Multiple sequence alignment - TraesCS5B01G228900

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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 TraesCS5B01G228900 chr5B 100.000 5553 0 0 1 5553 405721282 405726834 0.000000e+00 10255.0
1 TraesCS5B01G228900 chr5B 81.466 928 123 37 2059 2967 330169987 330169090 0.000000e+00 715.0
2 TraesCS5B01G228900 chr5B 80.485 989 122 38 2016 2970 638395286 638396237 0.000000e+00 691.0
3 TraesCS5B01G228900 chr5B 83.073 768 95 32 2219 2967 330485687 330484936 0.000000e+00 665.0
4 TraesCS5B01G228900 chr5B 80.508 118 17 5 2057 2169 608366322 608366206 9.910000e-13 86.1
5 TraesCS5B01G228900 chr5A 90.277 2201 117 41 2010 4158 445285292 445287447 0.000000e+00 2789.0
6 TraesCS5B01G228900 chr5A 88.187 1964 201 22 2 1956 445283270 445285211 0.000000e+00 2313.0
7 TraesCS5B01G228900 chr5A 90.145 1309 97 13 4254 5553 445287552 445288837 0.000000e+00 1674.0
8 TraesCS5B01G228900 chr5D 94.095 1050 28 16 3126 4158 345928108 345927076 0.000000e+00 1565.0
9 TraesCS5B01G228900 chr5D 88.635 1311 107 23 4254 5552 345926971 345925691 0.000000e+00 1557.0
10 TraesCS5B01G228900 chr5D 81.075 1358 207 31 2 1333 345932985 345931652 0.000000e+00 1038.0
11 TraesCS5B01G228900 chr7D 83.610 964 109 34 2010 2954 486550064 486550997 0.000000e+00 859.0
12 TraesCS5B01G228900 chr7D 82.609 897 122 26 2086 2965 256819294 256818415 0.000000e+00 761.0
13 TraesCS5B01G228900 chr3B 82.724 903 124 24 2058 2944 769397349 769396463 0.000000e+00 774.0
14 TraesCS5B01G228900 chr3B 89.091 55 5 1 4201 4255 114098867 114098920 3.590000e-07 67.6
15 TraesCS5B01G228900 chr2A 81.474 977 124 40 2010 2963 187487702 187486760 0.000000e+00 749.0
16 TraesCS5B01G228900 chr2A 89.474 57 5 1 4201 4257 362434718 362434663 2.780000e-08 71.3
17 TraesCS5B01G228900 chr4A 81.624 936 122 31 2057 2963 97251371 97252285 0.000000e+00 730.0
18 TraesCS5B01G228900 chr6B 82.127 884 124 27 2057 2921 51988729 51989597 0.000000e+00 726.0
19 TraesCS5B01G228900 chr6B 82.822 163 27 1 5392 5553 215147649 215147487 1.610000e-30 145.0
20 TraesCS5B01G228900 chr2B 81.655 894 115 27 2077 2962 122930778 122929926 0.000000e+00 697.0
21 TraesCS5B01G228900 chr2B 80.636 346 33 19 2057 2380 522212028 522211695 2.590000e-58 237.0
22 TraesCS5B01G228900 chr2B 95.556 45 2 0 4213 4257 575146520 575146476 7.720000e-09 73.1
23 TraesCS5B01G228900 chr2B 89.474 57 5 1 4201 4257 87922732 87922787 2.780000e-08 71.3
24 TraesCS5B01G228900 chr1D 80.752 878 128 31 2103 2963 468712129 468712982 0.000000e+00 647.0
25 TraesCS5B01G228900 chr1D 93.617 47 3 0 4211 4257 343363395 343363441 2.780000e-08 71.3
26 TraesCS5B01G228900 chr7B 85.556 90 11 2 2057 2145 670035550 670035638 5.920000e-15 93.5
27 TraesCS5B01G228900 chr7B 85.556 90 11 2 2057 2145 670052596 670052684 5.920000e-15 93.5
28 TraesCS5B01G228900 chr7A 71.698 371 82 16 776 1140 30673380 30673027 1.280000e-11 82.4
29 TraesCS5B01G228900 chr6D 89.474 57 4 2 4214 4268 128910423 128910367 2.780000e-08 71.3
30 TraesCS5B01G228900 chr3D 95.455 44 2 0 4214 4257 608238764 608238807 2.780000e-08 71.3
31 TraesCS5B01G228900 chr4B 90.196 51 5 0 4208 4258 27929234 27929284 3.590000e-07 67.6
32 TraesCS5B01G228900 chr2D 87.719 57 6 1 4201 4257 295155013 295154958 1.290000e-06 65.8
33 TraesCS5B01G228900 chr2D 100.000 29 0 0 1767 1795 64725373 64725401 3.000000e-03 54.7
34 TraesCS5B01G228900 chr1B 97.222 36 1 0 1760 1795 117589097 117589062 1.670000e-05 62.1


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 TraesCS5B01G228900 chr5B 405721282 405726834 5552 False 10255.000000 10255 100.000000 1 5553 1 chr5B.!!$F1 5552
1 TraesCS5B01G228900 chr5B 330169090 330169987 897 True 715.000000 715 81.466000 2059 2967 1 chr5B.!!$R1 908
2 TraesCS5B01G228900 chr5B 638395286 638396237 951 False 691.000000 691 80.485000 2016 2970 1 chr5B.!!$F2 954
3 TraesCS5B01G228900 chr5B 330484936 330485687 751 True 665.000000 665 83.073000 2219 2967 1 chr5B.!!$R2 748
4 TraesCS5B01G228900 chr5A 445283270 445288837 5567 False 2258.666667 2789 89.536333 2 5553 3 chr5A.!!$F1 5551
5 TraesCS5B01G228900 chr5D 345925691 345932985 7294 True 1386.666667 1565 87.935000 2 5552 3 chr5D.!!$R1 5550
6 TraesCS5B01G228900 chr7D 486550064 486550997 933 False 859.000000 859 83.610000 2010 2954 1 chr7D.!!$F1 944
7 TraesCS5B01G228900 chr7D 256818415 256819294 879 True 761.000000 761 82.609000 2086 2965 1 chr7D.!!$R1 879
8 TraesCS5B01G228900 chr3B 769396463 769397349 886 True 774.000000 774 82.724000 2058 2944 1 chr3B.!!$R1 886
9 TraesCS5B01G228900 chr2A 187486760 187487702 942 True 749.000000 749 81.474000 2010 2963 1 chr2A.!!$R1 953
10 TraesCS5B01G228900 chr4A 97251371 97252285 914 False 730.000000 730 81.624000 2057 2963 1 chr4A.!!$F1 906
11 TraesCS5B01G228900 chr6B 51988729 51989597 868 False 726.000000 726 82.127000 2057 2921 1 chr6B.!!$F1 864
12 TraesCS5B01G228900 chr2B 122929926 122930778 852 True 697.000000 697 81.655000 2077 2962 1 chr2B.!!$R1 885
