Multiple sequence alignment - TraesCS2A01G256600

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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 TraesCS2A01G256600 chr2A 100.000 3470 0 0 1 3470 393338575 393342044 0.000000e+00 6408
1 TraesCS2A01G256600 chr2D 96.162 1850 56 4 718 2554 324863265 324861418 0.000000e+00 3009
2 TraesCS2A01G256600 chr2D 92.431 872 45 7 2619 3470 324861414 324860544 0.000000e+00 1225
3 TraesCS2A01G256600 chr2D 94.100 678 38 1 1 678 324908097 324907422 0.000000e+00 1029
4 TraesCS2A01G256600 chr2B 96.005 1777 56 4 768 2542 393861058 393859295 0.000000e+00 2874
5 TraesCS2A01G256600 chr2B 92.009 876 44 8 2619 3468 393859276 393858401 0.000000e+00 1206
6 TraesCS2A01G256600 chr2B 89.104 569 55 5 4 572 393874944 393874383 0.000000e+00 701
7 TraesCS2A01G256600 chr2B 90.756 119 11 0 570 688 393873848 393873730 3.580000e-35 159
8 TraesCS2A01G256600 chr3D 92.108 1812 115 16 768 2560 481517073 481515271 0.000000e+00 2529
9 TraesCS2A01G256600 chr3B 91.889 1800 126 14 770 2557 642487124 642485333 0.000000e+00 2497
10 TraesCS2A01G256600 chr3A 91.217 1799 134 14 770 2554 624530274 624528486 0.000000e+00 2425
11 TraesCS2A01G256600 chr6A 90.828 338 28 3 2619 2953 4814869 4814532 1.900000e-122 449
12 TraesCS2A01G256600 chr6A 88.793 116 8 3 2443 2554 4814987 4814873 1.680000e-28 137


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 TraesCS2A01G256600 chr2A 393338575 393342044 3469 False 6408 6408 100.0000 1 3470 1 chr2A.!!$F1 3469
1 TraesCS2A01G256600 chr2D 324860544 324863265 2721 True 2117 3009 94.2965 718 3470 2 chr2D.!!$R2 2752
2 TraesCS2A01G256600 chr2D 324907422 324908097 675 True 1029 1029 94.1000 1 678 1 chr2D.!!$R1 677
3 TraesCS2A01G256600 chr2B 393858401 393861058 2657 True 2040 2874 94.0070 768 3468 2 chr2B.!!$R1 2700
4 TraesCS2A01G256600 chr2B 393873730 393874944 1214 True 430 701 89.9300 4 688 2 chr2B.!!$R2 684
5 TraesCS2A01G256600 chr3D 481515271 481517073 1802 True 2529 2529 92.1080 768 2560 1 chr3D.!!$R1 1792
6 TraesCS2A01G256600 chr3B 642485333 642487124 1791 True 2497 2497 91.8890 770 2557 1 chr3B.!!$R1 1787
7 TraesCS2A01G256600 chr3A 624528486 624530274 1788 True 2425 2425 91.2170 770 2554 1 chr3A.!!$R1 1784

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
234 235 0.036732 TGCGACAAGGAGCCAGAAAT 59.963 50.0 0.00 0.0 0.0 2.17 F
654 655 0.037326 CTTGCAAGACCGCCTCTGTA 60.037 55.0 22.31 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2278 0.745468 GTATCGGGCTCTCGAACCTT 59.255 55.0 0.0 0.0 42.69 3.50 R
2596 3096 0.467384 TAGTACTCCCTCCGTCCTCG 59.533 60.0 0.0 0.0 0.00 4.63 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
51 52 0.543749 GCCAAGTCCTGCTATCTGGT 59.456 55.000 0.00 0.00 33.50 4.00
159 160 1.376812 CTTACCAGGGCCGGTGTTC 60.377 63.158 24.24 0.00 40.39 3.18
234 235 0.036732 TGCGACAAGGAGCCAGAAAT 59.963 50.000 0.00 0.00 0.00 2.17
241 242 2.950309 CAAGGAGCCAGAAATCATCCAG 59.050 50.000 0.00 0.00 32.21 3.86
257 258 1.374758 CAGCACCTTCTCGTCACCC 60.375 63.158 0.00 0.00 0.00 4.61
267 268 1.001764 TCGTCACCCGCTCCTTCTA 60.002 57.895 0.00 0.00 36.19 2.10
268 269 1.139095 CGTCACCCGCTCCTTCTAC 59.861 63.158 0.00 0.00 0.00 2.59
291 292 2.224161 GCTAGGTGTGGTCATGAGATCC 60.224 54.545 0.00 0.00 0.00 3.36
302 303 1.992519 ATGAGATCCTGGCCTGGTGC 61.993 60.000 26.40 19.03 40.16 5.01
