Multiple sequence alignment - TraesCS5B01G448700

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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 TraesCS5B01G448700 chr5B 100.000 3158 0 0 1 3158 621239278 621236121 0.000000e+00 5832.0
1 TraesCS5B01G448700 chr5B 87.112 1645 189 15 943 2573 556795809 556794174 0.000000e+00 1842.0
2 TraesCS5B01G448700 chr5B 87.209 430 45 8 2738 3158 556624731 556624303 6.130000e-132 481.0
3 TraesCS5B01G448700 chr5B 81.015 453 66 14 2708 3158 556794056 556793622 3.020000e-90 342.0
4 TraesCS5B01G448700 chr5B 96.512 86 3 0 472 557 704532029 704531944 3.280000e-30 143.0
5 TraesCS5B01G448700 chr5D 93.684 1884 67 13 705 2574 499865358 499863513 0.000000e+00 2772.0
6 TraesCS5B01G448700 chr5D 81.824 1579 244 26 914 2476 42075979 42077530 0.000000e+00 1286.0
7 TraesCS5B01G448700 chr5D 95.763 590 21 2 2570 3158 499863402 499862816 0.000000e+00 948.0
8 TraesCS5B01G448700 chr5D 85.882 425 44 9 2738 3154 42077782 42078198 3.740000e-119 438.0
9 TraesCS5B01G448700 chr5D 92.105 152 9 3 556 705 499865612 499865462 8.870000e-51 211.0
10 TraesCS5B01G448700 chr5A 94.280 1416 56 12 1747 3158 624204955 624203561 0.000000e+00 2143.0
11 TraesCS5B01G448700 chr5A 93.038 474 16 2 857 1315 624205412 624204941 0.000000e+00 676.0
12 TraesCS5B01G448700 chr5A 87.313 134 17 0 1 134 624209253 624209120 1.520000e-33 154.0
13 TraesCS5B01G448700 chr1B 85.345 1665 201 20 991 2633 662037311 662038954 0.000000e+00 1683.0
14 TraesCS5B01G448700 chr1B 80.263 1672 258 34 988 2634 662153019 662154643 0.000000e+00 1194.0
15 TraesCS5B01G448700 chr1B 96.629 89 3 0 469 557 549520148 549520060 7.060000e-32 148.0
16 TraesCS5B01G448700 chr6B 85.547 1626 211 13 1013 2626 15381521 15379908 0.000000e+00 1679.0
17 TraesCS5B01G448700 chr6B 83.709 1596 205 27 993 2573 670592702 670591147 0.000000e+00 1456.0
18 TraesCS5B01G448700 chr6B 81.647 1542 234 30 1058 2581 15715152 15713642 0.000000e+00 1234.0
19 TraesCS5B01G448700 chr6B 81.582 1542 236 31 1115 2634 16320701 16322216 0.000000e+00 1230.0
20 TraesCS5B01G448700 chr6B 87.413 429 44 8 2738 3158 15233024 15232598 4.740000e-133 484.0
21 TraesCS5B01G448700 chr6B 86.150 426 38 7 2738 3155 16269167 16269579 1.040000e-119 440.0
22 TraesCS5B01G448700 chr6B 89.189 296 26 3 2869 3158 52979678 52979383 6.440000e-97 364.0
23 TraesCS5B01G448700 chr6B 80.795 453 69 16 2708 3158 15396256 15395820 3.900000e-89 339.0
24 TraesCS5B01G448700 chr2B 82.949 1736 227 37 922 2634 54016741 54015052 0.000000e+00 1502.0
25 TraesCS5B01G448700 chr2B 82.616 1720 218 44 941 2634 54044072 54042408 0.000000e+00 1445.0
26 TraesCS5B01G448700 chr2B 81.373 1471 236 22 1115 2572 709569639 709568194 0.000000e+00 1164.0
27 TraesCS5B01G448700 chr2B 83.482 448 53 12 2708 3139 89492321 89492763 6.350000e-107 398.0
28 TraesCS5B01G448700 chr2B 92.929 99 7 0 458 556 667782154 667782252 9.130000e-31 145.0
29 TraesCS5B01G448700 chr6D 82.325 1703 238 45 899 2573 33894942 33896609 0.000000e+00 1419.0
30 TraesCS5B01G448700 chr6D 83.052 1540 213 28 1115 2634 8987358 8988869 0.000000e+00 1354.0
31 TraesCS5B01G448700 chr6D 96.226 53 2 0 867 919 8402595 8402543 1.560000e-13 87.9
32 TraesCS5B01G448700 chr6D 96.226 53 2 0 867 919 8893879 8893931 1.560000e-13 87.9
33 TraesCS5B01G448700 chr6D 89.231 65 5 1 857 919 33894850 33894914 2.610000e-11 80.5
