Multiple sequence alignment - TraesCS2B01G577200

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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 TraesCS2B01G577200 chr2B 100.000 4998 0 0 1 4998 765579058 765584055 0.000000e+00 9230.0
1 TraesCS2B01G577200 chr2B 90.823 948 78 7 1125 2065 765572173 765573118 0.000000e+00 1260.0
2 TraesCS2B01G577200 chr2B 87.845 905 104 4 1164 2064 753829980 753829078 0.000000e+00 1057.0
3 TraesCS2B01G577200 chr2B 85.670 963 123 9 1145 2094 765594822 765593862 0.000000e+00 1000.0
4 TraesCS2B01G577200 chr2B 94.737 38 2 0 2169 2206 753829007 753828970 5.400000e-05 60.2
5 TraesCS2B01G577200 chr7D 87.895 2850 269 34 2185 4998 534371685 534368876 0.000000e+00 3282.0
6 TraesCS2B01G577200 chr7D 87.257 1797 140 46 345 2100 534473852 534472104 0.000000e+00 1967.0
7 TraesCS2B01G577200 chr7D 89.716 1410 135 8 2755 4156 534469454 534468047 0.000000e+00 1792.0
8 TraesCS2B01G577200 chr7D 86.210 1124 133 14 3091 4197 534620949 534619831 0.000000e+00 1197.0
9 TraesCS2B01G577200 chr7D 84.740 1114 137 20 3026 4116 534520994 534519891 0.000000e+00 1085.0
10 TraesCS2B01G577200 chr7D 88.089 403 23 7 252 637 534525481 534525087 5.900000e-124 455.0
11 TraesCS2B01G577200 chr7D 86.683 398 48 2 4203 4596 534467868 534467472 2.140000e-118 436.0
12 TraesCS2B01G577200 chr7D 85.577 312 36 5 2455 2757 534470947 534470636 8.070000e-83 318.0
13 TraesCS2B01G577200 chr7D 90.566 212 19 1 39 249 534525722 534525511 3.810000e-71 279.0
14 TraesCS2B01G577200 chr7D 80.328 305 37 15 2169 2466 534472085 534471797 5.070000e-50 209.0
15 TraesCS2B01G577200 chr7D 80.137 146 23 4 426 565 534625291 534625146 2.460000e-18 104.0
16 TraesCS2B01G577200 chr2A 93.065 1860 116 5 2638 4492 755113958 755115809 0.000000e+00 2708.0
17 TraesCS2B01G577200 chr2A 88.432 1435 76 23 1084 2474 755112242 755113630 0.000000e+00 1648.0
18 TraesCS2B01G577200 chr2A 86.811 1198 134 15 3013 4194 755087282 755088471 0.000000e+00 1315.0
19 TraesCS2B01G577200 chr2A 90.011 941 85 7 1132 2064 755251697 755250758 0.000000e+00 1208.0
20 TraesCS2B01G577200 chr2A 84.957 1037 139 14 3119 4144 755247710 755246680 0.000000e+00 1035.0
21 TraesCS2B01G577200 chr2A 86.674 923 117 4 1149 2068 748078214 748079133 0.000000e+00 1018.0
22 TraesCS2B01G577200 chr2A 86.559 186 15 4 2479 2654 755113760 755113945 3.950000e-46 196.0
23 TraesCS2B01G577200 chr2A 91.912 136 9 2 38 172 755091639 755091773 6.610000e-44 189.0
24 TraesCS2B01G577200 chr2A 84.167 120 14 5 4799 4916 603517173 603517289 1.470000e-20 111.0
25 TraesCS2B01G577200 chr2A 77.540 187 30 10 2318 2497 755086744 755086925 8.850000e-18 102.0
26 TraesCS2B01G577200 chr2D 88.896 1666 155 17 2517 4156 623913106 623914767 0.000000e+00 2025.0
27 TraesCS2B01G577200 chr2D 88.457 1542 114 32 960 2475 623910665 623912168 0.000000e+00 1803.0
28 TraesCS2B01G577200 chr2D 91.226 946 72 8 1124 2062 623895242 623896183 0.000000e+00 1277.0
29 TraesCS2B01G577200 chr2D 87.610 912 106 6 1145 2050 623958506 623957596 0.000000e+00 1051.0
