Multiple sequence alignment - TraesCS4A01G235300

Loading Multiple Alignment...

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 TraesCS4A01G235300 chr4A 100.000 4462 0 0 1 4462 544061908 544057447 0.000000e+00 8240.0
1 TraesCS4A01G235300 chr4D 90.452 1749 121 26 765 2495 52751228 52752948 0.000000e+00 2263.0
2 TraesCS4A01G235300 chr4D 94.419 1308 60 6 3168 4462 52753604 52754911 0.000000e+00 1999.0
3 TraesCS4A01G235300 chr4D 92.446 278 14 3 2591 2861 52752999 52753276 1.500000e-104 390.0
4 TraesCS4A01G235300 chr4D 83.375 397 27 20 340 736 52750871 52751228 9.250000e-87 331.0
5 TraesCS4A01G235300 chr4D 92.437 119 6 3 10 127 52749633 52749749 2.760000e-37 167.0
6 TraesCS4A01G235300 chr4D 89.286 84 9 0 185 268 52750762 52750845 6.100000e-19 106.0
7 TraesCS4A01G235300 chr4B 94.122 1259 70 2 3206 4462 77513873 77515129 0.000000e+00 1912.0
8 TraesCS4A01G235300 chr4B 90.644 1165 76 20 1340 2495 77512103 77513243 0.000000e+00 1517.0
9 TraesCS4A01G235300 chr4B 82.363 1168 131 30 972 2130 438098058 438099159 0.000000e+00 946.0
10 TraesCS4A01G235300 chr4B 91.985 524 35 3 2591 3107 77513294 77513817 0.000000e+00 728.0
11 TraesCS4A01G235300 chr4B 91.638 287 14 5 404 689 77510050 77510327 5.410000e-104 388.0
12 TraesCS4A01G235300 chr4B 81.458 480 56 14 2397 2854 438099446 438099914 3.280000e-96 363.0
13 TraesCS4A01G235300 chr4B 91.220 205 13 2 765 968 77510364 77510564 1.580000e-69 274.0
14 TraesCS4A01G235300 chr4B 91.379 174 15 0 1119 1292 77510946 77511119 5.770000e-59 239.0
15 TraesCS4A01G235300 chr4B 78.537 410 41 16 1 388 77509586 77509970 4.490000e-55 226.0
16 TraesCS4A01G235300 chr4B 91.304 46 0 1 3123 3168 70256673 70256632 4.820000e-05 60.2
17 TraesCS4A01G235300 chr2A 82.292 1440 145 57 972 2399 115433070 115434411 0.000000e+00 1146.0
18 TraesCS4A01G235300 chr2A 82.328 481 58 12 2397 2854 115434503 115434979 4.180000e-105 392.0
19 TraesCS4A01G235300 chr2A 86.411 287 34 4 2058 2343 687066999 687067281 4.330000e-80 309.0
20 TraesCS4A01G235300 chr7A 82.140 1439 147 46 972 2399 611770430 611771769 0.000000e+00 1133.0
21 TraesCS4A01G235300 chr7A 82.536 481 57 12 2397 2854 611771861 611772337 8.990000e-107 398.0
22 TraesCS4A01G235300 chr7A 85.714 287 32 5 2058 2343 642740675 642740953 1.210000e-75 294.0
23 TraesCS4A01G235300 chr7A 100.000 28 0 0 3123 3150 120981950 120981923 8.000000e-03 52.8
24 TraesCS4A01G235300 chr7A 87.500 48 2 1 3123 3170 210853607 210853650 8.000000e-03 52.8
25 TraesCS4A01G235300 chr1B 82.001 1439 150 53 972 2399 93952951 93954291 0.000000e+00 1122.0
26 TraesCS4A01G235300 chr1B 82.536 481 57 12 2397 2854 93954384 93954860 8.990000e-107 398.0
27 TraesCS4A01G235300 chr2D 81.040 1461 178 56 1428 2855 640354951 640356345 0.000000e+00 1072.0
28 TraesCS4A01G235300 chr2D 83.585 463 48 14 970 1431 640344643 640345078 4.150000e-110 409.0
29 TraesCS4A01G235300 chr7D 82.818 1164 126 36 970 2123 511059525 511060624 0.000000e+00 974.0
30 TraesCS4A01G235300 chr7D 80.517 1160 135 30 973 2123 580125606 580124529 0.000000e+00 806.0
31 TraesCS4A01G235300 chr7D 82.420 438 57 7 2434 2855 511060615 511061048 9.120000e-97 364.0
32 TraesCS4A01G235300 chr7D 81.306 444 63 7 2434 2861 580124538 580124099 4.270000e-90 342.0
33 TraesCS4A01G235300 chr7D 87.500 48 2 1 3123 3170 156217728 156217771 8.000000e-03 52.8
34 TraesCS4A01G235300 chr3B 82.332 849 107 23 1252 2093 71452989 71452177 0.000000e+00 697.0
35 TraesCS4A01G235300 chr3B 81.839 435 62 7 2434 2855 71452164 71451734 2.550000e-92 350.0
36 TraesCS4A01G235300 chr7B 84.272 426 44 11 973 1397 159183320 159182917 1.160000e-105 394.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G235300 chr4A 544057447 544061908 4461 True 8240.000000 8240 100.000000 1 4462 1 chr4A.!!$R1 4461
1 TraesCS4A01G235300 chr4D 52749633 52754911 5278 False 876.000000 2263 90.402500 10 4462 6 chr4D.!!$F1 4452
2 TraesCS4A01G235300 chr4B 77509586 77515129 5543 False 754.857143 1912 89.932143 1 4462 7 chr4B.!!$F1 4461
3 TraesCS4A01G235300 chr4B 438098058 438099914 1856 False 654.500000 946 81.910500 972 2854 2 chr4B.!!$F2 1882
4 TraesCS4A01G235300 chr2A 115433070 115434979 1909 False 769.000000 1146 82.310000 972 2854 2 chr2A.!!$F2 1882
5 TraesCS4A01G235300 chr7A 611770430 611772337 1907 False 765.500000 1133 82.338000 972 2854 2 chr7A.!!$F3 1882
6 TraesCS4A01G235300 chr1B 93952951 93954860 1909 False 760.000000 1122 82.268500 972 2854 2 chr1B.!!$F1 1882
7 TraesCS4A01G235300 chr2D 640354951 640356345 1394 False 1072.000000 1072 81.040000 1428 2855 1 chr2D.!!$F2 1427
8 TraesCS4A01G235300 chr7D 511059525 511061048 1523 False 669.000000 974 82.619000 970 2855 2 chr7D.!!$F2 1885
9 TraesCS4A01G235300 chr7D 580124099 580125606 1507 True 574.000000 806 80.911500 973 2861 2 chr7D.!!$R1 1888
10 TraesCS4A01G235300 chr3B 71451734 71452989 1255 True 523.500000 697 82.085500 1252 2855 2 chr3B.!!$R1 1603

