Multiple sequence alignment - TraesCS2A01G108100

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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 TraesCS2A01G108100 chr2A 100.000 3251 0 0 1 3251 60080424 60077174 0.000000e+00 6004
1 TraesCS2A01G108100 chr2A 95.629 572 17 1 1 564 669580380 669580951 0.000000e+00 911
2 TraesCS2A01G108100 chr2A 84.856 766 71 24 1593 2330 60068786 60068038 0.000000e+00 730
3 TraesCS2A01G108100 chr2A 82.991 682 101 15 815 1491 60069549 60068878 1.290000e-168 603
4 TraesCS2A01G108100 chr2A 87.778 540 30 14 2716 3251 761192982 761193489 1.670000e-167 599
5 TraesCS2A01G108100 chr2A 85.195 385 57 0 1868 2252 59873115 59872731 2.350000e-106 396
6 TraesCS2A01G108100 chr2A 84.715 386 57 2 1868 2252 59933142 59932758 5.090000e-103 385
7 TraesCS2A01G108100 chr2A 87.805 205 23 2 1290 1493 60760252 60760049 4.190000e-59 239
8 TraesCS2A01G108100 chr2A 83.945 218 31 4 1004 1218 59587320 59587536 4.250000e-49 206
9 TraesCS2A01G108100 chr2A 84.390 205 30 2 1007 1210 59880740 59880537 1.980000e-47 200
10 TraesCS2A01G108100 chr2A 83.902 205 31 2 1007 1210 59943412 59943209 9.200000e-46 195
11 TraesCS2A01G108100 chr2A 82.738 168 27 2 1044 1210 60195771 60195605 7.270000e-32 148
12 TraesCS2A01G108100 chr2B 89.162 1301 94 34 561 1838 93805459 93804183 0.000000e+00 1578
13 TraesCS2A01G108100 chr2B 89.162 1301 94 34 561 1838 93883496 93882220 0.000000e+00 1578
14 TraesCS2A01G108100 chr2B 85.214 771 71 24 1591 2341 93711999 93711252 0.000000e+00 752
15 TraesCS2A01G108100 chr2B 92.100 481 34 1 1850 2330 93804141 93803665 0.000000e+00 675
16 TraesCS2A01G108100 chr2B 92.100 481 34 1 1850 2330 93882178 93881702 0.000000e+00 675
17 TraesCS2A01G108100 chr2B 85.263 380 56 0 1868 2247 93638531 93638152 3.040000e-105 392
18 TraesCS2A01G108100 chr2B 80.440 409 65 13 819 1222 93714172 93713774 6.820000e-77 298
19 TraesCS2A01G108100 chr2B 88.780 205 21 2 1290 1493 94089910 94089707 1.940000e-62 250
20 TraesCS2A01G108100 chr2B 87.317 205 24 2 1290 1493 94099324 94099121 1.950000e-57 233
21 TraesCS2A01G108100 chr2B 89.116 147 14 2 2476 2622 93803509 93803365 7.170000e-42 182
22 TraesCS2A01G108100 chr2D 91.043 1150 69 13 1261 2400 60079087 60077962 0.000000e+00 1522
23 TraesCS2A01G108100 chr2D 94.895 666 33 1 561 1225 60079828 60079163 0.000000e+00 1040
24 TraesCS2A01G108100 chr2D 84.709 824 84 21 1591 2400 60064777 60063982 0.000000e+00 785
25 TraesCS2A01G108100 chr2D 80.144 695 78 34 815 1492 60065531 60064880 6.350000e-127 464
26 TraesCS2A01G108100 chr2D 85.366 205 28 2 1290 1493 60166994 60166791 9.140000e-51 211
27 TraesCS2A01G108100 chr7A 96.250 560 21 0 1 560 706166773 706167332 0.000000e+00 918
28 TraesCS2A01G108100 chr6A 95.775 568 17 1 1 561 588090073 588090640 0.000000e+00 909
29 TraesCS2A01G108100 chr6A 90.924 606 42 11 2641 3239 501235677 501235078 0.000000e+00 802
30 TraesCS2A01G108100 chr6A 90.415 626 33 9 2641 3243 52815033 52814412 0.000000e+00 798
