Multiple sequence alignment - TraesCS3B01G370000

Loading Multiple Alignment...

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 TraesCS3B01G370000 chr3B 100.000 3543 0 0 1 3543 581966765 581963223 0.000000e+00 6543.0
1 TraesCS3B01G370000 chr3B 95.161 62 3 0 2347 2408 581964359 581964298 8.090000e-17 99.0
2 TraesCS3B01G370000 chr3B 95.161 62 3 0 2407 2468 581964419 581964358 8.090000e-17 99.0
3 TraesCS3B01G370000 chr3A 91.419 2121 107 30 1456 3543 585022859 585020781 0.000000e+00 2839.0
4 TraesCS3B01G370000 chr3A 95.982 672 26 1 787 1457 585023582 585022911 0.000000e+00 1090.0
5 TraesCS3B01G370000 chr3A 92.443 397 25 3 20 413 585024133 585023739 2.390000e-156 562.0
6 TraesCS3B01G370000 chr3A 95.105 143 4 3 413 553 657422653 657422794 4.600000e-54 222.0
7 TraesCS3B01G370000 chr3A 95.105 143 3 3 400 539 662336206 662336065 4.600000e-54 222.0
8 TraesCS3B01G370000 chr3A 100.000 62 0 0 2407 2468 585021970 585021909 8.040000e-22 115.0
9 TraesCS3B01G370000 chr3A 95.745 47 2 0 3244 3290 585021106 585021060 3.790000e-10 76.8
10 TraesCS3B01G370000 chr3D 89.991 2118 132 36 1471 3543 444059774 444057692 0.000000e+00 2663.0
11 TraesCS3B01G370000 chr3D 96.471 680 20 4 787 1463 444060504 444059826 0.000000e+00 1120.0
12 TraesCS3B01G370000 chr3D 94.527 402 11 3 20 412 444061086 444060687 8.410000e-171 610.0
13 TraesCS3B01G370000 chr3D 91.525 118 8 2 662 779 578617864 578617979 1.020000e-35 161.0
14 TraesCS3B01G370000 chr3D 96.774 62 2 0 2407 2468 444058859 444058798 1.740000e-18 104.0
15 TraesCS3B01G370000 chr3D 95.161 62 3 0 2347 2408 444058799 444058738 8.090000e-17 99.0
16 TraesCS3B01G370000 chr6B 98.473 131 2 0 413 543 601881426 601881296 7.650000e-57 231.0
17 TraesCS3B01G370000 chr6B 86.029 136 13 1 663 798 205266618 205266489 1.330000e-29 141.0
18 TraesCS3B01G370000 chr5B 98.462 130 2 0 413 542 273304156 273304285 2.750000e-56 230.0
19 TraesCS3B01G370000 chr2B 97.015 134 4 0 412 545 794689063 794688930 3.560000e-55 226.0
20 TraesCS3B01G370000 chr2B 97.015 134 4 0 412 545 794797964 794797831 3.560000e-55 226.0
21 TraesCS3B01G370000 chrUn 92.857 154 10 1 400 553 322720548 322720396 4.600000e-54 222.0
22 TraesCS3B01G370000 chrUn 86.364 132 15 3 659 788 321894339 321894209 1.330000e-29 141.0
23 TraesCS3B01G370000 chr1B 93.878 147 6 3 413 557 623687580 623687725 5.960000e-53 219.0
24 TraesCS3B01G370000 chr4A 93.243 148 7 2 392 539 541579418 541579562 7.700000e-52 215.0
25 TraesCS3B01G370000 chr6D 89.922 129 13 0 663 791 115787735 115787607 2.190000e-37 167.0
26 TraesCS3B01G370000 chr5A 91.818 110 9 0 673 782 395300611 395300502 1.700000e-33 154.0
27 TraesCS3B01G370000 chr2D 91.818 110 9 0 670 779 480566684 480566575 1.700000e-33 154.0
28 TraesCS3B01G370000 chr2D 89.167 120 12 1 663 782 351973340 351973458 7.920000e-32 148.0
29 TraesCS3B01G370000 chr5D 93.137 102 7 0 673 774 444710083 444710184 2.200000e-32 150.0
30 TraesCS3B01G370000 chr6A 86.364 132 15 3 659 788 295818529 295818399 1.330000e-29 141.0


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 TraesCS3B01G370000 chr3B 581963223 581966765 3542 True 2247.00 6543 96.7740 1 3543 3 chr3B.!!$R1 3542
1 TraesCS3B01G370000 chr3A 585020781 585024133 3352 True 936.56 2839 95.1178 20 3543 5 chr3A.!!$R2 3523
2 TraesCS3B01G370000 chr3D 444057692 444061086 3394 True 919.20 2663 94.5848 20 3543 5 chr3D.!!$R1 3523

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
431 441 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.0 44.66 2.17 F
434 444 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 F
542 552 0.179009 CCGGACGGAGGGAGTACATA 60.179 60.0 4.40 0.0 37.50 2.29 F
2107 2232 0.104671 GCAGTGGCAGCAAAAAGGAA 59.895 50.0 0.00 0.0 40.72 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 2022 0.454957 CACGGCTTCCTTTCATTGCG 60.455 55.000 0.00 0.00 0.00 4.85 R
2086 2211 0.599204 CCTTTTTGCTGCCACTGCTG 60.599 55.000 0.00 0.00 38.71 4.41 R
2165 2290 1.520564 CGCCATTGCTACTGCGGTA 60.521 57.895 5.05 5.05 43.08 4.02 R
3293 3443 0.106149 CTACCCAAGGTCGGCATACC 59.894 60.000 0.00 0.00 37.09 2.73 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
128 129 2.434774 GTTTGCCTCCCCCTCGTT 59.565 61.111 0.00 0.00 0.00 3.85
194 195 0.108585 TTGTCTGGTTGTGAGGGCTC 59.891 55.000 0.00 0.00 0.00 4.70
195 196 0.764369 TGTCTGGTTGTGAGGGCTCT 60.764 55.000 0.00 0.00 0.00 4.09
199 200 1.344953 TGGTTGTGAGGGCTCTGTGT 61.345 55.000 0.00 0.00 0.00 3.72
217 218 4.460263 TGTGTTACATCTCTGCCTTTTGT 58.540 39.130 0.00 0.00 0.00 2.83
221 222 5.008613 TGTTACATCTCTGCCTTTTGTGTTC 59.991 40.000 0.00 0.00 0.00 3.18
293 294 1.632589 GATTTGGCCTGTTGGAGGTT 58.367 50.000 3.32 0.00 44.97 3.50
331 332 3.432326 CCGAGGAAAGAGGTATGGGAAAG 60.432 52.174 0.00 0.00 0.00 2.62
332 333 3.197983 CGAGGAAAGAGGTATGGGAAAGT 59.802 47.826 0.00 0.00 0.00 2.66
377 387 6.019779 TGTGTGAAAATATGCCAGTTTACC 57.980 37.500 0.00 0.00 0.00 2.85
