Multiple sequence alignment - TraesCS6B01G260400

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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 TraesCS6B01G260400 chr6B 100.000 4830 0 0 1 4830 470821368 470826197 0.000000e+00 8920.0
1 TraesCS6B01G260400 chr6D 92.305 2469 147 13 753 3198 305740401 305737953 0.000000e+00 3467.0
2 TraesCS6B01G260400 chr6D 93.581 701 35 3 68 766 305741125 305740433 0.000000e+00 1037.0
3 TraesCS6B01G260400 chr6D 92.491 586 29 8 3355 3925 305737947 305737362 0.000000e+00 824.0
4 TraesCS6B01G260400 chr6D 93.241 503 24 5 4331 4830 305736584 305736089 0.000000e+00 732.0
5 TraesCS6B01G260400 chr6D 91.646 395 25 6 3921 4313 305737052 305736664 1.530000e-149 540.0
6 TraesCS6B01G260400 chr6A 91.740 2034 135 12 1191 3198 440260972 440258946 0.000000e+00 2795.0
7 TraesCS6B01G260400 chr6A 93.750 1216 66 6 95 1306 440262126 440260917 0.000000e+00 1816.0
8 TraesCS6B01G260400 chr6A 88.187 855 69 17 1270 2101 447629532 447628687 0.000000e+00 990.0
9 TraesCS6B01G260400 chr6A 88.499 713 60 11 2503 3198 447627847 447627140 0.000000e+00 843.0
10 TraesCS6B01G260400 chr6A 88.907 613 28 19 3921 4528 440257879 440257302 0.000000e+00 719.0
11 TraesCS6B01G260400 chr6A 94.930 355 18 0 3571 3925 440258538 440258184 1.520000e-154 556.0
12 TraesCS6B01G260400 chr6A 90.909 308 15 8 4524 4830 440256227 440255932 7.530000e-108 401.0
13 TraesCS6B01G260400 chr6A 97.222 180 5 0 3354 3533 440258944 440258765 6.070000e-79 305.0
14 TraesCS6B01G260400 chr6A 87.687 268 25 3 3608 3874 447622641 447622381 6.070000e-79 305.0
15 TraesCS6B01G260400 chr6A 100.000 48 0 0 7 54 440262462 440262415 6.660000e-14 89.8
16 TraesCS6B01G260400 chr5A 94.937 158 7 1 3195 3352 320214243 320214399 3.730000e-61 246.0
17 TraesCS6B01G260400 chr5A 89.773 176 16 2 3195 3369 558675659 558675485 1.750000e-54 224.0
18 TraesCS6B01G260400 chr7A 92.771 166 11 1 3193 3358 494786993 494786829 6.250000e-59 239.0
19 TraesCS6B01G260400 chr7A 92.262 168 12 1 3195 3362 498937205 498937371 2.250000e-58 237.0
20 TraesCS6B01G260400 chr2B 94.194 155 9 0 3195 3349 361574994 361574840 2.250000e-58 237.0
21 TraesCS6B01G260400 chr7B 91.716 169 11 2 3192 3358 12186448 12186615 1.050000e-56 231.0
22 TraesCS6B01G260400 chr7B 90.698 172 15 1 3193 3364 176002828 176002998 1.350000e-55 228.0
23 TraesCS6B01G260400 chr7B 89.888 178 13 5 3193 3369 490208154 490207981 1.750000e-54 224.0
24 TraesCS6B01G260400 chr7D 91.124 169 14 1 3194 3362 183790425 183790258 1.350000e-55 228.0


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 TraesCS6B01G260400 chr6B 470821368 470826197 4829 False 8920.000000 8920 100.000000 1 4830 1 chr6B.!!$F1 4829
1 TraesCS6B01G260400 chr6D 305736089 305741125 5036 True 1320.000000 3467 92.652800 68 4830 5 chr6D.!!$R1 4762
2 TraesCS6B01G260400 chr6A 440255932 440262462 6530 True 954.542857 2795 93.922571 7 4830 7 chr6A.!!$R2 4823
3 TraesCS6B01G260400 chr6A 447627140 447629532 2392 True 916.500000 990 88.343000 1270 3198 2 chr6A.!!$R3 1928

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
190 440 0.343372 AGGATGCCCCCTTCTCTACA 59.657 55.0 0.0 0.0 30.99 2.74 F
1770 2129 0.746923 GGGGTTATGAGGACCGTTGC 60.747 60.0 0.0 0.0 38.08 4.17 F
2938 3784 0.395312 TTCAAACTCGGGTCCTCACC 59.605 55.0 0.0 0.0 42.90 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 2338 0.106268 TGGCTTTCCACCTTGCTTGA 60.106 50.0 0.00 0.00 37.47 3.02 R
3385 4237 0.818040 GTTTGGCACTTGACCGGTCT 60.818 55.0 33.39 12.78 0.00 3.85 R
4568 7075 0.543410 TTCCAGCCTGTAACCGAGGA 60.543 55.0 0.00 0.00 31.48 3.71 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
54 55 2.158971 GGCCCTTGAAACTCAGCAAAAA 60.159 45.455 0.00 0.00 0.00 1.94
139 388 1.841663 CTTCACACGCTTCCCCAACG 61.842 60.000 0.00 0.00 0.00 4.10
170 419 1.393539 CAACTGCGAATACGGTTCCAG 59.606 52.381 14.03 14.03 40.15 3.86
180 430 2.597903 GGTTCCAGAGGATGCCCC 59.402 66.667 0.00 0.00 0.00 5.80
190 440 0.343372 AGGATGCCCCCTTCTCTACA 59.657 55.000 0.00 0.00 30.99 2.74
227 477 3.006537 ACGAAGTCGAATCTGGGAAAGAA 59.993 43.478 7.87 0.00 29.74 2.52
270 520 2.029666 CGGAGGGTCGGCATGATC 59.970 66.667 0.00 0.00 0.00 2.92
314 564 5.799213 ACCACAAGAATTTTGGTTTGTTGA 58.201 33.333 0.00 0.00 40.98 3.18
393 643 1.135402 GCAATTTACTCAAGGGCACGG 60.135 52.381 0.00 0.00 0.00 4.94
445 695 2.168313 GGGTATGGGCACATTTTCTTGG 59.832 50.000 6.84 0.00 38.53 3.61
451 701 1.275856 GGCACATTTTCTTGGCCATGA 59.724 47.619 17.00 17.00 44.01 3.07
