Multiple sequence alignment - TraesCS7D01G408600

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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 TraesCS7D01G408600 chr7D 100.000 4359 0 0 1 4359 526381333 526376975 0.000000e+00 8050.0
1 TraesCS7D01G408600 chr7D 91.699 2048 131 20 554 2567 526529008 526526966 0.000000e+00 2804.0
2 TraesCS7D01G408600 chr7D 90.100 2000 164 19 600 2568 526976257 526974261 0.000000e+00 2566.0
3 TraesCS7D01G408600 chr7D 91.708 1628 121 7 947 2568 527197201 527195582 0.000000e+00 2246.0
4 TraesCS7D01G408600 chr7D 91.523 1628 118 10 947 2568 526804451 526802838 0.000000e+00 2224.0
5 TraesCS7D01G408600 chr7D 94.952 733 32 4 543 1273 526498644 526497915 0.000000e+00 1144.0
6 TraesCS7D01G408600 chr7D 94.816 733 33 4 543 1273 526446595 526445866 0.000000e+00 1138.0
7 TraesCS7D01G408600 chr7D 86.289 671 51 26 2938 3587 526973912 526973262 0.000000e+00 691.0
8 TraesCS7D01G408600 chr7D 85.650 669 57 26 2938 3586 527195201 527194552 0.000000e+00 667.0
9 TraesCS7D01G408600 chr7D 86.981 530 45 17 2940 3465 526526541 526526032 3.780000e-160 575.0
10 TraesCS7D01G408600 chr7D 86.867 533 45 18 2940 3465 526444226 526443712 1.360000e-159 573.0
11 TraesCS7D01G408600 chr7D 88.806 402 34 3 155 555 526529456 526529065 2.360000e-132 483.0
12 TraesCS7D01G408600 chr7D 87.895 380 34 4 178 555 526976737 526976368 1.860000e-118 436.0
13 TraesCS7D01G408600 chr7D 87.632 380 36 3 178 555 526805307 526804937 8.660000e-117 431.0
14 TraesCS7D01G408600 chr7D 87.368 380 37 3 178 555 527198057 527197687 4.030000e-115 425.0
15 TraesCS7D01G408600 chr7D 87.562 201 4 3 2 201 526446823 526446643 3.410000e-51 213.0
16 TraesCS7D01G408600 chr7D 87.065 201 5 5 2 201 526498872 526498692 1.590000e-49 207.0
17 TraesCS7D01G408600 chr7D 84.663 163 20 4 3603 3764 526525794 526525636 1.620000e-34 158.0
18 TraesCS7D01G408600 chr7D 94.915 59 2 1 2652 2709 526378499 526378441 1.670000e-14 91.6
19 TraesCS7D01G408600 chr7D 94.915 59 2 1 2835 2893 526378682 526378625 1.670000e-14 91.6
20 TraesCS7D01G408600 chr7D 83.529 85 9 4 3603 3686 526443310 526443230 1.680000e-09 75.0
21 TraesCS7D01G408600 chr7B 97.855 2098 38 3 626 2716 562995258 562993161 0.000000e+00 3618.0
22 TraesCS7D01G408600 chr7B 94.431 2029 106 5 543 2567 563478232 563476207 0.000000e+00 3114.0
23 TraesCS7D01G408600 chr7B 89.990 1978 162 21 543 2489 563737309 563735337 0.000000e+00 2523.0
24 TraesCS7D01G408600 chr7B 92.231 1506 67 32 2807 4296 562993067 562991596 0.000000e+00 2087.0
25 TraesCS7D01G408600 chr7B 86.012 672 59 22 2939 3592 563734911 563734257 0.000000e+00 688.0
26 TraesCS7D01G408600 chr7B 83.455 683 68 22 2938 3599 563475786 563475128 1.040000e-165 593.0
27 TraesCS7D01G408600 chr7B 88.250 400 34 3 155 550 563672609 563672219 2.370000e-127 466.0
28 TraesCS7D01G408600 chr7B 87.715 407 30 7 155 555 563737768 563737376 1.430000e-124 457.0
29 TraesCS7D01G408600 chr7B 95.604 273 12 0 283 555 563478571 563478299 5.180000e-119 438.0
30 TraesCS7D01G408600 chr7B 84.519 239 4 5 1 239 563478773 563478568 5.710000e-49 206.0
31 TraesCS7D01G408600 chr7B 90.845 142 2 1 1 142 562995474 562995344 3.460000e-41 180.0
32 TraesCS7D01G408600 chr7B 86.331 139 10 1 2807 2945 563475966 563475837 4.540000e-30 143.0
33 TraesCS7D01G408600 chr7B 91.954 87 6 1 2715 2800 562993067 562992981 2.130000e-23 121.0
34 TraesCS7D01G408600 chr7B 96.774 62 2 0 3861 3922 563462914 563462853 2.140000e-18 104.0
35 TraesCS7D01G408600 chr7B 88.235 68 7 1 2835 2902 562993225 562993159 3.610000e-11 80.5
36 TraesCS7D01G408600 chr7A 94.913 1848 78 11 2455 4290 606581817 606579974 0.000000e+00 2878.0