422 432 3.328382 TGAAATTGTGTACTCCCTCCG 57.672 47.619 0.00 0.00 0.00 4.63
423 433 2.635915 TGAAATTGTGTACTCCCTCCGT 59.364 45.455 0.00 0.00 0.00 4.69
424 434 3.259902 GAAATTGTGTACTCCCTCCGTC 58.740 50.000 0.00 0.00 0.00 4.79
425 435 1.192428 ATTGTGTACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
426 436 1.246056 TTGTGTACTCCCTCCGTCCG 61.246 60.000 0.00 0.00 0.00 4.79
427 437 2.044650 TGTACTCCCTCCGTCCGG 60.045 66.667 0.00 0.00 0.00 5.14
428 438 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
429 439 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
430 440 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
431 441 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
432 442 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
433 443 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
434 444 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
435 445 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
436 446 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
437 447 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
438 448 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
439 449 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
440 450 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
441 451 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
442 452 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
443 453 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
444 454 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
445 455 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
446 456 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
447 457 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
448 458 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
449 459 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
450 460 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
458 468 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
459 469 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
460 470 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
461 471 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
462 472 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
463 473 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
466 476 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
472 482 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
480 490 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
502 512 9.924650 TTAGTTCTAGATACACTCCTTTTTGTC 57.075 33.333 0.00 0.00 0.00 3.18
503 513 7.387643 AGTTCTAGATACACTCCTTTTTGTCC 58.612 38.462 0.00 0.00 0.00 4.02
504 514 6.928348 TCTAGATACACTCCTTTTTGTCCA 57.072 37.500 0.00 0.00 0.00 4.02
505 515 7.496346 TCTAGATACACTCCTTTTTGTCCAT 57.504 36.000 0.00 0.00 0.00 3.41
506 516 7.918076 TCTAGATACACTCCTTTTTGTCCATT 58.082 34.615 0.00 0.00 0.00 3.16
507 517 8.383175 TCTAGATACACTCCTTTTTGTCCATTT 58.617 33.333 0.00 0.00 0.00 2.32
508 518 7.839680 AGATACACTCCTTTTTGTCCATTTT 57.160 32.000 0.00 0.00 0.00 1.82
509 519 7.661040 AGATACACTCCTTTTTGTCCATTTTG 58.339 34.615 0.00 0.00 0.00 2.44
510 520 5.930837 ACACTCCTTTTTGTCCATTTTGA 57.069 34.783 0.00 0.00 0.00 2.69
511 521 6.484364 ACACTCCTTTTTGTCCATTTTGAT 57.516 33.333 0.00 0.00 0.00 2.57
512 522 6.282930 ACACTCCTTTTTGTCCATTTTGATG 58.717 36.000 0.00 0.00 0.00 3.07
513 523 6.098124 ACACTCCTTTTTGTCCATTTTGATGA 59.902 34.615 0.00 0.00 0.00 2.92
514 524 6.421801 CACTCCTTTTTGTCCATTTTGATGAC 59.578 38.462 0.00 0.00 0.00 3.06
515 525 6.098124 ACTCCTTTTTGTCCATTTTGATGACA 59.902 34.615 0.00 0.00 0.00 3.58
516 526 6.882656 TCCTTTTTGTCCATTTTGATGACAA 58.117 32.000 0.00 0.00 34.47 3.18
517 527 6.985645 TCCTTTTTGTCCATTTTGATGACAAG 59.014 34.615 0.00 0.00 37.13 3.16
518 528 6.762661 CCTTTTTGTCCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.13 3.16
519 529 7.280652 CCTTTTTGTCCATTTTGATGACAAGTT 59.719 33.333 0.00 0.00 37.13 2.66
520 530 8.558973 TTTTTGTCCATTTTGATGACAAGTTT 57.441 26.923 0.00 0.00 37.13 2.66
521 531 8.558973 TTTTGTCCATTTTGATGACAAGTTTT 57.441 26.923 0.00 0.00 37.13 2.43
522 532 8.558973 TTTGTCCATTTTGATGACAAGTTTTT 57.441 26.923 0.00 0.00 37.13 1.94
523 533 7.769272 TGTCCATTTTGATGACAAGTTTTTC 57.231 32.000 0.00 0.00 37.32 2.29
524 534 6.760770 TGTCCATTTTGATGACAAGTTTTTCC 59.239 34.615 0.00 0.00 37.32 3.13
525 535 5.982516 TCCATTTTGATGACAAGTTTTTCCG 59.017 36.000 0.00 0.00 37.32 4.30
526 536 5.177327 CCATTTTGATGACAAGTTTTTCCGG 59.823 40.000 0.00 0.00 37.32 5.14
527 537 5.584253 TTTTGATGACAAGTTTTTCCGGA 57.416 34.783 0.00 0.00 37.32 5.14
528 538 4.561735 TTGATGACAAGTTTTTCCGGAC 57.438 40.909 1.83 0.00 0.00 4.79
529 539 2.546368 TGATGACAAGTTTTTCCGGACG 59.454 45.455 1.83 0.00 0.00 4.79
530 540 1.301423 TGACAAGTTTTTCCGGACGG 58.699 50.000 1.83 3.96 0.00 4.79
531 541 1.134461 TGACAAGTTTTTCCGGACGGA 60.134 47.619 1.83 9.76 43.52 4.69
532 542 1.529865 GACAAGTTTTTCCGGACGGAG 59.470 52.381 13.64 3.15 46.06 4.63
