Multiple sequence alignment - TraesCS2B01G511100

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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 TraesCS2B01G511100 chr2B 100.000 3626 0 0 1 3626 706792565 706788940 0.000000e+00 6697.0
1 TraesCS2B01G511100 chr2B 85.865 1705 200 24 1716 3398 758898313 758899998 0.000000e+00 1775.0
2 TraesCS2B01G511100 chr2B 84.736 1533 219 12 1 1524 758896677 758898203 0.000000e+00 1520.0
3 TraesCS2B01G511100 chr2B 76.042 1152 245 20 3 1129 758666504 758667649 1.460000e-158 569.0
4 TraesCS2B01G511100 chr2B 78.223 349 52 9 3255 3579 706920915 706920567 6.140000e-48 202.0
5 TraesCS2B01G511100 chr2B 77.485 342 53 9 3262 3579 706729301 706728960 2.220000e-42 183.0
6 TraesCS2B01G511100 chr2B 74.545 440 87 22 2541 2970 707656576 707656152 6.230000e-38 169.0
7 TraesCS2B01G511100 chr2B 79.412 136 21 5 2858 2991 707518531 707518401 4.990000e-14 89.8
8 TraesCS2B01G511100 chr2D 81.512 3716 503 108 1 3626 585696009 585692388 0.000000e+00 2887.0
9 TraesCS2B01G511100 chr2D 85.815 1699 210 22 1716 3398 619575040 619576723 0.000000e+00 1773.0
10 TraesCS2B01G511100 chr2D 83.353 1658 218 23 1 1607 619573313 619574963 0.000000e+00 1480.0
11 TraesCS2B01G511100 chr2D 81.646 1106 198 5 7 1109 585740278 585739175 0.000000e+00 913.0
12 TraesCS2B01G511100 chr2D 82.993 1029 135 17 1758 2778 585738381 585737385 0.000000e+00 894.0
13 TraesCS2B01G511100 chr2D 76.087 1150 248 16 3 1129 619566217 619567362 3.140000e-160 575.0
14 TraesCS2B01G511100 chr2D 77.205 737 95 34 2869 3579 585684953 585684264 2.660000e-96 363.0
15 TraesCS2B01G511100 chr2A 85.074 1896 223 26 1757 3622 719737820 719735955 0.000000e+00 1879.0
16 TraesCS2B01G511100 chr2A 82.857 1995 262 46 1439 3394 751173081 751175034 0.000000e+00 1716.0
17 TraesCS2B01G511100 chr2A 85.776 1392 158 25 1659 3045 751014968 751016324 0.000000e+00 1437.0
18 TraesCS2B01G511100 chr2A 85.868 1302 144 24 1747 3045 751048515 751049779 0.000000e+00 1349.0
19 TraesCS2B01G511100 chr2A 84.207 1355 201 9 1 1343 751037492 751038845 0.000000e+00 1304.0
20 TraesCS2B01G511100 chr2A 82.632 1474 210 25 7 1470 751013524 751014961 0.000000e+00 1262.0
21 TraesCS2B01G511100 chr2A 84.713 870 130 3 1 868 751172153 751173021 0.000000e+00 867.0
22 TraesCS2B01G511100 chr2A 87.785 745 78 9 2063 2803 751055338 751056073 0.000000e+00 859.0
23 TraesCS2B01G511100 chr2A 78.444 617 114 12 2796 3398 751056917 751057528 5.680000e-103 385.0
24 TraesCS2B01G511100 chr6B 75.737 441 87 16 2540 2974 698990319 698990745 1.710000e-48 204.0


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 TraesCS2B01G511100 chr2B 706788940 706792565 3625 True 6697.0 6697 100.0000 1 3626 1 chr2B.!!$R2 3625
1 TraesCS2B01G511100 chr2B 758896677 758899998 3321 False 1647.5 1775 85.3005 1 3398 2 chr2B.!!$F2 3397
2 TraesCS2B01G511100 chr2B 758666504 758667649 1145 False 569.0 569 76.0420 3 1129 1 chr2B.!!$F1 1126
3 TraesCS2B01G511100 chr2D 585692388 585696009 3621 True 2887.0 2887 81.5120 1 3626 1 chr2D.!!$R2 3625
4 TraesCS2B01G511100 chr2D 619573313 619576723 3410 False 1626.5 1773 84.5840 1 3398 2 chr2D.!!$F2 3397
