Multiple sequence alignment - TraesCS1D01G427200

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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 TraesCS1D01G427200 chr1D 100.000 4290 0 0 1 4290 479772441 479776730 0.000000e+00 7923
1 TraesCS1D01G427200 chr1D 85.375 1053 109 19 1695 2733 460356992 460358013 0.000000e+00 1050
2 TraesCS1D01G427200 chr1D 85.375 1053 108 19 1698 2736 489736712 489735692 0.000000e+00 1050
3 TraesCS1D01G427200 chr1D 89.231 520 22 17 1135 1634 460356490 460356995 1.690000e-173 619
4 TraesCS1D01G427200 chr1D 87.172 343 13 12 2768 3100 489735410 489735089 1.130000e-95 361
5 TraesCS1D01G427200 chr1A 88.298 2239 125 43 1926 4077 576220704 576222892 0.000000e+00 2556
6 TraesCS1D01G427200 chr1A 85.936 1415 77 53 225 1586 576219025 576220370 0.000000e+00 1399
7 TraesCS1D01G427200 chr1A 88.339 283 31 2 1654 1935 576220397 576220678 5.310000e-89 339
8 TraesCS1D01G427200 chr1A 88.210 229 16 5 1 228 576218746 576218964 3.290000e-66 263
9 TraesCS1D01G427200 chr1A 82.432 148 11 6 4149 4290 576222915 576223053 9.750000e-22 115
10 TraesCS1D01G427200 chr1B 82.987 2022 165 81 855 2833 668053559 668055444 0.000000e+00 1663
11 TraesCS1D01G427200 chr1B 86.126 937 43 38 2768 3642 668055863 668056774 0.000000e+00 929
12 TraesCS1D01G427200 chr1B 98.000 100 2 0 4191 4290 668056827 668056926 1.590000e-39 174
13 TraesCS1D01G427200 chr1B 100.000 59 0 0 3685 3743 668056770 668056828 4.540000e-20 110
14 TraesCS1D01G427200 chr3B 89.772 1183 71 25 1926 3095 8943028 8944173 0.000000e+00 1469
15 TraesCS1D01G427200 chr7D 85.727 1149 115 22 1698 2833 179698976 179697864 0.000000e+00 1168
16 TraesCS1D01G427200 chr7D 86.076 1106 103 21 1698 2788 331779615 331778546 0.000000e+00 1142
17 TraesCS1D01G427200 chr7D 85.470 1053 108 18 1695 2733 31391711 31392732 0.000000e+00 1055
18 TraesCS1D01G427200 chr7D 89.231 520 22 17 1135 1634 31391209 31391714 1.690000e-173 619
19 TraesCS1D01G427200 chr7D 88.654 520 25 18 1135 1634 549498626 549499131 1.710000e-168 603
20 TraesCS1D01G427200 chr7D 87.252 353 13 11 2768 3109 31393017 31393348 1.460000e-99 374
21 TraesCS1D01G427200 chr7D 90.000 160 8 3 73 229 590367035 590367189 2.620000e-47 200
22 TraesCS1D01G427200 chr7D 87.975 158 11 3 73 227 603469185 603469033 3.410000e-41 180
23 TraesCS1D01G427200 chr7D 75.912 411 54 21 224 628 509830593 509830222 7.380000e-38 169
24 TraesCS1D01G427200 chr7D 75.912 411 54 22 224 628 590367258 590367629 7.380000e-38 169
25 TraesCS1D01G427200 chr7D 74.696 411 59 21 224 628 603468962 603468591 1.610000e-29 141
26 TraesCS1D01G427200 chr6D 85.755 1053 105 18 1698 2736 54417224 54416203 0.000000e+00 1072
27 TraesCS1D01G427200 chr6D 88.654 520 25 18 1135 1634 54417729 54417224 1.710000e-168 603
28 TraesCS1D01G427200 chr6D 76.413 814 129 37 2093 2881 449923815 449924590 8.710000e-102 381
29 TraesCS1D01G427200 chr6D 87.252 353 13 11 2768 3109 54415921 54415590 1.460000e-99 374
30 TraesCS1D01G427200 chr6D 79.953 424 51 21 1977 2380 449920663 449921072 9.080000e-72 281
31 TraesCS1D01G427200 chr6D 77.951 449 82 14 2356 2792 387600451 387600894 9.150000e-67 265
32 TraesCS1D01G427200 chr6D 86.364 242 19 7 1487 1720 449919037 449919272 7.120000e-63 252
33 TraesCS1D01G427200 chr6D 78.240 409 61 14 2516 2911 449991851 449992244 1.990000e-58 237
34 TraesCS1D01G427200 chr6D 89.873 158 8 3 73 227 432828964 432829116 3.380000e-46 196
35 TraesCS1D01G427200 chr6D 87.500 88 8 2 3204 3290 449992369 449992454 9.820000e-17 99
36 TraesCS1D01G427200 chr4D 85.551 1052 109 17 1695 2733 3463249 3464270 0.000000e+00 1061
37 TraesCS1D01G427200 chr4D 88.846 520 24 17 1135 1634 3462747 3463252 3.670000e-170 608
38 TraesCS1D01G427200 chr4D 86.977 430 22 13 2768 3184 3464554 3464962 1.820000e-123 453
39 TraesCS1D01G427200 chrUn 85.361 1052 111 17 1695 2733 105262032 105263053 0.000000e+00 1050
40 TraesCS1D01G427200 chrUn 89.423 520 21 17 1135 1634 105261530 105262035 3.640000e-175 625
41 TraesCS1D01G427200 chrUn 87.252 353 13 11 2768 3109 105263338 105263669 1.460000e-99 374
42 TraesCS1D01G427200 chr3D 85.375 1053 108 19 1695 2733 50834479 50835499 0.000000e+00 1050
43 TraesCS1D01G427200 chr3D 89.231 520 22 17 1135 1634 50833977 50834482 1.690000e-173 619
44 TraesCS1D01G427200 chr3D 87.252 353 13 11 2768 3109 50835784 50836115 1.460000e-99 374
45 TraesCS1D01G427200 chr5D 85.049 1030 108 19 1695 2709 442365302 442366300 0.000000e+00 1007
46 TraesCS1D01G427200 chr5D 89.038 520 23 17 1135 1634 442364800 442365305 7.880000e-172 614
47 TraesCS1D01G427200 chr5D 87.674 430 19 13 2768 3184 442366479 442366887 1.810000e-128 470
48 TraesCS1D01G427200 chr6A 89.844 512 38 5 1926 2431 324803205 324802702 0.000000e+00 645
49 TraesCS1D01G427200 chr6A 88.225 552 40 9 1048 1590 324804074 324803539 1.680000e-178 636
50 TraesCS1D01G427200 chr6A 88.333 180 15 2 2656 2835 595491670 595491843 1.210000e-50 211
51 TraesCS1D01G427200 chr6B 79.433 423 54 16 1977 2380 682121294 682121702 7.070000e-68 268
52 TraesCS1D01G427200 chr6B 83.813 278 34 5 1977 2254 682316810 682316544 1.980000e-63 254
53 TraesCS1D01G427200 chr6B 89.773 88 8 1 3204 3290 682123042 682123129 1.260000e-20 111
54 TraesCS1D01G427200 chr6B 88.636 88 9 1 3204 3290 682314976 682314889 5.870000e-19 106


