Multiple sequence alignment - TraesCS5D01G218100

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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 TraesCS5D01G218100 chr5D 100.000 3366 0 0 1 3366 326902729 326906094 0.000000e+00 6216.0
1 TraesCS5D01G218100 chr5D 84.411 1578 181 44 826 2379 318934396 318932860 0.000000e+00 1491.0
2 TraesCS5D01G218100 chr5D 80.082 728 120 17 1174 1893 319138528 319137818 4.980000e-143 518.0
3 TraesCS5D01G218100 chr5D 77.617 621 97 18 2502 3112 48847059 48846471 4.160000e-89 339.0
4 TraesCS5D01G218100 chr5B 92.293 2699 134 25 718 3366 379596599 379599273 0.000000e+00 3764.0
5 TraesCS5D01G218100 chr5B 83.830 1577 181 50 826 2370 368787297 368785763 0.000000e+00 1432.0
6 TraesCS5D01G218100 chr5B 91.019 579 37 5 1 573 379595905 379596474 0.000000e+00 767.0
7 TraesCS5D01G218100 chr5A 92.833 1786 66 26 721 2479 429657398 429655648 0.000000e+00 2532.0
8 TraesCS5D01G218100 chr5A 82.422 1115 129 44 823 1906 415430305 415431383 0.000000e+00 911.0
9 TraesCS5D01G218100 chr5A 89.831 413 41 1 1963 2375 415431402 415431813 2.300000e-146 529.0
10 TraesCS5D01G218100 chr5A 87.454 271 27 4 3 266 429712449 429712179 4.220000e-79 305.0
11 TraesCS5D01G218100 chr5A 84.375 320 29 9 264 573 429657809 429657501 9.130000e-76 294.0
12 TraesCS5D01G218100 chr5A 75.523 621 94 34 2502 3112 38543518 38542946 5.580000e-63 252.0
13 TraesCS5D01G218100 chr7A 87.791 516 63 0 1378 1893 138012319 138011804 3.710000e-169 604.0
14 TraesCS5D01G218100 chr7A 84.783 368 50 4 2002 2366 138011806 138011442 6.860000e-97 364.0
15 TraesCS5D01G218100 chr7A 81.232 357 46 11 2726 3077 301122337 301121997 5.540000e-68 268.0
16 TraesCS5D01G218100 chr7A 86.765 68 9 0 1015 1082 138012599 138012532 3.600000e-10 76.8
17 TraesCS5D01G218100 chr7D 87.403 516 64 1 1378 1893 138086557 138086043 2.890000e-165 592.0
18 TraesCS5D01G218100 chr7D 86.434 516 70 0 1378 1893 138038832 138038317 1.750000e-157 566.0
19 TraesCS5D01G218100 chr7D 83.333 564 71 12 2568 3115 520395125 520395681 1.800000e-137 499.0
20 TraesCS5D01G218100 chr7D 83.696 368 54 4 2002 2366 138038319 138037955 3.220000e-90 342.0
21 TraesCS5D01G218100 chr7D 83.469 369 53 7 2002 2366 138086045 138085681 1.500000e-88 337.0
22 TraesCS5D01G218100 chr7D 83.550 231 30 4 2729 2958 271053938 271053715 3.400000e-50 209.0
23 TraesCS5D01G218100 chr7D 86.765 68 9 0 1015 1082 138039104 138039037 3.600000e-10 76.8
24 TraesCS5D01G218100 chr2B 79.882 676 102 18 2600 3246 588929620 588930290 6.580000e-127 464.0
25 TraesCS5D01G218100 chr2B 85.145 276 34 5 3042 3312 610920591 610920864 3.310000e-70 276.0
26 TraesCS5D01G218100 chr3A 81.731 520 68 18 2797 3312 113257311 113256815 3.130000e-110 409.0
27 TraesCS5D01G218100 chr3A 78.070 342 60 13 3033 3366 113257116 113256782 5.690000e-48 202.0
28 TraesCS5D01G218100 chr3A 75.238 315 48 14 2791 3104 681445762 681445477 4.560000e-24 122.0
29 TraesCS5D01G218100 chr2A 78.649 459 58 28 2695 3148 70218207 70217784 5.540000e-68 268.0
30 TraesCS5D01G218100 chr7B 82.661 248 30 8 3063 3309 103574917 103575152 1.220000e-49 207.0
31 TraesCS5D01G218100 chr6D 80.144 277 45 10 2569 2840 227462474 227462745 7.370000e-47 198.0
32 TraesCS5D01G218100 chr6D 80.784 255 30 11 3099 3344 221221411 221221655 7.420000e-42 182.0
33 TraesCS5D01G218100 chr6D 77.155 232 41 7 3116 3344 409649573 409649795 1.270000e-24 124.0
34 TraesCS5D01G218100 chr6D 86.316 95 13 0 2251 2345 141930468 141930562 1.650000e-18 104.0
35 TraesCS5D01G218100 chr6B 80.755 265 38 6 3041 3293 436732503 436732766 9.530000e-46 195.0
