Multiple sequence alignment - TraesCS5A01G231400

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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 TraesCS5A01G231400 chr5A 100.000 3200 0 0 1 3200 447004384 447001185 0.000000e+00 5910.0
1 TraesCS5A01G231400 chr5A 86.147 231 20 4 2914 3134 446987533 446987305 4.130000e-59 239.0
2 TraesCS5A01G231400 chr5A 98.462 65 1 0 3136 3200 283660150 283660086 7.250000e-22 115.0
3 TraesCS5A01G231400 chr5A 95.652 69 1 2 3132 3198 194863451 194863383 3.370000e-20 110.0
4 TraesCS5A01G231400 chr5A 94.366 71 2 2 3132 3200 413121071 413121001 1.210000e-19 108.0
5 TraesCS5A01G231400 chr4D 93.648 2881 161 15 1 2868 202556148 202553277 0.000000e+00 4287.0
6 TraesCS5A01G231400 chr4D 93.296 2879 170 17 1 2866 144300243 144297375 0.000000e+00 4226.0
7 TraesCS5A01G231400 chr4D 90.566 2915 217 37 1 2868 151101065 151103968 0.000000e+00 3807.0
8 TraesCS5A01G231400 chr4D 94.245 2450 132 5 425 2868 202573898 202571452 0.000000e+00 3735.0
9 TraesCS5A01G231400 chr4D 93.306 2480 150 9 1 2472 395881934 395879463 0.000000e+00 3646.0
10 TraesCS5A01G231400 chr4D 88.076 2407 217 45 521 2868 267044396 267042001 0.000000e+00 2791.0
11 TraesCS5A01G231400 chr4D 90.217 184 17 1 2952 3134 329382866 329383049 4.130000e-59 239.0
12 TraesCS5A01G231400 chr3D 93.403 2880 160 23 1 2868 384053724 384050863 0.000000e+00 4239.0
13 TraesCS5A01G231400 chr3D 89.381 226 18 5 1 220 178348733 178348508 2.430000e-71 279.0
14 TraesCS5A01G231400 chr3D 89.427 227 16 4 1 219 384056330 384056104 2.430000e-71 279.0
15 TraesCS5A01G231400 chr3D 86.854 213 26 2 2922 3134 213255487 213255277 1.480000e-58 237.0
16 TraesCS5A01G231400 chr3D 84.211 209 22 8 2920 3117 508793228 508793436 3.260000e-45 193.0
17 TraesCS5A01G231400 chr3D 86.747 166 11 6 2869 3024 145436562 145436398 1.180000e-39 174.0
18 TraesCS5A01G231400 chr6D 91.389 2915 194 38 1 2868 300592424 300595328 0.000000e+00 3940.0
19 TraesCS5A01G231400 chr6D 85.987 157 11 2 2920 3066 74700909 74700754 1.190000e-34 158.0
20 TraesCS5A01G231400 chr6D 84.906 159 11 4 2920 3067 165903850 165904006 7.150000e-32 148.0
21 TraesCS5A01G231400 chr1D 93.750 2480 144 9 1 2472 123206095 123203619 0.000000e+00 3711.0
22 TraesCS5A01G231400 chr1D 87.500 216 21 4 2920 3134 156173990 156174200 8.870000e-61 244.0
23 TraesCS5A01G231400 chr1D 95.652 46 2 0 2823 2868 156172492 156172537 1.230000e-09 75.0
24 TraesCS5A01G231400 chr5D 93.355 2483 145 16 1 2472 164173481 164171008 0.000000e+00 3653.0
25 TraesCS5A01G231400 chr5D 86.333 300 30 2 2845 3134 143667980 143668278 1.850000e-82 316.0
26 TraesCS5A01G231400 chr5D 88.426 216 21 4 2920 3134 372650597 372650809 1.140000e-64 257.0
27 TraesCS5A01G231400 chr1B 84.283 509 51 17 1 496 513370925 513370433 1.340000e-128 470.0
28 TraesCS5A01G231400 chr1B 83.629 507 55 16 1 496 259360152 259360641 4.870000e-123 451.0
29 TraesCS5A01G231400 chr3B 82.798 529 51 22 2379 2868 108261619 108262146 1.360000e-118 436.0
30 TraesCS5A01G231400 chr2B 82.386 528 54 17 2379 2868 717994233 717994759 1.060000e-114 424.0
31 TraesCS5A01G231400 chr2B 83.158 475 41 15 2431 2868 268032911 268032439 6.430000e-107 398.0
32 TraesCS5A01G231400 chr2A 90.421 261 23 2 2609 2868 687644402 687644143 3.060000e-90 342.0
33 TraesCS5A01G231400 chr2A 90.234 256 23 2 2615 2868 495661096 495661351 1.840000e-87 333.0
34 TraesCS5A01G231400 chr2A 98.462 65 1 0 3136 3200 661054619 661054555 7.250000e-22 115.0
35 TraesCS5A01G231400 chr7A 90.385 260 23 2 2609 2867 69780252 69780510 1.100000e-89 340.0
36 TraesCS5A01G231400 chr7A 90.038 261 24 2 2609 2868 572403767 572404026 1.420000e-88 337.0
37 TraesCS5A01G231400 chr7A 98.462 65 1 0 3136 3200 308534236 308534172 7.250000e-22 115.0
38 TraesCS5A01G231400 chr7A 96.970 66 2 0 3135 3200 719933632 719933697 9.380000e-21 111.0
39 TraesCS5A01G231400 chr3A 89.734 263 23 4 2609 2868 394512823 394513084 1.840000e-87 333.0
40 TraesCS5A01G231400 chr3A 86.590 261 23 6 2869 3117 211801299 211801559 8.740000e-71 278.0
41 TraesCS5A01G231400 chr3A 98.462 65 1 0 3136 3200 60813376 60813312 7.250000e-22 115.0
42 TraesCS5A01G231400 chr3A 98.462 65 1 0 3136 3200 412222891 412222827 7.250000e-22 115.0
43 TraesCS5A01G231400 chr7D 88.053 226 15 6 2920 3134 444799976 444800200 1.140000e-64 257.0
44 TraesCS5A01G231400 chr7D 88.785 214 17 4 2920 3133 148612021 148611815 4.100000e-64 255.0
45 TraesCS5A01G231400 chr7D 87.665 227 13 6 2920 3134 362171220 362170997 1.910000e-62 250.0
46 TraesCS5A01G231400 chr7D 82.524 103 4 8 2907 2995 341808614 341808716 9.520000e-11 78.7
47 TraesCS5A01G231400 chr2D 90.710 183 15 2 2953 3134 229565829 229565648 3.190000e-60 243.0
48 TraesCS5A01G231400 chr2D 80.864 162 20 6 2866 3016 276223453 276223292 2.020000e-22 117.0
49 TraesCS5A01G231400 chr6B 85.333 225 20 5 2921 3134 60755986 60755764 1.490000e-53 220.0
50 TraesCS5A01G231400 chr6A 100.000 65 0 0 3136 3200 570707213 570707149 1.560000e-23 121.0


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 TraesCS5A01G231400 chr5A 447001185 447004384 3199 True 5910 5910 100.000 1 3200 1 chr5A.!!$R5 3199
