Multiple sequence alignment - TraesCS5A01G284200

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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 TraesCS5A01G284200 chr5A 100.000 6080 0 0 1 6080 492036096 492030017 0.000000e+00 11228.0
1 TraesCS5A01G284200 chr5A 80.785 739 89 17 2056 2783 489879943 489880639 4.170000e-146 529.0
2 TraesCS5A01G284200 chr5A 82.735 446 58 13 3815 4244 489899523 489899965 4.450000e-101 379.0
3 TraesCS5A01G284200 chr5A 81.481 405 43 10 4687 5062 489870720 489871121 2.750000e-78 303.0
4 TraesCS5A01G284200 chr5A 92.157 102 8 0 543 644 248535434 248535333 1.770000e-30 145.0
5 TraesCS5A01G284200 chr5B 96.150 5350 172 20 674 6002 467515768 467510432 0.000000e+00 8708.0
6 TraesCS5A01G284200 chr5B 89.937 159 10 1 386 544 467515988 467515836 3.720000e-47 200.0
7 TraesCS5A01G284200 chr5D 94.884 5395 211 34 637 6004 389114175 389108819 0.000000e+00 8373.0
8 TraesCS5A01G284200 chr5D 86.825 630 79 3 2146 2774 387114015 387114641 0.000000e+00 701.0
9 TraesCS5A01G284200 chr5D 82.830 728 87 20 3402 4112 387114900 387115606 8.660000e-173 617.0
10 TraesCS5A01G284200 chr5D 83.242 549 66 9 5 544 389114734 389114203 1.190000e-131 481.0
11 TraesCS5A01G284200 chr5D 86.777 121 12 4 4120 4239 387115688 387115805 1.380000e-26 132.0
12 TraesCS5A01G284200 chr7D 77.656 273 53 6 9 280 39771000 39770735 6.310000e-35 159.0
13 TraesCS5A01G284200 chr7D 89.216 102 11 0 543 644 4020106 4020207 1.780000e-25 128.0
14 TraesCS5A01G284200 chr7A 77.444 266 45 9 12 271 6661792 6661536 1.770000e-30 145.0
15 TraesCS5A01G284200 chr7A 77.068 266 46 9 12 271 628898224 628897968 8.220000e-29 139.0
16 TraesCS5A01G284200 chr2A 91.176 102 9 0 543 644 29955179 29955280 8.220000e-29 139.0
17 TraesCS5A01G284200 chr4A 91.667 96 8 0 549 644 175561789 175561694 3.820000e-27 134.0
18 TraesCS5A01G284200 chr4A 90.196 102 10 0 541 642 581861098 581860997 3.820000e-27 134.0
19 TraesCS5A01G284200 chr4A 96.970 33 1 0 511 543 631210937 631210905 8.510000e-04 56.5
20 TraesCS5A01G284200 chr3A 91.667 96 8 0 549 644 399421650 399421555 3.820000e-27 134.0
21 TraesCS5A01G284200 chr1A 89.623 106 10 1 540 644 82078364 82078259 3.820000e-27 134.0
22 TraesCS5A01G284200 chr1A 89.320 103 11 0 542 644 314477071 314476969 4.950000e-26 130.0
23 TraesCS5A01G284200 chr6B 84.252 127 20 0 518 644 675244499 675244625 2.300000e-24 124.0
24 TraesCS5A01G284200 chr7B 100.000 32 0 0 513 544 733050398 733050429 6.580000e-05 60.2
25 TraesCS5A01G284200 chr1B 94.737 38 2 0 506 543 564160723 564160760 6.580000e-05 60.2
26 TraesCS5A01G284200 chr1B 100.000 30 0 0 512 541 349839201 349839172 8.510000e-04 56.5
27 TraesCS5A01G284200 chr1D 100.000 31 0 0 513 543 415628057 415628087 2.370000e-04 58.4


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 TraesCS5A01G284200 chr5A 492030017 492036096 6079 True 11228.000000 11228 100.000000 1 6080 1 chr5A.!!$R2 6079
1 TraesCS5A01G284200 chr5A 489879943 489880639 696 False 529.000000 529 80.785000 2056 2783 1 chr5A.!!$F2 727
2 TraesCS5A01G284200 chr5B 467510432 467515988 5556 True 4454.000000 8708 93.043500 386 6002 2 chr5B.!!$R1 5616
3 TraesCS5A01G284200 chr5D 389108819 389114734 5915 True 4427.000000 8373 89.063000 5 6004 2 chr5D.!!$R1 5999
4 TraesCS5A01G284200 chr5D 387114015 387115805 1790 False 483.333333 701 85.477333 2146 4239 3 chr5D.!!$F1 2093

