Multiple sequence alignment - TraesCS6A01G214800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G214800 chr6A 100.000 3302 0 0 1 3302 393636171 393639472 0.000000e+00 6098
1 TraesCS6A01G214800 chr6A 93.478 736 45 3 2569 3302 475971402 475972136 0.000000e+00 1090
2 TraesCS6A01G214800 chr6A 92.799 736 51 2 2569 3302 464655649 464654914 0.000000e+00 1064
3 TraesCS6A01G214800 chr6A 92.750 731 51 1 2569 3297 513953496 513954226 0.000000e+00 1055
4 TraesCS6A01G214800 chr6D 97.158 1478 32 4 845 2319 274341749 274340279 0.000000e+00 2488
5 TraesCS6A01G214800 chr6D 87.647 850 58 15 1 844 274342606 274341798 0.000000e+00 944
6 TraesCS6A01G214800 chr6B 90.717 1465 79 21 428 1871 436710298 436708870 0.000000e+00 1899
7 TraesCS6A01G214800 chr6B 90.909 429 27 4 1976 2393 436672253 436671826 1.720000e-157 566
8 TraesCS6A01G214800 chr6B 82.422 256 42 3 106 359 436725955 436725701 1.540000e-53 220
9 TraesCS6A01G214800 chr6B 98.319 119 2 0 1862 1980 436708472 436708354 3.340000e-50 209
10 TraesCS6A01G214800 chr3A 92.935 736 49 3 2569 3302 11700032 11699298 0.000000e+00 1068
11 TraesCS6A01G214800 chr3A 92.663 736 52 2 2569 3302 7724978 7725713 0.000000e+00 1059
12 TraesCS6A01G214800 chr3A 92.663 736 51 3 2569 3302 11672582 11671848 0.000000e+00 1057
13 TraesCS6A01G214800 chr3A 92.537 737 50 5 2569 3302 340238464 340239198 0.000000e+00 1051
14 TraesCS6A01G214800 chr4A 92.663 736 51 3 2569 3302 680218699 680217965 0.000000e+00 1057
15 TraesCS6A01G214800 chr7A 92.527 736 53 1 2569 3302 522727781 522728516 0.000000e+00 1053
16 TraesCS6A01G214800 chr2D 81.793 357 63 2 1796 2151 441871325 441870970 6.930000e-77 298
17 TraesCS6A01G214800 chr2D 79.188 394 71 7 1027 1419 441872216 441871833 2.530000e-66 263
18 TraesCS6A01G214800 chr2D 85.417 144 20 1 1421 1564 441871703 441871561 7.380000e-32 148
19 TraesCS6A01G214800 chr2A 80.879 387 66 7 1796 2175 585741134 585740749 6.930000e-77 298
20 TraesCS6A01G214800 chr2A 79.449 399 61 15 1027 1419 585741983 585741600 2.530000e-66 263
21 TraesCS6A01G214800 chr2A 82.915 199 30 4 1223 1419 272968084 272967888 3.390000e-40 176
22 TraesCS6A01G214800 chr2A 86.111 144 19 1 1421 1564 585741515 585741373 1.590000e-33 154
23 TraesCS6A01G214800 chr2B 81.564 358 64 2 1796 2152 521517216 521516860 8.960000e-76 294
24 TraesCS6A01G214800 chr2B 79.093 397 63 16 1027 1419 521518102 521517722 4.230000e-64 255
25 TraesCS6A01G214800 chr2B 84.722 144 21 1 1421 1564 521517594 521517452 3.430000e-30 143


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G214800 chr6A 393636171 393639472 3301 False 6098.000000 6098 100.000000 1 3302 1 chr6A.!!$F1 3301
1 TraesCS6A01G214800 chr6A 475971402 475972136 734 False 1090.000000 1090 93.478000 2569 3302 1 chr6A.!!$F2 733
2 TraesCS6A01G214800 chr6A 464654914 464655649 735 True 1064.000000 1064 92.799000 2569 3302 1 chr6A.!!$R1 733
3 TraesCS6A01G214800 chr6A 513953496 513954226 730 False 1055.000000 1055 92.750000 2569 3297 1 chr6A.!!$F3 728
4 TraesCS6A01G214800 chr6D 274340279 274342606 2327 True 1716.000000 2488 92.402500 1 2319 2 chr6D.!!$R1 2318
5 TraesCS6A01G214800 chr6B 436708354 436710298 1944 True 1054.000000 1899 94.518000 428 1980 2 chr6B.!!$R3 1552
6 TraesCS6A01G214800 chr3A 11699298 11700032 734 True 1068.000000 1068 92.935000 2569 3302 1 chr3A.!!$R2 733
7 TraesCS6A01G214800 chr3A 7724978 7725713 735 False 1059.000000 1059 92.663000 2569 3302 1 chr3A.!!$F1 733
8 TraesCS6A01G214800 chr3A 11671848 11672582 734 True 1057.000000 1057 92.663000 2569 3302 1 chr3A.!!$R1 733
9 TraesCS6A01G214800 chr3A 340238464 340239198 734 False 1051.000000 1051 92.537000 2569 3302 1 chr3A.!!$F2 733
10 TraesCS6A01G214800 chr4A 680217965 680218699 734 True 1057.000000 1057 92.663000 2569 3302 1 chr4A.!!$R1 733
11 TraesCS6A01G214800 chr7A 522727781 522728516 735 False 1053.000000 1053 92.527000 2569 3302 1 chr7A.!!$F1 733
12 TraesCS6A01G214800 chr2D 441870970 441872216 1246 True 236.333333 298 82.132667 1027 2151 3 chr2D.!!$R1 1124
13 TraesCS6A01G214800 chr2A 585740749 585741983 1234 True 238.333333 298 82.146333 1027 2175 3 chr2A.!!$R2 1148
14 TraesCS6A01G214800 chr2B 521516860 521518102 1242 True 230.666667 294 81.793000 1027 2152 3 chr2B.!!$R1 1125

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
605 612 0.032117 ACCATCATCAGGACGGAGGA 60.032 55.0 0.0 0.0 31.52 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2498 3145 0.108138 GCTCCGGTGTGCATACTCTT 60.108 55.0 13.64 0.0 0.0 2.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.261671 CGCACTTGCCCGTCTACT 59.738 61.111 0.00 0.00 37.91 2.57
53 54 1.805945 CGCACTTGCCCGTCTACTC 60.806 63.158 0.00 0.00 37.91 2.59
54 55 1.805945 GCACTTGCCCGTCTACTCG 60.806 63.158 0.00 0.00 34.31 4.18
