Multiple sequence alignment - TraesCS5B01G436500

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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 TraesCS5B01G436500 chr5B 100.000 3473 0 0 1 3473 610283422 610279950 0.000000e+00 6414.0
1 TraesCS5B01G436500 chr5B 93.041 1667 82 18 835 2490 610108090 610106447 0.000000e+00 2405.0
2 TraesCS5B01G436500 chr5B 91.988 1635 113 10 865 2490 610206051 610204426 0.000000e+00 2278.0
3 TraesCS5B01G436500 chr5B 89.078 586 24 13 170 720 476074631 476075211 0.000000e+00 691.0
4 TraesCS5B01G436500 chr5B 94.203 69 4 0 103 171 476074254 476074322 4.740000e-19 106.0
5 TraesCS5B01G436500 chr5D 93.149 1810 103 9 835 2641 494079328 494077537 0.000000e+00 2636.0
6 TraesCS5B01G436500 chr5D 92.468 1633 99 12 863 2474 493912289 493913918 0.000000e+00 2313.0
7 TraesCS5B01G436500 chr5D 92.693 1177 73 6 1436 2611 494060014 494058850 0.000000e+00 1685.0
8 TraesCS5B01G436500 chr5D 82.890 1543 196 40 989 2482 542106120 542107643 0.000000e+00 1325.0
9 TraesCS5B01G436500 chr5D 89.474 513 43 6 2967 3473 494074607 494074100 3.780000e-179 638.0
10 TraesCS5B01G436500 chr5D 88.802 509 38 8 2967 3473 493842453 493842944 1.070000e-169 606.0
11 TraesCS5B01G436500 chr5D 79.188 394 52 21 379 753 113745110 113744728 2.680000e-61 246.0
12 TraesCS5B01G436500 chr5D 92.754 69 5 0 28 96 494066515 494066447 2.210000e-17 100.0
13 TraesCS5B01G436500 chr5D 88.235 68 2 1 28 95 493911735 493911796 3.720000e-10 76.8
14 TraesCS5B01G436500 chr5A 92.747 1751 112 5 835 2581 617123841 617122102 0.000000e+00 2516.0
15 TraesCS5B01G436500 chr5A 92.400 1658 103 8 835 2490 617097470 617095834 0.000000e+00 2342.0
16 TraesCS5B01G436500 chr5A 87.928 555 53 8 2088 2641 617111674 617111133 2.920000e-180 641.0
17 TraesCS5B01G436500 chr5A 83.616 708 87 19 2791 3473 617100124 617099421 3.780000e-179 638.0
18 TraesCS5B01G436500 chr5A 93.878 49 2 1 1 49 617097598 617097551 4.810000e-09 73.1
19 TraesCS5B01G436500 chr4A 82.790 1441 202 30 1019 2430 626954573 626953150 0.000000e+00 1245.0
20 TraesCS5B01G436500 chr4A 92.647 68 4 1 102 169 670212989 670213055 2.850000e-16 97.1
21 TraesCS5B01G436500 chr7A 89.270 671 23 24 102 725 124411174 124411842 0.000000e+00 795.0
22 TraesCS5B01G436500 chr7A 86.083 697 39 22 103 753 642531262 642530578 0.000000e+00 697.0
23 TraesCS5B01G436500 chr7A 85.038 655 35 21 102 704 79594503 79595146 2.960000e-170 608.0
24 TraesCS5B01G436500 chr4B 91.800 500 25 2 227 710 529339630 529340129 0.000000e+00 682.0
25 TraesCS5B01G436500 chr4B 96.053 76 3 0 101 176 529339459 529339534 1.310000e-24 124.0
26 TraesCS5B01G436500 chr2B 85.329 668 43 20 132 753 679813502 679814160 1.050000e-179 640.0
27 TraesCS5B01G436500 chr2B 90.411 73 5 2 99 170 796607815 796607886 1.030000e-15 95.3
28 TraesCS5B01G436500 chr2A 81.211 644 81 15 2853 3473 706581526 706582152 1.870000e-132 483.0
29 TraesCS5B01G436500 chr2D 77.208 566 87 28 224 754 540957455 540958013 3.390000e-75 292.0
30 TraesCS5B01G436500 chr2D 76.997 313 43 17 102 385 26777594 26777906 6.000000e-33 152.0
31 TraesCS5B01G436500 chr3D 75.485 722 102 45 100 754 14964818 14965531 2.040000e-72 283.0
