Multiple sequence alignment - TraesCS6D01G052900

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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 TraesCS6D01G052900 chr6D 100.000 3239 0 0 1 3239 25615769 25612531 0.000000e+00 5982.0
1 TraesCS6D01G052900 chr6D 77.540 748 131 23 1702 2435 459062920 459062196 1.800000e-112 416.0
2 TraesCS6D01G052900 chr6D 76.400 750 131 23 1702 2435 458989304 458988585 2.380000e-96 363.0
3 TraesCS6D01G052900 chr6D 92.857 70 5 0 2974 3043 469423237 469423168 5.720000e-18 102.0
4 TraesCS6D01G052900 chr6D 88.095 84 7 3 2962 3044 406205756 406205675 2.660000e-16 97.1
5 TraesCS6D01G052900 chr6B 94.385 1496 71 5 1 1486 41436094 41434602 0.000000e+00 2285.0
6 TraesCS6D01G052900 chr6B 92.259 956 68 5 1492 2442 41434508 41433554 0.000000e+00 1351.0
7 TraesCS6D01G052900 chr6A 94.834 1355 62 4 1 1350 23603073 23601722 0.000000e+00 2108.0
8 TraesCS6D01G052900 chr6A 90.748 1243 67 9 1479 2716 23595641 23594442 0.000000e+00 1615.0
9 TraesCS6D01G052900 chr6A 76.964 751 134 27 1702 2437 605343740 605343014 3.030000e-105 392.0
10 TraesCS6D01G052900 chr6A 83.805 389 42 4 972 1352 23595859 23595484 1.850000e-92 350.0
11 TraesCS6D01G052900 chr6A 93.333 225 11 2 2749 2972 23594440 23594219 2.410000e-86 329.0
12 TraesCS6D01G052900 chr6A 89.583 192 15 4 3050 3239 23594205 23594017 4.180000e-59 239.0
13 TraesCS6D01G052900 chr6A 95.172 145 1 2 1348 1486 23595861 23595717 1.170000e-54 224.0
14 TraesCS6D01G052900 chr4A 79.266 545 87 15 1724 2257 632617296 632617825 1.110000e-94 357.0
15 TraesCS6D01G052900 chr4A 79.431 457 83 8 1806 2257 615455696 615455246 2.430000e-81 313.0
16 TraesCS6D01G052900 chr4A 76.613 372 69 17 925 1287 616662906 616663268 4.270000e-44 189.0
17 TraesCS6D01G052900 chr5D 80.659 455 79 7 1806 2257 552685364 552685812 8.600000e-91 344.0
18 TraesCS6D01G052900 chr5D 79.564 367 67 8 925 1287 552408526 552408888 4.150000e-64 255.0
19 TraesCS6D01G052900 chr5D 79.245 371 54 17 999 1352 551545002 551544638 1.500000e-58 237.0
20 TraesCS6D01G052900 chr5D 77.128 376 68 15 924 1290 551469009 551468643 5.480000e-48 202.0
21 TraesCS6D01G052900 chr5D 77.982 327 65 4 934 1257 551408924 551408602 7.090000e-47 198.0
22 TraesCS6D01G052900 chr5D 77.879 330 61 9 928 1251 542410371 542410048 9.170000e-46 195.0
23 TraesCS6D01G052900 chr5D 93.421 76 1 3 2974 3046 41140032 41139958 3.420000e-20 110.0
24 TraesCS6D01G052900 chr2A 79.331 508 89 9 1754 2260 776169218 776168726 3.090000e-90 342.0
25 TraesCS6D01G052900 chrUn 78.416 505 87 13 1754 2257 23718812 23718329 3.140000e-80 309.0
26 TraesCS6D01G052900 chr2B 79.065 449 81 7 1807 2255 780873502 780873067 2.440000e-76 296.0
27 TraesCS6D01G052900 chr5B 79.186 442 77 12 1818 2257 699279886 699279458 3.160000e-75 292.0
28 TraesCS6D01G052900 chr3D 92.079 101 2 1 2635 2729 14157031 14157131 1.570000e-28 137.0
29 TraesCS6D01G052900 chr1D 96.970 66 2 0 2971 3036 15516953 15516888 9.500000e-21 111.0
30 TraesCS6D01G052900 chr1A 93.243 74 5 0 2971 3044 290331208 290331281 3.420000e-20 110.0
31 TraesCS6D01G052900 chr1A 91.892 74 3 2 2971 3043 399497076 399497147 2.060000e-17 100.0
32 TraesCS6D01G052900 chr5A 92.857 70 5 0 2967 3036 23817522 23817591 5.720000e-18 102.0
33 TraesCS6D01G052900 chr5A 92.857 70 5 0 2974 3043 619718948 619718879 5.720000e-18 102.0
34 TraesCS6D01G052900 chr7B 91.781 73 3 1 2968 3037 196961035 196961107 7.400000e-17 99.0


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 TraesCS6D01G052900 chr6D 25612531 25615769 3238 True 5982.0 5982 100.0000 1 3239 1 chr6D.!!$R1 3238