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
491 1512 0.179171 GACCGAGCGATCGACTTGAA 60.179 55.0 26.68 0.00 34.64 2.69 F
893 1916 0.183492 AAGAGCTGTGTTGGCCAAGA 59.817 50.0 21.21 16.53 0.00 3.02 F
1104 2394 0.602372 GCGGCAATCTCCTCATCCTC 60.602 60.0 0.00 0.00 0.00 3.71 F
2587 4949 0.388391 CGTTCATGGGCGCACATTTT 60.388 50.0 25.55 0.00 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2459 4816 1.063717 ACATGCACCAAATCCTAGGGG 60.064 52.381 9.46 4.44 0.0 4.79 R
2568 4925 0.388391 AAAATGTGCGCCCATGAACG 60.388 50.000 6.01 0.00 0.0 3.95 R
3080 5544 0.177836 TGGTCCAGAGTGTGTGTGTG 59.822 55.000 0.00 0.00 0.0 3.82 R
3712 6193 0.525668 AATCGCATGACTCGTCGGAC 60.526 55.000 0.00 0.00 0.0 4.79 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
52 53 7.418337 AATAAAACAGAACCTTGGTTCAGTT 57.582 32.000 26.70 26.70 42.24 3.16
106 107 3.317406 ACAGATGCTCATATACACCCCA 58.683 45.455 0.00 0.00 0.00 4.96
107 108 3.912528 ACAGATGCTCATATACACCCCAT 59.087 43.478 0.00 0.00 0.00 4.00
114 1049 4.058124 CTCATATACACCCCATGAACACG 58.942 47.826 0.00 0.00 0.00 4.49
126 1061 0.876342 TGAACACGCATACGCACACA 60.876 50.000 0.00 0.00 45.53 3.72
130 1065 1.277326 CACGCATACGCACACACTAT 58.723 50.000 0.00 0.00 45.53 2.12
138 1073 3.887621 ACGCACACACTATTCCTACAT 57.112 42.857 0.00 0.00 0.00 2.29
139 1074 3.521560 ACGCACACACTATTCCTACATG 58.478 45.455 0.00 0.00 0.00 3.21
153 1088 2.159043 CCTACATGCACCTTCGAGATGT 60.159 50.000 0.00 0.00 0.00 3.06
154 1089 2.479566 ACATGCACCTTCGAGATGTT 57.520 45.000 0.00 0.00 0.00 2.71
156 1091 1.399440 CATGCACCTTCGAGATGTTGG 59.601 52.381 0.00 0.00 0.00 3.77
158 1093 1.648467 GCACCTTCGAGATGTTGGGC 61.648 60.000 0.00 0.00 0.00 5.36
181 1116 4.336433 CCGGCACAACATCTTAAGATTGAT 59.664 41.667 20.54 6.78 31.21 2.57
184 1119 6.493116 GGCACAACATCTTAAGATTGATGAG 58.507 40.000 20.54 15.68 41.69 2.90
185 1120 5.970023 GCACAACATCTTAAGATTGATGAGC 59.030 40.000 20.54 19.75 41.69 4.26
186 1121 6.403964 GCACAACATCTTAAGATTGATGAGCA 60.404 38.462 23.95 0.00 41.69 4.26
187 1122 6.965500 CACAACATCTTAAGATTGATGAGCAC 59.035 38.462 20.54 0.00 41.69 4.40
188 1123 5.980698 ACATCTTAAGATTGATGAGCACG 57.019 39.130 15.49 3.24 41.69 5.34
189 1124 4.272018 ACATCTTAAGATTGATGAGCACGC 59.728 41.667 15.49 0.00 41.69 5.34
192 1149 1.089920 AAGATTGATGAGCACGCACC 58.910 50.000 0.00 0.00 0.00 5.01
222 1179 4.588899 CCCTACTTCACCATTCATTCACA 58.411 43.478 0.00 0.00 0.00 3.58
223 1180 5.009631 CCCTACTTCACCATTCATTCACAA 58.990 41.667 0.00 0.00 0.00 3.33
236 1193 0.858583 TTCACAACGTGATCTGTGCG 59.141 50.000 12.25 3.66 42.40 5.34
237 1194 0.249280 TCACAACGTGATCTGTGCGT 60.249 50.000 12.25 4.21 42.20 5.24
270 1227 4.625311 CCCGAAAATGCCTAAAAATCACAC 59.375 41.667 0.00 0.00 0.00 3.82
273 1230 6.081049 CGAAAATGCCTAAAAATCACACGTA 58.919 36.000 0.00 0.00 0.00 3.57
288 1245 1.014044 ACGTAAGCTGTGCACATCGG 61.014 55.000 22.00 10.29 45.62 4.18
290 1247 2.100031 TAAGCTGTGCACATCGGCG 61.100 57.895 22.00 9.47 41.47 6.46
305 1262 2.395360 GGCGCGTTGATGGCTGTAA 61.395 57.895 8.43 0.00 0.00 2.41
308 1265 1.882198 CGCGTTGATGGCTGTAAAAG 58.118 50.000 0.00 0.00 0.00 2.27
320 1277 3.963383 CTGTAAAAGCCGTTCAACAGT 57.037 42.857 0.00 0.00 32.37 3.55
321 1278 3.873529 CTGTAAAAGCCGTTCAACAGTC 58.126 45.455 0.00 0.00 32.37 3.51
322 1279 3.537580 TGTAAAAGCCGTTCAACAGTCT 58.462 40.909 0.00 0.00 0.00 3.24
323 1280 4.695396 TGTAAAAGCCGTTCAACAGTCTA 58.305 39.130 0.00 0.00 0.00 2.59
324 1281 4.748102 TGTAAAAGCCGTTCAACAGTCTAG 59.252 41.667 0.00 0.00 0.00 2.43
325 1282 3.470645 AAAGCCGTTCAACAGTCTAGT 57.529 42.857 0.00 0.00 0.00 2.57
331 1288 3.566523 CGTTCAACAGTCTAGTGACCTC 58.433 50.000 0.00 0.00 43.91 3.85
334 1291 2.812591 TCAACAGTCTAGTGACCTCGAC 59.187 50.000 0.00 0.00 43.91 4.20
397 1354 2.508300 ACTTTTATACTCCCCCGCACAT 59.492 45.455 0.00 0.00 0.00 3.21
433 1454 1.421382 CAAAGAAAAGGTGCGCATGG 58.579 50.000 15.91 0.00 0.00 3.66
469 1490 4.672542 CGATGTGCTTTGTTACCATCCTTG 60.673 45.833 0.00 0.00 0.00 3.61
481 1502 2.035155 TCCTTGAGGACCGAGCGA 59.965 61.111 0.00 0.00 39.78 4.93
484 1505 1.298713 CTTGAGGACCGAGCGATCG 60.299 63.158 17.57 17.57 0.00 3.69
485 1506 1.715862 CTTGAGGACCGAGCGATCGA 61.716 60.000 26.68 0.00 34.64 3.59
486 1507 1.989966 TTGAGGACCGAGCGATCGAC 61.990 60.000 26.68 17.31 34.64 4.20
488 1509 1.716826 GAGGACCGAGCGATCGACTT 61.717 60.000 26.68 14.27 34.64 3.01
491 1512 0.179171 GACCGAGCGATCGACTTGAA 60.179 55.000 26.68 0.00 34.64 2.69
496 1517 2.215138 CGAGCGATCGACTTGAATGAAG 59.785 50.000 20.02 0.00 37.73 3.02
499 1520 3.126831 GCGATCGACTTGAATGAAGGAT 58.873 45.455 21.57 0.00 35.78 3.24
511 1532 4.818005 TGAATGAAGGATCCATGAACGATG 59.182 41.667 15.82 0.00 0.00 3.84
557 1580 3.414700 GGTGCTCGTGCGGTTCTG 61.415 66.667 4.84 0.00 43.34 3.02
572 1595 2.541556 GTTCTGAAGGAGCCGACATAC 58.458 52.381 0.00 0.00 0.00 2.39
635 1658 2.282251 TCGTCCTGCTCAGACGGT 60.282 61.111 18.84 0.00 41.94 4.83
636 1659 2.126307 CGTCCTGCTCAGACGGTG 60.126 66.667 13.60 0.00 38.50 4.94
