Multiple sequence alignment - TraesCS3B01G203100

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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 TraesCS3B01G203100 chr3B 100.000 3077 0 0 1 3077 237330856 237333932 0.000000e+00 5683
1 TraesCS3B01G203100 chr3D 90.709 2185 153 21 77 2223 160697267 160699439 0.000000e+00 2865
2 TraesCS3B01G203100 chr3D 88.934 244 20 6 2833 3073 160700048 160700287 8.340000e-76 294
3 TraesCS3B01G203100 chr3D 85.091 275 23 9 2430 2703 160699786 160700043 6.540000e-67 265
4 TraesCS3B01G203100 chr3A 93.047 1697 84 13 687 2363 187247306 187248988 0.000000e+00 2449
5 TraesCS3B01G203100 chr3A 85.542 332 20 16 2363 2686 187249044 187249355 3.830000e-84 322
6 TraesCS3B01G203100 chr3A 88.710 248 20 7 2833 3077 187249364 187249606 2.320000e-76 296
7 TraesCS3B01G203100 chrUn 93.617 141 8 1 2689 2829 319650494 319650355 3.110000e-50 209
8 TraesCS3B01G203100 chr6B 96.094 128 5 0 2702 2829 220575563 220575436 3.110000e-50 209
9 TraesCS3B01G203100 chr6B 95.385 130 6 0 2700 2829 39206388 39206517 1.120000e-49 207
10 TraesCS3B01G203100 chr5D 94.203 138 7 1 2692 2829 392813716 392813852 3.110000e-50 209
11 TraesCS3B01G203100 chr4D 95.385 130 6 0 2701 2830 439129929 439129800 1.120000e-49 207
12 TraesCS3B01G203100 chr2B 93.007 143 8 2 2694 2834 536806172 536806030 1.120000e-49 207
13 TraesCS3B01G203100 chr6A 94.697 132 7 0 2702 2833 87926630 87926499 4.020000e-49 206
14 TraesCS3B01G203100 chr5A 94.074 135 7 1 2702 2836 243810111 243809978 1.450000e-48 204
15 TraesCS3B01G203100 chr4B 94.656 131 7 0 2700 2830 180671160 180671290 1.450000e-48 204


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 TraesCS3B01G203100 chr3B 237330856 237333932 3076 False 5683.000000 5683 100.000000 1 3077 1 chr3B.!!$F1 3076
1 TraesCS3B01G203100 chr3D 160697267 160700287 3020 False 1141.333333 2865 88.244667 77 3073 3 chr3D.!!$F1 2996
2 TraesCS3B01G203100 chr3A 187247306 187249606 2300 False 1022.333333 2449 89.099667 687 3077 3 chr3A.!!$F1 2390

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
750 762 0.0293 TCTTGTTGCAAAGCACTCGC 59.971 50.0 0.0 0.0 38.71 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2698 2960 0.613853 TGGGACGGAGGGAGTACAAG 60.614 60.0 0.0 0.0 0.0 3.16 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
20 21 3.723348 GTCCGCCGCACCTGAAAC 61.723 66.667 0.00 0.00 0.00 2.78
26 27 4.025401 CGCACCTGAAACGCCCAC 62.025 66.667 0.00 0.00 0.00 4.61
39 40 2.751436 CCCACGTGGCCATGGAAG 60.751 66.667 29.75 16.98 38.34 3.46
40 41 2.751436 CCACGTGGCCATGGAAGG 60.751 66.667 28.37 21.57 38.34 3.46
61 62 2.128035 CGGAGCAGATTACTAAAGGCG 58.872 52.381 0.00 0.00 0.00 5.52
62 63 2.481449 CGGAGCAGATTACTAAAGGCGT 60.481 50.000 0.00 0.00 0.00 5.68
63 64 3.124560 GGAGCAGATTACTAAAGGCGTC 58.875 50.000 0.00 0.00 0.00 5.19
64 65 2.789893 GAGCAGATTACTAAAGGCGTCG 59.210 50.000 0.00 0.00 0.00 5.12
65 66 2.426024 AGCAGATTACTAAAGGCGTCGA 59.574 45.455 0.00 0.00 0.00 4.20
66 67 3.068307 AGCAGATTACTAAAGGCGTCGAT 59.932 43.478 0.00 0.00 0.00 3.59
67 68 4.277672 AGCAGATTACTAAAGGCGTCGATA 59.722 41.667 0.00 0.00 0.00 2.92
68 69 4.980434 GCAGATTACTAAAGGCGTCGATAA 59.020 41.667 0.00 0.00 0.00 1.75
69 70 5.461078 GCAGATTACTAAAGGCGTCGATAAA 59.539 40.000 0.00 0.00 0.00 1.40
70 71 6.345882 GCAGATTACTAAAGGCGTCGATAAAG 60.346 42.308 0.00 0.00 0.00 1.85
71 72 6.144080 CAGATTACTAAAGGCGTCGATAAAGG 59.856 42.308 0.00 0.00 0.00 3.11
72 73 3.175109 ACTAAAGGCGTCGATAAAGGG 57.825 47.619 0.00 0.00 0.00 3.95
73 74 2.159000 ACTAAAGGCGTCGATAAAGGGG 60.159 50.000 0.00 0.00 0.00 4.79
74 75 0.746923 AAAGGCGTCGATAAAGGGGC 60.747 55.000 0.00 0.00 0.00 5.80
75 76 1.623542 AAGGCGTCGATAAAGGGGCT 61.624 55.000 0.00 0.00 34.74 5.19
81 82 3.576648 CGTCGATAAAGGGGCTCTAATC 58.423 50.000 0.00 0.00 0.00 1.75
87 88 2.877154 AAGGGGCTCTAATCTCCTCA 57.123 50.000 0.00 0.00 0.00 3.86
107 108 2.037367 TCGGGTGTGGAGGGAGAG 59.963 66.667 0.00 0.00 0.00 3.20
111 112 2.689034 GTGTGGAGGGAGAGGGGG 60.689 72.222 0.00 0.00 0.00 5.40
112 113 3.208592 TGTGGAGGGAGAGGGGGT 61.209 66.667 0.00 0.00 0.00 4.95
118 119 0.326618 GAGGGAGAGGGGGTGATTCA 60.327 60.000 0.00 0.00 0.00 2.57
129 130 3.711704 GGGGGTGATTCATGACTTCTCTA 59.288 47.826 0.00 0.00 0.00 2.43
134 135 6.881602 GGGTGATTCATGACTTCTCTAGTTTT 59.118 38.462 0.00 0.00 37.17 2.43
149 150 7.831753 TCTCTAGTTTTATGTGAGAGTTCCAG 58.168 38.462 0.00 0.00 36.01 3.86
184 185 6.899393 AAGATTAACAAGGCTGAATGAACA 57.101 33.333 0.00 0.00 0.00 3.18
198 199 7.912250 GGCTGAATGAACAAAATACACAGATAG 59.088 37.037 0.00 0.00 0.00 2.08
199 200 7.430502 GCTGAATGAACAAAATACACAGATAGC 59.569 37.037 0.00 0.00 0.00 2.97
201 202 8.668353 TGAATGAACAAAATACACAGATAGCTC 58.332 33.333 0.00 0.00 0.00 4.09
208 209 2.638556 ACACAGATAGCTCACGACAC 57.361 50.000 0.00 0.00 0.00 3.67
212 213 0.393944 AGATAGCTCACGACACCCGA 60.394 55.000 0.00 0.00 41.76 5.14
217 218 0.384309 GCTCACGACACCCGATGATA 59.616 55.000 0.00 0.00 41.76 2.15
254 255 0.322975 CTCCTCAAGGTCAGGTGTGG 59.677 60.000 0.00 0.00 36.34 4.17
262 263 1.545706 GGTCAGGTGTGGAGGGAGAC 61.546 65.000 0.00 0.00 0.00 3.36
