Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008655.1 Hibiscus syriacus cultivar Beakdansim tig00111649_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: 378222
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 3 of 3
Found at i:318923 original size:22 final size:24
Alignment explanation
Indices: 318890--318946 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 24
318880 AAGAATAATA
* *
318890 ATGCATTTGTGACAC-TTTT-TTT
1 ATGCCTTTGTGACACGTTTTGTCT
*
318912 ATGTCTTTGTGACACGTTTTGTCT
1 ATGCCTTTGTGACACGTTTTGTCT
318936 ATGCCTTTGTG
1 ATGCCTTTGTG
318947 GCATATTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 13 0.45
23 4 0.14
24 12 0.41
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (24 bp):
ATGCCTTTGTGACACGTTTTGTCT
Found at i:319329 original size:3 final size:3
Alignment explanation
Indices: 319311--319365 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
319301 TTGTCCGGGG
*
319311 TAT TAT TAA TATT TAT TAT TAT TAT TAT TA- TAT TAT TA- TAT T-T
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
319354 ATAT TAT T-T TAT
1 -TAT TAT TAT TAT
319366 GTAGTTCCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
2 7 0.16
3 34 0.77
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:319352 original size:19 final size:19
Alignment explanation
Indices: 319311--319362 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
319301 TTGTCCGGGG
*
319311 TATTATTAATATTTATTAT
1 TATTATTATTATTTATTAT
319330 TATTATTATTATATTATTA-
1 TATTATTATTAT-TTATTAT
319349 TATT-TATATTATTT
1 TATTAT-TATTATTT
319363 TATGTAGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.10
19 21 0.70
20 6 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTATTATTATTTATTAT
Found at i:327983 original size:18 final size:19
Alignment explanation
Indices: 327955--327993 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
327945 AAAACAAAAT
*
327955 AAGCGATTCCAGAATAATG
1 AAGCGATTCCACAATAATG
*
327974 AAGC-ATTCCACAATATTG
1 AAGCGATTCCACAATAATG
327992 AA
1 AA
327994 AGCAAATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (19 bp):
AAGCGATTCCACAATAATG
Found at i:329506 original size:257 final size:255
Alignment explanation
Indices: 328917--329568 Score: 919
Period size: 257 Copynumber: 2.5 Consensus size: 255
328907 TTTGGAAACA
* * * * * *
328917 AGAAAGCAATTTTCAAAGTTTTTCATTTATTGTTTTCAGAAAATGGAATTTTTGAAAAGTAATAA
1 AGAAAGCGATTTTCAAAGTTTCTCATTTACTATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAA
* * *
328982 AGCGATTTCCAAAGTTTATTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTCGGGCCATCA
66 AGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATT-GTAAATCATTCGGGCCATCA
* * *
329047 GTAAGTCTTTCGAGCATTATGATTAAATCCTTCAGATCACTGTAAGTCTTTCGAGAAATATGTAA
130 GTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGATCACTATAAGTCTTTCGAGAAAGATGTAA
* * *
329112 GTCTTTCGGGCCATCTATAAGACATTCTGGTAGGATGTTTCCACATGATTTTCAAAAAATG
195 GTCCTTCGGGCCATCTATAAGACATTCAGGCAGGATGTTTCCACATGATTTTCAAAAAATG
* *
329173 AGAAAGAGATTTTCAAAGTTTCTCATTTAAGTATTTTTCAGAAAATGAAATTTTTGAAAAGTAAG
1 AGAAAGCGATTTTCAAAGTTTCTCATTT-ACTA-TTTTCAGAAAATGAAATTTTTGAAAAGTAAG
* * * *
329238 AAAGCGATTTCCAAAGTATCTTTCCCAGTAAATTATTT-CAAAATTAGTAAATCATTCGGGCCAT
64 AAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATT-GTAAATCATTCGGGCCAT
* * * * *
329302 CTGTAAGTCTTTCGAGCATGATGATTAAATCTTTTAGGTCATCTATAAGTCTTTCGAGCAAGATG
128 CAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGATCA-CTATAAGTCTTTCGAGAAAGATG
* * *
329367 ATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCAGGATGTTTCCTCATGATTTTCGAAAAATG
192 -TAAGTCCTTCGGGCCATCTATAAGACATTCAGGCAGGATGTTTCCACATGATTTTCAAAAAATG
* *
329432 AGAAAGCGATTTCCAAAGTTTCTCATTTACTATTTTCAAAAAATGAAATTTTTGAAAAGTAAGAA
1 AGAAAGCGATTTTCAAAGTTTCTCATTTACTATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAA
* * * *
329497 AGTGATTTCCAAAATTTCTTACCCAGTAAACTATTTCCCAAATTGGAAAGTCTTTCGGGCCATCA
