Multiple sequence alignment - TraesCS3D01G204800

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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 TraesCS3D01G204800 chr3D 100.000 6554 0 0 1 6554 256991066 256984513 0.000000e+00 12104.0
1 TraesCS3D01G204800 chr3D 92.985 670 31 6 5898 6554 115642969 115643635 0.000000e+00 963.0
2 TraesCS3D01G204800 chr3D 93.323 659 30 6 5908 6554 607326566 607327222 0.000000e+00 961.0
3 TraesCS3D01G204800 chr3D 92.879 660 29 9 5907 6554 374392362 374393015 0.000000e+00 942.0
4 TraesCS3D01G204800 chr3D 85.096 416 42 13 4127 4525 598077430 598077018 2.200000e-109 407.0
5 TraesCS3D01G204800 chr3D 76.800 250 49 5 3530 3772 19914793 19914546 1.480000e-26 132.0
6 TraesCS3D01G204800 chr3D 97.727 44 1 0 3721 3764 598077837 598077794 7.050000e-10 76.8
7 TraesCS3D01G204800 chr3B 96.021 3041 80 17 748 3772 351287379 351290394 0.000000e+00 4907.0
8 TraesCS3D01G204800 chr3B 97.335 713 18 1 4629 5340 351291261 351291973 0.000000e+00 1210.0
9 TraesCS3D01G204800 chr3B 91.369 869 42 8 3757 4604 351290418 351291274 0.000000e+00 1158.0
10 TraesCS3D01G204800 chr3B 92.900 662 33 5 5907 6554 571135758 571135097 0.000000e+00 950.0
11 TraesCS3D01G204800 chr3B 90.092 434 36 4 283 711 351221877 351222308 2.060000e-154 556.0
12 TraesCS3D01G204800 chr3B 95.533 291 10 2 5456 5746 351291964 351292251 4.630000e-126 462.0
13 TraesCS3D01G204800 chr3B 79.607 407 64 12 3734 4127 578225195 578225595 2.330000e-69 274.0
14 TraesCS3D01G204800 chr3B 81.150 313 48 6 3765 4069 31593206 31593515 2.360000e-59 241.0
15 TraesCS3D01G204800 chr3B 90.132 152 5 2 5745 5893 351292305 351292449 8.680000e-44 189.0
16 TraesCS3D01G204800 chr3A 95.791 3017 65 16 766 3772 327295177 327292213 0.000000e+00 4811.0
17 TraesCS3D01G204800 chr3A 94.549 1174 30 17 4740 5907 327291198 327290053 0.000000e+00 1783.0
18 TraesCS3D01G204800 chr3A 92.810 904 40 6 3760 4642 327292186 327291287 0.000000e+00 1286.0
19 TraesCS3D01G204800 chr3A 89.843 699 51 5 1 695 327295858 327295176 0.000000e+00 880.0
20 TraesCS3D01G204800 chr3A 85.644 404 40 10 4138 4525 728098809 728098408 6.120000e-110 409.0
21 TraesCS3D01G204800 chr3A 85.678 398 43 4 4127 4512 728237276 728236881 2.200000e-109 407.0
22 TraesCS3D01G204800 chr3A 77.143 560 107 13 3231 3774 728238268 728237714 8.260000e-79 305.0
23 TraesCS3D01G204800 chr3A 81.600 250 40 6 3890 4135 247793219 247793466 1.110000e-47 202.0
24 TraesCS3D01G204800 chr3A 82.069 145 26 0 565 709 580459947 580460091 2.480000e-24 124.0
25 TraesCS3D01G204800 chr2D 92.365 668 32 8 5902 6554 537704564 537703901 0.000000e+00 933.0
26 TraesCS3D01G204800 chr2D 93.519 108 7 0 5340 5447 54095843 54095736 1.890000e-35 161.0
27 TraesCS3D01G204800 chr2D 100.000 38 0 0 4763 4800 577164126 577164089 3.280000e-08 71.3
28 TraesCS3D01G204800 chr7D 94.684 602 28 4 5900 6499 438546407 438545808 0.000000e+00 931.0
29 TraesCS3D01G204800 chr7D 93.355 617 37 3 5908 6522 38712405 38711791 0.000000e+00 909.0
30 TraesCS3D01G204800 chr7D 76.962 599 100 22 3531 4102 579140044 579139457 2.300000e-79 307.0
31 TraesCS3D01G204800 chr7D 80.622 418 54 13 4128 4522 603146541 603146954 1.380000e-76 298.0
32 TraesCS3D01G204800 chr7D 94.872 39 2 0 4762 4800 621084748 621084710 1.970000e-05 62.1
33 TraesCS3D01G204800 chr4D 94.676 601 29 3 5900 6499 468585819 468586417 0.000000e+00 929.0
34 TraesCS3D01G204800 chr4D 93.291 626 35 6 5900 6522 322076180 322076801 0.000000e+00 917.0