1 TraesCS5A01G231400 chr4D 202553277 202556148 2871 True 4287 4287 93.648 1 2868 1 chr4D.!!$R2 2867
2 TraesCS5A01G231400 chr4D 144297375 144300243 2868 True 4226 4226 93.296 1 2866 1 chr4D.!!$R1 2865
3 TraesCS5A01G231400 chr4D 151101065 151103968 2903 False 3807 3807 90.566 1 2868 1 chr4D.!!$F1 2867
4 TraesCS5A01G231400 chr4D 202571452 202573898 2446 True 3735 3735 94.245 425 2868 1 chr4D.!!$R3 2443
5 TraesCS5A01G231400 chr4D 395879463 395881934 2471 True 3646 3646 93.306 1 2472 1 chr4D.!!$R5 2471
6 TraesCS5A01G231400 chr4D 267042001 267044396 2395 True 2791 2791 88.076 521 2868 1 chr4D.!!$R4 2347
7 TraesCS5A01G231400 chr3D 384050863 384056330 5467 True 2259 4239 91.415 1 2868 2 chr3D.!!$R4 2867
8 TraesCS5A01G231400 chr6D 300592424 300595328 2904 False 3940 3940 91.389 1 2868 1 chr6D.!!$F2 2867
9 TraesCS5A01G231400 chr1D 123203619 123206095 2476 True 3711 3711 93.750 1 2472 1 chr1D.!!$R1 2471
10 TraesCS5A01G231400 chr5D 164171008 164173481 2473 True 3653 3653 93.355 1 2472 1 chr5D.!!$R1 2471
11 TraesCS5A01G231400 chr3B 108261619 108262146 527 False 436 436 82.798 2379 2868 1 chr3B.!!$F1 489
12 TraesCS5A01G231400 chr2B 717994233 717994759 526 False 424 424 82.386 2379 2868 1 chr2B.!!$F1 489

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
900 3518 1.132262 GAGAGCAGAGGAGAAGACACG 59.868 57.143 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2872 5565 0.108774 TGTGGGATTGTGCCGTTGTA 59.891 50.0 0.0 0.0 0.0 2.41 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
34 35 1.821753 AGTGACCAGAGGAGTTCGATG 59.178 52.381 0.00 0.00 0.00 3.84
38 39 1.513158 CAGAGGAGTTCGATGCGGT 59.487 57.895 0.00 0.00 0.00 5.68
63 64 3.550233 CCTCGCTAGCGCTTATAAACAGA 60.550 47.826 31.82 9.35 39.59 3.41
64 65 3.629058 TCGCTAGCGCTTATAAACAGAG 58.371 45.455 31.82 6.90 39.59 3.35
169 177 2.593956 GGGCCGAACTTCACTCCCT 61.594 63.158 0.00 0.00 0.00 4.20
288 2890 5.854431 ACAACAAAAGAAAAATGTGCGTT 57.146 30.435 0.00 0.00 0.00 4.84
307 2909 2.340210 TGCACAGCCAGAAACTACAA 57.660 45.000 0.00 0.00 0.00 2.41
348 2951 1.533731 CGCAGAAAGCCCGAAGTAAAA 59.466 47.619 0.00 0.00 41.38 1.52
414 3017 5.147162 GTGGAAGCACGAAGTATTCTTTTG 58.853 41.667 0.00 0.00 44.75 2.44
420 3024 5.177696 AGCACGAAGTATTCTTTTGTCTGAC 59.822 40.000 0.00 0.00 44.75 3.51
423 3027 7.148639 GCACGAAGTATTCTTTTGTCTGACATA 60.149 37.037 11.86 3.88 44.75 2.29
474 3079 4.774200 AGGCTAAAATGAAGAATGCAACCT 59.226 37.500 0.00 0.00 0.00 3.50
536 3141 4.401022 TGCATGAAAGAACTCCATCAAGT 58.599 39.130 0.00 0.00 0.00 3.16
573 3178 9.890629 GCATACATCTGTATAAATCCTAATCCA 57.109 33.333 2.65 0.00 39.06 3.41
602 3207 5.545658 TCCAGTGCACGAAGAATAAATTC 57.454 39.130 12.01 0.00 37.06 2.17
605 3210 5.163622 CCAGTGCACGAAGAATAAATTCCAT 60.164 40.000 12.01 0.00 37.51 3.41
635 3240 3.747099 GTACACTATGTGGACGTACGT 57.253 47.619 23.04 23.04 37.65 3.57
716 3322 4.579753 TCATCACATTTTCTGACAGTTGCA 59.420 37.500 1.59 0.00 0.00 4.08
726 3332 3.197549 TCTGACAGTTGCATGCATACCTA 59.802 43.478 23.37 2.36 0.00 3.08
782 3388 3.120304 GGATTTCCAACGCACTAACAGAC 60.120 47.826 0.00 0.00 35.64 3.51
794 3400 4.537751 CACTAACAGACCCTCCTCATAGA 58.462 47.826 0.00 0.00 0.00 1.98
824 3430 4.155462 TCTCTGTAGTTGCCACGTAACTAG 59.845 45.833 9.19 2.38 40.29 2.57
895 3513 2.166254 GTCAAGGAGAGCAGAGGAGAAG 59.834 54.545 0.00 0.00 0.00 2.85
900 3518 1.132262 GAGAGCAGAGGAGAAGACACG 59.868 57.143 0.00 0.00 0.00 4.49
959 3581 3.691575 TCCACACTTCCTTTCACAAACA 58.308 40.909 0.00 0.00 0.00 2.83
971 3598 5.532406 CCTTTCACAAACATCTTCTCTCCAA 59.468 40.000 0.00 0.00 0.00 3.53
990 3617 3.003689 CCAAAACAAACACGAGAGAGCAT 59.996 43.478 0.00 0.00 0.00 3.79
1028 3655 1.202806 TGCACCTCTTTACAAGCAGCT 60.203 47.619 0.00 0.00 0.00 4.24
1033 3660 0.321671 TCTTTACAAGCAGCTCCGCT 59.678 50.000 0.00 0.00 46.67 5.52
1043 3670 1.990060 AGCTCCGCTGGTACACCAT 60.990 57.895 0.60 0.00 46.46 3.55
1073 3700 4.129737 CGTCGACCTCCACGGCAT 62.130 66.667 10.58 0.00 34.98 4.40
1097 3724 1.001487 CAAGCTCCACGTCATTTGCAA 60.001 47.619 0.00 0.00 0.00 4.08
1101 3728 2.287547 GCTCCACGTCATTTGCAAAAGA 60.288 45.455 17.19 14.84 0.00 2.52
1104 3731 4.942852 TCCACGTCATTTGCAAAAGAAAT 58.057 34.783 17.91 7.19 0.00 2.17
1113 3740 7.172019 GTCATTTGCAAAAGAAATGGTGAAGAT 59.828 33.333 17.91 0.00 40.01 2.40
1306 3935 7.984050 ACAGGTCAGAATAACTATCAATCTGTG 59.016 37.037 0.00 0.00 38.83 3.66
1435 4064 0.687354 ATCCGGCTCCATGTATGTCC 59.313 55.000 0.00 0.00 0.00 4.02
1491 4120 8.937884 TCTAGCAATACACGCAGTTTTATTTTA 58.062 29.630 0.00 0.00 41.61 1.52
1588 4217 7.218228 ACAGTTCAAGAATACAATCATGCAA 57.782 32.000 0.00 0.00 0.00 4.08
1705 4340 8.975410 TTCATATTGCAGTTCAATTTCAGAAG 57.025 30.769 0.00 0.00 42.48 2.85
1769 4407 8.743085 ATTCACTCTATACAAACATCTTGCAT 57.257 30.769 0.00 0.00 0.00 3.96
1951 4589 5.869579 AGAAGTTTGACTCTTTGGCTGATA 58.130 37.500 0.00 0.00 0.00 2.15
2025 4664 2.307768 CGCAAGGAGGACCATACTCTA 58.692 52.381 0.00 0.00 38.94 2.43
2041 4680 7.487822 CATACTCTATGGGGATTCTACACAT 57.512 40.000 0.00 0.00 32.55 3.21
2155 4794 4.142160 ACAGGGCAAAAAGAGACAAAGAAC 60.142 41.667 0.00 0.00 0.00 3.01
2163 4802 7.278646 GCAAAAAGAGACAAAGAACCAAAGAAT 59.721 33.333 0.00 0.00 0.00 2.40
