Multiple sequence alignment - TraesCS6D01G005500

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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 TraesCS6D01G005500 chr6D 100.000 4150 0 0 1 4150 2357358 2353209 0.000000e+00 7664.0
1 TraesCS6D01G005500 chr6D 84.500 1671 214 20 948 2586 2336673 2335016 0.000000e+00 1609.0
2 TraesCS6D01G005500 chr6D 90.789 152 14 0 2875 3026 2334760 2334609 1.960000e-48 204.0
3 TraesCS6D01G005500 chr6B 95.740 2629 87 11 830 3450 3623427 3626038 0.000000e+00 4211.0
4 TraesCS6D01G005500 chr6B 87.176 772 98 1 960 1730 3643742 3644513 0.000000e+00 876.0
5 TraesCS6D01G005500 chr6B 80.565 921 152 18 1536 2432 22905 21988 0.000000e+00 684.0
6 TraesCS6D01G005500 chr6B 87.456 574 54 9 3506 4072 3626056 3626618 0.000000e+00 645.0
7 TraesCS6D01G005500 chr6B 91.473 129 10 1 2871 2999 20853 20726 4.260000e-40 176.0
8 TraesCS6D01G005500 chr6B 76.970 330 60 13 37 361 3642809 3643127 1.530000e-39 174.0
9 TraesCS6D01G005500 chr6B 84.906 159 21 3 2430 2585 21389 21231 1.540000e-34 158.0
10 TraesCS6D01G005500 chr6B 97.872 47 1 0 3415 3461 68514946 68514992 9.560000e-12 82.4
11 TraesCS6D01G005500 chr6B 97.826 46 1 0 3410 3455 22555686 22555641 3.440000e-11 80.5
12 TraesCS6D01G005500 chr6A 93.451 1649 74 18 1 1630 1420411 1418778 0.000000e+00 2416.0
13 TraesCS6D01G005500 chr6A 86.005 1915 237 16 994 2907 1397840 1395956 0.000000e+00 2023.0
14 TraesCS6D01G005500 chr6A 80.849 872 146 16 1751 2616 1418579 1417723 0.000000e+00 665.0
15 TraesCS6D01G005500 chr6A 79.819 332 51 12 37 361 1398604 1398282 1.160000e-55 228.0
16 TraesCS6D01G005500 chr6A 90.625 160 15 0 2870 3029 1417496 1417337 3.250000e-51 213.0
17 TraesCS6D01G005500 chr6A 90.323 93 9 0 2934 3026 1395958 1395866 5.630000e-24 122.0
18 TraesCS6D01G005500 chr5B 76.963 382 83 5 1219 1596 690362873 690362493 3.250000e-51 213.0
19 TraesCS6D01G005500 chr5B 72.043 465 97 23 1783 2232 690362264 690361818 1.580000e-19 108.0
20 TraesCS6D01G005500 chr2D 91.781 146 9 3 3938 4082 119281618 119281475 2.530000e-47 200.0
21 TraesCS6D01G005500 chr2D 95.918 49 0 1 3415 3463 233486507 233486553 1.240000e-10 78.7
22 TraesCS6D01G005500 chr4B 89.116 147 16 0 3938 4084 241347449 241347303 2.550000e-42 183.0
23 TraesCS6D01G005500 chr4B 88.514 148 17 0 3940 4087 593126731 593126878 3.300000e-41 180.0
24 TraesCS6D01G005500 chr4B 80.282 142 28 0 1316 1457 3627070 3626929 1.580000e-19 108.0
25 TraesCS6D01G005500 chr4B 92.308 52 4 0 3402 3453 348086048 348086099 1.600000e-09 75.0
26 TraesCS6D01G005500 chr7D 87.755 147 18 0 3938 4084 475875493 475875347 5.520000e-39 172.0
27 TraesCS6D01G005500 chr7D 87.586 145 17 1 3938 4082 398000463 398000606 2.570000e-37 167.0
28 TraesCS6D01G005500 chr7A 87.013 154 16 3 3934 4084 247640919 247641071 1.980000e-38 171.0
29 TraesCS6D01G005500 chr7A 84.706 85 13 0 1772 1856 19309138 19309222 7.390000e-13 86.1
30 TraesCS6D01G005500 chr5D 89.051 137 15 0 3938 4074 366679212 366679348 1.980000e-38 171.0
31 TraesCS6D01G005500 chr5D 97.727 44 1 0 3412 3455 548003510 548003553 4.450000e-10 76.8
32 TraesCS6D01G005500 chr1D 85.714 154 17 1 3938 4091 285318444 285318592 1.540000e-34 158.0
33 TraesCS6D01G005500 chr1D 85.135 74 11 0 2876 2949 469836327 469836254 4.450000e-10 76.8
34 TraesCS6D01G005500 chr2B 88.000 100 12 0 1322 1421 799548130 799548031 7.290000e-23 119.0
35 TraesCS6D01G005500 chr2B 79.592 98 16 4 2876 2971 13418655 13418560 2.680000e-07 67.6
36 TraesCS6D01G005500 chr1A 83.784 111 18 0 2876 2986 563163375 563163265 5.670000e-19 106.0
37 TraesCS6D01G005500 chr4A 90.323 62 6 0 1766 1827 710050966 710051027 9.560000e-12 82.4
38 TraesCS6D01G005500 chr4D 97.727 44 1 0 3412 3455 34978340 34978383 4.450000e-10 76.8
39 TraesCS6D01G005500 chr4D 97.727 44 1 0 3412 3455 317189868 317189911 4.450000e-10 76.8
40 TraesCS6D01G005500 chr3B 94.000 50 3 0 3403 3452 729205876 729205925 4.450000e-10 76.8
41 TraesCS6D01G005500 chr1B 84.507 71 11 0 1784 1854 651952748 651952678 2.070000e-08 71.3


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 TraesCS6D01G005500 chr6D 2353209 2357358 4149 True 7664.000000 7664 100.000000 1 4150 1 chr6D.!!$R1 4149
1 TraesCS6D01G005500 chr6D 2334609 2336673 2064 True 906.500000 1609 87.644500 948 3026 2 chr6D.!!$R2 2078
2 TraesCS6D01G005500 chr6B 3623427 3626618 3191 False 2428.000000 4211 91.598000 830 4072 2 chr6B.!!$F2 3242
3 TraesCS6D01G005500 chr6B 3642809 3644513 1704 False 525.000000 876 82.073000 37 1730 2 chr6B.!!$F3 1693
4 TraesCS6D01G005500 chr6B 20726 22905 2179 True 339.333333 684 85.648000 1536 2999 3 chr6B.!!$R2 1463