361 362 1.613437 CCACGAATGGTTTTCAGCCTT 59.387 47.619 0.00 0.00 41.64 4.35
366 367 3.428045 CGAATGGTTTTCAGCCTTCATCC 60.428 47.826 0.00 0.00 0.00 3.51
445 446 2.228822 GGCGAATCTGAAAACACCACAT 59.771 45.455 0.00 0.00 0.00 3.21
494 495 1.518056 CGGTTGTGCAGCTCACCAAT 61.518 55.000 11.99 0.00 45.03 3.16
510 511 3.061295 CACCAATGAGATCAAAGACGACG 59.939 47.826 0.00 0.00 0.00 5.12
516 517 3.374367 TGAGATCAAAGACGACGGTAGAG 59.626 47.826 0.00 0.00 0.00 2.43
560 561 1.509923 GCTTGGCCAGCTGATCAAC 59.490 57.895 17.39 9.74 46.27 3.18
561 562 1.246056 GCTTGGCCAGCTGATCAACA 61.246 55.000 17.39 3.45 46.27 3.33
562 563 0.524862 CTTGGCCAGCTGATCAACAC 59.475 55.000 17.39 0.00 0.00 3.32
581 582 4.734917 ACACGAGACATAGACTTTGTAGC 58.265 43.478 0.00 0.00 0.00 3.58
583 584 5.646793 ACACGAGACATAGACTTTGTAGCTA 59.353 40.000 0.00 0.00 0.00 3.32
584 585 5.966503 CACGAGACATAGACTTTGTAGCTAC 59.033 44.000 17.30 17.30 0.00 3.58
604 605 2.093500 ACCATTCTCATGCGCTCTTGTA 60.093 45.455 9.73 0.00 0.00 2.41
605 606 2.543012 CCATTCTCATGCGCTCTTGTAG 59.457 50.000 9.73 4.24 0.00 2.74
606 607 2.299993 TTCTCATGCGCTCTTGTAGG 57.700 50.000 9.73 0.00 0.00 3.18
607 608 0.179100 TCTCATGCGCTCTTGTAGGC 60.179 55.000 9.73 0.00 0.00 3.93
608 609 1.153369 TCATGCGCTCTTGTAGGCC 60.153 57.895 9.73 0.00 0.00 5.19
609 610 1.153289 CATGCGCTCTTGTAGGCCT 60.153 57.895 11.78 11.78 0.00 5.19
610 611 0.745845 CATGCGCTCTTGTAGGCCTT 60.746 55.000 12.58 0.00 0.00 4.35
611 612 0.745845 ATGCGCTCTTGTAGGCCTTG 60.746 55.000 12.58 0.00 0.00 3.61
612 613 1.079127 GCGCTCTTGTAGGCCTTGA 60.079 57.895 12.58 3.80 0.00 3.02
613 614 0.462759 GCGCTCTTGTAGGCCTTGAT 60.463 55.000 12.58 0.00 0.00 2.57
614 615 1.576356 CGCTCTTGTAGGCCTTGATC 58.424 55.000 12.58 0.00 0.00 2.92
615 616 1.134699 CGCTCTTGTAGGCCTTGATCA 60.135 52.381 12.58 2.74 0.00 2.92
616 617 2.284190 GCTCTTGTAGGCCTTGATCAC 58.716 52.381 12.58 2.24 0.00 3.06
617 618 2.355108 GCTCTTGTAGGCCTTGATCACA 60.355 50.000 12.58 5.72 0.00 3.58
618 619 3.265791 CTCTTGTAGGCCTTGATCACAC 58.734 50.000 12.58 0.38 0.00 3.82
619 620 2.027192 TCTTGTAGGCCTTGATCACACC 60.027 50.000 12.58 0.00 0.00 4.16
620 621 0.249120 TGTAGGCCTTGATCACACCG 59.751 55.000 12.58 0.00 0.00 4.94
621 622 1.090052 GTAGGCCTTGATCACACCGC 61.090 60.000 12.58 0.00 0.00 5.68
622 623 2.252072 TAGGCCTTGATCACACCGCC 62.252 60.000 12.58 11.73 39.40 6.13
623 624 2.045926 GCCTTGATCACACCGCCT 60.046 61.111 0.00 0.00 0.00 5.52
624 625 1.220749 GCCTTGATCACACCGCCTA 59.779 57.895 0.00 0.00 0.00 3.93
625 626 1.090052 GCCTTGATCACACCGCCTAC 61.090 60.000 0.00 0.00 0.00 3.18
626 627 0.806102 CCTTGATCACACCGCCTACG 60.806 60.000 0.00 0.00 39.67 3.51
627 628 0.108804 CTTGATCACACCGCCTACGT 60.109 55.000 0.00 0.00 37.70 3.57
628 629 0.389296 TTGATCACACCGCCTACGTG 60.389 55.000 0.00 0.00 37.70 4.49
629 630 1.214589 GATCACACCGCCTACGTGT 59.785 57.895 0.00 0.00 37.70 4.49
630 631 0.389426 GATCACACCGCCTACGTGTT 60.389 55.000 0.00 0.00 37.70 3.32
631 632 0.669318 ATCACACCGCCTACGTGTTG 60.669 55.000 0.00 0.00 37.70 3.33
632 633 2.029964 ACACCGCCTACGTGTTGG 59.970 61.111 0.00 0.00 37.70 3.77
633 634 2.029964 CACCGCCTACGTGTTGGT 59.970 61.111 0.00 0.00 37.70 3.67
634 635 2.029964 ACCGCCTACGTGTTGGTG 59.970 61.111 0.00 7.00 37.70 4.17
635 636 3.419759 CCGCCTACGTGTTGGTGC 61.420 66.667 0.00 0.00 37.70 5.01
636 637 2.357034 CGCCTACGTGTTGGTGCT 60.357 61.111 0.00 0.00 33.53 4.40
