Multiple sequence alignment - TraesCS4A01G178000

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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 TraesCS4A01G178000 chr4A 100.000 3880 0 0 1 3880 449897357 449893478 0.000000e+00 7166
1 TraesCS4A01G178000 chr4A 85.565 672 67 15 1 647 307830704 307830038 0.000000e+00 676
2 TraesCS4A01G178000 chr4A 85.435 666 69 12 7 646 285346717 285346054 0.000000e+00 667
3 TraesCS4A01G178000 chr4A 85.075 670 59 13 2 647 367734676 367735328 0.000000e+00 645
4 TraesCS4A01G178000 chr4A 84.314 663 84 9 1 647 283182369 283183027 7.070000e-177 630
5 TraesCS4A01G178000 chr4A 85.612 556 37 9 115 647 449902335 449901800 9.480000e-151 544
6 TraesCS4A01G178000 chr4A 82.132 666 50 17 7 648 285321876 285321256 1.240000e-139 507
7 TraesCS4A01G178000 chr4A 81.980 394 40 13 271 647 491098185 491097806 4.870000e-79 305
8 TraesCS4A01G178000 chr4D 97.010 2475 52 5 1397 3865 119418241 119415783 0.000000e+00 4141
9 TraesCS4A01G178000 chr4D 91.472 598 33 11 670 1264 119420094 119419512 0.000000e+00 806
10 TraesCS4A01G178000 chr4B 95.922 2305 57 13 1561 3865 181698905 181696638 0.000000e+00 3701
11 TraesCS4A01G178000 chr4B 90.783 575 41 10 709 1275 181699621 181699051 0.000000e+00 758
12 TraesCS4A01G178000 chr3A 90.085 585 46 3 1 573 259073251 259073835 0.000000e+00 749
13 TraesCS4A01G178000 chr3A 100.000 74 0 0 1273 1346 658902289 658902362 1.880000e-28 137
14 TraesCS4A01G178000 chr7A 89.573 585 48 4 1 573 348203707 348204290 0.000000e+00 730
15 TraesCS4A01G178000 chr7A 86.289 671 68 3 1 647 359059604 359058934 0.000000e+00 708
16 TraesCS4A01G178000 chr7A 84.650 671 79 3 1 647 357898247 357898917 0.000000e+00 647
17 TraesCS4A01G178000 chr7A 91.195 159 14 0 415 573 357906360 357906518 2.350000e-52 217
18 TraesCS4A01G178000 chrUn 86.462 650 62 10 23 647 436199991 436199343 0.000000e+00 689
19 TraesCS4A01G178000 chr6A 85.736 666 69 4 7 647 176190757 176190093 0.000000e+00 680
20 TraesCS4A01G178000 chr6A 84.940 664 53 8 1 639 288397705 288398346 2.540000e-176 628
21 TraesCS4A01G178000 chr6A 98.718 78 0 1 1273 1349 175625578 175625501 1.880000e-28 137
22 TraesCS4A01G178000 chr6B 80.597 670 96 21 1 647 685301946 685301288 1.620000e-133 486
23 TraesCS4A01G178000 chr6B 98.718 78 0 1 1273 1349 201225748 201225825 1.880000e-28 137
24 TraesCS4A01G178000 chr3D 80.556 612 80 21 1 576 557806261 557805653 5.950000e-118 435
25 TraesCS4A01G178000 chr2A 76.042 672 117 24 9 647 297048997 297048337 3.760000e-80 309
26 TraesCS4A01G178000 chr7B 100.000 74 0 0 1273 1346 698903161 698903234 1.880000e-28 137
27 TraesCS4A01G178000 chr2B 100.000 74 0 0 1273 1346 359864813 359864886 1.880000e-28 137
28 TraesCS4A01G178000 chr2B 98.701 77 1 0 1273 1349 481540414 481540490 1.880000e-28 137
29 TraesCS4A01G178000 chr1B 98.701 77 1 0 1273 1349 666817634 666817558 1.880000e-28 137
30 TraesCS4A01G178000 chr1B 97.500 80 0 2 1273 1351 669758484 669758406 6.760000e-28 135
