Multiple sequence alignment - TraesCS2A01G129000

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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 TraesCS2A01G129000 chr2A 100.000 4812 0 0 1 4812 77267187 77262376 0.000000e+00 8887.0
1 TraesCS2A01G129000 chr2A 89.723 506 27 11 232 721 73076808 73076312 1.470000e-174 623.0
2 TraesCS2A01G129000 chr2A 88.363 507 32 11 232 721 426132584 426133080 6.940000e-163 584.0
3 TraesCS2A01G129000 chr2A 85.830 494 35 13 873 1356 426133075 426133543 4.330000e-135 492.0
4 TraesCS2A01G129000 chr2A 85.020 494 39 13 873 1356 73076317 73075849 2.030000e-128 470.0
5 TraesCS2A01G129000 chr2A 83.457 405 50 4 2019 2423 86651366 86650979 1.270000e-95 361.0
6 TraesCS2A01G129000 chr2A 90.909 44 3 1 4180 4222 77237969 77237926 1.870000e-04 58.4
7 TraesCS2A01G129000 chr2B 89.902 3476 232 66 826 4256 118063571 118060170 0.000000e+00 4364.0
8 TraesCS2A01G129000 chr2B 83.564 1010 129 19 2089 3093 462941129 462942106 0.000000e+00 911.0
9 TraesCS2A01G129000 chr2B 89.180 573 37 16 4256 4812 118060141 118059578 0.000000e+00 691.0
10 TraesCS2A01G129000 chr2B 81.818 836 63 45 3 775 118064337 118063528 1.900000e-173 619.0
11 TraesCS2A01G129000 chr2D 93.871 2578 103 19 1290 3836 76764029 76761476 0.000000e+00 3834.0
12 TraesCS2A01G129000 chr2D 86.778 1316 95 36 22 1294 76765467 76764188 0.000000e+00 1393.0
13 TraesCS2A01G129000 chr2D 90.976 953 52 19 3887 4812 76761468 76760523 0.000000e+00 1253.0
14 TraesCS2A01G129000 chr2D 91.388 569 32 12 4256 4812 76760156 76759593 0.000000e+00 763.0
15 TraesCS2A01G129000 chr1A 85.390 1013 120 16 2089 3093 548472093 548471101 0.000000e+00 1026.0
16 TraesCS2A01G129000 chr1A 84.273 1011 118 26 2089 3093 94120147 94119172 0.000000e+00 948.0
17 TraesCS2A01G129000 chr7B 84.329 1021 124 16 2089 3093 569422663 569421663 0.000000e+00 966.0
18 TraesCS2A01G129000 chrUn 83.482 1011 121 26 2089 3093 10183878 10184848 0.000000e+00 900.0
19 TraesCS2A01G129000 chrUn 77.984 486 62 14 2089 2571 363625471 363625028 3.690000e-66 263.0
20 TraesCS2A01G129000 chr1B 81.439 959 134 27 2089 3041 9371700 9372620 0.000000e+00 745.0
21 TraesCS2A01G129000 chr1B 86.116 533 58 12 2564 3093 646829810 646829291 1.170000e-155 560.0
22 TraesCS2A01G129000 chr1B 78.189 486 61 14 2089 2571 646831559 646831116 7.940000e-68 268.0
23 TraesCS2A01G129000 chr1D 83.807 704 100 12 1678 2375 364492513 364493208 0.000000e+00 656.0
24 TraesCS2A01G129000 chr3A 89.941 507 26 11 232 721 7975676 7975178 8.790000e-177 630.0
25 TraesCS2A01G129000 chr3A 89.293 495 28 11 232 710 183811178 183811663 8.910000e-167 597.0
26 TraesCS2A01G129000 chr3A 85.216 487 42 9 878 1356 183811674 183812138 1.570000e-129 473.0
27 TraesCS2A01G129000 chr3A 84.413 494 42 13 873 1356 7975183 7974715 2.040000e-123 453.0
28 TraesCS2A01G129000 chr3A 79.560 318 63 2 3489 3805 155429516 155429200 4.850000e-55 226.0
29 TraesCS2A01G129000 chr7A 89.375 480 31 9 259 721 88306168 88305692 1.930000e-163 586.0
30 TraesCS2A01G129000 chr7A 84.818 494 40 13 873 1356 88305697 88305229 9.430000e-127 464.0
31 TraesCS2A01G129000 chr7A 88.166 338 28 7 2652 2988 150330513 150330839 4.510000e-105 392.0
32 TraesCS2A01G129000 chr7A 86.313 358 36 9 2278 2626 593450897 593451250 1.260000e-100 377.0
33 TraesCS2A01G129000 chr5A 87.179 507 34 12 232 721 701757750 701758242 9.110000e-152 547.0
34 TraesCS2A01G129000 chr5A 85.020 494 39 13 873 1356 701758237 701758705 2.030000e-128 470.0
35 TraesCS2A01G129000 chr3B 80.025 791 115 24 2089 2872 463207660 463206906 3.270000e-151 545.0
36 TraesCS2A01G129000 chr3B 78.549 317 66 2 3490 3805 200873669 200873354 1.760000e-49 207.0
37 TraesCS2A01G129000 chr4A 89.302 430 29 7 298 710 247023227 247022798 1.530000e-144 523.0
38 TraesCS2A01G129000 chr4A 85.656 488 39 10 877 1356 247022788 247022324 7.240000e-133 484.0
39 TraesCS2A01G129000 chr6D 88.060 335 39 1 2089 2423 421037000 421036667 3.490000e-106 396.0


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 TraesCS2A01G129000 chr2A 77262376 77267187 4811 True 8887.000000 8887 100.000000 1 4812 1 chr2A.!!$R2 4811
