Multiple sequence alignment - TraesCS6B01G132300

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 TraesCS6B01G132300 chr6B 100.000 7132 0 0 992 8123 129277106 129269975 0.000000e+00 13171.0
1 TraesCS6B01G132300 chr6B 100.000 618 0 0 1 618 129278097 129277480 0.000000e+00 1142.0
2 TraesCS6B01G132300 chr6B 83.333 858 82 21 2773 3608 618112901 618113719 0.000000e+00 736.0
3 TraesCS6B01G132300 chr6B 92.857 112 8 0 173 284 650598704 650598593 6.520000e-36 163.0
4 TraesCS6B01G132300 chr6A 93.456 6326 242 68 1191 7418 72437652 72431401 0.000000e+00 9230.0
5 TraesCS6B01G132300 chr6A 93.314 688 25 1 7457 8123 72431402 72430715 0.000000e+00 996.0
6 TraesCS6B01G132300 chr6A 86.667 270 20 6 20 284 72438622 72438364 1.330000e-72 285.0
7 TraesCS6B01G132300 chr6A 93.333 105 7 0 180 284 23496590 23496486 1.090000e-33 156.0
8 TraesCS6B01G132300 chr6D 93.316 3456 148 35 4016 7418 57220767 57217342 0.000000e+00 5025.0
9 TraesCS6B01G132300 chr6D 92.635 3028 143 38 998 3980 57223748 57220756 0.000000e+00 4283.0
10 TraesCS6B01G132300 chr6D 92.659 504 16 1 7457 7939 57217343 57216840 0.000000e+00 706.0
11 TraesCS6B01G132300 chr6D 86.012 336 22 8 287 618 57224182 57223868 3.630000e-88 337.0
12 TraesCS6B01G132300 chr6D 84.281 299 21 10 1 284 57224583 57224296 1.340000e-67 268.0
13 TraesCS6B01G132300 chr6D 94.595 148 8 0 7976 8123 57216843 57216696 6.340000e-56 230.0
14 TraesCS6B01G132300 chr6D 93.750 112 7 0 173 284 431160832 431160721 1.400000e-37 169.0
15 TraesCS6B01G132300 chr5A 80.312 2052 299 57 4116 6106 591092299 591090292 0.000000e+00 1454.0
16 TraesCS6B01G132300 chr5A 81.117 609 90 15 2012 2613 591094727 591094137 1.600000e-126 464.0
17 TraesCS6B01G132300 chr5D 82.374 1373 187 32 4763 6101 470386859 470385508 0.000000e+00 1144.0
18 TraesCS6B01G132300 chr5D 82.013 606 92 13 2012 2613 470389827 470389235 4.380000e-137 499.0
19 TraesCS6B01G132300 chr5D 76.295 869 152 32 2727 3566 470389180 470388337 1.630000e-111 414.0
20 TraesCS6B01G132300 chr5D 91.150 113 10 0 172 284 461072768 461072656 3.930000e-33 154.0
21 TraesCS6B01G132300 chr5B 81.958 1369 198 28 4763 6101 577695264 577693915 0.000000e+00 1114.0
22 TraesCS6B01G132300 chr5B 80.952 609 93 14 2012 2613 577698098 577697506 2.070000e-125 460.0
23 TraesCS6B01G132300 chr5B 76.464 871 147 37 2727 3566 577697451 577696608 3.510000e-113 420.0
24 TraesCS6B01G132300 chr4B 85.842 671 56 18 2950 3597 251664866 251665520 0.000000e+00 676.0
25 TraesCS6B01G132300 chr4B 85.395 671 59 12 2950 3597 251278206 251278860 0.000000e+00 660.0
26 TraesCS6B01G132300 chr4B 91.892 111 9 0 174 284 178081267 178081157 1.090000e-33 156.0
