Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001464.1 Hibiscus syriacus cultivar Beakdansim tig00002828_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: 60739
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1274 original size:13 final size:13
Alignment explanation
Indices: 1220--1276 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1210 GTTCAATGCA
*
1220 CGTCATAAATGAG
1 CGTCATAAATGTG
* *
1233 CGTAAAAAATGT-
1 CGTCATAAATGTG
*
1245 -GTCATAAATGCG
1 CGTCATAAATGTG
*
1257 TGTCATAAATGTG
1 CGTCATAAATGTG
1270 CGTCATA
1 CGTCATA
1277 GATTTATGAC
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 8 0.24
13 26 0.76
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (13 bp):
CGTCATAAATGTG
Found at i:2470 original size:24 final size:24
Alignment explanation
Indices: 2426--2472 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2416 ACGGACACAA
* **
2426 CTCTTGGCACTTCAAGTGACGTTT
1 CTCTTGGAACTTCAAAAGACGTTT
2450 CTCTTGGAACTTCAAAAGACGTT
1 CTCTTGGAACTTCAAAAGACGTT
2473 ATCTTTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (24 bp):
CTCTTGGAACTTCAAAAGACGTTT
Found at i:2488 original size:24 final size:24
Alignment explanation
Indices: 2443--2488 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2433 CACTTCAAGT
* *
2443 GACGTTTCTCTTGGAACTTCAAAA
1 GACGTTTCTCTTGAAACATCAAAA
2467 GACGTTATCT-TTGAAACATCAA
1 GACGTT-TCTCTTGAAACATCAA
2489 GAGATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (24 bp):
GACGTTTCTCTTGAAACATCAAAA
Found at i:4255 original size:35 final size:35
Alignment explanation
Indices: 4210--4319 Score: 175
Period size: 35 Copynumber: 3.1 Consensus size: 35
4200 TGGTAAGGGA
4210 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
* * *
4245 ATGGTGATGATATAGGCATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
*
4280 ATGGTGATGATATAGGCGTGAAAATGGTGATTGAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATAGAAG
4316 ATGG
1 ATGG
4320 GGATCAACAG
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 51 0.75
36 17 0.25
ACGTcount: A:0.33, C:0.04, G:0.37, T:0.26
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
Found at i:10982 original size:21 final size:21
Alignment explanation
Indices: 10935--10982 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
10925 CTACTATACT
*
10935 CGCAATAGCGCCCGCTATGGC
1 CGCAATAGCGCCCGCTATGAC
* * * *
10956 CACAATAGTGTCCGTTATGAC
1 CGCAATAGCGCCCGCTATGAC
10977 CGCAAT
1 CGCAAT
10983 CGAGGTAAAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (21 bp):
CGCAATAGCGCCCGCTATGAC
Found at i:14244 original size:43 final size:44
Alignment explanation
Indices: 14189--14317 Score: 185
Period size: 43 Copynumber: 3.0 Consensus size: 44
14179 GTTGATTTTA
*
14189 TTTAGACTTATTGAGACTTATTAGTGTTATGGTGTTATTTATTT
1 TTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTATTTATTT
* *
14233 TTTA-ACTTATTGAGACATAATAGTGTTCTGGTGTTATTTA--T
1 TTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTATTTATTT
*
14274 TTTAGACTTATTGAGACTTAAT-GATGTTATGGTGTTTTTTATTT
1 TTTAGACTTATTGAGACTTAATAG-TGTTATGGTGTTATTTATTT
14318 ACTTGCTTAT
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
41 6 0.08
42 31 0.41
43 33 0.44
44 5 0.07
ACGTcount: A:0.24, C:0.05, G:0.18, T:0.53
Consensus pattern (44 bp):
TTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTATTTATTT
Found at i:14307 original size:42 final size:42
Alignment explanation
Indices: 14185--14317 Score: 182
Period size: 42 Copynumber: 3.2 Consensus size: 42
14175 TGATGTTGAT
*
14185 TTTA-TTTAGACTTATTGAGACTTATTAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
* *
14226 TTTATTTTTTA-ACTTATTGAGACATAATAGTGTTCTGGTGTTA
1 TTTA--TTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
*
14269 TTTATTTTAGACTTATTGAGACTTAAT-GATGTTATGGTGTTT
1 TTTATTTTAGACTTATTGAGACTTAATAG-TGTTATGGTGTTA
14311 TTTATTT
1 TTTATTT
14318 ACTTGCTTAT
Statistics
Matches: 81, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
41 10 0.12
42 34 0.42
43 33 0.41
44 4 0.05
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.53
Consensus pattern (42 bp):
TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
Found at i:22842 original size:20 final size:20
