Multiple sequence alignment - TraesCS7A01G488600

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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 TraesCS7A01G488600 chr7A 100.000 3527 0 0 1 3527 678972043 678968517 0.000000e+00 6514
1 TraesCS7A01G488600 chr7A 73.667 619 87 27 1325 1903 675743389 675742807 1.680000e-38 171
2 TraesCS7A01G488600 chr7A 86.916 107 11 3 375 479 162776204 162776309 2.220000e-22 117
3 TraesCS7A01G488600 chr7A 86.792 106 13 1 375 479 175244588 175244693 2.220000e-22 117
4 TraesCS7A01G488600 chr7D 89.348 3023 236 49 476 3453 587121276 587118295 0.000000e+00 3720
5 TraesCS7A01G488600 chr7D 86.000 500 39 12 1 476 587123470 587122978 1.130000e-139 507
6 TraesCS7A01G488600 chr7D 89.474 95 8 2 375 468 136863649 136863556 6.180000e-23 119
7 TraesCS7A01G488600 chr7D 85.849 106 14 1 375 479 173020123 173020018 1.030000e-20 111
8 TraesCS7A01G488600 chr7B 89.270 2889 192 46 486 3333 658221845 658219034 0.000000e+00 3509
9 TraesCS7A01G488600 chr7B 88.830 376 23 10 1 372 658222235 658221875 8.980000e-121 444
10 TraesCS7A01G488600 chr6B 85.866 566 41 14 1681 2229 720405712 720406255 1.840000e-157 566
11 TraesCS7A01G488600 chr6B 82.927 246 25 11 1003 1243 213157494 213157261 4.620000e-49 206
12 TraesCS7A01G488600 chr6B 92.308 91 7 0 1528 1618 213157166 213157076 2.860000e-26 130
13 TraesCS7A01G488600 chrUn 75.243 618 80 29 1325 1903 329059252 329058669 3.540000e-55 226
14 TraesCS7A01G488600 chr6A 75.243 618 80 29 1325 1903 514350975 514350392 3.540000e-55 226
15 TraesCS7A01G488600 chr6A 80.226 177 26 1 1334 1501 588757105 588757281 1.330000e-24 124
16 TraesCS7A01G488600 chr6D 82.114 246 27 11 1003 1243 121093273 121093040 9.990000e-46 195
17 TraesCS7A01G488600 chr6D 81.122 196 30 1 1313 1501 223690371 223690566 2.190000e-32 150
18 TraesCS7A01G488600 chr6D 83.065 124 17 3 375 494 451017754 451017631 3.720000e-20 110
19 TraesCS7A01G488600 chr4A 73.701 616 92 27 1325 1903 504673704 504673122 3.620000e-40 176
20 TraesCS7A01G488600 chr5D 80.095 211 29 7 1003 1212 30555570 30555768 1.020000e-30 145
21 TraesCS7A01G488600 chr5D 80.000 210 29 7 1004 1212 525777385 525777582 3.670000e-30 143
22 TraesCS7A01G488600 chr4D 78.972 214 32 10 1003 1215 287300413 287300212 2.210000e-27 134
23 TraesCS7A01G488600 chr4B 79.070 215 30 10 1003 1215 216792034 216791833 2.210000e-27 134
24 TraesCS7A01G488600 chr2D 79.147 211 31 7 1003 1212 561922250 561922448 2.210000e-27 134
25 TraesCS7A01G488600 chr2D 86.290 124 16 1 1273 1396 561922559 561922681 2.210000e-27 134
26 TraesCS7A01G488600 chr2A 89.583 96 9 1 375 469 25378918 25378823 1.720000e-23 121
27 TraesCS7A01G488600 chr2A 85.981 107 12 3 375 480 278996347 278996451 1.030000e-20 111
28 TraesCS7A01G488600 chr3A 86.792 106 11 2 375 479 740079650 740079547 8.000000e-22 115


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 TraesCS7A01G488600 chr7A 678968517 678972043 3526 True 6514.0 6514 100.000 1 3527 1 chr7A.!!$R2 3526
1 TraesCS7A01G488600 chr7D 587118295 587123470 5175 True 2113.5 3720 87.674 1 3453 2 chr7D.!!$R3 3452
2 TraesCS7A01G488600 chr7B 658219034 658222235 3201 True 1976.5 3509 89.050 1 3333 2 chr7B.!!$R1 3332
3 TraesCS7A01G488600 chr6B 720405712 720406255 543 False 566.0 566 85.866 1681 2229 1 chr6B.!!$F1 548
4 TraesCS7A01G488600 chrUn 329058669 329059252 583 True 226.0 226 75.243 1325 1903 1 chrUn.!!$R1 578