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
206 207 0.031716 TCATCAGAGGAGTGGGGGAG 60.032 60.0 0.00 0.0 0.00 4.30 F
653 663 0.730840 GGAACGGAGGCATAAAACGG 59.269 55.0 0.00 0.0 0.00 4.44 F
1664 1689 0.529337 CCATCGAGCTGCCTGTAGTG 60.529 60.0 0.00 0.0 0.00 2.74 F
2502 2535 0.538057 CAACCAAGAGCTGAAGGCCA 60.538 55.0 5.01 0.0 43.05 5.36 F
3563 3646 1.221466 CCGCTGAAGAAACGAGTGCA 61.221 55.0 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1664 1689 1.355066 GCGCTGCTACAACTGTCTCC 61.355 60.0 0.0 0.0 0.00 3.71 R
2093 2118 1.422977 TTGTAGGAACCCCAGCAGCA 61.423 55.0 0.0 0.0 33.88 4.41 R
3050 3089 0.111061 ACAATGACAAGCAGCCCTCA 59.889 50.0 0.0 0.0 0.00 3.86 R
3581 3664 0.674581 TGCAAGAGGCCGAGTCATTG 60.675 55.0 0.0 0.0 43.89 2.82 R
5289 5474 0.120377 TTCCACCCCTCCACCTATGT 59.880 55.0 0.0 0.0 0.00 2.29 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
87 88 2.044650 TACAGGACGGACGAGGGG 60.045 66.667 0.00 0.00 0.00 4.79
91 92 2.993264 GGACGGACGAGGGGAACA 60.993 66.667 0.00 0.00 0.00 3.18
94 95 3.677648 CGGACGAGGGGAACACGT 61.678 66.667 0.00 0.00 44.70 4.49
97 98 3.048602 ACGAGGGGAACACGTCAG 58.951 61.111 0.00 0.00 39.83 3.51
105 106 4.681978 AACACGTCAGGAGCGGGC 62.682 66.667 0.00 0.00 35.99 6.13
206 207 0.031716 TCATCAGAGGAGTGGGGGAG 60.032 60.000 0.00 0.00 0.00 4.30
208 209 2.263099 ATCAGAGGAGTGGGGGAGGG 62.263 65.000 0.00 0.00 0.00 4.30
209 210 3.700350 AGAGGAGTGGGGGAGGGG 61.700 72.222 0.00 0.00 0.00 4.79
210 211 4.825679 GAGGAGTGGGGGAGGGGG 62.826 77.778 0.00 0.00 0.00 5.40
238 239 2.437281 AGAGGATTAGTGTCCATGGCAG 59.563 50.000 6.96 0.00 40.90 4.85
245 246 2.268920 GTCCATGGCAGCGGAAGA 59.731 61.111 6.96 0.00 31.67 2.87
259 260 2.452491 AAGAAGGGTGGGTGGGCT 60.452 61.111 0.00 0.00 0.00 5.19
262 263 4.974438 AAGGGTGGGTGGGCTCGA 62.974 66.667 0.00 0.00 0.00 4.04
266 267 2.747686 GTGGGTGGGCTCGAAAGA 59.252 61.111 0.00 0.00 39.12 2.52
271 272 1.613255 GGGTGGGCTCGAAAGAATTGA 60.613 52.381 0.00 0.00 41.32 2.57
297 305 8.786826 TTTCCTCTGTACCATATAAAAGTGTG 57.213 34.615 0.00 0.00 0.00 3.82
305 313 5.368989 ACCATATAAAAGTGTGCTCTAGCC 58.631 41.667 0.00 0.00 41.18 3.93
307 315 5.822519 CCATATAAAAGTGTGCTCTAGCCAA 59.177 40.000 0.00 0.00 41.18 4.52
312 320 1.167851 GTGTGCTCTAGCCAATGCAA 58.832 50.000 0.00 0.00 41.13 4.08
313 321 1.747355 GTGTGCTCTAGCCAATGCAAT 59.253 47.619 0.00 0.00 41.13 3.56
314 322 2.165030 GTGTGCTCTAGCCAATGCAATT 59.835 45.455 0.00 0.00 41.13 2.32
489 499 2.634982 TTGCAACTGATTCCGCATTC 57.365 45.000 0.00 0.00 33.71 2.67
496 506 3.123804 ACTGATTCCGCATTCGTGTATC 58.876 45.455 0.00 0.00 0.00 2.24
502 512 2.355444 TCCGCATTCGTGTATCGTCTAA 59.645 45.455 0.00 0.00 40.80 2.10
512 522 9.745880 ATTCGTGTATCGTCTAATGAATTACTT 57.254 29.630 0.00 0.00 40.80 2.24
553 563 8.108551 ACGCTCTTATATTATACTTTCTCCGT 57.891 34.615 0.00 0.00 0.00 4.69
554 564 8.574737 ACGCTCTTATATTATACTTTCTCCGTT 58.425 33.333 0.00 0.00 0.00 4.44
566 576 8.853469 ATACTTTCTCCGTTAAGAATTACTCG 57.147 34.615 0.00 0.00 35.30 4.18
567 577 6.685657 ACTTTCTCCGTTAAGAATTACTCGT 58.314 36.000 0.00 0.00 35.30 4.18
568 578 6.805760 ACTTTCTCCGTTAAGAATTACTCGTC 59.194 38.462 0.00 0.00 35.30 4.20
569 579 4.901814 TCTCCGTTAAGAATTACTCGTCG 58.098 43.478 0.00 0.00 0.00 5.12
570 580 3.429085 TCCGTTAAGAATTACTCGTCGC 58.571 45.455 0.00 0.00 0.00 5.19
571 581 3.119884 TCCGTTAAGAATTACTCGTCGCA 60.120 43.478 0.00 0.00 0.00 5.10