32 TraesCS5B01G436500 chr3D 78.445 283 35 16 2929 3207 148399740 148399480 9.980000e-36 161.0
33 TraesCS5B01G436500 chr1B 79.653 403 48 18 379 754 152516480 152516085 3.440000e-65 259.0
34 TraesCS5B01G436500 chr1B 75.873 315 45 19 101 385 152516874 152516561 7.820000e-27 132.0
35 TraesCS5B01G436500 chr1B 83.942 137 14 5 2929 3058 626134293 626134428 1.310000e-24 124.0
36 TraesCS5B01G436500 chr3A 78.611 360 53 15 407 753 142903800 142904148 2.100000e-52 217.0
37 TraesCS5B01G436500 chr1A 79.085 306 42 8 393 680 64835059 64835360 1.270000e-44 191.0
38 TraesCS5B01G436500 chr6A 75.394 317 47 17 98 384 563478696 563479011 1.310000e-24 124.0


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 TraesCS5B01G436500 chr5B 610279950 610283422 3472 True 6414.0 6414 100.000000 1 3473 1 chr5B.!!$R3 3472
1 TraesCS5B01G436500 chr5B 610106447 610108090 1643 True 2405.0 2405 93.041000 835 2490 1 chr5B.!!$R1 1655
2 TraesCS5B01G436500 chr5B 610204426 610206051 1625 True 2278.0 2278 91.988000 865 2490 1 chr5B.!!$R2 1625
3 TraesCS5B01G436500 chr5B 476074254 476075211 957 False 398.5 691 91.640500 103 720 2 chr5B.!!$F1 617
4 TraesCS5B01G436500 chr5D 494058850 494060014 1164 True 1685.0 1685 92.693000 1436 2611 1 chr5D.!!$R2 1175
5 TraesCS5B01G436500 chr5D 494074100 494079328 5228 True 1637.0 2636 91.311500 835 3473 2 chr5D.!!$R4 2638
6 TraesCS5B01G436500 chr5D 542106120 542107643 1523 False 1325.0 1325 82.890000 989 2482 1 chr5D.!!$F2 1493
7 TraesCS5B01G436500 chr5D 493911735 493913918 2183 False 1194.9 2313 90.351500 28 2474 2 chr5D.!!$F3 2446
8 TraesCS5B01G436500 chr5A 617122102 617123841 1739 True 2516.0 2516 92.747000 835 2581 1 chr5A.!!$R2 1746
9 TraesCS5B01G436500 chr5A 617095834 617100124 4290 True 1017.7 2342 89.964667 1 3473 3 chr5A.!!$R3 3472
10 TraesCS5B01G436500 chr5A 617111133 617111674 541 True 641.0 641 87.928000 2088 2641 1 chr5A.!!$R1 553
11 TraesCS5B01G436500 chr4A 626953150 626954573 1423 True 1245.0 1245 82.790000 1019 2430 1 chr4A.!!$R1 1411
12 TraesCS5B01G436500 chr7A 124411174 124411842 668 False 795.0 795 89.270000 102 725 1 chr7A.!!$F2 623
13 TraesCS5B01G436500 chr7A 642530578 642531262 684 True 697.0 697 86.083000 103 753 1 chr7A.!!$R1 650
14 TraesCS5B01G436500 chr7A 79594503 79595146 643 False 608.0 608 85.038000 102 704 1 chr7A.!!$F1 602
15 TraesCS5B01G436500 chr4B 529339459 529340129 670 False 403.0 682 93.926500 101 710 2 chr4B.!!$F1 609
16 TraesCS5B01G436500 chr2B 679813502 679814160 658 False 640.0 640 85.329000 132 753 1 chr2B.!!$F1 621
17 TraesCS5B01G436500 chr2A 706581526 706582152 626 False 483.0 483 81.211000 2853 3473 1 chr2A.!!$F1 620
18 TraesCS5B01G436500 chr2D 540957455 540958013 558 False 292.0 292 77.208000 224 754 1 chr2D.!!$F2 530
19 TraesCS5B01G436500 chr3D 14964818 14965531 713 False 283.0 283 75.485000 100 754 1 chr3D.!!$F1 654

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
815 3868 0.24746 CATCAGACAACGAGAGCCCA 59.753 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 5660 0.17576 TATGTCAGTGAAGCTCCGCC 59.824 55.0 0.0 0.0 0.0 6.13 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
50 2576 4.219115 TGCCAAGGTACCAAAATCTTCAA 58.781 39.130 15.94 0.00 0.00 2.69
