Multiple sequence alignment - TraesCS7A01G488500

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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 TraesCS7A01G488500 chr7A 100.000 3727 0 0 686 4412 678952963 678956689 0.000000e+00 6883
1 TraesCS7A01G488500 chr7A 97.965 344 7 0 688 1031 678951751 678951408 8.170000e-167 597
2 TraesCS7A01G488500 chr7A 97.177 248 7 0 784 1031 672177137 672176890 1.900000e-113 420
3 TraesCS7A01G488500 chr7A 100.000 189 0 0 1 189 678952278 678952466 2.530000e-92 350
4 TraesCS7A01G488500 chr7A 76.166 579 111 19 3706 4269 65159972 65159406 3.360000e-71 279
5 TraesCS7A01G488500 chr7D 95.081 3253 144 10 1032 4269 587102309 587105560 0.000000e+00 5107
6 TraesCS7A01G488500 chr7D 78.891 559 96 13 3706 4253 61232642 61232095 4.200000e-95 359
7 TraesCS7A01G488500 chr7B 91.283 2650 154 28 1079 3696 658173547 658176151 0.000000e+00 3542
8 TraesCS7A01G488500 chr7B 91.621 907 57 13 1119 2015 658139326 658140223 0.000000e+00 1236
9 TraesCS7A01G488500 chr7B 81.928 415 68 5 3706 4113 711736988 711736574 1.170000e-90 344
10 TraesCS7A01G488500 chr1D 86.287 2319 277 22 1079 3385 366873836 366876125 0.000000e+00 2483
11 TraesCS7A01G488500 chr1D 82.101 257 37 8 1311 1564 366872583 366872833 1.240000e-50 211
12 TraesCS7A01G488500 chr1A 86.165 2313 278 31 1085 3385 465343396 465341114 0.000000e+00 2460
13 TraesCS7A01G488500 chr1A 81.703 634 110 6 2241 2873 465340728 465340100 1.410000e-144 523
14 TraesCS7A01G488500 chr1A 98.400 250 4 0 784 1033 104588349 104588100 1.460000e-119 440
15 TraesCS7A01G488500 chr1A 82.677 254 34 9 1314 1564 465344607 465344361 2.670000e-52 217
16 TraesCS7A01G488500 chr1B 85.843 2324 280 30 1085 3394 490723024 490720736 0.000000e+00 2423
17 TraesCS7A01G488500 chr1B 87.412 993 111 11 1232 2222 490446639 490447619 0.000000e+00 1129
18 TraesCS7A01G488500 chr5A 99.424 347 2 0 686 1032 534075494 534075148 8.050000e-177 630
19 TraesCS7A01G488500 chr5A 97.810 274 3 1 761 1034 48476176 48476446 1.860000e-128 470
20 TraesCS7A01G488500 chr5A 98.374 246 4 0 786 1031 534076088 534076333 2.440000e-117 433
21 TraesCS7A01G488500 chr5A 97.967 246 2 1 786 1031 48475156 48474914 1.470000e-114 424
22 TraesCS7A01G488500 chr5A 98.942 189 2 0 1 189 48475505 48475693 5.470000e-89 339
23 TraesCS7A01G488500 chr5A 98.942 189 2 0 1 189 534075739 534075551 5.470000e-89 339
24 TraesCS7A01G488500 chr5A 73.898 590 120 21 3697 4269 697768051 697768623 5.780000e-49 206
25 TraesCS7A01G488500 chr5B 99.194 248 2 0 784 1031 373757075 373756828 8.700000e-122 448
26 TraesCS7A01G488500 chr5B 78.605 631 100 19 3699 4313 115312413 115313024 6.920000e-103 385
27 TraesCS7A01G488500 chr4A 96.400 250 9 0 784 1033 40239771 40239522 3.180000e-111 412
28 TraesCS7A01G488500 chr4A 83.333 126 21 0 2710 2835 546297261 546297136 2.790000e-22 117
29 TraesCS7A01G488500 chr3B 77.306 542 99 19 3699 4227 583006531 583007061 9.280000e-77 298
30 TraesCS7A01G488500 chr6D 94.271 192 8 1 1 189 60166748 60166939 1.550000e-74 291
31 TraesCS7A01G488500 chr6D 90.395 177 14 2 13 189 60166862 60167035 3.430000e-56 230
32 TraesCS7A01G488500 chr6D 87.432 183 22 1 3907 4088 341076499 341076681 4.470000e-50 209
33 TraesCS7A01G488500 chr6B 93.651 189 9 3 1 189 133998809 133998994 3.360000e-71 279
34 TraesCS7A01G488500 chr6B 88.820 161 15 2 13 173 133999013 133999170 1.250000e-45 195
