Multiple sequence alignment - TraesCS1A01G266100

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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 TraesCS1A01G266100 chr1A 100.000 4144 0 0 1 4144 461644961 461640818 0.000000e+00 7653.0
1 TraesCS1A01G266100 chr1A 88.166 938 77 14 804 1722 461524232 461523310 0.000000e+00 1086.0
2 TraesCS1A01G266100 chr1A 86.612 732 93 5 2545 3273 461522602 461521873 0.000000e+00 804.0
3 TraesCS1A01G266100 chr1A 77.670 618 106 19 1121 1710 573033373 573032760 8.530000e-92 348.0
4 TraesCS1A01G266100 chr1A 79.537 259 43 9 232 488 566041124 566041374 4.260000e-40 176.0
5 TraesCS1A01G266100 chr1D 95.795 1831 40 10 2335 4144 362131222 362129408 0.000000e+00 2920.0
6 TraesCS1A01G266100 chr1D 95.573 1039 36 7 753 1788 362132817 362131786 0.000000e+00 1655.0
7 TraesCS1A01G266100 chr1D 88.584 946 71 11 798 1722 362013419 362012490 0.000000e+00 1114.0
8 TraesCS1A01G266100 chr1D 85.679 810 103 12 2544 3348 362010696 362009895 0.000000e+00 841.0
9 TraesCS1A01G266100 chr1D 87.121 528 30 17 1840 2336 362131795 362131275 7.780000e-157 564.0
10 TraesCS1A01G266100 chr1B 90.590 1796 86 29 1 1788 484693788 484692068 0.000000e+00 2303.0
11 TraesCS1A01G266100 chr1B 92.612 961 66 4 3189 4144 484690002 484689042 0.000000e+00 1376.0
12 TraesCS1A01G266100 chr1B 91.613 930 69 9 2410 3335 484691258 484690334 0.000000e+00 1277.0
13 TraesCS1A01G266100 chr1B 88.173 947 73 13 798 1722 484465437 484464508 0.000000e+00 1092.0
14 TraesCS1A01G266100 chr1B 86.267 801 97 12 2544 3338 484463754 484462961 0.000000e+00 857.0
15 TraesCS1A01G266100 chr1B 93.117 247 14 2 1840 2083 484692077 484691831 3.940000e-95 359.0
16 TraesCS1A01G266100 chr1B 80.328 122 24 0 2543 2664 656183494 656183615 4.410000e-15 93.5
17 TraesCS1A01G266100 chr1B 100.000 45 0 0 2124 2168 484691701 484691657 2.650000e-12 84.2
18 TraesCS1A01G266100 chr1B 91.071 56 4 1 1781 1836 37800623 37800569 1.600000e-09 75.0
19 TraesCS1A01G266100 chr1B 95.745 47 1 1 2365 2410 484691409 484691363 1.600000e-09 75.0
20 TraesCS1A01G266100 chr4B 82.724 301 33 10 245 542 4550568 4550852 2.470000e-62 250.0
21 TraesCS1A01G266100 chr4B 81.200 250 37 5 241 488 481005306 481005065 4.230000e-45 193.0
22 TraesCS1A01G266100 chr4D 80.968 310 43 11 241 546 93436750 93437047 8.960000e-57 231.0
23 TraesCS1A01G266100 chr4D 77.328 247 35 12 283 529 7766155 7765930 4.350000e-25 126.0
24 TraesCS1A01G266100 chr7B 80.844 308 43 7 240 547 528751272 528751563 1.160000e-55 228.0
25 TraesCS1A01G266100 chr7B 79.688 128 14 6 434 561 368196076 368195961 9.550000e-12 82.4
26 TraesCS1A01G266100 chr7D 79.641 334 51 7 228 559 500618653 500618971 1.500000e-54 224.0
27 TraesCS1A01G266100 chr7D 92.727 55 4 0 1784 1838 509201650 509201704 3.430000e-11 80.5
28 TraesCS1A01G266100 chr7D 95.918 49 2 0 1788 1836 552322045 552321997 3.430000e-11 80.5
29 TraesCS1A01G266100 chr2B 79.677 310 36 17 241 546 272773498 272773784 9.090000e-47 198.0
30 TraesCS1A01G266100 chr2B 94.915 59 2 1 1778 1836 231671588 231671531 1.590000e-14 91.6
31 TraesCS1A01G266100 chr4A 82.710 214 27 5 278 488 654105300 654105094 9.150000e-42 182.0
32 TraesCS1A01G266100 chr4A 92.727 55 3 1 1784 1838 75354992 75354939 1.240000e-10 78.7
33 TraesCS1A01G266100 chr4A 91.071 56 3 1 1781 1836 684272635 684272688 1.600000e-09 75.0
34 TraesCS1A01G266100 chr5A 77.640 322 54 10 241 559 121412055 121411749 3.290000e-41 180.0
35 TraesCS1A01G266100 chr5A 79.079 239 39 11 241 476 216673357 216673587 1.990000e-33 154.0
