Multiple sequence alignment - TraesCS3D01G450600

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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 TraesCS3D01G450600 chr3D 100.000 4040 0 0 1 4040 558783177 558787216 0.000000e+00 7461.0
1 TraesCS3D01G450600 chr3D 84.421 1226 127 31 1919 3137 558938757 558939925 0.000000e+00 1147.0
2 TraesCS3D01G450600 chr3D 84.772 394 54 2 1500 1887 558938365 558938758 1.360000e-104 390.0
3 TraesCS3D01G450600 chr3D 81.224 245 36 7 18 254 565051682 565051440 5.330000e-44 189.0
4 TraesCS3D01G450600 chr3D 76.068 117 22 6 503 614 579959427 579959542 5.640000e-04 56.5
5 TraesCS3D01G450600 chr3A 95.054 2770 101 17 1238 3985 695130420 695133175 0.000000e+00 4324.0
6 TraesCS3D01G450600 chr3A 86.248 509 44 12 1 501 695129038 695129528 2.770000e-146 529.0
7 TraesCS3D01G450600 chr3A 83.556 450 50 15 2733 3170 695239597 695240034 2.260000e-107 399.0
8 TraesCS3D01G450600 chr3A 80.600 567 62 12 1919 2485 695224150 695224668 1.050000e-105 394.0
9 TraesCS3D01G450600 chr3A 89.811 265 22 4 2467 2729 695225732 695225993 6.470000e-88 335.0
10 TraesCS3D01G450600 chr3A 82.339 436 28 30 643 1047 695129542 695129959 2.330000e-87 333.0
11 TraesCS3D01G450600 chr3B 94.560 2794 121 14 1265 4040 741601296 741604076 0.000000e+00 4289.0
12 TraesCS3D01G450600 chr3B 84.584 1213 122 26 1919 3128 741713577 741714727 0.000000e+00 1144.0
13 TraesCS3D01G450600 chr3B 79.764 677 126 7 1610 2278 742524634 742523961 7.850000e-132 481.0
14 TraesCS3D01G450600 chr3B 86.234 385 50 2 2682 3063 742712806 742712422 8.080000e-112 414.0
15 TraesCS3D01G450600 chr3B 85.714 385 52 2 2682 3063 742550822 742550438 1.750000e-108 403.0
16 TraesCS3D01G450600 chr3B 85.279 394 52 2 1500 1887 741713185 741713578 6.290000e-108 401.0
17 TraesCS3D01G450600 chr3B 84.021 388 56 4 2682 3063 742672368 742671981 6.380000e-98 368.0
18 TraesCS3D01G450600 chr3B 91.964 224 10 3 612 830 741600298 741600518 1.410000e-79 307.0
19 TraesCS3D01G450600 chr3B 79.739 306 41 11 16 303 18789149 18789451 6.850000e-48 202.0
20 TraesCS3D01G450600 chr3B 86.339 183 9 2 863 1045 741600516 741600682 6.900000e-43 185.0
21 TraesCS3D01G450600 chr3B 82.716 162 10 3 348 509 741600154 741600297 1.180000e-25 128.0
22 TraesCS3D01G450600 chr4A 78.361 2075 338 71 1008 3042 113332131 113330128 0.000000e+00 1242.0
23 TraesCS3D01G450600 chr4A 80.233 258 33 10 55 296 621838846 621839101 1.150000e-40 178.0
24 TraesCS3D01G450600 chr4D 78.726 1946 316 61 1140 3042 352118217 352120107 0.000000e+00 1210.0
25 TraesCS3D01G450600 chr7B 86.156 679 89 4 3365 4040 552735209 552734533 0.000000e+00 728.0
26 TraesCS3D01G450600 chr7B 86.156 679 89 4 3365 4040 552776261 552775585 0.000000e+00 728.0
27 TraesCS3D01G450600 chr7B 85.777 682 91 3 3361 4040 553058509 553057832 0.000000e+00 717.0
28 TraesCS3D01G450600 chr7B 88.430 121 10 4 497 614 245073348 245073467 4.210000e-30 143.0
29 TraesCS3D01G450600 chr7A 85.294 680 92 7 3365 4040 595306701 595306026 0.000000e+00 695.0
