Multiple sequence alignment - TraesCS1D01G001900

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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 TraesCS1D01G001900 chr1D 100.000 2460 0 0 825 3284 465081 462622 0.000000e+00 4543.0
1 TraesCS1D01G001900 chr1D 100.000 394 0 0 1 394 465905 465512 0.000000e+00 728.0
2 TraesCS1D01G001900 chr1D 85.516 504 49 14 1461 1944 614742 615241 3.780000e-139 505.0
3 TraesCS1D01G001900 chr1D 88.276 290 31 3 1469 1757 398247 397960 8.720000e-91 344.0
4 TraesCS1D01G001900 chr1D 81.013 474 38 22 845 1289 692383 692833 2.440000e-86 329.0
5 TraesCS1D01G001900 chr1D 84.512 297 41 2 1456 1747 692952 693248 4.150000e-74 289.0
6 TraesCS1D01G001900 chr1D 87.805 246 23 3 975 1219 398659 398420 6.940000e-72 281.0
7 TraesCS1D01G001900 chr1D 86.730 211 21 5 2806 3011 396007 395799 9.170000e-56 228.0
8 TraesCS1D01G001900 chr1B 95.208 960 39 3 2329 3284 4099980 4099024 0.000000e+00 1511.0
9 TraesCS1D01G001900 chr1B 92.596 959 62 4 2329 3282 4528245 4529199 0.000000e+00 1369.0
10 TraesCS1D01G001900 chr1B 90.866 843 61 9 2401 3242 4861326 4862153 0.000000e+00 1116.0
11 TraesCS1D01G001900 chr1B 90.578 796 53 11 2496 3284 4820376 4821156 0.000000e+00 1035.0
12 TraesCS1D01G001900 chr1B 92.020 589 38 5 2329 2915 3968898 3968317 0.000000e+00 819.0
13 TraesCS1D01G001900 chr1B 93.449 519 32 2 2010 2526 4837919 4838437 0.000000e+00 769.0
14 TraesCS1D01G001900 chr1B 87.835 559 43 10 2715 3273 4840704 4841237 1.660000e-177 632.0
15 TraesCS1D01G001900 chr1B 93.797 403 20 3 1617 2015 4818728 4819129 4.690000e-168 601.0
16 TraesCS1D01G001900 chr1B 85.352 512 48 15 1456 1944 4477330 4477837 3.780000e-139 505.0
17 TraesCS1D01G001900 chr1B 83.190 583 54 22 1465 2006 3948148 3947569 8.190000e-136 494.0
18 TraesCS1D01G001900 chr1B 92.759 290 19 1 2010 2299 4497965 4498252 5.070000e-113 418.0
19 TraesCS1D01G001900 chr1B 92.069 290 21 1 2010 2299 4819747 4820034 1.100000e-109 407.0
20 TraesCS1D01G001900 chr1B 91.837 294 18 5 1 294 4201718 4201431 3.950000e-109 405.0
21 TraesCS1D01G001900 chr1B 88.724 337 29 3 2948 3284 3968320 3967993 1.420000e-108 403.0
22 TraesCS1D01G001900 chr1B 85.196 358 48 5 2806 3161 4154757 4154403 2.410000e-96 363.0
23 TraesCS1D01G001900 chr1B 93.388 242 16 0 1703 1944 4032004 4031763 3.120000e-95 359.0
24 TraesCS1D01G001900 chr1B 87.805 287 31 4 2014 2299 3969424 3969141 1.890000e-87 333.0
25 TraesCS1D01G001900 chr1B 82.687 387 56 8 2395 2774 4758201 4758583 1.890000e-87 333.0
26 TraesCS1D01G001900 chr1B 87.500 288 30 3 7 294 4817926 4818207 8.790000e-86 327.0
27 TraesCS1D01G001900 chr1B 92.478 226 12 3 19 243 4527132 4527353 5.290000e-83 318.0
28 TraesCS1D01G001900 chr1B 86.926 283 30 5 2329 2609 4498466 4498743 8.850000e-81 311.0
29 TraesCS1D01G001900 chr1B 86.207 290 22 5 2010 2299 4527704 4527975 6.890000e-77 298.0
30 TraesCS1D01G001900 chr1B 83.636 330 35 12 837 1148 4756328 4756656 3.210000e-75 292.0
31 TraesCS1D01G001900 chr1B 95.783 166 7 0 1850 2015 4497183 4497348 5.400000e-68 268.0
