Multiple sequence alignment - TraesCS4B01G097700

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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 TraesCS4B01G097700 chr4B 100.000 2339 0 0 1 2339 102457916 102455578 0.000000e+00 4320.0
1 TraesCS4B01G097700 chr4B 86.714 986 105 13 1379 2339 108415600 108414616 0.000000e+00 1072.0
2 TraesCS4B01G097700 chr4B 84.211 114 17 1 1376 1488 99014674 99014561 2.460000e-20 110.0
3 TraesCS4B01G097700 chr7D 91.647 838 68 2 1503 2339 557080125 557080961 0.000000e+00 1158.0
4 TraesCS4B01G097700 chr7D 90.271 812 75 4 1502 2311 58888188 58888997 0.000000e+00 1059.0
5 TraesCS4B01G097700 chr7D 85.321 109 15 1 1381 1488 223097363 223097255 6.830000e-21 111.0
6 TraesCS4B01G097700 chr7D 83.333 114 19 0 1372 1485 367576663 367576776 3.180000e-19 106.0
7 TraesCS4B01G097700 chr7D 89.394 66 7 0 601 666 296363173 296363108 1.490000e-12 84.2
8 TraesCS4B01G097700 chr5A 91.667 840 64 6 1503 2339 17601341 17602177 0.000000e+00 1158.0
9 TraesCS4B01G097700 chr5A 91.408 838 68 4 1503 2339 477428234 477429068 0.000000e+00 1146.0
10 TraesCS4B01G097700 chr5A 92.330 704 45 1 672 1366 503328083 503327380 0.000000e+00 992.0
11 TraesCS4B01G097700 chr5A 85.714 112 16 0 1379 1490 680739331 680739442 4.080000e-23 119.0
12 TraesCS4B01G097700 chr5A 85.586 111 12 4 1379 1488 632761207 632761314 1.900000e-21 113.0
13 TraesCS4B01G097700 chr7B 87.146 988 96 13 1377 2339 604664411 604665392 0.000000e+00 1092.0
14 TraesCS4B01G097700 chr7B 83.333 186 25 5 1189 1370 17518235 17518052 1.440000e-37 167.0
15 TraesCS4B01G097700 chr7B 83.333 186 25 5 1189 1370 17518736 17518553 1.440000e-37 167.0
16 TraesCS4B01G097700 chr2A 89.759 830 84 1 1511 2339 721476657 721477486 0.000000e+00 1061.0
17 TraesCS4B01G097700 chr2A 79.641 167 31 3 1203 1366 350428046 350428212 1.470000e-22 117.0
18 TraesCS4B01G097700 chr1A 89.576 825 82 4 1517 2339 499925682 499924860 0.000000e+00 1044.0
19 TraesCS4B01G097700 chr1A 86.148 989 104 17 1381 2339 452512537 452513522 0.000000e+00 1037.0
20 TraesCS4B01G097700 chr1D 86.224 980 114 11 1381 2339 414267195 414268174 0.000000e+00 1042.0
21 TraesCS4B01G097700 chr1D 94.318 176 9 1 1188 1363 6380901 6380727 3.830000e-68 268.0
22 TraesCS4B01G097700 chr1D 86.364 110 14 1 1381 1490 351547105 351547213 4.080000e-23 119.0
23 TraesCS4B01G097700 chr1D 85.455 110 16 0 1379 1488 233888578 233888687 5.280000e-22 115.0
24 TraesCS4B01G097700 chr1D 90.909 66 6 0 601 666 280171776 280171841 3.200000e-14 89.8
25 TraesCS4B01G097700 chr4D 89.467 826 79 4 1514 2338 439861788 439860970 0.000000e+00 1037.0
26 TraesCS4B01G097700 chr4D 93.421 380 13 3 1 369 69483206 69482828 9.450000e-154 553.0
27 TraesCS4B01G097700 chr4D 83.249 197 24 6 385 578 69482843 69482653 3.090000e-39 172.0
28 TraesCS4B01G097700 chr7A 92.525 709 43 2 667 1366 708380876 708381583 0.000000e+00 1007.0
29 TraesCS4B01G097700 chr7A 89.552 67 7 0 600 666 383095930 383095996 4.140000e-13 86.1
30 TraesCS4B01G097700 chr4A 92.348 379 12 7 1 369 521536789 521536418 7.410000e-145 523.0
31 TraesCS4B01G097700 chr2B 76.093 686 145 14 695 1365 635020922 635020241 8.010000e-90 340.0
32 TraesCS4B01G097700 chr2B 89.552 67 7 0 600 666 368177325 368177259 4.140000e-13 86.1
33 TraesCS4B01G097700 chr2B 89.394 66 7 0 601 666 360046246 360046311 1.490000e-12 84.2
34 TraesCS4B01G097700 chr6B 77.826 460 81 9 915 1366 124474373 124474819 4.960000e-67 265.0
35 TraesCS4B01G097700 chr6D 89.706 68 7 0 599 666 321163673 321163740 1.150000e-13 87.9
36 TraesCS4B01G097700 chr3A 89.552 67 7 0 600 666 546789271 546789205 4.140000e-13 86.1
37 TraesCS4B01G097700 chr2D 89.394 66 7 0 601 666 332586758 332586693 1.490000e-12 84.2
38 TraesCS4B01G097700 chr2D 92.857 56 4 0 611 666 125684303 125684248 5.360000e-12 82.4


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 TraesCS4B01G097700 chr4B 102455578 102457916 2338 True 4320.0 4320 100.000 1 2339 1 chr4B.!!$R2 2338
1 TraesCS4B01G097700 chr4B 108414616 108415600 984 True 1072.0 1072 86.714 1379 2339 1 chr4B.!!$R3 960
2 TraesCS4B01G097700 chr7D 557080125 557080961 836 False 1158.0 1158 91.647 1503 2339 1 chr7D.!!$F3 836
3 TraesCS4B01G097700 chr7D 58888188 58888997 809 False 1059.0 1059 90.271 1502 2311 1 chr7D.!!$F1 809
4 TraesCS4B01G097700 chr5A 17601341 17602177 836 False 1158.0 1158 91.667 1503 2339 1 chr5A.!!$F1 836
5 TraesCS4B01G097700 chr5A 477428234 477429068 834 False 1146.0 1146 91.408 1503 2339 1 chr5A.!!$F2 836
6 TraesCS4B01G097700 chr5A 503327380 503328083 703 True 992.0 992 92.330 672 1366 1 chr5A.!!$R1 694
7 TraesCS4B01G097700 chr7B 604664411 604665392 981 False 1092.0 1092 87.146 1377 2339 1 chr7B.!!$F1 962
8 TraesCS4B01G097700 chr2A 721476657 721477486 829 False 1061.0 1061 89.759 1511 2339 1 chr2A.!!$F2 828