35 TraesCS7A01G488500 chr6B 92.105 76 5 1 3622 3696 681075908 681075833 6.040000e-19 106
36 TraesCS7A01G488500 chr2D 82.492 297 44 5 3697 3985 542523734 542524030 2.040000e-63 254
37 TraesCS7A01G488500 chr2D 81.041 269 43 6 3697 3958 565935599 565935332 1.610000e-49 207
38 TraesCS7A01G488500 chr6A 91.975 162 10 2 28 189 76637480 76637638 1.600000e-54 224
39 TraesCS7A01G488500 chr6A 90.062 161 13 2 13 173 76637561 76637718 5.780000e-49 206
40 TraesCS7A01G488500 chr6A 100.000 67 0 0 123 189 76637476 76637542 1.670000e-24 124
41 TraesCS7A01G488500 chr6A 98.246 57 1 0 1 57 76637177 76637233 2.810000e-17 100
42 TraesCS7A01G488500 chr4B 83.740 123 20 0 2710 2832 74442814 74442936 2.790000e-22 117
43 TraesCS7A01G488500 chr4D 82.927 123 21 0 2710 2832 50642875 50642997 1.300000e-20 111


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 TraesCS7A01G488500 chr7A 678952278 678956689 4411 False 3616.500000 6883 100.000 1 4412 2 chr7A.!!$F1 4411
1 TraesCS7A01G488500 chr7A 65159406 65159972 566 True 279.000000 279 76.166 3706 4269 1 chr7A.!!$R1 563
2 TraesCS7A01G488500 chr7D 587102309 587105560 3251 False 5107.000000 5107 95.081 1032 4269 1 chr7D.!!$F1 3237
3 TraesCS7A01G488500 chr7D 61232095 61232642 547 True 359.000000 359 78.891 3706 4253 1 chr7D.!!$R1 547
4 TraesCS7A01G488500 chr7B 658173547 658176151 2604 False 3542.000000 3542 91.283 1079 3696 1 chr7B.!!$F2 2617
5 TraesCS7A01G488500 chr7B 658139326 658140223 897 False 1236.000000 1236 91.621 1119 2015 1 chr7B.!!$F1 896
6 TraesCS7A01G488500 chr1D 366872583 366876125 3542 False 1347.000000 2483 84.194 1079 3385 2 chr1D.!!$F1 2306
7 TraesCS7A01G488500 chr1A 465340100 465344607 4507 True 1066.666667 2460 83.515 1085 3385 3 chr1A.!!$R2 2300
8 TraesCS7A01G488500 chr1B 490720736 490723024 2288 True 2423.000000 2423 85.843 1085 3394 1 chr1B.!!$R1 2309
9 TraesCS7A01G488500 chr1B 490446639 490447619 980 False 1129.000000 1129 87.412 1232 2222 1 chr1B.!!$F1 990
10 TraesCS7A01G488500 chr5A 534075148 534075739 591 True 484.500000 630 99.183 1 1032 2 chr5A.!!$R2 1031
11 TraesCS7A01G488500 chr5A 48475505 48476446 941 False 404.500000 470 98.376 1 1034 2 chr5A.!!$F3 1033
12 TraesCS7A01G488500 chr5A 697768051 697768623 572 False 206.000000 206 73.898 3697 4269 1 chr5A.!!$F2 572
13 TraesCS7A01G488500 chr5B 115312413 115313024 611 False 385.000000 385 78.605 3699 4313 1 chr5B.!!$F1 614
14 TraesCS7A01G488500 chr3B 583006531 583007061 530 False 298.000000 298 77.306 3699 4227 1 chr3B.!!$F1 528

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
954 1323 3.194116 ACGGATTAGCGAGAAAGTGGTAA 59.806 43.478 0.00 0.00 33.18 2.85 F
1076 1445 0.384725 GCAGTAAATAGCCATGCGCG 60.385 55.000 0.00 0.00 44.76 6.86 F
1077 1446 0.384725 CAGTAAATAGCCATGCGCGC 60.385 55.000 27.26 27.26 44.76 6.86 F
1746 2128 0.392998 ACTCCAATGTGACCATCGCC 60.393 55.000 0.00 0.00 0.00 5.54 F
1839 2221 1.065928 CGCGTCCTTCTTCGGCTAT 59.934 57.895 0.00 0.00 0.00 2.97 F
2410 2795 1.593209 TTCCTGTCCAACGACACGC 60.593 57.895 0.00 0.00 44.20 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 2266 1.671054 CCACAGGGCCTTGTACACG 60.671 63.158 21.55 8.16 0.00 4.49 R
2843 3236 1.966451 GGAGCCAAGGTGTTGTCCG 60.966 63.158 0.00 0.00 30.95 4.79 R
2980 3376 2.674852 CGCACATGAGCTTGATGTAGTT 59.325 45.455 13.36 0.00 32.64 2.24 R
3235 3631 0.104487 TGCTTACCGTCGAACACCAA 59.896 50.000 0.00 0.00 0.00 3.67 R
