Multiple sequence alignment - TraesCS2D01G542300

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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 TraesCS2D01G542300 chr2D 100.000 3488 0 0 1 3488 620882364 620885851 0.000000e+00 6442.0
1 TraesCS2D01G542300 chr2D 78.717 1029 198 11 1543 2559 620921569 620922588 0.000000e+00 667.0
2 TraesCS2D01G542300 chr2D 80.410 439 84 2 2126 2563 620910674 620911111 2.010000e-87 333.0
3 TraesCS2D01G542300 chr2D 87.831 189 18 2 2748 2932 620911312 620911499 2.110000e-52 217.0
4 TraesCS2D01G542300 chr2D 86.076 158 17 3 3226 3379 620914532 620914688 7.750000e-37 165.0
5 TraesCS2D01G542300 chr2A 96.724 1740 37 3 833 2566 752748334 752750059 0.000000e+00 2880.0
6 TraesCS2D01G542300 chr2A 92.152 841 34 7 13 822 752747335 752748174 0.000000e+00 1158.0
7 TraesCS2D01G542300 chr2A 75.296 1182 233 40 1334 2489 752706762 752705614 8.640000e-141 510.0
8 TraesCS2D01G542300 chr2A 89.367 395 23 3 2747 3123 752750267 752750660 2.440000e-131 479.0
9 TraesCS2D01G542300 chr2A 93.939 297 15 3 3192 3488 752750664 752750957 2.470000e-121 446.0
10 TraesCS2D01G542300 chr2A 80.549 437 77 8 2138 2570 752758667 752759099 2.600000e-86 329.0
11 TraesCS2D01G542300 chr2A 92.366 131 7 2 2609 2736 752750058 752750188 2.140000e-42 183.0
12 TraesCS2D01G542300 chr2A 89.423 104 9 2 2609 2710 752759094 752759197 2.830000e-26 130.0
13 TraesCS2D01G542300 chr2B 75.702 1354 274 33 1233 2560 761984280 761985604 8.220000e-176 627.0
14 TraesCS2D01G542300 chr2B 78.596 855 149 20 1717 2562 761960538 761961367 5.120000e-148 534.0
15 TraesCS2D01G542300 chr2B 78.342 748 136 13 1820 2563 761888708 761889433 8.820000e-126 460.0
16 TraesCS2D01G542300 chr2B 83.002 453 60 11 3 447 420688347 420687904 9.070000e-106 394.0
17 TraesCS2D01G542300 chr2B 74.466 983 200 33 1550 2490 761721612 761720639 9.140000e-101 377.0
18 TraesCS2D01G542300 chr2B 89.474 190 14 2 2748 2932 761889630 761889818 5.820000e-58 235.0
19 TraesCS2D01G542300 chr6D 85.872 453 48 14 1 448 77520932 77521373 5.270000e-128 468.0
20 TraesCS2D01G542300 chr5D 86.667 420 41 11 3 417 37162201 37162610 5.310000e-123 451.0
21 TraesCS2D01G542300 chr7B 100.000 43 0 0 2564 2606 671276370 671276412 2.890000e-11 80.5
22 TraesCS2D01G542300 chr7B 97.778 45 1 0 2562 2606 593062789 593062833 1.040000e-10 78.7
23 TraesCS2D01G542300 chr4A 94.118 51 3 0 2562 2612 222527959 222527909 1.040000e-10 78.7
24 TraesCS2D01G542300 chr4A 91.379 58 3 2 2558 2613 729053791 729053848 1.040000e-10 78.7
25 TraesCS2D01G542300 chr4A 91.379 58 3 2 2558 2613 731065599 731065542 1.040000e-10 78.7
26 TraesCS2D01G542300 chr7D 95.745 47 2 0 2564 2610 532599549 532599503 3.730000e-10 76.8
27 TraesCS2D01G542300 chr5B 95.745 47 2 0 2564 2610 336765980 336765934 3.730000e-10 76.8
28 TraesCS2D01G542300 chr3D 93.878 49 3 0 2562 2610 435704515 435704563 1.340000e-09 75.0
29 TraesCS2D01G542300 chr1A 93.878 49 3 0 2562 2610 59930537 59930489 1.340000e-09 75.0


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 TraesCS2D01G542300 chr2D 620882364 620885851 3487 False 6442.000000 6442 100.000000 1 3488 1 chr2D.!!$F1 3487