5 TraesCS6D01G005500 chr6A 1417337 1420411 3074 True 1098.000000 2416 88.308333 1 3029 3 chr6A.!!$R2 3028
6 TraesCS6D01G005500 chr6A 1395866 1398604 2738 True 791.000000 2023 85.382333 37 3026 3 chr6A.!!$R1 2989

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
178 187 0.032815 AATTCAAAAACCCGCCGTGG 59.967 50.000 0.0 0.0 37.55 4.94 F
741 825 0.038166 TCGCATTTCCAAGGGCTTCT 59.962 50.000 0.0 0.0 0.00 2.85 F
1424 1677 2.746277 CCACGCCACCTGCTAACC 60.746 66.667 0.0 0.0 38.05 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1424 1677 0.383949 CAACGGTTTGGACACCAAGG 59.616 55.000 3.49 1.29 44.84 3.61 R
1839 2192 3.369052 CGGAGAAAGTAGCCATACCAACA 60.369 47.826 0.00 0.00 31.78 3.33 R
3259 4433 0.108186 ATGAAAGTGATCGCGCCTCA 60.108 50.000 0.00 3.83 0.00 3.86 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
60 61 6.476380 TCACAGTTCATTTTGTGCAGAATTTC 59.524 34.615 0.00 0.00 43.31 2.17
89 90 2.161012 CACACTGAGATGACATGTTGCC 59.839 50.000 0.00 0.00 0.00 4.52
174 183 1.337728 CCCAGAATTCAAAAACCCGCC 60.338 52.381 8.44 0.00 0.00 6.13
176 185 1.000717 CAGAATTCAAAAACCCGCCGT 60.001 47.619 8.44 0.00 0.00 5.68
178 187 0.032815 AATTCAAAAACCCGCCGTGG 59.967 50.000 0.00 0.00 37.55 4.94
272 291 0.684805 AGATTTCCGGCCTCGTCTCT 60.685 55.000 0.00 0.00 33.95 3.10
284 303 2.342179 CTCGTCTCTGCTTTTTCCTCC 58.658 52.381 0.00 0.00 0.00 4.30
390 409 3.107601 TCCTCTTTCCGATCACTCCATT 58.892 45.455 0.00 0.00 0.00 3.16
393 412 4.507710 CTCTTTCCGATCACTCCATTGAA 58.492 43.478 0.00 0.00 0.00 2.69
397 416 2.168521 TCCGATCACTCCATTGAACTCC 59.831 50.000 0.00 0.00 0.00 3.85
450 469 1.177401 GCCATGGACAACCCTTCTTC 58.823 55.000 18.40 0.00 35.38 2.87
458 477 0.605589 CAACCCTTCTTCGACCACCC 60.606 60.000 0.00 0.00 0.00 4.61
526 545 1.138266 GCCCGTAATCAGGTCTAGCAA 59.862 52.381 0.00 0.00 0.00 3.91
650 709 5.008613 TCAACAAGAAAATGTGGTGTCTAGC 59.991 40.000 0.00 0.00 33.98 3.42
651 710 4.718961 ACAAGAAAATGTGGTGTCTAGCT 58.281 39.130 0.00 0.00 30.82 3.32
652 711 5.865085 ACAAGAAAATGTGGTGTCTAGCTA 58.135 37.500 0.00 0.00 30.82 3.32
655 714 8.267894 ACAAGAAAATGTGGTGTCTAGCTATAT 58.732 33.333 0.00 0.00 30.82 0.86
741 825 0.038166 TCGCATTTCCAAGGGCTTCT 59.962 50.000 0.00 0.00 0.00 2.85
860 944 4.742659 CGGTTGAATCGTTTTGTTTTGGAT 59.257 37.500 0.00 0.00 0.00 3.41
1024 1276 5.234466 AGATAATCCATGGAGGTAGCAAC 57.766 43.478 21.33 6.09 39.02 4.17
1424 1677 2.746277 CCACGCCACCTGCTAACC 60.746 66.667 0.00 0.00 38.05 2.85
1457 1710 4.561735 AACCGTTGGAGTTTGTTATGTG 57.438 40.909 0.00 0.00 0.00 3.21
1482 1735 8.154203 TGATGTATAAACATATGACCCACGAAT 58.846 33.333 10.38 0.00 46.49 3.34
1839 2192 1.679944 CCAAGGCAACGATGATCCACT 60.680 52.381 0.00 0.00 46.39 4.00
2033 2389 3.569277 TGTCAACCTGGACATGTGATTTG 59.431 43.478 1.15 0.00 42.56 2.32
2154 2528 5.099575 CCGTTGGGCAGTATAATTTGTTTC 58.900 41.667 0.00 0.00 0.00 2.78
2300 2674 3.559655 TGTTGTATGAAGCGATATGGTGC 59.440 43.478 0.00 0.00 0.00 5.01
2306 2680 2.035321 TGAAGCGATATGGTGCACGATA 59.965 45.455 21.72 21.72 0.00 2.92
3033 4207 2.184579 GTCGGTGACCTGCTAGCC 59.815 66.667 13.29 0.00 0.00 3.93
3034 4208 3.449227 TCGGTGACCTGCTAGCCG 61.449 66.667 13.29 5.57 43.32 5.52
3049 4223 2.674796 AGCCGATCACAAGTCCTAAC 57.325 50.000 0.00 0.00 0.00 2.34
3055 4229 3.063997 CGATCACAAGTCCTAACATTGCC 59.936 47.826 0.00 0.00 0.00 4.52
3071 4245 1.376553 GCCAGGTTGAGCAGTCCTC 60.377 63.158 0.00 0.00 41.15 3.71
3072 4246 1.298014 CCAGGTTGAGCAGTCCTCC 59.702 63.158 0.00 0.00 39.98 4.30
3073 4247 1.197430 CCAGGTTGAGCAGTCCTCCT 61.197 60.000 0.00 0.00 39.98 3.69
3074 4248 0.248843 CAGGTTGAGCAGTCCTCCTC 59.751 60.000 0.00 0.00 39.98 3.71
3088 4262 2.317900 TCCTCCTCCTCCTCCATGTAAA 59.682 50.000 0.00 0.00 0.00 2.01
3092 4266 4.033709 TCCTCCTCCTCCATGTAAAGAAG 58.966 47.826 0.00 0.00 0.00 2.85
3116 4290 7.649057 AGACCACTTTATTCAAGTTTGTAAGC 58.351 34.615 0.00 0.00 43.89 3.09
3148 4322 1.968017 ACGCATGCTGTTGGTCCAG 60.968 57.895 17.13 0.00 35.49 3.86
3157 4331 2.673368 GCTGTTGGTCCAGAGTAAATCG 59.327 50.000 0.00 0.00 34.23 3.34
3176 4350 1.602377 CGAAGCTCGACCAACCTTTTT 59.398 47.619 0.00 0.00 43.74 1.94
3246 4420 7.483307 ACAAATTGAGTAAATTCCATCCATCG 58.517 34.615 0.00 0.00 37.51 3.84
3255 4429 3.643199 TTCCATCCATCGGACATCAAA 57.357 42.857 0.00 0.00 32.98 2.69
3257 4431 4.169059 TCCATCCATCGGACATCAAATT 57.831 40.909 0.00 0.00 32.98 1.82
3259 4433 3.633525 CCATCCATCGGACATCAAATTGT 59.366 43.478 0.00 0.00 32.98 2.71
3306 4484 5.524281 TGACGTTGTAAAGTGAATACAAGCA 59.476 36.000 0.00 0.00 42.24 3.91
3326 4504 2.095768 CAGACACCAATAACTGCAACCG 60.096 50.000 0.00 0.00 0.00 4.44
3374 4552 1.168714 CCAAGGTAGCCTCAAACTGC 58.831 55.000 0.00 0.00 30.89 4.40
