Multiple sequence alignment - TraesCS7B01G086500

Loading Multiple Alignment...

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 TraesCS7B01G086500 chr7B 100.000 3952 0 0 1 3952 99633278 99637229 0.000000e+00 7299.0
1 TraesCS7B01G086500 chr7B 81.356 118 21 1 3622 3739 66232669 66232785 1.170000e-15 95.3
2 TraesCS7B01G086500 chr7D 95.109 1288 48 7 2255 3542 136417137 136415865 0.000000e+00 2015.0
3 TraesCS7B01G086500 chr7D 94.329 864 41 5 1413 2275 136418212 136417356 0.000000e+00 1317.0
4 TraesCS7B01G086500 chr7D 95.406 653 29 1 717 1368 136418952 136418300 0.000000e+00 1038.0
5 TraesCS7B01G086500 chr7D 84.404 545 74 6 3 545 58136272 58135737 3.500000e-145 525.0
6 TraesCS7B01G086500 chr7D 90.769 390 32 3 3563 3949 136415305 136414917 5.850000e-143 518.0
7 TraesCS7B01G086500 chr7D 87.151 179 22 1 3563 3741 136415728 136415905 6.700000e-48 202.0
8 TraesCS7B01G086500 chr7A 92.832 1395 60 19 2113 3504 136168177 136166820 0.000000e+00 1986.0
9 TraesCS7B01G086500 chr7A 95.192 832 34 5 1415 2243 136169005 136168177 0.000000e+00 1310.0
10 TraesCS7B01G086500 chr7A 92.689 807 50 7 567 1366 136169920 136169116 0.000000e+00 1155.0
11 TraesCS7B01G086500 chr7A 85.273 550 68 10 1 546 729559125 729559665 4.460000e-154 555.0
12 TraesCS7B01G086500 chr2A 87.796 549 61 5 1 546 2741852 2742397 4.310000e-179 638.0
13 TraesCS7B01G086500 chr3B 85.009 547 80 2 2 546 184958089 184957543 4.460000e-154 555.0
14 TraesCS7B01G086500 chr5B 84.854 548 78 3 1 546 488188208 488187664 7.470000e-152 547.0
15 TraesCS7B01G086500 chr5B 84.699 549 77 5 1 546 467374606 467374062 3.470000e-150 542.0
16 TraesCS7B01G086500 chr3D 85.206 534 67 9 1 528 47748567 47748040 4.490000e-149 538.0
17 TraesCS7B01G086500 chr1A 84.095 547 81 4 1 545 7313510 7314052 1.260000e-144 523.0
18 TraesCS7B01G086500 chr6A 84.095 547 79 7 1 545 29792541 29793081 4.530000e-144 521.0
19 TraesCS7B01G086500 chr2D 85.632 174 22 3 3563 3735 459812268 459812439 3.140000e-41 180.0
20 TraesCS7B01G086500 chr5A 81.395 172 31 1 3567 3738 706050819 706050649 5.330000e-29 139.0
21 TraesCS7B01G086500 chr3A 81.143 175 28 5 3563 3735 212186836 212187007 6.890000e-28 135.0
22 TraesCS7B01G086500 chr5D 79.882 169 28 6 3572 3738 368562159 368561995 6.940000e-23 119.0
23 TraesCS7B01G086500 chr1B 89.394 66 6 1 3678 3742 652257242 652257307 9.100000e-12 82.4
24 TraesCS7B01G086500 chr4A 94.000 50 3 0 3694 3743 352482229 352482180 4.230000e-10 76.8


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 TraesCS7B01G086500 chr7B 99633278 99637229 3951 False 7299.000000 7299 100.00000 1 3952 1 chr7B.!!$F2 3951
1 TraesCS7B01G086500 chr7D 136414917 136418952 4035 True 1222.000000 2015 93.90325 717 3949 4 chr7D.!!$R2 3232
2 TraesCS7B01G086500 chr7D 58135737 58136272 535 True 525.000000 525 84.40400 3 545 1 chr7D.!!$R1 542
3 TraesCS7B01G086500 chr7A 136166820 136169920 3100 True 1483.666667 1986 93.57100 567 3504 3 chr7A.!!$R1 2937
4 TraesCS7B01G086500 chr7A 729559125 729559665 540 False 555.000000 555 85.27300 1 546 1 chr7A.!!$F1 545
5 TraesCS7B01G086500 chr2A 2741852 2742397 545 False 638.000000 638 87.79600 1 546 1 chr2A.!!$F1 545