30 TraesCS2B01G577200 chr2D 85.615 1008 117 15 3198 4193 623896412 623897403 0.000000e+00 1033.0
31 TraesCS2B01G577200 chr2D 87.367 657 41 9 27 645 623909385 623910037 0.000000e+00 715.0
32 TraesCS2B01G577200 chr2D 82.119 151 20 3 661 806 623910440 623910588 6.790000e-24 122.0
33 TraesCS2B01G577200 chr6D 75.862 290 39 10 4737 4998 15374623 15374337 8.790000e-23 119.0
34 TraesCS2B01G577200 chr6B 74.476 286 40 12 4742 4998 27119661 27119380 5.330000e-15 93.5
35 TraesCS2B01G577200 chr6B 83.133 83 5 6 4827 4907 688669169 688669094 3.230000e-07 67.6
36 TraesCS2B01G577200 chr6A 84.884 86 9 2 4818 4902 15949053 15948971 3.210000e-12 84.2


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 TraesCS2B01G577200 chr2B 765579058 765584055 4997 False 9230.000000 9230 100.00000 1 4998 1 chr2B.!!$F2 4997
1 TraesCS2B01G577200 chr2B 765572173 765573118 945 False 1260.000000 1260 90.82300 1125 2065 1 chr2B.!!$F1 940
2 TraesCS2B01G577200 chr2B 765593862 765594822 960 True 1000.000000 1000 85.67000 1145 2094 1 chr2B.!!$R1 949
3 TraesCS2B01G577200 chr2B 753828970 753829980 1010 True 558.600000 1057 91.29100 1164 2206 2 chr2B.!!$R2 1042
4 TraesCS2B01G577200 chr7D 534368876 534371685 2809 True 3282.000000 3282 87.89500 2185 4998 1 chr7D.!!$R1 2813
5 TraesCS2B01G577200 chr7D 534619831 534620949 1118 True 1197.000000 1197 86.21000 3091 4197 1 chr7D.!!$R3 1106
6 TraesCS2B01G577200 chr7D 534519891 534520994 1103 True 1085.000000 1085 84.74000 3026 4116 1 chr7D.!!$R2 1090
7 TraesCS2B01G577200 chr7D 534467472 534473852 6380 True 944.400000 1967 85.91220 345 4596 5 chr7D.!!$R5 4251
8 TraesCS2B01G577200 chr7D 534525087 534525722 635 True 367.000000 455 89.32750 39 637 2 chr7D.!!$R6 598
9 TraesCS2B01G577200 chr2A 755112242 755115809 3567 False 1517.333333 2708 89.35200 1084 4492 3 chr2A.!!$F4 3408
10 TraesCS2B01G577200 chr2A 755246680 755251697 5017 True 1121.500000 1208 87.48400 1132 4144 2 chr2A.!!$R1 3012
11 TraesCS2B01G577200 chr2A 748078214 748079133 919 False 1018.000000 1018 86.67400 1149 2068 1 chr2A.!!$F2 919
12 TraesCS2B01G577200 chr2A 755086744 755091773 5029 False 535.333333 1315 85.42100 38 4194 3 chr2A.!!$F3 4156
13 TraesCS2B01G577200 chr2D 623909385 623914767 5382 False 1166.250000 2025 86.70975 27 4156 4 chr2D.!!$F2 4129
14 TraesCS2B01G577200 chr2D 623895242 623897403 2161 False 1155.000000 1277 88.42050 1124 4193 2 chr2D.!!$F1 3069
15 TraesCS2B01G577200 chr2D 623957596 623958506 910 True 1051.000000 1051 87.61000 1145 2050 1 chr2D.!!$R1 905

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
412 457 1.007842 TGGAGGCATGTGTAGTCCCTA 59.992 52.381 0.00 0.0 0.00 3.53 F
1150 1643 0.598065 GCCGAACTGCACAAAGGAAT 59.402 50.000 0.00 0.0 0.00 3.01 F
1209 1714 0.743701 GGCTCGTCGTCTCTGTCCTA 60.744 60.000 0.00 0.0 0.00 2.94 F
1451 1980 1.146930 ATGATTCCGTGCTCGCCAT 59.853 52.632 1.89 0.0 35.54 4.40 F
2289 2866 0.321919 GAGATGGCTCAAGTGGCACA 60.322 55.000 21.41 0.0 45.12 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 2222 0.251916 TGGTGCGGGAGATAAGGTTG 59.748 55.000 0.00 0.0 0.00 3.77 R
