Multiple sequence alignment - TraesCS2A01G159300

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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 TraesCS2A01G159300 chr2A 100.000 6686 0 0 1 6686 106811108 106804423 0.000000e+00 12347.0
1 TraesCS2A01G159300 chr2A 93.478 92 4 2 4061 4150 570001449 570001540 1.170000e-27 135.0
2 TraesCS2A01G159300 chr2B 93.396 4815 164 43 10 4733 159897283 159892532 0.000000e+00 6988.0
3 TraesCS2A01G159300 chr2B 94.945 1543 45 11 4762 6298 159892533 159891018 0.000000e+00 2386.0
4 TraesCS2A01G159300 chr2B 87.870 338 25 6 6299 6634 159885993 159885670 3.780000e-102 383.0
5 TraesCS2A01G159300 chr2B 92.784 97 6 1 4057 4152 691994690 691994786 9.040000e-29 139.0
6 TraesCS2A01G159300 chr2D 89.625 3094 214 59 1 3011 110670898 110667829 0.000000e+00 3836.0
7 TraesCS2A01G159300 chr2D 91.395 2150 101 32 4548 6672 110666316 110664226 0.000000e+00 2868.0
8 TraesCS2A01G159300 chr2D 95.421 1070 35 6 3001 4065 110667806 110666746 0.000000e+00 1692.0
9 TraesCS2A01G159300 chr2D 93.046 417 25 4 4147 4561 110666747 110666333 2.060000e-169 606.0
10 TraesCS2A01G159300 chr2D 93.684 95 5 1 4061 4154 307490174 307490080 2.510000e-29 141.0
11 TraesCS2A01G159300 chr4A 95.455 88 3 1 4064 4150 570916153 570916240 9.040000e-29 139.0
12 TraesCS2A01G159300 chr7D 94.382 89 4 1 4062 4149 28032482 28032394 1.170000e-27 135.0
13 TraesCS2A01G159300 chr6B 94.382 89 4 1 4064 4151 96886077 96886165 1.170000e-27 135.0
14 TraesCS2A01G159300 chr4D 93.407 91 5 1 4063 4152 28237808 28237898 4.210000e-27 134.0
15 TraesCS2A01G159300 chr6D 90.099 101 9 1 4053 4152 399221350 399221450 5.440000e-26 130.0
16 TraesCS2A01G159300 chr5B 91.803 61 2 2 6610 6668 670789719 670789660 1.550000e-11 82.4


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 TraesCS2A01G159300 chr2A 106804423 106811108 6685 True 12347.0 12347 100.00000 1 6686 1 chr2A.!!$R1 6685
1 TraesCS2A01G159300 chr2B 159891018 159897283 6265 True 4687.0 6988 94.17050 10 6298 2 chr2B.!!$R2 6288
2 TraesCS2A01G159300 chr2D 110664226 110670898 6672 True 2250.5 3836 92.37175 1 6672 4 chr2D.!!$R2 6671

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
490 502 0.033504 GTGAAGGGAACTCGTGAGCA 59.966 55.000 0.00 0.00 42.68 4.26 F
1668 1771 0.027586 GATAAACGGTGATGGTGCGC 59.972 55.000 0.00 0.00 0.00 6.09 F
1736 1839 2.427095 ACAACACAAAAGCAACCTCTCC 59.573 45.455 0.00 0.00 0.00 3.71 F
2789 2906 4.036734 TGAAGATTGGTTTCAGTGAACAGC 59.963 41.667 4.68 7.55 31.35 4.40 F
4601 4787 2.076100 CTTATTTCGTGCTCACTGGCA 58.924 47.619 0.00 0.00 40.15 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 2296 0.179018 AGGTGCCTTCACAAGTGACC 60.179 55.000 1.73 1.34 44.87 4.02 R
3191 3342 1.915141 CATCTTCAAGCCAACCTGGT 58.085 50.000 0.00 0.00 40.46 4.00 R
3595 3746 7.175467 TCACCAGTAGAAGTATGTTCGTTAAGA 59.825 37.037 0.00 0.00 0.00 2.10 R
4719 4905 0.826715 GCCAGCTGACCAGACAGATA 59.173 55.000 17.39 0.00 39.94 1.98 R
6347 6554 0.321671 TCCTCCTGACGAAGCCTTTG 59.678 55.000 0.00 0.00 0.00 2.77 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
58 59 2.530801 CCCCACCACCAACCCAAT 59.469 61.111 0.00 0.00 0.00 3.16
59 60 1.912763 CCCCACCACCAACCCAATG 60.913 63.158 0.00 0.00 0.00 2.82