32 TraesCS1D01G001900 chr1B 94.074 135 8 0 1881 2015 3970102 3969968 4.300000e-49 206.0
33 TraesCS1D01G001900 chr1B 99.115 113 1 0 2186 2298 4757884 4757996 1.540000e-48 204.0
34 TraesCS1D01G001900 chr1B 94.656 131 4 2 2329 2458 4820250 4820378 2.000000e-47 200.0
35 TraesCS1D01G001900 chr1B 87.356 174 16 6 1007 1178 27092592 27092761 9.300000e-46 195.0
36 TraesCS1D01G001900 chr1B 86.857 175 13 6 975 1148 3974782 3974617 1.560000e-43 187.0
37 TraesCS1D01G001900 chr1B 83.908 174 22 5 2604 2774 4563856 4564026 9.430000e-36 161.0
38 TraesCS1D01G001900 chr1B 95.062 81 3 1 2251 2330 4100165 4100085 3.440000e-25 126.0
39 TraesCS1D01G001900 chr1B 80.645 124 19 4 839 961 4190241 4190122 1.250000e-14 91.6
40 TraesCS1D01G001900 chr1A 92.843 489 34 1 1456 1944 3448411 3448898 0.000000e+00 708.0
41 TraesCS1D01G001900 chr1A 88.281 512 36 14 1456 1944 2980384 2979874 2.820000e-165 592.0
42 TraesCS1D01G001900 chr1A 89.630 405 21 6 1456 1860 3469567 3469950 2.280000e-136 496.0
43 TraesCS1D01G001900 chr1A 83.510 473 56 10 1491 1943 27218556 27218086 3.920000e-114 422.0
44 TraesCS1D01G001900 chr1A 83.900 441 52 11 972 1399 3469127 3469561 1.420000e-108 403.0
45 TraesCS1D01G001900 chr1A 91.986 287 15 2 2013 2299 2987302 2987024 2.370000e-106 396.0
46 TraesCS1D01G001900 chr1A 91.379 290 23 1 2010 2299 3487149 3487436 2.370000e-106 396.0
47 TraesCS1D01G001900 chr1A 85.942 377 45 8 972 1340 3548249 3548625 2.370000e-106 396.0
48 TraesCS1D01G001900 chr1A 81.606 386 60 7 2395 2774 2986820 2986440 3.180000e-80 309.0
49 TraesCS1D01G001900 chr1A 84.965 286 30 8 2491 2774 3487668 3487942 8.970000e-71 278.0
50 TraesCS1D01G001900 chr1A 96.386 166 6 0 1850 2015 3486378 3486543 1.160000e-69 274.0
51 TraesCS1D01G001900 chr1A 100.000 55 0 0 1400 1454 238142352 238142406 5.800000e-18 102.0
52 TraesCS1D01G001900 chr1A 100.000 55 0 0 1400 1454 238144975 238145029 5.800000e-18 102.0
53 TraesCS1D01G001900 chr1A 100.000 55 0 0 1400 1454 334069256 334069310 5.800000e-18 102.0
54 TraesCS1D01G001900 chr1A 96.491 57 2 0 1343 1399 2980446 2980390 9.700000e-16 95.3
55 TraesCS1D01G001900 chr1A 82.051 78 10 2 940 1013 2996118 2996041 2.740000e-06 63.9
56 TraesCS1D01G001900 chr1A 97.222 36 0 1 981 1015 3675780 3675815 3.540000e-05 60.2
57 TraesCS1D01G001900 chr3D 82.759 464 55 8 2806 3267 560054215 560054655 1.100000e-104 390.0
58 TraesCS1D01G001900 chr6B 89.080 174 13 5 1007 1178 527629749 527629580 9.230000e-51 211.0
59 TraesCS1D01G001900 chr6B 88.889 45 5 0 91 135 693087868 693087912 4.580000e-04 56.5
60 TraesCS1D01G001900 chr4B 87.931 174 15 5 1007 1178 88708006 88707837 2.000000e-47 200.0
61 TraesCS1D01G001900 chr3B 87.931 174 15 5 1007 1178 442044197 442044366 2.000000e-47 200.0
62 TraesCS1D01G001900 chrUn 100.000 55 0 0 1400 1454 410093531 410093477 5.800000e-18 102.0
63 TraesCS1D01G001900 chrUn 100.000 55 0 0 1400 1454 439509604 439509658 5.800000e-18 102.0
64 TraesCS1D01G001900 chr4D 100.000 55 0 0 1400 1454 123379076 123379022 5.800000e-18 102.0
65 TraesCS1D01G001900 chr4D 100.000 55 0 0 1400 1454 123589861 123589807 5.800000e-18 102.0
