Multiple sequence alignment - TraesCS6D01G108000

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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 TraesCS6D01G108000 chr6D 100.000 5111 0 0 1 5111 72139885 72144995 0.000000e+00 9439.0
1 TraesCS6D01G108000 chr6D 98.930 187 1 1 4464 4650 72170488 72170673 2.950000e-87 333.0
2 TraesCS6D01G108000 chr6D 75.519 482 89 15 4644 5111 144020556 144020090 5.190000e-50 209.0
3 TraesCS6D01G108000 chr6A 92.834 3419 144 54 1 3394 88846958 88850300 0.000000e+00 4863.0
4 TraesCS6D01G108000 chr6A 95.770 922 25 8 3555 4469 88850302 88851216 0.000000e+00 1474.0
5 TraesCS6D01G108000 chr6A 93.949 661 27 8 4464 5111 518697124 518696464 0.000000e+00 987.0
6 TraesCS6D01G108000 chr6A 93.797 661 28 8 4464 5111 518776950 518776290 0.000000e+00 981.0
7 TraesCS6D01G108000 chr6A 96.237 186 7 0 4464 4649 518675632 518675447 6.430000e-79 305.0
8 TraesCS6D01G108000 chr6B 95.046 2947 94 20 489 3393 146696356 146699292 0.000000e+00 4586.0
9 TraesCS6D01G108000 chr6B 95.119 881 31 9 3550 4425 146699290 146700163 0.000000e+00 1378.0
10 TraesCS6D01G108000 chr6B 89.101 367 19 8 1 366 146695929 146696275 2.190000e-118 436.0
11 TraesCS6D01G108000 chr3B 96.520 661 10 4 4464 5111 119291967 119291307 0.000000e+00 1081.0
12 TraesCS6D01G108000 chr3B 98.930 187 2 0 4464 4650 119287393 119287207 8.200000e-88 335.0
13 TraesCS6D01G108000 chr1B 93.797 661 19 9 4465 5111 49109989 49109337 0.000000e+00 974.0
14 TraesCS6D01G108000 chr1B 97.561 164 4 0 3389 3552 626072059 626071896 1.080000e-71 281.0
15 TraesCS6D01G108000 chr4A 98.020 505 10 0 4465 4969 626783111 626783615 0.000000e+00 878.0
16 TraesCS6D01G108000 chr4A 97.849 186 4 0 4464 4649 626841081 626841266 6.380000e-84 322.0
17 TraesCS6D01G108000 chr4A 96.581 117 4 0 4995 5111 626837035 626837151 1.450000e-45 195.0
18 TraesCS6D01G108000 chrUn 96.188 341 13 0 4475 4815 41017356 41017016 4.470000e-155 558.0
19 TraesCS6D01G108000 chrUn 92.607 257 6 4 4868 5111 41017018 41016762 1.750000e-94 357.0
20 TraesCS6D01G108000 chrUn 97.414 116 3 0 4996 5111 337104386 337104271 1.120000e-46 198.0
21 TraesCS6D01G108000 chrUn 97.414 116 3 0 4996 5111 416889230 416889345 1.120000e-46 198.0
22 TraesCS6D01G108000 chrUn 76.812 138 30 2 4715 4851 340492328 340492464 5.490000e-10 76.8
23 TraesCS6D01G108000 chr2B 84.866 522 42 21 3886 4407 68602015 68602499 4.600000e-135 492.0
24 TraesCS6D01G108000 chr2B 83.208 530 54 20 3886 4414 145375935 145375440 2.170000e-123 453.0
25 TraesCS6D01G108000 chr2B 82.798 529 51 22 3886 4413 39734914 39735403 2.190000e-118 436.0
26 TraesCS6D01G108000 chr2B 85.878 262 21 9 2737 2993 68601680 68601930 1.090000e-66 265.0
27 TraesCS6D01G108000 chr1D 83.932 529 50 20 3886 4414 486701536 486701043 1.670000e-129 473.0
28 TraesCS6D01G108000 chr1D 81.937 537 54 24 3886 4420 308188483 308188978 1.020000e-111 414.0
29 TraesCS6D01G108000 chr1D 79.574 235 26 14 2848 3075 308188249 308188468 1.150000e-31 148.0
30 TraesCS6D01G108000 chr4B 83.365 529 53 19 3886 4414 566610707 566610214 1.680000e-124 457.0
31 TraesCS6D01G108000 chr4B 81.726 591 54 28 3886 4465 527326927 527326380 1.310000e-120 444.0
32 TraesCS6D01G108000 chr4B 79.149 235 26 15 2848 3075 527327160 527326942 1.920000e-29 141.0
33 TraesCS6D01G108000 chr7D 82.890 526 54 18 3886 4411 162186122 162185633 1.690000e-119 440.0
34 TraesCS6D01G108000 chr7D 80.985 589 65 27 3886 4465 298811879 298812429 1.700000e-114 424.0
35 TraesCS6D01G108000 chr1A 82.830 530 53 21 3886 4414 45647766 45647274 1.690000e-119 440.0
36 TraesCS6D01G108000 chr2D 82.609 529 56 17 3886 4414 408489820 408489328 7.860000e-118 435.0
37 TraesCS6D01G108000 chr2D 98.171 164 3 0 3391 3554 478874293 478874130 2.330000e-73 287.0
38 TraesCS6D01G108000 chr2D 78.723 235 27 15 2848 3075 136351591 136351809 8.930000e-28 135.0
39 TraesCS6D01G108000 chr2D 77.880 217 21 16 2848 3060 107843733 107843540 5.410000e-20 110.0