9 TraesCS4B01G097700 chr1A 499924860 499925682 822 True 1044.0 1044 89.576 1517 2339 1 chr1A.!!$R1 822
10 TraesCS4B01G097700 chr1A 452512537 452513522 985 False 1037.0 1037 86.148 1381 2339 1 chr1A.!!$F1 958
11 TraesCS4B01G097700 chr1D 414267195 414268174 979 False 1042.0 1042 86.224 1381 2339 1 chr1D.!!$F4 958
12 TraesCS4B01G097700 chr4D 439860970 439861788 818 True 1037.0 1037 89.467 1514 2338 1 chr4D.!!$R1 824
13 TraesCS4B01G097700 chr4D 69482653 69483206 553 True 362.5 553 88.335 1 578 2 chr4D.!!$R2 577
14 TraesCS4B01G097700 chr7A 708380876 708381583 707 False 1007.0 1007 92.525 667 1366 1 chr7A.!!$F2 699
15 TraesCS4B01G097700 chr2B 635020241 635020922 681 True 340.0 340 76.093 695 1365 1 chr2B.!!$R2 670

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
978 1002 0.031857 CGGCAGGAAACAATGTTGCA 59.968 50.0 6.42 0.0 36.53 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1858 0.320073 TTTCGGTGCCGTAGTTGGAG 60.32 55.0 10.6 0.0 40.74 3.86 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
19 20 1.739049 CCTGGCCAGAGAGATCGAC 59.261 63.158 34.91 0.00 0.00 4.20
21 22 1.077716 TGGCCAGAGAGATCGACGA 60.078 57.895 0.00 0.00 0.00 4.20
100 101 2.131067 GGCGGAGGAGAGAAGGAGG 61.131 68.421 0.00 0.00 0.00 4.30
160 161 0.107214 AGTGTGGGTGTGAACTGTGG 60.107 55.000 0.00 0.00 0.00 4.17
166 167 0.759346 GGTGTGAACTGTGGAGAGGT 59.241 55.000 0.00 0.00 0.00 3.85
167 168 1.541233 GGTGTGAACTGTGGAGAGGTG 60.541 57.143 0.00 0.00 0.00 4.00
171 172 1.133167 TGAACTGTGGAGAGGTGGAGA 60.133 52.381 0.00 0.00 0.00 3.71
186 187 2.880890 GTGGAGAGAGAGAGAGAGATGC 59.119 54.545 0.00 0.00 0.00 3.91
244 247 0.521735 GTGGGTCTTTTGCGGATCAC 59.478 55.000 0.00 0.00 0.00 3.06
253 256 0.904649 TTGCGGATCACTCCTGTCAT 59.095 50.000 0.00 0.00 39.65 3.06
260 263 3.589988 GATCACTCCTGTCATTTGTCGT 58.410 45.455 0.00 0.00 0.00 4.34
267 270 5.179368 ACTCCTGTCATTTGTCGTGTTATTG 59.821 40.000 0.00 0.00 0.00 1.90
275 278 3.846423 TGTCGTGTTATTGCGGTAGTA 57.154 42.857 0.00 0.00 0.00 1.82
356 368 1.866496 GTCGTACTACGCAGCGGTG 60.866 63.158 21.15 10.98 42.21 4.94
357 369 2.578713 CGTACTACGCAGCGGTGG 60.579 66.667 21.15 10.87 33.65 4.61
358 370 2.570181 GTACTACGCAGCGGTGGT 59.430 61.111 21.15 16.08 35.65 4.16
359 371 1.804326 GTACTACGCAGCGGTGGTG 60.804 63.158 21.15 6.49 33.42 4.17
360 372 2.997075 TACTACGCAGCGGTGGTGG 61.997 63.158 21.15 15.78 33.42 4.61
361 373 4.063967 CTACGCAGCGGTGGTGGA 62.064 66.667 21.15 0.00 0.00 4.02
362 374 3.583276 CTACGCAGCGGTGGTGGAA 62.583 63.158 21.15 0.00 0.00 3.53
363 375 3.583276 TACGCAGCGGTGGTGGAAG 62.583 63.158 21.15 0.00 0.00 3.46
405 417 2.877097 TGGTGGAAGCATTTAGAGCA 57.123 45.000 0.00 0.00 40.88 4.26
416 428 1.519408 TTTAGAGCACCTTCAACCGC 58.481 50.000 0.00 0.00 0.00 5.68
425 437 1.202557 ACCTTCAACCGCGTCAGTAAA 60.203 47.619 4.92 0.00 0.00 2.01
426 438 1.868498 CCTTCAACCGCGTCAGTAAAA 59.132 47.619 4.92 0.00 0.00 1.52
455 467 2.224549 TGTTTACGCGAAATTGGGTCAG 59.775 45.455 15.93 0.00 36.35 3.51
463 475 3.306710 GCGAAATTGGGTCAGGGAAATTT 60.307 43.478 0.00 0.00 35.50 1.82
470 482 2.826128 GGGTCAGGGAAATTTCTCCAAC 59.174 50.000 14.60 12.27 37.20 3.77
472 484 3.895041 GGTCAGGGAAATTTCTCCAACAA 59.105 43.478 14.60 1.24 37.20 2.83
485 497 9.541143 AATTTCTCCAACAATTTTCATAAACGT 57.459 25.926 0.00 0.00 0.00 3.99
492 504 7.854916 CCAACAATTTTCATAAACGTGCAAATT 59.145 29.630 0.00 0.00 36.05 1.82
501 513 8.858003 TCATAAACGTGCAAATTTTAGTGAAA 57.142 26.923 2.05 0.00 0.00 2.69
503 515 9.907576 CATAAACGTGCAAATTTTAGTGAAAAA 57.092 25.926 2.05 0.00 41.21 1.94
533 546 8.977267 AAAATGATTTTGGGAAGATGTTTTCA 57.023 26.923 1.78 0.00 0.00 2.69
534 547 8.611654 AAATGATTTTGGGAAGATGTTTTCAG 57.388 30.769 0.00 0.00 0.00 3.02
535 548 6.975196 TGATTTTGGGAAGATGTTTTCAGA 57.025 33.333 0.00 0.00 0.00 3.27
536 549 7.358770 TGATTTTGGGAAGATGTTTTCAGAA 57.641 32.000 0.00 0.00 0.00 3.02
537 550 7.790027 TGATTTTGGGAAGATGTTTTCAGAAA 58.210 30.769 0.00 0.00 0.00 2.52
538 551 7.710475 TGATTTTGGGAAGATGTTTTCAGAAAC 59.290 33.333 0.00 0.00 44.29 2.78
539 552 6.790232 TTTGGGAAGATGTTTTCAGAAACT 57.210 33.333 0.00 0.00 44.33 2.66
540 553 5.772825 TGGGAAGATGTTTTCAGAAACTG 57.227 39.130 0.00 0.00 44.33 3.16
541 554 5.445069 TGGGAAGATGTTTTCAGAAACTGA 58.555 37.500 0.00 0.00 44.33 3.41
542 555 5.532406 TGGGAAGATGTTTTCAGAAACTGAG 59.468 40.000 0.00 0.00 44.33 3.35
543 556 5.765182 GGGAAGATGTTTTCAGAAACTGAGA 59.235 40.000 0.00 0.00 44.33 3.27
544 557 6.263168 GGGAAGATGTTTTCAGAAACTGAGAA 59.737 38.462 0.00 0.00 44.33 2.87
545 558 7.201821 GGGAAGATGTTTTCAGAAACTGAGAAA 60.202 37.037 6.36 5.94 44.33 2.52
546 559 8.190784 GGAAGATGTTTTCAGAAACTGAGAAAA 58.809 33.333 6.36 2.68 44.33 2.29
547 560 9.230932 GAAGATGTTTTCAGAAACTGAGAAAAG 57.769 33.333 6.36 0.00 44.33 2.27
548 561 8.511604 AGATGTTTTCAGAAACTGAGAAAAGA 57.488 30.769 6.36 0.00 44.33 2.52
