Multiple sequence alignment - TraesCS2A01G467800

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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 TraesCS2A01G467800 chr2A 100.000 4153 0 0 1 4153 711973041 711977193 0.000000e+00 7670
1 TraesCS2A01G467800 chr2A 85.174 661 71 15 961 1606 111272113 111271465 0.000000e+00 652
2 TraesCS2A01G467800 chr2D 89.384 3523 178 53 143 3566 572783226 572786651 0.000000e+00 4253
3 TraesCS2A01G467800 chr2D 81.522 368 24 27 3793 4130 572786789 572787142 3.180000e-66 263
4 TraesCS2A01G467800 chr2D 93.103 145 8 1 1 143 572736335 572736479 1.170000e-50 211
5 TraesCS2A01G467800 chr2B 89.956 2967 207 41 485 3415 688456477 688459388 0.000000e+00 3744
6 TraesCS2A01G467800 chr2B 83.429 700 50 30 3469 4126 688459409 688460084 1.290000e-164 590
7 TraesCS2A01G467800 chr2B 84.842 442 39 10 2 423 688456042 688456475 1.790000e-113 420
8 TraesCS2A01G467800 chr3A 86.233 661 64 15 961 1606 703852648 703852000 0.000000e+00 691
9 TraesCS2A01G467800 chr3A 85.023 661 71 18 961 1606 58077477 58076830 0.000000e+00 647
10 TraesCS2A01G467800 chr6D 86.018 658 67 14 961 1606 150885755 150885111 0.000000e+00 682
11 TraesCS2A01G467800 chr7D 85.303 660 71 15 961 1606 180440546 180441193 0.000000e+00 658
12 TraesCS2A01G467800 chr3D 85.303 660 71 15 961 1606 86080485 86079838 0.000000e+00 658
13 TraesCS2A01G467800 chr1A 85.325 661 68 17 961 1606 67961321 67960675 0.000000e+00 656


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 TraesCS2A01G467800 chr2A 711973041 711977193 4152 False 7670.000000 7670 100.000000 1 4153 1 chr2A.!!$F1 4152
1 TraesCS2A01G467800 chr2A 111271465 111272113 648 True 652.000000 652 85.174000 961 1606 1 chr2A.!!$R1 645
2 TraesCS2A01G467800 chr2D 572783226 572787142 3916 False 2258.000000 4253 85.453000 143 4130 2 chr2D.!!$F2 3987
3 TraesCS2A01G467800 chr2B 688456042 688460084 4042 False 1584.666667 3744 86.075667 2 4126 3 chr2B.!!$F1 4124
4 TraesCS2A01G467800 chr3A 703852000 703852648 648 True 691.000000 691 86.233000 961 1606 1 chr3A.!!$R2 645
5 TraesCS2A01G467800 chr3A 58076830 58077477 647 True 647.000000 647 85.023000 961 1606 1 chr3A.!!$R1 645
6 TraesCS2A01G467800 chr6D 150885111 150885755 644 True 682.000000 682 86.018000 961 1606 1 chr6D.!!$R1 645
7 TraesCS2A01G467800 chr7D 180440546 180441193 647 False 658.000000 658 85.303000 961 1606 1 chr7D.!!$F1 645
8 TraesCS2A01G467800 chr3D 86079838 86080485 647 True 658.000000 658 85.303000 961 1606 1 chr3D.!!$R1 645
9 TraesCS2A01G467800 chr1A 67960675 67961321 646 True 656.000000 656 85.325000 961 1606 1 chr1A.!!$R1 645

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
460 492 0.108567 GTCCTCTCTTCCAAGTCGGC 60.109 60.0 0.0 0.0 33.14 5.54 F
481 513 0.179089 TCACCGTTTCCCGTCGAAAA 60.179 50.0 0.0 0.0 42.11 2.29 F
585 652 0.183971 ATCCGTCAGATCTCTCCCGT 59.816 55.0 0.0 0.0 0.00 5.28 F
1150 1223 0.460722 GTCCTCTTCCCTTACGGCTC 59.539 60.0 0.0 0.0 0.00 4.70 F
2013 2109 1.014044 CATGAACCAGTGACGACCCG 61.014 60.0 0.0 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 1943 0.469917 ACTCATTAGTGATGGCCCCG 59.530 55.000 0.00 0.00 36.37 5.73 R
2437 2552 1.435256 AGCCATAAATAGGGACGCCT 58.565 50.000 0.00 0.00 0.00 5.52 R
2568 2687 5.192927 GTGTTGTCAGGATATGAAATGGGA 58.807 41.667 0.00 0.00 40.43 4.37 R
2940 3085 1.305219 GCATGGCAAGCACGGTAAGA 61.305 55.000 10.23 0.00 0.00 2.10 R
3950 4160 0.179089 ATCAGTGAGCGATCAGTGGC 60.179 55.000 31.79 9.61 40.45 5.01 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