40 TraesCS6D01G108000 chr3D 81.474 529 55 23 3886 4411 173629205 173628717 1.330000e-105 394.0
41 TraesCS6D01G108000 chr3D 98.204 167 2 1 3392 3558 211947732 211947567 1.800000e-74 291.0
42 TraesCS6D01G108000 chr3D 96.552 174 6 0 3388 3561 536788501 536788328 6.470000e-74 289.0
43 TraesCS6D01G108000 chr3D 95.858 169 6 1 3392 3559 571465528 571465360 6.520000e-69 272.0
44 TraesCS6D01G108000 chr3D 96.386 166 5 1 3392 3556 579494792 579494957 6.520000e-69 272.0
45 TraesCS6D01G108000 chr3D 80.087 231 23 15 2852 3075 173629434 173629220 3.190000e-32 150.0
46 TraesCS6D01G108000 chr5D 98.773 163 2 0 3392 3554 476192534 476192372 1.800000e-74 291.0
47 TraesCS6D01G108000 chr5D 99.359 156 1 0 3392 3547 552059769 552059924 3.010000e-72 283.0
48 TraesCS6D01G108000 chr2A 94.652 187 9 1 4463 4649 757536612 757536797 6.470000e-74 289.0
49 TraesCS6D01G108000 chr4D 97.605 167 3 1 3388 3553 38450781 38450615 8.380000e-73 285.0
50 TraesCS6D01G108000 chr3A 93.382 136 6 2 2738 2871 688436502 688436636 1.120000e-46 198.0


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 TraesCS6D01G108000 chr6D 72139885 72144995 5110 False 9439.000000 9439 100.000000 1 5111 1 chr6D.!!$F1 5110
1 TraesCS6D01G108000 chr6A 88846958 88851216 4258 False 3168.500000 4863 94.302000 1 4469 2 chr6A.!!$F1 4468
2 TraesCS6D01G108000 chr6A 518696464 518697124 660 True 987.000000 987 93.949000 4464 5111 1 chr6A.!!$R2 647
3 TraesCS6D01G108000 chr6A 518776290 518776950 660 True 981.000000 981 93.797000 4464 5111 1 chr6A.!!$R3 647
4 TraesCS6D01G108000 chr6B 146695929 146700163 4234 False 2133.333333 4586 93.088667 1 4425 3 chr6B.!!$F1 4424
5 TraesCS6D01G108000 chr3B 119287207 119291967 4760 True 708.000000 1081 97.725000 4464 5111 2 chr3B.!!$R1 647
6 TraesCS6D01G108000 chr1B 49109337 49109989 652 True 974.000000 974 93.797000 4465 5111 1 chr1B.!!$R1 646
7 TraesCS6D01G108000 chr4A 626783111 626783615 504 False 878.000000 878 98.020000 4465 4969 1 chr4A.!!$F1 504
8 TraesCS6D01G108000 chr4A 626837035 626841266 4231 False 258.500000 322 97.215000 4464 5111 2 chr4A.!!$F2 647
9 TraesCS6D01G108000 chrUn 41016762 41017356 594 True 457.500000 558 94.397500 4475 5111 2 chrUn.!!$R2 636
10 TraesCS6D01G108000 chr2B 68601680 68602499 819 False 378.500000 492 85.372000 2737 4407 2 chr2B.!!$F2 1670
11 TraesCS6D01G108000 chr1D 308188249 308188978 729 False 281.000000 414 80.755500 2848 4420 2 chr1D.!!$F1 1572
12 TraesCS6D01G108000 chr4B 527326380 527327160 780 True 292.500000 444 80.437500 2848 4465 2 chr4B.!!$R2 1617
13 TraesCS6D01G108000 chr7D 298811879 298812429 550 False 424.000000 424 80.985000 3886 4465 1 chr7D.!!$F1 579
14 TraesCS6D01G108000 chr3D 173628717 173629434 717 True 272.000000 394 80.780500 2852 4411 2 chr3D.!!$R4 1559

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
365 373 0.105778 CCCGCAATTCCCTCTCTCTC 59.894 60.000 0.00 0.00 0.00 3.20 F
662 691 0.174845 GGGGCGGCCATTAGTTTTTC 59.825 55.000 30.95 3.87 0.00 2.29 F
2053 2104 0.985490 GATGGCCAAGGAGGAGGAGT 60.985 60.000 10.96 0.00 41.22 3.85 F
2436 2498 4.040755 AGCCCTGTAGATGATGTTACCTT 58.959 43.478 0.00 0.00 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 2282 1.954651 GATTCCGACGAATCCGGCC 60.955 63.158 0.00 0.00 45.95 6.13 R
2397 2454 4.635324 CAGGGCTTGTCAAATTTTGTGTTT 59.365 37.500 8.89 0.00 0.00 2.83 R
3158 3272 0.610232 GCTCAATTGCCTGTGGTCCT 60.610 55.000 0.00 0.00 0.00 3.85 R
4415 4553 0.102120 CCAACCGTGCACAACATGTT 59.898 50.000 18.64 4.92 33.01 2.71 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
67 69 1.619654 CAGGGCAAATTGGTCTCACA 58.380 50.000 0.00 0.00 0.00 3.58
72 74 3.559171 GGGCAAATTGGTCTCACACTCTA 60.559 47.826 0.00 0.00 0.00 2.43
83 85 5.393243 GGTCTCACACTCTACACTTATCCAC 60.393 48.000 0.00 0.00 0.00 4.02
92 94 6.070538 ACTCTACACTTATCCACTGCAAATCT 60.071 38.462 0.00 0.00 0.00 2.40
104 106 4.214758 CACTGCAAATCTCAGATGACACAA 59.785 41.667 0.00 0.00 35.61 3.33