1 TraesCS6D01G052900 chr6D 459062196 459062920 724 True 416.0 416 77.5400 1702 2435 1 chr6D.!!$R4 733
2 TraesCS6D01G052900 chr6D 458988585 458989304 719 True 363.0 363 76.4000 1702 2435 1 chr6D.!!$R3 733
3 TraesCS6D01G052900 chr6B 41433554 41436094 2540 True 1818.0 2285 93.3220 1 2442 2 chr6B.!!$R1 2441
4 TraesCS6D01G052900 chr6A 23601722 23603073 1351 True 2108.0 2108 94.8340 1 1350 1 chr6A.!!$R1 1349
5 TraesCS6D01G052900 chr6A 23594017 23595861 1844 True 551.4 1615 90.5282 972 3239 5 chr6A.!!$R3 2267
6 TraesCS6D01G052900 chr6A 605343014 605343740 726 True 392.0 392 76.9640 1702 2437 1 chr6A.!!$R2 735
7 TraesCS6D01G052900 chr4A 632617296 632617825 529 False 357.0 357 79.2660 1724 2257 1 chr4A.!!$F2 533

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
457 461 0.036765 TACACGAGGGGTCACAATGC 60.037 55.0 0.0 0.0 0.0 3.56 F
570 574 0.038251 TGGCAGCAGAGAGTACAACG 60.038 55.0 0.0 0.0 0.0 4.10 F
1409 1415 0.241749 CTTGCACGCACCACATGAAT 59.758 50.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2122 0.974383 GTCTTCCTCCAAGAACCCGA 59.026 55.0 0.00 0.0 43.1 5.14 R
2027 2131 1.801242 TGTCACCTTGTCTTCCTCCA 58.199 50.0 0.00 0.0 0.0 3.86 R
2612 2745 0.033601 ACTGCCGGCCATTTCCAATA 60.034 50.0 26.77 0.0 0.0 1.90 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
52 56 4.667573 AGATGGTCAGACAGAAGTAGTGA 58.332 43.478 2.17 0.00 0.00 3.41
250 254 2.613133 AGTGGAAGCTCTCGTACGATAC 59.387 50.000 19.87 11.08 0.00 2.24
299 303 3.574614 CGTTGGTGGTGAATTTGATTCC 58.425 45.455 0.00 0.00 38.50 3.01
310 314 7.153985 GGTGAATTTGATTCCAATTCAGACAA 58.846 34.615 20.36 2.48 38.50 3.18
320 324 4.017222 TCCAATTCAGACAATGGAAGGGAT 60.017 41.667 0.00 0.00 38.95 3.85
342 346 4.026744 TGACAAACTGGAACCAAAATGGA 58.973 39.130 2.85 0.00 40.96 3.41
457 461 0.036765 TACACGAGGGGTCACAATGC 60.037 55.000 0.00 0.00 0.00 3.56
469 473 2.165030 GTCACAATGCTGATGAAAGGGG 59.835 50.000 0.00 0.00 0.00 4.79
570 574 0.038251 TGGCAGCAGAGAGTACAACG 60.038 55.000 0.00 0.00 0.00 4.10
698 702 1.179174 CGAGGGGCGATGGATACTCA 61.179 60.000 0.00 0.00 44.57 3.41
740 744 1.519455 CAGCTCGATGGACCGGAAC 60.519 63.158 9.46 0.00 0.00 3.62
843 847 5.869888 AGTAAAGCTAATGTAGTCTGTGTGC 59.130 40.000 0.00 0.00 0.00 4.57
854 858 2.035449 AGTCTGTGTGCGTGCTAACTAA 59.965 45.455 0.00 0.00 0.00 2.24
1088 1094 8.095169 CCCTACTAATTTTATCTGGCTATCGTT 58.905 37.037 0.00 0.00 0.00 3.85
1342 1348 6.638610 TGTTTCCAAAATATTCGGCATCAAT 58.361 32.000 0.00 0.00 0.00 2.57
1359 1365 6.151648 GGCATCAATAACATACCATACTGCAT 59.848 38.462 0.00 0.00 0.00 3.96
1364 1370 6.686484 ATAACATACCATACTGCATCTCCA 57.314 37.500 0.00 0.00 0.00 3.86
1401 1407 2.350102 GGTAAGTTAACTTGCACGCACC 60.350 50.000 29.69 22.96 39.81 5.01
1409 1415 0.241749 CTTGCACGCACCACATGAAT 59.758 50.000 0.00 0.00 0.00 2.57
1411 1417 0.672889 TGCACGCACCACATGAATTT 59.327 45.000 0.00 0.00 0.00 1.82
1412 1418 1.335780 TGCACGCACCACATGAATTTC 60.336 47.619 0.00 0.00 0.00 2.17
1446 1455 9.159254 TCTACACATCATATGTTCTTCCCTAAT 57.841 33.333 1.90 0.00 42.70 1.73
1458 1467 5.725551 TCTTCCCTAATTTTATCTGCCCA 57.274 39.130 0.00 0.00 0.00 5.36
1461 1470 4.651778 TCCCTAATTTTATCTGCCCATCG 58.348 43.478 0.00 0.00 0.00 3.84
1504 1604 3.141272 TGGACCCAGTTTACCCTTGAAAT 59.859 43.478 0.00 0.00 0.00 2.17
1638 1738 2.095853 CGACATCAACAACATACCAGGC 59.904 50.000 0.00 0.00 0.00 4.85
1664 1764 9.552114 CAGTTGATCTGATTTTTAATCACTCAC 57.448 33.333 0.00 2.16 46.27 3.51
1875 1976 7.141363 GGCAAGATTAATTGACATGTGGTATC 58.859 38.462 1.15 0.00 38.15 2.24
