Multiple sequence alignment - TraesCS4A01G137200

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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 TraesCS4A01G137200 chr4A 100.000 3898 0 0 1 3898 196570432 196574329 0.000000e+00 7199.0
1 TraesCS4A01G137200 chr4D 92.454 1524 66 17 1783 3276 295434013 295432509 0.000000e+00 2132.0
2 TraesCS4A01G137200 chr4D 91.774 936 46 10 856 1791 295435084 295434180 0.000000e+00 1273.0
3 TraesCS4A01G137200 chr4D 86.682 871 109 7 1 868 446172826 446173692 0.000000e+00 959.0
4 TraesCS4A01G137200 chr4D 80.882 272 20 9 3275 3528 295432385 295432128 6.650000e-43 185.0
5 TraesCS4A01G137200 chr4B 85.412 1275 78 41 2556 3772 364182627 364183851 0.000000e+00 1225.0
6 TraesCS4A01G137200 chr4B 88.608 869 95 4 1 867 17486138 17487004 0.000000e+00 1053.0
7 TraesCS4A01G137200 chr4B 93.034 646 44 1 1626 2271 364163358 364164002 0.000000e+00 942.0
8 TraesCS4A01G137200 chr4B 94.583 240 13 0 868 1107 364151843 364152082 4.760000e-99 372.0
9 TraesCS4A01G137200 chr4B 90.000 260 20 4 1263 1518 364152077 364152334 8.070000e-87 331.0
10 TraesCS4A01G137200 chr4B 91.667 228 7 1 2267 2482 364165396 364165623 4.890000e-79 305.0
11 TraesCS4A01G137200 chr4B 96.667 60 1 1 2503 2561 364165615 364165674 8.910000e-17 99.0
12 TraesCS4A01G137200 chr5B 87.933 837 98 3 1 835 697677447 697676612 0.000000e+00 983.0
13 TraesCS4A01G137200 chr5B 88.029 827 89 9 46 867 459582634 459581813 0.000000e+00 970.0
14 TraesCS4A01G137200 chr5B 100.000 28 0 0 2079 2106 697609401 697609428 7.000000e-03 52.8
15 TraesCS4A01G137200 chr5D 87.666 827 84 11 43 866 535499715 535498904 0.000000e+00 946.0
16 TraesCS4A01G137200 chr5D 84.361 876 130 7 1 872 35807643 35806771 0.000000e+00 852.0
17 TraesCS4A01G137200 chr6B 86.207 870 114 6 1 866 617164792 617165659 0.000000e+00 937.0
18 TraesCS4A01G137200 chr6B 85.749 835 112 5 1 834 457871752 457872580 0.000000e+00 876.0
19 TraesCS4A01G137200 chr6B 80.941 871 155 10 1 867 562491351 562490488 0.000000e+00 678.0
20 TraesCS4A01G137200 chr6B 93.902 82 5 0 1009 1090 714702028 714701947 1.470000e-24 124.0
21 TraesCS4A01G137200 chr2D 84.356 326 31 4 2241 2554 60753375 60753692 6.330000e-78 302.0
22 TraesCS4A01G137200 chr2D 83.133 332 36 4 2241 2560 44087660 44087337 6.370000e-73 285.0
23 TraesCS4A01G137200 chr2D 93.893 131 7 1 984 1114 60751808 60751937 3.070000e-46 196.0
24 TraesCS4A01G137200 chr2D 92.029 138 10 1 984 1121 44089186 44089050 3.970000e-45 193.0
25 TraesCS4A01G137200 chr2D 94.737 38 0 1 2077 2112 325832455 325832418 1.510000e-04 58.4
26 TraesCS4A01G137200 chr2A 84.049 326 32 4 2241 2554 61286807 61287124 2.940000e-76 296.0
27 TraesCS4A01G137200 chr2A 83.133 332 36 4 2241 2560 47918600 47918277 6.370000e-73 285.0
28 TraesCS4A01G137200 chr2A 92.754 138 9 1 984 1121 47919650 47919514 8.540000e-47 198.0
29 TraesCS4A01G137200 chr2A 92.143 140 10 1 975 1114 61285258 61285396 3.070000e-46 196.0
30 TraesCS4A01G137200 chr2A 95.122 41 2 0 1083 1123 62918908 62918948 9.040000e-07 65.8
31 TraesCS4A01G137200 chr2B 82.831 332 37 4 2241 2560 69500956 69500633 2.970000e-71 279.0
32 TraesCS4A01G137200 chr2B 90.062 161 13 3 984 1142 69502453 69502294 5.110000e-49 206.0
33 TraesCS4A01G137200 chr2B 91.429 140 11 1 975 1114 94925509 94925647 1.430000e-44 191.0
34 TraesCS4A01G137200 chr2B 92.105 38 1 2 2077 2112 373484906 373484869 7.000000e-03 52.8
35 TraesCS4A01G137200 chr6D 100.000 28 0 0 2079 2106 139567518 139567491 7.000000e-03 52.8


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 TraesCS4A01G137200 chr4A 196570432 196574329 3897 False 7199.000000 7199 100.000000 1 3898 1 chr4A.!!$F1 3897
1 TraesCS4A01G137200 chr4D 295432128 295435084 2956 True 1196.666667 2132 88.370000 856 3528 3 chr4D.!!$R1 2672
2 TraesCS4A01G137200 chr4D 446172826 446173692 866 False 959.000000 959 86.682000 1 868 1 chr4D.!!$F1 867
3 TraesCS4A01G137200 chr4B 364182627 364183851 1224 False 1225.000000 1225 85.412000 2556 3772 1 chr4B.!!$F2 1216
4 TraesCS4A01G137200 chr4B 17486138 17487004 866 False 1053.000000 1053 88.608000 1 867 1 chr4B.!!$F1 866
5 TraesCS4A01G137200 chr4B 364163358 364165674 2316 False 448.666667 942 93.789333 1626 2561 3 chr4B.!!$F4 935
6 TraesCS4A01G137200 chr5B 697676612 697677447 835 True 983.000000 983 87.933000 1 835 1 chr5B.!!$R2 834
7 TraesCS4A01G137200 chr5B 459581813 459582634 821 True 970.000000 970 88.029000 46 867 1 chr5B.!!$R1 821
8 TraesCS4A01G137200 chr5D 535498904 535499715 811 True 946.000000 946 87.666000 43 866 1 chr5D.!!$R2 823
9 TraesCS4A01G137200 chr5D 35806771 35807643 872 True 852.000000 852 84.361000 1 872 1 chr5D.!!$R1 871
10 TraesCS4A01G137200 chr6B 617164792 617165659 867 False 937.000000 937 86.207000 1 866 1 chr6B.!!$F2 865
11 TraesCS4A01G137200 chr6B 457871752 457872580 828 False 876.000000 876 85.749000 1 834 1 chr6B.!!$F1 833
12 TraesCS4A01G137200 chr6B 562490488 562491351 863 True 678.000000 678 80.941000 1 867 1 chr6B.!!$R1 866
13 TraesCS4A01G137200 chr2D 60751808 60753692 1884 False 249.000000 302 89.124500 984 2554 2 chr2D.!!$F1 1570