35 TraesCS3D01G204800 chr4D 95.413 109 3 2 5340 5447 73247943 73248050 8.740000e-39 172.0
36 TraesCS3D01G204800 chr4D 90.435 115 9 2 5343 5457 215464569 215464457 4.090000e-32 150.0
37 TraesCS3D01G204800 chr2B 85.282 727 68 18 1 709 610390267 610389562 0.000000e+00 713.0
38 TraesCS3D01G204800 chr2B 90.909 286 20 3 430 710 671287360 671287076 4.800000e-101 379.0
39 TraesCS3D01G204800 chr2B 90.559 286 21 3 430 710 671266911 671266627 2.230000e-99 374.0
40 TraesCS3D01G204800 chr2B 81.864 397 59 11 4127 4521 405117293 405116908 8.200000e-84 322.0
41 TraesCS3D01G204800 chr2B 89.691 194 20 0 4297 4490 464669628 464669821 1.410000e-61 248.0
42 TraesCS3D01G204800 chr7B 86.170 376 44 3 4127 4502 460586803 460586436 3.680000e-107 399.0
43 TraesCS3D01G204800 chr7B 81.637 501 74 15 3284 3768 460587750 460587252 3.680000e-107 399.0
44 TraesCS3D01G204800 chr7B 83.541 401 49 8 4127 4512 138034835 138035233 6.250000e-95 359.0
45 TraesCS3D01G204800 chr7B 81.167 377 52 10 3765 4127 68584295 68584666 1.080000e-72 285.0
46 TraesCS3D01G204800 chr7B 78.488 344 62 6 3767 4101 529662129 529661789 1.430000e-51 215.0
47 TraesCS3D01G204800 chr7B 76.000 250 50 6 3521 3763 125381460 125381214 3.210000e-23 121.0
48 TraesCS3D01G204800 chr7B 97.436 39 1 0 4762 4800 689889100 689889062 4.240000e-07 67.6
49 TraesCS3D01G204800 chr1B 85.037 401 41 11 4127 4511 886941 887338 2.220000e-104 390.0
50 TraesCS3D01G204800 chr1B 81.469 286 38 7 3767 4038 604838902 604838618 3.080000e-53 220.0
51 TraesCS3D01G204800 chr5D 78.584 565 88 14 3231 3772 90312833 90312279 6.290000e-90 342.0
52 TraesCS3D01G204800 chr5D 78.933 375 60 13 3768 4129 460059152 460059520 3.050000e-58 237.0
53 TraesCS3D01G204800 chr5D 89.916 119 10 2 5331 5447 451709418 451709300 1.140000e-32 152.0
54 TraesCS3D01G204800 chr5D 77.723 202 32 8 3576 3768 497941156 497941353 1.930000e-20 111.0
55 TraesCS3D01G204800 chr7A 84.776 335 39 5 3778 4102 674275506 674275838 6.340000e-85 326.0
56 TraesCS3D01G204800 chr7A 80.978 368 46 10 4181 4526 732970797 732971162 3.010000e-68 270.0
57 TraesCS3D01G204800 chr5B 80.183 328 48 11 3772 4088 565490487 565490808 5.110000e-56 230.0
58 TraesCS3D01G204800 chrUn 89.362 141 9 2 4666 4800 29782610 29782750 8.740000e-39 172.0
59 TraesCS3D01G204800 chr4A 91.870 123 6 4 5331 5451 113601796 113601676 1.130000e-37 169.0
60 TraesCS3D01G204800 chr4A 80.833 120 22 1 4127 4246 158797307 158797189 7.000000e-15 93.5
61 TraesCS3D01G204800 chr1A 78.409 264 47 6 3516 3772 61004686 61004426 5.260000e-36 163.0
62 TraesCS3D01G204800 chr1A 92.035 113 9 0 5340 5452 587931547 587931659 6.800000e-35 159.0
63 TraesCS3D01G204800 chr1A 91.892 111 9 0 5342 5452 175176073 175176183 8.800000e-34 156.0
64 TraesCS3D01G204800 chr1A 75.198 379 68 15 4127 4488 250483996 250484365 8.800000e-34 156.0
65 TraesCS3D01G204800 chr1A 97.436 39 1 0 4762 4800 20515699 20515737 4.240000e-07 67.6
66 TraesCS3D01G204800 chr1A 97.436 39 1 0 4762 4800 20526393 20526431 4.240000e-07 67.6
67 TraesCS3D01G204800 chr5A 90.756 119 9 2 5331 5447 570525181 570525063 2.450000e-34 158.0
68 TraesCS3D01G204800 chr2A 83.766 154 23 2 557 709 516377716 516377868 1.900000e-30 145.0
69 TraesCS3D01G204800 chr2A 80.992 121 21 2 4127 4246 62132433 62132552 1.950000e-15 95.3
70 TraesCS3D01G204800 chr2A 97.436 39 1 0 4762 4800 764207132 764207170 4.240000e-07 67.6


