Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004727.1 Hibiscus syriacus cultivar Beakdansim tig00010659_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: 59261
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:12688 original size:20 final size:20
Alignment explanation
Indices: 12659--12697 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12649 AGAGCTCATA
*
12659 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
12679 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
12698 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:13485 original size:19 final size:21
Alignment explanation
Indices: 13441--13493 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
13431 GAAACCCCTT
13441 TGAAAATACATTGACTTTTAAA
1 TGAAAATACA-TGACTTTTAAA
13463 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
13482 TGAAGATACATG
1 TGAAAATACATG
13494 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 3 0.10
22 10 0.33
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:17633 original size:20 final size:22
Alignment explanation
Indices: 17591--17641 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
17581 AACCCCTTTG
17591 AAAATACATGACTTTTAAATGA
1 AAAATACATGACTTTTAAATGA
17613 AAAATACATGA-TTTT-AATG-
1 AAAATACATGACTTTTAAATGA
*
17632 AAGATACATG
1 AAAATACATG
17642 CTCGGGGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 9 0.32
20 4 0.14
21 4 0.14
22 11 0.39
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (22 bp):
AAAATACATGACTTTTAAATGA
Found at i:19873 original size:11 final size:11
Alignment explanation
Indices: 19857--19882 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19847 TTTGAGTTCA
19857 AGCTTGAATCG
1 AGCTTGAATCG
19868 AGCTTGAATCG
1 AGCTTGAATCG
19879 AGCT
1 AGCT
19883 CGAGTCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (11 bp):
AGCTTGAATCG
Found at i:24112 original size:21 final size:21
Alignment explanation
Indices: 24088--24146 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
24078 ATAAAACTAC
*
24088 TAATAGTAATAATAACTCATA
1 TAATATTAATAATAACTCATA
24109 TAATATTAATAATAACTCATA
1 TAATATTAATAATAACTCATA
24130 TAATATTAATAATAACT
1 TAATATTAATAATAACT
24147 ATTCCCTCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (21 bp):
TAATATTAATAATAACTCATA
Found at i:27244 original size:43 final size:43
Alignment explanation
Indices: 27176--27258 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
27166 TCAAGAATGA
* * *
27176 TTGTAATATGTTAGTTTGGTATATTTATGGATTGTTACTTTGG
1 TTGTAACATGTTAGTTTGATATATTTATAGATTGTTACTTTGG
* *
27219 TTGTAACATGTTAGTTTGATGTATTTGTAGATTGTTACTT
1 TTGTAACATGTTAGTTTGATATATTTATAGATTGTTACTT
27259 CGGAGTTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.53
Consensus pattern (43 bp):
TTGTAACATGTTAGTTTGATATATTTATAGATTGTTACTTTGG
Found at i:42883 original size:230 final size:227
Alignment explanation
Indices: 42476--42925 Score: 783
Period size: 230 Copynumber: 2.0 Consensus size: 227
42466 GTAAATTATC
* * *
42476 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
42541 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
42606 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATT
*
42671 GAAACATAAATTATATAACTTTCAAAAAAGTATA
195 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
42705 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
42770 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
42835 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
42900 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
42926 GCAGTTATAA
Statistics
Matches: 210, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
228 4 0.02
229 65 0.31
230 141 0.67
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:43013 original size:20 final size:19
Alignment explanation
Indices: 42990--43035 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
42980 CGATATACCA
42990 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
43010 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
43030 GGTAAA
1 GGTAAA
43036 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:43180 original size:20 final size:19
Alignment explanation
Indices: 43157--43203 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
43147 CGATATAACA
43157 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
43177 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
43197 GGTAAAA
1 GGTAAAA
43204 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:43205 original size:17 final size:19
Alignment explanation
Indices: 43166--43208 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
43156 AGGTAAAAAT
43166 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
43186 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
43203 ATGATA
1 ATGATA
43209 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:45484 original size:21 final size:21
Alignment explanation
Indices: 45437--45501 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
45427 AAGACAATCA
* *
45437 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