51 2577 4.837860 TGCCAAGGTACCAAAATCTTCAAT 59.162 37.500 15.94 0.00 0.00 2.57
52 2578 5.170748 GCCAAGGTACCAAAATCTTCAATG 58.829 41.667 15.94 0.00 0.00 2.82
53 2579 5.723295 CCAAGGTACCAAAATCTTCAATGG 58.277 41.667 15.94 1.26 38.91 3.16
54 2580 5.170748 CAAGGTACCAAAATCTTCAATGGC 58.829 41.667 15.94 0.00 36.37 4.40
55 2581 4.415596 AGGTACCAAAATCTTCAATGGCA 58.584 39.130 15.94 0.00 36.37 4.92
56 2582 4.463891 AGGTACCAAAATCTTCAATGGCAG 59.536 41.667 15.94 0.00 36.37 4.85
95 2621 3.184628 TGGAAGATGGAGATCACCAAGT 58.815 45.455 16.23 0.00 43.47 3.16
96 2622 3.198635 TGGAAGATGGAGATCACCAAGTC 59.801 47.826 16.23 10.02 43.47 3.01
97 2623 3.452474 GAAGATGGAGATCACCAAGTCG 58.548 50.000 16.23 0.00 43.47 4.18
98 2624 1.759445 AGATGGAGATCACCAAGTCGG 59.241 52.381 16.23 0.00 43.47 4.79
176 2772 7.182361 TGATTTTGCTTAGAGATTAGATGCG 57.818 36.000 0.00 0.00 0.00 4.73
233 3222 0.454600 CATGCAAGCAGATCCACCAC 59.545 55.000 0.00 0.00 0.00 4.16
234 3223 0.330604 ATGCAAGCAGATCCACCACT 59.669 50.000 0.00 0.00 0.00 4.00
411 3407 3.414700 GCGGAACACAGTGAGCCG 61.415 66.667 24.87 24.87 39.31 5.52
759 3808 3.931578 AGAAAATCCACTCTCCAAGTCG 58.068 45.455 0.00 0.00 35.45 4.18
774 3823 1.079057 GTCGGAAGCCACTTCTCCC 60.079 63.158 7.24 0.00 40.07 4.30
789 3842 3.001406 CCCGTTCCCCTTCCTCGT 61.001 66.667 0.00 0.00 0.00 4.18
807 3860 2.601481 GTTGCTTCCATCAGACAACG 57.399 50.000 0.00 0.00 32.24 4.10
808 3861 2.143122 GTTGCTTCCATCAGACAACGA 58.857 47.619 0.00 0.00 32.24 3.85
809 3862 2.084610 TGCTTCCATCAGACAACGAG 57.915 50.000 0.00 0.00 0.00 4.18
810 3863 1.618343 TGCTTCCATCAGACAACGAGA 59.382 47.619 0.00 0.00 0.00 4.04
811 3864 2.266554 GCTTCCATCAGACAACGAGAG 58.733 52.381 0.00 0.00 0.00 3.20
812 3865 2.266554 CTTCCATCAGACAACGAGAGC 58.733 52.381 0.00 0.00 0.00 4.09
813 3866 0.532573 TCCATCAGACAACGAGAGCC 59.467 55.000 0.00 0.00 0.00 4.70
814 3867 0.460987 CCATCAGACAACGAGAGCCC 60.461 60.000 0.00 0.00 0.00 5.19
815 3868 0.247460 CATCAGACAACGAGAGCCCA 59.753 55.000 0.00 0.00 0.00 5.36
816 3869 0.976641 ATCAGACAACGAGAGCCCAA 59.023 50.000 0.00 0.00 0.00 4.12
817 3870 0.756294 TCAGACAACGAGAGCCCAAA 59.244 50.000 0.00 0.00 0.00 3.28
818 3871 0.868406 CAGACAACGAGAGCCCAAAC 59.132 55.000 0.00 0.00 0.00 2.93
819 3872 0.759346 AGACAACGAGAGCCCAAACT 59.241 50.000 0.00 0.00 0.00 2.66
820 3873 1.141053 AGACAACGAGAGCCCAAACTT 59.859 47.619 0.00 0.00 0.00 2.66
821 3874 1.947456 GACAACGAGAGCCCAAACTTT 59.053 47.619 0.00 0.00 0.00 2.66
822 3875 2.357952 GACAACGAGAGCCCAAACTTTT 59.642 45.455 0.00 0.00 0.00 2.27
823 3876 2.758423 ACAACGAGAGCCCAAACTTTTT 59.242 40.909 0.00 0.00 0.00 1.94
848 3901 6.723298 TTGAATTTTGAGAGCCCAAACTTA 57.277 33.333 0.00 0.00 35.95 2.24
904 3966 0.806868 TCGTCTTAATCGCACCGAGT 59.193 50.000 0.00 0.00 39.91 4.18
937 4005 3.435566 TCTGCATTTGTACTCGATCGAC 58.564 45.455 15.15 6.06 0.00 4.20
970 4078 2.401766 CGGCCGTAGTACACTCCGT 61.402 63.158 19.50 0.00 36.66 4.69
972 4080 1.061570 GCCGTAGTACACTCCGTCG 59.938 63.158 0.38 0.00 0.00 5.12
973 4081 1.717937 CCGTAGTACACTCCGTCGG 59.282 63.158 4.39 4.39 0.00 4.79
974 4082 1.021390 CCGTAGTACACTCCGTCGGT 61.021 60.000 11.88 0.00 33.20 4.69
975 4083 0.371645 CGTAGTACACTCCGTCGGTC 59.628 60.000 11.88 0.00 0.00 4.79
