Multiple sequence alignment - TraesCS4B01G096100

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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 TraesCS4B01G096100 chr4B 100.000 4882 0 0 1 4882 99961325 99956444 0.000000e+00 9016.0
1 TraesCS4B01G096100 chr4B 94.094 508 30 0 4375 4882 2408558 2409065 0.000000e+00 773.0
2 TraesCS4B01G096100 chr4B 93.725 510 32 0 4373 4882 58059397 58058888 0.000000e+00 765.0
3 TraesCS4B01G096100 chr4B 100.000 29 0 0 995 1023 562400233 562400205 2.000000e-03 54.7
4 TraesCS4B01G096100 chr4A 94.367 3000 141 16 1397 4376 516893713 516890722 0.000000e+00 4578.0
5 TraesCS4B01G096100 chr4A 96.204 1291 39 7 1 1287 516895084 516893800 0.000000e+00 2104.0
6 TraesCS4B01G096100 chr4A 100.000 29 0 0 995 1023 727827201 727827173 2.000000e-03 54.7
7 TraesCS4B01G096100 chr4D 96.163 2554 82 7 1397 3937 67457161 67454611 0.000000e+00 4159.0
8 TraesCS4B01G096100 chr4D 95.929 1302 31 11 1 1287 67458540 67457246 0.000000e+00 2091.0
9 TraesCS4B01G096100 chr4D 94.457 451 16 7 3933 4376 67446515 67446067 0.000000e+00 686.0
10 TraesCS4B01G096100 chr5B 94.892 509 26 0 4374 4882 684443725 684443217 0.000000e+00 797.0
11 TraesCS4B01G096100 chr5B 94.499 509 28 0 4374 4882 611696126 611696634 0.000000e+00 785.0
12 TraesCS4B01G096100 chr2B 94.499 509 28 0 4374 4882 91496683 91497191 0.000000e+00 785.0
13 TraesCS4B01G096100 chr2B 93.898 508 30 1 4375 4882 673092511 673092005 0.000000e+00 765.0
14 TraesCS4B01G096100 chr2B 93.567 513 32 1 4370 4882 398048689 398049200 0.000000e+00 763.0
15 TraesCS4B01G096100 chr2B 94.595 37 0 2 995 1030 53398973 53399008 6.830000e-04 56.5
16 TraesCS4B01G096100 chr3B 94.094 508 27 1 4375 4882 679507762 679507258 0.000000e+00 769.0
17 TraesCS4B01G096100 chr3B 88.095 168 15 1 1992 2159 256888029 256888191 1.390000e-45 195.0
18 TraesCS4B01G096100 chr3B 100.000 29 0 0 995 1023 498412613 498412585 2.000000e-03 54.7
19 TraesCS4B01G096100 chr3B 100.000 29 0 0 995 1023 761840821 761840849 2.000000e-03 54.7
20 TraesCS4B01G096100 chr1D 93.725 510 32 0 4373 4882 12417067 12417576 0.000000e+00 765.0
21 TraesCS4B01G096100 chr1D 86.056 251 34 1 1730 1980 182526514 182526763 8.050000e-68 268.0
22 TraesCS4B01G096100 chr1D 97.727 44 1 0 2107 2150 182527572 182527615 5.240000e-10 76.8
23 TraesCS4B01G096100 chr3D 85.317 252 34 3 1730 1980 464127202 464126953 1.740000e-64 257.0
24 TraesCS4B01G096100 chr3A 92.453 159 12 0 1992 2150 393400599 393400757 1.370000e-55 228.0
25 TraesCS4B01G096100 chr1A 89.744 156 16 0 1992 2147 284331082 284331237 2.980000e-47 200.0
26 TraesCS4B01G096100 chr7B 100.000 29 0 0 995 1023 531228480 531228508 2.000000e-03 54.7


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 TraesCS4B01G096100 chr4B 99956444 99961325 4881 True 9016 9016 100.0000 1 4882 1 chr4B.!!$R2 4881
1 TraesCS4B01G096100 chr4B 2408558 2409065 507 False 773 773 94.0940 4375 4882 1 chr4B.!!$F1 507
