Multiple sequence alignment - TraesCS7D01G123300

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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 TraesCS7D01G123300 chr7D 100.000 4226 0 0 1 4226 76972484 76976709 0.000000e+00 7805.0
1 TraesCS7D01G123300 chr7D 86.033 2198 257 29 985 3171 76744541 76746699 0.000000e+00 2313.0
2 TraesCS7D01G123300 chr7D 85.844 2211 269 24 985 3176 76920270 76922455 0.000000e+00 2309.0
3 TraesCS7D01G123300 chr7D 85.259 2198 292 23 985 3174 76785157 76787330 0.000000e+00 2235.0
4 TraesCS7D01G123300 chr7D 85.830 1849 227 25 1323 3160 77045885 77047709 0.000000e+00 1930.0
5 TraesCS7D01G123300 chr7D 84.592 1947 245 27 1216 3145 76955728 76957636 0.000000e+00 1882.0
6 TraesCS7D01G123300 chr7D 84.509 1801 247 18 985 2780 76634883 76633110 0.000000e+00 1751.0
7 TraesCS7D01G123300 chr7D 97.487 995 15 1 1 985 568394273 568395267 0.000000e+00 1690.0
8 TraesCS7D01G123300 chr7D 82.741 788 131 3 985 1771 7562045 7562828 0.000000e+00 697.0
9 TraesCS7D01G123300 chr7D 90.377 239 19 4 751 986 568394342 568394105 1.140000e-80 311.0
10 TraesCS7D01G123300 chr7A 86.401 2184 260 20 985 3159 80862962 80865117 0.000000e+00 2353.0
11 TraesCS7D01G123300 chr7B 86.092 2193 266 25 986 3154 23525529 23527706 0.000000e+00 2324.0
12 TraesCS7D01G123300 chr7B 85.553 2208 298 10 985 3181 23517119 23519316 0.000000e+00 2290.0
13 TraesCS7D01G123300 chr7B 85.559 2209 287 26 985 3186 23958976 23961159 0.000000e+00 2283.0
14 TraesCS7D01G123300 chr7B 85.591 2200 276 24 978 3146 23583268 23585457 0.000000e+00 2268.0
15 TraesCS7D01G123300 chr7B 84.577 2185 299 29 985 3160 23597686 23599841 0.000000e+00 2134.0
16 TraesCS7D01G123300 chr7B 82.691 2155 313 27 1030 3181 23934365 23936462 0.000000e+00 1858.0
17 TraesCS7D01G123300 chr7B 83.731 1801 257 19 988 2781 23939503 23941274 0.000000e+00 1670.0
18 TraesCS7D01G123300 chr7B 85.152 1320 184 8 1871 3187 23639655 23640965 0.000000e+00 1341.0
19 TraesCS7D01G123300 chr7B 92.060 466 23 8 3746 4204 23903355 23903813 0.000000e+00 643.0
20 TraesCS7D01G123300 chr7B 87.257 565 50 9 3646 4203 23586432 23586981 3.590000e-175 625.0
21 TraesCS7D01G123300 chr7B 94.162 394 18 4 3636 4025 23925545 23925937 2.810000e-166 595.0
22 TraesCS7D01G123300 chr7B 83.384 331 26 15 3458 3762 23902880 23903207 3.220000e-71 279.0
23 TraesCS7D01G123300 chr7B 95.238 147 5 2 4060 4204 23925935 23926081 9.140000e-57 231.0
24 TraesCS7D01G123300 chr7B 89.313 131 13 1 3220 3349 23528671 23528801 3.380000e-36 163.0
25 TraesCS7D01G123300 chr2A 89.537 994 66 9 1 984 470052452 470053417 0.000000e+00 1225.0
26 TraesCS7D01G123300 chr2A 89.865 148 14 1 1 148 18004240 18004094 5.580000e-44 189.0
27 TraesCS7D01G123300 chr2A 94.872 39 2 0 335 373 25350546 25350508 1.270000e-05 62.1
28 TraesCS7D01G123300 chr5D 90.670 836 59 10 153 984 98668091 98667271 0.000000e+00 1094.0
29 TraesCS7D01G123300 chr3B 84.625 787 119 2 985 1770 741464137 741464922 0.000000e+00 782.0
30 TraesCS7D01G123300 chr3B 88.845 251 28 0 339 589 655317243 655317493 4.100000e-80 309.0
31 TraesCS7D01G123300 chr3B 92.000 100 8 0 203 302 655317146 655317245 1.580000e-29 141.0
32 TraesCS7D01G123300 chr4A 81.481 783 142 1 989 1771 732106437 732107216 1.280000e-179 640.0
33 TraesCS7D01G123300 chr4A 81.203 798 140 9 988 1780 731663155 731662363 5.960000e-178 634.0
34 TraesCS7D01G123300 chr4A 81.454 399 56 13 601 984 719984044 719984439 1.140000e-80 311.0
