Multiple sequence alignment - TraesCS3B01G349200

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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 TraesCS3B01G349200 chr3B 100.000 4824 0 0 1 4824 559344631 559339808 0.000000e+00 8909
1 TraesCS3B01G349200 chr3B 95.890 73 3 0 1543 1615 493857636 493857708 8.480000e-23 119
2 TraesCS3B01G349200 chr3B 94.667 75 4 0 1542 1616 4536843 4536769 3.050000e-22 117
3 TraesCS3B01G349200 chr3B 94.366 71 4 0 1546 1616 157251390 157251460 5.100000e-20 110
4 TraesCS3B01G349200 chr3D 93.987 3193 119 33 1635 4782 427818588 427815424 0.000000e+00 4765
5 TraesCS3B01G349200 chr3D 87.407 937 73 18 585 1488 427820004 427819080 0.000000e+00 1035
6 TraesCS3B01G349200 chr3D 89.679 591 49 6 1 582 427820623 427820036 0.000000e+00 743
7 TraesCS3B01G349200 chr3D 82.470 502 72 15 45 540 58597140 58597631 4.460000e-115 425
8 TraesCS3B01G349200 chr3D 100.000 66 0 0 1479 1544 427818658 427818593 6.560000e-24 122
9 TraesCS3B01G349200 chr3A 94.141 3004 112 27 1636 4603 557948066 557951041 0.000000e+00 4514
10 TraesCS3B01G349200 chr3A 89.064 1143 93 17 130 1250 557946611 557947743 0.000000e+00 1389
11 TraesCS3B01G349200 chr3A 92.347 196 13 1 4589 4782 557951059 557951254 1.320000e-70 278
12 TraesCS3B01G349200 chr3A 92.169 166 11 2 1379 1544 557947862 557948025 2.900000e-57 233
13 TraesCS3B01G349200 chr1D 81.873 502 81 10 45 542 491721982 491721487 9.660000e-112 414
14 TraesCS3B01G349200 chr5D 81.563 499 90 2 45 541 76031030 76030532 1.250000e-110 411
15 TraesCS3B01G349200 chr6D 81.437 501 88 5 45 541 253754279 253753780 5.810000e-109 405
16 TraesCS3B01G349200 chr2D 81.287 513 84 11 47 553 626117924 626118430 5.810000e-109 405
17 TraesCS3B01G349200 chr2D 80.488 451 58 22 3087 3521 616635294 616634858 7.790000e-83 318
18 TraesCS3B01G349200 chr1B 81.437 501 83 10 45 540 99692528 99693023 7.520000e-108 401
19 TraesCS3B01G349200 chr1B 95.775 71 3 0 1546 1616 674876130 674876200 1.100000e-21 115
20 TraesCS3B01G349200 chr1B 95.652 69 3 0 1545 1613 674620200 674620268 1.420000e-20 111
21 TraesCS3B01G349200 chr6A 81.176 510 84 8 47 553 51412073 51411573 2.700000e-107 399
22 TraesCS3B01G349200 chr6A 89.041 146 16 0 3313 3458 53156891 53156746 1.070000e-41 182
23 TraesCS3B01G349200 chr6A 97.183 71 2 0 1546 1616 551091867 551091797 2.360000e-23 121
24 TraesCS3B01G349200 chr2A 79.956 454 65 20 3083 3524 746852398 746851959 1.300000e-80 311
25 TraesCS3B01G349200 chr2B 79.825 456 64 21 3083 3525 751842242 751841802 1.690000e-79 307
26 TraesCS3B01G349200 chrUn 89.041 146 16 0 3313 3458 98211667 98211522 1.070000e-41 182
27 TraesCS3B01G349200 chr6B 89.041 146 16 0 3313 3458 107771879 107771734 1.070000e-41 182
28 TraesCS3B01G349200 chr5B 84.971 173 18 6 3294 3460 562048304 562048474 8.300000e-38 169
29 TraesCS3B01G349200 chr5B 94.595 74 4 0 1546 1619 6497341 6497268 1.100000e-21 115
30 TraesCS3B01G349200 chr5B 94.444 72 4 0 1545 1616 677752652 677752723 1.420000e-20 111
31 TraesCS3B01G349200 chr7B 95.775 71 3 0 1546 1616 126755149 126755219 1.100000e-21 115


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 TraesCS3B01G349200 chr3B 559339808 559344631 4823 True 8909.00 8909 100.00000 1 4824 1 chr3B.!!$R2 4823
1 TraesCS3B01G349200 chr3D 427815424 427820623 5199 True 1666.25 4765 92.76825 1 4782 4 chr3D.!!$R1 4781
2 TraesCS3B01G349200 chr3A 557946611 557951254 4643 False 1603.50 4514 91.93025 130 4782 4 chr3A.!!$F1 4652
3 TraesCS3B01G349200 chr2D 626117924 626118430 506 False 405.00 405 81.28700 47 553 1 chr2D.!!$F1 506
4 TraesCS3B01G349200 chr6A 51411573 51412073 500 True 399.00 399 81.17600 47 553 1 chr6A.!!$R1 506

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
45 46 0.042131 TATCCCGACCCTTGGTGAGT 59.958 55.0 0.00 0.0 35.25 3.41 F
307 320 0.309922 CTACTCTTTATCGGCGGCGA 59.690 55.0 36.40 36.4 0.00 5.54 F
1564 2084 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.0 44.66 2.17 F
1567 2087 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 F
1836 2363 0.306533 GTGTGTCGCCGTCACATTTT 59.693 50.0 19.18 0.0 45.43 1.82 F
1894 2422 0.510790 TGCGCGTGTTAATGTGACTG 59.489 50.0 8.43 0.0 0.00 3.51 F
1919 2447 1.075542 TGGTGCGTCGATCAACATTC 58.924 50.0 4.52 0.0 0.00 2.67 F
3282 3825 0.249699 TCGGTTTGATGCGTCAGTGT 60.250 50.0 8.93 0.0 35.39 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 2055 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12 R
