Multiple sequence alignment - TraesCS5B01G034500

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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 TraesCS5B01G034500 chr5B 100.000 3380 0 0 1 3380 37409333 37412712 0.000000e+00 6242.0
1 TraesCS5B01G034500 chr5B 92.955 582 32 5 63 636 458805509 458804929 0.000000e+00 839.0
2 TraesCS5B01G034500 chr4A 92.250 2516 151 23 665 3169 732362271 732364753 0.000000e+00 3526.0
3 TraesCS5B01G034500 chr4A 84.202 2513 335 34 910 3380 731875449 731872957 0.000000e+00 2385.0
4 TraesCS5B01G034500 chr4A 91.935 1674 112 14 1724 3380 731603493 731601826 0.000000e+00 2322.0
5 TraesCS5B01G034500 chr4A 81.315 2494 394 43 923 3380 732354808 732357265 0.000000e+00 1958.0
6 TraesCS5B01G034500 chr4A 86.592 1790 201 21 910 2665 731774377 731772593 0.000000e+00 1940.0
7 TraesCS5B01G034500 chr4A 79.977 2612 431 60 819 3380 732058484 732061053 0.000000e+00 1842.0
8 TraesCS5B01G034500 chr4A 84.658 717 98 4 2664 3380 731615054 731614350 0.000000e+00 704.0
9 TraesCS5B01G034500 chr4A 83.333 714 107 5 2663 3376 731860004 731859303 0.000000e+00 649.0
10 TraesCS5B01G034500 chr4A 82.711 723 118 5 2663 3380 731662338 731661618 1.320000e-178 636.0
11 TraesCS5B01G034500 chr4A 82.917 720 109 8 2662 3380 732379855 732380561 1.320000e-178 636.0
12 TraesCS5B01G034500 chr4A 82.138 683 115 7 2701 3380 731501553 731500875 2.260000e-161 579.0
13 TraesCS5B01G034500 chr4A 82.913 515 70 12 2869 3380 731751802 731751303 6.650000e-122 448.0
14 TraesCS5B01G034500 chr4A 88.587 368 39 3 3008 3374 732414608 732414973 8.610000e-121 444.0
15 TraesCS5B01G034500 chr4A 87.826 115 13 1 667 781 732105184 732105297 2.120000e-27 134.0
16 TraesCS5B01G034500 chr4A 88.889 108 9 2 667 774 732058315 732058419 2.740000e-26 130.0
17 TraesCS5B01G034500 chr4A 83.077 65 10 1 3316 3380 733766694 733766757 1.310000e-04 58.4
18 TraesCS5B01G034500 chr7D 85.802 2444 316 16 965 3380 8177062 8179502 0.000000e+00 2562.0
19 TraesCS5B01G034500 chr7D 85.386 2484 315 25 923 3374 7712568 7715035 0.000000e+00 2532.0
20 TraesCS5B01G034500 chr7D 86.575 2324 269 21 1082 3380 7606303 7608608 0.000000e+00 2523.0
21 TraesCS5B01G034500 chr7D 85.190 2505 316 30 910 3380 7749974 7752457 0.000000e+00 2519.0
22 TraesCS5B01G034500 chr7D 84.084 2488 353 30 918 3380 8233449 8235918 0.000000e+00 2361.0
23 TraesCS5B01G034500 chr7D 83.671 1923 250 33 778 2665 8256185 8254292 0.000000e+00 1753.0
24 TraesCS5B01G034500 chr7D 81.567 868 153 2 2514 3380 7655446 7656307 0.000000e+00 710.0
25 TraesCS5B01G034500 chr7D 84.254 724 111 3 2658 3380 8254262 8253541 0.000000e+00 702.0
26 TraesCS5B01G034500 chr7D 81.486 875 133 14 2509 3380 7598907 7599755 0.000000e+00 691.0
27 TraesCS5B01G034500 chr7D 83.840 724 112 4 2658 3380 8054587 8055306 0.000000e+00 684.0
28 TraesCS5B01G034500 chr7D 84.146 164 25 1 2510 2672 7925937 7926100 1.260000e-34 158.0
29 TraesCS5B01G034500 chr7D 94.444 54 3 0 12 65 7749589 7749642 2.160000e-12 84.2
30 TraesCS5B01G034500 chr7D 91.525 59 2 3 7 65 8256435 8256380 1.010000e-10 78.7
31 TraesCS5B01G034500 chr7D 91.489 47 3 1 704 750 7597066 7597111 2.820000e-06 63.9