34 TraesCS5B01G448700 chr6D 91.379 58 5 0 857 914 34006891 34006948 2.610000e-11 80.5
35 TraesCS5B01G448700 chr7B 84.762 840 110 9 988 1825 32348078 32347255 0.000000e+00 826.0
36 TraesCS5B01G448700 chr3D 91.156 294 19 6 2869 3155 582881304 582881597 2.950000e-105 392.0
37 TraesCS5B01G448700 chr3B 88.449 303 18 8 2869 3158 778341491 778341193 1.800000e-92 350.0
38 TraesCS5B01G448700 chr3A 94.681 94 5 0 464 557 69643865 69643772 2.540000e-31 147.0
39 TraesCS5B01G448700 chr3A 96.471 85 3 0 473 557 696373517 696373433 1.180000e-29 141.0
40 TraesCS5B01G448700 chr7D 93.750 96 4 2 463 557 180445021 180444927 3.280000e-30 143.0
41 TraesCS5B01G448700 chr4B 95.455 88 4 0 470 557 59873732 59873819 1.180000e-29 141.0
42 TraesCS5B01G448700 chr4B 93.617 94 4 2 468 559 384157933 384158026 4.250000e-29 139.0
43 TraesCS5B01G448700 chr7A 93.617 94 5 1 467 560 553036599 553036691 4.250000e-29 139.0


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 TraesCS5B01G448700 chr5B 621236121 621239278 3157 True 5832.000000 5832 100.000000 1 3158 1 chr5B.!!$R2 3157
1 TraesCS5B01G448700 chr5B 556793622 556795809 2187 True 1092.000000 1842 84.063500 943 3158 2 chr5B.!!$R4 2215
2 TraesCS5B01G448700 chr5D 499862816 499865612 2796 True 1310.333333 2772 93.850667 556 3158 3 chr5D.!!$R1 2602
3 TraesCS5B01G448700 chr5D 42075979 42078198 2219 False 862.000000 1286 83.853000 914 3154 2 chr5D.!!$F1 2240
4 TraesCS5B01G448700 chr5A 624203561 624209253 5692 True 991.000000 2143 91.543667 1 3158 3 chr5A.!!$R1 3157
5 TraesCS5B01G448700 chr1B 662037311 662038954 1643 False 1683.000000 1683 85.345000 991 2633 1 chr1B.!!$F1 1642
6 TraesCS5B01G448700 chr1B 662153019 662154643 1624 False 1194.000000 1194 80.263000 988 2634 1 chr1B.!!$F2 1646
7 TraesCS5B01G448700 chr6B 15379908 15381521 1613 True 1679.000000 1679 85.547000 1013 2626 1 chr6B.!!$R2 1613
8 TraesCS5B01G448700 chr6B 670591147 670592702 1555 True 1456.000000 1456 83.709000 993 2573 1 chr6B.!!$R6 1580
9 TraesCS5B01G448700 chr6B 15713642 15715152 1510 True 1234.000000 1234 81.647000 1058 2581 1 chr6B.!!$R4 1523
10 TraesCS5B01G448700 chr6B 16320701 16322216 1515 False 1230.000000 1230 81.582000 1115 2634 1 chr6B.!!$F2 1519
11 TraesCS5B01G448700 chr2B 54015052 54016741 1689 True 1502.000000 1502 82.949000 922 2634 1 chr2B.!!$R1 1712
12 TraesCS5B01G448700 chr2B 54042408 54044072 1664 True 1445.000000 1445 82.616000 941 2634 1 chr2B.!!$R2 1693
13 TraesCS5B01G448700 chr2B 709568194 709569639 1445 True 1164.000000 1164 81.373000 1115 2572 1 chr2B.!!$R3 1457
14 TraesCS5B01G448700 chr6D 8987358 8988869 1511 False 1354.000000 1354 83.052000 1115 2634 1 chr6D.!!$F2 1519
15 TraesCS5B01G448700 chr6D 33894850 33896609 1759 False 749.750000 1419 85.778000 857 2573 2 chr6D.!!$F4 1716
16 TraesCS5B01G448700 chr7B 32347255 32348078 823 True 826.000000 826 84.762000 988 1825 1 chr7B.!!$R1 837

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
183 184 0.246635 TACTCCTCGAGCAAGCAACC 59.753 55.0 6.99 0.0 32.04 3.77 F
937 4153 0.392193 ACGCAAATCCTCTGGCTCTG 60.392 55.0 0.00 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 5139 0.901124 AGCTCGCAGATGAGGAACTT 59.099 50.0 0.00 0.0 34.01 2.66 R
2802 6308 1.913778 TGCACATTTCATCCTGCAGT 58.086 45.0 13.81 0.0 34.73 4.40 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