27 TraesCS6B01G132300 chr4D 91.379 116 10 0 174 289 443723445 443723560 8.440000e-35 159.0
28 TraesCS6B01G132300 chr4D 92.593 108 8 0 177 284 25439796 25439903 1.090000e-33 156.0
29 TraesCS6B01G132300 chr3D 91.892 111 9 0 174 284 128214004 128214114 1.090000e-33 156.0
30 TraesCS6B01G132300 chr7A 90.517 116 9 2 171 284 524701248 524701363 1.410000e-32 152.0
31 TraesCS6B01G132300 chr7A 77.852 149 19 6 24 171 724507819 724507684 6.760000e-11 80.5


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 TraesCS6B01G132300 chr6B 129269975 129278097 8122 True 7156.500000 13171 100.000000 1 8123 2 chr6B.!!$R2 8122
1 TraesCS6B01G132300 chr6B 618112901 618113719 818 False 736.000000 736 83.333000 2773 3608 1 chr6B.!!$F1 835
2 TraesCS6B01G132300 chr6A 72430715 72438622 7907 True 3503.666667 9230 91.145667 20 8123 3 chr6A.!!$R2 8103
3 TraesCS6B01G132300 chr6D 57216696 57224583 7887 True 1808.166667 5025 90.583000 1 8123 6 chr6D.!!$R2 8122
4 TraesCS6B01G132300 chr5A 591090292 591094727 4435 True 959.000000 1454 80.714500 2012 6106 2 chr5A.!!$R1 4094
5 TraesCS6B01G132300 chr5D 470385508 470389827 4319 True 685.666667 1144 80.227333 2012 6101 3 chr5D.!!$R2 4089
6 TraesCS6B01G132300 chr5B 577693915 577698098 4183 True 664.666667 1114 79.791333 2012 6101 3 chr5B.!!$R1 4089
7 TraesCS6B01G132300 chr4B 251664866 251665520 654 False 676.000000 676 85.842000 2950 3597 1 chr4B.!!$F2 647
8 TraesCS6B01G132300 chr4B 251278206 251278860 654 False 660.000000 660 85.395000 2950 3597 1 chr4B.!!$F1 647

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
478 623 1.002134 GCTGGCACCTAGGAGCAAA 60.002 57.895 29.09 17.22 33.44 3.68 F
1294 1457 0.107410 TGAACAAGTGGCTGACGGTT 60.107 50.000 0.00 0.00 31.93 4.44 F
1580 1780 0.392193 AAGCCGGATCTGTGCTTGAG 60.392 55.000 22.07 0.00 43.30 3.02 F
2208 2424 1.077265 CAAGGGCCCACAACAGGAT 59.923 57.895 27.56 0.00 0.00 3.24 F
2667 2887 1.605710 GCTCAGTTGTGCACATCAGTT 59.394 47.619 25.59 6.51 34.92 3.16 F
4194 4949 0.675633 TTCTGCAGCTTTCTTTGGGC 59.324 50.000 9.47 0.00 0.00 5.36 F
4299 5054 1.003355 ATGTGCCAAGGAGGTCACG 60.003 57.895 0.00 0.00 43.20 4.35 F
6128 6983 1.271488 TGATGAGCCAACATGCTGTCA 60.271 47.619 0.00 0.00 42.95 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 1558 0.036590 CCGGGGGAAAAGGAAACGTA 59.963 55.000 0.00 0.00 0.00 3.57 R
2130 2346 1.002069 TCTGGTCCTTCATGGCCAAT 58.998 50.000 10.96 0.00 40.01 3.16 R
2644 2861 3.069289 CTGATGTGCACAACTGAGCTTA 58.931 45.455 25.72 2.11 32.76 3.09 R
4194 4949 0.597568 TGGCTGTTCTTGCATTTCCG 59.402 50.000 0.00 0.00 0.00 4.30 R
