Multiple sequence alignment - TraesCS3A01G050500

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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 TraesCS3A01G050500 chr3A 100.000 3277 0 0 1 3277 26827526 26830802 0.000000e+00 6052.0
1 TraesCS3A01G050500 chr3A 90.518 1951 119 23 992 2934 26872501 26870609 0.000000e+00 2518.0
2 TraesCS3A01G050500 chr3A 80.735 898 137 17 1 878 26873492 26872611 0.000000e+00 667.0
3 TraesCS3A01G050500 chr3A 98.182 220 4 0 3008 3227 26870606 26870387 5.740000e-103 385.0
4 TraesCS3A01G050500 chr3A 100.000 75 0 0 3589 3663 26831114 26831188 4.930000e-29 139.0
5 TraesCS3A01G050500 chr3A 92.857 56 4 0 2335 2390 95891687 95891742 8.430000e-12 82.4
6 TraesCS3A01G050500 chr3D 85.922 2891 279 62 1 2838 19303493 19300678 0.000000e+00 2966.0
7 TraesCS3A01G050500 chr3D 88.999 2127 171 36 437 2553 19286604 19288677 0.000000e+00 2573.0
8 TraesCS3A01G050500 chr3D 89.383 405 41 2 1 405 19285598 19286000 3.260000e-140 508.0
9 TraesCS3A01G050500 chr3D 96.825 63 1 1 3166 3227 19300224 19300162 1.800000e-18 104.0
10 TraesCS3A01G050500 chr3B 91.325 2144 147 17 1111 3227 31068236 31066105 0.000000e+00 2892.0
11 TraesCS3A01G050500 chr3B 87.236 2319 173 66 432 2728 31057809 31060026 0.000000e+00 2529.0
12 TraesCS3A01G050500 chr3B 88.770 374 39 2 1 372 31057442 31057814 4.310000e-124 455.0
13 TraesCS3A01G050500 chr2A 90.437 481 45 1 1415 1895 28200529 28200050 1.860000e-177 632.0
14 TraesCS3A01G050500 chr2A 89.952 209 20 1 1687 1895 690320635 690320428 6.030000e-68 268.0
15 TraesCS3A01G050500 chr2A 92.000 75 6 0 3589 3663 75640615 75640689 5.000000e-19 106.0
16 TraesCS3A01G050500 chr2A 90.667 75 7 0 3589 3663 628067078 628067004 2.330000e-17 100.0
17 TraesCS3A01G050500 chr2D 94.375 160 9 0 1566 1725 613336810 613336651 2.830000e-61 246.0
18 TraesCS3A01G050500 chr2D 95.238 42 2 0 161 202 10720839 10720798 2.360000e-07 67.6
19 TraesCS3A01G050500 chr1A 91.250 160 14 0 1566 1725 497924740 497924581 6.160000e-53 219.0
20 TraesCS3A01G050500 chr1A 92.000 75 6 0 3589 3663 63089918 63089844 5.000000e-19 106.0
21 TraesCS3A01G050500 chr1A 94.444 36 1 1 153 188 243619358 243619392 2.000000e-03 54.7
22 TraesCS3A01G050500 chr1D 91.558 154 13 0 1566 1719 419028818 419028971 2.870000e-51 213.0
23 TraesCS3A01G050500 chr6A 93.333 75 5 0 3589 3663 10139088 10139162 1.080000e-20 111.0
24 TraesCS3A01G050500 chr6A 92.000 75 6 0 3589 3663 384090271 384090197 5.000000e-19 106.0
25 TraesCS3A01G050500 chr6A 91.892 74 6 0 3589 3662 610123157 610123230 1.800000e-18 104.0
26 TraesCS3A01G050500 chr5A 91.892 74 6 0 3589 3662 327580902 327580975 1.800000e-18 104.0
27 TraesCS3A01G050500 chr5A 90.667 75 7 0 3589 3663 326431618 326431692 2.330000e-17 100.0
28 TraesCS3A01G050500 chr5A 96.875 32 1 0 161 192 41166270 41166239 2.000000e-03 54.7
29 TraesCS3A01G050500 chr1B 90.667 75 7 0 3589 3663 513461554 513461628 2.330000e-17 100.0
30 TraesCS3A01G050500 chr1B 94.444 36 1 1 153 188 270321353 270321319 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G050500 chr3A 26827526 26831188 3662 False 3095.5 6052 100.000000 1 3663 2 chr3A.!!$F2 3662