36 TraesCS1A01G266100 chr5A 83.333 108 12 1 373 480 703005265 703005366 1.230000e-15 95.3
37 TraesCS1A01G266100 chr6A 86.316 95 12 1 35 128 32030441 32030347 7.330000e-18 102.0
38 TraesCS1A01G266100 chr6A 90.164 61 4 2 1777 1836 46592889 46592948 1.240000e-10 78.7
39 TraesCS1A01G266100 chr7A 91.667 60 3 2 1778 1836 666991563 666991621 9.550000e-12 82.4
40 TraesCS1A01G266100 chr3A 91.228 57 5 0 1780 1836 688594503 688594559 1.240000e-10 78.7
41 TraesCS1A01G266100 chr2A 89.474 57 3 3 239 292 706204719 706204663 7.430000e-08 69.4
42 TraesCS1A01G266100 chr6D 85.714 56 8 0 5 60 317746653 317746598 4.470000e-05 60.2
43 TraesCS1A01G266100 chr5D 94.286 35 2 0 26 60 306659746 306659712 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 TraesCS1A01G266100 chr1A 461640818 461644961 4143 True 7653.000000 7653 100.000000 1 4144 1 chr1A.!!$R1 4143
1 TraesCS1A01G266100 chr1A 461521873 461524232 2359 True 945.000000 1086 87.389000 804 3273 2 chr1A.!!$R3 2469
2 TraesCS1A01G266100 chr1A 573032760 573033373 613 True 348.000000 348 77.670000 1121 1710 1 chr1A.!!$R2 589
3 TraesCS1A01G266100 chr1D 362129408 362132817 3409 True 1713.000000 2920 92.829667 753 4144 3 chr1D.!!$R2 3391
4 TraesCS1A01G266100 chr1D 362009895 362013419 3524 True 977.500000 1114 87.131500 798 3348 2 chr1D.!!$R1 2550
5 TraesCS1A01G266100 chr1B 484462961 484465437 2476 True 974.500000 1092 87.220000 798 3338 2 chr1B.!!$R2 2540
6 TraesCS1A01G266100 chr1B 484689042 484693788 4746 True 912.366667 2303 93.946167 1 4144 6 chr1B.!!$R3 4143

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
987 1011 0.035820 TCGGATTAACACCCACCAGC 60.036 55.0 0.00 0.0 0.0 4.85 F
1722 1777 0.033781 AGGTAAGTAACGCGCCACAA 59.966 50.0 5.73 0.0 0.0 3.33 F
2287 2560 0.035439 AACCATCCATCACCCACGAC 60.035 55.0 0.00 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2010 1.735376 TAGATCGTCGCCTTGCCTCC 61.735 60.000 0.0 0.0 0.0 4.30 R
3117 4772 1.265365 GTGCTTGAAGTCTTGGAGTGC 59.735 52.381 0.0 0.0 0.0 4.40 R
4033 6188 4.079787 ACCCAAATCATGTGTGTAGCCTAT 60.080 41.667 0.0 0.0 0.0 2.57 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
41 42 9.926158 ATAATGACTTTGCATTGTGAATGTTTA 57.074 25.926 0.00 0.00 41.01 2.01
74 75 9.878667 TCCTATAATGTTGATCAAACTTTACGA 57.121 29.630 10.35 7.41 39.71 3.43
86 87 6.778108 TCAAACTTTACGAAACTTGACTTCC 58.222 36.000 0.00 0.00 0.00 3.46
94 95 4.025145 ACGAAACTTGACTTCCGACAAATC 60.025 41.667 0.00 0.00 0.00 2.17
120 121 6.742559 ATATGTAGAGTAAAATGGACCGGT 57.257 37.500 6.92 6.92 0.00 5.28
122 123 2.781681 AGAGTAAAATGGACCGGTGG 57.218 50.000 14.63 0.00 0.00 4.61
229 232 6.887545 TGGAATTTTTACCTATGATCGGTTGT 59.112 34.615 0.00 0.00 35.98 3.32
245 248 5.713025 TCGGTTGTGTTATAGTTGTACTCC 58.287 41.667 0.00 0.00 0.00 3.85
248 251 6.104665 GGTTGTGTTATAGTTGTACTCCCTC 58.895 44.000 0.00 0.00 0.00 4.30
250 253 4.400251 TGTGTTATAGTTGTACTCCCTCCG 59.600 45.833 0.00 0.00 0.00 4.63
251 254 4.400567 GTGTTATAGTTGTACTCCCTCCGT 59.599 45.833 0.00 0.00 0.00 4.69
252 255 4.641989 TGTTATAGTTGTACTCCCTCCGTC 59.358 45.833 0.00 0.00 0.00 4.79
253 256 2.134789 TAGTTGTACTCCCTCCGTCC 57.865 55.000 0.00 0.00 0.00 4.79
254 257 0.113776 AGTTGTACTCCCTCCGTCCA 59.886 55.000 0.00 0.00 0.00 4.02
255 258 1.192428 GTTGTACTCCCTCCGTCCAT 58.808 55.000 0.00 0.00 0.00 3.41
256 259 1.134788 GTTGTACTCCCTCCGTCCATG 60.135 57.143 0.00 0.00 0.00 3.66
257 260 0.333652 TGTACTCCCTCCGTCCATGA 59.666 55.000 0.00 0.00 0.00 3.07
259 262 2.040178 GTACTCCCTCCGTCCATGAAT 58.960 52.381 0.00 0.00 0.00 2.57
260 263 2.471815 ACTCCCTCCGTCCATGAATA 57.528 50.000 0.00 0.00 0.00 1.75