1 TraesCS2A01G129000 chr2A 73075849 73076808 959 True 546.500000 623 87.371500 232 1356 2 chr2A.!!$R4 1124
2 TraesCS2A01G129000 chr2A 426132584 426133543 959 False 538.000000 584 87.096500 232 1356 2 chr2A.!!$F1 1124
3 TraesCS2A01G129000 chr2B 118059578 118064337 4759 True 1891.333333 4364 86.966667 3 4812 3 chr2B.!!$R1 4809
4 TraesCS2A01G129000 chr2B 462941129 462942106 977 False 911.000000 911 83.564000 2089 3093 1 chr2B.!!$F1 1004
5 TraesCS2A01G129000 chr2D 76759593 76765467 5874 True 1810.750000 3834 90.753250 22 4812 4 chr2D.!!$R1 4790
6 TraesCS2A01G129000 chr1A 548471101 548472093 992 True 1026.000000 1026 85.390000 2089 3093 1 chr1A.!!$R2 1004
7 TraesCS2A01G129000 chr1A 94119172 94120147 975 True 948.000000 948 84.273000 2089 3093 1 chr1A.!!$R1 1004
8 TraesCS2A01G129000 chr7B 569421663 569422663 1000 True 966.000000 966 84.329000 2089 3093 1 chr7B.!!$R1 1004
9 TraesCS2A01G129000 chrUn 10183878 10184848 970 False 900.000000 900 83.482000 2089 3093 1 chrUn.!!$F1 1004
10 TraesCS2A01G129000 chr1B 9371700 9372620 920 False 745.000000 745 81.439000 2089 3041 1 chr1B.!!$F1 952
11 TraesCS2A01G129000 chr1B 646829291 646831559 2268 True 414.000000 560 82.152500 2089 3093 2 chr1B.!!$R1 1004
12 TraesCS2A01G129000 chr1D 364492513 364493208 695 False 656.000000 656 83.807000 1678 2375 1 chr1D.!!$F1 697
13 TraesCS2A01G129000 chr3A 7974715 7975676 961 True 541.500000 630 87.177000 232 1356 2 chr3A.!!$R2 1124
14 TraesCS2A01G129000 chr3A 183811178 183812138 960 False 535.000000 597 87.254500 232 1356 2 chr3A.!!$F1 1124
15 TraesCS2A01G129000 chr7A 88305229 88306168 939 True 525.000000 586 87.096500 259 1356 2 chr7A.!!$R1 1097
16 TraesCS2A01G129000 chr5A 701757750 701758705 955 False 508.500000 547 86.099500 232 1356 2 chr5A.!!$F1 1124
17 TraesCS2A01G129000 chr3B 463206906 463207660 754 True 545.000000 545 80.025000 2089 2872 1 chr3B.!!$R2 783
18 TraesCS2A01G129000 chr4A 247022324 247023227 903 True 503.500000 523 87.479000 298 1356 2 chr4A.!!$R1 1058

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
20 21 0.114364 GCCTTTCCCTTCCCTCCAAA 59.886 55.000 0.00 0.0 0.00 3.28 F
396 428 0.243636 GGGTTGGATTTTGAGGTGCG 59.756 55.000 0.00 0.0 0.00 5.34 F
397 429 0.388520 GGTTGGATTTTGAGGTGCGC 60.389 55.000 0.00 0.0 0.00 6.09 F
398 430 0.729140 GTTGGATTTTGAGGTGCGCG 60.729 55.000 0.00 0.0 0.00 6.86 F
1206 1350 1.001181 CATGTCCTTGGTTGCCTTTGG 59.999 52.381 0.00 0.0 0.00 3.28 F
2423 2774 1.005805 TGGCTTTCCATGTGTATGCCT 59.994 47.619 12.76 0.0 37.47 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1075 1204 1.076727 GGTGGAACAGGAAAGGGGG 59.923 63.158 0.00 0.00 41.80 5.40 R
2226 2569 0.179234 TTGGTTTCGGTGAGTGCTCA 59.821 50.000 0.00 0.00 37.24 4.26 R
2295 2646 1.541233 GGAGGATACATGGCGACCAAG 60.541 57.143 0.00 1.53 36.95 3.61 R
2487 2838 2.106684 CCCTATTTTCCTCTGCCTACCC 59.893 54.545 0.00 0.00 0.00 3.69 R
2596 4264 0.817229 GCAGGGAGCTAATCACAGGC 60.817 60.000 0.00 0.00 41.15 4.85 R
3870 5577 0.025513 CTCGCGCATTGCTTCACTAC 59.974 55.000 8.75 0.00 43.27 2.73 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
18 19 2.238701 GGCCTTTCCCTTCCCTCCA 61.239 63.158 0.00 0.00 0.00 3.86
19 20 1.774300 GCCTTTCCCTTCCCTCCAA 59.226 57.895 0.00 0.00 0.00 3.53
20 21 0.114364 GCCTTTCCCTTCCCTCCAAA 59.886 55.000 0.00 0.00 0.00 3.28
40 41 0.893727 CCAAACCAAACCCCGAGGAG 60.894 60.000 0.00 0.00 36.73 3.69
55 56 3.948719 GAGAACACGCCCACCCCA 61.949 66.667 0.00 0.00 0.00 4.96
56 57 3.256960 AGAACACGCCCACCCCAT 61.257 61.111 0.00 0.00 0.00 4.00
58 59 4.360405 AACACGCCCACCCCATCC 62.360 66.667 0.00 0.00 0.00 3.51
72 75 1.407437 CCCATCCCCTTTCGTCAGAAG 60.407 57.143 0.00 0.00 37.70 2.85
182 197 2.284151 GTCCTCCCCCTCTCTCCC 59.716 72.222 0.00 0.00 0.00 4.30
183 198 3.036959 TCCTCCCCCTCTCTCCCC 61.037 72.222 0.00 0.00 0.00 4.81
184 199 4.179599 CCTCCCCCTCTCTCCCCC 62.180 77.778 0.00 0.00 0.00 5.40
249 269 1.345526 CCCCCATCCCCTATCTATCCC 60.346 61.905 0.00 0.00 0.00 3.85
376 405 2.615493 CCCTGTTTCTTGGATGCGTAGT 60.615 50.000 0.00 0.00 0.00 2.73
388 420 2.279935 TGCGTAGTGGGTTGGATTTT 57.720 45.000 0.00 0.00 0.00 1.82
389 421 1.883275 TGCGTAGTGGGTTGGATTTTG 59.117 47.619 0.00 0.00 0.00 2.44
390 422 2.156098 GCGTAGTGGGTTGGATTTTGA 58.844 47.619 0.00 0.00 0.00 2.69
