Multiple sequence alignment - TraesCS5A01G021000

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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 TraesCS5A01G021000 chr5A 100.000 3849 0 0 1 3849 17280199 17284047 0.000000e+00 7108.0
1 TraesCS5A01G021000 chr5A 99.885 873 0 1 1 873 2483674 2484545 0.000000e+00 1605.0
2 TraesCS5A01G021000 chr5A 91.364 880 70 2 873 1746 17371054 17370175 0.000000e+00 1199.0
3 TraesCS5A01G021000 chr5A 87.783 884 64 23 1 866 562921541 562922398 0.000000e+00 994.0
4 TraesCS5A01G021000 chr5A 92.135 178 6 3 3240 3417 17370179 17370010 1.070000e-60 244.0
5 TraesCS5A01G021000 chr5A 90.556 180 17 0 1597 1776 17472224 17472045 4.970000e-59 239.0
6 TraesCS5A01G021000 chr5A 92.361 144 11 0 873 1016 17472366 17472223 5.040000e-49 206.0
7 TraesCS5A01G021000 chr5A 95.604 91 4 0 1852 1942 17472053 17471963 3.100000e-31 147.0
8 TraesCS5A01G021000 chr5D 94.989 2854 77 24 873 3724 23675923 23678712 0.000000e+00 4418.0
9 TraesCS5A01G021000 chr5D 89.474 380 26 7 1614 1991 23836729 23837096 5.820000e-128 468.0
10 TraesCS5A01G021000 chr7A 86.378 1938 226 22 873 2794 726803611 726805526 0.000000e+00 2082.0
11 TraesCS5A01G021000 chr7A 92.593 351 24 2 3499 3849 465464192 465464540 1.600000e-138 503.0
12 TraesCS5A01G021000 chr7A 91.501 353 25 3 3497 3849 465382490 465382143 7.480000e-132 481.0
13 TraesCS5A01G021000 chr7A 91.483 317 23 1 3533 3849 297864801 297864489 2.120000e-117 433.0
14 TraesCS5A01G021000 chr7B 99.088 877 2 4 1 873 73658301 73659175 0.000000e+00 1570.0
15 TraesCS5A01G021000 chr6A 97.377 877 10 6 1 873 608131962 608132829 0.000000e+00 1480.0
16 TraesCS5A01G021000 chr4A 95.362 884 6 5 1 873 30404592 30405451 0.000000e+00 1373.0
17 TraesCS5A01G021000 chr4A 92.023 351 24 1 3499 3849 136384044 136384390 1.240000e-134 490.0
18 TraesCS5A01G021000 chr5B 85.396 1123 146 10 873 1991 17733368 17732260 0.000000e+00 1149.0
19 TraesCS5A01G021000 chr5B 90.598 351 29 1 3499 3849 52304429 52304775 2.710000e-126 462.0
20 TraesCS5A01G021000 chr5B 88.669 353 34 3 3497 3849 489819144 489818798 3.550000e-115 425.0
21 TraesCS5A01G021000 chr3A 88.058 896 49 24 1 873 647601322 647602182 0.000000e+00 1009.0
22 TraesCS5A01G021000 chr3A 89.466 655 45 15 236 873 649144190 649144837 0.000000e+00 806.0
23 TraesCS5A01G021000 chr3A 94.231 52 2 1 3488 3538 540492028 540492079 1.150000e-10 78.7
24 TraesCS5A01G021000 chrUn 87.263 581 48 11 1 572 84778092 84778655 1.170000e-179 640.0
25 TraesCS5A01G021000 chr1B 87.288 472 31 7 1 470 470543481 470543037 2.650000e-141 512.0
26 TraesCS5A01G021000 chr1B 91.150 339 26 3 3511 3849 5762808 5763142 1.260000e-124 457.0
27 TraesCS5A01G021000 chr1B 84.178 493 43 11 1 489 335492478 335492017 2.730000e-121 446.0
28 TraesCS5A01G021000 chr4D 91.738 351 25 1 3498 3848 75040621 75040967 5.780000e-133 484.0
29 TraesCS5A01G021000 chr6B 85.386 479 41 9 1 477 525400285 525399834 1.620000e-128 470.0


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 TraesCS5A01G021000 chr5A 17280199 17284047 3848 False 7108.0 7108 100.0000 1 3849 1 chr5A.!!$F2 3848