31 32 8.465273 ACTTAGTTATTCAACTTTTCAAGCCT 57.535 30.769 0.00 0.00 42.51 4.58
46 47 9.399403 CTTTTCAAGCCTAATCTTCTAACAAAC 57.601 33.333 0.00 0.00 0.00 2.93
47 48 8.691661 TTTCAAGCCTAATCTTCTAACAAACT 57.308 30.769 0.00 0.00 0.00 2.66
48 49 7.907214 TCAAGCCTAATCTTCTAACAAACTC 57.093 36.000 0.00 0.00 0.00 3.01
73 74 9.224267 TCTCACCTTTAAAATCTCATTCTCTTG 57.776 33.333 0.00 0.00 0.00 3.02
247 261 7.333672 ACTTTTACGATACCAAAGATTCCTCAC 59.666 37.037 0.00 0.00 32.73 3.51
395 427 2.997315 GCCCAAGCCCAAGGAACC 60.997 66.667 0.00 0.00 0.00 3.62
423 455 1.021920 GCGTTTCTGCCTCTCTTCCC 61.022 60.000 0.00 0.00 0.00 3.97
424 456 0.321671 CGTTTCTGCCTCTCTTCCCA 59.678 55.000 0.00 0.00 0.00 4.37
425 457 1.270839 CGTTTCTGCCTCTCTTCCCAA 60.271 52.381 0.00 0.00 0.00 4.12
426 458 2.431454 GTTTCTGCCTCTCTTCCCAAG 58.569 52.381 0.00 0.00 0.00 3.61
427 459 1.734655 TTCTGCCTCTCTTCCCAAGT 58.265 50.000 0.00 0.00 0.00 3.16
428 460 1.734655 TCTGCCTCTCTTCCCAAGTT 58.265 50.000 0.00 0.00 0.00 2.66
429 461 2.057922 TCTGCCTCTCTTCCCAAGTTT 58.942 47.619 0.00 0.00 0.00 2.66
430 462 2.443255 TCTGCCTCTCTTCCCAAGTTTT 59.557 45.455 0.00 0.00 0.00 2.43
431 463 3.117512 TCTGCCTCTCTTCCCAAGTTTTT 60.118 43.478 0.00 0.00 0.00 1.94
452 484 2.833631 TTTTGACGGTCCTCTCTTCC 57.166 50.000 5.55 0.00 0.00 3.46
453 485 1.712056 TTTGACGGTCCTCTCTTCCA 58.288 50.000 5.55 0.00 0.00 3.53
454 486 1.712056 TTGACGGTCCTCTCTTCCAA 58.288 50.000 5.55 0.00 0.00 3.53
455 487 1.257743 TGACGGTCCTCTCTTCCAAG 58.742 55.000 5.55 0.00 0.00 3.61
456 488 1.258676 GACGGTCCTCTCTTCCAAGT 58.741 55.000 0.00 0.00 0.00 3.16
457 489 1.202817 GACGGTCCTCTCTTCCAAGTC 59.797 57.143 0.00 0.00 0.00 3.01
458 490 0.171455 CGGTCCTCTCTTCCAAGTCG 59.829 60.000 0.00 0.00 0.00 4.18
459 491 0.533032 GGTCCTCTCTTCCAAGTCGG 59.467 60.000 0.00 0.00 0.00 4.79
460 492 0.108567 GTCCTCTCTTCCAAGTCGGC 60.109 60.000 0.00 0.00 33.14 5.54
461 493 1.153745 CCTCTCTTCCAAGTCGGCG 60.154 63.158 0.00 0.00 33.14 6.46
462 494 1.587054 CTCTCTTCCAAGTCGGCGT 59.413 57.895 6.85 0.00 33.14 5.68
463 495 0.456995 CTCTCTTCCAAGTCGGCGTC 60.457 60.000 6.85 0.00 33.14 5.19
464 496 1.176619 TCTCTTCCAAGTCGGCGTCA 61.177 55.000 6.85 0.00 33.14 4.35
465 497 1.006571 TCTTCCAAGTCGGCGTCAC 60.007 57.895 6.85 0.00 33.14 3.67
466 498 2.027625 CTTCCAAGTCGGCGTCACC 61.028 63.158 6.85 0.00 33.14 4.02
475 507 4.974989 GGCGTCACCGTTTCCCGT 62.975 66.667 0.00 0.00 36.15 5.28
476 508 3.408851 GCGTCACCGTTTCCCGTC 61.409 66.667 0.00 0.00 36.15 4.79
477 509 3.101428 CGTCACCGTTTCCCGTCG 61.101 66.667 0.00 0.00 33.66 5.12
478 510 2.336088 GTCACCGTTTCCCGTCGA 59.664 61.111 0.00 0.00 33.66 4.20
479 511 1.300080 GTCACCGTTTCCCGTCGAA 60.300 57.895 0.00 0.00 33.66 3.71
480 512 0.875474 GTCACCGTTTCCCGTCGAAA 60.875 55.000 0.00 0.00 38.16 3.46
481 513 0.179089 TCACCGTTTCCCGTCGAAAA 60.179 50.000 0.00 0.00 42.11 2.29
482 514 0.656785 CACCGTTTCCCGTCGAAAAA 59.343 50.000 0.00 0.00 42.11 1.94
507 574 4.651008 GGCGTCACCGTTCCGTCA 62.651 66.667 0.00 0.00 36.15 4.35
526 593 1.504275 ATCCAGTCCAAGGCTGCCTT 61.504 55.000 27.70 27.70 45.88 4.35
580 647 3.226777 CCACCTTATCCGTCAGATCTCT 58.773 50.000 0.00 0.00 36.33 3.10
585 652 0.183971 ATCCGTCAGATCTCTCCCGT 59.816 55.000 0.00 0.00 0.00 5.28
608 675 3.225061 GATCTCCCCCGTCCGTCC 61.225 72.222 0.00 0.00 0.00 4.79
647 714 4.179599 CCTCTCCCCCTCCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
648 715 4.179599 CTCTCCCCCTCCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
694 761 1.749638 GGAGCCGACGAAGAGGAGA 60.750 63.158 0.00 0.00 0.00 3.71
695 762 1.720694 GGAGCCGACGAAGAGGAGAG 61.721 65.000 0.00 0.00 0.00 3.20
