Multiple sequence alignment - TraesCS6D01G321600

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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 TraesCS6D01G321600 chr6D 100.000 3512 0 0 1 3512 429009197 429012708 0.000000e+00 6486.0
1 TraesCS6D01G321600 chr6D 87.500 376 36 7 2473 2840 429020497 429020869 1.170000e-114 424.0
2 TraesCS6D01G321600 chr6D 91.954 87 5 1 2952 3036 27511252 27511166 1.710000e-23 121.0
3 TraesCS6D01G321600 chr6D 95.745 47 1 1 2810 2856 245495235 245495190 1.350000e-09 75.0
4 TraesCS6D01G321600 chr6B 94.177 2851 121 15 1 2812 646239405 646242249 0.000000e+00 4303.0
5 TraesCS6D01G321600 chr6B 87.313 536 50 12 2850 3384 646242243 646242761 6.490000e-167 597.0
6 TraesCS6D01G321600 chr6B 86.316 380 37 7 2473 2840 646254179 646254555 1.960000e-107 399.0
7 TraesCS6D01G321600 chr6A 92.321 2865 146 33 1 2812 574241064 574243907 0.000000e+00 4004.0
8 TraesCS6D01G321600 chr6A 89.138 580 44 9 2850 3428 574243901 574244462 0.000000e+00 704.0
9 TraesCS6D01G321600 chr6A 86.559 372 30 8 2464 2816 574263277 574263647 3.290000e-105 392.0
10 TraesCS6D01G321600 chr3B 82.973 1574 248 14 887 2457 734437154 734435598 0.000000e+00 1404.0
11 TraesCS6D01G321600 chr3B 79.021 143 16 8 2908 3036 798335069 798334927 6.250000e-13 86.1
12 TraesCS6D01G321600 chr3B 93.478 46 3 0 2896 2941 526689808 526689853 6.290000e-08 69.4
13 TraesCS6D01G321600 chr3A 82.412 1592 258 12 883 2468 689502205 689500630 0.000000e+00 1369.0
14 TraesCS6D01G321600 chr3A 81.818 143 15 7 2897 3036 590234911 590234777 3.710000e-20 110.0
15 TraesCS6D01G321600 chr3D 82.197 1584 262 13 888 2468 553233505 553231939 0.000000e+00 1345.0
16 TraesCS6D01G321600 chr3D 100.000 28 0 0 1235 1262 6467695 6467668 6.000000e-03 52.8
17 TraesCS6D01G321600 chr7B 71.857 1066 259 34 1332 2378 130747054 130746011 5.780000e-68 268.0
18 TraesCS6D01G321600 chr7B 95.000 40 2 0 2898 2937 639499249 639499288 2.930000e-06 63.9
19 TraesCS6D01G321600 chr7A 71.764 1066 260 34 1332 2378 167904412 167903369 2.690000e-66 263.0
20 TraesCS6D01G321600 chr5B 93.103 87 4 1 2952 3036 208523365 208523451 3.680000e-25 126.0
21 TraesCS6D01G321600 chr4A 83.333 150 11 4 2901 3036 109850204 109850055 3.680000e-25 126.0
22 TraesCS6D01G321600 chr4A 92.135 89 6 1 2950 3037 9613099 9613011 1.320000e-24 124.0
23 TraesCS6D01G321600 chr5D 91.954 87 5 1 2952 3036 204323298 204323384 1.710000e-23 121.0
24 TraesCS6D01G321600 chr1D 81.646 158 15 7 2893 3037 450394114 450394270 6.160000e-23 119.0
25 TraesCS6D01G321600 chr1D 89.362 94 6 3 2946 3037 450454881 450454972 7.970000e-22 115.0
26 TraesCS6D01G321600 chrUn 80.667 150 13 8 2898 3031 10131951 10132100 6.200000e-18 102.0
27 TraesCS6D01G321600 chr2B 79.503 161 11 9 2898 3036 361574092 361573932 1.040000e-15 95.3