37 TraesCS7D01G408600 chr7A 89.840 2057 165 24 543 2562 606941746 606939697 0.000000e+00 2601.0
38 TraesCS7D01G408600 chr7A 94.079 1233 69 2 1339 2567 606637171 606635939 0.000000e+00 1869.0
39 TraesCS7D01G408600 chr7A 96.897 419 13 0 139 557 606638356 606637938 0.000000e+00 702.0
40 TraesCS7D01G408600 chr7A 86.176 680 55 23 2942 3599 606939345 606938683 0.000000e+00 699.0
41 TraesCS7D01G408600 chr7A 90.991 444 28 8 2940 3381 606635514 606635081 4.860000e-164 588.0
42 TraesCS7D01G408600 chr7A 87.811 402 36 3 155 555 606942201 606941812 3.970000e-125 459.0
43 TraesCS7D01G408600 chr7A 92.105 152 10 2 2743 2893 606581620 606581470 3.410000e-51 213.0
44 TraesCS7D01G408600 chr7A 79.525 337 30 18 3603 3931 606634712 606634407 2.060000e-48 204.0
45 TraesCS7D01G408600 chr7A 88.272 162 16 3 2743 2904 606939575 606939417 1.600000e-44 191.0
46 TraesCS7D01G408600 chr7A 96.842 95 3 0 1 95 606638453 606638359 4.510000e-35 159.0
47 TraesCS7D01G408600 chr7A 84.173 139 13 1 2807 2945 606635698 606635569 4.580000e-25 126.0
48 TraesCS7D01G408600 chr7A 90.722 97 5 3 543 637 606637871 606637777 4.580000e-25 126.0
49 TraesCS7D01G408600 chr7A 93.151 73 3 1 4289 4359 606579886 606579814 5.960000e-19 106.0
50 TraesCS7D01G408600 chr7A 90.141 71 6 1 3998 4068 28821193 28821124 1.670000e-14 91.6
51 TraesCS7D01G408600 chr7A 94.915 59 2 1 2835 2893 606581620 606581563 1.670000e-14 91.6
52 TraesCS7D01G408600 chr1D 88.889 72 8 0 3994 4065 477184229 477184300 6.000000e-14 89.8
53 TraesCS7D01G408600 chr1B 91.228 57 5 0 4002 4058 19045412 19045468 1.300000e-10 78.7
54 TraesCS7D01G408600 chr1B 95.122 41 2 0 3998 4038 333786179 333786219 1.010000e-06 65.8
55 TraesCS7D01G408600 chr3B 84.507 71 9 2 3999 4068 807969250 807969181 7.820000e-08 69.4
56 TraesCS7D01G408600 chr3D 100.000 31 0 0 3996 4026 59258648 59258678 1.690000e-04 58.4


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 TraesCS7D01G408600 chr7D 526376975 526381333 4358 True 2744.400000 8050 96.610000 1 4359 3 chr7D.!!$R1 4358
1 TraesCS7D01G408600 chr7D 526802838 526805307 2469 True 1327.500000 2224 89.577500 178 2568 2 chr7D.!!$R5 2390
2 TraesCS7D01G408600 chr7D 526973262 526976737 3475 True 1231.000000 2566 88.094667 178 3587 3 chr7D.!!$R6 3409
3 TraesCS7D01G408600 chr7D 527194552 527198057 3505 True 1112.666667 2246 88.242000 178 3586 3 chr7D.!!$R7 3408
4 TraesCS7D01G408600 chr7D 526525636 526529456 3820 True 1005.000000 2804 88.037250 155 3764 4 chr7D.!!$R4 3609
5 TraesCS7D01G408600 chr7D 526497915 526498872 957 True 675.500000 1144 91.008500 2 1273 2 chr7D.!!$R3 1271
6 TraesCS7D01G408600 chr7D 526443230 526446823 3593 True 499.750000 1138 88.193500 2 3686 4 chr7D.!!$R2 3684
7 TraesCS7D01G408600 chr7B 563734257 563737768 3511 True 1222.666667 2523 87.905667 155 3592 3 chr7B.!!$R5 3437
8 TraesCS7D01G408600 chr7B 562991596 562995474 3878 True 1217.300000 3618 92.224000 1 4296 5 chr7B.!!$R3 4295
9 TraesCS7D01G408600 chr7B 563475128 563478773 3645 True 898.800000 3114 88.868000 1 3599 5 chr7B.!!$R4 3598
10 TraesCS7D01G408600 chr7A 606938683 606942201 3518 True 987.500000 2601 88.024750 155 3599 4 chr7A.!!$R4 3444
11 TraesCS7D01G408600 chr7A 606579814 606581817 2003 True 822.150000 2878 93.771000 2455 4359 4 chr7A.!!$R2 1904
12 TraesCS7D01G408600 chr7A 606634407 606638453 4046 True 539.142857 1869 90.461286 1 3931 7 chr7A.!!$R3 3930

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
148 162 0.106217 GGGAGAGGAGGGTCTCAGAG 60.106 65.000 3.44 0.0 44.29 3.35 F
150 164 0.106217 GAGAGGAGGGTCTCAGAGGG 60.106 65.000 0.00 0.0 42.36 4.30 F
869 1033 0.251354 TGATCAGGAAGGCTGCAGAC 59.749 55.000 20.43 17.0 0.00 3.51 F
