Multiple sequence alignment - TraesCS2A01G273100

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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 TraesCS2A01G273100 chr2A 100.000 4654 0 0 1 4654 447283788 447288441 0.000000e+00 8595.0
1 TraesCS2A01G273100 chr2A 91.954 87 7 0 429 515 447284131 447284217 6.320000e-24 122.0
2 TraesCS2A01G273100 chr2A 91.954 87 7 0 344 430 447284216 447284302 6.320000e-24 122.0
3 TraesCS2A01G273100 chr2A 80.531 113 20 2 1580 1691 149209219 149209108 8.300000e-13 86.1
4 TraesCS2A01G273100 chr2D 93.919 2335 81 18 315 2626 337133456 337135752 0.000000e+00 3469.0
5 TraesCS2A01G273100 chr2D 95.594 1112 20 11 3322 4420 337137385 337138480 0.000000e+00 1755.0
6 TraesCS2A01G273100 chr2D 97.758 669 15 0 2618 3286 337136720 337137388 0.000000e+00 1153.0
7 TraesCS2A01G273100 chr2D 91.385 325 25 2 3 324 337132230 337132554 4.270000e-120 442.0
8 TraesCS2A01G273100 chr2D 96.277 188 7 0 4467 4654 337138894 337139081 4.520000e-80 309.0
9 TraesCS2A01G273100 chr2D 91.954 87 7 0 429 515 337133485 337133571 6.320000e-24 122.0
10 TraesCS2A01G273100 chr2D 81.250 112 21 0 1580 1691 152097993 152098104 1.780000e-14 91.6
11 TraesCS2A01G273100 chr3A 92.550 349 24 2 4307 4654 720479735 720480082 2.500000e-137 499.0
12 TraesCS2A01G273100 chr3A 89.459 351 29 6 4310 4654 593172412 593172760 1.990000e-118 436.0
13 TraesCS2A01G273100 chr7A 88.761 347 34 5 4310 4654 252172781 252173124 2.000000e-113 420.0
14 TraesCS2A01G273100 chr7A 77.273 286 48 15 4307 4585 81948475 81948200 8.070000e-33 152.0
15 TraesCS2A01G273100 chr2B 89.080 348 23 7 4308 4654 769265833 769266166 7.200000e-113 418.0
16 TraesCS2A01G273100 chr2B 92.079 202 8 2 4104 4305 404577128 404577321 1.280000e-70 278.0
17 TraesCS2A01G273100 chr2B 81.250 112 21 0 1580 1691 210457523 210457634 1.780000e-14 91.6
18 TraesCS2A01G273100 chr7B 87.896 347 40 2 4309 4654 518921963 518922308 1.560000e-109 407.0
19 TraesCS2A01G273100 chr6A 85.714 336 46 2 4321 4654 380159643 380159308 2.060000e-93 353.0
20 TraesCS2A01G273100 chr5A 91.623 191 15 1 4465 4654 429348838 429349028 3.570000e-66 263.0
21 TraesCS2A01G273100 chr3B 85.837 233 24 4 4399 4630 548041941 548042165 6.020000e-59 239.0
22 TraesCS2A01G273100 chr1B 87.374 198 23 2 4310 4506 638041036 638040840 4.690000e-55 226.0
23 TraesCS2A01G273100 chr1B 86.111 144 16 3 2227 2368 521218470 521218611 8.070000e-33 152.0


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 TraesCS2A01G273100 chr2A 447283788 447288441 4653 False 8595.000000 8595 100.000000 1 4654 1 chr2A.!!$F1 4653
1 TraesCS2A01G273100 chr2D 337132230 337139081 6851 False 1208.333333 3469 94.481167 3 4654 6 chr2D.!!$F2 4651

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
537 1451 0.250597 GAGCAACCCAACCCTAACGT 60.251 55.0 0.0 0.0 0.0 3.99 F
1715 2633 0.322277 ATCCATCCCATCTGCATCGC 60.322 55.0 0.0 0.0 0.0 4.58 F
2379 3308 0.035056 ATGAGAGGGGGAACAAAGCG 60.035 55.0 0.0 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 3297 0.034896 TCACCTCTCGCTTTGTTCCC 59.965 55.0 0.00 0.00 0.00 3.97 R
2765 4677 0.317938 GGCTCCGCTCATAGTACACG 60.318 60.0 0.00 0.00 0.00 4.49 R
4242 6167 0.815734 CTCTGCATTTGAAGGCTGGG 59.184 55.0 7.27 0.79 36.52 4.45 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
20 21 0.958876 AAACCCTTTAAGGCGAGCCG 60.959 55.000 5.29 0.00 41.95 5.52
93 96 3.270877 GCCAAATAGTCCAAGATGTCGT 58.729 45.455 0.00 0.00 0.00 4.34
123 126 2.687425 CAACATCAACCCTGACACAACA 59.313 45.455 0.00 0.00 33.30 3.33
140 143 2.234300 ACAGTGTTCACGACGGATTT 57.766 45.000 0.00 0.00 0.00 2.17
146 149 2.132762 GTTCACGACGGATTTGAGTGT 58.867 47.619 0.00 0.00 34.71 3.55
152 155 5.100259 CACGACGGATTTGAGTGTTACTAT 58.900 41.667 0.00 0.00 0.00 2.12
165 168 9.926158 TTGAGTGTTACTATCGGTAAAACATAA 57.074 29.630 10.28 3.90 46.05 1.90
166 169 9.357652 TGAGTGTTACTATCGGTAAAACATAAC 57.642 33.333 10.28 0.00 46.05 1.89
169 172 8.112449 GTGTTACTATCGGTAAAACATAACTGC 58.888 37.037 6.57 0.00 44.15 4.40
399 1313 5.047306 AGACACCAATCTTGATCTCGTGTAA 60.047 40.000 0.00 0.00 31.75 2.41
404 1318 7.065085 CACCAATCTTGATCTCGTGTAATTTCT 59.935 37.037 0.00 0.00 0.00 2.52
433 1347 7.954666 TGATCATCTATATGTATTCCACCGA 57.045 36.000 0.00 0.00 34.50 4.69
449 1363 4.405680 TCCACCGACAATGTCTATCTCAAT 59.594 41.667 11.92 0.00 0.00 2.57
475 1389 4.744570 TCATACGAGACACCAATCTTGAC 58.255 43.478 0.00 0.00 34.58 3.18
481 1395 3.162666 AGACACCAATCTTGACCTCGTA 58.837 45.455 0.00 0.00 0.00 3.43