6 TraesCS7B01G086500 chr3B 184957543 184958089 546 True 555.000000 555 85.00900 2 546 1 chr3B.!!$R1 544
7 TraesCS7B01G086500 chr5B 488187664 488188208 544 True 547.000000 547 84.85400 1 546 1 chr5B.!!$R2 545
8 TraesCS7B01G086500 chr5B 467374062 467374606 544 True 542.000000 542 84.69900 1 546 1 chr5B.!!$R1 545
9 TraesCS7B01G086500 chr3D 47748040 47748567 527 True 538.000000 538 85.20600 1 528 1 chr3D.!!$R1 527
10 TraesCS7B01G086500 chr1A 7313510 7314052 542 False 523.000000 523 84.09500 1 545 1 chr1A.!!$F1 544
11 TraesCS7B01G086500 chr6A 29792541 29793081 540 False 521.000000 521 84.09500 1 545 1 chr6A.!!$F1 544

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
267 274 0.758734 TGAATCCCGCGAGATCCAAT 59.241 50.000 8.23 0.0 0.0 3.16 F
462 473 1.211457 AGATCTTCCACACCTCCATGC 59.789 52.381 0.00 0.0 0.0 4.06 F
2393 2844 0.035820 TGACGTGCTAATTGGACCCC 60.036 55.000 0.00 0.0 33.1 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 1965 1.371467 TGATGGCTTTCCCTCTCCAA 58.629 50.000 0.00 0.0 31.66 3.53 R
2398 2849 1.225704 CCTCCTGCCATCAACTCCC 59.774 63.158 0.00 0.0 0.00 4.30 R
3551 4010 0.035056 GGGCAGTGCTAGTTCATGGT 60.035 55.000 16.11 0.0 0.00 3.55 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
123 125 2.124411 GCTAAGACCCCATAGGACCAA 58.876 52.381 0.00 0.00 39.89 3.67
125 127 2.053747 AAGACCCCATAGGACCAACA 57.946 50.000 0.00 0.00 39.89 3.33
128 132 1.564348 GACCCCATAGGACCAACACAT 59.436 52.381 0.00 0.00 39.89 3.21
196 203 7.007723 AGATCAAACCTGTAAACACCCAAATA 58.992 34.615 0.00 0.00 0.00 1.40
235 242 2.940994 TCCAAACAGATCCACCGAAA 57.059 45.000 0.00 0.00 0.00 3.46
267 274 0.758734 TGAATCCCGCGAGATCCAAT 59.241 50.000 8.23 0.00 0.00 3.16
310 317 2.809119 CTCCGACGATGCTAGATACACT 59.191 50.000 0.00 0.00 0.00 3.55
370 380 3.078196 TAAGGGACATCGCCGCCA 61.078 61.111 0.00 0.00 0.00 5.69
378 388 4.634703 ATCGCCGCCACCACACAA 62.635 61.111 0.00 0.00 0.00 3.33
379 389 4.858680 TCGCCGCCACCACACAAA 62.859 61.111 0.00 0.00 0.00 2.83
451 462 2.768344 GGGGGCCGAGATCTTCCA 60.768 66.667 0.00 0.00 0.00 3.53
462 473 1.211457 AGATCTTCCACACCTCCATGC 59.789 52.381 0.00 0.00 0.00 4.06
482 494 2.808919 CCCTAGAGGCCATCGAAGATA 58.191 52.381 5.01 0.00 45.12 1.98
525 537 3.984633 CGACGAGAGAAGAAGAGCTTTTT 59.015 43.478 0.00 0.00 36.83 1.94
546 558 4.559862 TTGGTGGAGGAAGAAAGAGATC 57.440 45.455 0.00 0.00 0.00 2.75
547 559 2.840651 TGGTGGAGGAAGAAAGAGATCC 59.159 50.000 0.00 0.00 0.00 3.36
548 560 3.111484 GGTGGAGGAAGAAAGAGATCCT 58.889 50.000 0.00 0.00 46.14 3.24
549 561 3.521531 GGTGGAGGAAGAAAGAGATCCTT 59.478 47.826 0.00 0.00 43.55 3.36
550 562 4.717280 GGTGGAGGAAGAAAGAGATCCTTA 59.283 45.833 0.00 0.00 43.55 2.69
551 563 5.189934 GGTGGAGGAAGAAAGAGATCCTTAA 59.810 44.000 0.00 0.00 43.55 1.85
552 564 6.110033 GTGGAGGAAGAAAGAGATCCTTAAC 58.890 44.000 0.00 0.00 43.55 2.01
553 565 5.189934 TGGAGGAAGAAAGAGATCCTTAACC 59.810 44.000 0.00 0.00 43.55 2.85
554 566 5.189934 GGAGGAAGAAAGAGATCCTTAACCA 59.810 44.000 0.00 0.00 43.55 3.67
555 567 6.126623 GGAGGAAGAAAGAGATCCTTAACCAT 60.127 42.308 0.00 0.00 43.55 3.55