573 583 4.093514 CGTTAAGAATTACTCGTCGCAGA 58.906 43.478 0.00 0.00 0.00 4.26
576 586 6.237490 CGTTAAGAATTACTCGTCGCAGAAAT 60.237 38.462 0.00 0.00 39.69 2.17
577 587 5.456192 AAGAATTACTCGTCGCAGAAATG 57.544 39.130 0.00 0.00 39.69 2.32
578 588 4.744570 AGAATTACTCGTCGCAGAAATGA 58.255 39.130 0.00 0.00 39.69 2.57
580 590 5.812642 AGAATTACTCGTCGCAGAAATGAAT 59.187 36.000 0.00 0.00 39.69 2.57
581 591 4.840401 TTACTCGTCGCAGAAATGAATG 57.160 40.909 0.00 0.00 39.69 2.67
582 592 2.688507 ACTCGTCGCAGAAATGAATGT 58.311 42.857 0.00 0.00 39.69 2.71
583 593 3.845178 ACTCGTCGCAGAAATGAATGTA 58.155 40.909 0.00 0.00 39.69 2.29
584 594 4.433615 ACTCGTCGCAGAAATGAATGTAT 58.566 39.130 0.00 0.00 39.69 2.29
585 595 4.504461 ACTCGTCGCAGAAATGAATGTATC 59.496 41.667 0.00 0.00 39.69 2.24
586 596 4.682787 TCGTCGCAGAAATGAATGTATCT 58.317 39.130 0.00 0.00 39.69 1.98
587 597 5.827666 TCGTCGCAGAAATGAATGTATCTA 58.172 37.500 0.00 0.00 39.69 1.98
588 598 5.915196 TCGTCGCAGAAATGAATGTATCTAG 59.085 40.000 0.00 0.00 39.69 2.43
590 600 6.584184 CGTCGCAGAAATGAATGTATCTAGAT 59.416 38.462 10.73 10.73 39.69 1.98
591 601 7.410193 CGTCGCAGAAATGAATGTATCTAGATG 60.410 40.741 15.79 0.00 39.69 2.90
592 602 7.383572 GTCGCAGAAATGAATGTATCTAGATGT 59.616 37.037 15.79 0.00 39.69 3.06
593 603 8.576442 TCGCAGAAATGAATGTATCTAGATGTA 58.424 33.333 15.79 4.44 0.00 2.29
594 604 9.363763 CGCAGAAATGAATGTATCTAGATGTAT 57.636 33.333 15.79 6.61 0.00 2.29
635 645 8.915871 ATTCATTTCTGTGACGAATAATTTGG 57.084 30.769 0.00 0.00 0.00 3.28
644 654 2.681344 ACGAATAATTTGGAACGGAGGC 59.319 45.455 0.00 0.00 0.00 4.70
647 657 4.513692 CGAATAATTTGGAACGGAGGCATA 59.486 41.667 0.00 0.00 0.00 3.14
651 661 3.926821 TTTGGAACGGAGGCATAAAAC 57.073 42.857 0.00 0.00 0.00 2.43
653 663 0.730840 GGAACGGAGGCATAAAACGG 59.269 55.000 0.00 0.00 0.00 4.44
655 665 1.664151 GAACGGAGGCATAAAACGGAG 59.336 52.381 0.00 0.00 0.00 4.63
661 671 1.917568 AGGCATAAAACGGAGGGGTAA 59.082 47.619 0.00 0.00 0.00 2.85
663 673 1.674441 GCATAAAACGGAGGGGTAAGC 59.326 52.381 0.00 0.00 0.00 3.09
664 674 2.294979 CATAAAACGGAGGGGTAAGCC 58.705 52.381 0.00 0.00 0.00 4.35
666 676 0.775542 AAAACGGAGGGGTAAGCCTT 59.224 50.000 0.00 0.00 34.45 4.35
667 677 0.775542 AAACGGAGGGGTAAGCCTTT 59.224 50.000 0.00 0.00 34.45 3.11
668 678 1.660242 AACGGAGGGGTAAGCCTTTA 58.340 50.000 0.00 0.00 34.45 1.85
669 679 1.660242 ACGGAGGGGTAAGCCTTTAA 58.340 50.000 0.00 0.00 34.45 1.52
670 680 1.558294 ACGGAGGGGTAAGCCTTTAAG 59.442 52.381 0.00 0.00 34.45 1.85
671 681 1.558294 CGGAGGGGTAAGCCTTTAAGT 59.442 52.381 0.00 0.00 34.45 2.24
672 682 2.419713 CGGAGGGGTAAGCCTTTAAGTC 60.420 54.545 0.00 0.00 34.45 3.01
988 1012 1.202177 CCCGATTTCGAGCATTGGTTG 60.202 52.381 0.67 0.00 43.02 3.77
989 1013 1.737236 CCGATTTCGAGCATTGGTTGA 59.263 47.619 0.67 1.57 43.02 3.18
990 1014 2.355756 CCGATTTCGAGCATTGGTTGAT 59.644 45.455 6.62 0.00 43.02 2.57
991 1015 3.181497 CCGATTTCGAGCATTGGTTGATT 60.181 43.478 6.62 0.00 43.02 2.57
1019 1043 1.338136 ATGACCATCCCGTCCTCCAC 61.338 60.000 0.00 0.00 31.35 4.02
1039 1064 1.805943 CCGGTTAGTTGTTAAACCCCG 59.194 52.381 0.00 0.00 41.81 5.73
1075 1100 3.170672 CCCATCTGGATCCGCCCA 61.171 66.667 7.39 0.00 37.39 5.36
1141 1166 1.275291 GGATCCGTGTGTTTCAGGAGA 59.725 52.381 0.00 0.00 36.08 3.71
1148 1173 1.630369 TGTGTTTCAGGAGAGATGGGG 59.370 52.381 0.00 0.00 0.00 4.96
1250 1275 2.507324 GTCGAGGAAGCGGCTGTC 60.507 66.667 1.81 3.43 32.23 3.51
