Multiple sequence alignment - TraesCS1D01G140700

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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 TraesCS1D01G140700 chr1D 100.000 4382 0 0 1 4382 193959135 193963516 0.000000e+00 8093
1 TraesCS1D01G140700 chr1D 95.290 276 9 3 3648 3923 194136628 194136899 6.730000e-118 435
2 TraesCS1D01G140700 chr1D 94.040 151 8 1 4031 4181 194136970 194137119 1.230000e-55 228
3 TraesCS1D01G140700 chr1B 96.760 2531 59 10 967 3486 268637915 268640433 0.000000e+00 4198
4 TraesCS1D01G140700 chr1B 96.479 426 15 0 3719 4144 268641210 268641635 0.000000e+00 704
5 TraesCS1D01G140700 chr1B 88.565 481 41 8 411 887 268637171 268637641 4.920000e-159 571
6 TraesCS1D01G140700 chr1B 88.235 408 42 5 6 412 268628243 268628645 2.370000e-132 483
7 TraesCS1D01G140700 chr1B 97.967 246 5 0 4137 4382 268649257 268649502 1.130000e-115 427
8 TraesCS1D01G140700 chr1B 93.907 279 10 5 3648 3923 268800243 268800517 8.770000e-112 414
9 TraesCS1D01G140700 chr1B 92.053 151 7 3 4031 4181 268800588 268800733 1.600000e-49 207
10 TraesCS1D01G140700 chr1B 88.793 116 5 5 3607 3717 268640766 268640878 7.640000e-28 135
11 TraesCS1D01G140700 chr1A 94.660 2116 88 11 1 2105 241167386 241169487 0.000000e+00 3258
12 TraesCS1D01G140700 chr1A 97.416 1393 33 2 2145 3535 241169479 241170870 0.000000e+00 2370
13 TraesCS1D01G140700 chr1A 97.345 452 12 0 3931 4382 241176770 241177221 0.000000e+00 769
14 TraesCS1D01G140700 chr1A 89.209 556 20 16 3648 4181 241317648 241318185 0.000000e+00 658
15 TraesCS1D01G140700 chr1A 95.640 344 10 5 3581 3923 241170984 241171323 8.290000e-152 547
16 TraesCS1D01G140700 chr1A 95.349 344 11 5 3581 3923 241171754 241172093 3.860000e-150 542
17 TraesCS1D01G140700 chr1A 97.093 172 5 0 3752 3923 241175055 241175226 1.540000e-74 291
18 TraesCS1D01G140700 chr1A 92.486 173 8 5 3581 3752 241172524 241172692 4.380000e-60 243
19 TraesCS1D01G140700 chr7B 77.291 1004 160 44 1522 2501 697028203 697027244 3.000000e-146 529
20 TraesCS1D01G140700 chr7B 79.542 655 95 24 1451 2095 693617837 693618462 8.710000e-117 431
21 TraesCS1D01G140700 chr7B 79.421 656 94 25 1451 2095 699177824 699178449 4.050000e-115 425
22 TraesCS1D01G140700 chr7B 80.198 606 84 23 1522 2105 697792145 697792736 5.240000e-114 422
23 TraesCS1D01G140700 chr7B 79.605 304 49 9 2203 2501 697366929 697366634 5.740000e-49 206
24 TraesCS1D01G140700 chr7B 77.841 352 61 13 2157 2501 696141136 696141477 7.430000e-48 202
25 TraesCS1D01G140700 chr7A 80.854 679 96 22 1451 2114 699916494 699915835 1.820000e-138 503
26 TraesCS1D01G140700 chr7A 78.254 676 112 19 1446 2114 700204618 700205265 6.830000e-108 401
27 TraesCS1D01G140700 chr7A 75.989 354 58 18 2164 2501 699915827 699915485 1.630000e-34 158
28 TraesCS1D01G140700 chr7D 78.758 612 97 21 1522 2114 609652043 609651446 3.200000e-101 379
29 TraesCS1D01G140700 chr7D 77.904 353 61 14 2157 2501 600237009 600236666 2.070000e-48 204
30 TraesCS1D01G140700 chr6B 82.836 134 15 5 3375 3505 399254913 399255041 3.580000e-21 113


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 TraesCS1D01G140700 chr1D 193959135 193963516 4381 False 8093.000000 8093 100.000000 1 4382 1 chr1D.!!$F1 4381
