Multiple sequence alignment - TraesCS3D01G194200

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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 TraesCS3D01G194200 chr3D 100.000 4179 0 0 1 4179 185234094 185238272 0.000000e+00 7718
1 TraesCS3D01G194200 chr3D 89.815 108 11 0 1566 1673 511322120 511322013 5.630000e-29 139
2 TraesCS3D01G194200 chr3B 95.620 1370 26 7 1991 3354 264008953 264010294 0.000000e+00 2167
3 TraesCS3D01G194200 chr3B 90.202 1041 35 28 521 1512 264007553 264008575 0.000000e+00 1295
4 TraesCS3D01G194200 chr3B 85.661 809 104 10 3375 4177 404417129 404416327 0.000000e+00 841
5 TraesCS3D01G194200 chr3B 84.988 806 112 9 3375 4177 241670650 241669851 0.000000e+00 809
6 TraesCS3D01G194200 chr3B 91.187 556 11 5 1 529 264005072 264005616 0.000000e+00 721
7 TraesCS3D01G194200 chr3B 99.673 306 1 0 1676 1981 264008670 264008975 1.010000e-155 560
8 TraesCS3D01G194200 chr3A 96.590 997 29 2 2384 3378 244352757 244353750 0.000000e+00 1648
9 TraesCS3D01G194200 chr3A 92.700 1000 29 21 600 1570 244350415 244351399 0.000000e+00 1402
10 TraesCS3D01G194200 chr3A 96.065 737 20 3 1672 2402 244351396 244352129 0.000000e+00 1192
11 TraesCS3D01G194200 chr3A 90.462 346 13 6 265 610 244307263 244307588 4.960000e-119 438
12 TraesCS3D01G194200 chr3A 93.609 266 15 2 1 264 244167376 244167641 3.030000e-106 396
13 TraesCS3D01G194200 chr3A 88.889 117 13 0 1559 1675 256934803 256934687 1.210000e-30 145
14 TraesCS3D01G194200 chr1D 86.940 781 95 7 3400 4177 250735000 250734224 0.000000e+00 870
15 TraesCS3D01G194200 chr6D 87.398 738 84 8 3443 4177 399025147 399025878 0.000000e+00 839
16 TraesCS3D01G194200 chr2D 85.644 808 105 7 3374 4177 177452944 177453744 0.000000e+00 839
17 TraesCS3D01G194200 chr2D 91.743 109 9 0 1567 1675 48182418 48182310 7.240000e-33 152
18 TraesCS3D01G194200 chr5B 84.852 812 107 14 3377 4179 80203229 80204033 0.000000e+00 804
19 TraesCS3D01G194200 chr5B 84.483 812 110 14 3377 4179 80607706 80608510 0.000000e+00 787
20 TraesCS3D01G194200 chr5B 85.000 120 18 0 2234 2353 256616250 256616131 5.670000e-24 122
21 TraesCS3D01G194200 chr5A 85.422 782 103 10 3400 4177 494284212 494283438 0.000000e+00 802
22 TraesCS3D01G194200 chr5A 85.369 786 101 8 3401 4177 584547000 584546220 0.000000e+00 802
23 TraesCS3D01G194200 chr5A 91.071 112 10 0 1566 1677 680344819 680344708 7.240000e-33 152
24 TraesCS3D01G194200 chr5A 82.517 143 23 2 2218 2359 311676126 311675985 1.580000e-24 124
25 TraesCS3D01G194200 chr5D 92.727 110 8 0 1566 1675 539873170 539873061 4.320000e-35 159
26 TraesCS3D01G194200 chr5D 85.000 120 18 0 2234 2353 241846366 241846247 5.670000e-24 122
27 TraesCS3D01G194200 chr1A 92.727 110 6 2 1565 1673 95100055 95100163 1.560000e-34 158
28 TraesCS3D01G194200 chr1A 90.179 112 11 0 1566 1677 535427470 535427581 3.370000e-31 147
29 TraesCS3D01G194200 chr7D 89.076 119 12 1 1566 1684 4020213 4020096 3.370000e-31 147
30 TraesCS3D01G194200 chr7D 89.655 116 10 2 1564 1678 615266719 615266605 3.370000e-31 147
31 TraesCS3D01G194200 chr4A 81.250 144 27 0 2610 2753 472197187 472197330 2.640000e-22 117
32 TraesCS3D01G194200 chr4D 84.956 113 17 0 2610 2722 102872288 102872176 9.490000e-22 115


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 TraesCS3D01G194200 chr3D 185234094 185238272 4178 False 7718.00 7718 100.000000 1 4179 1 chr3D.!!$F1 4178
1 TraesCS3D01G194200 chr3B 264005072 264010294 5222 False 1185.75 2167 94.170500 1 3354 4 chr3B.!!$F1 3353
2 TraesCS3D01G194200 chr3B 404416327 404417129 802 True 841.00 841 85.661000 3375 4177 1 chr3B.!!$R2 802