13 TraesCS5B01G228900 chr1D 468712129 468712982 853 False 647.000000 647 80.752000 2103 2963 1 chr1D.!!$F2 860

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
256 258 0.165944 CGGCAAGTAAAACGAGGCAG 59.834 55.000 0.00 0.00 0.00 4.85 F
1571 2013 0.390492 CTAGGGCATGCGACTGATGA 59.610 55.000 20.03 3.18 0.00 2.92 F
1983 2570 0.329261 TTCAAGCCATGAGACCAGGG 59.671 55.000 0.00 0.00 46.44 4.45 F
1984 2571 0.842030 TCAAGCCATGAGACCAGGGT 60.842 55.000 0.00 0.00 45.52 4.34 F
2014 2644 1.000896 CACATTTTCCCCTCCGGCT 60.001 57.895 0.00 0.00 0.00 5.52 F
3566 5725 0.615331 AGTTGTGGCATCTGATCCGT 59.385 50.000 0.00 0.00 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2553 0.038744 AACCCTGGTCTCATGGCTTG 59.961 55.000 0.00 0.0 32.73 4.01 R
2655 4329 0.683412 ACCACGAACTACTCCCAACC 59.317 55.000 0.00 0.0 0.00 3.77 R
3223 5377 1.003839 TGCACCGTTGGATGAGGAC 60.004 57.895 0.00 0.0 0.00 3.85 R
3434 5593 2.299297 GTTCAAGAGACGAAGGGAAGGA 59.701 50.000 0.00 0.0 0.00 3.36 R
3943 6124 2.412325 GCCGGAACACAATCAGTTAACG 60.412 50.000 5.05 0.0 32.62 3.18 R
4579 6774 0.596083 CGTCGCTCCTGATCATCCAC 60.596 60.000 0.00 0.0 0.00 4.02 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
70 71 3.124976 CACACCAACTTGGCAAAAGTTTG 59.875 43.478 12.62 12.02 42.67 2.93
71 72 2.677337 CACCAACTTGGCAAAAGTTTGG 59.323 45.455 19.96 19.96 42.67 3.28
88 89 1.001269 GGTCCTTCTTTTCCCCGGG 60.001 63.158 15.80 15.80 0.00 5.73
172 173 2.880890 AGTCAGCCTGTTCAATTCACAC 59.119 45.455 0.00 0.00 0.00 3.82
176 177 1.873591 GCCTGTTCAATTCACACGAGT 59.126 47.619 0.00 0.00 0.00 4.18
192 194 6.479990 TCACACGAGTCATGATCATTTTATCC 59.520 38.462 5.16 0.00 0.00 2.59
196 198 5.691754 CGAGTCATGATCATTTTATCCGACA 59.308 40.000 17.45 0.00 33.18 4.35
237 239 1.009335 GTTTGCCGAACCGAACCAC 60.009 57.895 0.00 0.00 31.85 4.16
256 258 0.165944 CGGCAAGTAAAACGAGGCAG 59.834 55.000 0.00 0.00 0.00 4.85
271 273 4.157840 ACGAGGCAGAAATAATTTGAACCC 59.842 41.667 0.00 0.00 0.00 4.11
276 278 5.095490 GCAGAAATAATTTGAACCCACGAG 58.905 41.667 0.00 0.00 0.00 4.18
305 308 3.556306 CCGGGTGCCCATATCCGT 61.556 66.667 8.14 0.00 40.78 4.69
316 319 2.106511 CCCATATCCGTCCCAAACATCT 59.893 50.000 0.00 0.00 0.00 2.90
320 323 1.285280 TCCGTCCCAAACATCTGGAT 58.715 50.000 0.00 0.00 38.96 3.41
328 331 1.952296 CAAACATCTGGATAGGCTGCC 59.048 52.381 11.65 11.65 0.00 4.85
330 333 1.004080 CATCTGGATAGGCTGCCCG 60.004 63.158 16.57 0.00 35.76 6.13
339 342 4.643387 GGCTGCCCGGTCACTGTT 62.643 66.667 7.66 0.00 0.00 3.16
370 373 2.403252 AAGCCATCCAACTAGGTTCG 57.597 50.000 0.00 0.00 39.02 3.95
373 376 1.922570 CCATCCAACTAGGTTCGTCG 58.077 55.000 0.00 0.00 39.02 5.12
381 384 1.970917 CTAGGTTCGTCGTACGCGGT 61.971 60.000 24.33 13.51 42.21 5.68
395 398 4.733542 CGGTCCAAATGCCCGGGT 62.734 66.667 24.63 0.00 38.09 5.28
505 530 3.219281 CATTGTCCCTATAAAACCCCCG 58.781 50.000 0.00 0.00 0.00 5.73
571 596 2.172505 CTCTCCCTCTCAGCTCTACTCA 59.827 54.545 0.00 0.00 0.00 3.41
573 598 2.886523 CTCCCTCTCAGCTCTACTCATG 59.113 54.545 0.00 0.00 0.00 3.07
581 609 2.622942 CAGCTCTACTCATGTCTCCTCC 59.377 54.545 0.00 0.00 0.00 4.30
582 610 2.513738 AGCTCTACTCATGTCTCCTCCT 59.486 50.000 0.00 0.00 0.00 3.69
583 611 3.052944 AGCTCTACTCATGTCTCCTCCTT 60.053 47.826 0.00 0.00 0.00 3.36
589 617 3.848975 ACTCATGTCTCCTCCTTTCCATT 59.151 43.478 0.00 0.00 0.00 3.16
608 636 2.988010 TTCCACAATCTCTCCCATCG 57.012 50.000 0.00 0.00 0.00 3.84
697 725 2.600731 CTTCGACTCGTCAAGCTCATT 58.399 47.619 0.00 0.00 0.00 2.57
698 726 2.264109 TCGACTCGTCAAGCTCATTC 57.736 50.000 0.00 0.00 0.00 2.67
700 728 0.642800 GACTCGTCAAGCTCATTCGC 59.357 55.000 0.00 0.00 0.00 4.70
707 735 1.153289 AAGCTCATTCGCGCTGGAT 60.153 52.632 5.56 0.00 36.45 3.41
736 765 1.059994 CGTGCTTCGCATTGCTCTC 59.940 57.895 7.12 0.00 41.91 3.20
746 775 4.778415 TTGCTCTCCGTCGCTCGC 62.778 66.667 0.00 0.00 38.35 5.03
754 783 4.753877 CGTCGCTCGCGGACAGAA 62.754 66.667 6.13 0.00 40.25 3.02
786 815 3.432588 CTCCTCCACGACGTCGCT 61.433 66.667 35.92 20.88 44.43 4.93
795 824 2.202623 GACGTCGCTGGTGGCTAG 60.203 66.667 0.00 0.00 39.13 3.42
911 940 2.350514 GCAGTTGCTCCTCCTGCT 59.649 61.111 3.75 0.00 46.23 4.24
912 941 2.039405 GCAGTTGCTCCTCCTGCTG 61.039 63.158 3.75 0.00 46.23 4.41
935 964 2.575993 CGCTCAGTGCTAGTGCCT 59.424 61.111 0.00 0.00 40.11 4.75
947 976 2.821366 GTGCCTGCACCATCGAGG 60.821 66.667 11.16 0.00 40.79 4.63
960 989 2.586079 CGAGGCCGCGATCACAAT 60.586 61.111 25.87 0.00 0.00 2.71
961 990 2.173669 CGAGGCCGCGATCACAATT 61.174 57.895 25.87 0.00 0.00 2.32
966 995 1.405469 GCCGCGATCACAATTGCAAC 61.405 55.000 8.23 0.00 41.71 4.17
971 1000 2.498905 CGATCACAATTGCAACAGACG 58.501 47.619 0.00 0.00 0.00 4.18
972 1001 2.157474 CGATCACAATTGCAACAGACGA 59.843 45.455 0.00 0.57 0.00 4.20
985 1419 3.379445 GACGAAGACGGAGGGGCA 61.379 66.667 0.00 0.00 44.46 5.36
992 1426 1.286248 AGACGGAGGGGCACTTATTT 58.714 50.000 0.00 0.00 0.00 1.40
1057 1492 0.468214 CTGCGGGTCCTCCAGATCTA 60.468 60.000 0.00 0.00 34.36 1.98
1083 1518 3.771160 CTGTTACCGCCCGCCTCT 61.771 66.667 0.00 0.00 0.00 3.69
