Multiple sequence alignment - TraesCS4A01G062200

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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 TraesCS4A01G062200 chr4A 100.000 8536 0 0 1 8536 58892098 58883563 0.000000e+00 15764.0
1 TraesCS4A01G062200 chr4A 75.758 198 38 8 332 523 723747464 723747657 3.280000e-14 91.6
2 TraesCS4A01G062200 chr4B 96.119 4664 144 16 587 5228 495604234 495599586 0.000000e+00 7576.0
3 TraesCS4A01G062200 chr4B 95.047 2463 97 14 5312 7757 495599585 495597131 0.000000e+00 3849.0
4 TraesCS4A01G062200 chr4B 92.662 804 32 8 7746 8536 495597109 495596320 0.000000e+00 1133.0
5 TraesCS4A01G062200 chr4B 87.332 521 57 8 11 523 495606483 495605964 9.550000e-164 588.0
6 TraesCS4A01G062200 chr4B 95.556 90 4 0 5227 5316 643774332 643774243 2.480000e-30 145.0
7 TraesCS4A01G062200 chr4D 95.934 4501 129 25 745 5228 401101190 401096727 0.000000e+00 7249.0
8 TraesCS4A01G062200 chr4D 96.001 3001 91 15 827 3813 417647670 417644685 0.000000e+00 4850.0
9 TraesCS4A01G062200 chr4D 96.264 1472 46 6 6182 7644 417634362 417632891 0.000000e+00 2405.0
10 TraesCS4A01G062200 chr4D 96.401 1417 36 6 3817 5228 417644175 417642769 0.000000e+00 2320.0
11 TraesCS4A01G062200 chr4D 96.072 891 29 4 6760 7644 401095014 401094124 0.000000e+00 1447.0
12 TraesCS4A01G062200 chr4D 96.216 872 29 2 5312 6183 401096726 401095859 0.000000e+00 1424.0
13 TraesCS4A01G062200 chr4D 94.266 872 29 6 5312 6183 417642768 417641918 0.000000e+00 1314.0
14 TraesCS4A01G062200 chr4D 93.225 797 36 7 7749 8536 417632362 417631575 0.000000e+00 1157.0
15 TraesCS4A01G062200 chr4D 94.281 647 28 4 7893 8536 401090781 401090141 0.000000e+00 981.0
16 TraesCS4A01G062200 chr4D 95.392 586 22 3 6182 6762 401095702 401095117 0.000000e+00 928.0
17 TraesCS4A01G062200 chr4D 89.691 194 14 6 8 196 470498283 470498475 8.560000e-60 243.0
18 TraesCS4A01G062200 chr4D 89.116 147 11 3 7746 7891 401092778 401092636 2.450000e-40 178.0
19 TraesCS4A01G062200 chr4D 88.430 121 13 1 7637 7757 417632509 417632390 2.480000e-30 145.0
20 TraesCS4A01G062200 chr7D 90.625 192 13 4 8 194 197293043 197293234 5.120000e-62 250.0
21 TraesCS4A01G062200 chr7D 90.576 191 13 5 8 193 349054977 349054787 1.840000e-61 248.0
22 TraesCS4A01G062200 chr7D 75.449 334 71 10 196 522 573909103 573909432 1.480000e-32 152.0
23 TraesCS4A01G062200 chr7D 95.652 92 4 0 5219 5310 633397813 633397722 1.920000e-31 148.0
24 TraesCS4A01G062200 chr7D 95.604 91 4 0 5220 5310 154378951 154379041 6.900000e-31 147.0
25 TraesCS4A01G062200 chr7D 91.346 104 7 2 5219 5321 141292080 141292182 3.210000e-29 141.0
26 TraesCS4A01G062200 chr7D 83.607 61 9 1 302 361 571809387 571809447 1.000000e-03 56.5
27 TraesCS4A01G062200 chr2D 90.576 191 12 6 8 193 359943001 359942812 1.840000e-61 248.0
28 TraesCS4A01G062200 chr2A 90.909 187 12 5 14 195 462827105 462826919 6.620000e-61 246.0
29 TraesCS4A01G062200 chr3D 90.052 191 15 3 8 194 317056410 317056220 2.380000e-60 244.0
30 TraesCS4A01G062200 chr5D 90.052 191 14 4 8 193 166929928 166930118 8.560000e-60 243.0
31 TraesCS4A01G062200 chr5D 94.845 97 3 2 5227 5321 545281810 545281906 5.340000e-32 150.0
32 TraesCS4A01G062200 chr5D 75.635 197 36 8 329 522 484660891 484660704 4.240000e-13 87.9
33 TraesCS4A01G062200 chr2B 88.557 201 17 6 8 202 158155414 158155214 1.110000e-58 239.0
34 TraesCS4A01G062200 chr2B 82.667 150 22 4 552 698 740548155 740548303 6.950000e-26 130.0
35 TraesCS4A01G062200 chr7A 98.810 84 1 0 5227 5310 485195289 485195206 5.340000e-32 150.0
36 TraesCS4A01G062200 chr7A 95.455 88 4 0 5223 5310 126927404 126927317 3.210000e-29 141.0
37 TraesCS4A01G062200 chr7A 72.892 332 70 13 196 522 54726358 54726674 7.050000e-16 97.1
38 TraesCS4A01G062200 chr6D 97.701 87 2 0 5224 5310 62245404 62245318 5.340000e-32 150.0
39 TraesCS4A01G062200 chr6B 94.681 94 5 0 5217 5310 14523416 14523323 6.900000e-31 147.0
40 TraesCS4A01G062200 chr5A 78.481 158 22 8 556 703 570473486 570473641 9.120000e-15 93.5
41 TraesCS4A01G062200 chr7B 88.060 67 6 2 457 522 696230363 696230428 2.550000e-10 78.7
42 TraesCS4A01G062200 chr3A 82.927 82 10 3 623 704 377804744 377804667 4.270000e-08 71.3
43 TraesCS4A01G062200 chr3A 85.185 54 5 2 533 583 708950496 708950549 1.500000e-02 52.8
44 TraesCS4A01G062200 chr1B 79.787 94 18 1 278 370 26260879 26260972 5.530000e-07 67.6


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 TraesCS4A01G062200 chr4A 58883563 58892098 8535 True 15764.000000 15764 100.000000 1 8536 1 chr4A.!!$R1 8535
1 TraesCS4A01G062200 chr4B 495596320 495606483 10163 True 3286.500000 7576 92.790000 11 8536 4 chr4B.!!$R2 8525
2 TraesCS4A01G062200 chr4D 417641918 417647670 5752 True 2828.000000 4850 95.556000 827 6183 3 chr4D.!!$R3 5356
3 TraesCS4A01G062200 chr4D 401090141 401101190 11049 True 2034.500000 7249 94.501833 745 8536 6 chr4D.!!$R1 7791
4 TraesCS4A01G062200 chr4D 417631575 417634362 2787 True 1235.666667 2405 92.639667 6182 8536 3 chr4D.!!$R2 2354

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
574 583 0.098728 GTGTGGCACGAACATATGGC 59.901 55.000 13.77 0.0 41.57 4.40 F
642 2317 0.887933 TTCCTTTTCGGATGGCAAGC 59.112 50.000 0.00 0.0 42.70 4.01 F
1591 3280 0.744771 CTAGTTTCTCTTGGGCGCCC 60.745 60.000 39.40 39.4 0.00 6.13 F
2102 3791 1.915769 AGCTTCCGTTCCAGGAGCT 60.916 57.895 1.28 0.0 41.98 4.09 F
3680 5371 0.846870 CACCCCTCCCCCTTCTCTTT 60.847 60.000 0.00 0.0 0.00 2.52 F