1914 2015 3.917380 GCATGAAGTTATCTCGATCTCGG 59.083 47.826 0.00 0.00 40.29 4.63
1926 2027 3.642705 TCGATCTCGGCATTTATGTCTG 58.357 45.455 0.00 0.00 40.29 3.51
2007 2108 6.524101 TTTAAGCACCTGAACTTGAAGTTT 57.476 33.333 12.37 0.00 38.80 2.66
2017 2121 5.928976 TGAACTTGAAGTTTCTCCAGATGA 58.071 37.500 12.37 0.00 38.80 2.92
2018 2122 6.537355 TGAACTTGAAGTTTCTCCAGATGAT 58.463 36.000 12.37 0.00 38.80 2.45
2026 2130 2.461300 TCTCCAGATGATCGGGTTCT 57.539 50.000 11.33 0.00 33.27 3.01
2027 2131 2.752030 TCTCCAGATGATCGGGTTCTT 58.248 47.619 11.33 0.00 33.27 2.52
2148 2261 1.338136 ATGCCTCCGACCCTAACAGG 61.338 60.000 0.00 0.00 34.30 4.00
2257 2373 4.927267 TGACAGGTATGGTCAAGGAATT 57.073 40.909 0.00 0.00 41.96 2.17
2272 2388 7.255001 GGTCAAGGAATTTAAGTTTCAGAACGA 60.255 37.037 0.00 0.00 40.75 3.85
2279 2396 1.714794 AGTTTCAGAACGATCGCAGG 58.285 50.000 16.60 2.49 40.75 4.85
2292 2416 0.748367 TCGCAGGTGCTAGATCGACT 60.748 55.000 0.00 0.00 39.32 4.18
2363 2493 4.556233 TGAGTACTTGATTGGTCTGAACG 58.444 43.478 0.00 0.00 0.00 3.95
2388 2518 5.991606 TCACAATGTAGCTAGATTATGTGCC 59.008 40.000 22.12 0.00 0.00 5.01
2393 2523 6.576662 TGTAGCTAGATTATGTGCCTACTC 57.423 41.667 0.00 0.00 0.00 2.59
2449 2579 3.131396 CGAGTAATTGCCTACCCATCAC 58.869 50.000 0.00 0.00 0.00 3.06
2450 2580 3.181465 CGAGTAATTGCCTACCCATCACT 60.181 47.826 0.00 0.00 0.00 3.41
2454 2585 3.737559 ATTGCCTACCCATCACTGAAA 57.262 42.857 0.00 0.00 0.00 2.69
2459 2590 3.879892 GCCTACCCATCACTGAAATTCTC 59.120 47.826 0.00 0.00 0.00 2.87
2495 2628 5.334724 GCTCTCTTTTCAGAACATCAACCAG 60.335 44.000 0.00 0.00 0.00 4.00
2604 2737 1.002502 AACGGGGTAGCAAGCCTTC 60.003 57.895 0.00 0.00 43.23 3.46
2608 2741 1.295423 GGGTAGCAAGCCTTCGACA 59.705 57.895 0.00 0.00 40.33 4.35
2610 2743 0.796927 GGTAGCAAGCCTTCGACAAC 59.203 55.000 0.00 0.00 0.00 3.32
2611 2744 1.508632 GTAGCAAGCCTTCGACAACA 58.491 50.000 0.00 0.00 0.00 3.33
2612 2745 2.076863 GTAGCAAGCCTTCGACAACAT 58.923 47.619 0.00 0.00 0.00 2.71
2613 2746 2.472695 AGCAAGCCTTCGACAACATA 57.527 45.000 0.00 0.00 0.00 2.29
2614 2747 2.991250 AGCAAGCCTTCGACAACATAT 58.009 42.857 0.00 0.00 0.00 1.78
2615 2748 3.347216 AGCAAGCCTTCGACAACATATT 58.653 40.909 0.00 0.00 0.00 1.28
2616 2749 3.127548 AGCAAGCCTTCGACAACATATTG 59.872 43.478 0.00 0.00 41.98 1.90
2617 2750 3.731867 GCAAGCCTTCGACAACATATTGG 60.732 47.826 0.00 0.00 40.42 3.16
2618 2751 3.627395 AGCCTTCGACAACATATTGGA 57.373 42.857 0.00 0.00 40.42 3.53
2619 2752 3.950397 AGCCTTCGACAACATATTGGAA 58.050 40.909 0.00 0.00 40.42 3.53
2620 2753 4.331968 AGCCTTCGACAACATATTGGAAA 58.668 39.130 0.00 0.00 40.42 3.13
2621 2754 4.949856 AGCCTTCGACAACATATTGGAAAT 59.050 37.500 0.00 0.00 40.42 2.17
2622 2755 5.036737 GCCTTCGACAACATATTGGAAATG 58.963 41.667 0.00 0.00 40.42 2.32
2623 2756 5.581605 CCTTCGACAACATATTGGAAATGG 58.418 41.667 0.00 0.00 40.42 3.16
2624 2757 4.630894 TCGACAACATATTGGAAATGGC 57.369 40.909 0.00 0.00 40.42 4.40
2625 2758 3.380004 TCGACAACATATTGGAAATGGCC 59.620 43.478 0.00 0.00 40.42 5.36
2626 2759 3.705604 GACAACATATTGGAAATGGCCG 58.294 45.455 0.00 0.00 40.42 6.13
2627 2760 2.430332 ACAACATATTGGAAATGGCCGG 59.570 45.455 0.00 0.00 40.42 6.13
2628 2761 1.039856 ACATATTGGAAATGGCCGGC 58.960 50.000 21.18 21.18 0.00 6.13
2643 2776 1.178534 CCGGCAGTTTGGTCCAACAT 61.179 55.000 2.98 0.00 0.00 2.71
2646 2779 3.275143 CGGCAGTTTGGTCCAACATATA 58.725 45.455 2.98 0.00 0.00 0.86
2653 2786 7.067008 GCAGTTTGGTCCAACATATAGTTACAT 59.933 37.037 2.98 0.00 38.74 2.29
2655 2788 9.609346 AGTTTGGTCCAACATATAGTTACATAC 57.391 33.333 2.98 0.00 38.74 2.39
