Multiple sequence alignment - TraesCS7D01G351200

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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 TraesCS7D01G351200 chr7D 100.000 4112 0 0 1 4112 451975857 451971746 0.000000e+00 7594.0
1 TraesCS7D01G351200 chr7D 80.808 396 54 18 186 572 204103742 204104124 1.450000e-74 291.0
2 TraesCS7D01G351200 chr7B 88.058 3023 233 65 1 2930 474414388 474411401 0.000000e+00 3465.0
3 TraesCS7D01G351200 chr7B 94.890 998 41 7 3116 4111 474409256 474408267 0.000000e+00 1552.0
4 TraesCS7D01G351200 chr7B 96.985 199 6 0 2922 3120 474409481 474409283 6.590000e-88 335.0
5 TraesCS7D01G351200 chr7A 86.048 1326 116 38 2206 3484 545541978 545543281 0.000000e+00 1360.0
6 TraesCS7D01G351200 chr7A 83.167 802 86 26 913 1700 545540752 545541518 0.000000e+00 688.0
7 TraesCS7D01G351200 chr7A 83.917 628 42 26 3513 4110 545543275 545543873 2.800000e-151 545.0
8 TraesCS7D01G351200 chr7A 90.306 392 30 4 1754 2142 545541590 545541976 1.320000e-139 507.0
9 TraesCS7D01G351200 chr7A 76.316 532 96 20 53 573 215929194 215929706 1.470000e-64 257.0
10 TraesCS7D01G351200 chr7A 74.645 422 91 10 160 573 672611810 672612223 5.460000e-39 172.0
11 TraesCS7D01G351200 chr7A 73.934 422 93 11 160 573 672637869 672638281 1.980000e-33 154.0
12 TraesCS7D01G351200 chr7A 88.000 75 3 2 742 811 545540563 545540636 2.630000e-12 84.2
13 TraesCS7D01G351200 chr6B 75.536 466 97 14 178 632 96887275 96887734 3.220000e-51 213.0
14 TraesCS7D01G351200 chr6A 76.982 391 77 11 178 559 51516057 51515671 1.160000e-50 211.0
15 TraesCS7D01G351200 chr2D 75.229 436 83 19 177 601 37941502 37941081 2.520000e-42 183.0
16 TraesCS7D01G351200 chr5B 75.000 412 81 16 173 573 617808031 617807631 1.970000e-38 171.0
17 TraesCS7D01G351200 chr5B 78.378 111 22 1 568 678 633526580 633526688 2.050000e-08 71.3
18 TraesCS7D01G351200 chr1A 79.752 242 43 6 336 573 547580511 547580750 1.970000e-38 171.0
19 TraesCS7D01G351200 chr1D 79.537 259 36 12 323 573 426872698 426872947 7.070000e-38 169.0
20 TraesCS7D01G351200 chr3D 95.745 47 2 0 565 611 120879955 120879909 4.410000e-10 76.8
21 TraesCS7D01G351200 chr2B 85.938 64 9 0 569 632 93647313 93647250 7.380000e-08 69.4
22 TraesCS7D01G351200 chr3B 84.375 64 10 0 569 632 398965891 398965828 3.430000e-06 63.9
23 TraesCS7D01G351200 chr3A 77.869 122 14 3 492 600 501030396 501030275 3.430000e-06 63.9
24 TraesCS7D01G351200 chr4D 82.812 64 11 0 569 632 47557186 47557123 1.600000e-04 58.4
25 TraesCS7D01G351200 chr5A 100.000 29 0 0 569 597 592518356 592518384 2.000000e-03 54.7


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 TraesCS7D01G351200 chr7D 451971746 451975857 4111 True 7594.00 7594 100.0000 1 4112 1 chr7D.!!$R1 4111
1 TraesCS7D01G351200 chr7B 474408267 474414388 6121 True 1784.00 3465 93.3110 1 4111 3 chr7B.!!$R1 4110
2 TraesCS7D01G351200 chr7A 545540563 545543873 3310 False 636.84 1360 86.2876 742 4110 5 chr7A.!!$F4 3368
3 TraesCS7D01G351200 chr7A 215929194 215929706 512 False 257.00 257 76.3160 53 573 1 chr7A.!!$F1 520

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
193 202 0.029681 AGTAGACCATGGGAGGCCAT 60.030 55.0 18.09 0.0 0.00 4.40 F
644 661 0.033796 CTGGTCCTGTAGGGTCCGTA 60.034 60.0 0.00 0.0 44.58 4.02 F
1341 1447 0.099259 CCCACGCATCGTACGTCTTA 59.901 55.0 16.05 0.0 42.96 2.10 F
