Multiple sequence alignment - TraesCS5D01G436300

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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 TraesCS5D01G436300 chr5D 100.000 2459 0 0 1 2459 490953443 490955901 0.000000e+00 4542
1 TraesCS5D01G436300 chr5D 82.041 490 49 21 1020 1470 491796990 491796501 4.960000e-102 381
2 TraesCS5D01G436300 chr5D 92.531 241 18 0 1230 1470 491846643 491846403 1.810000e-91 346
3 TraesCS5D01G436300 chr5D 91.393 244 20 1 1228 1470 490968901 490969144 1.410000e-87 333
4 TraesCS5D01G436300 chr5D 85.976 164 17 3 996 1153 490968592 490968755 1.170000e-38 171
5 TraesCS5D01G436300 chr5D 91.339 127 8 2 1020 1143 492222505 492222379 1.170000e-38 171
6 TraesCS5D01G436300 chr5D 90.551 127 9 2 1020 1143 491846895 491846769 5.440000e-37 165
7 TraesCS5D01G436300 chr5D 89.764 127 10 2 1020 1143 492068055 492067929 2.530000e-35 159
8 TraesCS5D01G436300 chr5B 92.246 993 60 9 665 1654 605512994 605513972 0.000000e+00 1391
9 TraesCS5D01G436300 chr5B 88.078 822 55 14 1652 2459 605514048 605514840 0.000000e+00 935
10 TraesCS5D01G436300 chr5B 92.250 529 40 1 5 533 605512067 605512594 0.000000e+00 749
11 TraesCS5D01G436300 chr5B 82.245 490 44 20 1020 1468 606853674 606853187 1.380000e-102 383
12 TraesCS5D01G436300 chr5B 81.148 488 50 18 1023 1468 606871155 606870668 1.080000e-93 353
13 TraesCS5D01G436300 chr5B 90.574 244 22 1 1228 1470 605518697 605518940 3.050000e-84 322
14 TraesCS5D01G436300 chr5B 86.471 170 16 4 991 1153 605518385 605518554 1.940000e-41 180
15 TraesCS5D01G436300 chr5B 91.935 124 2 6 547 662 605512835 605512958 1.510000e-37 167
16 TraesCS5D01G436300 chr5A 92.068 996 49 13 678 1654 613373810 613374794 0.000000e+00 1375
17 TraesCS5D01G436300 chr5A 84.544 537 39 15 1860 2395 613375523 613376016 2.200000e-135 492
18 TraesCS5D01G436300 chr5A 91.701 241 19 1 1228 1467 613457555 613457795 1.410000e-87 333
19 TraesCS5D01G436300 chr5A 86.585 164 16 3 996 1153 613457246 613457409 2.510000e-40 176
20 TraesCS5D01G436300 chr5A 90.476 126 6 1 1689 1814 613374964 613375083 7.040000e-36 161
21 TraesCS5D01G436300 chr4D 81.336 584 91 13 17 588 502028396 502028973 2.230000e-125 459
22 TraesCS5D01G436300 chr6D 79.865 591 98 16 10 588 10432778 10433359 1.760000e-111 412
23 TraesCS5D01G436300 chr2A 78.150 627 115 19 22 637 10633122 10632507 1.780000e-101 379
24 TraesCS5D01G436300 chr2A 78.286 525 102 9 18 536 129857567 129858085 6.560000e-86 327
25 TraesCS5D01G436300 chr1A 78.902 583 105 12 17 588 65236409 65235834 1.780000e-101 379
26 TraesCS5D01G436300 chr2D 78.709 573 106 11 27 588 480166250 480166817 3.860000e-98 368
27 TraesCS5D01G436300 chr7A 81.963 438 68 10 104 536 103106362 103105931 6.460000e-96 361
28 TraesCS5D01G436300 chr3A 78.957 537 89 22 18 536 238675553 238676083 6.510000e-91 344


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 TraesCS5D01G436300 chr5D 490953443 490955901 2458 False 4542.0 4542 100.000000 1 2459 1 chr5D.!!$F1 2458
1 TraesCS5D01G436300 chr5D 490968592 490969144 552 False 252.0 333 88.684500 996 1470 2 chr5D.!!$F2 474
2 TraesCS5D01G436300 chr5B 605512067 605518940 6873 False 624.0 1391 90.259000 5 2459 6 chr5B.!!$F1 2454
3 TraesCS5D01G436300 chr5A 613373810 613376016 2206 False 676.0 1375 89.029333 678 2395 3 chr5A.!!$F1 1717