5 TraesCS2B01G511100 chr2D 585737385 585740278 2893 True 903.5 913 82.3195 7 2778 2 chr2D.!!$R3 2771
6 TraesCS2B01G511100 chr2D 619566217 619567362 1145 False 575.0 575 76.0870 3 1129 1 chr2D.!!$F1 1126
7 TraesCS2B01G511100 chr2D 585684264 585684953 689 True 363.0 363 77.2050 2869 3579 1 chr2D.!!$R1 710
8 TraesCS2B01G511100 chr2A 719735955 719737820 1865 True 1879.0 1879 85.0740 1757 3622 1 chr2A.!!$R1 1865
9 TraesCS2B01G511100 chr2A 751013524 751016324 2800 False 1349.5 1437 84.2040 7 3045 2 chr2A.!!$F3 3038
10 TraesCS2B01G511100 chr2A 751048515 751049779 1264 False 1349.0 1349 85.8680 1747 3045 1 chr2A.!!$F2 1298
11 TraesCS2B01G511100 chr2A 751037492 751038845 1353 False 1304.0 1304 84.2070 1 1343 1 chr2A.!!$F1 1342
12 TraesCS2B01G511100 chr2A 751172153 751175034 2881 False 1291.5 1716 83.7850 1 3394 2 chr2A.!!$F5 3393
13 TraesCS2B01G511100 chr2A 751055338 751057528 2190 False 622.0 859 83.1145 2063 3398 2 chr2A.!!$F4 1335

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
275 276 0.038166 GAGCTTCCATCACCCAACCA 59.962 55.0 0.0 0.0 0.0 3.67 F
396 403 0.195096 TACTCCTTGGGTGGGGACTT 59.805 55.0 0.0 0.0 0.0 3.01 F
1624 1879 0.251165 TAGTTGCCCAGTTGCCCTTC 60.251 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1869 0.403271 ACTGCATGAGAAGGGCAACT 59.597 50.0 0.00 0.00 37.06 3.16 R
2198 2545 0.616891 GTCCCCTACGTGGTGGAATT 59.383 55.0 4.37 0.00 37.07 2.17 R
3467 4708 0.251354 GATTCTCCACCTGCAGCTGA 59.749 55.0 20.43 2.98 0.00 4.26 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
28 29 3.435026 GCATATGGTACCACAACATCCCT 60.435 47.826 19.09 0.00 0.00 4.20
30 31 1.440618 TGGTACCACAACATCCCTGT 58.559 50.000 11.60 0.00 37.12 4.00
31 32 1.349688 TGGTACCACAACATCCCTGTC 59.650 52.381 11.60 0.00 33.36 3.51
34 35 1.377202 CCACAACATCCCTGTCCGG 60.377 63.158 0.00 0.00 33.36 5.14
85 86 1.219124 GATCACCGGCAGCTCTTCA 59.781 57.895 0.00 0.00 0.00 3.02
124 125 0.895530 CCGGCTCTGACCTTGTCTTA 59.104 55.000 0.00 0.00 33.15 2.10
146 147 3.421567 GACTCCAAAGGCCACACTT 57.578 52.632 5.01 0.00 0.00 3.16
157 158 1.555477 GCCACACTTTTTGGACAACG 58.445 50.000 0.00 0.00 36.02 4.10
180 181 2.437651 TGAACAACATCACCACCAGAGA 59.562 45.455 0.00 0.00 0.00 3.10
192 193 3.136443 ACCACCAGAGACATCAAAACTGA 59.864 43.478 0.00 0.00 0.00 3.41
275 276 0.038166 GAGCTTCCATCACCCAACCA 59.962 55.000 0.00 0.00 0.00 3.67
304 305 6.364701 CATCCTCCCAAATATGAGTTTACCA 58.635 40.000 0.00 0.00 0.00 3.25
370 371 1.925285 GCCCTGATGACCCATCCACA 61.925 60.000 4.69 0.00 39.87 4.17
391 392 0.613777 GTGACTACTCCTTGGGTGGG 59.386 60.000 0.00 0.00 0.00 4.61
396 403 0.195096 TACTCCTTGGGTGGGGACTT 59.805 55.000 0.00 0.00 0.00 3.01
407 420 2.270527 GGGACTTGAGCCTCCAGC 59.729 66.667 0.00 0.00 44.25 4.85
474 487 3.696045 TGGATGGTGTATTGGTCTTTGG 58.304 45.455 0.00 0.00 0.00 3.28
477 494 2.235016 TGGTGTATTGGTCTTTGGCAC 58.765 47.619 0.00 0.00 0.00 5.01
482 499 3.687212 TGTATTGGTCTTTGGCACGTATG 59.313 43.478 0.00 0.00 0.00 2.39
499 516 4.466370 ACGTATGAGAGAAAATCAGGTCCA 59.534 41.667 0.00 0.00 0.00 4.02