31 TraesCS4A01G178000 chr1B 93.258 89 5 1 1273 1361 520262101 520262188 3.150000e-26 130


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 TraesCS4A01G178000 chr4A 449893478 449897357 3879 True 7166.0 7166 100.0000 1 3880 1 chr4A.!!$R4 3879
1 TraesCS4A01G178000 chr4A 307830038 307830704 666 True 676.0 676 85.5650 1 647 1 chr4A.!!$R3 646
2 TraesCS4A01G178000 chr4A 285346054 285346717 663 True 667.0 667 85.4350 7 646 1 chr4A.!!$R2 639
3 TraesCS4A01G178000 chr4A 367734676 367735328 652 False 645.0 645 85.0750 2 647 1 chr4A.!!$F2 645
4 TraesCS4A01G178000 chr4A 283182369 283183027 658 False 630.0 630 84.3140 1 647 1 chr4A.!!$F1 646
5 TraesCS4A01G178000 chr4A 449901800 449902335 535 True 544.0 544 85.6120 115 647 1 chr4A.!!$R5 532
6 TraesCS4A01G178000 chr4A 285321256 285321876 620 True 507.0 507 82.1320 7 648 1 chr4A.!!$R1 641
7 TraesCS4A01G178000 chr4D 119415783 119420094 4311 True 2473.5 4141 94.2410 670 3865 2 chr4D.!!$R1 3195
8 TraesCS4A01G178000 chr4B 181696638 181699621 2983 True 2229.5 3701 93.3525 709 3865 2 chr4B.!!$R1 3156
9 TraesCS4A01G178000 chr3A 259073251 259073835 584 False 749.0 749 90.0850 1 573 1 chr3A.!!$F1 572
10 TraesCS4A01G178000 chr7A 348203707 348204290 583 False 730.0 730 89.5730 1 573 1 chr7A.!!$F1 572
11 TraesCS4A01G178000 chr7A 359058934 359059604 670 True 708.0 708 86.2890 1 647 1 chr7A.!!$R1 646
12 TraesCS4A01G178000 chr7A 357898247 357898917 670 False 647.0 647 84.6500 1 647 1 chr7A.!!$F2 646
13 TraesCS4A01G178000 chrUn 436199343 436199991 648 True 689.0 689 86.4620 23 647 1 chrUn.!!$R1 624
14 TraesCS4A01G178000 chr6A 176190093 176190757 664 True 680.0 680 85.7360 7 647 1 chr6A.!!$R2 640
15 TraesCS4A01G178000 chr6A 288397705 288398346 641 False 628.0 628 84.9400 1 639 1 chr6A.!!$F1 638
16 TraesCS4A01G178000 chr6B 685301288 685301946 658 True 486.0 486 80.5970 1 647 1 chr6B.!!$R1 646
17 TraesCS4A01G178000 chr3D 557805653 557806261 608 True 435.0 435 80.5560 1 576 1 chr3D.!!$R1 575
18 TraesCS4A01G178000 chr2A 297048337 297048997 660 True 309.0 309 76.0420 9 647 1 chr2A.!!$R1 638

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
613 692 0.824595 TTTGGTGGGACGACGAGAGA 60.825 55.0 0.00 0.00 0.00 3.10 F
1342 1436 0.105964 TGCACCAGGTTGCCCTTTTA 60.106 50.0 10.46 0.00 42.25 1.52 F
1362 1456 0.953727 TATATGGGACGGACGAACGG 59.046 55.0 0.00 0.49 38.39 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 3335 0.238289 GAATGGTGACTGGCGTGTTG 59.762 55.0 0.0 0.0 0.00 3.33 R
2750 4070 0.685660 GGAAGTCCGACCCAAAGTCT 59.314 55.0 0.0 0.0 43.91 3.24 R
3357 4677 2.105477 GTCAGGGCACAGATACATCCAT 59.895 50.0 0.0 0.0 0.00 3.41 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
58 61 3.574395 AAGGGGGCGAAGGGGTACT 62.574 63.158 0.00 0.00 0.00 2.73
285 321 2.268920 CGGCTTCAGGGCAGCTTA 59.731 61.111 0.00 0.00 40.90 3.09
532 598 5.587443 CCAAGTCTCATATGCATTGAAGTGA 59.413 40.000 3.54 1.63 0.00 3.41
539 605 9.176460 TCTCATATGCATTGAAGTGAAATTGTA 57.824 29.630 3.54 0.00 0.00 2.41