391 423 2.161609 GCGTAGTGGGTTGGATTTTGAG 59.838 50.000 0.00 0.00 0.00 3.02
393 425 3.763057 GTAGTGGGTTGGATTTTGAGGT 58.237 45.455 0.00 0.00 0.00 3.85
395 427 1.000843 GTGGGTTGGATTTTGAGGTGC 59.999 52.381 0.00 0.00 0.00 5.01
396 428 0.243636 GGGTTGGATTTTGAGGTGCG 59.756 55.000 0.00 0.00 0.00 5.34
397 429 0.388520 GGTTGGATTTTGAGGTGCGC 60.389 55.000 0.00 0.00 0.00 6.09
398 430 0.729140 GTTGGATTTTGAGGTGCGCG 60.729 55.000 0.00 0.00 0.00 6.86
401 433 1.797537 GATTTTGAGGTGCGCGTGC 60.798 57.895 15.48 15.48 43.20 5.34
504 568 1.948611 GCGGCTTGTTGGGACTGATTA 60.949 52.381 0.00 0.00 0.00 1.75
582 656 2.292267 GGATGCAGTCAATCGATGGTT 58.708 47.619 0.00 0.00 0.00 3.67
595 670 5.740290 ATCGATGGTTAGATTATCCGGTT 57.260 39.130 0.00 0.00 0.00 4.44
596 671 6.845758 ATCGATGGTTAGATTATCCGGTTA 57.154 37.500 0.00 0.00 0.00 2.85
605 684 5.670792 AGATTATCCGGTTATATCGCCAA 57.329 39.130 0.00 0.00 0.00 4.52
634 716 1.758440 TACGGCTGATCTGATGGGGC 61.758 60.000 0.00 0.00 0.00 5.80
687 773 5.479716 AGTTTGTGTTTTCGAGTTAGGTG 57.520 39.130 0.00 0.00 0.00 4.00
700 786 4.437390 CGAGTTAGGTGATGATGTTTTGGC 60.437 45.833 0.00 0.00 0.00 4.52
710 796 2.034939 TGATGTTTTGGCTGCTCTGTTG 59.965 45.455 0.00 0.00 0.00 3.33
711 797 1.473258 TGTTTTGGCTGCTCTGTTGT 58.527 45.000 0.00 0.00 0.00 3.32
717 804 1.578423 GCTGCTCTGTTGTTCCTGC 59.422 57.895 0.00 0.00 0.00 4.85
734 821 3.751175 TCCTGCGTTTCCATTTACAAGAG 59.249 43.478 0.00 0.00 0.00 2.85
741 828 6.403636 GCGTTTCCATTTACAAGAGTCATGAT 60.404 38.462 1.66 0.00 0.00 2.45
743 830 7.693951 CGTTTCCATTTACAAGAGTCATGATTC 59.306 37.037 10.09 10.09 0.00 2.52
784 871 4.137543 AGACAAGATTCAGGGTTTGTGTC 58.862 43.478 0.00 0.00 34.18 3.67
805 896 6.253727 GTGTCTTCGAGTTAGGTAATGATGTG 59.746 42.308 0.00 0.00 0.00 3.21
851 961 8.482128 AGTCATGATTCCTAGTCTAAAAAGGAG 58.518 37.037 0.00 0.00 40.43 3.69
856 979 5.422214 TCCTAGTCTAAAAAGGAGCAAGG 57.578 43.478 0.00 0.00 34.46 3.61
857 980 4.225267 TCCTAGTCTAAAAAGGAGCAAGGG 59.775 45.833 0.00 0.00 34.46 3.95
858 981 3.441500 AGTCTAAAAAGGAGCAAGGGG 57.558 47.619 0.00 0.00 0.00 4.79
859 982 2.041755 AGTCTAAAAAGGAGCAAGGGGG 59.958 50.000 0.00 0.00 0.00 5.40
943 1067 5.355350 CCTTACATGAGGTGGAAAGATGTTC 59.645 44.000 0.00 0.00 27.83 3.18
945 1069 4.330250 ACATGAGGTGGAAAGATGTTCTG 58.670 43.478 0.00 0.00 0.00 3.02
985 1109 3.131046 CCCTGCACTTCTTGTTTGAGTTT 59.869 43.478 0.00 0.00 0.00 2.66
1041 1170 1.470098 GCTGTGAGTGCAATACAAGGG 59.530 52.381 0.00 0.00 0.00 3.95
1052 1181 1.508256 ATACAAGGGGTAGTGGAGGC 58.492 55.000 0.00 0.00 34.92 4.70
1112 1242 1.842562 CCACTCCATCATTCCCTCTGT 59.157 52.381 0.00 0.00 0.00 3.41
1127 1257 7.451731 TTCCCTCTGTTATCATATTTCCTGT 57.548 36.000 0.00 0.00 0.00 4.00
1145 1289 1.134220 TGTTCTTTCCAGTGAAGCGGT 60.134 47.619 0.00 0.00 0.00 5.68
1146 1290 1.947456 GTTCTTTCCAGTGAAGCGGTT 59.053 47.619 0.00 0.00 0.00 4.44
1147 1291 3.135994 GTTCTTTCCAGTGAAGCGGTTA 58.864 45.455 0.00 0.00 0.00 2.85
1148 1292 2.762745 TCTTTCCAGTGAAGCGGTTAC 58.237 47.619 0.00 0.00 0.00 2.50
1149 1293 2.367567 TCTTTCCAGTGAAGCGGTTACT 59.632 45.455 0.00 1.78 0.00 2.24
1150 1294 3.575256 TCTTTCCAGTGAAGCGGTTACTA 59.425 43.478 0.00 0.00 0.00 1.82
1151 1295 3.308438 TTCCAGTGAAGCGGTTACTAC 57.692 47.619 0.00 0.07 0.00 2.73
1206 1350 1.001181 CATGTCCTTGGTTGCCTTTGG 59.999 52.381 0.00 0.00 0.00 3.28
1357 1664 3.305398 ACTGACTAGAAAGCTGAACCG 57.695 47.619 0.00 0.00 0.00 4.44
1360 1667 4.202223 ACTGACTAGAAAGCTGAACCGAAA 60.202 41.667 0.00 0.00 0.00 3.46
1370 1677 4.557205 AGCTGAACCGAAAGTACAGTAAG 58.443 43.478 0.00 0.00 0.00 2.34
1371 1678 3.123116 GCTGAACCGAAAGTACAGTAAGC 59.877 47.826 0.00 0.00 0.00 3.09
1372 1679 4.557205 CTGAACCGAAAGTACAGTAAGCT 58.443 43.478 0.00 0.00 0.00 3.74
1373 1680 5.706916 CTGAACCGAAAGTACAGTAAGCTA 58.293 41.667 0.00 0.00 0.00 3.32
1376 1683 6.985645 TGAACCGAAAGTACAGTAAGCTAAAA 59.014 34.615 0.00 0.00 0.00 1.52
1377 1684 7.495279 TGAACCGAAAGTACAGTAAGCTAAAAA 59.505 33.333 0.00 0.00 0.00 1.94
1378 1685 7.182361 ACCGAAAGTACAGTAAGCTAAAAAC 57.818 36.000 0.00 0.00 0.00 2.43
1379 1686 6.203530 ACCGAAAGTACAGTAAGCTAAAAACC 59.796 38.462 0.00 0.00 0.00 3.27