4 TraesCS5D01G436300 chr5A 613457246 613457795 549 False 254.5 333 89.143000 996 1467 2 chr5A.!!$F2 471
5 TraesCS5D01G436300 chr4D 502028396 502028973 577 False 459.0 459 81.336000 17 588 1 chr4D.!!$F1 571
6 TraesCS5D01G436300 chr6D 10432778 10433359 581 False 412.0 412 79.865000 10 588 1 chr6D.!!$F1 578
7 TraesCS5D01G436300 chr2A 10632507 10633122 615 True 379.0 379 78.150000 22 637 1 chr2A.!!$R1 615
8 TraesCS5D01G436300 chr2A 129857567 129858085 518 False 327.0 327 78.286000 18 536 1 chr2A.!!$F1 518
9 TraesCS5D01G436300 chr1A 65235834 65236409 575 True 379.0 379 78.902000 17 588 1 chr1A.!!$R1 571
10 TraesCS5D01G436300 chr2D 480166250 480166817 567 False 368.0 368 78.709000 27 588 1 chr2D.!!$F1 561
11 TraesCS5D01G436300 chr3A 238675553 238676083 530 False 344.0 344 78.957000 18 536 1 chr3A.!!$F1 518

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
941 1241 0.173481 CACGATCGAAGAAGAGGGCA 59.827 55.0 24.34 0.0 43.58 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 8196 0.10852 GGGTGAATCTTGCCGACGTA 60.109 55.0 0.0 0.0 0.0 3.57 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
24 25 0.830444 TTAGAGCGAGTGTGGTGGGT 60.830 55.000 0.00 0.00 0.00 4.51
50 51 2.202623 ATCTCGTCGAGGTTGCGC 60.203 61.111 21.63 0.00 0.00 6.09
112 113 3.084039 TCCTCAGATGATTTGTGGTTGC 58.916 45.455 4.32 0.00 32.45 4.17
151 152 3.964411 TCTTCCTCCTCGTCACTATGAA 58.036 45.455 0.00 0.00 0.00 2.57
435 440 0.601046 TCTGCTTGAGTCTGGTTGCG 60.601 55.000 0.00 0.00 0.00 4.85
536 557 7.206687 TGGTTATTTTAAGGTGCTCTTTGTTG 58.793 34.615 0.00 0.00 36.93 3.33
537 558 6.645003 GGTTATTTTAAGGTGCTCTTTGTTGG 59.355 38.462 0.00 0.00 36.93 3.77
543 564 1.202348 GGTGCTCTTTGTTGGTATGGC 59.798 52.381 0.00 0.00 0.00 4.40
662 940 3.557264 GGTCTCATCCCGTCTGTCTTTTT 60.557 47.826 0.00 0.00 0.00 1.94
766 1055 0.732880 CCGTCACGGTGTCAGTCATC 60.733 60.000 8.54 0.00 42.73 2.92
775 1064 0.389037 TGTCAGTCATCTGCTCGCAC 60.389 55.000 0.00 0.00 41.10 5.34
780 1069 1.002366 GTCATCTGCTCGCACGATTT 58.998 50.000 0.00 0.00 0.00 2.17
875 1165 2.361610 CGAGCCAGGCCACCAAAT 60.362 61.111 8.22 0.00 0.00 2.32
906 1206 4.796231 ACTCGATCGCACCGCACC 62.796 66.667 11.09 0.00 0.00 5.01
941 1241 0.173481 CACGATCGAAGAAGAGGGCA 59.827 55.000 24.34 0.00 43.58 5.36
978 1278 2.174349 CCAGAGTTCAAAGCGCGC 59.826 61.111 26.66 26.66 0.00 6.86
1095 1401 4.699522 GGCTGCGGGTTCTTCGGT 62.700 66.667 0.00 0.00 0.00 4.69
1222 1600 2.390599 GCCGATGCTGCAGTCGAAA 61.391 57.895 23.81 3.42 40.11 3.46
1422 6949 2.212900 GAATCGCCAAGCACAACCCC 62.213 60.000 0.00 0.00 0.00 4.95
1473 7000 1.672356 CTGAAGCCCACAAGACCGG 60.672 63.158 0.00 0.00 0.00 5.28
1480 7007 1.026718 CCCACAAGACCGGCAGAATC 61.027 60.000 0.00 0.00 0.00 2.52
1521 7048 2.887733 GAACATGTGACGTTCGTTGTC 58.112 47.619 0.00 0.00 33.98 3.18
1562 7090 8.233190 CAGTCTTGGAAATGAACTTGTAAGATC 58.767 37.037 0.00 0.00 0.00 2.75
1564 7092 8.233190 GTCTTGGAAATGAACTTGTAAGATCAG 58.767 37.037 9.83 0.00 40.46 2.90
1565 7093 7.939039 TCTTGGAAATGAACTTGTAAGATCAGT 59.061 33.333 9.83 5.18 40.46 3.41
1567 7095 7.874940 TGGAAATGAACTTGTAAGATCAGTTG 58.125 34.615 17.94 0.00 43.09 3.16
1568 7096 7.719193 TGGAAATGAACTTGTAAGATCAGTTGA 59.281 33.333 17.94 6.04 43.09 3.18