1 TraesCS2D01G542300 chr2D 620921569 620922588 1019 False 667.000000 667 78.717000 1543 2559 1 chr2D.!!$F2 1016
2 TraesCS2D01G542300 chr2D 620910674 620914688 4014 False 238.333333 333 84.772333 2126 3379 3 chr2D.!!$F3 1253
3 TraesCS2D01G542300 chr2A 752747335 752750957 3622 False 1029.200000 2880 92.909600 13 3488 5 chr2A.!!$F1 3475
4 TraesCS2D01G542300 chr2A 752705614 752706762 1148 True 510.000000 510 75.296000 1334 2489 1 chr2A.!!$R1 1155
5 TraesCS2D01G542300 chr2A 752758667 752759197 530 False 229.500000 329 84.986000 2138 2710 2 chr2A.!!$F2 572
6 TraesCS2D01G542300 chr2B 761984280 761985604 1324 False 627.000000 627 75.702000 1233 2560 1 chr2B.!!$F2 1327
7 TraesCS2D01G542300 chr2B 761960538 761961367 829 False 534.000000 534 78.596000 1717 2562 1 chr2B.!!$F1 845
8 TraesCS2D01G542300 chr2B 761720639 761721612 973 True 377.000000 377 74.466000 1550 2490 1 chr2B.!!$R2 940
9 TraesCS2D01G542300 chr2B 761888708 761889818 1110 False 347.500000 460 83.908000 1820 2932 2 chr2B.!!$F3 1112

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
669 698 0.17668 AGTGTCCGGACAGCATGATC 59.823 55.0 37.04 22.62 42.74 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2515 5134 0.030908 CGGTCTCTTATCTGTCGGGC 59.969 60.0 0.0 0.0 0.0 6.13 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
77 78 6.327154 TCAAGCTGCACAAATCATTAAGATG 58.673 36.000 1.02 0.00 36.96 2.90
95 96 2.851263 TGGAGTAAACCATGAGCGTT 57.149 45.000 0.00 0.00 34.77 4.84
107 108 1.629013 TGAGCGTTGATAGCAGTTCG 58.371 50.000 0.00 0.00 37.01 3.95
135 136 8.638565 GTTAAATATTGCAACACATGACAAGTC 58.361 33.333 0.00 0.00 31.67 3.01
300 301 8.354426 TGCCAAGTAGAAACAATTAAAGTTACC 58.646 33.333 0.00 0.00 0.00 2.85
373 377 4.160439 TGCTGACACCCTAGAAGTTATCAG 59.840 45.833 13.97 13.97 36.30 2.90
375 379 3.451178 TGACACCCTAGAAGTTATCAGGC 59.549 47.826 0.00 0.00 0.00 4.85
421 425 4.568359 CACAAGCTGCATAACTTATCGAGT 59.432 41.667 1.02 0.00 41.47 4.18
440 444 4.642429 GAGTGGAAGTAAACCATGAGTGT 58.358 43.478 0.00 0.00 39.69 3.55
493 502 2.607635 GCGAAGTGTCAGTTGAAGTGAA 59.392 45.455 3.97 0.00 0.00 3.18
518 547 4.339530 CGAGAGAGAGAGAGAGAGAGAGAA 59.660 50.000 0.00 0.00 0.00 2.87
533 562 1.349357 AGAGAAGAGGTTTGTGGGAGC 59.651 52.381 0.00 0.00 0.00 4.70
571 600 2.255252 CGCCCGCAAACCTTTCTG 59.745 61.111 0.00 0.00 0.00 3.02
611 640 3.119955 TGTGATTTCAGACGTCTAGACCG 60.120 47.826 19.57 13.98 0.00 4.79
646 675 8.357796 AGTTTGATGTATGATGTTAGATGACG 57.642 34.615 0.00 0.00 0.00 4.35
662 691 1.001048 TGACGTAAAGTGTCCGGACAG 60.001 52.381 37.04 25.20 42.74 3.51
669 698 0.176680 AGTGTCCGGACAGCATGATC 59.823 55.000 37.04 22.62 42.74 2.92
673 705 1.134699 GTCCGGACAGCATGATCAAGA 60.135 52.381 29.75 0.00 39.69 3.02
686 718 2.743664 TGATCAAGACATTTGCAGACGG 59.256 45.455 0.00 0.00 0.00 4.79
691 723 1.608590 AGACATTTGCAGACGGTTTGG 59.391 47.619 0.55 0.00 0.00 3.28
698 730 1.064946 CAGACGGTTTGGCGCAAAA 59.935 52.632 10.83 8.15 35.03 2.44
746 778 7.685304 GTGTCATTTACGACGGTTATGTTTTAG 59.315 37.037 0.00 0.00 38.84 1.85
751 783 3.120923 ACGACGGTTATGTTTTAGCAACG 60.121 43.478 0.00 0.00 0.00 4.10
769 801 4.376311 GCAACGCTTTTGTGGATTGAAATC 60.376 41.667 0.00 0.00 34.66 2.17
801 833 5.929697 TGCTCACTTATTCAACAAGACAG 57.070 39.130 0.00 0.00 0.00 3.51
