Multiple sequence alignment - TraesCS2D01G410200

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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 TraesCS2D01G410200 chr2D 100.000 3256 0 0 1 3256 524585755 524582500 0.000000e+00 6013
1 TraesCS2D01G410200 chr2D 92.754 138 10 0 2999 3136 571556977 571557114 1.980000e-47 200
2 TraesCS2D01G410200 chr2B 95.241 1891 84 5 842 2732 620593376 620595260 0.000000e+00 2988
3 TraesCS2D01G410200 chr2B 93.086 405 19 4 2732 3134 620595340 620595737 4.680000e-163 584
4 TraesCS2D01G410200 chr2B 86.325 234 24 2 521 754 620824305 620824080 6.980000e-62 248
5 TraesCS2D01G410200 chr2B 92.806 139 10 0 2999 3137 683745013 683745151 5.510000e-48 202
6 TraesCS2D01G410200 chr2A 91.485 1832 122 18 1227 3054 670250302 670248501 0.000000e+00 2488
7 TraesCS2D01G410200 chr2A 96.653 239 7 1 883 1121 670251032 670250795 2.350000e-106 396
8 TraesCS2D01G410200 chr2A 87.658 316 36 3 522 836 670252219 670251906 6.640000e-97 364
9 TraesCS2D01G410200 chr2A 91.156 147 13 0 2071 2217 670238283 670238137 1.980000e-47 200
10 TraesCS2D01G410200 chr5D 96.558 523 16 2 1 522 175077557 175078078 0.000000e+00 865
11 TraesCS2D01G410200 chr5D 96.161 521 18 2 3 522 452398113 452398632 0.000000e+00 850
12 TraesCS2D01G410200 chr1D 96.353 521 17 2 1 520 255860190 255859671 0.000000e+00 856
13 TraesCS2D01G410200 chr1D 95.977 522 19 2 1 521 341905937 341905417 0.000000e+00 846
14 TraesCS2D01G410200 chr1D 95.644 528 19 4 1 527 220359535 220360059 0.000000e+00 845
15 TraesCS2D01G410200 chr1D 95.802 524 20 2 1 523 252063147 252062625 0.000000e+00 845
16 TraesCS2D01G410200 chr7D 95.985 523 17 4 3 523 144155384 144154864 0.000000e+00 846
17 TraesCS2D01G410200 chr4B 95.977 522 19 2 1 521 306133481 306132961 0.000000e+00 846
18 TraesCS2D01G410200 chr3D 95.969 521 19 2 1 520 334113084 334113603 0.000000e+00 845


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 TraesCS2D01G410200 chr2D 524582500 524585755 3255 True 6013.000000 6013 100.0000 1 3256 1 chr2D.!!$R1 3255
1 TraesCS2D01G410200 chr2B 620593376 620595737 2361 False 1786.000000 2988 94.1635 842 3134 2 chr2B.!!$F2 2292
2 TraesCS2D01G410200 chr2A 670248501 670252219 3718 True 1082.666667 2488 91.9320 522 3054 3 chr2A.!!$R2 2532
3 TraesCS2D01G410200 chr5D 175077557 175078078 521 False 865.000000 865 96.5580 1 522 1 chr5D.!!$F1 521
4 TraesCS2D01G410200 chr5D 452398113 452398632 519 False 850.000000 850 96.1610 3 522 1 chr5D.!!$F2 519
5 TraesCS2D01G410200 chr1D 255859671 255860190 519 True 856.000000 856 96.3530 1 520 1 chr1D.!!$R2 519
6 TraesCS2D01G410200 chr1D 341905417 341905937 520 True 846.000000 846 95.9770 1 521 1 chr1D.!!$R3 520
7 TraesCS2D01G410200 chr1D 220359535 220360059 524 False 845.000000 845 95.6440 1 527 1 chr1D.!!$F1 526
8 TraesCS2D01G410200 chr1D 252062625 252063147 522 True 845.000000 845 95.8020 1 523 1 chr1D.!!$R1 522
9 TraesCS2D01G410200 chr7D 144154864 144155384 520 True 846.000000 846 95.9850 3 523 1 chr7D.!!$R1 520
10 TraesCS2D01G410200 chr4B 306132961 306133481 520 True 846.000000 846 95.9770 1 521 1 chr4B.!!$R1 520
11 TraesCS2D01G410200 chr3D 334113084 334113603 519 False 845.000000 845 95.9690 1 520 1 chr3D.!!$F1 519

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
599 601 0.323302 TAGCATGTTCACGCTGGGAA 59.677 50.0 3.62 0.0 39.30 3.97 F
1704 2919 0.381089 CCATCGACTACCTCGTGGTC 59.619 60.0 13.38 0.0 44.78 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 3319 1.086696 ATGCTGCTACGACGCAAAAT 58.913 45.0 0.00 0.16 39.80 1.82 R