30 TraesCS3D01G450600 chr7A 89.565 115 9 3 503 614 70753378 70753264 4.210000e-30 143.0
31 TraesCS3D01G450600 chr2B 84.384 666 85 12 3352 4009 698948287 698947633 1.580000e-178 636.0
32 TraesCS3D01G450600 chr1D 76.943 1171 216 37 1500 2655 22625530 22624399 5.740000e-173 617.0
33 TraesCS3D01G450600 chr1D 81.107 307 37 12 16 305 226449732 226450034 4.060000e-55 226.0
34 TraesCS3D01G450600 chr1D 80.237 253 36 7 68 307 461273066 461273317 1.150000e-40 178.0
35 TraesCS3D01G450600 chr1D 80.751 213 41 0 2822 3034 22624259 22624047 2.500000e-37 167.0
36 TraesCS3D01G450600 chr1B 77.682 1044 184 33 1618 2652 38832656 38833659 3.480000e-165 592.0
37 TraesCS3D01G450600 chr7D 85.893 560 72 4 3485 4040 519677436 519676880 1.250000e-164 590.0
38 TraesCS3D01G450600 chr7D 90.909 110 7 2 504 610 132765372 132765263 1.170000e-30 145.0
39 TraesCS3D01G450600 chr7D 85.714 119 13 4 504 618 520951567 520951685 5.480000e-24 122.0
40 TraesCS3D01G450600 chr2D 86.117 461 61 2 3359 3816 628998120 628998580 1.010000e-135 494.0
41 TraesCS3D01G450600 chr2D 79.283 251 35 12 16 255 372800890 372800646 4.180000e-35 159.0
42 TraesCS3D01G450600 chr6D 80.328 305 39 14 16 305 309592314 309592612 1.140000e-50 211.0
43 TraesCS3D01G450600 chr6D 77.667 300 51 12 17 303 461683574 461683278 6.940000e-38 169.0
44 TraesCS3D01G450600 chr6B 79.934 304 42 13 16 305 477230161 477230459 5.290000e-49 206.0
45 TraesCS3D01G450600 chr6B 94.872 39 2 0 501 539 474814724 474814762 1.210000e-05 62.1
46 TraesCS3D01G450600 chr5A 85.965 114 13 3 504 614 580844086 580843973 7.090000e-23 119.0
47 TraesCS3D01G450600 chr5A 82.906 117 17 3 501 614 524221147 524221263 7.140000e-18 102.0
48 TraesCS3D01G450600 chr2A 100.000 29 0 0 3819 3847 555815564 555815536 2.000000e-03 54.7


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 TraesCS3D01G450600 chr3D 558783177 558787216 4039 False 7461.000000 7461 100.000000 1 4040 1 chr3D.!!$F1 4039
1 TraesCS3D01G450600 chr3D 558938365 558939925 1560 False 768.500000 1147 84.596500 1500 3137 2 chr3D.!!$F3 1637
2 TraesCS3D01G450600 chr3A 695129038 695133175 4137 False 1728.666667 4324 87.880333 1 3985 3 chr3A.!!$F2 3984
3 TraesCS3D01G450600 chr3A 695224150 695225993 1843 False 364.500000 394 85.205500 1919 2729 2 chr3A.!!$F3 810
4 TraesCS3D01G450600 chr3B 741600154 741604076 3922 False 1227.250000 4289 88.894750 348 4040 4 chr3B.!!$F2 3692
5 TraesCS3D01G450600 chr3B 741713185 741714727 1542 False 772.500000 1144 84.931500 1500 3128 2 chr3B.!!$F3 1628
6 TraesCS3D01G450600 chr3B 742523961 742524634 673 True 481.000000 481 79.764000 1610 2278 1 chr3B.!!$R1 668
7 TraesCS3D01G450600 chr4A 113330128 113332131 2003 True 1242.000000 1242 78.361000 1008 3042 1 chr4A.!!$R1 2034
8 TraesCS3D01G450600 chr4D 352118217 352120107 1890 False 1210.000000 1210 78.726000 1140 3042 1 chr4D.!!$F1 1902
9 TraesCS3D01G450600 chr7B 552734533 552735209 676 True 728.000000 728 86.156000 3365 4040 1 chr7B.!!$R1 675
