Multiple sequence alignment - TraesCS2B01G262600

Loading Multiple Alignment...

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 TraesCS2B01G262600 chr2B 100.000 3285 0 0 1 3285 346672010 346668726 0.000000e+00 6067.0
1 TraesCS2B01G262600 chr2B 83.736 787 92 20 2508 3285 4582630 4581871 0.000000e+00 712.0
2 TraesCS2B01G262600 chr2D 90.338 1925 111 33 633 2501 222646421 222648326 0.000000e+00 2455.0
3 TraesCS2B01G262600 chr2D 84.533 750 83 18 2543 3285 7952780 7953503 0.000000e+00 712.0
4 TraesCS2B01G262600 chr2A 88.550 1214 85 28 1327 2501 240759403 240760601 0.000000e+00 1423.0
5 TraesCS2B01G262600 chr2A 91.502 812 40 14 633 1419 240758595 240759402 0.000000e+00 1090.0
6 TraesCS2B01G262600 chr1B 92.710 631 42 3 1 628 49873637 49873008 0.000000e+00 907.0
7 TraesCS2B01G262600 chr1B 91.905 630 40 2 1 628 642096549 642095929 0.000000e+00 870.0
8 TraesCS2B01G262600 chr1B 93.264 193 13 0 826 1018 657319379 657319571 5.360000e-73 285.0
9 TraesCS2B01G262600 chr6B 92.540 630 38 4 1 628 591139435 591138813 0.000000e+00 894.0
10 TraesCS2B01G262600 chr6B 91.772 632 48 3 1 628 580967247 580966616 0.000000e+00 876.0
11 TraesCS2B01G262600 chr6B 91.534 626 37 7 1 623 32472439 32471827 0.000000e+00 848.0
12 TraesCS2B01G262600 chr6B 91.228 627 44 7 1 625 457426749 457427366 0.000000e+00 843.0
13 TraesCS2B01G262600 chr6B 87.861 346 21 6 2942 3285 615293234 615293560 1.430000e-103 387.0
14 TraesCS2B01G262600 chr4B 92.089 632 46 3 1 628 660340127 660339496 0.000000e+00 887.0
15 TraesCS2B01G262600 chr3A 92.344 627 37 2 1 625 677742817 677743434 0.000000e+00 881.0
16 TraesCS2B01G262600 chr5A 92.076 631 37 4 1 628 502609558 502608938 0.000000e+00 876.0
17 TraesCS2B01G262600 chr5A 88.656 573 56 6 1723 2288 334745287 334744717 0.000000e+00 689.0
18 TraesCS2B01G262600 chr5A 83.477 581 63 22 829 1392 334746326 334745762 8.130000e-141 510.0
19 TraesCS2B01G262600 chr5A 86.880 343 27 4 2942 3283 588850955 588851280 5.180000e-98 368.0
20 TraesCS2B01G262600 chr5D 89.492 571 53 7 1723 2288 251955375 251954807 0.000000e+00 715.0
21 TraesCS2B01G262600 chr5D 83.861 632 65 21 783 1392 251956387 251955771 4.760000e-158 568.0
22 TraesCS2B01G262600 chr5B 89.539 564 55 4 1727 2288 284000785 284000224 0.000000e+00 712.0
23 TraesCS2B01G262600 chr5B 87.856 527 40 15 782 1294 284001941 284001425 6.070000e-167 597.0
24 TraesCS2B01G262600 chr5B 85.321 109 8 4 1723 1830 407960659 407960558 4.480000e-19 106.0
25 TraesCS2B01G262600 chr5B 89.583 48 5 0 2518 2565 507540552 507540505 9.840000e-06 62.1
26 TraesCS2B01G262600 chr4D 88.010 392 42 3 1 388 360460625 360461015 2.990000e-125 459.0
27 TraesCS2B01G262600 chr4D 79.736 454 74 13 1823 2271 253867181 253866741 2.460000e-81 313.0
28 TraesCS2B01G262600 chr6A 87.121 132 15 2 2509 2638 256470708 256470839 7.340000e-32 148.0
29 TraesCS2B01G262600 chr4A 92.857 70 5 0 2509 2578 665729164 665729095 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 TraesCS2B01G262600 chr2B 346668726 346672010 3284 True 6067.0 6067 100.0000 1 3285 1 chr2B.!!$R2 3284
1 TraesCS2B01G262600 chr2B 4581871 4582630 759 True 712.0 712 83.7360 2508 3285 1 chr2B.!!$R1 777
2 TraesCS2B01G262600 chr2D 222646421 222648326 1905 False 2455.0 2455 90.3380 633 2501 1 chr2D.!!$F2 1868