3 TraesCS3D01G194200 chr3B 241669851 241670650 799 True 809.00 809 84.988000 3375 4177 1 chr3B.!!$R1 802
4 TraesCS3D01G194200 chr3A 244350415 244353750 3335 False 1414.00 1648 95.118333 600 3378 3 chr3A.!!$F3 2778
5 TraesCS3D01G194200 chr1D 250734224 250735000 776 True 870.00 870 86.940000 3400 4177 1 chr1D.!!$R1 777
6 TraesCS3D01G194200 chr6D 399025147 399025878 731 False 839.00 839 87.398000 3443 4177 1 chr6D.!!$F1 734
7 TraesCS3D01G194200 chr2D 177452944 177453744 800 False 839.00 839 85.644000 3374 4177 1 chr2D.!!$F1 803
8 TraesCS3D01G194200 chr5B 80203229 80204033 804 False 804.00 804 84.852000 3377 4179 1 chr5B.!!$F1 802
9 TraesCS3D01G194200 chr5B 80607706 80608510 804 False 787.00 787 84.483000 3377 4179 1 chr5B.!!$F2 802
10 TraesCS3D01G194200 chr5A 494283438 494284212 774 True 802.00 802 85.422000 3400 4177 1 chr5A.!!$R2 777
11 TraesCS3D01G194200 chr5A 584546220 584547000 780 True 802.00 802 85.369000 3401 4177 1 chr5A.!!$R3 776

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
489 517 0.379669 GAATGCCTCGTTGCTGGATG 59.620 55.000 1.05 0.0 0.0 3.51 F
1595 3675 1.136474 CGTTGCAAATTACTCGTCGCA 60.136 47.619 0.00 0.0 0.0 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 4076 1.072806 ACAGCAGGACAAGAATCAGCA 59.927 47.619 0.0 0.0 0.00 4.41 R
3535 6307 0.108804 CATGTTCTACGACTGCGGGT 60.109 55.000 0.0 0.0 43.17 5.28 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
44 45 3.572682 CCATCTTCCCATGTCATCCATTG 59.427 47.826 0.00 0.00 0.00 2.82
78 79 4.401925 AGTATGCAACTTCAGGAGCTTTT 58.598 39.130 0.00 0.00 33.35 2.27
84 85 5.301551 TGCAACTTCAGGAGCTTTTGATTAA 59.698 36.000 2.42 0.00 0.00 1.40
191 193 0.546122 GGATACCCACCAGATGCACA 59.454 55.000 0.00 0.00 0.00 4.57
234 236 4.092279 TGGAATCATGTTGTATGCCCAAA 58.908 39.130 0.00 0.00 0.00 3.28
244 246 7.954788 TGTTGTATGCCCAAAGAAAAATTAC 57.045 32.000 0.00 0.00 0.00 1.89
282 284 8.742554 TGATACTACATGACATGCTAAATACG 57.257 34.615 15.49 0.00 0.00 3.06
395 423 0.829990 CTGGTTTGCCCTGGTGTTTT 59.170 50.000 0.00 0.00 0.00 2.43
443 471 5.435686 TGTGATGTTACTAGAGGCCAAAT 57.564 39.130 5.01 0.00 0.00 2.32
479 507 2.945008 TCATGCTTTAAGGAATGCCTCG 59.055 45.455 0.00 0.00 46.28 4.63
480 508 2.489938 TGCTTTAAGGAATGCCTCGT 57.510 45.000 0.00 0.00 46.28 4.18
481 509 2.790433 TGCTTTAAGGAATGCCTCGTT 58.210 42.857 0.00 0.00 46.28 3.85
482 510 2.487762 TGCTTTAAGGAATGCCTCGTTG 59.512 45.455 0.00 0.00 46.28 4.10
483 511 2.732282 GCTTTAAGGAATGCCTCGTTGC 60.732 50.000 0.00 0.00 46.28 4.17
484 512 2.489938 TTAAGGAATGCCTCGTTGCT 57.510 45.000 0.00 0.00 46.28 3.91
485 513 1.737838 TAAGGAATGCCTCGTTGCTG 58.262 50.000 0.00 0.00 46.28 4.41
486 514 0.962356 AAGGAATGCCTCGTTGCTGG 60.962 55.000 0.00 0.00 46.28 4.85
487 515 1.377202 GGAATGCCTCGTTGCTGGA 60.377 57.895 1.05 0.00 0.00 3.86
488 516 0.749454 GGAATGCCTCGTTGCTGGAT 60.749 55.000 1.05 0.00 0.00 3.41
489 517 0.379669 GAATGCCTCGTTGCTGGATG 59.620 55.000 1.05 0.00 0.00 3.51
677 2650 8.494016 AGACCGAAATACAATCCTAAGAAAAG 57.506 34.615 0.00 0.00 0.00 2.27
1003 2985 1.153509 GTCATTGCCTTGGCCATGC 60.154 57.895 18.36 18.36 0.00 4.06
1006 3017 2.420568 ATTGCCTTGGCCATGCGAG 61.421 57.895 19.30 9.16 0.00 5.03
1010 3021 1.876497 GCCTTGGCCATGCGAGAAAA 61.876 55.000 6.09 0.00 0.00 2.29
1012 3023 1.403249 CCTTGGCCATGCGAGAAAAAG 60.403 52.381 6.09 0.00 0.00 2.27
1017 3028 1.812571 GCCATGCGAGAAAAAGGAGAA 59.187 47.619 0.00 0.00 0.00 2.87
1179 3207 3.788766 CGCGCCGTTTGGAGGAAG 61.789 66.667 0.00 0.00 37.49 3.46
1360 3392 4.145876 TGTGTGCTTGAATCTTTTAGCG 57.854 40.909 0.00 0.00 36.43 4.26
