Multiple sequence alignment - TraesCS3A01G240600

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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 TraesCS3A01G240600 chr3A 100.000 5106 0 0 1 5106 451719695 451714590 0.000000e+00 9430.0
1 TraesCS3A01G240600 chr3A 94.217 1003 37 6 1 995 715976333 715977322 0.000000e+00 1511.0
2 TraesCS3A01G240600 chr3A 85.946 185 22 4 139 320 737131584 737131401 1.450000e-45 195.0
3 TraesCS3A01G240600 chr3A 91.304 69 6 0 926 994 715975809 715975741 1.510000e-15 95.3
4 TraesCS3A01G240600 chr3A 89.855 69 7 0 926 994 451720231 451720299 7.040000e-14 89.8
5 TraesCS3A01G240600 chr3D 97.952 1611 19 5 2531 4133 333514376 333512772 0.000000e+00 2780.0
6 TraesCS3A01G240600 chr3D 95.458 1387 48 11 994 2369 333515760 333514378 0.000000e+00 2198.0
7 TraesCS3A01G240600 chr3D 91.048 983 71 14 4134 5106 464115583 464114608 0.000000e+00 1312.0
8 TraesCS3A01G240600 chr3D 93.258 178 12 0 2357 2534 545912344 545912167 3.920000e-66 263.0
9 TraesCS3A01G240600 chr3D 86.339 183 23 2 140 320 462806149 462806331 1.120000e-46 198.0
10 TraesCS3A01G240600 chr3B 93.991 1631 47 25 2530 4133 432831845 432833451 0.000000e+00 2422.0
11 TraesCS3A01G240600 chr3B 94.981 1295 50 9 994 2278 432830536 432831825 0.000000e+00 2017.0
12 TraesCS3A01G240600 chr4A 93.402 970 34 8 1 962 436397188 436396241 0.000000e+00 1410.0
13 TraesCS3A01G240600 chr4A 91.048 983 75 7 4133 5106 190831944 190830966 0.000000e+00 1315.0
14 TraesCS3A01G240600 chr4A 88.396 991 94 17 4133 5106 720363484 720362498 0.000000e+00 1173.0
15 TraesCS3A01G240600 chr4A 91.304 69 6 0 926 994 436397715 436397783 1.510000e-15 95.3
16 TraesCS3A01G240600 chr1B 90.182 988 79 15 4134 5106 44501079 44502063 0.000000e+00 1271.0
17 TraesCS3A01G240600 chr1B 89.206 982 94 5 4134 5106 302501748 302502726 0.000000e+00 1216.0
18 TraesCS3A01G240600 chr7D 89.725 983 87 11 4134 5106 42907193 42908171 0.000000e+00 1243.0
19 TraesCS3A01G240600 chr7D 88.945 986 93 13 4134 5106 394018030 394019012 0.000000e+00 1203.0
20 TraesCS3A01G240600 chr7D 96.386 166 6 0 2368 2533 363148997 363148832 1.810000e-69 274.0
21 TraesCS3A01G240600 chr6D 89.115 983 90 14 4133 5106 235783427 235782453 0.000000e+00 1206.0
22 TraesCS3A01G240600 chr6D 94.798 173 9 0 2360 2532 8921599 8921427 2.340000e-68 270.0
23 TraesCS3A01G240600 chr6D 92.818 181 11 2 2356 2534 308588169 308587989 1.410000e-65 261.0
24 TraesCS3A01G240600 chr5B 89.001 991 87 13 4134 5106 609261281 609262267 0.000000e+00 1206.0
25 TraesCS3A01G240600 chr7A 87.648 842 74 13 1 822 235692088 235692919 0.000000e+00 952.0
26 TraesCS3A01G240600 chr7A 96.386 166 6 0 2368 2533 195397169 195397334 1.810000e-69 274.0
27 TraesCS3A01G240600 chr7A 86.294 197 22 3 2366 2558 569407196 569407001 5.180000e-50 209.0
28 TraesCS3A01G240600 chr7A 90.435 115 5 3 834 942 235692903 235693017 4.120000e-31 147.0
29 TraesCS3A01G240600 chrUn 100.000 394 0 0 3283 3676 479525700 479526093 0.000000e+00 728.0