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 TraesCS3D01G204800 chr3D 256984513 256991066 6553 True 12104.0 12104 100.00000 1 6554 1 chr3D.!!$R2 6553
1 TraesCS3D01G204800 chr3D 115642969 115643635 666 False 963.0 963 92.98500 5898 6554 1 chr3D.!!$F1 656
2 TraesCS3D01G204800 chr3D 607326566 607327222 656 False 961.0 961 93.32300 5908 6554 1 chr3D.!!$F3 646
3 TraesCS3D01G204800 chr3D 374392362 374393015 653 False 942.0 942 92.87900 5907 6554 1 chr3D.!!$F2 647
4 TraesCS3D01G204800 chr3D 598077018 598077837 819 True 241.9 407 91.41150 3721 4525 2 chr3D.!!$R3 804
5 TraesCS3D01G204800 chr3B 351287379 351292449 5070 False 1585.2 4907 94.07800 748 5893 5 chr3B.!!$F4 5145
6 TraesCS3D01G204800 chr3B 571135097 571135758 661 True 950.0 950 92.90000 5907 6554 1 chr3B.!!$R1 647
7 TraesCS3D01G204800 chr3A 327290053 327295858 5805 True 2190.0 4811 93.24825 1 5907 4 chr3A.!!$R2 5906
8 TraesCS3D01G204800 chr3A 728236881 728238268 1387 True 356.0 407 81.41050 3231 4512 2 chr3A.!!$R3 1281
9 TraesCS3D01G204800 chr2D 537703901 537704564 663 True 933.0 933 92.36500 5902 6554 1 chr2D.!!$R2 652
10 TraesCS3D01G204800 chr7D 438545808 438546407 599 True 931.0 931 94.68400 5900 6499 1 chr7D.!!$R2 599
11 TraesCS3D01G204800 chr7D 38711791 38712405 614 True 909.0 909 93.35500 5908 6522 1 chr7D.!!$R1 614
12 TraesCS3D01G204800 chr7D 579139457 579140044 587 True 307.0 307 76.96200 3531 4102 1 chr7D.!!$R3 571
13 TraesCS3D01G204800 chr4D 468585819 468586417 598 False 929.0 929 94.67600 5900 6499 1 chr4D.!!$F3 599
14 TraesCS3D01G204800 chr4D 322076180 322076801 621 False 917.0 917 93.29100 5900 6522 1 chr4D.!!$F2 622
15 TraesCS3D01G204800 chr2B 610389562 610390267 705 True 713.0 713 85.28200 1 709 1 chr2B.!!$R2 708
16 TraesCS3D01G204800 chr7B 460586436 460587750 1314 True 399.0 399 83.90350 3284 4502 2 chr7B.!!$R4 1218
17 TraesCS3D01G204800 chr5D 90312279 90312833 554 True 342.0 342 78.58400 3231 3772 1 chr5D.!!$R1 541

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
737 767 0.034477 CGGGGGCTCCAACTATTGTT 60.034 55.0 4.16 0.0 36.75 2.83 F
837 869 0.326927 TTACTGTAACAGCCCAGGCC 59.673 55.0 4.70 0.0 43.17 5.19 F
1651 1691 1.700955 GCATCATCCCTGGCTTTCAT 58.299 50.0 0.00 0.0 0.00 2.57 F
3015 3055 0.743688 TTGGTTTGCTCAACATGCGT 59.256 45.0 0.00 0.0 37.07 5.24 F
4115 4247 0.392706 TCTGACATGCCGACAACAGT 59.607 50.0 0.00 0.0 31.81 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 2237 0.033503 TACAGACCATGGGCGAGAGA 60.034 55.000 18.09 2.72 0.00 3.10 R
2816 2856 6.454795 GGCTTCACAAGTGGAAAATGAATTA 58.545 36.000 0.00 0.00 0.00 1.40 R
3452 3518 2.284625 TGGCTGATCTCCACCCGT 60.285 61.111 3.58 0.00 0.00 5.28 R
4212 4406 0.613260 CACCGTCCCATCTTCAGGAA 59.387 55.000 0.00 0.00 32.81 3.36 R
5568 5816 0.890542 TGAAACCTTGCAGCGCAGAT 60.891 50.000 11.47 0.00 40.61 2.90 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
23 25 1.002087 GTTCCCTGAACTGATCGGTGT 59.998 52.381 8.25 0.00 39.23 4.16
32 34 1.691976 ACTGATCGGTGTGGTTCTTCA 59.308 47.619 6.33 0.00 0.00 3.02
65 67 5.528870 ACAATTCGGTTTTGAGAAATCACC 58.471 37.500 0.00 0.00 0.00 4.02
115 117 1.595929 GAGGTTCCGTTGCACCGAA 60.596 57.895 4.75 0.00 38.21 4.30
156 158 0.107410 GTGACCCAATGGCACCGATA 60.107 55.000 0.00 0.00 34.52 2.92
157 159 0.843309 TGACCCAATGGCACCGATAT 59.157 50.000 0.00 0.00 33.59 1.63
158 160 2.050918 TGACCCAATGGCACCGATATA 58.949 47.619 0.00 0.00 33.59 0.86
159 161 2.642311 TGACCCAATGGCACCGATATAT 59.358 45.455 0.00 0.00 33.59 0.86
160 162 3.841255 TGACCCAATGGCACCGATATATA 59.159 43.478 0.00 0.00 33.59 0.86