275 276 0.392595 GGGAGACGGGGACAATTCAC 60.393 60.000 0.00 0.00 0.00 3.18
276 277 0.323629 GGAGACGGGGACAATTCACA 59.676 55.000 0.00 0.00 0.00 3.58
285 286 3.753797 GGGGACAATTCACAACTTCTCTC 59.246 47.826 0.00 0.00 0.00 3.20
286 287 4.505742 GGGGACAATTCACAACTTCTCTCT 60.506 45.833 0.00 0.00 0.00 3.10
287 288 4.453819 GGGACAATTCACAACTTCTCTCTG 59.546 45.833 0.00 0.00 0.00 3.35
295 296 5.047847 TCACAACTTCTCTCTGGTTTTACG 58.952 41.667 0.00 0.00 0.00 3.18
340 342 9.922305 GATTAAGATTAACGAGGTTGAATGAAG 57.078 33.333 0.00 0.00 0.00 3.02
355 357 8.641499 GTTGAATGAAGTAATCAACTAACACG 57.359 34.615 9.86 0.00 45.86 4.49
356 358 7.359262 TGAATGAAGTAATCAACTAACACGG 57.641 36.000 0.00 0.00 42.54 4.94
369 371 7.444299 TCAACTAACACGGTACCTAGAAATTT 58.556 34.615 10.90 0.00 0.00 1.82
370 372 7.385752 TCAACTAACACGGTACCTAGAAATTTG 59.614 37.037 10.90 6.33 0.00 2.32
395 397 8.366401 TGTAATCCAATAAATTATGCATGGTGG 58.634 33.333 10.16 6.15 0.00 4.61
401 403 9.947433 CCAATAAATTATGCATGGTGGATTTAT 57.053 29.630 10.16 13.08 33.48 1.40
421 423 6.886178 TTATTCTAGGGTTGCTAAGAGGTT 57.114 37.500 0.00 0.00 0.00 3.50
425 427 5.525484 TCTAGGGTTGCTAAGAGGTTCATA 58.475 41.667 0.00 0.00 0.00 2.15
426 428 6.143915 TCTAGGGTTGCTAAGAGGTTCATAT 58.856 40.000 0.00 0.00 0.00 1.78
430 432 5.059833 GGTTGCTAAGAGGTTCATATCCAG 58.940 45.833 0.00 0.00 0.00 3.86
443 445 3.649502 TCATATCCAGATGCATGGTCAGT 59.350 43.478 2.46 0.00 41.43 3.41
458 460 1.001764 CAGTGAGGCCATGCAAGGA 60.002 57.895 13.26 0.00 0.00 3.36
474 480 2.584608 GATGGTGGGTGGAGGACG 59.415 66.667 0.00 0.00 0.00 4.79
477 483 2.920912 GGTGGGTGGAGGACGTCA 60.921 66.667 18.91 0.00 0.00 4.35
487 493 1.305297 AGGACGTCAGCCTGGATCA 60.305 57.895 18.91 0.00 33.59 2.92
492 498 1.142748 GTCAGCCTGGATCACTCGG 59.857 63.158 0.00 0.00 0.00 4.63
493 499 2.202987 CAGCCTGGATCACTCGGC 60.203 66.667 0.00 0.17 42.79 5.54
497 503 2.579201 CTGGATCACTCGGCGGTT 59.421 61.111 7.21 0.00 0.00 4.44
504 510 0.672401 TCACTCGGCGGTTGAATTCC 60.672 55.000 7.21 0.00 0.00 3.01
505 511 1.376812 ACTCGGCGGTTGAATTCCC 60.377 57.895 7.21 0.00 0.00 3.97
507 513 2.360600 CGGCGGTTGAATTCCCCA 60.361 61.111 2.27 0.00 0.00 4.96
526 532 1.550130 AAATTCCTCACCCTCCGCGA 61.550 55.000 8.23 0.00 0.00 5.87
527 533 2.240162 AATTCCTCACCCTCCGCGAC 62.240 60.000 8.23 0.00 0.00 5.19
532 538 4.530857 CACCCTCCGCGACCATCC 62.531 72.222 8.23 0.00 0.00 3.51
533 539 4.779733 ACCCTCCGCGACCATCCT 62.780 66.667 8.23 0.00 0.00 3.24
535 541 2.202932 CCTCCGCGACCATCCTTG 60.203 66.667 8.23 0.00 0.00 3.61
575 581 1.381928 GGGTGGTAGCGACTCGATCA 61.382 60.000 1.63 0.00 0.00 2.92
596 602 2.758130 TGTGGTCATGGGATAGCACTA 58.242 47.619 13.54 1.20 42.96 2.74
615 621 5.631026 CACTAGTGCGTATTTTTCATGCTT 58.369 37.500 10.54 0.00 0.00 3.91
650 662 3.374042 TTTTTGTGAGGTGGGAGTCAA 57.626 42.857 0.00 0.00 0.00 3.18
655 667 1.555075 GTGAGGTGGGAGTCAATGCTA 59.445 52.381 0.00 0.00 0.00 3.49
662 674 1.065126 GGGAGTCAATGCTAAGTGGCT 60.065 52.381 0.00 0.00 39.46 4.75
666 678 1.541147 GTCAATGCTAAGTGGCTTGCA 59.459 47.619 0.00 0.00 34.25 4.08
677 689 2.901839 AGTGGCTTGCAGATTTGGAATT 59.098 40.909 0.00 0.00 33.95 2.17
711 723 6.649973 CACCCACATATTGATTCTTTGCAAAA 59.350 34.615 13.84 0.00 0.00 2.44
717 729 3.641437 TGATTCTTTGCAAAACTCCCG 57.359 42.857 13.84 0.21 0.00 5.14
750 762 0.029300 TCTTGTTGCAAAGCACTCGC 59.971 50.000 0.00 0.00 38.71 5.03
751 763 1.264141 CTTGTTGCAAAGCACTCGCG 61.264 55.000 0.00 0.00 45.49 5.87
767 779 0.238289 CGCGGTGCAAATCTTTGAGT 59.762 50.000 0.00 0.00 40.55 3.41
780 792 2.802247 TCTTTGAGTGCAACATGACTCG 59.198 45.455 0.00 0.00 41.37 4.18
785 797 3.056891 TGAGTGCAACATGACTCGTGATA 60.057 43.478 0.00 0.00 41.37 2.15
807 820 4.947645 ACAAATCTCCAAACACAACATGG 58.052 39.130 0.00 0.00 35.49 3.66
809 822 2.064434 TCTCCAAACACAACATGGCA 57.936 45.000 0.00 0.00 34.13 4.92
826 839 3.753519 ATGGCACATGTTGTAAACCTCCA 60.754 43.478 0.00 0.00 44.91 3.86
833 846 3.349488 GTTGTAAACCTCCAAGCACAC 57.651 47.619 0.00 0.00 42.21 3.82
858 871 1.299541 CCCATGTTGCATACCTCGTC 58.700 55.000 0.00 0.00 0.00 4.20
859 872 0.930310 CCATGTTGCATACCTCGTCG 59.070 55.000 0.00 0.00 0.00 5.12
864 877 1.600511 TTGCATACCTCGTCGGCTGA 61.601 55.000 0.00 0.00 35.61 4.26
919 933 3.157087 ACCTTCAAGCCTAACATGGTTG 58.843 45.455 0.00 0.00 0.00 3.77
938 952 1.134189 TGCAAGCCTCATCAGGATCTG 60.134 52.381 0.00 0.00 43.65 2.90
963 977 1.437986 GATCCAACGGCTAGCGACT 59.562 57.895 9.00 0.00 0.00 4.18
1051 1070 2.025418 CCACGAAGCCACGTACCAC 61.025 63.158 5.52 0.00 44.76 4.16
1059 1078 3.455195 CACGTACCACGACACGCG 61.455 66.667 3.53 3.53 46.05 6.01
1101 1128 4.554036 GCTGCCCCTCCACGATCC 62.554 72.222 0.00 0.00 0.00 3.36
1118 1145 4.400251 CCTCCTCCCCCGTCAGGT 62.400 72.222 0.00 0.00 35.12 4.00
1119 1146 2.760385 CTCCTCCCCCGTCAGGTC 60.760 72.222 0.00 0.00 35.12 3.85
1120 1147 3.273654 TCCTCCCCCGTCAGGTCT 61.274 66.667 0.00 0.00 35.12 3.85
1169 1196 0.878523 CACAAAACCTCAGACGGCGA 60.879 55.000 16.62 0.00 0.00 5.54
1175 1202 2.259818 CTCAGACGGCGAACTGCT 59.740 61.111 24.52 8.85 45.43 4.24
1264 1291 1.901948 CGCTACCTATGCTCCGGGA 60.902 63.158 0.00 0.00 0.00 5.14