36 TraesCS5D01G218100 chr1D 78.970 233 38 7 3141 3362 329018757 329018525 7.520000e-32 148.0
37 TraesCS5D01G218100 chr4A 76.531 294 48 13 3054 3344 573376143 573375868 1.260000e-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 TraesCS5D01G218100 chr5D 326902729 326906094 3365 False 6216.000000 6216 100.000000 1 3366 1 chr5D.!!$F1 3365
1 TraesCS5D01G218100 chr5D 318932860 318934396 1536 True 1491.000000 1491 84.411000 826 2379 1 chr5D.!!$R2 1553
2 TraesCS5D01G218100 chr5D 319137818 319138528 710 True 518.000000 518 80.082000 1174 1893 1 chr5D.!!$R3 719
3 TraesCS5D01G218100 chr5D 48846471 48847059 588 True 339.000000 339 77.617000 2502 3112 1 chr5D.!!$R1 610
4 TraesCS5D01G218100 chr5B 379595905 379599273 3368 False 2265.500000 3764 91.656000 1 3366 2 chr5B.!!$F1 3365
5 TraesCS5D01G218100 chr5B 368785763 368787297 1534 True 1432.000000 1432 83.830000 826 2370 1 chr5B.!!$R1 1544
6 TraesCS5D01G218100 chr5A 429655648 429657809 2161 True 1413.000000 2532 88.604000 264 2479 2 chr5A.!!$R3 2215
7 TraesCS5D01G218100 chr5A 415430305 415431813 1508 False 720.000000 911 86.126500 823 2375 2 chr5A.!!$F1 1552
8 TraesCS5D01G218100 chr5A 38542946 38543518 572 True 252.000000 252 75.523000 2502 3112 1 chr5A.!!$R1 610
9 TraesCS5D01G218100 chr7A 138011442 138012599 1157 True 348.266667 604 86.446333 1015 2366 3 chr7A.!!$R2 1351
10 TraesCS5D01G218100 chr7D 520395125 520395681 556 False 499.000000 499 83.333000 2568 3115 1 chr7D.!!$F1 547
11 TraesCS5D01G218100 chr7D 138085681 138086557 876 True 464.500000 592 85.436000 1378 2366 2 chr7D.!!$R3 988
12 TraesCS5D01G218100 chr7D 138037955 138039104 1149 True 328.266667 566 85.631667 1015 2366 3 chr7D.!!$R2 1351
13 TraesCS5D01G218100 chr2B 588929620 588930290 670 False 464.000000 464 79.882000 2600 3246 1 chr2B.!!$F1 646
14 TraesCS5D01G218100 chr3A 113256782 113257311 529 True 305.500000 409 79.900500 2797 3366 2 chr3A.!!$R2 569

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
771 857 0.17899 AGTTGGGACTTGGGTCTTGC 60.179 55.0 0.0 0.0 41.82 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2452 2722 0.039256 CGCACCAACCCATTTGTGAG 60.039 55.0 0.0 0.0 32.71 3.51 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
44 45 7.282675 CGACTAGGTCTGATTTAGAGGAGTAAA 59.717 40.741 0.00 0.00 35.70 2.01
46 47 9.495382 ACTAGGTCTGATTTAGAGGAGTAAATT 57.505 33.333 0.00 0.00 35.70 1.82
48 49 7.569240 AGGTCTGATTTAGAGGAGTAAATTGG 58.431 38.462 0.00 0.00 35.70 3.16
49 50 7.403231 AGGTCTGATTTAGAGGAGTAAATTGGA 59.597 37.037 0.00 0.00 35.70 3.53
72 73 9.886132 TGGATTTATTACTTCTCTAACTGGTTC 57.114 33.333 0.00 0.00 0.00 3.62
82 83 3.563223 TCTAACTGGTTCTAGGGGATCG 58.437 50.000 0.00 0.00 0.00 3.69
87 88 0.468648 GGTTCTAGGGGATCGGTTGG 59.531 60.000 0.00 0.00 0.00 3.77
93 94 0.326618 AGGGGATCGGTTGGAGATGT 60.327 55.000 0.00 0.00 0.00 3.06
99 100 3.134081 GGATCGGTTGGAGATGTCCTTAA 59.866 47.826 10.72 0.00 44.30 1.85
103 104 4.773674 TCGGTTGGAGATGTCCTTAAGTTA 59.226 41.667 10.72 0.00 44.30 2.24
149 150 1.549243 TTAGTGTGGCCATCCGCTGA 61.549 55.000 9.72 2.51 43.26 4.26
167 168 7.306213 TCCGCTGATAGAAATATTAGTCTTCG 58.694 38.462 0.00 0.00 0.00 3.79
186 187 1.229076 GACAACCCCCACCACACTT 59.771 57.895 0.00 0.00 0.00 3.16
224 225 6.757237 TCTACGACTAGGGACATTAGAGTAG 58.243 44.000 0.00 10.40 36.07 2.57
225 226 5.370875 ACGACTAGGGACATTAGAGTAGT 57.629 43.478 0.00 0.00 0.00 2.73
226 227 5.124645 ACGACTAGGGACATTAGAGTAGTG 58.875 45.833 0.00 0.00 0.00 2.74
246 247 0.249120 CCATACAACTCGGAGCACCA 59.751 55.000 4.58 0.00 35.59 4.17
251 252 1.238439 CAACTCGGAGCACCACAAAT 58.762 50.000 4.58 0.00 35.59 2.32
