Multiple sequence alignment - TraesCS1D01G380000

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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 TraesCS1D01G380000 chr1D 100.000 4504 0 0 1 4504 455781623 455786126 0.000000e+00 8318.0
1 TraesCS1D01G380000 chr1D 95.556 90 4 0 1 90 234341984 234342073 1.310000e-30 145.0
2 TraesCS1D01G380000 chr1D 95.556 90 4 0 1 90 234347438 234347527 1.310000e-30 145.0
3 TraesCS1D01G380000 chr1A 90.252 3888 223 77 714 4504 549418050 549421878 0.000000e+00 4937.0
4 TraesCS1D01G380000 chr1A 95.556 90 4 0 1 90 432025497 432025586 1.310000e-30 145.0
5 TraesCS1D01G380000 chr1A 95.161 62 3 0 571 632 549414606 549414667 1.030000e-16 99.0
6 TraesCS1D01G380000 chr1B 88.365 1040 60 31 1528 2512 626225194 626226227 0.000000e+00 1194.0
7 TraesCS1D01G380000 chr1B 94.072 776 39 3 3736 4504 626227835 626228610 0.000000e+00 1171.0
8 TraesCS1D01G380000 chr1B 89.448 815 48 18 2899 3683 626227010 626227816 0.000000e+00 994.0
9 TraesCS1D01G380000 chr1B 84.574 927 59 32 634 1510 626224260 626225152 0.000000e+00 843.0
10 TraesCS1D01G380000 chr1B 89.655 58 1 1 572 629 626223590 626223642 8.080000e-08 69.4
11 TraesCS1D01G380000 chr7B 92.978 769 54 0 3736 4504 399793814 399794582 0.000000e+00 1122.0
12 TraesCS1D01G380000 chr7B 87.216 704 57 20 3007 3683 399793098 399793795 0.000000e+00 771.0
13 TraesCS1D01G380000 chr7B 83.754 357 23 13 1346 1676 399792676 399793023 5.660000e-79 305.0
14 TraesCS1D01G380000 chr7B 91.954 87 7 0 1122 1208 399792560 399792646 6.120000e-24 122.0
15 TraesCS1D01G380000 chr3B 92.228 772 56 3 3736 4504 237975439 237976209 0.000000e+00 1090.0
16 TraesCS1D01G380000 chr3B 86.648 704 60 21 3007 3683 237974724 237975420 0.000000e+00 749.0
17 TraesCS1D01G380000 chr3B 83.776 339 36 11 1355 1676 237974314 237974650 2.040000e-78 303.0
18 TraesCS1D01G380000 chr3A 91.753 776 56 3 3730 4504 707168059 707168827 0.000000e+00 1072.0
19 TraesCS1D01G380000 chr3A 88.205 390 30 5 1122 1510 707134884 707135258 6.870000e-123 451.0
20 TraesCS1D01G380000 chr3A 86.527 334 32 10 3007 3332 707135516 707135844 5.540000e-94 355.0
21 TraesCS1D01G380000 chr3A 85.405 370 20 12 3334 3683 707167691 707168046 1.990000e-93 353.0
22 TraesCS1D01G380000 chr3A 94.000 100 6 0 1577 1676 707135342 707135441 7.800000e-33 152.0
23 TraesCS1D01G380000 chr3D 97.018 436 13 0 136 571 528139092 528139527 0.000000e+00 734.0
24 TraesCS1D01G380000 chr3D 96.796 437 14 0 136 572 528144813 528145249 0.000000e+00 730.0
25 TraesCS1D01G380000 chr3D 94.749 438 23 0 136 573 103866999 103866562 0.000000e+00 682.0
26 TraesCS1D01G380000 chr3D 94.495 436 22 1 136 571 26846580 26846147 0.000000e+00 671.0
27 TraesCS1D01G380000 chr3D 92.727 440 31 1 136 575 332492104 332491666 6.360000e-178 634.0
28 TraesCS1D01G380000 chr3D 95.699 93 4 0 1 93 103872539 103872447 2.810000e-32 150.0
29 TraesCS1D01G380000 chr3D 96.667 90 3 0 1 90 528138999 528139088 2.810000e-32 150.0
30 TraesCS1D01G380000 chr3D 95.556 90 4 0 1 90 528144720 528144809 1.310000e-30 145.0
31 TraesCS1D01G380000 chr3D 100.000 28 0 0 2268 2295 132983990 132983963 8.000000e-03 52.8
32 TraesCS1D01G380000 chr6D 93.349 436 29 0 136 571 7699462 7699897 0.000000e+00 645.0
