Multiple sequence alignment - TraesCS5D01G050900

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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 TraesCS5D01G050900 chr5D 100.000 5191 0 0 1 5191 49016021 49021211 0.000000e+00 9587.0
1 TraesCS5D01G050900 chr5D 87.218 133 14 3 651 781 57843195 57843326 1.160000e-31 148.0
2 TraesCS5D01G050900 chr5D 87.121 132 16 1 651 781 503081260 503081391 1.160000e-31 148.0
3 TraesCS5D01G050900 chr5D 83.916 143 21 2 640 781 256208072 256207931 9.070000e-28 135.0
4 TraesCS5D01G050900 chr5A 96.820 3019 84 7 2178 5191 38712085 38715096 0.000000e+00 5033.0
5 TraesCS5D01G050900 chr5A 93.690 1363 57 14 836 2180 38710693 38712044 0.000000e+00 2013.0
6 TraesCS5D01G050900 chr5A 89.565 460 35 7 333 781 38708959 38709416 5.830000e-159 571.0
7 TraesCS5D01G050900 chr5A 86.828 372 16 3 7 345 38691149 38691520 8.150000e-103 385.0
8 TraesCS5D01G050900 chr5A 79.564 597 76 28 32 593 536466954 536466369 8.150000e-103 385.0
9 TraesCS5D01G050900 chr5B 92.460 2825 164 28 2183 4986 51790335 51793131 0.000000e+00 3991.0
10 TraesCS5D01G050900 chr5B 90.696 1365 81 13 832 2180 51788954 51790288 0.000000e+00 1775.0
11 TraesCS5D01G050900 chr5B 77.003 674 78 41 30 637 20644722 20644060 1.090000e-81 315.0
12 TraesCS5D01G050900 chr5B 92.821 195 12 2 4998 5191 51793173 51793366 1.100000e-71 281.0
13 TraesCS5D01G050900 chr7D 96.104 385 15 0 2387 2771 271751301 271751685 3.410000e-176 628.0
14 TraesCS5D01G050900 chr7D 86.929 482 46 11 1705 2180 271748227 271748697 4.600000e-145 525.0
15 TraesCS5D01G050900 chr7D 83.168 606 69 18 3111 3712 271752243 271752819 1.660000e-144 523.0
16 TraesCS5D01G050900 chr7D 87.285 291 18 11 3808 4089 271753163 271753443 1.090000e-81 315.0
17 TraesCS5D01G050900 chr7D 76.061 660 94 28 32 636 255304859 255305509 8.510000e-73 285.0
18 TraesCS5D01G050900 chr7D 84.286 140 19 3 643 781 564063176 564063313 3.260000e-27 134.0
19 TraesCS5D01G050900 chr7B 95.141 391 19 0 2387 2777 267337705 267337315 7.390000e-173 617.0
20 TraesCS5D01G050900 chr7B 82.975 605 64 24 3114 3712 267336765 267336194 1.290000e-140 510.0
21 TraesCS5D01G050900 chr7B 77.259 664 85 24 32 638 749501415 749500761 3.880000e-86 329.0
22 TraesCS5D01G050900 chr7B 86.195 297 22 11 3808 4095 267335951 267335665 2.350000e-78 303.0
23 TraesCS5D01G050900 chr7B 87.023 131 16 1 651 780 512694820 512694690 4.190000e-31 147.0
24 TraesCS5D01G050900 chr7B 84.783 138 18 3 645 781 28938356 28938491 9.070000e-28 135.0
25 TraesCS5D01G050900 chr7A 95.141 391 19 0 2387 2777 303955066 303955456 7.390000e-173 617.0
26 TraesCS5D01G050900 chr7A 83.828 606 65 18 3111 3712 303956020 303956596 3.530000e-151 545.0
27 TraesCS5D01G050900 chr7A 87.552 482 43 12 1705 2180 303950153 303950623 4.570000e-150 542.0
28 TraesCS5D01G050900 chr7A 77.521 605 88 16 30 593 725737359 725736762 2.330000e-83 320.0
29 TraesCS5D01G050900 chr7A 97.647 85 2 0 3808 3892 303956805 303956721 4.190000e-31 147.0
30 TraesCS5D01G050900 chr6D 79.431 598 79 19 27 594 293809330 293808747 2.930000e-102 383.0
31 TraesCS5D01G050900 chr6D 87.500 128 15 1 654 780 181729733 181729606 4.190000e-31 147.0
32 TraesCS5D01G050900 chr6A 78.912 588 72 24 27 574 426955665 426956240 8.270000e-93 351.0