1134 1569 2.566529 CGCTCCTACACGTCAGCA 59.433 61.111 0.00 0.00 0.00 4.41
1169 1604 2.859538 GCCGTCGGTAATACGAAAATGA 59.140 45.455 13.94 0.00 45.38 2.57
1266 1702 3.518590 GTCGTCGAAACAATCCCTATGT 58.481 45.455 0.00 0.00 0.00 2.29
1381 1821 4.350225 AGGAGGCATGAGATCACATAATGT 59.650 41.667 5.25 0.00 0.00 2.71
1404 1846 1.160329 CCGCTTGATCCCCATCGAAC 61.160 60.000 0.00 0.00 0.00 3.95
1411 1853 1.343465 GATCCCCATCGAACGGTACAT 59.657 52.381 0.00 0.00 0.00 2.29
1414 1856 1.487452 CCCATCGAACGGTACATGCG 61.487 60.000 0.00 0.00 0.00 4.73
1442 1884 4.574674 ATCCTTCACTGGATAGTTGCAA 57.425 40.909 0.00 0.00 44.36 4.08
1456 1898 4.085357 AGTTGCAAGCCGATCCATAATA 57.915 40.909 0.00 0.00 0.00 0.98
1459 1901 5.536161 AGTTGCAAGCCGATCCATAATAAAT 59.464 36.000 0.00 0.00 0.00 1.40
1463 1905 4.553330 AGCCGATCCATAATAAATCCGT 57.447 40.909 0.00 0.00 0.00 4.69
1469 1911 6.637254 CCGATCCATAATAAATCCGTCTATCG 59.363 42.308 0.00 0.00 39.52 2.92
1507 1949 2.439507 AGAGACATCAACAACCACCACT 59.560 45.455 0.00 0.00 0.00 4.00
1571 2013 0.390492 CTAGGGCATGCGACTGATGA 59.610 55.000 20.03 3.18 0.00 2.92
1660 2102 1.614583 CGGTGGAAGAGAGAGGACTCA 60.615 57.143 1.75 0.00 44.79 3.41
1695 2137 2.512896 GAGGCGGCATCAAGGGAT 59.487 61.111 13.08 0.00 0.00 3.85
1704 2146 2.301346 GCATCAAGGGATTTCCATCGT 58.699 47.619 0.00 0.00 38.24 3.73
1743 2186 0.602638 TGTCGTGTTCATGTGGCCTC 60.603 55.000 3.32 0.00 0.00 4.70
1747 2190 1.076332 GTGTTCATGTGGCCTCGTAC 58.924 55.000 3.32 0.00 0.00 3.67
1794 2237 8.838649 ATAATAAAGGGGTTATTGCTTCTGTT 57.161 30.769 2.35 0.00 41.55 3.16
1796 2239 2.711542 AGGGGTTATTGCTTCTGTTCG 58.288 47.619 0.00 0.00 0.00 3.95
1800 2243 1.132453 GTTATTGCTTCTGTTCGCCCC 59.868 52.381 0.00 0.00 0.00 5.80
1853 2296 0.621609 TTACCCACTATGCCACCCAC 59.378 55.000 0.00 0.00 0.00 4.61
1861 2304 1.812571 CTATGCCACCCACAAGTGAAC 59.187 52.381 0.94 0.00 40.34 3.18
1866 2309 2.887337 CCACCCACAAGTGAACAAAAC 58.113 47.619 0.94 0.00 40.34 2.43
1867 2310 2.232452 CCACCCACAAGTGAACAAAACA 59.768 45.455 0.94 0.00 40.34 2.83
1869 2312 4.502962 CACCCACAAGTGAACAAAACAAT 58.497 39.130 0.94 0.00 40.34 2.71
1870 2313 4.566360 CACCCACAAGTGAACAAAACAATC 59.434 41.667 0.94 0.00 40.34 2.67
1871 2314 4.466015 ACCCACAAGTGAACAAAACAATCT 59.534 37.500 0.94 0.00 0.00 2.40
1872 2315 4.805192 CCCACAAGTGAACAAAACAATCTG 59.195 41.667 0.94 0.00 0.00 2.90
1873 2316 4.805192 CCACAAGTGAACAAAACAATCTGG 59.195 41.667 0.94 0.00 0.00 3.86
1878 2465 7.117667 ACAAGTGAACAAAACAATCTGGTTTTC 59.882 33.333 1.38 0.00 45.20 2.29
1879 2466 6.935167 AGTGAACAAAACAATCTGGTTTTCT 58.065 32.000 1.38 0.00 45.20 2.52
1884 2471 8.614469 AACAAAACAATCTGGTTTTCTTTTCA 57.386 26.923 1.38 0.00 45.20 2.69
1890 2477 6.751888 ACAATCTGGTTTTCTTTTCAAAGTCG 59.248 34.615 0.00 0.00 37.31 4.18
1891 2478 5.243426 TCTGGTTTTCTTTTCAAAGTCGG 57.757 39.130 0.00 0.00 37.31 4.79
1896 2483 4.909696 TTTCTTTTCAAAGTCGGCATCA 57.090 36.364 0.00 0.00 37.31 3.07
1903 2490 0.729116 AAAGTCGGCATCATGCTTCG 59.271 50.000 10.11 5.72 44.28 3.79
1911 2498 4.104776 CGGCATCATGCTTCGTTATTTTT 58.895 39.130 10.11 0.00 44.28 1.94
1912 2499 5.065346 TCGGCATCATGCTTCGTTATTTTTA 59.935 36.000 10.11 0.00 44.28 1.52
1913 2500 5.914635 CGGCATCATGCTTCGTTATTTTTAT 59.085 36.000 10.11 0.00 44.28 1.40
1956 2543 2.159226 AGTCATAGACGCACAAGTAGCC 60.159 50.000 0.00 0.00 37.67 3.93
1959 2546 2.133281 TAGACGCACAAGTAGCCCTA 57.867 50.000 0.00 0.00 0.00 3.53
1960 2547 0.818296 AGACGCACAAGTAGCCCTAG 59.182 55.000 0.00 0.00 0.00 3.02
1961 2548 0.806492 GACGCACAAGTAGCCCTAGC 60.806 60.000 0.00 0.00 40.32 3.42
1979 2566 1.377536 GCTCTTCAAGCCATGAGACC 58.622 55.000 0.00 0.00 45.92 3.85
1980 2567 1.339438 GCTCTTCAAGCCATGAGACCA 60.339 52.381 0.00 0.00 45.92 4.02
1981 2568 2.630158 CTCTTCAAGCCATGAGACCAG 58.370 52.381 0.00 0.00 39.77 4.00
1982 2569 1.280133 TCTTCAAGCCATGAGACCAGG 59.720 52.381 0.00 0.00 39.77 4.45
1983 2570 0.329261 TTCAAGCCATGAGACCAGGG 59.671 55.000 0.00 0.00 46.44 4.45
1984 2571 0.842030 TCAAGCCATGAGACCAGGGT 60.842 55.000 0.00 0.00 45.52 4.34
2004 2591 2.299013 GTTCCCCAACCTCCACATTTTC 59.701 50.000 0.00 0.00 0.00 2.29
2005 2592 1.203125 TCCCCAACCTCCACATTTTCC 60.203 52.381 0.00 0.00 0.00 3.13
2008 2595 1.203174 CCAACCTCCACATTTTCCCCT 60.203 52.381 0.00 0.00 0.00 4.79
2014 2644 1.000896 CACATTTTCCCCTCCGGCT 60.001 57.895 0.00 0.00 0.00 5.52
2022 2652 4.100084 CCCTCCGGCTCATGTGCA 62.100 66.667 20.43 0.38 34.04 4.57
2039 3495 1.077212 CAGGGCTTGACTCCCCATG 60.077 63.158 0.00 0.00 45.03 3.66
2095 3558 9.801873 CATTCTGTTTTCTTCCTTCTTTAAACA 57.198 29.630 0.00 0.00 35.13 2.83
2495 4153 8.647143 AATGTTCATGAATTCGAAAACTGTTT 57.353 26.923 12.12 0.00 0.00 2.83
2591 4261 8.472683 AAAAATGATTCGAAAAACTGTTCACA 57.527 26.923 0.00 0.00 0.00 3.58
2655 4329 9.734984 TTTCCTAAAGTCTTTATTTGTCTAGGG 57.265 33.333 5.50 1.23 0.00 3.53
2827 4505 2.231380 ATTGGCGAGGGTGGGAAGT 61.231 57.895 0.00 0.00 0.00 3.01
2841 4525 5.130311 GGGTGGGAAGTAAAATAAATGGCAT 59.870 40.000 0.00 0.00 0.00 4.40
2871 4632 4.589908 AGCCACTGTGTTAAAATAGAGGG 58.410 43.478 7.08 4.78 0.00 4.30