32 TraesCS5B01G034500 chr7A 83.877 2512 338 32 910 3380 8653703 8656188 0.000000e+00 2333.0
33 TraesCS5B01G034500 chr7A 82.131 2496 397 33 908 3380 8634294 8636763 0.000000e+00 2093.0
34 TraesCS5B01G034500 chr7A 83.884 726 110 7 2658 3380 3430320 3429599 0.000000e+00 686.0
35 TraesCS5B01G034500 chr7A 90.741 108 10 0 667 774 8589471 8589578 9.770000e-31 145.0
36 TraesCS5B01G034500 chr1B 94.310 580 28 3 63 637 592237300 592237879 0.000000e+00 883.0
37 TraesCS5B01G034500 chr1B 93.610 579 32 3 63 636 592286140 592286718 0.000000e+00 859.0
38 TraesCS5B01G034500 chr1B 93.092 579 34 4 63 636 592327432 592328009 0.000000e+00 843.0
39 TraesCS5B01G034500 chr7B 93.643 582 33 2 63 640 153585168 153584587 0.000000e+00 867.0
40 TraesCS5B01G034500 chr4B 93.115 581 31 7 63 637 339149357 339149934 0.000000e+00 843.0
41 TraesCS5B01G034500 chr4B 92.241 580 39 4 63 637 652991240 652991818 0.000000e+00 817.0
42 TraesCS5B01G034500 chr6B 93.080 578 33 5 63 636 692560663 692560089 0.000000e+00 839.0
43 TraesCS5B01G034500 chr2A 92.374 577 37 5 63 635 430703303 430703876 0.000000e+00 815.0


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 TraesCS5B01G034500 chr5B 37409333 37412712 3379 False 6242.000000 6242 100.000000 1 3380 1 chr5B.!!$F1 3379
1 TraesCS5B01G034500 chr5B 458804929 458805509 580 True 839.000000 839 92.955000 63 636 1 chr5B.!!$R1 573
2 TraesCS5B01G034500 chr4A 732362271 732364753 2482 False 3526.000000 3526 92.250000 665 3169 1 chr4A.!!$F3 2504
3 TraesCS5B01G034500 chr4A 731872957 731875449 2492 True 2385.000000 2385 84.202000 910 3380 1 chr4A.!!$R8 2470
4 TraesCS5B01G034500 chr4A 731601826 731603493 1667 True 2322.000000 2322 91.935000 1724 3380 1 chr4A.!!$R2 1656
5 TraesCS5B01G034500 chr4A 732354808 732357265 2457 False 1958.000000 1958 81.315000 923 3380 1 chr4A.!!$F2 2457
6 TraesCS5B01G034500 chr4A 731772593 731774377 1784 True 1940.000000 1940 86.592000 910 2665 1 chr4A.!!$R6 1755
7 TraesCS5B01G034500 chr4A 732058315 732061053 2738 False 986.000000 1842 84.433000 667 3380 2 chr4A.!!$F7 2713
8 TraesCS5B01G034500 chr4A 731614350 731615054 704 True 704.000000 704 84.658000 2664 3380 1 chr4A.!!$R3 716
9 TraesCS5B01G034500 chr4A 731859303 731860004 701 True 649.000000 649 83.333000 2663 3376 1 chr4A.!!$R7 713
10 TraesCS5B01G034500 chr4A 731661618 731662338 720 True 636.000000 636 82.711000 2663 3380 1 chr4A.!!$R4 717
11 TraesCS5B01G034500 chr4A 732379855 732380561 706 False 636.000000 636 82.917000 2662 3380 1 chr4A.!!$F4 718
12 TraesCS5B01G034500 chr4A 731500875 731501553 678 True 579.000000 579 82.138000 2701 3380 1 chr4A.!!$R1 679
13 TraesCS5B01G034500 chr7D 8177062 8179502 2440 False 2562.000000 2562 85.802000 965 3380 1 chr7D.!!$F6 2415
14 TraesCS5B01G034500 chr7D 7712568 7715035 2467 False 2532.000000 2532 85.386000 923 3374 1 chr7D.!!$F3 2451
15 TraesCS5B01G034500 chr7D 7606303 7608608 2305 False 2523.000000 2523 86.575000 1082 3380 1 chr7D.!!$F1 2298
16 TraesCS5B01G034500 chr7D 8233449 8235918 2469 False 2361.000000 2361 84.084000 918 3380 1 chr7D.!!$F7 2462
17 TraesCS5B01G034500 chr7D 7749589 7752457 2868 False 1301.600000 2519 89.817000 12 3380 2 chr7D.!!$F9 3368