33 TraesCS1D01G380000 chr6D 92.906 437 31 0 136 572 7713511 7713947 1.770000e-178 636.0
34 TraesCS1D01G380000 chr5D 93.119 436 30 0 136 571 372057134 372056699 1.370000e-179 640.0
35 TraesCS1D01G380000 chr4D 92.906 437 31 0 136 572 6082479 6082915 1.770000e-178 636.0
36 TraesCS1D01G380000 chr4D 96.154 52 2 0 1121 1172 401236271 401236322 8.030000e-13 86.1
37 TraesCS1D01G380000 chr7D 96.667 90 3 0 1 90 627017298 627017387 2.810000e-32 150.0
38 TraesCS1D01G380000 chr4B 96.667 90 3 0 1 90 364166076 364166165 2.810000e-32 150.0
39 TraesCS1D01G380000 chr2B 96.667 90 3 0 1 90 214343380 214343469 2.810000e-32 150.0


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 TraesCS1D01G380000 chr1D 455781623 455786126 4503 False 8318.000000 8318 100.000000 1 4504 1 chr1D.!!$F3 4503
1 TraesCS1D01G380000 chr1A 549414606 549421878 7272 False 2518.000000 4937 92.706500 571 4504 2 chr1A.!!$F2 3933
2 TraesCS1D01G380000 chr1B 626223590 626228610 5020 False 854.280000 1194 89.222800 572 4504 5 chr1B.!!$F1 3932
3 TraesCS1D01G380000 chr7B 399792560 399794582 2022 False 580.000000 1122 88.975500 1122 4504 4 chr7B.!!$F1 3382
4 TraesCS1D01G380000 chr3B 237974314 237976209 1895 False 714.000000 1090 87.550667 1355 4504 3 chr3B.!!$F1 3149
5 TraesCS1D01G380000 chr3A 707167691 707168827 1136 False 712.500000 1072 88.579000 3334 4504 2 chr3A.!!$F2 1170
6 TraesCS1D01G380000 chr3A 707134884 707135844 960 False 319.333333 451 89.577333 1122 3332 3 chr3A.!!$F1 2210
7 TraesCS1D01G380000 chr3D 528138999 528139527 528 False 442.000000 734 96.842500 1 571 2 chr3D.!!$F1 570
8 TraesCS1D01G380000 chr3D 528144720 528145249 529 False 437.500000 730 96.176000 1 572 2 chr3D.!!$F2 571

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
105 106 0.329931 AGAGAGACCTCGCCTCTTGA 59.670 55.0 0.00 0.00 44.08 3.02 F
336 337 0.389391 ACATGACGATCGGGACATCC 59.611 55.0 20.98 0.08 0.00 3.51 F
1747 5750 0.530870 GCCGACCTCCTACATTCAGC 60.531 60.0 0.00 0.00 0.00 4.26 F
1932 5949 0.698818 GGTTGGTCCTCCACATTCCT 59.301 55.0 0.00 0.00 44.22 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 5847 0.234884 GCTTTTGTCGGTGAGGTTCG 59.765 55.0 0.00 0.0 0.00 3.95 R
2139 6179 0.106519 AGAGCTGCAACCAACCACTT 60.107 50.0 1.02 0.0 0.00 3.16 R
2581 6719 0.953960 AAAACTACCAGCGAAGGCCG 60.954 55.0 0.00 0.0 41.24 6.13 R
3853 8403 0.512952 CAAGAAGGAAGAACACGCCG 59.487 55.0 0.00 0.0 0.00 6.46 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
38 39 1.396301 CTCTTCGCATTGTTCCAGAGC 59.604 52.381 0.00 0.00 0.00 4.09
50 51 3.057548 CAGAGCATTGCACCGCCA 61.058 61.111 11.91 0.00 0.00 5.69
66 67 2.648059 CGCCAATCTCTTTCCCATCTT 58.352 47.619 0.00 0.00 0.00 2.40
93 94 2.179517 CGTGCACCGGAGAGAGAC 59.820 66.667 9.46 0.00 0.00 3.36
94 95 2.574399 GTGCACCGGAGAGAGACC 59.426 66.667 9.46 0.00 0.00 3.85
95 96 1.979693 GTGCACCGGAGAGAGACCT 60.980 63.158 9.46 0.00 0.00 3.85
96 97 1.679305 TGCACCGGAGAGAGACCTC 60.679 63.158 9.46 0.00 39.72 3.85
97 98 2.766400 GCACCGGAGAGAGACCTCG 61.766 68.421 9.46 0.00 44.08 4.63
98 99 2.438795 ACCGGAGAGAGACCTCGC 60.439 66.667 9.46 0.00 44.08 5.03
102 103 4.977393 GAGAGAGACCTCGCCTCT 57.023 61.111 12.07 0.00 44.08 3.69