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 TraesCS1D01G427200 chr1D 479772441 479776730 4289 False 7923.000000 7923 100.000000 1 4290 1 chr1D.!!$F1 4289
1 TraesCS1D01G427200 chr1D 460356490 460358013 1523 False 834.500000 1050 87.303000 1135 2733 2 chr1D.!!$F2 1598
2 TraesCS1D01G427200 chr1D 489735089 489736712 1623 True 705.500000 1050 86.273500 1698 3100 2 chr1D.!!$R1 1402
3 TraesCS1D01G427200 chr1A 576218746 576223053 4307 False 934.400000 2556 86.643000 1 4290 5 chr1A.!!$F1 4289
4 TraesCS1D01G427200 chr1B 668053559 668056926 3367 False 719.000000 1663 91.778250 855 4290 4 chr1B.!!$F1 3435
5 TraesCS1D01G427200 chr3B 8943028 8944173 1145 False 1469.000000 1469 89.772000 1926 3095 1 chr3B.!!$F1 1169
6 TraesCS1D01G427200 chr7D 179697864 179698976 1112 True 1168.000000 1168 85.727000 1698 2833 1 chr7D.!!$R1 1135
7 TraesCS1D01G427200 chr7D 331778546 331779615 1069 True 1142.000000 1142 86.076000 1698 2788 1 chr7D.!!$R2 1090
8 TraesCS1D01G427200 chr7D 31391209 31393348 2139 False 682.666667 1055 87.317667 1135 3109 3 chr7D.!!$F2 1974
9 TraesCS1D01G427200 chr7D 549498626 549499131 505 False 603.000000 603 88.654000 1135 1634 1 chr7D.!!$F1 499
10 TraesCS1D01G427200 chr6D 54415590 54417729 2139 True 683.000000 1072 87.220333 1135 3109 3 chr6D.!!$R1 1974
11 TraesCS1D01G427200 chr6D 449919037 449924590 5553 False 304.666667 381 80.910000 1487 2881 3 chr6D.!!$F3 1394
12 TraesCS1D01G427200 chr4D 3462747 3464962 2215 False 707.333333 1061 87.124667 1135 3184 3 chr4D.!!$F1 2049
13 TraesCS1D01G427200 chrUn 105261530 105263669 2139 False 683.000000 1050 87.345333 1135 3109 3 chrUn.!!$F1 1974
14 TraesCS1D01G427200 chr3D 50833977 50836115 2138 False 681.000000 1050 87.286000 1135 3109 3 chr3D.!!$F1 1974
15 TraesCS1D01G427200 chr5D 442364800 442366887 2087 False 697.000000 1007 87.253667 1135 3184 3 chr5D.!!$F1 2049
16 TraesCS1D01G427200 chr6A 324802702 324804074 1372 True 640.500000 645 89.034500 1048 2431 2 chr6A.!!$R1 1383

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
254 320 0.102844 CACCACAAACAACCCAGCAG 59.897 55.0 0.00 0.00 0.00 4.24 F
374 444 0.179134 CTCACCGACGATCTTGGGAC 60.179 60.0 7.27 0.00 0.00 4.46 F
1727 1903 0.179161 CGACGGTGAGAGCACTTAGG 60.179 60.0 0.00 0.00 44.52 2.69 F
2561 3983 0.739561 GCCCACGAGTACACTCTAGG 59.260 60.0 7.72 8.44 40.75 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1471 1626 0.471591 AGCTGAATGCCCCCAAACAA 60.472 50.0 0.00 0.0 44.23 2.83 R
2199 3585 0.471617 AGGCATCATAGGGCTGTCAC 59.528 55.0 0.00 0.0 39.98 3.67 R
2721 7213 0.107654 CCCTCCCGTTCAGGTGATTC 60.108 60.0 0.00 0.0 38.74 2.52 R
4082 9196 0.105453 ATCACTCGAGCCCCCTACAT 60.105 55.0 13.61 0.0 0.00 2.29 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
29 30 3.125316 CGGAGTAAATGACTTTGAGCCAC 59.875 47.826 0.00 0.00 39.06 5.01
35 36 1.082756 GACTTTGAGCCACGCAACG 60.083 57.895 0.00 0.00 0.00 4.10
36 37 2.427410 CTTTGAGCCACGCAACGC 60.427 61.111 0.00 0.00 0.00 4.84
38 39 2.660553 CTTTGAGCCACGCAACGCAA 62.661 55.000 0.00 0.00 0.00 4.85
39 40 2.928313 TTTGAGCCACGCAACGCAAC 62.928 55.000 0.00 0.00 0.00 4.17
40 41 4.683334 GAGCCACGCAACGCAACC 62.683 66.667 0.00 0.00 0.00 3.77
46 47 2.385091 ACGCAACGCAACCGGTATC 61.385 57.895 8.00 0.86 39.22 2.24
50 51 1.793714 GCAACGCAACCGGTATCAATG 60.794 52.381 8.00 2.39 39.22 2.82
52 53 2.673862 CAACGCAACCGGTATCAATGTA 59.326 45.455 8.00 0.00 39.22 2.29
63 64 6.126997 ACCGGTATCAATGTATGTACCTTTGA 60.127 38.462 4.49 7.60 35.38 2.69
75 76 8.421784 TGTATGTACCTTTGATCCTGAGTAATC 58.578 37.037 0.00 0.00 0.00 1.75
80 81 4.450419 CCTTTGATCCTGAGTAATCGATGC 59.550 45.833 0.00 0.00 0.00 3.91
81 82 3.667497 TGATCCTGAGTAATCGATGCC 57.333 47.619 0.00 0.00 0.00 4.40
102 103 0.475906 AAAGGAGCCTCACAGTTGCT 59.524 50.000 0.00 0.00 38.24 3.91
128 129 1.686428 CCTCTGAGTCAATCTCCCGGA 60.686 57.143 0.73 0.00 42.12 5.14
187 188 5.814188 TCAGCAGCAACATAACTTGATAGAG 59.186 40.000 0.00 0.00 0.00 2.43
190 191 5.814705 GCAGCAACATAACTTGATAGAGAGT 59.185 40.000 0.00 0.00 0.00 3.24
192 193 7.168972 GCAGCAACATAACTTGATAGAGAGTAG 59.831 40.741 0.00 0.00 0.00 2.57
198 199 8.062536 ACATAACTTGATAGAGAGTAGGTCCTT 58.937 37.037 0.00 0.00 0.00 3.36
199 200 6.783708 AACTTGATAGAGAGTAGGTCCTTG 57.216 41.667 0.00 0.00 0.00 3.61
200 201 4.647399 ACTTGATAGAGAGTAGGTCCTTGC 59.353 45.833 0.00 0.00 0.00 4.01
201 202 4.251103 TGATAGAGAGTAGGTCCTTGCA 57.749 45.455 0.00 0.00 0.00 4.08
202 203 4.809193 TGATAGAGAGTAGGTCCTTGCAT 58.191 43.478 0.00 0.00 0.00 3.96
203 204 5.211973 TGATAGAGAGTAGGTCCTTGCATT 58.788 41.667 0.00 0.00 0.00 3.56
215 216 2.107378 TCCTTGCATTGGTCCAACAGTA 59.893 45.455 6.41 0.00 0.00 2.74
233 299 7.542130 CCAACAGTAAGATAAATGCCAAGTTTC 59.458 37.037 0.00 0.00 0.00 2.78
234 300 7.158099 ACAGTAAGATAAATGCCAAGTTTCC 57.842 36.000 0.00 0.00 0.00 3.13
254 320 0.102844 CACCACAAACAACCCAGCAG 59.897 55.000 0.00 0.00 0.00 4.24
258 324 1.955778 CACAAACAACCCAGCAGATCA 59.044 47.619 0.00 0.00 0.00 2.92
272 338 5.509163 CCAGCAGATCATCCAAAATCAATCC 60.509 44.000 0.00 0.00 0.00 3.01
275 341 5.755813 CAGATCATCCAAAATCAATCCGAC 58.244 41.667 0.00 0.00 0.00 4.79
292 358 2.489971 CGACCAAGAGTAGCACCAAAA 58.510 47.619 0.00 0.00 0.00 2.44
366 436 0.386858 CGTGTGTTCTCACCGACGAT 60.387 55.000 0.00 0.00 42.50 3.73
374 444 0.179134 CTCACCGACGATCTTGGGAC 60.179 60.000 7.27 0.00 0.00 4.46
378 448 1.340795 ACCGACGATCTTGGGACTAGT 60.341 52.381 7.27 0.00 0.00 2.57
382 452 3.495377 CGACGATCTTGGGACTAGTAGAG 59.505 52.174 3.59 0.00 0.00 2.43