1698 1737 2.792290 CTTGGCATCAGCGTCGTCG 61.792 63.158 0.00 0.00 43.41 5.12
1701 1740 2.504026 GCATCAGCGTCGTCGTCA 60.504 61.111 3.66 0.00 39.49 4.35
1882 1921 0.608582 CAAGAAAGCTCTGCCCTGCT 60.609 55.000 0.00 0.00 41.82 4.24
1924 1963 0.666577 GTCAGTTTCGTCGGTCAGGG 60.667 60.000 0.00 0.00 0.00 4.45
1925 1964 2.027625 CAGTTTCGTCGGTCAGGGC 61.028 63.158 0.00 0.00 0.00 5.19
1926 1965 2.741211 GTTTCGTCGGTCAGGGCC 60.741 66.667 0.00 0.00 0.00 5.80
1986 2025 2.356313 CGCACAACGTCTCTGCCT 60.356 61.111 6.50 0.00 36.87 4.75
2020 2059 1.078143 GTTCTTGGATGCCTCGGCT 60.078 57.895 9.65 0.00 42.51 5.52
2225 2264 0.036732 TCAGCCGGCTCAATCTTTGT 59.963 50.000 30.29 0.00 0.00 2.83
2232 2271 3.181497 CCGGCTCAATCTTTGTTATGTGG 60.181 47.826 0.00 0.00 0.00 4.17
2240 2279 6.214615 TCAATCTTTGTTATGTGGGAGTCCTA 59.785 38.462 9.58 0.00 0.00 2.94
2241 2280 6.831664 ATCTTTGTTATGTGGGAGTCCTAT 57.168 37.500 9.58 4.39 0.00 2.57
2242 2281 6.636454 TCTTTGTTATGTGGGAGTCCTATT 57.364 37.500 9.58 0.00 0.00 1.73
2243 2282 7.027874 TCTTTGTTATGTGGGAGTCCTATTT 57.972 36.000 9.58 0.00 0.00 1.40
2244 2283 7.466804 TCTTTGTTATGTGGGAGTCCTATTTT 58.533 34.615 9.58 0.00 0.00 1.82
2245 2284 8.607713 TCTTTGTTATGTGGGAGTCCTATTTTA 58.392 33.333 9.58 0.00 0.00 1.52
2246 2285 8.801882 TTTGTTATGTGGGAGTCCTATTTTAG 57.198 34.615 9.58 0.00 0.00 1.85
2296 2335 9.793259 TTACCCATATCAATTCCTTACTTCATC 57.207 33.333 0.00 0.00 0.00 2.92
2297 2336 7.815383 ACCCATATCAATTCCTTACTTCATCA 58.185 34.615 0.00 0.00 0.00 3.07
2298 2337 8.451245 ACCCATATCAATTCCTTACTTCATCAT 58.549 33.333 0.00 0.00 0.00 2.45
2332 2371 8.992073 GGAATAAACATCTTTGTGCTGAATTTT 58.008 29.630 0.00 0.00 35.83 1.82
2333 2372 9.801714 GAATAAACATCTTTGTGCTGAATTTTG 57.198 29.630 0.00 0.00 35.83 2.44
2341 2380 5.534207 TTGTGCTGAATTTTGTTCTCCAT 57.466 34.783 0.00 0.00 0.00 3.41
2343 2382 5.291178 TGTGCTGAATTTTGTTCTCCATTG 58.709 37.500 0.00 0.00 0.00 2.82
2347 2386 5.984926 GCTGAATTTTGTTCTCCATTGTTCA 59.015 36.000 0.00 0.00 0.00 3.18
2363 2402 6.142161 CCATTGTTCATTGTGTTTCGTGTTAG 59.858 38.462 0.00 0.00 0.00 2.34
2365 2404 6.905544 TGTTCATTGTGTTTCGTGTTAGTA 57.094 33.333 0.00 0.00 0.00 1.82
2366 2405 6.707711 TGTTCATTGTGTTTCGTGTTAGTAC 58.292 36.000 0.00 0.00 0.00 2.73
2367 2406 6.313164 TGTTCATTGTGTTTCGTGTTAGTACA 59.687 34.615 0.00 0.00 0.00 2.90
2464 2723 6.482973 CCTGCAAACAAAACAATTACTGGATT 59.517 34.615 0.00 0.00 0.00 3.01
2488 2747 6.564709 AATATTGCAATCTCATGTATGCGT 57.435 33.333 16.86 0.00 41.61 5.24
2489 2748 4.906065 ATTGCAATCTCATGTATGCGTT 57.094 36.364 5.99 0.00 41.61 4.84
2490 2749 4.700268 TTGCAATCTCATGTATGCGTTT 57.300 36.364 0.00 0.00 41.61 3.60
2527 2786 8.874744 TTACTGGAGTACTACAAGTCTAATGT 57.125 34.615 9.61 3.52 34.81 2.71
2595 2854 6.423862 TCGATCAAAACCTTGTTTTAACGAG 58.576 36.000 16.00 3.33 39.63 4.18
2596 2855 6.258287 TCGATCAAAACCTTGTTTTAACGAGA 59.742 34.615 10.75 7.36 41.97 4.04
2597 2856 6.573725 CGATCAAAACCTTGTTTTAACGAGAG 59.426 38.462 10.75 4.71 41.97 3.20
2598 2857 6.988622 TCAAAACCTTGTTTTAACGAGAGA 57.011 33.333 10.75 0.00 41.97 3.10
2599 2858 7.380431 TCAAAACCTTGTTTTAACGAGAGAA 57.620 32.000 10.75 0.00 41.97 2.87
2690 2952 8.494433 AGAAGGGAGTTACATATCTAAAATGCA 58.506 33.333 0.00 0.00 0.00 3.96
2698 2960 9.931210 GTTACATATCTAAAATGCACCTTACAC 57.069 33.333 0.00 0.00 0.00 2.90
2703 2965 9.899661 ATATCTAAAATGCACCTTACACTTGTA 57.100 29.630 0.00 0.00 0.00 2.41
2704 2966 7.429636 TCTAAAATGCACCTTACACTTGTAC 57.570 36.000 0.00 0.00 0.00 2.90
2705 2967 7.221450 TCTAAAATGCACCTTACACTTGTACT 58.779 34.615 0.00 0.00 0.00 2.73
2707 2969 3.396260 TGCACCTTACACTTGTACTCC 57.604 47.619 0.00 0.00 0.00 3.85
2708 2970 2.038033 TGCACCTTACACTTGTACTCCC 59.962 50.000 0.00 0.00 0.00 4.30
2709 2971 2.302157 GCACCTTACACTTGTACTCCCT 59.698 50.000 0.00 0.00 0.00 4.20
2710 2972 3.616802 GCACCTTACACTTGTACTCCCTC 60.617 52.174 0.00 0.00 0.00 4.30
2711 2973 3.056035 CACCTTACACTTGTACTCCCTCC 60.056 52.174 0.00 0.00 0.00 4.30
2712 2974 2.165845 CCTTACACTTGTACTCCCTCCG 59.834 54.545 0.00 0.00 0.00 4.63
2713 2975 2.592102 TACACTTGTACTCCCTCCGT 57.408 50.000 0.00 0.00 0.00 4.69
2714 2976 1.254954 ACACTTGTACTCCCTCCGTC 58.745 55.000 0.00 0.00 0.00 4.79
2715 2977 0.531200 CACTTGTACTCCCTCCGTCC 59.469 60.000 0.00 0.00 0.00 4.79
2716 2978 0.614134 ACTTGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
2717 2979 0.613853 CTTGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
2718 2980 0.178926 TTGTACTCCCTCCGTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
2719 2981 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2720 2982 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2721 2983 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2722 2984 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2723 2985 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2724 2986 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2725 2987 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2726 2988 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2727 2989 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2728 2990 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2729 2991 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2730 2992 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2731 2993 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2732 2994 4.758165 TCCGTCCCAAAATTCTTGTCTTAC 59.242 41.667 0.00 0.00 0.00 2.34