1401 3433 9.211485 GTTCATCATTTTCTGGTCAAATTGATT 57.789 29.630 0.00 0.00 35.57 2.57
1402 3434 8.766000 TCATCATTTTCTGGTCAAATTGATTG 57.234 30.769 0.00 0.00 35.57 2.67
1403 3435 8.586744 TCATCATTTTCTGGTCAAATTGATTGA 58.413 29.630 0.00 0.00 45.71 2.57
1427 3459 6.531503 TCAACTGGTCCTCTGTATAAGAAG 57.468 41.667 0.00 0.00 33.37 2.85
1527 3606 2.921754 CTGTTACGTAGCTGTTAGCCAC 59.078 50.000 10.88 0.00 43.77 5.01
1568 3648 9.918630 ATGCATAATAAAAGCATTCATTCCTAC 57.081 29.630 0.00 0.00 45.98 3.18
1569 3649 9.135189 TGCATAATAAAAGCATTCATTCCTACT 57.865 29.630 0.00 0.00 32.55 2.57
1570 3650 9.617975 GCATAATAAAAGCATTCATTCCTACTC 57.382 33.333 0.00 0.00 0.00 2.59
1575 3655 6.765915 AAAGCATTCATTCCTACTCTTTCC 57.234 37.500 0.00 0.00 0.00 3.13
1576 3656 4.446371 AGCATTCATTCCTACTCTTTCCG 58.554 43.478 0.00 0.00 0.00 4.30
1577 3657 4.080863 AGCATTCATTCCTACTCTTTCCGT 60.081 41.667 0.00 0.00 0.00 4.69
1578 3658 4.636206 GCATTCATTCCTACTCTTTCCGTT 59.364 41.667 0.00 0.00 0.00 4.44
1579 3659 5.447818 GCATTCATTCCTACTCTTTCCGTTG 60.448 44.000 0.00 0.00 0.00 4.10
1580 3660 3.596214 TCATTCCTACTCTTTCCGTTGC 58.404 45.455 0.00 0.00 0.00 4.17
1581 3661 3.007506 TCATTCCTACTCTTTCCGTTGCA 59.992 43.478 0.00 0.00 0.00 4.08
1582 3662 3.478857 TTCCTACTCTTTCCGTTGCAA 57.521 42.857 0.00 0.00 0.00 4.08
1583 3663 3.478857 TCCTACTCTTTCCGTTGCAAA 57.521 42.857 0.00 0.00 0.00 3.68
1584 3664 4.015872 TCCTACTCTTTCCGTTGCAAAT 57.984 40.909 0.00 0.00 0.00 2.32
1585 3665 4.394729 TCCTACTCTTTCCGTTGCAAATT 58.605 39.130 0.00 0.00 0.00 1.82
1586 3666 5.553123 TCCTACTCTTTCCGTTGCAAATTA 58.447 37.500 0.00 0.00 0.00 1.40
1587 3667 5.410439 TCCTACTCTTTCCGTTGCAAATTAC 59.590 40.000 0.00 0.00 0.00 1.89
1588 3668 5.411669 CCTACTCTTTCCGTTGCAAATTACT 59.588 40.000 0.00 0.00 0.00 2.24
1589 3669 5.358298 ACTCTTTCCGTTGCAAATTACTC 57.642 39.130 0.00 0.00 0.00 2.59
1590 3670 4.084013 ACTCTTTCCGTTGCAAATTACTCG 60.084 41.667 0.00 0.00 0.00 4.18
1591 3671 3.810941 TCTTTCCGTTGCAAATTACTCGT 59.189 39.130 0.00 0.00 0.00 4.18
1592 3672 3.799137 TTCCGTTGCAAATTACTCGTC 57.201 42.857 0.00 0.00 0.00 4.20
1593 3673 1.722464 TCCGTTGCAAATTACTCGTCG 59.278 47.619 0.00 0.00 0.00 5.12
1594 3674 1.510007 CGTTGCAAATTACTCGTCGC 58.490 50.000 0.00 0.00 0.00 5.19
1595 3675 1.136474 CGTTGCAAATTACTCGTCGCA 60.136 47.619 0.00 0.00 0.00 5.10
1596 3676 2.660631 CGTTGCAAATTACTCGTCGCAA 60.661 45.455 0.00 0.00 37.05 4.85
1597 3677 3.293262 GTTGCAAATTACTCGTCGCAAA 58.707 40.909 0.00 0.00 40.67 3.68
1598 3678 3.610786 TGCAAATTACTCGTCGCAAAA 57.389 38.095 0.00 0.00 0.00 2.44
1599 3679 3.953766 TGCAAATTACTCGTCGCAAAAA 58.046 36.364 0.00 0.00 0.00 1.94
1600 3680 4.541779 TGCAAATTACTCGTCGCAAAAAT 58.458 34.783 0.00 0.00 0.00 1.82
1601 3681 4.979197 TGCAAATTACTCGTCGCAAAAATT 59.021 33.333 0.00 0.00 0.00 1.82
1602 3682 5.108065 TGCAAATTACTCGTCGCAAAAATTG 60.108 36.000 0.00 0.00 0.00 2.32
1603 3683 5.116377 GCAAATTACTCGTCGCAAAAATTGA 59.884 36.000 0.00 0.00 0.00 2.57
1604 3684 6.183359 GCAAATTACTCGTCGCAAAAATTGAT 60.183 34.615 0.00 0.00 0.00 2.57
1605 3685 6.853279 AATTACTCGTCGCAAAAATTGATG 57.147 33.333 0.00 0.00 0.00 3.07
1606 3686 3.896648 ACTCGTCGCAAAAATTGATGT 57.103 38.095 0.00 0.00 0.00 3.06
1607 3687 6.469139 TTACTCGTCGCAAAAATTGATGTA 57.531 33.333 0.00 0.00 0.00 2.29
1608 3688 5.545658 ACTCGTCGCAAAAATTGATGTAT 57.454 34.783 0.00 0.00 0.00 2.29
1609 3689 5.560148 ACTCGTCGCAAAAATTGATGTATC 58.440 37.500 0.00 0.00 0.00 2.24
1610 3690 5.351465 ACTCGTCGCAAAAATTGATGTATCT 59.649 36.000 0.00 0.00 0.00 1.98
1611 3691 6.533723 ACTCGTCGCAAAAATTGATGTATCTA 59.466 34.615 0.00 0.00 0.00 1.98
1612 3692 6.933130 TCGTCGCAAAAATTGATGTATCTAG 58.067 36.000 0.00 0.00 0.00 2.43