3223 4522 0.179179 GGCAATGCACTCGCTCTTTC 60.179 55.0 7.79 0.00 39.64 2.62 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
44 45 2.597510 GCCCGCCACCTTTTGACT 60.598 61.111 0.00 0.00 0.00 3.41
80 81 1.631405 CCTTTTCACAGGAATGGGCA 58.369 50.000 0.00 0.00 35.71 5.36
124 125 2.059541 GACGTATCATAGGCGCCTTTC 58.940 52.381 37.74 13.62 0.00 2.62
219 221 1.356059 TGGAAAATCCCCATTGGTCGA 59.644 47.619 1.20 0.00 35.03 4.20
242 244 2.805657 GCTGTTAGCGGGTTATCGGATT 60.806 50.000 0.00 0.00 0.00 3.01
320 322 2.103432 TCACCCTTGACGAAAGCACTTA 59.897 45.455 0.00 0.00 34.24 2.24
499 501 3.671459 GTGACAAACACGTATCATCACGA 59.329 43.478 2.26 0.00 44.69 4.35
540 542 3.133542 TGATAACATGTGAGCCTCTCCTG 59.866 47.826 0.00 0.00 0.00 3.86
542 544 0.612229 ACATGTGAGCCTCTCCTGTG 59.388 55.000 0.00 0.00 0.00 3.66
555 557 2.034879 CCTGTGGCGTCGCAATCTT 61.035 57.895 20.50 0.00 32.47 2.40
568 570 1.957113 GCAATCTTTAGCAGCCCCTGT 60.957 52.381 0.00 0.00 33.43 4.00
569 571 1.747355 CAATCTTTAGCAGCCCCTGTG 59.253 52.381 0.00 0.00 33.43 3.66
599 601 0.323302 TAGCATGTTCACGCTGGGAA 59.677 50.000 3.62 0.00 39.30 3.97
620 622 2.614259 ACCACCATGAAGTCTCAGTCT 58.386 47.619 0.00 0.00 34.23 3.24
625 627 4.220382 CACCATGAAGTCTCAGTCTCTTCT 59.780 45.833 0.00 0.00 38.52 2.85
639 641 0.811281 TCTTCTGCGAGCTTGATCGA 59.189 50.000 12.54 0.00 45.56 3.59
644 646 1.786004 CTGCGAGCTTGATCGAATCTC 59.214 52.381 12.54 3.03 45.56 2.75
669 671 1.452108 GAAACTCCTGGATGGCCCG 60.452 63.158 0.00 0.00 37.93 6.13
678 680 2.275380 GGATGGCCCGTTGCAAACT 61.275 57.895 0.00 0.00 46.99 2.66
687 689 1.661112 CCGTTGCAAACTAGAGCTAGC 59.339 52.381 6.62 6.62 46.99 3.42
715 717 2.809601 GGCGAAAAGAGCGAGCGA 60.810 61.111 0.00 0.00 35.00 4.93
738 740 1.454201 CTGTCGTGAGGAGAGCAGTA 58.546 55.000 0.00 0.00 0.00 2.74
742 744 3.008330 GTCGTGAGGAGAGCAGTAGTTA 58.992 50.000 0.00 0.00 0.00 2.24
743 745 3.628487 GTCGTGAGGAGAGCAGTAGTTAT 59.372 47.826 0.00 0.00 0.00 1.89
744 746 4.815308 GTCGTGAGGAGAGCAGTAGTTATA 59.185 45.833 0.00 0.00 0.00 0.98
745 747 5.296283 GTCGTGAGGAGAGCAGTAGTTATAA 59.704 44.000 0.00 0.00 0.00 0.98
768 770 3.029570 GGGTAAGTGAGTACCACCTAGG 58.970 54.545 7.41 7.41 46.87 3.02
776 778 0.916809 GTACCACCTAGGGGCACATT 59.083 55.000 14.81 0.00 43.89 2.71
808 810 4.961438 ATGATTTTGCAAGAGTTTGGGT 57.039 36.364 0.00 0.00 34.79 4.51
812 814 1.110442 TTGCAAGAGTTTGGGTGGTG 58.890 50.000 0.00 0.00 34.79 4.17
814 816 0.668535 GCAAGAGTTTGGGTGGTGAC 59.331 55.000 0.00 0.00 34.79 3.67
823 825 4.166531 AGTTTGGGTGGTGACTTAACCTTA 59.833 41.667 3.43 0.00 41.16 2.69
1020 1848 3.687102 CCACCGCGACCACCACTA 61.687 66.667 8.23 0.00 0.00 2.74
1101 1929 4.787280 CTCCTCCTCCGCCCCACT 62.787 72.222 0.00 0.00 0.00 4.00
1129 1957 3.839432 CGAACCCTCTCCTCCGCC 61.839 72.222 0.00 0.00 0.00 6.13
1133 1961 2.685380 CCCTCTCCTCCGCCTTGT 60.685 66.667 0.00 0.00 0.00 3.16
1704 2919 0.381089 CCATCGACTACCTCGTGGTC 59.619 60.000 13.38 0.00 44.78 4.02
1707 2922 1.378250 CGACTACCTCGTGGTCCCT 60.378 63.158 13.38 0.00 44.78 4.20
1743 2958 2.125350 CTTGCGCTCCCTGTCCTC 60.125 66.667 9.73 0.00 0.00 3.71
1746 2961 4.803426 GCGCTCCCTGTCCTCACG 62.803 72.222 0.00 0.00 0.00 4.35
1995 3210 3.674997 GTCTGCAGTGGTCATTTCCTTA 58.325 45.455 14.67 0.00 0.00 2.69
2001 3216 3.758554 CAGTGGTCATTTCCTTAGTTGGG 59.241 47.826 0.00 0.00 0.00 4.12
2064 3279 1.642037 CTGGTGCTGGTGATTCGCTG 61.642 60.000 0.00 0.00 0.00 5.18
