Multiple sequence alignment - TraesCS7D01G502800

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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 TraesCS7D01G502800 chr7D 100.000 3185 0 0 3310 6494 608206439 608203255 0.000000e+00 5882.0
1 TraesCS7D01G502800 chr7D 100.000 2973 0 0 1 2973 608209748 608206776 0.000000e+00 5491.0
2 TraesCS7D01G502800 chr7D 94.434 2084 78 13 919 2973 514901305 514899231 0.000000e+00 3171.0
3 TraesCS7D01G502800 chr7D 93.480 2086 84 18 919 2973 610479943 610482007 0.000000e+00 3051.0
4 TraesCS7D01G502800 chr7D 88.865 1410 123 14 3577 4958 610482558 610483961 0.000000e+00 1703.0
5 TraesCS7D01G502800 chr7D 87.900 1405 133 14 3572 4958 514898486 514897101 0.000000e+00 1618.0
6 TraesCS7D01G502800 chr7D 93.116 828 36 12 5239 6059 514896811 514895998 0.000000e+00 1194.0
7 TraesCS7D01G502800 chr7D 91.960 398 23 6 6103 6494 514895786 514895392 3.420000e-152 549.0
8 TraesCS7D01G502800 chr7D 83.753 437 53 13 5 432 197935688 197935261 1.310000e-106 398.0
9 TraesCS7D01G502800 chr7D 78.549 317 34 17 29 319 424487908 424488216 1.860000e-40 178.0
10 TraesCS7D01G502800 chr7D 86.250 160 5 3 678 821 514901458 514901300 2.420000e-34 158.0
11 TraesCS7D01G502800 chr7D 84.459 148 7 5 447 594 514901937 514901806 1.470000e-26 132.0
12 TraesCS7D01G502800 chr7B 95.916 2767 82 12 3310 6059 699192497 699189745 0.000000e+00 4455.0
13 TraesCS7D01G502800 chr7B 92.081 2134 99 26 878 2973 699194772 699192671 0.000000e+00 2940.0
14 TraesCS7D01G502800 chr7B 92.749 1448 73 16 1313 2755 694497573 694498993 0.000000e+00 2063.0
15 TraesCS7D01G502800 chr7B 87.652 1401 146 12 3581 4958 694447816 694446420 0.000000e+00 1604.0
16 TraesCS7D01G502800 chr7B 87.935 1235 110 23 1718 2931 697285348 697286564 0.000000e+00 1419.0
17 TraesCS7D01G502800 chr7B 91.908 828 46 11 5239 6059 694446129 694445316 0.000000e+00 1138.0
18 TraesCS7D01G502800 chr7B 87.635 833 69 18 1 817 694522341 694521527 0.000000e+00 937.0
19 TraesCS7D01G502800 chr7B 97.704 392 9 0 6103 6494 699189532 699189141 0.000000e+00 675.0
20 TraesCS7D01G502800 chr7B 92.214 411 29 1 1019 1426 697284013 697284423 4.370000e-161 579.0
21 TraesCS7D01G502800 chr7B 91.878 394 25 5 6103 6494 694445118 694444730 1.590000e-150 544.0
22 TraesCS7D01G502800 chr7B 78.238 749 145 14 4200 4939 697287198 697287937 1.280000e-126 464.0
23 TraesCS7D01G502800 chr7B 83.841 427 53 11 12 429 162149785 162149366 6.100000e-105 392.0
24 TraesCS7D01G502800 chr7B 92.576 229 5 1 2757 2973 694449128 694448900 1.050000e-82 318.0
25 TraesCS7D01G502800 chr7B 78.025 405 63 17 23 412 58883032 58882639 1.410000e-56 231.0
26 TraesCS7D01G502800 chr7B 83.045 289 15 13 545 821 699195062 699194796 1.410000e-56 231.0
27 TraesCS7D01G502800 chr7A 94.276 1974 79 14 927 2888 700286823 700284872 0.000000e+00 2988.0
28 TraesCS7D01G502800 chr7A 93.921 1859 80 16 1130 2973 700329136 700327296 0.000000e+00 2776.0