467 717 3.508840 GAGCGATGCCCAAACCCG 61.509 66.667 0.00 0.00 0.00 5.28
470 720 3.131478 CGATGCCCAAACCCGACC 61.131 66.667 0.00 0.00 0.00 4.79
484 734 0.750546 CCGACCCGACTAGTCATGGA 60.751 60.000 26.99 0.00 33.70 3.41
536 786 5.642063 TCGCACAAAAGTTATAAGCTAGCTT 59.358 36.000 31.38 31.38 39.83 3.74
592 844 7.172532 ACACAAACAACGTCATGAATATAGTGT 59.827 33.333 0.00 3.01 0.00 3.55
666 918 7.068470 TGCATATTCTCTATTTCATTTGGCACA 59.932 33.333 0.00 0.00 0.00 4.57
695 947 7.410800 TGTTTACGTTGGTTATAGAACTGTG 57.589 36.000 0.00 0.00 35.74 3.66
935 1234 2.646121 GCAAGTGCAAGGGCTAGTT 58.354 52.632 0.00 0.00 41.91 2.24
936 1235 0.961753 GCAAGTGCAAGGGCTAGTTT 59.038 50.000 0.00 0.00 41.91 2.66
977 1276 2.046023 CTGCCTGATTGCCACGGA 60.046 61.111 0.00 0.00 0.00 4.69
1110 1409 2.329267 TCAGGAACATCCCGCTATCAT 58.671 47.619 0.00 0.00 37.19 2.45
1202 1501 0.884704 AATGCGCGGGTGGTATCATC 60.885 55.000 8.83 0.00 0.00 2.92
1204 1503 1.522806 GCGCGGGTGGTATCATCAA 60.523 57.895 8.83 0.00 0.00 2.57
1219 1518 3.200483 TCATCAACAGCGGATGATTCAG 58.800 45.455 6.87 0.00 44.51 3.02
1299 1598 4.081420 TCAAGCAGTCTAGATCCCAGAAAC 60.081 45.833 0.00 0.00 0.00 2.78
1359 1718 4.796606 ACCATATGAAGCAGCTAACCAAT 58.203 39.130 3.65 0.00 0.00 3.16
1371 1730 2.027192 GCTAACCAATGTCTCCACTGGA 60.027 50.000 0.00 0.00 32.97 3.86
1506 1865 2.750888 GGTTCGCAGAATGGACGCC 61.751 63.158 0.00 0.00 45.90 5.68
1554 1913 1.153429 GGACATACCGTGTGGGCTC 60.153 63.158 0.00 0.00 42.36 4.70
1626 1985 6.542821 TGGTAACTTCTGGATTGATCTTGTT 58.457 36.000 0.00 0.00 37.61 2.83
1715 2074 1.172812 AAACTTGCTCAAGGTCCGGC 61.173 55.000 13.48 0.00 42.53 6.13
1764 2123 0.846693 ATGGCTGGGGTTATGAGGAC 59.153 55.000 0.00 0.00 0.00 3.85
1770 2129 0.746923 GGGGTTATGAGGACCGTTGC 60.747 60.000 0.00 0.00 38.08 4.17
1774 2133 0.912487 TTATGAGGACCGTTGCCCCT 60.912 55.000 0.00 0.00 0.00 4.79
1778 2137 1.833787 GAGGACCGTTGCCCCTACAA 61.834 60.000 0.00 0.00 0.00 2.41
1779 2138 1.205460 AGGACCGTTGCCCCTACAAT 61.205 55.000 0.00 0.00 0.00 2.71
1840 2203 9.262358 AGCTTATTAGTTGCTTATTACAGTAGC 57.738 33.333 0.00 0.00 32.61 3.58
1873 2236 5.073311 GTGCCTCACACTACTTATCTTGA 57.927 43.478 0.00 0.00 46.41 3.02
1874 2237 5.479306 GTGCCTCACACTACTTATCTTGAA 58.521 41.667 0.00 0.00 46.41 2.69
1875 2238 5.578727 GTGCCTCACACTACTTATCTTGAAG 59.421 44.000 0.00 0.00 46.41 3.02
1876 2239 5.246203 TGCCTCACACTACTTATCTTGAAGT 59.754 40.000 0.00 0.00 42.35 3.01
1907 2279 3.564644 CAGTGGATGATTTGGAGAGATGC 59.435 47.826 0.00 0.00 0.00 3.91
1942 2326 3.246226 GGCAGCATAATGAACTCTACACG 59.754 47.826 0.00 0.00 0.00 4.49
1954 2338 1.880675 CTCTACACGTCACACTGGTCT 59.119 52.381 0.00 0.00 0.00 3.85
1993 2377 6.633856 AGCCAAGCACATATTTTCCTTTTAG 58.366 36.000 0.00 0.00 0.00 1.85
2000 2384 4.405680 ACATATTTTCCTTTTAGGCAGGGC 59.594 41.667 0.00 0.00 34.61 5.19
2029 2413 3.057174 GCTATCACAACTCTCCGGATAGG 60.057 52.174 19.95 9.02 38.43 2.57
2101 2888 4.372656 GCATACAGAGCGGTAATCTTCTT 58.627 43.478 0.00 0.00 0.00 2.52
2122 2909 6.356556 TCTTCCGTGTGGATCATGAAATAAT 58.643 36.000 0.00 0.00 45.91 1.28
2125 2912 4.977963 CCGTGTGGATCATGAAATAATTGC 59.022 41.667 0.00 0.00 37.49 3.56
2126 2913 5.450274 CCGTGTGGATCATGAAATAATTGCA 60.450 40.000 0.00 0.00 37.49 4.08
2128 2915 6.698329 CGTGTGGATCATGAAATAATTGCAAT 59.302 34.615 5.99 5.99 35.23 3.56
2151 2939 5.437289 TGTTGCTCAAATCCTTACAGTTG 57.563 39.130 0.00 0.00 0.00 3.16
2154 2942 4.724399 TGCTCAAATCCTTACAGTTGGAA 58.276 39.130 0.00 0.00 35.81 3.53
2201 2989 1.886542 GGTTTGGCACTCAAGTAAGGG 59.113 52.381 0.00 0.00 36.62 3.95
2205 2993 3.306472 TGGCACTCAAGTAAGGGTTTT 57.694 42.857 0.00 0.00 0.00 2.43
2225 3013 2.462456 TGGTGACTTCAAGCTAGCAG 57.538 50.000 18.83 9.26 0.00 4.24
2290 3078 3.442977 ACAGCTTGGATCTTGAAATGCTC 59.557 43.478 0.00 0.00 0.00 4.26
2310 3098 4.125703 CTCAAGTCATCACCTATTCCAGC 58.874 47.826 0.00 0.00 0.00 4.85
2383 3171 0.597637 AGCGTAGAATGGCGATTCGG 60.598 55.000 14.76 9.93 42.61 4.30
2404 3192 2.802816 GAGGACGTGGATGCAATATGAC 59.197 50.000 0.00 0.00 0.00 3.06
2444 3232 0.513820 TGCGGTCCGATTTTTCGTTC 59.486 50.000 17.49 0.00 0.00 3.95
2456 3244 3.612472 TTTTCGTTCGCCTGGTAAAAG 57.388 42.857 0.00 0.00 0.00 2.27
2461 3249 2.665052 CGTTCGCCTGGTAAAAGACTAC 59.335 50.000 0.00 0.00 0.00 2.73
2534 3372 7.101054 ACTGCTTCCGTTTACATATTAAGACA 58.899 34.615 0.00 0.00 0.00 3.41
2656 3497 1.398692 TTCAGGTGTTGCCCTTTGTC 58.601 50.000 0.00 0.00 38.26 3.18
2671 3512 3.865745 CCTTTGTCGATTACTACAGCCTG 59.134 47.826 0.00 0.00 0.00 4.85
