Multiple sequence alignment - TraesCS7B01G414800

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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 TraesCS7B01G414800 chr7B 100.000 2891 0 0 1 2891 682792775 682789885 0.000000e+00 5339.0
1 TraesCS7B01G414800 chr7B 86.575 1162 89 28 1087 2209 681688471 681689604 0.000000e+00 1219.0
2 TraesCS7B01G414800 chr7B 78.322 858 112 55 989 1827 681750186 681750988 1.200000e-133 486.0
3 TraesCS7B01G414800 chr7B 85.843 445 31 15 1385 1816 682886390 682885965 7.350000e-121 444.0
4 TraesCS7B01G414800 chr7B 81.154 589 72 22 1 585 682887558 682887005 1.230000e-118 436.0
5 TraesCS7B01G414800 chr7B 91.525 236 11 2 1601 1827 681780146 681780381 1.670000e-82 316.0
6 TraesCS7B01G414800 chr7B 76.728 434 45 26 865 1275 682886852 682886452 1.060000e-44 191.0
7 TraesCS7B01G414800 chr7B 84.146 82 11 2 1863 1943 682885940 682885860 8.590000e-11 78.7
8 TraesCS7B01G414800 chr7D 86.011 1394 95 44 861 2193 602410396 602409042 0.000000e+00 1402.0
9 TraesCS7B01G414800 chr7D 82.749 1368 124 48 953 2277 602042468 602043766 0.000000e+00 1116.0
10 TraesCS7B01G414800 chr7D 81.668 971 87 51 871 1815 602295446 602294541 0.000000e+00 723.0
11 TraesCS7B01G414800 chr7D 76.574 1191 160 72 989 2143 602072501 602073608 7.050000e-151 544.0
12 TraesCS7B01G414800 chr7D 79.148 446 44 23 861 1275 602196574 602197001 2.210000e-66 263.0
13 TraesCS7B01G414800 chr7D 81.319 273 22 13 994 1251 602632846 602632588 8.170000e-46 195.0
14 TraesCS7B01G414800 chr7D 90.678 118 8 1 2478 2592 602409013 602408896 1.390000e-33 154.0
15 TraesCS7B01G414800 chr7A 85.092 1308 105 40 954 2209 693815150 693816419 0.000000e+00 1253.0
16 TraesCS7B01G414800 chr7A 84.829 1081 54 42 1881 2891 694075480 694074440 0.000000e+00 987.0
17 TraesCS7B01G414800 chr7A 76.619 988 124 61 989 1938 693838238 693839156 2.040000e-121 446.0
18 TraesCS7B01G414800 chr7A 82.340 470 50 13 1382 1827 694022578 694022118 7.560000e-101 377.0
19 TraesCS7B01G414800 chr7A 87.075 147 16 2 646 789 6527893 6527747 2.300000e-36 163.0
20 TraesCS7B01G414800 chrUn 81.034 986 99 48 998 1967 87232701 87231788 0.000000e+00 704.0
21 TraesCS7B01G414800 chrUn 78.428 598 80 25 1571 2142 87260256 87259682 7.670000e-91 344.0
22 TraesCS7B01G414800 chrUn 78.428 598 80 25 1571 2142 235076115 235075541 7.670000e-91 344.0
23 TraesCS7B01G414800 chr6B 78.165 545 97 19 292 821 245893792 245893255 7.720000e-86 327.0
24 TraesCS7B01G414800 chr1D 81.724 290 46 6 301 585 169066591 169066304 4.820000e-58 235.0
25 TraesCS7B01G414800 chr1D 81.250 288 48 6 294 579 233892788 233892505 8.060000e-56 228.0
26 TraesCS7B01G414800 chr2B 81.754 285 46 6 300 581 177133435 177133716 1.730000e-57 233.0
27 TraesCS7B01G414800 chr2B 80.969 289 51 4 302 588 697672328 697672042 2.900000e-55 226.0
28 TraesCS7B01G414800 chr3D 83.471 242 34 5 585 821 580990357 580990117 1.350000e-53 220.0
29 TraesCS7B01G414800 chr5D 83.197 244 32 7 585 821 451067421 451067180 6.270000e-52 215.0
30 TraesCS7B01G414800 chr5D 85.047 214 26 5 585 793 403049400 403049612 2.260000e-51 213.0
31 TraesCS7B01G414800 chr6A 81.008 258 44 4 301 555 404354820 404354565 1.760000e-47 200.0
32 TraesCS7B01G414800 chr6A 79.570 279 55 2 302 579 297628808 297628531 6.320000e-47 198.0