383 453 4.453751 GACGATCTTGGGACTAGTAGAGT 58.546 47.826 3.59 0.00 42.90 3.24
385 455 4.200874 CGATCTTGGGACTAGTAGAGTGT 58.799 47.826 3.59 0.00 39.06 3.55
419 489 4.761058 TCCGCTTCCTCCCGCTCT 62.761 66.667 0.00 0.00 0.00 4.09
500 574 1.265905 CGGACAAAAACCCTCGAAAGG 59.734 52.381 0.00 0.00 42.95 3.11
709 793 3.292481 ATGCTTGGGTGGCAGGGAG 62.292 63.158 0.00 0.00 43.15 4.30
722 806 2.066999 AGGGAGAGGGGAATGCGAC 61.067 63.158 0.00 0.00 0.00 5.19
757 841 3.412408 GGGGGCTGGGTTCCTCTC 61.412 72.222 0.00 0.00 0.00 3.20
758 842 3.787001 GGGGCTGGGTTCCTCTCG 61.787 72.222 0.00 0.00 0.00 4.04
759 843 3.787001 GGGCTGGGTTCCTCTCGG 61.787 72.222 0.00 0.00 0.00 4.63
760 844 2.683933 GGCTGGGTTCCTCTCGGA 60.684 66.667 0.00 0.00 37.60 4.55
761 845 2.726351 GGCTGGGTTCCTCTCGGAG 61.726 68.421 0.00 0.00 41.25 4.63
787 871 2.592861 GGCTCATCCGTCCATGGC 60.593 66.667 6.96 0.96 0.00 4.40
807 899 4.785453 CAAGAGCGGGAGGGTGGC 62.785 72.222 0.00 0.00 0.00 5.01
818 910 4.041762 GGGTGGCGGAATGGTGGA 62.042 66.667 0.00 0.00 0.00 4.02
828 920 1.683319 GGAATGGTGGAGAAGGCTTCC 60.683 57.143 23.09 10.99 0.00 3.46
942 1035 4.175337 GGCCGGGCTGCTCATGTA 62.175 66.667 22.87 0.00 0.00 2.29
943 1036 2.111878 GCCGGGCTGCTCATGTAT 59.888 61.111 12.87 0.00 0.00 2.29
944 1037 1.963338 GCCGGGCTGCTCATGTATC 60.963 63.158 12.87 0.00 0.00 2.24
961 1070 3.322466 CTCCTTCCGGGCCACAGT 61.322 66.667 4.39 0.00 34.39 3.55
1125 1266 2.969238 GACATGCGGGAGATGGCG 60.969 66.667 0.00 0.00 0.00 5.69
1293 1434 2.586792 GGAATCACGGGCTGAGCT 59.413 61.111 3.72 0.00 30.20 4.09
1295 1436 1.817099 GAATCACGGGCTGAGCTGG 60.817 63.158 3.72 0.00 30.20 4.85
1437 1585 2.091541 GCTCGATTTGGTTTGGATGGA 58.908 47.619 0.00 0.00 0.00 3.41
1438 1586 2.689983 GCTCGATTTGGTTTGGATGGAT 59.310 45.455 0.00 0.00 0.00 3.41
1439 1587 3.489738 GCTCGATTTGGTTTGGATGGATG 60.490 47.826 0.00 0.00 0.00 3.51
1440 1588 3.023119 TCGATTTGGTTTGGATGGATGG 58.977 45.455 0.00 0.00 0.00 3.51
1450 1598 1.301244 GATGGATGGCGCGTGATCT 60.301 57.895 8.43 0.00 0.00 2.75
1452 1600 0.882042 ATGGATGGCGCGTGATCTTC 60.882 55.000 8.43 3.42 0.00 2.87
1457 1605 1.234821 TGGCGCGTGATCTTCTTTTT 58.765 45.000 8.43 0.00 0.00 1.94
1482 1637 2.103941 TCTGAATTTGTTGTTTGGGGGC 59.896 45.455 0.00 0.00 0.00 5.80
1483 1638 1.839994 TGAATTTGTTGTTTGGGGGCA 59.160 42.857 0.00 0.00 0.00 5.36
1596 1751 3.396570 AAGGTAACCCCCTCCGCG 61.397 66.667 0.00 0.00 32.13 6.46
1634 1797 3.073798 TCAACAATGTTCAGGGGCTTCTA 59.926 43.478 0.00 0.00 0.00 2.10
1648 1811 2.541762 GGCTTCTAAACATAGCAGCGAG 59.458 50.000 0.00 0.00 37.24 5.03
1649 1812 2.541762 GCTTCTAAACATAGCAGCGAGG 59.458 50.000 0.00 0.00 35.05 4.63
1650 1813 3.786635 CTTCTAAACATAGCAGCGAGGT 58.213 45.455 0.00 0.00 0.00 3.85
1651 1814 3.438297 TCTAAACATAGCAGCGAGGTC 57.562 47.619 0.00 0.00 0.00 3.85
1652 1815 3.024547 TCTAAACATAGCAGCGAGGTCT 58.975 45.455 0.00 0.00 0.00 3.85
1703 1872 8.994429 TCTCTGAATTCTAAGTTTGTGATCTC 57.006 34.615 7.05 0.00 0.00 2.75
1711 1880 2.953020 AGTTTGTGATCTCTGCTCGAC 58.047 47.619 0.00 0.00 0.00 4.20
1727 1903 0.179161 CGACGGTGAGAGCACTTAGG 60.179 60.000 0.00 0.00 44.52 2.69
1736 1912 3.753272 TGAGAGCACTTAGGAAATGTTGC 59.247 43.478 0.00 0.00 0.00 4.17
1924 3301 1.059692 GTCGCATCATGTTCTGACGTG 59.940 52.381 0.00 0.00 42.87 4.49
1941 3318 6.039047 TCTGACGTGTCATAGGATTACCTTAC 59.961 42.308 2.72 0.00 40.32 2.34
1942 3319 5.653330 TGACGTGTCATAGGATTACCTTACA 59.347 40.000 0.00 0.00 39.97 2.41
1943 3320 6.145338 ACGTGTCATAGGATTACCTTACAG 57.855 41.667 0.00 0.00 45.36 2.74
1944 3321 5.655532 ACGTGTCATAGGATTACCTTACAGT 59.344 40.000 0.00 0.00 45.36 3.55
1945 3322 5.977725 CGTGTCATAGGATTACCTTACAGTG 59.022 44.000 0.00 0.00 45.36 3.66
1962 3339 7.489113 CCTTACAGTGTTGAAATATTGATTGGC 59.511 37.037 0.00 0.00 0.00 4.52
1987 3366 6.889301 AACTTGATCTCTTTCTGCAATTCA 57.111 33.333 0.00 0.00 0.00 2.57
1989 3368 8.571461 AACTTGATCTCTTTCTGCAATTCATA 57.429 30.769 0.00 0.00 0.00 2.15
2018 3397 2.413112 CGCATACTTGTCCAGTGAACAG 59.587 50.000 0.00 0.00 35.97 3.16
2023 3402 1.939934 CTTGTCCAGTGAACAGCGAAA 59.060 47.619 0.00 0.00 0.00 3.46
2126 3508 4.077108 AGGAAATTAAAACGGTGGACCTC 58.923 43.478 0.00 0.00 0.00 3.85
2171 3553 8.877779 GTTCATATATCATTATCTGGCACTGAC 58.122 37.037 0.00 0.00 39.59 3.51
2175 3557 1.212688 CATTATCTGGCACTGACCCCA 59.787 52.381 0.00 0.00 39.59 4.96
2202 3588 8.885722 GGTATGGATTTTGTAACTTAATCGTGA 58.114 33.333 0.00 0.00 0.00 4.35
2235 3621 6.256053 TGATGCCTTTATTTTCCTTCCTCTT 58.744 36.000 0.00 0.00 0.00 2.85
2284 3689 9.610705 ATCTGATGACATACTATGGATTTATGC 57.389 33.333 1.11 0.00 33.60 3.14
2307 3712 9.754382 ATGCTTGCAATTCCTGTAATAATTAAG 57.246 29.630 0.00 0.00 0.00 1.85
2324 3729 5.869753 ATTAAGCTCTGTGTCAACATGTC 57.130 39.130 0.00 0.00 35.22 3.06
2375 3780 2.033757 AGGCCACTGCTTGCAGAG 59.966 61.111 26.71 19.19 37.74 3.35
2450 3855 6.721321 TCGTTGGACTTTGACAATTTTAGAC 58.279 36.000 0.00 0.00 0.00 2.59
2561 3983 0.739561 GCCCACGAGTACACTCTAGG 59.260 60.000 7.72 8.44 40.75 3.02
2596 4018 8.897752 AGGATTTCAGAACTAATGTAAGAATGC 58.102 33.333 0.00 0.00 0.00 3.56
2653 7145 1.516161 GCAGACAGTTGCATGACTCA 58.484 50.000 0.00 0.00 43.53 3.41
2805 7779 5.420725 AAGTTGGATACTGTACATGCAGA 57.579 39.130 7.27 0.00 39.62 4.26
2806 7780 5.620738 AGTTGGATACTGTACATGCAGAT 57.379 39.130 7.27 0.00 39.62 2.90
2807 7781 5.363101 AGTTGGATACTGTACATGCAGATG 58.637 41.667 7.27 0.00 39.62 2.90
