Multiple sequence alignment - TraesCS5D01G155000

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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 TraesCS5D01G155000 chr5D 100.000 3110 0 0 1 3110 243218857 243221966 0.000000e+00 5744.0
1 TraesCS5D01G155000 chr5D 79.757 494 84 13 4 490 373201459 373201943 8.260000e-91 344.0
2 TraesCS5D01G155000 chr5D 82.353 408 51 11 2528 2933 35497904 35497516 4.970000e-88 335.0
3 TraesCS5D01G155000 chr5D 78.711 512 96 10 4 508 215872891 215872386 2.310000e-86 329.0
4 TraesCS5D01G155000 chr5B 93.184 2362 111 17 4 2326 255201591 255199241 0.000000e+00 3424.0
5 TraesCS5D01G155000 chr5B 84.261 629 56 7 2484 3110 255198590 255198003 9.670000e-160 573.0
6 TraesCS5D01G155000 chr5B 79.637 496 90 9 1 491 6724006 6724495 2.300000e-91 346.0
7 TraesCS5D01G155000 chr5B 79.435 496 91 9 1 491 6710904 6711393 1.070000e-89 340.0
8 TraesCS5D01G155000 chr5B 93.382 136 6 1 2319 2454 255199064 255198932 6.800000e-47 198.0
9 TraesCS5D01G155000 chr5B 82.723 191 30 2 2661 2850 48849130 48848942 1.920000e-37 167.0
10 TraesCS5D01G155000 chr5A 93.463 2050 79 30 513 2525 308377365 308375334 0.000000e+00 2992.0
11 TraesCS5D01G155000 chr5A 80.741 270 36 7 2527 2796 24061148 24060895 2.450000e-46 196.0
12 TraesCS5D01G155000 chr3A 84.516 930 125 15 1124 2048 575948930 575948015 0.000000e+00 902.0
13 TraesCS5D01G155000 chr3D 84.301 930 127 15 1124 2048 437779356 437778441 0.000000e+00 891.0
14 TraesCS5D01G155000 chr3B 83.978 930 130 14 1124 2048 572936854 572935939 0.000000e+00 874.0
15 TraesCS5D01G155000 chr3B 81.964 499 63 13 2527 3018 642871778 642872256 6.250000e-107 398.0
16 TraesCS5D01G155000 chr3B 78.088 502 83 11 2528 3022 728986498 728986017 3.030000e-75 292.0
17 TraesCS5D01G155000 chr1D 82.777 958 148 12 1091 2044 406973072 406974016 0.000000e+00 839.0
18 TraesCS5D01G155000 chr1D 79.651 516 89 15 1 508 343262050 343262557 1.060000e-94 357.0
19 TraesCS5D01G155000 chr1D 93.750 48 3 0 2479 2526 449595571 449595524 4.300000e-09 73.1
20 TraesCS5D01G155000 chr1D 91.837 49 4 0 2480 2528 478036333 478036285 5.570000e-08 69.4
21 TraesCS5D01G155000 chr1A 82.568 958 150 12 1091 2044 502677773 502678717 0.000000e+00 828.0
22 TraesCS5D01G155000 chr1A 95.652 46 2 0 2481 2526 53435291 53435336 1.200000e-09 75.0
23 TraesCS5D01G155000 chr1B 82.150 958 154 12 1091 2044 547281839 547282783 0.000000e+00 806.0
24 TraesCS5D01G155000 chr7B 86.124 418 55 3 4 419 126999095 126998679 6.120000e-122 448.0
25 TraesCS5D01G155000 chr7B 77.238 391 61 25 2660 3031 739961700 739962081 1.460000e-48 204.0
26 TraesCS5D01G155000 chr7B 80.682 88 15 2 2522 2608 568150367 568150453 2.000000e-07 67.6
27 TraesCS5D01G155000 chr4D 83.252 412 64 5 82 491 493927743 493927335 1.050000e-99 374.0
28 TraesCS5D01G155000 chr4D 75.615 447 82 22 2660 3095 277343334 277343764 2.450000e-46 196.0
29 TraesCS5D01G155000 chrUn 79.513 493 90 9 4 491 423979197 423978711 1.070000e-89 340.0