1861 2388 0.299300 CGCGCAATCGATCGGTTTTA 59.701 50.000 11.76 0.00 38.10 1.52 R
2767 3310 0.036010 CGAGCAGGAACTTGGTGGAT 60.036 55.000 0.00 0.00 34.60 3.41 R
3260 3803 0.298707 CTGACGCATCAAACCGATCG 59.701 55.000 8.51 8.51 33.30 3.69 R
3264 3807 0.586319 AACACTGACGCATCAAACCG 59.414 50.000 0.00 0.00 33.30 4.44 R
3266 3809 1.002468 AGCAACACTGACGCATCAAAC 60.002 47.619 0.00 0.00 33.30 2.93 R
3292 3853 1.154282 CTGCATGCACGCAACTCAG 60.154 57.895 18.46 0.00 42.45 3.35 R
4200 4764 0.173481 TATCTCTGTGCGTGGCTGTC 59.827 55.000 0.00 0.00 0.00 3.51 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
40 41 1.525442 GGTGTATCCCGACCCTTGG 59.475 63.158 0.00 0.00 0.00 3.61
45 46 0.042131 TATCCCGACCCTTGGTGAGT 59.958 55.000 0.00 0.00 35.25 3.41
49 50 1.687563 CCGACCCTTGGTGAGTTTTT 58.312 50.000 0.00 0.00 35.25 1.94
91 102 3.795688 AGGATTTCTGTCCTGCTCAAA 57.204 42.857 0.00 0.00 46.76 2.69
108 119 2.981977 AAAAAGACGAGACGGCGGCA 62.982 55.000 18.30 0.00 43.13 5.69
146 157 3.458163 CGTTCTCCCCGCCTAGCA 61.458 66.667 0.00 0.00 0.00 3.49
199 210 1.298667 GCGTGTGGGGGTGTATCTT 59.701 57.895 0.00 0.00 0.00 2.40
228 239 3.565307 TCTGTCTTTGGTGGATTTGCTT 58.435 40.909 0.00 0.00 0.00 3.91
241 252 4.278170 TGGATTTGCTTGAATCAGTTCGTT 59.722 37.500 9.24 0.00 37.69 3.85
264 277 1.679680 TCGTCTCCTTCGTGTGTCTTT 59.320 47.619 0.00 0.00 0.00 2.52
288 301 3.132289 TGTTGGATCCTTCCGATCTACAC 59.868 47.826 14.23 0.00 45.90 2.90
296 309 5.507637 TCCTTCCGATCTACACTACTCTTT 58.492 41.667 0.00 0.00 0.00 2.52
307 320 0.309922 CTACTCTTTATCGGCGGCGA 59.690 55.000 36.40 36.40 0.00 5.54
318 331 1.355796 CGGCGGCGATTGTTGTTCTA 61.356 55.000 29.19 0.00 0.00 2.10
334 347 4.606210 TGTTCTAGTGTGCTGGTCCTATA 58.394 43.478 0.00 0.00 0.00 1.31
339 352 1.367840 GTGCTGGTCCTATAGGGCG 59.632 63.158 18.97 6.43 41.79 6.13
365 378 1.137513 CGACAACTTTCCGACTGTCC 58.862 55.000 1.55 0.00 35.77 4.02
411 425 2.363795 AAGGAGGGGCGATGACGA 60.364 61.111 0.00 0.00 42.66 4.20
517 531 9.483916 TGGTGTTCGTTATACTATCATATTTGG 57.516 33.333 0.00 0.00 0.00 3.28
553 567 9.710900 GATTGGATGTTTTCCTGTAAAAGAAAT 57.289 29.630 0.00 0.00 45.68 2.17
582 596 3.372440 AAGCCCACCCTCTATTTTCTG 57.628 47.619 0.00 0.00 0.00 3.02
583 597 1.566231 AGCCCACCCTCTATTTTCTGG 59.434 52.381 0.00 0.00 0.00 3.86
605 648 1.927174 CGATGGACCAAGAACACGATC 59.073 52.381 0.00 0.00 0.00 3.69
713 761 1.079073 CCTTTGGACCAGGGCCAAT 59.921 57.895 28.95 0.00 44.30 3.16
726 774 2.108952 AGGGCCAATCTTTGAACTGTCT 59.891 45.455 6.18 0.00 0.00 3.41
738 786 2.743664 TGAACTGTCTGTGCATGCATAC 59.256 45.455 25.64 21.28 0.00 2.39
740 788 1.003464 ACTGTCTGTGCATGCATACCA 59.997 47.619 25.64 16.23 0.00 3.25
799 847 1.153005 AGCTACGTACTCCCTCCCG 60.153 63.158 0.00 0.00 0.00 5.14
801 849 1.452651 CTACGTACTCCCTCCCGCA 60.453 63.158 0.00 0.00 0.00 5.69
802 850 0.822532 CTACGTACTCCCTCCCGCAT 60.823 60.000 0.00 0.00 0.00 4.73
803 851 1.105167 TACGTACTCCCTCCCGCATG 61.105 60.000 0.00 0.00 0.00 4.06
805 853 3.536917 TACTCCCTCCCGCATGCG 61.537 66.667 32.60 32.60 39.44 4.73
819 871 2.195567 ATGCGCAACCACAGCAACT 61.196 52.632 17.11 0.00 44.51 3.16
829 881 1.085091 CACAGCAACTGCCATCTCTC 58.915 55.000 0.00 0.00 43.38 3.20
830 882 0.982704 ACAGCAACTGCCATCTCTCT 59.017 50.000 0.00 0.00 43.38 3.10
831 883 1.338864 ACAGCAACTGCCATCTCTCTG 60.339 52.381 0.00 0.00 43.38 3.35
903 955 2.035632 GAGTACCCTCCAGATCCACTG 58.964 57.143 0.00 0.00 45.36 3.66
921 973 1.990614 GGACAGTGACCCTCTCCCC 60.991 68.421 0.00 0.00 0.00 4.81
922 974 1.229209 GACAGTGACCCTCTCCCCA 60.229 63.158 0.00 0.00 0.00 4.96
923 975 0.836400 GACAGTGACCCTCTCCCCAA 60.836 60.000 0.00 0.00 0.00 4.12
967 1019 3.573967 GAGAGAAGAAGGCCTAGATCCAG 59.426 52.174 5.16 0.00 0.00 3.86
1015 1070 4.288105 AGAAGAAGATGGTGACCATGAAGT 59.712 41.667 23.89 3.64 45.26 3.01
1047 1102 1.064803 CCAGACATCTTCGTCCTCGAG 59.935 57.143 5.13 5.13 46.81 4.04
1092 1157 7.327214 CCTTCCTCATTTCATATACTCCTAGC 58.673 42.308 0.00 0.00 0.00 3.42
1102 1167 9.588096 TTTCATATACTCCTAGCTGATTACTCA 57.412 33.333 0.00 0.00 0.00 3.41
1128 1193 3.749609 CCCTCGGTTGATTTTTCTAACGT 59.250 43.478 0.00 0.00 0.00 3.99
1156 1222 4.541085 TGCACTTCGAGATGCATAATTG 57.459 40.909 18.59 0.00 46.63 2.32
1164 1230 6.594284 TCGAGATGCATAATTGTTCTCAAG 57.406 37.500 0.00 0.00 35.60 3.02
1171 1237 6.446318 TGCATAATTGTTCTCAAGGTTTGAC 58.554 36.000 0.00 0.00 36.97 3.18
1173 1239 6.516527 GCATAATTGTTCTCAAGGTTTGACCA 60.517 38.462 0.00 0.00 41.95 4.02
1179 1245 7.069331 ATTGTTCTCAAGGTTTGACCAAACATA 59.931 33.333 22.31 5.56 43.41 2.29