258 259 2.414559 CGGAGCACCACAAATGAATCAC 60.415 50.000 0.00 0.00 35.59 3.06
260 261 2.226437 GAGCACCACAAATGAATCACGT 59.774 45.455 0.00 0.00 0.00 4.49
404 414 3.355378 TGTGGCAAGATTCCGAATCATT 58.645 40.909 20.71 10.63 40.42 2.57
412 422 6.624423 CAAGATTCCGAATCATTCCTGTTTT 58.376 36.000 20.71 3.02 40.42 2.43
415 425 4.027674 TCCGAATCATTCCTGTTTTGGA 57.972 40.909 0.00 2.57 40.24 3.53
447 457 8.542497 TTGCAGTAACAATTACTAGTAGTTGG 57.458 34.615 30.37 18.71 44.32 3.77
448 458 7.101054 TGCAGTAACAATTACTAGTAGTTGGG 58.899 38.462 30.37 19.25 44.32 4.12
449 459 6.537660 GCAGTAACAATTACTAGTAGTTGGGG 59.462 42.308 30.37 19.49 44.32 4.96
451 461 8.752187 CAGTAACAATTACTAGTAGTTGGGGTA 58.248 37.037 30.37 20.38 44.32 3.69
452 462 8.753133 AGTAACAATTACTAGTAGTTGGGGTAC 58.247 37.037 30.37 26.51 44.30 3.34
453 463 7.981789 GTAACAATTACTAGTAGTTGGGGTACC 59.018 40.741 30.37 2.17 39.65 3.34
495 505 3.118629 TCTCTTCTCATGAATCGGGTTGG 60.119 47.826 0.00 0.00 0.00 3.77
499 509 3.104512 TCTCATGAATCGGGTTGGTAGT 58.895 45.455 0.00 0.00 0.00 2.73
502 512 5.018539 TCATGAATCGGGTTGGTAGTTAG 57.981 43.478 0.00 0.00 0.00 2.34
504 514 4.460948 TGAATCGGGTTGGTAGTTAGAC 57.539 45.455 0.00 0.00 0.00 2.59
506 516 1.176527 TCGGGTTGGTAGTTAGACGG 58.823 55.000 0.00 0.00 0.00 4.79
518 535 3.766545 AGTTAGACGGTGTGGTAGGTAA 58.233 45.455 0.00 0.00 0.00 2.85
535 552 0.389426 TAAGGTTCGTCTTCGCTGGC 60.389 55.000 0.00 0.00 36.96 4.85
539 556 4.778415 TCGTCTTCGCTGGCTCGC 62.778 66.667 0.00 0.00 36.96 5.03
550 567 4.382320 GGCTCGCCCGTTACCACA 62.382 66.667 0.00 0.00 0.00 4.17
557 574 1.530323 GCCCGTTACCACAAGACATT 58.470 50.000 0.00 0.00 0.00 2.71
593 648 1.134098 ACGATCATTGACCCCACATCC 60.134 52.381 0.00 0.00 0.00 3.51
595 650 2.301346 GATCATTGACCCCACATCCAC 58.699 52.381 0.00 0.00 0.00 4.02
601 656 1.463214 ACCCCACATCCACTGGACA 60.463 57.895 0.00 0.00 32.98 4.02
602 657 1.065410 ACCCCACATCCACTGGACAA 61.065 55.000 0.00 0.00 32.98 3.18
607 662 3.338249 CCACATCCACTGGACAACTTAG 58.662 50.000 0.00 0.00 32.98 2.18
608 663 2.744202 CACATCCACTGGACAACTTAGC 59.256 50.000 0.00 0.00 32.98 3.09
612 667 4.901197 TCCACTGGACAACTTAGCAATA 57.099 40.909 0.00 0.00 0.00 1.90
613 668 5.235850 TCCACTGGACAACTTAGCAATAA 57.764 39.130 0.00 0.00 0.00 1.40
614 669 5.815581 TCCACTGGACAACTTAGCAATAAT 58.184 37.500 0.00 0.00 0.00 1.28
619 674 6.127897 ACTGGACAACTTAGCAATAATTGAGC 60.128 38.462 0.00 0.00 0.00 4.26
621 676 6.208402 TGGACAACTTAGCAATAATTGAGCAA 59.792 34.615 0.00 0.00 0.00 3.91
622 677 6.749118 GGACAACTTAGCAATAATTGAGCAAG 59.251 38.462 0.00 0.00 0.00 4.01
623 678 7.362056 GGACAACTTAGCAATAATTGAGCAAGA 60.362 37.037 0.00 0.00 0.00 3.02
624 679 7.533426 ACAACTTAGCAATAATTGAGCAAGAG 58.467 34.615 0.00 6.29 0.00 2.85
625 680 7.175641 ACAACTTAGCAATAATTGAGCAAGAGT 59.824 33.333 0.00 6.69 0.00 3.24
626 681 7.081526 ACTTAGCAATAATTGAGCAAGAGTG 57.918 36.000 0.00 0.00 0.00 3.51
627 682 6.881065 ACTTAGCAATAATTGAGCAAGAGTGA 59.119 34.615 0.00 0.00 0.00 3.41
628 683 5.557891 AGCAATAATTGAGCAAGAGTGAC 57.442 39.130 0.00 0.00 0.00 3.67
629 684 4.397417 AGCAATAATTGAGCAAGAGTGACC 59.603 41.667 0.00 0.00 0.00 4.02
630 685 4.439289 GCAATAATTGAGCAAGAGTGACCC 60.439 45.833 0.00 0.00 0.00 4.46
631 686 2.957402 AATTGAGCAAGAGTGACCCA 57.043 45.000 0.00 0.00 0.00 4.51
632 687 2.486472 ATTGAGCAAGAGTGACCCAG 57.514 50.000 0.00 0.00 0.00 4.45
633 688 1.131638 TTGAGCAAGAGTGACCCAGT 58.868 50.000 0.00 0.00 0.00 4.00
634 689 0.394192 TGAGCAAGAGTGACCCAGTG 59.606 55.000 0.00 0.00 0.00 3.66
635 690 0.321122 GAGCAAGAGTGACCCAGTGG 60.321 60.000 0.63 0.63 37.80 4.00
