Multiple sequence alignment - TraesCS4D01G086400

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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 TraesCS4D01G086400 chr4D 100.000 3479 0 0 1 3479 61958909 61955431 0.000000e+00 6425
1 TraesCS4D01G086400 chr4A 95.395 2693 88 19 1 2677 535244987 535242315 0.000000e+00 4253
2 TraesCS4D01G086400 chr4A 83.008 512 58 16 2738 3240 535242321 535241830 1.480000e-118 436
3 TraesCS4D01G086400 chr4A 95.652 115 5 0 3340 3454 535241636 535241522 5.930000e-43 185
4 TraesCS4D01G086400 chr4B 96.022 1433 41 4 1 1430 90726635 90728054 0.000000e+00 2316
5 TraesCS4D01G086400 chr4B 96.072 1171 27 7 1513 2677 90728061 90729218 0.000000e+00 1890
6 TraesCS4D01G086400 chr4B 94.776 134 4 2 3335 3465 90750999 90751132 4.550000e-49 206
7 TraesCS4D01G086400 chr4B 91.837 98 3 2 2738 2830 90729212 90729309 7.840000e-27 132


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 TraesCS4D01G086400 chr4D 61955431 61958909 3478 True 6425.000000 6425 100.000000 1 3479 1 chr4D.!!$R1 3478
1 TraesCS4D01G086400 chr4A 535241522 535244987 3465 True 1624.666667 4253 91.351667 1 3454 3 chr4A.!!$R1 3453
2 TraesCS4D01G086400 chr4B 90726635 90729309 2674 False 1446.000000 2316 94.643667 1 2830 3 chr4B.!!$F2 2829

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
929 934 1.273211 CCCCACATTTCCCTCCACAAT 60.273 52.381 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2730 2753 0.319555 TCAAGTAGCAGTGTCGCACC 60.32 55.0 6.39 0.0 34.49 5.01 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
61 62 5.906113 AGTATTATCTCACCCTCGCATAG 57.094 43.478 0.00 0.00 0.00 2.23
207 211 4.841813 TCCTCTTCTCTATTCCAGGGAT 57.158 45.455 0.00 0.00 32.26 3.85
354 358 9.434275 TCTTAGATGGTGATTAGTTGGATAGAA 57.566 33.333 0.00 0.00 0.00 2.10
517 521 6.469782 AACCGATGGATGCTTTTTATGATT 57.530 33.333 0.00 0.00 0.00 2.57
522 526 6.291955 CGATGGATGCTTTTTATGATTGTTGC 60.292 38.462 0.00 0.00 0.00 4.17
548 552 5.648178 TGTCGGCTTATGTTCTGTTACTA 57.352 39.130 0.00 0.00 0.00 1.82
551 555 5.515626 GTCGGCTTATGTTCTGTTACTAGTG 59.484 44.000 5.39 0.00 0.00 2.74
565 569 7.339466 TCTGTTACTAGTGTTGCTCATCTCATA 59.661 37.037 5.39 0.00 0.00 2.15
567 571 9.131791 TGTTACTAGTGTTGCTCATCTCATATA 57.868 33.333 5.39 0.00 0.00 0.86
618 623 4.018141 TCAAATTGTGATGGATCTCTGGGT 60.018 41.667 0.00 0.00 0.00 4.51
864 869 1.500736 CCCCTTGGCCTATCCTTCATT 59.499 52.381 3.32 0.00 35.26 2.57
929 934 1.273211 CCCCACATTTCCCTCCACAAT 60.273 52.381 0.00 0.00 0.00 2.71
931 936 2.557229 CCCACATTTCCCTCCACAATCA 60.557 50.000 0.00 0.00 0.00 2.57
1350 1356 0.539986 GGATCTACTTGCCCAACGGA 59.460 55.000 0.00 0.00 0.00 4.69
1445 1452 5.898174 TCCATTTACTCTACACACCATACG 58.102 41.667 0.00 0.00 0.00 3.06
1446 1453 5.419788 TCCATTTACTCTACACACCATACGT 59.580 40.000 0.00 0.00 0.00 3.57
1447 1454 6.071221 TCCATTTACTCTACACACCATACGTT 60.071 38.462 0.00 0.00 0.00 3.99
1509 1518 3.490348 ACTGTTTCCTTTAGCAGCATGT 58.510 40.909 0.00 0.00 39.31 3.21
1523 1532 3.242543 GCAGCATGTAGTACATCACAAGC 60.243 47.826 13.00 12.64 36.53 4.01
1528 1537 4.720649 TGTAGTACATCACAAGCTCTCC 57.279 45.455 0.00 0.00 0.00 3.71