5 TraesCS7A01G488600 chr6A 514350392 514350975 583 True 226.0 226 75.243 1325 1903 1 chr6A.!!$R1 578

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
295 311 0.099436 GCCGACTTTCACATCATGCC 59.901 55.0 0.0 0.0 0.00 4.40 F
1911 3702 0.035725 CAGAGATCAAGCCAGTGCCA 60.036 55.0 0.0 0.0 38.69 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 3875 0.037512 GAAGCAGCAGAGAGAGTGCA 60.038 55.0 0.0 0.0 43.82 4.57 R
3469 5303 0.317519 TCTCTGTGTGTGTACGTGCG 60.318 55.0 0.0 0.0 0.00 5.34 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
79 80 3.496131 CGCACGCCCATGTGGTAC 61.496 66.667 0.00 0.00 40.26 3.34
105 110 4.020662 TGATGATAACCTTGTTTTTGCCCC 60.021 41.667 0.00 0.00 0.00 5.80
157 165 1.065782 GGCTGACTCTTCCCCTCTTTC 60.066 57.143 0.00 0.00 0.00 2.62
170 178 1.651240 CTCTTTCCGCAGCCACATGG 61.651 60.000 0.00 0.00 38.53 3.66
201 209 1.809207 GGGTGGCCACGAAATGATG 59.191 57.895 29.08 0.00 0.00 3.07
203 211 1.666209 GGTGGCCACGAAATGATGGG 61.666 60.000 29.08 0.00 36.41 4.00
205 213 0.964860 TGGCCACGAAATGATGGGTG 60.965 55.000 0.00 0.00 36.41 4.61
207 215 1.809207 CCACGAAATGATGGGTGGC 59.191 57.895 0.00 0.00 42.95 5.01
208 216 0.964860 CCACGAAATGATGGGTGGCA 60.965 55.000 0.00 0.00 42.95 4.92
209 217 0.171007 CACGAAATGATGGGTGGCAC 59.829 55.000 9.70 9.70 0.00 5.01
231 247 1.369692 CGCTGTTACTGTGGGTGGA 59.630 57.895 0.00 0.00 0.00 4.02
233 249 1.739067 GCTGTTACTGTGGGTGGATC 58.261 55.000 0.00 0.00 0.00 3.36
235 251 1.275291 CTGTTACTGTGGGTGGATCGT 59.725 52.381 0.00 0.00 0.00 3.73
236 252 1.695242 TGTTACTGTGGGTGGATCGTT 59.305 47.619 0.00 0.00 0.00 3.85
237 253 2.073816 GTTACTGTGGGTGGATCGTTG 58.926 52.381 0.00 0.00 0.00 4.10
247 263 2.356382 GGTGGATCGTTGTTGTTGTTGA 59.644 45.455 0.00 0.00 0.00 3.18
292 308 1.003580 AGGTGCCGACTTTCACATCAT 59.996 47.619 0.00 0.00 35.04 2.45
293 309 1.131126 GGTGCCGACTTTCACATCATG 59.869 52.381 0.00 0.00 35.04 3.07
294 310 0.804364 TGCCGACTTTCACATCATGC 59.196 50.000 0.00 0.00 0.00 4.06
295 311 0.099436 GCCGACTTTCACATCATGCC 59.901 55.000 0.00 0.00 0.00 4.40
296 312 1.742761 CCGACTTTCACATCATGCCT 58.257 50.000 0.00 0.00 0.00 4.75
337 353 0.962855 GAGCAGGAAGAAACAGGCCC 60.963 60.000 0.00 0.00 0.00 5.80
374 398 0.174845 CAGGCAAATCTGTGGGCATG 59.825 55.000 0.00 0.00 0.00 4.06
389 413 1.460359 GGCATGAAAATGTTTGCACGG 59.540 47.619 0.00 0.00 36.82 4.94
395 419 4.545610 TGAAAATGTTTGCACGGATCTTC 58.454 39.130 0.00 0.00 0.00 2.87
396 420 2.900122 AATGTTTGCACGGATCTTCG 57.100 45.000 0.00 0.00 0.00 3.79
415 439 9.559958 GATCTTCGTGTAAAATCAATGACATTT 57.440 29.630 0.00 0.00 0.00 2.32
416 440 8.726650 TCTTCGTGTAAAATCAATGACATTTG 57.273 30.769 0.00 0.00 0.00 2.32
508 2234 0.843872 GCAAAACGTGCGAGGTTTTC 59.156 50.000 13.20 0.00 45.10 2.29
511 2237 3.175929 CAAAACGTGCGAGGTTTTCTTT 58.824 40.909 13.20 0.00 42.19 2.52
530 2256 4.405680 TCTTTGGAGGCGAGATCTTCATAA 59.594 41.667 0.00 0.00 0.00 1.90
545 2271 4.895889 TCTTCATAAGATCCACGAGACCAT 59.104 41.667 0.00 0.00 31.20 3.55
616 2342 6.371548 CCGGATAACATAATCTGGTACCAATG 59.628 42.308 17.11 18.06 44.38 2.82
649 2375 4.572985 TGCAATCCGATTCATCCAATTC 57.427 40.909 0.00 0.00 0.00 2.17
650 2376 3.952967 TGCAATCCGATTCATCCAATTCA 59.047 39.130 0.00 0.00 0.00 2.57
654 2380 7.147312 GCAATCCGATTCATCCAATTCATTTA 58.853 34.615 0.00 0.00 0.00 1.40
657 2383 7.496529 TCCGATTCATCCAATTCATTTAGTC 57.503 36.000 0.00 0.00 0.00 2.59
660 2386 8.715998 CCGATTCATCCAATTCATTTAGTCTAG 58.284 37.037 0.00 0.00 0.00 2.43
690 2426 7.891183 TTTAACTACACTTTGAGCAGATCTC 57.109 36.000 0.00 0.00 42.23 2.75