14 TraesCS4A01G137200 chr2D 44087337 44089186 1849 True 239.000000 285 87.581000 984 2560 2 chr2D.!!$R2 1576
15 TraesCS4A01G137200 chr2A 61285258 61287124 1866 False 246.000000 296 88.096000 975 2554 2 chr2A.!!$F2 1579
16 TraesCS4A01G137200 chr2A 47918277 47919650 1373 True 241.500000 285 87.943500 984 2560 2 chr2A.!!$R1 1576
17 TraesCS4A01G137200 chr2B 69500633 69502453 1820 True 242.500000 279 86.446500 984 2560 2 chr2B.!!$R2 1576

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
346 349 0.807667 ATGAAGCACGAGTGATCCGC 60.808 55.000 7.5 0.0 0.00 5.54 F
1241 1422 1.135689 GCGATGTGGCTGTTCGAAAAT 60.136 47.619 0.0 0.0 34.92 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 1685 0.386113 GGATCTCCACTACGACAGGC 59.614 60.0 0.00 0.0 35.64 4.85 R
3114 5518 1.327303 GAGGAGGATCATCGCAGTCT 58.673 55.0 0.56 0.0 35.64 3.24 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
26 27 3.827898 GGAGCGGAGGAGGACACG 61.828 72.222 0.00 0.00 0.00 4.49
78 79 1.693606 CAAGATGGGTTTGGGCTTTGT 59.306 47.619 0.00 0.00 0.00 2.83
84 85 1.203013 GGGTTTGGGCTTTGTAGGACT 60.203 52.381 0.00 0.00 0.00 3.85
86 87 3.079578 GGTTTGGGCTTTGTAGGACTAC 58.920 50.000 2.57 2.57 36.63 2.73
177 178 6.826231 TGAGACAACAAATCAACAAGACCTAA 59.174 34.615 0.00 0.00 0.00 2.69
179 180 6.601613 AGACAACAAATCAACAAGACCTAACA 59.398 34.615 0.00 0.00 0.00 2.41
202 203 4.006989 CGAATTTTAGTGACCATGTGGGA 58.993 43.478 3.77 0.00 41.15 4.37
205 206 5.722021 ATTTTAGTGACCATGTGGGAAAC 57.278 39.130 3.77 0.00 41.15 2.78
248 249 5.919141 GGCTATGCATGAGAATGAATTTCAC 59.081 40.000 10.16 0.00 36.75 3.18
272 274 3.350833 CCTGCTTTCCACTATGAGCTTT 58.649 45.455 0.00 0.00 36.16 3.51
273 275 3.128242 CCTGCTTTCCACTATGAGCTTTG 59.872 47.826 0.00 0.00 36.16 2.77
295 298 6.808008 TGTAAAGAGATTTTTGAGGAGCTG 57.192 37.500 0.00 0.00 0.00 4.24
319 322 1.835494 TAGCTAACTCGCACAGACCT 58.165 50.000 0.00 0.00 0.00 3.85
346 349 0.807667 ATGAAGCACGAGTGATCCGC 60.808 55.000 7.50 0.00 0.00 5.54
351 354 3.066190 ACGAGTGATCCGCCGGAA 61.066 61.111 11.19 0.00 34.34 4.30
352 355 2.278857 CGAGTGATCCGCCGGAAG 60.279 66.667 11.19 0.00 34.34 3.46
423 428 1.373812 GGGCCTGTCAACGTTAGGT 59.626 57.895 15.32 0.00 34.06 3.08
440 445 3.286751 TGACAAAGGTGCAGCGGC 61.287 61.111 10.78 0.31 41.68 6.53
459 464 1.826327 CAGTTGTTTGCCGTGACAAG 58.174 50.000 0.00 0.00 36.52 3.16
462 467 1.917303 GTTGTTTGCCGTGACAAGTTG 59.083 47.619 0.00 0.00 36.52 3.16
491 496 4.920640 TTTTTGGGTATTTCAGCGTTGA 57.079 36.364 0.00 0.00 0.00 3.18
497 502 5.465935 TGGGTATTTCAGCGTTGATTTTTC 58.534 37.500 1.75 0.00 32.27 2.29
501 506 6.806249 GGTATTTCAGCGTTGATTTTTCATGA 59.194 34.615 1.75 0.00 32.27 3.07
561 566 1.306997 AAGCACTAGCCCTAGCCCA 60.307 57.895 2.31 0.00 43.56 5.36
640 645 4.253685 ACATCAAATCTACAGGTTCACCG 58.746 43.478 0.00 0.00 42.08 4.94
670 675 8.612486 ATGCTCATATCCTTAGAGAGATTCAT 57.388 34.615 0.00 0.00 0.00 2.57
717 722 8.601845 TCTGATGATTTTCGTTTTGAGAGTAA 57.398 30.769 0.00 0.00 0.00 2.24
719 724 9.663904 CTGATGATTTTCGTTTTGAGAGTAAAA 57.336 29.630 0.00 0.00 0.00 1.52
810 815 4.641989 GCTAGGAATTTTGCCAGAGATTGA 59.358 41.667 0.00 0.00 0.00 2.57
812 817 5.593679 AGGAATTTTGCCAGAGATTGATG 57.406 39.130 0.00 0.00 0.00 3.07
836 841 2.074547 TCCGGATGTCGTGAACTTTC 57.925 50.000 0.00 0.00 37.11 2.62
839 844 2.096417 CCGGATGTCGTGAACTTTCAAC 60.096 50.000 0.00 0.00 39.21 3.18
893 898 4.224991 ACTAAACTATAAAAGCCGCCCA 57.775 40.909 0.00 0.00 0.00 5.36
894 899 4.591929 ACTAAACTATAAAAGCCGCCCAA 58.408 39.130 0.00 0.00 0.00 4.12
915 920 4.426313 GCCCCTAGCGCAAACCCT 62.426 66.667 11.47 0.00 0.00 4.34
916 921 2.355115 CCCCTAGCGCAAACCCTT 59.645 61.111 11.47 0.00 0.00 3.95
917 922 2.046285 CCCCTAGCGCAAACCCTTG 61.046 63.158 11.47 0.00 35.49 3.61
954 959 2.516930 ACAGCCACACACCACAGC 60.517 61.111 0.00 0.00 0.00 4.40
1148 1322 3.069729 CCTTTCCCCTACCTCGTCTTATG 59.930 52.174 0.00 0.00 0.00 1.90
1149 1323 3.393426 TTCCCCTACCTCGTCTTATGT 57.607 47.619 0.00 0.00 0.00 2.29
1156 1330 5.319453 CCTACCTCGTCTTATGTGGGTATA 58.681 45.833 0.00 0.00 0.00 1.47
1241 1422 1.135689 GCGATGTGGCTGTTCGAAAAT 60.136 47.619 0.00 0.00 34.92 1.82
1246 1427 5.452302 CGATGTGGCTGTTCGAAAATTATTC 59.548 40.000 0.00 0.00 34.92 1.75
1296 1477 4.465632 TGTTATGGTAGCATGACGAGTT 57.534 40.909 20.66 0.00 0.00 3.01
1297 1478 4.827692 TGTTATGGTAGCATGACGAGTTT 58.172 39.130 20.66 0.00 0.00 2.66
1298 1479 4.629634 TGTTATGGTAGCATGACGAGTTTG 59.370 41.667 20.66 0.00 0.00 2.93
1299 1480 2.093306 TGGTAGCATGACGAGTTTGG 57.907 50.000 0.00 0.00 0.00 3.28
1300 1481 1.346395 TGGTAGCATGACGAGTTTGGT 59.654 47.619 0.00 0.00 0.00 3.67
1301 1482 1.732259 GGTAGCATGACGAGTTTGGTG 59.268 52.381 0.00 0.00 0.00 4.17
1302 1483 1.732259 GTAGCATGACGAGTTTGGTGG 59.268 52.381 0.00 0.00 0.00 4.61
1303 1484 1.210155 GCATGACGAGTTTGGTGGC 59.790 57.895 0.00 0.00 0.00 5.01
1305 1486 1.238439 CATGACGAGTTTGGTGGCTT 58.762 50.000 0.00 0.00 0.00 4.35
1306 1487 1.608590 CATGACGAGTTTGGTGGCTTT 59.391 47.619 0.00 0.00 0.00 3.51
1312 1493 2.351738 CGAGTTTGGTGGCTTTTGATCC 60.352 50.000 0.00 0.00 0.00 3.36
1317 1498 1.212751 GTGGCTTTTGATCCGTGGC 59.787 57.895 0.00 0.00 0.00 5.01
