Multiple sequence alignment - TraesCS5D01G245900

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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 TraesCS5D01G245900 chr5D 100.000 5193 0 0 1446 6638 354254851 354260043 0.000000e+00 9590.0
1 TraesCS5D01G245900 chr5D 100.000 1018 0 0 1 1018 354253406 354254423 0.000000e+00 1881.0
2 TraesCS5D01G245900 chr5D 90.608 362 33 1 5797 6158 412722495 412722135 4.660000e-131 479.0
3 TraesCS5D01G245900 chr5D 89.677 155 12 4 3384 3536 5794771 5794923 1.890000e-45 195.0
4 TraesCS5D01G245900 chr5D 92.553 94 5 2 3446 3538 257502198 257502290 4.180000e-27 134.0
5 TraesCS5D01G245900 chr5A 94.252 1531 60 11 5128 6638 455088090 455089612 0.000000e+00 2314.0
6 TraesCS5D01G245900 chr5A 94.162 1062 41 13 1455 2514 455082593 455083635 0.000000e+00 1598.0
7 TraesCS5D01G245900 chr5A 91.352 1006 56 8 16 1018 455081226 455082203 0.000000e+00 1347.0
8 TraesCS5D01G245900 chr5A 89.632 1061 79 19 2505 3540 455083666 455084720 0.000000e+00 1321.0
9 TraesCS5D01G245900 chr5A 94.277 629 31 4 4488 5114 455087404 455088029 0.000000e+00 957.0
10 TraesCS5D01G245900 chr5A 90.698 473 22 12 4036 4500 455084720 455085178 1.580000e-170 610.0
11 TraesCS5D01G245900 chr5A 94.286 70 4 0 3333 3402 185649700 185649769 2.530000e-19 108.0
12 TraesCS5D01G245900 chr5B 94.559 1452 68 6 5194 6638 418470977 418472424 0.000000e+00 2233.0
13 TraesCS5D01G245900 chr5B 92.646 1047 52 12 1518 2563 418464308 418465330 0.000000e+00 1483.0
14 TraesCS5D01G245900 chr5B 96.264 803 30 0 2708 3510 418466215 418467017 0.000000e+00 1317.0
15 TraesCS5D01G245900 chr5B 95.047 747 27 5 4036 4776 418467058 418467800 0.000000e+00 1166.0
16 TraesCS5D01G245900 chr5B 95.399 326 11 3 4772 5096 418470096 418470418 3.550000e-142 516.0
17 TraesCS5D01G245900 chr5B 91.033 368 29 3 5791 6158 709933557 709933920 1.660000e-135 494.0
18 TraesCS5D01G245900 chr5B 93.182 264 16 2 660 923 418463593 418463854 2.900000e-103 387.0
19 TraesCS5D01G245900 chr5B 93.684 95 2 4 3446 3538 291786916 291787008 8.980000e-29 139.0
20 TraesCS5D01G245900 chr5B 82.353 153 7 4 3405 3537 601414175 601414327 1.510000e-21 115.0
21 TraesCS5D01G245900 chr5B 94.286 70 4 0 3333 3402 187046450 187046381 2.530000e-19 108.0
22 TraesCS5D01G245900 chr5B 97.222 36 1 0 2555 2590 418466174 418466209 2.000000e-05 62.1
23 TraesCS5D01G245900 chr2D 97.421 504 8 2 3540 4038 113048193 113047690 0.000000e+00 854.0
24 TraesCS5D01G245900 chr2D 95.294 510 18 4 3540 4045 596815769 596816276 0.000000e+00 804.0
25 TraesCS5D01G245900 chr2D 95.030 503 17 5 3539 4038 116057013 116056516 0.000000e+00 784.0
26 TraesCS5D01G245900 chr2D 93.548 93 4 2 3446 3537 215831877 215831968 3.230000e-28 137.0
27 TraesCS5D01G245900 chr2D 95.588 68 3 0 3335 3402 548076875 548076808 7.040000e-20 110.0
28 TraesCS5D01G245900 chr7D 95.817 502 15 3 3540 4037 572176208 572176707 0.000000e+00 806.0
29 TraesCS5D01G245900 chr7D 95.050 505 17 5 3540 4037 418619196 418618693 0.000000e+00 787.0
30 TraesCS5D01G245900 chr7D 94.841 504 21 3 3538 4037 152081681 152082183 0.000000e+00 782.0
31 TraesCS5D01G245900 chr7D 94.186 86 5 0 3452 3537 617790676 617790591 1.500000e-26 132.0
32 TraesCS5D01G245900 chr1D 95.409 501 18 3 3540 4036 283421098 283421597 0.000000e+00 793.0
33 TraesCS5D01G245900 chr1D 94.488 508 21 5 3540 4042 493775120 493775625 0.000000e+00 776.0
34 TraesCS5D01G245900 chr1D 91.803 61 4 1 3402 3462 225939198 225939257 4.270000e-12 84.2
35 TraesCS5D01G245900 chr6D 94.675 507 21 4 3537 4038 104329897 104330402 0.000000e+00 782.0