1380 1687 6.426025 CCGAAAGTACAGTAAGCTAAAAACCT 59.574 38.462 0.00 0.00 0.00 3.50
1381 1688 7.041576 CCGAAAGTACAGTAAGCTAAAAACCTT 60.042 37.037 0.00 0.00 0.00 3.50
1382 1689 8.008279 CGAAAGTACAGTAAGCTAAAAACCTTC 58.992 37.037 0.00 0.00 0.00 3.46
1383 1690 8.741603 AAAGTACAGTAAGCTAAAAACCTTCA 57.258 30.769 0.00 0.00 0.00 3.02
1384 1691 7.964604 AGTACAGTAAGCTAAAAACCTTCAG 57.035 36.000 0.00 0.00 0.00 3.02
1415 1722 4.420168 CTGAAAAAGGTGAAAACAAGCGA 58.580 39.130 0.00 0.00 0.00 4.93
1539 1846 5.195940 CCTCATGATTAACTGACCAACCAT 58.804 41.667 0.00 0.00 0.00 3.55
1683 2000 7.905604 TTCAGTTACATGGATTCACACTAAG 57.094 36.000 0.00 0.00 0.00 2.18
1764 2082 9.558396 TCAAATCTTTTGCTGAAAAATGGTAAT 57.442 25.926 0.00 0.00 37.14 1.89
1767 2085 7.727331 TCTTTTGCTGAAAAATGGTAATTGG 57.273 32.000 0.00 0.00 37.14 3.16
1768 2086 5.938438 TTTGCTGAAAAATGGTAATTGGC 57.062 34.783 0.00 0.00 0.00 4.52
1770 2088 5.163281 TGCTGAAAAATGGTAATTGGCAT 57.837 34.783 0.00 0.00 0.00 4.40
1772 2090 5.046448 TGCTGAAAAATGGTAATTGGCATCT 60.046 36.000 0.00 0.00 0.00 2.90
1773 2091 6.154192 TGCTGAAAAATGGTAATTGGCATCTA 59.846 34.615 0.00 0.00 0.00 1.98
1774 2092 7.147689 TGCTGAAAAATGGTAATTGGCATCTAT 60.148 33.333 0.00 0.00 0.00 1.98
1775 2093 7.170320 GCTGAAAAATGGTAATTGGCATCTATG 59.830 37.037 0.00 0.00 0.00 2.23
1811 2142 6.537301 CGGTGTGTAATGATGTAACCTAACAT 59.463 38.462 0.00 0.00 42.75 2.71
1854 2187 7.807977 TTACAAACTTTTCTGAGATGAAGCT 57.192 32.000 6.14 0.00 0.00 3.74
1892 2232 2.881074 TCTGCATCGTTAGTGCTCTTC 58.119 47.619 0.00 0.00 42.92 2.87
1897 2237 5.419542 TGCATCGTTAGTGCTCTTCTTTAT 58.580 37.500 0.00 0.00 42.92 1.40
1905 2245 7.432838 CGTTAGTGCTCTTCTTTATAGAACCTC 59.567 40.741 0.00 0.00 35.49 3.85
1924 2264 3.433709 CTCTAAGTGCAGTCGAGTCATG 58.566 50.000 10.96 0.00 0.00 3.07
1981 2321 5.694910 TGCGTTCCTTAGAAAAGTGAGTTAG 59.305 40.000 0.00 0.00 32.58 2.34
2099 2441 6.884280 TCTCTTGATTTCTTTTTCCTCCAC 57.116 37.500 0.00 0.00 0.00 4.02
2205 2548 7.397194 CAAAGATTGAGATGTTAGATGTCACG 58.603 38.462 0.00 0.00 0.00 4.35
2226 2569 3.488721 CGGAACTCGTCGGTGATCTTATT 60.489 47.826 0.00 0.00 0.00 1.40
2295 2646 1.406539 CTATTGGAATGCCCTGTGTGC 59.593 52.381 0.00 0.00 35.38 4.57
2423 2774 1.005805 TGGCTTTCCATGTGTATGCCT 59.994 47.619 12.76 0.00 37.47 4.75
2460 2811 8.677300 TCAGATAAGAATATCCAGTTGCAAAAC 58.323 33.333 0.00 0.00 39.02 2.43
2511 2863 3.372440 AGGCAGAGGAAAATAGGGTTG 57.628 47.619 0.00 0.00 0.00 3.77
2543 2896 7.809806 GGTGACCTTTTTCTATGAATCACTTTG 59.190 37.037 0.00 0.00 36.36 2.77
2572 4240 7.937700 ATAAGTGATATCCCTTCCTTTCTGA 57.062 36.000 3.51 0.00 0.00 3.27
2575 4243 8.517323 AAGTGATATCCCTTCCTTTCTGATAT 57.483 34.615 0.00 0.00 32.74 1.63
3094 4777 5.027293 TCACTGGTGACATTCCATATCTG 57.973 43.478 0.00 0.00 41.51 2.90
3112 4795 4.008074 TCTGGTGAATCACTTGAAGGAC 57.992 45.455 13.53 0.00 34.40 3.85
3115 4798 2.737252 GGTGAATCACTTGAAGGACGAC 59.263 50.000 13.53 0.00 34.40 4.34
3226 4909 6.183360 TGCTTACGGTAATTATCAGCTACCTT 60.183 38.462 0.29 0.00 34.15 3.50
3352 5045 7.011482 GTCTTATGGATTGCTGATCGTTTACTT 59.989 37.037 0.00 0.00 35.49 2.24
3371 5064 7.571089 TTACTTAGTGTGTGCATACTTAACG 57.429 36.000 15.05 9.45 34.54 3.18
3376 5069 3.985279 GTGTGTGCATACTTAACGACTCA 59.015 43.478 15.05 0.00 0.00 3.41
3481 5174 8.534954 AGTTGTGGAACTAACTCTAGCATATA 57.465 34.615 0.00 0.00 40.85 0.86
3482 5175 8.414778 AGTTGTGGAACTAACTCTAGCATATAC 58.585 37.037 0.00 0.00 40.85 1.47
3529 5222 2.498167 CAGTACTTCTGCCTGCACTTT 58.502 47.619 0.00 0.00 37.36 2.66
3658 5351 0.981183 ACCGTAAGATGACCTGGCAA 59.019 50.000 0.00 0.00 43.02 4.52
3694 5387 1.500474 TCAGGGATAGCCACAGGAAG 58.500 55.000 0.00 0.00 35.15 3.46
3712 5405 2.125961 GGTCCGGGACAGCTACGAT 61.126 63.158 27.32 0.00 33.68 3.73
3730 5423 2.281345 GGGCTCATCATCCAGCGG 60.281 66.667 0.00 0.00 36.41 5.52
3843 5550 0.462047 ATGCTTAGAAGGCCGTTCGG 60.462 55.000 6.90 6.90 40.49 4.30
3847 5554 0.680618 TTAGAAGGCCGTTCGGTTCA 59.319 50.000 12.81 0.00 40.49 3.18
3854 5561 0.953960 GCCGTTCGGTTCATTCTGGT 60.954 55.000 12.81 0.00 0.00 4.00
3863 5570 2.555199 GTTCATTCTGGTGATCCGAGG 58.445 52.381 0.00 0.00 36.30 4.63
3864 5571 0.465705 TCATTCTGGTGATCCGAGGC 59.534 55.000 0.00 0.00 36.30 4.70
