Multiple sequence alignment - TraesCS2A01G435800

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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 TraesCS2A01G435800 chr2A 100.000 4059 0 0 1 4059 688229998 688234056 0.000000e+00 7496.0
1 TraesCS2A01G435800 chr2A 95.885 1701 54 6 1 1695 688208571 688210261 0.000000e+00 2739.0
2 TraesCS2A01G435800 chr2A 95.721 1706 51 8 1 1695 688219311 688221005 0.000000e+00 2726.0
3 TraesCS2A01G435800 chr2B 94.922 1536 58 12 938 2466 651934793 651933271 0.000000e+00 2386.0
4 TraesCS2A01G435800 chr2B 88.970 1514 101 37 2602 4058 651933151 651931647 0.000000e+00 1810.0
5 TraesCS2A01G435800 chr2B 94.359 195 10 1 227 421 651934976 651934783 8.530000e-77 298.0
6 TraesCS2A01G435800 chr2B 93.491 169 11 0 1 169 651935151 651934983 6.730000e-63 252.0
7 TraesCS2A01G435800 chr2D 95.793 1331 45 6 930 2252 545042895 545041568 0.000000e+00 2137.0
8 TraesCS2A01G435800 chr2D 94.127 1277 59 11 2655 3922 545040780 545039511 0.000000e+00 1929.0
9 TraesCS2A01G435800 chr2D 93.264 193 11 2 227 417 545043069 545042877 2.390000e-72 283.0
10 TraesCS2A01G435800 chr2D 92.746 193 13 1 1 193 545043261 545043070 1.110000e-70 278.0
11 TraesCS2A01G435800 chr6A 88.962 453 41 3 421 873 49501708 49502151 5.930000e-153 551.0
12 TraesCS2A01G435800 chr1D 85.138 471 57 9 416 876 339355898 339356365 1.710000e-128 470.0
13 TraesCS2A01G435800 chr6B 85.313 463 56 12 420 875 62817721 62818178 6.140000e-128 468.0
14 TraesCS2A01G435800 chr6B 85.176 425 58 5 410 829 6791946 6792370 8.060000e-117 431.0
15 TraesCS2A01G435800 chr1A 86.553 409 48 7 476 880 72499969 72499564 1.040000e-120 444.0
16 TraesCS2A01G435800 chr4A 84.334 383 37 5 446 827 620982889 620983249 1.790000e-93 353.0
17 TraesCS2A01G435800 chr4A 79.785 465 70 9 414 875 721420892 721421335 2.350000e-82 316.0
18 TraesCS2A01G435800 chr4A 96.774 31 1 0 2452 2482 724580703 724580673 7.000000e-03 52.8


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 TraesCS2A01G435800 chr2A 688229998 688234056 4058 False 7496.00 7496 100.0000 1 4059 1 chr2A.!!$F3 4058
1 TraesCS2A01G435800 chr2A 688208571 688210261 1690 False 2739.00 2739 95.8850 1 1695 1 chr2A.!!$F1 1694
2 TraesCS2A01G435800 chr2A 688219311 688221005 1694 False 2726.00 2726 95.7210 1 1695 1 chr2A.!!$F2 1694
3 TraesCS2A01G435800 chr2B 651931647 651935151 3504 True 1186.50 2386 92.9355 1 4058 4 chr2B.!!$R1 4057
4 TraesCS2A01G435800 chr2D 545039511 545043261 3750 True 1156.75 2137 93.9825 1 3922 4 chr2D.!!$R1 3921

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
858 885 1.741528 TTTAAAAGATCGGTCGGCCC 58.258 50.000 0.00 0.0 0.0 5.80 F
2056 2108 1.063649 GCTCGAGCGATCCGTGTTA 59.936 57.895 23.61 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2242 0.178068 CCGTGGTGATCCCCTGTTAG 59.822 60.0 0.0 0.0 0.0 2.34 R
3465 4012 0.447801 CTTTCGCCAGGAAATCACCG 59.552 55.0 0.0 0.0 43.4 4.94 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
788 815 8.231837 GTCCTTGTTGCAATAACGAAAATAGTA 58.768 33.333 0.59 0.00 0.00 1.82
850 877 6.912591 AGGCAGCGAATATTTTTAAAAGATCG 59.087 34.615 15.99 15.99 0.00 3.69
858 885 1.741528 TTTAAAAGATCGGTCGGCCC 58.258 50.000 0.00 0.00 0.00 5.80
875 902 2.824041 CACGCATAGTGTGGCCCC 60.824 66.667 0.00 0.00 45.51 5.80
970 1003 9.533831 AAGACCATGACTAAAAAGGATTACATT 57.466 29.630 0.00 0.00 0.00 2.71