31 TraesCS2A01G108100 chr3A 95.478 575 17 4 1 567 694492802 694493375 0.000000e+00 909
32 TraesCS2A01G108100 chr3A 95.398 565 22 2 1 561 713028264 713028828 0.000000e+00 896
33 TraesCS2A01G108100 chr3A 81.353 606 70 25 2641 3238 677841166 677840596 1.380000e-123 453
34 TraesCS2A01G108100 chr3A 80.542 627 77 28 2642 3238 617009194 617008583 1.070000e-119 440
35 TraesCS2A01G108100 chr5A 95.599 568 17 1 1 560 676328862 676328295 0.000000e+00 904
36 TraesCS2A01G108100 chr5A 95.599 568 17 4 1 560 699372659 699372092 0.000000e+00 904
37 TraesCS2A01G108100 chr5A 95.722 561 23 1 1 561 51939178 51939737 0.000000e+00 902
38 TraesCS2A01G108100 chr1A 95.423 568 17 5 1 560 507679429 507679995 0.000000e+00 896
39 TraesCS2A01G108100 chr7B 85.957 648 47 24 2641 3251 725391009 725391649 0.000000e+00 652
40 TraesCS2A01G108100 chr1D 86.120 598 64 10 2641 3234 35781803 35782385 7.660000e-176 627
41 TraesCS2A01G108100 chr6D 84.793 651 49 18 2641 3251 289632778 289632138 2.770000e-170 608
42 TraesCS2A01G108100 chr7D 86.916 535 62 8 2641 3172 579634207 579634736 7.770000e-166 593
43 TraesCS2A01G108100 chr6B 83.993 606 58 25 2641 3240 136791322 136790750 2.210000e-151 545


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 TraesCS2A01G108100 chr2A 60077174 60080424 3250 True 6004.000000 6004 100.0000 1 3251 1 chr2A.!!$R5 3250
1 TraesCS2A01G108100 chr2A 669580380 669580951 571 False 911.000000 911 95.6290 1 564 1 chr2A.!!$F2 563
2 TraesCS2A01G108100 chr2A 60068038 60069549 1511 True 666.500000 730 83.9235 815 2330 2 chr2A.!!$R8 1515
3 TraesCS2A01G108100 chr2A 761192982 761193489 507 False 599.000000 599 87.7780 2716 3251 1 chr2A.!!$F3 535
4 TraesCS2A01G108100 chr2B 93881702 93883496 1794 True 1126.500000 1578 90.6310 561 2330 2 chr2B.!!$R6 1769
5 TraesCS2A01G108100 chr2B 93803365 93805459 2094 True 811.666667 1578 90.1260 561 2622 3 chr2B.!!$R5 2061
6 TraesCS2A01G108100 chr2B 93711252 93714172 2920 True 525.000000 752 82.8270 819 2341 2 chr2B.!!$R4 1522
7 TraesCS2A01G108100 chr2D 60077962 60079828 1866 True 1281.000000 1522 92.9690 561 2400 2 chr2D.!!$R3 1839
8 TraesCS2A01G108100 chr2D 60063982 60065531 1549 True 624.500000 785 82.4265 815 2400 2 chr2D.!!$R2 1585
9 TraesCS2A01G108100 chr7A 706166773 706167332 559 False 918.000000 918 96.2500 1 560 1 chr7A.!!$F1 559
10 TraesCS2A01G108100 chr6A 588090073 588090640 567 False 909.000000 909 95.7750 1 561 1 chr6A.!!$F1 560
11 TraesCS2A01G108100 chr6A 501235078 501235677 599 True 802.000000 802 90.9240 2641 3239 1 chr6A.!!$R2 598
12 TraesCS2A01G108100 chr6A 52814412 52815033 621 True 798.000000 798 90.4150 2641 3243 1 chr6A.!!$R1 602
13 TraesCS2A01G108100 chr3A 694492802 694493375 573 False 909.000000 909 95.4780 1 567 1 chr3A.!!$F1 566
14 TraesCS2A01G108100 chr3A 713028264 713028828 564 False 896.000000 896 95.3980 1 561 1 chr3A.!!$F2 560
15 TraesCS2A01G108100 chr3A 677840596 677841166 570 True 453.000000 453 81.3530 2641 3238 1 chr3A.!!$R2 597