724 2460 0.736325 ATGAAAAGTCGCCGACGGAG 60.736 55.000 20.50 16.01 40.63 4.63
725 2461 2.727684 GAAAAGTCGCCGACGGAGC 61.728 63.158 20.50 10.94 40.63 4.70
783 2527 2.231529 CCTTACGAGGATCCGAGTCAT 58.768 52.381 16.61 0.00 46.74 3.06
941 2685 0.999228 GACAGACAGACAGACGCACG 60.999 60.000 0.00 0.00 0.00 5.34
972 2716 2.520020 ACCACCACCGTGACGAGA 60.520 61.111 6.54 0.00 43.14 4.04
1188 2932 4.729918 CTGCCGGGCCTCTGCTTT 62.730 66.667 17.97 0.00 37.74 3.51
1258 3002 2.017138 GCCTCTGCTTCTGTACCTTC 57.983 55.000 0.00 0.00 33.53 3.46
1297 3041 3.760684 ACTGAATTTTCATCCTGTGCTCC 59.239 43.478 0.00 0.00 36.46 4.70
1330 3074 1.377856 GAGCTGGAAGGGAGCAACC 60.378 63.158 0.00 0.00 39.05 3.77
1477 3228 4.441792 TGTTATCAGTATGCGCAGAATGT 58.558 39.130 28.60 19.11 34.70 2.71
1482 3233 4.441792 TCAGTATGCGCAGAATGTTGTAT 58.558 39.130 28.60 5.20 34.70 2.29
1507 3279 1.070134 AGTCAACACCTAGCGAGCAAA 59.930 47.619 0.00 0.00 0.00 3.68
1541 3313 2.223112 CCGCAGTGGATTTCATCGAAAG 60.223 50.000 0.00 0.00 42.00 2.62
1568 3340 7.630242 TTCTGAACAAAAGAGAAACATCACT 57.370 32.000 0.00 0.00 0.00 3.41
1613 3385 3.861840 TCGTCTGCTCCAAAATTCCTAG 58.138 45.455 0.00 0.00 0.00 3.02
1665 3437 6.058183 CCCTGGTCCAACATAGAAATAGAAG 58.942 44.000 0.00 0.00 0.00 2.85
1674 3446 9.823647 CCAACATAGAAATAGAAGTACACTGAT 57.176 33.333 0.00 0.00 0.00 2.90
1692 3472 6.003950 CACTGATTTTAGAGTTGGGAAGGAA 58.996 40.000 0.00 0.00 0.00 3.36
1830 3620 1.478510 AGCGAGTCATTGGTCGAGATT 59.521 47.619 11.91 0.00 38.50 2.40
1905 3696 2.121948 AGGTATGCAGAGATCAAGCCA 58.878 47.619 0.00 0.00 0.00 4.75
1911 3702 0.035725 CAGAGATCAAGCCAGTGCCA 60.036 55.000 0.00 0.00 38.69 4.92
1963 3759 5.234543 ACAAACTGCTTACGTTTCTTCTCTC 59.765 40.000 0.00 0.00 32.64 3.20
1971 3767 6.618805 GCTTACGTTTCTTCTCTCCAATGAAC 60.619 42.308 0.00 0.00 0.00 3.18
2046 3842 0.985490 GGTCCAGGAGGAGGAAGCAT 60.985 60.000 0.00 0.00 46.92 3.79
2077 3873 0.179020 TGACCTTGAGTTGCAGGTGG 60.179 55.000 0.00 0.00 34.38 4.61
2079 3875 0.773644 ACCTTGAGTTGCAGGTGGAT 59.226 50.000 0.00 0.00 32.77 3.41
2080 3876 1.171308 CCTTGAGTTGCAGGTGGATG 58.829 55.000 0.00 0.00 0.00 3.51
2088 3894 1.601171 GCAGGTGGATGCACTCTCT 59.399 57.895 17.44 3.00 45.77 3.10
2095 3901 0.810823 GGATGCACTCTCTCTGCTGC 60.811 60.000 0.00 0.00 35.53 5.25
2098 3906 0.037512 TGCACTCTCTCTGCTGCTTC 60.038 55.000 0.00 0.00 35.53 3.86
2117 3925 7.041848 GCTGCTTCATCAAACAAAAATTACCTT 60.042 33.333 0.00 0.00 0.00 3.50
2156 3964 3.151554 TCCTAATGCACATGCCATGATC 58.848 45.455 12.53 2.95 41.18 2.92
2262 4072 0.469494 TCAAGCAACTGACAGAGGCA 59.531 50.000 19.83 2.92 0.00 4.75
2265 4075 2.283145 AGCAACTGACAGAGGCAAAT 57.717 45.000 19.83 2.92 0.00 2.32
2352 4162 3.578716 TCAAGGTAACACTTCTCCTCTGG 59.421 47.826 0.00 0.00 41.41 3.86
2355 4168 4.087907 AGGTAACACTTCTCCTCTGGTAC 58.912 47.826 0.00 0.00 41.41 3.34
2358 4171 4.608948 AACACTTCTCCTCTGGTACAAG 57.391 45.455 0.00 0.00 38.70 3.16
2397 4211 6.865726 CCTCTAAACGATCATCAGTTCCATAG 59.134 42.308 0.00 0.00 0.00 2.23
2398 4212 6.216569 TCTAAACGATCATCAGTTCCATAGC 58.783 40.000 0.00 0.00 0.00 2.97
2399 4213 4.406648 AACGATCATCAGTTCCATAGCA 57.593 40.909 0.00 0.00 0.00 3.49
2400 4214 3.987547 ACGATCATCAGTTCCATAGCAG 58.012 45.455 0.00 0.00 0.00 4.24
2401 4215 3.638627 ACGATCATCAGTTCCATAGCAGA 59.361 43.478 0.00 0.00 0.00 4.26
2402 4216 4.100035 ACGATCATCAGTTCCATAGCAGAA 59.900 41.667 0.00 0.00 0.00 3.02
2403 4217 4.685165 CGATCATCAGTTCCATAGCAGAAG 59.315 45.833 0.00 0.00 0.00 2.85