636 691 1.968540 GCAAGAGTGACCCAGTGGC 60.969 63.158 2.61 0.00 33.59 5.01
637 692 1.302832 CAAGAGTGACCCAGTGGCC 60.303 63.158 2.61 0.00 33.59 5.36
638 693 2.529744 AAGAGTGACCCAGTGGCCC 61.530 63.158 2.61 0.00 33.59 5.80
639 694 3.249189 GAGTGACCCAGTGGCCCA 61.249 66.667 2.61 0.06 33.59 5.36
640 695 2.776526 AGTGACCCAGTGGCCCAA 60.777 61.111 2.61 0.00 33.59 4.12
641 696 2.597510 GTGACCCAGTGGCCCAAC 60.598 66.667 2.61 0.00 33.59 3.77
642 697 3.897122 TGACCCAGTGGCCCAACC 61.897 66.667 2.61 0.00 39.84 3.77
650 705 2.440065 TGGCCCAACCGCATCATC 60.440 61.111 0.00 0.00 43.94 2.92
651 706 3.585990 GGCCCAACCGCATCATCG 61.586 66.667 0.00 0.00 0.00 3.84
652 707 4.256090 GCCCAACCGCATCATCGC 62.256 66.667 0.00 0.00 0.00 4.58
653 708 2.514592 CCCAACCGCATCATCGCT 60.515 61.111 0.00 0.00 0.00 4.93
654 709 2.114670 CCCAACCGCATCATCGCTT 61.115 57.895 0.00 0.00 0.00 4.68
655 710 1.353103 CCAACCGCATCATCGCTTC 59.647 57.895 0.00 0.00 0.00 3.86
656 711 1.353103 CAACCGCATCATCGCTTCC 59.647 57.895 0.00 0.00 0.00 3.46
657 712 1.078497 AACCGCATCATCGCTTCCA 60.078 52.632 0.00 0.00 0.00 3.53
658 713 0.464373 AACCGCATCATCGCTTCCAT 60.464 50.000 0.00 0.00 0.00 3.41
659 714 0.464373 ACCGCATCATCGCTTCCATT 60.464 50.000 0.00 0.00 0.00 3.16
671 751 3.886505 TCGCTTCCATTGGTTTACAGTTT 59.113 39.130 1.86 0.00 0.00 2.66
672 752 4.023536 TCGCTTCCATTGGTTTACAGTTTC 60.024 41.667 1.86 0.00 0.00 2.78
673 753 4.023193 CGCTTCCATTGGTTTACAGTTTCT 60.023 41.667 1.86 0.00 0.00 2.52
674 754 5.507315 CGCTTCCATTGGTTTACAGTTTCTT 60.507 40.000 1.86 0.00 0.00 2.52
675 755 6.280643 GCTTCCATTGGTTTACAGTTTCTTT 58.719 36.000 1.86 0.00 0.00 2.52
676 756 6.420903 GCTTCCATTGGTTTACAGTTTCTTTC 59.579 38.462 1.86 0.00 0.00 2.62
677 757 7.654022 TTCCATTGGTTTACAGTTTCTTTCT 57.346 32.000 1.86 0.00 0.00 2.52
678 758 8.754991 TTCCATTGGTTTACAGTTTCTTTCTA 57.245 30.769 1.86 0.00 0.00 2.10
679 759 8.754991 TCCATTGGTTTACAGTTTCTTTCTAA 57.245 30.769 1.86 0.00 0.00 2.10
680 760 9.191479 TCCATTGGTTTACAGTTTCTTTCTAAA 57.809 29.630 1.86 0.00 0.00 1.85
681 761 9.981114 CCATTGGTTTACAGTTTCTTTCTAAAT 57.019 29.630 0.00 0.00 0.00 1.40
705 785 9.757227 AATTTGAATCGATTGGTTTAAAGTTGA 57.243 25.926 16.96 0.00 0.00 3.18
706 786 8.795786 TTTGAATCGATTGGTTTAAAGTTGAG 57.204 30.769 16.96 0.00 0.00 3.02
707 787 7.737972 TGAATCGATTGGTTTAAAGTTGAGA 57.262 32.000 16.96 0.00 0.00 3.27
708 788 7.806690 TGAATCGATTGGTTTAAAGTTGAGAG 58.193 34.615 16.96 0.00 0.00 3.20
709 789 7.659799 TGAATCGATTGGTTTAAAGTTGAGAGA 59.340 33.333 16.96 0.00 0.00 3.10
710 790 7.602517 ATCGATTGGTTTAAAGTTGAGAGAG 57.397 36.000 0.00 0.00 0.00 3.20
711 791 6.755206 TCGATTGGTTTAAAGTTGAGAGAGA 58.245 36.000 0.00 0.00 0.00 3.10
712 792 7.214381 TCGATTGGTTTAAAGTTGAGAGAGAA 58.786 34.615 0.00 0.00 0.00 2.87
713 793 7.385205 TCGATTGGTTTAAAGTTGAGAGAGAAG 59.615 37.037 0.00 0.00 0.00 2.85
714 794 7.385205 CGATTGGTTTAAAGTTGAGAGAGAAGA 59.615 37.037 0.00 0.00 0.00 2.87
715 795 8.980481 ATTGGTTTAAAGTTGAGAGAGAAGAA 57.020 30.769 0.00 0.00 0.00 2.52
716 796 7.787725 TGGTTTAAAGTTGAGAGAGAAGAAC 57.212 36.000 0.00 0.00 0.00 3.01
765 851 1.971695 GGCGAAGTTGGGACTTGGG 60.972 63.158 0.00 0.00 45.88 4.12
766 852 1.228154 GCGAAGTTGGGACTTGGGT 60.228 57.895 0.00 0.00 45.88 4.51
771 857 0.178990 AGTTGGGACTTGGGTCTTGC 60.179 55.000 0.00 0.00 41.82 4.01
779 865 2.737252 GACTTGGGTCTTGCGAGTAAAG 59.263 50.000 0.00 3.94 39.24 1.85
782 868 3.308438 TGGGTCTTGCGAGTAAAGTAC 57.692 47.619 0.00 0.00 0.00 2.73
803 892 1.336755 AGCATGTGTTTCCCGTTTGAC 59.663 47.619 0.00 0.00 0.00 3.18
824 913 2.815647 GCACCGCTGTAGCTGGAC 60.816 66.667 17.34 8.38 37.85 4.02