161 163 4.473196 TGACCCAATGGCACCGATATATAT 59.527 41.667 0.00 0.00 33.59 0.86
162 164 5.663556 TGACCCAATGGCACCGATATATATA 59.336 40.000 0.00 0.00 33.59 0.86
163 165 5.925509 ACCCAATGGCACCGATATATATAC 58.074 41.667 0.00 0.00 33.59 1.47
164 166 5.665812 ACCCAATGGCACCGATATATATACT 59.334 40.000 0.00 0.00 33.59 2.12
165 167 6.157994 ACCCAATGGCACCGATATATATACTT 59.842 38.462 0.00 0.00 33.59 2.24
166 168 7.346175 ACCCAATGGCACCGATATATATACTTA 59.654 37.037 0.00 0.00 33.59 2.24
167 169 8.375506 CCCAATGGCACCGATATATATACTTAT 58.624 37.037 0.00 0.00 0.00 1.73
278 297 3.242543 CGTGCTTGCCTGCTAAAAGATAG 60.243 47.826 0.00 0.00 0.00 2.08
366 391 8.918202 AACTCAATGCCGGAATTATCTTAATA 57.082 30.769 7.55 0.00 0.00 0.98
428 453 2.571757 CAGAGGTTAGTCGGCGCA 59.428 61.111 10.83 0.00 0.00 6.09
488 513 1.460689 TGCGGGGGATTAGGGTAGG 60.461 63.158 0.00 0.00 0.00 3.18
544 570 3.243737 GGCCTTCTTTTTACTGGGTGTTG 60.244 47.826 0.00 0.00 0.00 3.33
627 657 3.432933 GCAAACCGATTGTACTACCGAAA 59.567 43.478 0.00 0.00 41.32 3.46
689 719 2.224233 TGGTTCGGTACATCGGTTTTCA 60.224 45.455 0.00 0.00 0.00 2.69
693 723 2.037511 TCGGTACATCGGTTTTCAGGTT 59.962 45.455 0.00 0.00 0.00 3.50
694 724 3.257873 TCGGTACATCGGTTTTCAGGTTA 59.742 43.478 0.00 0.00 0.00 2.85
695 725 4.081531 TCGGTACATCGGTTTTCAGGTTAT 60.082 41.667 0.00 0.00 0.00 1.89
696 726 5.126869 TCGGTACATCGGTTTTCAGGTTATA 59.873 40.000 0.00 0.00 0.00 0.98
697 727 5.987347 CGGTACATCGGTTTTCAGGTTATAT 59.013 40.000 0.00 0.00 0.00 0.86
698 728 6.073980 CGGTACATCGGTTTTCAGGTTATATG 60.074 42.308 0.00 0.00 0.00 1.78
699 729 5.751243 ACATCGGTTTTCAGGTTATATGC 57.249 39.130 0.00 0.00 0.00 3.14
700 730 4.578928 ACATCGGTTTTCAGGTTATATGCC 59.421 41.667 0.00 0.00 0.00 4.40
701 731 3.547746 TCGGTTTTCAGGTTATATGCCC 58.452 45.455 0.00 0.00 0.00 5.36
702 732 3.054287 TCGGTTTTCAGGTTATATGCCCA 60.054 43.478 0.00 0.00 0.00 5.36
703 733 3.315191 CGGTTTTCAGGTTATATGCCCAG 59.685 47.826 0.00 0.00 0.00 4.45
704 734 3.068165 GGTTTTCAGGTTATATGCCCAGC 59.932 47.826 0.00 0.00 0.00 4.85
705 735 2.656947 TTCAGGTTATATGCCCAGCC 57.343 50.000 0.00 0.00 0.00 4.85
706 736 0.771127 TCAGGTTATATGCCCAGCCC 59.229 55.000 0.00 0.00 0.00 5.19
707 737 0.773644 CAGGTTATATGCCCAGCCCT 59.226 55.000 0.00 0.00 0.00 5.19
708 738 1.985159 CAGGTTATATGCCCAGCCCTA 59.015 52.381 0.00 0.00 0.00 3.53
709 739 2.026822 CAGGTTATATGCCCAGCCCTAG 60.027 54.545 0.00 0.00 0.00 3.02
710 740 1.282157 GGTTATATGCCCAGCCCTAGG 59.718 57.143 0.06 0.06 0.00 3.02
733 763 3.489513 GGCGGGGGCTCCAACTAT 61.490 66.667 4.16 0.00 34.36 2.12
734 764 2.595655 GCGGGGGCTCCAACTATT 59.404 61.111 4.16 0.00 34.36 1.73
735 765 1.823899 GCGGGGGCTCCAACTATTG 60.824 63.158 4.16 0.00 34.36 1.90
736 766 1.607612 CGGGGGCTCCAACTATTGT 59.392 57.895 4.16 0.00 34.36 2.71
737 767 0.034477 CGGGGGCTCCAACTATTGTT 60.034 55.000 4.16 0.00 36.75 2.83
738 768 1.615919 CGGGGGCTCCAACTATTGTTT 60.616 52.381 4.16 0.00 33.52 2.83
739 769 1.824852 GGGGGCTCCAACTATTGTTTG 59.175 52.381 4.16 0.00 33.52 2.93
740 770 1.824852 GGGGCTCCAACTATTGTTTGG 59.175 52.381 0.00 0.00 33.52 3.28
741 771 2.525368 GGGCTCCAACTATTGTTTGGT 58.475 47.619 1.21 0.00 33.52 3.67
742 772 2.231235 GGGCTCCAACTATTGTTTGGTG 59.769 50.000 1.21 0.52 33.52 4.17
743 773 2.352715 GGCTCCAACTATTGTTTGGTGC 60.353 50.000 16.25 16.25 39.78 5.01
744 774 2.558359 GCTCCAACTATTGTTTGGTGCT 59.442 45.455 16.94 0.00 38.80 4.40
745 775 3.756434 GCTCCAACTATTGTTTGGTGCTA 59.244 43.478 16.94 0.00 38.80 3.49