30 TraesCS5D01G155000 chr7A 80.144 277 50 5 2660 2933 637317686 637317412 5.260000e-48 202.0
31 TraesCS5D01G155000 chr7A 91.304 46 4 0 514 559 317900008 317899963 2.590000e-06 63.9
32 TraesCS5D01G155000 chr7D 76.109 293 46 13 2521 2809 17243064 17242792 7.000000e-27 132.0
33 TraesCS5D01G155000 chr7D 95.745 47 2 0 2480 2526 60301209 60301163 3.330000e-10 76.8
34 TraesCS5D01G155000 chr7D 83.333 66 9 2 2475 2538 563440142 563440207 3.350000e-05 60.2
35 TraesCS5D01G155000 chr2A 95.745 47 2 0 2479 2525 59705301 59705255 3.330000e-10 76.8
36 TraesCS5D01G155000 chr2A 95.349 43 2 0 2527 2569 366414164 366414206 5.570000e-08 69.4
37 TraesCS5D01G155000 chr6B 89.655 58 4 2 2481 2536 604077087 604077030 4.300000e-09 73.1
38 TraesCS5D01G155000 chr6B 92.157 51 3 1 2475 2525 597082327 597082376 1.550000e-08 71.3
39 TraesCS5D01G155000 chr6B 91.489 47 4 0 2522 2568 115236707 115236661 7.200000e-07 65.8
40 TraesCS5D01G155000 chr2D 87.273 55 7 0 2522 2576 82663658 82663712 2.590000e-06 63.9
41 TraesCS5D01G155000 chr4B 86.792 53 6 1 2517 2569 532459823 532459874 1.200000e-04 58.4
42 TraesCS5D01G155000 chr6A 87.500 48 6 0 2522 2569 55618155 55618108 4.330000e-04 56.5


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 TraesCS5D01G155000 chr5D 243218857 243221966 3109 False 5744.000000 5744 100.000000 1 3110 1 chr5D.!!$F1 3109
1 TraesCS5D01G155000 chr5D 215872386 215872891 505 True 329.000000 329 78.711000 4 508 1 chr5D.!!$R2 504
2 TraesCS5D01G155000 chr5B 255198003 255201591 3588 True 1398.333333 3424 90.275667 4 3110 3 chr5B.!!$R2 3106
3 TraesCS5D01G155000 chr5A 308375334 308377365 2031 True 2992.000000 2992 93.463000 513 2525 1 chr5A.!!$R2 2012
4 TraesCS5D01G155000 chr3A 575948015 575948930 915 True 902.000000 902 84.516000 1124 2048 1 chr3A.!!$R1 924
5 TraesCS5D01G155000 chr3D 437778441 437779356 915 True 891.000000 891 84.301000 1124 2048 1 chr3D.!!$R1 924
6 TraesCS5D01G155000 chr3B 572935939 572936854 915 True 874.000000 874 83.978000 1124 2048 1 chr3B.!!$R1 924
7 TraesCS5D01G155000 chr1D 406973072 406974016 944 False 839.000000 839 82.777000 1091 2044 1 chr1D.!!$F2 953
8 TraesCS5D01G155000 chr1D 343262050 343262557 507 False 357.000000 357 79.651000 1 508 1 chr1D.!!$F1 507
9 TraesCS5D01G155000 chr1A 502677773 502678717 944 False 828.000000 828 82.568000 1091 2044 1 chr1A.!!$F2 953
10 TraesCS5D01G155000 chr1B 547281839 547282783 944 False 806.000000 806 82.150000 1091 2044 1 chr1B.!!$F1 953

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
507 514 0.109039 AACGGTGTGCACAACCAAAC 60.109 50.0 28.5 11.7 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2261 2.918571 GCTTTTGCTTTTGGAGGGC 58.081 52.632 0.0 0.0 43.35 5.19 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
48 49 3.562557 AGTTTTAGGGTACAAGCACAACG 59.437 43.478 0.00 0.00 0.00 4.10
49 50 2.172851 TTAGGGTACAAGCACAACGG 57.827 50.000 0.00 0.00 0.00 4.44