62 63 0.112218 CCACCACCAACCCAATGAGA 59.888 55.000 0.00 0.00 0.00 3.27
103 104 3.825908 TTGGCAACCCCTTAAAGATCT 57.174 42.857 0.00 0.00 0.00 2.75
123 124 0.823460 GAAGAGCTAGCCTGAGTGCT 59.177 55.000 12.13 1.33 45.38 4.40
130 131 2.266554 CTAGCCTGAGTGCTTTCTTCG 58.733 52.381 0.95 0.00 42.75 3.79
158 167 1.571955 ATTTGTGCCTTGGGGAATCC 58.428 50.000 0.00 0.00 33.58 3.01
209 218 2.448453 ACTTACGAACCAGGGAGAGAG 58.552 52.381 0.00 0.00 0.00 3.20
302 311 0.534873 ATTTTGTAATGTGCGCCCCC 59.465 50.000 4.18 0.00 0.00 5.40
349 358 1.373435 GTGGTGGACCCGACAATCA 59.627 57.895 0.00 0.00 35.15 2.57
416 428 0.392863 CGGAGATGGTGGATGCAACA 60.393 55.000 7.64 7.64 0.00 3.33
449 461 6.128391 TGGACAACGACAATGCTAAATCTAAC 60.128 38.462 0.00 0.00 0.00 2.34
484 496 4.381411 AGAAAGAAAGTGAAGGGAACTCG 58.619 43.478 0.00 0.00 42.68 4.18
490 502 0.033504 GTGAAGGGAACTCGTGAGCA 59.966 55.000 0.00 0.00 42.68 4.26
495 507 0.741221 GGGAACTCGTGAGCATGTCC 60.741 60.000 0.00 0.00 0.00 4.02
504 516 0.398522 TGAGCATGTCCGGGGTAGAT 60.399 55.000 0.00 0.00 0.00 1.98
508 520 2.180276 GCATGTCCGGGGTAGATAGAT 58.820 52.381 0.00 0.00 0.00 1.98
509 521 3.011369 AGCATGTCCGGGGTAGATAGATA 59.989 47.826 0.00 0.00 0.00 1.98
510 522 3.381908 GCATGTCCGGGGTAGATAGATAG 59.618 52.174 0.00 0.00 0.00 2.08
511 523 4.856509 CATGTCCGGGGTAGATAGATAGA 58.143 47.826 0.00 0.00 0.00 1.98
512 524 5.450453 CATGTCCGGGGTAGATAGATAGAT 58.550 45.833 0.00 0.00 0.00 1.98
516 528 6.620267 TGTCCGGGGTAGATAGATAGATAGAT 59.380 42.308 0.00 0.00 0.00 1.98
520 532 9.053472 CCGGGGTAGATAGATAGATAGATAGAT 57.947 40.741 0.00 0.00 0.00 1.98
657 693 4.649088 AAACTTTGCCTTGTACACTTCC 57.351 40.909 0.00 0.00 0.00 3.46
765 801 0.465460 AGCGTGTGCCTTCAAGGAAA 60.465 50.000 7.98 0.00 44.31 3.13
794 830 1.817099 GAAGCACGCAGATCCCCAG 60.817 63.158 0.00 0.00 0.00 4.45
795 831 2.244117 GAAGCACGCAGATCCCCAGA 62.244 60.000 0.00 0.00 0.00 3.86
797 833 1.153086 GCACGCAGATCCCCAGAAT 60.153 57.895 0.00 0.00 0.00 2.40
802 838 1.925120 CAGATCCCCAGAATGCCCA 59.075 57.895 0.00 0.00 31.97 5.36
805 841 1.935400 ATCCCCAGAATGCCCACCA 60.935 57.895 0.00 0.00 31.97 4.17
1350 1415 4.254709 TGCACGCTCTGGCAGGTT 62.255 61.111 15.73 0.00 38.60 3.50
1372 1437 0.391130 TACTGACACGCATTGCCCTC 60.391 55.000 2.41 0.00 0.00 4.30
1375 1440 3.950794 GACACGCATTGCCCTCGGA 62.951 63.158 2.41 0.00 0.00 4.55
1430 1498 1.070843 CGTGCAACAGTAAACACTCGG 60.071 52.381 0.00 0.00 35.74 4.63
1431 1499 0.941542 TGCAACAGTAAACACTCGGC 59.058 50.000 0.00 0.00 0.00 5.54
1432 1500 1.226746 GCAACAGTAAACACTCGGCT 58.773 50.000 0.00 0.00 0.00 5.52
1433 1501 1.194772 GCAACAGTAAACACTCGGCTC 59.805 52.381 0.00 0.00 0.00 4.70
1434 1502 1.798813 CAACAGTAAACACTCGGCTCC 59.201 52.381 0.00 0.00 0.00 4.70
1436 1504 2.522185 ACAGTAAACACTCGGCTCCTA 58.478 47.619 0.00 0.00 0.00 2.94
1438 1506 3.322828 ACAGTAAACACTCGGCTCCTAAA 59.677 43.478 0.00 0.00 0.00 1.85
1440 1508 4.753107 CAGTAAACACTCGGCTCCTAAAAA 59.247 41.667 0.00 0.00 0.00 1.94
1482 1572 4.332819 GGTTGTCACTTGTCACATATAGGC 59.667 45.833 0.00 0.00 0.00 3.93
1495 1585 6.144080 GTCACATATAGGCACGATAGAAACAC 59.856 42.308 0.00 0.00 41.38 3.32
1496 1586 6.040504 TCACATATAGGCACGATAGAAACACT 59.959 38.462 0.00 0.00 41.38 3.55
1497 1587 7.229907 TCACATATAGGCACGATAGAAACACTA 59.770 37.037 0.00 0.00 41.38 2.74