30 TraesCS3A01G240600 chrUn 95.783 166 7 0 2367 2532 112299216 112299381 8.430000e-68 268.0
31 TraesCS3A01G240600 chr5D 95.238 168 8 0 2368 2535 491000573 491000740 3.030000e-67 267.0
32 TraesCS3A01G240600 chr5D 86.885 183 22 2 140 320 412064845 412064663 2.410000e-48 204.0
33 TraesCS3A01G240600 chr1D 95.238 168 8 0 2368 2535 286391231 286391064 3.030000e-67 267.0
34 TraesCS3A01G240600 chr4D 90.576 191 17 1 2358 2548 425058018 425057829 8.490000e-63 252.0
35 TraesCS3A01G240600 chr2B 86.413 184 22 3 140 320 689161362 689161545 1.120000e-46 198.0
36 TraesCS3A01G240600 chr2B 91.176 68 5 1 869 936 718216534 718216468 1.960000e-14 91.6
37 TraesCS3A01G240600 chr2A 86.022 186 22 4 138 320 266870397 266870581 4.030000e-46 196.0
38 TraesCS3A01G240600 chr6B 85.484 186 24 3 138 320 21108042 21107857 1.880000e-44 191.0


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 TraesCS3A01G240600 chr3A 451714590 451719695 5105 True 9430.0 9430 100.0000 1 5106 1 chr3A.!!$R1 5105
1 TraesCS3A01G240600 chr3A 715976333 715977322 989 False 1511.0 1511 94.2170 1 995 1 chr3A.!!$F2 994
2 TraesCS3A01G240600 chr3D 333512772 333515760 2988 True 2489.0 2780 96.7050 994 4133 2 chr3D.!!$R3 3139
3 TraesCS3A01G240600 chr3D 464114608 464115583 975 True 1312.0 1312 91.0480 4134 5106 1 chr3D.!!$R1 972
4 TraesCS3A01G240600 chr3B 432830536 432833451 2915 False 2219.5 2422 94.4860 994 4133 2 chr3B.!!$F1 3139
5 TraesCS3A01G240600 chr4A 436396241 436397188 947 True 1410.0 1410 93.4020 1 962 1 chr4A.!!$R2 961
6 TraesCS3A01G240600 chr4A 190830966 190831944 978 True 1315.0 1315 91.0480 4133 5106 1 chr4A.!!$R1 973
7 TraesCS3A01G240600 chr4A 720362498 720363484 986 True 1173.0 1173 88.3960 4133 5106 1 chr4A.!!$R3 973
8 TraesCS3A01G240600 chr1B 44501079 44502063 984 False 1271.0 1271 90.1820 4134 5106 1 chr1B.!!$F1 972
9 TraesCS3A01G240600 chr1B 302501748 302502726 978 False 1216.0 1216 89.2060 4134 5106 1 chr1B.!!$F2 972
10 TraesCS3A01G240600 chr7D 42907193 42908171 978 False 1243.0 1243 89.7250 4134 5106 1 chr7D.!!$F1 972
11 TraesCS3A01G240600 chr7D 394018030 394019012 982 False 1203.0 1203 88.9450 4134 5106 1 chr7D.!!$F2 972
12 TraesCS3A01G240600 chr6D 235782453 235783427 974 True 1206.0 1206 89.1150 4133 5106 1 chr6D.!!$R2 973
13 TraesCS3A01G240600 chr5B 609261281 609262267 986 False 1206.0 1206 89.0010 4134 5106 1 chr5B.!!$F1 972
14 TraesCS3A01G240600 chr7A 235692088 235693017 929 False 549.5 952 89.0415 1 942 2 chr7A.!!$F2 941

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
528 536 0.949397 CGATACCGTGGCTGCTACTA 59.051 55.000 14.29 1.25 0.00 1.82 F
1669 1710 0.187117 TTGGTGCACAGGGATCCAAA 59.813 50.000 20.43 0.00 35.61 3.28 F
2381 2423 1.063567 AGCATCTACTCCCTCCGTTCT 60.064 52.381 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2521 2563 0.037605 AAAGCGTTGTACTCCCTCCG 60.038 55.0 0.0 0.0 0.0 4.63 R
2522 2564 2.180432 AAAAGCGTTGTACTCCCTCC 57.820 50.0 0.0 0.0 0.0 4.30 R