3 TraesCS2B01G262600 chr2D 7952780 7953503 723 False 712.0 712 84.5330 2543 3285 1 chr2D.!!$F1 742
4 TraesCS2B01G262600 chr2A 240758595 240760601 2006 False 1256.5 1423 90.0260 633 2501 2 chr2A.!!$F1 1868
5 TraesCS2B01G262600 chr1B 49873008 49873637 629 True 907.0 907 92.7100 1 628 1 chr1B.!!$R1 627
6 TraesCS2B01G262600 chr1B 642095929 642096549 620 True 870.0 870 91.9050 1 628 1 chr1B.!!$R2 627
7 TraesCS2B01G262600 chr6B 591138813 591139435 622 True 894.0 894 92.5400 1 628 1 chr6B.!!$R3 627
8 TraesCS2B01G262600 chr6B 580966616 580967247 631 True 876.0 876 91.7720 1 628 1 chr6B.!!$R2 627
9 TraesCS2B01G262600 chr6B 32471827 32472439 612 True 848.0 848 91.5340 1 623 1 chr6B.!!$R1 622
10 TraesCS2B01G262600 chr6B 457426749 457427366 617 False 843.0 843 91.2280 1 625 1 chr6B.!!$F1 624
11 TraesCS2B01G262600 chr4B 660339496 660340127 631 True 887.0 887 92.0890 1 628 1 chr4B.!!$R1 627
12 TraesCS2B01G262600 chr3A 677742817 677743434 617 False 881.0 881 92.3440 1 625 1 chr3A.!!$F1 624
13 TraesCS2B01G262600 chr5A 502608938 502609558 620 True 876.0 876 92.0760 1 628 1 chr5A.!!$R1 627
14 TraesCS2B01G262600 chr5A 334744717 334746326 1609 True 599.5 689 86.0665 829 2288 2 chr5A.!!$R2 1459
15 TraesCS2B01G262600 chr5D 251954807 251956387 1580 True 641.5 715 86.6765 783 2288 2 chr5D.!!$R1 1505
16 TraesCS2B01G262600 chr5B 284000224 284001941 1717 True 654.5 712 88.6975 782 2288 2 chr5B.!!$R3 1506

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
690 702 0.534203 GAAAGCACACTCGAACCCCA 60.534 55.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2330 2707 0.370273 GGCGCAAACAGATACTGTCG 59.63 55.0 10.83 6.09 44.62 4.35 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
94 97 4.947147 GTGCGGGCCCACAAGACA 62.947 66.667 24.92 6.55 35.80 3.41
105 108 2.224621 CCCACAAGACACCATTCTGAGT 60.225 50.000 0.00 0.00 0.00 3.41
262 268 4.257731 TGTGTGCTCTTGTACTTGTTTCA 58.742 39.130 0.00 0.00 0.00 2.69
284 290 2.954611 GAGCCGGTGCACCTTTTC 59.045 61.111 32.28 21.41 41.13 2.29
453 463 4.684214 GCTCCACTCACATCCATTGACATA 60.684 45.833 0.00 0.00 0.00 2.29
507 519 2.882927 GTGCATACACCCAGATACGA 57.117 50.000 0.00 0.00 41.21 3.43
525 537 2.168936 ACGAATGGAGGCACCGTATTTA 59.831 45.455 0.00 0.00 42.61 1.40
532 544 4.156922 TGGAGGCACCGTATTTAAACAATG 59.843 41.667 0.00 0.00 42.61 2.82
536 548 5.420739 AGGCACCGTATTTAAACAATGGAAT 59.579 36.000 14.65 0.00 0.00 3.01
587 599 7.759489 TTACAAGTTTAGGCATCAAAGTGAT 57.241 32.000 0.00 0.00 37.65 3.06
597 609 2.509336 AAAGTGATCGCGCCGGAG 60.509 61.111 5.05 1.55 0.00 4.63
625 637 5.416083 TGAGACATCCGTGGTGTATTTAAG 58.584 41.667 0.00 0.00 0.00 1.85
628 640 5.046878 AGACATCCGTGGTGTATTTAAGTCA 60.047 40.000 0.00 0.00 0.00 3.41
629 641 5.175859 ACATCCGTGGTGTATTTAAGTCAG 58.824 41.667 0.00 0.00 0.00 3.51
630 642 4.877378 TCCGTGGTGTATTTAAGTCAGT 57.123 40.909 0.00 0.00 0.00 3.41
631 643 5.981088 TCCGTGGTGTATTTAAGTCAGTA 57.019 39.130 0.00 0.00 0.00 2.74
682 694 0.895100 TGGCCCATGAAAGCACACTC 60.895 55.000 0.00 0.00 0.00 3.51
684 696 0.955428 GCCCATGAAAGCACACTCGA 60.955 55.000 0.00 0.00 0.00 4.04
690 702 0.534203 GAAAGCACACTCGAACCCCA 60.534 55.000 0.00 0.00 0.00 4.96
750 762 4.147449 CACGCGCCCATCTCCTCA 62.147 66.667 5.73 0.00 0.00 3.86
780 792 2.511452 CCCTCCCCGCATCTTCGAT 61.511 63.158 0.00 0.00 0.00 3.59