5241 7466 1.078823 ACATGTACTCCCTCTGTCCCA 59.921 52.381 0.00 0.0 0.00 4.37 F
5286 7511 1.602377 AGTGTAGTGCCAAAAACGCTC 59.398 47.619 0.00 0.0 0.00 5.03 F
5310 7535 1.718280 ATTATGGGACGGAGGGAGTC 58.282 55.000 0.00 0.0 37.86 3.36 F
7027 9523 1.552337 CTTCTAGAGGCTTGCTGGACA 59.448 52.381 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 3276 1.281566 AAAGAAAAATTGCGCGGGCG 61.282 50.000 20.22 8.99 44.10 6.13 R
1992 3681 1.351350 ACTAAGAACTGGACCCTTGCC 59.649 52.381 0.00 0.00 0.00 4.52 R
2660 4349 1.005569 TCCTCCACTCGAGCTTTAGGA 59.994 52.381 13.61 16.19 37.27 2.94 R
3934 6131 2.024414 GCAGTTGGAGTTTTGGACTGT 58.976 47.619 0.00 0.00 39.19 3.55 R
5293 7518 0.185416 GAGACTCCCTCCGTCCCATA 59.815 60.000 0.00 0.00 35.87 2.74 R
6641 9031 0.106894 GGTAGTACTGCCATGCCTCC 59.893 60.000 23.63 0.00 35.28 4.30 R
7027 9523 3.254024 ATCCTGGTCGGCTGCGTTT 62.254 57.895 0.00 0.00 0.00 3.60 R
7299 9795 2.969238 CCGCCGTCATCATCAGCC 60.969 66.667 0.00 0.00 0.00 4.85 R
8357 13989 1.060937 GCCTGCACGCGAACAATAG 59.939 57.895 15.93 1.73 0.00 1.73 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
30 31 2.601266 CGCGTTTGGAGTTCGTTTGATT 60.601 45.455 0.00 0.00 0.00 2.57
40 43 5.343325 GGAGTTCGTTTGATTGATTTTCTGC 59.657 40.000 0.00 0.00 0.00 4.26
69 72 4.335400 AAAACATGCGAAAAACAGGGAT 57.665 36.364 0.00 0.00 0.00 3.85
70 73 5.461032 AAAACATGCGAAAAACAGGGATA 57.539 34.783 0.00 0.00 0.00 2.59
71 74 5.461032 AAACATGCGAAAAACAGGGATAA 57.539 34.783 0.00 0.00 0.00 1.75
81 85 3.175133 CAGGGATAACACTGGGCAC 57.825 57.895 0.00 0.00 43.19 5.01
97 101 5.104360 ACTGGGCACTGATCAATATGTTAGT 60.104 40.000 0.00 0.45 0.00 2.24
100 104 5.368145 GGCACTGATCAATATGTTAGTCCA 58.632 41.667 0.00 0.00 0.00 4.02
204 210 5.339875 CGAAGACGTATCAATGGATTAGACG 59.660 44.000 2.89 2.89 38.40 4.18
212 218 2.797156 CAATGGATTAGACGAAGCTCCG 59.203 50.000 0.00 0.00 0.00 4.63
215 221 1.404391 GGATTAGACGAAGCTCCGACA 59.596 52.381 0.00 0.00 0.00 4.35
216 222 2.034812 GGATTAGACGAAGCTCCGACAT 59.965 50.000 0.00 0.00 0.00 3.06
249 255 2.175035 CTCCTCGGGCCAACGGTTTA 62.175 60.000 4.39 0.00 0.00 2.01
253 259 3.066190 GGGCCAACGGTTTAGGGC 61.066 66.667 4.39 13.44 46.34 5.19
259 265 1.271163 CCAACGGTTTAGGGCTTCTCA 60.271 52.381 0.00 0.00 0.00 3.27
260 266 2.618045 CCAACGGTTTAGGGCTTCTCAT 60.618 50.000 0.00 0.00 0.00 2.90
265 271 1.666189 GTTTAGGGCTTCTCATCGTGC 59.334 52.381 0.00 0.00 0.00 5.34
269 275 1.146358 GGGCTTCTCATCGTGCGTAC 61.146 60.000 0.00 0.00 0.00 3.67
286 292 0.521867 TACGCGACGACGAGATTTGG 60.522 55.000 15.93 0.00 41.48 3.28
307 313 7.595819 TTGGTGTGAGGTTCTTTAAATCAAT 57.404 32.000 0.00 0.00 0.00 2.57
314 320 9.912634 GTGAGGTTCTTTAAATCAATTCAATGA 57.087 29.630 0.00 0.00 0.00 2.57
328 334 6.748658 TCAATTCAATGATTCAACTTCGATGC 59.251 34.615 0.00 0.00 0.00 3.91
330 336 5.225899 TCAATGATTCAACTTCGATGCTG 57.774 39.130 0.00 0.00 0.00 4.41
331 337 3.687572 ATGATTCAACTTCGATGCTGC 57.312 42.857 0.00 0.00 0.00 5.25
332 338 2.425539 TGATTCAACTTCGATGCTGCA 58.574 42.857 4.13 4.13 0.00 4.41
349 356 4.479993 AGCTCCATGGCGCTGGTC 62.480 66.667 28.03 8.59 34.64 4.02
361 368 2.602676 GCTGGTCCTTAGGGGCACA 61.603 63.158 0.00 0.00 39.39 4.57
401 409 8.258007 TCTGGTTATATCAACAAGGTTAGACTG 58.742 37.037 0.00 0.00 0.00 3.51
412 420 4.592485 AGGTTAGACTGGCTTCGATATG 57.408 45.455 0.00 0.00 0.00 1.78
427 435 2.743938 GATATGAGAGCGGCGAAAAGA 58.256 47.619 12.98 0.00 0.00 2.52
433 441 2.175811 GCGGCGAAAAGAATGCGT 59.824 55.556 12.98 0.00 0.00 5.24
434 442 1.863446 GCGGCGAAAAGAATGCGTC 60.863 57.895 12.98 0.00 0.00 5.19
439 447 0.433492 CGAAAAGAATGCGTCGACGT 59.567 50.000 35.48 19.18 42.22 4.34
445 454 1.070843 AGAATGCGTCGACGTTTGTTG 60.071 47.619 35.48 9.81 42.22 3.33
447 456 1.489574 ATGCGTCGACGTTTGTTGTA 58.510 45.000 35.48 14.36 42.22 2.41
450 459 0.179316 CGTCGACGTTTGTTGTAGCG 60.179 55.000 29.08 0.00 34.11 4.26
479 488 1.678728 GCTCATTCGGTGGTCCAATGA 60.679 52.381 0.00 0.00 38.08 2.57
523 532 5.676552 TGTTTGGAGTGCTTTGTACTTCTA 58.323 37.500 0.00 0.00 0.00 2.10
524 533 5.526111 TGTTTGGAGTGCTTTGTACTTCTAC 59.474 40.000 0.00 0.00 0.00 2.59
525 534 4.948341 TGGAGTGCTTTGTACTTCTACA 57.052 40.909 0.00 0.00 0.00 2.74
539 548 7.618137 TGTACTTCTACAAAACCTTAGGATCC 58.382 38.462 4.77 2.48 29.36 3.36
543 552 7.182930 ACTTCTACAAAACCTTAGGATCCTGAT 59.817 37.037 25.28 3.77 0.00 2.90
544 553 8.618240 TTCTACAAAACCTTAGGATCCTGATA 57.382 34.615 25.28 8.59 0.00 2.15
545 554 8.618240 TCTACAAAACCTTAGGATCCTGATAA 57.382 34.615 25.28 9.91 0.00 1.75
546 555 8.483758 TCTACAAAACCTTAGGATCCTGATAAC 58.516 37.037 25.28 0.00 0.00 1.89
549 558 7.037586 ACAAAACCTTAGGATCCTGATAACTGA 60.038 37.037 25.28 0.00 0.00 3.41
551 560 5.529289 ACCTTAGGATCCTGATAACTGACA 58.471 41.667 25.28 0.00 0.00 3.58
552 561 5.364157 ACCTTAGGATCCTGATAACTGACAC 59.636 44.000 25.28 0.00 0.00 3.67
553 562 5.363868 CCTTAGGATCCTGATAACTGACACA 59.636 44.000 25.28 0.00 0.00 3.72
556 565 4.780021 AGGATCCTGATAACTGACACAAGT 59.220 41.667 15.29 0.00 0.00 3.16
567 576 4.996113 CACAAGTGTGGCACGAAC 57.004 55.556 13.77 6.57 42.10 3.95
568 577 2.094060 CACAAGTGTGGCACGAACA 58.906 52.632 13.77 0.00 42.10 3.18
569 578 0.662619 CACAAGTGTGGCACGAACAT 59.337 50.000 13.77 0.00 42.10 2.71
570 579 1.870402 CACAAGTGTGGCACGAACATA 59.130 47.619 13.77 0.00 42.10 2.29
571 580 2.483877 CACAAGTGTGGCACGAACATAT 59.516 45.455 13.77 0.00 42.10 1.78
572 581 2.483877 ACAAGTGTGGCACGAACATATG 59.516 45.455 13.77 0.00 39.64 1.78