607 686 2.028385 ACTAGACATTTGGTGGGACGAC 60.028 50.000 0.00 0.00 0.00 4.34
613 692 0.824595 TTTGGTGGGACGACGAGAGA 60.825 55.000 0.00 0.00 0.00 3.10
620 699 1.309950 GGACGACGAGAGATCCATGA 58.690 55.000 0.00 0.00 33.43 3.07
621 700 1.676529 GGACGACGAGAGATCCATGAA 59.323 52.381 0.00 0.00 33.43 2.57
622 701 2.099263 GGACGACGAGAGATCCATGAAA 59.901 50.000 0.00 0.00 33.43 2.69
639 718 5.163343 CCATGAAAATGATCTTGGGATGCTT 60.163 40.000 0.00 0.00 39.67 3.91
653 732 2.845019 TGCTTCGCATCAGTTCCAG 58.155 52.632 0.00 0.00 31.71 3.86
654 733 1.300971 TGCTTCGCATCAGTTCCAGC 61.301 55.000 0.00 0.00 31.71 4.85
655 734 1.986575 GCTTCGCATCAGTTCCAGCC 61.987 60.000 0.00 0.00 0.00 4.85
656 735 1.699656 CTTCGCATCAGTTCCAGCCG 61.700 60.000 0.00 0.00 0.00 5.52
657 736 3.869272 CGCATCAGTTCCAGCCGC 61.869 66.667 0.00 0.00 0.00 6.53
658 737 3.512516 GCATCAGTTCCAGCCGCC 61.513 66.667 0.00 0.00 0.00 6.13
659 738 2.046023 CATCAGTTCCAGCCGCCA 60.046 61.111 0.00 0.00 0.00 5.69
660 739 2.110967 CATCAGTTCCAGCCGCCAG 61.111 63.158 0.00 0.00 0.00 4.85
661 740 3.335356 ATCAGTTCCAGCCGCCAGG 62.335 63.158 0.00 0.00 41.62 4.45
662 741 4.020617 CAGTTCCAGCCGCCAGGA 62.021 66.667 0.00 0.00 41.02 3.86
663 742 3.710722 AGTTCCAGCCGCCAGGAG 61.711 66.667 0.00 0.00 41.02 3.69
679 758 1.595466 GGAGCGAGAGACTCCGATTA 58.405 55.000 14.93 0.00 41.87 1.75
688 767 5.447144 CGAGAGACTCCGATTATAGATGCTG 60.447 48.000 0.00 0.00 0.00 4.41
707 786 3.826729 GCTGTTACCAACATTCTTCCCTT 59.173 43.478 0.00 0.00 41.26 3.95
722 801 4.465512 CTTGTGCGGTGCGGATGC 62.466 66.667 0.00 0.00 43.20 3.91
736 815 2.539142 GCGGATGCGTAGATAGATACGG 60.539 54.545 8.84 0.00 46.66 4.02
785 864 1.516161 GATGCTGCAGTGACAGTGAA 58.484 50.000 16.64 2.19 39.96 3.18
819 898 2.289320 TGCTTTCTCTCTCTCACCTTGC 60.289 50.000 0.00 0.00 0.00 4.01
835 914 2.826738 GCGCCTTTTCCGCCCATA 60.827 61.111 0.00 0.00 45.30 2.74
867 948 1.918293 CCTCCTGCTACCACCACCA 60.918 63.158 0.00 0.00 0.00 4.17
868 949 1.296715 CTCCTGCTACCACCACCAC 59.703 63.158 0.00 0.00 0.00 4.16
870 951 2.525124 CCTGCTACCACCACCACCA 61.525 63.158 0.00 0.00 0.00 4.17
871 952 1.302511 CTGCTACCACCACCACCAC 60.303 63.158 0.00 0.00 0.00 4.16
873 954 2.824880 GCTACCACCACCACCACCA 61.825 63.158 0.00 0.00 0.00 4.17
899 988 3.230134 CATCACCACCTTTTCCTTTCCA 58.770 45.455 0.00 0.00 0.00 3.53
1029 1122 1.048160 GCCTCCTCTTCCTCCTCCTG 61.048 65.000 0.00 0.00 0.00 3.86
1031 1124 1.002274 TCCTCTTCCTCCTCCTGCC 59.998 63.158 0.00 0.00 0.00 4.85
1176 1270 1.364626 CGGAGGCTCATCTGCACAAC 61.365 60.000 17.69 0.00 34.04 3.32
1179 1273 2.275318 GAGGCTCATCTGCACAACTAC 58.725 52.381 10.25 0.00 34.04 2.73
1217 1311 0.373716 CCGAAATGTACTCTTGCGCC 59.626 55.000 4.18 0.00 0.00 6.53
1233 1327 3.465403 CCTCTACCTGCGGCTGCT 61.465 66.667 20.27 0.14 43.34 4.24
1246 1340 1.575922 GCTGCTGCACACGATTTCA 59.424 52.632 11.11 0.00 39.41 2.69
1268 1362 8.696043 TTCATTTTCTTGAGGTGATATATGGG 57.304 34.615 0.00 0.00 0.00 4.00
1269 1363 8.044574 TCATTTTCTTGAGGTGATATATGGGA 57.955 34.615 0.00 0.00 0.00 4.37