1577 1602 3.136123 CATGCCAAGCAGGACCGG 61.136 66.667 0.00 0.00 43.36 5.28
1606 1631 1.939934 GGCTGCACGCTATGATAAACA 59.060 47.619 0.50 0.00 39.13 2.83
1610 1635 4.342772 CTGCACGCTATGATAAACAAACC 58.657 43.478 0.00 0.00 0.00 3.27
1611 1636 3.753797 TGCACGCTATGATAAACAAACCA 59.246 39.130 0.00 0.00 0.00 3.67
1616 1641 4.024893 CGCTATGATAAACAAACCATCGCT 60.025 41.667 0.00 0.00 0.00 4.93
1653 1678 2.029838 AAATGAGGTGTCCATCGAGC 57.970 50.000 0.00 0.00 0.00 5.03
1664 1689 0.529337 CCATCGAGCTGCCTGTAGTG 60.529 60.000 0.00 0.00 0.00 2.74
1718 1743 1.966451 GGTTCTTGGTGCGGTGGAG 60.966 63.158 0.00 0.00 0.00 3.86
1772 1797 1.392589 ATGTGATTAAAGGGCTGCCG 58.607 50.000 13.40 0.00 0.00 5.69
1835 1860 3.798202 CCTCCTAGCGCTTGATAAGTTT 58.202 45.455 18.68 0.00 0.00 2.66
1910 1935 4.728534 TGAAGAAGTTGTTTGTGGAAACG 58.271 39.130 0.00 0.00 43.92 3.60
1973 1998 3.308323 GCCTCTTCTCAAGTATTTGCTCG 59.692 47.826 0.00 0.00 34.21 5.03
2093 2118 1.992277 AGCGGAGGATGCTTCCAGT 60.992 57.895 19.98 0.67 45.30 4.00
2376 2409 4.862018 GCAGCAAAGAACAAGTACAAACAA 59.138 37.500 0.00 0.00 0.00 2.83
2414 2447 2.191400 TCCCAGATTCCAGGTTCAGAG 58.809 52.381 0.00 0.00 0.00 3.35
2417 2450 3.519510 CCCAGATTCCAGGTTCAGAGTTA 59.480 47.826 0.00 0.00 0.00 2.24
2456 2489 3.328931 AGAAAGAACATGAGCCCTCTGAA 59.671 43.478 0.00 0.00 0.00 3.02
2492 2525 1.882623 GCTTCTGTTCCCAACCAAGAG 59.117 52.381 0.00 0.00 0.00 2.85
2502 2535 0.538057 CAACCAAGAGCTGAAGGCCA 60.538 55.000 5.01 0.00 43.05 5.36
3050 3089 5.538813 TGATAGTAATGCTCCCGTATCAGTT 59.461 40.000 0.00 0.00 0.00 3.16
3153 3192 4.925054 CACAGCCAAACACCAATGAATTAG 59.075 41.667 0.00 0.00 0.00 1.73
3233 3272 3.387374 TGGCAAGTGGTGATGAAAAACAT 59.613 39.130 0.00 0.00 42.47 2.71
3563 3646 1.221466 CCGCTGAAGAAACGAGTGCA 61.221 55.000 0.00 0.00 0.00 4.57
3581 3664 1.227556 ACCAGTGAGTTGTGGCGAC 60.228 57.895 0.00 0.00 37.34 5.19
3756 3849 3.431486 CGGAAGGAGGAAGAGAATGAAGG 60.431 52.174 0.00 0.00 0.00 3.46
3863 3956 1.737838 TTCTTATCAGCAAGGCACCG 58.262 50.000 0.00 0.00 0.00 4.94
3899 3992 6.183360 CGATTACTTTGAACAGATTCAGCCAT 60.183 38.462 0.00 0.00 45.54 4.40
4491 4672 7.812309 TGATTTAGATTCGAAGGCATATACG 57.188 36.000 3.35 0.00 0.00 3.06
4647 4828 3.947910 TGTACAAGTGTAGGTGCCTAC 57.052 47.619 18.75 18.75 46.56 3.18
4714 4897 2.489938 TAGAACCCAAGTGACATGCC 57.510 50.000 0.00 0.00 0.00 4.40
4842 5025 5.585047 ACTGTTTTCCTTAATACGCAGATCC 59.415 40.000 0.00 0.00 0.00 3.36
5071 5254 2.885616 TCCTTTTCTACGAGAGGGTGT 58.114 47.619 0.00 0.00 0.00 4.16
5090 5273 5.068198 GGGTGTCCGAGTAAGACAATATGTA 59.932 44.000 0.00 0.00 45.37 2.29
5141 5324 6.644347 AGTAGTTAGGGACAAGATGAATGTG 58.356 40.000 0.00 0.00 0.00 3.21
5188 5371 4.689612 TTTGGGGATACTGCTATGACTC 57.310 45.455 0.00 0.00 0.00 3.36
5189 5372 3.328535 TGGGGATACTGCTATGACTCA 57.671 47.619 0.00 0.00 0.00 3.41
5197 5380 3.023119 ACTGCTATGACTCAGTCTCAGG 58.977 50.000 6.33 0.00 39.11 3.86
5258 5443 3.069289 CTGTTCATGCTGCTTACAGTGA 58.931 45.455 0.00 0.00 46.30 3.41
5289 5474 4.258457 TGGGTTTTCCTTTTCTGGAGAA 57.742 40.909 0.00 0.00 40.46 2.87
5292 5477 4.588951 GGGTTTTCCTTTTCTGGAGAACAT 59.411 41.667 15.50 0.00 46.69 2.71
5398 5583 3.917329 TGGTTTAGAGTCAGTCAGTCG 57.083 47.619 0.00 0.00 0.00 4.18
5412 5597 0.103208 CAGTCGGTCATAGACAGCCC 59.897 60.000 0.00 0.00 40.84 5.19
5436 5622 7.359595 CCGGTACATGTTTTTGATATATGTGG 58.640 38.462 2.30 0.00 34.22 4.17
