Multiple sequence alignment - TraesCS2B01G059400

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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 TraesCS2B01G059400 chr2B 100.000 4522 0 0 1 4522 28881969 28886490 0.000000e+00 8351.0
1 TraesCS2B01G059400 chr2B 98.462 65 1 0 768 832 357473103 357473039 1.030000e-21 115.0
2 TraesCS2B01G059400 chr2D 93.351 3414 176 19 717 4115 17010626 17014003 0.000000e+00 5000.0
3 TraesCS2B01G059400 chr2D 84.537 2451 309 44 1140 3564 16765264 16762858 0.000000e+00 2362.0
4 TraesCS2B01G059400 chr2D 88.445 701 29 14 1 671 17009851 17010529 0.000000e+00 798.0
5 TraesCS2B01G059400 chr2D 92.135 267 16 2 4128 4389 17013988 17014254 5.520000e-99 372.0
6 TraesCS2B01G059400 chr2D 93.023 129 8 1 4394 4522 17014644 17014771 2.150000e-43 187.0
7 TraesCS2B01G059400 chr2A 93.066 3173 165 18 958 4115 18425163 18422031 0.000000e+00 4590.0
8 TraesCS2B01G059400 chr2A 84.609 2456 302 38 1140 3572 18544619 18547021 0.000000e+00 2372.0
9 TraesCS2B01G059400 chr2A 93.464 306 20 0 1 306 18461130 18460825 5.330000e-124 455.0
10 TraesCS2B01G059400 chr2A 93.822 259 16 0 4131 4389 18422043 18421785 1.530000e-104 390.0
11 TraesCS2B01G059400 chr2A 96.596 235 7 1 717 951 18448059 18447826 5.490000e-104 388.0
12 TraesCS2B01G059400 chr2A 92.342 222 11 2 350 570 18448434 18448218 1.220000e-80 311.0
13 TraesCS2B01G059400 chr2A 95.455 66 3 0 575 640 18448157 18448092 6.190000e-19 106.0
14 TraesCS2B01G059400 chr2A 89.744 78 5 3 4394 4470 18421415 18421340 3.720000e-16 97.1
15 TraesCS2B01G059400 chr6A 86.818 2640 279 29 970 3570 28410320 28412929 0.000000e+00 2883.0
16 TraesCS2B01G059400 chr6A 89.189 74 8 0 3689 3762 28413127 28413200 4.820000e-15 93.5
17 TraesCS2B01G059400 chr6D 87.880 2467 241 33 1140 3570 27056851 27059295 0.000000e+00 2846.0
18 TraesCS2B01G059400 chr6D 79.126 2472 437 56 1142 3568 24377883 24375446 0.000000e+00 1633.0
19 TraesCS2B01G059400 chr6D 75.430 582 103 22 1281 1846 24294982 24294425 3.490000e-61 246.0
20 TraesCS2B01G059400 chr6D 95.385 65 3 0 768 832 370023585 370023649 2.230000e-18 104.0
21 TraesCS2B01G059400 chr6B 86.409 2612 284 29 1018 3590 49437949 49435370 0.000000e+00 2791.0
22 TraesCS2B01G059400 chr6B 86.231 2600 271 40 1018 3570 49733883 49736442 0.000000e+00 2737.0
23 TraesCS2B01G059400 chr6B 88.551 1712 182 12 1667 3371 49306006 49307710 0.000000e+00 2063.0
24 TraesCS2B01G059400 chr6B 89.288 1307 133 6 2265 3570 49537635 49538935 0.000000e+00 1631.0
25 TraesCS2B01G059400 chr6B 77.068 955 166 36 1181 2101 39367185 39368120 6.750000e-138 501.0
26 TraesCS2B01G059400 chrUn 76.298 1021 201 25 1231 2227 35132788 35133791 1.450000e-139 507.0
27 TraesCS2B01G059400 chrUn 95.385 65 3 0 768 832 417899689 417899753 2.230000e-18 104.0
28 TraesCS2B01G059400 chr3B 94.203 69 4 0 764 832 575838665 575838597 6.190000e-19 106.0
29 TraesCS2B01G059400 chr4D 95.385 65 3 0 768 832 123351203 123351267 2.230000e-18 104.0
30 TraesCS2B01G059400 chr4D 95.385 65 3 0 768 832 123562141 123562205 2.230000e-18 104.0
31 TraesCS2B01G059400 chr4D 95.385 65 3 0 768 832 450897111 450897047 2.230000e-18 104.0


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 TraesCS2B01G059400 chr2B 28881969 28886490 4521 False 8351.000000 8351 100.000000 1 4522 1 chr2B.!!$F1 4521