66 AGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGTAAA-TCATTCGGGCCATCA
329562 GTAAGTC
130 GTAAGTC
329569 CTTCAGGCAG
Statistics
Matches: 348, Mismatches: 42, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
256 25 0.07
257 127 0.36
258 112 0.32
259 84 0.24
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (255 bp):
AGAAAGCGATTTTCAAAGTTTCTCATTTACTATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAA
AGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGTAAATCATTCGGGCCATCAG
TAAGTCTTTCGAGCATGATGATTAAATCCTTCAGATCACTATAAGTCTTTCGAGAAAGATGTAAG
TCCTTCGGGCCATCTATAAGACATTCAGGCAGGATGTTTCCACATGATTTTCAAAAAATG
Found at i:329708 original size:42 final size:41
Alignment explanation
Indices: 329661--329763 Score: 102
Period size: 42 Copynumber: 2.5 Consensus size: 41
329651 AGTTGGTAAG
*
329661 TCCTTCGGGCCATCAGTAAG-TCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATC-GTAAGCTCTTTCGAGCAAGATGA-TAAA
* * * *
329703 TCCTTCGAGTCAT-TTATAGCTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGCCATCGTA-AGCTCTTTCGAGCAAGATGATAAA
*
329744 TCCTTCTGGCCATCCGTAAG
1 TCCTTCGGGCCAT-CGTAAG
329764 ACCTTCGGGT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
40 2 0.04
41 15 0.31
42 29 0.60
43 2 0.04
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGCCATCGTAAGCTCTTTCGAGCAAGATGATAAA
Found at i:329906 original size:372 final size:371
Alignment explanation
Indices: 329222--329957 Score: 1023
Period size: 372 Copynumber: 2.0 Consensus size: 371
329212 AGAAAATGAA
* * *
329222 ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTATCTTTCCCAGTAAATTATTTCAAAATTAGTA
1 ATTTTTGAAAAATAAGAAAGCGATTTCCAAAGTATCTTACCCAGTAAACTATTTCAAAATTAGTA
* **
329287 AATCATTCGGGCCATCTGTAAGTCTTTCGAGCATGATGATTAAATCTTTTAGGTCATCTATAAGT
66 AATCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTCGAGGTCATCTATAAGT
* * *
329352 CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCAGGATGTTTCCTCAT
131 CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAGGATATTTCCACAT
* * *
329417 GATTTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTACTATTTTCAAAAAATGAAATT
196 GATTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTACAATTTTCAAAAAATGAAATC
* *
329482 TTTGAAAAGTAAGAAAGTGATTTCCAAAATTTCTTACCCAGTAAACTATTTCCCAAATTGGAAAG
261 TTTGAAAAGTAAGAAAGTGATTTCCAAAATTTCTTACCCAGTAAACTATTTCCAAAATTAGAAAG
* **
329547 TCTTTCGGGCCATCAGTAAGTCCTTC-AGGCAGGATGTTTCCACATG
326 TCCTTCGACCCATCAGTAAGTCCTTCGA-GCAGGATGTTTCCACATG
* * * * *
329593 ATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAGTTGGT
1 ATTTTTGAAAAATAAGAAAGCGATTTCCAAAGTATCTTACCCAGTAAACTATTT-CAAAATTAGT
* * *
329658 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGA-GTCATTTAT-A
65 AAATCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAAT-CTTCGAGGTCATCTATAA
* * * * *
329721 GCTCTTTCGAGCAAGATGATAAGTCCTTCTGGCCATCCGTAAGACCTTCGGGTAGGATATTTTCA
129 G-TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAGGATATTTCCA
* * * *
329786 CATTATTTT-GAAAAATGAGAAAACGATTTTCAAAGTTTCTCATTTA-AATCTTTTATGAAAATG
193 CATGATTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTACAAT-TTTCA-AAAAATG
* *
329849 AAATCTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTA
256 AAATCTTTGAAAAGTAAGAAAGTGATTTCCAAAATTTCTTACCCAGTAAACTATTTCCAAAATTA
* * * *
329914 GCAGGTCCTTCGACCCATCAGTAAGTCTTTCGAGCATGATGTTT
321 GAAAGTCCTTCGACCCATCAGTAAGTCCTTCGAGCAGGATGTTT
329958 AAATCCTTTG
Statistics
Matches: 319, Mismatches: 40, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
370 2 0.01
371 90 0.28
372 222 0.70
373 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (371 bp):
ATTTTTGAAAAATAAGAAAGCGATTTCCAAAGTATCTTACCCAGTAAACTATTTCAAAATTAGTA
AATCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTCGAGGTCATCTATAAGT
CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAGGATATTTCCACAT
GATTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTACAATTTTCAAAAAATGAAATC
TTTGAAAAGTAAGAAAGTGATTTCCAAAATTTCTTACCCAGTAAACTATTTCCAAAATTAGAAAG
TCCTTCGACCCATCAGTAAGTCCTTCGAGCAGGATGTTTCCACATG
Found at i:330128 original size:12 final size:13
Alignment explanation
Indices: 330107--330148 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
330097 TCTGTCTGGG
330107 TTAT-TATTAATA
1 TTATATATTAATA
330119 TTA-ATATTAATA
1 TTATATATTAATA
*
330131 TTATTATATTTATA
1 TTA-TATATTAATA
330145 TTAT
1 TTAT
330149 TTTATGTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 14 0.54
13 1 0.04
14 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATATATTAATA
Found at i:330145 original size:14 final size:15
Alignment explanation
Indices: 330117--330149 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
330107 TTATTATTAA
330117 TATTAATATTAATAT
1 TATTAATATTAATAT
*
330132 TATT-ATATTTATAT
1 TATTAATATTAATAT
330146 TATT
1 TATT
330150 TTATGTAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTAATATTAATAT
Found at i:336968 original size:3 final size:3
Alignment explanation
Indices: 336960--337018 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
336950 TTTTTATCCA
*
336960 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
337008 TAT TAT TAT TA
1 TAT TAT TAT TA
337019 ATAAATATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:337033 original size:14 final size:14
Alignment explanation
Indices: 337014--337054 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
337004 TTATTATTAT
337014 TATTAATAAATATA
1 TATTAATAAATATA
337028 TATTAAATAAATATA
1 TATT-AATAAATATA
*
337043 TATAAATAAATA
1 TATTAATAAATA
337055 ATTACAGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATTAATAAATATA
Found at i:337038 original size:15 final size:15
Alignment explanation
Indices: 337014--337054 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
337004 TTATTATTAT
337014 TATT-AATAAATATA
1 TATTAAATAAATATA
337028 TATTAAATAAATATA
1 TATTAAATAAATATA
337043 TA-TAAATAAATA
1 TATTAAATAAATA
337055 ATTACAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTAAATAAATATA
Found at i:342580 original size:14 final size:15
Alignment explanation
Indices: 342550--342582 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
342540 TTATTATTTT
342550 ATTTATTAAGATAAA
1 ATTTATTAAGATAAA
*
342565 ATTTATTAA-TTAAA
1 ATTTATTAAGATAAA
342579 ATTT
1 ATTT
342583 GAAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTTATTAAGATAAA
Found at i:350194 original size:16 final size:16
Alignment explanation
Indices: 350168--350212 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
350158 TTTGAATACA
*
350168 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
350185 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
350200 ATTCAATTTATTT
1 ATTCAATTTATTT
350213 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:351277 original size:83 final size:83
Alignment explanation
Indices: 350994--351793 Score: 1378
Period size: 83 Copynumber: 9.7 Consensus size: 83
350984 AATTAAATGA
350994 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
** *
351058 AA-CAATCATTGTGTTTAG
65 AACCAATCATTGAATTTGG
* * *
351076 AAGATGAATTTG-CCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
* *
351139 GAA-CAATCATTGAGTTTAG
64 GAACCAATCATTGAATTTGG
* *
351158 AAGATAAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
351222 AACCAATCATTGAATTTGG
65 AACCAATCATTGAATTTGG
351241 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
351306 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
351324 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
351389 ACCAATCATTGAGTTTGG
66 ACCAATCATTGAATTTGG
*
351407 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTCGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
351472 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
*
351490 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTCGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