1862 1997 0.896940 ACTGCCATTTGCTGACCCTG 60.897 55.0 0.00 0.0 41.11 4.45 F
2452 2626 0.541998 GGGCCTTGGCAAACTTACCT 60.542 55.0 14.04 0.0 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1243 0.389948 CCAAGAAGACGGACGGAAGG 60.390 60.000 0.00 0.00 0.00 3.46 R
1862 1997 0.810031 AACTGACATGATACGGCCGC 60.810 55.000 28.58 10.14 0.00 6.53 R
2426 2567 1.044611 TTTGCCAAGGCCCAGTTAAC 58.955 50.000 8.89 0.00 41.09 2.01 R
2789 2963 1.066143 CAGGCAGAACGGTTACCAGAT 60.066 52.381 1.13 0.00 0.00 2.90 R
3977 6158 0.108615 CTCTTGCACCACCTCTACCG 60.109 60.000 0.00 0.00 0.00 4.02 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
23 24 3.173668 TGAAGTATCCCGACAAATCCG 57.826 47.619 0.00 0.00 0.00 4.18
25 26 2.884894 AGTATCCCGACAAATCCGTC 57.115 50.000 0.00 0.00 0.00 4.79
57 66 1.805945 GCAACGCGTAGGTGGAGAG 60.806 63.158 14.46 0.00 38.21 3.20
63 72 1.752683 GCGTAGGTGGAGAGAGAAGA 58.247 55.000 0.00 0.00 0.00 2.87
108 117 0.034089 GTGGAGGGATTTGACTGGGG 60.034 60.000 0.00 0.00 0.00 4.96
137 146 3.277742 GACGTCGCCAACTTCACGC 62.278 63.158 0.00 0.00 35.64 5.34
138 147 3.036084 CGTCGCCAACTTCACGCT 61.036 61.111 0.00 0.00 0.00 5.07
169 178 2.104253 CGCCACCACCAATACCGAC 61.104 63.158 0.00 0.00 0.00 4.79
193 202 0.029681 AGTAGACCATGGGAGGCCAT 60.030 55.000 18.09 0.00 0.00 4.40
196 205 3.482232 GACCATGGGAGGCCATCGG 62.482 68.421 18.09 0.00 0.00 4.18
204 213 4.431131 AGGCCATCGGTGCTTGGG 62.431 66.667 5.01 0.00 33.40 4.12
215 224 1.463214 TGCTTGGGTCCCAGGAAGA 60.463 57.895 23.95 1.22 31.89 2.87
289 298 2.986290 CGTAGGCCATGGTGACCA 59.014 61.111 14.67 6.84 38.19 4.02
321 331 2.235016 CCAAAAACCGACCCTGATTCA 58.765 47.619 0.00 0.00 0.00 2.57
330 340 4.102524 ACCGACCCTGATTCATGCTTTATA 59.897 41.667 0.00 0.00 0.00 0.98
387 398 4.106925 CCTCAGGGCTCAGGGTGC 62.107 72.222 0.00 0.00 0.00 5.01
388 399 3.324930 CTCAGGGCTCAGGGTGCA 61.325 66.667 0.00 0.00 0.00 4.57
404 415 1.895707 GCACCTGTGAGCTTGCTGT 60.896 57.895 0.00 0.00 32.00 4.40
415 426 1.296392 CTTGCTGTCGGACATGGGA 59.704 57.895 11.86 0.00 0.00 4.37
434 445 3.496331 GGAAAGACATGTCCTGGGAAAA 58.504 45.455 22.21 0.00 0.00 2.29
562 579 2.617308 TCAACCGGTTTGCACGAATTTA 59.383 40.909 19.55 0.00 34.88 1.40
582 599 7.696992 ATTTAGTCCGGTTTGAAATGTATGT 57.303 32.000 0.00 0.00 0.00 2.29
588 605 4.438200 CCGGTTTGAAATGTATGTGGCTAC 60.438 45.833 0.00 0.00 0.00 3.58
589 606 4.658071 GGTTTGAAATGTATGTGGCTACG 58.342 43.478 0.00 0.00 0.00 3.51
590 607 4.438200 GGTTTGAAATGTATGTGGCTACGG 60.438 45.833 0.00 0.00 0.00 4.02
591 608 3.620427 TGAAATGTATGTGGCTACGGT 57.380 42.857 0.00 0.00 0.00 4.83
592 609 3.945346 TGAAATGTATGTGGCTACGGTT 58.055 40.909 0.00 0.00 0.00 4.44
593 610 3.687212 TGAAATGTATGTGGCTACGGTTG 59.313 43.478 0.00 0.00 0.00 3.77
594 611 2.325583 ATGTATGTGGCTACGGTTGG 57.674 50.000 0.00 0.00 0.00 3.77
595 612 1.268066 TGTATGTGGCTACGGTTGGA 58.732 50.000 0.00 0.00 0.00 3.53
596 613 1.834896 TGTATGTGGCTACGGTTGGAT 59.165 47.619 0.00 0.00 0.00 3.41
601 618 2.270850 GCTACGGTTGGATGGCCA 59.729 61.111 8.56 8.56 44.17 5.36
633 650 0.946221 GTGTTCGCTGACTGGTCCTG 60.946 60.000 0.00 0.00 0.00 3.86
634 651 1.367840 GTTCGCTGACTGGTCCTGT 59.632 57.895 0.14 0.14 0.00 4.00
635 652 0.601558 GTTCGCTGACTGGTCCTGTA 59.398 55.000 0.65 0.00 0.00 2.74
636 653 0.888619 TTCGCTGACTGGTCCTGTAG 59.111 55.000 0.65 2.04 0.00 2.74