4376 5133 2.917713 ATGGGCAATGGAGTGGTAAA 57.082 45.000 0.00 0.00 0.00 2.01 R
5361 6210 1.621072 CCTGCTAGAAGAGTGGGGAGT 60.621 57.143 0.00 0.00 0.00 3.85 R
6235 7098 1.341852 ACTGCAGCAATGCACAAATGA 59.658 42.857 15.27 0.00 40.23 2.57 R
7950 8890 0.040958 CGTCTTGTTCAGCAACTGCC 60.041 55.000 0.00 0.00 43.38 4.85 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
72 74 9.516314 GGCTTAAACTTTGACCATATATTTGAC 57.484 33.333 0.00 0.00 0.00 3.18
203 207 9.084533 AGTCCATCTGTTTCTAGATATAAGACC 57.915 37.037 0.00 0.00 35.70 3.85
284 302 6.246449 CAGATTCACTCATTTTGCTTCGTAG 58.754 40.000 0.00 0.00 0.00 3.51
307 446 1.139095 GACGGAGGCAGTAAGTCGG 59.861 63.158 0.00 0.00 0.00 4.79
335 474 4.713824 ACGCTTGATGTACTACTTAGCA 57.286 40.909 0.00 0.00 0.00 3.49
360 499 6.260050 AGCGAAGAGTCAAAACACTAAATGAA 59.740 34.615 0.00 0.00 0.00 2.57
415 558 9.538508 GGAATTTAGCATGATTAATTCAAAGCT 57.461 29.630 27.09 15.43 45.85 3.74
421 564 5.517770 GCATGATTAATTCAAAGCTGTGGAC 59.482 40.000 3.47 0.00 38.03 4.02
478 623 1.002134 GCTGGCACCTAGGAGCAAA 60.002 57.895 29.09 17.22 33.44 3.68
537 682 3.896133 GCGATGCATGGCCCACTG 61.896 66.667 21.81 0.00 0.00 3.66
538 683 3.896133 CGATGCATGGCCCACTGC 61.896 66.667 2.46 13.53 38.87 4.40
574 719 3.093278 CCATCAAGAAGCGGCGAC 58.907 61.111 12.98 1.23 0.00 5.19
1010 1160 2.756283 AAGCCTCCTCGTCCTCGG 60.756 66.667 0.00 0.00 37.69 4.63
1013 1163 4.824515 CCTCCTCGTCCTCGGCCT 62.825 72.222 0.00 0.00 37.69 5.19
1014 1164 3.213402 CTCCTCGTCCTCGGCCTC 61.213 72.222 0.00 0.00 37.69 4.70
1083 1233 2.927014 GCTCTGGTGAGTGGTTTCTACG 60.927 54.545 0.00 0.00 42.13 3.51
1084 1234 1.000506 TCTGGTGAGTGGTTTCTACGC 59.999 52.381 0.00 0.00 0.00 4.42
1085 1235 1.000955 CTGGTGAGTGGTTTCTACGCT 59.999 52.381 0.00 0.00 0.00 5.07
1086 1236 2.230508 CTGGTGAGTGGTTTCTACGCTA 59.769 50.000 0.00 0.00 0.00 4.26
1087 1237 2.029649 TGGTGAGTGGTTTCTACGCTAC 60.030 50.000 0.00 0.00 0.00 3.58
1221 1371 4.724262 GTGGAACCCTCTTGAGGC 57.276 61.111 11.01 0.00 0.00 4.70
1289 1452 0.396435 ACCGATGAACAAGTGGCTGA 59.604 50.000 0.00 0.00 0.00 4.26
1293 1456 0.108585 ATGAACAAGTGGCTGACGGT 59.891 50.000 0.00 0.00 0.00 4.83
1294 1457 0.107410 TGAACAAGTGGCTGACGGTT 60.107 50.000 0.00 0.00 31.93 4.44
1297 1460 0.738389 ACAAGTGGCTGACGGTTTTG 59.262 50.000 0.00 0.00 0.00 2.44
1337 1510 3.447229 AGATTTGGAAATTAGTTGCCGGG 59.553 43.478 2.18 0.00 0.00 5.73
1356 1529 2.287849 GGGAGTGCTTTTCTGTTTCTGC 60.288 50.000 0.00 0.00 0.00 4.26
1378 1558 7.441157 TCTGCATAAGCGTTGCTATTAATTAGT 59.559 33.333 9.42 0.00 46.23 2.24
1379 1559 8.596271 TGCATAAGCGTTGCTATTAATTAGTA 57.404 30.769 9.42 0.00 46.23 1.82
