Multiple sequence alignment - TraesCS4A01G166400

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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 TraesCS4A01G166400 chr4A 100.000 2201 0 0 1 2201 401304756 401302556 0.000000e+00 4065.0
1 TraesCS4A01G166400 chr4A 90.334 1169 113 0 1 1169 401296789 401295621 0.000000e+00 1533.0
2 TraesCS4A01G166400 chr4A 87.812 681 46 7 1557 2201 401267476 401266797 0.000000e+00 763.0
3 TraesCS4A01G166400 chr4A 92.348 379 18 5 1819 2188 323786725 323787101 1.500000e-146 529.0
4 TraesCS4A01G166400 chr4A 88.274 307 28 4 1891 2190 429009289 429008984 5.780000e-96 361.0
5 TraesCS4A01G166400 chr4A 100.000 31 0 0 1541 1571 460028528 460028498 8.490000e-05 58.4
6 TraesCS4A01G166400 chr6A 84.112 1177 143 22 2 1171 462752770 462751631 0.000000e+00 1098.0
7 TraesCS4A01G166400 chr6A 83.713 1185 167 20 2 1171 243178846 243177673 0.000000e+00 1096.0
8 TraesCS4A01G166400 chr6A 83.488 1187 156 25 2 1171 243181216 243180053 0.000000e+00 1070.0
9 TraesCS4A01G166400 chr6A 84.975 599 61 10 573 1171 363052250 363051681 4.070000e-162 580.0
10 TraesCS4A01G166400 chr6A 87.580 467 57 1 573 1039 363013330 363012865 6.910000e-150 540.0
11 TraesCS4A01G166400 chr6A 90.214 327 32 0 845 1171 206269263 206269589 5.620000e-116 427.0
12 TraesCS4A01G166400 chr6A 94.737 152 8 0 1316 1467 250996082 250995931 1.020000e-58 237.0
13 TraesCS4A01G166400 chr6A 87.425 167 17 3 1160 1326 462751512 462751350 2.880000e-44 189.0
14 TraesCS4A01G166400 chr6A 87.037 162 18 3 1437 1598 461294809 461294967 1.740000e-41 180.0
15 TraesCS4A01G166400 chr6A 89.231 130 13 1 1338 1467 478107236 478107364 6.290000e-36 161.0
16 TraesCS4A01G166400 chr6A 91.892 111 9 0 577 687 65409655 65409765 2.930000e-34 156.0
17 TraesCS4A01G166400 chr6A 89.000 100 11 0 1160 1259 363012643 363012544 8.250000e-25 124.0
18 TraesCS4A01G166400 chr6A 97.674 43 0 1 1730 1772 261149805 261149764 3.030000e-09 73.1
19 TraesCS4A01G166400 chr6A 95.000 40 2 0 1673 1712 310998666 310998705 1.820000e-06 63.9
20 TraesCS4A01G166400 chr3B 82.580 597 88 14 1 593 461322015 461322599 1.510000e-141 512.0
21 TraesCS4A01G166400 chr3B 82.923 568 79 16 2 562 593505202 593505758 1.520000e-136 496.0
22 TraesCS4A01G166400 chr3B 82.432 592 73 24 3 587 242360763 242361330 2.540000e-134 488.0
23 TraesCS4A01G166400 chr2D 83.187 571 75 16 2 562 452641426 452640867 9.070000e-139 503.0
24 TraesCS4A01G166400 chr2D 88.018 217 24 2 956 1171 597695029 597695244 2.800000e-64 255.0
25 TraesCS4A01G166400 chr2D 89.116 147 14 2 1454 1598 541940222 541940368 4.830000e-42 182.0
26 TraesCS4A01G166400 chr4D 82.867 572 79 16 1 562 435549521 435548959 1.520000e-136 496.0
27 TraesCS4A01G166400 chr4D 88.018 217 24 2 956 1171 100169144 100169359 2.800000e-64 255.0
28 TraesCS4A01G166400 chr1D 83.069 567 74 19 2 562 312147920 312147370 1.520000e-136 496.0
29 TraesCS4A01G166400 chr4B 82.293 593 79 21 1 584 176999402 176998827 7.060000e-135 490.0
30 TraesCS4A01G166400 chr4B 94.203 69 4 0 1326 1394 409702213 409702281 2.990000e-19 106.0
31 TraesCS4A01G166400 chr3A 89.744 312 32 0 541 852 151226947 151227258 1.220000e-107 399.0
32 TraesCS4A01G166400 chr3A 88.621 290 22 7 1891 2171 364875596 364875883 2.090000e-90 342.0
33 TraesCS4A01G166400 chr3A 87.797 295 24 8 1891 2176 362416695 362416404 3.500000e-88 335.0
34 TraesCS4A01G166400 chr3A 90.945 254 15 4 1891 2136 364870629 364870882 3.500000e-88 335.0
35 TraesCS4A01G166400 chr3A 87.586 290 25 7 1891 2171 364895887 364896174 2.110000e-85 326.0