103 104 3.184736 GAGAGAGACCTCGCCTCTT 57.815 57.895 12.07 0.00 44.08 2.85
104 105 0.738389 GAGAGAGACCTCGCCTCTTG 59.262 60.000 12.07 0.00 44.08 3.02
105 106 0.329931 AGAGAGACCTCGCCTCTTGA 59.670 55.000 0.00 0.00 44.08 3.02
106 107 0.738389 GAGAGACCTCGCCTCTTGAG 59.262 60.000 0.00 0.00 40.78 3.02
107 108 1.140804 GAGACCTCGCCTCTTGAGC 59.859 63.158 0.00 0.00 31.98 4.26
108 109 1.599606 GAGACCTCGCCTCTTGAGCA 61.600 60.000 0.00 0.00 31.98 4.26
109 110 1.188219 AGACCTCGCCTCTTGAGCAA 61.188 55.000 0.00 0.00 31.98 3.91
110 111 0.739112 GACCTCGCCTCTTGAGCAAG 60.739 60.000 3.87 3.87 39.71 4.01
111 112 1.449246 CCTCGCCTCTTGAGCAAGG 60.449 63.158 10.09 0.00 38.88 3.61
115 116 3.130160 CCTCTTGAGCAAGGCGGC 61.130 66.667 0.00 0.00 38.88 6.53
116 117 3.494336 CTCTTGAGCAAGGCGGCG 61.494 66.667 0.51 0.51 38.88 6.46
131 132 3.368571 GCGCTTGAGCAAGGCCTT 61.369 61.111 13.78 13.78 42.21 4.35
132 133 2.873288 CGCTTGAGCAAGGCCTTC 59.127 61.111 17.29 10.91 42.21 3.46
133 134 2.694760 CGCTTGAGCAAGGCCTTCC 61.695 63.158 17.29 6.69 42.21 3.46
309 310 2.334946 CCCCGACGTCAACGACCTA 61.335 63.158 17.16 0.00 43.02 3.08
316 317 1.271379 ACGTCAACGACCTATTCAGCA 59.729 47.619 9.88 0.00 43.02 4.41
336 337 0.389391 ACATGACGATCGGGACATCC 59.611 55.000 20.98 0.08 0.00 3.51
380 381 6.017026 TCGTATGTCATCTTATCCTCACTGTC 60.017 42.308 0.00 0.00 0.00 3.51
426 427 6.377146 TGCTAGTAGCGATTGACATGGATATA 59.623 38.462 17.16 0.00 46.26 0.86
440 441 7.654116 TGACATGGATATAATGCATTTTGCTTG 59.346 33.333 18.75 16.59 45.31 4.01
603 604 1.261238 AAAGGGAGAGGCGAGGTGAG 61.261 60.000 0.00 0.00 0.00 3.51
604 605 3.151022 GGGAGAGGCGAGGTGAGG 61.151 72.222 0.00 0.00 0.00 3.86
605 606 2.363147 GGAGAGGCGAGGTGAGGT 60.363 66.667 0.00 0.00 0.00 3.85
638 1252 0.534203 ACCCCAATCACACACACGAC 60.534 55.000 0.00 0.00 0.00 4.34
643 1257 2.337583 CAATCACACACACGACCCTAG 58.662 52.381 0.00 0.00 0.00 3.02
651 1265 4.174009 CACACACGACCCTAGTTAATGAG 58.826 47.826 0.00 0.00 0.00 2.90
686 4580 4.380843 TCCTTATCCACCAAAGCAGAAA 57.619 40.909 0.00 0.00 0.00 2.52
864 4770 2.028020 CCCTATTTCTAGTCCATCGGCC 60.028 54.545 0.00 0.00 0.00 6.13
972 4910 3.093172 CAAGGGGAGGGAGGGCTC 61.093 72.222 0.00 0.00 0.00 4.70
973 4911 4.806339 AAGGGGAGGGAGGGCTCG 62.806 72.222 0.00 0.00 0.00 5.03
984 4922 3.808656 GGGCTCGCTTGCTTGCTC 61.809 66.667 6.64 0.24 0.00 4.26
986 4924 4.157958 GCTCGCTTGCTTGCTCGG 62.158 66.667 0.00 0.00 0.00 4.63
987 4925 4.157958 CTCGCTTGCTTGCTCGGC 62.158 66.667 0.00 0.00 0.00 5.54
1281 5231 3.444805 GAGGACTGGCGCGAGACT 61.445 66.667 26.95 21.54 42.42 3.24
1325 5278 2.525629 GGCTAGGGAGAGGAGGGC 60.526 72.222 0.00 0.00 0.00 5.19
1495 5451 4.988716 ACGGGGAGAGGCGACACA 62.989 66.667 0.00 0.00 0.00 3.72
1510 5466 2.224209 CGACACAGGGAGGTTTGTACTT 60.224 50.000 0.00 0.00 0.00 2.24
1511 5467 3.743269 CGACACAGGGAGGTTTGTACTTT 60.743 47.826 0.00 0.00 0.00 2.66
1512 5468 4.204799 GACACAGGGAGGTTTGTACTTTT 58.795 43.478 0.00 0.00 0.00 2.27
1513 5469 3.951680 ACACAGGGAGGTTTGTACTTTTG 59.048 43.478 0.00 0.00 0.00 2.44
1514 5470 2.956333 ACAGGGAGGTTTGTACTTTTGC 59.044 45.455 0.00 0.00 0.00 3.68
1515 5471 3.222603 CAGGGAGGTTTGTACTTTTGCT 58.777 45.455 0.00 0.00 0.00 3.91