4146 4222 1.107945 TGATCAACGGTATGCCTCGA 58.892 50.0 0.0 0.0 0.0 4.04 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
124 125 3.699894 CACACGAGAGCAGCCCCT 61.700 66.667 0.00 0.00 0.00 4.79
203 204 3.045518 GGTCCCCCGTTTCACATTT 57.954 52.632 0.00 0.00 0.00 2.32
210 211 6.295180 GGTCCCCCGTTTCACATTTTAAAATA 60.295 38.462 12.98 0.00 0.00 1.40
528 536 0.949397 CGATACCGTGGCTGCTACTA 59.051 55.000 14.29 1.25 0.00 1.82
657 666 2.597971 CGCAGAAAACGTTCGCTTTGTA 60.598 45.455 0.00 0.00 38.90 2.41
659 668 4.664640 CGCAGAAAACGTTCGCTTTGTATA 60.665 41.667 0.00 0.00 38.90 1.47
661 670 5.793457 GCAGAAAACGTTCGCTTTGTATATT 59.207 36.000 0.00 0.00 38.90 1.28
662 671 6.022484 GCAGAAAACGTTCGCTTTGTATATTC 60.022 38.462 0.00 0.00 38.90 1.75
671 680 5.597806 TCGCTTTGTATATTCGTCTCCAAT 58.402 37.500 0.00 0.00 0.00 3.16
696 705 6.088016 CAAATCTGAGTCAAATTTGGGACA 57.912 37.500 19.93 13.19 36.95 4.02
1000 1027 3.085439 TTATCCCCGTCCCCGCCTA 62.085 63.158 0.00 0.00 0.00 3.93
1074 1101 3.288381 ACCTCCTGCCCTCCTCCT 61.288 66.667 0.00 0.00 0.00 3.69
1279 1306 2.867429 CATCGCCAAGGTCAAACATTC 58.133 47.619 0.00 0.00 0.00 2.67
1346 1375 0.508641 CCGGCGAATCGAAGCTTATG 59.491 55.000 9.30 0.00 0.00 1.90
1349 1378 2.201732 GGCGAATCGAAGCTTATGTCA 58.798 47.619 6.91 0.00 0.00 3.58
1350 1379 2.033662 GGCGAATCGAAGCTTATGTCAC 60.034 50.000 6.91 0.00 0.00 3.67
1351 1380 2.603110 GCGAATCGAAGCTTATGTCACA 59.397 45.455 6.91 0.00 0.00 3.58
1352 1381 3.542291 GCGAATCGAAGCTTATGTCACAC 60.542 47.826 6.91 0.00 0.00 3.82
1353 1382 3.612423 CGAATCGAAGCTTATGTCACACA 59.388 43.478 0.00 0.00 0.00 3.72
1358 1395 3.247411 CGAAGCTTATGTCACACACACAA 59.753 43.478 0.00 0.00 38.04 3.33
1377 1414 7.117812 ACACACAACATTCTAGCACTACATTAC 59.882 37.037 0.00 0.00 0.00 1.89
1510 1547 4.155644 TCAGCGATGCTAGAGATGATAGTG 59.844 45.833 0.00 0.00 36.40 2.74
1574 1611 4.566488 CCCTTCTGCTAGAGGAACAACAAT 60.566 45.833 0.00 0.00 0.00 2.71
1603 1640 4.699637 TCGTTTTGTAGTTCTGGTCATGT 58.300 39.130 0.00 0.00 0.00 3.21
1669 1710 0.187117 TTGGTGCACAGGGATCCAAA 59.813 50.000 20.43 0.00 35.61 3.28
1796 1837 2.507484 TCCTCTGACATTTTGCACAGG 58.493 47.619 0.00 0.00 0.00 4.00
1857 1899 5.454187 GCTATGGCCTATTGGTGTGTTAGTA 60.454 44.000 3.32 0.00 35.27 1.82
1861 1903 4.036380 GGCCTATTGGTGTGTTAGTATTGC 59.964 45.833 0.00 0.00 35.27 3.56
1979 2021 5.180117 CCAGTTATAGCAATGGTATGAGCAC 59.820 44.000 14.50 6.53 0.00 4.40
2292 2334 8.576442 CCTTTTGAAGTTTATACATGTGGAACT 58.424 33.333 9.11 12.29 38.04 3.01
2354 2396 4.232221 GTGCAACATGATTTTCTCCACAG 58.768 43.478 0.00 0.00 36.32 3.66
2369 2411 4.402793 TCTCCACAGAACCTTAGCATCTAC 59.597 45.833 0.00 0.00 0.00 2.59
2370 2412 4.353777 TCCACAGAACCTTAGCATCTACT 58.646 43.478 0.00 0.00 0.00 2.57
2371 2413 4.402793 TCCACAGAACCTTAGCATCTACTC 59.597 45.833 0.00 0.00 0.00 2.59
2372 2414 4.442192 CCACAGAACCTTAGCATCTACTCC 60.442 50.000 0.00 0.00 0.00 3.85
2373 2415 3.707102 ACAGAACCTTAGCATCTACTCCC 59.293 47.826 0.00 0.00 0.00 4.30
2374 2416 3.964031 CAGAACCTTAGCATCTACTCCCT 59.036 47.826 0.00 0.00 0.00 4.20