351555 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
*
351573 AAGATGAATGTGTTCATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
351638 ACCAATCATTGAGTTTGG
66 ACCAATCATTGAATTTGG
351656 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
351721 ACCAATCATTGAATTCGG
66 ACCAATCATTGAATTTGG
351739 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
351794 ATTCAGTAGG
Statistics
Matches: 694, Mismatches: 20, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
81 1 0.00
82 134 0.19
83 557 0.80
84 2 0.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (83 bp):
AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAATTTGG
Found at i:352747 original size:116 final size:117
Alignment explanation
Indices: 352536--352814 Score: 442
Period size: 117 Copynumber: 2.4 Consensus size: 117
352526 TCGAATCCAC
*
352536 TTGATGGATCA-TTTCTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAG
1 TTGATGGATCAGTTT-TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAA
* *
352597 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-AATTGAATCCATCAT
65 AAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGAATTGAATCCATCAT
*
352649 TTGATGGATCAGTTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAA
1 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAA
**
352714 AGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAATCCATCAT
66 AGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGAATTGAATCCATCAT
* *
352766 TTGATGGATCAGCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATC
1 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC
352815 TAAAGAAGGA
Statistics
Matches: 152, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
113 38 0.25
114 3 0.02
115 1 0.01
116 51 0.34
117 59 0.39
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (117 bp):
TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAA
AGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGAATTGAATCCATCAT
Found at i:353092 original size:117 final size:116
Alignment explanation
Indices: 352885--353270 Score: 519
Period size: 117 Copynumber: 3.3 Consensus size: 116
352875 CCCCAGCGGA
* **
352885 AAGTTCATAATGAGAAGAACTTGTTCAATTTTTTTGGTTTGAATTCATCATTTGATGGATCAACA
1 AAGTTCATAATAAGAAGAACTTGTTCAA-CCTTTTGGTTTGAATTCATCATTTGATGGATCAACA
*
352950 TTACCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAAAG
65 TT-CCAGGAAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAAAG
353003 AAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACAT
1 AAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACAT
* * *
353068 TGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCGTCTGAAGAAGGAAGAAG
66 T-CCAGGAAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAAAG
* * * * * * * *
353120 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-ATCTGAATTCATCACTGGATGGATTATTTC
1 AAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCA--AC
* *
353184 -TTCCAGAGAA-AGTTCATAATGAGAAGAACTCCTCATATGAAGAA-GAAAGAAG
64 ATTCCAG-GAAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAA-AAG
*
353236 AAGTTCATAATAAGAAGAACTTGTTCAACTTTTTG
1 AAGTTCATAATAAGAAGAACTTGTTCAACCTTTTG
353271 CATAATTCTA
Statistics
Matches: 240, Mismatches: 23, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
115 3 0.01
116 90 0.38
117 119 0.50
118 28 0.12
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (116 bp):
AAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACAT
TCCAGGAAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAAAG
Found at i:353506 original size:3 final size:3
Alignment explanation
Indices: 353493--353542 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
353483 TTTTTATCCA
* *
353493 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
353541 TA
1 TA
353543 ATAAATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:353560 original size:13 final size:13