1203 1269 7.206981 AGTTTGGTACATGTGAATCTTTCTG 57.793 36.000 9.11 0.00 39.30 3.02
1250 1316 9.699410 TTTTCTTGTGGGTTTCTATATCATCAT 57.301 29.630 0.00 0.00 0.00 2.45
1263 1343 8.828688 TCTATATCATCATGCTCAGTTCAAAG 57.171 34.615 0.00 0.00 0.00 2.77
1295 1376 9.594936 TTTTTCTATTTTTCACCTTCCCTCATA 57.405 29.630 0.00 0.00 0.00 2.15
1296 1377 8.807948 TTTCTATTTTTCACCTTCCCTCATAG 57.192 34.615 0.00 0.00 0.00 2.23
1300 1381 6.894339 TTTTTCACCTTCCCTCATAGTTTC 57.106 37.500 0.00 0.00 0.00 2.78
1305 1386 4.938226 CACCTTCCCTCATAGTTTCAAGAC 59.062 45.833 0.00 0.00 0.00 3.01
1330 1411 6.098982 CCATAGTTTCCACTGTTAGAGGAGAT 59.901 42.308 0.00 0.00 36.36 2.75
1347 1428 3.753797 GGAGATGACAAAAACACTCCTCC 59.246 47.826 0.00 0.00 40.20 4.30
1368 1449 1.381191 TCCATGTCTAGGCGGCTCA 60.381 57.895 17.67 8.27 0.00 4.26
1371 1452 1.344438 CCATGTCTAGGCGGCTCAATA 59.656 52.381 17.67 3.27 0.00 1.90
1375 1456 2.297315 TGTCTAGGCGGCTCAATATGAG 59.703 50.000 17.67 5.40 46.90 2.90
1544 2055 9.622004 GTTTGTTTCGATCTATAAGATCCGATA 57.378 33.333 10.52 5.17 46.42 2.92
1557 2077 2.486472 TCCGATATACTCCCTCCGTC 57.514 55.000 0.00 0.00 0.00 4.79
1558 2078 1.004044 TCCGATATACTCCCTCCGTCC 59.996 57.143 0.00 0.00 0.00 4.79
1559 2079 1.085091 CGATATACTCCCTCCGTCCG 58.915 60.000 0.00 0.00 0.00 4.79
1560 2080 1.461559 GATATACTCCCTCCGTCCGG 58.538 60.000 0.00 0.00 0.00 5.14
1561 2081 1.004044 GATATACTCCCTCCGTCCGGA 59.996 57.143 0.00 0.00 42.90 5.14
1562 2082 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
1564 2084 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1566 2086 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1567 2087 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1568 2088 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1570 2090 2.631545 CCCTCCGTCCGGAAATACTTAT 59.368 50.000 5.23 0.00 44.66 1.73
1571 2091 3.305881 CCCTCCGTCCGGAAATACTTATC 60.306 52.174 5.23 0.00 44.66 1.75
1573 2093 4.021368 CCTCCGTCCGGAAATACTTATCAT 60.021 45.833 5.23 0.00 44.66 2.45
1574 2094 5.130292 TCCGTCCGGAAATACTTATCATC 57.870 43.478 5.23 0.00 42.05 2.92
1575 2095 4.585581 TCCGTCCGGAAATACTTATCATCA 59.414 41.667 5.23 0.00 42.05 3.07
1576 2096 5.069383 TCCGTCCGGAAATACTTATCATCAA 59.931 40.000 5.23 0.00 42.05 2.57
1577 2097 5.756347 CCGTCCGGAAATACTTATCATCAAA 59.244 40.000 5.23 0.00 37.50 2.69
1578 2098 6.259167 CCGTCCGGAAATACTTATCATCAAAA 59.741 38.462 5.23 0.00 37.50 2.44
1579 2099 7.041372 CCGTCCGGAAATACTTATCATCAAAAT 60.041 37.037 5.23 0.00 37.50 1.82
1580 2100 7.798516 CGTCCGGAAATACTTATCATCAAAATG 59.201 37.037 5.23 0.00 0.00 2.32
1581 2101 8.836413 GTCCGGAAATACTTATCATCAAAATGA 58.164 33.333 5.23 0.00 45.73 2.57
1582 2102 9.402320 TCCGGAAATACTTATCATCAAAATGAA 57.598 29.630 0.00 0.00 44.85 2.57
1647 2167 8.868522 AATGAAAATGGAATACTTCTCAGTCA 57.131 30.769 0.00 0.00 34.06 3.41
1649 2169 8.272545 TGAAAATGGAATACTTCTCAGTCATG 57.727 34.615 0.00 0.00 34.06 3.07
1655 2175 6.013379 TGGAATACTTCTCAGTCATGGTTTCT 60.013 38.462 0.00 0.00 34.06 2.52
1668 2188 2.876091 TGGTTTCTAAGATCACGAGCG 58.124 47.619 0.00 0.00 0.00 5.03
1675 2201 3.993234 GATCACGAGCGCGCATGG 61.993 66.667 35.10 23.13 42.48 3.66
1692 2218 5.292589 GCGCATGGAAATTTGATGAGAATTT 59.707 36.000 0.30 0.00 38.89 1.82
1719 2245 4.441792 TGTTTACGTGATCCATCCATCTG 58.558 43.478 0.00 0.00 0.00 2.90
1836 2363 0.306533 GTGTGTCGCCGTCACATTTT 59.693 50.000 19.18 0.00 45.43 1.82
1837 2364 1.018148 TGTGTCGCCGTCACATTTTT 58.982 45.000 12.94 0.00 40.26 1.94
1857 2384 3.829886 TTCGCATTCATCAACTGAACC 57.170 42.857 0.00 0.00 46.37 3.62
1859 2386 1.464608 CGCATTCATCAACTGAACCGT 59.535 47.619 0.00 0.00 46.37 4.83
1861 2388 3.309682 CGCATTCATCAACTGAACCGTAT 59.690 43.478 0.00 0.00 46.37 3.06
1865 2392 7.247728 GCATTCATCAACTGAACCGTATAAAA 58.752 34.615 0.00 0.00 46.37 1.52
1866 2393 7.218204 GCATTCATCAACTGAACCGTATAAAAC 59.782 37.037 0.00 0.00 46.37 2.43
1881 2409 1.632046 AAAACCGATCGATTGCGCGT 61.632 50.000 18.66 0.17 37.46 6.01
1894 2422 0.510790 TGCGCGTGTTAATGTGACTG 59.489 50.000 8.43 0.00 0.00 3.51
1906 2434 2.078849 TGTGACTGACTAATGGTGCG 57.921 50.000 0.00 0.00 0.00 5.34
1913 2441 1.474879 TGACTAATGGTGCGTCGATCA 59.525 47.619 0.00 0.00 0.00 2.92
1914 2442 2.094442 TGACTAATGGTGCGTCGATCAA 60.094 45.455 0.00 0.00 0.00 2.57
1919 2447 1.075542 TGGTGCGTCGATCAACATTC 58.924 50.000 4.52 0.00 0.00 2.67
1924 2452 2.263077 GCGTCGATCAACATTCTGAGT 58.737 47.619 0.00 0.00 0.00 3.41
1993 2521 4.509737 GAGTACCAGCCGCCGTCC 62.510 72.222 0.00 0.00 0.00 4.79
