Multiple sequence alignment - TraesCS7B01G001100

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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 TraesCS7B01G001100 chr7B 100.000 3368 0 0 1 3368 262915 266282 0.000000e+00 6220.0
1 TraesCS7B01G001100 chr5D 89.578 2111 99 48 617 2635 562344447 562342366 0.000000e+00 2567.0
2 TraesCS7B01G001100 chr5D 90.968 465 21 11 1 449 562345106 562344647 1.030000e-169 606.0
3 TraesCS7B01G001100 chr5D 78.157 586 84 25 788 1364 562349373 562348823 1.940000e-87 333.0
4 TraesCS7B01G001100 chr5D 89.179 268 11 4 3119 3368 562341803 562341536 5.420000e-83 318.0
5 TraesCS7B01G001100 chr5D 94.845 194 5 3 2935 3128 562342008 562341820 7.060000e-77 298.0
6 TraesCS7B01G001100 chr5D 98.765 162 2 0 2784 2945 562342215 562342054 4.250000e-74 289.0
7 TraesCS7B01G001100 chr5D 95.522 134 4 2 2654 2785 562342375 562342242 2.630000e-51 213.0
8 TraesCS7B01G001100 chr5B 86.817 1282 76 25 1410 2635 712856396 712855152 0.000000e+00 1345.0
9 TraesCS7B01G001100 chr5B 83.827 1484 94 61 1 1405 712857848 712856432 0.000000e+00 1277.0
10 TraesCS7B01G001100 chr5B 95.000 140 7 0 3229 3368 712854440 712854301 1.570000e-53 220.0
11 TraesCS7B01G001100 chr5B 91.667 60 5 0 3144 3203 712854567 712854508 2.150000e-12 84.2
12 TraesCS7B01G001100 chr3B 94.643 112 5 1 3258 3368 772894220 772894109 4.470000e-39 172.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G001100 chr7B 262915 266282 3367 False 6220.000000 6220 100.00000 1 3368 1 chr7B.!!$F1 3367
1 TraesCS7B01G001100 chr5D 562341536 562349373 7837 True 660.571429 2567 91.00200 1 3368 7 chr5D.!!$R1 3367
2 TraesCS7B01G001100 chr5B 712854301 712857848 3547 True 731.550000 1345 89.32775 1 3368 4 chr5B.!!$R1 3367

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
997 5384 1.047002 CTGCATTCAAACCCCCAACA 58.953 50.0 0.0 0.0 0.0 3.33 F
1020 5408 0.322975 TGAACTCTGCCCTCAAGCTC 59.677 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 6799 0.315886 ATACAACACGTCGAGCACCA 59.684 50.0 0.00 0.0 0.00 4.17 R
2605 7103 1.617755 CGTCCGTGCACTAACAGCAG 61.618 60.0 16.19 0.0 43.63 4.24 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 4291 3.181458 GGAAATGGTCGTTAGCATAGGGA 60.181 47.826 0.00 0.00 42.93 4.20
24 4292 4.505039 GGAAATGGTCGTTAGCATAGGGAT 60.505 45.833 0.00 0.00 42.93 3.85
25 4293 3.685139 ATGGTCGTTAGCATAGGGATG 57.315 47.619 0.00 0.00 41.96 3.51
44 4312 4.943705 GGATGCATGTATATAACCACAGGG 59.056 45.833 2.46 0.00 41.29 4.45
67 4335 6.128634 GGGTATTGTTGTAAGAAGAACTGACG 60.129 42.308 0.00 0.00 32.75 4.35
73 4341 6.643770 TGTTGTAAGAAGAACTGACGAATACC 59.356 38.462 0.00 0.00 32.75 2.73
87 4355 7.606456 ACTGACGAATACCATTGTTACATTCTT 59.394 33.333 0.00 0.00 0.00 2.52
113 4381 4.122776 CTGCGTACTAATTTCCAGCATCT 58.877 43.478 0.00 0.00 32.49 2.90
129 4397 4.525912 GCATCTAATAAAATGCCCCCAG 57.474 45.455 0.00 0.00 41.92 4.45
135 4403 6.731467 TCTAATAAAATGCCCCCAGGATATC 58.269 40.000 0.00 0.00 33.47 1.63
219 4488 9.926751 GTGTAGTTGTAGGTTTTTCTTTAAGAC 57.073 33.333 0.00 0.00 0.00 3.01
220 4489 9.112725 TGTAGTTGTAGGTTTTTCTTTAAGACC 57.887 33.333 0.00 0.00 0.00 3.85
221 4490 7.578310 AGTTGTAGGTTTTTCTTTAAGACCC 57.422 36.000 0.00 0.00 0.00 4.46
340 4638 8.725046 CGTGTGCTTTATCGAAAAATCTATTTC 58.275 33.333 0.00 0.00 36.24 2.17
344 4642 8.120465 TGCTTTATCGAAAAATCTATTTCCGTC 58.880 33.333 0.00 0.00 36.21 4.79
355 4653 7.948278 AATCTATTTCCGTCTGTAGCATTAC 57.052 36.000 0.00 0.00 0.00 1.89