549 562 8.401709 AGATGTTTTCAGAAACTGAGAAAAGAC 58.598 33.333 6.36 2.11 44.33 3.01
550 563 7.447374 TGTTTTCAGAAACTGAGAAAAGACA 57.553 32.000 6.36 0.23 44.33 3.41
551 564 7.530010 TGTTTTCAGAAACTGAGAAAAGACAG 58.470 34.615 6.36 0.00 44.33 3.51
552 565 5.741388 TTCAGAAACTGAGAAAAGACAGC 57.259 39.130 0.00 0.00 41.75 4.40
553 566 4.769688 TCAGAAACTGAGAAAAGACAGCA 58.230 39.130 0.00 0.00 35.39 4.41
554 567 5.371526 TCAGAAACTGAGAAAAGACAGCAT 58.628 37.500 0.00 0.00 35.39 3.79
555 568 5.468072 TCAGAAACTGAGAAAAGACAGCATC 59.532 40.000 0.00 0.00 35.39 3.91
556 569 5.237996 CAGAAACTGAGAAAAGACAGCATCA 59.762 40.000 0.00 0.00 37.61 3.07
557 570 5.238214 AGAAACTGAGAAAAGACAGCATCAC 59.762 40.000 0.00 0.00 37.61 3.06
558 571 3.062763 ACTGAGAAAAGACAGCATCACG 58.937 45.455 0.00 0.00 37.61 4.35
559 572 1.800586 TGAGAAAAGACAGCATCACGC 59.199 47.619 0.00 0.00 42.91 5.34
560 573 1.800586 GAGAAAAGACAGCATCACGCA 59.199 47.619 0.00 0.00 46.13 5.24
561 574 2.221169 AGAAAAGACAGCATCACGCAA 58.779 42.857 0.00 0.00 46.13 4.85
562 575 2.031682 AGAAAAGACAGCATCACGCAAC 60.032 45.455 0.00 0.00 46.13 4.17
563 576 1.597742 AAAGACAGCATCACGCAACT 58.402 45.000 0.00 0.00 46.13 3.16
564 577 1.597742 AAGACAGCATCACGCAACTT 58.402 45.000 0.00 0.00 46.13 2.66
565 578 1.151668 AGACAGCATCACGCAACTTC 58.848 50.000 0.00 0.00 46.13 3.01
566 579 0.166814 GACAGCATCACGCAACTTCC 59.833 55.000 0.00 0.00 46.13 3.46
567 580 1.237285 ACAGCATCACGCAACTTCCC 61.237 55.000 0.00 0.00 46.13 3.97
568 581 1.675641 AGCATCACGCAACTTCCCC 60.676 57.895 0.00 0.00 46.13 4.81
569 582 1.675641 GCATCACGCAACTTCCCCT 60.676 57.895 0.00 0.00 41.79 4.79
570 583 0.392461 GCATCACGCAACTTCCCCTA 60.392 55.000 0.00 0.00 41.79 3.53
571 584 1.948611 GCATCACGCAACTTCCCCTAA 60.949 52.381 0.00 0.00 41.79 2.69
572 585 2.432444 CATCACGCAACTTCCCCTAAA 58.568 47.619 0.00 0.00 0.00 1.85
573 586 2.871096 TCACGCAACTTCCCCTAAAT 57.129 45.000 0.00 0.00 0.00 1.40
574 587 3.149005 TCACGCAACTTCCCCTAAATT 57.851 42.857 0.00 0.00 0.00 1.82
575 588 3.492337 TCACGCAACTTCCCCTAAATTT 58.508 40.909 0.00 0.00 0.00 1.82
576 589 3.892588 TCACGCAACTTCCCCTAAATTTT 59.107 39.130 0.00 0.00 0.00 1.82
577 590 5.071370 TCACGCAACTTCCCCTAAATTTTA 58.929 37.500 0.00 0.00 0.00 1.52
578 591 5.535406 TCACGCAACTTCCCCTAAATTTTAA 59.465 36.000 0.00 0.00 0.00 1.52
579 592 6.209788 TCACGCAACTTCCCCTAAATTTTAAT 59.790 34.615 0.00 0.00 0.00 1.40
580 593 6.310224 CACGCAACTTCCCCTAAATTTTAATG 59.690 38.462 0.00 0.00 0.00 1.90
581 594 5.290885 CGCAACTTCCCCTAAATTTTAATGC 59.709 40.000 0.00 0.00 0.00 3.56
582 595 6.169800 GCAACTTCCCCTAAATTTTAATGCA 58.830 36.000 0.00 0.00 0.00 3.96
583 596 6.092122 GCAACTTCCCCTAAATTTTAATGCAC 59.908 38.462 0.00 0.00 0.00 4.57
584 597 7.386059 CAACTTCCCCTAAATTTTAATGCACT 58.614 34.615 0.00 0.00 0.00 4.40
585 598 7.553504 ACTTCCCCTAAATTTTAATGCACTT 57.446 32.000 0.00 0.00 0.00 3.16
586 599 7.973402 ACTTCCCCTAAATTTTAATGCACTTT 58.027 30.769 0.00 0.00 0.00 2.66
587 600 8.094548 ACTTCCCCTAAATTTTAATGCACTTTC 58.905 33.333 0.00 0.00 0.00 2.62
588 601 7.546250 TCCCCTAAATTTTAATGCACTTTCA 57.454 32.000 0.00 0.00 0.00 2.69
589 602 7.382898 TCCCCTAAATTTTAATGCACTTTCAC 58.617 34.615 0.00 0.00 0.00 3.18
590 603 6.310224 CCCCTAAATTTTAATGCACTTTCACG 59.690 38.462 0.00 0.00 0.00 4.35
591 604 7.087639 CCCTAAATTTTAATGCACTTTCACGA 58.912 34.615 0.00 0.00 0.00 4.35
592 605 7.273381 CCCTAAATTTTAATGCACTTTCACGAG 59.727 37.037 0.00 0.00 0.00 4.18
593 606 7.273381 CCTAAATTTTAATGCACTTTCACGAGG 59.727 37.037 0.00 0.00 0.00 4.63
594 607 5.957842 ATTTTAATGCACTTTCACGAGGA 57.042 34.783 0.00 0.00 0.00 3.71
595 608 5.759506 TTTTAATGCACTTTCACGAGGAA 57.240 34.783 0.00 0.00 0.00 3.36
596 609 5.957842 TTTAATGCACTTTCACGAGGAAT 57.042 34.783 0.00 0.00 34.91 3.01
597 610 5.957842 TTAATGCACTTTCACGAGGAATT 57.042 34.783 0.00 0.00 34.91 2.17
598 611 4.853924 AATGCACTTTCACGAGGAATTT 57.146 36.364 0.00 0.00 34.91 1.82
599 612 3.896648 TGCACTTTCACGAGGAATTTC 57.103 42.857 0.00 0.00 34.91 2.17
600 613 3.476552 TGCACTTTCACGAGGAATTTCT 58.523 40.909 0.00 0.00 34.91 2.52
601 614 3.882888 TGCACTTTCACGAGGAATTTCTT 59.117 39.130 0.00 0.00 34.91 2.52
602 615 5.060506 TGCACTTTCACGAGGAATTTCTTA 58.939 37.500 0.00 0.00 34.91 2.10
603 616 5.179368 TGCACTTTCACGAGGAATTTCTTAG 59.821 40.000 0.00 0.00 34.91 2.18
604 617 5.408604 GCACTTTCACGAGGAATTTCTTAGA 59.591 40.000 0.00 0.00 34.91 2.10
605 618 6.618805 GCACTTTCACGAGGAATTTCTTAGAC 60.619 42.308 0.00 0.00 34.91 2.59
606 619 6.647067 CACTTTCACGAGGAATTTCTTAGACT 59.353 38.462 0.00 0.00 34.91 3.24
607 620 7.813148 CACTTTCACGAGGAATTTCTTAGACTA 59.187 37.037 0.00 0.00 34.91 2.59
608 621 7.813627 ACTTTCACGAGGAATTTCTTAGACTAC 59.186 37.037 0.00 0.00 34.91 2.73
609 622 6.205101 TCACGAGGAATTTCTTAGACTACC 57.795 41.667 0.00 0.00 0.00 3.18
610 623 5.126707 TCACGAGGAATTTCTTAGACTACCC 59.873 44.000 0.00 0.00 0.00 3.69