746 776 4.142600 GCTCCAACTATTGTTTGGTGCTAG 60.143 45.833 16.94 3.04 38.80 3.42
754 784 5.567138 ATTGTTTGGTGCTAGCTAATGAC 57.433 39.130 17.23 4.85 0.00 3.06
805 837 7.811713 CGATTTCAGAGACTGCAGATATGAATA 59.188 37.037 23.35 15.98 0.00 1.75
811 843 9.269453 CAGAGACTGCAGATATGAATAATTTGA 57.731 33.333 23.35 0.00 0.00 2.69
833 865 5.482526 TGATAGAGTTTACTGTAACAGCCCA 59.517 40.000 0.00 0.00 34.37 5.36
834 866 4.273148 AGAGTTTACTGTAACAGCCCAG 57.727 45.455 0.00 0.00 34.37 4.45
835 867 3.008049 AGAGTTTACTGTAACAGCCCAGG 59.992 47.826 0.00 0.00 34.37 4.45
836 868 1.810755 GTTTACTGTAACAGCCCAGGC 59.189 52.381 0.00 0.00 42.33 4.85
837 869 0.326927 TTACTGTAACAGCCCAGGCC 59.673 55.000 4.70 0.00 43.17 5.19
1093 1128 3.558746 CCACAGGATTGCAGTCTCTCTTT 60.559 47.826 9.27 0.00 0.00 2.52
1413 1448 6.085416 CCTTACCTCTCCTTACCTGGATATT 58.915 44.000 0.00 0.00 35.30 1.28
1651 1691 1.700955 GCATCATCCCTGGCTTTCAT 58.299 50.000 0.00 0.00 0.00 2.57
1757 1797 3.409026 TTCCCTTCTTCAGTTCAGAGC 57.591 47.619 0.00 0.00 0.00 4.09
2190 2230 5.647225 ACAACGACCAGTAAAAGGTTACAAA 59.353 36.000 0.00 0.00 41.88 2.83
2710 2750 9.758651 ATGATGTATGATGAACAATTTCCATTG 57.241 29.630 0.00 0.00 44.90 2.82
2811 2851 6.811253 ATATCCAAACACTTAGCGAACAAA 57.189 33.333 0.00 0.00 0.00 2.83
2812 2852 4.966965 TCCAAACACTTAGCGAACAAAA 57.033 36.364 0.00 0.00 0.00 2.44
2813 2853 5.508200 TCCAAACACTTAGCGAACAAAAT 57.492 34.783 0.00 0.00 0.00 1.82
2814 2854 6.621316 TCCAAACACTTAGCGAACAAAATA 57.379 33.333 0.00 0.00 0.00 1.40
2815 2855 7.028926 TCCAAACACTTAGCGAACAAAATAA 57.971 32.000 0.00 0.00 0.00 1.40
2816 2856 7.653647 TCCAAACACTTAGCGAACAAAATAAT 58.346 30.769 0.00 0.00 0.00 1.28
3012 3052 2.546373 CCTGGTTGGTTTGCTCAACATG 60.546 50.000 8.82 0.00 44.38 3.21
3013 3053 1.202510 TGGTTGGTTTGCTCAACATGC 60.203 47.619 8.82 0.00 44.38 4.06
3014 3054 1.130955 GTTGGTTTGCTCAACATGCG 58.869 50.000 0.00 0.00 42.72 4.73
3015 3055 0.743688 TTGGTTTGCTCAACATGCGT 59.256 45.000 0.00 0.00 37.07 5.24
3016 3056 1.598882 TGGTTTGCTCAACATGCGTA 58.401 45.000 0.00 0.00 37.07 4.42
3091 3138 7.363181 CCTGTTTGCTGGATTATTTGAAGATGA 60.363 37.037 0.00 0.00 35.96 2.92
3465 3531 2.606213 TGGCACGGGTGGAGATCA 60.606 61.111 0.43 0.00 0.00 2.92
3639 3713 2.710902 CGGTGATCTGGTGCTCCGA 61.711 63.158 0.00 1.30 42.05 4.55
3828 3945 1.078497 TGGCCGGTGCACAAGATAG 60.078 57.895 20.43 0.93 40.13 2.08
4011 4141 2.740826 GGCGGCGCTTAAGTGTCA 60.741 61.111 32.30 0.00 0.00 3.58
4113 4245 1.441738 CATCTGACATGCCGACAACA 58.558 50.000 0.00 0.00 0.00 3.33
4115 4247 0.392706 TCTGACATGCCGACAACAGT 59.607 50.000 0.00 0.00 31.81 3.55
4123 4303 1.745890 CCGACAACAGTGGGTCTCA 59.254 57.895 13.27 0.00 31.88 3.27
4273 4480 1.597027 CCGTGTGTGTTGAGGGTCC 60.597 63.158 0.00 0.00 0.00 4.46
4334 4541 1.053424 GGCCACCGGATTAGATGGTA 58.947 55.000 9.46 0.00 33.82 3.25
4346 4553 0.761187 AGATGGTATGCGTGGATGCT 59.239 50.000 0.00 0.00 35.36 3.79
4437 4644 2.959516 TGCATCTACTTTGTCGGACTG 58.040 47.619 9.88 2.64 0.00 3.51
4572 4783 7.856145 AGCCTAGATTTTGTTAAGATCACTG 57.144 36.000 0.00 0.00 0.00 3.66
4574 4785 6.709643 CCTAGATTTTGTTAAGATCACTGCG 58.290 40.000 0.00 0.00 0.00 5.18
4611 4842 3.119137 CGACACAGAGAGAGAGAGAGAGA 60.119 52.174 0.00 0.00 0.00 3.10
4615 4846 4.403752 CACAGAGAGAGAGAGAGAGAGAGA 59.596 50.000 0.00 0.00 0.00 3.10