33 TraesCS5D01G050900 chr6A 77.628 666 80 30 32 640 552263572 552264225 1.790000e-89 340.0
34 TraesCS5D01G050900 chr2B 78.502 614 71 25 32 593 98440675 98441279 3.850000e-91 346.0
35 TraesCS5D01G050900 chr2B 76.568 606 89 17 32 593 767027996 767028592 3.060000e-72 283.0
36 TraesCS5D01G050900 chr2B 78.041 296 41 12 370 642 736890686 736890980 1.160000e-36 165.0
37 TraesCS5D01G050900 chr3A 78.525 610 67 35 28 593 699292903 699292314 4.980000e-90 342.0
38 TraesCS5D01G050900 chr3A 78.061 588 75 19 96 638 13011799 13012377 6.480000e-84 322.0
39 TraesCS5D01G050900 chr4A 78.311 604 75 21 32 593 708571348 708570759 6.440000e-89 339.0
40 TraesCS5D01G050900 chr4A 80.244 410 62 11 193 593 389620787 389620388 1.830000e-74 291.0
41 TraesCS5D01G050900 chr4A 79.518 415 62 13 193 593 95392635 95393040 1.840000e-69 274.0
42 TraesCS5D01G050900 chr4A 82.877 146 24 1 637 781 17882664 17882809 4.220000e-26 130.0
43 TraesCS5D01G050900 chr4D 77.074 663 88 33 32 638 496174543 496173889 1.800000e-84 324.0
44 TraesCS5D01G050900 chr3D 76.866 670 86 32 32 645 374957800 374957144 1.090000e-81 315.0
45 TraesCS5D01G050900 chr3D 85.185 135 17 2 643 775 526937241 526937374 9.070000e-28 135.0
46 TraesCS5D01G050900 chr3D 92.683 41 3 0 1377 1417 26665589 26665629 5.610000e-05 60.2
47 TraesCS5D01G050900 chr1D 77.176 609 87 22 28 593 101589556 101588957 1.820000e-79 307.0
48 TraesCS5D01G050900 chr1D 87.597 129 15 1 654 781 28560190 28560062 1.160000e-31 148.0
49 TraesCS5D01G050900 chr1D 86.822 129 16 1 654 781 457175600 457175472 5.420000e-30 143.0
50 TraesCS5D01G050900 chr1A 77.393 606 77 22 32 593 226767629 226768218 6.530000e-79 305.0
51 TraesCS5D01G050900 chr4B 86.861 137 14 3 648 781 79610259 79610394 3.240000e-32 150.0
52 TraesCS5D01G050900 chr2D 86.567 134 17 1 649 781 633559624 633559757 4.190000e-31 147.0
53 TraesCS5D01G050900 chr6B 73.176 466 92 23 193 638 404460380 404460832 2.520000e-28 137.0
54 TraesCS5D01G050900 chr3B 85.075 134 19 1 649 781 680757290 680757157 9.070000e-28 135.0


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 TraesCS5D01G050900 chr5D 49016021 49021211 5190 False 9587.000000 9587 100.000000 1 5191 1 chr5D.!!$F1 5190
1 TraesCS5D01G050900 chr5A 38708959 38715096 6137 False 2539.000000 5033 93.358333 333 5191 3 chr5A.!!$F2 4858
2 TraesCS5D01G050900 chr5A 536466369 536466954 585 True 385.000000 385 79.564000 32 593 1 chr5A.!!$R1 561
3 TraesCS5D01G050900 chr5B 51788954 51793366 4412 False 2015.666667 3991 91.992333 832 5191 3 chr5B.!!$F1 4359
4 TraesCS5D01G050900 chr5B 20644060 20644722 662 True 315.000000 315 77.003000 30 637 1 chr5B.!!$R1 607
5 TraesCS5D01G050900 chr7D 271748227 271753443 5216 False 497.750000 628 88.371500 1705 4089 4 chr7D.!!$F3 2384
6 TraesCS5D01G050900 chr7D 255304859 255305509 650 False 285.000000 285 76.061000 32 636 1 chr7D.!!$F1 604
7 TraesCS5D01G050900 chr7B 267335665 267337705 2040 True 476.666667 617 88.103667 2387 4095 3 chr7B.!!$R3 1708
8 TraesCS5D01G050900 chr7B 749500761 749501415 654 True 329.000000 329 77.259000 32 638 1 chr7B.!!$R2 606
9 TraesCS5D01G050900 chr7A 303955066 303956596 1530 False 581.000000 617 89.484500 2387 3712 2 chr7A.!!$F2 1325