64 65 2.827190 TCTACTCGGCGCCGACAT 60.827 61.111 45.37 35.73 44.01 3.06
96 97 4.539509 GAGATCTTCGACGATGTGTAGT 57.460 45.455 9.41 0.00 0.00 2.73
110 111 9.525409 GACGATGTGTAGTTTTTACCTATGTAT 57.475 33.333 0.00 0.00 0.00 2.29
135 136 9.811995 ATGTAGTACGTAGATTTCTATTTTGCA 57.188 29.630 0.00 0.00 0.00 4.08
136 137 9.811995 TGTAGTACGTAGATTTCTATTTTGCAT 57.188 29.630 0.00 0.00 0.00 3.96
139 140 9.477484 AGTACGTAGATTTCTATTTTGCATAGG 57.523 33.333 0.00 0.00 0.00 2.57
140 141 9.257651 GTACGTAGATTTCTATTTTGCATAGGT 57.742 33.333 0.00 0.00 0.00 3.08
141 142 8.142994 ACGTAGATTTCTATTTTGCATAGGTG 57.857 34.615 0.00 0.00 0.00 4.00
182 183 6.047870 TGAAATTTGAGTTTCATGGTTGTGG 58.952 36.000 0.00 0.00 41.70 4.17
187 188 3.074390 TGAGTTTCATGGTTGTGGAGGAT 59.926 43.478 0.00 0.00 0.00 3.24
194 195 3.025322 TGGTTGTGGAGGATGTTTTGT 57.975 42.857 0.00 0.00 0.00 2.83
204 205 3.631250 AGGATGTTTTGTTGTGGTGTCT 58.369 40.909 0.00 0.00 0.00 3.41
214 215 3.067106 GTTGTGGTGTCTGGTCACTATG 58.933 50.000 0.00 0.00 38.28 2.23
215 216 2.325484 TGTGGTGTCTGGTCACTATGT 58.675 47.619 0.00 0.00 38.28 2.29
217 218 2.037251 GTGGTGTCTGGTCACTATGTGT 59.963 50.000 0.00 0.00 38.28 3.72
219 220 2.612972 GGTGTCTGGTCACTATGTGTGG 60.613 54.545 0.00 0.00 46.20 4.17
220 221 2.037251 GTGTCTGGTCACTATGTGTGGT 59.963 50.000 0.00 0.00 46.20 4.16
223 224 0.320334 TGGTCACTATGTGTGGTGCG 60.320 55.000 0.00 0.00 46.20 5.34
225 226 1.508632 GTCACTATGTGTGGTGCGTT 58.491 50.000 0.00 0.00 46.20 4.84
232 233 4.920112 TGTGGTGCGTTCGTGGGG 62.920 66.667 0.00 0.00 0.00 4.96
261 262 0.606944 TCGGCTTTTGGGTATTGCGT 60.607 50.000 0.00 0.00 0.00 5.24
267 268 3.917985 GCTTTTGGGTATTGCGTTTGTAG 59.082 43.478 0.00 0.00 0.00 2.74
281 282 4.260375 GCGTTTGTAGATGCTCTAACCATG 60.260 45.833 0.00 0.00 29.58 3.66
288 289 1.264749 TGCTCTAACCATGGCGAGGT 61.265 55.000 21.16 0.00 42.34 3.85
294 295 3.402681 CCATGGCGAGGTGGGACT 61.403 66.667 0.00 0.00 0.00 3.85
327 328 2.448961 TCCCAAAGTTCCAATCCTTCCA 59.551 45.455 0.00 0.00 0.00 3.53
331 332 0.693049 AGTTCCAATCCTTCCACGCT 59.307 50.000 0.00 0.00 0.00 5.07
354 356 0.458669 TCGATCGGTTAACTGCCTCC 59.541 55.000 16.41 0.00 0.00 4.30
358 360 0.543410 TCGGTTAACTGCCTCCCTCA 60.543 55.000 9.72 0.00 0.00 3.86
359 361 0.323629 CGGTTAACTGCCTCCCTCAA 59.676 55.000 5.42 0.00 0.00 3.02
377 379 5.754890 CCCTCAAATCAAACACCAAAAAGAG 59.245 40.000 0.00 0.00 0.00 2.85
380 382 7.010460 CCTCAAATCAAACACCAAAAAGAGAAC 59.990 37.037 0.00 0.00 0.00 3.01
381 383 7.382110 TCAAATCAAACACCAAAAAGAGAACA 58.618 30.769 0.00 0.00 0.00 3.18
398 400 2.358322 ACACATGAAAAGGTTCCCGT 57.642 45.000 0.00 0.00 32.28 5.28
479 482 1.071699 AGTTGGAAGCCGTAGAAGCAA 59.928 47.619 0.00 0.00 0.00 3.91
592 599 0.878416 GCGTTGCAAGGTAACCATCA 59.122 50.000 19.45 0.00 37.17 3.07
593 600 1.472480 GCGTTGCAAGGTAACCATCAT 59.528 47.619 19.45 0.00 37.17 2.45
594 601 2.477863 GCGTTGCAAGGTAACCATCATC 60.478 50.000 19.45 0.00 37.17 2.92
595 602 2.746904 CGTTGCAAGGTAACCATCATCA 59.253 45.455 10.97 0.00 37.17 3.07
596 603 3.181507 CGTTGCAAGGTAACCATCATCAG 60.182 47.826 10.97 0.00 37.17 2.90
597 604 3.003394 TGCAAGGTAACCATCATCAGG 57.997 47.619 0.00 0.00 37.17 3.86
598 605 2.575735 TGCAAGGTAACCATCATCAGGA 59.424 45.455 0.00 0.00 37.17 3.86
599 606 2.945668 GCAAGGTAACCATCATCAGGAC 59.054 50.000 0.00 0.00 37.17 3.85
600 607 3.198068 CAAGGTAACCATCATCAGGACG 58.802 50.000 0.00 0.00 37.17 4.79
601 608 1.762957 AGGTAACCATCATCAGGACGG 59.237 52.381 0.00 0.00 37.17 4.79
602 609 1.760613 GGTAACCATCATCAGGACGGA 59.239 52.381 0.00 0.00 0.00 4.69
603 610 2.224066 GGTAACCATCATCAGGACGGAG 60.224 54.545 0.00 0.00 0.00 4.63
604 611 0.833287 AACCATCATCAGGACGGAGG 59.167 55.000 0.00 0.00 0.00 4.30
605 612 0.032117 ACCATCATCAGGACGGAGGA 60.032 55.000 0.00 0.00 31.52 3.71
606 613 0.390860 CCATCATCAGGACGGAGGAC 59.609 60.000 0.00 0.00 29.46 3.85
617 624 3.685435 GGAGGACGACGGTAACCA 58.315 61.111 0.00 0.00 0.00 3.67
618 625 2.196319 GGAGGACGACGGTAACCAT 58.804 57.895 0.00 0.00 0.00 3.55
619 626 0.101939 GGAGGACGACGGTAACCATC 59.898 60.000 0.00 0.00 0.00 3.51
747 754 2.694760 CCCGCTTCTTGCTCTTGCC 61.695 63.158 0.00 0.00 40.11 4.52
784 791 1.301244 CCGTTGTGAGCTGCTGTCT 60.301 57.895 7.01 0.00 0.00 3.41
798 805 2.758423 TGCTGTCTCTGTTCGGCTATAA 59.242 45.455 0.00 0.00 36.94 0.98
804 811 7.147143 TGTCTCTGTTCGGCTATAATAGATC 57.853 40.000 0.00 0.00 0.00 2.75
850 905 3.544285 GTGTCTCTTCGCTCGTTAATGAG 59.456 47.826 18.69 18.69 39.05 2.90
887 942 4.427394 GCCCATGCTAGTGACGAG 57.573 61.111 0.00 0.00 33.53 4.18
967 1022 4.527157 GTGCATGCTCGCGCTTCC 62.527 66.667 20.33 0.00 39.35 3.46
1497 1695 2.579201 CGTGACCTCAAGCCGGAT 59.421 61.111 5.05 0.00 0.00 4.18
1605 1818 3.430790 CGCCTGACACTAATTCTCCATCA 60.431 47.826 0.00 0.00 0.00 3.07