2808 7782 3.732212 TGGATACTGTACATGCAGATGC 58.268 45.455 7.27 0.00 39.62 3.91
2809 7783 8.535511 AGTTGGATACTGTACATGCAGATGCA 62.536 42.308 10.37 10.37 45.44 3.96
2882 7862 5.649782 AATCATTTCTAGTGTTTGCCTGG 57.350 39.130 0.00 0.00 0.00 4.45
2884 7864 1.616159 TTTCTAGTGTTTGCCTGGGC 58.384 50.000 4.43 4.43 42.35 5.36
2971 7962 4.097286 CCGTTGATACCCTGGTTTATTTGG 59.903 45.833 0.00 0.00 0.00 3.28
2980 7975 3.191791 CCTGGTTTATTTGGTTACCCGTG 59.808 47.826 0.00 0.00 0.00 4.94
3078 8082 4.161565 TGCGTAGAGGACTTGGATGTTTAT 59.838 41.667 0.00 0.00 0.00 1.40
3079 8083 5.361571 TGCGTAGAGGACTTGGATGTTTATA 59.638 40.000 0.00 0.00 0.00 0.98
3149 8155 1.037493 TTGTGCGAGTGGAGTAGTGT 58.963 50.000 0.00 0.00 0.00 3.55
3184 8191 5.760253 CAGAGATTGAACTGTGGTGTTACTT 59.240 40.000 0.00 0.00 0.00 2.24
3185 8192 6.929049 CAGAGATTGAACTGTGGTGTTACTTA 59.071 38.462 0.00 0.00 0.00 2.24
3186 8193 6.929606 AGAGATTGAACTGTGGTGTTACTTAC 59.070 38.462 0.00 0.00 0.00 2.34
3256 8263 1.072965 CAGCCTTTCCACTTCACCTCT 59.927 52.381 0.00 0.00 0.00 3.69
3302 8309 2.269023 TCAGGTGATGGTTCATGTCCT 58.731 47.619 10.06 0.00 33.56 3.85
3303 8310 2.644299 TCAGGTGATGGTTCATGTCCTT 59.356 45.455 10.06 5.02 33.56 3.36
3304 8311 3.012518 CAGGTGATGGTTCATGTCCTTC 58.987 50.000 13.94 13.94 33.56 3.46
3306 8313 3.267812 AGGTGATGGTTCATGTCCTTCAT 59.732 43.478 20.92 10.82 39.87 2.57
3307 8314 4.474651 AGGTGATGGTTCATGTCCTTCATA 59.525 41.667 20.92 6.56 39.87 2.15
3309 8316 4.576463 GTGATGGTTCATGTCCTTCATACC 59.424 45.833 20.92 11.54 39.87 2.73
3310 8317 3.260475 TGGTTCATGTCCTTCATACCG 57.740 47.619 10.06 0.00 37.76 4.02
3322 8354 0.907704 TCATACCGGAGCCAAGGTGT 60.908 55.000 9.46 0.00 41.51 4.16
3323 8355 0.744414 CATACCGGAGCCAAGGTGTG 60.744 60.000 9.46 4.93 41.83 3.82
3394 8438 3.303461 CGTAGTCTCTGAAGTATCCAGCG 60.303 52.174 0.00 0.00 0.00 5.18
3402 8446 2.036604 TGAAGTATCCAGCGTGTGTGAA 59.963 45.455 0.00 0.00 0.00 3.18
3429 8477 2.076100 TGTCGATTAAGTTGCTGCTGG 58.924 47.619 0.00 0.00 0.00 4.85
3464 8512 7.227049 TGTCTCTGTGAACATCTAACATGTA 57.773 36.000 0.00 0.00 0.00 2.29
3505 8553 8.889445 TGTATTCCATTCCATCCATGTATTCTA 58.111 33.333 0.00 0.00 0.00 2.10
3596 8665 1.002544 ACAGCTACAGTGGAAGCCTTC 59.997 52.381 14.20 0.00 39.64 3.46
3634 8703 2.270986 CCTCAGTTGCCACTTGCCC 61.271 63.158 0.00 0.00 40.16 5.36
3645 8714 0.538057 CACTTGCCCCTGCTGAAAGA 60.538 55.000 0.00 0.00 38.71 2.52
3648 8717 1.271656 CTTGCCCCTGCTGAAAGAAAG 59.728 52.381 0.00 0.00 38.71 2.62
3649 8718 1.181098 TGCCCCTGCTGAAAGAAAGC 61.181 55.000 0.00 0.00 41.22 3.51
3771 8849 2.595463 TGCCAGCCAGCAAGTGTC 60.595 61.111 0.00 0.00 40.56 3.67
3777 8855 0.250640 AGCCAGCAAGTGTCCTCTTG 60.251 55.000 5.05 5.05 45.09 3.02
3780 8858 1.876156 CCAGCAAGTGTCCTCTTGTTC 59.124 52.381 9.93 0.00 44.41 3.18
3810 8888 4.314708 CGTTGCTTCTTATCGTTTCGTTTG 59.685 41.667 0.00 0.00 0.00 2.93
3816 8894 3.430895 TCTTATCGTTTCGTTTGTCAGGC 59.569 43.478 0.00 0.00 0.00 4.85
3817 8895 0.872388 ATCGTTTCGTTTGTCAGGCC 59.128 50.000 0.00 0.00 0.00 5.19
3818 8896 1.161563 TCGTTTCGTTTGTCAGGCCC 61.162 55.000 0.00 0.00 0.00 5.80
3819 8897 1.440938 CGTTTCGTTTGTCAGGCCCA 61.441 55.000 0.00 0.00 0.00 5.36
3820 8898 0.741915 GTTTCGTTTGTCAGGCCCAA 59.258 50.000 0.00 0.00 0.00 4.12
3821 8899 1.135333 GTTTCGTTTGTCAGGCCCAAA 59.865 47.619 0.00 0.00 0.00 3.28
3822 8900 1.028905 TTCGTTTGTCAGGCCCAAAG 58.971 50.000 0.00 0.00 32.79 2.77
3823 8901 1.007387 CGTTTGTCAGGCCCAAAGC 60.007 57.895 0.00 0.00 42.60 3.51
3824 8902 1.733402 CGTTTGTCAGGCCCAAAGCA 61.733 55.000 0.00 0.00 46.50 3.91
3825 8903 0.463620 GTTTGTCAGGCCCAAAGCAA 59.536 50.000 0.00 0.00 46.50 3.91
3826 8904 0.752054 TTTGTCAGGCCCAAAGCAAG 59.248 50.000 0.00 0.00 46.50 4.01
3827 8905 0.106268 TTGTCAGGCCCAAAGCAAGA 60.106 50.000 0.00 0.00 46.50 3.02
3867 8955 6.273825 AGAAATACAACTGTATAGCTCCGTG 58.726 40.000 2.85 0.00 40.10 4.94
3868 8956 5.847111 AATACAACTGTATAGCTCCGTGA 57.153 39.130 2.85 0.00 40.10 4.35
3885 8974 7.039363 AGCTCCGTGAAGATAGATAAATTAGCT 60.039 37.037 0.00 0.00 0.00 3.32
3887 8976 9.134734 CTCCGTGAAGATAGATAAATTAGCTTC 57.865 37.037 0.00 0.00 41.53 3.86
3906 9016 5.654209 AGCTTCCCCTAAAGAAAATTAGCAG 59.346 40.000 0.00 0.00 32.62 4.24
3909 9019 5.506708 TCCCCTAAAGAAAATTAGCAGGTC 58.493 41.667 0.00 0.00 32.62 3.85
3915 9025 9.178758 CCTAAAGAAAATTAGCAGGTCTGTTAT 57.821 33.333 0.00 0.00 32.62 1.89
3927 9037 5.106908 GCAGGTCTGTTATTTTGTCTGTCTC 60.107 44.000 0.00 0.00 0.00 3.36
3943 9053 4.593634 TCTGTCTCGAGGGATCATAGAGTA 59.406 45.833 13.56 0.00 0.00 2.59
3946 9056 7.126573 TCTGTCTCGAGGGATCATAGAGTATAT 59.873 40.741 13.56 0.00 0.00 0.86
3968 9078 1.968704 TATCTGTCTCGGCGAGTCAT 58.031 50.000 33.31 22.34 28.80 3.06
3976 9086 2.991190 TCTCGGCGAGTCATAAACAAAC 59.009 45.455 33.31 0.00 0.00 2.93
3977 9087 2.070783 TCGGCGAGTCATAAACAAACC 58.929 47.619 4.99 0.00 0.00 3.27
3978 9088 2.073816 CGGCGAGTCATAAACAAACCT 58.926 47.619 0.00 0.00 0.00 3.50
3979 9089 2.159707 CGGCGAGTCATAAACAAACCTG 60.160 50.000 0.00 0.00 0.00 4.00
3980 9090 2.812011 GGCGAGTCATAAACAAACCTGT 59.188 45.455 0.00 0.00 37.39 4.00
3981 9091 3.120304 GGCGAGTCATAAACAAACCTGTC 60.120 47.826 0.00 0.00 33.45 3.51
3984 9094 5.504994 GCGAGTCATAAACAAACCTGTCAAA 60.505 40.000 0.00 0.00 33.45 2.69
4043 9157 3.857052 CGACAGTGTATGTGTATGGGTT 58.143 45.455 0.00 0.00 44.17 4.11
4055 9169 0.251564 TATGGGTTGGTGGCCACTTG 60.252 55.000 33.91 0.00 30.78 3.16