1334 1515 3.347216 GTGGCTTAGTTGTGGTGATGAT 58.653 45.455 0.00 0.00 0.00 2.45
1335 1516 3.127548 GTGGCTTAGTTGTGGTGATGATG 59.872 47.826 0.00 0.00 0.00 3.07
1336 1517 2.684881 GGCTTAGTTGTGGTGATGATGG 59.315 50.000 0.00 0.00 0.00 3.51
1347 1528 2.846371 GATGATGGGTAGCATCGGC 58.154 57.895 0.00 0.00 39.61 5.54
1383 1564 6.353323 TGGATTGTCTTCGATTAATTAGGCA 58.647 36.000 0.00 0.00 0.00 4.75
1499 1680 7.718314 TCCGTAGTATATGTAGCCTATACATGG 59.282 40.741 10.09 2.52 38.47 3.66
1500 1681 7.501559 CCGTAGTATATGTAGCCTATACATGGT 59.498 40.741 10.09 3.01 38.47 3.55
1501 1682 8.557864 CGTAGTATATGTAGCCTATACATGGTC 58.442 40.741 10.09 2.07 38.47 4.02
1504 1685 8.972127 AGTATATGTAGCCTATACATGGTCTTG 58.028 37.037 10.09 0.00 38.47 3.02
1506 1687 2.938956 AGCCTATACATGGTCTTGCC 57.061 50.000 0.00 0.00 37.90 4.52
1507 1688 2.412591 AGCCTATACATGGTCTTGCCT 58.587 47.619 0.00 0.00 38.35 4.75
1508 1689 2.105477 AGCCTATACATGGTCTTGCCTG 59.895 50.000 0.00 0.00 38.35 4.85
1567 1748 3.820557 CATCGTATTGGGGATTCTTGGT 58.179 45.455 0.00 0.00 0.00 3.67
1572 1753 2.674754 GGGGATTCTTGGTCGCCA 59.325 61.111 4.57 0.00 45.25 5.69
1594 1775 8.939929 CGCCAGTACTCATGAATAAATGATAAT 58.060 33.333 0.00 0.00 36.03 1.28
1750 2287 7.524717 ACTAAGATGCTTGTTTGGTTGTTAT 57.475 32.000 0.00 0.00 0.00 1.89
1903 2841 1.532868 GAGCAAGACGCATGACAGTTT 59.467 47.619 0.00 0.00 46.13 2.66
1907 2845 3.038017 CAAGACGCATGACAGTTTTGTG 58.962 45.455 0.00 0.00 37.76 3.33
2098 3044 2.576648 AGTACTCCCTCCATCCCAAAAC 59.423 50.000 0.00 0.00 0.00 2.43
2118 3064 7.148656 CCAAAACAAGTGTCAACTTTACAAAGG 60.149 37.037 6.66 0.00 44.47 3.11
2149 3095 5.716703 ACACTTATTTTGGGATTGAAGGAGG 59.283 40.000 0.00 0.00 0.00 4.30
2434 4827 0.883833 AGCATTCGCAAGTCAAAGGG 59.116 50.000 0.00 0.00 42.27 3.95
2482 4875 1.079503 GACCAGTTTGAGGCTAAGCG 58.920 55.000 0.00 0.00 0.00 4.68
2483 4876 0.685097 ACCAGTTTGAGGCTAAGCGA 59.315 50.000 0.00 0.00 0.00 4.93
2484 4877 1.338200 ACCAGTTTGAGGCTAAGCGAG 60.338 52.381 0.00 0.00 0.00 5.03
2485 4878 1.338200 CCAGTTTGAGGCTAAGCGAGT 60.338 52.381 0.00 0.00 0.00 4.18
2486 4879 2.094182 CCAGTTTGAGGCTAAGCGAGTA 60.094 50.000 0.00 0.00 0.00 2.59
2487 4880 3.585862 CAGTTTGAGGCTAAGCGAGTAA 58.414 45.455 0.00 0.00 0.00 2.24
2488 4881 3.614616 CAGTTTGAGGCTAAGCGAGTAAG 59.385 47.826 0.00 0.00 0.00 2.34
2489 4882 2.295253 TTGAGGCTAAGCGAGTAAGC 57.705 50.000 0.00 0.00 35.47 3.09
2572 4965 3.074390 AGGTCTGATGTCCAATGGTTCAA 59.926 43.478 0.00 0.00 0.00 2.69
2574 4967 4.463891 GGTCTGATGTCCAATGGTTCAAAT 59.536 41.667 0.00 0.00 0.00 2.32
2575 4968 5.047092 GGTCTGATGTCCAATGGTTCAAATT 60.047 40.000 0.00 0.00 0.00 1.82
2696 5090 4.640690 AGGGACCACTCCGCACCT 62.641 66.667 0.00 0.00 37.46 4.00
2697 5091 4.394712 GGGACCACTCCGCACCTG 62.395 72.222 0.00 0.00 37.46 4.00
2699 5093 4.008933 GACCACTCCGCACCTGCT 62.009 66.667 0.00 0.00 39.32 4.24
2756 5150 6.313905 CGTAAGCATATCTTCTGTTTTGACCT 59.686 38.462 0.00 0.00 36.25 3.85
2757 5151 6.506500 AAGCATATCTTCTGTTTTGACCTG 57.493 37.500 0.00 0.00 0.00 4.00
2767 5161 6.202516 TCTGTTTTGACCTGTTTTTACCAG 57.797 37.500 0.00 0.00 0.00 4.00
2799 5193 3.432890 CCTGTTTAGCTCCCCTGATCTTC 60.433 52.174 0.00 0.00 0.00 2.87
2813 5207 5.363939 CCTGATCTTCTGTTTATCCCTGAC 58.636 45.833 0.00 0.00 0.00 3.51
2856 5250 3.990469 GCAAAGAAGTGAAGATCTGACGA 59.010 43.478 0.00 0.00 0.00 4.20
3047 5449 1.666054 CTGATCTCTCTTGCCTTGCC 58.334 55.000 0.00 0.00 0.00 4.52
3083 5487 4.896482 TGGTTTTGGTATGTTAGCTTGGTT 59.104 37.500 0.00 0.00 0.00 3.67
3100 5504 3.745799 TGGTTTATCTTTTGCCACGAGA 58.254 40.909 0.00 0.00 0.00 4.04
3114 5518 2.807967 CCACGAGAACAGAATTTGAGCA 59.192 45.455 0.00 0.00 0.00 4.26
3173 5581 5.241064 TCCGGTTGCTATCTACTTGATCTAC 59.759 44.000 0.00 0.00 36.65 2.59
3184 5592 6.323266 TCTACTTGATCTACAAACGCTCTTC 58.677 40.000 0.00 0.00 38.08 2.87
3185 5593 4.883083 ACTTGATCTACAAACGCTCTTCA 58.117 39.130 0.00 0.00 38.08 3.02
3195 5603 9.431887 TCTACAAACGCTCTTCAAATACTTTAT 57.568 29.630 0.00 0.00 0.00 1.40
3268 5684 9.123902 TGTTATGATTCATTACTCCCATCTTTG 57.876 33.333 14.79 0.00 0.00 2.77
3276 5692 8.537728 TCATTACTCCCATCTTTGCAAAATAT 57.462 30.769 13.84 7.07 0.00 1.28
3277 5693 9.639563 TCATTACTCCCATCTTTGCAAAATATA 57.360 29.630 13.84 0.00 0.00 0.86
3280 5696 7.902920 ACTCCCATCTTTGCAAAATATATGT 57.097 32.000 13.84 4.66 0.00 2.29
3370 5913 9.722056 GCTTGTATATGTGGTTGATCTTTAAAG 57.278 33.333 9.04 9.04 0.00 1.85
3374 5917 9.916397 GTATATGTGGTTGATCTTTAAAGTTCG 57.084 33.333 14.74 0.00 0.00 3.95
3383 5940 8.645487 GTTGATCTTTAAAGTTCGACGAATAGT 58.355 33.333 22.30 4.49 32.45 2.12
3418 5975 4.336433 TGGCTGATTTAGAATGCTTGTAGC 59.664 41.667 0.00 0.00 42.82 3.58
3419 5976 4.578105 GGCTGATTTAGAATGCTTGTAGCT 59.422 41.667 0.00 0.00 42.97 3.32
3421 5978 6.405176 GGCTGATTTAGAATGCTTGTAGCTTT 60.405 38.462 0.00 0.03 42.97 3.51
3430 5988 1.201780 GCTTGTAGCTTTACGTCGCAC 60.202 52.381 0.00 0.00 38.45 5.34
3445 6003 4.084537 ACGTCGCACTTAATTCAGAAACAG 60.085 41.667 0.00 0.00 0.00 3.16
3457 6015 6.882768 ATTCAGAAACAGTCCTAATCCTCT 57.117 37.500 0.00 0.00 0.00 3.69
3461 6019 4.714308 AGAAACAGTCCTAATCCTCTGAGG 59.286 45.833 17.84 17.84 36.46 3.86