1380 1560 8.492748 TGCATAAGCGTTGCTATTAATTAGTAC 58.507 33.333 9.42 0.00 46.23 2.73
1398 1579 2.632544 CGTTTCCTTTTCCCCCGGC 61.633 63.158 0.00 0.00 0.00 6.13
1506 1706 8.494016 AGGACAGATTGCTTGTAAATTAGTAC 57.506 34.615 0.00 0.00 0.00 2.73
1507 1707 8.322091 AGGACAGATTGCTTGTAAATTAGTACT 58.678 33.333 0.00 0.00 0.00 2.73
1508 1708 9.595823 GGACAGATTGCTTGTAAATTAGTACTA 57.404 33.333 0.00 0.00 0.00 1.82
1536 1736 4.424061 TTCTTTGGATTCGCTTCATGTG 57.576 40.909 0.00 0.00 0.00 3.21
1548 1748 2.115595 CTTCATGTGATCGTCGCTCTC 58.884 52.381 0.00 0.00 0.00 3.20
1580 1780 0.392193 AAGCCGGATCTGTGCTTGAG 60.392 55.000 22.07 0.00 43.30 3.02
1587 1787 1.306642 ATCTGTGCTTGAGCTGCTGC 61.307 55.000 7.01 7.62 42.66 5.25
1598 1798 1.734465 GAGCTGCTGCGTAGTTGAATT 59.266 47.619 7.01 0.00 45.42 2.17
1606 1806 2.033550 TGCGTAGTTGAATTTGGCGTTT 59.966 40.909 0.00 0.00 0.00 3.60
1613 1813 3.378911 TGAATTTGGCGTTTCCTTTCC 57.621 42.857 0.00 0.00 35.26 3.13
1637 1840 7.593273 TCCAACGATCATACACATTTTTGAAAC 59.407 33.333 0.00 0.00 0.00 2.78
1650 1853 4.630894 TTTTGAAACATCGAACTGCTGT 57.369 36.364 0.00 0.00 0.00 4.40
1741 1945 6.260714 GTCTTCAATTTCCTTGGCAATTTGTT 59.739 34.615 0.00 0.00 35.43 2.83
1745 1949 9.784531 TTCAATTTCCTTGGCAATTTGTTAATA 57.215 25.926 0.00 0.00 35.43 0.98
1771 1975 8.760103 TTTGTGTTTATGATGAATGAATGGTG 57.240 30.769 0.00 0.00 0.00 4.17
1776 1980 8.407832 TGTTTATGATGAATGAATGGTGATGAC 58.592 33.333 0.00 0.00 0.00 3.06
1799 2005 9.420118 TGACCTGCCACTTCATTTTATATAATT 57.580 29.630 0.00 0.00 0.00 1.40
1841 2047 4.729227 ATTTTGAACCTGACCGTTGTTT 57.271 36.364 0.00 0.00 0.00 2.83
1856 2062 4.154015 CCGTTGTTTCATTGTAGCAGATCA 59.846 41.667 0.00 0.00 0.00 2.92
1857 2063 5.082059 CGTTGTTTCATTGTAGCAGATCAC 58.918 41.667 0.00 0.00 0.00 3.06
1858 2064 5.393962 GTTGTTTCATTGTAGCAGATCACC 58.606 41.667 0.00 0.00 0.00 4.02
1966 2175 5.049336 GCTTGAAAGACCTCTAGTTTTCCAC 60.049 44.000 0.00 0.00 30.68 4.02
1968 2177 5.611374 TGAAAGACCTCTAGTTTTCCACAG 58.389 41.667 0.00 0.00 30.68 3.66
1973 2182 3.974642 ACCTCTAGTTTTCCACAGACCTT 59.025 43.478 0.00 0.00 0.00 3.50
2130 2346 1.339055 CGACCATTGAGCAAGAGGGAA 60.339 52.381 8.67 0.00 0.00 3.97
2199 2415 3.785887 AGACAATCTTATACAAGGGCCCA 59.214 43.478 27.56 2.25 32.22 5.36
2201 2417 3.268334 ACAATCTTATACAAGGGCCCACA 59.732 43.478 27.56 5.73 32.22 4.17
2208 2424 1.077265 CAAGGGCCCACAACAGGAT 59.923 57.895 27.56 0.00 0.00 3.24
2260 2476 3.942829 ACACTGTCCAACGATTCATCAT 58.057 40.909 0.00 0.00 0.00 2.45
2285 2501 7.870509 TGAATAGCTGAAGCAATTCTGTATT 57.129 32.000 4.90 0.00 45.16 1.89
2290 2506 7.081526 AGCTGAAGCAATTCTGTATTGTAAG 57.918 36.000 4.90 3.64 44.52 2.34