16 TraesCS2A01G108100 chr3A 617008583 617009194 611 True 440.000000 440 80.5420 2642 3238 1 chr3A.!!$R1 596
17 TraesCS2A01G108100 chr5A 676328295 676328862 567 True 904.000000 904 95.5990 1 560 1 chr5A.!!$R1 559
18 TraesCS2A01G108100 chr5A 699372092 699372659 567 True 904.000000 904 95.5990 1 560 1 chr5A.!!$R2 559
19 TraesCS2A01G108100 chr5A 51939178 51939737 559 False 902.000000 902 95.7220 1 561 1 chr5A.!!$F1 560
20 TraesCS2A01G108100 chr1A 507679429 507679995 566 False 896.000000 896 95.4230 1 560 1 chr1A.!!$F1 559
21 TraesCS2A01G108100 chr7B 725391009 725391649 640 False 652.000000 652 85.9570 2641 3251 1 chr7B.!!$F1 610
22 TraesCS2A01G108100 chr1D 35781803 35782385 582 False 627.000000 627 86.1200 2641 3234 1 chr1D.!!$F1 593
23 TraesCS2A01G108100 chr6D 289632138 289632778 640 True 608.000000 608 84.7930 2641 3251 1 chr6D.!!$R1 610
24 TraesCS2A01G108100 chr7D 579634207 579634736 529 False 593.000000 593 86.9160 2641 3172 1 chr7D.!!$F1 531
25 TraesCS2A01G108100 chr6B 136790750 136791322 572 True 545.000000 545 83.9930 2641 3240 1 chr6B.!!$R1 599

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
439 448 0.110295 CGGGATCAATGGCCCACATA 59.890 55.0 0.0 0.0 44.94 2.29 F
1521 2654 0.174389 AGCTCTCATGCACGTACTGG 59.826 55.0 0.0 0.0 34.99 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 3088 0.250901 CACCCAGCTGCTTGGTAAGT 60.251 55.0 23.28 8.42 36.45 2.24 R
2607 4221 0.178924 ATTTGGCCCTGAAACCAGCT 60.179 50.0 0.00 0.00 37.24 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
261 270 2.615447 CGCGAGCGAGGGGTATATATAA 59.385 50.000 12.58 0.00 42.83 0.98
296 305 1.003839 GGTTGGTGACATGAGCCGA 60.004 57.895 0.00 0.00 42.32 5.54
307 316 1.757118 CATGAGCCGAGACTAAAGGGA 59.243 52.381 0.00 0.00 0.00 4.20
437 446 1.644437 ATCGGGATCAATGGCCCACA 61.644 55.000 0.00 0.00 44.94 4.17
439 448 0.110295 CGGGATCAATGGCCCACATA 59.890 55.000 0.00 0.00 44.94 2.29
478 487 0.533491 CTCACGAACCGGGACCAATA 59.467 55.000 6.32 0.00 32.99 1.90
591 601 5.852827 TCGAACTGACCATATGCAATCATA 58.147 37.500 0.00 0.00 39.31 2.15
647 657 0.458197 TGCGCCAATAATGCAGTTGC 60.458 50.000 4.18 0.00 42.50 4.17
662 672 4.519612 TGCTGCTGGTGTTGGCCA 62.520 61.111 0.00 0.00 36.97 5.36
737 747 1.666189 GAGAACGTTCCATGCTAAGCC 59.334 52.381 24.22 0.00 0.00 4.35
739 749 1.398390 GAACGTTCCATGCTAAGCCTG 59.602 52.381 17.68 0.00 0.00 4.85
745 755 1.027357 CCATGCTAAGCCTGCGAATT 58.973 50.000 0.00 0.00 0.00 2.17
758 769 4.436317 GCCTGCGAATTGTATTCGTTTGTA 60.436 41.667 19.27 4.93 43.24 2.41
778 789 1.369983 AGGGTATCCTTTCTCCAGGGT 59.630 52.381 0.00 0.00 41.56 4.34
810 821 1.607628 ACATGTCCGCTAGTATCGTCC 59.392 52.381 0.00 0.00 0.00 4.79
813 824 0.592148 GTCCGCTAGTATCGTCCCTG 59.408 60.000 0.00 0.00 0.00 4.45
1226 1258 3.939592 GCAAGTCCCATAACCTTACTCAC 59.060 47.826 0.00 0.00 0.00 3.51
1227 1259 4.181578 CAAGTCCCATAACCTTACTCACG 58.818 47.826 0.00 0.00 0.00 4.35
1230 1262 2.498481 TCCCATAACCTTACTCACGTGG 59.502 50.000 17.00 9.11 0.00 4.94