1623 1836 3.775654 CCCGGGAGCTCGCTTTCT 61.776 66.667 26.13 0.00 0.00 2.52
1624 1837 2.266055 CCGGGAGCTCGCTTTCTT 59.734 61.111 26.13 0.00 0.00 2.52
2158 2805 1.227438 CCGTTTATCCCGATGCCGT 60.227 57.895 0.00 0.00 0.00 5.68
2311 2958 7.993183 TCTCCATATTCTTTTAGATGAACACCC 59.007 37.037 0.00 0.00 0.00 4.61
2319 2966 1.302511 GATGAACACCCGTGCCAGT 60.303 57.895 0.00 0.00 0.00 4.00
2320 2967 1.577328 GATGAACACCCGTGCCAGTG 61.577 60.000 0.00 0.00 39.93 3.66
2321 2968 2.978010 GAACACCCGTGCCAGTGG 60.978 66.667 4.20 4.20 38.34 4.00
2322 2969 3.469863 GAACACCCGTGCCAGTGGA 62.470 63.158 15.20 0.00 38.34 4.02
2323 2970 2.951475 GAACACCCGTGCCAGTGGAA 62.951 60.000 15.20 0.00 38.34 3.53
2324 2971 2.669569 CACCCGTGCCAGTGGAAG 60.670 66.667 15.20 2.40 0.00 3.46
2325 2972 4.643387 ACCCGTGCCAGTGGAAGC 62.643 66.667 15.20 0.00 0.00 3.86
2326 2973 4.641645 CCCGTGCCAGTGGAAGCA 62.642 66.667 15.20 0.00 36.44 3.91
2330 2977 3.872603 TGCCAGTGGAAGCACCGT 61.873 61.111 15.20 0.00 42.61 4.83
2331 2978 2.594592 GCCAGTGGAAGCACCGTT 60.595 61.111 15.20 0.00 42.61 4.44
2332 2979 1.302192 GCCAGTGGAAGCACCGTTA 60.302 57.895 15.20 0.00 42.61 3.18
2333 2980 0.676782 GCCAGTGGAAGCACCGTTAT 60.677 55.000 15.20 0.00 42.61 1.89
2334 2981 1.369625 CCAGTGGAAGCACCGTTATC 58.630 55.000 1.68 0.00 42.61 1.75
2335 2982 1.369625 CAGTGGAAGCACCGTTATCC 58.630 55.000 0.00 0.00 42.61 2.59
2336 2983 1.066143 CAGTGGAAGCACCGTTATCCT 60.066 52.381 0.00 0.00 42.61 3.24
2337 2984 1.628846 AGTGGAAGCACCGTTATCCTT 59.371 47.619 0.00 0.00 42.61 3.36
2338 2985 1.737793 GTGGAAGCACCGTTATCCTTG 59.262 52.381 0.00 0.00 42.61 3.61
2339 2986 1.349688 TGGAAGCACCGTTATCCTTGT 59.650 47.619 0.00 0.00 42.61 3.16
2340 2987 2.224670 TGGAAGCACCGTTATCCTTGTT 60.225 45.455 0.00 0.00 42.61 2.83
2341 2988 2.817844 GGAAGCACCGTTATCCTTGTTT 59.182 45.455 0.00 0.00 0.00 2.83
2342 2989 4.004982 GGAAGCACCGTTATCCTTGTTTA 58.995 43.478 0.00 0.00 0.00 2.01
2343 2990 4.456566 GGAAGCACCGTTATCCTTGTTTAA 59.543 41.667 0.00 0.00 0.00 1.52
2344 2991 5.391629 GGAAGCACCGTTATCCTTGTTTAAG 60.392 44.000 0.00 0.00 0.00 1.85
2345 2992 4.648651 AGCACCGTTATCCTTGTTTAAGT 58.351 39.130 0.00 0.00 31.80 2.24
2346 2993 5.067954 AGCACCGTTATCCTTGTTTAAGTT 58.932 37.500 0.00 0.00 31.80 2.66
2347 2994 5.533528 AGCACCGTTATCCTTGTTTAAGTTT 59.466 36.000 0.00 0.00 31.80 2.66
2348 2995 6.040054 AGCACCGTTATCCTTGTTTAAGTTTT 59.960 34.615 0.00 0.00 31.80 2.43
2349 2996 6.698329 GCACCGTTATCCTTGTTTAAGTTTTT 59.302 34.615 0.00 0.00 31.80 1.94
2415 3062 4.783764 ATTTTTGCTAAAAGGACCTCGG 57.216 40.909 11.55 0.00 36.73 4.63
2416 3063 3.495434 TTTTGCTAAAAGGACCTCGGA 57.505 42.857 0.00 0.00 0.00 4.55
2417 3064 3.495434 TTTGCTAAAAGGACCTCGGAA 57.505 42.857 0.00 0.00 0.00 4.30
2418 3065 3.713826 TTGCTAAAAGGACCTCGGAAT 57.286 42.857 0.00 0.00 0.00 3.01
2419 3066 3.713826 TGCTAAAAGGACCTCGGAATT 57.286 42.857 0.00 0.00 0.00 2.17
2420 3067 4.028993 TGCTAAAAGGACCTCGGAATTT 57.971 40.909 0.00 0.00 0.00 1.82
2421 3068 3.756434 TGCTAAAAGGACCTCGGAATTTG 59.244 43.478 0.00 0.00 0.00 2.32
2422 3069 3.756963 GCTAAAAGGACCTCGGAATTTGT 59.243 43.478 0.00 0.00 0.00 2.83
2423 3070 4.939439 GCTAAAAGGACCTCGGAATTTGTA 59.061 41.667 0.00 0.00 0.00 2.41
2424 3071 5.589050 GCTAAAAGGACCTCGGAATTTGTAT 59.411 40.000 0.00 0.00 0.00 2.29
2425 3072 6.238402 GCTAAAAGGACCTCGGAATTTGTATC 60.238 42.308 0.00 0.00 0.00 2.24
2426 3073 3.454371 AGGACCTCGGAATTTGTATCG 57.546 47.619 0.00 0.00 0.00 2.92
2427 3074 3.028850 AGGACCTCGGAATTTGTATCGA 58.971 45.455 0.00 0.00 0.00 3.59
2428 3075 3.449737 AGGACCTCGGAATTTGTATCGAA 59.550 43.478 0.00 0.00 0.00 3.71
2429 3076 3.802685 GGACCTCGGAATTTGTATCGAAG 59.197 47.826 0.00 0.00 0.00 3.79
2430 3077 3.793559 ACCTCGGAATTTGTATCGAAGG 58.206 45.455 0.00 0.00 0.00 3.46
2431 3078 3.449737 ACCTCGGAATTTGTATCGAAGGA 59.550 43.478 0.00 0.00 0.00 3.36
2432 3079 4.101119 ACCTCGGAATTTGTATCGAAGGAT 59.899 41.667 0.00 0.00 36.65 3.24
2433 3080 4.686554 CCTCGGAATTTGTATCGAAGGATC 59.313 45.833 0.00 0.00 34.00 3.36
2434 3081 5.509840 CCTCGGAATTTGTATCGAAGGATCT 60.510 44.000 0.00 0.00 34.00 2.75
2435 3082 6.294564 CCTCGGAATTTGTATCGAAGGATCTA 60.295 42.308 0.00 0.00 34.00 1.98
2436 3083 7.046292 TCGGAATTTGTATCGAAGGATCTAA 57.954 36.000 0.00 0.00 34.00 2.10
2437 3084 7.494211 TCGGAATTTGTATCGAAGGATCTAAA 58.506 34.615 0.00 0.00 34.00 1.85
2438 3085 7.652105 TCGGAATTTGTATCGAAGGATCTAAAG 59.348 37.037 0.00 0.00 34.00 1.85
2439 3086 7.438459 CGGAATTTGTATCGAAGGATCTAAAGT 59.562 37.037 0.00 0.00 34.00 2.66
2440 3087 9.760077 GGAATTTGTATCGAAGGATCTAAAGTA 57.240 33.333 0.00 0.00 34.00 2.24
2445 3092 8.969260 TGTATCGAAGGATCTAAAGTAGTACA 57.031 34.615 2.52 0.00 34.00 2.90
2446 3093 9.399797 TGTATCGAAGGATCTAAAGTAGTACAA 57.600 33.333 2.52 0.00 34.00 2.41
2449 3096 7.256286 TCGAAGGATCTAAAGTAGTACAAAGC 58.744 38.462 2.52 0.00 0.00 3.51