36 TraesCS5D01G245900 chr1B 93.939 132 8 0 3405 3536 119126419 119126550 4.060000e-47 200.0
37 TraesCS5D01G245900 chr1B 94.118 68 4 0 3335 3402 332083873 332083806 3.270000e-18 104.0
38 TraesCS5D01G245900 chr4A 89.655 145 15 0 3396 3540 330087257 330087401 1.140000e-42 185.0
39 TraesCS5D01G245900 chr4A 79.355 155 13 6 3400 3535 507971458 507971304 2.550000e-14 91.6
40 TraesCS5D01G245900 chr4A 90.625 64 6 0 3399 3462 594141864 594141927 1.190000e-12 86.1
41 TraesCS5D01G245900 chr3D 95.294 85 4 0 3452 3536 26165779 26165695 1.160000e-27 135.0
42 TraesCS5D01G245900 chr6B 95.775 71 3 0 3466 3536 127608675 127608605 1.510000e-21 115.0
43 TraesCS5D01G245900 chr6B 92.754 69 5 0 3334 3402 146149433 146149365 4.240000e-17 100.0
44 TraesCS5D01G245900 chr1A 94.118 68 4 0 3335 3402 307037678 307037745 3.270000e-18 104.0
45 TraesCS5D01G245900 chr6A 92.754 69 5 0 3334 3402 88080389 88080321 4.240000e-17 100.0


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 TraesCS5D01G245900 chr5D 354253406 354260043 6637 False 5735.500000 9590 100.000000 1 6638 2 chr5D.!!$F3 6637
1 TraesCS5D01G245900 chr5A 455081226 455089612 8386 False 1357.833333 2314 92.395500 16 6638 6 chr5A.!!$F2 6622
2 TraesCS5D01G245900 chr5B 418463593 418472424 8831 False 1023.442857 2233 94.902714 660 6638 7 chr5B.!!$F4 5978
3 TraesCS5D01G245900 chr2D 113047690 113048193 503 True 854.000000 854 97.421000 3540 4038 1 chr2D.!!$R1 498
4 TraesCS5D01G245900 chr2D 596815769 596816276 507 False 804.000000 804 95.294000 3540 4045 1 chr2D.!!$F2 505
5 TraesCS5D01G245900 chr7D 418618693 418619196 503 True 787.000000 787 95.050000 3540 4037 1 chr7D.!!$R1 497
6 TraesCS5D01G245900 chr7D 152081681 152082183 502 False 782.000000 782 94.841000 3538 4037 1 chr7D.!!$F1 499
7 TraesCS5D01G245900 chr1D 493775120 493775625 505 False 776.000000 776 94.488000 3540 4042 1 chr1D.!!$F3 502
8 TraesCS5D01G245900 chr6D 104329897 104330402 505 False 782.000000 782 94.675000 3537 4038 1 chr6D.!!$F1 501

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
482 483 0.321298 TGGTTTCGCTAGCTTGGTCC 60.321 55.000 13.93 9.17 0.00 4.46 F
1904 1909 0.395036 TTGGGGTTGGATATGGTGCG 60.395 55.000 0.00 0.00 0.00 5.34 F
2598 3498 0.453390 GTTGCAATCCTAGCAGTGGC 59.547 55.000 0.59 0.00 43.75 5.01 F
3302 4217 1.115467 CAGTTCCCATCCTACGAGCT 58.885 55.000 0.00 0.00 0.00 4.09 F
3521 4466 1.412710 CTAAGCGTCCAAGGCAGGATA 59.587 52.381 1.91 0.00 40.42 2.59 F
4914 10416 1.067635 GTGGTTGTGTCCATGCCAATC 60.068 52.381 0.00 0.00 39.81 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2472 2479 0.037590 TCGCTGCAATTACCCAAGGT 59.962 50.000 0.00 0.00 40.16 3.50 R
2749 3650 0.765510 AGAAGTCCCAGTTGTCCCAC 59.234 55.000 0.00 0.00 0.00 4.61 R
3464 4398 1.334869 GCAGCGCCTTACAAATATGCT 59.665 47.619 2.29 0.00 0.00 3.79 R
4896 10398 1.067635 GTGATTGGCATGGACACAACC 60.068 52.381 0.00 0.00 0.00 3.77 R
5304 11282 1.047801 ACCCATCCACTGGCAAAAAC 58.952 50.000 0.00 0.00 44.46 2.43 R
6409 12393 0.251386 TCTCGAACCTCTGCAGGAGT 60.251 55.000 15.13 8.86 43.65 3.85 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
24 25 3.888930 TGTCCTCAAGAACAAATGGAACC 59.111 43.478 0.00 0.00 0.00 3.62
32 33 1.686355 ACAAATGGAACCGCTGACAA 58.314 45.000 0.00 0.00 0.00 3.18
67 68 4.760530 TCATGATCAGAGGTTAGGGTTG 57.239 45.455 0.09 0.00 0.00 3.77
76 77 2.239907 GAGGTTAGGGTTGGCTTCAGAT 59.760 50.000 0.00 0.00 0.00 2.90
112 113 1.028868 GCTAAGGAGCTTGGCACCAG 61.029 60.000 8.51 0.08 45.20 4.00
145 146 3.929002 CCATGTGGTGGCCATCTG 58.071 61.111 18.94 7.19 42.12 2.90
146 147 2.420568 CCATGTGGTGGCCATCTGC 61.421 63.158 18.94 10.82 42.12 4.26