2213 2786 1.554617 CCACCATTTGTTTGATCCCCC 59.445 52.381 0.00 0.0 0.00 5.40 R
2275 2852 2.531522 AATTTTGTGCCACTTGAGCC 57.468 45.000 0.00 0.0 0.00 4.70 R
3264 9093 5.907866 TGTGGTATAGAAGAATCGACACA 57.092 39.130 0.00 0.0 0.00 3.72 R
4117 9982 1.525619 GTGGATAACGAAGGCGCATAC 59.474 52.381 10.83 0.0 42.48 2.39 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
30 31 7.296628 ACAACTCTATTATTCTAGCAGGAGG 57.703 40.000 0.00 0.00 0.00 4.30
31 32 6.268847 ACAACTCTATTATTCTAGCAGGAGGG 59.731 42.308 0.00 0.00 0.00 4.30
32 33 5.337788 ACTCTATTATTCTAGCAGGAGGGG 58.662 45.833 0.00 0.00 0.00 4.79
64 65 2.034558 ACCGAAAAGCAAATGACACTGG 59.965 45.455 0.00 0.00 0.00 4.00
66 67 3.057315 CCGAAAAGCAAATGACACTGGAT 60.057 43.478 0.00 0.00 0.00 3.41
96 97 5.001237 TGCAAAACAGGCTAATGATGATG 57.999 39.130 0.00 0.00 0.00 3.07
149 151 5.069781 CCTCCTTTCTTCTCGGATGTATTCT 59.930 44.000 0.00 0.00 0.00 2.40
172 174 2.996249 TCATTGTCATCCTCCTGAGC 57.004 50.000 0.00 0.00 0.00 4.26
185 187 3.317430 CCTCCTGAGCAATTGATAAAGCC 59.683 47.826 10.34 0.00 0.00 4.35
249 251 1.544691 GTGTCTTCTTCTAGTCGGCCA 59.455 52.381 2.24 0.00 0.00 5.36
250 252 2.166664 GTGTCTTCTTCTAGTCGGCCAT 59.833 50.000 2.24 0.00 0.00 4.40
277 306 4.619227 CGTGTGAACCACCGCCCT 62.619 66.667 0.00 0.00 41.26 5.19
287 316 1.202952 ACCACCGCCCTAATGTCAAAA 60.203 47.619 0.00 0.00 0.00 2.44
408 453 5.590259 ACAATAATTGGAGGCATGTGTAGTC 59.410 40.000 0.00 0.00 34.12 2.59
412 457 1.007842 TGGAGGCATGTGTAGTCCCTA 59.992 52.381 0.00 0.00 0.00 3.53
444 489 6.183360 GGCCAGGAAAATAACAAATCGGATTA 60.183 38.462 3.22 0.00 0.00 1.75
458 504 1.406751 CGGATTACCTGTCATGCCACA 60.407 52.381 0.00 0.00 0.00 4.17
506 552 2.093447 AGGTAGCCTGTTGTGCTATGTC 60.093 50.000 0.00 0.00 42.80 3.06
691 1134 8.535690 AGGTGTTCTAAAATTTCTAGAAGTCG 57.464 34.615 16.45 0.00 36.34 4.18
710 1153 4.804139 AGTCGGACTTCATAATGCTTAACG 59.196 41.667 4.45 0.00 0.00 3.18
711 1154 4.565564 GTCGGACTTCATAATGCTTAACGT 59.434 41.667 0.00 0.00 0.00 3.99
734 1177 8.303876 ACGTAAATATCAAAAAGAATGCCAACT 58.696 29.630 0.00 0.00 0.00 3.16
838 1286 6.539649 TTCTTCAAAAACCTAGATCACACG 57.460 37.500 0.00 0.00 0.00 4.49
839 1287 4.994852 TCTTCAAAAACCTAGATCACACGG 59.005 41.667 0.00 0.00 0.00 4.94
846 1294 3.022406 ACCTAGATCACACGGAACTACC 58.978 50.000 0.00 0.00 30.42 3.18
914 1367 9.515020 TTTAGAACAGAGCAAGTAACATTTTTG 57.485 29.630 0.00 0.00 0.00 2.44
922 1375 7.920682 AGAGCAAGTAACATTTTTGAAACGAAT 59.079 29.630 0.00 0.00 0.00 3.34
930 1383 6.443792 ACATTTTTGAAACGAATGGAGTACC 58.556 36.000 7.12 0.00 35.60 3.34
940 1393 5.903810 ACGAATGGAGTACCTAAATCAGAC 58.096 41.667 0.00 0.00 37.04 3.51
941 1394 5.657302 ACGAATGGAGTACCTAAATCAGACT 59.343 40.000 0.00 0.00 37.04 3.24
942 1395 6.183360 ACGAATGGAGTACCTAAATCAGACTC 60.183 42.308 0.00 0.00 36.60 3.36
943 1396 6.039941 CGAATGGAGTACCTAAATCAGACTCT 59.960 42.308 0.00 0.00 37.33 3.24
944 1397 6.969993 ATGGAGTACCTAAATCAGACTCTC 57.030 41.667 0.00 0.00 37.33 3.20
945 1398 6.080969 TGGAGTACCTAAATCAGACTCTCT 57.919 41.667 0.00 0.00 37.33 3.10
946 1399 6.123651 TGGAGTACCTAAATCAGACTCTCTC 58.876 44.000 0.00 0.00 37.33 3.20