1 TraesCS5A01G021000 chr5A 2483674 2484545 871 False 1605.0 1605 99.8850 1 873 1 chr5A.!!$F1 872
2 TraesCS5A01G021000 chr5A 562921541 562922398 857 False 994.0 994 87.7830 1 866 1 chr5A.!!$F3 865
3 TraesCS5A01G021000 chr5A 17370010 17371054 1044 True 721.5 1199 91.7495 873 3417 2 chr5A.!!$R1 2544
4 TraesCS5A01G021000 chr5D 23675923 23678712 2789 False 4418.0 4418 94.9890 873 3724 1 chr5D.!!$F1 2851
5 TraesCS5A01G021000 chr7A 726803611 726805526 1915 False 2082.0 2082 86.3780 873 2794 1 chr7A.!!$F2 1921
6 TraesCS5A01G021000 chr7B 73658301 73659175 874 False 1570.0 1570 99.0880 1 873 1 chr7B.!!$F1 872
7 TraesCS5A01G021000 chr6A 608131962 608132829 867 False 1480.0 1480 97.3770 1 873 1 chr6A.!!$F1 872
8 TraesCS5A01G021000 chr4A 30404592 30405451 859 False 1373.0 1373 95.3620 1 873 1 chr4A.!!$F1 872
9 TraesCS5A01G021000 chr5B 17732260 17733368 1108 True 1149.0 1149 85.3960 873 1991 1 chr5B.!!$R1 1118
10 TraesCS5A01G021000 chr3A 647601322 647602182 860 False 1009.0 1009 88.0580 1 873 1 chr3A.!!$F2 872
11 TraesCS5A01G021000 chr3A 649144190 649144837 647 False 806.0 806 89.4660 236 873 1 chr3A.!!$F3 637
12 TraesCS5A01G021000 chrUn 84778092 84778655 563 False 640.0 640 87.2630 1 572 1 chrUn.!!$F1 571

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
1034 1084 9.920946 AGAAGTATTTAATCTGAAGGCCAAATA 57.079 29.63 5.01 0.69 0.0 1.4 F
2449 2524 0.252467 AGAAGAGTGTGAGGGGGAGG 60.252 60.00 0.00 0.00 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2451 2526 0.031616 ACATGGTCTCCTCCTCCTCC 60.032 60.0 0.00 0.0 0.0 4.30 R
3289 3366 0.035725 TGTGAGGAGGATGCAGCAAG 60.036 55.0 3.51 0.0 0.0 4.01 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
1034 1084 9.920946 AGAAGTATTTAATCTGAAGGCCAAATA 57.079 29.630 5.01 0.69 0.00 1.40
1787 1845 4.359706 GCCAAAGTGACACTTACCAAAAG 58.640 43.478 20.85 6.53 37.47 2.27
2274 2349 2.479837 CGTGAAGTTGCAGTCAGGTTA 58.520 47.619 8.04 0.00 0.00 2.85
2304 2379 5.207110 ACTGCGCATACTTGATAGATTCT 57.793 39.130 12.24 0.00 0.00 2.40
2437 2512 6.059787 AGGTCATGAAGCATTTAGAAGAGT 57.940 37.500 0.00 0.00 0.00 3.24
2438 2513 5.879223 AGGTCATGAAGCATTTAGAAGAGTG 59.121 40.000 0.00 0.00 0.00 3.51
2439 2514 5.645497 GGTCATGAAGCATTTAGAAGAGTGT 59.355 40.000 0.00 0.00 0.00 3.55
2440 2515 6.402983 GGTCATGAAGCATTTAGAAGAGTGTG 60.403 42.308 0.00 0.00 0.00 3.82
2441 2516 6.369890 GTCATGAAGCATTTAGAAGAGTGTGA 59.630 38.462 0.00 0.00 0.00 3.58
2442 2517 6.592994 TCATGAAGCATTTAGAAGAGTGTGAG 59.407 38.462 0.00 0.00 0.00 3.51
2443 2518 5.240891 TGAAGCATTTAGAAGAGTGTGAGG 58.759 41.667 0.00 0.00 0.00 3.86
2444 2519 4.213564 AGCATTTAGAAGAGTGTGAGGG 57.786 45.455 0.00 0.00 0.00 4.30
2445 2520 3.054802 AGCATTTAGAAGAGTGTGAGGGG 60.055 47.826 0.00 0.00 0.00 4.79
2446 2521 3.878778 CATTTAGAAGAGTGTGAGGGGG 58.121 50.000 0.00 0.00 0.00 5.40
2447 2522 3.269592 TTTAGAAGAGTGTGAGGGGGA 57.730 47.619 0.00 0.00 0.00 4.81
2448 2523 2.534042 TAGAAGAGTGTGAGGGGGAG 57.466 55.000 0.00 0.00 0.00 4.30