1 TraesCS1D01G140700 chr1B 268637171 268641635 4464 False 1402.000000 4198 92.649250 411 4144 4 chr1B.!!$F3 3733
2 TraesCS1D01G140700 chr1A 241167386 241177221 9835 False 1145.714286 3258 95.712714 1 4382 7 chr1A.!!$F2 4381
3 TraesCS1D01G140700 chr1A 241317648 241318185 537 False 658.000000 658 89.209000 3648 4181 1 chr1A.!!$F1 533
4 TraesCS1D01G140700 chr7B 697027244 697028203 959 True 529.000000 529 77.291000 1522 2501 1 chr7B.!!$R1 979
5 TraesCS1D01G140700 chr7B 693617837 693618462 625 False 431.000000 431 79.542000 1451 2095 1 chr7B.!!$F1 644
6 TraesCS1D01G140700 chr7B 699177824 699178449 625 False 425.000000 425 79.421000 1451 2095 1 chr7B.!!$F4 644
7 TraesCS1D01G140700 chr7B 697792145 697792736 591 False 422.000000 422 80.198000 1522 2105 1 chr7B.!!$F3 583
8 TraesCS1D01G140700 chr7A 700204618 700205265 647 False 401.000000 401 78.254000 1446 2114 1 chr7A.!!$F1 668
9 TraesCS1D01G140700 chr7A 699915485 699916494 1009 True 330.500000 503 78.421500 1451 2501 2 chr7A.!!$R1 1050
10 TraesCS1D01G140700 chr7D 609651446 609652043 597 True 379.000000 379 78.758000 1522 2114 1 chr7D.!!$R2 592

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
726 739 0.398318 AAACAAGCCTCTCGCCTCTT 59.602 50.0 0.00 0.0 38.78 2.85 F
1403 1612 0.389687 TGTCATTCATCGAGCGCACA 60.390 50.0 11.47 0.0 0.00 4.57 F
2145 2383 0.267356 AAGGGGGAGGAGGAGATCTG 59.733 60.0 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 2364 0.267356 CAGATCTCCTCCTCCCCCTT 59.733 60.0 0.00 0.00 0.00 3.95 R
2861 3203 7.244166 AGATTCATTGATGTTCGAACTGATC 57.756 36.0 27.32 21.83 0.00 2.92 R
3565 3907 0.031010 TTAAGAGAGCTCCCCTCCCC 60.031 60.0 10.93 0.00 41.74 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
27 28 5.787953 TTTCATTGTTCCACATCACATGT 57.212 34.783 0.00 0.00 46.22 3.21
43 44 5.132502 TCACATGTTCAGATTTTGAGGTGT 58.867 37.500 0.00 0.00 37.07 4.16
54 55 9.120538 TCAGATTTTGAGGTGTATTAAATAGCC 57.879 33.333 0.00 0.00 0.00 3.93
55 56 8.070171 CAGATTTTGAGGTGTATTAAATAGCCG 58.930 37.037 0.00 0.00 0.00 5.52
81 82 7.532884 GCAAGCAATGATCAAAAGAAAATTCAC 59.467 33.333 0.00 0.00 0.00 3.18
87 88 7.878477 TGATCAAAAGAAAATTCACTGATGC 57.122 32.000 0.00 0.00 0.00 3.91
103 104 4.460382 ACTGATGCATGTAAAAGTCCTTGG 59.540 41.667 2.46 0.00 0.00 3.61
110 111 6.183360 TGCATGTAAAAGTCCTTGGTCATTTT 60.183 34.615 0.00 0.00 0.00 1.82
111 112 6.146021 GCATGTAAAAGTCCTTGGTCATTTTG 59.854 38.462 0.00 0.00 0.00 2.44
118 119 3.573967 GTCCTTGGTCATTTTGTGGTCAT 59.426 43.478 0.00 0.00 0.00 3.06
125 126 6.241645 TGGTCATTTTGTGGTCATACATACA 58.758 36.000 0.00 0.00 0.00 2.29
130 131 5.977171 TTTGTGGTCATACATACATACGC 57.023 39.130 0.00 0.00 0.00 4.42
131 132 3.985008 TGTGGTCATACATACATACGCC 58.015 45.455 0.00 0.00 0.00 5.68
158 159 7.862372 ACAATTAATGCATCGGTAACATGATTC 59.138 33.333 0.00 0.00 0.00 2.52
165 166 7.471721 TGCATCGGTAACATGATTCTTTAAAG 58.528 34.615 9.04 9.04 0.00 1.85
166 167 7.335673 TGCATCGGTAACATGATTCTTTAAAGA 59.664 33.333 13.99 13.99 0.00 2.52
223 224 9.492730 AATTAGAGAAATTATTTCACCACCCAT 57.507 29.630 18.37 0.00 42.10 4.00