2450 3097 7.033791 CGAAGGATCTAAAGTAGTACAAAGCA 58.966 38.462 2.52 0.00 0.00 3.91
2451 3098 7.009357 CGAAGGATCTAAAGTAGTACAAAGCAC 59.991 40.741 2.52 0.00 0.00 4.40
2452 3099 6.641474 AGGATCTAAAGTAGTACAAAGCACC 58.359 40.000 2.52 4.17 0.00 5.01
2453 3100 5.816258 GGATCTAAAGTAGTACAAAGCACCC 59.184 44.000 2.52 0.00 0.00 4.61
2454 3101 5.811796 TCTAAAGTAGTACAAAGCACCCA 57.188 39.130 2.52 0.00 0.00 4.51
2455 3102 6.177310 TCTAAAGTAGTACAAAGCACCCAA 57.823 37.500 2.52 0.00 0.00 4.12
2456 3103 6.593807 TCTAAAGTAGTACAAAGCACCCAAA 58.406 36.000 2.52 0.00 0.00 3.28
2457 3104 7.055378 TCTAAAGTAGTACAAAGCACCCAAAA 58.945 34.615 2.52 0.00 0.00 2.44
2458 3105 6.532988 AAAGTAGTACAAAGCACCCAAAAA 57.467 33.333 2.52 0.00 0.00 1.94
2459 3106 5.767816 AGTAGTACAAAGCACCCAAAAAG 57.232 39.130 2.52 0.00 0.00 2.27
2460 3107 5.198207 AGTAGTACAAAGCACCCAAAAAGT 58.802 37.500 2.52 0.00 0.00 2.66
2461 3108 6.358991 AGTAGTACAAAGCACCCAAAAAGTA 58.641 36.000 2.52 0.00 0.00 2.24
2462 3109 6.829811 AGTAGTACAAAGCACCCAAAAAGTAA 59.170 34.615 2.52 0.00 0.00 2.24
2463 3110 6.532988 AGTACAAAGCACCCAAAAAGTAAA 57.467 33.333 0.00 0.00 0.00 2.01
2464 3111 6.937392 AGTACAAAGCACCCAAAAAGTAAAA 58.063 32.000 0.00 0.00 0.00 1.52
2465 3112 7.039270 AGTACAAAGCACCCAAAAAGTAAAAG 58.961 34.615 0.00 0.00 0.00 2.27
2466 3113 6.043854 ACAAAGCACCCAAAAAGTAAAAGA 57.956 33.333 0.00 0.00 0.00 2.52
2467 3114 6.468543 ACAAAGCACCCAAAAAGTAAAAGAA 58.531 32.000 0.00 0.00 0.00 2.52
2468 3115 6.937465 ACAAAGCACCCAAAAAGTAAAAGAAA 59.063 30.769 0.00 0.00 0.00 2.52
2469 3116 7.609918 ACAAAGCACCCAAAAAGTAAAAGAAAT 59.390 29.630 0.00 0.00 0.00 2.17
2470 3117 8.458052 CAAAGCACCCAAAAAGTAAAAGAAATT 58.542 29.630 0.00 0.00 0.00 1.82
2471 3118 9.674068 AAAGCACCCAAAAAGTAAAAGAAATTA 57.326 25.926 0.00 0.00 0.00 1.40
2472 3119 8.657074 AGCACCCAAAAAGTAAAAGAAATTAC 57.343 30.769 0.00 0.00 36.28 1.89
2473 3120 8.261522 AGCACCCAAAAAGTAAAAGAAATTACA 58.738 29.630 0.00 0.00 38.07 2.41
2474 3121 8.884726 GCACCCAAAAAGTAAAAGAAATTACAA 58.115 29.630 0.00 0.00 38.07 2.41
2476 3123 9.089601 ACCCAAAAAGTAAAAGAAATTACAACG 57.910 29.630 0.00 0.00 38.07 4.10
2477 3124 9.303537 CCCAAAAAGTAAAAGAAATTACAACGA 57.696 29.630 0.00 0.00 38.07 3.85
2487 3134 8.833231 AAAGAAATTACAACGAGATCTTCAGA 57.167 30.769 0.00 0.00 0.00 3.27
2488 3135 7.820044 AGAAATTACAACGAGATCTTCAGAC 57.180 36.000 0.00 0.00 0.00 3.51
2489 3136 6.814146 AGAAATTACAACGAGATCTTCAGACC 59.186 38.462 0.00 0.00 0.00 3.85
2490 3137 5.661056 ATTACAACGAGATCTTCAGACCA 57.339 39.130 0.00 0.00 0.00 4.02
2491 3138 3.305398 ACAACGAGATCTTCAGACCAC 57.695 47.619 0.00 0.00 0.00 4.16
2492 3139 2.894126 ACAACGAGATCTTCAGACCACT 59.106 45.455 0.00 0.00 0.00 4.00
2493 3140 3.322254 ACAACGAGATCTTCAGACCACTT 59.678 43.478 0.00 0.00 0.00 3.16
2494 3141 4.523173 ACAACGAGATCTTCAGACCACTTA 59.477 41.667 0.00 0.00 0.00 2.24
2495 3142 5.010719 ACAACGAGATCTTCAGACCACTTAA 59.989 40.000 0.00 0.00 0.00 1.85
2496 3143 5.923733 ACGAGATCTTCAGACCACTTAAT 57.076 39.130 0.00 0.00 0.00 1.40
2497 3144 5.655488 ACGAGATCTTCAGACCACTTAATG 58.345 41.667 0.00 0.00 0.00 1.90
2498 3145 5.419155 ACGAGATCTTCAGACCACTTAATGA 59.581 40.000 0.00 0.00 0.00 2.57
2499 3146 6.071334 ACGAGATCTTCAGACCACTTAATGAA 60.071 38.462 0.00 0.00 0.00 2.57
2500 3147 6.475076 CGAGATCTTCAGACCACTTAATGAAG 59.525 42.308 0.00 7.33 46.42 3.02
2507 3154 6.341316 TCAGACCACTTAATGAAGAGTATGC 58.659 40.000 0.00 0.00 34.54 3.14
2508 3155 6.070824 TCAGACCACTTAATGAAGAGTATGCA 60.071 38.462 0.00 0.00 34.54 3.96
2509 3156 6.036517 CAGACCACTTAATGAAGAGTATGCAC 59.963 42.308 0.00 0.00 36.45 4.57
2510 3157 5.804639 ACCACTTAATGAAGAGTATGCACA 58.195 37.500 0.00 0.00 36.45 4.57
2511 3158 5.643777 ACCACTTAATGAAGAGTATGCACAC 59.356 40.000 0.00 0.00 36.45 3.82
2512 3159 5.065218 CCACTTAATGAAGAGTATGCACACC 59.935 44.000 0.00 0.00 36.45 4.16
2513 3160 4.870426 ACTTAATGAAGAGTATGCACACCG 59.130 41.667 0.00 0.00 36.45 4.94
2514 3161 2.315925 ATGAAGAGTATGCACACCGG 57.684 50.000 0.00 0.00 0.00 5.28
2515 3162 1.262417 TGAAGAGTATGCACACCGGA 58.738 50.000 9.46 0.00 0.00 5.14
2516 3163 1.204704 TGAAGAGTATGCACACCGGAG 59.795 52.381 9.46 1.26 0.00 4.63
2517 3164 0.108138 AAGAGTATGCACACCGGAGC 60.108 55.000 9.46 10.17 0.00 4.70
2518 3165 1.878522 GAGTATGCACACCGGAGCG 60.879 63.158 9.46 0.00 32.83 5.03
2531 3178 4.899239 GAGCGGGATGAGGGCGTG 62.899 72.222 0.00 0.00 0.00 5.34
2542 3189 4.400961 GGGCGTGCAGCTCTCCTT 62.401 66.667 3.58 0.00 44.82 3.36
2544 3191 3.797546 GCGTGCAGCTCTCCTTGC 61.798 66.667 0.00 0.00 44.04 4.01
2545 3192 3.123620 CGTGCAGCTCTCCTTGCC 61.124 66.667 0.00 0.00 0.00 4.52
2546 3193 3.123620 GTGCAGCTCTCCTTGCCG 61.124 66.667 0.00 0.00 0.00 5.69
2547 3194 3.630013 TGCAGCTCTCCTTGCCGT 61.630 61.111 0.00 0.00 0.00 5.68
