Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003017.1 Hibiscus syriacus cultivar Beakdansim tig00006264_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: 251717
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:220472 original size:3 final size:3
Alignment explanation
Indices: 220464--220531 Score: 100
Period size: 3 Copynumber: 22.3 Consensus size: 3
220454 TTTGTATGTA
* *
220464 AAT AAT AAT AAT AAT AAT AAT AAG AAT AAG AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
220512 AATT TAT AAT AAT AAT AAT A
1 AA-T AAT AAT AAT AAT AAT A
220532 TTTAATGGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 56 0.97
4 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:221181 original size:3 final size:3
Alignment explanation
Indices: 221173--221242 Score: 106
Period size: 3 Copynumber: 23.3 Consensus size: 3
221163 TTTATATGTA
* *
221173 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATTT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
221219 AAT AAT AAT -AT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
221243 TTTAATGGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.95
4 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:221238 original size:708 final size:711
Alignment explanation
Indices: 219853--221530 Score: 2590
Period size: 709 Copynumber: 2.4 Consensus size: 711
219843 TTGGATATCG
* * *
219853 AATCCAACTTAATTCACAAGCCAAGAACC-TTTTTATAAAGTTAAAATAACAACAACTAACACCT
1 AATCCAACTTAATTCACAAGTCAAGAACCTTTTTTATAAAGTTAAAATAATAGCAACTAACACCT
* *
219917 AATACTTAAATTATAACTAATAGTTTTCCAAACAATTCTTATACAATATATAACATATATCATAA
66 AATACTTAAATTATAACTAATAGTTTCCCAAACAATTCTTAAACAATATATAACATATATCATAA
* * *
219982 AATTGATCAAATATAGACATTTTAATTAAAAATTAACAAAAATCTTGACA-TTTTTCCATATAAA
131 AATTGATCAGATATAGACATTTTAATTAAAAATTAACAAAAGTCTTGACATTTTTTCCAAATAAA
* * *
220046 GAAATCAAAAAATCCAAAAGCT-A-ACTTGTTTGACAAGTTAATTAAATTTGAAAATTTAAATAT
196 GAAATCAAAGAATCCAAATG-TGATA-TTGTTTGACAAGTTAATTAAATTTGGAAATTTAAATAT
* * * *
220109 GGGCATGTTTGATTAAGGCGGATTTAGATTCATTTGTGCTTATACACTTGGATGGGTGACTTGGT
259 GAGCATGTTTGATTAAGGCGGATTTAGATTCATTTGTGCTTATACACATGGATGGGTGACGTGGC
* *
220174 AAGCTCCTTACCCTTGGATCTAACCCTTCATCAATGGCTCACATGGGTTGTGTTTGTTTGACAAT
324 AAGCTCCTTACCCTTGGATCTAACCCTCCATCAATGGCTCACATGGGTTGTGTTTGTTTGACAAG
* *
220239 GATTGAAGAGATGATGGCCCTTGAATAAAAGCTAATCATGGGATGAAATCATTTTTTGTTTCTTT
389 GATTGAAGAGATGATGGCCCTTGAATAAAAGCTAATCAAGGGATGAAATCATTTTGTGTTTCTTT
* * *
220304 ACATGGATTGGTGATGTCATCACCTCAAAAGCTACACTAACAATAAATGCCTTATCCTTTTTTGA
454 ACATGGACTGGTGATGTCATCACCTCAAAAGCTACACCAACAATAAATGCCTTATCATTTTTTGA
* * *
220369 AATTCAAACTAAAAATATTTCTCCCACAAAAAAATCAGTGGCTACCCAGGAAATGGTACACTAGG
519 AATTCAAACTAAAAATATATCTCCCACAAAAAAATCAGCGACTACCCAGGAAATGGTACACTAGG
* *
220434 GTTTGAACATTGGGCTCGGTTTTGTATGTAAATAATAATAATAATAATAATAAGAATAAGAATAA
584 GTTTGAACATTGGGCCCGGTTTTATATGTAAATAATAATAATAATAATAATAAGAATAAGAATAA
* *
220499 TAATAATAATAATAATT--TATAATAATAATAATATTTAATGGTTGAAGAATGGTGATTATAA
649 TAATAATAATAATAATTAATATAATAATAATAATATTTAATGGTTGAAAAATGATGATTATAA
* * *
220560 AATCCAACTCAATTAACAAGTCAAGAACCTTTTTTATAAGGTTAAAATAATAGCAACTAACACCT