66 TraesCS1D01G001900 chr2D 100.000 55 0 0 1400 1454 635048507 635048453 5.800000e-18 102.0
67 TraesCS1D01G001900 chr2D 100.000 55 0 0 1400 1454 637324151 637324205 5.800000e-18 102.0


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 TraesCS1D01G001900 chr1D 462622 465905 3283 True 2635.500000 4543 100.000000 1 3284 2 chr1D.!!$R2 3283
1 TraesCS1D01G001900 chr1D 692383 693248 865 False 309.000000 329 82.762500 845 1747 2 chr1D.!!$F2 902
2 TraesCS1D01G001900 chr1D 395799 398659 2860 True 284.333333 344 87.603667 975 3011 3 chr1D.!!$R1 2036
3 TraesCS1D01G001900 chr1B 4861326 4862153 827 False 1116.000000 1116 90.866000 2401 3242 1 chr1B.!!$F3 841
4 TraesCS1D01G001900 chr1B 4099024 4100165 1141 True 818.500000 1511 95.135000 2251 3284 2 chr1B.!!$R8 1033
5 TraesCS1D01G001900 chr1B 4837919 4841237 3318 False 700.500000 769 90.642000 2010 3273 2 chr1B.!!$F9 1263
6 TraesCS1D01G001900 chr1B 4527132 4529199 2067 False 661.666667 1369 90.427000 19 3282 3 chr1B.!!$F6 3263
7 TraesCS1D01G001900 chr1B 4817926 4821156 3230 False 514.000000 1035 91.720000 7 3284 5 chr1B.!!$F8 3277
8 TraesCS1D01G001900 chr1B 4477330 4477837 507 False 505.000000 505 85.352000 1456 1944 1 chr1B.!!$F1 488
9 TraesCS1D01G001900 chr1B 3947569 3948148 579 True 494.000000 494 83.190000 1465 2006 1 chr1B.!!$R1 541
10 TraesCS1D01G001900 chr1B 3967993 3970102 2109 True 440.250000 819 90.655750 1881 3284 4 chr1B.!!$R7 1403
11 TraesCS1D01G001900 chr1B 4497183 4498743 1560 False 332.333333 418 91.822667 1850 2609 3 chr1B.!!$F5 759
12 TraesCS1D01G001900 chr1B 4756328 4758583 2255 False 276.333333 333 88.479333 837 2774 3 chr1B.!!$F7 1937
13 TraesCS1D01G001900 chr1A 3469127 3469950 823 False 449.500000 496 86.765000 972 1860 2 chr1A.!!$F5 888
14 TraesCS1D01G001900 chr1A 2986440 2987302 862 True 352.500000 396 86.796000 2013 2774 2 chr1A.!!$R4 761
15 TraesCS1D01G001900 chr1A 2979874 2980446 572 True 343.650000 592 92.386000 1343 1944 2 chr1A.!!$R3 601
16 TraesCS1D01G001900 chr1A 3486378 3487942 1564 False 316.000000 396 90.910000 1850 2774 3 chr1A.!!$F6 924

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
301 303 0.321210 TTGTACTGCATGTGTCCCCG 60.321 55.0 0.0 0.0 0.00 5.73 F
1329 1604 0.321671 ATGGACAAGACAGACGTGGG 59.678 55.0 0.0 0.0 32.54 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1732 0.094216 CACAGTGATCGAAAGCTGCG 59.906 55.000 0.0 3.05 32.65 5.18 R
2937 8094 1.349688 TCCGTAAAGCTTGGTCATGGT 59.650 47.619 0.0 0.00 0.00 3.55 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
197 198 9.980780 AACTTGTTTTCCAATTTTTCATTAACG 57.019 25.926 0.00 0.00 31.20 3.18
262 264 9.612066 AAATTTAATTGAGTGGTGTGATTTGTT 57.388 25.926 0.00 0.00 0.00 2.83
263 265 9.612066 AATTTAATTGAGTGGTGTGATTTGTTT 57.388 25.926 0.00 0.00 0.00 2.83
268 270 9.612066 AATTGAGTGGTGTGATTTGTTTAAATT 57.388 25.926 0.00 0.00 36.66 1.82
274 276 9.592720 GTGGTGTGATTTGTTTAAATTTTATGC 57.407 29.630 0.00 0.00 36.66 3.14
294 296 4.691175 TGCAAACAAATTGTACTGCATGT 58.309 34.783 23.44 0.00 41.45 3.21
296 298 4.507388 GCAAACAAATTGTACTGCATGTGT 59.493 37.500 21.11 0.00 41.32 3.72