45459 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
45479 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
45500 AG
1 AG
45502 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:45577 original size:33 final size:33
Alignment explanation
Indices: 45535--45600 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
45525 AAATAGATGG
*
45535 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
45568 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
45601 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:47403 original size:18 final size:19
Alignment explanation
Indices: 47365--47409 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
47355 GTAGGGTTAA
47365 TTTGTATAAGATTTATAAT
1 TTTGTATAAGATTTATAAT
*
47384 TTTGTATACGATTTAT-AT
1 TTTGTATAAGATTTATAAT
47402 TTTCGTAT
1 TTT-GTAT
47410 GTGAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTGTATAAGATTTATAAT
Found at i:48623 original size:196 final size:197
Alignment explanation
Indices: 47533--48991 Score: 2709
Period size: 195 Copynumber: 7.5 Consensus size: 197
47523 GGCCAAAAGG
*
47533 ATGTAATTTTTCAATCTAACTGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
47598 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
47663 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
47728 AAT
195 AAT
47731 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
47796 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CC
47861 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
47925 AAT
195 AAT
47928 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGT--GAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
47991 TGTCGACACT-A-ATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG-GCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
48053 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGAACCCAAAAG--TAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
48114 AAT
195 AAT
48117 ATGTAATTTTTCAATCT-ACCGGTACAATTATACCGG-TTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
48180 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
48245 TAAA--GTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
48308 AT
196 AT
48310 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
48375 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
48440 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
48505 AT
196 AT
*
48507 ATGTAATTTTTCAATCCAA-CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
48571 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTACACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
48636 TAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
48700 AT
196 AT
48702 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCT-AATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
48766 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
*
48831 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAGCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
48896 AT
196 AT
*
48898 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGATAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
48963 TGTCGACACTAATATAGTTTGTGTCGATA
66 TGTCGACACTAATATAGTTTGTGTCGATA
48992 CTAATTTAAA
Statistics
Matches: 1232, Mismatches: 10, Indels: 39
0.96 0.01 0.03
Matches are distributed among these distances:
187 7 0.01
188 19 0.02
189 68 0.06
190 58 0.05
191 64 0.05
192 23 0.02
193 45 0.04
194 48 0.04
195 279 0.23
196 267 0.22
197 207 0.17
198 147 0.12
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (197 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
AT
Found at i:48627 original size:391 final size:394
Alignment explanation
Indices: 47533--48991 Score: 2702
Period size: 391 Copynumber: 3.7 Consensus size: 394
47523 GGCCAAAAGG
*
47533 ATGTAATTTTTCAATCTAACTGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
47598 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
47663 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
131 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
47728 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
196 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
47793 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA
261 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA
47858 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAA
326 -CCATAAAG-GTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
47922 TGTAAT
389 TGTAAT
47928 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGT--GAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
47991 TGTCGACACT-A-ATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG-GCACC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
48053 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGAACCCAAAAG--TAATGT
131 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
48114 AATATGTAATTTTTCAATCT-ACCGGTACAATTATACCGG-TTTATGTGAGAATATGTCTAAATA
196 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
48177 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA
261 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA
48242 CCATAAA-GTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
326 CCATAAAGGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
48306 TAAT
391 TAAT
48310 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
48375 TGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
48439 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
131 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
48504 AATATGTAATTTTTCAATCCAA-CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
196 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
*
48568 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTACA
261 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA
48633 CCATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
326 CCATAAAG-GTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
48697 GTAAT
390 GTAAT
48702 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCT-AATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
48766 TGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
*
48830 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAGCCAAAAGTATAATGT
131 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
48895 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGATAATATGTCTAAATA
196 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
48960 ATGTGTCGACACTAATATAGTTTGTGTCGATA
261 ATGTGTCGACACTAATATAGTTTGTGTCGATA
48992 CTAATTTAAA
Statistics
Matches: 1042, Mismatches: 7, Indels: 33
0.96 0.01 0.03
Matches are distributed among these distances:
381 45 0.04
382 60 0.06
383 7 0.01
384 117 0.11
385 48 0.05
386 68 0.07
387 15 0.01
388 38 0.04
389 15 0.01
390 68 0.07
391 298 0.29
392 178 0.17
393 41 0.04
395 44 0.04
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (394 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
ATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA
CCATAAAGGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAAT
Found at i:50461 original size:3 final size:3
Alignment explanation
Indices: 50453--50531 Score: 68
Period size: 3 Copynumber: 26.3 Consensus size: 3
50443 AAAATGAAGC
* * * * * * * *
50453 TGA TGA TGA AGA TGA CGA TGA TGA TGA CGA TGA AGC TGG CGA TGA AGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
* *
50501 TGA TGA CGA TGA TGA TGA TGA AGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
50532 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.35, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
TGA
Found at i:50463 original size:12 final size:12
Alignment explanation
Indices: 50446--50531 Score: 91
Period size: 12 Copynumber: 7.2 Consensus size: 12
50436 GTCGCAGAAA
*
50446 ATGAAGCTGATG
1 ATGAAGATGATG
*
50458 ATGAAGATGACG
1 ATGAAGATGATG
* *
50470 ATGATGATGACG
1 ATGAAGATGATG
* **
50482 ATGAAGCTGGCG
1 ATGAAGATGATG
50494 ATGAAGATGATG
1 ATGAAGATGATG
* *
50506 ACGATGATGATG
1 ATGAAGATGATG
50518 ATGAAGATGATG
1 ATGAAGATGATG
50530 AT
1 AT
50532 CCAAACAAGT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 61 1.00
ACGTcount: A:0.36, C:0.07, G:0.34, T:0.23
Consensus pattern (12 bp):
ATGAAGATGATG
Found at i:50497 original size:36 final size:36
Alignment explanation
Indices: 50446--50523 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
50436 GTCGCAGAAA
* *
50446 ATGAAGCTGATGATGAAGATGACGATGATGATGACG
1 ATGAAGCTGACGATGAAGATGACGACGATGATGACG
* * *
50482 ATGAAGCTGGCGATGAAGATGATGACGATGATGATG
1 ATGAAGCTGACGATGAAGATGACGACGATGATGACG
50518 ATGAAG
1 ATGAAG
50524 ATGATGATCC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.22
Consensus pattern (36 bp):
ATGAAGCTGACGATGAAGATGACGACGATGATGACG
Found at i:52346 original size:180 final size:183
Alignment explanation
Indices: 51983--52602 Score: 1074
Period size: 181 Copynumber: 3.4 Consensus size: 183
51973 CTTTCAACAT
** * * * * * * *
51983 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCAAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
52048 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
52113 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAA-CCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
52165 ATTATAATGTAATAGATAATTTTGT-A-ATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
52228 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
52292 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
52345 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
52410 GG--TACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
52473 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * *
52526 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAA-A
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
*
52590 TGTCTACAACCTA
66 GGTCTACAACCTA
52603 AAATGTGTCG
Statistics
Matches: 419, Mismatches: 13, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
179 89 0.21
180 105 0.25
181 157 0.37
182 68 0.16
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:55067 original size:23 final size:21
Alignment explanation
Indices: 55021--55070 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