50 51 1.050204 TAGGGTACAAGCACAACGGT 58.950 50.000 0.00 0.00 0.00 4.83
67 72 2.299297 ACGGTCACAGAGGGTTTAAGAG 59.701 50.000 0.00 0.00 0.00 2.85
77 82 2.092375 AGGGTTTAAGAGTAGGCATGCC 60.092 50.000 30.12 30.12 0.00 4.40
113 118 3.260740 CTCCAAGTTTGTGCAAAAGCAA 58.739 40.909 6.22 0.00 31.33 3.91
155 160 2.288825 TGACAAGGTGGATCGTCAGTTC 60.289 50.000 0.00 0.00 33.61 3.01
195 200 1.079405 TTCGTCCAGTTCATCGCCC 60.079 57.895 0.00 0.00 0.00 6.13
209 214 2.186160 CGCCCTTGCAGTGTTGTGA 61.186 57.895 0.00 0.00 37.32 3.58
217 222 0.248054 GCAGTGTTGTGACGTTGGTG 60.248 55.000 0.00 0.00 0.00 4.17
224 229 1.590525 GTGACGTTGGTGTGCTCGA 60.591 57.895 0.00 0.00 0.00 4.04
231 236 0.249699 TTGGTGTGCTCGACGTGATT 60.250 50.000 0.00 0.00 0.00 2.57
244 249 5.886992 TCGACGTGATTGTGTGTAAGATAT 58.113 37.500 0.00 0.00 0.00 1.63
267 272 7.753309 ATAGTAGTAGTGGTAAGCTCATCAG 57.247 40.000 0.00 0.00 0.00 2.90
273 278 2.103263 GTGGTAAGCTCATCAGGTAGGG 59.897 54.545 0.00 0.00 0.00 3.53
284 289 5.030147 TCATCAGGTAGGGTACAAAGTGAT 58.970 41.667 0.00 0.00 0.00 3.06
296 301 7.399191 AGGGTACAAAGTGATCACAACTCTATA 59.601 37.037 27.02 7.66 0.00 1.31
297 302 7.491696 GGGTACAAAGTGATCACAACTCTATAC 59.508 40.741 27.02 17.16 0.00 1.47
300 305 7.030165 ACAAAGTGATCACAACTCTATACTCG 58.970 38.462 27.02 3.83 0.00 4.18
314 319 5.968254 TCTATACTCGTATGCAACCAAACA 58.032 37.500 0.00 0.00 0.00 2.83
319 324 3.129109 TCGTATGCAACCAAACAACGTA 58.871 40.909 0.00 0.00 0.00 3.57
320 325 3.747010 TCGTATGCAACCAAACAACGTAT 59.253 39.130 0.00 0.00 0.00 3.06
329 334 5.856126 ACCAAACAACGTATACTCATGTG 57.144 39.130 0.56 0.00 0.00 3.21
332 337 6.312918 ACCAAACAACGTATACTCATGTGATC 59.687 38.462 0.94 0.00 0.00 2.92
334 339 7.011389 CCAAACAACGTATACTCATGTGATCAT 59.989 37.037 0.00 0.00 34.21 2.45
353 358 5.079689 TCATAGACAATACGAGCAACCAA 57.920 39.130 0.00 0.00 0.00 3.67
359 364 3.568007 ACAATACGAGCAACCAAACACAT 59.432 39.130 0.00 0.00 0.00 3.21
363 368 2.946329 ACGAGCAACCAAACACATTACA 59.054 40.909 0.00 0.00 0.00 2.41
367 372 5.640732 GAGCAACCAAACACATTACATAGG 58.359 41.667 0.00 0.00 0.00 2.57
368 373 5.321102 AGCAACCAAACACATTACATAGGA 58.679 37.500 0.00 0.00 0.00 2.94
386 391 3.984508 GGAGCGTTGCTACTATACAGA 57.015 47.619 0.00 0.00 39.88 3.41
387 392 3.891324 GGAGCGTTGCTACTATACAGAG 58.109 50.000 0.00 0.00 39.88 3.35
389 394 4.036498 GGAGCGTTGCTACTATACAGAGAA 59.964 45.833 0.00 0.00 39.88 2.87
392 397 5.357314 AGCGTTGCTACTATACAGAGAAAGA 59.643 40.000 0.00 0.00 36.99 2.52
400 405 9.352784 GCTACTATACAGAGAAAGAATATGCAG 57.647 37.037 0.00 0.00 0.00 4.41
401 406 9.853555 CTACTATACAGAGAAAGAATATGCAGG 57.146 37.037 0.00 0.00 0.00 4.85
413 418 4.652421 AGAATATGCAGGCAACCAATCAAT 59.348 37.500 0.00 0.00 37.17 2.57
432 437 8.491152 CAATCAATATACAGACGATGGTTCTTC 58.509 37.037 0.00 0.00 0.00 2.87
433 438 6.206498 TCAATATACAGACGATGGTTCTTCG 58.794 40.000 0.00 2.41 42.20 3.79
434 439 2.273370 TACAGACGATGGTTCTTCGC 57.727 50.000 0.00 0.00 40.19 4.70