2449 2524 0.252467 AGAAGAGTGTGAGGGGGAGG 60.252 60.000 0.00 0.00 0.00 4.30
2450 2525 0.252284 GAAGAGTGTGAGGGGGAGGA 60.252 60.000 0.00 0.00 0.00 3.71
2451 2526 0.252467 AAGAGTGTGAGGGGGAGGAG 60.252 60.000 0.00 0.00 0.00 3.69
2452 2527 1.687493 GAGTGTGAGGGGGAGGAGG 60.687 68.421 0.00 0.00 0.00 4.30
2475 2550 0.041238 AGGAGGAGACCATGTTCCGA 59.959 55.000 0.00 0.00 38.54 4.55
2481 2556 1.153628 GACCATGTTCCGACGAGGG 60.154 63.158 0.00 0.00 41.52 4.30
2551 2626 0.394899 GGTGCTGGAGGAATTCTGGG 60.395 60.000 5.23 0.00 0.00 4.45
2553 2628 1.304282 GCTGGAGGAATTCTGGGCA 59.696 57.895 5.23 0.00 0.00 5.36
2577 2652 0.385751 CCATCGTCTACATCGCACCT 59.614 55.000 0.00 0.00 0.00 4.00
2658 2733 0.104777 TCTGGGCCCTGCTATCTCAT 60.105 55.000 25.70 0.00 0.00 2.90
2684 2759 1.342672 ATCCGGGCGATAAACAGGGT 61.343 55.000 0.00 0.00 0.00 4.34
2695 2770 4.260784 CGATAAACAGGGTGCAAGATAAGC 60.261 45.833 0.00 0.00 0.00 3.09
2715 2790 4.511246 ACCATGCCCAGCCATCCG 62.511 66.667 0.00 0.00 0.00 4.18
2737 2812 4.612614 CGTCCGAAGAAAATGTGTGATTTG 59.387 41.667 0.00 0.00 0.00 2.32
2744 2819 4.586001 AGAAAATGTGTGATTTGCCTCTGT 59.414 37.500 0.00 0.00 0.00 3.41
2807 2883 5.771602 AATTCAAAACCGTGTGTTTGTTC 57.228 34.783 0.00 0.00 46.39 3.18
2829 2905 8.919145 TGTTCTTTATTTCCTTTGAGCCTAAAA 58.081 29.630 0.00 0.00 0.00 1.52
2835 2911 6.391227 TTTCCTTTGAGCCTAAAAGTCTTG 57.609 37.500 0.89 0.00 33.61 3.02
2836 2912 5.048846 TCCTTTGAGCCTAAAAGTCTTGT 57.951 39.130 0.89 0.00 33.61 3.16
2884 2960 1.822371 TGCGTGTATACAAGAGCAGGA 59.178 47.619 21.04 3.93 32.28 3.86
2906 2982 1.243902 GGAGCTCTCCTACGATCAGG 58.756 60.000 14.64 0.00 46.16 3.86
2911 2987 2.030363 GCTCTCCTACGATCAGGACATG 60.030 54.545 0.00 0.00 39.89 3.21
2916 2992 4.533815 TCCTACGATCAGGACATGTAAGT 58.466 43.478 0.00 0.00 39.89 2.24
2919 2995 6.262496 TCCTACGATCAGGACATGTAAGTTAG 59.738 42.308 0.00 0.00 39.89 2.34
2920 2996 6.262496 CCTACGATCAGGACATGTAAGTTAGA 59.738 42.308 0.00 0.00 38.00 2.10
2921 2997 6.525578 ACGATCAGGACATGTAAGTTAGAA 57.474 37.500 0.00 0.00 0.00 2.10
2922 2998 7.113658 ACGATCAGGACATGTAAGTTAGAAT 57.886 36.000 0.00 0.00 0.00 2.40
2923 2999 6.980978 ACGATCAGGACATGTAAGTTAGAATG 59.019 38.462 0.00 4.61 0.00 2.67
2924 3000 6.422100 CGATCAGGACATGTAAGTTAGAATGG 59.578 42.308 0.00 0.00 0.00 3.16
2925 3001 5.989477 TCAGGACATGTAAGTTAGAATGGG 58.011 41.667 0.00 0.00 0.00 4.00
2926 3002 5.487488 TCAGGACATGTAAGTTAGAATGGGT 59.513 40.000 0.00 0.00 0.00 4.51
2927 3003 6.012858 TCAGGACATGTAAGTTAGAATGGGTT 60.013 38.462 0.00 0.00 0.00 4.11
2928 3004 6.659242 CAGGACATGTAAGTTAGAATGGGTTT 59.341 38.462 0.00 0.00 0.00 3.27
2929 3005 6.884836 AGGACATGTAAGTTAGAATGGGTTTC 59.115 38.462 0.00 0.64 34.31 2.78
2930 3006 6.657541 GGACATGTAAGTTAGAATGGGTTTCA 59.342 38.462 0.00 0.00 36.75 2.69
2931 3007 7.175990 GGACATGTAAGTTAGAATGGGTTTCAA 59.824 37.037 0.00 0.00 36.75 2.69
2932 3008 8.472007 ACATGTAAGTTAGAATGGGTTTCAAA 57.528 30.769 0.00 0.00 36.75 2.69
2933 3009 8.357402 ACATGTAAGTTAGAATGGGTTTCAAAC 58.643 33.333 0.00 0.00 36.75 2.93