2 TraesCS4B01G096100 chr4B 58058888 58059397 509 True 765 765 93.7250 4373 4882 1 chr4B.!!$R1 509
3 TraesCS4B01G096100 chr4A 516890722 516895084 4362 True 3341 4578 95.2855 1 4376 2 chr4A.!!$R2 4375
4 TraesCS4B01G096100 chr4D 67454611 67458540 3929 True 3125 4159 96.0460 1 3937 2 chr4D.!!$R2 3936
5 TraesCS4B01G096100 chr5B 684443217 684443725 508 True 797 797 94.8920 4374 4882 1 chr5B.!!$R1 508
6 TraesCS4B01G096100 chr5B 611696126 611696634 508 False 785 785 94.4990 4374 4882 1 chr5B.!!$F1 508
7 TraesCS4B01G096100 chr2B 91496683 91497191 508 False 785 785 94.4990 4374 4882 1 chr2B.!!$F2 508
8 TraesCS4B01G096100 chr2B 673092005 673092511 506 True 765 765 93.8980 4375 4882 1 chr2B.!!$R1 507
9 TraesCS4B01G096100 chr2B 398048689 398049200 511 False 763 763 93.5670 4370 4882 1 chr2B.!!$F3 512
10 TraesCS4B01G096100 chr3B 679507258 679507762 504 True 769 769 94.0940 4375 4882 1 chr3B.!!$R2 507
11 TraesCS4B01G096100 chr1D 12417067 12417576 509 False 765 765 93.7250 4373 4882 1 chr1D.!!$F1 509

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
785 795 0.320374 TCTTGTGTGGATCCCGTCAC 59.680 55.0 9.90 15.61 33.84 3.67 F
1369 1411 0.034380 AGTGGCTCTGCTGCAATCAT 60.034 50.0 3.02 0.00 34.04 2.45 F
1370 1412 0.100682 GTGGCTCTGCTGCAATCATG 59.899 55.0 3.02 0.00 34.04 3.07 F
1372 1414 0.100682 GGCTCTGCTGCAATCATGTG 59.899 55.0 3.02 0.00 34.04 3.21 F
1373 1415 0.100682 GCTCTGCTGCAATCATGTGG 59.899 55.0 3.02 0.00 0.00 4.17 F
2382 2435 0.545309 TGGAAGGACAGGAGGACCAG 60.545 60.0 0.00 0.00 38.94 4.00 F
3096 3159 0.906066 TACCAAGCGTTGCCTCCATA 59.094 50.0 0.00 0.00 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 1905 1.004440 GCCTCCGACAAGAGCAAGT 60.004 57.895 0.00 0.00 32.17 3.16 R
2353 2406 2.354259 CTGTCCTTCCATGTGCTCTTC 58.646 52.381 0.00 0.00 0.00 2.87 R
2894 2957 2.818130 AGCGGACAAATTTGCATTGT 57.182 40.000 18.12 3.87 43.37 2.71 R
3222 3285 4.054671 CTGTTCAACTGTCCTCTGAAGAC 58.945 47.826 0.00 0.00 30.00 3.01 R
3382 3445 3.877508 TCAGCAGATCATTCATTCAGCAG 59.122 43.478 0.00 0.00 0.00 4.24 R
3451 3516 0.458669 CCTGCCATTCACCAAGCATC 59.541 55.000 0.00 0.00 34.16 3.91 R
4082 4147 0.537143 ATCTGAAAACGGCACCTGCA 60.537 50.000 0.00 0.00 44.36 4.41 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
147 148 4.270084 TGAATAAACTCATTCCATCGCGTC 59.730 41.667 5.77 0.00 34.59 5.19
155 156 0.671796 TTCCATCGCGTCGATACCAT 59.328 50.000 5.77 0.00 45.19 3.55
258 261 1.946156 CCCGTGCATCGACGATGAG 60.946 63.158 35.61 24.92 42.09 2.90
330 333 2.115337 ATCTTCTCCATGAGAGGGGG 57.885 55.000 10.23 0.00 43.44 5.40
426 430 0.468029 CACCCCAAAGTCAAGCAGGT 60.468 55.000 0.00 0.00 0.00 4.00
514 522 4.709397 GGATCTAGGAGTATGTGAGATGGG 59.291 50.000 0.00 0.00 0.00 4.00
532 540 5.478332 AGATGGGTTGTCTGATTTTTCTTCC 59.522 40.000 0.00 0.00 0.00 3.46
538 546 6.459710 GGTTGTCTGATTTTTCTTCCGAAGTT 60.460 38.462 8.01 0.00 0.00 2.66
684 692 7.864379 TGTTTACTTAACGAGTAGACTTTCCTG 59.136 37.037 7.93 0.00 43.11 3.86