25 26 7.701445 AGATCAATTAGTGAAAACTAGCATGC 58.299 34.615 10.51 10.51 40.50 4.06
56 57 2.262915 CAGACACCTCAGCCGACC 59.737 66.667 0.00 0.00 0.00 4.79
69 70 1.749634 AGCCGACCTGACTACACATAC 59.250 52.381 0.00 0.00 0.00 2.39
80 81 4.159693 TGACTACACATACAGATCCACACC 59.840 45.833 0.00 0.00 0.00 4.16
86 87 1.261938 TACAGATCCACACCCCACCG 61.262 60.000 0.00 0.00 0.00 4.94
88 89 1.537889 AGATCCACACCCCACCGAA 60.538 57.895 0.00 0.00 0.00 4.30
89 90 0.914417 AGATCCACACCCCACCGAAT 60.914 55.000 0.00 0.00 0.00 3.34
94 95 1.191535 CACACCCCACCGAATAGAGA 58.808 55.000 0.00 0.00 0.00 3.10
103 104 4.372656 CCACCGAATAGAGAAACTCCATC 58.627 47.826 0.00 0.00 0.00 3.51
105 106 4.806247 CACCGAATAGAGAAACTCCATCAC 59.194 45.833 0.00 0.00 0.00 3.06
106 107 4.466370 ACCGAATAGAGAAACTCCATCACA 59.534 41.667 0.00 0.00 0.00 3.58
116 117 1.133823 ACTCCATCACAGTTGCCAACA 60.134 47.619 10.69 0.00 0.00 3.33
117 118 1.955778 CTCCATCACAGTTGCCAACAA 59.044 47.619 10.69 0.00 0.00 2.83
134 135 8.978874 TGCCAACAACTATTATCATAATCACT 57.021 30.769 0.00 0.00 0.00 3.41
135 136 9.407380 TGCCAACAACTATTATCATAATCACTT 57.593 29.630 0.00 0.00 0.00 3.16
136 137 9.884465 GCCAACAACTATTATCATAATCACTTC 57.116 33.333 0.00 0.00 0.00 3.01
182 183 1.067495 ACTACTCCTCGAGCAAGCAAC 60.067 52.381 6.99 0.00 32.04 4.17
183 184 0.246635 TACTCCTCGAGCAAGCAACC 59.753 55.000 6.99 0.00 32.04 3.77
185 186 3.793144 CCTCGAGCAAGCAACCGC 61.793 66.667 6.99 0.00 38.99 5.68
188 189 3.711842 CGAGCAAGCAACCGCGAA 61.712 61.111 8.23 0.00 45.49 4.70
189 190 2.870372 GAGCAAGCAACCGCGAAT 59.130 55.556 8.23 0.00 45.49 3.34
190 191 1.210155 GAGCAAGCAACCGCGAATT 59.790 52.632 8.23 0.00 45.49 2.17
196 197 2.380084 AGCAACCGCGAATTAGAGAA 57.620 45.000 8.23 0.00 45.49 2.87
209 1111 6.895040 GCGAATTAGAGAAAACTACAATCACG 59.105 38.462 0.00 0.00 0.00 4.35
211 1113 8.808529 CGAATTAGAGAAAACTACAATCACGAT 58.191 33.333 0.00 0.00 0.00 3.73
215 1117 3.689649 AGAAAACTACAATCACGATGGGC 59.310 43.478 0.00 0.00 0.00 5.36
218 1120 0.535102 CTACAATCACGATGGGCCCC 60.535 60.000 22.27 2.97 0.00 5.80
232 1134 1.745890 GCCCCCACCAGTTTGTTTC 59.254 57.895 0.00 0.00 0.00 2.78
234 1136 1.460273 CCCCCACCAGTTTGTTTCCG 61.460 60.000 0.00 0.00 0.00 4.30
267 1169 3.390639 TGTTTTTGCCCCACATCAAATCT 59.609 39.130 0.00 0.00 32.92 2.40
268 1170 4.141528 TGTTTTTGCCCCACATCAAATCTT 60.142 37.500 0.00 0.00 32.92 2.40
269 1171 3.959535 TTTGCCCCACATCAAATCTTC 57.040 42.857 0.00 0.00 0.00 2.87
270 1172 2.905415 TGCCCCACATCAAATCTTCT 57.095 45.000 0.00 0.00 0.00 2.85
271 1173 3.173953 TGCCCCACATCAAATCTTCTT 57.826 42.857 0.00 0.00 0.00 2.52
272 1174 3.091545 TGCCCCACATCAAATCTTCTTC 58.908 45.455 0.00 0.00 0.00 2.87
273 1175 3.245371 TGCCCCACATCAAATCTTCTTCT 60.245 43.478 0.00 0.00 0.00 2.85
274 1176 3.129988 GCCCCACATCAAATCTTCTTCTG 59.870 47.826 0.00 0.00 0.00 3.02
275 1177 4.338879 CCCCACATCAAATCTTCTTCTGT 58.661 43.478 0.00 0.00 0.00 3.41
276 1178 4.768968 CCCCACATCAAATCTTCTTCTGTT 59.231 41.667 0.00 0.00 0.00 3.16
281 1183 7.040892 CCACATCAAATCTTCTTCTGTTCTTCA 60.041 37.037 0.00 0.00 0.00 3.02
298 1200 8.287439 TGTTCTTCATTTGTTTTTACCTCTCA 57.713 30.769 0.00 0.00 0.00 3.27
302 1204 6.385649 TCATTTGTTTTTACCTCTCACACC 57.614 37.500 0.00 0.00 0.00 4.16
303 1205 6.126409 TCATTTGTTTTTACCTCTCACACCT 58.874 36.000 0.00 0.00 0.00 4.00