261 264 2.759355 ACTCCCTCCGTCCATGAATAA 58.241 47.619 0.00 0.00 0.00 1.40
264 267 2.434336 TCCCTCCGTCCATGAATAAGTG 59.566 50.000 0.00 0.00 0.00 3.16
265 268 2.170607 CCCTCCGTCCATGAATAAGTGT 59.829 50.000 0.00 0.00 0.00 3.55
266 269 3.386726 CCCTCCGTCCATGAATAAGTGTA 59.613 47.826 0.00 0.00 0.00 2.90
267 270 4.369182 CCTCCGTCCATGAATAAGTGTAC 58.631 47.826 0.00 0.00 0.00 2.90
269 272 5.453339 CCTCCGTCCATGAATAAGTGTACAT 60.453 44.000 0.00 0.00 0.00 2.29
271 274 7.297936 TCCGTCCATGAATAAGTGTACATAT 57.702 36.000 0.00 0.00 0.00 1.78
273 276 8.862085 TCCGTCCATGAATAAGTGTACATATAA 58.138 33.333 0.00 0.00 0.00 0.98
274 277 9.653287 CCGTCCATGAATAAGTGTACATATAAT 57.347 33.333 0.00 0.00 0.00 1.28
331 334 3.447918 GCATTAGAATGTGCAAGCCAT 57.552 42.857 4.27 0.00 40.94 4.40
356 359 8.024145 TCATCTCTCTTCTCTTTAATTACCCC 57.976 38.462 0.00 0.00 0.00 4.95
361 364 5.105853 TCTTCTCTTTAATTACCCCACCCT 58.894 41.667 0.00 0.00 0.00 4.34
362 365 4.855298 TCTCTTTAATTACCCCACCCTG 57.145 45.455 0.00 0.00 0.00 4.45
378 381 1.370609 CCTGAATGAGCTGAGTGCAG 58.629 55.000 0.00 0.00 45.94 4.41
404 407 4.593206 AGAAAGTGAGGAGACCATGTGTTA 59.407 41.667 0.00 0.00 0.00 2.41
409 412 5.003804 GTGAGGAGACCATGTGTTAAATGT 58.996 41.667 0.00 0.00 0.00 2.71
410 413 5.122396 GTGAGGAGACCATGTGTTAAATGTC 59.878 44.000 0.00 0.00 0.00 3.06
419 422 6.267471 ACCATGTGTTAAATGTCATTGGTCTT 59.733 34.615 0.00 0.00 31.87 3.01
420 423 6.587226 CCATGTGTTAAATGTCATTGGTCTTG 59.413 38.462 0.00 0.00 0.00 3.02
421 424 6.951062 TGTGTTAAATGTCATTGGTCTTGA 57.049 33.333 0.00 0.00 0.00 3.02
422 425 7.523293 TGTGTTAAATGTCATTGGTCTTGAT 57.477 32.000 0.00 0.00 0.00 2.57
423 426 7.950512 TGTGTTAAATGTCATTGGTCTTGATT 58.049 30.769 0.00 0.00 0.00 2.57
424 427 9.072375 TGTGTTAAATGTCATTGGTCTTGATTA 57.928 29.630 0.00 0.00 0.00 1.75
454 457 5.830912 TCGTGTGATGAAAAAGAAGCATTT 58.169 33.333 0.00 0.00 0.00 2.32
455 458 6.272318 TCGTGTGATGAAAAAGAAGCATTTT 58.728 32.000 0.00 0.00 33.86 1.82
481 484 9.474920 TTTCTACTTTAAAATGCATTGTGAAGG 57.525 29.630 28.28 18.28 0.00 3.46
500 503 9.256228 TGTGAAGGTAGAAGACTAGAAATACAT 57.744 33.333 0.00 0.00 0.00 2.29
549 552 6.630045 GTCAAACGTACACTTATTTGTGAACC 59.370 38.462 1.47 0.00 40.12 3.62
554 557 6.140110 CGTACACTTATTTGTGAACCAAAGG 58.860 40.000 1.47 0.00 45.79 3.11
584 587 5.018539 TGTATGTGAGGGATTTACTTCCG 57.981 43.478 0.00 0.00 36.58 4.30
591 594 3.361281 GGGATTTACTTCCGTCCCTTT 57.639 47.619 2.09 0.00 45.57 3.11
598 601 2.501261 ACTTCCGTCCCTTTTTGCTAC 58.499 47.619 0.00 0.00 0.00 3.58
601 604 4.202388 ACTTCCGTCCCTTTTTGCTACTTA 60.202 41.667 0.00 0.00 0.00 2.24
625 628 1.284785 ACATGGGGTAGTGGGAACATG 59.715 52.381 0.00 0.00 46.14 3.21
647 650 1.024579 CCCGTGGTTGGAGGAATTCG 61.025 60.000 0.00 0.00 0.00 3.34
648 651 0.321298 CCGTGGTTGGAGGAATTCGT 60.321 55.000 0.00 0.00 0.00 3.85
649 652 1.066716 CCGTGGTTGGAGGAATTCGTA 60.067 52.381 0.00 0.00 0.00 3.43
650 653 2.613474 CCGTGGTTGGAGGAATTCGTAA 60.613 50.000 0.00 0.00 0.00 3.18
651 654 3.267483 CGTGGTTGGAGGAATTCGTAAT 58.733 45.455 0.00 0.00 0.00 1.89
652 655 3.308866 CGTGGTTGGAGGAATTCGTAATC 59.691 47.826 0.00 0.00 0.00 1.75
653 656 3.626217 GTGGTTGGAGGAATTCGTAATCC 59.374 47.826 0.00 5.77 35.88 3.01
654 657 2.870411 GGTTGGAGGAATTCGTAATCCG 59.130 50.000 0.00 0.00 40.78 4.18
655 658 3.528532 GTTGGAGGAATTCGTAATCCGT 58.471 45.455 0.00 0.00 40.78 4.69
656 659 4.441913 GGTTGGAGGAATTCGTAATCCGTA 60.442 45.833 0.00 0.00 40.78 4.02
657 660 5.295152 GTTGGAGGAATTCGTAATCCGTAT 58.705 41.667 0.00 0.00 40.78 3.06
658 661 5.540400 TGGAGGAATTCGTAATCCGTATT 57.460 39.130 0.00 0.00 40.78 1.89