10 TraesCS3D01G450600 chr7B 552775585 552776261 676 True 728.000000 728 86.156000 3365 4040 1 chr7B.!!$R2 675
11 TraesCS3D01G450600 chr7B 553057832 553058509 677 True 717.000000 717 85.777000 3361 4040 1 chr7B.!!$R3 679
12 TraesCS3D01G450600 chr7A 595306026 595306701 675 True 695.000000 695 85.294000 3365 4040 1 chr7A.!!$R2 675
13 TraesCS3D01G450600 chr2B 698947633 698948287 654 True 636.000000 636 84.384000 3352 4009 1 chr2B.!!$R1 657
14 TraesCS3D01G450600 chr1D 22624047 22625530 1483 True 392.000000 617 78.847000 1500 3034 2 chr1D.!!$R1 1534
15 TraesCS3D01G450600 chr1B 38832656 38833659 1003 False 592.000000 592 77.682000 1618 2652 1 chr1B.!!$F1 1034
16 TraesCS3D01G450600 chr7D 519676880 519677436 556 True 590.000000 590 85.893000 3485 4040 1 chr7D.!!$R2 555

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
668 677 0.179045 GGTGAATCGGGATGGACCAG 60.179 60.0 0.0 0.0 41.20 4.00 F
669 678 0.541863 GTGAATCGGGATGGACCAGT 59.458 55.0 0.0 0.0 41.20 4.00 F
2094 2682 0.475906 AGGTCTGCCAGTTCAAGCTT 59.524 50.0 0.0 0.0 37.19 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2616 1.375098 CGGAGGACTCGACCCTGTAC 61.375 65.000 6.36 0.00 33.36 2.90 R
2233 2829 2.047274 CGTGTTGCGGACAGGGAT 60.047 61.111 5.19 0.00 39.39 3.85 R
3063 4790 1.069500 GTAAATGGCAGAACAACGCGT 60.069 47.619 5.58 5.58 0.00 6.01 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
18 19 3.437746 GTTTGAGTAGAGTCGGGGC 57.562 57.895 0.00 0.00 0.00 5.80
37 38 2.498885 GGCCTCTTTGATTGCAGGATTT 59.501 45.455 0.00 0.00 0.00 2.17
38 39 3.055602 GGCCTCTTTGATTGCAGGATTTT 60.056 43.478 0.00 0.00 0.00 1.82
45 46 7.083858 TCTTTGATTGCAGGATTTTAAAGACG 58.916 34.615 0.00 0.00 30.56 4.18
47 48 2.892373 TGCAGGATTTTAAAGACGCG 57.108 45.000 3.53 3.53 0.00 6.01
55 56 4.142556 GGATTTTAAAGACGCGAAATGGGA 60.143 41.667 15.93 0.00 0.00 4.37
61 62 1.268625 AGACGCGAAATGGGAAAAACC 59.731 47.619 15.93 0.00 38.08 3.27
62 63 1.001158 GACGCGAAATGGGAAAAACCA 60.001 47.619 15.93 0.00 46.24 3.67
75 76 6.746894 TGGGAAAAACCATAGGATTGGAATA 58.253 36.000 0.00 0.00 39.25 1.75
98 99 9.445878 AATATCATGGTCATCTCAATCATACAC 57.554 33.333 0.00 0.00 0.00 2.90
99 100 6.237887 TCATGGTCATCTCAATCATACACA 57.762 37.500 0.00 0.00 0.00 3.72
108 109 5.964758 TCTCAATCATACACAATTTTGGGC 58.035 37.500 0.00 0.00 34.06 5.36
118 119 4.575645 ACACAATTTTGGGCTGTTTGATTG 59.424 37.500 0.00 0.00 34.06 2.67
124 125 4.613925 TTGGGCTGTTTGATTGCATTAA 57.386 36.364 0.00 0.00 0.00 1.40
125 126 4.191033 TGGGCTGTTTGATTGCATTAAG 57.809 40.909 0.00 0.00 0.00 1.85
127 128 3.524541 GGCTGTTTGATTGCATTAAGGG 58.475 45.455 0.00 0.00 0.00 3.95
136 138 7.727331 TTGATTGCATTAAGGGAAAACAAAG 57.273 32.000 12.08 0.00 0.00 2.77
141 143 6.836242 TGCATTAAGGGAAAACAAAGGAATT 58.164 32.000 0.00 0.00 0.00 2.17
146 148 6.918892 AAGGGAAAACAAAGGAATTTTTCG 57.081 33.333 0.00 0.00 39.24 3.46
147 149 5.364778 AGGGAAAACAAAGGAATTTTTCGG 58.635 37.500 0.00 0.00 39.24 4.30
148 150 5.104693 AGGGAAAACAAAGGAATTTTTCGGT 60.105 36.000 0.00 0.00 39.24 4.69
149 151 5.587043 GGGAAAACAAAGGAATTTTTCGGTT 59.413 36.000 0.00 0.00 39.24 4.44
