Multiple sequence alignment - TraesCS4A01G421600

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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 TraesCS4A01G421600 chr4A 100.000 4123 0 0 1 4123 692086454 692090576 0.000000e+00 7614
1 TraesCS4A01G421600 chr4A 99.298 3276 20 1 851 4123 692164461 692167736 0.000000e+00 5919
2 TraesCS4A01G421600 chr4A 98.541 2330 26 2 851 3177 692260115 692262439 0.000000e+00 4108
3 TraesCS4A01G421600 chr4A 88.235 187 15 2 577 763 692164278 692164457 2.500000e-52 217
4 TraesCS4A01G421600 chr4A 88.235 187 14 3 577 763 692259933 692260111 2.500000e-52 217
5 TraesCS4A01G421600 chr7A 95.649 1471 52 6 1715 3180 33737074 33735611 0.000000e+00 2351
6 TraesCS4A01G421600 chr7A 89.510 1573 123 25 1833 3385 33985299 33983749 0.000000e+00 1953
7 TraesCS4A01G421600 chr7A 96.296 702 23 1 2445 3146 33664158 33663460 0.000000e+00 1149
8 TraesCS4A01G421600 chr7A 90.379 738 54 7 1833 2556 33971870 33971136 0.000000e+00 953
9 TraesCS4A01G421600 chr7A 92.012 676 41 11 1052 1719 33738574 33737904 0.000000e+00 937
10 TraesCS4A01G421600 chr7A 86.674 863 80 17 1575 2419 33666880 33666035 0.000000e+00 924
11 TraesCS4A01G421600 chr7A 85.591 694 47 21 845 1522 33972529 33971873 0.000000e+00 678
12 TraesCS4A01G421600 chr7A 87.338 616 47 13 846 1450 33679141 33678546 0.000000e+00 676
13 TraesCS4A01G421600 chr7A 85.923 547 75 2 8 554 83621692 83621148 2.140000e-162 582
14 TraesCS4A01G421600 chr7A 81.647 692 56 25 845 1522 33985936 33985302 3.680000e-140 508
15 TraesCS4A01G421600 chr7A 84.000 225 19 11 846 1059 33740886 33740668 2.510000e-47 200
16 TraesCS4A01G421600 chr7A 86.905 168 14 5 577 744 33679329 33679170 9.100000e-42 182
17 TraesCS4A01G421600 chr7A 95.062 81 3 1 3986 4065 53263381 53263461 4.330000e-25 126
18 TraesCS4A01G421600 chr7D 89.088 1677 130 30 1833 3488 33465141 33463497 0.000000e+00 2034
19 TraesCS4A01G421600 chr7D 85.591 694 47 21 845 1522 33465800 33465144 0.000000e+00 678
20 TraesCS4A01G421600 chr7D 86.909 550 71 1 5 554 80797815 80797267 2.110000e-172 616
21 TraesCS4A01G421600 chr7D 85.636 550 77 2 5 554 290865503 290864956 9.940000e-161 577
22 TraesCS4A01G421600 chr1D 86.996 546 68 3 5 549 293617119 293617662 2.720000e-171 612
23 TraesCS4A01G421600 chr1A 86.876 541 69 2 5 545 538801485 538802023 4.560000e-169 604
24 TraesCS4A01G421600 chr1B 85.981 535 68 6 18 548 679234302 679233771 2.150000e-157 566
25 TraesCS4A01G421600 chr2B 86.207 522 69 2 5 524 98290845 98291365 2.780000e-156 562
26 TraesCS4A01G421600 chr2B 85.502 538 72 5 12 548 690213174 690213706 1.290000e-154 556
27 TraesCS4A01G421600 chr2D 85.688 538 70 3 5 542 106963115 106962585 1.000000e-155 560
28 TraesCS4A01G421600 chrUn 95.062 81 3 1 3986 4065 52409505 52409425 4.330000e-25 126
29 TraesCS4A01G421600 chr6B 95.062 81 3 1 3986 4065 267020722 267020802 4.330000e-25 126
30 TraesCS4A01G421600 chr6A 95.062 81 3 1 3986 4065 32557813 32557733 4.330000e-25 126
31 TraesCS4A01G421600 chr5B 95.062 81 3 1 3986 4065 259549870 259549950 4.330000e-25 126
32 TraesCS4A01G421600 chr4B 95.062 81 3 1 3986 4065 18970542 18970622 4.330000e-25 126
33 TraesCS4A01G421600 chr4B 95.062 81 3 1 3986 4065 95680739 95680819 4.330000e-25 126