29 TraesCS7D01G502800 chr7A 91.677 829 46 12 5239 6059 700264631 700263818 0.000000e+00 1127.0
30 TraesCS7D01G502800 chr7A 91.011 712 48 9 5301 6009 700279862 700279164 0.000000e+00 946.0
31 TraesCS7D01G502800 chr7A 91.011 712 48 9 5301 6009 700284173 700283475 0.000000e+00 946.0
32 TraesCS7D01G502800 chr7A 89.026 647 66 5 4312 4958 700265576 700264935 0.000000e+00 797.0
33 TraesCS7D01G502800 chr7A 91.466 539 21 6 927 1445 700329682 700329149 0.000000e+00 717.0
34 TraesCS7D01G502800 chr7A 87.840 551 44 14 928 1464 699900808 699901349 5.530000e-175 625.0
35 TraesCS7D01G502800 chr7A 83.404 705 83 20 3348 4029 699903235 699903928 1.990000e-174 623.0
36 TraesCS7D01G502800 chr7A 90.886 395 29 4 6103 6493 700278910 700278519 2.070000e-144 523.0
37 TraesCS7D01G502800 chr7A 90.633 395 30 4 6103 6493 700283221 700282830 9.650000e-143 518.0
38 TraesCS7D01G502800 chr7A 90.704 398 20 10 6103 6494 700263602 700263216 1.250000e-141 514.0
39 TraesCS7D01G502800 chr7A 86.486 481 46 4 3780 4256 700266207 700265742 1.620000e-140 510.0
40 TraesCS7D01G502800 chr7A 82.562 562 46 19 5093 5645 699906581 699907099 1.280000e-121 448.0
41 TraesCS7D01G502800 chr7A 95.161 186 8 1 3321 3505 700284358 700284173 6.370000e-75 292.0
42 TraesCS7D01G502800 chr7A 94.118 187 9 2 3321 3505 700280048 700279862 3.830000e-72 283.0
43 TraesCS7D01G502800 chr7A 89.720 107 3 3 715 814 700286928 700286823 5.280000e-26 130.0
44 TraesCS7D01G502800 chr7A 96.875 32 0 1 783 814 700329712 700329682 1.200000e-02 52.8
45 TraesCS7D01G502800 chrUn 95.514 1761 61 7 4311 6059 77468068 77466314 0.000000e+00 2798.0
46 TraesCS7D01G502800 chrUn 91.161 1731 82 32 557 2266 77510491 77508811 0.000000e+00 2283.0
47 TraesCS7D01G502800 chrUn 94.066 1247 57 6 1511 2754 77470873 77469641 0.000000e+00 1877.0
48 TraesCS7D01G502800 chrUn 85.810 1346 129 22 3640 4958 77506319 77505009 0.000000e+00 1371.0
49 TraesCS7D01G502800 chrUn 95.063 790 20 6 3310 4084 77468859 77468074 0.000000e+00 1225.0
50 TraesCS7D01G502800 chrUn 90.953 829 50 12 5239 6059 77504718 77503907 0.000000e+00 1092.0
51 TraesCS7D01G502800 chrUn 88.172 930 43 19 557 1447 77471774 77470873 0.000000e+00 1046.0
52 TraesCS7D01G502800 chrUn 97.194 392 11 0 6103 6494 77466098 77465707 0.000000e+00 664.0
53 TraesCS7D01G502800 chrUn 92.978 413 14 4 2574 2973 77507367 77506957 7.250000e-164 588.0
54 TraesCS7D01G502800 chrUn 90.657 396 28 5 6103 6494 77503694 77503304 9.650000e-143 518.0
55 TraesCS7D01G502800 chrUn 91.542 201 5 1 2785 2973 77469640 77469440 3.860000e-67 267.0
56 TraesCS7D01G502800 chrUn 98.611 72 1 0 447 518 77471856 77471785 1.900000e-25 128.0
57 TraesCS7D01G502800 chrUn 98.611 72 1 0 447 518 77510573 77510502 1.900000e-25 128.0
58 TraesCS7D01G502800 chr4A 92.955 1604 85 11 1387 2973 662072283 662073875 0.000000e+00 2311.0
59 TraesCS7D01G502800 chr4A 90.109 829 45 11 5239 6059 662076368 662077167 0.000000e+00 1042.0