1116 1149 1.820481 CCTCTCCGACGACCTCCTC 60.820 68.421 0.00 0.00 0.00 3.71
1457 1490 4.873129 CGAGCCCATCGTCCACGG 62.873 72.222 0.00 0.00 46.62 4.94
1507 1552 2.833582 GGAGGGCGACGGAGATCA 60.834 66.667 0.00 0.00 0.00 2.92
1791 1836 3.470567 GAAGTGCTGGTCGCGTCG 61.471 66.667 5.77 0.00 43.27 5.12
2004 2049 4.201881 GCCCTCATTGTACGTCCAATTAAC 60.202 45.833 3.29 0.00 32.81 2.01
2019 2064 2.743636 TTAACTGGCTTCTCTCCGTG 57.256 50.000 0.00 0.00 0.00 4.94
2042 2094 3.129113 TGAATCCATGGATTGTTTGCTCG 59.871 43.478 38.61 0.00 43.98 5.03
2055 2107 2.202623 GCTCGAGCGATCCGTGTT 60.203 61.111 23.61 0.00 0.00 3.32
2056 2108 1.063649 GCTCGAGCGATCCGTGTTA 59.936 57.895 23.61 0.00 0.00 2.41
2057 2109 1.201098 GCTCGAGCGATCCGTGTTAC 61.201 60.000 23.61 0.00 0.00 2.50
2097 2149 5.886715 TTGATGATTCGTTTTTGTGCTTG 57.113 34.783 0.00 0.00 0.00 4.01
2132 2184 1.421646 CAGGGAATGGAGGGATACACC 59.578 57.143 0.00 0.00 39.74 4.16
2156 2208 6.088824 CAGCTTCTTGGATGATGTAAACAAC 58.911 40.000 0.00 0.00 0.00 3.32
2195 2247 4.973396 CCGTATTATCGGTATCGCTAACA 58.027 43.478 0.00 0.00 44.77 2.41
2257 2309 4.433615 CTCAGGAGAAGCAACGCTATAAA 58.566 43.478 0.00 0.00 38.25 1.40
2260 2312 4.870426 CAGGAGAAGCAACGCTATAAAGAA 59.130 41.667 0.00 0.00 38.25 2.52
2314 2366 8.179615 GGTACGTAATTTCTAGGGTTCATTTTG 58.820 37.037 0.00 0.00 0.00 2.44
2327 2379 5.922544 GGGTTCATTTTGTCAGTTCATTCAG 59.077 40.000 0.00 0.00 0.00 3.02
2338 2390 4.769488 TCAGTTCATTCAGAGACTGTAGCT 59.231 41.667 0.00 0.00 37.03 3.32
2361 2413 9.079833 AGCTCAAATATTCACGATTTTGAAATG 57.920 29.630 0.00 0.00 38.95 2.32
2386 2438 8.092687 TGAAGGAAACATGTTTAGGAGTAGTAC 58.907 37.037 23.33 7.22 32.11 2.73
2387 2439 7.793948 AGGAAACATGTTTAGGAGTAGTACT 57.206 36.000 23.33 1.37 32.11 2.73
2423 2776 4.222588 AGCCCATTGAAAAATCATCGGAAA 59.777 37.500 0.00 0.00 0.00 3.13
2425 2778 5.006941 GCCCATTGAAAAATCATCGGAAATG 59.993 40.000 0.00 0.00 0.00 2.32
2428 2781 7.763528 CCCATTGAAAAATCATCGGAAATGTTA 59.236 33.333 0.00 0.00 0.00 2.41
2429 2782 9.316730 CCATTGAAAAATCATCGGAAATGTTAT 57.683 29.630 0.00 0.00 0.00 1.89
2432 2785 9.571810 TTGAAAAATCATCGGAAATGTTATCTG 57.428 29.630 0.00 0.00 0.00 2.90
2433 2786 8.190122 TGAAAAATCATCGGAAATGTTATCTGG 58.810 33.333 0.00 0.00 0.00 3.86
2434 2787 5.695851 AATCATCGGAAATGTTATCTGGC 57.304 39.130 0.00 0.00 0.00 4.85
2435 2788 4.422073 TCATCGGAAATGTTATCTGGCT 57.578 40.909 0.00 0.00 0.00 4.75
2441 2794 3.696051 GGAAATGTTATCTGGCTGCTGAA 59.304 43.478 0.00 0.00 0.00 3.02
2444 2797 2.977914 TGTTATCTGGCTGCTGAAGTC 58.022 47.619 0.00 0.00 0.00 3.01
2446 2799 0.461548 TATCTGGCTGCTGAAGTCCG 59.538 55.000 0.00 0.00 0.00 4.79
2447 2800 2.866085 ATCTGGCTGCTGAAGTCCGC 62.866 60.000 0.00 0.00 0.00 5.54
2469 2893 1.644786 GGAGGGTGGCATTTCGAACG 61.645 60.000 0.00 0.00 0.00 3.95
2479 2903 2.786578 GCATTTCGAACGTTTTTGCTGA 59.213 40.909 0.46 0.00 0.00 4.26
2483 2907 1.112459 CGAACGTTTTTGCTGACAGC 58.888 50.000 20.86 20.86 42.82 4.40
2496 2920 2.872245 GCTGACAGCTTTAGTTGTGTCA 59.128 45.455 20.41 7.51 45.39 3.58
2498 2922 4.137116 TGACAGCTTTAGTTGTGTCAGT 57.863 40.909 3.88 0.00 43.33 3.41
2499 2923 4.119862 TGACAGCTTTAGTTGTGTCAGTC 58.880 43.478 3.88 0.00 43.33 3.51
2500 2924 3.467803 ACAGCTTTAGTTGTGTCAGTCC 58.532 45.455 0.00 0.00 38.07 3.85
2502 2926 4.130118 CAGCTTTAGTTGTGTCAGTCCTT 58.870 43.478 0.00 0.00 0.00 3.36
2503 2927 4.576463 CAGCTTTAGTTGTGTCAGTCCTTT 59.424 41.667 0.00 0.00 0.00 3.11