147 148 1.379443 CATGTGGTGGCCATCTGCT 60.379 57.895 18.94 0.00 40.92 4.24
148 149 0.968901 CATGTGGTGGCCATCTGCTT 60.969 55.000 18.94 5.68 40.92 3.91
159 160 2.354259 CCATCTGCTTCTTCAGGTCAC 58.646 52.381 0.00 0.00 34.91 3.67
191 192 2.303175 GACTGCTACTCCTAGAGGTGG 58.697 57.143 2.88 0.00 33.35 4.61
195 196 2.786445 TGCTACTCCTAGAGGTGGATCT 59.214 50.000 2.88 0.00 33.35 2.75
199 200 5.457052 GCTACTCCTAGAGGTGGATCTAGTT 60.457 48.000 9.30 0.00 44.93 2.24
212 213 8.432805 AGGTGGATCTAGTTATGGTTTCATTAG 58.567 37.037 0.00 0.00 34.96 1.73
220 221 9.817809 CTAGTTATGGTTTCATTAGTAAGCTCA 57.182 33.333 0.00 0.00 34.96 4.26
293 294 0.846427 TGGAAGGAGGGAATGTGGCT 60.846 55.000 0.00 0.00 0.00 4.75
300 301 1.559682 GAGGGAATGTGGCTGGTCTAA 59.440 52.381 0.00 0.00 0.00 2.10
311 312 2.838813 GGCTGGTCTAACTCTTACCCTT 59.161 50.000 0.00 0.00 31.97 3.95
314 315 4.439837 GCTGGTCTAACTCTTACCCTTACG 60.440 50.000 0.00 0.00 31.97 3.18
317 318 4.892345 GGTCTAACTCTTACCCTTACGGAT 59.108 45.833 0.00 0.00 34.64 4.18
345 346 0.611714 GCCCTAGGGAAACAAGACGA 59.388 55.000 33.21 0.00 37.50 4.20
346 347 1.405661 GCCCTAGGGAAACAAGACGAG 60.406 57.143 33.21 0.00 37.50 4.18
349 350 3.586892 CCTAGGGAAACAAGACGAGTTC 58.413 50.000 0.00 0.00 0.00 3.01
357 358 2.474816 ACAAGACGAGTTCAGTGCTTC 58.525 47.619 0.00 0.00 0.00 3.86
362 363 1.063806 CGAGTTCAGTGCTTCTTCGG 58.936 55.000 0.00 0.00 0.00 4.30
417 418 3.777818 GAGCTACCCCCTCCTCCCC 62.778 73.684 0.00 0.00 0.00 4.81
419 420 3.763757 CTACCCCCTCCTCCCCGT 61.764 72.222 0.00 0.00 0.00 5.28
462 463 2.079925 GTGGATCAACAACCTCTCTGC 58.920 52.381 0.00 0.00 0.00 4.26
479 480 1.796796 GCTGGTTTCGCTAGCTTGG 59.203 57.895 13.93 0.00 46.57 3.61
482 483 0.321298 TGGTTTCGCTAGCTTGGTCC 60.321 55.000 13.93 9.17 0.00 4.46
513 514 6.176183 CCTCTTCTTCAACCTTCACATGTAT 58.824 40.000 0.00 0.00 0.00 2.29
532 533 1.201429 TGTCCCTCTTCTCCTTGCCC 61.201 60.000 0.00 0.00 0.00 5.36
538 539 2.978278 CCTCTTCTCCTTGCCCTATGAT 59.022 50.000 0.00 0.00 0.00 2.45
539 540 3.007831 CCTCTTCTCCTTGCCCTATGATC 59.992 52.174 0.00 0.00 0.00 2.92
585 586 6.501781 GCTTCAGGATCCAATTGTATTCTTG 58.498 40.000 15.82 5.22 0.00 3.02
592 593 7.337942 AGGATCCAATTGTATTCTTGTTGTCTC 59.662 37.037 15.82 0.00 0.00 3.36
599 600 7.873719 TTGTATTCTTGTTGTCTCTTTTGGA 57.126 32.000 0.00 0.00 0.00 3.53
601 602 7.054124 TGTATTCTTGTTGTCTCTTTTGGAGT 58.946 34.615 0.00 0.00 42.40 3.85
606 607 3.142174 GTTGTCTCTTTTGGAGTCCTGG 58.858 50.000 11.33 0.00 42.40 4.45
609 610 3.202151 TGTCTCTTTTGGAGTCCTGGTTT 59.798 43.478 11.33 0.00 42.40 3.27
619 620 3.895041 GGAGTCCTGGTTTCAAAATGGAA 59.105 43.478 0.41 0.00 0.00 3.53
635 636 7.454380 TCAAAATGGAAGGACCTGATTGTAAAT 59.546 33.333 0.00 0.00 39.86 1.40
640 641 7.010160 TGGAAGGACCTGATTGTAAATTTTCT 58.990 34.615 0.00 0.00 39.86 2.52
678 680 1.441849 CGTTACACGCGTCGGGTTA 60.442 57.895 9.86 6.27 42.45 2.85
720 722 3.365265 GTTTGGCTGGGTGGAGCG 61.365 66.667 0.00 0.00 40.13 5.03
752 754 0.526211 GTGATCTGCCGGGAAAAACC 59.474 55.000 2.18 0.00 38.08 3.27
754 756 0.811281 GATCTGCCGGGAAAAACCTG 59.189 55.000 2.18 0.00 44.27 4.00
766 768 4.385825 GGAAAAACCTGAACCCAAATTCC 58.614 43.478 0.00 0.00 35.41 3.01
890 894 1.536662 GCCAGGATATCTCCCCCGT 60.537 63.158 2.05 0.00 43.21 5.28
949 954 3.615811 TCCCCCACTCCAGCCTCT 61.616 66.667 0.00 0.00 0.00 3.69
1004 1009 4.812476 CGTCCCCGCGAGCATGAA 62.812 66.667 8.23 0.00 0.00 2.57
1711 1716 0.903236 GTAAGAGGAGGTGGTGGGAC 59.097 60.000 0.00 0.00 0.00 4.46
1904 1909 0.395036 TTGGGGTTGGATATGGTGCG 60.395 55.000 0.00 0.00 0.00 5.34
1913 1918 5.277828 GGTTGGATATGGTGCGAATTCTTAC 60.278 44.000 3.52 2.37 0.00 2.34