1613 3693 6.754675 TCGTCGCAAAAATTGATGTATCTAGA 59.245 34.615 0.00 0.00 0.00 2.43
1614 3694 7.276878 TCGTCGCAAAAATTGATGTATCTAGAA 59.723 33.333 0.00 0.00 0.00 2.10
1615 3695 7.370836 CGTCGCAAAAATTGATGTATCTAGAAC 59.629 37.037 0.00 0.00 0.00 3.01
1616 3696 8.391106 GTCGCAAAAATTGATGTATCTAGAACT 58.609 33.333 0.00 0.00 0.00 3.01
1617 3697 9.594478 TCGCAAAAATTGATGTATCTAGAACTA 57.406 29.630 0.00 0.00 0.00 2.24
1658 3738 9.599866 ACAATCATATCTTCGACAAGTAATTCA 57.400 29.630 0.00 0.00 0.00 2.57
1662 3742 9.302345 TCATATCTTCGACAAGTAATTCAGAAC 57.698 33.333 0.00 0.00 0.00 3.01
1663 3743 6.633668 ATCTTCGACAAGTAATTCAGAACG 57.366 37.500 0.00 0.00 0.00 3.95
1664 3744 4.921515 TCTTCGACAAGTAATTCAGAACGG 59.078 41.667 0.00 0.00 0.00 4.44
1665 3745 4.508461 TCGACAAGTAATTCAGAACGGA 57.492 40.909 0.00 0.00 0.00 4.69
1666 3746 4.482386 TCGACAAGTAATTCAGAACGGAG 58.518 43.478 0.00 0.00 0.00 4.63
1667 3747 3.060895 CGACAAGTAATTCAGAACGGAGC 59.939 47.826 0.00 0.00 0.00 4.70
1668 3748 2.993899 ACAAGTAATTCAGAACGGAGCG 59.006 45.455 0.00 0.00 0.00 5.03
1669 3749 3.250744 CAAGTAATTCAGAACGGAGCGA 58.749 45.455 0.00 0.00 0.00 4.93
1670 3750 3.152261 AGTAATTCAGAACGGAGCGAG 57.848 47.619 0.00 0.00 0.00 5.03
1697 3777 2.083167 TCCAATTGACGGACGGTAAC 57.917 50.000 7.12 0.00 0.00 2.50
1978 4058 1.467734 CCACAGCTGCTGATTCTTGTC 59.532 52.381 34.28 0.00 35.18 3.18
1979 4059 1.467734 CACAGCTGCTGATTCTTGTCC 59.532 52.381 34.28 0.00 35.18 4.02
1980 4060 1.350351 ACAGCTGCTGATTCTTGTCCT 59.650 47.619 34.28 6.45 35.18 3.85
1981 4061 2.224719 ACAGCTGCTGATTCTTGTCCTT 60.225 45.455 34.28 5.91 35.18 3.36
1982 4062 2.818432 CAGCTGCTGATTCTTGTCCTTT 59.182 45.455 24.88 0.00 32.44 3.11
1983 4063 3.255149 CAGCTGCTGATTCTTGTCCTTTT 59.745 43.478 24.88 0.00 32.44 2.27
1984 4064 3.893813 AGCTGCTGATTCTTGTCCTTTTT 59.106 39.130 0.00 0.00 0.00 1.94
2005 4085 4.405116 TTTTTGCCAAAGTGCTGATTCT 57.595 36.364 0.00 0.00 0.00 2.40
2006 4086 4.405116 TTTTGCCAAAGTGCTGATTCTT 57.595 36.364 0.00 0.00 0.00 2.52
2007 4087 3.374220 TTGCCAAAGTGCTGATTCTTG 57.626 42.857 0.00 0.00 0.00 3.02
2008 4088 2.309613 TGCCAAAGTGCTGATTCTTGT 58.690 42.857 0.00 0.00 0.00 3.16
2322 4439 2.847234 TTCGACCACCACTGCCCT 60.847 61.111 0.00 0.00 0.00 5.19
2358 4475 0.977627 TCGGCCTGGTCAGTCATCAT 60.978 55.000 0.00 0.00 0.00 2.45
2448 5216 6.648725 GCTGATATAGATTCTGGTGTCCTTTC 59.351 42.308 0.00 0.00 0.00 2.62
2527 5295 0.037975 TTTACGTCTTCGCCCTGTCC 60.038 55.000 0.00 0.00 41.18 4.02
3093 5861 2.197324 CGGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
3094 5862 2.387772 CGGAGGAGGAGGAGGAGGA 61.388 68.421 0.00 0.00 0.00 3.71
3095 5863 1.541672 GGAGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
3096 5864 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
3100 5868 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
3133 5901 2.143925 GCAACTGTACAGGACCAAGAC 58.856 52.381 26.12 3.86 0.00 3.01
3215 5983 2.232756 TTCTTTTCCCTTTTTGGCGC 57.767 45.000 0.00 0.00 0.00 6.53
3329 6097 5.351189 GGGTCCGTAATTTCGCTTAGTTTAA 59.649 40.000 0.00 0.00 0.00 1.52
3357 6125 6.507900 TCTCTACTTCATTTGGAGAATAGCG 58.492 40.000 0.00 0.00 31.28 4.26
3362 6130 4.437682 TCATTTGGAGAATAGCGGGAAT 57.562 40.909 0.00 0.00 0.00 3.01
3363 6131 4.389374 TCATTTGGAGAATAGCGGGAATC 58.611 43.478 0.00 0.00 0.00 2.52
3395 6163 0.882474 AGAGCAACTCTAACGCGTCT 59.118 50.000 14.44 1.39 39.28 4.18
3412 6180 2.872245 CGTCTATTCAAATGGATGGCGT 59.128 45.455 1.50 0.00 31.51 5.68
3445 6214 2.193536 GTTTGCTTGGGTCAGCCGT 61.194 57.895 0.00 0.00 39.25 5.68
3446 6215 1.454847 TTTGCTTGGGTCAGCCGTT 60.455 52.632 0.00 0.00 39.25 4.44