822 854 2.735762 GCTGTCCTAGTGGAGCGTTTAG 60.736 54.545 0.00 0.00 44.16 1.85
823 855 2.753452 CTGTCCTAGTGGAGCGTTTAGA 59.247 50.000 0.00 0.00 44.16 2.10
824 856 3.159472 TGTCCTAGTGGAGCGTTTAGAA 58.841 45.455 0.00 0.00 44.16 2.10
825 857 3.057033 TGTCCTAGTGGAGCGTTTAGAAC 60.057 47.826 0.00 0.00 44.16 3.01
900 1081 1.639298 GCCGTGCCACACTTCTCATC 61.639 60.000 0.00 0.00 31.34 2.92
926 1107 1.453379 CCCTGCCTGCCAATCTCAG 60.453 63.158 0.00 0.00 0.00 3.35
1613 1813 1.282817 TTCGTCGATGTTATTGCCCG 58.717 50.000 4.21 0.00 0.00 6.13
1657 1857 0.447801 GGCCGTGCTAGACATGTTTG 59.552 55.000 0.00 0.00 33.01 2.93
1941 2147 2.591715 ACGCAGAACTGTGCACCC 60.592 61.111 15.69 0.79 44.21 4.61
2232 2462 3.609853 CAAATCGAGATTTCCTGGACCA 58.390 45.455 7.99 0.00 38.84 4.02
2383 2631 4.099120 CGAGAGAGTCATTTCAGGTTACG 58.901 47.826 0.00 0.00 0.00 3.18
2515 5134 2.376808 AGAGGCATCAAACAGAGTCG 57.623 50.000 0.00 0.00 0.00 4.18
2544 5164 6.363065 ACAGATAAGAGACCGGACTTATGTA 58.637 40.000 25.12 11.35 38.76 2.29
2569 5189 8.682936 ATCATCATTGTATTTGGAACTACTCC 57.317 34.615 0.00 0.00 45.64 3.85
2570 5190 7.054124 TCATCATTGTATTTGGAACTACTCCC 58.946 38.462 0.00 0.00 44.69 4.30
2571 5191 6.636454 TCATTGTATTTGGAACTACTCCCT 57.364 37.500 0.00 0.00 44.69 4.20
2572 5192 6.650120 TCATTGTATTTGGAACTACTCCCTC 58.350 40.000 0.00 0.00 44.69 4.30
2573 5193 5.431179 TTGTATTTGGAACTACTCCCTCC 57.569 43.478 0.00 0.00 44.69 4.30
2574 5194 3.449737 TGTATTTGGAACTACTCCCTCCG 59.550 47.826 0.00 0.00 44.69 4.63
2575 5195 2.019807 TTTGGAACTACTCCCTCCGT 57.980 50.000 0.00 0.00 44.69 4.69
2576 5196 2.019807 TTGGAACTACTCCCTCCGTT 57.980 50.000 0.00 0.00 44.69 4.44
2577 5197 1.553706 TGGAACTACTCCCTCCGTTC 58.446 55.000 0.00 0.00 44.69 3.95
2578 5198 0.822811 GGAACTACTCCCTCCGTTCC 59.177 60.000 4.51 4.51 45.79 3.62
2579 5199 1.553706 GAACTACTCCCTCCGTTCCA 58.446 55.000 0.00 0.00 31.89 3.53
2580 5200 2.108970 GAACTACTCCCTCCGTTCCAT 58.891 52.381 0.00 0.00 31.89 3.41
2581 5201 3.294214 GAACTACTCCCTCCGTTCCATA 58.706 50.000 0.00 0.00 31.89 2.74
2582 5202 3.393426 ACTACTCCCTCCGTTCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
2583 5203 3.924922 ACTACTCCCTCCGTTCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
2584 5204 5.070823 ACTACTCCCTCCGTTCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
2585 5205 5.652324 ACTACTCCCTCCGTTCCATAATAT 58.348 41.667 0.00 0.00 0.00 1.28
2586 5206 6.797707 ACTACTCCCTCCGTTCCATAATATA 58.202 40.000 0.00 0.00 0.00 0.86
2587 5207 7.243824 ACTACTCCCTCCGTTCCATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
2588 5208 6.607004 ACTCCCTCCGTTCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
2589 5209 6.320518 ACTCCCTCCGTTCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
2590 5210 6.437793 ACTCCCTCCGTTCCATAATATAAGAG 59.562 42.308 0.00 0.00 0.00 2.85
2591 5211 5.187186 TCCCTCCGTTCCATAATATAAGAGC 59.813 44.000 0.00 0.00 0.00 4.09
2592 5212 5.103000 CCTCCGTTCCATAATATAAGAGCG 58.897 45.833 3.06 3.06 33.46 5.03
2593 5213 5.336531 CCTCCGTTCCATAATATAAGAGCGT 60.337 44.000 7.53 0.00 32.01 5.07
2594 5214 6.092955 TCCGTTCCATAATATAAGAGCGTT 57.907 37.500 7.53 0.00 32.01 4.84