533 543 0.872388 CAAGTTTTTCCGGACGGAGG 59.128 55.000 13.64 0.00 46.06 4.30
534 544 0.250597 AAGTTTTTCCGGACGGAGGG 60.251 55.000 13.64 0.00 46.06 4.30
535 545 1.123246 AGTTTTTCCGGACGGAGGGA 61.123 55.000 13.64 1.83 46.06 4.20
536 546 0.672711 GTTTTTCCGGACGGAGGGAG 60.673 60.000 13.64 0.00 46.06 4.30
537 547 1.123246 TTTTTCCGGACGGAGGGAGT 61.123 55.000 13.64 0.00 46.06 3.85
538 548 0.251742 TTTTCCGGACGGAGGGAGTA 60.252 55.000 13.64 0.00 46.06 2.59
539 549 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
540 550 2.044650 CCGGACGGAGGGAGTACA 60.045 66.667 4.40 0.00 37.50 2.90
541 551 1.455217 CCGGACGGAGGGAGTACAT 60.455 63.158 4.40 0.00 37.50 2.29
542 552 0.179009 CCGGACGGAGGGAGTACATA 60.179 60.000 4.40 0.00 37.50 2.29
543 553 1.547223 CCGGACGGAGGGAGTACATAT 60.547 57.143 4.40 0.00 37.50 1.78
544 554 2.236766 CGGACGGAGGGAGTACATATT 58.763 52.381 0.00 0.00 0.00 1.28
549 559 5.337330 GGACGGAGGGAGTACATATTAATGG 60.337 48.000 0.00 0.00 37.43 3.16
560 570 9.485206 GAGTACATATTAATGGTGGAATTACGT 57.515 33.333 0.00 0.00 37.43 3.57
593 603 9.425893 CGAATATTTGTTGTCTTATGCAGTTAG 57.574 33.333 0.00 0.00 0.00 2.34
598 608 6.346477 TGTTGTCTTATGCAGTTAGACTCT 57.654 37.500 19.92 0.00 39.18 3.24
630 642 5.584067 TCATGGAGTGAATGCCCTTAGGC 62.584 52.174 0.00 0.00 46.86 3.93
646 658 6.521162 CCCTTAGGCTTTAAACATGTTTTGT 58.479 36.000 27.66 7.81 41.53 2.83
647 659 6.423604 CCCTTAGGCTTTAAACATGTTTTGTG 59.576 38.462 27.66 17.72 38.99 3.33
648 660 7.206687 CCTTAGGCTTTAAACATGTTTTGTGA 58.793 34.615 27.66 8.25 38.99 3.58
693 705 5.954752 TGCTACTCCCTCTGATCCATATTAG 59.045 44.000 0.00 0.00 0.00 1.73
696 708 6.678568 ACTCCCTCTGATCCATATTAGTTG 57.321 41.667 0.00 0.00 0.00 3.16
699 714 6.143206 TCCCTCTGATCCATATTAGTTGTCA 58.857 40.000 0.00 0.00 0.00 3.58
702 717 7.151308 CCTCTGATCCATATTAGTTGTCACTC 58.849 42.308 0.00 0.00 34.06 3.51
704 719 8.078060 TCTGATCCATATTAGTTGTCACTCAA 57.922 34.615 0.00 0.00 34.06 3.02
705 720 8.539544 TCTGATCCATATTAGTTGTCACTCAAA 58.460 33.333 0.00 0.00 37.81 2.69
707 722 9.112725 TGATCCATATTAGTTGTCACTCAAATG 57.887 33.333 0.00 0.00 37.81 2.32
709 724 7.629157 TCCATATTAGTTGTCACTCAAATGGA 58.371 34.615 0.00 0.00 37.81 3.41
710 725 8.274322 TCCATATTAGTTGTCACTCAAATGGAT 58.726 33.333 0.00 0.00 37.81 3.41
711 726 8.347771 CCATATTAGTTGTCACTCAAATGGATG 58.652 37.037 0.00 0.00 37.81 3.51
712 727 8.896744 CATATTAGTTGTCACTCAAATGGATGT 58.103 33.333 0.00 0.00 37.81 3.06
715 730 6.992063 AGTTGTCACTCAAATGGATGTATC 57.008 37.500 0.00 0.00 37.81 2.24
716 731 6.715280 AGTTGTCACTCAAATGGATGTATCT 58.285 36.000 0.00 0.00 37.81 1.98
718 733 7.984050 AGTTGTCACTCAAATGGATGTATCTAG 59.016 37.037 0.00 0.00 37.81 2.43
719 734 6.283694 TGTCACTCAAATGGATGTATCTAGC 58.716 40.000 0.00 0.00 0.00 3.42
720 735 6.127083 TGTCACTCAAATGGATGTATCTAGCA 60.127 38.462 0.00 0.00 0.00 3.49
721 736 6.201806 GTCACTCAAATGGATGTATCTAGCAC 59.798 42.308 0.00 0.00 0.00 4.40
722 737 6.098838 TCACTCAAATGGATGTATCTAGCACT 59.901 38.462 0.00 0.00 0.00 4.40
723 738 7.287696 TCACTCAAATGGATGTATCTAGCACTA 59.712 37.037 0.00 0.00 0.00 2.74
724 739 7.928167 CACTCAAATGGATGTATCTAGCACTAA 59.072 37.037 0.00 0.00 0.00 2.24
725 740 8.486210 ACTCAAATGGATGTATCTAGCACTAAA 58.514 33.333 0.00 0.00 0.00 1.85
726 741 9.330063 CTCAAATGGATGTATCTAGCACTAAAA 57.670 33.333 0.00 0.00 0.00 1.52
727 742 9.851686 TCAAATGGATGTATCTAGCACTAAAAT 57.148 29.630 0.00 0.00 0.00 1.82
744 759 9.077674 GCACTAAAATACATCTAGATACATCCG 57.922 37.037 4.54 0.00 0.00 4.18
750 765 9.698309 AAATACATCTAGATACATCCGTTTCAG 57.302 33.333 4.54 0.00 0.00 3.02
751 766 5.533482 ACATCTAGATACATCCGTTTCAGC 58.467 41.667 4.54 0.00 0.00 4.26
752 767 5.303078 ACATCTAGATACATCCGTTTCAGCT 59.697 40.000 4.54 0.00 0.00 4.24
753 768 6.490381 ACATCTAGATACATCCGTTTCAGCTA 59.510 38.462 4.54 0.00 0.00 3.32
754 769 6.315091 TCTAGATACATCCGTTTCAGCTAC 57.685 41.667 0.00 0.00 0.00 3.58
755 770 5.826208 TCTAGATACATCCGTTTCAGCTACA 59.174 40.000 0.00 0.00 0.00 2.74
756 771 5.339008 AGATACATCCGTTTCAGCTACAA 57.661 39.130 0.00 0.00 0.00 2.41
757 772 5.109903 AGATACATCCGTTTCAGCTACAAC 58.890 41.667 0.00 0.00 0.00 3.32
758 773 3.402628 ACATCCGTTTCAGCTACAACT 57.597 42.857 5.82 0.00 0.00 3.16
759 774 4.530710 ACATCCGTTTCAGCTACAACTA 57.469 40.909 5.82 0.00 0.00 2.24
760 775 4.890088 ACATCCGTTTCAGCTACAACTAA 58.110 39.130 5.82 0.00 0.00 2.24
761 776 5.488341 ACATCCGTTTCAGCTACAACTAAT 58.512 37.500 5.82 0.00 0.00 1.73
762 777 6.636705 ACATCCGTTTCAGCTACAACTAATA 58.363 36.000 5.82 0.00 0.00 0.98
763 778 7.272978 ACATCCGTTTCAGCTACAACTAATAT 58.727 34.615 5.82 0.00 0.00 1.28
764 779 7.224753 ACATCCGTTTCAGCTACAACTAATATG 59.775 37.037 5.82 6.22 0.00 1.78
765 780 6.046593 TCCGTTTCAGCTACAACTAATATGG 58.953 40.000 5.82 0.02 0.00 2.74
766 781 6.046593 CCGTTTCAGCTACAACTAATATGGA 58.953 40.000 5.82 0.00 0.00 3.41
767 782 6.706270 CCGTTTCAGCTACAACTAATATGGAT 59.294 38.462 5.82 0.00 0.00 3.41
768 783 7.095607 CCGTTTCAGCTACAACTAATATGGATC 60.096 40.741 5.82 0.00 0.00 3.36