637 638 1.959226 CGCCTACGTGTTGGTGCTT 60.959 57.895 0.00 0.00 33.53 3.91
638 639 1.574428 GCCTACGTGTTGGTGCTTG 59.426 57.895 0.00 0.00 0.00 4.01
639 640 1.574428 CCTACGTGTTGGTGCTTGC 59.426 57.895 0.00 0.00 0.00 4.01
640 641 1.163420 CCTACGTGTTGGTGCTTGCA 61.163 55.000 0.00 0.00 0.00 4.08
641 642 0.660488 CTACGTGTTGGTGCTTGCAA 59.340 50.000 0.00 0.00 0.00 4.08
642 643 0.660488 TACGTGTTGGTGCTTGCAAG 59.340 50.000 22.44 22.44 0.00 4.01
643 644 1.029408 ACGTGTTGGTGCTTGCAAGA 61.029 50.000 30.39 12.25 0.00 3.02
644 645 0.592247 CGTGTTGGTGCTTGCAAGAC 60.592 55.000 30.39 22.02 0.00 3.01
645 646 0.249031 GTGTTGGTGCTTGCAAGACC 60.249 55.000 30.39 28.63 0.00 3.85
646 647 1.008538 GTTGGTGCTTGCAAGACCG 60.009 57.895 30.39 4.69 32.41 4.79
647 648 2.844451 TTGGTGCTTGCAAGACCGC 61.844 57.895 30.39 18.36 32.41 5.68
648 649 4.043200 GGTGCTTGCAAGACCGCC 62.043 66.667 30.39 23.01 0.00 6.13
649 650 2.980233 GTGCTTGCAAGACCGCCT 60.980 61.111 30.39 0.00 0.00 5.52
650 651 2.669569 TGCTTGCAAGACCGCCTC 60.670 61.111 30.39 10.65 0.00 4.70
651 652 2.359230 GCTTGCAAGACCGCCTCT 60.359 61.111 30.39 0.00 0.00 3.69
652 653 2.684843 GCTTGCAAGACCGCCTCTG 61.685 63.158 30.39 0.22 0.00 3.35
653 654 1.302033 CTTGCAAGACCGCCTCTGT 60.302 57.895 22.31 0.00 0.00 3.41
654 655 0.037326 CTTGCAAGACCGCCTCTGTA 60.037 55.000 22.31 0.00 0.00 2.74
655 656 0.394938 TTGCAAGACCGCCTCTGTAA 59.605 50.000 0.00 0.00 0.00 2.41
656 657 0.613260 TGCAAGACCGCCTCTGTAAT 59.387 50.000 0.00 0.00 0.00 1.89
657 658 1.009829 GCAAGACCGCCTCTGTAATG 58.990 55.000 0.00 0.00 0.00 1.90
658 659 1.405526 GCAAGACCGCCTCTGTAATGA 60.406 52.381 0.00 0.00 0.00 2.57
659 660 2.271800 CAAGACCGCCTCTGTAATGAC 58.728 52.381 0.00 0.00 0.00 3.06
660 661 1.853963 AGACCGCCTCTGTAATGACT 58.146 50.000 0.00 0.00 0.00 3.41
661 662 2.180276 AGACCGCCTCTGTAATGACTT 58.820 47.619 0.00 0.00 0.00 3.01
662 663 2.166664 AGACCGCCTCTGTAATGACTTC 59.833 50.000 0.00 0.00 0.00 3.01
663 664 2.166664 GACCGCCTCTGTAATGACTTCT 59.833 50.000 0.00 0.00 0.00 2.85
664 665 2.567615 ACCGCCTCTGTAATGACTTCTT 59.432 45.455 0.00 0.00 0.00 2.52
665 666 3.008049 ACCGCCTCTGTAATGACTTCTTT 59.992 43.478 0.00 0.00 0.00 2.52
666 667 4.222145 ACCGCCTCTGTAATGACTTCTTTA 59.778 41.667 0.00 0.00 0.00 1.85
667 668 5.175859 CCGCCTCTGTAATGACTTCTTTAA 58.824 41.667 0.00 0.00 0.00 1.52
668 669 5.642063 CCGCCTCTGTAATGACTTCTTTAAA 59.358 40.000 0.00 0.00 0.00 1.52
669 670 6.402226 CCGCCTCTGTAATGACTTCTTTAAAC 60.402 42.308 0.00 0.00 0.00 2.01
670 671 6.402226 CGCCTCTGTAATGACTTCTTTAAACC 60.402 42.308 0.00 0.00 0.00 3.27
671 672 6.655425 GCCTCTGTAATGACTTCTTTAAACCT 59.345 38.462 0.00 0.00 0.00 3.50
672 673 7.175119 GCCTCTGTAATGACTTCTTTAAACCTT 59.825 37.037 0.00 0.00 0.00 3.50
673 674 8.722394 CCTCTGTAATGACTTCTTTAAACCTTC 58.278 37.037 0.00 0.00 0.00 3.46
674 675 9.495572 CTCTGTAATGACTTCTTTAAACCTTCT 57.504 33.333 0.00 0.00 0.00 2.85
675 676 9.847224 TCTGTAATGACTTCTTTAAACCTTCTT 57.153 29.630 0.00 0.00 0.00 2.52
677 678 9.847224 TGTAATGACTTCTTTAAACCTTCTTCT 57.153 29.630 0.00 0.00 0.00 2.85
714 715 8.988934 TGATACATAAGTCTTTTATGGATTCGC 58.011 33.333 10.59 0.00 36.38 4.70
715 716 6.287107 ACATAAGTCTTTTATGGATTCGCG 57.713 37.500 0.00 0.00 36.86 5.87
716 717 6.046593 ACATAAGTCTTTTATGGATTCGCGA 58.953 36.000 3.71 3.71 36.86 5.87
717 718 6.537301 ACATAAGTCTTTTATGGATTCGCGAA 59.463 34.615 25.66 25.66 36.86 4.70
718 719 5.873179 AAGTCTTTTATGGATTCGCGAAA 57.127 34.783 27.23 10.25 0.00 3.46