611 624 5.021458 ACGAGGAATTTCTTAGACTACCCA 58.979 41.667 0.00 0.00 0.00 4.51
612 625 5.661759 ACGAGGAATTTCTTAGACTACCCAT 59.338 40.000 0.00 0.00 0.00 4.00
613 626 6.837568 ACGAGGAATTTCTTAGACTACCCATA 59.162 38.462 0.00 0.00 0.00 2.74
614 627 7.014422 ACGAGGAATTTCTTAGACTACCCATAG 59.986 40.741 0.00 0.00 34.25 2.23
615 628 7.014422 CGAGGAATTTCTTAGACTACCCATAGT 59.986 40.741 0.00 0.00 44.74 2.12
616 629 8.024145 AGGAATTTCTTAGACTACCCATAGTG 57.976 38.462 0.00 0.00 41.98 2.74
617 630 7.844779 AGGAATTTCTTAGACTACCCATAGTGA 59.155 37.037 0.00 0.00 41.98 3.41
618 631 8.483758 GGAATTTCTTAGACTACCCATAGTGAA 58.516 37.037 0.00 0.00 41.98 3.18
619 632 9.535878 GAATTTCTTAGACTACCCATAGTGAAG 57.464 37.037 0.00 0.00 41.98 3.02
620 633 8.840200 ATTTCTTAGACTACCCATAGTGAAGA 57.160 34.615 0.00 0.00 41.98 2.87
621 634 7.883391 TTCTTAGACTACCCATAGTGAAGAG 57.117 40.000 0.00 0.00 41.98 2.85
622 635 6.971340 TCTTAGACTACCCATAGTGAAGAGT 58.029 40.000 0.00 0.00 41.98 3.24
623 636 8.098963 TCTTAGACTACCCATAGTGAAGAGTA 57.901 38.462 0.00 0.00 41.98 2.59
624 637 8.554870 TCTTAGACTACCCATAGTGAAGAGTAA 58.445 37.037 0.00 0.00 41.98 2.24
625 638 8.517062 TTAGACTACCCATAGTGAAGAGTAAC 57.483 38.462 0.00 0.00 41.98 2.50
626 639 6.733509 AGACTACCCATAGTGAAGAGTAACT 58.266 40.000 0.00 0.00 41.98 2.24
627 640 7.183460 AGACTACCCATAGTGAAGAGTAACTT 58.817 38.462 0.00 0.00 41.98 2.66
628 641 8.334734 AGACTACCCATAGTGAAGAGTAACTTA 58.665 37.037 0.00 0.00 41.98 2.24
629 642 8.291191 ACTACCCATAGTGAAGAGTAACTTAC 57.709 38.462 0.00 0.00 40.32 2.34
630 643 7.892241 ACTACCCATAGTGAAGAGTAACTTACA 59.108 37.037 1.79 0.00 40.32 2.41
631 644 6.932947 ACCCATAGTGAAGAGTAACTTACAC 58.067 40.000 1.79 0.00 39.13 2.90
632 645 6.070938 ACCCATAGTGAAGAGTAACTTACACC 60.071 42.308 1.79 0.00 39.13 4.16
633 646 6.070995 CCCATAGTGAAGAGTAACTTACACCA 60.071 42.308 1.79 0.00 39.13 4.17
634 647 7.036220 CCATAGTGAAGAGTAACTTACACCAG 58.964 42.308 1.79 0.00 39.13 4.00
635 648 7.309867 CCATAGTGAAGAGTAACTTACACCAGT 60.310 40.741 1.79 0.52 39.13 4.00
636 649 8.737175 CATAGTGAAGAGTAACTTACACCAGTA 58.263 37.037 1.79 2.33 39.13 2.74
637 650 7.592885 AGTGAAGAGTAACTTACACCAGTAA 57.407 36.000 1.79 0.00 39.13 2.24
638 651 7.432059 AGTGAAGAGTAACTTACACCAGTAAC 58.568 38.462 1.79 0.00 39.13 2.50
639 652 7.069085 AGTGAAGAGTAACTTACACCAGTAACA 59.931 37.037 1.79 0.00 39.13 2.41
640 653 7.871463 GTGAAGAGTAACTTACACCAGTAACAT 59.129 37.037 1.79 0.00 39.13 2.71
641 654 7.870954 TGAAGAGTAACTTACACCAGTAACATG 59.129 37.037 1.79 0.00 39.13 3.21
642 655 6.164176 AGAGTAACTTACACCAGTAACATGC 58.836 40.000 1.79 0.00 35.37 4.06
643 656 5.860611 AGTAACTTACACCAGTAACATGCA 58.139 37.500 1.79 0.00 35.37 3.96
644 657 5.699458 AGTAACTTACACCAGTAACATGCAC 59.301 40.000 0.00 0.00 35.37 4.57
645 658 4.079980 ACTTACACCAGTAACATGCACA 57.920 40.909 0.00 0.00 35.37 4.57
646 659 4.651778 ACTTACACCAGTAACATGCACAT 58.348 39.130 0.00 0.00 35.37 3.21
647 660 4.455533 ACTTACACCAGTAACATGCACATG 59.544 41.667 9.06 9.06 44.15 3.21
662 675 7.776933 CATGCACATGTTACTAGTCTATGTT 57.223 36.000 13.72 2.22 34.23 2.71
663 676 8.871686 CATGCACATGTTACTAGTCTATGTTA 57.128 34.615 13.72 8.80 34.23 2.41
664 677 8.755941 CATGCACATGTTACTAGTCTATGTTAC 58.244 37.037 13.72 10.81 34.23 2.50
665 678 8.063200 TGCACATGTTACTAGTCTATGTTACT 57.937 34.615 13.72 0.00 30.15 2.24
670 683 9.302345 CATGTTACTAGTCTATGTTACTTGTGG 57.698 37.037 0.00 0.00 35.18 4.17
687 700 1.143073 GTGGTGGGTCAGGAAAAGTCT 59.857 52.381 0.00 0.00 0.00 3.24
688 701 1.420138 TGGTGGGTCAGGAAAAGTCTC 59.580 52.381 0.00 0.00 0.00 3.36
758 771 7.406104 AGAAAACTAGTCCATAAGGAGCAAAT 58.594 34.615 0.00 0.00 46.92 2.32
763 776 8.090788 ACTAGTCCATAAGGAGCAAATAAAGA 57.909 34.615 0.00 0.00 46.92 2.52
764 777 7.988028 ACTAGTCCATAAGGAGCAAATAAAGAC 59.012 37.037 0.00 0.00 46.92 3.01
807 820 0.467844 TGAGAGGCCTTGCTGCAAAA 60.468 50.000 16.74 0.00 0.00 2.44
840 853 1.112916 CCCAACCCAAGGCGAAACTT 61.113 55.000 0.00 0.00 0.00 2.66
900 915 1.396653 AGCTTAATGTGGATGCAGCC 58.603 50.000 15.83 15.83 0.00 4.85
951 975 2.046864 TCGGGACAGCTCGAGGAAG 61.047 63.158 15.58 0.00 43.24 3.46
960 984 1.355066 GCTCGAGGAAGTTCTTGGCG 61.355 60.000 15.58 2.36 0.00 5.69
978 1002 0.031857 CGGCAGGAAACAATGTTGCA 59.968 50.000 6.42 0.00 36.53 4.08
979 1003 1.337074 CGGCAGGAAACAATGTTGCAT 60.337 47.619 6.42 0.00 36.53 3.96
1041 1065 1.807742 CGGTTCGGTCTTAATTTGGCA 59.192 47.619 0.00 0.00 0.00 4.92
1117 1141 1.187567 GGCAATGCAAGAGGGTGGTT 61.188 55.000 7.79 0.00 0.00 3.67
1167 1191 4.767578 AGATGATTGCTACCACATGTCT 57.232 40.909 0.00 0.00 0.00 3.41
1231 1255 1.068333 CAAATTCTGTTGCCCACGAGG 60.068 52.381 0.00 0.00 39.47 4.63
1273 1297 1.923395 CCCCCTAGCACCTGGTTCA 60.923 63.158 0.00 0.00 0.00 3.18
1305 1329 3.933861 AGTGCCTTACTTCCCCTTATG 57.066 47.619 0.00 0.00 35.67 1.90
1409 1435 3.827302 CTCTAGCAGACCCCGTATAATGT 59.173 47.826 0.00 0.00 0.00 2.71