1916 1921 6.061441 TGGATATGGTGCGAATTCTTACATT 58.939 36.000 3.52 0.00 0.00 2.71
1917 1922 6.545666 TGGATATGGTGCGAATTCTTACATTT 59.454 34.615 3.52 0.00 0.00 2.32
1939 1944 3.451141 TTGTTTGTGTGGCTTTGGATC 57.549 42.857 0.00 0.00 0.00 3.36
2213 2219 6.040391 ACTTGAGTTAAGGCTTGTTATTTGCA 59.960 34.615 10.69 0.00 40.84 4.08
2219 2225 4.192429 AGGCTTGTTATTTGCAACCATC 57.808 40.909 0.00 0.00 0.00 3.51
2255 2261 7.327032 GCTGTGATGAATTCTTACTTTGGAAAC 59.673 37.037 7.05 0.00 0.00 2.78
2266 2272 7.957002 TCTTACTTTGGAAACATAATTTGCCA 58.043 30.769 0.00 0.00 42.32 4.92
2281 2287 0.687920 TGCCATACAACCTTCACCGA 59.312 50.000 0.00 0.00 0.00 4.69
2310 2316 2.098831 GTTACTGGTCGAAGCCCGC 61.099 63.158 0.00 0.00 38.37 6.13
2314 2320 2.992689 TGGTCGAAGCCCGCTGTA 60.993 61.111 0.00 0.00 38.37 2.74
2322 2328 2.737359 CGAAGCCCGCTGTAGTTATGAA 60.737 50.000 0.00 0.00 0.00 2.57
2327 2333 5.433526 AGCCCGCTGTAGTTATGAAAATAA 58.566 37.500 0.00 0.00 0.00 1.40
2330 2336 6.204882 GCCCGCTGTAGTTATGAAAATAAGAT 59.795 38.462 0.00 0.00 0.00 2.40
2472 2479 7.397476 ACTCACATTTAGAACTGGATCAGTAGA 59.603 37.037 0.67 0.00 44.62 2.59
2514 2522 5.705609 AGTCGATAAATTTTGTGGTGCTT 57.294 34.783 0.00 0.00 0.00 3.91
2595 3495 4.826274 TCTTAGTTGCAATCCTAGCAGT 57.174 40.909 0.59 0.00 43.75 4.40
2598 3498 0.453390 GTTGCAATCCTAGCAGTGGC 59.547 55.000 0.59 0.00 43.75 5.01
2601 3501 2.182842 CAATCCTAGCAGTGGCCGC 61.183 63.158 8.71 8.71 42.56 6.53
2602 3502 2.669133 AATCCTAGCAGTGGCCGCA 61.669 57.895 20.59 0.00 42.56 5.69
2603 3503 2.196997 AATCCTAGCAGTGGCCGCAA 62.197 55.000 20.59 0.00 42.56 4.85
2604 3504 2.876368 ATCCTAGCAGTGGCCGCAAC 62.876 60.000 20.59 9.94 42.56 4.17
2659 3559 5.244785 TCGGCAGACTATAGTTAACACAG 57.755 43.478 6.88 4.14 0.00 3.66
2670 3570 4.320608 AGTTAACACAGCACATTTTGGG 57.679 40.909 8.61 0.00 0.00 4.12
2671 3571 3.704061 AGTTAACACAGCACATTTTGGGT 59.296 39.130 8.61 0.00 30.80 4.51
2672 3572 2.600470 AACACAGCACATTTTGGGTG 57.400 45.000 0.00 0.00 39.25 4.61
2673 3573 1.774110 ACACAGCACATTTTGGGTGA 58.226 45.000 0.00 0.00 38.54 4.02
2674 3574 1.682854 ACACAGCACATTTTGGGTGAG 59.317 47.619 0.00 0.00 38.54 3.51
2675 3575 1.955778 CACAGCACATTTTGGGTGAGA 59.044 47.619 0.00 0.00 38.54 3.27
2677 3577 3.006110 CACAGCACATTTTGGGTGAGATT 59.994 43.478 0.00 0.00 38.54 2.40
2699 3600 8.705594 AGATTGGTACTGCATAAACTACATACT 58.294 33.333 0.00 0.00 0.00 2.12
2732 3633 8.976471 CAATTATGTAGCTCTTGACATGTAGAG 58.024 37.037 17.83 17.83 40.66 2.43
2749 3650 9.823647 ACATGTAGAGGAATAACTAGTCAATTG 57.176 33.333 0.00 0.00 0.00 2.32
2782 3683 4.162320 TGGGACTTCTGTTAGCCTAGAATG 59.838 45.833 0.00 0.00 32.92 2.67
3017 3924 6.715280 ACATCTGACACTTAATTCTGTGGAT 58.285 36.000 13.13 5.81 38.39 3.41
3233 4148 3.717294 CCTTCCCCACCTCCACCG 61.717 72.222 0.00 0.00 0.00 4.94
3240 4155 3.941188 CACCTCCACCGCACACCT 61.941 66.667 0.00 0.00 0.00 4.00
3254 4169 2.936032 ACCTCCTTCACCCCCAGC 60.936 66.667 0.00 0.00 0.00 4.85
3302 4217 1.115467 CAGTTCCCATCCTACGAGCT 58.885 55.000 0.00 0.00 0.00 4.09
3464 4398 2.721945 GCTCTAGCGCCTAAGGAGA 58.278 57.895 2.29 0.00 0.00 3.71
3521 4466 1.412710 CTAAGCGTCCAAGGCAGGATA 59.587 52.381 1.91 0.00 40.42 2.59
3614 4561 1.981256 ACCTGTTGTGATTGACCCAC 58.019 50.000 0.00 0.00 35.23 4.61
4073 5029 9.945904 AGAGGGAGTATGTTAAAGAGTAAAAAG 57.054 33.333 0.00 0.00 0.00 2.27
4345 5302 1.468054 GCGCCAGCAAAATAAGGAGTG 60.468 52.381 0.00 0.00 44.35 3.51
4596 7798 2.686715 GCCCCACCTACTGCACATATTT 60.687 50.000 0.00 0.00 0.00 1.40
4779 10281 2.845363 TTTCGGGTAGTGGGAACTTC 57.155 50.000 0.00 0.00 0.00 3.01