2375 2417 4.038642 CAGAACCTTAGCATCTACTCCCTC 59.961 50.000 0.00 0.00 0.00 4.30
2376 2418 2.965562 ACCTTAGCATCTACTCCCTCC 58.034 52.381 0.00 0.00 0.00 4.30
2377 2419 1.889829 CCTTAGCATCTACTCCCTCCG 59.110 57.143 0.00 0.00 0.00 4.63
2378 2420 2.588620 CTTAGCATCTACTCCCTCCGT 58.411 52.381 0.00 0.00 0.00 4.69
2379 2421 2.750141 TAGCATCTACTCCCTCCGTT 57.250 50.000 0.00 0.00 0.00 4.44
2380 2422 1.404843 AGCATCTACTCCCTCCGTTC 58.595 55.000 0.00 0.00 0.00 3.95
2381 2423 1.063567 AGCATCTACTCCCTCCGTTCT 60.064 52.381 0.00 0.00 0.00 3.01
2382 2424 1.757699 GCATCTACTCCCTCCGTTCTT 59.242 52.381 0.00 0.00 0.00 2.52
2383 2425 2.957006 GCATCTACTCCCTCCGTTCTTA 59.043 50.000 0.00 0.00 0.00 2.10
2384 2426 3.383825 GCATCTACTCCCTCCGTTCTTAA 59.616 47.826 0.00 0.00 0.00 1.85
2385 2427 4.142004 GCATCTACTCCCTCCGTTCTTAAA 60.142 45.833 0.00 0.00 0.00 1.52
2386 2428 5.453480 GCATCTACTCCCTCCGTTCTTAAAT 60.453 44.000 0.00 0.00 0.00 1.40
2387 2429 6.239232 GCATCTACTCCCTCCGTTCTTAAATA 60.239 42.308 0.00 0.00 0.00 1.40
2388 2430 7.525692 GCATCTACTCCCTCCGTTCTTAAATAT 60.526 40.741 0.00 0.00 0.00 1.28
2389 2431 9.021807 CATCTACTCCCTCCGTTCTTAAATATA 57.978 37.037 0.00 0.00 0.00 0.86
2390 2432 9.597681 ATCTACTCCCTCCGTTCTTAAATATAA 57.402 33.333 0.00 0.00 0.00 0.98
2391 2433 9.075678 TCTACTCCCTCCGTTCTTAAATATAAG 57.924 37.037 0.00 0.00 39.97 1.73
2392 2434 7.672122 ACTCCCTCCGTTCTTAAATATAAGT 57.328 36.000 0.00 0.00 39.65 2.24
2393 2435 7.724287 ACTCCCTCCGTTCTTAAATATAAGTC 58.276 38.462 0.00 0.00 39.65 3.01
2394 2436 7.564292 ACTCCCTCCGTTCTTAAATATAAGTCT 59.436 37.037 0.00 0.00 39.65 3.24
2395 2437 8.315220 TCCCTCCGTTCTTAAATATAAGTCTT 57.685 34.615 0.00 0.00 39.65 3.01
2396 2438 8.765517 TCCCTCCGTTCTTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 39.65 2.52
2397 2439 9.392259 CCCTCCGTTCTTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 39.65 2.27
2425 2467 9.698309 AGAGATTCCAATAAATGACTACATACG 57.302 33.333 0.00 0.00 35.50 3.06
2426 2468 8.833231 AGATTCCAATAAATGACTACATACGG 57.167 34.615 0.00 0.00 35.50 4.02
2427 2469 8.647796 AGATTCCAATAAATGACTACATACGGA 58.352 33.333 0.00 0.00 35.50 4.69
2428 2470 8.833231 ATTCCAATAAATGACTACATACGGAG 57.167 34.615 0.00 0.00 35.50 4.63
2429 2471 6.220930 TCCAATAAATGACTACATACGGAGC 58.779 40.000 0.00 0.00 35.50 4.70
2430 2472 5.989168 CCAATAAATGACTACATACGGAGCA 59.011 40.000 0.00 0.00 35.50 4.26
2431 2473 6.481976 CCAATAAATGACTACATACGGAGCAA 59.518 38.462 0.00 0.00 35.50 3.91
2432 2474 7.011950 CCAATAAATGACTACATACGGAGCAAA 59.988 37.037 0.00 0.00 35.50 3.68
2433 2475 8.394877 CAATAAATGACTACATACGGAGCAAAA 58.605 33.333 0.00 0.00 35.50 2.44
2434 2476 8.677148 ATAAATGACTACATACGGAGCAAAAT 57.323 30.769 0.00 0.00 35.50 1.82
2435 2477 5.991328 ATGACTACATACGGAGCAAAATG 57.009 39.130 0.00 0.00 34.71 2.32
2436 2478 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
2437 2479 5.109210 TGACTACATACGGAGCAAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