573 582 1.737838 AGTGTGGCACGAACATATGG 58.262 50.000 13.77 0.00 39.64 2.74
574 583 0.098728 GTGTGGCACGAACATATGGC 59.901 55.000 13.77 0.00 41.57 4.40
577 586 3.622459 GGCACGAACATATGGCAAC 57.378 52.632 7.80 0.00 40.91 4.17
578 587 1.094785 GGCACGAACATATGGCAACT 58.905 50.000 7.80 0.00 40.91 3.16
579 588 1.064060 GGCACGAACATATGGCAACTC 59.936 52.381 7.80 0.00 40.91 3.01
581 590 1.327460 CACGAACATATGGCAACTCCG 59.673 52.381 7.80 2.50 37.80 4.63
583 592 2.158957 ACGAACATATGGCAACTCCGAT 60.159 45.455 7.80 0.00 37.80 4.18
584 593 2.476619 CGAACATATGGCAACTCCGATC 59.523 50.000 7.80 0.00 37.80 3.69
585 594 2.154854 ACATATGGCAACTCCGATCG 57.845 50.000 8.51 8.51 37.80 3.69
595 2270 3.544244 GCAACTCCGATCGTTTTCTATGC 60.544 47.826 15.09 10.84 0.00 3.14
598 2273 3.181465 ACTCCGATCGTTTTCTATGCCAT 60.181 43.478 15.09 0.00 0.00 4.40
609 2284 3.535280 TCTATGCCATGTTTAGCGACA 57.465 42.857 0.00 0.00 0.00 4.35
622 2297 1.815421 GCGACACGAGGATGGCAAT 60.815 57.895 0.00 0.00 0.00 3.56
625 2300 1.062587 CGACACGAGGATGGCAATTTC 59.937 52.381 0.00 0.00 0.00 2.17
633 2308 2.497273 AGGATGGCAATTTCCTTTTCGG 59.503 45.455 2.22 0.00 39.36 4.30
642 2317 0.887933 TTCCTTTTCGGATGGCAAGC 59.112 50.000 0.00 0.00 42.70 4.01
648 2323 1.614996 TTCGGATGGCAAGCTTCAAA 58.385 45.000 0.00 0.00 0.00 2.69
734 2413 2.249309 CAAGTGTGGCGCTTGTCG 59.751 61.111 7.64 0.00 44.10 4.35
762 2441 4.162509 GGAACCTTTATAGCAGTGAGTCCT 59.837 45.833 0.00 0.00 0.00 3.85
763 2442 5.338463 GGAACCTTTATAGCAGTGAGTCCTT 60.338 44.000 0.00 0.00 0.00 3.36
764 2443 5.763876 ACCTTTATAGCAGTGAGTCCTTT 57.236 39.130 0.00 0.00 0.00 3.11
816 2495 4.769688 TGGATTGCATGAAGAGTCGTAAT 58.230 39.130 0.00 0.00 0.00 1.89
825 2504 9.358872 TGCATGAAGAGTCGTAATAATCATATC 57.641 33.333 0.00 0.00 0.00 1.63
835 2514 9.347934 GTCGTAATAATCATATCTGAGGAAGTG 57.652 37.037 0.00 0.00 34.12 3.16
1032 2721 2.096248 CTAGTCGGAGAGCTTGAGGTT 58.904 52.381 0.00 0.00 36.95 3.50
1139 2828 2.692741 CCTTCACCCCCTCCTCCC 60.693 72.222 0.00 0.00 0.00 4.30
1173 2862 1.214305 CCCTTCCCCTGGTGGATTCA 61.214 60.000 4.97 0.00 35.39 2.57
1174 2863 0.929244 CCTTCCCCTGGTGGATTCAT 59.071 55.000 4.97 0.00 35.39 2.57
1563 3252 3.192212 CCAACCTTCTGCAGAGGAATTTC 59.808 47.826 28.29 0.00 0.00 2.17
1587 3276 3.259902 CGGTAACTAGTTTCTCTTGGGC 58.740 50.000 14.49 0.00 0.00 5.36
1591 3280 0.744771 CTAGTTTCTCTTGGGCGCCC 60.745 60.000 39.40 39.40 0.00 6.13
1697 3386 3.411446 TGTAGGTGGCATTGACAAAGAG 58.589 45.455 0.00 0.00 0.00 2.85
1919 3608 2.031258 TGTTGCACCGAAGAAGTTCA 57.969 45.000 5.50 0.00 32.36 3.18
1992 3681 7.763528 GGCCTGATATCTATGATGAAAGTAGTG 59.236 40.741 3.98 0.00 0.00 2.74
2076 3765 4.624015 TGTCTGTTACAGGTTTAACTCGG 58.376 43.478 12.79 0.00 33.73 4.63
2102 3791 1.915769 AGCTTCCGTTCCAGGAGCT 60.916 57.895 1.28 0.00 41.98 4.09
2196 3885 4.559862 ATTCACCGAAGAGAAGTCCATT 57.440 40.909 0.00 0.00 0.00 3.16
2616 4305 5.404066 CCATCCGAAAACAATGTGGTTAAAC 59.596 40.000 0.00 0.00 0.00 2.01
2618 4307 3.180782 CCGAAAACAATGTGGTTAAACGC 59.819 43.478 0.00 0.00 0.00 4.84
2945 4634 7.497909 GCAATACCTGAAAAGGCTGTATTAGTA 59.502 37.037 5.62 0.00 32.46 1.82
3162 4851 8.306313 TGAAGAGGCTGAGATGTTACTTAATA 57.694 34.615 0.00 0.00 0.00 0.98
3188 4877 8.149647 AGGCTGTTTCATGATTTTATTTTGTCA 58.850 29.630 0.00 0.00 0.00 3.58
3277 4966 5.511088 AACGTATTTGTTCGAGTAAGCAG 57.489 39.130 0.00 0.00 0.00 4.24
3344 5033 5.526506 AAGCTGAATTTCTTGCTTCAACT 57.473 34.783 17.88 3.71 41.21 3.16
3362 5051 4.462483 TCAACTATTGTTTCATCCCTTGCC 59.538 41.667 0.00 0.00 33.52 4.52
3570 5261 7.157347 TGTTCTTGCCTCTGCTATCTATATTG 58.843 38.462 0.00 0.00 38.71 1.90
3584 5275 8.013947 GCTATCTATATTGCACATTGTTGTCAG 58.986 37.037 0.00 0.00 34.46 3.51
3680 5371 0.846870 CACCCCTCCCCCTTCTCTTT 60.847 60.000 0.00 0.00 0.00 2.52
3736 5427 8.891501 TGATAGGACCTAGAGACTACAATATCA 58.108 37.037 7.43 0.00 0.00 2.15
3934 6131 2.839975 TCAAGCACACGTTTATCACCA 58.160 42.857 0.00 0.00 0.00 4.17
3946 6143 4.274950 CGTTTATCACCACAGTCCAAAACT 59.725 41.667 0.00 0.00 39.44 2.66
4063 6260 8.874744 AAGTTTTCTACAGTAGAGTTTCTGAC 57.125 34.615 10.27 3.97 35.96 3.51
4145 6342 3.021695 CACCCATCTGTTCAGATGCAAT 58.978 45.455 27.50 16.53 43.07 3.56
4195 6392 3.263170 TGACCTTAGTTCAGGCAGCATTA 59.737 43.478 0.00 0.00 37.47 1.90
4387 6584 3.387374 AGCTGGAAGGACTCACAGATATG 59.613 47.826 7.22 0.00 32.86 1.78
4409 6606 4.532126 TGCTACTGGAGGGATATATTGGTG 59.468 45.833 0.00 0.00 0.00 4.17
4563 6760 7.041098 GGTTTGGTCTAATTCTATGCCACTATG 60.041 40.741 0.00 0.00 0.00 2.23
4584 6781 8.349983 ACTATGTTCTTAATGTTTTTCTTGCGT 58.650 29.630 0.00 0.00 0.00 5.24
4836 7040 2.846193 TGTAGCAACTCACCCTTTCAC 58.154 47.619 0.00 0.00 0.00 3.18
4848 7052 1.398390 CCCTTTCACTACGCAATCTGC 59.602 52.381 0.00 0.00 40.69 4.26
4982 7190 9.571810 GCATTGACTAGTAATCTCTGATCATAG 57.428 37.037 0.00 0.00 0.00 2.23
4986 7194 7.721399 TGACTAGTAATCTCTGATCATAGCACA 59.279 37.037 0.00 0.00 0.00 4.57
4987 7195 8.648698 ACTAGTAATCTCTGATCATAGCACAT 57.351 34.615 3.26 0.00 0.00 3.21
4988 7196 8.522003 ACTAGTAATCTCTGATCATAGCACATG 58.478 37.037 3.26 0.00 0.00 3.21
4989 7197 7.300556 AGTAATCTCTGATCATAGCACATGT 57.699 36.000 3.26 0.00 0.00 3.21
4990 7198 8.414629 AGTAATCTCTGATCATAGCACATGTA 57.585 34.615 0.00 0.00 0.00 2.29
4991 7199 9.033711 AGTAATCTCTGATCATAGCACATGTAT 57.966 33.333 0.00 0.00 0.00 2.29
4992 7200 9.299963 GTAATCTCTGATCATAGCACATGTATC 57.700 37.037 0.00 0.00 0.00 2.24
4993 7201 6.906157 TCTCTGATCATAGCACATGTATCA 57.094 37.500 0.00 2.11 0.00 2.15