1 TraesCS2B01G059400 chr2D 16762858 16765264 2406 True 2362.000000 2362 84.537000 1140 3564 1 chr2D.!!$R1 2424
2 TraesCS2B01G059400 chr2D 17009851 17014771 4920 False 1589.250000 5000 91.738500 1 4522 4 chr2D.!!$F1 4521
3 TraesCS2B01G059400 chr2A 18544619 18547021 2402 False 2372.000000 2372 84.609000 1140 3572 1 chr2A.!!$F1 2432
4 TraesCS2B01G059400 chr2A 18421340 18425163 3823 True 1692.366667 4590 92.210667 958 4470 3 chr2A.!!$R2 3512
5 TraesCS2B01G059400 chr2A 18447826 18448434 608 True 268.333333 388 94.797667 350 951 3 chr2A.!!$R3 601
6 TraesCS2B01G059400 chr6A 28410320 28413200 2880 False 1488.250000 2883 88.003500 970 3762 2 chr6A.!!$F1 2792
7 TraesCS2B01G059400 chr6D 27056851 27059295 2444 False 2846.000000 2846 87.880000 1140 3570 1 chr6D.!!$F1 2430
8 TraesCS2B01G059400 chr6D 24375446 24377883 2437 True 1633.000000 1633 79.126000 1142 3568 1 chr6D.!!$R2 2426
9 TraesCS2B01G059400 chr6D 24294425 24294982 557 True 246.000000 246 75.430000 1281 1846 1 chr6D.!!$R1 565
10 TraesCS2B01G059400 chr6B 49435370 49437949 2579 True 2791.000000 2791 86.409000 1018 3590 1 chr6B.!!$R1 2572
11 TraesCS2B01G059400 chr6B 49733883 49736442 2559 False 2737.000000 2737 86.231000 1018 3570 1 chr6B.!!$F4 2552
12 TraesCS2B01G059400 chr6B 49306006 49307710 1704 False 2063.000000 2063 88.551000 1667 3371 1 chr6B.!!$F2 1704
13 TraesCS2B01G059400 chr6B 49537635 49538935 1300 False 1631.000000 1631 89.288000 2265 3570 1 chr6B.!!$F3 1305
14 TraesCS2B01G059400 chr6B 39367185 39368120 935 False 501.000000 501 77.068000 1181 2101 1 chr6B.!!$F1 920
15 TraesCS2B01G059400 chrUn 35132788 35133791 1003 False 507.000000 507 76.298000 1231 2227 1 chrUn.!!$F1 996

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
672 757 0.034896 TCGGGACTTGAAGCTTCACC 59.965 55.0 28.46 24.18 36.83 4.02 F
674 759 0.110486 GGGACTTGAAGCTTCACCCA 59.890 55.0 33.40 19.69 39.54 4.51 F
1765 1993 0.457853 GGATGCGAGCAACGAGTACA 60.458 55.0 0.57 0.00 45.77 2.90 F
2430 2690 0.794605 GCGAAAGATGAAGCAACGGC 60.795 55.0 0.00 0.00 41.61 5.68 F
2633 2893 1.496060 AAGGCATCATGTCGGACCTA 58.504 50.0 5.55 0.00 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 2019 0.110678 ACCATCCTCTCTCGGCGATA 59.889 55.0 11.27 1.34 0.00 2.92 R
2633 2893 0.246360 TCTTGATCGCCACGACATGT 59.754 50.0 0.00 0.00 39.18 3.21 R
3241 3502 0.040514 CTGAGGATCTAGCACGCGAG 60.041 60.0 15.93 5.97 34.92 5.03 R
3442 3703 0.996583 TTCCTCCATGTTGGTACCCC 59.003 55.0 10.07 0.00 39.03 4.95 R
4046 4415 1.025812 AACGAAAATTGGTGTGCGGA 58.974 45.0 0.00 0.00 0.00 5.54 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
75 76 2.875672 GCATCTTGCAGTAGGTTGGACA 60.876 50.000 0.00 0.00 44.26 4.02
126 130 7.917505 GGATGGACATTATTACAAAGCAGAAAG 59.082 37.037 0.00 0.00 0.00 2.62
128 132 6.719370 TGGACATTATTACAAAGCAGAAAGGT 59.281 34.615 0.00 0.00 0.00 3.50
129 133 7.885922 TGGACATTATTACAAAGCAGAAAGGTA 59.114 33.333 0.00 0.00 0.00 3.08
131 135 9.937175 GACATTATTACAAAGCAGAAAGGTATC 57.063 33.333 0.00 0.00 0.00 2.24
152 156 3.137544 TCTTGTTCCACTACCAACACCAT 59.862 43.478 0.00 0.00 32.19 3.55
158 162 2.486370 CCACTACCAACACCATCACACA 60.486 50.000 0.00 0.00 0.00 3.72