976 4084 1.442769 GTAGTACACTCCGTCGGTCA 58.557 55.000 11.88 0.00 0.00 4.02
977 4085 1.129437 GTAGTACACTCCGTCGGTCAC 59.871 57.143 11.88 3.56 0.00 3.67
1324 4448 3.068691 CGGTCAGGCTTCTCCGGA 61.069 66.667 2.93 2.93 40.77 5.14
1716 4843 0.882042 AGCACTTCCACAAGACGCTG 60.882 55.000 0.00 0.00 39.16 5.18
2249 5382 2.564975 CAAGGACTACGCGTCGGT 59.435 61.111 18.63 16.88 43.79 4.69
2311 5456 3.118992 CGAGTCCATTCAGAGGTTGATGA 60.119 47.826 0.00 0.00 35.27 2.92
2344 5489 0.674895 CCAGAAGAAGGCCAAGGACG 60.675 60.000 5.01 0.00 0.00 4.79
2468 5623 0.620556 GGAGAAGACATCCAGGCCAA 59.379 55.000 5.01 0.00 36.79 4.52
2525 5683 2.668457 CGGAGCTTCACTGACATAACAC 59.332 50.000 0.00 0.00 0.00 3.32
2526 5684 3.615110 CGGAGCTTCACTGACATAACACT 60.615 47.826 0.00 0.00 0.00 3.55
2594 5753 9.817809 GAATAGTTTCTTCCATCTATACACACA 57.182 33.333 0.00 0.00 0.00 3.72
2610 5769 1.078426 ACATAGCTGTGTTCGGGGC 60.078 57.895 10.73 0.00 33.22 5.80
2620 5779 3.575247 TTCGGGGCCAGCTTTGGA 61.575 61.111 4.39 0.00 0.00 3.53
2641 5800 5.779771 TGGACTTTCCTTTTGGCTGATTAAT 59.220 36.000 0.00 0.00 37.46 1.40
2642 5801 6.101997 GGACTTTCCTTTTGGCTGATTAATG 58.898 40.000 0.00 0.00 40.12 1.90
2643 5802 6.041423 ACTTTCCTTTTGGCTGATTAATGG 57.959 37.500 0.00 0.00 40.12 3.16
2655 6664 2.571653 TGATTAATGGCCCCTAGATCCG 59.428 50.000 0.00 0.00 0.00 4.18
2660 6669 2.294078 GGCCCCTAGATCCGATGGG 61.294 68.421 0.00 3.43 39.37 4.00
2688 6697 0.465705 CTACGACAGCCATGACCCAT 59.534 55.000 0.00 0.00 0.00 4.00
2704 6713 4.145052 GACCCATGGAGTCTTGTTTTTCT 58.855 43.478 15.22 0.00 0.00 2.52
2709 6718 4.385358 TGGAGTCTTGTTTTTCTTTGGC 57.615 40.909 0.00 0.00 0.00 4.52
2714 6723 5.793817 AGTCTTGTTTTTCTTTGGCAAACT 58.206 33.333 8.93 0.00 32.58 2.66
2715 6724 6.230472 AGTCTTGTTTTTCTTTGGCAAACTT 58.770 32.000 8.93 0.00 32.58 2.66
2733 6742 5.343307 AACTTGCTGCCTTTATTATTGGG 57.657 39.130 0.00 0.00 0.00 4.12
2751 8525 1.202651 GGGCGCTGATAAGTACCACAT 60.203 52.381 7.64 0.00 0.00 3.21
2758 8532 3.527533 TGATAAGTACCACATGTTCGGC 58.472 45.455 0.00 0.00 0.00 5.54
2761 8535 0.036388 AGTACCACATGTTCGGCCTG 60.036 55.000 0.00 0.00 0.00 4.85
2779 8553 3.319198 GGCACCTCCCAGACCGAA 61.319 66.667 0.00 0.00 0.00 4.30
2780 8554 2.047179 GCACCTCCCAGACCGAAC 60.047 66.667 0.00 0.00 0.00 3.95
2781 8555 2.584391 GCACCTCCCAGACCGAACT 61.584 63.158 0.00 0.00 0.00 3.01
2782 8556 1.255667 GCACCTCCCAGACCGAACTA 61.256 60.000 0.00 0.00 0.00 2.24
2783 8557 1.486211 CACCTCCCAGACCGAACTAT 58.514 55.000 0.00 0.00 0.00 2.12
2784 8558 1.409427 CACCTCCCAGACCGAACTATC 59.591 57.143 0.00 0.00 0.00 2.08
2785 8559 1.006758 ACCTCCCAGACCGAACTATCA 59.993 52.381 0.00 0.00 0.00 2.15
2786 8560 1.683917 CCTCCCAGACCGAACTATCAG 59.316 57.143 0.00 0.00 0.00 2.90
2787 8561 1.067821 CTCCCAGACCGAACTATCAGC 59.932 57.143 0.00 0.00 0.00 4.26
2788 8562 0.824109 CCCAGACCGAACTATCAGCA 59.176 55.000 0.00 0.00 0.00 4.41
2789 8563 1.202463 CCCAGACCGAACTATCAGCAG 60.202 57.143 0.00 0.00 0.00 4.24
2790 8564 1.565305 CAGACCGAACTATCAGCAGC 58.435 55.000 0.00 0.00 0.00 5.25
2791 8565 1.134995 CAGACCGAACTATCAGCAGCA 60.135 52.381 0.00 0.00 0.00 4.41
2792 8566 1.134965 AGACCGAACTATCAGCAGCAC 60.135 52.381 0.00 0.00 0.00 4.40