2596 3136 2.770048 CTCCTCCCGGGCCTGAAT 60.770 66.667 18.49 0.00 34.39 2.57
2619 3159 3.349006 CGCCAGCTTCAGCAACGT 61.349 61.111 0.75 0.00 45.16 3.99
2628 3168 1.831389 TTCAGCAACGTCAGCTTCGC 61.831 55.000 12.22 0.00 41.14 4.70
2629 3169 3.406361 AGCAACGTCAGCTTCGCG 61.406 61.111 9.42 0.00 39.87 5.87
2740 3283 2.187239 TCCTGGAGGAGATCATTGCT 57.813 50.000 0.00 0.00 39.78 3.91
2755 3298 2.669569 GCTCTGCTGCCGACCAAA 60.670 61.111 0.00 0.00 0.00 3.28
2767 3310 2.410466 GACCAAAAAGGGCGTCACA 58.590 52.632 0.00 0.00 43.89 3.58
2893 3436 2.757917 AGCCTCGAGGACCTGCTC 60.758 66.667 35.69 15.11 37.39 4.26
3143 3686 1.518903 GGACACCAACCTGAAGCTGC 61.519 60.000 0.00 0.00 0.00 5.25
3245 3788 2.620251 CCTCAAGGTGACAACTGACA 57.380 50.000 0.00 0.00 0.00 3.58
3247 3790 2.874701 CCTCAAGGTGACAACTGACAAG 59.125 50.000 0.00 0.00 0.00 3.16
3248 3791 3.535561 CTCAAGGTGACAACTGACAAGT 58.464 45.455 0.00 0.00 38.71 3.16
3253 3796 3.006940 GGTGACAACTGACAAGTGACAA 58.993 45.455 0.00 0.00 36.51 3.18
3255 3798 4.403453 GTGACAACTGACAAGTGACAAAC 58.597 43.478 0.00 0.00 36.51 2.93
3256 3799 4.068599 TGACAACTGACAAGTGACAAACA 58.931 39.130 0.00 0.00 36.51 2.83
3265 3808 1.129809 GTGACAAACACGGCGATCG 59.870 57.895 16.62 11.69 45.88 3.69
3266 3809 2.024868 TGACAAACACGGCGATCGG 61.025 57.895 16.62 3.26 44.45 4.18
3267 3810 2.025418 GACAAACACGGCGATCGGT 61.025 57.895 16.62 3.99 44.45 4.69
3268 3811 1.562575 GACAAACACGGCGATCGGTT 61.563 55.000 16.62 9.41 44.45 4.44
3269 3812 1.161563 ACAAACACGGCGATCGGTTT 61.162 50.000 16.62 14.89 44.45 3.27
3270 3813 0.724453 CAAACACGGCGATCGGTTTG 60.724 55.000 23.61 23.61 44.65 2.93
3271 3814 0.881159 AAACACGGCGATCGGTTTGA 60.881 50.000 16.62 0.00 44.45 2.69
3272 3815 0.672401 AACACGGCGATCGGTTTGAT 60.672 50.000 16.62 0.00 44.45 2.57
3275 3818 2.324477 GGCGATCGGTTTGATGCG 59.676 61.111 18.30 0.00 37.47 4.73
3277 3820 1.012234 GCGATCGGTTTGATGCGTC 60.012 57.895 18.30 0.00 37.47 5.19
3278 3821 1.692148 GCGATCGGTTTGATGCGTCA 61.692 55.000 18.30 3.97 37.47 4.35
3279 3822 0.298707 CGATCGGTTTGATGCGTCAG 59.701 55.000 7.38 0.00 37.47 3.51
3280 3823 1.359848 GATCGGTTTGATGCGTCAGT 58.640 50.000 8.93 0.00 37.47 3.41
3281 3824 1.061131 GATCGGTTTGATGCGTCAGTG 59.939 52.381 8.93 0.98 37.47 3.66
3282 3825 0.249699 TCGGTTTGATGCGTCAGTGT 60.250 50.000 8.93 0.00 35.39 3.55
3283 3826 0.586319 CGGTTTGATGCGTCAGTGTT 59.414 50.000 8.93 0.00 35.39 3.32
3284 3827 1.660052 CGGTTTGATGCGTCAGTGTTG 60.660 52.381 8.93 0.00 35.39 3.33
3285 3828 1.398595 GTTTGATGCGTCAGTGTTGC 58.601 50.000 8.93 2.94 35.39 4.17
3292 3853 1.798223 TGCGTCAGTGTTGCTAACATC 59.202 47.619 9.98 1.29 44.35 3.06
3297 3858 4.310769 GTCAGTGTTGCTAACATCTGAGT 58.689 43.478 20.46 0.00 43.43 3.41
3298 3859 4.752101 GTCAGTGTTGCTAACATCTGAGTT 59.248 41.667 20.46 0.00 43.43 3.01
3305 3866 2.068519 CTAACATCTGAGTTGCGTGCA 58.931 47.619 0.00 0.00 33.07 4.57
3701 4262 1.548357 GGAGCTGGAGAAGGAGTGCA 61.548 60.000 0.00 0.00 0.00 4.57
3867 4428 6.701145 AGAGTATGAAATCTCAGCTAACGA 57.299 37.500 0.00 0.00 34.23 3.85
4028 4592 9.273016 AGCACTTCACATACATAACCATAATAC 57.727 33.333 0.00 0.00 0.00 1.89
4065 4629 4.428209 CAAGCTCGTCAGAATAGTGATGT 58.572 43.478 0.00 0.00 35.33 3.06
4144 4708 5.248640 CCTAGGAAAGAAATGAAGCACTCA 58.751 41.667 1.05 0.00 38.81 3.41
4164 4728 9.979270 GCACTCATATATATTACAAGAATGCAC 57.021 33.333 7.97 0.00 0.00 4.57
4182 4746 5.767816 TGCACGAAGATCTATAGCTACAA 57.232 39.130 0.00 0.00 0.00 2.41
4200 4764 4.734398 ACAAGTATTCTCTCTCAGCCAG 57.266 45.455 0.00 0.00 0.00 4.85
4201 4765 4.348486 ACAAGTATTCTCTCTCAGCCAGA 58.652 43.478 0.00 0.00 0.00 3.86
4202 4766 4.159506 ACAAGTATTCTCTCTCAGCCAGAC 59.840 45.833 0.00 0.00 0.00 3.51
4203 4767 3.974719 AGTATTCTCTCTCAGCCAGACA 58.025 45.455 0.00 0.00 0.00 3.41
4204 4768 3.953612 AGTATTCTCTCTCAGCCAGACAG 59.046 47.826 0.00 0.00 0.00 3.51
4205 4769 0.894141 TTCTCTCTCAGCCAGACAGC 59.106 55.000 0.00 0.00 0.00 4.40
4206 4770 0.969917 TCTCTCTCAGCCAGACAGCC 60.970 60.000 0.00 0.00 0.00 4.85
4207 4771 1.228988 TCTCTCAGCCAGACAGCCA 60.229 57.895 0.00 0.00 0.00 4.75
4208 4772 1.079266 CTCTCAGCCAGACAGCCAC 60.079 63.158 0.00 0.00 0.00 5.01
4209 4773 2.433838 CTCAGCCAGACAGCCACG 60.434 66.667 0.00 0.00 0.00 4.94
4210 4774 4.687215 TCAGCCAGACAGCCACGC 62.687 66.667 0.00 0.00 0.00 5.34
4211 4775 4.994471 CAGCCAGACAGCCACGCA 62.994 66.667 0.00 0.00 0.00 5.24
4214 4778 3.046087 CCAGACAGCCACGCACAG 61.046 66.667 0.00 0.00 0.00 3.66
4287 4851 7.664318 CACATCCTATTCTCATCCATTCATCAA 59.336 37.037 0.00 0.00 0.00 2.57
