Multiple sequence alignment - TraesCS5B01G403900

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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 TraesCS5B01G403900 chr5B 100.000 3455 0 0 1 3455 580291383 580287929 0.000000e+00 6381.0
1 TraesCS5B01G403900 chr5B 93.333 90 5 1 2181 2270 27832922 27833010 7.780000e-27 132.0
2 TraesCS5B01G403900 chr5B 86.364 66 9 0 12 77 701557889 701557824 4.780000e-09 73.1
3 TraesCS5B01G403900 chr5B 91.837 49 3 1 28 75 701844283 701844235 2.230000e-07 67.6
4 TraesCS5B01G403900 chr5A 87.500 1328 99 35 894 2182 592623639 592622340 0.000000e+00 1471.0
5 TraesCS5B01G403900 chr5A 97.835 739 16 0 153 891 483275881 483276619 0.000000e+00 1277.0
6 TraesCS5B01G403900 chr5A 87.165 1083 80 30 2264 3330 592622341 592621302 0.000000e+00 1175.0
7 TraesCS5B01G403900 chr5A 82.468 154 11 7 3 152 592623767 592623626 1.680000e-23 121.0
8 TraesCS5B01G403900 chr6A 98.370 736 11 1 153 888 386108514 386109248 0.000000e+00 1291.0
9 TraesCS5B01G403900 chr6A 91.954 87 7 0 2179 2265 598614880 598614794 4.680000e-24 122.0
10 TraesCS5B01G403900 chr6A 91.954 87 7 0 2179 2265 598617187 598617101 4.680000e-24 122.0
11 TraesCS5B01G403900 chr4A 98.497 732 10 1 153 884 42774742 42774012 0.000000e+00 1290.0
12 TraesCS5B01G403900 chr4A 88.060 67 7 1 12 77 617718822 617718756 1.030000e-10 78.7
13 TraesCS5B01G403900 chr4A 88.060 67 7 1 12 77 617752013 617751947 1.030000e-10 78.7
14 TraesCS5B01G403900 chr4A 88.060 67 7 1 12 77 617784645 617784579 1.030000e-10 78.7
15 TraesCS5B01G403900 chr4A 86.567 67 8 1 12 77 617818063 617817997 4.780000e-09 73.1
16 TraesCS5B01G403900 chr7A 98.106 739 14 0 153 891 357348950 357348212 0.000000e+00 1288.0
17 TraesCS5B01G403900 chr2A 98.106 739 14 0 153 891 747620778 747621516 0.000000e+00 1288.0
18 TraesCS5B01G403900 chr2A 97.326 748 18 2 152 898 36033984 36033238 0.000000e+00 1269.0
19 TraesCS5B01G403900 chr2A 93.548 93 4 2 2180 2272 758599098 758599188 1.670000e-28 137.0
20 TraesCS5B01G403900 chr2A 91.860 86 7 0 2181 2266 518329816 518329731 1.680000e-23 121.0
21 TraesCS5B01G403900 chr1B 97.970 739 15 0 153 891 574237414 574238152 0.000000e+00 1282.0
22 TraesCS5B01G403900 chr2B 98.090 733 13 1 153 885 676548863 676549594 0.000000e+00 1275.0
23 TraesCS5B01G403900 chr2B 91.398 93 7 1 2180 2272 771822008 771821917 3.620000e-25 126.0
24 TraesCS5B01G403900 chrUn 97.826 736 16 0 153 888 17582800 17582065 0.000000e+00 1271.0
25 TraesCS5B01G403900 chrUn 88.060 67 7 1 12 77 382749144 382749078 1.030000e-10 78.7
26 TraesCS5B01G403900 chr5D 91.354 694 30 13 893 1586 472998227 472997564 0.000000e+00 922.0
27 TraesCS5B01G403900 chr5D 93.791 612 35 3 2264 2874 472996706 472996097 0.000000e+00 917.0
28 TraesCS5B01G403900 chr5D 91.745 424 17 4 1776 2182 472997127 472996705 1.080000e-159 573.0
29 TraesCS5B01G403900 chr5D 95.500 200 9 0 1583 1782 472997435 472997236 1.550000e-83 320.0
30 TraesCS5B01G403900 chr5D 85.906 298 24 11 2901 3184 472996038 472995745 5.600000e-78 302.0
31 TraesCS5B01G403900 chr5D 87.603 242 22 3 3219 3452 472995747 472995506 1.220000e-69 274.0
32 TraesCS5B01G403900 chr5D 85.806 155 16 3 3 152 472998366 472998213 3.570000e-35 159.0
33 TraesCS5B01G403900 chr3A 93.182 88 6 0 2178 2265 58929337 58929424 2.800000e-26 130.0
34 TraesCS5B01G403900 chr2D 91.398 93 7 1 2180 2272 628571534 628571443 3.620000e-25 126.0
35 TraesCS5B01G403900 chr1D 91.111 90 8 0 2176 2265 59875942 59876031 4.680000e-24 122.0


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 TraesCS5B01G403900 chr5B 580287929 580291383 3454 True 6381.000000 6381 100.000000 1 3455 1 chr5B.!!$R1 3454
1 TraesCS5B01G403900 chr5A 483275881 483276619 738 False 1277.000000 1277 97.835000 153 891 1 chr5A.!!$F1 738
2 TraesCS5B01G403900 chr5A 592621302 592623767 2465 True 922.333333 1471 85.711000 3 3330 3 chr5A.!!$R1 3327
3 TraesCS5B01G403900 chr6A 386108514 386109248 734 False 1291.000000 1291 98.370000 153 888 1 chr6A.!!$F1 735
4 TraesCS5B01G403900 chr4A 42774012 42774742 730 True 1290.000000 1290 98.497000 153 884 1 chr4A.!!$R1 731
5 TraesCS5B01G403900 chr7A 357348212 357348950 738 True 1288.000000 1288 98.106000 153 891 1 chr7A.!!$R1 738