2793 8567 0.608130 ACCGAACTATCAGCAGCACA 59.392 50.000 0.00 0.00 0.00 4.57
2794 8568 1.208052 ACCGAACTATCAGCAGCACAT 59.792 47.619 0.00 0.00 0.00 3.21
2795 8569 1.596260 CCGAACTATCAGCAGCACATG 59.404 52.381 0.00 0.00 0.00 3.21
2796 8570 2.274437 CGAACTATCAGCAGCACATGT 58.726 47.619 0.00 0.00 0.00 3.21
2797 8571 2.674852 CGAACTATCAGCAGCACATGTT 59.325 45.455 0.00 0.00 0.00 2.71
2798 8572 3.242220 CGAACTATCAGCAGCACATGTTC 60.242 47.826 0.00 0.00 0.00 3.18
2799 8573 2.274437 ACTATCAGCAGCACATGTTCG 58.726 47.619 0.00 0.00 0.00 3.95
2800 8574 2.094026 ACTATCAGCAGCACATGTTCGA 60.094 45.455 0.00 0.00 0.00 3.71
2801 8575 1.081892 ATCAGCAGCACATGTTCGAC 58.918 50.000 0.00 0.00 0.00 4.20
2802 8576 0.950555 TCAGCAGCACATGTTCGACC 60.951 55.000 0.00 0.00 0.00 4.79
2803 8577 0.952497 CAGCAGCACATGTTCGACCT 60.952 55.000 0.00 0.00 0.00 3.85
2804 8578 0.952497 AGCAGCACATGTTCGACCTG 60.952 55.000 0.00 0.00 0.00 4.00
2805 8579 1.915614 GCAGCACATGTTCGACCTGG 61.916 60.000 0.00 0.00 0.00 4.45
2806 8580 1.003355 AGCACATGTTCGACCTGGG 60.003 57.895 0.00 0.00 0.00 4.45
2807 8581 2.690778 GCACATGTTCGACCTGGGC 61.691 63.158 0.00 0.00 36.08 5.36
2808 8582 1.302431 CACATGTTCGACCTGGGCA 60.302 57.895 0.00 0.00 0.00 5.36
2809 8583 1.302511 ACATGTTCGACCTGGGCAC 60.303 57.895 0.00 0.00 0.00 5.01
2823 8597 1.003233 GGCACCTCCCAGACTGAAC 60.003 63.158 3.32 0.00 0.00 3.18
2859 8633 1.453762 GGGATCGATCCTCCGAACGT 61.454 60.000 36.72 0.00 46.35 3.99
2903 8678 3.691342 CCGAACGCCTCCCTGACA 61.691 66.667 0.00 0.00 0.00 3.58
2927 8702 6.868339 CACCAGGTCTTTTCCATGTAAAAATC 59.132 38.462 0.00 0.00 0.00 2.17
3024 8835 3.802866 AGCCTAGATTTTGCTCAGCTAC 58.197 45.455 0.00 0.00 0.00 3.58
3096 8911 4.895668 ATGCCATTTGAGTTTGACCAAT 57.104 36.364 0.00 0.00 0.00 3.16
3179 8994 3.523157 TGATTCCCTAGTGAAAGCATGGA 59.477 43.478 0.00 0.00 0.00 3.41
3180 8995 3.350219 TTCCCTAGTGAAAGCATGGAC 57.650 47.619 0.00 0.00 0.00 4.02
3187 9002 3.087031 AGTGAAAGCATGGACAATCTGG 58.913 45.455 0.00 0.00 0.00 3.86
3194 9009 2.371306 CATGGACAATCTGGCATGACA 58.629 47.619 0.00 0.00 0.00 3.58
3195 9010 2.583024 TGGACAATCTGGCATGACAA 57.417 45.000 1.11 0.00 0.00 3.18
3196 9011 2.874014 TGGACAATCTGGCATGACAAA 58.126 42.857 1.11 0.00 0.00 2.83
3233 9048 6.325919 AGTCATGGCTAAAAATTTGTTCGA 57.674 33.333 0.00 0.00 0.00 3.71
3246 9063 7.784633 AAATTTGTTCGAAAAATGACATGGT 57.215 28.000 0.61 0.00 0.00 3.55
3257 9074 7.118101 CGAAAAATGACATGGTGATTTTCCATT 59.882 33.333 16.51 0.00 42.92 3.16
3266 9083 4.039004 TGGTGATTTTCCATTTGTGTCCAG 59.961 41.667 0.00 0.00 0.00 3.86
3282 9099 1.487976 TCCAGCACCAAAAATTGCCAA 59.512 42.857 0.00 0.00 39.75 4.52
3287 9104 3.148412 GCACCAAAAATTGCCAAGGAAT 58.852 40.909 0.00 0.00 32.21 3.01
3304 9121 7.431960 GCCAAGGAATTTTTGAAAAACACAATC 59.568 33.333 5.08 0.46 0.00 2.67
3356 9188 2.662791 CGAACTTCAGAAACACCATGCG 60.663 50.000 0.00 0.00 0.00 4.73
3368 9200 0.955428 ACCATGCGTGTGTGTCCATC 60.955 55.000 4.96 0.00 0.00 3.51
3378 9210 2.757314 TGTGTGTCCATCAAAGTTGCAA 59.243 40.909 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.552890 GGGTTTGAACAGAGGTTTGCATC 60.553 47.826 0.00 0.00 37.36 3.91
2 3 1.754226 GGGTTTGAACAGAGGTTTGCA 59.246 47.619 0.00 0.00 37.36 4.08