10 TraesCS5D01G050900 chr7A 725736762 725737359 597 True 320.000000 320 77.521000 30 593 1 chr7A.!!$R2 563
11 TraesCS5D01G050900 chr6D 293808747 293809330 583 True 383.000000 383 79.431000 27 594 1 chr6D.!!$R2 567
12 TraesCS5D01G050900 chr6A 426955665 426956240 575 False 351.000000 351 78.912000 27 574 1 chr6A.!!$F1 547
13 TraesCS5D01G050900 chr6A 552263572 552264225 653 False 340.000000 340 77.628000 32 640 1 chr6A.!!$F2 608
14 TraesCS5D01G050900 chr2B 98440675 98441279 604 False 346.000000 346 78.502000 32 593 1 chr2B.!!$F1 561
15 TraesCS5D01G050900 chr2B 767027996 767028592 596 False 283.000000 283 76.568000 32 593 1 chr2B.!!$F3 561
16 TraesCS5D01G050900 chr3A 699292314 699292903 589 True 342.000000 342 78.525000 28 593 1 chr3A.!!$R1 565
17 TraesCS5D01G050900 chr3A 13011799 13012377 578 False 322.000000 322 78.061000 96 638 1 chr3A.!!$F1 542
18 TraesCS5D01G050900 chr4A 708570759 708571348 589 True 339.000000 339 78.311000 32 593 1 chr4A.!!$R2 561
19 TraesCS5D01G050900 chr4D 496173889 496174543 654 True 324.000000 324 77.074000 32 638 1 chr4D.!!$R1 606
20 TraesCS5D01G050900 chr3D 374957144 374957800 656 True 315.000000 315 76.866000 32 645 1 chr3D.!!$R1 613
21 TraesCS5D01G050900 chr1D 101588957 101589556 599 True 307.000000 307 77.176000 28 593 1 chr1D.!!$R2 565
22 TraesCS5D01G050900 chr1A 226767629 226768218 589 False 305.000000 305 77.393000 32 593 1 chr1A.!!$F1 561

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
660 748 0.397816 AGAGATGCTCTAAGGCCCGT 60.398 55.000 0.00 0.00 39.28 5.28 F
1404 2722 0.687354 CTCCGCCATAGGTAAGCCAT 59.313 55.000 0.00 0.00 37.19 4.40 F
1934 3270 1.301716 GTTCGAGTTCAGCCAGGCA 60.302 57.895 15.80 0.00 0.00 4.75 F
3369 7429 1.134280 ACTGGCTAGTATGCTTGGCTG 60.134 52.381 18.98 18.98 43.12 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1664 3000 0.457166 TCGAGGTTGCCGTATTCGTG 60.457 55.000 0.0 0.0 35.01 4.35 R
3369 7429 1.168714 GATGGTCCTGAAACAGTGCC 58.831 55.000 0.0 0.0 0.00 5.01 R
3730 8036 4.872691 GCTATAAGAGAGCAGAAACAGCAA 59.127 41.667 0.0 0.0 39.84 3.91 R
4962 9307 0.539669 CCAAACCAAGTCACCTCCCC 60.540 60.000 0.0 0.0 0.00 4.81 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
21 22 3.343380 ACTGAAAAACGCGTTTTAGGG 57.657 42.857 40.51 32.37 41.45 3.53
22 23 2.684374 ACTGAAAAACGCGTTTTAGGGT 59.316 40.909 40.51 32.89 41.45 4.34
23 24 3.242837 ACTGAAAAACGCGTTTTAGGGTC 60.243 43.478 40.51 33.43 41.45 4.46
24 25 2.944349 TGAAAAACGCGTTTTAGGGTCT 59.056 40.909 40.51 27.96 41.45 3.85
25 26 3.242804 TGAAAAACGCGTTTTAGGGTCTG 60.243 43.478 40.51 0.00 41.45 3.51
58 59 6.992123 GGAATGAAAATGGAGTGGAAAGTTTT 59.008 34.615 0.00 0.00 0.00 2.43
60 61 6.537453 TGAAAATGGAGTGGAAAGTTTTCA 57.463 33.333 6.90 6.91 40.90 2.69
189 204 0.460722 TTTCGGTGGAACAGACGTGA 59.539 50.000 0.00 0.00 41.81 4.35
198 234 5.180492 GGTGGAACAGACGTGAAAAATATGA 59.820 40.000 0.00 0.00 41.80 2.15
200 236 6.797033 GTGGAACAGACGTGAAAAATATGAAG 59.203 38.462 0.00 0.00 41.80 3.02
203 239 7.534239 GGAACAGACGTGAAAAATATGAAGTTC 59.466 37.037 0.00 0.00 0.00 3.01
302 363 7.339482 AGATTATTTGAGGACCAACTTCTACC 58.661 38.462 0.00 0.00 33.85 3.18