2438 2480 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2439 2481 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2440 2482 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2441 2483 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2442 2484 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2443 2485 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2444 2486 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2445 2487 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2446 2488 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2447 2489 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2448 2490 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2484 2526 9.143155 TGTCTACATACATCCATATGTTGTAGT 57.857 33.333 22.56 15.48 44.07 2.73
2485 2527 9.627395 GTCTACATACATCCATATGTTGTAGTC 57.373 37.037 22.56 18.41 44.07 2.59
2486 2528 9.588096 TCTACATACATCCATATGTTGTAGTCT 57.412 33.333 22.56 7.77 44.07 3.24
2527 2569 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2528 2570 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2529 2571 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
3091 3165 5.301805 TCCTGTTCATTCCTGTTCCTTTTTC 59.698 40.000 0.00 0.00 0.00 2.29
3094 3168 7.181569 TGTTCATTCCTGTTCCTTTTTCTTT 57.818 32.000 0.00 0.00 0.00 2.52
3676 3752 6.650807 ACCATGTACTTGATATATCCTTTGCG 59.349 38.462 10.25 0.00 0.00 4.85
3700 3776 1.000060 GCAGCTTGCTGATTTGGAACA 60.000 47.619 24.67 0.00 40.96 3.18
3810 3886 2.622436 GTCATGCTGGTCTTCAGGTAC 58.378 52.381 0.00 0.00 43.54 3.34
3908 3984 8.410912 GTCACATACACACATACTATGTCCTTA 58.589 37.037 0.00 0.00 42.70 2.69
4125 4201 0.695924 TTCCCCTCCTCGATTTGCAA 59.304 50.000 0.00 0.00 0.00 4.08
4228 4306 5.833406 TGTTAACGAGGTTCACCGATATA 57.167 39.130 0.26 0.00 42.08 0.86
4289 4369 1.001181 ACACCGTTACAATACCGCACT 59.999 47.619 0.00 0.00 0.00 4.40
4437 4536 8.884323 ACATGACTCCATATCCTATGTAAACAT 58.116 33.333 0.00 0.63 40.22 2.71
4460 4559 7.549488 ACATAATACAACTCCTAGTTCAACTGC 59.451 37.037 0.00 0.00 36.03 4.40
4503 4602 6.920569 ATTCGACACAACTCTAACAAACTT 57.079 33.333 0.00 0.00 0.00 2.66
4504 4603 6.730960 TTCGACACAACTCTAACAAACTTT 57.269 33.333 0.00 0.00 0.00 2.66
4572 4672 7.174253 GTCAAACTTCCATGTACATTGGACTTA 59.826 37.037 20.13 10.03 0.00 2.24
4574 4674 8.356657 CAAACTTCCATGTACATTGGACTTAAA 58.643 33.333 20.13 9.52 0.00 1.52
4593 4693 6.381994 ACTTAAACTTATCCCATGAGTACCGA 59.618 38.462 0.00 0.00 0.00 4.69
4616 4716 4.093743 TGCTACTCCAAAGACTCCATGTA 58.906 43.478 0.00 0.00 0.00 2.29
4617 4717 4.160439 TGCTACTCCAAAGACTCCATGTAG 59.840 45.833 0.00 0.00 0.00 2.74
4625 4725 1.195115 GACTCCATGTAGCTCCACCA 58.805 55.000 0.00 0.00 0.00 4.17
4706 4806 4.177026 CACATTACTCTAGTTTGCGCTCT 58.823 43.478 9.73 7.26 0.00 4.09
4722 4823 3.677424 GCGCTCTCAACTTCCAGAGTATT 60.677 47.826 0.00 0.00 38.78 1.89
4742 4851 2.503331 TCATCCACAACATCACACACC 58.497 47.619 0.00 0.00 0.00 4.16
4860 4969 4.830826 ACTTGAAGGAATTTCACCGTTC 57.169 40.909 0.00 0.00 45.22 3.95
5065 5177 2.027605 CCGATCATCACCGACCGG 59.972 66.667 6.94 6.94 42.03 5.28