1271 1365 8.790718 CATTTTCTTGAGGTGATATATGGGAAG 58.209 37.037 0.00 0.00 0.00 3.46
1272 1366 6.439636 TTCTTGAGGTGATATATGGGAAGG 57.560 41.667 0.00 0.00 0.00 3.46
1273 1367 5.726560 TCTTGAGGTGATATATGGGAAGGA 58.273 41.667 0.00 0.00 0.00 3.36
1274 1368 5.544176 TCTTGAGGTGATATATGGGAAGGAC 59.456 44.000 0.00 0.00 0.00 3.85
1289 1383 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
1290 1384 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
1291 1385 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
1292 1386 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
1293 1387 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
1294 1388 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
1295 1389 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
1296 1390 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
1297 1391 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
1298 1392 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
1299 1393 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
1300 1394 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
1301 1395 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
1302 1396 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
1303 1397 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
1304 1398 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
1305 1399 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
1306 1400 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
1307 1401 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
1308 1402 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
1333 1427 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
1334 1428 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
1335 1429 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
1336 1430 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
1337 1431 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
1338 1432 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
1339 1433 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
1340 1434 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
1341 1435 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
1342 1436 0.105964 TGCACCAGGTTGCCCTTTTA 60.106 50.000 10.46 0.00 42.25 1.52
1343 1437 1.266178 GCACCAGGTTGCCCTTTTAT 58.734 50.000 0.00 0.00 39.89 1.40
1344 1438 2.225142 TGCACCAGGTTGCCCTTTTATA 60.225 45.455 10.46 0.00 42.25 0.98
1345 1439 3.031013 GCACCAGGTTGCCCTTTTATAT 58.969 45.455 0.00 0.00 39.89 0.86
1346 1440 4.211920 GCACCAGGTTGCCCTTTTATATA 58.788 43.478 0.00 0.00 39.89 0.86
1347 1441 4.832823 GCACCAGGTTGCCCTTTTATATAT 59.167 41.667 0.00 0.00 39.89 0.86
1348 1442 5.278957 GCACCAGGTTGCCCTTTTATATATG 60.279 44.000 0.00 0.00 39.89 1.78
1349 1443 5.243730 CACCAGGTTGCCCTTTTATATATGG 59.756 44.000 0.00 0.00 39.89 2.74
1362 1456 0.953727 TATATGGGACGGACGAACGG 59.046 55.000 0.00 0.49 38.39 4.44
1389 1483 2.029649 TCTGAACTTAACGTCCCCTTCG 60.030 50.000 0.00 0.00 0.00 3.79