2713 3555 5.500234 GCAATATGCATCTATGGGGTAGAA 58.500 41.667 0.19 0.00 44.26 2.10
2883 3729 3.830755 TCTACTCCTCGGTAAAACAGCTT 59.169 43.478 0.00 0.00 0.00 3.74
2923 3769 3.561310 GCTCTATGGTCGCATCAATTCAA 59.439 43.478 0.00 0.00 0.00 2.69
2938 3784 0.395312 TTCAAACTCGGGTCCTCACC 59.605 55.000 0.00 0.00 42.90 4.02
2970 3816 1.633432 AGCAAGTGGTACATAAGCCCA 59.367 47.619 0.00 0.00 44.52 5.36
2990 3836 3.181454 CCAGAGGTAATGTCCCCACATAC 60.181 52.174 0.00 0.00 42.89 2.39
2998 3844 2.870175 TGTCCCCACATACAAAGGTTG 58.130 47.619 0.00 0.00 0.00 3.77
3010 3856 2.703007 ACAAAGGTTGGCTGCCATAAAA 59.297 40.909 24.03 4.08 31.53 1.52
3191 4043 5.127194 CAGAAGTGTAACCTATGGCTCTGTA 59.873 44.000 0.00 0.00 37.80 2.74
3198 4050 8.804204 GTGTAACCTATGGCTCTGTAATATACT 58.196 37.037 0.00 0.00 0.00 2.12
3199 4051 9.021807 TGTAACCTATGGCTCTGTAATATACTC 57.978 37.037 0.00 0.00 0.00 2.59
3200 4052 7.483580 AACCTATGGCTCTGTAATATACTCC 57.516 40.000 0.00 0.00 0.00 3.85
3201 4053 5.958987 ACCTATGGCTCTGTAATATACTCCC 59.041 44.000 0.00 0.00 0.00 4.30
3202 4054 6.198639 CCTATGGCTCTGTAATATACTCCCT 58.801 44.000 0.00 0.00 0.00 4.20
3203 4055 6.322712 CCTATGGCTCTGTAATATACTCCCTC 59.677 46.154 0.00 0.00 0.00 4.30
3204 4056 4.417437 TGGCTCTGTAATATACTCCCTCC 58.583 47.826 0.00 0.00 0.00 4.30
3205 4057 3.444388 GGCTCTGTAATATACTCCCTCCG 59.556 52.174 0.00 0.00 0.00 4.63
3206 4058 4.080687 GCTCTGTAATATACTCCCTCCGT 58.919 47.826 0.00 0.00 0.00 4.69
3207 4059 4.523558 GCTCTGTAATATACTCCCTCCGTT 59.476 45.833 0.00 0.00 0.00 4.44
3208 4060 5.335819 GCTCTGTAATATACTCCCTCCGTTC 60.336 48.000 0.00 0.00 0.00 3.95
3209 4061 5.075493 TCTGTAATATACTCCCTCCGTTCC 58.925 45.833 0.00 0.00 0.00 3.62
3210 4062 5.070823 TGTAATATACTCCCTCCGTTCCT 57.929 43.478 0.00 0.00 0.00 3.36
3211 4063 6.044754 TCTGTAATATACTCCCTCCGTTCCTA 59.955 42.308 0.00 0.00 0.00 2.94
3212 4064 6.613699 TGTAATATACTCCCTCCGTTCCTAA 58.386 40.000 0.00 0.00 0.00 2.69
3213 4065 7.068702 TGTAATATACTCCCTCCGTTCCTAAA 58.931 38.462 0.00 0.00 0.00 1.85
3214 4066 7.731688 TGTAATATACTCCCTCCGTTCCTAAAT 59.268 37.037 0.00 0.00 0.00 1.40
3215 4067 9.247861 GTAATATACTCCCTCCGTTCCTAAATA 57.752 37.037 0.00 0.00 0.00 1.40
3216 4068 8.912614 AATATACTCCCTCCGTTCCTAAATAT 57.087 34.615 0.00 0.00 0.00 1.28
3219 4071 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3220 4072 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3221 4073 6.614496 ACTCCCTCCGTTCCTAAATATAAGTT 59.386 38.462 0.00 0.00 0.00 2.66
3222 4074 7.126879 ACTCCCTCCGTTCCTAAATATAAGTTT 59.873 37.037 0.00 0.00 0.00 2.66
3223 4075 7.864770 TCCCTCCGTTCCTAAATATAAGTTTT 58.135 34.615 0.00 0.00 0.00 2.43
3224 4076 8.330993 TCCCTCCGTTCCTAAATATAAGTTTTT 58.669 33.333 0.00 0.00 0.00 1.94
3254 4106 9.179909 AGAGATTCCAATATAGACTACATACGG 57.820 37.037 0.00 0.00 0.00 4.02
3255 4107 9.175312 GAGATTCCAATATAGACTACATACGGA 57.825 37.037 0.00 0.00 0.00 4.69
3256 4108 9.179909 AGATTCCAATATAGACTACATACGGAG 57.820 37.037 0.00 0.00 0.00 4.63
3257 4109 6.754702 TCCAATATAGACTACATACGGAGC 57.245 41.667 0.00 0.00 0.00 4.70
3258 4110 6.243148 TCCAATATAGACTACATACGGAGCA 58.757 40.000 0.00 0.00 0.00 4.26
3259 4111 6.717997 TCCAATATAGACTACATACGGAGCAA 59.282 38.462 0.00 0.00 0.00 3.91
3260 4112 7.231925 TCCAATATAGACTACATACGGAGCAAA 59.768 37.037 0.00 0.00 0.00 3.68
3261 4113 7.870954 CCAATATAGACTACATACGGAGCAAAA 59.129 37.037 0.00 0.00 0.00 2.44
3262 4114 9.424319 CAATATAGACTACATACGGAGCAAAAT 57.576 33.333 0.00 0.00 0.00 1.82
3263 4115 8.988064 ATATAGACTACATACGGAGCAAAATG 57.012 34.615 0.00 0.00 0.00 2.32
3264 4116 5.339008 AGACTACATACGGAGCAAAATGA 57.661 39.130 0.00 0.00 0.00 2.57
3265 4117 5.352284 AGACTACATACGGAGCAAAATGAG 58.648 41.667 0.00 0.00 0.00 2.90
3266 4118 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3267 4119 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3268 4120 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3269 4121 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3270 4122 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3271 4123 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3272 4124 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3273 4125 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3274 4126 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3275 4127 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3276 4128 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3290 4142 9.030452 AGTGAATCTACACTCTGAAATAAGTCT 57.970 33.333 0.00 0.00 46.36 3.24