229 230 8.281531 AGAAATTATTTCACCACCCATCATCTA 58.718 33.333 18.37 0.00 42.10 1.98
230 231 9.082313 GAAATTATTTCACCACCCATCATCTAT 57.918 33.333 12.28 0.00 39.45 1.98
240 241 5.249163 CCACCCATCATCTATCTTGGATGTA 59.751 44.000 0.00 0.00 40.76 2.29
243 244 7.886970 CACCCATCATCTATCTTGGATGTAAAT 59.113 37.037 0.00 0.00 40.76 1.40
244 245 8.451245 ACCCATCATCTATCTTGGATGTAAATT 58.549 33.333 0.00 0.00 40.76 1.82
273 274 7.825331 TGAATTTGACCCATACAACTTAACA 57.175 32.000 0.00 0.00 0.00 2.41
317 318 7.797121 AATGTTATTTTGGAAAGATGGGAGT 57.203 32.000 0.00 0.00 0.00 3.85
321 322 7.454380 TGTTATTTTGGAAAGATGGGAGTGAAT 59.546 33.333 0.00 0.00 0.00 2.57
371 372 2.292292 GCACGTAATCCAACAACAACCT 59.708 45.455 0.00 0.00 0.00 3.50
443 448 9.317936 TCATATCTAATGACTTGTCACATCAAC 57.682 33.333 5.53 0.00 0.00 3.18
454 459 9.599322 GACTTGTCACATCAACTAAAACTTATG 57.401 33.333 0.00 0.00 0.00 1.90
487 498 1.678627 AGACATCCGGTGAATCTCTCG 59.321 52.381 0.00 0.00 0.00 4.04
495 506 4.081642 TCCGGTGAATCTCTCGAAAAGAAT 60.082 41.667 0.00 0.00 32.23 2.40
514 525 5.357257 AGAATATTACACCGGATGTCACAC 58.643 41.667 9.46 0.58 42.09 3.82
529 540 6.183360 GGATGTCACACCTAGTTTCAAAACAA 60.183 38.462 8.23 0.00 41.30 2.83
549 560 4.280929 ACAATTAACTTGCTTTGAGGTCCC 59.719 41.667 0.00 0.00 38.50 4.46
550 561 3.586470 TTAACTTGCTTTGAGGTCCCA 57.414 42.857 0.00 0.00 0.00 4.37
554 565 0.555769 TTGCTTTGAGGTCCCAAGGT 59.444 50.000 4.79 0.00 0.00 3.50
569 580 4.104831 CCCAAGGTATATAGAAGGGGAGG 58.895 52.174 0.00 0.00 36.40 4.30
570 581 4.202901 CCCAAGGTATATAGAAGGGGAGGA 60.203 50.000 0.00 0.00 36.40 3.71
571 582 5.412384 CCAAGGTATATAGAAGGGGAGGAA 58.588 45.833 0.00 0.00 0.00 3.36
573 584 6.331837 CCAAGGTATATAGAAGGGGAGGAAAA 59.668 42.308 0.00 0.00 0.00 2.29
574 585 7.225011 CAAGGTATATAGAAGGGGAGGAAAAC 58.775 42.308 0.00 0.00 0.00 2.43
588 601 1.684450 GGAAAACGCTCCCCTTCAAAA 59.316 47.619 0.00 0.00 0.00 2.44
594 607 2.820197 ACGCTCCCCTTCAAAATTTCTC 59.180 45.455 0.00 0.00 0.00 2.87
726 739 0.398318 AAACAAGCCTCTCGCCTCTT 59.602 50.000 0.00 0.00 38.78 2.85
728 741 0.902516 ACAAGCCTCTCGCCTCTTCT 60.903 55.000 0.00 0.00 38.78 2.85
731 744 2.411290 CCTCTCGCCTCTTCTCGC 59.589 66.667 0.00 0.00 0.00 5.03
737 750 2.277628 GCCTCTTCTCGCGTCTCG 60.278 66.667 5.77 0.00 40.15 4.04
774 787 2.492012 CACTCCAGAAGATATGCCTGC 58.508 52.381 0.00 0.00 0.00 4.85
1403 1612 0.389687 TGTCATTCATCGAGCGCACA 60.390 50.000 11.47 0.00 0.00 4.57
1480 1689 8.225603 TCTGAAAGAAGAGTTTTAAGCACAAT 57.774 30.769 0.00 0.00 42.31 2.71
1556 1771 7.873719 TCATCAACTTTCTGTTTAACTGGAA 57.126 32.000 2.32 0.00 36.63 3.53
1570 1789 6.633500 TTAACTGGAAGCAATATATGTGGC 57.367 37.500 0.00 0.00 37.60 5.01
1575 1794 4.350816 TGGAAGCAATATATGTGGCCTAGT 59.649 41.667 3.32 0.00 0.00 2.57
2115 2353 2.664851 CGCCTGCGTCACCAGAAA 60.665 61.111 2.83 0.00 34.77 2.52
2117 2355 2.617274 GCCTGCGTCACCAGAAACC 61.617 63.158 0.00 0.00 34.77 3.27
2118 2356 1.227823 CCTGCGTCACCAGAAACCA 60.228 57.895 0.00 0.00 34.77 3.67
2119 2357 0.817634 CCTGCGTCACCAGAAACCAA 60.818 55.000 0.00 0.00 34.77 3.67
2120 2358 0.588252 CTGCGTCACCAGAAACCAAG 59.412 55.000 0.00 0.00 34.77 3.61