1498 1588 7.539022 CACATATAGGCACGATAGAAACACTAG 59.461 40.741 0.00 0.00 41.38 2.57
1499 1589 7.447545 ACATATAGGCACGATAGAAACACTAGA 59.552 37.037 0.00 0.00 41.38 2.43
1500 1590 4.373348 AGGCACGATAGAAACACTAGAC 57.627 45.455 0.00 0.00 41.38 2.59
1501 1591 3.762288 AGGCACGATAGAAACACTAGACA 59.238 43.478 0.00 0.00 41.38 3.41
1593 1696 9.542462 ACAAATATACGATGTAGCACAGTTTAT 57.458 29.630 0.00 0.00 0.00 1.40
1668 1771 0.027586 GATAAACGGTGATGGTGCGC 59.972 55.000 0.00 0.00 0.00 6.09
1730 1833 5.445806 GGACATGAAACAACACAAAAGCAAC 60.446 40.000 0.00 0.00 0.00 4.17
1736 1839 2.427095 ACAACACAAAAGCAACCTCTCC 59.573 45.455 0.00 0.00 0.00 3.71
1816 1919 6.377146 GTCTGGGTTTTCCTATGCTATTTTGA 59.623 38.462 0.00 0.00 40.46 2.69
1820 1923 7.180051 TGGGTTTTCCTATGCTATTTTGATGTT 59.820 33.333 0.00 0.00 40.46 2.71
1822 1925 7.010460 GGTTTTCCTATGCTATTTTGATGTTGC 59.990 37.037 0.00 0.00 36.94 4.17
1984 2087 8.129211 GGACAGGTGATGCTTTATGTTAATTAC 58.871 37.037 0.00 0.00 0.00 1.89
2076 2179 6.655078 ATGGTAATAGGGAACATTCATTGC 57.345 37.500 0.00 0.00 0.00 3.56
2193 2296 6.494842 TCCTTTGTGAGTTTGAATTTCTTCG 58.505 36.000 0.00 0.00 33.86 3.79
2716 2833 9.699410 AATATTCTGGGTTTGAGAACATATTCA 57.301 29.630 0.00 0.00 37.29 2.57
2758 2875 6.036408 GCTCATTGACAAAAGAAAAGCACTTT 59.964 34.615 5.39 0.00 38.91 2.66
2789 2906 4.036734 TGAAGATTGGTTTCAGTGAACAGC 59.963 41.667 4.68 7.55 31.35 4.40
2968 3085 7.595819 TTCTTATTGGGAAAAACACATCTGT 57.404 32.000 0.00 0.00 0.00 3.41
3094 3245 4.082949 GCTGGTTTCCTTTACAAATACGCT 60.083 41.667 0.00 0.00 0.00 5.07
3191 3342 8.104566 GTCTATAGTGCTTATCTCCTCTTCCTA 58.895 40.741 0.00 0.00 0.00 2.94
3587 3738 6.949352 ATCATTTTTGCTGGTATACCTCAG 57.051 37.500 22.41 13.43 36.82 3.35
3616 3767 9.623350 GTTTCTCTTAACGAACATACTTCTACT 57.377 33.333 0.00 0.00 0.00 2.57
3780 3935 8.010733 TCAGTTCCTGTCAATTTGATTTTTCT 57.989 30.769 1.78 0.00 32.61 2.52
3864 4019 5.852282 ACACACTGTTTCCTTTGCTAAAT 57.148 34.783 0.00 0.00 0.00 1.40
3871 4026 7.599998 CACTGTTTCCTTTGCTAAATTTGCTAT 59.400 33.333 0.00 0.00 0.00 2.97
4086 4241 3.198853 ACTCCCTCCATCTCAAAGTAAGC 59.801 47.826 0.00 0.00 0.00 3.09
4449 4606 5.067805 CACTGGAGCCTTTTCTTTTAACTGT 59.932 40.000 0.00 0.00 0.00 3.55
4505 4662 3.176552 TGGTGGATTTGTGCAAACTTG 57.823 42.857 0.00 0.00 32.51 3.16
4601 4787 2.076100 CTTATTTCGTGCTCACTGGCA 58.924 47.619 0.00 0.00 40.15 4.92
4719 4905 9.336171 ACAACTATAATGTGGTTTTGCAAAAAT 57.664 25.926 25.40 15.51 27.74 1.82
4745 4931 1.925285 CTGGTCAGCTGGCCCCATAA 61.925 60.000 33.79 14.56 39.61 1.90
4762 4948 4.648762 CCCATAATCTTAATGTGGCAACCA 59.351 41.667 0.00 0.00 0.00 3.67
5480 5676 2.299297 ACACTCCAGCTACACAGGTTAC 59.701 50.000 0.00 0.00 0.00 2.50
5687 5883 2.125269 GTACGGCCGGCTGTGAAT 60.125 61.111 44.00 24.53 36.80 2.57
5692 5888 1.586154 CGGCCGGCTGTGAATTTCTT 61.586 55.000 27.83 0.00 0.00 2.52
5699 5895 3.004734 CGGCTGTGAATTTCTTGGTTCTT 59.995 43.478 0.00 0.00 0.00 2.52
5703 5899 5.186996 TGTGAATTTCTTGGTTCTTCAGC 57.813 39.130 0.00 0.00 0.00 4.26
5704 5900 4.644234 TGTGAATTTCTTGGTTCTTCAGCA 59.356 37.500 0.00 0.00 0.00 4.41
5705 5901 4.978580 GTGAATTTCTTGGTTCTTCAGCAC 59.021 41.667 0.00 0.00 30.58 4.40
5735 5931 2.560542 TGTTCTCTGTCTCTTCAGGCTC 59.439 50.000 0.00 0.00 36.25 4.70