36 TraesCS4A01G166400 chr3A 85.374 294 33 7 1891 2176 106230799 106231090 1.650000e-76 296.0
37 TraesCS4A01G166400 chr3A 90.370 135 10 3 1316 1448 505809218 505809351 8.080000e-40 174.0
38 TraesCS4A01G166400 chr3A 89.147 129 14 0 1316 1444 505838228 505838356 6.290000e-36 161.0
39 TraesCS4A01G166400 chr3A 90.625 96 9 0 1219 1314 505759397 505759492 6.380000e-26 128.0
40 TraesCS4A01G166400 chr3A 88.679 106 9 3 1316 1419 651055024 651055128 2.290000e-25 126.0
41 TraesCS4A01G166400 chr3A 88.542 96 11 0 1219 1314 505838102 505838197 1.380000e-22 117.0
42 TraesCS4A01G166400 chr3A 74.671 304 48 27 1890 2176 453368673 453368382 8.310000e-20 108.0
43 TraesCS4A01G166400 chr3A 94.118 51 2 1 1673 1722 453368843 453368793 2.340000e-10 76.8
44 TraesCS4A01G166400 chr3A 97.561 41 0 1 1778 1817 453350724 453350684 3.920000e-08 69.4
45 TraesCS4A01G166400 chr3A 100.000 30 0 0 1219 1248 351599396 351599367 3.050000e-04 56.5
46 TraesCS4A01G166400 chr3A 100.000 29 0 0 2173 2201 134819374 134819402 1.000000e-03 54.7
47 TraesCS4A01G166400 chr1A 75.318 786 134 37 2 745 281006103 281005336 2.730000e-84 322.0
48 TraesCS4A01G166400 chr1A 92.763 152 11 0 1316 1467 226901953 226901802 1.020000e-53 220.0
49 TraesCS4A01G166400 chr7A 85.424 295 31 9 1891 2177 481275778 481276068 1.650000e-76 296.0
50 TraesCS4A01G166400 chr7A 90.184 163 12 4 1437 1598 327697772 327697613 2.210000e-50 209.0
51 TraesCS4A01G166400 chr7A 88.344 163 15 4 1437 1598 327658236 327658077 2.230000e-45 193.0
52 TraesCS4A01G166400 chr7A 90.698 129 12 0 1316 1444 511396005 511396133 2.910000e-39 172.0
53 TraesCS4A01G166400 chr7A 80.000 255 22 18 1219 1444 298849487 298849233 6.290000e-36 161.0
54 TraesCS4A01G166400 chr7A 86.792 106 14 0 1219 1324 399823815 399823710 3.840000e-23 119.0
55 TraesCS4A01G166400 chr7A 94.118 51 2 1 1673 1722 335277546 335277496 2.340000e-10 76.8
56 TraesCS4A01G166400 chr7D 88.479 217 23 2 956 1171 140574818 140575033 6.030000e-66 261.0
57 TraesCS4A01G166400 chr6D 87.558 217 25 2 956 1171 186002620 186002835 1.300000e-62 250.0
58 TraesCS4A01G166400 chr3D 87.558 217 25 2 956 1171 146541645 146541860 1.300000e-62 250.0
59 TraesCS4A01G166400 chr3D 86.607 224 27 3 950 1171 146533216 146533438 6.070000e-61 244.0
60 TraesCS4A01G166400 chr2A 93.421 152 10 0 1316 1467 467789839 467789688 2.200000e-55 226.0
61 TraesCS4A01G166400 chr2A 94.118 51 2 1 1673 1722 346465164 346465114 2.340000e-10 76.8
62 TraesCS4A01G166400 chr2A 97.561 41 0 1 1778 1817 346465130 346465090 3.920000e-08 69.4
63 TraesCS4A01G166400 chr2A 97.561 41 0 1 1778 1817 346470680 346470640 3.920000e-08 69.4
64 TraesCS4A01G166400 chr2A 91.837 49 3 1 1202 1250 647013277 647013324 1.410000e-07 67.6
65 TraesCS4A01G166400 chr5A 89.394 66 7 0 1219 1284 282164451 282164516 1.400000e-12 84.2


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 TraesCS4A01G166400 chr4A 401302556 401304756 2200 True 4065.0 4065 100.0000 1 2201 1 chr4A.!!$R3 2200
1 TraesCS4A01G166400 chr4A 401295621 401296789 1168 True 1533.0 1533 90.3340 1 1169 1 chr4A.!!$R2 1168
2 TraesCS4A01G166400 chr4A 401266797 401267476 679 True 763.0 763 87.8120 1557 2201 1 chr4A.!!$R1 644
3 TraesCS4A01G166400 chr6A 243177673 243181216 3543 True 1083.0 1096 83.6005 2 1171 2 chr6A.!!$R4 1169
4 TraesCS4A01G166400 chr6A 462751350 462752770 1420 True 643.5 1098 85.7685 2 1326 2 chr6A.!!$R6 1324
5 TraesCS4A01G166400 chr6A 363051681 363052250 569 True 580.0 580 84.9750 573 1171 1 chr6A.!!$R3 598
6 TraesCS4A01G166400 chr6A 363012544 363013330 786 True 332.0 540 88.2900 573 1259 2 chr6A.!!$R5 686