501 518 6.323996 ACGTATGAGAGAAAATCAGGTCCATA 59.676 38.462 0.00 0.00 0.00 2.74
502 519 6.865726 CGTATGAGAGAAAATCAGGTCCATAG 59.134 42.308 0.00 0.00 0.00 2.23
513 531 1.278127 AGGTCCATAGTGTCCCAAACG 59.722 52.381 0.00 0.00 0.00 3.60
548 566 3.009143 GGGGGTGAGTTCTACTTGACATT 59.991 47.826 0.00 0.00 0.00 2.71
549 567 4.003648 GGGGTGAGTTCTACTTGACATTG 58.996 47.826 0.00 0.00 0.00 2.82
604 622 4.262089 TGCACCACACGGGCATGA 62.262 61.111 0.00 0.00 42.05 3.07
628 646 1.529796 TTCCTGGCGTGGAACAACT 59.470 52.632 7.56 0.00 44.16 3.16
645 663 7.110155 GGAACAACTACTCATTATCTTGGGAA 58.890 38.462 0.00 0.00 0.00 3.97
648 666 8.375493 ACAACTACTCATTATCTTGGGAAGTA 57.625 34.615 0.00 0.00 0.00 2.24
680 698 1.486726 CCCAGGTCCTAACTGTGATCC 59.513 57.143 0.00 0.00 34.16 3.36
684 702 3.385111 CAGGTCCTAACTGTGATCCCTAC 59.615 52.174 0.00 0.00 0.00 3.18
760 778 3.071874 AGTGCCTCGATGGATTTGAAA 57.928 42.857 5.24 0.00 38.35 2.69
805 823 3.774216 AGGATGTCAGAGAAAGAAGGAGG 59.226 47.826 0.00 0.00 0.00 4.30
842 860 5.360591 AGGAGATAGTTTCATTACCTTGCG 58.639 41.667 0.00 0.00 0.00 4.85
853 871 4.094294 TCATTACCTTGCGTAACATGAAGC 59.906 41.667 0.00 0.00 39.75 3.86
854 872 2.185004 ACCTTGCGTAACATGAAGCT 57.815 45.000 0.00 0.00 0.00 3.74
874 892 2.476619 CTGCCTGACAAGTTCTTGTACG 59.523 50.000 16.57 10.97 34.90 3.67
949 967 0.298707 CACTGCATACGCTTACGCTG 59.701 55.000 0.00 0.00 45.53 5.18
996 1023 0.889306 ACCAGTCGAGGTGCTTAGTC 59.111 55.000 0.00 0.00 41.30 2.59
1005 1032 0.912486 GGTGCTTAGTCTGGATGGGT 59.088 55.000 0.00 0.00 0.00 4.51
1021 1048 1.142667 TGGGTGAGCTTGTTGACATGA 59.857 47.619 0.00 0.00 0.00 3.07
1136 1175 5.356751 TGTGTGATGGATTGCCTATTAACAC 59.643 40.000 0.00 0.00 34.31 3.32
1138 1177 5.589855 TGTGATGGATTGCCTATTAACACAG 59.410 40.000 0.00 0.00 34.31 3.66
1145 1184 6.770785 GGATTGCCTATTAACACAGGATTACA 59.229 38.462 4.21 0.00 33.42 2.41
1150 1189 7.390440 TGCCTATTAACACAGGATTACATATGC 59.610 37.037 1.58 0.00 33.42 3.14
1155 1194 2.481568 CACAGGATTACATATGCGGCTG 59.518 50.000 1.58 0.00 0.00 4.85
1198 1250 7.307131 AGTTTACTAAGGTGGCTACTACAAA 57.693 36.000 0.00 0.00 0.00 2.83
1228 1280 3.198872 GTGGCAGTTAGAGCTATGTTCC 58.801 50.000 0.00 0.00 0.00 3.62
1269 1321 3.838244 TTGTGCTCTCCTGTTACAGTT 57.162 42.857 11.68 0.00 0.00 3.16
1283 1335 6.128282 CCTGTTACAGTTTGAAGACGCATAAT 60.128 38.462 11.68 0.00 0.00 1.28
1292 1344 4.252878 TGAAGACGCATAATGAGCTTTGA 58.747 39.130 0.00 0.00 0.00 2.69
1307 1359 8.707796 ATGAGCTTTGATATTGGATGAAGATT 57.292 30.769 0.00 0.00 0.00 2.40
1353 1433 6.735678 ATGTTCTTGCATACGTATGTTCAA 57.264 33.333 30.63 24.99 36.11 2.69
1388 1473 3.913799 TGTTCTCCCTACCCATCAAAAGA 59.086 43.478 0.00 0.00 0.00 2.52
1390 1475 5.163034 TGTTCTCCCTACCCATCAAAAGAAA 60.163 40.000 0.00 0.00 0.00 2.52
1414 1499 6.889301 TCATGTTTTCAGATTCTGCTTCTT 57.111 33.333 8.89 0.00 0.00 2.52
1453 1538 2.984471 GCATCGTCTTCGTCAGTGTTTA 59.016 45.455 0.00 0.00 38.33 2.01
1514 1607 3.129462 TCATGAGCCTATATGCTAGCGTC 59.871 47.826 14.00 0.00 42.95 5.19
1530 1623 1.157870 CGTCTTTGGTGACTGCGGTT 61.158 55.000 0.00 0.00 35.00 4.44
1532 1625 1.529865 GTCTTTGGTGACTGCGGTTAC 59.470 52.381 12.02 12.02 34.39 2.50