1516 5472 3.004734 CAGGGAGGTTTGTACTTTTGCTG 59.995 47.826 0.00 0.00 0.00 4.41
1517 5473 2.956333 GGGAGGTTTGTACTTTTGCTGT 59.044 45.455 0.00 0.00 0.00 4.40
1518 5474 3.004419 GGGAGGTTTGTACTTTTGCTGTC 59.996 47.826 0.00 0.00 0.00 3.51
1519 5475 3.004419 GGAGGTTTGTACTTTTGCTGTCC 59.996 47.826 0.00 0.00 0.00 4.02
1520 5476 2.956333 AGGTTTGTACTTTTGCTGTCCC 59.044 45.455 0.00 0.00 0.00 4.46
1550 5542 1.506718 CTTGCGTCTCTCCGTGCTA 59.493 57.895 0.00 0.00 0.00 3.49
1551 5543 0.798771 CTTGCGTCTCTCCGTGCTAC 60.799 60.000 0.00 0.00 0.00 3.58
1556 5548 1.466024 CGTCTCTCCGTGCTACAACTC 60.466 57.143 0.00 0.00 0.00 3.01
1559 5551 0.888619 TCTCCGTGCTACAACTCTGG 59.111 55.000 0.00 0.00 0.00 3.86
1567 5559 3.368236 GTGCTACAACTCTGGACGAATTC 59.632 47.826 0.00 0.00 0.00 2.17
1620 5623 5.667539 TCTGAATCGACTTCTGATTTCCT 57.332 39.130 10.72 0.00 37.03 3.36
1739 5742 3.129502 CACGACGCCGACCTCCTA 61.130 66.667 0.00 0.00 39.50 2.94
1747 5750 0.530870 GCCGACCTCCTACATTCAGC 60.531 60.000 0.00 0.00 0.00 4.26
1832 5835 3.587923 CATTCCACGCACCATTTCATTT 58.412 40.909 0.00 0.00 0.00 2.32
1837 5840 0.894141 CGCACCATTTCATTTCCCCA 59.106 50.000 0.00 0.00 0.00 4.96
1844 5847 1.347062 TTTCATTTCCCCAACCCTGC 58.653 50.000 0.00 0.00 0.00 4.85
1903 5917 6.071278 TCCAGCATTCATTTCATCATTGTTGA 60.071 34.615 0.00 0.00 36.00 3.18
1916 5933 4.260985 TCATTGTTGATGCACGATAGGTT 58.739 39.130 0.00 0.00 36.53 3.50
1932 5949 0.698818 GGTTGGTCCTCCACATTCCT 59.301 55.000 0.00 0.00 44.22 3.36
1961 5979 3.949754 TCATTCTGATTGGGCAATCTCAC 59.050 43.478 0.00 0.00 45.55 3.51
1993 6011 4.768448 TCGTAGGTGGTTTCAGACTATCAA 59.232 41.667 0.00 0.00 0.00 2.57
2006 6024 2.972713 GACTATCAAGGGGTCCATGCTA 59.027 50.000 0.00 0.00 0.00 3.49
2019 6037 6.013293 GGGGTCCATGCTAAATCTTATACTCT 60.013 42.308 0.00 0.00 0.00 3.24
2077 6101 6.935771 TGCTGATTTGGCATTTTTGTTTCTAT 59.064 30.769 0.00 0.00 34.56 1.98
2092 6116 4.019771 TGTTTCTATGCCATGGTACTCACA 60.020 41.667 14.67 5.89 0.00 3.58
2139 6179 4.272748 CGATCCTCACACGTTCTATACTGA 59.727 45.833 0.00 0.00 0.00 3.41
2199 6239 1.080638 TTTATCACCCCTGGCTGGTT 58.919 50.000 9.73 0.00 32.46 3.67
2229 6273 1.416373 TTATACGACACGCAACGCAA 58.584 45.000 0.00 0.00 0.00 4.85
2334 6379 5.426689 TTGAGTGTAGATGCAGATTTCCT 57.573 39.130 0.00 0.00 0.00 3.36
2340 6385 4.949856 TGTAGATGCAGATTTCCTTTTCCC 59.050 41.667 0.00 0.00 0.00 3.97
2342 6387 4.021916 AGATGCAGATTTCCTTTTCCCTG 58.978 43.478 0.00 0.00 0.00 4.45
2343 6388 3.243359 TGCAGATTTCCTTTTCCCTGT 57.757 42.857 0.00 0.00 0.00 4.00
2347 6399 4.797275 GCAGATTTCCTTTTCCCTGTTGTG 60.797 45.833 0.00 0.00 0.00 3.33
2380 6432 1.089112 CGCTGAATCATTGTGCTGGA 58.911 50.000 0.00 0.00 0.00 3.86
2458 6515 4.202030 TGGATGGTTGGTTCGTTGTTTAAC 60.202 41.667 0.00 0.00 0.00 2.01
2488 6546 1.417517 AGAATGTGGTGAGCACACTGA 59.582 47.619 20.52 0.00 45.32 3.41
2581 6719 2.796593 GCATGTTTGTGAGTCAAAAGGC 59.203 45.455 0.00 0.00 45.84 4.35
2621 6759 3.476552 TGACTTTGGGTTCTGCACTTAG 58.523 45.455 0.00 0.00 0.00 2.18
2718 6925 1.008079 GCTGCTGTGTGCCACTTTC 60.008 57.895 0.00 0.00 42.00 2.62
2737 6944 2.677199 TCGTGCTGATCAGTTCTGAAC 58.323 47.619 23.38 12.54 0.00 3.18
2738 6945 2.035832 TCGTGCTGATCAGTTCTGAACA 59.964 45.455 23.38 8.56 32.60 3.18