637 654 0.965866 TCGCTGACTGGTCCTGTAGG 60.966 60.000 0.65 0.00 0.00 3.18
638 655 1.901085 GCTGACTGGTCCTGTAGGG 59.099 63.158 0.65 0.00 35.41 3.53
640 657 1.187087 CTGACTGGTCCTGTAGGGTC 58.813 60.000 0.65 0.00 36.25 4.46
641 658 0.252103 TGACTGGTCCTGTAGGGTCC 60.252 60.000 0.65 2.60 42.47 4.46
642 659 1.305046 ACTGGTCCTGTAGGGTCCG 60.305 63.158 0.00 2.12 44.58 4.79
643 660 1.305046 CTGGTCCTGTAGGGTCCGT 60.305 63.158 0.00 0.00 44.58 4.69
644 661 0.033796 CTGGTCCTGTAGGGTCCGTA 60.034 60.000 0.00 0.00 44.58 4.02
645 662 0.033796 TGGTCCTGTAGGGTCCGTAG 60.034 60.000 0.00 0.00 44.58 3.51
646 663 0.257039 GGTCCTGTAGGGTCCGTAGA 59.743 60.000 0.00 0.00 33.89 2.59
647 664 1.387539 GTCCTGTAGGGTCCGTAGAC 58.612 60.000 0.00 0.00 42.73 2.59
648 665 0.107508 TCCTGTAGGGTCCGTAGACG 60.108 60.000 0.00 0.00 44.54 4.18
659 702 1.283793 CGTAGACGGACACGGTGTT 59.716 57.895 15.94 0.00 46.48 3.32
677 720 1.068055 GTTCGGTTTAGAGGTCAGCGA 60.068 52.381 0.00 0.00 38.58 4.93
680 723 1.134367 CGGTTTAGAGGTCAGCGATGA 59.866 52.381 0.00 0.00 33.26 2.92
688 731 0.462581 GGTCAGCGATGAAGATGCCA 60.463 55.000 4.22 0.00 0.00 4.92
690 733 1.263484 GTCAGCGATGAAGATGCCATG 59.737 52.381 4.22 0.00 0.00 3.66
691 734 1.134310 TCAGCGATGAAGATGCCATGT 60.134 47.619 0.00 0.00 0.00 3.21
696 739 3.801638 GCGATGAAGATGCCATGTCTAGT 60.802 47.826 0.00 0.00 0.00 2.57
697 740 4.375272 CGATGAAGATGCCATGTCTAGTT 58.625 43.478 0.00 0.00 0.00 2.24
698 741 5.532557 CGATGAAGATGCCATGTCTAGTTA 58.467 41.667 0.00 0.00 0.00 2.24
699 742 6.162079 CGATGAAGATGCCATGTCTAGTTAT 58.838 40.000 0.00 0.00 0.00 1.89
723 766 4.023878 TGTGTTTAATGAAGGCACGGTTAC 60.024 41.667 0.00 0.00 33.23 2.50
724 767 4.023878 GTGTTTAATGAAGGCACGGTTACA 60.024 41.667 0.00 0.00 0.00 2.41
726 769 5.106475 TGTTTAATGAAGGCACGGTTACATC 60.106 40.000 0.00 0.00 0.00 3.06
727 770 3.350219 AATGAAGGCACGGTTACATCT 57.650 42.857 0.00 0.00 0.00 2.90
729 772 3.241067 TGAAGGCACGGTTACATCTAC 57.759 47.619 0.00 0.00 0.00 2.59
735 778 4.214758 AGGCACGGTTACATCTACAAAAAC 59.785 41.667 0.00 0.00 0.00 2.43
736 779 4.023878 GGCACGGTTACATCTACAAAAACA 60.024 41.667 0.00 0.00 0.00 2.83
737 780 5.505985 GGCACGGTTACATCTACAAAAACAA 60.506 40.000 0.00 0.00 0.00 2.83
762 805 0.732880 CGGCACAACTCTAGACCACG 60.733 60.000 0.00 0.00 0.00 4.94
773 816 0.393820 TAGACCACGAAACACCACCC 59.606 55.000 0.00 0.00 0.00 4.61
822 870 0.915364 GAGCCCTGGACCTGATTCTT 59.085 55.000 0.00 0.00 0.00 2.52
886 934 1.696832 GAGATTGGTTGCGCTCGTCC 61.697 60.000 9.73 6.37 0.00 4.79
931 1009 1.590259 CTTAGCTTCGAGGAGCCGC 60.590 63.158 5.48 0.00 43.74 6.53
1208 1288 5.067805 GCATTTATCTTCCTTTTCCCGTCAT 59.932 40.000 0.00 0.00 0.00 3.06
1306 1406 0.176680 ATCTCAGCTGTTACCTGCCG 59.823 55.000 14.67 0.00 36.27 5.69
1315 1415 1.082117 GTTACCTGCCGACATCCACG 61.082 60.000 0.00 0.00 0.00 4.94
1321 1427 2.740714 GCCGACATCCACGTTCAGC 61.741 63.158 0.00 0.00 0.00 4.26
1330 1436 4.329545 ACGTTCAGCCCCACGCAT 62.330 61.111 0.00 0.00 40.16 4.73
1331 1437 3.499737 CGTTCAGCCCCACGCATC 61.500 66.667 0.00 0.00 41.38 3.91
1341 1447 0.099259 CCCACGCATCGTACGTCTTA 59.901 55.000 16.05 0.00 42.96 2.10
1344 1450 2.447250 CACGCATCGTACGTCTTACAT 58.553 47.619 16.05 0.00 42.96 2.29
1360 1466 6.587651 GTCTTACATACTGAACCGTCAAAAC 58.412 40.000 0.00 0.00 31.88 2.43