5041 7257 9.524106 CATGAATGTAAGTTTGTATGCATCAAT 57.476 29.630 0.19 0.00 0.00 2.57
5228 7453 7.229228 TGATGCGTTCATACTTAACATGTAC 57.771 36.000 0.00 0.00 31.96 2.90
5229 7454 7.039270 TGATGCGTTCATACTTAACATGTACT 58.961 34.615 0.00 0.00 31.96 2.73
5230 7455 6.880822 TGCGTTCATACTTAACATGTACTC 57.119 37.500 0.00 0.00 0.00 2.59
5231 7456 5.808540 TGCGTTCATACTTAACATGTACTCC 59.191 40.000 0.00 0.00 0.00 3.85
5232 7457 5.233689 GCGTTCATACTTAACATGTACTCCC 59.766 44.000 0.00 0.00 0.00 4.30
5233 7458 6.570692 CGTTCATACTTAACATGTACTCCCT 58.429 40.000 0.00 0.00 0.00 4.20
5234 7459 6.696148 CGTTCATACTTAACATGTACTCCCTC 59.304 42.308 0.00 0.00 0.00 4.30
5235 7460 7.416438 CGTTCATACTTAACATGTACTCCCTCT 60.416 40.741 0.00 0.00 0.00 3.69
5236 7461 7.348080 TCATACTTAACATGTACTCCCTCTG 57.652 40.000 0.00 0.00 0.00 3.35
5237 7462 6.895756 TCATACTTAACATGTACTCCCTCTGT 59.104 38.462 0.00 0.00 0.00 3.41
5238 7463 5.662674 ACTTAACATGTACTCCCTCTGTC 57.337 43.478 0.00 0.00 0.00 3.51
5239 7464 4.466726 ACTTAACATGTACTCCCTCTGTCC 59.533 45.833 0.00 0.00 0.00 4.02
5240 7465 1.867363 ACATGTACTCCCTCTGTCCC 58.133 55.000 0.00 0.00 0.00 4.46
5241 7466 1.078823 ACATGTACTCCCTCTGTCCCA 59.921 52.381 0.00 0.00 0.00 4.37
5242 7467 2.293184 ACATGTACTCCCTCTGTCCCAT 60.293 50.000 0.00 0.00 0.00 4.00
5243 7468 3.052109 ACATGTACTCCCTCTGTCCCATA 60.052 47.826 0.00 0.00 0.00 2.74
5244 7469 3.769189 TGTACTCCCTCTGTCCCATAA 57.231 47.619 0.00 0.00 0.00 1.90
5245 7470 4.280789 TGTACTCCCTCTGTCCCATAAT 57.719 45.455 0.00 0.00 0.00 1.28
5246 7471 5.412617 TGTACTCCCTCTGTCCCATAATA 57.587 43.478 0.00 0.00 0.00 0.98
5247 7472 5.977533 TGTACTCCCTCTGTCCCATAATAT 58.022 41.667 0.00 0.00 0.00 1.28
5248 7473 7.111136 TGTACTCCCTCTGTCCCATAATATA 57.889 40.000 0.00 0.00 0.00 0.86
5249 7474 7.541074 TGTACTCCCTCTGTCCCATAATATAA 58.459 38.462 0.00 0.00 0.00 0.98
5250 7475 7.674348 TGTACTCCCTCTGTCCCATAATATAAG 59.326 40.741 0.00 0.00 0.00 1.73
5251 7476 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
5252 7477 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
5253 7478 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
5254 7479 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
5255 7480 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
5256 7481 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
5257 7482 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
5258 7483 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
5259 7484 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
5284 7509 2.546789 ACTAGTGTAGTGCCAAAAACGC 59.453 45.455 0.00 0.00 37.69 4.84
5285 7510 1.675552 AGTGTAGTGCCAAAAACGCT 58.324 45.000 0.00 0.00 0.00 5.07
5286 7511 1.602377 AGTGTAGTGCCAAAAACGCTC 59.398 47.619 0.00 0.00 0.00 5.03
5287 7512 1.602377 GTGTAGTGCCAAAAACGCTCT 59.398 47.619 0.00 0.00 34.63 4.09
5288 7513 2.032924 GTGTAGTGCCAAAAACGCTCTT 59.967 45.455 0.00 0.00 32.65 2.85
5289 7514 3.249080 GTGTAGTGCCAAAAACGCTCTTA 59.751 43.478 0.00 0.00 32.65 2.10
5290 7515 4.069304 TGTAGTGCCAAAAACGCTCTTAT 58.931 39.130 0.00 0.00 32.65 1.73
5291 7516 5.121142 GTGTAGTGCCAAAAACGCTCTTATA 59.879 40.000 0.00 0.00 32.65 0.98
5292 7517 5.878116 TGTAGTGCCAAAAACGCTCTTATAT 59.122 36.000 0.00 0.00 32.65 0.86
5293 7518 5.897377 AGTGCCAAAAACGCTCTTATATT 57.103 34.783 0.00 0.00 0.00 1.28
5294 7519 6.995511 AGTGCCAAAAACGCTCTTATATTA 57.004 33.333 0.00 0.00 0.00 0.98
5295 7520 7.568199 AGTGCCAAAAACGCTCTTATATTAT 57.432 32.000 0.00 0.00 0.00 1.28
5296 7521 7.417612 AGTGCCAAAAACGCTCTTATATTATG 58.582 34.615 0.00 0.00 0.00 1.90
5297 7522 6.636850 GTGCCAAAAACGCTCTTATATTATGG 59.363 38.462 0.00 0.00 0.00 2.74
5298 7523 6.149633 GCCAAAAACGCTCTTATATTATGGG 58.850 40.000 0.00 0.00 0.00 4.00
5299 7524 6.016610 GCCAAAAACGCTCTTATATTATGGGA 60.017 38.462 0.00 0.00 0.00 4.37
5300 7525 7.360361 CCAAAAACGCTCTTATATTATGGGAC 58.640 38.462 0.00 0.00 0.00 4.46
5301 7526 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
5302 7527 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
5303 7528 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
5304 7529 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
5305 7530 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
5306 7531 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
5307 7532 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
5308 7533 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
5309 7534 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
5310 7535 1.718280 ATTATGGGACGGAGGGAGTC 58.282 55.000 0.00 0.00 37.86 3.36
5342 7567 2.936202 ACACTGTCAATGTTGGCTCTT 58.064 42.857 0.00 0.00 33.01 2.85
5386 7611 4.558715 TGGTACTACCTAATACATGCCCA 58.441 43.478 6.79 0.00 39.58 5.36
5565 7790 6.207417 CCTCCGCAATCTTATGGTAAAATCAT 59.793 38.462 0.00 0.00 0.00 2.45
5566 7791 6.969366 TCCGCAATCTTATGGTAAAATCATG 58.031 36.000 0.00 0.00 0.00 3.07
5589 7814 7.147958 TGTGATCATATCCCCAATTTGTCTA 57.852 36.000 0.00 0.00 0.00 2.59
5720 7946 5.128499 GCAGCATGATAGTATAGGACCTCAT 59.872 44.000 0.00 0.00 39.69 2.90
5762 7988 7.477494 ACGTTTTTAAACAGCTAATCAACAGT 58.523 30.769 6.21 0.00 38.81 3.55
5855 8081 2.163010 CAGCGATCTTTTGTGGCTTCAT 59.837 45.455 0.00 0.00 0.00 2.57
6164 8390 6.934645 ACAGCAGTAGTTTATCAAGTGCTAAA 59.065 34.615 3.75 0.00 45.69 1.85
6400 8787 9.069082 TCTTTTGTATTAATTCCCGTTTCTTCA 57.931 29.630 0.00 0.00 0.00 3.02