637 1660 2.626780 CGTCCTGCTCAGACGGTGA 61.627 63.158 13.60 0.00 38.50 4.02
638 1661 1.080434 GTCCTGCTCAGACGGTGAC 60.080 63.158 0.00 0.00 0.00 3.67
639 1662 2.262915 CCTGCTCAGACGGTGACC 59.737 66.667 0.00 0.00 0.00 4.02
679 1702 3.763360 TCATGGATCTTCGCCACAAATTT 59.237 39.130 0.00 0.00 38.44 1.82
718 1741 0.825425 TCTGCATCAACCCCGCAAAA 60.825 50.000 0.00 0.00 34.75 2.44
736 1759 3.394313 AAACAACGTTTGACGAAGACC 57.606 42.857 7.54 0.00 46.05 3.85
739 1762 1.493134 AACGTTTGACGAAGACCGCC 61.493 55.000 7.54 0.00 46.05 6.13
740 1763 2.851104 GTTTGACGAAGACCGCCG 59.149 61.111 0.00 0.00 43.32 6.46
741 1764 1.952635 GTTTGACGAAGACCGCCGT 60.953 57.895 0.00 0.00 43.32 5.68
747 1770 4.814294 GAAGACCGCCGTCCGCAT 62.814 66.667 1.30 0.00 40.12 4.73
748 1771 4.814294 AAGACCGCCGTCCGCATC 62.814 66.667 1.30 0.00 40.12 3.91
754 1777 3.195698 GCCGTCCGCATCAACCTC 61.196 66.667 0.00 0.00 37.47 3.85
755 1778 2.511600 CCGTCCGCATCAACCTCC 60.512 66.667 0.00 0.00 0.00 4.30
756 1779 2.885644 CGTCCGCATCAACCTCCG 60.886 66.667 0.00 0.00 0.00 4.63
757 1780 3.195698 GTCCGCATCAACCTCCGC 61.196 66.667 0.00 0.00 0.00 5.54
758 1781 4.467084 TCCGCATCAACCTCCGCC 62.467 66.667 0.00 0.00 0.00 6.13
761 1784 3.195698 GCATCAACCTCCGCCGTC 61.196 66.667 0.00 0.00 0.00 4.79
762 1785 2.511600 CATCAACCTCCGCCGTCC 60.512 66.667 0.00 0.00 0.00 4.79
763 1786 4.143333 ATCAACCTCCGCCGTCCG 62.143 66.667 0.00 0.00 0.00 4.79
790 1813 1.384222 CCTAGCATTTTCGCCCCACC 61.384 60.000 0.00 0.00 0.00 4.61
893 1916 0.183492 AAGAGCTGTGTTGGCCAAGA 59.817 50.000 21.21 16.53 0.00 3.02
905 1928 2.956987 CCAAGAAGGCGGCACAAG 59.043 61.111 13.08 1.67 0.00 3.16
950 1973 2.158623 ACTTCCAAACATCTGGCAGACA 60.159 45.455 21.37 0.00 33.80 3.41
1024 2314 1.338020 GCAAGAACAGGGGTTTGAGTG 59.662 52.381 0.00 0.00 37.36 3.51
1104 2394 0.602372 GCGGCAATCTCCTCATCCTC 60.602 60.000 0.00 0.00 0.00 3.71
1113 2403 3.999603 TCTCCTCATCCTCTGGAAATGA 58.000 45.455 0.00 0.00 34.34 2.57
1118 2408 5.907662 TCCTCATCCTCTGGAAATGACTTAT 59.092 40.000 0.00 0.00 34.34 1.73
1127 2418 4.599041 TGGAAATGACTTATCAGGGTTGG 58.401 43.478 0.00 0.00 38.57 3.77
1145 2436 4.736896 GTGCCCGACAGTCCCGAC 62.737 72.222 0.00 0.00 0.00 4.79
1397 3641 7.215085 CACAGAGAAGGAATCACATGATATGA 58.785 38.462 0.00 0.00 33.73 2.15
1399 3643 9.097946 ACAGAGAAGGAATCACATGATATGATA 57.902 33.333 0.00 0.00 35.72 2.15
1454 3698 1.873591 ACACCGCAGAAATTGTCAGTC 59.126 47.619 0.00 0.00 0.00 3.51
1455 3699 1.136252 CACCGCAGAAATTGTCAGTCG 60.136 52.381 0.00 0.00 0.00 4.18
1481 3726 1.479389 CCTTGCTTCCCTTCAACCACT 60.479 52.381 0.00 0.00 0.00 4.00
1507 3752 6.207417 GTCTCATTTTCTGAAGTTGATCCCAA 59.793 38.462 5.25 0.00 32.14 4.12
1510 3755 7.380536 TCATTTTCTGAAGTTGATCCCAATTG 58.619 34.615 0.00 0.00 34.39 2.32
1557 3807 3.169512 AGTACCCAATTCAACCCAAGG 57.830 47.619 0.00 0.00 0.00 3.61
1626 3876 4.811969 TCCAAGCCACGAGATAAAGTAA 57.188 40.909 0.00 0.00 0.00 2.24
1633 3883 6.704310 AGCCACGAGATAAAGTAACCTAAAA 58.296 36.000 0.00 0.00 0.00 1.52
1634 3884 6.592994 AGCCACGAGATAAAGTAACCTAAAAC 59.407 38.462 0.00 0.00 0.00 2.43
1635 3885 6.369615 GCCACGAGATAAAGTAACCTAAAACA 59.630 38.462 0.00 0.00 0.00 2.83
1636 3886 7.095102 GCCACGAGATAAAGTAACCTAAAACAA 60.095 37.037 0.00 0.00 0.00 2.83
1637 3887 8.225777 CCACGAGATAAAGTAACCTAAAACAAC 58.774 37.037 0.00 0.00 0.00 3.32
1638 3888 8.225777 CACGAGATAAAGTAACCTAAAACAACC 58.774 37.037 0.00 0.00 0.00 3.77
1639 3889 8.152898 ACGAGATAAAGTAACCTAAAACAACCT 58.847 33.333 0.00 0.00 0.00 3.50
1640 3890 9.643693 CGAGATAAAGTAACCTAAAACAACCTA 57.356 33.333 0.00 0.00 0.00 3.08
1658 3908 8.281212 ACAACCTAGAACAGCCTTATAATTTG 57.719 34.615 0.00 0.00 0.00 2.32
1663 3913 8.739972 CCTAGAACAGCCTTATAATTTGTTTGT 58.260 33.333 9.41 5.26 32.58 2.83
1713 3963 6.244552 TGATTTCCTCTTCAGATAGCATGT 57.755 37.500 0.00 0.00 0.00 3.21
1854 4104 1.965930 GGTGCGTGTTGATGCTCCA 60.966 57.895 0.00 0.00 44.17 3.86
1993 4243 5.188434 TCCACATCTTGTTCCAGATTGATC 58.812 41.667 0.00 0.00 30.50 2.92
2015 4265 8.949177 TGATCCATACACAATCATATTGCATAC 58.051 33.333 0.00 0.00 0.00 2.39
2061 4311 9.219603 CTTGGAAAATTGTACATCTGAGTTCTA 57.780 33.333 0.00 0.00 0.00 2.10
2132 4382 4.081406 AGCACACATCCTTCATTTAAGCA 58.919 39.130 0.00 0.00 33.49 3.91
2137 4387 7.707893 GCACACATCCTTCATTTAAGCATAATT 59.292 33.333 0.00 0.00 33.49 1.40
2264 4519 3.057245 CCTTAGCTCCAAAGGTTTGCTTC 60.057 47.826 5.69 0.00 38.98 3.86
2452 4809 6.779860 ACTGAACACAACCTTAGTATGGATT 58.220 36.000 9.01 0.00 0.00 3.01
2459 4816 7.770897 ACACAACCTTAGTATGGATTCATCTTC 59.229 37.037 9.01 0.00 34.96 2.87
2462 4819 5.310857 ACCTTAGTATGGATTCATCTTCCCC 59.689 44.000 9.01 0.00 34.96 4.81
2568 4925 8.654230 AGATTATGACCATATATGATTGACGC 57.346 34.615 14.54 0.00 0.00 5.19
2576 4933 5.446340 CCATATATGATTGACGCGTTCATGG 60.446 44.000 27.01 19.81 32.84 3.66
2587 4949 0.388391 CGTTCATGGGCGCACATTTT 60.388 50.000 25.55 0.00 0.00 1.82
2629 5012 3.113260 AGATAGCAGATTGGTAACCGC 57.887 47.619 0.00 0.00 33.73 5.68