3379 4557 1.375908 TAGCCTCAAACTGCTGCCG 60.376 57.895 0.00 0.00 38.52 5.69
3413 4591 2.627221 AGGACATCGATGATCAGAGGTG 59.373 50.000 31.33 9.00 31.14 4.00
3436 4614 4.141914 GCTCCCTCCGTCCCATAATATAAG 60.142 50.000 0.00 0.00 0.00 1.73
3437 4615 5.269991 CTCCCTCCGTCCCATAATATAAGA 58.730 45.833 0.00 0.00 0.00 2.10
3440 4618 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
3450 4628 9.233232 CCCATAATATAAGAACGTTTTTCAAGC 57.767 33.333 7.42 0.00 0.00 4.01
3457 4635 5.613358 AGAACGTTTTTCAAGCTATGAGG 57.387 39.130 0.46 0.00 39.77 3.86
3458 4636 4.455877 AGAACGTTTTTCAAGCTATGAGGG 59.544 41.667 0.46 0.00 39.77 4.30
3459 4637 4.015872 ACGTTTTTCAAGCTATGAGGGA 57.984 40.909 0.00 0.00 39.77 4.20
3460 4638 4.003648 ACGTTTTTCAAGCTATGAGGGAG 58.996 43.478 0.00 0.00 39.77 4.30
3461 4639 4.003648 CGTTTTTCAAGCTATGAGGGAGT 58.996 43.478 0.00 0.00 39.77 3.85
3466 4644 6.412362 TTTCAAGCTATGAGGGAGTATCTC 57.588 41.667 0.00 0.00 39.77 2.75
3479 4657 4.521256 GGGAGTATCTCTGTATCACCTCAC 59.479 50.000 0.00 0.00 33.73 3.51
3480 4658 5.133941 GGAGTATCTCTGTATCACCTCACA 58.866 45.833 0.00 0.00 33.73 3.58
3481 4659 5.240623 GGAGTATCTCTGTATCACCTCACAG 59.759 48.000 0.00 0.00 42.88 3.66
3482 4660 5.136828 AGTATCTCTGTATCACCTCACAGG 58.863 45.833 2.20 0.00 42.01 4.00
3483 4661 2.739943 TCTCTGTATCACCTCACAGGG 58.260 52.381 2.20 0.00 43.38 4.45
3484 4662 1.759445 CTCTGTATCACCTCACAGGGG 59.241 57.143 2.20 0.00 41.27 4.79
3485 4663 0.179000 CTGTATCACCTCACAGGGGC 59.821 60.000 0.00 0.00 39.16 5.80
3486 4664 0.252696 TGTATCACCTCACAGGGGCT 60.253 55.000 0.00 0.00 39.16 5.19
3487 4665 0.466124 GTATCACCTCACAGGGGCTC 59.534 60.000 0.00 0.00 39.16 4.70
3488 4666 0.042581 TATCACCTCACAGGGGCTCA 59.957 55.000 0.00 0.00 39.16 4.26
3489 4667 1.270414 ATCACCTCACAGGGGCTCAG 61.270 60.000 0.00 0.00 39.16 3.35
3490 4668 1.915266 CACCTCACAGGGGCTCAGA 60.915 63.158 0.00 0.00 40.58 3.27
3491 4669 1.081833 ACCTCACAGGGGCTCAGAT 59.918 57.895 0.00 0.00 40.58 2.90
3492 4670 0.980231 ACCTCACAGGGGCTCAGATC 60.980 60.000 0.00 0.00 40.58 2.75
3493 4671 0.690411 CCTCACAGGGGCTCAGATCT 60.690 60.000 0.00 0.00 0.00 2.75
3494 4672 1.202330 CTCACAGGGGCTCAGATCTT 58.798 55.000 0.00 0.00 0.00 2.40
3495 4673 0.907486 TCACAGGGGCTCAGATCTTG 59.093 55.000 0.00 0.00 0.00 3.02
3496 4674 0.617413 CACAGGGGCTCAGATCTTGT 59.383 55.000 0.00 0.00 0.00 3.16
3497 4675 0.908198 ACAGGGGCTCAGATCTTGTC 59.092 55.000 0.00 0.00 0.00 3.18
3498 4676 0.907486 CAGGGGCTCAGATCTTGTCA 59.093 55.000 0.00 0.00 0.00 3.58
3499 4677 1.134461 CAGGGGCTCAGATCTTGTCAG 60.134 57.143 0.00 0.00 0.00 3.51
3500 4678 0.179936 GGGGCTCAGATCTTGTCAGG 59.820 60.000 0.00 0.00 0.00 3.86
3501 4679 0.463474 GGGCTCAGATCTTGTCAGGC 60.463 60.000 0.00 0.00 0.00 4.85
3502 4680 0.251354 GGCTCAGATCTTGTCAGGCA 59.749 55.000 0.00 0.00 0.00 4.75
3503 4681 1.339438 GGCTCAGATCTTGTCAGGCAA 60.339 52.381 0.00 0.00 35.50 4.52
3504 4682 2.430465 GCTCAGATCTTGTCAGGCAAA 58.570 47.619 0.00 0.00 36.53 3.68
3505 4683 2.816087 GCTCAGATCTTGTCAGGCAAAA 59.184 45.455 0.00 0.00 36.53 2.44
3536 4714 1.180029 ACTGAGTTTCCCATGCATGC 58.820 50.000 21.69 11.82 0.00 4.06
3566 4744 3.064931 CGAGTCCAAGTAGTTTTCACCC 58.935 50.000 0.00 0.00 0.00 4.61
3567 4745 3.409570 GAGTCCAAGTAGTTTTCACCCC 58.590 50.000 0.00 0.00 0.00 4.95
3573 4751 4.202212 CCAAGTAGTTTTCACCCCTTTTGG 60.202 45.833 0.00 0.00 39.97 3.28
3607 4785 1.164411 TTTCTGCCGTGCACAATAGG 58.836 50.000 18.64 10.94 33.79 2.57
3614 4796 3.773860 CCGTGCACAATAGGCAATTAA 57.226 42.857 18.64 0.00 43.91 1.40
3617 4799 3.128589 CGTGCACAATAGGCAATTAAGGT 59.871 43.478 18.64 0.00 43.91 3.50
3622 4804 3.954258 ACAATAGGCAATTAAGGTGAGGC 59.046 43.478 0.00 0.00 0.00 4.70
3680 4862 4.709840 GCAGCTGCAGGAGAAAGA 57.290 55.556 33.36 0.00 41.59 2.52
3686 4868 2.028203 AGCTGCAGGAGAAAGAGAAGAC 60.028 50.000 17.12 0.00 0.00 3.01
3744 4926 4.946478 AGGCTAGCTGGTAAGAGTATTG 57.054 45.455 15.72 0.00 0.00 1.90
3783 4965 5.103290 TCGTGCTTTATTCCACAACTTTC 57.897 39.130 0.00 0.00 32.37 2.62
3784 4966 4.023536 TCGTGCTTTATTCCACAACTTTCC 60.024 41.667 0.00 0.00 32.37 3.13
3786 4968 5.507315 CGTGCTTTATTCCACAACTTTCCTT 60.507 40.000 0.00 0.00 32.37 3.36
3789 4971 6.097554 TGCTTTATTCCACAACTTTCCTTTGA 59.902 34.615 0.00 0.00 0.00 2.69
3795 4977 3.304659 CCACAACTTTCCTTTGATGTCCG 60.305 47.826 0.00 0.00 0.00 4.79
3808 4990 1.474478 GATGTCCGAGTCTCAAGAGCA 59.526 52.381 0.00 0.00 0.00 4.26
3826 5008 1.003116 GCATGAGCCACACGATCATTC 60.003 52.381 0.00 0.00 31.38 2.67
3830 5012 0.179100 AGCCACACGATCATTCTCCG 60.179 55.000 0.00 0.00 0.00 4.63
3834 5016 0.532573 ACACGATCATTCTCCGCAGT 59.467 50.000 0.00 0.00 0.00 4.40