1 AATCCAACTTAATTCACAAGTCAAGAACCTTTTTTATAAAGTTAAAATAATAGCAACTAACACCT
*
220625 ACTACTTAAATTATAACTAATAGTTTCCCAAACAATTCTTAAACAATATATAACATATATCATAA
66 AATACTTAAATTATAACTAATAGTTTCCCAAACAATTCTTAAACAATATATAACATATATCATAA
* * * *
220690 AATTGATCAGATAAAAACATTTTAACTAAAAATTAACTAAAGTCTTGACATTTTTTCCAAATAAA
131 AATTGATCAGATATAGACATTTTAATTAAAAATTAACAAAAGTCTTGACATTTTTTCCAAATAAA
* *
220755 GAAATCAAAGAATTCAAATGTGATATTGCTTGACAAGTTAATTAAATTTGGAAATTTAAATATGA
196 GAAATCAAAGAATCCAAATGTGATATTGTTTGACAAGTTAATTAAATTTGGAAATTTAAATATGA
* *
220820 GCATGTTTGATTAAGGCAGG-TTTAGATTCATTTGTGCTTCTTCACATGGATGGGTGACGTGGCA
261 GCATGTTTGATTAAGGC-GGATTTAGATTCATTTGTGCTTATACACATGGATGGGTGACGTGGCA
*
220884 AGTTCC-TAGCCCTTGGATCTAACCCTCCATCAATGGCTCACATGGGTTGTGTTTGTTTGAC-AG
325 AGCTCCTTA-CCCTTGGATCTAACCCTCCATCAATGGCTCACATGGGTTGTGTTTGTTTGACAAG
* * *
220947 GATTGAAGAGATGATGGCTCTTGGATGAAAA-CTAATCAAGGGATGAGATCATTTTGTGTTTCTT
389 GATTGAAGAGATGATGGCCCTTGAAT-AAAAGCTAATCAAGGGATGAAATCATTTTGTGTTTCTT
* * * * *
221011 TACATGGACTGGTGTTGTCATCACCTCAAAAGCTATACCAACTATAAATGTCTTATCATTTTTTT
453 TACATGGACTGGTGATGTCATCACCTCAAAAGCTACACCAACAATAAATGCCTTATCATTTTTTG
* * *
221076 AAATTCAAA-TAAAAA-ATATCTCCTCTGCCAAAAGAATCGGCGACTACCCAGGAAATGGTACAC
518 AAATTCAAACTAAAAATATATCTCC-C--ACAAAAAAATCAGCGACTACCCAGGAAATGGTACAC
* *
221139 TAGGGTTTGAACATTGGGCCCGGTTTTATATGTAAATAATAATAATAATAATAATAATAATAATA
580 TAGGGTTTGAACATTGGGCCCGGTTTTATATGTAAATAATAATAATAATAATAATAAGAATAAGA
* *
221204 ATAATATTTTATAATAATAA-TAATATAATAATAATAATATTTAATGGTTGAAAAATGATGATTA
645 ATAATA-ATAATAATAATAATTAATATAATAATAATAATATTTAATGGTTGAAAAATGATGATTA
*
221268 TAG
709 TAA
* * *
221271 AATCCAACTTAATTCACAAGTCAATAACCTTTTTTATAAACTTAAAATAATAGCAACTAACTCCT
1 AATCCAACTTAATTCACAAGTCAAGAACCTTTTTTATAAAGTTAAAATAATAGCAACTAACACCT
*
221336 AATACTTAAATTATAACTAATAGTTTCCCAAAAAATTCTTAAACAATATATAACATATATCATAA
66 AATACTTAAATTATAACTAATAGTTTCCCAAACAATTCTTAAACAATATATAACATATATCATAA
*
221401 AATTTATCAGATATAGACATTTTAATTAAAAATTAACAAAAGTCTTGACATTTTTTTCCAAATAA
131 AATTGATCAGATATAGACATTTTAATTAAAAATTAACAAAAGTCTTGACA-TTTTTTCCAAATAA
* *
221466 AGAAATCAAAGAATCCAAATGAGATCTTGTTTGACAAGTTAATTAAATTTGGAAATTTAAATATG
195 AGAAATCAAAGAATCCAAATGTGATATTGTTTGACAAGTTAATTAAATTTGGAAATTTAAATATG
221531 TTTGATTAAG
Statistics
Matches: 882, Mismatches: 75, Indels: 23
0.90 0.08 0.02
Matches are distributed among these distances:
706 7 0.01
707 33 0.04
708 262 0.30
709 283 0.32
710 14 0.02
711 208 0.24
712 75 0.09
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (711 bp):
AATCCAACTTAATTCACAAGTCAAGAACCTTTTTTATAAAGTTAAAATAATAGCAACTAACACCT
AATACTTAAATTATAACTAATAGTTTCCCAAACAATTCTTAAACAATATATAACATATATCATAA
AATTGATCAGATATAGACATTTTAATTAAAAATTAACAAAAGTCTTGACATTTTTTCCAAATAAA
GAAATCAAAGAATCCAAATGTGATATTGTTTGACAAGTTAATTAAATTTGGAAATTTAAATATGA
GCATGTTTGATTAAGGCGGATTTAGATTCATTTGTGCTTATACACATGGATGGGTGACGTGGCAA
GCTCCTTACCCTTGGATCTAACCCTCCATCAATGGCTCACATGGGTTGTGTTTGTTTGACAAGGA
TTGAAGAGATGATGGCCCTTGAATAAAAGCTAATCAAGGGATGAAATCATTTTGTGTTTCTTTAC
ATGGACTGGTGATGTCATCACCTCAAAAGCTACACCAACAATAAATGCCTTATCATTTTTTGAAA
TTCAAACTAAAAATATATCTCCCACAAAAAAATCAGCGACTACCCAGGAAATGGTACACTAGGGT