4831 10333 3.486383 TGTGTTTGGATTTGAGTCCTCC 58.514 45.455 0.00 0.00 39.12 4.30
4859 10361 4.268884 GCTCGTCAAATCTAAGCCAGTTAG 59.731 45.833 0.00 0.00 39.80 2.34
4896 10398 1.284982 CGACAGTTCTCAAGGCCGTG 61.285 60.000 13.08 13.08 0.00 4.94
4914 10416 1.067635 GTGGTTGTGTCCATGCCAATC 60.068 52.381 0.00 0.00 39.81 2.67
5032 10535 3.117738 CCAGATTCCTTGAGCCTAACCAT 60.118 47.826 0.00 0.00 0.00 3.55
5040 10543 3.408157 TGAGCCTAACCATGGGTAGTA 57.592 47.619 30.67 14.34 33.12 1.82
5069 10573 8.060075 AGGTTATGCTATATCCTACGGACTATT 58.940 37.037 0.00 0.00 32.98 1.73
5097 10601 3.944015 TGTTGGAAAAGGTGCAAAAATGG 59.056 39.130 0.00 0.00 39.54 3.16
5104 10608 6.317642 GGAAAAGGTGCAAAAATGGTAAAAGT 59.682 34.615 0.00 0.00 0.00 2.66
5105 10609 7.496263 GGAAAAGGTGCAAAAATGGTAAAAGTA 59.504 33.333 0.00 0.00 0.00 2.24
5106 10610 7.780008 AAAGGTGCAAAAATGGTAAAAGTAC 57.220 32.000 0.00 0.00 0.00 2.73
5107 10611 6.472686 AGGTGCAAAAATGGTAAAAGTACA 57.527 33.333 0.00 0.00 31.21 2.90
5109 10613 6.983890 AGGTGCAAAAATGGTAAAAGTACAAG 59.016 34.615 0.00 0.00 31.21 3.16
5137 10641 7.609760 GGTCTGAACCAAAATGTTTTTCTTT 57.390 32.000 0.00 0.00 45.68 2.52
5138 10642 8.039603 GGTCTGAACCAAAATGTTTTTCTTTT 57.960 30.769 0.00 0.00 45.68 2.27
5139 10643 8.511321 GGTCTGAACCAAAATGTTTTTCTTTTT 58.489 29.630 0.00 0.00 45.68 1.94
5172 11042 3.372822 CCCTGAAATGCATCAAATGTTGC 59.627 43.478 0.00 9.05 40.24 4.17
5215 11180 9.525409 GTGATACTAACTAATAACGACCACAAT 57.475 33.333 0.00 0.00 0.00 2.71
5259 11232 6.415573 ACCTGATACATGGAAGGTTAAACTC 58.584 40.000 0.00 0.00 40.14 3.01
5304 11282 5.018539 TGGAGGTGTCTTACATTATTCCG 57.981 43.478 0.00 0.00 0.00 4.30
5459 11437 5.355071 TCTTGACATCTTGTTCATACCATGC 59.645 40.000 0.00 0.00 0.00 4.06
5506 11484 6.549952 CATTCAGTACATTCCTTCTGAAAGC 58.450 40.000 9.82 0.00 45.58 3.51
5515 11493 3.632333 TCCTTCTGAAAGCGATCTAGGA 58.368 45.455 0.00 0.00 0.00 2.94
5580 11558 6.431198 TTTGTAGGCTATGTTCGGAAAATC 57.569 37.500 0.00 0.00 0.00 2.17
5589 11567 3.666274 TGTTCGGAAAATCACATACCGT 58.334 40.909 0.00 0.00 43.36 4.83
5619 11597 6.897986 AGCTGAAAATCTGGATGAGTTAGAT 58.102 36.000 0.00 0.00 32.22 1.98
5660 11638 0.385390 GTTGGTGCTGTCTGTTTGGG 59.615 55.000 0.00 0.00 0.00 4.12
5663 11641 1.150536 GTGCTGTCTGTTTGGGGGA 59.849 57.895 0.00 0.00 0.00 4.81
5668 11646 1.149854 GTCTGTTTGGGGGACGGTT 59.850 57.895 0.00 0.00 0.00 4.44
5701 11679 5.772521 ACTGGTGCTGAATATTTTGTGTTC 58.227 37.500 0.00 0.00 0.00 3.18
5708 11686 7.860373 GTGCTGAATATTTTGTGTTCACTACAA 59.140 33.333 4.59 0.00 38.80 2.41
5709 11687 8.409371 TGCTGAATATTTTGTGTTCACTACAAA 58.591 29.630 4.59 0.00 43.88 2.83
5723 11701 8.134895 TGTTCACTACAAATGATTCTTTTCACC 58.865 33.333 0.00 0.00 32.64 4.02
5729 11707 6.275335 ACAAATGATTCTTTTCACCACACAG 58.725 36.000 0.00 0.00 0.00 3.66
5746 11724 4.516698 CACACAGTTTCTATTTCAGGCACT 59.483 41.667 0.00 0.00 43.88 4.40
5781 11759 6.552350 AGGATGCCATTCTTTAAGCATTGTAT 59.448 34.615 0.00 0.00 45.57 2.29
5783 11761 8.359642 GGATGCCATTCTTTAAGCATTGTATAA 58.640 33.333 0.00 0.00 45.57 0.98
5784 11762 9.748708 GATGCCATTCTTTAAGCATTGTATAAA 57.251 29.630 0.00 0.00 45.57 1.40
5785 11763 8.925161 TGCCATTCTTTAAGCATTGTATAAAC 57.075 30.769 0.00 0.00 0.00 2.01
5904 11883 2.576615 GCTTTGGACCAGTTCTCAAGT 58.423 47.619 0.00 0.00 0.00 3.16
5913 11892 5.365619 GACCAGTTCTCAAGTAACCTTTCA 58.634 41.667 0.00 0.00 0.00 2.69
6104 12088 2.009051 TCTGTTCAGCACACAACAGTG 58.991 47.619 10.71 0.00 46.51 3.66
6175 12159 3.699411 ATAGCCTTCTCCATCATCTGC 57.301 47.619 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.524328 GGTTCCATTTGTTCTTGAGGACAT 59.476 41.667 0.00 0.00 0.00 3.06