825 914 2.973899 CACCGCTGTAGCTGGACT 59.026 61.111 17.34 0.00 37.85 3.85
826 915 1.446792 CACCGCTGTAGCTGGACTG 60.447 63.158 17.34 0.00 37.85 3.51
827 916 2.185350 CCGCTGTAGCTGGACTGG 59.815 66.667 0.00 0.00 39.32 4.00
828 917 2.351244 CCGCTGTAGCTGGACTGGA 61.351 63.158 0.00 0.00 39.32 3.86
829 918 1.140589 CGCTGTAGCTGGACTGGAG 59.859 63.158 0.00 0.00 39.32 3.86
830 919 1.599606 CGCTGTAGCTGGACTGGAGT 61.600 60.000 0.00 0.00 39.32 3.85
857 949 0.249911 GTATCTGACGTCCATGCCCC 60.250 60.000 14.12 0.00 0.00 5.80
898 990 0.535102 CAGTCCAACCCGTCAGCTTT 60.535 55.000 0.00 0.00 0.00 3.51
904 996 0.605589 AACCCGTCAGCTTTGCCTAC 60.606 55.000 0.00 0.00 0.00 3.18
933 1029 3.730761 CTCGTGGCTTGGCAGTGC 61.731 66.667 6.55 6.55 0.00 4.40
1011 1126 2.358957 CAGTCATCAATGGCGAAAGGA 58.641 47.619 0.00 0.00 37.51 3.36
1021 1136 2.793946 CGAAAGGAATGCCTGCGG 59.206 61.111 7.27 0.00 46.28 5.69
1098 1241 2.657143 AGGTCGTCTTCCTCTATCCAC 58.343 52.381 0.00 0.00 0.00 4.02
1099 1242 2.025226 AGGTCGTCTTCCTCTATCCACA 60.025 50.000 0.00 0.00 0.00 4.17
1100 1243 2.359531 GGTCGTCTTCCTCTATCCACAG 59.640 54.545 0.00 0.00 0.00 3.66
1102 1245 3.017442 TCGTCTTCCTCTATCCACAGTG 58.983 50.000 0.00 0.00 0.00 3.66
1103 1246 2.755655 CGTCTTCCTCTATCCACAGTGT 59.244 50.000 0.00 0.00 0.00 3.55
1139 1327 2.359107 CCTCTGCTTCTTGCGCCA 60.359 61.111 4.18 0.00 46.63 5.69
1222 1410 3.909086 AAGGTGCTCTTCTGCGGGC 62.909 63.158 0.00 0.00 35.36 6.13
1287 1475 3.207669 CTCTACCCCGTCGTCCCG 61.208 72.222 0.00 0.00 0.00 5.14
1353 1547 8.125978 TCCTCCAAATTTCTAGTAGTACGAAA 57.874 34.615 6.01 6.01 0.00 3.46
1471 1703 1.476891 GTGGGCTACTTCATCGACTCA 59.523 52.381 0.00 0.00 0.00 3.41
1477 1709 0.817654 ACTTCATCGACTCATGCCGA 59.182 50.000 7.03 7.03 39.25 5.54
1877 2116 4.648007 TCTTGGTCAGCCAGGACT 57.352 55.556 0.00 0.00 44.60 3.85
1896 2135 4.000988 GACTCCGAGCAAATGAAGGTTAA 58.999 43.478 0.00 0.00 0.00 2.01
1935 2174 4.855298 TCCCTCCATTAATCGACCTTTT 57.145 40.909 0.00 0.00 0.00 2.27
1962 2221 1.402968 GTGACGCATGATTCTTGGCAT 59.597 47.619 0.00 0.00 0.00 4.40
2452 2722 8.469125 GTGAAGTCGTGATTTGTTGTTTTATTC 58.531 33.333 0.00 0.00 0.00 1.75
2453 2723 8.402472 TGAAGTCGTGATTTGTTGTTTTATTCT 58.598 29.630 0.00 0.00 0.00 2.40
2583 2865 9.677567 TTACTTCATCAAAAGTGCATTTTACTC 57.322 29.630 7.69 0.00 39.11 2.59
2613 2897 2.832672 GGCAACTTCAACCGATGATC 57.167 50.000 0.00 0.00 38.03 2.92
2924 3256 1.210234 ACGGTGGCTTCATCATCATCA 59.790 47.619 0.00 0.00 0.00 3.07
2925 3257 2.158711 ACGGTGGCTTCATCATCATCAT 60.159 45.455 0.00 0.00 0.00 2.45
2926 3258 2.483106 CGGTGGCTTCATCATCATCATC 59.517 50.000 0.00 0.00 0.00 2.92
2950 3299 6.640499 TCAATGGCTTCTTTATCAACGTTTTG 59.360 34.615 0.00 0.00 0.00 2.44
2965 3314 2.598907 CGTTTTGATGCGTTGACGTCTT 60.599 45.455 17.92 0.00 42.22 3.01
2984 3333 0.178984 TAGTGTCGTGACCTCCACCA 60.179 55.000 0.00 0.00 42.76 4.17
3000 3349 2.233271 CACCAGAAGCACCTTCATTGT 58.767 47.619 7.62 0.00 42.37 2.71
3010 3359 1.339727 ACCTTCATTGTTACCTCCCGC 60.340 52.381 0.00 0.00 0.00 6.13
3040 3389 3.565307 TGTTTTCATCAAAGCCACCTCT 58.435 40.909 0.00 0.00 0.00 3.69
3111 3463 1.075482 CCCAAGCCACCTCACATGT 59.925 57.895 0.00 0.00 0.00 3.21
3113 3465 0.250858 CCAAGCCACCTCACATGTCA 60.251 55.000 0.00 0.00 0.00 3.58
3270 3680 1.152610 ATGGCACCTCCCATCATGC 60.153 57.895 0.00 0.00 41.75 4.06
3277 3687 1.133884 ACCTCCCATCATGCTCATGTG 60.134 52.381 9.41 7.36 39.72 3.21
3301 3711 0.837272 CCCATTCCACCGTCTATGGT 59.163 55.000 0.00 0.00 45.21 3.55
3361 3783 4.392940 CCCATTTCATCTATGACACCTCC 58.607 47.826 0.00 0.00 36.36 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 9.886132 GAACCAGTTAGAGAAGTAATAAATCCA 57.114 33.333 0.00 0.00 0.00 3.41
