Multiple sequence alignment - TraesCS5A01G064800

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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 TraesCS5A01G064800 chr5A 100.000 2396 0 0 1 2396 70174279 70171884 0.000000e+00 4425.0
1 TraesCS5A01G064800 chr5A 87.119 295 37 1 367 661 70173856 70173563 1.370000e-87 333.0
2 TraesCS5A01G064800 chr5A 87.119 295 37 1 424 717 70173913 70173619 1.370000e-87 333.0
3 TraesCS5A01G064800 chr5D 91.337 658 28 5 1610 2264 74717801 74717170 0.000000e+00 872.0
4 TraesCS5A01G064800 chr5D 92.308 611 24 6 1749 2355 74760799 74760208 0.000000e+00 846.0
5 TraesCS5A01G064800 chr5D 83.951 405 34 14 1055 1448 486832652 486833036 2.260000e-95 359.0
6 TraesCS5A01G064800 chr5D 86.909 275 19 8 1452 1720 74761046 74760783 2.330000e-75 292.0
7 TraesCS5A01G064800 chr5D 86.364 198 17 8 11 201 486831596 486831790 8.680000e-50 207.0
8 TraesCS5A01G064800 chr5D 84.375 96 11 2 1258 1350 196875514 196875608 9.120000e-15 91.6
9 TraesCS5A01G064800 chr5B 91.447 608 31 9 1749 2355 77587524 77588111 0.000000e+00 815.0
10 TraesCS5A01G064800 chr5B 88.591 298 14 5 1610 1907 77643946 77644223 6.340000e-91 344.0
11 TraesCS5A01G064800 chr5B 93.750 160 7 3 2153 2312 77644471 77644627 1.110000e-58 237.0
12 TraesCS5A01G064800 chr5B 90.728 151 7 4 1577 1720 77587390 77587540 6.760000e-46 195.0
13 TraesCS5A01G064800 chr5B 95.745 47 2 0 2350 2396 509485250 509485204 2.550000e-10 76.8
14 TraesCS5A01G064800 chr5B 97.561 41 1 0 2356 2396 480655716 480655756 1.190000e-08 71.3
15 TraesCS5A01G064800 chr7D 91.115 574 47 3 791 1360 564687581 564687008 0.000000e+00 774.0
16 TraesCS5A01G064800 chr7D 85.340 382 45 8 1078 1449 104923212 104923592 3.740000e-103 385.0
17 TraesCS5A01G064800 chr7D 86.691 278 27 5 1188 1455 126879389 126879112 1.390000e-77 300.0
18 TraesCS5A01G064800 chr7D 88.511 235 24 1 435 669 564687848 564687617 5.040000e-72 281.0
19 TraesCS5A01G064800 chr7D 84.549 233 33 3 380 612 564687846 564687617 6.660000e-56 228.0
20 TraesCS5A01G064800 chr3A 85.444 687 67 11 3 663 142978180 142977501 0.000000e+00 684.0
21 TraesCS5A01G064800 chr6D 83.624 574 52 26 916 1448 7294662 7294090 3.560000e-138 501.0
22 TraesCS5A01G064800 chr6A 85.604 389 43 10 1078 1455 539235223 539235609 1.730000e-106 396.0
23 TraesCS5A01G064800 chr6A 100.000 41 0 0 2356 2396 540315037 540314997 2.550000e-10 76.8
24 TraesCS5A01G064800 chr2D 88.108 185 15 5 11 190 261767074 261766892 1.870000e-51 213.0
25 TraesCS5A01G064800 chr1A 88.679 106 12 0 96 201 394030221 394030116 1.930000e-26 130.0
26 TraesCS5A01G064800 chr1A 100.000 34 0 0 438 471 394030072 394030039 1.990000e-06 63.9
27 TraesCS5A01G064800 chr1A 100.000 33 0 0 382 414 394030071 394030039 7.150000e-06 62.1
28 TraesCS5A01G064800 chr3B 95.652 46 2 0 2351 2396 705590926 705590881 9.190000e-10 75.0
29 TraesCS5A01G064800 chr1B 95.652 46 2 0 2351 2396 568324739 568324784 9.190000e-10 75.0
30 TraesCS5A01G064800 chr1B 97.619 42 1 0 2355 2396 25246028 25245987 3.300000e-09 73.1
31 TraesCS5A01G064800 chr1B 97.619 42 1 0 2355 2396 416827641 416827600 3.300000e-09 73.1
32 TraesCS5A01G064800 chr1B 97.619 42 1 0 2355 2396 588228375 588228334 3.300000e-09 73.1
33 TraesCS5A01G064800 chr1B 95.000 40 1 1 430 468 280756047 280756086 7.150000e-06 62.1
34 TraesCS5A01G064800 chr1B 86.792 53 4 3 361 411 280756035 280756086 3.330000e-04 56.5