2 3 3.888930 GGTTCCATTTGTTCTTGAGGACA 59.111 43.478 0.00 0.00 0.00 4.02
3 4 3.058224 CGGTTCCATTTGTTCTTGAGGAC 60.058 47.826 0.00 0.00 0.00 3.85
4 5 3.146066 CGGTTCCATTTGTTCTTGAGGA 58.854 45.455 0.00 0.00 0.00 3.71
5 6 2.351738 GCGGTTCCATTTGTTCTTGAGG 60.352 50.000 0.00 0.00 0.00 3.86
6 7 2.554032 AGCGGTTCCATTTGTTCTTGAG 59.446 45.455 0.00 0.00 0.00 3.02
7 8 2.293122 CAGCGGTTCCATTTGTTCTTGA 59.707 45.455 0.00 0.00 0.00 3.02
8 9 2.293122 TCAGCGGTTCCATTTGTTCTTG 59.707 45.455 0.00 0.00 0.00 3.02
9 10 2.293399 GTCAGCGGTTCCATTTGTTCTT 59.707 45.455 0.00 0.00 0.00 2.52
10 11 1.880027 GTCAGCGGTTCCATTTGTTCT 59.120 47.619 0.00 0.00 0.00 3.01
11 12 1.606668 TGTCAGCGGTTCCATTTGTTC 59.393 47.619 0.00 0.00 0.00 3.18
12 13 1.686355 TGTCAGCGGTTCCATTTGTT 58.314 45.000 0.00 0.00 0.00 2.83
13 14 1.686355 TTGTCAGCGGTTCCATTTGT 58.314 45.000 0.00 0.00 0.00 2.83
14 15 2.664916 CTTTGTCAGCGGTTCCATTTG 58.335 47.619 0.00 0.00 0.00 2.32
42 43 4.723789 ACCCTAACCTCTGATCATGAACAT 59.276 41.667 6.09 0.00 0.00 2.71
115 116 0.733150 CACATGGTGCAGCTCATGAG 59.267 55.000 25.65 18.84 42.25 2.90
138 139 1.339438 TGACCTGAAGAAGCAGATGGC 60.339 52.381 0.00 0.00 45.30 4.40
141 142 1.066573 CGGTGACCTGAAGAAGCAGAT 60.067 52.381 0.00 0.00 38.14 2.90
145 146 0.670854 GGACGGTGACCTGAAGAAGC 60.671 60.000 0.00 0.00 0.00 3.86
146 147 0.388649 CGGACGGTGACCTGAAGAAG 60.389 60.000 0.00 0.00 0.00 2.85
147 148 1.111116 ACGGACGGTGACCTGAAGAA 61.111 55.000 0.00 0.00 0.00 2.52
148 149 1.529948 ACGGACGGTGACCTGAAGA 60.530 57.895 0.00 0.00 0.00 2.87
199 200 6.257849 CGCTTGAGCTTACTAATGAAACCATA 59.742 38.462 1.07 0.00 39.32 2.74
212 213 2.453638 GGCGACCGCTTGAGCTTAC 61.454 63.158 14.25 0.00 41.60 2.34
220 221 0.603569 CCTAGATATGGCGACCGCTT 59.396 55.000 14.25 5.16 41.60 4.68
311 312 3.581332 CCTAGGGCTTATTGGAATCCGTA 59.419 47.826 0.00 0.00 0.00 4.02
314 315 2.986728 TCCCTAGGGCTTATTGGAATCC 59.013 50.000 24.42 0.00 34.68 3.01
317 318 3.594232 TGTTTCCCTAGGGCTTATTGGAA 59.406 43.478 24.42 6.57 34.68 3.53
345 346 0.106708 TGCCGAAGAAGCACTGAACT 59.893 50.000 0.00 0.00 34.69 3.01
346 347 0.944386 TTGCCGAAGAAGCACTGAAC 59.056 50.000 0.00 0.00 40.69 3.18
349 350 1.446907 ATCTTGCCGAAGAAGCACTG 58.553 50.000 0.00 0.00 41.64 3.66
357 358 5.385617 CAGTGTAAGAAAATCTTGCCGAAG 58.614 41.667 2.94 0.00 38.15 3.79
362 363 7.114953 GGTTAAAGCAGTGTAAGAAAATCTTGC 59.885 37.037 2.94 2.35 37.29 4.01
417 418 3.504043 CATTCATTGCAGCTCGACG 57.496 52.632 0.00 0.00 0.00 5.12
427 428 4.209538 TGATCCACCCTAAGCATTCATTG 58.790 43.478 0.00 0.00 0.00 2.82
462 463 1.079503 GACCAAGCTAGCGAAACCAG 58.920 55.000 9.55 0.00 0.00 4.00
479 480 1.556911 TGAAGAAGAGGGCATCAGGAC 59.443 52.381 0.58 0.00 0.00 3.85
482 483 2.026449 AGGTTGAAGAAGAGGGCATCAG 60.026 50.000 0.58 0.00 0.00 2.90
513 514 1.201429 GGGCAAGGAGAAGAGGGACA 61.201 60.000 0.00 0.00 0.00 4.02
585 586 3.142174 CCAGGACTCCAAAAGAGACAAC 58.858 50.000 0.00 0.00 46.50 3.32
592 593 5.337578 TTTTGAAACCAGGACTCCAAAAG 57.662 39.130 0.00 0.00 32.12 2.27
599 600 3.897505 CCTTCCATTTTGAAACCAGGACT 59.102 43.478 0.00 0.00 0.00 3.85
601 602 3.895041 GTCCTTCCATTTTGAAACCAGGA 59.105 43.478 0.00 0.00 0.00 3.86
606 607 5.728637 ATCAGGTCCTTCCATTTTGAAAC 57.271 39.130 0.00 0.00 39.02 2.78
609 610 4.739793 ACAATCAGGTCCTTCCATTTTGA 58.260 39.130 0.00 0.00 39.02 2.69
619 620 6.472887 TCGAGAAAATTTACAATCAGGTCCT 58.527 36.000 0.00 0.00 0.00 3.85
635 636 1.425412 GGTACTTGCGCTCGAGAAAA 58.575 50.000 18.75 5.66 0.00 2.29
720 722 2.202570 ATCACACTACGCGGTCGC 60.203 61.111 12.47 5.16 39.84 5.19
752 754 2.928694 CGTTTCGGAATTTGGGTTCAG 58.071 47.619 0.00 0.00 0.00 3.02