4619 4850 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4623 4854 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4627 4858 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4633 4864 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4657 4900 3.454082 AGAGAGACATTGGGAAAGCTAGG 59.546 47.826 0.00 0.00 0.00 3.02
4674 4917 3.813724 GCTAGGAAGGAAAAGAAACGTGT 59.186 43.478 0.00 0.00 0.00 4.49
5034 5278 0.953727 TGTGTGAATGCCAGCAACTC 59.046 50.000 0.00 0.00 0.00 3.01
5144 5388 8.450964 TCTGCAATAATTTAGAAAGTGTAGTGC 58.549 33.333 0.00 0.00 0.00 4.40
5204 5448 6.823689 ACAATACATCCATACTGACCAAAGAC 59.176 38.462 0.00 0.00 0.00 3.01
5206 5450 3.054361 ACATCCATACTGACCAAAGACCC 60.054 47.826 0.00 0.00 0.00 4.46
5375 5619 4.698201 TGGACCTCATGACTTTGTTACA 57.302 40.909 0.00 0.00 0.00 2.41
5441 5689 2.160646 GGGGTGGTCCTCCTTTTCA 58.839 57.895 9.84 0.00 35.33 2.69
5442 5690 0.481128 GGGGTGGTCCTCCTTTTCAA 59.519 55.000 9.84 0.00 35.33 2.69
5443 5691 1.133294 GGGGTGGTCCTCCTTTTCAAA 60.133 52.381 9.84 0.00 35.33 2.69
5444 5692 2.673258 GGGTGGTCCTCCTTTTCAAAA 58.327 47.619 9.84 0.00 34.23 2.44
5520 5768 8.704668 ACTAACTGATCCATTTTTCTTTTGGTT 58.295 29.630 0.00 0.00 0.00 3.67
5631 5879 2.998670 CTGGAGCAACAGACATACACAG 59.001 50.000 1.77 0.00 40.97 3.66
5671 5919 9.118300 GATTCAGATTTTCATTGTACAGGAGAT 57.882 33.333 0.00 0.00 0.00 2.75
5732 5980 3.493176 CGACCCAATCAGTCATGAGCATA 60.493 47.826 0.00 0.00 39.29 3.14
5826 6129 6.715344 ACATCTGCTTATTTGTGCAATTTG 57.285 33.333 0.00 0.00 38.81 2.32
5946 6253 0.179056 CGTGTGGTGGGAGTCAAACT 60.179 55.000 0.00 0.00 0.00 2.66
5986 6293 1.550524 ACACAGACTACGCCATGTCAT 59.449 47.619 0.00 0.00 35.81 3.06
6076 6383 5.897377 AATCCGATTGAAGATCCGTTTTT 57.103 34.783 0.00 0.00 0.00 1.94
6089 6396 8.589701 AAGATCCGTTTTTACCATTAAATCCT 57.410 30.769 0.00 0.00 0.00 3.24
6214 6529 7.826744 TGTTTACACTGAAGTTGCCATGATATA 59.173 33.333 0.00 0.00 0.00 0.86
6313 6629 6.318144 TGCCATGCACCATAAATTAAAATTGG 59.682 34.615 0.00 0.00 31.71 3.16
6327 6643 8.911918 AATTAAAATTGGCATGATACATGCAT 57.088 26.923 28.98 17.11 46.21 3.96
6419 6740 9.013490 CGAAAAACTAAAATTGCCATGATCTAG 57.987 33.333 0.00 0.00 0.00 2.43
6543 6875 6.819397 TCTCTAGTTTTGAAGATCTCGTCA 57.181 37.500 0.00 0.00 32.73 4.35
6544 6876 7.397892 TCTCTAGTTTTGAAGATCTCGTCAT 57.602 36.000 0.00 0.00 34.54 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 16 1.691976 ACTGAAGAACCACACCGATCA 59.308 47.619 0.00 0.00 0.00 2.92
23 25 3.351740 TGTTGCAGAAACTGAAGAACCA 58.648 40.909 2.81 0.00 39.70 3.67
32 34 4.385358 AAACCGAATTGTTGCAGAAACT 57.615 36.364 0.00 0.00 39.70 2.66
115 117 3.059603 CGATGACCGGACCGATTTT 57.940 52.632 17.49 0.00 33.91 1.82
179 195 3.326646 ATTCCTGCTGCTGCTCGCT 62.327 57.895 17.00 0.00 40.48 4.93
261 280 6.281405 GCTAGTACTATCTTTTAGCAGGCAA 58.719 40.000 2.33 0.00 37.33 4.52
278 297 0.464452 ATTGGCGTGGAGGCTAGTAC 59.536 55.000 0.00 0.00 46.88 2.73
316 341 1.339151 GGTCGATGCTTCCTGGTCTTT 60.339 52.381 0.00 0.00 0.00 2.52
319 344 0.179000 ATGGTCGATGCTTCCTGGTC 59.821 55.000 0.00 0.00 0.00 4.02
488 513 1.834263 CCTACTGCTATCCCTATGGGC 59.166 57.143 0.00 0.00 43.94 5.36
627 657 3.995705 TCGAATACACCGAAACCGAAAAT 59.004 39.130 0.00 0.00 32.64 1.82
655 685 1.474879 CCGAACCAAAATAACCGGCAT 59.525 47.619 0.00 0.00 0.00 4.40
689 719 2.269940 CTAGGGCTGGGCATATAACCT 58.730 52.381 0.00 0.00 0.00 3.50
693 723 3.417330 CCCTAGGGCTGGGCATATA 57.583 57.895 16.90 0.00 37.99 0.86
694 724 4.257890 CCCTAGGGCTGGGCATAT 57.742 61.111 16.90 0.00 37.99 1.78
716 746 3.056754 AATAGTTGGAGCCCCCGCC 62.057 63.158 0.00 0.00 37.93 6.13
717 747 1.823899 CAATAGTTGGAGCCCCCGC 60.824 63.158 0.00 0.00 37.93 6.13