35 TraesCS7D01G123300 chr6B 88.861 395 36 2 203 589 632560390 632560784 2.960000e-131 479.0
36 TraesCS7D01G123300 chr6B 83.791 401 49 7 601 986 61806495 61806894 2.400000e-97 366.0
37 TraesCS7D01G123300 chr3A 86.458 384 32 9 206 589 412934610 412934247 1.830000e-108 403.0
38 TraesCS7D01G123300 chr3A 88.845 251 28 0 339 589 123291918 123292168 4.100000e-80 309.0
39 TraesCS7D01G123300 chr3A 91.216 148 12 1 1 148 713995469 713995323 2.580000e-47 200.0
40 TraesCS7D01G123300 chr3A 93.000 100 7 0 203 302 123291821 123291920 3.400000e-31 147.0
41 TraesCS7D01G123300 chr1D 92.674 273 16 4 718 988 442449994 442449724 1.420000e-104 390.0
42 TraesCS7D01G123300 chr1D 91.760 267 22 0 718 984 430066947 430067213 5.160000e-99 372.0
43 TraesCS7D01G123300 chr5A 89.344 244 26 0 741 984 563100897 563100654 1.480000e-79 307.0
44 TraesCS7D01G123300 chr5A 88.525 244 28 0 741 984 563164776 563164533 3.190000e-76 296.0
45 TraesCS7D01G123300 chr3D 88.845 251 27 1 339 589 15412607 15412856 1.480000e-79 307.0
46 TraesCS7D01G123300 chr3D 90.541 148 14 0 1 148 963970 963823 3.330000e-46 196.0
47 TraesCS7D01G123300 chr3D 92.000 100 8 0 203 302 15412510 15412609 1.580000e-29 141.0
48 TraesCS7D01G123300 chr4D 89.865 148 14 1 1 148 483391964 483391818 5.580000e-44 189.0
49 TraesCS7D01G123300 chr2D 89.437 142 14 1 1 142 103134050 103133910 1.210000e-40 178.0
50 TraesCS7D01G123300 chr1B 88.514 148 16 1 1 148 655050624 655050770 1.210000e-40 178.0
51 TraesCS7D01G123300 chr1A 88.514 148 16 1 1 148 12219274 12219128 1.210000e-40 178.0


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 TraesCS7D01G123300 chr7D 76972484 76976709 4225 False 7805.0 7805 100.0000 1 4226 1 chr7D.!!$F6 4225
1 TraesCS7D01G123300 chr7D 76744541 76746699 2158 False 2313.0 2313 86.0330 985 3171 1 chr7D.!!$F2 2186
2 TraesCS7D01G123300 chr7D 76920270 76922455 2185 False 2309.0 2309 85.8440 985 3176 1 chr7D.!!$F4 2191
3 TraesCS7D01G123300 chr7D 76785157 76787330 2173 False 2235.0 2235 85.2590 985 3174 1 chr7D.!!$F3 2189
4 TraesCS7D01G123300 chr7D 77045885 77047709 1824 False 1930.0 1930 85.8300 1323 3160 1 chr7D.!!$F7 1837
5 TraesCS7D01G123300 chr7D 76955728 76957636 1908 False 1882.0 1882 84.5920 1216 3145 1 chr7D.!!$F5 1929
6 TraesCS7D01G123300 chr7D 76633110 76634883 1773 True 1751.0 1751 84.5090 985 2780 1 chr7D.!!$R1 1795
7 TraesCS7D01G123300 chr7D 568394273 568395267 994 False 1690.0 1690 97.4870 1 985 1 chr7D.!!$F8 984
8 TraesCS7D01G123300 chr7D 7562045 7562828 783 False 697.0 697 82.7410 985 1771 1 chr7D.!!$F1 786
9 TraesCS7D01G123300 chr7A 80862962 80865117 2155 False 2353.0 2353 86.4010 985 3159 1 chr7A.!!$F1 2174
10 TraesCS7D01G123300 chr7B 23517119 23519316 2197 False 2290.0 2290 85.5530 985 3181 1 chr7B.!!$F1 2196
11 TraesCS7D01G123300 chr7B 23958976 23961159 2183 False 2283.0 2283 85.5590 985 3186 1 chr7B.!!$F4 2201
12 TraesCS7D01G123300 chr7B 23597686 23599841 2155 False 2134.0 2134 84.5770 985 3160 1 chr7B.!!$F2 2175
13 TraesCS7D01G123300 chr7B 23934365 23941274 6909 False 1764.0 1858 83.2110 988 3181 2 chr7B.!!$F9 2193
14 TraesCS7D01G123300 chr7B 23583268 23586981 3713 False 1446.5 2268 86.4240 978 4203 2 chr7B.!!$F6 3225
15 TraesCS7D01G123300 chr7B 23639655 23640965 1310 False 1341.0 1341 85.1520 1871 3187 1 chr7B.!!$F3 1316
16 TraesCS7D01G123300 chr7B 23525529 23528801 3272 False 1243.5 2324 87.7025 986 3349 2 chr7B.!!$F5 2363