1533 1626 1.139256 TCTTTGGTGACTGCGGTTACA 59.861 47.619 20.87 8.17 34.21 2.41
1534 1627 1.531149 CTTTGGTGACTGCGGTTACAG 59.469 52.381 20.87 7.37 43.59 2.74
1598 1853 6.126409 ACCTTACTCCATGTTTTGTGAGAAA 58.874 36.000 1.97 0.00 0.00 2.52
1608 1863 9.912634 CCATGTTTTGTGAGAAAATACAATAGT 57.087 29.630 0.00 0.00 36.75 2.12
1611 1866 9.243637 TGTTTTGTGAGAAAATACAATAGTTGC 57.756 29.630 0.00 0.00 36.75 4.17
1612 1867 8.699749 GTTTTGTGAGAAAATACAATAGTTGCC 58.300 33.333 0.00 0.00 36.75 4.52
1613 1868 6.509418 TGTGAGAAAATACAATAGTTGCCC 57.491 37.500 0.00 0.00 0.00 5.36
1614 1869 6.007076 TGTGAGAAAATACAATAGTTGCCCA 58.993 36.000 0.00 0.00 0.00 5.36
1615 1870 6.150976 TGTGAGAAAATACAATAGTTGCCCAG 59.849 38.462 0.00 0.00 0.00 4.45
1616 1871 6.151144 GTGAGAAAATACAATAGTTGCCCAGT 59.849 38.462 0.00 0.00 0.00 4.00
1617 1872 6.719370 TGAGAAAATACAATAGTTGCCCAGTT 59.281 34.615 0.00 0.00 0.00 3.16
1618 1873 6.924111 AGAAAATACAATAGTTGCCCAGTTG 58.076 36.000 0.00 0.00 0.00 3.16
1619 1874 4.718940 AATACAATAGTTGCCCAGTTGC 57.281 40.909 0.00 0.00 0.00 4.17
1620 1875 1.256812 ACAATAGTTGCCCAGTTGCC 58.743 50.000 0.00 0.00 0.00 4.52
1621 1876 0.532115 CAATAGTTGCCCAGTTGCCC 59.468 55.000 0.00 0.00 0.00 5.36
1622 1877 0.409484 AATAGTTGCCCAGTTGCCCT 59.591 50.000 0.00 0.00 0.00 5.19
1623 1878 0.409484 ATAGTTGCCCAGTTGCCCTT 59.591 50.000 0.00 0.00 0.00 3.95
1624 1879 0.251165 TAGTTGCCCAGTTGCCCTTC 60.251 55.000 0.00 0.00 0.00 3.46
1669 1957 8.753497 ATATATGTTTTTGGTCTTTCTCTCCC 57.247 34.615 0.00 0.00 0.00 4.30
1673 1961 2.723530 TTGGTCTTTCTCTCCCCTCT 57.276 50.000 0.00 0.00 0.00 3.69
1693 1981 6.044871 CCCTCTCCTTCCACCTAAATCAATAT 59.955 42.308 0.00 0.00 0.00 1.28
1696 1984 8.980481 TCTCCTTCCACCTAAATCAATATTTC 57.020 34.615 0.00 0.00 36.67 2.17
1705 1993 6.207417 ACCTAAATCAATATTTCGCCTGGATG 59.793 38.462 0.00 0.00 36.67 3.51
1717 2005 2.009042 GCCTGGATGTACACAGTGCTC 61.009 57.143 11.36 0.00 32.90 4.26
1774 2110 5.822519 TGTTGTCTTTTGCAGTCAGTAAGAT 59.177 36.000 0.00 0.00 31.76 2.40
1787 2123 3.056536 TCAGTAAGATGACAGGTGCACTC 60.057 47.826 17.98 7.24 0.00 3.51
1817 2153 0.325933 TCCCAGTCATGGCAAGTCTG 59.674 55.000 9.49 9.49 46.19 3.51
1870 2206 1.063806 CGCAAGTCGAGAGGTTGAAG 58.936 55.000 0.00 0.00 41.67 3.02
1879 2215 3.506455 TCGAGAGGTTGAAGAAGATTCGT 59.494 43.478 0.00 0.00 0.00 3.85
1951 2296 2.603075 TTAATTCCTGGCAGGCAAGT 57.397 45.000 29.02 22.31 34.61 3.16
1956 2301 1.207488 TCCTGGCAGGCAAGTACCAT 61.207 55.000 29.02 0.00 34.61 3.55
1987 2332 3.327172 ACCCATGAATTTTGTGATGCCAA 59.673 39.130 0.00 0.00 0.00 4.52
2004 2349 2.802247 GCCAAAACAACTGAGCAATTCC 59.198 45.455 0.00 0.00 0.00 3.01
2059 2405 4.260170 GTGGATCAGCTTCAAAGACATCT 58.740 43.478 0.00 0.00 0.00 2.90
2072 2418 3.054802 AAAGACATCTTCCCTGCTACAGG 60.055 47.826 6.65 6.65 42.25 4.00
2163 2510 6.929049 TCCACTTTGACAATTACAGTAGTGAG 59.071 38.462 13.14 6.05 35.65 3.51
2165 2512 7.604164 CCACTTTGACAATTACAGTAGTGAGAT 59.396 37.037 13.14 0.00 35.65 2.75
2182 2529 6.686130 GTGAGATGCACTTTTTCATTTCTG 57.314 37.500 0.00 0.00 44.27 3.02