1258 1336 4.676924 ACGCTGTAAAAGACGTTAGTACAC 59.323 41.667 0.00 0.00 35.90 2.90
1405 2533 3.807622 ACGTCATCGACAACATCAAAACT 59.192 39.130 0.00 0.00 40.62 2.66
1435 2563 2.534019 CGTGTGCAAGCAGACCGTT 61.534 57.895 15.47 0.00 36.96 4.44
1514 2647 3.249559 GGCAATTACTAGCTCTCATGCAC 59.750 47.826 0.00 0.00 34.37 4.57
1518 2651 2.853731 ACTAGCTCTCATGCACGTAC 57.146 50.000 0.00 0.00 34.99 3.67
1521 2654 0.174389 AGCTCTCATGCACGTACTGG 59.826 55.000 0.00 0.00 34.99 4.00
1531 2664 4.063967 CGTACTGGTGCTGCCGGA 62.064 66.667 5.05 0.00 46.81 5.14
1549 2682 4.169696 CCAGCGACGCCCCCATAA 62.170 66.667 17.79 0.00 0.00 1.90
1550 2683 2.895372 CAGCGACGCCCCCATAAC 60.895 66.667 17.79 0.00 0.00 1.89
1551 2684 3.081409 AGCGACGCCCCCATAACT 61.081 61.111 17.79 0.00 0.00 2.24
1557 3064 1.483415 GACGCCCCCATAACTAACTGA 59.517 52.381 0.00 0.00 0.00 3.41
1577 3084 5.073144 ACTGAGGTTTGGAACTAATTCTGGA 59.927 40.000 0.00 0.00 34.98 3.86
1580 3087 5.892348 AGGTTTGGAACTAATTCTGGACAT 58.108 37.500 0.00 0.00 34.98 3.06
1581 3088 7.027874 AGGTTTGGAACTAATTCTGGACATA 57.972 36.000 0.00 0.00 34.98 2.29
1582 3089 6.884836 AGGTTTGGAACTAATTCTGGACATAC 59.115 38.462 0.00 0.00 34.98 2.39
1583 3090 6.884836 GGTTTGGAACTAATTCTGGACATACT 59.115 38.462 0.00 0.00 34.98 2.12
1623 3130 2.872038 GCCGACATGGACTGTTCTTCTT 60.872 50.000 0.00 0.00 42.00 2.52
1780 3295 4.710375 CAGGTACACCCCGCTAATATCTAT 59.290 45.833 0.00 0.00 36.42 1.98
1781 3296 4.710375 AGGTACACCCCGCTAATATCTATG 59.290 45.833 0.00 0.00 36.42 2.23
1782 3297 3.611766 ACACCCCGCTAATATCTATGC 57.388 47.619 0.00 0.00 0.00 3.14
1783 3298 2.903784 ACACCCCGCTAATATCTATGCA 59.096 45.455 0.00 0.00 0.00 3.96
1784 3299 3.519510 ACACCCCGCTAATATCTATGCAT 59.480 43.478 3.79 3.79 0.00 3.96
1785 3300 3.873361 CACCCCGCTAATATCTATGCATG 59.127 47.826 10.16 0.00 0.00 4.06
1787 3302 4.141846 ACCCCGCTAATATCTATGCATGAG 60.142 45.833 10.16 3.20 0.00 2.90
1789 3304 5.423015 CCCGCTAATATCTATGCATGAGTT 58.577 41.667 10.16 7.02 0.00 3.01
1790 3305 5.521735 CCCGCTAATATCTATGCATGAGTTC 59.478 44.000 10.16 0.00 0.00 3.01
1791 3306 6.336566 CCGCTAATATCTATGCATGAGTTCT 58.663 40.000 10.16 0.00 0.00 3.01
1792 3307 6.475076 CCGCTAATATCTATGCATGAGTTCTC 59.525 42.308 10.16 0.00 0.00 2.87
1793 3308 7.257003 CGCTAATATCTATGCATGAGTTCTCT 58.743 38.462 10.16 0.00 0.00 3.10
1794 3309 7.220491 CGCTAATATCTATGCATGAGTTCTCTG 59.780 40.741 10.16 0.00 0.00 3.35
1795 3310 8.249638 GCTAATATCTATGCATGAGTTCTCTGA 58.750 37.037 10.16 0.00 0.00 3.27
1813 3328 2.547211 CTGAGCTCAAACTTCACCACAG 59.453 50.000 18.85 0.00 0.00 3.66
1819 3334 2.682856 TCAAACTTCACCACAGCAACTC 59.317 45.455 0.00 0.00 0.00 3.01
1839 3367 2.943033 TCGCGAGAGATATTCTGACACA 59.057 45.455 3.71 0.00 35.87 3.72
1841 3369 4.105486 CGCGAGAGATATTCTGACACAAA 58.895 43.478 0.00 0.00 35.87 2.83
1843 3371 5.915196 CGCGAGAGATATTCTGACACAAATA 59.085 40.000 0.00 0.00 35.87 1.40
1844 3372 6.584184 CGCGAGAGATATTCTGACACAAATAT 59.416 38.462 0.00 0.10 35.87 1.28
1845 3373 7.410193 CGCGAGAGATATTCTGACACAAATATG 60.410 40.741 0.00 0.00 35.87 1.78