3 4 2.031870 AGGGTTTGAACAGAGGTTTGC 58.968 47.619 0.00 0.00 37.36 3.68
5 6 2.430694 GCAAGGGTTTGAACAGAGGTTT 59.569 45.455 0.00 0.00 37.36 3.27
6 7 2.031870 GCAAGGGTTTGAACAGAGGTT 58.968 47.619 0.00 0.00 40.76 3.50
7 8 1.064017 TGCAAGGGTTTGAACAGAGGT 60.064 47.619 0.00 0.00 36.36 3.85
9 10 2.608752 GCATGCAAGGGTTTGAACAGAG 60.609 50.000 14.21 0.00 36.36 3.35
10 11 1.340889 GCATGCAAGGGTTTGAACAGA 59.659 47.619 14.21 0.00 36.36 3.41
11 12 1.606224 GGCATGCAAGGGTTTGAACAG 60.606 52.381 21.36 0.00 36.36 3.16
51 2577 0.535780 CAGAAGCTTGTGGACTGCCA 60.536 55.000 15.62 0.00 43.47 4.92
52 2578 0.536006 ACAGAAGCTTGTGGACTGCC 60.536 55.000 25.62 0.00 32.67 4.85
53 2579 1.265365 GAACAGAAGCTTGTGGACTGC 59.735 52.381 25.62 1.86 32.67 4.40
54 2580 2.547211 CAGAACAGAAGCTTGTGGACTG 59.453 50.000 25.62 25.34 35.14 3.51
55 2581 2.486191 CCAGAACAGAAGCTTGTGGACT 60.486 50.000 25.62 19.88 34.62 3.85
56 2582 1.876156 CCAGAACAGAAGCTTGTGGAC 59.124 52.381 25.62 18.21 34.62 4.02
649 3686 6.850752 TCTACATGGTATTCTTCACTCACA 57.149 37.500 0.00 0.00 0.00 3.58
656 3693 9.862371 CCTACATACATCTACATGGTATTCTTC 57.138 37.037 0.00 0.00 33.82 2.87
736 3785 5.395768 CCGACTTGGAGAGTGGATTTTCTAT 60.396 44.000 0.00 0.00 42.00 1.98
759 3808 0.673956 GAACGGGAGAAGTGGCTTCC 60.674 60.000 5.38 0.00 40.98 3.46
774 3823 2.033194 GCAACGAGGAAGGGGAACG 61.033 63.158 0.00 0.00 0.00 3.95
789 3842 2.037121 TCTCGTTGTCTGATGGAAGCAA 59.963 45.455 0.00 0.00 0.00 3.91
822 3875 6.413892 AGTTTGGGCTCTCAAAATTCAAAAA 58.586 32.000 0.00 0.00 38.21 1.94
823 3876 5.988287 AGTTTGGGCTCTCAAAATTCAAAA 58.012 33.333 0.00 0.00 38.21 2.44
824 3877 5.612725 AGTTTGGGCTCTCAAAATTCAAA 57.387 34.783 0.00 0.00 38.21 2.69
825 3878 5.612725 AAGTTTGGGCTCTCAAAATTCAA 57.387 34.783 2.48 0.00 39.65 2.69
826 3879 6.916360 ATAAGTTTGGGCTCTCAAAATTCA 57.084 33.333 10.63 0.82 41.80 2.57
827 3880 6.967199 CGTATAAGTTTGGGCTCTCAAAATTC 59.033 38.462 10.63 0.00 41.80 2.17
828 3881 6.433093 ACGTATAAGTTTGGGCTCTCAAAATT 59.567 34.615 11.78 11.78 43.93 1.82
829 3882 5.944007 ACGTATAAGTTTGGGCTCTCAAAAT 59.056 36.000 0.00 0.00 38.21 1.82
830 3883 5.310451 ACGTATAAGTTTGGGCTCTCAAAA 58.690 37.500 0.00 0.00 38.21 2.44
831 3884 4.901868 ACGTATAAGTTTGGGCTCTCAAA 58.098 39.130 0.00 0.00 34.64 2.69
832 3885 4.546829 ACGTATAAGTTTGGGCTCTCAA 57.453 40.909 0.00 0.00 0.00 3.02
833 3886 5.361571 TCATACGTATAAGTTTGGGCTCTCA 59.638 40.000 7.96 0.00 0.00 3.27
904 3966 2.391616 AATGCAGATCAGACGCAAGA 57.608 45.000 0.00 0.00 39.48 3.02
972 4080 4.487412 CTACCGCGTCCCGTGACC 62.487 72.222 4.92 0.00 39.94 4.02
975 4083 4.849329 GAGCTACCGCGTCCCGTG 62.849 72.222 4.92 0.00 42.32 4.94
984 4092 4.227134 ATGGCTGGCGAGCTACCG 62.227 66.667 20.62 0.00 45.44 4.02
985 4093 2.590007 CATGGCTGGCGAGCTACC 60.590 66.667 20.62 4.58 45.44 3.18
986 4094 2.590007 CCATGGCTGGCGAGCTAC 60.590 66.667 20.62 5.34 45.44 3.58
1324 4448 2.346365 GAACCGGTCGAAGGGCTT 59.654 61.111 8.04 0.00 0.00 4.35
1680 4807 1.725665 CTCGACGTAATCCGGCTCA 59.274 57.895 0.00 0.00 44.70 4.26
2311 5456 1.888436 TTCTGGATGGCGTCGCTCTT 61.888 55.000 18.11 5.54 0.00 2.85
2344 5489 0.390472 CTCCTTGCCTTCAGACCGAC 60.390 60.000 0.00 0.00 0.00 4.79
2468 5623 2.418197 CGTCGGACCAATACCAATCAGT 60.418 50.000 1.91 0.00 0.00 3.41