1571 7099 9.903682 AAATGAACTTGTAAGATCAGTTGATTG 57.096 29.630 14.02 0.00 42.04 2.67
1572 7100 8.853077 ATGAACTTGTAAGATCAGTTGATTGA 57.147 30.769 9.83 0.00 40.46 2.57
1573 7101 8.853077 TGAACTTGTAAGATCAGTTGATTGAT 57.147 30.769 0.46 0.00 40.40 2.57
1574 7102 9.288576 TGAACTTGTAAGATCAGTTGATTGATT 57.711 29.630 0.46 0.00 37.90 2.57
1575 7103 9.552114 GAACTTGTAAGATCAGTTGATTGATTG 57.448 33.333 0.46 0.00 37.90 2.67
1579 7107 8.853077 TGTAAGATCAGTTGATTGATTGAGTT 57.147 30.769 0.00 0.00 37.90 3.01
1580 7108 8.939929 TGTAAGATCAGTTGATTGATTGAGTTC 58.060 33.333 0.00 0.00 37.90 3.01
1581 7109 9.160496 GTAAGATCAGTTGATTGATTGAGTTCT 57.840 33.333 0.00 0.00 37.90 3.01
1600 7135 9.653287 TGAGTTCTTGTAAATTACATAGTCTGG 57.347 33.333 6.67 0.00 38.68 3.86
1609 7144 9.614792 GTAAATTACATAGTCTGGGAAGTGAAT 57.385 33.333 0.00 0.00 0.00 2.57
1614 7149 5.940470 ACATAGTCTGGGAAGTGAATTTGTC 59.060 40.000 0.00 0.00 0.00 3.18
1645 7180 6.831553 CGTTGATCGGTTGAGTTCTTGTAAAG 60.832 42.308 0.00 0.00 39.74 1.85
1664 7352 8.028540 TGTAAAGTACATTATCTTGCAGTGTG 57.971 34.615 0.00 0.00 32.89 3.82
1677 7365 3.006659 GCAGTGTGCGTTAATTTTGGA 57.993 42.857 0.00 0.00 31.71 3.53
1678 7366 3.376540 GCAGTGTGCGTTAATTTTGGAA 58.623 40.909 0.00 0.00 31.71 3.53
1679 7367 3.799420 GCAGTGTGCGTTAATTTTGGAAA 59.201 39.130 0.00 0.00 31.71 3.13
1680 7368 4.447389 GCAGTGTGCGTTAATTTTGGAAAT 59.553 37.500 0.00 0.00 31.71 2.17
1681 7369 5.612276 GCAGTGTGCGTTAATTTTGGAAATG 60.612 40.000 0.00 0.00 31.71 2.32
1682 7370 4.447389 AGTGTGCGTTAATTTTGGAAATGC 59.553 37.500 0.00 0.00 36.02 3.56
1683 7371 3.426859 TGTGCGTTAATTTTGGAAATGCG 59.573 39.130 0.00 0.00 37.84 4.73
1684 7372 2.989840 TGCGTTAATTTTGGAAATGCGG 59.010 40.909 0.00 0.00 37.84 5.69
1685 7373 2.990514 GCGTTAATTTTGGAAATGCGGT 59.009 40.909 0.00 0.00 0.00 5.68
1686 7374 4.167268 GCGTTAATTTTGGAAATGCGGTA 58.833 39.130 0.00 0.00 0.00 4.02
1687 7375 4.264380 GCGTTAATTTTGGAAATGCGGTAG 59.736 41.667 0.00 0.00 0.00 3.18
1688 7376 5.632959 CGTTAATTTTGGAAATGCGGTAGA 58.367 37.500 0.00 0.00 0.00 2.59
1689 7377 6.262601 CGTTAATTTTGGAAATGCGGTAGAT 58.737 36.000 0.00 0.00 0.00 1.98
1697 7385 5.555966 TGGAAATGCGGTAGATAATATGCA 58.444 37.500 0.00 0.00 36.69 3.96
1731 7419 2.151202 CTCATGGTTGCCTACGTTTGT 58.849 47.619 0.00 0.00 0.00 2.83
1732 7420 3.331150 CTCATGGTTGCCTACGTTTGTA 58.669 45.455 0.00 0.00 0.00 2.41
1733 7421 3.068560 TCATGGTTGCCTACGTTTGTAC 58.931 45.455 0.00 0.00 0.00 2.90
1734 7422 2.914695 TGGTTGCCTACGTTTGTACT 57.085 45.000 0.00 0.00 0.00 2.73
1735 7423 4.021280 TCATGGTTGCCTACGTTTGTACTA 60.021 41.667 0.00 0.00 0.00 1.82
1736 7424 4.333913 TGGTTGCCTACGTTTGTACTAA 57.666 40.909 0.00 0.00 0.00 2.24
1746 7434 8.711457 GCCTACGTTTGTACTAATAAACAAAGA 58.289 33.333 0.00 0.00 43.99 2.52
1778 7466 7.768807 AAACATTTTAGGTATTGTGGCACTA 57.231 32.000 19.83 12.22 0.00 2.74
1783 7471 8.559536 CATTTTAGGTATTGTGGCACTATACTG 58.440 37.037 34.41 25.24 37.12 2.74
1798 7486 6.074088 GCACTATACTGAACGATTTGGAGATG 60.074 42.308 0.00 0.00 0.00 2.90
1809 7497 3.895232 TTTGGAGATGTAGGAGTGAGC 57.105 47.619 0.00 0.00 0.00 4.26
1820 7918 5.373222 TGTAGGAGTGAGCTTGCTTTAAAA 58.627 37.500 0.00 0.00 0.00 1.52
1823 7921 5.776744 AGGAGTGAGCTTGCTTTAAAAATG 58.223 37.500 0.00 0.00 0.00 2.32