3299 4151 9.593134 ACACTCTGAAATAAGTCTACATTCATC 57.407 33.333 0.00 0.00 30.39 2.92
3300 4152 9.039870 CACTCTGAAATAAGTCTACATTCATCC 57.960 37.037 0.00 0.00 30.39 3.51
3301 4153 7.923344 ACTCTGAAATAAGTCTACATTCATCCG 59.077 37.037 0.00 0.00 30.39 4.18
3302 4154 7.782049 TCTGAAATAAGTCTACATTCATCCGT 58.218 34.615 0.00 0.00 30.39 4.69
3303 4155 8.909923 TCTGAAATAAGTCTACATTCATCCGTA 58.090 33.333 0.00 0.00 30.39 4.02
3304 4156 9.698309 CTGAAATAAGTCTACATTCATCCGTAT 57.302 33.333 0.00 0.00 30.39 3.06
3305 4157 9.476202 TGAAATAAGTCTACATTCATCCGTATG 57.524 33.333 0.00 0.00 0.00 2.39
3306 4158 9.477484 GAAATAAGTCTACATTCATCCGTATGT 57.523 33.333 0.00 0.00 37.04 2.29
3309 4161 7.584122 AAGTCTACATTCATCCGTATGTAGT 57.416 36.000 17.13 2.37 46.08 2.73
3310 4162 7.204496 AGTCTACATTCATCCGTATGTAGTC 57.796 40.000 17.13 13.42 46.08 2.59
3311 4163 6.207025 AGTCTACATTCATCCGTATGTAGTCC 59.793 42.308 17.13 11.48 46.08 3.85
3312 4164 6.016527 GTCTACATTCATCCGTATGTAGTCCA 60.017 42.308 17.13 1.82 46.08 4.02
3313 4165 5.808366 ACATTCATCCGTATGTAGTCCAT 57.192 39.130 0.00 0.00 31.98 3.41
3314 4166 6.911250 ACATTCATCCGTATGTAGTCCATA 57.089 37.500 0.00 0.00 31.98 2.74
3315 4167 7.482169 ACATTCATCCGTATGTAGTCCATAT 57.518 36.000 0.00 0.00 38.29 1.78
3316 4168 7.907389 ACATTCATCCGTATGTAGTCCATATT 58.093 34.615 0.00 0.00 38.29 1.28
3317 4169 7.819415 ACATTCATCCGTATGTAGTCCATATTG 59.181 37.037 0.00 0.00 38.29 1.90
3318 4170 7.533289 TTCATCCGTATGTAGTCCATATTGA 57.467 36.000 0.00 0.00 38.29 2.57
3319 4171 7.533289 TCATCCGTATGTAGTCCATATTGAA 57.467 36.000 0.00 0.00 38.29 2.69
3320 4172 7.958088 TCATCCGTATGTAGTCCATATTGAAA 58.042 34.615 0.00 0.00 38.29 2.69
3321 4173 8.593679 TCATCCGTATGTAGTCCATATTGAAAT 58.406 33.333 0.00 0.00 38.29 2.17
3322 4174 8.873830 CATCCGTATGTAGTCCATATTGAAATC 58.126 37.037 0.00 0.00 38.29 2.17
3323 4175 8.190326 TCCGTATGTAGTCCATATTGAAATCT 57.810 34.615 0.00 0.00 38.29 2.40
3324 4176 8.304596 TCCGTATGTAGTCCATATTGAAATCTC 58.695 37.037 0.00 0.00 38.29 2.75
3325 4177 8.307483 CCGTATGTAGTCCATATTGAAATCTCT 58.693 37.037 0.00 0.00 38.29 3.10
3349 4201 9.985730 TCTAAAAAGACTTGTATTTAGGAACGA 57.014 29.630 13.94 0.00 36.48 3.85
3352 4204 8.897872 AAAAGACTTGTATTTAGGAACGAAGA 57.102 30.769 0.00 0.00 0.00 2.87
3417 4269 0.248866 GCCAAACCACAACCAAGTCG 60.249 55.000 0.00 0.00 0.00 4.18
3461 4313 5.422970 AGCAAAAATGAGCTATGATTTCCCA 59.577 36.000 0.00 0.00 39.78 4.37
3462 4314 6.070653 AGCAAAAATGAGCTATGATTTCCCAA 60.071 34.615 0.00 0.00 39.78 4.12
3559 4587 7.840210 ACTGTACCTAAGTCTAGCCTCTTATTT 59.160 37.037 0.00 0.00 0.00 1.40
3599 4642 9.319143 ACAGATTGTATAGCTAAACAAGATGTC 57.681 33.333 0.00 0.00 38.87 3.06
3643 4686 6.369890 TGCAGATGTTCAAACTAGAAGATGTC 59.630 38.462 0.00 0.00 32.35 3.06
3646 4689 3.673338 TGTTCAAACTAGAAGATGTCGCG 59.327 43.478 0.00 0.00 0.00 5.87
3720 4763 9.911788 ATACAAAACAGATAAGAGGATTCACAT 57.088 29.630 0.00 0.00 0.00 3.21
3751 4794 0.331616 AGGAGGGGTACATTGTTGCC 59.668 55.000 0.00 0.00 0.00 4.52
3814 4857 4.042187 ACACTCCTAAGGACAAATCAAGCT 59.958 41.667 0.00 0.00 0.00 3.74
3848 4891 8.381387 GCAACTAACTAACTAGTAATGCAGAAC 58.619 37.037 0.00 0.00 34.99 3.01
3938 5299 0.673333 CCAACAGCTGCATCCGTACA 60.673 55.000 15.27 0.00 0.00 2.90
3991 5353 2.615447 CCAGTCCCAATTCATGATCACG 59.385 50.000 0.00 0.00 0.00 4.35
4017 5379 9.099454 GAAATCCATAGAAACTGTAGGTACAAG 57.901 37.037 0.00 0.00 35.50 3.16
4020 5382 6.156256 TCCATAGAAACTGTAGGTACAAGCAT 59.844 38.462 0.00 0.00 35.50 3.79
4103 5466 8.815189 CACTATATGTCTGTTCACATCAGAAAG 58.185 37.037 0.00 0.00 42.42 2.62
4104 5467 8.753133 ACTATATGTCTGTTCACATCAGAAAGA 58.247 33.333 0.00 0.00 42.42 2.52
4185 5548 8.307582 ACATTACCACTGACTAGCTAATTAGT 57.692 34.615 13.91 0.00 36.61 2.24
4186 5549 8.414778 ACATTACCACTGACTAGCTAATTAGTC 58.585 37.037 13.91 7.32 46.27 2.59
4244 5607 4.690748 CACAGTTCACATTGTAACTCGGAT 59.309 41.667 8.01 0.00 33.72 4.18
4282 5645 2.937149 CAATGCATCAGAGGTGTCTCAG 59.063 50.000 0.00 0.00 42.34 3.35
4292 5655 5.706369 TCAGAGGTGTCTCAGTCTAACTAAC 59.294 44.000 0.00 0.00 42.34 2.34
4293 5656 5.473846 CAGAGGTGTCTCAGTCTAACTAACA 59.526 44.000 0.00 0.00 42.34 2.41
4302 5665 2.113052 AGTCTAACTAACACCCCCTCCA 59.887 50.000 0.00 0.00 0.00 3.86
4313 5676 1.061190 ACCCCCTCCATCCCGTAATAA 60.061 52.381 0.00 0.00 0.00 1.40
4314 5677 1.628846 CCCCCTCCATCCCGTAATAAG 59.371 57.143 0.00 0.00 0.00 1.73
4316 5679 3.182152 CCCCTCCATCCCGTAATAAGAT 58.818 50.000 0.00 0.00 0.00 2.40