TTGAACATTGGGCCCGGTTTTATATGTAAATAATAATAATAATAATAATAAGAATAAGAATAATA
ATAATAATAATAATTAATATAATAATAATAATATTTAATGGTTGAAAAATGATGATTATAA
Found at i:222725 original size:20 final size:20
Alignment explanation
Indices: 222700--222745 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
222690 TGGCTCACAT
222700 GGATTGTGTTTGTTTGACAA
1 GGATTGTGTTTGTTTGACAA
222720 GGATTGTGTTTGTTTGACAA
1 GGATTGTGTTTGTTTGACAA
222740 GGATTG
1 GGATTG
222746 AAGTGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.04, G:0.33, T:0.43
Consensus pattern (20 bp):
GGATTGTGTTTGTTTGACAA
Found at i:225391 original size:146 final size:146
Alignment explanation
Indices: 225156--225674 Score: 817
Period size: 146 Copynumber: 3.6 Consensus size: 146
225146 TCTGCCGTCA
* * * * * *
225156 TCCACCGTCCGATTGTCCTGATTTTTCAATAGGTTGTTTGTGTTGG-CATCGCGCAACTTTTCAC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTC-CGCAACTTTTGAC
** * * * ** * *
225220 CGTTCGGAATATTGATCGCAGATTCCGATCACCGACAAGAGGCTAAAAATCGTCCAGATTTATTT
65 CGTTCGGAATATTGATCAAATATTCCGATCACCGGCAAGAGGCTAAAAACCACCCGGATTTGTTT
225285 TCTCCGATCCGTCACCG
130 TCTCCGATCCGTCACCG
*
225302 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTGTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
*
225367 ATTCGGAATATTGATCAAATATTCCGATCACCGGCAAGAGGCTAAAAACCACCCGGATTTGTTTT
66 GTTCGGAATATTGATCAAATATTCCGATCACCGGCAAGAGGCTAAAAACCACCCGGATTTGTTTT
225432 CTCCGATCCGTCACCG
131 CTCCGATCCGTCACCG
225448 TCCACCG-CCTGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGAC
1 TCCACCGTCC-GATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGAC
*
225512 TGTTCGGAATATTGATCAAATATTCCGATCACCGGCAAGAGGCTAAAAACCACCCGGATTTGTTT
65 CGTTCGGAATATTGATCAAATATTCCGATCACCGGCAAGAGGCTAAAAACCACCCGGATTTGTTT
*
225577 TCTCCGATTCGTCACCG
130 TCTCCGATCCGTCACCG
* *
225594 TCCACCGTCTGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCACAACTTTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
225659 GTTCGGAATATTGATC
66 GTTCGGAATATTGATC
225675 GGAGATCCTG
Statistics
Matches: 346, Mismatches: 24, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
145 2 0.01
146 340 0.98
147 4 0.01
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.33
Consensus pattern (146 bp):
TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
GTTCGGAATATTGATCAAATATTCCGATCACCGGCAAGAGGCTAAAAACCACCCGGATTTGTTTT
CTCCGATCCGTCACCG
Found at i:226322 original size:55 final size:54
Alignment explanation
Indices: 226251--226599 Score: 273
Period size: 55 Copynumber: 6.3 Consensus size: 54
226241 TAACTAAATG
* * **
226251 AGACTTGAAAAATCTTCGGAAAACGTGTCCGCTCTCTATTCTTTCATAGAGTATA
1 AGACTCGAACAATCTTC-GAAAACGTGTCCGCTCTCTATTCTTTCAGGGAGTATA
* * *
226306 AGACTTGAACAATCTTCGACCAACGTGTCTGCT-TCCTATTCTTTCAGGGAGTAT-
1 AGACTCGAACAATCTTCGA-AAACGTGTCCGCTCT-CTATTCTTTCAGGGAGTATA
* * * * *
226360 AGAACTCGAACAACCTTCTGAAACCGGGTTCGCTCCCTATTGCTTT-AGGGAGTAT-
1 AG-ACTCGAACAATCTTC-GAAAACGTGTCCGCTCTCTATT-CTTTCAGGGAGTATA
* *
226415 AGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCATCT-TTCTTTCAGGGAGTATA
1 AG-ACTCGAACAATCTTC-GAAAACGTGTCCGCT-C-TCTATTCTTTCAGGGAGTATA
* * * * *
226472 AAACTCGAACAATCTTCAAAAATCGTGTCTGCTCTCTATTTCTTGCAGAGAGTATA