388 4687 5.381174 TGAAGCTTGAAATTGACTCCATG 57.619 39.130 2.10 0.00 0.00 3.66
451 4777 5.416952 CAGGTAAAGAATGCTTCAGTCCAAT 59.583 40.000 0.00 0.00 31.82 3.16
466 4792 4.869297 CAGTCCAATGCAAGACAAAACAAA 59.131 37.500 14.91 0.00 35.38 2.83
474 4800 9.409312 CAATGCAAGACAAAACAAATATCACTA 57.591 29.630 0.00 0.00 0.00 2.74
481 4808 9.003658 AGACAAAACAAATATCACTAGAGTTGG 57.996 33.333 0.00 0.00 0.00 3.77
483 4810 8.784043 ACAAAACAAATATCACTAGAGTTGGAC 58.216 33.333 0.00 0.00 0.00 4.02
511 4838 8.579850 AATGCTTACCAGAACTCAAATCATTA 57.420 30.769 0.00 0.00 0.00 1.90
515 4842 7.148474 GCTTACCAGAACTCAAATCATTAACGA 60.148 37.037 0.00 0.00 0.00 3.85
516 4843 6.481954 ACCAGAACTCAAATCATTAACGAC 57.518 37.500 0.00 0.00 0.00 4.34
517 4844 5.995282 ACCAGAACTCAAATCATTAACGACA 59.005 36.000 0.00 0.00 0.00 4.35
518 4845 6.655003 ACCAGAACTCAAATCATTAACGACAT 59.345 34.615 0.00 0.00 0.00 3.06
524 4851 9.773328 AACTCAAATCATTAACGACATTGTATG 57.227 29.630 0.00 0.00 0.00 2.39
536 4863 4.679106 CGACATTGTATGAGAGGCAGTCTT 60.679 45.833 0.00 0.00 34.71 3.01
539 4866 5.163364 ACATTGTATGAGAGGCAGTCTTAGG 60.163 44.000 0.00 0.00 34.71 2.69
547 4874 1.557371 AGGCAGTCTTAGGCTTCTTCC 59.443 52.381 0.00 0.00 38.98 3.46
585 4952 3.069586 CCAAACTTTCCCTTTCCCAAGAC 59.930 47.826 0.00 0.00 30.57 3.01
617 4985 5.997129 CAGCCTTCTCTTTCTCTTTCTCTTT 59.003 40.000 0.00 0.00 0.00 2.52
626 4994 9.196552 CTCTTTCTCTTTCTCTTTCTCTTTCTC 57.803 37.037 0.00 0.00 0.00 2.87
627 4995 8.923270 TCTTTCTCTTTCTCTTTCTCTTTCTCT 58.077 33.333 0.00 0.00 0.00 3.10
628 4996 9.546428 CTTTCTCTTTCTCTTTCTCTTTCTCTT 57.454 33.333 0.00 0.00 0.00 2.85
630 4998 9.541143 TTCTCTTTCTCTTTCTCTTTCTCTTTC 57.459 33.333 0.00 0.00 0.00 2.62
631 4999 8.923270 TCTCTTTCTCTTTCTCTTTCTCTTTCT 58.077 33.333 0.00 0.00 0.00 2.52
635 5003 9.898152 TTTCTCTTTCTCTTTCTCTTTCTCTTT 57.102 29.630 0.00 0.00 0.00 2.52
636 5004 9.541143 TTCTCTTTCTCTTTCTCTTTCTCTTTC 57.459 33.333 0.00 0.00 0.00 2.62
637 5005 8.923270 TCTCTTTCTCTTTCTCTTTCTCTTTCT 58.077 33.333 0.00 0.00 0.00 2.52
638 5006 9.196552 CTCTTTCTCTTTCTCTTTCTCTTTCTC 57.803 37.037 0.00 0.00 0.00 2.87
639 5007 8.923270 TCTTTCTCTTTCTCTTTCTCTTTCTCT 58.077 33.333 0.00 0.00 0.00 3.10
640 5008 9.546428 CTTTCTCTTTCTCTTTCTCTTTCTCTT 57.454 33.333 0.00 0.00 0.00 2.85
642 5010 9.898152 TTCTCTTTCTCTTTCTCTTTCTCTTTT 57.102 29.630 0.00 0.00 0.00 2.27
643 5011 9.898152 TCTCTTTCTCTTTCTCTTTCTCTTTTT 57.102 29.630 0.00 0.00 0.00 1.94
648 5016 8.669946 TCTCTTTCTCTTTCTCTTTTTCTTCC 57.330 34.615 0.00 0.00 0.00 3.46
649 5017 8.490311 TCTCTTTCTCTTTCTCTTTTTCTTCCT 58.510 33.333 0.00 0.00 0.00 3.36
650 5018 8.669946 TCTTTCTCTTTCTCTTTTTCTTCCTC 57.330 34.615 0.00 0.00 0.00 3.71
651 5019 7.717436 TCTTTCTCTTTCTCTTTTTCTTCCTCC 59.283 37.037 0.00 0.00 0.00 4.30
652 5020 5.870706 TCTCTTTCTCTTTTTCTTCCTCCC 58.129 41.667 0.00 0.00 0.00 4.30
653 5021 5.608860 TCTCTTTCTCTTTTTCTTCCTCCCT 59.391 40.000 0.00 0.00 0.00 4.20
654 5022 6.101881 TCTCTTTCTCTTTTTCTTCCTCCCTT 59.898 38.462 0.00 0.00 0.00 3.95
655 5023 6.299922 TCTTTCTCTTTTTCTTCCTCCCTTC 58.700 40.000 0.00 0.00 0.00 3.46
656 5024 5.646692 TTCTCTTTTTCTTCCTCCCTTCA 57.353 39.130 0.00 0.00 0.00 3.02
657 5025 4.974399 TCTCTTTTTCTTCCTCCCTTCAC 58.026 43.478 0.00 0.00 0.00 3.18
658 5026 4.412199 TCTCTTTTTCTTCCTCCCTTCACA 59.588 41.667 0.00 0.00 0.00 3.58
659 5027 5.104109 TCTCTTTTTCTTCCTCCCTTCACAA 60.104 40.000 0.00 0.00 0.00 3.33
660 5028 5.705400 TCTTTTTCTTCCTCCCTTCACAAT 58.295 37.500 0.00 0.00 0.00 2.71