2517 3006 6.547141 TGTCAGTCCTTTCAGAAAATGTCATT 59.453 34.615 0.00 0.00 0.00 2.57
2525 3014 8.084073 CCTTTCAGAAAATGTCATTTTGCTCTA 58.916 33.333 24.74 10.95 42.15 2.43
2540 3029 2.106511 TGCTCTAAAGAAACTGCCACCT 59.893 45.455 0.00 0.00 0.00 4.00
2564 3057 1.375908 ACATCGTGCCATGTCGCTT 60.376 52.632 0.00 0.00 30.76 4.68
2566 3059 0.521867 CATCGTGCCATGTCGCTTTG 60.522 55.000 0.00 0.00 0.00 2.77
2581 3074 3.498397 TCGCTTTGAAGAAACTGTCATCC 59.502 43.478 0.00 0.00 0.00 3.51
2582 3075 3.365364 CGCTTTGAAGAAACTGTCATCCC 60.365 47.826 0.00 0.00 0.00 3.85
2583 3076 3.569701 GCTTTGAAGAAACTGTCATCCCA 59.430 43.478 0.00 0.00 0.00 4.37
2584 3077 4.557496 GCTTTGAAGAAACTGTCATCCCAC 60.557 45.833 0.00 0.00 0.00 4.61
2585 3078 3.855255 TGAAGAAACTGTCATCCCACA 57.145 42.857 0.00 0.00 0.00 4.17
2586 3079 3.476552 TGAAGAAACTGTCATCCCACAC 58.523 45.455 0.00 0.00 0.00 3.82
2587 3080 3.118075 TGAAGAAACTGTCATCCCACACA 60.118 43.478 0.00 0.00 0.00 3.72
2588 3081 3.795688 AGAAACTGTCATCCCACACAT 57.204 42.857 0.00 0.00 0.00 3.21
2589 3082 3.415212 AGAAACTGTCATCCCACACATG 58.585 45.455 0.00 0.00 0.00 3.21
2590 3083 2.957402 AACTGTCATCCCACACATGT 57.043 45.000 0.00 0.00 0.00 3.21
2591 3084 2.479566 ACTGTCATCCCACACATGTC 57.520 50.000 0.00 0.00 0.00 3.06
2592 3085 1.338105 ACTGTCATCCCACACATGTCG 60.338 52.381 0.00 0.00 0.00 4.35
2593 3086 0.684535 TGTCATCCCACACATGTCGT 59.315 50.000 0.00 0.00 0.00 4.34
2594 3087 1.337728 TGTCATCCCACACATGTCGTC 60.338 52.381 0.00 0.00 0.00 4.20
2595 3088 0.249120 TCATCCCACACATGTCGTCC 59.751 55.000 0.00 0.00 0.00 4.79
2596 3089 0.250234 CATCCCACACATGTCGTCCT 59.750 55.000 0.00 0.00 0.00 3.85
2597 3090 0.537188 ATCCCACACATGTCGTCCTC 59.463 55.000 0.00 0.00 0.00 3.71
2598 3091 1.079127 CCCACACATGTCGTCCTCC 60.079 63.158 0.00 0.00 0.00 4.30
2599 3092 1.079127 CCACACATGTCGTCCTCCC 60.079 63.158 0.00 0.00 0.00 4.30
2600 3093 1.671166 CACACATGTCGTCCTCCCA 59.329 57.895 0.00 0.00 0.00 4.37
2601 3094 0.390340 CACACATGTCGTCCTCCCAG 60.390 60.000 0.00 0.00 0.00 4.45
2602 3095 0.541998 ACACATGTCGTCCTCCCAGA 60.542 55.000 0.00 0.00 0.00 3.86
2603 3096 0.608130 CACATGTCGTCCTCCCAGAA 59.392 55.000 0.00 0.00 0.00 3.02
2604 3097 1.001974 CACATGTCGTCCTCCCAGAAA 59.998 52.381 0.00 0.00 0.00 2.52
2605 3098 1.697432 ACATGTCGTCCTCCCAGAAAA 59.303 47.619 0.00 0.00 0.00 2.29
2606 3099 2.305927 ACATGTCGTCCTCCCAGAAAAT 59.694 45.455 0.00 0.00 0.00 1.82
2607 3100 2.472695 TGTCGTCCTCCCAGAAAATG 57.527 50.000 0.00 0.00 0.00 2.32
2608 3101 1.697432 TGTCGTCCTCCCAGAAAATGT 59.303 47.619 0.00 0.00 0.00 2.71
2609 3102 2.901192 TGTCGTCCTCCCAGAAAATGTA 59.099 45.455 0.00 0.00 0.00 2.29
2610 3103 3.325425 TGTCGTCCTCCCAGAAAATGTAA 59.675 43.478 0.00 0.00 0.00 2.41
2611 3104 4.019681 TGTCGTCCTCCCAGAAAATGTAAT 60.020 41.667 0.00 0.00 0.00 1.89
2612 3105 4.332819 GTCGTCCTCCCAGAAAATGTAATG 59.667 45.833 0.00 0.00 0.00 1.90
2613 3106 3.065371 CGTCCTCCCAGAAAATGTAATGC 59.935 47.826 0.00 0.00 0.00 3.56
2614 3107 3.381590 GTCCTCCCAGAAAATGTAATGCC 59.618 47.826 0.00 0.00 0.00 4.40
2615 3108 2.358898 CCTCCCAGAAAATGTAATGCCG 59.641 50.000 0.00 0.00 0.00 5.69
2616 3109 1.748493 TCCCAGAAAATGTAATGCCGC 59.252 47.619 0.00 0.00 0.00 6.53
2617 3110 1.750778 CCCAGAAAATGTAATGCCGCT 59.249 47.619 0.00 0.00 0.00 5.52
2618 3111 2.223572 CCCAGAAAATGTAATGCCGCTC 60.224 50.000 0.00 0.00 0.00 5.03