2966 3042 3.087031 ACATGAGAGCAAATGTCTTGGG 58.913 45.455 0.00 0.00 31.33 4.12
2967 3043 2.957402 TGAGAGCAAATGTCTTGGGT 57.043 45.000 0.00 0.00 0.00 4.51
2968 3044 3.228188 TGAGAGCAAATGTCTTGGGTT 57.772 42.857 0.00 0.00 0.00 4.11
2969 3045 2.886523 TGAGAGCAAATGTCTTGGGTTG 59.113 45.455 0.00 0.00 0.00 3.77
2970 3046 3.149196 GAGAGCAAATGTCTTGGGTTGA 58.851 45.455 0.00 0.00 0.00 3.18
2971 3047 3.565307 AGAGCAAATGTCTTGGGTTGAA 58.435 40.909 0.00 0.00 0.00 2.69
2972 3048 3.960102 AGAGCAAATGTCTTGGGTTGAAA 59.040 39.130 0.00 0.00 0.00 2.69
2973 3049 4.405358 AGAGCAAATGTCTTGGGTTGAAAA 59.595 37.500 0.00 0.00 0.00 2.29
3009 3085 2.737039 CGGGTTGAGTTGGTTTGGTTTG 60.737 50.000 0.00 0.00 0.00 2.93
3071 3147 2.766925 TTGTGGGCTGGGTTGCTCT 61.767 57.895 0.00 0.00 33.90 4.09
3073 3149 3.970410 TGGGCTGGGTTGCTCTGG 61.970 66.667 0.00 0.00 33.90 3.86
3086 3162 2.446435 TGCTCTGGCCTATTTGAAACC 58.554 47.619 3.32 0.00 37.74 3.27
3088 3164 2.164422 GCTCTGGCCTATTTGAAACCAC 59.836 50.000 3.32 0.00 0.00 4.16
3196 3272 6.444633 CCTAACGATATAACACCGATTCTGT 58.555 40.000 0.00 0.00 0.00 3.41
3289 3366 5.334260 GCTCTTGCTTGATTATGCATCTCTC 60.334 44.000 0.19 0.00 36.91 3.20
3332 3409 1.150827 CATCAGCAAGTGAGCGTTCA 58.849 50.000 0.00 0.00 39.07 3.18
3333 3410 1.736126 CATCAGCAAGTGAGCGTTCAT 59.264 47.619 4.92 0.00 39.07 2.57
3334 3411 2.741759 TCAGCAAGTGAGCGTTCATA 57.258 45.000 4.92 0.00 40.15 2.15
3335 3412 2.610433 TCAGCAAGTGAGCGTTCATAG 58.390 47.619 4.92 0.00 40.15 2.23
3338 3415 3.244814 CAGCAAGTGAGCGTTCATAGATC 59.755 47.826 4.92 0.00 40.15 2.75
3412 3489 4.688021 GCCATGTTACTAGAGAACCTGAG 58.312 47.826 14.39 8.79 0.00 3.35
3440 3517 1.134699 TGCACTAGCGCTCTAATGCTT 60.135 47.619 25.71 1.58 45.40 3.91
3487 3564 1.428869 ATCCCTAGTGTGCTGATCCC 58.571 55.000 0.00 0.00 0.00 3.85
3537 3614 2.570442 GTTGCAACGGGAGAAAACAA 57.430 45.000 14.90 0.00 0.00 2.83
3547 3624 1.602377 GGAGAAAACAACCCTCACACG 59.398 52.381 0.00 0.00 0.00 4.49
3554 3631 0.035439 CAACCCTCACACGCCCTTAT 60.035 55.000 0.00 0.00 0.00 1.73
3590 3667 4.083862 GACCTCACCCTCGTGCCC 62.084 72.222 0.00 0.00 40.04 5.36
3607 3684 7.389330 CCTCGTGCCCATAACATAATAAACATA 59.611 37.037 0.00 0.00 0.00 2.29
3611 3688 9.893305 GTGCCCATAACATAATAAACATAACTC 57.107 33.333 0.00 0.00 0.00 3.01
3630 3707 5.713792 ACTCATACCTTATCCTCATGTCG 57.286 43.478 0.00 0.00 0.00 4.35
3726 3803 2.038387 AACACCAGTTGTCACTCACC 57.962 50.000 0.00 0.00 37.51 4.02
3727 3804 0.908910 ACACCAGTTGTCACTCACCA 59.091 50.000 0.00 0.00 29.79 4.17
3728 3805 1.280710 ACACCAGTTGTCACTCACCAA 59.719 47.619 0.00 0.00 29.79 3.67
3729 3806 1.942657 CACCAGTTGTCACTCACCAAG 59.057 52.381 0.00 0.00 0.00 3.61
3730 3807 1.134098 ACCAGTTGTCACTCACCAAGG 60.134 52.381 0.00 0.00 0.00 3.61
3731 3808 1.134098 CCAGTTGTCACTCACCAAGGT 60.134 52.381 0.00 0.00 0.00 3.50
3732 3809 2.643551 CAGTTGTCACTCACCAAGGTT 58.356 47.619 0.00 0.00 0.00 3.50
3733 3810 2.355756 CAGTTGTCACTCACCAAGGTTG 59.644 50.000 0.00 0.00 0.00 3.77
3742 3819 2.283173 CCAAGGTTGGCCAGGTCC 60.283 66.667 5.11 10.56 42.21 4.46