732 802 3.471806 GGAAGACCTCCGCTCCCC 61.472 72.222 0.00 0.00 33.37 4.81
770 840 3.049344 ACCCTCCTCAAGATGGTAATCC 58.951 50.000 0.00 0.00 41.32 3.01
849 919 4.317529 GCGATCTGGCGAGAAGAG 57.682 61.111 1.37 0.00 0.00 2.85
863 933 2.892542 GAAGAGCTCGGCGGAGAACC 62.893 65.000 24.11 11.62 43.27 3.62
881 951 1.003233 ACCAGATCTCCCGGTGTTTTC 59.997 52.381 0.00 0.00 0.00 2.29
958 1028 3.981071 TCAGATCGATGGTGGAAAACT 57.019 42.857 0.54 0.00 0.00 2.66
991 1061 1.856265 GCCCTGCTTTGTCGAACTGG 61.856 60.000 0.00 0.00 0.00 4.00
1138 1211 1.895798 TGAAGCGATGTGAGTCCTCTT 59.104 47.619 0.00 0.00 0.00 2.85
1146 1219 2.168496 TGTGAGTCCTCTTCCCTTACG 58.832 52.381 0.00 0.00 0.00 3.18
1150 1223 0.460722 GTCCTCTTCCCTTACGGCTC 59.539 60.000 0.00 0.00 0.00 4.70
1162 1236 2.074230 TACGGCTCGTTCGTGTGGTT 62.074 55.000 5.57 0.00 41.54 3.67
1218 1296 3.266636 TGTGACGAGTTGTTTGATGTGT 58.733 40.909 0.00 0.00 0.00 3.72
1278 1356 1.677637 CGAGTAAGGGGGAGCCTGTC 61.678 65.000 0.00 0.00 0.00 3.51
1293 1371 1.874345 CTGTCGAGTACCGGTGCCTT 61.874 60.000 19.93 0.00 39.14 4.35
1336 1414 1.136500 GGAACATCTCCACCTCGGTAC 59.864 57.143 0.00 0.00 44.67 3.34
1506 1594 7.991084 TTGCATATTTCCTCTGGATATGAAG 57.009 36.000 9.95 0.00 36.37 3.02
1518 1606 5.869344 TCTGGATATGAAGTGAAACAACTCG 59.131 40.000 0.00 0.00 41.43 4.18
1562 1652 6.262601 AGAATGTTTGTTGGTTGTTACTTCG 58.737 36.000 0.00 0.00 0.00 3.79
1565 1655 4.095185 TGTTTGTTGGTTGTTACTTCGAGG 59.905 41.667 0.00 0.00 0.00 4.63
1581 1672 2.076863 CGAGGTGAGGATGGTTTGTTC 58.923 52.381 0.00 0.00 0.00 3.18
1751 1842 9.819267 GTATAAAGTTAGGACTGAAGCACTTAT 57.181 33.333 0.00 0.00 35.91 1.73
1764 1855 6.908825 TGAAGCACTTATGTTTGGTACATTC 58.091 36.000 0.00 0.00 45.19 2.67
1768 1859 6.886459 AGCACTTATGTTTGGTACATTCTGAT 59.114 34.615 0.00 0.00 45.19 2.90
1778 1869 5.917462 TGGTACATTCTGATCATAGTGGTG 58.083 41.667 8.20 0.43 0.00 4.17
1804 1897 5.411781 AGTCTTTTATGCAGTAACCTCTCG 58.588 41.667 0.00 0.00 0.00 4.04
1843 1939 4.079958 AGTTAAACTAATAGGGCAGTGGGG 60.080 45.833 0.00 0.00 0.00 4.96
1847 1943 1.694696 CTAATAGGGCAGTGGGGAGAC 59.305 57.143 0.00 0.00 0.00 3.36
1878 1974 7.225538 CCATCACTAATGAGTTGTCCTGATTAC 59.774 40.741 0.00 0.00 38.57 1.89
1928 2024 9.141400 GAGTTAGAACTTACCAGTGTTAAGATG 57.859 37.037 13.80 0.00 39.88 2.90
2007 2103 3.921119 TCAATTGCATGAACCAGTGAC 57.079 42.857 0.00 0.00 0.00 3.67
2013 2109 1.014044 CATGAACCAGTGACGACCCG 61.014 60.000 0.00 0.00 0.00 5.28
2045 2141 8.450578 TTGTTTCATCTTACATCAGTTGAACT 57.549 30.769 0.00 0.00 33.92 3.01
2117 2214 9.204337 TGAATGATATTTTCCCAAGATCATGTT 57.796 29.630 5.65 0.00 37.33 2.71
2219 2316 2.824936 TCGATGTGAACCCATGCATTTT 59.175 40.909 0.00 0.00 0.00 1.82
2220 2317 3.257873 TCGATGTGAACCCATGCATTTTT 59.742 39.130 0.00 0.00 0.00 1.94
2221 2318 3.613737 CGATGTGAACCCATGCATTTTTC 59.386 43.478 0.00 0.36 0.00 2.29
2222 2319 4.618927 CGATGTGAACCCATGCATTTTTCT 60.619 41.667 0.00 0.00 0.00 2.52
2223 2320 4.686191 TGTGAACCCATGCATTTTTCTT 57.314 36.364 0.00 0.00 0.00 2.52
2224 2321 5.033589 TGTGAACCCATGCATTTTTCTTT 57.966 34.783 0.00 0.00 0.00 2.52
2225 2322 5.055812 TGTGAACCCATGCATTTTTCTTTC 58.944 37.500 0.00 0.00 0.00 2.62
2226 2323 4.452114 GTGAACCCATGCATTTTTCTTTCC 59.548 41.667 0.00 0.00 0.00 3.13
2227 2324 4.102210 TGAACCCATGCATTTTTCTTTCCA 59.898 37.500 0.00 0.00 0.00 3.53
2228 2325 4.914177 ACCCATGCATTTTTCTTTCCAT 57.086 36.364 0.00 0.00 0.00 3.41
2229 2326 4.581868 ACCCATGCATTTTTCTTTCCATG 58.418 39.130 0.00 0.00 0.00 3.66
2230 2327 3.375922 CCCATGCATTTTTCTTTCCATGC 59.624 43.478 0.00 0.00 42.07 4.06