3850 5032 5.132502 TCCGCAGTATGAATGGATCATTTT 58.867 37.500 0.00 0.00 46.85 1.82
3861 5043 9.523168 ATGAATGGATCATTTTCCACAATTTTT 57.477 25.926 0.00 0.00 46.85 1.94
3864 5046 6.520272 TGGATCATTTTCCACAATTTTTCGT 58.480 32.000 0.00 0.00 40.90 3.85
3865 5047 7.661968 TGGATCATTTTCCACAATTTTTCGTA 58.338 30.769 0.00 0.00 40.90 3.43
3866 5048 7.596995 TGGATCATTTTCCACAATTTTTCGTAC 59.403 33.333 0.00 0.00 40.90 3.67
3867 5049 7.062956 GGATCATTTTCCACAATTTTTCGTACC 59.937 37.037 0.00 0.00 35.72 3.34
3868 5050 5.915758 TCATTTTCCACAATTTTTCGTACCG 59.084 36.000 0.00 0.00 0.00 4.02
3872 5054 3.002451 TCCACAATTTTTCGTACCGTGTG 59.998 43.478 0.00 0.00 35.72 3.82
3881 5063 1.014044 CGTACCGTGTGCTTGCTCAT 61.014 55.000 0.73 0.00 0.00 2.90
3887 5069 2.270257 TGTGCTTGCTCATGGTGGC 61.270 57.895 0.00 0.00 0.00 5.01
3908 5090 4.329545 GGTGGTCTTCAGCGGGCA 62.330 66.667 0.00 0.00 33.95 5.36
3926 5110 0.960364 CACGGTGCCTGGTTGCTAAT 60.960 55.000 0.00 0.00 0.00 1.73
3935 5119 3.382546 GCCTGGTTGCTAATGTGATCATT 59.617 43.478 0.00 0.00 45.00 2.57
3961 5145 8.103935 TGGTAACATCACATATACCAAGACAAA 58.896 33.333 1.21 0.00 46.17 2.83
3966 5150 8.896744 ACATCACATATACCAAGACAAAATGAG 58.103 33.333 0.00 0.00 0.00 2.90
3968 5152 8.492673 TCACATATACCAAGACAAAATGAGTC 57.507 34.615 0.00 0.00 36.26 3.36
3972 5156 8.755941 CATATACCAAGACAAAATGAGTCTACG 58.244 37.037 0.00 0.00 45.11 3.51
3975 5159 5.221461 ACCAAGACAAAATGAGTCTACGACT 60.221 40.000 0.00 0.00 45.11 4.18
4018 5202 7.307989 GCATAACATCACACATATGTTACTCCC 60.308 40.741 5.37 0.00 46.84 4.30
4021 5205 4.481368 TCACACATATGTTACTCCCCAC 57.519 45.455 5.37 0.00 36.72 4.61
4026 5210 7.232737 TCACACATATGTTACTCCCCACTATAG 59.767 40.741 5.37 0.00 36.72 1.31
4028 5212 7.451877 ACACATATGTTACTCCCCACTATAGAG 59.548 40.741 5.37 0.00 34.46 2.43
4067 5251 7.279536 GCATGTTACTAGTTTAAGTTACTCCCC 59.720 40.741 0.00 0.00 31.82 4.81
4068 5252 7.854166 TGTTACTAGTTTAAGTTACTCCCCA 57.146 36.000 0.00 0.00 31.82 4.96
4069 5253 7.670364 TGTTACTAGTTTAAGTTACTCCCCAC 58.330 38.462 0.00 0.00 31.82 4.61
4070 5254 7.510343 TGTTACTAGTTTAAGTTACTCCCCACT 59.490 37.037 0.00 0.00 31.82 4.00
4071 5255 9.025041 GTTACTAGTTTAAGTTACTCCCCACTA 57.975 37.037 0.00 0.00 0.00 2.74
4072 5256 9.774071 TTACTAGTTTAAGTTACTCCCCACTAT 57.226 33.333 0.00 0.00 0.00 2.12
4073 5257 8.075761 ACTAGTTTAAGTTACTCCCCACTATG 57.924 38.462 0.00 0.00 0.00 2.23
4074 5258 6.309389 AGTTTAAGTTACTCCCCACTATGG 57.691 41.667 0.00 0.00 37.25 2.74
4075 5259 6.027482 AGTTTAAGTTACTCCCCACTATGGA 58.973 40.000 0.00 0.00 40.96 3.41
4076 5260 6.677076 AGTTTAAGTTACTCCCCACTATGGAT 59.323 38.462 0.00 0.00 40.96 3.41
4077 5261 7.847848 AGTTTAAGTTACTCCCCACTATGGATA 59.152 37.037 0.00 0.00 40.96 2.59
4078 5262 7.850935 TTAAGTTACTCCCCACTATGGATAG 57.149 40.000 0.00 0.00 40.96 2.08
4079 5263 5.420215 AGTTACTCCCCACTATGGATAGT 57.580 43.478 0.00 2.28 44.03 2.12
4080 5264 5.395611 AGTTACTCCCCACTATGGATAGTC 58.604 45.833 0.00 0.00 41.44 2.59
4081 5265 5.136392 AGTTACTCCCCACTATGGATAGTCT 59.864 44.000 0.00 0.00 41.44 3.24
4082 5266 6.334774 AGTTACTCCCCACTATGGATAGTCTA 59.665 42.308 0.00 0.00 41.44 2.59
4083 5267 5.681494 ACTCCCCACTATGGATAGTCTAA 57.319 43.478 0.00 0.00 41.44 2.10
4084 5268 6.234404 ACTCCCCACTATGGATAGTCTAAT 57.766 41.667 0.00 0.00 41.44 1.73
4085 5269 6.019748 ACTCCCCACTATGGATAGTCTAATG 58.980 44.000 0.00 0.00 41.44 1.90
4086 5270 4.777896 TCCCCACTATGGATAGTCTAATGC 59.222 45.833 0.00 0.00 41.44 3.56
4087 5271 4.080863 CCCCACTATGGATAGTCTAATGCC 60.081 50.000 0.00 0.00 41.44 4.40
4088 5272 4.780021 CCCACTATGGATAGTCTAATGCCT 59.220 45.833 0.00 0.00 41.44 4.75
4089 5273 5.958380 CCCACTATGGATAGTCTAATGCCTA 59.042 44.000 0.00 0.00 41.44 3.93
4090 5274 6.613271 CCCACTATGGATAGTCTAATGCCTAT 59.387 42.308 0.00 0.00 41.44 2.57
4091 5275 7.126421 CCCACTATGGATAGTCTAATGCCTATT 59.874 40.741 0.00 0.00 41.44 1.73
4092 5276 7.984050 CCACTATGGATAGTCTAATGCCTATTG 59.016 40.741 0.00 0.00 41.44 1.90
4093 5277 8.535335 CACTATGGATAGTCTAATGCCTATTGT 58.465 37.037 0.00 0.00 41.44 2.71
4094 5278 9.105844 ACTATGGATAGTCTAATGCCTATTGTT 57.894 33.333 0.00 0.00 39.27 2.83
4095 5279 9.376075 CTATGGATAGTCTAATGCCTATTGTTG 57.624 37.037 0.00 0.00 0.00 3.33
4096 5280 7.136822 TGGATAGTCTAATGCCTATTGTTGT 57.863 36.000 0.00 0.00 0.00 3.32
4097 5281 6.992123 TGGATAGTCTAATGCCTATTGTTGTG 59.008 38.462 0.00 0.00 0.00 3.33
4098 5282 6.073003 GGATAGTCTAATGCCTATTGTTGTGC 60.073 42.308 0.00 0.00 0.00 4.57
4099 5283 4.848357 AGTCTAATGCCTATTGTTGTGCT 58.152 39.130 0.00 0.00 0.00 4.40
4100 5284 4.637534 AGTCTAATGCCTATTGTTGTGCTG 59.362 41.667 0.00 0.00 0.00 4.41