4539 5103 4.036262 CAGAACAGTCCGAATCCAACAAAA 59.964 41.667 0.00 0.00 0.00 2.44
4666 5275 4.320494 GCCATGCCAAATTAACTCGATAGG 60.320 45.833 0.00 0.00 0.00 2.57
4695 5304 9.411189 GAAATACTTACCCCCACAATAACATTA 57.589 33.333 0.00 0.00 0.00 1.90
4716 5325 2.009051 CTGCCTATGACGTCAATTGCA 58.991 47.619 26.84 26.84 0.00 4.08
4749 5358 5.533154 CCCACTGTAACACCAGAAACAATAA 59.467 40.000 0.00 0.00 36.30 1.40
4787 5396 9.914131 TTAGATAATCTGAATGAGTTGATACCG 57.086 33.333 0.00 0.00 0.00 4.02
4788 5397 8.183104 AGATAATCTGAATGAGTTGATACCGA 57.817 34.615 0.00 0.00 0.00 4.69
4789 5398 8.085296 AGATAATCTGAATGAGTTGATACCGAC 58.915 37.037 0.00 0.00 0.00 4.79
4790 5399 4.386867 TCTGAATGAGTTGATACCGACC 57.613 45.455 0.00 0.00 0.00 4.79
4791 5400 4.023980 TCTGAATGAGTTGATACCGACCT 58.976 43.478 0.00 0.00 0.00 3.85
4792 5401 5.198207 TCTGAATGAGTTGATACCGACCTA 58.802 41.667 0.00 0.00 0.00 3.08
4793 5402 5.833667 TCTGAATGAGTTGATACCGACCTAT 59.166 40.000 0.00 0.00 0.00 2.57
4794 5403 6.016192 TCTGAATGAGTTGATACCGACCTATC 60.016 42.308 0.00 0.00 0.00 2.08
4795 5404 5.833667 TGAATGAGTTGATACCGACCTATCT 59.166 40.000 0.00 0.00 0.00 1.98
4796 5405 7.002276 TGAATGAGTTGATACCGACCTATCTA 58.998 38.462 0.00 0.00 0.00 1.98
4797 5406 7.670140 TGAATGAGTTGATACCGACCTATCTAT 59.330 37.037 0.00 0.00 0.00 1.98
4798 5407 6.819397 TGAGTTGATACCGACCTATCTATG 57.181 41.667 0.00 0.00 0.00 2.23
4799 5408 6.540083 TGAGTTGATACCGACCTATCTATGA 58.460 40.000 0.00 0.00 0.00 2.15
4800 5409 7.175797 TGAGTTGATACCGACCTATCTATGAT 58.824 38.462 0.00 0.00 0.00 2.45
4801 5410 7.670140 TGAGTTGATACCGACCTATCTATGATT 59.330 37.037 0.00 0.00 0.00 2.57
4802 5411 8.423906 AGTTGATACCGACCTATCTATGATTT 57.576 34.615 0.00 0.00 0.00 2.17
4803 5412 8.307483 AGTTGATACCGACCTATCTATGATTTG 58.693 37.037 0.00 0.00 0.00 2.32
4804 5413 8.304596 GTTGATACCGACCTATCTATGATTTGA 58.695 37.037 0.00 0.00 0.00 2.69
4805 5414 8.417273 TGATACCGACCTATCTATGATTTGAA 57.583 34.615 0.00 0.00 0.00 2.69
4806 5415 8.866093 TGATACCGACCTATCTATGATTTGAAA 58.134 33.333 0.00 0.00 0.00 2.69
4807 5416 9.360093 GATACCGACCTATCTATGATTTGAAAG 57.640 37.037 0.00 0.00 0.00 2.62
4808 5417 6.525629 ACCGACCTATCTATGATTTGAAAGG 58.474 40.000 0.00 0.00 0.00 3.11
4809 5418 6.326583 ACCGACCTATCTATGATTTGAAAGGA 59.673 38.462 0.00 0.00 0.00 3.36
4810 5419 6.870965 CCGACCTATCTATGATTTGAAAGGAG 59.129 42.308 0.00 0.00 0.00 3.69
4811 5420 7.255977 CCGACCTATCTATGATTTGAAAGGAGA 60.256 40.741 0.00 0.00 0.00 3.71
4812 5421 7.812191 CGACCTATCTATGATTTGAAAGGAGAG 59.188 40.741 0.00 0.00 0.00 3.20
4813 5422 8.560124 ACCTATCTATGATTTGAAAGGAGAGT 57.440 34.615 0.00 0.00 0.00 3.24
4814 5423 8.428063 ACCTATCTATGATTTGAAAGGAGAGTG 58.572 37.037 0.00 0.00 0.00 3.51
4815 5424 7.877097 CCTATCTATGATTTGAAAGGAGAGTGG 59.123 40.741 0.00 0.00 0.00 4.00
4816 5425 6.874278 TCTATGATTTGAAAGGAGAGTGGA 57.126 37.500 0.00 0.00 0.00 4.02
4817 5426 7.443302 TCTATGATTTGAAAGGAGAGTGGAT 57.557 36.000 0.00 0.00 0.00 3.41
4818 5427 8.553085 TCTATGATTTGAAAGGAGAGTGGATA 57.447 34.615 0.00 0.00 0.00 2.59
4819 5428 8.646004 TCTATGATTTGAAAGGAGAGTGGATAG 58.354 37.037 0.00 0.00 0.00 2.08
4820 5429 6.627087 TGATTTGAAAGGAGAGTGGATAGT 57.373 37.500 0.00 0.00 0.00 2.12
4821 5430 6.644347 TGATTTGAAAGGAGAGTGGATAGTC 58.356 40.000 0.00 0.00 0.00 2.59
4822 5431 6.441924 TGATTTGAAAGGAGAGTGGATAGTCT 59.558 38.462 0.00 0.00 39.31 3.24
4823 5432 5.667539 TTGAAAGGAGAGTGGATAGTCTG 57.332 43.478 0.00 0.00 36.73 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.269703 ACCAAGGGTCGGGATACACC 61.270 60.000 0.00 0.00 39.74 4.16
26 27 0.042131 ACTCACCAAGGGTCGGGATA 59.958 55.000 0.00 0.00 31.02 2.59
33 34 6.311735 ACACATATAAAAACTCACCAAGGGT 58.688 36.000 0.00 0.00 35.62 4.34
90 101 2.737376 GCCGCCGTCTCGTCTTTT 60.737 61.111 0.00 0.00 0.00 2.27
91 102 3.296709 ATGCCGCCGTCTCGTCTTT 62.297 57.895 0.00 0.00 0.00 2.52
108 119 4.656112 ACGTTATTCCATCTTCAGGGAGAT 59.344 41.667 0.00 0.00 36.84 2.75
146 157 2.837031 GATGCACCACCGGAATGGGT 62.837 60.000 9.46 7.30 44.81 4.51
189 200 1.955080 AGATCCGTCGAAGATACACCC 59.045 52.381 0.00 0.00 40.67 4.61
199 210 1.067846 CACCAAAGACAGATCCGTCGA 60.068 52.381 3.44 0.00 40.98 4.20
228 239 3.713288 AGACGAACAACGAACTGATTCA 58.287 40.909 0.00 0.00 45.77 2.57
241 252 0.742505 ACACACGAAGGAGACGAACA 59.257 50.000 0.00 0.00 34.70 3.18
288 301 0.309922 TCGCCGCCGATAAAGAGTAG 59.690 55.000 0.00 0.00 38.82 2.57
307 320 3.815401 GACCAGCACACTAGAACAACAAT 59.185 43.478 0.00 0.00 0.00 2.71
318 331 1.794714 CCCTATAGGACCAGCACACT 58.205 55.000 21.07 0.00 38.24 3.55