33 TraesCS7B01G414800 chr1B 79.496 278 50 6 296 568 249623801 249624076 1.060000e-44 191.0
34 TraesCS7B01G414800 chr6D 78.472 288 51 11 307 590 356193221 356192941 8.230000e-41 178.0
35 TraesCS7B01G414800 chr3A 80.342 234 40 5 593 821 586084889 586084657 3.830000e-39 172.0
36 TraesCS7B01G414800 chr4A 81.081 222 32 9 585 802 163815448 163815663 4.950000e-38 169.0
37 TraesCS7B01G414800 chr4A 80.349 229 37 7 585 809 56712337 56712561 1.780000e-37 167.0
38 TraesCS7B01G414800 chr2D 79.339 242 36 10 586 821 311544216 311543983 1.070000e-34 158.0


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 TraesCS7B01G414800 chr7B 682789885 682792775 2890 True 5339.000 5339 100.00000 1 2891 1 chr7B.!!$R1 2890
1 TraesCS7B01G414800 chr7B 681688471 681689604 1133 False 1219.000 1219 86.57500 1087 2209 1 chr7B.!!$F1 1122
2 TraesCS7B01G414800 chr7B 681750186 681750988 802 False 486.000 486 78.32200 989 1827 1 chr7B.!!$F2 838
3 TraesCS7B01G414800 chr7B 682885860 682887558 1698 True 287.425 444 81.96775 1 1943 4 chr7B.!!$R2 1942
4 TraesCS7B01G414800 chr7D 602042468 602043766 1298 False 1116.000 1116 82.74900 953 2277 1 chr7D.!!$F1 1324
5 TraesCS7B01G414800 chr7D 602408896 602410396 1500 True 778.000 1402 88.34450 861 2592 2 chr7D.!!$R3 1731
6 TraesCS7B01G414800 chr7D 602294541 602295446 905 True 723.000 723 81.66800 871 1815 1 chr7D.!!$R1 944
7 TraesCS7B01G414800 chr7D 602072501 602073608 1107 False 544.000 544 76.57400 989 2143 1 chr7D.!!$F2 1154
8 TraesCS7B01G414800 chr7A 693815150 693816419 1269 False 1253.000 1253 85.09200 954 2209 1 chr7A.!!$F1 1255
9 TraesCS7B01G414800 chr7A 694074440 694075480 1040 True 987.000 987 84.82900 1881 2891 1 chr7A.!!$R3 1010
10 TraesCS7B01G414800 chr7A 693838238 693839156 918 False 446.000 446 76.61900 989 1938 1 chr7A.!!$F2 949
11 TraesCS7B01G414800 chrUn 87231788 87232701 913 True 704.000 704 81.03400 998 1967 1 chrUn.!!$R1 969
12 TraesCS7B01G414800 chrUn 87259682 87260256 574 True 344.000 344 78.42800 1571 2142 1 chrUn.!!$R2 571
13 TraesCS7B01G414800 chrUn 235075541 235076115 574 True 344.000 344 78.42800 1571 2142 1 chrUn.!!$R3 571
14 TraesCS7B01G414800 chr6B 245893255 245893792 537 True 327.000 327 78.16500 292 821 1 chr6B.!!$R1 529

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
585 593 0.871722 GCACGTGCATTGTCCAAGTA 59.128 50.0 34.52 0.0 41.59 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 2780 0.396811 CAACATATCCCCTCGGGTCC 59.603 60.0 0.55 0.0 44.74 4.46 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
88 89 3.882888 GTGGGTGAGTTTGTTGATTCTGA 59.117 43.478 0.00 0.00 0.00 3.27
90 91 4.520111 TGGGTGAGTTTGTTGATTCTGATG 59.480 41.667 0.00 0.00 0.00 3.07
91 92 4.761739 GGGTGAGTTTGTTGATTCTGATGA 59.238 41.667 0.00 0.00 0.00 2.92
194 195 6.789268 TCATGGTTCTTCTAGAATTTCCCAA 58.211 36.000 5.44 0.00 36.50 4.12
262 263 4.657436 TTTTTCAGGCATTTGTTACGGT 57.343 36.364 0.00 0.00 0.00 4.83
263 264 3.907894 TTTCAGGCATTTGTTACGGTC 57.092 42.857 0.00 0.00 0.00 4.79
264 265 1.434555 TCAGGCATTTGTTACGGTCG 58.565 50.000 0.00 0.00 0.00 4.79
288 289 7.454694 TCGCCCTATGCTGATACCATATATAAT 59.545 37.037 0.00 0.00 38.05 1.28
290 291 9.799106 GCCCTATGCTGATACCATATATAATTT 57.201 33.333 0.00 0.00 36.87 1.82