297 299 5.332506 GCAAACAAATTGTACTGCATGTGTC 60.333 40.000 21.11 0.00 41.32 3.67
298 300 4.503741 ACAAATTGTACTGCATGTGTCC 57.496 40.909 0.00 0.00 0.00 4.02
299 301 3.255642 ACAAATTGTACTGCATGTGTCCC 59.744 43.478 0.00 0.00 0.00 4.46
300 302 2.128771 ATTGTACTGCATGTGTCCCC 57.871 50.000 0.00 0.00 0.00 4.81
301 303 0.321210 TTGTACTGCATGTGTCCCCG 60.321 55.000 0.00 0.00 0.00 5.73
302 304 2.106683 GTACTGCATGTGTCCCCGC 61.107 63.158 0.00 0.00 0.00 6.13
303 305 3.323758 TACTGCATGTGTCCCCGCC 62.324 63.158 0.00 0.00 0.00 6.13
384 601 2.182030 GTCCGCCACCTCTTCTCG 59.818 66.667 0.00 0.00 0.00 4.04
389 606 4.821589 CCACCTCTTCTCGCCGCC 62.822 72.222 0.00 0.00 0.00 6.13
905 1122 1.386525 ATGCCATGCCACGGATGAAC 61.387 55.000 0.00 0.00 0.00 3.18
917 1147 2.034558 ACGGATGAACAAAACTGGCTTG 59.965 45.455 0.00 0.00 0.00 4.01
918 1148 2.293122 CGGATGAACAAAACTGGCTTGA 59.707 45.455 0.00 0.00 0.00 3.02
952 1182 2.851195 AGTTTGAGCACCGATTTCTGT 58.149 42.857 0.00 0.00 0.00 3.41
1079 1334 2.123428 GGTCCATGCTGCCATCCAC 61.123 63.158 0.00 0.00 0.00 4.02
1172 1437 5.939764 TGTGCTCTCATACACCTTTAGAT 57.060 39.130 0.00 0.00 35.90 1.98
1277 1552 8.466617 TCTCCTTAGGTTACTTGCTATAGAAG 57.533 38.462 3.21 7.10 0.00 2.85
1292 1567 2.029838 AGAAGCCGCTGATTTCGAAT 57.970 45.000 0.00 0.00 0.00 3.34
1300 1575 2.222678 CGCTGATTTCGAATGCTAGCAT 59.777 45.455 24.67 24.67 38.46 3.79
1308 1583 3.599343 TCGAATGCTAGCATGTTCTTGT 58.401 40.909 30.19 13.18 36.68 3.16
1325 1600 2.438868 TGTCATGGACAAGACAGACG 57.561 50.000 6.30 0.00 39.78 4.18
1329 1604 0.321671 ATGGACAAGACAGACGTGGG 59.678 55.000 0.00 0.00 32.54 4.61
1339 1614 2.609459 GACAGACGTGGGAATGCTATTG 59.391 50.000 0.00 0.00 0.00 1.90
1399 1709 2.484417 CCTCTTGTGGCAGTAGGCTATG 60.484 54.545 0.00 0.00 44.01 2.23
1400 1710 1.134401 TCTTGTGGCAGTAGGCTATGC 60.134 52.381 15.96 15.96 44.01 3.14
1403 1713 2.063979 TGGCAGTAGGCTATGCGGT 61.064 57.895 17.01 0.00 43.49 5.68
1405 1715 0.463833 GGCAGTAGGCTATGCGGTTT 60.464 55.000 17.01 0.00 43.49 3.27
1406 1716 0.938008 GCAGTAGGCTATGCGGTTTC 59.062 55.000 11.37 0.00 40.25 2.78
1408 1718 2.627945 CAGTAGGCTATGCGGTTTCAA 58.372 47.619 0.00 0.00 0.00 2.69
1409 1719 2.609459 CAGTAGGCTATGCGGTTTCAAG 59.391 50.000 0.00 0.00 0.00 3.02
1410 1720 2.236395 AGTAGGCTATGCGGTTTCAAGT 59.764 45.455 0.00 0.00 0.00 3.16
1411 1721 2.200373 AGGCTATGCGGTTTCAAGTT 57.800 45.000 0.00 0.00 0.00 2.66
1412 1722 1.812571 AGGCTATGCGGTTTCAAGTTG 59.187 47.619 0.00 0.00 0.00 3.16
1413 1723 1.539827 GGCTATGCGGTTTCAAGTTGT 59.460 47.619 2.11 0.00 0.00 3.32
1414 1724 2.030274 GGCTATGCGGTTTCAAGTTGTT 60.030 45.455 2.11 0.00 0.00 2.83
1415 1725 3.552068 GGCTATGCGGTTTCAAGTTGTTT 60.552 43.478 2.11 0.00 0.00 2.83
1416 1726 4.048504 GCTATGCGGTTTCAAGTTGTTTT 58.951 39.130 2.11 0.00 0.00 2.43
1417 1727 4.085107 GCTATGCGGTTTCAAGTTGTTTTG 60.085 41.667 2.11 0.00 0.00 2.44
1418 1728 2.611518 TGCGGTTTCAAGTTGTTTTGG 58.388 42.857 2.11 0.00 0.00 3.28
1419 1729 2.028930 TGCGGTTTCAAGTTGTTTTGGT 60.029 40.909 2.11 0.00 0.00 3.67
1420 1730 2.997303 GCGGTTTCAAGTTGTTTTGGTT 59.003 40.909 2.11 0.00 0.00 3.67