2619 3112 2.684881 CCAGAAAATGTAATGCCGCTCT 59.315 45.455 0.00 0.00 0.00 4.09
2620 3113 3.488047 CCAGAAAATGTAATGCCGCTCTG 60.488 47.826 0.00 0.00 0.00 3.35
2621 3114 3.374988 CAGAAAATGTAATGCCGCTCTGA 59.625 43.478 0.00 0.00 32.58 3.27
2622 3115 4.009675 AGAAAATGTAATGCCGCTCTGAA 58.990 39.130 0.00 0.00 0.00 3.02
2623 3116 4.095483 AGAAAATGTAATGCCGCTCTGAAG 59.905 41.667 0.00 0.00 0.00 3.02
2624 3117 2.988010 ATGTAATGCCGCTCTGAAGA 57.012 45.000 0.00 0.00 0.00 2.87
2625 3118 2.760634 TGTAATGCCGCTCTGAAGAA 57.239 45.000 0.00 0.00 0.00 2.52
2626 3119 3.052455 TGTAATGCCGCTCTGAAGAAA 57.948 42.857 0.00 0.00 0.00 2.52
2627 3120 2.742053 TGTAATGCCGCTCTGAAGAAAC 59.258 45.455 0.00 0.00 0.00 2.78
2628 3121 2.191128 AATGCCGCTCTGAAGAAACT 57.809 45.000 0.00 0.00 0.00 2.66
2629 3122 1.446907 ATGCCGCTCTGAAGAAACTG 58.553 50.000 0.00 0.00 0.00 3.16
2630 3123 0.603707 TGCCGCTCTGAAGAAACTGG 60.604 55.000 0.00 0.00 0.00 4.00
2631 3124 1.916697 GCCGCTCTGAAGAAACTGGC 61.917 60.000 0.00 0.00 0.00 4.85
2632 3125 0.603707 CCGCTCTGAAGAAACTGGCA 60.604 55.000 0.00 0.00 0.00 4.92
2633 3126 1.446907 CGCTCTGAAGAAACTGGCAT 58.553 50.000 0.00 0.00 0.00 4.40
2634 3127 2.621338 CGCTCTGAAGAAACTGGCATA 58.379 47.619 0.00 0.00 0.00 3.14
2635 3128 3.201290 CGCTCTGAAGAAACTGGCATAT 58.799 45.455 0.00 0.00 0.00 1.78
2812 3352 2.434185 TCGACGGCTTGTCCATGC 60.434 61.111 0.00 0.00 45.23 4.06
2991 3531 3.905784 AGTCGTACCTTGTTCCTTTACG 58.094 45.455 0.00 0.00 37.47 3.18
3069 3609 5.756347 TCGGATTACATTAAATCTCCAACGG 59.244 40.000 0.00 0.00 36.34 4.44
3089 3629 3.999001 CGGGAGGTTTTTAGAAGTGGTAC 59.001 47.826 0.00 0.00 0.00 3.34
3090 3630 4.262765 CGGGAGGTTTTTAGAAGTGGTACT 60.263 45.833 0.00 0.00 0.00 2.73
3091 3631 5.001874 GGGAGGTTTTTAGAAGTGGTACTG 58.998 45.833 0.00 0.00 0.00 2.74
3150 3697 1.454653 GTTTGTTAGTGGTCGTCTCGC 59.545 52.381 0.00 0.00 0.00 5.03
3170 3717 7.848051 GTCTCGCAAAAATACTTATGACTGATG 59.152 37.037 0.00 0.00 0.00 3.07
3180 3727 5.171476 ACTTATGACTGATGAACTTCGTGG 58.829 41.667 0.00 0.00 0.00 4.94
3316 3863 1.227853 GTCACCCACCGCTTTGTCT 60.228 57.895 0.00 0.00 0.00 3.41
3364 3911 0.921256 CCAGGATTTCAGGGGGAGGT 60.921 60.000 0.00 0.00 0.00 3.85
3439 3986 0.402121 GAACCTCTGGAGCTGGGTTT 59.598 55.000 0.00 0.00 41.44 3.27
3442 3989 0.674895 CCTCTGGAGCTGGGTTTTCG 60.675 60.000 0.00 0.00 0.00 3.46
3566 4113 1.486726 CTCTAGTTCTGCCCCCGATTT 59.513 52.381 0.00 0.00 0.00 2.17
3567 4114 1.913419 TCTAGTTCTGCCCCCGATTTT 59.087 47.619 0.00 0.00 0.00 1.82
3586 4133 7.333423 CCGATTTTATCAGTCTGAAACCTTGTA 59.667 37.037 6.64 0.00 0.00 2.41
3644 4191 3.802948 ACCAATAAGACAGTAGGCTCG 57.197 47.619 0.00 0.00 0.00 5.03
3647 4194 3.119291 CAATAAGACAGTAGGCTCGCTG 58.881 50.000 14.86 14.86 38.58 5.18
3651 4198 0.737715 GACAGTAGGCTCGCTGTTGG 60.738 60.000 20.63 0.87 44.89 3.77
3659 4236 1.442769 GCTCGCTGTTGGAATGAAGA 58.557 50.000 0.00 0.00 0.00 2.87
3678 4255 5.065346 TGAAGAAACAACAACAGCGACATAA 59.935 36.000 0.00 0.00 0.00 1.90
3680 4257 4.574828 AGAAACAACAACAGCGACATAACT 59.425 37.500 0.00 0.00 0.00 2.24
3684 4261 4.152402 ACAACAACAGCGACATAACTCATC 59.848 41.667 0.00 0.00 0.00 2.92
3685 4262 3.262420 ACAACAGCGACATAACTCATCC 58.738 45.455 0.00 0.00 0.00 3.51
3700 4277 3.006859 ACTCATCCGATTGACAGTCACAA 59.993 43.478 1.52 0.00 0.00 3.33
3701 4278 4.186926 CTCATCCGATTGACAGTCACAAT 58.813 43.478 1.52 0.00 40.08 2.71