17 TraesCS7D01G123300 chr7B 23902880 23903813 933 False 461.0 643 87.7220 3458 4204 2 chr7B.!!$F7 746
18 TraesCS7D01G123300 chr7B 23925545 23926081 536 False 413.0 595 94.7000 3636 4204 2 chr7B.!!$F8 568
19 TraesCS7D01G123300 chr2A 470052452 470053417 965 False 1225.0 1225 89.5370 1 984 1 chr2A.!!$F1 983
20 TraesCS7D01G123300 chr5D 98667271 98668091 820 True 1094.0 1094 90.6700 153 984 1 chr5D.!!$R1 831
21 TraesCS7D01G123300 chr3B 741464137 741464922 785 False 782.0 782 84.6250 985 1770 1 chr3B.!!$F1 785
22 TraesCS7D01G123300 chr4A 732106437 732107216 779 False 640.0 640 81.4810 989 1771 1 chr4A.!!$F2 782
23 TraesCS7D01G123300 chr4A 731662363 731663155 792 True 634.0 634 81.2030 988 1780 1 chr4A.!!$R1 792

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
512 513 1.443407 GAGCATTGGAGGCGAGCTA 59.557 57.895 0.00 0.00 35.36 3.32 F
1031 1065 1.202710 TCGAAGCAAACAAGTGGCCTA 60.203 47.619 3.32 0.00 0.00 3.93 F
1802 1901 0.179174 GATTTTAACCGGCTGCCACG 60.179 55.000 20.29 10.39 0.00 4.94 F
2670 2779 0.459489 GTTGGGCAGAAAACAGTGCA 59.541 50.000 0.00 0.00 41.75 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 1861 0.251386 TGGCAGCCGGTTAAAATCCA 60.251 50.0 7.03 0.0 0.0 3.41 R
2525 2634 0.041312 CTTCAGTTTGCCCACGTTCG 60.041 55.0 0.00 0.0 0.0 3.95 R
3108 3234 0.178990 ACTCCCCACCTTCTTTGCAC 60.179 55.0 0.00 0.0 0.0 4.57 R
4053 5604 0.034616 GAGGGGAGATGATGGAAGCG 59.965 60.0 0.00 0.0 0.0 4.68 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
512 513 1.443407 GAGCATTGGAGGCGAGCTA 59.557 57.895 0.00 0.00 35.36 3.32
535 536 4.624364 CCGCGGGCTGGATATGCA 62.624 66.667 20.10 0.00 0.00 3.96
540 541 1.839191 GGGCTGGATATGCAGTCCA 59.161 57.895 35.14 19.26 42.44 4.02
746 780 1.606601 CGGGAGCAGGATATCGGGA 60.607 63.158 0.00 0.00 0.00 5.14
870 904 4.355151 GGGCCAAATCACCCGATT 57.645 55.556 4.39 0.00 43.94 3.34
902 936 6.899393 TTGCAAGGAGTTTAGTGAAATCAT 57.101 33.333 0.00 0.00 34.12 2.45
999 1033 4.142609 TGACTCACCAGGAAGCATTATC 57.857 45.455 0.00 0.00 0.00 1.75
1000 1034 3.519107 TGACTCACCAGGAAGCATTATCA 59.481 43.478 0.00 0.00 0.00 2.15
1031 1065 1.202710 TCGAAGCAAACAAGTGGCCTA 60.203 47.619 3.32 0.00 0.00 3.93
1140 1175 2.703536 TGGTGTAGAGGAGCAAACAGAA 59.296 45.455 0.00 0.00 0.00 3.02
1159 1194 6.725364 ACAGAATTAATCACCACAGGAAGAT 58.275 36.000 0.00 0.00 0.00 2.40
1232 1267 4.222114 GGATTGCTGAGTTCAAAGAAACG 58.778 43.478 0.00 0.00 34.27 3.60
1236 1271 3.938963 TGCTGAGTTCAAAGAAACGAGTT 59.061 39.130 0.00 0.00 34.27 3.01
1479 1514 8.434589 TGGATTTAACATGGAAAGGAGAATTT 57.565 30.769 0.00 0.00 0.00 1.82
1504 1539 3.874383 TCCATGAGTTGGTTTGGAGAA 57.126 42.857 0.00 0.00 46.52 2.87
1521 1556 4.228210 TGGAGAACCTTCCTGCAAGATATT 59.772 41.667 0.00 0.00 38.12 1.28
1663 1713 8.786898 CCATAGAAGAATTGACTGAACAGAAAA 58.213 33.333 8.87 3.17 0.00 2.29
1731 1793 6.421377 TTGGAACATATCACTCGATTGTTG 57.579 37.500 2.44 2.85 39.30 3.33
1802 1901 0.179174 GATTTTAACCGGCTGCCACG 60.179 55.000 20.29 10.39 0.00 4.94
1903 2002 7.065923 GGTATCTTGACCTCTCCAATTGTAAAC 59.934 40.741 4.43 0.00 36.47 2.01
1923 2022 3.403038 ACCCAATGCTATATTGCTCGAC 58.597 45.455 10.48 0.00 0.00 4.20
1956 2055 5.990386 TCTGTTGTATAACCTGCAAACGTTA 59.010 36.000 0.00 3.87 35.92 3.18
1971 2070 5.460646 CAAACGTTAAGGCTCAATCATTGT 58.539 37.500 0.00 0.00 0.00 2.71
1984 2083 4.216902 TCAATCATTGTGAAGGACTGCAAG 59.783 41.667 0.00 0.00 42.29 4.01
2083 2182 1.244019 GCCTCGAAACATTGGCCAGT 61.244 55.000 5.11 0.00 39.49 4.00
