Multiple sequence alignment - TraesCS6A01G161400

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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 TraesCS6A01G161400 chr6A 100.000 2042 0 0 1 2042 156459496 156457455 0.000000e+00 3771.0
1 TraesCS6A01G161400 chr6A 100.000 180 0 0 2350 2529 156457147 156456968 1.450000e-87 333.0
2 TraesCS6A01G161400 chr6D 90.508 1201 66 17 838 2021 124834321 124835490 0.000000e+00 1543.0
3 TraesCS6A01G161400 chr6D 85.190 844 88 12 3 837 124833168 124833983 0.000000e+00 832.0
4 TraesCS6A01G161400 chr6B 91.277 642 40 4 838 1472 222424269 222424901 0.000000e+00 861.0
5 TraesCS6A01G161400 chr6B 84.260 845 95 27 1 837 222422668 222423482 0.000000e+00 789.0
6 TraesCS6A01G161400 chr6B 90.237 379 18 8 1478 1839 222424951 222425327 6.330000e-131 477.0
7 TraesCS6A01G161400 chr6B 79.545 352 68 4 2 351 518605787 518606136 5.400000e-62 248.0
8 TraesCS6A01G161400 chr6B 96.250 80 3 0 1839 1918 222427042 222427121 5.680000e-27 132.0
9 TraesCS6A01G161400 chr7D 78.672 497 86 14 14 509 442208517 442208040 1.890000e-81 313.0
10 TraesCS6A01G161400 chr7D 80.311 386 70 6 1 383 201982592 201982210 1.140000e-73 287.0
11 TraesCS6A01G161400 chr7D 79.830 352 65 6 2 351 47387300 47387647 4.180000e-63 252.0
12 TraesCS6A01G161400 chr5B 78.462 520 82 22 1 514 711337995 711338490 1.890000e-81 313.0
13 TraesCS6A01G161400 chr5D 80.000 380 70 6 6 383 388807669 388808044 2.480000e-70 276.0
14 TraesCS6A01G161400 chr3B 76.482 523 81 29 1 514 618162090 618161601 1.940000e-61 246.0
15 TraesCS6A01G161400 chr7A 80.508 118 21 2 157 273 690795662 690795546 3.470000e-14 89.8


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 TraesCS6A01G161400 chr6A 156456968 156459496 2528 True 2052.00 3771 100.000 1 2529 2 chr6A.!!$R1 2528
1 TraesCS6A01G161400 chr6D 124833168 124835490 2322 False 1187.50 1543 87.849 3 2021 2 chr6D.!!$F1 2018
2 TraesCS6A01G161400 chr6B 222422668 222427121 4453 False 564.75 861 90.506 1 1918 4 chr6B.!!$F2 1917

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
98 99 3.949113 GTGAAACAACCCACTGGAAAGTA 59.051 43.478 0.0 0.0 36.32 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 2692 0.03582 TGATTGGGGTAGTTGGTCGC 60.036 55.0 0.0 0.0 0.0 5.19 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
98 99 3.949113 GTGAAACAACCCACTGGAAAGTA 59.051 43.478 0.00 0.00 36.32 2.24
103 104 6.553953 AACAACCCACTGGAAAGTAAAATT 57.446 33.333 0.00 0.00 34.81 1.82
107 108 7.343574 ACAACCCACTGGAAAGTAAAATTTAGT 59.656 33.333 0.00 0.00 34.81 2.24
109 110 8.999905 ACCCACTGGAAAGTAAAATTTAGTTA 57.000 30.769 6.28 0.00 34.81 2.24
255 257 4.923281 GGTGTGATTTTTGCGAAATAAGCT 59.077 37.500 0.00 0.00 35.28 3.74
257 259 6.033513 GGTGTGATTTTTGCGAAATAAGCTAC 59.966 38.462 0.00 0.00 35.28 3.58
260 262 6.801862 GTGATTTTTGCGAAATAAGCTACTGT 59.198 34.615 0.00 0.00 35.28 3.55
647 656 9.598517 AACTAATTTTGTGAATGTGAAATGTGT 57.401 25.926 0.00 0.00 0.00 3.72
652 661 9.761504 ATTTTGTGAATGTGAAATGTGTATTCA 57.238 25.926 0.00 0.00 35.93 2.57
806 816 9.528018 GTCAAGGTCAAAAAGATGTTTGATTTA 57.472 29.630 1.66 0.00 46.31 1.40
837 847 8.928733 GTGTAGGAGAAGAGATATAGTAGTTCG 58.071 40.741 0.00 0.00 0.00 3.95
1056 1877 0.033894 AGGAGGAAGACGAGGAGGAC 60.034 60.000 0.00 0.00 0.00 3.85
1091 1912 1.226323 GTCATCGAGACCCACGACG 60.226 63.158 0.00 0.00 42.37 5.12
1147 1968 1.596260 GTCATCATCCTGTGCATGTCG 59.404 52.381 0.00 0.00 0.00 4.35