34 TraesCS4A01G421600 chr4B 90.426 94 7 2 3974 4065 599464413 599464506 5.600000e-24 122


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 TraesCS4A01G421600 chr4A 692086454 692090576 4122 False 7614.000000 7614 100.000000 1 4123 1 chr4A.!!$F1 4122
1 TraesCS4A01G421600 chr4A 692164278 692167736 3458 False 3068.000000 5919 93.766500 577 4123 2 chr4A.!!$F2 3546
2 TraesCS4A01G421600 chr4A 692259933 692262439 2506 False 2162.500000 4108 93.388000 577 3177 2 chr4A.!!$F3 2600
3 TraesCS4A01G421600 chr7A 33983749 33985936 2187 True 1230.500000 1953 85.578500 845 3385 2 chr7A.!!$R6 2540
4 TraesCS4A01G421600 chr7A 33735611 33740886 5275 True 1162.666667 2351 90.553667 846 3180 3 chr7A.!!$R4 2334
5 TraesCS4A01G421600 chr7A 33663460 33666880 3420 True 1036.500000 1149 91.485000 1575 3146 2 chr7A.!!$R2 1571
6 TraesCS4A01G421600 chr7A 33971136 33972529 1393 True 815.500000 953 87.985000 845 2556 2 chr7A.!!$R5 1711
7 TraesCS4A01G421600 chr7A 83621148 83621692 544 True 582.000000 582 85.923000 8 554 1 chr7A.!!$R1 546
8 TraesCS4A01G421600 chr7A 33678546 33679329 783 True 429.000000 676 87.121500 577 1450 2 chr7A.!!$R3 873
9 TraesCS4A01G421600 chr7D 33463497 33465800 2303 True 1356.000000 2034 87.339500 845 3488 2 chr7D.!!$R3 2643
10 TraesCS4A01G421600 chr7D 80797267 80797815 548 True 616.000000 616 86.909000 5 554 1 chr7D.!!$R1 549
11 TraesCS4A01G421600 chr7D 290864956 290865503 547 True 577.000000 577 85.636000 5 554 1 chr7D.!!$R2 549
12 TraesCS4A01G421600 chr1D 293617119 293617662 543 False 612.000000 612 86.996000 5 549 1 chr1D.!!$F1 544
13 TraesCS4A01G421600 chr1A 538801485 538802023 538 False 604.000000 604 86.876000 5 545 1 chr1A.!!$F1 540
14 TraesCS4A01G421600 chr1B 679233771 679234302 531 True 566.000000 566 85.981000 18 548 1 chr1B.!!$R1 530
15 TraesCS4A01G421600 chr2B 98290845 98291365 520 False 562.000000 562 86.207000 5 524 1 chr2B.!!$F1 519
16 TraesCS4A01G421600 chr2B 690213174 690213706 532 False 556.000000 556 85.502000 12 548 1 chr2B.!!$F2 536
17 TraesCS4A01G421600 chr2D 106962585 106963115 530 True 560.000000 560 85.688000 5 542 1 chr2D.!!$R1 537

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
824 829 0.036199 ACCCGCACGGTTGCTATAAA 60.036 50.000 8.49 0.0 45.36 1.40 F
825 830 1.611148 ACCCGCACGGTTGCTATAAAA 60.611 47.619 8.49 0.0 45.36 1.52 F
2230 5261 0.611714 AACCTTGTCGACGGGCTATT 59.388 50.000 22.04 10.3 0.00 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 5217 2.432874 TCTCTCTTTTGTCGACCCAACA 59.567 45.455 14.12 0.0 0.00 3.33 R
2757 7650 6.569179 AACCGCAGTTATTGTAAGTGAATT 57.431 33.333 8.35 0.0 33.27 2.17 R
3541 8444 2.113139 CCACTCCGTTGGCACCTT 59.887 61.111 0.00 0.0 0.00 3.50 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 6.059484 TCAACCTTTGGTCGAAGAAATACTT 58.941 36.000 0.00 0.00 39.69 2.24
50 51 9.444600 AATACTTCAAAAGCTTCGGTAAAGATA 57.555 29.630 0.00 0.00 37.12 1.98
207 210 4.723309 GGAATGATCCCTTAGAAGTGCAT 58.277 43.478 0.00 0.00 40.10 3.96
229 232 5.196341 TGCCGTCGAATCACTATATCTTT 57.804 39.130 0.00 0.00 0.00 2.52
232 235 6.016527 TGCCGTCGAATCACTATATCTTTACT 60.017 38.462 0.00 0.00 0.00 2.24
325 330 9.650539 CATAAACTCATCAGATCCGAATAATCT 57.349 33.333 0.00 0.00 33.74 2.40
349 354 4.060038 TCTGCGAGAACAGAAAACTCTT 57.940 40.909 0.00 0.00 43.59 2.85
