Multiple sequence alignment - TraesCS7D01G328400

Loading Multiple Alignment...

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 TraesCS7D01G328400 chr7D 100.000 8238 0 0 1 8238 419789865 419798102 0.000000e+00 15213.0
1 TraesCS7D01G328400 chr7D 95.062 81 3 1 3105 3185 596233619 596233540 8.680000e-25 126.0
2 TraesCS7D01G328400 chr7D 91.111 90 7 1 3090 3178 390929872 390929783 4.040000e-23 121.0
3 TraesCS7D01G328400 chr7D 87.778 90 11 0 3246 3335 563470240 563470329 1.130000e-18 106.0
4 TraesCS7D01G328400 chr7D 96.610 59 1 1 3034 3091 526495639 526495581 6.810000e-16 97.1
5 TraesCS7D01G328400 chr7D 92.424 66 3 2 8174 8238 419035806 419035870 8.800000e-15 93.5
6 TraesCS7D01G328400 chr7B 97.336 3078 52 12 1 3062 435807749 435810812 0.000000e+00 5203.0
7 TraesCS7D01G328400 chr7B 98.273 2142 30 3 3313 5454 435810960 435813094 0.000000e+00 3744.0
8 TraesCS7D01G328400 chr7B 96.477 1788 50 8 5891 7677 435813822 435815597 0.000000e+00 2940.0
9 TraesCS7D01G328400 chr7B 99.083 436 3 1 5458 5893 435813275 435813709 0.000000e+00 782.0
10 TraesCS7D01G328400 chr7B 93.527 448 28 1 7788 8235 435815608 435816054 0.000000e+00 665.0
11 TraesCS7D01G328400 chr7B 99.333 150 1 0 3125 3274 435810811 435810960 1.050000e-68 272.0
12 TraesCS7D01G328400 chr7B 89.157 83 5 4 3029 3108 594954296 594954377 5.260000e-17 100.0
13 TraesCS7D01G328400 chr7B 92.308 65 5 0 8174 8238 181408296 181408232 8.800000e-15 93.5
14 TraesCS7D01G328400 chr7A 91.751 2267 139 18 5449 7708 513219200 513216975 0.000000e+00 3107.0
15 TraesCS7D01G328400 chr7A 92.680 1776 107 9 1287 3047 513222995 513221228 0.000000e+00 2538.0
16 TraesCS7D01G328400 chr7A 94.085 1251 66 3 4208 5456 513220585 513219341 0.000000e+00 1893.0
17 TraesCS7D01G328400 chr7A 91.654 635 25 9 3178 3786 513221212 513220580 0.000000e+00 854.0
18 TraesCS7D01G328400 chr7A 85.971 613 65 14 619 1221 513223575 513222974 3.240000e-178 636.0
19 TraesCS7D01G328400 chr7A 90.710 183 11 4 7996 8173 513216420 513216239 1.070000e-58 239.0
20 TraesCS7D01G328400 chr7A 89.116 147 11 4 7766 7912 513216948 513216807 2.360000e-40 178.0
21 TraesCS7D01G328400 chr7A 93.243 74 5 0 4 77 513223598 513223525 8.740000e-20 110.0
22 TraesCS7D01G328400 chr7A 100.000 34 0 0 7940 7973 513216453 513216420 6.900000e-06 63.9
23 TraesCS7D01G328400 chr5B 96.512 86 3 0 3249 3334 706306879 706306964 8.620000e-30 143.0
24 TraesCS7D01G328400 chr5B 96.512 86 3 0 3249 3334 706306964 706306879 8.620000e-30 143.0
25 TraesCS7D01G328400 chr5B 97.297 74 1 1 1224 1296 109223394 109223321 3.120000e-24 124.0
26 TraesCS7D01G328400 chr1B 95.506 89 4 0 3246 3334 493871877 493871965 8.620000e-30 143.0
27 TraesCS7D01G328400 chr1B 96.512 86 3 0 3249 3334 493871965 493871880 8.620000e-30 143.0
28 TraesCS7D01G328400 chr1B 94.253 87 5 0 3249 3335 296488079 296487993 5.190000e-27 134.0
29 TraesCS7D01G328400 chr1B 98.611 72 1 0 1224 1295 5866000 5866071 2.410000e-25 128.0
30 TraesCS7D01G328400 chr1B 91.667 84 5 2 1208 1291 497844756 497844837 1.880000e-21 115.0
31 TraesCS7D01G328400 chr3A 95.402 87 4 0 3248 3334 593969916 593970002 1.110000e-28 139.0
32 TraesCS7D01G328400 chr3A 84.672 137 15 6 3044 3178 12376030 12375898 1.870000e-26 132.0
33 TraesCS7D01G328400 chr3A 89.888 89 5 3 1208 1295 113584499 113584414 2.430000e-20 111.0
34 TraesCS7D01G328400 chr3A 88.462 78 4 3 3036 3108 131651758 131651835 1.140000e-13 89.8
35 TraesCS7D01G328400 chr4D 95.349 86 4 0 3249 3334 450203706 450203791 4.010000e-28 137.0
36 TraesCS7D01G328400 chr4D 95.890 73 3 0 1224 1296 327574622 327574694 1.450000e-22 119.0