304 1206 6.605594 TCATTTGTTTTTACCTCTCACACCTT 59.394 34.615 0.00 0.00 0.00 3.50
305 1207 6.445357 TTTGTTTTTACCTCTCACACCTTC 57.555 37.500 0.00 0.00 0.00 3.46
306 1208 4.457466 TGTTTTTACCTCTCACACCTTCC 58.543 43.478 0.00 0.00 0.00 3.46
307 1209 3.782656 TTTTACCTCTCACACCTTCCC 57.217 47.619 0.00 0.00 0.00 3.97
308 1210 1.263356 TTACCTCTCACACCTTCCCG 58.737 55.000 0.00 0.00 0.00 5.14
309 1211 1.255667 TACCTCTCACACCTTCCCGC 61.256 60.000 0.00 0.00 0.00 6.13
310 1212 2.583441 CCTCTCACACCTTCCCGCA 61.583 63.158 0.00 0.00 0.00 5.69
311 1213 1.079543 CTCTCACACCTTCCCGCAG 60.080 63.158 0.00 0.00 0.00 5.18
358 1349 3.887621 AACGTATCAGTACATGTGCCT 57.112 42.857 9.11 0.87 0.00 4.75
360 1351 3.521560 ACGTATCAGTACATGTGCCTTG 58.478 45.455 9.11 2.53 0.00 3.61
365 1356 6.089954 CGTATCAGTACATGTGCCTTGATATG 59.910 42.308 20.81 20.71 32.21 1.78
366 1357 5.357742 TCAGTACATGTGCCTTGATATGT 57.642 39.130 9.11 0.00 37.51 2.29
367 1358 6.478512 TCAGTACATGTGCCTTGATATGTA 57.521 37.500 9.11 0.00 35.55 2.29
368 1359 7.066307 TCAGTACATGTGCCTTGATATGTAT 57.934 36.000 9.11 0.00 38.04 2.29
369 1360 7.154656 TCAGTACATGTGCCTTGATATGTATC 58.845 38.462 9.11 0.00 38.04 2.24
370 1361 6.930722 CAGTACATGTGCCTTGATATGTATCA 59.069 38.462 9.11 0.00 40.69 2.15
371 1362 7.117379 CAGTACATGTGCCTTGATATGTATCAG 59.883 40.741 9.11 0.00 42.99 2.90
372 1363 5.933617 ACATGTGCCTTGATATGTATCAGT 58.066 37.500 0.00 0.00 42.99 3.41
373 1364 5.761726 ACATGTGCCTTGATATGTATCAGTG 59.238 40.000 0.00 0.00 42.99 3.66
374 1365 5.357742 TGTGCCTTGATATGTATCAGTGT 57.642 39.130 3.23 0.00 42.99 3.55
375 1366 5.359756 TGTGCCTTGATATGTATCAGTGTC 58.640 41.667 3.23 0.00 42.99 3.67
376 1367 4.445718 GTGCCTTGATATGTATCAGTGTCG 59.554 45.833 3.23 0.00 42.99 4.35
377 1368 4.340950 TGCCTTGATATGTATCAGTGTCGA 59.659 41.667 3.23 0.00 42.99 4.20
378 1369 4.681942 GCCTTGATATGTATCAGTGTCGAC 59.318 45.833 9.11 9.11 42.99 4.20
379 1370 5.736207 GCCTTGATATGTATCAGTGTCGACA 60.736 44.000 15.76 15.76 42.99 4.35
380 1371 5.687730 CCTTGATATGTATCAGTGTCGACAC 59.312 44.000 35.83 35.83 42.99 3.67
430 1421 6.428083 TGACACTAAGGAAGACAAACCATA 57.572 37.500 0.00 0.00 0.00 2.74
435 1426 6.318900 CACTAAGGAAGACAAACCATATTCCC 59.681 42.308 0.00 0.00 40.26 3.97
443 1434 6.263754 AGACAAACCATATTCCCTCCATTTT 58.736 36.000 0.00 0.00 0.00 1.82
451 1442 7.455638 ACCATATTCCCTCCATTTTATGAATGG 59.544 37.037 13.67 13.67 46.59 3.16
490 1481 8.716674 AATATAATACTCCCTCTGTACCGAAA 57.283 34.615 0.00 0.00 0.00 3.46
491 1482 8.896722 ATATAATACTCCCTCTGTACCGAAAT 57.103 34.615 0.00 0.00 0.00 2.17
492 1483 9.986157 ATATAATACTCCCTCTGTACCGAAATA 57.014 33.333 0.00 0.00 0.00 1.40
493 1484 6.651975 AATACTCCCTCTGTACCGAAATAG 57.348 41.667 0.00 0.00 0.00 1.73
494 1485 3.978610 ACTCCCTCTGTACCGAAATAGT 58.021 45.455 0.00 0.00 0.00 2.12
497 1488 4.091549 TCCCTCTGTACCGAAATAGTTGT 58.908 43.478 0.00 0.00 0.00 3.32
499 1490 4.103357 CCTCTGTACCGAAATAGTTGTCG 58.897 47.826 0.00 0.00 37.01 4.35
500 1491 3.504863 TCTGTACCGAAATAGTTGTCGC 58.495 45.455 0.00 0.00 35.93 5.19
501 1492 3.192001 TCTGTACCGAAATAGTTGTCGCT 59.808 43.478 0.00 0.00 35.93 4.93
502 1493 3.247442 TGTACCGAAATAGTTGTCGCTG 58.753 45.455 0.00 0.00 35.93 5.18
503 1494 1.722011 ACCGAAATAGTTGTCGCTGG 58.278 50.000 0.00 0.00 35.93 4.85
504 1495 1.274167 ACCGAAATAGTTGTCGCTGGA 59.726 47.619 0.00 0.00 35.93 3.86