1421 2727 4.080863 ACAAATCCCACTCTATGTCTGGAC 60.081 45.833 0.00 0.00 31.72 4.02
1422 2728 3.697190 ATCCCACTCTATGTCTGGACT 57.303 47.619 2.38 0.00 31.72 3.85
1423 2729 3.019799 TCCCACTCTATGTCTGGACTC 57.980 52.381 2.38 0.00 0.00 3.36
1424 2730 2.583101 TCCCACTCTATGTCTGGACTCT 59.417 50.000 2.38 0.00 0.00 3.24
1425 2731 2.692557 CCCACTCTATGTCTGGACTCTG 59.307 54.545 2.38 0.00 0.00 3.35
1426 2732 2.100584 CCACTCTATGTCTGGACTCTGC 59.899 54.545 2.38 0.00 0.00 4.26
1427 2733 2.757314 CACTCTATGTCTGGACTCTGCA 59.243 50.000 2.38 0.00 0.00 4.41
1527 2841 1.588239 TCAGATTGGGGAGCATCACT 58.412 50.000 0.00 0.00 39.68 3.41
1557 2877 8.733092 AGATACATATACTGGGATGGGATATG 57.267 38.462 0.00 0.00 36.81 1.78
1699 3019 4.513318 GCATCTCATACCTACTTTCTTGCC 59.487 45.833 0.00 0.00 0.00 4.52
1715 3035 5.932619 TCTTGCCTACTTAGTTCTATGCA 57.067 39.130 0.00 0.00 0.00 3.96
1829 3149 2.573009 TGATGACTTGGATCCAGCTCAA 59.427 45.455 21.32 5.39 0.00 3.02
1875 3195 1.189524 AGTCCCATCGACGAACCCAA 61.190 55.000 0.00 0.00 46.92 4.12
2015 3335 1.450312 CCCTTCGACATCTGCACCC 60.450 63.158 0.00 0.00 0.00 4.61
2130 3450 1.595357 GGCACTACACCGCCTACTT 59.405 57.895 0.00 0.00 45.29 2.24
2159 3479 1.076350 ACTACTCCAGTCACAGCTCCT 59.924 52.381 0.00 0.00 28.33 3.69
2208 3528 2.825836 CCAAGGCCGGCTCATCAC 60.826 66.667 28.56 8.41 0.00 3.06
2479 3799 6.839124 TTGGTGTTCTGAAATATCATGCTT 57.161 33.333 0.00 0.00 34.37 3.91
2503 3823 1.002868 TCCTCTTTGCAGGCTCAGC 60.003 57.895 0.00 0.00 32.91 4.26
2568 3888 7.975616 GGTGAAGCTTATAAATTTGCATTCTGA 59.024 33.333 0.00 0.00 0.00 3.27
2592 3912 7.658167 TGATAACATGGAACTCTCGTGTTTAAA 59.342 33.333 6.93 0.00 34.67 1.52
2692 4012 4.353777 AGCCCTGTTACTAGTTCATCTGA 58.646 43.478 0.00 0.00 0.00 3.27
2750 4070 3.816994 CTCAGGCATTTCTGGATCATCA 58.183 45.455 0.00 0.00 35.58 3.07
3704 5024 1.456287 GTGTGCCCTTCTGTCCCTT 59.544 57.895 0.00 0.00 0.00 3.95
3843 5163 6.013379 TCCTCTTGGATGCTTTCTTTCTTCTA 60.013 38.462 0.00 0.00 37.46 2.10
3846 5166 7.227156 TCTTGGATGCTTTCTTTCTTCTACTT 58.773 34.615 0.00 0.00 0.00 2.24
3865 5185 9.699410 TTCTACTTATTCCATTTCACATGGATT 57.301 29.630 4.39 4.29 46.51 3.01
3866 5186 9.699410 TCTACTTATTCCATTTCACATGGATTT 57.301 29.630 4.39 0.00 46.51 2.17
3873 5193 9.603921 ATTCCATTTCACATGGATTTTATTGTC 57.396 29.630 4.39 0.00 46.51 3.18
3874 5194 8.131847 TCCATTTCACATGGATTTTATTGTCA 57.868 30.769 0.00 0.00 42.81 3.58
3875 5195 8.034215 TCCATTTCACATGGATTTTATTGTCAC 58.966 33.333 0.00 0.00 42.81 3.67
3876 5196 7.278424 CCATTTCACATGGATTTTATTGTCACC 59.722 37.037 0.00 0.00 41.64 4.02
3877 5197 5.559427 TCACATGGATTTTATTGTCACCG 57.441 39.130 0.00 0.00 0.00 4.94
3878 5198 5.249420 TCACATGGATTTTATTGTCACCGA 58.751 37.500 0.00 0.00 0.00 4.69
3879 5199 5.885352 TCACATGGATTTTATTGTCACCGAT 59.115 36.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.173965 CTCCTCCACCACTTTTCTAGGA 58.826 50.000 0.00 0.00 0.00 2.94
285 321 0.904865 TGGAGACCCGAGAGCAACAT 60.905 55.000 0.00 0.00 34.29 2.71
344 398 3.285371 GGACGATCCGGACACAGT 58.715 61.111 6.12 4.18 0.00 3.55