556 568 6.894682 AGGAAGAAAGAGATCCTTAACCATC 58.105 40.000 0.00 0.00 40.70 3.51
557 569 5.755861 GGAAGAAAGAGATCCTTAACCATCG 59.244 44.000 0.00 0.00 34.00 3.84
558 570 5.941555 AGAAAGAGATCCTTAACCATCGT 57.058 39.130 0.00 0.00 34.00 3.73
559 571 5.908341 AGAAAGAGATCCTTAACCATCGTC 58.092 41.667 0.00 0.00 34.00 4.20
560 572 5.659079 AGAAAGAGATCCTTAACCATCGTCT 59.341 40.000 0.00 0.00 34.00 4.18
561 573 5.941555 AAGAGATCCTTAACCATCGTCTT 57.058 39.130 0.00 0.00 32.24 3.01
562 574 5.941555 AGAGATCCTTAACCATCGTCTTT 57.058 39.130 0.00 0.00 0.00 2.52
563 575 5.665459 AGAGATCCTTAACCATCGTCTTTG 58.335 41.667 0.00 0.00 0.00 2.77
564 576 5.422331 AGAGATCCTTAACCATCGTCTTTGA 59.578 40.000 0.00 0.00 0.00 2.69
565 577 5.665459 AGATCCTTAACCATCGTCTTTGAG 58.335 41.667 0.00 0.00 0.00 3.02
566 578 5.422331 AGATCCTTAACCATCGTCTTTGAGA 59.578 40.000 0.00 0.00 0.00 3.27
567 579 5.477607 TCCTTAACCATCGTCTTTGAGAA 57.522 39.130 0.00 0.00 0.00 2.87
568 580 5.479306 TCCTTAACCATCGTCTTTGAGAAG 58.521 41.667 0.00 0.00 0.00 2.85
569 581 4.093556 CCTTAACCATCGTCTTTGAGAAGC 59.906 45.833 0.00 0.00 32.75 3.86
570 582 2.100605 ACCATCGTCTTTGAGAAGCC 57.899 50.000 0.00 0.00 32.75 4.35
571 583 1.347707 ACCATCGTCTTTGAGAAGCCA 59.652 47.619 0.00 0.00 32.75 4.75
580 592 2.346766 TTGAGAAGCCAAAGCACTGA 57.653 45.000 0.00 0.00 43.56 3.41
582 594 2.653726 TGAGAAGCCAAAGCACTGAAA 58.346 42.857 0.00 0.00 43.56 2.69
589 601 3.507622 AGCCAAAGCACTGAAAGATAACC 59.492 43.478 0.00 0.00 43.56 2.85
594 606 3.412386 AGCACTGAAAGATAACCCACAC 58.588 45.455 0.00 0.00 37.43 3.82
599 611 6.095440 GCACTGAAAGATAACCCACACATAAT 59.905 38.462 0.00 0.00 37.43 1.28
608 620 7.833682 AGATAACCCACACATAATCAATCACAA 59.166 33.333 0.00 0.00 0.00 3.33
609 621 6.855763 AACCCACACATAATCAATCACAAT 57.144 33.333 0.00 0.00 0.00 2.71
643 655 4.561735 ACCAATTGTTGTTTACCACTCG 57.438 40.909 4.43 0.00 0.00 4.18
671 683 9.715121 TTAATAAATCTTGGACGTAGAGTTGTT 57.285 29.630 11.78 11.78 35.92 2.83
672 684 5.924475 AAATCTTGGACGTAGAGTTGTTG 57.076 39.130 0.00 0.00 29.67 3.33
673 685 4.602340 ATCTTGGACGTAGAGTTGTTGT 57.398 40.909 0.00 0.00 0.00 3.32
698 710 6.474140 TTTTATATACAGCCCGAGAGTTGA 57.526 37.500 0.00 0.00 0.00 3.18
699 711 6.665992 TTTATATACAGCCCGAGAGTTGAT 57.334 37.500 0.00 0.00 0.00 2.57
738 752 9.485591 GATTGATGCAGAAATAAAAATTGCAAG 57.514 29.630 4.94 0.00 46.44 4.01
751 765 7.628769 AAAAATTGCAAGTTCTTTGGACAAT 57.371 28.000 13.16 0.00 36.80 2.71
767 782 5.815581 TGGACAATGCTGGAACTACTATTT 58.184 37.500 0.00 0.00 0.00 1.40
776 791 5.232414 GCTGGAACTACTATTTAGCGTTCAG 59.768 44.000 15.96 13.14 38.09 3.02
908 923 4.615541 CCGCGAGAAATAAACAAGGAAAAC 59.384 41.667 8.23 0.00 0.00 2.43
1041 1060 3.506096 CTGCCGCTCGTCCTCGTA 61.506 66.667 0.00 0.00 38.33 3.43
1143 1162 1.227764 CCTCAGGGCGATGATGGTG 60.228 63.158 0.00 0.00 0.00 4.17
1305 1324 1.418334 AGTCTGGTGCTGAAGTGTCT 58.582 50.000 0.00 0.00 0.00 3.41
1319 1338 6.017109 GCTGAAGTGTCTACAAATTCCTGAAA 60.017 38.462 6.78 0.00 0.00 2.69
1321 1340 9.219603 CTGAAGTGTCTACAAATTCCTGAAATA 57.780 33.333 6.78 0.00 0.00 1.40
1338 1357 9.929180 TCCTGAAATATATTCCATTTCTAGACG 57.071 33.333 0.00 0.00 41.13 4.18