3515 6286 1.406539 GCCTGCGATCCATTTCATGTT 59.593 47.619 0.00 0.00 0.00 2.71
3528 6299 5.331756 CCATTTCATGTTCGCGCATAAATTC 60.332 40.000 8.75 0.00 0.00 2.17
3534 6306 4.219802 TGTTCGCGCATAAATTCGAAAAA 58.780 34.783 8.75 0.00 41.65 1.94
3550 6322 2.243602 AAAAACCCGCAGTCGTAGAA 57.756 45.000 0.00 0.00 39.69 2.10
3556 6329 0.458543 CCGCAGTCGTAGAACATGCT 60.459 55.000 0.00 0.00 39.69 3.79
3654 6435 4.862641 AAACCATATAGTTCCTGCTGGT 57.137 40.909 9.73 0.00 38.60 4.00
3661 6442 0.536006 AGTTCCTGCTGGTGCACTTC 60.536 55.000 17.98 6.69 45.31 3.01
3699 6483 2.132996 CAGCACACAAAAGGGGGCA 61.133 57.895 0.00 0.00 0.00 5.36
3723 6507 1.369091 ATTCAACCACGCCATCTCGC 61.369 55.000 0.00 0.00 0.00 5.03
3793 6582 1.268589 CGTCGCCATAGATCACTCGTT 60.269 52.381 0.00 0.00 0.00 3.85
3800 6589 4.611943 CCATAGATCACTCGTTGTCGAAT 58.388 43.478 0.00 0.00 45.61 3.34
3821 6610 1.227645 GAGCATGTCGGCCTGCATA 60.228 57.895 19.43 0.00 38.47 3.14
3902 6691 1.447217 CCCCGTCATCATGCTAGCA 59.553 57.895 21.85 21.85 0.00 3.49
3992 6781 1.133853 GCCTCCATCTCAAGCATCCTT 60.134 52.381 0.00 0.00 0.00 3.36
4007 6796 1.014044 TCCTTGCTTGCTTCTACGCG 61.014 55.000 3.53 3.53 0.00 6.01
4021 6810 2.607668 TACGCGTCCATCTCAAGCCG 62.608 60.000 18.63 0.00 0.00 5.52
4050 6839 2.093500 TGGATCTCCATGAAGGTGTTCG 60.093 50.000 0.00 0.00 42.01 3.95
4060 6850 5.221048 CCATGAAGGTGTTCGTTTTCTCTTT 60.221 40.000 0.00 0.00 35.17 2.52
4082 6872 3.695606 TCTTGCCGGCGCTTCTCT 61.696 61.111 23.90 0.00 35.36 3.10
4139 6929 3.326210 GCGAGCAAGGCGATCGAG 61.326 66.667 21.57 6.11 38.72 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 9.334947 CATCTTTACCATTTGTATCTGAGATGT 57.665 33.333 4.96 0.00 33.66 3.06
244 246 9.599322 GTCATGTAGTATCAACAACAAGAAAAG 57.401 33.333 0.00 0.00 0.00 2.27
256 258 9.191995 CGTATTTAGCATGTCATGTAGTATCAA 57.808 33.333 14.26 0.00 0.00 2.57
282 284 8.321650 AGTTCTTCATGTTCAAGAGATTTCTC 57.678 34.615 0.00 0.00 43.17 2.87
395 423 7.894753 TTGTATCCAAATCAGCATTCCATTA 57.105 32.000 0.00 0.00 0.00 1.90
418 446 5.435686 TGGCCTCTAGTAACATCACAATT 57.564 39.130 3.32 0.00 0.00 2.32
443 471 3.315596 AGCATGAGATCTCCATTCTCCA 58.684 45.455 20.03 0.00 39.10 3.86
479 507 4.236935 CAAATACACCAACATCCAGCAAC 58.763 43.478 0.00 0.00 0.00 4.17
480 508 3.257873 CCAAATACACCAACATCCAGCAA 59.742 43.478 0.00 0.00 0.00 3.91
481 509 2.824936 CCAAATACACCAACATCCAGCA 59.175 45.455 0.00 0.00 0.00 4.41
482 510 3.088532 TCCAAATACACCAACATCCAGC 58.911 45.455 0.00 0.00 0.00 4.85
483 511 5.010516 TGTTTCCAAATACACCAACATCCAG 59.989 40.000 0.00 0.00 0.00 3.86
484 512 4.895889 TGTTTCCAAATACACCAACATCCA 59.104 37.500 0.00 0.00 0.00 3.41
485 513 5.461032 TGTTTCCAAATACACCAACATCC 57.539 39.130 0.00 0.00 0.00 3.51
486 514 8.050778 TCTATGTTTCCAAATACACCAACATC 57.949 34.615 0.00 0.00 36.50 3.06
487 515 8.415950 TTCTATGTTTCCAAATACACCAACAT 57.584 30.769 0.00 0.00 38.21 2.71
488 516 7.825331 TTCTATGTTTCCAAATACACCAACA 57.175 32.000 0.00 0.00 0.00 3.33
575 2548 8.755018 GGGCATCATTTATTTGAAGTAATTTCG 58.245 33.333 0.00 0.00 38.71 3.46
863 2837 1.738099 CTCAACGACCTTCCTGCCG 60.738 63.158 0.00 0.00 0.00 5.69
1003 2985 6.480320 TCTTCAGTTTCTTCTCCTTTTTCTCG 59.520 38.462 0.00 0.00 0.00 4.04
1006 3017 6.434596 GCTCTTCAGTTTCTTCTCCTTTTTC 58.565 40.000 0.00 0.00 0.00 2.29
1010 3021 3.556004 CCGCTCTTCAGTTTCTTCTCCTT 60.556 47.826 0.00 0.00 0.00 3.36
1012 3023 2.342179 CCGCTCTTCAGTTTCTTCTCC 58.658 52.381 0.00 0.00 0.00 3.71
1017 3028 0.321122 CTGGCCGCTCTTCAGTTTCT 60.321 55.000 0.00 0.00 0.00 2.52
1043 3054 2.887568 GCCTGCCGATCAGACGTG 60.888 66.667 0.00 0.00 45.72 4.49