719 720 5.873179 AGTCTTTTATGGATTCGCGAAAA 57.127 34.783 27.23 14.88 0.00 2.29
720 721 6.249035 AGTCTTTTATGGATTCGCGAAAAA 57.751 33.333 27.23 17.82 0.00 1.94
787 798 5.171476 GTCTCTGTAGCTGCTCAATTTGTA 58.829 41.667 4.91 0.00 0.00 2.41
803 817 6.315144 TCAATTTGTATGTACTCGGTGGAATG 59.685 38.462 0.00 0.00 0.00 2.67
833 855 7.255590 CGTAAGCATGATTCCCTCCAATAATTT 60.256 37.037 0.00 0.00 0.00 1.82
917 944 2.545946 GCTCGGATGTAGCTTTTGATCC 59.454 50.000 0.00 0.00 37.01 3.36
1045 1076 0.250234 AGCTCTTGCGGCAGTAATCA 59.750 50.000 1.67 0.00 45.42 2.57
1047 1078 1.262683 GCTCTTGCGGCAGTAATCATC 59.737 52.381 1.67 0.00 0.00 2.92
1262 1328 2.364317 CTCCCTCTTCGGCCTCCA 60.364 66.667 0.00 0.00 0.00 3.86
1312 1378 1.374758 AAGTTCCTCTTCGCCAGCG 60.375 57.895 5.50 5.50 41.35 5.18
1998 2065 4.148825 CCGGGGGAAGCTCTGTCG 62.149 72.222 0.00 0.00 0.00 4.35
2094 2161 2.110967 CATGCTCAAGAGGGCGGTG 61.111 63.158 0.00 0.00 0.00 4.94
2508 3004 1.730612 CCTGATCCGAATGATGCATCG 59.269 52.381 21.34 11.21 32.41 3.84
2561 3061 8.645814 AATGTACGATTACAGATATACCTCCA 57.354 34.615 0.00 0.00 41.62 3.86
2562 3062 8.824756 ATGTACGATTACAGATATACCTCCAT 57.175 34.615 0.00 0.00 41.62 3.41
2563 3063 8.277490 TGTACGATTACAGATATACCTCCATC 57.723 38.462 0.00 0.00 32.98 3.51
2564 3064 6.777213 ACGATTACAGATATACCTCCATCC 57.223 41.667 0.00 0.00 0.00 3.51
2565 3065 5.657302 ACGATTACAGATATACCTCCATCCC 59.343 44.000 0.00 0.00 0.00 3.85
2566 3066 5.656859 CGATTACAGATATACCTCCATCCCA 59.343 44.000 0.00 0.00 0.00 4.37
2567 3067 6.154534 CGATTACAGATATACCTCCATCCCAA 59.845 42.308 0.00 0.00 0.00 4.12
2568 3068 7.310423 CGATTACAGATATACCTCCATCCCAAA 60.310 40.741 0.00 0.00 0.00 3.28
2569 3069 7.888514 TTACAGATATACCTCCATCCCAAAT 57.111 36.000 0.00 0.00 0.00 2.32
2570 3070 6.786843 ACAGATATACCTCCATCCCAAATT 57.213 37.500 0.00 0.00 0.00 1.82
2571 3071 7.888514 ACAGATATACCTCCATCCCAAATTA 57.111 36.000 0.00 0.00 0.00 1.40
2572 3072 7.922382 ACAGATATACCTCCATCCCAAATTAG 58.078 38.462 0.00 0.00 0.00 1.73
2573 3073 7.739444 ACAGATATACCTCCATCCCAAATTAGA 59.261 37.037 0.00 0.00 0.00 2.10
2574 3074 8.043710 CAGATATACCTCCATCCCAAATTAGAC 58.956 40.741 0.00 0.00 0.00 2.59
2575 3075 7.739444 AGATATACCTCCATCCCAAATTAGACA 59.261 37.037 0.00 0.00 0.00 3.41
2576 3076 6.786843 ATACCTCCATCCCAAATTAGACAT 57.213 37.500 0.00 0.00 0.00 3.06
2577 3077 5.472301 ACCTCCATCCCAAATTAGACATT 57.528 39.130 0.00 0.00 0.00 2.71
2578 3078 6.590656 ACCTCCATCCCAAATTAGACATTA 57.409 37.500 0.00 0.00 0.00 1.90
2579 3079 6.365520 ACCTCCATCCCAAATTAGACATTAC 58.634 40.000 0.00 0.00 0.00 1.89
2580 3080 6.160459 ACCTCCATCCCAAATTAGACATTACT 59.840 38.462 0.00 0.00 0.00 2.24
2581 3081 7.062957 CCTCCATCCCAAATTAGACATTACTT 58.937 38.462 0.00 0.00 0.00 2.24
2582 3082 7.013655 CCTCCATCCCAAATTAGACATTACTTG 59.986 40.741 0.00 0.00 0.00 3.16
2583 3083 7.410174 TCCATCCCAAATTAGACATTACTTGT 58.590 34.615 0.00 0.00 42.79 3.16
2597 3097 7.028926 ACATTACTTGTCTGTCTAGATACCG 57.971 40.000 0.00 0.00 34.94 4.02
2598 3098 6.827251 ACATTACTTGTCTGTCTAGATACCGA 59.173 38.462 0.00 0.00 34.94 4.69
2599 3099 6.922247 TTACTTGTCTGTCTAGATACCGAG 57.078 41.667 0.00 0.00 34.94 4.63
2600 3100 4.200874 ACTTGTCTGTCTAGATACCGAGG 58.799 47.826 0.00 0.00 34.94 4.63
2601 3101 4.080469 ACTTGTCTGTCTAGATACCGAGGA 60.080 45.833 0.00 0.00 34.94 3.71
2602 3102 3.806380 TGTCTGTCTAGATACCGAGGAC 58.194 50.000 0.00 0.00 34.94 3.85