304 365 4.351874 TTTGAGGACCAACTTCTACCAG 57.648 45.455 0.00 0.00 33.85 4.00
318 379 3.148412 TCTACCAGCACACACGTACTTA 58.852 45.455 0.00 0.00 0.00 2.24
319 380 2.894763 ACCAGCACACACGTACTTAA 57.105 45.000 0.00 0.00 0.00 1.85
320 381 2.750948 ACCAGCACACACGTACTTAAG 58.249 47.619 0.00 0.00 0.00 1.85
321 382 2.101917 ACCAGCACACACGTACTTAAGT 59.898 45.455 13.68 13.68 0.00 2.24
322 383 3.318839 ACCAGCACACACGTACTTAAGTA 59.681 43.478 11.38 11.38 0.00 2.24
323 384 4.021719 ACCAGCACACACGTACTTAAGTAT 60.022 41.667 18.03 0.74 32.54 2.12
324 385 4.927425 CCAGCACACACGTACTTAAGTATT 59.073 41.667 18.03 6.29 32.54 1.89
659 747 1.621992 TAGAGATGCTCTAAGGCCCG 58.378 55.000 0.00 0.00 39.74 6.13
660 748 0.397816 AGAGATGCTCTAAGGCCCGT 60.398 55.000 0.00 0.00 39.28 5.28
661 749 1.133450 AGAGATGCTCTAAGGCCCGTA 60.133 52.381 0.00 0.00 39.28 4.02
662 750 1.896465 GAGATGCTCTAAGGCCCGTAT 59.104 52.381 0.00 0.00 0.00 3.06
673 762 4.634012 AAGGCCCGTATAATGCAAGATA 57.366 40.909 0.00 0.00 0.00 1.98
679 768 5.523916 GCCCGTATAATGCAAGATACATAGG 59.476 44.000 17.04 14.79 0.00 2.57
691 780 6.518032 GCAAGATACATAGGAGAGATGCTTGA 60.518 42.308 0.00 0.00 30.04 3.02
704 793 8.344098 GGAGAGATGCTTGAAGAAATAAATCAG 58.656 37.037 0.00 0.00 0.00 2.90
705 794 8.223177 AGAGATGCTTGAAGAAATAAATCAGG 57.777 34.615 0.00 0.00 0.00 3.86
720 809 9.489084 AAATAAATCAGGTTTTTCTTAAGCACC 57.511 29.630 0.00 1.55 0.00 5.01
723 812 2.621526 CAGGTTTTTCTTAAGCACCGGT 59.378 45.455 0.00 0.00 32.32 5.28
739 828 4.699637 CACCGGTGCTTATTTGTATAGGA 58.300 43.478 24.02 0.00 0.00 2.94
747 836 6.310711 GTGCTTATTTGTATAGGATAGACGCC 59.689 42.308 0.00 0.00 35.04 5.68
755 844 7.876936 TGTATAGGATAGACGCCTAATTAGG 57.123 40.000 24.90 24.90 41.10 2.69
756 845 7.408543 TGTATAGGATAGACGCCTAATTAGGT 58.591 38.462 28.31 13.14 41.10 3.08
764 853 3.372660 CGCCTAATTAGGTGTCTCTCC 57.627 52.381 29.49 12.56 46.35 3.71
766 855 3.243569 CGCCTAATTAGGTGTCTCTCCTG 60.244 52.174 29.49 5.06 46.35 3.86
769 858 5.010213 GCCTAATTAGGTGTCTCTCCTGTAG 59.990 48.000 28.31 2.31 45.42 2.74
803 913 9.292195 CACCTTATTTTTCTAAACACCTCCTTA 57.708 33.333 0.00 0.00 0.00 2.69
808 918 7.775053 TTTTTCTAAACACCTCCTTATGCAT 57.225 32.000 3.79 3.79 0.00 3.96
809 919 7.391148 TTTTCTAAACACCTCCTTATGCATC 57.609 36.000 0.19 0.00 0.00 3.91
812 922 7.432148 TCTAAACACCTCCTTATGCATCTAA 57.568 36.000 0.19 0.00 0.00 2.10
813 923 7.272978 TCTAAACACCTCCTTATGCATCTAAC 58.727 38.462 0.19 0.00 0.00 2.34
815 925 3.451178 ACACCTCCTTATGCATCTAACGT 59.549 43.478 0.19 0.00 0.00 3.99
817 927 3.704566 ACCTCCTTATGCATCTAACGTCA 59.295 43.478 0.19 0.00 0.00 4.35
819 929 5.163301 ACCTCCTTATGCATCTAACGTCATT 60.163 40.000 0.19 0.00 0.00 2.57
820 930 5.178252 CCTCCTTATGCATCTAACGTCATTG 59.822 44.000 0.19 0.00 0.00 2.82
821 931 5.670485 TCCTTATGCATCTAACGTCATTGT 58.330 37.500 0.19 0.00 0.00 2.71
823 933 6.700081 TCCTTATGCATCTAACGTCATTGTAC 59.300 38.462 0.19 0.00 0.00 2.90
824 934 6.478673 CCTTATGCATCTAACGTCATTGTACA 59.521 38.462 0.19 0.00 0.00 2.90
826 936 5.778161 TGCATCTAACGTCATTGTACAAG 57.222 39.130 14.65 6.58 0.00 3.16
828 938 4.494199 GCATCTAACGTCATTGTACAAGCC 60.494 45.833 14.65 3.43 0.00 4.35
830 940 2.561478 AACGTCATTGTACAAGCCCT 57.439 45.000 14.65 0.00 0.00 5.19
832 942 3.247006 ACGTCATTGTACAAGCCCTAG 57.753 47.619 14.65 5.86 0.00 3.02