7 TraesCS4A01G166400 chr3B 461322015 461322599 584 False 512.0 512 82.5800 1 593 1 chr3B.!!$F2 592
8 TraesCS4A01G166400 chr3B 593505202 593505758 556 False 496.0 496 82.9230 2 562 1 chr3B.!!$F3 560
9 TraesCS4A01G166400 chr3B 242360763 242361330 567 False 488.0 488 82.4320 3 587 1 chr3B.!!$F1 584
10 TraesCS4A01G166400 chr2D 452640867 452641426 559 True 503.0 503 83.1870 2 562 1 chr2D.!!$R1 560
11 TraesCS4A01G166400 chr4D 435548959 435549521 562 True 496.0 496 82.8670 1 562 1 chr4D.!!$R1 561
12 TraesCS4A01G166400 chr1D 312147370 312147920 550 True 496.0 496 83.0690 2 562 1 chr1D.!!$R1 560
13 TraesCS4A01G166400 chr4B 176998827 176999402 575 True 490.0 490 82.2930 1 584 1 chr4B.!!$R1 583
14 TraesCS4A01G166400 chr1A 281005336 281006103 767 True 322.0 322 75.3180 2 745 1 chr1A.!!$R2 743

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
784 856 0.036306 GGGTTTCGGTCATGGAGTGT 59.964 55.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 3917 0.467106 TCCCCATCTCTCTCTCGCAG 60.467 60.0 0.0 0.0 0.0 5.18 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
120 125 8.819015 GCATTTAAATGTTGTTATCATGATGCA 58.181 29.630 25.15 13.59 38.65 3.96
143 148 7.870445 TGCAAATGACCTAAACAAGTTTTATCC 59.130 33.333 3.25 0.00 34.23 2.59
232 245 1.024271 CATGGCAACGAATCCGGAAT 58.976 50.000 9.01 0.00 40.78 3.01
258 271 2.736081 GCCACGACAACATATCGGTACA 60.736 50.000 0.00 0.00 43.95 2.90
263 276 4.581824 ACGACAACATATCGGTACAGGTAT 59.418 41.667 0.00 0.00 43.95 2.73
353 380 0.254747 TTCATCGGGTTCCCATGGAC 59.745 55.000 15.22 3.80 0.00 4.02
435 471 3.200605 AGGGTGCATCTCATACATCACAA 59.799 43.478 0.00 0.00 0.00 3.33
531 573 4.563184 GCAATGTAGAGGAAGTAGACGTTG 59.437 45.833 0.00 0.00 39.13 4.10
623 694 4.819105 TGAGTTTCCATAGATGTTCGGT 57.181 40.909 0.00 0.00 0.00 4.69
638 709 2.432628 GGTGTCACGGCGAGGAAG 60.433 66.667 16.62 0.00 0.00 3.46
749 820 3.972133 TCGGAGATGGGAGTAGTACAAA 58.028 45.455 2.52 0.00 0.00 2.83
756 828 1.547372 GGGAGTAGTACAAAGTCGCCA 59.453 52.381 2.52 0.00 0.00 5.69
779 851 1.539827 GAACTTGGGTTTCGGTCATGG 59.460 52.381 0.00 0.00 35.58 3.66
784 856 0.036306 GGGTTTCGGTCATGGAGTGT 59.964 55.000 0.00 0.00 0.00 3.55
840 912 2.800159 ATCCAGTCTCCGGGGTCGTT 62.800 60.000 0.00 0.00 33.95 3.85
843 915 1.075482 AGTCTCCGGGGTCGTTGTA 59.925 57.895 0.00 0.00 33.95 2.41
878 950 2.473984 CGTGTAACTCCAAGGTTCGTTC 59.526 50.000 0.00 0.00 31.75 3.95
914 986 1.666189 GTCTTTGGTGAAGATAGCCGC 59.334 52.381 0.00 0.00 45.66 6.53
922 994 1.233019 GAAGATAGCCGCACATGCAT 58.767 50.000 4.49 0.00 42.21 3.96
962 1034 1.664321 ATCGACGTCCTGGTACCTGC 61.664 60.000 14.36 0.00 0.00 4.85
963 1035 2.341101 CGACGTCCTGGTACCTGCT 61.341 63.158 14.36 0.00 0.00 4.24
975 1047 0.541063 TACCTGCTGTCCTTCGACCA 60.541 55.000 0.00 0.00 38.32 4.02
992 1064 3.056536 CGACCATGAGAGAGAAGAAACCA 60.057 47.826 0.00 0.00 0.00 3.67
1017 1089 1.149174 GATGGTGCACGATGGGGAT 59.851 57.895 19.79 0.00 0.00 3.85
1031 1132 1.751927 GGGATGGTCCTGCAGCAAG 60.752 63.158 8.66 0.00 36.57 4.01
1047 1148 0.807667 CAAGAGGAGGTCGAATGGCG 60.808 60.000 0.00 0.00 42.69 5.69
1121 1222 1.200092 AGCAGAGCTTCTGGAGGCTT 61.200 55.000 8.54 0.00 44.18 4.35
1270 1501 2.121506 ATGGGGTCACAGGGTGGT 60.122 61.111 0.00 0.00 33.87 4.16
1288 1519 1.003839 TGCGGGGACAAAGCAGTAG 60.004 57.895 0.00 0.00 35.81 2.57
1314 2788 1.489230 ACGGAGTGGAGGAACAAAGTT 59.511 47.619 0.00 0.00 42.51 2.66
1320 2794 0.822121 GGAGGAACAAAGTTGCCGGT 60.822 55.000 1.90 0.00 0.00 5.28
1360 3458 4.988716 ACGACGAGGTCCCTGGCA 62.989 66.667 0.00 0.00 0.00 4.92
1361 3459 4.135153 CGACGAGGTCCCTGGCAG 62.135 72.222 7.75 7.75 0.00 4.85