3743 3820 2.520458 CAAGGTTGGCCAGGTCCA 59.480 61.111 20.51 0.00 37.19 4.02
3744 3821 1.152567 CAAGGTTGGCCAGGTCCAA 60.153 57.895 20.51 10.42 43.36 3.53
3745 3822 0.542702 CAAGGTTGGCCAGGTCCAAT 60.543 55.000 20.51 9.94 46.64 3.16
3746 3823 1.080638 AAGGTTGGCCAGGTCCAATA 58.919 50.000 20.51 0.00 46.64 1.90
3747 3824 1.080638 AGGTTGGCCAGGTCCAATAA 58.919 50.000 20.51 0.00 46.64 1.40
3748 3825 1.182667 GGTTGGCCAGGTCCAATAAC 58.817 55.000 15.86 0.00 46.64 1.89
3749 3826 1.272480 GGTTGGCCAGGTCCAATAACT 60.272 52.381 15.86 0.00 46.64 2.24
3750 3827 1.818674 GTTGGCCAGGTCCAATAACTG 59.181 52.381 15.86 0.00 46.64 3.16
3762 3839 3.951979 CAATAACTGGATTGTCGAGCC 57.048 47.619 0.00 0.00 33.01 4.70
3763 3840 2.225068 ATAACTGGATTGTCGAGCCG 57.775 50.000 0.00 0.00 36.27 5.52
3764 3841 0.459585 TAACTGGATTGTCGAGCCGC 60.460 55.000 0.00 0.00 36.27 6.53
3765 3842 2.892425 CTGGATTGTCGAGCCGCC 60.892 66.667 0.00 0.00 36.27 6.13
3766 3843 3.376935 CTGGATTGTCGAGCCGCCT 62.377 63.158 0.00 0.00 36.27 5.52
3767 3844 2.125106 GGATTGTCGAGCCGCCTT 60.125 61.111 0.00 0.00 0.00 4.35
3768 3845 2.174319 GGATTGTCGAGCCGCCTTC 61.174 63.158 0.00 0.00 0.00 3.46
3769 3846 2.509336 ATTGTCGAGCCGCCTTCG 60.509 61.111 0.00 0.00 39.33 3.79
3770 3847 3.296709 ATTGTCGAGCCGCCTTCGT 62.297 57.895 2.39 0.00 39.05 3.85
3771 3848 4.717629 TGTCGAGCCGCCTTCGTG 62.718 66.667 2.39 0.00 39.05 4.35
3772 3849 4.719369 GTCGAGCCGCCTTCGTGT 62.719 66.667 2.39 0.00 39.05 4.49
3773 3850 4.415332 TCGAGCCGCCTTCGTGTC 62.415 66.667 2.39 0.00 39.05 3.67
3787 3864 2.810486 GTGTCCGACGAAGACCAAG 58.190 57.895 0.00 0.00 33.09 3.61
3788 3865 0.313043 GTGTCCGACGAAGACCAAGA 59.687 55.000 0.00 0.00 33.09 3.02
3789 3866 0.596577 TGTCCGACGAAGACCAAGAG 59.403 55.000 0.00 0.00 33.09 2.85
3790 3867 0.733223 GTCCGACGAAGACCAAGAGC 60.733 60.000 0.00 0.00 0.00 4.09
3791 3868 1.801913 CCGACGAAGACCAAGAGCG 60.802 63.158 0.00 0.00 0.00 5.03
3792 3869 1.081376 CGACGAAGACCAAGAGCGT 60.081 57.895 0.00 0.00 37.97 5.07
3793 3870 0.663568 CGACGAAGACCAAGAGCGTT 60.664 55.000 0.00 0.00 35.09 4.84
3794 3871 0.784778 GACGAAGACCAAGAGCGTTG 59.215 55.000 0.00 0.00 35.09 4.10
3795 3872 0.387929 ACGAAGACCAAGAGCGTTGA 59.612 50.000 3.62 0.00 0.00 3.18
3796 3873 1.202486 ACGAAGACCAAGAGCGTTGAA 60.202 47.619 3.62 0.00 0.00 2.69
3797 3874 1.457303 CGAAGACCAAGAGCGTTGAAG 59.543 52.381 3.62 0.00 0.00 3.02
3798 3875 2.755650 GAAGACCAAGAGCGTTGAAGA 58.244 47.619 3.62 0.00 0.00 2.87
3799 3876 2.910688 AGACCAAGAGCGTTGAAGAA 57.089 45.000 3.62 0.00 0.00 2.52
3800 3877 3.194005 AGACCAAGAGCGTTGAAGAAA 57.806 42.857 3.62 0.00 0.00 2.52
3801 3878 3.134458 AGACCAAGAGCGTTGAAGAAAG 58.866 45.455 3.62 0.00 0.00 2.62
3802 3879 2.872858 GACCAAGAGCGTTGAAGAAAGT 59.127 45.455 3.62 0.00 0.00 2.66
3803 3880 3.279434 ACCAAGAGCGTTGAAGAAAGTT 58.721 40.909 3.62 0.00 0.00 2.66
3804 3881 3.694566 ACCAAGAGCGTTGAAGAAAGTTT 59.305 39.130 3.62 0.00 0.00 2.66
3805 3882 4.157840 ACCAAGAGCGTTGAAGAAAGTTTT 59.842 37.500 3.62 0.00 0.00 2.43