1833 7931 9.123902 AGCTTGCTTTAAAAATGAAAAAGGATT 57.876 25.926 0.00 0.00 31.83 3.01
1843 7941 9.594478 AAAAATGAAAAAGGATTTGTAACGTCT 57.406 25.926 0.00 0.00 39.02 4.18
1844 7942 8.797266 AAATGAAAAAGGATTTGTAACGTCTC 57.203 30.769 0.00 0.00 39.02 3.36
1845 7943 6.308371 TGAAAAAGGATTTGTAACGTCTCC 57.692 37.500 0.00 0.00 39.02 3.71
1846 7944 5.823570 TGAAAAAGGATTTGTAACGTCTCCA 59.176 36.000 0.00 0.00 39.02 3.86
1847 7945 6.319152 TGAAAAAGGATTTGTAACGTCTCCAA 59.681 34.615 0.00 0.00 39.02 3.53
1848 7946 5.684550 AAAGGATTTGTAACGTCTCCAAC 57.315 39.130 0.00 0.00 36.60 3.77
1868 7966 8.821147 TCCAACGTATATATAATTCGCTTTGT 57.179 30.769 0.00 0.00 0.00 2.83
1892 7990 4.008074 TGGTTGAACTCCTCATCAGTTC 57.992 45.455 5.75 5.75 46.85 3.01
1910 8008 8.910666 CATCAGTTCAGATAATTGATACGTCTC 58.089 37.037 0.00 0.00 0.00 3.36
1915 8013 7.107639 TCAGATAATTGATACGTCTCCAACA 57.892 36.000 0.00 0.00 0.00 3.33
1918 8016 8.916654 CAGATAATTGATACGTCTCCAACATAC 58.083 37.037 0.00 0.00 0.00 2.39
1973 8072 9.962809 TCACATCAATTATATATGATCTTGGCA 57.037 29.630 0.00 0.00 34.12 4.92
2058 8157 4.278170 TCCTAGTGTTTTTGCACATTCCAG 59.722 41.667 0.00 0.00 41.52 3.86
2065 8164 5.115480 GTTTTTGCACATTCCAGAAAAGGA 58.885 37.500 0.00 0.00 35.41 3.36
2079 8178 3.006859 AGAAAAGGAATTTTTGGGAGCGG 59.993 43.478 0.00 0.00 39.06 5.52
2081 8180 2.302587 AGGAATTTTTGGGAGCGGAA 57.697 45.000 0.00 0.00 0.00 4.30
2194 8293 2.042537 TCTCTCTCATGCGCCCCT 60.043 61.111 4.18 0.00 0.00 4.79
2195 8294 2.108566 CTCTCTCATGCGCCCCTG 59.891 66.667 4.18 0.00 0.00 4.45
2196 8295 3.457625 CTCTCTCATGCGCCCCTGG 62.458 68.421 4.18 0.00 0.00 4.45
2197 8296 4.559063 CTCTCATGCGCCCCTGGG 62.559 72.222 5.50 5.50 38.57 4.45
2207 8306 3.854669 CCCCTGGGCTACGAGCTG 61.855 72.222 7.39 0.00 41.99 4.24
2208 8307 2.759973 CCCTGGGCTACGAGCTGA 60.760 66.667 0.00 0.00 41.99 4.26
2211 8310 2.037367 TGGGCTACGAGCTGAGGT 59.963 61.111 0.00 0.00 41.99 3.85
2216 8315 1.213013 CTACGAGCTGAGGTTGCGT 59.787 57.895 0.00 3.95 38.81 5.24
2238 8337 1.079127 CACGTAGCAGGTCCCTTGG 60.079 63.158 0.00 0.00 0.00 3.61
2282 8381 0.040425 CTTCGGAAGTTTTGCCACCG 60.040 55.000 9.61 0.00 44.09 4.94
2283 8382 2.050442 CGGAAGTTTTGCCACCGC 60.050 61.111 0.00 0.00 37.32 5.68
2289 8388 0.251608 AGTTTTGCCACCGCCCTATT 60.252 50.000 0.00 0.00 0.00 1.73
2339 8438 2.542550 TCCGTGGAGGAGGTAAAATGA 58.457 47.619 0.00 0.00 45.98 2.57
2345 8444 4.878397 GTGGAGGAGGTAAAATGATGACAG 59.122 45.833 0.00 0.00 0.00 3.51
2346 8445 4.782691 TGGAGGAGGTAAAATGATGACAGA 59.217 41.667 0.00 0.00 0.00 3.41
2378 8477 7.681939 TTTCAACATCTAGAAAAATACCGCT 57.318 32.000 0.00 0.00 31.35 5.52
2386 8485 4.553330 AGAAAAATACCGCTCAAGGAGA 57.447 40.909 0.00 0.00 34.73 3.71
2403 8502 3.677002 GAGAGCCAATCTCGAAGGG 57.323 57.895 0.00 0.00 44.95 3.95
2404 8503 0.105778 GAGAGCCAATCTCGAAGGGG 59.894 60.000 0.00 0.00 44.95 4.79
2405 8504 1.147153 GAGCCAATCTCGAAGGGGG 59.853 63.158 0.00 0.00 31.20 5.40
2406 8505 2.517166 GCCAATCTCGAAGGGGGC 60.517 66.667 2.59 2.59 0.00 5.80
2407 8506 3.049080 GCCAATCTCGAAGGGGGCT 62.049 63.158 9.77 0.00 38.37 5.19
2408 8507 1.147153 CCAATCTCGAAGGGGGCTC 59.853 63.158 0.00 0.00 0.00 4.70
2409 8508 1.341156 CCAATCTCGAAGGGGGCTCT 61.341 60.000 0.00 0.00 0.00 4.09
2410 8509 0.105778 CAATCTCGAAGGGGGCTCTC 59.894 60.000 0.00 0.00 0.00 3.20