1 AGACTCGAACAATCTTCGAAAA-CGTGTCCGCTCTCTA-TTCTTTCAGGGAGTATA
* * * * *
226528 AGACTCGAACCATCTTCAACAAACGGGTTCACTCCCTCT-TTCTTTCAGGGAGTAT-
1 AGACTCGAACAATCTTCGA-AAACGTG-TC-CGCTCTCTATTCTTTCAGGGAGTATA
*
226583 GGAACTCGAAC-ATCTTC
1 AG-ACTCGAACAATCTTC
226600 TTCTTACGGG
Statistics
Matches: 245, Mismatches: 32, Indels: 34
0.79 0.10 0.11
Matches are distributed among these distances:
54 8 0.03
55 127 0.52
56 97 0.40
57 8 0.03
58 5 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (54 bp):
AGACTCGAACAATCTTCGAAAACGTGTCCGCTCTCTATTCTTTCAGGGAGTATA
Found at i:226780 original size:54 final size:54
Alignment explanation
Indices: 226351--227246 Score: 1135
Period size: 54 Copynumber: 16.5 Consensus size: 54
226341 CTATTCTTTC
* * * * * * *
226351 AGGGAGTATAGAACTCGAACAACCTTC-TGAAACCGGGTTCGCTCCCTATTGCTTT
1 AGGGAGTATGGAACTCGGAC-ATCTTCTTCAAA-CGGGTTCGCTCCCTCTTTCTCT
* * ** * *
226406 AGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCATCTTTCTTT
1 AGGGAGTATGGAACTCGGAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
** * ** * * *
226461 CAGGGAGTATAAAACTCGAACAATCTTC-AAAAATCGTG-TCTGCTCTCTATTTCT-T
1 -AGGGAGTATGGAACTCGGAC-ATCTTCTTCAAA-CGGGTTC-GCTCCCTCTTTCTCT
* * * ** * *
226516 GCAGAGAGTAT-AAGACTCGAACCATCTTCAACAAACGGGTTCACTCCCTCTTTCTTT
1 --AGGGAGTATGGA-ACTCGGA-CATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* ** *
226573 CAGGGAGTATGGAACTCGAACATCTTCTTCTTACGGGGTTCACTCCCTCTTTCTCT
1 -AGGGAGTATGGAACTCGGACATCTTCTTCAAAC-GGGTTCGCTCCCTCTTTCTCT
* * * * *
226629 AGGGAGTATGGAACTCAGACATC-TCTTCAAATGGGTTCACTCCTTCTTTCTTT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
226682 AAGGAGTATGGAACTCGGATATC-TCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
226735 AGGAAGTATGGAACTCGGAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
226789 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
226843 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
226897 TGGGAGTATGGAACTCAGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
226951 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
*
227005 AGGGAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
*
227059 AGGGAGTATGGAACTCGTACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * * *
227113 AGGGAGTATGGAAATCGTACATCTTCTTTAAACGGGTTCGCTCCCTCTTTCCCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
227167 AGGGAGTATGGAACTCGAACA--ATCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
227219 AGGGAGTATGGAACTCGAAAATCTTCTT
1 AGGGAGTATGGAACTCGGACATCTTCTT
227247 TTGCTTCACT
Statistics
Matches: 765, Mismatches: 61, Indels: 31
0.89 0.07 0.04
Matches are distributed among these distances:
52 48 0.06
53 85 0.11
54 425 0.56
55 85 0.11
56 113 0.15
57 9 0.01
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (54 bp):
AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
Found at i:227685 original size:36 final size:36
Alignment explanation
Indices: 227608--227809 Score: 124
Period size: 36 Copynumber: 5.6 Consensus size: 36
227598 GCTCCAACAC
* * * * *
227608 TCTTATGA-GAAGGCTTAAAATGGATTTCCTTCACGAC
1 TCTT-TGATGAAGACTTAAGATGG-TTTGCTTCACTAT