2236 2333 7.925043 TGCATTTTTCTTTCCATGCATTTAT 57.075 28.000 0.00 0.00 45.50 1.40
2258 2355 4.264253 TGCTCTCCGATGAAACAATTGAT 58.736 39.130 13.59 0.00 0.00 2.57
2329 2429 7.171630 AGTCTTAGTAATGAAATCACGGTCT 57.828 36.000 0.00 0.00 0.00 3.85
2387 2488 6.096846 CCTAATTCCCATGACCTAAGTTTTGG 59.903 42.308 0.00 0.00 0.00 3.28
2437 2552 4.979335 TGATGGTTGAAGTGGTGATGTAA 58.021 39.130 0.00 0.00 0.00 2.41
2568 2687 4.634199 CTGTCAATTTGGAAACATGCCTT 58.366 39.130 0.00 0.00 42.32 4.35
2586 2705 3.823304 GCCTTCCCATTTCATATCCTGAC 59.177 47.826 0.00 0.00 32.17 3.51
2626 2745 8.723942 ACTCACATGAACTAATCTGTTTATCC 57.276 34.615 0.00 0.00 0.00 2.59
2644 2763 7.068103 TGTTTATCCTTGTGCATACCTATTTGG 59.932 37.037 0.00 0.00 42.93 3.28
2664 2783 3.843893 GCCCCAGCCATATCAAATTTT 57.156 42.857 0.00 0.00 0.00 1.82
2673 2792 6.369340 CAGCCATATCAAATTTTTGCAACTCA 59.631 34.615 0.00 0.00 38.05 3.41
2745 2865 7.611855 GGATAAATATGTGCACTTAGGGCTTAT 59.388 37.037 19.41 15.36 0.00 1.73
2821 2941 7.232118 TCTGAAATGTCATCAGAGAACTGTA 57.768 36.000 2.57 0.00 46.23 2.74
2854 2987 6.824305 ATTGTTTTGGTTATGAGGACTGAG 57.176 37.500 0.00 0.00 0.00 3.35
2940 3085 4.159135 GCATTTCTGGACCAATCAGTGAAT 59.841 41.667 0.00 0.00 34.15 2.57
3161 3311 4.597004 CAGGGTCTAAGTAGTGAGGTACA 58.403 47.826 0.00 0.00 0.00 2.90
3217 3367 0.249322 CGGTCAAGACGTTGTCACCT 60.249 55.000 0.00 0.00 34.60 4.00
3308 3461 2.539274 GCATTTTGAAGCAGCGTTTTGA 59.461 40.909 0.00 0.00 0.00 2.69
3325 3478 3.350219 TTGATCTGGTTGTAAGCCTCC 57.650 47.619 0.00 0.00 0.00 4.30
3327 3480 1.840635 GATCTGGTTGTAAGCCTCCCT 59.159 52.381 0.00 0.00 0.00 4.20
3328 3481 0.984230 TCTGGTTGTAAGCCTCCCTG 59.016 55.000 0.00 0.00 0.00 4.45
3372 3530 2.238084 ACTGCTAGATCTGACCACCA 57.762 50.000 5.18 0.00 0.00 4.17
3400 3560 6.486993 AGTCTTAGTTCAGTTTGGAATGGTTC 59.513 38.462 0.00 0.00 0.00 3.62
3401 3561 6.262273 GTCTTAGTTCAGTTTGGAATGGTTCA 59.738 38.462 0.00 0.00 0.00 3.18
3446 3609 8.881743 GCCTATGATATGAATGAAGAATCTGTC 58.118 37.037 0.00 0.00 0.00 3.51
3484 3647 2.278854 GCAATGCTGGTGTGTTTTTGT 58.721 42.857 0.00 0.00 0.00 2.83
3553 3737 3.604024 GGTACGTTACCTCCCTCCT 57.396 57.895 0.00 0.00 45.52 3.69
3555 3739 1.064091 GGTACGTTACCTCCCTCCTCT 60.064 57.143 0.00 0.00 45.52 3.69
3569 3753 2.421670 CCTCCTCTGCTGCTGAATCAAT 60.422 50.000 10.47 0.00 0.00 2.57
3638 3830 5.538813 TGTCTATAGTCTTGGATGCCGTATT 59.461 40.000 0.00 0.00 0.00 1.89
3651 3843 0.664761 CCGTATTTGCATGGCCTCAG 59.335 55.000 3.32 0.00 0.00 3.35
3701 3893 2.053116 GATGCCAATGCGTACGCG 60.053 61.111 32.65 20.44 45.51 6.01
3702 3894 3.506312 GATGCCAATGCGTACGCGG 62.506 63.158 32.65 27.65 45.51 6.46
3709 3901 3.538028 ATGCGTACGCGGATCCTCG 62.538 63.158 32.65 22.16 45.95 4.63
3738 3933 2.743636 TTTCGTTAGTCTCTGCCCAG 57.256 50.000 0.00 0.00 0.00 4.45
3739 3934 1.629043 TTCGTTAGTCTCTGCCCAGT 58.371 50.000 0.00 0.00 0.00 4.00
3743 3938 2.480419 CGTTAGTCTCTGCCCAGTTTTG 59.520 50.000 0.00 0.00 0.00 2.44
3744 3939 2.185004 TAGTCTCTGCCCAGTTTTGC 57.815 50.000 0.00 0.00 0.00 3.68
3749 3944 1.007387 CTGCCCAGTTTTGCCGTTC 60.007 57.895 0.00 0.00 0.00 3.95
3756 3951 2.095567 CCAGTTTTGCCGTTCAGATCAG 60.096 50.000 0.00 0.00 0.00 2.90
3778 3974 8.868522 TCAGAATGGTTTTTATCTCAATCTGT 57.131 30.769 0.00 0.00 37.97 3.41
3779 3975 8.950210 TCAGAATGGTTTTTATCTCAATCTGTC 58.050 33.333 0.00 0.00 37.97 3.51
3780 3976 8.954350 CAGAATGGTTTTTATCTCAATCTGTCT 58.046 33.333 0.00 0.00 34.35 3.41
3781 3977 8.954350 AGAATGGTTTTTATCTCAATCTGTCTG 58.046 33.333 0.00 0.00 0.00 3.51
3782 3978 6.500684 TGGTTTTTATCTCAATCTGTCTGC 57.499 37.500 0.00 0.00 0.00 4.26