5529 5715 9.994432 CTTGAGGTAGAAATGACATGTTATTTC 57.006 33.333 32.97 32.97 42.42 2.17
5571 5757 3.190327 TGTACCATGCCACGAAAATCAAG 59.810 43.478 0.00 0.00 0.00 3.02
5573 5759 1.203052 CCATGCCACGAAAATCAAGCT 59.797 47.619 0.00 0.00 0.00 3.74
5576 5762 1.680735 TGCCACGAAAATCAAGCTTGT 59.319 42.857 25.19 10.69 0.00 3.16
5582 5768 5.625311 CCACGAAAATCAAGCTTGTAAGTTC 59.375 40.000 25.19 20.34 0.00 3.01
5827 6028 9.231297 GTATTATGTAATGGCTGGTATCATGTT 57.769 33.333 0.00 0.00 0.00 2.71
5829 6030 9.979897 ATTATGTAATGGCTGGTATCATGTTAT 57.020 29.630 0.00 0.00 0.00 1.89
5861 6062 2.080536 CCTGGGATCATGGGGCTCA 61.081 63.158 0.00 0.00 0.00 4.26
5918 6119 4.337060 GGGTGACGTTTTGCCCGC 62.337 66.667 0.00 0.00 0.00 6.13
5981 6185 4.472833 AGCAATCTAGAGGTGAACAGGAAT 59.527 41.667 9.80 0.00 0.00 3.01
6007 6211 2.743928 GGTGCTGCCGTCTCCAAG 60.744 66.667 0.00 0.00 0.00 3.61
6008 6212 2.743928 GTGCTGCCGTCTCCAAGG 60.744 66.667 0.00 0.00 0.00 3.61
6009 6213 3.241530 TGCTGCCGTCTCCAAGGT 61.242 61.111 0.00 0.00 0.00 3.50
6010 6214 2.435059 GCTGCCGTCTCCAAGGTC 60.435 66.667 0.00 0.00 0.00 3.85
6011 6215 2.125912 CTGCCGTCTCCAAGGTCG 60.126 66.667 0.00 0.00 0.00 4.79
6012 6216 3.649277 CTGCCGTCTCCAAGGTCGG 62.649 68.421 12.71 12.71 44.86 4.79
6014 6218 4.796231 CCGTCTCCAAGGTCGGCG 62.796 72.222 0.00 0.00 36.68 6.46
6015 6219 3.744719 CGTCTCCAAGGTCGGCGA 61.745 66.667 4.99 4.99 0.00 5.54
6016 6220 2.126031 GTCTCCAAGGTCGGCGAC 60.126 66.667 30.72 30.72 33.87 5.19
6017 6221 2.282958 TCTCCAAGGTCGGCGACT 60.283 61.111 35.42 20.74 32.47 4.18
6018 6222 2.125912 CTCCAAGGTCGGCGACTG 60.126 66.667 35.42 26.81 32.47 3.51
6019 6223 3.649277 CTCCAAGGTCGGCGACTGG 62.649 68.421 35.42 33.16 31.67 4.00
6034 6238 2.741985 TGGCGCAACCAGATGACG 60.742 61.111 10.83 0.00 46.36 4.35
6035 6239 4.166011 GGCGCAACCAGATGACGC 62.166 66.667 10.83 0.00 41.64 5.19
6036 6240 4.166011 GCGCAACCAGATGACGCC 62.166 66.667 0.30 0.00 38.77 5.68
6037 6241 3.499737 CGCAACCAGATGACGCCC 61.500 66.667 0.00 0.00 0.00 6.13
6038 6242 3.499737 GCAACCAGATGACGCCCG 61.500 66.667 0.00 0.00 0.00 6.13
6039 6243 3.499737 CAACCAGATGACGCCCGC 61.500 66.667 0.00 0.00 0.00 6.13
6040 6244 4.778143 AACCAGATGACGCCCGCC 62.778 66.667 0.00 0.00 0.00 6.13
6075 6279 4.629958 TGCGGGGCATGGGGTTTT 62.630 61.111 0.00 0.00 31.71 2.43
6076 6280 3.318384 GCGGGGCATGGGGTTTTT 61.318 61.111 0.00 0.00 0.00 1.94
6077 6281 2.661997 CGGGGCATGGGGTTTTTG 59.338 61.111 0.00 0.00 0.00 2.44
6078 6282 2.213513 CGGGGCATGGGGTTTTTGT 61.214 57.895 0.00 0.00 0.00 2.83
6079 6283 1.763546 CGGGGCATGGGGTTTTTGTT 61.764 55.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.585006 GACATCCGTCACCACGTCT 59.415 57.895 0.00 0.00 45.17 4.18
63 64 2.219458 TCGTCCGTCCTGTAGATGATC 58.781 52.381 0.00 0.00 32.76 2.92
71 72 3.518552 TTCCCCTCGTCCGTCCTGT 62.519 63.158 0.00 0.00 0.00 4.00
75 76 2.260743 GTGTTCCCCTCGTCCGTC 59.739 66.667 0.00 0.00 0.00 4.79
87 88 2.432628 CCCGCTCCTGACGTGTTC 60.433 66.667 0.00 0.00 0.00 3.18
148 149 2.202987 CGTCCTCCATGCTGCCTC 60.203 66.667 0.00 0.00 0.00 4.70
208 209 2.252714 CACTAATCCTCTAGCCTCCCC 58.747 57.143 0.00 0.00 0.00 4.81
209 210 2.894765 GACACTAATCCTCTAGCCTCCC 59.105 54.545 0.00 0.00 0.00 4.30
210 211 2.894765 GGACACTAATCCTCTAGCCTCC 59.105 54.545 0.00 0.00 35.68 4.30
211 212 3.567397 TGGACACTAATCCTCTAGCCTC 58.433 50.000 0.00 0.00 39.75 4.70
212 213 3.689872 TGGACACTAATCCTCTAGCCT 57.310 47.619 0.00 0.00 39.75 4.58
