Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008459.1 Hibiscus syriacus cultivar Beakdansim tig00111272_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: 632685
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:595537 original size:25 final size:25
Alignment explanation
Indices: 595492--595539 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
595482 TGATTTATTA
* *
595492 TTTTATTATTTTTTTTGTTTTTTGT
1 TTTTATTATTTGTTATGTTTTTTGT
595517 TTTTATTTATTTGTTAT-TTTTTT
1 TTTTA-TTATTTGTTATGTTTTTT
595540 CTAACCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.10, C:0.00, G:0.06, T:0.83
Consensus pattern (25 bp):
TTTTATTATTTGTTATGTTTTTTGT
Found at i:599337 original size:17 final size:18
Alignment explanation
Indices: 599310--599355 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
599300 TTTTACAAGT
*
599310 ATAAGAAAATATAAATTA-
1 ATAA-AAAATATAAATCAC
*
599328 ATTAAAAATA-AAATCAC
1 ATAAAAAATATAAATCAC
599345 ATAAAAAATAT
1 ATAAAAAATAT
599356 CTTATGGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.22
17 15 0.65
18 3 0.13
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (18 bp):
ATAAAAAATATAAATCAC
Found at i:601739 original size:223 final size:217
Alignment explanation
Indices: 601351--601785 Score: 671
Period size: 223 Copynumber: 2.0 Consensus size: 217
601341 GTAAATTATC
* * *
601351 TATCCTTTTTATAAAGTGTCAACTATTTCACTGTGAAAATATATTTATTATTATCTTTAGTTAAT
1 TATCATTTTTATAAAGTGTCAACTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAAT
**
601416 TGTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAATTTTTTGTGTAAA
66 TGTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAAAATTTTGTGTAAA
601481 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTA-TAAAAAAATTGAAACATAA
131 TGAAA-TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
601545 ATTACATAACTTTCAAAAAGTATA
195 ATTACATAACTTT-AAAAAGTATA
601569 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTT-G
1 TATCATTTTTAT-AAAGTGT-CA-AC-TATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
601633 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
61 TT-A-ATTG-TAAATTTAAAATCTAAATAATATTTTAT-AAATATCAAAACAATCAAATAAAATT
* *
601698 TTGTGTAAAT-TAA-ATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
122 TTGTGTAAATGAAATATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
601761 AAACATAAATTACATAACTTTAAAA
187 AAACATAAATTACATAACTTTAAAA
601786 GCAGTTATAA
Statistics
Matches: 199, Mismatches: 8, Indels: 15
0.90 0.04 0.07
Matches are distributed among these distances:
218 11 0.06
219 7 0.04
220 2 0.01
221 2 0.01
222 13 0.07
223 66 0.33
224 35 0.18
225 29 0.15
226 34 0.17
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (217 bp):
TATCATTTTTATAAAGTGTCAACTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAAT
TGTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAAAATTTTGTGTAAA
TGAAATATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAA
TTACATAACTTTAAAAAGTATA
Found at i:601873 original size:20 final size:19
Alignment explanation
Indices: 601850--601894 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
601840 CGATATACCA
601850 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
601870 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
601890 -GTAAA
1 GGTAAA
601895 TTTAAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.04
19 4 0.17
20 16 0.67
21 3 0.12
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.18
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:602037 original size:20 final size:19
Alignment explanation
Indices: 602014--602060 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
602004 CGATATAACA
602014 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
602034 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
602054 GGTAAAA
1 GGTAAAA
602061 TGATACCGAT
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:602062 original size:17 final size:19
Alignment explanation
Indices: 602023--602065 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
602013 AGGTAAAAAT
602023 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
602043 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
602060 ATGATA
1 ATGATA
602066 CCGATATATT
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:604313 original size:21 final size:21
Alignment explanation
Indices: 604266--604330 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
604256 AAGACAATCA
* *
604266 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
604288 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
604308 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
604329 AG
1 AG
604331 GCATAGGGGG