833 943 2.093658 ACGTCATTGTACAAGCCCTAGG 60.094 50.000 14.65 0.06 0.00 3.02
834 944 2.093658 CGTCATTGTACAAGCCCTAGGT 60.094 50.000 14.65 0.00 0.00 3.08
1106 2421 4.814294 CTAGGGTCACGGGCGCAC 62.814 72.222 10.83 3.71 0.00 5.34
1135 2450 4.463879 CTGCTGCTCCCTCCACGG 62.464 72.222 0.00 0.00 0.00 4.94
1241 2556 3.941188 CACCGACAGGGCCACAGT 61.941 66.667 6.18 0.01 43.47 3.55
1404 2722 0.687354 CTCCGCCATAGGTAAGCCAT 59.313 55.000 0.00 0.00 37.19 4.40
1406 2724 1.493022 TCCGCCATAGGTAAGCCATTT 59.507 47.619 0.00 0.00 37.19 2.32
1407 2725 2.706723 TCCGCCATAGGTAAGCCATTTA 59.293 45.455 0.00 0.00 37.19 1.40
1418 2736 6.974795 AGGTAAGCCATTTAGATTCCTCTTT 58.025 36.000 0.00 0.00 37.19 2.52
1430 2748 3.771577 TTCCTCTTTCTCCGCTTTCTT 57.228 42.857 0.00 0.00 0.00 2.52
1449 2767 3.622060 TAAGGTTCTGGGCTGCGGC 62.622 63.158 9.72 9.72 37.82 6.53
1570 2891 9.579768 GACTTATATCATGTGGAGCTTATAGTG 57.420 37.037 0.00 0.00 0.00 2.74
1584 2905 4.436584 GCTTATAGTGTGTTTCTGCTGCTG 60.437 45.833 0.00 0.00 0.00 4.41
1605 2926 4.910195 TGTGCATACTTCAAAGGACTGAT 58.090 39.130 0.00 0.00 0.00 2.90
1633 2958 7.512992 AGCCTAGCAAATAGTCATATTCTTGT 58.487 34.615 0.00 0.00 31.02 3.16
1664 3000 1.541588 GGGGACAGATTCTTGTGTTGC 59.458 52.381 0.00 0.00 27.72 4.17
1671 3007 4.754618 ACAGATTCTTGTGTTGCACGAATA 59.245 37.500 0.00 0.00 43.35 1.75
1934 3270 1.301716 GTTCGAGTTCAGCCAGGCA 60.302 57.895 15.80 0.00 0.00 4.75
1980 3316 3.463585 GGATACGCGGGGTCACCA 61.464 66.667 12.47 0.00 40.22 4.17
2071 3407 4.451774 CACTTCTTGCTCTCTCCTCTTTTG 59.548 45.833 0.00 0.00 0.00 2.44
2249 3634 7.153217 ACTGAACCATAATTTAGTTTTCCCG 57.847 36.000 0.00 0.00 0.00 5.14
2349 6084 1.859302 TCCCTTGTTTTTGCCTGTGT 58.141 45.000 0.00 0.00 0.00 3.72
2449 6209 8.632679 TGGCAGGTTGAAGATGATAAAATTATC 58.367 33.333 6.27 6.27 39.92 1.75
2791 6840 7.386025 TCTTCTGACTAATTCTTGTGTGACATG 59.614 37.037 0.00 0.00 0.00 3.21
2805 6854 3.004629 TGTGACATGTTGCATCCTTTGAC 59.995 43.478 0.00 0.00 0.00 3.18
2852 6901 2.457366 ATCTGTGAAACCACTCCGTC 57.543 50.000 0.00 0.00 35.63 4.79
2863 6912 3.818180 ACCACTCCGTCTTACTCGATAT 58.182 45.455 0.00 0.00 0.00 1.63
2909 6958 3.673543 AATTAAAATGACCCCCGCCTA 57.326 42.857 0.00 0.00 0.00 3.93
2959 7008 5.407407 TTTTGCAGTAGTGTTTCCCAAAA 57.593 34.783 8.21 8.21 0.00 2.44
3002 7059 5.529430 TGAAGAAAGACTCGTTTGCCAAATA 59.471 36.000 0.00 0.00 0.00 1.40
3042 7099 1.656652 CCTGGTTCTGCATTACCTCG 58.343 55.000 15.89 8.71 35.41 4.63
3175 7233 2.224892 TGGGCAGCATACCAAGTAACAA 60.225 45.455 0.00 0.00 32.89 2.83
3244 7303 9.646427 CAATACTAGAGCTCAAAACTAACTCTT 57.354 33.333 17.77 0.00 38.59 2.85
3245 7304 9.646427 AATACTAGAGCTCAAAACTAACTCTTG 57.354 33.333 17.77 0.00 38.59 3.02
3246 7305 7.056844 ACTAGAGCTCAAAACTAACTCTTGT 57.943 36.000 17.77 0.00 38.19 3.16
3247 7306 7.149307 ACTAGAGCTCAAAACTAACTCTTGTC 58.851 38.462 17.77 0.00 38.49 3.18
3274 7333 6.398918 ACTGATACAAGTTTCGCATACTTCT 58.601 36.000 0.00 0.00 33.73 2.85
3281 7340 3.071479 GTTTCGCATACTTCTGTGGGAA 58.929 45.455 1.44 1.44 42.94 3.97
3369 7429 1.134280 ACTGGCTAGTATGCTTGGCTG 60.134 52.381 18.98 18.98 43.12 4.85
3946 8279 5.006386 AGTTATTTCTGAAACTGGAGGCAG 58.994 41.667 4.73 0.00 34.70 4.85