1555 1564 7.920160 TGACTGAAATGCTCATGTATGTAAA 57.080 32.000 0.00 0.00 32.14 2.01
1671 1684 4.802999 ACTTCGCCAAGTAAGTACAGTAC 58.197 43.478 2.05 2.05 41.39 2.73
1767 1782 5.665812 ACTAAGCAATCCTGTCCTGGTATTA 59.334 40.000 0.00 0.00 0.00 0.98
1953 1971 2.670414 CACGGCTTCAGATTCAGAACTC 59.330 50.000 0.00 0.00 0.00 3.01
1956 1974 2.677337 GGCTTCAGATTCAGAACTCTGC 59.323 50.000 13.64 6.41 43.46 4.26
1997 2019 4.012374 CCATAAACAACATCCTGCAGACT 58.988 43.478 17.39 0.00 0.00 3.24
2167 2189 0.179073 AGATATTCGTTGCCGCAGCT 60.179 50.000 5.63 0.00 40.80 4.24
2168 2190 0.233332 GATATTCGTTGCCGCAGCTC 59.767 55.000 5.63 0.00 40.80 4.09
2169 2191 0.461870 ATATTCGTTGCCGCAGCTCA 60.462 50.000 5.63 0.00 40.80 4.26
2170 2192 1.083806 TATTCGTTGCCGCAGCTCAG 61.084 55.000 5.63 0.00 40.80 3.35
2322 2344 2.233922 GGTGAAGGAGATCAAGAACGGA 59.766 50.000 0.00 0.00 0.00 4.69
2489 2511 3.052082 CCTGTGAGCTGGCCGTTG 61.052 66.667 0.00 0.00 0.00 4.10
2521 2543 3.499737 GCCGTCGGCTGTTGATGG 61.500 66.667 28.98 5.49 46.69 3.51
2534 2556 1.371337 TTGATGGATCAGCTGCGTGC 61.371 55.000 9.47 6.16 38.19 5.34
2640 2663 4.038271 TCAAGGGCAGAAGAAACATGAT 57.962 40.909 0.00 0.00 0.00 2.45
2670 2693 1.996798 TCTGATGGGAGTATCGGACC 58.003 55.000 0.00 0.00 37.50 4.46
2671 2694 1.216930 TCTGATGGGAGTATCGGACCA 59.783 52.381 0.00 0.00 37.50 4.02
2672 2695 1.341531 CTGATGGGAGTATCGGACCAC 59.658 57.143 0.00 0.00 35.85 4.16
2673 2696 1.063190 TGATGGGAGTATCGGACCACT 60.063 52.381 0.00 0.00 35.52 4.00
2674 2697 1.341531 GATGGGAGTATCGGACCACTG 59.658 57.143 0.00 0.00 35.52 3.66
2675 2698 1.327690 TGGGAGTATCGGACCACTGC 61.328 60.000 4.98 4.98 34.37 4.40
2676 2699 1.043673 GGGAGTATCGGACCACTGCT 61.044 60.000 11.23 0.00 33.96 4.24
2677 2700 0.824759 GGAGTATCGGACCACTGCTT 59.175 55.000 6.02 0.00 34.37 3.91
2678 2701 1.202428 GGAGTATCGGACCACTGCTTC 60.202 57.143 6.02 0.00 34.37 3.86
2679 2702 1.476891 GAGTATCGGACCACTGCTTCA 59.523 52.381 0.00 0.00 0.00 3.02
2680 2703 1.478510 AGTATCGGACCACTGCTTCAG 59.521 52.381 0.00 0.00 37.52 3.02
2681 2704 0.175760 TATCGGACCACTGCTTCAGC 59.824 55.000 0.00 0.00 42.50 4.26
2682 2705 1.548357 ATCGGACCACTGCTTCAGCT 61.548 55.000 0.00 0.00 42.66 4.24
2683 2706 1.302033 CGGACCACTGCTTCAGCTT 60.302 57.895 0.00 0.00 42.66 3.74
2684 2707 1.572085 CGGACCACTGCTTCAGCTTG 61.572 60.000 0.00 0.00 42.66 4.01
2685 2708 0.536006 GGACCACTGCTTCAGCTTGT 60.536 55.000 0.00 0.00 42.66 3.16
2686 2709 0.590195 GACCACTGCTTCAGCTTGTG 59.410 55.000 14.44 14.44 41.76 3.33
2687 2710 1.285023 CCACTGCTTCAGCTTGTGC 59.715 57.895 15.39 0.00 41.24 4.57
2718 2741 8.785329 TTTTTATTTTCTTGCTGGAAACTTGT 57.215 26.923 4.62 0.00 35.31 3.16
2719 2742 7.769272 TTTATTTTCTTGCTGGAAACTTGTG 57.231 32.000 4.62 0.00 35.31 3.33
2720 2743 2.869233 TTCTTGCTGGAAACTTGTGC 57.131 45.000 0.00 0.00 0.00 4.57
2721 2744 2.057137 TCTTGCTGGAAACTTGTGCT 57.943 45.000 0.00 0.00 0.00 4.40
2722 2745 2.378038 TCTTGCTGGAAACTTGTGCTT 58.622 42.857 0.00 0.00 0.00 3.91
2723 2746 2.099592 TCTTGCTGGAAACTTGTGCTTG 59.900 45.455 0.00 0.00 0.00 4.01
2724 2747 1.761449 TGCTGGAAACTTGTGCTTGA 58.239 45.000 0.00 0.00 0.00 3.02
2725 2748 2.309613 TGCTGGAAACTTGTGCTTGAT 58.690 42.857 0.00 0.00 0.00 2.57