1 TraesCS3A01G050500 chr3A 26870387 26873492 3105 True 1190.0 2518 89.811667 1 3227 3 chr3A.!!$R1 3226
2 TraesCS3A01G050500 chr3D 19285598 19288677 3079 False 1540.5 2573 89.191000 1 2553 2 chr3D.!!$F1 2552
3 TraesCS3A01G050500 chr3D 19300162 19303493 3331 True 1535.0 2966 91.373500 1 3227 2 chr3D.!!$R1 3226
4 TraesCS3A01G050500 chr3B 31066105 31068236 2131 True 2892.0 2892 91.325000 1111 3227 1 chr3B.!!$R1 2116
5 TraesCS3A01G050500 chr3B 31057442 31060026 2584 False 1492.0 2529 88.003000 1 2728 2 chr3B.!!$F1 2727

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
796 1442 0.110644 GTAGCAATATCGCGCTTGGC 60.111 55.0 5.56 0.76 39.70 4.52 F
1978 2694 0.040603 CTACGACCCCGAAGCGTATC 60.041 60.0 0.00 0.00 39.42 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2593 3315 0.039618 ATTTCCGGCCAGGTTCACAT 59.960 50.0 2.24 0.0 41.99 3.21 R
2815 3568 0.471211 GAGGGGATGACCACGGGATA 60.471 60.0 0.00 0.0 45.76 2.59 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
26 27 8.246430 TCATCCATAGTATCCTTCGTTAAACT 57.754 34.615 0.00 0.00 0.00 2.66
43 44 9.247861 TCGTTAAACTTTAGGTACTTATCCTCT 57.752 33.333 0.00 0.00 41.75 3.69
112 116 6.718522 AAGTTATTTTTCCTCCGAAAACCA 57.281 33.333 0.00 0.00 45.43 3.67
118 122 4.376225 TTTCCTCCGAAAACCACCTTAT 57.624 40.909 0.00 0.00 35.02 1.73
122 126 3.192633 CCTCCGAAAACCACCTTATTTGG 59.807 47.826 0.00 0.00 40.32 3.28
272 280 9.909644 GTACAGAATCATATTAATACGGACAGT 57.090 33.333 0.00 0.00 0.00 3.55
282 290 9.970395 ATATTAATACGGACAGTTAAATCACGA 57.030 29.630 0.00 0.00 0.00 4.35
322 330 4.875544 TTATAGCCTGTTGAAACGCATC 57.124 40.909 0.00 0.00 0.00 3.91
329 337 3.186909 CTGTTGAAACGCATCGGAGATA 58.813 45.455 0.00 0.00 45.12 1.98
332 340 4.033932 TGTTGAAACGCATCGGAGATAATG 59.966 41.667 0.00 0.00 45.12 1.90
333 341 2.543848 TGAAACGCATCGGAGATAATGC 59.456 45.455 0.00 0.00 45.12 3.56
343 351 6.036517 GCATCGGAGATAATGCATTTACCTAG 59.963 42.308 18.75 6.28 45.97 3.02
376 384 4.640201 GGAGACATAGCCATTGTTTAAGCA 59.360 41.667 0.00 0.00 0.00 3.91
385 393 1.036707 TTGTTTAAGCACCCAGTGGC 58.963 50.000 2.61 0.00 33.64 5.01
412 420 0.321671 GCTGACTAGAGGTTGGTGCA 59.678 55.000 0.00 0.00 0.00 4.57
459 467 4.895297 TCTGCCAGGAAAACTTTCAATCTT 59.105 37.500 4.67 0.00 38.92 2.40
521 1129 7.469260 ACCACAAAAATTACATACAGATACGC 58.531 34.615 0.00 0.00 0.00 4.42
548 1165 2.885894 ACCTAGCGACTATAAGACCTGC 59.114 50.000 0.00 0.00 0.00 4.85
572 1189 0.379316 ACCCGAACGCAAACTCAAAC 59.621 50.000 0.00 0.00 0.00 2.93
629 1246 5.509498 TGGCTTTCTGGCAGATAAATAAGT 58.491 37.500 19.50 0.00 46.76 2.24
630 1247 6.658849 TGGCTTTCTGGCAGATAAATAAGTA 58.341 36.000 19.50 8.98 46.76 2.24
634 1251 8.766151 GCTTTCTGGCAGATAAATAAGTAGTAC 58.234 37.037 19.50 1.90 0.00 2.73
674 1295 4.874966 GTGGGATGAAGACTGAAGAGATTG 59.125 45.833 0.00 0.00 0.00 2.67
796 1442 0.110644 GTAGCAATATCGCGCTTGGC 60.111 55.000 5.56 0.76 39.70 4.52
861 1509 1.666888 CCCACACACGTCGTAGGTAAC 60.667 57.143 0.00 0.00 0.00 2.50
886 1534 4.634443 AGGTTGCCGCAAGTTAATTACTAG 59.366 41.667 5.91 0.00 35.54 2.57