1446 1472 7.033185 ACTTGTTTACAATTCGCTGAAAAACT 58.967 30.769 12.80 0.00 35.02 2.66
1457 1483 3.610585 CGCTGAAAAACTATTTTGCGGGA 60.611 43.478 9.51 0.00 42.49 5.14
1500 1553 2.816083 CCCGCGTCGGCACATTTA 60.816 61.111 4.92 0.00 46.86 1.40
1508 1561 2.970609 CGTCGGCACATTTACTGTTTTG 59.029 45.455 0.00 0.00 35.29 2.44
1567 1620 2.742774 GTCAGCTCGCAAACCAAAAAT 58.257 42.857 0.00 0.00 0.00 1.82
1621 1674 6.517714 CGACGATTGAGTTCAAATTCAAAGAG 59.482 38.462 5.01 3.24 38.01 2.85
1663 1717 7.148885 GCGCAAATAAAAGCATAGTTTTGTACA 60.149 33.333 0.30 0.00 31.96 2.90
1676 1730 6.526566 AGTTTTGTACAACAAACGCAAAAA 57.473 29.167 8.07 0.00 46.53 1.94
1695 1749 4.510038 AAAGACTTCATGCAAAAGCGAT 57.490 36.364 11.08 0.00 0.00 4.58
1722 1776 2.481969 CGTCCATCATCATCTTGGTCGT 60.482 50.000 0.00 0.00 37.32 4.34
1760 1814 1.002430 GATCTTCACTCTGCACCACCA 59.998 52.381 0.00 0.00 0.00 4.17
1804 1858 1.315257 AATCCATCACCGGCACTTGC 61.315 55.000 0.00 0.00 41.14 4.01
1812 1866 1.003839 CCGGCACTTGCTCCAACTA 60.004 57.895 0.38 0.00 41.70 2.24
1941 1997 4.383989 GCATCCTCCTCTTCAAGATGTCTT 60.384 45.833 0.00 0.00 37.30 3.01
2003 2060 2.863740 GTCATCGCGGTTCAATGTCATA 59.136 45.455 6.13 0.00 0.00 2.15
2047 2105 3.190878 GCCATGGCTTTGGTCTCG 58.809 61.111 29.98 0.00 39.11 4.04
2118 2176 3.084039 CCTTGAGCAATTGCCACTTCTA 58.916 45.455 26.45 13.06 43.38 2.10
2121 2179 5.357878 CCTTGAGCAATTGCCACTTCTATTA 59.642 40.000 26.45 6.23 43.38 0.98
2181 2239 1.879380 CTCCAATGTCTTCGCCAACAA 59.121 47.619 0.00 0.00 0.00 2.83
2198 2256 5.051816 CCAACAACAACTCATTTGATTGCT 58.948 37.500 0.00 0.00 38.73 3.91
2205 2263 3.705051 ACTCATTTGATTGCTCCATGGT 58.295 40.909 12.58 0.00 0.00 3.55
2248 2306 2.481276 CGATGCATCGTGTTCCCTCTTA 60.481 50.000 35.19 0.00 44.74 2.10
2314 2372 1.810755 CATGGGCCATCATCATCTTCG 59.189 52.381 18.16 0.00 0.00 3.79
2315 2373 0.535780 TGGGCCATCATCATCTTCGC 60.536 55.000 0.00 0.00 0.00 4.70
2319 2377 1.952296 GCCATCATCATCTTCGCCTTT 59.048 47.619 0.00 0.00 0.00 3.11
2320 2378 2.287427 GCCATCATCATCTTCGCCTTTG 60.287 50.000 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.405594 CTCTCCCGCTCTCGTTCG 59.594 66.667 0.00 0.00 0.00 3.95
21 22 2.756283 CCCTCTCCCGCTCTCGTT 60.756 66.667 0.00 0.00 0.00 3.85
160 161 2.771943 TCTCTCTCTCTCTCCACCTCTC 59.228 54.545 0.00 0.00 0.00 3.20
166 167 2.485302 CGCATCTCTCTCTCTCTCTCCA 60.485 54.545 0.00 0.00 0.00 3.86
167 168 2.146342 CGCATCTCTCTCTCTCTCTCC 58.854 57.143 0.00 0.00 0.00 3.71
171 172 2.358898 GCTTTCGCATCTCTCTCTCTCT 59.641 50.000 0.00 0.00 35.78 3.10
186 187 1.000274 CCCCTGTTCCAAAAGCTTTCG 60.000 52.381 13.10 0.00 0.00 3.46
244 247 5.621422 CAATAACACGACAAATGACAGGAG 58.379 41.667 0.00 0.00 0.00 3.69
253 256 3.391965 ACTACCGCAATAACACGACAAA 58.608 40.909 0.00 0.00 0.00 2.83
260 263 4.403113 TCCATGTCTACTACCGCAATAACA 59.597 41.667 0.00 0.00 0.00 2.41
267 270 0.030369 CCGTCCATGTCTACTACCGC 59.970 60.000 0.00 0.00 0.00 5.68
275 278 0.036952 CTTGACAGCCGTCCATGTCT 60.037 55.000 0.00 0.00 44.90 3.41
372 384 2.042843 ACCACCACCCCGCAAAAA 60.043 55.556 0.00 0.00 0.00 1.94
373 385 2.835431 CACCACCACCCCGCAAAA 60.835 61.111 0.00 0.00 0.00 2.44
374 386 4.904590 CCACCACCACCCCGCAAA 62.905 66.667 0.00 0.00 0.00 3.68
379 391 2.730129 AATGCTTCCACCACCACCCC 62.730 60.000 0.00 0.00 0.00 4.95
380 392 0.831711 AAATGCTTCCACCACCACCC 60.832 55.000 0.00 0.00 0.00 4.61
381 393 1.818674 CTAAATGCTTCCACCACCACC 59.181 52.381 0.00 0.00 0.00 4.61
382 394 2.749621 CTCTAAATGCTTCCACCACCAC 59.250 50.000 0.00 0.00 0.00 4.16
383 395 2.879756 GCTCTAAATGCTTCCACCACCA 60.880 50.000 0.00 0.00 0.00 4.17
384 396 1.745653 GCTCTAAATGCTTCCACCACC 59.254 52.381 0.00 0.00 0.00 4.61
385 397 2.162408 GTGCTCTAAATGCTTCCACCAC 59.838 50.000 0.00 0.00 0.00 4.16
386 398 2.436417 GTGCTCTAAATGCTTCCACCA 58.564 47.619 0.00 0.00 0.00 4.17
387 399 1.745653 GGTGCTCTAAATGCTTCCACC 59.254 52.381 0.00 0.00 35.10 4.61
405 417 0.390124 TTACTGACGCGGTTGAAGGT 59.610 50.000 12.47 1.74 0.00 3.50
416 428 7.005380 CGTAAACAGTGGTTATTTTACTGACG 58.995 38.462 3.46 0.00 43.35 4.35
425 437 5.616488 ATTTCGCGTAAACAGTGGTTATT 57.384 34.783 5.77 0.00 35.82 1.40
426 438 5.387279 CAATTTCGCGTAAACAGTGGTTAT 58.613 37.500 5.77 0.00 35.82 1.89
455 467 7.984422 ATGAAAATTGTTGGAGAAATTTCCC 57.016 32.000 14.61 14.92 35.47 3.97
463 475 5.918011 GCACGTTTATGAAAATTGTTGGAGA 59.082 36.000 0.00 0.00 0.00 3.71
509 521 8.431222 TCTGAAAACATCTTCCCAAAATCATTT 58.569 29.630 0.00 0.00 0.00 2.32
512 524 6.975196 TCTGAAAACATCTTCCCAAAATCA 57.025 33.333 0.00 0.00 0.00 2.57
513 525 7.928167 AGTTTCTGAAAACATCTTCCCAAAATC 59.072 33.333 4.09 0.00 45.94 2.17
515 527 7.041107 CAGTTTCTGAAAACATCTTCCCAAAA 58.959 34.615 4.09 0.00 45.94 2.44
516 528 6.379703 TCAGTTTCTGAAAACATCTTCCCAAA 59.620 34.615 4.09 0.00 45.94 3.28
518 530 5.445069 TCAGTTTCTGAAAACATCTTCCCA 58.555 37.500 4.09 0.00 45.94 4.37