3783 3979 5.122239 TGGTTTTTATCTCAATCTGTCTGCG 59.878 40.000 0.00 0.00 0.00 5.18
3784 3980 5.351465 GGTTTTTATCTCAATCTGTCTGCGA 59.649 40.000 0.00 0.00 0.00 5.10
3785 3981 6.037610 GGTTTTTATCTCAATCTGTCTGCGAT 59.962 38.462 0.00 0.00 0.00 4.58
3786 3982 7.414540 GGTTTTTATCTCAATCTGTCTGCGATT 60.415 37.037 0.00 0.00 0.00 3.34
3787 3983 7.615582 TTTTATCTCAATCTGTCTGCGATTT 57.384 32.000 0.00 0.00 0.00 2.17
3788 3984 6.594284 TTATCTCAATCTGTCTGCGATTTG 57.406 37.500 0.00 0.00 0.00 2.32
3789 3985 3.264947 TCTCAATCTGTCTGCGATTTGG 58.735 45.455 0.00 0.00 0.00 3.28
3790 3986 3.055891 TCTCAATCTGTCTGCGATTTGGA 60.056 43.478 0.00 0.00 0.00 3.53
3791 3987 3.002791 TCAATCTGTCTGCGATTTGGAC 58.997 45.455 0.00 0.00 0.00 4.02
3804 4000 4.453136 GCGATTTGGACTGTTTTACCACTA 59.547 41.667 0.00 0.00 33.20 2.74
3808 4004 7.041644 CGATTTGGACTGTTTTACCACTAGAAA 60.042 37.037 0.00 0.00 33.20 2.52
3837 4033 9.956720 AAGAATCTGTGAAGTGTTCTTTTTATG 57.043 29.630 0.00 0.00 36.11 1.90
3841 4037 7.054124 TCTGTGAAGTGTTCTTTTTATGGACT 58.946 34.615 0.00 0.00 33.64 3.85
3846 4042 4.213482 AGTGTTCTTTTTATGGACTCGCAC 59.787 41.667 0.00 0.00 0.00 5.34
3847 4043 4.024387 GTGTTCTTTTTATGGACTCGCACA 60.024 41.667 0.00 0.00 0.00 4.57
3848 4044 4.024387 TGTTCTTTTTATGGACTCGCACAC 60.024 41.667 0.00 0.00 0.00 3.82
3849 4045 2.734606 TCTTTTTATGGACTCGCACACG 59.265 45.455 0.00 0.00 42.01 4.49
3860 4070 2.480555 GCACACGATCTTTGCCCG 59.519 61.111 0.00 0.00 0.00 6.13
3936 4146 5.975693 AAATAATCCGAAAGCCAACAAGA 57.024 34.783 0.00 0.00 0.00 3.02
3938 4148 1.156736 ATCCGAAAGCCAACAAGACG 58.843 50.000 0.00 0.00 0.00 4.18
3939 4149 0.882927 TCCGAAAGCCAACAAGACGG 60.883 55.000 0.00 0.00 40.16 4.79
3944 4154 2.594592 GCCAACAAGACGGGCACT 60.595 61.111 0.00 0.00 46.92 4.40
3945 4155 2.908073 GCCAACAAGACGGGCACTG 61.908 63.158 0.00 0.00 46.92 3.66
3946 4156 1.227823 CCAACAAGACGGGCACTGA 60.228 57.895 0.00 0.00 38.67 3.41
3947 4157 1.507141 CCAACAAGACGGGCACTGAC 61.507 60.000 0.00 0.00 38.67 3.51
3948 4158 1.594293 AACAAGACGGGCACTGACG 60.594 57.895 0.00 0.00 38.67 4.35
3949 4159 3.414700 CAAGACGGGCACTGACGC 61.415 66.667 0.00 0.00 38.67 5.19
4040 4274 2.687566 ACCACCCACTCCCGATCC 60.688 66.667 0.00 0.00 0.00 3.36
4041 4275 3.849951 CCACCCACTCCCGATCCG 61.850 72.222 0.00 0.00 0.00 4.18
4046 4280 3.606662 CACTCCCGATCCGCCGAT 61.607 66.667 0.00 0.00 0.00 4.18
4047 4281 3.296054 ACTCCCGATCCGCCGATC 61.296 66.667 5.09 5.09 41.43 3.69
4098 4335 7.147497 ACCCCTCAAAATCTCATCTTTTGTTTT 60.147 33.333 8.00 0.00 41.88 2.43
4126 4363 4.995058 TCCCCCACCACCACTCCC 62.995 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
46 47 9.447157 AAGAGAATGAGATTTTAAAGGTGAGAG 57.553 33.333 0.00 0.00 0.00 3.20
47 48 9.224267 CAAGAGAATGAGATTTTAAAGGTGAGA 57.776 33.333 0.00 0.00 0.00 3.27
48 49 7.967303 GCAAGAGAATGAGATTTTAAAGGTGAG 59.033 37.037 0.00 0.00 0.00 3.51
73 74 6.183360 CCAAACATGTTTAGCAATATTTGGGC 60.183 38.462 22.87 0.00 40.25 5.36
359 391 1.599542 GCTGAACGGGATAAGCATGAC 59.400 52.381 0.00 0.00 35.69 3.06
361 393 0.947244 GGCTGAACGGGATAAGCATG 59.053 55.000 0.00 0.00 37.40 4.06
395 427 1.225745 GCAGAAACGCCGTGATTCG 60.226 57.895 0.00 0.00 34.76 3.34
432 464 2.436542 TGGAAGAGAGGACCGTCAAAAA 59.563 45.455 0.00 0.00 0.00 1.94
433 465 2.043992 TGGAAGAGAGGACCGTCAAAA 58.956 47.619 0.00 0.00 0.00 2.44
434 466 1.712056 TGGAAGAGAGGACCGTCAAA 58.288 50.000 0.00 0.00 0.00 2.69
435 467 1.618837 CTTGGAAGAGAGGACCGTCAA 59.381 52.381 0.00 0.00 0.00 3.18
436 468 1.257743 CTTGGAAGAGAGGACCGTCA 58.742 55.000 0.00 0.00 0.00 4.35