** *
227645 TCTTTGATGAAGACACAAGATGGTTTGCTTCATTAT
1 TCTTTGATGAAGACTTAAGATGGTTTGCTTCACTAT
* * * *
227681 TCTTTGGTGCATG-CTTAAGACGGTTTGCTTCACTAA
1 TCTTTGATG-AAGACTTAAGATGGTTTGCTTCACTAT
*
227717 TCTTT-AGTGAAGGCTTAAGATGG-TTGCTTCACTAT
1 TCTTTGA-TGAAGACTTAAGATGGTTTGCTTCACTAT
* * * * * **
227752 TATTTGGTGAAGACTTCAGATTGATCTGCTTCACTCC
1 TCTTTGATGAAGACTTAAGA-TGGTTTGCTTCACTAT
* * *
227789 TCTTCGGTGAAGGCTTAAGAT
1 TCTTTGATGAAGACTTAAGAT
227810 TGACTTTGCT
Statistics
Matches: 127, Mismatches: 31, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
35 28 0.22
36 57 0.45
37 42 0.33
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (36 bp):
TCTTTGATGAAGACTTAAGATGGTTTGCTTCACTAT
Found at i:229149 original size:125 final size:123
Alignment explanation
Indices: 228930--229289 Score: 420
Period size: 125 Copynumber: 2.9 Consensus size: 123
228920 ATCTTACATT
* * * * *
228930 GGTACGAGCCTTCAAAATGCCCCAACATCTCAGATTGTAAGGCT-TGCTCTCAATGCCTTCTTGG
1 GGTACGAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCTTCT-TC-ATGCCTTATTGG
* * * *
228994 TCTGAATCTTGTCATCTTC-ACACGATGTGGGTGCAGTCATGCCCCATCAGTGTCTTATACC
64 TTTGAATCTTGTCATC-TCAACATGATGTGGGTTCAGTCGTGCCCCAT-AGTGTCTTATACC
* * ** *
229055 GGTATGGGCCTTCAAAAAACCCCATCACCTCAAATTGTAAGGCTCCTTCTTCATGCCTTTTTGGT
1 GGTACGAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCT-CTTCTTCATGCCTTATTGGT
* * * *
229120 TTAAATCTTGTCATCTCAACATGACGTGGGTTCAGTCGTGCCCCAATATTGTCTTATACT
65 TTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCC-ATAGTGTCTTATACC
* * * *
229180 GGTACGAGCCTTTAAAATGCCTCATCACCTCAAATTCTAAGGCTCATTCTTCATGCCTCATT-GT
1 GGTACGAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTC-TTCTTCATGCCTTATTGGT
*
229244 TCTGAATCTTGTCATCTCAACCTGATGTGGGTTCAGTCGTGCCCCA
65 T-TGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCA
229290 ACATATCCTA
Statistics
Matches: 200, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
124 7 0.04
125 186 0.93
126 4 0.02
127 3 0.01
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (123 bp):
GGTACGAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCTTCTTCATGCCTTATTGGTT
TGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCATAGTGTCTTATACC
Found at i:230558 original size:14 final size:14
Alignment explanation
Indices: 230539--230590 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
230529 TCATTCTCTT
230539 TTTTTTTATTTTCA
1 TTTTTTTATTTTCA
* *
230553 TTTTTTCATTTACAA
1 TTTTTTTATTTTC-A
*
230568 TTTTTTCT-TTTTCT
1 TTTTTT-TATTTTCA
230582 TTTTTTTAT
1 TTTTTTTAT
230591 CTTTTCTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 11 0.37
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTATTTTCA
Found at i:230600 original size:12 final size:11
Alignment explanation
Indices: 230570--230607 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
230560 ATTTACAATT
230570 TTTTCTTTTTC
1 TTTTCTTTTTC
230581 TTTT-TTTTATC
1 TTTTCTTTT-TC
230592 TTTTCTTTTCTC
1 TTTTCTTTT-TC
230604 TTTT
1 TTTT
230608 AACATTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:230620 original size:44 final size:44
Alignment explanation
Indices: 230535--230621 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