520 532 6.867662 TCTCAGTTTCTGAAAACATCTTCC 57.132 37.500 4.09 0.00 45.94 3.46
531 544 4.769688 TGCTGTCTTTTCTCAGTTTCTGA 58.230 39.130 0.00 0.00 38.25 3.27
532 545 5.237996 TGATGCTGTCTTTTCTCAGTTTCTG 59.762 40.000 0.00 0.00 34.57 3.02
533 546 5.238214 GTGATGCTGTCTTTTCTCAGTTTCT 59.762 40.000 0.00 0.00 34.57 2.52
534 547 5.447573 GTGATGCTGTCTTTTCTCAGTTTC 58.552 41.667 0.00 0.00 34.57 2.78
535 548 4.024556 CGTGATGCTGTCTTTTCTCAGTTT 60.025 41.667 0.00 0.00 34.57 2.66
536 549 3.496130 CGTGATGCTGTCTTTTCTCAGTT 59.504 43.478 0.00 0.00 34.57 3.16
537 550 3.062763 CGTGATGCTGTCTTTTCTCAGT 58.937 45.455 0.00 0.00 34.57 3.41
538 551 2.159734 GCGTGATGCTGTCTTTTCTCAG 60.160 50.000 0.00 0.00 41.73 3.35
539 552 1.800586 GCGTGATGCTGTCTTTTCTCA 59.199 47.619 0.00 0.00 41.73 3.27
540 553 1.800586 TGCGTGATGCTGTCTTTTCTC 59.199 47.619 0.00 0.00 46.63 2.87
541 554 1.882912 TGCGTGATGCTGTCTTTTCT 58.117 45.000 0.00 0.00 46.63 2.52
542 555 2.031682 AGTTGCGTGATGCTGTCTTTTC 60.032 45.455 0.00 0.00 46.63 2.29
543 556 1.949525 AGTTGCGTGATGCTGTCTTTT 59.050 42.857 0.00 0.00 46.63 2.27
544 557 1.597742 AGTTGCGTGATGCTGTCTTT 58.402 45.000 0.00 0.00 46.63 2.52
545 558 1.532868 GAAGTTGCGTGATGCTGTCTT 59.467 47.619 0.00 0.04 46.63 3.01
546 559 1.151668 GAAGTTGCGTGATGCTGTCT 58.848 50.000 0.00 0.00 46.63 3.41
547 560 0.166814 GGAAGTTGCGTGATGCTGTC 59.833 55.000 0.00 0.00 46.63 3.51
548 561 1.237285 GGGAAGTTGCGTGATGCTGT 61.237 55.000 0.00 0.00 46.63 4.40
549 562 1.503542 GGGAAGTTGCGTGATGCTG 59.496 57.895 0.00 0.00 46.63 4.41
550 563 1.675641 GGGGAAGTTGCGTGATGCT 60.676 57.895 0.00 0.00 46.63 3.79
551 564 0.392461 TAGGGGAAGTTGCGTGATGC 60.392 55.000 0.00 0.00 46.70 3.91
552 565 2.107950 TTAGGGGAAGTTGCGTGATG 57.892 50.000 0.00 0.00 0.00 3.07
553 566 2.871096 TTTAGGGGAAGTTGCGTGAT 57.129 45.000 0.00 0.00 0.00 3.06
554 567 2.871096 ATTTAGGGGAAGTTGCGTGA 57.129 45.000 0.00 0.00 0.00 4.35
555 568 3.934457 AAATTTAGGGGAAGTTGCGTG 57.066 42.857 0.00 0.00 0.00 5.34
556 569 6.394809 CATTAAAATTTAGGGGAAGTTGCGT 58.605 36.000 0.00 0.00 0.00 5.24
557 570 5.290885 GCATTAAAATTTAGGGGAAGTTGCG 59.709 40.000 0.00 0.00 0.00 4.85
558 571 6.092122 GTGCATTAAAATTTAGGGGAAGTTGC 59.908 38.462 0.00 0.00 0.00 4.17
559 572 7.386059 AGTGCATTAAAATTTAGGGGAAGTTG 58.614 34.615 0.00 0.00 0.00 3.16
560 573 7.553504 AGTGCATTAAAATTTAGGGGAAGTT 57.446 32.000 0.00 0.00 0.00 2.66
561 574 7.553504 AAGTGCATTAAAATTTAGGGGAAGT 57.446 32.000 0.00 0.00 0.00 3.01
562 575 8.093927 TGAAAGTGCATTAAAATTTAGGGGAAG 58.906 33.333 0.00 0.00 0.00 3.46
563 576 7.875554 GTGAAAGTGCATTAAAATTTAGGGGAA 59.124 33.333 0.00 0.00 0.00 3.97
564 577 7.382898 GTGAAAGTGCATTAAAATTTAGGGGA 58.617 34.615 0.00 0.00 0.00 4.81
565 578 6.310224 CGTGAAAGTGCATTAAAATTTAGGGG 59.690 38.462 0.00 0.00 0.00 4.79
566 579 7.087639 TCGTGAAAGTGCATTAAAATTTAGGG 58.912 34.615 0.00 0.00 0.00 3.53
567 580 7.273381 CCTCGTGAAAGTGCATTAAAATTTAGG 59.727 37.037 0.00 0.00 0.00 2.69
568 581 8.020819 TCCTCGTGAAAGTGCATTAAAATTTAG 58.979 33.333 0.00 0.00 0.00 1.85
569 582 7.877003 TCCTCGTGAAAGTGCATTAAAATTTA 58.123 30.769 0.00 0.00 0.00 1.40
570 583 6.744112 TCCTCGTGAAAGTGCATTAAAATTT 58.256 32.000 0.00 0.00 0.00 1.82
571 584 6.325919 TCCTCGTGAAAGTGCATTAAAATT 57.674 33.333 0.00 0.00 0.00 1.82
572 585 5.957842 TCCTCGTGAAAGTGCATTAAAAT 57.042 34.783 0.00 0.00 0.00 1.82
573 586 5.759506 TTCCTCGTGAAAGTGCATTAAAA 57.240 34.783 0.00 0.00 0.00 1.52
574 587 5.957842 ATTCCTCGTGAAAGTGCATTAAA 57.042 34.783 0.00 0.00 36.33 1.52
575 588 5.957842 AATTCCTCGTGAAAGTGCATTAA 57.042 34.783 0.00 0.00 36.33 1.40
576 589 5.705441 AGAAATTCCTCGTGAAAGTGCATTA 59.295 36.000 0.00 0.00 36.33 1.90
577 590 4.520492 AGAAATTCCTCGTGAAAGTGCATT 59.480 37.500 0.00 0.00 36.33 3.56
578 591 4.074970 AGAAATTCCTCGTGAAAGTGCAT 58.925 39.130 0.00 0.00 36.33 3.96
579 592 3.476552 AGAAATTCCTCGTGAAAGTGCA 58.523 40.909 0.00 0.00 36.33 4.57
580 593 4.489679 AAGAAATTCCTCGTGAAAGTGC 57.510 40.909 0.00 0.00 36.33 4.40
581 594 6.647067 AGTCTAAGAAATTCCTCGTGAAAGTG 59.353 38.462 0.00 0.00 36.33 3.16
582 595 6.760291 AGTCTAAGAAATTCCTCGTGAAAGT 58.240 36.000 0.00 0.00 36.33 2.66
583 596 7.275999 GGTAGTCTAAGAAATTCCTCGTGAAAG 59.724 40.741 0.00 0.00 36.33 2.62
584 597 7.095270 GGTAGTCTAAGAAATTCCTCGTGAAA 58.905 38.462 0.00 0.00 36.33 2.69
585 598 6.350780 GGGTAGTCTAAGAAATTCCTCGTGAA 60.351 42.308 0.00 0.00 37.38 3.18
586 599 5.126707 GGGTAGTCTAAGAAATTCCTCGTGA 59.873 44.000 0.00 0.00 0.00 4.35
587 600 5.105473 TGGGTAGTCTAAGAAATTCCTCGTG 60.105 44.000 0.00 0.00 0.00 4.35
588 601 5.021458 TGGGTAGTCTAAGAAATTCCTCGT 58.979 41.667 0.00 0.00 0.00 4.18
589 602 5.593679 TGGGTAGTCTAAGAAATTCCTCG 57.406 43.478 0.00 0.00 0.00 4.63
590 603 8.145122 CACTATGGGTAGTCTAAGAAATTCCTC 58.855 40.741 0.00 0.00 39.12 3.71
591 604 7.844779 TCACTATGGGTAGTCTAAGAAATTCCT 59.155 37.037 0.00 0.00 39.12 3.36