659 662 5.294356 TGGAGGAATTCGTAATCCGTATTG 58.706 41.667 0.00 0.00 40.78 1.90
660 663 4.151867 GGAGGAATTCGTAATCCGTATTGC 59.848 45.833 0.00 0.00 42.29 3.56
661 664 4.699637 AGGAATTCGTAATCCGTATTGCA 58.300 39.130 0.00 0.00 43.65 4.08
662 665 4.510340 AGGAATTCGTAATCCGTATTGCAC 59.490 41.667 0.00 0.00 43.65 4.57
663 666 4.271533 GGAATTCGTAATCCGTATTGCACA 59.728 41.667 0.00 0.00 41.83 4.57
664 667 5.403897 AATTCGTAATCCGTATTGCACAG 57.596 39.130 0.00 0.00 35.56 3.66
665 668 2.816689 TCGTAATCCGTATTGCACAGG 58.183 47.619 0.00 0.00 37.94 4.00
666 669 2.427812 TCGTAATCCGTATTGCACAGGA 59.572 45.455 0.00 0.00 37.94 3.86
667 670 3.119065 TCGTAATCCGTATTGCACAGGAA 60.119 43.478 3.24 0.00 34.81 3.36
680 683 3.202097 GCACAGGAAAATCTCTCCTAGC 58.798 50.000 0.00 0.00 41.61 3.42
742 746 4.145807 TGAGCCCGGTGATTTCTTAAAAA 58.854 39.130 0.00 0.00 0.00 1.94
787 792 1.427368 ACTGGGAATGGCCACTTAACA 59.573 47.619 8.16 2.84 38.95 2.41
788 793 2.094675 CTGGGAATGGCCACTTAACAG 58.905 52.381 8.16 9.83 38.95 3.16
795 800 5.163237 GGAATGGCCACTTAACAGTAGGATA 60.163 44.000 8.16 0.00 36.34 2.59
985 1009 1.065053 CCATCGGATTAACACCCACCA 60.065 52.381 0.00 0.00 0.00 4.17
986 1010 2.288666 CATCGGATTAACACCCACCAG 58.711 52.381 0.00 0.00 0.00 4.00
987 1011 0.035820 TCGGATTAACACCCACCAGC 60.036 55.000 0.00 0.00 0.00 4.85
1314 1341 3.142838 GACCTACTGGCCGGCGTA 61.143 66.667 22.54 16.86 36.63 4.42
1722 1777 0.033781 AGGTAAGTAACGCGCCACAA 59.966 50.000 5.73 0.00 0.00 3.33
1730 1785 2.139888 AACGCGCCACAATGATGCAA 62.140 50.000 5.73 0.00 0.00 4.08
1776 1835 2.864343 GTCCAATAGATCAAACCGACCG 59.136 50.000 0.00 0.00 0.00 4.79
1777 1836 2.498481 TCCAATAGATCAAACCGACCGT 59.502 45.455 0.00 0.00 0.00 4.83
1778 1837 3.055675 TCCAATAGATCAAACCGACCGTT 60.056 43.478 0.00 0.00 35.70 4.44
1779 1838 4.160065 TCCAATAGATCAAACCGACCGTTA 59.840 41.667 0.00 0.00 33.05 3.18
1780 1839 5.054477 CCAATAGATCAAACCGACCGTTAT 58.946 41.667 0.00 0.00 33.05 1.89
1781 1840 6.040729 TCCAATAGATCAAACCGACCGTTATA 59.959 38.462 0.00 0.00 33.05 0.98
1782 1841 6.702723 CCAATAGATCAAACCGACCGTTATAA 59.297 38.462 0.00 0.00 33.05 0.98
1783 1842 7.225145 CCAATAGATCAAACCGACCGTTATAAA 59.775 37.037 0.00 0.00 33.05 1.40
1784 1843 8.770828 CAATAGATCAAACCGACCGTTATAAAT 58.229 33.333 0.00 0.00 33.05 1.40
1785 1844 9.985730 AATAGATCAAACCGACCGTTATAAATA 57.014 29.630 0.00 0.00 33.05 1.40
1786 1845 9.985730 ATAGATCAAACCGACCGTTATAAATAA 57.014 29.630 0.00 0.00 33.05 1.40
1787 1846 8.134905 AGATCAAACCGACCGTTATAAATAAC 57.865 34.615 0.00 3.25 39.32 1.89
1788 1847 7.765360 AGATCAAACCGACCGTTATAAATAACA 59.235 33.333 12.13 0.00 42.02 2.41
1789 1848 7.293402 TCAAACCGACCGTTATAAATAACAG 57.707 36.000 12.13 4.55 42.02 3.16
1790 1849 6.873076 TCAAACCGACCGTTATAAATAACAGT 59.127 34.615 12.13 7.38 42.02 3.55
1791 1850 7.387397 TCAAACCGACCGTTATAAATAACAGTT 59.613 33.333 12.13 0.00 42.02 3.16
1792 1851 7.671495 AACCGACCGTTATAAATAACAGTTT 57.329 32.000 12.13 0.00 42.02 2.66
1793 1852 7.671495 ACCGACCGTTATAAATAACAGTTTT 57.329 32.000 12.13 0.00 42.02 2.43
1794 1853 7.520686 ACCGACCGTTATAAATAACAGTTTTG 58.479 34.615 12.13 4.02 42.02 2.44
1795 1854 6.466730 CCGACCGTTATAAATAACAGTTTTGC 59.533 38.462 12.13 0.00 42.02 3.68
1796 1855 7.238571 CGACCGTTATAAATAACAGTTTTGCT 58.761 34.615 12.13 0.00 42.02 3.91
1797 1856 8.382130 CGACCGTTATAAATAACAGTTTTGCTA 58.618 33.333 12.13 0.00 42.02 3.49
1902 1992 5.791336 TCTTGACTAGACTGAAGCAAAGA 57.209 39.130 0.00 0.00 0.00 2.52
1915 2010 6.754209 ACTGAAGCAAAGAGATTGACTATACG 59.246 38.462 0.00 0.00 41.85 3.06
1935 2030 0.102481 GAGGCAAGGCGACGATCTAA 59.898 55.000 0.00 0.00 0.00 2.10