2726 2749 3.485394 TGCTGGAAACTTGTGCTTGATA 58.515 40.909 0.00 0.00 0.00 2.15
2727 2750 3.888323 TGCTGGAAACTTGTGCTTGATAA 59.112 39.130 0.00 0.00 0.00 1.75
2728 2751 4.229876 GCTGGAAACTTGTGCTTGATAAC 58.770 43.478 0.00 0.00 0.00 1.89
2729 2752 4.022849 GCTGGAAACTTGTGCTTGATAACT 60.023 41.667 0.00 0.00 0.00 2.24
2730 2753 5.437289 TGGAAACTTGTGCTTGATAACTG 57.563 39.130 0.00 0.00 0.00 3.16
2731 2754 4.278170 TGGAAACTTGTGCTTGATAACTGG 59.722 41.667 0.00 0.00 0.00 4.00
2732 2755 4.278419 GGAAACTTGTGCTTGATAACTGGT 59.722 41.667 0.00 0.00 0.00 4.00
2733 2756 4.836125 AACTTGTGCTTGATAACTGGTG 57.164 40.909 0.00 0.00 0.00 4.17
2734 2757 2.554032 ACTTGTGCTTGATAACTGGTGC 59.446 45.455 0.00 0.00 0.00 5.01
2735 2758 1.155889 TGTGCTTGATAACTGGTGCG 58.844 50.000 0.00 0.00 0.00 5.34
2736 2759 1.270571 TGTGCTTGATAACTGGTGCGA 60.271 47.619 0.00 0.00 0.00 5.10
2811 2836 8.786898 CCAGATTGACTCTTTGAAACTTGATTA 58.213 33.333 0.00 0.00 29.16 1.75
2835 2863 6.234177 AGTTAAGTCCTTGCATATAGATGGC 58.766 40.000 0.00 0.00 33.26 4.40
2836 2864 4.712051 AAGTCCTTGCATATAGATGGCA 57.288 40.909 0.00 0.00 33.26 4.92
2840 2868 4.823989 GTCCTTGCATATAGATGGCAAACT 59.176 41.667 0.00 0.00 32.43 2.66
2841 2869 5.300286 GTCCTTGCATATAGATGGCAAACTT 59.700 40.000 0.00 0.00 32.43 2.66
2847 2875 8.236585 TGCATATAGATGGCAAACTTGTTATT 57.763 30.769 0.00 0.00 33.26 1.40
2918 2949 7.201732 CGAATTTGAAGTGCTGGAATTATACCT 60.202 37.037 0.00 0.00 0.00 3.08
2952 2983 8.584157 ACAGATTCTAGGCTATATTCTTCACAG 58.416 37.037 0.00 0.00 0.00 3.66
2954 2985 8.802267 AGATTCTAGGCTATATTCTTCACAGAC 58.198 37.037 0.00 0.00 0.00 3.51
2969 3000 7.810658 TCTTCACAGACAGCAAAATTTCTATC 58.189 34.615 0.00 0.00 0.00 2.08
2971 3002 7.369803 TCACAGACAGCAAAATTTCTATCTC 57.630 36.000 0.00 0.00 0.00 2.75
3053 3084 7.707893 GCATCATATAGACCAAAGTTGCAAATT 59.292 33.333 6.26 6.26 0.00 1.82
3056 3087 8.801299 TCATATAGACCAAAGTTGCAAATTCAA 58.199 29.630 13.16 0.00 0.00 2.69
3060 3091 7.250445 AGACCAAAGTTGCAAATTCAAATTC 57.750 32.000 13.16 5.73 33.78 2.17
3065 3096 8.129840 CCAAAGTTGCAAATTCAAATTCAATCA 58.870 29.630 13.16 0.00 33.78 2.57
3080 3111 9.782028 CAAATTCAATCAAAATAGTTGACAACG 57.218 29.630 12.54 0.00 36.23 4.10
3174 3206 3.795623 ATTTGCTGCCATTGAGATCAC 57.204 42.857 0.00 0.00 0.00 3.06
3177 3209 3.564053 TGCTGCCATTGAGATCACATA 57.436 42.857 0.00 0.00 0.00 2.29
3178 3210 4.094830 TGCTGCCATTGAGATCACATAT 57.905 40.909 0.00 0.00 0.00 1.78
3180 3212 3.819337 GCTGCCATTGAGATCACATATGT 59.181 43.478 1.41 1.41 0.00 2.29
3219 3251 8.441312 TTCTCTACGTTTGGATTAAAGTTTGT 57.559 30.769 0.00 0.00 0.00 2.83
3222 3254 8.211116 TCTACGTTTGGATTAAAGTTTGTTCA 57.789 30.769 0.00 0.00 0.00 3.18
3252 3285 0.828022 TGGGACAAGACACTCGTGTT 59.172 50.000 3.97 0.00 39.12 3.32
3253 3286 1.208535 TGGGACAAGACACTCGTGTTT 59.791 47.619 3.97 0.00 39.12 2.83
3254 3287 2.285977 GGGACAAGACACTCGTGTTTT 58.714 47.619 3.97 2.19 45.05 2.43
3255 3288 2.681344 GGGACAAGACACTCGTGTTTTT 59.319 45.455 3.97 0.34 45.05 1.94
3277 3435 4.841443 TTAGCGAGTCTAACACACTTGA 57.159 40.909 0.00 0.00 32.57 3.02
3278 3436 3.014604 AGCGAGTCTAACACACTTGAC 57.985 47.619 0.00 0.00 0.00 3.18