507 1421 9.800433 ATAGTTTCTATTCTGATCATCTATGCG 57.200 33.333 0.00 0.00 0.00 4.73
534 1448 2.047769 TAGGAGCAACCCAACCCTAA 57.952 50.000 0.00 0.00 40.05 2.69
537 1451 0.250597 GAGCAACCCAACCCTAACGT 60.251 55.000 0.00 0.00 0.00 3.99
545 1459 2.290071 CCCAACCCTAACGTGTGATCTT 60.290 50.000 0.00 0.00 0.00 2.40
560 1474 4.039973 TGTGATCTTCCGGTATTATGGACC 59.960 45.833 0.00 0.00 32.95 4.46
763 1681 1.806623 GCCACCGGCTCTGTAGTAATG 60.807 57.143 0.00 0.00 46.69 1.90
825 1743 4.814294 GCTGATCGCCGTTCCCGT 62.814 66.667 0.00 0.00 0.00 5.28
845 1763 1.941377 TCTCCCCAAGCATTTGCAAT 58.059 45.000 0.00 0.00 45.16 3.56
850 1768 1.203052 CCCAAGCATTTGCAATCGAGT 59.797 47.619 0.00 0.00 45.16 4.18
881 1799 3.209097 AACCACGCAACGCAAGCT 61.209 55.556 0.00 0.00 45.62 3.74
960 1878 1.987704 GAAGCCACACACGCACAACA 61.988 55.000 0.00 0.00 0.00 3.33
1176 2094 3.060663 GCACTTCGCGAGCTTCGTC 62.061 63.158 9.59 0.00 42.81 4.20
1241 2159 2.283529 GGCTCTCCGTGTTCAGGGA 61.284 63.158 12.61 12.61 0.00 4.20
1500 2418 1.144936 CCAGGTCCGCCTCTGATTC 59.855 63.158 0.00 0.00 44.97 2.52
1508 2426 2.158900 TCCGCCTCTGATTCCATCTTTC 60.159 50.000 0.00 0.00 0.00 2.62
1525 2443 2.489938 TTCCTTGGATTCGGTTGGAG 57.510 50.000 0.00 0.00 0.00 3.86
1528 2446 1.533625 CTTGGATTCGGTTGGAGCAA 58.466 50.000 0.00 0.00 0.00 3.91
1529 2447 1.885887 CTTGGATTCGGTTGGAGCAAA 59.114 47.619 0.00 0.00 0.00 3.68
1555 2473 2.091541 GGTTGATTTGATTCCAGCCGA 58.908 47.619 0.00 0.00 0.00 5.54
1645 2563 2.283388 AACTACCTCGCCACCGGA 60.283 61.111 9.46 0.00 34.56 5.14
1708 2626 2.251818 CACGAGGTATCCATCCCATCT 58.748 52.381 0.00 0.00 0.00 2.90
1709 2627 2.028658 CACGAGGTATCCATCCCATCTG 60.029 54.545 0.00 0.00 0.00 2.90
1710 2628 1.066573 CGAGGTATCCATCCCATCTGC 60.067 57.143 0.00 0.00 0.00 4.26
1711 2629 1.980765 GAGGTATCCATCCCATCTGCA 59.019 52.381 0.00 0.00 0.00 4.41
1712 2630 2.575279 GAGGTATCCATCCCATCTGCAT 59.425 50.000 0.00 0.00 0.00 3.96
1713 2631 2.575279 AGGTATCCATCCCATCTGCATC 59.425 50.000 0.00 0.00 0.00 3.91
1714 2632 2.625737 GTATCCATCCCATCTGCATCG 58.374 52.381 0.00 0.00 0.00 3.84
1715 2633 0.322277 ATCCATCCCATCTGCATCGC 60.322 55.000 0.00 0.00 0.00 4.58
1716 2634 1.970114 CCATCCCATCTGCATCGCC 60.970 63.158 0.00 0.00 0.00 5.54
1717 2635 1.072678 CATCCCATCTGCATCGCCT 59.927 57.895 0.00 0.00 0.00 5.52
1718 2636 0.954449 CATCCCATCTGCATCGCCTC 60.954 60.000 0.00 0.00 0.00 4.70
1734 2652 2.202824 TCGTAGAATTGCCCCGCG 60.203 61.111 0.00 0.00 0.00 6.46
1802 2721 8.964476 ACAATAGTGGGTCTACTGATTTAATG 57.036 34.615 0.00 0.00 31.32 1.90
1808 2727 8.109634 AGTGGGTCTACTGATTTAATGAATGTT 58.890 33.333 0.00 0.00 0.00 2.71
1809 2728 9.391006 GTGGGTCTACTGATTTAATGAATGTTA 57.609 33.333 0.00 0.00 0.00 2.41
1902 2822 4.585879 TGCTTGTACCCAGAAAGTATTCC 58.414 43.478 0.00 0.00 36.12 3.01
1911 2831 4.443598 CCCAGAAAGTATTCCTAGGCTGTC 60.444 50.000 2.96 0.00 36.12 3.51
1953 2873 6.768381 CCAGATAAAATACTCCCAACTTCTCC 59.232 42.308 0.00 0.00 0.00 3.71
1982 2902 9.552114 TTCAATGTTTTGTGCTAATTGTTTTTG 57.448 25.926 0.00 0.00 34.32 2.44
1995 2916 7.870445 GCTAATTGTTTTTGTTCAATGGTCCTA 59.130 33.333 0.00 0.00 34.98 2.94
1996 2917 9.757227 CTAATTGTTTTTGTTCAATGGTCCTAA 57.243 29.630 0.00 0.00 34.98 2.69
1997 2918 8.661352 AATTGTTTTTGTTCAATGGTCCTAAG 57.339 30.769 0.00 0.00 34.98 2.18
2017 2938 6.151312 CCTAAGAAGTAGCAACTGACTAGTGA 59.849 42.308 0.00 0.00 37.19 3.41
2025 2946 4.219944 AGCAACTGACTAGTGATTACCGAA 59.780 41.667 0.00 0.00 37.19 4.30
2140 3061 8.652810 TCTTTACGGTTAACTAGATAATTGCC 57.347 34.615 5.42 0.00 0.00 4.52
2141 3062 7.436080 TCTTTACGGTTAACTAGATAATTGCCG 59.564 37.037 14.73 14.73 41.99 5.69
2142 3063 5.266733 ACGGTTAACTAGATAATTGCCGA 57.733 39.130 20.15 0.00 39.85 5.54
2191 3119 3.958798 TCTAGTAGCTTAATTCACCGGCT 59.041 43.478 0.00 0.00 37.08 5.52
2218 3146 9.950680 CATGTTAGTGTGATTGTTTAAGAAAGT 57.049 29.630 0.00 0.00 0.00 2.66
2373 3302 5.574970 AAATCATAGATGAGAGGGGGAAC 57.425 43.478 0.00 0.00 40.64 3.62
2376 3305 4.370776 TCATAGATGAGAGGGGGAACAAA 58.629 43.478 0.00 0.00 32.11 2.83
2377 3306 4.410228 TCATAGATGAGAGGGGGAACAAAG 59.590 45.833 0.00 0.00 32.11 2.77
2378 3307 1.283321 AGATGAGAGGGGGAACAAAGC 59.717 52.381 0.00 0.00 0.00 3.51
2379 3308 0.035056 ATGAGAGGGGGAACAAAGCG 60.035 55.000 0.00 0.00 0.00 4.68
2381 3310 0.391793 GAGAGGGGGAACAAAGCGAG 60.392 60.000 0.00 0.00 0.00 5.03
2383 3312 0.391793 GAGGGGGAACAAAGCGAGAG 60.392 60.000 0.00 0.00 0.00 3.20
2486 3422 9.259832 AGAAATTTAAAAGCCTATGGATTCTGT 57.740 29.630 0.00 0.00 27.99 3.41