971 1641 1.539157 AGATCGATCCATCAGCGCTA 58.461 50.000 21.66 0.00 0.00 4.26
981 1651 0.470833 ATCAGCGCTACCTCCATCCT 60.471 55.000 10.99 0.00 0.00 3.24
982 1652 1.068753 CAGCGCTACCTCCATCCTG 59.931 63.158 10.99 0.00 0.00 3.86
1044 1714 2.584835 TCTTCCCCACACAAATCCAG 57.415 50.000 0.00 0.00 0.00 3.86
1071 1741 0.812412 AACAAGAACACACCGACCGG 60.812 55.000 6.94 6.94 42.03 5.28
1083 1753 1.951130 CGACCGGCCATTGATCTCG 60.951 63.158 0.00 0.00 0.00 4.04
1141 1829 0.386113 CGAGGCAAGAGGTAGGTAGC 59.614 60.000 0.00 0.00 0.00 3.58
1144 1832 2.624364 GAGGCAAGAGGTAGGTAGCTAC 59.376 54.545 21.37 21.37 33.58 3.58
1170 1863 1.132721 CCATGTCTCCCTCCCCTGATA 60.133 57.143 0.00 0.00 0.00 2.15
1172 1865 3.246130 CCATGTCTCCCTCCCCTGATATA 60.246 52.174 0.00 0.00 0.00 0.86
1173 1866 4.429505 CATGTCTCCCTCCCCTGATATAA 58.570 47.826 0.00 0.00 0.00 0.98
1174 1867 4.569676 TGTCTCCCTCCCCTGATATAAA 57.430 45.455 0.00 0.00 0.00 1.40
1308 2013 2.552315 TCGTTGGAACTTGGAAGAATGC 59.448 45.455 0.00 0.00 0.00 3.56
1365 2075 0.337428 GGGAGTACCACCTGGACCTA 59.663 60.000 0.00 0.00 39.85 3.08
1501 2211 3.217743 CCTCCCTCTACGACGCCC 61.218 72.222 0.00 0.00 0.00 6.13
1502 2212 3.584052 CTCCCTCTACGACGCCCG 61.584 72.222 0.00 0.00 45.44 6.13
1548 2261 4.140599 CTCTCGCCGGAGCAGCTT 62.141 66.667 5.05 0.00 40.26 3.74
1719 2432 0.736053 GCTCTCTCTACCAGGACGTG 59.264 60.000 0.00 0.00 0.00 4.49
1739 2452 3.650950 GCAAGAGCTCCACCCCCA 61.651 66.667 10.93 0.00 37.91 4.96
1741 2454 2.612115 AAGAGCTCCACCCCCAGG 60.612 66.667 10.93 0.00 40.04 4.45
1742 2455 3.194025 AAGAGCTCCACCCCCAGGA 62.194 63.158 10.93 0.00 36.73 3.86
1785 2501 1.870901 CTACGCCAACTACGACGGC 60.871 63.158 0.00 0.00 42.64 5.68
1956 2672 2.423898 GGACGGGCTGATCGAAGGA 61.424 63.158 0.00 0.00 0.00 3.36
1971 2687 1.753073 GAAGGATTCTACGACCCCGAA 59.247 52.381 0.00 0.00 43.23 4.30
1977 2693 0.464373 TCTACGACCCCGAAGCGTAT 60.464 55.000 0.00 0.00 39.42 3.06
1978 2694 0.040603 CTACGACCCCGAAGCGTATC 60.041 60.000 0.00 0.00 39.42 2.24
2007 2723 0.685458 AGGGCAAGTTCATCATGGGC 60.685 55.000 0.00 0.00 0.00 5.36
2237 2959 1.372997 TCTCGCTCGCCAAGAACAC 60.373 57.895 0.00 0.00 0.00 3.32
2267 2989 4.954680 CAACAACACCGGTGCGCG 62.955 66.667 34.26 23.60 0.00 6.86
2405 3127 2.278596 CGCGTCCGGGTACATGAG 60.279 66.667 0.00 0.00 0.00 2.90
2465 3187 1.660560 GCGCTCATGGCCAAGATGTT 61.661 55.000 10.96 0.00 37.74 2.71
2466 3188 0.813184 CGCTCATGGCCAAGATGTTT 59.187 50.000 10.96 0.00 37.74 2.83
2577 3299 3.178540 AACCCTGCACGAGTGACCC 62.179 63.158 7.50 0.00 0.00 4.46
2578 3300 4.742201 CCCTGCACGAGTGACCCG 62.742 72.222 7.50 0.00 0.00 5.28
2579 3301 3.991051 CCTGCACGAGTGACCCGT 61.991 66.667 7.50 0.00 41.36 5.28
2584 3306 4.338539 ACGAGTGACCCGTGCGTC 62.339 66.667 0.00 0.00 38.97 5.19
2586 3308 3.681835 GAGTGACCCGTGCGTCCT 61.682 66.667 0.00 0.00 31.35 3.85
2587 3309 3.628280 GAGTGACCCGTGCGTCCTC 62.628 68.421 0.00 0.00 31.35 3.71
2588 3310 3.681835 GTGACCCGTGCGTCCTCT 61.682 66.667 0.00 0.00 31.35 3.69
2589 3311 3.680786 TGACCCGTGCGTCCTCTG 61.681 66.667 0.00 0.00 31.35 3.35