60 TraesCS7D01G502800 chr4A 89.574 681 56 11 3594 4263 662074545 662075221 0.000000e+00 850.0
61 TraesCS7D01G502800 chr4A 87.758 678 80 3 4281 4958 662075403 662076077 0.000000e+00 789.0
62 TraesCS7D01G502800 chr4A 88.979 617 46 15 881 1483 662071342 662071950 0.000000e+00 743.0
63 TraesCS7D01G502800 chr4A 89.673 397 29 9 6103 6494 662077379 662077768 4.520000e-136 496.0
64 TraesCS7D01G502800 chr4A 88.623 167 14 4 3310 3475 662074214 662074376 1.430000e-46 198.0
65 TraesCS7D01G502800 chr4A 79.018 224 27 10 213 432 742325261 742325468 1.140000e-27 135.0
66 TraesCS7D01G502800 chr4A 96.825 63 2 0 447 509 662058986 662059048 8.910000e-19 106.0
67 TraesCS7D01G502800 chr2D 82.451 359 49 6 77 432 53466719 53466372 1.060000e-77 302.0
68 TraesCS7D01G502800 chr4D 84.519 239 30 4 176 411 10485814 10486048 5.060000e-56 230.0
69 TraesCS7D01G502800 chr2A 76.263 396 73 12 52 436 14610905 14611290 2.390000e-44 191.0
70 TraesCS7D01G502800 chr2A 84.848 66 4 3 155 214 88006088 88006023 1.960000e-05 62.1
71 TraesCS7D01G502800 chr2B 88.800 125 14 0 1 125 84450248 84450372 3.140000e-33 154.0
72 TraesCS7D01G502800 chr6A 75.194 387 52 20 12 390 556516055 556516405 6.790000e-30 143.0


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 TraesCS7D01G502800 chr7D 608203255 608209748 6493 True 5686.500000 5882 100.000000 1 6494 2 chr7D.!!$R3 6493
1 TraesCS7D01G502800 chr7D 610479943 610483961 4018 False 2377.000000 3051 91.172500 919 4958 2 chr7D.!!$F2 4039
2 TraesCS7D01G502800 chr7D 514895392 514901937 6545 True 1137.000000 3171 89.686500 447 6494 6 chr7D.!!$R2 6047
3 TraesCS7D01G502800 chr7B 699189141 699195062 5921 True 2075.250000 4455 92.186500 545 6494 4 chr7B.!!$R5 5949
4 TraesCS7D01G502800 chr7B 694497573 694498993 1420 False 2063.000000 2063 92.749000 1313 2755 1 chr7B.!!$F1 1442
5 TraesCS7D01G502800 chr7B 694521527 694522341 814 True 937.000000 937 87.635000 1 817 1 chr7B.!!$R3 816
6 TraesCS7D01G502800 chr7B 694444730 694449128 4398 True 901.000000 1604 91.003500 2757 6494 4 chr7B.!!$R4 3737
7 TraesCS7D01G502800 chr7B 697284013 697287937 3924 False 820.666667 1419 86.129000 1019 4939 3 chr7B.!!$F2 3920
8 TraesCS7D01G502800 chr7A 700327296 700329712 2416 True 1181.933333 2776 94.087333 783 2973 3 chr7A.!!$R3 2190
9 TraesCS7D01G502800 chr7A 700278519 700286928 8409 True 828.250000 2988 92.102000 715 6493 8 chr7A.!!$R2 5778
10 TraesCS7D01G502800 chr7A 700263216 700266207 2991 True 737.000000 1127 89.473250 3780 6494 4 chr7A.!!$R1 2714
11 TraesCS7D01G502800 chr7A 699900808 699907099 6291 False 565.333333 625 84.602000 928 5645 3 chr7A.!!$F1 4717
12 TraesCS7D01G502800 chrUn 77465707 77471856 6149 True 1143.571429 2798 94.308857 447 6494 7 chrUn.!!$R1 6047
13 TraesCS7D01G502800 chrUn 77503304 77510573 7269 True 996.666667 2283 91.695000 447 6494 6 chrUn.!!$R2 6047