2595 5215 6.518493 TCCGTTCCATAATATAAGAGCGTTT 58.482 36.000 7.53 0.00 32.01 3.60
2596 5216 6.987992 TCCGTTCCATAATATAAGAGCGTTTT 59.012 34.615 7.53 0.00 32.01 2.43
2597 5217 7.496591 TCCGTTCCATAATATAAGAGCGTTTTT 59.503 33.333 7.53 0.00 32.01 1.94
2598 5218 7.586300 CCGTTCCATAATATAAGAGCGTTTTTG 59.414 37.037 7.53 0.00 32.01 2.44
2599 5219 8.332464 CGTTCCATAATATAAGAGCGTTTTTGA 58.668 33.333 0.00 0.00 0.00 2.69
2673 5293 3.439129 GGTTGCTTAAGCGTTGGATACTT 59.561 43.478 21.97 0.00 45.83 2.24
2690 5310 5.525378 GGATACTTCATCAACTGGTCACATC 59.475 44.000 0.00 0.00 35.11 3.06
2697 5317 3.930336 TCAACTGGTCACATCATCTGTC 58.070 45.455 0.00 0.00 35.29 3.51
2728 5363 7.915293 TTTTTATGTCCTGATTGTATGACGT 57.085 32.000 0.00 0.00 0.00 4.34
2736 5371 8.905850 TGTCCTGATTGTATGACGTATACTTTA 58.094 33.333 0.56 0.00 41.82 1.85
2737 5372 9.740239 GTCCTGATTGTATGACGTATACTTTAA 57.260 33.333 0.56 4.21 41.82 1.52
2738 5373 9.961265 TCCTGATTGTATGACGTATACTTTAAG 57.039 33.333 0.56 0.00 41.82 1.85
2739 5374 8.700644 CCTGATTGTATGACGTATACTTTAAGC 58.299 37.037 0.56 6.17 41.82 3.09
2740 5375 8.277270 TGATTGTATGACGTATACTTTAAGCG 57.723 34.615 0.56 0.00 41.82 4.68
2742 5377 8.638685 ATTGTATGACGTATACTTTAAGCGTT 57.361 30.769 0.56 0.00 41.82 4.84
2743 5378 7.440541 TGTATGACGTATACTTTAAGCGTTG 57.559 36.000 0.56 0.00 41.82 4.10
2744 5379 7.028962 TGTATGACGTATACTTTAAGCGTTGT 58.971 34.615 0.56 0.00 41.82 3.32
2745 5380 6.956299 ATGACGTATACTTTAAGCGTTGTT 57.044 33.333 0.56 0.00 35.86 2.83
2845 5549 4.963318 AAACAGAGTCCATTCTGACAGA 57.037 40.909 0.00 0.00 45.95 3.41
2880 5584 7.331026 TGGACAGATATACAAGGAGTTTCAAG 58.669 38.462 0.00 0.00 0.00 3.02
2986 6325 3.854286 GGTGAAGCACCGATATAAACG 57.146 47.619 0.22 0.00 44.95 3.60
2988 6327 2.864343 GTGAAGCACCGATATAAACGCT 59.136 45.455 0.00 0.00 0.00 5.07
3086 6425 2.675348 GCATGTAAGACAAGAGCCTCAC 59.325 50.000 0.00 0.00 0.00 3.51
3103 6443 2.093890 TCACCGAAATACGTGCCTAGA 58.906 47.619 0.00 0.00 40.78 2.43
3106 6446 2.957006 ACCGAAATACGTGCCTAGAGAT 59.043 45.455 0.00 0.00 40.78 2.75
3108 6448 3.227147 CGAAATACGTGCCTAGAGATCG 58.773 50.000 0.00 0.00 37.22 3.69
3116 6456 1.065701 TGCCTAGAGATCGTTTCGAGC 59.934 52.381 0.00 0.00 42.87 5.03
3123 6463 3.129462 AGAGATCGTTTCGAGCATGAAGA 59.871 43.478 9.83 0.00 45.07 2.87
3125 6465 3.614616 AGATCGTTTCGAGCATGAAGAAC 59.385 43.478 9.83 0.00 45.07 3.01
3126 6466 2.066262 TCGTTTCGAGCATGAAGAACC 58.934 47.619 0.00 0.00 0.00 3.62
3127 6467 1.128692 CGTTTCGAGCATGAAGAACCC 59.871 52.381 0.00 0.00 0.00 4.11
3128 6468 1.128692 GTTTCGAGCATGAAGAACCCG 59.871 52.381 0.00 0.00 0.00 5.28
3129 6469 0.391130 TTCGAGCATGAAGAACCCGG 60.391 55.000 0.00 0.00 0.00 5.73
3130 6470 2.464459 CGAGCATGAAGAACCCGGC 61.464 63.158 0.00 0.00 0.00 6.13
3131 6471 1.377202 GAGCATGAAGAACCCGGCA 60.377 57.895 0.00 0.00 0.00 5.69
3132 6472 0.749454 GAGCATGAAGAACCCGGCAT 60.749 55.000 0.00 0.00 0.00 4.40
3133 6473 0.546122 AGCATGAAGAACCCGGCATA 59.454 50.000 0.00 0.00 0.00 3.14
3134 6474 0.947244 GCATGAAGAACCCGGCATAG 59.053 55.000 0.00 0.00 0.00 2.23
3135 6475 1.475034 GCATGAAGAACCCGGCATAGA 60.475 52.381 0.00 0.00 0.00 1.98
3136 6476 2.213499 CATGAAGAACCCGGCATAGAC 58.787 52.381 0.00 0.00 0.00 2.59