2091 2190 4.379652 GAAACATTGGCCAGTTGAACAAT 58.620 39.130 21.00 0.71 34.13 2.71
2182 2282 3.126858 GCGACACCTTTGCAATAAGATGA 59.873 43.478 0.00 0.00 34.24 2.92
2241 2341 2.030007 CGCAAAAGAAGCCAATCTCCAA 60.030 45.455 0.00 0.00 0.00 3.53
2271 2371 5.585390 CAAAATCTGAGTGAGCTGTTGTTT 58.415 37.500 0.00 0.00 0.00 2.83
2306 2415 7.254932 CCTTAAAAGATATGAAGAGCCCGAAAG 60.255 40.741 0.00 0.00 0.00 2.62
2318 2427 1.747206 GCCCGAAAGTGAGGCATGTAT 60.747 52.381 0.00 0.00 46.34 2.29
2525 2634 7.093421 ACCTTCACTGGAGTACTTATCCTTAAC 60.093 40.741 0.00 0.00 37.74 2.01
2530 2639 5.883661 TGGAGTACTTATCCTTAACGAACG 58.116 41.667 0.00 0.00 37.74 3.95
2535 2644 2.298411 TATCCTTAACGAACGTGGGC 57.702 50.000 0.00 0.00 0.00 5.36
2576 2685 6.939730 TGTGATAACCTTTGCATAGAAGTTGA 59.060 34.615 5.65 0.00 0.00 3.18
2578 2687 8.296713 GTGATAACCTTTGCATAGAAGTTGAAA 58.703 33.333 5.65 0.00 0.00 2.69
2652 2761 3.672211 AGAGCTACCTAGTCTAGAGGGT 58.328 50.000 8.56 14.05 38.52 4.34
2670 2779 0.459489 GTTGGGCAGAAAACAGTGCA 59.541 50.000 0.00 0.00 41.75 4.57
2799 2911 4.513442 TGAGTTTATCAGAATTCCCGGTG 58.487 43.478 0.00 0.00 32.77 4.94
2838 2952 1.643286 TGGGATATTCCAAGGTTGCCA 59.357 47.619 0.00 0.00 38.64 4.92
2844 2970 2.380064 TTCCAAGGTTGCCAACATCT 57.620 45.000 10.18 0.00 0.00 2.90
2845 2971 1.619654 TCCAAGGTTGCCAACATCTG 58.380 50.000 10.18 4.02 0.00 2.90
2885 3011 1.072505 GCTTCGGAGGTTTGGTGGA 59.927 57.895 0.00 0.00 0.00 4.02
2945 3071 2.371841 ACCTACTGGTTCATGACTGCAA 59.628 45.455 0.00 0.00 46.05 4.08
2952 3078 3.820777 GTTCATGACTGCAAGAACCTC 57.179 47.619 0.00 0.00 43.38 3.85
3036 3162 1.987855 AGCGACGGAGGAATTCCCA 60.988 57.895 21.22 0.00 43.63 4.37
3042 3168 0.746659 CGGAGGAATTCCCAAATGGC 59.253 55.000 21.22 2.28 43.63 4.40
3053 3179 0.612732 CCAAATGGCCTCCTTCAGCA 60.613 55.000 3.32 0.00 0.00 4.41
3108 3234 1.856265 GCCCTGAGTTGCAAAGACGG 61.856 60.000 0.00 0.00 0.00 4.79
3176 3302 6.449698 CAGTTAAACACATTCCAGCAGAATT 58.550 36.000 0.00 0.00 42.86 2.17
3196 3334 7.141100 GAATTAGAATTCGGAACTGGAACAA 57.859 36.000 0.00 0.00 34.94 2.83
3197 3335 6.743575 ATTAGAATTCGGAACTGGAACAAG 57.256 37.500 0.00 0.00 38.70 3.16
3198 3336 4.086706 AGAATTCGGAACTGGAACAAGT 57.913 40.909 0.00 0.00 38.70 3.16
3199 3337 5.223449 AGAATTCGGAACTGGAACAAGTA 57.777 39.130 0.00 0.00 38.70 2.24
3200 3338 5.805728 AGAATTCGGAACTGGAACAAGTAT 58.194 37.500 0.00 0.00 38.70 2.12
3201 3339 5.875359 AGAATTCGGAACTGGAACAAGTATC 59.125 40.000 0.00 0.00 38.70 2.24
3202 3340 4.610605 TTCGGAACTGGAACAAGTATCA 57.389 40.909 0.00 0.00 38.70 2.15
3204 3342 3.000727 CGGAACTGGAACAAGTATCACC 58.999 50.000 0.00 0.00 38.70 4.02
3205 3343 3.306780 CGGAACTGGAACAAGTATCACCT 60.307 47.826 0.00 0.00 38.70 4.00
3206 3344 4.652822 GGAACTGGAACAAGTATCACCTT 58.347 43.478 0.00 0.00 38.70 3.50
3207 3345 4.695928 GGAACTGGAACAAGTATCACCTTC 59.304 45.833 0.00 0.00 38.70 3.46
3208 3346 4.974645 ACTGGAACAAGTATCACCTTCA 57.025 40.909 0.00 0.00 38.70 3.02
3209 3347 5.505181 ACTGGAACAAGTATCACCTTCAT 57.495 39.130 0.00 0.00 38.70 2.57
3210 3348 5.248640 ACTGGAACAAGTATCACCTTCATG 58.751 41.667 0.00 0.00 38.70 3.07
3211 3349 4.009675 TGGAACAAGTATCACCTTCATGC 58.990 43.478 0.00 0.00 31.92 4.06
3213 3351 4.095483 GGAACAAGTATCACCTTCATGCAG 59.905 45.833 0.00 0.00 0.00 4.41
3214 3352 3.012518 ACAAGTATCACCTTCATGCAGC 58.987 45.455 0.00 0.00 0.00 5.25
3215 3353 3.276857 CAAGTATCACCTTCATGCAGCT 58.723 45.455 0.00 0.00 0.00 4.24
3217 3355 2.770802 AGTATCACCTTCATGCAGCTCT 59.229 45.455 0.00 0.00 0.00 4.09