14 TraesCS7D01G502800 chr4A 662071342 662077768 6426 False 918.428571 2311 89.667286 881 6494 7 chr4A.!!$F3 5613

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
227 229 0.464036 TGAGGACGACAAAGCACAGT 59.536 50.000 0.00 0.0 0.00 3.55 F
1272 1640 0.104882 TCTACCTCACCAACCCCACA 60.105 55.000 0.00 0.0 0.00 4.17 F
2443 4527 1.228862 GGCACTTGTTGGGATGGGT 60.229 57.895 0.00 0.0 0.00 4.51 F
2749 5864 1.978580 ACCTCTTTCCCACACCTACAG 59.021 52.381 0.00 0.0 0.00 2.74 F
3826 7622 2.093890 TGTATGCATTGAGCCACCTTG 58.906 47.619 3.54 0.0 44.83 3.61 F
4784 8947 0.393077 CTGACCTTGGTCAGTCGGTT 59.607 55.000 31.13 0.0 44.16 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 3633 2.298411 TATGCCTTACGAACCCGAAC 57.702 50.000 0.00 0.00 39.50 3.95 R
2730 5845 1.978580 ACTGTAGGTGTGGGAAAGAGG 59.021 52.381 0.00 0.00 0.00 3.69 R
3776 7554 1.002366 CATGTCAAGTAGCTGCCGAC 58.998 55.000 13.09 13.09 0.00 4.79 R
4686 8849 1.212751 GCCAACAAACGAGGCCATC 59.787 57.895 5.01 0.00 42.58 3.51 R
4941 9105 0.397941 ATGACCACTGGTGTGACAGG 59.602 55.000 5.10 0.00 46.55 4.00 R
6073 16106 2.435805 TGGCTAAGCTCTGTTAGGATGG 59.564 50.000 0.00 0.00 31.60 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
52 53 4.755614 GCGAGCGACGACGAAGGT 62.756 66.667 12.29 0.00 45.77 3.50
64 65 4.317488 ACGACGAAGGTTGGCTTTTATAA 58.683 39.130 0.00 0.00 0.00 0.98
116 118 3.647771 AGGAAAGGGCGGGGACAC 61.648 66.667 0.00 0.00 0.00 3.67
144 146 1.745115 GCTCGCCATTACTGTGCCA 60.745 57.895 0.00 0.00 0.00 4.92
146 148 1.369091 CTCGCCATTACTGTGCCACC 61.369 60.000 0.00 0.00 0.00 4.61
162 164 1.352352 CCACCAGTCTTGATGGAAGGT 59.648 52.381 0.00 0.00 40.51 3.50
170 172 0.608035 TTGATGGAAGGTTGACCGGC 60.608 55.000 0.00 0.00 42.08 6.13
187 189 4.558309 CGACAGCATTGAATCGCG 57.442 55.556 0.00 0.00 0.00 5.87
218 220 2.761195 CGAGGCGATGAGGACGACA 61.761 63.158 0.00 0.00 41.61 4.35
226 228 1.728971 GATGAGGACGACAAAGCACAG 59.271 52.381 0.00 0.00 0.00 3.66
227 229 0.464036 TGAGGACGACAAAGCACAGT 59.536 50.000 0.00 0.00 0.00 3.55
272 274 2.683475 GGGGGAATCTGGTGTGGG 59.317 66.667 0.00 0.00 0.00 4.61
276 278 1.250840 GGGAATCTGGTGTGGGTTGC 61.251 60.000 0.00 0.00 0.00 4.17
291 293 0.858583 GTTGCTTTCGCGCCATTTTT 59.141 45.000 0.00 0.00 39.65 1.94
292 294 1.135867 TTGCTTTCGCGCCATTTTTC 58.864 45.000 0.00 0.00 39.65 2.29
304 306 0.707822 CATTTTTCTTTTCCGCGGCG 59.292 50.000 23.51 16.78 0.00 6.46
335 338 4.796231 CCAGCGCGCTAGGTTCGT 62.796 66.667 36.02 6.28 0.00 3.85
345 348 2.531852 AGGTTCGTCCTGGGTCCT 59.468 61.111 0.00 0.00 46.19 3.85
347 350 2.657066 GGTTCGTCCTGGGTCCTCC 61.657 68.421 0.00 0.00 0.00 4.30
359 362 2.437716 TCCTCCGGCGCCAATTTC 60.438 61.111 28.98 0.00 0.00 2.17
361 364 3.876198 CTCCGGCGCCAATTTCGG 61.876 66.667 28.98 20.48 43.42 4.30
406 410 4.520846 GCGCGACTGGCCGATTTG 62.521 66.667 12.10 0.00 38.94 2.32
414 418 1.616872 CTGGCCGATTTGTTTTGCGC 61.617 55.000 0.00 0.00 0.00 6.09