2750 5134 1.135575 GCAAAGCTTCATGGACTTCCG 60.136 52.381 0.00 0.00 39.43 4.30
2771 5155 3.063180 CGAAGATTGTGAGCATCCAGAAC 59.937 47.826 0.00 0.00 0.00 3.01
2822 5206 0.534412 AAGGTGAGGCAGAGATGTCG 59.466 55.000 0.00 0.00 0.00 4.35
2855 5240 8.099364 TCTATTCATTTTCAGTCACTTGAACC 57.901 34.615 0.00 0.00 36.84 3.62
2909 5373 1.392853 GTCGCAGTTGATCTTGCTGAG 59.607 52.381 13.29 10.76 32.39 3.35
2912 5376 2.157738 GCAGTTGATCTTGCTGAGGTT 58.842 47.619 13.29 0.00 32.39 3.50
2960 5424 3.597728 CTCGCCTACTCCCCGCTC 61.598 72.222 0.00 0.00 0.00 5.03
3001 5465 5.167121 CGGAAAGTATCTGGATGATAGCTG 58.833 45.833 0.00 0.00 38.23 4.24
3008 5472 1.945394 CTGGATGATAGCTGTGGCAAC 59.055 52.381 0.00 0.00 41.70 4.17
3080 5544 0.831307 CCCCTCTGGCTAAGGTACAC 59.169 60.000 0.00 0.00 31.51 2.90
3091 5555 3.740141 GCTAAGGTACACACACACACACT 60.740 47.826 0.00 0.00 0.00 3.55
3097 5561 1.290203 CACACACACACACTCTGGAC 58.710 55.000 0.00 0.00 0.00 4.02
3109 5573 2.104111 CACTCTGGACCACTACAACCAA 59.896 50.000 0.00 0.00 31.85 3.67
3110 5574 2.368875 ACTCTGGACCACTACAACCAAG 59.631 50.000 0.00 0.00 31.85 3.61
3111 5575 2.368875 CTCTGGACCACTACAACCAAGT 59.631 50.000 0.00 0.00 31.85 3.16
3112 5576 3.576982 CTCTGGACCACTACAACCAAGTA 59.423 47.826 0.00 0.00 31.85 2.24
3113 5577 3.322828 TCTGGACCACTACAACCAAGTAC 59.677 47.826 0.00 0.00 31.85 2.73
3114 5578 3.311091 TGGACCACTACAACCAAGTACT 58.689 45.455 0.00 0.00 0.00 2.73
3115 5579 3.322828 TGGACCACTACAACCAAGTACTC 59.677 47.826 0.00 0.00 0.00 2.59
3116 5580 3.306571 GGACCACTACAACCAAGTACTCC 60.307 52.174 0.00 0.00 0.00 3.85
3117 5581 2.636403 ACCACTACAACCAAGTACTCCC 59.364 50.000 0.00 0.00 0.00 4.30
3118 5582 2.904434 CCACTACAACCAAGTACTCCCT 59.096 50.000 0.00 0.00 0.00 4.20
3119 5583 3.056035 CCACTACAACCAAGTACTCCCTC 60.056 52.174 0.00 0.00 0.00 4.30
3120 5584 3.833070 CACTACAACCAAGTACTCCCTCT 59.167 47.826 0.00 0.00 0.00 3.69
3121 5585 4.283722 CACTACAACCAAGTACTCCCTCTT 59.716 45.833 0.00 0.00 0.00 2.85
3122 5586 5.479375 CACTACAACCAAGTACTCCCTCTTA 59.521 44.000 0.00 0.00 0.00 2.10
3123 5587 6.154706 CACTACAACCAAGTACTCCCTCTTAT 59.845 42.308 0.00 0.00 0.00 1.73
3124 5588 7.341256 CACTACAACCAAGTACTCCCTCTTATA 59.659 40.741 0.00 0.00 0.00 0.98
3125 5589 6.793505 ACAACCAAGTACTCCCTCTTATAG 57.206 41.667 0.00 0.00 0.00 1.31
3126 5590 6.262207 ACAACCAAGTACTCCCTCTTATAGT 58.738 40.000 0.00 0.00 0.00 2.12
3127 5591 6.154706 ACAACCAAGTACTCCCTCTTATAGTG 59.845 42.308 0.00 0.00 0.00 2.74
3128 5592 6.088541 ACCAAGTACTCCCTCTTATAGTGA 57.911 41.667 0.00 0.00 0.00 3.41
3129 5593 5.892686 ACCAAGTACTCCCTCTTATAGTGAC 59.107 44.000 0.00 0.00 0.00 3.67
3130 5594 5.302313 CCAAGTACTCCCTCTTATAGTGACC 59.698 48.000 0.00 0.00 0.00 4.02
3131 5595 5.998128 AGTACTCCCTCTTATAGTGACCT 57.002 43.478 0.00 0.00 0.00 3.85
3132 5596 7.288560 CAAGTACTCCCTCTTATAGTGACCTA 58.711 42.308 0.00 0.00 0.00 3.08
3133 5597 7.463054 AGTACTCCCTCTTATAGTGACCTAA 57.537 40.000 0.00 0.00 0.00 2.69
3134 5598 7.880623 AGTACTCCCTCTTATAGTGACCTAAA 58.119 38.462 0.00 0.00 0.00 1.85
3135 5599 8.342270 AGTACTCCCTCTTATAGTGACCTAAAA 58.658 37.037 0.00 0.00 0.00 1.52
3136 5600 7.421087 ACTCCCTCTTATAGTGACCTAAAAC 57.579 40.000 0.00 0.00 0.00 2.43
3137 5601 6.096564 ACTCCCTCTTATAGTGACCTAAAACG 59.903 42.308 0.00 0.00 0.00 3.60
3138 5602 5.954150 TCCCTCTTATAGTGACCTAAAACGT 59.046 40.000 0.00 0.00 0.00 3.99
3139 5603 6.096001 TCCCTCTTATAGTGACCTAAAACGTC 59.904 42.308 0.00 0.00 0.00 4.34
3140 5604 6.096564 CCCTCTTATAGTGACCTAAAACGTCT 59.903 42.308 0.00 0.00 0.00 4.18
3141 5605 7.363617 CCCTCTTATAGTGACCTAAAACGTCTT 60.364 40.741 0.00 0.00 0.00 3.01
3142 5606 8.680903 CCTCTTATAGTGACCTAAAACGTCTTA 58.319 37.037 0.00 0.00 0.00 2.10
3143 5607 9.500864 CTCTTATAGTGACCTAAAACGTCTTAC 57.499 37.037 0.00 0.00 0.00 2.34
3144 5608 9.013229 TCTTATAGTGACCTAAAACGTCTTACA 57.987 33.333 0.00 0.00 0.00 2.41
3145 5609 9.798994 CTTATAGTGACCTAAAACGTCTTACAT 57.201 33.333 0.00 0.00 0.00 2.29
3148 5612 7.186021 AGTGACCTAAAACGTCTTACATTTG 57.814 36.000 0.00 0.00 0.00 2.32
3149 5613 6.764560 AGTGACCTAAAACGTCTTACATTTGT 59.235 34.615 0.00 0.00 0.00 2.83
3150 5614 6.849305 GTGACCTAAAACGTCTTACATTTGTG 59.151 38.462 0.00 0.00 0.00 3.33
3151 5615 6.539464 TGACCTAAAACGTCTTACATTTGTGT 59.461 34.615 0.00 0.00 0.00 3.72
3152 5616 6.721321 ACCTAAAACGTCTTACATTTGTGTG 58.279 36.000 0.00 0.00 0.00 3.82
3153 5617 6.316890 ACCTAAAACGTCTTACATTTGTGTGT 59.683 34.615 0.00 0.00 36.13 3.72
3154 5618 7.148205 ACCTAAAACGTCTTACATTTGTGTGTT 60.148 33.333 0.00 0.00 33.62 3.32
3155 5619 7.698970 CCTAAAACGTCTTACATTTGTGTGTTT 59.301 33.333 0.00 0.00 33.62 2.83
3156 5620 9.705471 CTAAAACGTCTTACATTTGTGTGTTTA 57.295 29.630 0.00 0.00 33.62 2.01
3157 5621 7.958112 AAACGTCTTACATTTGTGTGTTTAC 57.042 32.000 0.00 0.00 33.62 2.01
3158 5622 6.665474 ACGTCTTACATTTGTGTGTTTACA 57.335 33.333 0.00 0.00 33.62 2.41
3159 5623 6.711579 ACGTCTTACATTTGTGTGTTTACAG 58.288 36.000 0.00 0.00 37.52 2.74
3160 5624 6.535865 ACGTCTTACATTTGTGTGTTTACAGA 59.464 34.615 0.00 0.00 37.52 3.41