Alignment explanation
Indices: 22790--22850 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
22780 TTCCCCTGTG
*
22790 GGGGGAATCGATTCTCCTTCAAA
1 GGGGGAATCGATTC-CC-TC-AT
*
22813 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
22833 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
22851 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 2 0.06
23 13 0.38
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:34288 original size:191 final size:187
Alignment explanation
Indices: 33931--34311 Score: 653
Period size: 191 Copynumber: 2.0 Consensus size: 187
33921 TTGGGTGTAT
33931 AAAGCTTAAGGAAATCTTATAAAGATTAAACAAGAGAGAGAATTAATAAGGGAATTGTAATAAGG
1 AAAGCTTAAGGAAATCTTATAAAGATTAAACAAGAGAGAGAATTAATAAGGGAATTGTAATAAGG
33996 GTGTAGAAATGAATTGTGGCATGAAGAGATTTTTGAAGTTCTATTGATAAATATGACTTTTATAA
66 GTGTAGAAATGAATTGTGGCATGAAGAGATTTTTGAAGTTC-ATTGATAAATATGACTTTTATAA
34061 GAAGATTAAGAAGTTTAAAGCAATAGAAATGAATTTAGAACACATGGAAAG-TTAGTAA
130 GAAGATTAAGAAGTTTAAAGCAATAGAAATGAATTTAGAACACATGG-AAGTTTAGTAA
34119 AAAGCTTAAGGAAATCTTATATAAGATTAAACATCAAGAGAAGAGAATTAATAAGGGAATTGTAA
1 AAAGCTTAAGGAAATCTTATA-AAGATT-AA-A-CAAGAG-AGAGAATTAATAAGGGAATTGTAA
34184 TAAGGGTGTAGAAATGAATTGCTGGCATGAAGAGATTTTTGAAGTTC-TTGAT-AA-ATGACTTT
61 TAAGGGTGTAGAAATGAATTG-TGGCATGAAGAGATTTTTGAAGTTCATTGATAAATATGAC-TT
34246 TTATAAGAAGATTAAGAAGTTTAAAGCAATAGAAATGAATTTAGAACACATGGAAGTTTAGTAA
124 TTATAAGAAGATTAAGAAGTTTAAAGCAATAGAAATGAATTTAGAACACATGGAAGTTTAGTAA
34310 AA
1 AA
34312 TTCTTTAATT
Statistics
Matches: 185, Mismatches: 0, Indels: 13
0.93 0.00 0.07
Matches are distributed among these distances:
188 21 0.11
189 6 0.03
190 10 0.05
191 67 0.36
192 11 0.06
193 45 0.24
194 25 0.14
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (187 bp):
AAAGCTTAAGGAAATCTTATAAAGATTAAACAAGAGAGAGAATTAATAAGGGAATTGTAATAAGG
GTGTAGAAATGAATTGTGGCATGAAGAGATTTTTGAAGTTCATTGATAAATATGACTTTTATAAG
AAGATTAAGAAGTTTAAAGCAATAGAAATGAATTTAGAACACATGGAAGTTTAGTAA
Found at i:41336 original size:3 final size:3
Alignment explanation
Indices: 41330--41435 Score: 119
Period size: 3 Copynumber: 35.3 Consensus size: 3
41320 AATAATAATA
41330 ATT ATT ATT ATT ATT ATT ATT A-T ATAT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
* * * * *
41375 ATA ATA ATA ATA ATA ATT ATT ATT ATT A-T ATAT ATT ATT A-T ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT AT-T
41420 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
41436 AAAAATAATT
Statistics
Matches: 95, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
2 6 0.06
3 80 0.84
4 9 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:41378 original size:63 final size:63
Alignment explanation
Indices: 41304--41435 Score: 239
Period size: 63 Copynumber: 2.1 Consensus size: 63
41294 ATTTATTTAT
41304 TTATTATTATAATAATAATAATAATAATTATTATTAT-TATTATTATTATATATATTATTATTA
1 TTATTATTATAATAATAATAATAATAATTATTATTATATA-TATTATTATATATATTATTATTA
*
41367 TTATTATTATAATAATAATAATAATTATTATTATTATATATATTATTATATATATTATTATTA
1 TTATTATTATAATAATAATAATAATAATTATTATTATATATATTATTATATATATTATTATTA
41430 TTATTA
1 TTATTA
41436 AAAAATAATT
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
63 65 0.97
64 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (63 bp):
TTATTATTATAATAATAATAATAATAATTATTATTATATATATTATTATATATATTATTATTA
Found at i:45097 original size:14 final size:14
Alignment explanation
Indices: 45059--45112 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
45049 ATTTTAAATA
**
45059 ATTTACATTTATAT
1 ATTTACATTTGCAT
*
45073 TTTTACATTTGCAT
1 ATTTACATTTGCAT
45087 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
45102 CTTTGCATTTG
1 ATTTACATTTG
45113 TATTTTTATG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:45110 original size:15 final size:15
Alignment explanation
Indices: 45074--45112 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
45064 CATTTATATT
45074 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
45088 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
45103 TTTGCATTTG
1 TTTACATTTG
45113 TATTTTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:48720 original size:21 final size:21
Alignment explanation