2404 4218 5.609423 GATCATCAGTTCCATAGCAGAAGT 58.391 41.667 0.00 0.00 0.00 3.01
2405 4219 4.763073 TCATCAGTTCCATAGCAGAAGTG 58.237 43.478 2.60 2.60 43.21 3.16
2629 4443 2.670414 GCTCTTCAAGTTCAGACATCGG 59.330 50.000 0.00 0.00 0.00 4.18
2669 4483 4.270834 AGTCTAGAGTGCTCGAATAACCA 58.729 43.478 0.00 0.00 34.09 3.67
2737 4551 1.453155 CCCGGAGATTCACACCAAAG 58.547 55.000 0.73 0.00 0.00 2.77
2788 4602 3.117926 TGGCTGTTGCATACCTGACATAT 60.118 43.478 0.00 0.00 41.91 1.78
2907 4721 5.172934 TGTTCATATACAACCAACCGAGTC 58.827 41.667 0.00 0.00 0.00 3.36
2923 4737 2.223294 CGAGTCGTCCTCTGTCCATTAC 60.223 54.545 3.82 0.00 38.11 1.89
2971 4785 7.907214 ATCTTTGTTCCATACTTGTACAGAC 57.093 36.000 0.00 0.00 0.00 3.51
2972 4786 7.062749 TCTTTGTTCCATACTTGTACAGACT 57.937 36.000 0.00 0.00 0.00 3.24
2973 4787 8.185506 TCTTTGTTCCATACTTGTACAGACTA 57.814 34.615 0.00 0.00 0.00 2.59
2974 4788 8.086522 TCTTTGTTCCATACTTGTACAGACTAC 58.913 37.037 0.00 0.00 0.00 2.73
2975 4789 6.904463 TGTTCCATACTTGTACAGACTACA 57.096 37.500 0.00 0.00 0.00 2.74
2976 4790 6.920817 TGTTCCATACTTGTACAGACTACAG 58.079 40.000 0.00 0.00 0.00 2.74
2977 4791 6.717997 TGTTCCATACTTGTACAGACTACAGA 59.282 38.462 0.00 0.00 0.00 3.41
2980 4794 8.185506 TCCATACTTGTACAGACTACAGAAAA 57.814 34.615 0.00 0.00 0.00 2.29
2996 4811 9.672673 ACTACAGAAAACTTAACTATGCATCAT 57.327 29.630 0.19 0.00 0.00 2.45
2999 4814 9.890629 ACAGAAAACTTAACTATGCATCATCTA 57.109 29.630 0.19 0.00 0.00 1.98
3031 4846 5.921962 TTGATGTAGCTCTGATGTACAGT 57.078 39.130 0.33 0.00 45.86 3.55
3066 4885 2.594303 TCTGTTGGCGTTGGCAGG 60.594 61.111 0.00 0.00 42.47 4.85
3075 4894 1.071471 CGTTGGCAGGTCTGAAGGT 59.929 57.895 1.65 0.00 0.00 3.50
3076 4895 0.951040 CGTTGGCAGGTCTGAAGGTC 60.951 60.000 1.65 0.00 0.00 3.85
3113 4932 1.227823 CCTCACACCTCAACCGCAA 60.228 57.895 0.00 0.00 0.00 4.85
3128 4947 1.675714 CCGCAATCAACTACCAGCTGA 60.676 52.381 17.39 0.00 0.00 4.26
3134 4953 5.464168 CAATCAACTACCAGCTGAAAAAGG 58.536 41.667 17.39 0.00 0.00 3.11
3136 4955 3.137544 TCAACTACCAGCTGAAAAAGGGA 59.862 43.478 17.39 6.26 0.00 4.20
3159 4978 6.472163 GGATTGTGTTTGTACAAAACTGTGAG 59.528 38.462 22.14 0.00 43.13 3.51
3163 4982 6.858993 TGTGTTTGTACAAAACTGTGAGAAAC 59.141 34.615 22.14 7.10 35.69 2.78
3190 5009 8.143193 AGAGTGCAAATGTAAATGAAATGACAA 58.857 29.630 0.00 0.00 0.00 3.18
3247 5066 7.707467 ATTAGGTAACCAGGTCATAAGGAAT 57.293 36.000 0.00 0.00 37.17 3.01
3258 5077 7.148000 CCAGGTCATAAGGAATTTTTCTTCTCC 60.148 40.741 0.00 0.00 0.00 3.71
3259 5078 6.892456 AGGTCATAAGGAATTTTTCTTCTCCC 59.108 38.462 0.00 0.00 0.00 4.30
3276 5095 8.404107 TCTTCTCCCGTTGAAGAAAATTTAAT 57.596 30.769 8.78 0.00 44.51 1.40
3333 5158 6.759497 AAGGAAGAAATATTCAGGGTTTCG 57.241 37.500 0.00 0.00 37.04 3.46
3335 5160 4.495844 GGAAGAAATATTCAGGGTTTCGCG 60.496 45.833 0.00 0.00 37.04 5.87
3341 5174 0.534203 TTCAGGGTTTCGCGCTCTTT 60.534 50.000 5.56 0.00 38.41 2.52
3350 5183 3.521524 TTCGCGCTCTTTCTCTTTTTC 57.478 42.857 5.56 0.00 0.00 2.29
3362 5195 8.379457 TCTTTCTCTTTTTCCTAACTACTTGC 57.621 34.615 0.00 0.00 0.00 4.01
3375 5208 1.993370 CTACTTGCGCAGTTGTCCTAC 59.007 52.381 11.31 0.00 36.88 3.18
3383 5217 2.552315 CGCAGTTGTCCTACCAAAACAT 59.448 45.455 0.00 0.00 0.00 2.71
3386 5220 5.458015 GCAGTTGTCCTACCAAAACATAAC 58.542 41.667 0.00 0.00 0.00 1.89
3390 5224 8.287503 CAGTTGTCCTACCAAAACATAACTTAC 58.712 37.037 0.00 0.00 0.00 2.34
3414 5248 8.888579 ACAAACATATACAGTAGAATGCTACC 57.111 34.615 7.29 0.00 46.59 3.18