6 TraesCS5B01G403900 chr2A 747620778 747621516 738 False 1288.000000 1288 98.106000 153 891 1 chr2A.!!$F1 738
7 TraesCS5B01G403900 chr2A 36033238 36033984 746 True 1269.000000 1269 97.326000 152 898 1 chr2A.!!$R1 746
8 TraesCS5B01G403900 chr1B 574237414 574238152 738 False 1282.000000 1282 97.970000 153 891 1 chr1B.!!$F1 738
9 TraesCS5B01G403900 chr2B 676548863 676549594 731 False 1275.000000 1275 98.090000 153 885 1 chr2B.!!$F1 732
10 TraesCS5B01G403900 chrUn 17582065 17582800 735 True 1271.000000 1271 97.826000 153 888 1 chrUn.!!$R1 735
11 TraesCS5B01G403900 chr5D 472995506 472998366 2860 True 495.285714 922 90.243571 3 3452 7 chr5D.!!$R1 3449

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
74 76 0.608640 AGTCGGAAGTTGGATTCGCT 59.391 50.0 0.0 0.0 0.0 4.93 F
1455 1470 0.521735 CGGCCTTTTTGCTAGTGTCC 59.478 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1514 1529 0.179225 GAGCACAACGCCACATAACG 60.179 55.0 0.0 0.0 44.04 3.18 R
2785 3072 0.175760 TCTGCCCGTCTGAATACTGC 59.824 55.0 0.0 0.0 0.00 4.40 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
64 66 1.587054 CCTTCAGCGAGTCGGAAGT 59.413 57.895 22.07 0.00 42.86 3.01
72 74 1.269166 CGAGTCGGAAGTTGGATTCG 58.731 55.000 4.10 4.71 36.36 3.34
73 75 1.000145 GAGTCGGAAGTTGGATTCGC 59.000 55.000 0.00 0.00 0.00 4.70
74 76 0.608640 AGTCGGAAGTTGGATTCGCT 59.391 50.000 0.00 0.00 0.00 4.93
75 77 0.721718 GTCGGAAGTTGGATTCGCTG 59.278 55.000 0.00 0.00 0.00 5.18
77 79 1.002366 CGGAAGTTGGATTCGCTGAG 58.998 55.000 0.00 0.00 0.00 3.35
106 108 4.821589 GAGGCGCCCGTTGGAGAG 62.822 72.222 26.15 0.00 32.25 3.20
118 120 0.902531 TTGGAGAGGCCCTAAACTCG 59.097 55.000 0.00 0.00 38.72 4.18
148 154 9.696917 CTAAATAAAATAAACATGGAGATGCCC 57.303 33.333 0.00 0.00 34.97 5.36
149 155 7.919385 AATAAAATAAACATGGAGATGCCCT 57.081 32.000 0.00 0.00 34.97 5.19
150 156 9.432982 AAATAAAATAAACATGGAGATGCCCTA 57.567 29.630 0.00 0.00 34.97 3.53
294 300 1.153086 GGATGGATGAAGTGGCGCT 60.153 57.895 7.64 0.00 0.00 5.92
545 551 3.571401 CACCAATTGAGGAGAAGCTTGTT 59.429 43.478 2.10 0.00 0.00 2.83
584 590 4.462394 GGGCATATTCAGCGCAGA 57.538 55.556 11.47 3.41 43.54 4.26
674 680 2.041081 ACCGATTTTGACATGGGAGGAA 59.959 45.455 0.00 0.00 0.00 3.36
695 701 5.163395 GGAATCCGTTAAGAGAGACCTGAAT 60.163 44.000 0.00 0.00 0.00 2.57
791 797 5.000591 TGAGTTGGTTGCGAAATCTTATGA 58.999 37.500 0.00 0.00 0.00 2.15
812 818 2.044630 AGTTTCACCTCTAGCCTACCCT 59.955 50.000 0.00 0.00 0.00 4.34
891 903 6.128282 TGTTGTTGTTGTTGTTGTTGTTGTTT 60.128 30.769 0.00 0.00 0.00 2.83
893 905 7.715265 TGTTGTTGTTGTTGTTGTTGTTTAT 57.285 28.000 0.00 0.00 0.00 1.40
898 910 6.516739 TGTTGTTGTTGTTGTTTATGGAGA 57.483 33.333 0.00 0.00 0.00 3.71
899 911 7.106439 TGTTGTTGTTGTTGTTTATGGAGAT 57.894 32.000 0.00 0.00 0.00 2.75
900 912 6.977502 TGTTGTTGTTGTTGTTTATGGAGATG 59.022 34.615 0.00 0.00 0.00 2.90
901 913 5.527951 TGTTGTTGTTGTTTATGGAGATGC 58.472 37.500 0.00 0.00 0.00 3.91
988 1000 1.157585 GCGACCCAAGAGAAGAAACC 58.842 55.000 0.00 0.00 0.00 3.27
989 1001 1.809684 CGACCCAAGAGAAGAAACCC 58.190 55.000 0.00 0.00 0.00 4.11
990 1002 1.610886 CGACCCAAGAGAAGAAACCCC 60.611 57.143 0.00 0.00 0.00 4.95
991 1003 0.778083 ACCCAAGAGAAGAAACCCCC 59.222 55.000 0.00 0.00 0.00 5.40
992 1004 0.777446 CCCAAGAGAAGAAACCCCCA 59.223 55.000 0.00 0.00 0.00 4.96
993 1005 1.146982 CCCAAGAGAAGAAACCCCCAA 59.853 52.381 0.00 0.00 0.00 4.12
1327 1342 3.423154 CACGCGAGCTCCCCAAAC 61.423 66.667 15.93 0.00 0.00 2.93
1345 1360 3.496438 CCCCTAGGTATCCCTTCCC 57.504 63.158 8.29 0.00 42.66 3.97
1354 1369 1.645402 TATCCCTTCCCTTGCCAGGC 61.645 60.000 3.66 3.66 39.20 4.85
1373 1388 1.389106 GCTGTTCGTTTGGCGTAGTAG 59.611 52.381 0.00 0.00 42.13 2.57
1376 1391 4.229096 CTGTTCGTTTGGCGTAGTAGTAA 58.771 43.478 0.00 0.00 42.13 2.24
1396 1411 9.774742 GTAGTAATTGATTTGGATGTGAAAGAC 57.225 33.333 0.00 0.00 0.00 3.01
1436 1451 3.917380 CGTAAGATGAGATGGAATCGCTC 59.083 47.826 0.00 0.00 46.32 5.03
1441 1456 2.423446 GATGGAATCGCTCGGCCT 59.577 61.111 0.00 0.00 31.13 5.19
1455 1470 0.521735 CGGCCTTTTTGCTAGTGTCC 59.478 55.000 0.00 0.00 0.00 4.02
1476 1491 3.626670 CCAACAGGAGCAAATCTGAGATC 59.373 47.826 0.00 0.00 35.20 2.75