1361 1467 6.201425 GTCTTACATACTGAACCGTCAAAACA 59.799 38.462 0.00 0.00 31.88 2.83
1405 1511 1.412710 TGTCAGTGACAACCAGACCTC 59.587 52.381 23.55 0.00 39.78 3.85
1410 1516 2.158900 AGTGACAACCAGACCTCACTTG 60.159 50.000 0.00 0.00 40.36 3.16
1426 1536 3.055819 TCACTTGCCTGATACTGAAGGTC 60.056 47.826 0.00 0.00 35.86 3.85
1509 1619 2.908073 GCCCAGCATTAATCGCCGG 61.908 63.158 0.00 0.00 0.00 6.13
1515 1625 1.139058 AGCATTAATCGCCGGAGAAGT 59.861 47.619 13.28 5.95 0.00 3.01
1547 1657 3.666253 GCGAAAACCCCACCACCG 61.666 66.667 0.00 0.00 0.00 4.94
1567 1677 2.854777 CGTCCTTGATCTCAATGTCGAC 59.145 50.000 9.11 9.11 36.07 4.20
1587 1697 1.423395 GGTGATGCTACTAGCGATGC 58.577 55.000 3.59 0.00 46.26 3.91
1592 1702 2.287393 TGCTACTAGCGATGCGAAAA 57.713 45.000 3.59 0.00 46.26 2.29
1624 1734 2.575532 CCAAGGAGTGCTGTTCTTCAA 58.424 47.619 0.00 0.00 0.00 2.69
1687 1797 4.374399 TCCTTCTTCGTGAGGTAAAACAC 58.626 43.478 0.00 0.00 0.00 3.32
1689 1799 4.814771 CCTTCTTCGTGAGGTAAAACACTT 59.185 41.667 0.00 0.00 35.23 3.16
1704 1814 2.958213 ACACTTTGTTTGCAGTGGTTG 58.042 42.857 6.49 0.00 44.12 3.77
1736 1867 4.853924 TTTCTCTGAACAAAGCCATTCC 57.146 40.909 0.00 0.00 0.00 3.01
1738 1869 3.415212 TCTCTGAACAAAGCCATTCCAG 58.585 45.455 0.00 0.00 0.00 3.86
1769 1904 8.841300 TGCATAATTCAGTAGTACTCTCTAGTG 58.159 37.037 0.00 0.00 40.62 2.74
1797 1932 6.493116 CAGAACATCCTAGTGATCAAAATGC 58.507 40.000 0.00 0.00 0.00 3.56
1862 1997 0.896940 ACTGCCATTTGCTGACCCTG 60.897 55.000 0.00 0.00 41.11 4.45
2150 2288 8.993121 AGTCTCATTTACTTACAAGTGTCATTG 58.007 33.333 4.86 0.00 40.07 2.82
2156 2294 5.186996 ACTTACAAGTGTCATTGGCAAAG 57.813 39.130 3.01 0.00 37.98 2.77
2188 2326 7.916914 ACTTTAGGTTACGATGCAGTATTTT 57.083 32.000 0.00 0.00 0.00 1.82
2271 2411 9.460019 TGTGAATTTGGATGAACTATACAATGA 57.540 29.630 0.00 0.00 39.34 2.57
2286 2426 6.892658 ATACAATGAACAACAAGGCTTGTA 57.107 33.333 31.34 17.00 44.59 2.41
2426 2567 6.141462 GCTCTTTTCTGATGTCACTTTCAAG 58.859 40.000 0.00 0.00 0.00 3.02
2452 2626 0.541998 GGGCCTTGGCAAACTTACCT 60.542 55.000 14.04 0.00 0.00 3.08
2455 2629 2.894765 GGCCTTGGCAAACTTACCTAAA 59.105 45.455 14.04 0.00 0.00 1.85
2536 2710 5.855988 ACCTCTTAGATCCTTACTTCCCTT 58.144 41.667 0.00 0.00 0.00 3.95
2584 2758 0.676736 GTCTCCCTGGGATAAGCGAG 59.323 60.000 17.51 2.40 0.00 5.03
2649 2823 8.560576 TTTATTTTCTTGAGAACAAAGCTTCG 57.439 30.769 0.00 0.00 35.49 3.79
2651 2825 6.671614 TTTTCTTGAGAACAAAGCTTCGTA 57.328 33.333 0.00 0.00 35.49 3.43
2789 2963 3.316029 CGGCAGGAGATATTCATTTGCAA 59.684 43.478 0.00 0.00 33.47 4.08
2805 2979 2.422597 TGCAATCTGGTAACCGTTCTG 58.577 47.619 0.00 0.00 0.00 3.02
2808 2982 1.276622 ATCTGGTAACCGTTCTGCCT 58.723 50.000 0.00 0.00 0.00 4.75
2811 2985 1.302192 GGTAACCGTTCTGCCTGCA 60.302 57.895 0.00 0.00 0.00 4.41
2832 3006 4.031878 GCAGTACTTTCGAACATGTCTAGC 59.968 45.833 0.00 0.00 0.00 3.42
2837 3011 4.686554 ACTTTCGAACATGTCTAGCAGAAC 59.313 41.667 0.00 0.00 0.00 3.01
2889 3066 4.367450 GCAGTTCTTAAAACATGCCAACA 58.633 39.130 0.00 0.00 0.00 3.33
3069 5176 9.354673 CACTCCATAAACAATATTATTGGAGGT 57.645 33.333 22.28 12.84 40.39 3.85
3099 5206 0.390998 GCTTCAGGGACAGCTCAGAC 60.391 60.000 0.00 0.00 32.87 3.51
3120 5227 6.534436 CAGACAGAGAAATGTAGATTGGACAG 59.466 42.308 0.00 0.00 32.25 3.51
3123 5261 8.083828 ACAGAGAAATGTAGATTGGACAGTAT 57.916 34.615 0.00 0.00 0.00 2.12