2590 3312 3.681835 GACCCGTGCGTCCTCTGT 61.682 66.667 0.00 0.00 0.00 3.41
2591 3313 3.628280 GACCCGTGCGTCCTCTGTC 62.628 68.421 0.00 0.00 0.00 3.51
2592 3314 3.374402 CCCGTGCGTCCTCTGTCT 61.374 66.667 0.00 0.00 0.00 3.41
2593 3315 2.044555 CCCGTGCGTCCTCTGTCTA 61.045 63.158 0.00 0.00 0.00 2.59
2641 3385 6.436847 TGCTTGGTTCATCAGAAATCCAAATA 59.563 34.615 0.00 0.00 38.60 1.40
2755 3508 2.755103 TCTAGCGCTGACTTTGATGAGA 59.245 45.455 22.90 7.72 0.00 3.27
2815 3568 5.120208 CGTTCGTAATTGAGGTGTCATTCTT 59.880 40.000 0.00 0.00 30.85 2.52
2820 3573 6.202954 CGTAATTGAGGTGTCATTCTTATCCC 59.797 42.308 0.00 0.00 30.85 3.85
2838 3592 1.436336 CGTGGTCATCCCCTCGTAC 59.564 63.158 0.00 0.00 36.88 3.67
2939 3696 4.101448 GTGCAGGAGGGGCGATGT 62.101 66.667 0.00 0.00 0.00 3.06
2952 3709 1.795170 GCGATGTTGTTGGTGCACCT 61.795 55.000 34.75 14.54 36.82 4.00
2953 3710 0.667993 CGATGTTGTTGGTGCACCTT 59.332 50.000 34.75 11.92 36.82 3.50
2968 3725 3.191539 CTTCGGCTCGGCTTGCTC 61.192 66.667 0.00 0.00 0.00 4.26
2971 3728 2.279120 CGGCTCGGCTTGCTCTAG 60.279 66.667 0.00 0.00 0.00 2.43
2982 3739 4.065789 GGCTTGCTCTAGTGTTTGTAGTT 58.934 43.478 0.00 0.00 0.00 2.24
2986 3743 6.202188 GCTTGCTCTAGTGTTTGTAGTTGTTA 59.798 38.462 0.00 0.00 0.00 2.41
2990 3747 9.419297 TGCTCTAGTGTTTGTAGTTGTTATTAG 57.581 33.333 0.00 0.00 0.00 1.73
2994 3751 7.739498 AGTGTTTGTAGTTGTTATTAGGTGG 57.261 36.000 0.00 0.00 0.00 4.61
3227 4202 1.089920 ATCTGCATGACGCCAGAAAC 58.910 50.000 0.00 0.00 41.33 2.78
3228 4203 0.250252 TCTGCATGACGCCAGAAACA 60.250 50.000 0.00 0.00 41.33 2.83
3229 4204 0.592637 CTGCATGACGCCAGAAACAA 59.407 50.000 0.00 0.00 41.33 2.83
3230 4205 1.200716 CTGCATGACGCCAGAAACAAT 59.799 47.619 0.00 0.00 41.33 2.71
3231 4206 2.419673 CTGCATGACGCCAGAAACAATA 59.580 45.455 0.00 0.00 41.33 1.90
3232 4207 2.816672 TGCATGACGCCAGAAACAATAA 59.183 40.909 0.00 0.00 41.33 1.40
3233 4208 3.443329 TGCATGACGCCAGAAACAATAAT 59.557 39.130 0.00 0.00 41.33 1.28
3234 4209 4.037690 GCATGACGCCAGAAACAATAATC 58.962 43.478 0.00 0.00 32.94 1.75
3235 4210 4.601019 CATGACGCCAGAAACAATAATCC 58.399 43.478 0.00 0.00 0.00 3.01
3236 4211 3.950397 TGACGCCAGAAACAATAATCCT 58.050 40.909 0.00 0.00 0.00 3.24
3237 4212 5.092554 TGACGCCAGAAACAATAATCCTA 57.907 39.130 0.00 0.00 0.00 2.94
3238 4213 4.873827 TGACGCCAGAAACAATAATCCTAC 59.126 41.667 0.00 0.00 0.00 3.18
3239 4214 3.869246 ACGCCAGAAACAATAATCCTACG 59.131 43.478 0.00 0.00 0.00 3.51
3240 4215 3.303132 CGCCAGAAACAATAATCCTACGC 60.303 47.826 0.00 0.00 0.00 4.42
3241 4216 3.003378 GCCAGAAACAATAATCCTACGCC 59.997 47.826 0.00 0.00 0.00 5.68
3242 4217 4.451900 CCAGAAACAATAATCCTACGCCT 58.548 43.478 0.00 0.00 0.00 5.52
3243 4218 5.607477 CCAGAAACAATAATCCTACGCCTA 58.393 41.667 0.00 0.00 0.00 3.93
3244 4219 5.465724 CCAGAAACAATAATCCTACGCCTAC 59.534 44.000 0.00 0.00 0.00 3.18
3246 4221 4.924305 AACAATAATCCTACGCCTACGA 57.076 40.909 0.00 0.00 43.93 3.43
3247 4222 4.924305 ACAATAATCCTACGCCTACGAA 57.076 40.909 0.00 0.00 43.93 3.85
3248 4223 5.266733 ACAATAATCCTACGCCTACGAAA 57.733 39.130 0.00 0.00 43.93 3.46
3249 4224 5.287226 ACAATAATCCTACGCCTACGAAAG 58.713 41.667 0.00 0.00 43.93 2.62