769 784 7.358435 CGTTTCAGCTACAACTAATATGGATCG 60.358 40.741 5.82 0.00 0.00 3.69
770 785 6.025749 TCAGCTACAACTAATATGGATCGG 57.974 41.667 0.00 0.00 0.00 4.18
771 786 5.773176 TCAGCTACAACTAATATGGATCGGA 59.227 40.000 0.00 0.00 0.00 4.55
772 787 6.071896 TCAGCTACAACTAATATGGATCGGAG 60.072 42.308 0.00 0.00 0.00 4.63
773 788 5.186021 AGCTACAACTAATATGGATCGGAGG 59.814 44.000 0.00 0.00 0.00 4.30
774 789 4.891992 ACAACTAATATGGATCGGAGGG 57.108 45.455 0.00 0.00 0.00 4.30
775 790 4.489737 ACAACTAATATGGATCGGAGGGA 58.510 43.478 0.00 0.00 0.00 4.20
776 791 4.528596 ACAACTAATATGGATCGGAGGGAG 59.471 45.833 0.00 0.00 0.00 4.30
777 792 4.405756 ACTAATATGGATCGGAGGGAGT 57.594 45.455 0.00 0.00 0.00 3.85
778 793 5.531753 ACTAATATGGATCGGAGGGAGTA 57.468 43.478 0.00 0.00 0.00 2.59
779 794 5.511363 ACTAATATGGATCGGAGGGAGTAG 58.489 45.833 0.00 0.00 0.00 2.57
780 795 4.405756 AATATGGATCGGAGGGAGTAGT 57.594 45.455 0.00 0.00 0.00 2.73
781 796 5.531753 AATATGGATCGGAGGGAGTAGTA 57.468 43.478 0.00 0.00 0.00 1.82
782 797 2.953284 TGGATCGGAGGGAGTAGTAG 57.047 55.000 0.00 0.00 0.00 2.57
785 800 3.398292 TGGATCGGAGGGAGTAGTAGATT 59.602 47.826 0.00 0.00 0.00 2.40
798 813 7.336176 GGGAGTAGTAGATTTTTGGTTTACCTG 59.664 40.741 0.00 0.00 36.82 4.00
819 834 4.870363 TGTTTTGCTAGAAATGTTGCCTC 58.130 39.130 0.00 0.00 0.00 4.70
879 894 9.100197 TGCACCTATTTCTATCATATGGTCTTA 57.900 33.333 2.13 0.00 0.00 2.10
1071 1088 4.694233 CTCAGCCGCAGCACCTGT 62.694 66.667 8.66 0.00 43.56 4.00
1273 1290 5.566469 ACGAAAATGGGGATTCACTTTCTA 58.434 37.500 0.00 0.00 0.00 2.10
1344 1361 0.390866 CATCGTCAGCCTTCACTGCT 60.391 55.000 0.00 0.00 40.41 4.24
1400 1417 5.012893 AGAGAATGGAAATTCCTCAACCAC 58.987 41.667 13.78 0.00 37.46 4.16
1404 1421 3.221771 TGGAAATTCCTCAACCACTGTG 58.778 45.455 13.78 0.00 37.46 3.66
1461 1534 7.220030 TCCTAATCTGTCTTATCTTGCCAATC 58.780 38.462 0.00 0.00 0.00 2.67
1516 1589 9.559958 CTATAAGTGTTGGATGCTTAGTTTTTG 57.440 33.333 0.00 0.00 0.00 2.44
1613 1689 4.261114 GCTCTTATGATTTGCTGCTCCTTC 60.261 45.833 0.00 0.00 0.00 3.46
1616 1692 6.653020 TCTTATGATTTGCTGCTCCTTCTTA 58.347 36.000 0.00 0.00 0.00 2.10
1651 1727 8.589338 AGGAGGTATCATATCTTGTCATTGTAC 58.411 37.037 0.00 0.00 0.00 2.90
1668 1744 4.688511 TGTACGGGTAAATTGATTGTGC 57.311 40.909 0.00 0.00 0.00 4.57
1680 1756 6.536731 AATTGATTGTGCTGATACGATCTC 57.463 37.500 11.53 0.00 40.57 2.75
1723 1803 5.739959 TGAATTGACCCGAGAATGATGTTA 58.260 37.500 0.00 0.00 0.00 2.41
1824 1933 2.554032 ACCTCAGTGTTATTGCTTGTGC 59.446 45.455 0.00 0.00 40.20 4.57
1856 1973 5.089970 TGTTCTCTACTTGGATGGTGATG 57.910 43.478 0.00 0.00 0.00 3.07
1860 1977 4.532126 TCTCTACTTGGATGGTGATGTGTT 59.468 41.667 0.00 0.00 0.00 3.32
1862 1979 6.212589 TCTCTACTTGGATGGTGATGTGTTAA 59.787 38.462 0.00 0.00 0.00 2.01
1865 1987 6.271488 ACTTGGATGGTGATGTGTTAAATG 57.729 37.500 0.00 0.00 0.00 2.32
1866 1988 5.774690 ACTTGGATGGTGATGTGTTAAATGT 59.225 36.000 0.00 0.00 0.00 2.71
1867 1989 6.267471 ACTTGGATGGTGATGTGTTAAATGTT 59.733 34.615 0.00 0.00 0.00 2.71
1900 2022 1.954382 GGGACTCAACTGTTGGTTTCC 59.046 52.381 19.55 19.43 35.74 3.13
2107 2232 0.104671 GCAGTGGCAGCAAAAAGGAA 59.895 50.000 0.00 0.00 40.72 3.36
2165 2290 5.487131 AGCAAGAGAGATAAGAAACCTTCCT 59.513 40.000 0.00 0.00 0.00 3.36
2182 2307 1.160329 CCTACCGCAGTAGCAATGGC 61.160 60.000 1.24 0.00 44.05 4.40
2278 2403 6.631016 TGACACTAGTGTTCCTGAATATCAC 58.369 40.000 28.49 11.96 45.05 3.06
2512 2637 4.560716 GCCAAGTACAAAGGGATGTTTTCC 60.561 45.833 0.00 0.00 44.62 3.13
2573 2699 1.407258 GAGACTCCTGCGCTATTCACT 59.593 52.381 9.73 1.36 0.00 3.41
2575 2701 0.460987 ACTCCTGCGCTATTCACTGC 60.461 55.000 9.73 0.00 0.00 4.40
2583 2709 0.804989 GCTATTCACTGCCGTGCTTT 59.195 50.000 2.98 0.00 40.99 3.51
2651 2778 3.384467 ACTTTTGTTTGGACATCAGTGGG 59.616 43.478 0.00 0.00 35.29 4.61
2838 2965 7.176589 TCTGTTTTATGTTTTGAGTTTGGGT 57.823 32.000 0.00 0.00 0.00 4.51
2908 3035 5.033589 ACTGATTCCTTCATGGATCAGAC 57.966 43.478 14.62 2.04 45.68 3.51
2916 3043 5.045359 TCCTTCATGGATCAGACAATGACTT 60.045 40.000 0.00 0.00 40.56 3.01
2917 3044 5.651139 CCTTCATGGATCAGACAATGACTTT 59.349 40.000 0.00 0.00 41.91 2.66
2946 3073 4.534500 AGTAACACATGGAGGGATGTAACA 59.466 41.667 0.00 0.00 34.69 2.41
2947 3074 4.380843 AACACATGGAGGGATGTAACAA 57.619 40.909 0.00 0.00 34.69 2.83
2948 3075 4.380843 ACACATGGAGGGATGTAACAAA 57.619 40.909 0.00 0.00 34.69 2.83
2949 3076 4.934356 ACACATGGAGGGATGTAACAAAT 58.066 39.130 0.00 0.00 34.69 2.32
2950 3077 4.706476 ACACATGGAGGGATGTAACAAATG 59.294 41.667 0.00 0.00 34.69 2.32
3052 3179 0.523966 CTTCGGTTCTCGTCTGCTCT 59.476 55.000 0.00 0.00 40.32 4.09
3053 3180 0.959553 TTCGGTTCTCGTCTGCTCTT 59.040 50.000 0.00 0.00 40.32 2.85
3090 3217 2.483363 GCCATCTCTGACTGTCTCCATG 60.483 54.545 9.51 6.10 0.00 3.66
3126 3276 2.050077 GTGCCGTCAAAGCCAAGC 60.050 61.111 0.00 0.00 0.00 4.01
3131 3281 1.134946 GCCGTCAAAGCCAAGCAATAT 59.865 47.619 0.00 0.00 0.00 1.28