213 214 3.007398 CCATGGACACTAATCCTCTAGCC 59.993 52.174 5.56 0.00 39.75 3.93
225 226 2.809861 CTTCCGCTGCCATGGACACT 62.810 60.000 18.40 0.00 32.95 3.55
238 239 2.359975 CACCCACCCTTCTTCCGC 60.360 66.667 0.00 0.00 0.00 5.54
245 246 4.974438 TCGAGCCCACCCACCCTT 62.974 66.667 0.00 0.00 0.00 3.95
259 260 6.594159 GGTACAGAGGAAATCAATTCTTTCGA 59.406 38.462 0.00 0.00 38.18 3.71
290 298 1.815003 GCATTGGCTAGAGCACACTTT 59.185 47.619 3.54 0.00 44.36 2.66
461 469 5.300752 CGGAATCAGTTGCAATATAGGAGT 58.699 41.667 0.59 0.00 0.00 3.85
462 470 4.153117 GCGGAATCAGTTGCAATATAGGAG 59.847 45.833 0.59 0.00 0.00 3.69
464 472 3.814842 TGCGGAATCAGTTGCAATATAGG 59.185 43.478 0.59 0.00 33.80 2.57
465 473 5.618056 ATGCGGAATCAGTTGCAATATAG 57.382 39.130 0.59 0.00 41.22 1.31
477 487 2.124122 CGATACACGAATGCGGAATCA 58.876 47.619 0.00 0.00 45.77 2.57
529 539 8.967552 AACGGAGAAAGTATAATATAAGAGCG 57.032 34.615 0.00 0.00 0.00 5.03
544 554 6.021626 CGACGAGTAATTCTTAACGGAGAAAG 60.022 42.308 0.00 0.00 38.98 2.62
546 556 5.327091 CGACGAGTAATTCTTAACGGAGAA 58.673 41.667 0.00 1.49 39.76 2.87
548 558 3.481388 GCGACGAGTAATTCTTAACGGAG 59.519 47.826 0.00 0.00 0.00 4.63
549 559 3.119884 TGCGACGAGTAATTCTTAACGGA 60.120 43.478 0.00 0.00 0.00 4.69
550 560 3.173599 TGCGACGAGTAATTCTTAACGG 58.826 45.455 0.00 0.00 0.00 4.44
551 561 4.093514 TCTGCGACGAGTAATTCTTAACG 58.906 43.478 0.00 0.00 0.00 3.18
553 563 6.809689 TCATTTCTGCGACGAGTAATTCTTAA 59.190 34.615 0.00 0.00 0.00 1.85
554 564 6.327154 TCATTTCTGCGACGAGTAATTCTTA 58.673 36.000 0.00 0.00 0.00 2.10
557 567 5.450376 TTCATTTCTGCGACGAGTAATTC 57.550 39.130 0.00 0.00 0.00 2.17
562 572 2.688507 ACATTCATTTCTGCGACGAGT 58.311 42.857 0.00 0.00 0.00 4.18
563 573 4.742167 AGATACATTCATTTCTGCGACGAG 59.258 41.667 0.00 0.00 0.00 4.18
564 574 4.682787 AGATACATTCATTTCTGCGACGA 58.317 39.130 0.00 0.00 0.00 4.20
565 575 5.915196 TCTAGATACATTCATTTCTGCGACG 59.085 40.000 0.00 0.00 0.00 5.12
566 576 7.383572 ACATCTAGATACATTCATTTCTGCGAC 59.616 37.037 4.54 0.00 0.00 5.19
567 577 7.436933 ACATCTAGATACATTCATTTCTGCGA 58.563 34.615 4.54 0.00 0.00 5.10
568 578 7.649370 ACATCTAGATACATTCATTTCTGCG 57.351 36.000 4.54 0.00 0.00 5.18
610 620 8.739039 TCCAAATTATTCGTCACAGAAATGAAT 58.261 29.630 0.00 0.00 33.43 2.57
611 621 8.105097 TCCAAATTATTCGTCACAGAAATGAA 57.895 30.769 0.00 0.00 33.43 2.57
612 622 7.680442 TCCAAATTATTCGTCACAGAAATGA 57.320 32.000 0.00 0.00 33.43 2.57
613 623 7.007367 CGTTCCAAATTATTCGTCACAGAAATG 59.993 37.037 0.00 0.00 33.43 2.32
614 624 7.021196 CGTTCCAAATTATTCGTCACAGAAAT 58.979 34.615 0.00 0.00 33.43 2.17
615 625 6.367421 CGTTCCAAATTATTCGTCACAGAAA 58.633 36.000 0.00 0.00 33.43 2.52
616 626 5.106869 CCGTTCCAAATTATTCGTCACAGAA 60.107 40.000 0.00 0.00 34.31 3.02
617 627 4.390603 CCGTTCCAAATTATTCGTCACAGA 59.609 41.667 0.00 0.00 0.00 3.41
618 628 4.390603 TCCGTTCCAAATTATTCGTCACAG 59.609 41.667 0.00 0.00 0.00 3.66
619 629 4.316645 TCCGTTCCAAATTATTCGTCACA 58.683 39.130 0.00 0.00 0.00 3.58
620 630 4.201783 CCTCCGTTCCAAATTATTCGTCAC 60.202 45.833 0.00 0.00 0.00 3.67
621 631 3.936453 CCTCCGTTCCAAATTATTCGTCA 59.064 43.478 0.00 0.00 0.00 4.35
622 632 3.242641 GCCTCCGTTCCAAATTATTCGTC 60.243 47.826 0.00 0.00 0.00 4.20
623 633 2.681344 GCCTCCGTTCCAAATTATTCGT 59.319 45.455 0.00 0.00 0.00 3.85
624 634 2.680841 TGCCTCCGTTCCAAATTATTCG 59.319 45.455 0.00 0.00 0.00 3.34