168 172 3.825585 ACACCATCACACATTGCATTACA 59.174 39.130 0.00 0.00 0.00 2.41
182 186 2.741517 GCATTACAAATTTGTGTGGCCC 59.258 45.455 29.72 13.68 42.31 5.80
209 213 1.069823 CTCTTCAGGATGCAGCCGTAT 59.930 52.381 16.75 0.00 34.76 3.06
212 216 0.313987 TCAGGATGCAGCCGTATACG 59.686 55.000 16.75 18.40 34.76 3.06
228 232 5.946298 CGTATACGGAGAGTGCCAATAATA 58.054 41.667 17.61 0.00 35.37 0.98
271 275 5.479124 AGGAATTGTACACGGTTAGAAGT 57.521 39.130 0.00 0.00 0.00 3.01
280 284 3.572255 ACACGGTTAGAAGTACGGGTTTA 59.428 43.478 0.00 0.00 40.47 2.01
306 310 4.155826 CGTCAAGGTATGGCTGAAAATCAA 59.844 41.667 0.00 0.00 0.00 2.57
307 311 5.335583 CGTCAAGGTATGGCTGAAAATCAAA 60.336 40.000 0.00 0.00 0.00 2.69
308 312 6.095377 GTCAAGGTATGGCTGAAAATCAAAG 58.905 40.000 0.00 0.00 0.00 2.77
323 351 6.408770 AAATCAAAGGAGGAGGGATTAGTT 57.591 37.500 0.00 0.00 0.00 2.24
328 356 2.966516 AGGAGGAGGGATTAGTTAAGCG 59.033 50.000 0.00 0.00 0.00 4.68
465 494 4.380867 GCCCATTTTTCACACCATCTACTG 60.381 45.833 0.00 0.00 0.00 2.74
484 513 4.901927 ACTGGGATAAGGAGAGGAGAAAT 58.098 43.478 0.00 0.00 0.00 2.17
507 536 2.801679 ACAATGCATTTTGTTGCTTCCG 59.198 40.909 9.83 0.00 43.18 4.30
538 567 0.687354 TGAGTCACCTTCAGCCTTCC 59.313 55.000 0.00 0.00 0.00 3.46
560 589 2.159324 GCTAATCTTGGCTTCTTGCACC 60.159 50.000 0.00 0.00 45.15 5.01
570 599 2.154462 CTTCTTGCACCCTCGAACAAT 58.846 47.619 0.00 0.00 0.00 2.71
572 601 2.582052 TCTTGCACCCTCGAACAATTT 58.418 42.857 0.00 0.00 0.00 1.82
573 602 2.955660 TCTTGCACCCTCGAACAATTTT 59.044 40.909 0.00 0.00 0.00 1.82
654 739 2.086054 ACTGTCGCTCACCTTCATTC 57.914 50.000 0.00 0.00 0.00 2.67
671 756 1.878953 TTCGGGACTTGAAGCTTCAC 58.121 50.000 28.46 16.88 36.83 3.18
672 757 0.034896 TCGGGACTTGAAGCTTCACC 59.965 55.000 28.46 24.18 36.83 4.02
673 758 0.955919 CGGGACTTGAAGCTTCACCC 60.956 60.000 30.69 30.69 37.55 4.61
674 759 0.110486 GGGACTTGAAGCTTCACCCA 59.890 55.000 33.40 19.69 39.54 4.51
675 760 1.272147 GGGACTTGAAGCTTCACCCAT 60.272 52.381 33.40 19.67 39.54 4.00
676 761 2.087646 GGACTTGAAGCTTCACCCATC 58.912 52.381 28.46 20.54 36.83 3.51
677 762 2.290577 GGACTTGAAGCTTCACCCATCT 60.291 50.000 28.46 7.45 36.83 2.90
679 764 2.089980 CTTGAAGCTTCACCCATCTGG 58.910 52.381 28.46 7.80 36.83 3.86
693 778 5.041191 CCCATCTGGTTTATAGTTGAGCT 57.959 43.478 0.00 0.00 0.00 4.09
694 779 4.818546 CCCATCTGGTTTATAGTTGAGCTG 59.181 45.833 0.00 0.00 0.00 4.24
698 789 5.876357 TCTGGTTTATAGTTGAGCTGGTTT 58.124 37.500 0.00 0.00 0.00 3.27
878 1014 8.916628 AACCAATAAAAAGTTATTTGCCATGT 57.083 26.923 0.00 0.00 37.75 3.21
909 1045 8.681806 TCCAATCGCATAGAAAATTCACAAATA 58.318 29.630 0.00 0.00 0.00 1.40
1021 1184 2.092291 CACGCGTGTTCGGTAGCAT 61.092 57.895 30.50 0.00 37.56 3.79
1074 1243 1.981256 CAACCTGCCCAACTTGTAGT 58.019 50.000 0.00 0.00 0.00 2.73
1107 1276 3.533606 AATGGATTGGAGAGACAGTCG 57.466 47.619 0.00 0.00 0.00 4.18
1296 1473 2.203015 CCGTTCGGCATCGGGAAT 60.203 61.111 0.00 0.00 42.61 3.01
1428 1611 2.029020 CACGGTGAGAATCTTGGACAGA 60.029 50.000 0.74 0.00 34.92 3.41
1479 1668 3.499737 CTCGATGGCAACGGCACC 61.500 66.667 17.21 0.00 41.84 5.01
1743 1971 1.519455 CGGCGTGGAGATGAAGTCC 60.519 63.158 0.00 0.00 34.31 3.85
1765 1993 0.457853 GGATGCGAGCAACGAGTACA 60.458 55.000 0.57 0.00 45.77 2.90