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:604405 original size:33 final size:33
Alignment explanation
Indices: 604363--604428 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
604353 AAATAGATGG
*
604363 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
604396 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
604429 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:606214 original size:19 final size:19
Alignment explanation
Indices: 606192--606240 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
606182 AAATGTAGGT
606192 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
606211 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
606230 T-ATTTTCGTAT
1 TAATTTT-GTAT
606241 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:607009 original size:196 final size:196
Alignment explanation
Indices: 606370--607827 Score: 2694
Period size: 196 Copynumber: 7.5 Consensus size: 196
606360 CCAAAAGGAT
606370 GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAA--TG
1 GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTG
606433 TCGACACT-A-ATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CCAT
66 TCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGG-AAACAGGGTGCACCCAT
606495 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
130 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
606560 TA
195 TA
606562 TGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGT
1 -GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGT
606627 GTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAACAGGGTGCACCCAT
65 GTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAACAGGGTGCACCCAT
606692 AAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
130 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
606755 TA
195 TA
606757 TGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGT
1 -GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGT
606822 GTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCCA
65 GTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGG-AAACAGGGTGCACCCA
606887 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
129 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
606952 ATA
194 ATA
606955 -TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTG
1 GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTG
*
607019 TCGACACTAATATAGTTTGTGTCGATATTT-TTTTCAGAATGAATGGAAACAGGGTGCACCCATA
66 TCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAACAGGGTGCACCCATA
607083 AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAAT
131 AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAAT
607148 A
196 A
607149 TGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGT
1 -GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGT
607214 GTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCCA
65 GTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGG-AAACAGGGTGCACCCA
607279 TAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
129 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
607343 ATA
194 ATA
* *
607346 TATAATTTTTCAATCTAACCGGTACAATTAT-CCGATTTTATGTGAGAATATGTCTAAATAATGT
1 -GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGT
*
607410 GTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAACAGGGTGCA-CCAT
65 GTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAACAGGGTGCACCCAT
607474 AAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
130 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
607538 TA
195 TA
607540 TGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGT
1 -GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGT
607604 GTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAACAGGGTGCACCCAT
65 GTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAACAGGGTGCACCCAT
607669 AAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
130 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
607733 TA
195 TA
607735 TGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGT
1 -GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGT
607800 GTCGACACTAATATAGTTTGTGTCGATA
65 GTCGACACTAATATAGTTTGTGTCGATA
607828 CTAATTTAAA
Statistics
Matches: 1242, Mismatches: 8, Indels: 27
0.97 0.01 0.02
Matches are distributed among these distances:
193 86 0.07
194 249 0.20
195 277 0.22
196 397 0.32
197 145 0.12
198 88 0.07
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (196 bp):
GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTG
TCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAACAGGGTGCACCCATA
AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAAT
A
Found at i:618860 original size:6 final size:6
Alignment explanation