4310 8644 0.171455 GCACGGTTGTGGTTGAACAA 59.829 50.000 0.00 0.00 46.51 2.83
4517 8855 3.886123 ACTTGGTTAGAGCAACTTGTGT 58.114 40.909 0.00 0.00 37.30 3.72
4726 9071 2.555199 CTTCTTTGGATCGTAGGCCTG 58.445 52.381 17.99 0.00 0.00 4.85
4742 9087 1.098050 CCTGTGCCTCCTTGCATAAC 58.902 55.000 0.00 0.00 44.30 1.89
4762 9107 3.117171 GTCACTGCAGCTGCCTCG 61.117 66.667 34.64 24.09 41.18 4.63
4862 9207 1.135257 CCTTAGTGAGTGAGCGGACTG 60.135 57.143 0.00 0.00 0.00 3.51
4874 9219 1.092345 GCGGACTGGGATTTCTCTGC 61.092 60.000 0.00 0.00 0.00 4.26
4882 9227 5.463154 ACTGGGATTTCTCTGCTACTAGAT 58.537 41.667 0.00 0.00 0.00 1.98
4930 9275 6.801539 ATTTAACTCAAAGCTCGATTGACA 57.198 33.333 0.00 0.00 33.47 3.58
4948 9293 7.269937 CGATTGACAAAGAATTAGCAAGAACAG 59.730 37.037 0.00 0.00 0.00 3.16
4962 9307 1.071385 AGAACAGAGCAACCACCTCAG 59.929 52.381 0.00 0.00 0.00 3.35
5150 9526 4.446371 AGATTTCTAGCTATGGTGCACAC 58.554 43.478 20.43 8.79 34.99 3.82
5162 9538 1.687563 GTGCACACTACCCCAAAAGT 58.312 50.000 13.17 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.684374 ACCCTAAAACGCGTTTTTCAGT 59.316 40.909 43.50 33.96 42.22 3.41
4 5 3.294102 CAGACCCTAAAACGCGTTTTTC 58.706 45.455 43.50 34.77 42.22 2.29
5 6 2.542205 GCAGACCCTAAAACGCGTTTTT 60.542 45.455 43.50 30.62 42.22 1.94
6 7 1.002142 GCAGACCCTAAAACGCGTTTT 60.002 47.619 41.13 41.13 44.16 2.43
7 8 0.589708 GCAGACCCTAAAACGCGTTT 59.410 50.000 30.36 30.36 0.00 3.60
8 9 0.250166 AGCAGACCCTAAAACGCGTT 60.250 50.000 20.79 20.79 0.00 4.84
9 10 0.604578 TAGCAGACCCTAAAACGCGT 59.395 50.000 5.58 5.58 0.00 6.01
10 11 1.135199 TCTAGCAGACCCTAAAACGCG 60.135 52.381 3.53 3.53 0.00 6.01
11 12 2.667473 TCTAGCAGACCCTAAAACGC 57.333 50.000 0.00 0.00 0.00 4.84
12 13 4.583489 TCCTATCTAGCAGACCCTAAAACG 59.417 45.833 0.00 0.00 0.00 3.60
13 14 6.481434 TTCCTATCTAGCAGACCCTAAAAC 57.519 41.667 0.00 0.00 0.00 2.43
14 15 6.844388 TCATTCCTATCTAGCAGACCCTAAAA 59.156 38.462 0.00 0.00 0.00 1.52
15 16 6.382087 TCATTCCTATCTAGCAGACCCTAAA 58.618 40.000 0.00 0.00 0.00 1.85
16 17 5.965486 TCATTCCTATCTAGCAGACCCTAA 58.035 41.667 0.00 0.00 0.00 2.69
17 18 5.600669 TCATTCCTATCTAGCAGACCCTA 57.399 43.478 0.00 0.00 0.00 3.53
18 19 4.477536 TCATTCCTATCTAGCAGACCCT 57.522 45.455 0.00 0.00 0.00 4.34
19 20 5.552870 TTTCATTCCTATCTAGCAGACCC 57.447 43.478 0.00 0.00 0.00 4.46
20 21 6.429385 CCATTTTCATTCCTATCTAGCAGACC 59.571 42.308 0.00 0.00 0.00 3.85
21 22 7.220030 TCCATTTTCATTCCTATCTAGCAGAC 58.780 38.462 0.00 0.00 0.00 3.51
22 23 7.071698 ACTCCATTTTCATTCCTATCTAGCAGA 59.928 37.037 0.00 0.00 0.00 4.26
23 24 7.172875 CACTCCATTTTCATTCCTATCTAGCAG 59.827 40.741 0.00 0.00 0.00 4.24
24 25 6.994496 CACTCCATTTTCATTCCTATCTAGCA 59.006 38.462 0.00 0.00 0.00 3.49
25 26 6.429385 CCACTCCATTTTCATTCCTATCTAGC 59.571 42.308 0.00 0.00 0.00 3.42
135 148 7.659390 TCCATTTTTGTTTCCATTTCCACATAC 59.341 33.333 0.00 0.00 0.00 2.39
203 239 9.167311 CAGCCATAAGCCTATAGTAAAAATAGG 57.833 37.037 5.01 5.01 46.01 2.57
277 329 7.037586 TGGTAGAAGTTGGTCCTCAAATAATCT 60.038 37.037 0.00 0.00 37.08 2.40
281 342 5.570844 GCTGGTAGAAGTTGGTCCTCAAATA 60.571 44.000 0.00 0.00 37.08 1.40
302 363 7.571089 TTAATACTTAAGTACGTGTGTGCTG 57.429 36.000 17.45 0.00 40.43 4.41
324 385 9.892444 TGGAGAATTTCATATAGGGTCTACTTA 57.108 33.333 0.00 0.00 0.00 2.24