625 635 4.918810 ATGCCTCCGTTCCAAATTATTC 57.081 40.909 0.00 0.00 0.00 1.75
626 636 6.783708 TTTATGCCTCCGTTCCAAATTATT 57.216 33.333 0.00 0.00 0.00 1.40
630 640 3.119637 CGTTTTATGCCTCCGTTCCAAAT 60.120 43.478 0.00 0.00 0.00 2.32
632 642 1.807742 CGTTTTATGCCTCCGTTCCAA 59.192 47.619 0.00 0.00 0.00 3.53
634 644 0.730840 CCGTTTTATGCCTCCGTTCC 59.269 55.000 0.00 0.00 0.00 3.62
635 645 1.664151 CTCCGTTTTATGCCTCCGTTC 59.336 52.381 0.00 0.00 0.00 3.95
644 654 2.092592 AGGCTTACCCCTCCGTTTTATG 60.093 50.000 0.00 0.00 36.11 1.90
647 657 0.775542 AAGGCTTACCCCTCCGTTTT 59.224 50.000 0.00 0.00 36.11 2.43
651 661 1.558294 ACTTAAAGGCTTACCCCTCCG 59.442 52.381 0.00 0.00 36.11 4.63
653 663 4.571369 AAGACTTAAAGGCTTACCCCTC 57.429 45.455 0.00 0.00 43.01 4.30
655 665 4.155462 CGAAAAGACTTAAAGGCTTACCCC 59.845 45.833 0.00 0.00 44.35 4.95
661 671 4.001652 GGCTACGAAAAGACTTAAAGGCT 58.998 43.478 0.00 0.00 32.54 4.58
663 673 4.579270 CGGCTACGAAAAGACTTAAAGG 57.421 45.455 0.00 0.00 44.60 3.11
691 701 4.678574 CGGGGTATGAACAATCTGTCGTAA 60.679 45.833 0.00 0.00 0.00 3.18
805 822 1.767672 TGGCTAGGGCAGGGAGATG 60.768 63.158 0.00 0.00 40.87 2.90
988 1012 3.008485 GGGATGGTCATACCTCAGGAATC 59.992 52.174 0.00 0.00 38.82 2.52
989 1013 2.982488 GGGATGGTCATACCTCAGGAAT 59.018 50.000 0.00 0.00 38.82 3.01
990 1014 2.408565 GGGATGGTCATACCTCAGGAA 58.591 52.381 0.00 0.00 38.82 3.36
991 1015 1.757764 CGGGATGGTCATACCTCAGGA 60.758 57.143 10.23 0.00 39.77 3.86
1019 1043 1.805943 CGGGGTTTAACAACTAACCGG 59.194 52.381 0.00 0.00 43.79 5.28
1039 1064 1.472878 GGGAAATTTCTGGAGTTCGGC 59.527 52.381 17.42 0.00 0.00 5.54
1102 1127 2.312741 TCCAATCAAGCCCAAGGAAGAT 59.687 45.455 0.00 0.00 0.00 2.40
1105 1130 2.624029 GGATCCAATCAAGCCCAAGGAA 60.624 50.000 6.95 0.00 0.00 3.36
1141 1166 1.918957 CCTTCACCTTCTTCCCCATCT 59.081 52.381 0.00 0.00 0.00 2.90
1148 1173 1.539157 CCTTGGCCTTCACCTTCTTC 58.461 55.000 3.32 0.00 0.00 2.87
1520 1545 1.421410 GCTTGGTATCTGACACGGCG 61.421 60.000 4.80 4.80 0.00 6.46
1616 1641 5.707931 TCATTTTCGCATGACAAGCAATAA 58.292 33.333 3.27 0.00 0.00 1.40
1664 1689 1.355066 GCGCTGCTACAACTGTCTCC 61.355 60.000 0.00 0.00 0.00 3.71
1718 1743 1.465777 GCCAAAACCAATGCATTGCTC 59.534 47.619 30.15 11.50 36.48 4.26
1772 1797 9.912634 TTGAAGAAACATGTATTTCCAAGATTC 57.087 29.630 0.00 1.10 39.05 2.52
1910 1935 2.751259 TCCTGCATCATTTGAAGCACTC 59.249 45.455 6.39 0.00 42.83 3.51
1973 1998 4.336280 AGCCTTTGAACTGAGGGTATTTC 58.664 43.478 0.00 0.00 41.69 2.17
2093 2118 1.422977 TTGTAGGAACCCCAGCAGCA 61.423 55.000 0.00 0.00 33.88 4.41
2414 2447 3.321111 TCTCACTGACAACCTGTCCTAAC 59.679 47.826 4.42 0.00 46.40 2.34
2417 2450 2.088104 TCTCACTGACAACCTGTCCT 57.912 50.000 4.42 0.00 46.40 3.85
2456 2489 2.082231 GAAGCACATGACTCACTGCAT 58.918 47.619 0.00 0.00 31.71 3.96
2502 2535 5.965033 ATGTCATCCTCCACATTAGAAGT 57.035 39.130 0.00 0.00 28.27 3.01
3050 3089 0.111061 ACAATGACAAGCAGCCCTCA 59.889 50.000 0.00 0.00 0.00 3.86
3090 3129 2.086869 CTCACAATGCCAAGATTCCGT 58.913 47.619 0.00 0.00 0.00 4.69
3153 3192 1.950973 GCCGTCTCCTCACCCTCTTC 61.951 65.000 0.00 0.00 0.00 2.87
3233 3272 2.158957 GCTCGGGACCTTATCATCAACA 60.159 50.000 0.00 0.00 0.00 3.33
3563 3646 1.227556 GTCGCCACAACTCACTGGT 60.228 57.895 0.00 0.00 0.00 4.00
3581 3664 0.674581 TGCAAGAGGCCGAGTCATTG 60.675 55.000 0.00 0.00 43.89 2.82
3756 3849 0.814457 TTGTGTGCCTTGACAACCAC 59.186 50.000 7.10 7.10 0.00 4.16