2302 2518 8.645814 TTCTGTATTGTAAGAGTGACCTTCTA 57.354 34.615 0.00 0.00 0.00 2.10
2405 2622 4.443457 GGAGCTAAGGATGTTGCTATGTCA 60.443 45.833 0.00 0.00 35.76 3.58
2624 2841 3.896648 AATGTGAGTAGTGGCAAAACG 57.103 42.857 0.00 0.00 0.00 3.60
2640 2857 4.909880 GCAAAACGTTTACCATCTGTCTTC 59.090 41.667 15.03 0.00 0.00 2.87
2644 2861 6.937436 AACGTTTACCATCTGTCTTCTTTT 57.063 33.333 0.00 0.00 0.00 2.27
2664 2884 1.971481 AAGCTCAGTTGTGCACATCA 58.029 45.000 25.59 8.84 37.04 3.07
2667 2887 1.605710 GCTCAGTTGTGCACATCAGTT 59.394 47.619 25.59 6.51 34.92 3.16
2725 2945 8.770438 TGTTTTCTAACAAGTTTGAAGCAAAT 57.230 26.923 9.15 0.00 41.15 2.32
3576 3849 6.143919 GCTAAGGTTTGGATTTCTCAAAAACG 59.856 38.462 0.00 0.00 37.13 3.60
3956 4686 6.403866 TCATGTTTCAAAAGTGGCTACATT 57.596 33.333 2.02 0.00 0.00 2.71
3960 4690 6.634805 TGTTTCAAAAGTGGCTACATTTTCA 58.365 32.000 2.02 0.00 35.76 2.69
4194 4949 0.675633 TTCTGCAGCTTTCTTTGGGC 59.324 50.000 9.47 0.00 0.00 5.36
4299 5054 1.003355 ATGTGCCAAGGAGGTCACG 60.003 57.895 0.00 0.00 43.20 4.35
4330 5085 6.770785 TGCAAAAGTTAACATGGTAAGAGTCT 59.229 34.615 2.67 0.00 0.00 3.24
4376 5133 7.173390 GTCTTACCTTTAGTTGCTGAAGTCAAT 59.827 37.037 0.00 0.00 0.00 2.57
4731 5523 6.715264 CAGTAAGGCCCTTTCTTTCTTTCTTA 59.285 38.462 0.00 0.00 0.00 2.10
4928 5756 7.395772 TCATCCACTGCTCCATTTATGTTAAAA 59.604 33.333 0.00 0.00 0.00 1.52
5087 5915 2.372264 GCAGAAATCAGGGAGATGCAA 58.628 47.619 0.00 0.00 36.96 4.08
5147 5975 3.944015 CAGATGAAGGAAATGGGTCTGAC 59.056 47.826 0.00 0.00 34.95 3.51
5246 6074 9.817809 GTACAGAGATCTATTGACAAATTGGTA 57.182 33.333 12.36 0.00 0.00 3.25
5258 6086 5.049060 TGACAAATTGGTAATGTCACTTCCG 60.049 40.000 5.92 0.00 46.11 4.30
5333 6176 2.173782 TCTTCCACTGGGTGTAAGCAAA 59.826 45.455 0.00 0.00 31.13 3.68
5677 6529 2.716217 CCAGGTTCTGGTTTCTGATCC 58.284 52.381 5.82 0.00 45.82 3.36
5807 6662 3.665745 AACGAAGGCAAAGCAAATGAT 57.334 38.095 0.00 0.00 0.00 2.45
6012 6867 3.681897 CGAGGTTGAAGTCAGAAGATTGG 59.318 47.826 0.00 0.00 0.00 3.16
6094 6949 1.280421 CCCTGCAGTTTCTCTAGCCTT 59.720 52.381 13.81 0.00 0.00 4.35
6106 6961 8.827758 AGTTTCTCTAGCCTTAAGGTAAAGATT 58.172 33.333 22.55 7.28 37.57 2.40
6128 6983 1.271488 TGATGAGCCAACATGCTGTCA 60.271 47.619 0.00 0.00 42.95 3.58
6142 6998 1.604278 GCTGTCAAGTGTCCTTTGGTC 59.396 52.381 0.00 0.00 0.00 4.02
6160 7018 3.142174 GGTCATATTGCTACCCTGCTTC 58.858 50.000 0.00 0.00 0.00 3.86
6172 7030 2.292267 CCCTGCTTCGTTATCTGCATT 58.708 47.619 0.00 0.00 34.79 3.56
6321 7184 1.271054 GGCTCAAGGCTGACAGAAGAA 60.271 52.381 6.65 0.00 41.46 2.52