505 1496 1.927174 CCGAAATAGTTGTCGCTGGAG 59.073 52.381 0.00 0.00 35.93 3.86
506 1497 2.607187 CGAAATAGTTGTCGCTGGAGT 58.393 47.619 0.00 0.00 0.00 3.85
508 1499 3.791887 CGAAATAGTTGTCGCTGGAGTAG 59.208 47.826 0.00 0.00 0.00 2.57
531 1522 2.626266 TGAACTTCAGCTACTCCAACGA 59.374 45.455 0.00 0.00 0.00 3.85
534 1525 2.364324 ACTTCAGCTACTCCAACGACAA 59.636 45.455 0.00 0.00 0.00 3.18
536 1527 1.961394 TCAGCTACTCCAACGACAACT 59.039 47.619 0.00 0.00 0.00 3.16
542 1533 5.408604 AGCTACTCCAACGACAACTATTTTG 59.591 40.000 0.00 0.00 0.00 2.44
543 1534 5.390567 GCTACTCCAACGACAACTATTTTGG 60.391 44.000 0.00 0.00 38.48 3.28
544 1535 4.457466 ACTCCAACGACAACTATTTTGGT 58.543 39.130 0.00 0.00 38.32 3.67
545 1536 5.613329 ACTCCAACGACAACTATTTTGGTA 58.387 37.500 0.00 0.00 38.32 3.25
547 1538 5.366460 TCCAACGACAACTATTTTGGTACA 58.634 37.500 0.00 0.00 38.32 2.90
548 1539 5.467399 TCCAACGACAACTATTTTGGTACAG 59.533 40.000 0.00 0.00 42.39 2.74
549 1540 5.467399 CCAACGACAACTATTTTGGTACAGA 59.533 40.000 0.00 0.00 42.39 3.41
551 1542 6.721571 ACGACAACTATTTTGGTACAGATG 57.278 37.500 0.00 0.00 42.39 2.90
552 1543 5.642063 ACGACAACTATTTTGGTACAGATGG 59.358 40.000 0.00 0.00 42.39 3.51
553 1544 5.872617 CGACAACTATTTTGGTACAGATGGA 59.127 40.000 0.00 0.00 42.39 3.41
554 1545 6.036083 CGACAACTATTTTGGTACAGATGGAG 59.964 42.308 0.00 0.00 42.39 3.86
559 3596 7.328737 ACTATTTTGGTACAGATGGAGTACAC 58.671 38.462 0.00 0.00 42.73 2.90
569 3606 7.584122 ACAGATGGAGTACACGTTTATCTAT 57.416 36.000 0.00 0.00 0.00 1.98
630 3667 3.774734 AGCATGCATGTGGATCCATAAT 58.225 40.909 26.79 12.29 0.00 1.28
768 3915 6.693315 AGTGTATGTTATTATTGTGGGCAC 57.307 37.500 0.00 0.00 0.00 5.01
769 3916 5.295787 AGTGTATGTTATTATTGTGGGCACG 59.704 40.000 0.00 0.00 0.00 5.34
770 3917 4.576873 TGTATGTTATTATTGTGGGCACGG 59.423 41.667 0.00 0.00 0.00 4.94
771 3918 1.746220 TGTTATTATTGTGGGCACGGC 59.254 47.619 0.00 0.00 0.00 5.68
850 4002 1.288508 ACCAGCCCAGCCCATTATCA 61.289 55.000 0.00 0.00 0.00 2.15
851 4003 0.538977 CCAGCCCAGCCCATTATCAG 60.539 60.000 0.00 0.00 0.00 2.90
852 4004 0.475475 CAGCCCAGCCCATTATCAGA 59.525 55.000 0.00 0.00 0.00 3.27
853 4005 0.769873 AGCCCAGCCCATTATCAGAG 59.230 55.000 0.00 0.00 0.00 3.35
854 4006 0.767375 GCCCAGCCCATTATCAGAGA 59.233 55.000 0.00 0.00 0.00 3.10
855 4007 1.143684 GCCCAGCCCATTATCAGAGAA 59.856 52.381 0.00 0.00 0.00 2.87
937 4153 0.392193 ACGCAAATCCTCTGGCTCTG 60.392 55.000 0.00 0.00 0.00 3.35
1049 4283 3.641046 CCCATCTCCTCTCTTCTTCTCA 58.359 50.000 0.00 0.00 0.00 3.27
1880 5152 3.204526 GCAGATCCAAGTTCCTCATCTG 58.795 50.000 3.34 3.34 42.28 2.90
1972 5249 1.304381 AGACCCCGGCACTACGTTA 60.304 57.895 0.00 0.00 0.00 3.18
2092 5369 0.901827 TCATAAGGAAGCTGCACCGA 59.098 50.000 1.02 0.00 0.00 4.69
2208 5485 0.391130 TGGTTGTCCGCTGCTGTATC 60.391 55.000 0.00 0.00 36.30 2.24
2209 5486 0.108138 GGTTGTCCGCTGCTGTATCT 60.108 55.000 0.00 0.00 0.00 1.98
2210 5487 1.002366 GTTGTCCGCTGCTGTATCTG 58.998 55.000 0.00 0.00 0.00 2.90
2211 5488 0.608130 TTGTCCGCTGCTGTATCTGT 59.392 50.000 0.00 0.00 0.00 3.41
2212 5489 1.470051 TGTCCGCTGCTGTATCTGTA 58.530 50.000 0.00 0.00 0.00 2.74
2213 5490 2.031870 TGTCCGCTGCTGTATCTGTAT 58.968 47.619 0.00 0.00 0.00 2.29
2318 5597 3.072184 ACTCAGCAGAGAAGAAACCATGT 59.928 43.478 13.73 0.00 44.98 3.21
2449 5740 4.868171 TCGTTGCTGGTGTATTGAGATAAC 59.132 41.667 0.00 0.00 0.00 1.89