37 TraesCS7D01G328400 chr4D 83.478 115 17 2 3246 3358 494801381 494801267 1.130000e-18 106.0
38 TraesCS7D01G328400 chr6D 93.333 90 6 0 3246 3335 292073369 292073458 5.190000e-27 134.0
39 TraesCS7D01G328400 chr6D 83.478 115 17 2 3246 3358 303549206 303549092 1.130000e-18 106.0
40 TraesCS7D01G328400 chr6D 87.778 90 11 0 3246 3335 333950516 333950605 1.130000e-18 106.0
41 TraesCS7D01G328400 chr6D 84.211 76 7 4 3090 3161 27202898 27202972 1.480000e-07 69.4
42 TraesCS7D01G328400 chr2D 96.250 80 2 1 1223 1301 199141567 199141646 6.710000e-26 130.0
43 TraesCS7D01G328400 chr2D 92.424 66 5 0 8173 8238 62416784 62416719 2.450000e-15 95.3
44 TraesCS7D01G328400 chr3B 95.062 81 4 0 3105 3185 189918626 189918546 2.410000e-25 128.0
45 TraesCS7D01G328400 chr3B 90.278 72 5 2 8164 8235 544545837 544545906 8.800000e-15 93.5
46 TraesCS7D01G328400 chr3B 90.769 65 4 2 3029 3091 44751061 44750997 1.470000e-12 86.1
47 TraesCS7D01G328400 chr5D 96.104 77 3 0 3105 3181 110378840 110378764 8.680000e-25 126.0
48 TraesCS7D01G328400 chr5D 83.478 115 17 2 3246 3358 351412815 351412701 1.130000e-18 106.0
49 TraesCS7D01G328400 chr2B 98.611 72 0 1 1224 1295 699072585 699072515 8.680000e-25 126.0
50 TraesCS7D01G328400 chr2B 91.765 85 7 0 3105 3189 17899904 17899820 1.450000e-22 119.0
51 TraesCS7D01G328400 chr2B 93.846 65 4 0 8174 8238 777651553 777651489 1.890000e-16 99.0
52 TraesCS7D01G328400 chr2B 96.610 59 1 1 3034 3091 197683230 197683288 6.810000e-16 97.1
53 TraesCS7D01G328400 chrUn 91.304 92 7 1 3105 3196 9840442 9840352 3.120000e-24 124.0
54 TraesCS7D01G328400 chrUn 92.537 67 5 0 8172 8238 170188938 170189004 6.810000e-16 97.1
55 TraesCS7D01G328400 chrUn 92.308 65 1 3 3027 3091 92814981 92814921 1.140000e-13 89.8
56 TraesCS7D01G328400 chr6A 95.000 80 2 2 1220 1299 563250024 563250101 3.120000e-24 124.0
57 TraesCS7D01G328400 chr6A 100.000 47 0 0 3045 3091 540126860 540126814 4.100000e-13 87.9
58 TraesCS7D01G328400 chr4B 94.872 78 4 0 3105 3182 552019752 552019829 1.120000e-23 122.0
59 TraesCS7D01G328400 chr4B 86.316 95 9 3 3085 3178 640009068 640009159 5.260000e-17 100.0
60 TraesCS7D01G328400 chr4B 92.424 66 4 1 8174 8238 5820981 5820916 8.800000e-15 93.5
61 TraesCS7D01G328400 chr4B 83.544 79 11 2 3090 3168 111787977 111788053 1.150000e-08 73.1
62 TraesCS7D01G328400 chr3D 87.778 90 11 0 3246 3335 531382394 531382483 1.130000e-18 106.0
63 TraesCS7D01G328400 chr3D 87.912 91 9 2 3246 3335 584272044 584272133 1.130000e-18 106.0
64 TraesCS7D01G328400 chr3D 93.846 65 2 2 3045 3107 590847236 590847172 6.810000e-16 97.1
65 TraesCS7D01G328400 chr3D 89.474 76 5 3 8164 8238 418215933 418216006 8.800000e-15 93.5
66 TraesCS7D01G328400 chr1D 87.778 90 11 0 3246 3335 61734278 61734367 1.130000e-18 106.0
67 TraesCS7D01G328400 chr6B 85.526 76 6 4 3090 3161 49665173 49665247 3.190000e-09 75.0
68 TraesCS7D01G328400 chr6B 88.710 62 5 2 3090 3150 49879485 49879545 3.190000e-09 75.0


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 TraesCS7D01G328400 chr7D 419789865 419798102 8237 False 15213.000000 15213 100.000000 1 8238 1 chr7D.!!$F2 8237
1 TraesCS7D01G328400 chr7B 435807749 435816054 8305 False 2267.666667 5203 97.338167 1 8235 6 chr7B.!!$F2 8234
2 TraesCS7D01G328400 chr7A 513216239 513223598 7359 True 1068.766667 3107 92.134444 4 8173 9 chr7A.!!$R1 8169

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
585 589 2.089980 TCTAGAAGGAGCGGTGTACAC 58.910 52.381 18.01 18.01 0.00 2.90 F
1076 1081 1.196354 CTGCTGCTTGAGAAGTTTCCG 59.804 52.381 0.00 0.00 0.00 4.30 F