361 365 5.429681 TCTTTATTCCGATGACCCTTTCA 57.570 39.130 0.00 0.00 39.11 2.69
372 376 2.225017 TGACCCTTTCATCCAACCTTCC 60.225 50.000 0.00 0.00 0.00 3.46
374 378 1.619704 CCCTTTCATCCAACCTTCCCC 60.620 57.143 0.00 0.00 0.00 4.81
375 379 1.359130 CCTTTCATCCAACCTTCCCCT 59.641 52.381 0.00 0.00 0.00 4.79
427 431 9.492973 CTTACATTTTGAGTCCATTCCATTTTT 57.507 29.630 0.00 0.00 0.00 1.94
532 540 1.544724 TGGGCAGGTAAATCACAAGC 58.455 50.000 0.00 0.00 0.00 4.01
534 542 1.474077 GGGCAGGTAAATCACAAGCTG 59.526 52.381 0.00 0.00 42.67 4.24
538 546 3.120060 GCAGGTAAATCACAAGCTGACAG 60.120 47.826 5.77 0.00 42.45 3.51
539 547 4.318332 CAGGTAAATCACAAGCTGACAGA 58.682 43.478 6.65 0.00 42.45 3.41
541 549 4.065088 GGTAAATCACAAGCTGACAGACA 58.935 43.478 6.65 0.00 0.00 3.41
549 557 6.233434 TCACAAGCTGACAGACAAGAATATT 58.767 36.000 6.65 0.00 0.00 1.28
571 579 7.709269 ATTTATATCATCTTACAACGCACGT 57.291 32.000 0.00 0.00 0.00 4.49
575 583 1.128507 CATCTTACAACGCACGTGCAT 59.871 47.619 37.03 23.73 42.21 3.96
576 584 1.222300 TCTTACAACGCACGTGCATT 58.778 45.000 37.03 28.37 42.21 3.56
579 587 3.814009 CAACGCACGTGCATTGTC 58.186 55.556 34.16 9.63 39.14 3.18
581 589 2.183504 AACGCACGTGCATTGTCCA 61.184 52.632 37.03 0.00 42.21 4.02
583 591 1.440850 CGCACGTGCATTGTCCAAG 60.441 57.895 37.03 15.87 42.21 3.61
584 592 1.654220 GCACGTGCATTGTCCAAGT 59.346 52.632 34.52 0.00 41.59 3.16
585 593 0.871722 GCACGTGCATTGTCCAAGTA 59.128 50.000 34.52 0.00 41.59 2.24
586 594 1.399727 GCACGTGCATTGTCCAAGTAC 60.400 52.381 34.52 0.00 41.59 2.73
587 595 2.143122 CACGTGCATTGTCCAAGTACT 58.857 47.619 0.82 0.00 0.00 2.73
588 596 2.548057 CACGTGCATTGTCCAAGTACTT 59.452 45.455 0.82 1.12 0.00 2.24
589 597 3.743911 CACGTGCATTGTCCAAGTACTTA 59.256 43.478 8.04 0.00 0.00 2.24
591 600 4.451096 ACGTGCATTGTCCAAGTACTTAAG 59.549 41.667 8.04 0.00 0.00 1.85
598 607 8.515414 GCATTGTCCAAGTACTTAAGAAGAATT 58.485 33.333 10.09 0.00 0.00 2.17
628 638 3.951680 TCACCTTTCACTTTCTTTCCACC 59.048 43.478 0.00 0.00 0.00 4.61
633 643 1.134220 TCACTTTCTTTCCACCACGCT 60.134 47.619 0.00 0.00 0.00 5.07
635 645 1.947456 ACTTTCTTTCCACCACGCTTC 59.053 47.619 0.00 0.00 0.00 3.86
636 646 1.946768 CTTTCTTTCCACCACGCTTCA 59.053 47.619 0.00 0.00 0.00 3.02
637 647 2.270352 TTCTTTCCACCACGCTTCAT 57.730 45.000 0.00 0.00 0.00 2.57
638 648 1.808411 TCTTTCCACCACGCTTCATC 58.192 50.000 0.00 0.00 0.00 2.92
646 657 1.247567 CCACGCTTCATCCAACCTTT 58.752 50.000 0.00 0.00 0.00 3.11
647 658 1.613437 CCACGCTTCATCCAACCTTTT 59.387 47.619 0.00 0.00 0.00 2.27
650 661 1.202348 CGCTTCATCCAACCTTTTCCC 59.798 52.381 0.00 0.00 0.00 3.97
658 669 6.841601 TCATCCAACCTTTTCCCTATGATAG 58.158 40.000 0.00 0.00 0.00 2.08
660 671 6.248569 TCCAACCTTTTCCCTATGATAGTC 57.751 41.667 0.00 0.00 0.00 2.59
682 693 8.803397 AGTCAATCACCTTAATTTACTTACCC 57.197 34.615 0.00 0.00 0.00 3.69
683 694 7.551617 AGTCAATCACCTTAATTTACTTACCCG 59.448 37.037 0.00 0.00 0.00 5.28
684 695 7.335171 GTCAATCACCTTAATTTACTTACCCGT 59.665 37.037 0.00 0.00 0.00 5.28
686 697 7.619964 ATCACCTTAATTTACTTACCCGTTG 57.380 36.000 0.00 0.00 0.00 4.10
693 704 6.904463 AATTTACTTACCCGTTGAACCAAT 57.096 33.333 0.00 0.00 0.00 3.16
694 705 6.904463 ATTTACTTACCCGTTGAACCAATT 57.096 33.333 0.00 0.00 0.00 2.32