4085 9199 4.576879 CAGGCATGCATGTAGATAGATGT 58.423 43.478 26.79 0.00 30.38 3.06
4086 9200 5.727434 CAGGCATGCATGTAGATAGATGTA 58.273 41.667 26.79 0.00 30.38 2.29
4087 9201 5.811100 CAGGCATGCATGTAGATAGATGTAG 59.189 44.000 26.79 0.00 30.38 2.74
4088 9202 5.105023 AGGCATGCATGTAGATAGATGTAGG 60.105 44.000 26.79 0.00 30.38 3.18
4089 9203 5.114780 GCATGCATGTAGATAGATGTAGGG 58.885 45.833 26.79 0.00 30.38 3.53
4093 9207 4.357325 CATGTAGATAGATGTAGGGGGCT 58.643 47.826 0.00 0.00 0.00 5.19
4094 9208 4.048970 TGTAGATAGATGTAGGGGGCTC 57.951 50.000 0.00 0.00 0.00 4.70
4095 9209 2.223803 AGATAGATGTAGGGGGCTCG 57.776 55.000 0.00 0.00 0.00 5.03
4096 9210 1.711375 AGATAGATGTAGGGGGCTCGA 59.289 52.381 0.00 0.00 0.00 4.04
4097 9211 2.096248 GATAGATGTAGGGGGCTCGAG 58.904 57.143 8.45 8.45 0.00 4.04
4099 9213 0.757188 AGATGTAGGGGGCTCGAGTG 60.757 60.000 15.13 0.00 0.00 3.51
4100 9214 0.755698 GATGTAGGGGGCTCGAGTGA 60.756 60.000 15.13 0.00 0.00 3.41
4101 9215 0.105453 ATGTAGGGGGCTCGAGTGAT 60.105 55.000 15.13 0.00 0.00 3.06
4102 9216 0.325296 TGTAGGGGGCTCGAGTGATT 60.325 55.000 15.13 0.00 0.00 2.57
4103 9217 1.063492 TGTAGGGGGCTCGAGTGATTA 60.063 52.381 15.13 0.00 0.00 1.75
4104 9218 1.614413 GTAGGGGGCTCGAGTGATTAG 59.386 57.143 15.13 0.00 0.00 1.73
4105 9219 1.069935 GGGGGCTCGAGTGATTAGC 59.930 63.158 15.13 0.00 35.47 3.09
4106 9220 1.300233 GGGGCTCGAGTGATTAGCG 60.300 63.158 15.13 0.00 37.11 4.26
4107 9221 1.300233 GGGCTCGAGTGATTAGCGG 60.300 63.158 15.13 0.00 37.11 5.52
4108 9222 1.951631 GGCTCGAGTGATTAGCGGC 60.952 63.158 15.13 0.00 37.11 6.53
4109 9223 2.296480 GCTCGAGTGATTAGCGGCG 61.296 63.158 15.13 0.51 0.00 6.46
4110 9224 1.658717 CTCGAGTGATTAGCGGCGG 60.659 63.158 9.78 0.00 0.00 6.13
4111 9225 2.104331 CGAGTGATTAGCGGCGGT 59.896 61.111 18.21 18.21 0.00 5.68
4112 9226 2.230940 CGAGTGATTAGCGGCGGTG 61.231 63.158 23.33 0.00 0.00 4.94
4113 9227 1.883084 GAGTGATTAGCGGCGGTGG 60.883 63.158 23.33 0.00 0.00 4.61
4114 9228 2.895372 GTGATTAGCGGCGGTGGG 60.895 66.667 23.33 0.00 0.00 4.61
4115 9229 3.395702 TGATTAGCGGCGGTGGGT 61.396 61.111 23.33 7.15 0.00 4.51
4116 9230 2.895372 GATTAGCGGCGGTGGGTG 60.895 66.667 23.33 0.00 0.00 4.61
4117 9231 4.483243 ATTAGCGGCGGTGGGTGG 62.483 66.667 23.33 0.00 0.00 4.61
4126 9240 4.115199 GGTGGGTGGGCTGGCTAG 62.115 72.222 0.00 0.00 0.00 3.42
4127 9241 3.330720 GTGGGTGGGCTGGCTAGT 61.331 66.667 0.00 0.00 0.00 2.57
4128 9242 3.329889 TGGGTGGGCTGGCTAGTG 61.330 66.667 0.00 0.00 0.00 2.74
4129 9243 4.115199 GGGTGGGCTGGCTAGTGG 62.115 72.222 0.00 0.00 0.00 4.00
4130 9244 3.330720 GGTGGGCTGGCTAGTGGT 61.331 66.667 0.00 0.00 0.00 4.16
4131 9245 1.993391 GGTGGGCTGGCTAGTGGTA 60.993 63.158 0.00 0.00 0.00 3.25
4132 9246 1.345715 GGTGGGCTGGCTAGTGGTAT 61.346 60.000 0.00 0.00 0.00 2.73
4133 9247 0.106894 GTGGGCTGGCTAGTGGTATC 59.893 60.000 0.00 0.00 0.00 2.24
4134 9248 0.326143 TGGGCTGGCTAGTGGTATCA 60.326 55.000 0.00 0.00 0.00 2.15
4135 9249 0.106894 GGGCTGGCTAGTGGTATCAC 59.893 60.000 0.00 0.00 43.93 3.06
4136 9250 0.830648 GGCTGGCTAGTGGTATCACA 59.169 55.000 9.22 0.00 45.91 3.58
4137 9251 1.202580 GGCTGGCTAGTGGTATCACAG 60.203 57.143 9.22 5.15 45.91 3.66
4138 9252 1.202580 GCTGGCTAGTGGTATCACAGG 60.203 57.143 9.22 1.44 45.91 4.00
4139 9253 1.414181 CTGGCTAGTGGTATCACAGGG 59.586 57.143 9.22 0.00 45.91 4.45
4140 9254 1.273609 TGGCTAGTGGTATCACAGGGT 60.274 52.381 9.22 0.00 45.91 4.34
4141 9255 2.023791 TGGCTAGTGGTATCACAGGGTA 60.024 50.000 9.22 0.00 45.91 3.69
4142 9256 3.240302 GGCTAGTGGTATCACAGGGTAT 58.760 50.000 9.22 0.00 45.91 2.73
4143 9257 3.646637 GGCTAGTGGTATCACAGGGTATT 59.353 47.826 9.22 0.00 45.91 1.89
4144 9258 4.102681 GGCTAGTGGTATCACAGGGTATTT 59.897 45.833 9.22 0.00 45.91 1.40
4145 9259 5.397559 GGCTAGTGGTATCACAGGGTATTTT 60.398 44.000 9.22 0.00 45.91 1.82
4146 9260 5.758784 GCTAGTGGTATCACAGGGTATTTTC 59.241 44.000 9.22 0.00 45.91 2.29
4147 9261 5.112129 AGTGGTATCACAGGGTATTTTCC 57.888 43.478 9.22 0.00 45.91 3.13
4158 9272 2.100197 GGTATTTTCCCCTTGGTGAGC 58.900 52.381 0.00 0.00 0.00 4.26
4165 9279 2.115910 CCTTGGTGAGCCCTTGCA 59.884 61.111 0.00 0.00 41.13 4.08
4171 9285 2.281970 TGAGCCCTTGCAGTGCAG 60.282 61.111 18.81 12.20 40.61 4.41
4172 9286 2.282040 GAGCCCTTGCAGTGCAGT 60.282 61.111 18.81 1.81 40.61 4.40
4173 9287 2.596631 AGCCCTTGCAGTGCAGTG 60.597 61.111 18.81 17.56 40.61 3.66
4174 9288 4.353437 GCCCTTGCAGTGCAGTGC 62.353 66.667 34.65 34.65 40.61 4.40
4186 9300 0.594540 TGCAGTGCAAACGTGAATGC 60.595 50.000 17.26 12.74 42.86 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.427410 GCGTTGCGTGGCTCAAAG 60.427 61.111 0.00 0.00 0.00 2.77
29 30 1.902716 TTGATACCGGTTGCGTTGCG 61.903 55.000 15.04 0.00 0.00 4.85
35 36 4.212636 GGTACATACATTGATACCGGTTGC 59.787 45.833 15.04 5.82 0.00 4.17
36 37 5.607477 AGGTACATACATTGATACCGGTTG 58.393 41.667 15.04 7.13 41.71 3.77
38 39 5.881923 AAGGTACATACATTGATACCGGT 57.118 39.130 13.98 13.98 41.71 5.28
39 40 6.285224 TCAAAGGTACATACATTGATACCGG 58.715 40.000 0.00 0.00 41.71 5.28
40 41 7.117812 GGATCAAAGGTACATACATTGATACCG 59.882 40.741 16.19 0.00 40.83 4.02
41 42 8.157476 AGGATCAAAGGTACATACATTGATACC 58.843 37.037 18.88 17.97 41.22 2.73
42 43 8.993121 CAGGATCAAAGGTACATACATTGATAC 58.007 37.037 16.71 16.71 40.83 2.24
43 44 8.933653 TCAGGATCAAAGGTACATACATTGATA 58.066 33.333 16.19 5.04 40.83 2.15
46 47 7.050377 ACTCAGGATCAAAGGTACATACATTG 58.950 38.462 0.00 0.00 29.85 2.82