451 522 2.715880 ACCGGAACTTAAAACCCCCTTA 59.284 45.455 9.46 0.00 0.00 2.69
589 662 3.326588 AGACCAAACTGTGTGCTACCATA 59.673 43.478 0.00 0.00 0.00 2.74
607 695 0.942252 AAACGAAGCGGAAACAGACC 59.058 50.000 0.00 0.00 0.00 3.85
658 746 8.678199 TCTCTCCTATGTATCTTGCATTATACG 58.322 37.037 12.00 0.00 32.34 3.06
661 749 7.986320 GCATCTCTCCTATGTATCTTGCATTAT 59.014 37.037 0.00 0.00 0.00 1.28
662 750 7.179872 AGCATCTCTCCTATGTATCTTGCATTA 59.820 37.037 0.00 0.00 0.00 1.90
673 762 5.946942 TTCTTCAAGCATCTCTCCTATGT 57.053 39.130 0.00 0.00 0.00 2.29
679 768 8.344098 CCTGATTTATTTCTTCAAGCATCTCTC 58.656 37.037 0.00 0.00 0.00 3.20
701 790 2.882137 CCGGTGCTTAAGAAAAACCTGA 59.118 45.455 6.67 0.00 0.00 3.86
704 793 3.007979 CACCGGTGCTTAAGAAAAACC 57.992 47.619 24.02 6.81 0.00 3.27
720 809 6.527023 CGTCTATCCTATACAAATAAGCACCG 59.473 42.308 0.00 0.00 0.00 4.94
723 812 6.210784 AGGCGTCTATCCTATACAAATAAGCA 59.789 38.462 0.00 0.00 30.79 3.91
735 824 5.709164 GACACCTAATTAGGCGTCTATCCTA 59.291 44.000 32.03 0.00 46.77 2.94
737 826 4.807443 GACACCTAATTAGGCGTCTATCC 58.193 47.826 32.03 15.55 46.77 2.59
747 836 7.883391 TTCTACAGGAGAGACACCTAATTAG 57.117 40.000 5.43 5.43 34.93 1.73
755 844 6.404954 GGTGTCTATTTCTACAGGAGAGACAC 60.405 46.154 18.64 18.64 46.35 3.67
756 845 5.652891 GGTGTCTATTTCTACAGGAGAGACA 59.347 44.000 0.00 0.00 37.51 3.41
803 913 5.220662 GCTTGTACAATGACGTTAGATGCAT 60.221 40.000 9.13 0.00 0.00 3.96
805 915 4.494199 GGCTTGTACAATGACGTTAGATGC 60.494 45.833 9.13 4.23 0.00 3.91
808 918 3.259876 AGGGCTTGTACAATGACGTTAGA 59.740 43.478 9.13 0.00 0.00 2.10
809 919 3.596214 AGGGCTTGTACAATGACGTTAG 58.404 45.455 9.13 0.00 0.00 2.34
812 922 2.093658 CCTAGGGCTTGTACAATGACGT 60.094 50.000 9.13 9.58 0.00 4.34
813 923 2.093658 ACCTAGGGCTTGTACAATGACG 60.094 50.000 14.81 0.00 0.00 4.35
815 925 4.080751 GGTTACCTAGGGCTTGTACAATGA 60.081 45.833 14.81 0.00 0.00 2.57
817 927 3.201487 GGGTTACCTAGGGCTTGTACAAT 59.799 47.826 14.81 0.00 0.00 2.71
819 929 2.190538 GGGTTACCTAGGGCTTGTACA 58.809 52.381 14.81 0.00 0.00 2.90
820 930 2.169978 CTGGGTTACCTAGGGCTTGTAC 59.830 54.545 14.81 1.50 37.76 2.90
821 931 2.044769 TCTGGGTTACCTAGGGCTTGTA 59.955 50.000 14.75 0.00 37.76 2.41
823 933 1.209747 GTCTGGGTTACCTAGGGCTTG 59.790 57.143 14.75 0.00 37.76 4.01
824 934 1.581223 GTCTGGGTTACCTAGGGCTT 58.419 55.000 14.75 0.00 37.76 4.35
826 936 0.974525 ACGTCTGGGTTACCTAGGGC 60.975 60.000 14.75 7.42 37.76 5.19
828 938 3.690475 AAAACGTCTGGGTTACCTAGG 57.310 47.619 14.75 7.41 37.76 3.02
830 940 3.140623 GCAAAAACGTCTGGGTTACCTA 58.859 45.455 0.00 0.00 37.76 3.08
832 942 1.677052 TGCAAAAACGTCTGGGTTACC 59.323 47.619 0.00 0.00 37.24 2.85
833 943 3.003897 TGATGCAAAAACGTCTGGGTTAC 59.996 43.478 0.00 0.00 0.00 2.50
834 944 3.003897 GTGATGCAAAAACGTCTGGGTTA 59.996 43.478 0.00 0.00 0.00 2.85
991 2306 4.947147 GTGGCCTGTGCGGTTGGA 62.947 66.667 3.32 0.00 38.85 3.53
1404 2722 5.422214 AAGCGGAGAAAGAGGAATCTAAA 57.578 39.130 0.00 0.00 0.00 1.85
1406 2724 4.712337 AGAAAGCGGAGAAAGAGGAATCTA 59.288 41.667 0.00 0.00 0.00 1.98
1407 2725 3.517500 AGAAAGCGGAGAAAGAGGAATCT 59.482 43.478 0.00 0.00 0.00 2.40
1418 2736 4.315803 CAGAACCTTAAAGAAAGCGGAGA 58.684 43.478 0.00 0.00 33.49 3.71