3806 3883 5.102313 CCAAGAGCGTTGAAGAAAGTTTTT 58.898 37.500 3.62 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1034 1084 5.440610 GGGTGATGGACATAGACTTGAAAT 58.559 41.667 0.00 0.00 0.00 2.17
1645 1703 2.031333 GCACCTCAATTATAGCAGCTGC 60.031 50.000 31.53 31.53 42.49 5.25
1803 1863 0.965363 AAGCATTGCCCCGGTAACAG 60.965 55.000 4.70 0.00 0.00 3.16
2274 2349 4.948847 TCAAGTATGCGCAGTATCTTGAT 58.051 39.130 28.22 11.07 39.52 2.57
2304 2379 0.538057 CTGAAAGCAGTTCTGGGGCA 60.538 55.000 1.97 0.00 37.37 5.36
2437 2512 2.780693 CTCCTCCTCCCCCTCACA 59.219 66.667 0.00 0.00 0.00 3.58
2438 2513 2.041405 CCTCCTCCTCCCCCTCAC 60.041 72.222 0.00 0.00 0.00 3.51
2439 2514 2.204624 TCCTCCTCCTCCCCCTCA 60.205 66.667 0.00 0.00 0.00 3.86
2440 2515 2.612251 CTCCTCCTCCTCCCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
2441 2516 3.039526 CCTCCTCCTCCTCCCCCT 61.040 72.222 0.00 0.00 0.00 4.79
2442 2517 3.036959 TCCTCCTCCTCCTCCCCC 61.037 72.222 0.00 0.00 0.00 5.40
2443 2518 2.612251 CTCCTCCTCCTCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
2444 2519 2.015726 TCCTCCTCCTCCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
2445 2520 0.996762 TCTCCTCCTCCTCCTCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
2446 2521 0.185175 GTCTCCTCCTCCTCCTCCTC 59.815 65.000 0.00 0.00 0.00 3.71
2447 2522 1.293683 GGTCTCCTCCTCCTCCTCCT 61.294 65.000 0.00 0.00 0.00 3.69
2448 2523 1.231928 GGTCTCCTCCTCCTCCTCC 59.768 68.421 0.00 0.00 0.00 4.30
2449 2524 0.560688 ATGGTCTCCTCCTCCTCCTC 59.439 60.000 0.00 0.00 0.00 3.71
2450 2525 0.264359 CATGGTCTCCTCCTCCTCCT 59.736 60.000 0.00 0.00 0.00 3.69
2451 2526 0.031616 ACATGGTCTCCTCCTCCTCC 60.032 60.000 0.00 0.00 0.00 4.30
2452 2527 1.760029 GAACATGGTCTCCTCCTCCTC 59.240 57.143 2.64 0.00 0.00 3.71
2475 2550 3.322466 CCCAGCTTGACCCCTCGT 61.322 66.667 0.00 0.00 0.00 4.18
2525 2600 1.075601 TTCCTCCAGCACCTTCCATT 58.924 50.000 0.00 0.00 0.00 3.16
2571 2646 4.260907 CCATTGACATTATCTGAAGGTGCG 60.261 45.833 0.00 0.00 0.00 5.34
2577 2652 4.858850 AGTGCCCATTGACATTATCTGAA 58.141 39.130 0.00 0.00 0.00 3.02
2622 2697 2.092914 CCAGATGTGGGTTAGGAACTCC 60.093 54.545 0.00 0.00 40.67 3.85
2646 2721 0.108019 TGCCAGCATGAGATAGCAGG 59.892 55.000 0.00 0.00 39.69 4.85
2695 2770 2.363276 ATGGCTGGGCATGGTGTG 60.363 61.111 8.82 0.00 0.00 3.82
2715 2790 4.382754 GCAAATCACACATTTTCTTCGGAC 59.617 41.667 0.00 0.00 0.00 4.79
2719 2794 5.632347 CAGAGGCAAATCACACATTTTCTTC 59.368 40.000 0.00 0.00 0.00 2.87
2737 2812 4.216472 CACTCCTTTTCCTTTTACAGAGGC 59.784 45.833 0.00 0.00 34.17 4.70
2744 2819 3.391955 TCGGACCACTCCTTTTCCTTTTA 59.608 43.478 0.00 0.00 33.79 1.52
2795 2871 7.486551 TCAAAGGAAATAAAGAACAAACACACG 59.513 33.333 0.00 0.00 0.00 4.49
2807 2883 8.797438 AGACTTTTAGGCTCAAAGGAAATAAAG 58.203 33.333 21.59 6.94 35.82 1.85
2862 2938 3.000041 CCTGCTCTTGTATACACGCAAA 59.000 45.455 18.62 0.79 0.00 3.68
2906 2982 7.681939 TGAAACCCATTCTAACTTACATGTC 57.318 36.000 0.00 0.00 38.92 3.06
2925 3001 3.383185 TGTGGTTCCAGATGGTTTGAAAC 59.617 43.478 0.00 0.00 36.34 2.78
2926 3002 3.636679 TGTGGTTCCAGATGGTTTGAAA 58.363 40.909 0.00 0.00 36.34 2.69