2121 2359 0.817634 TGCGTCACCAGAAACCAAGG 60.818 55.000 0.00 0.00 0.00 3.61
2122 2360 0.534203 GCGTCACCAGAAACCAAGGA 60.534 55.000 0.00 0.00 0.00 3.36
2123 2361 1.512926 CGTCACCAGAAACCAAGGAG 58.487 55.000 0.00 0.00 0.00 3.69
2124 2362 1.070134 CGTCACCAGAAACCAAGGAGA 59.930 52.381 0.00 0.00 0.00 3.71
2125 2363 2.289694 CGTCACCAGAAACCAAGGAGAT 60.290 50.000 0.00 0.00 0.00 2.75
2126 2364 3.056107 CGTCACCAGAAACCAAGGAGATA 60.056 47.826 0.00 0.00 0.00 1.98
2127 2365 4.562757 CGTCACCAGAAACCAAGGAGATAA 60.563 45.833 0.00 0.00 0.00 1.75
2128 2366 4.938226 GTCACCAGAAACCAAGGAGATAAG 59.062 45.833 0.00 0.00 0.00 1.73
2129 2367 4.019321 TCACCAGAAACCAAGGAGATAAGG 60.019 45.833 0.00 0.00 0.00 2.69
2130 2368 3.267031 ACCAGAAACCAAGGAGATAAGGG 59.733 47.826 0.00 0.00 0.00 3.95
2131 2369 3.372025 CCAGAAACCAAGGAGATAAGGGG 60.372 52.174 0.00 0.00 0.00 4.79
2132 2370 2.853077 AGAAACCAAGGAGATAAGGGGG 59.147 50.000 0.00 0.00 0.00 5.40
2133 2371 2.680439 AACCAAGGAGATAAGGGGGA 57.320 50.000 0.00 0.00 0.00 4.81
2134 2372 2.198334 ACCAAGGAGATAAGGGGGAG 57.802 55.000 0.00 0.00 0.00 4.30
2135 2373 1.345526 ACCAAGGAGATAAGGGGGAGG 60.346 57.143 0.00 0.00 0.00 4.30
2136 2374 1.061346 CCAAGGAGATAAGGGGGAGGA 60.061 57.143 0.00 0.00 0.00 3.71
2137 2375 2.334023 CAAGGAGATAAGGGGGAGGAG 58.666 57.143 0.00 0.00 0.00 3.69
2138 2376 0.871024 AGGAGATAAGGGGGAGGAGG 59.129 60.000 0.00 0.00 0.00 4.30
2139 2377 0.868186 GGAGATAAGGGGGAGGAGGA 59.132 60.000 0.00 0.00 0.00 3.71
2140 2378 1.203250 GGAGATAAGGGGGAGGAGGAG 60.203 61.905 0.00 0.00 0.00 3.69
2141 2379 1.790157 GAGATAAGGGGGAGGAGGAGA 59.210 57.143 0.00 0.00 0.00 3.71
2142 2380 2.385417 GAGATAAGGGGGAGGAGGAGAT 59.615 54.545 0.00 0.00 0.00 2.75
2143 2381 2.385417 AGATAAGGGGGAGGAGGAGATC 59.615 54.545 0.00 0.00 0.00 2.75
2144 2382 1.942882 TAAGGGGGAGGAGGAGATCT 58.057 55.000 0.00 0.00 0.00 2.75
2145 2383 0.267356 AAGGGGGAGGAGGAGATCTG 59.733 60.000 0.00 0.00 0.00 2.90
2146 2384 1.841103 GGGGGAGGAGGAGATCTGC 60.841 68.421 6.03 6.03 0.00 4.26
2147 2385 2.206536 GGGGAGGAGGAGATCTGCG 61.207 68.421 8.74 0.00 38.98 5.18
2148 2386 2.733945 GGAGGAGGAGATCTGCGC 59.266 66.667 9.51 9.51 38.98 6.09
2149 2387 2.733945 GAGGAGGAGATCTGCGCC 59.266 66.667 26.20 26.20 40.93 6.53
2150 2388 3.206211 GAGGAGGAGATCTGCGCCG 62.206 68.421 26.80 0.00 44.91 6.46
2151 2389 4.292178 GGAGGAGATCTGCGCCGG 62.292 72.222 20.51 0.00 41.97 6.13
2397 2739 7.440523 CTTGCCAGTCTCAAGTAGTTAAATT 57.559 36.000 0.00 0.00 36.93 1.82
2587 2929 5.685841 ACAAATTAGTATGTGTGCAACGAC 58.314 37.500 0.00 0.00 42.39 4.34
2861 3203 8.693542 AAGTTGAAACATGAGAACTTTTCAAG 57.306 30.769 15.84 0.00 44.49 3.02
2875 3217 6.867662 ACTTTTCAAGATCAGTTCGAACAT 57.132 33.333 28.78 15.33 0.00 2.71
2959 3301 5.343249 AGATGTTTTCTTTGCTTGTGACAC 58.657 37.500 0.00 0.00 0.00 3.67
2961 3303 3.256879 TGTTTTCTTTGCTTGTGACACCA 59.743 39.130 2.45 0.00 0.00 4.17
3026 3368 4.481930 TGCATCTATAATTTTTCCGCCG 57.518 40.909 0.00 0.00 0.00 6.46
3027 3369 3.880490 TGCATCTATAATTTTTCCGCCGT 59.120 39.130 0.00 0.00 0.00 5.68
3071 3413 8.090250 TGTTTGGTACATGTGTTCTATGTTAC 57.910 34.615 9.11 0.00 39.30 2.50
3132 3474 2.623418 TGTCCTAGGTCCACACTGAT 57.377 50.000 9.08 0.00 0.00 2.90