6411 8798 6.677781 TCCCGTTTCTTCAATGATATGTTC 57.322 37.500 0.00 0.00 0.00 3.18
6443 8830 3.556213 CGTGGTAAATGGACTCCTGACAA 60.556 47.826 0.00 0.00 0.00 3.18
6616 9006 2.036733 TCCAGACTTCAGTGTTAACGGG 59.963 50.000 0.26 0.00 0.00 5.28
6641 9031 7.436080 GGCATGTATTGAAGTATTCCATGTTTG 59.564 37.037 0.00 0.00 46.93 2.93
6691 9081 7.422399 TGAACTCCTACAAAGTTTTACAATGC 58.578 34.615 0.00 0.00 37.10 3.56
6763 9258 1.747355 ACTTGCTTGATGGCATGTAGC 59.253 47.619 18.61 18.61 44.75 3.58
6817 9312 4.974103 ACGCATAGCTGACGAAATAATC 57.026 40.909 11.16 0.00 0.00 1.75
7027 9523 1.552337 CTTCTAGAGGCTTGCTGGACA 59.448 52.381 0.00 0.00 0.00 4.02
7321 9817 2.125147 ATGATGACGGCGGTGGTG 60.125 61.111 13.24 0.00 0.00 4.17
7378 9874 0.837691 AGCCTGTGGACATGGACTCA 60.838 55.000 0.00 0.00 0.00 3.41
7436 9939 3.376546 GGAGTTCCAAATCATCAGTGCTC 59.623 47.826 0.00 0.00 35.64 4.26
7465 9968 3.585990 GGCCATGCAATCGTCGGG 61.586 66.667 0.00 0.00 0.00 5.14
7476 9979 2.320745 ATCGTCGGGGTTATTTGGTC 57.679 50.000 0.00 0.00 0.00 4.02
7494 9997 6.839124 TTGGTCGACTGGAATAGTAGTAAA 57.161 37.500 16.46 0.00 40.53 2.01
7533 10036 7.264221 TGGCCATGCAATAGTAAATTTTACTG 58.736 34.615 25.25 14.42 0.00 2.74
7536 10039 7.973388 GCCATGCAATAGTAAATTTTACTGTGA 59.027 33.333 25.25 11.11 0.00 3.58
7634 10144 5.273170 TCGAGCTGTGTTTTGAAAATTGAG 58.727 37.500 0.00 0.00 0.00 3.02
7635 10145 4.442073 CGAGCTGTGTTTTGAAAATTGAGG 59.558 41.667 0.00 0.00 0.00 3.86
7645 10155 2.253603 GAAAATTGAGGCATGCGTCAC 58.746 47.619 35.61 22.83 40.00 3.67
7752 11489 4.201676 CGGAGTTGGAAAAAGCAAAAACAC 60.202 41.667 0.00 0.00 0.00 3.32
7775 11554 1.924731 TCCAGTGACAGTGGTAGGAG 58.075 55.000 25.39 2.84 39.71 3.69
7778 11557 2.632996 CCAGTGACAGTGGTAGGAGAAA 59.367 50.000 19.70 0.00 33.97 2.52
7779 11558 3.071023 CCAGTGACAGTGGTAGGAGAAAA 59.929 47.826 19.70 0.00 33.97 2.29
7780 11559 4.263068 CCAGTGACAGTGGTAGGAGAAAAT 60.263 45.833 19.70 0.00 33.97 1.82
7781 11560 5.046591 CCAGTGACAGTGGTAGGAGAAAATA 60.047 44.000 19.70 0.00 33.97 1.40
7782 11561 6.464222 CAGTGACAGTGGTAGGAGAAAATAA 58.536 40.000 2.02 0.00 0.00 1.40
7786 11565 6.042781 TGACAGTGGTAGGAGAAAATAAGTGT 59.957 38.462 0.00 0.00 0.00 3.55
7852 11631 4.660938 GCCGGGCTTCTTGTGGGT 62.661 66.667 12.87 0.00 0.00 4.51
7871 11650 2.351455 GTTCTAAGTGAGCCTGCCTTC 58.649 52.381 0.00 0.00 0.00 3.46
7872 11651 1.644509 TCTAAGTGAGCCTGCCTTCA 58.355 50.000 0.00 0.00 0.00 3.02
7891 11670 1.676006 CAAACCCAACACTGACAGACC 59.324 52.381 10.08 0.00 0.00 3.85
7942 13574 2.029666 GATCCCAGACGGCCATCG 59.970 66.667 2.24 0.00 45.88 3.84
8334 13966 0.387622 GTCGTCCGTTGGTCGATTGA 60.388 55.000 8.31 0.00 43.79 2.57
8336 13968 1.744522 TCGTCCGTTGGTCGATTGATA 59.255 47.619 1.14 0.00 38.20 2.15
8357 13989 2.814336 ACCTGATTGCTCGTTTTCCTTC 59.186 45.455 0.00 0.00 0.00 3.46
8359 13991 4.253685 CCTGATTGCTCGTTTTCCTTCTA 58.746 43.478 0.00 0.00 0.00 2.10
8449 14081 2.231964 TGAGTCCATTCTGGCATTTTGC 59.768 45.455 0.00 0.00 44.08 3.68
8454 14086 3.579586 TCCATTCTGGCATTTTGCTCTTT 59.420 39.130 0.00 0.00 44.28 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.757745 ACTCCAAACGCGATTTTATGG 57.242 42.857 15.93 5.67 0.00 2.74
1 2 3.778718 CGAACTCCAAACGCGATTTTATG 59.221 43.478 15.93 0.00 0.00 1.90
2 3 3.434299 ACGAACTCCAAACGCGATTTTAT 59.566 39.130 15.93 0.00 0.00 1.40
3 4 2.801679 ACGAACTCCAAACGCGATTTTA 59.198 40.909 15.93 0.00 0.00 1.52
4 5 1.600485 ACGAACTCCAAACGCGATTTT 59.400 42.857 15.93 0.00 0.00 1.82
5 6 1.223187 ACGAACTCCAAACGCGATTT 58.777 45.000 15.93 7.01 0.00 2.17
6 7 1.223187 AACGAACTCCAAACGCGATT 58.777 45.000 15.93 3.59 0.00 3.34
7 8 1.070175 CAAACGAACTCCAAACGCGAT 60.070 47.619 15.93 0.00 0.00 4.58
8 9 0.302288 CAAACGAACTCCAAACGCGA 59.698 50.000 15.93 0.00 0.00 5.87
9 10 0.302288 TCAAACGAACTCCAAACGCG 59.698 50.000 3.53 3.53 0.00 6.01
19 20 4.909305 TCGCAGAAAATCAATCAAACGAAC 59.091 37.500 0.00 0.00 0.00 3.95
57 60 3.056821 GCCCAGTGTTATCCCTGTTTTTC 60.057 47.826 0.00 0.00 0.00 2.29
67 70 3.266510 TGATCAGTGCCCAGTGTTATC 57.733 47.619 0.00 1.62 33.58 1.75
69 72 3.719268 ATTGATCAGTGCCCAGTGTTA 57.281 42.857 0.00 0.00 33.58 2.41
70 73 2.592102 ATTGATCAGTGCCCAGTGTT 57.408 45.000 0.00 0.00 33.58 3.32
71 74 3.054139 ACATATTGATCAGTGCCCAGTGT 60.054 43.478 0.13 0.00 33.58 3.55
117 121 9.341899 CTACAACTTTCATATACTTTTGGCAAC 57.658 33.333 0.00 0.00 0.00 4.17
119 123 8.856153 TCTACAACTTTCATATACTTTTGGCA 57.144 30.769 0.00 0.00 0.00 4.92
180 186 5.339875 CGTCTAATCCATTGATACGTCTTCG 59.660 44.000 0.00 0.00 43.34 3.79
182 188 6.387041 TCGTCTAATCCATTGATACGTCTT 57.613 37.500 0.00 0.00 0.00 3.01
183 189 6.387041 TTCGTCTAATCCATTGATACGTCT 57.613 37.500 0.00 0.00 0.00 4.18
204 210 3.046390 CACGAATCTATGTCGGAGCTTC 58.954 50.000 0.00 0.00 42.82 3.86
212 218 2.131183 GAGCTGGCACGAATCTATGTC 58.869 52.381 0.00 0.00 0.00 3.06
215 221 1.342819 GAGGAGCTGGCACGAATCTAT 59.657 52.381 0.00 0.00 0.00 1.98
216 222 0.747255 GAGGAGCTGGCACGAATCTA 59.253 55.000 0.00 0.00 0.00 1.98
246 252 1.739035 CGCACGATGAGAAGCCCTAAA 60.739 52.381 0.00 0.00 0.00 1.85
249 255 1.320344 TACGCACGATGAGAAGCCCT 61.320 55.000 0.00 0.00 0.00 5.19
269 275 1.800315 ACCAAATCTCGTCGTCGCG 60.800 57.895 0.00 0.00 36.96 5.87
274 280 1.336887 ACCTCACACCAAATCTCGTCG 60.337 52.381 0.00 0.00 0.00 5.12
286 292 9.696917 ATTGAATTGATTTAAAGAACCTCACAC 57.303 29.630 0.00 0.00 0.00 3.82
307 313 5.633927 CAGCATCGAAGTTGAATCATTGAA 58.366 37.500 0.00 0.00 0.00 2.69
314 320 1.131883 GCTGCAGCATCGAAGTTGAAT 59.868 47.619 33.36 0.00 41.59 2.57