2733 2995 4.517453 CCGTCCCAAAATTCTTGTCTTACA 59.483 41.667 0.00 0.00 0.00 2.41
2734 2996 5.183140 CCGTCCCAAAATTCTTGTCTTACAT 59.817 40.000 0.00 0.00 0.00 2.29
2735 2997 6.294508 CCGTCCCAAAATTCTTGTCTTACATT 60.295 38.462 0.00 0.00 0.00 2.71
2736 2998 7.145323 CGTCCCAAAATTCTTGTCTTACATTT 58.855 34.615 0.00 0.00 0.00 2.32
2737 2999 8.293867 CGTCCCAAAATTCTTGTCTTACATTTA 58.706 33.333 0.00 0.00 0.00 1.40
2756 3018 8.880991 ACATTTATCTAGATACGGATGTACCT 57.119 34.615 22.14 8.27 36.31 3.08
2757 3019 9.970553 ACATTTATCTAGATACGGATGTACCTA 57.029 33.333 22.14 2.50 36.31 3.08
2770 3032 8.882415 ACGGATGTACCTAATACTAAAATGTG 57.118 34.615 0.00 0.00 34.56 3.21
2771 3033 8.698210 ACGGATGTACCTAATACTAAAATGTGA 58.302 33.333 0.00 0.00 34.56 3.58
2772 3034 8.975439 CGGATGTACCTAATACTAAAATGTGAC 58.025 37.037 0.00 0.00 34.56 3.67
2779 3041 8.893727 ACCTAATACTAAAATGTGACTTGATGC 58.106 33.333 0.00 0.00 0.00 3.91
2780 3042 8.892723 CCTAATACTAAAATGTGACTTGATGCA 58.107 33.333 0.00 0.00 0.00 3.96
2783 3045 6.199937 ACTAAAATGTGACTTGATGCATCC 57.800 37.500 23.67 8.87 0.00 3.51
2784 3046 3.770263 AAATGTGACTTGATGCATCCG 57.230 42.857 23.67 16.46 0.00 4.18
2785 3047 2.408271 ATGTGACTTGATGCATCCGT 57.592 45.000 23.67 19.44 0.00 4.69
2786 3048 3.541996 ATGTGACTTGATGCATCCGTA 57.458 42.857 23.67 8.47 0.00 4.02
2787 3049 3.541996 TGTGACTTGATGCATCCGTAT 57.458 42.857 23.67 6.88 0.00 3.06
2788 3050 3.872696 TGTGACTTGATGCATCCGTATT 58.127 40.909 23.67 3.78 0.00 1.89
2789 3051 4.260985 TGTGACTTGATGCATCCGTATTT 58.739 39.130 23.67 2.33 0.00 1.40
2790 3052 4.094739 TGTGACTTGATGCATCCGTATTTG 59.905 41.667 23.67 8.30 0.00 2.32
2791 3053 3.627123 TGACTTGATGCATCCGTATTTGG 59.373 43.478 23.67 7.34 0.00 3.28
2792 3054 3.876914 GACTTGATGCATCCGTATTTGGA 59.123 43.478 23.67 0.00 43.58 3.53
2793 3055 3.627577 ACTTGATGCATCCGTATTTGGAC 59.372 43.478 23.67 0.00 41.85 4.02
2794 3056 3.274095 TGATGCATCCGTATTTGGACA 57.726 42.857 23.67 0.00 41.85 4.02
2795 3057 3.615155 TGATGCATCCGTATTTGGACAA 58.385 40.909 23.67 0.00 41.85 3.18
2796 3058 4.013050 TGATGCATCCGTATTTGGACAAA 58.987 39.130 23.67 0.00 41.85 2.83
2797 3059 4.644234 TGATGCATCCGTATTTGGACAAAT 59.356 37.500 23.67 14.02 41.85 2.32
2798 3060 4.630894 TGCATCCGTATTTGGACAAATC 57.369 40.909 13.07 5.63 41.85 2.17
2799 3061 4.269183 TGCATCCGTATTTGGACAAATCT 58.731 39.130 13.07 0.00 41.85 2.40
2800 3062 5.432645 TGCATCCGTATTTGGACAAATCTA 58.567 37.500 13.07 0.00 41.85 1.98
2801 3063 5.883115 TGCATCCGTATTTGGACAAATCTAA 59.117 36.000 13.07 0.00 41.85 2.10
2802 3064 6.038161 TGCATCCGTATTTGGACAAATCTAAG 59.962 38.462 13.07 1.07 41.85 2.18
2803 3065 6.260050 GCATCCGTATTTGGACAAATCTAAGA 59.740 38.462 13.07 7.57 41.85 2.10
2804 3066 7.630924 CATCCGTATTTGGACAAATCTAAGAC 58.369 38.462 13.07 5.74 41.85 3.01
2805 3067 6.703319 TCCGTATTTGGACAAATCTAAGACA 58.297 36.000 13.07 0.00 40.99 3.41
2806 3068 7.162761 TCCGTATTTGGACAAATCTAAGACAA 58.837 34.615 13.07 0.00 40.99 3.18
2807 3069 7.333423 TCCGTATTTGGACAAATCTAAGACAAG 59.667 37.037 13.07 2.30 40.99 3.16
2808 3070 7.333423 CCGTATTTGGACAAATCTAAGACAAGA 59.667 37.037 13.07 0.00 40.99 3.02
2809 3071 8.717821 CGTATTTGGACAAATCTAAGACAAGAA 58.282 33.333 13.07 0.00 40.99 2.52
2819 3081 9.760660 CAAATCTAAGACAAGAATTTTAGGACG 57.239 33.333 0.00 0.00 0.00 4.79
2820 3082 8.494016 AATCTAAGACAAGAATTTTAGGACGG 57.506 34.615 0.00 0.00 0.00 4.79
2821 3083 7.235935 TCTAAGACAAGAATTTTAGGACGGA 57.764 36.000 0.00 0.00 0.00 4.69
2822 3084 7.321153 TCTAAGACAAGAATTTTAGGACGGAG 58.679 38.462 0.00 0.00 0.00 4.63
2823 3085 4.833390 AGACAAGAATTTTAGGACGGAGG 58.167 43.478 0.00 0.00 0.00 4.30
2824 3086 4.530946 AGACAAGAATTTTAGGACGGAGGA 59.469 41.667 0.00 0.00 0.00 3.71
2825 3087 5.012768 AGACAAGAATTTTAGGACGGAGGAA 59.987 40.000 0.00 0.00 0.00 3.36
2826 3088 5.246307 ACAAGAATTTTAGGACGGAGGAAG 58.754 41.667 0.00 0.00 0.00 3.46
2827 3089 5.221864 ACAAGAATTTTAGGACGGAGGAAGT 60.222 40.000 0.00 0.00 0.00 3.01
2828 3090 6.013984 ACAAGAATTTTAGGACGGAGGAAGTA 60.014 38.462 0.00 0.00 0.00 2.24
2829 3091 6.809976 AGAATTTTAGGACGGAGGAAGTAT 57.190 37.500 0.00 0.00 0.00 2.12
2830 3092 7.196637 AGAATTTTAGGACGGAGGAAGTATT 57.803 36.000 0.00 0.00 0.00 1.89
2831 3093 8.315220 AGAATTTTAGGACGGAGGAAGTATTA 57.685 34.615 0.00 0.00 0.00 0.98
2865 3127 0.756294 AGTCCGAATGTCACACACCA 59.244 50.000 0.00 0.00 0.00 4.17
2880 3142 4.758674 CACACACCAATCAAGAGAAGTGAT 59.241 41.667 0.00 0.00 37.31 3.06
2881 3143 4.758674 ACACACCAATCAAGAGAAGTGATG 59.241 41.667 0.00 0.00 35.87 3.07
2884 3146 4.094590 CACCAATCAAGAGAAGTGATGAGC 59.905 45.833 0.00 0.00 35.87 4.26
2899 3161 5.101628 GTGATGAGCGGCATAATTCAAAAA 58.898 37.500 1.45 0.00 37.34 1.94
2900 3162 5.750067 GTGATGAGCGGCATAATTCAAAAAT 59.250 36.000 1.45 0.00 37.34 1.82