1362 3460 3.775654 GACGAGGTCCCTGGCAGG 61.776 72.222 27.04 27.04 34.30 4.85
1380 3478 4.803426 GCAGGGCGACGACTCTGG 62.803 72.222 17.38 0.31 0.00 3.86
1385 3483 3.063084 GCGACGACTCTGGGAGGT 61.063 66.667 0.00 0.00 33.35 3.85
1387 3485 1.716826 GCGACGACTCTGGGAGGTAG 61.717 65.000 0.00 0.00 33.35 3.18
1388 3486 1.096386 CGACGACTCTGGGAGGTAGG 61.096 65.000 0.00 0.00 33.35 3.18
1389 3487 0.752376 GACGACTCTGGGAGGTAGGG 60.752 65.000 0.00 0.00 33.35 3.53
1390 3488 1.212934 ACGACTCTGGGAGGTAGGGA 61.213 60.000 0.00 0.00 33.35 4.20
1391 3489 0.752376 CGACTCTGGGAGGTAGGGAC 60.752 65.000 0.00 0.00 33.35 4.46
1392 3490 0.752376 GACTCTGGGAGGTAGGGACG 60.752 65.000 0.00 0.00 33.35 4.79
1393 3491 1.455959 CTCTGGGAGGTAGGGACGG 60.456 68.421 0.00 0.00 0.00 4.79
1394 3492 3.155167 CTGGGAGGTAGGGACGGC 61.155 72.222 0.00 0.00 0.00 5.68
1425 3624 3.414193 TCTCGCGGTAGGAGGGGA 61.414 66.667 6.13 0.00 32.34 4.81
1426 3625 2.907917 CTCGCGGTAGGAGGGGAG 60.908 72.222 6.13 0.00 36.98 4.30
1427 3626 4.517934 TCGCGGTAGGAGGGGAGG 62.518 72.222 6.13 0.00 0.00 4.30
1430 3629 2.122813 CGGTAGGAGGGGAGGCAT 60.123 66.667 0.00 0.00 0.00 4.40
1431 3630 2.511452 CGGTAGGAGGGGAGGCATG 61.511 68.421 0.00 0.00 0.00 4.06
1432 3631 1.384643 GGTAGGAGGGGAGGCATGT 60.385 63.158 0.00 0.00 0.00 3.21
1433 3632 1.411651 GGTAGGAGGGGAGGCATGTC 61.412 65.000 0.00 0.00 0.00 3.06
1434 3633 1.074471 TAGGAGGGGAGGCATGTCC 60.074 63.158 0.00 0.00 35.64 4.02
1443 3642 2.423446 GGCATGTCCTAGCCGGAG 59.577 66.667 5.05 0.00 44.20 4.63
1444 3643 2.435693 GGCATGTCCTAGCCGGAGT 61.436 63.158 5.05 0.00 44.20 3.85
1445 3644 1.068250 GCATGTCCTAGCCGGAGTC 59.932 63.158 5.05 0.00 44.20 3.36
1446 3645 1.676678 GCATGTCCTAGCCGGAGTCA 61.677 60.000 5.05 0.00 44.20 3.41
1447 3646 0.387202 CATGTCCTAGCCGGAGTCAG 59.613 60.000 5.05 0.00 44.20 3.51
1448 3647 1.395826 ATGTCCTAGCCGGAGTCAGC 61.396 60.000 5.05 0.00 44.20 4.26
1449 3648 2.052690 GTCCTAGCCGGAGTCAGCA 61.053 63.158 5.05 0.00 44.20 4.41
1450 3649 1.754621 TCCTAGCCGGAGTCAGCAG 60.755 63.158 5.05 3.10 36.69 4.24
1451 3650 2.790791 CCTAGCCGGAGTCAGCAGG 61.791 68.421 5.05 7.51 33.16 4.85
1452 3651 2.759973 TAGCCGGAGTCAGCAGGG 60.760 66.667 5.05 0.00 0.00 4.45
1472 3671 3.142838 GCGATGCCATGGCCTTGT 61.143 61.111 33.44 16.86 41.09 3.16
1473 3672 2.802792 CGATGCCATGGCCTTGTG 59.197 61.111 33.44 14.96 41.09 3.33
1474 3673 2.777972 CGATGCCATGGCCTTGTGG 61.778 63.158 33.44 16.08 41.09 4.17
1475 3674 2.364579 ATGCCATGGCCTTGTGGG 60.365 61.111 33.44 3.68 41.09 4.61
1485 3684 4.711949 CTTGTGGGCAGGCGAGCT 62.712 66.667 5.04 0.00 34.17 4.09
1486 3685 4.704833 TTGTGGGCAGGCGAGCTC 62.705 66.667 2.73 2.73 34.90 4.09
1489 3688 4.478371 TGGGCAGGCGAGCTCATG 62.478 66.667 15.40 10.19 40.79 3.07
1493 3692 3.790437 CAGGCGAGCTCATGGGGT 61.790 66.667 15.40 0.00 0.00 4.95
1494 3693 3.474570 AGGCGAGCTCATGGGGTC 61.475 66.667 15.01 15.01 0.00 4.46
1498 3697 4.899239 GAGCTCATGGGGTCGCGG 62.899 72.222 9.41 0.00 0.00 6.46
1513 3712 2.751436 CGGGGTGGTTGGCATGAG 60.751 66.667 0.00 0.00 0.00 2.90
1514 3713 2.362889 GGGGTGGTTGGCATGAGG 60.363 66.667 0.00 0.00 0.00 3.86
1515 3714 2.362889 GGGTGGTTGGCATGAGGG 60.363 66.667 0.00 0.00 0.00 4.30
1516 3715 2.362889 GGTGGTTGGCATGAGGGG 60.363 66.667 0.00 0.00 0.00 4.79
1517 3716 2.440599 GTGGTTGGCATGAGGGGT 59.559 61.111 0.00 0.00 0.00 4.95
1518 3717 1.228862 GTGGTTGGCATGAGGGGTT 60.229 57.895 0.00 0.00 0.00 4.11
1519 3718 0.831711 GTGGTTGGCATGAGGGGTTT 60.832 55.000 0.00 0.00 0.00 3.27
1520 3719 0.541764 TGGTTGGCATGAGGGGTTTC 60.542 55.000 0.00 0.00 0.00 2.78