2487 3423 9.305925 GAAATTTAAAAGCCTATGGATTCTGTG 57.694 33.333 0.00 0.00 27.99 3.66
2488 3424 8.593945 AATTTAAAAGCCTATGGATTCTGTGA 57.406 30.769 0.00 0.00 27.99 3.58
2489 3425 8.593945 ATTTAAAAGCCTATGGATTCTGTGAA 57.406 30.769 0.00 0.00 27.99 3.18
2490 3426 8.415950 TTTAAAAGCCTATGGATTCTGTGAAA 57.584 30.769 0.00 0.00 27.99 2.69
2491 3427 6.521151 AAAAGCCTATGGATTCTGTGAAAG 57.479 37.500 0.00 0.00 27.99 2.62
2570 3506 7.119846 ACCAGAGATGCACTAGAATTTGTTAAC 59.880 37.037 0.00 0.00 0.00 2.01
2647 4559 3.261580 CAATCAGTCAGTCACGCCATAA 58.738 45.455 0.00 0.00 0.00 1.90
2719 4631 3.449746 TTAATCTTGGTTGGACCTGGG 57.550 47.619 0.00 0.00 39.58 4.45
2765 4677 3.057526 AGGCGCTAAAACCATTTTCTGTC 60.058 43.478 7.64 0.00 34.19 3.51
2774 4686 7.739498 AAAACCATTTTCTGTCGTGTACTAT 57.261 32.000 0.00 0.00 0.00 2.12
2777 4689 6.100004 ACCATTTTCTGTCGTGTACTATGAG 58.900 40.000 0.00 0.00 0.00 2.90
2779 4691 3.400505 TTCTGTCGTGTACTATGAGCG 57.599 47.619 0.00 0.00 0.00 5.03
3038 4950 1.375908 AGAACCACGCGCATGTGAT 60.376 52.632 15.84 5.41 42.55 3.06
3092 5004 1.656652 TCAGCTATCTCGCAAAAGCC 58.343 50.000 0.00 0.00 35.54 4.35
3122 5034 3.178865 AGAAACCGAGAAGGATTACCCA 58.821 45.455 0.00 0.00 45.00 4.51
3221 5133 4.084118 GCTATTGACGAAGATCAGATTGCC 60.084 45.833 0.00 0.00 0.00 4.52
3269 5181 5.244626 ACTTGCAAGTAAGAATCCAAAGCAT 59.755 36.000 30.25 0.00 37.52 3.79
3288 5200 8.500753 AAAGCATTTGCATATTTGATCATTGT 57.499 26.923 5.20 0.00 45.16 2.71
3289 5201 7.477144 AGCATTTGCATATTTGATCATTGTG 57.523 32.000 5.20 0.00 45.16 3.33
3290 5202 7.045416 AGCATTTGCATATTTGATCATTGTGT 58.955 30.769 5.20 0.00 45.16 3.72
3291 5203 7.223971 AGCATTTGCATATTTGATCATTGTGTC 59.776 33.333 5.20 0.00 45.16 3.67
3292 5204 7.223971 GCATTTGCATATTTGATCATTGTGTCT 59.776 33.333 0.00 0.00 41.59 3.41
3293 5205 9.093970 CATTTGCATATTTGATCATTGTGTCTT 57.906 29.630 0.00 0.00 0.00 3.01
3294 5206 8.692110 TTTGCATATTTGATCATTGTGTCTTC 57.308 30.769 0.00 0.00 0.00 2.87
3295 5207 7.393841 TGCATATTTGATCATTGTGTCTTCA 57.606 32.000 0.00 0.00 0.00 3.02
3296 5208 7.477494 TGCATATTTGATCATTGTGTCTTCAG 58.523 34.615 0.00 0.00 0.00 3.02
3297 5209 6.417044 GCATATTTGATCATTGTGTCTTCAGC 59.583 38.462 0.00 0.00 0.00 4.26
3298 5210 4.771590 TTTGATCATTGTGTCTTCAGCC 57.228 40.909 0.00 0.00 0.00 4.85
3299 5211 2.349590 TGATCATTGTGTCTTCAGCCG 58.650 47.619 0.00 0.00 0.00 5.52
3300 5212 2.289631 TGATCATTGTGTCTTCAGCCGT 60.290 45.455 0.00 0.00 0.00 5.68
3301 5213 2.254546 TCATTGTGTCTTCAGCCGTT 57.745 45.000 0.00 0.00 0.00 4.44
3302 5214 3.394674 TCATTGTGTCTTCAGCCGTTA 57.605 42.857 0.00 0.00 0.00 3.18
3303 5215 3.325870 TCATTGTGTCTTCAGCCGTTAG 58.674 45.455 0.00 0.00 0.00 2.34
3304 5216 2.902705 TTGTGTCTTCAGCCGTTAGT 57.097 45.000 0.00 0.00 0.00 2.24
3305 5217 2.148916 TGTGTCTTCAGCCGTTAGTG 57.851 50.000 0.00 0.00 0.00 2.74
3306 5218 1.684450 TGTGTCTTCAGCCGTTAGTGA 59.316 47.619 0.00 0.00 0.00 3.41
3307 5219 2.299013 TGTGTCTTCAGCCGTTAGTGAT 59.701 45.455 0.00 0.00 0.00 3.06
3308 5220 2.924290 GTGTCTTCAGCCGTTAGTGATC 59.076 50.000 0.00 0.00 0.00 2.92
3309 5221 2.826128 TGTCTTCAGCCGTTAGTGATCT 59.174 45.455 0.00 0.00 0.00 2.75
3310 5222 3.182967 GTCTTCAGCCGTTAGTGATCTG 58.817 50.000 0.00 0.00 0.00 2.90
3311 5223 1.929836 CTTCAGCCGTTAGTGATCTGC 59.070 52.381 0.00 0.00 0.00 4.26
3312 5224 1.186200 TCAGCCGTTAGTGATCTGCT 58.814 50.000 0.00 0.00 0.00 4.24
3313 5225 1.550524 TCAGCCGTTAGTGATCTGCTT 59.449 47.619 0.00 0.00 0.00 3.91
3314 5226 2.758423 TCAGCCGTTAGTGATCTGCTTA 59.242 45.455 0.00 0.00 0.00 3.09
3315 5227 3.384789 TCAGCCGTTAGTGATCTGCTTAT 59.615 43.478 0.00 0.00 0.00 1.73
3316 5228 3.492383 CAGCCGTTAGTGATCTGCTTATG 59.508 47.826 0.00 0.00 0.00 1.90
3317 5229 3.133003 AGCCGTTAGTGATCTGCTTATGT 59.867 43.478 0.00 0.00 0.00 2.29
3318 5230 4.341235 AGCCGTTAGTGATCTGCTTATGTA 59.659 41.667 0.00 0.00 0.00 2.29
3319 5231 5.011125 AGCCGTTAGTGATCTGCTTATGTAT 59.989 40.000 0.00 0.00 0.00 2.29
3320 5232 5.119279 GCCGTTAGTGATCTGCTTATGTATG 59.881 44.000 0.00 0.00 0.00 2.39
3321 5233 6.216569 CCGTTAGTGATCTGCTTATGTATGT 58.783 40.000 0.00 0.00 0.00 2.29
3322 5234 6.363626 CCGTTAGTGATCTGCTTATGTATGTC 59.636 42.308 0.00 0.00 0.00 3.06
3323 5235 6.918022 CGTTAGTGATCTGCTTATGTATGTCA 59.082 38.462 0.00 0.00 0.00 3.58
3324 5236 7.596621 CGTTAGTGATCTGCTTATGTATGTCAT 59.403 37.037 0.00 0.00 40.25 3.06
3669 5581 9.702253 AGAAGGAATAAGATCTTGTAGTACTCA 57.298 33.333 18.47 0.00 0.00 3.41