661 5029 5.770162 TCTTTTTCTTCCTCCCTTCACAATC 59.230 40.000 0.00 0.00 0.00 2.67
662 5030 4.722526 TTTCTTCCTCCCTTCACAATCA 57.277 40.909 0.00 0.00 0.00 2.57
663 5031 3.703001 TCTTCCTCCCTTCACAATCAC 57.297 47.619 0.00 0.00 0.00 3.06
664 5032 2.978978 TCTTCCTCCCTTCACAATCACA 59.021 45.455 0.00 0.00 0.00 3.58
665 5033 3.394274 TCTTCCTCCCTTCACAATCACAA 59.606 43.478 0.00 0.00 0.00 3.33
666 5034 3.423539 TCCTCCCTTCACAATCACAAG 57.576 47.619 0.00 0.00 0.00 3.16
667 5035 2.711009 TCCTCCCTTCACAATCACAAGT 59.289 45.455 0.00 0.00 0.00 3.16
668 5036 3.077359 CCTCCCTTCACAATCACAAGTC 58.923 50.000 0.00 0.00 0.00 3.01
669 5037 3.496692 CCTCCCTTCACAATCACAAGTCA 60.497 47.826 0.00 0.00 0.00 3.41
745 5114 6.883744 AGCATAAAGAAAACCAAGGAACAAA 58.116 32.000 0.00 0.00 0.00 2.83
746 5115 6.986231 AGCATAAAGAAAACCAAGGAACAAAG 59.014 34.615 0.00 0.00 0.00 2.77
748 5117 7.279981 GCATAAAGAAAACCAAGGAACAAAGTT 59.720 33.333 0.00 0.00 0.00 2.66
749 5118 9.810545 CATAAAGAAAACCAAGGAACAAAGTTA 57.189 29.630 0.00 0.00 0.00 2.24
754 5125 4.741928 ACCAAGGAACAAAGTTATCCCT 57.258 40.909 0.00 0.00 33.55 4.20
861 5248 3.363970 GCACCACGCTAATTATTCCATCG 60.364 47.826 0.00 0.00 37.77 3.84
961 5348 5.305644 ACACTATATCACACCTCATTCCTCC 59.694 44.000 0.00 0.00 0.00 4.30
990 5377 5.125100 TCACATCTTTCTGCATTCAAACC 57.875 39.130 0.00 0.00 0.00 3.27
996 5383 1.337118 TCTGCATTCAAACCCCCAAC 58.663 50.000 0.00 0.00 0.00 3.77
997 5384 1.047002 CTGCATTCAAACCCCCAACA 58.953 50.000 0.00 0.00 0.00 3.33
1016 5404 1.067295 ACCATGAACTCTGCCCTCAA 58.933 50.000 0.00 0.00 0.00 3.02
1020 5408 0.322975 TGAACTCTGCCCTCAAGCTC 59.677 55.000 0.00 0.00 0.00 4.09
1032 5420 2.333014 CTCAAGCTCGTCTCTTTCCAC 58.667 52.381 0.00 0.00 0.00 4.02
1034 5422 3.154710 TCAAGCTCGTCTCTTTCCACTA 58.845 45.455 0.00 0.00 0.00 2.74
1035 5423 3.764434 TCAAGCTCGTCTCTTTCCACTAT 59.236 43.478 0.00 0.00 0.00 2.12
1036 5424 4.109050 CAAGCTCGTCTCTTTCCACTATC 58.891 47.826 0.00 0.00 0.00 2.08
1037 5425 3.357203 AGCTCGTCTCTTTCCACTATCA 58.643 45.455 0.00 0.00 0.00 2.15
1130 5518 2.387757 ACAATATTCGCCAAAGCCCAT 58.612 42.857 0.00 0.00 34.57 4.00
1145 5533 0.959553 CCCATACGAGCGATACCAGT 59.040 55.000 0.00 0.00 0.00 4.00
1224 5612 5.078949 TCTTCACCCATGACAAATGTGATT 58.921 37.500 0.00 0.00 36.00 2.57
1263 5651 1.325640 CTCAATGACAAGGACATCGCG 59.674 52.381 0.00 0.00 0.00 5.87
1297 5685 1.075212 TGATTCACCCTGATTGCACCA 59.925 47.619 0.00 0.00 0.00 4.17
1299 5687 1.548081 TTCACCCTGATTGCACCATG 58.452 50.000 0.00 0.00 0.00 3.66
1355 5743 1.890489 GGTTTTACCCGCACCTCATTT 59.110 47.619 0.00 0.00 30.04 2.32
1361 5749 0.804989 CCCGCACCTCATTTTCTCAC 59.195 55.000 0.00 0.00 0.00 3.51
1366 5754 2.416431 GCACCTCATTTTCTCACATGCC 60.416 50.000 0.00 0.00 0.00 4.40
1371 5759 2.562298 TCATTTTCTCACATGCCCCAAC 59.438 45.455 0.00 0.00 0.00 3.77
1394 5782 1.133181 TCATGGTTGAGTCCCCTGCA 61.133 55.000 0.00 0.00 0.00 4.41
1401 5789 3.620488 GTTGAGTCCCCTGCATATTTGA 58.380 45.455 0.00 0.00 0.00 2.69
1405 5793 2.024414 GTCCCCTGCATATTTGACCAC 58.976 52.381 0.00 0.00 0.00 4.16
1406 5794 1.922447 TCCCCTGCATATTTGACCACT 59.078 47.619 0.00 0.00 0.00 4.00
1407 5795 2.026641 CCCCTGCATATTTGACCACTG 58.973 52.381 0.00 0.00 0.00 3.66
1408 5796 2.026641 CCCTGCATATTTGACCACTGG 58.973 52.381 0.00 0.00 0.00 4.00
1415 5834 4.022416 GCATATTTGACCACTGGACAACAA 60.022 41.667 11.89 4.75 37.13 2.83
1419 5838 3.188159 TGACCACTGGACAACAACTAC 57.812 47.619 0.71 0.00 0.00 2.73
1427 5846 2.357637 TGGACAACAACTACTTTGCTGC 59.642 45.455 0.00 0.00 39.01 5.25