4317 5680 4.359105 CCCCTCCATCCCGTAATAAGATA 58.641 47.826 0.00 0.00 0.00 1.98
4319 5682 5.428783 CCCCTCCATCCCGTAATAAGATAAT 59.571 44.000 0.00 0.00 0.00 1.28
4320 5683 6.069615 CCCCTCCATCCCGTAATAAGATAATT 60.070 42.308 0.00 0.00 0.00 1.40
4323 5686 8.730680 CCTCCATCCCGTAATAAGATAATTTTG 58.269 37.037 0.00 0.00 0.00 2.44
4324 5687 8.106247 TCCATCCCGTAATAAGATAATTTTGC 57.894 34.615 0.00 0.00 0.00 3.68
4325 5688 7.721842 TCCATCCCGTAATAAGATAATTTTGCA 59.278 33.333 0.00 0.00 0.00 4.08
4327 5690 9.912634 CATCCCGTAATAAGATAATTTTGCAAT 57.087 29.630 0.00 0.00 0.00 3.56
4329 5692 9.349713 TCCCGTAATAAGATAATTTTGCAATCT 57.650 29.630 0.00 0.00 0.00 2.40
4358 5783 9.187455 GTACCAATACAAGTTTTAAACCATGTG 57.813 33.333 20.03 10.36 34.82 3.21
4365 5790 6.978080 ACAAGTTTTAAACCATGTGCAGTTAG 59.022 34.615 13.57 0.00 32.67 2.34
4474 5902 7.495934 AGGAAAATGGACTCTACATATTTGTCG 59.504 37.037 0.00 0.00 37.28 4.35
4554 7061 7.789202 ATAGTAGCACATGAGAAGTATCCAT 57.211 36.000 0.00 0.00 0.00 3.41
4566 7073 6.665248 TGAGAAGTATCCATTGTGAAGAGAGA 59.335 38.462 0.00 0.00 0.00 3.10
4567 7074 7.111247 AGAAGTATCCATTGTGAAGAGAGAG 57.889 40.000 0.00 0.00 0.00 3.20
4568 7075 6.667414 AGAAGTATCCATTGTGAAGAGAGAGT 59.333 38.462 0.00 0.00 0.00 3.24
4618 7126 1.367346 TAAGGGTTGCACATCCTGGA 58.633 50.000 0.00 0.00 0.00 3.86
4635 7143 3.599285 GACCGATGGCCCGTGTGAA 62.599 63.158 0.00 0.00 0.00 3.18
4665 7173 1.435515 GCCAGCCGTCAAACAAACA 59.564 52.632 0.00 0.00 0.00 2.83
4730 7238 0.040958 CCGCTGCATTAAATCGGCTC 60.041 55.000 0.00 0.00 33.36 4.70
4741 7249 2.604046 AATCGGCTCATACACCTCAC 57.396 50.000 0.00 0.00 0.00 3.51
4753 7261 1.204941 ACACCTCACGTATCCTGCTTC 59.795 52.381 0.00 0.00 0.00 3.86
4776 7284 9.649167 CTTCTCTGCATTCACATATATATCACA 57.351 33.333 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.096001 CCCCTGAGTCCTAAAAATTCAAGATG 59.904 42.308 0.00 0.00 0.00 2.90
1 2 6.190587 CCCCTGAGTCCTAAAAATTCAAGAT 58.809 40.000 0.00 0.00 0.00 2.40
2 3 5.570320 CCCCTGAGTCCTAAAAATTCAAGA 58.430 41.667 0.00 0.00 0.00 3.02
3 4 4.158579 GCCCCTGAGTCCTAAAAATTCAAG 59.841 45.833 0.00 0.00 0.00 3.02
4 5 4.086457 GCCCCTGAGTCCTAAAAATTCAA 58.914 43.478 0.00 0.00 0.00 2.69
5 6 3.333680 AGCCCCTGAGTCCTAAAAATTCA 59.666 43.478 0.00 0.00 0.00 2.57
139 388 0.955428 TCGCAGTTGCTGATGGGAAC 60.955 55.000 2.29 0.00 44.89 3.62
165 414 1.230281 AAGGGGGCATCCTCTGGAA 60.230 57.895 0.00 0.00 44.92 3.53
170 419 1.052617 GTAGAGAAGGGGGCATCCTC 58.947 60.000 0.00 0.00 35.80 3.71
180 430 0.528017 TGTCGCAGCTGTAGAGAAGG 59.472 55.000 16.64 0.00 0.00 3.46
227 477 5.499004 TGTTATGGTGAGGTTAGAAGCTT 57.501 39.130 0.00 0.00 36.78 3.74
270 520 4.330074 GGTAAGTTCACCATGATCGACTTG 59.670 45.833 0.00 0.00 38.55 3.16
302 552 4.285863 AGTCCAAGGATCAACAAACCAAA 58.714 39.130 0.00 0.00 0.00 3.28
314 564 4.449081 CCTCTCTAGATGGAGTCCAAGGAT 60.449 50.000 17.71 0.00 36.95 3.24
409 659 1.192146 TACCCTATCCATGCGAGCCC 61.192 60.000 0.00 0.00 0.00 5.19
415 665 0.698238 TGCCCATACCCTATCCATGC 59.302 55.000 0.00 0.00 0.00 4.06
451 701 4.028490 TCGGGTTTGGGCATCGCT 62.028 61.111 0.00 0.00 0.00 4.93
467 717 2.820787 CCTATCCATGACTAGTCGGGTC 59.179 54.545 24.64 3.20 0.00 4.46
470 720 3.156288 TCCCTATCCATGACTAGTCGG 57.844 52.381 17.85 13.59 0.00 4.79
522 772 7.600375 TGCATCTATCACAAGCTAGCTTATAAC 59.400 37.037 28.87 12.75 34.50 1.89
560 812 3.463533 TGACGTTGTTTGTGTGTCTTG 57.536 42.857 0.00 0.00 0.00 3.02
592 844 8.091449 ACAATGATCGTTATGCCCTTTTAAAAA 58.909 29.630 0.00 0.00 0.00 1.94
597 849 4.097892 GGACAATGATCGTTATGCCCTTTT 59.902 41.667 0.00 0.00 0.00 2.27
609 861 4.570772 ACTTTAATCGTGGGACAATGATCG 59.429 41.667 0.00 0.00 44.16 3.69
668 920 9.709495 ACAGTTCTATAACCAACGTAAACATTA 57.291 29.630 0.00 0.00 36.15 1.90
878 1177 1.464608 CCTGTCGATGCAATTGTCGTT 59.535 47.619 15.52 0.00 38.85 3.85
935 1234 4.751098 GCACTGCTGATTTGAATGGAAAAA 59.249 37.500 0.00 0.00 0.00 1.94
936 1235 4.309099 GCACTGCTGATTTGAATGGAAAA 58.691 39.130 0.00 0.00 0.00 2.29
977 1276 5.389520 TCTCCGATCTCACTTTCTATGGAT 58.610 41.667 0.00 0.00 0.00 3.41
1110 1409 2.431997 AGGGGATTGGCATGGAGAATA 58.568 47.619 0.00 0.00 0.00 1.75
1190 1489 1.299541 CGCTGTTGATGATACCACCC 58.700 55.000 0.00 0.00 0.00 4.61
1202 1501 0.379669 GCCTGAATCATCCGCTGTTG 59.620 55.000 0.00 0.00 0.00 3.33
1204 1503 0.463295 CTGCCTGAATCATCCGCTGT 60.463 55.000 0.00 0.00 0.00 4.40
1299 1598 4.020543 AGTGTAGCCTTTCAGTAGAGGAG 58.979 47.826 0.00 0.00 34.91 3.69
1359 1718 0.836400 GGGGAAGTCCAGTGGAGACA 60.836 60.000 13.61 0.00 36.68 3.41