50 51 7.595502 CGATTACTCAGGATCAAAGGTACATAC 59.404 40.741 0.00 0.00 0.00 2.39
52 53 6.323996 TCGATTACTCAGGATCAAAGGTACAT 59.676 38.462 0.00 0.00 0.00 2.29
63 64 4.422073 TTTGGCATCGATTACTCAGGAT 57.578 40.909 0.00 0.00 0.00 3.24
75 76 0.677731 TGAGGCTCCTTTTGGCATCG 60.678 55.000 12.86 0.00 41.34 3.84
80 81 1.610522 CAACTGTGAGGCTCCTTTTGG 59.389 52.381 12.86 0.00 42.21 3.28
81 82 1.000938 GCAACTGTGAGGCTCCTTTTG 60.001 52.381 12.86 10.84 0.00 2.44
102 103 3.708631 GGAGATTGACTCAGAGGATTCCA 59.291 47.826 5.29 0.00 46.54 3.53
187 188 2.633488 GACCAATGCAAGGACCTACTC 58.367 52.381 14.81 0.00 0.00 2.59
190 191 1.367346 TGGACCAATGCAAGGACCTA 58.633 50.000 23.24 12.09 40.88 3.08
192 193 0.603065 GTTGGACCAATGCAAGGACC 59.397 55.000 18.60 18.60 36.75 4.46
198 199 3.500448 TCTTACTGTTGGACCAATGCA 57.500 42.857 10.83 3.71 0.00 3.96
199 200 6.509418 TTTATCTTACTGTTGGACCAATGC 57.491 37.500 10.83 0.00 0.00 3.56
200 201 6.974622 GCATTTATCTTACTGTTGGACCAATG 59.025 38.462 10.83 9.22 0.00 2.82
201 202 6.096846 GGCATTTATCTTACTGTTGGACCAAT 59.903 38.462 10.83 0.00 0.00 3.16
202 203 5.417580 GGCATTTATCTTACTGTTGGACCAA 59.582 40.000 1.69 1.69 0.00 3.67
203 204 4.947388 GGCATTTATCTTACTGTTGGACCA 59.053 41.667 0.00 0.00 0.00 4.02
215 216 4.222810 GGTGGGAAACTTGGCATTTATCTT 59.777 41.667 0.00 0.00 0.00 2.40
233 299 2.026945 GCTGGGTTGTTTGTGGTGGG 62.027 60.000 0.00 0.00 0.00 4.61
234 300 1.326213 TGCTGGGTTGTTTGTGGTGG 61.326 55.000 0.00 0.00 0.00 4.61
254 320 4.580167 TGGTCGGATTGATTTTGGATGATC 59.420 41.667 0.00 0.00 0.00 2.92
258 324 4.599041 TCTTGGTCGGATTGATTTTGGAT 58.401 39.130 0.00 0.00 0.00 3.41
272 338 2.163818 TTTGGTGCTACTCTTGGTCG 57.836 50.000 0.00 0.00 0.00 4.79
275 341 3.380004 TGTTGTTTTGGTGCTACTCTTGG 59.620 43.478 0.00 0.00 0.00 3.61
292 358 4.706842 ACCTGTAATCTCACCTTGTTGT 57.293 40.909 0.00 0.00 0.00 3.32
366 436 4.994282 TCAACACTCTACTAGTCCCAAGA 58.006 43.478 0.00 0.00 35.76 3.02
374 444 4.438472 GGCCTACGTTCAACACTCTACTAG 60.438 50.000 0.00 0.00 0.00 2.57
378 448 1.200716 CGGCCTACGTTCAACACTCTA 59.799 52.381 0.00 0.00 37.93 2.43
401 471 3.771160 GAGCGGGAGGAAGCGGAA 61.771 66.667 0.00 0.00 38.61 4.30
419 489 2.186903 GCGATTCAAGGCGGAGGA 59.813 61.111 0.00 0.00 0.00 3.71
474 548 2.989166 CGAGGGTTTTTGTCCGTACTAC 59.011 50.000 0.00 0.00 0.00 2.73
475 549 2.890311 TCGAGGGTTTTTGTCCGTACTA 59.110 45.455 0.00 0.00 0.00 1.82
476 550 1.688197 TCGAGGGTTTTTGTCCGTACT 59.312 47.619 0.00 0.00 0.00 2.73
500 574 1.984020 AGCCTTCGAGGGTTTCCTC 59.016 57.895 15.82 2.50 45.25 3.71
513 587 2.348998 CTTCGCCAGGTGAGCCTT 59.651 61.111 2.13 0.00 44.18 4.35
695 769 2.935481 CCTCTCCCTGCCACCCAA 60.935 66.667 0.00 0.00 0.00 4.12
740 824 3.412408 GAGAGGAACCCAGCCCCC 61.412 72.222 0.00 0.00 0.00 5.40
779 863 3.512516 GCTCTTGCCGCCATGGAC 61.513 66.667 18.40 5.97 42.00 4.02
802 894 2.438434 CTCCACCATTCCGCCACC 60.438 66.667 0.00 0.00 0.00 4.61
807 899 0.035056 AAGCCTTCTCCACCATTCCG 60.035 55.000 0.00 0.00 0.00 4.30
808 900 1.683319 GGAAGCCTTCTCCACCATTCC 60.683 57.143 4.15 0.00 0.00 3.01
809 901 1.683319 GGGAAGCCTTCTCCACCATTC 60.683 57.143 4.15 0.00 0.00 2.67
818 910 2.291856 CTTCTCGGGGAAGCCTTCT 58.708 57.895 4.39 0.00 43.88 2.85
828 920 1.446272 GTCAAGGACGCTTCTCGGG 60.446 63.158 0.00 0.00 43.86 5.14
961 1070 3.618171 GGTTTGCCCTTACGACTGA 57.382 52.632 0.00 0.00 0.00 3.41
1125 1266 4.821589 CTCCAGGCCGCCGTCTTC 62.822 72.222 3.05 0.00 0.00 2.87
1314 1458 1.877443 CCGTCCGACCTGACAAAAATT 59.123 47.619 0.00 0.00 34.88 1.82
1437 1585 1.453155 AAAAGAAGATCACGCGCCAT 58.547 45.000 5.73 0.00 0.00 4.40
1438 1586 1.234821 AAAAAGAAGATCACGCGCCA 58.765 45.000 5.73 0.00 0.00 5.69
1457 1605 5.396213 CCCCCAAACAACAAATTCAGAAGAA 60.396 40.000 0.00 0.00 38.31 2.52
1471 1626 0.471591 AGCTGAATGCCCCCAAACAA 60.472 50.000 0.00 0.00 44.23 2.83
1474 1629 0.471591 ACAAGCTGAATGCCCCCAAA 60.472 50.000 0.00 0.00 44.23 3.28
1475 1630 0.471591 AACAAGCTGAATGCCCCCAA 60.472 50.000 0.00 0.00 44.23 4.12
1482 1637 3.424039 CGTAGAGCACAACAAGCTGAATG 60.424 47.826 0.00 0.00 43.58 2.67
1483 1638 2.738846 CGTAGAGCACAACAAGCTGAAT 59.261 45.455 0.00 0.00 43.58 2.57
1634 1797 1.406069 CCAGACCTCGCTGCTATGTTT 60.406 52.381 0.00 0.00 34.56 2.83
1711 1880 2.743636 TTTCCTAAGTGCTCTCACCG 57.256 50.000 0.00 0.00 44.16 4.94
1727 1903 3.508762 CATCCTCAAGCAGCAACATTTC 58.491 45.455 0.00 0.00 0.00 2.17
1736 1912 2.097036 TCAAATGCCATCCTCAAGCAG 58.903 47.619 0.00 0.00 40.40 4.24
1924 3301 7.553334 TCAACACTGTAAGGTAATCCTATGAC 58.447 38.462 0.00 0.00 44.35 3.06
1941 3318 7.385752 AGTTTGCCAATCAATATTTCAACACTG 59.614 33.333 0.00 0.00 34.12 3.66
1942 3319 7.444299 AGTTTGCCAATCAATATTTCAACACT 58.556 30.769 0.00 0.00 34.12 3.55
1943 3320 7.656707 AGTTTGCCAATCAATATTTCAACAC 57.343 32.000 0.00 0.00 34.12 3.32
1944 3321 7.930325 TCAAGTTTGCCAATCAATATTTCAACA 59.070 29.630 0.00 0.00 34.12 3.33
1945 3322 8.309163 TCAAGTTTGCCAATCAATATTTCAAC 57.691 30.769 0.00 0.00 34.12 3.18
1962 3339 7.143340 TGAATTGCAGAAAGAGATCAAGTTTG 58.857 34.615 0.00 0.00 0.00 2.93
2018 3397 6.949578 TTGAATTTTCAAGGATCATTTCGC 57.050 33.333 1.66 0.00 41.88 4.70
2097 3479 3.057806 ACCGTTTTAATTTCCTGGAAGCG 60.058 43.478 9.42 1.27 0.00 4.68
2126 3508 1.561542 ACCCATCCTACTGGCTTCAAG 59.438 52.381 0.00 0.00 34.77 3.02
2171 3553 4.867086 AGTTACAAAATCCATACCTGGGG 58.133 43.478 0.00 0.00 43.34 4.96
2175 3557 8.889717 CACGATTAAGTTACAAAATCCATACCT 58.110 33.333 0.00 0.00 0.00 3.08