2190 4829 7.349598 AGAAGAACAAGGCTGTAATCCAATAT 58.650 34.615 0.00 0.00 33.45 1.28
2429 5073 9.463443 GCTGAAATTAGTTTGTGTTAGAACAAT 57.537 29.630 0.00 0.00 41.21 2.71
2507 5153 9.502145 ACATACATAACATATTCAAAAACAGCG 57.498 29.630 0.00 0.00 0.00 5.18
2753 5445 2.348998 CAGAACGAAGGGGCTGCT 59.651 61.111 0.00 0.00 0.00 4.24
2773 5465 1.675483 TGCAACTTTCGTTCAGTGCAT 59.325 42.857 0.00 0.00 0.00 3.96
2789 5481 3.941483 AGTGCATAACATACAGACTTGGC 59.059 43.478 0.00 0.00 0.00 4.52
2856 5549 6.706716 TGACATCATTTGTACTACCACGAAAA 59.293 34.615 0.00 0.00 39.18 2.29
2870 5563 8.365647 ACTACCACGAAAAATATATACTCCTGG 58.634 37.037 0.00 0.00 0.00 4.45
2871 5564 5.995897 ACCACGAAAAATATATACTCCTGGC 59.004 40.000 0.00 0.00 0.00 4.85
2872 5565 6.183361 ACCACGAAAAATATATACTCCTGGCT 60.183 38.462 0.00 0.00 0.00 4.75
2873 5566 7.015877 ACCACGAAAAATATATACTCCTGGCTA 59.984 37.037 0.00 0.00 0.00 3.93
2874 5567 7.331193 CCACGAAAAATATATACTCCTGGCTAC 59.669 40.741 0.00 0.00 0.00 3.58
2875 5568 7.870954 CACGAAAAATATATACTCCTGGCTACA 59.129 37.037 0.00 0.00 0.00 2.74
2876 5569 8.426489 ACGAAAAATATATACTCCTGGCTACAA 58.574 33.333 0.00 0.00 0.00 2.41
2877 5570 8.709646 CGAAAAATATATACTCCTGGCTACAAC 58.290 37.037 0.00 0.00 0.00 3.32
2878 5571 8.603242 AAAAATATATACTCCTGGCTACAACG 57.397 34.615 0.00 0.00 0.00 4.10
2879 5572 5.916661 ATATATACTCCTGGCTACAACGG 57.083 43.478 0.00 0.00 0.00 4.44
2880 5573 0.464452 ATACTCCTGGCTACAACGGC 59.536 55.000 0.00 0.00 0.00 5.68
2881 5574 0.901114 TACTCCTGGCTACAACGGCA 60.901 55.000 0.00 0.00 37.89 5.69
2882 5575 1.741770 CTCCTGGCTACAACGGCAC 60.742 63.158 0.00 0.00 35.46 5.01
2883 5576 2.031919 CCTGGCTACAACGGCACA 59.968 61.111 0.00 0.00 35.46 4.57
2884 5577 1.599518 CCTGGCTACAACGGCACAA 60.600 57.895 0.00 0.00 35.46 3.33
2885 5578 0.960364 CCTGGCTACAACGGCACAAT 60.960 55.000 0.00 0.00 35.46 2.71
2886 5579 0.447801 CTGGCTACAACGGCACAATC 59.552 55.000 0.00 0.00 35.46 2.67
2887 5580 0.958382 TGGCTACAACGGCACAATCC 60.958 55.000 0.00 0.00 34.24 3.01
2888 5581 1.654023 GGCTACAACGGCACAATCCC 61.654 60.000 0.00 0.00 0.00 3.85
2889 5582 0.958382 GCTACAACGGCACAATCCCA 60.958 55.000 0.00 0.00 0.00 4.37
2890 5583 0.802494 CTACAACGGCACAATCCCAC 59.198 55.000 0.00 0.00 0.00 4.61
2891 5584 0.108774 TACAACGGCACAATCCCACA 59.891 50.000 0.00 0.00 0.00 4.17
2892 5585 0.539438 ACAACGGCACAATCCCACAT 60.539 50.000 0.00 0.00 0.00 3.21
2893 5586 0.171007 CAACGGCACAATCCCACATC 59.829 55.000 0.00 0.00 0.00 3.06
2894 5587 0.251121 AACGGCACAATCCCACATCA 60.251 50.000 0.00 0.00 0.00 3.07
2895 5588 0.960364 ACGGCACAATCCCACATCAC 60.960 55.000 0.00 0.00 0.00 3.06
2896 5589 0.959867 CGGCACAATCCCACATCACA 60.960 55.000 0.00 0.00 0.00 3.58
2897 5590 1.477553 GGCACAATCCCACATCACAT 58.522 50.000 0.00 0.00 0.00 3.21
2898 5591 1.406539 GGCACAATCCCACATCACATC 59.593 52.381 0.00 0.00 0.00 3.06
2899 5592 1.406539 GCACAATCCCACATCACATCC 59.593 52.381 0.00 0.00 0.00 3.51
2900 5593 2.947243 GCACAATCCCACATCACATCCT 60.947 50.000 0.00 0.00 0.00 3.24
2901 5594 2.686405 CACAATCCCACATCACATCCTG 59.314 50.000 0.00 0.00 0.00 3.86
2902 5595 2.304092 CAATCCCACATCACATCCTGG 58.696 52.381 0.00 0.00 0.00 4.45
2903 5596 0.184451 ATCCCACATCACATCCTGGC 59.816 55.000 0.00 0.00 0.00 4.85
2904 5597 0.915872 TCCCACATCACATCCTGGCT 60.916 55.000 0.00 0.00 0.00 4.75
2905 5598 0.839277 CCCACATCACATCCTGGCTA 59.161 55.000 0.00 0.00 0.00 3.93
2906 5599 1.202734 CCCACATCACATCCTGGCTAG 60.203 57.143 0.00 0.00 0.00 3.42
2907 5600 1.202734 CCACATCACATCCTGGCTAGG 60.203 57.143 10.47 10.47 46.06 3.02
2908 5601 1.487976 CACATCACATCCTGGCTAGGT 59.512 52.381 16.69 0.41 44.88 3.08
2909 5602 2.092753 CACATCACATCCTGGCTAGGTT 60.093 50.000 16.69 4.72 44.88 3.50
2910 5603 2.092753 ACATCACATCCTGGCTAGGTTG 60.093 50.000 21.95 21.95 45.42 3.77
2911 5604 1.951209 TCACATCCTGGCTAGGTTGA 58.049 50.000 28.26 19.70 43.56 3.18
2912 5605 1.555075 TCACATCCTGGCTAGGTTGAC 59.445 52.381 28.26 0.00 43.56 3.18
2913 5606 1.278985 CACATCCTGGCTAGGTTGACA 59.721 52.381 28.26 5.57 43.56 3.58
2914 5607 1.556911 ACATCCTGGCTAGGTTGACAG 59.443 52.381 28.26 11.11 43.56 3.51
2916 5609 4.625800 CTGGCTAGGTTGACAGGC 57.374 61.111 0.00 0.00 39.32 4.85
2917 5610 1.679311 CTGGCTAGGTTGACAGGCA 59.321 57.895 0.00 0.00 44.20 4.75
2918 5611 0.674895 CTGGCTAGGTTGACAGGCAC 60.675 60.000 0.00 0.00 41.86 5.01
2919 5612 1.374947 GGCTAGGTTGACAGGCACA 59.625 57.895 0.00 0.00 37.30 4.57
2920 5613 0.955919 GGCTAGGTTGACAGGCACAC 60.956 60.000 0.00 0.00 37.30 3.82
2921 5614 1.291877 GCTAGGTTGACAGGCACACG 61.292 60.000 0.00 0.00 0.00 4.49
2922 5615 0.670546 CTAGGTTGACAGGCACACGG 60.671 60.000 0.00 0.00 0.00 4.94
2923 5616 2.107041 TAGGTTGACAGGCACACGGG 62.107 60.000 0.00 0.00 0.00 5.28
2924 5617 2.978010 GTTGACAGGCACACGGGG 60.978 66.667 0.00 0.00 0.00 5.73
2925 5618 3.484806 TTGACAGGCACACGGGGT 61.485 61.111 0.00 0.00 0.00 4.95
2936 5629 3.300765 ACGGGGTGTGACGGACTC 61.301 66.667 0.00 0.00 0.00 3.36
2937 5630 4.415332 CGGGGTGTGACGGACTCG 62.415 72.222 0.00 0.00 43.02 4.18
2938 5631 4.736896 GGGGTGTGACGGACTCGC 62.737 72.222 0.00 0.00 40.63 5.03
2939 5632 4.736896 GGGTGTGACGGACTCGCC 62.737 72.222 4.01 4.01 40.59 5.54