2901 3163 5.978919 TGATGAGCGGCATAATTCAAAAATC 59.021 36.000 1.45 0.00 37.34 2.17
2911 3173 7.113965 GGCATAATTCAAAAATCTAGTGCATCG 59.886 37.037 0.00 0.00 0.00 3.84
2914 3176 5.545658 TTCAAAAATCTAGTGCATCGTCC 57.454 39.130 0.00 0.00 0.00 4.79
2918 3180 4.744795 AAATCTAGTGCATCGTCCTTCT 57.255 40.909 0.00 0.00 0.00 2.85
2920 3182 5.446143 AATCTAGTGCATCGTCCTTCTAG 57.554 43.478 0.00 0.00 0.00 2.43
2923 3185 4.948004 TCTAGTGCATCGTCCTTCTAGAAA 59.052 41.667 6.63 0.00 33.49 2.52
2934 3196 4.000988 TCCTTCTAGAAACAAATGGCGAC 58.999 43.478 6.63 0.00 0.00 5.19
2953 3215 2.605366 GACGCTATCTTTTCTCTGTGCC 59.395 50.000 0.00 0.00 0.00 5.01
2984 3248 3.003793 GGGACTGCTTGTTCTCAAAGTTC 59.996 47.826 0.00 0.00 32.87 3.01
2985 3249 3.879892 GGACTGCTTGTTCTCAAAGTTCT 59.120 43.478 0.00 0.00 32.87 3.01
2986 3250 5.057149 GGACTGCTTGTTCTCAAAGTTCTA 58.943 41.667 0.00 0.00 32.87 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.723348 GTTTCAGGTGCGGCGGAC 61.723 66.667 23.91 23.91 0.00 4.79
9 10 4.025401 GTGGGCGTTTCAGGTGCG 62.025 66.667 0.00 0.00 0.00 5.34
10 11 4.025401 CGTGGGCGTTTCAGGTGC 62.025 66.667 0.00 0.00 0.00 5.01
24 25 3.443045 GCCTTCCATGGCCACGTG 61.443 66.667 8.16 9.08 46.82 4.49
31 32 2.335092 ATCTGCTCCGCCTTCCATGG 62.335 60.000 4.97 4.97 0.00 3.66
32 33 0.465097 AATCTGCTCCGCCTTCCATG 60.465 55.000 0.00 0.00 0.00 3.66
33 34 1.131638 TAATCTGCTCCGCCTTCCAT 58.868 50.000 0.00 0.00 0.00 3.41
34 35 0.178068 GTAATCTGCTCCGCCTTCCA 59.822 55.000 0.00 0.00 0.00 3.53
35 36 0.466124 AGTAATCTGCTCCGCCTTCC 59.534 55.000 0.00 0.00 0.00 3.46
36 37 3.454371 TTAGTAATCTGCTCCGCCTTC 57.546 47.619 0.00 0.00 0.00 3.46
37 38 3.432326 CCTTTAGTAATCTGCTCCGCCTT 60.432 47.826 0.00 0.00 0.00 4.35
38 39 2.103263 CCTTTAGTAATCTGCTCCGCCT 59.897 50.000 0.00 0.00 0.00 5.52
39 40 2.484889 CCTTTAGTAATCTGCTCCGCC 58.515 52.381 0.00 0.00 0.00 6.13
40 41 1.867865 GCCTTTAGTAATCTGCTCCGC 59.132 52.381 0.00 0.00 0.00 5.54
41 42 2.128035 CGCCTTTAGTAATCTGCTCCG 58.872 52.381 0.00 0.00 0.00 4.63
42 43 3.124560 GACGCCTTTAGTAATCTGCTCC 58.875 50.000 0.00 0.00 0.00 4.70
43 44 2.789893 CGACGCCTTTAGTAATCTGCTC 59.210 50.000 0.00 0.00 0.00 4.26
44 45 2.426024 TCGACGCCTTTAGTAATCTGCT 59.574 45.455 0.00 0.00 0.00 4.24
45 46 2.805845 TCGACGCCTTTAGTAATCTGC 58.194 47.619 0.00 0.00 0.00 4.26
46 47 6.144080 CCTTTATCGACGCCTTTAGTAATCTG 59.856 42.308 0.00 0.00 0.00 2.90
47 48 6.214399 CCTTTATCGACGCCTTTAGTAATCT 58.786 40.000 0.00 0.00 0.00 2.40
48 49 5.404667 CCCTTTATCGACGCCTTTAGTAATC 59.595 44.000 0.00 0.00 0.00 1.75
49 50 5.295152 CCCTTTATCGACGCCTTTAGTAAT 58.705 41.667 0.00 0.00 0.00 1.89
50 51 4.441913 CCCCTTTATCGACGCCTTTAGTAA 60.442 45.833 0.00 0.00 0.00 2.24
51 52 3.068590 CCCCTTTATCGACGCCTTTAGTA 59.931 47.826 0.00 0.00 0.00 1.82
52 53 2.159000 CCCCTTTATCGACGCCTTTAGT 60.159 50.000 0.00 0.00 0.00 2.24
53 54 2.480845 CCCCTTTATCGACGCCTTTAG 58.519 52.381 0.00 0.00 0.00 1.85
54 55 1.473788 GCCCCTTTATCGACGCCTTTA 60.474 52.381 0.00 0.00 0.00 1.85
55 56 0.746923 GCCCCTTTATCGACGCCTTT 60.747 55.000 0.00 0.00 0.00 3.11
56 57 1.153229 GCCCCTTTATCGACGCCTT 60.153 57.895 0.00 0.00 0.00 4.35
57 58 2.029307 GAGCCCCTTTATCGACGCCT 62.029 60.000 0.00 0.00 0.00 5.52
58 59 1.594564 GAGCCCCTTTATCGACGCC 60.595 63.158 0.00 0.00 0.00 5.68
59 60 0.672342 TAGAGCCCCTTTATCGACGC 59.328 55.000 0.00 0.00 0.00 5.19
60 61 3.256136 AGATTAGAGCCCCTTTATCGACG 59.744 47.826 0.00 0.00 0.00 5.12
61 62 4.322123 GGAGATTAGAGCCCCTTTATCGAC 60.322 50.000 0.00 0.00 0.00 4.20
62 63 3.833070 GGAGATTAGAGCCCCTTTATCGA 59.167 47.826 0.00 0.00 0.00 3.59
63 64 3.835395 AGGAGATTAGAGCCCCTTTATCG 59.165 47.826 0.00 0.00 0.00 2.92
64 65 4.841246 TGAGGAGATTAGAGCCCCTTTATC 59.159 45.833 0.00 0.00 0.00 1.75
65 66 4.832492 TGAGGAGATTAGAGCCCCTTTAT 58.168 43.478 0.00 0.00 0.00 1.40
66 67 4.227197 CTGAGGAGATTAGAGCCCCTTTA 58.773 47.826 0.00 0.00 0.00 1.85
67 68 3.044894 CTGAGGAGATTAGAGCCCCTTT 58.955 50.000 0.00 0.00 0.00 3.11
68 69 2.688477 CTGAGGAGATTAGAGCCCCTT 58.312 52.381 0.00 0.00 0.00 3.95
69 70 1.132881 CCTGAGGAGATTAGAGCCCCT 60.133 57.143 0.00 0.00 0.00 4.79
70 71 1.347062 CCTGAGGAGATTAGAGCCCC 58.653 60.000 0.00 0.00 0.00 5.80
71 72 1.967779 GACCTGAGGAGATTAGAGCCC 59.032 57.143 4.99 0.00 0.00 5.19
72 73 1.611491 CGACCTGAGGAGATTAGAGCC 59.389 57.143 4.99 0.00 0.00 4.70
73 74 1.611491 CCGACCTGAGGAGATTAGAGC 59.389 57.143 4.99 0.00 0.00 4.09
74 75 2.235016 CCCGACCTGAGGAGATTAGAG 58.765 57.143 4.99 0.00 0.00 2.43
75 76 1.569548 ACCCGACCTGAGGAGATTAGA 59.430 52.381 4.99 0.00 0.00 2.10
81 82 2.650116 CCACACCCGACCTGAGGAG 61.650 68.421 4.99 0.00 0.00 3.69
87 88 3.907027 CTCCCTCCACACCCGACCT 62.907 68.421 0.00 0.00 0.00 3.85
107 108 2.507471 AGAGAAGTCATGAATCACCCCC 59.493 50.000 0.00 0.00 0.00 5.40
118 119 9.030452 ACTCTCACATAAAACTAGAGAAGTCAT 57.970 33.333 0.00 0.00 37.50 3.06
129 130 8.598041 AGAATACTGGAACTCTCACATAAAACT 58.402 33.333 0.00 0.00 0.00 2.66
134 135 9.647918 AATCTAGAATACTGGAACTCTCACATA 57.352 33.333 0.00 0.00 37.20 2.29
157 158 9.508567 GTTCATTCAGCCTTGTTAATCTTAATC 57.491 33.333 0.00 0.00 0.00 1.75
174 175 8.671921 AGCTATCTGTGTATTTTGTTCATTCAG 58.328 33.333 0.00 0.00 0.00 3.02