3208 3550 1.822506 GGTCAGGCCCACTTCTAAAC 58.177 55.000 0.00 0.00 0.00 2.01
3209 3551 1.439679 GTCAGGCCCACTTCTAAACG 58.560 55.000 0.00 0.00 0.00 3.60
3223 3565 7.201582 CCACTTCTAAACGGAATGTTGTATACC 60.202 40.741 0.00 0.00 40.84 2.73
3276 3618 7.385752 CACCACTGATTTGCATTTCTTACATTT 59.614 33.333 0.00 0.00 0.00 2.32
3277 3619 7.599998 ACCACTGATTTGCATTTCTTACATTTC 59.400 33.333 0.00 0.00 0.00 2.17
3421 3763 9.314321 CATTGTATAGTACTTTTGGTGTAGGAG 57.686 37.037 0.00 0.00 0.00 3.69
3425 3767 5.211174 AGTACTTTTGGTGTAGGAGTGAC 57.789 43.478 0.00 0.00 0.00 3.67
3510 3852 8.725405 TTGAGTGTGTAGAGAGTAGAGATTAG 57.275 38.462 0.00 0.00 0.00 1.73
3535 3877 6.536941 GCAGCTTATATATCCTTCCTAACTGC 59.463 42.308 0.00 0.00 37.69 4.40
3536 3878 7.580495 GCAGCTTATATATCCTTCCTAACTGCT 60.580 40.741 0.00 0.00 40.69 4.24
3537 3879 8.317679 CAGCTTATATATCCTTCCTAACTGCTT 58.682 37.037 0.00 0.00 0.00 3.91
3538 3880 8.317679 AGCTTATATATCCTTCCTAACTGCTTG 58.682 37.037 0.00 0.00 0.00 4.01
3539 3881 8.097662 GCTTATATATCCTTCCTAACTGCTTGT 58.902 37.037 0.00 0.00 0.00 3.16
3566 3908 8.943909 AAGTACTCTCTTATTAATGAAACGGG 57.056 34.615 0.00 0.00 0.00 5.28
3567 3909 7.498443 AGTACTCTCTTATTAATGAAACGGGG 58.502 38.462 0.00 0.00 0.00 5.73
3568 3910 5.681639 ACTCTCTTATTAATGAAACGGGGG 58.318 41.667 0.00 0.00 0.00 5.40
3569 3911 5.427481 ACTCTCTTATTAATGAAACGGGGGA 59.573 40.000 0.00 0.00 0.00 4.81
3570 3912 5.925509 TCTCTTATTAATGAAACGGGGGAG 58.074 41.667 0.00 0.00 0.00 4.30
3571 3913 5.043737 TCTTATTAATGAAACGGGGGAGG 57.956 43.478 0.00 0.00 0.00 4.30
3572 3914 2.748209 ATTAATGAAACGGGGGAGGG 57.252 50.000 0.00 0.00 0.00 4.30
3573 3915 0.626916 TTAATGAAACGGGGGAGGGG 59.373 55.000 0.00 0.00 0.00 4.79
3574 3916 0.253254 TAATGAAACGGGGGAGGGGA 60.253 55.000 0.00 0.00 0.00 4.81
3575 3917 1.571773 AATGAAACGGGGGAGGGGAG 61.572 60.000 0.00 0.00 0.00 4.30
3576 3918 4.111053 GAAACGGGGGAGGGGAGC 62.111 72.222 0.00 0.00 0.00 4.70
3577 3919 4.677151 AAACGGGGGAGGGGAGCT 62.677 66.667 0.00 0.00 0.00 4.09
3601 4012 7.800847 GCTCTCTTAATCAACTTTTCTGTCAAC 59.199 37.037 0.00 0.00 0.00 3.18
3688 4246 1.560146 AGGTACTTAAGCTGAAGCCCC 59.440 52.381 11.06 10.60 37.19 5.80
3902 8363 2.703416 CAGATAGAACAGTGGCTGCAA 58.297 47.619 0.50 0.00 34.37 4.08
3923 8384 5.105146 GCAACTCCTCTTGATCTTCCTCTTA 60.105 44.000 0.00 0.00 0.00 2.10
3926 8387 5.128663 ACTCCTCTTGATCTTCCTCTTAAGC 59.871 44.000 0.00 0.00 0.00 3.09
3943 9940 9.232473 CCTCTTAAGCCTTAGAAGTTTAACATT 57.768 33.333 0.00 0.00 0.00 2.71
4097 10094 6.979817 GCATTATGCATCATTGTTGGTCTTAA 59.020 34.615 12.80 0.00 44.26 1.85
4158 10155 4.826733 TGCAGAATGACTTGCCTCTTTTTA 59.173 37.500 0.00 0.00 39.69 1.52
4231 10228 6.197981 GCTCTCTGCATTTCTTAACATTAGC 58.802 40.000 0.00 0.00 42.31 3.09
4320 10317 1.798813 GGCAACTGTTCCGTAACTCTG 59.201 52.381 0.00 0.00 36.51 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.264970 TCAAAATCTGAACATGTGATGTGGAA 59.735 34.615 0.00 0.00 44.07 3.53
43 44 6.206438 TGATCATTGCTTGCGGCTATTTAATA 59.794 34.615 0.00 0.00 42.39 0.98
54 55 5.579384 TTTTCTTTTGATCATTGCTTGCG 57.421 34.783 0.00 0.00 0.00 4.85