2674 2808 5.980116 ACATACAGCATCAGTCGAACTATTC 59.020 40.000 0.00 0.00 0.00 1.75
2680 2814 4.759782 CATCAGTCGAACTATTCCCAACT 58.240 43.478 0.00 0.00 0.00 3.16
2716 2851 0.534412 AGCAGAGATACGCAGCAAGT 59.466 50.000 0.00 0.00 0.00 3.16
2717 2852 0.649475 GCAGAGATACGCAGCAAGTG 59.351 55.000 0.00 0.00 0.00 3.16
2727 2862 1.792301 CAGCAAGTGCAGATGACCG 59.208 57.895 6.00 0.00 45.16 4.79
2728 2863 2.037136 AGCAAGTGCAGATGACCGC 61.037 57.895 6.00 0.00 45.16 5.68
2729 2864 3.044059 GCAAGTGCAGATGACCGCC 62.044 63.158 2.92 0.00 41.59 6.13
2730 2865 2.045926 AAGTGCAGATGACCGCCC 60.046 61.111 0.00 0.00 0.00 6.13
2731 2866 2.894257 AAGTGCAGATGACCGCCCA 61.894 57.895 0.00 0.00 0.00 5.36
2732 2867 2.359850 GTGCAGATGACCGCCCAA 60.360 61.111 0.00 0.00 0.00 4.12
2733 2868 2.046023 TGCAGATGACCGCCCAAG 60.046 61.111 0.00 0.00 0.00 3.61
2734 2869 2.268920 GCAGATGACCGCCCAAGA 59.731 61.111 0.00 0.00 0.00 3.02
2735 2870 1.377202 GCAGATGACCGCCCAAGAA 60.377 57.895 0.00 0.00 0.00 2.52
2736 2871 0.749454 GCAGATGACCGCCCAAGAAT 60.749 55.000 0.00 0.00 0.00 2.40
2737 2872 1.475034 GCAGATGACCGCCCAAGAATA 60.475 52.381 0.00 0.00 0.00 1.75
2738 2873 2.917933 CAGATGACCGCCCAAGAATAA 58.082 47.619 0.00 0.00 0.00 1.40
2739 2874 3.480470 CAGATGACCGCCCAAGAATAAT 58.520 45.455 0.00 0.00 0.00 1.28
2740 2875 4.641396 CAGATGACCGCCCAAGAATAATA 58.359 43.478 0.00 0.00 0.00 0.98
2741 2876 4.452455 CAGATGACCGCCCAAGAATAATAC 59.548 45.833 0.00 0.00 0.00 1.89
2742 2877 4.348168 AGATGACCGCCCAAGAATAATACT 59.652 41.667 0.00 0.00 0.00 2.12
2743 2878 5.542635 AGATGACCGCCCAAGAATAATACTA 59.457 40.000 0.00 0.00 0.00 1.82
2744 2879 5.209818 TGACCGCCCAAGAATAATACTAG 57.790 43.478 0.00 0.00 0.00 2.57
2745 2880 4.652421 TGACCGCCCAAGAATAATACTAGT 59.348 41.667 0.00 0.00 0.00 2.57
2746 2881 5.834742 TGACCGCCCAAGAATAATACTAGTA 59.165 40.000 4.77 4.77 0.00 1.82
2747 2882 6.094193 ACCGCCCAAGAATAATACTAGTAC 57.906 41.667 4.31 0.00 0.00 2.73
2810 2946 8.402798 TCACAAACTCCATTATTAAAGCTCAA 57.597 30.769 0.00 0.00 0.00 3.02
2868 3004 6.959311 CGTAAAAAGGACGTATCAAGAAATGG 59.041 38.462 0.00 0.00 35.58 3.16
2893 3029 2.610433 TGTAGAAGAGCTTGTGCGATG 58.390 47.619 0.00 0.00 45.42 3.84
2900 3036 2.959030 AGAGCTTGTGCGATGGTATCTA 59.041 45.455 0.00 0.00 45.42 1.98
2915 3051 7.201830 CGATGGTATCTAGTTCTCTCAAAGGAA 60.202 40.741 0.00 0.00 0.00 3.36
2935 3071 4.575645 GGAAATCTGAGAATTCTCCAGCTG 59.424 45.833 28.40 6.78 42.20 4.24
2944 3080 3.567478 ATTCTCCAGCTGGAACATACC 57.433 47.619 34.30 0.00 44.91 2.73
2976 3112 8.579850 TTATTCCATCATATGCTGTTATTCCC 57.420 34.615 5.86 0.00 0.00 3.97
2977 3113 5.848286 TCCATCATATGCTGTTATTCCCT 57.152 39.130 5.86 0.00 0.00 4.20
2978 3114 5.809001 TCCATCATATGCTGTTATTCCCTC 58.191 41.667 5.86 0.00 0.00 4.30
2979 3115 5.549228 TCCATCATATGCTGTTATTCCCTCT 59.451 40.000 5.86 0.00 0.00 3.69
2980 3116 5.646793 CCATCATATGCTGTTATTCCCTCTG 59.353 44.000 5.86 0.00 0.00 3.35
2981 3117 5.894298 TCATATGCTGTTATTCCCTCTGT 57.106 39.130 0.00 0.00 0.00 3.41
2982 3118 6.994421 TCATATGCTGTTATTCCCTCTGTA 57.006 37.500 0.00 0.00 0.00 2.74
2985 3121 7.933577 TCATATGCTGTTATTCCCTCTGTAAAG 59.066 37.037 0.00 0.00 0.00 1.85
2986 3122 5.755409 TGCTGTTATTCCCTCTGTAAAGA 57.245 39.130 0.00 0.00 0.00 2.52
2987 3123 6.121776 TGCTGTTATTCCCTCTGTAAAGAA 57.878 37.500 0.00 0.00 0.00 2.52
2988 3124 6.539173 TGCTGTTATTCCCTCTGTAAAGAAA 58.461 36.000 0.00 0.00 0.00 2.52
2989 3125 7.175104 TGCTGTTATTCCCTCTGTAAAGAAAT 58.825 34.615 0.00 0.00 0.00 2.17