35 TraesCS5A01G064800 chr2A 95.455 44 2 0 2353 2396 39464347 39464390 1.190000e-08 71.3


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 TraesCS5A01G064800 chr5A 70171884 70174279 2395 True 1697.000000 4425 91.412667 1 2396 3 chr5A.!!$R1 2395
1 TraesCS5A01G064800 chr5D 74717170 74717801 631 True 872.000000 872 91.337000 1610 2264 1 chr5D.!!$R1 654
2 TraesCS5A01G064800 chr5D 74760208 74761046 838 True 569.000000 846 89.608500 1452 2355 2 chr5D.!!$R2 903
3 TraesCS5A01G064800 chr5D 486831596 486833036 1440 False 283.000000 359 85.157500 11 1448 2 chr5D.!!$F2 1437
4 TraesCS5A01G064800 chr5B 77587390 77588111 721 False 505.000000 815 91.087500 1577 2355 2 chr5B.!!$F2 778
5 TraesCS5A01G064800 chr5B 77643946 77644627 681 False 290.500000 344 91.170500 1610 2312 2 chr5B.!!$F3 702
6 TraesCS5A01G064800 chr7D 564687008 564687848 840 True 427.666667 774 88.058333 380 1360 3 chr7D.!!$R2 980
7 TraesCS5A01G064800 chr3A 142977501 142978180 679 True 684.000000 684 85.444000 3 663 1 chr3A.!!$R1 660
8 TraesCS5A01G064800 chr6D 7294090 7294662 572 True 501.000000 501 83.624000 916 1448 1 chr6D.!!$R1 532

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
51 54 0.106419 TGCAATTAATCCCCCGTCCC 60.106 55.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 2186 0.107361 TCTGACCTCCTGCATGCATG 60.107 55.0 22.97 22.7 0.0 4.06 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
27 28 1.376037 CGGTGGCTCTCTGGAAACC 60.376 63.158 0.00 0.00 0.00 3.27
36 39 1.768275 TCTCTGGAAACCTGTCTGCAA 59.232 47.619 0.00 0.00 0.00 4.08
45 48 3.018423 ACCTGTCTGCAATTAATCCCC 57.982 47.619 0.00 0.00 0.00 4.81
47 50 1.949525 CTGTCTGCAATTAATCCCCCG 59.050 52.381 0.00 0.00 0.00 5.73
49 52 1.947456 GTCTGCAATTAATCCCCCGTC 59.053 52.381 0.00 0.00 0.00 4.79
51 54 0.106419 TGCAATTAATCCCCCGTCCC 60.106 55.000 0.00 0.00 0.00 4.46
79 85 2.765689 TCAATCCCCTCTCTCTCTCC 57.234 55.000 0.00 0.00 0.00 3.71
80 86 2.222271 TCAATCCCCTCTCTCTCTCCT 58.778 52.381 0.00 0.00 0.00 3.69
133 145 4.180946 CCTCGTCCGCGGAGTCAG 62.181 72.222 31.97 23.06 38.89 3.51
154 166 2.061773 CGACGCTGTTGATCAAGAAGT 58.938 47.619 8.80 10.47 0.00 3.01
210 273 3.256960 GTGTCCCCAGGCTTCCCA 61.257 66.667 0.00 0.00 0.00 4.37
270 333 1.825474 CCGACTCTAGAGGCCAAGAAA 59.175 52.381 23.50 0.00 30.97 2.52
366 590 4.475135 GCTCCCTCCGCCTTCCAC 62.475 72.222 0.00 0.00 0.00 4.02
378 602 3.883744 CTTCCACGCGCTCCAAGGT 62.884 63.158 5.73 0.00 0.00 3.50
549 811 1.736586 CTTAGTCGCGCTCCAGGAT 59.263 57.895 5.56 0.00 0.00 3.24
550 812 0.596083 CTTAGTCGCGCTCCAGGATG 60.596 60.000 5.56 0.00 0.00 3.51
561 823 4.457496 CAGGATGCCGCAGACCGT 62.457 66.667 11.93 0.00 34.38 4.83
562 824 4.148825 AGGATGCCGCAGACCGTC 62.149 66.667 11.93 0.00 34.38 4.79
579 841 4.735132 CGCGCTCCGGTCCAAGAA 62.735 66.667 5.56 0.00 0.00 2.52
580 842 2.815647 GCGCTCCGGTCCAAGAAG 60.816 66.667 0.00 0.00 0.00 2.85
581 843 2.815647 CGCTCCGGTCCAAGAAGC 60.816 66.667 0.00 0.00 0.00 3.86
582 844 2.436824 GCTCCGGTCCAAGAAGCC 60.437 66.667 0.00 0.00 0.00 4.35
583 845 2.125512 CTCCGGTCCAAGAAGCCG 60.126 66.667 0.00 0.00 44.55 5.52
591 853 2.435938 CAAGAAGCCGGCGCCTTA 60.436 61.111 27.59 0.00 34.57 2.69
595 857 3.659089 GAAGCCGGCGCCTTAGTCA 62.659 63.158 26.68 0.00 34.57 3.41
634 896 4.166011 GTGCCGCTCCGATGCAAC 62.166 66.667 0.00 0.00 36.65 4.17
635 897 4.695993 TGCCGCTCCGATGCAACA 62.696 61.111 0.00 0.00 30.85 3.33