339 352 2.097056 GTCGGAAAGTTGTCGTGCTAAC 60.097 50.000 0.00 0.00 0.00 2.34
350 363 2.299297 CCTAGTGGACAGTCGGAAAGTT 59.701 50.000 0.00 0.00 34.57 2.66
411 425 1.153168 CGAACCGAAGATGCCCCAT 60.153 57.895 0.00 0.00 0.00 4.00
549 563 5.804639 AGGGTGGGCTTAAAATTGAATTTC 58.195 37.500 3.32 0.00 0.00 2.17
553 567 4.126520 AGAGGGTGGGCTTAAAATTGAA 57.873 40.909 0.00 0.00 0.00 2.69
582 596 1.002624 TGTTCTTGGTCCATCGGCC 60.003 57.895 0.00 0.00 0.00 6.13
583 597 1.635663 CGTGTTCTTGGTCCATCGGC 61.636 60.000 0.00 0.00 0.00 5.54
605 648 2.417379 CCTACCTGTCAGTCGATTGTGG 60.417 54.545 7.87 10.82 0.00 4.17
713 761 2.291465 GCATGCACAGACAGTTCAAAGA 59.709 45.455 14.21 0.00 0.00 2.52
726 774 0.036483 ACGAGTGGTATGCATGCACA 60.036 50.000 25.37 9.23 0.00 4.57
738 786 2.353607 GCGCGATAGGACGAGTGG 60.354 66.667 12.10 0.00 35.70 4.00
740 788 1.167155 AGATGCGCGATAGGACGAGT 61.167 55.000 12.10 0.00 35.70 4.18
799 847 3.844858 TTGCTGTGGTTGCGCATGC 62.845 57.895 12.75 7.91 43.20 4.06
801 849 2.195567 AGTTGCTGTGGTTGCGCAT 61.196 52.632 12.75 0.00 33.15 4.73
802 850 2.828095 AGTTGCTGTGGTTGCGCA 60.828 55.556 5.66 5.66 0.00 6.09
803 851 2.353839 CAGTTGCTGTGGTTGCGC 60.354 61.111 0.00 0.00 0.00 6.09
805 853 2.028043 GGCAGTTGCTGTGGTTGC 59.972 61.111 3.88 0.00 41.70 4.17
807 855 0.178981 AGATGGCAGTTGCTGTGGTT 60.179 50.000 3.88 0.00 41.70 3.67
808 856 0.607489 GAGATGGCAGTTGCTGTGGT 60.607 55.000 3.88 0.00 41.70 4.16
811 859 0.982704 AGAGAGATGGCAGTTGCTGT 59.017 50.000 3.88 0.00 41.70 4.40
812 860 1.338864 ACAGAGAGATGGCAGTTGCTG 60.339 52.381 3.88 0.00 41.70 4.41
813 861 0.982704 ACAGAGAGATGGCAGTTGCT 59.017 50.000 3.88 0.00 41.70 3.91
819 871 4.824479 TTATTGTCACAGAGAGATGGCA 57.176 40.909 0.00 0.00 0.00 4.92
829 881 4.728882 GCGAGCAAGGATTTATTGTCACAG 60.729 45.833 0.00 0.00 0.00 3.66
830 882 3.126858 GCGAGCAAGGATTTATTGTCACA 59.873 43.478 0.00 0.00 0.00 3.58
831 883 3.375299 AGCGAGCAAGGATTTATTGTCAC 59.625 43.478 0.00 0.00 0.00 3.67
940 992 0.040499 AGGCCTTCTTCTCTCGGACT 59.960 55.000 0.00 0.00 0.00 3.85
946 998 3.052186 ACTGGATCTAGGCCTTCTTCTCT 60.052 47.826 12.58 0.00 0.00 3.10
967 1019 4.137543 CAGAATTATTCCACCTAGGCCAC 58.862 47.826 9.30 0.00 37.29 5.01
1015 1070 0.482446 ATGTCTGGCTTGGAACCCAA 59.518 50.000 0.00 0.00 41.69 4.12
1047 1102 0.178990 GGGATAACCATGTGAGGCCC 60.179 60.000 0.00 0.00 39.85 5.80
1092 1157 3.226777 ACCGAGGGAGATGAGTAATCAG 58.773 50.000 0.00 0.00 37.81 2.90
1102 1167 4.576330 AGAAAAATCAACCGAGGGAGAT 57.424 40.909 0.00 0.00 0.00 2.75
1151 1217 7.262048 GTTTGGTCAAACCTTGAGAACAATTA 58.738 34.615 13.81 0.00 43.52 1.40
1173 1239 8.635765 AGATTCACATGTACCAAACTATGTTT 57.364 30.769 0.00 0.00 31.59 2.83
1179 1245 6.772716 ACAGAAAGATTCACATGTACCAAACT 59.227 34.615 0.00 0.00 0.00 2.66
1203 1269 2.200373 ATGGAACCAGTTGTGCCTAC 57.800 50.000 0.00 0.00 44.13 3.18
1238 1304 8.645110 TCTTTGAACTGAGCATGATGATATAGA 58.355 33.333 0.00 0.00 0.00 1.98
1271 1351 8.390921 ACTATGAGGGAAGGTGAAAAATAGAAA 58.609 33.333 0.00 0.00 0.00 2.52
1274 1354 8.581253 AAACTATGAGGGAAGGTGAAAAATAG 57.419 34.615 0.00 0.00 0.00 1.73
1276 1356 7.010160 TGAAACTATGAGGGAAGGTGAAAAAT 58.990 34.615 0.00 0.00 0.00 1.82
1277 1357 6.369629 TGAAACTATGAGGGAAGGTGAAAAA 58.630 36.000 0.00 0.00 0.00 1.94
1284 1364 4.019321 TGGTCTTGAAACTATGAGGGAAGG 60.019 45.833 0.00 0.00 0.00 3.46
1288 1368 6.240549 ACTATGGTCTTGAAACTATGAGGG 57.759 41.667 0.00 0.00 0.00 4.30
1295 1376 5.765182 CAGTGGAAACTATGGTCTTGAAACT 59.235 40.000 0.00 0.00 0.00 2.66
1296 1377 5.531287 ACAGTGGAAACTATGGTCTTGAAAC 59.469 40.000 0.00 0.00 0.00 2.78
1300 1381 6.464222 TCTAACAGTGGAAACTATGGTCTTG 58.536 40.000 0.00 0.00 0.00 3.02
1305 1386 5.422331 TCTCCTCTAACAGTGGAAACTATGG 59.578 44.000 0.00 0.00 37.43 2.74
1330 1411 3.181454 GGAGAGGAGGAGTGTTTTTGTCA 60.181 47.826 0.00 0.00 0.00 3.58
1347 1428 1.112315 AGCCGCCTAGACATGGAGAG 61.112 60.000 0.00 0.00 0.00 3.20
1368 1449 6.478016 CACAATCGATATCCGCATCTCATATT 59.522 38.462 0.00 0.00 38.37 1.28
1371 1452 4.179298 CACAATCGATATCCGCATCTCAT 58.821 43.478 0.00 0.00 38.37 2.90
1375 1456 2.068519 TGCACAATCGATATCCGCATC 58.931 47.619 0.00 0.00 38.37 3.91
1420 1501 3.057315 ACTTGATTCGCCAATGGAACTTG 60.057 43.478 2.05 0.00 0.00 3.16
1544 2055 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
1633 2153 8.816894 TCTTAGAAACCATGACTGAGAAGTATT 58.183 33.333 0.00 0.00 0.00 1.89
1647 2167 3.448686 CGCTCGTGATCTTAGAAACCAT 58.551 45.455 0.00 0.00 0.00 3.55
1649 2169 1.588861 GCGCTCGTGATCTTAGAAACC 59.411 52.381 0.00 0.00 0.00 3.27