2548 3195 2.359230 GCAGCTCTCCTTGCCGTT 60.359 61.111 0.00 0.00 0.00 4.44
2549 3196 2.684843 GCAGCTCTCCTTGCCGTTG 61.685 63.158 0.00 0.00 0.00 4.10
2550 3197 2.359230 AGCTCTCCTTGCCGTTGC 60.359 61.111 0.00 0.00 38.26 4.17
2551 3198 2.359230 GCTCTCCTTGCCGTTGCT 60.359 61.111 0.00 0.00 38.71 3.91
2552 3199 2.394563 GCTCTCCTTGCCGTTGCTC 61.395 63.158 0.00 0.00 38.71 4.26
2553 3200 1.743252 CTCTCCTTGCCGTTGCTCC 60.743 63.158 0.00 0.00 38.71 4.70
2554 3201 2.747855 CTCCTTGCCGTTGCTCCC 60.748 66.667 0.00 0.00 38.71 4.30
2555 3202 4.344865 TCCTTGCCGTTGCTCCCC 62.345 66.667 0.00 0.00 38.71 4.81
2557 3204 4.697756 CTTGCCGTTGCTCCCCGA 62.698 66.667 0.00 0.00 38.71 5.14
2558 3205 4.697756 TTGCCGTTGCTCCCCGAG 62.698 66.667 0.00 0.00 38.71 4.63
2567 3214 2.125350 CTCCCCGAGCAAGCACTC 60.125 66.667 0.00 0.00 0.00 3.51
2577 3224 0.319900 GCAAGCACTCTCCGTCTGAA 60.320 55.000 0.00 0.00 0.00 3.02
2580 3227 2.872245 CAAGCACTCTCCGTCTGAAAAA 59.128 45.455 0.00 0.00 0.00 1.94
2660 3307 2.657620 GCCGCGGTAATCGAGACC 60.658 66.667 28.70 8.87 41.18 3.85
2772 3419 3.005472 CCTACAAGTCAGTCACTCGGAAA 59.995 47.826 0.00 0.00 32.30 3.13
2779 3426 2.231478 TCAGTCACTCGGAAATGTCCTC 59.769 50.000 0.00 0.00 42.44 3.71
2859 3507 3.612247 ATTTCTCCGCTGCGCCTGT 62.612 57.895 18.00 0.00 0.00 4.00
2925 3573 0.473117 TGGGGAAGGAGAAGACGGTT 60.473 55.000 0.00 0.00 0.00 4.44
2981 3629 1.073923 GAAAGGAAAGAGGACCAGCCA 59.926 52.381 0.00 0.00 40.02 4.75
3076 3724 1.370609 AGACGACATCGACGATCTGT 58.629 50.000 7.54 5.50 43.02 3.41
3135 3785 1.072505 GGGAAACAAGACCGAGCCA 59.927 57.895 0.00 0.00 0.00 4.75
3189 3841 0.511221 CTCATGTCGACCGCGTTTTT 59.489 50.000 14.12 0.00 38.98 1.94
3208 3860 0.030603 TTTTGCCTCCCCACCCTTTT 60.031 50.000 0.00 0.00 0.00 2.27
3297 3949 1.270571 TGCTGCCTTCGTGTCAATGTA 60.271 47.619 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.262915 CTCCTTCGTCTGCGCCTT 59.737 61.111 4.18 0.00 38.14 4.35
10 11 2.581354 CAGGGCCTCCTTCGTCTG 59.419 66.667 0.95 0.00 42.67 3.51
11 12 2.685380 CCAGGGCCTCCTTCGTCT 60.685 66.667 0.95 0.00 42.67 4.18
16 17 2.204213 AAGCTCCAGGGCCTCCTT 60.204 61.111 0.95 0.85 42.67 3.36
53 54 4.592192 ATCTCCATGTCGGCGCCG 62.592 66.667 42.13 42.13 41.35 6.46
54 55 2.663188 GATCTCCATGTCGGCGCC 60.663 66.667 19.07 19.07 33.14 6.53
55 56 3.032609 CGATCTCCATGTCGGCGC 61.033 66.667 0.00 0.00 34.39 6.53
56 57 1.658717 GACGATCTCCATGTCGGCG 60.659 63.158 0.00 0.00 41.87 6.46
57 58 4.327885 GACGATCTCCATGTCGGC 57.672 61.111 8.14 1.20 41.87 5.54
82 83 5.125100 AGGTAAAAACTACACATCGTCGA 57.875 39.130 0.00 0.00 0.00 4.20
110 111 9.811995 ATGCAAAATAGAAATCTACGTACTACA 57.188 29.630 0.00 0.00 0.00 2.74
134 135 9.710900 TCATAACTCAAATACATAGCACCTATG 57.289 33.333 9.95 9.95 46.43 2.23
137 138 9.632638 ATTTCATAACTCAAATACATAGCACCT 57.367 29.630 0.00 0.00 0.00 4.00
175 176 3.132111 ACAACAAAACATCCTCCACAACC 59.868 43.478 0.00 0.00 0.00 3.77
176 177 4.111916 CACAACAAAACATCCTCCACAAC 58.888 43.478 0.00 0.00 0.00 3.32
182 183 3.632145 AGACACCACAACAAAACATCCTC 59.368 43.478 0.00 0.00 0.00 3.71
187 188 2.490115 GACCAGACACCACAACAAAACA 59.510 45.455 0.00 0.00 0.00 2.83
194 195 2.703536 ACATAGTGACCAGACACCACAA 59.296 45.455 0.00 0.00 41.12 3.33
214 215 3.645975 CCCACGAACGCACCACAC 61.646 66.667 0.00 0.00 0.00 3.82
215 216 4.920112 CCCCACGAACGCACCACA 62.920 66.667 0.00 0.00 0.00 4.17
219 220 3.351416 GAACCCCCACGAACGCAC 61.351 66.667 0.00 0.00 0.00 5.34
220 221 3.818121 CTGAACCCCCACGAACGCA 62.818 63.158 0.00 0.00 0.00 5.24
223 224 2.033602 CCCTGAACCCCCACGAAC 59.966 66.667 0.00 0.00 0.00 3.95
225 226 4.585216 ACCCCTGAACCCCCACGA 62.585 66.667 0.00 0.00 0.00 4.35
232 233 1.228459 AAAAGCCGACCCCTGAACC 60.228 57.895 0.00 0.00 0.00 3.62
267 268 1.506493 CTCGCCATGGTTAGAGCATC 58.494 55.000 14.67 0.00 33.46 3.91
281 282 2.128507 CCTCTAGTCCCACCTCGCC 61.129 68.421 0.00 0.00 0.00 5.54
294 295 2.621070 ACTTTGGGAGCAAGACCTCTA 58.379 47.619 0.00 0.00 32.43 2.43
327 328 0.108992 TTAACCGATCGAGCAAGCGT 60.109 50.000 18.66 0.17 0.00 5.07
331 332 1.355971 GCAGTTAACCGATCGAGCAA 58.644 50.000 18.66 3.86 0.00 3.91
354 356 6.572519 TCTCTTTTTGGTGTTTGATTTGAGG 58.427 36.000 0.00 0.00 0.00 3.86
358 360 7.158021 TGTGTTCTCTTTTTGGTGTTTGATTT 58.842 30.769 0.00 0.00 0.00 2.17
359 361 6.696411 TGTGTTCTCTTTTTGGTGTTTGATT 58.304 32.000 0.00 0.00 0.00 2.57
415 417 3.665323 CGCCAAAGATAGATATGCAACGC 60.665 47.826 0.00 0.00 0.00 4.84
416 418 3.494626 ACGCCAAAGATAGATATGCAACG 59.505 43.478 0.00 0.00 0.00 4.10
417 419 5.237344 AGAACGCCAAAGATAGATATGCAAC 59.763 40.000 0.00 0.00 0.00 4.17
479 482 4.320456 CCACAGCTCTGCCCGTGT 62.320 66.667 0.00 0.00 32.74 4.49
592 599 2.113433 CGTCGTCCTCCGTCCTGAT 61.113 63.158 0.00 0.00 37.94 2.90
593 600 2.745100 CGTCGTCCTCCGTCCTGA 60.745 66.667 0.00 0.00 37.94 3.86