28 TraesCS6D01G321600 chr1A 78.912 147 13 7 2897 3031 440793052 440793192 2.250000e-12 84.2
29 TraesCS6D01G321600 chr5A 90.741 54 3 2 2810 2863 622999341 622999392 1.750000e-08 71.3
30 TraesCS6D01G321600 chr2D 93.182 44 2 1 2815 2858 443729207 443729249 2.930000e-06 63.9
31 TraesCS6D01G321600 chr4B 100.000 31 0 0 2908 2938 89507059 89507029 1.360000e-04 58.4


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 TraesCS6D01G321600 chr6D 429009197 429012708 3511 False 6486 6486 100.0000 1 3512 1 chr6D.!!$F1 3511
1 TraesCS6D01G321600 chr6B 646239405 646242761 3356 False 2450 4303 90.7450 1 3384 2 chr6B.!!$F2 3383
2 TraesCS6D01G321600 chr6A 574241064 574244462 3398 False 2354 4004 90.7295 1 3428 2 chr6A.!!$F2 3427
3 TraesCS6D01G321600 chr3B 734435598 734437154 1556 True 1404 1404 82.9730 887 2457 1 chr3B.!!$R1 1570
4 TraesCS6D01G321600 chr3A 689500630 689502205 1575 True 1369 1369 82.4120 883 2468 1 chr3A.!!$R2 1585
5 TraesCS6D01G321600 chr3D 553231939 553233505 1566 True 1345 1345 82.1970 888 2468 1 chr3D.!!$R2 1580
6 TraesCS6D01G321600 chr7B 130746011 130747054 1043 True 268 268 71.8570 1332 2378 1 chr7B.!!$R1 1046
7 TraesCS6D01G321600 chr7A 167903369 167904412 1043 True 263 263 71.7640 1332 2378 1 chr7A.!!$R1 1046

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
337 346 1.228215 TCCGTATATGGGACCGCGA 60.228 57.895 8.23 0.0 0.00 5.87 F
497 517 1.990563 CCTAGCCGTTGTCGTTGTAAG 59.009 52.381 0.00 0.0 35.01 2.34 F
1700 1732 1.477295 GAGGAACCTTCTACAGACCGG 59.523 57.143 0.00 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1505 0.171231 CGTCGATGGCTGAGAAGACA 59.829 55.0 0.0 0.0 0.00 3.41 R
2052 2084 0.675633 GTGCCACAAAGGACATTGCT 59.324 50.0 0.0 0.0 41.22 3.91 R
3386 3453 0.106708 TCAAAGTTGTCGCTGCCTCT 59.893 50.0 0.0 0.0 0.00 3.69 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
218 227 8.443937 GTGATATAGTTCAGACAAAGAAACACC 58.556 37.037 0.00 0.00 0.00 4.16
219 228 8.154203 TGATATAGTTCAGACAAAGAAACACCA 58.846 33.333 0.00 0.00 0.00 4.17
220 229 4.965119 AGTTCAGACAAAGAAACACCAC 57.035 40.909 0.00 0.00 0.00 4.16
263 272 6.742926 TTGAAGTGTCAAAGGAACGATCCATA 60.743 38.462 14.80 0.00 42.49 2.74
321 330 1.303074 GGTTTGAACCTCCCCGTCC 60.303 63.158 5.66 0.00 45.75 4.79
337 346 1.228215 TCCGTATATGGGACCGCGA 60.228 57.895 8.23 0.00 0.00 5.87
366 375 3.329386 CACACCAGCCATATTCTATCCG 58.671 50.000 0.00 0.00 0.00 4.18
384 393 3.449227 TACAGCCTCTCCCGTGCG 61.449 66.667 0.00 0.00 0.00 5.34
409 424 4.250431 AAACACAGGTGCGCGCAC 62.250 61.111 46.90 46.90 45.49 5.34
428 448 2.352651 CACGCCACCTCAAATATGTGAG 59.647 50.000 15.13 15.13 43.98 3.51
497 517 1.990563 CCTAGCCGTTGTCGTTGTAAG 59.009 52.381 0.00 0.00 35.01 2.34
500 520 3.096489 AGCCGTTGTCGTTGTAAGTAA 57.904 42.857 0.00 0.00 35.01 2.24
712 736 7.519008 GCAAGAGTTCCCGTTATCAGAAATATG 60.519 40.741 0.00 0.00 0.00 1.78