Indices: 618836--618921 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
618826 AGCGGTCGCA
* * * * * **
618836 GAAGAT GAAGCT GACGAT GAAGAT GATGAT GACGAT GAAGCT GGCGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * *
618884 GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
618922 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:618865 original size:3 final size:3
Alignment explanation
Indices: 618851--618925 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
618841 TGAAGCTGAC
* * * * ** * *
618851 GAT GAA GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
618899 GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
618926 CCAAACAAGT
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.36, C:0.05, G:0.35, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:618875 original size:30 final size:30
Alignment explanation
Indices: 618839--618925 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
618829 GGTCGCAGAA
618839 GATGAAGCTGACGATGAAGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGATGATGAC
* * *
618869 GATGAAGCTGGCGATGAAGATGATGACGAT
1 GATGAAGCTGACGATGAAGATGATGATGAC
* * *
618899 GATGATGATGATGATGAAGATGATGAT
1 GATGAAGCTGACGATGAAGATGATGAT
618926 CCAAACAAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.36, C:0.07, G:0.34, T:0.23
Consensus pattern (30 bp):
GATGAAGCTGACGATGAAGATGATGATGAC
Found at i:618922 original size:12 final size:12
Alignment explanation
Indices: 618839--618925 Score: 75
Period size: 12 Copynumber: 7.2 Consensus size: 12
618829 GGTCGCAGAA
* *
618839 GATGAAGCTGAC
1 GATGAAGATGAT
618851 GATGAAGATGAT
1 GATGAAGATGAT
* *
618863 GATGACGATGAA
1 GATGAAGATGAT
* ** *
618875 GCTGGCGATGAA
1 GATGAAGATGAT
* *
618887 GATGATGACGAT
1 GATGAAGATGAT
*
618899 GATGATGATGAT
1 GATGAAGATGAT
618911 GATGAAGATGAT
1 GATGAAGATGAT
618923 GAT
1 GAT
618926 CCAAACAAGT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 62 1.00
ACGTcount: A:0.36, C:0.07, G:0.34, T:0.23
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:618924 original size:18 final size:18
Alignment explanation
Indices: 618836--618921 Score: 73
Period size: 18 Copynumber: 4.8 Consensus size: 18
618826 AGCGGTCGCA
* *
618836 GAAGATGAAGCTGACGAT
1 GAAGATGATGATGACGAT
618854 GAAGATGATGATGACGAT
1 GAAGATGATGATGACGAT
* ** *
618872 GAAGCTGGCGATGAAGAT
1 GAAGATGATGATGACGAT
* * *
618890 GATGACGATGATGATGAT
1 GAAGATGATGATGACGAT
* *
618908 GATGATGAAGATGA
1 GAAGATGATGATGA
618922 TGATCCAAAC
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGATGATGACGAT
Found at i:620696 original size:183 final size:183
Alignment explanation
Indices: 620388--620831 Score: 798
Period size: 183 Copynumber: 2.4 Consensus size: 183
620378 CTTTCAACAT
** * * *
620388 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
620453 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
620518 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * * *
620571 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGAGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
620636 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
620701 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
620754 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
*
620819 TGTCTACAACCTA
66 GGTCTACAACCTA
620832 AAATGTGTCG
Statistics
Matches: 247, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 247 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:621521 original size:18 final size:18
Alignment explanation
Indices: 621500--621536 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
621490 GTAATTGGAG
621500 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
621518 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
621536 T
1 T
621537 ATATATTTCG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:621544 original size:24 final size:24
Alignment explanation
Indices: 621492--621538 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
621482 TTTCATATGT
* *
621492 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
621516 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
621539 ATATTTCGGC
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:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:621836 original size:39 final size:39
Alignment explanation
Indices: 621793--621879 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
621783 TCCGATGCTC
*
621793 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
621832 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
621871 ATCAAAATC
1 ATCAAAATC
621880 TACAACTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:622348 original size:22 final size:23
Alignment explanation
Indices: 622299--622370 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