947 1400 6.069323 TGGAGTACCTAAATCAGACTCTCTCT 60.069 42.308 0.00 0.00 37.33 3.10
948 1401 6.831868 GGAGTACCTAAATCAGACTCTCTCTT 59.168 42.308 0.00 0.00 37.33 2.85
949 1402 7.340999 GGAGTACCTAAATCAGACTCTCTCTTT 59.659 40.741 0.00 0.00 37.33 2.52
950 1403 8.658840 AGTACCTAAATCAGACTCTCTCTTTT 57.341 34.615 0.00 0.00 0.00 2.27
951 1404 9.095700 AGTACCTAAATCAGACTCTCTCTTTTT 57.904 33.333 0.00 0.00 0.00 1.94
983 1457 2.434336 TCCTTCCTCACATATCGGTTGG 59.566 50.000 0.00 0.00 0.00 3.77
989 1463 5.853936 TCCTCACATATCGGTTGGAATAAG 58.146 41.667 0.00 0.00 0.00 1.73
990 1464 4.997395 CCTCACATATCGGTTGGAATAAGG 59.003 45.833 0.00 0.00 0.00 2.69
991 1465 5.221641 CCTCACATATCGGTTGGAATAAGGA 60.222 44.000 0.00 0.00 0.00 3.36
992 1466 5.607477 TCACATATCGGTTGGAATAAGGAC 58.393 41.667 0.00 0.00 0.00 3.85
995 1469 6.017934 CACATATCGGTTGGAATAAGGACTTG 60.018 42.308 0.00 0.00 0.00 3.16
1012 1487 5.604650 AGGACTTGTATTATGAGAAGGAGGG 59.395 44.000 0.00 0.00 0.00 4.30
1020 1495 7.894364 TGTATTATGAGAAGGAGGGGTACTATC 59.106 40.741 0.00 0.00 0.00 2.08
1023 1498 6.547396 ATGAGAAGGAGGGGTACTATCTTA 57.453 41.667 0.00 0.00 0.00 2.10
1032 1507 9.739737 AGGAGGGGTACTATCTTAAAAGAAATA 57.260 33.333 0.00 0.00 38.77 1.40
1150 1643 0.598065 GCCGAACTGCACAAAGGAAT 59.402 50.000 0.00 0.00 0.00 3.01
1204 1709 1.875813 GCATGGCTCGTCGTCTCTG 60.876 63.158 0.00 0.00 0.00 3.35
1209 1714 0.743701 GGCTCGTCGTCTCTGTCCTA 60.744 60.000 0.00 0.00 0.00 2.94
1219 1724 4.409574 TCGTCTCTGTCCTATCCTTCTACT 59.590 45.833 0.00 0.00 0.00 2.57
1233 1738 5.900437 TCCTTCTACTTTCTCAACCTCCTA 58.100 41.667 0.00 0.00 0.00 2.94
1404 1918 2.037527 GTGGTCGTCTCCTCCCCT 59.962 66.667 0.00 0.00 0.00 4.79
1451 1980 1.146930 ATGATTCCGTGCTCGCCAT 59.853 52.632 1.89 0.00 35.54 4.40
1626 2159 1.367840 GGAGCTCACAGACCACGTT 59.632 57.895 17.19 0.00 0.00 3.99
1689 2222 2.507324 GCCTTCACGACGAGCCTC 60.507 66.667 0.00 0.00 0.00 4.70
2149 2695 6.916387 ACACTCGATGTATTATACCGTTTGAG 59.084 38.462 0.00 6.40 40.88 3.02
2164 2710 3.753272 CGTTTGAGTGATTCCATGAACCT 59.247 43.478 0.00 0.00 0.00 3.50
2213 2786 4.434685 GCTGATTGAGCCTCTCCG 57.565 61.111 0.00 0.00 42.54 4.63
2275 2852 5.163933 CCAAAACAAAAATGGCATCGAGATG 60.164 40.000 0.00 8.62 41.60 2.90
2289 2866 0.321919 GAGATGGCTCAAGTGGCACA 60.322 55.000 21.41 0.00 45.12 4.57
2304 2885 5.969423 AGTGGCACAAAATTTCATATCCAG 58.031 37.500 21.41 0.00 44.16 3.86
2373 2958 8.723942 ACTATAGAGTAGCCAATTTGTTTCTG 57.276 34.615 6.78 0.00 32.65 3.02
2382 2967 4.815846 GCCAATTTGTTTCTGTTGATGGTT 59.184 37.500 0.00 0.00 0.00 3.67
2385 2970 6.707161 CCAATTTGTTTCTGTTGATGGTTGAT 59.293 34.615 0.00 0.00 0.00 2.57
2386 2971 7.227116 CCAATTTGTTTCTGTTGATGGTTGATT 59.773 33.333 0.00 0.00 0.00 2.57
2453 3042 6.982160 ATGTGGATATTTGTGGCATGTTAT 57.018 33.333 0.00 0.00 0.00 1.89
2475 3925 9.319143 GTTATTCATCTACTGCTGTCAATAACT 57.681 33.333 0.00 0.00 34.66 2.24
2483 4818 8.318412 TCTACTGCTGTCAATAACTCCAAATAA 58.682 33.333 0.00 0.00 0.00 1.40
2601 6519 0.811915 TGGACCAAACCACACAAACG 59.188 50.000 0.00 0.00 34.77 3.60
2657 6605 5.977635 TCTAAAATCGGCATCTCTTGAGAA 58.022 37.500 4.33 0.00 0.00 2.87