1477 1492 3.557228 ACAGGAGCAAATCTGAGATCC 57.443 47.619 0.00 0.00 35.20 3.36
1481 1496 2.220313 GAGCAAATCTGAGATCCTGCC 58.780 52.381 19.81 11.47 0.00 4.85
1513 1528 3.503891 GTGTAAAACTGTTGTTGGCGTT 58.496 40.909 0.00 0.00 36.39 4.84
1514 1529 3.544682 GTGTAAAACTGTTGTTGGCGTTC 59.455 43.478 0.00 0.00 36.39 3.95
1515 1530 1.902840 AAAACTGTTGTTGGCGTTCG 58.097 45.000 0.00 0.00 36.39 3.95
1516 1531 0.806241 AAACTGTTGTTGGCGTTCGT 59.194 45.000 0.00 0.00 36.39 3.85
1517 1532 0.806241 AACTGTTGTTGGCGTTCGTT 59.194 45.000 0.00 0.00 34.71 3.85
1528 1543 0.787908 GCGTTCGTTATGTGGCGTTG 60.788 55.000 0.00 0.00 0.00 4.10
1557 1572 1.003355 CCGCCTCACTGTCCATGTT 60.003 57.895 0.00 0.00 0.00 2.71
1562 1577 1.354337 CTCACTGTCCATGTTCGCCG 61.354 60.000 0.00 0.00 0.00 6.46
1616 1763 0.794473 GAACGTCCCGTCATGTTTCC 59.206 55.000 0.00 0.00 39.99 3.13
1626 1773 1.197721 GTCATGTTTCCGTCTTGCTGG 59.802 52.381 0.00 0.00 0.00 4.85
1687 1834 2.544721 TCTTGCTCTTGTCTGATCCCT 58.455 47.619 0.00 0.00 0.00 4.20
1723 1870 4.154918 GTGTTCTTTCTATCTGCTTGTGGG 59.845 45.833 0.00 0.00 0.00 4.61
1747 1894 0.806868 ACAGATGATTTGCTGCCACG 59.193 50.000 0.00 0.00 35.57 4.94
1843 2105 6.587206 TGTGATGCTTCCAATGTGATAAAA 57.413 33.333 0.00 0.00 0.00 1.52
1855 2117 7.665145 TCCAATGTGATAAAACTGACTGATGAA 59.335 33.333 0.00 0.00 0.00 2.57
1856 2118 8.464404 CCAATGTGATAAAACTGACTGATGAAT 58.536 33.333 0.00 0.00 0.00 2.57
1870 2133 5.862845 ACTGATGAATGTCTGAAACAGAGT 58.137 37.500 1.53 0.00 41.46 3.24
1962 2239 2.493278 GGCTGTGCAATTACTGAATGGT 59.507 45.455 0.00 0.00 0.00 3.55
2051 2332 3.502211 ACTTGCCTCCTTATGTTCAAACG 59.498 43.478 0.00 0.00 0.00 3.60
2081 2362 6.273825 AGCTACTCGTCATACAACTATTTGG 58.726 40.000 0.00 0.00 37.00 3.28
2094 2379 4.574674 ACTATTTGGGTGAAGCATGAGA 57.425 40.909 0.00 0.00 0.00 3.27
2100 2385 2.749076 TGGGTGAAGCATGAGATTTTCG 59.251 45.455 0.00 0.00 0.00 3.46
2113 2398 4.023279 TGAGATTTTCGTTCATTGGTGTGG 60.023 41.667 0.00 0.00 0.00 4.17
2182 2467 6.402226 GCAGCAACATACAAGGACTTAACTAC 60.402 42.308 0.00 0.00 0.00 2.73
2183 2468 6.874134 CAGCAACATACAAGGACTTAACTACT 59.126 38.462 0.00 0.00 0.00 2.57
2184 2469 7.063544 CAGCAACATACAAGGACTTAACTACTC 59.936 40.741 0.00 0.00 0.00 2.59
2185 2470 6.313164 GCAACATACAAGGACTTAACTACTCC 59.687 42.308 0.00 0.00 0.00 3.85
2186 2471 6.541934 ACATACAAGGACTTAACTACTCCC 57.458 41.667 0.00 0.00 0.00 4.30
2187 2472 6.262207 ACATACAAGGACTTAACTACTCCCT 58.738 40.000 0.00 0.00 0.00 4.20
2188 2473 6.380560 ACATACAAGGACTTAACTACTCCCTC 59.619 42.308 0.00 0.00 0.00 4.30
2189 2474 4.095211 ACAAGGACTTAACTACTCCCTCC 58.905 47.826 0.00 0.00 0.00 4.30
2190 2475 4.094476 CAAGGACTTAACTACTCCCTCCA 58.906 47.826 0.00 0.00 0.00 3.86
2191 2476 4.628661 AGGACTTAACTACTCCCTCCAT 57.371 45.455 0.00 0.00 0.00 3.41
2192 2477 4.548669 AGGACTTAACTACTCCCTCCATC 58.451 47.826 0.00 0.00 0.00 3.51
2193 2478 3.642377 GGACTTAACTACTCCCTCCATCC 59.358 52.174 0.00 0.00 0.00 3.51
2194 2479 3.642377 GACTTAACTACTCCCTCCATCCC 59.358 52.174 0.00 0.00 0.00 3.85
2195 2480 3.013648 ACTTAACTACTCCCTCCATCCCA 59.986 47.826 0.00 0.00 0.00 4.37
2196 2481 2.897823 AACTACTCCCTCCATCCCAT 57.102 50.000 0.00 0.00 0.00 4.00
2197 2482 5.102783 ACTTAACTACTCCCTCCATCCCATA 60.103 44.000 0.00 0.00 0.00 2.74
2198 2483 4.295905 AACTACTCCCTCCATCCCATAA 57.704 45.455 0.00 0.00 0.00 1.90
2199 2484 4.510303 ACTACTCCCTCCATCCCATAAT 57.490 45.455 0.00 0.00 0.00 1.28
2200 2485 5.633473 ACTACTCCCTCCATCCCATAATA 57.367 43.478 0.00 0.00 0.00 0.98
2201 2486 6.185677 ACTACTCCCTCCATCCCATAATAT 57.814 41.667 0.00 0.00 0.00 1.28
2202 2487 7.312162 ACTACTCCCTCCATCCCATAATATA 57.688 40.000 0.00 0.00 0.00 0.86
2203 2488 7.729350 ACTACTCCCTCCATCCCATAATATAA 58.271 38.462 0.00 0.00 0.00 0.98
2204 2489 7.846823 ACTACTCCCTCCATCCCATAATATAAG 59.153 40.741 0.00 0.00 0.00 1.73
2205 2490 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
2206 2491 7.442655 ACTCCCTCCATCCCATAATATAAGAT 58.557 38.462 0.00 0.00 0.00 2.40
2207 2492 7.570607 ACTCCCTCCATCCCATAATATAAGATC 59.429 40.741 0.00 0.00 0.00 2.75
2208 2493 6.554982 TCCCTCCATCCCATAATATAAGATCG 59.445 42.308 0.00 0.00 0.00 3.69
2209 2494 6.327626 CCCTCCATCCCATAATATAAGATCGT 59.672 42.308 0.00 0.00 0.00 3.73
2210 2495 7.147479 CCCTCCATCCCATAATATAAGATCGTT 60.147 40.741 0.00 0.00 0.00 3.85