793 805 4.537965 CATCTTCGATACCCTAAGTCACG 58.462 47.826 0.00 0.00 0.00 4.35
895 915 3.074369 TCCCGCAATCTCGCCTGA 61.074 61.111 0.00 0.00 0.00 3.86
1038 1058 1.292223 GCGTTGCTGGGAGTACAGA 59.708 57.895 0.00 0.00 40.97 3.41
1135 1160 4.896482 AGCAGGTTTATCTCTTAGATCCGT 59.104 41.667 0.00 0.00 36.20 4.69
1142 1167 3.955524 TCTCTTAGATCCGTTCCTCCT 57.044 47.619 0.00 0.00 0.00 3.69
1143 1168 4.252570 TCTCTTAGATCCGTTCCTCCTT 57.747 45.455 0.00 0.00 0.00 3.36
1144 1169 4.611367 TCTCTTAGATCCGTTCCTCCTTT 58.389 43.478 0.00 0.00 0.00 3.11
1157 1182 5.106277 CGTTCCTCCTTTTTATGTTCCTTCC 60.106 44.000 0.00 0.00 0.00 3.46
1254 1295 0.375454 TGTTCGTTGTGCGTGGAAAG 59.625 50.000 0.00 0.00 42.13 2.62
1262 1304 3.455990 TGTGCGTGGAAAGTGTACTTA 57.544 42.857 0.00 0.00 34.61 2.24
1294 1336 5.858581 TCGTCGAAGCTAGGTTTAGTTTTAC 59.141 40.000 8.87 0.79 31.43 2.01
1296 1338 6.183359 CGTCGAAGCTAGGTTTAGTTTTACTG 60.183 42.308 8.87 0.00 31.43 2.74
1297 1339 6.865205 GTCGAAGCTAGGTTTAGTTTTACTGA 59.135 38.462 8.87 0.00 31.43 3.41
1298 1340 7.544915 GTCGAAGCTAGGTTTAGTTTTACTGAT 59.455 37.037 8.87 0.00 31.43 2.90
1299 1341 7.758528 TCGAAGCTAGGTTTAGTTTTACTGATC 59.241 37.037 8.87 0.00 31.43 2.92
1302 1346 8.549338 AGCTAGGTTTAGTTTTACTGATCAAC 57.451 34.615 0.00 0.00 0.00 3.18
1312 1356 8.451908 AGTTTTACTGATCAACTTATATGCCC 57.548 34.615 0.00 0.00 0.00 5.36
1355 1446 2.996621 CAGTTTGTCCTGAACGGATCTC 59.003 50.000 0.00 0.00 45.44 2.75
1419 1568 8.484799 GTTTTAACAGCTTTAGTTAATTGCACC 58.515 33.333 8.26 0.00 40.11 5.01
1461 1708 5.957842 TTGGACCATGTCATTCAGTTTAC 57.042 39.130 0.00 0.00 33.68 2.01
1476 1723 6.920569 TCAGTTTACTGTTCCTGAAACTTC 57.079 37.500 9.53 0.00 44.12 3.01
1535 1843 6.697455 CACTGAAGTATGTTCACATATACGCT 59.303 38.462 3.00 0.00 40.53 5.07
1547 1855 5.872617 TCACATATACGCTGTAAGTTGCTTT 59.127 36.000 0.00 0.00 35.30 3.51
1568 1876 8.828644 TGCTTTTGTTTATACTAACTCGTGAAA 58.171 29.630 0.00 0.00 0.00 2.69
1611 1947 8.686334 AGTACCATTTAGTTAAATTGCTCCATG 58.314 33.333 0.00 0.00 33.88 3.66
1612 1948 7.480760 ACCATTTAGTTAAATTGCTCCATGT 57.519 32.000 0.00 0.00 33.88 3.21
1615 1951 9.868277 CCATTTAGTTAAATTGCTCCATGTTTA 57.132 29.630 0.00 0.00 33.88 2.01
1627 1963 4.702131 GCTCCATGTTTATGTTTCCTCTGT 59.298 41.667 0.00 0.00 32.21 3.41
1630 1966 6.303054 TCCATGTTTATGTTTCCTCTGTGAA 58.697 36.000 0.00 0.00 32.21 3.18
1650 1986 8.279970 TGTGAATTTAGTCCAATAACTGATGG 57.720 34.615 0.00 0.00 38.09 3.51
1668 2011 6.876257 ACTGATGGTTGTCTCTGTAATTCTTC 59.124 38.462 0.00 0.00 0.00 2.87
1674 2017 6.128418 GGTTGTCTCTGTAATTCTTCTTGCTC 60.128 42.308 0.00 0.00 0.00 4.26
1676 2019 6.763355 TGTCTCTGTAATTCTTCTTGCTCTT 58.237 36.000 0.00 0.00 0.00 2.85
1679 2047 9.377312 GTCTCTGTAATTCTTCTTGCTCTTATT 57.623 33.333 0.00 0.00 0.00 1.40
1690 2058 8.105829 TCTTCTTGCTCTTATTCTTTCTCCATT 58.894 33.333 0.00 0.00 0.00 3.16
1713 2082 9.540431 CATTTTATAATTGCTTTTGTTTTCCCG 57.460 29.630 0.00 0.00 0.00 5.14
1878 2249 0.868406 GGAACAAGAGGTCTGTTGCG 59.132 55.000 7.63 0.00 37.36 4.85
1917 2288 1.302192 GCTTGGTGGCCTTCGTGTA 60.302 57.895 3.32 0.00 0.00 2.90
1947 2318 5.784023 TCCTACTGGGTGAATGAGGTATAA 58.216 41.667 0.00 0.00 36.25 0.98
1954 2325 5.890985 TGGGTGAATGAGGTATAACATTTGG 59.109 40.000 0.00 0.00 36.94 3.28
1958 2330 7.415206 GGTGAATGAGGTATAACATTTGGTCAC 60.415 40.741 0.00 0.00 36.94 3.67