435 440 0.732880 ACAGACGATGGTTCTTCGCG 60.733 55.000 0.00 0.00 40.19 5.87
436 441 0.732880 CAGACGATGGTTCTTCGCGT 60.733 55.000 5.77 0.00 40.19 6.01
437 442 0.732880 AGACGATGGTTCTTCGCGTG 60.733 55.000 5.77 0.00 40.19 5.34
454 459 2.288666 CGTGCATATGCTTAACCAGGT 58.711 47.619 27.13 0.00 42.66 4.00
455 460 2.287915 CGTGCATATGCTTAACCAGGTC 59.712 50.000 27.13 5.45 42.66 3.85
456 461 3.278574 GTGCATATGCTTAACCAGGTCA 58.721 45.455 27.13 0.47 42.66 4.02
457 462 3.885297 GTGCATATGCTTAACCAGGTCAT 59.115 43.478 27.13 0.00 42.66 3.06
458 463 5.063204 GTGCATATGCTTAACCAGGTCATA 58.937 41.667 27.13 0.00 42.66 2.15
459 464 5.707298 GTGCATATGCTTAACCAGGTCATAT 59.293 40.000 27.13 5.90 42.66 1.78
461 466 7.065085 GTGCATATGCTTAACCAGGTCATATAG 59.935 40.741 27.13 7.26 42.66 1.31
462 467 7.106239 GCATATGCTTAACCAGGTCATATAGT 58.894 38.462 20.64 0.00 38.21 2.12
464 469 6.747414 ATGCTTAACCAGGTCATATAGTGA 57.253 37.500 0.00 0.00 0.00 3.41
492 499 7.810759 ACAAATATGTAAAGTGCCTAAAAACGG 59.189 33.333 0.00 0.00 38.24 4.44
497 504 0.666374 AGTGCCTAAAAACGGTGTGC 59.334 50.000 0.00 0.00 0.00 4.57
507 514 0.109039 AACGGTGTGCACAACCAAAC 60.109 50.000 28.50 11.70 0.00 2.93
508 515 0.963355 ACGGTGTGCACAACCAAACT 60.963 50.000 28.50 3.66 0.00 2.66
544 561 1.227002 GGAAAGAGGCCTACGCTCG 60.227 63.158 4.42 0.00 34.44 5.03
559 576 1.068753 CTCGAGCCAATCCAGCGAT 59.931 57.895 0.00 0.00 34.64 4.58
566 584 0.374758 CCAATCCAGCGATGTTGACG 59.625 55.000 5.66 0.00 0.00 4.35
751 778 0.972134 TCAGAGAGCTGACCTTGGTG 59.028 55.000 0.00 0.00 45.88 4.17
921 966 0.179134 GCGCGTCTCCTAGTCAACAT 60.179 55.000 8.43 0.00 0.00 2.71
922 967 1.828832 CGCGTCTCCTAGTCAACATC 58.171 55.000 0.00 0.00 0.00 3.06
923 968 1.132453 CGCGTCTCCTAGTCAACATCA 59.868 52.381 0.00 0.00 0.00 3.07
924 969 2.223595 CGCGTCTCCTAGTCAACATCAT 60.224 50.000 0.00 0.00 0.00 2.45
925 970 3.003378 CGCGTCTCCTAGTCAACATCATA 59.997 47.826 0.00 0.00 0.00 2.15
964 1009 2.034221 GGGAGCTTCACCACCACC 59.966 66.667 0.00 0.00 0.00 4.61
1116 1163 4.363990 AGGTCCGTGCTGCTGTCG 62.364 66.667 0.00 3.47 0.00 4.35
1146 1193 2.821366 GCGGTGTGGATCAGCCTG 60.821 66.667 0.00 0.00 40.98 4.85
1188 1235 1.933021 ACAAGTACATCCTCGACCCA 58.067 50.000 0.00 0.00 0.00 4.51
1298 1345 3.060615 CTTCGTCGACCTCCCCGT 61.061 66.667 10.58 0.00 0.00 5.28
2161 2277 0.692419 TGGGCCCTCCAAAAGCAAAA 60.692 50.000 25.70 0.00 43.84 2.44
2237 2356 5.330233 TCAGCCATAGGATATCCGAACTAA 58.670 41.667 16.21 0.00 42.08 2.24
2244 2364 9.021807 CCATAGGATATCCGAACTAAGAGTTAA 57.978 37.037 16.21 0.00 38.80 2.01
2249 2369 9.930693 GGATATCCGAACTAAGAGTTAATTCAT 57.069 33.333 5.86 0.00 38.80 2.57
2316 2441 5.631512 TGATTGGCATTTGTTTTAAGCGTAC 59.368 36.000 0.00 0.00 0.00 3.67
2446 2759 1.350193 CGAGCAACGAGTGTAGCATT 58.650 50.000 0.00 0.00 45.77 3.56
2479 2806 1.599606 AACACCACCGCAAAGCAACA 61.600 50.000 0.00 0.00 0.00 3.33
2486 3116 1.196808 ACCGCAAAGCAACATACTTCG 59.803 47.619 0.00 0.00 0.00 3.79