3262 4237 4.240175 CTACGAAAGGACTATGTAGGGC 57.760 50.000 0.00 0.00 31.19 5.19
3263 4238 2.748388 ACGAAAGGACTATGTAGGGCT 58.252 47.619 0.00 0.00 0.00 5.19
3264 4239 3.907221 ACGAAAGGACTATGTAGGGCTA 58.093 45.455 0.00 0.00 0.00 3.93
3265 4240 3.635836 ACGAAAGGACTATGTAGGGCTAC 59.364 47.826 0.00 0.00 36.63 3.58
3266 4241 3.304525 CGAAAGGACTATGTAGGGCTACG 60.305 52.174 0.00 0.00 38.85 3.51
3267 4242 3.309600 AAGGACTATGTAGGGCTACGT 57.690 47.619 0.00 0.00 38.85 3.57
3268 4243 4.443978 AAGGACTATGTAGGGCTACGTA 57.556 45.455 0.00 0.00 38.85 3.57
3269 4244 4.443978 AGGACTATGTAGGGCTACGTAA 57.556 45.455 0.00 0.00 37.17 3.18
3270 4245 4.796606 AGGACTATGTAGGGCTACGTAAA 58.203 43.478 0.00 0.00 37.17 2.01
3271 4246 4.582240 AGGACTATGTAGGGCTACGTAAAC 59.418 45.833 0.00 0.00 37.17 2.01
3272 4247 4.261783 GGACTATGTAGGGCTACGTAAACC 60.262 50.000 7.03 7.03 37.17 3.27
3273 4248 4.540715 ACTATGTAGGGCTACGTAAACCT 58.459 43.478 18.45 18.45 37.17 3.50
3274 4249 4.958581 ACTATGTAGGGCTACGTAAACCTT 59.041 41.667 19.32 12.17 37.17 3.50
3275 4250 3.874392 TGTAGGGCTACGTAAACCTTC 57.126 47.619 19.32 15.54 38.85 3.46
3276 4251 2.497273 TGTAGGGCTACGTAAACCTTCC 59.503 50.000 19.32 12.58 38.85 3.46
3632 4607 4.830765 TGCTCCCGCATACGTGGC 62.831 66.667 0.00 0.21 42.25 5.01
3633 4608 4.830765 GCTCCCGCATACGTGGCA 62.831 66.667 13.38 0.00 41.87 4.92
3634 4609 2.108976 CTCCCGCATACGTGGCAT 59.891 61.111 13.38 0.00 41.87 4.40
3635 4610 2.203001 TCCCGCATACGTGGCATG 60.203 61.111 4.87 4.87 41.87 4.06
3636 4611 3.279116 CCCGCATACGTGGCATGG 61.279 66.667 12.05 9.25 41.87 3.66
3637 4612 2.513666 CCGCATACGTGGCATGGT 60.514 61.111 12.05 5.53 35.59 3.55
3638 4613 2.112198 CCGCATACGTGGCATGGTT 61.112 57.895 12.05 0.00 35.59 3.67
3639 4614 1.653094 CCGCATACGTGGCATGGTTT 61.653 55.000 12.05 0.00 35.59 3.27
3640 4615 0.523125 CGCATACGTGGCATGGTTTG 60.523 55.000 12.05 9.27 33.53 2.93
3641 4616 0.808125 GCATACGTGGCATGGTTTGA 59.192 50.000 12.05 0.00 0.00 2.69
3642 4617 1.405105 GCATACGTGGCATGGTTTGAT 59.595 47.619 12.05 0.00 0.00 2.57
3643 4618 2.159254 GCATACGTGGCATGGTTTGATT 60.159 45.455 12.05 0.00 0.00 2.57
3644 4619 3.437428 CATACGTGGCATGGTTTGATTG 58.563 45.455 12.05 0.00 0.00 2.67
3645 4620 1.614996 ACGTGGCATGGTTTGATTGA 58.385 45.000 12.05 0.00 0.00 2.57
3646 4621 1.959985 ACGTGGCATGGTTTGATTGAA 59.040 42.857 12.05 0.00 0.00 2.69
3647 4622 2.363680 ACGTGGCATGGTTTGATTGAAA 59.636 40.909 12.05 0.00 0.00 2.69
3648 4623 3.006752 ACGTGGCATGGTTTGATTGAAAT 59.993 39.130 12.05 0.00 0.00 2.17
3649 4624 3.613737 CGTGGCATGGTTTGATTGAAATC 59.386 43.478 0.00 0.00 35.97 2.17
3650 4625 4.567971 GTGGCATGGTTTGATTGAAATCA 58.432 39.130 1.55 1.55 43.28 2.57
3662 4637 5.659463 TGATTGAAATCAAATAAAGCCCGG 58.341 37.500 3.24 0.00 42.11 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 116 1.716503 AGAAGGTGGGCCAAATAAGGT 59.283 47.619 8.40 0.00 37.19 3.50
118 122 3.756082 ATCAATAGAAGGTGGGCCAAA 57.244 42.857 8.40 0.00 37.19 3.28
122 126 7.530426 AATGATAAATCAATAGAAGGTGGGC 57.470 36.000 0.00 0.00 40.69 5.36