5084 5196 1.488527 GTGACGAGTTTCACGCTTCT 58.511 50.000 0.00 0.00 36.79 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
625 634 3.095738 CGTTTTCTGCGTTTTCTTCGTT 58.904 40.909 0.00 0.00 0.00 3.85
657 666 6.830912 TCAGATTTGGATTGGAGACGAATAT 58.169 36.000 0.00 0.00 0.00 1.28
659 668 5.102953 TCAGATTTGGATTGGAGACGAAT 57.897 39.130 0.00 0.00 0.00 3.34
661 670 3.515502 ACTCAGATTTGGATTGGAGACGA 59.484 43.478 0.00 0.00 0.00 4.20
662 671 3.866651 ACTCAGATTTGGATTGGAGACG 58.133 45.455 0.00 0.00 0.00 4.18
696 705 4.196193 TGTGTCTGTTCGGACAAATCTTT 58.804 39.130 14.83 0.00 46.00 2.52
699 708 4.545823 TTTGTGTCTGTTCGGACAAATC 57.454 40.909 14.83 5.29 46.00 2.17
918 938 0.327924 ATCCAACGGCCATCAAGTGA 59.672 50.000 2.24 0.00 0.00 3.41
919 939 0.452987 CATCCAACGGCCATCAAGTG 59.547 55.000 2.24 0.00 0.00 3.16
920 940 0.038166 ACATCCAACGGCCATCAAGT 59.962 50.000 2.24 0.00 0.00 3.16
921 941 0.452987 CACATCCAACGGCCATCAAG 59.547 55.000 2.24 0.00 0.00 3.02
950 977 0.038251 TCAGGCAGTCACGCTGTAAG 60.038 55.000 0.00 0.00 46.64 2.34
1142 1169 4.485834 TGTACGCGCCGGTAGCTG 62.486 66.667 19.02 14.98 40.39 4.24
1279 1306 0.252742 AGGGGTGTTGGTAGGAGAGG 60.253 60.000 0.00 0.00 0.00 3.69
1346 1375 3.559655 TGCTAGAATGTTGTGTGTGTGAC 59.440 43.478 0.00 0.00 0.00 3.67
1349 1378 3.808728 AGTGCTAGAATGTTGTGTGTGT 58.191 40.909 0.00 0.00 0.00 3.72
1350 1379 4.749598 TGTAGTGCTAGAATGTTGTGTGTG 59.250 41.667 0.00 0.00 0.00 3.82
1351 1380 4.956085 TGTAGTGCTAGAATGTTGTGTGT 58.044 39.130 0.00 0.00 0.00 3.72
1352 1381 6.486253 AATGTAGTGCTAGAATGTTGTGTG 57.514 37.500 0.00 0.00 0.00 3.82
1353 1382 7.331934 CAGTAATGTAGTGCTAGAATGTTGTGT 59.668 37.037 0.00 0.00 0.00 3.72
1377 1414 8.028354 TGCAATGAGTCAAACCATTAAATACAG 58.972 33.333 0.00 0.00 32.31 2.74
1389 1426 6.476380 TGAACAAGAAATGCAATGAGTCAAAC 59.524 34.615 0.00 0.00 0.00 2.93
1510 1547 4.837567 GTCAATATGACAACTCCAATCGC 58.162 43.478 5.65 0.00 46.22 4.58
1574 1611 9.491675 TGACCAGAACTACAAAACGATAAAATA 57.508 29.630 0.00 0.00 0.00 1.40
1588 1625 4.574828 ACAACACAACATGACCAGAACTAC 59.425 41.667 0.00 0.00 0.00 2.73
1603 1640 7.703197 ACATCGATTCGTACATATACAACACAA 59.297 33.333 5.89 0.00 0.00 3.33
1669 1710 1.450312 GCCACCGCTACAGAATGCT 60.450 57.895 0.00 0.00 42.53 3.79
1796 1837 1.274447 ACCGTAAGCAAGTAGGTCACC 59.726 52.381 0.00 0.00 0.00 4.02
1857 1899 1.527034 ATGACGCTGAACAGTGCAAT 58.473 45.000 14.11 6.46 42.40 3.56
1861 1903 2.545526 ACAGAAATGACGCTGAACAGTG 59.454 45.455 12.86 12.86 44.11 3.66
2230 2272 7.716799 TCATACAGGATTTAAAACTGGCAAT 57.283 32.000 20.61 11.92 36.57 3.56
2292 2334 2.983229 TGCAAAAAGAAGGCAAGCAAA 58.017 38.095 0.00 0.00 34.05 3.68
2354 2396 3.322541 GGAGGGAGTAGATGCTAAGGTTC 59.677 52.174 0.00 0.00 0.00 3.62
2369 2411 7.953752 AGACTTATATTTAAGAACGGAGGGAG 58.046 38.462 9.58 0.00 38.56 4.30
2370 2412 7.909485 AGACTTATATTTAAGAACGGAGGGA 57.091 36.000 9.58 0.00 38.56 4.20
2371 2413 8.959705 AAAGACTTATATTTAAGAACGGAGGG 57.040 34.615 9.58 0.00 38.56 4.30