2498 5656 4.443266 AGTGAAGCTCCGCCGCTC 62.443 66.667 0.00 0.00 39.86 5.03
2499 5657 4.749310 CAGTGAAGCTCCGCCGCT 62.749 66.667 0.00 0.00 43.31 5.52
2500 5658 4.742201 TCAGTGAAGCTCCGCCGC 62.742 66.667 0.00 0.00 0.00 6.53
2501 5659 2.811317 GTCAGTGAAGCTCCGCCG 60.811 66.667 0.00 0.00 0.00 6.46
2502 5660 0.175760 TATGTCAGTGAAGCTCCGCC 59.824 55.000 0.00 0.00 0.00 6.13
2503 5661 1.661112 GTTATGTCAGTGAAGCTCCGC 59.339 52.381 0.00 0.00 0.00 5.54
2504 5662 2.668457 GTGTTATGTCAGTGAAGCTCCG 59.332 50.000 0.00 0.00 0.00 4.63
2505 5663 3.681897 CAGTGTTATGTCAGTGAAGCTCC 59.318 47.826 0.00 0.00 40.11 4.70
2512 5670 2.183478 TGCCCAGTGTTATGTCAGTG 57.817 50.000 0.00 0.00 38.18 3.66
2525 5683 2.496871 TCATAATTTGCCTGTTGCCCAG 59.503 45.455 0.00 0.00 40.16 4.45
2526 5684 2.533916 TCATAATTTGCCTGTTGCCCA 58.466 42.857 0.00 0.00 40.16 5.36
2592 5751 1.078426 GCCCCGAACACAGCTATGT 60.078 57.895 0.00 0.00 41.57 2.29
2593 5752 1.819632 GGCCCCGAACACAGCTATG 60.820 63.158 0.00 0.00 0.00 2.23
2594 5753 2.257409 CTGGCCCCGAACACAGCTAT 62.257 60.000 0.00 0.00 0.00 2.97
2595 5754 2.925706 TGGCCCCGAACACAGCTA 60.926 61.111 0.00 0.00 0.00 3.32
2605 5764 3.868200 AAGTCCAAAGCTGGCCCCG 62.868 63.158 0.00 0.00 43.17 5.73
2606 5765 1.533994 AAAGTCCAAAGCTGGCCCC 60.534 57.895 0.00 0.00 43.17 5.80
2610 5769 3.493176 CCAAAAGGAAAGTCCAAAGCTGG 60.493 47.826 0.00 0.00 45.08 4.85
2620 5779 5.569428 GCCATTAATCAGCCAAAAGGAAAGT 60.569 40.000 0.00 0.00 0.00 2.66
2641 5800 1.536418 CCATCGGATCTAGGGGCCA 60.536 63.158 4.39 0.00 0.00 5.36
2642 5801 2.294078 CCCATCGGATCTAGGGGCC 61.294 68.421 0.00 0.00 37.66 5.80
2643 5802 3.393360 CCCATCGGATCTAGGGGC 58.607 66.667 5.58 0.00 37.66 5.80
2655 6664 2.158957 TGTCGTAGCAAAGATCCCCATC 60.159 50.000 0.00 0.00 0.00 3.51
2688 6697 3.766591 TGCCAAAGAAAAACAAGACTCCA 59.233 39.130 0.00 0.00 0.00 3.86
2691 6700 5.793817 AGTTTGCCAAAGAAAAACAAGACT 58.206 33.333 0.00 0.00 36.48 3.24
2709 6718 5.581874 CCCAATAATAAAGGCAGCAAGTTTG 59.418 40.000 0.00 0.00 0.00 2.93
2714 6723 2.100584 CGCCCAATAATAAAGGCAGCAA 59.899 45.455 0.00 0.00 46.08 3.91
2715 6724 1.680735 CGCCCAATAATAAAGGCAGCA 59.319 47.619 0.00 0.00 46.08 4.41
2717 6726 1.956477 AGCGCCCAATAATAAAGGCAG 59.044 47.619 2.29 0.00 46.08 4.85
2733 6742 2.550978 ACATGTGGTACTTATCAGCGC 58.449 47.619 0.00 0.00 0.00 5.92
2770 8544 1.804372 GCTGCTGATAGTTCGGTCTGG 60.804 57.143 0.00 0.00 0.00 3.86
2771 8545 1.134995 TGCTGCTGATAGTTCGGTCTG 60.135 52.381 0.00 0.00 0.00 3.51
2777 8551 3.242220 CGAACATGTGCTGCTGATAGTTC 60.242 47.826 0.00 8.08 0.00 3.01
2778 8552 2.674852 CGAACATGTGCTGCTGATAGTT 59.325 45.455 0.00 0.00 0.00 2.24
2779 8553 2.094026 TCGAACATGTGCTGCTGATAGT 60.094 45.455 0.00 0.00 0.00 2.12
2780 8554 2.283617 GTCGAACATGTGCTGCTGATAG 59.716 50.000 0.00 0.00 0.00 2.08
2781 8555 2.270923 GTCGAACATGTGCTGCTGATA 58.729 47.619 0.00 0.00 0.00 2.15
2782 8556 1.081892 GTCGAACATGTGCTGCTGAT 58.918 50.000 0.00 0.00 0.00 2.90
2783 8557 0.950555 GGTCGAACATGTGCTGCTGA 60.951 55.000 0.00 0.00 0.00 4.26
2784 8558 0.952497 AGGTCGAACATGTGCTGCTG 60.952 55.000 1.87 0.00 0.00 4.41
2785 8559 0.952497 CAGGTCGAACATGTGCTGCT 60.952 55.000 1.87 0.00 0.00 4.24