3279 3437 2.361119 AGCGAGTCTAACACACTTGACA 59.639 45.455 0.00 0.00 32.41 3.58
3280 3438 2.471743 GCGAGTCTAACACACTTGACAC 59.528 50.000 0.00 0.00 32.41 3.67
3282 3440 4.360563 CGAGTCTAACACACTTGACACTT 58.639 43.478 0.00 0.00 32.41 3.16
3283 3441 4.804139 CGAGTCTAACACACTTGACACTTT 59.196 41.667 0.00 0.00 32.41 2.66
3284 3442 5.291128 CGAGTCTAACACACTTGACACTTTT 59.709 40.000 0.00 0.00 32.41 2.27
3285 3443 6.183360 CGAGTCTAACACACTTGACACTTTTT 60.183 38.462 0.00 0.00 32.41 1.94
3286 3444 7.073342 AGTCTAACACACTTGACACTTTTTC 57.927 36.000 0.00 0.00 32.41 2.29
3287 3445 6.879458 AGTCTAACACACTTGACACTTTTTCT 59.121 34.615 0.00 0.00 32.41 2.52
3289 3447 8.662141 GTCTAACACACTTGACACTTTTTCTTA 58.338 33.333 0.00 0.00 0.00 2.10
3290 3448 8.879759 TCTAACACACTTGACACTTTTTCTTAG 58.120 33.333 0.00 0.00 0.00 2.18
3291 3449 6.436843 ACACACTTGACACTTTTTCTTAGG 57.563 37.500 0.00 0.00 0.00 2.69
3292 3450 5.944007 ACACACTTGACACTTTTTCTTAGGT 59.056 36.000 0.00 0.00 0.00 3.08
3293 3451 6.128007 ACACACTTGACACTTTTTCTTAGGTG 60.128 38.462 0.00 0.00 35.99 4.00
3295 3453 7.065324 CACACTTGACACTTTTTCTTAGGTGTA 59.935 37.037 0.00 0.00 42.01 2.90
3296 3454 7.065443 ACACTTGACACTTTTTCTTAGGTGTAC 59.935 37.037 0.00 0.00 42.01 2.90
3297 3455 7.065324 CACTTGACACTTTTTCTTAGGTGTACA 59.935 37.037 0.00 0.00 42.01 2.90
3298 3456 6.913873 TGACACTTTTTCTTAGGTGTACAC 57.086 37.500 18.01 18.01 42.01 2.90
3299 3457 6.408035 TGACACTTTTTCTTAGGTGTACACA 58.592 36.000 26.51 5.07 42.01 3.72
3300 3458 6.314400 TGACACTTTTTCTTAGGTGTACACAC 59.686 38.462 26.51 15.88 42.01 3.82
3301 3459 6.412214 ACACTTTTTCTTAGGTGTACACACT 58.588 36.000 26.51 21.38 45.73 3.55
3302 3460 6.882678 ACACTTTTTCTTAGGTGTACACACTT 59.117 34.615 26.51 13.99 45.73 3.16
3303 3461 8.042515 ACACTTTTTCTTAGGTGTACACACTTA 58.957 33.333 26.51 13.86 45.73 2.24
3304 3462 8.333186 CACTTTTTCTTAGGTGTACACACTTAC 58.667 37.037 26.51 9.52 45.73 2.34
3305 3463 8.042515 ACTTTTTCTTAGGTGTACACACTTACA 58.957 33.333 26.51 4.33 45.73 2.41
3312 3470 4.789095 GTGTACACACTTACACTTGTGG 57.211 45.455 21.14 0.00 46.21 4.17
3313 3471 3.558418 GTGTACACACTTACACTTGTGGG 59.442 47.826 21.14 0.00 46.21 4.61
3317 3475 2.612212 CACACTTACACTTGTGGGTGTC 59.388 50.000 18.40 0.00 45.94 3.67
3318 3476 2.218603 CACTTACACTTGTGGGTGTCC 58.781 52.381 3.48 0.00 45.94 4.02
3319 3477 1.142262 ACTTACACTTGTGGGTGTCCC 59.858 52.381 3.48 0.00 45.94 4.46
3354 3512 5.426504 TGGTAAAAGCCCATGCAAATAATG 58.573 37.500 0.00 0.00 41.13 1.90
3358 3516 6.543430 AAAAGCCCATGCAAATAATGTCTA 57.457 33.333 0.00 0.00 41.13 2.59
3419 3577 1.327690 ATGCAATGGGCCAAGCTGAG 61.328 55.000 27.51 9.98 43.89 3.35
3443 3601 1.870064 CCCATCAGAAGGCCCAAATT 58.130 50.000 0.00 0.00 0.00 1.82
3446 3604 3.969312 CCCATCAGAAGGCCCAAATTATT 59.031 43.478 0.00 0.00 0.00 1.40
3454 3612 3.387012 AGGCCCAAATTATTCATTGCCT 58.613 40.909 0.00 0.00 37.10 4.75
3455 3613 3.781965 AGGCCCAAATTATTCATTGCCTT 59.218 39.130 0.00 0.00 38.20 4.35
3456 3614 3.878699 GGCCCAAATTATTCATTGCCTTG 59.121 43.478 0.00 0.00 31.45 3.61
3457 3615 4.516323 GCCCAAATTATTCATTGCCTTGT 58.484 39.130 0.00 0.00 0.00 3.16
3458 3616 4.571984 GCCCAAATTATTCATTGCCTTGTC 59.428 41.667 0.00 0.00 0.00 3.18