3239 4311 5.899547 TCTCTGGATGAGTATCTGCCTTTTA 59.100 40.000 0.00 0.00 43.13 1.52
3255 4327 7.719633 TCTGCCTTTTATTGGACAAGTATATCC 59.280 37.037 0.00 0.00 35.37 2.59
3279 4351 1.691215 GCTTACTGCTCTGTGCTCGC 61.691 60.000 3.20 0.00 43.37 5.03
3280 4352 1.409227 CTTACTGCTCTGTGCTCGCG 61.409 60.000 0.00 0.00 43.37 5.87
3325 4398 9.174166 GCATAAAGAGGTAAACTTCTAATCCAA 57.826 33.333 0.00 0.00 31.62 3.53
3350 4423 6.058833 TGACATCTCTAGTACTTCCTGCTAG 58.941 44.000 0.00 0.00 36.71 3.42
3355 4428 2.239681 AGTACTTCCTGCTAGTGCCT 57.760 50.000 0.00 0.00 38.71 4.75
3359 4432 2.104170 ACTTCCTGCTAGTGCCTAGTC 58.896 52.381 9.93 4.75 36.53 2.59
3368 4441 4.956700 TGCTAGTGCCTAGTCTTAATCTGT 59.043 41.667 9.93 0.00 36.53 3.41
3371 4444 6.477360 GCTAGTGCCTAGTCTTAATCTGTTTC 59.523 42.308 9.93 0.00 36.53 2.78
3373 4446 5.485708 AGTGCCTAGTCTTAATCTGTTTCCT 59.514 40.000 0.00 0.00 0.00 3.36
3374 4447 6.668283 AGTGCCTAGTCTTAATCTGTTTCCTA 59.332 38.462 0.00 0.00 0.00 2.94
3375 4448 7.180408 AGTGCCTAGTCTTAATCTGTTTCCTAA 59.820 37.037 0.00 0.00 0.00 2.69
3376 4449 7.988028 GTGCCTAGTCTTAATCTGTTTCCTAAT 59.012 37.037 0.00 0.00 0.00 1.73
3378 4451 8.204836 GCCTAGTCTTAATCTGTTTCCTAATGA 58.795 37.037 0.00 0.00 0.00 2.57
3404 4525 5.716703 AGTTTATCAATCCTTTCAGGTTGGG 59.283 40.000 5.71 0.00 36.53 4.12
3405 4526 2.603075 TCAATCCTTTCAGGTTGGGG 57.397 50.000 5.71 0.00 36.53 4.96
3406 4527 2.069775 TCAATCCTTTCAGGTTGGGGA 58.930 47.619 0.00 0.00 36.53 4.81
3411 4532 3.057586 TCCTTTCAGGTTGGGGAAGTTA 58.942 45.455 0.00 0.00 36.53 2.24
3416 4537 6.183361 CCTTTCAGGTTGGGGAAGTTAAAATT 60.183 38.462 0.00 0.00 0.00 1.82
3418 4539 5.459505 TCAGGTTGGGGAAGTTAAAATTCA 58.540 37.500 4.57 0.00 0.00 2.57
3419 4540 6.081356 TCAGGTTGGGGAAGTTAAAATTCAT 58.919 36.000 4.57 0.00 0.00 2.57
3428 4549 6.528072 GGGAAGTTAAAATTCATCAAAGCTCG 59.472 38.462 0.00 0.00 0.00 5.03
3442 4563 0.249398 AGCTCGGTATGTTGGTGTCC 59.751 55.000 0.00 0.00 0.00 4.02
3469 4609 2.072298 GCTTCTTTCACGAGCATGACT 58.928 47.619 0.00 0.00 36.45 3.41
3472 4612 3.599730 TCTTTCACGAGCATGACTGAT 57.400 42.857 0.00 0.00 0.00 2.90
3494 4634 4.259356 TGAAGAGGCAAATCTGATCACAG 58.741 43.478 0.00 0.00 44.66 3.66
3495 4635 2.641305 AGAGGCAAATCTGATCACAGC 58.359 47.619 0.00 0.00 43.17 4.40
3497 4637 0.743097 GGCAAATCTGATCACAGCCC 59.257 55.000 9.92 0.00 43.17 5.19
3512 4652 4.080356 TCACAGCCCTCTAATACTGCAAAT 60.080 41.667 0.00 0.00 33.35 2.32
3518 4658 5.645497 GCCCTCTAATACTGCAAATCCATAG 59.355 44.000 0.00 0.00 0.00 2.23
3528 4669 3.881089 TGCAAATCCATAGAGCACATGAG 59.119 43.478 0.00 0.00 0.00 2.90
3593 4738 5.633830 ACTTTGTACTTTCCTCATGCATG 57.366 39.130 21.07 21.07 0.00 4.06
3650 5031 9.651913 TGGGAATTACAATTTTCATTAGCTTTC 57.348 29.630 0.00 0.00 0.00 2.62
3653 5034 7.755582 ATTACAATTTTCATTAGCTTTCGGC 57.244 32.000 0.00 0.00 42.19 5.54
3660 5041 2.487762 TCATTAGCTTTCGGCCAACAAG 59.512 45.455 2.24 1.99 43.05 3.16
3661 5042 1.243902 TTAGCTTTCGGCCAACAAGG 58.756 50.000 2.24 0.00 43.05 3.61
3801 5348 2.359967 AACCTACGGGCTGAGCTCC 61.360 63.158 12.15 2.90 35.63 4.70
3863 5411 2.352323 CCAACGGCCCTTGAACAAATAC 60.352 50.000 15.24 0.00 0.00 1.89
3919 5467 2.968574 TGGAAGGTATGCTCCATCTCTC 59.031 50.000 0.00 0.00 36.79 3.20
4141 5709 3.387699 TGTCTGTCAGGAATCAAGTGACA 59.612 43.478 10.53 10.53 46.43 3.58
4177 5746 3.242936 GCAGCACCGTTTTGTTCTTAAGA 60.243 43.478 0.00 0.00 0.00 2.10
4202 5771 5.238006 ACGAGAGTAAGCAGATAACACTC 57.762 43.478 0.00 0.00 46.88 3.51