721 745 9.366216 CCCGTTATCAGAAATATGAAATATCGA 57.634 33.333 0.00 0.00 38.94 3.59
725 749 7.834068 ATCAGAAATATGAAATATCGACCGG 57.166 36.000 0.00 0.00 38.94 5.28
1066 1095 5.251764 AGCTCGTAGTAGACAACTTCCTAA 58.748 41.667 0.00 0.00 39.80 2.69
1081 1110 2.104967 TCCTAACCATGGTGACCGTAG 58.895 52.381 20.60 15.36 0.00 3.51
1449 1481 7.104290 GGAACAAGTACTTAACATTAGAGGCT 58.896 38.462 8.04 0.00 0.00 4.58
1451 1483 6.407202 ACAAGTACTTAACATTAGAGGCTGG 58.593 40.000 8.04 0.00 0.00 4.85
1473 1505 2.705821 CGAGGAGGCTGAGCTCGTT 61.706 63.158 9.64 0.00 33.50 3.85
1622 1654 4.819761 GCTGCGAGGCGACATCCA 62.820 66.667 0.00 0.00 0.00 3.41
1700 1732 1.477295 GAGGAACCTTCTACAGACCGG 59.523 57.143 0.00 0.00 0.00 5.28
2514 2549 4.712476 AGCAGTTGAGAGACACTTGAAAT 58.288 39.130 0.00 0.00 0.00 2.17
2517 2552 4.818546 CAGTTGAGAGACACTTGAAATGGT 59.181 41.667 0.00 0.00 0.00 3.55
2519 2554 4.008074 TGAGAGACACTTGAAATGGTCC 57.992 45.455 0.00 0.00 0.00 4.46
2523 2575 5.449553 AGAGACACTTGAAATGGTCCTTTT 58.550 37.500 2.45 2.45 0.00 2.27
2560 2612 9.797556 ACCCGCTTTGATTTCTAAAATAAATAC 57.202 29.630 0.00 0.00 0.00 1.89
2561 2613 9.796120 CCCGCTTTGATTTCTAAAATAAATACA 57.204 29.630 0.00 0.00 0.00 2.29
2652 2714 6.472887 TGTACTCAATCTTTTCTTACCCTGG 58.527 40.000 0.00 0.00 0.00 4.45
2655 2717 6.004574 ACTCAATCTTTTCTTACCCTGGAAC 58.995 40.000 0.00 0.00 0.00 3.62
2729 2795 7.967890 ATGTCGTTGCTGATATGATTATTGA 57.032 32.000 0.00 0.00 0.00 2.57
2772 2838 8.989131 ACTAGTGTAACAAATATAGTGATGGGT 58.011 33.333 0.00 0.00 41.43 4.51
2779 2845 5.163343 ACAAATATAGTGATGGGTACACGCT 60.163 40.000 0.00 0.00 42.25 5.07
2819 2885 2.779506 CTTAAAAAGCACTCCCTCCGT 58.220 47.619 0.00 0.00 0.00 4.69
2820 2886 3.934068 CTTAAAAAGCACTCCCTCCGTA 58.066 45.455 0.00 0.00 0.00 4.02
2821 2887 2.943036 AAAAAGCACTCCCTCCGTAA 57.057 45.000 0.00 0.00 0.00 3.18
2822 2888 2.943036 AAAAGCACTCCCTCCGTAAA 57.057 45.000 0.00 0.00 0.00 2.01
2823 2889 2.943036 AAAGCACTCCCTCCGTAAAA 57.057 45.000 0.00 0.00 0.00 1.52
2824 2890 2.943036 AAGCACTCCCTCCGTAAAAA 57.057 45.000 0.00 0.00 0.00 1.94
2921 2987 8.387813 AGTACTCCCTTGGTTCACAAATATAAA 58.612 33.333 0.00 0.00 38.91 1.40
2958 3024 6.707440 TTTGTGAATCCATGTGTTTAGTGT 57.293 33.333 0.00 0.00 0.00 3.55
2959 3025 7.809546 TTTGTGAATCCATGTGTTTAGTGTA 57.190 32.000 0.00 0.00 0.00 2.90
2962 3028 8.402798 TGTGAATCCATGTGTTTAGTGTATTT 57.597 30.769 0.00 0.00 0.00 1.40
2963 3029 8.296000 TGTGAATCCATGTGTTTAGTGTATTTG 58.704 33.333 0.00 0.00 0.00 2.32
2964 3030 7.273381 GTGAATCCATGTGTTTAGTGTATTTGC 59.727 37.037 0.00 0.00 0.00 3.68
2965 3031 7.176515 TGAATCCATGTGTTTAGTGTATTTGCT 59.823 33.333 0.00 0.00 0.00 3.91
2967 3033 6.000840 TCCATGTGTTTAGTGTATTTGCTCA 58.999 36.000 0.00 0.00 0.00 4.26
2968 3034 6.072728 TCCATGTGTTTAGTGTATTTGCTCAC 60.073 38.462 0.00 0.00 35.13 3.51
2969 3035 6.072508 CCATGTGTTTAGTGTATTTGCTCACT 60.073 38.462 0.00 0.00 45.21 3.41