2927 3003 3.304911 TGTGGTTCCAGATGGTTTGAA 57.695 42.857 0.00 0.00 36.34 2.69
2928 3004 3.156293 CATGTGGTTCCAGATGGTTTGA 58.844 45.455 17.67 0.00 35.09 2.69
2929 3005 3.156293 TCATGTGGTTCCAGATGGTTTG 58.844 45.455 22.69 5.06 38.00 2.93
2930 3006 3.074390 TCTCATGTGGTTCCAGATGGTTT 59.926 43.478 22.69 0.00 38.00 3.27
2931 3007 2.644299 TCTCATGTGGTTCCAGATGGTT 59.356 45.455 22.69 0.00 38.00 3.67
2932 3008 2.238144 CTCTCATGTGGTTCCAGATGGT 59.762 50.000 22.69 0.00 38.00 3.55
2933 3009 2.915349 CTCTCATGTGGTTCCAGATGG 58.085 52.381 22.69 15.65 38.00 3.51
2934 3010 2.286872 GCTCTCATGTGGTTCCAGATG 58.713 52.381 18.88 18.88 38.54 2.90
2935 3011 1.911357 TGCTCTCATGTGGTTCCAGAT 59.089 47.619 0.00 0.00 0.00 2.90
2936 3012 1.351076 TGCTCTCATGTGGTTCCAGA 58.649 50.000 0.00 0.00 0.00 3.86
2937 3013 2.189594 TTGCTCTCATGTGGTTCCAG 57.810 50.000 0.00 0.00 0.00 3.86
2938 3014 2.655090 TTTGCTCTCATGTGGTTCCA 57.345 45.000 0.00 0.00 0.00 3.53
2939 3015 2.821969 ACATTTGCTCTCATGTGGTTCC 59.178 45.455 0.00 0.00 32.19 3.62
2966 3042 5.912955 CCGGACTGTATTTCAAGTTTTCAAC 59.087 40.000 0.00 0.00 0.00 3.18
2967 3043 5.009210 CCCGGACTGTATTTCAAGTTTTCAA 59.991 40.000 0.73 0.00 0.00 2.69
2968 3044 4.517453 CCCGGACTGTATTTCAAGTTTTCA 59.483 41.667 0.73 0.00 0.00 2.69
2969 3045 4.517832 ACCCGGACTGTATTTCAAGTTTTC 59.482 41.667 0.73 0.00 0.00 2.29
2970 3046 4.466827 ACCCGGACTGTATTTCAAGTTTT 58.533 39.130 0.73 0.00 0.00 2.43
2971 3047 4.094830 ACCCGGACTGTATTTCAAGTTT 57.905 40.909 0.73 0.00 0.00 2.66
2972 3048 3.782656 ACCCGGACTGTATTTCAAGTT 57.217 42.857 0.73 0.00 0.00 2.66
2973 3049 3.071892 TCAACCCGGACTGTATTTCAAGT 59.928 43.478 0.73 0.00 0.00 3.16
2974 3050 3.670625 TCAACCCGGACTGTATTTCAAG 58.329 45.455 0.73 0.00 0.00 3.02
2975 3051 3.071892 ACTCAACCCGGACTGTATTTCAA 59.928 43.478 0.73 0.00 0.00 2.69
3009 3085 4.067896 ACCCGATCAGCATTTCATCATAC 58.932 43.478 0.00 0.00 0.00 2.39
3071 3147 3.245087 TGCTAGTGGTTTCAAATAGGCCA 60.245 43.478 5.01 0.00 0.00 5.36
3073 3149 3.378427 CCTGCTAGTGGTTTCAAATAGGC 59.622 47.826 0.00 0.00 0.00 3.93
3289 3366 0.035725 TGTGAGGAGGATGCAGCAAG 60.036 55.000 3.51 0.00 0.00 4.01
3332 3409 9.684448 CACAACATTTACAGTCTATCGATCTAT 57.316 33.333 0.00 0.00 0.00 1.98
3333 3410 7.648112 GCACAACATTTACAGTCTATCGATCTA 59.352 37.037 0.00 0.00 0.00 1.98
3334 3411 6.477033 GCACAACATTTACAGTCTATCGATCT 59.523 38.462 0.00 0.00 0.00 2.75
3335 3412 6.292381 GGCACAACATTTACAGTCTATCGATC 60.292 42.308 0.00 0.00 0.00 3.69
3338 3415 4.870426 AGGCACAACATTTACAGTCTATCG 59.130 41.667 0.00 0.00 0.00 2.92
3412 3489 1.855360 GAGCGCTAGTGCACTCATAAC 59.145 52.381 28.83 10.56 44.99 1.89
3467 3544 1.771255 GGGATCAGCACACTAGGGATT 59.229 52.381 0.00 0.00 0.00 3.01
3475 3552 2.103094 TGCATACTAGGGATCAGCACAC 59.897 50.000 0.00 0.00 0.00 3.82
3528 3605 1.002792 GCGTGTGAGGGTTGTTTTCTC 60.003 52.381 0.00 0.00 0.00 2.87
3537 3614 1.623542 GGATAAGGGCGTGTGAGGGT 61.624 60.000 0.00 0.00 0.00 4.34
3607 3684 5.833667 TCGACATGAGGATAAGGTATGAGTT 59.166 40.000 0.00 0.00 0.00 3.01