6620 7483 3.444034 TCGACTCCATTACAGTGAGGAAG 59.556 47.826 0.00 0.00 0.00 3.46
6652 7515 5.610557 TGATACATTTCATACTGGGGATGGA 59.389 40.000 0.00 0.00 0.00 3.41
6786 7649 8.730680 TGTAGATAGCTCAAAATTCTTTGGAAC 58.269 33.333 0.00 0.00 41.98 3.62
6798 7661 5.828299 TTCTTTGGAACGTTCATGACTTT 57.172 34.783 28.24 0.00 0.00 2.66
6818 7681 5.471456 ACTTTTTGTCATCTACCTTCTGCAG 59.529 40.000 7.63 7.63 0.00 4.41
6900 7764 3.068873 AGGCAATTGTCGGTGCTTAAAAA 59.931 39.130 7.40 0.00 40.70 1.94
6901 7765 3.428534 GGCAATTGTCGGTGCTTAAAAAG 59.571 43.478 7.40 0.00 40.70 2.27
6902 7766 3.428534 GCAATTGTCGGTGCTTAAAAAGG 59.571 43.478 7.40 0.00 37.78 3.11
6937 7804 6.775142 TGTTCAATCAGGTGGTTGATTTCTAA 59.225 34.615 6.50 0.00 43.41 2.10
6983 7850 6.991485 ATGCAAAATTTTAGACTGTTCACG 57.009 33.333 2.44 0.00 0.00 4.35
6995 7862 6.496338 AGACTGTTCACGGAATTTTTATCC 57.504 37.500 0.00 0.00 0.00 2.59
7056 7937 1.419381 TGGCAGAGTGGAGTGTGTTA 58.581 50.000 0.00 0.00 0.00 2.41
7071 7952 4.772100 AGTGTGTTATGCCAGCCTAAAATT 59.228 37.500 0.00 0.00 0.00 1.82
7079 7960 5.116084 TGCCAGCCTAAAATTAGAGTGAT 57.884 39.130 1.75 0.00 32.47 3.06
7085 7966 8.778358 CCAGCCTAAAATTAGAGTGATAATGAC 58.222 37.037 1.75 0.00 32.47 3.06
7148 8029 7.762615 ACATTATCAAATTTGCATTCCTGACTG 59.237 33.333 13.54 2.99 0.00 3.51
7161 8057 6.736794 GCATTCCTGACTGTGAAAATGACTTT 60.737 38.462 6.32 0.00 0.00 2.66
7162 8058 5.756195 TCCTGACTGTGAAAATGACTTTG 57.244 39.130 0.00 0.00 0.00 2.77
7172 8068 8.062065 TGTGAAAATGACTTTGAAAAGGTACT 57.938 30.769 7.65 0.00 35.70 2.73
7173 8069 7.973388 TGTGAAAATGACTTTGAAAAGGTACTG 59.027 33.333 7.65 0.00 35.70 2.74
7174 8070 8.188139 GTGAAAATGACTTTGAAAAGGTACTGA 58.812 33.333 7.65 0.00 35.70 3.41
7239 8145 2.287103 CAGTCATGAACCATCAGATGCG 59.713 50.000 4.68 1.39 39.39 4.73
7240 8146 1.600957 GTCATGAACCATCAGATGCGG 59.399 52.381 4.68 0.00 39.39 5.69
7241 8147 1.485895 TCATGAACCATCAGATGCGGA 59.514 47.619 4.68 0.00 39.39 5.54
7245 8159 2.093021 TGAACCATCAGATGCGGAATGA 60.093 45.455 4.68 0.00 0.00 2.57
7266 8180 1.442526 GGATGAACATGGCGAGCAGG 61.443 60.000 0.00 0.00 0.00 4.85
7277 8191 1.227764 CGAGCAGGGCACAGCATAT 60.228 57.895 5.99 0.00 33.33 1.78
7278 8192 0.816825 CGAGCAGGGCACAGCATATT 60.817 55.000 5.99 0.00 33.33 1.28
7279 8193 0.950116 GAGCAGGGCACAGCATATTC 59.050 55.000 5.99 0.00 33.33 1.75
7323 8242 0.473755 TCCAGGCATGTGAACACACT 59.526 50.000 9.83 0.71 45.05 3.55
7332 8251 4.597079 CATGTGAACACACTACCACAAAC 58.403 43.478 9.83 0.00 45.05 2.93
7365 8284 1.414550 TGTCATTCTCCCAACACACGA 59.585 47.619 0.00 0.00 0.00 4.35
7366 8285 2.038426 TGTCATTCTCCCAACACACGAT 59.962 45.455 0.00 0.00 0.00 3.73