1371 1730 2.521958 CTTCGGTCGCATGGGGAAGT 62.522 60.000 10.21 0.00 31.73 3.01
1554 1913 1.659098 GTTATGGAAGAACCTGCGACG 59.341 52.381 0.00 0.00 39.86 5.12
1715 2074 3.816537 GTGAAGGCGTTCTGCACTATGG 61.817 54.545 19.07 0.00 46.38 2.74
1764 2123 2.285977 GAGTTATTGTAGGGGCAACGG 58.714 52.381 0.00 0.00 37.60 4.44
1770 2129 4.097892 GCATTGTTGGAGTTATTGTAGGGG 59.902 45.833 0.00 0.00 0.00 4.79
1774 2133 6.488344 TGAGTTGCATTGTTGGAGTTATTGTA 59.512 34.615 0.00 0.00 0.00 2.41
1778 2137 5.047802 CCTTGAGTTGCATTGTTGGAGTTAT 60.048 40.000 0.00 0.00 0.00 1.89
1779 2138 4.278170 CCTTGAGTTGCATTGTTGGAGTTA 59.722 41.667 0.00 0.00 0.00 2.24
1814 2176 9.262358 GCTACTGTAATAAGCAACTAATAAGCT 57.738 33.333 0.00 0.00 41.03 3.74
1831 2193 6.053005 GGCACCACAATAATAGCTACTGTAA 58.947 40.000 0.00 0.00 0.00 2.41
1871 2234 6.358974 TCATCCACTGTGAAAGATACTTCA 57.641 37.500 9.86 0.00 32.89 3.02
1872 2235 7.856145 AATCATCCACTGTGAAAGATACTTC 57.144 36.000 9.86 0.00 0.00 3.01
1873 2236 7.121759 CCAAATCATCCACTGTGAAAGATACTT 59.878 37.037 9.86 0.00 0.00 2.24
1874 2237 6.600822 CCAAATCATCCACTGTGAAAGATACT 59.399 38.462 9.86 0.00 0.00 2.12
1875 2238 6.599244 TCCAAATCATCCACTGTGAAAGATAC 59.401 38.462 9.86 0.00 0.00 2.24
1876 2239 6.720309 TCCAAATCATCCACTGTGAAAGATA 58.280 36.000 9.86 0.00 0.00 1.98
1907 2279 1.259142 TGCTGCCCACCATGGAATTG 61.259 55.000 21.47 6.27 40.96 2.32
1942 2326 1.869767 CTTGCTTGAGACCAGTGTGAC 59.130 52.381 0.00 0.00 0.00 3.67
1954 2338 0.106268 TGGCTTTCCACCTTGCTTGA 60.106 50.000 0.00 0.00 37.47 3.02
1993 2377 0.250510 GATAGCAAGGTAGCCCTGCC 60.251 60.000 11.77 0.00 41.56 4.85
2000 2384 4.688021 GGAGAGTTGTGATAGCAAGGTAG 58.312 47.826 0.00 0.00 0.00 3.18
2029 2413 3.921021 CGTCATATGTATTCCTTCGAGCC 59.079 47.826 1.90 0.00 0.00 4.70
2125 2912 6.449698 ACTGTAAGGATTTGAGCAACAATTG 58.550 36.000 3.24 3.24 39.30 2.32
2126 2913 6.655078 ACTGTAAGGATTTGAGCAACAATT 57.345 33.333 0.00 0.00 39.30 2.32
2128 2915 5.221224 CCAACTGTAAGGATTTGAGCAACAA 60.221 40.000 0.00 0.00 39.30 2.83
2151 2939 3.561725 CGAGCCCTGATAACAGAAATTCC 59.438 47.826 0.79 0.00 46.03 3.01
2154 2942 2.771943 TCCGAGCCCTGATAACAGAAAT 59.228 45.455 0.79 0.00 46.03 2.17
2201 2989 4.202010 TGCTAGCTTGAAGTCACCAAAAAC 60.202 41.667 17.23 0.00 0.00 2.43
2205 2993 2.550855 CCTGCTAGCTTGAAGTCACCAA 60.551 50.000 17.23 0.00 0.00 3.67
2266 3054 4.082354 AGCATTTCAAGATCCAAGCTGTTC 60.082 41.667 0.00 0.00 0.00 3.18
2269 3057 3.442625 TGAGCATTTCAAGATCCAAGCTG 59.557 43.478 0.00 0.00 31.34 4.24
2290 3078 3.209410 GGCTGGAATAGGTGATGACTTG 58.791 50.000 0.00 0.00 0.00 3.16
2310 3098 0.108138 AAGGTCGAGATCTTTGCCGG 60.108 55.000 0.00 0.00 0.00 6.13
2383 3171 2.802816 GTCATATTGCATCCACGTCCTC 59.197 50.000 0.00 0.00 0.00 3.71
2444 3232 3.034721 TGTGTAGTCTTTTACCAGGCG 57.965 47.619 0.00 0.00 0.00 5.52
2534 3372 2.030027 TGGTGTCAGGATTCTGGACT 57.970 50.000 0.00 0.00 41.23 3.85
2596 3437 3.445857 CTCGTTCCGGAGTTCCTTATTC 58.554 50.000 3.34 0.00 0.00 1.75
2624 3465 1.200716 CACCTGAATGTCACCATGTGC 59.799 52.381 0.00 0.00 32.98 4.57
2627 3468 2.352030 GCAACACCTGAATGTCACCATG 60.352 50.000 0.00 0.00 30.55 3.66
2656 3497 5.635280 CCATGTAATCAGGCTGTAGTAATCG 59.365 44.000 15.27 0.00 0.00 3.34
2671 3512 3.609853 TGCCAGTGTCTTCCATGTAATC 58.390 45.455 0.00 0.00 0.00 1.75
2754 3596 4.506758 AGTTGAGCACACAAAAGCAAAAT 58.493 34.783 0.00 0.00 0.00 1.82
2883 3729 1.438651 GCAGACCGTTGCTGACATTA 58.561 50.000 0.00 0.00 40.89 1.90
2938 3784 3.074412 ACCACTTGCTTTCACTATTCCG 58.926 45.455 0.00 0.00 0.00 4.30
2940 3786 6.743575 ATGTACCACTTGCTTTCACTATTC 57.256 37.500 0.00 0.00 0.00 1.75
2970 3816 3.731431 TGTATGTGGGGACATTACCTCT 58.269 45.455 0.00 0.00 46.14 3.69
2990 3836 3.399440 TTTTATGGCAGCCAACCTTTG 57.601 42.857 20.84 0.00 36.95 2.77
2998 3844 1.743431 GCACCCATTTTTATGGCAGCC 60.743 52.381 3.66 3.66 40.35 4.85
3010 3856 5.513233 ACATCAGAAATCTTAGCACCCATT 58.487 37.500 0.00 0.00 0.00 3.16
3106 3953 4.408993 TGATTGTCTTTGCGATGTCTTG 57.591 40.909 0.00 0.00 0.00 3.02
3114 3961 4.050553 ACCAAATGTTGATTGTCTTTGCG 58.949 39.130 0.00 0.00 0.00 4.85
3163 4015 3.535561 CCATAGGTTACACTTCTGCCTG 58.464 50.000 0.00 0.00 0.00 4.85
3191 4043 8.912614 ATATTTAGGAACGGAGGGAGTATATT 57.087 34.615 0.00 0.00 0.00 1.28
3198 4050 7.441903 AAACTTATATTTAGGAACGGAGGGA 57.558 36.000 0.00 0.00 0.00 4.20
3199 4051 8.515695 AAAAACTTATATTTAGGAACGGAGGG 57.484 34.615 0.00 0.00 0.00 4.30
3228 4080 9.179909 CCGTATGTAGTCTATATTGGAATCTCT 57.820 37.037 0.00 0.00 0.00 3.10