2751 6701 1.106285 CCTTTGAGGCCCTGTATTGC 58.894 55.000 0.00 0.00 0.00 3.56
2764 7898 5.534654 GCCCTGTATTGCATATACCTTGAAA 59.465 40.000 13.15 0.00 0.00 2.69
2794 7928 3.883830 ACAACAACATGGAAGCACAAA 57.116 38.095 0.00 0.00 0.00 2.83
2848 7982 6.981722 ACCAGAAACATGAAAACTGATAACC 58.018 36.000 0.00 0.00 0.00 2.85
2855 7989 9.883142 AAACATGAAAACTGATAACCTGAAAAA 57.117 25.926 0.00 0.00 0.00 1.94
3150 8956 8.879227 TGAAAAAGGAAATATTGGGTCAAGAAT 58.121 29.630 0.00 0.00 0.00 2.40
3577 9435 5.409826 AGCTGTCATAAAAGAGACTTTTCGG 59.590 40.000 11.81 6.98 35.81 4.30
3723 9581 4.404073 AGATGTATGGACTGAACCTGAGAC 59.596 45.833 0.00 0.00 0.00 3.36
3923 9781 3.189287 GGAACGTGATGGGATTGATATGC 59.811 47.826 0.00 0.00 0.00 3.14
3987 9845 7.855904 CCTTTGTATTATAGCAACACCGATTTC 59.144 37.037 0.00 0.00 0.00 2.17
4008 9872 7.546250 TTTCAGGAAAATAAAAGGCACCATA 57.454 32.000 0.00 0.00 0.00 2.74
4018 9883 8.823220 AATAAAAGGCACCATATTAAGAGTGT 57.177 30.769 0.00 0.00 32.75 3.55
4025 9890 7.553044 AGGCACCATATTAAGAGTGTTTTAGAC 59.447 37.037 0.00 0.00 32.75 2.59
4117 9982 6.333416 TGATATTCTCTCAGAGTTCAAACCG 58.667 40.000 0.36 0.00 0.00 4.44
4129 9994 1.060308 CAAACCGTATGCGCCTTCG 59.940 57.895 4.18 4.55 36.67 3.79
4167 10046 9.748708 TTTTTCACCAAGAATATGAACAAGAAG 57.251 29.630 0.00 0.00 35.83 2.85
4270 11029 3.118038 GCTACTTTGGGATGGTGATGGTA 60.118 47.826 0.00 0.00 0.00 3.25
4343 11102 6.325919 TGGTGATGGAAAGAAATACACAAC 57.674 37.500 0.00 0.00 0.00 3.32
4354 11113 8.845942 AAAGAAATACACAACGTTAAAGTTCC 57.154 30.769 0.00 0.00 30.96 3.62
4427 11193 8.612619 AGAATAAAGTTAATACTGCCATGAACG 58.387 33.333 0.00 0.00 34.01 3.95
4506 11275 3.270877 ACTTGCAAATATCTCCACGTCC 58.729 45.455 0.00 0.00 0.00 4.79
4520 11289 3.388676 TCCACGTCCTTTTGTTCTCCTTA 59.611 43.478 0.00 0.00 0.00 2.69
4596 11368 8.514594 CAATACTCTCAAAAGGTCATTGCTTAA 58.485 33.333 0.00 0.00 0.00 1.85
4597 11369 8.814038 ATACTCTCAAAAGGTCATTGCTTAAT 57.186 30.769 0.00 0.00 0.00 1.40
4598 11370 7.530426 ACTCTCAAAAGGTCATTGCTTAATT 57.470 32.000 0.00 0.00 0.00 1.40
4599 11371 8.635765 ACTCTCAAAAGGTCATTGCTTAATTA 57.364 30.769 0.00 0.00 0.00 1.40
4668 11440 8.586570 TTGTGCTAGTGACCAAATAAAAATTG 57.413 30.769 0.00 0.00 0.00 2.32
4692 11464 5.355910 GGGGTTATTGTTGAGAAGCGATTTA 59.644 40.000 0.00 0.00 0.00 1.40
4697 11469 3.342719 TGTTGAGAAGCGATTTATGGCA 58.657 40.909 0.00 0.00 33.65 4.92
4698 11470 3.374988 TGTTGAGAAGCGATTTATGGCAG 59.625 43.478 0.00 0.00 33.65 4.85
4714 11486 1.610624 GGCAGGAACATCCTCGAACAA 60.611 52.381 0.00 0.00 45.66 2.83
4718 11490 1.076332 GAACATCCTCGAACAACCCG 58.924 55.000 0.00 0.00 0.00 5.28
4732 11504 0.893727 AACCCGGATTTGTGCTCACC 60.894 55.000 0.73 0.00 0.00 4.02
4735 11507 2.398554 CGGATTTGTGCTCACCCGG 61.399 63.158 12.77 0.00 33.94 5.73
4750 11522 0.037697 CCCGGTTGTCTCGTGATTCA 60.038 55.000 0.00 0.00 0.00 2.57
4758 11530 6.853872 CGGTTGTCTCGTGATTCAAAAATTAA 59.146 34.615 0.00 0.00 0.00 1.40
4786 11558 3.272334 GCATCCGCGTTAGCCCTG 61.272 66.667 4.92 0.00 41.18 4.45
4812 11584 1.681780 CCTTACATGGGGTCAATGCGT 60.682 52.381 0.00 0.00 0.00 5.24