3245 3641 0.388649 CTGCTTCTCGTGCTTACCGT 60.389 55.000 0.00 0.00 0.00 4.83 R
4386 5143 0.107654 CCTCCCCGGTGAAGCTAAAG 60.108 60.000 0.00 0.00 0.00 1.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
954 1323 3.194116 ACGGATTAGCGAGAAAGTGGTAA 59.806 43.478 0.00 0.00 33.18 2.85
1000 1369 2.027003 AGTTTTTCGTCACGGTTCCA 57.973 45.000 0.00 0.00 0.00 3.53
1034 1403 8.631797 TGGTAGTTTTTGGTTAAATACTCCAAC 58.368 33.333 0.00 0.00 40.32 3.77
1035 1404 8.084073 GGTAGTTTTTGGTTAAATACTCCAACC 58.916 37.037 0.00 0.00 40.32 3.77
1039 1408 3.677190 TGGTTAAATACTCCAACCACCG 58.323 45.455 1.38 0.00 45.15 4.94
1040 1409 3.327172 TGGTTAAATACTCCAACCACCGA 59.673 43.478 1.38 0.00 45.15 4.69
1041 1410 4.202440 TGGTTAAATACTCCAACCACCGAA 60.202 41.667 1.38 0.00 45.15 4.30
1042 1411 4.393990 GGTTAAATACTCCAACCACCGAAG 59.606 45.833 0.00 0.00 41.17 3.79
1043 1412 6.600811 GGTTAAATACTCCAACCACCGAAGG 61.601 48.000 0.00 0.00 42.66 3.46
1044 1413 8.700984 GGTTAAATACTCCAACCACCGAAGGA 62.701 46.154 0.00 0.00 45.86 3.36
1063 1432 3.777465 GAGTCGTACTCCATGCAGTAA 57.223 47.619 0.00 0.00 39.28 2.24
1064 1433 4.106029 GAGTCGTACTCCATGCAGTAAA 57.894 45.455 0.00 0.00 39.28 2.01
1065 1434 4.683832 GAGTCGTACTCCATGCAGTAAAT 58.316 43.478 0.00 0.00 39.28 1.40
1066 1435 5.828747 GAGTCGTACTCCATGCAGTAAATA 58.171 41.667 0.00 0.00 39.28 1.40
1067 1436 5.833082 AGTCGTACTCCATGCAGTAAATAG 58.167 41.667 0.00 0.00 30.47 1.73
1068 1437 4.444720 GTCGTACTCCATGCAGTAAATAGC 59.555 45.833 0.00 0.00 30.47 2.97
1069 1438 3.741344 CGTACTCCATGCAGTAAATAGCC 59.259 47.826 0.00 0.00 30.47 3.93
1070 1439 3.931907 ACTCCATGCAGTAAATAGCCA 57.068 42.857 0.00 0.00 0.00 4.75
1071 1440 4.443978 ACTCCATGCAGTAAATAGCCAT 57.556 40.909 0.00 0.00 0.00 4.40
1072 1441 4.139786 ACTCCATGCAGTAAATAGCCATG 58.860 43.478 0.00 0.00 0.00 3.66
1073 1442 2.886523 TCCATGCAGTAAATAGCCATGC 59.113 45.455 0.00 0.00 37.40 4.06
1074 1443 2.351060 CCATGCAGTAAATAGCCATGCG 60.351 50.000 0.00 0.00 39.74 4.73
1075 1444 0.662619 TGCAGTAAATAGCCATGCGC 59.337 50.000 0.00 0.00 39.74 6.09
1076 1445 0.384725 GCAGTAAATAGCCATGCGCG 60.385 55.000 0.00 0.00 44.76 6.86
1077 1446 0.384725 CAGTAAATAGCCATGCGCGC 60.385 55.000 27.26 27.26 44.76 6.86
1078 1447 1.082104 GTAAATAGCCATGCGCGCC 60.082 57.895 30.77 13.41 44.76 6.53
1079 1448 2.603247 TAAATAGCCATGCGCGCCG 61.603 57.895 30.77 19.84 44.76 6.46
1190 1560 3.155167 CCTGGTCGCCCTCTACCC 61.155 72.222 0.00 0.00 34.69 3.69
1286 1665 2.741092 GGTGTTCTCGAGCCACCA 59.259 61.111 32.25 15.57 46.33 4.17
1404 1783 2.586792 GATGGGCTCGACAGGCTT 59.413 61.111 0.00 0.00 44.88 4.35
1524 1903 2.452116 CGGAGGAATATGGGAGGCA 58.548 57.895 0.00 0.00 0.00 4.75
1746 2128 0.392998 ACTCCAATGTGACCATCGCC 60.393 55.000 0.00 0.00 0.00 5.54
1839 2221 1.065928 CGCGTCCTTCTTCGGCTAT 59.934 57.895 0.00 0.00 0.00 2.97
1927 2309 2.565394 GACGCGTACGCTTCCGATG 61.565 63.158 34.69 20.89 45.53 3.84
1983 2365 2.795297 GACGTGCTCTCCCTCTCG 59.205 66.667 0.00 0.00 0.00 4.04
2410 2795 1.593209 TTCCTGTCCAACGACACGC 60.593 57.895 0.00 0.00 44.20 5.34
2899 3292 2.202743 GCATCGAGTACGCAGCCA 60.203 61.111 0.00 0.00 39.58 4.75
2900 3293 2.233654 GCATCGAGTACGCAGCCAG 61.234 63.158 0.00 0.00 39.58 4.85
2952 3348 4.658786 AACCGCTCCCTGGACCCT 62.659 66.667 0.00 0.00 0.00 4.34
3042 3438 2.497138 CAGATCAAGACTGTGGTGCAA 58.503 47.619 0.00 0.00 0.00 4.08