2211 2496 8.267894 CCTCCATCCCATAATATAAGATCGTTT 58.732 37.037 0.00 0.00 0.00 3.60
2212 2497 9.672673 CTCCATCCCATAATATAAGATCGTTTT 57.327 33.333 0.00 0.00 0.00 2.43
2218 2503 9.612620 CCCATAATATAAGATCGTTTTTCAAGC 57.387 33.333 0.00 0.00 0.00 4.01
2240 2525 5.704217 CTATGTTAGCTTGAGAAACGGTC 57.296 43.478 0.00 0.00 0.00 4.79
2241 2526 3.746045 TGTTAGCTTGAGAAACGGTCT 57.254 42.857 0.00 0.00 40.25 3.85
2242 2527 4.067972 TGTTAGCTTGAGAAACGGTCTT 57.932 40.909 0.00 0.00 36.41 3.01
2243 2528 5.204409 TGTTAGCTTGAGAAACGGTCTTA 57.796 39.130 0.00 0.00 36.41 2.10
2244 2529 5.790593 TGTTAGCTTGAGAAACGGTCTTAT 58.209 37.500 0.00 0.00 36.41 1.73
2245 2530 6.927416 TGTTAGCTTGAGAAACGGTCTTATA 58.073 36.000 0.00 0.00 36.41 0.98
2246 2531 7.553334 TGTTAGCTTGAGAAACGGTCTTATAT 58.447 34.615 0.00 0.00 36.41 0.86
2247 2532 8.038944 TGTTAGCTTGAGAAACGGTCTTATATT 58.961 33.333 0.00 0.00 36.41 1.28
2248 2533 6.910536 AGCTTGAGAAACGGTCTTATATTG 57.089 37.500 0.00 0.00 36.41 1.90
2249 2534 6.407202 AGCTTGAGAAACGGTCTTATATTGT 58.593 36.000 0.00 0.00 36.41 2.71
2250 2535 6.313905 AGCTTGAGAAACGGTCTTATATTGTG 59.686 38.462 0.00 0.00 36.41 3.33
2251 2536 6.456988 GCTTGAGAAACGGTCTTATATTGTGG 60.457 42.308 0.00 0.00 36.41 4.17
2252 2537 5.424757 TGAGAAACGGTCTTATATTGTGGG 58.575 41.667 0.00 0.00 36.41 4.61
2253 2538 5.188163 TGAGAAACGGTCTTATATTGTGGGA 59.812 40.000 0.00 0.00 36.41 4.37
2254 2539 5.425630 AGAAACGGTCTTATATTGTGGGAC 58.574 41.667 0.00 0.00 29.66 4.46
2255 2540 4.829872 AACGGTCTTATATTGTGGGACA 57.170 40.909 0.00 0.00 0.00 4.02
2256 2541 4.829872 ACGGTCTTATATTGTGGGACAA 57.170 40.909 0.00 0.00 44.16 3.18
2257 2542 5.168647 ACGGTCTTATATTGTGGGACAAA 57.831 39.130 0.00 0.00 44.16 2.83
2258 2543 5.183228 ACGGTCTTATATTGTGGGACAAAG 58.817 41.667 0.00 0.00 44.16 2.77
2259 2544 4.574828 CGGTCTTATATTGTGGGACAAAGG 59.425 45.833 0.00 0.00 44.16 3.11
2260 2545 4.887655 GGTCTTATATTGTGGGACAAAGGG 59.112 45.833 0.00 0.00 44.16 3.95
2261 2546 5.339695 GGTCTTATATTGTGGGACAAAGGGA 60.340 44.000 0.00 0.00 44.16 4.20
2262 2547 5.823045 GTCTTATATTGTGGGACAAAGGGAG 59.177 44.000 0.00 0.00 44.16 4.30
2263 2548 5.491078 TCTTATATTGTGGGACAAAGGGAGT 59.509 40.000 0.00 0.00 44.16 3.85
2264 2549 6.674861 TCTTATATTGTGGGACAAAGGGAGTA 59.325 38.462 0.00 0.00 44.16 2.59
2270 2555 4.224370 TGTGGGACAAAGGGAGTAAGTATC 59.776 45.833 0.00 0.00 44.16 2.24
2293 2578 8.662781 ATCTACATACGAACATGCTATTTTGT 57.337 30.769 0.00 0.00 0.00 2.83
2572 2858 3.446516 TCGACTTCTAGGGTTCTTTAGCC 59.553 47.826 0.00 0.00 45.13 3.93
2591 2877 2.941415 GCCCTCTGTGGACAATGTTAGG 60.941 54.545 0.00 0.00 38.35 2.69
2592 2878 2.356125 CCCTCTGTGGACAATGTTAGGG 60.356 54.545 0.00 0.00 38.35 3.53
2624 2910 5.065731 GGCAGTAGAAATCTGGAACATCTTG 59.934 44.000 0.00 0.00 38.20 3.02
2704 2990 1.486310 TCTGGAATCTAAGCGTGGCAT 59.514 47.619 0.00 0.00 0.00 4.40
2785 3072 0.813610 TCCACCAAACTGAGCACACG 60.814 55.000 0.00 0.00 0.00 4.49
2786 3073 1.009675 CACCAAACTGAGCACACGC 60.010 57.895 0.00 0.00 38.99 5.34
2787 3074 1.451207 ACCAAACTGAGCACACGCA 60.451 52.632 0.00 0.00 42.27 5.24
2820 3107 3.216800 GGCAGAGATTGTCCAATATGCA 58.783 45.455 18.28 0.00 36.95 3.96
2825 3128 2.874701 AGATTGTCCAATATGCACTCGC 59.125 45.455 0.00 0.00 39.24 5.03
2826 3129 1.006086 TTGTCCAATATGCACTCGCG 58.994 50.000 0.00 0.00 42.97 5.87
2827 3130 0.108377 TGTCCAATATGCACTCGCGT 60.108 50.000 5.77 0.00 42.97 6.01
2828 3131 1.006832 GTCCAATATGCACTCGCGTT 58.993 50.000 5.77 0.00 42.97 4.84
2829 3132 1.004927 GTCCAATATGCACTCGCGTTC 60.005 52.381 5.77 0.00 42.97 3.95
2830 3133 0.043053 CCAATATGCACTCGCGTTCG 60.043 55.000 5.77 0.00 42.97 3.95
2831 3134 0.651610 CAATATGCACTCGCGTTCGC 60.652 55.000 5.77 7.77 42.97 4.70
2832 3135 0.806102 AATATGCACTCGCGTTCGCT 60.806 50.000 14.92 0.45 42.97 4.93
2833 3136 1.482621 ATATGCACTCGCGTTCGCTG 61.483 55.000 14.92 7.90 42.97 5.18
2834 3137 2.812542 TATGCACTCGCGTTCGCTGT 62.813 55.000 14.92 10.46 42.97 4.40
2835 3138 3.702555 GCACTCGCGTTCGCTGTT 61.703 61.111 14.92 0.00 35.26 3.16
2836 3139 2.465920 CACTCGCGTTCGCTGTTC 59.534 61.111 14.92 0.00 35.26 3.18
2837 3140 2.016704 CACTCGCGTTCGCTGTTCT 61.017 57.895 14.92 0.00 35.26 3.01