594 601 3.812019 CCGTCGTCCTCCGTCCTG 61.812 72.222 0.00 0.00 37.94 3.86
595 602 2.469465 TTACCGTCGTCCTCCGTCCT 62.469 60.000 0.00 0.00 37.94 3.85
596 603 2.040544 TTACCGTCGTCCTCCGTCC 61.041 63.158 0.00 0.00 37.94 4.79
597 604 1.135523 GTTACCGTCGTCCTCCGTC 59.864 63.158 0.00 0.00 37.94 4.79
598 605 2.335712 GGTTACCGTCGTCCTCCGT 61.336 63.158 0.00 0.00 37.94 4.69
599 606 1.660560 ATGGTTACCGTCGTCCTCCG 61.661 60.000 0.00 0.00 38.13 4.63
600 607 0.101939 GATGGTTACCGTCGTCCTCC 59.898 60.000 7.95 0.00 29.33 4.30
601 608 3.637297 GATGGTTACCGTCGTCCTC 57.363 57.895 7.95 0.00 29.33 3.71
608 615 0.529378 GTCCTGACGATGGTTACCGT 59.471 55.000 0.00 0.00 42.17 4.83
609 616 3.340727 GTCCTGACGATGGTTACCG 57.659 57.895 0.00 0.00 0.00 4.02
732 739 2.608998 GGAAAAGGCAAGAGCAAGAAGC 60.609 50.000 0.00 0.00 44.61 3.86
747 754 0.310854 GCAACAGACGTGGGGAAAAG 59.689 55.000 0.00 0.00 0.00 2.27
784 791 5.619309 GCGTGATCTATTATAGCCGAACAGA 60.619 44.000 0.00 0.00 0.00 3.41
798 805 1.029681 TACGGCACAGCGTGATCTAT 58.970 50.000 11.94 0.00 35.23 1.98
804 811 1.897398 GAAGGTTACGGCACAGCGTG 61.897 60.000 0.00 4.61 36.51 5.34
850 905 5.468409 TGGGCTTTTGCTTAAATTAACAAGC 59.532 36.000 10.78 10.78 45.90 4.01
1497 1695 0.325296 AGCCCTGGATGAGGACGTTA 60.325 55.000 0.00 0.00 46.33 3.18
1605 1818 4.083862 GAAAGCGAGCTCCCGGGT 62.084 66.667 22.86 0.00 0.00 5.28
1623 1836 2.666508 GCAGCGACGTGAAGAATTAGAA 59.333 45.455 0.00 0.00 0.00 2.10
1624 1837 2.259618 GCAGCGACGTGAAGAATTAGA 58.740 47.619 0.00 0.00 0.00 2.10
2158 2805 1.904852 GAGTCGGCACTGTCGTCGTA 61.905 60.000 2.41 0.00 30.63 3.43
2209 2856 1.967319 AACGTCTCATGCACAACCTT 58.033 45.000 0.00 0.00 0.00 3.50
2309 2956 4.641645 TGCTTCCACTGGCACGGG 62.642 66.667 0.00 0.00 40.47 5.28
2319 2966 1.349688 ACAAGGATAACGGTGCTTCCA 59.650 47.619 6.93 0.00 35.57 3.53
2320 2967 2.109425 ACAAGGATAACGGTGCTTCC 57.891 50.000 0.00 0.00 0.00 3.46
2321 2968 5.180680 ACTTAAACAAGGATAACGGTGCTTC 59.819 40.000 0.00 0.00 0.00 3.86
2322 2969 5.067954 ACTTAAACAAGGATAACGGTGCTT 58.932 37.500 0.00 0.00 0.00 3.91
2323 2970 4.648651 ACTTAAACAAGGATAACGGTGCT 58.351 39.130 0.00 0.00 0.00 4.40
2324 2971 5.366829 AACTTAAACAAGGATAACGGTGC 57.633 39.130 0.00 0.00 0.00 5.01
2389 3036 8.463607 CCGAGGTCCTTTTAGCAAAAATAATAA 58.536 33.333 0.00 0.00 34.18 1.40
2390 3037 7.830201 TCCGAGGTCCTTTTAGCAAAAATAATA 59.170 33.333 0.00 0.00 34.18 0.98
2391 3038 6.661805 TCCGAGGTCCTTTTAGCAAAAATAAT 59.338 34.615 0.00 0.00 34.18 1.28
2392 3039 6.005198 TCCGAGGTCCTTTTAGCAAAAATAA 58.995 36.000 0.00 0.00 34.18 1.40
2393 3040 5.562635 TCCGAGGTCCTTTTAGCAAAAATA 58.437 37.500 0.00 0.00 34.18 1.40
2394 3041 4.403734 TCCGAGGTCCTTTTAGCAAAAAT 58.596 39.130 0.00 0.00 34.18 1.82
2395 3042 3.822940 TCCGAGGTCCTTTTAGCAAAAA 58.177 40.909 0.00 0.00 33.58 1.94
2396 3043 3.495434 TCCGAGGTCCTTTTAGCAAAA 57.505 42.857 0.00 0.00 0.00 2.44
2397 3044 3.495434 TTCCGAGGTCCTTTTAGCAAA 57.505 42.857 0.00 0.00 0.00 3.68
2398 3045 3.713826 ATTCCGAGGTCCTTTTAGCAA 57.286 42.857 0.00 0.00 0.00 3.91
2399 3046 3.713826 AATTCCGAGGTCCTTTTAGCA 57.286 42.857 0.00 0.00 0.00 3.49
2400 3047 3.756963 ACAAATTCCGAGGTCCTTTTAGC 59.243 43.478 0.00 0.00 0.00 3.09
2401 3048 6.018994 CGATACAAATTCCGAGGTCCTTTTAG 60.019 42.308 0.00 0.00 0.00 1.85
2402 3049 5.813672 CGATACAAATTCCGAGGTCCTTTTA 59.186 40.000 0.00 0.00 0.00 1.52
2403 3050 4.634443 CGATACAAATTCCGAGGTCCTTTT 59.366 41.667 0.00 0.00 0.00 2.27
2404 3051 4.081309 TCGATACAAATTCCGAGGTCCTTT 60.081 41.667 0.00 0.00 0.00 3.11
2405 3052 3.449737 TCGATACAAATTCCGAGGTCCTT 59.550 43.478 0.00 0.00 0.00 3.36
2406 3053 3.028850 TCGATACAAATTCCGAGGTCCT 58.971 45.455 0.00 0.00 0.00 3.85
2407 3054 3.447918 TCGATACAAATTCCGAGGTCC 57.552 47.619 0.00 0.00 0.00 4.46
2408 3055 3.802685 CCTTCGATACAAATTCCGAGGTC 59.197 47.826 0.00 0.00 32.41 3.85
2409 3056 3.449737 TCCTTCGATACAAATTCCGAGGT 59.550 43.478 0.00 0.00 32.41 3.85
2410 3057 4.054780 TCCTTCGATACAAATTCCGAGG 57.945 45.455 0.00 0.00 32.41 4.63
2411 3058 5.533482 AGATCCTTCGATACAAATTCCGAG 58.467 41.667 0.00 0.00 32.41 4.63
2412 3059 5.531122 AGATCCTTCGATACAAATTCCGA 57.469 39.130 0.00 0.00 0.00 4.55
2413 3060 7.438459 ACTTTAGATCCTTCGATACAAATTCCG 59.562 37.037 0.00 0.00 0.00 4.30
2414 3061 8.664211 ACTTTAGATCCTTCGATACAAATTCC 57.336 34.615 0.00 0.00 0.00 3.01
2419 3066 9.399797 TGTACTACTTTAGATCCTTCGATACAA 57.600 33.333 0.00 0.00 0.00 2.41
2420 3067 8.969260 TGTACTACTTTAGATCCTTCGATACA 57.031 34.615 0.00 0.00 0.00 2.29
2423 3070 7.921745 GCTTTGTACTACTTTAGATCCTTCGAT 59.078 37.037 0.00 0.00 0.00 3.59
2424 3071 7.094075 TGCTTTGTACTACTTTAGATCCTTCGA 60.094 37.037 0.00 0.00 0.00 3.71
2425 3072 7.009357 GTGCTTTGTACTACTTTAGATCCTTCG 59.991 40.741 0.00 0.00 0.00 3.79
2426 3073 7.278203 GGTGCTTTGTACTACTTTAGATCCTTC 59.722 40.741 0.00 0.00 0.00 3.46