2073 3288 1.667510 TGATTCGCTGAAGCACGCA 60.668 52.632 2.79 0.00 42.21 5.24
2094 3309 0.847373 TGGGTTAAGGCAAGACCACA 59.153 50.000 5.71 0.00 43.14 4.17
2096 3311 1.073284 GGGTTAAGGCAAGACCACAGA 59.927 52.381 5.71 0.00 43.14 3.41
2097 3312 2.427506 GGTTAAGGCAAGACCACAGAG 58.572 52.381 0.00 0.00 43.14 3.35
2104 3319 2.487265 GGCAAGACCACAGAGGAGAAAA 60.487 50.000 0.00 0.00 41.22 2.29
2117 3332 4.389077 AGAGGAGAAAATTTTGCGTCGTAG 59.611 41.667 8.47 0.00 0.00 3.51
2131 3346 3.120991 GCGTCGTAGCAGCATAATTTAGG 60.121 47.826 0.00 0.00 37.05 2.69
2194 3409 1.074319 GCATTGCAACATCAGCCACG 61.074 55.000 0.00 0.00 0.00 4.94
2251 3466 7.875327 TCCTTTGGAAGTAAACTATTATGCC 57.125 36.000 0.00 0.00 0.00 4.40
2303 3518 8.089597 TCAATTGTTTGCATCTGATTTGTGTAT 58.910 29.630 5.13 0.00 32.61 2.29
2399 3614 7.113694 AAAGCATTTTAAGATCAGCTCAAGCG 61.114 38.462 0.00 0.00 40.39 4.68
2471 3686 5.063880 GTGAGGAAACTACAGTGAATTGGT 58.936 41.667 0.00 0.00 44.43 3.67
2477 3692 6.128172 GGAAACTACAGTGAATTGGTGATCAG 60.128 42.308 0.00 0.00 0.00 2.90
2512 3727 1.346395 TGCAACGTTGTACTCCAGGAT 59.654 47.619 27.78 0.00 0.00 3.24
2528 3743 6.070538 ACTCCAGGATATCACATACATTAGGC 60.071 42.308 4.83 0.00 0.00 3.93
2539 3754 9.726438 ATCACATACATTAGGCCTTATTAAGAC 57.274 33.333 12.58 0.00 0.00 3.01
2552 3767 6.768381 GCCTTATTAAGACTAGTGGCAATTCT 59.232 38.462 0.00 0.00 38.99 2.40
2602 3817 6.498304 TGAGAAGAACTGCAGAATTTTTGTC 58.502 36.000 23.35 14.35 0.00 3.18
2605 3820 4.848757 AGAACTGCAGAATTTTTGTCGAC 58.151 39.130 23.35 9.11 0.00 4.20
2658 3873 0.179124 TTGTCAAGGCAAACAACGGC 60.179 50.000 0.00 0.00 30.73 5.68
2764 4058 4.315803 AGACCACGAATTTGAGTACCTTG 58.684 43.478 0.00 0.00 0.00 3.61
2873 4167 4.520492 CACTCTTACACCTTTGATTTGCCT 59.480 41.667 0.00 0.00 0.00 4.75
2916 4210 1.605710 CTGTCACCACTCTGGCAAAAG 59.394 52.381 0.00 0.00 42.67 2.27
2979 4274 6.753107 TCTGACGTACATGAATCTGACTAA 57.247 37.500 0.00 0.00 0.00 2.24
3003 4298 7.765695 AGAAAATCATGTGTTGGTGAACTAT 57.234 32.000 0.00 0.00 32.79 2.12
3134 4433 3.753272 CCAGTGGTCCTATGTTTTCTGTG 59.247 47.826 0.00 0.00 0.00 3.66
3135 4434 4.389374 CAGTGGTCCTATGTTTTCTGTGT 58.611 43.478 0.00 0.00 0.00 3.72
3136 4435 4.821805 CAGTGGTCCTATGTTTTCTGTGTT 59.178 41.667 0.00 0.00 0.00 3.32
3137 4436 5.299279 CAGTGGTCCTATGTTTTCTGTGTTT 59.701 40.000 0.00 0.00 0.00 2.83
3138 4437 5.891551 AGTGGTCCTATGTTTTCTGTGTTTT 59.108 36.000 0.00 0.00 0.00 2.43
3139 4438 6.379988 AGTGGTCCTATGTTTTCTGTGTTTTT 59.620 34.615 0.00 0.00 0.00 1.94
3163 4462 7.744087 TTTACAGCATCTATGTTTTCTGTGT 57.256 32.000 9.74 0.00 36.37 3.72
3164 4463 7.744087 TTACAGCATCTATGTTTTCTGTGTT 57.256 32.000 9.74 0.00 36.37 3.32
3165 4464 6.005583 ACAGCATCTATGTTTTCTGTGTTG 57.994 37.500 0.00 0.00 34.00 3.33
3166 4465 5.532406 ACAGCATCTATGTTTTCTGTGTTGT 59.468 36.000 0.00 0.00 34.00 3.32
3167 4466 5.854866 CAGCATCTATGTTTTCTGTGTTGTG 59.145 40.000 0.00 0.00 0.00 3.33
3168 4467 4.618489 GCATCTATGTTTTCTGTGTTGTGC 59.382 41.667 0.00 0.00 0.00 4.57
3169 4468 5.563475 GCATCTATGTTTTCTGTGTTGTGCT 60.563 40.000 0.00 0.00 0.00 4.40
3170 4469 5.422666 TCTATGTTTTCTGTGTTGTGCTG 57.577 39.130 0.00 0.00 0.00 4.41
3171 4470 4.881273 TCTATGTTTTCTGTGTTGTGCTGT 59.119 37.500 0.00 0.00 0.00 4.40
3172 4471 3.214697 TGTTTTCTGTGTTGTGCTGTG 57.785 42.857 0.00 0.00 0.00 3.66
3173 4472 1.919918 GTTTTCTGTGTTGTGCTGTGC 59.080 47.619 0.00 0.00 0.00 4.57
3174 4473 1.462616 TTTCTGTGTTGTGCTGTGCT 58.537 45.000 0.00 0.00 0.00 4.40
3175 4474 1.462616 TTCTGTGTTGTGCTGTGCTT 58.537 45.000 0.00 0.00 0.00 3.91