1215 2036 2.612746 CGGGGAAGGGGAAGGGAA 60.613 66.667 0.00 0.00 0.00 3.97
1218 2039 2.272471 GGAAGGGGAAGGGAAGCG 59.728 66.667 0.00 0.00 0.00 4.68
1380 2203 2.738321 CGCTCCACATGTACATACAGCA 60.738 50.000 8.32 0.00 39.92 4.41
1394 2217 0.034756 ACAGCATGGACGCACTTACA 59.965 50.000 0.00 0.00 43.62 2.41
1419 2246 1.467678 AAGGAGGAGCATCGATCGGG 61.468 60.000 16.41 9.28 34.37 5.14
1459 2287 3.062774 GCATGGCTACTCGTTCTTCTTTC 59.937 47.826 0.00 0.00 0.00 2.62
1461 2289 4.602340 TGGCTACTCGTTCTTCTTTCTT 57.398 40.909 0.00 0.00 0.00 2.52
1468 2296 5.525199 ACTCGTTCTTCTTTCTTCTCTGTC 58.475 41.667 0.00 0.00 0.00 3.51
1574 2446 1.073964 CATCGATCCATGTGCGATCC 58.926 55.000 10.44 0.00 42.23 3.36
1576 2448 1.007387 CGATCCATGTGCGATCCGA 60.007 57.895 5.25 0.00 33.91 4.55
1603 2477 8.967918 TGCTTCTTCTACTACTTTAGCTGATAA 58.032 33.333 0.00 0.00 0.00 1.75
1670 2553 3.193691 CCCATATGCTCCTACCGTTCTAG 59.806 52.174 0.00 0.00 0.00 2.43
1676 2561 2.351932 GCTCCTACCGTTCTAGCTATGC 60.352 54.545 0.00 0.00 0.00 3.14
1691 2578 0.878416 TATGCTCGTTTGTTGGGCAC 59.122 50.000 0.00 0.00 35.72 5.01
1749 2639 3.564225 GTGTTTGGACCAGAAGACGAAAT 59.436 43.478 0.00 0.00 0.00 2.17
1753 2643 1.679032 GGACCAGAAGACGAAATGGGG 60.679 57.143 0.00 0.00 37.13 4.96
1754 2644 1.278127 GACCAGAAGACGAAATGGGGA 59.722 52.381 0.00 0.00 37.13 4.81
1757 2647 2.488153 CCAGAAGACGAAATGGGGAAAC 59.512 50.000 0.00 0.00 0.00 2.78
1763 2653 0.970427 CGAAATGGGGAAACTGGGGG 60.970 60.000 0.00 0.00 0.00 5.40
1764 2654 1.229496 AAATGGGGAAACTGGGGGC 60.229 57.895 0.00 0.00 0.00 5.80
1802 2692 2.432628 GAGACAACGACGCCCAGG 60.433 66.667 0.00 0.00 0.00 4.45
1859 4464 1.471287 GGAATTCGGCACCTAAACCAC 59.529 52.381 0.00 0.00 0.00 4.16
1878 4483 0.447801 CCAACTATTCGGTGCTGCAC 59.552 55.000 24.02 24.02 0.00 4.57
1952 4557 2.948979 TCTTTGCACGGTGTTGAGAATT 59.051 40.909 10.24 0.00 0.00 2.17
1953 4558 4.130857 TCTTTGCACGGTGTTGAGAATTA 58.869 39.130 10.24 0.00 0.00 1.40
1960 4565 5.177696 GCACGGTGTTGAGAATTATATCCTC 59.822 44.000 10.24 0.00 0.00 3.71
1961 4566 6.516718 CACGGTGTTGAGAATTATATCCTCT 58.483 40.000 0.00 0.00 0.00 3.69
1962 4567 6.642950 CACGGTGTTGAGAATTATATCCTCTC 59.357 42.308 0.00 0.00 36.85 3.20
1966 4571 9.646427 GGTGTTGAGAATTATATCCTCTCATAC 57.354 37.037 10.50 11.61 43.76 2.39
1978 4583 6.949117 ATCCTCTCATACATTATGAAGCCT 57.051 37.500 0.00 0.00 43.98 4.58
1979 4584 6.753913 TCCTCTCATACATTATGAAGCCTT 57.246 37.500 0.00 0.00 43.98 4.35
2366 4973 3.267233 ATGCCACCCCTTGCCTCA 61.267 61.111 0.00 0.00 0.00 3.86
2367 4974 3.590466 ATGCCACCCCTTGCCTCAC 62.590 63.158 0.00 0.00 0.00 3.51
2369 4976 4.366684 CCACCCCTTGCCTCACCC 62.367 72.222 0.00 0.00 0.00 4.61
2370 4977 4.366684 CACCCCTTGCCTCACCCC 62.367 72.222 0.00 0.00 0.00 4.95
2371 4978 4.617595 ACCCCTTGCCTCACCCCT 62.618 66.667 0.00 0.00 0.00 4.79
2372 4979 3.732849 CCCCTTGCCTCACCCCTC 61.733 72.222 0.00 0.00 0.00 4.30
2373 4980 3.732849 CCCTTGCCTCACCCCTCC 61.733 72.222 0.00 0.00 0.00 4.30
2374 4981 3.732849 CCTTGCCTCACCCCTCCC 61.733 72.222 0.00 0.00 0.00 4.30
2375 4982 3.732849 CTTGCCTCACCCCTCCCC 61.733 72.222 0.00 0.00 0.00 4.81
2387 4994 3.646715 CTCCCCCGCCAAGTCCAA 61.647 66.667 0.00 0.00 0.00 3.53
2388 4995 2.938798 TCCCCCGCCAAGTCCAAT 60.939 61.111 0.00 0.00 0.00 3.16
2389 4996 2.440247 CCCCCGCCAAGTCCAATC 60.440 66.667 0.00 0.00 0.00 2.67
2390 4997 2.440247 CCCCGCCAAGTCCAATCC 60.440 66.667 0.00 0.00 0.00 3.01
2391 4998 2.677228 CCCGCCAAGTCCAATCCT 59.323 61.111 0.00 0.00 0.00 3.24