1851 2079 2.330372 CCTCAACGACTCGACCGGA 61.330 63.158 9.46 0.00 0.00 5.14
1898 2126 1.366366 CCGTCGTCCTGGACTTTGT 59.634 57.895 23.49 0.00 34.75 2.83
2001 2235 2.420568 CCATGCTTCCTGCCGCAAT 61.421 57.895 0.00 0.00 39.89 3.56
2028 2262 1.016130 GCATGTATCGCAGCGGCTAT 61.016 55.000 16.42 3.96 38.10 2.97
2142 2379 4.012895 GAGTGCACCAACACGGCG 62.013 66.667 14.63 4.80 45.45 6.46
2166 2403 4.108299 CACCTATGCCGGTGCCCA 62.108 66.667 1.90 0.00 46.98 5.36
2276 2528 2.608467 GCACAGTTCATGCTCTGTTC 57.392 50.000 16.15 10.43 42.05 3.18
2281 2536 5.233225 CACAGTTCATGCTCTGTTCTAGAA 58.767 41.667 16.15 0.00 42.05 2.10
2282 2537 5.873712 CACAGTTCATGCTCTGTTCTAGAAT 59.126 40.000 8.75 0.00 42.05 2.40
2283 2538 7.038048 CACAGTTCATGCTCTGTTCTAGAATA 58.962 38.462 8.75 4.98 42.05 1.75
2284 2539 7.710044 CACAGTTCATGCTCTGTTCTAGAATAT 59.290 37.037 8.75 0.00 42.05 1.28
2285 2540 7.710044 ACAGTTCATGCTCTGTTCTAGAATATG 59.290 37.037 8.75 1.12 41.33 1.78
2381 2641 1.078567 CAGTGGAGCCAGCCTTCTC 60.079 63.158 0.00 0.00 0.00 2.87
2411 2671 4.223320 ACTTGGTGCTATTTTTGTGACG 57.777 40.909 0.00 0.00 0.00 4.35
2430 2690 0.794605 GCGAAAGATGAAGCAACGGC 60.795 55.000 0.00 0.00 41.61 5.68
2633 2893 1.496060 AAGGCATCATGTCGGACCTA 58.504 50.000 5.55 0.00 0.00 3.08
2795 3055 2.688507 CTGCTGGTGTACGAGTTCATT 58.311 47.619 0.00 0.00 0.00 2.57
2796 3056 2.668457 CTGCTGGTGTACGAGTTCATTC 59.332 50.000 0.00 0.00 0.00 2.67
3179 3440 4.130118 GGAAGAAACCATGCTCATATCGT 58.870 43.478 0.00 0.00 0.00 3.73
3527 3788 1.206878 GGTACCCCCGGTAGTCAATT 58.793 55.000 0.00 0.00 39.02 2.32
3533 3794 5.713760 ACCCCCGGTAGTCAATTTATTTA 57.286 39.130 0.00 0.00 32.11 1.40
3650 3953 5.983720 TCTGAAGGAAACAACGAGACTTAAG 59.016 40.000 0.00 0.00 0.00 1.85
3701 4046 6.145048 GCGTAGTTTTGCTCTGTCTTAAACTA 59.855 38.462 0.00 0.00 39.17 2.24
3766 4111 1.055338 GCAACAGAAATGCAAGCGTC 58.945 50.000 0.00 0.00 43.29 5.19
3769 4114 2.693797 ACAGAAATGCAAGCGTCAAG 57.306 45.000 0.00 0.00 0.00 3.02
3798 4143 7.584987 ACAAAGATGGAACGATACTTTCAAAG 58.415 34.615 0.00 0.00 0.00 2.77
3799 4144 7.228706 ACAAAGATGGAACGATACTTTCAAAGT 59.771 33.333 8.15 8.15 45.40 2.66
3801 4146 7.133891 AGATGGAACGATACTTTCAAAGTTG 57.866 36.000 8.41 1.84 42.81 3.16
3802 4147 6.710744 AGATGGAACGATACTTTCAAAGTTGT 59.289 34.615 8.41 2.49 42.81 3.32
3808 4153 6.962686 ACGATACTTTCAAAGTTGTTTACCC 58.037 36.000 8.41 0.00 42.81 3.69
3826 4171 8.442374 TGTTTACCCCCAAAGATAATATACCTC 58.558 37.037 0.00 0.00 0.00 3.85
3925 4270 9.469807 GAGATGATCACAGTTTCGAATATAACT 57.530 33.333 0.00 0.00 35.06 2.24
3927 4272 8.594881 ATGATCACAGTTTCGAATATAACTCC 57.405 34.615 0.00 0.00 32.50 3.85
3934 4279 9.583765 ACAGTTTCGAATATAACTCCTTTAGAC 57.416 33.333 0.00 0.00 32.50 2.59
3936 4281 8.755977 AGTTTCGAATATAACTCCTTTAGACCA 58.244 33.333 0.00 0.00 28.79 4.02
3965 4310 9.658799 TTAGGAATGTTTCAACAACAATTTGAA 57.341 25.926 2.79 0.00 43.03 2.69
3971 4316 8.484641 TGTTTCAACAACAATTTGAAGCATAA 57.515 26.923 9.44 0.00 44.38 1.90
3972 4317 9.107177 TGTTTCAACAACAATTTGAAGCATAAT 57.893 25.926 9.44 0.00 44.38 1.28
3977 4322 7.656707 ACAACAATTTGAAGCATAATTGGAC 57.343 32.000 2.79 0.00 42.96 4.02
3992 4337 2.198827 TGGACGCAAATTCACCATCT 57.801 45.000 0.00 0.00 0.00 2.90