315 321 0.518636 GCTGCAGCATCGAAGTTGAA 59.481 50.000 33.36 0.00 41.59 2.69
322 328 1.523032 CATGGAGCTGCAGCATCGA 60.523 57.895 38.24 27.40 45.16 3.59
323 329 2.543802 CCATGGAGCTGCAGCATCG 61.544 63.158 38.24 21.27 45.16 3.84
373 380 9.614792 GTCTAACCTTGTTGATATAACCAGAAT 57.385 33.333 0.00 0.00 0.00 2.40
382 389 5.700402 AGCCAGTCTAACCTTGTTGATAT 57.300 39.130 0.00 0.00 0.00 1.63
384 391 4.327680 GAAGCCAGTCTAACCTTGTTGAT 58.672 43.478 0.00 0.00 0.00 2.57
385 392 3.740115 GAAGCCAGTCTAACCTTGTTGA 58.260 45.455 0.00 0.00 0.00 3.18
386 393 2.480419 CGAAGCCAGTCTAACCTTGTTG 59.520 50.000 0.00 0.00 0.00 3.33
387 394 2.367567 TCGAAGCCAGTCTAACCTTGTT 59.632 45.455 0.00 0.00 0.00 2.83
395 403 3.504134 GCTCTCATATCGAAGCCAGTCTA 59.496 47.826 0.00 0.00 0.00 2.59
397 405 2.671596 GCTCTCATATCGAAGCCAGTC 58.328 52.381 0.00 0.00 0.00 3.51
401 409 1.011451 GCCGCTCTCATATCGAAGCC 61.011 60.000 0.00 0.00 0.00 4.35
412 420 0.247854 GCATTCTTTTCGCCGCTCTC 60.248 55.000 0.00 0.00 0.00 3.20
427 435 0.653636 ACAACAAACGTCGACGCATT 59.346 45.000 35.92 27.21 44.43 3.56
433 441 0.248990 ACCGCTACAACAAACGTCGA 60.249 50.000 0.00 0.00 0.00 4.20
434 442 0.111442 CACCGCTACAACAAACGTCG 60.111 55.000 0.00 0.00 0.00 5.12
439 447 2.739913 GCACTATCACCGCTACAACAAA 59.260 45.455 0.00 0.00 0.00 2.83
445 454 2.802787 ATGAGCACTATCACCGCTAC 57.197 50.000 0.00 0.00 35.75 3.58
447 456 1.536922 CGAATGAGCACTATCACCGCT 60.537 52.381 0.00 0.00 39.12 5.52
450 459 2.205074 CACCGAATGAGCACTATCACC 58.795 52.381 0.00 0.00 30.46 4.02
479 488 9.153721 CAAACATAATGCAAATTACATCAAGGT 57.846 29.630 0.00 0.00 0.00 3.50
494 503 4.559153 ACAAAGCACTCCAAACATAATGC 58.441 39.130 0.00 0.00 0.00 3.56
523 532 7.037586 TCAGTTATCAGGATCCTAAGGTTTTGT 60.038 37.037 15.67 0.00 0.00 2.83
524 533 7.281100 GTCAGTTATCAGGATCCTAAGGTTTTG 59.719 40.741 15.67 8.25 0.00 2.44
525 534 7.037586 TGTCAGTTATCAGGATCCTAAGGTTTT 60.038 37.037 15.67 0.00 0.00 2.43
530 539 6.471233 TGTGTCAGTTATCAGGATCCTAAG 57.529 41.667 15.67 2.88 0.00 2.18
531 540 6.440647 ACTTGTGTCAGTTATCAGGATCCTAA 59.559 38.462 15.67 0.00 0.00 2.69
537 546 4.503123 CCACACTTGTGTCAGTTATCAGGA 60.503 45.833 8.52 0.00 44.21 3.86
539 548 3.187227 GCCACACTTGTGTCAGTTATCAG 59.813 47.826 8.52 0.00 44.21 2.90
543 552 2.285083 GTGCCACACTTGTGTCAGTTA 58.715 47.619 8.52 0.00 44.21 2.24
544 553 1.094785 GTGCCACACTTGTGTCAGTT 58.905 50.000 8.52 0.00 44.21 3.16
545 554 1.089481 CGTGCCACACTTGTGTCAGT 61.089 55.000 8.52 0.00 44.21 3.41
546 555 0.809636 TCGTGCCACACTTGTGTCAG 60.810 55.000 8.52 0.26 44.21 3.51
549 558 0.675208 TGTTCGTGCCACACTTGTGT 60.675 50.000 8.52 0.00 44.21 3.72
551 560 2.248280 TATGTTCGTGCCACACTTGT 57.752 45.000 0.00 0.00 31.34 3.16
552 561 2.159531 CCATATGTTCGTGCCACACTTG 60.160 50.000 1.24 0.00 31.34 3.16
553 562 2.083774 CCATATGTTCGTGCCACACTT 58.916 47.619 1.24 0.00 31.34 3.16
556 565 0.322008 TGCCATATGTTCGTGCCACA 60.322 50.000 1.24 0.00 0.00 4.17
558 567 0.808125 GTTGCCATATGTTCGTGCCA 59.192 50.000 1.24 0.00 0.00 4.92
561 570 1.327460 CGGAGTTGCCATATGTTCGTG 59.673 52.381 1.24 0.00 35.94 4.35
562 571 1.206132 TCGGAGTTGCCATATGTTCGT 59.794 47.619 1.24 0.00 35.94 3.85
563 572 1.934589 TCGGAGTTGCCATATGTTCG 58.065 50.000 1.24 0.00 35.94 3.95
564 573 2.476619 CGATCGGAGTTGCCATATGTTC 59.523 50.000 7.38 0.00 35.94 3.18
565 574 2.158957 ACGATCGGAGTTGCCATATGTT 60.159 45.455 20.98 0.00 35.94 2.71
567 576 2.154854 ACGATCGGAGTTGCCATATG 57.845 50.000 20.98 0.00 35.94 1.78
568 577 2.910688 AACGATCGGAGTTGCCATAT 57.089 45.000 20.98 0.00 35.94 1.78
569 578 2.684001 AAACGATCGGAGTTGCCATA 57.316 45.000 20.98 0.00 35.94 2.74
570 579 1.737793 GAAAACGATCGGAGTTGCCAT 59.262 47.619 20.98 0.00 35.94 4.40
571 580 1.153353 GAAAACGATCGGAGTTGCCA 58.847 50.000 20.98 0.00 35.94 4.92
572 581 1.439679 AGAAAACGATCGGAGTTGCC 58.560 50.000 20.98 6.54 31.43 4.52
573 582 3.544244 GCATAGAAAACGATCGGAGTTGC 60.544 47.826 20.98 14.10 31.43 4.17
574 583 3.001330 GGCATAGAAAACGATCGGAGTTG 59.999 47.826 20.98 8.42 31.43 3.16
575 584 3.195661 GGCATAGAAAACGATCGGAGTT 58.804 45.455 20.98 9.92 0.00 3.01
576 585 2.167693 TGGCATAGAAAACGATCGGAGT 59.832 45.455 20.98 2.95 0.00 3.85
577 586 2.821546 TGGCATAGAAAACGATCGGAG 58.178 47.619 20.98 0.90 0.00 4.63
578 587 2.971660 TGGCATAGAAAACGATCGGA 57.028 45.000 20.98 0.00 0.00 4.55
579 588 2.872245 ACATGGCATAGAAAACGATCGG 59.128 45.455 20.98 1.23 0.00 4.18
581 590 5.909610 GCTAAACATGGCATAGAAAACGATC 59.090 40.000 0.00 0.00 0.00 3.69
583 592 4.201773 CGCTAAACATGGCATAGAAAACGA 60.202 41.667 0.00 0.00 0.00 3.85
584 593 4.028383 CGCTAAACATGGCATAGAAAACG 58.972 43.478 0.00 0.00 0.00 3.60
585 594 5.028375 GTCGCTAAACATGGCATAGAAAAC 58.972 41.667 0.00 0.00 0.00 2.43
595 2270 0.999406 CCTCGTGTCGCTAAACATGG 59.001 55.000 0.00 0.00 36.90 3.66
598 2273 1.403647 CCATCCTCGTGTCGCTAAACA 60.404 52.381 0.00 0.00 0.00 2.83
609 2284 2.514458 AAGGAAATTGCCATCCTCGT 57.486 45.000 4.92 0.00 45.33 4.18
625 2300 0.890683 AAGCTTGCCATCCGAAAAGG 59.109 50.000 0.00 0.00 42.97 3.11
715 2394 1.771073 CGACAAGCGCCACACTTGAA 61.771 55.000 12.64 0.00 45.99 2.69
720 2399 1.654137 CAAACGACAAGCGCCACAC 60.654 57.895 2.29 0.00 46.04 3.82
727 2406 1.029681 AAGGTTCCCAAACGACAAGC 58.970 50.000 0.00 0.00 36.16 4.01
734 2413 5.007682 TCACTGCTATAAAGGTTCCCAAAC 58.992 41.667 0.00 0.00 34.46 2.93
799 2478 9.358872 GATATGATTATTACGACTCTTCATGCA 57.641 33.333 0.00 0.00 0.00 3.96