4866 11638 4.862574 ACCGTGCTTTTTCTTTTGACTTTC 59.137 37.500 0.00 0.00 0.00 2.62
4921 11693 7.972832 AAAGTACAATATTCGTGTTCCTTGA 57.027 32.000 0.00 0.00 0.00 3.02
4922 11694 6.963049 AGTACAATATTCGTGTTCCTTGAC 57.037 37.500 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.861086 CCTCCTGCTAGAATAATAGAGTTGTTA 58.139 37.037 0.00 0.00 0.00 2.41
6 7 6.268847 CCCTCCTGCTAGAATAATAGAGTTGT 59.731 42.308 0.00 0.00 0.00 3.32
7 8 6.295575 CCCCTCCTGCTAGAATAATAGAGTTG 60.296 46.154 0.00 0.00 0.00 3.16
8 9 5.782845 CCCCTCCTGCTAGAATAATAGAGTT 59.217 44.000 0.00 0.00 0.00 3.01
9 10 5.337788 CCCCTCCTGCTAGAATAATAGAGT 58.662 45.833 0.00 0.00 0.00 3.24
10 11 4.714308 CCCCCTCCTGCTAGAATAATAGAG 59.286 50.000 0.00 0.00 0.00 2.43
11 12 4.109765 ACCCCCTCCTGCTAGAATAATAGA 59.890 45.833 0.00 0.00 0.00 1.98
12 13 4.430441 ACCCCCTCCTGCTAGAATAATAG 58.570 47.826 0.00 0.00 0.00 1.73
13 14 4.503685 ACCCCCTCCTGCTAGAATAATA 57.496 45.455 0.00 0.00 0.00 0.98
14 15 3.368921 ACCCCCTCCTGCTAGAATAAT 57.631 47.619 0.00 0.00 0.00 1.28
15 16 2.889522 ACCCCCTCCTGCTAGAATAA 57.110 50.000 0.00 0.00 0.00 1.40
16 17 2.520980 TGTACCCCCTCCTGCTAGAATA 59.479 50.000 0.00 0.00 0.00 1.75
17 18 1.294068 TGTACCCCCTCCTGCTAGAAT 59.706 52.381 0.00 0.00 0.00 2.40
18 19 0.714180 TGTACCCCCTCCTGCTAGAA 59.286 55.000 0.00 0.00 0.00 2.10
19 20 0.941963 ATGTACCCCCTCCTGCTAGA 59.058 55.000 0.00 0.00 0.00 2.43
20 21 2.696526 TATGTACCCCCTCCTGCTAG 57.303 55.000 0.00 0.00 0.00 3.42
21 22 2.453212 TGATATGTACCCCCTCCTGCTA 59.547 50.000 0.00 0.00 0.00 3.49
22 23 1.223077 TGATATGTACCCCCTCCTGCT 59.777 52.381 0.00 0.00 0.00 4.24
23 24 1.729586 TGATATGTACCCCCTCCTGC 58.270 55.000 0.00 0.00 0.00 4.85
24 25 2.372172 GGTTGATATGTACCCCCTCCTG 59.628 54.545 0.00 0.00 0.00 3.86
25 26 2.702748 GGTTGATATGTACCCCCTCCT 58.297 52.381 0.00 0.00 0.00 3.69
26 27 1.346722 CGGTTGATATGTACCCCCTCC 59.653 57.143 0.00 0.00 0.00 4.30
27 28 2.322658 TCGGTTGATATGTACCCCCTC 58.677 52.381 0.00 0.00 0.00 4.30
28 29 2.482414 TCGGTTGATATGTACCCCCT 57.518 50.000 0.00 0.00 0.00 4.79
29 30 3.564053 TTTCGGTTGATATGTACCCCC 57.436 47.619 0.00 0.00 0.00 5.40
30 31 3.314357 GCTTTTCGGTTGATATGTACCCC 59.686 47.826 0.00 0.00 0.00 4.95
31 32 3.942748 TGCTTTTCGGTTGATATGTACCC 59.057 43.478 0.00 0.00 0.00 3.69
32 33 5.554822 TTGCTTTTCGGTTGATATGTACC 57.445 39.130 0.00 0.00 0.00 3.34
66 67 9.964354 ATCATTAGCCTGTTTTGCATATCTATA 57.036 29.630 0.00 0.00 0.00 1.31
149 151 4.685302 GCTCAGGAGGATGACAATGAATCA 60.685 45.833 0.00 0.00 0.00 2.57
172 174 4.944962 TCGACACAGGCTTTATCAATTG 57.055 40.909 0.00 0.00 0.00 2.32
209 211 3.928992 CACGTGCACATTCTCTCACTAAT 59.071 43.478 18.64 0.00 0.00 1.73
249 251 3.057033 GTGGTTCACACGTACTACTCCAT 60.057 47.826 0.00 0.00 40.85 3.41
250 252 2.294233 GTGGTTCACACGTACTACTCCA 59.706 50.000 0.00 0.00 40.85 3.86
277 306 3.064682 CGCCGTCATGGATTTTGACATTA 59.935 43.478 4.86 0.00 42.90 1.90
287 316 2.842462 TAGGGCGCCGTCATGGAT 60.842 61.111 27.35 3.10 42.00 3.41
425 470 8.455682 TGACAGGTAATCCGATTTGTTATTTTC 58.544 33.333 0.00 0.00 39.05 2.29