2188 2210 1.477553 ATTCATGTGGATGTGTGCCC 58.522 50.000 0.00 0.00 0.00 5.36 F
2790 2823 1.390123 CGAGCAGTTTCATGTACGGTG 59.610 52.381 0.00 0.00 0.00 4.94 F
2950 2984 1.646912 TCCACGGTGGTTTCCTATCA 58.353 50.000 25.53 1.07 39.03 2.15 F
4138 4196 1.503542 GGCACACTTGGAAGATGCG 59.496 57.895 11.59 0.00 40.27 4.73 F
5340 5399 0.179150 GGAGTGCTAGACTGTCGCTG 60.179 60.000 1.52 0.00 33.83 5.18 F
5341 5400 0.179150 GAGTGCTAGACTGTCGCTGG 60.179 60.000 1.52 0.00 33.83 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 2210 1.633561 CTCTCATGCACACACTACCG 58.366 55.000 0.00 0.0 0.00 4.02 R
2759 2792 2.001812 AACTGCTCGTGCTATCACTG 57.998 50.000 11.19 0.0 40.99 3.66 R
3922 3980 1.679032 GCCTCACGCCCTTCATTAGTT 60.679 52.381 0.00 0.0 0.00 2.24 R
4138 4196 3.467803 CCATCGGAATTGGGTAGAACTC 58.532 50.000 0.00 0.0 0.00 3.01 R
4764 4823 5.827797 ACTCTGTAAGAAAACATTTCCAGCA 59.172 36.000 0.00 0.0 46.34 4.41 R
5541 5778 3.679980 AGCAGTCACTTGTACGCAAATAG 59.320 43.478 0.00 0.0 33.73 1.73 R
7136 7492 1.089920 CGGGTTGCATTTCTCCTCAG 58.910 55.000 0.00 0.0 0.00 3.35 R
7318 7674 1.961277 CAGCTCGCCTTTGAACCGT 60.961 57.895 0.00 0.0 0.00 4.83 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
131 135 7.331791 AGTTTATCAGGAGAATGTAAGGACAC 58.668 38.462 0.00 0.00 38.76 3.67
138 142 7.987458 TCAGGAGAATGTAAGGACACATATTTC 59.013 37.037 0.00 0.00 38.19 2.17
387 391 4.612264 TTTAATACGGCTGGGATACTCC 57.388 45.455 0.00 0.00 35.23 3.85
585 589 2.089980 TCTAGAAGGAGCGGTGTACAC 58.910 52.381 18.01 18.01 0.00 2.90
656 660 5.242838 TGTCTTGTTACCTTTATTTGGCTGG 59.757 40.000 0.00 0.00 0.00 4.85
670 674 4.363991 TTGGCTGGCAAAATTTAACCAT 57.636 36.364 14.75 0.00 0.00 3.55
881 886 6.607689 TGTTGTCTTGTTGTGTAGAAAGTTG 58.392 36.000 0.00 0.00 0.00 3.16
985 990 3.664107 CACTCTTGGCTGCTAACTGTTA 58.336 45.455 0.00 0.00 0.00 2.41
1076 1081 1.196354 CTGCTGCTTGAGAAGTTTCCG 59.804 52.381 0.00 0.00 0.00 4.30
1144 1151 1.946768 AGTTAGCAACGCAACACATGT 59.053 42.857 0.00 0.00 36.23 3.21
1183 1197 4.730042 CGCAACACATGTGAATAATAGTGC 59.270 41.667 31.94 21.48 42.32 4.40
1251 1265 4.263018 GCATTCTTTTGCCCTTCTTCTT 57.737 40.909 0.00 0.00 36.60 2.52
1428 1443 7.352079 ACACATTTTCCTCTCTTTCAAACAT 57.648 32.000 0.00 0.00 0.00 2.71
1456 1471 6.238897 CCAACACAAGTTTGTCTGGCTTTATA 60.239 38.462 8.81 0.00 39.91 0.98
1515 1537 2.024414 GTTCTGAGTGTTTTGCCTGGT 58.976 47.619 0.00 0.00 0.00 4.00
1831 1853 9.587772 CTATATCCCGGTTATCAGTGATAAAAG 57.412 37.037 23.88 19.49 36.46 2.27
1997 2019 5.714806 TGTATTGGTCGAGGATAGATATGCA 59.285 40.000 0.00 0.00 0.00 3.96
2188 2210 1.477553 ATTCATGTGGATGTGTGCCC 58.522 50.000 0.00 0.00 0.00 5.36
2291 2317 6.801539 TGCCTGTTTCAAGAGTTATACTTG 57.198 37.500 0.00 0.00 43.92 3.16
2759 2792 4.917415 AGCTGTTCGTTTTTGCAATATGAC 59.083 37.500 0.00 0.00 0.00 3.06
2790 2823 1.390123 CGAGCAGTTTCATGTACGGTG 59.610 52.381 0.00 0.00 0.00 4.94
2842 2875 3.665745 AAGTTTGGCATGCGATTTTCT 57.334 38.095 12.44 2.42 0.00 2.52
2950 2984 1.646912 TCCACGGTGGTTTCCTATCA 58.353 50.000 25.53 1.07 39.03 2.15
3060 3094 6.786461 ACTAAAAGGTACTCCCTCTGTAAACT 59.214 38.462 0.00 0.00 45.47 2.66
3061 3095 7.952368 ACTAAAAGGTACTCCCTCTGTAAACTA 59.048 37.037 0.00 0.00 45.47 2.24
3062 3096 7.622502 AAAAGGTACTCCCTCTGTAAACTAA 57.377 36.000 0.00 0.00 45.47 2.24
3063 3097 7.809880 AAAGGTACTCCCTCTGTAAACTAAT 57.190 36.000 0.00 0.00 45.47 1.73
3064 3098 8.906238 AAAGGTACTCCCTCTGTAAACTAATA 57.094 34.615 0.00 0.00 45.47 0.98
3065 3099 9.503369 AAAGGTACTCCCTCTGTAAACTAATAT 57.497 33.333 0.00 0.00 45.47 1.28
3071 3105 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
3072 3106 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