232 239 7.821595 TGATTCTGTACATAAGTGTTTACCG 57.178 36.000 0.00 0.00 39.77 4.02
265 273 2.955614 AGGTCGTGATTTAACTGTCCG 58.044 47.619 0.00 0.00 0.00 4.79
268 276 4.530710 TGCTAGGTCGTGATTTAACTGT 57.469 40.909 0.00 0.00 0.00 3.55
322 330 5.120830 GTGCTAGGTAAATGCATTATCTCCG 59.879 44.000 13.39 6.84 36.37 4.63
329 337 6.594937 CCAAAATTGTGCTAGGTAAATGCATT 59.405 34.615 5.99 5.99 39.00 3.56
332 340 5.719173 TCCAAAATTGTGCTAGGTAAATGC 58.281 37.500 0.00 0.00 0.00 3.56
333 341 7.029563 GTCTCCAAAATTGTGCTAGGTAAATG 58.970 38.462 0.00 0.00 0.00 2.32
343 351 3.193267 TGGCTATGTCTCCAAAATTGTGC 59.807 43.478 0.00 0.00 0.00 4.57
385 393 1.440938 CCTCTAGTCAGCCTCCGTCG 61.441 65.000 0.00 0.00 0.00 5.12
398 406 1.271054 ACAGCTTGCACCAACCTCTAG 60.271 52.381 0.00 0.00 0.00 2.43
439 447 6.048509 TGAAAAGATTGAAAGTTTTCCTGGC 58.951 36.000 10.84 0.00 38.75 4.85
491 1097 7.367285 TCTGTATGTAATTTTTGTGGTTCTGC 58.633 34.615 0.00 0.00 0.00 4.26
497 1103 7.468441 TGCGTATCTGTATGTAATTTTTGTGG 58.532 34.615 0.00 0.00 0.00 4.17
521 1129 5.505985 GGTCTTATAGTCGCTAGGTGTTCTG 60.506 48.000 0.00 0.00 0.00 3.02
561 1178 6.913170 TGGATTAGATGAAGTTTGAGTTTGC 58.087 36.000 0.00 0.00 0.00 3.68
572 1189 4.578105 GGGCTCTGTTTGGATTAGATGAAG 59.422 45.833 0.00 0.00 0.00 3.02
628 1245 9.988350 CCACAATGACATAAAAATCAGTACTAC 57.012 33.333 0.00 0.00 0.00 2.73
629 1246 9.173021 CCCACAATGACATAAAAATCAGTACTA 57.827 33.333 0.00 0.00 0.00 1.82
630 1247 7.888021 TCCCACAATGACATAAAAATCAGTACT 59.112 33.333 0.00 0.00 0.00 2.73
634 1251 7.774134 TCATCCCACAATGACATAAAAATCAG 58.226 34.615 0.00 0.00 30.76 2.90
674 1295 1.734465 GCATATGCTACGGATTGCTCC 59.266 52.381 20.64 0.00 38.21 4.70
704 1325 2.810274 GTGATTGACGCATATCCAGCAT 59.190 45.455 0.00 0.00 0.00 3.79
749 1370 8.854117 TGCACCCAAAAATAAGCATTTAAAAAT 58.146 25.926 0.00 0.00 33.09 1.82
861 1509 0.802494 ATTAACTTGCGGCAACCTCG 59.198 50.000 12.11 4.68 0.00 4.63
864 1512 3.842732 AGTAATTAACTTGCGGCAACC 57.157 42.857 12.11 0.00 33.35 3.77
867 1515 5.969423 ACTACTAGTAATTAACTTGCGGCA 58.031 37.500 3.76 0.00 39.80 5.69
869 1517 7.859875 GGAGTACTACTAGTAATTAACTTGCGG 59.140 40.741 3.76 0.00 39.80 5.69
918 1566 9.506018 AAAATCATTTAATTCCAAAACTGGAGG 57.494 29.630 0.00 0.00 39.43 4.30
939 1587 7.329471 TGATGGATCGATCTTATCACGAAAATC 59.671 37.037 27.05 12.94 39.38 2.17
971 1641 2.090324 TCAGGATGATCAGGATGGAGGT 60.090 50.000 0.09 0.00 42.56 3.85
1044 1714 3.517602 GGTGTGTTCTTGTTGGTTTTCC 58.482 45.455 0.00 0.00 41.14 3.13
1071 1741 1.134401 TGGAGGTTCGAGATCAATGGC 60.134 52.381 0.00 0.00 0.00 4.40
1083 1753 2.495084 GAAGGACTTGTGTGGAGGTTC 58.505 52.381 0.00 0.00 0.00 3.62
1141 1829 1.133009 AGGGAGACATGGCTAGGGTAG 60.133 57.143 0.00 0.00 0.00 3.18
1144 1832 1.124477 GGAGGGAGACATGGCTAGGG 61.124 65.000 0.00 0.00 0.00 3.53
1170 1863 2.587889 CACGCGGGGGAGGTTTAT 59.412 61.111 12.47 0.00 0.00 1.40
1308 2013 3.306917 TGCAAATGTCAGCAATTGGAG 57.693 42.857 7.72 0.00 37.90 3.86
1698 2411 0.394488 CGTCCTGGTAGAGAGAGCCA 60.394 60.000 0.00 0.00 0.00 4.75
1704 2417 0.680280 GCTCCACGTCCTGGTAGAGA 60.680 60.000 0.00 0.00 41.52 3.10