3425 5259 3.522553 AGAATGCTACCGTTCTTGCTAC 58.477 45.455 0.00 0.00 43.12 3.58
3430 5264 3.878103 TGCTACCGTTCTTGCTACAAAAA 59.122 39.130 0.00 0.00 0.00 1.94
3436 5270 5.008316 ACCGTTCTTGCTACAAAAAGGTAAG 59.992 40.000 9.32 0.00 32.77 2.34
3443 5277 5.378332 TGCTACAAAAAGGTAAGCAGGTTA 58.622 37.500 0.00 0.00 0.00 2.85
3456 5290 4.484872 GGTTAGGACCCGGCCAGC 62.485 72.222 2.24 0.00 40.25 4.85
3457 5291 4.832608 GTTAGGACCCGGCCAGCG 62.833 72.222 2.24 0.00 0.00 5.18
3481 5315 4.054455 CGCACCGCACGTACACAC 62.054 66.667 0.00 0.00 0.00 3.82
3482 5316 2.962786 GCACCGCACGTACACACA 60.963 61.111 0.00 0.00 0.00 3.72
3483 5317 2.925352 CACCGCACGTACACACAC 59.075 61.111 0.00 0.00 0.00 3.82
3484 5318 1.878975 CACCGCACGTACACACACA 60.879 57.895 0.00 0.00 0.00 3.72
3485 5319 1.590525 ACCGCACGTACACACACAG 60.591 57.895 0.00 0.00 0.00 3.66
3486 5320 1.299544 CCGCACGTACACACACAGA 60.300 57.895 0.00 0.00 0.00 3.41
3487 5321 1.275471 CCGCACGTACACACACAGAG 61.275 60.000 0.00 0.00 0.00 3.35
3488 5322 0.317519 CGCACGTACACACACAGAGA 60.318 55.000 0.00 0.00 0.00 3.10
3489 5323 1.409412 GCACGTACACACACAGAGAG 58.591 55.000 0.00 0.00 0.00 3.20
3490 5324 1.001706 GCACGTACACACACAGAGAGA 60.002 52.381 0.00 0.00 0.00 3.10
3491 5325 2.651701 CACGTACACACACAGAGAGAC 58.348 52.381 0.00 0.00 0.00 3.36
3492 5326 2.032924 CACGTACACACACAGAGAGACA 59.967 50.000 0.00 0.00 0.00 3.41
3493 5327 2.290916 ACGTACACACACAGAGAGACAG 59.709 50.000 0.00 0.00 0.00 3.51
3494 5328 2.548480 CGTACACACACAGAGAGACAGA 59.452 50.000 0.00 0.00 0.00 3.41
3495 5329 3.607310 CGTACACACACAGAGAGACAGAC 60.607 52.174 0.00 0.00 0.00 3.51
3496 5330 2.379005 ACACACACAGAGAGACAGACA 58.621 47.619 0.00 0.00 0.00 3.41
3497 5331 2.099921 ACACACACAGAGAGACAGACAC 59.900 50.000 0.00 0.00 0.00 3.67
3498 5332 2.099756 CACACACAGAGAGACAGACACA 59.900 50.000 0.00 0.00 0.00 3.72
3499 5333 2.099921 ACACACAGAGAGACAGACACAC 59.900 50.000 0.00 0.00 0.00 3.82
3500 5334 1.683917 ACACAGAGAGACAGACACACC 59.316 52.381 0.00 0.00 0.00 4.16
3501 5335 1.683385 CACAGAGAGACAGACACACCA 59.317 52.381 0.00 0.00 0.00 4.17
3502 5336 1.959985 ACAGAGAGACAGACACACCAG 59.040 52.381 0.00 0.00 0.00 4.00
3503 5337 1.959985 CAGAGAGACAGACACACCAGT 59.040 52.381 0.00 0.00 0.00 4.00
3504 5338 3.149981 CAGAGAGACAGACACACCAGTA 58.850 50.000 0.00 0.00 0.00 2.74
3505 5339 3.057876 CAGAGAGACAGACACACCAGTAC 60.058 52.174 0.00 0.00 0.00 2.73
3506 5340 1.880675 AGAGACAGACACACCAGTACG 59.119 52.381 0.00 0.00 0.00 3.67
3507 5341 1.607628 GAGACAGACACACCAGTACGT 59.392 52.381 0.00 0.00 0.00 3.57
3508 5342 2.029623 AGACAGACACACCAGTACGTT 58.970 47.619 0.00 0.00 0.00 3.99
3509 5343 2.429610 AGACAGACACACCAGTACGTTT 59.570 45.455 0.00 0.00 0.00 3.60
3510 5344 3.118884 AGACAGACACACCAGTACGTTTT 60.119 43.478 0.00 0.00 0.00 2.43
3511 5345 3.602483 ACAGACACACCAGTACGTTTTT 58.398 40.909 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 5.634859 GGCAAAAACAAGGTTATCATCAGTG 59.365 40.000 0.00 0.00 0.00 3.66
105 110 2.776072 CTAAAAGCGTGTCGGCCG 59.224 61.111 22.12 22.12 0.00 6.13
127 132 1.153469 GAGTCAGCCAGGCACTAGC 60.153 63.158 15.80 0.00 45.27 3.42
157 165 0.109319 GTTAAACCATGTGGCTGCGG 60.109 55.000 0.00 0.00 39.32 5.69
170 178 2.036571 CCACCCGAGCCGGTTAAAC 61.037 63.158 1.90 0.00 46.80 2.01
195 203 4.023137 GCAGTGCCACCCATCATT 57.977 55.556 2.85 0.00 0.00 2.57
205 213 2.358737 AGTAACAGCGGCAGTGCC 60.359 61.111 25.07 25.07 46.75 5.01
207 215 1.568612 CCACAGTAACAGCGGCAGTG 61.569 60.000 1.45 0.00 0.00 3.66