2427 3074 7.104290 GGTGCTTTGTACTACTTTAGATCCTT 58.896 38.462 0.00 0.00 0.00 3.36
2428 3075 6.351966 GGGTGCTTTGTACTACTTTAGATCCT 60.352 42.308 0.00 0.00 0.00 3.24
2429 3076 5.816258 GGGTGCTTTGTACTACTTTAGATCC 59.184 44.000 0.00 0.00 0.00 3.36
2430 3077 6.403878 TGGGTGCTTTGTACTACTTTAGATC 58.596 40.000 0.00 0.00 0.00 2.75
2431 3078 6.368779 TGGGTGCTTTGTACTACTTTAGAT 57.631 37.500 0.00 0.00 0.00 1.98
2432 3079 5.811796 TGGGTGCTTTGTACTACTTTAGA 57.188 39.130 0.00 0.00 0.00 2.10
2433 3080 6.870971 TTTGGGTGCTTTGTACTACTTTAG 57.129 37.500 0.00 0.00 0.00 1.85
2434 3081 7.339976 ACTTTTTGGGTGCTTTGTACTACTTTA 59.660 33.333 0.00 0.00 0.00 1.85
2435 3082 6.153851 ACTTTTTGGGTGCTTTGTACTACTTT 59.846 34.615 0.00 0.00 0.00 2.66
2436 3083 5.655090 ACTTTTTGGGTGCTTTGTACTACTT 59.345 36.000 0.00 0.00 0.00 2.24
2437 3084 5.198207 ACTTTTTGGGTGCTTTGTACTACT 58.802 37.500 0.00 0.00 0.00 2.57
2438 3085 5.509716 ACTTTTTGGGTGCTTTGTACTAC 57.490 39.130 0.00 0.00 0.00 2.73
2439 3086 7.642082 TTTACTTTTTGGGTGCTTTGTACTA 57.358 32.000 0.00 0.00 0.00 1.82
2440 3087 6.532988 TTTACTTTTTGGGTGCTTTGTACT 57.467 33.333 0.00 0.00 0.00 2.73
2441 3088 7.036829 TCTTTTACTTTTTGGGTGCTTTGTAC 58.963 34.615 0.00 0.00 0.00 2.90
2442 3089 7.171630 TCTTTTACTTTTTGGGTGCTTTGTA 57.828 32.000 0.00 0.00 0.00 2.41
2443 3090 6.043854 TCTTTTACTTTTTGGGTGCTTTGT 57.956 33.333 0.00 0.00 0.00 2.83
2444 3091 6.976636 TTCTTTTACTTTTTGGGTGCTTTG 57.023 33.333 0.00 0.00 0.00 2.77
2445 3092 8.574251 AATTTCTTTTACTTTTTGGGTGCTTT 57.426 26.923 0.00 0.00 0.00 3.51
2446 3093 9.104965 GTAATTTCTTTTACTTTTTGGGTGCTT 57.895 29.630 0.00 0.00 0.00 3.91
2447 3094 8.261522 TGTAATTTCTTTTACTTTTTGGGTGCT 58.738 29.630 0.00 0.00 33.99 4.40
2448 3095 8.426881 TGTAATTTCTTTTACTTTTTGGGTGC 57.573 30.769 0.00 0.00 33.99 5.01
2450 3097 9.089601 CGTTGTAATTTCTTTTACTTTTTGGGT 57.910 29.630 0.00 0.00 33.99 4.51
2451 3098 9.303537 TCGTTGTAATTTCTTTTACTTTTTGGG 57.696 29.630 0.00 0.00 33.99 4.12
2461 3108 9.273016 TCTGAAGATCTCGTTGTAATTTCTTTT 57.727 29.630 0.00 0.00 0.00 2.27
2462 3109 8.713271 GTCTGAAGATCTCGTTGTAATTTCTTT 58.287 33.333 0.00 0.00 0.00 2.52
2463 3110 7.332182 GGTCTGAAGATCTCGTTGTAATTTCTT 59.668 37.037 0.00 0.00 0.00 2.52
2464 3111 6.814146 GGTCTGAAGATCTCGTTGTAATTTCT 59.186 38.462 0.00 0.00 0.00 2.52
2465 3112 6.590292 TGGTCTGAAGATCTCGTTGTAATTTC 59.410 38.462 0.00 0.00 0.00 2.17
2466 3113 6.369065 GTGGTCTGAAGATCTCGTTGTAATTT 59.631 38.462 0.00 0.00 0.00 1.82
2467 3114 5.869888 GTGGTCTGAAGATCTCGTTGTAATT 59.130 40.000 0.00 0.00 0.00 1.40
2468 3115 5.186021 AGTGGTCTGAAGATCTCGTTGTAAT 59.814 40.000 0.00 0.00 0.00 1.89
2469 3116 4.523173 AGTGGTCTGAAGATCTCGTTGTAA 59.477 41.667 0.00 0.00 0.00 2.41
2470 3117 4.079970 AGTGGTCTGAAGATCTCGTTGTA 58.920 43.478 0.00 0.00 0.00 2.41
2471 3118 2.894126 AGTGGTCTGAAGATCTCGTTGT 59.106 45.455 0.00 0.00 0.00 3.32
2472 3119 3.584406 AGTGGTCTGAAGATCTCGTTG 57.416 47.619 0.00 0.00 0.00 4.10
2473 3120 5.723672 TTAAGTGGTCTGAAGATCTCGTT 57.276 39.130 0.00 0.00 0.00 3.85
2474 3121 5.419155 TCATTAAGTGGTCTGAAGATCTCGT 59.581 40.000 0.00 0.00 0.00 4.18
2475 3122 5.895928 TCATTAAGTGGTCTGAAGATCTCG 58.104 41.667 0.00 0.00 0.00 4.04
2476 3123 7.551585 TCTTCATTAAGTGGTCTGAAGATCTC 58.448 38.462 11.22 0.00 45.17 2.75
2477 3124 7.487822 TCTTCATTAAGTGGTCTGAAGATCT 57.512 36.000 11.22 0.00 45.17 2.75
2480 3127 6.672266 ACTCTTCATTAAGTGGTCTGAAGA 57.328 37.500 13.55 13.55 46.84 2.87
2481 3128 7.010923 GCATACTCTTCATTAAGTGGTCTGAAG 59.989 40.741 7.60 7.60 43.73 3.02
2482 3129 6.818644 GCATACTCTTCATTAAGTGGTCTGAA 59.181 38.462 0.00 0.00 34.13 3.02
2483 3130 6.070824 TGCATACTCTTCATTAAGTGGTCTGA 60.071 38.462 0.00 0.00 34.13 3.27
2484 3131 6.036517 GTGCATACTCTTCATTAAGTGGTCTG 59.963 42.308 0.00 0.00 34.13 3.51
2485 3132 6.109359 GTGCATACTCTTCATTAAGTGGTCT 58.891 40.000 0.00 0.00 34.13 3.85
2486 3133 5.874810 TGTGCATACTCTTCATTAAGTGGTC 59.125 40.000 0.00 0.00 34.13 4.02
2487 3134 5.643777 GTGTGCATACTCTTCATTAAGTGGT 59.356 40.000 6.31 0.00 34.13 4.16
2488 3135 5.065218 GGTGTGCATACTCTTCATTAAGTGG 59.935 44.000 13.64 0.00 34.13 4.00
2489 3136 5.220472 CGGTGTGCATACTCTTCATTAAGTG 60.220 44.000 13.64 0.00 34.13 3.16
2490 3137 4.870426 CGGTGTGCATACTCTTCATTAAGT 59.130 41.667 13.64 0.00 34.13 2.24
2491 3138 4.271049 CCGGTGTGCATACTCTTCATTAAG 59.729 45.833 13.64 0.00 0.00 1.85
2492 3139 4.081365 TCCGGTGTGCATACTCTTCATTAA 60.081 41.667 13.64 0.00 0.00 1.40
2493 3140 3.449377 TCCGGTGTGCATACTCTTCATTA 59.551 43.478 13.64 0.00 0.00 1.90
2494 3141 2.236146 TCCGGTGTGCATACTCTTCATT 59.764 45.455 13.64 0.00 0.00 2.57
2495 3142 1.831106 TCCGGTGTGCATACTCTTCAT 59.169 47.619 13.64 0.00 0.00 2.57
2496 3143 1.204704 CTCCGGTGTGCATACTCTTCA 59.795 52.381 13.64 0.00 0.00 3.02