1491 1694 0.317160 TCGTAAGTGTCCTGGTGCAG 59.683 55.000 0.00 0.0 39.48 4.41 F
2777 3184 1.074405 TCAACTTCTCTGCATTGGCCT 59.926 47.619 3.32 0.0 40.13 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1694 1.207593 CTGCGTACCTTTGCTGCAC 59.792 57.895 0.00 0.00 0.00 4.57 R
1978 2184 1.862008 GCTCTGGATACGCTCGAACAG 60.862 57.143 0.00 0.00 42.51 3.16 R
2757 3164 1.074405 AGGCCAATGCAGAGAAGTTGA 59.926 47.619 5.01 0.00 40.13 3.18 R
3357 3938 0.759346 AACTGAAGGCCGTCTCACTT 59.241 50.000 19.81 6.03 0.00 3.16 R
3835 4761 0.741221 CTAAGCGGCAGGGAACAGAC 60.741 60.000 1.45 0.00 0.00 3.51 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
48 49 2.190578 GCTGGACTTCGGGATGGG 59.809 66.667 0.00 0.00 0.00 4.00
103 104 3.569701 GCTCTTTGTTGTGGAGGAATTGA 59.430 43.478 0.00 0.00 0.00 2.57
143 157 3.756783 CGGGGGAGAGGAGGGTCT 61.757 72.222 0.00 0.00 0.00 3.85
144 158 2.284151 GGGGGAGAGGAGGGTCTC 59.716 72.222 0.00 0.00 42.11 3.36
145 159 2.637640 GGGGGAGAGGAGGGTCTCA 61.638 68.421 3.44 0.00 44.29 3.27
146 160 1.075600 GGGGAGAGGAGGGTCTCAG 60.076 68.421 3.44 0.00 44.29 3.35
147 161 1.585651 GGGGAGAGGAGGGTCTCAGA 61.586 65.000 3.44 0.00 44.29 3.27
148 162 0.106217 GGGAGAGGAGGGTCTCAGAG 60.106 65.000 3.44 0.00 44.29 3.35
149 163 0.106217 GGAGAGGAGGGTCTCAGAGG 60.106 65.000 0.00 0.00 44.29 3.69
150 164 0.106217 GAGAGGAGGGTCTCAGAGGG 60.106 65.000 0.00 0.00 42.36 4.30
151 165 1.760480 GAGGAGGGTCTCAGAGGGC 60.760 68.421 0.00 0.00 34.13 5.19
152 166 2.236959 GAGGAGGGTCTCAGAGGGCT 62.237 65.000 0.00 0.00 34.13 5.19
153 167 2.063378 GGAGGGTCTCAGAGGGCTG 61.063 68.421 0.00 0.00 43.67 4.85
187 206 9.542462 GTATGTTACTGGCTTTGTAAGATCATA 57.458 33.333 0.00 7.10 36.05 2.15
252 318 9.975218 AAAACTACATATTACTCCAATTGTCCT 57.025 29.630 4.43 0.00 0.00 3.85
253 319 8.964476 AACTACATATTACTCCAATTGTCCTG 57.036 34.615 4.43 0.00 0.00 3.86
254 320 8.090788 ACTACATATTACTCCAATTGTCCTGT 57.909 34.615 4.43 0.49 0.00 4.00
255 321 7.987458 ACTACATATTACTCCAATTGTCCTGTG 59.013 37.037 4.43 0.00 0.00 3.66
256 322 6.721318 ACATATTACTCCAATTGTCCTGTGT 58.279 36.000 4.43 0.00 0.00 3.72
257 323 6.599244 ACATATTACTCCAATTGTCCTGTGTG 59.401 38.462 4.43 0.00 0.00 3.82
258 324 4.698201 TTACTCCAATTGTCCTGTGTGA 57.302 40.909 4.43 0.00 0.00 3.58
259 325 3.795688 ACTCCAATTGTCCTGTGTGAT 57.204 42.857 4.43 0.00 0.00 3.06
260 326 4.908601 ACTCCAATTGTCCTGTGTGATA 57.091 40.909 4.43 0.00 0.00 2.15
261 327 4.836825 ACTCCAATTGTCCTGTGTGATAG 58.163 43.478 4.43 0.00 0.00 2.08
262 328 4.287067 ACTCCAATTGTCCTGTGTGATAGT 59.713 41.667 4.43 0.00 0.00 2.12
263 329 5.483937 ACTCCAATTGTCCTGTGTGATAGTA 59.516 40.000 4.43 0.00 0.00 1.82
264 330 5.730550 TCCAATTGTCCTGTGTGATAGTAC 58.269 41.667 4.43 0.00 0.00 2.73
265 331 4.876107 CCAATTGTCCTGTGTGATAGTACC 59.124 45.833 4.43 0.00 0.00 3.34
266 332 3.861276 TTGTCCTGTGTGATAGTACCG 57.139 47.619 0.00 0.00 0.00 4.02
267 333 3.076079 TGTCCTGTGTGATAGTACCGA 57.924 47.619 0.00 0.00 0.00 4.69
268 334 3.423749 TGTCCTGTGTGATAGTACCGAA 58.576 45.455 0.00 0.00 0.00 4.30
269 335 3.827876 TGTCCTGTGTGATAGTACCGAAA 59.172 43.478 0.00 0.00 0.00 3.46
270 336 4.464951 TGTCCTGTGTGATAGTACCGAAAT 59.535 41.667 0.00 0.00 0.00 2.17
271 337 5.653330 TGTCCTGTGTGATAGTACCGAAATA 59.347 40.000 0.00 0.00 0.00 1.40
272 338 6.183360 TGTCCTGTGTGATAGTACCGAAATAG 60.183 42.308 0.00 0.00 0.00 1.73
273 339 5.889853 TCCTGTGTGATAGTACCGAAATAGT 59.110 40.000 0.00 0.00 0.00 2.12
274 340 6.379133 TCCTGTGTGATAGTACCGAAATAGTT 59.621 38.462 0.00 0.00 0.00 2.24
275 341 7.557358 TCCTGTGTGATAGTACCGAAATAGTTA 59.443 37.037 0.00 0.00 0.00 2.24
276 342 8.192774 CCTGTGTGATAGTACCGAAATAGTTAA 58.807 37.037 0.00 0.00 0.00 2.01