3137 6477 0.174845 TGAAGAACCCGGCATAGACG 59.825 55.000 0.00 0.00 0.00 4.18
3138 6478 1.152383 GAAGAACCCGGCATAGACGC 61.152 60.000 0.00 0.00 29.68 5.19
3139 6479 1.895020 AAGAACCCGGCATAGACGCA 61.895 55.000 0.00 0.00 29.68 5.24
3140 6480 1.883084 GAACCCGGCATAGACGCAG 60.883 63.158 0.00 0.00 29.68 5.18
3154 6494 0.038159 ACGCAGTCAAGGTACAGAGC 60.038 55.000 0.00 0.00 29.74 4.09
3155 6495 0.038251 CGCAGTCAAGGTACAGAGCA 60.038 55.000 0.00 0.00 0.00 4.26
3156 6496 1.404717 CGCAGTCAAGGTACAGAGCAT 60.405 52.381 0.00 0.00 0.00 3.79
3157 6497 2.275318 GCAGTCAAGGTACAGAGCATC 58.725 52.381 0.00 0.00 0.00 3.91
3158 6498 2.354103 GCAGTCAAGGTACAGAGCATCA 60.354 50.000 0.00 0.00 37.82 3.07
3159 6499 3.519579 CAGTCAAGGTACAGAGCATCAG 58.480 50.000 0.00 0.00 37.82 2.90
3160 6500 2.499289 AGTCAAGGTACAGAGCATCAGG 59.501 50.000 0.00 0.00 37.82 3.86
3161 6501 2.234908 GTCAAGGTACAGAGCATCAGGT 59.765 50.000 0.00 0.00 37.82 4.00
3162 6502 3.447586 GTCAAGGTACAGAGCATCAGGTA 59.552 47.826 0.00 0.00 37.82 3.08
3163 6503 4.100189 GTCAAGGTACAGAGCATCAGGTAT 59.900 45.833 0.00 0.00 37.82 2.73
3164 6504 5.302059 GTCAAGGTACAGAGCATCAGGTATA 59.698 44.000 0.00 0.00 37.82 1.47
3172 6512 9.579768 GTACAGAGCATCAGGTATAATGATAAG 57.420 37.037 2.26 0.00 35.64 1.73
3179 6519 9.323985 GCATCAGGTATAATGATAAGAGAATCC 57.676 37.037 2.26 0.00 35.64 3.01
3217 6557 3.572255 AGTTGTAAATCGGCCACATGTTT 59.428 39.130 2.24 0.00 0.00 2.83
3275 6619 5.481473 CCAAAATATGTATGGGGAATCTGGG 59.519 44.000 0.00 0.00 0.00 4.45
3282 6626 3.424105 GGGAATCTGGGGCCAGCT 61.424 66.667 4.39 0.00 43.31 4.24
3286 6630 2.850828 GAATCTGGGGCCAGCTTGCT 62.851 60.000 9.95 0.00 43.31 3.91
3369 6713 2.124529 GCCTAAGTGGGAGCCAGC 60.125 66.667 0.00 0.00 32.34 4.85
3423 6767 1.135689 GCCAGCCGTTGTAACAAGATG 60.136 52.381 0.00 0.00 0.00 2.90
3459 6803 0.170561 CAGCAGCTCAAAGACCATGC 59.829 55.000 0.00 0.00 0.00 4.06
3461 6805 0.170561 GCAGCTCAAAGACCATGCAG 59.829 55.000 0.00 0.00 33.92 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.719355 TTGATAACTTTAAGTAAGTCAGCATGA 57.281 29.630 0.00 0.00 46.34 3.07
2 3 9.979270 CTTGATAACTTTAAGTAAGTCAGCATG 57.021 33.333 0.00 0.00 46.34 4.06
3 4 9.726438 ACTTGATAACTTTAAGTAAGTCAGCAT 57.274 29.630 0.00 0.00 46.34 3.79
39 40 5.529060 GTGCAGCTTGAGCCTAATAACTTAT 59.471 40.000 0.00 0.00 43.38 1.73
77 78 2.695359 TCAACGCTCATGGTTTACTCC 58.305 47.619 0.00 0.00 0.00 3.85
95 96 7.494298 TGCAATATTTAACTCGAACTGCTATCA 59.506 33.333 0.00 0.00 0.00 2.15
107 108 8.741101 TTGTCATGTGTTGCAATATTTAACTC 57.259 30.769 0.59 9.29 0.00 3.01
373 377 3.379372 TGATACCTTGTACTACGTCAGCC 59.621 47.826 0.00 0.00 0.00 4.85
375 379 4.497674 GCCTGATACCTTGTACTACGTCAG 60.498 50.000 0.00 1.15 33.46 3.51
386 390 1.741706 CAGCTTGTGCCTGATACCTTG 59.258 52.381 0.00 0.00 40.80 3.61
398 402 4.568359 ACTCGATAAGTTATGCAGCTTGTG 59.432 41.667 0.00 2.43 33.03 3.33
421 425 5.042463 TCAACACTCATGGTTTACTTCCA 57.958 39.130 0.00 0.00 39.41 3.53
462 471 1.004440 ACACTTCGCTCTTCCAGCC 60.004 57.895 0.00 0.00 46.74 4.85
466 475 1.795286 CAACTGACACTTCGCTCTTCC 59.205 52.381 0.00 0.00 0.00 3.46
493 502 4.023980 TCTCTCTCTCTCTCTCTCTCGTT 58.976 47.826 0.00 0.00 0.00 3.85
518 547 1.841556 TCGGCTCCCACAAACCTCT 60.842 57.895 0.00 0.00 0.00 3.69