3528 6086 5.410439 ACATTGTAACATCGTTTGGTACTCC 59.590 40.000 14.36 0.00 46.80 3.85
3530 6088 5.155278 TGTAACATCGTTTGGTACTCCAT 57.845 39.130 14.36 0.00 46.80 3.41
3531 6089 4.932799 TGTAACATCGTTTGGTACTCCATG 59.067 41.667 14.36 0.00 46.80 3.66
3532 6090 2.985896 ACATCGTTTGGTACTCCATGG 58.014 47.619 4.97 4.97 43.91 3.66
3533 6091 2.304761 ACATCGTTTGGTACTCCATGGT 59.695 45.455 12.58 0.00 43.91 3.55
3534 6092 2.754946 TCGTTTGGTACTCCATGGTC 57.245 50.000 12.58 1.23 43.91 4.02
3535 6093 2.253610 TCGTTTGGTACTCCATGGTCT 58.746 47.619 12.58 0.00 43.91 3.85
3536 6094 3.433343 TCGTTTGGTACTCCATGGTCTA 58.567 45.455 12.58 0.00 43.91 2.59
3537 6095 3.194116 TCGTTTGGTACTCCATGGTCTAC 59.806 47.826 12.58 11.71 43.91 2.59
3547 6127 1.152963 ATGGTCTACCGGCCATTGC 60.153 57.895 0.00 0.00 42.34 3.56
3583 6173 1.686115 CCTAGCCACCCATTCCCTTTG 60.686 57.143 0.00 0.00 0.00 2.77
3584 6174 0.324275 TAGCCACCCATTCCCTTTGC 60.324 55.000 0.00 0.00 0.00 3.68
3596 6186 3.222173 TCCCTTTGCTGCTAGTTGAAA 57.778 42.857 0.00 0.00 0.00 2.69
3605 6195 1.349026 TGCTAGTTGAAAGGCTCTGCT 59.651 47.619 0.00 0.00 0.00 4.24
3640 6230 3.900971 TGATCATTGGAGCTTGCCATAA 58.099 40.909 0.00 0.00 37.86 1.90
3642 6232 2.658285 TCATTGGAGCTTGCCATAAGG 58.342 47.619 0.00 0.00 37.86 2.69
3666 6256 0.036010 CGGCTTCACCATTCCTGAGT 60.036 55.000 0.00 0.00 39.03 3.41
3669 6259 1.612726 GCTTCACCATTCCTGAGTGCT 60.613 52.381 0.00 0.00 0.00 4.40
3672 6262 2.540383 TCACCATTCCTGAGTGCTACT 58.460 47.619 0.00 0.00 0.00 2.57
3673 6263 2.906389 TCACCATTCCTGAGTGCTACTT 59.094 45.455 0.00 0.00 0.00 2.24
3677 6267 3.054802 CCATTCCTGAGTGCTACTTCCTT 60.055 47.826 0.00 0.00 0.00 3.36
3732 6322 1.730547 GCTGCGTGATTTGGTGTGC 60.731 57.895 0.00 0.00 0.00 4.57
3733 6323 1.951510 CTGCGTGATTTGGTGTGCT 59.048 52.632 0.00 0.00 0.00 4.40
3734 6324 0.386352 CTGCGTGATTTGGTGTGCTG 60.386 55.000 0.00 0.00 0.00 4.41
3735 6325 0.817229 TGCGTGATTTGGTGTGCTGA 60.817 50.000 0.00 0.00 0.00 4.26
3736 6326 0.110056 GCGTGATTTGGTGTGCTGAG 60.110 55.000 0.00 0.00 0.00 3.35
3737 6327 0.518636 CGTGATTTGGTGTGCTGAGG 59.481 55.000 0.00 0.00 0.00 3.86
3761 6354 2.223641 CGAATTGTGGATCATGCCTTGG 60.224 50.000 0.00 0.00 0.00 3.61
3773 6366 3.423154 CCTTGGTGGAAGCGCGTC 61.423 66.667 15.40 15.40 38.35 5.19
3774 6367 3.777925 CTTGGTGGAAGCGCGTCG 61.778 66.667 17.05 0.00 36.92 5.12
3775 6368 4.595538 TTGGTGGAAGCGCGTCGT 62.596 61.111 17.05 0.00 36.92 4.34
3779 6372 4.287781 TGGAAGCGCGTCGTGGAA 62.288 61.111 17.05 0.00 0.00 3.53
3780 6373 2.813908 GGAAGCGCGTCGTGGAAT 60.814 61.111 17.05 0.00 0.00 3.01
3781 6374 2.388232 GGAAGCGCGTCGTGGAATT 61.388 57.895 17.05 0.00 0.00 2.17
3782 6375 1.225745 GAAGCGCGTCGTGGAATTG 60.226 57.895 7.77 0.00 0.00 2.32
3783 6376 1.897398 GAAGCGCGTCGTGGAATTGT 61.897 55.000 7.77 0.00 0.00 2.71
3784 6377 1.503818 AAGCGCGTCGTGGAATTGTT 61.504 50.000 8.43 0.00 0.00 2.83
3785 6378 0.668096 AGCGCGTCGTGGAATTGTTA 60.668 50.000 8.43 0.00 0.00 2.41
3786 6379 0.247145 GCGCGTCGTGGAATTGTTAG 60.247 55.000 8.43 0.00 0.00 2.34
3787 6380 1.342555 CGCGTCGTGGAATTGTTAGA 58.657 50.000 0.00 0.00 0.00 2.10
3788 6381 1.320555 CGCGTCGTGGAATTGTTAGAG 59.679 52.381 0.00 0.00 0.00 2.43
3789 6382 2.334838 GCGTCGTGGAATTGTTAGAGT 58.665 47.619 0.00 0.00 0.00 3.24
3790 6383 3.504863 GCGTCGTGGAATTGTTAGAGTA 58.495 45.455 0.00 0.00 0.00 2.59
3791 6384 3.546670 GCGTCGTGGAATTGTTAGAGTAG 59.453 47.826 0.00 0.00 0.00 2.57
3792 6385 3.546670 CGTCGTGGAATTGTTAGAGTAGC 59.453 47.826 0.00 0.00 0.00 3.58
3793 6386 4.674623 CGTCGTGGAATTGTTAGAGTAGCT 60.675 45.833 0.00 0.00 0.00 3.32
3794 6387 4.799428 GTCGTGGAATTGTTAGAGTAGCTC 59.201 45.833 0.00 0.00 0.00 4.09
3795 6388 3.791887 CGTGGAATTGTTAGAGTAGCTCG 59.208 47.826 0.00 0.00 35.36 5.03
3796 6389 4.438336 CGTGGAATTGTTAGAGTAGCTCGA 60.438 45.833 0.00 0.00 35.36 4.04
3797 6390 5.408356 GTGGAATTGTTAGAGTAGCTCGAA 58.592 41.667 0.00 0.00 35.36 3.71
3798 6391 5.517054 GTGGAATTGTTAGAGTAGCTCGAAG 59.483 44.000 0.00 0.00 35.36 3.79
3799 6392 4.504826 GGAATTGTTAGAGTAGCTCGAAGC 59.495 45.833 0.00 0.00 42.84 3.86
3810 6403 2.126463 TCGAAGCTGCCGAGAACG 60.126 61.111 7.30 0.00 39.43 3.95
3811 6404 2.126463 CGAAGCTGCCGAGAACGA 60.126 61.111 2.94 0.00 42.66 3.85
3812 6405 2.437343 CGAAGCTGCCGAGAACGAC 61.437 63.158 2.94 0.00 42.66 4.34
3813 6406 2.430921 AAGCTGCCGAGAACGACG 60.431 61.111 0.00 0.00 42.66 5.12
3814 6407 2.797866 GAAGCTGCCGAGAACGACGA 62.798 60.000 0.00 0.00 42.66 4.20
3815 6408 2.202623 GCTGCCGAGAACGACGAT 60.203 61.111 0.00 0.00 42.66 3.73
3816 6409 2.508891 GCTGCCGAGAACGACGATG 61.509 63.158 0.00 0.00 42.66 3.84
3817 6410 1.136774 CTGCCGAGAACGACGATGA 59.863 57.895 0.00 0.00 42.66 2.92
3818 6411 0.863538 CTGCCGAGAACGACGATGAG 60.864 60.000 0.00 0.00 42.66 2.90
3819 6412 2.224885 GCCGAGAACGACGATGAGC 61.225 63.158 0.00 0.00 42.66 4.26
3820 6413 1.586564 CCGAGAACGACGATGAGCC 60.587 63.158 0.00 0.00 42.66 4.70
3821 6414 1.934956 CGAGAACGACGATGAGCCG 60.935 63.158 0.00 0.00 42.66 5.52
3822 6415 1.428219 GAGAACGACGATGAGCCGA 59.572 57.895 0.00 0.00 0.00 5.54
3823 6416 0.862283 GAGAACGACGATGAGCCGAC 60.862 60.000 0.00 0.00 0.00 4.79