2110 2211 3.191371 GGCAACCATCAGACGAAAGATTT 59.809 43.478 0.00 0.00 0.00 2.17
2200 2416 7.575414 TTTTTGTTGATAGCTTGTCAAGGTA 57.425 32.000 23.04 23.04 44.64 3.08
2209 2425 2.287608 GCTTGTCAAGGTAACCACTTGC 60.288 50.000 14.40 0.00 43.77 4.01
2287 2560 0.035439 AACCATCCATCACCCACGAC 60.035 55.000 0.00 0.00 0.00 4.34
2306 2579 2.964768 GACAATTGAACGCGTCAGAAAC 59.035 45.455 14.44 0.80 37.61 2.78
2322 2642 6.161381 GTCAGAAACGGAAGGATAACAAGTA 58.839 40.000 0.00 0.00 0.00 2.24
2494 4149 9.330063 GAATATCACACATGACTATTTTCAGGA 57.670 33.333 0.00 0.00 37.79 3.86
3117 4772 1.451936 GGGAAGGATGGACGATGGG 59.548 63.158 0.00 0.00 0.00 4.00
3193 5301 6.551975 TGCATTATCCCTTGATGTGATTCATT 59.448 34.615 0.00 0.00 36.83 2.57
3209 5317 8.321353 TGTGATTCATTGTGTCTTACTCCTTAT 58.679 33.333 0.00 0.00 0.00 1.73
3235 5370 7.662669 TGAAGGTTCTTAAATAAAAGCTACGGT 59.337 33.333 0.00 0.00 31.02 4.83
3344 5483 3.751175 TGAAACACTTCCCATCGACAATC 59.249 43.478 0.00 0.00 0.00 2.67
3346 5485 1.909302 ACACTTCCCATCGACAATCCT 59.091 47.619 0.00 0.00 0.00 3.24
3349 5488 4.019681 ACACTTCCCATCGACAATCCTTTA 60.020 41.667 0.00 0.00 0.00 1.85
3350 5489 4.572389 CACTTCCCATCGACAATCCTTTAG 59.428 45.833 0.00 0.00 0.00 1.85
3351 5490 4.225267 ACTTCCCATCGACAATCCTTTAGT 59.775 41.667 0.00 0.00 0.00 2.24
3352 5491 4.137116 TCCCATCGACAATCCTTTAGTG 57.863 45.455 0.00 0.00 0.00 2.74
3353 5492 3.517901 TCCCATCGACAATCCTTTAGTGT 59.482 43.478 0.00 0.00 39.59 3.55
3354 5493 4.019681 TCCCATCGACAATCCTTTAGTGTT 60.020 41.667 0.00 0.00 36.31 3.32
3355 5494 4.332819 CCCATCGACAATCCTTTAGTGTTC 59.667 45.833 0.00 0.00 36.31 3.18
3356 5495 5.178797 CCATCGACAATCCTTTAGTGTTCT 58.821 41.667 0.00 0.00 36.31 3.01
3357 5496 5.643777 CCATCGACAATCCTTTAGTGTTCTT 59.356 40.000 0.00 0.00 36.31 2.52
3358 5497 6.183360 CCATCGACAATCCTTTAGTGTTCTTC 60.183 42.308 0.00 0.00 36.31 2.87
3359 5498 5.849510 TCGACAATCCTTTAGTGTTCTTCA 58.150 37.500 0.00 0.00 36.31 3.02
3360 5499 6.464222 TCGACAATCCTTTAGTGTTCTTCAT 58.536 36.000 0.00 0.00 36.31 2.57
3361 5500 7.608153 TCGACAATCCTTTAGTGTTCTTCATA 58.392 34.615 0.00 0.00 36.31 2.15
3362 5501 7.544566 TCGACAATCCTTTAGTGTTCTTCATAC 59.455 37.037 0.00 0.00 36.31 2.39
3363 5502 7.201530 CGACAATCCTTTAGTGTTCTTCATACC 60.202 40.741 0.00 0.00 36.31 2.73
3364 5503 7.458397 ACAATCCTTTAGTGTTCTTCATACCA 58.542 34.615 0.00 0.00 30.72 3.25
3365 5504 7.942341 ACAATCCTTTAGTGTTCTTCATACCAA 59.058 33.333 0.00 0.00 30.72 3.67
3366 5505 8.792633 CAATCCTTTAGTGTTCTTCATACCAAA 58.207 33.333 0.00 0.00 0.00 3.28
3367 5506 9.533831 AATCCTTTAGTGTTCTTCATACCAAAT 57.466 29.630 0.00 0.00 0.00 2.32
3395 5549 8.892723 TCTTCATGACATATGTGTATTTGGTTC 58.107 33.333 14.43 0.00 39.09 3.62
3527 5681 5.312443 AGTGGGGTTAGTTGATCTAAAGGTT 59.688 40.000 0.00 0.00 39.88 3.50
3533 5687 9.420551 GGGTTAGTTGATCTAAAGGTTATATCG 57.579 37.037 0.00 0.00 39.88 2.92
3540 5694 7.658261 TGATCTAAAGGTTATATCGTCCACAG 58.342 38.462 0.00 0.00 0.00 3.66
3548 5702 8.190326 AGGTTATATCGTCCACAGATATTTGA 57.810 34.615 0.00 0.00 40.55 2.69
3556 5710 4.393062 GTCCACAGATATTTGACACACCAG 59.607 45.833 0.00 0.00 0.00 4.00
3557 5711 4.285775 TCCACAGATATTTGACACACCAGA 59.714 41.667 0.00 0.00 0.00 3.86
3807 5961 8.294954 TGACTTTTACCATTTAAGGAAACACA 57.705 30.769 0.00 0.00 0.00 3.72
4033 6188 2.380932 TCATAGGACGGGGCTTATCCTA 59.619 50.000 11.73 11.73 46.59 2.94
4070 6225 7.288389 ACATGATTTGGGTACAAGCATGATTAT 59.712 33.333 22.21 4.47 44.81 1.28
4116 6271 5.537300 AGATTGAATCAGTACCATACGCT 57.463 39.130 8.03 0.00 0.00 5.07