3611 3688 5.453567 TGTCGACATGAGGATAAGGTATG 57.546 43.478 15.76 0.00 0.00 2.39
3618 3695 4.725490 TGTAGGATGTCGACATGAGGATA 58.275 43.478 34.48 16.04 36.57 2.59
3626 3703 9.256477 GTTATATTGAAATGTAGGATGTCGACA 57.744 33.333 22.48 22.48 35.54 4.35
3696 3773 2.358125 TGGTGTTGCGACCATCGG 60.358 61.111 0.45 0.00 41.30 4.18
3707 3784 1.280710 TGGTGAGTGACAACTGGTGTT 59.719 47.619 0.00 0.00 41.96 3.32
3708 3785 0.908910 TGGTGAGTGACAACTGGTGT 59.091 50.000 0.00 0.00 45.74 4.16
3726 3803 1.152567 TTGGACCTGGCCAACCTTG 60.153 57.895 19.46 3.71 42.75 3.61
3727 3804 3.352512 TTGGACCTGGCCAACCTT 58.647 55.556 19.46 0.48 42.75 3.50
3732 3809 3.976704 CAGTTATTGGACCTGGCCA 57.023 52.632 4.71 4.71 35.78 5.36
3742 3819 2.285220 CGGCTCGACAATCCAGTTATTG 59.715 50.000 0.00 0.00 41.65 1.90
3743 3820 2.550978 CGGCTCGACAATCCAGTTATT 58.449 47.619 0.00 0.00 0.00 1.40
3744 3821 1.806623 GCGGCTCGACAATCCAGTTAT 60.807 52.381 0.00 0.00 0.00 1.89
3745 3822 0.459585 GCGGCTCGACAATCCAGTTA 60.460 55.000 0.00 0.00 0.00 2.24
3746 3823 1.741770 GCGGCTCGACAATCCAGTT 60.742 57.895 0.00 0.00 0.00 3.16
3747 3824 2.125512 GCGGCTCGACAATCCAGT 60.126 61.111 0.00 0.00 0.00 4.00
3748 3825 2.859273 AAGGCGGCTCGACAATCCAG 62.859 60.000 13.70 0.00 37.34 3.86
3749 3826 2.852495 GAAGGCGGCTCGACAATCCA 62.852 60.000 13.70 0.00 37.34 3.41
3750 3827 2.125106 AAGGCGGCTCGACAATCC 60.125 61.111 13.70 0.00 37.34 3.01
3751 3828 2.517450 CGAAGGCGGCTCGACAATC 61.517 63.158 13.70 3.68 37.34 2.67
3752 3829 2.509336 CGAAGGCGGCTCGACAAT 60.509 61.111 13.70 0.00 37.34 2.71
3753 3830 3.986006 ACGAAGGCGGCTCGACAA 61.986 61.111 27.86 0.00 43.17 3.18
3754 3831 4.717629 CACGAAGGCGGCTCGACA 62.718 66.667 27.86 0.00 43.17 4.35
3755 3832 4.719369 ACACGAAGGCGGCTCGAC 62.719 66.667 27.86 16.01 43.17 4.20
3756 3833 4.415332 GACACGAAGGCGGCTCGA 62.415 66.667 27.86 0.00 43.17 4.04
3769 3846 0.313043 TCTTGGTCTTCGTCGGACAC 59.687 55.000 9.10 0.00 35.61 3.67
3770 3847 0.596577 CTCTTGGTCTTCGTCGGACA 59.403 55.000 9.10 0.00 35.61 4.02
3771 3848 0.733223 GCTCTTGGTCTTCGTCGGAC 60.733 60.000 0.00 0.00 0.00 4.79
3772 3849 1.585006 GCTCTTGGTCTTCGTCGGA 59.415 57.895 0.00 0.00 0.00 4.55
3773 3850 1.801913 CGCTCTTGGTCTTCGTCGG 60.802 63.158 0.00 0.00 0.00 4.79
3774 3851 0.663568 AACGCTCTTGGTCTTCGTCG 60.664 55.000 0.00 0.00 32.53 5.12
3775 3852 0.784778 CAACGCTCTTGGTCTTCGTC 59.215 55.000 0.00 0.00 32.53 4.20
3776 3853 0.387929 TCAACGCTCTTGGTCTTCGT 59.612 50.000 0.00 0.00 34.63 3.85
3777 3854 1.457303 CTTCAACGCTCTTGGTCTTCG 59.543 52.381 0.00 0.00 0.00 3.79
3778 3855 2.755650 TCTTCAACGCTCTTGGTCTTC 58.244 47.619 0.00 0.00 0.00 2.87
3779 3856 2.910688 TCTTCAACGCTCTTGGTCTT 57.089 45.000 0.00 0.00 0.00 3.01
3780 3857 2.910688 TTCTTCAACGCTCTTGGTCT 57.089 45.000 0.00 0.00 0.00 3.85
3781 3858 2.872858 ACTTTCTTCAACGCTCTTGGTC 59.127 45.455 0.00 0.00 0.00 4.02
3782 3859 2.919228 ACTTTCTTCAACGCTCTTGGT 58.081 42.857 0.00 0.00 0.00 3.67
3783 3860 3.971032 AACTTTCTTCAACGCTCTTGG 57.029 42.857 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.