5803 5999 0.744414 TCTGGCTGCTATTGTTCCGC 60.744 55.000 0.00 0.00 0.00 5.54
5858 6054 5.500825 GTTGTGTTGATTGGTTGCAAATTC 58.499 37.500 0.00 0.00 0.00 2.17
5895 6091 2.510615 GCGTCTTGCATGTCTACAAC 57.489 50.000 0.00 0.00 45.45 3.32
5899 6095 3.494626 CGTCTTGCATGTCTACAACTTGT 59.505 43.478 0.00 0.00 35.87 3.16
5900 6096 4.024893 CGTCTTGCATGTCTACAACTTGTT 60.025 41.667 0.00 0.00 35.87 2.83
6000 6197 4.892433 ACTCATGAGTCTTGGAACTCTTG 58.108 43.478 22.89 11.58 45.68 3.02
6112 6309 1.694048 CCCTCAGCTGGAAGGAGGTAT 60.694 57.143 20.42 0.00 45.42 2.73
6113 6310 2.426414 CCCTCAGCTGGAAGGAGGTATA 60.426 54.545 20.42 0.00 45.42 1.47
6223 6421 6.414732 TCTTGGTTATACAGTATGCTTGCTT 58.585 36.000 3.03 0.00 42.53 3.91
6279 6486 6.755141 GTGTTAGTAACTCCAGCATTCGAATA 59.245 38.462 10.97 0.00 0.00 1.75
6291 6498 7.011763 TCCAGCATTCGAATAGAAAAGATGAAG 59.988 37.037 10.97 0.00 42.91 3.02
6293 6500 7.850003 CAGCATTCGAATAGAAAAGATGAAGAC 59.150 37.037 10.97 0.00 42.91 3.01
6294 6501 7.550551 AGCATTCGAATAGAAAAGATGAAGACA 59.449 33.333 10.97 0.00 42.91 3.41
6295 6502 7.850003 GCATTCGAATAGAAAAGATGAAGACAG 59.150 37.037 10.97 0.00 42.91 3.51
6296 6503 9.091784 CATTCGAATAGAAAAGATGAAGACAGA 57.908 33.333 10.97 0.00 42.91 3.41
6297 6504 8.467402 TTCGAATAGAAAAGATGAAGACAGAC 57.533 34.615 0.00 0.00 35.61 3.51
6298 6505 6.747739 TCGAATAGAAAAGATGAAGACAGACG 59.252 38.462 0.00 0.00 0.00 4.18
6299 6506 6.528423 CGAATAGAAAAGATGAAGACAGACGT 59.472 38.462 0.00 0.00 0.00 4.34
6301 6508 9.355215 GAATAGAAAAGATGAAGACAGACGTAA 57.645 33.333 0.00 0.00 0.00 3.18
6302 6509 8.690680 ATAGAAAAGATGAAGACAGACGTAAC 57.309 34.615 0.00 0.00 0.00 2.50
6303 6510 6.513180 AGAAAAGATGAAGACAGACGTAACA 58.487 36.000 0.00 0.00 0.00 2.41
6304 6511 6.421202 AGAAAAGATGAAGACAGACGTAACAC 59.579 38.462 0.00 0.00 0.00 3.32
6306 6513 5.196341 AGATGAAGACAGACGTAACACAA 57.804 39.130 0.00 0.00 0.00 3.33
6308 6515 5.692204 AGATGAAGACAGACGTAACACAAAG 59.308 40.000 0.00 0.00 0.00 2.77
6347 6554 1.966451 CACCGTCCTCAAGGGCAAC 60.966 63.158 0.95 0.00 40.62 4.17
6348 6555 2.429930 CCGTCCTCAAGGGCAACA 59.570 61.111 0.95 0.00 40.62 3.33
6349 6556 1.228124 CCGTCCTCAAGGGCAACAA 60.228 57.895 0.95 0.00 40.62 2.83
6350 6557 0.821711 CCGTCCTCAAGGGCAACAAA 60.822 55.000 0.95 0.00 40.62 2.83
6351 6558 0.593128 CGTCCTCAAGGGCAACAAAG 59.407 55.000 0.95 0.00 40.62 2.77
6358 6565 0.755327 AAGGGCAACAAAGGCTTCGT 60.755 50.000 0.00 0.00 39.74 3.85
6359 6566 1.172812 AGGGCAACAAAGGCTTCGTC 61.173 55.000 0.00 0.00 39.74 4.20
6375 6582 1.597461 GTCAGGAGGAAAGGGACCG 59.403 63.158 0.00 0.00 0.00 4.79
6376 6583 1.612442 TCAGGAGGAAAGGGACCGG 60.612 63.158 0.00 0.00 0.00 5.28
6385 6592 2.224597 GGAAAGGGACCGGTTTGTTAGA 60.225 50.000 9.42 0.00 0.00 2.10
6386 6593 2.853235 AAGGGACCGGTTTGTTAGAG 57.147 50.000 9.42 0.00 0.00 2.43
6405 6613 9.436957 TGTTAGAGAAAGGAGTAATGAAATGAC 57.563 33.333 0.00 0.00 0.00 3.06
6406 6614 9.436957 GTTAGAGAAAGGAGTAATGAAATGACA 57.563 33.333 0.00 0.00 0.00 3.58
6417 6625 8.048534 AGTAATGAAATGACACATGAGGAAAG 57.951 34.615 0.00 0.00 0.00 2.62
6418 6626 4.771590 TGAAATGACACATGAGGAAAGC 57.228 40.909 0.00 0.00 0.00 3.51
6436 6644 8.763424 AGGAAAGCCTGGGCATATATATATAT 57.237 34.615 14.39 9.12 44.90 0.86
6437 6645 9.858868 AGGAAAGCCTGGGCATATATATATATA 57.141 33.333 13.72 13.60 44.90 0.86