2954 5101 2.222508 CGTTGCAACGCTACTGACATAC 60.223 50.000 35.89 1.96 46.06 2.39
2994 5143 5.649782 ACAAGGGTAATGCTTTCTTCATG 57.350 39.130 0.00 0.00 0.00 3.07
3172 5326 2.496899 TGTTGCTTTGATCCTCCTCC 57.503 50.000 0.00 0.00 0.00 4.30
3175 5329 3.157087 GTTGCTTTGATCCTCCTCCAAA 58.843 45.455 0.00 0.00 0.00 3.28
3191 5345 7.064728 CCTCCTCCAAAGTAAAAATAGACGAAG 59.935 40.741 0.00 0.00 0.00 3.79
3227 5381 4.954118 TGGCGTCCACTGGGTCCT 62.954 66.667 0.00 0.00 34.93 3.85
3452 5611 1.402984 CGTCCTTCCCTTCGTCTCTTG 60.403 57.143 0.00 0.00 0.00 3.02
3529 5688 2.618053 GCTAACCACAGCTTCGTACAT 58.382 47.619 0.00 0.00 38.57 2.29
3530 5689 3.777478 GCTAACCACAGCTTCGTACATA 58.223 45.455 0.00 0.00 38.57 2.29
3531 5690 3.797256 GCTAACCACAGCTTCGTACATAG 59.203 47.826 0.00 0.00 38.57 2.23
3532 5691 2.961526 ACCACAGCTTCGTACATAGG 57.038 50.000 0.00 0.00 0.00 2.57
3533 5692 2.453521 ACCACAGCTTCGTACATAGGA 58.546 47.619 0.00 0.00 0.00 2.94
3534 5693 2.427453 ACCACAGCTTCGTACATAGGAG 59.573 50.000 0.00 0.00 0.00 3.69
3566 5725 0.615331 AGTTGTGGCATCTGATCCGT 59.385 50.000 0.00 0.00 0.00 4.69
3707 5886 7.959718 ATTTCATTTGATCTTGAACGAATCG 57.040 32.000 0.00 0.00 31.87 3.34
3710 5889 3.722555 TTGATCTTGAACGAATCGCAC 57.277 42.857 1.15 0.00 0.00 5.34
3782 5963 2.358615 TGTCCATGCGTGCAGGTC 60.359 61.111 8.40 1.24 0.00 3.85
3943 6124 3.732048 TTTGGGGAAGAGTAATGGGTC 57.268 47.619 0.00 0.00 0.00 4.46
4127 6311 5.066505 GCTGCTGCTTAGTGGTTATTACAAT 59.933 40.000 8.53 0.00 36.03 2.71
4132 6316 9.285770 GCTGCTTAGTGGTTATTACAATTAAAC 57.714 33.333 0.00 0.00 0.00 2.01
4158 6342 2.939103 ACAATCAAGGCAAGCTCGATAC 59.061 45.455 0.00 0.00 0.00 2.24
4160 6344 2.988010 TCAAGGCAAGCTCGATACAT 57.012 45.000 0.00 0.00 0.00 2.29
4162 6346 3.198068 TCAAGGCAAGCTCGATACATTC 58.802 45.455 0.00 0.00 0.00 2.67
4174 6358 4.631133 CGATACATTCGGTAACATCTGC 57.369 45.455 0.00 0.00 44.28 4.26
4175 6359 3.119628 CGATACATTCGGTAACATCTGCG 59.880 47.826 0.00 0.00 44.28 5.18
4176 6360 2.665649 ACATTCGGTAACATCTGCGA 57.334 45.000 0.00 0.00 0.00 5.10
4177 6361 3.179443 ACATTCGGTAACATCTGCGAT 57.821 42.857 0.00 0.00 0.00 4.58
4178 6362 3.531538 ACATTCGGTAACATCTGCGATT 58.468 40.909 0.00 0.00 0.00 3.34
4179 6363 3.309682 ACATTCGGTAACATCTGCGATTG 59.690 43.478 0.00 0.00 0.00 2.67
4180 6364 2.665649 TCGGTAACATCTGCGATTGT 57.334 45.000 0.00 0.00 0.00 2.71
4181 6365 3.786516 TCGGTAACATCTGCGATTGTA 57.213 42.857 0.00 0.00 0.00 2.41
4182 6366 4.112716 TCGGTAACATCTGCGATTGTAA 57.887 40.909 0.00 0.00 0.00 2.41
4183 6367 4.689071 TCGGTAACATCTGCGATTGTAAT 58.311 39.130 0.00 0.00 0.00 1.89
4184 6368 4.506288 TCGGTAACATCTGCGATTGTAATG 59.494 41.667 0.00 0.00 0.00 1.90
4189 6373 6.735678 AACATCTGCGATTGTAATGTGTTA 57.264 33.333 0.00 0.00 31.29 2.41
4190 6374 6.349973 ACATCTGCGATTGTAATGTGTTAG 57.650 37.500 0.00 0.00 0.00 2.34
4191 6375 6.106003 ACATCTGCGATTGTAATGTGTTAGA 58.894 36.000 0.00 0.00 0.00 2.10
4192 6376 6.593770 ACATCTGCGATTGTAATGTGTTAGAA 59.406 34.615 0.00 0.00 0.00 2.10
4193 6377 7.119116 ACATCTGCGATTGTAATGTGTTAGAAA 59.881 33.333 0.00 0.00 28.39 2.52
4195 6379 7.866729 TCTGCGATTGTAATGTGTTAGAAAAA 58.133 30.769 0.00 0.00 28.39 1.94
4232 6416 9.874215 CCTTACTTTAGTTTAAAACTGCTACAC 57.126 33.333 0.00 0.00 42.84 2.90
4241 6425 9.744468 AGTTTAAAACTGCTACACTTATTTTGG 57.256 29.630 0.00 0.00 41.01 3.28
4245 6429 6.422776 AACTGCTACACTTATTTTGGATCG 57.577 37.500 0.00 0.00 0.00 3.69
4246 6430 4.876107 ACTGCTACACTTATTTTGGATCGG 59.124 41.667 0.00 0.00 0.00 4.18
4247 6431 5.092554 TGCTACACTTATTTTGGATCGGA 57.907 39.130 0.00 0.00 0.00 4.55
4248 6432 5.116180 TGCTACACTTATTTTGGATCGGAG 58.884 41.667 0.00 0.00 0.00 4.63
4249 6433 4.511826 GCTACACTTATTTTGGATCGGAGG 59.488 45.833 0.00 0.00 0.00 4.30
4251 6435 3.521937 ACACTTATTTTGGATCGGAGGGA 59.478 43.478 0.00 0.00 0.00 4.20
4268 6461 4.322123 GGAGGGAGTAGTTCAGTTGAGAAC 60.322 50.000 0.00 0.00 46.35 3.01
4308 6501 6.183360 CGTATCCTTGTACAACCATCTTTTCC 60.183 42.308 3.59 0.00 0.00 3.13
4317 6510 8.194769 TGTACAACCATCTTTTCCTTTTCTTTC 58.805 33.333 0.00 0.00 0.00 2.62
4318 6511 6.582636 ACAACCATCTTTTCCTTTTCTTTCC 58.417 36.000 0.00 0.00 0.00 3.13
4383 6578 8.682936 ACCCTCAATAATATCATCAACTGAAC 57.317 34.615 0.00 0.00 37.44 3.18
4386 6581 8.706936 CCTCAATAATATCATCAACTGAACTCG 58.293 37.037 0.00 0.00 37.44 4.18
4398 6593 4.679373 ACTGAACTCGGCATCTATTCAT 57.321 40.909 0.00 0.00 0.00 2.57
4468 6663 6.068498 TCCCAAGGGATAAAACCATGAAGTAT 60.068 38.462 3.04 0.00 39.76 2.12
4689 6885 3.164269 CTAGGGCCCGCCATGAGT 61.164 66.667 18.44 0.00 37.98 3.41
4690 6886 3.466791 CTAGGGCCCGCCATGAGTG 62.467 68.421 18.44 0.00 37.98 3.51
4751 6947 1.131504 GACGTGTTTGGTTGCTCACAA 59.868 47.619 0.00 0.00 0.00 3.33
4804 7000 4.431131 CAGGCGGGGAATGCAGGT 62.431 66.667 0.00 0.00 0.00 4.00
4810 7006 1.691219 GGGGAATGCAGGTTCTGGA 59.309 57.895 0.00 0.00 36.05 3.86
4817 7013 2.885135 TGCAGGTTCTGGATCATGTT 57.115 45.000 0.00 0.00 31.21 2.71
4825 7021 5.012354 AGGTTCTGGATCATGTTTTTGCAAT 59.988 36.000 0.00 0.00 0.00 3.56
4837 7033 9.334693 TCATGTTTTTGCAATTTGTTTTGTTAC 57.665 25.926 0.00 0.00 0.00 2.50