2747 6954 6.429624 TGATCAGTTCTGAACATGTTTTTCG 58.570 36.000 21.50 2.10 0.00 3.46
2779 7148 2.371841 ACTAGTTGTTGGCATCAGGTCA 59.628 45.455 0.00 0.00 0.00 4.02
2780 7149 2.592102 AGTTGTTGGCATCAGGTCAT 57.408 45.000 0.00 0.00 0.00 3.06
2781 7150 2.440409 AGTTGTTGGCATCAGGTCATC 58.560 47.619 0.00 0.00 0.00 2.92
2838 7212 6.875972 AAGCTCTTTAGATCCCTTGAGTAA 57.124 37.500 0.00 0.00 0.00 2.24
2875 7249 9.003658 GGATATATGTAGCATGCACTTTAAACT 57.996 33.333 21.98 0.00 29.56 2.66
2884 7258 7.253422 AGCATGCACTTTAAACTCATGTTATC 58.747 34.615 21.98 5.13 37.44 1.75
2897 7396 9.877178 AAACTCATGTTATCTGTTACTCCTAAG 57.123 33.333 0.00 0.00 34.96 2.18
3005 7504 2.409870 CCAGGATTGGCGCCTTGAC 61.410 63.158 29.70 15.52 37.73 3.18
3033 7532 6.516194 CGATAACATGAATTACGAGGTACCCT 60.516 42.308 8.74 0.00 36.03 4.34
3310 7823 3.380393 TCCTTTCGATTCAGTCCCCATA 58.620 45.455 0.00 0.00 0.00 2.74
3317 7830 3.999001 CGATTCAGTCCCCATATCACATG 59.001 47.826 0.00 0.00 0.00 3.21
3332 7845 2.109799 ATGGGCATCGGCTCTTCG 59.890 61.111 0.00 0.00 42.67 3.79
3351 7871 6.884187 TCTTCGCAAGTTAACATGAACTTAC 58.116 36.000 14.72 6.29 45.70 2.34
3352 7872 6.480651 TCTTCGCAAGTTAACATGAACTTACA 59.519 34.615 14.72 0.00 45.70 2.41
3353 7873 6.606234 TCGCAAGTTAACATGAACTTACAA 57.394 33.333 14.72 0.01 45.70 2.41
3354 7874 7.017498 TCGCAAGTTAACATGAACTTACAAA 57.983 32.000 14.72 0.00 45.70 2.83
3355 7875 7.644490 TCGCAAGTTAACATGAACTTACAAAT 58.356 30.769 14.72 0.00 45.70 2.32
3356 7876 7.801315 TCGCAAGTTAACATGAACTTACAAATC 59.199 33.333 14.72 0.00 45.70 2.17
3357 7877 7.589587 CGCAAGTTAACATGAACTTACAAATCA 59.410 33.333 14.72 0.00 45.70 2.57
3377 7897 8.561212 CAAATCATTGCAATTTTTCAGGAAGAA 58.439 29.630 9.83 0.00 0.00 2.52
3395 7915 4.008074 AGAATTTGAAGCGAGTGAGGAA 57.992 40.909 0.00 0.00 0.00 3.36
3613 8157 1.078143 CTTGTACAGCCCCCTCTGC 60.078 63.158 0.00 0.00 37.59 4.26
3632 8176 3.135994 TGCTGCTCTGCATATACACATG 58.864 45.455 0.00 0.00 38.13 3.21
3700 8246 1.348064 TTCTTGTCCCCATCGTCTGT 58.652 50.000 0.00 0.00 0.00 3.41
3909 8474 1.811266 CCTTCACCATCACGGCTCG 60.811 63.158 0.00 0.00 39.03 5.03
3959 8524 4.459089 GTGTCCTCCGCTGCTCCC 62.459 72.222 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.813184 AAGAGATTGGCGGTGCAATG 59.187 50.000 0.00 0.00 0.00 2.82
50 51 4.017683 AGGAAGCAAGATGGGAAAGAGATT 60.018 41.667 0.00 0.00 0.00 2.40
90 91 1.188219 TTGCTCAAGAGGCGAGGTCT 61.188 55.000 0.00 0.00 0.00 3.85
93 94 4.198625 CTTGCTCAAGAGGCGAGG 57.801 61.111 3.64 0.00 40.79 4.63
94 95 4.198625 CCTTGCTCAAGAGGCGAG 57.801 61.111 10.94 0.00 40.79 5.03
98 99 3.130160 GCCGCCTTGCTCAAGAGG 61.130 66.667 10.94 13.37 40.79 3.69
99 100 3.494336 CGCCGCCTTGCTCAAGAG 61.494 66.667 10.94 4.99 40.79 2.85
114 115 3.333898 GAAGGCCTTGCTCAAGCGC 62.334 63.158 26.25 0.00 45.83 5.92
115 116 2.694760 GGAAGGCCTTGCTCAAGCG 61.695 63.158 28.21 0.06 45.83 4.68
116 117 1.303970 AGGAAGGCCTTGCTCAAGC 60.304 57.895 31.94 11.51 43.90 4.01
117 118 0.037303 TCAGGAAGGCCTTGCTCAAG 59.963 55.000 34.32 23.68 43.90 3.02
118 119 0.250901 GTCAGGAAGGCCTTGCTCAA 60.251 55.000 34.32 22.91 43.90 3.02
119 120 1.376466 GTCAGGAAGGCCTTGCTCA 59.624 57.895 34.32 22.49 43.90 4.26
120 121 0.676151 CTGTCAGGAAGGCCTTGCTC 60.676 60.000 34.32 24.51 43.90 4.26