53 54 6.612049 CCCCTAGAACCAGTTAGAGAAGTAAT 59.388 42.308 0.00 0.00 0.00 1.89
66 67 1.139058 CAACCGATCCCCTAGAACCAG 59.861 57.143 0.00 0.00 0.00 4.00
72 73 1.620819 CATCTCCAACCGATCCCCTAG 59.379 57.143 0.00 0.00 0.00 3.02
82 83 7.065923 GTCAATAACTTAAGGACATCTCCAACC 59.934 40.741 7.53 0.00 39.39 3.77
93 94 6.443849 ACAGGGAGATGTCAATAACTTAAGGA 59.556 38.462 7.53 0.00 0.00 3.36
149 150 8.148999 GGGTTGTCCGAAGACTAATATTTCTAT 58.851 37.037 0.00 0.00 43.91 1.98
167 168 2.203437 GTGTGGTGGGGGTTGTCC 60.203 66.667 0.00 0.00 0.00 4.02
186 187 3.053842 AGTCGTAGAGGATGGGAAGTGTA 60.054 47.826 0.00 0.00 36.95 2.90
224 225 0.391130 TGCTCCGAGTTGTATGGCAC 60.391 55.000 0.00 0.00 0.00 5.01
225 226 0.391130 GTGCTCCGAGTTGTATGGCA 60.391 55.000 0.00 0.00 0.00 4.92
226 227 1.090052 GGTGCTCCGAGTTGTATGGC 61.090 60.000 0.00 0.00 0.00 4.40
404 414 3.131223 TGCAATTCGTTTCCAAAACAGGA 59.869 39.130 3.72 0.00 35.41 3.86
412 422 4.902443 TTGTTACTGCAATTCGTTTCCA 57.098 36.364 0.00 0.00 0.00 3.53
415 425 8.780249 ACTAGTAATTGTTACTGCAATTCGTTT 58.220 29.630 11.54 0.00 45.58 3.60
421 431 9.162764 CCAACTACTAGTAATTGTTACTGCAAT 57.837 33.333 19.60 0.00 45.58 3.56
495 505 3.084786 ACCTACCACACCGTCTAACTAC 58.915 50.000 0.00 0.00 0.00 2.73
499 509 3.091545 CCTTACCTACCACACCGTCTAA 58.908 50.000 0.00 0.00 0.00 2.10
502 512 1.260544 ACCTTACCTACCACACCGTC 58.739 55.000 0.00 0.00 0.00 4.79
504 514 1.403249 CGAACCTTACCTACCACACCG 60.403 57.143 0.00 0.00 0.00 4.94
506 516 2.560105 AGACGAACCTTACCTACCACAC 59.440 50.000 0.00 0.00 0.00 3.82
518 535 2.048127 GCCAGCGAAGACGAACCT 60.048 61.111 0.00 0.00 42.66 3.50
535 552 1.012486 GTCTTGTGGTAACGGGCGAG 61.012 60.000 0.00 0.00 42.51 5.03
539 556 2.158841 CGAAATGTCTTGTGGTAACGGG 59.841 50.000 0.00 0.00 42.51 5.28
593 648 7.144722 TCAATTATTGCTAAGTTGTCCAGTG 57.855 36.000 0.00 0.00 0.00 3.66
595 650 6.127925 TGCTCAATTATTGCTAAGTTGTCCAG 60.128 38.462 0.00 0.00 0.00 3.86
601 656 7.391554 TCACTCTTGCTCAATTATTGCTAAGTT 59.608 33.333 0.00 0.00 0.00 2.66
602 657 6.881065 TCACTCTTGCTCAATTATTGCTAAGT 59.119 34.615 0.00 0.00 0.00 2.24
607 662 4.439289 GGGTCACTCTTGCTCAATTATTGC 60.439 45.833 0.00 0.00 0.00 3.56
608 663 4.701651 TGGGTCACTCTTGCTCAATTATTG 59.298 41.667 0.00 0.00 0.00 1.90
612 667 2.107204 ACTGGGTCACTCTTGCTCAATT 59.893 45.455 0.00 0.00 0.00 2.32
613 668 1.701847 ACTGGGTCACTCTTGCTCAAT 59.298 47.619 0.00 0.00 0.00 2.57
614 669 1.131638 ACTGGGTCACTCTTGCTCAA 58.868 50.000 0.00 0.00 0.00 3.02
619 674 1.302832 GGCCACTGGGTCACTCTTG 60.303 63.158 0.00 0.00 39.19 3.02
621 676 2.930562 GGGCCACTGGGTCACTCT 60.931 66.667 4.39 0.00 42.08 3.24
622 677 2.829384 TTGGGCCACTGGGTCACTC 61.829 63.158 5.23 0.00 42.08 3.51
623 678 2.776526 TTGGGCCACTGGGTCACT 60.777 61.111 5.23 0.00 42.08 3.41
624 679 2.597510 GTTGGGCCACTGGGTCAC 60.598 66.667 5.23 0.00 42.08 3.67
625 680 3.897122 GGTTGGGCCACTGGGTCA 61.897 66.667 5.23 0.00 42.08 4.02
630 685 3.443045 GATGCGGTTGGGCCACTG 61.443 66.667 5.23 8.21 36.97 3.66
631 686 3.286694 ATGATGCGGTTGGGCCACT 62.287 57.895 5.23 0.00 36.97 4.00
632 687 2.755469 ATGATGCGGTTGGGCCAC 60.755 61.111 5.23 0.85 36.97 5.01
633 688 2.440065 GATGATGCGGTTGGGCCA 60.440 61.111 0.00 0.00 36.97 5.36
634 689 3.585990 CGATGATGCGGTTGGGCC 61.586 66.667 0.00 0.00 0.00 5.80
635 690 4.256090 GCGATGATGCGGTTGGGC 62.256 66.667 0.00 0.00 0.00 5.36
636 691 2.514592 AGCGATGATGCGGTTGGG 60.515 61.111 0.00 0.00 39.14 4.12
640 695 0.464373 AATGGAAGCGATGATGCGGT 60.464 50.000 0.00 0.00 44.70 5.68
641 696 0.040692 CAATGGAAGCGATGATGCGG 60.041 55.000 0.00 0.00 40.67 5.69