6469 6677 0.673644 TAGGGAGCAGAGCGCAAAAC 60.674 55.000 11.47 0.00 46.13 2.43
6489 6697 1.585006 TCGAAAGAGCACCGTCCTC 59.415 57.895 0.00 0.00 34.84 3.71
6493 6701 1.122019 AAAGAGCACCGTCCTCCAGT 61.122 55.000 0.00 0.00 0.00 4.00
6517 6727 4.140994 TGGAGGACCTCGTTAGAAGGATAT 60.141 45.833 15.46 0.00 37.04 1.63
6520 6730 4.140994 AGGACCTCGTTAGAAGGATATGGA 60.141 45.833 0.00 0.00 0.00 3.41
6525 6735 3.005897 TCGTTAGAAGGATATGGAGCAGC 59.994 47.826 0.00 0.00 0.00 5.25
6571 6782 4.385358 AAGCAACGAAAGGACACAAAAT 57.615 36.364 0.00 0.00 0.00 1.82
6608 6819 6.634039 GCCTATCTGAAAAATACCAGGTACCA 60.634 42.308 15.94 0.00 0.00 3.25
6609 6820 6.992715 CCTATCTGAAAAATACCAGGTACCAG 59.007 42.308 15.94 5.89 0.00 4.00
6612 6823 1.746470 AAAATACCAGGTACCAGCGC 58.254 50.000 15.94 0.00 0.00 5.92
6614 6825 1.324740 AATACCAGGTACCAGCGCGA 61.325 55.000 15.94 0.00 0.00 5.87
6615 6826 1.735376 ATACCAGGTACCAGCGCGAG 61.735 60.000 15.94 0.00 0.00 5.03
6657 6868 1.906966 CATTTCTCGATTTGTGCGTGC 59.093 47.619 0.00 0.00 0.00 5.34
6674 6885 3.515286 CCATCCTTGCGCAGGCTG 61.515 66.667 15.01 16.54 43.55 4.85
6675 6886 2.749044 CATCCTTGCGCAGGCTGT 60.749 61.111 15.01 0.00 43.55 4.40
6676 6887 1.450134 CATCCTTGCGCAGGCTGTA 60.450 57.895 15.01 0.00 43.55 2.74
6677 6888 0.816825 CATCCTTGCGCAGGCTGTAT 60.817 55.000 15.01 3.33 43.55 2.29
6678 6889 0.533755 ATCCTTGCGCAGGCTGTATC 60.534 55.000 15.01 6.13 43.55 2.24
6679 6890 2.528743 CCTTGCGCAGGCTGTATCG 61.529 63.158 15.01 12.32 40.82 2.92
6680 6891 1.811266 CTTGCGCAGGCTGTATCGT 60.811 57.895 17.16 0.00 40.82 3.73
6681 6892 1.361668 CTTGCGCAGGCTGTATCGTT 61.362 55.000 17.16 0.00 40.82 3.85
6682 6893 1.358725 TTGCGCAGGCTGTATCGTTC 61.359 55.000 17.16 0.48 40.82 3.95
6683 6894 2.526120 GCGCAGGCTGTATCGTTCC 61.526 63.158 17.16 0.00 35.83 3.62
6684 6895 1.153647 CGCAGGCTGTATCGTTCCA 60.154 57.895 17.16 0.00 0.00 3.53
6685 6896 0.739462 CGCAGGCTGTATCGTTCCAA 60.739 55.000 17.16 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.477295 GCTAGGCTTGGACGAACTACT 59.523 52.381 0.00 0.00 0.00 2.57
54 55 3.641434 ACACCATCTCCTTCTCATTGG 57.359 47.619 0.00 0.00 0.00 3.16
58 59 2.553028 GCCAAACACCATCTCCTTCTCA 60.553 50.000 0.00 0.00 0.00 3.27
59 60 2.087646 GCCAAACACCATCTCCTTCTC 58.912 52.381 0.00 0.00 0.00 2.87
62 63 0.779997 AGGCCAAACACCATCTCCTT 59.220 50.000 5.01 0.00 0.00 3.36
103 104 0.534412 GCACTCAGGCTAGCTCTTCA 59.466 55.000 15.72 0.00 0.00 3.02
123 124 6.708949 AGGCACAAATTTAGAGTACGAAGAAA 59.291 34.615 0.00 0.00 0.00 2.52
130 131 4.157840 CCCCAAGGCACAAATTTAGAGTAC 59.842 45.833 0.00 0.00 0.00 2.73
194 203 0.533032 GGTTCTCTCTCCCTGGTTCG 59.467 60.000 0.00 0.00 0.00 3.95
209 218 5.318630 AGGTCGGATCTTAGATCTAGGTTC 58.681 45.833 20.01 11.89 0.00 3.62
302 311 2.490217 CACTCCTCCAGCGTACCG 59.510 66.667 0.00 0.00 0.00 4.02
349 358 2.886523 CACCACACATCAAACACTCCAT 59.113 45.455 0.00 0.00 0.00 3.41
416 428 2.448926 TGTCGTTGTCCATCATCGTT 57.551 45.000 0.00 0.00 39.41 3.85
459 471 4.339530 AGTTCCCTTCACTTTCTTTCTTGC 59.660 41.667 0.00 0.00 0.00 4.01
484 496 1.144057 CTACCCCGGACATGCTCAC 59.856 63.158 0.73 0.00 0.00 3.51
490 502 5.735733 ATCTATCTATCTACCCCGGACAT 57.264 43.478 0.73 0.00 0.00 3.06
532 544 7.175119 CGACTTCTCTCTCTCTCTCTCTATCTA 59.825 44.444 0.00 0.00 0.00 1.98