1445 5864 3.243201 GCTGCCTGCAGAATACAATTACC 60.243 47.826 22.64 0.00 46.30 2.85
1493 5912 7.009907 GCTATGAGAAAGAATGTCAAATTTGCC 59.990 37.037 13.54 2.32 34.60 4.52
1505 5924 4.866486 GTCAAATTTGCCATTGATGAGGTC 59.134 41.667 13.54 0.00 37.82 3.85
1511 5930 2.012673 GCCATTGATGAGGTCTGTCAC 58.987 52.381 0.00 0.00 0.00 3.67
1597 6016 3.385193 AACAAATAAGTGGCAGGCAAC 57.615 42.857 0.00 0.00 0.00 4.17
1651 6070 4.202121 GCAGAGTGGAACGGTAAGATCATA 60.202 45.833 0.00 0.00 45.86 2.15
1680 6099 2.030805 CCAAAGGCTGCAGTTTCTACAC 60.031 50.000 16.64 0.00 0.00 2.90
1726 6145 7.348201 CGCTTCTTATTAGGTAGCTGAAATTG 58.652 38.462 4.27 0.00 31.44 2.32
1733 6152 9.692749 TTATTAGGTAGCTGAAATTGATACTCG 57.307 33.333 4.27 0.00 0.00 4.18
1773 6204 1.896220 ACACAACATCGTGCTTCCAT 58.104 45.000 0.00 0.00 40.73 3.41
1782 6213 2.905075 TCGTGCTTCCATCTTGGTATG 58.095 47.619 0.00 0.00 39.03 2.39
1795 6230 6.206243 CCATCTTGGTATGCTCTTTCTAATGG 59.794 42.308 0.00 0.00 31.35 3.16
1801 6236 3.192541 TGCTCTTTCTAATGGCGCATA 57.807 42.857 10.83 0.00 0.00 3.14
1926 6361 3.566742 TGCTGCTGCATCCAACTATATTG 59.433 43.478 14.93 0.00 45.31 1.90
1953 6404 3.026694 AGCTAATTGCCTTCCATGGAAC 58.973 45.455 23.63 15.03 44.23 3.62
2040 6510 7.766278 ACAAGCTGAAGGTATGTATAAACTCTG 59.234 37.037 0.00 0.00 0.00 3.35
2041 6511 7.425224 AGCTGAAGGTATGTATAAACTCTGT 57.575 36.000 0.00 0.00 0.00 3.41
2238 6713 3.565482 TCTGGTCATTTGTTGTGAAGCTC 59.435 43.478 0.00 0.00 0.00 4.09
2307 6782 1.808411 TCCGCTTCTGGTCATTTGTC 58.192 50.000 0.00 0.00 0.00 3.18
2317 6792 1.732259 GGTCATTTGTCGCACGAAGAT 59.268 47.619 0.00 0.00 0.00 2.40
2324 6799 3.452755 TGTCGCACGAAGATTGGATAT 57.547 42.857 0.00 0.00 0.00 1.63
2372 6847 6.899393 ATTCAAGCAGTTCATGTAAGGAAA 57.101 33.333 0.00 0.00 38.90 3.13
2373 6848 6.707440 TTCAAGCAGTTCATGTAAGGAAAA 57.293 33.333 0.00 0.00 38.90 2.29
2374 6849 6.707440 TCAAGCAGTTCATGTAAGGAAAAA 57.293 33.333 0.00 0.00 38.90 1.94
2465 6944 7.509141 TGCAATCAATTACCGACAATATCAT 57.491 32.000 0.00 0.00 0.00 2.45
2521 7019 3.055591 CGATGGATCAGAATCTTCCACG 58.944 50.000 5.86 8.18 42.09 4.94
2522 7020 2.315925 TGGATCAGAATCTTCCACGC 57.684 50.000 0.00 0.00 34.65 5.34
2605 7103 9.788960 GACATCATTTCACCCTTATAAGAAAAC 57.211 33.333 14.28 0.00 34.13 2.43
2619 7117 3.971032 AGAAAACTGCTGTTAGTGCAC 57.029 42.857 9.40 9.40 34.96 4.57
2628 7126 2.478370 GCTGTTAGTGCACGGACGTATA 60.478 50.000 12.01 0.00 0.00 1.47
2629 7127 3.794475 GCTGTTAGTGCACGGACGTATAT 60.794 47.826 12.01 0.00 0.00 0.86
2630 7128 4.555313 GCTGTTAGTGCACGGACGTATATA 60.555 45.833 12.01 0.00 0.00 0.86
2631 7129 5.694231 TGTTAGTGCACGGACGTATATAT 57.306 39.130 12.01 0.00 0.00 0.86
2632 7130 6.621380 GCTGTTAGTGCACGGACGTATATATA 60.621 42.308 12.01 0.00 0.00 0.86
2633 7131 7.381766 TGTTAGTGCACGGACGTATATATAT 57.618 36.000 12.01 0.00 0.00 0.86
2634 7132 8.491331 TGTTAGTGCACGGACGTATATATATA 57.509 34.615 12.01 0.00 0.00 0.86
2635 7133 9.112725 TGTTAGTGCACGGACGTATATATATAT 57.887 33.333 12.01 10.10 0.00 0.86
2696 7194 9.119329 GATAGATATTGCTGTAACAAGTACTCG 57.881 37.037 0.00 0.00 33.46 4.18
2760 7317 6.697455 GTCATTCTACAATCTATCTGTTCGCA 59.303 38.462 0.00 0.00 0.00 5.10
2774 7333 6.028146 TCTGTTCGCATAGTGTAGGTTTTA 57.972 37.500 0.00 0.00 0.00 1.52
2780 7339 8.378421 GTTCGCATAGTGTAGGTTTTACTTTAG 58.622 37.037 0.00 0.00 0.00 1.85
2781 7340 7.829725 TCGCATAGTGTAGGTTTTACTTTAGA 58.170 34.615 0.00 0.00 0.00 2.10
2782 7341 7.972277 TCGCATAGTGTAGGTTTTACTTTAGAG 59.028 37.037 0.00 0.00 0.00 2.43