1846 3374 7.621013 GCGAGAGATATTCTGACACAAATATGC 60.621 40.741 0.00 0.00 35.87 3.14
1847 3375 7.598118 CGAGAGATATTCTGACACAAATATGCT 59.402 37.037 3.97 2.48 35.87 3.79
1848 3376 9.270640 GAGAGATATTCTGACACAAATATGCTT 57.729 33.333 3.97 0.00 35.87 3.91
1855 3413 7.776933 TCTGACACAAATATGCTTGATCTAC 57.223 36.000 0.00 0.00 0.00 2.59
2304 3874 3.887621 TGAACTGAATAAGGTCTCGGG 57.112 47.619 0.00 0.00 43.71 5.14
2362 3935 3.808726 TGGTTACGTATGTGTGTTGGTTC 59.191 43.478 0.00 0.00 0.00 3.62
2367 3940 3.001533 ACGTATGTGTGTTGGTTCGAAAC 59.998 43.478 6.16 6.16 0.00 2.78
2372 3945 3.619483 TGTGTGTTGGTTCGAAACTGTAG 59.381 43.478 15.41 0.00 0.00 2.74
2381 3954 2.337583 TCGAAACTGTAGCTGTGCATC 58.662 47.619 0.00 0.00 0.00 3.91
2434 4048 3.126073 GTCATGCTGCGAGATGATAACA 58.874 45.455 4.71 0.00 31.40 2.41
2456 4070 2.027625 GCCACTTTCCACTCGACGG 61.028 63.158 0.00 0.00 0.00 4.79
2461 4075 2.837371 CTTTCCACTCGACGGCCCTC 62.837 65.000 0.00 0.00 0.00 4.30
2464 4078 2.202797 CACTCGACGGCCCTCATG 60.203 66.667 0.00 0.00 0.00 3.07
2474 4088 2.445845 CCCTCATGTCCGCCCCTA 60.446 66.667 0.00 0.00 0.00 3.53
2504 4118 4.082523 CACGGACGGACTGCCCAT 62.083 66.667 0.00 0.00 34.14 4.00
2538 4152 1.228862 ACAGCCCAGCCCGAAAAAT 60.229 52.632 0.00 0.00 0.00 1.82
2542 4156 1.540435 GCCCAGCCCGAAAAATCCAA 61.540 55.000 0.00 0.00 0.00 3.53
2545 4159 0.890683 CAGCCCGAAAAATCCAAGCT 59.109 50.000 0.00 0.00 0.00 3.74
2552 4166 2.351738 CGAAAAATCCAAGCTGGGTCAC 60.352 50.000 7.13 0.00 38.32 3.67
2556 4170 2.527951 ATCCAAGCTGGGTCACGCTC 62.528 60.000 7.13 0.00 38.32 5.03
2597 4211 1.953311 GCCTCATTTTACAGCCCGGAA 60.953 52.381 0.73 0.00 0.00 4.30
2607 4221 1.152735 AGCCCGGAAGCTAGATCGA 60.153 57.895 0.73 0.00 42.70 3.59
2617 4231 2.586258 GCTAGATCGAGCTGGTTTCA 57.414 50.000 19.36 0.00 39.50 2.69
2620 4234 0.539051 AGATCGAGCTGGTTTCAGGG 59.461 55.000 0.39 0.00 41.19 4.45
2621 4235 1.078143 ATCGAGCTGGTTTCAGGGC 60.078 57.895 0.00 0.00 41.19 5.19
2622 4236 2.543067 ATCGAGCTGGTTTCAGGGCC 62.543 60.000 0.00 0.00 41.19 5.80
2623 4237 2.436109 GAGCTGGTTTCAGGGCCA 59.564 61.111 6.18 0.00 41.19 5.36
2624 4238 1.228552 GAGCTGGTTTCAGGGCCAA 60.229 57.895 6.18 0.00 41.19 4.52
2625 4239 0.827507 GAGCTGGTTTCAGGGCCAAA 60.828 55.000 6.18 0.00 41.19 3.28
2626 4240 0.178924 AGCTGGTTTCAGGGCCAAAT 60.179 50.000 6.18 0.00 41.19 2.32
2627 4241 0.247460 GCTGGTTTCAGGGCCAAATC 59.753 55.000 6.18 0.00 41.19 2.17
2628 4242 0.897621 CTGGTTTCAGGGCCAAATCC 59.102 55.000 6.18 8.94 37.36 3.01
2629 4243 0.486879 TGGTTTCAGGGCCAAATCCT 59.513 50.000 6.18 0.00 34.39 3.24
2630 4244 1.713647 TGGTTTCAGGGCCAAATCCTA 59.286 47.619 6.18 0.00 32.49 2.94
2631 4245 2.314549 TGGTTTCAGGGCCAAATCCTAT 59.685 45.455 6.18 0.00 32.49 2.57
2632 4246 3.245948 TGGTTTCAGGGCCAAATCCTATT 60.246 43.478 6.18 0.00 32.49 1.73
2633 4247 3.384789 GGTTTCAGGGCCAAATCCTATTC 59.615 47.826 6.18 0.00 32.49 1.75
2634 4248 2.638480 TCAGGGCCAAATCCTATTCG 57.362 50.000 6.18 0.00 32.49 3.34