3161 5625 7.063456 CGTCTTACATTTGTGTGTTTACAGAG 58.937 38.462 0.00 0.00 37.52 3.35
3162 5626 7.352739 GTCTTACATTTGTGTGTTTACAGAGG 58.647 38.462 0.00 0.00 37.52 3.69
3163 5627 6.485313 TCTTACATTTGTGTGTTTACAGAGGG 59.515 38.462 0.00 0.00 37.52 4.30
3164 5628 4.787551 ACATTTGTGTGTTTACAGAGGGA 58.212 39.130 0.00 0.00 37.52 4.20
3165 5629 4.821805 ACATTTGTGTGTTTACAGAGGGAG 59.178 41.667 0.00 0.00 37.52 4.30
3166 5630 4.497291 TTTGTGTGTTTACAGAGGGAGT 57.503 40.909 0.00 0.00 37.52 3.85
3176 5640 7.652507 GTGTTTACAGAGGGAGTAGTATATTGC 59.347 40.741 0.00 0.00 0.00 3.56
3182 5646 5.186021 AGAGGGAGTAGTATATTGCCATTCG 59.814 44.000 0.00 0.00 41.33 3.34
3227 5706 2.822561 TGTGTTGTTTTGACAGGAAGCA 59.177 40.909 0.00 0.00 0.00 3.91
3261 5740 0.371645 CAAGGTCGCGAAGAAGCATC 59.628 55.000 12.06 0.00 36.85 3.91
3368 5847 2.562738 TCAGCTGAAGGAGAACATCGAA 59.437 45.455 15.67 0.00 0.00 3.71
3421 5900 4.232221 CCACAAGTTCTTGATGACATTGC 58.768 43.478 17.75 0.00 0.00 3.56
3635 6116 1.202687 TGCATCGGATGTCCAGATTCC 60.203 52.381 18.54 0.38 35.14 3.01
3731 6212 0.525668 GTCCGACGAGTCATGCGATT 60.526 55.000 0.00 0.00 0.00 3.34
3734 6215 0.842613 CGACGAGTCATGCGATTGAG 59.157 55.000 4.02 0.00 0.00 3.02
3754 6235 8.768501 ATTGAGTTCTCTACCATCTATACACA 57.231 34.615 1.53 0.00 0.00 3.72
3755 6236 7.569639 TGAGTTCTCTACCATCTATACACAC 57.430 40.000 1.53 0.00 0.00 3.82
4122 6605 0.540597 AAGGGCTGGCAAAGAAGACC 60.541 55.000 2.88 0.00 42.53 3.85
4239 6722 6.435292 AAAGGACTACAATACAGAACAGGT 57.565 37.500 0.00 0.00 0.00 4.00
4261 6744 6.708054 AGGTATGAACAAAGTCAACTGAGAAG 59.292 38.462 0.00 0.00 0.00 2.85
4262 6745 6.483640 GGTATGAACAAAGTCAACTGAGAAGT 59.516 38.462 0.00 0.00 0.00 3.01
4265 6748 6.403049 TGAACAAAGTCAACTGAGAAGTACA 58.597 36.000 0.00 0.00 0.00 2.90
4285 6768 3.005897 ACATACTATCCGCAGATGGTGTC 59.994 47.826 9.04 0.00 43.41 3.67
4291 6774 2.528743 CGCAGATGGTGTCGATGCC 61.529 63.158 0.00 0.00 33.32 4.40
4383 6866 7.607991 GTGGATCTATGGAATAATGGATTTCGT 59.392 37.037 0.00 0.00 28.81 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 1049 2.550978 AGGAATAGTGTGTGCGTATGC 58.449 47.619 0.00 0.00 43.20 3.14
126 1061 3.704566 TCGAAGGTGCATGTAGGAATAGT 59.295 43.478 0.00 0.00 0.00 2.12
130 1065 2.176045 TCTCGAAGGTGCATGTAGGAA 58.824 47.619 0.00 0.00 0.00 3.36
138 1073 0.321564 CCCAACATCTCGAAGGTGCA 60.322 55.000 0.00 0.00 0.00 4.57
139 1074 1.648467 GCCCAACATCTCGAAGGTGC 61.648 60.000 0.00 0.00 0.00 5.01
153 1088 2.988684 GATGTTGTGCCGGCCCAA 60.989 61.111 26.77 23.77 0.00 4.12
154 1089 2.130821 TAAGATGTTGTGCCGGCCCA 62.131 55.000 26.77 17.94 0.00 5.36
156 1091 0.451783 CTTAAGATGTTGTGCCGGCC 59.548 55.000 26.77 16.24 0.00 6.13
158 1093 3.689161 TCAATCTTAAGATGTTGTGCCGG 59.311 43.478 18.61 0.00 34.49 6.13
188 1123 2.124942 GTAGGGCTGAGCAGGTGC 60.125 66.667 6.82 0.00 42.49 5.01
189 1124 0.107945 GAAGTAGGGCTGAGCAGGTG 60.108 60.000 6.82 0.00 0.00 4.00
192 1149 0.107945 GGTGAAGTAGGGCTGAGCAG 60.108 60.000 6.82 0.00 0.00 4.24
223 1180 1.795768 AATGAACGCACAGATCACGT 58.204 45.000 0.00 0.00 42.81 4.49
236 1193 2.157474 GCATTTTCGGGTGCAAATGAAC 59.843 45.455 10.07 0.00 39.96 3.18
237 1194 2.411904 GCATTTTCGGGTGCAAATGAA 58.588 42.857 10.07 1.77 39.96 2.57
270 1227 1.709760 CCGATGTGCACAGCTTACG 59.290 57.895 30.29 23.49 0.00 3.18
273 1230 3.425713 CGCCGATGTGCACAGCTT 61.426 61.111 30.29 12.51 0.00 3.74
288 1245 0.109964 TTTTACAGCCATCAACGCGC 60.110 50.000 5.73 0.00 0.00 6.86
290 1247 1.617740 GCTTTTACAGCCATCAACGC 58.382 50.000 0.00 0.00 43.65 4.84
305 1262 3.131396 CACTAGACTGTTGAACGGCTTT 58.869 45.455 3.64 0.00 0.00 3.51
308 1265 2.059541 GTCACTAGACTGTTGAACGGC 58.940 52.381 3.64 0.00 41.64 5.68
309 1266 2.296471 AGGTCACTAGACTGTTGAACGG 59.704 50.000 1.93 1.93 44.36 4.44
310 1267 3.566523 GAGGTCACTAGACTGTTGAACG 58.433 50.000 0.00 0.00 44.36 3.95
311 1268 3.252701 TCGAGGTCACTAGACTGTTGAAC 59.747 47.826 0.00 0.00 44.36 3.18
312 1269 3.252701 GTCGAGGTCACTAGACTGTTGAA 59.747 47.826 0.00 0.00 43.46 2.69
313 1270 2.812591 GTCGAGGTCACTAGACTGTTGA 59.187 50.000 0.00 0.00 43.46 3.18
314 1271 2.412977 CGTCGAGGTCACTAGACTGTTG 60.413 54.545 0.00 0.00 44.28 3.33
315 1272 1.805345 CGTCGAGGTCACTAGACTGTT 59.195 52.381 0.00 0.00 44.28 3.16
316 1273 1.270732 ACGTCGAGGTCACTAGACTGT 60.271 52.381 4.63 4.03 44.28 3.55
317 1274 1.440708 ACGTCGAGGTCACTAGACTG 58.559 55.000 4.63 3.54 44.28 3.51
318 1275 2.891112 CTACGTCGAGGTCACTAGACT 58.109 52.381 15.00 0.00 44.28 3.24
319 1276 1.327156 GCTACGTCGAGGTCACTAGAC 59.673 57.143 15.00 0.10 43.39 2.59
320 1277 1.206610 AGCTACGTCGAGGTCACTAGA 59.793 52.381 15.00 0.00 0.00 2.43
321 1278 1.654317 AGCTACGTCGAGGTCACTAG 58.346 55.000 15.00 7.68 0.00 2.57
322 1279 2.105006 AAGCTACGTCGAGGTCACTA 57.895 50.000 15.00 0.00 0.00 2.74
323 1280 1.245732 AAAGCTACGTCGAGGTCACT 58.754 50.000 15.00 10.34 0.00 3.41
324 1281 2.061740 AAAAGCTACGTCGAGGTCAC 57.938 50.000 15.00 8.11 0.00 3.67