18 TraesCS5B01G034500 chr7D 8253541 8256435 2894 True 844.566667 1753 86.483333 7 3380 3 chr7D.!!$R1 3373
19 TraesCS5B01G034500 chr7D 7655446 7656307 861 False 710.000000 710 81.567000 2514 3380 1 chr7D.!!$F2 866
20 TraesCS5B01G034500 chr7D 8054587 8055306 719 False 684.000000 684 83.840000 2658 3380 1 chr7D.!!$F5 722
21 TraesCS5B01G034500 chr7D 7597066 7599755 2689 False 377.450000 691 86.487500 704 3380 2 chr7D.!!$F8 2676
22 TraesCS5B01G034500 chr7A 8653703 8656188 2485 False 2333.000000 2333 83.877000 910 3380 1 chr7A.!!$F3 2470
23 TraesCS5B01G034500 chr7A 8634294 8636763 2469 False 2093.000000 2093 82.131000 908 3380 1 chr7A.!!$F2 2472
24 TraesCS5B01G034500 chr7A 3429599 3430320 721 True 686.000000 686 83.884000 2658 3380 1 chr7A.!!$R1 722
25 TraesCS5B01G034500 chr1B 592237300 592237879 579 False 883.000000 883 94.310000 63 637 1 chr1B.!!$F1 574
26 TraesCS5B01G034500 chr1B 592286140 592286718 578 False 859.000000 859 93.610000 63 636 1 chr1B.!!$F2 573
27 TraesCS5B01G034500 chr1B 592327432 592328009 577 False 843.000000 843 93.092000 63 636 1 chr1B.!!$F3 573
28 TraesCS5B01G034500 chr7B 153584587 153585168 581 True 867.000000 867 93.643000 63 640 1 chr7B.!!$R1 577
29 TraesCS5B01G034500 chr4B 339149357 339149934 577 False 843.000000 843 93.115000 63 637 1 chr4B.!!$F1 574
30 TraesCS5B01G034500 chr4B 652991240 652991818 578 False 817.000000 817 92.241000 63 637 1 chr4B.!!$F2 574
31 TraesCS5B01G034500 chr6B 692560089 692560663 574 True 839.000000 839 93.080000 63 636 1 chr6B.!!$R1 573
32 TraesCS5B01G034500 chr2A 430703303 430703876 573 False 815.000000 815 92.374000 63 635 1 chr2A.!!$F1 572

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
597 604 0.24636 TGGCCGTGTACATCACTCTG 59.754 55.0 0.0 0.0 44.16 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2572 2834 0.179119 GCCTCTGACATTTGCATGGC 60.179 55.0 0.0 0.0 39.21 4.4 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
36 37 3.681897 CAGTCAACATACAGCTCTTGGAC 59.318 47.826 0.00 0.00 0.00 4.02
78 79 0.250727 CTTCCAAGGTCCTTTGGCGA 60.251 55.000 0.00 0.00 45.83 5.54
200 205 3.256879 TGTTGGAGTTTGCTTTGTTGTGA 59.743 39.130 0.00 0.00 0.00 3.58
214 219 8.417106 TGCTTTGTTGTGAACTATTTGGAATTA 58.583 29.630 0.00 0.00 0.00 1.40
280 285 3.700538 TGCAGGTTATTTTCTGAGCCAT 58.299 40.909 0.00 0.00 33.11 4.40
299 304 2.416680 TGGCATTGATCCATTCGTGA 57.583 45.000 0.00 0.00 0.00 4.35
409 414 4.365514 TTGGATGGCGGTCATGTAATAT 57.634 40.909 0.00 0.00 35.97 1.28
546 553 2.505819 ACTGTTGGAGACTTTGACACCT 59.494 45.455 0.00 0.00 0.00 4.00
547 554 3.054361 ACTGTTGGAGACTTTGACACCTT 60.054 43.478 0.00 0.00 0.00 3.50
548 555 3.278574 TGTTGGAGACTTTGACACCTTG 58.721 45.455 0.00 0.00 0.00 3.61
549 556 3.279434 GTTGGAGACTTTGACACCTTGT 58.721 45.455 0.00 0.00 0.00 3.16
550 557 3.644966 TGGAGACTTTGACACCTTGTT 57.355 42.857 0.00 0.00 0.00 2.83
551 558 3.963129 TGGAGACTTTGACACCTTGTTT 58.037 40.909 0.00 0.00 0.00 2.83
552 559 3.694072 TGGAGACTTTGACACCTTGTTTG 59.306 43.478 0.00 0.00 0.00 2.93
553 560 3.945285 GGAGACTTTGACACCTTGTTTGA 59.055 43.478 0.00 0.00 0.00 2.69