149 151 3.547054 ACGTACCACCTAGAGAGAGAG 57.453 52.381 0.00 0.00 0.00 3.20
150 152 2.839425 ACGTACCACCTAGAGAGAGAGT 59.161 50.000 0.00 0.00 0.00 3.24
151 153 3.199677 CGTACCACCTAGAGAGAGAGTG 58.800 54.545 0.00 0.00 0.00 3.51
153 155 2.065899 CCACCTAGAGAGAGAGTGGG 57.934 60.000 4.62 0.00 43.47 4.61
154 156 1.566703 CCACCTAGAGAGAGAGTGGGA 59.433 57.143 4.62 0.00 43.47 4.37
155 157 2.024846 CCACCTAGAGAGAGAGTGGGAA 60.025 54.545 4.62 0.00 43.47 3.97
157 159 3.053991 CACCTAGAGAGAGAGTGGGAAGA 60.054 52.174 0.00 0.00 0.00 2.87
158 160 3.594232 ACCTAGAGAGAGAGTGGGAAGAA 59.406 47.826 0.00 0.00 0.00 2.52
161 163 4.396357 AGAGAGAGAGTGGGAAGAAGAA 57.604 45.455 0.00 0.00 0.00 2.52
163 165 5.151454 AGAGAGAGAGTGGGAAGAAGAAAA 58.849 41.667 0.00 0.00 0.00 2.29
164 166 5.245977 AGAGAGAGAGTGGGAAGAAGAAAAG 59.754 44.000 0.00 0.00 0.00 2.27
171 178 2.040412 TGGGAAGAAGAAAAGGAGAGGC 59.960 50.000 0.00 0.00 0.00 4.70
178 185 0.254462 GAAAAGGAGAGGCAGGGAGG 59.746 60.000 0.00 0.00 0.00 4.30
180 187 2.125066 AAAGGAGAGGCAGGGAGGGA 62.125 60.000 0.00 0.00 0.00 4.20
365 373 0.105778 CCCGCAATTCCCTCTCTCTC 59.894 60.000 0.00 0.00 0.00 3.20
375 383 3.668821 TCCCTCTCTCTCTCTCATCTCT 58.331 50.000 0.00 0.00 0.00 3.10
376 384 3.648067 TCCCTCTCTCTCTCTCATCTCTC 59.352 52.174 0.00 0.00 0.00 3.20
377 385 3.392285 CCCTCTCTCTCTCTCATCTCTCA 59.608 52.174 0.00 0.00 0.00 3.27
378 386 4.042560 CCCTCTCTCTCTCTCATCTCTCAT 59.957 50.000 0.00 0.00 0.00 2.90
379 387 5.243981 CCTCTCTCTCTCTCATCTCTCATC 58.756 50.000 0.00 0.00 0.00 2.92
381 389 6.106648 TCTCTCTCTCTCATCTCTCATCTC 57.893 45.833 0.00 0.00 0.00 2.75
382 390 5.842874 TCTCTCTCTCTCATCTCTCATCTCT 59.157 44.000 0.00 0.00 0.00 3.10
383 391 6.014755 TCTCTCTCTCTCATCTCTCATCTCTC 60.015 46.154 0.00 0.00 0.00 3.20
422 430 4.810790 CGTAGGATCCCTAGTTAGCATTG 58.189 47.826 8.55 0.00 36.71 2.82
430 438 4.471386 TCCCTAGTTAGCATTGCTCTTCTT 59.529 41.667 15.81 0.68 40.44 2.52
562 591 1.751924 GACAGAGGAGTACGGCAGAAT 59.248 52.381 0.00 0.00 0.00 2.40
564 593 1.067821 CAGAGGAGTACGGCAGAATCC 59.932 57.143 0.00 0.00 0.00 3.01
661 690 1.261938 GGGGGCGGCCATTAGTTTTT 61.262 55.000 30.95 0.00 0.00 1.94
662 691 0.174845 GGGGCGGCCATTAGTTTTTC 59.825 55.000 30.95 3.87 0.00 2.29
663 692 1.182667 GGGCGGCCATTAGTTTTTCT 58.817 50.000 25.33 0.00 0.00 2.52
664 693 1.548719 GGGCGGCCATTAGTTTTTCTT 59.451 47.619 25.33 0.00 0.00 2.52
754 787 3.305403 CCCTCGGAAAAGGAAGAAAAAGC 60.305 47.826 0.00 0.00 38.87 3.51
790 823 2.610873 ACCTTTTCTCCGTCTTCCTCT 58.389 47.619 0.00 0.00 0.00 3.69
820 853 2.009888 CTTTCATCGGCCGAGAAGC 58.990 57.895 33.87 0.00 0.00 3.86
826 859 2.303549 ATCGGCCGAGAAGCAAGGAG 62.304 60.000 33.87 0.00 0.00 3.69
888 928 5.560966 TTAGGAATTCATTCGGTTCTTGC 57.439 39.130 7.93 0.00 37.67 4.01
962 1007 3.100671 AGAGCTGGAGTAAATTCTCGGT 58.899 45.455 0.00 0.00 35.52 4.69
2053 2104 0.985490 GATGGCCAAGGAGGAGGAGT 60.985 60.000 10.96 0.00 41.22 3.85
2054 2105 0.985490 ATGGCCAAGGAGGAGGAGTC 60.985 60.000 10.96 0.00 41.22 3.36
2103 2154 4.681978 GGAACAGTGGACGCGGCT 62.682 66.667 13.91 0.00 0.00 5.52
2379 2435 9.950680 TTCTTTTCAGTTTGCTATTTAAGTCAG 57.049 29.630 0.00 0.00 0.00 3.51
2436 2498 4.040755 AGCCCTGTAGATGATGTTACCTT 58.959 43.478 0.00 0.00 0.00 3.50
2500 2564 7.542477 AGACGTGTTCAAACTGATATGAGTTAG 59.458 37.037 8.05 0.00 35.01 2.34
2914 3003 8.565416 AGTAACCATAAAACAGAAGCAGTAAAC 58.435 33.333 0.00 0.00 0.00 2.01
3067 3159 6.005198 TGTGGGTGAATAACGGTAGAAATTT 58.995 36.000 0.00 0.00 0.00 1.82
3134 3248 9.627123 TTTAACCATTCTATTATGCTGTTAGCT 57.373 29.630 2.24 0.00 42.97 3.32
3137 3251 7.967908 ACCATTCTATTATGCTGTTAGCTAGT 58.032 34.615 2.24 0.00 42.97 2.57
3138 3252 8.432805 ACCATTCTATTATGCTGTTAGCTAGTT 58.567 33.333 2.24 0.00 42.97 2.24
3139 3253 9.929180 CCATTCTATTATGCTGTTAGCTAGTTA 57.071 33.333 2.24 0.00 42.97 2.24
3142 3256 9.745880 TTCTATTATGCTGTTAGCTAGTTACAC 57.254 33.333 2.24 0.00 42.97 2.90
3143 3257 9.132923 TCTATTATGCTGTTAGCTAGTTACACT 57.867 33.333 2.24 0.00 42.97 3.55