2183 2530 5.118203 GTGAGATGCACTTTTTCATTTCTGC 59.882 40.000 0.00 0.00 44.27 4.26
2184 2531 4.232221 AGATGCACTTTTTCATTTCTGCG 58.768 39.130 0.00 0.00 0.00 5.18
2185 2532 2.741612 TGCACTTTTTCATTTCTGCGG 58.258 42.857 0.00 0.00 0.00 5.69
2198 2545 8.675705 TTCATTTCTGCGGATTAATCTGAATA 57.324 30.769 25.44 7.32 35.13 1.75
2201 2548 9.903682 CATTTCTGCGGATTAATCTGAATAATT 57.096 29.630 25.44 9.50 35.13 1.40
2215 2562 3.118186 TGAATAATTCCACCACGTAGGGG 60.118 47.826 0.00 0.00 43.89 4.79
2359 2706 8.923683 GTTAGACTTCTTGGTTACTGTATTCAC 58.076 37.037 0.00 0.00 0.00 3.18
2423 2770 7.556635 ACAAAAGCTTAGACTACTTCCTGTTTT 59.443 33.333 0.00 0.00 0.00 2.43
2429 2776 7.817962 GCTTAGACTACTTCCTGTTTTGTATGA 59.182 37.037 0.00 0.00 0.00 2.15
2430 2777 9.706691 CTTAGACTACTTCCTGTTTTGTATGAA 57.293 33.333 0.00 0.00 0.00 2.57
2593 2941 4.016851 TCAAAGGGGTAGCTAGAGGACTTA 60.017 45.833 0.00 0.00 0.00 2.24
2657 3006 5.942236 AGATCTCAAAGCAAGCAACATCTTA 59.058 36.000 0.00 0.00 0.00 2.10
2687 3036 4.752101 GTGGAGATGAGACCCAAAATATCG 59.248 45.833 0.00 0.00 0.00 2.92
2708 3057 3.118665 CGGATTTTGGAATGGCAAGGATT 60.119 43.478 0.00 0.00 0.00 3.01
2717 3066 4.323715 GGAATGGCAAGGATTTTTGGTGAT 60.324 41.667 0.00 0.00 0.00 3.06
2785 3142 5.817784 AGTAGTAACTCCTGCACTCTAGAA 58.182 41.667 0.00 0.00 0.00 2.10
2835 4045 5.825507 AGCTTCAACTCATCAGTTTTTGTC 58.174 37.500 0.00 0.00 41.24 3.18
2977 4187 0.931005 GGTTAAAGATCAGCTCGCCG 59.069 55.000 0.00 0.00 0.00 6.46
3038 4253 3.636300 TGTAAGTGTTGCCAAATGCTTCT 59.364 39.130 0.00 0.00 42.00 2.85
3096 4318 5.106712 TGTTTATGAATGCTCGACCTTGTTC 60.107 40.000 0.00 0.00 0.00 3.18
3131 4353 4.634012 TCCTGAAAGAAGGAAAATCCGA 57.366 40.909 0.00 0.00 43.57 4.55
3155 4377 3.402628 TTTCCTAGACACAGTGCTTCC 57.597 47.619 0.00 0.00 0.00 3.46
3157 4379 0.108615 CCTAGACACAGTGCTTCCGG 60.109 60.000 0.00 0.00 0.00 5.14
3205 4427 2.295349 CTGTGCATCCATATTGGCCTTC 59.705 50.000 3.32 0.00 37.47 3.46
3329 4551 2.106683 CCGTCGGGAGGAAACATGC 61.107 63.158 2.34 0.00 34.06 4.06
3357 4579 2.301583 AGAAGCAAGGGAGAACTCTGTC 59.698 50.000 1.86 0.00 0.00 3.51
3363 4585 4.392940 CAAGGGAGAACTCTGTCAACAAT 58.607 43.478 1.86 0.00 0.00 2.71
3467 4708 0.755327 GCCAAGTGGGTTTCAGTGGT 60.755 55.000 0.00 0.00 39.65 4.16
3524 4770 3.522553 CCCTCGTCTGATGGTTAGTTTC 58.477 50.000 0.00 0.00 0.00 2.78
3623 4869 0.915872 ACTGCTGGGATCCATGACCA 60.916 55.000 15.23 0.29 30.82 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.435026 GGGATGTTGTGGTACCATATGCT 60.435 47.826 19.72 3.29 0.00 3.79
28 29 0.539518 CCCACACATATGTCCGGACA 59.460 55.000 37.79 37.79 46.44 4.02
30 31 0.828022 GACCCACACATATGTCCGGA 59.172 55.000 17.98 0.00 36.72 5.14
31 32 0.529773 CGACCCACACATATGTCCGG 60.530 60.000 5.07 9.13 36.72 5.14
34 35 2.864343 GTTAGCGACCCACACATATGTC 59.136 50.000 5.07 0.00 36.72 3.06
124 125 1.299976 GTGGCCTTTGGAGTCCGAT 59.700 57.895 3.32 0.00 0.00 4.18
141 142 4.156922 TGTTCATCGTTGTCCAAAAAGTGT 59.843 37.500 0.00 0.00 0.00 3.55
146 147 4.703645 TGTTGTTCATCGTTGTCCAAAA 57.296 36.364 0.00 0.00 0.00 2.44
192 193 1.069204 CGGTGTCCAGCAGTATAGCAT 59.931 52.381 0.00 0.00 36.85 3.79