4879 7077 2.440980 GGCCTCAATGCTCCCCAC 60.441 66.667 0.00 0.00 0.00 4.61
4916 7114 3.460868 CGGGATTTTGGCCTGGGC 61.461 66.667 14.23 14.23 41.06 5.36
4941 7139 4.142093 GGGCTGATGCAGATATTGTGTTTT 60.142 41.667 0.00 0.00 41.91 2.43
4968 7166 4.445385 GCACATTTTTGACCTGTTGTGATC 59.555 41.667 5.14 0.00 37.28 2.92
5009 7207 4.589798 TGGTGAGTTTACCAGCTACAACTA 59.410 41.667 0.00 0.00 45.46 2.24
5034 7232 7.552458 TTGTCATCGCATTGTACTTATGATT 57.448 32.000 11.27 0.00 0.00 2.57
5069 7268 9.926158 TTAGGAAACTACAAATATACAACGACA 57.074 29.630 0.00 0.00 44.30 4.35
5122 7321 5.657745 TCAACCTACTTAACCCGATATGACA 59.342 40.000 0.00 0.00 0.00 3.58
5145 7346 0.916358 ACCCTTGCCTACTCCATGCT 60.916 55.000 0.00 0.00 0.00 3.79
5165 7366 3.366476 GCTCGCTCTTCTCTTTGACTACA 60.366 47.826 0.00 0.00 0.00 2.74
5232 7433 8.993424 ACCCTCTATGACAACTATTCTTGTAAT 58.007 33.333 0.00 0.00 34.40 1.89
5264 7465 2.877975 ATGGCAAGCCTGTCATGAC 58.122 52.632 19.27 19.27 46.25 3.06
5275 7476 3.891977 GCCTGTCATGACCTATAGACTCA 59.108 47.826 22.85 2.01 32.41 3.41
5289 7490 6.778069 CCTATAGACTCATGAAACCCTCACTA 59.222 42.308 0.00 0.00 36.69 2.74
5297 7498 5.305902 TCATGAAACCCTCACTAAGTACACA 59.694 40.000 0.00 0.00 36.69 3.72
5304 7505 5.100259 CCCTCACTAAGTACACAACATACG 58.900 45.833 0.00 0.00 0.00 3.06
5316 7517 5.408356 ACACAACATACGACTTCATCTACC 58.592 41.667 0.00 0.00 0.00 3.18
5374 7576 8.894592 ACAAGAATCATATATGGTGGATAAGGT 58.105 33.333 12.78 0.00 0.00 3.50
5378 7580 7.829224 ATCATATATGGTGGATAAGGTTGGA 57.171 36.000 12.78 0.00 0.00 3.53
5382 7584 9.312904 CATATATGGTGGATAAGGTTGGATTTT 57.687 33.333 4.68 0.00 0.00 1.82
5413 7615 5.499004 TTAGGGCATGACTAAACTCAACT 57.501 39.130 0.00 0.00 0.00 3.16
5433 7635 6.489700 TCAACTTCTTTCAATGCCTACAATGA 59.510 34.615 0.00 0.00 33.85 2.57
5444 7646 3.817084 TGCCTACAATGATTAGCATCAGC 59.183 43.478 0.00 0.00 42.93 4.26
5452 7654 6.208797 ACAATGATTAGCATCAGCAATAGCAT 59.791 34.615 0.00 0.00 42.93 3.79
5546 7748 5.649831 GGTAAGGCTTGAATGATCTTCACTT 59.350 40.000 10.69 9.26 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 1.001269 CCCGGGGAAAAGAAGGACC 60.001 63.158 14.71 0.00 0.00 4.46
71 72 0.322277 GACCCGGGGAAAAGAAGGAC 60.322 60.000 27.92 0.00 0.00 3.85
88 89 1.135575 GCAGCACAGGCACAAATAGAC 60.136 52.381 0.00 0.00 44.61 2.59
172 173 5.691754 TGTCGGATAAAATGATCATGACTCG 59.308 40.000 9.46 9.11 35.45 4.18
176 177 8.367156 TGATACTGTCGGATAAAATGATCATGA 58.633 33.333 9.46 0.00 0.00 3.07
192 194 2.695666 AGATCCAACCCTGATACTGTCG 59.304 50.000 0.00 0.00 0.00 4.35
196 198 4.585162 CGAGTAAGATCCAACCCTGATACT 59.415 45.833 0.00 0.00 0.00 2.12
237 239 0.165944 CTGCCTCGTTTTACTTGCCG 59.834 55.000 0.00 0.00 0.00 5.69
256 258 5.106317 TGCTCTCGTGGGTTCAAATTATTTC 60.106 40.000 0.00 0.00 0.00 2.17
271 273 1.550065 CGGTTGTAGATGCTCTCGTG 58.450 55.000 0.00 0.00 0.00 4.35
276 278 1.090052 GCACCCGGTTGTAGATGCTC 61.090 60.000 0.00 0.00 0.00 4.26
293 295 0.106918 GTTTGGGACGGATATGGGCA 60.107 55.000 0.00 0.00 0.00 5.36
305 308 2.173356 CAGCCTATCCAGATGTTTGGGA 59.827 50.000 0.00 0.00 38.81 4.37
316 319 3.161450 GACCGGGCAGCCTATCCA 61.161 66.667 12.43 0.00 0.00 3.41
320 323 3.390521 CAGTGACCGGGCAGCCTA 61.391 66.667 12.52 0.00 0.00 3.93
328 331 1.372997 CTGTCCGAACAGTGACCGG 60.373 63.158 17.54 17.54 46.52 5.28
357 360 1.464608 CGTACGACGAACCTAGTTGGA 59.535 52.381 10.44 0.00 46.05 3.53
370 373 1.705727 CATTTGGACCGCGTACGAC 59.294 57.895 21.65 9.57 43.93 4.34
373 376 2.757056 GGGCATTTGGACCGCGTAC 61.757 63.158 4.92 0.00 32.42 3.67
381 384 1.152440 AACAACCCGGGCATTTGGA 60.152 52.632 24.08 0.00 0.00 3.53
395 398 2.684192 ATTCGCCCCACACCGAACAA 62.684 55.000 0.00 0.00 44.89 2.83
482 507 2.963101 GGGGTTTTATAGGGACAATGGC 59.037 50.000 0.00 0.00 0.00 4.40
518 543 1.278413 GAGTGGGGTTTGACTAGGGTC 59.722 57.143 0.00 0.00 42.42 4.46
549 574 1.133792 AGTAGAGCTGAGAGGGAGAGC 60.134 57.143 0.00 0.00 0.00 4.09
571 596 3.593328 TGGAAATGGAAAGGAGGAGACAT 59.407 43.478 0.00 0.00 0.00 3.06
573 598 3.244911 TGTGGAAATGGAAAGGAGGAGAC 60.245 47.826 0.00 0.00 0.00 3.36
581 609 4.400567 GGGAGAGATTGTGGAAATGGAAAG 59.599 45.833 0.00 0.00 0.00 2.62
582 610 4.202663 TGGGAGAGATTGTGGAAATGGAAA 60.203 41.667 0.00 0.00 0.00 3.13
583 611 3.333381 TGGGAGAGATTGTGGAAATGGAA 59.667 43.478 0.00 0.00 0.00 3.53
589 617 1.134401 GCGATGGGAGAGATTGTGGAA 60.134 52.381 0.00 0.00 0.00 3.53
624 652 2.232298 CTCTCAGGTCCACTTCCGGC 62.232 65.000 0.00 0.00 0.00 6.13
625 653 1.893786 CTCTCAGGTCCACTTCCGG 59.106 63.158 0.00 0.00 0.00 5.14
626 654 1.216710 GCTCTCAGGTCCACTTCCG 59.783 63.158 0.00 0.00 0.00 4.30
628 656 1.216710 CCGCTCTCAGGTCCACTTC 59.783 63.158 0.00 0.00 0.00 3.01
630 658 3.386237 GCCGCTCTCAGGTCCACT 61.386 66.667 0.00 0.00 0.00 4.00
631 659 3.363844 GAGCCGCTCTCAGGTCCAC 62.364 68.421 13.42 0.00 41.51 4.02
632 660 3.071206 GAGCCGCTCTCAGGTCCA 61.071 66.667 13.42 0.00 41.51 4.02
633 661 3.844090 GGAGCCGCTCTCAGGTCC 61.844 72.222 19.68 0.00 43.70 4.46
679 707 1.465856 CGAATGAGCTTGACGAGTCGA 60.466 52.381 21.50 0.00 0.00 4.20