386 391 3.065925 CGCCAAAAGGATGAGAGGAAATC 59.934 47.826 0.00 0.00 0.00 2.17
396 401 4.230314 TGAGAGGAAATCTATTCTCGCG 57.770 45.455 0.00 0.00 38.84 5.87
403 408 6.570692 AGGAAATCTATTCTCGCGAAACTAA 58.429 36.000 11.33 2.62 31.91 2.24
404 409 7.210873 AGGAAATCTATTCTCGCGAAACTAAT 58.789 34.615 11.33 10.22 31.91 1.73
408 413 9.915629 AAATCTATTCTCGCGAAACTAATATCT 57.084 29.630 11.33 0.77 31.91 1.98
458 463 0.466124 CTTGAAGATCCGAGGTCCCC 59.534 60.000 0.00 0.00 0.00 4.81
459 464 0.981277 TTGAAGATCCGAGGTCCCCC 60.981 60.000 0.00 0.00 0.00 5.40
474 479 3.775654 CCCCCACCTCTCAGCGTC 61.776 72.222 0.00 0.00 0.00 5.19
475 480 2.997315 CCCCACCTCTCAGCGTCA 60.997 66.667 0.00 0.00 0.00 4.35
476 481 2.583441 CCCCACCTCTCAGCGTCAA 61.583 63.158 0.00 0.00 0.00 3.18
477 482 1.079543 CCCACCTCTCAGCGTCAAG 60.080 63.158 0.00 0.00 0.00 3.02
478 483 1.536073 CCCACCTCTCAGCGTCAAGA 61.536 60.000 0.00 0.00 0.00 3.02
479 484 0.534412 CCACCTCTCAGCGTCAAGAT 59.466 55.000 0.00 0.00 0.00 2.40
480 485 1.751351 CCACCTCTCAGCGTCAAGATA 59.249 52.381 0.00 0.00 0.00 1.98
481 486 2.223688 CCACCTCTCAGCGTCAAGATAG 60.224 54.545 0.00 0.00 0.00 2.08
482 487 1.407258 ACCTCTCAGCGTCAAGATAGC 59.593 52.381 0.00 0.00 0.00 2.97
483 488 1.406898 CCTCTCAGCGTCAAGATAGCA 59.593 52.381 0.00 0.00 0.00 3.49
484 489 2.543445 CCTCTCAGCGTCAAGATAGCAG 60.543 54.545 0.00 0.00 0.00 4.24
485 490 1.202348 TCTCAGCGTCAAGATAGCAGC 60.202 52.381 0.00 0.00 0.00 5.25
486 491 0.179100 TCAGCGTCAAGATAGCAGCC 60.179 55.000 0.00 0.00 0.00 4.85
487 492 1.227089 AGCGTCAAGATAGCAGCCG 60.227 57.895 0.00 0.00 0.00 5.52
488 493 2.240500 GCGTCAAGATAGCAGCCGG 61.241 63.158 0.00 0.00 0.00 6.13
489 494 1.437573 CGTCAAGATAGCAGCCGGA 59.562 57.895 5.05 0.00 0.00 5.14
490 495 0.596083 CGTCAAGATAGCAGCCGGAG 60.596 60.000 5.05 0.00 0.00 4.63
517 522 4.417426 GGGACCTAAATTTCTCGGATGA 57.583 45.455 0.00 0.00 0.00 2.92
518 523 4.127907 GGGACCTAAATTTCTCGGATGAC 58.872 47.826 0.00 0.00 0.00 3.06
519 524 4.383770 GGGACCTAAATTTCTCGGATGACA 60.384 45.833 0.00 0.00 0.00 3.58
520 525 5.183228 GGACCTAAATTTCTCGGATGACAA 58.817 41.667 0.00 0.00 0.00 3.18
521 526 5.064834 GGACCTAAATTTCTCGGATGACAAC 59.935 44.000 0.00 0.00 0.00 3.32
522 527 4.630069 ACCTAAATTTCTCGGATGACAACG 59.370 41.667 0.00 0.00 0.00 4.10
523 528 4.868171 CCTAAATTTCTCGGATGACAACGA 59.132 41.667 0.00 5.63 37.56 3.85
524 529 4.663636 AAATTTCTCGGATGACAACGAC 57.336 40.909 1.96 0.00 35.04 4.34
525 530 1.693467 TTTCTCGGATGACAACGACG 58.307 50.000 0.00 0.00 35.04 5.12
526 531 0.109458 TTCTCGGATGACAACGACGG 60.109 55.000 0.00 0.00 35.04 4.79
527 532 2.126228 TCGGATGACAACGACGGC 60.126 61.111 0.00 0.00 33.69 5.68
528 533 3.541831 CGGATGACAACGACGGCG 61.542 66.667 10.39 10.39 44.79 6.46
529 534 3.186047 GGATGACAACGACGGCGG 61.186 66.667 18.49 0.00 43.17 6.13
530 535 3.849953 GATGACAACGACGGCGGC 61.850 66.667 18.49 7.52 43.17 6.53
550 555 1.886886 GGCACGAGAAAACCCTAACA 58.113 50.000 0.00 0.00 0.00 2.41
551 556 1.804748 GGCACGAGAAAACCCTAACAG 59.195 52.381 0.00 0.00 0.00 3.16
552 557 2.549349 GGCACGAGAAAACCCTAACAGA 60.549 50.000 0.00 0.00 0.00 3.41
553 558 3.335579 GCACGAGAAAACCCTAACAGAT 58.664 45.455 0.00 0.00 0.00 2.90
554 559 4.501071 GCACGAGAAAACCCTAACAGATA 58.499 43.478 0.00 0.00 0.00 1.98