636 898 3.430862 GCCGCTCCGATGCAACAA 61.431 61.111 0.00 0.00 0.00 2.83
637 899 2.787249 CCGCTCCGATGCAACAAG 59.213 61.111 0.00 0.00 0.00 3.16
638 900 2.753966 CCGCTCCGATGCAACAAGG 61.754 63.158 0.00 0.00 0.00 3.61
639 901 2.034879 CGCTCCGATGCAACAAGGT 61.035 57.895 0.00 0.00 0.00 3.50
640 902 1.503542 GCTCCGATGCAACAAGGTG 59.496 57.895 0.00 0.00 0.00 4.00
641 903 0.955428 GCTCCGATGCAACAAGGTGA 60.955 55.000 0.00 0.00 0.00 4.02
642 904 0.798776 CTCCGATGCAACAAGGTGAC 59.201 55.000 0.00 0.00 0.00 3.67
643 905 0.948623 TCCGATGCAACAAGGTGACG 60.949 55.000 0.00 0.00 0.00 4.35
644 906 1.154413 CGATGCAACAAGGTGACGC 60.154 57.895 0.00 0.00 0.00 5.19
645 907 1.210155 GATGCAACAAGGTGACGCC 59.790 57.895 0.00 0.00 37.58 5.68
695 958 2.040544 CCGCTCCGATGCAAAAGGT 61.041 57.895 0.00 0.00 0.00 3.50
717 980 2.701780 GCCTTCGTCGCTCTCCAGA 61.702 63.158 0.00 0.00 0.00 3.86
733 1056 3.512516 GAATGCTGCTCGTGGCCC 61.513 66.667 0.00 0.00 40.92 5.80
740 1063 4.643387 GCTCGTGGCCCTGTTGGT 62.643 66.667 0.00 0.00 36.04 3.67
743 1066 2.113139 CGTGGCCCTGTTGGTCTT 59.887 61.111 0.00 0.00 40.46 3.01
749 1072 1.752198 CCCTGTTGGTCTTGTCCGA 59.248 57.895 0.00 0.00 0.00 4.55
786 1109 4.980805 GCAACGCCCACGAGACCA 62.981 66.667 0.00 0.00 43.93 4.02
787 1110 2.280524 CAACGCCCACGAGACCAA 60.281 61.111 0.00 0.00 43.93 3.67
788 1111 2.280592 AACGCCCACGAGACCAAC 60.281 61.111 0.00 0.00 43.93 3.77
789 1112 3.819877 AACGCCCACGAGACCAACC 62.820 63.158 0.00 0.00 43.93 3.77
800 1123 4.681978 ACCAACCAGACGAGCGCC 62.682 66.667 2.29 0.00 0.00 6.53
944 1267 4.067913 TCGTCTGCGATGCCTGCA 62.068 61.111 0.00 0.00 42.81 4.41
956 1279 1.676635 GCCTGCAGCAACTCCATCA 60.677 57.895 8.66 0.00 42.97 3.07
963 1286 2.390599 GCAACTCCATCAAGCGCGA 61.391 57.895 12.10 0.00 0.00 5.87
1001 1324 2.670148 GGTCAAGGAGGACGGCCAT 61.670 63.158 11.69 0.00 38.70 4.40
1168 1532 2.267961 GTCCATGGTCACCGGGAC 59.732 66.667 18.88 18.88 46.20 4.46
1201 1566 0.911045 TGATGGCAGAGGAAGCTCCA 60.911 55.000 0.00 0.00 39.61 3.86
1218 1583 1.351707 CAGCGCACTCAACGTGTTT 59.648 52.632 11.47 0.00 45.57 2.83
1300 1668 2.088423 GTATGCAACCAAACATCGGGA 58.912 47.619 0.00 0.00 0.00 5.14
1322 1690 5.449588 GGACAAAATTGCATCTCGATGACAT 60.450 40.000 10.91 0.00 41.20 3.06
1324 1692 3.620929 AATTGCATCTCGATGACATGC 57.379 42.857 10.91 10.34 41.20 4.06
1363 1737 9.638239 GGCAACTAATCAAATTGACATCTTTTA 57.362 29.630 0.00 0.00 31.26 1.52
1367 1741 8.470002 ACTAATCAAATTGACATCTTTTAGCCC 58.530 33.333 0.00 0.00 0.00 5.19
1385 1759 1.758592 CCGTTTTCCCTCACCCAGA 59.241 57.895 0.00 0.00 0.00 3.86
1393 1767 1.763770 CCTCACCCAGAACCTGCTT 59.236 57.895 0.00 0.00 0.00 3.91
1396 1770 1.902508 CTCACCCAGAACCTGCTTAGA 59.097 52.381 0.00 0.00 0.00 2.10
1409 1783 2.413453 CTGCTTAGACTGGCTCGTTTTC 59.587 50.000 0.00 0.00 0.00 2.29
1415 1791 1.549170 GACTGGCTCGTTTTCCCTCTA 59.451 52.381 0.00 0.00 0.00 2.43
1418 1794 1.975680 TGGCTCGTTTTCCCTCTAAGT 59.024 47.619 0.00 0.00 0.00 2.24
1421 1797 3.556423 GGCTCGTTTTCCCTCTAAGTCAA 60.556 47.826 0.00 0.00 0.00 3.18
1432 1808 0.321919 CTAAGTCAAGCCCAGCAGCA 60.322 55.000 0.00 0.00 34.23 4.41
1448 1824 2.533942 GCAGCAAAAGTAACCAAACACG 59.466 45.455 0.00 0.00 0.00 4.49
1449 1825 3.765026 CAGCAAAAGTAACCAAACACGT 58.235 40.909 0.00 0.00 0.00 4.49
1450 1826 3.789224 CAGCAAAAGTAACCAAACACGTC 59.211 43.478 0.00 0.00 0.00 4.34
1461 1837 0.320697 AAACACGTCCTAGGCTGTCC 59.679 55.000 2.96 0.00 0.00 4.02