3137 3287 5.450412 CGTCAAAGCCAAGCAATATGGTTAT 60.450 40.000 0.00 0.00 40.23 1.89
3172 3322 0.534203 GCTTCCAGTTCCGGTCAACA 60.534 55.000 0.00 0.00 0.00 3.33
3193 3343 4.625800 GGCACGAGAGCTTTGGAT 57.374 55.556 0.00 0.00 34.17 3.41
3210 3360 1.207089 GGATCACGACATGTTCCTCCA 59.793 52.381 0.00 0.00 42.09 3.86
3220 3370 1.217916 TGTTCCTCCACCACCTTTGA 58.782 50.000 0.00 0.00 0.00 2.69
3245 3395 0.868602 AAACACGACAGACCACGACG 60.869 55.000 0.00 0.00 0.00 5.12
3246 3396 1.717791 AACACGACAGACCACGACGA 61.718 55.000 0.00 0.00 0.00 4.20
3247 3397 1.724929 CACGACAGACCACGACGAC 60.725 63.158 0.00 0.00 0.00 4.34
3251 3401 1.344942 GACAGACCACGACGACATGC 61.345 60.000 0.00 0.00 0.00 4.06
3293 3443 4.354155 ACACGACATGTTCCACCG 57.646 55.556 0.00 0.33 38.98 4.94
3398 3549 1.908344 CACACCATGTGGATTGTGGA 58.092 50.000 5.96 0.00 44.27 4.02
3509 3660 4.398988 TGTGCATCCAATGATAGTTCCAAC 59.601 41.667 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.471806 GGAGGCCTCGGAGTTCCC 61.472 72.222 26.36 6.90 0.00 3.97
6 7 1.962321 GAAGGAGGCCTCGGAGTTCC 61.962 65.000 26.36 11.82 30.89 3.62
7 8 0.973496 AGAAGGAGGCCTCGGAGTTC 60.973 60.000 26.36 22.67 30.89 3.01
8 9 0.545548 AAGAAGGAGGCCTCGGAGTT 60.546 55.000 26.36 16.19 30.89 3.01
9 10 0.973496 GAAGAAGGAGGCCTCGGAGT 60.973 60.000 26.36 11.10 30.89 3.85
10 11 1.681486 GGAAGAAGGAGGCCTCGGAG 61.681 65.000 26.36 0.00 30.89 4.63
11 12 1.686110 GGAAGAAGGAGGCCTCGGA 60.686 63.158 26.36 0.00 30.89 4.55
12 13 2.736826 GGGAAGAAGGAGGCCTCGG 61.737 68.421 26.36 0.00 30.89 4.63
13 14 2.736826 GGGGAAGAAGGAGGCCTCG 61.737 68.421 26.36 0.00 30.89 4.63
14 15 1.307430 AGGGGAAGAAGGAGGCCTC 60.307 63.158 25.59 25.59 30.89 4.70
15 16 1.617839 CAGGGGAAGAAGGAGGCCT 60.618 63.158 3.86 3.86 33.87 5.19
16 17 3.002371 CAGGGGAAGAAGGAGGCC 58.998 66.667 0.00 0.00 0.00 5.19
17 18 2.264120 GAGCAGGGGAAGAAGGAGGC 62.264 65.000 0.00 0.00 0.00 4.70
18 19 1.911471 GAGCAGGGGAAGAAGGAGG 59.089 63.158 0.00 0.00 0.00 4.30
194 195 4.516698 ACAAAAGGCAGAGATGTAACACAG 59.483 41.667 0.00 0.00 0.00 3.66
195 196 4.275689 CACAAAAGGCAGAGATGTAACACA 59.724 41.667 0.00 0.00 0.00 3.72
199 200 4.213270 CGAACACAAAAGGCAGAGATGTAA 59.787 41.667 0.00 0.00 0.00 2.41
293 294 1.256812 TCGGAGAGACAGCAATCACA 58.743 50.000 0.00 0.00 0.00 3.58
354 355 5.047660 GGGTAAACTGGCATATTTTCACACA 60.048 40.000 2.63 0.00 0.00 3.72
355 356 5.185056 AGGGTAAACTGGCATATTTTCACAC 59.815 40.000 2.63 0.00 0.00 3.82
377 387 3.592059 CATTTGCAATTCCACCAGAAGG 58.408 45.455 0.00 0.00 38.07 3.46
413 423 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
415 425 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
416 426 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
417 427 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
418 428 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
420 430 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
421 431 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
422 432 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
423 433 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
424 434 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
425 435 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
432 442 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
433 443 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
434 444 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
435 445 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
436 446 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
437 447 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
440 450 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
446 456 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
454 464 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
476 486 9.924650 GACAAAAAGGAGTGTATCTAGAACTAA 57.075 33.333 0.00 0.00 0.00 2.24
477 487 8.529476 GGACAAAAAGGAGTGTATCTAGAACTA 58.471 37.037 0.00 0.00 0.00 2.24
478 488 7.016268 TGGACAAAAAGGAGTGTATCTAGAACT 59.984 37.037 0.00 0.00 0.00 3.01
479 489 7.159372 TGGACAAAAAGGAGTGTATCTAGAAC 58.841 38.462 0.00 0.00 0.00 3.01
480 490 7.311092 TGGACAAAAAGGAGTGTATCTAGAA 57.689 36.000 0.00 0.00 0.00 2.10
481 491 6.928348 TGGACAAAAAGGAGTGTATCTAGA 57.072 37.500 0.00 0.00 0.00 2.43
482 492 8.567285 AAATGGACAAAAAGGAGTGTATCTAG 57.433 34.615 0.00 0.00 0.00 2.43
483 493 8.792633 CAAAATGGACAAAAAGGAGTGTATCTA 58.207 33.333 0.00 0.00 0.00 1.98
484 494 7.505585 TCAAAATGGACAAAAAGGAGTGTATCT 59.494 33.333 0.00 0.00 0.00 1.98
485 495 7.657336 TCAAAATGGACAAAAAGGAGTGTATC 58.343 34.615 0.00 0.00 0.00 2.24
486 496 7.595819 TCAAAATGGACAAAAAGGAGTGTAT 57.404 32.000 0.00 0.00 0.00 2.29
487 497 7.286546 TCATCAAAATGGACAAAAAGGAGTGTA 59.713 33.333 0.00 0.00 33.42 2.90
488 498 5.930837 TCAAAATGGACAAAAAGGAGTGT 57.069 34.783 0.00 0.00 0.00 3.55
489 499 6.421801 GTCATCAAAATGGACAAAAAGGAGTG 59.578 38.462 0.00 0.00 33.42 3.51
490 500 6.098124 TGTCATCAAAATGGACAAAAAGGAGT 59.902 34.615 0.00 0.00 33.42 3.85