785 795 0.320374 TCTTGTGTGGATCCCGTCAC 59.680 55.000 9.90 15.61 33.84 3.67
908 918 5.261216 TGTGGAGTTTTCAGTTCTTTCCTT 58.739 37.500 0.00 0.00 0.00 3.36
1227 1243 6.670695 ATTACTTCCTTGATGCTTGGTTTT 57.329 33.333 0.00 0.00 0.00 2.43
1228 1244 4.326504 ACTTCCTTGATGCTTGGTTTTG 57.673 40.909 0.00 0.00 0.00 2.44
1229 1245 3.706086 ACTTCCTTGATGCTTGGTTTTGT 59.294 39.130 0.00 0.00 0.00 2.83
1230 1246 3.731652 TCCTTGATGCTTGGTTTTGTG 57.268 42.857 0.00 0.00 0.00 3.33
1231 1247 2.364970 TCCTTGATGCTTGGTTTTGTGG 59.635 45.455 0.00 0.00 0.00 4.17
1232 1248 2.548493 CCTTGATGCTTGGTTTTGTGGG 60.548 50.000 0.00 0.00 0.00 4.61
1302 1343 5.934781 AGAAATGGTGTTTTCAGAGAGAGT 58.065 37.500 0.00 0.00 37.93 3.24
1303 1344 7.067496 AGAAATGGTGTTTTCAGAGAGAGTA 57.933 36.000 0.00 0.00 37.93 2.59
1308 1349 7.730364 TGGTGTTTTCAGAGAGAGTATTTTC 57.270 36.000 0.00 0.00 0.00 2.29
1309 1350 7.279615 TGGTGTTTTCAGAGAGAGTATTTTCA 58.720 34.615 0.00 0.00 0.00 2.69
1354 1396 8.511604 AGTTGATGATTTGTTAATAGGAGTGG 57.488 34.615 0.00 0.00 0.00 4.00
1355 1397 6.942532 TGATGATTTGTTAATAGGAGTGGC 57.057 37.500 0.00 0.00 0.00 5.01
1356 1398 6.662755 TGATGATTTGTTAATAGGAGTGGCT 58.337 36.000 0.00 0.00 0.00 4.75
1357 1399 6.767902 TGATGATTTGTTAATAGGAGTGGCTC 59.232 38.462 0.00 0.00 0.00 4.70
1358 1400 6.313519 TGATTTGTTAATAGGAGTGGCTCT 57.686 37.500 0.00 0.00 0.00 4.09
1359 1401 6.115446 TGATTTGTTAATAGGAGTGGCTCTG 58.885 40.000 0.00 0.00 0.00 3.35
1360 1402 3.543680 TGTTAATAGGAGTGGCTCTGC 57.456 47.619 0.00 0.00 34.62 4.26
1361 1403 3.107601 TGTTAATAGGAGTGGCTCTGCT 58.892 45.455 14.90 14.90 46.34 4.24
1362 1404 3.118629 TGTTAATAGGAGTGGCTCTGCTG 60.119 47.826 19.08 0.00 44.41 4.41
1363 1405 0.179936 AATAGGAGTGGCTCTGCTGC 59.820 55.000 19.08 0.00 44.41 5.25
1364 1406 0.979709 ATAGGAGTGGCTCTGCTGCA 60.980 55.000 19.08 0.88 44.41 4.41
1365 1407 1.194121 TAGGAGTGGCTCTGCTGCAA 61.194 55.000 19.08 0.00 44.41 4.08
1366 1408 1.378250 GGAGTGGCTCTGCTGCAAT 60.378 57.895 3.02 0.00 34.04 3.56
1367 1409 1.375098 GGAGTGGCTCTGCTGCAATC 61.375 60.000 3.02 0.00 34.04 2.67
1368 1410 0.675837 GAGTGGCTCTGCTGCAATCA 60.676 55.000 3.02 0.00 34.04 2.57
1369 1411 0.034380 AGTGGCTCTGCTGCAATCAT 60.034 50.000 3.02 0.00 34.04 2.45
1370 1412 0.100682 GTGGCTCTGCTGCAATCATG 59.899 55.000 3.02 0.00 34.04 3.07
1371 1413 0.323087 TGGCTCTGCTGCAATCATGT 60.323 50.000 3.02 0.00 34.04 3.21
1372 1414 0.100682 GGCTCTGCTGCAATCATGTG 59.899 55.000 3.02 0.00 34.04 3.21
1373 1415 0.100682 GCTCTGCTGCAATCATGTGG 59.899 55.000 3.02 0.00 0.00 4.17
1374 1416 1.746470 CTCTGCTGCAATCATGTGGA 58.254 50.000 3.02 0.00 0.00 4.02
1375 1417 2.089201 CTCTGCTGCAATCATGTGGAA 58.911 47.619 3.02 0.00 0.00 3.53
1376 1418 2.490509 CTCTGCTGCAATCATGTGGAAA 59.509 45.455 3.02 0.00 0.00 3.13
1377 1419 2.892215 TCTGCTGCAATCATGTGGAAAA 59.108 40.909 3.02 0.00 0.00 2.29
1378 1420 3.512329 TCTGCTGCAATCATGTGGAAAAT 59.488 39.130 3.02 0.00 0.00 1.82
1379 1421 3.591023 TGCTGCAATCATGTGGAAAATG 58.409 40.909 0.00 0.00 30.82 2.32