2411 8510 1.395826 AATCTCGAAGGGGGCTCTCG 61.396 60.000 0.00 0.00 0.00 4.04
2412 8511 4.214327 CTCGAAGGGGGCTCTCGC 62.214 72.222 0.00 0.00 0.00 5.03
2422 8521 2.185608 GCTCTCGCCTTCCAGGAC 59.814 66.667 0.00 0.00 37.67 3.85
2423 8522 2.896443 CTCTCGCCTTCCAGGACC 59.104 66.667 0.00 0.00 37.67 4.46
2424 8523 1.984570 CTCTCGCCTTCCAGGACCA 60.985 63.158 0.00 0.00 37.67 4.02
2425 8524 1.306141 TCTCGCCTTCCAGGACCAT 60.306 57.895 0.00 0.00 37.67 3.55
2426 8525 0.032515 TCTCGCCTTCCAGGACCATA 60.033 55.000 0.00 0.00 37.67 2.74
2427 8526 0.830648 CTCGCCTTCCAGGACCATAA 59.169 55.000 0.00 0.00 37.67 1.90
2428 8527 1.209504 CTCGCCTTCCAGGACCATAAA 59.790 52.381 0.00 0.00 37.67 1.40
2429 8528 1.631388 TCGCCTTCCAGGACCATAAAA 59.369 47.619 0.00 0.00 37.67 1.52
2430 8529 1.743394 CGCCTTCCAGGACCATAAAAC 59.257 52.381 0.00 0.00 37.67 2.43
2431 8530 2.100197 GCCTTCCAGGACCATAAAACC 58.900 52.381 0.00 0.00 37.67 3.27
2432 8531 2.556559 GCCTTCCAGGACCATAAAACCA 60.557 50.000 0.00 0.00 37.67 3.67
2433 8532 3.773560 CCTTCCAGGACCATAAAACCAA 58.226 45.455 0.00 0.00 37.67 3.67
2434 8533 4.352893 CCTTCCAGGACCATAAAACCAAT 58.647 43.478 0.00 0.00 37.67 3.16
2435 8534 4.160252 CCTTCCAGGACCATAAAACCAATG 59.840 45.833 0.00 0.00 37.67 2.82
2436 8535 4.666412 TCCAGGACCATAAAACCAATGA 57.334 40.909 0.00 0.00 0.00 2.57
2437 8536 4.340617 TCCAGGACCATAAAACCAATGAC 58.659 43.478 0.00 0.00 0.00 3.06
2438 8537 4.044065 TCCAGGACCATAAAACCAATGACT 59.956 41.667 0.00 0.00 0.00 3.41
2439 8538 5.251932 TCCAGGACCATAAAACCAATGACTA 59.748 40.000 0.00 0.00 0.00 2.59
2440 8539 5.590259 CCAGGACCATAAAACCAATGACTAG 59.410 44.000 0.00 0.00 0.00 2.57
2441 8540 6.414732 CAGGACCATAAAACCAATGACTAGA 58.585 40.000 0.00 0.00 0.00 2.43
2442 8541 6.540189 CAGGACCATAAAACCAATGACTAGAG 59.460 42.308 0.00 0.00 0.00 2.43
2443 8542 5.823045 GGACCATAAAACCAATGACTAGAGG 59.177 44.000 0.00 0.00 0.00 3.69
2444 8543 6.352737 GGACCATAAAACCAATGACTAGAGGA 60.353 42.308 0.00 0.00 0.00 3.71
2445 8544 6.653989 ACCATAAAACCAATGACTAGAGGAG 58.346 40.000 0.00 0.00 0.00 3.69
2446 8545 6.058183 CCATAAAACCAATGACTAGAGGAGG 58.942 44.000 0.00 0.00 0.00 4.30
2447 8546 6.126768 CCATAAAACCAATGACTAGAGGAGGA 60.127 42.308 0.00 0.00 0.00 3.71
2448 8547 5.843019 AAAACCAATGACTAGAGGAGGAA 57.157 39.130 0.00 0.00 0.00 3.36
2449 8548 4.828072 AACCAATGACTAGAGGAGGAAC 57.172 45.455 0.00 0.00 0.00 3.62
2450 8549 3.108376 ACCAATGACTAGAGGAGGAACC 58.892 50.000 0.00 0.00 39.35 3.62
2458 8557 1.229853 GAGGAGGAACCTTCCCCCA 60.230 63.158 7.34 0.00 46.92 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.522180 ACCACACTCGCTCTAAGTCG 59.478 55.000 0.00 0.00 0.00 4.18
3 4 0.603569 CCACCACACTCGCTCTAAGT 59.396 55.000 0.00 0.00 0.00 2.24
6 7 0.038599 TACCCACCACACTCGCTCTA 59.961 55.000 0.00 0.00 0.00 2.43
24 25 0.321387 CTCGACGAGATCCGGGGATA 60.321 60.000 20.25 0.00 43.93 2.59
50 51 1.335415 CGACCTCCAGACATCATAGCG 60.335 57.143 0.00 0.00 0.00 4.26
112 113 4.390297 GGAAGAAAAATCTCTGTCTCCACG 59.610 45.833 0.00 0.00 0.00 4.94
151 152 5.176741 AGAGGAAGAACATCAGCAGAAAT 57.823 39.130 0.00 0.00 0.00 2.17
237 239 7.257790 TGGAAGAGAATTGGATCTTGTTCTA 57.742 36.000 6.90 0.00 35.93 2.10
243 245 5.431073 TCCAGATGGAAGAGAATTGGATCTT 59.569 40.000 0.00 0.00 42.18 2.40
435 440 3.382546 AGGCTCATGCAACACAATAATCC 59.617 43.478 0.00 0.00 41.91 3.01