2603 3103 2.801679 GTCTGTCTAGATACCGAGGACG 59.198 54.545 0.00 0.00 34.94 4.79
2613 3113 3.824810 CGAGGACGGAGGGAGTAC 58.175 66.667 0.00 0.00 35.72 2.73
2614 3114 1.224039 CGAGGACGGAGGGAGTACT 59.776 63.158 0.00 0.00 35.04 2.73
2615 3115 0.467384 CGAGGACGGAGGGAGTACTA 59.533 60.000 0.00 0.00 31.89 1.82
2616 3116 1.540797 CGAGGACGGAGGGAGTACTAG 60.541 61.905 0.00 0.00 31.89 2.57
2617 3117 1.490069 GAGGACGGAGGGAGTACTAGT 59.510 57.143 0.00 0.00 31.89 2.57
2625 3125 4.623171 CGGAGGGAGTACTAGTTTGCAATT 60.623 45.833 0.00 0.00 0.00 2.32
2659 3160 9.965824 GTATTTCTCACATTCTTGAAAGGAAAA 57.034 29.630 0.00 0.00 32.91 2.29
2697 3198 5.091261 ACATCATCTACTCCAAACCAGTC 57.909 43.478 0.00 0.00 0.00 3.51
2699 3200 5.013079 ACATCATCTACTCCAAACCAGTCAA 59.987 40.000 0.00 0.00 0.00 3.18
2706 3207 3.875134 ACTCCAAACCAGTCAAACTTACG 59.125 43.478 0.00 0.00 0.00 3.18
2734 3235 5.253330 TGACTTTTAAGGCCCTCTACAATG 58.747 41.667 0.00 0.00 31.13 2.82
2760 3261 7.094805 GCACACATAATTCAAGAGACTGGTAAA 60.095 37.037 0.00 0.00 0.00 2.01
2800 3302 1.922135 AAGCGGCATAACCAGCAACG 61.922 55.000 1.45 0.00 39.49 4.10
2822 3324 2.752354 CTCCGATGGTAAACATGGCAAA 59.248 45.455 0.00 0.00 40.72 3.68
2823 3325 2.752354 TCCGATGGTAAACATGGCAAAG 59.248 45.455 0.00 0.00 40.72 2.77
2866 3368 5.998363 GGATAAACATCAGGGAATCCACTAC 59.002 44.000 0.09 0.00 34.34 2.73
2894 3396 5.375283 TCTCCTCTACTAGAGCAAAGCTA 57.625 43.478 7.50 0.00 40.98 3.32
2897 3399 4.757657 TCCTCTACTAGAGCAAAGCTATCG 59.242 45.833 7.50 0.00 40.98 2.92
2912 3414 3.013921 GCTATCGACCAAATTCCACCAA 58.986 45.455 0.00 0.00 0.00 3.67
2945 3448 2.413371 GCAGAAGACGGAAATTCACTGC 60.413 50.000 0.00 0.00 37.96 4.40
2952 3455 3.467803 ACGGAAATTCACTGCTATAGGC 58.532 45.455 1.04 0.00 42.22 3.93
2959 3462 0.764369 CACTGCTATAGGCCCCCTGA 60.764 60.000 0.00 0.00 40.92 3.86
3060 3576 4.502105 AATTTTGGGCACTTCCAAGTTT 57.498 36.364 0.00 0.00 46.19 2.66
3072 3588 7.203218 GCACTTCCAAGTTTATCCATTATTCC 58.797 38.462 0.00 0.00 37.08 3.01
3132 3649 0.603707 AGGGTGATATTGCGCCGATG 60.604 55.000 4.18 0.00 39.34 3.84
3234 3752 3.808174 GGAGTGTGTGTAAAGACAGGAAC 59.192 47.826 0.00 0.00 35.82 3.62
3238 3756 6.646267 AGTGTGTGTAAAGACAGGAACTAAA 58.354 36.000 0.00 0.00 36.02 1.85
3388 3906 5.455326 CCACCTATGATCAAGTAAGAAGGGG 60.455 48.000 0.00 0.00 0.00 4.79
3398 3917 1.564818 GTAAGAAGGGGGAAAGGGAGG 59.435 57.143 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 0.972471 TGCGGATCCAGAGAAGAGCA 60.972 55.000 13.41 7.59 0.00 4.26
116 117 5.573380 AGCCATAGGAAGATCTTTATGCA 57.427 39.130 16.79 0.00 0.00 3.96
119 120 6.198237 AGCAAGCCATAGGAAGATCTTTAT 57.802 37.500 9.87 1.56 0.00 1.40
159 160 2.456119 GCCAATCTGTCTGCGGTCG 61.456 63.158 0.00 0.00 0.00 4.79
234 235 0.532573 GACGAGAAGGTGCTGGATGA 59.467 55.000 0.00 0.00 0.00 2.92
257 258 1.102222 ACCTAGCGGTAGAAGGAGCG 61.102 60.000 22.81 6.73 43.29 5.03
268 269 0.179100 CTCATGACCACACCTAGCGG 60.179 60.000 0.00 0.00 0.00 5.52
361 362 0.991920 GGTTGGGGAGTCTTGGATGA 59.008 55.000 0.00 0.00 0.00 2.92
366 367 2.359975 GGCGGTTGGGGAGTCTTG 60.360 66.667 0.00 0.00 0.00 3.02
403 404 0.317160 AGCGGTGAGAATGAACACGA 59.683 50.000 0.00 0.00 37.82 4.35
445 446 3.669536 TCATTGTTGAACATGCTACCGA 58.330 40.909 0.00 0.00 0.00 4.69
494 495 3.340928 TCTACCGTCGTCTTTGATCTCA 58.659 45.455 0.00 0.00 0.00 3.27
560 561 4.987832 AGCTACAAAGTCTATGTCTCGTG 58.012 43.478 0.00 0.00 32.27 4.35