622289 ATAGGTAAAA
*
622299 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
622322 ATATAATGTAATAGGTA-CGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
622344 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
622367 ATAT
1 ATAT
622371 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 21 0.48
23 23 0.52
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:622773 original size:21 final size:23
Alignment explanation
Indices: 622731--622793 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 23
622721 AAAAATATGA
622731 TAATAGGTAGCGCTTATATAATG
1 TAATAGGTAGCGCTTATATAATG
*
622754 TAATAGGTATCG-TT-TATAATG
1 TAATAGGTAGCGCTTATATAATG
* *
622775 TAATAGGTAGTGGTTATAT
1 TAATAGGTAGCGCTTATAT
622794 TGTAAAGTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 17 0.49
22 4 0.11
23 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (23 bp):
TAATAGGTAGCGCTTATATAATG
Found at i:622882 original size:423 final size:425
Alignment explanation
Indices: 622089--623130 Score: 1840
Period size: 423 Copynumber: 2.5 Consensus size: 425
622079 TTATCTTTGG
*
622089 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAAATC-AATAATTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAAATAA-TT
622153 TTTGTGCAAATG-AATTATT-AATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAA
64 TTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAA
*
622216 TTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAATGTATGGACACTT
128 TTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTT
622281 TCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTACGTTTAT
193 TC-ATATAATAGGTAAAAATATGA-GTAATAGGTAGCGCTTATATAATGTAATAGGTACGTTTAT
622346 ATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCATTTTTATAAAAGTGTCCATACTTT
256 ATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCATTTTTATAAAAGTGTCCATACTTT
622411 TTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTA
321 TTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTA
622476 ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
386 ATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGATATA
622517 TTTTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAA-T
1 --TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATT
622581 TTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
64 TTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
622646 TGAAAC-TAAA-TACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTT
129 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTT
622709 CATATAATAGGTAAAAATATGA-TAATAGGTAGCGCTTATATAATGTAATAGGTATCG-TT-TAT
194 CATATAATAGGTAAAAATATGAGTAATAGGTAGCGCTTATATAATGTAATAGGTA-CGTTTATAT
*
622771 AATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTT
258 AATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCATTTTTATAAAAGTGTCCATACTTTTT
*
622836 TCACTGTTGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAAT
323 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAAT
622901 TATAGGCGTCTAATGATTTATTTTTACGTTACGATATA
388 TATAGGCGTCTAATGATTTATTTTTACGTTACGATATA
*
622939 TT-A--TTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAA-TTT
* *
623001 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTCAAAAAATT
65 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
623066 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCC-TTTTATAAAAAGTATGGACACTTTC
130 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
623130 A
195 A
623131 ACATATATAA
Statistics
Matches: 597, Mismatches: 7, Indels: 26
0.95 0.01 0.04
Matches are distributed among these distances:
417 54 0.09
419 71 0.12
420 32 0.05
421 28 0.05
422 18 0.03
423 151 0.25
424 34 0.06
425 2 0.00
426 21 0.04
427 53 0.09
428 17 0.03
429 28 0.05
430 88 0.15
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (425 bp):
TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCA
TATAATAGGTAAAAATATGAGTAATAGGTAGCGCTTATATAATGTAATAGGTACGTTTATATAAT
GTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCATTTTTATAAAAGTGTCCATACTTTTTTCA
CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAATTAT
AGGCGTCTAATGATTTATTTTTACGTTACGATATA
Found at i:625555 original size:26 final size:28
Alignment explanation
Indices: 625496--625560 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
625486 ATTCAAATTT
* ** *
625496 TATTAATTAAATTTTTTTCTCCATTAAC
1 TATTAATTGAATTTTTTTCTCCAAAAAA
625524 TATTAATTGAATTTTTTTCT-CAAAAAA
1 TATTAATTGAATTTTTTTCTCCAAAAAA
*
625551 T-TTAACTGAA
1 TATTAATTGAA
625561 CCGATCTAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 8 0.25
27 5 0.16
28 19 0.59
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (28 bp):
TATTAATTGAATTTTTTTCTCCAAAAAA