3149 5287 5.301805 TCCCCTTGAACAGAAGTTTTCATTC 59.698 40.000 0.00 0.00 38.30 2.67
3243 5383 6.183360 TGCATGTATTATCCGTGGGTAAGTAA 60.183 38.462 0.00 0.00 0.00 2.24
3320 5460 5.124297 TGTGTCATGTTATCTTCCATGCTTG 59.876 40.000 0.00 0.00 38.63 4.01
3321 5461 4.096833 TGTCATGTTATCTTCCATGCTTGC 59.903 41.667 0.00 0.00 38.63 4.01
3348 5488 3.487372 TGCTGATACTCTGGCGTATACT 58.513 45.455 0.56 0.00 30.57 2.12
3526 5675 6.708054 CCATGTAGTTGAAACTCAGACTTTCT 59.292 38.462 0.00 0.00 40.37 2.52
3721 5897 8.362464 ACCTGTAAACAGTATCAGTTCATAGA 57.638 34.615 9.17 0.00 42.27 1.98
3731 5907 8.795513 CAGTATCAGTTCATAGATGTCATCTCT 58.204 37.037 18.74 6.76 40.76 3.10
3734 5910 5.361857 TCAGTTCATAGATGTCATCTCTGCA 59.638 40.000 18.74 7.48 40.76 4.41
3757 5933 8.024865 TGCACATCTATTTCAAGAAAATCAGTG 58.975 33.333 0.00 6.70 38.53 3.66
3802 5978 7.697710 ACAAATGTATGTATTCTGCGAATGTTG 59.302 33.333 12.17 0.00 0.00 3.33
3844 6020 0.463654 TACATGGCGGCACAATCTCC 60.464 55.000 16.34 0.00 0.00 3.71
3845 6021 1.452651 CATGGCGGCACAATCTCCT 60.453 57.895 16.34 0.00 0.00 3.69
3846 6022 0.179048 CATGGCGGCACAATCTCCTA 60.179 55.000 16.34 0.00 0.00 2.94
3847 6023 0.546122 ATGGCGGCACAATCTCCTAA 59.454 50.000 16.34 0.00 0.00 2.69
3900 6077 1.669779 GCTGTGGAGAAGCATCATGAC 59.330 52.381 0.00 0.00 40.52 3.06
3907 6088 4.163649 TGGAGAAGCATCATGACAAGAGAT 59.836 41.667 0.00 0.00 0.00 2.75
3908 6089 5.124645 GGAGAAGCATCATGACAAGAGATT 58.875 41.667 0.00 0.00 0.00 2.40
3917 6098 7.279536 GCATCATGACAAGAGATTGAGAGTTTA 59.720 37.037 0.00 0.00 0.00 2.01
3977 6158 2.727544 CTCCTCGAGCTAGCTGCC 59.272 66.667 24.99 7.77 44.23 4.85
3998 6179 1.834263 GGTAGAGGTGGTGCAAGAGAT 59.166 52.381 0.00 0.00 0.00 2.75
4060 6241 5.909621 ATCCTCATGAAAATGGTCTTGTG 57.090 39.130 0.00 0.00 0.00 3.33
4111 6295 0.677731 GCTGATAGCAACACCAGGCA 60.678 55.000 0.00 0.00 41.89 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.175109 GACGGATTTGTCGGGATACTT 57.825 47.619 0.00 0.00 0.00 2.24
6 7 2.884894 GACGGATTTGTCGGGATACT 57.115 50.000 0.00 0.00 0.00 2.12
15 16 1.019278 ATCGCTTGCGACGGATTTGT 61.019 50.000 20.01 0.00 0.00 2.83
27 28 4.817063 CGTTGCCGCCATCGCTTG 62.817 66.667 0.00 0.00 0.00 4.01
38 39 2.813908 CTCCACCTACGCGTTGCC 60.814 66.667 20.78 0.00 0.00 4.52
51 52 2.834549 GGGAACATGTCTTCTCTCTCCA 59.165 50.000 0.00 0.00 0.00 3.86
57 66 2.569404 ACCTCTGGGAACATGTCTTCTC 59.431 50.000 0.00 0.00 41.51 2.87
63 72 0.608640 GTCGACCTCTGGGAACATGT 59.391 55.000 3.51 0.00 41.51 3.21
155 164 2.224354 ACTTTTCGTCGGTATTGGTGGT 60.224 45.455 0.00 0.00 0.00 4.16
169 178 2.906354 CCTCCCATGGTCTACTTTTCG 58.094 52.381 11.73 0.00 0.00 3.46
193 202 3.636231 CTGGGACCCAAGCACCGA 61.636 66.667 15.87 0.00 30.80 4.69
196 205 1.303643 CTTCCTGGGACCCAAGCAC 60.304 63.158 15.87 0.00 30.80 4.40
204 213 1.375326 GTGGTGGTCTTCCTGGGAC 59.625 63.158 0.00 0.00 34.23 4.46
215 224 2.592993 CCGAGGTGATGGTGGTGGT 61.593 63.158 0.00 0.00 0.00 4.16
237 246 1.645034 CAAGTCACCGACTATGCAGG 58.355 55.000 0.00 0.00 42.59 4.85
289 298 3.167374 TTTTTGGGGCGGGGGACAT 62.167 57.895 0.00 0.00 0.00 3.06
291 300 3.307906 GTTTTTGGGGCGGGGGAC 61.308 66.667 0.00 0.00 0.00 4.46
321 331 7.285858 AGAGTAGTCTCCGTTTCTATAAAGCAT 59.714 37.037 0.00 0.00 41.26 3.79
330 340 3.510753 GGGAAAGAGTAGTCTCCGTTTCT 59.489 47.826 0.00 0.00 41.26 2.52
385 396 1.895231 CAGCAAGCTCACAGGTGCA 60.895 57.895 8.43 0.00 36.01 4.57