2263 2640 0.037232 GGAAGAGGAACCAGACCGTG 60.037 60.000 0.00 0.00 0.00 4.94
2289 2666 1.713830 GCCGCTACCGTTAAGCTTG 59.286 57.895 9.86 0.00 37.85 4.01
2294 2671 2.140717 GCTACCGTTAAGCTTGTGTGT 58.859 47.619 9.86 4.07 37.01 3.72
2305 2682 4.568152 AGCTTGTGTGTTGTTATGTTCC 57.432 40.909 0.00 0.00 0.00 3.62
2330 2707 2.089600 ACCTGTCCTATGCCTACCTC 57.910 55.000 0.00 0.00 0.00 3.85
2347 2724 1.920574 CCTCGACAGTATCTGTTTGCG 59.079 52.381 3.91 3.99 45.44 4.85
2378 2755 1.334160 TGCTACCTTCGTTCTGTGGA 58.666 50.000 0.00 0.00 0.00 4.02
2385 2762 2.289694 CCTTCGTTCTGTGGATGAACCT 60.290 50.000 0.00 0.00 40.26 3.50
2386 2763 3.403038 CTTCGTTCTGTGGATGAACCTT 58.597 45.455 0.00 0.00 40.26 3.50
2387 2764 3.485463 TCGTTCTGTGGATGAACCTTT 57.515 42.857 0.00 0.00 40.26 3.11
2388 2765 3.815809 TCGTTCTGTGGATGAACCTTTT 58.184 40.909 0.00 0.00 40.26 2.27
2389 2766 4.963373 TCGTTCTGTGGATGAACCTTTTA 58.037 39.130 0.00 0.00 40.26 1.52
2390 2767 5.556915 TCGTTCTGTGGATGAACCTTTTAT 58.443 37.500 0.00 0.00 40.26 1.40
2391 2768 5.411361 TCGTTCTGTGGATGAACCTTTTATG 59.589 40.000 0.00 0.00 40.26 1.90
2421 2798 6.024049 GCATGTCTGTTGAACTATTTGCTAC 58.976 40.000 0.00 0.00 0.00 3.58
2442 2819 2.159627 CGTGCCTGTGTTACCTGAAATC 59.840 50.000 0.00 0.00 0.00 2.17
2444 2821 2.107378 TGCCTGTGTTACCTGAAATCCA 59.893 45.455 0.00 0.00 0.00 3.41
2473 2851 9.665719 TGATTTTAGTAATCTTGATGTGTGCTA 57.334 29.630 0.00 0.00 0.00 3.49
2476 2854 8.437360 TTTAGTAATCTTGATGTGTGCTATGG 57.563 34.615 0.00 0.00 0.00 2.74
2477 2855 5.994250 AGTAATCTTGATGTGTGCTATGGT 58.006 37.500 0.00 0.00 0.00 3.55
2478 2856 5.819379 AGTAATCTTGATGTGTGCTATGGTG 59.181 40.000 0.00 0.00 0.00 4.17
2501 2881 7.855409 GGTGGTTTTAATGCTTTGATGTTTTTC 59.145 33.333 0.00 0.00 0.00 2.29
2502 2882 8.611757 GTGGTTTTAATGCTTTGATGTTTTTCT 58.388 29.630 0.00 0.00 0.00 2.52
2503 2883 9.171877 TGGTTTTAATGCTTTGATGTTTTTCTT 57.828 25.926 0.00 0.00 0.00 2.52
2504 2884 9.437045 GGTTTTAATGCTTTGATGTTTTTCTTG 57.563 29.630 0.00 0.00 0.00 3.02
2505 2885 8.946935 GTTTTAATGCTTTGATGTTTTTCTTGC 58.053 29.630 0.00 0.00 0.00 4.01
2506 2886 8.436046 TTTAATGCTTTGATGTTTTTCTTGCT 57.564 26.923 0.00 0.00 0.00 3.91
2575 2955 2.189521 CCCAGCCACCCGATACAC 59.810 66.667 0.00 0.00 0.00 2.90
2585 2965 1.002468 ACCCGATACACGCACGTATAC 60.002 52.381 0.00 0.00 41.07 1.47
2587 2967 1.664016 CCGATACACGCACGTATACCC 60.664 57.143 0.00 0.00 41.07 3.69
2610 2990 0.104120 CGATTGGACCCAGCGTCATA 59.896 55.000 0.00 0.00 43.95 2.15
2617 2997 2.484889 GACCCAGCGTCATATTCTTCC 58.515 52.381 0.00 0.00 41.54 3.46
2674 3056 1.663643 GTCGCCGTGAGATGCAATTTA 59.336 47.619 0.00 0.00 0.00 1.40
2699 3084 4.824515 CCCTCGTCGCCTCCTCCT 62.825 72.222 0.00 0.00 0.00 3.69
2700 3085 2.192443 CCTCGTCGCCTCCTCCTA 59.808 66.667 0.00 0.00 0.00 2.94
2702 3087 2.124403 TCGTCGCCTCCTCCTACC 60.124 66.667 0.00 0.00 0.00 3.18
2703 3088 3.217743 CGTCGCCTCCTCCTACCC 61.218 72.222 0.00 0.00 0.00 3.69
2705 3090 4.153330 TCGCCTCCTCCTACCCCC 62.153 72.222 0.00 0.00 0.00 5.40
2727 3112 0.327259 TGATCTCCTGCTTGCAGCTT 59.673 50.000 16.37 1.53 42.97 3.74
2729 3114 0.619505 ATCTCCTGCTTGCAGCTTCT 59.380 50.000 16.37 0.00 42.97 2.85
2736 3121 1.670406 CTTGCAGCTTCTCGTGCCT 60.670 57.895 0.00 0.00 39.04 4.75
2738 3123 3.797546 GCAGCTTCTCGTGCCTGC 61.798 66.667 8.19 8.19 33.29 4.85