554 561 4.398044 GGAGACTTTGACACCTTGTTTGAA 59.602 41.667 0.00 0.00 0.00 2.69
555 562 5.105917 GGAGACTTTGACACCTTGTTTGAAA 60.106 40.000 0.00 0.00 0.00 2.69
556 563 5.709966 AGACTTTGACACCTTGTTTGAAAC 58.290 37.500 0.14 0.14 0.00 2.78
557 564 4.816392 ACTTTGACACCTTGTTTGAAACC 58.184 39.130 5.50 0.00 0.00 3.27
558 565 4.526650 ACTTTGACACCTTGTTTGAAACCT 59.473 37.500 5.50 0.00 0.00 3.50
559 566 5.011635 ACTTTGACACCTTGTTTGAAACCTT 59.988 36.000 5.50 0.00 0.00 3.50
560 567 5.476091 TTGACACCTTGTTTGAAACCTTT 57.524 34.783 5.50 0.00 0.00 3.11
561 568 5.476091 TGACACCTTGTTTGAAACCTTTT 57.524 34.783 5.50 0.00 0.00 2.27
562 569 5.859495 TGACACCTTGTTTGAAACCTTTTT 58.141 33.333 5.50 0.00 0.00 1.94
563 570 6.994221 TGACACCTTGTTTGAAACCTTTTTA 58.006 32.000 5.50 0.00 0.00 1.52
564 571 7.616313 TGACACCTTGTTTGAAACCTTTTTAT 58.384 30.769 5.50 0.00 0.00 1.40
565 572 8.097662 TGACACCTTGTTTGAAACCTTTTTATT 58.902 29.630 5.50 0.00 0.00 1.40
566 573 8.856153 ACACCTTGTTTGAAACCTTTTTATTT 57.144 26.923 5.50 0.00 0.00 1.40
567 574 8.726068 ACACCTTGTTTGAAACCTTTTTATTTG 58.274 29.630 5.50 0.00 0.00 2.32
568 575 8.180920 CACCTTGTTTGAAACCTTTTTATTTGG 58.819 33.333 5.50 0.00 0.00 3.28
569 576 7.885922 ACCTTGTTTGAAACCTTTTTATTTGGT 59.114 29.630 5.50 0.00 35.29 3.67
570 577 8.735315 CCTTGTTTGAAACCTTTTTATTTGGTT 58.265 29.630 5.50 0.00 44.92 3.67
585 592 8.480643 TTTATTTGGTTAATAAAATGGCCGTG 57.519 30.769 0.00 0.00 42.72 4.94
586 593 5.470047 TTTGGTTAATAAAATGGCCGTGT 57.530 34.783 0.00 0.00 0.00 4.49
587 594 6.585695 TTTGGTTAATAAAATGGCCGTGTA 57.414 33.333 0.00 0.00 0.00 2.90
588 595 5.564048 TGGTTAATAAAATGGCCGTGTAC 57.436 39.130 0.00 0.00 0.00 2.90
589 596 5.008331 TGGTTAATAAAATGGCCGTGTACA 58.992 37.500 0.00 0.00 0.00 2.90
590 597 5.652891 TGGTTAATAAAATGGCCGTGTACAT 59.347 36.000 0.00 0.00 0.00 2.29
591 598 6.183360 TGGTTAATAAAATGGCCGTGTACATC 60.183 38.462 0.00 0.00 0.00 3.06
592 599 6.183360 GGTTAATAAAATGGCCGTGTACATCA 60.183 38.462 0.00 0.00 0.00 3.07
593 600 4.893424 ATAAAATGGCCGTGTACATCAC 57.107 40.909 0.00 0.00 43.03 3.06
594 601 2.489938 AAATGGCCGTGTACATCACT 57.510 45.000 0.00 0.00 44.16 3.41
595 602 2.024176 AATGGCCGTGTACATCACTC 57.976 50.000 0.00 0.00 44.16 3.51
596 603 1.195115 ATGGCCGTGTACATCACTCT 58.805 50.000 0.00 0.00 44.16 3.24
597 604 0.246360 TGGCCGTGTACATCACTCTG 59.754 55.000 0.00 0.00 44.16 3.35
598 605 0.530744 GGCCGTGTACATCACTCTGA 59.469 55.000 0.00 0.00 44.16 3.27
599 606 1.137086 GGCCGTGTACATCACTCTGAT 59.863 52.381 0.00 0.00 44.16 2.90
611 618 3.473647 TCTGATGCAGAGGCCGGG 61.474 66.667 2.18 0.00 35.39 5.73
612 619 4.559063 CTGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
614 621 4.247380 GATGCAGAGGCCGGGGAG 62.247 72.222 2.18 0.00 40.13 4.30
615 622 4.804420 ATGCAGAGGCCGGGGAGA 62.804 66.667 2.18 0.00 40.13 3.71
617 624 4.475135 GCAGAGGCCGGGGAGAAC 62.475 72.222 2.18 0.00 0.00 3.01
618 625 3.787001 CAGAGGCCGGGGAGAACC 61.787 72.222 2.18 0.00 39.11 3.62
628 635 4.736739 GGAGAACCCCCTTTTCGG 57.263 61.111 0.00 0.00 0.00 4.30
629 636 2.072366 GGAGAACCCCCTTTTCGGA 58.928 57.895 0.00 0.00 33.16 4.55
630 637 0.402887 GGAGAACCCCCTTTTCGGAA 59.597 55.000 0.00 0.00 33.16 4.30