1379 1431 9.889128 ATTTCAGGAAATTGGTAATGGTAAATG 57.111 29.630 1.50 0.00 37.74 2.32
1380 1432 8.429237 TTCAGGAAATTGGTAATGGTAAATGT 57.571 30.769 0.00 0.00 0.00 2.71
1384 1436 8.340757 AGGAAATTGGTAATGGTAAATGTCCTA 58.659 33.333 4.49 0.00 42.49 2.94
1449 1529 6.678900 GCATCTCTTATTGGCAAGTGTAAAGG 60.679 42.308 5.96 0.00 0.00 3.11
1456 1536 3.408634 TGGCAAGTGTAAAGGCTAAGTC 58.591 45.455 0.00 0.00 0.00 3.01
1459 1539 4.459337 GGCAAGTGTAAAGGCTAAGTCATT 59.541 41.667 0.00 0.00 0.00 2.57
1471 1551 7.187824 AGGCTAAGTCATTTCAGTTATGAGA 57.812 36.000 0.00 0.00 36.61 3.27
1473 1553 8.270744 AGGCTAAGTCATTTCAGTTATGAGATT 58.729 33.333 0.00 0.00 36.61 2.40
1546 1629 9.907576 GTTTATGTCTTCGTCAGAAATCTATTG 57.092 33.333 0.00 0.00 35.71 1.90
1554 1637 6.817396 TCGTCAGAAATCTATTGAAACAACG 58.183 36.000 0.00 0.00 0.00 4.10
1698 1781 5.833667 TCCTCTTCATATCGTGTTAGGTGAT 59.166 40.000 0.00 0.00 0.00 3.06
1712 1795 2.643551 AGGTGATAAAGATGTTGGCGG 58.356 47.619 0.00 0.00 0.00 6.13
1745 1828 2.175202 GGATGGTAAATTGGTGCACCA 58.825 47.619 34.74 34.74 44.76 4.17
1782 1865 2.237392 GCCAGGACTAGATTCAAGTGGT 59.763 50.000 0.00 0.00 0.00 4.16
1833 1916 6.205853 TCAGTTTTATGTCACTAAATGCGGTT 59.794 34.615 0.00 0.00 0.00 4.44
1850 1933 1.526686 TTGCACTGCTCTGTGGTGG 60.527 57.895 1.98 0.00 38.31 4.61
1868 1951 4.680349 CAACACGTTGCGCTTCAA 57.320 50.000 9.73 0.00 33.45 2.69
1882 1965 3.550842 GCGCTTCAATGTTGAGAAGGTTT 60.551 43.478 0.00 0.00 41.13 3.27
1889 1972 5.532406 TCAATGTTGAGAAGGTTTTGGAGAG 59.468 40.000 0.00 0.00 32.50 3.20
2138 2221 0.250770 GTTCCCCCGAGTTCAAAGCT 60.251 55.000 0.00 0.00 0.00 3.74
2393 2844 0.035820 TGACGTGCTAATTGGACCCC 60.036 55.000 0.00 0.00 33.10 4.95
2458 2909 2.029649 CCTCCCTGCAAATTCAACACAG 60.030 50.000 0.00 0.00 0.00 3.66
2667 3118 1.280421 AGTCTGTTCCTCAAGGATGGC 59.720 52.381 0.00 0.00 44.98 4.40
2956 3407 5.434182 TGGTCACACTGGATATGAAATGA 57.566 39.130 0.00 0.00 0.00 2.57
3118 3569 0.788391 GATCAAACGAAGCGAACCGT 59.212 50.000 0.00 0.00 41.14 4.83
3244 3700 9.471084 TTTTGTCTTCTTCTTTTTCTTTTTCGT 57.529 25.926 0.00 0.00 0.00 3.85
3245 3701 9.471084 TTTGTCTTCTTCTTTTTCTTTTTCGTT 57.529 25.926 0.00 0.00 0.00 3.85
3246 3702 9.471084 TTGTCTTCTTCTTTTTCTTTTTCGTTT 57.529 25.926 0.00 0.00 0.00 3.60
3247 3703 9.471084 TGTCTTCTTCTTTTTCTTTTTCGTTTT 57.529 25.926 0.00 0.00 0.00 2.43
3248 3704 9.939047 GTCTTCTTCTTTTTCTTTTTCGTTTTC 57.061 29.630 0.00 0.00 0.00 2.29
3249 3705 8.846607 TCTTCTTCTTTTTCTTTTTCGTTTTCG 58.153 29.630 0.00 0.00 45.64 3.46
3298 3755 2.789409 ATCTTCTGTTTTCCCCCTCG 57.211 50.000 0.00 0.00 0.00 4.63
3308 3765 2.366972 CCCCCTCGTCCATCCCTT 60.367 66.667 0.00 0.00 0.00 3.95
3309 3766 2.444256 CCCCCTCGTCCATCCCTTC 61.444 68.421 0.00 0.00 0.00 3.46
3508 3967 2.357637 TCAGCCCAAAAACGTTTGAGAG 59.642 45.455 15.46 5.71 45.99 3.20
3526 3985 4.346709 TGAGAGAAGTCCACATTACAACCA 59.653 41.667 0.00 0.00 0.00 3.67
3542 4001 4.985538 ACAACCATGAACTAACCACTCAT 58.014 39.130 0.00 0.00 0.00 2.90
3543 4002 4.761739 ACAACCATGAACTAACCACTCATG 59.238 41.667 0.00 4.63 43.95 3.07
3574 4572 0.764890 TGAACTAGCACTGCCCAGTT 59.235 50.000 15.24 15.24 40.20 3.16
3600 4599 0.666374 CAACTCCGTCAAAACCACCC 59.334 55.000 0.00 0.00 0.00 4.61