208 216 1.301716 CCACAGTAACAGCGGCAGT 60.302 57.895 1.45 0.00 0.00 4.40
209 217 2.034879 CCCACAGTAACAGCGGCAG 61.035 63.158 1.45 0.00 0.00 4.85
213 229 0.036388 ATCCACCCACAGTAACAGCG 60.036 55.000 0.00 0.00 0.00 5.18
231 247 7.964559 CAGATTATCATCAACAACAACAACGAT 59.035 33.333 0.00 0.00 0.00 3.73
233 249 7.297391 TCAGATTATCATCAACAACAACAACG 58.703 34.615 0.00 0.00 0.00 4.10
235 251 9.628746 CAATCAGATTATCATCAACAACAACAA 57.371 29.630 0.00 0.00 0.00 2.83
236 252 7.756272 GCAATCAGATTATCATCAACAACAACA 59.244 33.333 0.00 0.00 0.00 3.33
237 253 7.221452 GGCAATCAGATTATCATCAACAACAAC 59.779 37.037 0.00 0.00 0.00 3.32
247 263 4.147321 GGTGGTGGCAATCAGATTATCAT 58.853 43.478 0.00 0.00 0.00 2.45
279 295 1.133790 GGCAGGCATGATGTGAAAGTC 59.866 52.381 0.62 0.00 0.00 3.01
281 297 1.134367 CAGGCAGGCATGATGTGAAAG 59.866 52.381 0.62 0.00 0.00 2.62
374 398 3.603770 CGAAGATCCGTGCAAACATTTTC 59.396 43.478 0.00 0.00 0.00 2.29
389 413 9.559958 AAATGTCATTGATTTTACACGAAGATC 57.440 29.630 0.00 0.00 0.00 2.75
395 419 6.932901 AGCAAATGTCATTGATTTTACACG 57.067 33.333 0.00 0.00 31.84 4.49
424 448 9.881649 CATCTAGATGTGCCATAAGTATTACAT 57.118 33.333 22.42 0.00 31.36 2.29
500 2226 1.807142 CTCGCCTCCAAAGAAAACCTC 59.193 52.381 0.00 0.00 0.00 3.85
508 2234 2.680312 TGAAGATCTCGCCTCCAAAG 57.320 50.000 0.00 0.00 0.00 2.77
511 2237 3.566351 TCTTATGAAGATCTCGCCTCCA 58.434 45.455 0.00 0.00 31.20 3.86
530 2256 1.852633 TGTCATGGTCTCGTGGATCT 58.147 50.000 0.00 0.00 0.00 2.75
535 2261 1.354337 CGCCTTGTCATGGTCTCGTG 61.354 60.000 6.62 0.00 0.00 4.35
539 2265 1.296715 GTCCGCCTTGTCATGGTCT 59.703 57.895 6.62 0.00 0.00 3.85
545 2271 1.005867 GGTTACGTCCGCCTTGTCA 60.006 57.895 0.00 0.00 0.00 3.58
616 2342 6.203530 TGAATCGGATTGCATTCAGTTATCTC 59.796 38.462 8.18 0.00 34.71 2.75
660 2386 8.770828 TCTGCTCAAAGTGTAGTTAAATAACAC 58.229 33.333 6.13 7.73 43.02 3.32
690 2426 4.342092 ACTTTTCATTGGGTTGAGGACTTG 59.658 41.667 0.00 0.00 0.00 3.16
698 2434 1.665735 CGGCGACTTTTCATTGGGTTG 60.666 52.381 0.00 0.00 0.00 3.77
783 2527 2.501223 GAATGGACAGTGACGCGGGA 62.501 60.000 12.47 0.00 0.00 5.14
941 2685 0.878961 GGTGGTGTTGTCGTCACTCC 60.879 60.000 0.00 0.00 36.25 3.85
972 2716 3.764466 CGCCTGCCTCTCCGTCTT 61.764 66.667 0.00 0.00 0.00 3.01
994 2738 1.424493 GCGCACTTCTTCATCTCCGG 61.424 60.000 0.30 0.00 0.00 5.14
1095 2839 3.914117 TCGTCGTTTCCGTGGCCA 61.914 61.111 0.00 0.00 35.01 5.36
1188 2932 4.056125 CTGCTCACCGAGTCGCCA 62.056 66.667 7.12 0.00 31.39 5.69
1215 2959 0.179070 CTAAGAGGGAAGCTTCGGGC 60.179 60.000 19.91 11.06 42.19 6.13
1228 2972 3.665544 GCAGAGGCTGAGCTAAGAG 57.334 57.895 0.74 0.00 36.96 2.85
1297 3041 2.435586 CTCCAGGGCGTTCTGCTG 60.436 66.667 2.31 0.00 45.43 4.41
1427 3178 0.250640 CTCTGTTGCAGGCTGAAGGT 60.251 55.000 20.86 0.00 31.51 3.50
1482 3233 3.859627 GCTCGCTAGGTGTTGACTTAACA 60.860 47.826 0.00 0.00 46.62 2.41
1507 3279 4.634703 TGCGGTTCACATGGGCGT 62.635 61.111 0.00 0.00 0.00 5.68
1511 3283 0.677731 ATCCACTGCGGTTCACATGG 60.678 55.000 0.00 0.00 35.57 3.66
1541 3313 8.962111 GTGATGTTTCTCTTTTGTTCAGAATTC 58.038 33.333 0.00 0.00 0.00 2.17
1665 3437 6.371825 CCTTCCCAACTCTAAAATCAGTGTAC 59.628 42.308 0.00 0.00 0.00 2.90
1674 3446 9.243105 CTATCAATTTCCTTCCCAACTCTAAAA 57.757 33.333 0.00 0.00 0.00 1.52
1692 3472 3.846588 ACCCTGGTGTGTCTCTATCAATT 59.153 43.478 0.00 0.00 0.00 2.32
1905 3696 8.409358 AATTAGAATTTACAGAACTTGGCACT 57.591 30.769 0.00 0.00 0.00 4.40
1934 3725 4.634443 AGAAACGTAAGCAGTTTGTTCAGT 59.366 37.500 0.00 0.00 41.32 3.41