175 176 8.565896 AGCTATCTGTGTATTTTGTTCATTCA 57.434 30.769 0.00 0.00 0.00 2.57
184 185 5.577164 GTGTCGTGAGCTATCTGTGTATTTT 59.423 40.000 0.00 0.00 0.00 1.82
198 199 0.384309 TATCATCGGGTGTCGTGAGC 59.616 55.000 0.00 0.00 40.32 4.26
199 200 1.001268 CCTATCATCGGGTGTCGTGAG 60.001 57.143 0.00 0.00 40.32 3.51
201 202 0.032130 CCCTATCATCGGGTGTCGTG 59.968 60.000 0.00 0.00 40.32 4.35
208 209 2.028020 GGTTTCTAGCCCTATCATCGGG 60.028 54.545 0.00 0.00 44.89 5.14
254 255 0.178301 GAATTGTCCCCGTCTCCCTC 59.822 60.000 0.00 0.00 0.00 4.30
262 263 2.484264 GAGAAGTTGTGAATTGTCCCCG 59.516 50.000 0.00 0.00 0.00 5.73
275 276 5.529791 TCTCGTAAAACCAGAGAGAAGTTG 58.470 41.667 0.00 0.00 36.25 3.16
276 277 5.786264 TCTCGTAAAACCAGAGAGAAGTT 57.214 39.130 0.00 0.00 36.25 2.66
285 286 3.258622 AGGGAACTCTCTCGTAAAACCAG 59.741 47.826 0.00 0.00 32.90 4.00
286 287 3.236896 AGGGAACTCTCTCGTAAAACCA 58.763 45.455 0.00 0.00 32.90 3.67
287 288 3.957591 AGGGAACTCTCTCGTAAAACC 57.042 47.619 0.00 0.00 32.90 3.27
295 296 9.802039 TCTTAATCTAGAATAGGGAACTCTCTC 57.198 37.037 0.00 0.00 43.67 3.20
324 326 6.710744 AGTTGATTACTTCATTCAACCTCGTT 59.289 34.615 10.47 0.00 46.58 3.85
327 329 8.999431 TGTTAGTTGATTACTTCATTCAACCTC 58.001 33.333 10.47 4.09 46.58 3.85
328 330 8.784043 GTGTTAGTTGATTACTTCATTCAACCT 58.216 33.333 10.47 3.11 46.58 3.50
340 342 7.088589 TCTAGGTACCGTGTTAGTTGATTAC 57.911 40.000 6.18 0.00 0.00 1.89
369 371 8.366401 CCACCATGCATAATTTATTGGATTACA 58.634 33.333 0.00 0.00 0.00 2.41
370 372 8.584157 TCCACCATGCATAATTTATTGGATTAC 58.416 33.333 0.00 0.00 0.00 1.89
391 393 4.793201 AGCAACCCTAGAATAAATCCACC 58.207 43.478 0.00 0.00 0.00 4.61
395 397 7.510407 ACCTCTTAGCAACCCTAGAATAAATC 58.490 38.462 0.00 0.00 0.00 2.17
401 403 4.164981 TGAACCTCTTAGCAACCCTAGAA 58.835 43.478 0.00 0.00 0.00 2.10
421 423 3.649502 ACTGACCATGCATCTGGATATGA 59.350 43.478 13.35 0.00 39.73 2.15
425 427 1.841919 TCACTGACCATGCATCTGGAT 59.158 47.619 13.35 0.00 39.73 3.41
426 428 1.208776 CTCACTGACCATGCATCTGGA 59.791 52.381 13.35 0.00 39.73 3.86
430 432 1.099879 GGCCTCACTGACCATGCATC 61.100 60.000 0.00 0.00 0.00 3.91
443 445 1.076559 CCATCCTTGCATGGCCTCA 60.077 57.895 13.75 0.00 37.12 3.86
458 460 2.203938 ACGTCCTCCACCCACCAT 60.204 61.111 0.00 0.00 0.00 3.55
474 480 1.142748 CCGAGTGATCCAGGCTGAC 59.857 63.158 17.94 5.96 0.00 3.51
477 483 3.842923 CGCCGAGTGATCCAGGCT 61.843 66.667 13.43 0.00 46.85 4.58
487 493 1.376812 GGGAATTCAACCGCCGAGT 60.377 57.895 7.93 0.00 0.00 4.18
492 498 2.760634 AATTTGGGGAATTCAACCGC 57.239 45.000 7.93 0.00 40.13 5.68
504 510 0.394352 CGGAGGGTGAGGAATTTGGG 60.394 60.000 0.00 0.00 0.00 4.12
505 511 1.032114 GCGGAGGGTGAGGAATTTGG 61.032 60.000 0.00 0.00 0.00 3.28
507 513 1.078426 CGCGGAGGGTGAGGAATTT 60.078 57.895 0.00 0.00 34.98 1.82
516 522 4.779733 AGGATGGTCGCGGAGGGT 62.780 66.667 6.13 0.00 42.82 4.34
532 538 2.780010 ACTAGGTGATGAATCCCCCAAG 59.220 50.000 0.00 0.00 0.00 3.61
533 539 2.858644 ACTAGGTGATGAATCCCCCAA 58.141 47.619 0.00 0.00 0.00 4.12
535 541 3.328050 CCTAACTAGGTGATGAATCCCCC 59.672 52.174 0.00 0.00 38.69 5.40
555 561 1.076923 ATCGAGTCGCTACCACCCT 60.077 57.895 7.92 0.00 0.00 4.34
575 581 2.130193 AGTGCTATCCCATGACCACAT 58.870 47.619 0.00 0.00 37.19 3.21
596 602 3.674753 GCAAAGCATGAAAAATACGCACT 59.325 39.130 0.00 0.00 0.00 4.40
603 609 9.452287 AAAACATATAGGCAAAGCATGAAAAAT 57.548 25.926 0.00 0.00 0.00 1.82
636 648 1.951209 TAGCATTGACTCCCACCTCA 58.049 50.000 0.00 0.00 0.00 3.86
641 653 1.340017 GCCACTTAGCATTGACTCCCA 60.340 52.381 0.00 0.00 0.00 4.37
642 654 1.065126 AGCCACTTAGCATTGACTCCC 60.065 52.381 0.00 0.00 34.23 4.30
650 662 2.431954 ATCTGCAAGCCACTTAGCAT 57.568 45.000 0.00 0.00 36.28 3.79
655 667 1.999648 TCCAAATCTGCAAGCCACTT 58.000 45.000 0.00 0.00 0.00 3.16
662 674 4.422840 CGCACATAATTCCAAATCTGCAA 58.577 39.130 0.00 0.00 0.00 4.08
666 678 3.023119 TGGCGCACATAATTCCAAATCT 58.977 40.909 10.83 0.00 0.00 2.40
711 723 2.434884 CATGTTGCGCTCGGGAGT 60.435 61.111 9.73 0.00 0.00 3.85
750 762 1.001487 TGCACTCAAAGATTTGCACCG 60.001 47.619 0.30 0.00 40.01 4.94
751 763 2.796593 GTTGCACTCAAAGATTTGCACC 59.203 45.455 0.30 0.00 44.44 5.01
767 779 3.311486 TGTATCACGAGTCATGTTGCA 57.689 42.857 0.00 0.00 0.00 4.08
780 792 6.734137 TGTTGTGTTTGGAGATTTGTATCAC 58.266 36.000 0.00 0.00 32.95 3.06
785 797 4.740334 GCCATGTTGTGTTTGGAGATTTGT 60.740 41.667 0.00 0.00 31.94 2.83
807 820 3.857010 GCTTGGAGGTTTACAACATGTGC 60.857 47.826 0.00 0.00 0.00 4.57
809 822 3.317993 GTGCTTGGAGGTTTACAACATGT 59.682 43.478 0.00 0.00 0.00 3.21
826 839 0.112995 ACATGGGTCATGGTGTGCTT 59.887 50.000 11.85 0.00 45.16 3.91
833 846 1.682854 GGTATGCAACATGGGTCATGG 59.317 52.381 11.85 0.00 45.16 3.66
858 871 1.880340 GCTCGGTCTGATTCAGCCG 60.880 63.158 28.50 28.50 45.29 5.52
859 872 1.880340 CGCTCGGTCTGATTCAGCC 60.880 63.158 8.89 11.87 0.00 4.85
864 877 0.391661 ATGTTGCGCTCGGTCTGATT 60.392 50.000 9.73 0.00 0.00 2.57
908 922 2.161855 TGAGGCTTGCAACCATGTTAG 58.838 47.619 16.93 0.00 0.00 2.34
919 933 1.140452 TCAGATCCTGATGAGGCTTGC 59.860 52.381 0.00 0.00 39.57 4.01