121 122 1.377994 CTGTCAGGAAGGCCTTGCT 59.622 57.895 31.94 31.94 43.90 3.91
122 123 2.338785 GCTGTCAGGAAGGCCTTGC 61.339 63.158 28.27 28.27 43.90 4.01
123 124 0.959372 CTGCTGTCAGGAAGGCCTTG 60.959 60.000 26.25 10.14 43.90 3.61
124 125 1.377994 CTGCTGTCAGGAAGGCCTT 59.622 57.895 20.65 20.65 43.90 4.35
133 134 2.454832 TTTCGGAGGCCTGCTGTCAG 62.455 60.000 23.05 6.21 40.02 3.51
134 135 2.515979 TTTCGGAGGCCTGCTGTCA 61.516 57.895 23.05 0.16 0.00 3.58
182 183 1.266178 CCCAAAAACCTGATCACCCC 58.734 55.000 0.00 0.00 0.00 4.95
220 221 3.338249 CCACGATGAACAAGAATCCAGT 58.662 45.455 0.00 0.00 0.00 4.00
309 310 1.935873 CCGATCGTCATGTTGCTGAAT 59.064 47.619 15.09 0.00 0.00 2.57
316 317 1.202533 GGATGTCCCGATCGTCATGTT 60.203 52.381 15.09 0.00 0.00 2.71
380 381 4.685924 CAATAAACCAAATGCTAGCCCTG 58.314 43.478 13.29 6.54 0.00 4.45
440 441 7.541091 TGAGACTAGTCATGTAATCGAAAACAC 59.459 37.037 24.44 0.00 0.00 3.32
603 604 1.745489 GGTGATTGAGCCGTCCACC 60.745 63.158 0.00 0.00 40.20 4.61
604 605 1.745489 GGGTGATTGAGCCGTCCAC 60.745 63.158 0.00 0.00 30.84 4.02
605 606 2.668632 GGGTGATTGAGCCGTCCA 59.331 61.111 0.00 0.00 30.84 4.02
651 1265 6.464607 GGTGGATAAGGATTAAGGAGGAAGAC 60.465 46.154 0.00 0.00 32.17 3.01
686 4580 3.756783 AGTAGGCTCCTCCCGGCT 61.757 66.667 0.00 0.00 40.64 5.52
728 4631 2.757077 GGGTCAGTGGGTCAAGGG 59.243 66.667 0.00 0.00 0.00 3.95
835 4741 3.116668 GGACTAGAAATAGGGAGGGAGGT 60.117 52.174 0.00 0.00 0.00 3.85
837 4743 4.200447 TGGACTAGAAATAGGGAGGGAG 57.800 50.000 0.00 0.00 0.00 4.30
838 4744 4.753186 GATGGACTAGAAATAGGGAGGGA 58.247 47.826 0.00 0.00 0.00 4.20
839 4745 3.511934 CGATGGACTAGAAATAGGGAGGG 59.488 52.174 0.00 0.00 0.00 4.30
877 4799 0.034477 AGGCAGTTGGTTATTCGGGG 60.034 55.000 0.00 0.00 0.00 5.73
963 4901 4.416738 AAGCAAGCGAGCCCTCCC 62.417 66.667 0.00 0.00 34.23 4.30
964 4902 3.130160 CAAGCAAGCGAGCCCTCC 61.130 66.667 0.00 0.00 34.23 4.30
965 4903 3.808656 GCAAGCAAGCGAGCCCTC 61.809 66.667 0.00 0.00 34.23 4.30
966 4904 4.341783 AGCAAGCAAGCGAGCCCT 62.342 61.111 7.87 0.00 40.15 5.19
967 4905 3.808656 GAGCAAGCAAGCGAGCCC 61.809 66.667 7.87 0.00 40.15 5.19
968 4906 4.157958 CGAGCAAGCAAGCGAGCC 62.158 66.667 7.87 1.04 40.15 4.70
969 4907 4.157958 CCGAGCAAGCAAGCGAGC 62.158 66.667 4.06 4.06 40.15 5.03
970 4908 4.157958 GCCGAGCAAGCAAGCGAG 62.158 66.667 0.00 0.00 40.15 5.03
971 4909 4.687215 AGCCGAGCAAGCAAGCGA 62.687 61.111 0.00 0.00 40.15 4.93
972 4910 4.456253 CAGCCGAGCAAGCAAGCG 62.456 66.667 0.00 0.00 40.15 4.68
973 4911 4.112341 CCAGCCGAGCAAGCAAGC 62.112 66.667 0.00 0.00 0.00 4.01
974 4912 4.112341 GCCAGCCGAGCAAGCAAG 62.112 66.667 0.00 0.00 0.00 4.01
1071 5009 1.454295 GGGAGAGGACGAGGAGGAC 60.454 68.421 0.00 0.00 0.00 3.85
1235 5179 2.837291 CCTCCTCCTCCTCCGCTG 60.837 72.222 0.00 0.00 0.00 5.18
1247 5194 0.933700 CTCCTCCTCTTCCTCCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
1299 5249 4.089757 TCCCTAGCCCTCCGCCTT 62.090 66.667 0.00 0.00 38.78 4.35
1310 5260 2.203567 CGGCCCTCCTCTCCCTAG 60.204 72.222 0.00 0.00 0.00 3.02
1311 5261 4.541648 GCGGCCCTCCTCTCCCTA 62.542 72.222 0.00 0.00 0.00 3.53
1495 5451 3.222603 CAGCAAAAGTACAAACCTCCCT 58.777 45.455 0.00 0.00 0.00 4.20