3459 3617 5.627503 GCCCAAATTATTCATTGCCTTGTCT 60.628 40.000 0.00 0.00 0.00 3.41
3460 3618 6.044682 CCCAAATTATTCATTGCCTTGTCTC 58.955 40.000 0.00 0.00 0.00 3.36
3461 3619 6.127253 CCCAAATTATTCATTGCCTTGTCTCT 60.127 38.462 0.00 0.00 0.00 3.10
3462 3620 7.325694 CCAAATTATTCATTGCCTTGTCTCTT 58.674 34.615 0.00 0.00 0.00 2.85
3463 3621 7.490402 CCAAATTATTCATTGCCTTGTCTCTTC 59.510 37.037 0.00 0.00 0.00 2.87
3464 3622 7.951347 AATTATTCATTGCCTTGTCTCTTCT 57.049 32.000 0.00 0.00 0.00 2.85
3465 3623 6.748333 TTATTCATTGCCTTGTCTCTTCTG 57.252 37.500 0.00 0.00 0.00 3.02
3466 3624 3.777106 TCATTGCCTTGTCTCTTCTGT 57.223 42.857 0.00 0.00 0.00 3.41
3467 3625 3.668447 TCATTGCCTTGTCTCTTCTGTC 58.332 45.455 0.00 0.00 0.00 3.51
3468 3626 3.326006 TCATTGCCTTGTCTCTTCTGTCT 59.674 43.478 0.00 0.00 0.00 3.41
3469 3627 3.845781 TTGCCTTGTCTCTTCTGTCTT 57.154 42.857 0.00 0.00 0.00 3.01
3470 3628 3.393089 TGCCTTGTCTCTTCTGTCTTC 57.607 47.619 0.00 0.00 0.00 2.87
3471 3629 2.968574 TGCCTTGTCTCTTCTGTCTTCT 59.031 45.455 0.00 0.00 0.00 2.85
3472 3630 3.389329 TGCCTTGTCTCTTCTGTCTTCTT 59.611 43.478 0.00 0.00 0.00 2.52
3473 3631 4.141620 TGCCTTGTCTCTTCTGTCTTCTTT 60.142 41.667 0.00 0.00 0.00 2.52
3474 3632 4.450757 GCCTTGTCTCTTCTGTCTTCTTTC 59.549 45.833 0.00 0.00 0.00 2.62
3475 3633 5.741673 GCCTTGTCTCTTCTGTCTTCTTTCT 60.742 44.000 0.00 0.00 0.00 2.52
3476 3634 6.287525 CCTTGTCTCTTCTGTCTTCTTTCTT 58.712 40.000 0.00 0.00 0.00 2.52
3477 3635 6.765512 CCTTGTCTCTTCTGTCTTCTTTCTTT 59.234 38.462 0.00 0.00 0.00 2.52
3478 3636 7.042119 CCTTGTCTCTTCTGTCTTCTTTCTTTC 60.042 40.741 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 7.370383 TCAACCATGAGAAACAAAGATTAAGC 58.630 34.615 0.00 0.00 0.00 3.09
144 145 7.232330 TGGAACAATACACATTCTTTTCCATGA 59.768 33.333 0.00 0.00 33.54 3.07
207 211 3.243234 CGTCAAACAAACCAGCAATGGTA 60.243 43.478 0.00 0.00 42.20 3.25
216 220 2.438411 ACCAACTCGTCAAACAAACCA 58.562 42.857 0.00 0.00 0.00 3.67
354 358 7.857456 TGGGATATTAATGTGACACAGTAGTT 58.143 34.615 14.91 10.06 29.95 2.24
522 526 3.002791 ACAGAACATAAGCCGACATGTG 58.997 45.455 1.15 0.00 35.59 3.21
567 571 7.014615 AGCACCAAATCAGACTCAAGTTTTAAT 59.985 33.333 0.00 0.00 0.00 1.40
580 584 4.341806 ACAATTTGACAGCACCAAATCAGA 59.658 37.500 2.79 0.00 41.71 3.27
618 623 0.908910 AGTTCCAGACCACACACACA 59.091 50.000 0.00 0.00 0.00 3.72
864 869 1.724148 TTGGAGGATGTTGTGGGCCA 61.724 55.000 0.00 0.00 0.00 5.36
929 934 0.918983 GGGAGGATGTGATGGGTTGA 59.081 55.000 0.00 0.00 0.00 3.18
931 936 1.566231 GAAGGGAGGATGTGATGGGTT 59.434 52.381 0.00 0.00 0.00 4.11
1303 1308 4.522789 GTCAGGGCCTGAAACAAATAGAAA 59.477 41.667 36.54 8.28 42.46 2.52
1350 1356 1.977544 CTCCGACCGGTCAAGGAGT 60.978 63.158 33.85 3.64 43.82 3.85
1445 1452 5.814705 AGAGCTATGACAAAGCATGACTAAC 59.185 40.000 0.00 0.00 42.62 2.34
1446 1453 5.814188 CAGAGCTATGACAAAGCATGACTAA 59.186 40.000 0.88 0.00 42.62 2.24
1447 1454 5.354767 CAGAGCTATGACAAAGCATGACTA 58.645 41.667 0.88 0.00 42.62 2.59
1486 1495 4.455877 ACATGCTGCTAAAGGAAACAGTAC 59.544 41.667 0.00 0.00 32.65 2.73
1509 1518 3.708451 TGGGAGAGCTTGTGATGTACTA 58.292 45.455 0.00 0.00 0.00 1.82