3073 3107 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
3074 3108 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
3075 3109 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
3090 3124 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
3091 3125 7.627298 AGAGCGTTTAGATCACTAAAGTAGA 57.373 36.000 0.00 0.00 45.42 2.59
3092 3126 7.699566 AGAGCGTTTAGATCACTAAAGTAGAG 58.300 38.462 0.00 0.00 45.42 2.43
3093 3127 6.267070 AGCGTTTAGATCACTAAAGTAGAGC 58.733 40.000 0.00 0.00 45.42 4.09
3094 3128 5.171695 GCGTTTAGATCACTAAAGTAGAGCG 59.828 44.000 0.00 0.00 45.42 5.03
3095 3129 6.256686 CGTTTAGATCACTAAAGTAGAGCGT 58.743 40.000 0.00 0.00 45.42 5.07
3096 3130 6.746364 CGTTTAGATCACTAAAGTAGAGCGTT 59.254 38.462 0.00 0.00 45.42 4.84
3097 3131 7.272948 CGTTTAGATCACTAAAGTAGAGCGTTT 59.727 37.037 0.00 0.00 45.42 3.60
3098 3132 9.565213 GTTTAGATCACTAAAGTAGAGCGTTTA 57.435 33.333 0.00 0.00 45.42 2.01
3099 3133 9.784680 TTTAGATCACTAAAGTAGAGCGTTTAG 57.215 33.333 0.00 0.00 41.71 1.85
3100 3134 7.627298 AGATCACTAAAGTAGAGCGTTTAGA 57.373 36.000 8.46 0.00 38.14 2.10
3101 3135 8.228035 AGATCACTAAAGTAGAGCGTTTAGAT 57.772 34.615 8.46 0.00 38.14 1.98
3102 3136 8.347035 AGATCACTAAAGTAGAGCGTTTAGATC 58.653 37.037 8.46 0.00 38.14 2.75
3103 3137 7.387119 TCACTAAAGTAGAGCGTTTAGATCA 57.613 36.000 8.46 0.00 38.14 2.92
3104 3138 7.997482 TCACTAAAGTAGAGCGTTTAGATCAT 58.003 34.615 8.46 0.00 38.14 2.45
3105 3139 9.117183 TCACTAAAGTAGAGCGTTTAGATCATA 57.883 33.333 8.46 0.00 38.14 2.15
3106 3140 9.731819 CACTAAAGTAGAGCGTTTAGATCATAA 57.268 33.333 8.46 0.00 38.14 1.90
4138 4196 1.503542 GGCACACTTGGAAGATGCG 59.496 57.895 11.59 0.00 40.27 4.73
4142 4200 2.146342 CACACTTGGAAGATGCGAGTT 58.854 47.619 0.00 0.00 29.26 3.01
4143 4201 2.158449 CACACTTGGAAGATGCGAGTTC 59.842 50.000 0.00 0.00 29.26 3.01
4321 4379 3.119173 TGGTTTCCACTTTTTGCAGTCTG 60.119 43.478 0.00 0.00 0.00 3.51
4324 4382 5.393678 GGTTTCCACTTTTTGCAGTCTGTTA 60.394 40.000 0.93 0.00 0.00 2.41
4436 4494 8.647226 GTTATTTGCAATGGTCAATTACTCAAC 58.353 33.333 0.00 0.00 0.00 3.18
4761 4820 3.446873 GTGGGAATGGTGATACAAATGCA 59.553 43.478 0.00 0.00 0.00 3.96
4762 4821 4.081752 GTGGGAATGGTGATACAAATGCAA 60.082 41.667 0.00 0.00 0.00 4.08
4763 4822 4.529769 TGGGAATGGTGATACAAATGCAAA 59.470 37.500 0.00 0.00 0.00 3.68
4764 4823 5.189342 TGGGAATGGTGATACAAATGCAAAT 59.811 36.000 0.00 0.00 0.00 2.32
4765 4824 5.524646 GGGAATGGTGATACAAATGCAAATG 59.475 40.000 0.00 0.00 0.00 2.32
4766 4825 5.006941 GGAATGGTGATACAAATGCAAATGC 59.993 40.000 0.00 0.00 42.50 3.56
4810 4869 5.185056 AGTGTTTGCATTCCAAGTATAACCC 59.815 40.000 0.00 0.00 34.34 4.11
4957 5016 4.376450 GTCTAAAGACGAAACTGCACTG 57.624 45.455 0.00 0.00 35.12 3.66
5340 5399 0.179150 GGAGTGCTAGACTGTCGCTG 60.179 60.000 1.52 0.00 33.83 5.18
5341 5400 0.179150 GAGTGCTAGACTGTCGCTGG 60.179 60.000 1.52 0.00 33.83 4.85
6190 6542 5.411361 CACCGAATCATCCAAGTTTTGACTA 59.589 40.000 0.00 0.00 0.00 2.59
6294 6646 4.761739 TGTCCAGCCTTTGTTTCTAATCTG 59.238 41.667 0.00 0.00 0.00 2.90
6338 6692 8.225777 CCATTTATTCATGTGTGATCAGTATCG 58.774 37.037 0.00 0.00 34.60 2.92
6440 6796 9.511144 CACACGTTTTTAAGTTTTTAAGGAGAT 57.489 29.630 0.00 0.00 30.84 2.75
6754 7110 2.744202 TCTGAAAAGCGGAGATTTCTGC 59.256 45.455 9.01 9.01 45.91 4.26
7069 7425 2.084101 CGCGATTGTGAACGACGGA 61.084 57.895 0.00 0.00 0.00 4.69
7075 7431 0.320073 TTGTGAACGACGGATCCACC 60.320 55.000 13.41 1.11 0.00 4.61
7150 7506 1.139654 CGGATCCTGAGGAGAAATGCA 59.860 52.381 7.50 0.00 34.05 3.96
7277 7633 5.182950 TGATGGTGTTATTTTCTGCACGATT 59.817 36.000 0.00 0.00 32.08 3.34