4002 4347 7.336931 ACGCAAATTCACCATCTAATACTTCTT 59.663 33.333 0.00 0.00 0.00 2.52
4021 4390 8.392372 ACTTCTTTTATGTACCTCTTGGTTTC 57.608 34.615 0.00 0.00 46.05 2.78
4039 4408 3.788227 TTCTCACTGCACCTTTACCAT 57.212 42.857 0.00 0.00 0.00 3.55
4046 4415 2.691526 CTGCACCTTTACCATGATGCAT 59.308 45.455 0.00 0.00 41.83 3.96
4048 4417 2.035066 GCACCTTTACCATGATGCATCC 59.965 50.000 23.67 6.71 33.27 3.51
4063 4432 1.616620 CATCCGCACACCAATTTTCG 58.383 50.000 0.00 0.00 0.00 3.46
4067 4436 1.520590 CCGCACACCAATTTTCGTTTG 59.479 47.619 0.00 0.00 0.00 2.93
4102 4471 7.063308 CCAATGCATTGTTGTAGTTGGTTAATC 59.937 37.037 31.87 0.00 36.06 1.75
4103 4472 6.641169 TGCATTGTTGTAGTTGGTTAATCA 57.359 33.333 0.00 0.00 0.00 2.57
4104 4473 7.225784 TGCATTGTTGTAGTTGGTTAATCAT 57.774 32.000 0.00 0.00 0.00 2.45
4105 4474 7.665690 TGCATTGTTGTAGTTGGTTAATCATT 58.334 30.769 0.00 0.00 0.00 2.57
4106 4475 8.147058 TGCATTGTTGTAGTTGGTTAATCATTT 58.853 29.630 0.00 0.00 0.00 2.32
4107 4476 9.632807 GCATTGTTGTAGTTGGTTAATCATTTA 57.367 29.630 0.00 0.00 0.00 1.40
4111 4480 9.562408 TGTTGTAGTTGGTTAATCATTTACAGA 57.438 29.630 10.77 3.26 0.00 3.41
4113 4482 8.786826 TGTAGTTGGTTAATCATTTACAGAGG 57.213 34.615 8.13 0.00 0.00 3.69
4114 4483 6.759497 AGTTGGTTAATCATTTACAGAGGC 57.241 37.500 0.00 0.00 0.00 4.70
4115 4484 6.485171 AGTTGGTTAATCATTTACAGAGGCT 58.515 36.000 0.00 0.00 0.00 4.58
4116 4485 6.599638 AGTTGGTTAATCATTTACAGAGGCTC 59.400 38.462 6.34 6.34 0.00 4.70
4117 4486 5.437060 TGGTTAATCATTTACAGAGGCTCC 58.563 41.667 11.71 0.00 0.00 4.70
4118 4487 5.191722 TGGTTAATCATTTACAGAGGCTCCT 59.808 40.000 11.71 0.00 0.00 3.69
4119 4488 5.760743 GGTTAATCATTTACAGAGGCTCCTC 59.239 44.000 11.71 7.84 43.03 3.71
4120 4489 3.742433 ATCATTTACAGAGGCTCCTCG 57.258 47.619 11.71 2.55 46.90 4.63
4121 4490 2.735151 TCATTTACAGAGGCTCCTCGA 58.265 47.619 11.71 0.00 46.90 4.04
4122 4491 3.096852 TCATTTACAGAGGCTCCTCGAA 58.903 45.455 11.71 2.17 46.90 3.71
4123 4492 3.513912 TCATTTACAGAGGCTCCTCGAAA 59.486 43.478 11.71 11.60 46.90 3.46
4124 4493 4.020573 TCATTTACAGAGGCTCCTCGAAAA 60.021 41.667 11.71 11.45 46.90 2.29
4125 4494 4.345859 TTTACAGAGGCTCCTCGAAAAA 57.654 40.909 11.71 8.75 46.90 1.94
4188 4557 5.747951 AGTAATTGCTTCTATTGCAGAGC 57.252 39.130 0.00 0.00 41.71 4.09
4231 4600 5.297776 AGAAACAACCTGTTGATGAGTTCAG 59.702 40.000 16.41 0.00 40.14 3.02
4234 4603 4.576463 ACAACCTGTTGATGAGTTCAGAAC 59.424 41.667 16.41 5.00 42.93 3.01
4235 4604 3.393800 ACCTGTTGATGAGTTCAGAACG 58.606 45.455 7.68 0.00 35.27 3.95
4238 4607 3.390135 TGTTGATGAGTTCAGAACGGAC 58.610 45.455 7.68 4.75 35.27 4.79
4242 4611 5.400066 TGATGAGTTCAGAACGGACATAA 57.600 39.130 17.27 11.31 36.23 1.90
4285 4655 9.178758 ACTTAATTATTTGGAACAGATCACTCC 57.821 33.333 0.00 0.00 42.39 3.85
4389 4763 3.440173 GCTACAGCTTACAAGATTTGGCA 59.560 43.478 0.00 0.00 38.21 4.92
4390 4764 4.096984 GCTACAGCTTACAAGATTTGGCAT 59.903 41.667 0.00 0.00 38.21 4.40
4391 4765 5.393461 GCTACAGCTTACAAGATTTGGCATT 60.393 40.000 0.00 0.00 38.21 3.56
4394 4768 4.624024 CAGCTTACAAGATTTGGCATTGTG 59.376 41.667 13.06 0.82 37.69 3.33
4395 4769 4.281688 AGCTTACAAGATTTGGCATTGTGT 59.718 37.500 13.06 5.11 37.69 3.72
4396 4770 4.990426 GCTTACAAGATTTGGCATTGTGTT 59.010 37.500 13.06 0.00 37.69 3.32