387 398 1.563435 CGACAGCAAGCTCACAGGTG 61.563 60.000 0.00 0.00 36.86 4.00
388 399 1.301244 CGACAGCAAGCTCACAGGT 60.301 57.895 0.00 0.00 0.00 4.00
391 402 1.300931 GTCCGACAGCAAGCTCACA 60.301 57.895 0.00 0.00 0.00 3.58
404 415 2.401583 CATGTCTTTCCCATGTCCGA 57.598 50.000 0.00 0.00 35.94 4.55
415 426 3.500343 CCTTTTCCCAGGACATGTCTTT 58.500 45.455 24.50 11.23 35.71 2.52
548 565 2.224784 ACCGGACTAAATTCGTGCAAAC 59.775 45.455 9.46 0.00 0.00 2.93
562 579 3.756434 CCACATACATTTCAAACCGGACT 59.244 43.478 9.46 0.00 0.00 3.85
582 599 2.270850 GCCATCCAACCGTAGCCA 59.729 61.111 0.00 0.00 0.00 4.75
588 605 2.825836 GAGCTGGCCATCCAACCG 60.826 66.667 5.51 0.00 42.91 4.44
589 606 2.440980 GGAGCTGGCCATCCAACC 60.441 66.667 18.89 9.44 42.91 3.77
590 607 2.440980 GGGAGCTGGCCATCCAAC 60.441 66.667 23.85 6.78 42.91 3.77
591 608 4.113815 CGGGAGCTGGCCATCCAA 62.114 66.667 23.85 0.00 42.91 3.53
612 629 2.022129 GACCAGTCAGCGAACACCG 61.022 63.158 0.00 0.00 42.21 4.94
641 658 0.727122 GAACACCGTGTCCGTCTACG 60.727 60.000 4.23 0.00 39.83 3.51
642 659 0.727122 CGAACACCGTGTCCGTCTAC 60.727 60.000 4.23 0.00 0.00 2.59
643 660 1.575922 CGAACACCGTGTCCGTCTA 59.424 57.895 4.23 0.00 0.00 2.59
644 661 2.333938 CGAACACCGTGTCCGTCT 59.666 61.111 4.23 0.00 0.00 4.18
645 662 2.732094 CCGAACACCGTGTCCGTC 60.732 66.667 9.55 0.93 36.31 4.79
646 663 2.576643 AAACCGAACACCGTGTCCGT 62.577 55.000 9.55 1.47 36.31 4.69
647 664 0.597118 TAAACCGAACACCGTGTCCG 60.597 55.000 2.90 2.90 36.31 4.79
648 665 1.142474 CTAAACCGAACACCGTGTCC 58.858 55.000 4.23 0.00 36.31 4.02
649 666 2.056577 CTCTAAACCGAACACCGTGTC 58.943 52.381 4.23 0.00 36.31 3.67
650 667 1.269936 CCTCTAAACCGAACACCGTGT 60.270 52.381 0.00 0.00 36.31 4.49
651 668 1.269936 ACCTCTAAACCGAACACCGTG 60.270 52.381 0.00 0.00 36.31 4.94
654 671 2.685100 CTGACCTCTAAACCGAACACC 58.315 52.381 0.00 0.00 0.00 4.16
659 702 1.134367 CATCGCTGACCTCTAAACCGA 59.866 52.381 0.00 0.00 0.00 4.69
677 720 7.228108 CACAATAACTAGACATGGCATCTTCAT 59.772 37.037 0.00 0.00 0.00 2.57
680 723 6.418101 ACACAATAACTAGACATGGCATCTT 58.582 36.000 0.00 0.00 0.00 2.40
690 733 8.726988 TGCCTTCATTAAACACAATAACTAGAC 58.273 33.333 0.00 0.00 0.00 2.59
691 734 8.726988 GTGCCTTCATTAAACACAATAACTAGA 58.273 33.333 0.00 0.00 0.00 2.43
696 739 5.241949 ACCGTGCCTTCATTAAACACAATAA 59.758 36.000 0.00 0.00 0.00 1.40
697 740 4.762765 ACCGTGCCTTCATTAAACACAATA 59.237 37.500 0.00 0.00 0.00 1.90
698 741 3.572255 ACCGTGCCTTCATTAAACACAAT 59.428 39.130 0.00 0.00 0.00 2.71
699 742 2.952978 ACCGTGCCTTCATTAAACACAA 59.047 40.909 0.00 0.00 0.00 3.33
723 766 4.798387 GCCGCCTATTTGTTTTTGTAGATG 59.202 41.667 0.00 0.00 0.00 2.90
724 767 4.461081 TGCCGCCTATTTGTTTTTGTAGAT 59.539 37.500 0.00 0.00 0.00 1.98
726 769 3.917985 GTGCCGCCTATTTGTTTTTGTAG 59.082 43.478 0.00 0.00 0.00 2.74
727 770 3.318275 TGTGCCGCCTATTTGTTTTTGTA 59.682 39.130 0.00 0.00 0.00 2.41
729 772 2.748605 TGTGCCGCCTATTTGTTTTTG 58.251 42.857 0.00 0.00 0.00 2.44
735 778 1.453155 AGAGTTGTGCCGCCTATTTG 58.547 50.000 0.00 0.00 0.00 2.32
736 779 2.500098 TCTAGAGTTGTGCCGCCTATTT 59.500 45.455 0.00 0.00 0.00 1.40
737 780 2.108168 TCTAGAGTTGTGCCGCCTATT 58.892 47.619 0.00 0.00 0.00 1.73
762 805 2.600470 GGCTGGGGGTGGTGTTTC 60.600 66.667 0.00 0.00 0.00 2.78
773 816 1.754226 GAGTTCAGACTAGAGGCTGGG 59.246 57.143 12.50 0.00 35.88 4.45