695 706 6.712179 TTTACTTACCCGTTGAACCAATTT 57.288 33.333 0.00 0.00 0.00 1.82
696 707 6.712179 TTACTTACCCGTTGAACCAATTTT 57.288 33.333 0.00 0.00 0.00 1.82
697 708 7.814264 TTACTTACCCGTTGAACCAATTTTA 57.186 32.000 0.00 0.00 0.00 1.52
701 712 8.205512 ACTTACCCGTTGAACCAATTTTATTTT 58.794 29.630 0.00 0.00 0.00 1.82
909 1071 7.763528 TGTTGAGTGCTGAAAATTGTAAAACAT 59.236 29.630 0.00 0.00 0.00 2.71
910 1072 7.697352 TGAGTGCTGAAAATTGTAAAACATG 57.303 32.000 0.00 0.00 0.00 3.21
911 1073 7.487484 TGAGTGCTGAAAATTGTAAAACATGA 58.513 30.769 0.00 0.00 0.00 3.07
912 1074 8.143193 TGAGTGCTGAAAATTGTAAAACATGAT 58.857 29.630 0.00 0.00 0.00 2.45
913 1075 8.891671 AGTGCTGAAAATTGTAAAACATGATT 57.108 26.923 0.00 0.00 0.00 2.57
943 1108 4.631813 ACATCACGTGAAAGCTTCCTATTC 59.368 41.667 24.13 0.00 0.00 1.75
948 1113 4.389077 ACGTGAAAGCTTCCTATTCTTTCG 59.611 41.667 0.00 3.40 45.09 3.46
1046 1228 0.386478 GCCGAGCTTTTTGTCTGCAG 60.386 55.000 7.63 7.63 0.00 4.41
1063 1245 2.791331 GCGAAACGTGCGAGCAAC 60.791 61.111 14.31 0.00 0.00 4.17
1158 1373 1.901085 GCCTCCTCCGCCCTATATG 59.099 63.158 0.00 0.00 0.00 1.78
1160 1375 1.938585 CCTCCTCCGCCCTATATGAA 58.061 55.000 0.00 0.00 0.00 2.57
1168 1383 0.396811 GCCCTATATGAACCCACGCT 59.603 55.000 0.00 0.00 0.00 5.07
1199 1415 2.512515 GACACATCCGCTCCAGGC 60.513 66.667 0.00 0.00 37.64 4.85
1200 1416 4.101448 ACACATCCGCTCCAGGCC 62.101 66.667 0.00 0.00 37.74 5.19
1209 1425 3.004951 CTCCAGGCCTCCAGCAAT 58.995 61.111 0.00 0.00 46.50 3.56
1682 2000 2.495366 ATCAACGCGGCGTACCAGAA 62.495 55.000 29.63 10.77 39.99 3.02
1683 2001 2.029369 AACGCGGCGTACCAGAAA 59.971 55.556 29.63 0.00 39.99 2.52
1819 2145 0.596577 CGACTGGTTCTCCGACTTCA 59.403 55.000 0.00 0.00 36.30 3.02
1839 2165 3.883744 AAGTCTCAAGGGCCGCGTG 62.884 63.158 4.92 0.00 0.00 5.34
1861 2194 3.451894 GCCAACGGCCATTCCTGG 61.452 66.667 2.24 2.12 44.06 4.45
1944 2282 5.076873 CCTGTTTTATTGTGGAGGGAAGAA 58.923 41.667 0.00 0.00 0.00 2.52
1972 2321 6.790232 AGAAAGAAATTCAGGGTTCAAACA 57.210 33.333 0.00 0.00 40.72 2.83
2092 2460 0.250553 ATTTCGAACAAGGGGACGCA 60.251 50.000 0.00 0.00 0.00 5.24
2109 2477 2.032030 ACGCATCTTTCGTTTTCAGTGG 60.032 45.455 0.00 0.00 36.72 4.00
2179 2548 6.474751 GGATTCAGATCTTTGCTGTAAAATGC 59.525 38.462 0.00 0.00 34.98 3.56
2218 2588 4.039488 TCTTGCAGGTGAAAATGAAATGCT 59.961 37.500 0.00 0.00 33.47 3.79
2227 2609 4.220382 TGAAAATGAAATGCTACCACTGGG 59.780 41.667 0.00 0.00 41.29 4.45
2278 2660 4.453478 TCTTCTGCAGCAACTGTTATCTTG 59.547 41.667 9.47 0.00 33.43 3.02
2299 2684 5.818678 TGTCTACCCACTTTGTGTTCTAT 57.181 39.130 0.00 0.00 0.00 1.98
2313 2698 3.111484 TGTTCTATGGGCCACACATCTA 58.889 45.455 9.28 0.00 0.00 1.98
2329 2714 7.023575 CACACATCTAGTACAGAAAAATTGCC 58.976 38.462 0.00 0.00 36.67 4.52
2367 2755 3.990959 TGTGATGCTACATGGGTACAA 57.009 42.857 0.00 0.00 0.00 2.41
2379 2767 5.831103 ACATGGGTACAAGATTTCAGGAAT 58.169 37.500 0.00 0.00 0.00 3.01
2380 2768 5.653769 ACATGGGTACAAGATTTCAGGAATG 59.346 40.000 0.00 0.00 0.00 2.67
2391 2779 1.097232 TCAGGAATGCGGCTTGATTG 58.903 50.000 0.00 0.00 0.00 2.67
2392 2780 0.101759 CAGGAATGCGGCTTGATTGG 59.898 55.000 0.00 0.00 0.00 3.16
2401 2789 1.452108 GCTTGATTGGGACCCGAGG 60.452 63.158 6.61 0.00 0.00 4.63
2421 2809 5.395324 CGAGGGGATATGTTGTTCAAGTAGT 60.395 44.000 0.00 0.00 0.00 2.73