444 489 0.478072 TTCCTTGTGGCATGACAGGT 59.522 50.000 0.00 0.00 0.00 4.00
458 504 2.110721 AGCAAGGTGGGATCTTTTCCTT 59.889 45.455 0.00 0.00 44.75 3.36
645 701 7.454380 ACACCTCAAATTTTGAAATGGAGGATA 59.546 33.333 27.17 0.00 44.93 2.59
663 1106 9.847224 ACTTCTAGAAATTTTAGAACACCTCAA 57.153 29.630 6.63 0.25 34.40 3.02
718 1161 6.507023 AGTGTAGAAGTTGGCATTCTTTTTG 58.493 36.000 8.52 0.00 38.05 2.44
785 1233 8.373048 TCAACATCTACAACGTTGAATTAGTT 57.627 30.769 33.66 24.96 44.38 2.24
835 1283 6.821031 AGCTTATCTATAGGTAGTTCCGTG 57.179 41.667 0.00 0.00 41.99 4.94
836 1284 7.002879 TCAAGCTTATCTATAGGTAGTTCCGT 58.997 38.462 0.00 0.00 41.99 4.69
837 1285 7.175293 AGTCAAGCTTATCTATAGGTAGTTCCG 59.825 40.741 0.00 0.00 41.99 4.30
838 1286 8.411991 AGTCAAGCTTATCTATAGGTAGTTCC 57.588 38.462 0.00 0.00 0.00 3.62
878 1327 8.669243 ACTTGCTCTGTTCTAAAATATAAGTGC 58.331 33.333 0.00 0.00 0.00 4.40
911 1364 7.662258 TGATTTAGGTACTCCATTCGTTTCAAA 59.338 33.333 0.00 0.00 41.75 2.69
913 1366 6.703319 TGATTTAGGTACTCCATTCGTTTCA 58.297 36.000 0.00 0.00 41.75 2.69
914 1367 7.010275 GTCTGATTTAGGTACTCCATTCGTTTC 59.990 40.741 0.00 0.00 41.75 2.78
922 1375 6.069323 AGAGAGAGTCTGATTTAGGTACTCCA 60.069 42.308 0.00 0.00 37.82 3.86
951 1404 3.460340 TGTGAGGAAGGAGTACCCAAAAA 59.540 43.478 3.60 0.00 37.41 1.94
956 1409 3.256136 CGATATGTGAGGAAGGAGTACCC 59.744 52.174 0.00 0.00 36.73 3.69
957 1410 3.256136 CCGATATGTGAGGAAGGAGTACC 59.744 52.174 0.00 0.00 0.00 3.34
958 1411 3.890147 ACCGATATGTGAGGAAGGAGTAC 59.110 47.826 0.00 0.00 0.00 2.73
963 1416 2.434336 TCCAACCGATATGTGAGGAAGG 59.566 50.000 0.00 0.00 0.00 3.46
989 1463 5.221742 CCCCTCCTTCTCATAATACAAGTCC 60.222 48.000 0.00 0.00 0.00 3.85
990 1464 5.367060 ACCCCTCCTTCTCATAATACAAGTC 59.633 44.000 0.00 0.00 0.00 3.01
991 1465 5.289510 ACCCCTCCTTCTCATAATACAAGT 58.710 41.667 0.00 0.00 0.00 3.16
992 1466 5.896073 ACCCCTCCTTCTCATAATACAAG 57.104 43.478 0.00 0.00 0.00 3.16
995 1469 8.117312 AGATAGTACCCCTCCTTCTCATAATAC 58.883 40.741 0.00 0.00 0.00 1.89
1006 1480 8.640033 ATTTCTTTTAAGATAGTACCCCTCCT 57.360 34.615 0.00 0.00 34.49 3.69
1032 1507 9.973450 CAATCAGCTGTATATAAGTTGTACTCT 57.027 33.333 14.67 0.00 0.00 3.24
1041 1516 8.817100 TGTTTTCGACAATCAGCTGTATATAAG 58.183 33.333 14.67 1.74 34.69 1.73
1042 1517 8.710835 TGTTTTCGACAATCAGCTGTATATAA 57.289 30.769 14.67 0.00 34.69 0.98
1043 1518 8.194769 TCTGTTTTCGACAATCAGCTGTATATA 58.805 33.333 14.67 0.00 37.93 0.86
1049 1534 4.024556 AGTTCTGTTTTCGACAATCAGCTG 60.025 41.667 7.63 7.63 37.93 4.24
1150 1643 3.267233 AGCCAGGGCCACCATTGA 61.267 61.111 6.18 0.00 43.17 2.57
1204 1709 6.381707 AGGTTGAGAAAGTAGAAGGATAGGAC 59.618 42.308 0.00 0.00 0.00 3.85
1209 1714 5.346270 AGGAGGTTGAGAAAGTAGAAGGAT 58.654 41.667 0.00 0.00 0.00 3.24
1219 1724 0.973632 TGCGCTAGGAGGTTGAGAAA 59.026 50.000 9.73 0.00 0.00 2.52
1598 2131 3.072476 TGAGCTCCCTCACCTTGC 58.928 61.111 12.15 0.00 42.98 4.01
1689 2222 0.251916 TGGTGCGGGAGATAAGGTTG 59.748 55.000 0.00 0.00 0.00 3.77
1996 2529 2.437897 CAGCAGGTCCTTGCCCTT 59.562 61.111 9.02 0.00 45.18 3.95
2149 2695 2.743183 CGGGAGAGGTTCATGGAATCAC 60.743 54.545 0.00 0.00 0.00 3.06