218 219 1.619654 TTTGGCAACCTGATGACCAG 58.380 50.000 0.00 0.00 42.55 4.00
242 243 5.157940 TGGAAGCTCTGCCATATATCTTC 57.842 43.478 0.00 0.00 0.00 2.87
243 244 5.250082 TGATGGAAGCTCTGCCATATATCTT 59.750 40.000 9.35 0.00 44.60 2.40
275 276 4.230502 ACTCATATTTGGGAGGATGGTGTT 59.769 41.667 0.00 0.00 35.45 3.32
304 305 1.102978 GGTTGGTGTTGTTGCTCAGT 58.897 50.000 0.00 0.00 0.00 3.41
370 371 1.978580 CCACCCAAGGAGTAGTCACTT 59.021 52.381 0.00 0.00 34.21 3.16
442 455 0.957395 CACCATCCAACGCAGCTCTT 60.957 55.000 0.00 0.00 0.00 2.85
474 487 4.184629 ACCTGATTTTCTCTCATACGTGC 58.815 43.478 0.00 0.00 0.00 5.34
477 494 5.011090 TGGACCTGATTTTCTCTCATACG 57.989 43.478 0.00 0.00 0.00 3.06
482 499 5.983540 ACACTATGGACCTGATTTTCTCTC 58.016 41.667 0.00 0.00 0.00 3.20
499 516 2.631062 TGACAGTCGTTTGGGACACTAT 59.369 45.455 0.00 0.00 39.29 2.12
501 518 0.828022 TGACAGTCGTTTGGGACACT 59.172 50.000 0.00 0.00 39.29 3.55
502 519 1.658994 TTGACAGTCGTTTGGGACAC 58.341 50.000 0.00 0.00 39.29 3.67
513 531 2.432510 CTCACCCCCTCTATTGACAGTC 59.567 54.545 0.00 0.00 0.00 3.51
604 622 2.214376 TTCCACGCCAGGAATTTCAT 57.786 45.000 0.57 0.00 42.56 2.57
651 669 1.485294 TAGGACCTGGGCGCTCAAAA 61.485 55.000 13.01 0.00 0.00 2.44
663 681 2.950990 AGGGATCACAGTTAGGACCT 57.049 50.000 0.00 0.00 0.00 3.85
760 778 5.584551 AGGGAAAAGTTAAGACCATCAGT 57.415 39.130 0.00 0.00 0.00 3.41
805 823 0.037326 TCTCCTCGACCACAATGCAC 60.037 55.000 0.00 0.00 0.00 4.57
842 860 2.426522 TGTCAGGCAGCTTCATGTTAC 58.573 47.619 0.00 0.00 0.00 2.50
874 892 3.119101 TGGTCGAAGCTTCTATTCCTGAC 60.119 47.826 23.50 19.09 0.00 3.51
949 967 1.066303 CATGCCGAGACTACTCAGGTC 59.934 57.143 0.00 0.00 42.72 3.85
996 1023 1.171308 CAACAAGCTCACCCATCCAG 58.829 55.000 0.00 0.00 0.00 3.86
1005 1032 3.251729 GCTTCTTCATGTCAACAAGCTCA 59.748 43.478 0.00 0.00 34.64 4.26
1021 1048 0.687354 AGACCATCACCACGCTTCTT 59.313 50.000 0.00 0.00 0.00 2.52
1136 1175 3.044235 TCAGCCGCATATGTAATCCTG 57.956 47.619 4.29 4.93 0.00 3.86
1138 1177 6.494893 TTTTATCAGCCGCATATGTAATCC 57.505 37.500 4.29 0.00 0.00 3.01
1145 1184 6.264292 TGGTACAAATTTTATCAGCCGCATAT 59.736 34.615 0.00 0.00 31.92 1.78
1150 1189 5.560966 AGTGGTACAAATTTTATCAGCCG 57.439 39.130 0.00 0.00 44.16 5.52
1198 1250 3.629398 GCTCTAACTGCCACATGCTTTAT 59.371 43.478 0.00 0.00 42.00 1.40
1228 1280 5.406175 ACAAATGCGGAAGAATGTTTCAATG 59.594 36.000 0.00 0.00 0.00 2.82
1269 1321 4.694982 TCAAAGCTCATTATGCGTCTTCAA 59.305 37.500 0.00 0.00 35.28 2.69
1283 1335 9.803507 ATAATCTTCATCCAATATCAAAGCTCA 57.196 29.630 0.00 0.00 0.00 4.26
1330 1387 6.735678 TTGAACATACGTATGCAAGAACAT 57.264 33.333 30.68 9.94 37.19 2.71
1353 1433 2.766828 GGGAGAACACAGCTGGTAGTAT 59.233 50.000 19.93 6.17 0.00 2.12
1388 1473 7.893658 AGAAGCAGAATCTGAAAACATGATTT 58.106 30.769 15.38 0.00 32.44 2.17
1390 1475 7.463961 AAGAAGCAGAATCTGAAAACATGAT 57.536 32.000 15.38 0.00 32.44 2.45
1408 1493 6.920210 GCCAAATGACAGGATTATAAAGAAGC 59.080 38.462 0.00 0.00 0.00 3.86
1414 1499 6.061441 ACGATGCCAAATGACAGGATTATAA 58.939 36.000 0.00 0.00 0.00 0.98
1514 1607 1.531149 CTGTAACCGCAGTCACCAAAG 59.469 52.381 0.00 0.00 0.00 2.77