1470 1846 1.202533 CCTAGGCTGTCCAACCATACG 60.203 57.143 0.00 0.00 33.74 3.06
1473 1849 1.206371 AGGCTGTCCAACCATACGTAC 59.794 52.381 0.00 0.00 33.74 3.67
1475 1851 2.268298 GCTGTCCAACCATACGTACAG 58.732 52.381 0.00 1.52 37.87 2.74
1485 1861 3.056322 ACCATACGTACAGGGACAGTTTC 60.056 47.826 17.44 0.00 0.00 2.78
1490 1866 2.296471 CGTACAGGGACAGTTTCAGAGT 59.704 50.000 0.00 0.00 0.00 3.24
1517 1893 5.957771 TTGGAGATGCTTAAGATGTAGGT 57.042 39.130 6.67 0.00 0.00 3.08
1568 1950 4.419522 CCAGATGGTACCTTTTTGAACG 57.580 45.455 14.36 0.00 0.00 3.95
1569 1951 3.818773 CCAGATGGTACCTTTTTGAACGT 59.181 43.478 14.36 0.00 0.00 3.99
1570 1952 4.083484 CCAGATGGTACCTTTTTGAACGTC 60.083 45.833 14.36 0.00 0.00 4.34
1571 1953 4.070009 AGATGGTACCTTTTTGAACGTCC 58.930 43.478 14.36 0.00 0.00 4.79
1572 1954 2.211806 TGGTACCTTTTTGAACGTCCG 58.788 47.619 14.36 0.00 0.00 4.79
1573 1955 1.532437 GGTACCTTTTTGAACGTCCGG 59.468 52.381 4.06 0.00 0.00 5.14
1574 1956 1.532437 GTACCTTTTTGAACGTCCGGG 59.468 52.381 0.00 0.00 0.00 5.73
1575 1957 0.820482 ACCTTTTTGAACGTCCGGGG 60.820 55.000 0.00 0.00 0.00 5.73
1605 1995 2.023888 ACTAGCTGTGGTCTAGGGTCAT 60.024 50.000 0.00 0.00 38.21 3.06
1606 1996 1.958288 AGCTGTGGTCTAGGGTCATT 58.042 50.000 0.00 0.00 0.00 2.57
1720 2139 6.183360 TGTGCATTAACTGATTGATTCGTACC 60.183 38.462 0.00 0.00 0.00 3.34
1721 2140 5.877564 TGCATTAACTGATTGATTCGTACCA 59.122 36.000 0.00 0.00 0.00 3.25
1722 2141 6.542005 TGCATTAACTGATTGATTCGTACCAT 59.458 34.615 0.00 0.00 0.00 3.55
1723 2142 7.066887 TGCATTAACTGATTGATTCGTACCATT 59.933 33.333 0.00 0.00 0.00 3.16
1724 2143 7.587757 GCATTAACTGATTGATTCGTACCATTC 59.412 37.037 0.00 0.00 0.00 2.67
1725 2144 8.830580 CATTAACTGATTGATTCGTACCATTCT 58.169 33.333 0.00 0.00 0.00 2.40
1726 2145 6.910536 AACTGATTGATTCGTACCATTCTC 57.089 37.500 0.00 0.00 0.00 2.87
1727 2146 5.977635 ACTGATTGATTCGTACCATTCTCA 58.022 37.500 0.00 0.00 0.00 3.27
1728 2147 6.406370 ACTGATTGATTCGTACCATTCTCAA 58.594 36.000 0.00 0.00 0.00 3.02
1729 2148 6.878923 ACTGATTGATTCGTACCATTCTCAAA 59.121 34.615 0.00 0.00 0.00 2.69
1730 2149 7.390440 ACTGATTGATTCGTACCATTCTCAAAA 59.610 33.333 0.00 0.00 0.00 2.44
1731 2150 7.751732 TGATTGATTCGTACCATTCTCAAAAG 58.248 34.615 0.00 0.00 0.00 2.27
1732 2151 5.545658 TGATTCGTACCATTCTCAAAAGC 57.454 39.130 0.00 0.00 0.00 3.51
1733 2152 5.000591 TGATTCGTACCATTCTCAAAAGCA 58.999 37.500 0.00 0.00 0.00 3.91
1734 2153 5.471797 TGATTCGTACCATTCTCAAAAGCAA 59.528 36.000 0.00 0.00 0.00 3.91
1735 2154 5.356882 TTCGTACCATTCTCAAAAGCAAG 57.643 39.130 0.00 0.00 0.00 4.01
1736 2155 4.637276 TCGTACCATTCTCAAAAGCAAGA 58.363 39.130 0.00 0.00 0.00 3.02
1737 2156 4.451096 TCGTACCATTCTCAAAAGCAAGAC 59.549 41.667 0.00 0.00 0.00 3.01
1738 2157 4.213270 CGTACCATTCTCAAAAGCAAGACA 59.787 41.667 0.00 0.00 0.00 3.41
1739 2158 5.277779 CGTACCATTCTCAAAAGCAAGACAA 60.278 40.000 0.00 0.00 0.00 3.18
1740 2159 4.936891 ACCATTCTCAAAAGCAAGACAAC 58.063 39.130 0.00 0.00 0.00 3.32
1741 2160 4.202151 ACCATTCTCAAAAGCAAGACAACC 60.202 41.667 0.00 0.00 0.00 3.77
1742 2161 4.301628 CATTCTCAAAAGCAAGACAACCC 58.698 43.478 0.00 0.00 0.00 4.11
1743 2162 3.011566 TCTCAAAAGCAAGACAACCCA 57.988 42.857 0.00 0.00 0.00 4.51
1744 2163 3.360867 TCTCAAAAGCAAGACAACCCAA 58.639 40.909 0.00 0.00 0.00 4.12
1745 2164 3.766591 TCTCAAAAGCAAGACAACCCAAA 59.233 39.130 0.00 0.00 0.00 3.28