1380 1422 3.007074 TGCTGCAATCATGTGGAAAATGT 59.993 39.130 0.00 0.00 31.84 2.71
1381 1423 4.220163 TGCTGCAATCATGTGGAAAATGTA 59.780 37.500 0.00 0.00 31.84 2.29
1382 1424 5.105269 TGCTGCAATCATGTGGAAAATGTAT 60.105 36.000 0.00 0.00 31.84 2.29
1383 1425 6.096564 TGCTGCAATCATGTGGAAAATGTATA 59.903 34.615 0.00 0.00 31.84 1.47
1384 1426 7.149973 GCTGCAATCATGTGGAAAATGTATAT 58.850 34.615 0.00 0.00 31.84 0.86
1385 1427 7.327761 GCTGCAATCATGTGGAAAATGTATATC 59.672 37.037 0.00 0.00 31.84 1.63
1386 1428 7.660112 TGCAATCATGTGGAAAATGTATATCC 58.340 34.615 0.00 0.00 31.84 2.59
1387 1429 7.506599 TGCAATCATGTGGAAAATGTATATCCT 59.493 33.333 0.00 0.00 31.84 3.24
1388 1430 7.811236 GCAATCATGTGGAAAATGTATATCCTG 59.189 37.037 0.00 0.00 31.84 3.86
1389 1431 8.853126 CAATCATGTGGAAAATGTATATCCTGT 58.147 33.333 0.00 0.00 31.84 4.00
1390 1432 8.627208 ATCATGTGGAAAATGTATATCCTGTC 57.373 34.615 0.00 0.00 31.84 3.51
1391 1433 7.805163 TCATGTGGAAAATGTATATCCTGTCT 58.195 34.615 0.00 0.00 31.84 3.41
1392 1434 7.716560 TCATGTGGAAAATGTATATCCTGTCTG 59.283 37.037 0.00 0.00 31.84 3.51
1393 1435 6.957631 TGTGGAAAATGTATATCCTGTCTGT 58.042 36.000 0.00 0.00 34.24 3.41
1394 1436 7.402054 TGTGGAAAATGTATATCCTGTCTGTT 58.598 34.615 0.00 0.00 34.24 3.16
1395 1437 7.888021 TGTGGAAAATGTATATCCTGTCTGTTT 59.112 33.333 0.00 0.00 34.24 2.83
1396 1438 8.739972 GTGGAAAATGTATATCCTGTCTGTTTT 58.260 33.333 0.00 0.00 34.24 2.43
1397 1439 8.739039 TGGAAAATGTATATCCTGTCTGTTTTG 58.261 33.333 0.00 0.00 34.24 2.44
1447 1490 5.474532 TGTCAAAGCATATCTTCTGTTTGCT 59.525 36.000 0.00 0.00 45.06 3.91
1466 1509 7.010923 TGTTTGCTTATTGTTCATGAAAACCAC 59.989 33.333 10.35 0.00 0.00 4.16
1491 1534 6.317391 CAGATTCCCTGGAAAAACTATCAGTC 59.683 42.308 2.15 0.00 39.23 3.51
1492 1535 4.569719 TCCCTGGAAAAACTATCAGTCC 57.430 45.455 0.00 0.00 0.00 3.85
1523 1566 7.806409 TGATTAACCATGTAATGTGGATCAG 57.194 36.000 0.00 0.00 44.81 2.90
1557 1600 6.042552 TCCTATTAGAAAAGCCTCCTCTGATG 59.957 42.308 0.00 0.00 0.00 3.07
1632 1675 3.077484 TCAAAGCAGAATCAGGGAAGG 57.923 47.619 0.00 0.00 0.00 3.46
1642 1685 2.612115 AGGGAAGGCACCAGGGAG 60.612 66.667 0.00 0.00 0.00 4.30
1691 1734 0.940126 GCATCAGGTCCTGTATTGCG 59.060 55.000 18.65 3.67 32.61 4.85
1862 1905 6.040278 TGGTTTCAGATGATTGCAACAAGTTA 59.960 34.615 0.00 0.00 0.00 2.24
1879 1922 2.028930 AGTTACTTGCTCTTGTCGGAGG 60.029 50.000 0.00 0.00 34.21 4.30
2382 2435 0.545309 TGGAAGGACAGGAGGACCAG 60.545 60.000 0.00 0.00 38.94 4.00
2682 2738 9.435688 TCTTCAAGAAATACGAAGATGAATCAA 57.564 29.630 0.00 0.00 40.06 2.57
2706 2762 3.557264 GGAAGTGAAAGGGACGATTCAGT 60.557 47.826 0.00 0.00 41.79 3.41
2732 2788 2.626255 TAGGGTCTGCCGATCTCGCT 62.626 60.000 3.65 0.00 38.18 4.93
2867 2930 7.832503 TGTAGTGACATAAACACATCATCAG 57.167 36.000 0.00 0.00 40.25 2.90
2894 2957 4.822685 TTAGTTCCGCCCATAGTTTACA 57.177 40.909 0.00 0.00 0.00 2.41
2993 3056 4.016444 GCCCAACTTGGATGATCAAAGTA 58.984 43.478 15.19 0.00 40.96 2.24