7318 7674 2.871022 TGTTGCTTACGGTTTTCGCTAA 59.129 40.909 0.00 0.00 43.89 3.09
7399 7775 4.142425 GCTACCTGGTCTAGACAGTAACAC 60.142 50.000 23.91 5.72 34.16 3.32
7400 7776 4.115398 ACCTGGTCTAGACAGTAACACT 57.885 45.455 23.91 0.00 34.16 3.55
7401 7777 5.252586 ACCTGGTCTAGACAGTAACACTA 57.747 43.478 23.91 0.00 34.16 2.74
7402 7778 5.254901 ACCTGGTCTAGACAGTAACACTAG 58.745 45.833 23.91 3.05 36.10 2.57
7403 7779 5.013913 ACCTGGTCTAGACAGTAACACTAGA 59.986 44.000 23.91 0.00 39.78 2.43
7404 7780 6.123651 CCTGGTCTAGACAGTAACACTAGAT 58.876 44.000 23.91 0.00 42.53 1.98
7405 7781 6.603997 CCTGGTCTAGACAGTAACACTAGATT 59.396 42.308 23.91 0.00 42.53 2.40
7406 7782 7.122948 CCTGGTCTAGACAGTAACACTAGATTT 59.877 40.741 23.91 0.00 42.53 2.17
7407 7783 7.827701 TGGTCTAGACAGTAACACTAGATTTG 58.172 38.462 23.91 0.00 42.53 2.32
7408 7784 6.752815 GGTCTAGACAGTAACACTAGATTTGC 59.247 42.308 23.91 0.00 42.53 3.68
7409 7785 7.363094 GGTCTAGACAGTAACACTAGATTTGCT 60.363 40.741 23.91 0.00 42.53 3.91
7410 7786 8.030106 GTCTAGACAGTAACACTAGATTTGCTT 58.970 37.037 18.20 0.00 42.53 3.91
7411 7787 8.029522 TCTAGACAGTAACACTAGATTTGCTTG 58.970 37.037 0.00 0.00 38.02 4.01
7412 7788 6.525629 AGACAGTAACACTAGATTTGCTTGT 58.474 36.000 0.00 0.03 32.68 3.16
7413 7789 7.667557 AGACAGTAACACTAGATTTGCTTGTA 58.332 34.615 0.00 0.00 31.27 2.41
7414 7790 8.314751 AGACAGTAACACTAGATTTGCTTGTAT 58.685 33.333 0.00 0.00 31.27 2.29
7415 7791 9.582431 GACAGTAACACTAGATTTGCTTGTATA 57.418 33.333 0.00 0.00 31.27 1.47
7462 7838 7.849804 TTTGATTAGTAATCTGGTCTTCTGC 57.150 36.000 20.80 0.00 38.72 4.26
7466 7842 4.899352 AGTAATCTGGTCTTCTGCACTT 57.101 40.909 0.00 0.00 0.00 3.16
7469 7845 2.827800 TCTGGTCTTCTGCACTTCTG 57.172 50.000 0.00 0.00 0.00 3.02
7470 7846 1.345741 TCTGGTCTTCTGCACTTCTGG 59.654 52.381 0.00 0.00 0.00 3.86
7486 7862 5.334421 ACTTCTGGTGATGGAGTACTACTT 58.666 41.667 6.66 0.00 0.00 2.24
7487 7863 5.780793 ACTTCTGGTGATGGAGTACTACTTT 59.219 40.000 6.66 0.00 0.00 2.66
7489 7865 5.084519 TCTGGTGATGGAGTACTACTTTGT 58.915 41.667 6.66 0.00 0.00 2.83
7716 8092 6.588348 AACTTAAAAGTTGATGTGCTTTGC 57.412 33.333 7.29 0.00 46.80 3.68
7718 8094 7.038154 ACTTAAAAGTTGATGTGCTTTGCTA 57.962 32.000 0.00 0.00 35.21 3.49
7719 8095 7.488322 ACTTAAAAGTTGATGTGCTTTGCTAA 58.512 30.769 0.00 0.00 35.21 3.09
7720 8096 7.978975 ACTTAAAAGTTGATGTGCTTTGCTAAA 59.021 29.630 0.00 0.00 35.21 1.85
7721 8097 6.833342 AAAAGTTGATGTGCTTTGCTAAAG 57.167 33.333 4.78 4.78 41.46 1.85
7723 8099 5.520376 AGTTGATGTGCTTTGCTAAAGTT 57.480 34.783 9.40 0.00 40.64 2.66
7724 8100 6.633500 AGTTGATGTGCTTTGCTAAAGTTA 57.367 33.333 9.40 0.00 40.64 2.24
7725 8101 6.672147 AGTTGATGTGCTTTGCTAAAGTTAG 58.328 36.000 9.40 0.00 40.64 2.34
7726 8102 5.627499 TGATGTGCTTTGCTAAAGTTAGG 57.373 39.130 9.40 0.00 40.64 2.69
7728 8104 5.181245 TGATGTGCTTTGCTAAAGTTAGGAC 59.819 40.000 9.40 0.00 40.64 3.85
7740 8121 6.711194 GCTAAAGTTAGGACAGAACCTTCTTT 59.289 38.462 3.17 3.17 41.14 2.52
7741 8122 7.228906 GCTAAAGTTAGGACAGAACCTTCTTTT 59.771 37.037 15.93 8.11 40.10 2.27
7742 8123 7.956328 AAAGTTAGGACAGAACCTTCTTTTT 57.044 32.000 0.00 0.00 38.46 1.94
7772 8153 8.990163 TTTTTGATAAACTAGGACAGAACCTT 57.010 30.769 0.00 0.00 41.00 3.50
7773 8154 8.617290 TTTTGATAAACTAGGACAGAACCTTC 57.383 34.615 0.00 0.00 41.00 3.46
7774 8155 7.554959 TTGATAAACTAGGACAGAACCTTCT 57.445 36.000 0.00 0.00 41.00 2.85
7775 8156 7.554959 TGATAAACTAGGACAGAACCTTCTT 57.445 36.000 0.00 0.00 41.00 2.52
7776 8157 7.974504 TGATAAACTAGGACAGAACCTTCTTT 58.025 34.615 0.00 0.00 41.00 2.52
7777 8158 9.096823 TGATAAACTAGGACAGAACCTTCTTTA 57.903 33.333 0.00 0.00 41.00 1.85