697 725 3.531207 CCTCCTCATCCAGCGCGA 61.531 66.667 12.10 0.00 0.00 5.87
698 726 3.531207 TCCTCCTCATCCAGCGCG 61.531 66.667 0.00 0.00 0.00 6.86
700 728 1.739049 GAGTCCTCCTCATCCAGCG 59.261 63.158 0.00 0.00 40.17 5.18
707 735 1.587043 CGAAGCACGAGTCCTCCTCA 61.587 60.000 0.00 0.00 45.77 3.86
724 753 2.202610 CGACGGAGAGCAATGCGA 60.203 61.111 8.97 0.00 37.47 5.10
746 775 2.738521 CCCGTGCAGTTCTGTCCG 60.739 66.667 0.00 4.47 0.00 4.79
751 780 2.659610 GAGCTCCCGTGCAGTTCT 59.340 61.111 0.87 0.00 34.99 3.01
754 783 3.386237 GAGGAGCTCCCGTGCAGT 61.386 66.667 29.54 8.83 40.87 4.40
786 815 1.229690 TTGCCTACCCTAGCCACCA 60.230 57.895 0.00 0.00 0.00 4.17
793 822 4.408276 CAGAGCTATAGTTGCCTACCCTA 58.592 47.826 0.84 0.00 0.00 3.53
795 824 2.289133 GCAGAGCTATAGTTGCCTACCC 60.289 54.545 12.27 0.00 0.00 3.69
947 976 1.154054 TTGCAATTGTGATCGCGGC 60.154 52.632 6.13 0.00 0.00 6.53
952 981 3.811722 TCGTCTGTTGCAATTGTGATC 57.188 42.857 0.59 0.00 0.00 2.92
960 989 0.103390 TCCGTCTTCGTCTGTTGCAA 59.897 50.000 0.00 0.00 35.01 4.08
961 990 0.318699 CTCCGTCTTCGTCTGTTGCA 60.319 55.000 0.00 0.00 35.01 4.08
966 995 2.885861 CCCCTCCGTCTTCGTCTG 59.114 66.667 0.00 0.00 35.01 3.51
971 1000 0.831307 ATAAGTGCCCCTCCGTCTTC 59.169 55.000 0.00 0.00 0.00 2.87
972 1001 1.286248 AATAAGTGCCCCTCCGTCTT 58.714 50.000 0.00 0.00 0.00 3.01
985 1419 6.828785 ACCTTCTTCATGGCGATAAAATAAGT 59.171 34.615 0.00 0.00 0.00 2.24
992 1426 2.917933 CCACCTTCTTCATGGCGATAA 58.082 47.619 0.00 0.00 0.00 1.75
1043 1478 1.413077 CCGGTTTAGATCTGGAGGACC 59.587 57.143 5.18 5.26 33.49 4.46
1057 1492 1.670083 GCGGTAACAGCTCCGGTTT 60.670 57.895 12.92 0.00 45.85 3.27
1134 1569 2.267681 GACGGCGGTCATTCGTCTCT 62.268 60.000 18.61 0.00 46.49 3.10
1159 1594 1.647346 AGCGCCGATTCATTTTCGTA 58.353 45.000 2.29 0.00 34.85 3.43
1160 1595 0.802494 AAGCGCCGATTCATTTTCGT 59.198 45.000 2.29 0.00 34.85 3.85
1266 1702 4.038642 GGAACCAACCAATGCTAGACAAAA 59.961 41.667 0.00 0.00 0.00 2.44
1381 1821 0.397941 GATGGGGATCAAGCGGATGA 59.602 55.000 0.00 0.00 36.00 2.92
1404 1846 0.248054 GATTTGGCACGCATGTACCG 60.248 55.000 0.00 0.00 33.87 4.02
1411 1853 0.537143 AGTGAAGGATTTGGCACGCA 60.537 50.000 0.00 0.00 36.43 5.24
1414 1856 1.909700 TCCAGTGAAGGATTTGGCAC 58.090 50.000 0.00 0.00 31.23 5.01
1434 1876 3.552132 TTATGGATCGGCTTGCAACTA 57.448 42.857 0.00 0.00 0.00 2.24
1442 1884 4.223032 AGACGGATTTATTATGGATCGGCT 59.777 41.667 0.00 0.00 0.00 5.52
1456 1898 5.768662 TGTCCTTATCTCGATAGACGGATTT 59.231 40.000 0.00 0.00 42.67 2.17
1459 1901 4.347360 TGTCCTTATCTCGATAGACGGA 57.653 45.455 0.00 0.00 42.67 4.69
1469 1911 3.067040 GTCTCTCGGGTTGTCCTTATCTC 59.933 52.174 0.00 0.00 0.00 2.75
1507 1949 4.021104 CCAAATGATCAGCGTCCTAGGATA 60.021 45.833 16.27 0.00 0.00 2.59
1559 2001 3.141398 AGTTGTTTGTCATCAGTCGCAT 58.859 40.909 0.00 0.00 0.00 4.73
1565 2007 7.038048 TGCTAGATCTAGTTGTTTGTCATCAG 58.962 38.462 26.73 3.01 35.65 2.90
1566 2008 6.935167 TGCTAGATCTAGTTGTTTGTCATCA 58.065 36.000 26.73 11.60 35.65 3.07
1571 2013 9.319143 GTCATTATGCTAGATCTAGTTGTTTGT 57.681 33.333 26.73 10.69 35.65 2.83
1660 2102 1.556911 CTCCTTCCACCTATGTGCACT 59.443 52.381 19.41 6.22 41.35 4.40
1695 2137 7.230108 CCCTAGTCTGTACTTATACGATGGAAA 59.770 40.741 0.00 0.00 37.15 3.13
1704 2146 6.183361 ACGACATCCCCTAGTCTGTACTTATA 60.183 42.308 0.00 0.00 37.15 0.98
1778 2221 1.132453 GGCGAACAGAAGCAATAACCC 59.868 52.381 0.00 0.00 34.54 4.11
1817 2260 8.913487 AGTGGGTAATTTATAGTAATTTCGGG 57.087 34.615 0.00 0.00 0.00 5.14
1837 2280 0.680921 CTTGTGGGTGGCATAGTGGG 60.681 60.000 0.00 0.00 0.00 4.61
1853 2296 6.966435 AAACCAGATTGTTTTGTTCACTTG 57.034 33.333 0.00 0.00 34.92 3.16
1861 2304 9.545611 CTTTGAAAAGAAAACCAGATTGTTTTG 57.454 29.630 6.62 0.00 45.72 2.44
1866 2309 6.198966 CCGACTTTGAAAAGAAAACCAGATTG 59.801 38.462 9.71 0.00 39.31 2.67
1867 2310 6.273071 CCGACTTTGAAAAGAAAACCAGATT 58.727 36.000 9.71 0.00 39.31 2.40
1869 2312 4.439563 GCCGACTTTGAAAAGAAAACCAGA 60.440 41.667 9.71 0.00 39.31 3.86
1870 2313 3.796717 GCCGACTTTGAAAAGAAAACCAG 59.203 43.478 9.71 0.00 39.31 4.00
1871 2314 3.193691 TGCCGACTTTGAAAAGAAAACCA 59.806 39.130 9.71 0.00 39.31 3.67
1872 2315 3.776340 TGCCGACTTTGAAAAGAAAACC 58.224 40.909 9.71 0.00 39.31 3.27
1873 2316 5.040635 TGATGCCGACTTTGAAAAGAAAAC 58.959 37.500 9.71 0.00 39.31 2.43
1878 2465 2.919229 GCATGATGCCGACTTTGAAAAG 59.081 45.455 6.04 1.22 37.42 2.27
1879 2466 2.557924 AGCATGATGCCGACTTTGAAAA 59.442 40.909 14.72 0.00 46.52 2.29
1884 2471 0.729116 CGAAGCATGATGCCGACTTT 59.271 50.000 14.72 0.61 46.52 2.66
1890 2477 7.222611 ACAATAAAAATAACGAAGCATGATGCC 59.777 33.333 14.72 0.00 46.52 4.40
1891 2478 8.118893 ACAATAAAAATAACGAAGCATGATGC 57.881 30.769 9.89 9.89 45.46 3.91
1927 2514 6.701841 ACTTGTGCGTCTATGACTTATATTGG 59.298 38.462 0.00 0.00 0.00 3.16
1936 2523 2.194271 GGCTACTTGTGCGTCTATGAC 58.806 52.381 0.00 0.00 0.00 3.06
1961 2548 2.630158 CTGGTCTCATGGCTTGAAGAG 58.370 52.381 4.53 0.00 32.78 2.85
1962 2549 1.280133 CCTGGTCTCATGGCTTGAAGA 59.720 52.381 4.53 2.27 32.78 2.87