522 543 2.795329 CCATACCAACAAAGAGCACCT 58.205 47.619 0.00 0.00 0.00 4.00
536 557 1.396996 CTTAACACGCACAGCCATACC 59.603 52.381 0.00 0.00 0.00 2.73
537 558 1.396996 CCTTAACACGCACAGCCATAC 59.603 52.381 0.00 0.00 0.00 2.39
543 564 0.041312 GCACACCTTAACACGCACAG 60.041 55.000 0.00 0.00 0.00 3.66
662 940 7.516198 AGTAGACGGTAGACTGTTCTAAAAA 57.484 36.000 0.00 0.00 36.03 1.94
722 1011 2.801699 CGCAGTTGCCACGGATAATCTA 60.802 50.000 0.00 0.00 37.91 1.98
766 1055 1.849219 GAGTCTAAATCGTGCGAGCAG 59.151 52.381 0.00 0.00 0.00 4.24
775 1064 0.249489 CCCAGCCGGAGTCTAAATCG 60.249 60.000 5.05 0.00 0.00 3.34
875 1165 2.049802 GAGTTTGGGACGCGACGA 60.050 61.111 15.93 0.00 0.00 4.20
906 1206 4.794439 TGATCCCTCGTGCGTGCG 62.794 66.667 0.00 0.00 0.00 5.34
907 1207 3.188786 GTGATCCCTCGTGCGTGC 61.189 66.667 0.00 0.00 0.00 5.34
908 1208 2.613739 ATCGTGATCCCTCGTGCGTG 62.614 60.000 0.00 0.00 0.00 5.34
909 1209 2.337749 GATCGTGATCCCTCGTGCGT 62.338 60.000 0.00 0.00 31.76 5.24
910 1210 1.658717 GATCGTGATCCCTCGTGCG 60.659 63.158 0.00 0.00 31.76 5.34
954 1254 3.825160 TTTGAACTCTGGCGCCGCT 62.825 57.895 23.90 3.25 0.00 5.52
955 1255 3.314388 CTTTGAACTCTGGCGCCGC 62.314 63.158 23.90 0.00 0.00 6.53
956 1256 2.863153 CTTTGAACTCTGGCGCCG 59.137 61.111 23.90 16.91 0.00 6.46
957 1257 2.563427 GCTTTGAACTCTGGCGCC 59.437 61.111 22.73 22.73 0.00 6.53
963 1263 3.050275 GGGCGCGCTTTGAACTCT 61.050 61.111 32.29 0.00 0.00 3.24
967 1267 2.903547 GAACAGGGCGCGCTTTGAA 61.904 57.895 32.29 0.00 0.00 2.69
968 1268 3.353836 GAACAGGGCGCGCTTTGA 61.354 61.111 32.29 0.00 0.00 2.69
978 1278 0.457851 CTACTGCTCCTCGAACAGGG 59.542 60.000 8.66 0.00 43.67 4.45
1422 6949 4.986587 TTGTCCGCGACCACGACG 62.987 66.667 8.23 0.00 42.66 5.12
1423 6950 2.814183 ATCTTGTCCGCGACCACGAC 62.814 60.000 8.23 6.59 42.66 4.34
1473 7000 1.134530 CGTCGTCTGGTCGATTCTGC 61.135 60.000 0.00 0.00 41.78 4.26
1480 7007 0.388134 ATGGTTTCGTCGTCTGGTCG 60.388 55.000 0.00 0.00 0.00 4.79
1521 7048 6.151287 CCAAGACTGATTACAGGTTTGGCG 62.151 50.000 15.93 0.00 45.26 5.69
1562 7090 9.903682 ATTTACAAGAACTCAATCAATCAACTG 57.096 29.630 0.00 0.00 0.00 3.16
1574 7102 9.653287 CCAGACTATGTAATTTACAAGAACTCA 57.347 33.333 12.96 0.00 42.76 3.41
1575 7103 9.099454 CCCAGACTATGTAATTTACAAGAACTC 57.901 37.037 12.96 4.73 42.76 3.01
1579 7107 8.822805 ACTTCCCAGACTATGTAATTTACAAGA 58.177 33.333 12.96 4.27 42.76 3.02
1580 7108 8.883731 CACTTCCCAGACTATGTAATTTACAAG 58.116 37.037 12.96 12.94 42.76 3.16
1581 7109 8.598916 TCACTTCCCAGACTATGTAATTTACAA 58.401 33.333 12.96 3.11 42.76 2.41
1600 7135 2.351726 CGGATCGGACAAATTCACTTCC 59.648 50.000 0.00 0.00 0.00 3.46
1645 7180 3.370978 ACGCACACTGCAAGATAATGTAC 59.629 43.478 0.00 0.00 45.36 2.90
1664 7352 2.990514 ACCGCATTTCCAAAATTAACGC 59.009 40.909 0.00 0.00 0.00 4.84
1672 7360 6.488344 TGCATATTATCTACCGCATTTCCAAA 59.512 34.615 0.00 0.00 0.00 3.28
1673 7361 6.000840 TGCATATTATCTACCGCATTTCCAA 58.999 36.000 0.00 0.00 0.00 3.53
1674 7362 5.555966 TGCATATTATCTACCGCATTTCCA 58.444 37.500 0.00 0.00 0.00 3.53
1675 7363 6.458751 CCATGCATATTATCTACCGCATTTCC 60.459 42.308 0.00 0.00 37.98 3.13
1676 7364 6.316140 TCCATGCATATTATCTACCGCATTTC 59.684 38.462 0.00 0.00 37.98 2.17
1677 7365 6.179756 TCCATGCATATTATCTACCGCATTT 58.820 36.000 0.00 0.00 37.98 2.32