389 443 1.988107 AGAAATCAGCCAAGTCCCAGA 59.012 47.619 0.00 0.00 0.00 3.86
532 598 5.940470 GGTGACATCACTCCTCTTACAATTT 59.060 40.000 11.63 0.00 45.73 1.82
539 605 2.894731 TGAGGTGACATCACTCCTCTT 58.105 47.619 15.75 0.00 45.30 2.85
594 672 0.824595 TCTCTCGTCGTCCCACCAAA 60.825 55.000 0.00 0.00 0.00 3.28
607 686 6.073167 CCAAGATCATTTTCATGGATCTCTCG 60.073 42.308 10.63 4.79 36.76 4.04
613 692 5.011738 GCATCCCAAGATCATTTTCATGGAT 59.988 40.000 0.00 0.00 36.76 3.41
620 699 4.644103 CGAAGCATCCCAAGATCATTTT 57.356 40.909 0.00 0.00 0.00 1.82
639 718 2.125552 CGGCTGGAACTGATGCGA 60.126 61.111 0.00 0.00 0.00 5.10
656 735 2.781158 GGAGTCTCTCGCTCCTGGC 61.781 68.421 0.00 0.00 46.71 4.85
657 736 3.520402 GGAGTCTCTCGCTCCTGG 58.480 66.667 0.00 0.00 46.71 4.45
660 739 1.595466 TAATCGGAGTCTCTCGCTCC 58.405 55.000 0.00 1.50 46.75 4.70
661 740 4.247258 TCTATAATCGGAGTCTCTCGCTC 58.753 47.826 0.00 0.00 0.00 5.03
662 741 4.274602 TCTATAATCGGAGTCTCTCGCT 57.725 45.455 0.00 0.00 0.00 4.93
663 742 4.729458 GCATCTATAATCGGAGTCTCTCGC 60.729 50.000 0.00 0.00 0.00 5.03
664 743 4.634004 AGCATCTATAATCGGAGTCTCTCG 59.366 45.833 0.00 2.29 0.00 4.04
665 744 5.414454 ACAGCATCTATAATCGGAGTCTCTC 59.586 44.000 0.00 0.00 0.00 3.20
666 745 5.321102 ACAGCATCTATAATCGGAGTCTCT 58.679 41.667 0.00 0.00 0.00 3.10
667 746 5.637006 ACAGCATCTATAATCGGAGTCTC 57.363 43.478 0.00 0.00 0.00 3.36
668 747 6.071840 GGTAACAGCATCTATAATCGGAGTCT 60.072 42.308 0.00 0.00 0.00 3.24
688 767 4.558697 GCACAAGGGAAGAATGTTGGTAAC 60.559 45.833 0.00 0.00 0.00 2.50
722 801 8.060679 CGAATACAATACCCGTATCTATCTACG 58.939 40.741 0.00 0.00 43.13 3.51
736 815 6.938030 TGGAATGGAATACCGAATACAATACC 59.062 38.462 0.00 0.00 39.42 2.73
785 864 3.537206 AAAGCACGCTCCCTCGCTT 62.537 57.895 0.00 0.00 46.26 4.68
819 898 2.478033 GGTATGGGCGGAAAAGGCG 61.478 63.158 0.00 0.00 37.59 5.52
835 914 1.379309 GGAGGCACGAGAGAGAGGT 60.379 63.158 0.00 0.00 0.00 3.85
867 948 2.081787 TGGTGATGGTGGTGGTGGT 61.082 57.895 0.00 0.00 0.00 4.16
868 949 1.603455 GTGGTGATGGTGGTGGTGG 60.603 63.158 0.00 0.00 0.00 4.61
870 951 1.360393 AAGGTGGTGATGGTGGTGGT 61.360 55.000 0.00 0.00 0.00 4.16
871 952 0.178964 AAAGGTGGTGATGGTGGTGG 60.179 55.000 0.00 0.00 0.00 4.61
873 954 1.480498 GGAAAAGGTGGTGATGGTGGT 60.480 52.381 0.00 0.00 0.00 4.16
962 1051 1.532868 CCGCAACCAGACAAGAAAGAG 59.467 52.381 0.00 0.00 0.00 2.85
1005 1098 1.258445 GGAGGAAGAGGAGGCGAACA 61.258 60.000 0.00 0.00 0.00 3.18
1031 1124 4.168291 GGAGGGAGCAAGCGAGGG 62.168 72.222 0.00 0.00 0.00 4.30
1176 1270 4.025145 GGAATCTAAAAATGTCCGCGGTAG 60.025 45.833 27.15 17.16 0.00 3.18
1179 1273 2.286184 CGGAATCTAAAAATGTCCGCGG 60.286 50.000 22.12 22.12 44.13 6.46
1233 1327 5.180367 TCAAGAAAATGAAATCGTGTGCA 57.820 34.783 0.00 0.00 0.00 4.57
1246 1340 7.946776 CCTTCCCATATATCACCTCAAGAAAAT 59.053 37.037 0.00 0.00 0.00 1.82
1273 1367 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
1274 1368 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