2497 3144 1.927895 CTCCGGTGTGCATACTCTTC 58.072 55.000 13.64 0.00 0.00 2.87
2498 3145 0.108138 GCTCCGGTGTGCATACTCTT 60.108 55.000 13.64 0.00 0.00 2.85
2499 3146 1.517832 GCTCCGGTGTGCATACTCT 59.482 57.895 13.64 0.00 0.00 3.24
2500 3147 1.878522 CGCTCCGGTGTGCATACTC 60.879 63.158 13.64 3.02 0.00 2.59
2501 3148 2.184322 CGCTCCGGTGTGCATACT 59.816 61.111 13.64 0.00 0.00 2.12
2502 3149 2.890474 CCGCTCCGGTGTGCATAC 60.890 66.667 11.57 4.79 42.73 2.39
2503 3150 4.155733 CCCGCTCCGGTGTGCATA 62.156 66.667 11.57 0.00 46.80 3.14
2507 3154 3.723235 CTCATCCCGCTCCGGTGTG 62.723 68.421 10.11 10.11 46.80 3.82
2508 3155 3.461773 CTCATCCCGCTCCGGTGT 61.462 66.667 0.00 0.00 46.80 4.16
2509 3156 4.227134 CCTCATCCCGCTCCGGTG 62.227 72.222 0.00 0.00 46.80 4.94
2514 3161 4.899239 CACGCCCTCATCCCGCTC 62.899 72.222 0.00 0.00 0.00 5.03
2519 3166 4.479993 AGCTGCACGCCCTCATCC 62.480 66.667 1.02 0.00 40.39 3.51
2520 3167 2.894387 GAGCTGCACGCCCTCATC 60.894 66.667 1.02 0.00 40.39 2.92
2521 3168 3.382803 GAGAGCTGCACGCCCTCAT 62.383 63.158 12.48 0.00 42.52 2.90
2522 3169 4.074526 GAGAGCTGCACGCCCTCA 62.075 66.667 12.48 0.00 42.52 3.86
2523 3170 4.828925 GGAGAGCTGCACGCCCTC 62.829 72.222 8.56 9.96 42.27 4.30
2525 3172 4.400961 AAGGAGAGCTGCACGCCC 62.401 66.667 15.37 9.35 40.39 6.13
2526 3173 3.123620 CAAGGAGAGCTGCACGCC 61.124 66.667 11.57 11.57 40.39 5.68
2527 3174 3.797546 GCAAGGAGAGCTGCACGC 61.798 66.667 1.02 0.00 38.48 5.34
2528 3175 3.123620 GGCAAGGAGAGCTGCACG 61.124 66.667 1.02 0.00 40.46 5.34
2529 3176 3.123620 CGGCAAGGAGAGCTGCAC 61.124 66.667 1.02 0.00 40.46 4.57
2530 3177 3.182590 AACGGCAAGGAGAGCTGCA 62.183 57.895 1.02 0.00 42.07 4.41
2531 3178 2.359230 AACGGCAAGGAGAGCTGC 60.359 61.111 0.00 0.00 42.07 5.25
2532 3179 2.684843 GCAACGGCAAGGAGAGCTG 61.685 63.158 0.00 0.00 43.90 4.24
2533 3180 2.359230 GCAACGGCAAGGAGAGCT 60.359 61.111 0.00 0.00 40.72 4.09
2534 3181 2.359230 AGCAACGGCAAGGAGAGC 60.359 61.111 0.00 0.00 44.61 4.09
2535 3182 1.743252 GGAGCAACGGCAAGGAGAG 60.743 63.158 0.00 0.00 44.61 3.20
2536 3183 2.347490 GGAGCAACGGCAAGGAGA 59.653 61.111 0.00 0.00 44.61 3.71
2537 3184 2.747855 GGGAGCAACGGCAAGGAG 60.748 66.667 0.00 0.00 44.61 3.69
2538 3185 4.344865 GGGGAGCAACGGCAAGGA 62.345 66.667 0.00 0.00 44.61 3.36
2540 3187 4.697756 TCGGGGAGCAACGGCAAG 62.698 66.667 0.00 0.00 44.61 4.01
2541 3188 4.697756 CTCGGGGAGCAACGGCAA 62.698 66.667 0.00 0.00 44.61 4.52
2550 3197 2.125350 GAGTGCTTGCTCGGGGAG 60.125 66.667 0.00 0.00 0.00 4.30
2551 3198 2.604686 AGAGTGCTTGCTCGGGGA 60.605 61.111 0.00 0.00 40.26 4.81
2552 3199 2.125350 GAGAGTGCTTGCTCGGGG 60.125 66.667 0.00 0.00 40.26 5.73
2553 3200 2.125350 GGAGAGTGCTTGCTCGGG 60.125 66.667 0.00 0.00 40.26 5.14
2554 3201 2.507992 CGGAGAGTGCTTGCTCGG 60.508 66.667 0.00 0.00 40.26 4.63
2555 3202 1.803519 GACGGAGAGTGCTTGCTCG 60.804 63.158 0.00 0.00 40.26 5.03
2556 3203 0.735632 CAGACGGAGAGTGCTTGCTC 60.736 60.000 0.00 0.00 35.82 4.26
2557 3204 1.181741 TCAGACGGAGAGTGCTTGCT 61.182 55.000 0.00 0.00 0.00 3.91
2558 3205 0.319900 TTCAGACGGAGAGTGCTTGC 60.320 55.000 0.00 0.00 0.00 4.01
2559 3206 2.154854 TTTCAGACGGAGAGTGCTTG 57.845 50.000 0.00 0.00 0.00 4.01
2560 3207 2.910688 TTTTCAGACGGAGAGTGCTT 57.089 45.000 0.00 0.00 0.00 3.91
2561 3208 2.910688 TTTTTCAGACGGAGAGTGCT 57.089 45.000 0.00 0.00 0.00 4.40
2562 3209 3.251004 ACAATTTTTCAGACGGAGAGTGC 59.749 43.478 0.00 0.00 0.00 4.40
2563 3210 5.237344 AGAACAATTTTTCAGACGGAGAGTG 59.763 40.000 7.08 0.00 0.00 3.51
2564 3211 5.237344 CAGAACAATTTTTCAGACGGAGAGT 59.763 40.000 7.08 0.00 0.00 3.24
2565 3212 5.683859 CAGAACAATTTTTCAGACGGAGAG 58.316 41.667 7.08 0.00 0.00 3.20
2566 3213 4.024048 GCAGAACAATTTTTCAGACGGAGA 60.024 41.667 7.08 0.00 0.00 3.71
2567 3214 4.023707 AGCAGAACAATTTTTCAGACGGAG 60.024 41.667 7.08 0.00 0.00 4.63
2577 3224 2.034558 CCACGGACAGCAGAACAATTTT 59.965 45.455 0.00 0.00 0.00 1.82
2580 3227 0.396435 TCCACGGACAGCAGAACAAT 59.604 50.000 0.00 0.00 0.00 2.71
2660 3307 1.609072 TCGAGATGACCTGCCTAATCG 59.391 52.381 0.00 0.00 0.00 3.34
2772 3419 2.643551 CGGTGCCTTTTATGAGGACAT 58.356 47.619 0.00 0.00 39.25 3.06
2779 3426 1.373590 CCGGTCCGGTGCCTTTTATG 61.374 60.000 23.02 0.00 42.73 1.90
2925 3573 3.179869 CTTTGCACGCTCCAACGCA 62.180 57.895 0.00 0.00 36.19 5.24
2981 3629 2.596776 CTTGACGAGGATCCACCCT 58.403 57.895 15.82 0.00 40.05 4.34
3053 3701 1.063616 GATCGTCGATGTCGTCTTGGA 59.936 52.381 13.54 0.00 40.80 3.53
3111 3761 1.759236 GGTCTTGTTTCCCGGGAGT 59.241 57.895 25.26 0.00 0.00 3.85
3120 3770 4.043168 CGTGGCTCGGTCTTGTTT 57.957 55.556 0.13 0.00 35.71 2.83
3189 3841 0.030603 AAAAGGGTGGGGAGGCAAAA 60.031 50.000 0.00 0.00 0.00 2.44
3276 3928 0.806868 CATTGACACGAAGGCAGCAT 59.193 50.000 0.00 0.00 0.00 3.79


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.