325 1282 4.445452 AATAAAAGCTACGTCGAGGTCA 57.555 40.909 15.00 1.01 0.00 4.02
331 1288 6.292168 CCTCAACCATAATAAAAGCTACGTCG 60.292 42.308 0.00 0.00 0.00 5.12
334 1291 6.715464 CACCTCAACCATAATAAAAGCTACG 58.285 40.000 0.00 0.00 0.00 3.51
397 1354 4.004314 TCTTTGGAAAAATATCCGACGCA 58.996 39.130 0.00 0.00 42.76 5.24
401 1422 7.375053 CACCTTTTCTTTGGAAAAATATCCGA 58.625 34.615 5.61 0.00 46.57 4.55
402 1423 6.090763 GCACCTTTTCTTTGGAAAAATATCCG 59.909 38.462 5.61 0.00 46.57 4.18
433 1454 2.484264 AGCACATCGTTTTCTTACAGGC 59.516 45.455 0.00 0.00 0.00 4.85
469 1490 1.716826 AAGTCGATCGCTCGGTCCTC 61.717 60.000 11.09 0.00 45.10 3.71
479 1500 3.738282 GGATCCTTCATTCAAGTCGATCG 59.262 47.826 9.36 9.36 33.61 3.69
481 1502 4.760530 TGGATCCTTCATTCAAGTCGAT 57.239 40.909 14.23 0.00 0.00 3.59
484 1505 5.220739 CGTTCATGGATCCTTCATTCAAGTC 60.221 44.000 14.23 0.00 0.00 3.01
485 1506 4.637534 CGTTCATGGATCCTTCATTCAAGT 59.362 41.667 14.23 0.00 0.00 3.16
486 1507 4.877823 TCGTTCATGGATCCTTCATTCAAG 59.122 41.667 14.23 0.00 0.00 3.02
488 1509 4.486125 TCGTTCATGGATCCTTCATTCA 57.514 40.909 14.23 0.00 0.00 2.57
491 1512 4.694760 TCATCGTTCATGGATCCTTCAT 57.305 40.909 14.23 0.00 32.64 2.57
496 1517 3.407424 TGGATCATCGTTCATGGATCC 57.593 47.619 15.65 15.65 38.47 3.36
499 1520 2.880268 GCAATGGATCATCGTTCATGGA 59.120 45.455 0.00 0.00 32.64 3.41
511 1532 2.939103 ACTAAACGAGCAGCAATGGATC 59.061 45.455 0.00 0.00 0.00 3.36
557 1580 2.005971 AAACGTATGTCGGCTCCTTC 57.994 50.000 0.00 0.00 44.69 3.46
635 1658 1.337447 GGAAAAGACGGTCATCGGTCA 60.337 52.381 11.27 0.00 43.36 4.02
636 1659 1.067071 AGGAAAAGACGGTCATCGGTC 60.067 52.381 11.27 0.43 44.45 4.79
637 1660 0.974383 AGGAAAAGACGGTCATCGGT 59.026 50.000 11.27 0.00 44.45 4.69
638 1661 2.000447 GAAGGAAAAGACGGTCATCGG 59.000 52.381 11.27 0.00 44.45 4.18
639 1662 2.683968 TGAAGGAAAAGACGGTCATCG 58.316 47.619 11.27 0.00 45.88 3.84
640 1663 3.375299 CCATGAAGGAAAAGACGGTCATC 59.625 47.826 11.27 5.58 41.22 2.92
641 1664 3.009033 TCCATGAAGGAAAAGACGGTCAT 59.991 43.478 11.27 0.00 45.65 3.06
701 1724 1.365633 GTTTTGCGGGGTTGATGCA 59.634 52.632 0.00 0.00 36.72 3.96
718 1741 0.925466 CGGTCTTCGTCAAACGTTGT 59.075 50.000 0.00 0.00 43.14 3.32
739 1762 2.885644 CGGAGGTTGATGCGGACG 60.886 66.667 0.00 0.00 0.00 4.79
740 1763 3.195698 GCGGAGGTTGATGCGGAC 61.196 66.667 0.00 0.00 34.24 4.79
741 1764 4.467084 GGCGGAGGTTGATGCGGA 62.467 66.667 0.00 0.00 34.24 5.54
744 1767 3.195698 GACGGCGGAGGTTGATGC 61.196 66.667 13.24 0.00 0.00 3.91
745 1768 2.511600 GGACGGCGGAGGTTGATG 60.512 66.667 13.24 0.00 0.00 3.07
746 1769 4.143333 CGGACGGCGGAGGTTGAT 62.143 66.667 13.24 0.00 0.00 2.57
757 1780 3.432051 CTAGGAAGCCAGCGGACGG 62.432 68.421 0.00 0.00 0.00 4.79
758 1781 2.105128 CTAGGAAGCCAGCGGACG 59.895 66.667 0.00 0.00 0.00 4.79
759 1782 2.202946 GCTAGGAAGCCAGCGGAC 60.203 66.667 0.00 0.00 43.40 4.79
776 1799 2.573340 GCAGGTGGGGCGAAAATG 59.427 61.111 0.00 0.00 0.00 2.32
853 1876 3.031660 GTTCACCGGCGAACTAGAG 57.968 57.895 24.72 0.00 41.70 2.43
893 1916 1.004440 GTCTCTCTTGTGCCGCCTT 60.004 57.895 0.00 0.00 0.00 4.35
898 1921 1.298014 CCCTGGTCTCTCTTGTGCC 59.702 63.158 0.00 0.00 0.00 5.01
905 1928 5.422214 TGAAAGAAATACCCTGGTCTCTC 57.578 43.478 0.00 0.00 0.00 3.20
950 1973 1.888512 CACCAGTATGCAGCCACTTTT 59.111 47.619 0.00 0.00 31.97 2.27
988 2011 3.779759 TCTTGCACATTCCAACAAACAC 58.220 40.909 0.00 0.00 0.00 3.32
1051 2341 4.625742 AGCATCATTTGTCGCGTATATACC 59.374 41.667 5.77 0.00 0.00 2.73
1104 2394 4.641989 CCAACCCTGATAAGTCATTTCCAG 59.358 45.833 0.00 0.00 32.98 3.86
1113 2403 0.331616 GGCACCCAACCCTGATAAGT 59.668 55.000 0.00 0.00 0.00 2.24
1134 2425 2.202756 GCCATCGTCGGGACTGTC 60.203 66.667 0.00 0.00 0.00 3.51
1280 2571 8.317891 ACAACGACAACATTAGAAACATGATA 57.682 30.769 0.00 0.00 0.00 2.15
1338 3582 9.454859 CTCCAAAGGTCATCTAAAAGAAGTAAT 57.545 33.333 0.00 0.00 0.00 1.89
1397 3641 9.240734 GATGCCCTGATCAAAAGAATAAGATAT 57.759 33.333 0.00 0.00 0.00 1.63
1399 3643 7.064866 TGATGCCCTGATCAAAAGAATAAGAT 58.935 34.615 0.00 0.00 29.11 2.40
1454 3698 1.740025 GAAGGGAAGCAAGGAATGTCG 59.260 52.381 0.00 0.00 0.00 4.35
1455 3699 2.795329 TGAAGGGAAGCAAGGAATGTC 58.205 47.619 0.00 0.00 0.00 3.06
1465 3709 1.202818 AGACAGTGGTTGAAGGGAAGC 60.203 52.381 0.00 0.00 0.00 3.86
1481 3726 5.707298 GGGATCAACTTCAGAAAATGAGACA 59.293 40.000 0.00 0.00 39.68 3.41
1522 3767 6.732896 TTGGGTACTAAAAGGCAATGAAAA 57.267 33.333 0.00 0.00 0.00 2.29
1557 3807 2.495669 CAGTCCTTCCTTGAGTCTCCTC 59.504 54.545 0.00 0.00 38.27 3.71
1626 3876 4.104261 AGGCTGTTCTAGGTTGTTTTAGGT 59.896 41.667 0.00 0.00 0.00 3.08
1633 3883 7.888546 ACAAATTATAAGGCTGTTCTAGGTTGT 59.111 33.333 0.00 0.00 0.00 3.32
1634 3884 8.281212 ACAAATTATAAGGCTGTTCTAGGTTG 57.719 34.615 0.00 0.00 0.00 3.77
1635 3885 8.879427 AACAAATTATAAGGCTGTTCTAGGTT 57.121 30.769 0.00 0.00 0.00 3.50
1636 3886 8.739972 CAAACAAATTATAAGGCTGTTCTAGGT 58.260 33.333 9.01 0.00 30.16 3.08
1637 3887 8.739972 ACAAACAAATTATAAGGCTGTTCTAGG 58.260 33.333 9.01 4.59 30.16 3.02