3096 3159 0.906066 TACCAAGCGTTGCCTCCATA 59.094 50.000 0.00 0.00 0.00 2.74
3133 3196 7.153985 CCATACAAACCAAGTTGAAATGTCAT 58.846 34.615 3.87 0.00 32.48 3.06
3165 3228 6.775594 AGAAAAGGTAGCAACTGTTTTCTT 57.224 33.333 11.10 0.63 41.24 2.52
3169 3232 5.036117 AGGTAGCAACTGTTTTCTTCAGA 57.964 39.130 0.00 0.00 36.81 3.27
3170 3233 4.816925 AGGTAGCAACTGTTTTCTTCAGAC 59.183 41.667 0.00 0.00 36.81 3.51
3222 3285 1.746470 TCTGATCTTGGCATGTGCTG 58.254 50.000 4.84 0.00 41.70 4.41
3356 3419 8.200120 TGAACATACACAACAAATTCATCCAAA 58.800 29.630 0.00 0.00 0.00 3.28
3368 3431 8.859090 ACAAATTCATCCAAACATCTCAACTAA 58.141 29.630 0.00 0.00 0.00 2.24
3440 3505 5.503634 TTTCTCCATTCTGAACATCAGGA 57.496 39.130 7.47 0.00 44.39 3.86
3451 3516 3.550431 ATCAGGATGGGGCGTCGG 61.550 66.667 0.00 0.00 36.16 4.79
3512 3577 5.955961 TGATCCTATTGTCCACATTCTCA 57.044 39.130 0.00 0.00 0.00 3.27
3866 3931 8.156820 CCCATATCAATGATAACTGTACAGGAA 58.843 37.037 26.12 14.12 34.84 3.36
3942 4007 2.700371 TCAGTGAGCCGATAACCATGAT 59.300 45.455 0.00 0.00 0.00 2.45
3952 4017 4.449068 CCGATAACCATGATCAACTAGTGC 59.551 45.833 0.00 0.00 0.00 4.40
3999 4064 2.588989 CCTGAGGGAGCAGCTTCC 59.411 66.667 12.63 12.63 34.56 3.46
4002 4067 0.327591 CTGAGGGAGCAGCTTCCTTT 59.672 55.000 24.48 1.68 40.10 3.11
4015 4080 5.052481 CAGCTTCCTTTCCTTTTTCCAAAG 58.948 41.667 0.00 0.00 39.45 2.77
4024 4089 7.201947 CCTTTCCTTTTTCCAAAGAAGAGTGAT 60.202 37.037 0.00 0.00 41.97 3.06
4034 4099 7.551585 TCCAAAGAAGAGTGATCTGATAGAAC 58.448 38.462 0.00 0.00 0.00 3.01
4057 4122 8.970691 AACTATACAAGTGTTCATGCAAATTC 57.029 30.769 0.00 0.00 38.88 2.17
4082 4147 2.906389 TGCAGGGAGAGTGTTGATAGTT 59.094 45.455 0.00 0.00 0.00 2.24
4092 4157 0.447801 GTTGATAGTTGCAGGTGCCG 59.552 55.000 0.00 0.00 41.18 5.69
4101 4166 0.537143 TGCAGGTGCCGTTTTCAGAT 60.537 50.000 0.00 0.00 41.18 2.90
4110 4175 5.353123 GGTGCCGTTTTCAGATGAATTAGTA 59.647 40.000 0.00 0.00 33.54 1.82
4111 4176 6.456988 GGTGCCGTTTTCAGATGAATTAGTAG 60.457 42.308 0.00 0.00 33.54 2.57
4126 4191 8.877864 TGAATTAGTAGATTGAAATTGGTGGT 57.122 30.769 0.00 0.00 0.00 4.16
4143 4208 3.477530 GTGGTGGTTTAGCTGAGACTTT 58.522 45.455 0.00 0.00 0.00 2.66
4210 4275 6.828785 TCCAGAAATCAGGGAATTTAGCTTAC 59.171 38.462 0.00 0.00 0.00 2.34
4286 4351 3.386078 TGGTGTTGGTGCAATACATTTGT 59.614 39.130 0.00 0.00 37.23 2.83
4422 4490 6.491403 AGCTCTGCCTTTTCATTAAGAAGAAA 59.509 34.615 0.00 0.00 37.57 2.52
4459 4527 6.844097 TTATAAGGAAAACTGGCCGAAAAT 57.156 33.333 0.00 0.00 0.00 1.82
4670 4738 1.964373 AAAGCCAACACCCTACGCG 60.964 57.895 3.53 3.53 0.00 6.01
4671 4739 2.669777 AAAGCCAACACCCTACGCGT 62.670 55.000 19.17 19.17 0.00 6.01
4682 4750 1.500108 CCTACGCGTACGAGATCTCT 58.500 55.000 25.90 10.02 43.93 3.10
4708 4777 2.651361 CGCACCGACTTCCACTCT 59.349 61.111 0.00 0.00 0.00 3.24
4714 4783 2.583441 CGACTTCCACTCTGGCCCA 61.583 63.158 0.00 0.00 37.47 5.36
4734 4803 2.282603 GGCCGCAAACCCACCTAA 60.283 61.111 0.00 0.00 0.00 2.69