2970 3036 6.539649 TGTGTTTAGTGTATTTGCTCACTC 57.460 37.500 1.08 0.00 42.77 3.51
2971 3037 6.052360 TGTGTTTAGTGTATTTGCTCACTCA 58.948 36.000 1.08 0.00 42.77 3.41
2972 3038 6.710295 TGTGTTTAGTGTATTTGCTCACTCAT 59.290 34.615 1.08 0.00 42.77 2.90
2973 3039 7.228507 TGTGTTTAGTGTATTTGCTCACTCATT 59.771 33.333 1.08 0.00 42.77 2.57
2974 3040 8.076178 GTGTTTAGTGTATTTGCTCACTCATTT 58.924 33.333 1.08 0.00 42.77 2.32
2975 3041 8.289618 TGTTTAGTGTATTTGCTCACTCATTTC 58.710 33.333 1.08 0.00 42.77 2.17
2976 3042 7.977789 TTAGTGTATTTGCTCACTCATTTCA 57.022 32.000 1.08 0.00 42.77 2.69
2977 3043 6.492007 AGTGTATTTGCTCACTCATTTCAG 57.508 37.500 0.00 0.00 40.28 3.02
2978 3044 6.000219 AGTGTATTTGCTCACTCATTTCAGT 59.000 36.000 0.00 0.00 40.28 3.41
2979 3045 6.148480 AGTGTATTTGCTCACTCATTTCAGTC 59.852 38.462 0.00 0.00 40.28 3.51
2980 3046 5.412594 TGTATTTGCTCACTCATTTCAGTCC 59.587 40.000 0.00 0.00 0.00 3.85
2981 3047 2.084610 TGCTCACTCATTTCAGTCCG 57.915 50.000 0.00 0.00 0.00 4.79
2982 3048 1.344438 TGCTCACTCATTTCAGTCCGT 59.656 47.619 0.00 0.00 0.00 4.69
2983 3049 2.560981 TGCTCACTCATTTCAGTCCGTA 59.439 45.455 0.00 0.00 0.00 4.02
2995 3061 9.304335 TCATTTCAGTCCGTATAGTCCATATTA 57.696 33.333 0.00 0.00 0.00 0.98
3031 3097 6.884832 ACATCTTATATTTGTGAACGGAGGA 58.115 36.000 0.00 0.00 0.00 3.71
3055 3121 2.396608 AGGTGACAGAGGGATGATCAG 58.603 52.381 0.09 0.00 0.00 2.90
3068 3134 8.182885 AGAGGGATGATCAGAAATAGGATAGAA 58.817 37.037 0.09 0.00 0.00 2.10
3097 3163 6.016276 AGGCCACATTCAAACTACACTAAAAG 60.016 38.462 5.01 0.00 0.00 2.27
3099 3165 6.515035 GCCACATTCAAACTACACTAAAAGCT 60.515 38.462 0.00 0.00 0.00 3.74
3162 3229 2.081425 GATCGCTGATCTCGCCACCT 62.081 60.000 10.15 0.00 36.27 4.00
3168 3235 0.103026 TGATCTCGCCACCTCATTCG 59.897 55.000 0.00 0.00 0.00 3.34
3190 3257 3.886123 CCCCCATTTTCTAAGACGACAT 58.114 45.455 0.00 0.00 0.00 3.06
3197 3264 1.170442 TCTAAGACGACATGACGGCA 58.830 50.000 24.68 0.00 44.44 5.69
3215 3282 2.260434 GCTACGAACACCTGCCGA 59.740 61.111 0.00 0.00 0.00 5.54
3358 3425 1.927174 CTCGTACAATAGTGTGCTGGC 59.073 52.381 5.98 0.00 38.14 4.85
3394 3461 1.694150 TGACCCATGTATAGAGGCAGC 59.306 52.381 0.00 0.00 0.00 5.25
3428 3495 1.345112 ACCTATTACCACCAGGAGGGG 60.345 57.143 7.97 0.84 42.91 4.79
3429 3496 0.765510 CTATTACCACCAGGAGGGGC 59.234 60.000 7.97 0.00 42.91 5.80
3430 3497 0.345502 TATTACCACCAGGAGGGGCT 59.654 55.000 7.97 0.00 42.91 5.19
3431 3498 0.988678 ATTACCACCAGGAGGGGCTC 60.989 60.000 7.97 0.00 42.91 4.70
3432 3499 3.976490 TACCACCAGGAGGGGCTCG 62.976 68.421 7.97 0.00 42.91 5.03
3459 3526 2.517598 CACGGAGAGTGGAACGTTG 58.482 57.895 5.00 0.00 46.77 4.10
3460 3527 1.300697 ACGGAGAGTGGAACGTTGC 60.301 57.895 13.47 13.47 45.86 4.17
3461 3528 1.300620 CGGAGAGTGGAACGTTGCA 60.301 57.895 19.24 19.24 45.86 4.08
3462 3529 0.670546 CGGAGAGTGGAACGTTGCAT 60.671 55.000 25.53 14.17 45.86 3.96