1965 2552 0.842030 ACCCTGGTCTCATGGCTTGA 60.842 55.000 2.86 2.86 32.73 3.02
1966 2553 0.038744 AACCCTGGTCTCATGGCTTG 59.961 55.000 0.00 0.00 32.73 4.01
1967 2554 0.329596 GAACCCTGGTCTCATGGCTT 59.670 55.000 0.00 0.00 32.73 4.35
1968 2555 1.566298 GGAACCCTGGTCTCATGGCT 61.566 60.000 0.00 0.00 32.73 4.75
1969 2556 1.077429 GGAACCCTGGTCTCATGGC 60.077 63.158 0.00 0.00 32.73 4.40
1983 2570 2.009681 AAATGTGGAGGTTGGGGAAC 57.990 50.000 0.00 0.00 0.00 3.62
1984 2571 2.604139 GAAAATGTGGAGGTTGGGGAA 58.396 47.619 0.00 0.00 0.00 3.97
2008 2595 4.100084 CCCTGCACATGAGCCGGA 62.100 66.667 23.58 0.60 40.88 5.14
2014 2644 0.321919 GAGTCAAGCCCTGCACATGA 60.322 55.000 0.00 0.00 0.00 3.07
2022 2652 1.142688 AACATGGGGAGTCAAGCCCT 61.143 55.000 0.00 0.00 45.30 5.19
2054 3510 9.755804 GAAAACAGAATGAGAAAAGGAAAGAAT 57.244 29.630 0.00 0.00 39.69 2.40
2055 3511 8.971073 AGAAAACAGAATGAGAAAAGGAAAGAA 58.029 29.630 0.00 0.00 39.69 2.52
2061 3517 7.282332 AGGAAGAAAACAGAATGAGAAAAGG 57.718 36.000 0.00 0.00 39.69 3.11
2311 3837 7.646130 TGTTTTGAATACACGGTCATTTTTCTC 59.354 33.333 0.00 0.00 0.00 2.87
2312 3838 7.484975 TGTTTTGAATACACGGTCATTTTTCT 58.515 30.769 0.00 0.00 0.00 2.52
2646 4320 2.113052 ACTACTCCCAACCCCTAGACAA 59.887 50.000 0.00 0.00 0.00 3.18
2655 4329 0.683412 ACCACGAACTACTCCCAACC 59.317 55.000 0.00 0.00 0.00 3.77
2827 4505 6.462768 GGCTCACCATGATGCCATTTATTTTA 60.463 38.462 11.88 0.00 39.14 1.52
2871 4632 6.940739 ACTCAATACCCTGATATATGAGTGC 58.059 40.000 4.85 0.00 33.54 4.40
3050 5202 8.359875 TGTAAATTGGATGTGTGGAATAACAT 57.640 30.769 0.00 0.00 39.69 2.71
3051 5203 7.767250 TGTAAATTGGATGTGTGGAATAACA 57.233 32.000 0.00 0.00 0.00 2.41
3172 5326 6.148811 TGCCTCCTTCGTCTATTTTTACTTTG 59.851 38.462 0.00 0.00 0.00 2.77
3175 5329 5.416271 TGCCTCCTTCGTCTATTTTTACT 57.584 39.130 0.00 0.00 0.00 2.24
3223 5377 1.003839 TGCACCGTTGGATGAGGAC 60.004 57.895 0.00 0.00 0.00 3.85
3227 5381 2.359850 GCCTGCACCGTTGGATGA 60.360 61.111 0.00 0.00 0.00 2.92
3278 5433 2.612746 GGGGGTGGCTAAGGACCA 60.613 66.667 0.00 0.00 33.48 4.02
3434 5593 2.299297 GTTCAAGAGACGAAGGGAAGGA 59.701 50.000 0.00 0.00 0.00 3.36
3452 5611 2.586357 GGAGATCGCCGGCTGTTC 60.586 66.667 26.68 20.41 0.00 3.18
3524 5683 7.368833 ACTCGCAAATACATACTCCTATGTAC 58.631 38.462 3.28 0.00 44.90 2.90
3525 5684 7.520451 ACTCGCAAATACATACTCCTATGTA 57.480 36.000 3.63 3.63 45.73 2.29
3529 5688 6.040247 CACAACTCGCAAATACATACTCCTA 58.960 40.000 0.00 0.00 0.00 2.94
3530 5689 4.870426 CACAACTCGCAAATACATACTCCT 59.130 41.667 0.00 0.00 0.00 3.69
3531 5690 4.034048 CCACAACTCGCAAATACATACTCC 59.966 45.833 0.00 0.00 0.00 3.85
3532 5691 4.494199 GCCACAACTCGCAAATACATACTC 60.494 45.833 0.00 0.00 0.00 2.59
3533 5692 3.374058 GCCACAACTCGCAAATACATACT 59.626 43.478 0.00 0.00 0.00 2.12
3534 5693 3.126171 TGCCACAACTCGCAAATACATAC 59.874 43.478 0.00 0.00 30.46 2.39
3710 5889 7.443259 TCACTGATTAATATCCATGCATGTG 57.557 36.000 24.58 15.94 0.00 3.21
3943 6124 2.412325 GCCGGAACACAATCAGTTAACG 60.412 50.000 5.05 0.00 32.62 3.18
4127 6311 6.597280 AGCTTGCCTTGATTGTTTTTGTTTAA 59.403 30.769 0.00 0.00 0.00 1.52
4132 6316 3.182972 CGAGCTTGCCTTGATTGTTTTTG 59.817 43.478 0.00 0.00 0.00 2.44
4158 6342 3.309682 ACAATCGCAGATGTTACCGAATG 59.690 43.478 0.00 0.00 45.12 2.67
4160 6344 2.967362 ACAATCGCAGATGTTACCGAA 58.033 42.857 0.00 0.00 45.12 4.30
4162 6346 4.270084 ACATTACAATCGCAGATGTTACCG 59.730 41.667 0.00 0.00 45.12 4.02
4163 6347 5.064707 ACACATTACAATCGCAGATGTTACC 59.935 40.000 0.00 0.00 45.12 2.85
4164 6348 6.106877 ACACATTACAATCGCAGATGTTAC 57.893 37.500 0.00 0.00 45.12 2.50
4165 6349 6.735678 AACACATTACAATCGCAGATGTTA 57.264 33.333 0.00 0.00 45.12 2.41
4166 6350 5.627499 AACACATTACAATCGCAGATGTT 57.373 34.783 0.00 0.00 45.12 2.71
4167 6351 6.106003 TCTAACACATTACAATCGCAGATGT 58.894 36.000 0.00 0.00 45.12 3.06
4168 6352 6.588348 TCTAACACATTACAATCGCAGATG 57.412 37.500 0.00 0.00 45.12 2.90
4170 6354 7.428282 TTTTCTAACACATTACAATCGCAGA 57.572 32.000 0.00 0.00 45.75 4.26
4205 6389 9.617523 TGTAGCAGTTTTAAACTAAAGTAAGGT 57.382 29.630 10.21 4.79 40.46 3.50
4206 6390 9.874215 GTGTAGCAGTTTTAAACTAAAGTAAGG 57.126 33.333 10.21 0.00 40.46 2.69
4215 6399 9.744468 CCAAAATAAGTGTAGCAGTTTTAAACT 57.256 29.630 4.30 4.30 44.06 2.66
4216 6400 9.738832 TCCAAAATAAGTGTAGCAGTTTTAAAC 57.261 29.630 0.00 0.00 0.00 2.01
4220 6404 7.305474 CGATCCAAAATAAGTGTAGCAGTTTT 58.695 34.615 0.00 0.00 0.00 2.43
4221 6405 6.128007 CCGATCCAAAATAAGTGTAGCAGTTT 60.128 38.462 0.00 0.00 0.00 2.66
4222 6406 5.354234 CCGATCCAAAATAAGTGTAGCAGTT 59.646 40.000 0.00 0.00 0.00 3.16
4224 6408 5.116180 TCCGATCCAAAATAAGTGTAGCAG 58.884 41.667 0.00 0.00 0.00 4.24
4225 6409 5.092554 TCCGATCCAAAATAAGTGTAGCA 57.907 39.130 0.00 0.00 0.00 3.49
4226 6410 4.511826 CCTCCGATCCAAAATAAGTGTAGC 59.488 45.833 0.00 0.00 0.00 3.58
4227 6411 5.057149 CCCTCCGATCCAAAATAAGTGTAG 58.943 45.833 0.00 0.00 0.00 2.74
4228 6412 4.717778 TCCCTCCGATCCAAAATAAGTGTA 59.282 41.667 0.00 0.00 0.00 2.90
4229 6413 3.521937 TCCCTCCGATCCAAAATAAGTGT 59.478 43.478 0.00 0.00 0.00 3.55