4118 6273 6.682746 AGATTGAATCAGTACCATACGCTAG 58.317 40.000 8.03 0.00 0.00 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 9.019764 CAAGTTTCGTAAAGTTTGATCAACATT 57.980 29.630 7.89 6.24 37.93 2.71
55 56 8.402472 TCAAGTTTCGTAAAGTTTGATCAACAT 58.598 29.630 7.89 0.00 37.93 2.71
56 57 7.694784 GTCAAGTTTCGTAAAGTTTGATCAACA 59.305 33.333 7.89 0.00 37.93 3.33
58 59 7.981142 AGTCAAGTTTCGTAAAGTTTGATCAA 58.019 30.769 3.38 3.38 31.88 2.57
59 60 7.548196 AGTCAAGTTTCGTAAAGTTTGATCA 57.452 32.000 0.00 0.00 31.88 2.92
60 61 7.586664 GGAAGTCAAGTTTCGTAAAGTTTGATC 59.413 37.037 0.00 0.00 31.88 2.92
61 62 7.415229 GGAAGTCAAGTTTCGTAAAGTTTGAT 58.585 34.615 0.00 0.00 31.88 2.57
62 63 6.455913 CGGAAGTCAAGTTTCGTAAAGTTTGA 60.456 38.462 0.00 0.00 31.88 2.69
63 64 5.675444 CGGAAGTCAAGTTTCGTAAAGTTTG 59.325 40.000 0.00 0.00 31.88 2.93
64 65 5.581874 TCGGAAGTCAAGTTTCGTAAAGTTT 59.418 36.000 0.00 0.00 31.88 2.66
65 66 5.006068 GTCGGAAGTCAAGTTTCGTAAAGTT 59.994 40.000 0.00 0.00 34.46 2.66
66 67 4.505556 GTCGGAAGTCAAGTTTCGTAAAGT 59.494 41.667 0.00 0.00 0.00 2.66
67 68 4.505191 TGTCGGAAGTCAAGTTTCGTAAAG 59.495 41.667 0.00 0.00 0.00 1.85
68 69 4.431809 TGTCGGAAGTCAAGTTTCGTAAA 58.568 39.130 0.00 0.00 0.00 2.01
69 70 4.044336 TGTCGGAAGTCAAGTTTCGTAA 57.956 40.909 0.00 0.00 0.00 3.18
70 71 3.713858 TGTCGGAAGTCAAGTTTCGTA 57.286 42.857 0.00 0.00 0.00 3.43
71 72 2.589798 TGTCGGAAGTCAAGTTTCGT 57.410 45.000 0.00 0.00 0.00 3.85
72 73 3.936902 TTTGTCGGAAGTCAAGTTTCG 57.063 42.857 0.00 0.00 40.04 3.46
73 74 5.674933 AGATTTGTCGGAAGTCAAGTTTC 57.325 39.130 0.00 0.00 40.04 2.78
74 75 7.745620 ATAAGATTTGTCGGAAGTCAAGTTT 57.254 32.000 0.00 0.00 40.04 2.66
75 76 8.883731 CATATAAGATTTGTCGGAAGTCAAGTT 58.116 33.333 0.00 0.00 40.04 2.66
76 77 8.041323 ACATATAAGATTTGTCGGAAGTCAAGT 58.959 33.333 0.00 0.00 40.04 3.16
77 78 8.425577 ACATATAAGATTTGTCGGAAGTCAAG 57.574 34.615 0.00 0.00 40.04 3.02
94 95 8.365647 ACCGGTCCATTTTACTCTACATATAAG 58.634 37.037 0.00 0.00 0.00 1.73
112 113 1.364269 AAATTACTCCCACCGGTCCA 58.636 50.000 2.59 0.00 0.00 4.02
113 114 2.502142 AAAATTACTCCCACCGGTCC 57.498 50.000 2.59 0.00 0.00 4.46
200 202 9.635404 ACCGATCATAGGTAAAAATTCCATAAA 57.365 29.630 0.00 0.00 40.80 1.40
203 205 7.559897 ACAACCGATCATAGGTAAAAATTCCAT 59.440 33.333 0.00 0.00 41.95 3.41
204 206 6.887545 ACAACCGATCATAGGTAAAAATTCCA 59.112 34.615 0.00 0.00 41.95 3.53
205 207 7.148137 ACACAACCGATCATAGGTAAAAATTCC 60.148 37.037 0.00 0.00 41.95 3.01
218 221 7.553334 AGTACAACTATAACACAACCGATCAT 58.447 34.615 0.00 0.00 0.00 2.45
224 227 6.046290 AGGGAGTACAACTATAACACAACC 57.954 41.667 0.00 0.00 0.00 3.77
229 232 4.603131 ACGGAGGGAGTACAACTATAACA 58.397 43.478 0.00 0.00 0.00 2.41
245 248 3.543680 ACACTTATTCATGGACGGAGG 57.456 47.619 0.00 0.00 0.00 4.30
248 251 9.653287 ATTATATGTACACTTATTCATGGACGG 57.347 33.333 0.00 0.00 31.76 4.79
316 319 2.950309 GAGATGATGGCTTGCACATTCT 59.050 45.455 0.00 0.00 0.00 2.40
328 331 9.487790 GGTAATTAAAGAGAAGAGAGATGATGG 57.512 37.037 0.00 0.00 0.00 3.51
331 334 7.623677 TGGGGTAATTAAAGAGAAGAGAGATGA 59.376 37.037 0.00 0.00 0.00 2.92
356 359 1.735386 CACTCAGCTCATTCAGGGTG 58.265 55.000 0.00 0.00 0.00 4.61
361 364 0.689055 ACCTGCACTCAGCTCATTCA 59.311 50.000 0.00 0.00 45.94 2.57
362 365 2.167281 TCTACCTGCACTCAGCTCATTC 59.833 50.000 0.00 0.00 45.94 2.67
378 381 3.515901 ACATGGTCTCCTCACTTTCTACC 59.484 47.826 0.00 0.00 0.00 3.18
409 412 8.992073 CACGATAATCATAATCAAGACCAATGA 58.008 33.333 0.00 0.00 0.00 2.57
410 413 8.777413 ACACGATAATCATAATCAAGACCAATG 58.223 33.333 0.00 0.00 0.00 2.82
424 427 7.912250 GCTTCTTTTTCATCACACGATAATCAT 59.088 33.333 0.00 0.00 0.00 2.45