555 560 4.567159 GCACGAGAAAACCCTAACAGATAG 59.433 45.833 0.00 0.00 0.00 2.08
556 561 5.623824 GCACGAGAAAACCCTAACAGATAGA 60.624 44.000 0.00 0.00 33.04 1.98
557 562 6.395629 CACGAGAAAACCCTAACAGATAGAA 58.604 40.000 0.00 0.00 33.04 2.10
558 563 6.531948 CACGAGAAAACCCTAACAGATAGAAG 59.468 42.308 0.00 0.00 33.04 2.85
559 564 6.436532 ACGAGAAAACCCTAACAGATAGAAGA 59.563 38.462 0.00 0.00 33.04 2.87
560 565 7.039223 ACGAGAAAACCCTAACAGATAGAAGAA 60.039 37.037 0.00 0.00 33.04 2.52
561 566 7.489757 CGAGAAAACCCTAACAGATAGAAGAAG 59.510 40.741 0.00 0.00 33.04 2.85
562 567 8.437274 AGAAAACCCTAACAGATAGAAGAAGA 57.563 34.615 0.00 0.00 33.04 2.87
563 568 8.881262 AGAAAACCCTAACAGATAGAAGAAGAA 58.119 33.333 0.00 0.00 33.04 2.52
564 569 9.503399 GAAAACCCTAACAGATAGAAGAAGAAA 57.497 33.333 0.00 0.00 33.04 2.52
568 573 8.414778 ACCCTAACAGATAGAAGAAGAAATACG 58.585 37.037 0.00 0.00 33.04 3.06
569 574 8.414778 CCCTAACAGATAGAAGAAGAAATACGT 58.585 37.037 0.00 0.00 33.04 3.57
572 577 8.859517 AACAGATAGAAGAAGAAATACGTAGC 57.140 34.615 0.08 0.00 0.00 3.58
573 578 7.997482 ACAGATAGAAGAAGAAATACGTAGCA 58.003 34.615 0.08 0.00 0.00 3.49
574 579 8.467598 ACAGATAGAAGAAGAAATACGTAGCAA 58.532 33.333 0.08 0.00 0.00 3.91
575 580 8.747666 CAGATAGAAGAAGAAATACGTAGCAAC 58.252 37.037 0.08 0.00 0.00 4.17
584 589 9.601971 GAAGAAATACGTAGCAACACATTTTTA 57.398 29.630 0.08 0.00 0.00 1.52
632 637 7.806690 ACATGATCGTAATATTCAATTTCGGG 58.193 34.615 0.00 0.00 0.00 5.14
642 647 4.487714 TTCAATTTCGGGCTGACTATCT 57.512 40.909 0.00 0.00 0.00 1.98
643 648 5.607939 TTCAATTTCGGGCTGACTATCTA 57.392 39.130 0.00 0.00 0.00 1.98
644 649 5.808366 TCAATTTCGGGCTGACTATCTAT 57.192 39.130 0.00 0.00 0.00 1.98
645 650 5.784177 TCAATTTCGGGCTGACTATCTATC 58.216 41.667 0.00 0.00 0.00 2.08
646 651 5.304357 TCAATTTCGGGCTGACTATCTATCA 59.696 40.000 0.00 0.00 0.00 2.15
647 652 4.585955 TTTCGGGCTGACTATCTATCAC 57.414 45.455 0.00 0.00 0.00 3.06
688 693 2.768022 CCCATTAGTCCCCTGCCCC 61.768 68.421 0.00 0.00 0.00 5.80
725 730 1.172180 GCCCATTAGCCGCTATTGCA 61.172 55.000 14.32 0.00 39.64 4.08
727 732 1.267806 CCCATTAGCCGCTATTGCAAG 59.732 52.381 14.32 0.00 39.64 4.01
745 750 1.446966 GGAGTCAGCAGCGAAGTCC 60.447 63.158 7.86 7.86 0.00 3.85
755 760 2.125512 CGAAGTCCCGCCCAAGAG 60.126 66.667 0.00 0.00 0.00 2.85
763 768 1.265454 CCCGCCCAAGAGGAAGTAGT 61.265 60.000 0.00 0.00 38.24 2.73
765 770 1.409427 CCGCCCAAGAGGAAGTAGTAG 59.591 57.143 0.00 0.00 38.24 2.57
766 771 2.376109 CGCCCAAGAGGAAGTAGTAGA 58.624 52.381 0.00 0.00 38.24 2.59
767 772 2.359531 CGCCCAAGAGGAAGTAGTAGAG 59.640 54.545 0.00 0.00 38.24 2.43
768 773 3.367321 GCCCAAGAGGAAGTAGTAGAGT 58.633 50.000 0.00 0.00 38.24 3.24
769 774 3.770388 GCCCAAGAGGAAGTAGTAGAGTT 59.230 47.826 0.00 0.00 38.24 3.01
770 775 4.382147 GCCCAAGAGGAAGTAGTAGAGTTG 60.382 50.000 0.00 0.00 38.24 3.16
771 776 4.382147 CCCAAGAGGAAGTAGTAGAGTTGC 60.382 50.000 0.00 0.00 38.24 4.17
772 777 4.464597 CCAAGAGGAAGTAGTAGAGTTGCT 59.535 45.833 0.00 0.00 41.53 3.91
777 782 6.420913 AGGAAGTAGTAGAGTTGCTCAAAA 57.579 37.500 0.00 0.00 34.20 2.44
778 783 6.827727 AGGAAGTAGTAGAGTTGCTCAAAAA 58.172 36.000 0.00 0.00 34.20 1.94
804 809 6.769134 AAAAGAGAGAGAGGAAGTAGTAGC 57.231 41.667 0.00 0.00 0.00 3.58
805 810 5.444744 AAGAGAGAGAGGAAGTAGTAGCA 57.555 43.478 0.00 0.00 0.00 3.49