3218 3614 1.764571 CTGGACGGGGTGAAGGTGAA 61.765 60.000 0.00 0.00 0.00 3.18
3235 3631 3.394635 AACGTCGTGCCCAACAGGT 62.395 57.895 0.00 0.00 38.26 4.00
3317 3713 2.552743 GCCAAATAATCCCCGAAGTAGC 59.447 50.000 0.00 0.00 0.00 3.58
3704 4305 2.203788 TCCTCCTCCACTGCGGTT 60.204 61.111 0.00 0.00 35.57 4.44
3802 4479 4.619973 GAAACTTTGTGGCATGTCAATCA 58.380 39.130 0.00 0.00 0.00 2.57
3897 4644 2.438975 ATGCCGCCATCCACACAG 60.439 61.111 0.00 0.00 0.00 3.66
4014 4761 6.008960 AGATCTGAAGACTGGCAAGAAAATT 58.991 36.000 0.00 0.00 0.00 1.82
4052 4800 0.185901 ACCGCCCATTAGAATGCCAT 59.814 50.000 0.00 0.00 35.08 4.40
4119 4868 2.158638 TGCCCAGCATTGATGTAGCATA 60.159 45.455 11.45 0.00 31.71 3.14
4128 4877 6.996879 AGCATTGATGTAGCATATCTGAAAGT 59.003 34.615 0.00 0.00 33.76 2.66
4212 4961 1.681793 GCTGGAGCAGTAGACGGATAA 59.318 52.381 0.00 0.00 41.59 1.75
4237 4986 2.264794 GACCCATCGTCGGCACTT 59.735 61.111 0.00 0.00 0.00 3.16
4259 5012 2.508526 CCAGTGTTGAGGAAGGAAAGG 58.491 52.381 0.00 0.00 0.00 3.11
4260 5013 2.158608 CCAGTGTTGAGGAAGGAAAGGT 60.159 50.000 0.00 0.00 0.00 3.50
4263 5016 1.157585 GTTGAGGAAGGAAAGGTCGC 58.842 55.000 0.00 0.00 0.00 5.19
4265 5018 0.836400 TGAGGAAGGAAAGGTCGCCT 60.836 55.000 0.00 0.00 35.61 5.52
4271 5024 2.184579 GAAAGGTCGCCTCCTCCG 59.815 66.667 0.00 0.00 36.74 4.63
4273 5026 4.698625 AAGGTCGCCTCCTCCGGT 62.699 66.667 0.00 0.00 36.74 5.28
4278 5035 4.135153 CGCCTCCTCCGGTCTGTG 62.135 72.222 0.00 0.00 0.00 3.66
4280 5037 2.973899 CCTCCTCCGGTCTGTGTG 59.026 66.667 0.00 0.00 0.00 3.82
4284 5041 2.923035 CTCCGGTCTGTGTGGGGT 60.923 66.667 0.00 0.00 0.00 4.95
4292 5049 1.002087 GTCTGTGTGGGGTGGTTCTAG 59.998 57.143 0.00 0.00 0.00 2.43
4300 5057 1.278413 GGGGTGGTTCTAGGAGTGAAC 59.722 57.143 0.00 0.00 42.00 3.18
4302 5059 1.617357 GGTGGTTCTAGGAGTGAACGT 59.383 52.381 0.00 0.00 43.21 3.99
4315 5072 3.975992 GAACGTAGCGGTTCGTAGA 57.024 52.632 19.31 0.00 39.39 2.59
4316 5073 1.807738 GAACGTAGCGGTTCGTAGAG 58.192 55.000 19.31 0.00 39.39 2.43
4317 5074 0.179179 AACGTAGCGGTTCGTAGAGC 60.179 55.000 19.31 0.00 39.39 4.09
4324 5081 3.676742 GTTCGTAGAGCCGAAGCG 58.323 61.111 0.00 0.00 46.45 4.68
4325 5082 1.154073 GTTCGTAGAGCCGAAGCGT 60.154 57.895 0.00 0.00 46.45 5.07
4326 5083 0.731855 GTTCGTAGAGCCGAAGCGTT 60.732 55.000 0.00 0.00 46.45 4.84
4327 5084 0.731514 TTCGTAGAGCCGAAGCGTTG 60.732 55.000 0.00 0.00 46.67 4.10
4328 5085 2.158959 CGTAGAGCCGAAGCGTTGG 61.159 63.158 0.75 0.75 46.67 3.77
4329 5086 1.214589 GTAGAGCCGAAGCGTTGGA 59.785 57.895 10.51 0.00 46.67 3.53
4330 5087 0.802607 GTAGAGCCGAAGCGTTGGAG 60.803 60.000 10.51 0.00 46.67 3.86
4331 5088 1.248785 TAGAGCCGAAGCGTTGGAGT 61.249 55.000 10.51 0.00 46.67 3.85
4332 5089 2.048127 AGCCGAAGCGTTGGAGTC 60.048 61.111 10.51 0.00 46.67 3.36
4333 5090 2.357034 GCCGAAGCGTTGGAGTCA 60.357 61.111 10.51 0.00 0.00 3.41
4334 5091 2.383527 GCCGAAGCGTTGGAGTCAG 61.384 63.158 10.51 0.00 0.00 3.51
4335 5092 2.383527 CCGAAGCGTTGGAGTCAGC 61.384 63.158 0.00 0.00 0.00 4.26
4336 5093 2.383527 CGAAGCGTTGGAGTCAGCC 61.384 63.158 0.00 0.00 0.00 4.85
4337 5094 1.004440 GAAGCGTTGGAGTCAGCCT 60.004 57.895 0.00 0.00 0.00 4.58
4338 5095 0.603975 GAAGCGTTGGAGTCAGCCTT 60.604 55.000 0.00 0.00 0.00 4.35
4339 5096 0.179018 AAGCGTTGGAGTCAGCCTTT 60.179 50.000 0.00 0.00 0.00 3.11
4340 5097 0.603975 AGCGTTGGAGTCAGCCTTTC 60.604 55.000 0.00 0.00 0.00 2.62