1755 2471 2.106683 GGCGTAGTCCATGTGGCAC 61.107 63.158 11.55 11.55 34.44 5.01
1956 2672 1.318158 ACGCTTCGGGGTCGTAGAAT 61.318 55.000 0.00 0.00 39.69 2.40
2007 2723 2.606519 TCCGGGTGGAACTGGAGG 60.607 66.667 0.00 0.00 42.85 4.30
2168 2890 3.891366 CTCCATTTCCTGGTTCAGTTTGT 59.109 43.478 0.00 0.00 46.08 2.83
2237 2959 0.382151 GTTGTTGCCGAACACGTACG 60.382 55.000 15.01 15.01 41.92 3.67
2317 3039 2.380410 GCGCCGTGTTCGACTCAAT 61.380 57.895 0.00 0.00 39.71 2.57
2319 3041 3.973516 AGCGCCGTGTTCGACTCA 61.974 61.111 2.29 0.00 39.71 3.41
2394 3116 1.227380 GAGCCTGCTCATGTACCCG 60.227 63.158 14.07 0.00 42.31 5.28
2577 3299 0.452184 ACATAGACAGAGGACGCACG 59.548 55.000 0.00 0.00 0.00 5.34
2578 3300 1.472878 TCACATAGACAGAGGACGCAC 59.527 52.381 0.00 0.00 0.00 5.34
2579 3301 1.834188 TCACATAGACAGAGGACGCA 58.166 50.000 0.00 0.00 0.00 5.24
2580 3302 2.531206 GTTCACATAGACAGAGGACGC 58.469 52.381 0.00 0.00 0.00 5.19
2581 3303 2.755655 AGGTTCACATAGACAGAGGACG 59.244 50.000 0.00 0.00 0.00 4.79
2582 3304 3.118956 CCAGGTTCACATAGACAGAGGAC 60.119 52.174 0.00 0.00 0.00 3.85
2583 3305 3.099905 CCAGGTTCACATAGACAGAGGA 58.900 50.000 0.00 0.00 0.00 3.71
2584 3306 2.419297 GCCAGGTTCACATAGACAGAGG 60.419 54.545 0.00 0.00 0.00 3.69
2585 3307 2.419297 GGCCAGGTTCACATAGACAGAG 60.419 54.545 0.00 0.00 0.00 3.35
2586 3308 1.555075 GGCCAGGTTCACATAGACAGA 59.445 52.381 0.00 0.00 0.00 3.41
2587 3309 1.740380 CGGCCAGGTTCACATAGACAG 60.740 57.143 2.24 0.00 0.00 3.51
2588 3310 0.249120 CGGCCAGGTTCACATAGACA 59.751 55.000 2.24 0.00 0.00 3.41
2589 3311 0.462047 CCGGCCAGGTTCACATAGAC 60.462 60.000 2.24 0.00 34.51 2.59
2590 3312 0.616395 TCCGGCCAGGTTCACATAGA 60.616 55.000 2.24 0.00 41.99 1.98
2591 3313 0.251916 TTCCGGCCAGGTTCACATAG 59.748 55.000 2.24 0.00 41.99 2.23
2592 3314 0.693622 TTTCCGGCCAGGTTCACATA 59.306 50.000 2.24 0.00 41.99 2.29
2593 3315 0.039618 ATTTCCGGCCAGGTTCACAT 59.960 50.000 2.24 0.00 41.99 3.21
2641 3385 5.818678 ATTAATTCAGGATGCCATGCAAT 57.181 34.783 0.00 0.00 43.62 3.56
2755 3508 8.091449 ACTTACTCTCTTCGTCTTTCATTTCAT 58.909 33.333 0.00 0.00 0.00 2.57
2815 3568 0.471211 GAGGGGATGACCACGGGATA 60.471 60.000 0.00 0.00 45.76 2.59
2820 3573 1.436336 GTACGAGGGGATGACCACG 59.564 63.158 0.00 0.00 45.76 4.94
2838 3592 6.317140 TGGTACACAAGTTAGATAGGAGTACG 59.683 42.308 0.00 0.00 32.37 3.67
2952 3709 2.284798 CTAGAGCAAGCCGAGCCGAA 62.285 60.000 0.00 0.00 0.00 4.30
2953 3710 2.754254 TAGAGCAAGCCGAGCCGA 60.754 61.111 0.00 0.00 0.00 5.54
2968 3725 8.932791 CCACCTAATAACAACTACAAACACTAG 58.067 37.037 0.00 0.00 0.00 2.57
2971 3728 7.500720 ACCACCTAATAACAACTACAAACAC 57.499 36.000 0.00 0.00 0.00 3.32
3227 4202 4.684703 CCTTTCGTAGGCGTAGGATTATTG 59.315 45.833 9.40 0.49 40.61 1.90
3228 4203 4.586001 TCCTTTCGTAGGCGTAGGATTATT 59.414 41.667 9.40 0.00 44.37 1.40
3229 4204 4.022503 GTCCTTTCGTAGGCGTAGGATTAT 60.023 45.833 9.40 0.00 44.65 1.28
3230 4205 3.316308 GTCCTTTCGTAGGCGTAGGATTA 59.684 47.826 9.40 1.64 44.65 1.75
3231 4206 2.100418 GTCCTTTCGTAGGCGTAGGATT 59.900 50.000 9.40 0.00 44.65 3.01
3232 4207 1.680207 GTCCTTTCGTAGGCGTAGGAT 59.320 52.381 9.40 0.00 44.65 3.24