55011 TAACTACAAG
*
55021 TATATAATGTAATAGGTCGTT
1 TATATAATGTAATAGGTCGCT
55042 TATATAATGTAATAGGTAGCGCT
1 TATATAATGTAATAGGT--CGCT
55065 TATATA
1 TATATA
55071 TATTGTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 17 0.65
23 9 0.35
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.40
Consensus pattern (21 bp):
TATATAATGTAATAGGTCGCT
Found at i:55837 original size:38 final size:39
Alignment explanation
Indices: 55773--55858 Score: 113
Period size: 37 Copynumber: 2.2 Consensus size: 39
55763 TCCGATGCTC
* * *
55773 ATCAAAATCCAAAGTCATATGGTGCC-AAGCAAAA-GAA
1 ATCAAAATCCAAACTCATATGATGCCAAAACAAAAGGAA
*
55810 ATCAAAATTCAAATCTCATATGATGCCAAAACAAAAGGAA
1 ATCAAAATCCAAA-CTCATATGATGCCAAAACAAAAGGAA
55850 ATCAAAATC
1 ATCAAAATC
55859 TACAACTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 12 0.29
38 11 0.27
39 7 0.17
40 11 0.27
ACGTcount: A:0.51, C:0.19, G:0.12, T:0.19
Consensus pattern (39 bp):
ATCAAAATCCAAACTCATATGATGCCAAAACAAAAGGAA
Found at i:56300 original size:23 final size:23
Alignment explanation
Indices: 56269--56341 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
56259 ATAGGTAAAA
*
56269 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
56292 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
56315 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
56338 ATAT
1 ATAT
56342 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:56744 original size:22 final size:22
Alignment explanation
Indices: 56695--56766 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 22
56685 TAATAGGTAA
* *
56695 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTATCG-TT
56718 ATATAATGTAATAGGTATCGTT
1 ATATAATGTAATAGGTATCGTT
*
56740 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTA-TCGTT
56763 ATAT
1 ATAT
56767 TGTAAAGTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 19 0.42
23 26 0.58
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (22 bp):
ATATAATGTAATAGGTATCGTT
Found at i:56888 original size:425 final size:428
Alignment explanation
Indices: 56061--57103 Score: 1875
Period size: 425 Copynumber: 2.5 Consensus size: 428
56051 TATTATTTGG
56061 TTAATGTTGTTAAATTAAAAATTCTAAATAATA-TTTATAAAATATCAAATAATCAAATAA-TTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
56124 TTGTGCAAATGAAA-TATTAAA-TAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
66 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
*
56187 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAGGTATGGACACTTT
131 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTT
56252 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTAT
196 CAATATAATAGGT-AAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTAT
56317 ATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTT
260 ATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTT
56382 TTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATGTAGTA
325 TTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATGTAGTA
*
56447 ATTATAGGCGTAATGA-TTATTTTTTACGTTACGATATA
390 ATTATAAGCGTAATGATTTATTTTTTACGTTACGATATA
56485 TTTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAA-AATCAAATAATTT
1 -TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTT
56549 TTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAACATGAAACACTATTAAAAAAA
65 TTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGG-AAAACATGAAACACTATTAAAAAAA
56614 ATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCC-TTTTATAAAAAGTATGGACACT
129 ATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACT
56678 TTCAATATAATAGGT-AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCG-TTA
194 TTCAATATAATAGGTAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTA
56741 TATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTT
259 TATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTT
* *
56806 TTTT-ACTGTTGAAAACATTAATTTAAGGTTATCTTTTGAGTGAG-TTTAAGATTTTAATTTAGT
324 TTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATGTAGT
56869 AATTATAAGCGTCTAATGATTTATTTTTTACGTTACGATATA
389 AATTATAAGCG--TAATGATTTATTTTTTACGTTACGATATA
*
56911 -T-A--TTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
*
56972 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-CAAAAAAT
66 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
57036 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTT
131 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTT
57101 CAA
196 CAA
57104 CATATTATAA
Statistics
Matches: 602, Mismatches: 6, Indels: 24
0.95 0.01 0.04
Matches are distributed among these distances:
420 47 0.08
421 88 0.15
422 52 0.09
423 29 0.05
424 40 0.07
425 121 0.20
426 100 0.17
427 7 0.01
428 51 0.08
429 67 0.11
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (428 bp):
TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTT
CAATATAATAGGTAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATA
TAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTT
TTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATGTAGTAA
TTATAAGCGTAATGATTTATTTTTTACGTTACGATATA
Done.