150 152 6.094325 GGGAAAACAAAGGAATTTTTCGGTTT 59.906 34.615 0.00 0.00 39.24 3.27
169 176 7.748847 TCGGTTTAAGTGAATGCTAGAAATTC 58.251 34.615 10.25 10.25 35.10 2.17
170 177 7.606456 TCGGTTTAAGTGAATGCTAGAAATTCT 59.394 33.333 15.58 0.00 35.48 2.40
179 186 7.859875 GTGAATGCTAGAAATTCTATGGAAAGC 59.140 37.037 15.58 4.84 35.48 3.51
229 236 9.699410 AATTCCTACACAATTCAATCCTATGAA 57.301 29.630 0.00 0.00 43.03 2.57
236 243 8.805175 ACACAATTCAATCCTATGAATCAAACA 58.195 29.630 3.26 0.00 46.57 2.83
246 253 8.279970 TCCTATGAATCAAACAACCAACATAG 57.720 34.615 0.00 0.00 37.06 2.23
248 255 8.739039 CCTATGAATCAAACAACCAACATAGAA 58.261 33.333 0.00 0.00 38.53 2.10
249 256 9.778993 CTATGAATCAAACAACCAACATAGAAG 57.221 33.333 0.00 0.00 38.53 2.85
322 330 4.360563 GAGTCTTCAAGTTGAACGTCAGA 58.639 43.478 14.35 7.13 32.21 3.27
334 342 0.888619 ACGTCAGAGGCTTCGAATCA 59.111 50.000 0.00 0.00 0.00 2.57
335 343 1.478510 ACGTCAGAGGCTTCGAATCAT 59.521 47.619 0.00 0.00 0.00 2.45
411 420 7.565680 AGATAGTAAGTATTTTGGTCCTGGTG 58.434 38.462 0.00 0.00 0.00 4.17
419 428 5.578157 ATTTTGGTCCTGGTGTTACTACT 57.422 39.130 0.00 0.00 0.00 2.57
429 438 6.495872 TCCTGGTGTTACTACTCATTTAGTGT 59.504 38.462 0.00 0.00 39.39 3.55
432 441 7.318141 TGGTGTTACTACTCATTTAGTGTAGC 58.682 38.462 0.00 0.00 44.34 3.58
464 473 2.355444 CGTTCAATGGTCATGCATGCTA 59.645 45.455 22.25 14.73 0.00 3.49
509 518 6.726230 TGCAAATCGTACTACTGATACTCTC 58.274 40.000 0.00 0.00 0.00 3.20
510 519 6.542735 TGCAAATCGTACTACTGATACTCTCT 59.457 38.462 0.00 0.00 0.00 3.10
511 520 7.073265 GCAAATCGTACTACTGATACTCTCTC 58.927 42.308 0.00 0.00 0.00 3.20
513 522 4.869215 TCGTACTACTGATACTCTCTCCG 58.131 47.826 0.00 0.00 0.00 4.63
514 523 4.340666 TCGTACTACTGATACTCTCTCCGT 59.659 45.833 0.00 0.00 0.00 4.69
515 524 4.681025 CGTACTACTGATACTCTCTCCGTC 59.319 50.000 0.00 0.00 0.00 4.79
516 525 4.075963 ACTACTGATACTCTCTCCGTCC 57.924 50.000 0.00 0.00 0.00 4.79
517 526 1.956297 ACTGATACTCTCTCCGTCCG 58.044 55.000 0.00 0.00 0.00 4.79
518 527 1.485480 ACTGATACTCTCTCCGTCCGA 59.515 52.381 0.00 0.00 0.00 4.55
519 528 2.093075 ACTGATACTCTCTCCGTCCGAA 60.093 50.000 0.00 0.00 0.00 4.30
520 529 2.943690 CTGATACTCTCTCCGTCCGAAA 59.056 50.000 0.00 0.00 0.00 3.46
521 530 3.349927 TGATACTCTCTCCGTCCGAAAA 58.650 45.455 0.00 0.00 0.00 2.29
522 531 3.952323 TGATACTCTCTCCGTCCGAAAAT 59.048 43.478 0.00 0.00 0.00 1.82
523 532 5.128205 TGATACTCTCTCCGTCCGAAAATA 58.872 41.667 0.00 0.00 0.00 1.40
524 533 3.779271 ACTCTCTCCGTCCGAAAATAC 57.221 47.619 0.00 0.00 0.00 1.89
525 534 3.354467 ACTCTCTCCGTCCGAAAATACT 58.646 45.455 0.00 0.00 0.00 2.12
526 535 3.762823 ACTCTCTCCGTCCGAAAATACTT 59.237 43.478 0.00 0.00 0.00 2.24
527 536 4.946157 ACTCTCTCCGTCCGAAAATACTTA 59.054 41.667 0.00 0.00 0.00 2.24
528 537 5.593502 ACTCTCTCCGTCCGAAAATACTTAT 59.406 40.000 0.00 0.00 0.00 1.73
529 538 6.069684 TCTCTCCGTCCGAAAATACTTATC 57.930 41.667 0.00 0.00 0.00 1.75
530 539 5.009410 TCTCTCCGTCCGAAAATACTTATCC 59.991 44.000 0.00 0.00 0.00 2.59