1421 1731 3.181525 GCGGTTTCAAGTTGTTTTGGTTG 60.182 43.478 2.11 0.00 0.00 3.77
1422 1732 3.181525 CGGTTTCAAGTTGTTTTGGTTGC 60.182 43.478 2.11 0.00 0.00 4.17
1423 1733 3.181525 GGTTTCAAGTTGTTTTGGTTGCG 60.182 43.478 2.11 0.00 0.00 4.85
1424 1734 1.634702 TCAAGTTGTTTTGGTTGCGC 58.365 45.000 0.00 0.00 0.00 6.09
1425 1735 1.067565 TCAAGTTGTTTTGGTTGCGCA 60.068 42.857 5.66 5.66 0.00 6.09
1426 1736 1.324134 CAAGTTGTTTTGGTTGCGCAG 59.676 47.619 11.31 0.00 0.00 5.18
1440 1750 2.449548 CGCAGCTTTCGATCACTGT 58.550 52.632 9.85 0.00 32.65 3.55
1441 1751 0.094216 CGCAGCTTTCGATCACTGTG 59.906 55.000 0.17 0.17 34.67 3.66
1442 1752 1.151668 GCAGCTTTCGATCACTGTGT 58.848 50.000 7.79 0.00 32.65 3.72
1443 1753 1.127582 GCAGCTTTCGATCACTGTGTC 59.872 52.381 7.79 4.25 32.65 3.67
1444 1754 2.407090 CAGCTTTCGATCACTGTGTCA 58.593 47.619 7.79 0.00 0.00 3.58
1445 1755 2.411069 CAGCTTTCGATCACTGTGTCAG 59.589 50.000 7.79 0.69 37.52 3.51
1446 1756 1.127582 GCTTTCGATCACTGTGTCAGC 59.872 52.381 7.79 6.57 34.37 4.26
1447 1757 1.728971 CTTTCGATCACTGTGTCAGCC 59.271 52.381 7.79 0.00 34.37 4.85
1448 1758 0.388520 TTCGATCACTGTGTCAGCCG 60.389 55.000 7.79 5.85 34.37 5.52
1449 1759 1.212751 CGATCACTGTGTCAGCCGA 59.787 57.895 7.79 0.00 34.37 5.54
1450 1760 0.799917 CGATCACTGTGTCAGCCGAG 60.800 60.000 7.79 0.00 34.37 4.63
1451 1761 1.079543 ATCACTGTGTCAGCCGAGC 60.080 57.895 7.79 0.00 34.37 5.03
1452 1762 1.539560 ATCACTGTGTCAGCCGAGCT 61.540 55.000 7.79 0.00 40.77 4.09
1453 1763 1.735920 CACTGTGTCAGCCGAGCTC 60.736 63.158 2.73 2.73 36.40 4.09
1454 1764 2.203082 ACTGTGTCAGCCGAGCTCA 61.203 57.895 15.40 0.00 36.40 4.26
1458 1768 0.249238 GTGTCAGCCGAGCTCATAGG 60.249 60.000 15.40 8.19 36.40 2.57
1482 1797 7.885399 AGGGCTCAAATATTTATACTCCACATC 59.115 37.037 0.00 0.00 0.00 3.06
1531 1846 1.886542 GACATCCTGTCCAACCAAACC 59.113 52.381 0.00 0.00 41.37 3.27
1609 1924 5.003804 ACTGTATGTTGCCTTAGTTTCCTG 58.996 41.667 0.00 0.00 0.00 3.86
1700 2779 3.184541 CTGCAATGAAAGCTGCCAATAC 58.815 45.455 0.00 0.00 37.79 1.89
1752 2831 9.814899 GTCAGGATTGAAGATATAGATGTATGG 57.185 37.037 0.00 0.00 34.49 2.74
1768 2861 7.966812 AGATGTATGGAGCATAACTGTTCATA 58.033 34.615 0.00 0.00 34.54 2.15
1822 2935 1.831106 ACATCTGAATCCGTACCTGCA 59.169 47.619 0.00 0.00 0.00 4.41
1937 3053 3.496337 CCAGATGACATTGATGAGGAGGG 60.496 52.174 0.00 0.00 0.00 4.30
2075 4465 2.096248 AGCAAAAACAACTCACGGGAA 58.904 42.857 0.00 0.00 0.00 3.97
2100 4490 2.588620 TCCAAACCACTTTAACGCCAT 58.411 42.857 0.00 0.00 0.00 4.40
2102 4492 4.337145 TCCAAACCACTTTAACGCCATAT 58.663 39.130 0.00 0.00 0.00 1.78
2346 4992 8.842280 TCGTTGTATTGAATTTTAAGGTGAACT 58.158 29.630 0.00 0.00 0.00 3.01
2485 5133 8.212995 TCATATCATCTCATCCTTTGTTAAGCA 58.787 33.333 0.00 0.00 0.00 3.91
2489 5137 7.541162 TCATCTCATCCTTTGTTAAGCATTTG 58.459 34.615 0.00 0.00 0.00 2.32
2494 5142 8.402798 TCATCCTTTGTTAAGCATTTGTTAGA 57.597 30.769 0.00 0.00 0.00 2.10
2543 5195 2.487762 TGTTCCATTTCAATCTCGCCAC 59.512 45.455 0.00 0.00 0.00 5.01
2544 5196 1.750193 TCCATTTCAATCTCGCCACC 58.250 50.000 0.00 0.00 0.00 4.61