1179 3207 1.093159 CCATCCTGCTTGACTGCTTC 58.907 55.000 0.00 0.00 0.00 3.86
1360 3392 7.475771 AATGATGAACGCTAGATCTTCTTTC 57.524 36.000 0.00 3.96 0.00 2.62
1367 3399 5.525378 ACCAGAAAATGATGAACGCTAGATC 59.475 40.000 0.00 0.00 0.00 2.75
1374 3406 6.862608 TCAATTTGACCAGAAAATGATGAACG 59.137 34.615 0.00 0.00 0.00 3.95
1401 3433 6.194967 TCTTATACAGAGGACCAGTTGATCA 58.805 40.000 0.00 0.00 0.00 2.92
1402 3434 6.716934 TCTTATACAGAGGACCAGTTGATC 57.283 41.667 0.00 0.00 0.00 2.92
1403 3435 6.098982 CCTTCTTATACAGAGGACCAGTTGAT 59.901 42.308 0.00 0.00 29.63 2.57
1409 3441 6.697641 AAAACCTTCTTATACAGAGGACCA 57.302 37.500 0.00 0.00 29.63 4.02
1561 3641 3.695830 TGCAACGGAAAGAGTAGGAAT 57.304 42.857 0.00 0.00 0.00 3.01
1562 3642 3.478857 TTGCAACGGAAAGAGTAGGAA 57.521 42.857 0.00 0.00 0.00 3.36
1564 3644 4.766404 AATTTGCAACGGAAAGAGTAGG 57.234 40.909 0.00 0.00 0.00 3.18
1566 3646 5.119588 CGAGTAATTTGCAACGGAAAGAGTA 59.880 40.000 0.00 0.00 0.00 2.59
1568 3648 4.084013 ACGAGTAATTTGCAACGGAAAGAG 60.084 41.667 0.00 0.00 0.00 2.85
1569 3649 3.810941 ACGAGTAATTTGCAACGGAAAGA 59.189 39.130 0.00 0.00 0.00 2.52
1570 3650 4.141855 ACGAGTAATTTGCAACGGAAAG 57.858 40.909 0.00 0.00 0.00 2.62
1571 3651 3.363182 CGACGAGTAATTTGCAACGGAAA 60.363 43.478 0.00 0.00 0.00 3.13
1572 3652 2.156117 CGACGAGTAATTTGCAACGGAA 59.844 45.455 0.00 0.00 0.00 4.30
1573 3653 1.722464 CGACGAGTAATTTGCAACGGA 59.278 47.619 0.00 0.00 0.00 4.69
1574 3654 1.785518 GCGACGAGTAATTTGCAACGG 60.786 52.381 0.00 0.00 0.00 4.44
1575 3655 1.136474 TGCGACGAGTAATTTGCAACG 60.136 47.619 0.00 0.11 0.00 4.10
1576 3656 2.587612 TGCGACGAGTAATTTGCAAC 57.412 45.000 0.00 0.00 0.00 4.17
1577 3657 3.610786 TTTGCGACGAGTAATTTGCAA 57.389 38.095 0.00 0.00 40.22 4.08
1578 3658 3.610786 TTTTGCGACGAGTAATTTGCA 57.389 38.095 0.00 0.00 0.00 4.08
1579 3659 5.116377 TCAATTTTTGCGACGAGTAATTTGC 59.884 36.000 0.00 0.00 0.00 3.68
1580 3660 6.667981 TCAATTTTTGCGACGAGTAATTTG 57.332 33.333 0.00 2.44 0.00 2.32
1581 3661 6.861055 ACATCAATTTTTGCGACGAGTAATTT 59.139 30.769 0.00 0.00 0.00 1.82
1582 3662 6.378582 ACATCAATTTTTGCGACGAGTAATT 58.621 32.000 0.00 0.00 0.00 1.40
1583 3663 5.938322 ACATCAATTTTTGCGACGAGTAAT 58.062 33.333 0.00 0.00 0.00 1.89
1584 3664 5.351233 ACATCAATTTTTGCGACGAGTAA 57.649 34.783 0.00 0.00 0.00 2.24
1585 3665 6.533723 AGATACATCAATTTTTGCGACGAGTA 59.466 34.615 0.00 0.00 0.00 2.59
1586 3666 3.896648 ACATCAATTTTTGCGACGAGT 57.103 38.095 0.00 0.00 0.00 4.18
1587 3667 5.799960 AGATACATCAATTTTTGCGACGAG 58.200 37.500 0.00 0.00 0.00 4.18
1588 3668 5.794687 AGATACATCAATTTTTGCGACGA 57.205 34.783 0.00 0.00 0.00 4.20
1589 3669 6.933130 TCTAGATACATCAATTTTTGCGACG 58.067 36.000 0.00 0.00 0.00 5.12
1590 3670 8.391106 AGTTCTAGATACATCAATTTTTGCGAC 58.609 33.333 0.00 0.00 0.00 5.19
1591 3671 8.492673 AGTTCTAGATACATCAATTTTTGCGA 57.507 30.769 0.00 0.00 0.00 5.10
1632 3712 9.599866 TGAATTACTTGTCGAAGATATGATTGT 57.400 29.630 0.00 0.00 40.67 2.71
1636 3716 9.302345 GTTCTGAATTACTTGTCGAAGATATGA 57.698 33.333 0.00 0.00 40.67 2.15
1637 3717 8.262588 CGTTCTGAATTACTTGTCGAAGATATG 58.737 37.037 0.00 0.00 40.67 1.78
1638 3718 7.435488 CCGTTCTGAATTACTTGTCGAAGATAT 59.565 37.037 0.00 0.00 40.67 1.63
1639 3719 6.750501 CCGTTCTGAATTACTTGTCGAAGATA 59.249 38.462 0.00 0.00 40.67 1.98
1640 3720 5.577164 CCGTTCTGAATTACTTGTCGAAGAT 59.423 40.000 0.00 0.00 40.67 2.40
1641 3721 4.921515 CCGTTCTGAATTACTTGTCGAAGA 59.078 41.667 0.00 0.00 32.98 2.87
1642 3722 4.921515 TCCGTTCTGAATTACTTGTCGAAG 59.078 41.667 0.00 0.00 35.07 3.79
1643 3723 4.873817 TCCGTTCTGAATTACTTGTCGAA 58.126 39.130 0.00 0.00 0.00 3.71