2199 3585 0.471617 AGGCATCATAGGGCTGTCAC 59.528 55.000 0.00 0.00 39.98 3.67
2202 3588 4.459852 AATAAAGGCATCATAGGGCTGT 57.540 40.909 0.00 0.00 41.44 4.40
2235 3621 6.159299 TGTCTTTCTGAAATTTCAATGCCA 57.841 33.333 20.82 10.51 36.64 4.92
2284 3689 9.455847 GAGCTTAATTATTACAGGAATTGCAAG 57.544 33.333 4.94 0.00 0.00 4.01
2307 3712 2.759191 TCTGACATGTTGACACAGAGC 58.241 47.619 9.48 0.00 35.94 4.09
2324 3729 6.866770 AGTGTGCTGAAAATTTGAATCATCTG 59.133 34.615 0.00 0.00 0.00 2.90
2399 3804 2.984471 CAGCTGCTAGCAAAACAACATG 59.016 45.455 19.86 4.63 45.56 3.21
2450 3855 7.222417 CAGATATTCTTGCACTTAGACAGAGTG 59.778 40.741 0.00 0.10 45.64 3.51
2596 4018 3.624777 AGCAGTGGGATCCAAACAATAG 58.375 45.455 15.23 4.53 34.18 1.73
2653 7145 6.040209 TCTGCACAAATATGCCAAGAAAAT 57.960 33.333 0.00 0.00 45.50 1.82
2721 7213 0.107654 CCCTCCCGTTCAGGTGATTC 60.108 60.000 0.00 0.00 38.74 2.52
2805 7779 4.070265 ATGGCTGGGTGGCTGCAT 62.070 61.111 0.50 0.00 42.34 3.96
2806 7780 4.746309 GATGGCTGGGTGGCTGCA 62.746 66.667 0.50 0.00 42.34 4.41
2807 7781 2.349100 ATAGATGGCTGGGTGGCTGC 62.349 60.000 0.00 0.00 42.34 5.25
2808 7782 0.184451 AATAGATGGCTGGGTGGCTG 59.816 55.000 0.00 0.00 42.34 4.85
2809 7783 1.701847 CTAATAGATGGCTGGGTGGCT 59.298 52.381 0.00 0.00 42.34 4.75
2810 7784 1.884067 GCTAATAGATGGCTGGGTGGC 60.884 57.143 0.00 0.00 42.18 5.01
2853 7827 8.947115 GGCAAACACTAGAAATGATTTACTACT 58.053 33.333 0.00 0.00 0.00 2.57
2854 7828 8.947115 AGGCAAACACTAGAAATGATTTACTAC 58.053 33.333 0.00 0.00 0.00 2.73
2882 7862 1.067354 CATTTGGCCTCTTGTCTTGCC 60.067 52.381 3.32 0.00 44.27 4.52
2884 7864 1.614903 TGCATTTGGCCTCTTGTCTTG 59.385 47.619 3.32 0.00 43.89 3.02
2892 7872 1.079612 GGTGCTTGCATTTGGCCTC 60.080 57.895 3.32 0.00 43.89 4.70
2929 7920 2.755655 CGGTACACTCTTCCTGTCAGAT 59.244 50.000 0.00 0.00 0.00 2.90
2971 7962 2.027469 AGGAAATCTGACCACGGGTAAC 60.027 50.000 0.00 0.00 35.25 2.50
2980 7975 4.565022 GCATCTAGCTAGGAAATCTGACC 58.435 47.826 20.58 0.00 41.15 4.02
3051 8049 1.001633 TCCAAGTCCTCTACGCAAACC 59.998 52.381 0.00 0.00 0.00 3.27
3149 8155 1.839354 TCAATCTCTGGTGCAGGCATA 59.161 47.619 0.00 0.00 31.51 3.14
3184 8191 2.093181 ACAGCAACGCATTAGGATGGTA 60.093 45.455 0.00 0.00 33.72 3.25
3185 8192 1.340017 ACAGCAACGCATTAGGATGGT 60.340 47.619 0.00 0.00 33.72 3.55
3186 8193 1.382522 ACAGCAACGCATTAGGATGG 58.617 50.000 0.00 0.00 33.72 3.51
3256 8263 3.973305 TGGAGTACATGATGCATTCCCTA 59.027 43.478 0.00 0.00 0.00 3.53
3296 8303 0.759346 GGCTCCGGTATGAAGGACAT 59.241 55.000 0.00 0.00 42.39 3.06
3299 8306 0.830648 CTTGGCTCCGGTATGAAGGA 59.169 55.000 0.00 0.00 34.93 3.36
3300 8307 0.179045 CCTTGGCTCCGGTATGAAGG 60.179 60.000 0.00 6.03 0.00 3.46
3302 8309 0.251916 CACCTTGGCTCCGGTATGAA 59.748 55.000 0.00 0.00 30.91 2.57
3303 8310 0.907704 ACACCTTGGCTCCGGTATGA 60.908 55.000 0.00 0.00 30.91 2.15
3304 8311 0.744414 CACACCTTGGCTCCGGTATG 60.744 60.000 0.00 0.00 30.91 2.39
3306 8313 2.589157 CCACACCTTGGCTCCGGTA 61.589 63.158 0.00 0.00 39.07 4.02
3307 8314 3.953775 CCACACCTTGGCTCCGGT 61.954 66.667 0.00 0.00 39.07 5.28
3309 8316 2.358737 GTCCACACCTTGGCTCCG 60.359 66.667 0.00 0.00 46.47 4.63
3310 8317 2.034221 GGTCCACACCTTGGCTCC 59.966 66.667 0.00 0.00 46.47 4.70
3322 8354 1.918293 AGGCCACGATCAAGGTCCA 60.918 57.895 5.01 0.00 0.00 4.02
3323 8355 1.450312 CAGGCCACGATCAAGGTCC 60.450 63.158 5.01 4.21 0.00 4.46
3324 8356 2.109126 GCAGGCCACGATCAAGGTC 61.109 63.158 5.01 0.00 0.00 3.85
3325 8357 2.045926 GCAGGCCACGATCAAGGT 60.046 61.111 5.01 0.00 0.00 3.50
3326 8358 3.197790 CGCAGGCCACGATCAAGG 61.198 66.667 12.47 0.00 0.00 3.61
3327 8359 3.869272 GCGCAGGCCACGATCAAG 61.869 66.667 20.97 0.00 0.00 3.02
3371 8406 3.549221 GCTGGATACTTCAGAGACTACGC 60.549 52.174 0.00 0.00 34.36 4.42
3379 8423 1.893137 ACACACGCTGGATACTTCAGA 59.107 47.619 0.00 0.00 34.36 3.27
3394 8438 5.530519 AATCGACATACATGTTCACACAC 57.469 39.130 2.30 0.00 41.95 3.82
3402 8446 5.220662 GCAGCAACTTAATCGACATACATGT 60.221 40.000 2.69 2.69 45.16 3.21
3505 8553 8.971073 CATTAAATGGAGGAAAAAGATGTACCT 58.029 33.333 0.00 0.00 0.00 3.08
3596 8665 5.415077 TGAGGCAAAATGGCAATAAAAATGG 59.585 36.000 6.68 0.00 46.46 3.16
3645 8714 4.366684 CCCCGGCCTTCCTGCTTT 62.367 66.667 0.00 0.00 0.00 3.51
3652 8721 4.410400 CACAGGTCCCCGGCCTTC 62.410 72.222 0.00 0.00 33.31 3.46
3770 8848 3.004315 GCAACGGAATTTGAACAAGAGGA 59.996 43.478 0.00 0.00 0.00 3.71
3771 8849 3.004734 AGCAACGGAATTTGAACAAGAGG 59.995 43.478 0.00 0.00 0.00 3.69
3777 8855 5.508224 CGATAAGAAGCAACGGAATTTGAAC 59.492 40.000 0.00 0.00 0.00 3.18
3780 8858 4.969816 ACGATAAGAAGCAACGGAATTTG 58.030 39.130 0.00 0.00 0.00 2.32
3810 8888 0.529378 CATCTTGCTTTGGGCCTGAC 59.471 55.000 4.53 0.00 40.92 3.51
3816 8894 3.059603 GCATGCATCTTGCTTTGGG 57.940 52.632 14.21 0.00 45.31 4.12
3822 8900 0.815213 TACCGGAGCATGCATCTTGC 60.815 55.000 21.98 0.00 45.29 4.01
3823 8901 1.202568 TCTACCGGAGCATGCATCTTG 60.203 52.381 21.98 11.39 0.00 3.02
3824 8902 1.069823 CTCTACCGGAGCATGCATCTT 59.930 52.381 21.98 0.00 35.08 2.40
3825 8903 0.678395 CTCTACCGGAGCATGCATCT 59.322 55.000 21.98 0.00 35.08 2.90
3826 8904 0.676184 TCTCTACCGGAGCATGCATC 59.324 55.000 21.98 13.95 41.60 3.91
3827 8905 1.123077 TTCTCTACCGGAGCATGCAT 58.877 50.000 21.98 4.75 41.60 3.96
3885 8974 5.899278 ACCTGCTAATTTTCTTTAGGGGAA 58.101 37.500 0.00 0.00 31.19 3.97
3887 8976 5.358160 CAGACCTGCTAATTTTCTTTAGGGG 59.642 44.000 0.00 0.00 31.19 4.79