3827 6420 4.492160 GACGATGAGCCGACGCCA 62.492 66.667 0.00 0.00 34.57 5.69
3828 6421 3.774959 GACGATGAGCCGACGCCAT 62.775 63.158 0.00 0.00 34.57 4.40
3829 6422 3.333189 CGATGAGCCGACGCCATG 61.333 66.667 0.00 0.00 34.57 3.66
3830 6423 3.643978 GATGAGCCGACGCCATGC 61.644 66.667 0.00 0.00 34.57 4.06
3831 6424 4.471908 ATGAGCCGACGCCATGCA 62.472 61.111 0.00 0.00 34.57 3.96
3832 6425 3.762429 ATGAGCCGACGCCATGCAT 62.762 57.895 0.00 0.00 34.57 3.96
3833 6426 3.204827 GAGCCGACGCCATGCATT 61.205 61.111 0.00 0.00 34.57 3.56
3834 6427 3.173390 GAGCCGACGCCATGCATTC 62.173 63.158 0.00 0.00 34.57 2.67
3835 6428 4.596180 GCCGACGCCATGCATTCG 62.596 66.667 14.47 14.47 34.73 3.34
3836 6429 4.596180 CCGACGCCATGCATTCGC 62.596 66.667 15.61 10.89 33.97 4.70
3837 6430 4.596180 CGACGCCATGCATTCGCC 62.596 66.667 15.61 6.26 37.32 5.54
3838 6431 3.204827 GACGCCATGCATTCGCCT 61.205 61.111 15.61 3.01 37.32 5.52
3839 6432 3.459378 GACGCCATGCATTCGCCTG 62.459 63.158 15.61 4.10 37.32 4.85
3840 6433 4.918129 CGCCATGCATTCGCCTGC 62.918 66.667 0.00 2.48 42.62 4.85
3841 6434 3.524606 GCCATGCATTCGCCTGCT 61.525 61.111 0.00 0.00 42.75 4.24
3842 6435 2.411701 CCATGCATTCGCCTGCTG 59.588 61.111 0.00 6.21 42.75 4.41
3843 6436 2.278596 CATGCATTCGCCTGCTGC 60.279 61.111 0.00 0.00 42.75 5.25
3844 6437 3.524606 ATGCATTCGCCTGCTGCC 61.525 61.111 9.87 0.00 42.75 4.85
3846 6439 3.751246 GCATTCGCCTGCTGCCAA 61.751 61.111 0.00 0.00 39.12 4.52
3847 6440 3.072486 GCATTCGCCTGCTGCCAAT 62.072 57.895 0.00 0.00 39.12 3.16
3848 6441 1.226859 CATTCGCCTGCTGCCAATG 60.227 57.895 0.00 5.18 41.18 2.82
3849 6442 1.679977 ATTCGCCTGCTGCCAATGT 60.680 52.632 0.00 0.00 36.24 2.71
3850 6443 1.660560 ATTCGCCTGCTGCCAATGTC 61.661 55.000 0.00 0.00 36.24 3.06
3851 6444 3.818787 CGCCTGCTGCCAATGTCC 61.819 66.667 0.00 0.00 36.24 4.02
3852 6445 2.677524 GCCTGCTGCCAATGTCCA 60.678 61.111 0.00 0.00 0.00 4.02
3853 6446 2.998279 GCCTGCTGCCAATGTCCAC 61.998 63.158 0.00 0.00 0.00 4.02
3854 6447 1.604308 CCTGCTGCCAATGTCCACA 60.604 57.895 0.00 0.00 0.00 4.17
3855 6448 1.180456 CCTGCTGCCAATGTCCACAA 61.180 55.000 0.00 0.00 0.00 3.33
3856 6449 0.242825 CTGCTGCCAATGTCCACAAG 59.757 55.000 0.00 0.00 0.00 3.16
3857 6450 0.467844 TGCTGCCAATGTCCACAAGT 60.468 50.000 0.00 0.00 0.00 3.16
3858 6451 0.242017 GCTGCCAATGTCCACAAGTC 59.758 55.000 0.00 0.00 0.00 3.01
3859 6452 0.883833 CTGCCAATGTCCACAAGTCC 59.116 55.000 0.00 0.00 0.00 3.85
3860 6453 0.184692 TGCCAATGTCCACAAGTCCA 59.815 50.000 0.00 0.00 0.00 4.02
3861 6454 1.203038 TGCCAATGTCCACAAGTCCAT 60.203 47.619 0.00 0.00 0.00 3.41
3862 6455 1.474077 GCCAATGTCCACAAGTCCATC 59.526 52.381 0.00 0.00 0.00 3.51
3863 6456 2.094675 CCAATGTCCACAAGTCCATCC 58.905 52.381 0.00 0.00 0.00 3.51
3864 6457 1.739466 CAATGTCCACAAGTCCATCCG 59.261 52.381 0.00 0.00 0.00 4.18
3865 6458 0.392998 ATGTCCACAAGTCCATCCGC 60.393 55.000 0.00 0.00 0.00 5.54
3866 6459 1.296715 GTCCACAAGTCCATCCGCT 59.703 57.895 0.00 0.00 0.00 5.52
3867 6460 0.741221 GTCCACAAGTCCATCCGCTC 60.741 60.000 0.00 0.00 0.00 5.03
3868 6461 0.904865 TCCACAAGTCCATCCGCTCT 60.905 55.000 0.00 0.00 0.00 4.09
3869 6462 0.460987 CCACAAGTCCATCCGCTCTC 60.461 60.000 0.00 0.00 0.00 3.20
3870 6463 0.460987 CACAAGTCCATCCGCTCTCC 60.461 60.000 0.00 0.00 0.00 3.71
3871 6464 1.227089 CAAGTCCATCCGCTCTCCG 60.227 63.158 0.00 0.00 0.00 4.63
3872 6465 1.379977 AAGTCCATCCGCTCTCCGA 60.380 57.895 0.00 0.00 40.02 4.55
3873 6466 1.668101 AAGTCCATCCGCTCTCCGAC 61.668 60.000 0.00 0.00 40.02 4.79
3874 6467 3.209812 TCCATCCGCTCTCCGACG 61.210 66.667 0.00 0.00 40.02 5.12
3881 6474 3.148279 GCTCTCCGACGGGGTGAT 61.148 66.667 19.73 0.00 37.65 3.06
3882 6475 3.121019 CTCTCCGACGGGGTGATC 58.879 66.667 14.78 0.00 37.65 2.92
3883 6476 2.827190 TCTCCGACGGGGTGATCG 60.827 66.667 14.78 0.00 33.46 3.69
3884 6477 2.827190 CTCCGACGGGGTGATCGA 60.827 66.667 15.25 0.00 40.86 3.59
3885 6478 2.827190 TCCGACGGGGTGATCGAG 60.827 66.667 15.25 0.00 40.86 4.04
3886 6479 4.570663 CCGACGGGGTGATCGAGC 62.571 72.222 5.81 0.00 40.86 5.03
3887 6480 3.518998 CGACGGGGTGATCGAGCT 61.519 66.667 0.90 0.00 40.86 4.09
3888 6481 2.413765 GACGGGGTGATCGAGCTC 59.586 66.667 2.73 2.73 0.00 4.09
3889 6482 2.043852 ACGGGGTGATCGAGCTCT 60.044 61.111 12.85 0.00 0.00 4.09
3890 6483 2.065906 GACGGGGTGATCGAGCTCTC 62.066 65.000 12.85 3.94 0.00 3.20
3891 6484 2.851071 CGGGGTGATCGAGCTCTCC 61.851 68.421 11.61 11.61 0.00 3.71
3892 6485 1.456705 GGGGTGATCGAGCTCTCCT 60.457 63.158 14.24 0.00 0.00 3.69
3893 6486 1.045911 GGGGTGATCGAGCTCTCCTT 61.046 60.000 14.24 0.00 0.00 3.36
3894 6487 0.103937 GGGTGATCGAGCTCTCCTTG 59.896 60.000 12.85 0.00 0.00 3.61
3895 6488 0.103937 GGTGATCGAGCTCTCCTTGG 59.896 60.000 12.85 0.00 0.00 3.61
3896 6489 1.107114 GTGATCGAGCTCTCCTTGGA 58.893 55.000 12.85 0.20 0.00 3.53
3897 6490 1.066908 GTGATCGAGCTCTCCTTGGAG 59.933 57.143 12.85 10.28 36.50 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.287977 AGTCCTACAAAGCCCAAACC 57.712 50.000 0.00 0.00 0.00 3.27
78 79 0.538584 TCGACCAGCTCGTAGTCCTA 59.461 55.000 0.00 0.00 43.45 2.94
177 178 4.215399 CCACATGGTCACTAAAATTCGTGT 59.785 41.667 0.00 0.00 33.07 4.49