1276 1370 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
1277 1371 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
1278 1372 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
1279 1373 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
1280 1374 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
1281 1375 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
1282 1376 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
1283 1377 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
1284 1378 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
1285 1379 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
1286 1380 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
1287 1381 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
1288 1382 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
1289 1383 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
1290 1384 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
1291 1385 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
1303 1397 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
1306 1400 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
1307 1401 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
1308 1402 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
1309 1403 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
1315 1409 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
1316 1410 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
1317 1411 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
1318 1412 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
1319 1413 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
1331 1425 4.457949 CCGTCCCATATATAAAAGGGCAAC 59.542 45.833 11.55 6.68 41.22 4.17
1332 1426 4.351407 TCCGTCCCATATATAAAAGGGCAA 59.649 41.667 11.55 0.00 41.22 4.52
1333 1427 3.911260 TCCGTCCCATATATAAAAGGGCA 59.089 43.478 11.55 1.92 41.22 5.36
1334 1428 4.259356 GTCCGTCCCATATATAAAAGGGC 58.741 47.826 11.55 2.99 41.22 5.19
1335 1429 4.221262 TCGTCCGTCCCATATATAAAAGGG 59.779 45.833 10.55 10.55 42.86 3.95
1336 1430 5.395682 TCGTCCGTCCCATATATAAAAGG 57.604 43.478 0.00 0.00 0.00 3.11
1337 1431 5.344128 CGTTCGTCCGTCCCATATATAAAAG 59.656 44.000 0.00 0.00 0.00 2.27
1338 1432 5.221880 CGTTCGTCCGTCCCATATATAAAA 58.778 41.667 0.00 0.00 0.00 1.52
1339 1433 4.321156 CCGTTCGTCCGTCCCATATATAAA 60.321 45.833 0.00 0.00 0.00 1.40
1340 1434 3.191162 CCGTTCGTCCGTCCCATATATAA 59.809 47.826 0.00 0.00 0.00 0.98
1341 1435 2.749076 CCGTTCGTCCGTCCCATATATA 59.251 50.000 0.00 0.00 0.00 0.86
1342 1436 1.542915 CCGTTCGTCCGTCCCATATAT 59.457 52.381 0.00 0.00 0.00 0.86
1343 1437 0.953727 CCGTTCGTCCGTCCCATATA 59.046 55.000 0.00 0.00 0.00 0.86
1344 1438 1.039233 ACCGTTCGTCCGTCCCATAT 61.039 55.000 0.00 0.00 0.00 1.78
1345 1439 1.250154 AACCGTTCGTCCGTCCCATA 61.250 55.000 0.00 0.00 0.00 2.74
1346 1440 1.250154 TAACCGTTCGTCCGTCCCAT 61.250 55.000 0.00 0.00 0.00 4.00
1347 1441 1.459455 TTAACCGTTCGTCCGTCCCA 61.459 55.000 0.00 0.00 0.00 4.37