Alignment explanation
Indices: 353538--353578 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 13
353528 TCATTATTAT
353538 TATT-AATAAATA
1 TATTAAATAAATA
353550 TATTAAATAAATA
1 TATTAAATAAATA
353563 TA-TAAATAAATA
1 TATTAAATAAATA
353575 -ATTA
1 TATTA
353579 CAGACCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.04
12 16 0.59
13 10 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATTAAATAAATA
Found at i:356350 original size:23 final size:23
Alignment explanation
Indices: 356323--356382 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
356313 ACTTAAAACT
356323 TGTCCCGAATGACCACACATATAA
1 TGTCCCGAATGACCACACATA-AA
* *
356347 -GTCCCTAA-GAAC-CACATAAA
1 TGTCCCGAATGACCACACATAAA
*
356367 TATCCCGAATGACCAC
1 TGTCCCGAATGACCAC
356383 TCCTTAAGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 7
0.70 0.12 0.17
Matches are distributed among these distances:
20 2 0.07
21 12 0.43
22 6 0.21
23 8 0.29
ACGTcount: A:0.38, C:0.32, G:0.12, T:0.18
Consensus pattern (23 bp):
TGTCCCGAATGACCACACATAAA
Found at i:356381 original size:21 final size:23
Alignment explanation
Indices: 356324--356382 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
356314 CTTAAAACTT
*
356324 GTCCCGAATGACCACACATATAA
1 GTCCCGAATGACCACACAAATAA
* *
356347 GTCCCTAA-GAACCACATAAAT-A
1 GTCCCGAATG-ACCACACAAATAA
356369 -TCCCGAATGACCAC
1 GTCCCGAATGACCAC
356383 TCCTTAAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 11 0.37
22 3 0.10
23 16 0.53
ACGTcount: A:0.39, C:0.32, G:0.12, T:0.17
Consensus pattern (23 bp):
GTCCCGAATGACCACACAAATAA
Found at i:357081 original size:19 final size:19
Alignment explanation
Indices: 357057--357106 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
357047 CCCTAGCTGT
* *
357057 GGTATCGATGCCAGGCCTG
1 GGTATCGATACCAAGCCTG
357076 GGTATCGATACCAAGCCTG
1 GGTATCGATACCAAGCCTG
357095 GGTATCGATACC
1 GGTATCGATACC
357107 CATTTTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (19 bp):
GGTATCGATACCAAGCCTG
Found at i:362273 original size:23 final size:23
Alignment explanation
Indices: 362243--362290 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
362233 CCACGAGGTC
362243 CCACTGCATCATTCCAACATTCT
1 CCACTGCATCATTCCAACATTCT
362266 CCACTGCATCATTCCAACATTCT
1 CCACTGCATCATTCCAACATTCT
362289 CC
1 CC
362291 GCAATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.42, G:0.04, T:0.29
Consensus pattern (23 bp):
CCACTGCATCATTCCAACATTCT
Found at i:365893 original size:15 final size:16
Alignment explanation
Indices: 365875--365909 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
365865 TTATTTTAAT
*
365875 AATATTGTTTTA-CTA
1 AATATTGTTTAACCTA
365890 AATATTGTTTAACCTA
1 AATATTGTTTAACCTA
365906 AATA
1 AATA
365910 CAATGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (16 bp):
AATATTGTTTAACCTA
Found at i:373107 original size:13 final size:13
Alignment explanation
Indices: 373089--373133 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
373079 ATTATTATAT
373089 ATTTTAAATATTA
1 ATTTTAAATATTA
*
373102 ATTTTATAT-TATA
1 ATTTTAAATAT-TA
373115 TATTTTAAATATTA
1 -ATTTTAAATATTA
373129 ATTTT
1 ATTTT
373134 CTATTTCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 1 0.04
13 15 0.56
14 10 0.37
15 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTTAAATATTA
Found at i:373116 original size:27 final size:27
Alignment explanation
Indices: 373081--373159 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
373071 AGTTTGAAAT
373081 TATTATATATTTTAAATATTAATTTTA
1 TATTATATATTTTAAATATTAATTTTA
*
373108 TATTATATATTTTAAATATTAATTTTC
1 TATTATATATTTTAAATATTAATTTTA
*
373135 TATT-TCTA-TTTATAATA-TAATTTTA
1 TATTATATATTTTA-AATATTAATTTTA
373160 CTCTTTAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
25 11 0.23
26 7 0.15
27 30 0.62
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (27 bp):
TATTATATATTTTAAATATTAATTTTA
Done.