4341 5098 0.884704 GCGTTGGAGTCAGCCTTTCA 60.885 55.000 0.00 0.00 0.00 2.69
4342 5099 1.593196 CGTTGGAGTCAGCCTTTCAA 58.407 50.000 0.00 0.00 0.00 2.69
4343 5100 1.946768 CGTTGGAGTCAGCCTTTCAAA 59.053 47.619 0.00 0.00 0.00 2.69
4344 5101 2.554032 CGTTGGAGTCAGCCTTTCAAAT 59.446 45.455 0.00 0.00 0.00 2.32
4345 5102 3.610114 CGTTGGAGTCAGCCTTTCAAATG 60.610 47.826 0.00 0.00 0.00 2.32
4346 5103 3.507162 TGGAGTCAGCCTTTCAAATGA 57.493 42.857 0.00 0.00 0.00 2.57
4347 5104 4.038271 TGGAGTCAGCCTTTCAAATGAT 57.962 40.909 0.00 0.00 0.00 2.45
4348 5105 5.178096 TGGAGTCAGCCTTTCAAATGATA 57.822 39.130 0.00 0.00 0.00 2.15
4349 5106 5.759059 TGGAGTCAGCCTTTCAAATGATAT 58.241 37.500 0.00 0.00 0.00 1.63
4350 5107 5.824624 TGGAGTCAGCCTTTCAAATGATATC 59.175 40.000 0.00 0.00 0.00 1.63
4351 5108 5.824624 GGAGTCAGCCTTTCAAATGATATCA 59.175 40.000 8.10 8.10 0.00 2.15
4352 5109 6.489361 GGAGTCAGCCTTTCAAATGATATCAT 59.511 38.462 12.62 12.62 38.41 2.45
4366 5123 5.645056 TGATATCATTTGGGCTACCTTCA 57.355 39.130 0.00 0.00 37.76 3.02
4367 5124 5.624159 TGATATCATTTGGGCTACCTTCAG 58.376 41.667 0.00 0.00 37.76 3.02
4368 5125 5.132648 TGATATCATTTGGGCTACCTTCAGT 59.867 40.000 0.00 0.00 37.76 3.41
4369 5126 3.806949 TCATTTGGGCTACCTTCAGTT 57.193 42.857 0.00 0.00 37.76 3.16
4370 5127 4.919774 TCATTTGGGCTACCTTCAGTTA 57.080 40.909 0.00 0.00 37.76 2.24
4371 5128 5.249780 TCATTTGGGCTACCTTCAGTTAA 57.750 39.130 0.00 0.00 37.76 2.01
4372 5129 5.826643 TCATTTGGGCTACCTTCAGTTAAT 58.173 37.500 0.00 0.00 37.76 1.40
4373 5130 6.964464 TCATTTGGGCTACCTTCAGTTAATA 58.036 36.000 0.00 0.00 37.76 0.98
4374 5131 7.406916 TCATTTGGGCTACCTTCAGTTAATAA 58.593 34.615 0.00 0.00 37.76 1.40
4375 5132 8.058847 TCATTTGGGCTACCTTCAGTTAATAAT 58.941 33.333 0.00 0.00 37.76 1.28
4376 5133 8.695456 CATTTGGGCTACCTTCAGTTAATAATT 58.305 33.333 0.00 0.00 37.76 1.40
4377 5134 8.658840 TTTGGGCTACCTTCAGTTAATAATTT 57.341 30.769 0.00 0.00 37.76 1.82
4378 5135 8.658840 TTGGGCTACCTTCAGTTAATAATTTT 57.341 30.769 0.00 0.00 37.76 1.82
4379 5136 8.288689 TGGGCTACCTTCAGTTAATAATTTTC 57.711 34.615 0.00 0.00 37.76 2.29
4380 5137 8.113462 TGGGCTACCTTCAGTTAATAATTTTCT 58.887 33.333 0.00 0.00 37.76 2.52
4381 5138 8.622157 GGGCTACCTTCAGTTAATAATTTTCTC 58.378 37.037 0.00 0.00 0.00 2.87
4382 5139 8.336080 GGCTACCTTCAGTTAATAATTTTCTCG 58.664 37.037 0.00 0.00 0.00 4.04
4383 5140 8.880750 GCTACCTTCAGTTAATAATTTTCTCGT 58.119 33.333 0.00 0.00 0.00 4.18
4386 5143 8.021396 ACCTTCAGTTAATAATTTTCTCGTTGC 58.979 33.333 0.00 0.00 0.00 4.17
4387 5144 8.237267 CCTTCAGTTAATAATTTTCTCGTTGCT 58.763 33.333 0.00 0.00 0.00 3.91
4388 5145 9.612620 CTTCAGTTAATAATTTTCTCGTTGCTT 57.387 29.630 0.00 0.00 0.00 3.91
4389 5146 9.959749 TTCAGTTAATAATTTTCTCGTTGCTTT 57.040 25.926 0.00 0.00 0.00 3.51
4392 5149 9.556030 AGTTAATAATTTTCTCGTTGCTTTAGC 57.444 29.630 0.00 0.00 42.50 3.09
4393 5150 9.556030 GTTAATAATTTTCTCGTTGCTTTAGCT 57.444 29.630 3.10 0.00 42.66 3.32
4395 5152 8.675040 AATAATTTTCTCGTTGCTTTAGCTTC 57.325 30.769 0.00 0.00 42.66 3.86
4396 5153 5.689383 ATTTTCTCGTTGCTTTAGCTTCA 57.311 34.783 0.00 0.00 42.66 3.02
4397 5154 4.468095 TTTCTCGTTGCTTTAGCTTCAC 57.532 40.909 0.00 0.00 42.66 3.18
4398 5155 2.413837 TCTCGTTGCTTTAGCTTCACC 58.586 47.619 0.00 0.00 42.66 4.02
4399 5156 1.126846 CTCGTTGCTTTAGCTTCACCG 59.873 52.381 0.00 0.00 42.66 4.94
4400 5157 0.165944 CGTTGCTTTAGCTTCACCGG 59.834 55.000 0.00 0.00 42.66 5.28