631 638 1.202964 GGAGAACCCCCTTTTCGGAAA 60.203 52.381 0.00 0.00 33.16 3.13
632 639 2.589720 GAGAACCCCCTTTTCGGAAAA 58.410 47.619 14.64 14.64 33.16 2.29
633 640 2.960384 GAGAACCCCCTTTTCGGAAAAA 59.040 45.455 15.99 2.14 33.42 1.94
654 661 2.071778 AGCAACCACACAACTCCATT 57.928 45.000 0.00 0.00 0.00 3.16
655 662 2.387757 AGCAACCACACAACTCCATTT 58.612 42.857 0.00 0.00 0.00 2.32
656 663 2.101249 AGCAACCACACAACTCCATTTG 59.899 45.455 0.00 0.00 0.00 2.32
657 664 2.472816 CAACCACACAACTCCATTTGC 58.527 47.619 0.00 0.00 0.00 3.68
658 665 2.071778 ACCACACAACTCCATTTGCT 57.928 45.000 0.00 0.00 0.00 3.91
659 666 2.387757 ACCACACAACTCCATTTGCTT 58.612 42.857 0.00 0.00 0.00 3.91
661 668 2.288395 CCACACAACTCCATTTGCTTCC 60.288 50.000 0.00 0.00 0.00 3.46
663 670 3.068590 CACACAACTCCATTTGCTTCCTT 59.931 43.478 0.00 0.00 0.00 3.36
776 797 1.755783 GCTCAATCCTTGGCCTGGG 60.756 63.158 3.32 6.23 0.00 4.45
832 887 7.908082 CACTGGAATTTTTATGTATGTGTACCG 59.092 37.037 0.00 0.00 0.00 4.02
921 1122 9.496710 TGTGGAACTAGGAAATAGGAGTATTAA 57.503 33.333 0.00 0.00 38.04 1.40
938 1140 7.254863 GGAGTATTAAAAGGTTGTTCGTGTTCA 60.255 37.037 0.00 0.00 0.00 3.18
950 1152 4.211164 TGTTCGTGTTCAATCAGTGCTAAG 59.789 41.667 0.00 0.00 0.00 2.18
957 1167 5.185828 TGTTCAATCAGTGCTAAGCTCTCTA 59.814 40.000 0.00 0.00 29.56 2.43
973 1185 4.615949 CTCTCTACTTTCATACGCTGCAT 58.384 43.478 0.00 0.00 0.00 3.96
980 1195 4.218417 ACTTTCATACGCTGCATTTCCTTT 59.782 37.500 0.00 0.00 0.00 3.11
1065 1281 1.745115 GGCCGCAGATGCACTTGTA 60.745 57.895 5.55 0.00 42.21 2.41
1074 1290 4.511527 CAGATGCACTTGTAGAGACCATT 58.488 43.478 0.00 0.00 0.00 3.16
1103 1319 2.678580 TGGCCTCGACGATGACCA 60.679 61.111 3.32 6.54 0.00 4.02
1146 1362 2.154798 TAGCCGTCGAGTGCAAGCTT 62.155 55.000 8.63 0.00 0.00 3.74
1267 1483 1.153489 CAGTATGAGGCACTGCGCT 60.153 57.895 9.73 0.00 41.55 5.92
1271 1487 2.889154 TATGAGGCACTGCGCTGTCG 62.889 60.000 17.75 13.57 41.55 4.35
1319 1535 2.418197 GCAAGGTACTCGGCTACATCAA 60.418 50.000 0.00 0.00 38.49 2.57
1335 1551 3.636231 AAGCACCACAGCCCGCTA 61.636 61.111 0.00 0.00 33.45 4.26
1342 1558 1.608717 CCACAGCCCGCTACTCTTCT 61.609 60.000 0.00 0.00 0.00 2.85
1356 1572 6.146184 CGCTACTCTTCTGTTTTGAAATGAGA 59.854 38.462 0.00 0.00 0.00 3.27
1376 1592 5.751990 TGAGAAAGAAACTCAAGAACGTACC 59.248 40.000 0.00 0.00 40.70 3.34
1415 1635 5.560722 TTGGTTGAGGAGATGAACAAGTA 57.439 39.130 0.00 0.00 0.00 2.24
1419 1639 5.338381 GGTTGAGGAGATGAACAAGTATGGA 60.338 44.000 0.00 0.00 0.00 3.41
1532 1752 3.281727 TGATGATAAGGAAGTGGTGGC 57.718 47.619 0.00 0.00 0.00 5.01
1536 1756 2.007608 GATAAGGAAGTGGTGGCGAAC 58.992 52.381 0.00 0.00 0.00 3.95
1562 1782 2.486472 CTGGACCAGCAAGATCAGTT 57.514 50.000 8.99 0.00 0.00 3.16
1575 1795 2.079925 GATCAGTTGAAGGTGCAGGTC 58.920 52.381 0.00 0.00 0.00 3.85
1686 1906 3.015293 GATGTGGCACTGCGTGTCG 62.015 63.158 19.83 0.00 41.53 4.35
1928 2149 4.878439 AGCGTAATAGTTGTCACAACTCA 58.122 39.130 26.61 13.36 0.00 3.41
1994 2215 1.923204 GCTAGCATGTCTGAGTGAACG 59.077 52.381 10.63 0.00 0.00 3.95
2029 2250 8.553696 GGGAATTATTTGCAAAGAAAGCATATG 58.446 33.333 21.85 0.00 42.33 1.78
2081 2303 0.453782 GTCGGCATTGGCAAACGTAC 60.454 55.000 17.55 12.38 43.71 3.67