531 540 4.891756 TCTCCGTCCGAAAATACTTATCCT 59.108 41.667 0.00 0.00 0.00 3.24
532 541 6.064060 TCTCCGTCCGAAAATACTTATCCTA 58.936 40.000 0.00 0.00 0.00 2.94
533 542 6.547141 TCTCCGTCCGAAAATACTTATCCTAA 59.453 38.462 0.00 0.00 0.00 2.69
534 543 7.068593 TCTCCGTCCGAAAATACTTATCCTAAA 59.931 37.037 0.00 0.00 0.00 1.85
535 544 7.555087 TCCGTCCGAAAATACTTATCCTAAAA 58.445 34.615 0.00 0.00 0.00 1.52
536 545 8.040132 TCCGTCCGAAAATACTTATCCTAAAAA 58.960 33.333 0.00 0.00 0.00 1.94
537 546 8.833493 CCGTCCGAAAATACTTATCCTAAAAAT 58.167 33.333 0.00 0.00 0.00 1.82
538 547 9.646336 CGTCCGAAAATACTTATCCTAAAAATG 57.354 33.333 0.00 0.00 0.00 2.32
539 548 9.946165 GTCCGAAAATACTTATCCTAAAAATGG 57.054 33.333 0.00 0.00 0.00 3.16
540 549 9.689501 TCCGAAAATACTTATCCTAAAAATGGT 57.310 29.630 0.00 0.00 0.00 3.55
610 619 2.685850 AAAGTATTTCCGGACGGAGG 57.314 50.000 13.64 0.00 46.06 4.30
616 625 4.689549 TCCGGACGGAGGGAGCAA 62.690 66.667 9.76 0.00 39.76 3.91
660 669 1.514087 GTGCTACGGTGAATCGGGA 59.486 57.895 0.00 0.00 0.00 5.14
668 677 0.179045 GGTGAATCGGGATGGACCAG 60.179 60.000 0.00 0.00 41.20 4.00
669 678 0.541863 GTGAATCGGGATGGACCAGT 59.458 55.000 0.00 0.00 41.20 4.00
670 679 0.830648 TGAATCGGGATGGACCAGTC 59.169 55.000 0.00 0.00 41.20 3.51
777 791 1.302033 AGCACGGGAGTCTGCAAAG 60.302 57.895 5.73 0.00 44.67 2.77
810 824 1.082104 GCAAAGCGGAAACCTGTCG 60.082 57.895 0.00 0.00 0.00 4.35
858 880 3.803082 CGTTCCACATGCCAGCCG 61.803 66.667 0.00 0.00 0.00 5.52
885 907 2.084546 GACCGGAGTAAAAAGCAGCAT 58.915 47.619 9.46 0.00 0.00 3.79
894 916 1.926511 AAAAGCAGCATCGCCTTCCG 61.927 55.000 0.00 0.00 38.61 4.30
897 919 3.257561 CAGCATCGCCTTCCGTCG 61.258 66.667 0.00 0.00 38.35 5.12
1605 2160 4.101448 GACATGCGGGCCCTCAGT 62.101 66.667 21.21 17.29 0.00 3.41
1917 2472 2.932234 CGACCAGGAGTTCCAGCGT 61.932 63.158 0.00 0.00 38.89 5.07
2028 2616 1.264557 CTCTACGTCTACGATGGCCTG 59.735 57.143 9.86 0.00 43.02 4.85
2033 2621 1.268589 CGTCTACGATGGCCTGTACAG 60.269 57.143 16.34 16.34 43.02 2.74
2094 2682 0.475906 AGGTCTGCCAGTTCAAGCTT 59.524 50.000 0.00 0.00 37.19 3.74
2238 2834 2.367512 GAGGCTGTCCCCATCCCT 60.368 66.667 0.00 0.00 0.00 4.20
2529 4238 3.747579 CCCAGGAGCTGCCCCAAT 61.748 66.667 2.14 0.00 37.37 3.16
2552 4261 4.241555 GACGCAGCGGGGGATGAT 62.242 66.667 21.15 0.00 0.00 2.45
2970 4694 3.637273 GAGTCGTGCCCCCACCTT 61.637 66.667 0.00 0.00 38.79 3.50
3145 4889 1.869767 GTAGCATGGATGAAAGCGAGG 59.130 52.381 0.00 0.00 0.00 4.63
3221 4965 5.917462 TCTCAGTCTCAGTCAATTGTTCAA 58.083 37.500 5.13 0.00 0.00 2.69
3242 4986 6.542821 TCAAATCCAACTTGTCCTGACTTAT 58.457 36.000 0.00 0.00 0.00 1.73
3243 4987 7.685481 TCAAATCCAACTTGTCCTGACTTATA 58.315 34.615 0.00 0.00 0.00 0.98
3244 4988 8.160765 TCAAATCCAACTTGTCCTGACTTATAA 58.839 33.333 0.00 0.00 0.00 0.98
3245 4989 8.454106 CAAATCCAACTTGTCCTGACTTATAAG 58.546 37.037 11.05 11.05 0.00 1.73
3246 4990 6.049955 TCCAACTTGTCCTGACTTATAAGG 57.950 41.667 16.73 0.00 34.65 2.69
3247 4991 5.783360 TCCAACTTGTCCTGACTTATAAGGA 59.217 40.000 16.73 2.10 40.36 3.36