2565 3196 1.971481 TACGCGGAGGCTTATCAGTA 58.029 50.000 12.47 0.00 36.88 2.74
2566 3197 0.669077 ACGCGGAGGCTTATCAGTAG 59.331 55.000 12.47 0.00 36.88 2.57
2567 3198 0.664767 CGCGGAGGCTTATCAGTAGC 60.665 60.000 0.00 0.00 36.88 3.58
2568 3199 0.664767 GCGGAGGCTTATCAGTAGCG 60.665 60.000 0.00 0.00 39.54 4.26
2569 3200 0.039074 CGGAGGCTTATCAGTAGCGG 60.039 60.000 0.00 0.00 39.54 5.52
2570 3201 0.318762 GGAGGCTTATCAGTAGCGGG 59.681 60.000 0.00 0.00 39.54 6.13
2571 3202 0.318762 GAGGCTTATCAGTAGCGGGG 59.681 60.000 0.00 0.00 39.54 5.73
2572 3203 1.301795 GGCTTATCAGTAGCGGGGC 60.302 63.158 0.00 0.00 39.54 5.80
2573 3204 1.301795 GCTTATCAGTAGCGGGGCC 60.302 63.158 0.00 0.00 0.00 5.80
2574 3205 1.759459 GCTTATCAGTAGCGGGGCCT 61.759 60.000 0.84 0.00 0.00 5.19
2575 3206 1.629043 CTTATCAGTAGCGGGGCCTA 58.371 55.000 0.84 0.00 0.00 3.93
2576 3207 2.180276 CTTATCAGTAGCGGGGCCTAT 58.820 52.381 0.84 0.00 0.00 2.57
2577 3208 1.848652 TATCAGTAGCGGGGCCTATC 58.151 55.000 0.84 0.00 0.00 2.08
2578 3209 0.178932 ATCAGTAGCGGGGCCTATCA 60.179 55.000 0.84 0.00 0.00 2.15
2579 3210 0.827925 TCAGTAGCGGGGCCTATCAG 60.828 60.000 0.84 0.00 0.00 2.90
2702 3333 1.077212 CTGCTGCTAAGTGGGCCAT 60.077 57.895 10.70 0.00 0.00 4.40
2703 3334 1.378911 TGCTGCTAAGTGGGCCATG 60.379 57.895 10.70 1.65 0.00 3.66
2734 3365 2.028930 CCGGGTCTAGCCTTATTAGCAG 60.029 54.545 0.00 0.00 37.43 4.24
2735 3366 2.610727 CGGGTCTAGCCTTATTAGCAGC 60.611 54.545 3.66 0.00 37.43 5.25
2743 3374 1.268032 CCTTATTAGCAGCGCGGTTTG 60.268 52.381 8.73 0.00 0.00 2.93
2774 3405 4.038763 ACGCCACAACTAATATGCTAGCTA 59.961 41.667 17.23 6.33 0.00 3.32
2778 3409 7.324178 GCCACAACTAATATGCTAGCTATAGT 58.676 38.462 17.23 14.63 0.00 2.12
2780 3411 8.307483 CCACAACTAATATGCTAGCTATAGTGT 58.693 37.037 17.23 14.14 0.00 3.55
2816 3447 1.256376 CGCTGCTACTAAATCTGCACG 59.744 52.381 0.00 0.00 0.00 5.34
2844 3475 0.614415 TGGTGGGCCCAAATTAGCAG 60.614 55.000 30.64 0.00 41.50 4.24
2870 3501 2.740055 GGTGCCAGACGAGTGCTG 60.740 66.667 0.00 0.00 0.00 4.41
2872 3503 4.687215 TGCCAGACGAGTGCTGCC 62.687 66.667 0.00 0.00 32.06 4.85
2877 3508 2.881352 GACGAGTGCTGCCGCTAC 60.881 66.667 0.70 0.00 36.97 3.58
2888 3519 0.533491 TGCCGCTACGTCCATTAACT 59.467 50.000 0.00 0.00 0.00 2.24
2889 3520 0.928229 GCCGCTACGTCCATTAACTG 59.072 55.000 0.00 0.00 0.00 3.16
2896 3527 0.570734 CGTCCATTAACTGTAGCGCG 59.429 55.000 0.00 0.00 0.00 6.86
2937 3569 6.239232 GCTACTGCTAAGCCACCTTATACTAA 60.239 42.308 0.00 0.00 33.31 2.24
2966 3598 0.546747 TCGGTTTCCTCCCTCACCAT 60.547 55.000 0.00 0.00 0.00 3.55
2970 3602 2.576648 GGTTTCCTCCCTCACCATACTT 59.423 50.000 0.00 0.00 0.00 2.24
2988 3620 7.668052 ACCATACTTACTCTCACTCCATATCTC 59.332 40.741 0.00 0.00 0.00 2.75
2992 3624 4.534647 ACTCTCACTCCATATCTCTGGT 57.465 45.455 0.00 0.00 37.57 4.00
2996 3628 3.106827 TCACTCCATATCTCTGGTGCAA 58.893 45.455 0.00 0.00 37.57 4.08
3001 3633 2.812591 CCATATCTCTGGTGCAATGCTC 59.187 50.000 6.82 2.08 0.00 4.26