561 562 5.066246 GGTAGCTACAAAGTCTATGTCTCGT 59.934 44.000 24.75 0.00 32.27 4.18
562 563 5.066117 TGGTAGCTACAAAGTCTATGTCTCG 59.934 44.000 24.75 0.00 32.27 4.04
581 582 2.522836 AGAGCGCATGAGAATGGTAG 57.477 50.000 11.47 0.00 0.00 3.18
583 584 1.339438 ACAAGAGCGCATGAGAATGGT 60.339 47.619 11.47 0.00 0.00 3.55
584 585 1.376543 ACAAGAGCGCATGAGAATGG 58.623 50.000 11.47 0.00 0.00 3.16
604 605 2.045926 GCGGTGTGATCAAGGCCT 60.046 61.111 0.00 0.00 0.00 5.19
605 606 2.252072 TAGGCGGTGTGATCAAGGCC 62.252 60.000 15.86 15.86 41.50 5.19
606 607 1.090052 GTAGGCGGTGTGATCAAGGC 61.090 60.000 0.00 2.00 0.00 4.35
607 608 0.806102 CGTAGGCGGTGTGATCAAGG 60.806 60.000 0.00 0.00 0.00 3.61
608 609 0.108804 ACGTAGGCGGTGTGATCAAG 60.109 55.000 0.00 0.00 43.45 3.02
609 610 0.389296 CACGTAGGCGGTGTGATCAA 60.389 55.000 0.00 0.00 43.45 2.57
610 611 1.214325 CACGTAGGCGGTGTGATCA 59.786 57.895 0.00 0.00 43.45 2.92
611 612 0.389426 AACACGTAGGCGGTGTGATC 60.389 55.000 11.65 0.00 43.45 2.92
612 613 0.669318 CAACACGTAGGCGGTGTGAT 60.669 55.000 11.65 0.00 43.45 3.06
613 614 1.300311 CAACACGTAGGCGGTGTGA 60.300 57.895 11.65 0.00 43.45 3.58
614 615 2.314647 CCAACACGTAGGCGGTGTG 61.315 63.158 11.65 8.30 43.45 3.82
615 616 2.029964 CCAACACGTAGGCGGTGT 59.970 61.111 6.27 6.27 43.45 4.16
616 617 2.029964 ACCAACACGTAGGCGGTG 59.970 61.111 0.00 5.11 43.45 4.94
617 618 2.029964 CACCAACACGTAGGCGGT 59.970 61.111 0.00 0.00 43.45 5.68
618 619 3.419759 GCACCAACACGTAGGCGG 61.420 66.667 0.00 0.00 43.45 6.13
619 620 1.959226 AAGCACCAACACGTAGGCG 60.959 57.895 0.00 0.00 44.93 5.52
620 621 1.574428 CAAGCACCAACACGTAGGC 59.426 57.895 0.00 0.00 0.00 3.93
621 622 1.163420 TGCAAGCACCAACACGTAGG 61.163 55.000 0.00 0.00 0.00 3.18
622 623 0.660488 TTGCAAGCACCAACACGTAG 59.340 50.000 0.00 0.00 0.00 3.51
623 624 0.660488 CTTGCAAGCACCAACACGTA 59.340 50.000 14.65 0.00 0.00 3.57
624 625 1.029408 TCTTGCAAGCACCAACACGT 61.029 50.000 21.99 0.00 0.00 4.49
625 626 0.592247 GTCTTGCAAGCACCAACACG 60.592 55.000 21.99 0.00 0.00 4.49
626 627 0.249031 GGTCTTGCAAGCACCAACAC 60.249 55.000 28.50 18.34 0.00 3.32
627 628 1.723608 CGGTCTTGCAAGCACCAACA 61.724 55.000 30.46 11.69 0.00 3.33
628 629 1.008538 CGGTCTTGCAAGCACCAAC 60.009 57.895 30.46 20.93 0.00 3.77
629 630 2.844451 GCGGTCTTGCAAGCACCAA 61.844 57.895 30.46 12.88 34.15 3.67
630 631 3.286751 GCGGTCTTGCAAGCACCA 61.287 61.111 30.46 13.18 34.15 4.17
631 632 4.043200 GGCGGTCTTGCAAGCACC 62.043 66.667 25.84 25.84 36.28 5.01
632 633 2.970974 GAGGCGGTCTTGCAAGCAC 61.971 63.158 21.99 18.52 36.28 4.40
633 634 2.669569 GAGGCGGTCTTGCAAGCA 60.670 61.111 21.99 7.99 36.28 3.91
634 635 2.359230 AGAGGCGGTCTTGCAAGC 60.359 61.111 21.99 15.82 36.28 4.01
635 636 0.037326 TACAGAGGCGGTCTTGCAAG 60.037 55.000 20.81 20.81 36.28 4.01
636 637 0.394938 TTACAGAGGCGGTCTTGCAA 59.605 50.000 0.00 0.00 36.28 4.08
637 638 0.613260 ATTACAGAGGCGGTCTTGCA 59.387 50.000 0.00 0.00 36.28 4.08
638 639 1.009829 CATTACAGAGGCGGTCTTGC 58.990 55.000 0.00 0.00 30.64 4.01
639 640 2.093973 AGTCATTACAGAGGCGGTCTTG 60.094 50.000 0.00 0.00 30.64 3.02
640 641 2.180276 AGTCATTACAGAGGCGGTCTT 58.820 47.619 0.00 0.00 30.64 3.01
641 642 1.853963 AGTCATTACAGAGGCGGTCT 58.146 50.000 0.00 0.00 35.00 3.85
642 643 2.166664 AGAAGTCATTACAGAGGCGGTC 59.833 50.000 0.00 0.00 0.00 4.79
643 644 2.180276 AGAAGTCATTACAGAGGCGGT 58.820 47.619 0.00 0.00 0.00 5.68