1644 3724 4.482386 CTCCGTTCTGAATTACTTGTCGA 58.518 43.478 0.00 0.00 0.00 4.20
1645 3725 3.060895 GCTCCGTTCTGAATTACTTGTCG 59.939 47.826 0.00 0.00 0.00 4.35
1646 3726 3.060895 CGCTCCGTTCTGAATTACTTGTC 59.939 47.826 0.00 0.00 0.00 3.18
1647 3727 2.993899 CGCTCCGTTCTGAATTACTTGT 59.006 45.455 0.00 0.00 0.00 3.16
1648 3728 3.250744 TCGCTCCGTTCTGAATTACTTG 58.749 45.455 0.00 0.00 0.00 3.16
1649 3729 3.056749 ACTCGCTCCGTTCTGAATTACTT 60.057 43.478 0.00 0.00 0.00 2.24
1650 3730 2.492484 ACTCGCTCCGTTCTGAATTACT 59.508 45.455 0.00 0.00 0.00 2.24
1651 3731 2.877335 ACTCGCTCCGTTCTGAATTAC 58.123 47.619 0.00 0.00 0.00 1.89
1652 3732 3.693085 AGTACTCGCTCCGTTCTGAATTA 59.307 43.478 0.00 0.00 0.00 1.40
1653 3733 2.492484 AGTACTCGCTCCGTTCTGAATT 59.508 45.455 0.00 0.00 0.00 2.17
1654 3734 2.093106 AGTACTCGCTCCGTTCTGAAT 58.907 47.619 0.00 0.00 0.00 2.57
1655 3735 1.531423 AGTACTCGCTCCGTTCTGAA 58.469 50.000 0.00 0.00 0.00 3.02
1656 3736 2.277969 CTAGTACTCGCTCCGTTCTGA 58.722 52.381 0.00 0.00 0.00 3.27
1657 3737 2.008329 ACTAGTACTCGCTCCGTTCTG 58.992 52.381 0.00 0.00 0.00 3.02
1658 3738 2.399916 ACTAGTACTCGCTCCGTTCT 57.600 50.000 0.00 0.00 0.00 3.01
1659 3739 2.223226 GGAACTAGTACTCGCTCCGTTC 60.223 54.545 0.00 4.40 32.79 3.95
1660 3740 1.742268 GGAACTAGTACTCGCTCCGTT 59.258 52.381 0.00 0.00 0.00 4.44
1661 3741 1.339438 TGGAACTAGTACTCGCTCCGT 60.339 52.381 11.12 0.00 0.00 4.69
1662 3742 1.376543 TGGAACTAGTACTCGCTCCG 58.623 55.000 11.12 0.00 0.00 4.63
1663 3743 4.113354 CAATTGGAACTAGTACTCGCTCC 58.887 47.826 9.38 9.38 0.00 4.70
1664 3744 4.799428 GTCAATTGGAACTAGTACTCGCTC 59.201 45.833 5.42 0.00 0.00 5.03
1665 3745 4.674623 CGTCAATTGGAACTAGTACTCGCT 60.675 45.833 5.42 0.00 0.00 4.93
1666 3746 3.546670 CGTCAATTGGAACTAGTACTCGC 59.453 47.826 5.42 0.00 0.00 5.03
1667 3747 4.103357 CCGTCAATTGGAACTAGTACTCG 58.897 47.826 5.42 0.00 0.00 4.18
1668 3748 5.100943 GTCCGTCAATTGGAACTAGTACTC 58.899 45.833 5.42 0.00 37.23 2.59
1669 3749 4.380233 CGTCCGTCAATTGGAACTAGTACT 60.380 45.833 5.42 0.00 37.23 2.73
1670 3750 3.855950 CGTCCGTCAATTGGAACTAGTAC 59.144 47.826 5.42 0.00 37.23 2.73
1697 3777 5.009210 TGAAATCGTTTTGGTGGGAGTAAAG 59.991 40.000 0.00 0.00 0.00 1.85
1984 4064 4.405116 AGAATCAGCACTTTGGCAAAAA 57.595 36.364 14.43 0.00 35.83 1.94
1985 4065 4.121317 CAAGAATCAGCACTTTGGCAAAA 58.879 39.130 14.43 0.00 35.83 2.44
1986 4066 3.132646 ACAAGAATCAGCACTTTGGCAAA 59.867 39.130 12.79 12.79 35.83 3.68
1987 4067 2.694628 ACAAGAATCAGCACTTTGGCAA 59.305 40.909 0.00 0.00 35.83 4.52
1988 4068 2.294233 GACAAGAATCAGCACTTTGGCA 59.706 45.455 0.00 0.00 35.83 4.92
1989 4069 2.352127 GGACAAGAATCAGCACTTTGGC 60.352 50.000 0.00 0.00 0.00 4.52
1990 4070 3.057736 CAGGACAAGAATCAGCACTTTGG 60.058 47.826 0.00 0.00 0.00 3.28
1991 4071 3.611057 GCAGGACAAGAATCAGCACTTTG 60.611 47.826 0.00 0.00 0.00 2.77
1992 4072 2.555757 GCAGGACAAGAATCAGCACTTT 59.444 45.455 0.00 0.00 0.00 2.66
1993 4073 2.157738 GCAGGACAAGAATCAGCACTT 58.842 47.619 0.00 0.00 0.00 3.16
1994 4074 1.350351 AGCAGGACAAGAATCAGCACT 59.650 47.619 0.00 0.00 0.00 4.40
1995 4075 1.467734 CAGCAGGACAAGAATCAGCAC 59.532 52.381 0.00 0.00 0.00 4.40
1996 4076 1.072806 ACAGCAGGACAAGAATCAGCA 59.927 47.619 0.00 0.00 0.00 4.41
1997 4077 1.818642 ACAGCAGGACAAGAATCAGC 58.181 50.000 0.00 0.00 0.00 4.26
1998 4078 5.413833 ACATTTACAGCAGGACAAGAATCAG 59.586 40.000 0.00 0.00 0.00 2.90
1999 4079 5.316167 ACATTTACAGCAGGACAAGAATCA 58.684 37.500 0.00 0.00 0.00 2.57
2000 4080 5.886960 ACATTTACAGCAGGACAAGAATC 57.113 39.130 0.00 0.00 0.00 2.52
2001 4081 6.655078 AAACATTTACAGCAGGACAAGAAT 57.345 33.333 0.00 0.00 0.00 2.40