3748 5662 8.372031 GGTTATTCCAGTATTGCCTTGCAATTC 61.372 40.741 18.29 13.63 44.97 2.17
3957 5871 7.130917 GTCTGATGATGATAATGTTTCACTGC 58.869 38.462 0.00 0.00 0.00 4.40
3970 5884 2.836636 TCACTGCATCTAGAGGAGGT 57.163 50.000 8.95 2.78 0.00 3.85
3977 5891 2.700897 GCATCTAGAGGAGGTTGCCTTA 59.299 50.000 8.95 0.00 38.73 2.69
3978 5892 3.493524 GCATCTAGAGGAGGTTGCCTTAC 60.494 52.174 8.95 0.00 38.73 2.34
3979 5893 3.759815 TCTAGAGGAGGTTGCCTTACT 57.240 47.619 0.00 0.00 38.73 2.24
3980 5894 4.062490 TCTAGAGGAGGTTGCCTTACTT 57.938 45.455 0.00 0.00 38.73 2.24
4002 5916 7.470079 ACTTCGTTTTCAACCTCTTTCTAAAC 58.530 34.615 0.00 0.00 0.00 2.01
4024 5938 3.563808 CGAAGAAACATTCAAGGACACCA 59.436 43.478 0.00 0.00 0.00 4.17
4074 5988 8.973835 TCGATAATGGGAAAATTGTAACAAAC 57.026 30.769 0.00 0.00 0.00 2.93
4106 6031 4.137543 GGAGAGGAAAACAACATGACTGT 58.862 43.478 0.00 0.00 37.12 3.55
4179 6104 6.128688 GCAAAGAAAGCAAAACAAACTGTACA 60.129 34.615 0.00 0.00 0.00 2.90
4180 6105 7.447430 CAAAGAAAGCAAAACAAACTGTACAG 58.553 34.615 21.44 21.44 0.00 2.74
4220 6145 5.266733 ACAACAGAACAAGCATCAACATT 57.733 34.783 0.00 0.00 0.00 2.71
4263 6188 0.815734 CAGCCTTCAAATGCAGAGGG 59.184 55.000 0.00 0.00 35.51 4.30
4264 6189 0.407139 AGCCTTCAAATGCAGAGGGT 59.593 50.000 4.78 3.77 34.92 4.34
4297 6222 6.403866 TTGACAAACCAAATGCAGAGTATT 57.596 33.333 0.00 0.00 0.00 1.89
4305 6230 6.917533 ACCAAATGCAGAGTATTTCTTCTTG 58.082 36.000 0.00 0.00 32.41 3.02
4306 6231 6.491403 ACCAAATGCAGAGTATTTCTTCTTGT 59.509 34.615 0.00 0.00 32.41 3.16
4307 6232 7.014615 ACCAAATGCAGAGTATTTCTTCTTGTT 59.985 33.333 0.00 0.00 32.41 2.83
4415 6340 2.930040 AGAACGGCATGACAATTACTCG 59.070 45.455 0.00 0.00 0.00 4.18
4420 6345 2.218759 GGCATGACAATTACTCGCGTAG 59.781 50.000 5.77 4.90 0.00 3.51
4423 6348 4.085721 GCATGACAATTACTCGCGTAGTAC 60.086 45.833 15.03 6.97 40.48 2.73
4424 6349 4.683501 TGACAATTACTCGCGTAGTACA 57.316 40.909 15.03 8.87 40.48 2.90
4425 6350 5.045668 TGACAATTACTCGCGTAGTACAA 57.954 39.130 15.03 7.00 40.48 2.41
4426 6351 5.459768 TGACAATTACTCGCGTAGTACAAA 58.540 37.500 15.03 6.45 40.48 2.83
4427 6352 6.094719 TGACAATTACTCGCGTAGTACAAAT 58.905 36.000 15.03 8.05 40.48 2.32
4428 6353 6.587226 TGACAATTACTCGCGTAGTACAAATT 59.413 34.615 15.03 12.16 40.48 1.82
4429 6354 7.116662 TGACAATTACTCGCGTAGTACAAATTT 59.883 33.333 15.03 7.96 40.48 1.82
4430 6355 7.450627 ACAATTACTCGCGTAGTACAAATTTC 58.549 34.615 15.03 0.00 40.48 2.17
4431 6356 6.579491 ATTACTCGCGTAGTACAAATTTCC 57.421 37.500 15.03 0.00 40.48 3.13
4432 6357 3.256558 ACTCGCGTAGTACAAATTTCCC 58.743 45.455 5.77 0.00 36.36 3.97
4433 6358 3.056322 ACTCGCGTAGTACAAATTTCCCT 60.056 43.478 5.77 0.00 36.36 4.20
4434 6359 4.158394 ACTCGCGTAGTACAAATTTCCCTA 59.842 41.667 5.77 0.00 36.36 3.53
4435 6360 5.070770 TCGCGTAGTACAAATTTCCCTAA 57.929 39.130 5.77 0.00 0.00 2.69
4436 6361 5.663456 TCGCGTAGTACAAATTTCCCTAAT 58.337 37.500 5.77 0.00 0.00 1.73
4437 6362 6.108015 TCGCGTAGTACAAATTTCCCTAATT 58.892 36.000 5.77 0.00 38.08 1.40
4438 6363 6.594937 TCGCGTAGTACAAATTTCCCTAATTT 59.405 34.615 5.77 0.00 45.14 1.82
4439 6364 6.903479 CGCGTAGTACAAATTTCCCTAATTTC 59.097 38.462 0.00 0.00 43.00 2.17
4440 6365 7.201582 CGCGTAGTACAAATTTCCCTAATTTCT 60.202 37.037 0.00 0.00 43.00 2.52
4441 6366 8.456471 GCGTAGTACAAATTTCCCTAATTTCTT 58.544 33.333 0.38 0.00 43.00 2.52
4442 6367 9.983804 CGTAGTACAAATTTCCCTAATTTCTTC 57.016 33.333 0.38 0.00 43.00 2.87
4443 6368 9.983804 GTAGTACAAATTTCCCTAATTTCTTCG 57.016 33.333 0.00 0.00 43.00 3.79
4444 6369 7.535997 AGTACAAATTTCCCTAATTTCTTCGC 58.464 34.615 0.00 0.00 43.00 4.70
4445 6370 5.720202 ACAAATTTCCCTAATTTCTTCGCC 58.280 37.500 0.00 0.00 43.00 5.54
4446 6371 5.109210 CAAATTTCCCTAATTTCTTCGCCC 58.891 41.667 0.00 0.00 43.00 6.13
4447 6372 2.430248 TTCCCTAATTTCTTCGCCCC 57.570 50.000 0.00 0.00 0.00 5.80
4448 6373 1.591768 TCCCTAATTTCTTCGCCCCT 58.408 50.000 0.00 0.00 0.00 4.79
4449 6374 1.211949 TCCCTAATTTCTTCGCCCCTG 59.788 52.381 0.00 0.00 0.00 4.45
4450 6375 1.025041 CCTAATTTCTTCGCCCCTGC 58.975 55.000 0.00 0.00 0.00 4.85
4451 6376 1.681780 CCTAATTTCTTCGCCCCTGCA 60.682 52.381 0.00 0.00 37.32 4.41
4452 6377 1.672881 CTAATTTCTTCGCCCCTGCAG 59.327 52.381 6.78 6.78 37.32 4.41
4453 6378 0.251341 AATTTCTTCGCCCCTGCAGT 60.251 50.000 13.81 0.00 37.32 4.40
4454 6379 0.618458 ATTTCTTCGCCCCTGCAGTA 59.382 50.000 13.81 0.00 37.32 2.74
4455 6380 0.398696 TTTCTTCGCCCCTGCAGTAA 59.601 50.000 13.81 0.00 37.32 2.24
4456 6381 0.321298 TTCTTCGCCCCTGCAGTAAC 60.321 55.000 13.81 0.00 37.32 2.50