417 421 2.085844 CCGATTTGTTTTGCGCCCG 61.086 57.895 4.18 0.00 0.00 6.13
438 442 1.532604 GAAAAAGAAGGCGGGGGTGG 61.533 60.000 0.00 0.00 0.00 4.61
439 443 2.014033 AAAAAGAAGGCGGGGGTGGA 62.014 55.000 0.00 0.00 0.00 4.02
482 486 7.318401 AGGGGTATAGGGAAATGACACTATTA 58.682 38.462 0.00 0.00 37.60 0.98
1272 1640 0.104882 TCTACCTCACCAACCCCACA 60.105 55.000 0.00 0.00 0.00 4.17
1447 2602 7.365117 CCCCTGAGTTAGAAGTCATAGATTTGT 60.365 40.741 0.35 0.00 37.70 2.83
1448 2603 8.043710 CCCTGAGTTAGAAGTCATAGATTTGTT 58.956 37.037 0.35 0.00 37.70 2.83
1463 2618 9.612620 CATAGATTTGTTGGACTCTGTTTTTAC 57.387 33.333 0.00 0.00 0.00 2.01
2443 4527 1.228862 GGCACTTGTTGGGATGGGT 60.229 57.895 0.00 0.00 0.00 4.51
2749 5864 1.978580 ACCTCTTTCCCACACCTACAG 59.021 52.381 0.00 0.00 0.00 2.74
2755 5870 3.756933 TTCCCACACCTACAGTACAAC 57.243 47.619 0.00 0.00 0.00 3.32
3392 7096 6.693315 TGTTTTGTTTCTCTTAAGTCCTGG 57.307 37.500 1.63 0.00 0.00 4.45
3589 7296 7.692460 ACTCATAAAATCAGTTCAGCATTCA 57.308 32.000 0.00 0.00 0.00 2.57
3715 7471 5.826208 AGAACTCCAAAACCGTCTAAAACAT 59.174 36.000 0.00 0.00 0.00 2.71
3754 7510 6.567769 AAAATGTGCACTTTGTTAGTTTCG 57.432 33.333 19.41 0.00 33.85 3.46
3755 7511 5.493133 AATGTGCACTTTGTTAGTTTCGA 57.507 34.783 19.41 0.00 33.85 3.71
3756 7512 4.948608 TGTGCACTTTGTTAGTTTCGAA 57.051 36.364 19.41 0.00 33.85 3.71
3826 7622 2.093890 TGTATGCATTGAGCCACCTTG 58.906 47.619 3.54 0.00 44.83 3.61
4363 8503 2.245287 TGGGTTGTGGGTTAGGTTTTCT 59.755 45.455 0.00 0.00 0.00 2.52
4514 8674 3.964221 TTGTCAGCTACGCGGCTCG 62.964 63.158 12.47 5.82 41.00 5.03
4686 8849 0.671781 CTGTCCAAGAAGGCCAGTCG 60.672 60.000 5.01 0.00 38.58 4.18
4727 8890 1.209019 CTGCAGTGGAGCTATTGTCCT 59.791 52.381 5.25 0.00 34.86 3.85
4737 8900 1.772182 CTATTGTCCTCCATCGTCGC 58.228 55.000 0.00 0.00 0.00 5.19
4777 8940 0.842030 ATGGCCTCTGACCTTGGTCA 60.842 55.000 19.86 19.86 39.95 4.02
4784 8947 0.393077 CTGACCTTGGTCAGTCGGTT 59.607 55.000 31.13 0.00 44.16 4.44
4973 9137 4.344968 CCAGTGGTCATCATCCATGTACTA 59.655 45.833 0.00 0.00 37.30 1.82
5080 9668 5.163913 GGTTCAGTCAATCTTTCATCGTGAG 60.164 44.000 0.00 0.00 0.00 3.51
5317 11024 5.687285 CCTACACAGTTGCTTCATTGTTTTC 59.313 40.000 0.00 0.00 0.00 2.29
5318 11025 5.329035 ACACAGTTGCTTCATTGTTTTCT 57.671 34.783 0.00 0.00 0.00 2.52
5348 11055 2.841266 GGTTAGAGAAGGAAGAAGGCCT 59.159 50.000 0.00 0.00 37.35 5.19
5352 11059 1.746991 GAAGGAAGAAGGCCTGGCG 60.747 63.158 5.69 0.00 35.50 5.69
5586 15606 9.124807 GGTTGTGTCTAGCAAAATAATAACAAC 57.875 33.333 0.00 0.00 41.65 3.32
5706 15726 1.964223 CTACATCCTGGTGGCGACTAT 59.036 52.381 0.00 0.00 0.00 2.12
5961 15984 3.876309 TTGGGACAGAAGTTAGCCTTT 57.124 42.857 0.00 0.00 42.39 3.11
5971 15994 9.601217 GACAGAAGTTAGCCTTTCTATTTATCA 57.399 33.333 0.00 0.00 32.03 2.15
6031 16058 3.507622 GCCAGTTCTTCTTAGCCAAACAT 59.492 43.478 0.00 0.00 0.00 2.71
6059 16092 5.674052 TTAAAGCCATGCATATTGGTGTT 57.326 34.783 0.00 0.00 36.57 3.32