4397 4771 5.107375 GCTTACAAGATTTGGCATTGTGTTG 60.107 40.000 13.06 8.10 37.69 3.33
4398 4772 3.132925 ACAAGATTTGGCATTGTGTTGC 58.867 40.909 3.54 0.00 42.01 4.17
4451 5209 5.123820 GCATTGTGTTGCTATAACTGGAGAA 59.876 40.000 0.00 0.00 39.57 2.87
4453 5211 6.741992 TTGTGTTGCTATAACTGGAGAATG 57.258 37.500 0.00 0.00 0.00 2.67
4454 5212 5.185454 TGTGTTGCTATAACTGGAGAATGG 58.815 41.667 0.00 0.00 0.00 3.16
4472 5230 0.179163 GGCGCCTTTGCACACTAATC 60.179 55.000 22.15 0.00 37.32 1.75
4490 5248 6.757010 CACTAATCTGTAATTGCTAGGACGTT 59.243 38.462 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.562143 GCAAGATGCCAGGATTCAAAAGTT 60.562 41.667 0.00 0.00 37.42 2.66
41 42 3.056393 TGCAAGATGCCAGGATTCAAAAG 60.056 43.478 0.00 0.00 44.23 2.27
44 45 2.097036 CTGCAAGATGCCAGGATTCAA 58.903 47.619 0.00 0.00 44.23 2.69
126 130 4.694037 GTGTTGGTAGTGGAACAAGATACC 59.306 45.833 0.00 0.00 44.16 2.73
128 132 4.348461 TGGTGTTGGTAGTGGAACAAGATA 59.652 41.667 0.00 0.00 44.16 1.98
129 133 3.137544 TGGTGTTGGTAGTGGAACAAGAT 59.862 43.478 0.00 0.00 44.16 2.40
131 135 2.925724 TGGTGTTGGTAGTGGAACAAG 58.074 47.619 0.00 0.00 44.16 3.16
152 156 7.175073 CACAAATTTGTAATGCAATGTGTGA 57.825 32.000 22.87 0.00 41.22 3.58
158 162 4.455190 GGCCACACAAATTTGTAATGCAAT 59.545 37.500 22.87 0.00 39.91 3.56
209 213 5.382616 TCTCTATTATTGGCACTCTCCGTA 58.617 41.667 0.00 0.00 0.00 4.02
212 216 5.563867 CGTCTCTCTATTATTGGCACTCTCC 60.564 48.000 0.00 0.00 0.00 3.71
213 217 5.457140 CGTCTCTCTATTATTGGCACTCTC 58.543 45.833 0.00 0.00 0.00 3.20
228 232 1.838715 TCCTAGGTGTAGCGTCTCTCT 59.161 52.381 9.08 0.00 0.00 3.10
256 260 2.488153 ACCCGTACTTCTAACCGTGTAC 59.512 50.000 0.00 0.00 33.89 2.90
261 265 4.415735 GTCTAAACCCGTACTTCTAACCG 58.584 47.826 0.00 0.00 0.00 4.44
271 275 2.238521 ACCTTGACGTCTAAACCCGTA 58.761 47.619 17.92 0.00 37.44 4.02
280 284 1.557099 TCAGCCATACCTTGACGTCT 58.443 50.000 17.92 0.00 0.00 4.18
306 310 3.388350 CGCTTAACTAATCCCTCCTCCTT 59.612 47.826 0.00 0.00 0.00 3.36
307 311 2.966516 CGCTTAACTAATCCCTCCTCCT 59.033 50.000 0.00 0.00 0.00 3.69
308 312 2.963782 TCGCTTAACTAATCCCTCCTCC 59.036 50.000 0.00 0.00 0.00 4.30
323 351 5.128827 ACTTATTGACCCATCTCTTCGCTTA 59.871 40.000 0.00 0.00 0.00 3.09
439 468 0.387202 TGGTGTGAAAAATGGGCACG 59.613 50.000 0.00 0.00 35.37 5.34
465 494 6.749036 TGTTATTTCTCCTCTCCTTATCCC 57.251 41.667 0.00 0.00 0.00 3.85
507 536 1.906824 TGACTCAGGGTCCGGTGAC 60.907 63.158 0.00 0.00 43.89 3.67
522 551 2.035442 GCGGAAGGCTGAAGGTGAC 61.035 63.158 0.00 0.00 39.11 3.67
538 567 1.739466 TGCAAGAAGCCAAGATTAGCG 59.261 47.619 0.00 0.00 44.83 4.26
549 578 0.884704 TGTTCGAGGGTGCAAGAAGC 60.885 55.000 0.00 0.00 45.96 3.86
654 739 0.955919 GGGTGAAGCTTCAAGTCCCG 60.956 60.000 28.42 0.00 39.21 5.14
671 756 4.818546 CAGCTCAACTATAAACCAGATGGG 59.181 45.833 3.48 0.00 44.81 4.00
672 757 4.818546 CCAGCTCAACTATAAACCAGATGG 59.181 45.833 0.00 0.00 42.17 3.51
673 758 5.431765 ACCAGCTCAACTATAAACCAGATG 58.568 41.667 0.00 0.00 0.00 2.90
674 759 5.700402 ACCAGCTCAACTATAAACCAGAT 57.300 39.130 0.00 0.00 0.00 2.90
675 760 5.499004 AACCAGCTCAACTATAAACCAGA 57.501 39.130 0.00 0.00 0.00 3.86
676 761 7.308782 CTAAACCAGCTCAACTATAAACCAG 57.691 40.000 0.00 0.00 0.00 4.00