2990 3126 8.325787 TGCTGTTATTCCCTCTGTAAAGAAATA 58.674 33.333 0.00 0.00 0.00 1.40
2991 3127 9.343539 GCTGTTATTCCCTCTGTAAAGAAATAT 57.656 33.333 0.00 0.00 0.00 1.28
2997 3133 9.785982 ATTCCCTCTGTAAAGAAATATAAGAGC 57.214 33.333 0.00 0.00 0.00 4.09
2998 3134 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
2999 3135 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
3000 3136 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
3001 3137 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
3010 3146 9.685828 AGAAATATAAGAGCGTTTAGATCACTC 57.314 33.333 0.00 0.00 37.82 3.51
3011 3147 9.685828 GAAATATAAGAGCGTTTAGATCACTCT 57.314 33.333 0.00 0.00 39.34 3.24
3019 3155 9.685828 AGAGCGTTTAGATCACTCTTATATTTC 57.314 33.333 0.00 0.00 37.82 2.17
3020 3156 9.685828 GAGCGTTTAGATCACTCTTATATTTCT 57.314 33.333 0.00 0.00 34.89 2.52
3048 3184 8.830915 ATAGAGGGAGTACATGATAATACCTG 57.169 38.462 10.15 0.00 0.00 4.00
3049 3185 5.482175 AGAGGGAGTACATGATAATACCTGC 59.518 44.000 10.15 4.44 0.00 4.85
3050 3186 4.220821 AGGGAGTACATGATAATACCTGCG 59.779 45.833 0.00 0.00 0.00 5.18
3051 3187 4.021368 GGGAGTACATGATAATACCTGCGT 60.021 45.833 0.00 0.00 0.00 5.24
3052 3188 5.510861 GGGAGTACATGATAATACCTGCGTT 60.511 44.000 0.00 0.00 0.00 4.84
3089 3226 5.441718 AAATCAAGAGGATAGCTCAACCA 57.558 39.130 0.00 0.00 34.28 3.67
3101 3238 1.926510 GCTCAACCAAACAAACAGCAC 59.073 47.619 0.00 0.00 0.00 4.40
3102 3239 2.184448 CTCAACCAAACAAACAGCACG 58.816 47.619 0.00 0.00 0.00 5.34
3107 3244 2.098443 ACCAAACAAACAGCACGTAAGG 59.902 45.455 0.00 0.00 46.39 2.69
3124 3261 2.048444 AGGGCATCTACAACAGCATG 57.952 50.000 0.00 0.00 46.00 4.06
3134 3271 2.769893 ACAACAGCATGCCCAAATTTC 58.230 42.857 15.66 0.00 42.53 2.17
3138 3275 2.289819 ACAGCATGCCCAAATTTCCTTG 60.290 45.455 15.66 3.72 42.53 3.61
3164 3301 7.093068 GGAATACCCCAAAACAGAAAATATGGT 60.093 37.037 0.00 0.00 0.00 3.55
3200 3338 2.102588 ACGTATCTCCAGCAACATACCC 59.897 50.000 0.00 0.00 0.00 3.69
3205 3343 3.355378 TCTCCAGCAACATACCCAAATG 58.645 45.455 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 56 1.271127 GGGAGGCTTCCTTCTGCTCT 61.271 60.000 15.38 0.00 43.49 4.09
137 141 3.420397 CGACTCGGAGAAAGAACCC 57.580 57.895 12.86 0.00 34.09 4.11
250 254 1.965935 TCGTATCACATTGCCATGGG 58.034 50.000 15.13 0.00 34.72 4.00
299 303 4.951715 TCATCCCTTCCATTGTCTGAATTG 59.048 41.667 0.00 0.00 0.00 2.32
310 314 2.649312 TCCAGTTTGTCATCCCTTCCAT 59.351 45.455 0.00 0.00 0.00 3.41
320 324 4.026744 TCCATTTTGGTTCCAGTTTGTCA 58.973 39.130 0.00 0.00 39.03 3.58
342 346 1.499870 ACTAGACCTATTCGGGGCTCT 59.500 52.381 0.00 0.00 41.78 4.09
457 461 3.834231 ACCAAATTGACCCCTTTCATCAG 59.166 43.478 0.00 0.00 0.00 2.90
469 473 2.729360 GCAAAGCCGTTACCAAATTGAC 59.271 45.455 0.00 0.00 0.00 3.18
570 574 8.207545 ACTCCTGAATCTACTTTTCATATCACC 58.792 37.037 0.00 0.00 32.94 4.02
626 630 4.732647 GCGTTCATCACAGGACGAGTATTA 60.733 45.833 0.00 0.00 37.69 0.98
628 632 2.479730 GCGTTCATCACAGGACGAGTAT 60.480 50.000 0.00 0.00 37.69 2.12
686 690 2.876550 TGGTCGTAGTGAGTATCCATCG 59.123 50.000 0.00 0.00 0.00 3.84
698 702 3.259064 CAATTCCGATGTTGGTCGTAGT 58.741 45.455 0.00 0.00 39.89 2.73
740 744 2.824041 CTGAATTGCCGTCCCCCG 60.824 66.667 0.00 0.00 0.00 5.73
752 756 5.144100 AGTGAATATCCGTCTCCTCTGAAT 58.856 41.667 0.00 0.00 0.00 2.57
843 847 5.459107 GTCTGGTCATACATTAGTTAGCACG 59.541 44.000 0.00 0.00 0.00 5.34
1015 1021 6.150641 GCAGAAGATATTCATGTGGTGCATAT 59.849 38.462 2.42 0.00 35.74 1.78
1088 1094 5.508489 CCAAATCTGCAGCAAGAAGAAGAAA 60.508 40.000 9.47 0.00 34.86 2.52