3144 3258 9.400638 CTATTATGCTGTTAGCTAGTTACACTC 57.599 37.037 2.24 0.00 42.97 3.51
3145 3259 5.661056 ATGCTGTTAGCTAGTTACACTCA 57.339 39.130 2.24 0.00 42.97 3.41
3147 3261 6.037786 TGCTGTTAGCTAGTTACACTCAAT 57.962 37.500 2.24 0.00 42.97 2.57
3158 3272 7.331934 GCTAGTTACACTCAATGATTCAACAGA 59.668 37.037 0.00 0.00 0.00 3.41
3336 3450 4.492494 TTGCTCTGATAGATGGCAAGAA 57.508 40.909 0.00 0.00 32.63 2.52
3368 3482 7.320443 TGTCATAAGTGGCAAGAATCATTAC 57.680 36.000 0.00 0.00 36.93 1.89
3369 3483 6.883756 TGTCATAAGTGGCAAGAATCATTACA 59.116 34.615 0.00 0.00 36.93 2.41
3397 3511 2.038557 TGTCCAGCTTCTTTGTACTCCC 59.961 50.000 0.00 0.00 0.00 4.30
3400 3514 2.355209 CCAGCTTCTTTGTACTCCCTCC 60.355 54.545 0.00 0.00 0.00 4.30
3401 3515 1.550976 AGCTTCTTTGTACTCCCTCCG 59.449 52.381 0.00 0.00 0.00 4.63
3402 3516 1.275573 GCTTCTTTGTACTCCCTCCGT 59.724 52.381 0.00 0.00 0.00 4.69
3404 3518 3.586892 CTTCTTTGTACTCCCTCCGTTC 58.413 50.000 0.00 0.00 0.00 3.95
3406 3520 1.900486 CTTTGTACTCCCTCCGTTCCT 59.100 52.381 0.00 0.00 0.00 3.36
3407 3521 2.905415 TTGTACTCCCTCCGTTCCTA 57.095 50.000 0.00 0.00 0.00 2.94
3408 3522 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3409 3523 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3411 3525 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3412 3526 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
3414 3528 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
3415 3529 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3416 3530 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3419 3533 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3420 3534 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3421 3535 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
3422 3536 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
3438 3552 6.702329 AGTCTTTGTAGAGGTTTCACTATGG 58.298 40.000 0.00 0.00 0.00 2.74
3439 3553 6.497259 AGTCTTTGTAGAGGTTTCACTATGGA 59.503 38.462 0.00 0.00 0.00 3.41
3440 3554 6.590677 GTCTTTGTAGAGGTTTCACTATGGAC 59.409 42.308 0.00 0.00 0.00 4.02
3441 3555 6.497259 TCTTTGTAGAGGTTTCACTATGGACT 59.503 38.462 0.00 0.00 0.00 3.85
3442 3556 7.672660 TCTTTGTAGAGGTTTCACTATGGACTA 59.327 37.037 0.00 0.00 0.00 2.59
3444 3558 6.250711 TGTAGAGGTTTCACTATGGACTACA 58.749 40.000 0.00 0.00 36.46 2.74
3446 3560 8.057011 TGTAGAGGTTTCACTATGGACTACATA 58.943 37.037 0.00 0.00 41.03 2.29
3447 3561 7.349412 AGAGGTTTCACTATGGACTACATAC 57.651 40.000 0.00 0.00 41.03 2.39
3448 3562 6.039493 AGAGGTTTCACTATGGACTACATACG 59.961 42.308 0.00 0.00 41.03 3.06
3449 3563 5.068723 AGGTTTCACTATGGACTACATACGG 59.931 44.000 0.00 0.00 41.03 4.02
3451 3565 6.207213 GTTTCACTATGGACTACATACGGAG 58.793 44.000 0.00 0.00 41.03 4.63
3452 3566 3.819337 TCACTATGGACTACATACGGAGC 59.181 47.826 0.00 0.00 41.03 4.70
3453 3567 3.568430 CACTATGGACTACATACGGAGCA 59.432 47.826 0.00 0.00 41.03 4.26
3454 3568 4.037565 CACTATGGACTACATACGGAGCAA 59.962 45.833 0.00 0.00 41.03 3.91
3456 3570 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
3457 3571 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
3458 3572 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
3459 3573 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
3460 3574 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
3461 3575 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3462 3576 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3464 3578 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3465 3579 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3466 3580 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3467 3581 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3469 3583 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3470 3584 4.872691 CGGAGCAAAATGAGTGAATCTACT 59.127 41.667 0.00 0.00 0.00 2.57
3471 3585 5.352569 CGGAGCAAAATGAGTGAATCTACTT 59.647 40.000 0.00 0.00 0.00 2.24