7821 8202 1.834188 ACCGTGTGATCCAAATTCCC 58.166 50.000 0.00 0.00 0.00 3.97
7834 8215 1.530323 AATTCCCGTACTGTGTTGGC 58.470 50.000 0.00 0.00 0.00 4.52
7924 8305 5.663158 ATTGCACTTTATACATACCCCCT 57.337 39.130 0.00 0.00 0.00 4.79
7999 8706 7.360113 TGTGTCTTACCATGAGCAGATAATA 57.640 36.000 0.00 0.00 0.00 0.98
8054 8761 7.876068 ACGAGACACCATTAGTTTCATTTTCTA 59.124 33.333 0.00 0.00 0.00 2.10
8088 8795 7.176515 TGCAAAGCTTCATAAACCTCATTAAGA 59.823 33.333 0.00 0.00 0.00 2.10
8101 8808 8.546083 AACCTCATTAAGAGTGAGAGTATCAT 57.454 34.615 6.20 0.00 44.57 2.45
8111 8818 7.398829 AGAGTGAGAGTATCATGGTCGTATAT 58.601 38.462 0.00 0.00 40.92 0.86
8155 8862 6.844696 TGTAAGAACTTGACAGTGAACATC 57.155 37.500 0.00 0.00 31.60 3.06
8216 8923 1.367840 GCTCCACGCCCCTATACAG 59.632 63.158 0.00 0.00 0.00 2.74
8218 8925 0.674534 CTCCACGCCCCTATACAGAC 59.325 60.000 0.00 0.00 0.00 3.51
8224 8931 4.056050 CACGCCCCTATACAGACATTAAC 58.944 47.826 0.00 0.00 0.00 2.01
8226 8933 4.038883 ACGCCCCTATACAGACATTAACTC 59.961 45.833 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 135 4.412207 TCACGACTCACGAGTGAAATATG 58.588 43.478 4.01 4.59 42.66 1.78
138 142 2.096657 AGATCATCACGACTCACGAGTG 59.903 50.000 4.01 0.00 42.66 3.51
193 197 1.068434 CTAGCCAGCTAGCTTCAGGTC 59.932 57.143 16.46 9.79 41.41 3.85
194 198 1.118838 CTAGCCAGCTAGCTTCAGGT 58.881 55.000 16.46 14.65 41.41 4.00
195 199 0.392336 CCTAGCCAGCTAGCTTCAGG 59.608 60.000 16.46 14.96 41.41 3.86
417 421 5.998454 ATCGTTTGATCATAGCCAAGAAG 57.002 39.130 0.00 0.00 0.00 2.85
608 612 7.124298 ACAGCAAGAGTAAATACTGGACAGATA 59.876 37.037 6.29 0.00 36.50 1.98
881 886 9.382244 CAAGTATAAGTAAGAGCAACAAACAAC 57.618 33.333 0.00 0.00 0.00 3.32
985 990 3.718434 TCCATCATTATCTCCACCAAGCT 59.282 43.478 0.00 0.00 0.00 3.74
1076 1081 6.039616 TGCAAGTTTGACAAACCATTTCTAC 58.960 36.000 24.09 8.76 42.34 2.59
1183 1197 7.150640 ACTCTTGTTTACTTAAGGAACTACCG 58.849 38.462 18.73 10.94 44.74 4.02
1274 1288 8.317891 TGTACTTTCTTTTTCTCGAATATGCA 57.682 30.769 0.00 0.00 0.00 3.96
1276 1290 9.708222 CCATGTACTTTCTTTTTCTCGAATATG 57.292 33.333 0.00 0.00 0.00 1.78
1278 1292 9.496873 TTCCATGTACTTTCTTTTTCTCGAATA 57.503 29.630 0.00 0.00 0.00 1.75
1280 1294 7.517734 CGTTCCATGTACTTTCTTTTTCTCGAA 60.518 37.037 0.00 0.00 0.00 3.71
1281 1295 6.073980 CGTTCCATGTACTTTCTTTTTCTCGA 60.074 38.462 0.00 0.00 0.00 4.04
1282 1296 6.071463 CGTTCCATGTACTTTCTTTTTCTCG 58.929 40.000 0.00 0.00 0.00 4.04
1283 1297 6.956047 ACGTTCCATGTACTTTCTTTTTCTC 58.044 36.000 0.00 0.00 0.00 2.87
1284 1298 6.937436 ACGTTCCATGTACTTTCTTTTTCT 57.063 33.333 0.00 0.00 0.00 2.52
1285 1299 6.416750 CCAACGTTCCATGTACTTTCTTTTTC 59.583 38.462 0.00 0.00 0.00 2.29
1286 1300 6.127563 ACCAACGTTCCATGTACTTTCTTTTT 60.128 34.615 0.00 0.00 0.00 1.94
1287 1301 5.358725 ACCAACGTTCCATGTACTTTCTTTT 59.641 36.000 0.00 0.00 0.00 2.27
1288 1302 4.885325 ACCAACGTTCCATGTACTTTCTTT 59.115 37.500 0.00 0.00 0.00 2.52
1289 1303 4.274950 CACCAACGTTCCATGTACTTTCTT 59.725 41.667 0.00 0.00 0.00 2.52
1290 1304 3.813166 CACCAACGTTCCATGTACTTTCT 59.187 43.478 0.00 0.00 0.00 2.52
1291 1305 3.608474 GCACCAACGTTCCATGTACTTTC 60.608 47.826 0.00 0.00 0.00 2.62
1428 1443 3.129638 GCCAGACAAACTTGTGTTGGTTA 59.870 43.478 17.50 0.00 40.20 2.85
1515 1537 6.829811 TCCTGAAATCTGCACATATCATCAAA 59.170 34.615 0.00 0.00 0.00 2.69
1831 1853 4.137543 CCTATCCAAATACCAGCAAGGAC 58.862 47.826 1.83 0.00 41.22 3.85
1997 2019 4.137116 TGACAGATACCGCTTTGCTATT 57.863 40.909 0.00 0.00 0.00 1.73
2164 2186 5.477510 GGCACACATCCACATGAATAAAAA 58.522 37.500 0.00 0.00 33.72 1.94
2188 2210 1.633561 CTCTCATGCACACACTACCG 58.366 55.000 0.00 0.00 0.00 4.02