1640 3890 9.297037 ACTACAAACAAATTATAAGGCTGTTCT 57.703 29.630 9.01 3.23 30.16 3.01
1641 3891 9.908152 AACTACAAACAAATTATAAGGCTGTTC 57.092 29.630 9.01 0.00 30.16 3.18
1643 3893 9.908152 GAAACTACAAACAAATTATAAGGCTGT 57.092 29.630 0.00 0.00 0.00 4.40
1658 3908 6.443792 ACAAATGGATTCGGAAACTACAAAC 58.556 36.000 0.00 0.00 0.00 2.93
1663 3913 6.110707 GGACTACAAATGGATTCGGAAACTA 58.889 40.000 0.00 0.00 0.00 2.24
1713 3963 4.438065 CGTGTTTCAGTGACACCATTCAAA 60.438 41.667 6.95 0.00 43.38 2.69
1753 4003 8.792633 CAAAATTACCTGGTCAGAAACAGAATA 58.207 33.333 0.63 0.00 36.86 1.75
1968 4218 5.005740 TCAATCTGGAACAAGATGTGGAAG 58.994 41.667 0.00 0.00 38.70 3.46
1971 4221 4.337555 GGATCAATCTGGAACAAGATGTGG 59.662 45.833 0.00 0.00 38.70 4.17
1993 4243 9.401873 CAAAGTATGCAATATGATTGTGTATGG 57.598 33.333 0.00 0.00 0.00 2.74
2049 4299 8.404000 CAAAGGATGGAAAATAGAACTCAGATG 58.596 37.037 0.00 0.00 0.00 2.90
2076 4326 9.235537 GTCTATATAAGACGACAAAAAGACTCC 57.764 37.037 0.00 0.00 45.05 3.85
2246 4501 2.071778 TGAAGCAAACCTTTGGAGCT 57.928 45.000 0.00 0.00 38.57 4.09
2264 4519 2.437281 ACCTATCTGGCCTGAAGACATG 59.563 50.000 17.04 5.14 40.22 3.21
2356 4611 6.809630 ATTAGTTCCTGAAGAGCTTTCAAC 57.190 37.500 10.97 7.73 37.26 3.18
2429 4785 6.878923 TGAATCCATACTAAGGTTGTGTTCAG 59.121 38.462 0.00 0.00 0.00 3.02
2439 4795 5.549619 AGGGGAAGATGAATCCATACTAAGG 59.450 44.000 0.00 0.00 38.80 2.69
2452 4809 3.459598 CACCAAATCCTAGGGGAAGATGA 59.540 47.826 9.46 0.00 45.78 2.92
2459 4816 1.063717 ACATGCACCAAATCCTAGGGG 60.064 52.381 9.46 4.44 0.00 4.79
2462 4819 5.750067 GCAAAATACATGCACCAAATCCTAG 59.250 40.000 0.00 0.00 43.29 3.02
2552 4909 5.446340 CCATGAACGCGTCAATCATATATGG 60.446 44.000 20.99 16.60 40.50 2.74
2558 4915 1.016627 CCCATGAACGCGTCAATCAT 58.983 50.000 14.44 16.05 40.50 2.45
2559 4916 1.643868 GCCCATGAACGCGTCAATCA 61.644 55.000 14.44 14.14 40.50 2.57
2568 4925 0.388391 AAAATGTGCGCCCATGAACG 60.388 50.000 6.01 0.00 0.00 3.95
2576 4933 2.536803 CTGCATATTCAAAATGTGCGCC 59.463 45.455 4.18 0.00 38.58 6.53
2587 4949 3.632643 TGGCTGTCTTCTGCATATTCA 57.367 42.857 0.00 0.00 39.69 2.57
2629 5012 6.936900 CCAACAGGGAATTATATACTGGTCTG 59.063 42.308 0.00 0.00 40.01 3.51
2750 5134 3.063180 CGTTCTGGATGCTCACAATCTTC 59.937 47.826 0.00 0.00 0.00 2.87
2771 5155 4.761235 TCTCACAAGTAGACTGTAACCG 57.239 45.455 0.00 0.00 0.00 4.44
2810 5194 0.532573 TCTTGGTCGACATCTCTGCC 59.467 55.000 18.91 0.00 0.00 4.85
2822 5206 8.394121 GTGACTGAAAATGAATAGATCTTGGTC 58.606 37.037 0.00 0.00 0.00 4.02
2855 5240 5.482908 GTGCAGACTCCATTATACCATAGG 58.517 45.833 0.00 0.00 0.00 2.57
2912 5376 1.260538 TGCAGTTGTTTGGGTGGCAA 61.261 50.000 0.00 0.00 0.00 4.52
2960 5424 3.414700 GTCAGAACACCGCTGCCG 61.415 66.667 0.00 0.00 33.45 5.69
3001 5465 1.405105 TGAAACTCTTGCTGTTGCCAC 59.595 47.619 0.00 0.00 38.71 5.01
3008 5472 4.699257 AGATTTAGCCTGAAACTCTTGCTG 59.301 41.667 0.00 0.00 33.63 4.41
3062 5526 1.207329 GTGTGTACCTTAGCCAGAGGG 59.793 57.143 3.06 0.00 38.65 4.30
3066 5530 2.224185 TGTGTGTGTGTACCTTAGCCAG 60.224 50.000 0.00 0.00 0.00 4.85
3071 5535 3.702548 AGAGTGTGTGTGTGTGTACCTTA 59.297 43.478 0.00 0.00 0.00 2.69
3074 5538 2.201732 CAGAGTGTGTGTGTGTGTACC 58.798 52.381 0.00 0.00 0.00 3.34
3078 5542 1.290203 GTCCAGAGTGTGTGTGTGTG 58.710 55.000 0.00 0.00 0.00 3.82
3080 5544 0.177836 TGGTCCAGAGTGTGTGTGTG 59.822 55.000 0.00 0.00 0.00 3.82
3091 5555 2.404559 ACTTGGTTGTAGTGGTCCAGA 58.595 47.619 0.00 0.00 0.00 3.86
3097 5561 2.904434 AGGGAGTACTTGGTTGTAGTGG 59.096 50.000 0.00 0.00 0.00 4.00
3109 5573 5.998128 AGGTCACTATAAGAGGGAGTACT 57.002 43.478 0.00 0.00 38.68 2.73
3110 5574 8.412456 GTTTTAGGTCACTATAAGAGGGAGTAC 58.588 40.741 0.00 0.00 38.68 2.73
3111 5575 7.284034 CGTTTTAGGTCACTATAAGAGGGAGTA 59.716 40.741 0.00 0.00 38.68 2.59
3112 5576 6.096564 CGTTTTAGGTCACTATAAGAGGGAGT 59.903 42.308 0.00 0.00 38.68 3.85
3113 5577 6.096564 ACGTTTTAGGTCACTATAAGAGGGAG 59.903 42.308 0.00 0.00 38.68 4.30
3114 5578 5.954150 ACGTTTTAGGTCACTATAAGAGGGA 59.046 40.000 0.00 0.00 34.12 4.20
3115 5579 6.096564 AGACGTTTTAGGTCACTATAAGAGGG 59.903 42.308 0.00 0.00 35.60 4.30
3116 5580 7.098074 AGACGTTTTAGGTCACTATAAGAGG 57.902 40.000 0.00 0.00 35.60 3.69
3117 5581 9.500864 GTAAGACGTTTTAGGTCACTATAAGAG 57.499 37.037 0.00 0.00 35.60 2.85
3118 5582 9.013229 TGTAAGACGTTTTAGGTCACTATAAGA 57.987 33.333 0.00 0.00 35.60 2.10
3119 5583 9.798994 ATGTAAGACGTTTTAGGTCACTATAAG 57.201 33.333 0.00 0.00 35.60 1.73
3122 5586 8.932791 CAAATGTAAGACGTTTTAGGTCACTAT 58.067 33.333 0.00 0.00 35.31 2.12
3123 5587 7.927629 ACAAATGTAAGACGTTTTAGGTCACTA 59.072 33.333 0.00 0.00 35.31 2.74
3124 5588 6.764560 ACAAATGTAAGACGTTTTAGGTCACT 59.235 34.615 0.00 0.00 35.31 3.41
3125 5589 6.849305 CACAAATGTAAGACGTTTTAGGTCAC 59.151 38.462 0.00 0.00 35.31 3.67
3126 5590 6.539464 ACACAAATGTAAGACGTTTTAGGTCA 59.461 34.615 0.00 0.00 35.31 4.02
3127 5591 6.849305 CACACAAATGTAAGACGTTTTAGGTC 59.151 38.462 0.00 0.00 35.31 3.85