3608 4607 1.534163 GTCAAAACCACCCGACTTAGC 59.466 52.381 0.00 0.00 0.00 3.09
3614 4613 0.879090 CCACCCGACTTAGCCAAAAC 59.121 55.000 0.00 0.00 0.00 2.43
3617 4616 0.879090 CCCGACTTAGCCAAAACCAC 59.121 55.000 0.00 0.00 0.00 4.16
3621 4620 1.197036 GACTTAGCCAAAACCACGAGC 59.803 52.381 0.00 0.00 0.00 5.03
3630 4629 0.535102 AAACCACGAGCAGGGTTGAG 60.535 55.000 0.00 0.00 46.33 3.02
3640 4639 1.404315 GCAGGGTTGAGTTCTAGACCG 60.404 57.143 0.00 0.00 32.91 4.79
3699 4698 8.477419 TTGAAGTTCAGGGTTGAATTCTAAAT 57.523 30.769 5.56 0.00 44.62 1.40
3717 4716 3.611766 AATCGAGTGGTTAGTTCAGGG 57.388 47.619 0.00 0.00 0.00 4.45
3735 4734 5.205056 TCAGGGTTGTAATGTGGACTTTTT 58.795 37.500 0.00 0.00 0.00 1.94
3769 4769 2.624838 CCCATATGAGCATTGGACAACC 59.375 50.000 3.65 0.00 31.94 3.77
3779 4779 0.884704 TTGGACAACCTGAAGCGAGC 60.885 55.000 0.00 0.00 37.04 5.03
3781 4781 2.357517 ACAACCTGAAGCGAGCCG 60.358 61.111 0.00 0.00 0.00 5.52
3793 4793 1.953138 CGAGCCGTGGAGATGATGC 60.953 63.158 0.00 0.00 0.00 3.91
3799 4799 0.866427 CGTGGAGATGATGCTCATGC 59.134 55.000 3.76 0.00 37.20 4.06
3834 4834 3.332919 CTCACCATTCAGTTGAGGAGTG 58.667 50.000 0.00 0.00 0.00 3.51
3837 4837 3.997021 CACCATTCAGTTGAGGAGTGTAC 59.003 47.826 0.00 0.00 0.00 2.90
3849 4849 1.547372 GGAGTGTACGGTATGGTGTGT 59.453 52.381 0.00 0.00 0.00 3.72
3853 4853 1.345089 TGTACGGTATGGTGTGTTGCT 59.655 47.619 0.00 0.00 0.00 3.91
3871 4871 2.742053 TGCTTGACGATGCCTAAGTTTC 59.258 45.455 0.00 0.00 0.00 2.78
3880 4880 5.163754 ACGATGCCTAAGTTTCTGCAATAAC 60.164 40.000 0.00 3.08 37.27 1.89
3905 4905 5.345702 GTTAAAAGCTTTTGACCGGAGTTT 58.654 37.500 30.21 5.83 32.44 2.66
3910 4910 3.751698 AGCTTTTGACCGGAGTTTCATAC 59.248 43.478 9.46 0.00 0.00 2.39
3950 4950 5.966742 ATTTTTACCTCCTCTCAGTTTGC 57.033 39.130 0.00 0.00 0.00 3.68
3951 4951 3.418684 TTTACCTCCTCTCAGTTTGCC 57.581 47.619 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 3.261039 TTTGCCCGGCTCCGATGAA 62.261 57.895 11.61 0.00 42.83 2.57
123 125 4.748892 CGATGGTTTCTACTCTGATGTGT 58.251 43.478 0.00 0.00 0.00 3.72
125 127 3.449018 AGCGATGGTTTCTACTCTGATGT 59.551 43.478 0.00 0.00 0.00 3.06
128 132 3.089284 TCAGCGATGGTTTCTACTCTGA 58.911 45.455 0.00 0.00 0.00 3.27
196 203 3.439129 GGATCCGGTCTTCATTCGTTTTT 59.561 43.478 0.00 0.00 0.00 1.94
235 242 0.321653 GGATTCAGTCGGTGCTGGTT 60.322 55.000 0.00 0.00 37.12 3.67
267 274 2.614481 GGCGTGTGAAGGTTTATCTCCA 60.614 50.000 0.00 0.00 0.00 3.86
310 317 1.881973 CGTTCTATCCCCGTTCCGATA 59.118 52.381 0.00 0.00 0.00 2.92
370 380 1.190643 CTTGGTTGGGTTTGTGTGGT 58.809 50.000 0.00 0.00 0.00 4.16
378 388 1.544759 GGTCATCGTCTTGGTTGGGTT 60.545 52.381 0.00 0.00 0.00 4.11
379 389 0.036306 GGTCATCGTCTTGGTTGGGT 59.964 55.000 0.00 0.00 0.00 4.51
447 458 0.548926 TAGGGCATGGAGGTGTGGAA 60.549 55.000 0.00 0.00 0.00 3.53
451 462 2.922162 CTCTAGGGCATGGAGGTGT 58.078 57.895 4.46 0.00 33.01 4.16
462 473 1.638529 ATCTTCGATGGCCTCTAGGG 58.361 55.000 3.32 0.00 35.18 3.53
525 537 3.264450 GGATCTCTTTCTTCCTCCACCAA 59.736 47.826 0.00 0.00 0.00 3.67
536 548 5.659079 AGACGATGGTTAAGGATCTCTTTCT 59.341 40.000 0.00 0.00 36.93 2.52