2392 4999 1.452108 CCCGCCAAGTCCAATCCTC 60.452 63.158 0.00 0.00 0.00 3.71
2393 5000 1.299648 CCGCCAAGTCCAATCCTCA 59.700 57.895 0.00 0.00 0.00 3.86
2394 5001 0.107017 CCGCCAAGTCCAATCCTCAT 60.107 55.000 0.00 0.00 0.00 2.90
2395 5002 1.019673 CGCCAAGTCCAATCCTCATG 58.980 55.000 0.00 0.00 0.00 3.07
2396 5003 0.743097 GCCAAGTCCAATCCTCATGC 59.257 55.000 0.00 0.00 0.00 4.06
2397 5004 1.684248 GCCAAGTCCAATCCTCATGCT 60.684 52.381 0.00 0.00 0.00 3.79
2398 5005 2.731572 CCAAGTCCAATCCTCATGCTT 58.268 47.619 0.00 0.00 0.00 3.91
2399 5006 2.686915 CCAAGTCCAATCCTCATGCTTC 59.313 50.000 0.00 0.00 0.00 3.86
2400 5007 2.322355 AGTCCAATCCTCATGCTTCG 57.678 50.000 0.00 0.00 0.00 3.79
2401 5008 1.134280 AGTCCAATCCTCATGCTTCGG 60.134 52.381 0.00 0.00 0.00 4.30
2402 5009 0.181114 TCCAATCCTCATGCTTCGGG 59.819 55.000 0.00 0.00 0.00 5.14
2403 5010 0.107017 CCAATCCTCATGCTTCGGGT 60.107 55.000 0.00 0.00 0.00 5.28
2404 5011 1.019673 CAATCCTCATGCTTCGGGTG 58.980 55.000 0.00 0.00 0.00 4.61
2405 5012 0.107017 AATCCTCATGCTTCGGGTGG 60.107 55.000 0.00 0.00 0.00 4.61
2406 5013 2.615227 ATCCTCATGCTTCGGGTGGC 62.615 60.000 0.00 0.00 0.00 5.01
2407 5014 2.046023 CTCATGCTTCGGGTGGCA 60.046 61.111 0.00 0.00 42.80 4.92
2409 5016 0.179048 CTCATGCTTCGGGTGGCATA 60.179 55.000 0.00 0.00 45.82 3.14
2410 5017 0.179048 TCATGCTTCGGGTGGCATAG 60.179 55.000 0.00 0.00 45.82 2.23
2411 5018 1.526917 ATGCTTCGGGTGGCATAGC 60.527 57.895 0.00 0.00 45.74 2.97
2412 5019 1.987807 ATGCTTCGGGTGGCATAGCT 61.988 55.000 0.00 0.00 45.74 3.32
2413 5020 1.889573 GCTTCGGGTGGCATAGCTC 60.890 63.158 0.00 0.00 0.00 4.09
2414 5021 1.227674 CTTCGGGTGGCATAGCTCC 60.228 63.158 0.00 0.00 0.00 4.70
2415 5022 2.666596 CTTCGGGTGGCATAGCTCCC 62.667 65.000 0.00 0.04 38.47 4.30
2416 5023 4.256180 CGGGTGGCATAGCTCCCC 62.256 72.222 4.66 1.70 38.56 4.81
2417 5024 2.774351 GGGTGGCATAGCTCCCCT 60.774 66.667 0.00 0.00 36.97 4.79
2418 5025 2.386935 GGGTGGCATAGCTCCCCTT 61.387 63.158 0.00 0.00 36.97 3.95
2419 5026 1.149401 GGTGGCATAGCTCCCCTTC 59.851 63.158 0.00 0.00 0.00 3.46
2420 5027 1.149401 GTGGCATAGCTCCCCTTCC 59.851 63.158 0.00 0.00 0.00 3.46
2421 5028 1.307778 TGGCATAGCTCCCCTTCCA 60.308 57.895 0.00 0.00 0.00 3.53
2422 5029 1.348008 TGGCATAGCTCCCCTTCCAG 61.348 60.000 0.00 0.00 0.00 3.86
2423 5030 1.348775 GGCATAGCTCCCCTTCCAGT 61.349 60.000 0.00 0.00 0.00 4.00
2424 5031 0.179034 GCATAGCTCCCCTTCCAGTG 60.179 60.000 0.00 0.00 0.00 3.66
2425 5032 1.500474 CATAGCTCCCCTTCCAGTGA 58.500 55.000 0.00 0.00 0.00 3.41
2426 5033 2.053244 CATAGCTCCCCTTCCAGTGAT 58.947 52.381 0.00 0.00 0.00 3.06
2427 5034 1.500474 TAGCTCCCCTTCCAGTGATG 58.500 55.000 0.00 0.00 0.00 3.07
2428 5035 0.252881 AGCTCCCCTTCCAGTGATGA 60.253 55.000 0.00 0.00 0.00 2.92
2429 5036 0.107459 GCTCCCCTTCCAGTGATGAC 60.107 60.000 0.00 0.00 0.00 3.06
2430 5037 0.176680 CTCCCCTTCCAGTGATGACG 59.823 60.000 0.00 0.00 0.00 4.35
2431 5038 1.221840 CCCCTTCCAGTGATGACGG 59.778 63.158 0.00 0.00 0.00 4.79
2432 5039 1.450312 CCCTTCCAGTGATGACGGC 60.450 63.158 0.00 0.00 0.00 5.68
2433 5040 1.450312 CCTTCCAGTGATGACGGCC 60.450 63.158 0.00 0.00 0.00 6.13
2434 5041 1.450312 CTTCCAGTGATGACGGCCC 60.450 63.158 0.00 0.00 0.00 5.80
2435 5042 1.903877 CTTCCAGTGATGACGGCCCT 61.904 60.000 0.00 0.00 0.00 5.19
2436 5043 0.616395 TTCCAGTGATGACGGCCCTA 60.616 55.000 0.00 0.00 0.00 3.53
2437 5044 1.043116 TCCAGTGATGACGGCCCTAG 61.043 60.000 0.00 0.00 0.00 3.02
2438 5045 1.227380 CAGTGATGACGGCCCTAGC 60.227 63.158 0.00 0.00 38.76 3.42