3722 4299 4.364415 TGTAATGAAATTAAGCGTGGGC 57.636 40.909 0.00 0.00 41.12 5.36
3726 4303 3.951775 TGAAATTAAGCGTGGGCAAAT 57.048 38.095 0.00 0.00 43.41 2.32
3727 4304 3.843999 TGAAATTAAGCGTGGGCAAATC 58.156 40.909 0.00 0.00 43.41 2.17
3728 4305 3.256879 TGAAATTAAGCGTGGGCAAATCA 59.743 39.130 0.00 0.00 43.41 2.57
3862 4441 2.037121 CCAAACATCCCCAACTCCAAAC 59.963 50.000 0.00 0.00 0.00 2.93
3925 4504 8.706322 ACAGAAGGATACCAAAATTAAACACT 57.294 30.769 0.00 0.00 37.17 3.55
3931 4510 9.869757 AGGATACCAAAATTAAACACTAATTGC 57.130 29.630 0.00 0.00 37.17 3.56
3932 4511 9.869757 GGATACCAAAATTAAACACTAATTGCT 57.130 29.630 0.00 0.00 0.00 3.91
3953 4555 8.896320 TTGCTATTCGTTATATTAAAGGCTCA 57.104 30.769 0.00 0.00 0.00 4.26
3960 4562 9.997482 TTCGTTATATTAAAGGCTCATTTTGTC 57.003 29.630 0.00 0.00 0.00 3.18
3969 4571 3.960102 AGGCTCATTTTGTCTTTTCCACA 59.040 39.130 0.00 0.00 0.00 4.17
3993 4595 7.670364 CAAAATTATTTTGGGTCCTCACTTCT 58.330 34.615 19.38 0.00 44.75 2.85
3997 4599 3.492102 TTTGGGTCCTCACTTCTCTTG 57.508 47.619 0.00 0.00 0.00 3.02
4010 4612 3.244215 ACTTCTCTTGCCAGATCGAACAA 60.244 43.478 0.00 0.00 0.00 2.83
4011 4613 3.401033 TCTCTTGCCAGATCGAACAAA 57.599 42.857 0.00 0.00 0.00 2.83
4012 4614 3.329386 TCTCTTGCCAGATCGAACAAAG 58.671 45.455 0.00 0.00 0.00 2.77
4024 4626 6.591834 CAGATCGAACAAAGTAGATGGAAAGT 59.408 38.462 0.00 0.00 0.00 2.66
4052 4654 8.589338 AGAAACATACAGAGAAGATGTGTTAGT 58.411 33.333 0.00 0.00 36.64 2.24
4058 4660 6.456501 ACAGAGAAGATGTGTTAGTTGGTAC 58.543 40.000 0.00 0.00 29.32 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
584 611 5.357032 ACTTTTGTTGTCCTCATTTCTTCGT 59.643 36.000 0.00 0.00 0.00 3.85
850 877 4.157120 ACTATGCGTGGGCCGACC 62.157 66.667 12.80 5.90 39.56 4.79
1021 1054 2.689553 TTAGATGGATGTGCGCAGAA 57.310 45.000 12.22 1.62 0.00 3.02
1116 1149 4.271816 CGGAGGAGGATGTCGCGG 62.272 72.222 6.13 0.00 0.00 6.46
1453 1486 4.742201 CTCCTGTCCGTGGCCGTG 62.742 72.222 0.00 0.00 0.00 4.94
1456 1489 4.083862 GACCTCCTGTCCGTGGCC 62.084 72.222 0.00 0.00 38.09 5.36
1457 1490 4.436998 CGACCTCCTGTCCGTGGC 62.437 72.222 0.00 0.00 41.18 5.01
1489 1534 2.519780 GATCTCCGTCGCCCTCCT 60.520 66.667 0.00 0.00 0.00 3.69
1791 1836 3.948719 TGGGCGTGGTGGAGGAAC 61.949 66.667 0.00 0.00 0.00 3.62
2004 2049 0.318441 TTCACACGGAGAGAAGCCAG 59.682 55.000 0.00 0.00 0.00 4.85
2019 2064 4.427312 GAGCAAACAATCCATGGATTCAC 58.573 43.478 32.87 20.59 42.30 3.18
2042 2094 3.489785 CCAATTAGTAACACGGATCGCTC 59.510 47.826 0.00 0.00 0.00 5.03
2055 2107 9.527157 TCATCAAAATCAAAGGACCAATTAGTA 57.473 29.630 0.00 0.00 0.00 1.82
2056 2108 8.421249 TCATCAAAATCAAAGGACCAATTAGT 57.579 30.769 0.00 0.00 0.00 2.24
2057 2109 9.880157 AATCATCAAAATCAAAGGACCAATTAG 57.120 29.630 0.00 0.00 0.00 1.73
2097 2149 5.519927 CCATTCCCTGAAAAACAATAATCGC 59.480 40.000 0.00 0.00 0.00 4.58
2132 2184 5.885230 TGTTTACATCATCCAAGAAGCTG 57.115 39.130 0.00 0.00 0.00 4.24
2156 2208 1.004918 GGTCTGACACACGGGAAGG 60.005 63.158 10.38 0.00 0.00 3.46
2190 2242 0.178068 CCGTGGTGATCCCCTGTTAG 59.822 60.000 0.00 0.00 0.00 2.34
2195 2247 2.231380 AAAGCCGTGGTGATCCCCT 61.231 57.895 0.00 0.00 0.00 4.79
2302 2354 5.598005 TGAATGAACTGACAAAATGAACCCT 59.402 36.000 0.00 0.00 0.00 4.34
2314 2366 4.862018 GCTACAGTCTCTGAATGAACTGAC 59.138 45.833 8.24 0.00 35.18 3.51
2327 2379 6.266323 TCGTGAATATTTGAGCTACAGTCTC 58.734 40.000 0.00 0.00 0.00 3.36