491 501 6.514947 TGTCATCAAAATGGACAAAAAGGAG 58.485 36.000 0.00 0.00 33.42 3.69
492 502 6.477053 TGTCATCAAAATGGACAAAAAGGA 57.523 33.333 0.00 0.00 33.42 3.36
493 503 6.762661 ACTTGTCATCAAAATGGACAAAAAGG 59.237 34.615 7.70 0.11 34.98 3.11
494 504 7.775397 ACTTGTCATCAAAATGGACAAAAAG 57.225 32.000 7.70 0.11 34.98 2.27
495 505 8.558973 AAACTTGTCATCAAAATGGACAAAAA 57.441 26.923 7.70 0.00 34.98 1.94
496 506 8.558973 AAAACTTGTCATCAAAATGGACAAAA 57.441 26.923 7.70 0.00 34.98 2.44
497 507 8.558973 AAAAACTTGTCATCAAAATGGACAAA 57.441 26.923 7.70 0.00 34.98 2.83
498 508 7.279758 GGAAAAACTTGTCATCAAAATGGACAA 59.720 33.333 0.00 0.00 34.59 3.18
499 509 6.760770 GGAAAAACTTGTCATCAAAATGGACA 59.239 34.615 0.00 0.00 33.42 4.02
500 510 6.074356 CGGAAAAACTTGTCATCAAAATGGAC 60.074 38.462 0.00 0.00 33.42 4.02
501 511 5.982516 CGGAAAAACTTGTCATCAAAATGGA 59.017 36.000 0.00 0.00 33.42 3.41
502 512 5.177327 CCGGAAAAACTTGTCATCAAAATGG 59.823 40.000 0.00 0.00 33.42 3.16
503 513 5.982516 TCCGGAAAAACTTGTCATCAAAATG 59.017 36.000 0.00 0.00 32.87 2.32
504 514 5.983118 GTCCGGAAAAACTTGTCATCAAAAT 59.017 36.000 5.23 0.00 32.87 1.82
505 515 5.344884 GTCCGGAAAAACTTGTCATCAAAA 58.655 37.500 5.23 0.00 32.87 2.44
506 516 4.496673 CGTCCGGAAAAACTTGTCATCAAA 60.497 41.667 5.23 0.00 32.87 2.69
507 517 3.002862 CGTCCGGAAAAACTTGTCATCAA 59.997 43.478 5.23 0.00 0.00 2.57
508 518 2.546368 CGTCCGGAAAAACTTGTCATCA 59.454 45.455 5.23 0.00 0.00 3.07
509 519 2.095919 CCGTCCGGAAAAACTTGTCATC 60.096 50.000 5.23 0.00 37.50 2.92
510 520 1.877443 CCGTCCGGAAAAACTTGTCAT 59.123 47.619 5.23 0.00 37.50 3.06
511 521 1.134461 TCCGTCCGGAAAAACTTGTCA 60.134 47.619 5.23 0.00 42.05 3.58
512 522 1.529865 CTCCGTCCGGAAAAACTTGTC 59.470 52.381 5.23 0.00 44.66 3.18
513 523 1.589803 CTCCGTCCGGAAAAACTTGT 58.410 50.000 5.23 0.00 44.66 3.16
514 524 0.872388 CCTCCGTCCGGAAAAACTTG 59.128 55.000 5.23 0.00 44.66 3.16
515 525 0.250597 CCCTCCGTCCGGAAAAACTT 60.251 55.000 5.23 0.00 44.66 2.66
516 526 1.123246 TCCCTCCGTCCGGAAAAACT 61.123 55.000 5.23 0.00 44.66 2.66
517 527 0.672711 CTCCCTCCGTCCGGAAAAAC 60.673 60.000 5.23 0.00 44.66 2.43
518 528 1.123246 ACTCCCTCCGTCCGGAAAAA 61.123 55.000 5.23 0.00 44.66 1.94
519 529 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
520 530 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
521 531 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
522 532 1.929860 ATGTACTCCCTCCGTCCGGA 61.930 60.000 0.00 0.00 42.90 5.14
523 533 0.179009 TATGTACTCCCTCCGTCCGG 60.179 60.000 0.00 0.00 0.00 5.14
524 534 1.906990 ATATGTACTCCCTCCGTCCG 58.093 55.000 0.00 0.00 0.00 4.79
525 535 5.337330 CCATTAATATGTACTCCCTCCGTCC 60.337 48.000 0.00 0.00 0.00 4.79
526 536 5.245526 ACCATTAATATGTACTCCCTCCGTC 59.754 44.000 0.00 0.00 0.00 4.79
527 537 5.011738 CACCATTAATATGTACTCCCTCCGT 59.988 44.000 0.00 0.00 0.00 4.69
528 538 5.479306 CACCATTAATATGTACTCCCTCCG 58.521 45.833 0.00 0.00 0.00 4.63
529 539 5.546499 TCCACCATTAATATGTACTCCCTCC 59.454 44.000 0.00 0.00 0.00 4.30
530 540 6.681729 TCCACCATTAATATGTACTCCCTC 57.318 41.667 0.00 0.00 0.00 4.30
531 541 7.648177 ATTCCACCATTAATATGTACTCCCT 57.352 36.000 0.00 0.00 0.00 4.20
532 542 9.227777 GTAATTCCACCATTAATATGTACTCCC 57.772 37.037 0.00 0.00 0.00 4.30
533 543 8.932791 CGTAATTCCACCATTAATATGTACTCC 58.067 37.037 0.00 0.00 0.00 3.85
534 544 9.485206 ACGTAATTCCACCATTAATATGTACTC 57.515 33.333 0.00 0.00 0.00 2.59
535 545 9.841295 AACGTAATTCCACCATTAATATGTACT 57.159 29.630 0.00 0.00 0.00 2.73
562 572 7.967854 TGCATAAGACAACAAATATTCGAAAGG 59.032 33.333 0.00 0.00 0.00 3.11
576 586 7.659652 AAAGAGTCTAACTGCATAAGACAAC 57.340 36.000 19.47 14.32 41.69 3.32
598 608 9.023962 GGGCATTCACTCCATGATATAATTAAA 57.976 33.333 0.00 0.00 37.11 1.52
655 667 9.435570 AGAGGGAGTAGCAGTATTTTATAAAGA 57.564 33.333 0.00 0.00 0.00 2.52
659 671 8.958060 ATCAGAGGGAGTAGCAGTATTTTATA 57.042 34.615 0.00 0.00 0.00 0.98
670 682 5.955355 ACTAATATGGATCAGAGGGAGTAGC 59.045 44.000 0.00 0.00 0.00 3.58
673 685 6.146760 ACAACTAATATGGATCAGAGGGAGT 58.853 40.000 0.00 0.00 0.00 3.85
674 686 6.268617 TGACAACTAATATGGATCAGAGGGAG 59.731 42.308 0.00 0.00 0.00 4.30
675 687 6.042093 GTGACAACTAATATGGATCAGAGGGA 59.958 42.308 0.00 0.00 0.00 4.20
677 689 7.060383 AGTGACAACTAATATGGATCAGAGG 57.940 40.000 0.00 0.00 33.79 3.69
678 690 7.720442 TGAGTGACAACTAATATGGATCAGAG 58.280 38.462 0.00 0.00 36.52 3.35
679 691 7.660030 TGAGTGACAACTAATATGGATCAGA 57.340 36.000 0.00 0.00 36.52 3.27
680 692 8.722480 TTTGAGTGACAACTAATATGGATCAG 57.278 34.615 0.00 0.00 36.52 2.90
693 705 6.992063 AGATACATCCATTTGAGTGACAAC 57.008 37.500 0.00 0.00 38.29 3.32
696 708 6.201806 GTGCTAGATACATCCATTTGAGTGAC 59.798 42.308 0.00 0.00 0.00 3.67
699 714 6.491714 AGTGCTAGATACATCCATTTGAGT 57.508 37.500 0.00 0.00 0.00 3.41
718 733 9.077674 CGGATGTATCTAGATGTATTTTAGTGC 57.922 37.037 15.79 0.00 0.00 4.40
724 739 9.698309 CTGAAACGGATGTATCTAGATGTATTT 57.302 33.333 15.79 6.16 0.00 1.40