55 56 7.532884 GTGAATTTTCTTTTGATCATTGCTTGC 59.467 33.333 0.00 0.00 0.00 4.01
64 65 7.878477 TGCATCAGTGAATTTTCTTTTGATC 57.122 32.000 0.00 0.00 0.00 2.92
81 82 4.460382 ACCAAGGACTTTTACATGCATCAG 59.540 41.667 0.00 0.00 0.00 2.90
86 87 5.391312 AATGACCAAGGACTTTTACATGC 57.609 39.130 0.00 0.00 0.00 4.06
87 88 7.169645 CACAAAATGACCAAGGACTTTTACATG 59.830 37.037 0.00 0.00 0.00 3.21
103 104 8.061857 CGTATGTATGTATGACCACAAAATGAC 58.938 37.037 0.00 0.00 30.84 3.06
110 111 3.385111 TGGCGTATGTATGTATGACCACA 59.615 43.478 0.00 0.00 0.00 4.17
111 112 3.739300 GTGGCGTATGTATGTATGACCAC 59.261 47.826 0.00 0.00 34.16 4.16
118 119 6.483640 TGCATTAATTGTGGCGTATGTATGTA 59.516 34.615 0.00 0.00 0.00 2.29
125 126 3.058293 CCGATGCATTAATTGTGGCGTAT 60.058 43.478 0.00 0.00 0.00 3.06
130 131 5.242069 TGTTACCGATGCATTAATTGTGG 57.758 39.130 0.00 0.00 0.00 4.17
131 132 6.493978 TCATGTTACCGATGCATTAATTGTG 58.506 36.000 0.00 0.00 0.00 3.33
165 166 9.463443 AATACTCAATTAGTGTGCTTGTTTTTC 57.537 29.630 0.00 0.00 39.39 2.29
166 167 9.816354 AAATACTCAATTAGTGTGCTTGTTTTT 57.184 25.926 0.00 0.00 39.39 1.94
167 168 9.816354 AAAATACTCAATTAGTGTGCTTGTTTT 57.184 25.926 0.00 0.00 39.39 2.43
249 250 7.721842 TCTGTTAAGTTGTATGGGTCAAATTCA 59.278 33.333 0.00 0.00 35.35 2.57
250 251 8.106247 TCTGTTAAGTTGTATGGGTCAAATTC 57.894 34.615 0.00 0.00 35.35 2.17
251 252 7.176690 CCTCTGTTAAGTTGTATGGGTCAAATT 59.823 37.037 0.00 0.00 37.04 1.82
294 295 6.953520 TCACTCCCATCTTTCCAAAATAACAT 59.046 34.615 0.00 0.00 0.00 2.71
295 296 6.310941 TCACTCCCATCTTTCCAAAATAACA 58.689 36.000 0.00 0.00 0.00 2.41
296 297 6.834168 TCACTCCCATCTTTCCAAAATAAC 57.166 37.500 0.00 0.00 0.00 1.89
335 336 8.145122 TGGATTACGTGCAGTCACATATTATAA 58.855 33.333 0.00 0.00 43.28 0.98
344 345 2.139917 TGTTGGATTACGTGCAGTCAC 58.860 47.619 0.00 0.00 39.78 3.67
388 389 3.317603 TGATGCGACAAGTCATTGAGA 57.682 42.857 0.72 0.00 38.83 3.27
460 471 5.083122 AGATTCACCGGATGTCTCATCTAT 58.917 41.667 9.46 0.00 0.00 1.98
487 498 7.065324 TGTGACATCCGGTGTAATATTCTTTTC 59.935 37.037 0.00 0.00 42.36 2.29
495 506 3.101437 AGGTGTGACATCCGGTGTAATA 58.899 45.455 0.00 0.00 42.36 0.98
514 525 8.871686 AGCAAGTTAATTGTTTTGAAACTAGG 57.128 30.769 7.97 0.00 41.29 3.02
529 540 4.112634 TGGGACCTCAAAGCAAGTTAAT 57.887 40.909 0.00 0.00 0.00 1.40
549 560 7.225011 GTTTTCCTCCCCTTCTATATACCTTG 58.775 42.308 0.00 0.00 0.00 3.61
550 561 6.042897 CGTTTTCCTCCCCTTCTATATACCTT 59.957 42.308 0.00 0.00 0.00 3.50
554 565 5.152934 AGCGTTTTCCTCCCCTTCTATATA 58.847 41.667 0.00 0.00 0.00 0.86
569 580 3.660501 ATTTTGAAGGGGAGCGTTTTC 57.339 42.857 0.00 0.00 0.00 2.29
570 581 4.100963 AGAAATTTTGAAGGGGAGCGTTTT 59.899 37.500 0.00 0.00 0.00 2.43
571 582 3.641436 AGAAATTTTGAAGGGGAGCGTTT 59.359 39.130 0.00 0.00 0.00 3.60
573 584 2.820197 GAGAAATTTTGAAGGGGAGCGT 59.180 45.455 0.00 0.00 0.00 5.07
574 585 2.164422 GGAGAAATTTTGAAGGGGAGCG 59.836 50.000 0.00 0.00 0.00 5.03
923 936 2.276740 CCCCTGCAATCTGACCCC 59.723 66.667 0.00 0.00 0.00 4.95
1020 1227 3.009714 GGAAAGCTCCCCGTCCCT 61.010 66.667 0.00 0.00 35.42 4.20
1480 1689 8.684386 TCAGTACTTTGTATTGACCATTTTGA 57.316 30.769 0.00 0.00 0.00 2.69
1556 1771 5.544176 ACTGTACTAGGCCACATATATTGCT 59.456 40.000 5.01 0.00 0.00 3.91