230525 TCTTTCATTC
* *
230535 TCTTTTTTTTTATTTTCATTTTTTCATTTACAATTTTTTCTTTT
1 TCTTTTTTTTTATTTTCATTTTCTCATTTACAATTTCTTCTTTT
* *
230579 TCTTTTTTTTATCTTTTC-TTTTCTCTTTTA-ACATTTCTTCTTT
1 TCTTTTTTTT-TATTTTCATTTTCTCATTTACA-ATTTCTTCTTT
230622 CTCTCATGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 1 0.03
44 30 0.81
45 6 0.16
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (44 bp):
TCTTTTTTTTTATTTTCATTTTCTCATTTACAATTTCTTCTTTT
Found at i:236508 original size:146 final size:146
Alignment explanation
Indices: 235990--236508 Score: 815
Period size: 146 Copynumber: 3.6 Consensus size: 146
235980 TCTGCCGTCA
* * * * * *
235990 TCCACCGTCCGATTGTCCTGATTTTTCAATAGGTTGTTTGTGTTGG-CATCGCGCAACTTTTCAC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTC-CGCAACTTTTGAC
** * * ** * *
236054 CGTTCGGAATATTGATCGCAGATTCCGATCACCGGCAAGAGGCTAAAAATCGTCTGGATTTATTT
65 CGTTCGGAATATTGATCAAATATTCCGATCACCGGCAAGAGGCTAAAAACCACCCGGATTTGTTT
236119 TCTCCGATCCGTCACCG
130 TCTCCGATCCGTCACCG
236136 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
* * * *
236201 GTTCGTAATATTGATGAAATATTCCGATCACTGGCAAGAGGCTAAAAACCACCCAGATTTGTTTT
66 GTTCGGAATATTGATCAAATATTCCGATCACCGGCAAGAGGCTAAAAACCACCCGGATTTGTTTT
236266 CTCCGATCCGTCACCG
131 CTCCGATCCGTCACCG
* * *
236282 TCCACCGTCTGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGCCCTTCCGCAACTTTTGACT
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
236347 GTTCGGAATATTGATCAAATATTCCGATCACCGGCAAGAGGCTAAAAACCACCCGGATTTGTTTT
66 GTTCGGAATATTGATCAAATATTCCGATCACCGGCAAGAGGCTAAAAACCACCCGGATTTGTTTT
*
236412 CTCCGATTCGTCACCG
131 CTCCGATCCGTCACCG
*
236428 TCCACCGTCTGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
1 TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
236493 GTTCGGAATATTGATC
66 GTTCGGAATATTGATC
236509 GGTGATCCTG
Statistics
Matches: 344, Mismatches: 28, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
146 341 0.99
147 3 0.01
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (146 bp):
TCCACCGTCCGATCGTCCTGATTTTTCAATATGTTGTTCGTGATGGCCTTCCGCAACTTTTGACC
GTTCGGAATATTGATCAAATATTCCGATCACCGGCAAGAGGCTAAAAACCACCCGGATTTGTTTT
CTCCGATCCGTCACCG
Found at i:238646 original size:28 final size:28
Alignment explanation
Indices: 238615--238670 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
238605 TCTCATAAAA
238615 TGTAATAATACCTAAGAAAATAAGAGGT
1 TGTAATAATACCTAAGAAAATAAGAGGT
* *
238643 TGTAATATTATCTAAGAAAATAAGAGGT
1 TGTAATAATACCTAAGAAAATAAGAGGT
238671 AATGAGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (28 bp):
TGTAATAATACCTAAGAAAATAAGAGGT
Found at i:238680 original size:28 final size:28
Alignment explanation
Indices: 238626--238680 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
238616 GTAATAATAC
** *
238626 CTAAGAAAATAAGAGGTTGTAATATTAT
1 CTAAGAAAATAAGAGGTAATAAGATTAT
*
238654 CTAAGAAAATAAGAGGTAATGAGATTA
1 CTAAGAAAATAAGAGGTAATAAGATTA
238681 CTATTGTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.20, T:0.27
Consensus pattern (28 bp):
CTAAGAAAATAAGAGGTAATAAGATTAT
Found at i:242246 original size:24 final size:23
Alignment explanation