3472 3586 6.456181 CGGAGCAAAATGAGTGAATCTACTTC 60.456 42.308 0.00 0.00 0.00 3.01
3473 3587 6.597280 GGAGCAAAATGAGTGAATCTACTTCT 59.403 38.462 0.00 0.00 34.75 2.85
3474 3588 7.766278 GGAGCAAAATGAGTGAATCTACTTCTA 59.234 37.037 0.00 0.00 34.75 2.10
3475 3589 9.155975 GAGCAAAATGAGTGAATCTACTTCTAA 57.844 33.333 0.00 0.00 34.75 2.10
3476 3590 9.507329 AGCAAAATGAGTGAATCTACTTCTAAA 57.493 29.630 0.00 0.00 34.75 1.85
3482 3596 9.624373 ATGAGTGAATCTACTTCTAAAATGCAT 57.376 29.630 0.00 0.00 34.75 3.96
3483 3597 9.102757 TGAGTGAATCTACTTCTAAAATGCATC 57.897 33.333 0.00 0.00 34.75 3.91
3484 3598 9.323985 GAGTGAATCTACTTCTAAAATGCATCT 57.676 33.333 0.00 0.00 34.75 2.90
3501 3615 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
3502 3616 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
3504 3618 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
3505 3619 7.435488 GCATCTATATACATCCGTATGTGGTTC 59.565 40.741 3.56 0.00 45.99 3.62
3506 3620 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
3507 3621 8.589701 TCTATATACATCCGTATGTGGTTCAT 57.410 34.615 3.56 0.00 45.99 2.57
3508 3622 9.689501 TCTATATACATCCGTATGTGGTTCATA 57.310 33.333 3.56 0.00 45.99 2.15
3509 3623 9.952188 CTATATACATCCGTATGTGGTTCATAG 57.048 37.037 3.56 0.80 45.99 2.23
3510 3624 6.665992 ATACATCCGTATGTGGTTCATAGT 57.334 37.500 3.56 0.00 45.99 2.12
3511 3625 4.693283 ACATCCGTATGTGGTTCATAGTG 58.307 43.478 0.00 0.00 44.79 2.74
3512 3626 4.404394 ACATCCGTATGTGGTTCATAGTGA 59.596 41.667 0.00 0.00 44.79 3.41
3513 3627 5.105106 ACATCCGTATGTGGTTCATAGTGAA 60.105 40.000 0.00 0.00 44.79 3.18
3514 3628 5.408880 TCCGTATGTGGTTCATAGTGAAA 57.591 39.130 0.00 0.00 38.22 2.69
3515 3629 5.984725 TCCGTATGTGGTTCATAGTGAAAT 58.015 37.500 0.00 0.00 38.22 2.17
3516 3630 6.046593 TCCGTATGTGGTTCATAGTGAAATC 58.953 40.000 0.00 0.00 38.22 2.17
3517 3631 6.049149 CCGTATGTGGTTCATAGTGAAATCT 58.951 40.000 0.00 0.00 38.22 2.40
3518 3632 6.538742 CCGTATGTGGTTCATAGTGAAATCTT 59.461 38.462 0.00 0.00 38.22 2.40
3519 3633 7.065803 CCGTATGTGGTTCATAGTGAAATCTTT 59.934 37.037 0.00 0.00 38.22 2.52
3522 3636 8.862325 ATGTGGTTCATAGTGAAATCTTTACA 57.138 30.769 0.00 0.00 38.22 2.41
3524 3638 9.126151 TGTGGTTCATAGTGAAATCTTTACAAA 57.874 29.630 0.00 0.00 38.22 2.83
3525 3639 9.612620 GTGGTTCATAGTGAAATCTTTACAAAG 57.387 33.333 0.00 0.00 38.22 2.77
3526 3640 9.567776 TGGTTCATAGTGAAATCTTTACAAAGA 57.432 29.630 6.85 6.85 39.16 2.52
3546 3660 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
3547 3661 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3549 3663 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
3550 3664 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
3551 3665 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
4029 4145 4.899502 AGTCTTCAGGGTTTACTGATGTG 58.100 43.478 0.00 0.00 46.07 3.21
4035 4151 2.639839 AGGGTTTACTGATGTGCTCTGT 59.360 45.455 0.00 0.00 39.20 3.41
4036 4152 3.073062 AGGGTTTACTGATGTGCTCTGTT 59.927 43.478 0.00 0.00 37.28 3.16
4037 4153 3.821033 GGGTTTACTGATGTGCTCTGTTT 59.179 43.478 0.00 0.00 37.28 2.83
4135 4253 5.878406 ATAGTGATACTTGTTGCTAGCCT 57.122 39.130 13.29 0.00 0.00 4.58
4243 4368 6.227624 TCCCTCCCCTTTTTATCTTTTCTT 57.772 37.500 0.00 0.00 0.00 2.52
4296 4434 0.605589 GAGGAGGATAGTGATGCCCG 59.394 60.000 0.00 0.00 0.00 6.13
4428 4566 0.385029 TCCAGCAACATGTTGTGCAC 59.615 50.000 33.01 19.77 42.31 4.57
4429 4567 0.935831 CCAGCAACATGTTGTGCACG 60.936 55.000 33.01 18.68 42.31 5.34
4431 4569 1.065600 GCAACATGTTGTGCACGGT 59.934 52.632 33.01 2.25 42.31 4.83
4436 4579 0.947960 CATGTTGTGCACGGTTGGTA 59.052 50.000 13.13 0.00 0.00 3.25
4437 4580 1.335182 CATGTTGTGCACGGTTGGTAA 59.665 47.619 13.13 0.00 0.00 2.85
4456 4599 9.482627 GTTGGTAATGTTTCATCCATTTTTACA 57.517 29.630 0.00 0.00 34.51 2.41
4992 5136 1.470098 AGCGCCTTGTATTCAGCTTTG 59.530 47.619 2.29 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.541863 GGATCCCACGGTCACAAGAT 59.458 55.000 0.00 0.00 0.00 2.40