1963 3759 5.808540 CACAGGCAATTCATTAGTTCATTGG 59.191 40.000 0.00 0.00 0.00 3.16
1971 3767 8.984891 TGAAATTTACACAGGCAATTCATTAG 57.015 30.769 0.00 0.00 0.00 1.73
2046 3842 3.169155 AAGGTCAGTCAGCTGCGCA 62.169 57.895 10.98 10.98 42.29 6.09
2055 3851 1.202698 ACCTGCAACTCAAGGTCAGTC 60.203 52.381 0.00 0.00 0.00 3.51
2077 3873 0.176219 AGCAGCAGAGAGAGTGCATC 59.824 55.000 0.00 0.00 43.82 3.91
2079 3875 0.037512 GAAGCAGCAGAGAGAGTGCA 60.038 55.000 0.00 0.00 43.82 4.57
2080 3876 0.037512 TGAAGCAGCAGAGAGAGTGC 60.038 55.000 0.00 0.00 41.54 4.40
2082 3888 2.177734 TGATGAAGCAGCAGAGAGAGT 58.822 47.619 0.00 0.00 0.00 3.24
2084 3890 3.244318 TGTTTGATGAAGCAGCAGAGAGA 60.244 43.478 0.00 0.00 29.47 3.10
2088 3894 4.652421 TTTTGTTTGATGAAGCAGCAGA 57.348 36.364 0.00 0.00 29.47 4.26
2156 3964 4.800471 GTCAGAAGCTTGAAACAAACTTGG 59.200 41.667 2.10 0.00 0.00 3.61
2262 4072 1.238439 CGGTGGTGAACTGCTGATTT 58.762 50.000 0.00 0.00 0.00 2.17
2289 4099 4.286808 TCTGATTTGAGGATCCTGTTGTCA 59.713 41.667 22.02 16.20 0.00 3.58
2341 4151 4.090090 TCTTCCTTGTACCAGAGGAGAAG 58.910 47.826 9.01 6.96 42.67 2.85
2352 4162 6.937392 AGAGGTGACTATTTCTTCCTTGTAC 58.063 40.000 0.00 0.00 44.43 2.90
2355 4168 7.063544 CGTTTAGAGGTGACTATTTCTTCCTTG 59.936 40.741 0.00 0.00 44.43 3.61
2358 4171 6.628185 TCGTTTAGAGGTGACTATTTCTTCC 58.372 40.000 0.00 0.00 44.43 3.46
2397 4211 4.730657 CCAATTTCAGATGTCACTTCTGC 58.269 43.478 14.57 0.00 40.35 4.26
2398 4212 4.458295 AGCCAATTTCAGATGTCACTTCTG 59.542 41.667 13.43 13.43 41.61 3.02
2399 4213 4.660168 AGCCAATTTCAGATGTCACTTCT 58.340 39.130 0.00 0.00 0.00 2.85
2400 4214 4.142513 GGAGCCAATTTCAGATGTCACTTC 60.143 45.833 0.00 0.00 0.00 3.01
2401 4215 3.760684 GGAGCCAATTTCAGATGTCACTT 59.239 43.478 0.00 0.00 0.00 3.16
2402 4216 3.350833 GGAGCCAATTTCAGATGTCACT 58.649 45.455 0.00 0.00 0.00 3.41
2403 4217 2.096496 CGGAGCCAATTTCAGATGTCAC 59.904 50.000 0.00 0.00 0.00 3.67
2404 4218 2.358957 CGGAGCCAATTTCAGATGTCA 58.641 47.619 0.00 0.00 0.00 3.58
2608 4422 2.670414 CCGATGTCTGAACTTGAAGAGC 59.330 50.000 0.00 0.00 0.00 4.09
2629 4443 2.227968 CTTGCAGTGCTTCGTACCGC 62.228 60.000 17.60 0.00 0.00 5.68
2669 4483 4.809496 CTGGGCAAGCGGGCATCT 62.809 66.667 7.25 0.00 45.66 2.90
2737 4551 4.689345 CGTTACTATACATAAAGGCCCTGC 59.311 45.833 0.00 0.00 0.00 4.85
2891 4705 1.067354 GGACGACTCGGTTGGTTGTAT 60.067 52.381 2.98 0.00 32.13 2.29
2907 4721 5.263968 ACATAAGTAATGGACAGAGGACG 57.736 43.478 0.00 0.00 40.16 4.79
2972 4786 9.890629 AGATGATGCATAGTTAAGTTTTCTGTA 57.109 29.630 0.00 0.00 0.00 2.74
2973 4787 8.798859 AGATGATGCATAGTTAAGTTTTCTGT 57.201 30.769 0.00 0.00 0.00 3.41
2977 4791 9.035607 CGACTAGATGATGCATAGTTAAGTTTT 57.964 33.333 0.00 0.00 30.04 2.43
2980 4794 6.265649 ACCGACTAGATGATGCATAGTTAAGT 59.734 38.462 0.00 0.80 30.04 2.24
2996 4811 4.705507 AGCTACATCAAAGAACCGACTAGA 59.294 41.667 0.00 0.00 0.00 2.43
2997 4812 5.000012 AGCTACATCAAAGAACCGACTAG 58.000 43.478 0.00 0.00 0.00 2.57
2999 4814 3.511934 AGAGCTACATCAAAGAACCGACT 59.488 43.478 0.00 0.00 0.00 4.18
3031 4846 6.438763 CAACAGACGATACTATGCACTGATA 58.561 40.000 0.00 0.00 0.00 2.15
3039 4854 3.079960 ACGCCAACAGACGATACTATG 57.920 47.619 0.00 0.00 0.00 2.23
3066 4885 5.422214 TCATTTCCTAAGGACCTTCAGAC 57.578 43.478 10.87 0.00 0.00 3.51
3075 4894 7.110155 GTGAGGTTTACATCATTTCCTAAGGA 58.890 38.462 0.24 0.00 38.98 3.36
3076 4895 6.884295 TGTGAGGTTTACATCATTTCCTAAGG 59.116 38.462 0.24 0.00 38.98 2.69