1521 3720 0.541764 GGTTGGCATGAGGGGTTTCA 60.542 55.000 0.00 0.00 0.00 2.69
1522 3721 0.603065 GTTGGCATGAGGGGTTTCAC 59.397 55.000 0.00 0.00 0.00 3.18
1523 3722 0.482446 TTGGCATGAGGGGTTTCACT 59.518 50.000 0.00 0.00 0.00 3.41
1524 3723 0.038166 TGGCATGAGGGGTTTCACTC 59.962 55.000 0.00 0.00 0.00 3.51
1525 3724 0.681243 GGCATGAGGGGTTTCACTCC 60.681 60.000 0.00 0.00 39.74 3.85
1531 3730 3.090504 GGGGTTTCACTCCTCTCCT 57.909 57.895 0.00 0.00 35.29 3.69
1532 3731 1.363246 GGGGTTTCACTCCTCTCCTT 58.637 55.000 0.00 0.00 35.29 3.36
1533 3732 1.705745 GGGGTTTCACTCCTCTCCTTT 59.294 52.381 0.00 0.00 35.29 3.11
1534 3733 2.290387 GGGGTTTCACTCCTCTCCTTTC 60.290 54.545 0.00 0.00 35.29 2.62
1535 3734 2.290387 GGGTTTCACTCCTCTCCTTTCC 60.290 54.545 0.00 0.00 0.00 3.13
1536 3735 2.640332 GGTTTCACTCCTCTCCTTTCCT 59.360 50.000 0.00 0.00 0.00 3.36
1537 3736 3.558109 GGTTTCACTCCTCTCCTTTCCTG 60.558 52.174 0.00 0.00 0.00 3.86
1538 3737 1.270907 TCACTCCTCTCCTTTCCTGC 58.729 55.000 0.00 0.00 0.00 4.85
1539 3738 0.979665 CACTCCTCTCCTTTCCTGCA 59.020 55.000 0.00 0.00 0.00 4.41
1540 3739 1.066286 CACTCCTCTCCTTTCCTGCAG 60.066 57.143 6.78 6.78 0.00 4.41
1541 3740 0.540923 CTCCTCTCCTTTCCTGCAGG 59.459 60.000 27.87 27.87 0.00 4.85
1542 3741 0.178891 TCCTCTCCTTTCCTGCAGGT 60.179 55.000 31.58 0.00 36.34 4.00
1543 3742 0.035630 CCTCTCCTTTCCTGCAGGTG 60.036 60.000 31.58 21.25 36.34 4.00
1544 3743 0.035630 CTCTCCTTTCCTGCAGGTGG 60.036 60.000 31.58 27.94 36.34 4.61
1545 3744 1.676967 CTCCTTTCCTGCAGGTGGC 60.677 63.158 31.58 0.00 45.13 5.01
1580 3779 3.306780 GGAGAGGGAGAGATCGAGAGTAG 60.307 56.522 0.00 0.00 0.00 2.57
1613 3812 2.746277 GGCGGTGGCTCGTTGATT 60.746 61.111 3.22 0.00 39.81 2.57
1627 3826 2.203070 GATTGGGCGATGCGAGGT 60.203 61.111 0.00 0.00 0.00 3.85
1664 3885 4.586235 GCCATGGGGATCGGGTGG 62.586 72.222 15.13 1.87 35.59 4.61
1696 3917 1.201429 TGGGACTGGGAGAAAGAGGC 61.201 60.000 0.00 0.00 0.00 4.70
1703 3924 1.608717 GGGAGAAAGAGGCTGCGAGA 61.609 60.000 0.00 0.00 0.00 4.04
1726 3947 4.648626 ATGGGGATCGGGCGCATG 62.649 66.667 10.83 0.00 0.00 4.06
1739 3960 2.124403 GCATGCCCTCTGTCCCTG 60.124 66.667 6.36 0.00 0.00 4.45
1773 3994 3.003173 CAGGGGAAGGGAGCGACA 61.003 66.667 0.00 0.00 0.00 4.35
1793 4014 1.608717 GGTGAGTGAGTGATCGGGCT 61.609 60.000 0.00 0.00 0.00 5.19
1818 4039 0.988832 TAAGGTTAGGTGGGCCTGTG 59.011 55.000 4.53 0.00 46.47 3.66
1841 4062 2.592861 GCTAAGCAGATGGGCCGG 60.593 66.667 0.00 0.00 0.00 6.13
1855 4076 3.702048 CCGGCGGAGAGGGAAACA 61.702 66.667 24.41 0.00 0.00 2.83
1856 4077 2.125512 CGGCGGAGAGGGAAACAG 60.126 66.667 0.00 0.00 0.00 3.16
1918 4147 9.541143 CTCTCTCTCCCTCATATTTTCTTTAAC 57.459 37.037 0.00 0.00 0.00 2.01
1941 4176 8.614469 AACAGAAAACAATAGAGAGAAGGAAG 57.386 34.615 0.00 0.00 0.00 3.46
1967 4202 4.081642 GGAGGTTTAGGGAAAGGAATTTGC 60.082 45.833 0.00 0.00 0.00 3.68
1972 4207 3.243359 AGGGAAAGGAATTTGCACTCA 57.757 42.857 0.00 0.00 0.00 3.41
2014 4249 6.232581 TCACAAAAATGAGTTTGACCCAAT 57.767 33.333 4.76 0.00 40.29 3.16
2094 4329 4.622260 AATGGGTTTGAACTGGGAATTG 57.378 40.909 0.00 0.00 0.00 2.32
2120 4355 5.897377 AAAGGAAGGTCCATAAATGTTCG 57.103 39.130 0.00 0.00 39.61 3.95
2143 4378 5.983720 CGAATTTTTAGAGGAGCCTCGATAA 59.016 40.000 10.69 4.90 46.90 1.75
2169 4404 6.012745 AGAGATAAAGAATTGTTGCCAAGGT 58.987 36.000 0.00 0.00 33.17 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 7.353414 TCCAGAATTGTTATTTGTTGTTCCA 57.647 32.000 0.00 0.00 0.00 3.53
232 245 2.607180 CGATATGTTGTCGTGGCATCAA 59.393 45.455 0.00 0.00 34.56 2.57
258 271 5.611374 CACCGGTATTTCAATGAGATACCT 58.389 41.667 28.87 16.06 43.39 3.08