277 343 8.915871 TGTGTGATAGTACCGAAATAGTTAAC 57.084 34.615 0.00 0.00 0.00 2.01
278 344 7.975616 TGTGTGATAGTACCGAAATAGTTAACC 59.024 37.037 0.88 0.00 0.00 2.85
279 345 8.193438 GTGTGATAGTACCGAAATAGTTAACCT 58.807 37.037 0.88 0.00 0.00 3.50
280 346 8.752187 TGTGATAGTACCGAAATAGTTAACCTT 58.248 33.333 0.88 0.00 0.00 3.50
281 347 9.591792 GTGATAGTACCGAAATAGTTAACCTTT 57.408 33.333 0.88 2.75 0.00 3.11
362 431 9.918630 ATCAAATTTTAGAATGTTTGTGAGGAG 57.081 29.630 0.00 0.00 34.20 3.69
687 851 3.942829 TGTGCTGTCATTAAGAGGAAGG 58.057 45.455 0.00 0.00 0.00 3.46
730 894 5.508825 GGTGGAATGTTGCACTCATGTTTTA 60.509 40.000 15.38 0.00 46.96 1.52
790 954 4.758674 TCTCTCATTGCTTTTCTTCAGGTG 59.241 41.667 0.00 0.00 0.00 4.00
791 955 3.822735 TCTCATTGCTTTTCTTCAGGTGG 59.177 43.478 0.00 0.00 0.00 4.61
869 1033 0.251354 TGATCAGGAAGGCTGCAGAC 59.749 55.000 20.43 17.00 0.00 3.51
886 1056 3.332919 CAGACTGAGCTGCAATTACTGT 58.667 45.455 1.02 0.00 0.00 3.55
915 1085 1.219646 GTTTCGAGTTACAACCGCCA 58.780 50.000 0.00 0.00 0.00 5.69
1202 1405 1.569072 ACTGAAACCCAAGGTTGAGGT 59.431 47.619 0.00 0.00 46.20 3.85
1235 1438 3.334691 TCGATTCTCCGTCAGCAAAATT 58.665 40.909 0.00 0.00 0.00 1.82
1320 1523 2.593026 GAGATGGTTGTGTTTCCCCAA 58.407 47.619 0.00 0.00 0.00 4.12
1491 1694 0.317160 TCGTAAGTGTCCTGGTGCAG 59.683 55.000 0.00 0.00 39.48 4.41
1527 1730 3.743584 CGCAGTTCCTCAGATCCATTGAT 60.744 47.826 0.00 0.00 0.00 2.57
1973 2179 2.742372 CTCGGGTTGGGCTTGTCG 60.742 66.667 0.00 0.00 0.00 4.35
1978 2184 1.305930 GGGTTGGGCTTGTCGTGATC 61.306 60.000 0.00 0.00 0.00 2.92
2017 2223 6.017026 CCAGAGCATAGTAAAGACAGACGATA 60.017 42.308 0.00 0.00 0.00 2.92
2750 3157 7.538678 GCTAAAAGGTTTACAGATGAATGTGTG 59.461 37.037 3.49 0.00 34.91 3.82
2751 3158 5.964958 AAGGTTTACAGATGAATGTGTGG 57.035 39.130 3.49 0.00 34.91 4.17
2752 3159 5.241403 AGGTTTACAGATGAATGTGTGGA 57.759 39.130 3.49 0.00 34.91 4.02
2753 3160 5.630121 AGGTTTACAGATGAATGTGTGGAA 58.370 37.500 3.49 0.00 34.91 3.53
2754 3161 6.248433 AGGTTTACAGATGAATGTGTGGAAT 58.752 36.000 3.49 0.00 34.91 3.01
2755 3162 6.151648 AGGTTTACAGATGAATGTGTGGAATG 59.848 38.462 3.49 0.00 34.91 2.67
2756 3163 6.150976 GGTTTACAGATGAATGTGTGGAATGA 59.849 38.462 3.49 0.00 34.91 2.57
2757 3164 7.148018 GGTTTACAGATGAATGTGTGGAATGAT 60.148 37.037 3.49 0.00 34.91 2.45
2758 3165 7.558161 TTACAGATGAATGTGTGGAATGATC 57.442 36.000 3.49 0.00 34.91 2.92
2759 3166 5.503002 ACAGATGAATGTGTGGAATGATCA 58.497 37.500 0.00 0.00 32.57 2.92
2760 3167 5.947566 ACAGATGAATGTGTGGAATGATCAA 59.052 36.000 0.00 0.00 32.57 2.57
2761 3168 6.127814 ACAGATGAATGTGTGGAATGATCAAC 60.128 38.462 0.00 0.00 32.57 3.18
2762 3169 6.095021 CAGATGAATGTGTGGAATGATCAACT 59.905 38.462 0.00 0.00 30.17 3.16
2763 3170 6.662234 AGATGAATGTGTGGAATGATCAACTT 59.338 34.615 0.00 0.00 30.17 2.66
2764 3171 6.258230 TGAATGTGTGGAATGATCAACTTC 57.742 37.500 0.00 0.00 30.17 3.01
2765 3172 6.005823 TGAATGTGTGGAATGATCAACTTCT 58.994 36.000 0.00 0.00 30.17 2.85
2766 3173 6.149973 TGAATGTGTGGAATGATCAACTTCTC 59.850 38.462 0.00 0.00 30.17 2.87
2767 3174 5.233083 TGTGTGGAATGATCAACTTCTCT 57.767 39.130 0.00 0.00 30.17 3.10
2768 3175 4.999311 TGTGTGGAATGATCAACTTCTCTG 59.001 41.667 0.00 0.00 30.17 3.35
2769 3176 4.005650 TGTGGAATGATCAACTTCTCTGC 58.994 43.478 0.00 0.00 30.17 4.26
2770 3177 4.005650 GTGGAATGATCAACTTCTCTGCA 58.994 43.478 0.00 0.00 0.00 4.41
2771 3178 4.639310 GTGGAATGATCAACTTCTCTGCAT 59.361 41.667 0.00 0.00 0.00 3.96
2772 3179 5.125097 GTGGAATGATCAACTTCTCTGCATT 59.875 40.000 0.00 0.00 0.00 3.56
2773 3180 5.124936 TGGAATGATCAACTTCTCTGCATTG 59.875 40.000 0.00 0.00 0.00 2.82
2774 3181 5.450137 GGAATGATCAACTTCTCTGCATTGG 60.450 44.000 0.00 0.00 0.00 3.16