2870 7458 7.812690 ATGCAAGACAGAAGCATCATAATTA 57.187 32.000 0.00 0.00 45.11 1.40
3039 7735 7.220030 TGCAGTGGAATTTCTATAGATCCTTC 58.780 38.462 17.78 13.41 0.00 3.46
3073 7770 3.429960 GCCCCTGAAAGAATCTTGCATTC 60.430 47.826 3.79 0.00 34.07 2.67
3095 7792 4.165565 TCTTCTTCTCATCATCCCATGCTT 59.834 41.667 0.00 0.00 0.00 3.91
3129 7852 4.613031 CGTCGAAAGAAATGGCTCTTTTTC 59.387 41.667 2.26 0.00 43.97 2.29
3191 7914 4.148128 ACCTGGCATAGAGAAACAGATG 57.852 45.455 0.00 0.00 0.00 2.90
3203 7926 2.438868 AACAGATGATAGCGCGCATA 57.561 45.000 35.10 21.96 0.00 3.14
3204 7927 1.988063 ACAGATGATAGCGCGCATAG 58.012 50.000 35.10 15.46 0.00 2.23
3279 8044 9.605275 CTGAAAGGATATTCTGAAATACTGTGA 57.395 33.333 0.00 0.00 31.96 3.58
3310 8075 0.538287 AACTCCAGTGCCTTCCTTGC 60.538 55.000 0.00 0.00 0.00 4.01
3311 8076 1.073722 CTCCAGTGCCTTCCTTGCA 59.926 57.895 0.00 0.00 36.12 4.08
3331 8096 3.608073 GCAATATTTTCTGCGACAACCAC 59.392 43.478 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 4291 5.582950 ACCCTGTGGTTATATACATGCAT 57.417 39.130 0.00 0.00 44.75 3.96
24 4292 6.696042 ATACCCTGTGGTTATATACATGCA 57.304 37.500 0.00 0.00 44.75 3.96
25 4293 6.940298 ACAATACCCTGTGGTTATATACATGC 59.060 38.462 0.00 0.00 44.75 4.06
26 4294 8.783093 CAACAATACCCTGTGGTTATATACATG 58.217 37.037 0.00 0.00 44.75 3.21
44 4312 7.633361 TCGTCAGTTCTTCTTACAACAATAC 57.367 36.000 0.00 0.00 0.00 1.89
91 4359 4.122776 AGATGCTGGAAATTAGTACGCAG 58.877 43.478 0.00 0.00 0.00 5.18
93 4361 6.787085 ATTAGATGCTGGAAATTAGTACGC 57.213 37.500 0.00 0.00 0.00 4.42
113 4381 5.559545 AGGATATCCTGGGGGCATTTTATTA 59.440 40.000 23.95 0.00 46.55 0.98
128 4396 4.421131 AGAATCCGTAAGCAGGATATCCT 58.579 43.478 19.18 19.18 46.99 3.24
129 4397 4.810191 AGAATCCGTAAGCAGGATATCC 57.190 45.455 14.41 14.41 46.99 2.59
135 4403 2.699954 ACACAAGAATCCGTAAGCAGG 58.300 47.619 0.00 0.00 0.00 4.85
145 4413 3.499918 ACTGCAGCTGTTACACAAGAATC 59.500 43.478 15.27 0.00 0.00 2.52
219 4488 0.320771 GTGCAGACTGTACTGTGGGG 60.321 60.000 15.61 0.97 39.73 4.96
220 4489 0.681733 AGTGCAGACTGTACTGTGGG 59.318 55.000 23.39 3.37 41.73 4.61
221 4490 2.224042 TGAAGTGCAGACTGTACTGTGG 60.224 50.000 24.49 3.72 42.47 4.17
340 4638 5.538118 TGGAATATGTAATGCTACAGACGG 58.462 41.667 0.00 0.00 41.33 4.79
344 4642 9.888878 CTTCAAATGGAATATGTAATGCTACAG 57.111 33.333 0.00 0.00 36.84 2.74
355 4653 9.373603 TCAATTTCAAGCTTCAAATGGAATATG 57.626 29.630 10.19 3.89 34.32 1.78
388 4687 7.387673 CCACAAAAAGGGAAAATAATCTGGAAC 59.612 37.037 0.00 0.00 0.00 3.62
451 4777 8.389779 TCTAGTGATATTTGTTTTGTCTTGCA 57.610 30.769 0.00 0.00 0.00 4.08
466 4792 8.200024 AGCATTATGTCCAACTCTAGTGATAT 57.800 34.615 0.00 0.00 0.00 1.63
474 4800 5.189736 TCTGGTAAGCATTATGTCCAACTCT 59.810 40.000 0.00 0.00 30.46 3.24
480 4807 5.428253 TGAGTTCTGGTAAGCATTATGTCC 58.572 41.667 0.00 0.00 30.46 4.02
481 4808 6.985188 TTGAGTTCTGGTAAGCATTATGTC 57.015 37.500 0.00 0.00 30.46 3.06
483 4810 7.988737 TGATTTGAGTTCTGGTAAGCATTATG 58.011 34.615 0.00 0.00 30.46 1.90
488 4815 7.360861 CGTTAATGATTTGAGTTCTGGTAAGCA 60.361 37.037 0.00 0.00 0.00 3.91
511 4838 3.055819 ACTGCCTCTCATACAATGTCGTT 60.056 43.478 0.00 0.00 0.00 3.85
515 4842 4.833478 AAGACTGCCTCTCATACAATGT 57.167 40.909 0.00 0.00 0.00 2.71
516 4843 5.295950 CCTAAGACTGCCTCTCATACAATG 58.704 45.833 0.00 0.00 0.00 2.82
517 4844 4.202305 GCCTAAGACTGCCTCTCATACAAT 60.202 45.833 0.00 0.00 0.00 2.71
518 4845 3.133003 GCCTAAGACTGCCTCTCATACAA 59.867 47.826 0.00 0.00 0.00 2.41
524 4851 2.107366 AGAAGCCTAAGACTGCCTCTC 58.893 52.381 0.00 0.00 0.00 3.20