4101 5285 4.396166 GTCTAATGCCTATTGTTGTGCTGT 59.604 41.667 0.00 0.00 0.00 4.40
4102 5286 5.009631 TCTAATGCCTATTGTTGTGCTGTT 58.990 37.500 0.00 0.00 0.00 3.16
4103 5287 6.093495 GTCTAATGCCTATTGTTGTGCTGTTA 59.907 38.462 0.00 0.00 0.00 2.41
4104 5288 5.720371 AATGCCTATTGTTGTGCTGTTAA 57.280 34.783 0.00 0.00 0.00 2.01
4105 5289 5.720371 ATGCCTATTGTTGTGCTGTTAAA 57.280 34.783 0.00 0.00 0.00 1.52
4106 5290 5.521906 TGCCTATTGTTGTGCTGTTAAAA 57.478 34.783 0.00 0.00 0.00 1.52
4107 5291 5.907207 TGCCTATTGTTGTGCTGTTAAAAA 58.093 33.333 0.00 0.00 0.00 1.94
4108 5292 5.982516 TGCCTATTGTTGTGCTGTTAAAAAG 59.017 36.000 0.00 0.00 0.00 2.27
4109 5293 5.405269 GCCTATTGTTGTGCTGTTAAAAAGG 59.595 40.000 0.00 0.00 0.00 3.11
4110 5294 6.512297 CCTATTGTTGTGCTGTTAAAAAGGT 58.488 36.000 0.00 0.00 0.00 3.50
4111 5295 6.420604 CCTATTGTTGTGCTGTTAAAAAGGTG 59.579 38.462 0.00 0.00 0.00 4.00
4112 5296 5.392767 TTGTTGTGCTGTTAAAAAGGTGA 57.607 34.783 0.00 0.00 0.00 4.02
4113 5297 5.392767 TGTTGTGCTGTTAAAAAGGTGAA 57.607 34.783 0.00 0.00 0.00 3.18
4114 5298 5.784177 TGTTGTGCTGTTAAAAAGGTGAAA 58.216 33.333 0.00 0.00 0.00 2.69
4115 5299 5.866633 TGTTGTGCTGTTAAAAAGGTGAAAG 59.133 36.000 0.00 0.00 0.00 2.62
4116 5300 4.429108 TGTGCTGTTAAAAAGGTGAAAGC 58.571 39.130 0.00 0.00 0.00 3.51
4117 5301 4.081972 TGTGCTGTTAAAAAGGTGAAAGCA 60.082 37.500 0.00 0.00 37.10 3.91
4118 5302 4.504097 GTGCTGTTAAAAAGGTGAAAGCAG 59.496 41.667 0.00 0.00 39.86 4.24
4119 5303 3.490896 GCTGTTAAAAAGGTGAAAGCAGC 59.509 43.478 0.00 0.00 42.72 5.25
4120 5304 3.701241 TGTTAAAAAGGTGAAAGCAGCG 58.299 40.909 0.00 0.00 46.76 5.18
4121 5305 3.049912 GTTAAAAAGGTGAAAGCAGCGG 58.950 45.455 0.00 0.00 46.76 5.52
4122 5306 1.111277 AAAAAGGTGAAAGCAGCGGT 58.889 45.000 0.00 0.00 46.76 5.68
4123 5307 0.385390 AAAAGGTGAAAGCAGCGGTG 59.615 50.000 10.98 10.98 46.76 4.94
4124 5308 0.465460 AAAGGTGAAAGCAGCGGTGA 60.465 50.000 20.69 0.00 46.76 4.02
4125 5309 0.886490 AAGGTGAAAGCAGCGGTGAG 60.886 55.000 20.69 0.00 46.76 3.51
4126 5310 2.328099 GGTGAAAGCAGCGGTGAGG 61.328 63.158 20.69 0.00 32.24 3.86
4127 5311 2.669569 TGAAAGCAGCGGTGAGGC 60.670 61.111 20.69 2.44 0.00 4.70
4128 5312 2.669569 GAAAGCAGCGGTGAGGCA 60.670 61.111 20.69 0.00 34.64 4.75
4129 5313 2.203337 AAAGCAGCGGTGAGGCAA 60.203 55.556 20.69 0.00 34.64 4.52
4130 5314 2.463675 GAAAGCAGCGGTGAGGCAAC 62.464 60.000 20.69 0.00 34.64 4.17
4133 5317 2.594303 CAGCGGTGAGGCAACCAA 60.594 61.111 9.50 0.00 40.53 3.67
4134 5318 1.973281 CAGCGGTGAGGCAACCAAT 60.973 57.895 9.50 0.00 40.53 3.16
4135 5319 1.675641 AGCGGTGAGGCAACCAATC 60.676 57.895 9.68 0.00 40.53 2.67
4136 5320 3.039202 GCGGTGAGGCAACCAATCG 62.039 63.158 9.68 3.25 40.53 3.34
4137 5321 1.375396 CGGTGAGGCAACCAATCGA 60.375 57.895 9.68 0.00 40.53 3.59
4138 5322 1.635663 CGGTGAGGCAACCAATCGAC 61.636 60.000 9.68 0.00 40.53 4.20
4139 5323 0.605319 GGTGAGGCAACCAATCGACA 60.605 55.000 4.63 0.00 40.22 4.35
4140 5324 0.517316 GTGAGGCAACCAATCGACAC 59.483 55.000 0.00 0.00 37.17 3.67
4141 5325 0.605319 TGAGGCAACCAATCGACACC 60.605 55.000 0.00 0.00 37.17 4.16
4142 5326 1.303317 AGGCAACCAATCGACACCC 60.303 57.895 0.00 0.00 37.17 4.61
4143 5327 1.602323 GGCAACCAATCGACACCCA 60.602 57.895 0.00 0.00 0.00 4.51
4144 5328 0.965363 GGCAACCAATCGACACCCAT 60.965 55.000 0.00 0.00 0.00 4.00
4145 5329 0.451783 GCAACCAATCGACACCCATC 59.548 55.000 0.00 0.00 0.00 3.51
4146 5330 1.094785 CAACCAATCGACACCCATCC 58.905 55.000 0.00 0.00 0.00 3.51
4147 5331 0.034477 AACCAATCGACACCCATCCC 60.034 55.000 0.00 0.00 0.00 3.85
4148 5332 1.204786 ACCAATCGACACCCATCCCA 61.205 55.000 0.00 0.00 0.00 4.37
4149 5333 0.034574 CCAATCGACACCCATCCCAA 60.035 55.000 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 3.055602 TGTCATCTCAGTGTGATTGGAGG 60.056 47.826 4.94 0.00 0.00 4.30
213 232 0.869068 TTGTGAACGCGGTTGGTATG 59.131 50.000 12.47 0.00 0.00 2.39
272 291 4.583073 GTGGTAAAGAAGGAGGAAAAAGCA 59.417 41.667 0.00 0.00 0.00 3.91
390 409 0.323629 CTAGGGGTTTGCGGAGTTCA 59.676 55.000 0.00 0.00 0.00 3.18
393 412 0.616679 TAGCTAGGGGTTTGCGGAGT 60.617 55.000 0.00 0.00 32.48 3.85
397 416 0.392461 TTGCTAGCTAGGGGTTTGCG 60.392 55.000 22.10 0.00 32.48 4.85
458 477 1.958205 GGATTCTGATGCGAGGCCG 60.958 63.158 0.00 0.00 39.16 6.13
517 536 1.222113 GGCCACCTCTTGCTAGACC 59.778 63.158 0.00 0.00 0.00 3.85
563 622 9.860650 ACTTATATAGCCACCACATTTGATAAA 57.139 29.630 0.00 0.00 0.00 1.40
860 944 7.148356 GCATGAAAAGCCATATCGATCTTATCA 60.148 37.037 0.00 0.00 0.00 2.15
1114 1366 1.067212 GTACGAGGACTTGGATCGCAT 59.933 52.381 0.00 0.00 40.02 4.73
1424 1677 0.383949 CAACGGTTTGGACACCAAGG 59.616 55.000 3.49 1.29 44.84 3.61