3176 4475 1.462616 TCTGTGTTGTGCTGTGCTTT 58.537 45.000 0.00 0.00 0.00 3.51
3177 4476 2.637947 TCTGTGTTGTGCTGTGCTTTA 58.362 42.857 0.00 0.00 0.00 1.85
3178 4477 2.613595 TCTGTGTTGTGCTGTGCTTTAG 59.386 45.455 0.00 0.00 0.00 1.85
3179 4478 1.065401 TGTGTTGTGCTGTGCTTTAGC 59.935 47.619 0.00 0.00 41.49 3.09
3196 4495 7.812309 GCTTTAGCAAAACATACCCTTAAAG 57.188 36.000 0.00 0.00 41.59 1.85
3197 4496 6.811665 GCTTTAGCAAAACATACCCTTAAAGG 59.188 38.462 0.00 0.00 41.59 3.11
3198 4497 7.524863 GCTTTAGCAAAACATACCCTTAAAGGT 60.525 37.037 0.48 0.48 41.58 3.50
3199 4498 5.722021 AGCAAAACATACCCTTAAAGGTG 57.278 39.130 5.98 0.00 41.42 4.00
3200 4499 4.021456 AGCAAAACATACCCTTAAAGGTGC 60.021 41.667 5.98 0.00 41.42 5.01
3201 4500 4.262249 GCAAAACATACCCTTAAAGGTGCA 60.262 41.667 5.98 0.00 41.42 4.57
3202 4501 5.740513 GCAAAACATACCCTTAAAGGTGCAA 60.741 40.000 5.98 0.00 41.42 4.08
3203 4502 6.463360 CAAAACATACCCTTAAAGGTGCAAT 58.537 36.000 5.98 0.00 41.42 3.56
3204 4503 5.659440 AACATACCCTTAAAGGTGCAATG 57.341 39.130 5.98 4.71 41.42 2.82
3205 4504 4.672899 ACATACCCTTAAAGGTGCAATGT 58.327 39.130 5.98 5.32 41.42 2.71
3206 4505 5.822204 ACATACCCTTAAAGGTGCAATGTA 58.178 37.500 5.98 0.00 41.42 2.29
3207 4506 5.650703 ACATACCCTTAAAGGTGCAATGTAC 59.349 40.000 5.98 0.00 41.42 2.90
3208 4507 4.382386 ACCCTTAAAGGTGCAATGTACT 57.618 40.909 0.87 0.00 39.24 2.73
3209 4508 4.736473 ACCCTTAAAGGTGCAATGTACTT 58.264 39.130 0.87 0.00 39.24 2.24
3210 4509 5.883180 ACCCTTAAAGGTGCAATGTACTTA 58.117 37.500 0.87 0.00 39.24 2.24
3211 4510 6.308566 ACCCTTAAAGGTGCAATGTACTTAA 58.691 36.000 0.87 0.00 39.24 1.85
3212 4511 6.433093 ACCCTTAAAGGTGCAATGTACTTAAG 59.567 38.462 12.73 12.73 39.24 1.85
3213 4512 6.322491 CCTTAAAGGTGCAATGTACTTAAGC 58.678 40.000 13.66 0.00 0.00 3.09
3214 4513 6.151144 CCTTAAAGGTGCAATGTACTTAAGCT 59.849 38.462 13.66 0.00 0.00 3.74
3215 4514 5.376854 AAAGGTGCAATGTACTTAAGCTG 57.623 39.130 1.29 0.00 0.00 4.24
3216 4515 4.021102 AGGTGCAATGTACTTAAGCTGT 57.979 40.909 1.29 0.00 0.00 4.40
3217 4516 5.160607 AGGTGCAATGTACTTAAGCTGTA 57.839 39.130 1.29 0.00 0.00 2.74
3218 4517 4.935808 AGGTGCAATGTACTTAAGCTGTAC 59.064 41.667 1.29 6.00 40.27 2.90
3219 4518 4.935808 GGTGCAATGTACTTAAGCTGTACT 59.064 41.667 12.51 0.00 40.44 2.73
3220 4519 5.411669 GGTGCAATGTACTTAAGCTGTACTT 59.588 40.000 12.51 5.28 40.44 2.24
3221 4520 6.402226 GGTGCAATGTACTTAAGCTGTACTTC 60.402 42.308 12.51 2.64 40.44 3.01
3222 4521 6.369065 GTGCAATGTACTTAAGCTGTACTTCT 59.631 38.462 12.51 0.00 40.44 2.85
3223 4522 6.368791 TGCAATGTACTTAAGCTGTACTTCTG 59.631 38.462 12.51 8.66 40.44 3.02
3224 4523 6.590292 GCAATGTACTTAAGCTGTACTTCTGA 59.410 38.462 12.51 0.00 40.44 3.27
3225 4524 7.117812 GCAATGTACTTAAGCTGTACTTCTGAA 59.882 37.037 12.51 0.00 40.44 3.02
3226 4525 8.988934 CAATGTACTTAAGCTGTACTTCTGAAA 58.011 33.333 12.51 0.00 40.44 2.69
3227 4526 8.764524 ATGTACTTAAGCTGTACTTCTGAAAG 57.235 34.615 12.51 2.51 40.44 2.62
3228 4527 7.948357 TGTACTTAAGCTGTACTTCTGAAAGA 58.052 34.615 12.51 0.00 39.97 2.52
3229 4528 8.082852 TGTACTTAAGCTGTACTTCTGAAAGAG 58.917 37.037 12.51 0.00 40.20 2.85
3230 4529 7.062488 GTACTTAAGCTGTACTTCTGAAAGAGC 59.938 40.741 1.29 3.71 39.97 4.09
3239 4538 2.462456 TCTGAAAGAGCGAGTGCATT 57.538 45.000 0.00 0.00 46.23 3.56
3240 4539 2.071540 TCTGAAAGAGCGAGTGCATTG 58.928 47.619 0.00 0.00 46.23 2.82
3241 4540 0.518636 TGAAAGAGCGAGTGCATTGC 59.481 50.000 0.46 0.46 46.23 3.56