Indices: 242215--242260 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
242205 AATTTTTTAT
**
242215 ATAAATAATATTTTATAATAATA
1 ATAAATAATATAATATAATAATA
242238 ATAATATAATATAATATAATAAT
1 ATAA-ATAATATAATATAATAAT
242261 GGTTGAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAAATAATATAATATAATAATA
Found at i:243503 original size:24 final size:24
Alignment explanation
Indices: 243427--243535 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
243417 AAACGGATAC
* * * *
243427 ATCAGAAATTAAAACAGAATTCAG
1 ATCAGAAATCAGAATAGAATCCAG
* * *
243451 ATGAGATATCAGAATAGAATCCAT
1 ATCAGAAATCAGAATAGAATCCAG
243475 ATCAGAAATCAGAATAGAATCCAG
1 ATCAGAAATCAGAATAGAATCCAG
* ** * * *
243499 GTCAGGTATCAGAACAGAATTCAA
1 ATCAGAAATCAGAATAGAATCCAG
243523 ATC-GAAAATCAGA
1 ATCAG-AAATCAGA
243536 TAAAATATTC
Statistics
Matches: 65, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
23 1 0.02
24 64 0.98
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAATAGAATCCAG
Found at i:245680 original size:13 final size:14
Alignment explanation
Indices: 245661--245693 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
245651 TCAAAGTCAA
245661 CGAGTTGACCCAGT
1 CGAGTTGACCCAGT
*
245675 -GAGTTGACTCAGT
1 CGAGTTGACCCAGT
245688 CGAGTT
1 CGAGTT
245694 AACTCAGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (14 bp):
CGAGTTGACCCAGT
Found at i:245701 original size:27 final size:29
Alignment explanation
Indices: 245661--245717 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
245651 TCAAAGTCAA
*
245661 CGAGTTGACCCAGTG-AG-TTGACTCAGT
1 CGAGTTAACCCAGTGCAGATTGACTCAGT
* *
245688 CGAGTTAACTCAGTGCGGATTGACTCAGT
1 CGAGTTAACCCAGTGCAGATTGACTCAGT
245717 C
1 C
245718 AAGTCAAGCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 13 0.52
28 1 0.04
29 11 0.44
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (29 bp):
CGAGTTAACCCAGTGCAGATTGACTCAGT
Found at i:245715 original size:15 final size:14
Alignment explanation
Indices: 245661--245717 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
245651 TCAAAGTCAA
*
245661 CGAGTTGACCCAGT
1 CGAGTTGACTCAGT
245675 -GAGTTGACTCAGT
1 CGAGTTGACTCAGT
*
245688 CGAGTTAACTCAGT
1 CGAGTTGACTCAGT
245702 GCG-GATTGACTCAGT
1 -CGAG-TTGACTCAGT
245717 C
1 C
245718 AAGTCAAGCG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 12 0.32
14 14 0.38
15 11 0.30
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (14 bp):
CGAGTTGACTCAGT
Found at i:247851 original size:19 final size:20
Alignment explanation
Indices: 247827--247869 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
247817 AGCATTTATC
*
247827 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
247846 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
247866 TTCA
1 TTCA
247870 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:251486 original size:19 final size:20
Alignment explanation
Indices: 251462--251504 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
251452 AGCATTTATC
*
251462 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
251481 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
251501 TTCA
1 TTCA
251505 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Done.