3423 5169 7.309177 TGTCGTTTACAATGTGGGAAATAATG 58.691 34.615 0.00 0.00 34.29 1.90
3453 5199 4.273969 GGGATAGTAGAGTCACAGAGTTCG 59.726 50.000 0.00 0.00 0.00 3.95
3542 5288 2.817901 ACCGTAGTCAATATTGGCGAC 58.182 47.619 19.70 19.70 37.98 5.19
3622 5373 0.679505 TGCTCGTGTAACAGCCTCTT 59.320 50.000 0.00 0.00 39.26 2.85
3684 5435 4.963318 TCCAATTCTCCATGCTAGGTAG 57.037 45.455 0.00 0.00 0.00 3.18
3713 5464 4.471904 TCCGAATAGCACTCAATTCTGT 57.528 40.909 0.00 0.00 31.29 3.41
3816 5572 4.026744 CTGGATCCTGAGAGTGTTTCCTA 58.973 47.826 14.23 0.00 0.00 2.94
3933 5697 3.699067 CTCTGACAAAGTTTGTTGCCAG 58.301 45.455 21.70 21.56 45.52 4.85
3955 5719 3.626028 ACTTTGATTGAAACAGCCGAC 57.374 42.857 0.00 0.00 0.00 4.79
4013 5778 2.516930 GCCGCTGCCACCATATGT 60.517 61.111 1.24 0.00 0.00 2.29
4019 5784 1.581934 CTGCCACCATATGTACCACG 58.418 55.000 1.24 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.657751 GCAATCAAAGAGGCCCCGAC 61.658 60.000 0.00 0.00 0.00 4.79
18 19 7.543520 GTCTTTAAAATCCTGCAATCAAAGAGG 59.456 37.037 0.00 0.00 32.96 3.69
37 38 4.832590 TTTTCCCATTTCGCGTCTTTAA 57.167 36.364 5.77 0.00 0.00 1.52
38 39 4.538917 GTTTTTCCCATTTCGCGTCTTTA 58.461 39.130 5.77 0.00 0.00 1.85
45 46 3.445805 TCCTATGGTTTTTCCCATTTCGC 59.554 43.478 0.00 0.00 42.70 4.70
47 48 6.156083 TCCAATCCTATGGTTTTTCCCATTTC 59.844 38.462 0.00 0.00 42.70 2.17
55 56 8.873144 CCATGATATTCCAATCCTATGGTTTTT 58.127 33.333 0.00 0.00 41.46 1.94
61 62 8.272889 AGATGACCATGATATTCCAATCCTATG 58.727 37.037 0.00 0.00 0.00 2.23
62 63 8.403292 AGATGACCATGATATTCCAATCCTAT 57.597 34.615 0.00 0.00 0.00 2.57
63 64 7.458806 TGAGATGACCATGATATTCCAATCCTA 59.541 37.037 0.00 0.00 0.00 2.94
64 65 6.273965 TGAGATGACCATGATATTCCAATCCT 59.726 38.462 0.00 0.00 0.00 3.24
65 66 6.479006 TGAGATGACCATGATATTCCAATCC 58.521 40.000 0.00 0.00 0.00 3.01
75 76 6.834107 TGTGTATGATTGAGATGACCATGAT 58.166 36.000 0.00 0.00 0.00 2.45
98 99 3.564644 TGCAATCAAACAGCCCAAAATTG 59.435 39.130 0.00 0.00 0.00 2.32
99 100 3.818180 TGCAATCAAACAGCCCAAAATT 58.182 36.364 0.00 0.00 0.00 1.82
108 109 6.705381 TGTTTTCCCTTAATGCAATCAAACAG 59.295 34.615 0.00 0.00 0.00 3.16
118 119 7.744087 AAATTCCTTTGTTTTCCCTTAATGC 57.256 32.000 0.00 0.00 0.00 3.56
124 125 5.104693 ACCGAAAAATTCCTTTGTTTTCCCT 60.105 36.000 0.00 0.00 37.77 4.20
125 126 5.120399 ACCGAAAAATTCCTTTGTTTTCCC 58.880 37.500 0.00 0.00 37.77 3.97
127 128 9.697250 CTTAAACCGAAAAATTCCTTTGTTTTC 57.303 29.630 0.00 0.00 37.71 2.29
136 138 6.645003 AGCATTCACTTAAACCGAAAAATTCC 59.355 34.615 0.00 0.00 0.00 3.01
141 143 7.499321 TTCTAGCATTCACTTAAACCGAAAA 57.501 32.000 0.00 0.00 0.00 2.29
202 209 9.699410 TCATAGGATTGAATTGTGTAGGAATTT 57.301 29.630 0.00 0.00 0.00 1.82
203 210 9.699410 TTCATAGGATTGAATTGTGTAGGAATT 57.301 29.630 0.00 0.00 30.82 2.17
213 220 9.090692 GGTTGTTTGATTCATAGGATTGAATTG 57.909 33.333 1.60 0.00 44.35 2.32
214 221 8.814931 TGGTTGTTTGATTCATAGGATTGAATT 58.185 29.630 1.60 0.00 44.35 2.17
303 311 3.717707 CCTCTGACGTTCAACTTGAAGA 58.282 45.455 4.36 0.00 37.00 2.87