536 548 4.341235 CCGACTTCTCTCTCTCTCTCTCTA 59.659 50.000 0.00 0.00 0.00 2.43
545 561 1.751162 CCGCCCGACTTCTCTCTCT 60.751 63.158 0.00 0.00 0.00 3.10
576 611 2.048597 TTCATCAGGCGTCGCGTT 60.049 55.556 10.16 0.00 0.00 4.84
603 639 8.993121 CACTATCTCCTATCATAAAAACGCATT 58.007 33.333 0.00 0.00 0.00 3.56
657 693 6.901887 CCATTTCTTCTCGTCAAAACATATCG 59.098 38.462 0.00 0.00 0.00 2.92
746 782 0.465460 TTTCCTTGAAGGCACACGCT 60.465 50.000 6.30 0.00 38.60 5.07
759 795 5.560183 CGTGCTTCTGAAATACGTTTTCCTT 60.560 40.000 15.71 0.00 0.00 3.36
765 801 2.139917 TGCGTGCTTCTGAAATACGTT 58.860 42.857 20.04 0.00 37.12 3.99
794 830 1.169661 TTGACACGTGGTGGGCATTC 61.170 55.000 21.57 6.04 37.94 2.67
795 831 1.152860 TTGACACGTGGTGGGCATT 60.153 52.632 21.57 0.00 37.94 3.56
797 833 2.515057 GTTGACACGTGGTGGGCA 60.515 61.111 21.57 6.85 37.94 5.36
805 841 3.932313 GTTGCGCCGTTGACACGT 61.932 61.111 4.18 0.00 45.62 4.49
1076 1126 3.332393 ATTGCGGGGAGGAGGAGGA 62.332 63.158 0.00 0.00 0.00 3.71
1332 1397 4.996434 ACCTGCCAGAGCGTGCAC 62.996 66.667 6.82 6.82 44.31 4.57
1350 1415 2.093181 AGGGCAATGCGTGTCAGTAATA 60.093 45.455 0.00 0.00 31.37 0.98
1440 1508 3.575805 ACCCAACATCCACATCAGTTTT 58.424 40.909 0.00 0.00 0.00 2.43
1441 1509 3.243359 ACCCAACATCCACATCAGTTT 57.757 42.857 0.00 0.00 0.00 2.66
1442 1510 2.892852 CAACCCAACATCCACATCAGTT 59.107 45.455 0.00 0.00 0.00 3.16
1444 1512 2.489329 GACAACCCAACATCCACATCAG 59.511 50.000 0.00 0.00 0.00 2.90
1446 1514 2.228822 GTGACAACCCAACATCCACATC 59.771 50.000 0.00 0.00 0.00 3.06
1447 1515 2.158475 AGTGACAACCCAACATCCACAT 60.158 45.455 0.00 0.00 0.00 3.21
1482 1572 7.064847 AGTCTAGTGTCTAGTGTTTCTATCGTG 59.935 40.741 4.13 0.00 0.00 4.35
1495 1585 9.360093 CCAATTTCTAAACAGTCTAGTGTCTAG 57.640 37.037 0.00 0.00 0.00 2.43
1496 1586 9.085645 TCCAATTTCTAAACAGTCTAGTGTCTA 57.914 33.333 0.00 0.00 0.00 2.59
1497 1587 7.963532 TCCAATTTCTAAACAGTCTAGTGTCT 58.036 34.615 0.00 0.00 0.00 3.41
1498 1588 8.603242 TTCCAATTTCTAAACAGTCTAGTGTC 57.397 34.615 0.00 0.00 0.00 3.67
1499 1589 9.220767 GATTCCAATTTCTAAACAGTCTAGTGT 57.779 33.333 0.00 0.00 0.00 3.55
1500 1590 9.219603 TGATTCCAATTTCTAAACAGTCTAGTG 57.780 33.333 0.00 0.00 0.00 2.74
1501 1591 9.220767 GTGATTCCAATTTCTAAACAGTCTAGT 57.779 33.333 0.00 0.00 0.00 2.57
1577 1677 6.909357 GCAAGAATGATAAACTGTGCTACATC 59.091 38.462 0.00 0.00 0.00 3.06
1593 1696 2.357327 GCAATGTGCAGCAAGAATGA 57.643 45.000 0.00 0.00 44.26 2.57
1646 1749 0.300491 CACCATCACCGTTTATCGCG 59.700 55.000 0.00 0.00 38.35 5.87
1668 1771 0.670546 ACTGCCCGATCACTGTTTCG 60.671 55.000 0.00 3.57 35.19 3.46
1730 1833 2.099405 GTCAGAGAGAACAGGGAGAGG 58.901 57.143 0.00 0.00 0.00 3.69
1816 1919 1.398692 AAAGGACACAACCGCAACAT 58.601 45.000 0.00 0.00 34.73 2.71
1820 1923 3.797184 GCAATTAAAAGGACACAACCGCA 60.797 43.478 0.00 0.00 34.73 5.69
1822 1925 3.005367 AGGCAATTAAAAGGACACAACCG 59.995 43.478 0.00 0.00 34.73 4.44
1984 2087 6.507023 ACTCTGAAATAGGCAAACAAAGTTG 58.493 36.000 0.00 0.00 0.00 3.16
2193 2296 0.179018 AGGTGCCTTCACAAGTGACC 60.179 55.000 1.73 1.34 44.87 4.02
2698 2815 9.921637 TGTTTTTATGAATATGTTCTCAAACCC 57.078 29.630 3.72 0.00 35.33 4.11
2758 2875 8.102676 TCACTGAAACCAATCTTCATGATAGAA 58.897 33.333 0.00 0.00 34.45 2.10
3191 3342 1.915141 CATCTTCAAGCCAACCTGGT 58.085 50.000 0.00 0.00 40.46 4.00