890 894 3.369410 ATAGGTGGGGACGGCGAGA 62.369 63.158 16.62 0.00 0.00 4.04
900 904 0.764752 GGAGGAGGGTGATAGGTGGG 60.765 65.000 0.00 0.00 0.00 4.61
1450 1455 4.787280 AGGGAGAGGAGCGGGGTG 62.787 72.222 0.00 0.00 0.00 4.61
1451 1456 4.787280 CAGGGAGAGGAGCGGGGT 62.787 72.222 0.00 0.00 0.00 4.95
1711 1716 3.612247 CTTGTCCCTGGACCAGCGG 62.612 68.421 16.72 17.69 43.97 5.52
1865 1870 5.137403 CCAAATAACTCGAAAACACAGACG 58.863 41.667 0.00 0.00 0.00 4.18
1916 1921 4.008074 TCCAAAGCCACACAAACAAAAA 57.992 36.364 0.00 0.00 0.00 1.94
1917 1922 3.685139 TCCAAAGCCACACAAACAAAA 57.315 38.095 0.00 0.00 0.00 2.44
1939 1944 3.242413 CGAAACCATCTTGCATTCCTACG 60.242 47.826 0.00 0.00 0.00 3.51
2188 2194 6.040391 TGCAAATAACAAGCCTTAACTCAAGT 59.960 34.615 0.00 0.00 31.77 3.16
2213 2219 2.555325 CACAGCAACATCACAGATGGTT 59.445 45.455 11.29 1.67 0.00 3.67
2219 2225 4.696899 ATTCATCACAGCAACATCACAG 57.303 40.909 0.00 0.00 0.00 3.66
2255 2261 6.042143 GGTGAAGGTTGTATGGCAAATTATG 58.958 40.000 0.00 0.00 39.03 1.90
2266 2272 1.346395 TGCTGTCGGTGAAGGTTGTAT 59.654 47.619 0.00 0.00 0.00 2.29
2301 2307 1.202371 TCATAACTACAGCGGGCTTCG 60.202 52.381 0.00 0.00 42.76 3.79
2327 2333 7.264294 ACTTAAAAACAGAGATGGAGGATCT 57.736 36.000 0.00 0.00 44.78 2.75
2330 2336 5.473504 GCAACTTAAAAACAGAGATGGAGGA 59.526 40.000 0.00 0.00 0.00 3.71
2384 2390 0.319813 GTGAACTTGGTGCCATTGCC 60.320 55.000 0.00 0.00 36.33 4.52
2391 2397 1.061131 CGATCATCGTGAACTTGGTGC 59.939 52.381 0.00 0.00 34.72 5.01
2472 2479 0.037590 TCGCTGCAATTACCCAAGGT 59.962 50.000 0.00 0.00 40.16 3.50
2595 3495 1.093972 CATCAGTATTGTTGCGGCCA 58.906 50.000 2.24 0.00 0.00 5.36
2598 3498 2.223112 GCTGTCATCAGTATTGTTGCGG 60.223 50.000 0.00 0.00 43.05 5.69
2634 3534 7.337480 TGTGTTAACTATAGTCTGCCGATTA 57.663 36.000 5.70 0.00 0.00 1.75
2639 3539 4.567159 GTGCTGTGTTAACTATAGTCTGCC 59.433 45.833 5.70 0.84 0.00 4.85
2640 3540 5.168569 TGTGCTGTGTTAACTATAGTCTGC 58.831 41.667 5.70 9.25 0.00 4.26
2641 3541 7.834068 AATGTGCTGTGTTAACTATAGTCTG 57.166 36.000 5.70 0.00 0.00 3.51
2650 3550 3.801594 CACCCAAAATGTGCTGTGTTAAC 59.198 43.478 0.00 0.00 0.00 2.01
2659 3559 2.299867 ACCAATCTCACCCAAAATGTGC 59.700 45.455 0.00 0.00 33.71 4.57
2670 3570 6.816640 TGTAGTTTATGCAGTACCAATCTCAC 59.183 38.462 0.00 0.00 0.00 3.51
2671 3571 6.941857 TGTAGTTTATGCAGTACCAATCTCA 58.058 36.000 0.00 0.00 0.00 3.27
2672 3572 8.979574 GTATGTAGTTTATGCAGTACCAATCTC 58.020 37.037 0.00 0.00 0.00 2.75
2673 3573 8.705594 AGTATGTAGTTTATGCAGTACCAATCT 58.294 33.333 0.00 0.00 0.00 2.40
2674 3574 8.765219 CAGTATGTAGTTTATGCAGTACCAATC 58.235 37.037 0.00 0.00 0.00 2.67
2675 3575 8.662781 CAGTATGTAGTTTATGCAGTACCAAT 57.337 34.615 0.00 0.00 0.00 3.16
2732 3633 6.177610 TGTCCCACAATTGACTAGTTATTCC 58.822 40.000 13.59 0.00 32.67 3.01
2749 3650 0.765510 AGAAGTCCCAGTTGTCCCAC 59.234 55.000 0.00 0.00 0.00 4.61
2782 3683 7.476667 AGATACGACAGACTAATGCATATAGC 58.523 38.462 0.00 1.86 45.96 2.97
3017 3924 7.824289 GCCAGCTATCTGTCATAAACCATAATA 59.176 37.037 0.00 0.00 38.66 0.98
3027 3934 3.899980 ACATCTGCCAGCTATCTGTCATA 59.100 43.478 0.00 0.00 38.66 2.15
3233 4148 2.034221 GGGGTGAAGGAGGTGTGC 59.966 66.667 0.00 0.00 0.00 4.57
3240 4155 2.121963 ACAGCTGGGGGTGAAGGA 60.122 61.111 19.93 0.00 42.91 3.36
3254 4169 3.004629 TGCTATTGTTTTCAGTGGCACAG 59.995 43.478 21.41 12.62 45.48 3.66
3391 4306 9.793245 CGCCTTATAAACAAAGAATATAAGACG 57.207 33.333 11.45 8.83 39.98 4.18
3462 4396 2.874701 CAGCGCCTTACAAATATGCTCT 59.125 45.455 2.29 0.00 0.00 4.09
3464 4398 1.334869 GCAGCGCCTTACAAATATGCT 59.665 47.619 2.29 0.00 0.00 3.79