806 811 4.777463 AGAGAGAGAGGAAGTAGTAGCAC 58.223 47.826 0.00 0.00 0.00 4.40
807 812 3.881089 GAGAGAGAGGAAGTAGTAGCACC 59.119 52.174 0.00 0.00 0.00 5.01
808 813 2.953648 GAGAGAGGAAGTAGTAGCACCC 59.046 54.545 0.00 0.00 0.00 4.61
809 814 1.677052 GAGAGGAAGTAGTAGCACCCG 59.323 57.143 0.00 0.00 0.00 5.28
810 815 0.102663 GAGGAAGTAGTAGCACCCGC 59.897 60.000 0.00 0.00 38.99 6.13
811 816 0.613853 AGGAAGTAGTAGCACCCGCA 60.614 55.000 0.00 0.00 42.27 5.69
812 817 0.459759 GGAAGTAGTAGCACCCGCAC 60.460 60.000 0.00 0.00 42.27 5.34
813 818 0.801067 GAAGTAGTAGCACCCGCACG 60.801 60.000 0.00 0.00 42.27 5.34
814 819 2.202703 GTAGTAGCACCCGCACGG 60.203 66.667 1.02 1.02 42.27 4.94
816 821 2.277591 TAGTAGCACCCGCACGGTT 61.278 57.895 8.49 0.00 45.36 4.44
817 822 2.495366 TAGTAGCACCCGCACGGTTG 62.495 60.000 8.49 5.17 45.36 3.77
821 826 2.435938 CACCCGCACGGTTGCTAT 60.436 61.111 8.49 0.00 45.36 2.97
822 827 1.153529 CACCCGCACGGTTGCTATA 60.154 57.895 8.49 0.00 45.36 1.31
823 828 0.741574 CACCCGCACGGTTGCTATAA 60.742 55.000 8.49 0.00 45.36 0.98
824 829 0.036199 ACCCGCACGGTTGCTATAAA 60.036 50.000 8.49 0.00 45.36 1.40
825 830 1.611148 ACCCGCACGGTTGCTATAAAA 60.611 47.619 8.49 0.00 45.36 1.52
826 831 3.134786 ACCCGCACGGTTGCTATAAAAA 61.135 45.455 8.49 0.00 45.36 1.94
960 986 2.504367 CTCCTTTCTTCGCCTTTTCCA 58.496 47.619 0.00 0.00 0.00 3.53
2070 5097 6.800072 AGTCTTCCTTGGGTTCTATTCTAG 57.200 41.667 0.00 0.00 0.00 2.43
2230 5261 0.611714 AACCTTGTCGACGGGCTATT 59.388 50.000 22.04 10.30 0.00 1.73
3376 8278 3.974871 TTGGTTTTTGTCGCTTAGTCC 57.025 42.857 0.00 0.00 0.00 3.85
3428 8330 2.745698 CACTGCTCCTGCCACTCA 59.254 61.111 0.00 0.00 38.71 3.41
3541 8444 1.592400 CGGCAAGTAGGACACGAGGA 61.592 60.000 0.00 0.00 0.00 3.71
3669 8572 2.295885 CTTGATGGAATGCACTCCCTC 58.704 52.381 12.49 12.22 34.22 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.556915 TCTTCGACCAAAGGTTGATATTGT 58.443 37.500 6.94 0.00 44.60 2.71
1 2 6.494893 TTCTTCGACCAAAGGTTGATATTG 57.505 37.500 6.94 0.11 44.60 1.90
2 3 7.703058 ATTTCTTCGACCAAAGGTTGATATT 57.297 32.000 6.94 0.00 44.60 1.28
3 4 8.047310 AGTATTTCTTCGACCAAAGGTTGATAT 58.953 33.333 6.94 2.76 44.60 1.63
30 31 7.380536 TGTAGTATCTTTACCGAAGCTTTTGA 58.619 34.615 0.00 0.00 35.24 2.69
36 37 6.759827 TCCAATTGTAGTATCTTTACCGAAGC 59.240 38.462 4.43 0.00 35.24 3.86
50 51 3.788227 TTGCTCCAGTCCAATTGTAGT 57.212 42.857 4.43 0.00 0.00 2.73
140 141 7.414429 CGATCAAGACTTATCATCTTTTTGGCA 60.414 37.037 0.00 0.00 34.08 4.92
141 142 6.909357 CGATCAAGACTTATCATCTTTTTGGC 59.091 38.462 0.00 0.00 34.08 4.52
187 189 3.887716 GCATGCACTTCTAAGGGATCATT 59.112 43.478 14.21 0.00 0.00 2.57
207 210 4.848562 AAGATATAGTGATTCGACGGCA 57.151 40.909 0.00 0.00 0.00 5.69
229 232 4.937201 ATCTTGCATCGACACCATAGTA 57.063 40.909 0.00 0.00 0.00 1.82
232 235 4.332543 GTGAAATCTTGCATCGACACCATA 59.667 41.667 0.00 0.00 0.00 2.74
325 330 3.990469 GAGTTTTCTGTTCTCGCAGATCA 59.010 43.478 0.00 0.00 43.99 2.92
349 354 4.312052 GCGGTGCCATGAGGTTAA 57.688 55.556 0.00 0.00 37.19 2.01
396 401 9.784680 TCAACGTCTAGTGAAGATATTAGTTTC 57.215 33.333 0.00 0.00 36.36 2.78
403 408 6.315642 TCTTCGTCAACGTCTAGTGAAGATAT 59.684 38.462 13.03 0.00 34.95 1.63
404 409 5.640783 TCTTCGTCAACGTCTAGTGAAGATA 59.359 40.000 13.03 1.39 34.95 1.98