2635 4249 1.142870 TCAGGGCCAAATCCTATTCGG 59.857 52.381 6.18 0.00 32.49 4.30
2636 4250 0.178990 AGGGCCAAATCCTATTCGGC 60.179 55.000 6.18 0.00 42.21 5.54
2637 4251 1.515521 GGGCCAAATCCTATTCGGCG 61.516 60.000 4.39 0.00 43.93 6.46
2638 4252 1.282875 GCCAAATCCTATTCGGCGC 59.717 57.895 0.00 0.00 32.14 6.53
2639 4253 1.949257 CCAAATCCTATTCGGCGCC 59.051 57.895 19.07 19.07 0.00 6.53
2724 4340 4.002316 AGTGCAAAAGCAAAAGAAAAGCA 58.998 34.783 0.00 0.00 0.00 3.91
2725 4341 4.090729 GTGCAAAAGCAAAAGAAAAGCAC 58.909 39.130 0.00 0.00 42.21 4.40
2767 4383 3.259064 GGTAGCTGCTGTTTCATCGTAA 58.741 45.455 13.43 0.00 0.00 3.18
2784 4400 4.706035 TCGTAAACTACACAAACCACCAT 58.294 39.130 0.00 0.00 0.00 3.55
2829 4445 7.316544 TGTGTTCACCTTTTCTAGTTCTTTC 57.683 36.000 0.37 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
307 316 1.228459 GAACCGGGACCAAAGGCTT 60.228 57.895 6.32 0.00 0.00 4.35
419 428 1.644437 ATGTGGGCCATTGATCCCGA 61.644 55.000 10.70 0.78 45.60 5.14
478 487 0.549469 GAACCGGGACCAATATGGGT 59.451 55.000 6.32 0.00 43.37 4.51
530 539 1.911057 AAACAGGGCTTTGGTCTAGC 58.089 50.000 0.00 0.00 37.91 3.42
647 657 1.255882 TATTTGGCCAACACCAGCAG 58.744 50.000 20.35 0.00 41.82 4.24
650 660 5.610235 CAAATTTATTTGGCCAACACCAG 57.390 39.130 20.35 0.00 42.51 4.00
737 747 5.255596 CCTACAAACGAATACAATTCGCAG 58.744 41.667 18.97 12.47 44.98 5.18
739 749 4.093850 ACCCTACAAACGAATACAATTCGC 59.906 41.667 18.97 0.00 44.98 4.70
745 755 6.549433 AAGGATACCCTACAAACGAATACA 57.451 37.500 0.00 0.00 43.48 2.29
778 789 2.098934 GCGGACATGTTGGCAATCATTA 59.901 45.455 14.88 0.00 0.00 1.90
810 821 1.202758 TGTGCCTAACTTGTCCACAGG 60.203 52.381 0.00 0.00 33.07 4.00
813 824 2.294074 TGTTGTGCCTAACTTGTCCAC 58.706 47.619 2.47 0.00 0.00 4.02
1226 1258 1.990563 CTTTTACAGCGTACTCCCACG 59.009 52.381 0.00 0.00 44.71 4.94
1227 1259 2.991866 GTCTTTTACAGCGTACTCCCAC 59.008 50.000 0.00 0.00 0.00 4.61
1230 1262 2.938869 ACGTCTTTTACAGCGTACTCC 58.061 47.619 0.00 0.00 34.69 3.85
1258 1336 7.801547 AATTCAGAAACACTAATCATTTGCG 57.198 32.000 0.00 0.00 0.00 4.85
1405 2533 3.625897 CACACGGCCTCCACCTGA 61.626 66.667 0.00 0.00 0.00 3.86
1435 2563 3.371097 GAGGATGTCGGCGCAGGAA 62.371 63.158 10.83 0.00 0.00 3.36
1514 2647 4.063967 TCCGGCAGCACCAGTACG 62.064 66.667 0.00 0.00 39.03 3.67
1537 2670 1.483415 TCAGTTAGTTATGGGGGCGTC 59.517 52.381 0.00 0.00 0.00 5.19
1538 2671 1.485066 CTCAGTTAGTTATGGGGGCGT 59.515 52.381 0.00 0.00 0.00 5.68
1542 2675 4.018779 TCCAAACCTCAGTTAGTTATGGGG 60.019 45.833 0.00 0.00 43.21 4.96
1543 2676 5.174037 TCCAAACCTCAGTTAGTTATGGG 57.826 43.478 0.00 0.00 34.19 4.00
1544 2677 6.238648 AGTTCCAAACCTCAGTTAGTTATGG 58.761 40.000 0.00 0.00 34.19 2.74
1545 2678 8.842358 TTAGTTCCAAACCTCAGTTAGTTATG 57.158 34.615 0.00 0.00 34.19 1.90
1548 2681 8.218488 AGAATTAGTTCCAAACCTCAGTTAGTT 58.782 33.333 0.00 0.00 32.94 2.24
1549 2682 7.661847 CAGAATTAGTTCCAAACCTCAGTTAGT 59.338 37.037 0.00 0.00 32.94 2.24
1550 2683 7.119846 CCAGAATTAGTTCCAAACCTCAGTTAG 59.880 40.741 0.00 0.00 32.94 2.34