2439 5046 1.381872 AGTGATGACGGCCCTAGCT 60.382 57.895 0.00 0.00 39.73 3.32
2440 5047 0.106167 AGTGATGACGGCCCTAGCTA 60.106 55.000 0.00 0.00 39.73 3.32
2441 5048 0.032267 GTGATGACGGCCCTAGCTAC 59.968 60.000 0.00 0.00 39.73 3.58
2442 5049 1.286260 GATGACGGCCCTAGCTACG 59.714 63.158 0.00 0.00 39.73 3.51
2443 5050 1.152819 ATGACGGCCCTAGCTACGA 60.153 57.895 8.31 0.00 39.73 3.43
2444 5051 1.453762 ATGACGGCCCTAGCTACGAC 61.454 60.000 8.31 3.27 39.73 4.34
2445 5052 2.044650 ACGGCCCTAGCTACGACA 60.045 61.111 8.31 0.00 39.73 4.35
2446 5053 1.453762 GACGGCCCTAGCTACGACAT 61.454 60.000 8.31 0.00 39.73 3.06
2447 5054 1.007271 CGGCCCTAGCTACGACATG 60.007 63.158 0.00 0.00 39.73 3.21
2448 5055 1.735376 CGGCCCTAGCTACGACATGT 61.735 60.000 0.00 0.00 39.73 3.21
2449 5056 0.464452 GGCCCTAGCTACGACATGTT 59.536 55.000 0.00 0.00 39.73 2.71
2450 5057 1.538419 GGCCCTAGCTACGACATGTTC 60.538 57.143 0.00 0.00 39.73 3.18
2451 5058 1.538419 GCCCTAGCTACGACATGTTCC 60.538 57.143 0.00 0.00 35.50 3.62
2452 5059 1.068741 CCCTAGCTACGACATGTTCCC 59.931 57.143 0.00 0.00 0.00 3.97
2453 5060 1.269102 CCTAGCTACGACATGTTCCCG 60.269 57.143 0.00 1.18 0.00 5.14
2454 5061 1.404391 CTAGCTACGACATGTTCCCGT 59.596 52.381 14.46 14.46 39.94 5.28
2455 5062 0.172803 AGCTACGACATGTTCCCGTC 59.827 55.000 13.59 2.46 37.69 4.79
2456 5063 0.172803 GCTACGACATGTTCCCGTCT 59.827 55.000 13.59 0.00 37.69 4.18
2457 5064 1.403780 GCTACGACATGTTCCCGTCTT 60.404 52.381 13.59 0.00 37.69 3.01
2458 5065 2.929592 GCTACGACATGTTCCCGTCTTT 60.930 50.000 13.59 0.00 37.69 2.52
2459 5066 1.508632 ACGACATGTTCCCGTCTTTG 58.491 50.000 0.00 0.00 29.82 2.77
2460 5067 0.796312 CGACATGTTCCCGTCTTTGG 59.204 55.000 0.00 0.00 0.00 3.28
2461 5068 1.606994 CGACATGTTCCCGTCTTTGGA 60.607 52.381 0.00 0.00 0.00 3.53
2462 5069 2.711542 GACATGTTCCCGTCTTTGGAT 58.288 47.619 0.00 0.00 0.00 3.41
2463 5070 2.678336 GACATGTTCCCGTCTTTGGATC 59.322 50.000 0.00 0.00 0.00 3.36
2464 5071 2.017049 CATGTTCCCGTCTTTGGATCC 58.983 52.381 4.20 4.20 0.00 3.36
2465 5072 1.060729 TGTTCCCGTCTTTGGATCCA 58.939 50.000 11.44 11.44 0.00 3.41
2466 5073 1.003118 TGTTCCCGTCTTTGGATCCAG 59.997 52.381 15.53 4.43 0.00 3.86
2467 5074 1.003233 GTTCCCGTCTTTGGATCCAGT 59.997 52.381 15.53 0.00 0.00 4.00
2468 5075 0.902531 TCCCGTCTTTGGATCCAGTC 59.097 55.000 15.53 6.07 0.00 3.51
2480 5087 4.660789 GGATCCAGTCCCAATGATTTTG 57.339 45.455 6.95 0.00 41.50 2.44
2481 5088 3.385755 GGATCCAGTCCCAATGATTTTGG 59.614 47.826 6.95 0.00 41.50 3.28
2491 5098 4.183101 CCAATGATTTTGGGATTGTTCGG 58.817 43.478 0.00 0.00 35.96 4.30
2492 5099 4.081752 CCAATGATTTTGGGATTGTTCGGA 60.082 41.667 0.00 0.00 35.96 4.55
2493 5100 4.718940 ATGATTTTGGGATTGTTCGGAC 57.281 40.909 0.00 0.00 0.00 4.79
2494 5101 3.491342 TGATTTTGGGATTGTTCGGACA 58.509 40.909 0.00 0.00 0.00 4.02
2495 5102 4.085733 TGATTTTGGGATTGTTCGGACAT 58.914 39.130 0.00 0.00 35.29 3.06
2496 5103 4.526262 TGATTTTGGGATTGTTCGGACATT 59.474 37.500 0.00 0.00 35.29 2.71
2497 5104 3.932545 TTTGGGATTGTTCGGACATTG 57.067 42.857 0.00 0.00 35.29 2.82
2498 5105 2.577606 TGGGATTGTTCGGACATTGT 57.422 45.000 0.00 0.00 35.29 2.71
2499 5106 3.704800 TGGGATTGTTCGGACATTGTA 57.295 42.857 0.00 0.00 35.29 2.41
2500 5107 3.340034 TGGGATTGTTCGGACATTGTAC 58.660 45.455 0.00 0.00 35.29 2.90
2501 5108 3.244596 TGGGATTGTTCGGACATTGTACA 60.245 43.478 0.00 0.00 35.29 2.90
2502 5109 3.374058 GGGATTGTTCGGACATTGTACAG 59.626 47.826 0.00 0.00 35.29 2.74