2803 7938 0.179000 ATGAACTCATCCCGAGGCAC 59.821 55.000 0.00 0.00 46.98 5.01
2863 8014 1.885887 TCTGTGTAAACCATTGCAGCC 59.114 47.619 0.00 0.00 31.46 4.85
2952 8109 1.342174 CTTGCACCATGACCAAGCTTT 59.658 47.619 0.00 0.00 30.83 3.51
3038 8195 2.796193 CCATCCCACGAGGCGATCA 61.796 63.158 0.00 0.00 34.51 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.877178 TGTTAAACATGTACTTGAAAAATGGTT 57.123 25.926 15.13 5.79 33.05 3.67
242 244 9.612066 AATTTAAACAAATCACACCACTCAATT 57.388 25.926 0.00 0.00 0.00 2.32
274 276 5.175491 GGACACATGCAGTACAATTTGTTTG 59.825 40.000 7.45 8.13 41.36 2.93
285 287 2.267642 GCGGGGACACATGCAGTA 59.732 61.111 0.00 0.00 0.00 2.74
322 324 4.702081 ACACCGCAGTCGCTCGAC 62.702 66.667 13.92 13.92 44.86 4.20
323 325 4.400109 GACACCGCAGTCGCTCGA 62.400 66.667 0.00 0.00 35.30 4.04
327 329 4.664677 AGTGGACACCGCAGTCGC 62.665 66.667 4.21 0.00 39.42 5.19
328 330 2.430921 GAGTGGACACCGCAGTCG 60.431 66.667 4.21 0.00 39.42 4.18
329 331 2.430921 CGAGTGGACACCGCAGTC 60.431 66.667 4.21 0.00 36.32 3.51
330 332 3.208884 GACGAGTGGACACCGCAGT 62.209 63.158 11.40 3.64 36.32 4.40
331 333 2.430921 GACGAGTGGACACCGCAG 60.431 66.667 11.40 0.66 36.32 5.18
332 334 4.337060 CGACGAGTGGACACCGCA 62.337 66.667 11.40 0.00 36.32 5.69
335 337 3.509137 TTGCCGACGAGTGGACACC 62.509 63.158 0.00 0.00 0.00 4.16
336 338 2.028484 TTGCCGACGAGTGGACAC 59.972 61.111 0.00 0.00 0.00 3.67
337 339 2.028484 GTTGCCGACGAGTGGACA 59.972 61.111 0.00 0.00 0.00 4.02
375 592 1.884926 GAATGGCGGCGAGAAGAGG 60.885 63.158 12.98 0.00 0.00 3.69
824 1041 2.623889 ACCTACTGACACCGATATGAGC 59.376 50.000 0.00 0.00 0.00 4.26
825 1042 3.551046 GCACCTACTGACACCGATATGAG 60.551 52.174 0.00 0.00 0.00 2.90
826 1043 2.361119 GCACCTACTGACACCGATATGA 59.639 50.000 0.00 0.00 0.00 2.15
827 1044 2.362397 AGCACCTACTGACACCGATATG 59.638 50.000 0.00 0.00 0.00 1.78
828 1045 2.623889 GAGCACCTACTGACACCGATAT 59.376 50.000 0.00 0.00 0.00 1.63
829 1046 2.022195 GAGCACCTACTGACACCGATA 58.978 52.381 0.00 0.00 0.00 2.92
830 1047 0.818296 GAGCACCTACTGACACCGAT 59.182 55.000 0.00 0.00 0.00 4.18
831 1048 0.251209 AGAGCACCTACTGACACCGA 60.251 55.000 0.00 0.00 0.00 4.69
832 1049 0.171455 GAGAGCACCTACTGACACCG 59.829 60.000 0.00 0.00 0.00 4.94
833 1050 1.474879 GAGAGAGCACCTACTGACACC 59.525 57.143 0.00 0.00 0.00 4.16
834 1051 1.131504 CGAGAGAGCACCTACTGACAC 59.868 57.143 0.00 0.00 0.00 3.67
835 1052 1.271434 ACGAGAGAGCACCTACTGACA 60.271 52.381 0.00 0.00 0.00 3.58
917 1147 5.098211 GCTCAAACTACCAAAATCAGCATC 58.902 41.667 0.00 0.00 0.00 3.91
918 1148 4.523943 TGCTCAAACTACCAAAATCAGCAT 59.476 37.500 0.00 0.00 29.56 3.79
952 1182 2.721167 CCGAATCCTCGTCCTGCCA 61.721 63.158 0.00 0.00 43.87 4.92
1067 1322 0.542467 AACATTGGTGGATGGCAGCA 60.542 50.000 4.64 0.00 0.00 4.41
1079 1334 9.398170 CTTTTAGATGTTGACTTGTAACATTGG 57.602 33.333 5.02 0.00 45.82 3.16
1178 1445 7.964666 TGGTTTATTATTGTAAAGAAGGGGG 57.035 36.000 0.00 0.00 26.60 5.40
1198 1465 9.755804 AAATTTTGAAACAACACAAAAATGGTT 57.244 22.222 0.00 0.00 44.91 3.67
1199 1466 9.404348 GAAATTTTGAAACAACACAAAAATGGT 57.596 25.926 0.00 0.00 44.91 3.55