263 276 3.342377 TGCACCGGTATTTCAATGAGA 57.658 42.857 6.87 0.00 0.00 3.27
353 380 4.459331 CGTTTGCCATGCCGTCGG 62.459 66.667 6.99 6.99 0.00 4.79
435 471 2.577606 TGACCCGTGGATGAATGTTT 57.422 45.000 0.00 0.00 0.00 2.83
531 573 1.959042 TCCACTACGACTATCCCGAC 58.041 55.000 0.00 0.00 0.00 4.79
598 669 4.571984 CGAACATCTATGGAAACTCATGCA 59.428 41.667 0.00 0.00 0.00 3.96
623 694 1.300620 CAACTTCCTCGCCGTGACA 60.301 57.895 0.00 0.00 0.00 3.58
638 709 2.298300 CAAGTTCAACGATGCGTCAAC 58.702 47.619 6.75 2.84 39.99 3.18
692 763 1.080974 CCGTCAAGTTCGGCTACGT 60.081 57.895 0.00 0.00 41.48 3.57
749 820 1.002134 CCCAAGTTCCATGGCGACT 60.002 57.895 6.96 10.80 36.58 4.18
756 828 1.144093 TGACCGAAACCCAAGTTCCAT 59.856 47.619 0.00 0.00 34.19 3.41
779 851 3.447586 TCCACTGATGCCTAGTAACACTC 59.552 47.826 0.00 0.00 0.00 3.51
784 856 3.898123 GGAGATCCACTGATGCCTAGTAA 59.102 47.826 0.00 0.00 35.64 2.24
840 912 6.881065 AGTTACACGAGATACCAAGTACTACA 59.119 38.462 0.00 0.00 0.00 2.74
843 915 5.356470 GGAGTTACACGAGATACCAAGTACT 59.644 44.000 0.00 0.00 0.00 2.73
914 986 4.348656 GCAAGTTCATCTACATGCATGTG 58.651 43.478 36.72 26.36 41.14 3.21
922 994 0.981183 ACCCGGCAAGTTCATCTACA 59.019 50.000 0.00 0.00 0.00 2.74
962 1034 2.095461 TCTCTCATGGTCGAAGGACAG 58.905 52.381 0.00 0.00 45.28 3.51
963 1035 2.095461 CTCTCTCATGGTCGAAGGACA 58.905 52.381 0.00 0.00 45.28 4.02
975 1047 5.762218 CACTGTTTGGTTTCTTCTCTCTCAT 59.238 40.000 0.00 0.00 0.00 2.90
992 1064 1.536766 CATCGTGCACCATCACTGTTT 59.463 47.619 12.15 0.00 34.92 2.83
1017 1089 1.834856 CTCCTCTTGCTGCAGGACCA 61.835 60.000 17.12 1.56 34.87 4.02
1031 1132 2.107141 CCGCCATTCGACCTCCTC 59.893 66.667 0.00 0.00 41.67 3.71
1047 1148 1.633852 CTTCGTCTTGCTGCTGCTCC 61.634 60.000 17.00 1.33 40.48 4.70
1155 1256 3.068691 TTGTCTCGCCTCCTCCCG 61.069 66.667 0.00 0.00 0.00 5.14
1169 1400 2.657237 CTTCCTCCGACGCCTTGT 59.343 61.111 0.00 0.00 0.00 3.16
1198 1429 1.455959 GCCTCCGCCTCTCCTCTTA 60.456 63.158 0.00 0.00 0.00 2.10
1254 1485 3.174987 CACCACCCTGTGACCCCA 61.175 66.667 0.00 0.00 38.55 4.96
1270 1501 1.003839 CTACTGCTTTGTCCCCGCA 60.004 57.895 0.00 0.00 0.00 5.69
1279 1510 2.096248 CTCCGTCTCTCCTACTGCTTT 58.904 52.381 0.00 0.00 0.00 3.51
1288 1519 0.323542 TTCCTCCACTCCGTCTCTCC 60.324 60.000 0.00 0.00 0.00 3.71
1300 2774 0.821711 CCGGCAACTTTGTTCCTCCA 60.822 55.000 0.00 0.00 0.00 3.86
1301 2775 0.822121 ACCGGCAACTTTGTTCCTCC 60.822 55.000 0.00 0.00 0.00 4.30
1340 3438 4.436998 CAGGGACCTCGTCGTGGC 62.437 72.222 13.13 6.28 32.65 5.01
1342 3440 4.436998 GCCAGGGACCTCGTCGTG 62.437 72.222 0.00 0.00 32.65 4.35
1362 3460 4.803426 CAGAGTCGTCGCCCTGCC 62.803 72.222 0.00 0.00 0.00 4.85
1363 3461 4.803426 CCAGAGTCGTCGCCCTGC 62.803 72.222 0.00 0.00 0.00 4.85
1364 3462 4.135153 CCCAGAGTCGTCGCCCTG 62.135 72.222 0.00 0.00 0.00 4.45
1365 3463 4.361971 TCCCAGAGTCGTCGCCCT 62.362 66.667 0.00 0.00 0.00 5.19
1366 3464 3.827898 CTCCCAGAGTCGTCGCCC 61.828 72.222 0.00 0.00 0.00 6.13
1368 3466 1.716826 CTACCTCCCAGAGTCGTCGC 61.717 65.000 0.00 0.00 0.00 5.19
1370 3468 0.752376 CCCTACCTCCCAGAGTCGTC 60.752 65.000 0.00 0.00 0.00 4.20
1371 3469 1.212934 TCCCTACCTCCCAGAGTCGT 61.213 60.000 0.00 0.00 0.00 4.34
1372 3470 0.752376 GTCCCTACCTCCCAGAGTCG 60.752 65.000 0.00 0.00 0.00 4.18
1375 3473 1.455959 CCGTCCCTACCTCCCAGAG 60.456 68.421 0.00 0.00 0.00 3.35
1376 3474 2.687902 CCGTCCCTACCTCCCAGA 59.312 66.667 0.00 0.00 0.00 3.86
1377 3475 3.155167 GCCGTCCCTACCTCCCAG 61.155 72.222 0.00 0.00 0.00 4.45
1407 3606 3.217743 CCCCTCCTACCGCGAGAC 61.218 72.222 8.23 0.00 0.00 3.36