4203 5772 4.275662 CGAGAGTAAGCAGATAACACTCG 58.724 47.826 0.00 0.00 43.90 4.18
4205 5774 4.270834 AGAGTAAGCAGATAACACTCGGA 58.729 43.478 0.00 0.00 40.41 4.55
4206 5775 4.705507 AGAGTAAGCAGATAACACTCGGAA 59.294 41.667 0.00 0.00 40.41 4.30
4207 5776 5.185249 AGAGTAAGCAGATAACACTCGGAAA 59.815 40.000 0.00 0.00 40.41 3.13
4208 5777 5.978814 AGTAAGCAGATAACACTCGGAAAT 58.021 37.500 0.00 0.00 0.00 2.17
4212 5781 3.938963 GCAGATAACACTCGGAAATCCAA 59.061 43.478 0.00 0.00 35.14 3.53
4213 5782 4.201822 GCAGATAACACTCGGAAATCCAAC 60.202 45.833 0.00 0.00 35.14 3.77
4215 5784 6.338146 CAGATAACACTCGGAAATCCAACTA 58.662 40.000 0.00 0.00 35.14 2.24
4216 5785 6.477033 CAGATAACACTCGGAAATCCAACTAG 59.523 42.308 0.00 0.00 35.14 2.57
4217 5786 3.611766 ACACTCGGAAATCCAACTAGG 57.388 47.619 0.00 0.00 39.47 3.02
4218 5787 2.904434 ACACTCGGAAATCCAACTAGGT 59.096 45.455 0.00 0.00 39.02 3.08
4219 5788 4.091549 ACACTCGGAAATCCAACTAGGTA 58.908 43.478 0.00 0.00 39.02 3.08
4221 5790 4.868734 CACTCGGAAATCCAACTAGGTAAC 59.131 45.833 0.00 0.00 39.02 2.50
4222 5791 4.529377 ACTCGGAAATCCAACTAGGTAACA 59.471 41.667 0.00 0.00 39.02 2.41
4223 5792 4.824289 TCGGAAATCCAACTAGGTAACAC 58.176 43.478 0.00 0.00 39.02 3.32
4224 5793 4.529377 TCGGAAATCCAACTAGGTAACACT 59.471 41.667 0.00 0.00 39.02 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 1.269309 GCAATAGACATCTCCGACGCT 60.269 52.381 0.00 0.00 0.00 5.07
290 291 4.850193 CCAACAGGAATGGTGGCT 57.150 55.556 0.00 0.00 40.09 4.75
540 541 3.361977 AACTTTTGCGGCGGCGAT 61.362 55.556 36.87 9.21 44.10 4.58
746 780 0.613012 GCAAGCAATCAACCCCTCCT 60.613 55.000 0.00 0.00 0.00 3.69
1000 1034 2.183478 TTGCTTCGACATGTGACCAT 57.817 45.000 1.15 0.00 0.00 3.55
1140 1175 8.055181 ACAATACATCTTCCTGTGGTGATTAAT 58.945 33.333 0.00 0.00 0.00 1.40
1182 1217 4.282703 ATTGTCTTCAAAGCAAGAGGCAAT 59.717 37.500 0.00 0.00 39.16 3.56
1232 1267 1.004745 TGGCCTTCCATTCCTCAACTC 59.995 52.381 3.32 0.00 37.47 3.01
1429 1464 9.350357 CATTGTTCCATCTTCTTGAATAAAGTG 57.650 33.333 0.00 0.00 37.18 3.16
1466 1501 8.753133 ACTCATGGAAAATAAATTCTCCTTTCC 58.247 33.333 11.55 11.55 43.50 3.13
1504 1539 5.888161 CCACTTTAATATCTTGCAGGAAGGT 59.112 40.000 1.33 0.00 31.85 3.50
1521 1556 5.880332 GCCATCAGATTTGACTACCACTTTA 59.120 40.000 0.00 0.00 35.83 1.85
1731 1793 1.740025 CGGAGAGATGTTTTGCCTTCC 59.260 52.381 0.00 0.00 0.00 3.46
1781 1861 0.251386 TGGCAGCCGGTTAAAATCCA 60.251 50.000 7.03 0.00 0.00 3.41
1791 1871 2.890474 GATACACGTGGCAGCCGG 60.890 66.667 21.57 0.00 0.00 6.13
1802 1901 4.794248 TGCAATGCTCGTAATGATACAC 57.206 40.909 6.82 0.00 32.02 2.90
1834 1933 2.280592 GAAACTGGCACCCGACGT 60.281 61.111 0.00 0.00 0.00 4.34
1835 1934 1.841663 CTTGAAACTGGCACCCGACG 61.842 60.000 0.00 0.00 0.00 5.12
1875 1974 1.112113 TGGAGAGGTCAAGATACCGC 58.888 55.000 0.00 0.00 44.77 5.68
1903 2002 3.668447 AGTCGAGCAATATAGCATTGGG 58.332 45.455 0.00 0.00 36.85 4.12
1923 2022 7.495606 TGCAGGTTATACAACAGACATATTGAG 59.504 37.037 0.00 0.00 36.29 3.02
1956 2055 3.760684 GTCCTTCACAATGATTGAGCCTT 59.239 43.478 12.80 0.00 0.00 4.35
1971 2070 1.276421 GGTAGCTCTTGCAGTCCTTCA 59.724 52.381 0.00 0.00 42.74 3.02
1984 2083 2.961741 TCATCATGTCCTCTGGTAGCTC 59.038 50.000 0.00 0.00 0.00 4.09
2083 2182 4.572795 TGTTAGTGTGCGAAGATTGTTCAA 59.427 37.500 0.00 0.00 0.00 2.69
2091 2190 4.814234 ACAAATCTTGTTAGTGTGCGAAGA 59.186 37.500 0.00 0.00 42.22 2.87
2241 2341 3.501445 GCTCACTCAGATTTTGCTTCTGT 59.499 43.478 1.07 0.00 41.13 3.41