3016 3648 4.838486 CTCTCTGGTCGCCGTCGC 62.838 72.222 0.00 0.00 35.26 5.19
3037 3669 4.552365 CCATCGCCGCCCATCACT 62.552 66.667 0.00 0.00 0.00 3.41
3038 3670 3.274586 CATCGCCGCCCATCACTG 61.275 66.667 0.00 0.00 0.00 3.66
3039 3671 3.785859 ATCGCCGCCCATCACTGT 61.786 61.111 0.00 0.00 0.00 3.55
3040 3672 3.740128 ATCGCCGCCCATCACTGTC 62.740 63.158 0.00 0.00 0.00 3.51
3041 3673 4.758251 CGCCGCCCATCACTGTCA 62.758 66.667 0.00 0.00 0.00 3.58
3046 3678 2.268920 CCCATCACTGTCACCCGG 59.731 66.667 0.00 0.00 0.00 5.73
3050 3682 3.296709 ATCACTGTCACCCGGCGTC 62.297 63.158 6.01 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.701651 TGTTCATTACAAGCTTCCCATGAG 59.298 41.667 0.00 0.00 32.64 2.90
48 49 4.081586 CCTACTCTTAAACCCTCTGTGACC 60.082 50.000 0.00 0.00 0.00 4.02
49 50 4.621038 GCCTACTCTTAAACCCTCTGTGAC 60.621 50.000 0.00 0.00 0.00 3.67
50 51 3.514309 GCCTACTCTTAAACCCTCTGTGA 59.486 47.826 0.00 0.00 0.00 3.58
67 72 0.392461 TTCTTCCACGGCATGCCTAC 60.392 55.000 33.07 8.82 0.00 3.18
77 82 2.743636 TGGAGTAAGCTTCTTCCACG 57.256 50.000 21.72 0.00 0.00 4.94
113 118 3.131709 ACTTCAACACTGCTACATGCT 57.868 42.857 0.00 0.00 43.37 3.79
155 160 2.099141 TGATGAAGTTCTTCAGCCCG 57.901 50.000 22.24 0.00 36.59 6.13
195 200 1.531677 CCAACGTCACAACACTGCAAG 60.532 52.381 0.00 0.00 42.29 4.01
209 214 2.657296 CGTCGAGCACACCAACGT 60.657 61.111 0.00 0.00 0.00 3.99
217 222 0.161658 CACACAATCACGTCGAGCAC 59.838 55.000 0.00 0.00 0.00 4.40
224 229 8.900781 ACTACTATATCTTACACACAATCACGT 58.099 33.333 0.00 0.00 0.00 4.49
244 249 6.062749 CCTGATGAGCTTACCACTACTACTA 58.937 44.000 0.00 0.00 0.00 1.82
260 265 4.466370 TCACTTTGTACCCTACCTGATGAG 59.534 45.833 0.00 0.00 0.00 2.90
267 272 4.546829 TGTGATCACTTTGTACCCTACC 57.453 45.455 25.55 0.00 0.00 3.18
273 278 9.291664 GAGTATAGAGTTGTGATCACTTTGTAC 57.708 37.037 25.55 17.06 0.00 2.90
284 289 6.263344 GTTGCATACGAGTATAGAGTTGTGA 58.737 40.000 0.00 0.00 0.00 3.58
296 301 2.032377 CGTTGTTTGGTTGCATACGAGT 60.032 45.455 0.00 0.00 0.00 4.18
297 302 2.032377 ACGTTGTTTGGTTGCATACGAG 60.032 45.455 0.00 0.00 0.00 4.18
300 305 6.128499 TGAGTATACGTTGTTTGGTTGCATAC 60.128 38.462 0.00 0.00 0.00 2.39
314 319 8.166422 TGTCTATGATCACATGAGTATACGTT 57.834 34.615 0.00 0.00 37.87 3.99
319 324 9.014297 TCGTATTGTCTATGATCACATGAGTAT 57.986 33.333 0.00 0.00 37.87 2.12
320 325 8.391075 TCGTATTGTCTATGATCACATGAGTA 57.609 34.615 0.00 0.00 37.87 2.59
329 334 5.289595 TGGTTGCTCGTATTGTCTATGATC 58.710 41.667 0.00 0.00 0.00 2.92
332 337 5.121611 TGTTTGGTTGCTCGTATTGTCTATG 59.878 40.000 0.00 0.00 0.00 2.23
334 339 4.449743 GTGTTTGGTTGCTCGTATTGTCTA 59.550 41.667 0.00 0.00 0.00 2.59
353 358 3.374058 GCAACGCTCCTATGTAATGTGTT 59.626 43.478 0.00 0.00 32.55 3.32
359 364 6.487668 TGTATAGTAGCAACGCTCCTATGTAA 59.512 38.462 10.36 0.00 38.09 2.41
363 368 5.314529 TCTGTATAGTAGCAACGCTCCTAT 58.685 41.667 6.37 6.37 40.15 2.57