179 180 3.756434 CCCACATGGTCACTAAAATTCGT 59.244 43.478 0.00 0.00 0.00 3.85
217 218 4.492494 TTCTCATGCATAGCCTTTCTCA 57.508 40.909 0.00 0.00 0.00 3.27
230 231 4.110482 GGCTGTGAAATTCATTCTCATGC 58.890 43.478 0.00 0.00 39.90 4.06
248 249 2.286872 CTCATAGTGGAAAGCAGGCTG 58.713 52.381 10.94 10.94 0.00 4.85
272 274 5.707298 CCAGCTCCTCAAAAATCTCTTTACA 59.293 40.000 0.00 0.00 0.00 2.41
273 275 5.940470 TCCAGCTCCTCAAAAATCTCTTTAC 59.060 40.000 0.00 0.00 0.00 2.01
295 298 2.099263 TCTGTGCGAGTTAGCTATGTCC 59.901 50.000 0.00 0.00 38.13 4.02
319 322 1.003118 ACTCGTGCTTCATTTGCCCTA 59.997 47.619 0.00 0.00 0.00 3.53
346 349 2.265589 ACCACACTTTTACCTTCCGG 57.734 50.000 0.00 0.00 0.00 5.14
351 354 2.497138 GCGGTAACCACACTTTTACCT 58.503 47.619 8.49 0.00 43.54 3.08
352 355 1.536766 GGCGGTAACCACACTTTTACC 59.463 52.381 1.12 1.12 42.67 2.85
354 357 2.550639 GGAGGCGGTAACCACACTTTTA 60.551 50.000 0.00 0.00 0.00 1.52
423 428 3.286751 GCCGCTGCACCTTTGTCA 61.287 61.111 0.00 0.00 37.47 3.58
440 445 1.132262 ACTTGTCACGGCAAACAACTG 59.868 47.619 0.00 0.00 32.28 3.16
447 452 2.485795 GCCCAACTTGTCACGGCAA 61.486 57.895 2.78 0.00 39.50 4.52
474 479 5.010112 TGAAAAATCAACGCTGAAATACCCA 59.990 36.000 0.00 0.00 34.49 4.51
479 484 5.634859 GGTCATGAAAAATCAACGCTGAAAT 59.365 36.000 0.00 0.00 34.49 2.17
480 485 4.981674 GGTCATGAAAAATCAACGCTGAAA 59.018 37.500 0.00 0.00 34.49 2.69
491 496 3.081804 GGTCGGTGAGGTCATGAAAAAT 58.918 45.455 0.00 0.00 0.00 1.82
497 502 2.184322 CGGGTCGGTGAGGTCATG 59.816 66.667 0.00 0.00 0.00 3.07
501 506 2.522436 TTGTCGGGTCGGTGAGGT 60.522 61.111 0.00 0.00 0.00 3.85
561 566 5.011943 GCAAGATCCTGTAGATTCAGATCCT 59.988 44.000 0.00 0.00 37.61 3.24
566 571 4.412796 TGGCAAGATCCTGTAGATTCAG 57.587 45.455 0.00 0.00 34.42 3.02
629 634 1.623811 AGCATAAGACGGTGAACCTGT 59.376 47.619 0.00 0.00 0.00 4.00
640 645 8.574251 TCTCTCTAAGGATATGAGCATAAGAC 57.426 38.462 0.00 0.00 0.00 3.01
690 695 7.355778 ACTCTCAAAACGAAAATCATCAGAAC 58.644 34.615 0.00 0.00 0.00 3.01
793 798 7.418254 GGAATACCATCAATCTCTGGCAAAATT 60.418 37.037 0.00 0.00 35.88 1.82
794 799 6.041296 GGAATACCATCAATCTCTGGCAAAAT 59.959 38.462 0.00 0.00 35.88 1.82
810 815 2.036387 TCACGACATCCGGAATACCAT 58.964 47.619 9.01 0.00 43.93 3.55
812 817 2.159142 AGTTCACGACATCCGGAATACC 60.159 50.000 9.01 0.00 43.93 2.73
874 879 3.379057 GCTTGGGCGGCTTTTATAGTTTA 59.621 43.478 9.56 0.00 0.00 2.01
875 880 2.165641 GCTTGGGCGGCTTTTATAGTTT 59.834 45.455 9.56 0.00 0.00 2.66
877 882 1.389555 GCTTGGGCGGCTTTTATAGT 58.610 50.000 9.56 0.00 0.00 2.12
941 946 1.003355 CCCTAGCTGTGGTGTGTGG 60.003 63.158 0.00 0.00 0.00 4.17
954 959 1.146982 CTTCTCTCCTCCCTCCCCTAG 59.853 61.905 0.00 0.00 0.00 3.02
1148 1322 1.343465 CCTGGGACACGATATACCCAC 59.657 57.143 0.00 0.00 46.04 4.61
1156 1330 1.852157 ATGGCAACCTGGGACACGAT 61.852 55.000 0.00 0.00 0.00 3.73
1241 1422 6.053005 GTCCGTAGAATTGACATGGGAATAA 58.947 40.000 0.00 0.00 0.00 1.40
1246 1427 3.260475 TGTCCGTAGAATTGACATGGG 57.740 47.619 0.00 0.00 0.00 4.00
1296 1477 0.958091 CACGGATCAAAAGCCACCAA 59.042 50.000 0.00 0.00 0.00 3.67
1297 1478 0.893270 CCACGGATCAAAAGCCACCA 60.893 55.000 0.00 0.00 0.00 4.17
1298 1479 1.883021 CCACGGATCAAAAGCCACC 59.117 57.895 0.00 0.00 0.00 4.61
1299 1480 1.212751 GCCACGGATCAAAAGCCAC 59.787 57.895 0.00 0.00 0.00 5.01
1300 1481 0.539438 AAGCCACGGATCAAAAGCCA 60.539 50.000 0.00 0.00 0.00 4.75
1301 1482 1.401905 CTAAGCCACGGATCAAAAGCC 59.598 52.381 0.00 0.00 0.00 4.35
1302 1483 2.084546 ACTAAGCCACGGATCAAAAGC 58.915 47.619 0.00 0.00 0.00 3.51
1303 1484 3.502211 ACAACTAAGCCACGGATCAAAAG 59.498 43.478 0.00 0.00 0.00 2.27
1305 1486 2.811431 CACAACTAAGCCACGGATCAAA 59.189 45.455 0.00 0.00 0.00 2.69
1306 1487 2.422597 CACAACTAAGCCACGGATCAA 58.577 47.619 0.00 0.00 0.00 2.57
1312 1493 1.464608 CATCACCACAACTAAGCCACG 59.535 52.381 0.00 0.00 0.00 4.94
1317 1498 3.955471 ACCCATCATCACCACAACTAAG 58.045 45.455 0.00 0.00 0.00 2.18
1347 1528 1.200020 GACAATCCAAACGGCTCCAAG 59.800 52.381 0.00 0.00 0.00 3.61
1383 1564 3.056678 TGCAAAAGCATTCATGGTTCGAT 60.057 39.130 4.75 0.00 46.62 3.59
1405 1586 8.870116 TCATATATAGGTCTAATGTTGCACAGT 58.130 33.333 0.00 0.00 0.00 3.55
1406 1587 9.710900 TTCATATATAGGTCTAATGTTGCACAG 57.289 33.333 0.00 0.00 0.00 3.66
1467 1648 6.921914 AGGCTACATATACTACGGATTTCAC 58.078 40.000 0.00 0.00 0.00 3.18
1499 1680 0.601558 TCCACTACGACAGGCAAGAC 59.398 55.000 0.00 0.00 0.00 3.01
1500 1681 0.888619 CTCCACTACGACAGGCAAGA 59.111 55.000 0.00 0.00 0.00 3.02
1501 1682 0.888619 TCTCCACTACGACAGGCAAG 59.111 55.000 0.00 0.00 0.00 4.01
1503 1684 1.103803 GATCTCCACTACGACAGGCA 58.896 55.000 0.00 0.00 0.00 4.75
1504 1685 0.386113 GGATCTCCACTACGACAGGC 59.614 60.000 0.00 0.00 35.64 4.85
1567 1748 5.912892 TCATTTATTCATGAGTACTGGCGA 58.087 37.500 0.00 0.00 0.00 5.54
1750 2287 9.793259 GAAATTCATATAATACCCACTTCAGGA 57.207 33.333 0.00 0.00 0.00 3.86
1855 2793 4.202050 CCAGAAAACAGCTTAGCAACACTT 60.202 41.667 7.07 0.00 0.00 3.16
1903 2841 1.818060 GGCCTGCATACAACATCACAA 59.182 47.619 0.00 0.00 0.00 3.33
1907 2845 2.042686 TCTGGCCTGCATACAACATC 57.957 50.000 3.32 0.00 0.00 3.06