2458 2846 5.968254 TGATTAGCCACGATGTGTTAACTA 58.032 37.500 7.22 0.00 0.00 2.24
2461 2849 7.865889 TGATTAGCCACGATGTGTTAACTATAG 59.134 37.037 7.22 0.00 0.00 1.31
2462 2850 5.593679 AGCCACGATGTGTTAACTATAGT 57.406 39.130 7.22 0.00 0.00 2.12
2463 2851 5.974108 AGCCACGATGTGTTAACTATAGTT 58.026 37.500 21.35 21.35 41.73 2.24
2464 2852 6.403878 AGCCACGATGTGTTAACTATAGTTT 58.596 36.000 22.66 4.21 39.31 2.66
2465 2853 6.877322 AGCCACGATGTGTTAACTATAGTTTT 59.123 34.615 22.66 2.80 39.31 2.43
2466 2854 7.389607 AGCCACGATGTGTTAACTATAGTTTTT 59.610 33.333 22.66 2.04 39.31 1.94
2467 2855 7.691050 GCCACGATGTGTTAACTATAGTTTTTC 59.309 37.037 22.66 13.48 39.31 2.29
2468 2856 8.932791 CCACGATGTGTTAACTATAGTTTTTCT 58.067 33.333 22.66 1.27 39.31 2.52
2474 2862 9.729281 TGTGTTAACTATAGTTTTTCTTAGGGG 57.271 33.333 22.66 0.00 39.31 4.79
2475 2863 9.948964 GTGTTAACTATAGTTTTTCTTAGGGGA 57.051 33.333 22.66 0.00 39.31 4.81
2476 2864 9.948964 TGTTAACTATAGTTTTTCTTAGGGGAC 57.051 33.333 22.66 0.92 39.31 4.46
2477 2865 9.091784 GTTAACTATAGTTTTTCTTAGGGGACG 57.908 37.037 22.66 0.00 39.31 4.79
2478 2866 6.864151 ACTATAGTTTTTCTTAGGGGACGT 57.136 37.500 0.00 0.00 0.00 4.34
2479 2867 6.637657 ACTATAGTTTTTCTTAGGGGACGTG 58.362 40.000 0.00 0.00 0.00 4.49
2480 2868 3.851458 AGTTTTTCTTAGGGGACGTGT 57.149 42.857 0.00 0.00 0.00 4.49
2481 2869 4.160642 AGTTTTTCTTAGGGGACGTGTT 57.839 40.909 0.00 0.00 0.00 3.32
2482 2870 5.294734 AGTTTTTCTTAGGGGACGTGTTA 57.705 39.130 0.00 0.00 0.00 2.41
2483 2871 5.683681 AGTTTTTCTTAGGGGACGTGTTAA 58.316 37.500 0.00 0.00 0.00 2.01
2484 2872 5.528690 AGTTTTTCTTAGGGGACGTGTTAAC 59.471 40.000 0.00 0.00 0.00 2.01
2485 2873 4.961438 TTTCTTAGGGGACGTGTTAACT 57.039 40.909 7.22 0.00 0.00 2.24
2486 2874 6.418057 TTTTCTTAGGGGACGTGTTAACTA 57.582 37.500 7.22 0.00 0.00 2.24
2530 2921 9.699410 TTCATGTCAATTAGTGATAAATTCCCT 57.301 29.630 0.00 0.00 38.90 4.20
2540 2931 5.012893 GTGATAAATTCCCTCCATCCATCC 58.987 45.833 0.00 0.00 0.00 3.51
2596 3014 3.243035 CGTGCAAAACCTTTGATCAGACA 60.243 43.478 3.35 0.00 0.00 3.41
2605 3023 5.678583 ACCTTTGATCAGACATATGTCCAG 58.321 41.667 28.26 21.71 45.85 3.86
2621 3040 0.974010 CCAGCCAGGGTGATGCAATT 60.974 55.000 20.97 0.00 32.22 2.32
2689 3127 2.482316 CGTCGGGCCAAGTACATTATCA 60.482 50.000 4.39 0.00 0.00 2.15
2698 3136 7.363793 GGGCCAAGTACATTATCAATCTTTGTT 60.364 37.037 4.39 0.00 0.00 2.83
2700 3138 9.423061 GCCAAGTACATTATCAATCTTTGTTTT 57.577 29.630 0.00 0.00 0.00 2.43
2748 3186 9.220767 GTCTAAGGGATTTATGCTTTTATCGAT 57.779 33.333 2.16 2.16 0.00 3.59
2839 3281 4.142534 GGACGCTTTTGAAATACCCTAACC 60.143 45.833 0.00 0.00 0.00 2.85
2863 3305 1.827681 TCCTTCAGAGTGAGGTCGAG 58.172 55.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 5.983540 ACTCACCCACTATCTCTCAAAATC 58.016 41.667 0.00 0.00 0.00 2.17
191 192 6.239289 ACACTATTTGGTGTCCAATTTCTTGG 60.239 38.462 1.97 0.00 45.94 3.61
194 195 9.920946 ATATACACTATTTGGTGTCCAATTTCT 57.079 29.630 2.77 0.00 45.94 2.52
241 242 4.612943 GACCGTAACAAATGCCTGAAAAA 58.387 39.130 0.00 0.00 0.00 1.94
244 245 1.801771 CGACCGTAACAAATGCCTGAA 59.198 47.619 0.00 0.00 0.00 3.02
246 247 0.179200 GCGACCGTAACAAATGCCTG 60.179 55.000 0.00 0.00 0.00 4.85
247 248 1.303091 GGCGACCGTAACAAATGCCT 61.303 55.000 0.00 0.00 38.00 4.75