2741 3126 2.359230 GCTTCTCGTGCCTGCCTT 60.359 61.111 0.00 0.00 0.00 4.35
2750 3135 3.064324 GCCTGCCTTGCCGTCATT 61.064 61.111 0.00 0.00 0.00 2.57
2755 3140 2.032634 GCCTTGCCGTCATTGTCGA 61.033 57.895 4.86 0.00 0.00 4.20
2789 3174 0.869454 GCTCGTCGGCTCAGAGATTG 60.869 60.000 0.00 0.00 34.13 2.67
2831 3216 2.555199 GTTCTACCACCTATGCAGCAG 58.445 52.381 0.00 0.00 0.00 4.24
2838 3223 0.321671 ACCTATGCAGCAGAACGTGT 59.678 50.000 0.00 0.00 0.00 4.49
2862 3247 3.084039 CTGGTTCCAGCAAATTAGCTCA 58.916 45.455 5.89 0.00 44.54 4.26
2868 3253 5.887214 TCCAGCAAATTAGCTCATAGGTA 57.113 39.130 0.00 0.00 44.54 3.08
2953 3340 4.240103 CATCTCGCCATGGCCGGA 62.240 66.667 30.79 26.29 37.98 5.14
3030 3418 2.202743 CATCATGTCGCCGTCGGT 60.203 61.111 13.94 0.00 36.13 4.69
3037 3428 4.141965 TCGCCGTCGGTGCATCAT 62.142 61.111 20.16 0.00 36.13 2.45
3063 3454 3.181534 CGTGAACGGTTGTAGCATTAGTG 60.182 47.826 0.00 0.00 35.37 2.74
3074 3465 2.006772 CATTAGTGGGCGACGCTTC 58.993 57.895 20.77 12.81 41.07 3.86
3075 3466 1.153429 ATTAGTGGGCGACGCTTCC 60.153 57.895 20.77 13.92 41.07 3.46
3095 3486 2.610694 CGGTTGCAGCTCCAGTGTG 61.611 63.158 0.00 0.00 0.00 3.82
3111 3502 0.034756 TGTGCGTGGTTGTAGCATCT 59.965 50.000 0.00 0.00 43.17 2.90
3112 3503 0.721718 GTGCGTGGTTGTAGCATCTC 59.278 55.000 0.00 0.00 43.17 2.75
3113 3504 0.391130 TGCGTGGTTGTAGCATCTCC 60.391 55.000 0.00 0.00 35.81 3.71
3114 3505 1.421410 GCGTGGTTGTAGCATCTCCG 61.421 60.000 0.00 0.00 0.00 4.63
3115 3506 0.108804 CGTGGTTGTAGCATCTCCGT 60.109 55.000 0.00 0.00 0.00 4.69
3116 3507 1.359848 GTGGTTGTAGCATCTCCGTG 58.640 55.000 0.00 0.00 0.00 4.94
3117 3508 0.249120 TGGTTGTAGCATCTCCGTGG 59.751 55.000 0.00 0.00 0.00 4.94
3118 3509 0.249398 GGTTGTAGCATCTCCGTGGT 59.751 55.000 0.00 0.00 0.00 4.16
3119 3510 1.338769 GGTTGTAGCATCTCCGTGGTT 60.339 52.381 0.00 0.00 0.00 3.67
3120 3511 1.732259 GTTGTAGCATCTCCGTGGTTG 59.268 52.381 0.00 0.00 0.00 3.77
3121 3512 0.973632 TGTAGCATCTCCGTGGTTGT 59.026 50.000 0.00 0.00 0.00 3.32
3122 3513 2.172679 TGTAGCATCTCCGTGGTTGTA 58.827 47.619 0.00 0.00 0.00 2.41
3123 3514 2.165641 TGTAGCATCTCCGTGGTTGTAG 59.834 50.000 0.00 0.00 0.00 2.74
3124 3515 0.108138 AGCATCTCCGTGGTTGTAGC 60.108 55.000 0.00 0.00 0.00 3.58
3125 3516 0.391130 GCATCTCCGTGGTTGTAGCA 60.391 55.000 0.00 0.00 0.00 3.49
3126 3517 1.743772 GCATCTCCGTGGTTGTAGCAT 60.744 52.381 0.00 0.00 0.00 3.79
3127 3518 2.205074 CATCTCCGTGGTTGTAGCATC 58.795 52.381 0.00 0.00 0.00 3.91
3137 3528 0.032130 TTGTAGCATCTCCGCGGATC 59.968 55.000 31.19 17.63 36.85 3.36
3161 3552 1.079612 CAGCTCCTGCGACACATGA 60.080 57.895 0.00 0.00 45.42 3.07
3167 3558 3.461061 CTCCTGCGACACATGATTGTAT 58.539 45.455 0.00 0.00 33.76 2.29
3207 3598 2.125106 GCCTGGCTACAACTCCGG 60.125 66.667 12.43 0.00 0.00 5.14
3242 3633 3.126000 GCAACTCTAGAGAATGTGGTTGC 59.874 47.826 26.57 23.19 46.49 4.17
3246 3637 2.302733 TCTAGAGAATGTGGTTGCAGCA 59.697 45.455 2.05 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 97 3.588842 TGAATCCAGGAACTCAGAATGGT 59.411 43.478 0.00 0.00 34.60 3.55
105 108 1.613255 GCCGGAAGTTGAATCCAGGAA 60.613 52.381 5.05 0.00 36.74 3.36
191 196 5.934625 GTGGTATGAGCAGTATGGAAATAGG 59.065 44.000 0.00 0.00 35.86 2.57
249 254 4.319190 CGGCTCGATTTGAAACAAGTACAA 60.319 41.667 0.00 0.00 0.00 2.41