1551 2684 6.940298 CCAGAATTAGTTCCAAACCTCAGTTA 59.060 38.462 0.00 0.00 32.94 2.24
1557 3064 5.319043 TGTCCAGAATTAGTTCCAAACCT 57.681 39.130 0.00 0.00 34.81 3.50
1577 3084 2.356125 CCCAGCTGCTTGGTAAGTATGT 60.356 50.000 8.66 0.00 36.45 2.29
1580 3087 1.003118 CACCCAGCTGCTTGGTAAGTA 59.997 52.381 23.28 0.00 36.45 2.24
1581 3088 0.250901 CACCCAGCTGCTTGGTAAGT 60.251 55.000 23.28 8.42 36.45 2.24
1582 3089 0.962356 CCACCCAGCTGCTTGGTAAG 60.962 60.000 23.28 14.68 36.45 2.34
1583 3090 1.074775 CCACCCAGCTGCTTGGTAA 59.925 57.895 23.28 0.00 36.45 2.85
1780 3295 1.897802 TGAGCTCAGAGAACTCATGCA 59.102 47.619 13.74 0.00 35.58 3.96
1781 3296 2.669300 TGAGCTCAGAGAACTCATGC 57.331 50.000 13.74 5.39 35.58 4.06
1782 3297 4.567971 AGTTTGAGCTCAGAGAACTCATG 58.432 43.478 21.35 0.00 39.99 3.07
1783 3298 4.888326 AGTTTGAGCTCAGAGAACTCAT 57.112 40.909 21.35 5.59 39.99 2.90
1784 3299 4.100035 TGAAGTTTGAGCTCAGAGAACTCA 59.900 41.667 25.20 21.16 38.62 3.41
1785 3300 4.447389 GTGAAGTTTGAGCTCAGAGAACTC 59.553 45.833 25.20 19.55 30.77 3.01
1787 3302 3.496507 GGTGAAGTTTGAGCTCAGAGAAC 59.503 47.826 17.43 17.84 0.00 3.01
1789 3304 2.700371 TGGTGAAGTTTGAGCTCAGAGA 59.300 45.455 17.43 4.46 0.00 3.10
1790 3305 2.805099 GTGGTGAAGTTTGAGCTCAGAG 59.195 50.000 17.43 0.00 0.00 3.35
1791 3306 2.170397 TGTGGTGAAGTTTGAGCTCAGA 59.830 45.455 17.43 10.10 0.00 3.27
1792 3307 2.547211 CTGTGGTGAAGTTTGAGCTCAG 59.453 50.000 17.43 0.00 30.09 3.35
1793 3308 2.564771 CTGTGGTGAAGTTTGAGCTCA 58.435 47.619 13.74 13.74 0.00 4.26
1794 3309 1.265365 GCTGTGGTGAAGTTTGAGCTC 59.735 52.381 6.82 6.82 0.00 4.09
1795 3310 1.312815 GCTGTGGTGAAGTTTGAGCT 58.687 50.000 0.00 0.00 0.00 4.09
1813 3328 2.723658 CAGAATATCTCTCGCGAGTTGC 59.276 50.000 33.33 17.12 38.45 4.17
1819 3334 3.340337 TGTGTCAGAATATCTCTCGCG 57.660 47.619 0.00 0.00 29.07 5.87
1839 3367 5.068636 CCTGCAGGTAGATCAAGCATATTT 58.931 41.667 25.53 0.00 34.35 1.40
1841 3369 4.283363 CCTGCAGGTAGATCAAGCATAT 57.717 45.455 25.53 0.00 34.35 1.78
1843 3371 2.634815 CCTGCAGGTAGATCAAGCAT 57.365 50.000 25.53 0.00 34.35 3.79
2304 3874 4.202441 TCCGTAGATTCTGGTACTGGTAC 58.798 47.826 0.00 2.58 35.40 3.34
2331 3904 2.070783 CATACGTAACCACACACCACC 58.929 52.381 0.00 0.00 0.00 4.61
2336 3909 3.455990 ACACACATACGTAACCACACA 57.544 42.857 0.00 0.00 0.00 3.72
2337 3910 3.059461 CCAACACACATACGTAACCACAC 60.059 47.826 0.00 0.00 0.00 3.82
2362 3935 2.341257 AGATGCACAGCTACAGTTTCG 58.659 47.619 0.00 0.00 0.00 3.46
2372 3945 0.389817 TGTGGACGTAGATGCACAGC 60.390 55.000 0.00 0.00 44.85 4.40
2400 3979 4.319984 CGCAGCATGACATACAATTAGCAT 60.320 41.667 0.00 0.00 39.69 3.79
2401 3980 3.002553 CGCAGCATGACATACAATTAGCA 59.997 43.478 0.00 0.00 39.69 3.49
2402 3981 3.248363 TCGCAGCATGACATACAATTAGC 59.752 43.478 0.00 0.00 39.69 3.09
2403 3982 4.746611 TCTCGCAGCATGACATACAATTAG 59.253 41.667 0.00 0.00 39.69 1.73
2405 3984 3.534554 TCTCGCAGCATGACATACAATT 58.465 40.909 0.00 0.00 39.69 2.32
2406 3985 3.183793 TCTCGCAGCATGACATACAAT 57.816 42.857 0.00 0.00 39.69 2.71