2838 3141 2.016704 ACTCGCGTTCGCTGTTCTG 61.017 57.895 14.92 0.00 35.26 3.02
2839 3142 3.340721 CTCGCGTTCGCTGTTCTGC 62.341 63.158 14.92 0.00 35.26 4.26
2858 3161 2.617274 GCCCTCAGCCGTGTTTCAC 61.617 63.158 0.00 0.00 34.35 3.18
2874 3177 0.465705 TCACTGAGGCCGATCATTCC 59.534 55.000 0.00 0.00 0.00 3.01
2875 3178 0.178767 CACTGAGGCCGATCATTCCA 59.821 55.000 0.00 0.00 0.00 3.53
2879 3220 0.465705 GAGGCCGATCATTCCACTCA 59.534 55.000 0.00 0.00 0.00 3.41
2881 3222 2.300152 GAGGCCGATCATTCCACTCATA 59.700 50.000 0.00 0.00 0.00 2.15
2891 3232 0.419865 TCCACTCATACCCCCTTCCA 59.580 55.000 0.00 0.00 0.00 3.53
2898 3239 0.261696 ATACCCCCTTCCAACATGGC 59.738 55.000 0.00 0.00 37.47 4.40
2899 3240 1.143329 TACCCCCTTCCAACATGGCA 61.143 55.000 0.00 0.00 37.47 4.92
2900 3241 1.229145 CCCCCTTCCAACATGGCAA 60.229 57.895 0.00 0.00 37.47 4.52
2901 3242 0.618393 CCCCCTTCCAACATGGCAAT 60.618 55.000 0.00 0.00 37.47 3.56
2902 3243 0.538118 CCCCTTCCAACATGGCAATG 59.462 55.000 0.00 0.00 37.47 2.82
2903 3244 0.538118 CCCTTCCAACATGGCAATGG 59.462 55.000 5.94 10.18 37.47 3.16
2904 3245 1.269012 CCTTCCAACATGGCAATGGT 58.731 50.000 5.94 0.00 37.47 3.55
2905 3246 1.205417 CCTTCCAACATGGCAATGGTC 59.795 52.381 5.94 0.00 37.47 4.02
2906 3247 1.205417 CTTCCAACATGGCAATGGTCC 59.795 52.381 5.94 0.00 37.47 4.46
2935 3276 1.956636 GCCATGCCTCAAATGAGACCA 60.957 52.381 11.94 8.69 44.74 4.02
2955 3296 0.105778 GAGGATGCTCTGGTAGGTGC 59.894 60.000 7.03 0.00 0.00 5.01
2957 3298 1.676678 GGATGCTCTGGTAGGTGCGA 61.677 60.000 0.00 0.00 0.00 5.10
2965 3306 2.202756 GTAGGTGCGAGGAAGGCG 60.203 66.667 0.00 0.00 0.00 5.52
2966 3307 2.361992 TAGGTGCGAGGAAGGCGA 60.362 61.111 0.00 0.00 0.00 5.54
3028 3377 1.103803 GGGAGTGCAGTCGATAGTCA 58.896 55.000 15.26 0.00 37.40 3.41
3055 3407 5.358160 CCTTCTTCAACTCTGGTCAGTTTTT 59.642 40.000 0.00 0.00 34.17 1.94
3109 3461 5.477607 TTCCTGTTAATTCCTCGAGACAA 57.522 39.130 15.71 6.62 0.00 3.18
3115 3467 0.732880 ATTCCTCGAGACAACACGCG 60.733 55.000 15.71 3.53 34.70 6.01
3147 3502 2.626266 GGCCTTTTCTTTTTCCCTCGAA 59.374 45.455 0.00 0.00 0.00 3.71
3198 3553 3.438216 TTGCCAAGATCAACCTGATGA 57.562 42.857 0.00 0.00 37.20 2.92
3199 3554 3.657398 TGCCAAGATCAACCTGATGAT 57.343 42.857 0.00 0.00 42.62 2.45
3200 3555 3.284617 TGCCAAGATCAACCTGATGATG 58.715 45.455 0.00 0.00 40.08 3.07
3205 3560 0.820891 ATCAACCTGATGATGGCCGC 60.821 55.000 0.00 0.00 38.59 6.53
3206 3561 2.124151 AACCTGATGATGGCCGCC 60.124 61.111 1.04 1.04 0.00 6.13
3207 3562 2.683465 AACCTGATGATGGCCGCCT 61.683 57.895 11.61 0.00 0.00 5.52
3211 3566 3.877450 GATGATGGCCGCCTGGGA 61.877 66.667 11.61 0.00 38.47 4.37
3239 3594 2.486191 CCACCACCAGCTAGAATGATCC 60.486 54.545 0.00 0.00 0.00 3.36
3240 3595 2.437281 CACCACCAGCTAGAATGATCCT 59.563 50.000 0.00 0.00 0.00 3.24
3250 3605 6.015918 AGCTAGAATGATCCTACTACATGCT 58.984 40.000 0.00 0.00 34.69 3.79
3393 3757 0.534203 ACCAACAGTGCCCTTACACG 60.534 55.000 0.00 0.00 45.45 4.49
3395 3759 0.865769 CAACAGTGCCCTTACACGAC 59.134 55.000 0.00 0.00 45.45 4.34
3396 3760 0.250166 AACAGTGCCCTTACACGACC 60.250 55.000 0.00 0.00 45.45 4.79
3414 3778 1.367471 CTCCGGCACACACTTGAGA 59.633 57.895 0.00 0.00 0.00 3.27
3415 3779 0.249868 CTCCGGCACACACTTGAGAA 60.250 55.000 0.00 0.00 0.00 2.87
3421 3785 2.880890 GGCACACACTTGAGAATGTTCT 59.119 45.455 0.00 0.00 41.00 3.01
3446 3810 9.424319 CTTTTTGCGTAGTCCATATACAGATAT 57.576 33.333 0.00 0.00 0.00 1.63
3447 3811 8.757164 TTTTGCGTAGTCCATATACAGATATG 57.243 34.615 0.00 0.00 43.20 1.78
3452 3816 6.238786 CGTAGTCCATATACAGATATGCTCCC 60.239 46.154 0.27 0.00 42.52 4.30
3453 3817 5.848004 AGTCCATATACAGATATGCTCCCT 58.152 41.667 0.27 0.00 42.52 4.20
3454 3818 5.896678 AGTCCATATACAGATATGCTCCCTC 59.103 44.000 0.27 0.00 42.52 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.153025 GAGATGGCCAGCTCATGCA 60.153 57.895 39.37 0.25 42.95 3.96
26 27 4.218578 CGAGCGAGATGGCCAGCT 62.219 66.667 26.67 26.67 43.33 4.24
72 74 1.748493 CCTCTATATCTCGCCCTCAGC 59.252 57.143 0.00 0.00 38.52 4.26
73 75 1.748493 GCCTCTATATCTCGCCCTCAG 59.252 57.143 0.00 0.00 0.00 3.35
74 76 1.840737 GCCTCTATATCTCGCCCTCA 58.159 55.000 0.00 0.00 0.00 3.86
75 77 0.736053 CGCCTCTATATCTCGCCCTC 59.264 60.000 0.00 0.00 0.00 4.30