1457 1710 7.956420 TTCGTGGGTCATATGTTTATACATC 57.044 36.000 1.77 0.00 43.81 3.06
1482 1735 1.603842 CTGCTACCACCATGGCTGA 59.396 57.895 13.04 0.00 42.67 4.26
1839 2192 3.369052 CGGAGAAAGTAGCCATACCAACA 60.369 47.826 0.00 0.00 31.78 3.33
2033 2389 3.954258 CCCATCCTCCTTTATTGTCCAAC 59.046 47.826 0.00 0.00 0.00 3.77
2306 2680 6.471146 CCCGGAGAGATCATCATTATTCTTT 58.529 40.000 0.73 0.00 0.00 2.52
2742 3750 2.290206 ATGGAGTTCATTGGCGGAAGC 61.290 52.381 0.00 0.00 45.53 3.86
2743 3751 1.755179 ATGGAGTTCATTGGCGGAAG 58.245 50.000 0.00 0.00 30.55 3.46
2744 3752 2.503765 TCTATGGAGTTCATTGGCGGAA 59.496 45.455 0.00 0.00 37.30 4.30
2745 3753 2.115427 TCTATGGAGTTCATTGGCGGA 58.885 47.619 0.00 0.00 37.30 5.54
2746 3754 2.620251 TCTATGGAGTTCATTGGCGG 57.380 50.000 0.00 0.00 37.30 6.13
3033 4207 3.063997 GGCAATGTTAGGACTTGTGATCG 59.936 47.826 0.00 0.00 0.00 3.69
3034 4208 4.009675 TGGCAATGTTAGGACTTGTGATC 58.990 43.478 0.00 0.00 0.00 2.92
3049 4223 0.524862 GACTGCTCAACCTGGCAATG 59.475 55.000 0.00 0.00 38.02 2.82
3055 4229 0.248843 GAGGAGGACTGCTCAACCTG 59.751 60.000 14.85 0.00 45.78 4.00
3071 4245 4.033709 TCTTCTTTACATGGAGGAGGAGG 58.966 47.826 0.00 0.00 0.00 4.30
3072 4246 4.141824 GGTCTTCTTTACATGGAGGAGGAG 60.142 50.000 0.00 0.00 0.00 3.69
3073 4247 3.775316 GGTCTTCTTTACATGGAGGAGGA 59.225 47.826 0.00 0.00 0.00 3.71
3074 4248 3.519510 TGGTCTTCTTTACATGGAGGAGG 59.480 47.826 0.00 0.00 0.00 4.30
3137 4311 4.188247 TCGATTTACTCTGGACCAACAG 57.812 45.455 0.00 0.00 39.84 3.16
3138 4312 4.566004 CTTCGATTTACTCTGGACCAACA 58.434 43.478 0.00 0.00 0.00 3.33
3139 4313 3.371285 GCTTCGATTTACTCTGGACCAAC 59.629 47.826 0.00 0.00 0.00 3.77
3176 4350 3.118702 TGTGTGTCCGTACAGAGGAAAAA 60.119 43.478 0.00 0.00 39.84 1.94
3177 4351 2.431419 TGTGTGTCCGTACAGAGGAAAA 59.569 45.455 0.00 0.00 39.84 2.29
3178 4352 2.033372 TGTGTGTCCGTACAGAGGAAA 58.967 47.619 0.00 0.00 39.84 3.13
3179 4353 1.694844 TGTGTGTCCGTACAGAGGAA 58.305 50.000 0.00 0.00 39.84 3.36
3180 4354 1.919240 ATGTGTGTCCGTACAGAGGA 58.081 50.000 0.00 0.00 35.91 3.71
3237 4411 3.633525 ACAATTTGATGTCCGATGGATGG 59.366 43.478 2.79 0.00 32.73 3.51
3246 4420 1.468054 GCGCCTCACAATTTGATGTCC 60.468 52.381 2.79 0.00 32.17 4.02
3255 4429 0.391661 AAGTGATCGCGCCTCACAAT 60.392 50.000 30.23 20.89 44.37 2.71
3257 4431 1.005037 AAAGTGATCGCGCCTCACA 60.005 52.632 30.23 12.30 44.37 3.58
3259 4433 0.108186 ATGAAAGTGATCGCGCCTCA 60.108 50.000 0.00 3.83 0.00 3.86
3306 4484 2.151202 CGGTTGCAGTTATTGGTGTCT 58.849 47.619 0.00 0.00 0.00 3.41
3326 4504 5.959618 TCGATTTCCCCTTCTTCTTTTTC 57.040 39.130 0.00 0.00 0.00 2.29
3379 4557 3.426568 GTCCTGTTCCGCAGCAGC 61.427 66.667 0.00 0.00 43.71 5.25
3387 4565 3.068732 TCTGATCATCGATGTCCTGTTCC 59.931 47.826 24.09 7.09 0.00 3.62
3391 4569 2.627221 ACCTCTGATCATCGATGTCCTG 59.373 50.000 24.09 18.61 0.00 3.86
3413 4591 1.640917 TATTATGGGACGGAGGGAGC 58.359 55.000 0.00 0.00 0.00 4.70
3436 4614 4.454504 TCCCTCATAGCTTGAAAAACGTTC 59.545 41.667 0.00 0.00 32.78 3.95
3437 4615 4.394729 TCCCTCATAGCTTGAAAAACGTT 58.605 39.130 0.00 0.00 32.78 3.99
3440 4618 7.051000 AGATACTCCCTCATAGCTTGAAAAAC 58.949 38.462 0.00 0.00 32.78 2.43
3450 4628 6.601613 GGTGATACAGAGATACTCCCTCATAG 59.398 46.154 0.00 0.00 33.25 2.23
3451 4629 6.275855 AGGTGATACAGAGATACTCCCTCATA 59.724 42.308 0.00 0.00 33.25 2.15
3452 4630 5.075761 AGGTGATACAGAGATACTCCCTCAT 59.924 44.000 0.00 0.00 33.25 2.90
3453 4631 4.417183 AGGTGATACAGAGATACTCCCTCA 59.583 45.833 0.00 0.00 33.25 3.86
3454 4632 4.993028 AGGTGATACAGAGATACTCCCTC 58.007 47.826 0.00 0.00 0.00 4.30
3455 4633 4.417183 TGAGGTGATACAGAGATACTCCCT 59.583 45.833 0.00 0.00 0.00 4.20
3456 4634 4.521256 GTGAGGTGATACAGAGATACTCCC 59.479 50.000 0.00 0.00 0.00 4.30
3457 4635 5.133941 TGTGAGGTGATACAGAGATACTCC 58.866 45.833 0.00 0.00 0.00 3.85
3458 4636 5.240623 CCTGTGAGGTGATACAGAGATACTC 59.759 48.000 5.99 0.00 45.46 2.59
3459 4637 5.136828 CCTGTGAGGTGATACAGAGATACT 58.863 45.833 5.99 0.00 45.46 2.12
3460 4638 4.279671 CCCTGTGAGGTGATACAGAGATAC 59.720 50.000 5.99 0.00 45.46 2.24
3461 4639 4.474394 CCCTGTGAGGTGATACAGAGATA 58.526 47.826 5.99 0.00 45.46 1.98
3466 4644 0.179000 GCCCCTGTGAGGTGATACAG 59.821 60.000 0.00 0.00 42.97 2.74
3479 4657 0.907486 TGACAAGATCTGAGCCCCTG 59.093 55.000 0.00 0.00 0.00 4.45
3480 4658 1.202330 CTGACAAGATCTGAGCCCCT 58.798 55.000 0.00 0.00 0.00 4.79
3481 4659 0.179936 CCTGACAAGATCTGAGCCCC 59.820 60.000 0.00 0.00 0.00 5.80
3482 4660 0.463474 GCCTGACAAGATCTGAGCCC 60.463 60.000 0.00 0.00 0.00 5.19
3483 4661 0.251354 TGCCTGACAAGATCTGAGCC 59.749 55.000 0.00 0.00 0.00 4.70
3484 4662 2.105006 TTGCCTGACAAGATCTGAGC 57.895 50.000 0.00 0.00 33.24 4.26