6060 16093 4.556592 AAAGCCATGCATATTGGTGTTT 57.443 36.364 0.00 0.38 36.57 2.83
6061 16094 4.556592 AAGCCATGCATATTGGTGTTTT 57.443 36.364 0.00 0.00 36.57 2.43
6062 16095 4.127566 AGCCATGCATATTGGTGTTTTC 57.872 40.909 0.00 0.00 36.57 2.29
6065 16098 4.330620 GCCATGCATATTGGTGTTTTCTTG 59.669 41.667 0.00 0.00 36.57 3.02
6066 16099 4.871557 CCATGCATATTGGTGTTTTCTTGG 59.128 41.667 0.00 0.00 0.00 3.61
6067 16100 5.481105 CATGCATATTGGTGTTTTCTTGGT 58.519 37.500 0.00 0.00 0.00 3.67
6068 16101 4.880759 TGCATATTGGTGTTTTCTTGGTG 58.119 39.130 0.00 0.00 0.00 4.17
6069 16102 4.586421 TGCATATTGGTGTTTTCTTGGTGA 59.414 37.500 0.00 0.00 0.00 4.02
6070 16103 4.923281 GCATATTGGTGTTTTCTTGGTGAC 59.077 41.667 0.00 0.00 0.00 3.67
6071 16104 5.508825 GCATATTGGTGTTTTCTTGGTGACA 60.509 40.000 0.00 0.00 39.83 3.58
6085 16118 3.695830 GGTGACAACCATCCTAACAGA 57.304 47.619 0.00 0.00 46.75 3.41
6086 16119 3.600388 GGTGACAACCATCCTAACAGAG 58.400 50.000 0.00 0.00 46.75 3.35
6087 16120 3.003480 GTGACAACCATCCTAACAGAGC 58.997 50.000 0.00 0.00 0.00 4.09
6090 16123 4.530553 TGACAACCATCCTAACAGAGCTTA 59.469 41.667 0.00 0.00 0.00 3.09
6091 16124 5.091261 ACAACCATCCTAACAGAGCTTAG 57.909 43.478 0.00 0.00 0.00 2.18
6092 16125 3.828875 ACCATCCTAACAGAGCTTAGC 57.171 47.619 0.00 0.00 0.00 3.09
6093 16126 2.436173 ACCATCCTAACAGAGCTTAGCC 59.564 50.000 0.00 0.00 0.00 3.93
6096 16129 4.517285 CATCCTAACAGAGCTTAGCCAAA 58.483 43.478 0.00 0.00 0.00 3.28
6097 16130 3.939066 TCCTAACAGAGCTTAGCCAAAC 58.061 45.455 0.00 0.00 0.00 2.93
6098 16131 3.326588 TCCTAACAGAGCTTAGCCAAACA 59.673 43.478 0.00 0.00 0.00 2.83
6099 16132 4.072131 CCTAACAGAGCTTAGCCAAACAA 58.928 43.478 0.00 0.00 0.00 2.83
6101 16134 5.183904 CCTAACAGAGCTTAGCCAAACAAAT 59.816 40.000 0.00 0.00 0.00 2.32
6288 16506 5.081394 GTGCTTTTTCAACAGTTGCTTTTG 58.919 37.500 8.58 0.46 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.249073 CCATCTCTTCGCCTACACCG 60.249 60.000 0.00 0.00 0.00 4.94
9 10 0.318275 CTCGCCATCTCTTCGCCTAC 60.318 60.000 0.00 0.00 0.00 3.18
46 47 3.729762 GCCGTTATAAAAGCCAACCTTCG 60.730 47.826 0.00 0.00 31.99 3.79
52 53 2.933906 CTCTCGCCGTTATAAAAGCCAA 59.066 45.455 3.14 0.00 0.00 4.52
82 83 4.710695 TGCCACGCGTCTACACCG 62.711 66.667 9.86 0.00 0.00 4.94
108 109 4.415332 CACCGTCTCGTGTCCCCG 62.415 72.222 0.00 0.00 0.00 5.73
144 146 2.711009 TCAACCTTCCATCAAGACTGGT 59.289 45.455 0.00 0.00 33.29 4.00
146 148 3.077359 GGTCAACCTTCCATCAAGACTG 58.923 50.000 0.00 0.00 33.29 3.51
162 164 2.031919 AATGCTGTCGCCGGTCAA 59.968 55.556 1.90 0.00 34.43 3.18
170 172 1.649348 GCGCGATTCAATGCTGTCG 60.649 57.895 12.10 0.00 37.17 4.35
206 208 1.728971 CTGTGCTTTGTCGTCCTCATC 59.271 52.381 0.00 0.00 0.00 2.92
209 211 1.140816 GACTGTGCTTTGTCGTCCTC 58.859 55.000 0.00 0.00 0.00 3.71
218 220 0.941463 CGAGTCAGCGACTGTGCTTT 60.941 55.000 14.47 0.00 44.46 3.51
276 278 3.121025 GGAAAAGAAAAATGGCGCGAAAG 60.121 43.478 12.10 0.00 0.00 2.62