1678 7366 5.744171 TCCATGCATATTATCTACCGCATT 58.256 37.500 0.00 0.00 37.98 3.56
1679 7367 5.357742 TCCATGCATATTATCTACCGCAT 57.642 39.130 0.00 0.00 40.55 4.73
1680 7368 4.817318 TCCATGCATATTATCTACCGCA 57.183 40.909 0.00 0.00 0.00 5.69
1681 7369 6.094048 ACAAATCCATGCATATTATCTACCGC 59.906 38.462 0.00 0.00 0.00 5.68
1682 7370 7.615582 ACAAATCCATGCATATTATCTACCG 57.384 36.000 0.00 0.00 0.00 4.02
1686 7374 9.305555 AGCTAAACAAATCCATGCATATTATCT 57.694 29.630 0.00 0.00 0.00 1.98
1687 7375 9.565213 GAGCTAAACAAATCCATGCATATTATC 57.435 33.333 0.00 0.00 0.00 1.75
1688 7376 9.081204 TGAGCTAAACAAATCCATGCATATTAT 57.919 29.630 0.00 0.00 0.00 1.28
1689 7377 8.462589 TGAGCTAAACAAATCCATGCATATTA 57.537 30.769 0.00 0.00 0.00 0.98
1697 7385 5.625197 GCAACCATGAGCTAAACAAATCCAT 60.625 40.000 0.00 0.00 0.00 3.41
1778 7466 6.323996 TCCTACATCTCCAAATCGTTCAGTAT 59.676 38.462 0.00 0.00 0.00 2.12
1783 7471 4.806247 CACTCCTACATCTCCAAATCGTTC 59.194 45.833 0.00 0.00 0.00 3.95
1798 7486 5.941948 TTTTAAAGCAAGCTCACTCCTAC 57.058 39.130 0.00 0.00 0.00 3.18
1820 7918 7.013846 TGGAGACGTTACAAATCCTTTTTCATT 59.986 33.333 0.00 0.00 0.00 2.57
1823 7921 6.308371 TGGAGACGTTACAAATCCTTTTTC 57.692 37.500 0.00 0.00 0.00 2.29
1840 7938 8.684973 AAGCGAATTATATATACGTTGGAGAC 57.315 34.615 0.00 0.00 0.00 3.36
1841 7939 9.135843 CAAAGCGAATTATATATACGTTGGAGA 57.864 33.333 0.00 0.00 0.00 3.71
1842 7940 8.922676 ACAAAGCGAATTATATATACGTTGGAG 58.077 33.333 0.00 0.65 0.00 3.86
1843 7941 8.821147 ACAAAGCGAATTATATATACGTTGGA 57.179 30.769 0.00 0.00 0.00 3.53
1853 7951 9.730420 GTTCAACCAATACAAAGCGAATTATAT 57.270 29.630 0.00 0.00 0.00 0.86
1854 7952 8.952278 AGTTCAACCAATACAAAGCGAATTATA 58.048 29.630 0.00 0.00 0.00 0.98
1855 7953 7.826690 AGTTCAACCAATACAAAGCGAATTAT 58.173 30.769 0.00 0.00 0.00 1.28
1856 7954 7.209471 AGTTCAACCAATACAAAGCGAATTA 57.791 32.000 0.00 0.00 0.00 1.40
1857 7955 6.084326 AGTTCAACCAATACAAAGCGAATT 57.916 33.333 0.00 0.00 0.00 2.17
1858 7956 5.335661 GGAGTTCAACCAATACAAAGCGAAT 60.336 40.000 0.00 0.00 0.00 3.34
1868 7966 5.762179 ACTGATGAGGAGTTCAACCAATA 57.238 39.130 0.00 0.00 39.77 1.90
1892 7990 7.953158 ATGTTGGAGACGTATCAATTATCTG 57.047 36.000 12.92 0.00 0.00 2.90
2058 8157 3.006430 TCCGCTCCCAAAAATTCCTTTTC 59.994 43.478 0.00 0.00 34.91 2.29
2086 8185 9.493206 GAATCTTGCCGACGTATTTTATTTTTA 57.507 29.630 0.00 0.00 0.00 1.52
2087 8186 8.024285 TGAATCTTGCCGACGTATTTTATTTTT 58.976 29.630 0.00 0.00 0.00 1.94
2088 8187 7.483691 GTGAATCTTGCCGACGTATTTTATTTT 59.516 33.333 0.00 0.00 0.00 1.82
2089 8188 6.964934 GTGAATCTTGCCGACGTATTTTATTT 59.035 34.615 0.00 0.00 0.00 1.40
2090 8189 6.457799 GGTGAATCTTGCCGACGTATTTTATT 60.458 38.462 0.00 0.00 0.00 1.40
2091 8190 5.007332 GGTGAATCTTGCCGACGTATTTTAT 59.993 40.000 0.00 0.00 0.00 1.40
2092 8191 4.330620 GGTGAATCTTGCCGACGTATTTTA 59.669 41.667 0.00 0.00 0.00 1.52
2093 8192 3.126343 GGTGAATCTTGCCGACGTATTTT 59.874 43.478 0.00 0.00 0.00 1.82
2094 8193 2.676342 GGTGAATCTTGCCGACGTATTT 59.324 45.455 0.00 0.00 0.00 1.40
2095 8194 2.277084 GGTGAATCTTGCCGACGTATT 58.723 47.619 0.00 0.00 0.00 1.89
2096 8195 1.472728 GGGTGAATCTTGCCGACGTAT 60.473 52.381 0.00 0.00 0.00 3.06
2097 8196 0.108520 GGGTGAATCTTGCCGACGTA 60.109 55.000 0.00 0.00 0.00 3.57