1746 2165 4.221703 TCTCAAAAGCAAGACAACCCAAAA 59.778 37.500 0.00 0.00 0.00 2.44
1747 2166 4.899502 TCAAAAGCAAGACAACCCAAAAA 58.100 34.783 0.00 0.00 0.00 1.94
1767 2186 4.946784 AAAACTGATTGATCCGTACTGC 57.053 40.909 0.00 0.00 0.00 4.40
1768 2187 3.610040 AACTGATTGATCCGTACTGCA 57.390 42.857 0.00 0.00 0.00 4.41
1916 2338 6.424683 CGAACCTCATGATAATGAACACATG 58.575 40.000 0.00 0.00 40.65 3.21
1927 2349 1.293924 GAACACATGATGCCGGAGAG 58.706 55.000 5.05 0.00 0.00 3.20
2092 2590 4.662961 CTGTGCAGGCGACCGTGA 62.663 66.667 0.00 0.00 0.00 4.35
2298 2798 1.854126 CAACAAAAGCAAGAGCAACCG 59.146 47.619 0.00 0.00 45.49 4.44
2304 2804 1.160329 AGCAAGAGCAACCGTGTGAC 61.160 55.000 0.00 0.00 45.49 3.67
2343 2845 4.035324 CGAGCTAGTCCTCTGATCGTTTTA 59.965 45.833 0.00 0.00 0.00 1.52
2355 2857 8.770828 CCTCTGATCGTTTTAACTGAGTTTTAA 58.229 33.333 1.97 0.00 0.00 1.52
2356 2858 9.582223 CTCTGATCGTTTTAACTGAGTTTTAAC 57.418 33.333 1.97 7.57 0.00 2.01
2357 2859 9.100554 TCTGATCGTTTTAACTGAGTTTTAACA 57.899 29.630 1.97 1.16 0.00 2.41
2358 2860 9.370126 CTGATCGTTTTAACTGAGTTTTAACAG 57.630 33.333 1.97 5.70 39.65 3.16
2368 2870 7.859325 ACTGAGTTTTAACAGTTTTGCTAGA 57.141 32.000 0.00 0.00 43.52 2.43
2369 2871 8.276252 ACTGAGTTTTAACAGTTTTGCTAGAA 57.724 30.769 0.00 0.00 43.52 2.10
2370 2872 8.182227 ACTGAGTTTTAACAGTTTTGCTAGAAC 58.818 33.333 0.00 0.00 43.52 3.01
2371 2873 8.276252 TGAGTTTTAACAGTTTTGCTAGAACT 57.724 30.769 0.00 0.00 34.72 3.01
2372 2874 8.395633 TGAGTTTTAACAGTTTTGCTAGAACTC 58.604 33.333 11.41 11.41 42.08 3.01
2373 2875 8.276252 AGTTTTAACAGTTTTGCTAGAACTCA 57.724 30.769 0.00 0.00 35.26 3.41
2374 2876 8.903820 AGTTTTAACAGTTTTGCTAGAACTCAT 58.096 29.630 0.00 0.00 35.26 2.90
2375 2877 9.170584 GTTTTAACAGTTTTGCTAGAACTCATC 57.829 33.333 0.00 0.00 35.26 2.92
2376 2878 8.677148 TTTAACAGTTTTGCTAGAACTCATCT 57.323 30.769 0.00 0.00 42.48 2.90
2377 2879 9.772973 TTTAACAGTTTTGCTAGAACTCATCTA 57.227 29.630 0.00 0.00 39.71 1.98
2378 2880 9.772973 TTAACAGTTTTGCTAGAACTCATCTAA 57.227 29.630 0.00 0.00 40.12 2.10
2379 2881 8.677148 AACAGTTTTGCTAGAACTCATCTAAA 57.323 30.769 0.00 0.00 40.12 1.85
2380 2882 8.854614 ACAGTTTTGCTAGAACTCATCTAAAT 57.145 30.769 0.00 0.00 40.12 1.40
2381 2883 8.725148 ACAGTTTTGCTAGAACTCATCTAAATG 58.275 33.333 0.00 0.00 40.12 2.32
2382 2884 8.939929 CAGTTTTGCTAGAACTCATCTAAATGA 58.060 33.333 0.00 0.00 40.12 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.812019 AGAGAGCCACCGCGTACG 61.812 66.667 11.84 11.84 41.18 3.67
4 5 2.202623 CAGAGAGCCACCGCGTAC 60.203 66.667 4.92 0.00 41.18 3.67
5 6 3.449227 CCAGAGAGCCACCGCGTA 61.449 66.667 4.92 0.00 41.18 4.42
7 8 3.589654 TTTCCAGAGAGCCACCGCG 62.590 63.158 0.00 0.00 41.18 6.46
9 10 1.376037 GGTTTCCAGAGAGCCACCG 60.376 63.158 0.00 0.00 0.00 4.94
27 28 1.949525 CGGGGGATTAATTGCAGACAG 59.050 52.381 0.00 0.00 0.00 3.51
36 39 2.917600 GGATTAGGGACGGGGGATTAAT 59.082 50.000 0.00 0.00 0.00 1.40
45 48 3.197983 GGGATTGATAGGATTAGGGACGG 59.802 52.174 0.00 0.00 0.00 4.79
47 50 4.439860 AGGGGATTGATAGGATTAGGGAC 58.560 47.826 0.00 0.00 0.00 4.46
49 52 4.704403 AGAGGGGATTGATAGGATTAGGG 58.296 47.826 0.00 0.00 0.00 3.53
51 54 6.502138 AGAGAGAGGGGATTGATAGGATTAG 58.498 44.000 0.00 0.00 0.00 1.73
79 85 0.103937 GGGATCGACTGGAGCAGAAG 59.896 60.000 0.00 0.00 35.18 2.85
80 86 1.667154 CGGGATCGACTGGAGCAGAA 61.667 60.000 0.00 0.00 39.00 3.02
132 144 0.038251 TCTTGATCAACAGCGTCGCT 60.038 50.000 15.47 15.47 40.77 4.93