2271 2371 6.086011 TCATATCTTTTAAGGCCCCAAGAA 57.914 37.500 0.00 0.00 0.00 2.52
2306 2415 4.142609 TCTTCCTCAATACATGCCTCAC 57.857 45.455 0.00 0.00 0.00 3.51
2318 2427 2.172505 TGCTGGAACACTTCTTCCTCAA 59.827 45.455 0.00 0.00 40.56 3.02
2525 2634 0.041312 CTTCAGTTTGCCCACGTTCG 60.041 55.000 0.00 0.00 0.00 3.95
2530 2639 2.362077 ACAATGTCTTCAGTTTGCCCAC 59.638 45.455 0.00 0.00 0.00 4.61
2535 2644 6.857964 GGTTATCACACAATGTCTTCAGTTTG 59.142 38.462 0.00 0.00 0.00 2.93
2576 2685 5.091552 TCTGTAGAGGGGTATTGTGTCTTT 58.908 41.667 0.00 0.00 0.00 2.52
2578 2687 4.332683 TCTGTAGAGGGGTATTGTGTCT 57.667 45.455 0.00 0.00 0.00 3.41
2652 2761 0.746063 CTGCACTGTTTTCTGCCCAA 59.254 50.000 0.00 0.00 31.97 4.12
2670 2779 0.921896 AGCTATCAATGGCCACACCT 59.078 50.000 8.16 0.00 40.22 4.00
2799 2911 1.737793 CATAAACACTTCACCTCCCGC 59.262 52.381 0.00 0.00 0.00 6.13
2838 2952 7.986320 TGAATCCACAAAATTTCAACAGATGTT 59.014 29.630 0.00 0.00 39.12 2.71
2844 2970 6.766944 AGCATTGAATCCACAAAATTTCAACA 59.233 30.769 0.00 0.00 39.94 3.33
2845 2971 7.193377 AGCATTGAATCCACAAAATTTCAAC 57.807 32.000 0.00 0.00 39.94 3.18
2885 3011 1.302832 CCAAGGTTCGAAGGCAGCT 60.303 57.895 0.00 0.00 0.00 4.24
2952 3078 0.251742 TCCCATCAGGCAACCCTTTG 60.252 55.000 0.00 0.00 40.33 2.77
3036 3162 0.407139 ACTGCTGAAGGAGGCCATTT 59.593 50.000 5.01 0.00 37.85 2.32
3042 3168 0.959372 CTGGCAACTGCTGAAGGAGG 60.959 60.000 3.77 0.00 41.70 4.30
3053 3179 0.825010 CTTGTCAAGGGCTGGCAACT 60.825 55.000 4.52 0.00 44.74 3.16
3108 3234 0.178990 ACTCCCCACCTTCTTTGCAC 60.179 55.000 0.00 0.00 0.00 4.57
3113 3239 3.010250 GTGGAAATACTCCCCACCTTCTT 59.990 47.826 0.00 0.00 44.69 2.52
3146 3272 5.163652 GCTGGAATGTGTTTAACTGGGATAC 60.164 44.000 0.00 0.00 0.00 2.24
3176 3302 5.223449 ACTTGTTCCAGTTCCGAATTCTA 57.777 39.130 3.52 0.00 0.00 2.10
3193 3331 3.012518 GCTGCATGAAGGTGATACTTGT 58.987 45.455 1.96 0.00 0.00 3.16
3196 3334 2.770802 AGAGCTGCATGAAGGTGATACT 59.229 45.455 10.98 0.00 0.00 2.12
3197 3335 3.129871 GAGAGCTGCATGAAGGTGATAC 58.870 50.000 10.98 0.00 0.00 2.24
3198 3336 3.036819 AGAGAGCTGCATGAAGGTGATA 58.963 45.455 10.98 0.00 0.00 2.15
3199 3337 1.838715 AGAGAGCTGCATGAAGGTGAT 59.161 47.619 10.98 0.00 0.00 3.06
3200 3338 1.066358 CAGAGAGCTGCATGAAGGTGA 60.066 52.381 10.98 0.00 34.95 4.02
3201 3339 1.370609 CAGAGAGCTGCATGAAGGTG 58.629 55.000 10.98 0.00 34.95 4.00
3202 3340 0.252479 CCAGAGAGCTGCATGAAGGT 59.748 55.000 4.67 4.67 40.91 3.50
3204 3342 2.158943 TCATCCAGAGAGCTGCATGAAG 60.159 50.000 1.02 0.00 44.28 3.02
3205 3343 1.835531 TCATCCAGAGAGCTGCATGAA 59.164 47.619 1.02 0.00 44.28 2.57
3206 3344 1.413077 CTCATCCAGAGAGCTGCATGA 59.587 52.381 1.02 0.00 44.87 3.07
3217 3355 6.753913 ATAAAAGGCAGATACTCATCCAGA 57.246 37.500 0.00 0.00 0.00 3.86
3223 4295 6.061022 TGTCCAATAAAAGGCAGATACTCA 57.939 37.500 0.00 0.00 0.00 3.41
3224 4296 6.599638 ACTTGTCCAATAAAAGGCAGATACTC 59.400 38.462 0.00 0.00 0.00 2.59
3239 4311 4.134563 GCAACGGGATATACTTGTCCAAT 58.865 43.478 0.00 0.00 34.91 3.16
3279 4351 4.793071 TGCTAATTTTGGTGATGTTGACG 58.207 39.130 0.00 0.00 0.00 4.35
3280 4352 8.755696 TTTATGCTAATTTTGGTGATGTTGAC 57.244 30.769 0.00 0.00 0.00 3.18
3318 4391 8.861086 GGAAGTACTAGAGATGTCATTGGATTA 58.139 37.037 0.00 0.00 0.00 1.75
3325 4398 5.454062 AGCAGGAAGTACTAGAGATGTCAT 58.546 41.667 0.00 0.00 0.00 3.06
3350 4423 5.735766 AGGAAACAGATTAAGACTAGGCAC 58.264 41.667 0.00 0.00 0.00 5.01
3392 4513 5.862678 TTTTAACTTCCCCAACCTGAAAG 57.137 39.130 0.00 0.00 0.00 2.62