2466 5757 4.654724 AGATAACTAGCCAAGGTAAGGTCC 59.345 45.833 0.00 0.00 28.96 4.46
2547 5852 8.324306 GTGGATAATTGGAGGATCAATCTGATA 58.676 37.037 0.00 0.00 37.20 2.15
2680 6183 2.973945 AGTAAAGATGGAGGCGTTCAC 58.026 47.619 0.00 0.00 0.00 3.18
2802 6308 6.617784 TGGTCATATTGGAAATACCTACTGGA 59.382 38.462 0.00 0.00 39.86 3.86
2861 6372 2.879002 TCTGCTAAAGAGAGATGCCG 57.121 50.000 0.00 0.00 0.00 5.69
2862 6373 1.410517 TCTGCTAAAGAGAGATGCCGG 59.589 52.381 0.00 0.00 0.00 6.13
3001 6516 3.436704 GCACTTGCTGCTAGTGATGTTAA 59.563 43.478 36.32 5.16 44.52 2.01
3110 6651 6.677913 TGGCAGCTTAAGATTTTTAGTTCAC 58.322 36.000 6.67 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.588899 ACATGGCATGCTAGTTTTCACTA 58.411 39.130 26.70 0.00 34.06 2.74
15 16 1.004628 TGTGGACATGGCATGCTAGTT 59.995 47.619 26.70 7.35 0.00 2.24
56 57 5.344066 GTGTGGATCTGTATGTGTAGTCAG 58.656 45.833 0.00 0.00 0.00 3.51
59 60 3.451178 GGGTGTGGATCTGTATGTGTAGT 59.549 47.826 0.00 0.00 0.00 2.73
69 70 1.836999 TTCGGTGGGGTGTGGATCTG 61.837 60.000 0.00 0.00 0.00 2.90
80 81 2.500098 TGGAGTTTCTCTATTCGGTGGG 59.500 50.000 0.00 0.00 0.00 4.61
86 87 6.183360 GCAACTGTGATGGAGTTTCTCTATTC 60.183 42.308 0.00 0.00 31.94 1.75
88 89 5.181748 GCAACTGTGATGGAGTTTCTCTAT 58.818 41.667 0.00 0.00 34.44 1.98
89 90 4.563580 GGCAACTGTGATGGAGTTTCTCTA 60.564 45.833 0.00 0.00 31.05 2.43
94 95 2.362077 GTTGGCAACTGTGATGGAGTTT 59.638 45.455 22.66 0.00 31.05 2.66
164 165 0.246635 GGTTGCTTGCTCGAGGAGTA 59.753 55.000 15.58 2.38 31.39 2.59
182 183 5.773239 TTGTAGTTTTCTCTAATTCGCGG 57.227 39.130 6.13 0.00 0.00 6.46
183 184 6.895040 GTGATTGTAGTTTTCTCTAATTCGCG 59.105 38.462 0.00 0.00 0.00 5.87
185 186 8.169839 TCGTGATTGTAGTTTTCTCTAATTCG 57.830 34.615 0.00 0.00 0.00 3.34
188 189 7.495934 CCCATCGTGATTGTAGTTTTCTCTAAT 59.504 37.037 0.00 0.00 0.00 1.73
189 190 6.816640 CCCATCGTGATTGTAGTTTTCTCTAA 59.183 38.462 0.00 0.00 0.00 2.10
190 191 6.338146 CCCATCGTGATTGTAGTTTTCTCTA 58.662 40.000 0.00 0.00 0.00 2.43
196 197 2.365582 GGCCCATCGTGATTGTAGTTT 58.634 47.619 0.00 0.00 0.00 2.66
211 1113 4.232061 CAAACTGGTGGGGGCCCA 62.232 66.667 26.86 7.88 45.02 5.36
215 1117 1.460273 CGGAAACAAACTGGTGGGGG 61.460 60.000 0.00 0.00 0.00 5.40
218 1120 2.951457 AAACGGAAACAAACTGGTGG 57.049 45.000 0.00 0.00 0.00 4.61
243 1145 3.853355 TTGATGTGGGGCAAAAACATT 57.147 38.095 0.00 0.00 34.74 2.71
258 1160 9.909644 AAATGAAGAACAGAAGAAGATTTGATG 57.090 29.630 0.00 0.00 0.00 3.07
267 1169 9.581099 GGTAAAAACAAATGAAGAACAGAAGAA 57.419 29.630 0.00 0.00 0.00 2.52
268 1170 8.966868 AGGTAAAAACAAATGAAGAACAGAAGA 58.033 29.630 0.00 0.00 0.00 2.87
269 1171 9.237846 GAGGTAAAAACAAATGAAGAACAGAAG 57.762 33.333 0.00 0.00 0.00 2.85
270 1172 8.966868 AGAGGTAAAAACAAATGAAGAACAGAA 58.033 29.630 0.00 0.00 0.00 3.02
271 1173 8.519799 AGAGGTAAAAACAAATGAAGAACAGA 57.480 30.769 0.00 0.00 0.00 3.41
272 1174 8.405531 TGAGAGGTAAAAACAAATGAAGAACAG 58.594 33.333 0.00 0.00 0.00 3.16
273 1175 8.188139 GTGAGAGGTAAAAACAAATGAAGAACA 58.812 33.333 0.00 0.00 0.00 3.18
274 1176 8.188139 TGTGAGAGGTAAAAACAAATGAAGAAC 58.812 33.333 0.00 0.00 0.00 3.01
275 1177 8.188139 GTGTGAGAGGTAAAAACAAATGAAGAA 58.812 33.333 0.00 0.00 0.00 2.52
276 1178 7.201785 GGTGTGAGAGGTAAAAACAAATGAAGA 60.202 37.037 0.00 0.00 0.00 2.87
281 1183 6.040504 GGAAGGTGTGAGAGGTAAAAACAAAT 59.959 38.462 0.00 0.00 0.00 2.32