4401 5158 0.521735 GTTGCTTTAGCTTCACCGGG 59.478 55.000 6.32 0.00 42.66 5.73
4402 5159 0.608035 TTGCTTTAGCTTCACCGGGG 60.608 55.000 6.32 0.00 42.66 5.73
4403 5160 1.298667 GCTTTAGCTTCACCGGGGA 59.701 57.895 0.00 0.00 38.21 4.81
4404 5161 0.744771 GCTTTAGCTTCACCGGGGAG 60.745 60.000 6.46 2.19 38.21 4.30
4406 5163 0.545787 TTTAGCTTCACCGGGGAGGA 60.546 55.000 21.86 0.00 45.00 3.71
4407 5164 1.262640 TTAGCTTCACCGGGGAGGAC 61.263 60.000 21.86 11.05 45.00 3.85
4408 5165 4.097361 GCTTCACCGGGGAGGACC 62.097 72.222 21.86 0.00 45.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
954 1323 6.146898 CACTTTACGATTTTGTCCCGAAAAT 58.853 36.000 0.00 0.00 38.07 1.82
1043 1412 3.777465 TTACTGCATGGAGTACGACTC 57.223 47.619 24.86 6.50 44.32 3.36
1044 1413 4.737855 ATTTACTGCATGGAGTACGACT 57.262 40.909 24.86 8.59 0.00 4.18
1045 1414 4.444720 GCTATTTACTGCATGGAGTACGAC 59.555 45.833 24.86 10.54 0.00 4.34
1046 1415 4.500887 GGCTATTTACTGCATGGAGTACGA 60.501 45.833 24.86 17.06 0.00 3.43
1047 1416 3.741344 GGCTATTTACTGCATGGAGTACG 59.259 47.826 24.86 14.76 0.00 3.67
1048 1417 4.703897 TGGCTATTTACTGCATGGAGTAC 58.296 43.478 24.86 13.70 0.00 2.73
1049 1418 5.308014 CATGGCTATTTACTGCATGGAGTA 58.692 41.667 21.77 21.77 0.00 2.59
1050 1419 3.931907 TGGCTATTTACTGCATGGAGT 57.068 42.857 24.00 24.00 0.00 3.85
1051 1420 3.057736 GCATGGCTATTTACTGCATGGAG 60.058 47.826 13.34 13.34 33.13 3.86
1052 1421 2.886523 GCATGGCTATTTACTGCATGGA 59.113 45.455 0.00 0.00 33.13 3.41
1053 1422 2.351060 CGCATGGCTATTTACTGCATGG 60.351 50.000 0.00 0.00 33.13 3.66
1054 1423 2.919387 GCGCATGGCTATTTACTGCATG 60.919 50.000 0.30 0.00 39.11 4.06
1055 1424 1.267806 GCGCATGGCTATTTACTGCAT 59.732 47.619 0.30 0.00 39.11 3.96
1056 1425 0.662619 GCGCATGGCTATTTACTGCA 59.337 50.000 0.30 0.00 39.11 4.41
1057 1426 0.384725 CGCGCATGGCTATTTACTGC 60.385 55.000 8.75 0.00 40.44 4.40
1058 1427 0.384725 GCGCGCATGGCTATTTACTG 60.385 55.000 29.10 0.00 40.44 2.74
1059 1428 1.507141 GGCGCGCATGGCTATTTACT 61.507 55.000 34.42 0.00 40.44 2.24
1060 1429 1.082104 GGCGCGCATGGCTATTTAC 60.082 57.895 34.42 6.62 40.44 2.01
1061 1430 2.603247 CGGCGCGCATGGCTATTTA 61.603 57.895 34.42 0.00 40.44 1.40
1062 1431 3.952675 CGGCGCGCATGGCTATTT 61.953 61.111 34.42 0.00 40.44 1.40
1079 1448 2.090524 CGGTGTCTTAACGGGCGAC 61.091 63.158 0.00 0.00 0.00 5.19
1080 1449 2.259204 CGGTGTCTTAACGGGCGA 59.741 61.111 0.00 0.00 0.00 5.54
1081 1450 2.812178 CCGGTGTCTTAACGGGCG 60.812 66.667 0.00 0.00 43.69 6.13
1085 1454 2.048877 ACGGCCGGTGTCTTAACG 60.049 61.111 31.76 0.00 0.00 3.18
1086 1455 2.090524 CGACGGCCGGTGTCTTAAC 61.091 63.158 31.76 7.68 34.17 2.01
1087 1456 1.240641 TACGACGGCCGGTGTCTTAA 61.241 55.000 31.76 9.09 43.93 1.85
1088 1457 1.673993 TACGACGGCCGGTGTCTTA 60.674 57.895 31.76 13.11 43.93 2.10
1089 1458 2.985282 TACGACGGCCGGTGTCTT 60.985 61.111 31.76 14.21 43.93 3.01
1090 1459 3.741476 GTACGACGGCCGGTGTCT 61.741 66.667 31.76 7.71 43.93 3.41
1286 1665 2.675423 TGGACTCGTACCAGCGCT 60.675 61.111 2.64 2.64 33.22 5.92
1323 1702 1.905512 GTAGAACATGTCCGCCCCT 59.094 57.895 0.00 0.00 0.00 4.79
1509 1888 0.987294 CGGATGCCTCCCATATTCCT 59.013 55.000 2.04 0.00 38.45 3.36
1698 2077 1.170290 GGCCCTTGTTGTACTTGCGT 61.170 55.000 0.00 0.00 0.00 5.24
1884 2266 1.671054 CCACAGGGCCTTGTACACG 60.671 63.158 21.55 8.16 0.00 4.49
1927 2309 2.585247 GTCCATGGCGGCGAGTAC 60.585 66.667 12.98 0.00 33.14 2.73