547 4874 1.948104 TTGGTTGTCTGTCACTTCCG 58.052 50.000 0.00 0.00 0.00 4.30
557 4884 3.704566 GGAAAGGGAAAGTTTGGTTGTCT 59.295 43.478 0.00 0.00 0.00 3.41
585 4952 6.815089 AGAGAAAGAGAAGGCTGTATGTATG 58.185 40.000 0.00 0.00 0.00 2.39
617 4985 9.898152 AAAAAGAGAAAGAGAAAGAGAAAGAGA 57.102 29.630 0.00 0.00 0.00 3.10
626 4994 7.040755 GGGAGGAAGAAAAAGAGAAAGAGAAAG 60.041 40.741 0.00 0.00 0.00 2.62
627 4995 6.773200 GGGAGGAAGAAAAAGAGAAAGAGAAA 59.227 38.462 0.00 0.00 0.00 2.52
628 4996 6.101881 AGGGAGGAAGAAAAAGAGAAAGAGAA 59.898 38.462 0.00 0.00 0.00 2.87
630 4998 5.875224 AGGGAGGAAGAAAAAGAGAAAGAG 58.125 41.667 0.00 0.00 0.00 2.85
631 4999 5.913946 AGGGAGGAAGAAAAAGAGAAAGA 57.086 39.130 0.00 0.00 0.00 2.52
635 5003 4.412199 TGTGAAGGGAGGAAGAAAAAGAGA 59.588 41.667 0.00 0.00 0.00 3.10
636 5004 4.718961 TGTGAAGGGAGGAAGAAAAAGAG 58.281 43.478 0.00 0.00 0.00 2.85
637 5005 4.788925 TGTGAAGGGAGGAAGAAAAAGA 57.211 40.909 0.00 0.00 0.00 2.52
638 5006 5.536161 TGATTGTGAAGGGAGGAAGAAAAAG 59.464 40.000 0.00 0.00 0.00 2.27
639 5007 5.301805 GTGATTGTGAAGGGAGGAAGAAAAA 59.698 40.000 0.00 0.00 0.00 1.94
640 5008 4.827284 GTGATTGTGAAGGGAGGAAGAAAA 59.173 41.667 0.00 0.00 0.00 2.29
642 5010 3.394274 TGTGATTGTGAAGGGAGGAAGAA 59.606 43.478 0.00 0.00 0.00 2.52
643 5011 2.978978 TGTGATTGTGAAGGGAGGAAGA 59.021 45.455 0.00 0.00 0.00 2.87
646 5014 2.711009 ACTTGTGATTGTGAAGGGAGGA 59.289 45.455 0.00 0.00 0.00 3.71
647 5015 3.077359 GACTTGTGATTGTGAAGGGAGG 58.923 50.000 0.00 0.00 0.00 4.30
648 5016 3.499918 GTGACTTGTGATTGTGAAGGGAG 59.500 47.826 0.00 0.00 0.00 4.30
649 5017 3.136443 AGTGACTTGTGATTGTGAAGGGA 59.864 43.478 0.00 0.00 0.00 4.20
650 5018 3.480470 AGTGACTTGTGATTGTGAAGGG 58.520 45.455 0.00 0.00 0.00 3.95
651 5019 6.652481 AGATAAGTGACTTGTGATTGTGAAGG 59.348 38.462 8.33 0.00 0.00 3.46
652 5020 7.664082 AGATAAGTGACTTGTGATTGTGAAG 57.336 36.000 8.33 0.00 0.00 3.02
653 5021 7.933577 AGAAGATAAGTGACTTGTGATTGTGAA 59.066 33.333 8.33 0.00 0.00 3.18
654 5022 7.445121 AGAAGATAAGTGACTTGTGATTGTGA 58.555 34.615 8.33 0.00 0.00 3.58
655 5023 7.664082 AGAAGATAAGTGACTTGTGATTGTG 57.336 36.000 8.33 0.00 0.00 3.33
656 5024 8.682936 AAAGAAGATAAGTGACTTGTGATTGT 57.317 30.769 8.33 0.00 0.00 2.71
657 5025 9.604626 GAAAAGAAGATAAGTGACTTGTGATTG 57.395 33.333 8.33 0.00 0.00 2.67
658 5026 9.566432 AGAAAAGAAGATAAGTGACTTGTGATT 57.434 29.630 8.33 0.00 0.00 2.57
659 5027 8.997323 CAGAAAAGAAGATAAGTGACTTGTGAT 58.003 33.333 8.33 0.00 0.00 3.06
660 5028 7.987458 ACAGAAAAGAAGATAAGTGACTTGTGA 59.013 33.333 8.33 0.00 0.00 3.58
661 5029 8.147642 ACAGAAAAGAAGATAAGTGACTTGTG 57.852 34.615 8.33 0.00 0.00 3.33
662 5030 9.482627 CTACAGAAAAGAAGATAAGTGACTTGT 57.517 33.333 8.33 0.00 0.00 3.16
663 5031 9.698309 TCTACAGAAAAGAAGATAAGTGACTTG 57.302 33.333 8.33 0.00 0.00 3.16
664 5032 9.699703 GTCTACAGAAAAGAAGATAAGTGACTT 57.300 33.333 2.37 2.37 0.00 3.01
665 5033 8.861086 TGTCTACAGAAAAGAAGATAAGTGACT 58.139 33.333 0.00 0.00 0.00 3.41
666 5034 9.477484 TTGTCTACAGAAAAGAAGATAAGTGAC 57.523 33.333 0.00 0.00 0.00 3.67
667 5035 9.477484 GTTGTCTACAGAAAAGAAGATAAGTGA 57.523 33.333 0.00 0.00 0.00 3.41
668 5036 8.713271 GGTTGTCTACAGAAAAGAAGATAAGTG 58.287 37.037 0.00 0.00 0.00 3.16
669 5037 8.429641 TGGTTGTCTACAGAAAAGAAGATAAGT 58.570 33.333 0.00 0.00 0.00 2.24
745 5114 6.252995 TGCCAATCTGTAAAAAGGGATAACT 58.747 36.000 0.00 0.00 0.00 2.24
746 5115 6.524101 TGCCAATCTGTAAAAAGGGATAAC 57.476 37.500 0.00 0.00 0.00 1.89