592 605 8.019656 TCACTATGGGTAGTCTAAGAAATTCC 57.980 38.462 0.00 0.00 39.12 3.01
593 606 9.535878 CTTCACTATGGGTAGTCTAAGAAATTC 57.464 37.037 0.00 0.00 39.12 2.17
594 607 9.268282 TCTTCACTATGGGTAGTCTAAGAAATT 57.732 33.333 7.14 0.00 39.12 1.82
595 608 8.840200 TCTTCACTATGGGTAGTCTAAGAAAT 57.160 34.615 7.14 0.00 39.12 2.17
596 609 7.894364 ACTCTTCACTATGGGTAGTCTAAGAAA 59.106 37.037 9.43 0.00 39.12 2.52
597 610 7.411808 ACTCTTCACTATGGGTAGTCTAAGAA 58.588 38.462 9.43 0.00 39.12 2.52
598 611 6.971340 ACTCTTCACTATGGGTAGTCTAAGA 58.029 40.000 8.48 8.48 39.12 2.10
599 612 8.623030 GTTACTCTTCACTATGGGTAGTCTAAG 58.377 40.741 0.00 0.00 39.12 2.18
600 613 8.334734 AGTTACTCTTCACTATGGGTAGTCTAA 58.665 37.037 0.00 0.00 39.12 2.10
601 614 7.870027 AGTTACTCTTCACTATGGGTAGTCTA 58.130 38.462 0.00 0.00 39.12 2.59
602 615 6.733509 AGTTACTCTTCACTATGGGTAGTCT 58.266 40.000 0.00 0.00 39.12 3.24
603 616 7.407393 AAGTTACTCTTCACTATGGGTAGTC 57.593 40.000 0.00 0.00 39.12 2.59
604 617 7.892241 TGTAAGTTACTCTTCACTATGGGTAGT 59.108 37.037 14.00 0.00 38.28 2.73
605 618 8.189460 GTGTAAGTTACTCTTCACTATGGGTAG 58.811 40.741 14.00 0.00 37.56 3.18
606 619 7.123247 GGTGTAAGTTACTCTTCACTATGGGTA 59.877 40.741 14.00 0.00 37.56 3.69
607 620 6.070938 GGTGTAAGTTACTCTTCACTATGGGT 60.071 42.308 14.00 0.00 37.56 4.51
608 621 6.070995 TGGTGTAAGTTACTCTTCACTATGGG 60.071 42.308 14.00 0.00 37.56 4.00
609 622 6.931838 TGGTGTAAGTTACTCTTCACTATGG 58.068 40.000 14.00 0.00 37.56 2.74
610 623 7.603651 ACTGGTGTAAGTTACTCTTCACTATG 58.396 38.462 14.00 2.14 37.56 2.23
611 624 7.778185 ACTGGTGTAAGTTACTCTTCACTAT 57.222 36.000 14.00 0.00 37.56 2.12
612 625 8.571336 GTTACTGGTGTAAGTTACTCTTCACTA 58.429 37.037 14.00 1.30 39.09 2.74
613 626 7.069085 TGTTACTGGTGTAAGTTACTCTTCACT 59.931 37.037 14.00 0.00 39.09 3.41
614 627 7.205297 TGTTACTGGTGTAAGTTACTCTTCAC 58.795 38.462 14.00 3.67 39.09 3.18
615 628 7.350744 TGTTACTGGTGTAAGTTACTCTTCA 57.649 36.000 14.00 4.68 39.09 3.02
616 629 7.148623 GCATGTTACTGGTGTAAGTTACTCTTC 60.149 40.741 14.00 0.50 39.09 2.87
617 630 6.649557 GCATGTTACTGGTGTAAGTTACTCTT 59.350 38.462 14.00 3.06 39.09 2.85
618 631 6.164176 GCATGTTACTGGTGTAAGTTACTCT 58.836 40.000 14.00 0.00 39.09 3.24
619 632 5.929992 TGCATGTTACTGGTGTAAGTTACTC 59.070 40.000 14.00 10.18 39.09 2.59
620 633 5.699458 GTGCATGTTACTGGTGTAAGTTACT 59.301 40.000 14.00 0.00 39.09 2.24
621 634 5.467399 TGTGCATGTTACTGGTGTAAGTTAC 59.533 40.000 6.06 6.06 39.09 2.50
622 635 5.612351 TGTGCATGTTACTGGTGTAAGTTA 58.388 37.500 0.00 0.00 39.09 2.24
623 636 4.456535 TGTGCATGTTACTGGTGTAAGTT 58.543 39.130 0.00 0.00 39.09 2.66
624 637 4.079980 TGTGCATGTTACTGGTGTAAGT 57.920 40.909 0.00 0.00 39.09 2.24
625 638 4.973396 CATGTGCATGTTACTGGTGTAAG 58.027 43.478 4.13 0.00 39.09 2.34
638 651 7.776933 AACATAGACTAGTAACATGTGCATG 57.223 36.000 14.07 10.31 44.15 4.06
639 652 8.696374 AGTAACATAGACTAGTAACATGTGCAT 58.304 33.333 14.07 5.21 30.55 3.96
640 653 8.063200 AGTAACATAGACTAGTAACATGTGCA 57.937 34.615 14.07 6.09 30.55 4.57
641 654 8.808529 CAAGTAACATAGACTAGTAACATGTGC 58.191 37.037 14.07 11.16 30.55 4.57
642 655 9.856488 ACAAGTAACATAGACTAGTAACATGTG 57.144 33.333 14.07 5.18 30.55 3.21
643 656 9.856488 CACAAGTAACATAGACTAGTAACATGT 57.144 33.333 0.00 3.02 0.00 3.21
644 657 9.302345 CCACAAGTAACATAGACTAGTAACATG 57.698 37.037 0.00 2.36 0.00 3.21
645 658 9.032624 ACCACAAGTAACATAGACTAGTAACAT 57.967 33.333 0.00 0.00 0.00 2.71
646 659 8.301720 CACCACAAGTAACATAGACTAGTAACA 58.698 37.037 0.00 0.00 0.00 2.41
647 660 7.758528 CCACCACAAGTAACATAGACTAGTAAC 59.241 40.741 0.00 0.00 0.00 2.50
648 661 7.093640 CCCACCACAAGTAACATAGACTAGTAA 60.094 40.741 0.00 0.00 0.00 2.24
649 662 6.379133 CCCACCACAAGTAACATAGACTAGTA 59.621 42.308 0.00 0.00 0.00 1.82
650 663 5.187186 CCCACCACAAGTAACATAGACTAGT 59.813 44.000 0.00 0.00 0.00 2.57
651 664 5.187186 ACCCACCACAAGTAACATAGACTAG 59.813 44.000 0.00 0.00 0.00 2.57
652 665 5.088730 ACCCACCACAAGTAACATAGACTA 58.911 41.667 0.00 0.00 0.00 2.59
653 666 3.908103 ACCCACCACAAGTAACATAGACT 59.092 43.478 0.00 0.00 0.00 3.24
654 667 4.251268 GACCCACCACAAGTAACATAGAC 58.749 47.826 0.00 0.00 0.00 2.59
655 668 3.904965 TGACCCACCACAAGTAACATAGA 59.095 43.478 0.00 0.00 0.00 1.98
656 669 4.253685 CTGACCCACCACAAGTAACATAG 58.746 47.826 0.00 0.00 0.00 2.23
657 670 3.008594 CCTGACCCACCACAAGTAACATA 59.991 47.826 0.00 0.00 0.00 2.29
658 671 2.224769 CCTGACCCACCACAAGTAACAT 60.225 50.000 0.00 0.00 0.00 2.71
659 672 1.142060 CCTGACCCACCACAAGTAACA 59.858 52.381 0.00 0.00 0.00 2.41
660 673 1.418637 TCCTGACCCACCACAAGTAAC 59.581 52.381 0.00 0.00 0.00 2.50
661 674 1.809133 TCCTGACCCACCACAAGTAA 58.191 50.000 0.00 0.00 0.00 2.24
662 675 1.809133 TTCCTGACCCACCACAAGTA 58.191 50.000 0.00 0.00 0.00 2.24
663 676 0.923358 TTTCCTGACCCACCACAAGT 59.077 50.000 0.00 0.00 0.00 3.16
664 677 1.956477 CTTTTCCTGACCCACCACAAG 59.044 52.381 0.00 0.00 0.00 3.16