546 558 4.093556 GCTTCTCAAAGACGATGGTTAAGG 59.906 45.833 0.00 0.00 34.14 2.69
547 559 4.093556 GGCTTCTCAAAGACGATGGTTAAG 59.906 45.833 0.00 0.00 34.14 1.85
548 560 4.000988 GGCTTCTCAAAGACGATGGTTAA 58.999 43.478 0.00 0.00 34.14 2.01
549 561 3.007506 TGGCTTCTCAAAGACGATGGTTA 59.992 43.478 0.00 0.00 44.17 2.85
550 562 2.224523 TGGCTTCTCAAAGACGATGGTT 60.225 45.455 0.00 0.00 44.17 3.67
551 563 1.347707 TGGCTTCTCAAAGACGATGGT 59.652 47.619 0.00 0.00 44.17 3.55
552 564 2.099141 TGGCTTCTCAAAGACGATGG 57.901 50.000 0.00 0.00 44.17 3.51
560 572 2.653726 TCAGTGCTTTGGCTTCTCAAA 58.346 42.857 0.00 0.00 39.59 2.69
561 573 2.346766 TCAGTGCTTTGGCTTCTCAA 57.653 45.000 0.00 0.00 39.59 3.02
562 574 2.346766 TTCAGTGCTTTGGCTTCTCA 57.653 45.000 0.00 0.00 39.59 3.27
563 575 2.880890 TCTTTCAGTGCTTTGGCTTCTC 59.119 45.455 0.00 0.00 39.59 2.87
564 576 2.936202 TCTTTCAGTGCTTTGGCTTCT 58.064 42.857 0.00 0.00 39.59 2.85
565 577 3.930634 ATCTTTCAGTGCTTTGGCTTC 57.069 42.857 0.00 0.00 39.59 3.86
566 578 4.021981 GGTTATCTTTCAGTGCTTTGGCTT 60.022 41.667 0.00 0.00 39.59 4.35
567 579 3.507622 GGTTATCTTTCAGTGCTTTGGCT 59.492 43.478 0.00 0.00 39.59 4.75
568 580 3.367395 GGGTTATCTTTCAGTGCTTTGGC 60.367 47.826 0.00 0.00 39.26 4.52
569 581 3.826157 TGGGTTATCTTTCAGTGCTTTGG 59.174 43.478 0.00 0.00 0.00 3.28
570 582 4.278170 TGTGGGTTATCTTTCAGTGCTTTG 59.722 41.667 0.00 0.00 0.00 2.77
571 583 4.278419 GTGTGGGTTATCTTTCAGTGCTTT 59.722 41.667 0.00 0.00 0.00 3.51
578 590 8.821686 ATTGATTATGTGTGGGTTATCTTTCA 57.178 30.769 0.00 0.00 0.00 2.69
580 592 8.686334 GTGATTGATTATGTGTGGGTTATCTTT 58.314 33.333 0.00 0.00 0.00 2.52
582 594 7.345691 TGTGATTGATTATGTGTGGGTTATCT 58.654 34.615 0.00 0.00 0.00 1.98
599 611 9.904198 TGGTTAGATGATTAGAATTGTGATTGA 57.096 29.630 0.00 0.00 0.00 2.57
643 655 8.601476 CAACTCTACGTCCAAGATTTATTAACC 58.399 37.037 0.00 0.00 0.00 2.85
678 690 7.956328 ATTATCAACTCTCGGGCTGTATATA 57.044 36.000 0.00 0.00 0.00 0.86
686 698 4.054780 TGTGTATTATCAACTCTCGGGC 57.945 45.455 0.00 0.00 0.00 6.13
715 727 7.966246 ACTTGCAATTTTTATTTCTGCATCA 57.034 28.000 0.00 0.00 42.22 3.07
738 752 3.319122 AGTTCCAGCATTGTCCAAAGAAC 59.681 43.478 0.00 0.00 34.09 3.01
751 765 4.730949 ACGCTAAATAGTAGTTCCAGCA 57.269 40.909 6.07 0.00 0.00 4.41
767 782 0.888619 AGTAGCTGCACTGAACGCTA 59.111 50.000 4.12 0.00 34.14 4.26
776 791 2.478831 GGCTTAGATCAGTAGCTGCAC 58.521 52.381 4.12 0.00 35.30 4.57
1143 1162 3.453070 GAGGAGCATCAGGTCGGCC 62.453 68.421 0.00 0.00 43.12 6.13
1275 1294 5.567430 TCAGCACCAGACTACTAAGAACTA 58.433 41.667 0.00 0.00 0.00 2.24
1285 1304 2.598565 AGACACTTCAGCACCAGACTA 58.401 47.619 0.00 0.00 0.00 2.59
1325 1344 8.687242 CAGCCTATATAATCGTCTAGAAATGGA 58.313 37.037 0.00 0.00 0.00 3.41
1370 1389 9.343539 GAAAATAGCTTCTAGGACATTTACCAT 57.656 33.333 0.00 0.00 0.00 3.55
1379 1431 7.100409 ACTGAAGTGAAAATAGCTTCTAGGAC 58.900 38.462 0.00 0.00 39.30 3.85
1380 1432 7.039011 TGACTGAAGTGAAAATAGCTTCTAGGA 60.039 37.037 0.00 0.00 39.30 2.94
1384 1436 9.507329 TTTATGACTGAAGTGAAAATAGCTTCT 57.493 29.630 0.00 0.00 39.30 2.85
1411 1463 8.312564 CCAATAAGAGATGCATCTTCTATCAGA 58.687 37.037 29.26 9.40 40.08 3.27