432 435 6.515043 AAAATGCTTCTTTTTCATCACACG 57.485 33.333 0.00 0.00 0.00 4.49
455 458 9.474920 CCTTCACAATGCATTTTAAAGTAGAAA 57.525 29.630 9.83 0.00 0.00 2.52
549 552 5.586243 CCCTCACATACAACATACTCCTTTG 59.414 44.000 0.00 0.00 0.00 2.77
554 557 8.204836 AGTAAATCCCTCACATACAACATACTC 58.795 37.037 0.00 0.00 0.00 2.59
584 587 3.190744 GTGCCTAAGTAGCAAAAAGGGAC 59.809 47.826 0.00 0.00 43.02 4.46
591 594 2.620367 CCCCATGTGCCTAAGTAGCAAA 60.620 50.000 0.00 0.00 43.02 3.68
598 601 1.134098 CCACTACCCCATGTGCCTAAG 60.134 57.143 0.00 0.00 33.26 2.18
601 604 2.308722 CCCACTACCCCATGTGCCT 61.309 63.158 0.00 0.00 33.26 4.75
625 628 1.848886 ATTCCTCCAACCACGGGGAC 61.849 60.000 12.96 0.00 38.05 4.46
647 650 5.554822 TTTTCCTGTGCAATACGGATTAC 57.445 39.130 0.00 0.00 37.93 1.89
648 651 6.119536 AGATTTTCCTGTGCAATACGGATTA 58.880 36.000 0.00 0.00 37.93 1.75
649 652 4.949856 AGATTTTCCTGTGCAATACGGATT 59.050 37.500 0.00 0.00 37.93 3.01
650 653 4.526970 AGATTTTCCTGTGCAATACGGAT 58.473 39.130 0.00 0.00 37.93 4.18
651 654 3.938963 GAGATTTTCCTGTGCAATACGGA 59.061 43.478 0.00 0.00 37.93 4.69
652 655 3.941483 AGAGATTTTCCTGTGCAATACGG 59.059 43.478 0.00 0.00 35.32 4.02
653 656 4.034510 GGAGAGATTTTCCTGTGCAATACG 59.965 45.833 0.00 0.00 0.00 3.06
654 657 5.189180 AGGAGAGATTTTCCTGTGCAATAC 58.811 41.667 0.00 0.00 43.38 1.89
655 658 5.441718 AGGAGAGATTTTCCTGTGCAATA 57.558 39.130 0.00 0.00 43.38 1.90
656 659 4.313020 AGGAGAGATTTTCCTGTGCAAT 57.687 40.909 0.00 0.00 43.38 3.56
657 660 3.795688 AGGAGAGATTTTCCTGTGCAA 57.204 42.857 0.00 0.00 43.38 4.08
658 661 3.369892 GCTAGGAGAGATTTTCCTGTGCA 60.370 47.826 4.11 0.00 44.65 4.57
659 662 3.202097 GCTAGGAGAGATTTTCCTGTGC 58.798 50.000 4.11 5.05 44.65 4.57
660 663 3.452474 CGCTAGGAGAGATTTTCCTGTG 58.548 50.000 4.11 0.00 44.65 3.66
661 664 2.432510 CCGCTAGGAGAGATTTTCCTGT 59.567 50.000 4.11 0.00 44.65 4.00
662 665 2.804933 GCCGCTAGGAGAGATTTTCCTG 60.805 54.545 4.11 0.00 44.65 3.86
663 666 1.414550 GCCGCTAGGAGAGATTTTCCT 59.585 52.381 0.00 0.00 46.58 3.36
664 667 1.414550 AGCCGCTAGGAGAGATTTTCC 59.585 52.381 0.00 0.00 41.02 3.13
665 668 2.900716 AGCCGCTAGGAGAGATTTTC 57.099 50.000 0.00 0.00 41.02 2.29
666 669 4.636249 CAATAGCCGCTAGGAGAGATTTT 58.364 43.478 6.23 0.00 41.02 1.82
667 670 3.556004 GCAATAGCCGCTAGGAGAGATTT 60.556 47.826 6.23 0.00 41.02 2.17
698 701 5.076873 CAAATCAGTTAGTTGGGGAGGAAA 58.923 41.667 0.00 0.00 29.47 3.13
742 746 3.196039 TGCATGATGCTGGCATACTTTTT 59.804 39.130 19.19 0.00 45.31 1.94
747 751 2.861935 GTTTTGCATGATGCTGGCATAC 59.138 45.455 19.19 4.73 45.31 2.39
748 752 2.761767 AGTTTTGCATGATGCTGGCATA 59.238 40.909 19.19 0.00 45.31 3.14
787 792 9.290988 CTGTCAATCACTGTACTATATCCTACT 57.709 37.037 0.00 0.00 0.00 2.57
788 793 9.069082 ACTGTCAATCACTGTACTATATCCTAC 57.931 37.037 0.00 0.00 35.50 3.18
795 800 8.462811 CAGTCTTACTGTCAATCACTGTACTAT 58.537 37.037 0.00 0.00 41.19 2.12
1056 1080 1.301479 ACGCGGTTTCTCTTGGTCC 60.301 57.895 12.47 0.00 0.00 4.46
1417 1468 4.980805 GCTCCACACGTCCGGCAA 62.981 66.667 0.00 0.00 0.00 4.52
1428 1482 1.079750 GTTGGACTCTCGGCTCCAC 60.080 63.158 0.00 0.00 36.24 4.02
1722 1777 6.982141 ACGCTCATTTATGAAAATTGCATCAT 59.018 30.769 5.86 5.86 39.50 2.45
1730 1785 6.745450 CGTACCAAACGCTCATTTATGAAAAT 59.255 34.615 0.00 0.00 46.10 1.82
1762 1821 7.765360 TGTTATTTATAACGGTCGGTTTGATCT 59.235 33.333 0.67 0.00 44.21 2.75
1800 1859 8.441608 CAATACTTGAAGCACATCTAGATATGC 58.558 37.037 25.34 25.34 41.29 3.14
1801 1860 8.441608 GCAATACTTGAAGCACATCTAGATATG 58.558 37.037 6.64 6.64 0.00 1.78
1802 1861 8.152898 TGCAATACTTGAAGCACATCTAGATAT 58.847 33.333 4.54 0.00 31.05 1.63