1655 2175 1.065764 ATGCGCGCTCGTGATCTTA 59.934 52.632 33.29 7.91 38.14 2.10
1668 2188 3.425577 TCTCATCAAATTTCCATGCGC 57.574 42.857 0.00 0.00 0.00 6.09
1692 2218 4.161377 TGGATGGATCACGTAAACATCTGA 59.839 41.667 16.21 0.00 38.33 3.27
1719 2245 1.412343 GCATCTCCTGGAGAAGAGTCC 59.588 57.143 28.84 9.19 42.27 3.85
1724 2250 2.485124 GGTCATGCATCTCCTGGAGAAG 60.485 54.545 28.84 24.97 42.27 2.85
1728 2255 0.687427 TCGGTCATGCATCTCCTGGA 60.687 55.000 0.00 0.00 0.00 3.86
1775 2302 4.372656 GGAGATAAAAGGACATGTCTCCG 58.627 47.826 24.50 0.00 41.44 4.63
1847 2374 4.880759 TCGGTTTTATACGGTTCAGTTGA 58.119 39.130 0.00 0.00 0.00 3.18
1857 2384 3.707179 CGCAATCGATCGGTTTTATACG 58.293 45.455 11.76 6.84 38.10 3.06
1859 2386 2.154198 CGCGCAATCGATCGGTTTTATA 59.846 45.455 11.76 0.00 38.10 0.98
1861 2388 0.299300 CGCGCAATCGATCGGTTTTA 59.701 50.000 11.76 0.00 38.10 1.52
1865 2392 3.254654 CACGCGCAATCGATCGGT 61.255 61.111 16.41 4.70 38.10 4.69
1866 2393 1.476235 TAACACGCGCAATCGATCGG 61.476 55.000 16.41 0.00 38.10 4.18
1881 2409 5.411361 GCACCATTAGTCAGTCACATTAACA 59.589 40.000 0.00 0.00 0.00 2.41
1894 2422 2.203800 TGATCGACGCACCATTAGTC 57.796 50.000 0.00 0.00 0.00 2.59
1906 2434 4.805719 TGCATACTCAGAATGTTGATCGAC 59.194 41.667 6.11 6.11 37.40 4.20
1913 2441 4.265073 GGGAACTGCATACTCAGAATGTT 58.735 43.478 0.00 0.00 37.51 2.71
1914 2442 3.679917 CGGGAACTGCATACTCAGAATGT 60.680 47.826 0.00 0.00 37.51 2.71
2137 2671 1.830145 GTCCGTCATGCCCAGGTAT 59.170 57.895 0.00 0.00 0.00 2.73
2488 3028 1.675310 CAGCCGCTTGAACATGGGA 60.675 57.895 0.00 0.00 0.00 4.37
2515 3055 1.453762 GCATGCTCTTGGCCTCCATC 61.454 60.000 11.37 0.00 40.92 3.51
2740 3283 1.172180 CCTTTTTGGTCGGCAGCAGA 61.172 55.000 0.00 0.00 0.00 4.26
2755 3298 1.303317 GGTGGATGTGACGCCCTTT 60.303 57.895 0.00 0.00 32.38 3.11
2767 3310 0.036010 CGAGCAGGAACTTGGTGGAT 60.036 55.000 0.00 0.00 34.60 3.41
3143 3686 2.747855 GAGCGCCTGGAACTTGGG 60.748 66.667 2.29 0.00 0.00 4.12
3235 3778 4.403453 GTGTTTGTCACTTGTCAGTTGTC 58.597 43.478 0.00 0.00 43.13 3.18
3241 3784 0.730265 GCCGTGTTTGTCACTTGTCA 59.270 50.000 0.00 0.00 44.16 3.58
3242 3785 0.315869 CGCCGTGTTTGTCACTTGTC 60.316 55.000 0.00 0.00 44.16 3.18
3243 3786 0.741574 TCGCCGTGTTTGTCACTTGT 60.742 50.000 0.00 0.00 44.16 3.16
3244 3787 0.586319 ATCGCCGTGTTTGTCACTTG 59.414 50.000 0.00 0.00 44.16 3.16
3245 3788 0.865769 GATCGCCGTGTTTGTCACTT 59.134 50.000 0.00 0.00 44.16 3.16
3247 3790 1.129809 CGATCGCCGTGTTTGTCAC 59.870 57.895 0.26 0.00 43.03 3.67
3248 3791 2.024868 CCGATCGCCGTGTTTGTCA 61.025 57.895 10.32 0.00 36.31 3.58
3253 3796 0.672401 ATCAAACCGATCGCCGTGTT 60.672 50.000 10.32 5.59 34.66 3.32
3255 3798 1.348250 CATCAAACCGATCGCCGTG 59.652 57.895 10.32 6.70 36.31 4.94
3256 3799 2.461110 GCATCAAACCGATCGCCGT 61.461 57.895 10.32 0.00 36.31 5.68
3258 3801 2.324477 CGCATCAAACCGATCGCC 59.676 61.111 10.32 0.00 29.21 5.54
3260 3803 0.298707 CTGACGCATCAAACCGATCG 59.701 55.000 8.51 8.51 33.30 3.69
3261 3804 1.061131 CACTGACGCATCAAACCGATC 59.939 52.381 0.00 0.00 33.30 3.69
3262 3805 1.078709 CACTGACGCATCAAACCGAT 58.921 50.000 0.00 0.00 33.30 4.18
3264 3807 0.586319 AACACTGACGCATCAAACCG 59.414 50.000 0.00 0.00 33.30 4.44
3265 3808 1.925946 GCAACACTGACGCATCAAACC 60.926 52.381 0.00 0.00 33.30 3.27
3266 3809 1.002468 AGCAACACTGACGCATCAAAC 60.002 47.619 0.00 0.00 33.30 2.93
3267 3810 1.308047 AGCAACACTGACGCATCAAA 58.692 45.000 0.00 0.00 33.30 2.69
3268 3811 2.162319 TAGCAACACTGACGCATCAA 57.838 45.000 0.00 0.00 33.30 2.57
3269 3812 1.798223 GTTAGCAACACTGACGCATCA 59.202 47.619 0.00 0.00 0.00 3.07
3270 3813 1.798223 TGTTAGCAACACTGACGCATC 59.202 47.619 0.00 0.00 37.70 3.91
3271 3814 1.877637 TGTTAGCAACACTGACGCAT 58.122 45.000 0.00 0.00 37.70 4.73
3272 3815 1.798223 GATGTTAGCAACACTGACGCA 59.202 47.619 4.23 0.00 45.50 5.24
3275 3818 4.310769 ACTCAGATGTTAGCAACACTGAC 58.689 43.478 18.41 8.33 45.50 3.51
3277 3820 4.612259 GCAACTCAGATGTTAGCAACACTG 60.612 45.833 16.15 16.15 45.50 3.66
3278 3821 3.499918 GCAACTCAGATGTTAGCAACACT 59.500 43.478 4.23 2.60 45.50 3.55
3279 3822 3.665323 CGCAACTCAGATGTTAGCAACAC 60.665 47.826 4.23 0.78 45.50 3.32
3280 3823 2.480037 CGCAACTCAGATGTTAGCAACA 59.520 45.455 4.56 4.56 46.94 3.33
3281 3824 2.480419 ACGCAACTCAGATGTTAGCAAC 59.520 45.455 0.00 0.00 0.00 4.17
3282 3825 2.480037 CACGCAACTCAGATGTTAGCAA 59.520 45.455 0.00 0.00 0.00 3.91
3283 3826 2.068519 CACGCAACTCAGATGTTAGCA 58.931 47.619 0.00 0.00 0.00 3.49