4737 4806 0.963355 GCCGCAAACCCACCTAATCA 60.963 55.000 0.00 0.00 0.00 2.57
4779 4848 1.379309 AAAGCCAACCACCACACGT 60.379 52.632 0.00 0.00 0.00 4.49
4837 4906 3.506096 CTCGAGGCCGCGTACTCA 61.506 66.667 28.27 7.96 33.36 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 4.271049 CGCGATGGAATGAGTTTATTCAGT 59.729 41.667 0.00 0.00 38.51 3.41
147 148 3.869246 GTGTTGAGGTGGTAATGGTATCG 59.131 47.826 0.00 0.00 0.00 2.92
155 156 3.968649 TCTTAGTGGTGTTGAGGTGGTAA 59.031 43.478 0.00 0.00 0.00 2.85
258 261 2.018542 TGTATTCCTTACACGGCTGC 57.981 50.000 0.00 0.00 35.86 5.25
330 333 1.021968 AATACCGAATGCCTTTCCGC 58.978 50.000 0.00 0.00 0.00 5.54
392 396 6.162241 ACTTTGGGGTGGATTAGGATAATTCT 59.838 38.462 0.00 0.00 0.00 2.40
401 405 2.755103 GCTTGACTTTGGGGTGGATTAG 59.245 50.000 0.00 0.00 0.00 1.73
684 692 2.736531 CAGTTTGCAAGTGGGGGC 59.263 61.111 0.00 0.00 0.00 5.80
737 747 3.201290 CGAAGGAGATGACCAGGAAATG 58.799 50.000 0.00 0.00 0.00 2.32
785 795 3.273434 TGCAAGAATCGGGAGAAATCAG 58.727 45.455 0.00 0.00 45.37 2.90
908 918 3.587498 ACCCATCTTCCTCAATCCGATA 58.413 45.455 0.00 0.00 0.00 2.92
1227 1243 2.853542 TCCAAGCAGGAGCCCACA 60.854 61.111 0.00 0.00 43.07 4.17
1277 1293 7.684529 ACTCTCTCTGAAAACACCATTTCTAT 58.315 34.615 1.99 0.00 39.51 1.98
1283 1324 7.939039 TGAAAATACTCTCTCTGAAAACACCAT 59.061 33.333 0.00 0.00 0.00 3.55
1293 1334 9.076781 TCCTAGATGATGAAAATACTCTCTCTG 57.923 37.037 0.00 0.00 0.00 3.35
1294 1335 9.827198 ATCCTAGATGATGAAAATACTCTCTCT 57.173 33.333 0.00 0.00 0.00 3.10
1354 1396 0.100682 CCACATGATTGCAGCAGAGC 59.899 55.000 0.00 0.00 0.00 4.09
1355 1397 1.746470 TCCACATGATTGCAGCAGAG 58.254 50.000 0.00 0.00 0.00 3.35
1356 1398 2.203470 TTCCACATGATTGCAGCAGA 57.797 45.000 0.00 0.00 0.00 4.26
1357 1399 3.306917 TTTTCCACATGATTGCAGCAG 57.693 42.857 0.00 0.00 0.00 4.24
1358 1400 3.007074 ACATTTTCCACATGATTGCAGCA 59.993 39.130 0.00 0.00 0.00 4.41
1359 1401 3.592059 ACATTTTCCACATGATTGCAGC 58.408 40.909 0.00 0.00 0.00 5.25
1360 1402 7.811236 GGATATACATTTTCCACATGATTGCAG 59.189 37.037 0.00 0.00 0.00 4.41
1361 1403 7.506599 AGGATATACATTTTCCACATGATTGCA 59.493 33.333 0.00 0.00 31.65 4.08
1362 1404 7.811236 CAGGATATACATTTTCCACATGATTGC 59.189 37.037 0.00 0.00 31.65 3.56
1363 1405 8.853126 ACAGGATATACATTTTCCACATGATTG 58.147 33.333 0.00 0.00 31.65 2.67
1364 1406 9.071276 GACAGGATATACATTTTCCACATGATT 57.929 33.333 0.00 0.00 31.65 2.57
1365 1407 8.443176 AGACAGGATATACATTTTCCACATGAT 58.557 33.333 0.00 0.00 31.65 2.45
1366 1408 7.716560 CAGACAGGATATACATTTTCCACATGA 59.283 37.037 0.00 0.00 31.65 3.07
1367 1409 7.500227 ACAGACAGGATATACATTTTCCACATG 59.500 37.037 0.00 0.00 31.65 3.21
1368 1410 7.577303 ACAGACAGGATATACATTTTCCACAT 58.423 34.615 0.00 0.00 31.65 3.21
1369 1411 6.957631 ACAGACAGGATATACATTTTCCACA 58.042 36.000 0.00 0.00 31.65 4.17
1370 1412 7.865706 AACAGACAGGATATACATTTTCCAC 57.134 36.000 0.00 0.00 31.65 4.02
1371 1413 8.739039 CAAAACAGACAGGATATACATTTTCCA 58.261 33.333 0.00 0.00 31.65 3.53