77 79 1.139947 GCGCCTCTATATCTCGCCC 59.860 63.158 0.00 0.00 39.91 6.13
136 142 2.641321 TCCTCATTAGGGCATCTCCATG 59.359 50.000 0.00 0.00 43.84 3.66
147 153 2.785357 ACCTCCTCCTCCTCATTAGG 57.215 55.000 0.00 0.00 45.21 2.69
148 154 3.576550 GCTAACCTCCTCCTCCTCATTAG 59.423 52.174 0.00 0.00 0.00 1.73
149 155 3.577919 GCTAACCTCCTCCTCCTCATTA 58.422 50.000 0.00 0.00 0.00 1.90
150 156 2.403561 GCTAACCTCCTCCTCCTCATT 58.596 52.381 0.00 0.00 0.00 2.57
294 300 3.261643 TCACAGAGAATGCCAGAAGCTTA 59.738 43.478 0.00 0.00 44.23 3.09
545 551 4.023279 CCAAACCATCTCAAACGATGTTGA 60.023 41.667 0.00 0.00 39.26 3.18
584 590 1.835927 GCACTGGAGCTTCTGGAGGT 61.836 60.000 3.68 0.00 39.22 3.85
674 680 4.956700 TCATTCAGGTCTCTCTTAACGGAT 59.043 41.667 0.00 0.00 0.00 4.18
695 701 4.160439 AGCTCTTTGTCGATACTCCAATCA 59.840 41.667 0.00 0.00 0.00 2.57
782 788 6.385467 AGGCTAGAGGTGAAACTCATAAGATT 59.615 38.462 0.00 0.00 39.97 2.40
791 797 2.044630 AGGGTAGGCTAGAGGTGAAACT 59.955 50.000 0.00 0.00 36.74 2.66
812 818 5.056553 AGCCTTTAGTCCCAAACAAGTTA 57.943 39.130 0.00 0.00 0.00 2.24
891 903 2.979678 GAGGGTTTAGGGCATCTCCATA 59.020 50.000 0.00 0.00 36.21 2.74
893 905 1.213296 GAGGGTTTAGGGCATCTCCA 58.787 55.000 0.00 0.00 36.21 3.86
898 910 2.179427 GCTTTTGAGGGTTTAGGGCAT 58.821 47.619 0.00 0.00 0.00 4.40
899 911 1.627864 GCTTTTGAGGGTTTAGGGCA 58.372 50.000 0.00 0.00 0.00 5.36
900 912 0.895530 GGCTTTTGAGGGTTTAGGGC 59.104 55.000 0.00 0.00 0.00 5.19
901 913 1.203125 TGGGCTTTTGAGGGTTTAGGG 60.203 52.381 0.00 0.00 0.00 3.53
988 1000 3.389662 CGCCATTTGGGGTTGGGG 61.390 66.667 5.53 0.00 42.54 4.96
989 1001 3.389662 CCGCCATTTGGGGTTGGG 61.390 66.667 12.12 0.00 45.67 4.12
1319 1334 1.345734 GGATACCTAGGGGTTTGGGGA 60.346 57.143 14.81 0.00 44.73 4.81
1341 1356 1.228552 GAACAGCCTGGCAAGGGAA 60.229 57.895 22.65 0.00 44.67 3.97
1342 1357 2.436109 GAACAGCCTGGCAAGGGA 59.564 61.111 22.65 0.00 44.67 4.20
1343 1358 3.058160 CGAACAGCCTGGCAAGGG 61.058 66.667 22.65 9.66 44.67 3.95
1345 1360 0.318107 CAAACGAACAGCCTGGCAAG 60.318 55.000 22.65 15.30 0.00 4.01
1373 1388 7.526608 TCGTCTTTCACATCCAAATCAATTAC 58.473 34.615 0.00 0.00 0.00 1.89
1376 1391 6.207417 ACTTCGTCTTTCACATCCAAATCAAT 59.793 34.615 0.00 0.00 0.00 2.57
1396 1411 0.370273 CGCAATCCTTTCCGACTTCG 59.630 55.000 0.00 0.00 39.44 3.79
1411 1426 4.051237 CGATTCCATCTCATCTTACGCAA 58.949 43.478 0.00 0.00 0.00 4.85
1436 1451 0.521735 GGACACTAGCAAAAAGGCCG 59.478 55.000 0.00 0.00 0.00 6.13
1440 1455 3.882888 TCCTGTTGGACACTAGCAAAAAG 59.117 43.478 0.00 0.00 37.46 2.27
1441 1456 3.882888 CTCCTGTTGGACACTAGCAAAAA 59.117 43.478 0.00 0.00 37.46 1.94
1455 1470 3.626670 GGATCTCAGATTTGCTCCTGTTG 59.373 47.826 0.00 0.00 0.00 3.33
1477 1492 0.976641 TACACCTGTCCTGAAGGCAG 59.023 55.000 11.59 11.59 38.48 4.85
1481 1496 4.451900 ACAGTTTTACACCTGTCCTGAAG 58.548 43.478 0.00 0.00 37.34 3.02
1506 1521 1.870383 GCCACATAACGAACGCCAA 59.130 52.632 0.00 0.00 0.00 4.52
1507 1522 2.384309 CGCCACATAACGAACGCCA 61.384 57.895 0.00 0.00 0.00 5.69
1513 1528 0.601576 AGCACAACGCCACATAACGA 60.602 50.000 0.00 0.00 44.04 3.85
1514 1529 0.179225 GAGCACAACGCCACATAACG 60.179 55.000 0.00 0.00 44.04 3.18
1515 1530 1.156736 AGAGCACAACGCCACATAAC 58.843 50.000 0.00 0.00 44.04 1.89
1516 1531 2.232696 TCTAGAGCACAACGCCACATAA 59.767 45.455 0.00 0.00 44.04 1.90
1517 1532 1.822371 TCTAGAGCACAACGCCACATA 59.178 47.619 0.00 0.00 44.04 2.29
1557 1572 2.792947 GGGCTTCTACATCCGGCGA 61.793 63.158 9.30 0.00 0.00 5.54
1562 1577 1.117150 TACACCGGGCTTCTACATCC 58.883 55.000 6.32 0.00 0.00 3.51
1626 1773 1.130561 GAAGAACCCAACGCTGCATAC 59.869 52.381 0.00 0.00 0.00 2.39
1687 1834 5.904941 AGAAAGAACACATCAATTTGCACA 58.095 33.333 0.00 0.00 0.00 4.57
1723 1870 3.192001 TGGCAGCAAATCATCTGTTCTTC 59.808 43.478 0.00 0.00 33.09 2.87
1747 1894 2.794350 GTGCAACACATACCAGCAAAAC 59.206 45.455 0.00 0.00 36.91 2.43
1843 2105 5.614308 TGTTTCAGACATTCATCAGTCAGT 58.386 37.500 0.00 0.00 37.23 3.41
1893 2156 2.815503 TCAGCAAGGATGTCAACATGTG 59.184 45.455 0.00 0.00 36.57 3.21
1897 2160 2.880268 CTGTTCAGCAAGGATGTCAACA 59.120 45.455 0.00 0.00 0.00 3.33
1962 2239 9.382275 CACTATATATATTGTGCAAGCATACCA 57.618 33.333 19.67 0.00 33.94 3.25
2051 2332 5.749109 AGTTGTATGACGAGTAGCTTAATGC 59.251 40.000 0.00 0.00 43.29 3.56