2135 2359 1.205417 CAAGACAATGGGTGGATTGCC 59.795 52.381 0.00 0.00 36.89 4.52
2220 2450 7.868792 TGATAGAGGGAAAGATGAGATCATT 57.131 36.000 0.00 0.00 36.57 2.57
2244 2474 6.420913 TCCATCCTAAAGTTGAGCTATACC 57.579 41.667 0.00 0.00 0.00 2.73
2263 2493 4.443978 ACCCACCTATCATCTGAAATGG 57.556 45.455 0.00 0.00 0.00 3.16
2315 2545 4.901849 TCCCAAGGACTATAAGATGGACAG 59.098 45.833 0.00 0.00 0.00 3.51
2317 2547 4.901849 CCAAGGACTATAAGATGGACAGGA 59.098 45.833 0.00 0.00 0.00 3.86
2511 2772 5.979993 TGTAAAATGCATGATTTGGCTCAT 58.020 33.333 0.00 0.00 34.30 2.90
2546 2807 7.436673 GTGCAAGTATAGAAGAATTGACTCGAT 59.563 37.037 0.00 0.00 0.00 3.59
2573 2835 9.986833 AGAAAGAATTGTTAAAAATGTTTGTGC 57.013 25.926 4.43 0.00 0.00 4.57
2619 2884 4.929479 TGGAACAAATTAGTGGGCTATGT 58.071 39.130 0.00 0.00 31.92 2.29
2644 2909 0.868406 CAGAACAAACCTCCGCACTC 59.132 55.000 0.00 0.00 0.00 3.51
2646 2911 1.149148 GAACAAACCTCCGCACTCTC 58.851 55.000 0.00 0.00 0.00 3.20
2810 3118 4.242475 TGGTCTAACATCACTAAGTTGCG 58.758 43.478 0.00 0.00 0.00 4.85
2873 3181 5.001874 CCTCATACATTGTCATATGCTGCT 58.998 41.667 0.00 0.00 0.00 4.24
2980 3288 5.008316 CCAAACTTTGGCGTACTAAAGAACT 59.992 40.000 7.63 3.49 45.17 3.01
2988 3296 7.534085 TGGCGTACTAAAGAACTTTCATATG 57.466 36.000 2.99 0.00 34.23 1.78
3169 3484 1.215423 AGTTGTTGTTCTCTTGGGGCT 59.785 47.619 0.00 0.00 0.00 5.19
3193 3511 7.064490 GCTAAGAAATAGATGATGAGCCTAAGC 59.936 40.741 0.00 0.00 34.50 3.09
3194 3512 5.803552 AGAAATAGATGATGAGCCTAAGCC 58.196 41.667 0.00 0.00 41.25 4.35
3276 3598 4.150359 AGTTAGAGATACGTGGGTATGGG 58.850 47.826 0.00 0.00 39.44 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.519799 TGTATGTTGACTGATAGACTGATACA 57.480 34.615 0.00 0.00 0.00 2.29
6 7 5.900425 AGCTGTATGTTGACTGATAGACTG 58.100 41.667 0.00 0.00 0.00 3.51
7 8 5.890985 AGAGCTGTATGTTGACTGATAGACT 59.109 40.000 0.00 0.00 0.00 3.24
8 9 6.142818 AGAGCTGTATGTTGACTGATAGAC 57.857 41.667 0.00 0.00 0.00 2.59
9 10 6.406288 CCAAGAGCTGTATGTTGACTGATAGA 60.406 42.308 0.00 0.00 0.00 1.98
10 11 5.752472 CCAAGAGCTGTATGTTGACTGATAG 59.248 44.000 0.00 0.00 0.00 2.08
11 12 5.422012 TCCAAGAGCTGTATGTTGACTGATA 59.578 40.000 0.00 0.00 0.00 2.15
13 14 3.578282 TCCAAGAGCTGTATGTTGACTGA 59.422 43.478 0.00 0.00 0.00 3.41
14 15 3.681897 GTCCAAGAGCTGTATGTTGACTG 59.318 47.826 0.00 0.00 0.00 3.51
15 16 3.580458 AGTCCAAGAGCTGTATGTTGACT 59.420 43.478 0.00 0.00 0.00 3.41
16 17 3.929610 GAGTCCAAGAGCTGTATGTTGAC 59.070 47.826 0.00 0.00 0.00 3.18
17 18 3.055819 GGAGTCCAAGAGCTGTATGTTGA 60.056 47.826 3.60 0.00 0.00 3.18
18 19 3.055530 AGGAGTCCAAGAGCTGTATGTTG 60.056 47.826 12.86 0.00 0.00 3.33
19 20 3.177228 AGGAGTCCAAGAGCTGTATGTT 58.823 45.455 12.86 0.00 0.00 2.71
20 21 2.826488 AGGAGTCCAAGAGCTGTATGT 58.174 47.619 12.86 0.00 0.00 2.29
21 22 3.196469 TCAAGGAGTCCAAGAGCTGTATG 59.804 47.826 12.86 0.00 0.00 2.39
36 37 6.297582 AGCAAATGGAGATAAGATCAAGGAG 58.702 40.000 0.00 0.00 0.00 3.69
214 219 9.883142 TTCTGTTAAAAACCAAATCATTTCTGT 57.117 25.926 0.00 0.00 0.00 3.41
255 260 4.686091 GGCTCAGAAAATAACCTGCAAAAC 59.314 41.667 0.00 0.00 0.00 2.43
280 285 2.416680 TCACGAATGGATCAATGCCA 57.583 45.000 0.00 0.00 40.24 4.92