437 469 1.202817 GACTTGGAAGAGAGGACCGTC 59.797 57.143 0.00 0.00 0.00 4.79
438 470 1.258676 GACTTGGAAGAGAGGACCGT 58.741 55.000 0.00 0.00 0.00 4.83
439 471 0.171455 CGACTTGGAAGAGAGGACCG 59.829 60.000 0.00 0.00 0.00 4.79
440 472 0.533032 CCGACTTGGAAGAGAGGACC 59.467 60.000 0.00 0.00 42.00 4.46
441 473 0.108567 GCCGACTTGGAAGAGAGGAC 60.109 60.000 0.00 0.00 42.00 3.85
442 474 1.595993 CGCCGACTTGGAAGAGAGGA 61.596 60.000 0.00 0.00 42.00 3.71
443 475 1.153745 CGCCGACTTGGAAGAGAGG 60.154 63.158 0.00 0.00 42.00 3.69
444 476 0.456995 GACGCCGACTTGGAAGAGAG 60.457 60.000 0.00 0.00 42.00 3.20
445 477 1.176619 TGACGCCGACTTGGAAGAGA 61.177 55.000 0.00 0.00 42.00 3.10
446 478 1.009389 GTGACGCCGACTTGGAAGAG 61.009 60.000 0.00 0.00 42.00 2.85
447 479 1.006571 GTGACGCCGACTTGGAAGA 60.007 57.895 0.00 0.00 42.00 2.87
448 480 2.027625 GGTGACGCCGACTTGGAAG 61.028 63.158 0.00 0.00 42.00 3.46
449 481 2.029964 GGTGACGCCGACTTGGAA 59.970 61.111 0.00 0.00 42.00 3.53
507 574 1.504275 AAGGCAGCCTTGGACTGGAT 61.504 55.000 26.87 0.00 42.96 3.41
526 593 0.179020 CAGGGGCTGTGAACTTGTGA 60.179 55.000 0.00 0.00 0.00 3.58
585 652 4.070265 ACGGGGGAGATCACGGGA 62.070 66.667 0.00 0.00 0.00 5.14
608 675 0.919289 AGGGTGGGGTATTGTGGGAG 60.919 60.000 0.00 0.00 0.00 4.30
646 713 4.853142 CGGGTCGGAGATGGGGGA 62.853 72.222 0.00 0.00 40.67 4.81
647 714 4.853142 TCGGGTCGGAGATGGGGG 62.853 72.222 0.00 0.00 40.67 5.40
648 715 2.762459 TTCGGGTCGGAGATGGGG 60.762 66.667 0.00 0.00 40.67 4.96
649 716 2.499685 GTTCGGGTCGGAGATGGG 59.500 66.667 0.00 0.00 40.67 4.00
650 717 2.499685 GGTTCGGGTCGGAGATGG 59.500 66.667 0.00 0.00 40.67 3.51
746 816 1.225704 CCATCTTGAGGAGGGTGGC 59.774 63.158 0.00 0.00 40.66 5.01
849 919 2.962697 GATCTGGTTCTCCGCCGAGC 62.963 65.000 0.00 0.00 35.94 5.03
863 933 1.359848 CGAAAACACCGGGAGATCTG 58.640 55.000 6.32 0.00 0.00 2.90
881 951 1.014352 CGGTTCCAAATTCTAGGGCG 58.986 55.000 0.00 0.00 0.00 6.13
991 1061 2.531206 GCGAGTAGACATGGTCAGAAC 58.469 52.381 0.00 0.00 34.60 3.01
1146 1219 1.278637 CAAACCACACGAACGAGCC 59.721 57.895 0.14 0.00 0.00 4.70
1150 1223 0.248296 CAACCCAAACCACACGAACG 60.248 55.000 0.00 0.00 0.00 3.95
1162 1236 2.255406 CCCATCAAATCCACAACCCAA 58.745 47.619 0.00 0.00 0.00 4.12
1218 1296 1.006220 ACACTTCATCGACGCTGCA 60.006 52.632 0.00 0.00 0.00 4.41
1278 1356 1.445582 GACAAGGCACCGGTACTCG 60.446 63.158 6.87 0.00 38.88 4.18
1336 1414 4.094590 CAGCAGCAGGAAGAAAGTGAATAG 59.905 45.833 0.00 0.00 0.00 1.73
1506 1594 1.133407 TGCAAACCCGAGTTGTTTCAC 59.867 47.619 0.00 0.00 35.97 3.18
1562 1652 2.076863 CGAACAAACCATCCTCACCTC 58.923 52.381 0.00 0.00 0.00 3.85
1565 1655 4.693566 TCAATACGAACAAACCATCCTCAC 59.306 41.667 0.00 0.00 0.00 3.51
1581 1672 9.976511 TTACCTACCTATCAATTTCTCAATACG 57.023 33.333 0.00 0.00 0.00 3.06
1614 1705 9.836179 ATCCTCTCTACATATTCAGGTAATTCT 57.164 33.333 0.00 0.00 0.00 2.40
1619 1710 8.670490 AGTGTATCCTCTCTACATATTCAGGTA 58.330 37.037 0.00 0.00 32.13 3.08
1649 1740 7.479980 TCGCGATATGACACAATGATCATATA 58.520 34.615 9.04 2.40 44.73 0.86
1734 1825 5.221843 ACCAAACATAAGTGCTTCAGTCCTA 60.222 40.000 0.00 0.00 0.00 2.94
1739 1830 5.940192 TGTACCAAACATAAGTGCTTCAG 57.060 39.130 0.00 0.00 31.43 3.02
1751 1842 6.823182 CCACTATGATCAGAATGTACCAAACA 59.177 38.462 0.09 0.00 43.86 2.83
1764 1855 4.134379 AGACTTGCACCACTATGATCAG 57.866 45.455 0.09 0.00 0.00 2.90
1768 1859 5.123820 GCATAAAAGACTTGCACCACTATGA 59.876 40.000 0.00 0.00 36.40 2.15
1778 1869 5.412904 AGAGGTTACTGCATAAAAGACTTGC 59.587 40.000 0.00 0.00 36.91 4.01
1798 1891 2.099921 ACAGCTGTAGCAATACGAGAGG 59.900 50.000 20.16 0.00 45.16 3.69