3242 4541 0.179179 GAAAGAGCGAGTGCATTGCC 60.179 55.000 6.12 0.00 46.23 4.52
3243 4542 0.607489 AAAGAGCGAGTGCATTGCCT 60.607 50.000 6.12 2.70 46.23 4.75
3244 4543 0.607489 AAGAGCGAGTGCATTGCCTT 60.607 50.000 6.12 0.00 46.23 4.35
3245 4544 0.607489 AGAGCGAGTGCATTGCCTTT 60.607 50.000 6.12 0.00 46.23 3.11
3246 4545 0.455633 GAGCGAGTGCATTGCCTTTG 60.456 55.000 6.12 0.00 46.23 2.77
3247 4546 1.444895 GCGAGTGCATTGCCTTTGG 60.445 57.895 6.12 0.00 42.15 3.28
3248 4547 1.865788 GCGAGTGCATTGCCTTTGGA 61.866 55.000 6.12 0.00 42.15 3.53
3249 4548 0.813184 CGAGTGCATTGCCTTTGGAT 59.187 50.000 6.12 0.00 0.00 3.41
3250 4549 1.468565 CGAGTGCATTGCCTTTGGATG 60.469 52.381 6.12 0.00 0.00 3.51
3251 4550 1.547372 GAGTGCATTGCCTTTGGATGT 59.453 47.619 6.12 0.00 0.00 3.06
3252 4551 1.972795 AGTGCATTGCCTTTGGATGTT 59.027 42.857 6.12 0.00 0.00 2.71
3253 4552 3.164268 AGTGCATTGCCTTTGGATGTTA 58.836 40.909 6.12 0.00 0.00 2.41
3254 4553 3.770933 AGTGCATTGCCTTTGGATGTTAT 59.229 39.130 6.12 0.00 0.00 1.89
3255 4554 4.114794 GTGCATTGCCTTTGGATGTTATC 58.885 43.478 6.12 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.757980 TAGTCAAAAGGTGGCGGGCC 62.758 60.000 1.86 1.86 36.74 5.80
44 45 1.379309 GGCCGGCCCATTTGACTTA 60.379 57.895 36.64 0.00 0.00 2.24
219 221 0.104304 CGATAACCCGCTAACAGCCT 59.896 55.000 0.00 0.00 38.18 4.58
242 244 0.108041 GCTATCGGGTCCGGTTTTGA 60.108 55.000 9.68 0.00 40.25 2.69
320 322 1.566404 TGATAAATCGCGCGTCACAT 58.434 45.000 30.98 18.43 0.00 3.21
523 525 0.612229 CACAGGAGAGGCTCACATGT 59.388 55.000 23.18 23.18 31.08 3.21
524 526 0.107800 CCACAGGAGAGGCTCACATG 60.108 60.000 21.94 21.94 31.08 3.21
525 527 1.908340 GCCACAGGAGAGGCTCACAT 61.908 60.000 18.26 5.06 46.56 3.21
526 528 2.587247 GCCACAGGAGAGGCTCACA 61.587 63.158 18.26 0.00 46.56 3.58
527 529 2.267324 GCCACAGGAGAGGCTCAC 59.733 66.667 18.26 10.70 46.56 3.51
531 533 4.803426 CGACGCCACAGGAGAGGC 62.803 72.222 0.00 0.00 46.60 4.70
532 534 4.803426 GCGACGCCACAGGAGAGG 62.803 72.222 9.14 0.00 0.00 3.69
540 542 0.247695 GCTAAAGATTGCGACGCCAC 60.248 55.000 18.69 8.57 0.00 5.01
542 544 0.026803 CTGCTAAAGATTGCGACGCC 59.973 55.000 18.69 1.34 0.00 5.68
544 546 0.026803 GGCTGCTAAAGATTGCGACG 59.973 55.000 0.00 0.00 0.00 5.12
555 557 1.073025 CACACACAGGGGCTGCTAA 59.927 57.895 0.00 0.00 34.37 3.09
568 570 1.079197 CATGCTAGTCGCCCACACA 60.079 57.895 0.00 0.00 38.05 3.72
569 571 0.673644 AACATGCTAGTCGCCCACAC 60.674 55.000 0.00 0.00 38.05 3.82
599 601 2.975489 AGACTGAGACTTCATGGTGGTT 59.025 45.455 0.00 0.00 31.68 3.67
607 609 2.227626 CGCAGAAGAGACTGAGACTTCA 59.772 50.000 15.79 0.00 41.37 3.02
608 610 2.486203 TCGCAGAAGAGACTGAGACTTC 59.514 50.000 0.00 0.00 40.55 3.01
611 613 1.467374 GCTCGCAGAAGAGACTGAGAC 60.467 57.143 0.00 0.00 40.55 3.36
620 622 0.811281 TCGATCAAGCTCGCAGAAGA 59.189 50.000 0.00 0.00 38.52 2.87
625 627 1.845266 GAGATTCGATCAAGCTCGCA 58.155 50.000 7.19 0.00 37.76 5.10
639 641 0.802607 GGAGTTTCGCGCTCGAGATT 60.803 55.000 18.75 0.00 46.34 2.40
644 646 2.890847 ATCCAGGAGTTTCGCGCTCG 62.891 60.000 5.56 0.00 34.00 5.03
649 651 2.115291 GGCCATCCAGGAGTTTCGC 61.115 63.158 0.00 0.00 41.22 4.70
658 660 2.274645 TTTGCAACGGGCCATCCAG 61.275 57.895 4.39 0.00 43.89 3.86
669 671 2.338500 ACGCTAGCTCTAGTTTGCAAC 58.662 47.619 13.93 0.00 35.65 4.17
702 704 3.112709 GCCGTCGCTCGCTCTTTT 61.113 61.111 0.00 0.00 38.35 2.27
725 727 5.540337 CCCATTATAACTACTGCTCTCCTCA 59.460 44.000 0.00 0.00 0.00 3.86
736 738 8.917088 TGGTACTCACTTACCCATTATAACTAC 58.083 37.037 0.00 0.00 40.96 2.73