1523 1532 3.204526 GAGCATTTCAGTCATGGGAGAG 58.795 50.000 0.00 0.00 0.00 3.20
1700 1713 6.949352 ATTTGACAGAACACTTCACAGATT 57.051 33.333 0.00 0.00 0.00 2.40
1701 1714 6.949352 AATTTGACAGAACACTTCACAGAT 57.051 33.333 0.00 0.00 0.00 2.90
1731 1746 5.594725 AGGATTGCTTAGTCGAGAGAACATA 59.405 40.000 0.00 0.00 45.01 2.29
1734 1749 4.109050 CAGGATTGCTTAGTCGAGAGAAC 58.891 47.826 0.00 0.00 45.01 3.01
1767 1782 4.019174 CCTGGTACCTGCAGAATTGAAAT 58.981 43.478 17.39 0.00 0.00 2.17
1953 1971 1.670811 ACCGTGAGTTCAAACTTGCAG 59.329 47.619 0.00 0.00 39.88 4.41
1956 1974 1.268539 GGCACCGTGAGTTCAAACTTG 60.269 52.381 1.65 0.00 39.88 3.16
1997 2019 2.927856 TCAAGGAGAAGGGCGCCA 60.928 61.111 30.85 0.00 39.21 5.69
2167 2189 1.911269 TACAAGGACGCCTGGCTGA 60.911 57.895 17.92 0.00 32.13 4.26
2168 2190 1.741770 GTACAAGGACGCCTGGCTG 60.742 63.158 17.92 12.68 32.13 4.85
2169 2191 1.913762 AGTACAAGGACGCCTGGCT 60.914 57.895 17.92 3.54 32.13 4.75
2170 2192 1.741770 CAGTACAAGGACGCCTGGC 60.742 63.158 9.11 9.11 32.13 4.85
2171 2193 0.389948 GTCAGTACAAGGACGCCTGG 60.390 60.000 0.00 0.00 32.13 4.45
2207 2229 1.945394 CATCAAATTCCTGCCGGAGAG 59.055 52.381 5.05 0.00 41.25 3.20
2322 2344 2.045926 GAGAACATGGCCAGCCGT 60.046 61.111 13.05 5.37 39.42 5.68
2388 2410 4.600576 TGCGCGCACAGGTTCTCA 62.601 61.111 33.09 2.14 0.00 3.27
2521 2543 2.624811 CATCGCACGCAGCTGATC 59.375 61.111 20.43 0.00 42.61 2.92
2640 2663 3.515502 ACTCCCATCAGAAATCAGAACGA 59.484 43.478 0.00 0.00 0.00 3.85
2670 2693 4.937781 GCACAAGCTGAAGCAGTG 57.062 55.556 18.14 18.14 45.63 3.66
2693 2716 8.663911 CACAAGTTTCCAGCAAGAAAATAAAAA 58.336 29.630 3.06 0.00 37.49 1.94
2694 2717 7.201600 GCACAAGTTTCCAGCAAGAAAATAAAA 60.202 33.333 3.06 0.00 37.49 1.52
2695 2718 6.257630 GCACAAGTTTCCAGCAAGAAAATAAA 59.742 34.615 3.06 0.00 37.49 1.40
2696 2719 5.752955 GCACAAGTTTCCAGCAAGAAAATAA 59.247 36.000 3.06 0.00 37.49 1.40
2697 2720 5.068987 AGCACAAGTTTCCAGCAAGAAAATA 59.931 36.000 3.06 0.00 37.49 1.40
2698 2721 4.122046 GCACAAGTTTCCAGCAAGAAAAT 58.878 39.130 3.06 0.00 37.49 1.82
2699 2722 3.195396 AGCACAAGTTTCCAGCAAGAAAA 59.805 39.130 3.06 0.00 37.49 2.29
2700 2723 2.760092 AGCACAAGTTTCCAGCAAGAAA 59.240 40.909 0.00 0.00 33.40 2.52
2701 2724 2.378038 AGCACAAGTTTCCAGCAAGAA 58.622 42.857 0.00 0.00 0.00 2.52
2702 2725 2.057137 AGCACAAGTTTCCAGCAAGA 57.943 45.000 0.00 0.00 0.00 3.02
2703 2726 2.099592 TCAAGCACAAGTTTCCAGCAAG 59.900 45.455 0.00 0.00 0.00 4.01
2704 2727 2.098614 TCAAGCACAAGTTTCCAGCAA 58.901 42.857 0.00 0.00 0.00 3.91
2705 2728 1.761449 TCAAGCACAAGTTTCCAGCA 58.239 45.000 0.00 0.00 0.00 4.41
2706 2729 4.022849 AGTTATCAAGCACAAGTTTCCAGC 60.023 41.667 0.00 0.00 0.00 4.85
2707 2730 5.455392 CAGTTATCAAGCACAAGTTTCCAG 58.545 41.667 0.00 0.00 0.00 3.86
2708 2731 4.278170 CCAGTTATCAAGCACAAGTTTCCA 59.722 41.667 0.00 0.00 0.00 3.53
2709 2732 4.278419 ACCAGTTATCAAGCACAAGTTTCC 59.722 41.667 0.00 0.00 0.00 3.13
2710 2733 5.215160 CACCAGTTATCAAGCACAAGTTTC 58.785 41.667 0.00 0.00 0.00 2.78
2711 2734 4.499696 GCACCAGTTATCAAGCACAAGTTT 60.500 41.667 0.00 0.00 0.00 2.66
2712 2735 3.004734 GCACCAGTTATCAAGCACAAGTT 59.995 43.478 0.00 0.00 0.00 2.66