67 69 5.483685 TTTGCAGTGGATAAGTGTAGAGT 57.516 39.130 0.00 0.00 0.00 3.24
72 74 4.910195 TGAGATTTGCAGTGGATAAGTGT 58.090 39.130 0.00 0.00 0.00 3.55
83 85 4.214758 TGTTGTGTCATCTGAGATTTGCAG 59.785 41.667 0.00 0.00 34.71 4.41
92 94 4.971939 TGGAATCTTGTTGTGTCATCTGA 58.028 39.130 0.00 0.00 0.00 3.27
104 106 6.258230 CATGTACATGTGTTGGAATCTTGT 57.742 37.500 24.91 0.00 34.23 3.16
149 151 3.680490 CCTCTCCTTTTCTTCTTCCCAC 58.320 50.000 0.00 0.00 0.00 4.61
150 152 2.040412 GCCTCTCCTTTTCTTCTTCCCA 59.960 50.000 0.00 0.00 0.00 4.37
151 153 2.040412 TGCCTCTCCTTTTCTTCTTCCC 59.960 50.000 0.00 0.00 0.00 3.97
153 155 3.342719 CCTGCCTCTCCTTTTCTTCTTC 58.657 50.000 0.00 0.00 0.00 2.87
154 156 2.040947 CCCTGCCTCTCCTTTTCTTCTT 59.959 50.000 0.00 0.00 0.00 2.52
155 157 1.632920 CCCTGCCTCTCCTTTTCTTCT 59.367 52.381 0.00 0.00 0.00 2.85
157 159 1.632920 CTCCCTGCCTCTCCTTTTCTT 59.367 52.381 0.00 0.00 0.00 2.52
158 160 1.284313 CTCCCTGCCTCTCCTTTTCT 58.716 55.000 0.00 0.00 0.00 2.52
161 163 1.617839 CCCTCCCTGCCTCTCCTTT 60.618 63.158 0.00 0.00 0.00 3.11
163 165 2.955246 TCCCTCCCTGCCTCTCCT 60.955 66.667 0.00 0.00 0.00 3.69
164 166 2.445654 CTCCCTCCCTGCCTCTCC 60.446 72.222 0.00 0.00 0.00 3.71
365 373 6.473758 AGAGATGAGAGATGAGAGATGAGAG 58.526 44.000 0.00 0.00 0.00 3.20
375 383 4.999469 AGGCTAGAGAGATGAGAGATGA 57.001 45.455 0.00 0.00 0.00 2.92
376 384 4.460382 GGAAGGCTAGAGAGATGAGAGATG 59.540 50.000 0.00 0.00 0.00 2.90
377 385 4.509122 GGGAAGGCTAGAGAGATGAGAGAT 60.509 50.000 0.00 0.00 0.00 2.75
378 386 3.181434 GGGAAGGCTAGAGAGATGAGAGA 60.181 52.174 0.00 0.00 0.00 3.10
379 387 3.157087 GGGAAGGCTAGAGAGATGAGAG 58.843 54.545 0.00 0.00 0.00 3.20
381 389 1.885887 CGGGAAGGCTAGAGAGATGAG 59.114 57.143 0.00 0.00 0.00 2.90
382 390 1.215673 ACGGGAAGGCTAGAGAGATGA 59.784 52.381 0.00 0.00 0.00 2.92
383 391 1.698506 ACGGGAAGGCTAGAGAGATG 58.301 55.000 0.00 0.00 0.00 2.90
422 430 0.805614 GGCGAAGGGAAAAGAAGAGC 59.194 55.000 0.00 0.00 0.00 4.09
430 438 1.204786 TGGAGATGGGCGAAGGGAAA 61.205 55.000 0.00 0.00 0.00 3.13
562 591 1.941403 ATAGGGGACGGACGGAAGGA 61.941 60.000 0.00 0.00 0.00 3.36
564 593 0.828677 AAATAGGGGACGGACGGAAG 59.171 55.000 0.00 0.00 0.00 3.46
640 669 3.655350 AACTAATGGCCGCCCCCAC 62.655 63.158 7.03 0.00 37.79 4.61
754 787 2.583593 GTAGCGAGGAAGCGGCAG 60.584 66.667 1.45 0.00 43.00 4.85
790 823 0.458543 GATGAAAGCTGCGAGACGGA 60.459 55.000 0.00 0.00 0.00 4.69
820 853 2.668457 CGTCAACCGAGAAATCTCCTTG 59.332 50.000 4.90 6.92 39.79 3.61
909 949 1.942657 CGATCAATCAATTCCACCGCT 59.057 47.619 0.00 0.00 0.00 5.52
962 1007 1.077357 ACAACCACCACCGCTCAAA 60.077 52.632 0.00 0.00 0.00 2.69
1341 1392 3.641925 GAGGTCGGAGGAGGACGGT 62.642 68.421 0.00 0.00 35.24 4.83
1809 1860 4.280019 AGGTTGGGGCGGGTGTTC 62.280 66.667 0.00 0.00 0.00 3.18
2053 2104 2.413963 CGCATTTCCCATTGGCCGA 61.414 57.895 0.00 0.00 0.00 5.54
2054 2105 2.104729 CGCATTTCCCATTGGCCG 59.895 61.111 0.00 0.00 0.00 6.13
2231 2282 1.954651 GATTCCGACGAATCCGGCC 60.955 63.158 0.00 0.00 45.95 6.13
2306 2362 7.615582 TCAAAATTATGTTGCACTCTCCTAG 57.384 36.000 0.00 0.00 0.00 3.02
2395 2452 5.709631 AGGGCTTGTCAAATTTTGTGTTTTT 59.290 32.000 8.89 0.00 0.00 1.94
2396 2453 5.123661 CAGGGCTTGTCAAATTTTGTGTTTT 59.876 36.000 8.89 0.00 0.00 2.43
2397 2454 4.635324 CAGGGCTTGTCAAATTTTGTGTTT 59.365 37.500 8.89 0.00 0.00 2.83
2436 2498 9.168451 CTGAACTAGTAAGACTGTCATAGAAGA 57.832 37.037 10.88 0.00 0.00 2.87
2572 2648 5.669798 AATGGGGAGTGGAGCTATAATTT 57.330 39.130 0.00 0.00 0.00 1.82
2933 3024 6.614694 TTGCTGGGACTCACTATTTAGTTA 57.385 37.500 0.00 0.00 33.46 2.24
2967 3058 6.297694 GCTAAAATCAGCTCATCGAATCTT 57.702 37.500 0.00 0.00 38.57 2.40
2993 3084 6.808008 AAACTCATATGTTCACTGGACTTG 57.192 37.500 1.90 0.00 0.00 3.16
3137 3251 6.650807 GTCCTCTGTTGAATCATTGAGTGTAA 59.349 38.462 0.00 0.00 0.00 2.41
3138 3252 6.166279 GTCCTCTGTTGAATCATTGAGTGTA 58.834 40.000 0.00 0.00 0.00 2.90
3139 3253 4.999950 GTCCTCTGTTGAATCATTGAGTGT 59.000 41.667 0.00 0.00 0.00 3.55