367 372 4.815040 TCTCTGTATAGTAGCAACGCTC 57.185 45.455 0.00 0.00 40.44 5.03
368 373 5.357314 TCTTTCTCTGTATAGTAGCAACGCT 59.643 40.000 0.00 0.00 43.41 5.07
379 384 7.066307 TGCCTGCATATTCTTTCTCTGTATA 57.934 36.000 0.00 0.00 0.00 1.47
382 387 4.226427 TGCCTGCATATTCTTTCTCTGT 57.774 40.909 0.00 0.00 0.00 3.41
386 391 3.700538 TGGTTGCCTGCATATTCTTTCT 58.299 40.909 0.00 0.00 0.00 2.52
387 392 4.454728 TTGGTTGCCTGCATATTCTTTC 57.545 40.909 0.00 0.00 0.00 2.62
389 394 4.025360 TGATTGGTTGCCTGCATATTCTT 58.975 39.130 0.00 0.00 0.00 2.52
392 397 6.675413 ATATTGATTGGTTGCCTGCATATT 57.325 33.333 0.00 0.00 0.00 1.28
400 405 4.814234 TCGTCTGTATATTGATTGGTTGCC 59.186 41.667 0.00 0.00 0.00 4.52
401 406 5.984233 TCGTCTGTATATTGATTGGTTGC 57.016 39.130 0.00 0.00 0.00 4.17
413 418 3.547413 CGCGAAGAACCATCGTCTGTATA 60.547 47.826 0.00 0.00 42.15 1.47
432 437 0.655208 TGGTTAAGCATATGCACGCG 59.345 50.000 28.62 3.53 45.16 6.01
433 438 1.002468 CCTGGTTAAGCATATGCACGC 60.002 52.381 28.62 15.05 45.16 5.34
434 439 2.287915 GACCTGGTTAAGCATATGCACG 59.712 50.000 28.62 8.99 45.16 5.34
435 440 3.278574 TGACCTGGTTAAGCATATGCAC 58.721 45.455 28.62 17.81 45.16 4.57
436 441 3.643199 TGACCTGGTTAAGCATATGCA 57.357 42.857 28.62 7.07 45.16 3.96
437 442 7.065085 CACTATATGACCTGGTTAAGCATATGC 59.935 40.741 20.36 20.36 42.49 3.14
457 462 9.542462 GGCACTTTACATATTTGTCTCACTATA 57.458 33.333 0.00 0.00 37.28 1.31
458 463 8.267894 AGGCACTTTACATATTTGTCTCACTAT 58.732 33.333 0.00 0.00 33.40 2.12
459 464 7.620880 AGGCACTTTACATATTTGTCTCACTA 58.379 34.615 0.00 0.00 33.40 2.74
461 466 6.743575 AGGCACTTTACATATTTGTCTCAC 57.256 37.500 0.00 0.00 33.40 3.51
462 467 8.856153 TTTAGGCACTTTACATATTTGTCTCA 57.144 30.769 0.00 0.00 41.75 3.27
464 469 9.908152 GTTTTTAGGCACTTTACATATTTGTCT 57.092 29.630 0.00 0.00 41.75 3.41
492 499 2.286184 CGACTAGTTTGGTTGTGCACAC 60.286 50.000 21.56 14.55 0.00 3.82
497 504 4.317839 CGAGTTTCGACTAGTTTGGTTGTG 60.318 45.833 0.00 0.00 43.74 3.33
507 514 0.179134 CCTGGCCGAGTTTCGACTAG 60.179 60.000 0.00 0.00 43.74 2.57
508 515 1.601419 CCCTGGCCGAGTTTCGACTA 61.601 60.000 0.00 0.00 43.74 2.59
544 561 0.379669 CAACATCGCTGGATTGGCTC 59.620 55.000 0.00 0.00 0.00 4.70
549 566 0.249120 TCCGTCAACATCGCTGGATT 59.751 50.000 0.00 0.00 0.00 3.01
566 584 2.347755 GCCACTCGATAAAACGTTCTCC 59.652 50.000 0.00 0.00 34.70 3.71
751 778 8.330302 GTGGTAGCAATTGCAATTGAAAATATC 58.670 33.333 42.21 29.48 46.72 1.63
921 966 1.141019 GCGGTGAGCTTCGGTATGA 59.859 57.895 0.00 0.00 44.04 2.15
922 967 2.230940 CGCGGTGAGCTTCGGTATG 61.231 63.158 0.00 0.00 45.59 2.39
923 968 2.104331 CGCGGTGAGCTTCGGTAT 59.896 61.111 0.00 0.00 45.59 2.73
924 969 4.789075 GCGCGGTGAGCTTCGGTA 62.789 66.667 8.83 0.00 45.59 4.02
1188 1235 1.276622 AGGGCCAGTCGTACATCTTT 58.723 50.000 6.18 0.00 0.00 2.52
2145 2261 2.918571 GCTTTTGCTTTTGGAGGGC 58.081 52.632 0.00 0.00 43.35 5.19
2161 2277 4.147321 ACTCTTTCAATCCATGTGTTGCT 58.853 39.130 0.00 0.00 0.00 3.91