361 364 1.059942 CAAATTTCGCCGGTTTGAGC 58.940 50.000 1.90 0.00 35.43 4.26
372 375 1.214325 GCCCGGAACCCAAATTTCG 59.786 57.895 0.73 0.00 0.00 3.46
405 409 2.884087 TTTTTCGCGGGCGCAAAACA 62.884 50.000 17.06 1.61 38.95 2.83
406 410 2.141225 CTTTTTCGCGGGCGCAAAAC 62.141 55.000 17.06 0.00 38.95 2.43
414 418 2.175811 CGCCTTCTTTTTCGCGGG 59.824 61.111 6.13 0.00 40.91 6.13
417 421 2.566529 CCCCGCCTTCTTTTTCGC 59.433 61.111 0.00 0.00 0.00 4.70
424 428 3.642741 ATCTCCACCCCCGCCTTCT 62.643 63.158 0.00 0.00 0.00 2.85
438 442 3.989934 CCCTTCGGGTTTAAGAGCATCTC 60.990 52.174 0.00 0.00 41.33 2.75
439 443 2.092914 CCCTTCGGGTTTAAGAGCATCT 60.093 50.000 0.00 0.00 43.32 2.90
482 486 8.667463 GGCATTTTTGTTGTAATATGCTCAAAT 58.333 29.630 0.00 0.00 40.25 2.32
530 534 3.432051 TTTTTGCGCGTGGGGGTTG 62.432 57.895 8.43 0.00 0.00 3.77
531 535 3.148279 TTTTTGCGCGTGGGGGTT 61.148 55.556 8.43 0.00 0.00 4.11
655 940 1.078567 GGAGCTGCTCACAAGGGAG 60.079 63.158 28.95 0.00 37.97 4.30
835 1161 2.896443 GAACTGAGAGGAGGGCGG 59.104 66.667 0.00 0.00 0.00 6.13
836 1162 1.030488 TACGAACTGAGAGGAGGGCG 61.030 60.000 0.00 0.00 0.00 6.13
846 1172 1.079819 GGCAGCTGCTACGAACTGA 60.080 57.895 35.82 0.00 41.70 3.41
1286 1654 3.449227 CCCGTAGCGTGGAGAGCA 61.449 66.667 0.00 0.00 37.01 4.26
1299 2006 4.778143 GAGATGTTGGCGGCCCGT 62.778 66.667 17.97 2.72 0.00 5.28
1625 3581 6.599244 CCAGTTTCAGCATTCCTAAATACAGA 59.401 38.462 0.00 0.00 0.00 3.41
1636 3592 4.525912 ACCAATTCCAGTTTCAGCATTC 57.474 40.909 0.00 0.00 0.00 2.67
1676 3633 2.298411 TATGCCTTACGAACCCGAAC 57.702 50.000 0.00 0.00 39.50 3.95
1749 3706 6.266558 ACAATGGTAGCCAAAAACAGTTCATA 59.733 34.615 0.00 0.00 36.95 2.15
2085 4047 8.186163 TGAAATCATTCGATTCTTCATGGAAAG 58.814 33.333 0.00 0.00 41.12 2.62
2086 4048 8.054152 TGAAATCATTCGATTCTTCATGGAAA 57.946 30.769 0.00 0.00 41.12 3.13
2443 4527 3.068732 CGATTACCATCTGCTCTGAGGAA 59.931 47.826 6.83 0.00 0.00 3.36
2730 5845 1.978580 ACTGTAGGTGTGGGAAAGAGG 59.021 52.381 0.00 0.00 0.00 3.69
2764 5879 9.812347 AAAGATGCCCAGAACAAATATATGATA 57.188 29.630 0.00 0.00 0.00 2.15
3392 7096 3.243839 TGAAGCTTGAATTCCCAGCAAAC 60.244 43.478 22.36 15.09 0.00 2.93
3754 7510 9.166126 CCGACTTAGTCAAAATAACTTTGTTTC 57.834 33.333 13.14 0.00 44.18 2.78
3755 7511 7.646526 GCCGACTTAGTCAAAATAACTTTGTTT 59.353 33.333 13.14 0.00 44.18 2.83
3756 7512 7.136772 GCCGACTTAGTCAAAATAACTTTGTT 58.863 34.615 13.14 0.00 44.18 2.83
3776 7554 1.002366 CATGTCAAGTAGCTGCCGAC 58.998 55.000 13.09 13.09 0.00 4.79
3826 7622 5.263968 TGGTTAAGATAGTAGCTGACTGC 57.736 43.478 0.00 0.00 39.39 4.40
4363 8503 1.725557 GAGAGTAGCGGTGGCGATGA 61.726 60.000 0.00 0.00 46.35 2.92
4514 8674 2.151369 TGGAACCCCACAGTTCTCC 58.849 57.895 4.58 0.00 44.56 3.71
4576 8736 2.665185 GGCCAAGAACGTGTCGCT 60.665 61.111 0.00 0.00 0.00 4.93
4686 8849 1.212751 GCCAACAAACGAGGCCATC 59.787 57.895 5.01 0.00 42.58 3.51
4777 8940 1.073199 CCAGCCCAAAGAACCGACT 59.927 57.895 0.00 0.00 0.00 4.18