2940 5633 3.681835 GGTGTGACGGACTCGCCT 61.682 66.667 5.16 0.00 38.94 5.52
2941 5634 2.430921 GTGTGACGGACTCGCCTG 60.431 66.667 0.00 0.00 40.63 4.85
2942 5635 2.910479 TGTGACGGACTCGCCTGT 60.910 61.111 0.00 0.00 40.63 4.00
2943 5636 2.430921 GTGACGGACTCGCCTGTG 60.431 66.667 0.00 0.00 40.63 3.66
2944 5637 4.357947 TGACGGACTCGCCTGTGC 62.358 66.667 0.00 0.00 40.63 4.57
2945 5638 4.357947 GACGGACTCGCCTGTGCA 62.358 66.667 0.00 0.00 40.63 4.57
2946 5639 3.649277 GACGGACTCGCCTGTGCAT 62.649 63.158 0.00 0.00 40.63 3.96
2947 5640 3.190849 CGGACTCGCCTGTGCATG 61.191 66.667 0.00 0.00 37.32 4.06
2948 5641 3.503363 GGACTCGCCTGTGCATGC 61.503 66.667 11.82 11.82 37.32 4.06
2980 5673 2.104530 GCCTACTCCGGCTCGTTC 59.895 66.667 0.00 0.00 46.63 3.95
2981 5674 2.806237 CCTACTCCGGCTCGTTCC 59.194 66.667 0.00 0.00 0.00 3.62
2982 5675 2.050350 CCTACTCCGGCTCGTTCCA 61.050 63.158 0.00 0.00 0.00 3.53
2983 5676 1.433879 CTACTCCGGCTCGTTCCAG 59.566 63.158 0.00 0.00 0.00 3.86
2984 5677 2.005960 CTACTCCGGCTCGTTCCAGG 62.006 65.000 0.00 0.00 0.00 4.45
2985 5678 4.821589 CTCCGGCTCGTTCCAGGC 62.822 72.222 0.00 0.00 35.59 4.85
2987 5680 4.821589 CCGGCTCGTTCCAGGCTC 62.822 72.222 0.00 0.00 36.80 4.70
2989 5682 4.821589 GGCTCGTTCCAGGCTCGG 62.822 72.222 0.00 0.00 36.04 4.63
3048 5741 4.864334 CACCCCCTGCTCGGCATC 62.864 72.222 0.00 0.00 38.13 3.91
3050 5743 4.864334 CCCCCTGCTCGGCATCAC 62.864 72.222 0.00 0.00 38.13 3.06
3053 5746 4.827087 CCTGCTCGGCATCACGCT 62.827 66.667 0.00 0.00 41.91 5.07
3054 5747 2.104928 CTGCTCGGCATCACGCTA 59.895 61.111 0.00 0.00 41.91 4.26
3055 5748 2.202743 TGCTCGGCATCACGCTAC 60.203 61.111 0.00 0.00 41.91 3.58
3056 5749 2.962253 GCTCGGCATCACGCTACC 60.962 66.667 0.00 0.00 41.91 3.18
3057 5750 2.494445 CTCGGCATCACGCTACCA 59.506 61.111 0.00 0.00 41.91 3.25
3058 5751 1.878522 CTCGGCATCACGCTACCAC 60.879 63.158 0.00 0.00 41.91 4.16
3059 5752 2.125713 CGGCATCACGCTACCACA 60.126 61.111 0.00 0.00 41.91 4.17
3060 5753 2.452813 CGGCATCACGCTACCACAC 61.453 63.158 0.00 0.00 41.91 3.82
3061 5754 2.452813 GGCATCACGCTACCACACG 61.453 63.158 0.00 0.00 41.91 4.49
3062 5755 3.081133 CATCACGCTACCACACGC 58.919 61.111 0.00 0.00 0.00 5.34
3063 5756 1.736282 CATCACGCTACCACACGCA 60.736 57.895 0.00 0.00 0.00 5.24
3064 5757 1.446099 ATCACGCTACCACACGCAG 60.446 57.895 0.00 0.00 0.00 5.18
3076 5769 3.110139 ACGCAGTGCACTTGGTTG 58.890 55.556 18.94 7.73 42.51 3.77
3077 5770 1.451207 ACGCAGTGCACTTGGTTGA 60.451 52.632 18.94 0.00 42.51 3.18
3078 5771 0.819259 ACGCAGTGCACTTGGTTGAT 60.819 50.000 18.94 0.00 42.51 2.57
3079 5772 1.155889 CGCAGTGCACTTGGTTGATA 58.844 50.000 18.94 0.00 0.00 2.15
3080 5773 1.129251 CGCAGTGCACTTGGTTGATAG 59.871 52.381 18.94 3.41 0.00 2.08
3081 5774 1.470098 GCAGTGCACTTGGTTGATAGG 59.530 52.381 18.94 2.59 0.00 2.57
3082 5775 2.783135 CAGTGCACTTGGTTGATAGGT 58.217 47.619 18.94 0.00 0.00 3.08
3083 5776 2.485426 CAGTGCACTTGGTTGATAGGTG 59.515 50.000 18.94 0.00 0.00 4.00
3087 5780 2.783135 CACTTGGTTGATAGGTGCAGT 58.217 47.619 0.00 0.00 0.00 4.40
3088 5781 2.485426 CACTTGGTTGATAGGTGCAGTG 59.515 50.000 0.00 0.00 0.00 3.66
3089 5782 1.470098 CTTGGTTGATAGGTGCAGTGC 59.530 52.381 8.58 8.58 0.00 4.40
3090 5783 0.673333 TGGTTGATAGGTGCAGTGCG 60.673 55.000 11.20 0.00 0.00 5.34
3091 5784 1.369091 GGTTGATAGGTGCAGTGCGG 61.369 60.000 11.20 0.00 0.00 5.69
3092 5785 0.391130 GTTGATAGGTGCAGTGCGGA 60.391 55.000 11.20 0.00 0.00 5.54
3093 5786 0.391130 TTGATAGGTGCAGTGCGGAC 60.391 55.000 11.20 0.00 34.64 4.79
3094 5787 1.218047 GATAGGTGCAGTGCGGACA 59.782 57.895 10.52 0.00 37.78 4.02
3095 5788 0.179073 GATAGGTGCAGTGCGGACAT 60.179 55.000 10.52 4.22 37.78 3.06
3096 5789 0.253044 ATAGGTGCAGTGCGGACATT 59.747 50.000 10.52 0.00 37.78 2.71
3097 5790 0.391130 TAGGTGCAGTGCGGACATTC 60.391 55.000 10.52 0.00 37.78 2.67
3098 5791 1.672356 GGTGCAGTGCGGACATTCT 60.672 57.895 10.52 0.00 37.78 2.40
3099 5792 0.391130 GGTGCAGTGCGGACATTCTA 60.391 55.000 10.52 0.00 37.78 2.10
3100 5793 1.656652 GTGCAGTGCGGACATTCTAT 58.343 50.000 10.52 0.00 35.67 1.98
3101 5794 2.009774 GTGCAGTGCGGACATTCTATT 58.990 47.619 10.52 0.00 35.67 1.73
3102 5795 2.420022 GTGCAGTGCGGACATTCTATTT 59.580 45.455 10.52 0.00 35.67 1.40
3103 5796 3.081061 TGCAGTGCGGACATTCTATTTT 58.919 40.909 10.52 0.00 0.00 1.82
3104 5797 3.505680 TGCAGTGCGGACATTCTATTTTT 59.494 39.130 10.52 0.00 0.00 1.94
3105 5798 4.098416 GCAGTGCGGACATTCTATTTTTC 58.902 43.478 10.52 0.00 0.00 2.29
3106 5799 4.662145 CAGTGCGGACATTCTATTTTTCC 58.338 43.478 10.52 0.00 0.00 3.13
3107 5800 4.155826 CAGTGCGGACATTCTATTTTTCCA 59.844 41.667 10.52 0.00 0.00 3.53
3108 5801 4.764823 AGTGCGGACATTCTATTTTTCCAA 59.235 37.500 10.52 0.00 0.00 3.53
3109 5802 5.095490 GTGCGGACATTCTATTTTTCCAAG 58.905 41.667 0.63 0.00 0.00 3.61
3110 5803 5.007034 TGCGGACATTCTATTTTTCCAAGA 58.993 37.500 0.00 0.00 0.00 3.02
3111 5804 5.475220 TGCGGACATTCTATTTTTCCAAGAA 59.525 36.000 0.00 0.00 34.00 2.52
3112 5805 6.152661 TGCGGACATTCTATTTTTCCAAGAAT 59.847 34.615 0.00 0.00 39.87 2.40
3113 5806 7.338196 TGCGGACATTCTATTTTTCCAAGAATA 59.662 33.333 0.00 0.00 37.76 1.75
3114 5807 7.857885 GCGGACATTCTATTTTTCCAAGAATAG 59.142 37.037 4.06 4.06 37.76 1.73