1430 2748 1.002624 CCGCAGCCCAGAACCTTAA 60.003 57.895 0.00 0.00 0.00 1.85
1449 2767 4.921470 ACGTTTCTATCACAAACCATCG 57.079 40.909 0.00 0.00 31.12 3.84
1554 2872 5.877012 CAGAAACACACTATAAGCTCCACAT 59.123 40.000 0.00 0.00 0.00 3.21
1570 2891 1.729276 TGCACAGCAGCAGAAACAC 59.271 52.632 0.00 0.00 40.11 3.32
1584 2905 4.937620 TCATCAGTCCTTTGAAGTATGCAC 59.062 41.667 0.00 0.00 0.00 4.57
1605 2926 7.739825 AGAATATGACTATTTGCTAGGCTTCA 58.260 34.615 0.00 0.00 36.32 3.02
1648 2984 2.560504 TCGTGCAACACAAGAATCTGT 58.439 42.857 0.00 0.00 33.56 3.41
1664 3000 0.457166 TCGAGGTTGCCGTATTCGTG 60.457 55.000 0.00 0.00 35.01 4.35
1671 3007 2.338984 GTCACTCGAGGTTGCCGT 59.661 61.111 18.41 0.00 0.00 5.68
1934 3270 3.140141 CCCACGCAAATCCCGCAT 61.140 61.111 0.00 0.00 0.00 4.73
2071 3407 9.282247 GAACTGTTGACATGAATTATTGATGAC 57.718 33.333 11.10 5.75 0.00 3.06
2245 3630 9.796120 GAAATGTAACAAAATGATTTATCGGGA 57.204 29.630 0.00 0.00 0.00 5.14
2290 6015 1.679977 GCATGCCACACCCACTCAT 60.680 57.895 6.36 0.00 0.00 2.90
2349 6084 9.772973 TTCTATAGTACAGCAAAGAAACTGAAA 57.227 29.630 0.00 0.00 37.35 2.69
2791 6840 2.774439 AACGTGTCAAAGGATGCAAC 57.226 45.000 0.00 0.00 0.00 4.17
2805 6854 2.704725 AGCTAAATGTGGCAAACGTG 57.295 45.000 0.00 0.00 32.62 4.49
3002 7059 6.143915 CAGGCCCCTATATAGTACCATATGT 58.856 44.000 8.92 0.00 0.00 2.29
3042 7099 6.038603 TGCCATCACTTGATAAGAAATGCTAC 59.961 38.462 0.00 0.00 32.63 3.58
3102 7159 6.317140 GGAAAACATGTTGATGCTCAGAGATA 59.683 38.462 12.82 0.00 32.14 1.98
3203 7262 7.982354 GCTCTAGTATTGTAAAGATGACCAAGT 59.018 37.037 0.00 0.00 0.00 3.16
3244 7303 4.572795 TGCGAAACTTGTATCAGTTTGACA 59.427 37.500 3.59 0.00 45.23 3.58
3245 7304 5.090652 TGCGAAACTTGTATCAGTTTGAC 57.909 39.130 3.59 0.00 45.23 3.18
3246 7305 5.940192 ATGCGAAACTTGTATCAGTTTGA 57.060 34.783 3.59 0.00 45.23 2.69
3247 7306 6.831769 AGTATGCGAAACTTGTATCAGTTTG 58.168 36.000 3.59 0.00 45.23 2.93
3274 7333 2.315176 CAGTTCAACCCAATTCCCACA 58.685 47.619 0.00 0.00 0.00 4.17
3281 7340 4.961438 ATTTTCAGCAGTTCAACCCAAT 57.039 36.364 0.00 0.00 0.00 3.16
3369 7429 1.168714 GATGGTCCTGAAACAGTGCC 58.831 55.000 0.00 0.00 0.00 5.01
3730 8036 4.872691 GCTATAAGAGAGCAGAAACAGCAA 59.127 41.667 0.00 0.00 39.84 3.91
3946 8279 3.320826 AGGACACATGTAAAAACCTTGCC 59.679 43.478 0.00 0.00 0.00 4.52
4205 8539 6.685828 CGTGTCAAGAATGCAGAAAAGATATG 59.314 38.462 0.00 0.00 0.00 1.78
4310 8644 5.133221 ACTAGCAAATTCCTTGTTCACACT 58.867 37.500 0.00 0.00 37.36 3.55
4649 8994 2.034221 GGACAGGGTTGTGGCCTC 59.966 66.667 3.32 0.00 43.21 4.70
4742 9087 3.054503 GGCAGCTGCAGTGACCTG 61.055 66.667 37.63 14.53 44.36 4.00
4762 9107 3.282885 AGGAAGGCGATCAAAATTCCTC 58.717 45.455 10.98 0.00 45.10 3.71
4862 9207 5.799827 ACATCTAGTAGCAGAGAAATCCC 57.200 43.478 0.00 0.00 0.00 3.85
4895 9240 8.860088 AGCTTTGAGTTAAATATGTTTCCACTT 58.140 29.630 0.00 0.00 0.00 3.16
4930 9275 6.442112 GTTGCTCTGTTCTTGCTAATTCTTT 58.558 36.000 0.00 0.00 0.00 2.52
4948 9293 2.190488 CTCCCCTGAGGTGGTTGCTC 62.190 65.000 0.00 0.00 34.80 4.26
4962 9307 0.539669 CCAAACCAAGTCACCTCCCC 60.540 60.000 0.00 0.00 0.00 4.81
5162 9538 4.020617 CTCCTCGGTGCCTTGCCA 62.021 66.667 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.