3233 4208 1.098050 GTCCTTTCGTAGGCGTAGGA 58.902 55.000 4.79 4.79 44.37 2.94
3234 4209 1.101331 AGTCCTTTCGTAGGCGTAGG 58.899 55.000 0.00 0.00 44.37 3.18
3235 4210 3.314635 ACATAGTCCTTTCGTAGGCGTAG 59.685 47.826 2.03 0.00 44.37 3.51
3236 4211 3.282021 ACATAGTCCTTTCGTAGGCGTA 58.718 45.455 2.03 0.00 44.37 4.42
3237 4212 2.097825 ACATAGTCCTTTCGTAGGCGT 58.902 47.619 2.03 0.00 44.37 5.68
3238 4213 2.865343 ACATAGTCCTTTCGTAGGCG 57.135 50.000 2.03 0.00 44.37 5.52
3239 4214 3.005578 CCCTACATAGTCCTTTCGTAGGC 59.994 52.174 8.15 0.00 45.20 3.93
3240 4215 3.005578 GCCCTACATAGTCCTTTCGTAGG 59.994 52.174 6.89 6.89 45.82 3.18
3241 4216 3.890147 AGCCCTACATAGTCCTTTCGTAG 59.110 47.826 0.00 0.00 0.00 3.51
3242 4217 3.907221 AGCCCTACATAGTCCTTTCGTA 58.093 45.455 0.00 0.00 0.00 3.43
3243 4218 2.748388 AGCCCTACATAGTCCTTTCGT 58.252 47.619 0.00 0.00 0.00 3.85
3244 4219 3.304525 CGTAGCCCTACATAGTCCTTTCG 60.305 52.174 6.30 0.00 35.87 3.46
3245 4220 3.635836 ACGTAGCCCTACATAGTCCTTTC 59.364 47.826 6.30 0.00 35.87 2.62
3246 4221 3.639952 ACGTAGCCCTACATAGTCCTTT 58.360 45.455 6.30 0.00 35.87 3.11
3247 4222 3.309600 ACGTAGCCCTACATAGTCCTT 57.690 47.619 6.30 0.00 35.87 3.36
3248 4223 4.443978 TTACGTAGCCCTACATAGTCCT 57.556 45.455 6.30 0.00 35.87 3.85
3249 4224 4.261783 GGTTTACGTAGCCCTACATAGTCC 60.262 50.000 6.30 0.00 35.87 3.85
3250 4225 4.582240 AGGTTTACGTAGCCCTACATAGTC 59.418 45.833 12.09 0.00 35.87 2.59
3251 4226 4.540715 AGGTTTACGTAGCCCTACATAGT 58.459 43.478 12.09 0.00 35.87 2.12
3252 4227 5.508657 GGAAGGTTTACGTAGCCCTACATAG 60.509 48.000 13.62 0.00 35.87 2.23
3253 4228 4.342092 GGAAGGTTTACGTAGCCCTACATA 59.658 45.833 13.62 0.00 35.87 2.29
3254 4229 3.133542 GGAAGGTTTACGTAGCCCTACAT 59.866 47.826 13.62 1.50 35.87 2.29
3255 4230 2.497273 GGAAGGTTTACGTAGCCCTACA 59.503 50.000 13.62 0.00 35.87 2.74
3256 4231 3.170791 GGAAGGTTTACGTAGCCCTAC 57.829 52.381 13.62 7.96 0.00 3.18
3617 4592 2.108976 ATGCCACGTATGCGGGAG 59.891 61.111 7.15 0.00 45.97 4.30
3618 4593 2.203001 CATGCCACGTATGCGGGA 60.203 61.111 7.15 0.00 45.97 5.14
3619 4594 3.279116 CCATGCCACGTATGCGGG 61.279 66.667 8.39 2.48 43.45 6.13
3620 4595 1.653094 AAACCATGCCACGTATGCGG 61.653 55.000 8.39 3.82 43.45 5.69
3621 4596 0.523125 CAAACCATGCCACGTATGCG 60.523 55.000 0.19 0.19 44.93 4.73
3622 4597 0.808125 TCAAACCATGCCACGTATGC 59.192 50.000 2.46 2.46 0.00 3.14
3623 4598 3.128415 TCAATCAAACCATGCCACGTATG 59.872 43.478 0.00 0.00 0.00 2.39
3624 4599 3.351740 TCAATCAAACCATGCCACGTAT 58.648 40.909 0.00 0.00 0.00 3.06
3625 4600 2.784347 TCAATCAAACCATGCCACGTA 58.216 42.857 0.00 0.00 0.00 3.57
3626 4601 1.614996 TCAATCAAACCATGCCACGT 58.385 45.000 0.00 0.00 0.00 4.49
3627 4602 2.721274 TTCAATCAAACCATGCCACG 57.279 45.000 0.00 0.00 0.00 4.94
3628 4603 4.567971 TGATTTCAATCAAACCATGCCAC 58.432 39.130 0.00 0.00 42.11 5.01
3629 4604 4.886496 TGATTTCAATCAAACCATGCCA 57.114 36.364 0.00 0.00 42.11 4.92
3639 4614 5.659463 CCGGGCTTTATTTGATTTCAATCA 58.341 37.500 0.00 0.00 43.28 2.57


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

AutoCloner maintained by Alex Coulton.