1293 1299 4.202202 GCCATACTAGAATGAGTCACAGCT 60.202 45.833 0.00 0.00 0.00 4.24
1342 1348 5.602561 ACTGGAGATGCAGTATGGTATGTTA 59.397 40.000 5.07 0.00 35.86 2.41
1359 1365 3.321682 CCATTTGGCAGAAAAACTGGAGA 59.678 43.478 0.00 0.00 45.82 3.71
1364 1370 5.869649 ACTTACCATTTGGCAGAAAAACT 57.130 34.783 0.00 0.00 39.32 2.66
1401 1407 6.965500 GTGTAGATGCAGAAGAAATTCATGTG 59.035 38.462 0.00 0.00 0.00 3.21
1409 1415 7.989170 ACATATGATGTGTAGATGCAGAAGAAA 59.011 33.333 10.38 0.00 43.01 2.52
1411 1417 7.059202 ACATATGATGTGTAGATGCAGAAGA 57.941 36.000 10.38 0.00 43.01 2.87
1412 1418 7.656542 AGAACATATGATGTGTAGATGCAGAAG 59.343 37.037 10.38 0.00 44.07 2.85
1446 1455 5.242838 AGAAAAACACGATGGGCAGATAAAA 59.757 36.000 0.00 0.00 0.00 1.52
1455 1464 2.664916 CAGCAAGAAAAACACGATGGG 58.335 47.619 0.00 0.00 0.00 4.00
1458 1467 2.618241 TCTGCAGCAAGAAAAACACGAT 59.382 40.909 9.47 0.00 0.00 3.73
1461 1470 4.025480 CCAAATCTGCAGCAAGAAAAACAC 60.025 41.667 9.47 0.00 0.00 3.32
1504 1604 5.652014 CCAAAATTCTACAGGGATAGTGCAA 59.348 40.000 0.00 0.00 0.00 4.08
1562 1662 3.056250 TCACAGCCTCTGAGATTCTGAAC 60.056 47.826 20.30 0.00 35.18 3.18
1571 1671 4.734398 AGAATAAGTCACAGCCTCTGAG 57.266 45.455 0.00 0.00 35.18 3.35
1638 1738 9.552114 GTGAGTGATTAAAAATCAGATCAACTG 57.448 33.333 14.40 0.00 46.97 3.16
1914 2015 3.557595 CGGGAGTTCTCAGACATAAATGC 59.442 47.826 2.24 0.00 0.00 3.56
1926 2027 2.289133 GGCAATATCCTCGGGAGTTCTC 60.289 54.545 0.00 0.00 34.05 2.87
2007 2108 2.432146 CAAGAACCCGATCATCTGGAGA 59.568 50.000 1.38 0.00 0.00 3.71
2017 2121 1.555533 GTCTTCCTCCAAGAACCCGAT 59.444 52.381 0.00 0.00 43.10 4.18
2018 2122 0.974383 GTCTTCCTCCAAGAACCCGA 59.026 55.000 0.00 0.00 43.10 5.14
2026 2130 2.123589 TGTCACCTTGTCTTCCTCCAA 58.876 47.619 0.00 0.00 0.00 3.53
2027 2131 1.801242 TGTCACCTTGTCTTCCTCCA 58.199 50.000 0.00 0.00 0.00 3.86
2134 2238 1.835531 GGATTTCCTGTTAGGGTCGGA 59.164 52.381 0.00 0.00 35.59 4.55
2227 2340 5.730550 TGACCATACCTGTCAACAGATTAC 58.269 41.667 11.70 0.00 46.59 1.89
2257 2373 3.678072 CCTGCGATCGTTCTGAAACTTAA 59.322 43.478 17.81 0.00 32.95 1.85
2279 2396 3.686128 CACACAGTAGTCGATCTAGCAC 58.314 50.000 0.00 0.00 0.00 4.40
2340 2470 4.988540 CGTTCAGACCAATCAAGTACTCAA 59.011 41.667 0.00 0.00 0.00 3.02
2341 2471 4.038763 ACGTTCAGACCAATCAAGTACTCA 59.961 41.667 0.00 0.00 0.00 3.41
2363 2493 6.073548 GGCACATAATCTAGCTACATTGTGAC 60.074 42.308 20.13 12.65 36.26 3.67
2388 2518 3.649981 ACCATGATCCCAGATTGGAGTAG 59.350 47.826 0.00 0.00 40.96 2.57
2393 2523 4.284178 AGAAAACCATGATCCCAGATTGG 58.716 43.478 0.00 0.00 37.25 3.16
2437 2567 3.879892 GAGAATTTCAGTGATGGGTAGGC 59.120 47.826 0.00 0.00 0.00 3.93
2449 2579 4.615452 GCCTCAGCAAGTTGAGAATTTCAG 60.615 45.833 14.42 0.00 45.95 3.02
2450 2580 3.254166 GCCTCAGCAAGTTGAGAATTTCA 59.746 43.478 14.42 0.00 45.95 2.69
2454 2585 2.305343 AGAGCCTCAGCAAGTTGAGAAT 59.695 45.455 14.42 3.57 45.95 2.40
2459 2590 2.181954 AAGAGAGCCTCAGCAAGTTG 57.818 50.000 0.00 0.00 43.56 3.16
2495 2628 4.746115 TCTGCACAATTTTCAGTCAAATGC 59.254 37.500 0.00 0.00 30.08 3.56
2572 2705 1.515954 CCGTTCTACTGCCGGTCAT 59.484 57.895 1.90 0.00 37.00 3.06
2575 2708 2.786512 TACCCCGTTCTACTGCCGGT 62.787 60.000 1.90 0.00 40.10 5.28
2577 2710 1.436336 CTACCCCGTTCTACTGCCG 59.564 63.158 0.00 0.00 0.00 5.69
2604 2737 3.705604 GGCCATTTCCAATATGTTGTCG 58.294 45.455 0.00 0.00 33.36 4.35
2608 2741 1.412343 GCCGGCCATTTCCAATATGTT 59.588 47.619 18.11 0.00 0.00 2.71
2610 2743 1.000060 CTGCCGGCCATTTCCAATATG 60.000 52.381 26.77 0.00 0.00 1.78
2611 2744 1.331214 CTGCCGGCCATTTCCAATAT 58.669 50.000 26.77 0.00 0.00 1.28