299 304 0.955178 CCATCGGAGTGAGTAGCGAT 59.045 55.000 0.00 0.00 0.00 4.58
326 331 2.614057 GGATCCAGTAACCAAATGCTCG 59.386 50.000 6.95 0.00 0.00 5.03
560 567 8.095169 ACACGGCCATTTTATTAACCAAATAAA 58.905 29.630 2.24 0.06 44.54 1.40
561 568 7.612677 ACACGGCCATTTTATTAACCAAATAA 58.387 30.769 2.24 0.00 38.09 1.40
562 569 7.171630 ACACGGCCATTTTATTAACCAAATA 57.828 32.000 2.24 0.00 0.00 1.40
563 570 6.043854 ACACGGCCATTTTATTAACCAAAT 57.956 33.333 2.24 0.00 0.00 2.32
564 571 5.470047 ACACGGCCATTTTATTAACCAAA 57.530 34.783 2.24 0.00 0.00 3.28
565 572 5.475909 TGTACACGGCCATTTTATTAACCAA 59.524 36.000 2.24 0.00 0.00 3.67
566 573 5.008331 TGTACACGGCCATTTTATTAACCA 58.992 37.500 2.24 0.00 0.00 3.67
567 574 5.564048 TGTACACGGCCATTTTATTAACC 57.436 39.130 2.24 0.00 0.00 2.85
568 575 6.689669 GTGATGTACACGGCCATTTTATTAAC 59.310 38.462 2.24 0.00 39.78 2.01
569 576 6.787225 GTGATGTACACGGCCATTTTATTAA 58.213 36.000 2.24 0.00 39.78 1.40
570 577 6.366315 GTGATGTACACGGCCATTTTATTA 57.634 37.500 2.24 0.00 39.78 0.98
571 578 5.243426 GTGATGTACACGGCCATTTTATT 57.757 39.130 2.24 0.00 39.78 1.40
572 579 4.893424 GTGATGTACACGGCCATTTTAT 57.107 40.909 2.24 0.00 39.78 1.40
594 601 3.473647 CCCGGCCTCTGCATCAGA 61.474 66.667 0.00 0.00 38.25 3.27
595 602 4.559063 CCCCGGCCTCTGCATCAG 62.559 72.222 0.00 0.00 40.13 2.90
597 604 4.247380 CTCCCCGGCCTCTGCATC 62.247 72.222 0.00 0.00 40.13 3.91
598 605 4.804420 TCTCCCCGGCCTCTGCAT 62.804 66.667 0.00 0.00 40.13 3.96
600 607 4.475135 GTTCTCCCCGGCCTCTGC 62.475 72.222 0.00 0.00 0.00 4.26
601 608 3.787001 GGTTCTCCCCGGCCTCTG 61.787 72.222 0.00 0.00 0.00 3.35
611 618 0.402887 TTCCGAAAAGGGGGTTCTCC 59.597 55.000 0.00 0.00 41.52 3.71
612 619 2.281539 TTTCCGAAAAGGGGGTTCTC 57.718 50.000 0.00 0.00 41.52 2.87
613 620 2.759839 TTTTCCGAAAAGGGGGTTCT 57.240 45.000 2.01 0.00 41.52 3.01
631 638 2.564947 TGGAGTTGTGTGGTTGCTTTTT 59.435 40.909 0.00 0.00 0.00 1.94
632 639 2.175202 TGGAGTTGTGTGGTTGCTTTT 58.825 42.857 0.00 0.00 0.00 2.27
633 640 1.846007 TGGAGTTGTGTGGTTGCTTT 58.154 45.000 0.00 0.00 0.00 3.51
634 641 2.071778 ATGGAGTTGTGTGGTTGCTT 57.928 45.000 0.00 0.00 0.00 3.91
654 661 0.178992 CCCTGTGTGGAAGGAAGCAA 60.179 55.000 0.00 0.00 36.91 3.91
655 662 1.455849 CCCTGTGTGGAAGGAAGCA 59.544 57.895 0.00 0.00 36.91 3.91
656 663 1.303643 CCCCTGTGTGGAAGGAAGC 60.304 63.158 0.00 0.00 36.91 3.86
657 664 1.303643 GCCCCTGTGTGGAAGGAAG 60.304 63.158 0.00 0.00 36.91 3.46
658 665 2.843545 GCCCCTGTGTGGAAGGAA 59.156 61.111 0.00 0.00 36.91 3.36
659 666 3.636231 CGCCCCTGTGTGGAAGGA 61.636 66.667 0.00 0.00 36.91 3.36
661 668 4.722700 CCCGCCCCTGTGTGGAAG 62.723 72.222 0.00 0.00 38.18 3.46
790 844 2.611224 CCAGTGGGAATTTTGCTTGCTC 60.611 50.000 0.00 0.00 35.59 4.26
803 858 6.951198 ACACATACATAAAAATTCCAGTGGGA 59.049 34.615 9.92 0.00 43.03 4.37
832 887 9.242477 GTATATCCCTCTTGTACGTACTTTTTC 57.758 37.037 25.12 0.00 0.00 2.29
841 896 6.879276 TCTCTTGTATATCCCTCTTGTACG 57.121 41.667 0.00 0.00 0.00 3.67
921 1122 4.398044 ACTGATTGAACACGAACAACCTTT 59.602 37.500 0.00 0.00 0.00 3.11
938 1140 5.930837 AAGTAGAGAGCTTAGCACTGATT 57.069 39.130 9.20 0.00 28.14 2.57
950 1152 2.792116 GCAGCGTATGAAAGTAGAGAGC 59.208 50.000 0.00 0.00 0.00 4.09