642 697 0.040692 CCAATGGAAGCGATGATGCG 60.041 55.000 0.00 0.00 40.67 4.73
643 698 1.027357 ACCAATGGAAGCGATGATGC 58.973 50.000 6.16 0.00 0.00 3.91
644 699 3.788333 AAACCAATGGAAGCGATGATG 57.212 42.857 6.16 0.00 0.00 3.07
645 700 4.269183 TGTAAACCAATGGAAGCGATGAT 58.731 39.130 6.16 0.00 0.00 2.45
646 701 3.680490 TGTAAACCAATGGAAGCGATGA 58.320 40.909 6.16 0.00 0.00 2.92
647 702 3.440173 ACTGTAAACCAATGGAAGCGATG 59.560 43.478 6.16 0.00 0.00 3.84
648 703 3.686016 ACTGTAAACCAATGGAAGCGAT 58.314 40.909 6.16 0.00 0.00 4.58
649 704 3.134574 ACTGTAAACCAATGGAAGCGA 57.865 42.857 6.16 0.00 0.00 4.93
650 705 3.915437 AACTGTAAACCAATGGAAGCG 57.085 42.857 6.16 0.00 0.00 4.68
651 706 5.453567 AGAAACTGTAAACCAATGGAAGC 57.546 39.130 6.16 0.00 0.00 3.86
652 707 7.716612 AGAAAGAAACTGTAAACCAATGGAAG 58.283 34.615 6.16 0.00 0.00 3.46
653 708 7.654022 AGAAAGAAACTGTAAACCAATGGAA 57.346 32.000 6.16 0.00 0.00 3.53
654 709 8.754991 TTAGAAAGAAACTGTAAACCAATGGA 57.245 30.769 6.16 0.00 0.00 3.41
655 710 9.981114 ATTTAGAAAGAAACTGTAAACCAATGG 57.019 29.630 0.00 0.00 0.00 3.16
679 759 9.757227 TCAACTTTAAACCAATCGATTCAAATT 57.243 25.926 7.92 4.19 0.00 1.82
680 760 9.410556 CTCAACTTTAAACCAATCGATTCAAAT 57.589 29.630 7.92 0.00 0.00 2.32
681 761 8.625651 TCTCAACTTTAAACCAATCGATTCAAA 58.374 29.630 7.92 3.47 0.00 2.69
682 762 8.160521 TCTCAACTTTAAACCAATCGATTCAA 57.839 30.769 7.92 0.00 0.00 2.69
683 763 7.659799 TCTCTCAACTTTAAACCAATCGATTCA 59.340 33.333 7.92 0.00 0.00 2.57
684 764 8.029642 TCTCTCAACTTTAAACCAATCGATTC 57.970 34.615 7.92 0.00 0.00 2.52
685 765 7.878127 TCTCTCTCAACTTTAAACCAATCGATT 59.122 33.333 4.39 4.39 0.00 3.34
686 766 7.386851 TCTCTCTCAACTTTAAACCAATCGAT 58.613 34.615 0.00 0.00 0.00 3.59
687 767 6.755206 TCTCTCTCAACTTTAAACCAATCGA 58.245 36.000 0.00 0.00 0.00 3.59
688 768 7.385205 TCTTCTCTCTCAACTTTAAACCAATCG 59.615 37.037 0.00 0.00 0.00 3.34
689 769 8.608844 TCTTCTCTCTCAACTTTAAACCAATC 57.391 34.615 0.00 0.00 0.00 2.67
690 770 8.841300 GTTCTTCTCTCTCAACTTTAAACCAAT 58.159 33.333 0.00 0.00 0.00 3.16
691 771 7.011109 CGTTCTTCTCTCTCAACTTTAAACCAA 59.989 37.037 0.00 0.00 0.00 3.67
692 772 6.479001 CGTTCTTCTCTCTCAACTTTAAACCA 59.521 38.462 0.00 0.00 0.00 3.67
693 773 6.564312 GCGTTCTTCTCTCTCAACTTTAAACC 60.564 42.308 0.00 0.00 0.00 3.27
694 774 6.018994 TGCGTTCTTCTCTCTCAACTTTAAAC 60.019 38.462 0.00 0.00 0.00 2.01
695 775 6.046593 TGCGTTCTTCTCTCTCAACTTTAAA 58.953 36.000 0.00 0.00 0.00 1.52
696 776 5.597806 TGCGTTCTTCTCTCTCAACTTTAA 58.402 37.500 0.00 0.00 0.00 1.52
697 777 5.196341 TGCGTTCTTCTCTCTCAACTTTA 57.804 39.130 0.00 0.00 0.00 1.85
698 778 4.054671 CTGCGTTCTTCTCTCTCAACTTT 58.945 43.478 0.00 0.00 0.00 2.66
699 779 3.648009 CTGCGTTCTTCTCTCTCAACTT 58.352 45.455 0.00 0.00 0.00 2.66
700 780 2.609244 GCTGCGTTCTTCTCTCTCAACT 60.609 50.000 0.00 0.00 0.00 3.16
701 781 1.724082 GCTGCGTTCTTCTCTCTCAAC 59.276 52.381 0.00 0.00 0.00 3.18
702 782 1.341209 TGCTGCGTTCTTCTCTCTCAA 59.659 47.619 0.00 0.00 0.00 3.02
703 783 0.961753 TGCTGCGTTCTTCTCTCTCA 59.038 50.000 0.00 0.00 0.00 3.27
704 784 1.345410 GTGCTGCGTTCTTCTCTCTC 58.655 55.000 0.00 0.00 0.00 3.20
705 785 0.387878 CGTGCTGCGTTCTTCTCTCT 60.388 55.000 0.00 0.00 35.54 3.10
706 786 0.387367 TCGTGCTGCGTTCTTCTCTC 60.387 55.000 0.00 0.00 42.13 3.20
707 787 0.387878 CTCGTGCTGCGTTCTTCTCT 60.388 55.000 0.00 0.00 42.13 3.10
708 788 1.950098 GCTCGTGCTGCGTTCTTCTC 61.950 60.000 1.41 0.00 42.13 2.87
709 789 2.024319 GCTCGTGCTGCGTTCTTCT 61.024 57.895 1.41 0.00 42.13 2.85
710 790 2.472049 GCTCGTGCTGCGTTCTTC 59.528 61.111 1.41 0.00 42.13 2.87