2503 5110 3.374058 GGATTGTTCGGACATTGTACAGG 59.626 47.826 0.00 0.00 35.29 4.00
2504 5111 2.465860 TGTTCGGACATTGTACAGGG 57.534 50.000 0.00 0.00 0.00 4.45
2505 5112 1.695242 TGTTCGGACATTGTACAGGGT 59.305 47.619 0.00 0.00 0.00 4.34
2506 5113 2.073816 GTTCGGACATTGTACAGGGTG 58.926 52.381 6.26 5.11 0.00 4.61
2507 5114 1.634960 TCGGACATTGTACAGGGTGA 58.365 50.000 6.26 0.00 0.00 4.02
2508 5115 1.972075 TCGGACATTGTACAGGGTGAA 59.028 47.619 6.26 0.00 0.00 3.18
2509 5116 2.369203 TCGGACATTGTACAGGGTGAAA 59.631 45.455 6.26 0.00 0.00 2.69
2510 5117 3.008594 TCGGACATTGTACAGGGTGAAAT 59.991 43.478 6.26 0.00 0.00 2.17
2511 5118 3.374058 CGGACATTGTACAGGGTGAAATC 59.626 47.826 6.26 0.00 0.00 2.17
2512 5119 3.694566 GGACATTGTACAGGGTGAAATCC 59.305 47.826 6.26 2.96 0.00 3.01
2520 5127 3.670105 GGGTGAAATCCCTGCTTGA 57.330 52.632 0.00 0.00 43.85 3.02
2521 5128 2.149973 GGGTGAAATCCCTGCTTGAT 57.850 50.000 0.00 0.00 43.85 2.57
2522 5129 1.753073 GGGTGAAATCCCTGCTTGATG 59.247 52.381 0.00 0.00 43.85 3.07
2523 5130 1.753073 GGTGAAATCCCTGCTTGATGG 59.247 52.381 0.00 0.00 0.00 3.51
2524 5131 2.621407 GGTGAAATCCCTGCTTGATGGA 60.621 50.000 0.00 0.00 0.00 3.41
2525 5132 3.091545 GTGAAATCCCTGCTTGATGGAA 58.908 45.455 0.00 0.00 0.00 3.53
2526 5133 3.511146 GTGAAATCCCTGCTTGATGGAAA 59.489 43.478 0.00 0.00 0.00 3.13
2527 5134 3.511146 TGAAATCCCTGCTTGATGGAAAC 59.489 43.478 0.00 0.00 0.00 2.78
2528 5135 2.149973 ATCCCTGCTTGATGGAAACC 57.850 50.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 9.074576 ACTAACTAAATTTTACTTTCCAGTGGG 57.925 33.333 9.92 0.00 34.06 4.61
220 222 7.147976 GCAAAAATCACACCTATTTCACTTCT 58.852 34.615 0.00 0.00 0.00 2.85
221 223 6.088085 CGCAAAAATCACACCTATTTCACTTC 59.912 38.462 0.00 0.00 0.00 3.01
224 226 5.457140 TCGCAAAAATCACACCTATTTCAC 58.543 37.500 0.00 0.00 0.00 3.18
301 304 7.873719 TCAGTTCCTCAAGTTGACATTTTAA 57.126 32.000 0.08 0.00 0.00 1.52
303 306 6.966534 ATCAGTTCCTCAAGTTGACATTTT 57.033 33.333 0.08 0.00 0.00 1.82
541 547 6.220726 TCCATGATCTGTAATTTCACTCGA 57.779 37.500 0.00 0.00 0.00 4.04
616 622 9.645059 TTTCACATTCACAAAATTAGTTTCACA 57.355 25.926 0.00 0.00 0.00 3.58
621 627 9.598517 ACACATTTCACATTCACAAAATTAGTT 57.401 25.926 0.00 0.00 0.00 2.24
626 632 9.761504 TGAATACACATTTCACATTCACAAAAT 57.238 25.926 0.00 0.00 32.25 1.82
661 670 8.187913 TCAATCTTGGATATTTTTCAACCACA 57.812 30.769 0.00 0.00 0.00 4.17
828 838 0.749454 GGACTCCGGCCGAACTACTA 60.749 60.000 30.73 1.33 0.00 1.82
832 842 2.866523 TATGGGACTCCGGCCGAACT 62.867 60.000 30.73 7.55 35.24 3.01
837 847 2.032681 GCATATGGGACTCCGGCC 59.967 66.667 4.56 0.00 35.24 6.13
1110 1931 3.403057 CGCAGAACACCACGTCCG 61.403 66.667 0.00 0.00 0.00 4.79
1147 1968 1.078143 GATGACCAGGGACAGCACC 60.078 63.158 1.32 0.00 0.00 5.01
1315 2136 2.941064 CGGTGATCACGAGAGGTAAGTA 59.059 50.000 19.33 0.00 0.00 2.24
1318 2139 0.454600 GCGGTGATCACGAGAGGTAA 59.545 55.000 19.33 0.00 0.00 2.85
1355 2176 2.509336 GTACATGTGGAGCGCGCT 60.509 61.111 37.28 37.28 0.00 5.92
1380 2203 0.321671 ACTGCTGTAAGTGCGTCCAT 59.678 50.000 0.00 0.00 35.30 3.41
1394 2217 0.749649 CGATGCTCCTCCTTACTGCT 59.250 55.000 0.00 0.00 0.00 4.24
1433 2260 1.756375 GAACGAGTAGCCATGCGCAG 61.756 60.000 18.32 3.80 41.38 5.18
1459 2287 7.647318 CAGTAGTAATATGCACAGACAGAGAAG 59.353 40.741 0.00 0.00 0.00 2.85
1461 2289 6.828785 TCAGTAGTAATATGCACAGACAGAGA 59.171 38.462 0.00 0.00 0.00 3.10
1468 2296 6.309980 GCAGCTATCAGTAGTAATATGCACAG 59.690 42.308 0.00 0.00 0.00 3.66