718 748 0.034477 AACAATAGTTGGAGCCCCCG 60.034 55.000 0.00 0.00 36.39 5.73
719 749 1.824852 CAAACAATAGTTGGAGCCCCC 59.175 52.381 0.00 0.00 38.17 5.40
720 750 1.824852 CCAAACAATAGTTGGAGCCCC 59.175 52.381 0.00 0.00 38.17 5.80
721 751 2.231235 CACCAAACAATAGTTGGAGCCC 59.769 50.000 10.07 0.00 38.17 5.19
722 752 2.352715 GCACCAAACAATAGTTGGAGCC 60.353 50.000 12.76 0.00 38.17 4.70
723 753 2.558359 AGCACCAAACAATAGTTGGAGC 59.442 45.455 15.13 15.13 39.86 4.70
724 754 4.142600 GCTAGCACCAAACAATAGTTGGAG 60.143 45.833 10.63 3.44 38.17 3.86
725 755 3.756434 GCTAGCACCAAACAATAGTTGGA 59.244 43.478 10.63 0.00 38.17 3.53
726 756 3.758554 AGCTAGCACCAAACAATAGTTGG 59.241 43.478 18.83 1.65 38.17 3.77
727 757 6.494893 TTAGCTAGCACCAAACAATAGTTG 57.505 37.500 18.83 0.00 38.17 3.16
728 758 6.884295 TCATTAGCTAGCACCAAACAATAGTT 59.116 34.615 18.83 0.00 40.40 2.24
729 759 6.316390 GTCATTAGCTAGCACCAAACAATAGT 59.684 38.462 18.83 0.00 0.00 2.12
730 760 6.510157 CGTCATTAGCTAGCACCAAACAATAG 60.510 42.308 18.83 0.00 0.00 1.73
731 761 5.293324 CGTCATTAGCTAGCACCAAACAATA 59.707 40.000 18.83 0.00 0.00 1.90
732 762 4.094887 CGTCATTAGCTAGCACCAAACAAT 59.905 41.667 18.83 1.76 0.00 2.71
733 763 3.435327 CGTCATTAGCTAGCACCAAACAA 59.565 43.478 18.83 0.00 0.00 2.83
734 764 3.000041 CGTCATTAGCTAGCACCAAACA 59.000 45.455 18.83 0.00 0.00 2.83
735 765 3.000727 ACGTCATTAGCTAGCACCAAAC 58.999 45.455 18.83 8.37 0.00 2.93
736 766 3.328382 ACGTCATTAGCTAGCACCAAA 57.672 42.857 18.83 5.90 0.00 3.28
737 767 3.193903 TGTACGTCATTAGCTAGCACCAA 59.806 43.478 18.83 8.18 0.00 3.67
738 768 2.756207 TGTACGTCATTAGCTAGCACCA 59.244 45.455 18.83 0.00 0.00 4.17
739 769 3.431922 TGTACGTCATTAGCTAGCACC 57.568 47.619 18.83 0.00 0.00 5.01
740 770 4.421948 AGTTGTACGTCATTAGCTAGCAC 58.578 43.478 18.83 4.68 0.00 4.40
741 771 4.713824 AGTTGTACGTCATTAGCTAGCA 57.286 40.909 18.83 0.00 0.00 3.49
742 772 5.341617 AGAAGTTGTACGTCATTAGCTAGC 58.658 41.667 6.62 6.62 0.00 3.42
743 773 7.470079 TGTAGAAGTTGTACGTCATTAGCTAG 58.530 38.462 5.77 0.00 0.00 3.42
744 774 7.381766 TGTAGAAGTTGTACGTCATTAGCTA 57.618 36.000 5.77 0.00 0.00 3.32
745 775 6.263516 TGTAGAAGTTGTACGTCATTAGCT 57.736 37.500 5.77 0.00 0.00 3.32
746 776 6.939551 TTGTAGAAGTTGTACGTCATTAGC 57.060 37.500 5.77 0.00 0.00 3.09
754 784 7.943065 CGTTTTGTAGATTGTAGAAGTTGTACG 59.057 37.037 5.77 0.00 0.00 3.67
805 837 8.947115 GGCTGTTACAGTAAACTCTATCAAATT 58.053 33.333 14.23 0.00 33.43 1.82
811 843 5.104900 CCTGGGCTGTTACAGTAAACTCTAT 60.105 44.000 14.23 0.00 33.43 1.98
836 868 2.507992 CTTCGTCGGCTGCTCAGG 60.508 66.667 0.00 0.00 0.00 3.86
837 869 3.184683 GCTTCGTCGGCTGCTCAG 61.185 66.667 0.00 0.00 0.00 3.35
1077 1112 6.040842 AGGATAGAGAAAGAGAGACTGCAATC 59.959 42.308 0.00 0.00 0.00 2.67
1297 1332 4.141892 TGGTTCTCTAGTCTCTCCTACTCG 60.142 50.000 0.00 0.00 0.00 4.18
1563 1603 1.209504 TGCCCAGCATTCCTACTGTAC 59.790 52.381 0.00 0.00 31.71 2.90
1651 1691 3.220222 CCATAGAGGCACTGGCGA 58.780 61.111 0.00 0.00 41.55 5.54
1757 1797 0.321564 TCCTGTCAGGCAATTGGTCG 60.322 55.000 14.64 0.00 34.61 4.79
1954 1994 3.290710 GTCATCCACATTAACCTGGCAT 58.709 45.455 0.00 0.00 0.00 4.40
2163 2203 3.200483 ACCTTTTACTGGTCGTTGTCAC 58.800 45.455 0.00 0.00 31.03 3.67
2190 2230 4.137543 GACCATGGGCGAGAGAAATAATT 58.862 43.478 18.09 0.00 0.00 1.40
2197 2237 0.033503 TACAGACCATGGGCGAGAGA 60.034 55.000 18.09 2.72 0.00 3.10
2710 2750 9.124807 GGTATAAAACAGCACAATACTGAAAAC 57.875 33.333 0.00 0.00 38.55 2.43