133 145 0.790207 TTCTTGATCAACAGCGTCGC 59.210 50.000 9.80 9.80 0.00 5.19
136 148 1.532868 GCACTTCTTGATCAACAGCGT 59.467 47.619 3.38 0.00 0.00 5.07
154 166 2.032528 CACCGCTGGAAGAAGGCA 59.967 61.111 1.50 0.00 36.86 4.75
505 729 1.674057 CTTCTTGGACCGGAGTGCT 59.326 57.895 9.46 0.00 34.93 4.40
508 732 2.943978 CGGCTTCTTGGACCGGAGT 61.944 63.158 9.46 0.00 43.23 3.85
562 824 4.735132 TTCTTGGACCGGAGCGCG 62.735 66.667 9.46 0.00 0.00 6.86
563 825 2.815647 CTTCTTGGACCGGAGCGC 60.816 66.667 9.46 0.00 0.00 5.92
564 826 2.815647 GCTTCTTGGACCGGAGCG 60.816 66.667 9.46 0.00 0.00 5.03
565 827 2.436824 GGCTTCTTGGACCGGAGC 60.437 66.667 9.46 4.04 0.00 4.70
566 828 2.125512 CGGCTTCTTGGACCGGAG 60.126 66.667 9.46 0.00 43.23 4.63
573 835 3.969250 TAAGGCGCCGGCTTCTTGG 62.969 63.158 29.73 15.07 45.21 3.61
574 836 2.435938 TAAGGCGCCGGCTTCTTG 60.436 61.111 29.73 15.71 45.21 3.02
575 837 2.125106 CTAAGGCGCCGGCTTCTT 60.125 61.111 29.73 26.55 45.21 2.52
576 838 3.372554 GACTAAGGCGCCGGCTTCT 62.373 63.158 29.73 18.46 45.21 2.85
577 839 2.890961 GACTAAGGCGCCGGCTTC 60.891 66.667 29.73 12.30 45.21 3.86
579 841 4.452733 GTGACTAAGGCGCCGGCT 62.453 66.667 26.68 7.62 41.24 5.52
585 847 1.517257 CTGGAGCGTGACTAAGGCG 60.517 63.158 0.00 0.00 44.54 5.52
586 848 1.153549 CCTGGAGCGTGACTAAGGC 60.154 63.158 0.00 0.00 40.06 4.35
587 849 0.173708 GTCCTGGAGCGTGACTAAGG 59.826 60.000 0.00 0.00 34.77 2.69
588 850 0.179161 CGTCCTGGAGCGTGACTAAG 60.179 60.000 0.00 0.00 0.00 2.18
589 851 1.880894 CGTCCTGGAGCGTGACTAA 59.119 57.895 0.00 0.00 0.00 2.24
590 852 2.697761 GCGTCCTGGAGCGTGACTA 61.698 63.158 16.20 0.00 0.00 2.59
591 853 4.057428 GCGTCCTGGAGCGTGACT 62.057 66.667 16.20 0.00 0.00 3.41
617 879 4.166011 GTTGCATCGGAGCGGCAC 62.166 66.667 1.45 0.00 36.16 5.01
618 880 4.695993 TGTTGCATCGGAGCGGCA 62.696 61.111 1.45 0.00 37.31 5.69
619 881 3.386867 CTTGTTGCATCGGAGCGGC 62.387 63.158 0.00 0.00 37.31 6.53
620 882 2.753966 CCTTGTTGCATCGGAGCGG 61.754 63.158 0.00 0.00 37.31 5.52
621 883 2.034879 ACCTTGTTGCATCGGAGCG 61.035 57.895 0.00 0.00 37.31 5.03
622 884 0.955428 TCACCTTGTTGCATCGGAGC 60.955 55.000 0.00 0.00 0.00 4.70
623 885 0.798776 GTCACCTTGTTGCATCGGAG 59.201 55.000 0.00 0.00 0.00 4.63
624 886 0.948623 CGTCACCTTGTTGCATCGGA 60.949 55.000 0.00 0.00 0.00 4.55
625 887 1.497278 CGTCACCTTGTTGCATCGG 59.503 57.895 0.00 0.00 0.00 4.18
626 888 1.154413 GCGTCACCTTGTTGCATCG 60.154 57.895 0.00 0.00 0.00 3.84
627 889 1.210155 GGCGTCACCTTGTTGCATC 59.790 57.895 0.00 0.00 34.51 3.91
628 890 3.354678 GGCGTCACCTTGTTGCAT 58.645 55.556 0.00 0.00 34.51 3.96
642 904 4.116328 TGGAGAGCGACGAAGGCG 62.116 66.667 0.00 0.00 44.79 5.52
643 905 2.202676 CTGGAGAGCGACGAAGGC 60.203 66.667 0.00 0.00 0.00 4.35
644 906 2.046864 TCCTGGAGAGCGACGAAGG 61.047 63.158 0.00 0.00 0.00 3.46
645 907 1.137825 GTCCTGGAGAGCGACGAAG 59.862 63.158 0.00 0.00 0.00 3.79
646 908 3.275088 GTCCTGGAGAGCGACGAA 58.725 61.111 0.00 0.00 0.00 3.85
649 911 4.500116 GGCGTCCTGGAGAGCGAC 62.500 72.222 15.21 6.64 0.00 5.19
717 980 4.039092 AGGGCCACGAGCAGCATT 62.039 61.111 6.18 0.00 46.50 3.56
733 1056 0.951040 GCCTCGGACAAGACCAACAG 60.951 60.000 0.00 0.00 0.00 3.16
740 1063 3.003173 CTGGGGCCTCGGACAAGA 61.003 66.667 5.06 0.00 0.00 3.02
769 1092 4.980805 TGGTCTCGTGGGCGTTGC 62.981 66.667 0.00 0.00 39.49 4.17
771 1094 2.280592 GTTGGTCTCGTGGGCGTT 60.281 61.111 0.00 0.00 39.49 4.84