3140 3254 4.394300 GGTCCTCTGTTGAATCATTGAGTG 59.606 45.833 0.00 0.00 0.00 3.51
3141 3255 4.042062 TGGTCCTCTGTTGAATCATTGAGT 59.958 41.667 0.00 0.00 0.00 3.41
3142 3256 4.394300 GTGGTCCTCTGTTGAATCATTGAG 59.606 45.833 0.00 0.00 0.00 3.02
3143 3257 4.202451 TGTGGTCCTCTGTTGAATCATTGA 60.202 41.667 0.00 0.00 0.00 2.57
3144 3258 4.074259 TGTGGTCCTCTGTTGAATCATTG 58.926 43.478 0.00 0.00 0.00 2.82
3145 3259 4.330250 CTGTGGTCCTCTGTTGAATCATT 58.670 43.478 0.00 0.00 0.00 2.57
3147 3261 2.038952 CCTGTGGTCCTCTGTTGAATCA 59.961 50.000 0.00 0.00 0.00 2.57
3158 3272 0.610232 GCTCAATTGCCTGTGGTCCT 60.610 55.000 0.00 0.00 0.00 3.85
3336 3450 1.747355 GCCACTTATGACAGCTGCAAT 59.253 47.619 15.27 10.34 0.00 3.56
3368 3482 3.331478 AAGAAGCTGGACAGATCTGTG 57.669 47.619 32.50 18.91 45.05 3.66
3397 3511 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
3411 3525 9.877178 CATAGTGAAACCTCTACAAAGACTTAT 57.123 33.333 0.00 0.00 37.80 1.73
3412 3526 8.311836 CCATAGTGAAACCTCTACAAAGACTTA 58.688 37.037 0.00 0.00 37.80 2.24
3414 3528 6.497259 TCCATAGTGAAACCTCTACAAAGACT 59.503 38.462 0.00 0.00 37.80 3.24
3415 3529 6.590677 GTCCATAGTGAAACCTCTACAAAGAC 59.409 42.308 0.00 0.00 37.80 3.01
3416 3530 6.497259 AGTCCATAGTGAAACCTCTACAAAGA 59.503 38.462 0.00 0.00 37.80 2.52
3419 3533 6.722590 TGTAGTCCATAGTGAAACCTCTACAA 59.277 38.462 0.00 0.00 37.80 2.41
3420 3534 6.250711 TGTAGTCCATAGTGAAACCTCTACA 58.749 40.000 0.00 0.00 37.80 2.74
3421 3535 6.770746 TGTAGTCCATAGTGAAACCTCTAC 57.229 41.667 0.00 0.00 37.80 2.59
3422 3536 7.228108 CGTATGTAGTCCATAGTGAAACCTCTA 59.772 40.741 0.00 0.00 36.71 2.43
3424 3538 6.207213 CGTATGTAGTCCATAGTGAAACCTC 58.793 44.000 0.00 0.00 36.71 3.85
3425 3539 5.068723 CCGTATGTAGTCCATAGTGAAACCT 59.931 44.000 0.00 0.00 36.71 3.50
3426 3540 5.068198 TCCGTATGTAGTCCATAGTGAAACC 59.932 44.000 0.00 0.00 36.71 3.27
3427 3541 6.140303 TCCGTATGTAGTCCATAGTGAAAC 57.860 41.667 0.00 0.00 36.71 2.78
3429 3543 4.277672 GCTCCGTATGTAGTCCATAGTGAA 59.722 45.833 0.00 0.00 36.71 3.18
3431 3545 3.568430 TGCTCCGTATGTAGTCCATAGTG 59.432 47.826 0.00 0.00 36.71 2.74
3432 3546 3.828921 TGCTCCGTATGTAGTCCATAGT 58.171 45.455 0.00 0.00 36.71 2.12
3433 3547 4.848562 TTGCTCCGTATGTAGTCCATAG 57.151 45.455 0.00 0.00 36.71 2.23
3435 3549 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
3436 3550 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
3438 3552 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3439 3553 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3440 3554 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3441 3555 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3442 3556 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3444 3558 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3446 3560 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3447 3561 4.872691 AGTAGATTCACTCATTTTGCTCCG 59.127 41.667 0.00 0.00 0.00 4.63
3448 3562 6.597280 AGAAGTAGATTCACTCATTTTGCTCC 59.403 38.462 0.00 0.00 40.67 4.70
3449 3563 7.608308 AGAAGTAGATTCACTCATTTTGCTC 57.392 36.000 0.00 0.00 40.67 4.26
3456 3570 9.624373 ATGCATTTTAGAAGTAGATTCACTCAT 57.376 29.630 0.00 0.00 40.67 2.90
3457 3571 9.102757 GATGCATTTTAGAAGTAGATTCACTCA 57.897 33.333 0.00 0.00 40.67 3.41
3458 3572 9.323985 AGATGCATTTTAGAAGTAGATTCACTC 57.676 33.333 0.00 0.00 40.67 3.51
3474 3588 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
3475 3589 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
3476 3590 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
3477 3591 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
3478 3592 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
3479 3593 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
3482 3596 8.589701 ATGAACCACATACGGATGTATATAGA 57.410 34.615 14.23 0.00 44.82 1.98
3483 3597 9.952188 CTATGAACCACATACGGATGTATATAG 57.048 37.037 14.23 12.28 44.82 1.31
3484 3598 9.470399 ACTATGAACCACATACGGATGTATATA 57.530 33.333 14.23 7.10 44.82 0.86