822 870 3.096852 ACGTATGAGTGTCCAGATTGGA 58.903 45.455 0.00 0.00 45.98 3.53
886 934 1.952296 GCATCACTTAGGCCAGATTGG 59.048 52.381 5.01 0.00 41.55 3.16
931 1009 2.107141 GGACGCCGAGATTGGAGG 59.893 66.667 0.00 0.00 32.43 4.30
944 1022 1.755008 GGGACAGGGAGAGAGGACG 60.755 68.421 0.00 0.00 0.00 4.79
1165 1243 0.389948 CCAAGAAGACGGACGGAAGG 60.390 60.000 0.00 0.00 0.00 3.46
1214 1294 8.196771 TCAAAATGATGACATAATTAAGTGCCC 58.803 33.333 0.00 0.00 35.50 5.36
1306 1406 1.745489 GGGGCTGAACGTGGATGTC 60.745 63.158 0.00 0.00 0.00 3.06
1315 1415 2.845752 TACGATGCGTGGGGCTGAAC 62.846 60.000 2.33 0.00 41.39 3.18
1321 1427 2.552585 AAGACGTACGATGCGTGGGG 62.553 60.000 24.41 0.00 43.04 4.96
1330 1436 4.201714 CGGTTCAGTATGTAAGACGTACGA 60.202 45.833 24.41 0.00 43.48 3.43
1331 1437 4.024438 CGGTTCAGTATGTAAGACGTACG 58.976 47.826 15.01 15.01 43.48 3.67
1341 1447 6.038825 TGAATTGTTTTGACGGTTCAGTATGT 59.961 34.615 0.00 0.00 37.40 2.29
1344 1450 6.055231 CTGAATTGTTTTGACGGTTCAGTA 57.945 37.500 11.99 0.00 38.33 2.74
1360 1466 3.408634 ACACGGGGAACTAACTGAATTG 58.591 45.455 0.00 0.00 0.00 2.32
1361 1467 3.782656 ACACGGGGAACTAACTGAATT 57.217 42.857 0.00 0.00 0.00 2.17
1405 1511 3.055530 AGACCTTCAGTATCAGGCAAGTG 60.056 47.826 0.00 0.00 32.79 3.16
1410 1516 3.895232 TGAAGACCTTCAGTATCAGGC 57.105 47.619 8.27 0.00 43.90 4.85
1434 1544 7.066645 TCCTCTCATTATTCTTTGTTGCAGATG 59.933 37.037 0.00 0.00 0.00 2.90
1523 1633 4.351938 GGGGTTTTCGCCGTTGCC 62.352 66.667 0.00 0.00 42.85 4.52
1547 1657 2.854777 CGTCGACATTGAGATCAAGGAC 59.145 50.000 17.16 6.89 39.74 3.85
1567 1677 1.691127 CATCGCTAGTAGCATCACCG 58.309 55.000 21.70 4.66 42.58 4.94
1624 1734 1.134580 CCGGATGTGAGAGTGCAAGAT 60.135 52.381 0.00 0.00 0.00 2.40
1704 1814 4.743493 TGTTCAGAGAAAACCAGTTTTGC 58.257 39.130 12.97 5.51 42.26 3.68
1707 1817 5.410924 GCTTTGTTCAGAGAAAACCAGTTT 58.589 37.500 0.00 0.00 0.00 2.66
1709 1819 3.381590 GGCTTTGTTCAGAGAAAACCAGT 59.618 43.478 0.00 0.00 27.82 4.00
1712 1822 4.590850 ATGGCTTTGTTCAGAGAAAACC 57.409 40.909 0.00 0.00 0.00 3.27
1736 1867 6.927936 AGTACTACTGAATTATGCATGCTCTG 59.072 38.462 20.33 13.40 0.00 3.35
1738 1869 7.151308 AGAGTACTACTGAATTATGCATGCTC 58.849 38.462 20.33 8.13 0.00 4.26
1769 1904 3.118629 TGATCACTAGGATGTTCTGCCAC 60.119 47.826 0.00 0.00 36.00 5.01
1797 1932 4.780815 TGCCTGTAAAAGAGATGGTATGG 58.219 43.478 0.00 0.00 0.00 2.74
1862 1997 0.810031 AACTGACATGATACGGCCGC 60.810 55.000 28.58 10.14 0.00 6.53
2156 2294 6.018262 TGCATCGTAACCTAAAGTATTGCATC 60.018 38.462 0.00 0.00 32.01 3.91
2188 2326 7.978975 GCAGAAAGCATAATTATGTACCCAAAA 59.021 33.333 23.14 0.00 44.79 2.44
2191 2329 6.633500 GCAGAAAGCATAATTATGTACCCA 57.367 37.500 23.14 0.00 44.79 4.51
2242 2382 8.862325 TGTATAGTTCATCCAAATTCACAAGT 57.138 30.769 0.00 0.00 0.00 3.16
2323 2463 1.313772 ATTGTGTACGTGCAAGGCAA 58.686 45.000 8.25 9.22 41.47 4.52
2397 2537 2.289010 TGACATCAGAAAAGAGCGCAGA 60.289 45.455 11.47 0.00 0.00 4.26
2398 2538 2.071540 TGACATCAGAAAAGAGCGCAG 58.928 47.619 11.47 0.00 0.00 5.18
2426 2567 1.044611 TTTGCCAAGGCCCAGTTAAC 58.955 50.000 8.89 0.00 41.09 2.01
2452 2626 8.542926 GGGGACTTTCACTAGTTAATACCTTTA 58.457 37.037 0.00 0.00 0.00 1.85
2455 2629 6.269974 AGGGGACTTTCACTAGTTAATACCT 58.730 40.000 0.00 0.00 37.44 3.08