1822 1915 4.113085 TCCCCACTGCCCTATTAGTTTAA 58.887 43.478 0.00 0.00 0.00 1.52
1823 1916 3.714798 CTCCCCACTGCCCTATTAGTTTA 59.285 47.826 0.00 0.00 0.00 2.01
1843 1939 0.759346 ATTAGTGATGGCCCCGTCTC 59.241 55.000 0.00 4.56 33.41 3.36
1847 1943 0.469917 ACTCATTAGTGATGGCCCCG 59.530 55.000 0.00 0.00 36.37 5.73
1878 1974 8.752005 TCTTTCCCATTCAGTAATAAGATTGG 57.248 34.615 0.00 0.00 35.87 3.16
2007 2103 3.479505 TGAAACAATTAATGCGGGTCG 57.520 42.857 0.00 0.00 0.00 4.79
2013 2109 9.793252 ACTGATGTAAGATGAAACAATTAATGC 57.207 29.630 0.00 0.00 0.00 3.56
2117 2214 4.226384 AGGTGATATCATGAGGTGCTACA 58.774 43.478 9.02 0.00 0.00 2.74
2230 2327 5.739752 TGTTTCATCGGAGAGCATAAATG 57.260 39.130 0.00 0.00 43.63 2.32
2231 2328 6.949352 ATTGTTTCATCGGAGAGCATAAAT 57.051 33.333 0.00 0.00 43.63 1.40
2232 2329 6.374053 TCAATTGTTTCATCGGAGAGCATAAA 59.626 34.615 5.13 0.00 43.63 1.40
2233 2330 5.879777 TCAATTGTTTCATCGGAGAGCATAA 59.120 36.000 5.13 0.00 43.63 1.90
2234 2331 5.427378 TCAATTGTTTCATCGGAGAGCATA 58.573 37.500 5.13 0.00 43.63 3.14
2235 2332 4.264253 TCAATTGTTTCATCGGAGAGCAT 58.736 39.130 5.13 0.00 43.63 3.79
2236 2333 3.673902 TCAATTGTTTCATCGGAGAGCA 58.326 40.909 5.13 0.00 43.63 4.26
2246 2343 9.491675 AAAAGATGCACATAATCAATTGTTTCA 57.508 25.926 5.13 0.00 0.00 2.69
2437 2552 1.435256 AGCCATAAATAGGGACGCCT 58.565 50.000 0.00 0.00 0.00 5.52
2568 2687 5.192927 GTGTTGTCAGGATATGAAATGGGA 58.807 41.667 0.00 0.00 40.43 4.37
2586 2705 7.984002 TCATGTGAGTATTTGTTTTGTGTTG 57.016 32.000 0.00 0.00 0.00 3.33
2626 2745 2.362077 GGGCCAAATAGGTATGCACAAG 59.638 50.000 4.39 0.00 40.61 3.16
2644 2763 3.843893 AAAATTTGATATGGCTGGGGC 57.156 42.857 0.00 0.00 37.82 5.80
2664 2783 2.304761 CCCCTACTTAGGTGAGTTGCAA 59.695 50.000 0.00 0.00 42.03 4.08
2696 2815 1.745653 CCCTAAGCTAAAGCACTTGGC 59.254 52.381 4.54 0.00 45.16 4.52
2745 2865 9.625747 TCAGAAATATAGCATGAACATTTACCA 57.374 29.630 0.00 0.00 0.00 3.25
2821 2941 9.590451 CTCATAACCAAAACAATATTGCAGATT 57.410 29.630 15.48 5.62 0.00 2.40
2873 3006 5.936187 ATGTTCAATAATGCCACCATGAA 57.064 34.783 0.00 0.00 0.00 2.57
2874 3007 7.005902 AGATATGTTCAATAATGCCACCATGA 58.994 34.615 0.00 0.00 0.00 3.07
2875 3008 7.088272 CAGATATGTTCAATAATGCCACCATG 58.912 38.462 0.00 0.00 0.00 3.66
2940 3085 1.305219 GCATGGCAAGCACGGTAAGA 61.305 55.000 10.23 0.00 0.00 2.10
3137 3287 2.225293 ACCTCACTACTTAGACCCTGCA 60.225 50.000 0.00 0.00 0.00 4.41
3161 3311 3.914426 AGGTCTCGGTAAATTCTGCAT 57.086 42.857 0.00 0.00 0.00 3.96
3217 3367 5.106078 GCGGACATGAATTAAGGGTAAAACA 60.106 40.000 0.00 0.00 0.00 2.83
3308 3461 1.561542 CAGGGAGGCTTACAACCAGAT 59.438 52.381 0.00 0.00 0.00 2.90
3325 3478 2.200370 ATGCCCATGCCATCCAGG 59.800 61.111 0.00 0.00 41.84 4.45
3372 3530 7.342026 ACCATTCCAAACTGAACTAAGACTTTT 59.658 33.333 0.00 0.00 0.00 2.27
3401 3561 2.758423 GGCCTAAAACCATCAAACCGAT 59.242 45.455 0.00 0.00 33.27 4.18
3446 3609 0.597377 GCCTTTCCAACAACCAAGCG 60.597 55.000 0.00 0.00 0.00 4.68
3484 3647 3.073678 CACTTGACATGGGATCACGAAA 58.926 45.455 0.00 0.00 0.00 3.46
3539 3706 0.684805 AGCAGAGGAGGGAGGTAACG 60.685 60.000 0.00 0.00 46.39 3.18
3548 3732 0.540454 TGATTCAGCAGCAGAGGAGG 59.460 55.000 0.00 0.00 0.00 4.30
3552 3736 5.511571 CATGTTATTGATTCAGCAGCAGAG 58.488 41.667 0.00 0.00 0.00 3.35
3553 3737 4.201980 GCATGTTATTGATTCAGCAGCAGA 60.202 41.667 0.00 0.00 0.00 4.26
3555 3739 3.444388 TGCATGTTATTGATTCAGCAGCA 59.556 39.130 0.00 0.00 0.00 4.41
3569 3753 1.561076 ACCAGGCTCAGATGCATGTTA 59.439 47.619 2.46 0.00 42.34 2.41
3606 3790 7.386299 GCATCCAAGACTATAGACAAACATAGG 59.614 40.741 6.78 0.00 0.00 2.57