738 740 7.147602 GGTGGTACTCACTTACCCATTATAACT 60.148 40.741 12.36 0.00 45.38 2.24
742 744 5.286221 AGGTGGTACTCACTTACCCATTAT 58.714 41.667 12.36 0.00 45.38 1.28
743 745 4.691238 AGGTGGTACTCACTTACCCATTA 58.309 43.478 12.36 0.00 45.38 1.90
744 746 3.527937 AGGTGGTACTCACTTACCCATT 58.472 45.455 12.36 0.00 45.38 3.16
745 747 3.200958 AGGTGGTACTCACTTACCCAT 57.799 47.619 12.36 0.00 45.38 4.00
768 770 5.070770 TCATACAAATCACAAATGTGCCC 57.929 39.130 8.67 0.00 45.25 5.36
776 778 8.143193 ACTCTTGCAAAATCATACAAATCACAA 58.857 29.630 0.00 0.00 0.00 3.33
847 886 1.880027 CCCCGTCCAACTCAAAAGAAG 59.120 52.381 0.00 0.00 0.00 2.85
850 889 2.641197 CCCCCGTCCAACTCAAAAG 58.359 57.895 0.00 0.00 0.00 2.27
1101 1929 4.668118 GGGTTCGTCGTGGCGGAA 62.668 66.667 0.00 0.00 0.00 4.30
1129 1957 4.748144 GGGGCAGGGGCTGACAAG 62.748 72.222 0.00 0.00 42.18 3.16
1133 1961 3.275271 ATTTGGGGCAGGGGCTGA 61.275 61.111 0.00 0.00 40.87 4.26
1704 2919 2.125912 CAAGCGAGGACACGAGGG 60.126 66.667 0.00 0.00 35.09 4.30
1707 2922 3.973516 ACGCAAGCGAGGACACGA 61.974 61.111 22.30 0.00 42.83 4.35
1851 3066 1.596934 GCTGATCAAGTCCCACGGA 59.403 57.895 0.00 0.00 0.00 4.69
1854 3069 2.109126 GGCGCTGATCAAGTCCCAC 61.109 63.158 7.64 0.00 0.00 4.61
1995 3210 4.154942 AGTCTGCAATGAAAATCCCAACT 58.845 39.130 0.00 0.00 0.00 3.16
2001 3216 3.174375 GGCGAAGTCTGCAATGAAAATC 58.826 45.455 0.00 0.00 0.00 2.17
2064 3279 1.135402 CCTTAACCCATTGCGTGCTTC 60.135 52.381 0.00 0.00 0.00 3.86
2073 3288 2.158385 TGTGGTCTTGCCTTAACCCATT 60.158 45.455 0.00 0.00 38.35 3.16
2094 3309 3.139077 ACGACGCAAAATTTTCTCCTCT 58.861 40.909 0.00 0.00 0.00 3.69
2096 3311 3.120304 GCTACGACGCAAAATTTTCTCCT 60.120 43.478 0.00 0.00 0.00 3.69
2097 3312 3.161306 GCTACGACGCAAAATTTTCTCC 58.839 45.455 0.00 0.00 0.00 3.71
2104 3319 1.086696 ATGCTGCTACGACGCAAAAT 58.913 45.000 0.00 0.16 39.80 1.82
2117 3332 6.867662 ATGTACAGACCTAAATTATGCTGC 57.132 37.500 0.33 0.00 0.00 5.25
2131 3346 5.989777 ACTACACTTTGGTCAATGTACAGAC 59.010 40.000 0.33 4.15 0.00 3.51
2194 3409 5.904362 AAAATAACTCATTCACCTGGAGC 57.096 39.130 0.00 0.00 31.88 4.70
2399 3614 2.766970 TTTTACAGTGCCGCTTGAAC 57.233 45.000 0.00 0.00 0.00 3.18
2458 3673 7.394016 ACAATACTGATCACCAATTCACTGTA 58.606 34.615 0.00 0.00 0.00 2.74
2477 3692 6.143758 ACAACGTTGCAATTGATCAACAATAC 59.856 34.615 27.61 5.06 46.90 1.89
2528 3743 8.738645 AAGAATTGCCACTAGTCTTAATAAGG 57.261 34.615 0.00 0.00 0.00 2.69
2539 3754 4.095483 AGCATCGAAAAGAATTGCCACTAG 59.905 41.667 1.48 0.00 35.92 2.57
2552 3767 5.123820 CCAAGGATGACTAAAGCATCGAAAA 59.876 40.000 0.00 0.00 42.32 2.29
2602 3817 6.030548 ACTCACATATTCCCAGATATGTCG 57.969 41.667 7.37 5.42 45.47 4.35
2605 3820 6.652481 GTCCAACTCACATATTCCCAGATATG 59.348 42.308 3.92 3.92 42.84 1.78
2621 3836 4.279922 TGACAAAGACTATCGTCCAACTCA 59.720 41.667 0.00 0.00 41.16 3.41
2658 3873 1.275291 TCGTACTGGAAGCCAAAGGAG 59.725 52.381 0.00 0.00 37.60 3.69
2821 4115 1.334556 GCACACAATTGAGACACTGCA 59.665 47.619 13.59 0.00 0.00 4.41
2873 4167 3.490439 TTGTCATCAAGGTGAAGCTCA 57.510 42.857 0.00 0.00 0.00 4.26
2979 4274 7.765695 ATAGTTCACCAACACATGATTTTCT 57.234 32.000 0.00 0.00 34.60 2.52
3003 4298 7.559897 TGGTCATGCGATAGAGATACCATAATA 59.440 37.037 0.00 0.00 39.76 0.98
3006 4301 5.261216 TGGTCATGCGATAGAGATACCATA 58.739 41.667 0.00 0.00 39.76 2.74
3087 4386 6.703165 GTGCTGAAACTGAAATGAAATTCCTT 59.297 34.615 0.00 0.00 33.67 3.36
3137 4436 8.629158 ACACAGAAAACATAGATGCTGTAAAAA 58.371 29.630 0.00 0.00 35.09 1.94