4457 6382 1.745489 CTTCGCCCCTGCAGTAACC 60.745 63.158 13.81 0.00 37.32 2.85
4458 6383 3.262448 TTCGCCCCTGCAGTAACCC 62.262 63.158 13.81 0.00 37.32 4.11
4459 6384 4.028490 CGCCCCTGCAGTAACCCA 62.028 66.667 13.81 0.00 37.32 4.51
4460 6385 2.438795 GCCCCTGCAGTAACCCAA 59.561 61.111 13.81 0.00 37.47 4.12
4461 6386 1.228737 GCCCCTGCAGTAACCCAAA 60.229 57.895 13.81 0.00 37.47 3.28
4462 6387 1.250840 GCCCCTGCAGTAACCCAAAG 61.251 60.000 13.81 0.00 37.47 2.77
4463 6388 0.611896 CCCCTGCAGTAACCCAAAGG 60.612 60.000 13.81 2.82 40.04 3.11
4520 6812 1.565156 GCGGTGCATTCTTGTGACGA 61.565 55.000 0.00 0.00 0.00 4.20
4525 6817 3.035942 GTGCATTCTTGTGACGAAACAC 58.964 45.455 0.00 0.00 40.68 3.32
4584 6876 0.475906 ATGGTAAGAGAGGCCATGGC 59.524 55.000 29.47 29.47 41.05 4.40
4615 6907 2.890311 TGGATTGCTCAAATTGGTTCGT 59.110 40.909 0.00 0.00 0.00 3.85
4616 6908 3.057596 TGGATTGCTCAAATTGGTTCGTC 60.058 43.478 0.00 0.00 0.00 4.20
4631 6923 0.750546 TCGTCTATCCCACCACTCCG 60.751 60.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.526211 GGCTCGCCTTAAAGGGTTTG 59.474 55.000 0.00 0.00 35.37 2.93
2 3 1.376812 CGGCTCGCCTTAAAGGGTT 60.377 57.895 6.35 0.00 35.37 4.11
3 4 2.267961 CGGCTCGCCTTAAAGGGT 59.732 61.111 6.35 0.00 35.37 4.34
4 5 1.814169 GTCGGCTCGCCTTAAAGGG 60.814 63.158 6.35 0.00 35.37 3.95
6 7 0.389948 AGTGTCGGCTCGCCTTAAAG 60.390 55.000 6.35 0.00 0.00 1.85
9 10 0.679002 ACTAGTGTCGGCTCGCCTTA 60.679 55.000 6.35 0.00 0.00 2.69
37 38 6.157123 AGGGACTTCCTGAGTATTCCTAAAAG 59.843 42.308 0.00 0.00 46.07 2.27
39 40 5.600749 AGGGACTTCCTGAGTATTCCTAAA 58.399 41.667 0.00 0.00 46.07 1.85
42 43 3.786213 AGGGACTTCCTGAGTATTCCT 57.214 47.619 0.00 0.00 46.07 3.36
55 58 1.545706 GGCGAGGTCTTGAGGGACTT 61.546 60.000 0.00 0.00 41.55 3.01
93 96 1.617850 GGGTTGATGTTGAACCATGCA 59.382 47.619 0.00 0.00 44.17 3.96
123 126 2.223971 ACTCAAATCCGTCGTGAACACT 60.224 45.455 3.51 0.00 0.00 3.55
140 143 9.357652 GTTATGTTTTACCGATAGTAACACTCA 57.642 33.333 0.00 0.00 40.69 3.41
146 149 6.476380 CCGCAGTTATGTTTTACCGATAGTAA 59.524 38.462 0.00 0.00 39.22 2.24
152 155 3.042871 ACCGCAGTTATGTTTTACCGA 57.957 42.857 0.00 0.00 0.00 4.69
195 198 2.204291 ATCCCTTCTGGTGGGCCA 60.204 61.111 0.00 0.00 44.23 5.36
197 200 0.681243 GTTGATCCCTTCTGGTGGGC 60.681 60.000 0.00 0.00 44.23 5.36
199 202 2.224867 ACAAGTTGATCCCTTCTGGTGG 60.225 50.000 10.54 0.00 34.77 4.61
204 207 2.576648 GGGGTACAAGTTGATCCCTTCT 59.423 50.000 26.36 2.81 35.47 2.85
272 275 3.261137 GGGCTATGTGGGTCCTATTAGAC 59.739 52.174 0.00 0.00 35.95 2.59
287 290 4.081198 GGATGGATGAGAAGTAGGGCTATG 60.081 50.000 0.00 0.00 0.00 2.23
335 1249 1.195448 GACATTGTCGGTGCTGACTTG 59.805 52.381 11.82 11.21 39.64 3.16
413 1327 7.819415 ACATTGTCGGTGGAATACATATAGATG 59.181 37.037 0.00 0.00 39.16 2.90
420 1334 4.487714 AGACATTGTCGGTGGAATACAT 57.512 40.909 11.01 0.00 37.67 2.29
458 1372 2.611518 GAGGTCAAGATTGGTGTCTCG 58.388 52.381 0.00 0.00 0.00 4.04
475 1389 9.781834 GATGATCAGAATAGAAACTATACGAGG 57.218 37.037 0.09 0.00 0.00 4.63
481 1395 9.800433 CGCATAGATGATCAGAATAGAAACTAT 57.200 33.333 0.09 0.00 0.00 2.12
522 1436 0.838608 TCACACGTTAGGGTTGGGTT 59.161 50.000 0.00 0.00 0.00 4.11
523 1437 1.002773 GATCACACGTTAGGGTTGGGT 59.997 52.381 0.00 0.00 0.00 4.51
524 1438 1.278127 AGATCACACGTTAGGGTTGGG 59.722 52.381 0.00 0.00 0.00 4.12
525 1439 2.762535 AGATCACACGTTAGGGTTGG 57.237 50.000 0.00 0.00 0.00 3.77
526 1440 3.000727 GGAAGATCACACGTTAGGGTTG 58.999 50.000 0.00 0.00 0.00 3.77
534 1448 4.500887 CCATAATACCGGAAGATCACACGT 60.501 45.833 9.46 0.00 0.00 4.49
537 1451 4.039973 GGTCCATAATACCGGAAGATCACA 59.960 45.833 9.46 0.00 31.67 3.58
647 1561 9.801873 AATTTTATGCCATGTGTAATAACTGTC 57.198 29.630 0.00 0.00 0.00 3.51
654 1568 9.762933 GACCATTAATTTTATGCCATGTGTAAT 57.237 29.630 0.00 0.00 0.00 1.89
718 1632 2.189499 GGTGGATTCATCAGCGGCC 61.189 63.158 0.00 0.00 0.00 6.13
763 1681 1.787155 CGTCGCTAATGGTGATGTAGC 59.213 52.381 0.00 0.00 36.87 3.58
768 1686 0.454600 ACGACGTCGCTAATGGTGAT 59.545 50.000 35.92 11.23 44.43 3.06
778 1696 2.708059 GCTGTGAGAACGACGTCGC 61.708 63.158 35.92 21.50 44.43 5.19
825 1743 1.714541 TTGCAAATGCTTGGGGAGAA 58.285 45.000 6.97 0.00 42.66 2.87
845 1763 0.312729 TGCTTTGTGCTCGTACTCGA 59.687 50.000 0.00 0.00 43.37 4.04
850 1768 0.941542 GTGGTTGCTTTGTGCTCGTA 59.058 50.000 0.00 0.00 43.37 3.43
881 1799 1.177895 TGGTGTACGGCGTTGGAGTA 61.178 55.000 21.24 0.00 0.00 2.59
938 1856 4.539083 TGCGTGTGTGGCTTCGGT 62.539 61.111 0.00 0.00 0.00 4.69