304 1206 4.145807 TCTTTTTATGTTTTCCTGCGGGA 58.854 39.130 11.27 11.27 40.36 5.14
305 1207 4.513198 TCTTTTTATGTTTTCCTGCGGG 57.487 40.909 4.71 4.71 0.00 6.13
306 1208 9.796120 TTATATTCTTTTTATGTTTTCCTGCGG 57.204 29.630 0.00 0.00 0.00 5.69
340 1331 3.780902 TCAAGGCACATGTACTGATACG 58.219 45.455 0.00 0.00 33.60 3.06
342 1333 7.066307 ACATATCAAGGCACATGTACTGATA 57.934 36.000 15.23 15.23 30.04 2.15
350 1341 5.761726 ACACTGATACATATCAAGGCACATG 59.238 40.000 3.30 0.00 41.72 3.21
387 1378 4.075682 TCAACACTGATATCCCGCAAAAA 58.924 39.130 0.00 0.00 0.00 1.94
388 1379 3.438781 GTCAACACTGATATCCCGCAAAA 59.561 43.478 0.00 0.00 33.05 2.44
389 1380 3.006940 GTCAACACTGATATCCCGCAAA 58.993 45.455 0.00 0.00 33.05 3.68
390 1381 2.027653 TGTCAACACTGATATCCCGCAA 60.028 45.455 0.00 0.00 33.05 4.85
391 1382 1.552792 TGTCAACACTGATATCCCGCA 59.447 47.619 0.00 0.00 33.05 5.69
392 1383 1.933853 GTGTCAACACTGATATCCCGC 59.066 52.381 6.03 0.00 43.25 6.13
404 1395 4.879545 GGTTTGTCTTCCTTAGTGTCAACA 59.120 41.667 0.00 0.00 0.00 3.33
407 1398 4.764050 TGGTTTGTCTTCCTTAGTGTCA 57.236 40.909 0.00 0.00 0.00 3.58
471 1462 5.703310 ACTATTTCGGTACAGAGGGAGTAT 58.297 41.667 0.00 0.00 0.00 2.12
472 1463 5.121380 ACTATTTCGGTACAGAGGGAGTA 57.879 43.478 0.00 0.00 0.00 2.59
474 1465 4.159879 ACAACTATTTCGGTACAGAGGGAG 59.840 45.833 0.00 0.00 0.00 4.30
475 1466 4.091549 ACAACTATTTCGGTACAGAGGGA 58.908 43.478 0.00 0.00 0.00 4.20
476 1467 4.430908 GACAACTATTTCGGTACAGAGGG 58.569 47.826 0.00 0.00 0.00 4.30
477 1468 4.103357 CGACAACTATTTCGGTACAGAGG 58.897 47.826 0.00 0.00 0.00 3.69
478 1469 3.546670 GCGACAACTATTTCGGTACAGAG 59.453 47.826 0.00 0.00 35.73 3.35
479 1470 3.192001 AGCGACAACTATTTCGGTACAGA 59.808 43.478 0.00 0.00 43.71 3.41
480 1471 3.303495 CAGCGACAACTATTTCGGTACAG 59.697 47.826 0.00 0.00 43.70 2.74
481 1472 3.247442 CAGCGACAACTATTTCGGTACA 58.753 45.455 0.00 0.00 43.70 2.90
482 1473 2.601763 CCAGCGACAACTATTTCGGTAC 59.398 50.000 0.00 0.00 43.70 3.34
483 1474 2.492881 TCCAGCGACAACTATTTCGGTA 59.507 45.455 0.00 0.00 43.70 4.02
484 1475 1.274167 TCCAGCGACAACTATTTCGGT 59.726 47.619 0.00 0.00 46.29 4.69
485 1476 1.927174 CTCCAGCGACAACTATTTCGG 59.073 52.381 0.00 0.00 35.73 4.30
486 1477 2.607187 ACTCCAGCGACAACTATTTCG 58.393 47.619 0.00 0.00 38.31 3.46
487 1478 3.552294 GCTACTCCAGCGACAACTATTTC 59.448 47.826 0.00 0.00 41.37 2.17
490 1481 2.873133 GCTACTCCAGCGACAACTAT 57.127 50.000 0.00 0.00 41.37 2.12
509 1500 2.989840 CGTTGGAGTAGCTGAAGTTCAG 59.010 50.000 25.68 25.68 46.90 3.02
510 1501 2.626266 TCGTTGGAGTAGCTGAAGTTCA 59.374 45.455 5.25 5.25 0.00 3.18
511 1502 2.987821 GTCGTTGGAGTAGCTGAAGTTC 59.012 50.000 0.00 0.00 0.00 3.01
512 1503 2.364324 TGTCGTTGGAGTAGCTGAAGTT 59.636 45.455 0.00 0.00 0.00 2.66
513 1504 1.961394 TGTCGTTGGAGTAGCTGAAGT 59.039 47.619 0.00 0.00 0.00 3.01
515 1506 2.364324 AGTTGTCGTTGGAGTAGCTGAA 59.636 45.455 0.00 0.00 0.00 3.02
516 1507 1.961394 AGTTGTCGTTGGAGTAGCTGA 59.039 47.619 0.00 0.00 0.00 4.26
517 1508 2.440539 AGTTGTCGTTGGAGTAGCTG 57.559 50.000 0.00 0.00 0.00 4.24
518 1509 4.803098 AATAGTTGTCGTTGGAGTAGCT 57.197 40.909 0.00 0.00 0.00 3.32
521 1512 5.613329 ACCAAAATAGTTGTCGTTGGAGTA 58.387 37.500 7.69 0.00 41.05 2.59
522 1513 4.457466 ACCAAAATAGTTGTCGTTGGAGT 58.543 39.130 7.69 0.00 41.05 3.85
523 1514 5.467399 TGTACCAAAATAGTTGTCGTTGGAG 59.533 40.000 7.69 0.00 41.05 3.86