545 574 3.876589 TTTGCGGGCGTCAGACCTC 62.877 63.158 0.00 0.00 45.93 3.85
571 600 3.315191 TCACACAAACTAGAAGCAAAGCC 59.685 43.478 0.00 0.00 0.00 4.35
611 640 6.223138 TCATACATCAAACTTTCACGACAC 57.777 37.500 0.00 0.00 0.00 3.67
646 675 1.732259 CATGCTGTCCGGACACTTTAC 59.268 52.381 33.23 19.07 36.21 2.01
662 691 4.103357 GTCTGCAAATGTCTTGATCATGC 58.897 43.478 8.01 8.01 0.00 4.06
669 698 3.044986 CAAACCGTCTGCAAATGTCTTG 58.955 45.455 0.00 0.00 0.00 3.02
673 705 0.031994 GCCAAACCGTCTGCAAATGT 59.968 50.000 0.00 0.00 0.00 2.71
686 718 1.526464 CCTCAATGTTTTGCGCCAAAC 59.474 47.619 25.51 25.51 32.79 2.93
691 723 0.508213 GCAACCTCAATGTTTTGCGC 59.492 50.000 0.00 0.00 35.41 6.09
698 730 4.586001 ACTGAAATCAAGCAACCTCAATGT 59.414 37.500 0.00 0.00 0.00 2.71
746 778 2.132740 TCAATCCACAAAAGCGTTGC 57.867 45.000 3.38 0.00 0.00 4.17
796 828 1.846007 CTCCACTAGGACAGCTGTCT 58.154 55.000 38.17 27.71 44.20 3.41
801 833 0.037232 AAACGCTCCACTAGGACAGC 60.037 55.000 0.00 0.00 39.61 4.40
828 860 2.619840 ATACGAGCAGCTGAGGCGTG 62.620 60.000 27.64 11.57 44.37 5.34
829 861 2.343163 GATACGAGCAGCTGAGGCGT 62.343 60.000 24.76 24.76 44.37 5.68
830 862 1.659954 GATACGAGCAGCTGAGGCG 60.660 63.158 20.43 18.77 44.37 5.52
831 863 1.659954 CGATACGAGCAGCTGAGGC 60.660 63.158 20.43 1.09 39.06 4.70
900 1081 4.106925 GCAGGCAGGGGAGTGAGG 62.107 72.222 0.00 0.00 0.00 3.86
1226 1413 2.114670 ATTTGGCGAGCGACCATGG 61.115 57.895 11.19 11.19 36.96 3.66
1227 1414 1.063006 CATTTGGCGAGCGACCATG 59.937 57.895 6.82 0.00 36.96 3.66
1228 1415 2.114670 CCATTTGGCGAGCGACCAT 61.115 57.895 6.82 0.00 36.96 3.55
1229 1416 2.173758 TACCATTTGGCGAGCGACCA 62.174 55.000 0.00 0.00 39.32 4.02
1230 1417 1.022451 TTACCATTTGGCGAGCGACC 61.022 55.000 0.00 0.00 39.32 4.79
1231 1418 0.373716 CTTACCATTTGGCGAGCGAC 59.626 55.000 0.00 0.00 39.32 5.19
1449 1645 2.109126 GTCTTGGAGCCATGACGCC 61.109 63.158 16.63 0.00 39.88 5.68
1613 1813 5.350640 CGTAAATTCTCCACCCTAAGAACAC 59.649 44.000 0.00 0.00 34.52 3.32
1657 1857 1.814394 TGATGCATTGGAGACACAAGC 59.186 47.619 0.00 0.00 42.67 4.01
1941 2147 1.673920 AGGTTTACGGTGTTGTTGCTG 59.326 47.619 0.00 0.00 0.00 4.41
2247 2480 4.967084 TTTGGCTAGTGAAGAGGTGTTA 57.033 40.909 0.00 0.00 0.00 2.41
2334 2582 0.248990 CTCTCCGCAGCACATCTCTC 60.249 60.000 0.00 0.00 0.00 3.20
2383 2631 1.142097 GCTCTTCCAGGTAGTCGCC 59.858 63.158 0.00 0.00 0.00 5.54
2515 5134 0.030908 CGGTCTCTTATCTGTCGGGC 59.969 60.000 0.00 0.00 0.00 6.13
2544 5164 8.682936 GGAGTAGTTCCAAATACAATGATGAT 57.317 34.615 0.23 0.00 46.01 2.45
2564 5184 7.472741 TCTTATATTATGGAACGGAGGGAGTA 58.527 38.462 0.00 0.00 0.00 2.59
2566 5186 6.628398 GCTCTTATATTATGGAACGGAGGGAG 60.628 46.154 0.00 0.00 0.00 4.30
2567 5187 5.187186 GCTCTTATATTATGGAACGGAGGGA 59.813 44.000 0.00 0.00 0.00 4.20
2568 5188 5.420409 GCTCTTATATTATGGAACGGAGGG 58.580 45.833 0.00 0.00 0.00 4.30
2569 5189 5.103000 CGCTCTTATATTATGGAACGGAGG 58.897 45.833 0.00 0.00 0.00 4.30
2570 5190 5.710984 ACGCTCTTATATTATGGAACGGAG 58.289 41.667 0.00 0.00 0.00 4.63
2571 5191 5.717078 ACGCTCTTATATTATGGAACGGA 57.283 39.130 0.00 0.00 0.00 4.69
2572 5192 6.780706 AAACGCTCTTATATTATGGAACGG 57.219 37.500 0.00 0.00 0.00 4.44