Found at i:625652 original size:13 final size:13
Alignment explanation
Indices: 625634--625660 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
625624 TTTTGTTTAT
625634 TCGGTTAATTTGG
1 TCGGTTAATTTGG
625647 TCGGTTAATTTGG
1 TCGGTTAATTTGG
625660 T
1 T
625661 AAAAATCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.30, T:0.48
Consensus pattern (13 bp):
TCGGTTAATTTGG
Found at i:631938 original size:32 final size:32
Alignment explanation
Indices: 631883--632065 Score: 99
Period size: 31 Copynumber: 5.4 Consensus size: 32
631873 TATAGTATAC
*
631883 ACTATATAATATATATTTCAAAAATATTTTT-TAA
1 ACTATAT-AT-TATATTTCAAAAA-ATTTTTCAAA
* *
631917 ATTATATATTATATTTTAAAAAATTTTTCAAA
1 ACTATATATTATATTTCAAAAAATTTTTCAAA
*
631949 ACTATATATTATATAGTTTTC-AAAAATGATTT-AAA
1 ACTATATA-T-TATA--TTTCAAAAAAT-TTTTCAAA
* * *
631984 AATAT-TA-TATAAGTTT-AAAATATTTTTTAAA
1 ACTATATATTAT-A-TTTCAAAAAATTTTTCAAA
* *
632015 ACTATATATTATATAATTTCTCAAAAAGTTTTTTTAAA
1 ACTATATA-T-TAT-A-TT-TCAAAAA-ATTTTTCAAA
632053 ACTATATATTATA
1 ACTATATATTATA
632066 AAGTTTTTCA
Statistics
Matches: 119, Mismatches: 14, Indels: 31
0.73 0.09 0.19
Matches are distributed among these distances:
30 3 0.03
31 24 0.20
32 24 0.20
33 3 0.03
34 12 0.10
35 21 0.18
36 10 0.08
37 5 0.04
38 17 0.14
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (32 bp):
ACTATATATTATATTTCAAAAAATTTTTCAAA
Found at i:632054 original size:38 final size:37
Alignment explanation
Indices: 631883--632269 Score: 230
Period size: 38 Copynumber: 10.6 Consensus size: 37
631873 TATAGTATAC
*
631883 ACTATATAATATAT-A-TTTCAAAAA-TATTTTT-TAA
1 ACTATATAATATATAATTTTCAAAAAGT-TTTTTAAAA
* * *
631917 ATTATAT-AT-TAT-ATTTT-AAAAA-ATTTTTCAAA
1 ACTATATAATATATAATTTTCAAAAAGTTTTTTAAAA
* * **
631949 ACTATATATTATATAGTTTTCAAAAA-TGATTT-AAA
1 ACTATATAATATATAATTTTCAAAAAGTTTTTTAAAA
*
631984 A--ATAT--TATATAAGTTT-AAAATA-TTTTTT-AAA
1 ACTATATAATATATAATTTTCAAAA-AGTTTTTTAAAA
* *
632015 ACTATATATTATATAATTTCTCAAAAAGTTTTTTTAAA
1 ACTATATAATATATAATTT-TCAAAAAGTTTTTTAAAA
* * *
632053 ACTATATATTATA-AAGTTTTTCAAAATA-CTTTCTAAAA
1 ACTATATAATATATAA--TTTTCAAAA-AGTTTTTTAAAA
** *
632091 A-TATATTATATATATTTTTTTCAAAATGATTTTTTAAAA
1 ACTATA-TA-ATATATAATTTTCAAAAAG-TTTTTTAAAA
*
632130 ACCT-TATAATATATATATTTTCAAAATGATTTTTTAAAA
1 A-CTATATAATATATA-ATTTTCAAAAAG-TTTTTTAAAA
632169 ACTATATAATATAT-ATTTTCAAAATGAGTTTTTTAAAA
1 ACTATATAATATATAATTTTCAAAA--AGTTTTTTAAAA
* *
632207 ACTATATAATATATATATATGATTTC-AAAA-TGTTTTCAAA
1 ACTATAT-A-ATATATA-AT--TTTCAAAAAGTTTTTTAAAA
632247 ACTATATATATTATATAATTTTC
1 ACTATATA-A-TATATAATTTTC
632270 TTAACTATAT
Statistics
Matches: 289, Mismatches: 28, Indels: 69
0.75 0.07 0.18
Matches are distributed among these distances:
30 4 0.01
31 23 0.08
32 17 0.06
33 14 0.05
34 9 0.03
35 17 0.06
36 10 0.03
37 30 0.10
38 66 0.23
39 59 0.20
40 29 0.10
41 2 0.01
42 2 0.01
43 3 0.01
44 4 0.01
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (37 bp):
ACTATATAATATATAATTTTCAAAAAGTTTTTTAAAA
Found at i:632155 original size:77 final size:77
Alignment explanation
Indices: 632012--632224 Score: 251
Period size: 77 Copynumber: 2.8 Consensus size: 77
632002 AATATTTTTT
* * * *
632012 AAAACTATATATTATATAATTTCTCAAAA--AGTTTTTTTAAAACTATATATTATAAAGT-TTTT
1 AAAACTATATAATATAT-ATTT-TCAAAATGAGTTTTTTAAAAACTATATAATATATA-TATTTT
632074 CAAAAT-ACTTTCTA
63 CAAAATGACTTTCTA
*
632088 AAAA-TATATTATATATATTTTTTTCAAAATGA-TTTTTTAAAAACCT-TATAATATATATATTT
1 AAAACTATA-TA-ATATA-TATTTTCAAAATGAGTTTTTTAAAAA-CTATATAATATATATATTT
* *
632150 TCAAAATGATTTTTTA
62 TCAAAATGACTTTCTA
632166 AAAACTATATAATATATATTTTCAAAATGAGTTTTTTAAAAACTATATAATATATATAT
1 AAAACTATATAATATATATTTTCAAAATGAGTTTTTTAAAAACTATATAATATATATAT
632225 ATGATTTCAA
Statistics
Matches: 118, Mismatches: 8, Indels: 21
0.80 0.05 0.14
Matches are distributed among these distances:
75 4 0.03
76 28 0.24
77 66 0.56
78 16 0.14
79 4 0.03
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.46
Consensus pattern (77 bp):
AAAACTATATAATATATATTTTCAAAATGAGTTTTTTAAAAACTATATAATATATATATTTTCAA
AATGACTTTCTA
Found at i:632343 original size:2 final size:2
Alignment explanation
Indices: 632336--632368 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
632326 AAAATGTTTA
632336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
632369 TAGTTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:632406 original size:9 final size:9
Alignment explanation
Indices: 632392--632426 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
632382 CATTTGCAAC
632392 TATATAATA
1 TATATAATA
632401 TATATAATA
1 TATATAATA
*
632410 TATATATGTA
1 TATATA-ATA
632420 TATATAA
1 TATATAA
632427 AAAATATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (9 bp):
TATATAATA
Done.