3115 5808 8.345565 CGGACATTCTATTTTTCCAAGAATAGG 58.654 37.037 8.85 0.00 37.76 2.57
3116 5809 9.408648 GGACATTCTATTTTTCCAAGAATAGGA 57.591 33.333 8.85 2.59 37.76 2.94
3118 5811 8.893727 ACATTCTATTTTTCCAAGAATAGGACG 58.106 33.333 8.85 0.00 37.76 4.79
3119 5812 6.920569 TCTATTTTTCCAAGAATAGGACGC 57.079 37.500 8.85 0.00 36.79 5.19
3120 5813 6.411376 TCTATTTTTCCAAGAATAGGACGCA 58.589 36.000 8.85 0.00 36.79 5.24
3121 5814 4.759516 TTTTTCCAAGAATAGGACGCAC 57.240 40.909 0.00 0.00 34.19 5.34
3122 5815 2.004583 TTCCAAGAATAGGACGCACG 57.995 50.000 0.00 0.00 34.19 5.34
3123 5816 0.459585 TCCAAGAATAGGACGCACGC 60.460 55.000 0.00 0.00 0.00 5.34
3124 5817 0.739462 CCAAGAATAGGACGCACGCA 60.739 55.000 0.00 0.00 0.00 5.24
3125 5818 1.075542 CAAGAATAGGACGCACGCAA 58.924 50.000 0.00 0.00 0.00 4.85
3126 5819 1.076332 AAGAATAGGACGCACGCAAC 58.924 50.000 0.00 0.00 0.00 4.17
3127 5820 0.739813 AGAATAGGACGCACGCAACC 60.740 55.000 0.00 0.00 0.00 3.77
3128 5821 1.702491 GAATAGGACGCACGCAACCC 61.702 60.000 0.00 0.00 0.00 4.11
3129 5822 3.675619 ATAGGACGCACGCAACCCC 62.676 63.158 0.00 0.00 0.00 4.95
3132 5825 4.980805 GACGCACGCAACCCCAGA 62.981 66.667 0.00 0.00 0.00 3.86
3133 5826 4.988598 ACGCACGCAACCCCAGAG 62.989 66.667 0.00 0.00 0.00 3.35
3134 5827 4.680237 CGCACGCAACCCCAGAGA 62.680 66.667 0.00 0.00 0.00 3.10
3135 5828 2.045926 GCACGCAACCCCAGAGAT 60.046 61.111 0.00 0.00 0.00 2.75
3136 5829 2.401766 GCACGCAACCCCAGAGATG 61.402 63.158 0.00 0.00 0.00 2.90
3137 5830 1.296392 CACGCAACCCCAGAGATGA 59.704 57.895 0.00 0.00 0.00 2.92
3138 5831 0.321564 CACGCAACCCCAGAGATGAA 60.322 55.000 0.00 0.00 0.00 2.57
3139 5832 0.400213 ACGCAACCCCAGAGATGAAA 59.600 50.000 0.00 0.00 0.00 2.69
3140 5833 1.089920 CGCAACCCCAGAGATGAAAG 58.910 55.000 0.00 0.00 0.00 2.62
3141 5834 1.611673 CGCAACCCCAGAGATGAAAGT 60.612 52.381 0.00 0.00 0.00 2.66
3142 5835 1.815003 GCAACCCCAGAGATGAAAGTG 59.185 52.381 0.00 0.00 0.00 3.16
3143 5836 2.815589 GCAACCCCAGAGATGAAAGTGT 60.816 50.000 0.00 0.00 0.00 3.55
3144 5837 2.816087 CAACCCCAGAGATGAAAGTGTG 59.184 50.000 0.00 0.00 0.00 3.82
3145 5838 2.057922 ACCCCAGAGATGAAAGTGTGT 58.942 47.619 0.00 0.00 0.00 3.72
3146 5839 2.443255 ACCCCAGAGATGAAAGTGTGTT 59.557 45.455 0.00 0.00 0.00 3.32
3147 5840 3.650942 ACCCCAGAGATGAAAGTGTGTTA 59.349 43.478 0.00 0.00 0.00 2.41
3148 5841 4.289672 ACCCCAGAGATGAAAGTGTGTTAT 59.710 41.667 0.00 0.00 0.00 1.89
3149 5842 5.487488 ACCCCAGAGATGAAAGTGTGTTATA 59.513 40.000 0.00 0.00 0.00 0.98
3150 5843 6.158695 ACCCCAGAGATGAAAGTGTGTTATAT 59.841 38.462 0.00 0.00 0.00 0.86
3151 5844 7.056635 CCCCAGAGATGAAAGTGTGTTATATT 58.943 38.462 0.00 0.00 0.00 1.28
3152 5845 7.012704 CCCCAGAGATGAAAGTGTGTTATATTG 59.987 40.741 0.00 0.00 0.00 1.90
3153 5846 7.770433 CCCAGAGATGAAAGTGTGTTATATTGA 59.230 37.037 0.00 0.00 0.00 2.57
3154 5847 8.607459 CCAGAGATGAAAGTGTGTTATATTGAC 58.393 37.037 0.00 0.00 0.00 3.18
3155 5848 9.376075 CAGAGATGAAAGTGTGTTATATTGACT 57.624 33.333 0.00 0.00 0.00 3.41
3160 5853 9.823647 ATGAAAGTGTGTTATATTGACTAGAGG 57.176 33.333 0.00 0.00 0.00 3.69
3161 5854 8.258007 TGAAAGTGTGTTATATTGACTAGAGGG 58.742 37.037 0.00 0.00 0.00 4.30
3162 5855 6.732896 AGTGTGTTATATTGACTAGAGGGG 57.267 41.667 0.00 0.00 0.00 4.79
3163 5856 5.602978 AGTGTGTTATATTGACTAGAGGGGG 59.397 44.000 0.00 0.00 0.00 5.40
3182 5875 5.887214 GGGGGTGAATAGGCAATTTTTAT 57.113 39.130 0.00 0.00 0.00 1.40
3183 5876 5.610398 GGGGGTGAATAGGCAATTTTTATG 58.390 41.667 0.00 0.00 0.00 1.90
3184 5877 5.365314 GGGGGTGAATAGGCAATTTTTATGA 59.635 40.000 0.00 0.00 0.00 2.15
3185 5878 6.126911 GGGGGTGAATAGGCAATTTTTATGAA 60.127 38.462 0.00 0.00 0.00 2.57
3186 5879 7.334858 GGGGTGAATAGGCAATTTTTATGAAA 58.665 34.615 0.00 0.00 0.00 2.69
3187 5880 7.495606 GGGGTGAATAGGCAATTTTTATGAAAG 59.504 37.037 0.00 0.00 0.00 2.62
3188 5881 8.040727 GGGTGAATAGGCAATTTTTATGAAAGT 58.959 33.333 0.00 0.00 0.00 2.66
3189 5882 9.087424 GGTGAATAGGCAATTTTTATGAAAGTC 57.913 33.333 0.00 0.00 0.00 3.01
3190 5883 9.860898 GTGAATAGGCAATTTTTATGAAAGTCT 57.139 29.630 0.00 0.00 0.00 3.24
3196 5889 9.612066 AGGCAATTTTTATGAAAGTCTTCAAAA 57.388 25.926 0.00 0.00 44.64 2.44
3197 5890 9.650371 GGCAATTTTTATGAAAGTCTTCAAAAC 57.350 29.630 0.00 0.00 44.64 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.526524 CGCATCGAACTCCTCTGGTC 60.527 60.000 0.00 0.00 0.00 4.02
133 136 1.303888 CAAGTGGGCCTGTGAGCAT 60.304 57.895 4.53 0.00 0.00 3.79
146 149 0.535102 AGTGAAGTTCGGCCCAAGTG 60.535 55.000 0.00 0.00 0.00 3.16
156 159 3.134458 CTGTGTTCAGGGAGTGAAGTTC 58.866 50.000 0.00 0.00 46.18 3.01
169 177 2.805897 CCTTGTTGGGCTGTGTTCA 58.194 52.632 0.00 0.00 0.00 3.18
288 2890 2.340210 TTGTAGTTTCTGGCTGTGCA 57.660 45.000 0.00 0.00 0.00 4.57
293 2895 8.556213 TTAATAACGAATTGTAGTTTCTGGCT 57.444 30.769 0.00 0.00 0.00 4.75
348 2951 0.037697 TCGCGGACTGCATTTGTACT 60.038 50.000 6.13 0.00 46.97 2.73
414 3017 5.652994 AGAAGGAGAACTGTATGTCAGAC 57.347 43.478 6.72 0.00 46.27 3.51
420 3024 5.330455 TGCAGTAGAAGGAGAACTGTATG 57.670 43.478 3.89 0.00 42.10 2.39
423 3027 4.573900 CAATGCAGTAGAAGGAGAACTGT 58.426 43.478 0.00 0.00 42.10 3.55
451 3055 4.774200 AGGTTGCATTCTTCATTTTAGCCT 59.226 37.500 0.00 0.00 0.00 4.58