2573 5193 8.332464 TCAAAAACGCTCTTATATTATGGAACG 58.668 33.333 0.00 0.00 0.00 3.95
2585 5205 9.865321 AATACAGTAGTATCAAAAACGCTCTTA 57.135 29.630 0.00 0.00 40.00 2.10
2586 5206 8.773404 AATACAGTAGTATCAAAAACGCTCTT 57.227 30.769 0.00 0.00 40.00 2.85
2587 5207 8.773404 AAATACAGTAGTATCAAAAACGCTCT 57.227 30.769 0.00 0.00 40.00 4.09
2588 5208 8.870879 AGAAATACAGTAGTATCAAAAACGCTC 58.129 33.333 0.00 0.00 40.00 5.03
2589 5209 8.773404 AGAAATACAGTAGTATCAAAAACGCT 57.227 30.769 0.00 0.00 40.00 5.07
2590 5210 9.821662 AAAGAAATACAGTAGTATCAAAAACGC 57.178 29.630 0.00 0.00 40.00 4.84
2601 5221 9.628500 ACTTCAAAAGGAAAGAAATACAGTAGT 57.372 29.630 0.00 0.00 34.44 2.73
2602 5222 9.884465 CACTTCAAAAGGAAAGAAATACAGTAG 57.116 33.333 0.00 0.00 34.44 2.57
2603 5223 9.621629 TCACTTCAAAAGGAAAGAAATACAGTA 57.378 29.630 0.00 0.00 34.44 2.74
2604 5224 8.519799 TCACTTCAAAAGGAAAGAAATACAGT 57.480 30.769 0.00 0.00 34.44 3.55
2605 5225 9.455847 CTTCACTTCAAAAGGAAAGAAATACAG 57.544 33.333 0.00 0.00 34.44 2.74
2606 5226 8.966868 ACTTCACTTCAAAAGGAAAGAAATACA 58.033 29.630 9.10 0.00 34.44 2.29
2607 5227 9.803315 AACTTCACTTCAAAAGGAAAGAAATAC 57.197 29.630 9.10 0.00 34.44 1.89
2673 5293 4.019950 ACAGATGATGTGACCAGTTGATGA 60.020 41.667 0.00 0.00 41.91 2.92
2708 5343 8.631480 AGTATACGTCATACAATCAGGACATA 57.369 34.615 13.82 0.00 41.84 2.29
2737 5372 4.142469 ACTGAAAACTAAGCAAACAACGCT 60.142 37.500 0.00 0.00 42.98 5.07
2738 5373 4.102649 ACTGAAAACTAAGCAAACAACGC 58.897 39.130 0.00 0.00 0.00 4.84
2739 5374 6.626199 AAACTGAAAACTAAGCAAACAACG 57.374 33.333 0.00 0.00 0.00 4.10
2756 5459 7.223971 GTGCGGATAGAATGTTGTATAAACTGA 59.776 37.037 0.00 0.00 0.00 3.41
2757 5460 7.224753 AGTGCGGATAGAATGTTGTATAAACTG 59.775 37.037 0.00 0.00 0.00 3.16
2777 5480 6.313905 ACTGAACTAGATGAAAATAAGTGCGG 59.686 38.462 0.00 0.00 0.00 5.69
2845 5549 7.503566 CCTTGTATATCTGTCCATCCATTGTTT 59.496 37.037 0.00 0.00 0.00 2.83
2880 5584 7.131302 ATCACCTCTTGATCACGGAAGTACC 62.131 48.000 10.88 0.00 41.53 3.34
2986 6325 5.556355 TGACTGATTGATTGTTGATCAGC 57.444 39.130 11.34 2.05 46.72 4.26
2988 6327 7.748691 TTCTTGACTGATTGATTGTTGATCA 57.251 32.000 0.00 0.00 42.95 2.92
3076 6415 1.549170 ACGTATTTCGGTGAGGCTCTT 59.451 47.619 16.72 0.00 44.69 2.85
3086 6425 3.566523 GATCTCTAGGCACGTATTTCGG 58.433 50.000 0.00 0.00 44.69 4.30
3103 6443 3.510388 TCTTCATGCTCGAAACGATCT 57.490 42.857 0.00 0.00 34.61 2.75
3106 6446 2.066262 GGTTCTTCATGCTCGAAACGA 58.934 47.619 0.00 0.00 0.00 3.85
3108 6448 1.128692 CGGGTTCTTCATGCTCGAAAC 59.871 52.381 0.00 0.00 0.00 2.78
3116 6456 2.213499 GTCTATGCCGGGTTCTTCATG 58.787 52.381 2.18 0.00 0.00 3.07
3123 6463 2.186903 CTGCGTCTATGCCGGGTT 59.813 61.111 2.18 0.00 0.00 4.11
3125 6465 2.279517 GACTGCGTCTATGCCGGG 60.280 66.667 2.18 0.00 0.00 5.73
3126 6466 1.148157 CTTGACTGCGTCTATGCCGG 61.148 60.000 0.00 0.00 33.15 6.13
3127 6467 1.148157 CCTTGACTGCGTCTATGCCG 61.148 60.000 9.49 0.00 33.15 5.69
3128 6468 0.108138 ACCTTGACTGCGTCTATGCC 60.108 55.000 9.49 0.00 33.15 4.40
3129 6469 2.194271 GTACCTTGACTGCGTCTATGC 58.806 52.381 9.49 0.00 33.15 3.14
3130 6470 3.128764 TCTGTACCTTGACTGCGTCTATG 59.871 47.826 9.49 3.21 33.15 2.23