3128 5592 6.316890 ACACACAAATGTAAGACGTTTTAGGT 59.683 34.615 0.00 0.00 35.31 3.08
3129 5593 6.721321 ACACACAAATGTAAGACGTTTTAGG 58.279 36.000 0.00 0.00 35.31 2.69
3130 5594 8.609478 AAACACACAAATGTAAGACGTTTTAG 57.391 30.769 0.00 0.00 35.31 1.85
3131 5595 9.488124 GTAAACACACAAATGTAAGACGTTTTA 57.512 29.630 0.00 0.00 35.31 1.52
3132 5596 8.021973 TGTAAACACACAAATGTAAGACGTTTT 58.978 29.630 0.00 0.00 35.31 2.43
3133 5597 7.528307 TGTAAACACACAAATGTAAGACGTTT 58.472 30.769 0.00 0.00 37.78 3.60
3134 5598 7.064847 TCTGTAAACACACAAATGTAAGACGTT 59.935 33.333 0.00 0.00 36.72 3.99
3135 5599 6.535865 TCTGTAAACACACAAATGTAAGACGT 59.464 34.615 0.00 0.00 36.72 4.34
3136 5600 6.939627 TCTGTAAACACACAAATGTAAGACG 58.060 36.000 0.00 0.00 36.72 4.18
3137 5601 7.352739 CCTCTGTAAACACACAAATGTAAGAC 58.647 38.462 0.00 0.00 36.72 3.01
3138 5602 6.485313 CCCTCTGTAAACACACAAATGTAAGA 59.515 38.462 0.00 0.00 36.72 2.10
3139 5603 6.485313 TCCCTCTGTAAACACACAAATGTAAG 59.515 38.462 0.00 0.00 36.72 2.34
3140 5604 6.358178 TCCCTCTGTAAACACACAAATGTAA 58.642 36.000 0.00 0.00 36.72 2.41
3141 5605 5.931294 TCCCTCTGTAAACACACAAATGTA 58.069 37.500 0.00 0.00 36.72 2.29
3142 5606 4.787551 TCCCTCTGTAAACACACAAATGT 58.212 39.130 0.00 0.00 40.80 2.71
3143 5607 4.821805 ACTCCCTCTGTAAACACACAAATG 59.178 41.667 0.00 0.00 0.00 2.32
3144 5608 5.048846 ACTCCCTCTGTAAACACACAAAT 57.951 39.130 0.00 0.00 0.00 2.32
3145 5609 4.497291 ACTCCCTCTGTAAACACACAAA 57.503 40.909 0.00 0.00 0.00 2.83
3146 5610 4.652421 ACTACTCCCTCTGTAAACACACAA 59.348 41.667 0.00 0.00 0.00 3.33
3147 5611 4.220724 ACTACTCCCTCTGTAAACACACA 58.779 43.478 0.00 0.00 0.00 3.72
3148 5612 4.868314 ACTACTCCCTCTGTAAACACAC 57.132 45.455 0.00 0.00 0.00 3.82
3149 5613 8.692710 CAATATACTACTCCCTCTGTAAACACA 58.307 37.037 0.00 0.00 0.00 3.72
3150 5614 7.652507 GCAATATACTACTCCCTCTGTAAACAC 59.347 40.741 0.00 0.00 0.00 3.32
3151 5615 7.201974 GGCAATATACTACTCCCTCTGTAAACA 60.202 40.741 0.00 0.00 0.00 2.83
3152 5616 7.153315 GGCAATATACTACTCCCTCTGTAAAC 58.847 42.308 0.00 0.00 0.00 2.01
3153 5617 6.842280 TGGCAATATACTACTCCCTCTGTAAA 59.158 38.462 0.00 0.00 0.00 2.01
3154 5618 6.378745 TGGCAATATACTACTCCCTCTGTAA 58.621 40.000 0.00 0.00 0.00 2.41
3155 5619 5.960704 TGGCAATATACTACTCCCTCTGTA 58.039 41.667 0.00 0.00 0.00 2.74
3156 5620 4.816126 TGGCAATATACTACTCCCTCTGT 58.184 43.478 0.00 0.00 0.00 3.41
3157 5621 6.365970 AATGGCAATATACTACTCCCTCTG 57.634 41.667 0.00 0.00 0.00 3.35
3158 5622 5.186021 CGAATGGCAATATACTACTCCCTCT 59.814 44.000 0.00 0.00 0.00 3.69
3159 5623 5.185249 TCGAATGGCAATATACTACTCCCTC 59.815 44.000 0.00 0.00 0.00 4.30
3160 5624 5.084519 TCGAATGGCAATATACTACTCCCT 58.915 41.667 0.00 0.00 0.00 4.20
3161 5625 5.401531 TCGAATGGCAATATACTACTCCC 57.598 43.478 0.00 0.00 0.00 4.30
3162 5626 7.907214 ATTTCGAATGGCAATATACTACTCC 57.093 36.000 0.00 0.00 0.00 3.85
3202 5669 5.708948 CTTCCTGTCAAAACAACACAAGAA 58.291 37.500 0.00 0.00 34.24 2.52
3204 5671 3.859386 GCTTCCTGTCAAAACAACACAAG 59.141 43.478 0.00 0.00 34.24 3.16
3296 5775 3.124921 GTGAATGGGCGGTCACGG 61.125 66.667 0.00 0.00 41.36 4.94
3299 5778 1.549243 TAGCTGTGAATGGGCGGTCA 61.549 55.000 0.00 0.00 0.00 4.02
3308 5787 3.474600 GATGATGGTGCTAGCTGTGAAT 58.525 45.455 17.23 2.78 0.00 2.57
3401 5880 3.814842 TCGCAATGTCATCAAGAACTTGT 59.185 39.130 13.15 0.48 41.16 3.16
3421 5900 6.306837 GTCTCTGTATCTCTTGAAAACAGTCG 59.693 42.308 0.00 0.00 39.38 4.18
3596 6077 7.652105 CCGATGCACTTTATTAACTCTTAGCTA 59.348 37.037 0.00 0.00 0.00 3.32
3597 6078 6.480320 CCGATGCACTTTATTAACTCTTAGCT 59.520 38.462 0.00 0.00 0.00 3.32
3599 6080 8.491152 CATCCGATGCACTTTATTAACTCTTAG 58.509 37.037 0.00 0.00 0.00 2.18
3635 6116 1.134367 CATTCAGTGCTGCAATGGAGG 59.866 52.381 27.09 18.67 29.97 4.30
3656 6137 1.595794 GTGTGGGTTGTAACTCGTGTG 59.404 52.381 0.00 0.00 29.87 3.82
3712 6193 0.525668 AATCGCATGACTCGTCGGAC 60.526 55.000 0.00 0.00 0.00 4.79
3731 6212 7.067129 GTGTGTGTATAGATGGTAGAGAACTCA 59.933 40.741 4.64 0.00 0.00 3.41
3734 6215 6.973474 GTGTGTGTGTATAGATGGTAGAGAAC 59.027 42.308 0.00 0.00 0.00 3.01
3754 6235 5.650266 TGTAAAACTGAATGGAAGTGTGTGT 59.350 36.000 0.00 0.00 0.00 3.72
3755 6236 6.130298 TGTAAAACTGAATGGAAGTGTGTG 57.870 37.500 0.00 0.00 0.00 3.82
4068 6551 5.475564 GGATAACCGGCAATACAAACCATAT 59.524 40.000 0.00 0.00 0.00 1.78
4122 6605 0.886490 AAAGGCTTCGTCTGTGGCAG 60.886 55.000 0.00 0.00 0.00 4.85
4171 6654 9.653287 TTACTGTCTTCTGTTGTATCAATTAGG 57.347 33.333 0.00 0.00 0.00 2.69
4239 6722 8.201464 TGTACTTCTCAGTTGACTTTGTTCATA 58.799 33.333 0.00 0.00 34.06 2.15
4261 6744 4.022242 ACACCATCTGCGGATAGTATGTAC 60.022 45.833 7.96 0.00 0.00 2.90
4262 6745 4.149598 ACACCATCTGCGGATAGTATGTA 58.850 43.478 7.96 0.00 0.00 2.29
4265 6748 2.229062 CGACACCATCTGCGGATAGTAT 59.771 50.000 7.96 0.00 0.00 2.12
4409 6892 9.744468 GTTGGTCTTGAAAATACTTTTGTATGT 57.256 29.630 0.00 0.00 44.21 2.29


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

AutoCloner maintained by Alex Coulton.