2813 2853 9.638239 GCTTCACAAGTGGAAAATGAATTATTA 57.362 29.630 0.00 0.00 0.00 0.98
2814 2854 7.603784 GGCTTCACAAGTGGAAAATGAATTATT 59.396 33.333 0.00 0.00 0.00 1.40
2815 2855 7.099120 GGCTTCACAAGTGGAAAATGAATTAT 58.901 34.615 0.00 0.00 0.00 1.28
2816 2856 6.454795 GGCTTCACAAGTGGAAAATGAATTA 58.545 36.000 0.00 0.00 0.00 1.40
2912 2952 9.183368 TGACACAAAATATCAACTATATTGCCA 57.817 29.630 0.00 0.00 39.41 4.92
3012 3052 4.334203 TGGATACATCAACAACCATTACGC 59.666 41.667 0.00 0.00 46.17 4.42
3452 3518 2.284625 TGGCTGATCTCCACCCGT 60.285 61.111 3.58 0.00 0.00 5.28
3465 3531 2.389449 CCCACCCCATCATCTGGCT 61.389 63.158 0.00 0.00 44.46 4.75
3617 3685 4.760047 GCACCAGATCACCGGCGT 62.760 66.667 6.01 0.00 0.00 5.68
3639 3713 6.761714 GTCACCGTCACTAATCTAATCCAATT 59.238 38.462 0.00 0.00 0.00 2.32
3652 3728 0.669619 TTTGCTCGTCACCGTCACTA 59.330 50.000 0.00 0.00 35.01 2.74
3828 3945 2.106683 CCCACGAGAATCCAACCGC 61.107 63.158 0.00 0.00 0.00 5.68
4113 4245 1.305297 TCCATCGCTGAGACCCACT 60.305 57.895 0.00 0.00 0.00 4.00
4115 4247 2.710902 CGTCCATCGCTGAGACCCA 61.711 63.158 0.00 0.00 0.00 4.51
4212 4406 0.613260 CACCGTCCCATCTTCAGGAA 59.387 55.000 0.00 0.00 32.81 3.36
4346 4553 1.080907 TCTCATGGAGTGCCCTGGA 59.919 57.895 0.00 0.00 35.38 3.86
4572 4783 3.000022 GTGTCGTAGCTCTAAAATTCCGC 60.000 47.826 0.00 0.00 0.00 5.54
4574 4785 5.408356 TCTGTGTCGTAGCTCTAAAATTCC 58.592 41.667 0.00 0.00 0.00 3.01
4611 4842 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4615 4846 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4619 4850 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
4623 4854 5.397221 CCAATGTCTCTCTCTCTCTCTCTCT 60.397 48.000 0.00 0.00 0.00 3.10
4627 4858 3.527253 TCCCAATGTCTCTCTCTCTCTCT 59.473 47.826 0.00 0.00 0.00 3.10
4633 4864 3.180507 AGCTTTCCCAATGTCTCTCTCT 58.819 45.455 0.00 0.00 0.00 3.10
4657 4900 5.736486 AAGAGACACGTTTCTTTTCCTTC 57.264 39.130 5.56 0.00 30.94 3.46
4760 5004 1.369625 CCGGCTTTAGCGAACTGAAT 58.630 50.000 0.00 0.00 43.26 2.57
5144 5388 3.081061 TGCAAAGCACCTAGTAACATGG 58.919 45.455 0.00 0.00 31.71 3.66
5454 5702 9.979578 TGTGTGCAAAATATTTAGTCAGAATTT 57.020 25.926 0.01 0.00 0.00 1.82
5469 5717 6.892658 TTACAGGAATAGTGTGTGCAAAAT 57.107 33.333 0.00 0.00 0.00 1.82
5568 5816 0.890542 TGAAACCTTGCAGCGCAGAT 60.891 50.000 11.47 0.00 40.61 2.90
5631 5879 7.507733 AAATCTGAATCCTATGCTGAATGAC 57.492 36.000 0.00 0.00 0.00 3.06
5671 5919 8.525316 AGATCAAATTACAACATGAGAATGCAA 58.475 29.630 0.00 0.00 0.00 4.08
5732 5980 9.567848 CATCGGTAAAAGCTAACAATTTACAAT 57.432 29.630 16.08 8.72 39.90 2.71
5895 6202 6.432107 GTTAGCGTTGTCCTTGTTTTAATCA 58.568 36.000 0.00 0.00 0.00 2.57
5946 6253 2.442458 TATAGGGCGTGTGGGCGA 60.442 61.111 0.00 0.00 43.46 5.54
6076 6383 3.117794 CGTCGCGAAGGATTTAATGGTA 58.882 45.455 12.06 0.00 0.00 3.25
6089 6396 4.664792 CGAAGATCTCGTCGCGAA 57.335 55.556 12.06 0.00 42.89 4.70
6140 6450 5.047188 CACGGCAACTTTTACCAAAGAAAT 58.953 37.500 1.73 0.00 41.97 2.17
6144 6459 3.066203 AGACACGGCAACTTTTACCAAAG 59.934 43.478 0.00 0.00 44.57 2.77
6149 6464 4.156182 GCAATAGACACGGCAACTTTTAC 58.844 43.478 0.00 0.00 0.00 2.01
6313 6629 7.073265 GGCAATTTTAAATGCATGTATCATGC 58.927 34.615 22.59 22.59 44.32 4.06
6327 6643 8.908786 TTTGTATGAACCATGGCAATTTTAAA 57.091 26.923 13.04 3.97 0.00 1.52
6367 6688 3.826524 TGGCAATTCCAGTACTTTGACA 58.173 40.909 9.11 9.11 40.72 3.58


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

AutoCloner maintained by Alex Coulton.