4784 8947 3.170362 CACCTCCCAGCCCAAAGA 58.830 61.111 0.00 0.00 0.00 2.52
4941 9105 0.397941 ATGACCACTGGTGTGACAGG 59.602 55.000 5.10 0.00 46.55 4.00
5080 9668 8.186821 CCTAGTGGTTTCTGATGAATTGAATTC 58.813 37.037 10.85 10.85 39.70 2.17
5081 9669 7.671398 ACCTAGTGGTTTCTGATGAATTGAATT 59.329 33.333 0.00 0.00 46.05 2.17
5113 10802 9.700831 AATCCAAAGCTATACTTTTACTTCCAT 57.299 29.630 0.00 0.00 46.73 3.41
5348 11055 1.948834 CAAATGTCCTATCATGCGCCA 59.051 47.619 4.18 0.00 0.00 5.69
5352 11059 6.511767 CGGAGTAAACAAATGTCCTATCATGC 60.512 42.308 0.00 0.00 0.00 4.06
5706 15726 6.158986 TCTAGGATCTCCTTCCTACTCCTAA 58.841 44.000 3.64 0.00 46.09 2.69
5961 15984 5.826208 TCGGAGTGCTACACTGATAAATAGA 59.174 40.000 4.71 0.00 45.44 1.98
6031 16058 8.575589 CACCAATATGCATGGCTTTAAAGTATA 58.424 33.333 16.38 4.19 41.89 1.47
6053 16086 2.494073 GGTTGTCACCAAGAAAACACCA 59.506 45.455 0.00 0.00 44.78 4.17
6065 16098 3.600388 CTCTGTTAGGATGGTTGTCACC 58.400 50.000 0.00 0.00 44.56 4.02
6066 16099 3.003480 GCTCTGTTAGGATGGTTGTCAC 58.997 50.000 0.00 0.00 0.00 3.67
6067 16100 2.906389 AGCTCTGTTAGGATGGTTGTCA 59.094 45.455 0.00 0.00 0.00 3.58
6068 16101 3.618690 AGCTCTGTTAGGATGGTTGTC 57.381 47.619 0.00 0.00 0.00 3.18
6069 16102 4.624125 GCTAAGCTCTGTTAGGATGGTTGT 60.624 45.833 0.00 0.00 31.60 3.32
6070 16103 3.873952 GCTAAGCTCTGTTAGGATGGTTG 59.126 47.826 0.00 0.00 31.60 3.77
6071 16104 3.118223 GGCTAAGCTCTGTTAGGATGGTT 60.118 47.826 0.00 0.00 31.60 3.67
6073 16106 2.435805 TGGCTAAGCTCTGTTAGGATGG 59.564 50.000 0.00 0.00 31.60 3.51
6074 16107 3.827008 TGGCTAAGCTCTGTTAGGATG 57.173 47.619 0.00 0.00 31.60 3.51
6075 16108 4.019321 TGTTTGGCTAAGCTCTGTTAGGAT 60.019 41.667 0.00 0.00 31.60 3.24
6076 16109 3.326588 TGTTTGGCTAAGCTCTGTTAGGA 59.673 43.478 0.00 0.00 31.60 2.94
6078 16111 5.689383 TTTGTTTGGCTAAGCTCTGTTAG 57.311 39.130 0.00 0.00 33.74 2.34
6079 16112 5.534654 ACATTTGTTTGGCTAAGCTCTGTTA 59.465 36.000 0.00 0.00 0.00 2.41
6082 16115 4.510038 ACATTTGTTTGGCTAAGCTCTG 57.490 40.909 0.00 0.00 0.00 3.35
6090 16123 7.714813 GGGCAAATATTATACATTTGTTTGGCT 59.285 33.333 17.02 0.00 44.74 4.75
6091 16124 7.497249 TGGGCAAATATTATACATTTGTTTGGC 59.503 33.333 15.44 11.49 42.67 4.52
6092 16125 8.825745 GTGGGCAAATATTATACATTTGTTTGG 58.174 33.333 15.44 0.00 42.67 3.28
6093 16126 9.376075 TGTGGGCAAATATTATACATTTGTTTG 57.624 29.630 15.44 0.00 42.67 2.93
6096 16129 7.984617 GGTTGTGGGCAAATATTATACATTTGT 59.015 33.333 15.44 0.00 42.67 2.83
6097 16130 7.984050 TGGTTGTGGGCAAATATTATACATTTG 59.016 33.333 11.94 11.94 43.27 2.32
6098 16131 8.083828 TGGTTGTGGGCAAATATTATACATTT 57.916 30.769 0.00 0.00 36.22 2.32
6099 16132 7.667575 TGGTTGTGGGCAAATATTATACATT 57.332 32.000 0.00 0.00 36.22 2.71
6101 16134 6.041409 CCATGGTTGTGGGCAAATATTATACA 59.959 38.462 2.57 0.00 36.22 2.29


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

AutoCloner maintained by Alex Coulton.