250 256 3.185594 CGGCTCGATTTGAAACAAGTACA 59.814 43.478 0.00 0.00 0.00 2.90
262 268 2.746277 GGTGCACCGGCTCGATTT 60.746 61.111 22.49 0.00 41.91 2.17
363 373 1.192980 GCAAAAGCACCTCGCATTTTG 59.807 47.619 12.93 12.93 46.13 2.44
507 519 4.337145 TGTTTAAATACGGTGCCTCCATT 58.663 39.130 0.00 0.00 35.57 3.16
546 558 9.530633 AAACTTGTAAAATACGCAAAATTGGTA 57.469 25.926 0.00 0.00 0.00 3.25
587 599 3.626680 CTCAACTTCTCCGGCGCGA 62.627 63.158 12.10 0.00 0.00 5.87
597 609 2.069273 CACCACGGATGTCTCAACTTC 58.931 52.381 0.00 0.00 0.00 3.01
625 637 2.269241 GGCACCTGGGCTACTGAC 59.731 66.667 0.00 0.00 39.42 3.51
628 640 3.706373 CGTGGCACCTGGGCTACT 61.706 66.667 12.86 0.00 42.40 2.57
629 641 4.778143 CCGTGGCACCTGGGCTAC 62.778 72.222 12.86 11.71 43.83 3.58
690 702 3.000819 TGGAATGGTCGGCCGTCT 61.001 61.111 27.15 3.22 37.67 4.18
750 762 1.359168 GGGGAGGGCGGTCTTATATT 58.641 55.000 0.00 0.00 0.00 1.28
780 792 2.440409 GGAGTGTCGTGACTTAGGGTA 58.560 52.381 1.23 0.00 0.00 3.69
1135 1160 5.773176 GTGGAAGGAACATAAAAAGGAGGAA 59.227 40.000 0.00 0.00 0.00 3.36
1142 1167 4.082463 GGCATCGTGGAAGGAACATAAAAA 60.082 41.667 0.00 0.00 32.76 1.94
1143 1168 3.442273 GGCATCGTGGAAGGAACATAAAA 59.558 43.478 0.00 0.00 32.76 1.52
1144 1169 3.013921 GGCATCGTGGAAGGAACATAAA 58.986 45.455 0.00 0.00 32.76 1.40
1157 1182 3.214123 CCCAGCCATGGCATCGTG 61.214 66.667 37.18 25.58 46.19 4.35
1186 1211 4.833478 ACCTAAGACAGCACAGAATGAT 57.167 40.909 0.00 0.00 39.69 2.45
1187 1212 5.939764 ATACCTAAGACAGCACAGAATGA 57.060 39.130 0.00 0.00 39.69 2.57
1188 1213 8.580720 ACTATATACCTAAGACAGCACAGAATG 58.419 37.037 0.00 0.00 46.00 2.67
1189 1214 8.713708 ACTATATACCTAAGACAGCACAGAAT 57.286 34.615 0.00 0.00 0.00 2.40
1190 1215 8.534954 AACTATATACCTAAGACAGCACAGAA 57.465 34.615 0.00 0.00 0.00 3.02
1191 1216 8.534954 AAACTATATACCTAAGACAGCACAGA 57.465 34.615 0.00 0.00 0.00 3.41
1192 1217 9.250624 GAAAACTATATACCTAAGACAGCACAG 57.749 37.037 0.00 0.00 0.00 3.66
1193 1218 8.978472 AGAAAACTATATACCTAAGACAGCACA 58.022 33.333 0.00 0.00 0.00 4.57
1254 1295 5.213913 TCGACGAGACAGAATAAGTACAC 57.786 43.478 0.00 0.00 0.00 2.90
1262 1304 2.356382 CCTAGCTTCGACGAGACAGAAT 59.644 50.000 0.00 0.00 0.00 2.40
1294 1336 7.172875 CAGAAGAAGGGCATATAAGTTGATCAG 59.827 40.741 0.00 0.00 0.00 2.90
1296 1338 6.072783 GCAGAAGAAGGGCATATAAGTTGATC 60.073 42.308 0.00 0.00 0.00 2.92
1297 1339 5.767168 GCAGAAGAAGGGCATATAAGTTGAT 59.233 40.000 0.00 0.00 0.00 2.57
1298 1340 5.126067 GCAGAAGAAGGGCATATAAGTTGA 58.874 41.667 0.00 0.00 0.00 3.18
1299 1341 4.883585 TGCAGAAGAAGGGCATATAAGTTG 59.116 41.667 0.00 0.00 31.58 3.16
1302 1346 7.750229 TTATTGCAGAAGAAGGGCATATAAG 57.250 36.000 0.00 0.00 37.39 1.73
1312 1356 5.879237 TGCCGTTTATTATTGCAGAAGAAG 58.121 37.500 0.00 0.00 0.00 2.85
1343 1387 4.389077 GGTTGTAAGTTGAGATCCGTTCAG 59.611 45.833 0.00 0.00 0.00 3.02
1355 1446 4.426416 CATGGCATCATGGTTGTAAGTTG 58.574 43.478 0.00 0.00 45.19 3.16
1407 1556 3.004315 CAGAAACACGGGTGCAATTAACT 59.996 43.478 0.00 0.00 0.00 2.24
1419 1568 5.929992 TCCAAATTACTACTCAGAAACACGG 59.070 40.000 0.00 0.00 0.00 4.94
1461 1708 2.291741 GCCACAGAAGTTTCAGGAACAG 59.708 50.000 0.00 0.00 40.84 3.16
1476 1723 1.812571 GTAAACCATGTCAGGCCACAG 59.187 52.381 5.01 0.00 0.00 3.66
1595 1903 9.423061 GAAACATAAACATGGAGCAATTTAACT 57.577 29.630 0.00 0.00 0.00 2.24