4195 5151 9.542462 TCTAGATATTACAGGTGTTACATTTGC 57.458 33.333 0.00 0.00 0.00 3.68
4523 7725 9.193806 AGTGTGCCATTCTTGATATTTCTTTAT 57.806 29.630 0.00 0.00 0.00 1.40
4779 10281 7.194278 TCTTTCGTCTAATCAACTTCCTATCG 58.806 38.462 0.00 0.00 0.00 2.92
4831 10333 2.349886 GCTTAGATTTGACGAGCTGGTG 59.650 50.000 5.94 0.00 0.00 4.17
4896 10398 1.067635 GTGATTGGCATGGACACAACC 60.068 52.381 0.00 0.00 0.00 3.77
5032 10535 3.700863 AGCATAACCTCCTACTACCCA 57.299 47.619 0.00 0.00 0.00 4.51
5069 10573 3.295093 TGCACCTTTTCCAACATCTTCA 58.705 40.909 0.00 0.00 0.00 3.02
5137 10641 3.390175 TTTCAGGGTTCCACTGGAAAA 57.610 42.857 12.33 0.08 43.86 2.29
5138 10642 3.230134 CATTTCAGGGTTCCACTGGAAA 58.770 45.455 12.33 0.00 43.86 3.13
5139 10643 2.875296 CATTTCAGGGTTCCACTGGAA 58.125 47.619 6.39 6.39 39.66 3.53
5140 10644 1.547675 GCATTTCAGGGTTCCACTGGA 60.548 52.381 0.00 0.00 36.62 3.86
5142 10646 1.619654 TGCATTTCAGGGTTCCACTG 58.380 50.000 0.00 0.00 37.30 3.66
5143 10647 2.225091 TGATGCATTTCAGGGTTCCACT 60.225 45.455 0.00 0.00 0.00 4.00
5144 10648 2.170166 TGATGCATTTCAGGGTTCCAC 58.830 47.619 0.00 0.00 0.00 4.02
5145 10649 2.601240 TGATGCATTTCAGGGTTCCA 57.399 45.000 0.00 0.00 0.00 3.53
5215 11180 6.436218 TCAGGTCAGAATAGTTGCAGTACTAA 59.564 38.462 2.47 0.00 34.50 2.24
5259 11232 3.132160 GTCATGTGCAGATCTCATCAGG 58.868 50.000 0.00 0.00 0.00 3.86
5304 11282 1.047801 ACCCATCCACTGGCAAAAAC 58.952 50.000 0.00 0.00 44.46 2.43
5403 11381 2.564947 ACAAGCTCTACTGGAAGGTCTG 59.435 50.000 0.00 0.00 39.30 3.51
5474 11452 5.473931 AGGAATGTACTGAATGCTATAGCG 58.526 41.667 19.55 7.56 45.83 4.26
5480 11458 5.426689 TCAGAAGGAATGTACTGAATGCT 57.573 39.130 0.00 0.00 36.63 3.79
5506 11484 4.647424 AAAGAAGTCAGCTCCTAGATCG 57.353 45.455 0.00 0.00 0.00 3.69
5515 11493 2.659428 AGGCACAAAAAGAAGTCAGCT 58.341 42.857 0.00 0.00 0.00 4.24
5589 11567 2.269023 TCCAGATTTTCAGCTCCCTCA 58.731 47.619 0.00 0.00 0.00 3.86
5619 11597 6.086011 ACAAATTATGGTGGTCTCCCATTA 57.914 37.500 0.00 0.00 44.35 1.90
5660 11638 6.678655 GCACCAGTTAATAAAATAACCGTCCC 60.679 42.308 0.00 0.00 36.62 4.46
5663 11641 6.655848 TCAGCACCAGTTAATAAAATAACCGT 59.344 34.615 0.00 0.00 36.62 4.83
5692 11670 9.868277 AAAGAATCATTTGTAGTGAACACAAAA 57.132 25.926 7.68 5.58 45.95 2.44
5693 11671 9.868277 AAAAGAATCATTTGTAGTGAACACAAA 57.132 25.926 7.68 3.39 46.64 2.83
5701 11679 7.379529 GTGTGGTGAAAAGAATCATTTGTAGTG 59.620 37.037 0.00 0.00 0.00 2.74
5708 11686 6.469782 AACTGTGTGGTGAAAAGAATCATT 57.530 33.333 0.00 0.00 0.00 2.57
5709 11687 6.322201 AGAAACTGTGTGGTGAAAAGAATCAT 59.678 34.615 0.00 0.00 0.00 2.45
5723 11701 4.516698 AGTGCCTGAAATAGAAACTGTGTG 59.483 41.667 0.00 0.00 0.00 3.82
5729 11707 5.122396 CCTGTACAGTGCCTGAAATAGAAAC 59.878 44.000 21.18 0.00 35.18 2.78
5746 11724 3.266772 AGAATGGCATCCTTTCCTGTACA 59.733 43.478 0.00 0.00 38.10 2.90
5755 11733 5.188359 ACAATGCTTAAAGAATGGCATCCTT 59.812 36.000 0.00 0.00 43.39 3.36
5788 11766 9.355215 CGTGTACAATAACTAGACAGAAAAGAT 57.645 33.333 0.00 0.00 0.00 2.40
5790 11768 7.328737 AGCGTGTACAATAACTAGACAGAAAAG 59.671 37.037 0.00 0.00 0.00 2.27
5875 11853 2.005451 CTGGTCCAAAGCGATCTCTTG 58.995 52.381 0.00 0.00 0.00 3.02
6104 12088 3.570125 GCCCTTGATGAAGGTTTATAGGC 59.430 47.826 10.28 0.47 46.84 3.93
6292 12276 4.021925 GACTGCTGCCGGTCCCTT 62.022 66.667 1.90 0.00 40.73 3.95
6314 12298 3.056179 TCGTCAGGCTTGTACATCATCAA 60.056 43.478 0.00 0.00 0.00 2.57
6409 12393 0.251386 TCTCGAACCTCTGCAGGAGT 60.251 55.000 15.13 8.86 43.65 3.85
6601 12585 1.433879 GACGTCCATCACCTCCTCG 59.566 63.158 3.51 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.