407 412 4.143194 TCTTCGTCAACGTCTAGTGAAG 57.857 45.455 2.09 9.79 40.80 3.02
408 413 4.201940 TGTTCTTCGTCAACGTCTAGTGAA 60.202 41.667 2.09 0.00 40.80 3.18
458 463 2.513026 CTTGACGCTGAGAGGTGGGG 62.513 65.000 0.00 0.00 0.00 4.96
459 464 1.079543 CTTGACGCTGAGAGGTGGG 60.080 63.158 0.00 0.00 0.00 4.61
460 465 0.534412 ATCTTGACGCTGAGAGGTGG 59.466 55.000 0.00 0.00 0.00 4.61
461 466 2.797792 GCTATCTTGACGCTGAGAGGTG 60.798 54.545 0.00 0.00 0.00 4.00
462 467 1.407258 GCTATCTTGACGCTGAGAGGT 59.593 52.381 0.00 0.00 0.00 3.85
463 468 1.406898 TGCTATCTTGACGCTGAGAGG 59.593 52.381 0.00 0.00 0.00 3.69
464 469 2.730069 CTGCTATCTTGACGCTGAGAG 58.270 52.381 0.00 0.00 0.00 3.20
465 470 1.202348 GCTGCTATCTTGACGCTGAGA 60.202 52.381 0.00 0.00 0.00 3.27
466 471 1.207390 GCTGCTATCTTGACGCTGAG 58.793 55.000 0.00 0.00 0.00 3.35
467 472 0.179100 GGCTGCTATCTTGACGCTGA 60.179 55.000 0.00 0.00 0.00 4.26
468 473 1.485838 CGGCTGCTATCTTGACGCTG 61.486 60.000 0.00 0.00 0.00 5.18
469 474 1.227089 CGGCTGCTATCTTGACGCT 60.227 57.895 0.00 0.00 0.00 5.07
470 475 2.240500 CCGGCTGCTATCTTGACGC 61.241 63.158 0.00 0.00 0.00 5.19
471 476 0.596083 CTCCGGCTGCTATCTTGACG 60.596 60.000 0.00 0.00 0.00 4.35
472 477 0.249657 CCTCCGGCTGCTATCTTGAC 60.250 60.000 0.00 0.00 0.00 3.18
473 478 0.687757 ACCTCCGGCTGCTATCTTGA 60.688 55.000 0.00 0.00 0.00 3.02
474 479 1.040646 TACCTCCGGCTGCTATCTTG 58.959 55.000 0.00 0.00 0.00 3.02
475 480 1.689273 CTTACCTCCGGCTGCTATCTT 59.311 52.381 0.00 0.00 0.00 2.40
476 481 1.333177 CTTACCTCCGGCTGCTATCT 58.667 55.000 0.00 0.00 0.00 1.98
477 482 0.318762 CCTTACCTCCGGCTGCTATC 59.681 60.000 0.00 0.00 0.00 2.08
478 483 1.122019 CCCTTACCTCCGGCTGCTAT 61.122 60.000 0.00 0.00 0.00 2.97
479 484 1.760875 CCCTTACCTCCGGCTGCTA 60.761 63.158 0.00 0.00 0.00 3.49
480 485 3.083997 CCCTTACCTCCGGCTGCT 61.084 66.667 0.00 0.00 0.00 4.24
481 486 4.176752 CCCCTTACCTCCGGCTGC 62.177 72.222 0.00 0.00 0.00 5.25
482 487 2.365105 TCCCCTTACCTCCGGCTG 60.365 66.667 0.00 0.00 0.00 4.85
483 488 2.365237 GTCCCCTTACCTCCGGCT 60.365 66.667 0.00 0.00 0.00 5.52
484 489 3.477346 GGTCCCCTTACCTCCGGC 61.477 72.222 0.00 0.00 36.53 6.13
490 495 4.449131 CGAGAAATTTAGGTCCCCTTACC 58.551 47.826 0.00 0.00 40.06 2.85
491 496 4.162888 TCCGAGAAATTTAGGTCCCCTTAC 59.837 45.833 0.00 0.00 34.61 2.34
492 497 4.364470 TCCGAGAAATTTAGGTCCCCTTA 58.636 43.478 0.00 0.00 34.61 2.69
493 498 3.187112 TCCGAGAAATTTAGGTCCCCTT 58.813 45.455 0.00 0.00 34.61 3.95
494 499 2.841795 TCCGAGAAATTTAGGTCCCCT 58.158 47.619 0.00 0.00 37.71 4.79
495 500 3.135895 TCATCCGAGAAATTTAGGTCCCC 59.864 47.826 0.00 0.00 0.00 4.81
496 501 4.127907 GTCATCCGAGAAATTTAGGTCCC 58.872 47.826 0.00 0.00 0.00 4.46
497 502 4.766375 TGTCATCCGAGAAATTTAGGTCC 58.234 43.478 0.00 0.00 0.00 4.46
498 503 5.220416 CGTTGTCATCCGAGAAATTTAGGTC 60.220 44.000 0.00 0.00 0.00 3.85
499 504 4.630069 CGTTGTCATCCGAGAAATTTAGGT 59.370 41.667 0.00 0.00 0.00 3.08
500 505 4.868171 TCGTTGTCATCCGAGAAATTTAGG 59.132 41.667 0.00 0.00 0.00 2.69
501 506 5.498700 CGTCGTTGTCATCCGAGAAATTTAG 60.499 44.000 0.00 0.00 33.10 1.85
502 507 4.325204 CGTCGTTGTCATCCGAGAAATTTA 59.675 41.667 0.00 0.00 33.10 1.40
503 508 3.122948 CGTCGTTGTCATCCGAGAAATTT 59.877 43.478 0.00 0.00 33.10 1.82