3587 3738 7.384387 AGAAGTATGTTCGTTAAGAGAAACCAC 59.616 37.037 0.00 0.00 0.00 4.16
3595 3746 7.175467 TCACCAGTAGAAGTATGTTCGTTAAGA 59.825 37.037 0.00 0.00 0.00 2.10
3597 3748 7.218228 TCACCAGTAGAAGTATGTTCGTTAA 57.782 36.000 0.00 0.00 0.00 2.01
3780 3935 4.034742 GGAAACGCAACAGACAAGAACTAA 59.965 41.667 0.00 0.00 0.00 2.24
3831 3986 5.712917 AGGAAACAGTGTGTTCAACCTTTTA 59.287 36.000 15.43 0.00 40.14 1.52
3864 4019 3.699411 ATGGGCTGCAAAAATAGCAAA 57.301 38.095 0.50 0.00 42.17 3.68
3871 4026 3.577848 AGTCATACAATGGGCTGCAAAAA 59.422 39.130 0.50 0.00 0.00 1.94
4081 4236 6.640092 AGTTAGTACAAAGTTGAGTCGCTTAC 59.360 38.462 0.00 0.00 0.00 2.34
4086 4241 8.571461 ACTAAAGTTAGTACAAAGTTGAGTCG 57.429 34.615 1.81 0.00 41.92 4.18
4449 4606 7.385752 GCATTTGATTCCAGATTTCACTTTCAA 59.614 33.333 0.00 0.00 0.00 2.69
4687 4873 9.632807 GCAAAACCACATTATAGTTGTCAAATA 57.367 29.630 0.00 0.00 0.00 1.40
4688 4874 8.147058 TGCAAAACCACATTATAGTTGTCAAAT 58.853 29.630 0.00 0.00 0.00 2.32
4689 4875 7.492524 TGCAAAACCACATTATAGTTGTCAAA 58.507 30.769 0.00 0.00 0.00 2.69
4690 4876 7.043961 TGCAAAACCACATTATAGTTGTCAA 57.956 32.000 0.00 0.00 0.00 3.18
4691 4877 6.641169 TGCAAAACCACATTATAGTTGTCA 57.359 33.333 0.00 0.00 0.00 3.58
4692 4878 7.938563 TTTGCAAAACCACATTATAGTTGTC 57.061 32.000 10.02 0.00 0.00 3.18
4719 4905 0.826715 GCCAGCTGACCAGACAGATA 59.173 55.000 17.39 0.00 39.94 1.98
4762 4948 6.992063 AAGAGAATCATAAGCATGAAACGT 57.008 33.333 0.00 0.00 44.27 3.99
4763 4949 7.964559 TGAAAAGAGAATCATAAGCATGAAACG 59.035 33.333 0.00 0.00 44.27 3.60
4764 4950 9.798994 ATGAAAAGAGAATCATAAGCATGAAAC 57.201 29.630 0.00 0.00 44.27 2.78
5699 5895 2.220953 AACACAGGAGTGGTGCTGA 58.779 52.632 0.50 0.00 45.92 4.26
5735 5931 1.445582 GTACCGTCTGGCAGTTCCG 60.446 63.158 15.27 14.50 39.70 4.30
5803 5999 2.034066 ACAGGTGCCAACATCCCG 59.966 61.111 0.00 0.00 0.00 5.14
5858 6054 2.287188 ACGCTTCAAGTTCAAGCATGTG 60.287 45.455 12.22 0.00 45.66 3.21
5930 6126 9.777008 TGGGAAAATAAAGGACTACCATTTTAT 57.223 29.630 0.00 0.00 38.94 1.40
5931 6127 9.777008 ATGGGAAAATAAAGGACTACCATTTTA 57.223 29.630 0.00 0.00 38.94 1.52
5932 6128 8.679344 ATGGGAAAATAAAGGACTACCATTTT 57.321 30.769 0.00 0.00 38.94 1.82
5933 6129 8.679344 AATGGGAAAATAAAGGACTACCATTT 57.321 30.769 0.00 0.00 41.84 2.32
5934 6130 8.679344 AAATGGGAAAATAAAGGACTACCATT 57.321 30.769 0.00 0.00 45.22 3.16
5935 6131 7.068226 CGAAATGGGAAAATAAAGGACTACCAT 59.932 37.037 0.00 0.00 37.77 3.55
5936 6132 6.376018 CGAAATGGGAAAATAAAGGACTACCA 59.624 38.462 0.00 0.00 38.94 3.25
5950 6146 8.262227 ACAATAGTACATAGACGAAATGGGAAA 58.738 33.333 0.00 0.00 0.00 3.13
6000 6197 9.209175 GAACTTGATACACATATCCCACTTATC 57.791 37.037 0.00 0.00 37.04 1.75
6048 6245 8.113173 ACAAAAGTAAACCTTAACACACAGAA 57.887 30.769 0.00 0.00 31.48 3.02
6135 6332 6.599638 AGTTTCGCCTAAAAGCAGATTAATCT 59.400 34.615 12.37 12.37 37.72 2.40
6223 6421 2.945008 CTGTGCTTTCTTCACAACAGGA 59.055 45.455 0.00 0.00 43.02 3.86
6279 6486 6.421202 GTGTTACGTCTGTCTTCATCTTTTCT 59.579 38.462 0.00 0.00 0.00 2.52
6291 6498 3.120649 GCATCCTTTGTGTTACGTCTGTC 60.121 47.826 0.00 0.00 0.00 3.51
6293 6500 2.805671 TGCATCCTTTGTGTTACGTCTG 59.194 45.455 0.00 0.00 0.00 3.51
6294 6501 3.120321 TGCATCCTTTGTGTTACGTCT 57.880 42.857 0.00 0.00 0.00 4.18