1611 1947 9.827411 GACTAAATTCACAGAGGAAACATAAAC 57.173 33.333 0.00 0.00 0.00 2.01
1612 1948 9.010029 GGACTAAATTCACAGAGGAAACATAAA 57.990 33.333 0.00 0.00 0.00 1.40
1615 1951 6.542821 TGGACTAAATTCACAGAGGAAACAT 58.457 36.000 0.00 0.00 0.00 2.71
1627 1963 8.739039 CAACCATCAGTTATTGGACTAAATTCA 58.261 33.333 0.00 0.00 36.18 2.57
1630 1966 8.109634 AGACAACCATCAGTTATTGGACTAAAT 58.890 33.333 0.00 0.00 36.18 1.40
1650 1986 6.648725 AGAGCAAGAAGAATTACAGAGACAAC 59.351 38.462 0.00 0.00 0.00 3.32
1690 2058 9.413048 CTACGGGAAAACAAAAGCAATTATAAA 57.587 29.630 0.00 0.00 0.00 1.40
1703 2071 2.922740 AGTCAGCTACGGGAAAACAA 57.077 45.000 0.00 0.00 0.00 2.83
1713 2082 6.631962 ACAAGAAACATAGGTAGTCAGCTAC 58.368 40.000 0.00 0.00 45.13 3.58
1878 2249 2.124942 CGCCCAGCTCTTTCCTCC 60.125 66.667 0.00 0.00 0.00 4.30
1908 2279 3.757493 AGTAGGAGTTGAGTACACGAAGG 59.243 47.826 0.00 0.00 0.00 3.46
1917 2288 2.696526 TCACCCAGTAGGAGTTGAGT 57.303 50.000 0.00 0.00 39.89 3.41
1947 2318 4.942761 AATTTCAGCAGTGACCAAATGT 57.057 36.364 0.00 0.00 30.10 2.71
1954 2325 6.476380 TCATTTCAACAAATTTCAGCAGTGAC 59.524 34.615 0.00 0.00 28.97 3.67
1958 2330 6.698329 TCAGTCATTTCAACAAATTTCAGCAG 59.302 34.615 0.00 0.00 28.97 4.24
1997 2374 7.522725 CGGGCAAGCAGAGAAATTGATAATATT 60.523 37.037 0.00 0.00 0.00 1.28
2020 2397 3.000727 GTCCTACATCACAAGAAACGGG 58.999 50.000 0.00 0.00 0.00 5.28
2289 2666 2.873472 TCCACGGAACATAACAACACAC 59.127 45.455 0.00 0.00 0.00 3.82
2324 2701 4.106197 GCAAACAGATACTGTCGAGGTAG 58.894 47.826 4.88 0.00 44.62 3.18
2330 2707 0.370273 GGCGCAAACAGATACTGTCG 59.630 55.000 10.83 6.09 44.62 4.35
2347 2724 3.242518 GAAGGTAGCAAAATTTGACGGC 58.757 45.455 10.26 0.00 0.00 5.68
2378 2755 4.046286 TGCCTGGACATAAAAGGTTCAT 57.954 40.909 0.00 0.00 33.34 2.57
2385 2762 4.032960 ACAGACATGCCTGGACATAAAA 57.967 40.909 13.95 0.00 38.44 1.52
2386 2763 3.719268 ACAGACATGCCTGGACATAAA 57.281 42.857 13.95 0.00 38.44 1.40
2387 2764 3.008923 TCAACAGACATGCCTGGACATAA 59.991 43.478 13.95 0.00 38.44 1.90
2388 2765 2.571202 TCAACAGACATGCCTGGACATA 59.429 45.455 13.95 0.00 38.44 2.29
2389 2766 1.352017 TCAACAGACATGCCTGGACAT 59.648 47.619 13.95 0.00 38.44 3.06
2390 2767 0.764271 TCAACAGACATGCCTGGACA 59.236 50.000 13.95 0.00 38.44 4.02
2391 2768 1.537202 GTTCAACAGACATGCCTGGAC 59.463 52.381 13.95 3.15 38.44 4.02
2421 2798 1.588674 TTTCAGGTAACACAGGCACG 58.411 50.000 0.00 0.00 41.41 5.34
2453 2830 6.986231 CACCATAGCACACATCAAGATTACTA 59.014 38.462 0.00 0.00 0.00 1.82
2458 2835 3.054139 ACCACCATAGCACACATCAAGAT 60.054 43.478 0.00 0.00 0.00 2.40
2473 2851 6.112927 ACATCAAAGCATTAAAACCACCAT 57.887 33.333 0.00 0.00 0.00 3.55
2474 2852 5.543507 ACATCAAAGCATTAAAACCACCA 57.456 34.783 0.00 0.00 0.00 4.17
2475 2853 6.859420 AAACATCAAAGCATTAAAACCACC 57.141 33.333 0.00 0.00 0.00 4.61
2476 2854 8.611757 AGAAAAACATCAAAGCATTAAAACCAC 58.388 29.630 0.00 0.00 0.00 4.16
2477 2855 8.729805 AGAAAAACATCAAAGCATTAAAACCA 57.270 26.923 0.00 0.00 0.00 3.67
2478 2856 9.437045 CAAGAAAAACATCAAAGCATTAAAACC 57.563 29.630 0.00 0.00 0.00 3.27
2504 2884 2.751837 GCCCAGTACTGCCCAAGC 60.752 66.667 17.86 10.26 40.48 4.01
2505 2885 2.436646 CGCCCAGTACTGCCCAAG 60.437 66.667 17.86 3.23 0.00 3.61
2506 2886 3.246112 ACGCCCAGTACTGCCCAA 61.246 61.111 17.86 0.00 0.00 4.12
2531 2911 2.561373 GCCGAAACTTTCAGCCGG 59.439 61.111 0.00 0.00 42.74 6.13