3138 4437 8.165239 ACACAGAAAACATAGATGCTGTAAAA 57.835 30.769 0.00 0.00 35.09 1.52
3139 4438 7.744087 ACACAGAAAACATAGATGCTGTAAA 57.256 32.000 0.00 0.00 35.09 2.01
3140 4439 7.228507 ACAACACAGAAAACATAGATGCTGTAA 59.771 33.333 0.00 0.00 35.09 2.41
3141 4440 6.710295 ACAACACAGAAAACATAGATGCTGTA 59.290 34.615 0.00 0.00 35.09 2.74
3142 4441 5.532406 ACAACACAGAAAACATAGATGCTGT 59.468 36.000 0.00 0.00 37.09 4.40
3143 4442 5.854866 CACAACACAGAAAACATAGATGCTG 59.145 40.000 0.00 0.00 0.00 4.41
3144 4443 5.563475 GCACAACACAGAAAACATAGATGCT 60.563 40.000 0.00 0.00 0.00 3.79
3145 4444 4.618489 GCACAACACAGAAAACATAGATGC 59.382 41.667 0.00 0.00 0.00 3.91
3146 4445 5.854866 CAGCACAACACAGAAAACATAGATG 59.145 40.000 0.00 0.00 0.00 2.90
3147 4446 5.532406 ACAGCACAACACAGAAAACATAGAT 59.468 36.000 0.00 0.00 0.00 1.98
3148 4447 4.881273 ACAGCACAACACAGAAAACATAGA 59.119 37.500 0.00 0.00 0.00 1.98
3149 4448 4.971830 CACAGCACAACACAGAAAACATAG 59.028 41.667 0.00 0.00 0.00 2.23
3150 4449 4.733230 GCACAGCACAACACAGAAAACATA 60.733 41.667 0.00 0.00 0.00 2.29
3151 4450 3.772932 CACAGCACAACACAGAAAACAT 58.227 40.909 0.00 0.00 0.00 2.71
3152 4451 2.670789 GCACAGCACAACACAGAAAACA 60.671 45.455 0.00 0.00 0.00 2.83
3153 4452 1.919918 GCACAGCACAACACAGAAAAC 59.080 47.619 0.00 0.00 0.00 2.43
3154 4453 1.818060 AGCACAGCACAACACAGAAAA 59.182 42.857 0.00 0.00 0.00 2.29
3155 4454 1.462616 AGCACAGCACAACACAGAAA 58.537 45.000 0.00 0.00 0.00 2.52
3156 4455 1.462616 AAGCACAGCACAACACAGAA 58.537 45.000 0.00 0.00 0.00 3.02
3157 4456 1.462616 AAAGCACAGCACAACACAGA 58.537 45.000 0.00 0.00 0.00 3.41
3158 4457 2.855953 GCTAAAGCACAGCACAACACAG 60.856 50.000 0.00 0.00 41.59 3.66
3159 4458 1.065401 GCTAAAGCACAGCACAACACA 59.935 47.619 0.00 0.00 41.59 3.72
3160 4459 1.758783 GCTAAAGCACAGCACAACAC 58.241 50.000 0.00 0.00 41.59 3.32
3172 4471 6.811665 CCTTTAAGGGTATGTTTTGCTAAAGC 59.188 38.462 2.44 0.00 42.50 3.51
3173 4472 7.812669 CACCTTTAAGGGTATGTTTTGCTAAAG 59.187 37.037 16.10 0.00 40.58 1.85
3174 4473 7.662897 CACCTTTAAGGGTATGTTTTGCTAAA 58.337 34.615 16.10 0.00 40.58 1.85
3175 4474 6.294843 GCACCTTTAAGGGTATGTTTTGCTAA 60.295 38.462 16.10 0.00 40.58 3.09
3176 4475 5.184287 GCACCTTTAAGGGTATGTTTTGCTA 59.816 40.000 16.10 0.00 40.58 3.49
3177 4476 4.021456 GCACCTTTAAGGGTATGTTTTGCT 60.021 41.667 16.10 0.00 40.58 3.91
3178 4477 4.242475 GCACCTTTAAGGGTATGTTTTGC 58.758 43.478 16.10 9.32 40.58 3.68
3179 4478 5.461032 TGCACCTTTAAGGGTATGTTTTG 57.539 39.130 16.10 2.96 40.58 2.44
3180 4479 6.042666 ACATTGCACCTTTAAGGGTATGTTTT 59.957 34.615 16.10 0.00 40.58 2.43
3181 4480 5.542251 ACATTGCACCTTTAAGGGTATGTTT 59.458 36.000 16.10 0.00 40.58 2.83
3182 4481 5.083821 ACATTGCACCTTTAAGGGTATGTT 58.916 37.500 16.10 3.79 40.58 2.71
3183 4482 4.672899 ACATTGCACCTTTAAGGGTATGT 58.327 39.130 16.10 14.70 40.58 2.29
3184 4483 5.885912 AGTACATTGCACCTTTAAGGGTATG 59.114 40.000 16.10 11.94 40.58 2.39
3185 4484 6.074698 AGTACATTGCACCTTTAAGGGTAT 57.925 37.500 16.10 0.00 40.58 2.73
3186 4485 5.508280 AGTACATTGCACCTTTAAGGGTA 57.492 39.130 16.10 3.91 40.58 3.69
3187 4486 4.382386 AGTACATTGCACCTTTAAGGGT 57.618 40.909 16.10 2.85 40.58 4.34
3188 4487 6.625081 GCTTAAGTACATTGCACCTTTAAGGG 60.625 42.308 16.10 1.27 40.58 3.95
3189 4488 6.151144 AGCTTAAGTACATTGCACCTTTAAGG 59.849 38.462 9.81 9.81 42.49 2.69
3190 4489 7.023575 CAGCTTAAGTACATTGCACCTTTAAG 58.976 38.462 4.02 0.00 0.00 1.85
3191 4490 6.488683 ACAGCTTAAGTACATTGCACCTTTAA 59.511 34.615 4.02 0.00 0.00 1.52