3404 4525 6.528072 CCGAGCTTTGATGAATTTTAACTTCC 59.472 38.462 0.00 0.00 0.00 3.46
3405 4526 7.084486 ACCGAGCTTTGATGAATTTTAACTTC 58.916 34.615 0.00 0.00 0.00 3.01
3406 4527 6.981722 ACCGAGCTTTGATGAATTTTAACTT 58.018 32.000 0.00 0.00 0.00 2.66
3411 4532 6.515272 ACATACCGAGCTTTGATGAATTTT 57.485 33.333 0.00 0.00 0.00 1.82
3416 4537 3.270027 CCAACATACCGAGCTTTGATGA 58.730 45.455 0.00 0.00 0.00 2.92
3418 4539 3.009723 CACCAACATACCGAGCTTTGAT 58.990 45.455 0.00 0.00 0.00 2.57
3419 4540 2.224426 ACACCAACATACCGAGCTTTGA 60.224 45.455 0.00 0.00 0.00 2.69
3428 4549 2.073816 CTTCGTGGACACCAACATACC 58.926 52.381 0.00 0.00 34.18 2.73
3442 4563 1.457303 CTCGTGAAAGAAGCCTTCGTG 59.543 52.381 0.00 0.00 34.02 4.35
3469 4609 4.880120 GTGATCAGATTTGCCTCTTCATCA 59.120 41.667 0.00 0.00 0.00 3.07
3472 4612 4.259356 CTGTGATCAGATTTGCCTCTTCA 58.741 43.478 0.00 0.00 43.76 3.02
3494 4634 3.820557 TGGATTTGCAGTATTAGAGGGC 58.179 45.455 0.00 0.00 0.00 5.19
3495 4635 7.009179 TCTATGGATTTGCAGTATTAGAGGG 57.991 40.000 0.00 0.00 0.00 4.30
3497 4637 7.117523 GTGCTCTATGGATTTGCAGTATTAGAG 59.882 40.741 12.44 12.44 34.15 2.43
3512 4652 3.099141 TGTCACTCATGTGCTCTATGGA 58.901 45.455 0.00 0.00 43.49 3.41
3518 4658 1.193203 CACGTTGTCACTCATGTGCTC 59.807 52.381 0.00 0.00 43.49 4.26
3528 4669 4.603231 TTTACCTGAAACACGTTGTCAC 57.397 40.909 0.00 0.00 0.00 3.67
3534 4675 6.039941 TCCATCAAATTTTACCTGAAACACGT 59.960 34.615 0.00 0.00 0.00 4.49
3535 4676 6.442952 TCCATCAAATTTTACCTGAAACACG 58.557 36.000 0.00 0.00 0.00 4.49
3570 4711 5.182001 ACATGCATGAGGAAAGTACAAAGTC 59.818 40.000 32.75 0.00 0.00 3.01
3612 4776 8.608185 AATTGTAATTCCCACCATGTTAGAAT 57.392 30.769 0.00 0.00 0.00 2.40
3618 4782 6.678568 TGAAAATTGTAATTCCCACCATGT 57.321 33.333 0.00 0.00 0.00 3.21
3624 4788 9.651913 GAAAGCTAATGAAAATTGTAATTCCCA 57.348 29.630 0.00 0.00 0.00 4.37
3625 4789 8.807581 CGAAAGCTAATGAAAATTGTAATTCCC 58.192 33.333 0.00 0.00 0.00 3.97
3627 4791 8.321005 GCCGAAAGCTAATGAAAATTGTAATTC 58.679 33.333 0.00 0.00 38.99 2.17
3630 4794 6.096695 GGCCGAAAGCTAATGAAAATTGTAA 58.903 36.000 0.00 0.00 43.05 2.41
3631 4795 5.184096 TGGCCGAAAGCTAATGAAAATTGTA 59.816 36.000 0.00 0.00 43.05 2.41
3632 4796 4.021544 TGGCCGAAAGCTAATGAAAATTGT 60.022 37.500 0.00 0.00 43.05 2.71
3650 5031 1.202533 AGATATCGTCCTTGTTGGCCG 60.203 52.381 0.00 0.00 38.75 6.13
3653 5034 5.011090 TCTTGAGATATCGTCCTTGTTGG 57.989 43.478 0.00 0.00 37.10 3.77
3660 5041 9.349713 AGGATAATAGATCTTGAGATATCGTCC 57.650 37.037 0.00 0.00 34.37 4.79
3801 5348 9.893305 AATGTAACTAAAAGATTTTTCCTGACG 57.107 29.630 0.00 0.00 0.00 4.35
3854 5402 6.151817 AGAGCTTGGAGGAAATGTATTTGTTC 59.848 38.462 0.00 0.00 0.00 3.18
3863 5411 2.548875 CTCGAGAGCTTGGAGGAAATG 58.451 52.381 6.58 0.00 0.00 2.32
3919 5467 7.068593 TGAGCATAGTTGGGGATGAAATTAAAG 59.931 37.037 0.00 0.00 0.00 1.85
4053 5604 0.034616 GAGGGGAGATGATGGAAGCG 59.965 60.000 0.00 0.00 0.00 4.68
4141 5709 1.447489 GCTGCAGCTGACGTCATCT 60.447 57.895 31.33 17.98 38.21 2.90
4177 5746 6.456501 AGTGTTATCTGCTTACTCTCGTTTT 58.543 36.000 0.00 0.00 0.00 2.43
4199 5768 4.529377 TGTTACCTAGTTGGATTTCCGAGT 59.471 41.667 0.00 0.00 39.43 4.18
4200 5769 4.868734 GTGTTACCTAGTTGGATTTCCGAG 59.131 45.833 0.00 0.00 39.43 4.63
4201 5770 4.529377 AGTGTTACCTAGTTGGATTTCCGA 59.471 41.667 0.00 0.00 39.43 4.55
4202 5771 4.828829 AGTGTTACCTAGTTGGATTTCCG 58.171 43.478 0.00 0.00 39.43 4.30


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

AutoCloner maintained by Alex Coulton.