1803 1862 7.500141 TGCAATACTTGAAGCACATCTAGATA 58.500 34.615 4.54 0.00 31.05 1.98
1804 1863 6.351711 TGCAATACTTGAAGCACATCTAGAT 58.648 36.000 0.00 0.00 31.05 1.98
1805 1864 5.733676 TGCAATACTTGAAGCACATCTAGA 58.266 37.500 0.00 0.00 31.05 2.43
1813 1872 6.816134 TTTAGATGTGCAATACTTGAAGCA 57.184 33.333 0.00 0.00 34.10 3.91
1814 1873 8.693542 AAATTTAGATGTGCAATACTTGAAGC 57.306 30.769 0.00 0.00 0.00 3.86
1902 1992 3.322254 CCTTGCCTCCGTATAGTCAATCT 59.678 47.826 0.00 0.00 0.00 2.40
1915 2010 1.735376 TAGATCGTCGCCTTGCCTCC 61.735 60.000 0.00 0.00 0.00 4.30
1935 2030 4.408182 AAACTGACTTGCTGTGTCTAGT 57.592 40.909 0.00 0.00 35.63 2.57
2017 2117 9.528018 GTGTTTTGAACCTTGATAAAAATCTCA 57.472 29.630 0.00 0.00 0.00 3.27
2064 2165 6.351202 CCCATCATGTCTTATTTTTCTGGCAA 60.351 38.462 0.00 0.00 0.00 4.52
2099 2200 4.328712 GGCTCTCTCAGAAAATCTTTCGTC 59.671 45.833 0.00 0.00 0.00 4.20
2110 2211 3.864789 AGTTTTTGGGCTCTCTCAGAA 57.135 42.857 0.00 0.00 0.00 3.02
2189 2405 3.214328 AGCAAGTGGTTACCTTGACAAG 58.786 45.455 8.31 8.31 0.00 3.16
2191 2407 4.425180 TTAGCAAGTGGTTACCTTGACA 57.575 40.909 2.07 0.00 0.00 3.58
2192 2408 5.061179 TCTTTAGCAAGTGGTTACCTTGAC 58.939 41.667 2.07 0.00 0.00 3.18
2193 2409 5.298989 TCTTTAGCAAGTGGTTACCTTGA 57.701 39.130 2.07 0.00 0.00 3.02
2198 2414 6.803154 AGTCATTCTTTAGCAAGTGGTTAC 57.197 37.500 0.00 0.00 0.00 2.50
2200 2416 8.299570 CAATAAGTCATTCTTTAGCAAGTGGTT 58.700 33.333 0.00 0.00 37.56 3.67
2209 2425 5.584649 TGCGGGTCAATAAGTCATTCTTTAG 59.415 40.000 0.00 0.00 37.56 1.85
2261 2477 2.301346 GGTGATGGATGGTTTAGCCTG 58.699 52.381 0.00 0.00 35.30 4.85
2287 2560 1.962547 CGTTTCTGACGCGTTCAATTG 59.037 47.619 15.53 0.00 45.86 2.32
2306 2579 8.446599 ACCATTTTATACTTGTTATCCTTCCG 57.553 34.615 0.00 0.00 0.00 4.30
2494 4149 2.631062 GGAAACCGGGAGAAAACCATTT 59.369 45.455 6.32 0.00 0.00 2.32
2657 4312 2.646175 GGCGCCACTAGACACCAGA 61.646 63.158 24.80 0.00 0.00 3.86
3117 4772 1.265365 GTGCTTGAAGTCTTGGAGTGC 59.735 52.381 0.00 0.00 0.00 4.40
3209 5317 7.662669 ACCGTAGCTTTTATTTAAGAACCTTCA 59.337 33.333 0.00 0.00 0.00 3.02
3344 5483 9.626045 GAAATTTGGTATGAAGAACACTAAAGG 57.374 33.333 0.00 0.00 0.00 3.11
3349 5488 8.463930 TGAAGAAATTTGGTATGAAGAACACT 57.536 30.769 0.00 0.00 0.00 3.55
3350 5489 9.132521 CATGAAGAAATTTGGTATGAAGAACAC 57.867 33.333 0.00 0.00 0.00 3.32
3351 5490 9.076781 TCATGAAGAAATTTGGTATGAAGAACA 57.923 29.630 0.00 0.00 0.00 3.18
3352 5491 9.346725 GTCATGAAGAAATTTGGTATGAAGAAC 57.653 33.333 0.00 0.00 0.00 3.01
3353 5492 9.076781 TGTCATGAAGAAATTTGGTATGAAGAA 57.923 29.630 0.00 0.00 0.00 2.52
3354 5493 8.634335 TGTCATGAAGAAATTTGGTATGAAGA 57.366 30.769 0.00 0.00 0.00 2.87
3360 5499 9.241919 ACACATATGTCATGAAGAAATTTGGTA 57.758 29.630 5.07 0.00 31.55 3.25
3361 5500 8.125978 ACACATATGTCATGAAGAAATTTGGT 57.874 30.769 5.07 0.00 31.55 3.67
3367 5506 9.241919 ACCAAATACACATATGTCATGAAGAAA 57.758 29.630 5.07 0.00 40.48 2.52
3527 5681 7.865889 GTGTGTCAAATATCTGTGGACGATATA 59.134 37.037 0.00 0.00 34.01 0.86
3533 5687 4.323417 TGGTGTGTCAAATATCTGTGGAC 58.677 43.478 0.00 0.00 0.00 4.02
3540 5694 9.643693 AATTGAAATTCTGGTGTGTCAAATATC 57.356 29.630 0.00 0.00 0.00 1.63
3548 5702 9.665719 AAAGTTAAAATTGAAATTCTGGTGTGT 57.334 25.926 0.00 0.00 0.00 3.72
3836 5990 6.791867 TCTTGCTCATACTAGTAACCATGT 57.208 37.500 6.70 0.00 0.00 3.21
4033 6188 4.079787 ACCCAAATCATGTGTGTAGCCTAT 60.080 41.667 0.00 0.00 0.00 2.57
4118 6273 5.823045 AGTAAGGATGTTAGCATTAGGTTGC 59.177 40.000 0.00 0.00 43.09 4.17


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

AutoCloner maintained by Alex Coulton.