305 313 2.158957 AGCCTCTGACGTTCAACTTGAA 60.159 45.455 0.00 0.00 33.32 2.69
322 330 1.009829 GAACGCATGATTCGAAGCCT 58.990 50.000 11.45 0.00 0.00 4.58
334 342 5.631096 CGACAATCATACATAGAGAACGCAT 59.369 40.000 0.00 0.00 0.00 4.73
335 343 4.976116 CGACAATCATACATAGAGAACGCA 59.024 41.667 0.00 0.00 0.00 5.24
401 410 3.247948 TGAGTAGTAACACCAGGACCA 57.752 47.619 0.00 0.00 0.00 4.02
411 420 7.318141 TGGTGCTACACTAAATGAGTAGTAAC 58.682 38.462 0.00 0.00 40.48 2.50
419 428 6.037062 CGAATTGATGGTGCTACACTAAATGA 59.963 38.462 0.00 0.00 34.40 2.57
429 438 4.096231 CCATTGAACGAATTGATGGTGCTA 59.904 41.667 0.00 0.00 34.06 3.49
432 441 4.439305 ACCATTGAACGAATTGATGGTG 57.561 40.909 5.59 0.00 46.37 4.17
464 473 5.163804 TGCAAATTATTAAGCGATCGTGTGT 60.164 36.000 17.81 2.20 0.00 3.72
501 510 4.571372 ATTTTCGGACGGAGAGAGTATC 57.429 45.455 0.00 0.00 0.00 2.24
502 511 5.131784 AGTATTTTCGGACGGAGAGAGTAT 58.868 41.667 0.00 0.00 0.00 2.12
509 518 5.197682 AGGATAAGTATTTTCGGACGGAG 57.802 43.478 0.00 0.00 0.00 4.63
510 519 6.713762 TTAGGATAAGTATTTTCGGACGGA 57.286 37.500 0.00 0.00 0.00 4.69
511 520 7.775397 TTTTAGGATAAGTATTTTCGGACGG 57.225 36.000 0.00 0.00 0.00 4.79
513 522 9.946165 CCATTTTTAGGATAAGTATTTTCGGAC 57.054 33.333 0.00 0.00 0.00 4.79
514 523 9.689501 ACCATTTTTAGGATAAGTATTTTCGGA 57.310 29.630 0.00 0.00 0.00 4.55
578 587 9.962809 TCCGGAAATACTTTCTAAAAAGGATAA 57.037 29.630 0.00 0.00 43.90 1.75
579 588 9.387257 GTCCGGAAATACTTTCTAAAAAGGATA 57.613 33.333 5.23 0.00 43.90 2.59
580 589 7.065443 CGTCCGGAAATACTTTCTAAAAAGGAT 59.935 37.037 5.23 0.00 46.15 3.24
581 590 6.369615 CGTCCGGAAATACTTTCTAAAAAGGA 59.630 38.462 5.23 0.00 45.15 3.36
582 591 6.402875 CCGTCCGGAAATACTTTCTAAAAAGG 60.403 42.308 5.23 0.00 41.01 3.11
583 592 6.369615 TCCGTCCGGAAATACTTTCTAAAAAG 59.630 38.462 5.23 0.00 43.25 2.27
584 593 6.229733 TCCGTCCGGAAATACTTTCTAAAAA 58.770 36.000 5.23 0.00 42.05 1.94
585 594 5.792741 TCCGTCCGGAAATACTTTCTAAAA 58.207 37.500 5.23 0.00 42.05 1.52
586 595 5.404466 TCCGTCCGGAAATACTTTCTAAA 57.596 39.130 5.23 0.00 42.05 1.85
587 596 4.142093 CCTCCGTCCGGAAATACTTTCTAA 60.142 45.833 5.23 0.00 44.66 2.10
588 597 3.382546 CCTCCGTCCGGAAATACTTTCTA 59.617 47.826 5.23 0.00 44.66 2.10
589 598 2.167900 CCTCCGTCCGGAAATACTTTCT 59.832 50.000 5.23 0.00 44.66 2.52
590 599 2.547826 CCTCCGTCCGGAAATACTTTC 58.452 52.381 5.23 0.00 44.66 2.62
591 600 1.208776 CCCTCCGTCCGGAAATACTTT 59.791 52.381 5.23 0.00 44.66 2.66
592 601 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
593 602 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
594 603 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
595 604 1.397390 GCTCCCTCCGTCCGGAAATA 61.397 60.000 5.23 0.00 44.66 1.40
596 605 2.732619 GCTCCCTCCGTCCGGAAAT 61.733 63.158 5.23 0.00 44.66 2.17
597 606 3.387947 GCTCCCTCCGTCCGGAAA 61.388 66.667 5.23 0.00 44.66 3.13
598 607 4.689549 TGCTCCCTCCGTCCGGAA 62.690 66.667 5.23 0.00 44.66 4.30
599 608 3.976490 ATTGCTCCCTCCGTCCGGA 62.976 63.158 0.00 0.00 42.90 5.14
600 609 3.470888 ATTGCTCCCTCCGTCCGG 61.471 66.667 0.00 0.00 0.00 5.14