748 5117 6.321181 GTCATGCCAATCTGTAAAAAGGGATA 59.679 38.462 0.00 0.00 0.00 2.59
749 5118 5.127682 GTCATGCCAATCTGTAAAAAGGGAT 59.872 40.000 0.00 0.00 0.00 3.85
750 5119 4.462483 GTCATGCCAATCTGTAAAAAGGGA 59.538 41.667 0.00 0.00 0.00 4.20
754 5125 5.076182 TGGAGTCATGCCAATCTGTAAAAA 58.924 37.500 0.00 0.00 31.13 1.94
961 5348 2.490509 TGCAGAAAGATGTGAAGGCATG 59.509 45.455 0.00 0.00 0.00 4.06
990 5377 1.538047 CAGAGTTCATGGTGTTGGGG 58.462 55.000 0.00 0.00 0.00 4.96
996 5383 0.325933 TGAGGGCAGAGTTCATGGTG 59.674 55.000 0.00 0.00 0.00 4.17
997 5384 1.004044 CTTGAGGGCAGAGTTCATGGT 59.996 52.381 0.00 0.00 0.00 3.55
1016 5404 3.357203 TGATAGTGGAAAGAGACGAGCT 58.643 45.455 0.00 0.00 0.00 4.09
1020 5408 3.639094 AGGGATGATAGTGGAAAGAGACG 59.361 47.826 0.00 0.00 0.00 4.18
1032 5420 7.829211 TGTTTTAGGTTGAAAGAGGGATGATAG 59.171 37.037 0.00 0.00 0.00 2.08
1034 5422 6.552008 TGTTTTAGGTTGAAAGAGGGATGAT 58.448 36.000 0.00 0.00 0.00 2.45
1035 5423 5.947663 TGTTTTAGGTTGAAAGAGGGATGA 58.052 37.500 0.00 0.00 0.00 2.92
1036 5424 6.447162 GTTGTTTTAGGTTGAAAGAGGGATG 58.553 40.000 0.00 0.00 0.00 3.51
1037 5425 5.240844 CGTTGTTTTAGGTTGAAAGAGGGAT 59.759 40.000 0.00 0.00 0.00 3.85
1091 5479 3.787001 GCCTCTTCCCCCACTCGG 61.787 72.222 0.00 0.00 0.00 4.63
1130 5518 1.033202 TGGCACTGGTATCGCTCGTA 61.033 55.000 0.00 0.00 0.00 3.43
1224 5612 3.333980 TGAGGGAAGAGTAGAACTCCTGA 59.666 47.826 3.49 0.00 46.18 3.86
1273 5661 1.404391 GCAATCAGGGTGAATCAGCTG 59.596 52.381 7.63 7.63 31.98 4.24
1282 5670 1.475280 CTTCATGGTGCAATCAGGGTG 59.525 52.381 0.00 0.00 0.00 4.61
1355 5743 1.133513 AGTTGTTGGGGCATGTGAGAA 60.134 47.619 0.00 0.00 0.00 2.87
1361 5749 0.533491 CCATGAGTTGTTGGGGCATG 59.467 55.000 0.00 0.00 36.87 4.06
1394 5782 5.385198 AGTTGTTGTCCAGTGGTCAAATAT 58.615 37.500 21.20 7.32 33.16 1.28
1401 5789 3.926058 AAGTAGTTGTTGTCCAGTGGT 57.074 42.857 9.54 0.00 0.00 4.16
1405 5793 3.548818 GCAGCAAAGTAGTTGTTGTCCAG 60.549 47.826 5.09 0.00 46.88 3.86
1406 5794 2.357637 GCAGCAAAGTAGTTGTTGTCCA 59.642 45.455 5.09 0.00 46.88 4.02
1407 5795 2.287608 GGCAGCAAAGTAGTTGTTGTCC 60.288 50.000 0.00 3.69 44.66 4.02
1408 5796 3.000082 GGCAGCAAAGTAGTTGTTGTC 58.000 47.619 0.00 0.00 46.88 3.18
1427 5846 6.201044 CGAAGTAGGTAATTGTATTCTGCAGG 59.799 42.308 15.13 0.00 0.00 4.85
1434 5853 5.296035 GCCTTGCGAAGTAGGTAATTGTATT 59.704 40.000 0.00 0.00 34.67 1.89
1439 5858 3.629142 AGCCTTGCGAAGTAGGTAATT 57.371 42.857 0.00 0.00 34.67 1.40
1443 5862 2.420129 CCATAAGCCTTGCGAAGTAGGT 60.420 50.000 0.00 0.00 34.67 3.08
1445 5864 3.179443 TCCATAAGCCTTGCGAAGTAG 57.821 47.619 0.00 0.00 0.00 2.57
1493 5912 2.094026 TCCGTGACAGACCTCATCAATG 60.094 50.000 0.00 0.00 0.00 2.82
1505 5924 1.067776 GTGGGTTCTACTCCGTGACAG 60.068 57.143 0.00 0.00 0.00 3.51
1511 5930 1.939838 GCAACAGTGGGTTCTACTCCG 60.940 57.143 0.00 0.00 37.72 4.63
1541 5960 1.202891 AGGAACTTACCAAGGTGCCAC 60.203 52.381 1.07 0.00 37.23 5.01
1651 6070 1.895131 CTGCAGCCTTTGGTAAATGGT 59.105 47.619 0.00 0.00 33.94 3.55
1680 6099 2.603173 GCTTCTCCTTTTGCTGAACACG 60.603 50.000 0.00 0.00 0.00 4.49
1726 6145 9.296400 GAAATTAGAGAATATGGAGCGAGTATC 57.704 37.037 0.00 0.00 0.00 2.24
1731 6150 8.082852 GTGTAGAAATTAGAGAATATGGAGCGA 58.917 37.037 0.00 0.00 0.00 4.93
1733 6152 9.547753 TTGTGTAGAAATTAGAGAATATGGAGC 57.452 33.333 0.00 0.00 0.00 4.70
1773 6204 5.126067 GCCATTAGAAAGAGCATACCAAGA 58.874 41.667 0.00 0.00 0.00 3.02
1782 6213 4.453819 AGAATATGCGCCATTAGAAAGAGC 59.546 41.667 4.18 0.00 0.00 4.09