728 808 3.646715 CAGGCACCGGGAAAGGGA 61.647 66.667 6.32 0.00 35.02 4.20
765 851 3.314553 TGCTGTACTTTACTCGCAAGAC 58.685 45.455 0.00 0.00 45.01 3.01
771 857 5.389516 GGAAACACATGCTGTACTTTACTCG 60.390 44.000 0.00 0.00 30.51 4.18
779 865 1.519408 ACGGGAAACACATGCTGTAC 58.481 50.000 0.00 0.00 30.51 2.90
782 868 1.336440 TCAAACGGGAAACACATGCTG 59.664 47.619 0.00 0.00 0.00 4.41
824 913 6.392353 CGTCAGATACTACGTATACTCCAG 57.608 45.833 0.00 0.00 34.48 3.86
888 980 2.380084 TAAGTAGGCAAAGCTGACGG 57.620 50.000 0.00 0.00 34.77 4.79
898 990 2.124411 GAGGTTGGGGATAAGTAGGCA 58.876 52.381 0.00 0.00 0.00 4.75
904 996 0.463833 GCCACGAGGTTGGGGATAAG 60.464 60.000 0.00 0.00 37.10 1.73
933 1029 3.254166 CCTGCTCAAAAATATCCGGATGG 59.746 47.826 27.55 10.78 0.00 3.51
1098 1241 3.801698 CATGATAGGGACTGGAACACTG 58.198 50.000 0.00 0.00 41.52 3.66
1099 1242 2.171448 GCATGATAGGGACTGGAACACT 59.829 50.000 0.00 0.00 41.52 3.55
1100 1243 2.565841 GCATGATAGGGACTGGAACAC 58.434 52.381 0.00 0.00 41.52 3.32
1102 1245 1.202818 GGGCATGATAGGGACTGGAAC 60.203 57.143 0.00 0.00 41.52 3.62
1103 1246 1.140312 GGGCATGATAGGGACTGGAA 58.860 55.000 0.00 0.00 41.52 3.53
1139 1327 2.764572 ACGTAGGGGAATTCGTCAGATT 59.235 45.455 0.00 0.00 30.71 2.40
1222 1410 2.262915 GAGGTCGGTGTGGCAGAG 59.737 66.667 0.00 0.00 0.00 3.35
1287 1475 2.600470 GCAAGGTTCACCCACCCC 60.600 66.667 0.00 0.00 37.58 4.95
1353 1547 2.421073 CGCCGCATGAATCCATCATTAT 59.579 45.455 0.00 0.00 46.85 1.28
1471 1703 2.107750 CTCACGCAGGATCGGCAT 59.892 61.111 8.47 0.00 0.00 4.40
1477 1709 4.827087 CCGCAGCTCACGCAGGAT 62.827 66.667 0.04 0.00 39.10 3.24
1877 2116 2.747446 GCTTAACCTTCATTTGCTCGGA 59.253 45.455 0.00 0.00 0.00 4.55
1896 2135 2.101415 GGGAAGCAACTGAAACAAAGCT 59.899 45.455 0.00 0.00 0.00 3.74
1962 2221 2.609299 TCAATGGCTCCCGTCCCA 60.609 61.111 0.00 0.00 35.21 4.37
2224 2493 2.045926 GTGATGCCGTGCTTCCCT 60.046 61.111 8.55 0.00 32.74 4.20
2452 2722 0.039256 CGCACCAACCCATTTGTGAG 60.039 55.000 0.00 0.00 32.71 3.51
2453 2723 0.753479 ACGCACCAACCCATTTGTGA 60.753 50.000 0.00 0.00 32.71 3.58
2566 2848 9.640974 CTTTTTGATGAGTAAAATGCACTTTTG 57.359 29.630 0.00 0.00 37.61 2.44
2582 2864 5.451798 GGTTGAAGTTGCCTCTTTTTGATGA 60.452 40.000 0.00 0.00 0.00 2.92
2583 2865 4.746611 GGTTGAAGTTGCCTCTTTTTGATG 59.253 41.667 0.00 0.00 0.00 3.07
2601 2885 6.160576 TCATCAATGTAGATCATCGGTTGA 57.839 37.500 0.00 0.00 39.12 3.18
2640 2924 8.636213 ACATCTTCAATTTGCCTTATCTATTGG 58.364 33.333 0.00 0.00 0.00 3.16
2651 2935 5.519722 CCGGTTATACATCTTCAATTTGCC 58.480 41.667 0.00 0.00 0.00 4.52
2924 3256 6.515272 AACGTTGATAAAGAAGCCATTGAT 57.485 33.333 0.00 0.00 0.00 2.57
2925 3257 5.957842 AACGTTGATAAAGAAGCCATTGA 57.042 34.783 0.00 0.00 0.00 2.57
2926 3258 6.640499 TCAAAACGTTGATAAAGAAGCCATTG 59.360 34.615 0.00 0.00 38.88 2.82
2950 3299 2.325761 ACACTAAGACGTCAACGCATC 58.674 47.619 19.50 0.00 44.43 3.91
2965 3314 0.178984 TGGTGGAGGTCACGACACTA 60.179 55.000 0.00 0.00 46.96 2.74
2984 3333 4.327680 GAGGTAACAATGAAGGTGCTTCT 58.672 43.478 0.00 0.00 39.30 2.85
3000 3349 1.597797 ATGAACGACGCGGGAGGTAA 61.598 55.000 12.47 0.00 0.00 2.85
3010 3359 4.087085 GCTTTGATGAAAACATGAACGACG 59.913 41.667 0.00 0.00 0.00 5.12
3218 3604 1.772971 TGGCAACATGGATGGTGGA 59.227 52.632 6.79 0.00 45.44 4.02
3270 3680 2.440796 AATGGGCGGCCACATGAG 60.441 61.111 35.30 0.00 0.00 2.90
3285 3695 2.963782 GAGGTACCATAGACGGTGGAAT 59.036 50.000 15.94 0.00 40.39 3.01
3301 3711 2.092429 GCCATGAGTGAAATGGGAGGTA 60.092 50.000 0.00 0.00 44.13 3.08


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

AutoCloner maintained by Alex Coulton.