504 509 2.666508 CGTCGTTGTCATCCGAGAAATT 59.333 45.455 0.00 0.00 33.10 1.82
505 510 2.259618 CGTCGTTGTCATCCGAGAAAT 58.740 47.619 0.00 0.00 33.10 2.17
506 511 1.667756 CCGTCGTTGTCATCCGAGAAA 60.668 52.381 0.00 0.00 33.10 2.52
507 512 0.109458 CCGTCGTTGTCATCCGAGAA 60.109 55.000 0.00 0.00 33.10 2.87
508 513 1.504900 CCGTCGTTGTCATCCGAGA 59.495 57.895 0.00 0.00 33.10 4.04
509 514 2.158959 GCCGTCGTTGTCATCCGAG 61.159 63.158 0.00 0.00 33.10 4.63
510 515 2.126228 GCCGTCGTTGTCATCCGA 60.126 61.111 0.00 0.00 0.00 4.55
511 516 3.541831 CGCCGTCGTTGTCATCCG 61.542 66.667 0.00 0.00 0.00 4.18
512 517 3.186047 CCGCCGTCGTTGTCATCC 61.186 66.667 0.00 0.00 0.00 3.51
513 518 3.849953 GCCGCCGTCGTTGTCATC 61.850 66.667 0.00 0.00 0.00 2.92
526 531 4.736631 GTTTTCTCGTGCCGCCGC 62.737 66.667 0.00 0.00 0.00 6.53
527 532 4.084888 GGTTTTCTCGTGCCGCCG 62.085 66.667 0.00 0.00 0.00 6.46
528 533 2.791501 TAGGGTTTTCTCGTGCCGCC 62.792 60.000 0.00 0.00 0.00 6.13
529 534 0.952010 TTAGGGTTTTCTCGTGCCGC 60.952 55.000 0.00 0.00 0.00 6.53
530 535 0.794473 GTTAGGGTTTTCTCGTGCCG 59.206 55.000 0.00 0.00 0.00 5.69
531 536 1.804748 CTGTTAGGGTTTTCTCGTGCC 59.195 52.381 0.00 0.00 0.00 5.01
532 537 2.762745 TCTGTTAGGGTTTTCTCGTGC 58.237 47.619 0.00 0.00 0.00 5.34
533 538 5.962433 TCTATCTGTTAGGGTTTTCTCGTG 58.038 41.667 0.00 0.00 0.00 4.35
534 539 6.436532 TCTTCTATCTGTTAGGGTTTTCTCGT 59.563 38.462 0.00 0.00 0.00 4.18
535 540 6.864342 TCTTCTATCTGTTAGGGTTTTCTCG 58.136 40.000 0.00 0.00 0.00 4.04
536 541 8.532819 TCTTCTTCTATCTGTTAGGGTTTTCTC 58.467 37.037 0.00 0.00 0.00 2.87
537 542 8.437274 TCTTCTTCTATCTGTTAGGGTTTTCT 57.563 34.615 0.00 0.00 0.00 2.52
538 543 9.503399 TTTCTTCTTCTATCTGTTAGGGTTTTC 57.497 33.333 0.00 0.00 0.00 2.29
542 547 8.414778 CGTATTTCTTCTTCTATCTGTTAGGGT 58.585 37.037 0.00 0.00 0.00 4.34
543 548 8.414778 ACGTATTTCTTCTTCTATCTGTTAGGG 58.585 37.037 0.00 0.00 0.00 3.53
546 551 9.947669 GCTACGTATTTCTTCTTCTATCTGTTA 57.052 33.333 0.00 0.00 0.00 2.41
547 552 8.467598 TGCTACGTATTTCTTCTTCTATCTGTT 58.532 33.333 0.00 0.00 0.00 3.16
548 553 7.997482 TGCTACGTATTTCTTCTTCTATCTGT 58.003 34.615 0.00 0.00 0.00 3.41
549 554 8.747666 GTTGCTACGTATTTCTTCTTCTATCTG 58.252 37.037 0.00 0.00 0.00 2.90
550 555 8.467598 TGTTGCTACGTATTTCTTCTTCTATCT 58.532 33.333 0.00 0.00 0.00 1.98
551 556 8.533153 GTGTTGCTACGTATTTCTTCTTCTATC 58.467 37.037 0.00 0.00 0.00 2.08
552 557 8.033038 TGTGTTGCTACGTATTTCTTCTTCTAT 58.967 33.333 0.00 0.00 0.00 1.98
553 558 7.372714 TGTGTTGCTACGTATTTCTTCTTCTA 58.627 34.615 0.00 0.00 0.00 2.10
554 559 6.220930 TGTGTTGCTACGTATTTCTTCTTCT 58.779 36.000 0.00 0.00 0.00 2.85
555 560 6.462073 TGTGTTGCTACGTATTTCTTCTTC 57.538 37.500 0.00 0.00 0.00 2.87
556 561 7.435068 AATGTGTTGCTACGTATTTCTTCTT 57.565 32.000 0.00 0.00 0.00 2.52
557 562 7.435068 AAATGTGTTGCTACGTATTTCTTCT 57.565 32.000 0.00 0.00 0.00 2.85
558 563 8.502161 AAAAATGTGTTGCTACGTATTTCTTC 57.498 30.769 10.98 0.00 0.00 2.87
563 568 9.997482 CCTAATAAAAATGTGTTGCTACGTATT 57.003 29.630 0.00 0.00 0.00 1.89
564 569 9.386010 TCCTAATAAAAATGTGTTGCTACGTAT 57.614 29.630 0.00 0.00 0.00 3.06
565 570 8.774890 TCCTAATAAAAATGTGTTGCTACGTA 57.225 30.769 0.00 0.00 0.00 3.57
566 571 7.675962 TCCTAATAAAAATGTGTTGCTACGT 57.324 32.000 0.00 0.00 0.00 3.57
567 572 8.234546 ACTTCCTAATAAAAATGTGTTGCTACG 58.765 33.333 0.00 0.00 0.00 3.51