3463 3530 1.523758 GGAGAGTGGAACGTTGCATT 58.476 50.000 25.53 21.44 45.86 3.56
3464 3531 1.880027 GGAGAGTGGAACGTTGCATTT 59.120 47.619 25.53 16.56 45.86 2.32
3465 3532 2.350772 GGAGAGTGGAACGTTGCATTTG 60.351 50.000 25.53 0.00 45.86 2.32
3466 3533 2.290641 GAGAGTGGAACGTTGCATTTGT 59.709 45.455 25.53 15.06 45.86 2.83
3467 3534 3.472652 AGAGTGGAACGTTGCATTTGTA 58.527 40.909 25.53 0.00 45.86 2.41
3468 3535 3.498397 AGAGTGGAACGTTGCATTTGTAG 59.502 43.478 25.53 0.00 45.86 2.74
3469 3536 3.472652 AGTGGAACGTTGCATTTGTAGA 58.527 40.909 25.53 0.00 45.86 2.59
3470 3537 3.250040 AGTGGAACGTTGCATTTGTAGAC 59.750 43.478 25.53 9.98 45.86 2.59
3471 3538 3.002862 GTGGAACGTTGCATTTGTAGACA 59.997 43.478 25.53 0.00 0.00 3.41
3472 3539 3.818210 TGGAACGTTGCATTTGTAGACAT 59.182 39.130 19.24 0.00 0.00 3.06
3473 3540 4.158384 GGAACGTTGCATTTGTAGACATG 58.842 43.478 15.52 0.00 0.00 3.21
3474 3541 3.829886 ACGTTGCATTTGTAGACATGG 57.170 42.857 0.00 0.00 0.00 3.66
3475 3542 3.407698 ACGTTGCATTTGTAGACATGGA 58.592 40.909 0.00 0.00 0.00 3.41
3476 3543 4.009675 ACGTTGCATTTGTAGACATGGAT 58.990 39.130 0.00 0.00 0.00 3.41
3477 3544 4.142622 ACGTTGCATTTGTAGACATGGATG 60.143 41.667 0.00 0.00 0.00 3.51
3478 3545 4.142622 CGTTGCATTTGTAGACATGGATGT 60.143 41.667 0.00 0.00 45.16 3.06
3479 3546 5.619757 CGTTGCATTTGTAGACATGGATGTT 60.620 40.000 0.00 0.00 41.95 2.71
3480 3547 5.565592 TGCATTTGTAGACATGGATGTTC 57.434 39.130 0.00 0.00 41.95 3.18
3481 3548 5.255687 TGCATTTGTAGACATGGATGTTCT 58.744 37.500 0.00 0.00 41.95 3.01
3482 3549 6.413892 TGCATTTGTAGACATGGATGTTCTA 58.586 36.000 0.00 0.00 41.95 2.10
3483 3550 6.316140 TGCATTTGTAGACATGGATGTTCTAC 59.684 38.462 11.60 11.60 41.95 2.59
3484 3551 6.316140 GCATTTGTAGACATGGATGTTCTACA 59.684 38.462 15.48 15.48 42.53 2.74
3485 3552 7.012704 GCATTTGTAGACATGGATGTTCTACAT 59.987 37.037 18.53 7.13 43.02 2.29
3486 3553 7.848223 TTTGTAGACATGGATGTTCTACATG 57.152 36.000 18.53 0.00 43.02 3.21
3487 3554 5.917462 TGTAGACATGGATGTTCTACATGG 58.083 41.667 15.48 0.00 44.65 3.66
3489 3556 2.545526 GACATGGATGTTCTACATGGCG 59.454 50.000 8.51 0.00 44.65 5.69
3490 3557 1.875514 CATGGATGTTCTACATGGCGG 59.124 52.381 0.00 0.00 39.27 6.13
3491 3558 0.463654 TGGATGTTCTACATGGCGGC 60.464 55.000 0.00 0.00 39.27 6.53
3492 3559 0.463654 GGATGTTCTACATGGCGGCA 60.464 55.000 16.34 16.34 39.27 5.69
3493 3560 1.597742 GATGTTCTACATGGCGGCAT 58.402 50.000 20.18 20.18 39.27 4.40
3494 3561 1.265095 GATGTTCTACATGGCGGCATG 59.735 52.381 40.61 40.61 39.27 4.06
3495 3562 0.251634 TGTTCTACATGGCGGCATGA 59.748 50.000 46.23 31.32 36.48 3.07
3496 3563 0.657840 GTTCTACATGGCGGCATGAC 59.342 55.000 46.23 33.14 36.48 3.06
3497 3564 0.463654 TTCTACATGGCGGCATGACC 60.464 55.000 46.23 13.22 36.48 4.02
3498 3565 1.893808 CTACATGGCGGCATGACCC 60.894 63.158 46.23 12.45 36.48 4.46