644 645 2.969628 AGAAGTCATTACAGAGGCGG 57.030 50.000 0.00 0.00 0.00 6.13
645 646 6.402226 GGTTTAAAGAAGTCATTACAGAGGCG 60.402 42.308 0.00 0.00 0.00 5.52
646 647 6.655425 AGGTTTAAAGAAGTCATTACAGAGGC 59.345 38.462 0.00 0.00 0.00 4.70
647 648 8.622948 AAGGTTTAAAGAAGTCATTACAGAGG 57.377 34.615 0.00 0.00 0.00 3.69
648 649 9.495572 AGAAGGTTTAAAGAAGTCATTACAGAG 57.504 33.333 0.00 0.00 0.00 3.35
649 650 9.847224 AAGAAGGTTTAAAGAAGTCATTACAGA 57.153 29.630 0.00 0.00 0.00 3.41
651 652 9.847224 AGAAGAAGGTTTAAAGAAGTCATTACA 57.153 29.630 0.00 0.00 0.00 2.41
688 689 8.988934 GCGAATCCATAAAAGACTTATGTATCA 58.011 33.333 0.00 0.00 32.07 2.15
689 690 8.162880 CGCGAATCCATAAAAGACTTATGTATC 58.837 37.037 0.00 0.23 32.07 2.24
690 691 7.870954 TCGCGAATCCATAAAAGACTTATGTAT 59.129 33.333 6.20 0.00 32.07 2.29
691 692 7.204604 TCGCGAATCCATAAAAGACTTATGTA 58.795 34.615 6.20 0.00 32.07 2.29
692 693 6.046593 TCGCGAATCCATAAAAGACTTATGT 58.953 36.000 6.20 0.00 32.07 2.29
693 694 6.525121 TCGCGAATCCATAAAAGACTTATG 57.475 37.500 6.20 0.00 33.39 1.90
694 695 7.548196 TTTCGCGAATCCATAAAAGACTTAT 57.452 32.000 24.05 0.00 0.00 1.73
695 696 6.971527 TTTCGCGAATCCATAAAAGACTTA 57.028 33.333 24.05 0.00 0.00 2.24
696 697 5.873179 TTTCGCGAATCCATAAAAGACTT 57.127 34.783 24.05 0.00 0.00 3.01
697 698 5.873179 TTTTCGCGAATCCATAAAAGACT 57.127 34.783 24.05 0.00 0.00 3.24
741 742 6.837312 ACGATTAATTAATCCATCCTCACCA 58.163 36.000 25.51 0.00 39.04 4.17
787 798 2.803133 CGATGCATTCCACCGAGTACAT 60.803 50.000 0.00 0.00 0.00 2.29
803 817 2.481952 GAGGGAATCATGCTTACGATGC 59.518 50.000 0.00 0.00 0.00 3.91
876 902 7.556275 TCCGAGCTTAATATTTTGATTGGTCTT 59.444 33.333 0.00 0.00 0.00 3.01
899 926 2.917933 TGGGATCAAAAGCTACATCCG 58.082 47.619 0.00 0.00 36.41 4.18
917 944 7.011109 CCACTGTCTAGTAAATTAAACCGATGG 59.989 40.741 0.00 0.00 34.74 3.51
1045 1076 5.677091 GCAATACCAACAAGATGAAAGCGAT 60.677 40.000 0.00 0.00 0.00 4.58
1047 1078 3.853671 GCAATACCAACAAGATGAAAGCG 59.146 43.478 0.00 0.00 0.00 4.68
1077 1108 3.248495 TGAGATGAGCTCTGCTTTCTG 57.752 47.619 16.19 0.00 44.27 3.02
1262 1328 4.052229 CGACGAGGAAGGCCGTGT 62.052 66.667 0.00 0.00 39.30 4.49
1404 1470 1.150081 CTGGACCATCATGGCCCTC 59.850 63.158 10.89 0.00 41.15 4.30
1998 2065 3.934391 CTTGCCGAGGTCGTCCCAC 62.934 68.421 0.00 0.00 37.74 4.61
2094 2161 1.557443 CGTCAAACTCCACGTCTGCC 61.557 60.000 0.00 0.00 0.00 4.85
2096 2163 1.557443 GCCGTCAAACTCCACGTCTG 61.557 60.000 0.00 0.00 34.06 3.51
2211 2278 0.745468 GTATCGGGCTCTCGAACCTT 59.255 55.000 0.00 0.00 42.69 3.50
2452 2946 3.428452 CGAAATCATTTGCTGATGCCTGT 60.428 43.478 0.00 0.00 44.03 4.00
2487 2981 2.775890 GATGCATCATTCGGATCAGGT 58.224 47.619 21.92 0.00 32.57 4.00
2508 3004 3.628942 TGCAATCATACAGCTGAATGGTC 59.371 43.478 23.35 2.88 0.00 4.02
2554 3054 6.590656 AATGTCTAATTTGGGATGGAGGTA 57.409 37.500 0.00 0.00 0.00 3.08
2555 3055 5.472301 AATGTCTAATTTGGGATGGAGGT 57.528 39.130 0.00 0.00 0.00 3.85
2558 3058 7.410174 ACAAGTAATGTCTAATTTGGGATGGA 58.590 34.615 0.00 0.00 37.96 3.41
2559 3059 7.645058 ACAAGTAATGTCTAATTTGGGATGG 57.355 36.000 0.00 0.00 37.96 3.51
2574 3074 7.260558 TCGGTATCTAGACAGACAAGTAATG 57.739 40.000 0.00 0.00 32.25 1.90
2575 3075 6.487331 CCTCGGTATCTAGACAGACAAGTAAT 59.513 42.308 0.00 0.00 32.25 1.89
2576 3076 5.821470 CCTCGGTATCTAGACAGACAAGTAA 59.179 44.000 0.00 0.00 32.25 2.24
2577 3077 5.129980 TCCTCGGTATCTAGACAGACAAGTA 59.870 44.000 0.00 0.00 32.25 2.24