1795 6230 4.376413 CGGTGTCAATTAGAGAATATGCGC 60.376 45.833 0.00 0.00 0.00 6.09
1801 6236 3.197766 TCCTGCGGTGTCAATTAGAGAAT 59.802 43.478 0.00 0.00 0.00 2.40
1926 6361 2.158755 TGGAAGGCAATTAGCTAGAGGC 60.159 50.000 0.00 0.60 44.79 4.70
1953 6404 8.511604 AAGTATGTCCTGTAAGAATTGGAATG 57.488 34.615 0.00 0.00 34.07 2.67
2070 6545 9.723601 TTCATGCTTAGCTGGATTTTAATTTTT 57.276 25.926 5.60 0.00 0.00 1.94
2071 6546 9.723601 TTTCATGCTTAGCTGGATTTTAATTTT 57.276 25.926 5.60 0.00 0.00 1.82
2072 6547 9.374838 CTTTCATGCTTAGCTGGATTTTAATTT 57.625 29.630 5.60 0.00 0.00 1.82
2073 6548 8.534496 ACTTTCATGCTTAGCTGGATTTTAATT 58.466 29.630 5.60 0.00 0.00 1.40
2074 6549 8.071177 ACTTTCATGCTTAGCTGGATTTTAAT 57.929 30.769 5.60 0.00 0.00 1.40
2238 6713 9.871238 ATAATAGGCTCCACGTATAATTTGTAG 57.129 33.333 0.00 0.00 0.00 2.74
2307 6782 2.221749 CACCATATCCAATCTTCGTGCG 59.778 50.000 0.00 0.00 0.00 5.34
2317 6792 0.821517 ACGTCGAGCACCATATCCAA 59.178 50.000 0.00 0.00 0.00 3.53
2324 6799 0.315886 ATACAACACGTCGAGCACCA 59.684 50.000 0.00 0.00 0.00 4.17
2349 6824 6.899393 TTTCCTTACATGAACTGCTTGAAT 57.101 33.333 0.00 0.00 0.00 2.57
2419 6898 5.566826 GCATCCACACGGTGTATATATCTGT 60.567 44.000 14.30 0.00 0.00 3.41
2423 6902 4.882842 TGCATCCACACGGTGTATATAT 57.117 40.909 14.30 2.54 0.00 0.86
2424 6903 4.674281 TTGCATCCACACGGTGTATATA 57.326 40.909 14.30 0.10 0.00 0.86
2434 6913 3.376859 TCGGTAATTGATTGCATCCACAC 59.623 43.478 0.00 0.00 0.00 3.82
2465 6944 2.103373 CCTTCTCGGATCCTTCACTCA 58.897 52.381 10.75 0.00 33.16 3.41
2521 7019 4.086199 TCGGGAAACAAATAAACATCGC 57.914 40.909 0.00 0.00 0.00 4.58
2522 7020 4.658071 CCTCGGGAAACAAATAAACATCG 58.342 43.478 0.00 0.00 0.00 3.84
2605 7103 1.617755 CGTCCGTGCACTAACAGCAG 61.618 60.000 16.19 0.00 43.63 4.24
2669 7167 9.413048 GAGTACTTGTTACAGCAATATCTATCC 57.587 37.037 0.00 0.00 32.41 2.59
2696 7194 7.716998 TCAGAAGAATACATAGGCAGAATTTCC 59.283 37.037 0.00 0.00 0.00 3.13
2760 7317 8.376803 AGCCTCTAAAGTAAAACCTACACTAT 57.623 34.615 0.00 0.00 0.00 2.12
2774 7333 8.844244 CATGCAGAAATAAATAGCCTCTAAAGT 58.156 33.333 0.00 0.00 0.00 2.66
2780 7339 7.072030 CGTTACATGCAGAAATAAATAGCCTC 58.928 38.462 0.00 0.00 0.00 4.70
2781 7340 6.513393 GCGTTACATGCAGAAATAAATAGCCT 60.513 38.462 0.00 0.00 0.00 4.58
2782 7341 5.625311 GCGTTACATGCAGAAATAAATAGCC 59.375 40.000 0.00 0.00 0.00 3.93
2870 7458 7.231317 TCAATGATTTGCTTGGTCTAAACTCTT 59.769 33.333 0.00 0.00 32.61 2.85
2954 7601 7.218614 CCATTCTGAATCAAGCTCTCTTAGAT 58.781 38.462 0.00 0.00 0.00 1.98
3039 7735 1.969862 CAGGGGCCTTTTGCTCTTG 59.030 57.895 0.84 0.00 41.61 3.02
3073 7770 4.088056 AGCATGGGATGATGAGAAGAAG 57.912 45.455 0.00 0.00 0.00 2.85
3095 7792 1.000717 TCTTTCGACGTCTGCACATCA 60.001 47.619 14.70 0.00 0.00 3.07
3129 7852 4.144297 TGGATTTCCAGTTTTCCACTCAG 58.856 43.478 0.00 0.00 42.01 3.35
3161 7884 2.366916 CTCTATGCCAGGTTCTCGGATT 59.633 50.000 0.00 0.00 0.00 3.01
3191 7914 1.630148 CCTAACCTATGCGCGCTATC 58.370 55.000 33.29 3.05 0.00 2.08
3203 7926 3.135530 GGATGAAGAGTGATGCCTAACCT 59.864 47.826 0.00 0.00 0.00 3.50
3204 7927 3.135530 AGGATGAAGAGTGATGCCTAACC 59.864 47.826 0.00 0.00 0.00 2.85
3261 8026 6.931281 CCATCGGTCACAGTATTTCAGAATAT 59.069 38.462 0.00 0.00 30.84 1.28
3310 8075 4.793071 TGTGGTTGTCGCAGAAAATATTG 58.207 39.130 0.00 0.00 35.51 1.90
3311 8076 5.182950 TGATGTGGTTGTCGCAGAAAATATT 59.817 36.000 0.00 0.00 35.51 1.28
3331 8096 4.556942 TTTTGCGAGCTCCATAATGATG 57.443 40.909 8.47 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.