3284 3827 1.201965 GCACGCAACTCAGATGTTAGC 60.202 52.381 0.00 0.00 0.00 3.09
3285 3828 2.068519 TGCACGCAACTCAGATGTTAG 58.931 47.619 0.00 0.00 0.00 2.34
3292 3853 1.154282 CTGCATGCACGCAACTCAG 60.154 57.895 18.46 0.00 42.45 3.35
3318 3879 4.778415 CCGACTCCGACAGCCACG 62.778 72.222 0.00 0.00 38.22 4.94
3319 3880 3.343788 CTCCGACTCCGACAGCCAC 62.344 68.421 0.00 0.00 38.22 5.01
3701 4262 2.224572 GGATCTCCTGCTTCATGCTCAT 60.225 50.000 0.00 0.00 43.37 2.90
3863 4424 5.642919 AGACGAATCTACTAACTCTGTCGTT 59.357 40.000 0.00 0.00 40.27 3.85
3867 4428 4.883006 GGGAGACGAATCTACTAACTCTGT 59.117 45.833 0.00 0.00 35.87 3.41
3876 4437 6.927294 AATGAAAATGGGAGACGAATCTAC 57.073 37.500 0.00 0.00 34.34 2.59
3964 4527 1.654954 CCCATGCAGAGCTGAAGCAC 61.655 60.000 4.90 0.00 45.16 4.40
4028 4592 1.000607 AGCTTGCTTGCAATGTCACTG 60.001 47.619 8.55 0.00 34.99 3.66
4164 4728 9.982291 GAGAATACTTGTAGCTATAGATCTTCG 57.018 37.037 0.00 0.00 0.00 3.79
4182 4746 3.953612 CTGTCTGGCTGAGAGAGAATACT 59.046 47.826 12.39 0.00 43.51 2.12
4200 4764 0.173481 TATCTCTGTGCGTGGCTGTC 59.827 55.000 0.00 0.00 0.00 3.51
4201 4765 0.826715 ATATCTCTGTGCGTGGCTGT 59.173 50.000 0.00 0.00 0.00 4.40
4202 4766 1.215244 CATATCTCTGTGCGTGGCTG 58.785 55.000 0.00 0.00 0.00 4.85
4203 4767 0.826715 ACATATCTCTGTGCGTGGCT 59.173 50.000 0.00 0.00 0.00 4.75
4204 4768 2.509052 TACATATCTCTGTGCGTGGC 57.491 50.000 0.00 0.00 0.00 5.01
4205 4769 4.380973 CCCTATACATATCTCTGTGCGTGG 60.381 50.000 0.00 0.00 0.00 4.94
4206 4770 4.459337 TCCCTATACATATCTCTGTGCGTG 59.541 45.833 0.00 0.00 0.00 5.34
4207 4771 4.663334 TCCCTATACATATCTCTGTGCGT 58.337 43.478 0.00 0.00 0.00 5.24
4208 4772 5.126222 ACATCCCTATACATATCTCTGTGCG 59.874 44.000 0.00 0.00 0.00 5.34
4209 4773 6.537453 ACATCCCTATACATATCTCTGTGC 57.463 41.667 0.00 0.00 0.00 4.57
4210 4774 8.581253 TGTACATCCCTATACATATCTCTGTG 57.419 38.462 0.00 0.00 0.00 3.66
4211 4775 9.601810 TTTGTACATCCCTATACATATCTCTGT 57.398 33.333 0.00 0.00 31.55 3.41
4287 4851 1.944024 CTTCTGATAGAGCGGTCTCGT 59.056 52.381 22.33 11.37 44.02 4.18
4436 5000 2.806745 CGTGCCTTCTGTTTCCTTCTCA 60.807 50.000 0.00 0.00 0.00 3.27
4438 5002 1.543429 CCGTGCCTTCTGTTTCCTTCT 60.543 52.381 0.00 0.00 0.00 2.85
4539 5103 8.773033 ACATTTTCTCCTGGCAGATATTTTAT 57.227 30.769 17.94 0.00 0.00 1.40
4614 5221 1.003003 TGGGTGTTCGATGAAGCATCA 59.997 47.619 8.02 0.00 40.54 3.07
4626 5233 0.315251 GGCTGCTTTTCTGGGTGTTC 59.685 55.000 0.00 0.00 0.00 3.18
4666 5275 3.359695 TGTGGGGGTAAGTATTTCTGC 57.640 47.619 0.00 0.00 0.00 4.26
4695 5304 2.009774 GCAATTGACGTCATAGGCAGT 58.990 47.619 20.80 0.00 0.00 4.40
4716 5325 2.429250 GTGTTACAGTGGGTTTTTGCCT 59.571 45.455 0.00 0.00 0.00 4.75
4749 5358 7.187824 TCAGATTATCTAACTTTGCCTGTCT 57.812 36.000 0.00 0.00 0.00 3.41
4770 5379 4.392921 AGGTCGGTATCAACTCATTCAG 57.607 45.455 0.00 0.00 0.00 3.02
4782 5391 8.314751 CCTTTCAAATCATAGATAGGTCGGTAT 58.685 37.037 0.00 0.00 31.03 2.73
4783 5392 7.507956 TCCTTTCAAATCATAGATAGGTCGGTA 59.492 37.037 0.00 0.00 35.36 4.02
4784 5393 6.326583 TCCTTTCAAATCATAGATAGGTCGGT 59.673 38.462 0.00 0.00 35.36 4.69
4785 5394 6.759272 TCCTTTCAAATCATAGATAGGTCGG 58.241 40.000 0.00 0.00 35.36 4.79
4786 5395 7.661968 TCTCCTTTCAAATCATAGATAGGTCG 58.338 38.462 0.00 0.00 35.36 4.79
4787 5396 8.646900 ACTCTCCTTTCAAATCATAGATAGGTC 58.353 37.037 0.00 0.00 35.36 3.85
4788 5397 8.428063 CACTCTCCTTTCAAATCATAGATAGGT 58.572 37.037 0.00 0.00 35.36 3.08
4789 5398 7.877097 CCACTCTCCTTTCAAATCATAGATAGG 59.123 40.741 0.00 0.00 35.20 2.57
4790 5399 8.646004 TCCACTCTCCTTTCAAATCATAGATAG 58.354 37.037 0.00 0.00 0.00 2.08
4791 5400 8.553085 TCCACTCTCCTTTCAAATCATAGATA 57.447 34.615 0.00 0.00 0.00 1.98
4792 5401 7.443302 TCCACTCTCCTTTCAAATCATAGAT 57.557 36.000 0.00 0.00 0.00 1.98
4793 5402 6.874278 TCCACTCTCCTTTCAAATCATAGA 57.126 37.500 0.00 0.00 0.00 1.98
4794 5403 8.428063 ACTATCCACTCTCCTTTCAAATCATAG 58.572 37.037 0.00 0.00 0.00 2.23
4795 5404 8.324191 ACTATCCACTCTCCTTTCAAATCATA 57.676 34.615 0.00 0.00 0.00 2.15
4796 5405 7.127032 AGACTATCCACTCTCCTTTCAAATCAT 59.873 37.037 0.00 0.00 0.00 2.45
4797 5406 6.441924 AGACTATCCACTCTCCTTTCAAATCA 59.558 38.462 0.00 0.00 0.00 2.57
4798 5407 6.760770 CAGACTATCCACTCTCCTTTCAAATC 59.239 42.308 0.00 0.00 0.00 2.17
4799 5408 6.648192 CAGACTATCCACTCTCCTTTCAAAT 58.352 40.000 0.00 0.00 0.00 2.32
4800 5409 6.042638 CAGACTATCCACTCTCCTTTCAAA 57.957 41.667 0.00 0.00 0.00 2.69
4801 5410 5.667539 CAGACTATCCACTCTCCTTTCAA 57.332 43.478 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.