2532 2912 2.561373 GGCCGAAACTTTCAGCCG 59.439 61.111 12.10 0.00 42.81 5.52
2536 2916 1.957186 CGACCGGCCGAAACTTTCA 60.957 57.895 30.73 0.00 0.00 2.69
2565 2945 1.002468 GTATACGTGCGTGTATCGGGT 60.002 52.381 7.55 0.00 40.26 5.28
2631 3013 3.001330 GGAATCGCGTTGACTTAGATTGG 59.999 47.826 5.77 0.00 32.42 3.16
2658 3040 3.056952 GCAGTAAATTGCATCTCACGG 57.943 47.619 0.00 0.00 43.53 4.94
2702 3087 0.106819 CAAGCAGGAGATCAAGGGGG 60.107 60.000 0.00 0.00 0.00 5.40
2703 3088 0.750911 GCAAGCAGGAGATCAAGGGG 60.751 60.000 0.00 0.00 0.00 4.79
2705 3090 1.380524 CTGCAAGCAGGAGATCAAGG 58.619 55.000 14.10 0.00 38.04 3.61
2727 3112 4.704833 GGCAAGGCAGGCACGAGA 62.705 66.667 0.00 0.00 0.00 4.04
2736 3121 2.324330 CGACAATGACGGCAAGGCA 61.324 57.895 0.00 0.00 45.56 4.75
2738 3123 1.787847 GTCGACAATGACGGCAAGG 59.212 57.895 11.55 0.00 35.39 3.61
2819 3204 0.321671 ACACGTTCTGCTGCATAGGT 59.678 50.000 1.31 3.65 0.00 3.08
2831 3216 0.307760 CTGGAACCAGCAACACGTTC 59.692 55.000 7.95 0.00 37.24 3.95
2862 3247 1.432024 ACGGGGGATGCTACTACCTAT 59.568 52.381 0.00 0.00 0.00 2.57
2868 3253 0.617820 AACTGACGGGGGATGCTACT 60.618 55.000 0.00 0.00 0.00 2.57
2901 3287 0.623723 ATGCTTCAACCGGGTATGGT 59.376 50.000 6.32 0.00 46.67 3.55
2902 3288 1.308998 GATGCTTCAACCGGGTATGG 58.691 55.000 6.32 0.00 0.00 2.74
2970 3357 0.948678 TTGTGAAAGCTACAACCGGC 59.051 50.000 0.00 0.00 33.43 6.13
3030 3418 2.451990 CGTTCACGGCGATGATGCA 61.452 57.895 16.62 0.00 36.28 3.96
3075 3466 4.335647 ACTGGAGCTGCAACCGGG 62.336 66.667 22.03 14.32 36.91 5.73
3090 3481 0.250295 ATGCTACAACCACGCACACT 60.250 50.000 0.00 0.00 36.37 3.55
3095 3486 1.421410 CGGAGATGCTACAACCACGC 61.421 60.000 0.00 0.00 0.00 5.34
3111 3502 0.535335 GGAGATGCTACAACCACGGA 59.465 55.000 0.00 0.00 0.00 4.69
3112 3503 0.806102 CGGAGATGCTACAACCACGG 60.806 60.000 0.00 0.00 0.00 4.94
3113 3504 1.421410 GCGGAGATGCTACAACCACG 61.421 60.000 0.00 0.00 0.00 4.94
3114 3505 1.421410 CGCGGAGATGCTACAACCAC 61.421 60.000 0.00 0.00 0.00 4.16
3115 3506 1.153647 CGCGGAGATGCTACAACCA 60.154 57.895 0.00 0.00 0.00 3.67
3116 3507 1.883084 CCGCGGAGATGCTACAACC 60.883 63.158 24.07 0.00 0.00 3.77
3117 3508 0.249489 ATCCGCGGAGATGCTACAAC 60.249 55.000 33.87 0.00 0.00 3.32
3118 3509 0.032130 GATCCGCGGAGATGCTACAA 59.968 55.000 33.87 6.09 0.00 2.41
3119 3510 1.660355 GATCCGCGGAGATGCTACA 59.340 57.895 33.87 6.96 0.00 2.74
3120 3511 1.442857 CGATCCGCGGAGATGCTAC 60.443 63.158 33.87 15.75 36.03 3.58
3121 3512 2.954611 CGATCCGCGGAGATGCTA 59.045 61.111 33.87 8.71 36.03 3.49
3143 3534 0.461516 ATCATGTGTCGCAGGAGCTG 60.462 55.000 6.89 0.00 41.47 4.24
3159 3550 6.509997 CGTCATCAGCGAAAATGATACAATCA 60.510 38.462 0.00 0.00 44.55 2.57
3161 3552 5.277490 CCGTCATCAGCGAAAATGATACAAT 60.277 40.000 0.00 0.00 35.64 2.71
3167 3558 0.726827 GCCGTCATCAGCGAAAATGA 59.273 50.000 0.00 0.00 0.00 2.57
3191 3582 2.125106 GCCGGAGTTGTAGCCAGG 60.125 66.667 5.05 0.00 0.00 4.45
3207 3598 2.622436 AGAGTTGCTATCCGAGTTTGC 58.378 47.619 0.00 0.00 0.00 3.68
3217 3608 6.344500 CAACCACATTCTCTAGAGTTGCTAT 58.656 40.000 19.21 4.39 0.00 2.97
3242 3633 3.004315 ACAACCGTTCACCTAAAATGCTG 59.996 43.478 0.00 0.00 0.00 4.41
3246 3637 4.648651 AGCTACAACCGTTCACCTAAAAT 58.351 39.130 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.