1514 2386 2.936919 ACACTCCATGTTCTTGCAGA 57.063 45.000 0.00 0.00 38.98 4.26
1574 2446 6.416455 CAGCTAAAGTAGTAGAAGAAGCATCG 59.584 42.308 0.00 0.00 0.00 3.84
1576 2448 7.411486 TCAGCTAAAGTAGTAGAAGAAGCAT 57.589 36.000 0.00 0.00 0.00 3.79
1603 2477 3.169512 ACCGAACCCAAATCCAGAAAT 57.830 42.857 0.00 0.00 0.00 2.17
1670 2553 0.179163 GCCCAACAAACGAGCATAGC 60.179 55.000 0.00 0.00 0.00 2.97
1676 2561 0.738389 ACAAGTGCCCAACAAACGAG 59.262 50.000 0.00 0.00 0.00 4.18
1691 2578 2.746362 GGCAAGATGTCTCTCCAACAAG 59.254 50.000 0.00 0.00 0.00 3.16
1753 2643 2.282180 TTCTGCGCCCCCAGTTTC 60.282 61.111 4.18 0.00 34.47 2.78
1754 2644 2.597510 GTTCTGCGCCCCCAGTTT 60.598 61.111 4.18 0.00 34.47 2.66
1764 2654 3.181967 CTCTTCGGCGGTTCTGCG 61.182 66.667 7.21 0.00 35.06 5.18
1800 2690 1.205460 ATTGGGGTAGTTGGTCGCCT 61.205 55.000 0.00 0.00 37.52 5.52
1802 2692 0.035820 TGATTGGGGTAGTTGGTCGC 60.036 55.000 0.00 0.00 0.00 5.19
1859 4464 0.447801 GTGCAGCACCGAATAGTTGG 59.552 55.000 15.27 0.00 0.00 3.77
1878 4483 5.985526 ACGTTTGTTTTCTTTTCTTCACG 57.014 34.783 0.00 0.00 0.00 4.35
1952 4557 9.720874 AGGCTTCATAATGTATGAGAGGATATA 57.279 33.333 0.00 0.00 45.15 0.86
1953 4558 8.621126 AGGCTTCATAATGTATGAGAGGATAT 57.379 34.615 0.00 0.00 45.15 1.63
2352 4959 4.366684 GGGTGAGGCAAGGGGTGG 62.367 72.222 0.00 0.00 0.00 4.61
2353 4960 4.366684 GGGGTGAGGCAAGGGGTG 62.367 72.222 0.00 0.00 0.00 4.61
2354 4961 4.617595 AGGGGTGAGGCAAGGGGT 62.618 66.667 0.00 0.00 0.00 4.95
2355 4962 3.732849 GAGGGGTGAGGCAAGGGG 61.733 72.222 0.00 0.00 0.00 4.79
2356 4963 3.732849 GGAGGGGTGAGGCAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
2357 4964 3.732849 GGGAGGGGTGAGGCAAGG 61.733 72.222 0.00 0.00 0.00 3.61
2358 4965 3.732849 GGGGAGGGGTGAGGCAAG 61.733 72.222 0.00 0.00 0.00 4.01
2370 4977 2.893682 GATTGGACTTGGCGGGGGAG 62.894 65.000 0.00 0.00 0.00 4.30
2371 4978 2.938798 ATTGGACTTGGCGGGGGA 60.939 61.111 0.00 0.00 0.00 4.81
2372 4979 2.440247 GATTGGACTTGGCGGGGG 60.440 66.667 0.00 0.00 0.00 5.40
2373 4980 2.440247 GGATTGGACTTGGCGGGG 60.440 66.667 0.00 0.00 0.00 5.73
2374 4981 1.452108 GAGGATTGGACTTGGCGGG 60.452 63.158 0.00 0.00 0.00 6.13
2375 4982 0.107017 ATGAGGATTGGACTTGGCGG 60.107 55.000 0.00 0.00 0.00 6.13
2376 4983 1.019673 CATGAGGATTGGACTTGGCG 58.980 55.000 0.00 0.00 0.00 5.69
2377 4984 0.743097 GCATGAGGATTGGACTTGGC 59.257 55.000 0.00 0.00 0.00 4.52
2378 4985 2.431954 AGCATGAGGATTGGACTTGG 57.568 50.000 0.00 0.00 0.00 3.61
2379 4986 2.353889 CGAAGCATGAGGATTGGACTTG 59.646 50.000 0.00 0.00 0.00 3.16
2380 4987 2.636830 CGAAGCATGAGGATTGGACTT 58.363 47.619 0.00 0.00 0.00 3.01
2381 4988 1.134280 CCGAAGCATGAGGATTGGACT 60.134 52.381 0.00 0.00 0.00 3.85
2382 4989 1.303309 CCGAAGCATGAGGATTGGAC 58.697 55.000 0.00 0.00 0.00 4.02
2383 4990 0.181114 CCCGAAGCATGAGGATTGGA 59.819 55.000 0.00 0.00 0.00 3.53
2384 4991 0.107017 ACCCGAAGCATGAGGATTGG 60.107 55.000 0.00 0.00 0.00 3.16
2385 4992 1.019673 CACCCGAAGCATGAGGATTG 58.980 55.000 0.00 0.00 0.00 2.67
2386 4993 0.107017 CCACCCGAAGCATGAGGATT 60.107 55.000 0.00 0.00 0.00 3.01
2387 4994 1.528824 CCACCCGAAGCATGAGGAT 59.471 57.895 0.00 0.00 0.00 3.24
2388 4995 2.989639 CCACCCGAAGCATGAGGA 59.010 61.111 0.00 0.00 0.00 3.71
2389 4996 2.825836 GCCACCCGAAGCATGAGG 60.826 66.667 0.00 0.00 0.00 3.86
2390 4997 2.046023 TGCCACCCGAAGCATGAG 60.046 61.111 0.00 0.00 33.08 2.90
2394 5001 2.124736 GCTATGCCACCCGAAGCA 60.125 61.111 0.00 0.00 44.45 3.91