1530 1623 5.054477 GGAAGCAAGTTTGTGTCTACTGTA 58.946 41.667 0.00 0.00 0.00 2.74
1532 1625 3.251004 GGGAAGCAAGTTTGTGTCTACTG 59.749 47.826 0.00 0.00 0.00 2.74
1533 1626 3.118038 TGGGAAGCAAGTTTGTGTCTACT 60.118 43.478 0.00 0.00 0.00 2.57
1534 1627 3.211045 TGGGAAGCAAGTTTGTGTCTAC 58.789 45.455 0.00 0.00 0.00 2.59
1537 1739 1.269257 GCTGGGAAGCAAGTTTGTGTC 60.269 52.381 0.00 0.00 34.41 3.67
1562 1764 6.264518 ACATGGAGTAAGGTACAACAAAAAGG 59.735 38.462 0.00 0.00 0.00 3.11
1563 1818 7.272037 ACATGGAGTAAGGTACAACAAAAAG 57.728 36.000 0.00 0.00 0.00 2.27
1598 1853 3.447229 GGCAACTGGGCAACTATTGTATT 59.553 43.478 0.00 0.00 42.77 1.89
1607 1862 1.527433 GAGAAGGGCAACTGGGCAAC 61.527 60.000 0.00 0.00 45.66 4.17
1608 1863 1.228552 GAGAAGGGCAACTGGGCAA 60.229 57.895 0.00 0.00 45.66 4.52
1609 1864 1.792757 ATGAGAAGGGCAACTGGGCA 61.793 55.000 0.00 0.00 45.66 5.36
1610 1865 1.000396 ATGAGAAGGGCAACTGGGC 60.000 57.895 0.00 0.00 42.44 5.36
1611 1866 1.318158 GCATGAGAAGGGCAACTGGG 61.318 60.000 0.00 0.00 0.00 4.45
1612 1867 0.609957 TGCATGAGAAGGGCAACTGG 60.610 55.000 0.00 0.00 34.05 4.00
1613 1868 0.809385 CTGCATGAGAAGGGCAACTG 59.191 55.000 0.00 0.00 37.06 3.16
1614 1869 0.403271 ACTGCATGAGAAGGGCAACT 59.597 50.000 0.00 0.00 37.06 3.16
1615 1870 2.113860 TACTGCATGAGAAGGGCAAC 57.886 50.000 0.00 0.00 37.06 4.17
1616 1871 4.712051 ATATACTGCATGAGAAGGGCAA 57.288 40.909 0.00 0.00 37.06 4.52
1617 1872 5.723405 AGATATATACTGCATGAGAAGGGCA 59.277 40.000 0.00 0.00 35.96 5.36
1618 1873 6.232581 AGATATATACTGCATGAGAAGGGC 57.767 41.667 0.00 0.00 0.00 5.19
1656 1911 1.007842 AGGAGAGGGGAGAGAAAGACC 59.992 57.143 0.00 0.00 0.00 3.85
1666 1954 1.098589 TTAGGTGGAAGGAGAGGGGA 58.901 55.000 0.00 0.00 0.00 4.81
1669 1957 4.844349 TTGATTTAGGTGGAAGGAGAGG 57.156 45.455 0.00 0.00 0.00 3.69
1673 1961 6.262273 GCGAAATATTGATTTAGGTGGAAGGA 59.738 38.462 0.00 0.00 35.33 3.36
1693 1981 1.346395 ACTGTGTACATCCAGGCGAAA 59.654 47.619 15.62 0.00 32.90 3.46
1696 1984 1.361668 GCACTGTGTACATCCAGGCG 61.362 60.000 15.62 8.80 32.90 5.52
1705 1993 4.457834 AGTAGATTGGAGCACTGTGTAC 57.542 45.455 9.86 3.96 0.00 2.90
1774 2110 2.497138 CAATCTTGAGTGCACCTGTCA 58.503 47.619 14.63 8.31 0.00 3.58
1778 2114 3.731716 TGCAATCTTGAGTGCACCT 57.268 47.368 19.57 0.04 45.52 4.00
1787 2123 2.189594 TGACTGGGAGTGCAATCTTG 57.810 50.000 14.60 7.03 0.00 3.02
1817 2153 4.083110 AGACAAATGCACACAAGTATCAGC 60.083 41.667 0.00 0.00 0.00 4.26
1951 2296 2.131854 CATGGGTCCCTTGGTATGGTA 58.868 52.381 14.88 0.00 0.00 3.25
1956 2301 4.093011 CAAAATTCATGGGTCCCTTGGTA 58.907 43.478 20.87 11.58 30.78 3.25
1987 2332 3.820467 TCATCGGAATTGCTCAGTTGTTT 59.180 39.130 0.00 0.00 0.00 2.83
2004 2349 9.852091 TCTGAATTCTCATCATATAGTTCATCG 57.148 33.333 7.05 0.00 0.00 3.84
2072 2418 3.499918 CACATTGGAGTCAGAGAAACCAC 59.500 47.826 0.00 0.00 0.00 4.16
2139 2486 6.929049 TCTCACTACTGTAATTGTCAAAGTGG 59.071 38.462 17.30 4.78 33.52 4.00
2163 2510 3.365820 CCGCAGAAATGAAAAAGTGCATC 59.634 43.478 0.00 0.00 0.00 3.91
2165 2512 2.360483 TCCGCAGAAATGAAAAAGTGCA 59.640 40.909 0.00 0.00 0.00 4.57