2775 3182 2.751259 TGATCAACTTCTCTGCATTGGC 59.249 45.455 0.00 0.00 41.68 4.52
2776 3183 1.538047 TCAACTTCTCTGCATTGGCC 58.462 50.000 0.00 0.00 40.13 5.36
2777 3184 1.074405 TCAACTTCTCTGCATTGGCCT 59.926 47.619 3.32 0.00 40.13 5.19
2778 3185 2.305635 TCAACTTCTCTGCATTGGCCTA 59.694 45.455 3.32 0.00 40.13 3.93
2779 3186 3.084039 CAACTTCTCTGCATTGGCCTAA 58.916 45.455 3.32 0.00 40.13 2.69
2780 3187 2.716217 ACTTCTCTGCATTGGCCTAAC 58.284 47.619 3.32 0.00 40.13 2.34
2781 3188 2.307098 ACTTCTCTGCATTGGCCTAACT 59.693 45.455 3.32 0.00 40.13 2.24
2782 3189 3.245052 ACTTCTCTGCATTGGCCTAACTT 60.245 43.478 3.32 0.00 40.13 2.66
2783 3190 2.715046 TCTCTGCATTGGCCTAACTTG 58.285 47.619 3.32 0.00 40.13 3.16
2784 3191 2.040278 TCTCTGCATTGGCCTAACTTGT 59.960 45.455 3.32 0.00 40.13 3.16
2785 3192 2.421424 CTCTGCATTGGCCTAACTTGTC 59.579 50.000 3.32 0.00 40.13 3.18
2786 3193 2.161855 CTGCATTGGCCTAACTTGTCA 58.838 47.619 3.32 0.00 40.13 3.58
2787 3194 2.557924 CTGCATTGGCCTAACTTGTCAA 59.442 45.455 3.32 0.00 40.13 3.18
2788 3195 2.295909 TGCATTGGCCTAACTTGTCAAC 59.704 45.455 3.32 0.00 40.13 3.18
2789 3196 2.295909 GCATTGGCCTAACTTGTCAACA 59.704 45.455 3.32 0.00 0.00 3.33
2790 3197 3.056607 GCATTGGCCTAACTTGTCAACAT 60.057 43.478 3.32 0.00 0.00 2.71
2791 3198 4.157656 GCATTGGCCTAACTTGTCAACATA 59.842 41.667 3.32 0.00 0.00 2.29
2792 3199 5.677091 GCATTGGCCTAACTTGTCAACATAG 60.677 44.000 3.32 0.00 0.00 2.23
2793 3200 3.343617 TGGCCTAACTTGTCAACATAGC 58.656 45.455 3.32 0.00 0.00 2.97
2794 3201 3.009033 TGGCCTAACTTGTCAACATAGCT 59.991 43.478 3.32 0.00 0.00 3.32
2795 3202 3.375299 GGCCTAACTTGTCAACATAGCTG 59.625 47.826 0.00 0.00 0.00 4.24
2796 3203 4.003648 GCCTAACTTGTCAACATAGCTGT 58.996 43.478 0.00 0.00 37.12 4.40
2797 3204 4.455877 GCCTAACTTGTCAACATAGCTGTT 59.544 41.667 0.00 0.00 46.54 3.16
2798 3205 5.048713 GCCTAACTTGTCAACATAGCTGTTT 60.049 40.000 0.00 0.00 43.05 2.83
2799 3206 6.148811 GCCTAACTTGTCAACATAGCTGTTTA 59.851 38.462 0.00 0.00 43.05 2.01
2800 3207 7.308348 GCCTAACTTGTCAACATAGCTGTTTAA 60.308 37.037 0.00 0.00 43.05 1.52
2801 3208 8.564574 CCTAACTTGTCAACATAGCTGTTTAAA 58.435 33.333 0.00 0.00 43.05 1.52
2831 3238 7.608308 AGCAGAGAAGCTAAAAGAATTACAG 57.392 36.000 0.00 0.00 44.50 2.74
2832 3239 7.390027 AGCAGAGAAGCTAAAAGAATTACAGA 58.610 34.615 0.00 0.00 44.50 3.41
2833 3240 8.046107 AGCAGAGAAGCTAAAAGAATTACAGAT 58.954 33.333 0.00 0.00 44.50 2.90
2834 3241 8.121708 GCAGAGAAGCTAAAAGAATTACAGATG 58.878 37.037 0.00 0.00 0.00 2.90
2835 3242 9.376075 CAGAGAAGCTAAAAGAATTACAGATGA 57.624 33.333 0.00 0.00 0.00 2.92
2836 3243 9.950496 AGAGAAGCTAAAAGAATTACAGATGAA 57.050 29.630 0.00 0.00 0.00 2.57
2841 3248 9.236006 AGCTAAAAGAATTACAGATGAATGTGT 57.764 29.630 0.00 0.00 38.00 3.72
3539 4228 2.276732 TTTCTTGAACTCCTGCTGGG 57.723 50.000 10.07 3.31 0.00 4.45
3576 4265 1.476488 GTTGTGTTGAAACCCTGCTGT 59.524 47.619 0.00 0.00 0.00 4.40
3587 4277 5.362430 TGAAACCCTGCTGTATTTCAAGTTT 59.638 36.000 13.61 0.00 37.94 2.66
3835 4761 0.450583 CACATAGCAGCTGCACCAAG 59.549 55.000 38.24 24.24 45.16 3.61
3847 4773 1.518903 GCACCAAGTCTGTTCCCTGC 61.519 60.000 0.00 0.00 0.00 4.85
3857 4783 0.398696 TGTTCCCTGCCGCTTAGAAA 59.601 50.000 0.00 0.00 0.00 2.52
3907 4833 4.362476 GCAACAAAGGGCGGCCAG 62.362 66.667 31.59 21.05 0.00 4.85
3944 4870 7.012232 CACAAAGGGAAAGCAAAAATGTATGTT 59.988 33.333 0.00 0.00 0.00 2.71
4010 4936 5.395611 AGTTCCATGTATAGTACTCCCTCC 58.604 45.833 0.00 0.00 0.00 4.30
4025 4954 5.078256 ACTCCCTCCGTCCTATAATGTAAG 58.922 45.833 0.00 0.00 0.00 2.34
4026 4955 4.413760 TCCCTCCGTCCTATAATGTAAGG 58.586 47.826 0.00 0.00 0.00 2.69
4050 4979 1.873698 TTTTGACTCCGGTGTAGTGC 58.126 50.000 9.57 0.00 0.00 4.40
4054 4983 0.034337 GACTCCGGTGTAGTGCCAAA 59.966 55.000 9.57 0.00 0.00 3.28