725 740 7.815068 GCTGAAACGGATGTATCTAGATGTATT 59.185 37.037 15.79 0.00 0.00 1.89
726 741 7.177568 AGCTGAAACGGATGTATCTAGATGTAT 59.822 37.037 15.79 9.11 0.00 2.29
727 742 6.490381 AGCTGAAACGGATGTATCTAGATGTA 59.510 38.462 15.79 4.44 0.00 2.29
728 743 5.303078 AGCTGAAACGGATGTATCTAGATGT 59.697 40.000 15.79 0.32 0.00 3.06
729 744 5.777802 AGCTGAAACGGATGTATCTAGATG 58.222 41.667 15.79 0.00 0.00 2.90
730 745 6.490381 TGTAGCTGAAACGGATGTATCTAGAT 59.510 38.462 10.73 10.73 0.00 1.98
731 746 5.826208 TGTAGCTGAAACGGATGTATCTAGA 59.174 40.000 0.00 0.00 0.00 2.43
732 747 6.073327 TGTAGCTGAAACGGATGTATCTAG 57.927 41.667 0.00 0.00 0.00 2.43
733 748 6.096423 AGTTGTAGCTGAAACGGATGTATCTA 59.904 38.462 0.00 0.00 0.00 1.98
734 749 5.105310 AGTTGTAGCTGAAACGGATGTATCT 60.105 40.000 0.00 0.00 0.00 1.98
735 750 5.109903 AGTTGTAGCTGAAACGGATGTATC 58.890 41.667 0.00 0.00 0.00 2.24
736 751 5.086104 AGTTGTAGCTGAAACGGATGTAT 57.914 39.130 0.00 0.00 0.00 2.29
737 752 4.530710 AGTTGTAGCTGAAACGGATGTA 57.469 40.909 0.00 0.00 0.00 2.29
738 753 3.402628 AGTTGTAGCTGAAACGGATGT 57.597 42.857 0.00 0.00 0.00 3.06
739 754 7.307396 CCATATTAGTTGTAGCTGAAACGGATG 60.307 40.741 0.00 5.05 0.00 3.51
740 755 6.706270 CCATATTAGTTGTAGCTGAAACGGAT 59.294 38.462 0.00 3.58 0.00 4.18
741 756 6.046593 CCATATTAGTTGTAGCTGAAACGGA 58.953 40.000 0.00 0.00 0.00 4.69
742 757 6.046593 TCCATATTAGTTGTAGCTGAAACGG 58.953 40.000 0.00 0.00 0.00 4.44
743 758 7.358435 CGATCCATATTAGTTGTAGCTGAAACG 60.358 40.741 0.00 0.00 0.00 3.60
744 759 7.095607 CCGATCCATATTAGTTGTAGCTGAAAC 60.096 40.741 0.00 0.19 0.00 2.78
745 760 6.929049 CCGATCCATATTAGTTGTAGCTGAAA 59.071 38.462 0.00 0.00 0.00 2.69
746 761 6.266786 TCCGATCCATATTAGTTGTAGCTGAA 59.733 38.462 0.00 0.00 0.00 3.02
747 762 5.773176 TCCGATCCATATTAGTTGTAGCTGA 59.227 40.000 0.00 0.00 0.00 4.26
748 763 6.025749 TCCGATCCATATTAGTTGTAGCTG 57.974 41.667 0.00 0.00 0.00 4.24
749 764 5.186021 CCTCCGATCCATATTAGTTGTAGCT 59.814 44.000 0.00 0.00 0.00 3.32
750 765 5.411781 CCTCCGATCCATATTAGTTGTAGC 58.588 45.833 0.00 0.00 0.00 3.58
751 766 5.715279 TCCCTCCGATCCATATTAGTTGTAG 59.285 44.000 0.00 0.00 0.00 2.74
752 767 5.647230 TCCCTCCGATCCATATTAGTTGTA 58.353 41.667 0.00 0.00 0.00 2.41
753 768 4.489737 TCCCTCCGATCCATATTAGTTGT 58.510 43.478 0.00 0.00 0.00 3.32
754 769 4.528596 ACTCCCTCCGATCCATATTAGTTG 59.471 45.833 0.00 0.00 0.00 3.16
755 770 4.753186 ACTCCCTCCGATCCATATTAGTT 58.247 43.478 0.00 0.00 0.00 2.24
756 771 4.405756 ACTCCCTCCGATCCATATTAGT 57.594 45.455 0.00 0.00 0.00 2.24
757 772 5.511363 ACTACTCCCTCCGATCCATATTAG 58.489 45.833 0.00 0.00 0.00 1.73
758 773 5.531753 ACTACTCCCTCCGATCCATATTA 57.468 43.478 0.00 0.00 0.00 0.98
759 774 4.405756 ACTACTCCCTCCGATCCATATT 57.594 45.455 0.00 0.00 0.00 1.28
760 775 4.789159 TCTACTACTCCCTCCGATCCATAT 59.211 45.833 0.00 0.00 0.00 1.78
761 776 4.173594 TCTACTACTCCCTCCGATCCATA 58.826 47.826 0.00 0.00 0.00 2.74
762 777 2.987437 TCTACTACTCCCTCCGATCCAT 59.013 50.000 0.00 0.00 0.00 3.41
763 778 2.415624 TCTACTACTCCCTCCGATCCA 58.584 52.381 0.00 0.00 0.00 3.41
764 779 3.724732 ATCTACTACTCCCTCCGATCC 57.275 52.381 0.00 0.00 0.00 3.36
765 780 6.217294 CAAAAATCTACTACTCCCTCCGATC 58.783 44.000 0.00 0.00 0.00 3.69
766 781 5.070580 CCAAAAATCTACTACTCCCTCCGAT 59.929 44.000 0.00 0.00 0.00 4.18
767 782 4.404715 CCAAAAATCTACTACTCCCTCCGA 59.595 45.833 0.00 0.00 0.00 4.55
768 783 4.161754 ACCAAAAATCTACTACTCCCTCCG 59.838 45.833 0.00 0.00 0.00 4.63
769 784 5.695424 ACCAAAAATCTACTACTCCCTCC 57.305 43.478 0.00 0.00 0.00 4.30
770 785 7.551974 GGTAAACCAAAAATCTACTACTCCCTC 59.448 40.741 0.00 0.00 35.64 4.30
771 786 7.239143 AGGTAAACCAAAAATCTACTACTCCCT 59.761 37.037 1.26 0.00 38.89 4.20
772 787 7.336176 CAGGTAAACCAAAAATCTACTACTCCC 59.664 40.741 1.26 0.00 38.89 4.30
773 788 7.881751 ACAGGTAAACCAAAAATCTACTACTCC 59.118 37.037 1.26 0.00 38.89 3.85
774 789 8.843885 ACAGGTAAACCAAAAATCTACTACTC 57.156 34.615 1.26 0.00 38.89 2.59
775 790 9.636789 AAACAGGTAAACCAAAAATCTACTACT 57.363 29.630 1.26 0.00 38.89 2.57
778 793 7.709182 GCAAAACAGGTAAACCAAAAATCTACT 59.291 33.333 1.26 0.00 38.89 2.57
779 794 7.709182 AGCAAAACAGGTAAACCAAAAATCTAC 59.291 33.333 1.26 0.00 38.89 2.59
780 795 7.787028 AGCAAAACAGGTAAACCAAAAATCTA 58.213 30.769 1.26 0.00 38.89 1.98
781 796 6.649155 AGCAAAACAGGTAAACCAAAAATCT 58.351 32.000 1.26 0.00 38.89 2.40
782 797 6.918892 AGCAAAACAGGTAAACCAAAAATC 57.081 33.333 1.26 0.00 38.89 2.17
785 800 6.777213 TCTAGCAAAACAGGTAAACCAAAA 57.223 33.333 1.26 0.00 38.89 2.44
798 813 4.870363 TGAGGCAACATTTCTAGCAAAAC 58.130 39.130 0.00 0.00 41.41 2.43
819 834 8.768019 TGCTCATATTTAAGTTCATTCGATCTG 58.232 33.333 0.00 0.00 0.00 2.90
879 894 9.978044 CGCCCTAGTTTACTAGATAAAGTTAAT 57.022 33.333 16.57 0.00 46.80 1.40
897 913 1.192428 CTTAAGGACCACGCCCTAGT 58.808 55.000 0.00 0.00 32.77 2.57
904 920 3.679824 AAGGACTTCTTAAGGACCACG 57.320 47.619 1.85 0.00 33.14 4.94