957 1167 3.347216 AGGAAATGCAGCGTATGAAAGT 58.653 40.909 0.00 0.00 0.00 2.66
973 1185 4.615513 TGAAGGTTGGAGGAAAAAGGAAA 58.384 39.130 0.00 0.00 0.00 3.13
980 1195 5.046663 GCCATATTTTGAAGGTTGGAGGAAA 60.047 40.000 0.00 0.00 0.00 3.13
1065 1281 2.912956 ACACATGTGGGTAATGGTCTCT 59.087 45.455 28.64 0.77 34.19 3.10
1267 1483 2.301870 ACTTGCCAATCTTAGACCGACA 59.698 45.455 0.00 0.00 0.00 4.35
1271 1487 3.350219 TGGACTTGCCAATCTTAGACC 57.650 47.619 0.00 0.00 45.87 3.85
1319 1535 4.394712 GTAGCGGGCTGTGGTGCT 62.395 66.667 2.86 0.00 41.32 4.40
1335 1551 8.511604 TCTTTCTCATTTCAAAACAGAAGAGT 57.488 30.769 0.00 0.00 0.00 3.24
1342 1558 9.357652 CTTGAGTTTCTTTCTCATTTCAAAACA 57.642 29.630 0.00 0.00 40.83 2.83
1356 1572 3.805971 CGGGTACGTTCTTGAGTTTCTTT 59.194 43.478 0.00 0.00 34.81 2.52
1376 1592 7.320443 TCAACCAATTTATTGATCTTCTCGG 57.680 36.000 4.07 0.00 40.14 4.63
1415 1635 5.965033 ATGTACAGAATTCTCCAGTCCAT 57.035 39.130 4.57 0.99 0.00 3.41
1419 1639 5.529289 TCCCTATGTACAGAATTCTCCAGT 58.471 41.667 4.57 3.52 0.00 4.00
1532 1752 1.572085 CTGGTCCAGCAGCAAGTTCG 61.572 60.000 5.79 0.00 30.08 3.95
1686 1906 2.028748 AGCAATGGCATCAAAGTTGTCC 60.029 45.455 0.00 0.00 44.61 4.02
1945 2166 3.565902 GGTTGAAGGGTCTGCATTATAGC 59.434 47.826 0.00 0.00 0.00 2.97
1994 2215 8.199449 TCTTTGCAAATAATTCCCATGAATCTC 58.801 33.333 13.23 0.00 40.34 2.75
2029 2250 1.741770 CCTGCTCTACACCGTTGCC 60.742 63.158 0.00 0.00 0.00 4.52
2081 2303 0.604578 CCCCCTGCATTTGTTGACAG 59.395 55.000 0.00 0.00 32.55 3.51
2220 2450 6.183361 GGGTATAGCTCAACTTTAGGATGGAA 60.183 42.308 1.32 0.00 0.00 3.53
2244 2474 4.070716 GCTCCATTTCAGATGATAGGTGG 58.929 47.826 0.00 0.00 0.00 4.61
2315 2545 3.567164 CCATAGCTGGATCAACATGTTCC 59.433 47.826 8.48 8.17 46.37 3.62
2317 2547 4.508551 TCCATAGCTGGATCAACATGTT 57.491 40.909 4.92 4.92 46.95 2.71
2431 2663 2.831526 TGTGTGCACTCCTGCTTATCTA 59.168 45.455 19.41 0.00 44.57 1.98
2572 2834 0.179119 GCCTCTGACATTTGCATGGC 60.179 55.000 0.00 0.00 39.21 4.40
2573 2835 1.134367 CAGCCTCTGACATTTGCATGG 59.866 52.381 0.00 0.00 34.27 3.66
2619 2884 2.500229 CGGAGGTTTGTTCTGCCTTTA 58.500 47.619 0.00 0.00 31.89 1.85
2644 2909 5.108517 GTGTGATTCTGAAGGAGCTAAGAG 58.891 45.833 0.00 0.00 0.00 2.85
2646 2911 4.825422 TGTGTGATTCTGAAGGAGCTAAG 58.175 43.478 0.00 0.00 0.00 2.18
2753 3061 7.681125 AGATATCGTAGACGTTTCACATTTC 57.319 36.000 1.46 0.00 42.51 2.17
2841 3149 4.637091 TGACAATGTATGAGGCTCAATGTG 59.363 41.667 22.84 16.45 0.00 3.21
2873 3181 4.412843 TGACATGTCTCCTGGTAACTACA 58.587 43.478 25.55 0.00 37.61 2.74
3001 3309 7.682459 TCCAAGGCCATCTATAGTATCCATAAA 59.318 37.037 5.01 0.00 0.00 1.40
3004 3312 5.603750 TCCAAGGCCATCTATAGTATCCAT 58.396 41.667 5.01 0.00 0.00 3.41
3014 3322 3.317406 TGCTCTATTCCAAGGCCATCTA 58.683 45.455 5.01 0.00 0.00 1.98
3169 3484 7.236432 AGGCTTAGGCTCATCATCTATTTCTTA 59.764 37.037 1.28 0.00 38.73 2.10
3193 3511 4.717877 TCTTCCACATTACATGCCATAGG 58.282 43.478 0.00 0.00 0.00 2.57
3194 3512 5.824624 ACTTCTTCCACATTACATGCCATAG 59.175 40.000 0.00 0.00 0.00 2.23
3276 3598 4.985538 TCCATTGTGATATTTCTAGGCCC 58.014 43.478 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.