2399 2441 9.698309 CGTATGTAGTCATTTATTGGAATCTCT 57.302 33.333 0.00 0.00 35.70 3.10
2400 2442 8.926710 CCGTATGTAGTCATTTATTGGAATCTC 58.073 37.037 0.00 0.00 35.70 2.75
2401 2443 8.647796 TCCGTATGTAGTCATTTATTGGAATCT 58.352 33.333 0.00 0.00 35.70 2.40
2402 2444 8.827177 TCCGTATGTAGTCATTTATTGGAATC 57.173 34.615 0.00 0.00 35.70 2.52
2403 2445 7.387948 GCTCCGTATGTAGTCATTTATTGGAAT 59.612 37.037 0.00 0.00 35.70 3.01
2404 2446 6.704493 GCTCCGTATGTAGTCATTTATTGGAA 59.296 38.462 0.00 0.00 35.70 3.53
2405 2447 6.183360 TGCTCCGTATGTAGTCATTTATTGGA 60.183 38.462 0.00 0.00 35.70 3.53
2406 2448 5.989168 TGCTCCGTATGTAGTCATTTATTGG 59.011 40.000 0.00 0.00 35.70 3.16
2407 2449 7.477144 TTGCTCCGTATGTAGTCATTTATTG 57.523 36.000 0.00 0.00 35.70 1.90
2408 2450 8.500753 TTTTGCTCCGTATGTAGTCATTTATT 57.499 30.769 0.00 0.00 35.70 1.40
2409 2451 8.559536 CATTTTGCTCCGTATGTAGTCATTTAT 58.440 33.333 0.00 0.00 35.70 1.40
2410 2452 7.766738 TCATTTTGCTCCGTATGTAGTCATTTA 59.233 33.333 0.00 0.00 35.70 1.40
2411 2453 6.597672 TCATTTTGCTCCGTATGTAGTCATTT 59.402 34.615 0.00 0.00 35.70 2.32
2412 2454 6.112734 TCATTTTGCTCCGTATGTAGTCATT 58.887 36.000 0.00 0.00 35.70 2.57
2413 2455 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
2414 2456 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2415 2457 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2416 2458 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2417 2459 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2418 2460 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2419 2461 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2420 2462 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2421 2463 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2422 2464 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2423 2465 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2424 2466 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2425 2467 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2426 2468 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2458 2500 9.143155 ACTACAACATATGGATGTATGTAGACA 57.857 33.333 26.03 7.65 45.93 3.41
2459 2501 9.627395 GACTACAACATATGGATGTATGTAGAC 57.373 37.037 26.03 21.22 45.93 2.59
2460 2502 9.588096 AGACTACAACATATGGATGTATGTAGA 57.412 33.333 26.03 8.59 45.93 2.59
2501 2543 8.645110 CCCTCCGTTCCTAAATATAAGTCTTTA 58.355 37.037 0.00 0.00 0.00 1.85
2502 2544 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2503 2545 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2504 2546 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2505 2547 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2506 2548 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2507 2549 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2508 2550 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
2509 2551 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
2510 2552 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
2511 2553 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