1510 5466 0.772124 AGGAGAAGGGGGACAGCAAA 60.772 55.000 0.00 0.00 0.00 3.68
1511 5467 0.772124 AAGGAGAAGGGGGACAGCAA 60.772 55.000 0.00 0.00 0.00 3.91
1512 5468 1.151810 AAGGAGAAGGGGGACAGCA 60.152 57.895 0.00 0.00 0.00 4.41
1513 5469 1.301293 CAAGGAGAAGGGGGACAGC 59.699 63.158 0.00 0.00 0.00 4.40
1514 5470 1.204113 AGCAAGGAGAAGGGGGACAG 61.204 60.000 0.00 0.00 0.00 3.51
1515 5471 0.772124 AAGCAAGGAGAAGGGGGACA 60.772 55.000 0.00 0.00 0.00 4.02
1516 5472 0.322906 CAAGCAAGGAGAAGGGGGAC 60.323 60.000 0.00 0.00 0.00 4.46
1517 5473 2.078452 CAAGCAAGGAGAAGGGGGA 58.922 57.895 0.00 0.00 0.00 4.81
1518 5474 1.680314 GCAAGCAAGGAGAAGGGGG 60.680 63.158 0.00 0.00 0.00 5.40
1519 5475 2.042831 CGCAAGCAAGGAGAAGGGG 61.043 63.158 0.00 0.00 0.00 4.79
1520 5476 1.301677 GACGCAAGCAAGGAGAAGGG 61.302 60.000 0.00 0.00 45.62 3.95
1550 5542 2.037772 AGCAGAATTCGTCCAGAGTTGT 59.962 45.455 0.00 0.00 0.00 3.32
1551 5543 2.670414 GAGCAGAATTCGTCCAGAGTTG 59.330 50.000 0.00 0.00 0.00 3.16
1556 5548 3.064545 GGATTTGAGCAGAATTCGTCCAG 59.935 47.826 0.00 0.00 0.00 3.86
1559 5551 4.154918 AGTTGGATTTGAGCAGAATTCGTC 59.845 41.667 0.00 0.00 0.00 4.20
1567 5559 4.096081 GGAGATTCAGTTGGATTTGAGCAG 59.904 45.833 0.00 0.00 0.00 4.24
1620 5623 2.741092 GGCGGTCCTCTGTCAACA 59.259 61.111 0.00 0.00 0.00 3.33
1832 5835 3.961414 GGTTCGCAGGGTTGGGGA 61.961 66.667 0.00 0.00 37.80 4.81
1837 5840 2.430367 GGTGAGGTTCGCAGGGTT 59.570 61.111 0.00 0.00 0.00 4.11
1844 5847 0.234884 GCTTTTGTCGGTGAGGTTCG 59.765 55.000 0.00 0.00 0.00 3.95
1903 5917 3.780624 GGACCAACCTATCGTGCAT 57.219 52.632 0.00 0.00 35.41 3.96
1916 5933 1.630369 CTTGAGGAATGTGGAGGACCA 59.370 52.381 0.00 0.00 44.76 4.02
1961 5979 1.522355 CCACCTACGATGGCTGCTG 60.522 63.158 0.00 0.00 0.00 4.41
1993 6011 5.852250 AGTATAAGATTTAGCATGGACCCCT 59.148 40.000 0.00 0.00 0.00 4.79
2019 6037 4.160439 GGCTGCATATGATGGCTACTAGTA 59.840 45.833 6.97 1.89 0.00 1.82
2077 6101 1.627834 TGTGATGTGAGTACCATGGCA 59.372 47.619 13.04 0.00 0.00 4.92
2108 6135 3.921677 ACGTGTGAGGATCGTTTTGTAT 58.078 40.909 0.00 0.00 38.61 2.29
2139 6179 0.106519 AGAGCTGCAACCAACCACTT 60.107 50.000 1.02 0.00 0.00 3.16
2199 6239 6.320944 TGCGTGTCGTATAAACATAACTACA 58.679 36.000 0.00 0.00 0.00 2.74
2237 6281 3.957535 CCATCCAATCTGCCGCGC 61.958 66.667 0.00 0.00 0.00 6.86
2305 6349 1.656652 CATCTACACTCAAAGGGCCG 58.343 55.000 0.00 0.00 0.00 6.13
2347 6399 3.392769 TTCAGCGTTTTGTGTGTGTAC 57.607 42.857 0.00 0.00 0.00 2.90
2358 6410 2.352030 CCAGCACAATGATTCAGCGTTT 60.352 45.455 0.00 0.00 0.00 3.60
2360 6412 0.806868 CCAGCACAATGATTCAGCGT 59.193 50.000 0.00 0.00 0.00 5.07
2361 6413 1.089112 TCCAGCACAATGATTCAGCG 58.911 50.000 0.00 0.00 0.00 5.18
2362 6414 2.089980 AGTCCAGCACAATGATTCAGC 58.910 47.619 0.00 0.00 0.00 4.26
2363 6415 3.340928 TCAGTCCAGCACAATGATTCAG 58.659 45.455 0.00 0.00 0.00 3.02
2380 6432 2.653726 TCAGCAACATGGTTGTTCAGT 58.346 42.857 10.44 0.00 44.24 3.41
2458 6515 5.088739 GCTCACCACATTCTAAAAATCACG 58.911 41.667 0.00 0.00 0.00 4.35
2474 6532 1.059098 ATCCTTCAGTGTGCTCACCA 58.941 50.000 14.99 0.00 44.83 4.17
2488 6546 3.167485 TGCTCAGGCATTCAAAATCCTT 58.833 40.909 0.00 0.00 44.28 3.36
2509 6642 6.213525 AGGAGGTCAGGTTCTTATTATCCTT 58.786 40.000 0.00 0.00 29.21 3.36