2612 2745 0.033601 ACTGCCGGCCATTTCCAATA 60.034 50.000 26.77 0.00 0.00 1.90
2613 2746 0.904394 AACTGCCGGCCATTTCCAAT 60.904 50.000 26.77 0.00 0.00 3.16
2614 2747 1.118356 AAACTGCCGGCCATTTCCAA 61.118 50.000 26.77 0.19 0.00 3.53
2615 2748 1.532794 AAACTGCCGGCCATTTCCA 60.533 52.632 26.77 1.11 0.00 3.53
2616 2749 1.079888 CAAACTGCCGGCCATTTCC 60.080 57.895 26.77 0.00 0.00 3.13
2617 2750 1.079888 CCAAACTGCCGGCCATTTC 60.080 57.895 26.77 0.00 0.00 2.17
2618 2751 1.815817 GACCAAACTGCCGGCCATTT 61.816 55.000 26.77 21.03 0.00 2.32
2619 2752 2.203625 ACCAAACTGCCGGCCATT 60.204 55.556 26.77 15.75 0.00 3.16
2620 2753 2.676471 GACCAAACTGCCGGCCAT 60.676 61.111 26.77 9.26 0.00 4.40
2621 2754 4.966787 GGACCAAACTGCCGGCCA 62.967 66.667 26.77 11.42 0.00 5.36
2622 2755 4.966787 TGGACCAAACTGCCGGCC 62.967 66.667 26.77 6.44 0.00 6.13
2623 2756 2.909965 TTGGACCAAACTGCCGGC 60.910 61.111 22.73 22.73 0.00 6.13
2624 2757 1.178534 ATGTTGGACCAAACTGCCGG 61.179 55.000 8.94 0.00 0.00 6.13
2625 2758 1.529226 TATGTTGGACCAAACTGCCG 58.471 50.000 8.94 0.00 0.00 5.69
2626 2759 4.270008 ACTATATGTTGGACCAAACTGCC 58.730 43.478 8.94 0.00 0.00 4.85
2627 2760 5.897377 AACTATATGTTGGACCAAACTGC 57.103 39.130 8.94 0.00 37.52 4.40
2628 2761 7.915293 TGTAACTATATGTTGGACCAAACTG 57.085 36.000 8.94 0.00 39.55 3.16
2643 2776 7.739498 TCGACTGATGCTGTATGTAACTATA 57.261 36.000 0.00 0.00 0.00 1.31
2646 2779 4.983671 TCGACTGATGCTGTATGTAACT 57.016 40.909 0.00 0.00 0.00 2.24
2653 2786 4.202121 GGGAATAGTTCGACTGATGCTGTA 60.202 45.833 0.00 0.00 0.00 2.74
2655 2788 3.126831 GGGAATAGTTCGACTGATGCTG 58.873 50.000 0.00 0.00 0.00 4.41
2674 2808 1.184431 TGCATGTTGCCATAGTTGGG 58.816 50.000 0.00 0.00 44.23 4.12
2680 2814 2.875087 GCTGAATGCATGTTGCCATA 57.125 45.000 0.00 0.00 44.23 2.74
2716 2851 2.046023 CTTGGGCGGTCATCTGCA 60.046 61.111 1.58 0.00 46.81 4.41
2717 2852 0.749454 ATTCTTGGGCGGTCATCTGC 60.749 55.000 0.00 0.00 44.51 4.26
2718 2853 2.620251 TATTCTTGGGCGGTCATCTG 57.380 50.000 0.00 0.00 0.00 2.90
2719 2854 3.864789 ATTATTCTTGGGCGGTCATCT 57.135 42.857 0.00 0.00 0.00 2.90
2720 2855 4.642429 AGTATTATTCTTGGGCGGTCATC 58.358 43.478 0.00 0.00 0.00 2.92
2721 2856 4.706842 AGTATTATTCTTGGGCGGTCAT 57.293 40.909 0.00 0.00 0.00 3.06
2722 2857 4.652421 ACTAGTATTATTCTTGGGCGGTCA 59.348 41.667 0.00 0.00 0.00 4.02
2723 2858 5.211174 ACTAGTATTATTCTTGGGCGGTC 57.789 43.478 0.00 0.00 0.00 4.79
2724 2859 5.599656 TGTACTAGTATTATTCTTGGGCGGT 59.400 40.000 5.75 0.00 0.00 5.68
2725 2860 6.092955 TGTACTAGTATTATTCTTGGGCGG 57.907 41.667 5.75 0.00 0.00 6.13
2726 2861 6.746120 ACTGTACTAGTATTATTCTTGGGCG 58.254 40.000 5.75 0.00 38.04 6.13
2727 2862 8.636213 TGTACTGTACTAGTATTATTCTTGGGC 58.364 37.037 17.98 0.00 43.44 5.36
2737 2872 9.332502 CAGACTCTGATGTACTGTACTAGTATT 57.667 37.037 17.98 0.00 37.67 1.89
2738 2873 7.442969 GCAGACTCTGATGTACTGTACTAGTAT 59.557 40.741 17.98 4.11 37.67 2.12
2739 2874 6.762187 GCAGACTCTGATGTACTGTACTAGTA 59.238 42.308 17.98 0.00 35.76 1.82
2740 2875 5.587043 GCAGACTCTGATGTACTGTACTAGT 59.413 44.000 17.98 12.68 37.23 2.57
2741 2876 5.586643 TGCAGACTCTGATGTACTGTACTAG 59.413 44.000 17.98 13.17 32.44 2.57
2742 2877 5.497474 TGCAGACTCTGATGTACTGTACTA 58.503 41.667 17.98 6.12 32.44 1.82
2743 2878 4.336280 TGCAGACTCTGATGTACTGTACT 58.664 43.478 17.98 4.82 32.44 2.73
2744 2879 4.703645 TGCAGACTCTGATGTACTGTAC 57.296 45.455 10.45 10.98 32.44 2.90
2745 2880 5.921962 AATGCAGACTCTGATGTACTGTA 57.078 39.130 10.45 0.00 32.44 2.74
2746 2881 4.815533 AATGCAGACTCTGATGTACTGT 57.184 40.909 10.45 0.00 32.44 3.55