1222 1489 9.589111 GAACAAAACCTTTTACATGTAAGGAAA 57.411 29.630 27.08 15.10 42.90 3.13
1230 1497 9.626045 GGAGATAAGAACAAAACCTTTTACATG 57.374 33.333 0.00 0.00 0.00 3.21
1240 1507 9.722184 AGTAACCTAAGGAGATAAGAACAAAAC 57.278 33.333 0.00 0.00 0.00 2.43
1242 1509 9.720769 CAAGTAACCTAAGGAGATAAGAACAAA 57.279 33.333 0.00 0.00 0.00 2.83
1243 1510 7.822822 GCAAGTAACCTAAGGAGATAAGAACAA 59.177 37.037 0.00 0.00 0.00 2.83
1277 1552 0.937304 TAGCATTCGAAATCAGCGGC 59.063 50.000 0.00 0.00 0.00 6.53
1279 1554 1.594397 TGCTAGCATTCGAAATCAGCG 59.406 47.619 14.93 0.00 0.00 5.18
1292 1567 3.011818 CCATGACAAGAACATGCTAGCA 58.988 45.455 21.85 21.85 42.31 3.49
1308 1583 1.000843 CCACGTCTGTCTTGTCCATGA 59.999 52.381 0.00 0.00 0.00 3.07
1324 1599 4.202010 CCTTTAACCAATAGCATTCCCACG 60.202 45.833 0.00 0.00 0.00 4.94
1325 1600 4.099419 CCCTTTAACCAATAGCATTCCCAC 59.901 45.833 0.00 0.00 0.00 4.61
1329 1604 3.795488 GCGCCCTTTAACCAATAGCATTC 60.795 47.826 0.00 0.00 0.00 2.67
1339 1614 1.674441 GGTAATCAGCGCCCTTTAACC 59.326 52.381 2.29 1.15 0.00 2.85
1399 1709 2.612604 ACCAAAACAACTTGAAACCGC 58.387 42.857 0.00 0.00 0.00 5.68
1400 1710 3.181525 GCAACCAAAACAACTTGAAACCG 60.182 43.478 0.00 0.00 0.00 4.44
1403 1713 2.413453 GCGCAACCAAAACAACTTGAAA 59.587 40.909 0.30 0.00 0.00 2.69
1405 1715 1.067565 TGCGCAACCAAAACAACTTGA 60.068 42.857 8.16 0.00 0.00 3.02
1406 1716 1.324134 CTGCGCAACCAAAACAACTTG 59.676 47.619 13.05 0.00 0.00 3.16
1408 1718 0.805711 GCTGCGCAACCAAAACAACT 60.806 50.000 13.05 0.00 0.00 3.16
1409 1719 0.805711 AGCTGCGCAACCAAAACAAC 60.806 50.000 13.05 0.00 0.00 3.32
1410 1720 0.108424 AAGCTGCGCAACCAAAACAA 60.108 45.000 13.05 0.00 0.00 2.83
1411 1721 0.108424 AAAGCTGCGCAACCAAAACA 60.108 45.000 13.05 0.00 0.00 2.83
1412 1722 0.576798 GAAAGCTGCGCAACCAAAAC 59.423 50.000 13.05 0.00 0.00 2.43
1413 1723 0.869454 CGAAAGCTGCGCAACCAAAA 60.869 50.000 13.05 0.00 0.00 2.44
1414 1724 1.299014 CGAAAGCTGCGCAACCAAA 60.299 52.632 13.05 0.00 0.00 3.28
1415 1725 1.514678 ATCGAAAGCTGCGCAACCAA 61.515 50.000 13.05 0.00 0.00 3.67
1416 1726 1.911293 GATCGAAAGCTGCGCAACCA 61.911 55.000 13.05 0.00 0.00 3.67
1417 1727 1.226128 GATCGAAAGCTGCGCAACC 60.226 57.895 13.05 5.46 0.00 3.77
1418 1728 0.790866 GTGATCGAAAGCTGCGCAAC 60.791 55.000 13.05 7.27 0.00 4.17
1419 1729 0.950555 AGTGATCGAAAGCTGCGCAA 60.951 50.000 13.05 0.00 0.00 4.85
1420 1730 1.374631 AGTGATCGAAAGCTGCGCA 60.375 52.632 10.98 10.98 0.00 6.09
1421 1731 1.059994 CAGTGATCGAAAGCTGCGC 59.940 57.895 0.00 0.00 0.00 6.09
1422 1732 0.094216 CACAGTGATCGAAAGCTGCG 59.906 55.000 0.00 3.05 32.65 5.18
1423 1733 1.127582 GACACAGTGATCGAAAGCTGC 59.872 52.381 7.81 0.00 32.65 5.25
1424 1734 2.407090 TGACACAGTGATCGAAAGCTG 58.593 47.619 7.81 10.57 35.31 4.24
1425 1735 2.681706 CTGACACAGTGATCGAAAGCT 58.318 47.619 7.81 0.00 0.00 3.74
1426 1736 1.127582 GCTGACACAGTGATCGAAAGC 59.872 52.381 7.81 3.19 33.43 3.51
1427 1737 1.728971 GGCTGACACAGTGATCGAAAG 59.271 52.381 7.81 0.00 33.43 2.62
1428 1738 1.795768 GGCTGACACAGTGATCGAAA 58.204 50.000 7.81 0.00 33.43 3.46