2361 2413 8.312564 AGTACTACTCCTAAACATGTTTCCTTC 58.687 37.037 26.46 8.11 34.23 3.46
2386 2438 6.224665 TCAATGGGCTTCCAAATCATAAAG 57.775 37.500 0.00 0.00 44.86 1.85
2387 2439 6.617782 TTCAATGGGCTTCCAAATCATAAA 57.382 33.333 0.00 0.00 44.86 1.40
2400 2452 3.364549 TCCGATGATTTTTCAATGGGCT 58.635 40.909 0.00 0.00 0.00 5.19
2423 2776 3.539604 GACTTCAGCAGCCAGATAACAT 58.460 45.455 0.00 0.00 0.00 2.71
2425 2778 2.284190 GGACTTCAGCAGCCAGATAAC 58.716 52.381 0.00 0.00 0.00 1.89
2428 2781 1.220206 CGGACTTCAGCAGCCAGAT 59.780 57.895 0.00 0.00 0.00 2.90
2429 2782 2.659016 CGGACTTCAGCAGCCAGA 59.341 61.111 0.00 0.00 0.00 3.86
2430 2783 3.123620 GCGGACTTCAGCAGCCAG 61.124 66.667 0.00 0.00 37.03 4.85
2446 2799 4.759205 AAATGCCACCCTCCCCGC 62.759 66.667 0.00 0.00 0.00 6.13
2447 2800 2.440247 GAAATGCCACCCTCCCCG 60.440 66.667 0.00 0.00 0.00 5.73
2469 2893 5.004726 CACAACTAAAGCTGTCAGCAAAAAC 59.995 40.000 26.23 0.00 45.56 2.43
2479 2903 3.134804 AGGACTGACACAACTAAAGCTGT 59.865 43.478 0.00 0.00 0.00 4.40
2483 2907 6.049149 TCTGAAAGGACTGACACAACTAAAG 58.951 40.000 0.00 0.00 0.00 1.85
2496 2920 6.703165 GCAAAATGACATTTTCTGAAAGGACT 59.297 34.615 20.73 0.00 40.27 3.85
2497 2921 6.703165 AGCAAAATGACATTTTCTGAAAGGAC 59.297 34.615 20.73 7.02 40.27 3.85
2498 2922 6.819284 AGCAAAATGACATTTTCTGAAAGGA 58.181 32.000 20.73 0.00 40.27 3.36
2499 2923 6.927381 AGAGCAAAATGACATTTTCTGAAAGG 59.073 34.615 20.73 10.70 40.27 3.11
2500 2924 7.941795 AGAGCAAAATGACATTTTCTGAAAG 57.058 32.000 20.73 11.30 40.27 2.62
2502 2926 9.467258 CTTTAGAGCAAAATGACATTTTCTGAA 57.533 29.630 20.73 16.42 40.27 3.02
2503 2927 8.849168 TCTTTAGAGCAAAATGACATTTTCTGA 58.151 29.630 20.73 11.08 40.27 3.27
2517 3006 3.317993 GGTGGCAGTTTCTTTAGAGCAAA 59.682 43.478 0.00 0.00 0.00 3.68
2525 3014 2.024414 GTGTGAGGTGGCAGTTTCTTT 58.976 47.619 0.00 0.00 0.00 2.52
2564 3057 3.882888 GTGTGGGATGACAGTTTCTTCAA 59.117 43.478 0.00 0.00 31.26 2.69
2566 3059 3.476552 TGTGTGGGATGACAGTTTCTTC 58.523 45.455 0.00 0.00 0.00 2.87
2581 3074 1.079127 GGGAGGACGACATGTGTGG 60.079 63.158 1.15 0.00 0.00 4.17
2582 3075 0.390340 CTGGGAGGACGACATGTGTG 60.390 60.000 1.15 0.00 0.00 3.82
2583 3076 0.541998 TCTGGGAGGACGACATGTGT 60.542 55.000 1.15 1.22 0.00 3.72
2584 3077 0.608130 TTCTGGGAGGACGACATGTG 59.392 55.000 1.15 0.00 0.00 3.21
2585 3078 1.348064 TTTCTGGGAGGACGACATGT 58.652 50.000 0.00 0.00 0.00 3.21
2586 3079 2.472695 TTTTCTGGGAGGACGACATG 57.527 50.000 0.00 0.00 0.00 3.21
2587 3080 2.305927 ACATTTTCTGGGAGGACGACAT 59.694 45.455 0.00 0.00 0.00 3.06
2588 3081 1.697432 ACATTTTCTGGGAGGACGACA 59.303 47.619 0.00 0.00 0.00 4.35
2589 3082 2.474410 ACATTTTCTGGGAGGACGAC 57.526 50.000 0.00 0.00 0.00 4.34
2590 3083 4.513442 CATTACATTTTCTGGGAGGACGA 58.487 43.478 0.00 0.00 0.00 4.20
2591 3084 3.065371 GCATTACATTTTCTGGGAGGACG 59.935 47.826 0.00 0.00 0.00 4.79
2592 3085 3.381590 GGCATTACATTTTCTGGGAGGAC 59.618 47.826 0.00 0.00 0.00 3.85
2593 3086 3.631250 GGCATTACATTTTCTGGGAGGA 58.369 45.455 0.00 0.00 0.00 3.71
2594 3087 2.358898 CGGCATTACATTTTCTGGGAGG 59.641 50.000 0.00 0.00 0.00 4.30
2595 3088 2.223572 GCGGCATTACATTTTCTGGGAG 60.224 50.000 0.00 0.00 0.00 4.30
2596 3089 1.748493 GCGGCATTACATTTTCTGGGA 59.252 47.619 0.00 0.00 0.00 4.37
2597 3090 1.750778 AGCGGCATTACATTTTCTGGG 59.249 47.619 1.45 0.00 0.00 4.45
2598 3091 2.684881 AGAGCGGCATTACATTTTCTGG 59.315 45.455 1.45 0.00 0.00 3.86