3131 6471 3.353557 TCTGTACCTTGACTGCGTCTAT 58.646 45.455 9.49 0.00 33.15 1.98
3132 6472 2.747989 CTCTGTACCTTGACTGCGTCTA 59.252 50.000 9.49 2.46 33.15 2.59
3133 6473 1.542030 CTCTGTACCTTGACTGCGTCT 59.458 52.381 9.49 0.00 33.15 4.18
3134 6474 1.983972 CTCTGTACCTTGACTGCGTC 58.016 55.000 0.00 2.32 0.00 5.19
3135 6475 0.038159 GCTCTGTACCTTGACTGCGT 60.038 55.000 0.00 0.00 0.00 5.24
3136 6476 0.038251 TGCTCTGTACCTTGACTGCG 60.038 55.000 0.00 0.00 0.00 5.18
3137 6477 2.275318 GATGCTCTGTACCTTGACTGC 58.725 52.381 0.00 0.00 0.00 4.40
3138 6478 3.519579 CTGATGCTCTGTACCTTGACTG 58.480 50.000 0.00 0.00 0.00 3.51
3139 6479 2.499289 CCTGATGCTCTGTACCTTGACT 59.501 50.000 0.00 0.00 0.00 3.41
3140 6480 2.234908 ACCTGATGCTCTGTACCTTGAC 59.765 50.000 0.00 0.00 0.00 3.18
3141 6481 2.540383 ACCTGATGCTCTGTACCTTGA 58.460 47.619 0.00 0.00 0.00 3.02
3142 6482 4.679373 ATACCTGATGCTCTGTACCTTG 57.321 45.455 0.00 0.00 0.00 3.61
3143 6483 6.554982 TCATTATACCTGATGCTCTGTACCTT 59.445 38.462 0.00 0.00 0.00 3.50
3144 6484 6.077993 TCATTATACCTGATGCTCTGTACCT 58.922 40.000 0.00 0.00 0.00 3.08
3145 6485 6.346477 TCATTATACCTGATGCTCTGTACC 57.654 41.667 0.00 0.00 0.00 3.34
3146 6486 9.579768 CTTATCATTATACCTGATGCTCTGTAC 57.420 37.037 7.08 0.00 35.12 2.90
3147 6487 9.533831 TCTTATCATTATACCTGATGCTCTGTA 57.466 33.333 7.08 0.00 35.12 2.74
3148 6488 8.427902 TCTTATCATTATACCTGATGCTCTGT 57.572 34.615 7.08 0.00 35.12 3.41
3149 6489 8.747471 TCTCTTATCATTATACCTGATGCTCTG 58.253 37.037 7.08 0.00 35.12 3.35
3150 6490 8.891985 TCTCTTATCATTATACCTGATGCTCT 57.108 34.615 7.08 0.00 35.12 4.09
3153 6493 9.323985 GGATTCTCTTATCATTATACCTGATGC 57.676 37.037 7.08 0.00 35.12 3.91
3156 6496 9.607333 ACAGGATTCTCTTATCATTATACCTGA 57.393 33.333 0.50 0.00 41.36 3.86
3157 6497 9.650539 CACAGGATTCTCTTATCATTATACCTG 57.349 37.037 0.00 0.00 43.47 4.00
3158 6498 8.820831 CCACAGGATTCTCTTATCATTATACCT 58.179 37.037 0.00 0.00 0.00 3.08
3159 6499 8.043710 CCCACAGGATTCTCTTATCATTATACC 58.956 40.741 0.00 0.00 33.47 2.73
3160 6500 7.550906 GCCCACAGGATTCTCTTATCATTATAC 59.449 40.741 0.00 0.00 33.47 1.47
3161 6501 7.579531 CGCCCACAGGATTCTCTTATCATTATA 60.580 40.741 0.00 0.00 33.47 0.98
3162 6502 6.479884 GCCCACAGGATTCTCTTATCATTAT 58.520 40.000 0.00 0.00 33.47 1.28
3163 6503 5.511373 CGCCCACAGGATTCTCTTATCATTA 60.511 44.000 0.00 0.00 33.47 1.90
3164 6504 4.723309 GCCCACAGGATTCTCTTATCATT 58.277 43.478 0.00 0.00 33.47 2.57
3172 6512 2.109126 GTGCGCCCACAGGATTCTC 61.109 63.158 4.18 0.00 41.67 2.87
3204 6544 2.851263 AGTTCTAAACATGTGGCCGA 57.149 45.000 0.00 0.00 0.00 5.54
3217 6557 1.919240 TCTGCCTGTCCGAAGTTCTA 58.081 50.000 0.56 0.00 0.00 2.10
3275 6619 1.669999 CCCATACAAGCAAGCTGGCC 61.670 60.000 10.23 0.00 0.00 5.36
3282 6626 2.371841 AGTGAGTGACCCATACAAGCAA 59.628 45.455 0.00 0.00 0.00 3.91
3411 6755 5.122519 TCTTCAGTGCACATCTTGTTACAA 58.877 37.500 21.04 0.00 0.00 2.41
3423 6767 1.598924 GCTGCAACTTCTTCAGTGCAC 60.599 52.381 9.40 9.40 35.73 4.57
3459 6803 1.466025 TTGGGCCTTCTTTGCTGCTG 61.466 55.000 4.53 0.00 0.00 4.41
3461 6805 1.291272 CTTGGGCCTTCTTTGCTGC 59.709 57.895 4.53 0.00 0.00 5.25
3466 6810 2.745968 TGTTCAACTTGGGCCTTCTTT 58.254 42.857 4.53 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.