3869 5576 1.949847 CTGGTGATCCGAGGCGAACT 61.950 60.000 0.00 0.00 36.30 3.01
3870 5577 1.519455 GGTGATCCGAGGCGAACTG 60.519 63.158 0.00 0.00 0.00 3.16
3871 5578 1.215647 GTGATCCGAGGCGAACTGT 59.784 57.895 0.00 0.00 0.00 3.55
3872 5579 0.454600 GTGATCCGAGGCGAACTGTA 59.545 55.000 0.00 0.00 0.00 2.74
3873 5580 0.738975 TGATCCGAGGCGAACTGTAG 59.261 55.000 0.00 0.00 0.00 2.74
3874 5581 0.739561 GATCCGAGGCGAACTGTAGT 59.260 55.000 0.00 0.00 0.00 2.73
3875 5582 0.456221 ATCCGAGGCGAACTGTAGTG 59.544 55.000 0.00 0.00 0.00 2.74
3876 5583 0.607217 TCCGAGGCGAACTGTAGTGA 60.607 55.000 0.00 0.00 0.00 3.41
3877 5584 0.242825 CCGAGGCGAACTGTAGTGAA 59.757 55.000 0.00 0.00 0.00 3.18
3878 5585 1.618861 CGAGGCGAACTGTAGTGAAG 58.381 55.000 0.00 0.00 0.00 3.02
3879 5586 1.351153 GAGGCGAACTGTAGTGAAGC 58.649 55.000 0.00 0.00 0.00 3.86
3880 5587 0.679505 AGGCGAACTGTAGTGAAGCA 59.320 50.000 0.00 0.00 0.00 3.91
3881 5588 1.070134 AGGCGAACTGTAGTGAAGCAA 59.930 47.619 0.00 0.00 0.00 3.91
3882 5589 2.076863 GGCGAACTGTAGTGAAGCAAT 58.923 47.619 0.00 0.00 0.00 3.56
3883 5590 2.159653 GGCGAACTGTAGTGAAGCAATG 60.160 50.000 0.00 0.00 0.00 2.82
3884 5591 2.726066 GCGAACTGTAGTGAAGCAATGC 60.726 50.000 0.00 0.00 0.00 3.56
3885 5592 2.472886 CGAACTGTAGTGAAGCAATGCG 60.473 50.000 0.00 0.00 0.00 4.73
3886 5593 0.798776 ACTGTAGTGAAGCAATGCGC 59.201 50.000 0.00 0.00 42.91 6.09
3895 5602 2.202349 GCAATGCGCGAGTGAACC 60.202 61.111 12.10 0.00 0.00 3.62
3896 5603 2.096406 CAATGCGCGAGTGAACCG 59.904 61.111 12.10 0.00 0.00 4.44
3939 5648 5.778542 AGGACTAGGTAATGGTGTGTAGAT 58.221 41.667 0.00 0.00 0.00 1.98
3946 5655 5.721960 AGGTAATGGTGTGTAGATTGTCTCT 59.278 40.000 0.00 0.00 38.06 3.10
3963 5672 9.791820 GATTGTCTCTTTAGGTTCTAGTAGTTC 57.208 37.037 0.00 0.00 0.00 3.01
3974 5683 8.196378 AGGTTCTAGTAGTTCTGAGATGTTTT 57.804 34.615 0.00 0.00 0.00 2.43
4072 5781 1.601759 GAACAAGAGCTGGCTGGCA 60.602 57.895 3.18 3.18 34.17 4.92
4142 5852 3.391296 TGTAAATGATGTAGCCCCTCTCC 59.609 47.826 0.00 0.00 0.00 3.71
4143 5853 2.503869 AATGATGTAGCCCCTCTCCT 57.496 50.000 0.00 0.00 0.00 3.69
4175 5886 6.174760 ACTCGTATCTATCTATGTCAGACCC 58.825 44.000 0.00 0.00 35.62 4.46
4284 6942 2.698855 ACTCGTATTTGCATCAGCCT 57.301 45.000 0.00 0.00 41.13 4.58
4381 7040 5.649831 GCTTCCACTGGAATATGTCTTCTTT 59.350 40.000 11.09 0.00 41.23 2.52
4384 7043 7.452880 TCCACTGGAATATGTCTTCTTTTTG 57.547 36.000 0.00 0.00 0.00 2.44
4385 7044 6.071952 TCCACTGGAATATGTCTTCTTTTTGC 60.072 38.462 0.00 0.00 0.00 3.68
4386 7045 6.294675 CCACTGGAATATGTCTTCTTTTTGCA 60.295 38.462 0.00 0.00 0.00 4.08
4387 7046 7.318141 CACTGGAATATGTCTTCTTTTTGCAT 58.682 34.615 0.00 0.00 0.00 3.96
4409 7070 7.176165 TGCATCAAATCAGAAGATGTTTTCTCT 59.824 33.333 10.73 0.00 40.86 3.10
4410 7071 7.697291 GCATCAAATCAGAAGATGTTTTCTCTC 59.303 37.037 10.73 0.00 40.86 3.20
4411 7072 8.948145 CATCAAATCAGAAGATGTTTTCTCTCT 58.052 33.333 0.00 0.00 35.28 3.10
4463 7124 4.035102 GGGCAGCGGGTTCCTTCT 62.035 66.667 0.00 0.00 0.00 2.85
4521 7185 6.373759 AGAAAACTAGACCCAAAAACCTCAT 58.626 36.000 0.00 0.00 0.00 2.90
4600 7273 3.741245 ACACTAGAGCTTAGGGACAGA 57.259 47.619 10.85 0.00 0.00 3.41
4639 7312 1.918262 TCAAGGGGCATCATCTGAGTT 59.082 47.619 0.00 0.00 0.00 3.01
4700 7373 0.449786 CACGTGCAACCAAACTGACA 59.550 50.000 0.82 0.00 0.00 3.58
4725 7398 3.075148 ACTCGTCGAAGAGAACTCATCA 58.925 45.455 30.95 0.00 40.57 3.07
4726 7399 3.126171 ACTCGTCGAAGAGAACTCATCAG 59.874 47.826 30.95 5.49 40.57 2.90
4727 7400 2.159503 TCGTCGAAGAGAACTCATCAGC 60.160 50.000 0.00 0.00 36.95 4.26
4728 7401 2.181205 GTCGAAGAGAACTCATCAGCG 58.819 52.381 4.64 0.00 36.95 5.18
4729 7402 1.813178 TCGAAGAGAACTCATCAGCGT 59.187 47.619 4.64 0.00 0.00 5.07
4730 7403 2.159503 TCGAAGAGAACTCATCAGCGTC 60.160 50.000 4.64 0.00 0.00 5.19
4731 7404 2.181205 GAAGAGAACTCATCAGCGTCG 58.819 52.381 4.64 0.00 0.00 5.12
4735 7415 3.628032 AGAGAACTCATCAGCGTCGAATA 59.372 43.478 0.00 0.00 0.00 1.75
4772 7452 6.730507 TCATCCTAGAAACATCATGGGCTATA 59.269 38.462 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.800229 TTGGAGGGAAGGGAAAGGCC 61.800 60.000 0.00 0.00 0.00 5.19
1 2 0.114364 TTTGGAGGGAAGGGAAAGGC 59.886 55.000 0.00 0.00 0.00 4.35
14 15 1.140052 GGGGTTTGGTTTGGTTTGGAG 59.860 52.381 0.00 0.00 0.00 3.86