601 610 2.202932 CATTGCTCCCTCCGTCCG 60.203 66.667 0.00 0.00 0.00 4.79
602 611 2.514824 GCATTGCTCCCTCCGTCC 60.515 66.667 0.16 0.00 0.00 4.79
603 612 2.586792 AGCATTGCTCCCTCCGTC 59.413 61.111 5.03 0.00 30.62 4.79
616 625 0.798776 CCTCGACGCAAAAAGAGCAT 59.201 50.000 0.00 0.00 0.00 3.79
660 669 2.639347 TGAACATGACTGACTGGTCCAT 59.361 45.455 0.00 0.00 35.54 3.41
668 677 4.176271 TCGATGACATGAACATGACTGAC 58.824 43.478 19.56 9.17 41.20 3.51
669 678 4.427312 CTCGATGACATGAACATGACTGA 58.573 43.478 19.56 12.02 41.20 3.41
670 679 3.554731 CCTCGATGACATGAACATGACTG 59.445 47.826 19.56 9.12 41.20 3.51
810 824 1.678360 CACGGTCGTGTGTACTGTAC 58.322 55.000 14.51 10.98 40.91 2.90
858 880 0.035739 TTTTACTCCGGTCCACTGCC 59.964 55.000 0.00 0.00 0.00 4.85
863 885 1.880646 GCTGCTTTTTACTCCGGTCCA 60.881 52.381 0.00 0.00 0.00 4.02
866 888 2.084546 GATGCTGCTTTTTACTCCGGT 58.915 47.619 0.00 0.00 0.00 5.28
940 994 4.116328 TTGTCTCGCCTCGCCTCG 62.116 66.667 0.00 0.00 0.00 4.63
941 995 2.202676 CTTGTCTCGCCTCGCCTC 60.203 66.667 0.00 0.00 0.00 4.70
942 996 1.816863 TTTCTTGTCTCGCCTCGCCT 61.817 55.000 0.00 0.00 0.00 5.52
1202 1655 2.434359 GGTTGGCGAAGTCGGAGG 60.434 66.667 2.47 0.00 40.23 4.30
1587 2142 4.864334 CTGAGGGCCCGCATGTCC 62.864 72.222 29.81 7.56 0.00 4.02
1605 2160 2.762043 TCCCCGTCGATCATGGCA 60.762 61.111 0.00 0.00 0.00 4.92
1809 2364 2.043752 TCATCGAGGTACCCGCCA 60.044 61.111 8.74 0.00 0.00 5.69
2028 2616 1.375098 CGGAGGACTCGACCCTGTAC 61.375 65.000 6.36 0.00 33.36 2.90
2033 2621 3.711059 TAGGCGGAGGACTCGACCC 62.711 68.421 5.84 0.00 36.06 4.46
2184 2780 2.838225 ATCGTGAGGTAGCCGGGG 60.838 66.667 2.18 0.00 0.00 5.73
2233 2829 2.047274 CGTGTTGCGGACAGGGAT 60.047 61.111 5.19 0.00 39.39 3.85
2291 2889 3.072468 CCGGGAACTCAGGGCGTA 61.072 66.667 0.00 0.00 0.00 4.42
3063 4790 1.069500 GTAAATGGCAGAACAACGCGT 60.069 47.619 5.58 5.58 0.00 6.01
3064 4791 1.069568 TGTAAATGGCAGAACAACGCG 60.070 47.619 3.53 3.53 0.00 6.01
3221 4965 7.037586 TCCTTATAAGTCAGGACAAGTTGGATT 60.038 37.037 11.50 0.00 33.99 3.01
3252 4996 9.511272 ACTTAACTCGGGACAGTTATTATTTTT 57.489 29.630 0.00 0.00 38.40 1.94
3269 5015 7.653767 AAATAAGTGTCTGGAACTTAACTCG 57.346 36.000 0.58 0.00 41.96 4.18
3423 5169 3.565063 GTGACTCTACTATCCCCGACTTC 59.435 52.174 0.00 0.00 0.00 3.01
3453 5199 8.851960 AACTTTCTTTTGTTTCTAATTCGTCC 57.148 30.769 0.00 0.00 0.00 4.79
3542 5288 4.773323 TGTATCCATCTCGCTACAGATG 57.227 45.455 9.24 9.24 46.61 2.90
3684 5435 1.202698 AGTGCTATTCGGAATGGCCTC 60.203 52.381 28.74 22.34 43.87 4.70
3713 5464 2.028839 CCCATGTTTGCAGCAGAATCAA 60.029 45.455 0.00 0.00 0.00 2.57
3816 5572 3.940209 ATGTGGATGCATCGTTTTGTT 57.060 38.095 20.15 0.00 0.00 2.83
3933 5697 3.975035 GTCGGCTGTTTCAATCAAAGTTC 59.025 43.478 0.00 0.00 0.00 3.01
3955 5719 1.332195 TGATACAGGAGCCTGATCGG 58.668 55.000 22.62 0.00 46.30 4.18
4013 5778 4.647853 ACTAATCCTGATTGCTACGTGGTA 59.352 41.667 0.00 0.00 32.50 3.25


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

AutoCloner maintained by Alex Coulton.