6295 6502 3.810373 CTTGCATCCTTTGTGTTACGTC 58.190 45.455 0.00 0.00 0.00 4.34
6296 6503 2.031157 GCTTGCATCCTTTGTGTTACGT 60.031 45.455 0.00 0.00 0.00 3.57
6297 6504 2.031245 TGCTTGCATCCTTTGTGTTACG 60.031 45.455 0.00 0.00 0.00 3.18
6298 6505 3.243367 TGTGCTTGCATCCTTTGTGTTAC 60.243 43.478 0.00 0.00 0.00 2.50
6299 6506 2.954989 TGTGCTTGCATCCTTTGTGTTA 59.045 40.909 0.00 0.00 0.00 2.41
6301 6508 1.401761 TGTGCTTGCATCCTTTGTGT 58.598 45.000 0.00 0.00 0.00 3.72
6302 6509 2.512485 TTGTGCTTGCATCCTTTGTG 57.488 45.000 0.00 0.00 0.00 3.33
6303 6510 2.804212 GCTTTGTGCTTGCATCCTTTGT 60.804 45.455 0.00 0.00 38.95 2.83
6304 6511 1.796459 GCTTTGTGCTTGCATCCTTTG 59.204 47.619 0.00 0.00 38.95 2.77
6306 6513 1.000506 CTGCTTTGTGCTTGCATCCTT 59.999 47.619 0.00 0.00 43.37 3.36
6308 6515 0.599558 TCTGCTTTGTGCTTGCATCC 59.400 50.000 0.00 0.00 43.37 3.51
6347 6554 0.321671 TCCTCCTGACGAAGCCTTTG 59.678 55.000 0.00 0.00 0.00 2.77
6348 6555 1.056660 TTCCTCCTGACGAAGCCTTT 58.943 50.000 0.00 0.00 0.00 3.11
6349 6556 1.002544 CTTTCCTCCTGACGAAGCCTT 59.997 52.381 0.00 0.00 0.00 4.35
6350 6557 0.610687 CTTTCCTCCTGACGAAGCCT 59.389 55.000 0.00 0.00 0.00 4.58
6351 6558 0.391793 CCTTTCCTCCTGACGAAGCC 60.392 60.000 0.00 0.00 0.00 4.35
6358 6565 1.612442 CCGGTCCCTTTCCTCCTGA 60.612 63.158 0.00 0.00 0.00 3.86
6359 6566 1.489560 AACCGGTCCCTTTCCTCCTG 61.490 60.000 8.04 0.00 0.00 3.86
6375 6582 8.617290 TTCATTACTCCTTTCTCTAACAAACC 57.383 34.615 0.00 0.00 0.00 3.27
6385 6592 7.884877 TCATGTGTCATTTCATTACTCCTTTCT 59.115 33.333 0.00 0.00 0.00 2.52
6386 6593 8.044060 TCATGTGTCATTTCATTACTCCTTTC 57.956 34.615 0.00 0.00 0.00 2.62
6405 6613 1.318158 GCCCAGGCTTTCCTCATGTG 61.318 60.000 0.08 0.00 41.93 3.21
6406 6614 1.000396 GCCCAGGCTTTCCTCATGT 60.000 57.895 0.08 0.00 41.93 3.21
6435 6643 9.087871 CTCTGCTCCCTAGTATATTGCATATAT 57.912 37.037 0.00 0.00 30.98 0.86
6436 6644 7.014711 GCTCTGCTCCCTAGTATATTGCATATA 59.985 40.741 0.00 0.00 0.00 0.86
6437 6645 6.183360 GCTCTGCTCCCTAGTATATTGCATAT 60.183 42.308 0.00 0.00 0.00 1.78
6456 6664 1.841663 TTCGAGGTTTTGCGCTCTGC 61.842 55.000 9.73 0.00 46.70 4.26
6460 6668 0.868406 CTCTTTCGAGGTTTTGCGCT 59.132 50.000 9.73 0.00 33.51 5.92
6469 6677 1.446272 GGACGGTGCTCTTTCGAGG 60.446 63.158 0.00 0.00 37.75 4.63
6489 6697 1.204941 CTAACGAGGTCCTCCAACTGG 59.795 57.143 13.54 0.53 35.89 4.00
6493 6701 2.176889 CCTTCTAACGAGGTCCTCCAA 58.823 52.381 13.54 0.00 35.89 3.53
6517 6727 2.298335 TAGATCCCTCCGCTGCTCCA 62.298 60.000 0.00 0.00 0.00 3.86
6520 6730 2.206536 GCTAGATCCCTCCGCTGCT 61.207 63.158 0.00 0.00 0.00 4.24
6525 6735 0.882474 CTTACGGCTAGATCCCTCCG 59.118 60.000 13.48 13.48 46.61 4.63
6550 6760 3.859411 TTTTGTGTCCTTTCGTTGCTT 57.141 38.095 0.00 0.00 0.00 3.91
6556 6767 3.735746 GGCTTTCATTTTGTGTCCTTTCG 59.264 43.478 0.00 0.00 0.00 3.46
6557 6768 3.735746 CGGCTTTCATTTTGTGTCCTTTC 59.264 43.478 0.00 0.00 0.00 2.62
6559 6770 2.955660 TCGGCTTTCATTTTGTGTCCTT 59.044 40.909 0.00 0.00 0.00 3.36
6588 6799 4.585879 GCTGGTACCTGGTATTTTTCAGA 58.414 43.478 19.31 0.00 33.11 3.27
6592 6803 2.089201 GCGCTGGTACCTGGTATTTTT 58.911 47.619 19.31 0.00 0.00 1.94
6631 6842 3.057596 GCACAAATCGAGAAATGGTCCAA 60.058 43.478 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.