665 678 1.286553 ACTTTTCCTGACCCACCACAA 59.713 47.619 0.00 0.00 0.00 3.33
670 683 2.495084 GTGAGACTTTTCCTGACCCAC 58.505 52.381 0.00 0.00 0.00 4.61
687 700 1.273048 GCAATTGCCACAATCAGGTGA 59.727 47.619 20.06 0.00 41.32 4.02
688 701 1.717194 GCAATTGCCACAATCAGGTG 58.283 50.000 20.06 0.00 38.52 4.00
720 733 3.782656 AGTTTTCTACGTTCCCACCAT 57.217 42.857 0.00 0.00 0.00 3.55
758 771 8.725405 TGTAACAATTTCAGACACTGTCTTTA 57.275 30.769 9.11 1.64 41.37 1.85
763 776 6.767902 ACTGATGTAACAATTTCAGACACTGT 59.232 34.615 9.08 0.00 38.25 3.55
764 777 7.041848 TCACTGATGTAACAATTTCAGACACTG 60.042 37.037 9.08 0.00 38.25 3.66
807 820 2.297880 GGGTTGGGTAGCAACGAAATTT 59.702 45.455 0.00 0.00 33.65 1.82
809 822 1.202952 TGGGTTGGGTAGCAACGAAAT 60.203 47.619 0.00 0.00 33.65 2.17
813 826 1.241315 CCTTGGGTTGGGTAGCAACG 61.241 60.000 0.00 0.00 33.65 4.10
815 828 1.228737 GCCTTGGGTTGGGTAGCAA 60.229 57.895 0.00 0.00 0.00 3.91
820 833 1.830847 GTTTCGCCTTGGGTTGGGT 60.831 57.895 0.00 0.00 0.00 4.51
828 841 2.169832 TCCTCTGAAGTTTCGCCTTG 57.830 50.000 0.00 0.00 0.00 3.61
864 877 8.714906 ACATTAAGCTTAATCATACCTGTAGGT 58.285 33.333 25.49 14.35 40.36 3.08
877 890 4.038402 GGCTGCATCCACATTAAGCTTAAT 59.962 41.667 23.22 23.22 33.82 1.40
900 915 4.169508 CAACTGTACAGTCAGGATCGAAG 58.830 47.826 28.04 5.53 41.58 3.79
946 970 1.302832 CTGCCGCCAAGAACTTCCT 60.303 57.895 0.00 0.00 0.00 3.36
951 975 1.285950 GTTTCCTGCCGCCAAGAAC 59.714 57.895 0.00 0.00 0.00 3.01
960 984 2.070783 CATGCAACATTGTTTCCTGCC 58.929 47.619 8.33 0.00 31.92 4.85
1014 1038 0.387622 TAAGACCGAACCGAAGTGCG 60.388 55.000 0.00 0.00 45.35 5.34
1117 1141 2.438795 GGCCGGTCCCGCAAATAA 60.439 61.111 1.90 0.00 38.24 1.40
1167 1191 3.696548 ACTGAGCTATGACAAGATCACGA 59.303 43.478 0.00 0.00 41.24 4.35
1231 1255 6.399639 AGAGAACCTAGCTAATCTTGCTAC 57.600 41.667 0.00 0.00 41.46 3.58
1305 1329 7.096884 AGAAACCAACAAAGAGTCTTTTACC 57.903 36.000 15.60 0.59 0.00 2.85
1367 1393 7.606456 GCTAGAGATGCTCTAACATAGACTAGT 59.394 40.741 0.00 0.00 41.74 2.57
1368 1394 7.606073 TGCTAGAGATGCTCTAACATAGACTAG 59.394 40.741 5.75 0.00 41.74 2.57
1369 1395 7.454225 TGCTAGAGATGCTCTAACATAGACTA 58.546 38.462 5.75 0.00 41.74 2.59
1370 1396 6.303054 TGCTAGAGATGCTCTAACATAGACT 58.697 40.000 5.75 0.00 41.74 3.24
1371 1397 6.429692 TCTGCTAGAGATGCTCTAACATAGAC 59.570 42.308 7.72 0.00 41.74 2.59
1372 1398 6.429692 GTCTGCTAGAGATGCTCTAACATAGA 59.570 42.308 7.72 5.70 41.74 1.98
1373 1399 6.349280 GGTCTGCTAGAGATGCTCTAACATAG 60.349 46.154 7.72 0.00 41.74 2.23
1374 1400 5.475220 GGTCTGCTAGAGATGCTCTAACATA 59.525 44.000 7.72 0.19 41.74 2.29
1375 1401 4.280677 GGTCTGCTAGAGATGCTCTAACAT 59.719 45.833 7.72 0.00 41.74 2.71
1409 1435 1.096416 AAACAAGTTTTGCGGGTCGA 58.904 45.000 0.00 0.00 0.00 4.20
1490 1516 1.713404 CGCAAAACAGTAAATGTGCCG 59.287 47.619 0.00 0.00 43.00 5.69
1492 1518 3.006659 TCCGCAAAACAGTAAATGTGC 57.993 42.857 0.00 0.00 43.00 4.57
1494 1520 3.119990 CCGATCCGCAAAACAGTAAATGT 60.120 43.478 0.00 0.00 46.97 2.71
1495 1521 3.425404 CCGATCCGCAAAACAGTAAATG 58.575 45.455 0.00 0.00 0.00 2.32
1498 1551 0.800012 GCCGATCCGCAAAACAGTAA 59.200 50.000 0.82 0.00 0.00 2.24
1500 1553 0.036765 TAGCCGATCCGCAAAACAGT 60.037 50.000 8.76 0.00 0.00 3.55
1550 1603 1.000843 GGGATTTTTGGTTTGCGAGCT 59.999 47.619 0.00 0.00 0.00 4.09
1567 1620 2.093394 TGTCAAATTCGCTAATCGGGGA 60.093 45.455 0.00 0.00 39.05 4.81
1621 1674 1.201834 TGCGCGCGAACTATGTTTTAC 60.202 47.619 37.18 11.40 0.00 2.01
1663 1717 4.032786 GCATGAAGTCTTTTTGCGTTTGTT 59.967 37.500 0.00 0.00 0.00 2.83
1695 1749 2.110578 AGATGATGATGGACGTGGTCA 58.889 47.619 0.00 0.00 33.68 4.02
1722 1776 2.242047 TCATGACGACGGGTGAAAAA 57.758 45.000 0.00 0.00 0.00 1.94
1760 1814 1.386525 GCGGTGATGGCATTGATGGT 61.387 55.000 0.00 0.00 0.00 3.55
1784 1838 1.176527 CAAGTGCCGGTGATGGATTT 58.823 50.000 1.90 0.00 0.00 2.17
1804 1858 0.320073 TTTCGGTGCCGTAGTTGGAG 60.320 55.000 10.60 0.00 40.74 3.86
1812 1866 3.118454 CGATGCTTTCGGTGCCGT 61.118 61.111 10.60 0.00 44.28 5.68
1978 2035 1.665169 CATTGAACCGCGATGACATGA 59.335 47.619 8.23 0.00 40.29 3.07
2047 2105 1.069978 GAGAGAAGAGCCTATGCCACC 59.930 57.143 0.00 0.00 38.69 4.61
2118 2176 4.464597 AGAAGAAGGCACGAGAGAAGTAAT 59.535 41.667 0.00 0.00 0.00 1.89
2121 2179 2.230266 GAGAAGAAGGCACGAGAGAAGT 59.770 50.000 0.00 0.00 0.00 3.01
2181 2239 4.081862 CCATGGAGCAATCAAATGAGTTGT 60.082 41.667 5.56 0.00 38.47 3.32
2198 2256 3.832490 CGGGACAAGATAGATACCATGGA 59.168 47.826 21.47 2.01 0.00 3.41
2248 2306 5.309282 AGACAAGAAGACAAGGGAGAAGATT 59.691 40.000 0.00 0.00 0.00 2.40
2314 2372 4.458989 TCACTTATGAACATGGACAAAGGC 59.541 41.667 0.00 0.00 0.00 4.35
2315 2373 6.573664 TTCACTTATGAACATGGACAAAGG 57.426 37.500 0.00 0.00 40.01 3.11


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

AutoCloner maintained by Alex Coulton.