2103 8202 1.141858 CTCCTAGGGGTGAATCTTGCC 59.858 57.143 9.46 0.00 0.00 4.52
2147 8246 2.767496 CCCTCTGGCTCCCCTCTG 60.767 72.222 0.00 0.00 0.00 3.35
2148 8247 4.101077 CCCCTCTGGCTCCCCTCT 62.101 72.222 0.00 0.00 0.00 3.69
2166 8265 3.363844 GAGAGAGAGGCGTGTGGGC 62.364 68.421 0.00 0.00 42.69 5.36
2194 8293 1.609501 AACCTCAGCTCGTAGCCCA 60.610 57.895 3.66 0.00 43.77 5.36
2195 8294 1.153549 CAACCTCAGCTCGTAGCCC 60.154 63.158 3.66 0.00 43.77 5.19
2196 8295 1.811679 GCAACCTCAGCTCGTAGCC 60.812 63.158 3.66 0.00 43.77 3.93
2197 8296 2.161486 CGCAACCTCAGCTCGTAGC 61.161 63.158 0.00 0.00 42.84 3.58
2198 8297 1.073216 CACGCAACCTCAGCTCGTAG 61.073 60.000 0.00 0.00 0.00 3.51
2199 8298 1.080772 CACGCAACCTCAGCTCGTA 60.081 57.895 0.00 0.00 0.00 3.43
2200 8299 2.356313 CACGCAACCTCAGCTCGT 60.356 61.111 0.00 0.00 0.00 4.18
2201 8300 2.356313 ACACGCAACCTCAGCTCG 60.356 61.111 0.00 0.00 0.00 5.03
2202 8301 2.029844 GGACACGCAACCTCAGCTC 61.030 63.158 0.00 0.00 0.00 4.09
2203 8302 2.031163 GGACACGCAACCTCAGCT 59.969 61.111 0.00 0.00 0.00 4.24
2204 8303 2.280797 TGGACACGCAACCTCAGC 60.281 61.111 0.00 0.00 0.00 4.26
2205 8304 3.642755 GTGGACACGCAACCTCAG 58.357 61.111 0.00 0.00 0.00 3.35
2216 8315 2.280552 GGGACCTGCTACGTGGACA 61.281 63.158 1.81 0.00 0.00 4.02
2226 8325 0.464554 GATGCTACCAAGGGACCTGC 60.465 60.000 0.00 0.00 0.00 4.85
2238 8337 1.401905 CCTGCGGAAAAAGGATGCTAC 59.598 52.381 0.00 0.00 35.40 3.58
2266 8365 2.050442 GCGGTGGCAAAACTTCCG 60.050 61.111 7.52 7.52 43.37 4.30
2289 8388 9.442047 CCTAGCTCTGAAAAATCTAGAGAAAAA 57.558 33.333 0.00 0.00 40.21 1.94
2311 8410 3.590643 TCCTCCACGGAGTTCCTAG 57.409 57.895 12.08 0.00 41.61 3.02
2386 8485 1.341156 CCCCCTTCGAGATTGGCTCT 61.341 60.000 0.00 0.00 41.66 4.09
2413 8512 5.016173 TCATTGGTTTTATGGTCCTGGAAG 58.984 41.667 0.00 0.00 0.00 3.46
2414 8513 4.770010 GTCATTGGTTTTATGGTCCTGGAA 59.230 41.667 0.00 0.00 0.00 3.53
2415 8514 4.044065 AGTCATTGGTTTTATGGTCCTGGA 59.956 41.667 0.00 0.00 0.00 3.86
2416 8515 4.344104 AGTCATTGGTTTTATGGTCCTGG 58.656 43.478 0.00 0.00 0.00 4.45
2417 8516 6.414732 TCTAGTCATTGGTTTTATGGTCCTG 58.585 40.000 0.00 0.00 0.00 3.86
2418 8517 6.353082 CCTCTAGTCATTGGTTTTATGGTCCT 60.353 42.308 0.00 0.00 0.00 3.85
2419 8518 5.823045 CCTCTAGTCATTGGTTTTATGGTCC 59.177 44.000 0.00 0.00 0.00 4.46
2420 8519 6.650120 TCCTCTAGTCATTGGTTTTATGGTC 58.350 40.000 0.00 0.00 0.00 4.02
2421 8520 6.353082 CCTCCTCTAGTCATTGGTTTTATGGT 60.353 42.308 0.00 0.00 0.00 3.55
2422 8521 6.058183 CCTCCTCTAGTCATTGGTTTTATGG 58.942 44.000 0.00 0.00 0.00 2.74
2423 8522 6.889198 TCCTCCTCTAGTCATTGGTTTTATG 58.111 40.000 0.00 0.00 0.00 1.90
2424 8523 7.339482 GTTCCTCCTCTAGTCATTGGTTTTAT 58.661 38.462 0.00 0.00 0.00 1.40
2425 8524 6.296259 GGTTCCTCCTCTAGTCATTGGTTTTA 60.296 42.308 0.00 0.00 0.00 1.52
2426 8525 5.515008 GGTTCCTCCTCTAGTCATTGGTTTT 60.515 44.000 0.00 0.00 0.00 2.43
2427 8526 4.019231 GGTTCCTCCTCTAGTCATTGGTTT 60.019 45.833 0.00 0.00 0.00 3.27
2428 8527 3.519913 GGTTCCTCCTCTAGTCATTGGTT 59.480 47.826 0.00 0.00 0.00 3.67
2429 8528 3.108376 GGTTCCTCCTCTAGTCATTGGT 58.892 50.000 0.00 0.00 0.00 3.67
2430 8529 3.379452 AGGTTCCTCCTCTAGTCATTGG 58.621 50.000 0.00 0.00 44.42 3.16


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

AutoCloner maintained by Alex Coulton.