694 779 0.323957 AGGACCGGTTCAGCTAAACC 59.676 55.000 17.22 8.95 44.40 3.27
698 789 1.255667 GGTGAGGACCGGTTCAGCTA 61.256 60.000 24.55 3.20 38.45 3.32
865 1001 6.400940 CGATTGGAAAACACATGGCAAATAAC 60.401 38.462 0.00 0.00 0.00 1.89
878 1014 7.328249 GTGAATTTTCTATGCGATTGGAAAACA 59.672 33.333 10.10 4.60 39.42 2.83
916 1052 9.770097 CCATTGTATCTACATTCTCACATTACT 57.230 33.333 0.00 0.00 35.89 2.24
917 1053 9.547753 ACCATTGTATCTACATTCTCACATTAC 57.452 33.333 0.00 0.00 35.89 1.89
921 1057 9.952030 TTTTACCATTGTATCTACATTCTCACA 57.048 29.630 0.00 0.00 35.89 3.58
953 1106 6.715718 TGGTCTAGGCTACACAGAGATATAAC 59.284 42.308 2.33 0.00 0.00 1.89
1021 1184 2.098607 CGCAACCTACCGTGATAGAGAA 59.901 50.000 0.00 0.00 0.00 2.87
1107 1276 0.390735 ATACCAGCCGGTTGTTCGAC 60.391 55.000 17.69 0.00 46.31 4.20
1363 1540 3.842923 CTGGAGGTCGCTGCCGAT 61.843 66.667 0.00 0.00 46.38 4.18
1428 1611 3.255397 AGCTTGACCTGGCCTGCT 61.255 61.111 3.32 0.00 0.00 4.24
1743 1971 2.125552 TCGTTGCTCGCATCCAGG 60.126 61.111 0.00 0.00 39.67 4.45
1765 1993 4.101448 GATGGGCAGCCTGTCGGT 62.101 66.667 12.43 0.00 0.00 4.69
1791 2019 0.110678 ACCATCCTCTCTCGGCGATA 59.889 55.000 11.27 1.34 0.00 2.92
1875 2103 4.988716 TCCAGGACGACGGGCACT 62.989 66.667 0.00 0.00 34.03 4.40
1898 2126 2.354729 CCGGCTTGGAATCCACCA 59.645 61.111 0.00 0.00 42.00 4.17
2001 2235 1.067416 GCGATACATGCCGGAGACA 59.933 57.895 5.05 0.00 0.00 3.41
2142 2379 2.808206 CCGGCATAGGTGTCCTCCC 61.808 68.421 0.00 0.00 34.61 4.30
2276 2528 8.514594 CAAGGAAGAGTCTCTAGCATATTCTAG 58.485 40.741 1.88 3.23 37.87 2.43
2281 2536 8.802267 GTTATCAAGGAAGAGTCTCTAGCATAT 58.198 37.037 1.88 0.00 0.00 1.78
2282 2537 7.780271 TGTTATCAAGGAAGAGTCTCTAGCATA 59.220 37.037 1.88 0.00 0.00 3.14
2283 2538 6.609212 TGTTATCAAGGAAGAGTCTCTAGCAT 59.391 38.462 1.88 0.00 0.00 3.79
2284 2539 5.952347 TGTTATCAAGGAAGAGTCTCTAGCA 59.048 40.000 1.88 0.00 0.00 3.49
2285 2540 6.458232 TGTTATCAAGGAAGAGTCTCTAGC 57.542 41.667 1.88 0.00 0.00 3.42
2381 2641 3.845781 ATAGCACCAAGTACCATGAGG 57.154 47.619 0.00 0.00 42.21 3.86
2411 2671 0.794605 GCCGTTGCTTCATCTTTCGC 60.795 55.000 0.00 0.00 33.53 4.70
2633 2893 0.246360 TCTTGATCGCCACGACATGT 59.754 50.000 0.00 0.00 39.18 3.21
2796 3056 0.623324 TGGTAGAGGGTCCCATTGGG 60.623 60.000 16.26 16.26 46.11 4.12
2856 3116 1.269778 TGCGATCCTTAGCCGATCTTG 60.270 52.381 0.00 0.00 35.06 3.02
2894 3154 1.226717 CGAGTGAAGGTAGCCGAGC 60.227 63.158 0.00 0.00 0.00 5.03
3179 3440 0.909623 GGGTTTCCTCCTCGGATGAA 59.090 55.000 0.29 0.29 42.70 2.57
3241 3502 0.040514 CTGAGGATCTAGCACGCGAG 60.041 60.000 15.93 5.97 34.92 5.03
3371 3632 2.677848 GAGCCCCCAAGGTTCTCC 59.322 66.667 0.00 0.00 42.45 3.71
3442 3703 0.996583 TTCCTCCATGTTGGTACCCC 59.003 55.000 10.07 0.00 39.03 4.95
3449 3710 1.962807 TGGCTTGTTTCCTCCATGTTG 59.037 47.619 0.00 0.00 0.00 3.33
3533 3794 9.985730 ATTGTCAAATTAAACTGATCACACAAT 57.014 25.926 0.00 0.00 0.00 2.71
3650 3953 7.865706 ACTTCAAAAGGTATGGACACATATC 57.134 36.000 0.00 0.00 41.34 1.63
3766 4111 7.584987 AGTATCGTTCCATCTTTGTTTTCTTG 58.415 34.615 0.00 0.00 0.00 3.02
3769 4114 8.073768 TGAAAGTATCGTTCCATCTTTGTTTTC 58.926 33.333 0.00 0.00 0.00 2.29
3798 4143 8.853126 GGTATATTATCTTTGGGGGTAAACAAC 58.147 37.037 0.00 0.00 0.00 3.32