474 3079 5.588648 ACAGACTGCTTTGCTTAACTAACAA 59.411 36.000 1.25 0.00 0.00 2.83
561 3166 9.247861 GCACTGGATTATATTGGATTAGGATTT 57.752 33.333 0.00 0.00 0.00 2.17
573 3178 8.902540 TTATTCTTCGTGCACTGGATTATATT 57.097 30.769 16.19 0.00 0.00 1.28
581 3186 4.155826 TGGAATTTATTCTTCGTGCACTGG 59.844 41.667 16.19 4.80 37.00 4.00
602 3207 4.883585 ACATAGTGTACTGCATGGAAATGG 59.116 41.667 0.00 0.00 0.00 3.16
605 3210 4.019771 TCCACATAGTGTACTGCATGGAAA 60.020 41.667 9.27 0.00 32.19 3.13
716 3322 4.827692 TCGTGACTTGTTTAGGTATGCAT 58.172 39.130 3.79 3.79 0.00 3.96
754 3360 0.535328 TGCGTTGGAAATCCGGAACA 60.535 50.000 9.01 2.37 39.43 3.18
782 3388 3.895041 GAGAGGTTCTTCTATGAGGAGGG 59.105 52.174 0.00 0.00 0.00 4.30
794 3400 2.972713 TGGCAACTACAGAGAGGTTCTT 59.027 45.455 0.00 0.00 32.44 2.52
824 3430 1.966451 CGTGGTGGGCCTCTGTTTC 60.966 63.158 4.53 0.00 35.27 2.78
921 3542 5.249393 AGTGTGGAGAAGAAGATGTAATGGT 59.751 40.000 0.00 0.00 0.00 3.55
927 3549 3.906846 AGGAAGTGTGGAGAAGAAGATGT 59.093 43.478 0.00 0.00 0.00 3.06
959 3581 5.123227 TCGTGTTTGTTTTGGAGAGAAGAT 58.877 37.500 0.00 0.00 0.00 2.40
971 3598 3.997021 CCTATGCTCTCTCGTGTTTGTTT 59.003 43.478 0.00 0.00 0.00 2.83
990 3617 1.332195 CATCCGCCATGACTCTCCTA 58.668 55.000 0.00 0.00 33.80 2.94
1043 3670 3.733960 CGACGTCGTGGAGCTCCA 61.734 66.667 32.00 32.00 45.30 3.86
1073 3700 0.396435 AATGACGTGGAGCTTGTGGA 59.604 50.000 0.00 0.00 0.00 4.02
1097 3724 5.139727 TGTCCACATCTTCACCATTTCTTT 58.860 37.500 0.00 0.00 0.00 2.52
1101 3728 4.728772 TCTTGTCCACATCTTCACCATTT 58.271 39.130 0.00 0.00 0.00 2.32
1104 3731 3.072915 ACATCTTGTCCACATCTTCACCA 59.927 43.478 0.00 0.00 0.00 4.17
1164 3791 4.109766 CGACATCAATGCCGACTAGTTTA 58.890 43.478 0.00 0.00 35.63 2.01
1419 4048 0.034059 GAGGGACATACATGGAGCCG 59.966 60.000 0.00 0.00 0.00 5.52
1769 4407 4.462483 GGAATTTGTCTAGTTCCATTGGCA 59.538 41.667 0.00 0.00 40.82 4.92
1867 4505 4.866508 TGTAGTTGTCGGAGTTGATCTT 57.133 40.909 0.00 0.00 0.00 2.40
1896 4534 1.280457 GGTCTCTCCATTCCACCTGT 58.720 55.000 0.00 0.00 35.97 4.00
1951 4589 1.059098 TCTATCATCCTGCCGGCAAT 58.941 50.000 32.09 22.48 0.00 3.56
1998 4637 1.353022 TGGTCCTCCTTGCGGTTAATT 59.647 47.619 0.00 0.00 34.23 1.40
2025 4664 2.244510 TGGCAATGTGTAGAATCCCCAT 59.755 45.455 0.00 0.00 0.00 4.00
2036 4675 4.523943 TGATAAGCTTTTCTGGCAATGTGT 59.476 37.500 16.42 0.00 0.00 3.72
2038 4677 5.244626 ACTTGATAAGCTTTTCTGGCAATGT 59.755 36.000 16.42 3.56 0.00 2.71
2041 4680 6.658816 TCATACTTGATAAGCTTTTCTGGCAA 59.341 34.615 16.42 4.10 0.00 4.52
2155 4794 6.015940 ACAGCCTTGTTCTTCTTATTCTTTGG 60.016 38.462 0.00 0.00 32.28 3.28
2163 4802 6.121776 TGGATTACAGCCTTGTTCTTCTTA 57.878 37.500 0.00 0.00 38.76 2.10
2368 5010 8.374327 TGATCAGAAGCAAACTATGATACATG 57.626 34.615 0.00 0.00 34.33 3.21
2488 5134 9.745880 TTTTAACCGCTGTTTTTGAATATGTTA 57.254 25.926 0.00 0.00 35.87 2.41
2773 5465 2.935849 CGCATGCCAAGTCTGTATGTTA 59.064 45.455 13.15 0.00 0.00 2.41
2807 5500 6.518208 TTTGTACTACTTGCACCAACTTTT 57.482 33.333 0.00 0.00 0.00 2.27
2810 5503 5.238650 GTCATTTGTACTACTTGCACCAACT 59.761 40.000 0.00 0.00 0.00 3.16
2856 5549 5.337330 GCCGTTGTAGCCAGGAGTATATATT 60.337 44.000 0.00 0.00 0.00 1.28
2868 5561 0.958382 GGATTGTGCCGTTGTAGCCA 60.958 55.000 0.00 0.00 0.00 4.75
2869 5562 1.654023 GGGATTGTGCCGTTGTAGCC 61.654 60.000 0.00 0.00 0.00 3.93
2870 5563 0.958382 TGGGATTGTGCCGTTGTAGC 60.958 55.000 0.00 0.00 0.00 3.58
2871 5564 0.802494 GTGGGATTGTGCCGTTGTAG 59.198 55.000 0.00 0.00 0.00 2.74
2872 5565 0.108774 TGTGGGATTGTGCCGTTGTA 59.891 50.000 0.00 0.00 0.00 2.41
2873 5566 0.539438 ATGTGGGATTGTGCCGTTGT 60.539 50.000 0.00 0.00 0.00 3.32
2874 5567 0.171007 GATGTGGGATTGTGCCGTTG 59.829 55.000 0.00 0.00 0.00 4.10
2875 5568 0.251121 TGATGTGGGATTGTGCCGTT 60.251 50.000 0.00 0.00 0.00 4.44
2876 5569 0.960364 GTGATGTGGGATTGTGCCGT 60.960 55.000 0.00 0.00 0.00 5.68
2877 5570 0.959867 TGTGATGTGGGATTGTGCCG 60.960 55.000 0.00 0.00 0.00 5.69
2878 5571 1.406539 GATGTGATGTGGGATTGTGCC 59.593 52.381 0.00 0.00 0.00 5.01
2879 5572 1.406539 GGATGTGATGTGGGATTGTGC 59.593 52.381 0.00 0.00 0.00 4.57
2880 5573 2.686405 CAGGATGTGATGTGGGATTGTG 59.314 50.000 0.00 0.00 0.00 3.33
2881 5574 2.357465 CCAGGATGTGATGTGGGATTGT 60.357 50.000 0.00 0.00 0.00 2.71
2882 5575 2.304092 CCAGGATGTGATGTGGGATTG 58.696 52.381 0.00 0.00 0.00 2.67
2883 5576 1.410648 GCCAGGATGTGATGTGGGATT 60.411 52.381 0.00 0.00 0.00 3.01
2884 5577 0.184451 GCCAGGATGTGATGTGGGAT 59.816 55.000 0.00 0.00 0.00 3.85
2885 5578 0.915872 AGCCAGGATGTGATGTGGGA 60.916 55.000 0.00 0.00 0.00 4.37
2886 5579 0.839277 TAGCCAGGATGTGATGTGGG 59.161 55.000 0.00 0.00 0.00 4.61
2887 5580 1.202734 CCTAGCCAGGATGTGATGTGG 60.203 57.143 0.00 0.00 45.91 4.17
2888 5581 1.487976 ACCTAGCCAGGATGTGATGTG 59.512 52.381 4.75 0.00 45.91 3.21
2889 5582 1.885049 ACCTAGCCAGGATGTGATGT 58.115 50.000 4.75 0.00 45.91 3.06
2890 5583 2.171237 TCAACCTAGCCAGGATGTGATG 59.829 50.000 4.75 0.00 45.91 3.07
2891 5584 2.171448 GTCAACCTAGCCAGGATGTGAT 59.829 50.000 4.75 0.00 45.91 3.06
2892 5585 1.555075 GTCAACCTAGCCAGGATGTGA 59.445 52.381 4.75 2.59 45.91 3.58
2893 5586 1.278985 TGTCAACCTAGCCAGGATGTG 59.721 52.381 4.75 0.02 45.91 3.21