2238 2620 3.782443 ACGATCCTGGCGTTCCCC 61.782 66.667 0.00 0.00 39.18 4.81
2410 2795 3.482436 AGTTCTCGTATAGCTCCCTCAG 58.518 50.000 0.00 0.00 0.00 3.35
2843 3236 1.966451 GGAGCCAAGGTGTTGTCCG 60.966 63.158 0.00 0.00 30.95 4.79
2976 3372 4.934001 CACATGAGCTTGATGTAGTTGTCT 59.066 41.667 10.96 0.00 32.64 3.41
2980 3376 2.674852 CGCACATGAGCTTGATGTAGTT 59.325 45.455 13.36 0.00 32.64 2.24
3218 3614 3.394635 AACCTGTTGGGCACGACGT 62.395 57.895 0.89 0.00 39.10 4.34
3235 3631 0.104487 TGCTTACCGTCGAACACCAA 59.896 50.000 0.00 0.00 0.00 3.67
3245 3641 0.388649 CTGCTTCTCGTGCTTACCGT 60.389 55.000 0.00 0.00 0.00 4.83
3317 3713 3.001228 CCATGTCAACGATCCATACAACG 59.999 47.826 0.00 0.00 0.00 4.10
3704 4305 6.506661 AGATGCTCCTCCATATCTTGGTATA 58.493 40.000 0.00 0.00 46.52 1.47
3814 4556 4.443457 CGGTGATGGAATCTAGTGGACATT 60.443 45.833 0.00 0.00 45.81 2.71
3897 4644 3.002348 GTGTTTGGTGTCTTGTAGTGAGC 59.998 47.826 0.00 0.00 0.00 4.26
4030 4777 1.103398 GCATTCTAATGGGCGGTGCT 61.103 55.000 4.93 0.00 36.90 4.40
4052 4800 2.079170 ATGCTCTTCCTCCATCTCGA 57.921 50.000 0.00 0.00 0.00 4.04
4212 4961 2.359404 ACGATGGGTCCTCGTCCT 59.641 61.111 0.46 0.00 45.63 3.85
4237 4986 0.843309 TTCCTTCCTCAACACTGGCA 59.157 50.000 0.00 0.00 0.00 4.92
4241 4990 2.224305 CGACCTTTCCTTCCTCAACACT 60.224 50.000 0.00 0.00 0.00 3.55
4271 5024 1.228154 GAACCACCCCACACAGACC 60.228 63.158 0.00 0.00 0.00 3.85
4273 5026 1.348064 CTAGAACCACCCCACACAGA 58.652 55.000 0.00 0.00 0.00 3.41
4278 5035 0.613777 CACTCCTAGAACCACCCCAC 59.386 60.000 0.00 0.00 0.00 4.61
4280 5037 1.278413 GTTCACTCCTAGAACCACCCC 59.722 57.143 0.00 0.00 39.48 4.95
4284 5041 2.490903 GCTACGTTCACTCCTAGAACCA 59.509 50.000 0.00 0.00 41.72 3.67
4292 5049 1.069378 CGAACCGCTACGTTCACTCC 61.069 60.000 0.00 0.00 41.89 3.85
4300 5057 1.298190 GGCTCTACGAACCGCTACG 60.298 63.158 0.00 0.00 0.00 3.51
4302 5059 1.026182 TTCGGCTCTACGAACCGCTA 61.026 55.000 1.09 0.00 46.68 4.26
4313 5070 2.262915 CTCCAACGCTTCGGCTCT 59.737 61.111 0.00 0.00 39.13 4.09
4314 5071 2.048127 ACTCCAACGCTTCGGCTC 60.048 61.111 0.00 0.00 39.13 4.70
4315 5072 2.048127 GACTCCAACGCTTCGGCT 60.048 61.111 0.00 0.00 39.13 5.52
4316 5073 2.357034 TGACTCCAACGCTTCGGC 60.357 61.111 0.00 0.00 37.65 5.54
4317 5074 2.383527 GCTGACTCCAACGCTTCGG 61.384 63.158 0.00 0.00 0.00 4.30
4318 5075 2.383527 GGCTGACTCCAACGCTTCG 61.384 63.158 0.00 0.00 0.00 3.79
4319 5076 0.603975 AAGGCTGACTCCAACGCTTC 60.604 55.000 0.00 0.00 0.00 3.86
4320 5077 0.179018 AAAGGCTGACTCCAACGCTT 60.179 50.000 0.00 0.00 0.00 4.68
4321 5078 0.603975 GAAAGGCTGACTCCAACGCT 60.604 55.000 0.00 0.00 0.00 5.07
4322 5079 0.884704 TGAAAGGCTGACTCCAACGC 60.885 55.000 0.00 0.00 0.00 4.84
4323 5080 1.593196 TTGAAAGGCTGACTCCAACG 58.407 50.000 0.00 0.00 0.00 4.10
4324 5081 3.569701 TCATTTGAAAGGCTGACTCCAAC 59.430 43.478 0.00 0.00 0.00 3.77
4325 5082 3.831323 TCATTTGAAAGGCTGACTCCAA 58.169 40.909 0.00 0.00 0.00 3.53
4326 5083 3.507162 TCATTTGAAAGGCTGACTCCA 57.493 42.857 0.00 0.00 0.00 3.86
4327 5084 5.824624 TGATATCATTTGAAAGGCTGACTCC 59.175 40.000 0.00 0.00 0.00 3.85
4328 5085 6.932356 TGATATCATTTGAAAGGCTGACTC 57.068 37.500 0.00 0.00 0.00 3.36
4329 5086 7.893124 AATGATATCATTTGAAAGGCTGACT 57.107 32.000 22.65 0.00 43.48 3.41
4343 5100 6.183361 ACTGAAGGTAGCCCAAATGATATCAT 60.183 38.462 12.62 12.62 38.41 2.45
4344 5101 5.132648 ACTGAAGGTAGCCCAAATGATATCA 59.867 40.000 8.10 8.10 0.00 2.15