248 249 1.135939 GGCGACCGTAACAAATGCC 59.864 57.895 0.00 0.00 0.00 4.40
249 250 1.135939 GGGCGACCGTAACAAATGC 59.864 57.895 0.00 0.00 43.64 3.56
264 265 9.799106 AAATTATATATGGTATCAGCATAGGGC 57.201 33.333 0.00 0.00 41.23 5.19
351 355 2.225017 GGAAGGTTGGATGAAAGGGTCA 60.225 50.000 0.00 0.00 41.67 4.02
352 356 2.447443 GGAAGGTTGGATGAAAGGGTC 58.553 52.381 0.00 0.00 0.00 4.46
361 365 8.300752 TGATTATTATAAGGGGAAGGTTGGAT 57.699 34.615 0.00 0.00 0.00 3.41
495 500 7.018149 ACCTGCCCATATTAATAGGATTGTGTA 59.982 37.037 8.68 0.00 0.00 2.90
504 509 8.862325 TGTGATTTACCTGCCCATATTAATAG 57.138 34.615 1.02 0.00 0.00 1.73
505 510 9.295825 CTTGTGATTTACCTGCCCATATTAATA 57.704 33.333 0.00 0.00 0.00 0.98
510 515 3.891366 GCTTGTGATTTACCTGCCCATAT 59.109 43.478 0.00 0.00 0.00 1.78
514 519 1.474077 CAGCTTGTGATTTACCTGCCC 59.526 52.381 0.00 0.00 0.00 5.36
516 521 2.813754 TGTCAGCTTGTGATTTACCTGC 59.186 45.455 0.00 0.00 37.56 4.85
517 522 4.153117 GTCTGTCAGCTTGTGATTTACCTG 59.847 45.833 0.00 0.00 37.56 4.00
549 557 5.051307 GCACGTGCGTTGTAAGATGATATAA 60.051 40.000 26.77 0.00 0.00 0.98
556 564 1.438651 ATGCACGTGCGTTGTAAGAT 58.561 45.000 33.22 17.03 45.83 2.40
557 565 2.907431 ATGCACGTGCGTTGTAAGA 58.093 47.368 33.22 15.42 45.83 2.10
571 579 6.530120 TCTTCTTAAGTACTTGGACAATGCA 58.470 36.000 18.56 0.00 0.00 3.96
609 618 3.243068 CGTGGTGGAAAGAAAGTGAAAGG 60.243 47.826 0.00 0.00 0.00 3.11
610 619 3.792124 GCGTGGTGGAAAGAAAGTGAAAG 60.792 47.826 0.00 0.00 0.00 2.62
614 623 1.308998 AGCGTGGTGGAAAGAAAGTG 58.691 50.000 0.00 0.00 0.00 3.16
628 638 2.351738 GGAAAAGGTTGGATGAAGCGTG 60.352 50.000 0.00 0.00 37.13 5.34
633 643 5.528600 TCATAGGGAAAAGGTTGGATGAA 57.471 39.130 0.00 0.00 0.00 2.57
635 645 6.605119 ACTATCATAGGGAAAAGGTTGGATG 58.395 40.000 0.00 0.00 0.00 3.51
636 646 6.389869 TGACTATCATAGGGAAAAGGTTGGAT 59.610 38.462 0.00 0.00 0.00 3.41
637 647 5.729229 TGACTATCATAGGGAAAAGGTTGGA 59.271 40.000 0.00 0.00 0.00 3.53
638 648 6.001449 TGACTATCATAGGGAAAAGGTTGG 57.999 41.667 0.00 0.00 0.00 3.77
646 657 8.561536 TTAAGGTGATTGACTATCATAGGGAA 57.438 34.615 2.88 0.00 44.75 3.97
647 658 8.742125 ATTAAGGTGATTGACTATCATAGGGA 57.258 34.615 2.88 0.00 44.75 4.20
658 669 7.335171 ACGGGTAAGTAAATTAAGGTGATTGAC 59.665 37.037 0.00 0.00 0.00 3.18
660 671 7.619964 ACGGGTAAGTAAATTAAGGTGATTG 57.380 36.000 0.00 0.00 0.00 2.67
854 919 4.036971 CCGGGTACACATTGAAAAGTTTCA 59.963 41.667 2.32 2.32 44.78 2.69
855 920 4.037089 ACCGGGTACACATTGAAAAGTTTC 59.963 41.667 6.32 0.00 37.69 2.78
858 923 3.143728 GACCGGGTACACATTGAAAAGT 58.856 45.455 6.32 0.00 0.00 2.66
859 924 3.142951 TGACCGGGTACACATTGAAAAG 58.857 45.455 6.32 0.00 0.00 2.27
863 1024 3.078097 CAATTGACCGGGTACACATTGA 58.922 45.455 6.32 0.00 0.00 2.57
943 1108 4.373348 ACTATTCCTTCCGTCTCGAAAG 57.627 45.455 0.00 0.00 0.00 2.62
948 1113 4.670347 GTGTGTACTATTCCTTCCGTCTC 58.330 47.826 0.00 0.00 0.00 3.36
1030 1212 0.588252 TCGCTGCAGACAAAAAGCTC 59.412 50.000 20.43 0.00 33.41 4.09
1033 1215 1.775208 CGTTTCGCTGCAGACAAAAAG 59.225 47.619 20.43 11.92 0.00 2.27
1046 1228 2.791331 GTTGCTCGCACGTTTCGC 60.791 61.111 2.38 0.00 0.00 4.70
1063 1245 2.330041 GTGTTTCCCACGTTGCCG 59.670 61.111 0.00 0.00 40.83 5.69
1149 1352 0.396811 AGCGTGGGTTCATATAGGGC 59.603 55.000 0.00 0.00 0.00 5.19