1413 3612 2.122813 ATGCCTCCCCTCCTACCG 60.123 66.667 0.00 0.00 0.00 4.02
1416 3615 1.074471 GGACATGCCTCCCCTCCTA 60.074 63.158 0.00 0.00 0.00 2.94
1417 3616 1.603633 TAGGACATGCCTCCCCTCCT 61.604 60.000 11.35 7.81 46.97 3.69
1426 3625 2.370647 GACTCCGGCTAGGACATGCC 62.371 65.000 0.00 0.00 45.98 4.40
1427 3626 1.068250 GACTCCGGCTAGGACATGC 59.932 63.158 0.00 0.00 45.98 4.06
1428 3627 0.387202 CTGACTCCGGCTAGGACATG 59.613 60.000 0.00 0.00 45.98 3.21
1429 3628 1.395826 GCTGACTCCGGCTAGGACAT 61.396 60.000 0.00 0.00 45.98 3.06
1430 3629 2.052690 GCTGACTCCGGCTAGGACA 61.053 63.158 0.00 0.00 45.98 4.02
1431 3630 2.010582 CTGCTGACTCCGGCTAGGAC 62.011 65.000 0.00 0.00 45.98 3.85
1433 3632 2.790791 CCTGCTGACTCCGGCTAGG 61.791 68.421 0.00 0.00 44.89 3.02
1434 3633 2.790791 CCCTGCTGACTCCGGCTAG 61.791 68.421 0.00 0.00 44.89 3.42
1435 3634 2.759973 CCCTGCTGACTCCGGCTA 60.760 66.667 0.00 0.00 44.89 3.93
1455 3654 3.142838 ACAAGGCCATGGCATCGC 61.143 61.111 36.56 20.07 44.11 4.58
1456 3655 2.777972 CCACAAGGCCATGGCATCG 61.778 63.158 36.56 24.05 44.11 3.84
1457 3656 2.428925 CCCACAAGGCCATGGCATC 61.429 63.158 36.56 21.21 44.11 3.91
1458 3657 2.364579 CCCACAAGGCCATGGCAT 60.365 61.111 36.56 29.47 44.11 4.40
1468 3667 4.711949 AGCTCGCCTGCCCACAAG 62.712 66.667 0.00 0.00 0.00 3.16
1469 3668 4.704833 GAGCTCGCCTGCCCACAA 62.705 66.667 0.00 0.00 0.00 3.33
1471 3670 4.479993 ATGAGCTCGCCTGCCCAC 62.480 66.667 9.64 0.00 0.00 4.61
1472 3671 4.478371 CATGAGCTCGCCTGCCCA 62.478 66.667 9.64 0.00 0.00 5.36
1476 3675 3.746949 GACCCCATGAGCTCGCCTG 62.747 68.421 9.64 6.51 0.00 4.85
1477 3676 3.474570 GACCCCATGAGCTCGCCT 61.475 66.667 9.64 0.00 0.00 5.52
1478 3677 4.899239 CGACCCCATGAGCTCGCC 62.899 72.222 9.64 0.00 0.00 5.54
1481 3680 4.899239 CCGCGACCCCATGAGCTC 62.899 72.222 8.23 6.82 0.00 4.09
1496 3695 2.751436 CTCATGCCAACCACCCCG 60.751 66.667 0.00 0.00 0.00 5.73
1497 3696 2.362889 CCTCATGCCAACCACCCC 60.363 66.667 0.00 0.00 0.00 4.95
1498 3697 2.362889 CCCTCATGCCAACCACCC 60.363 66.667 0.00 0.00 0.00 4.61
1499 3698 2.362889 CCCCTCATGCCAACCACC 60.363 66.667 0.00 0.00 0.00 4.61
1500 3699 0.831711 AAACCCCTCATGCCAACCAC 60.832 55.000 0.00 0.00 0.00 4.16
1501 3700 0.541764 GAAACCCCTCATGCCAACCA 60.542 55.000 0.00 0.00 0.00 3.67
1502 3701 0.541764 TGAAACCCCTCATGCCAACC 60.542 55.000 0.00 0.00 0.00 3.77
1503 3702 0.603065 GTGAAACCCCTCATGCCAAC 59.397 55.000 0.00 0.00 0.00 3.77
1504 3703 0.482446 AGTGAAACCCCTCATGCCAA 59.518 50.000 0.00 0.00 37.80 4.52
1505 3704 0.038166 GAGTGAAACCCCTCATGCCA 59.962 55.000 0.00 0.00 37.80 4.92
1506 3705 0.681243 GGAGTGAAACCCCTCATGCC 60.681 60.000 0.00 0.00 37.80 4.40
1507 3706 0.329596 AGGAGTGAAACCCCTCATGC 59.670 55.000 0.00 0.00 37.80 4.06
1508 3707 1.912043 AGAGGAGTGAAACCCCTCATG 59.088 52.381 10.18 0.00 46.74 3.07
1509 3708 2.192263 GAGAGGAGTGAAACCCCTCAT 58.808 52.381 10.18 0.00 46.74 2.90
1510 3709 1.645710 GAGAGGAGTGAAACCCCTCA 58.354 55.000 10.18 0.00 46.74 3.86
1511 3710 0.906066 GGAGAGGAGTGAAACCCCTC 59.094 60.000 0.00 0.00 45.16 4.30
1512 3711 0.494095 AGGAGAGGAGTGAAACCCCT 59.506 55.000 0.00 0.00 37.80 4.79
1513 3712 1.363246 AAGGAGAGGAGTGAAACCCC 58.637 55.000 0.00 0.00 37.80 4.95
1514 3713 2.290387 GGAAAGGAGAGGAGTGAAACCC 60.290 54.545 0.00 0.00 37.80 4.11
1515 3714 2.640332 AGGAAAGGAGAGGAGTGAAACC 59.360 50.000 0.00 0.00 37.80 3.27
1516 3715 3.669536 CAGGAAAGGAGAGGAGTGAAAC 58.330 50.000 0.00 0.00 0.00 2.78
1517 3716 2.039084 GCAGGAAAGGAGAGGAGTGAAA 59.961 50.000 0.00 0.00 0.00 2.69
1518 3717 1.625818 GCAGGAAAGGAGAGGAGTGAA 59.374 52.381 0.00 0.00 0.00 3.18