2894 5587 1.556911 CTGTCAACCTAGCCAGGATGT 59.443 52.381 4.75 0.00 45.91 3.06
2895 5588 1.134280 CCTGTCAACCTAGCCAGGATG 60.134 57.143 4.75 3.15 45.97 3.51
2896 5589 1.207791 CCTGTCAACCTAGCCAGGAT 58.792 55.000 4.75 0.00 45.97 3.24
2897 5590 1.553690 GCCTGTCAACCTAGCCAGGA 61.554 60.000 4.75 0.00 45.97 3.86
2899 5592 0.674895 GTGCCTGTCAACCTAGCCAG 60.675 60.000 0.00 0.00 0.00 4.85
2900 5593 1.374947 GTGCCTGTCAACCTAGCCA 59.625 57.895 0.00 0.00 0.00 4.75
2901 5594 0.955919 GTGTGCCTGTCAACCTAGCC 60.956 60.000 0.00 0.00 0.00 3.93
2902 5595 1.291877 CGTGTGCCTGTCAACCTAGC 61.292 60.000 0.00 0.00 0.00 3.42
2903 5596 0.670546 CCGTGTGCCTGTCAACCTAG 60.671 60.000 0.00 0.00 0.00 3.02
2904 5597 1.369692 CCGTGTGCCTGTCAACCTA 59.630 57.895 0.00 0.00 0.00 3.08
2905 5598 2.111043 CCGTGTGCCTGTCAACCT 59.889 61.111 0.00 0.00 0.00 3.50
2906 5599 2.978010 CCCGTGTGCCTGTCAACC 60.978 66.667 0.00 0.00 0.00 3.77
2907 5600 2.978010 CCCCGTGTGCCTGTCAAC 60.978 66.667 0.00 0.00 0.00 3.18
2908 5601 3.484806 ACCCCGTGTGCCTGTCAA 61.485 61.111 0.00 0.00 0.00 3.18
2909 5602 4.248842 CACCCCGTGTGCCTGTCA 62.249 66.667 0.00 0.00 38.34 3.58
2919 5612 3.300765 GAGTCCGTCACACCCCGT 61.301 66.667 0.00 0.00 0.00 5.28
2920 5613 4.415332 CGAGTCCGTCACACCCCG 62.415 72.222 0.00 0.00 0.00 5.73
2921 5614 4.736896 GCGAGTCCGTCACACCCC 62.737 72.222 0.00 0.00 38.24 4.95
2922 5615 4.736896 GGCGAGTCCGTCACACCC 62.737 72.222 0.00 0.00 40.69 4.61
2923 5616 3.681835 AGGCGAGTCCGTCACACC 61.682 66.667 0.00 0.00 44.02 4.16
2924 5617 2.430921 CAGGCGAGTCCGTCACAC 60.431 66.667 0.00 0.00 44.02 3.82
2925 5618 2.910479 ACAGGCGAGTCCGTCACA 60.910 61.111 0.00 0.00 44.02 3.58
2926 5619 2.430921 CACAGGCGAGTCCGTCAC 60.431 66.667 0.00 0.00 44.02 3.67
2927 5620 4.357947 GCACAGGCGAGTCCGTCA 62.358 66.667 0.00 0.00 44.02 4.35
2928 5621 3.649277 ATGCACAGGCGAGTCCGTC 62.649 63.158 0.00 0.00 45.35 4.79
2929 5622 3.695606 ATGCACAGGCGAGTCCGT 61.696 61.111 0.00 0.00 45.35 4.69
2930 5623 3.190849 CATGCACAGGCGAGTCCG 61.191 66.667 0.00 0.00 45.35 4.79
2931 5624 3.503363 GCATGCACAGGCGAGTCC 61.503 66.667 14.21 0.00 45.35 3.85
2956 5649 4.570663 CCGGAGTAGGCGGCGAAG 62.571 72.222 12.98 0.00 0.00 3.79
2964 5657 2.005960 CTGGAACGAGCCGGAGTAGG 62.006 65.000 5.05 0.00 36.35 3.18
2965 5658 1.433879 CTGGAACGAGCCGGAGTAG 59.566 63.158 5.05 0.00 36.35 2.57
2966 5659 2.050350 CCTGGAACGAGCCGGAGTA 61.050 63.158 5.05 0.00 36.35 2.59
2967 5660 3.382832 CCTGGAACGAGCCGGAGT 61.383 66.667 5.05 0.00 36.35 3.85
2968 5661 4.821589 GCCTGGAACGAGCCGGAG 62.822 72.222 5.05 0.00 36.35 4.63
2970 5663 4.821589 GAGCCTGGAACGAGCCGG 62.822 72.222 0.00 0.00 0.00 6.13
2972 5665 4.821589 CCGAGCCTGGAACGAGCC 62.822 72.222 12.93 0.00 0.00 4.70
2974 5667 4.821589 GGCCGAGCCTGGAACGAG 62.822 72.222 12.93 6.02 46.69 4.18
3031 5724 4.864334 GATGCCGAGCAGGGGGTG 62.864 72.222 4.90 0.00 43.65 4.61
3033 5726 4.864334 GTGATGCCGAGCAGGGGG 62.864 72.222 4.90 0.00 43.65 5.40
3044 5737 3.081133 CGTGTGGTAGCGTGATGC 58.919 61.111 0.00 0.00 46.98 3.91
3045 5738 1.686566 CTGCGTGTGGTAGCGTGATG 61.687 60.000 0.00 0.00 35.87 3.07
3046 5739 1.446099 CTGCGTGTGGTAGCGTGAT 60.446 57.895 0.00 0.00 35.87 3.06
3047 5740 2.049526 CTGCGTGTGGTAGCGTGA 60.050 61.111 0.00 0.00 35.87 4.35
3048 5741 2.355837 ACTGCGTGTGGTAGCGTG 60.356 61.111 0.00 0.00 35.87 5.34
3049 5742 2.355837 CACTGCGTGTGGTAGCGT 60.356 61.111 2.18 0.00 42.68 5.07
3050 5743 3.777925 GCACTGCGTGTGGTAGCG 61.778 66.667 10.89 0.00 46.27 4.26
3051 5744 2.664851 TGCACTGCGTGTGGTAGC 60.665 61.111 10.89 0.00 46.27 3.58
3052 5745 0.880278 AAGTGCACTGCGTGTGGTAG 60.880 55.000 22.49 0.00 46.27 3.18
3053 5746 1.145156 AAGTGCACTGCGTGTGGTA 59.855 52.632 22.49 0.00 46.27 3.25
3054 5747 2.124736 AAGTGCACTGCGTGTGGT 60.125 55.556 22.49 0.00 46.27 4.16
3055 5748 2.328989 CAAGTGCACTGCGTGTGG 59.671 61.111 22.49 0.50 46.27 4.17
3057 5750 1.748879 AACCAAGTGCACTGCGTGT 60.749 52.632 22.49 12.26 35.75 4.49
3058 5751 1.298563 CAACCAAGTGCACTGCGTG 60.299 57.895 22.49 15.13 36.51 5.34
3059 5752 0.819259 ATCAACCAAGTGCACTGCGT 60.819 50.000 22.49 16.47 0.00 5.24
3060 5753 1.129251 CTATCAACCAAGTGCACTGCG 59.871 52.381 22.49 15.76 0.00 5.18
3061 5754 1.470098 CCTATCAACCAAGTGCACTGC 59.530 52.381 22.49 0.00 0.00 4.40
3062 5755 2.485426 CACCTATCAACCAAGTGCACTG 59.515 50.000 22.49 11.68 0.00 3.66
3063 5756 2.783135 CACCTATCAACCAAGTGCACT 58.217 47.619 15.25 15.25 0.00 4.40
3067 5760 2.485426 CACTGCACCTATCAACCAAGTG 59.515 50.000 0.00 0.00 0.00 3.16
3068 5761 2.783135 CACTGCACCTATCAACCAAGT 58.217 47.619 0.00 0.00 0.00 3.16
3069 5762 1.470098 GCACTGCACCTATCAACCAAG 59.530 52.381 0.00 0.00 0.00 3.61
3070 5763 1.533625 GCACTGCACCTATCAACCAA 58.466 50.000 0.00 0.00 0.00 3.67
3071 5764 0.673333 CGCACTGCACCTATCAACCA 60.673 55.000 1.11 0.00 0.00 3.67
3072 5765 1.369091 CCGCACTGCACCTATCAACC 61.369 60.000 1.11 0.00 0.00 3.77
3073 5766 0.391130 TCCGCACTGCACCTATCAAC 60.391 55.000 1.11 0.00 0.00 3.18
3074 5767 0.391130 GTCCGCACTGCACCTATCAA 60.391 55.000 1.11 0.00 0.00 2.57
3075 5768 1.218047 GTCCGCACTGCACCTATCA 59.782 57.895 1.11 0.00 0.00 2.15
3076 5769 0.179073 ATGTCCGCACTGCACCTATC 60.179 55.000 1.11 0.00 0.00 2.08