3229 4081 9.175312 TCCGTATGTAGTCTATATTGGAATCTC 57.825 37.037 7.43 0.00 0.00 2.75
3230 4082 9.179909 CTCCGTATGTAGTCTATATTGGAATCT 57.820 37.037 9.87 0.00 0.00 2.40
3231 4083 7.916450 GCTCCGTATGTAGTCTATATTGGAATC 59.084 40.741 9.87 4.29 0.00 2.52
3232 4084 7.396339 TGCTCCGTATGTAGTCTATATTGGAAT 59.604 37.037 9.87 0.00 0.00 3.01
3233 4085 6.717997 TGCTCCGTATGTAGTCTATATTGGAA 59.282 38.462 9.87 0.00 0.00 3.53
3234 4086 6.243148 TGCTCCGTATGTAGTCTATATTGGA 58.757 40.000 8.84 8.84 0.00 3.53
3235 4087 6.510879 TGCTCCGTATGTAGTCTATATTGG 57.489 41.667 0.00 0.00 0.00 3.16
3236 4088 8.812147 TTTTGCTCCGTATGTAGTCTATATTG 57.188 34.615 0.00 0.00 0.00 1.90
3237 4089 9.424319 CATTTTGCTCCGTATGTAGTCTATATT 57.576 33.333 0.00 0.00 0.00 1.28
3238 4090 8.803235 TCATTTTGCTCCGTATGTAGTCTATAT 58.197 33.333 0.00 0.00 0.00 0.86
3239 4091 8.173542 TCATTTTGCTCCGTATGTAGTCTATA 57.826 34.615 0.00 0.00 0.00 1.31
3240 4092 7.050970 TCATTTTGCTCCGTATGTAGTCTAT 57.949 36.000 0.00 0.00 0.00 1.98
3241 4093 6.096423 ACTCATTTTGCTCCGTATGTAGTCTA 59.904 38.462 0.00 0.00 0.00 2.59
3242 4094 5.105310 ACTCATTTTGCTCCGTATGTAGTCT 60.105 40.000 0.00 0.00 0.00 3.24
3243 4095 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3244 4096 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3245 4097 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3246 4098 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3247 4099 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3248 4100 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3249 4101 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3250 4102 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3251 4103 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3252 4104 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3253 4105 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3254 4106 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3273 4125 9.593134 GATGAATGTAGACTTATTTCAGAGTGT 57.407 33.333 0.00 0.00 0.00 3.55
3274 4126 9.039870 GGATGAATGTAGACTTATTTCAGAGTG 57.960 37.037 0.00 0.00 0.00 3.51
3275 4127 7.923344 CGGATGAATGTAGACTTATTTCAGAGT 59.077 37.037 0.00 0.00 0.00 3.24
3276 4128 7.923344 ACGGATGAATGTAGACTTATTTCAGAG 59.077 37.037 0.00 0.00 0.00 3.35
3277 4129 7.782049 ACGGATGAATGTAGACTTATTTCAGA 58.218 34.615 0.00 0.00 0.00 3.27
3278 4130 9.698309 ATACGGATGAATGTAGACTTATTTCAG 57.302 33.333 0.00 0.00 0.00 3.02
3279 4131 9.476202 CATACGGATGAATGTAGACTTATTTCA 57.524 33.333 0.00 0.00 34.73 2.69
3280 4132 9.477484 ACATACGGATGAATGTAGACTTATTTC 57.523 33.333 16.36 0.00 34.61 2.17
3290 4142 6.911250 ATGGACTACATACGGATGAATGTA 57.089 37.500 16.36 5.74 38.26 2.29
3291 4143 5.808366 ATGGACTACATACGGATGAATGT 57.192 39.130 16.36 9.52 38.26 2.71
3292 4144 8.034804 TCAATATGGACTACATACGGATGAATG 58.965 37.037 16.36 6.19 44.41 2.67
3293 4145 8.134202 TCAATATGGACTACATACGGATGAAT 57.866 34.615 16.36 0.00 44.41 2.57
3294 4146 7.533289 TCAATATGGACTACATACGGATGAA 57.467 36.000 16.36 0.00 44.41 2.57
3295 4147 7.533289 TTCAATATGGACTACATACGGATGA 57.467 36.000 16.36 0.00 44.41 2.92
3296 4148 8.777865 ATTTCAATATGGACTACATACGGATG 57.222 34.615 5.94 5.94 44.41 3.51
3297 4149 8.816894 AGATTTCAATATGGACTACATACGGAT 58.183 33.333 0.00 0.00 44.41 4.18
3298 4150 8.190326 AGATTTCAATATGGACTACATACGGA 57.810 34.615 0.00 0.00 44.41 4.69
3299 4151 8.307483 AGAGATTTCAATATGGACTACATACGG 58.693 37.037 0.00 0.00 44.41 4.02
3323 4175 9.985730 TCGTTCCTAAATACAAGTCTTTTTAGA 57.014 29.630 13.43 2.40 34.90 2.10
3326 4178 9.333724 TCTTCGTTCCTAAATACAAGTCTTTTT 57.666 29.630 0.00 0.00 0.00 1.94
3327 4179 8.897872 TCTTCGTTCCTAAATACAAGTCTTTT 57.102 30.769 0.00 0.00 0.00 2.27
3328 4180 8.897872 TTCTTCGTTCCTAAATACAAGTCTTT 57.102 30.769 0.00 0.00 0.00 2.52
3329 4181 8.897872 TTTCTTCGTTCCTAAATACAAGTCTT 57.102 30.769 0.00 0.00 0.00 3.01
3330 4182 8.148999 ACTTTCTTCGTTCCTAAATACAAGTCT 58.851 33.333 0.00 0.00 0.00 3.24
3331 4183 8.307921 ACTTTCTTCGTTCCTAAATACAAGTC 57.692 34.615 0.00 0.00 0.00 3.01
3332 4184 9.201127 GTACTTTCTTCGTTCCTAAATACAAGT 57.799 33.333 0.00 0.00 0.00 3.16
3333 4185 9.199982 TGTACTTTCTTCGTTCCTAAATACAAG 57.800 33.333 0.00 0.00 0.00 3.16
3334 4186 9.715121 ATGTACTTTCTTCGTTCCTAAATACAA 57.285 29.630 0.00 0.00 0.00 2.41
3335 4187 9.146984 CATGTACTTTCTTCGTTCCTAAATACA 57.853 33.333 0.00 0.00 0.00 2.29
3336 4188 8.114905 GCATGTACTTTCTTCGTTCCTAAATAC 58.885 37.037 0.00 0.00 0.00 1.89
3337 4189 8.038944 AGCATGTACTTTCTTCGTTCCTAAATA 58.961 33.333 0.00 0.00 0.00 1.40