1967 2913 2.041620 CCTTGAGTGGATCTTTTGGGGA 59.958 50.000 0.00 0.00 0.00 4.81
2098 3044 6.093495 TCTCACCTTTGTAAAGTTGACACTTG 59.907 38.462 1.12 0.00 42.89 3.16
2118 3064 6.655003 TCAATCCCAAAATAAGTGTCTCTCAC 59.345 38.462 0.00 0.00 46.46 3.51
2234 3180 1.471287 CCCCTGCGCTTACCTAAAAAC 59.529 52.381 9.73 0.00 0.00 2.43
2325 4706 1.601903 CTTTGCTTCACGGTACTTGCA 59.398 47.619 0.00 0.00 0.00 4.08
2422 4815 1.882623 CCTTCTCACCCTTTGACTTGC 59.117 52.381 0.00 0.00 0.00 4.01
2434 4827 3.584834 GTCTTCTCTCTTGCCTTCTCAC 58.415 50.000 0.00 0.00 0.00 3.51
2482 4875 2.082354 GCTCTTGGCACGCTTACTC 58.918 57.895 0.00 0.00 41.35 2.59
2483 4876 4.285851 GCTCTTGGCACGCTTACT 57.714 55.556 0.00 0.00 41.35 2.24
2575 4968 7.489574 AGCAACTGACAAAAAGAAACAAAAA 57.510 28.000 0.00 0.00 0.00 1.94
2620 5014 7.600065 ACAATCTGAAGAATTTCATCAACAGG 58.400 34.615 5.88 0.50 42.19 4.00
2756 5150 5.554437 GGAAATTTCCCCTGGTAAAAACA 57.446 39.130 24.44 0.00 41.62 2.83
2799 5193 2.416547 CTGCAACGTCAGGGATAAACAG 59.583 50.000 0.00 0.00 0.00 3.16
2856 5250 4.454504 CACCCAGTAAACAGAACGCTTAAT 59.545 41.667 0.00 0.00 0.00 1.40
3083 5487 4.637276 TCTGTTCTCGTGGCAAAAGATAA 58.363 39.130 0.00 0.00 0.00 1.75
3100 5504 2.225019 CGCAGTCTGCTCAAATTCTGTT 59.775 45.455 22.13 0.00 42.25 3.16
3114 5518 1.327303 GAGGAGGATCATCGCAGTCT 58.673 55.000 0.56 0.00 35.64 3.24
3213 5621 1.355043 ACTCCCTCTGTCTAGGACGTT 59.645 52.381 0.00 0.00 39.15 3.99
3348 5888 9.916397 CGAACTTTAAAGATCAACCACATATAC 57.084 33.333 21.92 0.00 0.00 1.47
3354 5894 5.176223 TCGTCGAACTTTAAAGATCAACCAC 59.824 40.000 21.92 11.48 0.00 4.16
3370 5913 8.951969 CATAAAGGTAAGTACTATTCGTCGAAC 58.048 37.037 10.39 0.00 0.00 3.95
3374 5917 7.381678 CAGCCATAAAGGTAAGTACTATTCGTC 59.618 40.741 0.00 0.00 40.61 4.20
3388 5945 6.131961 AGCATTCTAAATCAGCCATAAAGGT 58.868 36.000 0.00 0.00 40.61 3.50
3418 5975 5.756950 TCTGAATTAAGTGCGACGTAAAG 57.243 39.130 0.00 0.00 0.00 1.85
3419 5976 6.018913 TGTTTCTGAATTAAGTGCGACGTAAA 60.019 34.615 0.00 0.00 0.00 2.01
3421 5978 4.983538 TGTTTCTGAATTAAGTGCGACGTA 59.016 37.500 0.00 0.00 0.00 3.57
3430 5988 9.103861 GAGGATTAGGACTGTTTCTGAATTAAG 57.896 37.037 0.00 0.00 0.00 1.85
3445 6003 4.187506 AGGTACCTCAGAGGATTAGGAC 57.812 50.000 24.45 9.98 37.67 3.85
3493 6051 6.487331 ACGATGTTACAATGTTGGTTTAAGGA 59.513 34.615 0.00 0.00 0.00 3.36
3505 6063 5.410132 TGGAGTACCAAACGATGTTACAATG 59.590 40.000 0.00 0.00 43.91 2.82
3528 6086 1.447317 GCAATGGCCGGTAGACCATG 61.447 60.000 11.57 7.66 46.04 3.66
3530 6088 2.270850 GCAATGGCCGGTAGACCA 59.729 61.111 1.90 1.17 41.06 4.02
3547 6127 4.103153 TGGCTAGGGTTTAGATGATTCAGG 59.897 45.833 0.00 0.00 0.00 3.86
3555 6135 2.280308 TGGGTGGCTAGGGTTTAGAT 57.720 50.000 0.00 0.00 0.00 1.98
3583 6173 1.736681 CAGAGCCTTTCAACTAGCAGC 59.263 52.381 0.00 0.00 0.00 5.25
3584 6174 1.736681 GCAGAGCCTTTCAACTAGCAG 59.263 52.381 0.00 0.00 0.00 4.24
3605 6195 2.037049 ATCAACAATGGGGCGGCA 59.963 55.556 12.47 0.00 0.00 5.69
3640 6230 2.129555 AATGGTGAAGCCGTGAGCCT 62.130 55.000 0.00 0.00 45.47 4.58
3642 6232 1.648467 GGAATGGTGAAGCCGTGAGC 61.648 60.000 0.00 0.00 41.21 4.26
3643 6233 0.036010 AGGAATGGTGAAGCCGTGAG 60.036 55.000 0.00 0.00 41.21 3.51
3644 6234 0.321564 CAGGAATGGTGAAGCCGTGA 60.322 55.000 0.00 0.00 41.21 4.35
3645 6235 0.321564 TCAGGAATGGTGAAGCCGTG 60.322 55.000 0.00 0.00 41.21 4.94
3646 6236 0.036010 CTCAGGAATGGTGAAGCCGT 60.036 55.000 0.00 0.00 41.21 5.68
3647 6237 0.036010 ACTCAGGAATGGTGAAGCCG 60.036 55.000 0.00 0.00 41.21 5.52
3666 6256 2.028748 GGTAACGGACAAGGAAGTAGCA 60.029 50.000 0.00 0.00 0.00 3.49
3669 6259 2.030007 CGTGGTAACGGACAAGGAAGTA 60.030 50.000 0.00 0.00 46.25 2.24
3672 6262 3.591979 CGTGGTAACGGACAAGGAA 57.408 52.632 0.00 0.00 46.25 3.36
3732 6322 1.091771 ATCCACAATTCGCGCCTCAG 61.092 55.000 0.00 0.00 0.00 3.35
3733 6323 1.078497 ATCCACAATTCGCGCCTCA 60.078 52.632 0.00 0.00 0.00 3.86
3734 6324 1.089481 TGATCCACAATTCGCGCCTC 61.089 55.000 0.00 0.00 0.00 4.70
3735 6325 0.464373 ATGATCCACAATTCGCGCCT 60.464 50.000 0.00 0.00 0.00 5.52
3736 6326 0.317269 CATGATCCACAATTCGCGCC 60.317 55.000 0.00 0.00 0.00 6.53
3737 6327 0.931662 GCATGATCCACAATTCGCGC 60.932 55.000 0.00 0.00 0.00 6.86
3744 6337 1.548081 CACCAAGGCATGATCCACAA 58.452 50.000 0.00 0.00 0.00 3.33
3745 6338 0.323633 CCACCAAGGCATGATCCACA 60.324 55.000 0.00 0.00 0.00 4.17
3772 6365 4.438336 CGAGCTACTCTAACAATTCCACGA 60.438 45.833 0.00 0.00 0.00 4.35
3773 6366 3.791887 CGAGCTACTCTAACAATTCCACG 59.208 47.826 0.00 0.00 0.00 4.94
3774 6367 4.995124 TCGAGCTACTCTAACAATTCCAC 58.005 43.478 0.00 0.00 0.00 4.02
3775 6368 5.651530 CTTCGAGCTACTCTAACAATTCCA 58.348 41.667 0.00 0.00 0.00 3.53
3776 6369 4.504826 GCTTCGAGCTACTCTAACAATTCC 59.495 45.833 0.00 0.00 38.45 3.01
3777 6370 5.629348 GCTTCGAGCTACTCTAACAATTC 57.371 43.478 0.00 0.00 38.45 2.17
3793 6386 2.126463 CGTTCTCGGCAGCTTCGA 60.126 61.111 8.40 8.40 35.24 3.71
3794 6387 2.126463 TCGTTCTCGGCAGCTTCG 60.126 61.111 0.00 0.16 37.69 3.79
3795 6388 2.437343 CGTCGTTCTCGGCAGCTTC 61.437 63.158 0.00 0.00 42.21 3.86
3796 6389 2.214181 ATCGTCGTTCTCGGCAGCTT 62.214 55.000 0.00 0.00 42.21 3.74