2578 3078 4.080469 TCCTCGGTATCTAGACAGACAAGT 60.080 45.833 0.00 0.00 32.25 3.16
2579 3079 4.273969 GTCCTCGGTATCTAGACAGACAAG 59.726 50.000 0.00 0.00 32.25 3.16
2580 3080 4.197750 GTCCTCGGTATCTAGACAGACAA 58.802 47.826 0.00 0.00 32.25 3.18
2581 3081 3.740452 CGTCCTCGGTATCTAGACAGACA 60.740 52.174 0.00 0.00 32.25 3.41
2582 3082 2.801679 CGTCCTCGGTATCTAGACAGAC 59.198 54.545 0.00 0.00 32.25 3.51
2583 3083 3.109044 CGTCCTCGGTATCTAGACAGA 57.891 52.381 0.00 0.00 34.56 3.41
2596 3096 0.467384 TAGTACTCCCTCCGTCCTCG 59.533 60.000 0.00 0.00 0.00 4.63
2597 3097 1.490069 ACTAGTACTCCCTCCGTCCTC 59.510 57.143 0.00 0.00 0.00 3.71
2598 3098 1.594129 ACTAGTACTCCCTCCGTCCT 58.406 55.000 0.00 0.00 0.00 3.85
2599 3099 2.426381 CAAACTAGTACTCCCTCCGTCC 59.574 54.545 0.00 0.00 0.00 4.79
2600 3100 2.159268 GCAAACTAGTACTCCCTCCGTC 60.159 54.545 0.00 0.00 0.00 4.79
2601 3101 1.823610 GCAAACTAGTACTCCCTCCGT 59.176 52.381 0.00 0.00 0.00 4.69
2602 3102 1.822990 TGCAAACTAGTACTCCCTCCG 59.177 52.381 0.00 0.00 0.00 4.63
2603 3103 3.975168 TTGCAAACTAGTACTCCCTCC 57.025 47.619 0.00 0.00 0.00 4.30
2604 3104 7.484035 CATAATTGCAAACTAGTACTCCCTC 57.516 40.000 1.71 0.00 0.00 4.30
2625 3125 7.828717 TCAAGAATGTGAGAAATACTTGGCATA 59.171 33.333 0.00 0.00 35.49 3.14
2659 3160 0.744414 ATGTCCTGCGCGTTGCTAAT 60.744 50.000 8.43 0.00 46.63 1.73
2662 3163 3.121030 GATGTCCTGCGCGTTGCT 61.121 61.111 8.43 0.00 46.63 3.91
2697 3198 9.274065 GCCTTAAAAGTCATATTCGTAAGTTTG 57.726 33.333 0.00 0.00 39.48 2.93
2699 3200 7.066645 GGGCCTTAAAAGTCATATTCGTAAGTT 59.933 37.037 0.84 0.00 39.48 2.66
2706 3207 7.280356 TGTAGAGGGCCTTAAAAGTCATATTC 58.720 38.462 7.89 0.00 0.00 1.75
2719 3220 0.698238 TGTGCATTGTAGAGGGCCTT 59.302 50.000 7.89 0.00 0.00 4.35
2734 3235 4.697352 ACCAGTCTCTTGAATTATGTGTGC 59.303 41.667 0.00 0.00 0.00 4.57
2760 3261 7.920682 CCGCTTGGAGCTTAATATTTGTAAATT 59.079 33.333 0.00 0.00 39.60 1.82
2782 3284 2.398554 CGTTGCTGGTTATGCCGCT 61.399 57.895 0.00 0.00 41.21 5.52
2783 3285 2.100216 CGTTGCTGGTTATGCCGC 59.900 61.111 0.00 0.00 41.21 6.53
2800 3302 0.663153 GCCATGTTTACCATCGGAGC 59.337 55.000 0.00 0.00 0.00 4.70
2822 3324 1.531149 CGAGTCGTTTTGTGATTGCCT 59.469 47.619 3.82 0.00 0.00 4.75
2823 3325 1.399727 CCGAGTCGTTTTGTGATTGCC 60.400 52.381 12.31 0.00 0.00 4.52
2866 3368 5.759506 TGCTCTAGTAGAGGAGAAAATCG 57.240 43.478 25.20 0.98 42.54 3.34
2894 3396 4.946478 TTTTTGGTGGAATTTGGTCGAT 57.054 36.364 0.00 0.00 0.00 3.59
2916 3418 2.910688 TCCGTCTTCTGCTTGTTCTT 57.089 45.000 0.00 0.00 0.00 2.52
2945 3448 0.398318 GCAGTTCAGGGGGCCTATAG 59.602 60.000 0.84 0.00 29.64 1.31
2952 3455 1.880819 GCAATGTGCAGTTCAGGGGG 61.881 60.000 0.00 0.00 44.26 5.40
2974 3477 3.313012 TCGAAGTGTTGTCGATGGATT 57.687 42.857 0.00 0.00 42.31 3.01
3024 3540 5.741673 GCCCAAAATTTTACATGTCTGGTGT 60.742 40.000 0.00 0.00 0.00 4.16
3060 3576 9.758021 ATGATGTTATGCTTGGAATAATGGATA 57.242 29.630 0.00 0.00 0.00 2.59
3072 3588 7.641760 TGTGCTTATGTATGATGTTATGCTTG 58.358 34.615 0.00 0.00 0.00 4.01
3132 3649 3.801129 GCTTCCACCTAAGCGAGC 58.199 61.111 0.00 0.00 42.21 5.03
3255 3773 6.053005 TCGAAAAGTCATTACCATGGTATCC 58.947 40.000 25.12 12.78 0.00 2.59
3388 3906 4.912317 ACTTCTAAGTTCCTCCCTTTCC 57.088 45.455 0.00 0.00 35.21 3.13
3417 3936 6.071784 ACGTGTATATACTTGTGTCCTGTTGA 60.072 38.462 13.89 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.