938 952 0.387929 TAGCCGTTGGATCCATCGTC 59.612 55.000 32.63 25.44 37.42 4.20
963 977 6.427853 ACTGATGTTTTGAAATGATCGACTGA 59.572 34.615 0.00 0.00 0.00 3.41
1059 1078 1.337167 GGTATATGTAACGGCGGGGTC 60.337 57.143 13.24 0.00 0.00 4.46
1101 1128 4.400251 ACCTGACGGGGGAGGAGG 62.400 72.222 5.03 0.00 40.03 4.30
1117 1144 4.838486 CGAGCCGGCGAGACAGAC 62.838 72.222 23.20 5.42 0.00 3.51
1142 1169 0.106918 TGAGGTTTTGTGGCGAAGGT 60.107 50.000 0.00 0.00 0.00 3.50
1152 1179 0.234884 GTTCGCCGTCTGAGGTTTTG 59.765 55.000 0.00 0.00 0.00 2.44
1169 1196 2.486636 TTCGATCGACGCCAGCAGTT 62.487 55.000 19.26 0.00 42.26 3.16
1175 1202 1.420641 CTGCATTTCGATCGACGCCA 61.421 55.000 19.26 11.48 42.26 5.69
1243 1270 1.661821 CGGAGCATAGGTAGCGTGC 60.662 63.158 14.80 14.80 39.10 5.34
1264 1291 0.534427 TCGTCACACTCACCGTCTCT 60.534 55.000 0.00 0.00 0.00 3.10
1466 1493 2.034687 AGCTCATGGTGGTGGTGC 59.965 61.111 0.00 0.00 0.00 5.01
1524 1551 3.554342 CGGATGGGGGAGAGGCAG 61.554 72.222 0.00 0.00 0.00 4.85
1698 1737 2.091333 AGAGGAAGAGGAGGAGGATGAC 60.091 54.545 0.00 0.00 0.00 3.06
1701 1740 1.412937 GCAGAGGAAGAGGAGGAGGAT 60.413 57.143 0.00 0.00 0.00 3.24
1824 1863 1.066585 ATGGCAGCCAGGATCCTGAT 61.067 55.000 38.37 24.97 46.30 2.90
1855 1894 4.643387 AGCTTTCTTGGCCCGCGT 62.643 61.111 4.92 0.00 0.00 6.01
2164 2203 9.663904 ATTTGCGATGTATACATAACATTGTTC 57.336 29.630 18.28 3.06 39.81 3.18
2323 2362 5.984926 TGAACAATGGAGAACAAAATTCAGC 59.015 36.000 0.00 0.00 0.00 4.26
2332 2371 5.850557 AACACAATGAACAATGGAGAACA 57.149 34.783 0.00 0.00 0.00 3.18
2333 2372 5.399301 CGAAACACAATGAACAATGGAGAAC 59.601 40.000 0.00 0.00 0.00 3.01
2341 2380 6.184580 ACTAACACGAAACACAATGAACAA 57.815 33.333 0.00 0.00 0.00 2.83
2343 2382 6.707711 TGTACTAACACGAAACACAATGAAC 58.292 36.000 0.00 0.00 0.00 3.18
2419 2519 4.746611 CAGGATTGTTTGTCAAAGCCTTTC 59.253 41.667 0.00 0.00 40.45 2.62
2464 2723 7.671495 ACGCATACATGAGATTGCAATATTA 57.329 32.000 12.97 6.44 34.80 0.98
2469 2728 4.700268 AAACGCATACATGAGATTGCAA 57.300 36.364 0.00 0.00 34.80 4.08
2502 2761 8.874744 ACATTAGACTTGTAGTACTCCAGTAA 57.125 34.615 0.00 0.00 31.52 2.24
2503 2762 8.105197 TGACATTAGACTTGTAGTACTCCAGTA 58.895 37.037 0.00 0.00 0.00 2.74
2504 2763 6.946583 TGACATTAGACTTGTAGTACTCCAGT 59.053 38.462 0.00 0.00 0.00 4.00
2505 2764 7.392494 TGACATTAGACTTGTAGTACTCCAG 57.608 40.000 0.00 0.00 0.00 3.86
2506 2765 7.956328 ATGACATTAGACTTGTAGTACTCCA 57.044 36.000 0.00 0.00 0.00 3.86
2571 2830 6.258287 TCTCGTTAAAACAAGGTTTTGATCGA 59.742 34.615 15.27 17.36 37.73 3.59
2573 2832 7.636326 TCTCTCGTTAAAACAAGGTTTTGATC 58.364 34.615 15.27 6.44 37.73 2.92
2576 2835 8.455598 TTTTCTCTCGTTAAAACAAGGTTTTG 57.544 30.769 15.27 1.81 40.24 2.44
2623 2882 6.732896 TGACTTCAGTAACTTCCTTCTTCT 57.267 37.500 0.00 0.00 0.00 2.85
2624 2883 5.407084 GCTGACTTCAGTAACTTCCTTCTTC 59.593 44.000 8.04 0.00 45.45 2.87
2625 2884 5.163301 TGCTGACTTCAGTAACTTCCTTCTT 60.163 40.000 8.04 0.00 45.45 2.52
2686 2948 3.307480 GGGAGTACAAGTGTAAGGTGCAT 60.307 47.826 0.00 0.00 31.52 3.96
2687 2949 2.038033 GGGAGTACAAGTGTAAGGTGCA 59.962 50.000 0.00 0.00 31.52 4.57
2690 2952 3.171528 GGAGGGAGTACAAGTGTAAGGT 58.828 50.000 0.00 0.00 31.52 3.50
2698 2960 0.613853 TGGGACGGAGGGAGTACAAG 60.614 60.000 0.00 0.00 0.00 3.16
2703 2965 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2704 2966 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2705 2967 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2707 2969 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2708 2970 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2709 2971 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2710 2972 4.517453 TGTAAGACAAGAATTTTGGGACGG 59.483 41.667 0.00 0.00 0.00 4.79
2711 2973 5.682943 TGTAAGACAAGAATTTTGGGACG 57.317 39.130 5.68 0.00 0.00 4.79
2730 2992 9.970553 AGGTACATCCGTATCTAGATAAATGTA 57.029 33.333 23.81 23.81 37.29 2.29
2731 2993 8.880991 AGGTACATCCGTATCTAGATAAATGT 57.119 34.615 25.07 25.07 37.29 2.71
2744 3006 9.970395 CACATTTTAGTATTAGGTACATCCGTA 57.030 33.333 0.00 0.00 41.99 4.02
2745 3007 8.698210 TCACATTTTAGTATTAGGTACATCCGT 58.302 33.333 0.00 0.00 41.99 4.69
2746 3008 8.975439 GTCACATTTTAGTATTAGGTACATCCG 58.025 37.037 0.00 0.00 41.99 4.18
2753 3015 8.893727 GCATCAAGTCACATTTTAGTATTAGGT 58.106 33.333 0.00 0.00 0.00 3.08
2754 3016 8.892723 TGCATCAAGTCACATTTTAGTATTAGG 58.107 33.333 0.00 0.00 0.00 2.69
2757 3019 8.408601 GGATGCATCAAGTCACATTTTAGTATT 58.591 33.333 27.25 0.00 0.00 1.89
2758 3020 7.254898 CGGATGCATCAAGTCACATTTTAGTAT 60.255 37.037 27.25 0.00 0.00 2.12
2759 3021 6.037062 CGGATGCATCAAGTCACATTTTAGTA 59.963 38.462 27.25 0.00 0.00 1.82
2760 3022 5.163723 CGGATGCATCAAGTCACATTTTAGT 60.164 40.000 27.25 0.00 0.00 2.24
2761 3023 5.163723 ACGGATGCATCAAGTCACATTTTAG 60.164 40.000 27.25 4.11 0.00 1.85
2762 3024 4.699735 ACGGATGCATCAAGTCACATTTTA 59.300 37.500 27.25 0.00 0.00 1.52
2763 3025 3.507233 ACGGATGCATCAAGTCACATTTT 59.493 39.130 27.25 0.78 0.00 1.82
2764 3026 3.084039 ACGGATGCATCAAGTCACATTT 58.916 40.909 27.25 1.45 0.00 2.32
2765 3027 2.715046 ACGGATGCATCAAGTCACATT 58.285 42.857 27.25 2.11 0.00 2.71