4345 5102 5.625150 ACTGAAGGTAGCCCAAATGATATC 58.375 41.667 0.00 0.00 0.00 1.63
4346 5103 5.653255 ACTGAAGGTAGCCCAAATGATAT 57.347 39.130 0.00 0.00 0.00 1.63
4347 5104 5.450818 AACTGAAGGTAGCCCAAATGATA 57.549 39.130 0.00 0.00 0.00 2.15
4348 5105 4.322057 AACTGAAGGTAGCCCAAATGAT 57.678 40.909 0.00 0.00 0.00 2.45
4349 5106 3.806949 AACTGAAGGTAGCCCAAATGA 57.193 42.857 0.00 0.00 0.00 2.57
4350 5107 7.639113 TTATTAACTGAAGGTAGCCCAAATG 57.361 36.000 0.00 0.00 0.00 2.32
4351 5108 8.838649 AATTATTAACTGAAGGTAGCCCAAAT 57.161 30.769 0.00 0.00 0.00 2.32
4352 5109 8.658840 AAATTATTAACTGAAGGTAGCCCAAA 57.341 30.769 0.00 0.00 0.00 3.28
4353 5110 8.658840 AAAATTATTAACTGAAGGTAGCCCAA 57.341 30.769 0.00 0.00 0.00 4.12
4354 5111 8.113462 AGAAAATTATTAACTGAAGGTAGCCCA 58.887 33.333 0.00 0.00 0.00 5.36
4355 5112 8.521170 AGAAAATTATTAACTGAAGGTAGCCC 57.479 34.615 0.00 0.00 0.00 5.19
4356 5113 8.336080 CGAGAAAATTATTAACTGAAGGTAGCC 58.664 37.037 0.00 0.00 0.00 3.93
4357 5114 8.880750 ACGAGAAAATTATTAACTGAAGGTAGC 58.119 33.333 0.00 0.00 0.00 3.58
4360 5117 8.021396 GCAACGAGAAAATTATTAACTGAAGGT 58.979 33.333 0.00 0.00 0.00 3.50
4361 5118 8.237267 AGCAACGAGAAAATTATTAACTGAAGG 58.763 33.333 0.00 0.00 0.00 3.46
4362 5119 9.612620 AAGCAACGAGAAAATTATTAACTGAAG 57.387 29.630 0.00 0.00 0.00 3.02
4363 5120 9.959749 AAAGCAACGAGAAAATTATTAACTGAA 57.040 25.926 0.00 0.00 0.00 3.02
4366 5123 9.556030 GCTAAAGCAACGAGAAAATTATTAACT 57.444 29.630 0.00 0.00 41.59 2.24
4367 5124 9.556030 AGCTAAAGCAACGAGAAAATTATTAAC 57.444 29.630 4.54 0.00 45.16 2.01
4369 5126 9.769093 GAAGCTAAAGCAACGAGAAAATTATTA 57.231 29.630 4.54 0.00 45.16 0.98
4370 5127 8.296713 TGAAGCTAAAGCAACGAGAAAATTATT 58.703 29.630 4.54 0.00 45.16 1.40
4371 5128 7.750903 GTGAAGCTAAAGCAACGAGAAAATTAT 59.249 33.333 4.54 0.00 45.16 1.28
4372 5129 7.075741 GTGAAGCTAAAGCAACGAGAAAATTA 58.924 34.615 4.54 0.00 45.16 1.40
4373 5130 5.915196 GTGAAGCTAAAGCAACGAGAAAATT 59.085 36.000 4.54 0.00 45.16 1.82
4374 5131 5.452777 GTGAAGCTAAAGCAACGAGAAAAT 58.547 37.500 4.54 0.00 45.16 1.82
4375 5132 4.261031 GGTGAAGCTAAAGCAACGAGAAAA 60.261 41.667 4.54 0.00 45.16 2.29
4376 5133 3.250040 GGTGAAGCTAAAGCAACGAGAAA 59.750 43.478 4.54 0.00 45.16 2.52
4377 5134 2.806244 GGTGAAGCTAAAGCAACGAGAA 59.194 45.455 4.54 0.00 45.16 2.87
4378 5135 2.413837 GGTGAAGCTAAAGCAACGAGA 58.586 47.619 4.54 0.00 45.16 4.04
4379 5136 1.126846 CGGTGAAGCTAAAGCAACGAG 59.873 52.381 9.72 0.00 44.87 4.18
4380 5137 1.144969 CGGTGAAGCTAAAGCAACGA 58.855 50.000 9.72 0.00 44.87 3.85
4381 5138 0.165944 CCGGTGAAGCTAAAGCAACG 59.834 55.000 4.54 8.66 45.16 4.10
4382 5139 0.521735 CCCGGTGAAGCTAAAGCAAC 59.478 55.000 0.00 0.00 45.16 4.17
4383 5140 0.608035 CCCCGGTGAAGCTAAAGCAA 60.608 55.000 0.00 0.00 45.16 3.91
4384 5141 1.002624 CCCCGGTGAAGCTAAAGCA 60.003 57.895 0.00 0.00 45.16 3.91
4385 5142 0.744771 CTCCCCGGTGAAGCTAAAGC 60.745 60.000 0.00 0.00 42.49 3.51
4386 5143 0.107654 CCTCCCCGGTGAAGCTAAAG 60.108 60.000 0.00 0.00 0.00 1.85
4387 5144 0.545787 TCCTCCCCGGTGAAGCTAAA 60.546 55.000 0.00 0.00 0.00 1.85
4388 5145 1.079621 TCCTCCCCGGTGAAGCTAA 59.920 57.895 0.00 0.00 0.00 3.09
4389 5146 1.684734 GTCCTCCCCGGTGAAGCTA 60.685 63.158 0.00 0.00 0.00 3.32
4390 5147 3.003763 GTCCTCCCCGGTGAAGCT 61.004 66.667 0.00 0.00 0.00 3.74
4391 5148 4.097361 GGTCCTCCCCGGTGAAGC 62.097 72.222 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.