3499 3566 2.329539 CTACATGGCGGCATGACCCT 62.330 60.000 46.23 31.04 36.48 4.34
3500 3567 2.607411 TACATGGCGGCATGACCCTG 62.607 60.000 46.23 28.22 36.48 4.45
3501 3568 4.511246 ATGGCGGCATGACCCTGG 62.511 66.667 25.20 0.00 33.26 4.45
3505 3572 4.100084 CGGCATGACCCTGGCTCA 62.100 66.667 0.00 0.00 39.42 4.26
3506 3573 2.124403 GGCATGACCCTGGCTCAG 60.124 66.667 0.00 0.00 38.58 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 227 5.761003 TCAACAAACTAAGCATGTCATGTG 58.239 37.500 14.26 5.40 0.00 3.21
219 228 6.039717 ACTTCAACAAACTAAGCATGTCATGT 59.960 34.615 14.26 0.00 0.00 3.21
220 229 6.361481 CACTTCAACAAACTAAGCATGTCATG 59.639 38.462 8.56 8.56 0.00 3.07
312 321 0.251474 TCCCATATACGGACGGGGAG 60.251 60.000 0.00 0.00 42.75 4.30
321 330 1.202222 GGTATCGCGGTCCCATATACG 60.202 57.143 6.13 0.00 0.00 3.06
337 346 4.109675 GGCTGGTGTGCCCGGTAT 62.110 66.667 0.00 0.00 46.82 2.73
345 354 3.244215 ACGGATAGAATATGGCTGGTGTG 60.244 47.826 0.00 0.00 0.00 3.82
346 355 2.972713 ACGGATAGAATATGGCTGGTGT 59.027 45.455 0.00 0.00 0.00 4.16
366 375 2.184579 GCACGGGAGAGGCTGTAC 59.815 66.667 0.00 0.00 0.00 2.90
384 393 2.594592 ACCTGTGTTTCTGGGCGC 60.595 61.111 0.00 0.00 39.12 6.53
409 424 1.331756 GCTCACATATTTGAGGTGGCG 59.668 52.381 18.26 0.00 42.95 5.69
428 448 1.532868 AGTTGTTCACGCTGATCTTGC 59.467 47.619 0.00 0.00 0.00 4.01
497 517 8.630278 TTCGCTGAAGAACTATTCTGTATTAC 57.370 34.615 0.00 0.00 40.59 1.89
500 520 6.276847 CCTTCGCTGAAGAACTATTCTGTAT 58.723 40.000 16.51 0.00 41.71 2.29
519 539 2.404186 GGGGTTTAAGCGCCCTTCG 61.404 63.158 13.63 0.00 44.25 3.79
997 1026 4.441079 CCAAATTCCTGATGAACTCATGCC 60.441 45.833 0.00 0.00 36.57 4.40
1066 1095 0.618458 ATTGCTACGGTCACCATGGT 59.382 50.000 13.00 13.00 0.00 3.55
1081 1110 1.523711 TAGTGGCTGCCGCTATTGC 60.524 57.895 32.21 9.06 43.18 3.56
1473 1505 0.171231 CGTCGATGGCTGAGAAGACA 59.829 55.000 0.00 0.00 0.00 3.41
1622 1654 1.644509 TCCAGATAGGTGCACACTGT 58.355 50.000 20.43 11.49 39.02 3.55
2052 2084 0.675633 GTGCCACAAAGGACATTGCT 59.324 50.000 0.00 0.00 41.22 3.91
2649 2711 7.497909 ACCAAGGATATACAAATAACGTTCCAG 59.502 37.037 2.82 0.00 0.00 3.86
2652 2714 8.671028 ACAACCAAGGATATACAAATAACGTTC 58.329 33.333 2.82 0.00 0.00 3.95
2655 2717 7.981142 ACACAACCAAGGATATACAAATAACG 58.019 34.615 0.00 0.00 0.00 3.18
2709 2775 6.959871 GCAGATCAATAATCATATCAGCAACG 59.040 38.462 0.00 0.00 36.79 4.10
2772 2838 4.814234 CCTAATTTTAGGCATGAGCGTGTA 59.186 41.667 0.00 0.00 43.43 2.90
2805 2871 2.943036 TTTTTACGGAGGGAGTGCTT 57.057 45.000 0.00 0.00 0.00 3.91
2832 2898 9.736414 TGTAGTACTTAGTGATCTAAACACTCT 57.264 33.333 0.00 0.00 45.58 3.24
2898 2964 8.531146 CATTTTATATTTGTGAACCAAGGGAGT 58.469 33.333 0.00 0.00 33.75 3.85
2947 3013 6.052360 TGAGTGAGCAAATACACTAAACACA 58.948 36.000 0.00 0.00 45.54 3.72
2953 3019 7.161404 ACTGAAATGAGTGAGCAAATACACTA 58.839 34.615 0.00 0.00 45.54 2.74