960 1878 5.523438 TTATTTTTCCTGCGGTTTCTTGT 57.477 34.783 0.00 0.00 0.00 3.16
1500 2418 3.004752 ACCGAATCCAAGGAAAGATGG 57.995 47.619 0.00 0.00 38.09 3.51
1508 2426 0.322456 TGCTCCAACCGAATCCAAGG 60.322 55.000 0.00 0.00 0.00 3.61
1525 2443 3.110447 TCAAATCAACCTGCCTTTTGC 57.890 42.857 0.00 0.00 41.77 3.68
1528 2446 3.903090 TGGAATCAAATCAACCTGCCTTT 59.097 39.130 0.00 0.00 0.00 3.11
1529 2447 3.509442 TGGAATCAAATCAACCTGCCTT 58.491 40.909 0.00 0.00 0.00 4.35
1555 2473 5.337169 CGAACCCTGAAGAGAAGAGAAAGAT 60.337 44.000 0.00 0.00 0.00 2.40
1594 2512 1.509923 CCCCGACGTACTGAAGGAC 59.490 63.158 0.00 0.00 0.00 3.85
1645 2563 1.303155 GCTGAGCACCTCCAGCTTT 60.303 57.895 0.00 0.00 43.58 3.51
1708 2626 1.570813 CAATTCTACGAGGCGATGCA 58.429 50.000 0.00 0.00 0.00 3.96
1709 2627 0.233332 GCAATTCTACGAGGCGATGC 59.767 55.000 0.00 0.00 0.00 3.91
1710 2628 0.861837 GGCAATTCTACGAGGCGATG 59.138 55.000 0.00 0.00 0.00 3.84
1711 2629 0.249911 GGGCAATTCTACGAGGCGAT 60.250 55.000 0.00 0.00 0.00 4.58
1712 2630 1.143183 GGGCAATTCTACGAGGCGA 59.857 57.895 0.00 0.00 0.00 5.54
1713 2631 1.887707 GGGGCAATTCTACGAGGCG 60.888 63.158 0.00 0.00 0.00 5.52
1714 2632 1.887707 CGGGGCAATTCTACGAGGC 60.888 63.158 0.00 0.00 0.00 4.70
1715 2633 1.887707 GCGGGGCAATTCTACGAGG 60.888 63.158 0.00 0.00 0.00 4.63
1716 2634 2.237751 CGCGGGGCAATTCTACGAG 61.238 63.158 0.00 0.00 0.00 4.18
1717 2635 2.202824 CGCGGGGCAATTCTACGA 60.203 61.111 0.00 0.00 0.00 3.43
1718 2636 2.202824 TCGCGGGGCAATTCTACG 60.203 61.111 6.13 0.00 0.00 3.51
1734 2652 6.780706 TCACCAAGAACGAAAAATCTAGTC 57.219 37.500 0.00 0.00 0.00 2.59
1764 2682 5.949952 ACCCACTATTGTCCCTACATTTTTC 59.050 40.000 0.00 0.00 34.97 2.29
1842 2761 7.615582 TCATTCTTTACTGCAAAGTGGATAG 57.384 36.000 0.61 0.00 43.58 2.08
1871 2790 1.000731 TGGGTACAAGCAAGCAAATGC 59.999 47.619 0.00 0.00 46.78 3.56
1872 2791 2.557924 TCTGGGTACAAGCAAGCAAATG 59.442 45.455 0.00 0.00 0.00 2.32
1902 2822 0.792640 CGTTTGCAGTGACAGCCTAG 59.207 55.000 0.00 0.00 0.00 3.02
1953 2873 7.467557 ACAATTAGCACAAAACATTGAACAG 57.532 32.000 0.00 0.00 0.00 3.16
1982 2902 5.488341 TGCTACTTCTTAGGACCATTGAAC 58.512 41.667 0.00 0.00 0.00 3.18
1995 2916 6.597832 ATCACTAGTCAGTTGCTACTTCTT 57.402 37.500 0.00 0.00 30.46 2.52
1996 2917 6.597832 AATCACTAGTCAGTTGCTACTTCT 57.402 37.500 0.00 3.31 30.46 2.85
1997 2918 6.752815 GGTAATCACTAGTCAGTTGCTACTTC 59.247 42.308 0.00 0.00 30.46 3.01
2017 2938 4.379082 GCCACTCGTTCAAATTTCGGTAAT 60.379 41.667 0.00 0.00 0.00 1.89
2025 2946 2.742774 GCTTTGCCACTCGTTCAAATT 58.257 42.857 0.00 0.00 0.00 1.82
2052 2973 1.112113 GATAGTTCCCCTGTGCTCGA 58.888 55.000 0.00 0.00 0.00 4.04
2055 2976 1.008938 AGAGGATAGTTCCCCTGTGCT 59.991 52.381 0.00 0.00 43.76 4.40
2140 3061 1.063006 CCTCCGTTGCAATGCATCG 59.937 57.895 26.14 26.14 46.84 3.84
2141 3062 1.434696 CCCTCCGTTGCAATGCATC 59.565 57.895 9.39 7.58 38.76 3.91
2142 3063 2.713967 GCCCTCCGTTGCAATGCAT 61.714 57.895 9.39 0.00 38.76 3.96
2188 3116 5.376854 AAACAATCACACTAACATGAGCC 57.623 39.130 0.00 0.00 0.00 4.70
2219 3147 9.541884 AGGGTTTACCAAATAAAATCATACTGT 57.458 29.630 0.69 0.00 43.89 3.55
2312 3240 1.234615 AAACGGCATCAACTGTCCCG 61.235 55.000 0.00 0.00 0.00 5.14
2357 3286 2.505819 GCTTTGTTCCCCCTCTCATCTA 59.494 50.000 0.00 0.00 0.00 1.98
2363 3292 0.836400 TCTCGCTTTGTTCCCCCTCT 60.836 55.000 0.00 0.00 0.00 3.69
2368 3297 0.034896 TCACCTCTCGCTTTGTTCCC 59.965 55.000 0.00 0.00 0.00 3.97
2369 3298 1.433534 CTCACCTCTCGCTTTGTTCC 58.566 55.000 0.00 0.00 0.00 3.62
2370 3299 1.000955 TCCTCACCTCTCGCTTTGTTC 59.999 52.381 0.00 0.00 0.00 3.18
2373 3302 0.891373 TCTCCTCACCTCTCGCTTTG 59.109 55.000 0.00 0.00 0.00 2.77
2376 3305 1.077068 CCTCTCCTCACCTCTCGCT 60.077 63.158 0.00 0.00 0.00 4.93
2377 3306 2.124693 CCCTCTCCTCACCTCTCGC 61.125 68.421 0.00 0.00 0.00 5.03
2378 3307 0.465460 CTCCCTCTCCTCACCTCTCG 60.465 65.000 0.00 0.00 0.00 4.04
2379 3308 0.106217 CCTCCCTCTCCTCACCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
2381 3310 1.075600 CCCTCCCTCTCCTCACCTC 60.076 68.421 0.00 0.00 0.00 3.85
2383 3312 1.075600 CTCCCTCCCTCTCCTCACC 60.076 68.421 0.00 0.00 0.00 4.02
2385 3314 1.093408 TTTCTCCCTCCCTCTCCTCA 58.907 55.000 0.00 0.00 0.00 3.86
2472 3408 4.156455 TCCTTTCACAGAATCCATAGGC 57.844 45.455 0.00 0.00 0.00 3.93
2482 3418 5.780282 TGAGGTTCTTCTATCCTTTCACAGA 59.220 40.000 0.00 0.00 0.00 3.41
2485 3421 6.043854 ACTGAGGTTCTTCTATCCTTTCAC 57.956 41.667 0.00 0.00 0.00 3.18