18 19 1.116308 CTCGGGGTTTGGTTTGGTTT 58.884 50.000 0.00 0.00 0.00 3.27
19 20 0.757561 CCTCGGGGTTTGGTTTGGTT 60.758 55.000 0.00 0.00 0.00 3.67
20 21 1.152631 CCTCGGGGTTTGGTTTGGT 60.153 57.895 0.00 0.00 0.00 3.67
40 41 2.750237 GATGGGGTGGGCGTGTTC 60.750 66.667 0.00 0.00 0.00 3.18
55 56 1.952621 TCCTTCTGACGAAAGGGGAT 58.047 50.000 2.29 0.00 0.00 3.85
56 57 1.724545 TTCCTTCTGACGAAAGGGGA 58.275 50.000 2.29 0.00 0.00 4.81
58 59 3.067833 GTCTTTCCTTCTGACGAAAGGG 58.932 50.000 18.94 4.15 43.34 3.95
72 75 2.070028 GTCGCCTCTTTCAGTCTTTCC 58.930 52.381 0.00 0.00 0.00 3.13
182 197 2.746359 GGCTCGAGATGGATGGGG 59.254 66.667 18.75 0.00 0.00 4.96
183 198 1.825281 GAGGGCTCGAGATGGATGGG 61.825 65.000 18.75 0.00 0.00 4.00
184 199 1.670590 GAGGGCTCGAGATGGATGG 59.329 63.158 18.75 0.00 0.00 3.51
185 200 1.670590 GGAGGGCTCGAGATGGATG 59.329 63.158 18.75 0.00 0.00 3.51
186 201 1.905843 CGGAGGGCTCGAGATGGAT 60.906 63.158 18.75 0.00 0.00 3.41
187 202 2.519541 CGGAGGGCTCGAGATGGA 60.520 66.667 18.75 0.00 0.00 3.41
249 269 2.230660 GGTTTGACCTTCACTTCCCTG 58.769 52.381 0.00 0.00 34.73 4.45
257 277 1.896660 GCGGCTGGTTTGACCTTCA 60.897 57.895 0.00 0.00 39.58 3.02
277 297 3.157949 CCGGAGAAGAGGAGGGGC 61.158 72.222 0.00 0.00 0.00 5.80
376 405 1.337118 GCACCTCAAAATCCAACCCA 58.663 50.000 0.00 0.00 0.00 4.51
397 429 3.423154 GAGCCAGAAACCCGCACG 61.423 66.667 0.00 0.00 0.00 5.34
398 430 3.423154 CGAGCCAGAAACCCGCAC 61.423 66.667 0.00 0.00 0.00 5.34
401 433 1.815421 CATCCGAGCCAGAAACCCG 60.815 63.158 0.00 0.00 0.00 5.28
402 434 2.115291 GCATCCGAGCCAGAAACCC 61.115 63.158 0.00 0.00 0.00 4.11
504 568 3.497942 GGGAATACTGTGACCCACAAGTT 60.498 47.826 11.81 0.00 44.08 2.66
553 627 2.672961 TGACTGCATCCCGAGTTAAG 57.327 50.000 0.00 0.00 0.00 1.85
555 629 2.481276 CGATTGACTGCATCCCGAGTTA 60.481 50.000 0.00 0.00 0.00 2.24
582 656 6.183360 CCTTGGCGATATAACCGGATAATCTA 60.183 42.308 9.46 0.00 0.00 1.98
595 670 0.682852 CGAACCCCCTTGGCGATATA 59.317 55.000 0.00 0.00 37.83 0.86
596 671 1.342672 ACGAACCCCCTTGGCGATAT 61.343 55.000 0.00 0.00 37.83 1.63
605 684 3.387947 CAGCCGTACGAACCCCCT 61.388 66.667 18.76 0.00 0.00 4.79
634 716 1.168714 GGCTGAGGCTTTACACCAAG 58.831 55.000 0.00 0.00 38.73 3.61
687 773 2.490903 ACAGAGCAGCCAAAACATCATC 59.509 45.455 0.00 0.00 0.00 2.92
700 786 0.882042 ACGCAGGAACAACAGAGCAG 60.882 55.000 0.00 0.00 0.00 4.24
710 796 3.907894 TGTAAATGGAAACGCAGGAAC 57.092 42.857 0.00 0.00 0.00 3.62
711 797 4.138290 TCTTGTAAATGGAAACGCAGGAA 58.862 39.130 0.00 0.00 0.00 3.36
717 804 6.480524 TCATGACTCTTGTAAATGGAAACG 57.519 37.500 0.00 0.00 0.00 3.60
734 821 9.487790 CTTCCTTTCTAGATTAGGAATCATGAC 57.512 37.037 25.57 0.00 44.65 3.06
741 828 8.666129 TGTCTTCTTCCTTTCTAGATTAGGAA 57.334 34.615 24.55 24.55 43.81 3.36
743 830 8.754080 TCTTGTCTTCTTCCTTTCTAGATTAGG 58.246 37.037 12.98 12.98 0.00 2.69
784 871 6.036083 CCAACACATCATTACCTAACTCGAAG 59.964 42.308 0.00 0.00 0.00 3.79
805 896 6.966021 TGACTAAATAAACAGAGCAACCAAC 58.034 36.000 0.00 0.00 0.00 3.77
839 949 2.447443 CCCCCTTGCTCCTTTTTAGAC 58.553 52.381 0.00 0.00 0.00 2.59
856 979 1.530183 GCATGCCTGAATCTCCCCC 60.530 63.158 6.36 0.00 0.00 5.40
857 980 0.822532 CAGCATGCCTGAATCTCCCC 60.823 60.000 15.66 0.00 44.64 4.81
858 981 0.106819 ACAGCATGCCTGAATCTCCC 60.107 55.000 15.66 0.00 44.64 4.30
859 982 1.404391 CAACAGCATGCCTGAATCTCC 59.596 52.381 15.66 0.00 44.64 3.71
860 983 2.362736 TCAACAGCATGCCTGAATCTC 58.637 47.619 15.66 0.00 44.64 2.75
861 984 2.502142 TCAACAGCATGCCTGAATCT 57.498 45.000 15.66 0.00 44.64 2.40
862 985 3.444916 CAATCAACAGCATGCCTGAATC 58.555 45.455 15.66 0.00 44.64 2.52
863 986 2.167693 CCAATCAACAGCATGCCTGAAT 59.832 45.455 15.66 5.44 44.64 2.57
864 987 1.546923 CCAATCAACAGCATGCCTGAA 59.453 47.619 15.66 0.00 44.64 3.02
865 988 1.179152 CCAATCAACAGCATGCCTGA 58.821 50.000 15.66 15.19 44.64 3.86
943 1067 1.741706 GGCATGGAGTTCATCACACAG 59.258 52.381 0.00 0.00 32.92 3.66
945 1069 1.098050 GGGCATGGAGTTCATCACAC 58.902 55.000 0.00 0.00 32.92 3.82
1011 1135 2.668550 CTCACAGCAGCAGCAGCA 60.669 61.111 12.92 0.00 45.49 4.41
1024 1148 2.200373 ACCCCTTGTATTGCACTCAC 57.800 50.000 0.00 0.00 0.00 3.51