2515 6648 5.310857 ACTTGAAGGAGGTCAGGTTCTTATT 59.689 40.000 0.00 0.00 34.43 1.40
2523 6656 2.370189 AGTTCACTTGAAGGAGGTCAGG 59.630 50.000 0.00 0.00 34.27 3.86
2581 6719 0.953960 AAAACTACCAGCGAAGGCCG 60.954 55.000 0.00 0.00 41.24 6.13
2590 6728 4.887655 AGAACCCAAAGTCAAAACTACCAG 59.112 41.667 0.00 0.00 33.48 4.00
2621 6759 9.668497 AGAACAACTAGGTATTTTTCTGTATCC 57.332 33.333 0.00 0.00 0.00 2.59
2718 6925 2.407090 TGTTCAGAACTGATCAGCACG 58.593 47.619 22.83 8.96 39.64 5.34
2737 6944 6.287107 AGTGTAGAACAGACGAAAAACATG 57.713 37.500 0.00 0.00 0.00 3.21
2738 6945 7.208080 ACTAGTGTAGAACAGACGAAAAACAT 58.792 34.615 0.00 0.00 0.00 2.71
2747 6954 4.448060 GCCAACAACTAGTGTAGAACAGAC 59.552 45.833 0.00 0.00 40.60 3.51
2779 7148 6.947733 TGAACTGGAACAACCTATCAAATGAT 59.052 34.615 1.01 1.01 38.70 2.45
2780 7149 6.206634 GTGAACTGGAACAACCTATCAAATGA 59.793 38.462 0.00 0.00 38.70 2.57
2781 7150 6.207417 AGTGAACTGGAACAACCTATCAAATG 59.793 38.462 0.00 0.00 38.70 2.32
2814 7188 7.973048 TTACTCAAGGGATCTAAAGAGCTTA 57.027 36.000 0.00 0.00 0.00 3.09
2838 7212 9.557061 CATGCTACATATATCCATTAGCAGAAT 57.443 33.333 15.12 3.07 46.14 2.40
2871 7245 9.877178 CTTAGGAGTAACAGATAACATGAGTTT 57.123 33.333 0.00 0.00 39.15 2.66
2919 7418 8.390354 TCGAAACATCATTATCTGAATGTTGTC 58.610 33.333 12.13 5.47 38.75 3.18
3005 7504 4.974275 ACCTCGTAATTCATGTTATCGACG 59.026 41.667 0.00 0.00 0.00 5.12
3033 7532 2.329539 GATGATGGGCAGCGGAAGGA 62.330 60.000 0.00 0.00 0.00 3.36
3078 7578 8.958043 CAATGTTCTTTGTTAAGTAAAGACAGC 58.042 33.333 12.16 8.07 42.15 4.40
3310 7823 1.228063 GAGCCGATGCCCATGTGAT 60.228 57.895 0.00 0.00 38.69 3.06
3332 7845 8.795786 TGATTTGTAAGTTCATGTTAACTTGC 57.204 30.769 18.17 17.22 46.49 4.01
3351 7871 8.090250 TCTTCCTGAAAAATTGCAATGATTTG 57.910 30.769 21.56 11.98 35.85 2.32
3352 7872 8.680039 TTCTTCCTGAAAAATTGCAATGATTT 57.320 26.923 13.82 16.64 0.00 2.17
3353 7873 8.857694 ATTCTTCCTGAAAAATTGCAATGATT 57.142 26.923 13.82 11.04 38.29 2.57
3354 7874 8.857694 AATTCTTCCTGAAAAATTGCAATGAT 57.142 26.923 13.82 2.11 38.29 2.45
3355 7875 8.561212 CAAATTCTTCCTGAAAAATTGCAATGA 58.439 29.630 13.82 0.63 38.29 2.57
3356 7876 8.561212 TCAAATTCTTCCTGAAAAATTGCAATG 58.439 29.630 13.82 0.00 38.29 2.82
3357 7877 8.680039 TCAAATTCTTCCTGAAAAATTGCAAT 57.320 26.923 5.99 5.99 38.29 3.56
3377 7897 3.409026 ACTTCCTCACTCGCTTCAAAT 57.591 42.857 0.00 0.00 0.00 2.32
3395 7915 2.063378 GCAGCTCAGCCTCCCTACT 61.063 63.158 0.00 0.00 0.00 2.57
3507 8028 1.045407 ACAAACTGTGGCGTAGGAGA 58.955 50.000 0.00 0.00 0.00 3.71
3613 8157 3.736720 ACCATGTGTATATGCAGAGCAG 58.263 45.455 0.00 0.00 43.65 4.24
3632 8176 7.360361 CCTGTGTATCTTTTCTTACAACAACC 58.640 38.462 0.00 0.00 30.59 3.77
3700 8246 1.580942 GTGCAGCTCAAATGGCGAA 59.419 52.632 0.00 0.00 34.52 4.70
3853 8403 0.512952 CAAGAAGGAAGAACACGCCG 59.487 55.000 0.00 0.00 0.00 6.46
3859 8409 1.456165 GCGACGTCAAGAAGGAAGAAC 59.544 52.381 17.16 0.00 0.00 3.01
3860 8410 1.604693 GGCGACGTCAAGAAGGAAGAA 60.605 52.381 17.16 0.00 0.00 2.52
3892 8454 2.456119 GCGAGCCGTGATGGTGAAG 61.456 63.158 0.00 0.00 41.21 3.02
4324 8892 3.823330 GTCCAGGACGACGCGGAT 61.823 66.667 12.47 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.