2599 3092 3.374988 TCAGAGCGGCATTACATTTTCTG 59.625 43.478 1.45 3.25 33.81 3.02
2600 3093 3.609853 TCAGAGCGGCATTACATTTTCT 58.390 40.909 1.45 0.00 0.00 2.52
2601 3094 4.094887 TCTTCAGAGCGGCATTACATTTTC 59.905 41.667 1.45 0.00 0.00 2.29
2602 3095 4.009675 TCTTCAGAGCGGCATTACATTTT 58.990 39.130 1.45 0.00 0.00 1.82
2603 3096 3.609853 TCTTCAGAGCGGCATTACATTT 58.390 40.909 1.45 0.00 0.00 2.32
2604 3097 3.266510 TCTTCAGAGCGGCATTACATT 57.733 42.857 1.45 0.00 0.00 2.71
2605 3098 2.988010 TCTTCAGAGCGGCATTACAT 57.012 45.000 1.45 0.00 0.00 2.29
2606 3099 2.742053 GTTTCTTCAGAGCGGCATTACA 59.258 45.455 1.45 0.00 0.00 2.41
2607 3100 3.003480 AGTTTCTTCAGAGCGGCATTAC 58.997 45.455 1.45 0.00 0.00 1.89
2608 3101 3.002791 CAGTTTCTTCAGAGCGGCATTA 58.997 45.455 1.45 0.00 0.00 1.90
2609 3102 1.808945 CAGTTTCTTCAGAGCGGCATT 59.191 47.619 1.45 0.00 0.00 3.56
2610 3103 1.446907 CAGTTTCTTCAGAGCGGCAT 58.553 50.000 1.45 0.00 0.00 4.40
2611 3104 0.603707 CCAGTTTCTTCAGAGCGGCA 60.604 55.000 1.45 0.00 0.00 5.69
2612 3105 1.916697 GCCAGTTTCTTCAGAGCGGC 61.917 60.000 0.00 0.00 0.00 6.53
2613 3106 0.603707 TGCCAGTTTCTTCAGAGCGG 60.604 55.000 0.00 0.00 0.00 5.52
2614 3107 1.446907 ATGCCAGTTTCTTCAGAGCG 58.553 50.000 0.00 0.00 0.00 5.03
2615 3108 4.450053 AGATATGCCAGTTTCTTCAGAGC 58.550 43.478 0.00 0.00 0.00 4.09
2616 3109 8.498054 TTTTAGATATGCCAGTTTCTTCAGAG 57.502 34.615 0.00 0.00 0.00 3.35
2617 3110 8.862325 TTTTTAGATATGCCAGTTTCTTCAGA 57.138 30.769 0.00 0.00 0.00 3.27
2618 3111 9.512435 CATTTTTAGATATGCCAGTTTCTTCAG 57.488 33.333 0.00 0.00 0.00 3.02
2619 3112 7.975616 GCATTTTTAGATATGCCAGTTTCTTCA 59.024 33.333 0.00 0.00 40.93 3.02
2620 3113 8.345224 GCATTTTTAGATATGCCAGTTTCTTC 57.655 34.615 0.00 0.00 40.93 2.87
2630 3123 6.144402 CCGTTTGATGGCATTTTTAGATATGC 59.856 38.462 0.00 0.00 44.93 3.14
2631 3124 6.642131 CCCGTTTGATGGCATTTTTAGATATG 59.358 38.462 0.00 0.00 0.00 1.78
2632 3125 6.239289 CCCCGTTTGATGGCATTTTTAGATAT 60.239 38.462 0.00 0.00 0.00 1.63
2633 3126 5.068460 CCCCGTTTGATGGCATTTTTAGATA 59.932 40.000 0.00 0.00 0.00 1.98
2634 3127 4.141959 CCCCGTTTGATGGCATTTTTAGAT 60.142 41.667 0.00 0.00 0.00 1.98
2635 3128 3.194542 CCCCGTTTGATGGCATTTTTAGA 59.805 43.478 0.00 0.00 0.00 2.10
2646 3139 1.333177 TTTTGGACCCCCGTTTGATG 58.667 50.000 0.00 0.00 34.29 3.07
2653 3146 4.367039 ACTATATGATTTTGGACCCCCG 57.633 45.455 0.00 0.00 34.29 5.73
2695 3231 4.764172 ACATTAGGCAAAGAGCTAGAGTG 58.236 43.478 0.00 0.00 44.79 3.51
2812 3352 1.810030 GTAACTCTCCGGCAAGCGG 60.810 63.158 0.00 0.00 0.00 5.52
2991 3531 3.022607 TCTCGGAAACTTTCTCGGTTC 57.977 47.619 1.57 0.00 0.00 3.62
3069 3609 4.454847 GCAGTACCACTTCTAAAAACCTCC 59.545 45.833 0.00 0.00 0.00 4.30
3089 3629 3.902881 AGGATCCACTTCTTACAGCAG 57.097 47.619 15.82 0.00 0.00 4.24
3090 3630 4.443457 GCATAGGATCCACTTCTTACAGCA 60.443 45.833 15.82 0.00 0.00 4.41
3091 3631 4.061596 GCATAGGATCCACTTCTTACAGC 58.938 47.826 15.82 1.17 0.00 4.40
3170 3717 1.278238 CACCTATCGCCACGAAGTTC 58.722 55.000 0.00 0.00 41.61 3.01
3180 3727 2.579207 TTAGAGCACACACCTATCGC 57.421 50.000 0.00 0.00 0.00 4.58
3316 3863 7.962995 ATGTGAGTTCTTAGAACCTCTATCA 57.037 36.000 20.05 14.06 0.00 2.15
3364 3911 3.077088 AGAGTAACCTTGTCAGGGGAGTA 59.923 47.826 5.89 0.00 46.01 2.59
3439 3986 3.001902 ATCGCCGCTGTTCCTCGAA 62.002 57.895 0.00 0.00 32.74 3.71
3442 3989 3.567797 GCATCGCCGCTGTTCCTC 61.568 66.667 0.00 0.00 0.00 3.71