2955 3021 6.246420 ACTGAAATGAGTGAGCAAATACAC 57.754 37.500 0.00 0.00 37.30 2.90
2956 3022 5.412594 GGACTGAAATGAGTGAGCAAATACA 59.587 40.000 0.00 0.00 0.00 2.29
2957 3023 5.446473 CGGACTGAAATGAGTGAGCAAATAC 60.446 44.000 0.00 0.00 0.00 1.89
2958 3024 4.631377 CGGACTGAAATGAGTGAGCAAATA 59.369 41.667 0.00 0.00 0.00 1.40
2959 3025 3.438087 CGGACTGAAATGAGTGAGCAAAT 59.562 43.478 0.00 0.00 0.00 2.32
2962 3028 1.344438 ACGGACTGAAATGAGTGAGCA 59.656 47.619 0.00 0.00 0.00 4.26
2963 3029 2.086054 ACGGACTGAAATGAGTGAGC 57.914 50.000 0.00 0.00 0.00 4.26
2964 3030 6.137794 ACTATACGGACTGAAATGAGTGAG 57.862 41.667 0.00 0.00 0.00 3.51
2965 3031 5.067413 GGACTATACGGACTGAAATGAGTGA 59.933 44.000 0.00 0.00 0.00 3.41
2967 3033 4.954202 TGGACTATACGGACTGAAATGAGT 59.046 41.667 0.00 0.00 0.00 3.41
2968 3034 5.515797 TGGACTATACGGACTGAAATGAG 57.484 43.478 0.00 0.00 0.00 2.90
2969 3035 7.776618 ATATGGACTATACGGACTGAAATGA 57.223 36.000 0.00 0.00 0.00 2.57
2970 3036 9.923143 TTAATATGGACTATACGGACTGAAATG 57.077 33.333 0.00 0.00 0.00 2.32
3031 3097 3.474798 TCATCCCTCTGTCACCTACTT 57.525 47.619 0.00 0.00 0.00 2.24
3055 3121 5.885912 TGTGGCCTGTTTTCTATCCTATTTC 59.114 40.000 3.32 0.00 0.00 2.17
3068 3134 3.957497 TGTAGTTTGAATGTGGCCTGTTT 59.043 39.130 3.32 0.00 0.00 2.83
3097 3163 5.924786 GATATGTCACTTGTGCATATCAGC 58.075 41.667 28.21 16.48 45.09 4.26
3162 3229 3.053991 TCTTAGAAAATGGGGGCGAATGA 60.054 43.478 0.00 0.00 0.00 2.57
3168 3235 2.014857 GTCGTCTTAGAAAATGGGGGC 58.985 52.381 0.00 0.00 0.00 5.80
3172 3239 4.032900 CCGTCATGTCGTCTTAGAAAATGG 59.967 45.833 11.29 0.00 0.00 3.16
3190 3257 1.372499 GTGTTCGTAGCTGCCGTCA 60.372 57.895 0.00 0.81 0.00 4.35
3197 3264 2.261671 CGGCAGGTGTTCGTAGCT 59.738 61.111 0.00 0.00 0.00 3.32
3215 3282 2.040606 AGATGGCCCTACCGGTGT 59.959 61.111 19.93 0.00 43.94 4.16
3222 3289 0.547712 GCCCTATGGAGATGGCCCTA 60.548 60.000 0.00 0.00 37.94 3.53
3292 3359 2.743928 GTCCTCTGGCAAGCCGTG 60.744 66.667 6.60 2.16 39.42 4.94
3293 3360 4.379243 CGTCCTCTGGCAAGCCGT 62.379 66.667 6.60 0.00 39.42 5.68
3303 3370 3.758133 ATGGATCCCGGCGTCCTCT 62.758 63.158 20.11 8.41 35.49 3.69
3328 3395 1.553690 ATTGTACGAGCACTGGCCCT 61.554 55.000 0.00 0.00 42.56 5.19
3384 3451 2.028112 TCAAAGTTGTCGCTGCCTCTAT 60.028 45.455 0.00 0.00 0.00 1.98
3385 3452 1.343142 TCAAAGTTGTCGCTGCCTCTA 59.657 47.619 0.00 0.00 0.00 2.43
3386 3453 0.106708 TCAAAGTTGTCGCTGCCTCT 59.893 50.000 0.00 0.00 0.00 3.69
3394 3461 4.390909 GGTAATAGGTGGTCAAAGTTGTCG 59.609 45.833 0.00 0.00 0.00 4.35
3441 3508 1.557443 GCAACGTTCCACTCTCCGTG 61.557 60.000 0.00 0.00 43.41 4.94
3442 3509 1.300697 GCAACGTTCCACTCTCCGT 60.301 57.895 0.00 0.00 34.56 4.69
3443 3510 0.670546 ATGCAACGTTCCACTCTCCG 60.671 55.000 0.00 0.00 0.00 4.63
3444 3511 1.523758 AATGCAACGTTCCACTCTCC 58.476 50.000 0.00 0.00 0.00 3.71