1158 1373 2.668550 GTGGTGGAGCGTGGGTTC 60.669 66.667 0.00 0.00 0.00 3.62
1183 1398 4.101448 GGCCTGGAGCGGATGTGT 62.101 66.667 0.00 0.00 45.17 3.72
1185 1400 3.474570 GAGGCCTGGAGCGGATGT 61.475 66.667 12.00 0.00 45.17 3.06
1199 1415 2.301346 GGAATGGTGTATTGCTGGAGG 58.699 52.381 0.00 0.00 34.59 4.30
1200 1416 2.947652 CTGGAATGGTGTATTGCTGGAG 59.052 50.000 0.00 0.00 37.91 3.86
1207 1423 2.357154 GGTGGAGCTGGAATGGTGTATT 60.357 50.000 0.00 0.00 0.00 1.89
1209 1425 0.618458 GGTGGAGCTGGAATGGTGTA 59.382 55.000 0.00 0.00 0.00 2.90
1375 1648 1.414866 GCCATTCCTCCTCCTCCTCC 61.415 65.000 0.00 0.00 0.00 4.30
1376 1649 1.753368 CGCCATTCCTCCTCCTCCTC 61.753 65.000 0.00 0.00 0.00 3.71
1377 1650 1.764054 CGCCATTCCTCCTCCTCCT 60.764 63.158 0.00 0.00 0.00 3.69
1378 1651 2.825264 CGCCATTCCTCCTCCTCC 59.175 66.667 0.00 0.00 0.00 4.30
1379 1652 2.110006 GCGCCATTCCTCCTCCTC 59.890 66.667 0.00 0.00 0.00 3.71
1380 1653 2.366167 AGCGCCATTCCTCCTCCT 60.366 61.111 2.29 0.00 0.00 3.69
1519 1798 2.284995 GTCCTCCTCCAGCACCCT 60.285 66.667 0.00 0.00 0.00 4.34
1569 1848 2.285368 TTGACCTCGCCCCTGGAT 60.285 61.111 0.00 0.00 0.00 3.41
1682 2000 0.806868 CCGCATGTTGCTCATCACTT 59.193 50.000 0.00 0.00 42.25 3.16
1683 2001 1.028330 CCCGCATGTTGCTCATCACT 61.028 55.000 0.00 0.00 42.25 3.41
1819 2145 2.665603 GCGGCCCTTGAGACTTCT 59.334 61.111 0.00 0.00 0.00 2.85
1853 2179 1.107538 CCTCTGCCATGCCAGGAATG 61.108 60.000 3.50 0.00 31.52 2.67
1856 2182 4.119363 GCCTCTGCCATGCCAGGA 62.119 66.667 3.50 0.00 31.52 3.86
1944 2282 6.059484 TGAACCCTGAATTTCTTTCTACGTT 58.941 36.000 0.00 0.00 35.23 3.99
2022 2379 4.383552 GCCACAATCTAGATCAACTCCTGT 60.384 45.833 5.51 1.87 0.00 4.00
2028 2385 3.553511 CGTGAGCCACAATCTAGATCAAC 59.446 47.826 5.51 0.00 33.40 3.18
2037 2395 2.536928 GCGTTAATCGTGAGCCACAATC 60.537 50.000 6.21 0.00 42.13 2.67
2092 2460 4.755123 CCACTACCACTGAAAACGAAAGAT 59.245 41.667 0.00 0.00 0.00 2.40
2109 2477 1.071471 AGTGCCAGTGTGCCACTAC 59.929 57.895 7.41 3.82 43.43 2.73
2179 2548 3.258872 TGCAAGAAACTGGAAATGGATGG 59.741 43.478 0.00 0.00 0.00 3.51
2195 2565 4.039488 AGCATTTCATTTTCACCTGCAAGA 59.961 37.500 0.00 0.00 34.07 3.02
2218 2588 3.054287 TCAAACTCAAACACCCAGTGGTA 60.054 43.478 8.74 0.00 45.57 3.25
2227 2609 1.067060 GGCAGGGTCAAACTCAAACAC 59.933 52.381 0.00 0.00 0.00 3.32
2232 2614 1.228245 GCAGGCAGGGTCAAACTCA 60.228 57.895 0.00 0.00 0.00 3.41
2278 2660 4.935808 CCATAGAACACAAAGTGGGTAGAC 59.064 45.833 1.93 0.00 28.95 2.59
2299 2684 1.831106 CTGTACTAGATGTGTGGCCCA 59.169 52.381 0.00 0.00 0.00 5.36
2329 2714 8.671921 AGCATCACATGACAAACTCTTATAAAG 58.328 33.333 0.00 0.00 0.00 1.85
2334 2719 6.463360 TGTAGCATCACATGACAAACTCTTA 58.537 36.000 0.00 0.00 0.00 2.10
2367 2755 1.747355 CAAGCCGCATTCCTGAAATCT 59.253 47.619 0.00 0.00 0.00 2.40
2379 2767 2.361104 GGTCCCAATCAAGCCGCA 60.361 61.111 0.00 0.00 0.00 5.69
2380 2768 3.140814 GGGTCCCAATCAAGCCGC 61.141 66.667 1.78 0.00 0.00 6.53
2391 2779 0.767060 AACATATCCCCTCGGGTCCC 60.767 60.000 0.00 0.00 44.74 4.46
2392 2780 0.396811 CAACATATCCCCTCGGGTCC 59.603 60.000 0.55 0.00 44.74 4.46
2421 2809 9.416284 TCGTGGCTAATCAATATGGATATAGTA 57.584 33.333 0.00 0.00 0.00 1.82
2458 2846 5.494390 ACACGTCCCCTAAGAAAAACTAT 57.506 39.130 0.00 0.00 0.00 2.12
2461 2849 5.528690 AGTTAACACGTCCCCTAAGAAAAAC 59.471 40.000 8.61 0.00 0.00 2.43