3503 4681 8.482128 TGGGAAACTCAGTTTGTATCAATTTTT 58.518 29.630 7.75 0.00 35.77 1.94
3504 4682 8.017418 TGGGAAACTCAGTTTGTATCAATTTT 57.983 30.769 7.75 0.00 35.77 1.82
3505 4683 7.595819 TGGGAAACTCAGTTTGTATCAATTT 57.404 32.000 7.75 0.00 35.77 1.82
3518 4696 1.134367 CAGCATGCATGGGAAACTCAG 59.866 52.381 27.34 2.74 0.00 3.35
3527 4705 3.023118 CTCGCTCAGCATGCATGG 58.977 61.111 27.34 12.41 34.76 3.66
3536 4714 1.515952 CTTGGACTCGCTCGCTCAG 60.516 63.158 0.00 0.00 0.00 3.35
3566 4744 0.517316 CGAAAGAGTCGCCCAAAAGG 59.483 55.000 0.00 0.00 44.14 3.11
3587 4765 1.539388 CCTATTGTGCACGGCAGAAAA 59.461 47.619 13.13 0.00 44.48 2.29
3589 4767 1.305219 GCCTATTGTGCACGGCAGAA 61.305 55.000 23.58 8.60 45.32 3.02
3607 4785 1.810151 TCGTTGCCTCACCTTAATTGC 59.190 47.619 0.00 0.00 0.00 3.56
3608 4786 3.181497 CCATCGTTGCCTCACCTTAATTG 60.181 47.826 0.00 0.00 0.00 2.32
3614 4796 0.036010 CTTCCATCGTTGCCTCACCT 60.036 55.000 0.00 0.00 0.00 4.00
3617 4799 1.554617 TCATCTTCCATCGTTGCCTCA 59.445 47.619 0.00 0.00 0.00 3.86
3622 4804 4.388773 TCTTCGTTTCATCTTCCATCGTTG 59.611 41.667 0.00 0.00 0.00 4.10
3678 4860 5.712917 ACACCTTATCTTCTTCGTCTTCTCT 59.287 40.000 0.00 0.00 0.00 3.10
3680 4862 5.336849 CCACACCTTATCTTCTTCGTCTTCT 60.337 44.000 0.00 0.00 0.00 2.85
3686 4868 3.252974 AGCCACACCTTATCTTCTTCG 57.747 47.619 0.00 0.00 0.00 3.79
3737 4919 5.376625 TGGACCAATAATGCTCCAATACTC 58.623 41.667 0.00 0.00 38.17 2.59
3738 4920 5.387113 TGGACCAATAATGCTCCAATACT 57.613 39.130 0.00 0.00 38.17 2.12
3739 4921 5.106555 CGATGGACCAATAATGCTCCAATAC 60.107 44.000 0.00 0.00 43.01 1.89
3740 4922 5.003160 CGATGGACCAATAATGCTCCAATA 58.997 41.667 0.00 0.00 43.01 1.90
3741 4923 3.822735 CGATGGACCAATAATGCTCCAAT 59.177 43.478 0.00 0.00 43.01 3.16
3742 4924 3.213506 CGATGGACCAATAATGCTCCAA 58.786 45.455 0.00 0.00 43.01 3.53
3743 4925 2.172505 ACGATGGACCAATAATGCTCCA 59.827 45.455 0.00 0.00 43.70 3.86
3744 4926 2.549754 CACGATGGACCAATAATGCTCC 59.450 50.000 0.00 0.00 32.70 4.70
3783 4965 3.056536 TCTTGAGACTCGGACATCAAAGG 60.057 47.826 0.00 0.00 31.70 3.11
3784 4966 4.172505 CTCTTGAGACTCGGACATCAAAG 58.827 47.826 0.00 0.00 31.70 2.77
3786 4968 2.094494 GCTCTTGAGACTCGGACATCAA 60.094 50.000 1.30 0.00 0.00 2.57
3789 4971 1.550327 TGCTCTTGAGACTCGGACAT 58.450 50.000 1.30 0.00 0.00 3.06
3795 4977 1.938625 GGCTCATGCTCTTGAGACTC 58.061 55.000 14.56 0.00 46.44 3.36
3808 4990 2.484417 GGAGAATGATCGTGTGGCTCAT 60.484 50.000 0.00 0.00 0.00 2.90
3826 5008 3.391506 TGATCCATTCATACTGCGGAG 57.608 47.619 0.85 0.85 0.00 4.63
3830 5012 6.395426 TGGAAAATGATCCATTCATACTGC 57.605 37.500 0.00 0.00 44.51 4.40
3863 5045 0.443869 CATGAGCAAGCACACGGTAC 59.556 55.000 0.00 0.00 0.00 3.34
3864 5046 0.673333 CCATGAGCAAGCACACGGTA 60.673 55.000 0.00 0.00 0.00 4.02
3865 5047 1.968017 CCATGAGCAAGCACACGGT 60.968 57.895 0.00 0.00 0.00 4.83
3866 5048 1.968017 ACCATGAGCAAGCACACGG 60.968 57.895 3.13 3.13 0.00 4.94
3867 5049 1.208358 CACCATGAGCAAGCACACG 59.792 57.895 0.00 0.00 0.00 4.49
3868 5050 1.582968 CCACCATGAGCAAGCACAC 59.417 57.895 0.00 0.00 0.00 3.82
3872 5054 3.818787 CCGCCACCATGAGCAAGC 61.819 66.667 0.00 0.00 0.00 4.01
3881 5063 4.954118 AGACCACCTCCGCCACCA 62.954 66.667 0.00 0.00 0.00 4.17
3887 5069 2.125912 CGCTGAAGACCACCTCCG 60.126 66.667 0.00 0.00 0.00 4.63
3907 5089 0.960364 ATTAGCAACCAGGCACCGTG 60.960 55.000 0.00 0.00 35.83 4.94
3908 5090 0.960364 CATTAGCAACCAGGCACCGT 60.960 55.000 0.00 0.00 35.83 4.83
3917 5101 4.989279 ACCAATGATCACATTAGCAACC 57.011 40.909 0.00 0.00 43.76 3.77
3935 5119 7.189079 TGTCTTGGTATATGTGATGTTACCA 57.811 36.000 0.00 0.00 41.69 3.25
3948 5132 8.058667 TCGTAGACTCATTTTGTCTTGGTATA 57.941 34.615 1.67 0.00 41.45 1.47
3984 5168 9.603298 CATATGTGTGATGTTATGCAATACTTC 57.397 33.333 0.00 0.38 0.00 3.01
3989 5173 9.123902 AGTAACATATGTGTGATGTTATGCAAT 57.876 29.630 9.63 0.00 46.23 3.56
3996 5180 5.045213 TGGGGAGTAACATATGTGTGATGTT 60.045 40.000 9.63 6.29 46.59 2.71
4000 5184 4.101114 AGTGGGGAGTAACATATGTGTGA 58.899 43.478 9.63 0.00 38.92 3.58
4002 5186 7.302948 TCTATAGTGGGGAGTAACATATGTGT 58.697 38.462 9.63 2.63 41.28 3.72
4018 5202 8.349568 TGCATATGTTACTACCTCTATAGTGG 57.650 38.462 17.49 17.49 36.09 4.00
4054 5238 7.367828 ACTATCCATAGTGGGGAGTAACTTAA 58.632 38.462 0.00 0.00 41.77 1.85
4058 5242 5.395611 AGACTATCCATAGTGGGGAGTAAC 58.604 45.833 3.88 0.00 43.27 2.50
4067 5251 8.535335 ACAATAGGCATTAGACTATCCATAGTG 58.465 37.037 3.88 0.00 45.51 2.74
4068 5252 8.671987 ACAATAGGCATTAGACTATCCATAGT 57.328 34.615 0.00 0.00 45.51 2.12
4069 5253 9.376075 CAACAATAGGCATTAGACTATCCATAG 57.624 37.037 0.00 0.00 45.51 2.23