2512 2554 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
2513 2555 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
2514 2556 2.827921 GTTGTACTCCCTCCGTTCCTAA 59.172 50.000 0.00 0.00 0.00 2.69
2515 2557 2.450476 GTTGTACTCCCTCCGTTCCTA 58.550 52.381 0.00 0.00 0.00 2.94
2516 2558 1.264295 GTTGTACTCCCTCCGTTCCT 58.736 55.000 0.00 0.00 0.00 3.36
2517 2559 0.108945 CGTTGTACTCCCTCCGTTCC 60.109 60.000 0.00 0.00 0.00 3.62
2518 2560 0.735287 GCGTTGTACTCCCTCCGTTC 60.735 60.000 0.00 0.00 0.00 3.95
2519 2561 1.183676 AGCGTTGTACTCCCTCCGTT 61.184 55.000 0.00 0.00 0.00 4.44
2520 2562 1.183676 AAGCGTTGTACTCCCTCCGT 61.184 55.000 0.00 0.00 0.00 4.69
2521 2563 0.037605 AAAGCGTTGTACTCCCTCCG 60.038 55.000 0.00 0.00 0.00 4.63
2522 2564 2.180432 AAAAGCGTTGTACTCCCTCC 57.820 50.000 0.00 0.00 0.00 4.30
3059 3133 5.449553 ACAGGAATGAACAGGAGAAAAAGT 58.550 37.500 0.00 0.00 0.00 2.66
3065 3139 3.251484 AGGAACAGGAATGAACAGGAGA 58.749 45.455 0.00 0.00 0.00 3.71
3700 3776 1.336755 GGCACCATTTCACAGTTTCGT 59.663 47.619 0.00 0.00 0.00 3.85
3810 3886 7.973388 TGACTTTTTGACACTCCACAAATTAAG 59.027 33.333 0.00 0.00 36.21 1.85
3908 3984 7.977853 CACAAGTCCCGTTACATTACTAGTTAT 59.022 37.037 0.00 0.00 0.00 1.89
3915 3991 3.124636 CAGCACAAGTCCCGTTACATTAC 59.875 47.826 0.00 0.00 0.00 1.89
4125 4201 9.372369 CCTCGAATTTATTCTAACAGTTCTTCT 57.628 33.333 0.00 0.00 34.69 2.85
4146 4222 1.107945 TGATCAACGGTATGCCTCGA 58.892 50.000 0.00 0.00 0.00 4.04
4228 4306 4.499116 AGGCCCCGGGATGTAGCT 62.499 66.667 26.32 3.39 0.00 3.32
4320 4419 1.954146 ATAATAGCACGGGCACGCG 60.954 57.895 14.57 3.53 46.04 6.01
4328 4427 4.065088 ACCTATGCCAACATAATAGCACG 58.935 43.478 0.00 0.00 38.29 5.34
4437 4536 6.999950 TGCAGTTGAACTAGGAGTTGTATTA 58.000 36.000 0.00 0.00 38.80 0.98
4453 4552 3.134985 TGTACAAGGTAGGTTGCAGTTGA 59.865 43.478 0.00 0.00 0.00 3.18
4460 4559 7.646922 GTCGAATATAGTGTACAAGGTAGGTTG 59.353 40.741 0.00 0.00 0.00 3.77
4572 4672 5.611374 CATCGGTACTCATGGGATAAGTTT 58.389 41.667 0.00 0.00 0.00 2.66
4574 4674 3.006967 GCATCGGTACTCATGGGATAAGT 59.993 47.826 0.00 0.00 0.00 2.24
4593 4693 3.521126 ACATGGAGTCTTTGGAGTAGCAT 59.479 43.478 0.00 0.00 0.00 3.79
4625 4725 4.439253 AAAGAAGGGACTACAAGTTGCT 57.561 40.909 1.81 0.00 38.49 3.91
4665 4765 3.430895 TGTGGAACTTAATTTCGCTCGAC 59.569 43.478 0.05 0.00 38.04 4.20
4706 4806 5.248248 TGTGGATGAATACTCTGGAAGTTGA 59.752 40.000 0.00 0.00 39.55 3.18
4722 4823 2.503331 GGTGTGTGATGTTGTGGATGA 58.497 47.619 0.00 0.00 0.00 2.92
4742 4851 0.232303 GTTCACTTTCACGCAGGTCG 59.768 55.000 0.00 0.00 45.38 4.79
4774 4883 6.437477 TCAGATAACTCTTATGTGTGACACCT 59.563 38.462 13.85 5.96 37.92 4.00
4860 4969 1.546029 TGACTCAGGATGACGACAAGG 59.454 52.381 0.00 0.00 42.56 3.61
5065 5177 1.488527 AGAAGCGTGAAACTCGTCAC 58.511 50.000 0.00 0.00 43.75 3.67
5084 5196 0.042581 TGGAGCCCAGTGGTCTGATA 59.957 55.000 8.74 0.00 43.76 2.15


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

AutoCloner maintained by Alex Coulton.