1570 1789 7.290110 TGGATCATGTATGAACTGTACTAGG 57.710 40.000 0.00 0.00 40.69 3.02
1575 1794 7.851228 AGAACTTGGATCATGTATGAACTGTA 58.149 34.615 0.00 0.00 40.69 2.74
2105 2343 2.930826 TCTCCTTGGTTTCTGGTGAC 57.069 50.000 0.00 0.00 0.00 3.67
2106 2344 4.019321 CCTTATCTCCTTGGTTTCTGGTGA 60.019 45.833 0.00 0.00 0.00 4.02
2114 2352 2.493091 CTCCCCCTTATCTCCTTGGTT 58.507 52.381 0.00 0.00 0.00 3.67
2115 2353 1.345526 CCTCCCCCTTATCTCCTTGGT 60.346 57.143 0.00 0.00 0.00 3.67
2117 2355 2.334023 CTCCTCCCCCTTATCTCCTTG 58.666 57.143 0.00 0.00 0.00 3.61
2118 2356 1.224381 CCTCCTCCCCCTTATCTCCTT 59.776 57.143 0.00 0.00 0.00 3.36
2119 2357 0.871024 CCTCCTCCCCCTTATCTCCT 59.129 60.000 0.00 0.00 0.00 3.69
2120 2358 0.868186 TCCTCCTCCCCCTTATCTCC 59.132 60.000 0.00 0.00 0.00 3.71
2121 2359 1.790157 TCTCCTCCTCCCCCTTATCTC 59.210 57.143 0.00 0.00 0.00 2.75
2122 2360 1.942882 TCTCCTCCTCCCCCTTATCT 58.057 55.000 0.00 0.00 0.00 1.98
2123 2361 2.385417 AGATCTCCTCCTCCCCCTTATC 59.615 54.545 0.00 0.00 0.00 1.75
2124 2362 2.113414 CAGATCTCCTCCTCCCCCTTAT 59.887 54.545 0.00 0.00 0.00 1.73
2125 2363 1.505538 CAGATCTCCTCCTCCCCCTTA 59.494 57.143 0.00 0.00 0.00 2.69
2126 2364 0.267356 CAGATCTCCTCCTCCCCCTT 59.733 60.000 0.00 0.00 0.00 3.95
2127 2365 1.945447 CAGATCTCCTCCTCCCCCT 59.055 63.158 0.00 0.00 0.00 4.79
2128 2366 1.841103 GCAGATCTCCTCCTCCCCC 60.841 68.421 0.00 0.00 0.00 5.40
2129 2367 2.206536 CGCAGATCTCCTCCTCCCC 61.207 68.421 0.00 0.00 0.00 4.81
2130 2368 2.866726 GCGCAGATCTCCTCCTCCC 61.867 68.421 0.30 0.00 0.00 4.30
2131 2369 2.733945 GCGCAGATCTCCTCCTCC 59.266 66.667 0.30 0.00 0.00 4.30
2132 2370 2.733945 GGCGCAGATCTCCTCCTC 59.266 66.667 10.83 0.00 0.00 3.71
2133 2371 3.222855 CGGCGCAGATCTCCTCCT 61.223 66.667 10.83 0.00 0.00 3.69
2134 2372 4.292178 CCGGCGCAGATCTCCTCC 62.292 72.222 10.83 0.00 0.00 4.30
2135 2373 4.959596 GCCGGCGCAGATCTCCTC 62.960 72.222 12.58 0.00 34.03 3.71
2861 3203 7.244166 AGATTCATTGATGTTCGAACTGATC 57.756 36.000 27.32 21.83 0.00 2.92
3198 3540 7.332430 TGGTATACAACATTCCGTTTAGAAGTG 59.668 37.037 5.01 0.00 34.86 3.16
3276 3618 8.429237 TTTTAGCATTTCCCTGGAATTTAAGA 57.571 30.769 0.00 0.00 33.79 2.10
3421 3763 2.139118 GAACTCCTGTTGCTGAGTCAC 58.861 52.381 0.00 0.00 40.84 3.67
3510 3852 6.536941 GCAGTTAGGAAGGATATATAAGCTGC 59.463 42.308 0.00 0.00 36.74 5.25
3540 3882 9.379791 CCCGTTTCATTAATAAGAGAGTACTTT 57.620 33.333 0.00 0.00 0.00 2.66
3541 3883 7.985752 CCCCGTTTCATTAATAAGAGAGTACTT 59.014 37.037 0.00 0.00 0.00 2.24
3542 3884 7.418712 CCCCCGTTTCATTAATAAGAGAGTACT 60.419 40.741 0.00 0.00 0.00 2.73
3543 3885 6.704937 CCCCCGTTTCATTAATAAGAGAGTAC 59.295 42.308 0.00 0.00 0.00 2.73
3544 3886 6.612456 TCCCCCGTTTCATTAATAAGAGAGTA 59.388 38.462 0.00 0.00 0.00 2.59
3545 3887 5.427481 TCCCCCGTTTCATTAATAAGAGAGT 59.573 40.000 0.00 0.00 0.00 3.24
3546 3888 5.925509 TCCCCCGTTTCATTAATAAGAGAG 58.074 41.667 0.00 0.00 0.00 3.20
3547 3889 5.163237 CCTCCCCCGTTTCATTAATAAGAGA 60.163 44.000 0.00 0.00 0.00 3.10
3548 3890 5.063880 CCTCCCCCGTTTCATTAATAAGAG 58.936 45.833 0.00 0.00 0.00 2.85
3549 3891 4.141344 CCCTCCCCCGTTTCATTAATAAGA 60.141 45.833 0.00 0.00 0.00 2.10