3465 4012 0.447801 CTTTCGCCAGGAAATCACCG 59.552 55.000 0.00 0.00 43.40 4.94
3467 4014 0.811281 CCCTTTCGCCAGGAAATCAC 59.189 55.000 0.00 0.00 43.40 3.06
3469 4016 0.965363 TGCCCTTTCGCCAGGAAATC 60.965 55.000 0.00 0.00 43.40 2.17
3566 4113 5.932303 GTGCTACAAGGTTTCAGACTGATAA 59.068 40.000 5.87 1.28 0.00 1.75
3567 4114 5.011635 TGTGCTACAAGGTTTCAGACTGATA 59.988 40.000 5.87 0.00 0.00 2.15
3644 4191 4.681744 TGTTGTTTCTTCATTCCAACAGC 58.318 39.130 0.00 0.00 40.12 4.40
3647 4194 5.005682 GCTGTTGTTGTTTCTTCATTCCAAC 59.994 40.000 0.00 0.00 36.74 3.77
3651 4198 4.437820 GTCGCTGTTGTTGTTTCTTCATTC 59.562 41.667 0.00 0.00 0.00 2.67
3659 4236 4.334203 TGAGTTATGTCGCTGTTGTTGTTT 59.666 37.500 0.00 0.00 0.00 2.83
3678 4255 2.562738 TGTGACTGTCAATCGGATGAGT 59.437 45.455 12.81 0.00 0.00 3.41
3680 4257 3.676291 TTGTGACTGTCAATCGGATGA 57.324 42.857 12.81 0.00 0.00 2.92
3684 4261 5.351189 TCATTACATTGTGACTGTCAATCGG 59.649 40.000 12.81 5.73 33.92 4.18
3685 4262 6.407475 TCATTACATTGTGACTGTCAATCG 57.593 37.500 12.81 4.32 33.92 3.34
3700 4277 4.400884 TGCCCACGCTTAATTTCATTACAT 59.599 37.500 0.00 0.00 35.36 2.29
3701 4278 3.759086 TGCCCACGCTTAATTTCATTACA 59.241 39.130 0.00 0.00 35.36 2.41
3722 4299 7.439056 GGCTGATTTATGGGTATGTTTGATTTG 59.561 37.037 0.00 0.00 0.00 2.32
3726 4303 4.892934 GGGCTGATTTATGGGTATGTTTGA 59.107 41.667 0.00 0.00 0.00 2.69
3727 4304 4.648762 TGGGCTGATTTATGGGTATGTTTG 59.351 41.667 0.00 0.00 0.00 2.93
3728 4305 4.877773 TGGGCTGATTTATGGGTATGTTT 58.122 39.130 0.00 0.00 0.00 2.83
3784 4363 2.035704 TGCAAAGCGAATGTCCAATGTT 59.964 40.909 0.00 0.00 0.00 2.71
3862 4441 5.521372 TGACAGCATGAACTATCTGAAATCG 59.479 40.000 0.00 0.00 39.69 3.34
3927 4506 9.502091 TGAGCCTTTAATATAACGAATAGCAAT 57.498 29.630 0.00 0.00 0.00 3.56
3928 4507 8.896320 TGAGCCTTTAATATAACGAATAGCAA 57.104 30.769 0.00 0.00 0.00 3.91
3929 4508 9.502091 AATGAGCCTTTAATATAACGAATAGCA 57.498 29.630 0.00 0.00 0.00 3.49
3934 4513 9.997482 GACAAAATGAGCCTTTAATATAACGAA 57.003 29.630 0.00 0.00 0.00 3.85
3935 4514 9.391006 AGACAAAATGAGCCTTTAATATAACGA 57.609 29.630 0.00 0.00 0.00 3.85
3941 4520 8.865090 TGGAAAAGACAAAATGAGCCTTTAATA 58.135 29.630 0.00 0.00 0.00 0.98
3942 4521 7.657354 GTGGAAAAGACAAAATGAGCCTTTAAT 59.343 33.333 0.00 0.00 0.00 1.40
3959 4561 7.717436 GGACCCAAAATAATTTTGTGGAAAAGA 59.283 33.333 13.53 0.00 46.53 2.52
3960 4562 7.719193 AGGACCCAAAATAATTTTGTGGAAAAG 59.281 33.333 13.53 3.48 46.53 2.27
3965 4567 5.931724 GTGAGGACCCAAAATAATTTTGTGG 59.068 40.000 0.00 1.01 46.53 4.17
3969 4571 7.730332 AGAGAAGTGAGGACCCAAAATAATTTT 59.270 33.333 0.00 0.00 0.00 1.82
3982 4584 1.620819 TCTGGCAAGAGAAGTGAGGAC 59.379 52.381 0.00 0.00 0.00 3.85
3983 4585 2.015456 TCTGGCAAGAGAAGTGAGGA 57.985 50.000 0.00 0.00 0.00 3.71
3985 4587 2.165234 TCGATCTGGCAAGAGAAGTGAG 59.835 50.000 0.00 0.00 35.37 3.51
3993 4595 3.126001 ACTTTGTTCGATCTGGCAAGA 57.874 42.857 0.00 0.00 36.69 3.02
3997 4599 3.557595 CCATCTACTTTGTTCGATCTGGC 59.442 47.826 0.00 0.00 0.00 4.85
4011 4613 9.877178 CTGTATGTTTCTTACTTTCCATCTACT 57.123 33.333 0.00 0.00 0.00 2.57
4012 4614 9.871238 TCTGTATGTTTCTTACTTTCCATCTAC 57.129 33.333 0.00 0.00 0.00 2.59
4034 4636 5.552870 ACCAACTAACACATCTTCTCTGT 57.447 39.130 0.00 0.00 0.00 3.41
4035 4637 6.952935 GTACCAACTAACACATCTTCTCTG 57.047 41.667 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.