2462 2850 5.683681 AGTTAACACGTCCCCTAAGAAAAA 58.316 37.500 8.61 0.00 0.00 1.94
2463 2851 5.294734 AGTTAACACGTCCCCTAAGAAAA 57.705 39.130 8.61 0.00 0.00 2.29
2464 2852 4.961438 AGTTAACACGTCCCCTAAGAAA 57.039 40.909 8.61 0.00 0.00 2.52
2465 2853 6.891908 ACTATAGTTAACACGTCCCCTAAGAA 59.108 38.462 8.61 0.00 0.00 2.52
2466 2854 6.426587 ACTATAGTTAACACGTCCCCTAAGA 58.573 40.000 8.61 0.00 0.00 2.10
2467 2855 6.705863 ACTATAGTTAACACGTCCCCTAAG 57.294 41.667 8.61 0.00 0.00 2.18
2468 2856 6.437162 ACAACTATAGTTAACACGTCCCCTAA 59.563 38.462 17.62 0.00 36.32 2.69
2469 2857 5.951747 ACAACTATAGTTAACACGTCCCCTA 59.048 40.000 17.62 0.00 36.32 3.53
2470 2858 4.774200 ACAACTATAGTTAACACGTCCCCT 59.226 41.667 17.62 0.00 36.32 4.79
2471 2859 5.077134 ACAACTATAGTTAACACGTCCCC 57.923 43.478 17.62 0.00 36.32 4.81
2472 2860 5.574443 GTGACAACTATAGTTAACACGTCCC 59.426 44.000 24.75 14.60 36.32 4.46
2473 2861 6.385033 AGTGACAACTATAGTTAACACGTCC 58.615 40.000 28.35 19.63 42.36 4.79
2474 2862 7.060403 GTGAGTGACAACTATAGTTAACACGTC 59.940 40.741 28.35 25.75 42.36 4.34
2475 2863 6.860023 GTGAGTGACAACTATAGTTAACACGT 59.140 38.462 28.35 22.19 42.36 4.49
2476 2864 7.060748 CAGTGAGTGACAACTATAGTTAACACG 59.939 40.741 28.35 17.37 42.36 4.49
2477 2865 8.080417 TCAGTGAGTGACAACTATAGTTAACAC 58.920 37.037 28.06 28.06 40.27 3.32
2478 2866 8.173542 TCAGTGAGTGACAACTATAGTTAACA 57.826 34.615 17.62 16.27 36.52 2.41
2479 2867 9.640963 AATCAGTGAGTGACAACTATAGTTAAC 57.359 33.333 17.62 15.17 38.28 2.01
2480 2868 9.856488 GAATCAGTGAGTGACAACTATAGTTAA 57.144 33.333 17.62 4.49 38.28 2.01
2481 2869 9.020731 TGAATCAGTGAGTGACAACTATAGTTA 57.979 33.333 17.62 0.00 38.28 2.24
2482 2870 7.896811 TGAATCAGTGAGTGACAACTATAGTT 58.103 34.615 12.50 12.50 38.28 2.24
2483 2871 7.468141 TGAATCAGTGAGTGACAACTATAGT 57.532 36.000 0.00 0.00 38.28 2.12
2484 2872 7.978414 ACATGAATCAGTGAGTGACAACTATAG 59.022 37.037 0.00 0.00 38.28 1.31
2485 2873 7.840931 ACATGAATCAGTGAGTGACAACTATA 58.159 34.615 0.00 0.00 38.28 1.31
2486 2874 6.705302 ACATGAATCAGTGAGTGACAACTAT 58.295 36.000 0.00 0.00 38.28 2.12
2530 2921 3.266513 TGATGTGAACTTGGATGGATGGA 59.733 43.478 0.00 0.00 0.00 3.41
2540 2931 9.285770 CATTAGTCATTGATTGATGTGAACTTG 57.714 33.333 5.95 0.00 36.54 3.16
2596 3014 1.422781 CATCACCCTGGCTGGACATAT 59.577 52.381 12.58 0.00 38.35 1.78
2605 3023 3.825143 ATAAAATTGCATCACCCTGGC 57.175 42.857 0.00 0.00 0.00 4.85
2635 3054 5.617528 ACGGGAAATGGGTTTAAAAAGTT 57.382 34.783 0.00 0.00 0.00 2.66
2638 3057 4.163649 ACCAACGGGAAATGGGTTTAAAAA 59.836 37.500 0.00 0.00 41.17 1.94
2643 3062 2.679429 TACCAACGGGAAATGGGTTT 57.321 45.000 0.00 0.00 41.17 3.27
2647 3066 2.215196 CGGTATACCAACGGGAAATGG 58.785 52.381 21.76 0.00 42.60 3.16
2673 3092 7.100458 ACAAAGATTGATAATGTACTTGGCC 57.900 36.000 0.00 0.00 0.00 5.36
2716 3154 5.788450 AGCATAAATCCCTTAGACTCGATG 58.212 41.667 0.00 0.00 0.00 3.84
2748 3186 7.882791 TCCTCTAATGTCAAGCTAACAAAATGA 59.117 33.333 6.00 0.00 0.00 2.57
2820 3262 6.340962 ACAAGGTTAGGGTATTTCAAAAGC 57.659 37.500 0.00 0.00 0.00 3.51
2831 3273 3.323775 TCTGAAGGAACAAGGTTAGGGT 58.676 45.455 0.00 0.00 0.00 4.34
2839 3281 3.658709 GACCTCACTCTGAAGGAACAAG 58.341 50.000 0.98 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.