1424 1504 5.818136 TTACACTTGCCAATAAGAGATGC 57.182 39.130 0.00 0.00 0.00 3.91
1508 1588 7.298122 ACGAAGACATAAACACAGCAAATTAG 58.702 34.615 0.00 0.00 0.00 1.73
1518 1601 7.352719 AGATTTCTGACGAAGACATAAACAC 57.647 36.000 0.00 0.00 32.52 3.32
1546 1629 7.482654 TGATCATATCTGGATTCGTTGTTTC 57.517 36.000 0.00 0.00 0.00 2.78
1554 1637 7.986320 CCAAGGACTATGATCATATCTGGATTC 59.014 40.741 15.71 0.00 0.00 2.52
1698 1781 2.675844 CGAACATCCGCCAACATCTTTA 59.324 45.455 0.00 0.00 0.00 1.85
1712 1795 5.873179 TTTACCATCCAAACTCGAACATC 57.127 39.130 0.00 0.00 0.00 3.06
1782 1865 2.685897 ACTAAACTCAAAAGCGCCACAA 59.314 40.909 2.29 0.00 0.00 3.33
1833 1916 2.111669 CCACCACAGAGCAGTGCA 59.888 61.111 19.20 0.00 38.18 4.57
1863 1946 6.039717 TCTCCAAAACCTTCTCAACATTGAAG 59.960 38.462 0.00 0.00 39.32 3.02
1868 1951 4.401925 CCTCTCCAAAACCTTCTCAACAT 58.598 43.478 0.00 0.00 0.00 2.71
1882 1965 1.371467 TGATGGCTTTCCCTCTCCAA 58.629 50.000 0.00 0.00 31.66 3.53
1915 1998 5.136105 AGAATGATCTGCTCCATTTAACCC 58.864 41.667 0.00 0.00 33.57 4.11
2297 2748 7.965655 CACATTGTACGCTATTTAATGTTCCAA 59.034 33.333 0.00 0.00 39.25 3.53
2298 2749 7.468441 CACATTGTACGCTATTTAATGTTCCA 58.532 34.615 0.00 0.00 39.25 3.53
2317 2768 3.978855 CAGAGACACACAAATGCACATTG 59.021 43.478 11.46 11.46 0.00 2.82
2393 2844 2.825836 GCCATCAACTCCCCTGCG 60.826 66.667 0.00 0.00 0.00 5.18
2398 2849 1.225704 CCTCCTGCCATCAACTCCC 59.774 63.158 0.00 0.00 0.00 4.30
2458 2909 7.011828 TGGTTTAAGCGCTTGAAGAATATAC 57.988 36.000 32.23 16.28 0.00 1.47
2502 2953 7.809331 ACAGATATACATTTGCCAAAATATGCG 59.191 33.333 0.00 0.00 34.14 4.73
2583 3034 4.371855 TCACACACGGTTAAAATTGCAA 57.628 36.364 0.00 0.00 0.00 4.08
2667 3118 3.902881 ATGAGAGTAGGCCTTCAAGTG 57.097 47.619 12.58 0.00 0.00 3.16
3118 3569 2.567497 GGTTCACCCGTCTGACCGA 61.567 63.158 1.55 0.00 0.00 4.69
3243 3699 5.524511 AAAGCAACAGGAAAAACGAAAAC 57.475 34.783 0.00 0.00 0.00 2.43
3244 3700 5.615764 GCAAAAGCAACAGGAAAAACGAAAA 60.616 36.000 0.00 0.00 0.00 2.29
3245 3701 4.143009 GCAAAAGCAACAGGAAAAACGAAA 60.143 37.500 0.00 0.00 0.00 3.46
3246 3702 3.369451 GCAAAAGCAACAGGAAAAACGAA 59.631 39.130 0.00 0.00 0.00 3.85
3247 3703 2.926838 GCAAAAGCAACAGGAAAAACGA 59.073 40.909 0.00 0.00 0.00 3.85
3248 3704 2.030335 GGCAAAAGCAACAGGAAAAACG 59.970 45.455 0.00 0.00 0.00 3.60
3249 3705 3.270027 AGGCAAAAGCAACAGGAAAAAC 58.730 40.909 0.00 0.00 0.00 2.43
3508 3967 5.473504 AGTTCATGGTTGTAATGTGGACTTC 59.526 40.000 0.00 0.00 0.00 3.01
3526 3985 5.698741 TCATCCATGAGTGGTTAGTTCAT 57.301 39.130 0.00 0.00 46.16 2.57
3542 4001 4.458989 GTGCTAGTTCATGGTTTTCATCCA 59.541 41.667 0.00 0.00 39.41 3.41
3543 4002 4.702131 AGTGCTAGTTCATGGTTTTCATCC 59.298 41.667 0.00 0.00 32.92 3.51
3544 4003 5.634896 CAGTGCTAGTTCATGGTTTTCATC 58.365 41.667 0.00 0.00 32.92 2.92
3545 4004 4.082571 GCAGTGCTAGTTCATGGTTTTCAT 60.083 41.667 8.18 0.00 36.31 2.57
3546 4005 3.253188 GCAGTGCTAGTTCATGGTTTTCA 59.747 43.478 8.18 0.00 0.00 2.69
3550 4009 1.614317 GGGCAGTGCTAGTTCATGGTT 60.614 52.381 16.11 0.00 0.00 3.67
3551 4010 0.035056 GGGCAGTGCTAGTTCATGGT 60.035 55.000 16.11 0.00 0.00 3.55