2517 2691 6.609616 AGACTCAAGGGAAGTAAGGATCTAAG 59.390 42.308 0.00 0.00 0.00 2.18
2536 2710 7.323420 CAACTACAATGTAATCCAGAGACTCA 58.677 38.462 5.02 0.00 0.00 3.41
2649 2823 9.699703 GGAACTCCTGATATCAAAAGTAGATAC 57.300 37.037 16.15 3.24 31.32 2.24
2651 2825 8.560124 AGGAACTCCTGATATCAAAAGTAGAT 57.440 34.615 16.15 5.30 46.55 1.98
2789 2963 1.066143 CAGGCAGAACGGTTACCAGAT 60.066 52.381 1.13 0.00 0.00 2.90
2805 2979 1.508632 TGTTCGAAAGTACTGCAGGC 58.491 50.000 19.93 10.58 32.11 4.85
2808 2982 3.990092 AGACATGTTCGAAAGTACTGCA 58.010 40.909 0.00 0.00 32.11 4.41
2811 2985 5.183331 TCTGCTAGACATGTTCGAAAGTACT 59.817 40.000 0.00 0.00 32.11 2.73
2848 3022 2.745281 TGCGAACAAATAGCCCTTACAC 59.255 45.455 0.00 0.00 0.00 2.90
2849 3023 3.006940 CTGCGAACAAATAGCCCTTACA 58.993 45.455 0.00 0.00 0.00 2.41
2889 3066 4.354087 ACTCCCTCAAGATAAAAGGTGGTT 59.646 41.667 0.00 0.00 0.00 3.67
2962 5067 3.473923 AACAAATGTTGCCCTGGAAAG 57.526 42.857 0.00 0.00 36.80 2.62
2997 5104 4.142609 TGAGGAAGCTATGGTTGCTAAG 57.857 45.455 3.71 0.00 41.37 2.18
3069 5176 1.202830 TCCCTGAAGCGCCAAAGTAAA 60.203 47.619 2.29 0.00 0.00 2.01
3099 5206 8.954950 AATACTGTCCAATCTACATTTCTCTG 57.045 34.615 0.00 0.00 0.00 3.35
3120 5227 6.650427 AAACTTCTGTTCAAGGGGAAATAC 57.350 37.500 0.00 0.00 37.23 1.89
3123 5261 5.020132 TGAAAACTTCTGTTCAAGGGGAAA 58.980 37.500 0.00 0.00 37.23 3.13
3149 5287 3.318017 AGTGCTACAAGTAGAAGTTGCG 58.682 45.455 11.25 0.00 38.92 4.85
3243 5383 6.268387 ACTTCACCACCAAATGATTTGAAGAT 59.732 34.615 18.82 0.00 43.26 2.40
3320 5460 1.538634 CCAGAGTATCAGCAGCTCAGC 60.539 57.143 0.00 0.00 37.82 4.26
3321 5461 1.538634 GCCAGAGTATCAGCAGCTCAG 60.539 57.143 0.00 0.00 37.82 3.35
3526 5675 8.341903 CGGCATGATTTTGTAGTAAATACATCA 58.658 33.333 0.00 0.00 43.87 3.07
3612 5788 6.539649 TGTGAAAAGTGCTGTGAGTAATAC 57.460 37.500 0.00 0.00 0.00 1.89
3621 5797 2.825532 ACCTGTTTGTGAAAAGTGCTGT 59.174 40.909 0.00 0.00 0.00 4.40
3721 5897 6.589135 TGAAATAGATGTGCAGAGATGACAT 58.411 36.000 0.00 0.00 32.95 3.06
3731 5907 8.024865 CACTGATTTTCTTGAAATAGATGTGCA 58.975 33.333 0.00 0.00 38.06 4.57
3757 5933 9.691362 ACATTTGTTACAAAACATACTGGAATC 57.309 29.630 14.70 0.00 44.85 2.52
3793 5969 3.002791 TCATCAGTCTTCCAACATTCGC 58.997 45.455 0.00 0.00 0.00 4.70
3802 5978 2.751259 TGCTTTGCATCATCAGTCTTCC 59.249 45.455 0.00 0.00 31.71 3.46
3844 6020 9.241317 CTTTGACATGCTTTTGGCTATTATTAG 57.759 33.333 0.00 0.00 42.39 1.73
3845 6021 7.706179 GCTTTGACATGCTTTTGGCTATTATTA 59.294 33.333 0.00 0.00 42.39 0.98
3846 6022 6.536224 GCTTTGACATGCTTTTGGCTATTATT 59.464 34.615 0.00 0.00 42.39 1.40
3847 6023 6.044682 GCTTTGACATGCTTTTGGCTATTAT 58.955 36.000 0.00 0.00 42.39 1.28
3884 6060 3.516700 TCTCTTGTCATGATGCTTCTCCA 59.483 43.478 0.00 0.00 0.00 3.86
3888 6065 5.816258 TCTCAATCTCTTGTCATGATGCTTC 59.184 40.000 0.00 0.00 33.87 3.86
3900 6077 7.846644 ATCTGCTTAAACTCTCAATCTCTTG 57.153 36.000 0.00 0.00 0.00 3.02
3907 6088 6.650807 CAGTGGTAATCTGCTTAAACTCTCAA 59.349 38.462 0.00 0.00 0.00 3.02
3908 6089 6.014584 TCAGTGGTAATCTGCTTAAACTCTCA 60.015 38.462 0.00 0.00 33.48 3.27
3917 6098 6.886459 ACATTGTTATCAGTGGTAATCTGCTT 59.114 34.615 0.00 0.00 35.94 3.91
3977 6158 0.108615 CTCTTGCACCACCTCTACCG 60.109 60.000 0.00 0.00 0.00 4.02
4060 6241 1.012841 GCTCAACATGTCTGCTAGCC 58.987 55.000 13.29 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.