3192 4491 6.001460 ACAGCTTAAGTACATTGCACCTTTA 58.999 36.000 4.02 0.00 0.00 1.85
3193 4492 4.827284 ACAGCTTAAGTACATTGCACCTTT 59.173 37.500 4.02 0.00 0.00 3.11
3194 4493 4.398319 ACAGCTTAAGTACATTGCACCTT 58.602 39.130 4.02 0.00 0.00 3.50
3195 4494 4.021102 ACAGCTTAAGTACATTGCACCT 57.979 40.909 4.02 0.00 0.00 4.00
3196 4495 4.935808 AGTACAGCTTAAGTACATTGCACC 59.064 41.667 13.53 0.00 43.24 5.01
3197 4496 6.369065 AGAAGTACAGCTTAAGTACATTGCAC 59.631 38.462 13.53 0.00 43.24 4.57
3198 4497 6.368791 CAGAAGTACAGCTTAAGTACATTGCA 59.631 38.462 13.53 0.00 43.24 4.08
3199 4498 6.590292 TCAGAAGTACAGCTTAAGTACATTGC 59.410 38.462 13.53 0.00 43.24 3.56
3200 4499 8.534333 TTCAGAAGTACAGCTTAAGTACATTG 57.466 34.615 13.53 9.08 43.24 2.82
3201 4500 9.209175 CTTTCAGAAGTACAGCTTAAGTACATT 57.791 33.333 13.53 6.48 43.24 2.71
3202 4501 8.585881 TCTTTCAGAAGTACAGCTTAAGTACAT 58.414 33.333 13.53 3.50 43.24 2.29
3203 4502 7.948357 TCTTTCAGAAGTACAGCTTAAGTACA 58.052 34.615 13.53 0.00 43.24 2.90
3204 4503 7.062488 GCTCTTTCAGAAGTACAGCTTAAGTAC 59.938 40.741 4.02 4.99 41.59 2.73
3205 4504 7.091443 GCTCTTTCAGAAGTACAGCTTAAGTA 58.909 38.462 4.02 0.00 37.59 2.24
3206 4505 5.929415 GCTCTTTCAGAAGTACAGCTTAAGT 59.071 40.000 4.02 0.00 37.59 2.24
3207 4506 5.061560 CGCTCTTTCAGAAGTACAGCTTAAG 59.938 44.000 0.00 0.00 37.59 1.85
3208 4507 4.923871 CGCTCTTTCAGAAGTACAGCTTAA 59.076 41.667 0.00 0.00 37.59 1.85
3209 4508 4.217767 TCGCTCTTTCAGAAGTACAGCTTA 59.782 41.667 0.00 0.00 37.59 3.09
3210 4509 3.005897 TCGCTCTTTCAGAAGTACAGCTT 59.994 43.478 0.00 0.00 40.76 3.74
3211 4510 2.558795 TCGCTCTTTCAGAAGTACAGCT 59.441 45.455 0.00 0.00 31.51 4.24
3212 4511 2.920490 CTCGCTCTTTCAGAAGTACAGC 59.080 50.000 0.00 0.00 34.41 4.40
3213 4512 3.917380 CACTCGCTCTTTCAGAAGTACAG 59.083 47.826 0.00 0.00 34.41 2.74
3214 4513 3.857383 GCACTCGCTCTTTCAGAAGTACA 60.857 47.826 0.00 0.00 34.41 2.90
3215 4514 2.664085 GCACTCGCTCTTTCAGAAGTAC 59.336 50.000 0.00 0.00 34.41 2.73
3216 4515 2.296190 TGCACTCGCTCTTTCAGAAGTA 59.704 45.455 0.00 0.00 39.64 2.24
3217 4516 1.069204 TGCACTCGCTCTTTCAGAAGT 59.931 47.619 0.00 0.00 39.64 3.01
3218 4517 1.788258 TGCACTCGCTCTTTCAGAAG 58.212 50.000 0.00 0.00 39.64 2.85
3219 4518 2.462456 ATGCACTCGCTCTTTCAGAA 57.538 45.000 0.00 0.00 39.64 3.02
3220 4519 2.071540 CAATGCACTCGCTCTTTCAGA 58.928 47.619 0.00 0.00 39.64 3.27
3221 4520 1.465354 GCAATGCACTCGCTCTTTCAG 60.465 52.381 0.00 0.00 39.64 3.02
3222 4521 0.518636 GCAATGCACTCGCTCTTTCA 59.481 50.000 0.00 0.00 39.64 2.69
3223 4522 0.179179 GGCAATGCACTCGCTCTTTC 60.179 55.000 7.79 0.00 39.64 2.62
3224 4523 0.607489 AGGCAATGCACTCGCTCTTT 60.607 50.000 7.79 0.00 39.64 2.52
3225 4524 0.607489 AAGGCAATGCACTCGCTCTT 60.607 50.000 7.79 0.00 39.64 2.85
3226 4525 0.607489 AAAGGCAATGCACTCGCTCT 60.607 50.000 7.79 0.00 39.64 4.09
3227 4526 0.455633 CAAAGGCAATGCACTCGCTC 60.456 55.000 7.79 0.00 39.64 5.03
3228 4527 1.582968 CAAAGGCAATGCACTCGCT 59.417 52.632 7.79 0.00 39.64 4.93
3229 4528 1.444895 CCAAAGGCAATGCACTCGC 60.445 57.895 7.79 0.00 39.24 5.03
3230 4529 0.813184 ATCCAAAGGCAATGCACTCG 59.187 50.000 7.79 0.00 0.00 4.18
3231 4530 1.547372 ACATCCAAAGGCAATGCACTC 59.453 47.619 7.79 0.00 0.00 3.51
3232 4531 1.636148 ACATCCAAAGGCAATGCACT 58.364 45.000 7.79 0.00 0.00 4.40
3233 4532 2.460757 AACATCCAAAGGCAATGCAC 57.539 45.000 7.79 0.00 0.00 4.57
3234 4533 4.389890 GATAACATCCAAAGGCAATGCA 57.610 40.909 7.79 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.