Indices: 48693--48753 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 21
48683 CTCATCCAAC
48693 AAAAAAAGAAGAAGGAAAAAAG
1 AAAAAAA-AAGAAGGAAAAAAG
*
48715 AAAAAAAAAAGAA-AAAAAAAG
1 -AAAAAAAAAGAAGGAAAAAAG
*
48736 -GAAAAAAA-AAGGAAAAAA
1 AAAAAAAAAGAAGGAAAAAA
48754 AAGGGAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.06
19 13 0.38
21 7 0.21
22 5 0.15
23 7 0.21
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAGAAGGAAAAAAG
Found at i:48722 original size:11 final size:11
Alignment explanation
Indices: 48693--48755 Score: 81
Period size: 11 Copynumber: 5.7 Consensus size: 11
48683 CTCATCCAAC
*
48693 AAAAAAAGAAG
1 AAAAAAAAAAG
**
48704 AAGGAAAAAAG
1 AAAAAAAAAAG
48715 AAAAAAAAAAG
1 AAAAAAAAAAG
*
48726 AAAAAAAAAGG
1 AAAAAAAAAAG
*
48737 AAAAAAAAAGG
1 AAAAAAAAAAG
48748 AAAAAAAA
1 AAAAAAAA
48756 GGGAGAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 46 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:48757 original size:10 final size:10
Alignment explanation
Indices: 48704--48757 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
48694 AAAAAAGAAG
48704 AAGGAAAAAA
1 AAGGAAAAAA
48714 GAA--AAAAAA
1 -AAGGAAAAAA
*
48723 AAGAAAAAAA
1 AAGGAAAAAA
48733 AAGGAAAAAAA
1 AAGG-AAAAAA
48744 AAGGAAAAAA
1 AAGGAAAAAA
48754 AAGG
1 AAGG
48758 GAGAAATTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 2 0.05
9 6 0.15
10 19 0.49
11 12 0.31
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAGGAAAAAA
Found at i:53482 original size:22 final size:22
Alignment explanation
Indices: 53456--53529 Score: 139
Period size: 22 Copynumber: 3.4 Consensus size: 22
53446 TACACTCTTC
53456 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTT
53478 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTT
*
53500 AAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCTCTTTTT
53522 AAAGATGA
1 AAAGATGA
53530 AAGCTTTATG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTT
Found at i:54557 original size:341 final size:339
Alignment explanation
Indices: 53936--54608 Score: 1024
Period size: 341 Copynumber: 2.0 Consensus size: 339
53926 GATTCAAATC
* *
53936 CATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGA
1 CATCACTTGATAGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
54001 AAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
66 AAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTCGCTCAAATCCATCATTTGATGGATCA
** **
54066 GTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
131 GCATCCCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * *
54131 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGT
196 AGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAAAAAGT
* *
54196 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGGGAAGAAATTGTTCAAC
261 TCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAAATTGTTCAAC
54261 CTTTTGCTTGAATT
326 CTTTTGCTTGAATT
* * *
54275 CATCACTTGATAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAAGTCATCTGAAGAAGGA
1 CATCACTTGATAGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * * ** *
54340 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAATCTTTCGTTTGAATTCATCATTTGATGGATCA
66 AAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTCGCTCAAATCCATCATTTGATGGATCA
* *
54405 GCATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
131 GCATCCCCA--GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAA
* * *
54470 TGAGAAGAACTTGTTCAA-CTTTTCGCTCAAATTCATCACTCGATGGATCAACTTTTCCAGAGAG
194 TGAGAAGAACTTGTTCAACCTTTT-GCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAAAA
* **
54534 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
258 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAAATTGTTC
*
54599 GACCTTTTGC
323 AACCTTTTGC
54609 ATGACTCTAT
Statistics
Matches: 299, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
339 122 0.41
340 5 0.02
341 172 0.58
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (339 bp):
CATCACTTGATAGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTCGCTCAAATCCATCATTTGATGGATCA
GCATCCCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
AGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAAAAAGT
TCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAAATTGTTCAAC
CTTTTGCTTGAATT
Found at i:54621 original size:113 final size:113
Alignment explanation
Indices: 53929--54608 Score: 984
Period size: 113 Copynumber: 6.0 Consensus size: 113
53919 TAGCAAAGAT
* * *
53929 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
53994 AGAAGGAAAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
54042 TCAAATCCATCATTTGATGGATCAGTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
54107 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
54155 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
54220 AGAAGGAAGAAGAAATTCATAATGGGAAGAAATTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * *
54268 TTGAATTCATCACTTGATAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAAGTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
54333 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAATCTTTCGT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * ** *
54381 TTGAATTCATCATTTGATGGATCAGCATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCT
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCA--GAAAAAGTTCATAATGAGAAGAACTCATCT
* *
54446 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
* * * *
54496 TCAAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * ** *
54561 AGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
54609 ATGACTCTAT
Statistics
Matches: 519, Mismatches: 44, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
113 416 0.80
114 9 0.02
115 94 0.18
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
TCAAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:54672 original size:124 final size:119
Alignment explanation
Indices: 54523--54751 Score: 329
Period size: 120 Copynumber: 1.9 Consensus size: 119
54513 TGGATCAACT
* *
54523 TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAGAGTTCACAATGAGAAGAACTCATCT---G-AAGAAGAAGAAGTTCACAATGAGA
*
54588 AGAGCTTGTTCGACCTTTTGC-ATGACT-CTATCACAGAAGGAGATATATCATTATCAGCA
62 AGAGCTTGTTCAACC-TTTGCTA-GACTAC-ATCACAGAAGGAGATATATCATTATCAGCA
54647 TTTCCAGA-AGAAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGA
1 TTTCCAGAGAG-AGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGA
*
54711 GCTTGTTCAACCTTTGCTAGATTACATCACAGAAGGAGATA
65 GCTTGTTCAACCTTTGCTAGACTACATCACAGAAGGAGATA
54752 AATTGTCATC
Statistics
Matches: 98, Mismatches: 4, Indels: 11
0.87 0.04 0.10
Matches are distributed among these distances:
119 24 0.24
120 39 0.40
121 1 0.01
123 2 0.02
124 32 0.33
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (119 bp):
TTTCCAGAGAGAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAG
CTTGTTCAACCTTTGCTAGACTACATCACAGAAGGAGATATATCATTATCAGCA
Found at i:54674 original size:17 final size:17
Alignment explanation
Indices: 54652--54710 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
54642 CAGCATTTCC
54652 AGAAGAAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
54669 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
54687 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
54705 AGAAGA
1 AGAAGA
54711 GCTTGTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 3 0.09
17 16 0.47
18 2 0.06
19 10 0.29
20 3 0.09
ACGTcount: A:0.49, C:0.12, G:0.24, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:54964 original size:3 final size:3
Alignment explanation
Indices: 54956--55016 Score: 86
Period size: 3 Copynumber: 19.0 Consensus size: 3
54946 TTTTATTTAT
54956 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TATA TATA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA T-TA TTA
55005 TTA TTA TTA TTA
1 TTA TTA TTA TTA
55017 AAAAATAATT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 42 0.74
4 15 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:59145 original size:20 final size:20
Alignment explanation
Indices: 59097--59148 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
59087 TGACCTTACA
* *
59097 ATATCGATACCATCTCTTAAG
1 ATATCGATACC-CCACTTAAG
*
59118 -TATTGATACCCCACTTAAG
1 ATATCGATACCCCACTTAAG
59137 ATATCGATACCC
1 ATATCGATACCC
59149 TAGTTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.31
Consensus pattern (20 bp):
ATATCGATACCCCACTTAAG
Done.