2081 2362 4.083324 TGAACGAAAATCTCATGCTTCACC 60.083 41.667 0.00 0.00 0.00 4.02
2094 2379 3.888930 ACTCCACACCAATGAACGAAAAT 59.111 39.130 0.00 0.00 0.00 1.82
2100 2385 3.149196 ACATCACTCCACACCAATGAAC 58.851 45.455 0.00 0.00 0.00 3.18
2182 2467 7.256119 CGATCTTATATTATGGGATGGAGGGAG 60.256 44.444 0.00 0.00 0.00 4.30
2183 2468 6.554982 CGATCTTATATTATGGGATGGAGGGA 59.445 42.308 0.00 0.00 0.00 4.20
2184 2469 6.327626 ACGATCTTATATTATGGGATGGAGGG 59.672 42.308 0.00 0.00 0.00 4.30
2185 2470 7.366847 ACGATCTTATATTATGGGATGGAGG 57.633 40.000 0.00 0.00 0.00 4.30
2186 2471 9.672673 AAAACGATCTTATATTATGGGATGGAG 57.327 33.333 0.00 0.00 0.00 3.86
2192 2477 9.612620 GCTTGAAAAACGATCTTATATTATGGG 57.387 33.333 0.00 0.00 0.00 4.00
2217 2502 7.559406 AAGACCGTTTCTCAAGCTAACATAGC 61.559 42.308 1.12 1.12 42.54 2.97
2218 2503 5.411781 AGACCGTTTCTCAAGCTAACATAG 58.588 41.667 0.00 0.00 0.00 2.23
2219 2504 5.401531 AGACCGTTTCTCAAGCTAACATA 57.598 39.130 0.00 0.00 0.00 2.29
2220 2505 4.273148 AGACCGTTTCTCAAGCTAACAT 57.727 40.909 0.00 0.00 0.00 2.71
2221 2506 3.746045 AGACCGTTTCTCAAGCTAACA 57.254 42.857 0.00 0.00 0.00 2.41
2222 2507 8.328864 CAATATAAGACCGTTTCTCAAGCTAAC 58.671 37.037 0.00 0.00 31.02 2.34
2223 2508 8.038944 ACAATATAAGACCGTTTCTCAAGCTAA 58.961 33.333 0.00 0.00 31.02 3.09
2224 2509 7.491372 CACAATATAAGACCGTTTCTCAAGCTA 59.509 37.037 0.00 0.00 31.02 3.32
2225 2510 6.313905 CACAATATAAGACCGTTTCTCAAGCT 59.686 38.462 0.00 0.00 31.02 3.74
2226 2511 6.456988 CCACAATATAAGACCGTTTCTCAAGC 60.457 42.308 0.00 0.00 31.02 4.01
2227 2512 6.037172 CCCACAATATAAGACCGTTTCTCAAG 59.963 42.308 0.00 0.00 31.02 3.02
2228 2513 5.878116 CCCACAATATAAGACCGTTTCTCAA 59.122 40.000 0.00 0.00 31.02 3.02
2229 2514 5.188163 TCCCACAATATAAGACCGTTTCTCA 59.812 40.000 0.00 0.00 31.02 3.27
2230 2515 5.522824 GTCCCACAATATAAGACCGTTTCTC 59.477 44.000 0.00 0.00 31.02 2.87
2231 2516 5.046159 TGTCCCACAATATAAGACCGTTTCT 60.046 40.000 0.00 0.00 35.32 2.52
2232 2517 5.180271 TGTCCCACAATATAAGACCGTTTC 58.820 41.667 0.00 0.00 0.00 2.78
2233 2518 5.168647 TGTCCCACAATATAAGACCGTTT 57.831 39.130 0.00 0.00 0.00 3.60
2234 2519 4.829872 TGTCCCACAATATAAGACCGTT 57.170 40.909 0.00 0.00 0.00 4.44
2235 2520 4.829872 TTGTCCCACAATATAAGACCGT 57.170 40.909 0.00 0.00 32.34 4.83
2236 2521 4.574828 CCTTTGTCCCACAATATAAGACCG 59.425 45.833 0.00 0.00 38.00 4.79
2237 2522 4.887655 CCCTTTGTCCCACAATATAAGACC 59.112 45.833 0.00 0.00 38.00 3.85
2238 2523 5.751586 TCCCTTTGTCCCACAATATAAGAC 58.248 41.667 0.00 0.00 38.00 3.01
2239 2524 5.491078 ACTCCCTTTGTCCCACAATATAAGA 59.509 40.000 0.00 0.00 38.00 2.10
2240 2525 5.755849 ACTCCCTTTGTCCCACAATATAAG 58.244 41.667 0.00 0.00 38.00 1.73
2241 2526 5.789574 ACTCCCTTTGTCCCACAATATAA 57.210 39.130 0.00 0.00 38.00 0.98
2242 2527 6.445786 ACTTACTCCCTTTGTCCCACAATATA 59.554 38.462 0.00 0.00 38.00 0.86
2243 2528 5.253096 ACTTACTCCCTTTGTCCCACAATAT 59.747 40.000 0.00 0.00 38.00 1.28
2244 2529 4.600111 ACTTACTCCCTTTGTCCCACAATA 59.400 41.667 0.00 0.00 38.00 1.90
2245 2530 3.397955 ACTTACTCCCTTTGTCCCACAAT 59.602 43.478 0.00 0.00 38.00 2.71
2246 2531 2.781174 ACTTACTCCCTTTGTCCCACAA 59.219 45.455 0.00 0.00 36.11 3.33
2247 2532 2.414612 ACTTACTCCCTTTGTCCCACA 58.585 47.619 0.00 0.00 0.00 4.17
2248 2533 4.470304 AGATACTTACTCCCTTTGTCCCAC 59.530 45.833 0.00 0.00 0.00 4.61
2249 2534 4.695606 AGATACTTACTCCCTTTGTCCCA 58.304 43.478 0.00 0.00 0.00 4.37
2250 2535 5.659971 TGTAGATACTTACTCCCTTTGTCCC 59.340 44.000 0.00 0.00 0.00 4.46
2251 2536 6.786967 TGTAGATACTTACTCCCTTTGTCC 57.213 41.667 0.00 0.00 0.00 4.02
2252 2537 8.074972 CGTATGTAGATACTTACTCCCTTTGTC 58.925 40.741 8.27 0.00 35.73 3.18
2253 2538 7.776969 TCGTATGTAGATACTTACTCCCTTTGT 59.223 37.037 8.27 0.00 35.73 2.83
2254 2539 8.162878 TCGTATGTAGATACTTACTCCCTTTG 57.837 38.462 8.27 0.00 35.73 2.77
2255 2540 8.628280 GTTCGTATGTAGATACTTACTCCCTTT 58.372 37.037 8.27 0.00 35.73 3.11
2256 2541 7.776969 TGTTCGTATGTAGATACTTACTCCCTT 59.223 37.037 8.27 0.00 35.73 3.95
2257 2542 7.285566 TGTTCGTATGTAGATACTTACTCCCT 58.714 38.462 8.27 0.00 35.73 4.20
2258 2543 7.502120 TGTTCGTATGTAGATACTTACTCCC 57.498 40.000 8.27 3.46 35.73 4.30