3799 4144 8.793720 AGGTATATTATCTTTGGGGGTAAACAA 58.206 33.333 0.00 0.00 0.00 2.83
3801 4146 8.666821 AGAGGTATATTATCTTTGGGGGTAAAC 58.333 37.037 0.00 0.00 0.00 2.01
3802 4147 8.823810 AGAGGTATATTATCTTTGGGGGTAAA 57.176 34.615 0.00 0.00 0.00 2.01
3836 4181 9.908152 GCCTACTTTTGTTGTGTTAATAGAAAT 57.092 29.630 0.00 0.00 0.00 2.17
3837 4182 8.904834 TGCCTACTTTTGTTGTGTTAATAGAAA 58.095 29.630 0.00 0.00 0.00 2.52
3838 4183 8.453238 TGCCTACTTTTGTTGTGTTAATAGAA 57.547 30.769 0.00 0.00 0.00 2.10
3839 4184 8.630054 ATGCCTACTTTTGTTGTGTTAATAGA 57.370 30.769 0.00 0.00 0.00 1.98
3840 4185 9.341899 GAATGCCTACTTTTGTTGTGTTAATAG 57.658 33.333 0.00 0.00 0.00 1.73
3841 4186 9.073475 AGAATGCCTACTTTTGTTGTGTTAATA 57.927 29.630 0.00 0.00 0.00 0.98
3891 4236 6.454848 CGAAACTGTGATCATCTCTAAACTGC 60.455 42.308 0.00 0.00 0.00 4.40
3925 4270 4.529377 ACATTCCTAACGTGGTCTAAAGGA 59.471 41.667 0.00 0.00 0.00 3.36
3927 4272 6.425721 TGAAACATTCCTAACGTGGTCTAAAG 59.574 38.462 0.00 0.00 0.00 1.85
3931 4276 4.345859 TGAAACATTCCTAACGTGGTCT 57.654 40.909 0.00 0.00 0.00 3.85
3934 4279 4.822036 TGTTGAAACATTCCTAACGTGG 57.178 40.909 0.00 0.00 33.17 4.94
3936 4281 5.821516 TGTTGTTGAAACATTCCTAACGT 57.178 34.783 0.00 0.00 38.95 3.99
3965 4310 4.423732 GTGAATTTGCGTCCAATTATGCT 58.576 39.130 0.00 0.00 32.39 3.79
3968 4313 5.360714 AGATGGTGAATTTGCGTCCAATTAT 59.639 36.000 0.00 0.00 0.00 1.28
3971 4316 3.091545 AGATGGTGAATTTGCGTCCAAT 58.908 40.909 0.00 0.00 0.00 3.16
3972 4317 2.513753 AGATGGTGAATTTGCGTCCAA 58.486 42.857 0.00 0.00 0.00 3.53
3977 4322 7.251704 AGAAGTATTAGATGGTGAATTTGCG 57.748 36.000 0.00 0.00 0.00 4.85
4021 4390 3.057969 TCATGGTAAAGGTGCAGTGAG 57.942 47.619 0.00 0.00 0.00 3.51
4046 4415 1.025812 AACGAAAATTGGTGTGCGGA 58.974 45.000 0.00 0.00 0.00 5.54
4048 4417 2.189342 ACAAACGAAAATTGGTGTGCG 58.811 42.857 0.00 0.00 28.33 5.34
4067 4436 1.340889 ACAATGCATTGGTGTGGTGAC 59.659 47.619 35.85 0.00 41.96 3.67
4102 4471 3.526931 TTCGAGGAGCCTCTGTAAATG 57.473 47.619 14.19 0.00 40.69 2.32
4103 4472 4.553330 TTTTCGAGGAGCCTCTGTAAAT 57.447 40.909 14.19 0.00 40.69 1.40
4104 4473 4.345859 TTTTTCGAGGAGCCTCTGTAAA 57.654 40.909 14.19 10.56 40.69 2.01
4125 4494 4.996758 GGCAATGCCTCAGTAAATGTTTTT 59.003 37.500 18.47 0.00 46.69 1.94
4126 4495 4.568956 GGCAATGCCTCAGTAAATGTTTT 58.431 39.130 18.47 0.00 46.69 2.43
4127 4496 4.192429 GGCAATGCCTCAGTAAATGTTT 57.808 40.909 18.47 0.00 46.69 2.83
4128 4497 3.874392 GGCAATGCCTCAGTAAATGTT 57.126 42.857 18.47 0.00 46.69 2.71
4156 4525 4.430908 AGAAGCAATTACTACTGGCGTAC 58.569 43.478 0.00 0.00 0.00 3.67
4160 4529 5.296780 TGCAATAGAAGCAATTACTACTGGC 59.703 40.000 0.00 0.00 39.39 4.85
4264 4634 9.293404 CATATGGAGTGATCTGTTCCAAATAAT 57.707 33.333 14.49 4.24 43.69 1.28
4285 4655 7.442062 TCCTGCATAATGTGTAGTGAACATATG 59.558 37.037 0.00 0.00 38.83 1.78
4288 4658 5.744171 TCCTGCATAATGTGTAGTGAACAT 58.256 37.500 0.00 0.00 41.10 2.71
4389 4763 5.426504 TCAATGTGAAAAAGGCAACACAAT 58.573 33.333 0.00 0.00 44.36 2.71
4390 4764 4.825422 TCAATGTGAAAAAGGCAACACAA 58.175 34.783 0.00 0.00 44.36 3.33
4391 4765 4.462508 TCAATGTGAAAAAGGCAACACA 57.537 36.364 0.00 0.00 45.06 3.72
4472 5230 6.903883 ATGTTAACGTCCTAGCAATTACAG 57.096 37.500 0.26 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.