3113 4932 4.082125 CCCTTTTTCAGCTGGTAGTTGAT 58.918 43.478 15.13 0.00 35.39 2.57
3128 4947 7.880713 AGTTTTGTACAAACACAATCCCTTTTT 59.119 29.630 20.43 1.23 38.18 1.94
3134 4953 6.326375 TCACAGTTTTGTACAAACACAATCC 58.674 36.000 20.43 3.58 38.18 3.01
3136 4955 7.151999 TCTCACAGTTTTGTACAAACACAAT 57.848 32.000 20.43 3.12 38.18 2.71
3159 4978 7.928908 TTCATTTACATTTGCACTCTGTTTC 57.071 32.000 0.00 0.00 0.00 2.78
3163 4982 7.595875 TGTCATTTCATTTACATTTGCACTCTG 59.404 33.333 0.00 0.00 0.00 3.35
3190 5009 7.480760 ACTTTGAAATTGGTGGCTATTATGT 57.519 32.000 0.00 0.00 0.00 2.29
3273 5092 5.885912 GTGACCAAGGCCTAATTCTTCATTA 59.114 40.000 5.16 0.00 0.00 1.90
3276 5095 3.561313 GGTGACCAAGGCCTAATTCTTCA 60.561 47.826 5.16 0.00 0.00 3.02
3333 5158 4.452795 AGTTAGGAAAAAGAGAAAGAGCGC 59.547 41.667 0.00 0.00 0.00 5.92
3335 5160 8.499967 CAAGTAGTTAGGAAAAAGAGAAAGAGC 58.500 37.037 0.00 0.00 0.00 4.09
3341 5174 4.689345 GCGCAAGTAGTTAGGAAAAAGAGA 59.311 41.667 0.30 0.00 41.68 3.10
3362 5195 1.944024 TGTTTTGGTAGGACAACTGCG 59.056 47.619 0.00 0.00 31.84 5.18
3390 5224 8.007821 CGGTAGCATTCTACTGTATATGTTTG 57.992 38.462 3.41 0.00 43.80 2.93
3414 5248 4.909880 GCTTACCTTTTTGTAGCAAGAACG 59.090 41.667 0.00 0.00 0.00 3.95
3425 5259 4.217767 GGTCCTAACCTGCTTACCTTTTTG 59.782 45.833 0.00 0.00 42.80 2.44
3430 5264 1.581223 GGGTCCTAACCTGCTTACCT 58.419 55.000 0.00 0.00 45.66 3.08
3464 5298 4.054455 GTGTGTACGTGCGGTGCG 62.054 66.667 0.00 0.00 33.41 5.34
3465 5299 2.962786 TGTGTGTACGTGCGGTGC 60.963 61.111 0.00 0.00 0.00 5.01
3466 5300 1.817217 CTGTGTGTGTACGTGCGGTG 61.817 60.000 0.00 0.00 0.00 4.94
3467 5301 1.590525 CTGTGTGTGTACGTGCGGT 60.591 57.895 0.00 0.00 0.00 5.68
3468 5302 1.275471 CTCTGTGTGTGTACGTGCGG 61.275 60.000 0.00 0.00 0.00 5.69
3469 5303 0.317519 TCTCTGTGTGTGTACGTGCG 60.318 55.000 0.00 0.00 0.00 5.34
3470 5304 1.001706 TCTCTCTGTGTGTGTACGTGC 60.002 52.381 0.00 0.00 0.00 5.34
3471 5305 2.032924 TGTCTCTCTGTGTGTGTACGTG 59.967 50.000 0.00 0.00 0.00 4.49
3472 5306 2.290916 CTGTCTCTCTGTGTGTGTACGT 59.709 50.000 0.00 0.00 0.00 3.57
3473 5307 2.548480 TCTGTCTCTCTGTGTGTGTACG 59.452 50.000 0.00 0.00 0.00 3.67
3474 5308 3.315470 TGTCTGTCTCTCTGTGTGTGTAC 59.685 47.826 0.00 0.00 0.00 2.90
3475 5309 3.315470 GTGTCTGTCTCTCTGTGTGTGTA 59.685 47.826 0.00 0.00 0.00 2.90
3476 5310 2.099921 GTGTCTGTCTCTCTGTGTGTGT 59.900 50.000 0.00 0.00 0.00 3.72
3477 5311 2.099756 TGTGTCTGTCTCTCTGTGTGTG 59.900 50.000 0.00 0.00 0.00 3.82
3478 5312 2.099921 GTGTGTCTGTCTCTCTGTGTGT 59.900 50.000 0.00 0.00 0.00 3.72
3479 5313 2.544694 GGTGTGTCTGTCTCTCTGTGTG 60.545 54.545 0.00 0.00 0.00 3.82
3480 5314 1.683917 GGTGTGTCTGTCTCTCTGTGT 59.316 52.381 0.00 0.00 0.00 3.72
3481 5315 1.683385 TGGTGTGTCTGTCTCTCTGTG 59.317 52.381 0.00 0.00 0.00 3.66
3482 5316 1.959985 CTGGTGTGTCTGTCTCTCTGT 59.040 52.381 0.00 0.00 0.00 3.41
3483 5317 1.959985 ACTGGTGTGTCTGTCTCTCTG 59.040 52.381 0.00 0.00 0.00 3.35
3484 5318 2.373335 ACTGGTGTGTCTGTCTCTCT 57.627 50.000 0.00 0.00 0.00 3.10
3485 5319 2.095668 CGTACTGGTGTGTCTGTCTCTC 60.096 54.545 0.00 0.00 0.00 3.20
3486 5320 1.880675 CGTACTGGTGTGTCTGTCTCT 59.119 52.381 0.00 0.00 0.00 3.10
3487 5321 1.607628 ACGTACTGGTGTGTCTGTCTC 59.392 52.381 0.00 0.00 0.00 3.36
3488 5322 1.688772 ACGTACTGGTGTGTCTGTCT 58.311 50.000 0.00 0.00 0.00 3.41
3489 5323 2.503920 AACGTACTGGTGTGTCTGTC 57.496 50.000 0.00 0.00 0.00 3.51
3490 5324 2.973694 AAACGTACTGGTGTGTCTGT 57.026 45.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.