3863 3956 6.128391 TGTTCAAAGTAATCGTCAATACAGGC 60.128 38.462 0.00 0.00 0.00 4.85
3899 3992 1.546029 CTGAACCGACCATGAGAGTCA 59.454 52.381 0.00 0.00 33.70 3.41
4366 4547 7.171337 GGCAGACTTGAATCAGAGAATAAGATC 59.829 40.741 0.00 0.00 0.00 2.75
4444 4625 8.491045 TCATATATGTAACCTCCAGATTCACA 57.509 34.615 12.42 0.00 0.00 3.58
4478 4659 2.987149 CAGCTTACCGTATATGCCTTCG 59.013 50.000 0.00 0.00 0.00 3.79
4647 4828 7.254252 GCATACTAAACTTGAGAGCTACACATG 60.254 40.741 0.00 0.00 0.00 3.21
4714 4897 4.618920 ATAGGTCCCTAAACTTATGCGG 57.381 45.455 0.00 0.00 31.73 5.69
4842 5025 7.095481 CGATAAGTGGTGATGTCATTATCCTTG 60.095 40.741 7.80 0.00 0.00 3.61
4881 5064 1.375908 GCTTCCCATGTGCTCGACA 60.376 57.895 0.00 0.00 39.53 4.35
4920 5103 5.294734 TCTTGCCAGATCTTACATATGCA 57.705 39.130 1.58 0.00 0.00 3.96
5071 5254 6.776116 ACCAGATACATATTGTCTTACTCGGA 59.224 38.462 0.00 0.00 0.00 4.55
5090 5273 3.404869 TCCATGAGTAGGTCACCAGAT 57.595 47.619 0.00 0.00 38.28 2.90
5141 5324 1.967319 TGTTTGTCACCTCTTGCTCC 58.033 50.000 0.00 0.00 0.00 4.70
5188 5371 2.524306 AGAACTCTCCACCTGAGACTG 58.476 52.381 0.00 0.00 45.29 3.51
5189 5372 2.990740 AGAACTCTCCACCTGAGACT 57.009 50.000 0.00 0.00 45.29 3.24
5238 5423 3.069289 CTCACTGTAAGCAGCATGAACA 58.931 45.455 0.00 0.00 46.30 3.18
5258 5443 6.384015 AGAAAAGGAAAACCCAAAGAATGACT 59.616 34.615 0.00 0.00 37.41 3.41
5289 5474 0.120377 TTCCACCCCTCCACCTATGT 59.880 55.000 0.00 0.00 0.00 2.29
5292 5477 1.638589 CAATTTCCACCCCTCCACCTA 59.361 52.381 0.00 0.00 0.00 3.08
5398 5583 0.388294 GTACCGGGCTGTCTATGACC 59.612 60.000 6.32 0.00 0.00 4.02
5412 5597 8.148807 TCCACATATATCAAAAACATGTACCG 57.851 34.615 0.00 0.00 0.00 4.02
5436 5622 1.735700 GCAAAATTTAGGGGCGCACTC 60.736 52.381 10.74 0.00 0.00 3.51
5571 5757 6.016276 TCCAGAATTTCTTGGAACTTACAAGC 60.016 38.462 8.71 0.00 43.77 4.01
5573 5759 8.477419 AATCCAGAATTTCTTGGAACTTACAA 57.523 30.769 16.44 0.00 31.10 2.41
5582 5768 9.709495 TCACAAAATAAATCCAGAATTTCTTGG 57.291 29.630 0.00 2.77 38.53 3.61
5624 5817 8.483758 TGGAGTTTTTAGGGATTCTAGACATAC 58.516 37.037 0.00 0.00 0.00 2.39
5633 5826 9.725019 ATTCAAATTTGGAGTTTTTAGGGATTC 57.275 29.630 17.90 0.00 0.00 2.52
5704 5897 7.340999 GCCTACAATCCCTAAAAACTCCAAATA 59.659 37.037 0.00 0.00 0.00 1.40
5713 5906 4.004982 GACGTGCCTACAATCCCTAAAAA 58.995 43.478 0.00 0.00 0.00 1.94
5882 6083 4.120331 GGAACATGCCGCTGTGCC 62.120 66.667 4.72 4.72 37.68 5.01
5918 6119 1.137825 GTCGTCCTCAGCTTCTCGG 59.862 63.158 0.00 0.00 0.00 4.63
5953 6157 1.406898 TCACCTCTAGATTGCTCTGCG 59.593 52.381 0.00 0.00 32.66 5.18
6017 6221 2.741985 CGTCATCTGGTTGCGCCA 60.742 61.111 4.18 0.00 46.95 5.69
6018 6222 4.166011 GCGTCATCTGGTTGCGCC 62.166 66.667 4.18 0.00 41.93 6.53
6019 6223 4.166011 GGCGTCATCTGGTTGCGC 62.166 66.667 0.00 0.00 46.24 6.09
6020 6224 3.499737 GGGCGTCATCTGGTTGCG 61.500 66.667 0.00 0.00 0.00 4.85
6021 6225 3.499737 CGGGCGTCATCTGGTTGC 61.500 66.667 0.00 0.00 0.00 4.17
6022 6226 3.499737 GCGGGCGTCATCTGGTTG 61.500 66.667 0.00 0.00 0.00 3.77
6023 6227 4.778143 GGCGGGCGTCATCTGGTT 62.778 66.667 0.00 0.00 0.00 3.67
6058 6262 4.629958 AAAACCCCATGCCCCGCA 62.630 61.111 0.00 0.00 44.86 5.69
6059 6263 3.318384 AAAAACCCCATGCCCCGC 61.318 61.111 0.00 0.00 0.00 6.13
6060 6264 1.763546 AACAAAAACCCCATGCCCCG 61.764 55.000 0.00 0.00 0.00 5.73
6061 6265 2.150449 AACAAAAACCCCATGCCCC 58.850 52.632 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.