816 2495 7.921041 AAGGTCACTTCCTCAGATATGATTA 57.079 36.000 0.00 0.00 36.74 1.75
825 2504 3.492102 TGGAAAAGGTCACTTCCTCAG 57.508 47.619 2.77 0.00 41.52 3.35
835 2514 5.791336 AAACCAGAGAAATGGAAAAGGTC 57.209 39.130 0.00 0.00 43.57 3.85
1563 3252 2.921754 CAAGAGAAACTAGTTACCGGCG 59.078 50.000 8.92 0.00 0.00 6.46
1587 3276 1.281566 AAAGAAAAATTGCGCGGGCG 61.282 50.000 20.22 8.99 44.10 6.13
1919 3608 3.181445 TGTTGCAGAGGATAACACCAGTT 60.181 43.478 0.00 0.00 41.74 3.16
1992 3681 1.351350 ACTAAGAACTGGACCCTTGCC 59.649 52.381 0.00 0.00 0.00 4.52
2056 3745 4.942761 ACCGAGTTAAACCTGTAACAGA 57.057 40.909 0.00 0.00 36.59 3.41
2076 3765 1.810151 TGGAACGGAAGCTGCAATTAC 59.190 47.619 1.02 0.00 0.00 1.89
2102 3791 4.790444 GCAATCGCAATACATTCATGAGCA 60.790 41.667 0.00 0.00 38.36 4.26
2196 3885 9.314133 AGTAGCATTATCTCCTAATGTATCACA 57.686 33.333 6.78 0.00 45.73 3.58
2616 4305 2.766970 TTCTCCAAAAACCTTTCGCG 57.233 45.000 0.00 0.00 0.00 5.87
2660 4349 1.005569 TCCTCCACTCGAGCTTTAGGA 59.994 52.381 13.61 16.19 37.27 2.94
2945 4634 2.936032 GGAGGCTCAACCCCACCT 60.936 66.667 17.69 0.00 40.58 4.00
3162 4851 8.149647 TGACAAAATAAAATCATGAAACAGCCT 58.850 29.630 0.00 0.00 0.00 4.58
3188 4877 2.437359 GCCTCATGAACAGCGCCT 60.437 61.111 2.29 0.00 0.00 5.52
3344 5033 3.054728 TCTCGGCAAGGGATGAAACAATA 60.055 43.478 0.00 0.00 0.00 1.90
3362 5051 5.078153 TCTCATGTTTTTGACGTTTCTCG 57.922 39.130 0.00 0.00 46.00 4.04
3480 5169 7.116736 ACAGGGATAATACGAGTCCAAAATTT 58.883 34.615 0.00 0.00 33.62 1.82
3481 5170 6.659824 ACAGGGATAATACGAGTCCAAAATT 58.340 36.000 0.00 0.00 33.62 1.82
3542 5231 4.853007 AGATAGCAGAGGCAAGAACAATT 58.147 39.130 0.00 0.00 44.61 2.32
3570 5261 5.118050 CACATCAATTCTGACAACAATGTGC 59.882 40.000 0.00 0.00 40.74 4.57
3736 5427 9.151177 TCAGTTCCCCTTACGTCTATATAAATT 57.849 33.333 0.00 0.00 0.00 1.82
3749 5440 5.678955 AGAACAGTATCAGTTCCCCTTAC 57.321 43.478 0.00 0.00 44.91 2.34
3813 5504 2.158505 AGCATTGCAGCTCCTATGGAAT 60.159 45.455 11.91 0.00 42.18 3.01
3934 6131 2.024414 GCAGTTGGAGTTTTGGACTGT 58.976 47.619 0.00 0.00 39.19 3.55
4195 6392 2.195741 TGTACTCCGCTCTGTAGTGT 57.804 50.000 0.00 0.00 0.00 3.55
4387 6584 4.532521 ACACCAATATATCCCTCCAGTAGC 59.467 45.833 0.00 0.00 0.00 3.58
4409 6606 6.088883 CCACGTTCAAATTTGGCAGTTAATAC 59.911 38.462 17.90 2.91 0.00 1.89
4554 6751 8.177119 AGAAAAACATTAAGAACATAGTGGCA 57.823 30.769 0.00 0.00 0.00 4.92
4563 6760 6.806120 ACACGCAAGAAAAACATTAAGAAC 57.194 33.333 0.00 0.00 43.62 3.01
4584 6781 9.926158 ACATCATGAACTTGCAAAATATAAACA 57.074 25.926 0.00 0.00 0.00 2.83
4721 6925 0.981183 AATTGGTACGGGACAGCTGA 59.019 50.000 23.35 0.00 0.00 4.26
4722 6926 1.468520 CAAATTGGTACGGGACAGCTG 59.531 52.381 13.48 13.48 0.00 4.24
4730 6934 0.446222 CAGTCCGCAAATTGGTACGG 59.554 55.000 4.50 4.50 46.97 4.02
4848 7052 3.957468 TCTCATCTGAATGTCGATGTCG 58.043 45.455 0.00 0.00 38.47 4.35
4982 7190 6.611381 ACAAAACATACACTGATACATGTGC 58.389 36.000 9.11 0.69 37.68 4.57
4986 7194 9.453572 AGATGAACAAAACATACACTGATACAT 57.546 29.630 0.00 0.00 0.00 2.29
4987 7195 8.720562 CAGATGAACAAAACATACACTGATACA 58.279 33.333 0.00 0.00 0.00 2.29
4988 7196 8.935844 TCAGATGAACAAAACATACACTGATAC 58.064 33.333 0.00 0.00 0.00 2.24
4989 7197 8.935844 GTCAGATGAACAAAACATACACTGATA 58.064 33.333 0.00 0.00 32.75 2.15
4990 7198 7.445096 TGTCAGATGAACAAAACATACACTGAT 59.555 33.333 0.00 0.00 32.75 2.90
4991 7199 6.765512 TGTCAGATGAACAAAACATACACTGA 59.234 34.615 0.00 0.00 0.00 3.41
4992 7200 6.958255 TGTCAGATGAACAAAACATACACTG 58.042 36.000 0.00 0.00 0.00 3.66
4993 7201 7.445096 TCATGTCAGATGAACAAAACATACACT 59.555 33.333 0.00 0.00 0.00 3.55
5041 7257 7.781324 TGATGTCAAGCTATCATCCACTATA 57.219 36.000 17.18 2.23 37.67 1.31
5263 7488 2.546789 GCGTTTTTGGCACTACACTAGT 59.453 45.455 0.00 0.00 40.28 2.57
5264 7489 2.806244 AGCGTTTTTGGCACTACACTAG 59.194 45.455 0.00 0.00 0.00 2.57
5265 7490 2.803956 GAGCGTTTTTGGCACTACACTA 59.196 45.455 0.00 0.00 0.00 2.74
5266 7491 1.602377 GAGCGTTTTTGGCACTACACT 59.398 47.619 0.00 0.00 0.00 3.55
5267 7492 1.602377 AGAGCGTTTTTGGCACTACAC 59.398 47.619 0.00 0.00 29.39 2.90
5268 7493 1.961793 AGAGCGTTTTTGGCACTACA 58.038 45.000 0.00 0.00 29.39 2.74
5269 7494 4.680171 ATAAGAGCGTTTTTGGCACTAC 57.320 40.909 0.00 0.00 31.01 2.73
5270 7495 6.995511 AATATAAGAGCGTTTTTGGCACTA 57.004 33.333 0.00 0.00 31.01 2.74
5271 7496 5.897377 AATATAAGAGCGTTTTTGGCACT 57.103 34.783 0.00 0.00 32.60 4.40
5272 7497 6.636850 CCATAATATAAGAGCGTTTTTGGCAC 59.363 38.462 0.00 0.00 0.00 5.01
5273 7498 6.238897 CCCATAATATAAGAGCGTTTTTGGCA 60.239 38.462 0.00 0.00 0.00 4.92
5274 7499 6.016610 TCCCATAATATAAGAGCGTTTTTGGC 60.017 38.462 0.00 0.00 0.00 4.52
5275 7500 7.360361 GTCCCATAATATAAGAGCGTTTTTGG 58.640 38.462 0.00 0.00 0.00 3.28
5276 7501 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
5277 7502 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
5278 7503 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
5279 7504 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
5280 7505 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
5281 7506 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
5282 7507 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
5283 7508 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
5284 7509 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
5285 7510 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
5286 7511 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