3898 8987 7.448469 ACAGACAAAATAACAGACCTGCTAATT 59.552 33.333 0.00 0.00 0.00 1.40
3900 8989 6.296026 ACAGACAAAATAACAGACCTGCTAA 58.704 36.000 0.00 0.00 0.00 3.09
3901 8990 5.865085 ACAGACAAAATAACAGACCTGCTA 58.135 37.500 0.00 0.00 0.00 3.49
3902 8991 4.718961 ACAGACAAAATAACAGACCTGCT 58.281 39.130 0.00 0.00 0.00 4.24
3903 8992 4.757149 AGACAGACAAAATAACAGACCTGC 59.243 41.667 0.00 0.00 0.00 4.85
3906 9016 5.227908 TCGAGACAGACAAAATAACAGACC 58.772 41.667 0.00 0.00 0.00 3.85
3909 9019 4.627467 CCCTCGAGACAGACAAAATAACAG 59.373 45.833 15.71 0.00 0.00 3.16
3915 9025 2.897326 TGATCCCTCGAGACAGACAAAA 59.103 45.455 15.71 0.00 0.00 2.44
3943 9053 5.009710 TGACTCGCCGAGACAGATAAAATAT 59.990 40.000 22.80 0.00 31.65 1.28
3946 9056 2.490509 TGACTCGCCGAGACAGATAAAA 59.509 45.455 22.80 0.00 31.65 1.52
3984 9094 8.148999 ACCTACGAACAGAGTAATCTTTCTTTT 58.851 33.333 0.00 0.00 0.00 2.27
3987 9097 6.433404 TGACCTACGAACAGAGTAATCTTTCT 59.567 38.462 0.00 0.00 0.00 2.52
3988 9098 6.618811 TGACCTACGAACAGAGTAATCTTTC 58.381 40.000 0.00 0.00 0.00 2.62
3989 9099 6.585695 TGACCTACGAACAGAGTAATCTTT 57.414 37.500 0.00 0.00 0.00 2.52
3990 9100 5.393243 GCTGACCTACGAACAGAGTAATCTT 60.393 44.000 0.00 0.00 34.07 2.40
4004 9118 2.185350 CCTGCCTGCTGACCTACG 59.815 66.667 0.00 0.00 0.00 3.51
4043 9157 1.824230 GCAATATTCAAGTGGCCACCA 59.176 47.619 32.29 14.07 0.00 4.17
4077 9191 2.096248 CTCGAGCCCCCTACATCTATC 58.904 57.143 0.00 0.00 0.00 2.08
4080 9194 0.757188 CACTCGAGCCCCCTACATCT 60.757 60.000 13.61 0.00 0.00 2.90
4081 9195 0.755698 TCACTCGAGCCCCCTACATC 60.756 60.000 13.61 0.00 0.00 3.06
4082 9196 0.105453 ATCACTCGAGCCCCCTACAT 60.105 55.000 13.61 0.00 0.00 2.29
4083 9197 0.325296 AATCACTCGAGCCCCCTACA 60.325 55.000 13.61 0.00 0.00 2.74
4085 9199 1.996798 CTAATCACTCGAGCCCCCTA 58.003 55.000 13.61 0.00 0.00 3.53
4086 9200 1.403687 GCTAATCACTCGAGCCCCCT 61.404 60.000 13.61 0.00 0.00 4.79
4087 9201 1.069935 GCTAATCACTCGAGCCCCC 59.930 63.158 13.61 0.00 0.00 5.40
4088 9202 1.300233 CGCTAATCACTCGAGCCCC 60.300 63.158 13.61 0.00 32.35 5.80
4089 9203 1.300233 CCGCTAATCACTCGAGCCC 60.300 63.158 13.61 0.00 32.35 5.19
4093 9207 2.411701 CCGCCGCTAATCACTCGA 59.588 61.111 0.00 0.00 0.00 4.04
4094 9208 2.104331 ACCGCCGCTAATCACTCG 59.896 61.111 0.00 0.00 0.00 4.18
4095 9209 1.883084 CCACCGCCGCTAATCACTC 60.883 63.158 0.00 0.00 0.00 3.51
4096 9210 2.186903 CCACCGCCGCTAATCACT 59.813 61.111 0.00 0.00 0.00 3.41
4097 9211 2.895372 CCCACCGCCGCTAATCAC 60.895 66.667 0.00 0.00 0.00 3.06
4099 9213 2.895372 CACCCACCGCCGCTAATC 60.895 66.667 0.00 0.00 0.00 1.75
4100 9214 4.483243 CCACCCACCGCCGCTAAT 62.483 66.667 0.00 0.00 0.00 1.73
4109 9223 4.115199 CTAGCCAGCCCACCCACC 62.115 72.222 0.00 0.00 0.00 4.61
4110 9224 3.330720 ACTAGCCAGCCCACCCAC 61.331 66.667 0.00 0.00 0.00 4.61
4111 9225 3.329889 CACTAGCCAGCCCACCCA 61.330 66.667 0.00 0.00 0.00 4.51
4112 9226 4.115199 CCACTAGCCAGCCCACCC 62.115 72.222 0.00 0.00 0.00 4.61
4113 9227 1.345715 ATACCACTAGCCAGCCCACC 61.346 60.000 0.00 0.00 0.00 4.61
4114 9228 0.106894 GATACCACTAGCCAGCCCAC 59.893 60.000 0.00 0.00 0.00 4.61
4115 9229 0.326143 TGATACCACTAGCCAGCCCA 60.326 55.000 0.00 0.00 0.00 5.36
4116 9230 0.106894 GTGATACCACTAGCCAGCCC 59.893 60.000 0.00 0.00 40.10 5.19
4117 9231 0.830648 TGTGATACCACTAGCCAGCC 59.169 55.000 0.00 0.00 43.55 4.85
4118 9232 1.202580 CCTGTGATACCACTAGCCAGC 60.203 57.143 0.00 0.00 43.55 4.85
4119 9233 1.414181 CCCTGTGATACCACTAGCCAG 59.586 57.143 0.00 0.00 43.55 4.85
4120 9234 1.273609 ACCCTGTGATACCACTAGCCA 60.274 52.381 0.00 0.00 43.55 4.75
4121 9235 1.497161 ACCCTGTGATACCACTAGCC 58.503 55.000 0.00 0.00 43.55 3.93
4122 9236 4.957684 AATACCCTGTGATACCACTAGC 57.042 45.455 0.00 0.00 43.55 3.42
4123 9237 6.289064 GGAAAATACCCTGTGATACCACTAG 58.711 44.000 0.00 0.00 43.55 2.57
4124 9238 5.131475 GGGAAAATACCCTGTGATACCACTA 59.869 44.000 0.00 0.00 45.90 2.74
4125 9239 4.079958 GGGAAAATACCCTGTGATACCACT 60.080 45.833 0.00 0.00 45.90 4.00
4126 9240 4.204799 GGGAAAATACCCTGTGATACCAC 58.795 47.826 0.00 0.00 45.90 4.16
4127 9241 4.513406 GGGAAAATACCCTGTGATACCA 57.487 45.455 0.00 0.00 45.90 3.25
4138 9252 2.100197 GCTCACCAAGGGGAAAATACC 58.900 52.381 0.00 0.00 38.05 2.73
4139 9253 2.100197 GGCTCACCAAGGGGAAAATAC 58.900 52.381 0.00 0.00 38.05 1.89
4140 9254 1.006639 GGGCTCACCAAGGGGAAAATA 59.993 52.381 0.00 0.00 39.85 1.40
4141 9255 0.252239 GGGCTCACCAAGGGGAAAAT 60.252 55.000 0.00 0.00 39.85 1.82
4142 9256 1.155155 GGGCTCACCAAGGGGAAAA 59.845 57.895 0.00 0.00 39.85 2.29
4143 9257 1.368268 AAGGGCTCACCAAGGGGAAA 61.368 55.000 0.00 0.00 43.89 3.13
4144 9258 1.778383 AAGGGCTCACCAAGGGGAA 60.778 57.895 0.00 0.00 43.89 3.97
4145 9259 2.121506 AAGGGCTCACCAAGGGGA 60.122 61.111 0.00 0.00 43.89 4.81
4146 9260 2.036256 CAAGGGCTCACCAAGGGG 59.964 66.667 0.00 0.00 43.89 4.79
4147 9261 2.677875 GCAAGGGCTCACCAAGGG 60.678 66.667 0.00 0.00 43.89 3.95
4158 9272 2.908428 TGCACTGCACTGCAAGGG 60.908 61.111 17.27 2.04 44.28 3.95
4165 9279 1.024271 ATTCACGTTTGCACTGCACT 58.976 45.000 2.26 0.00 38.71 4.40
4171 9285 1.780860 GAACTGCATTCACGTTTGCAC 59.219 47.619 12.22 2.08 43.54 4.57
4172 9286 1.403323 TGAACTGCATTCACGTTTGCA 59.597 42.857 14.69 14.69 46.03 4.08
4173 9287 2.118228 TGAACTGCATTCACGTTTGC 57.882 45.000 7.72 7.72 42.62 3.68


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

AutoCloner maintained by Alex Coulton.