1372 1414 8.739972 ACAAAACAGACAGGATATACATTTTCC 58.260 33.333 0.00 0.00 0.00 3.13
1373 1415 9.559958 CACAAAACAGACAGGATATACATTTTC 57.440 33.333 0.00 0.00 0.00 2.29
1374 1416 8.522830 CCACAAAACAGACAGGATATACATTTT 58.477 33.333 0.00 0.00 0.00 1.82
1375 1417 7.669722 ACCACAAAACAGACAGGATATACATTT 59.330 33.333 0.00 0.00 0.00 2.32
1376 1418 7.175104 ACCACAAAACAGACAGGATATACATT 58.825 34.615 0.00 0.00 0.00 2.71
1377 1419 6.721318 ACCACAAAACAGACAGGATATACAT 58.279 36.000 0.00 0.00 0.00 2.29
1378 1420 6.121776 ACCACAAAACAGACAGGATATACA 57.878 37.500 0.00 0.00 0.00 2.29
1379 1421 6.653320 TCAACCACAAAACAGACAGGATATAC 59.347 38.462 0.00 0.00 0.00 1.47
1380 1422 6.774673 TCAACCACAAAACAGACAGGATATA 58.225 36.000 0.00 0.00 0.00 0.86
1381 1423 5.630121 TCAACCACAAAACAGACAGGATAT 58.370 37.500 0.00 0.00 0.00 1.63
1382 1424 5.042463 TCAACCACAAAACAGACAGGATA 57.958 39.130 0.00 0.00 0.00 2.59
1383 1425 3.897239 TCAACCACAAAACAGACAGGAT 58.103 40.909 0.00 0.00 0.00 3.24
1384 1426 3.358111 TCAACCACAAAACAGACAGGA 57.642 42.857 0.00 0.00 0.00 3.86
1385 1427 4.448537 TTTCAACCACAAAACAGACAGG 57.551 40.909 0.00 0.00 0.00 4.00
1386 1428 7.706179 ACATAATTTCAACCACAAAACAGACAG 59.294 33.333 0.00 0.00 0.00 3.51
1387 1429 7.551585 ACATAATTTCAACCACAAAACAGACA 58.448 30.769 0.00 0.00 0.00 3.41
1388 1430 8.419076 AACATAATTTCAACCACAAAACAGAC 57.581 30.769 0.00 0.00 0.00 3.51
1416 1458 8.800332 ACAGAAGATATGCTTTGACAAGAAAAT 58.200 29.630 0.00 0.00 36.83 1.82
1447 1490 8.087750 GGAATCTGTGGTTTTCATGAACAATAA 58.912 33.333 7.89 0.00 0.00 1.40
1466 1509 6.183347 ACTGATAGTTTTTCCAGGGAATCTG 58.817 40.000 0.83 2.68 43.00 2.90
1506 1549 2.934887 TGGCTGATCCACATTACATGG 58.065 47.619 0.00 0.00 40.72 3.66
1523 1566 6.773200 AGGCTTTTCTAATAGGATAGTTTGGC 59.227 38.462 0.00 0.00 0.00 4.52
1557 1600 4.997395 TGCCTGTAAGATCAAAGAGACAAC 59.003 41.667 0.00 0.00 34.07 3.32
1632 1675 1.610886 GGTACTTGAACTCCCTGGTGC 60.611 57.143 0.00 0.00 0.00 5.01
1642 1685 1.532437 CGGTTTTCGGGGTACTTGAAC 59.468 52.381 0.00 0.00 34.75 3.18
1691 1734 5.497474 TCTATTGTCCTAGTTTCTTTGGCC 58.503 41.667 0.00 0.00 0.00 5.36
1862 1905 1.004440 GCCTCCGACAAGAGCAAGT 60.004 57.895 0.00 0.00 32.17 3.16
1978 2021 7.127339 TCCTCCCTGCATATATAAATTAGACCC 59.873 40.741 0.00 0.00 0.00 4.46
2181 2234 4.748892 ACTATGAATGAGTCAACTGACCG 58.251 43.478 6.23 0.00 45.85 4.79
2353 2406 2.354259 CTGTCCTTCCATGTGCTCTTC 58.646 52.381 0.00 0.00 0.00 2.87
2382 2435 6.147821 TCGAAAGAGATTGGATTGAACAGAAC 59.852 38.462 0.00 0.00 34.84 3.01
2682 2738 3.009033 TGAATCGTCCCTTTCACTTCCAT 59.991 43.478 0.00 0.00 0.00 3.41
2706 2762 3.773119 AGATCGGCAGACCCTAAAGTTAA 59.227 43.478 0.00 0.00 0.00 2.01
2732 2788 5.503662 AAATGATGTTCGCATAATGCAGA 57.496 34.783 0.00 0.00 45.36 4.26
2867 2930 4.324267 ACTATGGGCGGAACTAATTATGC 58.676 43.478 0.00 0.00 0.00 3.14
2894 2957 2.818130 AGCGGACAAATTTGCATTGT 57.182 40.000 18.12 3.87 43.37 2.71
2993 3056 7.341256 AGCCATGATCAGAAACAAATAAGACAT 59.659 33.333 0.09 0.00 0.00 3.06