2786 8560 1.499056 CAGGTCGAACATGTGCTGC 59.501 57.895 1.87 0.00 0.00 5.25
2787 8561 1.300971 CCCAGGTCGAACATGTGCTG 61.301 60.000 1.87 0.00 0.00 4.41
2788 8562 1.003355 CCCAGGTCGAACATGTGCT 60.003 57.895 1.87 0.00 0.00 4.40
2789 8563 2.690778 GCCCAGGTCGAACATGTGC 61.691 63.158 1.87 0.00 0.00 4.57
2790 8564 1.302431 TGCCCAGGTCGAACATGTG 60.302 57.895 1.87 0.00 0.00 3.21
2791 8565 1.302511 GTGCCCAGGTCGAACATGT 60.303 57.895 1.87 0.00 0.00 3.21
2792 8566 2.040544 GGTGCCCAGGTCGAACATG 61.041 63.158 1.87 0.00 0.00 3.21
2793 8567 2.185310 GAGGTGCCCAGGTCGAACAT 62.185 60.000 1.87 0.00 0.00 2.71
2794 8568 2.847234 AGGTGCCCAGGTCGAACA 60.847 61.111 1.87 0.00 0.00 3.18
2795 8569 2.047179 GAGGTGCCCAGGTCGAAC 60.047 66.667 0.00 0.00 0.00 3.95
2796 8570 3.319198 GGAGGTGCCCAGGTCGAA 61.319 66.667 0.00 0.00 0.00 3.71
2805 8579 1.003233 GTTCAGTCTGGGAGGTGCC 60.003 63.158 0.00 0.00 0.00 5.01
2806 8580 1.374758 CGTTCAGTCTGGGAGGTGC 60.375 63.158 0.00 0.00 0.00 5.01
2807 8581 0.898320 ATCGTTCAGTCTGGGAGGTG 59.102 55.000 0.00 0.00 0.00 4.00
2808 8582 1.276421 CAATCGTTCAGTCTGGGAGGT 59.724 52.381 0.00 0.00 0.00 3.85
2809 8583 1.276421 ACAATCGTTCAGTCTGGGAGG 59.724 52.381 0.00 0.00 0.00 4.30
2810 8584 2.751166 ACAATCGTTCAGTCTGGGAG 57.249 50.000 0.00 0.00 0.00 4.30
2859 8633 1.266160 TTCCCCCTGCCGAACGAATA 61.266 55.000 0.00 0.00 0.00 1.75
2870 8644 0.689745 TCGGACTATGGTTCCCCCTG 60.690 60.000 0.00 0.00 0.00 4.45
2881 8655 1.076192 AGGGAGGCGTTCGGACTAT 60.076 57.895 0.00 0.00 29.96 2.12
2882 8656 2.050350 CAGGGAGGCGTTCGGACTA 61.050 63.158 0.00 0.00 29.96 2.59
2883 8657 3.382832 CAGGGAGGCGTTCGGACT 61.383 66.667 0.00 0.00 35.84 3.85
2884 8658 3.379445 TCAGGGAGGCGTTCGGAC 61.379 66.667 0.00 0.00 0.00 4.79
2885 8659 3.379445 GTCAGGGAGGCGTTCGGA 61.379 66.667 0.00 0.00 0.00 4.55
2903 8678 6.553100 TGATTTTTACATGGAAAAGACCTGGT 59.447 34.615 15.28 0.00 30.30 4.00
2938 8713 9.811995 TCTAATTCATTACTAGCGAGCTTTTTA 57.188 29.630 1.86 0.00 0.00 1.52
2946 8721 8.765219 GCTTTTCATCTAATTCATTACTAGCGA 58.235 33.333 0.00 0.00 0.00 4.93
2952 8727 8.225603 TCTGGGCTTTTCATCTAATTCATTAC 57.774 34.615 0.00 0.00 0.00 1.89
2963 8738 6.866010 AAACAAAAATCTGGGCTTTTCATC 57.134 33.333 0.00 0.00 0.00 2.92
3073 8885 4.686191 TGGTCAAACTCAAATGGCATTT 57.314 36.364 19.39 19.39 0.00 2.32
3150 8965 7.118723 TGCTTTCACTAGGGAATCAAATATGT 58.881 34.615 8.58 0.00 0.00 2.29
3167 8982 2.416431 GCCAGATTGTCCATGCTTTCAC 60.416 50.000 0.00 0.00 0.00 3.18
3210 9025 6.325919 TCGAACAAATTTTTAGCCATGACT 57.674 33.333 0.00 0.00 0.00 3.41
3212 9027 8.425577 TTTTTCGAACAAATTTTTAGCCATGA 57.574 26.923 0.00 0.00 0.00 3.07
3226 9041 5.506686 TCACCATGTCATTTTTCGAACAA 57.493 34.783 0.00 0.00 0.00 2.83
3233 9048 8.569641 CAAATGGAAAATCACCATGTCATTTTT 58.430 29.630 0.00 2.21 45.89 1.94
3246 9063 3.640498 TGCTGGACACAAATGGAAAATCA 59.360 39.130 0.00 0.00 0.00 2.57
3266 9083 2.252976 TCCTTGGCAATTTTTGGTGC 57.747 45.000 0.00 0.00 0.00 5.01
3282 9099 8.623030 CATGGATTGTGTTTTTCAAAAATTCCT 58.377 29.630 0.00 0.00 0.00 3.36
3304 9121 1.092348 CTGATGCTGGACACACATGG 58.908 55.000 0.00 0.00 0.00 3.66
3356 9188 2.098934 TGCAACTTTGATGGACACACAC 59.901 45.455 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.