4131 5064 3.139850 CCAGCCATGCTCTGAATTCTAG 58.860 50.000 7.05 5.59 36.40 2.43
4332 5358 6.372937 TCACAAATCACAAATATCTTACCGCA 59.627 34.615 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.680352 TCGCCACCCTCTCTCCAC 60.680 66.667 0.00 0.00 0.00 4.02
103 104 0.397816 CTTGATCTCCCTCCTCCGGT 60.398 60.000 0.00 0.00 0.00 5.28
143 157 2.366167 CCCCTCTCAGCCCTCTGA 59.634 66.667 0.00 0.00 46.43 3.27
144 158 2.243774 TACCCCCTCTCAGCCCTCTG 62.244 65.000 0.00 0.00 41.67 3.35
145 159 1.307976 ATACCCCCTCTCAGCCCTCT 61.308 60.000 0.00 0.00 0.00 3.69
146 160 1.124477 CATACCCCCTCTCAGCCCTC 61.124 65.000 0.00 0.00 0.00 4.30
147 161 1.074167 CATACCCCCTCTCAGCCCT 60.074 63.158 0.00 0.00 0.00 5.19
148 162 0.988678 AACATACCCCCTCTCAGCCC 60.989 60.000 0.00 0.00 0.00 5.19
149 163 1.416772 GTAACATACCCCCTCTCAGCC 59.583 57.143 0.00 0.00 0.00 4.85
150 164 2.103263 CAGTAACATACCCCCTCTCAGC 59.897 54.545 0.00 0.00 0.00 4.26
151 165 2.700897 CCAGTAACATACCCCCTCTCAG 59.299 54.545 0.00 0.00 0.00 3.35
152 166 2.759355 CCAGTAACATACCCCCTCTCA 58.241 52.381 0.00 0.00 0.00 3.27
153 167 1.416772 GCCAGTAACATACCCCCTCTC 59.583 57.143 0.00 0.00 0.00 3.20
187 206 5.104941 TGTGGTATAAGCATAAGACTGCACT 60.105 40.000 0.00 0.00 44.77 4.40
239 305 3.795688 ATCACACAGGACAATTGGAGT 57.204 42.857 10.83 0.00 0.00 3.85
240 306 4.836825 ACTATCACACAGGACAATTGGAG 58.163 43.478 10.83 0.00 0.00 3.86
241 307 4.908601 ACTATCACACAGGACAATTGGA 57.091 40.909 10.83 0.00 0.00 3.53
242 308 4.876107 GGTACTATCACACAGGACAATTGG 59.124 45.833 10.83 0.00 0.00 3.16
244 310 4.464951 TCGGTACTATCACACAGGACAATT 59.535 41.667 0.00 0.00 0.00 2.32
245 311 4.021229 TCGGTACTATCACACAGGACAAT 58.979 43.478 0.00 0.00 0.00 2.71
246 312 3.423749 TCGGTACTATCACACAGGACAA 58.576 45.455 0.00 0.00 0.00 3.18
247 313 3.076079 TCGGTACTATCACACAGGACA 57.924 47.619 0.00 0.00 0.00 4.02
248 314 4.445452 TTTCGGTACTATCACACAGGAC 57.555 45.455 0.00 0.00 0.00 3.85
249 315 5.889853 ACTATTTCGGTACTATCACACAGGA 59.110 40.000 0.00 0.00 0.00 3.86
250 316 6.145338 ACTATTTCGGTACTATCACACAGG 57.855 41.667 0.00 0.00 0.00 4.00
251 317 9.017669 GTTAACTATTTCGGTACTATCACACAG 57.982 37.037 0.00 0.00 0.00 3.66
252 318 7.975616 GGTTAACTATTTCGGTACTATCACACA 59.024 37.037 5.42 0.00 0.00 3.72
253 319 8.193438 AGGTTAACTATTTCGGTACTATCACAC 58.807 37.037 5.42 0.00 0.00 3.82
254 320 8.297470 AGGTTAACTATTTCGGTACTATCACA 57.703 34.615 5.42 0.00 0.00 3.58
255 321 9.591792 AAAGGTTAACTATTTCGGTACTATCAC 57.408 33.333 5.42 0.00 0.00 3.06
269 335 8.843262 GGCCGATGTAAATAAAAGGTTAACTAT 58.157 33.333 5.42 0.00 0.00 2.12
270 336 8.048514 AGGCCGATGTAAATAAAAGGTTAACTA 58.951 33.333 5.42 0.00 0.00 2.24
271 337 6.888088 AGGCCGATGTAAATAAAAGGTTAACT 59.112 34.615 5.42 0.00 0.00 2.24
272 338 7.092137 AGGCCGATGTAAATAAAAGGTTAAC 57.908 36.000 0.00 0.00 0.00 2.01
273 339 8.983702 ATAGGCCGATGTAAATAAAAGGTTAA 57.016 30.769 0.00 0.00 0.00 2.01
274 340 8.983702 AATAGGCCGATGTAAATAAAAGGTTA 57.016 30.769 0.00 0.00 0.00 2.85
275 341 7.891498 AATAGGCCGATGTAAATAAAAGGTT 57.109 32.000 0.00 0.00 0.00 3.50
276 342 7.255001 CGAAATAGGCCGATGTAAATAAAAGGT 60.255 37.037 0.00 0.00 0.00 3.50
277 343 7.075741 CGAAATAGGCCGATGTAAATAAAAGG 58.924 38.462 0.00 0.00 0.00 3.11
278 344 7.636326 ACGAAATAGGCCGATGTAAATAAAAG 58.364 34.615 0.00 0.00 0.00 2.27
279 345 7.556733 ACGAAATAGGCCGATGTAAATAAAA 57.443 32.000 0.00 0.00 0.00 1.52
280 346 8.714179 CATACGAAATAGGCCGATGTAAATAAA 58.286 33.333 0.00 0.00 0.00 1.40
281 347 7.332430 CCATACGAAATAGGCCGATGTAAATAA 59.668 37.037 0.00 0.00 0.00 1.40
282 348 6.814644 CCATACGAAATAGGCCGATGTAAATA 59.185 38.462 0.00 0.00 0.00 1.40
283 349 5.642063 CCATACGAAATAGGCCGATGTAAAT 59.358 40.000 0.00 0.00 0.00 1.40