3445 3512 2.290641 ACAAATGCAACGTTCCACTCTC 59.709 45.455 0.00 0.00 0.00 3.20
3446 3513 2.297701 ACAAATGCAACGTTCCACTCT 58.702 42.857 0.00 0.00 0.00 3.24
3447 3514 2.774439 ACAAATGCAACGTTCCACTC 57.226 45.000 0.00 0.00 0.00 3.51
3448 3515 3.250040 GTCTACAAATGCAACGTTCCACT 59.750 43.478 0.00 0.00 0.00 4.00
3449 3516 3.002862 TGTCTACAAATGCAACGTTCCAC 59.997 43.478 0.00 0.00 0.00 4.02
3450 3517 3.206964 TGTCTACAAATGCAACGTTCCA 58.793 40.909 0.00 0.00 0.00 3.53
3451 3518 3.889196 TGTCTACAAATGCAACGTTCC 57.111 42.857 0.00 0.00 0.00 3.62
3452 3519 4.083537 TCCATGTCTACAAATGCAACGTTC 60.084 41.667 0.00 0.00 0.00 3.95
3453 3520 3.818210 TCCATGTCTACAAATGCAACGTT 59.182 39.130 0.00 0.00 0.00 3.99
3454 3521 3.407698 TCCATGTCTACAAATGCAACGT 58.592 40.909 0.00 0.00 0.00 3.99
3455 3522 4.142622 ACATCCATGTCTACAAATGCAACG 60.143 41.667 0.00 0.00 35.87 4.10
3456 3523 5.314923 ACATCCATGTCTACAAATGCAAC 57.685 39.130 0.00 0.00 35.87 4.17
3457 3524 5.711506 AGAACATCCATGTCTACAAATGCAA 59.288 36.000 0.00 0.00 40.80 4.08
3458 3525 5.255687 AGAACATCCATGTCTACAAATGCA 58.744 37.500 0.00 0.00 40.80 3.96
3459 3526 5.824904 AGAACATCCATGTCTACAAATGC 57.175 39.130 0.00 0.00 40.80 3.56
3460 3527 7.848223 TGTAGAACATCCATGTCTACAAATG 57.152 36.000 16.58 2.00 42.01 2.32
3461 3528 7.500227 CCATGTAGAACATCCATGTCTACAAAT 59.500 37.037 20.59 8.27 44.48 2.32
3462 3529 6.823182 CCATGTAGAACATCCATGTCTACAAA 59.177 38.462 20.59 5.50 44.48 2.83
3463 3530 6.348498 CCATGTAGAACATCCATGTCTACAA 58.652 40.000 20.59 9.57 44.48 2.41
3464 3531 5.684813 GCCATGTAGAACATCCATGTCTACA 60.685 44.000 19.57 19.57 44.86 2.74
3465 3532 4.752101 GCCATGTAGAACATCCATGTCTAC 59.248 45.833 11.60 11.60 40.80 2.59
3466 3533 4.501400 CGCCATGTAGAACATCCATGTCTA 60.501 45.833 0.00 0.00 40.80 2.59
3467 3534 3.742327 CGCCATGTAGAACATCCATGTCT 60.742 47.826 0.00 0.00 40.80 3.41
3468 3535 2.545526 CGCCATGTAGAACATCCATGTC 59.454 50.000 0.00 0.00 40.80 3.06
3469 3536 2.564771 CGCCATGTAGAACATCCATGT 58.435 47.619 0.00 0.00 44.20 3.21
3470 3537 1.875514 CCGCCATGTAGAACATCCATG 59.124 52.381 0.00 0.00 36.53 3.66
3471 3538 1.815408 GCCGCCATGTAGAACATCCAT 60.815 52.381 0.00 0.00 36.53 3.41
3472 3539 0.463654 GCCGCCATGTAGAACATCCA 60.464 55.000 0.00 0.00 36.53 3.41
3473 3540 0.463654 TGCCGCCATGTAGAACATCC 60.464 55.000 0.00 0.00 36.53 3.51
3474 3541 1.265095 CATGCCGCCATGTAGAACATC 59.735 52.381 0.00 0.00 43.07 3.06
3475 3542 1.311859 CATGCCGCCATGTAGAACAT 58.688 50.000 0.00 0.00 43.07 2.71
3476 3543 2.779282 CATGCCGCCATGTAGAACA 58.221 52.632 0.00 0.00 43.07 3.18
3484 3551 4.511246 CCAGGGTCATGCCGCCAT 62.511 66.667 0.00 0.00 38.44 4.40
3488 3555 4.100084 TGAGCCAGGGTCATGCCG 62.100 66.667 17.89 0.00 35.04 5.69
3489 3556 2.124403 CTGAGCCAGGGTCATGCC 60.124 66.667 21.85 0.00 39.36 4.40


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

AutoCloner maintained by Alex Coulton.