772 1095 4.309950 GGTTGGTCTCGTGGGCGT 62.310 66.667 0.00 0.00 39.49 5.68
773 1096 4.308458 TGGTTGGTCTCGTGGGCG 62.308 66.667 0.00 0.00 39.92 6.13
774 1097 2.358737 CTGGTTGGTCTCGTGGGC 60.359 66.667 0.00 0.00 0.00 5.36
775 1098 1.004918 GTCTGGTTGGTCTCGTGGG 60.005 63.158 0.00 0.00 0.00 4.61
776 1099 1.372997 CGTCTGGTTGGTCTCGTGG 60.373 63.158 0.00 0.00 0.00 4.94
777 1100 0.387367 CTCGTCTGGTTGGTCTCGTG 60.387 60.000 0.00 0.00 0.00 4.35
778 1101 1.957562 CTCGTCTGGTTGGTCTCGT 59.042 57.895 0.00 0.00 0.00 4.18
779 1102 1.444553 GCTCGTCTGGTTGGTCTCG 60.445 63.158 0.00 0.00 0.00 4.04
780 1103 1.444553 CGCTCGTCTGGTTGGTCTC 60.445 63.158 0.00 0.00 0.00 3.36
781 1104 2.651361 CGCTCGTCTGGTTGGTCT 59.349 61.111 0.00 0.00 0.00 3.85
782 1105 3.112709 GCGCTCGTCTGGTTGGTC 61.113 66.667 0.00 0.00 0.00 4.02
783 1106 4.681978 GGCGCTCGTCTGGTTGGT 62.682 66.667 7.64 0.00 0.00 3.67
784 1107 4.680237 TGGCGCTCGTCTGGTTGG 62.680 66.667 7.64 0.00 0.00 3.77
785 1108 3.114616 CTGGCGCTCGTCTGGTTG 61.115 66.667 7.64 0.00 0.00 3.77
786 1109 4.379243 CCTGGCGCTCGTCTGGTT 62.379 66.667 7.64 0.00 34.69 3.67
788 1111 4.504916 CTCCTGGCGCTCGTCTGG 62.505 72.222 7.64 12.61 39.70 3.86
843 1166 4.664677 GACACGGTGCGGCTCACT 62.665 66.667 8.30 0.00 44.98 3.41
944 1267 2.393768 CGCGCTTGATGGAGTTGCT 61.394 57.895 5.56 0.00 0.00 3.91
947 1270 1.016130 CAGTCGCGCTTGATGGAGTT 61.016 55.000 5.56 0.00 0.00 3.01
956 1279 1.153745 GATGAGTCCAGTCGCGCTT 60.154 57.895 5.56 0.00 0.00 4.68
963 1286 3.069980 GCGAGGCGATGAGTCCAGT 62.070 63.158 0.00 0.00 0.00 4.00
977 1300 1.216710 GTCCTCCTTGACCAGCGAG 59.783 63.158 0.00 0.00 0.00 5.03
1001 1324 4.129737 GCCGCCAGCGAGTAGACA 62.130 66.667 14.67 0.00 42.83 3.41
1168 1532 4.511246 ATCATGCCCACCGCCAGG 62.511 66.667 0.00 0.00 45.13 4.45
1218 1583 2.552315 GGTTTGGCTTCTCATTTCGTCA 59.448 45.455 0.00 0.00 0.00 4.35
1294 1662 2.355756 CGAGATGCAATTTTGTCCCGAT 59.644 45.455 0.00 0.00 0.00 4.18
1295 1663 1.737236 CGAGATGCAATTTTGTCCCGA 59.263 47.619 0.00 0.00 0.00 5.14
1300 1668 5.337554 CATGTCATCGAGATGCAATTTTGT 58.662 37.500 8.14 0.00 38.65 2.83
1343 1711 7.416213 CGGGGCTAAAAGATGTCAATTTGATTA 60.416 37.037 1.78 0.00 0.00 1.75
1350 1718 3.366052 ACGGGGCTAAAAGATGTCAAT 57.634 42.857 0.00 0.00 0.00 2.57
1363 1737 2.434774 GTGAGGGAAAACGGGGCT 59.565 61.111 0.00 0.00 0.00 5.19
1367 1741 0.109723 TTCTGGGTGAGGGAAAACGG 59.890 55.000 0.00 0.00 0.00 4.44
1385 1759 0.247736 CGAGCCAGTCTAAGCAGGTT 59.752 55.000 0.00 0.00 0.00 3.50
1393 1767 1.549170 GAGGGAAAACGAGCCAGTCTA 59.451 52.381 0.00 0.00 0.00 2.59
1396 1770 1.640917 TAGAGGGAAAACGAGCCAGT 58.359 50.000 0.00 0.00 0.00 4.00
1409 1783 0.107459 GCTGGGCTTGACTTAGAGGG 60.107 60.000 0.00 0.00 0.00 4.30
1415 1791 0.756442 TTTGCTGCTGGGCTTGACTT 60.756 50.000 0.00 0.00 0.00 3.01
1418 1794 0.756442 ACTTTTGCTGCTGGGCTTGA 60.756 50.000 0.00 0.00 0.00 3.02
1421 1797 0.961753 GTTACTTTTGCTGCTGGGCT 59.038 50.000 0.00 0.00 0.00 5.19
1432 1808 4.818005 CCTAGGACGTGTTTGGTTACTTTT 59.182 41.667 1.05 0.00 0.00 2.27
1448 1824 0.912486 ATGGTTGGACAGCCTAGGAC 59.088 55.000 14.75 3.76 32.40 3.85
1449 1825 2.116238 GTATGGTTGGACAGCCTAGGA 58.884 52.381 14.75 0.00 32.40 2.94
1450 1826 1.202533 CGTATGGTTGGACAGCCTAGG 60.203 57.143 3.67 3.67 32.40 3.02
1461 1837 2.232941 ACTGTCCCTGTACGTATGGTTG 59.767 50.000 13.95 3.37 0.00 3.77
1470 1846 3.306156 GGACTCTGAAACTGTCCCTGTAC 60.306 52.174 3.13 0.00 43.10 2.90