1041 1170 1.139853 CTTCCATGAGCCTCCACTACC 59.860 57.143 0.00 0.00 0.00 3.18
1075 1204 1.076727 GGTGGAACAGGAAAGGGGG 59.923 63.158 0.00 0.00 41.80 5.40
1112 1242 9.177608 CACTGGAAAGAACAGGAAATATGATAA 57.822 33.333 0.00 0.00 40.23 1.75
1127 1257 2.341846 AACCGCTTCACTGGAAAGAA 57.658 45.000 0.00 0.00 31.35 2.52
1206 1350 2.159085 AGTGCCGCTTCTCCAACTATAC 60.159 50.000 0.00 0.00 0.00 1.47
1302 1609 5.882557 AGTGTCAATCCATGTAACTGAATCC 59.117 40.000 0.00 0.00 0.00 3.01
1357 1664 8.833493 TGAAGGTTTTTAGCTTACTGTACTTTC 58.167 33.333 0.00 0.00 0.00 2.62
1360 1667 7.732996 TCTGAAGGTTTTTAGCTTACTGTACT 58.267 34.615 0.00 0.00 0.00 2.73
1370 1677 6.364435 CAGCAAAAGATCTGAAGGTTTTTAGC 59.636 38.462 0.00 0.00 32.26 3.09
1371 1678 7.651808 TCAGCAAAAGATCTGAAGGTTTTTAG 58.348 34.615 0.00 0.00 36.50 1.85
1372 1679 7.581213 TCAGCAAAAGATCTGAAGGTTTTTA 57.419 32.000 0.00 0.00 36.50 1.52
1373 1680 6.469782 TCAGCAAAAGATCTGAAGGTTTTT 57.530 33.333 0.00 0.00 36.50 1.94
1376 1683 6.469782 TTTTCAGCAAAAGATCTGAAGGTT 57.530 33.333 0.00 0.00 46.22 3.50
1377 1684 6.469782 TTTTTCAGCAAAAGATCTGAAGGT 57.530 33.333 0.00 0.00 46.22 3.50
1449 1756 5.009610 CCAGCAAGTGTTGTTAGGTTACATT 59.990 40.000 0.00 0.00 0.00 2.71
1571 1881 3.939740 AGACCACATCAATGCCACTAT 57.060 42.857 0.00 0.00 0.00 2.12
1572 1882 3.008923 TGAAGACCACATCAATGCCACTA 59.991 43.478 0.00 0.00 0.00 2.74
1655 1972 6.092670 AGTGTGAATCCATGTAACTGAATTCG 59.907 38.462 0.04 0.00 0.00 3.34
1657 1974 8.862325 TTAGTGTGAATCCATGTAACTGAATT 57.138 30.769 0.00 0.00 0.00 2.17
1683 2000 4.319549 CCGCTTTCTAGTCAACTGTTTTCC 60.320 45.833 0.00 0.00 0.00 3.13
1811 2142 5.565509 TGTAATATTTGACCCAGCAAGTCA 58.434 37.500 0.00 0.00 42.36 3.41
1854 2187 5.617252 TGCAGAAATCATGAGCTCATATGA 58.383 37.500 28.27 23.54 37.68 2.15
1892 2232 6.693545 CGACTGCACTTAGAGGTTCTATAAAG 59.306 42.308 0.00 0.00 0.00 1.85
1897 2237 3.682696 TCGACTGCACTTAGAGGTTCTA 58.317 45.455 0.00 0.00 0.00 2.10
1905 2245 3.223423 ACATGACTCGACTGCACTTAG 57.777 47.619 0.00 0.00 0.00 2.18
2205 2548 3.712091 ATAAGATCACCGACGAGTTCC 57.288 47.619 0.00 0.00 0.00 3.62
2226 2569 0.179234 TTGGTTTCGGTGAGTGCTCA 59.821 50.000 0.00 0.00 37.24 4.26
2295 2646 1.541233 GGAGGATACATGGCGACCAAG 60.541 57.143 0.00 1.53 36.95 3.61
2487 2838 2.106684 CCCTATTTTCCTCTGCCTACCC 59.893 54.545 0.00 0.00 0.00 3.69
2543 2896 6.441088 AGGAAGGGATATCACTTATTGGTC 57.559 41.667 20.21 6.86 40.21 4.02
2551 2906 7.181845 GGATATCAGAAAGGAAGGGATATCACT 59.818 40.741 0.15 0.15 44.20 3.41
2556 2911 5.548056 GGTGGATATCAGAAAGGAAGGGATA 59.452 44.000 4.83 0.00 0.00 2.59
2572 4240 1.356738 CCTGATGCATGGGGTGGATAT 59.643 52.381 2.46 0.00 39.19 1.63
2575 4243 3.009275 CCTGATGCATGGGGTGGA 58.991 61.111 2.46 0.00 0.00 4.02
2596 4264 0.817229 GCAGGGAGCTAATCACAGGC 60.817 60.000 0.00 0.00 41.15 4.85
2604 4272 3.894427 TCAAAATGTTTGCAGGGAGCTAA 59.106 39.130 0.00 0.00 45.94 3.09
2638 4307 7.169158 TGAAAATGAAAAGGAAGACTGTTGT 57.831 32.000 0.00 0.00 0.00 3.32
3058 4741 1.802960 CCAGTGACAGTGCATTCAGAC 59.197 52.381 4.63 0.00 0.00 3.51
3094 4777 2.737252 GTCGTCCTTCAAGTGATTCACC 59.263 50.000 13.14 0.00 34.49 4.02
3115 4798 3.084039 ACTGTGCATGTCAACCTTATGG 58.916 45.455 0.00 0.00 39.83 2.74
3352 5045 5.048573 TGAGTCGTTAAGTATGCACACACTA 60.049 40.000 0.00 0.00 0.00 2.74
3371 5064 8.025445 TCGACAGTAACCTTACTTAATTGAGTC 58.975 37.037 6.09 0.00 41.82 3.36
3376 5069 7.597743 CAGTGTCGACAGTAACCTTACTTAATT 59.402 37.037 24.83 0.00 41.82 1.40
3529 5222 4.020617 CCCAGCTGGAACGCCTCA 62.021 66.667 34.91 0.00 37.39 3.86
3628 5321 0.539986 TCTTACGGTTGATGCCTCCC 59.460 55.000 0.00 0.00 0.00 4.30
3661 5354 3.057749 CCTGATGCTCCGAGGGATA 57.942 57.895 0.00 0.00 0.00 2.59
3694 5387 2.125961 ATCGTAGCTGTCCCGGACC 61.126 63.158 15.24 0.28 0.00 4.46
3712 5405 2.507452 CGCTGGATGATGAGCCCA 59.493 61.111 0.00 0.00 30.98 5.36
3730 5423 0.610232 AGAAGCACAGGGCCATGTTC 60.610 55.000 22.77 17.36 46.50 3.18
3824 5525 0.462047 CCGAACGGCCTTCTAAGCAT 60.462 55.000 0.00 0.00 0.00 3.79
3843 5550 2.555199 CCTCGGATCACCAGAATGAAC 58.445 52.381 0.00 0.00 39.69 3.18
3847 5554 1.043116 TCGCCTCGGATCACCAGAAT 61.043 55.000 0.00 0.00 35.59 2.40
3854 5561 0.738975 CTACAGTTCGCCTCGGATCA 59.261 55.000 0.00 0.00 0.00 2.92