284 350 4.992319 CCATACGAAATAGGCCGATGTAAA 59.008 41.667 0.00 0.00 0.00 2.01
285 351 4.039488 ACCATACGAAATAGGCCGATGTAA 59.961 41.667 0.00 0.00 0.00 2.41
286 352 3.575256 ACCATACGAAATAGGCCGATGTA 59.425 43.478 0.00 0.00 0.00 2.29
287 353 2.367567 ACCATACGAAATAGGCCGATGT 59.632 45.455 0.00 0.00 0.00 3.06
288 354 3.040147 ACCATACGAAATAGGCCGATG 57.960 47.619 0.00 0.00 0.00 3.84
289 355 3.070446 TGAACCATACGAAATAGGCCGAT 59.930 43.478 0.00 0.00 0.00 4.18
290 356 2.431419 TGAACCATACGAAATAGGCCGA 59.569 45.455 0.00 0.00 0.00 5.54
349 418 2.880890 GACAGTTGCTCCTCACAAACAT 59.119 45.455 0.00 0.00 0.00 2.71
362 431 9.974750 GTAACTTCAATTAGATTAGACAGTTGC 57.025 33.333 0.00 0.00 0.00 4.17
687 851 8.455903 TTCCACCAATGATTAGATTTCATCTC 57.544 34.615 0.00 0.00 40.76 2.75
710 874 6.012658 TCCTAAAACATGAGTGCAACATTC 57.987 37.500 0.00 0.00 41.43 2.67
790 954 6.640518 TGTCTGAGGATATTGTACAGAAACC 58.359 40.000 0.00 0.00 38.90 3.27
791 955 7.819900 ACTTGTCTGAGGATATTGTACAGAAAC 59.180 37.037 0.00 0.00 38.90 2.78
854 1018 0.391395 CTCAGTCTGCAGCCTTCCTG 60.391 60.000 9.47 9.47 44.67 3.86
869 1033 2.430465 ACCACAGTAATTGCAGCTCAG 58.570 47.619 0.00 0.00 0.00 3.35
886 1056 3.387374 TGTAACTCGAAACCACCTTACCA 59.613 43.478 0.00 0.00 0.00 3.25
915 1085 1.272092 TGCCTGCTAAATGGTGCTCTT 60.272 47.619 0.00 0.00 0.00 2.85
1202 1405 6.094464 TGACGGAGAATCGAAGTAATCACTTA 59.906 38.462 0.00 0.00 45.18 2.24
1235 1438 6.070538 AGCTTCAGAGAAGAACTTGCCTATTA 60.071 38.462 10.72 0.00 0.00 0.98
1491 1694 1.207593 CTGCGTACCTTTGCTGCAC 59.792 57.895 0.00 0.00 0.00 4.57
1527 1730 4.155709 AGTCCTCAGTGATTTCAGAGACA 58.844 43.478 0.00 0.00 0.00 3.41
1973 2179 2.223502 TGGATACGCTCGAACAGATCAC 60.224 50.000 0.00 0.00 42.51 3.06
1978 2184 1.862008 GCTCTGGATACGCTCGAACAG 60.862 57.143 0.00 0.00 42.51 3.16
2451 2657 7.769044 GCATTTTGTAAGAGATTAGGGTGTAGA 59.231 37.037 0.00 0.00 0.00 2.59
2750 3157 5.450137 CCAATGCAGAGAAGTTGATCATTCC 60.450 44.000 0.00 0.00 0.00 3.01
2751 3158 5.579718 CCAATGCAGAGAAGTTGATCATTC 58.420 41.667 0.00 0.00 0.00 2.67
2752 3159 4.142227 GCCAATGCAGAGAAGTTGATCATT 60.142 41.667 0.00 0.00 37.47 2.57
2753 3160 3.380637 GCCAATGCAGAGAAGTTGATCAT 59.619 43.478 0.00 0.00 37.47 2.45
2754 3161 2.751259 GCCAATGCAGAGAAGTTGATCA 59.249 45.455 0.00 0.00 37.47 2.92
2755 3162 2.098770 GGCCAATGCAGAGAAGTTGATC 59.901 50.000 0.00 0.00 40.13 2.92
2756 3163 2.097825 GGCCAATGCAGAGAAGTTGAT 58.902 47.619 0.00 0.00 40.13 2.57
2757 3164 1.074405 AGGCCAATGCAGAGAAGTTGA 59.926 47.619 5.01 0.00 40.13 3.18
2758 3165 1.542492 AGGCCAATGCAGAGAAGTTG 58.458 50.000 5.01 0.00 40.13 3.16
2759 3166 3.084786 GTTAGGCCAATGCAGAGAAGTT 58.915 45.455 5.01 0.00 40.13 2.66
2760 3167 2.307098 AGTTAGGCCAATGCAGAGAAGT 59.693 45.455 5.01 0.00 40.13 3.01
2761 3168 2.996631 AGTTAGGCCAATGCAGAGAAG 58.003 47.619 5.01 0.00 40.13 2.85
2762 3169 3.084039 CAAGTTAGGCCAATGCAGAGAA 58.916 45.455 5.01 0.00 40.13 2.87
2763 3170 2.040278 ACAAGTTAGGCCAATGCAGAGA 59.960 45.455 5.01 0.00 40.13 3.10
2764 3171 2.421424 GACAAGTTAGGCCAATGCAGAG 59.579 50.000 5.01 0.00 40.13 3.35
2765 3172 2.224744 TGACAAGTTAGGCCAATGCAGA 60.225 45.455 5.01 0.00 40.13 4.26
2766 3173 2.161855 TGACAAGTTAGGCCAATGCAG 58.838 47.619 5.01 0.00 40.13 4.41
2767 3174 2.284754 TGACAAGTTAGGCCAATGCA 57.715 45.000 5.01 0.00 40.13 3.96
2768 3175 2.295909 TGTTGACAAGTTAGGCCAATGC 59.704 45.455 5.01 0.00 0.00 3.56
2769 3176 4.789012 ATGTTGACAAGTTAGGCCAATG 57.211 40.909 5.01 0.00 0.00 2.82
2770 3177 4.399303 GCTATGTTGACAAGTTAGGCCAAT 59.601 41.667 5.01 0.00 0.00 3.16
2771 3178 3.756434 GCTATGTTGACAAGTTAGGCCAA 59.244 43.478 5.01 0.00 0.00 4.52