2407 3986 2.671130 TCTCGCAGCATGACATACAA 57.329 45.000 0.00 0.00 39.69 2.41
2408 3987 2.101249 TCATCTCGCAGCATGACATACA 59.899 45.455 0.00 0.00 39.69 2.29
2434 4048 0.976641 TCGAGTGGAAAGTGGCAGAT 59.023 50.000 0.00 0.00 0.00 2.90
2436 4050 1.284982 CGTCGAGTGGAAAGTGGCAG 61.285 60.000 0.00 0.00 0.00 4.85
2437 4051 1.300620 CGTCGAGTGGAAAGTGGCA 60.301 57.895 0.00 0.00 0.00 4.92
2438 4052 2.027625 CCGTCGAGTGGAAAGTGGC 61.028 63.158 0.00 0.00 0.00 5.01
2439 4053 2.027625 GCCGTCGAGTGGAAAGTGG 61.028 63.158 7.80 0.00 0.00 4.00
2440 4054 2.027625 GGCCGTCGAGTGGAAAGTG 61.028 63.158 7.80 0.00 0.00 3.16
2441 4055 2.342648 GGCCGTCGAGTGGAAAGT 59.657 61.111 7.80 0.00 0.00 2.66
2442 4056 2.434359 GGGCCGTCGAGTGGAAAG 60.434 66.667 7.80 0.00 0.00 2.62
2443 4057 2.920912 AGGGCCGTCGAGTGGAAA 60.921 61.111 7.80 0.00 0.00 3.13
2444 4058 3.379445 GAGGGCCGTCGAGTGGAA 61.379 66.667 10.16 0.00 0.00 3.53
2445 4059 3.957435 ATGAGGGCCGTCGAGTGGA 62.957 63.158 19.99 2.13 0.00 4.02
2446 4060 3.461773 ATGAGGGCCGTCGAGTGG 61.462 66.667 19.99 0.00 0.00 4.00
2461 4075 0.751277 TTTGCATAGGGGCGGACATG 60.751 55.000 0.00 0.00 36.28 3.21
2464 4078 0.751643 ACATTTGCATAGGGGCGGAC 60.752 55.000 0.00 0.00 36.28 4.79
2469 4083 2.291465 CGTGATGACATTTGCATAGGGG 59.709 50.000 0.00 0.00 0.00 4.79
2470 4084 2.291465 CCGTGATGACATTTGCATAGGG 59.709 50.000 0.00 0.00 0.00 3.53
2471 4085 3.002656 GTCCGTGATGACATTTGCATAGG 59.997 47.826 0.00 0.00 35.29 2.57
2472 4086 3.302675 CGTCCGTGATGACATTTGCATAG 60.303 47.826 0.00 0.00 34.88 2.23
2473 4087 2.607180 CGTCCGTGATGACATTTGCATA 59.393 45.455 0.00 0.00 34.88 3.14
2474 4088 1.398041 CGTCCGTGATGACATTTGCAT 59.602 47.619 0.00 0.00 34.88 3.96
2504 4118 0.911769 CTGTCCATGCCCAGGTCTAA 59.088 55.000 2.73 0.00 0.00 2.10
2538 4152 3.240134 GAGCGTGACCCAGCTTGGA 62.240 63.158 11.55 0.00 44.69 3.53
2560 4174 2.124570 CCCATGACCAGCCCGAAG 60.125 66.667 0.00 0.00 0.00 3.79
2573 4187 1.780503 GGCTGTAAAATGAGGCCCAT 58.219 50.000 0.00 0.00 37.12 4.00
2579 4193 1.401905 GCTTCCGGGCTGTAAAATGAG 59.598 52.381 0.00 0.00 0.00 2.90
2607 4221 0.178924 ATTTGGCCCTGAAACCAGCT 60.179 50.000 0.00 0.00 37.24 4.24
2613 4227 3.287222 CGAATAGGATTTGGCCCTGAAA 58.713 45.455 0.00 0.00 35.30 2.69
2617 4231 0.178990 GCCGAATAGGATTTGGCCCT 60.179 55.000 16.66 0.00 45.00 5.19
2620 4234 1.282875 GCGCCGAATAGGATTTGGC 59.717 57.895 17.29 17.29 45.00 4.52
2621 4235 1.841663 CGGCGCCGAATAGGATTTGG 61.842 60.000 44.86 9.17 45.00 3.28
2622 4236 1.569493 CGGCGCCGAATAGGATTTG 59.431 57.895 44.86 9.41 45.00 2.32
2623 4237 4.043168 CGGCGCCGAATAGGATTT 57.957 55.556 44.86 0.00 45.00 2.17
2724 4340 1.544691 AGTTCGATTCCTACTGCACGT 59.455 47.619 0.00 0.00 0.00 4.49
2725 4341 1.920574 CAGTTCGATTCCTACTGCACG 59.079 52.381 1.49 0.00 33.63 5.34
2767 4383 1.960689 GGCATGGTGGTTTGTGTAGTT 59.039 47.619 0.00 0.00 0.00 2.24
2784 4400 0.680921 GCAGAATAGGCTTGGTGGCA 60.681 55.000 0.00 0.00 44.55 4.92


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

AutoCloner maintained by Alex Coulton.