2164 2710 1.615124 TGCTTTGATCCCCGGGAGA 60.615 57.895 26.32 18.63 34.05 3.71
2213 2786 1.554617 CCACCATTTGTTTGATCCCCC 59.445 52.381 0.00 0.00 0.00 5.40
2275 2852 2.531522 AATTTTGTGCCACTTGAGCC 57.468 45.000 0.00 0.00 0.00 4.70
2279 2856 6.164876 TGGATATGAAATTTTGTGCCACTTG 58.835 36.000 0.00 0.00 0.00 3.16
2343 2926 8.723942 ACAAATTGGCTACTCTATAGTCTTTG 57.276 34.615 0.00 0.00 37.15 2.77
2453 3042 6.070824 TGGAGTTATTGACAGCAGTAGATGAA 60.071 38.462 0.00 0.00 34.60 2.57
2764 7898 8.584157 TGCTTCCATGTTGTTGTATTTCTAAAT 58.416 29.630 0.00 0.00 0.00 1.40
2907 8041 7.911130 TGATTCCTATAAAATTTCCATGCCA 57.089 32.000 0.00 0.00 0.00 4.92
3242 9069 7.117454 CACAACTCTAAACTACACTTTCGTTG 58.883 38.462 0.00 0.00 35.46 4.10
3263 9092 6.275494 TGTGGTATAGAAGAATCGACACAA 57.725 37.500 0.00 0.00 0.00 3.33
3264 9093 5.907866 TGTGGTATAGAAGAATCGACACA 57.092 39.130 0.00 0.00 0.00 3.72
3468 9326 2.289547 GCAAGCTCGTCACAAACCTTAA 59.710 45.455 0.00 0.00 0.00 1.85
3577 9435 4.416738 GGTGCAGGAGGGTGGAGC 62.417 72.222 0.00 0.00 0.00 4.70
3723 9581 3.252974 AGAACCTCTCAGGCATAAACG 57.747 47.619 0.00 0.00 39.63 3.60
3923 9781 2.227388 GTGTCAGGCCAAAGTGATCTTG 59.773 50.000 5.01 0.00 33.79 3.02
3987 9845 9.533253 CTTAATATGGTGCCTTTTATTTTCCTG 57.467 33.333 0.00 0.00 0.00 3.86
4117 9982 1.525619 GTGGATAACGAAGGCGCATAC 59.474 52.381 10.83 0.00 42.48 2.39
4129 9994 4.846779 TGGTGAAAAAGCAGTGGATAAC 57.153 40.909 0.00 0.00 0.00 1.89
4270 11029 5.351465 CAGCCTAATGTGTTATCTTGACGTT 59.649 40.000 0.00 0.00 0.00 3.99
4318 11077 6.513806 TGTGTATTTCTTTCCATCACCATG 57.486 37.500 0.00 0.00 0.00 3.66
4343 11102 8.339714 TCTGTTATTTGAACAGGAACTTTAACG 58.660 33.333 15.44 0.00 45.66 3.18
4411 11177 4.403113 TGTAGTCCGTTCATGGCAGTATTA 59.597 41.667 0.00 0.00 0.00 0.98
4427 11193 7.923414 ATTGTCCTTTTGAAGTATGTAGTCC 57.077 36.000 0.00 0.00 0.00 3.85
4495 11261 3.557264 GGAGAACAAAAGGACGTGGAGAT 60.557 47.826 0.00 0.00 0.00 2.75
4520 11289 3.852286 TCGTTGTGCGGTTCACTATTAT 58.148 40.909 0.00 0.00 45.81 1.28
4599 11371 8.870116 ACAAAGCCTTCAAAAATATTAGGAGTT 58.130 29.630 5.54 0.00 0.00 3.01
4668 11440 2.706890 TCGCTTCTCAACAATAACCCC 58.293 47.619 0.00 0.00 0.00 4.95
4698 11470 1.450025 GGGTTGTTCGAGGATGTTCC 58.550 55.000 0.00 0.00 36.58 3.62
4714 11486 1.303317 GGTGAGCACAAATCCGGGT 60.303 57.895 0.00 0.00 0.00 5.28
4718 11490 0.893727 AACCGGGTGAGCACAAATCC 60.894 55.000 6.32 0.00 0.00 3.01
4732 11504 1.790755 TTGAATCACGAGACAACCGG 58.209 50.000 0.00 0.00 0.00 5.28
4762 11534 0.026803 CTAACGCGGATGCAAAGAGC 59.973 55.000 12.47 0.00 42.97 4.09
4774 11546 0.935196 GGTAATTCAGGGCTAACGCG 59.065 55.000 3.53 3.53 36.88 6.01
4777 11549 5.531287 CCATGTAAGGTAATTCAGGGCTAAC 59.469 44.000 0.00 0.00 0.00 2.34
4786 11558 5.221244 GCATTGACCCCATGTAAGGTAATTC 60.221 44.000 0.00 0.00 36.17 2.17
4902 11674 5.607119 GTGTCAAGGAACACGAATATTGT 57.393 39.130 0.00 0.00 40.09 2.71
4921 11693 4.216902 GGTATTGTTTTAAAGCCCTCGTGT 59.783 41.667 0.00 0.00 0.00 4.49
4922 11694 4.216687 TGGTATTGTTTTAAAGCCCTCGTG 59.783 41.667 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.