2002 4082 6.096141 TGAAAACATTTACAGCAGGACAAGAA 59.904 34.615 0.00 0.00 0.00 2.52
2003 4083 5.592282 TGAAAACATTTACAGCAGGACAAGA 59.408 36.000 0.00 0.00 0.00 3.02
2004 4084 5.830912 TGAAAACATTTACAGCAGGACAAG 58.169 37.500 0.00 0.00 0.00 3.16
2005 4085 5.221224 CCTGAAAACATTTACAGCAGGACAA 60.221 40.000 0.00 0.00 43.03 3.18
2006 4086 4.278170 CCTGAAAACATTTACAGCAGGACA 59.722 41.667 0.00 0.00 43.03 4.02
2007 4087 4.518970 TCCTGAAAACATTTACAGCAGGAC 59.481 41.667 0.00 0.00 43.81 3.85
2008 4088 4.724399 TCCTGAAAACATTTACAGCAGGA 58.276 39.130 0.00 0.00 45.75 3.86
2322 4439 3.918253 GATGCACTGGCCGACCCAA 62.918 63.158 0.00 0.00 44.81 4.12
2358 4475 7.839680 TGCAGTTACTCCTATATGAATGAGA 57.160 36.000 0.00 0.00 0.00 3.27
2448 5216 2.879462 GGTAGTTCCGCTGCGACG 60.879 66.667 25.45 7.89 0.00 5.12
2761 5529 1.945394 GTACAGAAGACCTCGGCGATA 59.055 52.381 11.27 0.00 0.00 2.92
3093 5861 2.433146 GGGCTACGTTCCCCTCCTC 61.433 68.421 14.18 0.00 38.30 3.71
3094 5862 2.365237 GGGCTACGTTCCCCTCCT 60.365 66.667 14.18 0.00 38.30 3.69
3100 5868 3.122971 GTTGCGGGGCTACGTTCC 61.123 66.667 0.00 0.00 35.98 3.62
3133 5901 0.315251 TCACAAGTGTCCTCTCAGCG 59.685 55.000 0.00 0.00 0.00 5.18
3254 6022 8.430063 CACGTATAAAATTTACAGTTCAGTCGT 58.570 33.333 0.00 0.00 0.00 4.34
3336 6104 4.752101 CCCGCTATTCTCCAAATGAAGTAG 59.248 45.833 0.00 0.00 0.00 2.57
3357 6125 2.975489 TCTTAGAGATGCCCTGATTCCC 59.025 50.000 0.00 0.00 0.00 3.97
3362 6130 2.165357 TGCTCTTAGAGATGCCCTGA 57.835 50.000 14.14 0.00 0.00 3.86
3363 6131 2.170187 AGTTGCTCTTAGAGATGCCCTG 59.830 50.000 14.14 0.00 0.00 4.45
3395 6163 5.788450 ACAAAAACGCCATCCATTTGAATA 58.212 33.333 3.81 0.00 35.52 1.75
3432 6201 2.644992 GCAAACGGCTGACCCAAG 59.355 61.111 0.00 0.00 40.25 3.61
3534 6306 0.606604 ATGTTCTACGACTGCGGGTT 59.393 50.000 0.00 0.00 43.17 4.11
3535 6307 0.108804 CATGTTCTACGACTGCGGGT 60.109 55.000 0.00 0.00 43.17 5.28
3541 6313 1.065701 CCGCTAGCATGTTCTACGACT 59.934 52.381 16.45 0.00 0.00 4.18
3543 6315 0.248907 GCCGCTAGCATGTTCTACGA 60.249 55.000 16.45 0.00 42.97 3.43
3550 6322 2.903855 GCATGGCCGCTAGCATGT 60.904 61.111 16.45 0.00 46.50 3.21
3575 6349 2.284754 TGGTGCCAGCATGAACTTTA 57.715 45.000 0.00 0.00 39.69 1.85
3631 6407 6.299141 CACCAGCAGGAACTATATGGTTTAT 58.701 40.000 5.87 0.00 42.55 1.40
3632 6408 5.680619 CACCAGCAGGAACTATATGGTTTA 58.319 41.667 5.87 0.00 42.55 2.01
3634 6411 3.685550 GCACCAGCAGGAACTATATGGTT 60.686 47.826 3.84 3.84 42.55 3.67
3675 6459 2.546373 CCCCTTTTGTGTGCTGACATTG 60.546 50.000 0.00 0.00 33.63 2.82
3676 6460 1.688197 CCCCTTTTGTGTGCTGACATT 59.312 47.619 0.00 0.00 33.63 2.71
3699 6483 3.157087 AGATGGCGTGGTTGAATTTCTT 58.843 40.909 0.00 0.00 0.00 2.52
3723 6507 4.720902 TGCTGGCATGACCACGGG 62.721 66.667 0.00 0.00 46.36 5.28
3793 6582 1.731709 CCGACATGCTCAAATTCGACA 59.268 47.619 0.00 0.00 0.00 4.35
3800 6589 2.334946 GCAGGCCGACATGCTCAAA 61.335 57.895 0.00 0.00 39.38 2.69
3821 6610 1.218316 GAGGCCGTGGTTCGAGAAT 59.782 57.895 0.00 0.00 42.86 2.40
3902 6691 0.398318 AGGCGAAAGAAGTGGCTCTT 59.602 50.000 0.67 0.67 37.24 2.85
3992 6781 1.736645 GGACGCGTAGAAGCAAGCA 60.737 57.895 13.97 0.00 36.85 3.91
4003 6792 2.125512 GGCTTGAGATGGACGCGT 60.126 61.111 13.85 13.85 0.00 6.01
4007 6796 1.522580 GAGGCGGCTTGAGATGGAC 60.523 63.158 14.76 0.00 0.00 4.02
4050 6839 4.282873 CGGCAAGACAAGAAAGAGAAAAC 58.717 43.478 0.00 0.00 0.00 2.43
4060 6850 3.825160 AAGCGCCGGCAAGACAAGA 62.825 57.895 28.98 0.00 43.41 3.02
4082 6872 2.372172 GACCAAGAAGGACTCAAGGGAA 59.628 50.000 0.00 0.00 41.22 3.97


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

AutoCloner maintained by Alex Coulton.