1519 3718 1.270907 GCAGGAAAGGAGAGGAGTGA 58.729 55.000 0.00 0.00 0.00 3.41
1520 3719 0.979665 TGCAGGAAAGGAGAGGAGTG 59.020 55.000 0.00 0.00 0.00 3.51
1521 3720 1.274712 CTGCAGGAAAGGAGAGGAGT 58.725 55.000 5.57 0.00 0.00 3.85
1522 3721 0.540923 CCTGCAGGAAAGGAGAGGAG 59.459 60.000 29.88 0.00 36.91 3.69
1523 3722 0.178891 ACCTGCAGGAAAGGAGAGGA 60.179 55.000 39.19 0.00 38.27 3.71
1524 3723 0.035630 CACCTGCAGGAAAGGAGAGG 60.036 60.000 39.19 9.95 38.27 3.69
1525 3724 0.035630 CCACCTGCAGGAAAGGAGAG 60.036 60.000 39.19 15.94 38.27 3.20
1526 3725 2.069776 CCACCTGCAGGAAAGGAGA 58.930 57.895 39.19 0.00 38.27 3.71
1527 3726 1.676967 GCCACCTGCAGGAAAGGAG 60.677 63.158 39.19 19.44 40.77 3.69
1528 3727 2.436109 GCCACCTGCAGGAAAGGA 59.564 61.111 39.19 0.00 40.77 3.36
1529 3728 3.058160 CGCCACCTGCAGGAAAGG 61.058 66.667 39.19 32.41 41.33 3.11
1530 3729 3.058160 CCGCCACCTGCAGGAAAG 61.058 66.667 39.19 25.24 41.33 2.62
1545 3744 4.193334 TCTCCATCGCTCGTGCCG 62.193 66.667 3.52 0.00 35.36 5.69
1546 3745 2.279120 CTCTCCATCGCTCGTGCC 60.279 66.667 3.52 0.00 35.36 5.01
1547 3746 2.279120 CCTCTCCATCGCTCGTGC 60.279 66.667 0.00 0.00 0.00 5.34
1548 3747 2.069465 CTCCCTCTCCATCGCTCGTG 62.069 65.000 0.00 0.00 0.00 4.35
1549 3748 1.826054 CTCCCTCTCCATCGCTCGT 60.826 63.158 0.00 0.00 0.00 4.18
1550 3749 1.514678 CTCTCCCTCTCCATCGCTCG 61.515 65.000 0.00 0.00 0.00 5.03
1551 3750 0.179004 TCTCTCCCTCTCCATCGCTC 60.179 60.000 0.00 0.00 0.00 5.03
1552 3751 0.482446 ATCTCTCCCTCTCCATCGCT 59.518 55.000 0.00 0.00 0.00 4.93
1553 3752 0.887933 GATCTCTCCCTCTCCATCGC 59.112 60.000 0.00 0.00 0.00 4.58
1554 3753 1.164411 CGATCTCTCCCTCTCCATCG 58.836 60.000 0.00 0.00 0.00 3.84
1555 3754 2.039746 TCTCGATCTCTCCCTCTCCATC 59.960 54.545 0.00 0.00 0.00 3.51
1560 3759 2.637872 CCTACTCTCGATCTCTCCCTCT 59.362 54.545 0.00 0.00 0.00 3.69
1607 3806 1.353103 CTCGCATCGCCCAATCAAC 59.647 57.895 0.00 0.00 0.00 3.18
1644 3865 4.586235 CCCGATCCCCATGGCCAC 62.586 72.222 8.16 0.00 0.00 5.01
1646 3867 4.586235 CACCCGATCCCCATGGCC 62.586 72.222 6.09 0.00 0.00 5.36
1696 3917 0.467106 TCCCCATCTCTCTCTCGCAG 60.467 60.000 0.00 0.00 0.00 5.18
1703 3924 1.535202 GCCCGATCCCCATCTCTCT 60.535 63.158 0.00 0.00 0.00 3.10
1724 3945 3.415087 GCCAGGGACAGAGGGCAT 61.415 66.667 0.00 0.00 45.70 4.40
1773 3994 1.608717 GCCCGATCACTCACTCACCT 61.609 60.000 0.00 0.00 0.00 4.00
1793 4014 2.199208 GCCCACCTAACCTTAACCCTA 58.801 52.381 0.00 0.00 0.00 3.53
1818 4039 1.527844 CCATCTGCTTAGCCCAGCC 60.528 63.158 0.29 0.00 39.25 4.85
1841 4062 2.436824 GGCTGTTTCCCTCTCCGC 60.437 66.667 0.00 0.00 0.00 5.54
1870 4091 2.821366 CAACTAGCAGCCCAGCCG 60.821 66.667 0.00 0.00 34.23 5.52
1880 4101 2.099098 GGAGAGAGAGAGCACAACTAGC 59.901 54.545 0.00 0.00 0.00 3.42
1918 4147 7.548780 CCTCTTCCTTCTCTCTATTGTTTTCTG 59.451 40.741 0.00 0.00 0.00 3.02
1924 4153 5.208121 CTCCCTCTTCCTTCTCTCTATTGT 58.792 45.833 0.00 0.00 0.00 2.71
1934 4163 2.506231 CCCTAAACCTCCCTCTTCCTTC 59.494 54.545 0.00 0.00 0.00 3.46
1941 4176 2.558974 TCCTTTCCCTAAACCTCCCTC 58.441 52.381 0.00 0.00 0.00 4.30
2014 4249 9.734620 CTTTCGATCATGCCATTTCTAATTTTA 57.265 29.630 0.00 0.00 0.00 1.52
2078 4313 5.989168 CCTTTTACCAATTCCCAGTTCAAAC 59.011 40.000 0.00 0.00 0.00 2.93
2091 4326 7.678171 ACATTTATGGACCTTCCTTTTACCAAT 59.322 33.333 0.00 0.00 37.46 3.16
2094 4329 7.476540 AACATTTATGGACCTTCCTTTTACC 57.523 36.000 0.00 0.00 37.46 2.85
2120 4355 7.787725 TTTATCGAGGCTCCTCTAAAAATTC 57.212 36.000 9.32 0.00 40.69 2.17
2169 4404 4.647399 CCCACTTTAAGTTTCACCTCCAAA 59.353 41.667 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.