1348 1442 0.108662 ATTAACCGTTCGTCCGTCCC 60.109 55.000 0.00 0.00 0.00 4.46
1349 1443 1.655597 GAATTAACCGTTCGTCCGTCC 59.344 52.381 0.00 0.00 0.00 4.79
1362 1456 5.936372 AGGGGACGTTAAGTTCAGAATTAAC 59.064 40.000 13.16 13.16 38.13 2.01
1389 1483 5.091261 AGAGTGGGATTTGTGTACAGATC 57.909 43.478 0.00 6.92 36.91 2.75
1421 2727 8.244802 AGTAAGTAGTATTGTGTTACTGCAGAG 58.755 37.037 23.35 0.00 37.30 3.35
1422 2728 8.118976 AGTAAGTAGTATTGTGTTACTGCAGA 57.881 34.615 23.35 0.48 37.30 4.26
1423 2729 8.758633 AAGTAAGTAGTATTGTGTTACTGCAG 57.241 34.615 13.48 13.48 37.30 4.41
1424 2730 8.361889 TGAAGTAAGTAGTATTGTGTTACTGCA 58.638 33.333 0.00 0.00 37.06 4.41
1425 2731 8.752766 TGAAGTAAGTAGTATTGTGTTACTGC 57.247 34.615 0.00 0.00 34.83 4.40
1426 2732 8.861101 GCTGAAGTAAGTAGTATTGTGTTACTG 58.139 37.037 0.00 0.00 34.83 2.74
1427 2733 8.582437 TGCTGAAGTAAGTAGTATTGTGTTACT 58.418 33.333 0.00 0.00 35.85 2.24
1527 2841 8.797674 TCCCATCCCAGTATATGTATCTATACA 58.202 37.037 5.33 5.33 46.21 2.29
1557 2877 1.259840 AAGGAATGGGCCACACATGC 61.260 55.000 9.28 0.43 0.00 4.06
1646 2966 3.057033 CCAAGAGGGCTGTGAAATGAAAG 60.057 47.826 0.00 0.00 0.00 2.62
1699 3019 6.511416 AGAGCACATGCATAGAACTAAGTAG 58.489 40.000 6.64 0.00 45.16 2.57
1715 3035 6.413052 AGTTTCATGTTCTGATAGAGCACAT 58.587 36.000 0.00 0.00 38.26 3.21
1829 3149 2.826702 GTGGTCGGGTTGGTCACT 59.173 61.111 0.00 0.00 0.00 3.41
1875 3195 1.879380 CACGGTGATGATTGTTGGTGT 59.121 47.619 0.74 0.00 0.00 4.16
2015 3335 0.238289 GAATGGTGACTGGCGTGTTG 59.762 55.000 0.00 0.00 0.00 3.33
2130 3450 0.697079 ACTGGAGTAGTGGTCGGAGA 59.303 55.000 0.00 0.00 38.49 3.71
2159 3479 1.077140 TTGCTGCCCTGACACAACA 60.077 52.632 0.00 0.00 0.00 3.33
2208 3528 3.423154 GTCCTGGAGCGCGGTTTG 61.423 66.667 14.00 5.69 0.00 2.93
2270 3590 1.142465 CAGCTCCCTGATGGCTGTATT 59.858 52.381 6.07 0.00 45.59 1.89
2479 3799 2.169352 GAGCCTGCAAAGAGGAGATGTA 59.831 50.000 0.00 0.00 38.04 2.29
2503 3823 3.695556 TGATGATGCCAATACACAGGTTG 59.304 43.478 0.00 0.00 0.00 3.77
2568 3888 7.360946 GCTTTAAACACGAGAGTTCCATGTTAT 60.361 37.037 0.00 0.00 46.40 1.89
2592 3912 4.592942 AGTTCACCATACACATCATTGCT 58.407 39.130 0.00 0.00 0.00 3.91
2750 4070 0.685660 GGAAGTCCGACCCAAAGTCT 59.314 55.000 0.00 0.00 43.91 3.24
3350 4670 4.139786 GCACAGATACATCCATTGACCAT 58.860 43.478 0.00 0.00 0.00 3.55
3351 4671 3.544684 GCACAGATACATCCATTGACCA 58.455 45.455 0.00 0.00 0.00 4.02
3352 4672 2.880890 GGCACAGATACATCCATTGACC 59.119 50.000 0.00 0.00 0.00 4.02
3353 4673 2.880890 GGGCACAGATACATCCATTGAC 59.119 50.000 0.00 0.00 0.00 3.18
3354 4674 2.779430 AGGGCACAGATACATCCATTGA 59.221 45.455 0.00 0.00 0.00 2.57
3355 4675 2.882761 CAGGGCACAGATACATCCATTG 59.117 50.000 0.00 0.00 0.00 2.82
3356 4676 2.779430 TCAGGGCACAGATACATCCATT 59.221 45.455 0.00 0.00 0.00 3.16
3357 4677 2.105477 GTCAGGGCACAGATACATCCAT 59.895 50.000 0.00 0.00 0.00 3.41
3523 4843 2.562298 GAGGACCAACAATTGAATGCCA 59.438 45.455 13.59 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.