2395 5002 1.889573 GAGCTATGCCACCCGAAGC 60.890 63.158 0.00 0.00 0.00 3.86
2396 5003 1.227674 GGAGCTATGCCACCCGAAG 60.228 63.158 0.00 0.00 0.00 3.79
2397 5004 2.742116 GGGAGCTATGCCACCCGAA 61.742 63.158 6.65 0.00 36.38 4.30
2398 5005 3.161450 GGGAGCTATGCCACCCGA 61.161 66.667 6.65 0.00 36.38 5.14
2399 5006 4.256180 GGGGAGCTATGCCACCCG 62.256 72.222 13.23 0.00 43.13 5.28
2400 5007 2.344878 GAAGGGGAGCTATGCCACCC 62.345 65.000 10.08 10.08 42.79 4.61
2401 5008 1.149401 GAAGGGGAGCTATGCCACC 59.851 63.158 0.00 0.00 39.08 4.61
2402 5009 1.149401 GGAAGGGGAGCTATGCCAC 59.851 63.158 0.00 0.00 39.08 5.01
2403 5010 1.307778 TGGAAGGGGAGCTATGCCA 60.308 57.895 0.00 0.00 39.08 4.92
2404 5011 1.348775 ACTGGAAGGGGAGCTATGCC 61.349 60.000 0.00 0.00 39.30 4.40
2405 5012 0.179034 CACTGGAAGGGGAGCTATGC 60.179 60.000 0.00 0.00 39.30 3.14
2406 5013 1.500474 TCACTGGAAGGGGAGCTATG 58.500 55.000 0.00 0.00 38.52 2.23
2407 5014 2.053244 CATCACTGGAAGGGGAGCTAT 58.947 52.381 0.00 0.00 38.52 2.97
2408 5015 1.008327 TCATCACTGGAAGGGGAGCTA 59.992 52.381 0.00 0.00 38.52 3.32
2409 5016 0.252881 TCATCACTGGAAGGGGAGCT 60.253 55.000 0.00 0.00 38.52 4.09
2410 5017 0.107459 GTCATCACTGGAAGGGGAGC 60.107 60.000 0.00 0.00 38.52 4.70
2411 5018 0.176680 CGTCATCACTGGAAGGGGAG 59.823 60.000 0.00 0.00 38.52 4.30
2412 5019 1.264749 CCGTCATCACTGGAAGGGGA 61.265 60.000 0.00 0.00 38.52 4.81
2413 5020 1.221840 CCGTCATCACTGGAAGGGG 59.778 63.158 0.00 0.00 38.52 4.79
2414 5021 1.450312 GCCGTCATCACTGGAAGGG 60.450 63.158 0.00 0.00 40.34 3.95
2415 5022 1.450312 GGCCGTCATCACTGGAAGG 60.450 63.158 0.00 0.00 39.30 3.46
2416 5023 1.450312 GGGCCGTCATCACTGGAAG 60.450 63.158 0.00 0.00 42.29 3.46
2417 5024 0.616395 TAGGGCCGTCATCACTGGAA 60.616 55.000 0.00 0.00 0.00 3.53
2418 5025 1.001120 TAGGGCCGTCATCACTGGA 59.999 57.895 0.00 0.00 0.00 3.86
2419 5026 1.443407 CTAGGGCCGTCATCACTGG 59.557 63.158 0.00 0.00 0.00 4.00
2420 5027 1.227380 GCTAGGGCCGTCATCACTG 60.227 63.158 0.00 0.00 0.00 3.66
2421 5028 0.106167 TAGCTAGGGCCGTCATCACT 60.106 55.000 0.00 0.00 39.73 3.41
2422 5029 0.032267 GTAGCTAGGGCCGTCATCAC 59.968 60.000 0.00 0.00 39.73 3.06
2423 5030 1.452953 CGTAGCTAGGGCCGTCATCA 61.453 60.000 0.00 0.00 39.73 3.07
2424 5031 1.170919 TCGTAGCTAGGGCCGTCATC 61.171 60.000 13.23 0.00 39.73 2.92
2425 5032 1.152819 TCGTAGCTAGGGCCGTCAT 60.153 57.895 13.23 0.00 39.73 3.06
2426 5033 2.117156 GTCGTAGCTAGGGCCGTCA 61.117 63.158 13.23 0.00 39.73 4.35
2427 5034 1.453762 ATGTCGTAGCTAGGGCCGTC 61.454 60.000 14.99 4.01 39.73 4.79
2428 5035 1.455217 ATGTCGTAGCTAGGGCCGT 60.455 57.895 14.99 2.24 39.73 5.68
2429 5036 1.007271 CATGTCGTAGCTAGGGCCG 60.007 63.158 14.99 5.41 39.73 6.13
2430 5037 0.464452 AACATGTCGTAGCTAGGGCC 59.536 55.000 14.99 0.00 39.73 5.80
2431 5038 1.538419 GGAACATGTCGTAGCTAGGGC 60.538 57.143 11.06 11.06 39.06 5.19
2432 5039 1.068741 GGGAACATGTCGTAGCTAGGG 59.931 57.143 13.23 0.00 0.00 3.53
2433 5040 1.269102 CGGGAACATGTCGTAGCTAGG 60.269 57.143 7.12 7.12 0.00 3.02
2434 5041 1.404391 ACGGGAACATGTCGTAGCTAG 59.596 52.381 9.10 0.00 35.23 3.42
2435 5042 1.402968 GACGGGAACATGTCGTAGCTA 59.597 52.381 10.63 0.00 37.25 3.32
2436 5043 0.172803 GACGGGAACATGTCGTAGCT 59.827 55.000 10.63 0.00 37.25 3.32
2437 5044 0.172803 AGACGGGAACATGTCGTAGC 59.827 55.000 10.63 1.05 39.67 3.58
2438 5045 2.649331 AAGACGGGAACATGTCGTAG 57.351 50.000 10.63 1.08 39.67 3.51
2439 5046 2.610976 CCAAAGACGGGAACATGTCGTA 60.611 50.000 10.63 0.00 39.67 3.43