2747 2882 5.063186 GTGAAATGCAGACTCTGATGTACTG 59.937 44.000 10.45 0.00 32.44 2.74
2760 2895 0.605319 GTCCGGTGGTGAAATGCAGA 60.605 55.000 0.00 0.00 0.00 4.26
2848 2984 6.414732 TGATCCATTTCTTGATACGTCCTTT 58.585 36.000 0.00 0.00 0.00 3.11
2849 2985 5.989477 TGATCCATTTCTTGATACGTCCTT 58.011 37.500 0.00 0.00 0.00 3.36
2850 2986 5.614324 TGATCCATTTCTTGATACGTCCT 57.386 39.130 0.00 0.00 0.00 3.85
2851 2987 5.760253 ACATGATCCATTTCTTGATACGTCC 59.240 40.000 0.00 0.00 0.00 4.79
2852 2988 6.851222 ACATGATCCATTTCTTGATACGTC 57.149 37.500 0.00 0.00 0.00 4.34
2853 2989 7.726216 TCTACATGATCCATTTCTTGATACGT 58.274 34.615 0.00 0.00 0.00 3.57
2868 3004 3.244814 CGCACAAGCTCTTCTACATGATC 59.755 47.826 0.00 0.00 39.10 2.92
2893 3029 8.700973 AGATTTCCTTTGAGAGAACTAGATACC 58.299 37.037 0.00 0.00 0.00 2.73
2900 3036 6.678568 TCTCAGATTTCCTTTGAGAGAACT 57.321 37.500 0.00 0.00 41.62 3.01
2915 3051 3.779183 TCCAGCTGGAGAATTCTCAGATT 59.221 43.478 32.00 14.73 44.60 2.40
2935 3071 7.556275 TGATGGAATAAAAGACTGGTATGTTCC 59.444 37.037 0.00 0.00 34.61 3.62
2944 3080 8.162878 ACAGCATATGATGGAATAAAAGACTG 57.837 34.615 23.87 10.06 35.42 3.51
2972 3108 7.926555 CGCTCTTATATTTCTTTACAGAGGGAA 59.073 37.037 4.76 0.00 40.49 3.97
2973 3109 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
2974 3110 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
2975 3111 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
2994 3130 9.685828 AGAAATATAAGAGTGATCTAAACGCTC 57.314 33.333 0.00 0.00 42.81 5.03
3022 3158 9.922477 CAGGTATTATCATGTACTCCCTCTATA 57.078 37.037 0.00 0.00 0.00 1.31
3023 3159 7.343316 GCAGGTATTATCATGTACTCCCTCTAT 59.657 40.741 0.00 0.00 0.00 1.98
3024 3160 6.663953 GCAGGTATTATCATGTACTCCCTCTA 59.336 42.308 0.00 0.00 0.00 2.43
3025 3161 5.482175 GCAGGTATTATCATGTACTCCCTCT 59.518 44.000 0.00 0.00 0.00 3.69
3026 3162 5.622460 CGCAGGTATTATCATGTACTCCCTC 60.622 48.000 0.00 0.00 0.00 4.30
3027 3163 4.220821 CGCAGGTATTATCATGTACTCCCT 59.779 45.833 0.00 0.00 0.00 4.20
3028 3164 4.021368 ACGCAGGTATTATCATGTACTCCC 60.021 45.833 0.00 0.00 0.00 4.30
3029 3165 5.135508 ACGCAGGTATTATCATGTACTCC 57.864 43.478 0.00 0.00 0.00 3.85
3030 3166 7.478520 AAAACGCAGGTATTATCATGTACTC 57.521 36.000 0.00 0.00 0.00 2.59
3031 3167 7.859325 AAAAACGCAGGTATTATCATGTACT 57.141 32.000 0.00 0.00 0.00 2.73
3061 3197 9.943163 GTTGAGCTATCCTCTTGATTTTATTTC 57.057 33.333 0.00 0.00 41.35 2.17
3072 3208 4.640771 TGTTTGGTTGAGCTATCCTCTT 57.359 40.909 0.00 0.00 41.35 2.85
3077 3213 4.229876 GCTGTTTGTTTGGTTGAGCTATC 58.770 43.478 0.00 0.00 0.00 2.08
3078 3214 3.636300 TGCTGTTTGTTTGGTTGAGCTAT 59.364 39.130 0.00 0.00 0.00 2.97
3079 3215 3.020274 TGCTGTTTGTTTGGTTGAGCTA 58.980 40.909 0.00 0.00 0.00 3.32
3089 3226 1.066454 GCCCTTACGTGCTGTTTGTTT 59.934 47.619 0.00 0.00 0.00 2.83
3101 3238 1.933853 GCTGTTGTAGATGCCCTTACG 59.066 52.381 0.00 0.00 0.00 3.18
3102 3239 2.985896 TGCTGTTGTAGATGCCCTTAC 58.014 47.619 0.00 0.00 0.00 2.34
3106 3243 0.383231 GCATGCTGTTGTAGATGCCC 59.617 55.000 11.37 0.00 35.61 5.36
3107 3244 0.383231 GGCATGCTGTTGTAGATGCC 59.617 55.000 18.92 0.00 44.79 4.40
3124 3261 3.118408 GGGTATTCCAAGGAAATTTGGGC 60.118 47.826 5.52 0.00 46.16 5.36
3134 3271 3.773560 TCTGTTTTGGGGTATTCCAAGG 58.226 45.455 0.00 0.00 46.19 3.61
3138 3275 7.093068 ACCATATTTTCTGTTTTGGGGTATTCC 60.093 37.037 0.00 0.00 0.00 3.01
3164 3301 8.338072 TGGAGATACGTTTTTAGCCAAAATAA 57.662 30.769 0.00 0.00 36.72 1.40


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

AutoCloner maintained by Alex Coulton.