2713 2736 2.554032 GCACCAGTTATCAAGCACAAGT 59.446 45.455 0.00 0.00 0.00 3.16
2714 2737 2.413239 CGCACCAGTTATCAAGCACAAG 60.413 50.000 0.00 0.00 0.00 3.16
2715 2738 1.535028 CGCACCAGTTATCAAGCACAA 59.465 47.619 0.00 0.00 0.00 3.33
2716 2739 1.155889 CGCACCAGTTATCAAGCACA 58.844 50.000 0.00 0.00 0.00 4.57
2717 2740 1.128692 GTCGCACCAGTTATCAAGCAC 59.871 52.381 0.00 0.00 0.00 4.40
2718 2741 1.270571 TGTCGCACCAGTTATCAAGCA 60.271 47.619 0.00 0.00 0.00 3.91
2719 2742 1.128692 GTGTCGCACCAGTTATCAAGC 59.871 52.381 0.00 0.00 0.00 4.01
2720 2743 2.413112 CAGTGTCGCACCAGTTATCAAG 59.587 50.000 6.39 0.00 34.49 3.02
2721 2744 2.412870 CAGTGTCGCACCAGTTATCAA 58.587 47.619 6.39 0.00 34.49 2.57
2722 2745 1.939381 GCAGTGTCGCACCAGTTATCA 60.939 52.381 6.39 0.00 34.49 2.15
2723 2746 0.721718 GCAGTGTCGCACCAGTTATC 59.278 55.000 6.39 0.00 34.49 1.75
2724 2747 0.321671 AGCAGTGTCGCACCAGTTAT 59.678 50.000 6.39 0.00 34.49 1.89
2725 2748 0.963225 TAGCAGTGTCGCACCAGTTA 59.037 50.000 6.39 1.17 34.49 2.24
2726 2749 0.600255 GTAGCAGTGTCGCACCAGTT 60.600 55.000 6.39 1.95 34.49 3.16
2727 2750 1.006102 GTAGCAGTGTCGCACCAGT 60.006 57.895 6.39 0.00 34.49 4.00
2728 2751 0.319900 AAGTAGCAGTGTCGCACCAG 60.320 55.000 6.39 2.19 34.49 4.00
2729 2752 0.599991 CAAGTAGCAGTGTCGCACCA 60.600 55.000 6.39 0.00 34.49 4.17
2730 2753 0.319555 TCAAGTAGCAGTGTCGCACC 60.320 55.000 6.39 0.00 34.49 5.01
2731 2754 1.063806 CTCAAGTAGCAGTGTCGCAC 58.936 55.000 2.28 2.28 34.10 5.34
2732 2755 0.673985 ACTCAAGTAGCAGTGTCGCA 59.326 50.000 0.00 0.00 0.00 5.10
2733 2756 2.631418 TACTCAAGTAGCAGTGTCGC 57.369 50.000 0.00 0.00 0.00 5.19
2734 2757 5.864474 AGAAATTACTCAAGTAGCAGTGTCG 59.136 40.000 0.00 0.00 0.00 4.35
2735 2758 6.868864 TCAGAAATTACTCAAGTAGCAGTGTC 59.131 38.462 0.00 0.00 0.00 3.67
2736 2759 6.759272 TCAGAAATTACTCAAGTAGCAGTGT 58.241 36.000 0.00 0.00 0.00 3.55
2770 2793 7.782049 AGTCAATCTGGTTCTTAACGATGATA 58.218 34.615 0.00 0.00 0.00 2.15
2782 2805 6.625873 AGTTTCAAAGAGTCAATCTGGTTC 57.374 37.500 0.00 0.00 38.67 3.62
2811 2836 6.183361 TGCCATCTATATGCAAGGACTTAACT 60.183 38.462 0.00 0.00 0.00 2.24
2830 2858 8.931385 ATGTAATCAATAACAAGTTTGCCATC 57.069 30.769 0.00 0.00 0.00 3.51
2882 2913 8.567948 CCAGCACTTCAAATTCGGTAATAATAT 58.432 33.333 0.00 0.00 0.00 1.28
2884 2915 6.601613 TCCAGCACTTCAAATTCGGTAATAAT 59.398 34.615 0.00 0.00 0.00 1.28
2885 2916 5.941058 TCCAGCACTTCAAATTCGGTAATAA 59.059 36.000 0.00 0.00 0.00 1.40
2886 2917 5.492895 TCCAGCACTTCAAATTCGGTAATA 58.507 37.500 0.00 0.00 0.00 0.98
2887 2918 4.331968 TCCAGCACTTCAAATTCGGTAAT 58.668 39.130 0.00 0.00 0.00 1.89
2888 2919 3.745799 TCCAGCACTTCAAATTCGGTAA 58.254 40.909 0.00 0.00 0.00 2.85
2889 2920 3.410631 TCCAGCACTTCAAATTCGGTA 57.589 42.857 0.00 0.00 0.00 4.02
2890 2921 2.270352 TCCAGCACTTCAAATTCGGT 57.730 45.000 0.00 0.00 0.00 4.69
2897 2928 9.120538 GATTTAGGTATAATTCCAGCACTTCAA 57.879 33.333 0.00 0.00 0.00 2.69
2931 2962 7.470702 GCTGTCTGTGAAGAATATAGCCTAGAA 60.471 40.741 0.00 0.00 0.00 2.10
2942 2973 7.047460 AGAAATTTTGCTGTCTGTGAAGAAT 57.953 32.000 0.00 0.00 0.00 2.40
2952 2983 8.897752 ACTATTGGAGATAGAAATTTTGCTGTC 58.102 33.333 0.00 0.00 0.00 3.51