2367 2393 7.278875 TGGGAACTGCAAATTACAGAAAATTT 58.721 30.769 13.73 0.00 39.14 1.82
2759 2792 2.001812 AACTGCTCGTGCTATCACTG 57.998 50.000 11.19 0.00 40.99 3.66
2842 2875 3.547746 GCCCCCATCGACAAAGTTAATA 58.452 45.455 0.00 0.00 0.00 0.98
2950 2984 3.058224 GCGCCAAGTAGAATTTTCACACT 60.058 43.478 0.00 0.00 0.00 3.55
3064 3098 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
3065 3099 9.170734 TCTACTTTAGTGATCTAAACGCTCTTA 57.829 33.333 0.00 0.00 40.05 2.10
3066 3100 8.053026 TCTACTTTAGTGATCTAAACGCTCTT 57.947 34.615 0.00 0.00 40.05 2.85
3067 3101 7.627298 TCTACTTTAGTGATCTAAACGCTCT 57.373 36.000 0.00 0.00 40.05 4.09
3068 3102 6.415573 GCTCTACTTTAGTGATCTAAACGCTC 59.584 42.308 0.00 0.00 40.05 5.03
3069 3103 6.267070 GCTCTACTTTAGTGATCTAAACGCT 58.733 40.000 0.00 0.00 40.05 5.07
3070 3104 5.171695 CGCTCTACTTTAGTGATCTAAACGC 59.828 44.000 0.00 0.00 40.05 4.84
3071 3105 6.256686 ACGCTCTACTTTAGTGATCTAAACG 58.743 40.000 0.00 0.00 40.05 3.60
3072 3106 8.463456 AAACGCTCTACTTTAGTGATCTAAAC 57.537 34.615 0.00 0.00 40.05 2.01
3073 3107 9.784680 CTAAACGCTCTACTTTAGTGATCTAAA 57.215 33.333 0.00 0.00 41.87 1.85
3074 3108 9.170734 TCTAAACGCTCTACTTTAGTGATCTAA 57.829 33.333 0.00 0.00 33.44 2.10
3075 3109 8.728337 TCTAAACGCTCTACTTTAGTGATCTA 57.272 34.615 0.00 0.00 33.44 1.98
3076 3110 7.627298 TCTAAACGCTCTACTTTAGTGATCT 57.373 36.000 0.00 0.00 33.44 2.75
3077 3111 8.129840 TGATCTAAACGCTCTACTTTAGTGATC 58.870 37.037 0.00 0.00 33.44 2.92
3078 3112 7.997482 TGATCTAAACGCTCTACTTTAGTGAT 58.003 34.615 0.00 0.00 33.44 3.06
3079 3113 7.387119 TGATCTAAACGCTCTACTTTAGTGA 57.613 36.000 0.00 0.00 33.44 3.41
3080 3114 9.731819 TTATGATCTAAACGCTCTACTTTAGTG 57.268 33.333 0.00 0.00 33.44 2.74
3155 3189 8.544687 AACTACTCCCTCCGTAAACTAATATT 57.455 34.615 0.00 0.00 0.00 1.28
3304 3351 4.178540 TCCGATCCAAAATAAGTGTCGTC 58.821 43.478 0.00 0.00 0.00 4.20
3922 3980 1.679032 GCCTCACGCCCTTCATTAGTT 60.679 52.381 0.00 0.00 0.00 2.24
4029 4087 6.933521 ACATTTGCAGCATTATTTACAACCAA 59.066 30.769 0.00 0.00 0.00 3.67
4138 4196 3.467803 CCATCGGAATTGGGTAGAACTC 58.532 50.000 0.00 0.00 0.00 3.01
4417 4475 6.215845 ACAAAGTTGAGTAATTGACCATTGC 58.784 36.000 0.00 0.00 0.00 3.56
4761 4820 7.725251 TCTGTAAGAAAACATTTCCAGCATTT 58.275 30.769 0.00 0.00 42.31 2.32
4762 4821 7.014615 ACTCTGTAAGAAAACATTTCCAGCATT 59.985 33.333 0.00 0.00 46.34 3.56
4763 4822 6.491403 ACTCTGTAAGAAAACATTTCCAGCAT 59.509 34.615 0.00 0.00 46.34 3.79
4764 4823 5.827797 ACTCTGTAAGAAAACATTTCCAGCA 59.172 36.000 0.00 0.00 46.34 4.41
4765 4824 6.145535 CACTCTGTAAGAAAACATTTCCAGC 58.854 40.000 0.00 0.00 46.34 4.85
4766 4825 7.264373 ACACTCTGTAAGAAAACATTTCCAG 57.736 36.000 0.00 1.48 46.34 3.86
5541 5778 3.679980 AGCAGTCACTTGTACGCAAATAG 59.320 43.478 0.00 0.00 33.73 1.73
6294 6646 2.368439 TGGGCAATACTTCAGATGCAC 58.632 47.619 0.00 0.00 42.47 4.57
6440 6796 5.562298 AGTTGCTACCTTAAAGTTCAGGA 57.438 39.130 7.86 0.00 33.90 3.86
6445 6801 7.926018 CCATCAAAAAGTTGCTACCTTAAAGTT 59.074 33.333 0.00 0.00 34.50 2.66
6754 7110 1.134965 CAGGTAAGAAGCTCCTCACCG 60.135 57.143 0.00 0.00 0.00 4.94
6995 7351 2.865119 TCCATCTTCTTTCTGCAGCA 57.135 45.000 9.47 0.00 0.00 4.41
7069 7425 1.519719 GAAGCTGAGCGAGGTGGAT 59.480 57.895 0.00 0.00 30.84 3.41
7075 7431 3.184683 GCACCGAAGCTGAGCGAG 61.185 66.667 0.00 0.00 0.00 5.03
7136 7492 1.089920 CGGGTTGCATTTCTCCTCAG 58.910 55.000 0.00 0.00 0.00 3.35
7318 7674 1.961277 CAGCTCGCCTTTGAACCGT 60.961 57.895 0.00 0.00 0.00 4.83
7356 7712 9.322773 AGGTAGCAATATATCATCATTCAATCG 57.677 33.333 0.00 0.00 0.00 3.34