4070 5254 8.880244 ACAACAATAGGCATTAGACTATCCATA 58.120 33.333 0.00 0.00 45.51 2.74
4071 5255 7.663081 CACAACAATAGGCATTAGACTATCCAT 59.337 37.037 0.00 0.00 45.51 3.41
4072 5256 6.992123 CACAACAATAGGCATTAGACTATCCA 59.008 38.462 0.00 0.00 45.51 3.41
4073 5257 6.073003 GCACAACAATAGGCATTAGACTATCC 60.073 42.308 0.00 0.00 45.51 2.59
4074 5258 6.708054 AGCACAACAATAGGCATTAGACTATC 59.292 38.462 0.00 0.00 45.51 2.08
4076 5260 5.817296 CAGCACAACAATAGGCATTAGACTA 59.183 40.000 0.00 0.00 40.37 2.59
4077 5261 4.637534 CAGCACAACAATAGGCATTAGACT 59.362 41.667 0.00 0.00 36.68 3.24
4078 5262 4.396166 ACAGCACAACAATAGGCATTAGAC 59.604 41.667 0.00 0.00 0.00 2.59
4079 5263 4.588899 ACAGCACAACAATAGGCATTAGA 58.411 39.130 0.00 0.00 0.00 2.10
4080 5264 4.970662 ACAGCACAACAATAGGCATTAG 57.029 40.909 0.00 0.00 0.00 1.73
4081 5265 6.825944 TTAACAGCACAACAATAGGCATTA 57.174 33.333 0.00 0.00 0.00 1.90
4082 5266 5.720371 TTAACAGCACAACAATAGGCATT 57.280 34.783 0.00 0.00 0.00 3.56
4083 5267 5.720371 TTTAACAGCACAACAATAGGCAT 57.280 34.783 0.00 0.00 0.00 4.40
4084 5268 5.521906 TTTTAACAGCACAACAATAGGCA 57.478 34.783 0.00 0.00 0.00 4.75
4085 5269 5.405269 CCTTTTTAACAGCACAACAATAGGC 59.595 40.000 0.00 0.00 0.00 3.93
4086 5270 6.420604 CACCTTTTTAACAGCACAACAATAGG 59.579 38.462 0.00 0.00 0.00 2.57
4087 5271 7.199766 TCACCTTTTTAACAGCACAACAATAG 58.800 34.615 0.00 0.00 0.00 1.73
4088 5272 7.101652 TCACCTTTTTAACAGCACAACAATA 57.898 32.000 0.00 0.00 0.00 1.90
4089 5273 5.971763 TCACCTTTTTAACAGCACAACAAT 58.028 33.333 0.00 0.00 0.00 2.71
4090 5274 5.392767 TCACCTTTTTAACAGCACAACAA 57.607 34.783 0.00 0.00 0.00 2.83
4091 5275 5.392767 TTCACCTTTTTAACAGCACAACA 57.607 34.783 0.00 0.00 0.00 3.33
4092 5276 5.220397 GCTTTCACCTTTTTAACAGCACAAC 60.220 40.000 0.00 0.00 0.00 3.32
4093 5277 4.867608 GCTTTCACCTTTTTAACAGCACAA 59.132 37.500 0.00 0.00 0.00 3.33
4094 5278 4.081972 TGCTTTCACCTTTTTAACAGCACA 60.082 37.500 0.00 0.00 31.17 4.57
4095 5279 4.429108 TGCTTTCACCTTTTTAACAGCAC 58.571 39.130 0.00 0.00 31.17 4.40
4096 5280 4.681744 CTGCTTTCACCTTTTTAACAGCA 58.318 39.130 0.00 0.00 34.88 4.41
4097 5281 3.490896 GCTGCTTTCACCTTTTTAACAGC 59.509 43.478 0.00 0.00 40.89 4.40
4098 5282 3.730715 CGCTGCTTTCACCTTTTTAACAG 59.269 43.478 0.00 0.00 0.00 3.16
4099 5283 3.490078 CCGCTGCTTTCACCTTTTTAACA 60.490 43.478 0.00 0.00 0.00 2.41
4100 5284 3.049912 CCGCTGCTTTCACCTTTTTAAC 58.950 45.455 0.00 0.00 0.00 2.01
4101 5285 2.691011 ACCGCTGCTTTCACCTTTTTAA 59.309 40.909 0.00 0.00 0.00 1.52
4102 5286 2.034053 CACCGCTGCTTTCACCTTTTTA 59.966 45.455 0.00 0.00 0.00 1.52
4103 5287 1.111277 ACCGCTGCTTTCACCTTTTT 58.889 45.000 0.00 0.00 0.00 1.94
4104 5288 0.385390 CACCGCTGCTTTCACCTTTT 59.615 50.000 0.00 0.00 0.00 2.27
4105 5289 0.465460 TCACCGCTGCTTTCACCTTT 60.465 50.000 0.00 0.00 0.00 3.11
4106 5290 0.886490 CTCACCGCTGCTTTCACCTT 60.886 55.000 0.00 0.00 0.00 3.50
4107 5291 1.302033 CTCACCGCTGCTTTCACCT 60.302 57.895 0.00 0.00 0.00 4.00
4108 5292 2.328099 CCTCACCGCTGCTTTCACC 61.328 63.158 0.00 0.00 0.00 4.02
4109 5293 2.970974 GCCTCACCGCTGCTTTCAC 61.971 63.158 0.00 0.00 0.00 3.18
4110 5294 2.669569 GCCTCACCGCTGCTTTCA 60.670 61.111 0.00 0.00 0.00 2.69
4111 5295 2.260869 TTGCCTCACCGCTGCTTTC 61.261 57.895 0.00 0.00 0.00 2.62
4112 5296 2.203337 TTGCCTCACCGCTGCTTT 60.203 55.556 0.00 0.00 0.00 3.51
4113 5297 2.980233 GTTGCCTCACCGCTGCTT 60.980 61.111 0.00 0.00 0.00 3.91
4116 5300 1.926511 GATTGGTTGCCTCACCGCTG 61.927 60.000 0.00 0.00 40.09 5.18
4117 5301 1.675641 GATTGGTTGCCTCACCGCT 60.676 57.895 0.00 0.00 40.09 5.52
4118 5302 2.877691 GATTGGTTGCCTCACCGC 59.122 61.111 0.00 0.00 40.09 5.68
4119 5303 1.375396 TCGATTGGTTGCCTCACCG 60.375 57.895 0.00 0.00 40.09 4.94
4120 5304 0.605319 TGTCGATTGGTTGCCTCACC 60.605 55.000 0.00 0.00 37.34 4.02
4121 5305 0.517316 GTGTCGATTGGTTGCCTCAC 59.483 55.000 0.00 0.00 0.00 3.51
4122 5306 0.605319 GGTGTCGATTGGTTGCCTCA 60.605 55.000 0.00 0.00 0.00 3.86
4123 5307 1.305930 GGGTGTCGATTGGTTGCCTC 61.306 60.000 0.00 0.00 0.00 4.70
4124 5308 1.303317 GGGTGTCGATTGGTTGCCT 60.303 57.895 0.00 0.00 0.00 4.75
4125 5309 0.965363 ATGGGTGTCGATTGGTTGCC 60.965 55.000 0.00 0.00 0.00 4.52
4126 5310 0.451783 GATGGGTGTCGATTGGTTGC 59.548 55.000 0.00 0.00 0.00 4.17
4127 5311 1.094785 GGATGGGTGTCGATTGGTTG 58.905 55.000 0.00 0.00 0.00 3.77
4128 5312 0.034477 GGGATGGGTGTCGATTGGTT 60.034 55.000 0.00 0.00 0.00 3.67
4129 5313 1.204786 TGGGATGGGTGTCGATTGGT 61.205 55.000 0.00 0.00 0.00 3.67
4130 5314 0.034574 TTGGGATGGGTGTCGATTGG 60.035 55.000 0.00 0.00 0.00 3.16
4131 5315 3.568000 TTGGGATGGGTGTCGATTG 57.432 52.632 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.