2171 2518 7.389803 TCAGATTAATCCGCAGAAATGAAAA 57.610 32.000 11.92 0.00 0.00 2.29
2179 2526 7.173218 GTGGAATTATTCAGATTAATCCGCAGA 59.827 37.037 11.92 3.04 0.00 4.26
2180 2527 7.301054 GTGGAATTATTCAGATTAATCCGCAG 58.699 38.462 11.92 0.72 0.00 5.18
2181 2528 6.206634 GGTGGAATTATTCAGATTAATCCGCA 59.793 38.462 11.92 0.00 0.00 5.69
2182 2529 6.206634 TGGTGGAATTATTCAGATTAATCCGC 59.793 38.462 11.92 0.98 0.00 5.54
2183 2530 7.571244 CGTGGTGGAATTATTCAGATTAATCCG 60.571 40.741 11.92 1.83 0.00 4.18
2184 2531 7.228706 ACGTGGTGGAATTATTCAGATTAATCC 59.771 37.037 11.92 0.00 0.00 3.01
2185 2532 8.154649 ACGTGGTGGAATTATTCAGATTAATC 57.845 34.615 7.41 7.41 0.00 1.75
2198 2545 0.616891 GTCCCCTACGTGGTGGAATT 59.383 55.000 4.37 0.00 37.07 2.17
2201 2548 1.909781 GTGTCCCCTACGTGGTGGA 60.910 63.158 0.00 0.00 34.28 4.02
2215 2562 0.890996 CCTTGCCACCTTCCAGTGTC 60.891 60.000 0.00 0.00 35.93 3.67
2287 2634 8.994429 TTGAGATGAGAACTACTTCATTTCTC 57.006 34.615 4.02 4.02 43.75 2.87
2309 2656 2.754552 AGTTTCTGTGCTGCACTTTTGA 59.245 40.909 30.43 19.98 35.11 2.69
2315 2662 3.971032 AACTAAGTTTCTGTGCTGCAC 57.029 42.857 25.15 25.15 34.56 4.57
2442 2789 9.894783 CTCCTATTCTAAATGCAAGAATCATTG 57.105 33.333 13.99 5.56 41.61 2.82
2455 2802 5.573380 TCAGGCATGCTCCTATTCTAAAT 57.427 39.130 18.92 0.00 33.95 1.40
2458 2805 3.906218 ACATCAGGCATGCTCCTATTCTA 59.094 43.478 18.92 0.00 35.65 2.10
2463 2810 3.711190 TCTTAACATCAGGCATGCTCCTA 59.289 43.478 18.92 1.15 35.65 2.94
2536 2884 2.101783 TGTTGGCCAATCAAGCATAGG 58.898 47.619 23.66 0.00 0.00 2.57
2593 2941 4.474651 TCTTGAATCATGGTGGAGGTACAT 59.525 41.667 0.00 0.00 0.00 2.29
2657 3006 2.441001 GGGTCTCATCTCCACATCCAAT 59.559 50.000 0.00 0.00 0.00 3.16
2687 3036 4.492494 AATCCTTGCCATTCCAAAATCC 57.508 40.909 0.00 0.00 0.00 3.01
2696 3045 4.914177 ATCACCAAAAATCCTTGCCATT 57.086 36.364 0.00 0.00 0.00 3.16
2717 3066 3.670625 AGTATTCGCTTGTTGCTGGTTA 58.329 40.909 0.00 0.00 40.11 2.85
2732 3081 3.131396 CCCGACAACATGCCTAGTATTC 58.869 50.000 0.00 0.00 0.00 1.75
2812 4022 5.221126 GGACAAAAACTGATGAGTTGAAGCT 60.221 40.000 0.00 0.00 41.87 3.74
2822 4032 4.311816 AGCAAGTGGACAAAAACTGATG 57.688 40.909 0.00 0.00 0.00 3.07
2825 4035 3.613737 CACAAGCAAGTGGACAAAAACTG 59.386 43.478 0.97 0.00 35.88 3.16
2827 4037 3.843999 TCACAAGCAAGTGGACAAAAAC 58.156 40.909 8.43 0.00 39.93 2.43
2835 4045 3.243035 TGAATCGTTTCACAAGCAAGTGG 60.243 43.478 4.80 0.00 36.94 4.00
2977 4187 7.288810 TGGAAAATCCATTATAAGGTGATGC 57.711 36.000 0.00 0.00 42.67 3.91
3096 4318 0.329261 TCAGGAAGTTCCATGCCTGG 59.671 55.000 23.87 0.78 46.14 4.45
3155 4377 2.508887 GCAGTGAGCAGCTCTCCG 60.509 66.667 23.15 13.12 44.79 4.63
3205 4427 0.886490 GGGCAGTCTTGGACACACAG 60.886 60.000 0.52 0.00 34.60 3.66
3329 4551 1.002888 TCTCCCTTGCTTCTTCTGCAG 59.997 52.381 7.63 7.63 41.71 4.41
3357 4579 0.592637 TCGTCAGGCTTGCATTGTTG 59.407 50.000 0.00 0.00 0.00 3.33
3363 4585 2.819117 CTAGCGTCGTCAGGCTTGCA 62.819 60.000 0.00 0.00 41.03 4.08
3467 4708 0.251354 GATTCTCCACCTGCAGCTGA 59.749 55.000 20.43 2.98 0.00 4.26


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

AutoCloner maintained by Alex Coulton.