2440 5047 1.508632 CAAAGACGGGAACATGTCGT 58.491 50.000 10.47 10.47 39.67 4.34
2441 5048 0.796312 CCAAAGACGGGAACATGTCG 59.204 55.000 0.00 0.54 39.67 4.35
2442 5049 2.178912 TCCAAAGACGGGAACATGTC 57.821 50.000 0.00 0.00 35.85 3.06
2443 5050 2.618045 GGATCCAAAGACGGGAACATGT 60.618 50.000 6.95 0.00 38.09 3.21
2444 5051 2.017049 GGATCCAAAGACGGGAACATG 58.983 52.381 6.95 0.00 38.09 3.21
2445 5052 1.633432 TGGATCCAAAGACGGGAACAT 59.367 47.619 13.46 0.00 38.09 2.71
2446 5053 1.003118 CTGGATCCAAAGACGGGAACA 59.997 52.381 17.00 0.00 38.09 3.18
2447 5054 1.003233 ACTGGATCCAAAGACGGGAAC 59.997 52.381 17.00 0.00 38.09 3.62
2448 5055 1.278127 GACTGGATCCAAAGACGGGAA 59.722 52.381 17.00 0.00 38.09 3.97
2449 5056 0.902531 GACTGGATCCAAAGACGGGA 59.097 55.000 17.00 0.00 39.14 5.14
2450 5057 3.460648 GACTGGATCCAAAGACGGG 57.539 57.895 17.00 4.55 0.00 5.28
2460 5067 4.660789 CCAAAATCATTGGGACTGGATC 57.339 45.455 0.00 0.00 35.96 3.36
2469 5076 4.081752 TCCGAACAATCCCAAAATCATTGG 60.082 41.667 0.15 0.15 39.25 3.16
2470 5077 4.864247 GTCCGAACAATCCCAAAATCATTG 59.136 41.667 0.00 0.00 34.29 2.82
2471 5078 4.526262 TGTCCGAACAATCCCAAAATCATT 59.474 37.500 0.00 0.00 30.70 2.57
2472 5079 4.085733 TGTCCGAACAATCCCAAAATCAT 58.914 39.130 0.00 0.00 30.70 2.45
2473 5080 3.491342 TGTCCGAACAATCCCAAAATCA 58.509 40.909 0.00 0.00 30.70 2.57
2474 5081 4.718940 ATGTCCGAACAATCCCAAAATC 57.281 40.909 0.00 0.00 39.30 2.17
2475 5082 4.283212 ACAATGTCCGAACAATCCCAAAAT 59.717 37.500 0.00 0.00 39.30 1.82
2476 5083 3.639094 ACAATGTCCGAACAATCCCAAAA 59.361 39.130 0.00 0.00 39.30 2.44
2477 5084 3.226777 ACAATGTCCGAACAATCCCAAA 58.773 40.909 0.00 0.00 39.30 3.28
2478 5085 2.870175 ACAATGTCCGAACAATCCCAA 58.130 42.857 0.00 0.00 39.30 4.12
2479 5086 2.577606 ACAATGTCCGAACAATCCCA 57.422 45.000 0.00 0.00 39.30 4.37
2480 5087 3.340034 TGTACAATGTCCGAACAATCCC 58.660 45.455 0.00 0.00 39.30 3.85
2481 5088 3.374058 CCTGTACAATGTCCGAACAATCC 59.626 47.826 0.00 0.00 39.30 3.01
2482 5089 3.374058 CCCTGTACAATGTCCGAACAATC 59.626 47.826 0.00 0.00 39.30 2.67
2483 5090 3.244770 ACCCTGTACAATGTCCGAACAAT 60.245 43.478 0.00 0.00 39.30 2.71
2484 5091 2.105134 ACCCTGTACAATGTCCGAACAA 59.895 45.455 0.00 0.00 39.30 2.83
2485 5092 1.695242 ACCCTGTACAATGTCCGAACA 59.305 47.619 0.00 0.00 40.38 3.18
2486 5093 2.073816 CACCCTGTACAATGTCCGAAC 58.926 52.381 0.00 0.00 0.00 3.95
2487 5094 1.972075 TCACCCTGTACAATGTCCGAA 59.028 47.619 0.00 0.00 0.00 4.30
2488 5095 1.634960 TCACCCTGTACAATGTCCGA 58.365 50.000 0.00 0.00 0.00 4.55
2489 5096 2.465860 TTCACCCTGTACAATGTCCG 57.534 50.000 0.00 0.00 0.00 4.79
2490 5097 3.694566 GGATTTCACCCTGTACAATGTCC 59.305 47.826 0.00 0.00 0.00 4.02
2491 5098 3.694566 GGGATTTCACCCTGTACAATGTC 59.305 47.826 0.00 0.00 45.90 3.06
2492 5099 3.697166 GGGATTTCACCCTGTACAATGT 58.303 45.455 0.00 0.00 45.90 2.71
2503 5110 1.753073 CCATCAAGCAGGGATTTCACC 59.247 52.381 0.00 0.00 0.00 4.02
2504 5111 2.726821 TCCATCAAGCAGGGATTTCAC 58.273 47.619 0.00 0.00 0.00 3.18
2505 5112 3.454719 TTCCATCAAGCAGGGATTTCA 57.545 42.857 0.00 0.00 0.00 2.69
2506 5113 3.118992 GGTTTCCATCAAGCAGGGATTTC 60.119 47.826 0.00 0.00 0.00 2.17
2507 5114 2.833943 GGTTTCCATCAAGCAGGGATTT 59.166 45.455 0.00 0.00 0.00 2.17
2508 5115 2.460669 GGTTTCCATCAAGCAGGGATT 58.539 47.619 0.00 0.00 0.00 3.01
2509 5116 2.149973 GGTTTCCATCAAGCAGGGAT 57.850 50.000 0.00 0.00 0.00 3.85
2510 5117 3.670105 GGTTTCCATCAAGCAGGGA 57.330 52.632 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.