3096 3159 4.202441 GGTTTGTATGGCTGATCTGACAT 58.798 43.478 22.80 22.80 39.35 3.06
3133 3196 6.260050 CAGTTGCTACCTTTTCTTTGTACTCA 59.740 38.462 0.00 0.00 0.00 3.41
3165 3228 7.685481 TGATAAAACCTATCAAGTTGGTCTGA 58.315 34.615 2.34 0.00 34.70 3.27
3169 3232 6.891908 AGCATGATAAAACCTATCAAGTTGGT 59.108 34.615 2.34 0.00 37.47 3.67
3170 3233 7.067372 TGAGCATGATAAAACCTATCAAGTTGG 59.933 37.037 2.34 0.00 37.47 3.77
3222 3285 4.054671 CTGTTCAACTGTCCTCTGAAGAC 58.945 47.826 0.00 0.00 30.00 3.01
3382 3445 3.877508 TCAGCAGATCATTCATTCAGCAG 59.122 43.478 0.00 0.00 0.00 4.24
3440 3505 3.797353 AAGCATCCGACGCCCCAT 61.797 61.111 0.00 0.00 0.00 4.00
3451 3516 0.458669 CCTGCCATTCACCAAGCATC 59.541 55.000 0.00 0.00 34.16 3.91
3503 3568 3.373130 CACACCTAGTGCATGAGAATGTG 59.627 47.826 14.80 14.80 42.15 3.21
3866 3931 4.159879 AGCTGAACCTAACGCTGTATACTT 59.840 41.667 4.17 0.00 0.00 2.24
3942 4007 1.005037 CGGCCACAGCACTAGTTGA 60.005 57.895 2.24 0.00 42.56 3.18
3999 4064 7.100458 TCACTCTTCTTTGGAAAAAGGAAAG 57.900 36.000 0.00 0.00 0.00 2.62
4002 4067 6.488006 CAGATCACTCTTCTTTGGAAAAAGGA 59.512 38.462 0.00 0.00 0.00 3.36
4034 4099 7.699391 CCAGAATTTGCATGAACACTTGTATAG 59.301 37.037 0.00 0.00 0.00 1.31
4057 4122 0.604780 CAACACTCTCCCTGCACCAG 60.605 60.000 0.00 0.00 0.00 4.00
4066 4131 3.265791 CCTGCAACTATCAACACTCTCC 58.734 50.000 0.00 0.00 0.00 3.71
4082 4147 0.537143 ATCTGAAAACGGCACCTGCA 60.537 50.000 0.00 0.00 44.36 4.41
4101 4166 8.739039 CACCACCAATTTCAATCTACTAATTCA 58.261 33.333 0.00 0.00 0.00 2.57
4110 4175 5.279456 GCTAAACCACCACCAATTTCAATCT 60.279 40.000 0.00 0.00 0.00 2.40
4111 4176 4.929211 GCTAAACCACCACCAATTTCAATC 59.071 41.667 0.00 0.00 0.00 2.67
4181 4246 6.261158 GCTAAATTCCCTGATTTCTGGACTAC 59.739 42.308 5.16 0.00 37.15 2.73
4210 4275 6.705381 TGTTTCTAAAATTGTTTGATGGGCTG 59.295 34.615 0.00 0.00 0.00 4.85
4261 4326 1.683917 TGTATTGCACCAACACCAACC 59.316 47.619 0.00 0.00 0.00 3.77
4354 4422 2.363147 GAGAGGGCGTGAGAGGGT 60.363 66.667 0.00 0.00 0.00 4.34
4422 4490 7.790782 TTTCCTTATAAACTGGCCAATTCTT 57.209 32.000 7.01 0.00 0.00 2.52
4459 4527 3.183237 CGTGTATCGCAGATGTATCGA 57.817 47.619 0.00 0.00 45.12 3.59
4502 4570 1.596203 TCGTCGACTCGAGTGGTGT 60.596 57.895 25.58 0.00 36.23 4.16
4670 4738 1.008309 GGCGCCAGAGATCTCGTAC 60.008 63.158 24.80 9.13 34.09 3.67
4671 4739 2.543802 CGGCGCCAGAGATCTCGTA 61.544 63.158 28.98 0.00 34.09 3.43
4714 4783 4.660938 GGTGGGTTTGCGGCCTCT 62.661 66.667 0.00 0.00 0.00 3.69
4734 4803 0.548031 AGGGCGACATGGTCATTGAT 59.452 50.000 0.00 0.00 32.09 2.57
4737 4806 4.643795 CAGGGCGACATGGTCATT 57.356 55.556 0.00 0.00 38.79 2.57
4779 4848 1.074423 CGGCTCCGGGTATCTCCTA 59.926 63.158 0.00 0.00 36.25 2.94
4832 4901 1.086067 CGTCGTCGGCTAGGTGAGTA 61.086 60.000 0.00 0.00 0.00 2.59
4837 4906 1.239968 AACTTCGTCGTCGGCTAGGT 61.240 55.000 1.55 0.00 37.69 3.08


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

AutoCloner maintained by Alex Coulton.