7417 7793 6.767423 TCAAATCACACCATCACCTATATGTG 59.233 38.462 1.97 1.97 36.13 3.21
7418 7794 6.899089 TCAAATCACACCATCACCTATATGT 58.101 36.000 0.00 0.00 0.00 2.29
7428 7804 8.562892 CCAGATTACTAATCAAATCACACCATC 58.437 37.037 10.76 0.00 40.42 3.51
7466 7842 5.047306 CACAAAGTAGTACTCCATCACCAGA 60.047 44.000 2.58 0.00 0.00 3.86
7469 7845 3.933332 GCACAAAGTAGTACTCCATCACC 59.067 47.826 2.58 0.00 0.00 4.02
7470 7846 4.566004 TGCACAAAGTAGTACTCCATCAC 58.434 43.478 2.58 0.00 0.00 3.06
7472 7848 3.619038 GCTGCACAAAGTAGTACTCCATC 59.381 47.826 2.58 0.00 31.85 3.51
7475 7851 2.347731 GGCTGCACAAAGTAGTACTCC 58.652 52.381 2.58 0.00 31.85 3.85
7476 7852 2.289444 TGGGCTGCACAAAGTAGTACTC 60.289 50.000 0.00 0.00 31.85 2.59
7477 7853 1.697432 TGGGCTGCACAAAGTAGTACT 59.303 47.619 0.00 0.00 31.85 2.73
7478 7854 2.076863 CTGGGCTGCACAAAGTAGTAC 58.923 52.381 5.89 0.00 31.85 2.73
7479 7855 1.697432 ACTGGGCTGCACAAAGTAGTA 59.303 47.619 5.89 0.00 31.85 1.82
7480 7856 0.474184 ACTGGGCTGCACAAAGTAGT 59.526 50.000 5.89 0.00 31.85 2.73
7481 7857 1.160137 GACTGGGCTGCACAAAGTAG 58.840 55.000 5.89 0.00 0.00 2.57
7484 7860 1.228367 AGGACTGGGCTGCACAAAG 60.228 57.895 5.89 0.00 0.00 2.77
7486 7862 1.708993 AAGAGGACTGGGCTGCACAA 61.709 55.000 5.89 0.00 0.00 3.33
7487 7863 1.708993 AAAGAGGACTGGGCTGCACA 61.709 55.000 3.77 3.77 0.00 4.57
7489 7865 1.073722 CAAAGAGGACTGGGCTGCA 59.926 57.895 0.50 0.00 0.00 4.41
7698 8074 6.340522 ACTTTAGCAAAGCACATCAACTTTT 58.659 32.000 8.09 0.00 42.27 2.27
7708 8084 4.755123 TCTGTCCTAACTTTAGCAAAGCAC 59.245 41.667 8.09 1.18 42.27 4.40
7710 8086 5.334957 GGTTCTGTCCTAACTTTAGCAAAGC 60.335 44.000 8.09 0.00 42.27 3.51
7711 8087 5.998363 AGGTTCTGTCCTAACTTTAGCAAAG 59.002 40.000 6.98 6.98 39.04 2.77
7712 8088 5.937111 AGGTTCTGTCCTAACTTTAGCAAA 58.063 37.500 0.00 0.00 35.87 3.68
7713 8089 5.562298 AGGTTCTGTCCTAACTTTAGCAA 57.438 39.130 0.00 0.00 35.87 3.91
7714 8090 5.307196 AGAAGGTTCTGTCCTAACTTTAGCA 59.693 40.000 0.00 0.00 36.74 3.49
7715 8091 5.795972 AGAAGGTTCTGTCCTAACTTTAGC 58.204 41.667 0.00 0.00 36.74 3.09
7716 8092 8.678593 AAAAGAAGGTTCTGTCCTAACTTTAG 57.321 34.615 16.68 0.00 40.10 1.85
7718 8094 7.956328 AAAAAGAAGGTTCTGTCCTAACTTT 57.044 32.000 0.00 0.00 41.29 2.66
7747 8128 8.990163 AAGGTTCTGTCCTAGTTTATCAAAAA 57.010 30.769 0.00 0.00 36.74 1.94
7748 8129 8.437575 AGAAGGTTCTGTCCTAGTTTATCAAAA 58.562 33.333 0.00 0.00 36.74 2.44
7749 8130 7.974504 AGAAGGTTCTGTCCTAGTTTATCAAA 58.025 34.615 0.00 0.00 36.74 2.69
7750 8131 7.554959 AGAAGGTTCTGTCCTAGTTTATCAA 57.445 36.000 0.00 0.00 36.74 2.57
7751 8132 7.554959 AAGAAGGTTCTGTCCTAGTTTATCA 57.445 36.000 0.00 0.00 37.65 2.15
7804 8185 1.448985 ACGGGAATTTGGATCACACG 58.551 50.000 0.00 0.00 0.00 4.49
7821 8202 1.458064 CGTAAAGGCCAACACAGTACG 59.542 52.381 5.01 4.07 0.00 3.67
7907 8288 4.688874 GCTGCAAGGGGGTATGTATAAAGT 60.689 45.833 0.00 0.00 0.00 2.66
7924 8305 2.266554 CAAAAGTTCAAACGGCTGCAA 58.733 42.857 0.50 0.00 0.00 4.08
7983 8690 4.763793 GCCAACATATTATCTGCTCATGGT 59.236 41.667 0.00 0.00 0.00 3.55
7990 8697 4.144297 TCCCAAGCCAACATATTATCTGC 58.856 43.478 0.00 0.00 0.00 4.26
7999 8706 2.564062 CAAGTTCATCCCAAGCCAACAT 59.436 45.455 0.00 0.00 0.00 2.71
8054 8761 6.372381 GGTTTATGAAGCTTTGCATTCCAAAT 59.628 34.615 0.00 0.00 42.22 2.32
8088 8795 7.168905 TCATATACGACCATGATACTCTCACT 58.831 38.462 0.00 0.00 36.48 3.41
8131 8838 6.992123 TGATGTTCACTGTCAAGTTCTTACAT 59.008 34.615 0.00 0.00 32.98 2.29
8155 8862 4.154918 GCTTCCGAAGATATGGGCTTAATG 59.845 45.833 12.54 0.00 0.00 1.90
8205 8912 4.347000 TGGAGTTAATGTCTGTATAGGGGC 59.653 45.833 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.