3638 3830 4.728110 AGCGCTGAGGCCATGCAA 62.728 61.111 10.39 0.00 34.44 4.08
3651 3843 4.410743 GCCAGGAAGCAACAGCGC 62.411 66.667 0.00 0.00 0.00 5.92
3722 3914 2.457366 AAACTGGGCAGAGACTAACG 57.543 50.000 0.00 0.00 0.00 3.18
3723 3915 2.226674 GCAAAACTGGGCAGAGACTAAC 59.773 50.000 0.00 0.00 0.00 2.34
3726 3918 0.538287 GGCAAAACTGGGCAGAGACT 60.538 55.000 0.00 0.00 0.00 3.24
3728 3920 1.600636 CGGCAAAACTGGGCAGAGA 60.601 57.895 0.00 0.00 0.00 3.10
3729 3921 1.455383 AACGGCAAAACTGGGCAGAG 61.455 55.000 0.00 0.00 0.00 3.35
3730 3922 1.452145 GAACGGCAAAACTGGGCAGA 61.452 55.000 0.00 0.00 0.00 4.26
3733 3925 1.007387 CTGAACGGCAAAACTGGGC 60.007 57.895 0.00 0.00 0.00 5.36
3734 3926 1.200020 GATCTGAACGGCAAAACTGGG 59.800 52.381 0.00 0.00 0.00 4.45
3738 3933 3.896648 TTCTGATCTGAACGGCAAAAC 57.103 42.857 10.68 0.00 0.00 2.43
3739 3934 3.191162 CCATTCTGATCTGAACGGCAAAA 59.809 43.478 16.26 0.00 0.00 2.44
3743 3938 2.029838 ACCATTCTGATCTGAACGGC 57.970 50.000 22.67 0.00 33.09 5.68
3744 3939 5.376854 AAAAACCATTCTGATCTGAACGG 57.623 39.130 21.55 21.55 35.64 4.44
3749 3944 9.947669 GATTGAGATAAAAACCATTCTGATCTG 57.052 33.333 0.00 0.00 0.00 2.90
3756 3951 7.699812 GCAGACAGATTGAGATAAAAACCATTC 59.300 37.037 0.00 0.00 0.00 2.67
3761 3956 6.408858 TCGCAGACAGATTGAGATAAAAAC 57.591 37.500 0.00 0.00 0.00 2.43
3778 3974 3.500680 GGTAAAACAGTCCAAATCGCAGA 59.499 43.478 0.00 0.00 45.75 4.26
3779 3975 3.252215 TGGTAAAACAGTCCAAATCGCAG 59.748 43.478 0.00 0.00 0.00 5.18
3780 3976 3.003897 GTGGTAAAACAGTCCAAATCGCA 59.996 43.478 0.00 0.00 32.82 5.10
3781 3977 3.252458 AGTGGTAAAACAGTCCAAATCGC 59.748 43.478 0.00 0.00 32.82 4.58
3782 3978 5.929992 TCTAGTGGTAAAACAGTCCAAATCG 59.070 40.000 0.00 0.00 32.82 3.34
3783 3979 7.739498 TTCTAGTGGTAAAACAGTCCAAATC 57.261 36.000 0.00 0.00 32.82 2.17
3784 3980 7.255486 GCTTTCTAGTGGTAAAACAGTCCAAAT 60.255 37.037 0.00 0.00 32.82 2.32
3785 3981 6.038936 GCTTTCTAGTGGTAAAACAGTCCAAA 59.961 38.462 0.00 0.00 32.82 3.28
3786 3982 5.529800 GCTTTCTAGTGGTAAAACAGTCCAA 59.470 40.000 0.00 0.00 32.82 3.53
3787 3983 5.061179 GCTTTCTAGTGGTAAAACAGTCCA 58.939 41.667 0.00 0.00 0.00 4.02
3788 3984 5.061179 TGCTTTCTAGTGGTAAAACAGTCC 58.939 41.667 0.00 0.00 0.00 3.85
3789 3985 6.482308 TCTTGCTTTCTAGTGGTAAAACAGTC 59.518 38.462 0.00 0.00 0.00 3.51
3790 3986 6.354130 TCTTGCTTTCTAGTGGTAAAACAGT 58.646 36.000 0.00 0.00 0.00 3.55
3791 3987 6.861065 TCTTGCTTTCTAGTGGTAAAACAG 57.139 37.500 0.00 0.00 0.00 3.16
3804 4000 5.128919 ACACTTCACAGATTCTTGCTTTCT 58.871 37.500 0.00 0.00 0.00 2.52
3808 4004 4.712476 AGAACACTTCACAGATTCTTGCT 58.288 39.130 0.00 0.00 29.74 3.91
3846 4042 1.361668 CTCACCGGGCAAAGATCGTG 61.362 60.000 6.32 0.00 0.00 4.35
3847 4043 1.079127 CTCACCGGGCAAAGATCGT 60.079 57.895 6.32 0.00 0.00 3.73
3848 4044 1.815421 CCTCACCGGGCAAAGATCG 60.815 63.158 6.32 0.00 0.00 3.69
3849 4045 4.225497 CCTCACCGGGCAAAGATC 57.775 61.111 6.32 0.00 0.00 2.75
3860 4070 2.680352 TGACGGCTCTCCCTCACC 60.680 66.667 0.00 0.00 0.00 4.02
3941 4151 2.433145 ATCAGTGGCGCGTCAGTG 60.433 61.111 36.36 36.36 38.93 3.66
3942 4152 2.125912 GATCAGTGGCGCGTCAGT 60.126 61.111 16.68 16.73 0.00 3.41
3943 4153 3.250323 CGATCAGTGGCGCGTCAG 61.250 66.667 16.68 2.79 0.00 3.51
3949 4159 2.163390 CAGTGAGCGATCAGTGGCG 61.163 63.158 26.94 5.33 37.39 5.69
3950 4160 0.179089 ATCAGTGAGCGATCAGTGGC 60.179 55.000 31.79 9.61 40.45 5.01
3951 4161 1.537776 GGATCAGTGAGCGATCAGTGG 60.538 57.143 31.79 17.18 40.93 4.00
4098 4335 3.632049 TGGGGGAGTGGGATGGGA 61.632 66.667 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.