2772 3179 3.009033 AGCTATGTTGACAAGTTAGGCCA 59.991 43.478 5.01 0.00 0.00 5.36
2773 3180 3.375299 CAGCTATGTTGACAAGTTAGGCC 59.625 47.826 0.00 0.00 0.00 5.19
2774 3181 4.003648 ACAGCTATGTTGACAAGTTAGGC 58.996 43.478 0.00 0.00 35.63 3.93
2791 3198 8.401709 GCTTCTCTGCTATTTATTTAAACAGCT 58.598 33.333 12.92 0.00 43.92 4.24
2792 3199 8.401709 AGCTTCTCTGCTATTTATTTAAACAGC 58.598 33.333 6.42 6.42 43.87 4.40
2804 3211 9.672673 TGTAATTCTTTTAGCTTCTCTGCTATT 57.327 29.630 0.00 0.00 43.92 1.73
2805 3212 9.323985 CTGTAATTCTTTTAGCTTCTCTGCTAT 57.676 33.333 0.00 0.00 43.92 2.97
2806 3213 8.531982 TCTGTAATTCTTTTAGCTTCTCTGCTA 58.468 33.333 0.00 0.00 43.74 3.49
2807 3214 7.390027 TCTGTAATTCTTTTAGCTTCTCTGCT 58.610 34.615 0.00 0.00 46.11 4.24
2808 3215 7.602517 TCTGTAATTCTTTTAGCTTCTCTGC 57.397 36.000 0.00 0.00 0.00 4.26
2809 3216 9.376075 TCATCTGTAATTCTTTTAGCTTCTCTG 57.624 33.333 0.00 0.00 0.00 3.35
2810 3217 9.950496 TTCATCTGTAATTCTTTTAGCTTCTCT 57.050 29.630 0.00 0.00 0.00 3.10
2815 3222 9.236006 ACACATTCATCTGTAATTCTTTTAGCT 57.764 29.630 0.00 0.00 0.00 3.32
2826 3233 9.889128 TTGATCATTCTACACATTCATCTGTAA 57.111 29.630 0.00 0.00 0.00 2.41
2827 3234 9.317936 GTTGATCATTCTACACATTCATCTGTA 57.682 33.333 0.00 0.00 0.00 2.74
2828 3235 8.045507 AGTTGATCATTCTACACATTCATCTGT 58.954 33.333 0.00 0.00 31.04 3.41
2829 3236 8.434733 AGTTGATCATTCTACACATTCATCTG 57.565 34.615 0.00 0.00 31.04 2.90
2830 3237 9.107177 GAAGTTGATCATTCTACACATTCATCT 57.893 33.333 0.00 0.00 31.04 2.90
2831 3238 9.107177 AGAAGTTGATCATTCTACACATTCATC 57.893 33.333 9.38 0.00 34.04 2.92
2832 3239 9.107177 GAGAAGTTGATCATTCTACACATTCAT 57.893 33.333 10.80 0.00 35.93 2.57
2833 3240 8.316946 AGAGAAGTTGATCATTCTACACATTCA 58.683 33.333 10.80 0.00 35.93 2.57
2834 3241 8.602328 CAGAGAAGTTGATCATTCTACACATTC 58.398 37.037 10.80 4.95 35.93 2.67
2835 3242 7.065563 GCAGAGAAGTTGATCATTCTACACATT 59.934 37.037 10.80 0.00 35.93 2.71
2836 3243 6.538021 GCAGAGAAGTTGATCATTCTACACAT 59.462 38.462 10.80 0.00 35.93 3.21
2837 3244 5.871524 GCAGAGAAGTTGATCATTCTACACA 59.128 40.000 10.80 0.00 35.93 3.72
2838 3245 5.871524 TGCAGAGAAGTTGATCATTCTACAC 59.128 40.000 10.80 0.00 35.93 2.90
2839 3246 6.041423 TGCAGAGAAGTTGATCATTCTACA 57.959 37.500 10.80 7.76 35.93 2.74
2840 3247 6.760298 TGATGCAGAGAAGTTGATCATTCTAC 59.240 38.462 10.80 0.00 35.93 2.59
2841 3248 6.881570 TGATGCAGAGAAGTTGATCATTCTA 58.118 36.000 10.80 0.00 35.93 2.10
3182 3754 1.741770 GTTCGGGCAGCGTCATCTT 60.742 57.895 0.00 0.00 0.00 2.40
3357 3938 0.759346 AACTGAAGGCCGTCTCACTT 59.241 50.000 19.81 6.03 0.00 3.16
3462 4104 1.337728 CCAGTACGACATTGCCACTCA 60.338 52.381 0.00 0.00 0.00 3.41
3539 4228 7.755822 TCAACACAACATAACAAACTTGGTAAC 59.244 33.333 0.00 0.00 33.45 2.50
3767 4687 8.753175 GGCTTGTTGATTAATAGTAGTACTTCG 58.247 37.037 8.40 0.00 0.00 3.79
3835 4761 0.741221 CTAAGCGGCAGGGAACAGAC 60.741 60.000 1.45 0.00 0.00 3.51
3847 4773 5.351465 TGCTTCTAAGTTGATTTCTAAGCGG 59.649 40.000 0.00 0.00 40.65 5.52
3857 4783 4.592942 TGGATGCTTGCTTCTAAGTTGAT 58.407 39.130 8.11 0.00 0.00 2.57
3907 4833 1.754226 TCCCTTTGTGTTTTGACAGCC 59.246 47.619 0.00 0.00 0.00 4.85
3944 4870 1.341852 TGTAACGACACCAGCTTGCTA 59.658 47.619 0.00 0.00 0.00 3.49
4010 4936 5.978934 AAAACGCCTTACATTATAGGACG 57.021 39.130 0.00 0.00 37.21 4.79
4054 4983 7.377766 AGCATACAACGATGTAAGACATTTT 57.622 32.000 9.74 0.00 44.81 1.82
4069 4998 3.585862 TCTCTTGTTCCGAGCATACAAC 58.414 45.455 0.00 0.00 0.00 3.32
4131 5064 6.314648 CGGGGTTATCCAAAACTTAGTTACTC 59.685 42.308 0.00 0.00 37.22 2.59
4327 5353 4.681978 GCGGTCTTCTGGTGCGGT 62.682 66.667 0.00 0.00 0.00 5.68
4332 5358 2.338984 GTCACGCGGTCTTCTGGT 59.661 61.111 12.47 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.