568 573 9.908152 AACTTCCTAATAAAAATGTGTTGCTAC 57.092 29.630 0.00 0.00 0.00 3.58
646 651 9.755804 GGGCTTTCTACTAGTATTATTTTACGT 57.244 33.333 2.33 0.00 0.00 3.57
647 652 9.754382 TGGGCTTTCTACTAGTATTATTTTACG 57.246 33.333 2.33 0.00 0.00 3.18
688 693 2.347731 GGCTTTCTACTTCTGAACCCG 58.652 52.381 0.00 0.00 0.00 5.28
696 701 2.872858 CGGCTAATGGGCTTTCTACTTC 59.127 50.000 0.00 0.00 38.46 3.01
725 730 0.037790 GACTTCGCTGCTGACTCCTT 60.038 55.000 0.00 0.00 0.00 3.36
727 732 1.446966 GGACTTCGCTGCTGACTCC 60.447 63.158 0.00 0.76 0.00 3.85
745 750 1.409427 CTACTACTTCCTCTTGGGCGG 59.591 57.143 0.00 0.00 34.39 6.13
751 756 5.326069 TGAGCAACTCTACTACTTCCTCTT 58.674 41.667 0.00 0.00 0.00 2.85
752 757 4.924625 TGAGCAACTCTACTACTTCCTCT 58.075 43.478 0.00 0.00 0.00 3.69
780 785 6.722129 TGCTACTACTTCCTCTCTCTCTTTTT 59.278 38.462 0.00 0.00 0.00 1.94
781 786 6.152154 GTGCTACTACTTCCTCTCTCTCTTTT 59.848 42.308 0.00 0.00 0.00 2.27
782 787 5.650703 GTGCTACTACTTCCTCTCTCTCTTT 59.349 44.000 0.00 0.00 0.00 2.52
783 788 5.190677 GTGCTACTACTTCCTCTCTCTCTT 58.809 45.833 0.00 0.00 0.00 2.85
784 789 4.384868 GGTGCTACTACTTCCTCTCTCTCT 60.385 50.000 0.00 0.00 0.00 3.10
785 790 3.881089 GGTGCTACTACTTCCTCTCTCTC 59.119 52.174 0.00 0.00 0.00 3.20
786 791 3.372241 GGGTGCTACTACTTCCTCTCTCT 60.372 52.174 0.00 0.00 0.00 3.10
787 792 2.953648 GGGTGCTACTACTTCCTCTCTC 59.046 54.545 0.00 0.00 0.00 3.20
788 793 2.684334 CGGGTGCTACTACTTCCTCTCT 60.684 54.545 0.00 0.00 0.00 3.10
789 794 1.677052 CGGGTGCTACTACTTCCTCTC 59.323 57.143 0.00 0.00 0.00 3.20
790 795 1.765230 CGGGTGCTACTACTTCCTCT 58.235 55.000 0.00 0.00 0.00 3.69
791 796 0.102663 GCGGGTGCTACTACTTCCTC 59.897 60.000 0.00 0.00 38.39 3.71
792 797 0.613853 TGCGGGTGCTACTACTTCCT 60.614 55.000 0.00 0.00 43.34 3.36
793 798 0.459759 GTGCGGGTGCTACTACTTCC 60.460 60.000 0.00 0.00 43.34 3.46
794 799 0.801067 CGTGCGGGTGCTACTACTTC 60.801 60.000 0.00 0.00 43.34 3.01
795 800 1.214589 CGTGCGGGTGCTACTACTT 59.785 57.895 0.00 0.00 43.34 2.24
796 801 2.707849 CCGTGCGGGTGCTACTACT 61.708 63.158 2.15 0.00 43.34 2.57
797 802 2.202703 CCGTGCGGGTGCTACTAC 60.203 66.667 2.15 0.00 43.34 2.73
825 830 2.611224 CGAGGTGCGGGTACTACTTTTT 60.611 50.000 0.00 0.00 36.03 1.94
826 831 1.067354 CGAGGTGCGGGTACTACTTTT 60.067 52.381 0.00 0.00 36.03 2.27
827 832 0.529378 CGAGGTGCGGGTACTACTTT 59.471 55.000 0.00 0.00 36.03 2.66
828 833 1.941999 GCGAGGTGCGGGTACTACTT 61.942 60.000 0.00 0.00 41.29 2.24
829 834 2.413142 GCGAGGTGCGGGTACTACT 61.413 63.158 0.00 0.00 41.29 2.57
830 835 2.103736 GCGAGGTGCGGGTACTAC 59.896 66.667 0.00 0.00 41.29 2.73
960 986 1.740380 CGCAAGGACAGATTCACGGAT 60.740 52.381 0.00 0.00 0.00 4.18
2070 5097 7.384387 GTCATACGGATTAGAACTTGGGAATAC 59.616 40.741 0.00 0.00 0.00 1.89
2186 5217 2.432874 TCTCTCTTTTGTCGACCCAACA 59.567 45.455 14.12 0.00 0.00 3.33
2757 7650 6.569179 AACCGCAGTTATTGTAAGTGAATT 57.431 33.333 8.35 0.00 33.27 2.17
3219 8120 4.955925 TGTCACAAACGATGAAACTTGT 57.044 36.364 0.00 0.00 32.31 3.16
3541 8444 2.113139 CCACTCCGTTGGCACCTT 59.887 61.111 0.00 0.00 0.00 3.50
3669 8572 3.640967 AGAGCTATTTGTCCCTCAGCTAG 59.359 47.826 0.00 0.00 42.44 3.42


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

AutoCloner maintained by Alex Coulton.