3485 3599 8.251026 CACTATGAACCACATACGGATGTATAT 58.749 37.037 14.23 1.68 44.82 0.86
3486 3600 7.449086 TCACTATGAACCACATACGGATGTATA 59.551 37.037 14.23 6.48 44.82 1.47
3487 3601 6.266786 TCACTATGAACCACATACGGATGTAT 59.733 38.462 14.23 5.54 44.82 2.29
3488 3602 5.595133 TCACTATGAACCACATACGGATGTA 59.405 40.000 14.23 0.00 44.82 2.29
3489 3603 5.105106 TTCACTATGAACCACATACGGATGT 60.105 40.000 7.68 7.68 37.89 3.06
3490 3604 4.944048 TCACTATGAACCACATACGGATG 58.056 43.478 5.94 5.94 40.07 3.51
3491 3605 5.607939 TTCACTATGAACCACATACGGAT 57.392 39.130 0.00 0.00 40.07 4.18
3492 3606 5.408880 TTTCACTATGAACCACATACGGA 57.591 39.130 0.00 0.00 35.89 4.69
3493 3607 6.049149 AGATTTCACTATGAACCACATACGG 58.951 40.000 0.00 0.00 35.89 4.02
3494 3608 7.539712 AAGATTTCACTATGAACCACATACG 57.460 36.000 0.00 0.00 35.89 3.06
3496 3610 9.952030 TGTAAAGATTTCACTATGAACCACATA 57.048 29.630 0.00 0.00 35.89 2.29
3497 3611 8.862325 TGTAAAGATTTCACTATGAACCACAT 57.138 30.769 0.00 0.00 35.89 3.21
3498 3612 8.684386 TTGTAAAGATTTCACTATGAACCACA 57.316 30.769 0.00 0.00 35.89 4.17
3501 3615 9.827411 GTCTTTGTAAAGATTTCACTATGAACC 57.173 33.333 9.98 0.00 45.83 3.62
3521 3635 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
3522 3636 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3524 3638 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3525 3639 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3526 3640 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3528 3642 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
3530 3644 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
3532 3646 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3534 3648 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
3535 3649 3.094572 CAAACTACTCCCTCCGTTCCTA 58.905 50.000 0.00 0.00 0.00 2.94
3536 3650 1.900486 CAAACTACTCCCTCCGTTCCT 59.100 52.381 0.00 0.00 0.00 3.36
3540 3654 3.166560 ACTACAAACTACTCCCTCCGT 57.833 47.619 0.00 0.00 0.00 4.69
3542 3656 4.285260 TCCAAACTACAAACTACTCCCTCC 59.715 45.833 0.00 0.00 0.00 4.30
3543 3657 5.221581 TGTCCAAACTACAAACTACTCCCTC 60.222 44.000 0.00 0.00 0.00 4.30
3546 3660 5.235831 GTGTGTCCAAACTACAAACTACTCC 59.764 44.000 0.00 0.00 33.15 3.85
3547 3661 5.051240 CGTGTGTCCAAACTACAAACTACTC 60.051 44.000 0.00 0.00 33.65 2.59
3549 3663 4.805192 TCGTGTGTCCAAACTACAAACTAC 59.195 41.667 0.00 0.00 33.65 2.73
3550 3664 5.008619 TCGTGTGTCCAAACTACAAACTA 57.991 39.130 0.00 0.00 33.65 2.24
3551 3665 3.864243 TCGTGTGTCCAAACTACAAACT 58.136 40.909 0.00 0.00 33.65 2.66
3602 3716 8.421701 CAGTTTTACATTGTTATTAAACCGTGC 58.578 33.333 0.00 0.00 34.49 5.34
3674 3788 6.320164 TCCTTGATTAGTGAGACTCTAAGAGC 59.680 42.308 3.68 0.00 32.04 4.09
4135 4253 6.052360 GCCAAAAAGAGGTGTCCATTTAAAA 58.948 36.000 0.00 0.00 0.00 1.52
4176 4294 4.336993 CACTGAGGTCTCTTAGCTAACGAT 59.663 45.833 0.86 0.00 35.60 3.73
4234 4359 7.543756 TCCGAAACACAAAGAAAAGAAAAGAT 58.456 30.769 0.00 0.00 0.00 2.40
4243 4368 4.623595 GCAAAACTCCGAAACACAAAGAAA 59.376 37.500 0.00 0.00 0.00 2.52
4296 4434 0.466922 CTCTGATCCCCATGGCAACC 60.467 60.000 6.09 0.00 0.00 3.77
4397 4535 7.066307 ACATGTTGCTGGATATATGACTGTA 57.934 36.000 0.00 0.00 0.00 2.74
4414 4552 1.198767 CAACCGTGCACAACATGTTG 58.801 50.000 32.03 32.03 45.58 3.33
4415 4553 0.102120 CCAACCGTGCACAACATGTT 59.898 50.000 18.64 4.92 33.01 2.71
4417 4555 0.947960 TACCAACCGTGCACAACATG 59.052 50.000 18.64 9.57 34.83 3.21
4428 4566 4.981806 ATGGATGAAACATTACCAACCG 57.018 40.909 0.00 0.00 34.28 4.44
4429 4567 7.977789 AAAAATGGATGAAACATTACCAACC 57.022 32.000 0.00 0.00 37.55 3.77
4436 4579 9.865321 CAGAGATGTAAAAATGGATGAAACATT 57.135 29.630 0.00 0.00 40.07 2.71
4437 4580 9.246670 TCAGAGATGTAAAAATGGATGAAACAT 57.753 29.630 0.00 0.00 0.00 2.71
4992 5136 1.299850 GAAAGCAACCAACGGTGCC 60.300 57.895 0.00 0.00 35.34 5.01


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

AutoCloner maintained by Alex Coulton.