3077 5770 0.253044 AATGTCCGCACTGCACCTAT 59.747 50.000 1.11 0.00 0.00 2.57
3078 5771 0.391130 GAATGTCCGCACTGCACCTA 60.391 55.000 1.11 0.00 0.00 3.08
3079 5772 1.672356 GAATGTCCGCACTGCACCT 60.672 57.895 1.11 0.00 0.00 4.00
3080 5773 0.391130 TAGAATGTCCGCACTGCACC 60.391 55.000 1.11 0.00 0.00 5.01
3081 5774 1.656652 ATAGAATGTCCGCACTGCAC 58.343 50.000 1.11 0.00 0.00 4.57
3082 5775 2.401583 AATAGAATGTCCGCACTGCA 57.598 45.000 1.11 0.00 0.00 4.41
3083 5776 3.764885 AAAATAGAATGTCCGCACTGC 57.235 42.857 0.00 0.00 0.00 4.40
3084 5777 4.155826 TGGAAAAATAGAATGTCCGCACTG 59.844 41.667 0.00 0.00 0.00 3.66
3085 5778 4.331968 TGGAAAAATAGAATGTCCGCACT 58.668 39.130 0.00 0.00 0.00 4.40
3086 5779 4.695217 TGGAAAAATAGAATGTCCGCAC 57.305 40.909 0.00 0.00 0.00 5.34
3087 5780 5.007034 TCTTGGAAAAATAGAATGTCCGCA 58.993 37.500 0.00 0.00 0.00 5.69
3088 5781 5.560966 TCTTGGAAAAATAGAATGTCCGC 57.439 39.130 0.00 0.00 0.00 5.54
3089 5782 8.345565 CCTATTCTTGGAAAAATAGAATGTCCG 58.654 37.037 0.00 0.00 38.64 4.79
3090 5783 9.408648 TCCTATTCTTGGAAAAATAGAATGTCC 57.591 33.333 0.00 0.00 38.64 4.02
3092 5785 8.893727 CGTCCTATTCTTGGAAAAATAGAATGT 58.106 33.333 0.00 0.00 38.64 2.71
3093 5786 7.857885 GCGTCCTATTCTTGGAAAAATAGAATG 59.142 37.037 0.00 0.00 38.64 2.67
3094 5787 7.556275 TGCGTCCTATTCTTGGAAAAATAGAAT 59.444 33.333 0.00 0.00 40.61 2.40
3095 5788 6.882140 TGCGTCCTATTCTTGGAAAAATAGAA 59.118 34.615 4.17 0.00 37.56 2.10
3096 5789 6.315393 GTGCGTCCTATTCTTGGAAAAATAGA 59.685 38.462 4.17 0.00 37.56 1.98
3097 5790 6.487103 GTGCGTCCTATTCTTGGAAAAATAG 58.513 40.000 0.00 0.00 35.93 1.73
3098 5791 5.064198 CGTGCGTCCTATTCTTGGAAAAATA 59.936 40.000 0.00 0.00 35.10 1.40
3099 5792 4.142687 CGTGCGTCCTATTCTTGGAAAAAT 60.143 41.667 0.00 0.00 35.10 1.82
3100 5793 3.187637 CGTGCGTCCTATTCTTGGAAAAA 59.812 43.478 0.00 0.00 35.10 1.94
3101 5794 2.739913 CGTGCGTCCTATTCTTGGAAAA 59.260 45.455 0.00 0.00 35.10 2.29
3102 5795 2.343101 CGTGCGTCCTATTCTTGGAAA 58.657 47.619 0.00 0.00 35.10 3.13
3103 5796 2.004583 CGTGCGTCCTATTCTTGGAA 57.995 50.000 0.00 0.00 35.10 3.53
3104 5797 0.459585 GCGTGCGTCCTATTCTTGGA 60.460 55.000 0.00 0.00 0.00 3.53
3105 5798 0.739462 TGCGTGCGTCCTATTCTTGG 60.739 55.000 0.00 0.00 0.00 3.61
3106 5799 1.075542 TTGCGTGCGTCCTATTCTTG 58.924 50.000 0.00 0.00 0.00 3.02
3107 5800 1.076332 GTTGCGTGCGTCCTATTCTT 58.924 50.000 0.00 0.00 0.00 2.52
3108 5801 0.739813 GGTTGCGTGCGTCCTATTCT 60.740 55.000 0.00 0.00 0.00 2.40
3109 5802 1.702491 GGGTTGCGTGCGTCCTATTC 61.702 60.000 5.40 0.00 0.00 1.75
3110 5803 1.743995 GGGTTGCGTGCGTCCTATT 60.744 57.895 5.40 0.00 0.00 1.73
3111 5804 2.125269 GGGTTGCGTGCGTCCTAT 60.125 61.111 5.40 0.00 0.00 2.57
3112 5805 4.382320 GGGGTTGCGTGCGTCCTA 62.382 66.667 5.40 0.00 0.00 2.94
3115 5808 4.980805 TCTGGGGTTGCGTGCGTC 62.981 66.667 0.00 0.00 0.00 5.19
3116 5809 4.988598 CTCTGGGGTTGCGTGCGT 62.989 66.667 0.00 0.00 0.00 5.24
3117 5810 3.958147 ATCTCTGGGGTTGCGTGCG 62.958 63.158 0.00 0.00 0.00 5.34
3118 5811 2.045926 ATCTCTGGGGTTGCGTGC 60.046 61.111 0.00 0.00 0.00 5.34
3119 5812 0.321564 TTCATCTCTGGGGTTGCGTG 60.322 55.000 0.00 0.00 0.00 5.34
3120 5813 0.400213 TTTCATCTCTGGGGTTGCGT 59.600 50.000 0.00 0.00 0.00 5.24
3121 5814 1.089920 CTTTCATCTCTGGGGTTGCG 58.910 55.000 0.00 0.00 0.00 4.85
3122 5815 1.815003 CACTTTCATCTCTGGGGTTGC 59.185 52.381 0.00 0.00 0.00 4.17
3123 5816 2.816087 CACACTTTCATCTCTGGGGTTG 59.184 50.000 0.00 0.00 0.00 3.77
3124 5817 2.443255 ACACACTTTCATCTCTGGGGTT 59.557 45.455 0.00 0.00 0.00 4.11
3125 5818 2.057922 ACACACTTTCATCTCTGGGGT 58.942 47.619 0.00 0.00 0.00 4.95
3126 5819 2.867109 ACACACTTTCATCTCTGGGG 57.133 50.000 0.00 0.00 0.00 4.96
3127 5820 7.770433 TCAATATAACACACTTTCATCTCTGGG 59.230 37.037 0.00 0.00 0.00 4.45
3128 5821 8.607459 GTCAATATAACACACTTTCATCTCTGG 58.393 37.037 0.00 0.00 0.00 3.86
3129 5822 9.376075 AGTCAATATAACACACTTTCATCTCTG 57.624 33.333 0.00 0.00 0.00 3.35
3134 5827 9.823647 CCTCTAGTCAATATAACACACTTTCAT 57.176 33.333 0.00 0.00 0.00 2.57
3135 5828 8.258007 CCCTCTAGTCAATATAACACACTTTCA 58.742 37.037 0.00 0.00 0.00 2.69
3136 5829 7.711339 CCCCTCTAGTCAATATAACACACTTTC 59.289 40.741 0.00 0.00 0.00 2.62
3137 5830 7.365652 CCCCCTCTAGTCAATATAACACACTTT 60.366 40.741 0.00 0.00 0.00 2.66
3138 5831 6.099845 CCCCCTCTAGTCAATATAACACACTT 59.900 42.308 0.00 0.00 0.00 3.16
3139 5832 5.602978 CCCCCTCTAGTCAATATAACACACT 59.397 44.000 0.00 0.00 0.00 3.55
3140 5833 5.855045 CCCCCTCTAGTCAATATAACACAC 58.145 45.833 0.00 0.00 0.00 3.82
3160 5853 5.365314 TCATAAAAATTGCCTATTCACCCCC 59.635 40.000 0.00 0.00 0.00 5.40
3161 5854 6.478512 TCATAAAAATTGCCTATTCACCCC 57.521 37.500 0.00 0.00 0.00 4.95
3162 5855 8.040727 ACTTTCATAAAAATTGCCTATTCACCC 58.959 33.333 0.00 0.00 0.00 4.61
3163 5856 9.087424 GACTTTCATAAAAATTGCCTATTCACC 57.913 33.333 0.00 0.00 0.00 4.02
3164 5857 9.860898 AGACTTTCATAAAAATTGCCTATTCAC 57.139 29.630 0.00 0.00 0.00 3.18
3170 5863 9.612066 TTTTGAAGACTTTCATAAAAATTGCCT 57.388 25.926 0.00 0.00 42.60 4.75
3171 5864 9.650371 GTTTTGAAGACTTTCATAAAAATTGCC 57.350 29.630 0.00 0.00 42.60 4.52


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

AutoCloner maintained by Alex Coulton.