3553 4012 1.339438 ACTGGGCAGTGCTAGTTCATG 60.339 52.381 16.11 0.00 40.75 3.07
3555 4014 0.764890 AACTGGGCAGTGCTAGTTCA 59.235 50.000 23.48 11.68 41.58 3.18
3556 4015 2.028020 ACTAACTGGGCAGTGCTAGTTC 60.028 50.000 28.78 9.94 41.58 3.01
3557 4016 1.978580 ACTAACTGGGCAGTGCTAGTT 59.021 47.619 28.29 28.29 41.58 2.24
3558 4017 1.276421 CACTAACTGGGCAGTGCTAGT 59.724 52.381 16.11 16.29 41.58 2.57
3559 4018 1.406069 CCACTAACTGGGCAGTGCTAG 60.406 57.143 16.11 15.65 41.58 3.42
3560 4019 0.613260 CCACTAACTGGGCAGTGCTA 59.387 55.000 16.11 3.70 41.58 3.49
3600 4599 1.459592 CTCGTGGTTTTGGCTAAGTCG 59.540 52.381 0.00 0.00 0.00 4.18
3608 4607 1.106944 AACCCTGCTCGTGGTTTTGG 61.107 55.000 0.00 0.00 42.09 3.28
3614 4613 0.951040 GAACTCAACCCTGCTCGTGG 60.951 60.000 0.00 0.00 0.00 4.94
3617 4616 1.819288 TCTAGAACTCAACCCTGCTCG 59.181 52.381 0.00 0.00 0.00 5.03
3621 4620 1.404315 GCGGTCTAGAACTCAACCCTG 60.404 57.143 6.16 0.00 0.00 4.45
3640 4639 1.228337 ACCCCCAAACTAACCACGC 60.228 57.895 0.00 0.00 0.00 5.34
3670 4669 4.729227 TTCAACCCTGAACTTCAAAACC 57.271 40.909 0.00 0.00 36.62 3.27
3678 4677 6.472887 TCGATTTAGAATTCAACCCTGAACT 58.527 36.000 8.44 0.00 44.28 3.01
3699 4698 2.005370 ACCCTGAACTAACCACTCGA 57.995 50.000 0.00 0.00 0.00 4.04
3735 4734 5.177326 GCTCATATGGGCAAACATTTTGAA 58.823 37.500 22.95 0.00 32.39 2.69
3741 4740 3.070446 CCAATGCTCATATGGGCAAACAT 59.930 43.478 32.84 14.89 41.90 2.71
3742 4741 2.431419 CCAATGCTCATATGGGCAAACA 59.569 45.455 32.84 11.20 41.90 2.83
3743 4742 2.694628 TCCAATGCTCATATGGGCAAAC 59.305 45.455 32.84 2.46 41.90 2.93
3746 4745 1.214923 TGTCCAATGCTCATATGGGCA 59.785 47.619 31.52 31.52 46.01 5.36
3747 4746 1.985473 TGTCCAATGCTCATATGGGC 58.015 50.000 21.18 21.18 39.31 5.36
3748 4747 2.624838 GGTTGTCCAATGCTCATATGGG 59.375 50.000 2.13 0.00 34.89 4.00
3751 4750 4.508551 TCAGGTTGTCCAATGCTCATAT 57.491 40.909 0.00 0.00 35.89 1.78
3752 4751 3.998913 TCAGGTTGTCCAATGCTCATA 57.001 42.857 0.00 0.00 35.89 2.15
3753 4752 2.885135 TCAGGTTGTCCAATGCTCAT 57.115 45.000 0.00 0.00 35.89 2.90
3754 4753 2.507484 CTTCAGGTTGTCCAATGCTCA 58.493 47.619 0.00 0.00 35.89 4.26
3755 4754 1.200948 GCTTCAGGTTGTCCAATGCTC 59.799 52.381 0.00 0.00 35.89 4.26
3756 4755 1.251251 GCTTCAGGTTGTCCAATGCT 58.749 50.000 0.00 0.00 35.89 3.79
3769 4769 2.290122 ATCTCCACGGCTCGCTTCAG 62.290 60.000 0.00 0.00 0.00 3.02
3793 4793 1.935194 CTGAGCGCATGAGCATGAG 59.065 57.895 23.73 11.75 41.20 2.90
3799 4799 2.172372 GTGAGGCTGAGCGCATGAG 61.172 63.158 11.47 2.63 41.67 2.90
3818 4818 3.254060 CCGTACACTCCTCAACTGAATG 58.746 50.000 0.00 0.00 0.00 2.67
3834 4834 2.088950 AGCAACACACCATACCGTAC 57.911 50.000 0.00 0.00 0.00 3.67
3837 4837 1.196808 GTCAAGCAACACACCATACCG 59.803 52.381 0.00 0.00 0.00 4.02
3849 4849 2.472695 ACTTAGGCATCGTCAAGCAA 57.527 45.000 0.00 0.00 0.00 3.91
3853 4853 2.742053 GCAGAAACTTAGGCATCGTCAA 59.258 45.455 0.00 0.00 0.00 3.18
3871 4871 6.419413 TCAAAAGCTTTTAACGGTTATTGCAG 59.581 34.615 23.44 6.92 0.00 4.41
3880 4880 2.291190 TCCGGTCAAAAGCTTTTAACGG 59.709 45.455 33.07 33.07 39.27 4.44
3930 4930 3.751518 GGCAAACTGAGAGGAGGTAAAA 58.248 45.455 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.