2766 3028 2.408271 ACGGATGCATCAAGTCACAT 57.592 45.000 27.25 2.78 0.00 3.21
2767 3029 3.541996 ATACGGATGCATCAAGTCACA 57.458 42.857 27.25 12.28 0.00 3.58
2768 3030 4.496341 CCAAATACGGATGCATCAAGTCAC 60.496 45.833 27.25 8.53 0.00 3.67
2769 3031 3.627123 CCAAATACGGATGCATCAAGTCA 59.373 43.478 27.25 14.60 0.00 3.41
2770 3032 3.876914 TCCAAATACGGATGCATCAAGTC 59.123 43.478 27.25 9.62 0.00 3.01
2771 3033 3.627577 GTCCAAATACGGATGCATCAAGT 59.372 43.478 27.25 25.40 37.41 3.16
2772 3034 3.627123 TGTCCAAATACGGATGCATCAAG 59.373 43.478 27.25 21.48 37.41 3.02
2773 3035 3.615155 TGTCCAAATACGGATGCATCAA 58.385 40.909 27.25 12.93 37.41 2.57
2774 3036 3.274095 TGTCCAAATACGGATGCATCA 57.726 42.857 27.25 8.37 37.41 3.07
2775 3037 4.630894 TTTGTCCAAATACGGATGCATC 57.369 40.909 18.81 18.81 37.41 3.91
2776 3038 4.889409 AGATTTGTCCAAATACGGATGCAT 59.111 37.500 0.00 0.00 40.77 3.96
2777 3039 4.269183 AGATTTGTCCAAATACGGATGCA 58.731 39.130 5.29 0.00 40.77 3.96
2778 3040 4.900635 AGATTTGTCCAAATACGGATGC 57.099 40.909 5.29 0.00 40.77 3.91
2779 3041 7.279981 TGTCTTAGATTTGTCCAAATACGGATG 59.720 37.037 5.29 0.00 40.77 3.51
2780 3042 7.335627 TGTCTTAGATTTGTCCAAATACGGAT 58.664 34.615 5.29 0.00 40.77 4.18
2781 3043 6.703319 TGTCTTAGATTTGTCCAAATACGGA 58.297 36.000 5.29 0.82 40.77 4.69
2782 3044 6.978343 TGTCTTAGATTTGTCCAAATACGG 57.022 37.500 5.29 0.00 40.77 4.02
2783 3045 8.251750 TCTTGTCTTAGATTTGTCCAAATACG 57.748 34.615 5.29 0.00 40.77 3.06
2793 3055 9.760660 CGTCCTAAAATTCTTGTCTTAGATTTG 57.239 33.333 0.00 0.00 0.00 2.32
2794 3056 8.947115 CCGTCCTAAAATTCTTGTCTTAGATTT 58.053 33.333 0.00 0.00 0.00 2.17
2795 3057 8.319146 TCCGTCCTAAAATTCTTGTCTTAGATT 58.681 33.333 0.00 0.00 0.00 2.40
2796 3058 7.848128 TCCGTCCTAAAATTCTTGTCTTAGAT 58.152 34.615 0.00 0.00 0.00 1.98
2797 3059 7.235935 TCCGTCCTAAAATTCTTGTCTTAGA 57.764 36.000 0.00 0.00 0.00 2.10
2798 3060 6.535508 CCTCCGTCCTAAAATTCTTGTCTTAG 59.464 42.308 0.00 0.00 0.00 2.18
2799 3061 6.211986 TCCTCCGTCCTAAAATTCTTGTCTTA 59.788 38.462 0.00 0.00 0.00 2.10
2800 3062 5.012768 TCCTCCGTCCTAAAATTCTTGTCTT 59.987 40.000 0.00 0.00 0.00 3.01
2801 3063 4.530946 TCCTCCGTCCTAAAATTCTTGTCT 59.469 41.667 0.00 0.00 0.00 3.41
2802 3064 4.828829 TCCTCCGTCCTAAAATTCTTGTC 58.171 43.478 0.00 0.00 0.00 3.18
2803 3065 4.903045 TCCTCCGTCCTAAAATTCTTGT 57.097 40.909 0.00 0.00 0.00 3.16
2804 3066 5.246307 ACTTCCTCCGTCCTAAAATTCTTG 58.754 41.667 0.00 0.00 0.00 3.02
2805 3067 5.500546 ACTTCCTCCGTCCTAAAATTCTT 57.499 39.130 0.00 0.00 0.00 2.52
2806 3068 6.809976 ATACTTCCTCCGTCCTAAAATTCT 57.190 37.500 0.00 0.00 0.00 2.40
2807 3069 8.202811 AGTAATACTTCCTCCGTCCTAAAATTC 58.797 37.037 0.00 0.00 0.00 2.17
2808 3070 8.087303 AGTAATACTTCCTCCGTCCTAAAATT 57.913 34.615 0.00 0.00 0.00 1.82
2809 3071 7.564292 AGAGTAATACTTCCTCCGTCCTAAAAT 59.436 37.037 0.00 0.00 0.00 1.82
2810 3072 6.894103 AGAGTAATACTTCCTCCGTCCTAAAA 59.106 38.462 0.00 0.00 0.00 1.52
2811 3073 6.320672 CAGAGTAATACTTCCTCCGTCCTAAA 59.679 42.308 0.00 0.00 0.00 1.85
2812 3074 5.826737 CAGAGTAATACTTCCTCCGTCCTAA 59.173 44.000 0.00 0.00 0.00 2.69
2813 3075 5.104193 ACAGAGTAATACTTCCTCCGTCCTA 60.104 44.000 0.00 0.00 0.00 2.94
2814 3076 4.208746 CAGAGTAATACTTCCTCCGTCCT 58.791 47.826 0.00 0.00 0.00 3.85
2815 3077 3.952967 ACAGAGTAATACTTCCTCCGTCC 59.047 47.826 0.00 0.00 0.00 4.79
2816 3078 5.579564 AACAGAGTAATACTTCCTCCGTC 57.420 43.478 0.00 0.00 0.00 4.79
2817 3079 5.997384 AAACAGAGTAATACTTCCTCCGT 57.003 39.130 0.00 0.00 0.00 4.69
2844 3106 1.270094 GGTGTGTGACATTCGGACTCA 60.270 52.381 0.00 0.00 0.00 3.41
2851 3113 4.756642 TCTCTTGATTGGTGTGTGACATTC 59.243 41.667 0.00 0.00 0.00 2.67
2852 3114 4.717877 TCTCTTGATTGGTGTGTGACATT 58.282 39.130 0.00 0.00 0.00 2.71
2853 3115 4.356405 TCTCTTGATTGGTGTGTGACAT 57.644 40.909 0.00 0.00 0.00 3.06
2865 3127 3.529533 CCGCTCATCACTTCTCTTGATT 58.470 45.455 0.00 0.00 30.98 2.57
2880 3142 5.581126 AGATTTTTGAATTATGCCGCTCA 57.419 34.783 0.00 0.00 0.00 4.26
2881 3143 6.634436 CACTAGATTTTTGAATTATGCCGCTC 59.366 38.462 0.00 0.00 0.00 5.03
2884 3146 6.264832 TGCACTAGATTTTTGAATTATGCCG 58.735 36.000 0.00 0.00 0.00 5.69
2899 3161 4.720046 TCTAGAAGGACGATGCACTAGAT 58.280 43.478 0.00 0.00 33.82 1.98
2900 3162 4.152284 TCTAGAAGGACGATGCACTAGA 57.848 45.455 0.00 0.00 35.53 2.43
2901 3163 4.902443 TTCTAGAAGGACGATGCACTAG 57.098 45.455 0.00 0.00 0.00 2.57
2911 3173 4.000988 TCGCCATTTGTTTCTAGAAGGAC 58.999 43.478 5.12 2.85 0.00 3.85
2914 3176 3.725010 GCGTCGCCATTTGTTTCTAGAAG 60.725 47.826 5.75 0.00 0.00 2.85
2918 3180 1.803334 AGCGTCGCCATTTGTTTCTA 58.197 45.000 14.86 0.00 0.00 2.10
2920 3182 2.351726 AGATAGCGTCGCCATTTGTTTC 59.648 45.455 14.86 0.00 0.00 2.78
2923 3185 2.024176 AAGATAGCGTCGCCATTTGT 57.976 45.000 14.86 0.00 0.00 2.83
2934 3196 2.863137 GAGGCACAGAGAAAAGATAGCG 59.137 50.000 0.00 0.00 0.00 4.26
2953 3215 1.064906 ACAAGCAGTCCCCATCATGAG 60.065 52.381 0.09 0.00 0.00 2.90
3050 3314 6.906901 ACTACTTATGGAAAGGGACATTAGGA 59.093 38.462 0.00 0.00 30.36 2.94


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

AutoCloner maintained by Alex Coulton.