3797 6390 2.701780 ATCGTCGTTCTCGGCAGCT 61.702 57.895 0.00 0.00 42.21 4.24
3798 6391 2.202623 ATCGTCGTTCTCGGCAGC 60.203 61.111 0.00 0.00 42.21 5.25
3799 6392 0.863538 CTCATCGTCGTTCTCGGCAG 60.864 60.000 0.00 0.00 42.21 4.85
3800 6393 1.136774 CTCATCGTCGTTCTCGGCA 59.863 57.895 0.00 0.00 42.21 5.69
3801 6394 2.224885 GCTCATCGTCGTTCTCGGC 61.225 63.158 0.00 0.00 38.40 5.54
3802 6395 1.586564 GGCTCATCGTCGTTCTCGG 60.587 63.158 0.00 0.00 37.69 4.63
3803 6396 1.934956 CGGCTCATCGTCGTTCTCG 60.935 63.158 0.00 0.00 35.63 4.04
3804 6397 0.862283 GTCGGCTCATCGTCGTTCTC 60.862 60.000 0.00 0.00 42.47 2.87
3805 6398 1.136984 GTCGGCTCATCGTCGTTCT 59.863 57.895 0.00 0.00 42.47 3.01
3806 6399 2.215604 CGTCGGCTCATCGTCGTTC 61.216 63.158 0.00 0.00 42.47 3.95
3807 6400 2.202440 CGTCGGCTCATCGTCGTT 60.202 61.111 0.00 0.00 42.47 3.85
3808 6401 4.831307 GCGTCGGCTCATCGTCGT 62.831 66.667 0.00 0.00 42.47 4.34
3810 6403 3.774959 ATGGCGTCGGCTCATCGTC 62.775 63.158 20.29 0.00 39.81 4.20
3811 6404 3.838271 ATGGCGTCGGCTCATCGT 61.838 61.111 20.29 0.00 39.81 3.73
3812 6405 3.333189 CATGGCGTCGGCTCATCG 61.333 66.667 20.29 0.10 39.81 3.84
3813 6406 3.643978 GCATGGCGTCGGCTCATC 61.644 66.667 20.29 3.05 39.81 2.92
3814 6407 3.762429 ATGCATGGCGTCGGCTCAT 62.762 57.895 20.29 15.98 39.81 2.90
3815 6408 3.974835 AATGCATGGCGTCGGCTCA 62.975 57.895 20.29 14.52 39.81 4.26
3816 6409 3.173390 GAATGCATGGCGTCGGCTC 62.173 63.158 20.29 9.47 39.81 4.70
3817 6410 3.204827 GAATGCATGGCGTCGGCT 61.205 61.111 20.29 2.64 39.81 5.52
3818 6411 4.596180 CGAATGCATGGCGTCGGC 62.596 66.667 12.58 12.58 35.86 5.54
3819 6412 4.596180 GCGAATGCATGGCGTCGG 62.596 66.667 17.57 3.11 42.15 4.79
3820 6413 4.596180 GGCGAATGCATGGCGTCG 62.596 66.667 19.36 16.40 45.35 5.12
3821 6414 3.204827 AGGCGAATGCATGGCGTC 61.205 61.111 16.31 16.31 45.35 5.19
3829 6422 3.751246 TTGGCAGCAGGCGAATGC 61.751 61.111 4.26 4.26 46.16 3.56
3832 6425 2.282391 ACATTGGCAGCAGGCGAA 60.282 55.556 0.00 0.00 46.16 4.70
3833 6426 2.747460 GACATTGGCAGCAGGCGA 60.747 61.111 0.00 0.00 46.16 5.54
3834 6427 3.818787 GGACATTGGCAGCAGGCG 61.819 66.667 0.00 0.00 46.16 5.52
3835 6428 2.677524 TGGACATTGGCAGCAGGC 60.678 61.111 0.00 0.00 43.74 4.85
3836 6429 1.180456 TTGTGGACATTGGCAGCAGG 61.180 55.000 0.00 0.00 0.00 4.85
3837 6430 0.242825 CTTGTGGACATTGGCAGCAG 59.757 55.000 0.00 0.00 0.00 4.24
3838 6431 0.467844 ACTTGTGGACATTGGCAGCA 60.468 50.000 0.00 0.00 0.00 4.41
3839 6432 0.242017 GACTTGTGGACATTGGCAGC 59.758 55.000 0.00 0.00 0.00 5.25
3840 6433 0.883833 GGACTTGTGGACATTGGCAG 59.116 55.000 0.00 0.00 0.00 4.85
3841 6434 0.184692 TGGACTTGTGGACATTGGCA 59.815 50.000 0.00 0.00 0.00 4.92
3842 6435 1.474077 GATGGACTTGTGGACATTGGC 59.526 52.381 0.00 0.00 0.00 4.52
3843 6436 2.094675 GGATGGACTTGTGGACATTGG 58.905 52.381 0.00 0.00 0.00 3.16
3844 6437 1.739466 CGGATGGACTTGTGGACATTG 59.261 52.381 0.00 0.00 0.00 2.82
3845 6438 1.950484 GCGGATGGACTTGTGGACATT 60.950 52.381 0.00 0.00 0.00 2.71
3846 6439 0.392998 GCGGATGGACTTGTGGACAT 60.393 55.000 0.00 0.00 0.00 3.06
3847 6440 1.003839 GCGGATGGACTTGTGGACA 60.004 57.895 0.00 0.00 0.00 4.02
3848 6441 0.741221 GAGCGGATGGACTTGTGGAC 60.741 60.000 0.00 0.00 0.00 4.02
3849 6442 0.904865 AGAGCGGATGGACTTGTGGA 60.905 55.000 0.00 0.00 0.00 4.02
3850 6443 0.460987 GAGAGCGGATGGACTTGTGG 60.461 60.000 0.00 0.00 0.00 4.17
3851 6444 0.460987 GGAGAGCGGATGGACTTGTG 60.461 60.000 0.00 0.00 0.00 3.33
3852 6445 1.901085 GGAGAGCGGATGGACTTGT 59.099 57.895 0.00 0.00 0.00 3.16
3853 6446 1.227089 CGGAGAGCGGATGGACTTG 60.227 63.158 0.00 0.00 0.00 3.16
3854 6447 1.379977 TCGGAGAGCGGATGGACTT 60.380 57.895 0.00 0.00 0.00 3.01
3855 6448 2.122167 GTCGGAGAGCGGATGGACT 61.122 63.158 0.00 0.00 36.95 3.85
3856 6449 2.413765 GTCGGAGAGCGGATGGAC 59.586 66.667 0.00 0.00 36.95 4.02
3857 6450 3.209812 CGTCGGAGAGCGGATGGA 61.210 66.667 0.00 0.00 36.95 3.41
3864 6457 3.140225 GATCACCCCGTCGGAGAGC 62.140 68.421 14.39 6.84 36.95 4.09
3865 6458 2.835705 CGATCACCCCGTCGGAGAG 61.836 68.421 14.39 0.00 36.95 3.20
3866 6459 2.827190 CGATCACCCCGTCGGAGA 60.827 66.667 14.39 8.18 35.49 3.71
3867 6460 2.827190 TCGATCACCCCGTCGGAG 60.827 66.667 14.39 0.52 38.34 4.63
3868 6461 2.827190 CTCGATCACCCCGTCGGA 60.827 66.667 14.39 0.00 38.34 4.55
3869 6462 4.570663 GCTCGATCACCCCGTCGG 62.571 72.222 3.60 3.60 38.34 4.79
3870 6463 3.471244 GAGCTCGATCACCCCGTCG 62.471 68.421 0.00 0.00 39.11 5.12
3871 6464 2.065906 GAGAGCTCGATCACCCCGTC 62.066 65.000 8.37 0.00 0.00 4.79
3872 6465 2.043852 AGAGCTCGATCACCCCGT 60.044 61.111 8.37 0.00 0.00 5.28
3873 6466 2.725008 GAGAGCTCGATCACCCCG 59.275 66.667 8.37 0.00 0.00 5.73
3874 6467 1.045911 AAGGAGAGCTCGATCACCCC 61.046 60.000 8.37 2.61 30.88 4.95
3875 6468 0.103937 CAAGGAGAGCTCGATCACCC 59.896 60.000 8.37 4.34 30.88 4.61
3876 6469 0.103937 CCAAGGAGAGCTCGATCACC 59.896 60.000 8.37 8.26 0.00 4.02
3877 6470 1.066908 CTCCAAGGAGAGCTCGATCAC 59.933 57.143 10.66 0.00 44.53 3.06
3878 6471 1.397672 CTCCAAGGAGAGCTCGATCA 58.602 55.000 10.66 0.00 44.53 2.92


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

AutoCloner maintained by Alex Coulton.