5287 7512 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5288 7513 4.294168 AGACTCCCTCCGTCCCATAATATA 59.706 45.833 0.00 0.00 31.83 0.86
5289 7514 3.077695 AGACTCCCTCCGTCCCATAATAT 59.922 47.826 0.00 0.00 31.83 1.28
5290 7515 2.449730 AGACTCCCTCCGTCCCATAATA 59.550 50.000 0.00 0.00 31.83 0.98
5291 7516 1.220750 AGACTCCCTCCGTCCCATAAT 59.779 52.381 0.00 0.00 31.83 1.28
5292 7517 0.635009 AGACTCCCTCCGTCCCATAA 59.365 55.000 0.00 0.00 31.83 1.90
5293 7518 0.185416 GAGACTCCCTCCGTCCCATA 59.815 60.000 0.00 0.00 35.87 2.74
5294 7519 1.075896 GAGACTCCCTCCGTCCCAT 60.076 63.158 0.00 0.00 35.87 4.00
5295 7520 1.875422 ATGAGACTCCCTCCGTCCCA 61.875 60.000 0.00 0.00 41.25 4.37
5296 7521 0.688087 AATGAGACTCCCTCCGTCCC 60.688 60.000 0.00 0.00 41.25 4.46
5297 7522 1.196012 AAATGAGACTCCCTCCGTCC 58.804 55.000 0.00 0.00 41.25 4.79
5298 7523 4.674281 ATAAAATGAGACTCCCTCCGTC 57.326 45.455 0.00 0.00 41.25 4.79
5299 7524 6.070424 TGTTTATAAAATGAGACTCCCTCCGT 60.070 38.462 0.00 0.00 41.25 4.69
5300 7525 6.258068 GTGTTTATAAAATGAGACTCCCTCCG 59.742 42.308 0.00 0.00 41.25 4.63
5301 7526 7.281100 CAGTGTTTATAAAATGAGACTCCCTCC 59.719 40.741 0.00 0.00 41.25 4.30
5302 7527 7.824779 ACAGTGTTTATAAAATGAGACTCCCTC 59.175 37.037 0.00 0.00 42.30 4.30
5303 7528 7.690256 ACAGTGTTTATAAAATGAGACTCCCT 58.310 34.615 0.00 0.00 0.00 4.20
5304 7529 7.606456 TGACAGTGTTTATAAAATGAGACTCCC 59.394 37.037 0.00 0.00 0.00 4.30
5305 7530 8.547967 TGACAGTGTTTATAAAATGAGACTCC 57.452 34.615 0.00 0.00 0.00 3.85
5386 7611 5.600484 CCTTCACTTGACTCCTGGTAGATAT 59.400 44.000 0.00 0.00 0.00 1.63
5565 7790 6.017211 AGACAAATTGGGGATATGATCACA 57.983 37.500 0.00 0.00 33.20 3.58
5566 7791 6.656693 CCTAGACAAATTGGGGATATGATCAC 59.343 42.308 0.00 0.00 0.00 3.06
5589 7814 6.610075 ACAACAAGGCATAAAAATGATCCT 57.390 33.333 0.00 0.00 0.00 3.24
5720 7946 2.262637 ACGTAGAAACTGAATCCCCCA 58.737 47.619 0.00 0.00 0.00 4.96
5834 8060 1.536766 TGAAGCCACAAAAGATCGCTG 59.463 47.619 0.00 0.00 0.00 5.18
5855 8081 9.102757 GTTGAGAACTGATTTAAGCATATCTCA 57.897 33.333 17.81 17.81 36.21 3.27
6041 8267 6.464465 GCATAGCTGGAGGTATAGAAGGAAAA 60.464 42.308 0.00 0.00 36.68 2.29
6094 8320 9.084533 TGGAAGCCAGTTTTACATAAACTTATT 57.915 29.630 0.42 0.00 38.32 1.40
6127 8353 7.440523 AAACTACTGCTGTCCATCTTAAAAG 57.559 36.000 0.00 0.00 0.00 2.27
6184 8568 9.649167 GTGAAAAATTCAATGATGGAGAGAATT 57.351 29.630 0.00 0.00 42.15 2.17
6203 8587 6.293955 GCTACAAGTCCTAAGCATGTGAAAAA 60.294 38.462 0.00 0.00 35.05 1.94
6400 8787 7.174946 ACCACGAAAAGAACAGAACATATCATT 59.825 33.333 0.00 0.00 0.00 2.57
6411 8798 5.238650 AGTCCATTTACCACGAAAAGAACAG 59.761 40.000 0.00 0.00 0.00 3.16
6443 8830 9.744468 CTTACCTACTTGTTAAAAACTGCAATT 57.256 29.630 0.00 0.00 0.00 2.32
6616 9006 7.436080 CCAAACATGGAATACTTCAATACATGC 59.564 37.037 0.00 0.00 38.14 4.06
6641 9031 0.106894 GGTAGTACTGCCATGCCTCC 59.893 60.000 23.63 0.00 35.28 4.30
6763 9258 5.709164 CCCTTAGAAATGATAAGGCATCCAG 59.291 44.000 6.28 0.00 45.37 3.86
6817 9312 8.904099 TCTCTTCCTGTAAAGAAAAGGTAAAG 57.096 34.615 0.00 0.00 34.95 1.85
7027 9523 3.254024 ATCCTGGTCGGCTGCGTTT 62.254 57.895 0.00 0.00 0.00 3.60
7159 9655 3.598715 TCGAACACCACCGCGTCT 61.599 61.111 4.92 0.00 0.00 4.18
7299 9795 2.969238 CCGCCGTCATCATCAGCC 60.969 66.667 0.00 0.00 0.00 4.85
7321 9817 1.452833 GGACAGCTCCTTGCCCATC 60.453 63.158 0.00 0.00 44.23 3.51
7378 9874 0.472543 TCCCTCTCCGGCATGATCAT 60.473 55.000 1.18 1.18 0.00 2.45
7436 9939 0.947180 GCATGGCCACACAAAGCAAG 60.947 55.000 8.16 0.00 0.00 4.01
7465 9968 5.425630 ACTATTCCAGTCGACCAAATAACC 58.574 41.667 13.01 0.00 28.33 2.85
7494 9997 2.799126 TGGCCATCACGGAGTAAAAT 57.201 45.000 0.00 0.00 41.61 1.82
7533 10036 2.545526 CGACAATGGGCATCAGTATCAC 59.454 50.000 0.00 0.00 0.00 3.06
7536 10039 2.260844 CCGACAATGGGCATCAGTAT 57.739 50.000 0.00 0.00 0.00 2.12
7545 10052 0.808755 GGTTTACAGCCGACAATGGG 59.191 55.000 0.00 0.00 0.00 4.00
7672 10579 9.243637 GCTAGTTGTAGTATCAGAATTTCTCAG 57.756 37.037 0.00 0.00 0.00 3.35
7752 11489 2.232452 CCTACCACTGTCACTGGAAGAG 59.768 54.545 5.60 0.95 37.43 2.85
7775 11554 7.323656 CACAATTCTCGGTTCACACTTATTTTC 59.676 37.037 0.00 0.00 0.00 2.29
7778 11557 5.181245 CCACAATTCTCGGTTCACACTTATT 59.819 40.000 0.00 0.00 0.00 1.40
7779 11558 4.695455 CCACAATTCTCGGTTCACACTTAT 59.305 41.667 0.00 0.00 0.00 1.73
7780 11559 4.062293 CCACAATTCTCGGTTCACACTTA 58.938 43.478 0.00 0.00 0.00 2.24
7781 11560 2.878406 CCACAATTCTCGGTTCACACTT 59.122 45.455 0.00 0.00 0.00 3.16
7782 11561 2.494059 CCACAATTCTCGGTTCACACT 58.506 47.619 0.00 0.00 0.00 3.55
7786 11565 0.608035 GGGCCACAATTCTCGGTTCA 60.608 55.000 4.39 0.00 0.00 3.18
7852 11631 1.977854 TGAAGGCAGGCTCACTTAGAA 59.022 47.619 0.00 0.00 0.00 2.10
7871 11650 1.676006 GGTCTGTCAGTGTTGGGTTTG 59.324 52.381 0.00 0.00 0.00 2.93
7872 11651 1.409661 GGGTCTGTCAGTGTTGGGTTT 60.410 52.381 0.00 0.00 0.00 3.27
7942 13574 1.301677 CTTCGGCTGAGGAGTTTGGC 61.302 60.000 0.00 0.00 0.00 4.52
7991 13623 2.451132 GAGTTCGCGATCTCAATTCGA 58.549 47.619 32.13 4.09 38.88 3.71
8266 13898 3.226429 AAGAGCGCGCACCTTCTGA 62.226 57.895 35.10 0.00 0.00 3.27
8334 13966 4.222124 AGGAAAACGAGCAATCAGGTAT 57.778 40.909 0.00 0.00 0.00 2.73
8336 13968 2.568623 AGGAAAACGAGCAATCAGGT 57.431 45.000 0.00 0.00 0.00 4.00
8357 13989 1.060937 GCCTGCACGCGAACAATAG 59.939 57.895 15.93 1.73 0.00 1.73


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

AutoCloner maintained by Alex Coulton.