3863 5570 2.726066 GCATTGCTTCACTACAGTTCGC 60.726 50.000 0.16 0.00 0.00 4.70
3864 5571 2.472886 CGCATTGCTTCACTACAGTTCG 60.473 50.000 7.12 0.00 0.00 3.95
3869 5576 0.669012 TCGCGCATTGCTTCACTACA 60.669 50.000 8.75 0.00 43.27 2.74
3870 5577 0.025513 CTCGCGCATTGCTTCACTAC 59.974 55.000 8.75 0.00 43.27 2.73
3871 5578 0.389817 ACTCGCGCATTGCTTCACTA 60.390 50.000 8.75 0.00 43.27 2.74
3872 5579 1.669115 ACTCGCGCATTGCTTCACT 60.669 52.632 8.75 0.00 43.27 3.41
3873 5580 1.510623 CACTCGCGCATTGCTTCAC 60.511 57.895 8.75 0.00 43.27 3.18
3874 5581 1.227342 TTCACTCGCGCATTGCTTCA 61.227 50.000 8.75 0.00 43.27 3.02
3875 5582 0.790866 GTTCACTCGCGCATTGCTTC 60.791 55.000 8.75 0.00 43.27 3.86
3876 5583 1.207593 GTTCACTCGCGCATTGCTT 59.792 52.632 8.75 0.00 43.27 3.91
3877 5584 2.680913 GGTTCACTCGCGCATTGCT 61.681 57.895 8.75 0.00 43.27 3.91
3878 5585 2.202349 GGTTCACTCGCGCATTGC 60.202 61.111 8.75 0.00 41.47 3.56
3879 5586 2.096406 CGGTTCACTCGCGCATTG 59.904 61.111 8.75 0.00 0.00 2.82
3880 5587 3.788766 GCGGTTCACTCGCGCATT 61.789 61.111 8.75 0.00 43.71 3.56
3897 5604 2.923426 TAATCAAGCCCTCGCAGCGG 62.923 60.000 16.42 5.58 37.52 5.52
3898 5605 1.493950 CTAATCAAGCCCTCGCAGCG 61.494 60.000 9.06 9.06 37.52 5.18
3899 5606 1.162800 CCTAATCAAGCCCTCGCAGC 61.163 60.000 0.00 0.00 37.52 5.25
3900 5607 0.465705 TCCTAATCAAGCCCTCGCAG 59.534 55.000 0.00 0.00 37.52 5.18
3901 5608 0.178068 GTCCTAATCAAGCCCTCGCA 59.822 55.000 0.00 0.00 37.52 5.10
3902 5609 0.466124 AGTCCTAATCAAGCCCTCGC 59.534 55.000 0.00 0.00 0.00 5.03
3903 5610 2.297597 CCTAGTCCTAATCAAGCCCTCG 59.702 54.545 0.00 0.00 0.00 4.63
3939 5648 8.794553 CAGAACTACTAGAACCTAAAGAGACAA 58.205 37.037 0.00 0.00 0.00 3.18
3946 5655 8.880991 ACATCTCAGAACTACTAGAACCTAAA 57.119 34.615 0.00 0.00 0.00 1.85
3963 5672 5.184479 ACAACCATCCATGAAAACATCTCAG 59.816 40.000 0.00 0.00 0.00 3.35
3974 5683 4.264253 GTTCTCATCACAACCATCCATGA 58.736 43.478 0.00 0.00 0.00 3.07
4090 5799 1.162698 CACCAGCAACATCTCACCAG 58.837 55.000 0.00 0.00 0.00 4.00
4142 5852 9.594478 ACATAGATAGATACGAGTCTCATACAG 57.406 37.037 0.00 0.00 0.00 2.74
4143 5853 9.589111 GACATAGATAGATACGAGTCTCATACA 57.411 37.037 0.00 0.00 0.00 2.29
4175 5886 4.472691 TCAGAAGTTCAGAACATTTGCG 57.527 40.909 15.85 0.00 0.00 4.85
4284 6942 2.355716 GGAATTCTGAACATCGGTGGGA 60.356 50.000 5.23 0.00 0.00 4.37
4381 7040 8.145767 AGAAAACATCTTCTGATTTGATGCAAA 58.854 29.630 12.52 0.00 40.66 3.68
4384 7043 7.536855 AGAGAAAACATCTTCTGATTTGATGC 58.463 34.615 12.52 0.00 40.66 3.91
4385 7044 8.948145 AGAGAGAAAACATCTTCTGATTTGATG 58.052 33.333 11.58 11.58 38.96 3.07
4386 7045 9.517868 AAGAGAGAAAACATCTTCTGATTTGAT 57.482 29.630 0.00 0.00 38.96 2.57
4387 7046 8.915057 AAGAGAGAAAACATCTTCTGATTTGA 57.085 30.769 0.00 0.00 38.96 2.69
4432 7093 0.036952 CTGCCCTCACAAGTCACGAT 60.037 55.000 0.00 0.00 0.00 3.73
4497 7161 5.762279 TGAGGTTTTTGGGTCTAGTTTTCT 58.238 37.500 0.00 0.00 0.00 2.52
4505 7169 5.186198 CGAGAATATGAGGTTTTTGGGTCT 58.814 41.667 0.00 0.00 0.00 3.85
4600 7273 4.717233 TGATGTTGCAGTTGTTTTGTCT 57.283 36.364 0.00 0.00 0.00 3.41
4639 7312 0.464036 CCTTGGCGCTATGGTGTCTA 59.536 55.000 16.43 0.00 0.00 2.59
4662 7335 1.729881 GGCCAAGCCTAATTGCTCG 59.270 57.895 0.00 0.00 46.69 5.03
4680 7353 0.248458 GTCAGTTTGGTTGCACGTGG 60.248 55.000 18.88 0.00 0.00 4.94
4700 7373 3.502595 TGAGTTCTCTTCGACGAGTGATT 59.497 43.478 17.45 5.94 32.83 2.57
4725 7398 1.798079 GCGGAAGAGTTATTCGACGCT 60.798 52.381 0.00 0.00 40.92 5.07
4726 7399 0.571197 GCGGAAGAGTTATTCGACGC 59.429 55.000 0.00 0.00 38.86 5.19
4727 7400 1.197910 GGCGGAAGAGTTATTCGACG 58.802 55.000 0.00 0.00 0.00 5.12
4728 7401 2.159282 TGAGGCGGAAGAGTTATTCGAC 60.159 50.000 0.00 0.00 0.00 4.20
4729 7402 2.097036 TGAGGCGGAAGAGTTATTCGA 58.903 47.619 0.00 0.00 0.00 3.71
4730 7403 2.579207 TGAGGCGGAAGAGTTATTCG 57.421 50.000 0.00 0.00 0.00 3.34
4731 7404 3.070302 AGGATGAGGCGGAAGAGTTATTC 59.930 47.826 0.00 0.00 0.00 1.75
4735 7415 2.035632 CTAGGATGAGGCGGAAGAGTT 58.964 52.381 0.00 0.00 0.00 3.01
4778 7458 6.096705 AGACCTTTCATGATGTTTTTCACACA 59.903 34.615 0.00 0.00 38.61 3.72


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

AutoCloner maintained by Alex Coulton.