2486 3422 6.688073 AACTGAGGTTCTTCTATCCTTTCA 57.312 37.500 0.00 0.00 0.00 2.69
2487 3423 8.478877 TCATAACTGAGGTTCTTCTATCCTTTC 58.521 37.037 0.00 0.00 36.92 2.62
2488 3424 8.380742 TCATAACTGAGGTTCTTCTATCCTTT 57.619 34.615 0.00 0.00 36.92 3.11
2489 3425 7.979786 TCATAACTGAGGTTCTTCTATCCTT 57.020 36.000 0.00 0.00 36.92 3.36
2490 3426 7.595819 CTCATAACTGAGGTTCTTCTATCCT 57.404 40.000 0.00 0.00 44.40 3.24
2522 3458 2.358015 ACGTTTCTTCACCGTTTCCAA 58.642 42.857 0.00 0.00 0.00 3.53
2523 3459 2.027003 ACGTTTCTTCACCGTTTCCA 57.973 45.000 0.00 0.00 0.00 3.53
2524 3460 3.303329 GGTTACGTTTCTTCACCGTTTCC 60.303 47.826 0.00 0.00 36.12 3.13
2570 3506 7.784037 TCCCCAAATGATTCTTTGACATATTG 58.216 34.615 9.00 0.00 38.17 1.90
2582 3518 6.263168 CAGGTATTACACTCCCCAAATGATTC 59.737 42.308 0.00 0.00 0.00 2.52
2719 4631 7.307337 CCTCATTGGTGTAAGTTTGAATTTTGC 60.307 37.037 0.00 0.00 0.00 3.68
2765 4677 0.317938 GGCTCCGCTCATAGTACACG 60.318 60.000 0.00 0.00 0.00 4.49
2774 4686 2.751436 GGCAAATGGCTCCGCTCA 60.751 61.111 0.00 0.00 44.01 4.26
2777 4689 3.056313 GACTGGCAAATGGCTCCGC 62.056 63.158 8.50 0.00 44.01 5.54
2779 4691 0.610232 ACAGACTGGCAAATGGCTCC 60.610 55.000 7.51 0.00 44.01 4.70
2922 4834 7.229506 AGCCAGCAGGAATAAATTCAATAGTAC 59.770 37.037 0.00 0.00 38.53 2.73
2935 4847 3.976654 AGAATAGGAAGCCAGCAGGAATA 59.023 43.478 0.00 0.00 36.89 1.75
2938 4850 1.885049 AGAATAGGAAGCCAGCAGGA 58.115 50.000 0.00 0.00 36.89 3.86
3221 5133 2.668279 GCCATGTTTCACAAGGTTAGCG 60.668 50.000 0.47 0.00 39.07 4.26
3269 5181 8.305317 TGAAGACACAATGATCAAATATGCAAA 58.695 29.630 0.00 0.00 0.00 3.68
3286 5198 1.684450 TCACTAACGGCTGAAGACACA 59.316 47.619 0.00 0.00 0.00 3.72
3287 5199 2.433868 TCACTAACGGCTGAAGACAC 57.566 50.000 0.00 0.00 0.00 3.67
3288 5200 2.826128 AGATCACTAACGGCTGAAGACA 59.174 45.455 0.00 0.00 0.00 3.41
3289 5201 3.182967 CAGATCACTAACGGCTGAAGAC 58.817 50.000 0.00 0.00 0.00 3.01
3290 5202 2.417379 GCAGATCACTAACGGCTGAAGA 60.417 50.000 0.00 0.00 0.00 2.87
3291 5203 1.929836 GCAGATCACTAACGGCTGAAG 59.070 52.381 0.00 0.00 0.00 3.02
3292 5204 1.550524 AGCAGATCACTAACGGCTGAA 59.449 47.619 0.00 0.00 36.36 3.02
3293 5205 1.186200 AGCAGATCACTAACGGCTGA 58.814 50.000 0.00 0.00 36.36 4.26
3294 5206 2.015736 AAGCAGATCACTAACGGCTG 57.984 50.000 0.00 0.00 37.58 4.85
3295 5207 3.133003 ACATAAGCAGATCACTAACGGCT 59.867 43.478 0.00 0.00 38.96 5.52
3296 5208 3.458189 ACATAAGCAGATCACTAACGGC 58.542 45.455 0.00 0.00 0.00 5.68
3297 5209 6.216569 ACATACATAAGCAGATCACTAACGG 58.783 40.000 0.00 0.00 0.00 4.44
3298 5210 6.918022 TGACATACATAAGCAGATCACTAACG 59.082 38.462 0.00 0.00 0.00 3.18
3299 5211 8.706936 CATGACATACATAAGCAGATCACTAAC 58.293 37.037 0.00 0.00 37.46 2.34
3300 5212 7.874528 CCATGACATACATAAGCAGATCACTAA 59.125 37.037 0.00 0.00 37.46 2.24
3301 5213 7.233348 TCCATGACATACATAAGCAGATCACTA 59.767 37.037 0.00 0.00 37.46 2.74
3302 5214 6.042437 TCCATGACATACATAAGCAGATCACT 59.958 38.462 0.00 0.00 37.46 3.41
3303 5215 6.226052 TCCATGACATACATAAGCAGATCAC 58.774 40.000 0.00 0.00 37.46 3.06
3304 5216 6.423776 TCCATGACATACATAAGCAGATCA 57.576 37.500 0.00 0.00 37.46 2.92
3305 5217 7.734924 TTTCCATGACATACATAAGCAGATC 57.265 36.000 0.00 0.00 37.46 2.75
3306 5218 8.701908 AATTTCCATGACATACATAAGCAGAT 57.298 30.769 0.00 0.00 37.46 2.90
3307 5219 9.056005 GTAATTTCCATGACATACATAAGCAGA 57.944 33.333 0.00 0.00 37.46 4.26
3308 5220 9.060347 AGTAATTTCCATGACATACATAAGCAG 57.940 33.333 0.00 0.00 37.46 4.24
3309 5221 8.839343 CAGTAATTTCCATGACATACATAAGCA 58.161 33.333 0.00 0.00 37.46 3.91
3310 5222 8.840321 ACAGTAATTTCCATGACATACATAAGC 58.160 33.333 0.00 0.00 37.46 3.09
3312 5224 9.119418 CCACAGTAATTTCCATGACATACATAA 57.881 33.333 0.00 0.00 37.46 1.90
3313 5225 7.228507 GCCACAGTAATTTCCATGACATACATA 59.771 37.037 0.00 0.00 37.46 2.29
3314 5226 6.039717 GCCACAGTAATTTCCATGACATACAT 59.960 38.462 0.00 0.00 40.17 2.29
3315 5227 5.356751 GCCACAGTAATTTCCATGACATACA 59.643 40.000 0.00 0.00 0.00 2.29
3316 5228 5.590259 AGCCACAGTAATTTCCATGACATAC 59.410 40.000 0.00 0.00 0.00 2.39
3317 5229 5.589855 CAGCCACAGTAATTTCCATGACATA 59.410 40.000 0.00 0.00 0.00 2.29
3318 5230 4.400251 CAGCCACAGTAATTTCCATGACAT 59.600 41.667 0.00 0.00 0.00 3.06
3319 5231 3.758023 CAGCCACAGTAATTTCCATGACA 59.242 43.478 0.00 0.00 0.00 3.58
3320 5232 4.009675 TCAGCCACAGTAATTTCCATGAC 58.990 43.478 0.00 0.00 0.00 3.06
3321 5233 4.299586 TCAGCCACAGTAATTTCCATGA 57.700 40.909 0.00 0.00 0.00 3.07
3322 5234 4.735578 GCATCAGCCACAGTAATTTCCATG 60.736 45.833 0.00 0.00 33.58 3.66