1473 1849 1.337260 CGGACTCTGAAACTGTCCCTG 60.337 57.143 7.89 0.00 45.31 4.45
1475 1851 0.966920 TCGGACTCTGAAACTGTCCC 59.033 55.000 7.89 0.00 45.31 4.46
1485 1861 1.411977 AGCATCTCCAATCGGACTCTG 59.588 52.381 0.00 0.00 35.91 3.35
1490 1866 4.101585 ACATCTTAAGCATCTCCAATCGGA 59.898 41.667 0.00 0.00 39.79 4.55
1493 1869 6.529220 ACCTACATCTTAAGCATCTCCAATC 58.471 40.000 0.00 0.00 0.00 2.67
1494 1870 6.506538 ACCTACATCTTAAGCATCTCCAAT 57.493 37.500 0.00 0.00 0.00 3.16
1562 1944 3.628982 GGACCCCCGGACGTTCAA 61.629 66.667 0.73 0.00 0.00 2.69
1572 1954 3.232483 GCTAGTAGCCGGACCCCC 61.232 72.222 11.33 0.00 34.48 5.40
1573 1955 2.123382 AGCTAGTAGCCGGACCCC 60.123 66.667 18.65 0.00 43.77 4.95
1574 1956 1.757340 ACAGCTAGTAGCCGGACCC 60.757 63.158 18.65 0.00 43.77 4.46
1575 1957 1.437986 CACAGCTAGTAGCCGGACC 59.562 63.158 18.65 0.00 43.77 4.46
1605 1995 4.792068 CCATATGGTGCCCTCTAGAAAAA 58.208 43.478 14.09 0.00 0.00 1.94
1606 1996 4.437682 CCATATGGTGCCCTCTAGAAAA 57.562 45.455 14.09 0.00 0.00 2.29
1720 2139 4.202141 TGGGTTGTCTTGCTTTTGAGAATG 60.202 41.667 0.00 0.00 0.00 2.67
1721 2140 3.960102 TGGGTTGTCTTGCTTTTGAGAAT 59.040 39.130 0.00 0.00 0.00 2.40
1722 2141 3.360867 TGGGTTGTCTTGCTTTTGAGAA 58.639 40.909 0.00 0.00 0.00 2.87
1723 2142 3.011566 TGGGTTGTCTTGCTTTTGAGA 57.988 42.857 0.00 0.00 0.00 3.27
1724 2143 3.799281 TTGGGTTGTCTTGCTTTTGAG 57.201 42.857 0.00 0.00 0.00 3.02
1725 2144 4.543590 TTTTGGGTTGTCTTGCTTTTGA 57.456 36.364 0.00 0.00 0.00 2.69
1745 2164 4.759693 TGCAGTACGGATCAATCAGTTTTT 59.240 37.500 0.00 0.00 36.61 1.94
1746 2165 4.323417 TGCAGTACGGATCAATCAGTTTT 58.677 39.130 0.00 0.00 36.61 2.43
1747 2166 3.937814 TGCAGTACGGATCAATCAGTTT 58.062 40.909 0.00 0.00 36.61 2.66
1748 2167 3.610040 TGCAGTACGGATCAATCAGTT 57.390 42.857 0.00 0.00 36.61 3.16
1749 2168 3.461061 CATGCAGTACGGATCAATCAGT 58.539 45.455 0.00 1.54 38.69 3.41
1750 2169 2.222678 GCATGCAGTACGGATCAATCAG 59.777 50.000 14.21 0.00 0.00 2.90
1751 2170 2.212652 GCATGCAGTACGGATCAATCA 58.787 47.619 14.21 0.00 0.00 2.57
1752 2171 2.212652 TGCATGCAGTACGGATCAATC 58.787 47.619 18.46 0.00 0.00 2.67
1753 2172 2.330440 TGCATGCAGTACGGATCAAT 57.670 45.000 18.46 0.00 0.00 2.57
1754 2173 1.941975 CATGCATGCAGTACGGATCAA 59.058 47.619 26.69 0.00 0.00 2.57
1755 2174 1.585297 CATGCATGCAGTACGGATCA 58.415 50.000 26.69 0.00 0.00 2.92
1767 2186 0.107361 TCTGACCTCCTGCATGCATG 60.107 55.000 22.97 22.70 0.00 4.06
1768 2187 0.180642 CTCTGACCTCCTGCATGCAT 59.819 55.000 22.97 5.46 0.00 3.96
1874 2296 1.516423 GGAGGTCGTCAGGTAAGGC 59.484 63.158 0.00 0.00 0.00 4.35
1997 2462 2.661566 GGTCTCGTCGACGTCGTCA 61.662 63.158 34.40 16.49 43.79 4.35
2101 2599 3.964875 CCATAACCATGGCCGCGC 61.965 66.667 13.04 0.00 45.29 6.86
2119 2617 0.831288 CCTCATCTCCAGGCTCGGAT 60.831 60.000 6.21 0.00 33.56 4.18
2265 2763 9.332502 TCTTGCTTTTGTTGAGTACAGTAATAA 57.667 29.630 0.00 0.00 38.19 1.40
2272 2770 3.944650 TGCTCTTGCTTTTGTTGAGTACA 59.055 39.130 0.00 0.00 40.48 2.90
2298 2798 2.464157 AGCTAGCTTTGAGGTCACAC 57.536 50.000 12.68 0.00 0.00 3.82
2304 2804 1.867698 GCTCGCTAGCTAGCTTTGAGG 60.868 57.143 36.02 22.75 46.85 3.86
2355 2857 8.725148 CATTTAGATGAGTTCTAGCAAAACTGT 58.275 33.333 0.32 0.00 38.19 3.55
2356 2858 8.939929 TCATTTAGATGAGTTCTAGCAAAACTG 58.060 33.333 0.32 0.00 38.19 3.16


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

AutoCloner maintained by Alex Coulton.