2983 3014 9.853177 ATTCTCGGGATATATCAAAAGAGTTTT 57.147 29.630 14.60 4.58 0.00 2.43
3028 3059 9.241317 GAATTTGCAACTTTGGTCTATATGATG 57.759 33.333 0.00 0.00 0.00 3.07
3056 3087 9.743057 TTCGTTGTCAACTATTTTGATTGAATT 57.257 25.926 13.67 0.00 34.28 2.17
3145 3177 6.487331 TCTCAATGGCAGCAAATTTGATTTTT 59.513 30.769 22.31 3.58 0.00 1.94
3146 3178 5.998981 TCTCAATGGCAGCAAATTTGATTTT 59.001 32.000 22.31 3.92 0.00 1.82
3147 3179 5.553123 TCTCAATGGCAGCAAATTTGATTT 58.447 33.333 22.31 3.82 0.00 2.17
3148 3180 5.155278 TCTCAATGGCAGCAAATTTGATT 57.845 34.783 22.31 9.04 0.00 2.57
3149 3181 4.811969 TCTCAATGGCAGCAAATTTGAT 57.188 36.364 22.31 13.31 0.00 2.57
3192 3224 9.893305 CAAACTTTAATCCAAACGTAGAGAAAT 57.107 29.630 0.00 0.00 0.00 2.17
3199 3231 9.635520 TTTTGAACAAACTTTAATCCAAACGTA 57.364 25.926 0.00 0.00 0.00 3.57
3253 3286 6.019318 GTCAAGTGTGTTAGACTCGCTAAAAA 60.019 38.462 0.00 0.00 40.60 1.94
3254 3287 5.461078 GTCAAGTGTGTTAGACTCGCTAAAA 59.539 40.000 0.00 0.00 40.60 1.52
3255 3288 4.980434 GTCAAGTGTGTTAGACTCGCTAAA 59.020 41.667 0.00 0.00 40.60 1.85
3257 3290 3.566742 TGTCAAGTGTGTTAGACTCGCTA 59.433 43.478 0.00 0.00 32.07 4.26
3258 3291 2.361119 TGTCAAGTGTGTTAGACTCGCT 59.639 45.455 0.00 0.00 34.36 4.93
3259 3292 2.471743 GTGTCAAGTGTGTTAGACTCGC 59.528 50.000 0.00 0.00 32.41 5.03
3260 3293 3.966154 AGTGTCAAGTGTGTTAGACTCG 58.034 45.455 0.00 0.00 31.79 4.18
3261 3294 6.663944 AAAAGTGTCAAGTGTGTTAGACTC 57.336 37.500 0.00 0.00 32.41 3.36
3262 3295 6.879458 AGAAAAAGTGTCAAGTGTGTTAGACT 59.121 34.615 0.00 0.00 32.41 3.24
3263 3296 7.073342 AGAAAAAGTGTCAAGTGTGTTAGAC 57.927 36.000 0.00 0.00 0.00 2.59
3277 3435 6.673154 GTGTGTACACCTAAGAAAAAGTGT 57.327 37.500 22.91 0.00 45.06 3.55
3292 3450 3.198200 ACCCACAAGTGTAAGTGTGTACA 59.802 43.478 0.00 0.00 42.95 2.90
3293 3451 3.558418 CACCCACAAGTGTAAGTGTGTAC 59.442 47.826 3.38 0.00 42.95 2.90
3295 3453 2.639065 CACCCACAAGTGTAAGTGTGT 58.361 47.619 3.38 0.00 42.95 3.72
3311 3469 3.723245 GGTGGTAGAGGGACACCC 58.277 66.667 0.00 0.00 46.90 4.61
3313 3471 1.065418 CCATTGGTGGTAGAGGGACAC 60.065 57.143 0.00 0.00 40.83 3.67
3314 3472 1.285280 CCATTGGTGGTAGAGGGACA 58.715 55.000 0.00 0.00 40.83 4.02
3333 3491 6.340522 AGACATTATTTGCATGGGCTTTTAC 58.659 36.000 0.00 0.00 41.91 2.01
3334 3492 6.543430 AGACATTATTTGCATGGGCTTTTA 57.457 33.333 0.00 0.00 41.91 1.52
3335 3493 5.425196 AGACATTATTTGCATGGGCTTTT 57.575 34.783 0.00 0.00 41.91 2.27
3336 3494 6.340522 GTTAGACATTATTTGCATGGGCTTT 58.659 36.000 0.00 0.00 41.91 3.51
3337 3495 5.450412 CGTTAGACATTATTTGCATGGGCTT 60.450 40.000 0.00 0.00 41.91 4.35
3338 3496 4.036734 CGTTAGACATTATTTGCATGGGCT 59.963 41.667 0.00 0.00 41.91 5.19
3354 3512 2.224113 TGGACCAAACTCACCGTTAGAC 60.224 50.000 0.00 0.00 33.90 2.59
3358 3516 1.604604 CATGGACCAAACTCACCGTT 58.395 50.000 0.00 0.00 37.47 4.44
3419 3577 3.608432 GCCTTCTGATGGGCCAAC 58.392 61.111 11.89 9.11 42.30 3.77
3443 3601 5.809001 ACAGAAGAGACAAGGCAATGAATA 58.191 37.500 0.00 0.00 0.00 1.75
3446 3604 3.326006 AGACAGAAGAGACAAGGCAATGA 59.674 43.478 0.00 0.00 0.00 2.57
3454 3612 7.778470 GAAAGAAAGAAGACAGAAGAGACAA 57.222 36.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.