2227 2346 9.099454 GAACATGAATTAACTCTTAGTTCGGAT 57.901 33.333 0.00 0.00 39.51 4.18
2237 2356 9.793252 GCATACAATTGAACATGAATTAACTCT 57.207 29.630 13.59 0.00 0.00 3.24
2413 2726 2.932614 GTTGCTCGCATCAAGTGATAGT 59.067 45.455 0.00 0.00 35.91 2.12
2446 2759 3.444388 GGTGGTGTTTGTCTTTGGTGTTA 59.556 43.478 0.00 0.00 0.00 2.41
2513 3144 7.989947 TCCCTAGTAGTGGTATTGAAATCTT 57.010 36.000 0.00 0.00 0.00 2.40
2548 3179 0.664767 GCTACTGATAAGCCTCCGCG 60.665 60.000 0.00 0.00 41.18 6.46
2551 3182 0.318762 CCCGCTACTGATAAGCCTCC 59.681 60.000 0.00 0.00 36.60 4.30
2552 3183 0.318762 CCCCGCTACTGATAAGCCTC 59.681 60.000 0.00 0.00 36.60 4.70
2565 3196 1.534235 CCTACTGATAGGCCCCGCT 60.534 63.158 0.00 0.00 41.80 5.52
2566 3197 3.060866 CCTACTGATAGGCCCCGC 58.939 66.667 0.00 0.00 41.80 6.13
2573 3204 6.001460 AGTTAGCAGTAGAGCCTACTGATAG 58.999 44.000 30.59 15.03 44.08 2.08
2574 3205 5.942961 AGTTAGCAGTAGAGCCTACTGATA 58.057 41.667 30.59 27.44 45.69 2.15
2575 3206 4.798882 AGTTAGCAGTAGAGCCTACTGAT 58.201 43.478 30.59 28.18 45.69 2.90
2576 3207 4.237976 AGTTAGCAGTAGAGCCTACTGA 57.762 45.455 30.59 17.09 45.69 3.41
2577 3208 5.682943 CTAGTTAGCAGTAGAGCCTACTG 57.317 47.826 25.84 25.84 45.62 2.74
2628 3259 3.696898 CGCTACTGCTAAGTCTTACCTG 58.303 50.000 0.00 0.00 37.88 4.00
2686 3317 1.077501 TCATGGCCCACTTAGCAGC 60.078 57.895 0.00 0.00 0.00 5.25
2743 3374 1.515081 TAGTTGTGGCGTGGTTTAGC 58.485 50.000 0.00 0.00 0.00 3.09
2751 3382 3.131396 GCTAGCATATTAGTTGTGGCGT 58.869 45.455 10.63 0.00 0.00 5.68
2755 3386 9.347934 GACACTATAGCTAGCATATTAGTTGTG 57.652 37.037 18.83 15.40 0.00 3.33
2829 3460 1.032794 GCTACTGCTAATTTGGGCCC 58.967 55.000 17.59 17.59 36.03 5.80
2833 3464 1.331756 CTGCCGCTACTGCTAATTTGG 59.668 52.381 0.00 0.00 36.97 3.28
2852 3483 2.919856 AGCACTCGTCTGGCACCT 60.920 61.111 0.00 0.00 0.00 4.00
2870 3501 0.928229 CAGTTAATGGACGTAGCGGC 59.072 55.000 0.00 0.00 0.00 6.53
2872 3503 2.787680 GCTACAGTTAATGGACGTAGCG 59.212 50.000 0.00 0.00 39.85 4.26
2877 3508 0.570734 CGCGCTACAGTTAATGGACG 59.429 55.000 5.56 0.00 0.00 4.79
2918 3549 4.639334 GGGTTAGTATAAGGTGGCTTAGC 58.361 47.826 0.00 0.00 0.00 3.09
2950 3582 4.470304 AGTAAGTATGGTGAGGGAGGAAAC 59.530 45.833 0.00 0.00 0.00 2.78
2966 3598 7.147284 ACCAGAGATATGGAGTGAGAGTAAGTA 60.147 40.741 0.00 0.00 43.57 2.24
2970 3602 5.380900 CACCAGAGATATGGAGTGAGAGTA 58.619 45.833 0.00 0.00 43.57 2.59
2988 3620 0.322277 ACCAGAGAGCATTGCACCAG 60.322 55.000 11.91 0.00 0.00 4.00
2992 3624 1.742880 GCGACCAGAGAGCATTGCA 60.743 57.895 11.91 0.00 0.00 4.08
2996 3628 3.069980 GACGGCGACCAGAGAGCAT 62.070 63.158 16.62 0.00 0.00 3.79
3025 3657 3.127533 GTGACAGTGATGGGCGGC 61.128 66.667 0.00 0.00 0.00 6.53
3031 3663 2.815211 CGCCGGGTGACAGTGATG 60.815 66.667 2.18 0.00 0.00 3.07
3032 3664 3.296709 GACGCCGGGTGACAGTGAT 62.297 63.158 15.77 0.00 0.00 3.06
3033 3665 3.986006 GACGCCGGGTGACAGTGA 61.986 66.667 15.77 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.