1071 1088 2.106566 TGCTCAAAACCTGCTTTTCCA 58.893 42.857 0.00 0.00 28.85 3.53
1344 1361 2.093021 TGATGATTCAGACGCATTCCCA 60.093 45.455 0.00 0.00 0.00 4.37
1400 1417 6.537566 GTGTACTGCAATCAAATACTCACAG 58.462 40.000 0.00 0.00 0.00 3.66
1404 1421 4.092821 TGCGTGTACTGCAATCAAATACTC 59.907 41.667 10.34 0.00 39.87 2.59
1504 1577 8.621532 AGAGTCAATATGTCAAAAACTAAGCA 57.378 30.769 0.00 0.00 0.00 3.91
1516 1589 8.599774 GTTCTAAGAAGCAAGAGTCAATATGTC 58.400 37.037 0.00 0.00 0.00 3.06
1602 1678 3.107601 ACAGGTATAAGAAGGAGCAGCA 58.892 45.455 0.00 0.00 0.00 4.41
1638 1714 6.231951 TCAATTTACCCGTACAATGACAAGA 58.768 36.000 0.00 0.00 0.00 3.02
1651 1727 4.637483 ATCAGCACAATCAATTTACCCG 57.363 40.909 0.00 0.00 0.00 5.28
1689 1769 6.657117 TCTCGGGTCAATTCAAACAATTATCA 59.343 34.615 0.00 0.00 0.00 2.15
1694 1774 5.476599 TCATTCTCGGGTCAATTCAAACAAT 59.523 36.000 0.00 0.00 0.00 2.71
1760 1844 6.935167 TCAGAGCAACAGTCAGACAATAATA 58.065 36.000 2.66 0.00 0.00 0.98
1770 1854 4.341366 TCAGAATTCAGAGCAACAGTCA 57.659 40.909 8.44 0.00 0.00 3.41
1824 1933 8.877779 CATCCAAGTAGAGAACAGAACATTTAG 58.122 37.037 0.00 0.00 0.00 1.85
1856 1973 7.417612 CCCTGCATATACAGAACATTTAACAC 58.582 38.462 4.39 0.00 40.25 3.32
1860 1977 6.101150 AGTCCCCTGCATATACAGAACATTTA 59.899 38.462 4.39 0.00 40.25 1.40
1862 1979 4.413520 AGTCCCCTGCATATACAGAACATT 59.586 41.667 4.39 0.00 40.25 2.71
1865 1987 3.388024 TGAGTCCCCTGCATATACAGAAC 59.612 47.826 4.39 0.69 40.25 3.01
1866 1988 3.653164 TGAGTCCCCTGCATATACAGAA 58.347 45.455 4.39 0.00 40.25 3.02
1867 1989 3.328535 TGAGTCCCCTGCATATACAGA 57.671 47.619 4.39 0.00 40.25 3.41
1900 2022 0.454957 CACGGCTTCCTTTCATTGCG 60.455 55.000 0.00 0.00 0.00 4.85
2006 2128 1.070758 TGAACTTCTCTGGTGTGGCTC 59.929 52.381 0.00 0.00 0.00 4.70
2011 2133 3.711704 TCTTCCTTGAACTTCTCTGGTGT 59.288 43.478 0.00 0.00 0.00 4.16
2086 2211 0.599204 CCTTTTTGCTGCCACTGCTG 60.599 55.000 0.00 0.00 38.71 4.41
2107 2232 2.555757 GCTGTGGTGAGAATGCTTCTTT 59.444 45.455 0.86 0.00 40.87 2.52
2143 2268 7.269316 GGTAGGAAGGTTTCTTATCTCTCTTG 58.731 42.308 0.00 0.00 32.52 3.02
2146 2271 5.736777 GCGGTAGGAAGGTTTCTTATCTCTC 60.737 48.000 0.00 0.00 32.52 3.20
2165 2290 1.520564 CGCCATTGCTACTGCGGTA 60.521 57.895 5.05 5.05 43.08 4.02
2278 2403 1.715585 CTGCCACGGCGATAACTTG 59.284 57.895 16.62 0.00 45.51 3.16
2314 2439 2.409870 GGGCATGGCTTCTTCCACG 61.410 63.158 19.78 0.00 39.25 4.94
2371 2496 1.579932 CTTGCAGCAGCTGGAACTG 59.420 57.895 24.30 12.79 36.92 3.16
2512 2637 4.260948 GCAAGTTGGTTCTGACTCAAGAAG 60.261 45.833 4.75 0.00 36.86 2.85
2573 2699 1.539388 CTGATAACCAAAAGCACGGCA 59.461 47.619 0.00 0.00 0.00 5.69
2575 2701 1.539388 TGCTGATAACCAAAAGCACGG 59.461 47.619 0.00 0.00 40.59 4.94
2583 2709 3.495331 TGAAAGCCTTGCTGATAACCAA 58.505 40.909 0.00 0.00 39.62 3.67
2651 2778 6.375945 ACCAAAGAATTTTCAAAACCATGC 57.624 33.333 0.00 0.00 35.03 4.06
2689 2816 8.311836 AGGAAAGACAGTTAATAATCTCAACGA 58.688 33.333 0.00 0.00 0.00 3.85
2865 2992 3.375438 TTTTTGGCGGGGCATGAG 58.625 55.556 0.00 0.00 0.00 2.90
2916 3043 6.938698 TCCCTCCATGTGTTACTTTACTAA 57.061 37.500 0.00 0.00 0.00 2.24
2917 3044 6.442564 ACATCCCTCCATGTGTTACTTTACTA 59.557 38.462 0.00 0.00 35.57 1.82
2948 3075 9.474313 AGATACATTGTTACCATTTGTTACCAT 57.526 29.630 0.00 0.00 0.00 3.55
2949 3076 8.735315 CAGATACATTGTTACCATTTGTTACCA 58.265 33.333 0.00 0.00 0.00 3.25
2950 3077 8.736244 ACAGATACATTGTTACCATTTGTTACC 58.264 33.333 0.00 0.00 0.00 2.85
2956 3083 7.615365 ACATCCACAGATACATTGTTACCATTT 59.385 33.333 0.00 0.00 0.00 2.32
3026 3153 2.818432 AGACGAGAACCGAAGCTAAGAA 59.182 45.455 0.00 0.00 41.76 2.52
3090 3217 1.798813 ACGATTGAGCTTTTCGTGTCC 59.201 47.619 15.76 0.00 43.80 4.02
3126 3276 8.294341 ACGATCGTAAGTTCATAACCATATTG 57.706 34.615 21.32 0.00 35.82 1.90
3131 3281 4.327898 GCAACGATCGTAAGTTCATAACCA 59.672 41.667 23.04 0.00 35.82 3.67
3137 3287 2.991190 GGAAGCAACGATCGTAAGTTCA 59.009 45.455 23.04 0.00 35.82 3.18
3172 3322 4.008933 AAAGCTCTCGTGCCGGCT 62.009 61.111 29.70 0.07 36.53 5.52
3193 3343 0.320374 GGTGGAGGAACATGTCGTGA 59.680 55.000 0.00 0.00 0.00 4.35
3210 3360 1.111277 GTTTGCCAGTCAAAGGTGGT 58.889 50.000 0.00 0.00 44.59 4.16
3220 3370 0.814010 GGTCTGTCGTGTTTGCCAGT 60.814 55.000 0.00 0.00 0.00 4.00
3251 3401 1.676967 GGCAAAGGTGGCTGAGGAG 60.677 63.158 0.00 0.00 46.62 3.69
3293 3443 0.106149 CTACCCAAGGTCGGCATACC 59.894 60.000 0.00 0.00 37.09 2.73
3392 3543 1.132977 TCAGTCCTACACCCTCCACAA 60.133 52.381 0.00 0.00 0.00 3.33
3393 3544 0.485543 TCAGTCCTACACCCTCCACA 59.514 55.000 0.00 0.00 0.00 4.17
3394 3545 1.187087 CTCAGTCCTACACCCTCCAC 58.813 60.000 0.00 0.00 0.00 4.02
3395 3546 0.614979 GCTCAGTCCTACACCCTCCA 60.615 60.000 0.00 0.00 0.00 3.86
3396 3547 0.614979 TGCTCAGTCCTACACCCTCC 60.615 60.000 0.00 0.00 0.00 4.30
3397 3548 1.410882 GATGCTCAGTCCTACACCCTC 59.589 57.143 0.00 0.00 0.00 4.30
3398 3549 1.273267 TGATGCTCAGTCCTACACCCT 60.273 52.381 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.