4230 6414 4.130118 CTCCCTCCGATCCAAAATAAGTG 58.870 47.826 0.00 0.00 0.00 3.16
4232 6416 4.423625 ACTCCCTCCGATCCAAAATAAG 57.576 45.455 0.00 0.00 0.00 1.73
4233 6417 4.966805 ACTACTCCCTCCGATCCAAAATAA 59.033 41.667 0.00 0.00 0.00 1.40
4234 6418 4.553678 ACTACTCCCTCCGATCCAAAATA 58.446 43.478 0.00 0.00 0.00 1.40
4235 6419 3.385115 ACTACTCCCTCCGATCCAAAAT 58.615 45.455 0.00 0.00 0.00 1.82
4236 6420 2.829023 ACTACTCCCTCCGATCCAAAA 58.171 47.619 0.00 0.00 0.00 2.44
4237 6421 2.544844 ACTACTCCCTCCGATCCAAA 57.455 50.000 0.00 0.00 0.00 3.28
4238 6422 2.291996 TGAACTACTCCCTCCGATCCAA 60.292 50.000 0.00 0.00 0.00 3.53
4240 6424 1.957877 CTGAACTACTCCCTCCGATCC 59.042 57.143 0.00 0.00 0.00 3.36
4241 6425 2.657143 ACTGAACTACTCCCTCCGATC 58.343 52.381 0.00 0.00 0.00 3.69
4243 6427 2.168496 CAACTGAACTACTCCCTCCGA 58.832 52.381 0.00 0.00 0.00 4.55
4244 6428 2.164624 CTCAACTGAACTACTCCCTCCG 59.835 54.545 0.00 0.00 0.00 4.63
4245 6429 3.432378 TCTCAACTGAACTACTCCCTCC 58.568 50.000 0.00 0.00 0.00 4.30
4246 6430 4.322123 GGTTCTCAACTGAACTACTCCCTC 60.322 50.000 7.22 0.00 44.02 4.30
4247 6431 3.579151 GGTTCTCAACTGAACTACTCCCT 59.421 47.826 7.22 0.00 44.02 4.20
4248 6432 3.579151 AGGTTCTCAACTGAACTACTCCC 59.421 47.826 7.22 0.00 44.02 4.30
4249 6433 4.875561 AGGTTCTCAACTGAACTACTCC 57.124 45.455 7.22 0.00 44.02 3.85
4251 6435 6.149142 CGTACTAGGTTCTCAACTGAACTACT 59.851 42.308 7.22 0.94 44.02 2.57
4268 6461 4.626042 AGGATACGTACTGTCGTACTAGG 58.374 47.826 0.00 0.00 46.43 3.02
4271 6464 4.256920 ACAAGGATACGTACTGTCGTACT 58.743 43.478 0.00 6.12 46.43 2.73
4274 6467 4.002982 TGTACAAGGATACGTACTGTCGT 58.997 43.478 0.00 9.50 45.97 4.34
4317 6510 7.361457 TCTACTGATATACACTTCCCTTTGG 57.639 40.000 0.00 0.00 0.00 3.28
4318 6511 9.838339 ATTTCTACTGATATACACTTCCCTTTG 57.162 33.333 0.00 0.00 0.00 2.77
4383 6578 2.994578 CTGCAGATGAATAGATGCCGAG 59.005 50.000 8.42 0.00 37.89 4.63
4386 6581 3.137446 ACCTGCAGATGAATAGATGCC 57.863 47.619 17.39 0.00 37.89 4.40
4398 6593 0.607217 CCACAGCATCAACCTGCAGA 60.607 55.000 17.39 0.00 44.77 4.26
4568 6763 7.194112 TCCTGATCATCCACTGTATTTTACA 57.806 36.000 0.00 0.00 37.13 2.41
4569 6764 6.203723 GCTCCTGATCATCCACTGTATTTTAC 59.796 42.308 0.00 0.00 0.00 2.01
4570 6765 6.291377 GCTCCTGATCATCCACTGTATTTTA 58.709 40.000 0.00 0.00 0.00 1.52
4573 6768 3.244009 CGCTCCTGATCATCCACTGTATT 60.244 47.826 0.00 0.00 0.00 1.89
4575 6770 1.683385 CGCTCCTGATCATCCACTGTA 59.317 52.381 0.00 0.00 0.00 2.74
4577 6772 0.749049 TCGCTCCTGATCATCCACTG 59.251 55.000 0.00 0.00 0.00 3.66
4579 6774 0.596083 CGTCGCTCCTGATCATCCAC 60.596 60.000 0.00 0.00 0.00 4.02
4689 6885 3.520317 TCCCCTAGATTTTCCTTTACGCA 59.480 43.478 0.00 0.00 0.00 5.24
4690 6886 4.146745 TCCCCTAGATTTTCCTTTACGC 57.853 45.455 0.00 0.00 0.00 4.42
4751 6947 1.029681 GTGGAAGAGGCCAAAAACGT 58.970 50.000 5.01 0.00 40.20 3.99
4804 7000 6.766944 ACAAATTGCAAAAACATGATCCAGAA 59.233 30.769 1.71 0.00 0.00 3.02
4810 7006 8.983307 AACAAAACAAATTGCAAAAACATGAT 57.017 23.077 1.71 0.00 33.52 2.45
4817 7013 6.206634 TGTGGGTAACAAAACAAATTGCAAAA 59.793 30.769 1.71 0.00 35.24 2.44
4837 7033 1.281867 TGCAGACTAGGGATTTGTGGG 59.718 52.381 0.00 0.00 0.00 4.61
4916 7114 2.552743 CACAATATCTGCATCAGCCCAG 59.447 50.000 0.00 0.00 41.13 4.45
4968 7166 0.752743 CACATAGGGGGTGCATGGTG 60.753 60.000 0.00 0.00 0.00 4.17
4999 7197 4.123497 TGCGATGACAATAGTTGTAGCT 57.877 40.909 0.00 0.00 45.52 3.32
5005 7203 6.985188 AAGTACAATGCGATGACAATAGTT 57.015 33.333 0.00 0.00 0.00 2.24
5009 7207 7.734924 ATCATAAGTACAATGCGATGACAAT 57.265 32.000 0.00 0.00 0.00 2.71
5145 7346 4.848562 TTGTAGTCAAAGAGAAGAGCGA 57.151 40.909 0.00 0.00 0.00 4.93
5165 7366 7.690256 AGGTAGACAATGATTACTCCAAGTTT 58.310 34.615 0.00 0.00 0.00 2.66
5182 7383 4.363573 TGAGACTAGAGAGGAGGTAGACA 58.636 47.826 0.00 0.00 0.00 3.41
5183 7384 5.362105 TTGAGACTAGAGAGGAGGTAGAC 57.638 47.826 0.00 0.00 0.00 2.59
5232 7433 2.543578 GCCATGAGCAAGTGAACGA 58.456 52.632 0.00 0.00 42.97 3.85
5264 7465 5.600484 AGTGAGGGTTTCATGAGTCTATAGG 59.400 44.000 0.00 0.00 38.29 2.57
5275 7476 5.818678 TGTGTACTTAGTGAGGGTTTCAT 57.181 39.130 0.00 0.00 38.29 2.57
5289 7490 6.688578 AGATGAAGTCGTATGTTGTGTACTT 58.311 36.000 0.00 0.00 0.00 2.24
5297 7498 5.661458 CCTTGGTAGATGAAGTCGTATGTT 58.339 41.667 0.00 0.00 0.00 2.71
5304 7505 3.895232 TCTGCCTTGGTAGATGAAGTC 57.105 47.619 3.33 0.00 0.00 3.01
5374 7576 5.011125 TGCCCTAATTTTGTCGAAAATCCAA 59.989 36.000 0.00 0.00 40.27 3.53
5378 7580 6.071391 AGTCATGCCCTAATTTTGTCGAAAAT 60.071 34.615 0.00 0.00 42.49 1.82
5382 7584 3.950397 AGTCATGCCCTAATTTTGTCGA 58.050 40.909 0.00 0.00 0.00 4.20
5413 7615 7.122501 TGCTAATCATTGTAGGCATTGAAAGAA 59.877 33.333 0.00 0.00 38.15 2.52
5433 7635 5.533528 TCACAATGCTATTGCTGATGCTAAT 59.466 36.000 0.00 0.00 40.48 1.73
5444 7646 7.878477 ATTGTTCTTGTTCACAATGCTATTG 57.122 32.000 7.16 7.16 41.18 1.90
5452 7654 5.042593 GTGATGCATTGTTCTTGTTCACAA 58.957 37.500 0.00 0.00 37.31 3.33


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

AutoCloner maintained by Alex Coulton.