531 1522 6.779860 ACTCCATCTGTACCAAAATAGTTGT 58.220 36.000 0.00 0.00 0.00 3.32
534 1525 7.328737 GTGTACTCCATCTGTACCAAAATAGT 58.671 38.462 0.00 0.00 39.42 2.12
536 1527 6.071221 ACGTGTACTCCATCTGTACCAAAATA 60.071 38.462 0.00 0.00 39.42 1.40
542 1533 3.863142 AACGTGTACTCCATCTGTACC 57.137 47.619 0.00 0.00 39.42 3.34
543 1534 6.793349 AGATAAACGTGTACTCCATCTGTAC 58.207 40.000 0.00 0.00 40.27 2.90
544 1535 8.687292 ATAGATAAACGTGTACTCCATCTGTA 57.313 34.615 0.00 0.00 0.00 2.74
545 1536 5.916661 AGATAAACGTGTACTCCATCTGT 57.083 39.130 0.00 0.00 0.00 3.41
559 3596 9.647797 TTACCCTGCACATTATATAGATAAACG 57.352 33.333 0.00 0.00 31.28 3.60
569 3606 6.773685 GGTATTTGGTTACCCTGCACATTATA 59.226 38.462 0.00 0.00 36.42 0.98
590 3627 6.147821 GCATGCTATGTTAAAGTCGATGGTAT 59.852 38.462 11.37 0.00 0.00 2.73
705 3745 2.948315 ACTACGTTTTTACCCCGCAAAA 59.052 40.909 0.00 0.00 0.00 2.44
707 3747 2.252976 ACTACGTTTTTACCCCGCAA 57.747 45.000 0.00 0.00 0.00 4.85
708 3748 3.608316 ATACTACGTTTTTACCCCGCA 57.392 42.857 0.00 0.00 0.00 5.69
709 3749 6.603237 AAATATACTACGTTTTTACCCCGC 57.397 37.500 0.00 0.00 0.00 6.13
711 3751 8.279970 ACCAAAATATACTACGTTTTTACCCC 57.720 34.615 0.00 0.00 0.00 4.95
809 3956 1.134128 TGGACTGACACTGTGCAATGT 60.134 47.619 7.90 1.99 31.87 2.71
818 3970 1.476007 GGCTGGTCTGGACTGACACT 61.476 60.000 10.76 0.00 38.61 3.55
850 4002 1.543802 CACGCCAGTCTCTCTTTCTCT 59.456 52.381 0.00 0.00 0.00 3.10
851 4003 1.271102 ACACGCCAGTCTCTCTTTCTC 59.729 52.381 0.00 0.00 0.00 2.87
852 4004 1.333177 ACACGCCAGTCTCTCTTTCT 58.667 50.000 0.00 0.00 0.00 2.52
853 4005 2.416162 CCTACACGCCAGTCTCTCTTTC 60.416 54.545 0.00 0.00 0.00 2.62
854 4006 1.546476 CCTACACGCCAGTCTCTCTTT 59.454 52.381 0.00 0.00 0.00 2.52
855 4007 1.178276 CCTACACGCCAGTCTCTCTT 58.822 55.000 0.00 0.00 0.00 2.85
1049 4283 3.011517 ATGCGGGAGAGGTGGCTT 61.012 61.111 0.00 0.00 0.00 4.35
1867 5139 0.901124 AGCTCGCAGATGAGGAACTT 59.099 50.000 0.00 0.00 34.01 2.66
1880 5152 3.056328 GTTCCAACCCCAGCTCGC 61.056 66.667 0.00 0.00 0.00 5.03
1972 5249 9.933723 CAATCCATTTTCCTTGAGAAACTTTAT 57.066 29.630 0.00 0.00 44.20 1.40
2092 5369 5.416952 CAGCATCATAGTCTTTTTCCAGGTT 59.583 40.000 0.00 0.00 0.00 3.50
2318 5597 6.596497 GGGGACGAAAAAGTTCATAACTGATA 59.404 38.462 0.00 0.00 41.91 2.15
2466 5757 3.614092 AGTGCATTACTGACATGAAGGG 58.386 45.455 0.00 0.00 38.49 3.95
2547 5852 7.658260 ACTATTTACCTAAATTTGGGATGGGT 58.342 34.615 25.78 13.10 37.16 4.51
2653 6156 5.658468 ACGCCTCCATCTTTACTTAGTTAC 58.342 41.667 0.00 0.00 0.00 2.50
2680 6183 2.096417 CGCTAAAGTTTCCACGGTTGAG 60.096 50.000 0.00 0.00 0.00 3.02
2715 6218 5.489792 ACTCATCTGTGTACACTTTCCAT 57.510 39.130 25.60 8.38 0.00 3.41
2802 6308 1.913778 TGCACATTTCATCCTGCAGT 58.086 45.000 13.81 0.00 34.73 4.40
2861 6372 4.246458 AGAGTTCGATGTTTAGTCAAGCC 58.754 43.478 0.00 0.00 0.00 4.35
2862 6373 4.923871 TGAGAGTTCGATGTTTAGTCAAGC 59.076 41.667 0.00 0.00 0.00 4.01
2927 6442 7.614494 AGCATAAAAATAAACAGAGGCATGTT 58.386 30.769 2.62 2.62 45.18 2.71
2930 6445 8.525290 ACTAGCATAAAAATAAACAGAGGCAT 57.475 30.769 0.00 0.00 0.00 4.40
3030 6545 5.047164 TGCAGAGCATAAAAATCCACAACAT 60.047 36.000 0.00 0.00 31.71 2.71
3110 6651 3.188460 CCCACAGGACGAAAACACAATAG 59.812 47.826 0.00 0.00 33.47 1.73


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

AutoCloner maintained by Alex Coulton.