2259 2544 7.537991 GCATGTTCGTATGTAGATACTTACTCC 59.462 40.741 8.27 3.70 35.73 3.85
2260 2545 8.291032 AGCATGTTCGTATGTAGATACTTACTC 58.709 37.037 8.27 5.71 35.73 2.59
2261 2546 8.167605 AGCATGTTCGTATGTAGATACTTACT 57.832 34.615 8.27 0.00 35.73 2.24
2264 2549 9.982651 AAATAGCATGTTCGTATGTAGATACTT 57.017 29.630 8.27 0.00 33.43 2.24
2270 2555 9.031360 ACTACAAAATAGCATGTTCGTATGTAG 57.969 33.333 18.02 18.02 41.21 2.74
2292 2577 4.390297 GGACAGAATGAGAAGTGCAACTAC 59.610 45.833 0.00 0.00 45.31 2.73
2293 2578 4.284490 AGGACAGAATGAGAAGTGCAACTA 59.716 41.667 0.00 0.00 45.31 2.24
2336 2621 1.002087 ACACGATGACCTTCTTGTCCC 59.998 52.381 0.00 0.00 34.25 4.46
2502 2787 1.600916 GCACCCTCAAGACCACCAC 60.601 63.158 0.00 0.00 0.00 4.16
2572 2858 2.305927 ACCCTAACATTGTCCACAGAGG 59.694 50.000 0.00 0.00 39.47 3.69
2578 2864 3.517901 CAGAGGTACCCTAACATTGTCCA 59.482 47.826 8.74 0.00 31.76 4.02
2591 2877 3.707102 AGATTTCTACTGCCAGAGGTACC 59.293 47.826 2.73 2.73 0.00 3.34
2592 2878 4.442192 CCAGATTTCTACTGCCAGAGGTAC 60.442 50.000 0.00 0.00 34.47 3.34
2597 2883 3.582647 TGTTCCAGATTTCTACTGCCAGA 59.417 43.478 0.00 0.00 34.47 3.86
2608 2894 4.660168 AGCTGTCAAGATGTTCCAGATTT 58.340 39.130 3.65 0.00 0.00 2.17
2785 3072 0.175760 TCTGCCCGTCTGAATACTGC 59.824 55.000 0.00 0.00 0.00 4.40
2786 3073 1.751351 TCTCTGCCCGTCTGAATACTG 59.249 52.381 0.00 0.00 0.00 2.74
2787 3074 2.145397 TCTCTGCCCGTCTGAATACT 57.855 50.000 0.00 0.00 0.00 2.12
2788 3075 3.126831 CAATCTCTGCCCGTCTGAATAC 58.873 50.000 0.00 0.00 0.00 1.89
2830 3133 3.123620 CTGAGGGCGCAGAACAGC 61.124 66.667 10.83 0.00 38.14 4.40
2831 3134 3.123620 GCTGAGGGCGCAGAACAG 61.124 66.667 10.83 13.68 38.14 3.16
2832 3135 4.704833 GGCTGAGGGCGCAGAACA 62.705 66.667 10.83 2.50 42.94 3.18
2840 3143 2.281484 TGAAACACGGCTGAGGGC 60.281 61.111 0.00 0.00 40.90 5.19
2841 3144 1.071471 AGTGAAACACGGCTGAGGG 59.929 57.895 0.00 0.00 41.43 4.30
2858 3161 0.467384 AGTGGAATGATCGGCCTCAG 59.533 55.000 0.00 0.00 0.00 3.35
2874 3177 1.633432 TGTTGGAAGGGGGTATGAGTG 59.367 52.381 0.00 0.00 0.00 3.51
2875 3178 2.053747 TGTTGGAAGGGGGTATGAGT 57.946 50.000 0.00 0.00 0.00 3.41
2879 3220 0.261696 GCCATGTTGGAAGGGGGTAT 59.738 55.000 0.00 0.00 40.96 2.73
2881 3222 2.029892 TTGCCATGTTGGAAGGGGGT 62.030 55.000 0.00 0.00 40.96 4.95
2891 3232 3.287445 GCGGACCATTGCCATGTT 58.713 55.556 0.00 0.00 0.00 2.71
2898 3239 3.197790 CAGCTCGGCGGACCATTG 61.198 66.667 7.21 0.00 34.57 2.82
2952 3293 2.048127 AGTTCGCCTTCCTCGCAC 60.048 61.111 0.00 0.00 0.00 5.34
2955 3296 2.048222 TGCAGTTCGCCTTCCTCG 60.048 61.111 0.00 0.00 41.33 4.63
2957 3298 2.359230 GCTGCAGTTCGCCTTCCT 60.359 61.111 16.64 0.00 41.33 3.36
2974 3315 3.244009 ACCCTCAGATCACATCGCATAAG 60.244 47.826 0.00 0.00 0.00 1.73
2975 3316 2.700371 ACCCTCAGATCACATCGCATAA 59.300 45.455 0.00 0.00 0.00 1.90
2985 3326 2.644676 CGTCTGTCTACCCTCAGATCA 58.355 52.381 0.00 0.00 41.67 2.92
2986 3327 1.335496 GCGTCTGTCTACCCTCAGATC 59.665 57.143 0.00 0.00 41.67 2.75
3028 3377 1.349357 GACCAGAGTTGAAGAAGGCCT 59.651 52.381 0.00 0.00 0.00 5.19
3055 3407 2.934553 CGCATTGATCAGAGCAAAGAGA 59.065 45.455 17.96 0.00 0.00 3.10
3200 3555 4.440829 TTTGGATCCCAGGCGGCC 62.441 66.667 12.11 12.11 33.81 6.13
3205 3560 0.611896 GTGGTGGTTTGGATCCCAGG 60.612 60.000 9.90 0.00 33.81 4.45
3206 3561 0.611896 GGTGGTGGTTTGGATCCCAG 60.612 60.000 9.90 0.00 33.81 4.45
3207 3562 1.364317 TGGTGGTGGTTTGGATCCCA 61.364 55.000 9.90 0.00 0.00 4.37
3211 3566 1.004745 CTAGCTGGTGGTGGTTTGGAT 59.995 52.381 0.00 0.00 0.00 3.41
3216 3571 1.985159 TCATTCTAGCTGGTGGTGGTT 59.015 47.619 0.00 0.00 0.00 3.67
3257 3613 6.594937 CCACATTTTGTGCTGCCTAATAATTT 59.405 34.615 0.00 0.00 46.51 1.82
3267 3623 1.202394 TGTGTCCACATTTTGTGCTGC 60.202 47.619 2.09 0.00 46.51 5.25
3313 3669 3.503748 ACAACTCACCTACGTACTGTACC 59.496 47.826 12.08 0.00 0.00 3.34
3396 3760 0.249868 TTCTCAAGTGTGTGCCGGAG 60.250 55.000 5.05 0.00 0.00 4.63
3414 3778 5.705609 ATGGACTACGCAAAAAGAACATT 57.294 34.783 0.00 0.00 0.00 2.71
3415 3779 7.551262 TGTATATGGACTACGCAAAAAGAACAT 59.449 33.333 0.00 0.00 0.00 2.71
3421 3785 9.203421 CATATCTGTATATGGACTACGCAAAAA 57.797 33.333 0.00 0.00 40.85 1.94


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

AutoCloner maintained by Alex Coulton.