3323 5235 3.382546 GCATCAGCCACAGTAATTTCCAT 59.617 43.478 0.00 0.00 33.58 3.41
3324 5236 2.754552 GCATCAGCCACAGTAATTTCCA 59.245 45.455 0.00 0.00 33.58 3.53
3660 5572 3.702045 AGGCAATCCAGACTGAGTACTAC 59.298 47.826 3.32 0.00 33.74 2.73
3669 5581 4.262808 GCATGTCTATAGGCAATCCAGACT 60.263 45.833 11.80 0.00 35.24 3.24
3739 5653 8.181573 ACATATTTACTGGTTACGAATTGCAAG 58.818 33.333 4.94 0.00 0.00 4.01
3748 5662 8.932791 AGAAGTTTCACATATTTACTGGTTACG 58.067 33.333 0.00 0.00 0.00 3.18
3957 5871 3.964031 AGTAAGGCAACCTCCTCTAGATG 59.036 47.826 0.00 0.00 34.82 2.90
3979 5893 7.148440 TTCGTTTAGAAAGAGGTTGAAAACGAA 60.148 33.333 21.70 21.70 46.95 3.85
3980 5894 6.313411 TTCGTTTAGAAAGAGGTTGAAAACGA 59.687 34.615 14.00 14.00 43.80 3.85
4002 5916 3.563808 TGGTGTCCTTGAATGTTTCTTCG 59.436 43.478 0.00 0.00 0.00 3.79
4155 6080 7.328249 TCTGTACAGTTTGTTTTGCTTTCTTTG 59.672 33.333 21.99 0.00 0.00 2.77
4189 6114 6.751514 TGCTTGTTCTGTTGTTCTCTTTTA 57.248 33.333 0.00 0.00 0.00 1.52
4190 6115 5.643379 TGCTTGTTCTGTTGTTCTCTTTT 57.357 34.783 0.00 0.00 0.00 2.27
4191 6116 5.357878 TGATGCTTGTTCTGTTGTTCTCTTT 59.642 36.000 0.00 0.00 0.00 2.52
4192 6117 4.883585 TGATGCTTGTTCTGTTGTTCTCTT 59.116 37.500 0.00 0.00 0.00 2.85
4193 6118 4.454678 TGATGCTTGTTCTGTTGTTCTCT 58.545 39.130 0.00 0.00 0.00 3.10
4205 6130 9.630098 CAGATAGTTTAAATGTTGATGCTTGTT 57.370 29.630 0.00 0.00 0.00 2.83
4220 6145 7.695055 TGGGTCCAAGATTTCAGATAGTTTAA 58.305 34.615 0.00 0.00 0.00 1.52
4242 6167 0.815734 CTCTGCATTTGAAGGCTGGG 59.184 55.000 7.27 0.79 36.52 4.45
4312 6237 4.920376 TCTTTTGCCTCAGTTTCGAAAAG 58.080 39.130 13.10 8.66 33.60 2.27
4313 6238 4.974368 TCTTTTGCCTCAGTTTCGAAAA 57.026 36.364 13.10 0.00 0.00 2.29
4374 6299 3.575256 TCTCTCGGCCTTTTGTAACACTA 59.425 43.478 0.00 0.00 0.00 2.74
4415 6340 7.982224 AGAAATTAGGGAAATTTGTACTACGC 58.018 34.615 0.00 0.00 45.70 4.42
4420 6345 6.750501 GGCGAAGAAATTAGGGAAATTTGTAC 59.249 38.462 0.00 0.00 45.70 2.90
4423 6348 5.109210 GGGCGAAGAAATTAGGGAAATTTG 58.891 41.667 0.00 0.00 45.70 2.32
4425 6350 3.704566 GGGGCGAAGAAATTAGGGAAATT 59.295 43.478 0.00 0.00 39.56 1.82
4426 6351 3.052869 AGGGGCGAAGAAATTAGGGAAAT 60.053 43.478 0.00 0.00 0.00 2.17
4427 6352 2.310647 AGGGGCGAAGAAATTAGGGAAA 59.689 45.455 0.00 0.00 0.00 3.13
4428 6353 1.920351 AGGGGCGAAGAAATTAGGGAA 59.080 47.619 0.00 0.00 0.00 3.97
4429 6354 1.211949 CAGGGGCGAAGAAATTAGGGA 59.788 52.381 0.00 0.00 0.00 4.20
4430 6355 1.680338 CAGGGGCGAAGAAATTAGGG 58.320 55.000 0.00 0.00 0.00 3.53
4431 6356 1.025041 GCAGGGGCGAAGAAATTAGG 58.975 55.000 0.00 0.00 0.00 2.69
4432 6357 1.672881 CTGCAGGGGCGAAGAAATTAG 59.327 52.381 5.57 0.00 45.35 1.73
4433 6358 1.004277 ACTGCAGGGGCGAAGAAATTA 59.996 47.619 19.93 0.00 45.35 1.40
4434 6359 0.251341 ACTGCAGGGGCGAAGAAATT 60.251 50.000 19.93 0.00 45.35 1.82
4435 6360 0.618458 TACTGCAGGGGCGAAGAAAT 59.382 50.000 19.93 0.00 45.35 2.17
4436 6361 0.398696 TTACTGCAGGGGCGAAGAAA 59.601 50.000 19.93 0.00 45.35 2.52
4437 6362 0.321298 GTTACTGCAGGGGCGAAGAA 60.321 55.000 19.93 0.00 45.35 2.52
4438 6363 1.295423 GTTACTGCAGGGGCGAAGA 59.705 57.895 19.93 0.00 45.35 2.87
4439 6364 1.745489 GGTTACTGCAGGGGCGAAG 60.745 63.158 19.93 0.00 45.35 3.79
4440 6365 2.349755 GGTTACTGCAGGGGCGAA 59.650 61.111 19.93 0.92 45.35 4.70
4441 6366 3.712907 GGGTTACTGCAGGGGCGA 61.713 66.667 19.93 0.00 45.35 5.54
4442 6367 3.561120 TTGGGTTACTGCAGGGGCG 62.561 63.158 19.93 0.00 45.35 6.13
4443 6368 1.228737 TTTGGGTTACTGCAGGGGC 60.229 57.895 19.93 6.89 41.68 5.80
4444 6369 0.611896 CCTTTGGGTTACTGCAGGGG 60.612 60.000 19.93 0.00 0.00 4.79
4445 6370 0.112412 ACCTTTGGGTTACTGCAGGG 59.888 55.000 19.93 8.48 44.73 4.45
4446 6371 3.745723 ACCTTTGGGTTACTGCAGG 57.254 52.632 19.93 0.00 44.73 4.85
4462 6387 2.435372 TATTGTGGATGAGGCCAACC 57.565 50.000 5.01 2.77 40.20 3.77
4463 6388 2.099756 GCTTATTGTGGATGAGGCCAAC 59.900 50.000 5.01 0.00 40.20 3.77
4464 6389 2.025037 AGCTTATTGTGGATGAGGCCAA 60.025 45.455 5.01 0.00 40.20 4.52
4465 6390 1.565759 AGCTTATTGTGGATGAGGCCA 59.434 47.619 5.01 0.00 35.02 5.36
4590 6882 5.622914 CGAACCAATTTGAGCAATCCAGATT 60.623 40.000 0.00 0.00 0.00 2.40
4615 6907 2.108168 CTTTCGGAGTGGTGGGATAGA 58.892 52.381 0.00 0.00 0.00 1.98
4616 6908 1.139058 CCTTTCGGAGTGGTGGGATAG 59.861 57.143 0.00 0.00 0.00 2.08
4631 6923 1.032114 CACCTTGCGGGATCCCTTTC 61.032 60.000 28.42 16.93 38.76 2.62


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

AutoCloner maintained by Alex Coulton.