3550 3892 4.142038 CCCTCCCCCGTTTCATTAATAAG 58.858 47.826 0.00 0.00 0.00 1.73
3551 3893 3.117436 CCCCTCCCCCGTTTCATTAATAA 60.117 47.826 0.00 0.00 0.00 1.40
3552 3894 2.444010 CCCCTCCCCCGTTTCATTAATA 59.556 50.000 0.00 0.00 0.00 0.98
3553 3895 1.216930 CCCCTCCCCCGTTTCATTAAT 59.783 52.381 0.00 0.00 0.00 1.40
3554 3896 0.626916 CCCCTCCCCCGTTTCATTAA 59.373 55.000 0.00 0.00 0.00 1.40
3555 3897 0.253254 TCCCCTCCCCCGTTTCATTA 60.253 55.000 0.00 0.00 0.00 1.90
3556 3898 1.542881 TCCCCTCCCCCGTTTCATT 60.543 57.895 0.00 0.00 0.00 2.57
3557 3899 2.001269 CTCCCCTCCCCCGTTTCAT 61.001 63.158 0.00 0.00 0.00 2.57
3558 3900 2.609610 CTCCCCTCCCCCGTTTCA 60.610 66.667 0.00 0.00 0.00 2.69
3559 3901 4.111053 GCTCCCCTCCCCCGTTTC 62.111 72.222 0.00 0.00 0.00 2.78
3560 3902 4.677151 AGCTCCCCTCCCCCGTTT 62.677 66.667 0.00 0.00 0.00 3.60
3564 3906 1.962570 TAAGAGAGCTCCCCTCCCCC 61.963 65.000 10.93 0.00 41.74 5.40
3565 3907 0.031010 TTAAGAGAGCTCCCCTCCCC 60.031 60.000 10.93 0.00 41.74 4.81
3566 3908 1.974957 GATTAAGAGAGCTCCCCTCCC 59.025 57.143 10.93 0.00 41.74 4.30
3567 3909 2.683768 TGATTAAGAGAGCTCCCCTCC 58.316 52.381 10.93 0.00 41.74 4.30
3568 3910 3.709141 AGTTGATTAAGAGAGCTCCCCTC 59.291 47.826 10.93 1.12 41.07 4.30
3569 3911 3.730269 AGTTGATTAAGAGAGCTCCCCT 58.270 45.455 10.93 5.16 0.00 4.79
3570 3912 4.495690 AAGTTGATTAAGAGAGCTCCCC 57.504 45.455 10.93 2.49 0.00 4.81
3571 3913 6.093357 CAGAAAAGTTGATTAAGAGAGCTCCC 59.907 42.308 10.93 0.00 0.00 4.30
3572 3914 6.652900 ACAGAAAAGTTGATTAAGAGAGCTCC 59.347 38.462 10.93 1.70 0.00 4.70
3573 3915 7.386299 TGACAGAAAAGTTGATTAAGAGAGCTC 59.614 37.037 5.27 5.27 0.00 4.09
3574 3916 7.220030 TGACAGAAAAGTTGATTAAGAGAGCT 58.780 34.615 0.00 0.00 0.00 4.09
3575 3917 7.426929 TGACAGAAAAGTTGATTAAGAGAGC 57.573 36.000 0.00 0.00 0.00 4.09
3576 3918 8.830580 TGTTGACAGAAAAGTTGATTAAGAGAG 58.169 33.333 0.00 0.00 0.00 3.20
3577 3919 8.612619 GTGTTGACAGAAAAGTTGATTAAGAGA 58.387 33.333 0.00 0.00 0.00 3.10
3578 3920 8.397906 TGTGTTGACAGAAAAGTTGATTAAGAG 58.602 33.333 0.00 0.00 0.00 2.85
3579 3921 8.275015 TGTGTTGACAGAAAAGTTGATTAAGA 57.725 30.769 0.00 0.00 0.00 2.10
3625 4179 6.654793 GAGTATCTGATGTGACAGGAAAAC 57.345 41.667 0.00 0.00 38.31 2.43
3711 4269 0.600557 TGCTTACCGTTGGCAAATGG 59.399 50.000 10.81 10.81 46.49 3.16
3902 8363 5.128663 GCTTAAGAGGAAGATCAAGAGGAGT 59.871 44.000 6.67 0.00 0.00 3.85
3923 8384 8.478775 AGGAAAATGTTAAACTTCTAAGGCTT 57.521 30.769 4.58 4.58 0.00 4.35
3943 9940 5.544176 ACCAGTGATTGAAGAGTCTAGGAAA 59.456 40.000 0.00 0.00 0.00 3.13
4044 10041 4.945543 AGTTATGAATCAGCATCAGCACAA 59.054 37.500 0.00 0.00 45.49 3.33
4134 10131 2.803030 AGAGGCAAGTCATTCTGCAT 57.197 45.000 0.00 0.00 0.00 3.96
4216 10213 9.177608 TGCACATAAGAGCTAATGTTAAGAAAT 57.822 29.630 6.18 0.00 34.12 2.17
4230 10227 1.747355 ACTGCCAATGCACATAAGAGC 59.253 47.619 0.00 0.00 44.23 4.09
4231 10228 4.637534 ACTTACTGCCAATGCACATAAGAG 59.362 41.667 15.48 0.00 44.23 2.85
4258 10255 4.786507 TGAACAAGCGAACATCATTCTTG 58.213 39.130 0.00 0.00 39.79 3.02


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

AutoCloner maintained by Alex Coulton.