3338 4190 6.879458 AGCATGTACTTTCTTCGTTCCTAAAT 59.121 34.615 0.00 0.00 0.00 1.40
3339 4191 6.228258 AGCATGTACTTTCTTCGTTCCTAAA 58.772 36.000 0.00 0.00 0.00 1.85
3340 4192 5.790593 AGCATGTACTTTCTTCGTTCCTAA 58.209 37.500 0.00 0.00 0.00 2.69
3341 4193 5.401531 AGCATGTACTTTCTTCGTTCCTA 57.598 39.130 0.00 0.00 0.00 2.94
3342 4194 4.273148 AGCATGTACTTTCTTCGTTCCT 57.727 40.909 0.00 0.00 0.00 3.36
3343 4195 5.408356 TCTAGCATGTACTTTCTTCGTTCC 58.592 41.667 0.00 0.00 0.00 3.62
3344 4196 6.752351 TCATCTAGCATGTACTTTCTTCGTTC 59.248 38.462 0.00 0.00 0.00 3.95
3345 4197 6.631016 TCATCTAGCATGTACTTTCTTCGTT 58.369 36.000 0.00 0.00 0.00 3.85
3346 4198 6.208988 TCATCTAGCATGTACTTTCTTCGT 57.791 37.500 0.00 0.00 0.00 3.85
3347 4199 7.525688 TTTCATCTAGCATGTACTTTCTTCG 57.474 36.000 0.00 0.00 0.00 3.79
3348 4200 8.940952 AGTTTTCATCTAGCATGTACTTTCTTC 58.059 33.333 0.00 0.00 0.00 2.87
3349 4201 8.854614 AGTTTTCATCTAGCATGTACTTTCTT 57.145 30.769 0.00 0.00 0.00 2.52
3350 4202 9.944376 TTAGTTTTCATCTAGCATGTACTTTCT 57.056 29.630 0.00 0.00 0.00 2.52
3385 4237 0.818040 GTTTGGCACTTGACCGGTCT 60.818 55.000 33.39 12.78 0.00 3.85
3417 4269 8.848474 TTTGCTAAATCAATATACCTCTAGGC 57.152 34.615 0.00 0.00 39.32 3.93
3461 4313 5.067805 CAGCTAGTTTTTCCTTGTTCCAGTT 59.932 40.000 0.00 0.00 0.00 3.16
3462 4314 4.580580 CAGCTAGTTTTTCCTTGTTCCAGT 59.419 41.667 0.00 0.00 0.00 4.00
3472 4324 3.821033 TGCCTCTTTCAGCTAGTTTTTCC 59.179 43.478 0.00 0.00 0.00 3.13
3599 4642 5.995897 TCTGCATGAATGAAGGATGTAGATG 59.004 40.000 0.00 0.00 34.94 2.90
3617 4660 6.883217 ACATCTTCTAGTTTGAACATCTGCAT 59.117 34.615 0.00 0.00 0.00 3.96
3643 4686 1.600636 AACCCATATGCCCATCGCG 60.601 57.895 0.00 0.00 42.08 5.87
3646 4689 1.202758 TCGTCAACCCATATGCCCATC 60.203 52.381 0.00 0.00 0.00 3.51
3698 4741 8.868522 TCAATGTGAATCCTCTTATCTGTTTT 57.131 30.769 0.00 0.00 0.00 2.43
3720 4763 2.354328 ACCCCTCCTTACAACCATCAA 58.646 47.619 0.00 0.00 0.00 2.57
3751 4794 6.016777 GCATATTCCTTGGTTCTTGATAGTGG 60.017 42.308 0.00 0.00 0.00 4.00
3814 4857 6.931838 ACTAGTTAGTTAGTTGCAGCACATA 58.068 36.000 2.55 0.00 31.13 2.29
3938 5299 2.287393 TGCGTCATAGCAACGTACAT 57.713 45.000 0.00 0.00 45.06 2.29
3991 5353 9.099454 CTTGTACCTACAGTTTCTATGGATTTC 57.901 37.037 0.00 0.00 37.52 2.17
4017 5379 3.585862 TCTTGTGTCTACCGAGAAATGC 58.414 45.455 0.00 0.00 31.96 3.56
4020 5382 5.243060 TGAAGATCTTGTGTCTACCGAGAAA 59.757 40.000 14.00 0.00 31.96 2.52
4104 5467 9.512588 CCCTTGATAGCTCATGAGTTAATTAAT 57.487 33.333 21.25 7.35 0.00 1.40
4185 5548 6.111382 TGTTGCTTTGATTGGTTTTGATTGA 58.889 32.000 0.00 0.00 0.00 2.57
4186 5549 6.360844 TGTTGCTTTGATTGGTTTTGATTG 57.639 33.333 0.00 0.00 0.00 2.67
4187 5550 6.458615 GCTTGTTGCTTTGATTGGTTTTGATT 60.459 34.615 0.00 0.00 38.95 2.57
4188 5551 5.007921 GCTTGTTGCTTTGATTGGTTTTGAT 59.992 36.000 0.00 0.00 38.95 2.57
4195 5558 2.739913 CCATGCTTGTTGCTTTGATTGG 59.260 45.455 0.00 0.00 43.37 3.16
4244 5607 3.243704 GCATTGGGCACAAAACAGAGTAA 60.244 43.478 4.97 0.00 43.97 2.24
4282 5645 2.543635 TGGAGGGGGTGTTAGTTAGAC 58.456 52.381 0.00 0.00 0.00 2.59
4292 5655 1.060163 ATTACGGGATGGAGGGGGTG 61.060 60.000 0.00 0.00 0.00 4.61
4293 5656 0.569204 TATTACGGGATGGAGGGGGT 59.431 55.000 0.00 0.00 0.00 4.95
4319 5682 9.019656 ACTTGTATTGGTACATAGATTGCAAAA 57.980 29.630 1.71 0.00 40.35 2.44
4320 5683 8.574251 ACTTGTATTGGTACATAGATTGCAAA 57.426 30.769 1.71 0.00 40.35 3.68
4474 5902 2.297701 TGGTGAAAGTCTGAACTTGCC 58.702 47.619 0.00 0.00 45.07 4.52
4554 7061 2.163509 CCGAGGACTCTCTCTTCACAA 58.836 52.381 0.00 0.00 37.86 3.33
4566 7073 1.258445 CCAGCCTGTAACCGAGGACT 61.258 60.000 0.00 0.00 31.48 3.85
4567 7074 1.218316 CCAGCCTGTAACCGAGGAC 59.782 63.158 0.00 0.00 31.48 3.85
4568 7075 0.543410 TTCCAGCCTGTAACCGAGGA 60.543 55.000 0.00 0.00 31.48 3.71
4618 7126 2.478335 AATTCACACGGGCCATCGGT 62.478 55.000 4.39 0.00 0.00 4.69
4629 7137 0.645868 GCGCTACTCCGAATTCACAC 59.354 55.000 0.00 0.00 0.00 3.82
4635 7143 2.107141 GCTGGCGCTACTCCGAAT 59.893 61.111 7.64 0.00 0.00 3.34
4665 7173 5.009911 TGTGAAGATTGCTGTTATGTTGCTT 59.990 36.000 0.00 0.00 0.00 3.91
4712 7220 0.657312 TGAGCCGATTTAATGCAGCG 59.343 50.000 0.00 0.00 0.00 5.18
4730 7238 2.362397 AGCAGGATACGTGAGGTGTATG 59.638 50.000 0.00 0.00 46.39 2.39
4776 7284 5.237344 GGAGATGTGCGCTAGATGTATTTTT 59.763 40.000 9.73 0.00 0.00 1.94
4791 7299 4.565564 GCAATTTCTTGATTGGAGATGTGC 59.434 41.667 0.00 0.00 37.47 4.57


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

AutoCloner maintained by Alex Coulton.