1429 1739 0.388520 CGGCTGACACAGTGATCGAA 60.389 55.000 7.81 0.00 33.43 3.71
1430 1740 1.212751 CGGCTGACACAGTGATCGA 59.787 57.895 7.81 0.00 33.43 3.59
1431 1741 0.799917 CTCGGCTGACACAGTGATCG 60.800 60.000 7.81 3.78 33.43 3.69
1432 1742 1.080995 GCTCGGCTGACACAGTGATC 61.081 60.000 7.81 1.90 33.43 2.92
1433 1743 1.079543 GCTCGGCTGACACAGTGAT 60.080 57.895 7.81 0.00 33.43 3.06
1434 1744 2.147315 GAGCTCGGCTGACACAGTGA 62.147 60.000 7.81 0.00 39.88 3.41
1435 1745 1.735920 GAGCTCGGCTGACACAGTG 60.736 63.158 0.00 0.00 39.88 3.66
1436 1746 1.539560 ATGAGCTCGGCTGACACAGT 61.540 55.000 9.64 0.00 39.88 3.55
1437 1747 0.457443 TATGAGCTCGGCTGACACAG 59.543 55.000 9.64 0.00 39.88 3.66
1438 1748 0.457443 CTATGAGCTCGGCTGACACA 59.543 55.000 9.64 0.00 39.88 3.72
1439 1749 0.249238 CCTATGAGCTCGGCTGACAC 60.249 60.000 9.64 0.00 39.88 3.67
1440 1750 1.395045 CCCTATGAGCTCGGCTGACA 61.395 60.000 9.64 0.00 39.88 3.58
1441 1751 1.365633 CCCTATGAGCTCGGCTGAC 59.634 63.158 9.64 0.00 39.88 3.51
1442 1752 2.502492 GCCCTATGAGCTCGGCTGA 61.502 63.158 19.63 0.00 39.88 4.26
1443 1753 2.030262 GCCCTATGAGCTCGGCTG 59.970 66.667 19.63 6.08 39.88 4.85
1444 1754 2.123077 AGCCCTATGAGCTCGGCT 60.123 61.111 22.76 22.76 46.96 5.52
1445 1755 2.341911 GAGCCCTATGAGCTCGGC 59.658 66.667 19.38 19.38 46.58 5.54
1449 1759 8.830741 AGTATAAATATTTGAGCCCTATGAGCT 58.169 33.333 11.05 0.00 45.23 4.09
1450 1760 9.103861 GAGTATAAATATTTGAGCCCTATGAGC 57.896 37.037 11.05 0.00 0.00 4.26
1451 1761 9.606631 GGAGTATAAATATTTGAGCCCTATGAG 57.393 37.037 11.05 0.00 0.00 2.90
1452 1762 9.111519 TGGAGTATAAATATTTGAGCCCTATGA 57.888 33.333 11.05 0.00 0.00 2.15
1453 1763 9.167311 GTGGAGTATAAATATTTGAGCCCTATG 57.833 37.037 11.05 0.00 0.00 2.23
1454 1764 8.890472 TGTGGAGTATAAATATTTGAGCCCTAT 58.110 33.333 11.05 0.00 0.00 2.57
1458 1768 7.885399 AGGATGTGGAGTATAAATATTTGAGCC 59.115 37.037 11.05 5.86 0.00 4.70
1463 1778 9.588096 GGGAAAGGATGTGGAGTATAAATATTT 57.412 33.333 5.89 5.89 0.00 1.40
1482 1797 3.780850 ACCTTCATACCTGTAGGGAAAGG 59.219 47.826 10.77 10.77 42.61 3.11
1531 1846 7.182761 CGAAAGCAAGTTGGTCAAGATTATAG 58.817 38.462 8.24 0.00 0.00 1.31
1700 2779 3.555527 TCATCATCCCTTTCAGCTCTG 57.444 47.619 0.00 0.00 0.00 3.35
1760 2839 8.675504 AGCTGAAGATCTTGAAAATATGAACAG 58.324 33.333 14.00 9.97 0.00 3.16
1822 2935 2.486982 GCATGCTCTGCGGATTATGAAT 59.513 45.455 11.37 0.00 41.97 2.57
2075 4465 3.243267 GCGTTAAAGTGGTTTGGATGTGT 60.243 43.478 0.00 0.00 0.00 3.72
2346 4992 7.804147 TCTTTTTACCAGAAAAGTAGGTACCA 58.196 34.615 15.94 0.00 43.65 3.25
2760 7517 3.055819 ACTCATTGTAAGTGGTCGATGCT 60.056 43.478 0.00 0.00 0.00 3.79
2803 7938 3.350833 CACTGATTCTTTTCCCTCCCTG 58.649 50.000 0.00 0.00 0.00 4.45
2863 8014 5.764487 AAAGAGGAGAACAAAGCAGAAAG 57.236 39.130 0.00 0.00 0.00 2.62
2937 8094 1.349688 TCCGTAAAGCTTGGTCATGGT 59.650 47.619 0.00 0.00 0.00 3.55
2952 8109 1.524961 GTGGGATGGCATGTCCGTA 59.475 57.895 3.81 0.00 36.58 4.02
3038 8195 6.877855 CCAGATCAGTAGTTGCATGCTATTAT 59.122 38.462 20.33 4.59 0.00 1.28


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

AutoCloner maintained by Alex Coulton.