7367 8286 3.259625 TGTCATTCTCCCAACACACGATA 59.740 43.478 0.00 0.00 0.00 2.92
7368 8287 4.250464 GTCATTCTCCCAACACACGATAA 58.750 43.478 0.00 0.00 0.00 1.75
7369 8288 4.693566 GTCATTCTCCCAACACACGATAAA 59.306 41.667 0.00 0.00 0.00 1.40
7370 8289 5.180492 GTCATTCTCCCAACACACGATAAAA 59.820 40.000 0.00 0.00 0.00 1.52
7371 8290 5.765677 TCATTCTCCCAACACACGATAAAAA 59.234 36.000 0.00 0.00 0.00 1.94
7417 8336 5.472137 AGTTCGACAAAATTAAGCTTGCCTA 59.528 36.000 9.86 0.00 0.00 3.93
7418 8337 5.950758 TCGACAAAATTAAGCTTGCCTAA 57.049 34.783 9.86 0.00 0.00 2.69
7419 8338 5.695818 TCGACAAAATTAAGCTTGCCTAAC 58.304 37.500 9.86 0.00 0.00 2.34
7420 8339 5.239744 TCGACAAAATTAAGCTTGCCTAACA 59.760 36.000 9.86 0.00 0.00 2.41
7421 8340 6.072175 TCGACAAAATTAAGCTTGCCTAACAT 60.072 34.615 9.86 0.00 0.00 2.71
7422 8341 6.251376 CGACAAAATTAAGCTTGCCTAACATC 59.749 38.462 9.86 0.00 0.00 3.06
7423 8342 6.991938 ACAAAATTAAGCTTGCCTAACATCA 58.008 32.000 9.86 0.00 0.00 3.07
7424 8343 7.614494 ACAAAATTAAGCTTGCCTAACATCAT 58.386 30.769 9.86 0.00 0.00 2.45
7425 8344 7.546667 ACAAAATTAAGCTTGCCTAACATCATG 59.453 33.333 9.86 0.00 0.00 3.07
7426 8345 6.780457 AATTAAGCTTGCCTAACATCATGT 57.220 33.333 9.86 0.00 0.00 3.21
7427 8346 5.818136 TTAAGCTTGCCTAACATCATGTC 57.182 39.130 9.86 0.00 0.00 3.06
7428 8347 3.641434 AGCTTGCCTAACATCATGTCT 57.359 42.857 0.00 0.00 0.00 3.41
7429 8348 3.960571 AGCTTGCCTAACATCATGTCTT 58.039 40.909 0.00 0.00 0.00 3.01
7430 8349 3.693085 AGCTTGCCTAACATCATGTCTTG 59.307 43.478 0.00 0.00 0.00 3.02
7431 8350 3.733077 GCTTGCCTAACATCATGTCTTGC 60.733 47.826 0.00 0.00 0.00 4.01
7432 8351 2.009051 TGCCTAACATCATGTCTTGCG 58.991 47.619 0.00 0.00 0.00 4.85
7433 8352 2.009774 GCCTAACATCATGTCTTGCGT 58.990 47.619 0.00 0.00 0.00 5.24
7434 8353 3.194861 GCCTAACATCATGTCTTGCGTA 58.805 45.455 0.00 0.00 0.00 4.42
7435 8354 3.621268 GCCTAACATCATGTCTTGCGTAA 59.379 43.478 0.00 0.00 0.00 3.18
7436 8355 4.094294 GCCTAACATCATGTCTTGCGTAAA 59.906 41.667 0.00 0.00 0.00 2.01
7437 8356 5.560148 CCTAACATCATGTCTTGCGTAAAC 58.440 41.667 0.00 0.00 0.00 2.01
7438 8357 5.121611 CCTAACATCATGTCTTGCGTAAACA 59.878 40.000 0.00 4.41 0.00 2.83
7439 8358 5.627499 AACATCATGTCTTGCGTAAACAT 57.373 34.783 0.00 7.74 34.03 2.71
7441 8360 3.469899 TCATGTCTTGCGTAAACATGC 57.530 42.857 23.30 2.65 46.25 4.06
7442 8361 3.073678 TCATGTCTTGCGTAAACATGCT 58.926 40.909 23.30 3.56 46.25 3.79
7443 8362 3.501828 TCATGTCTTGCGTAAACATGCTT 59.498 39.130 23.30 0.00 46.25 3.91
7444 8363 4.693095 TCATGTCTTGCGTAAACATGCTTA 59.307 37.500 23.30 12.61 46.25 3.09
7445 8364 5.180304 TCATGTCTTGCGTAAACATGCTTAA 59.820 36.000 23.30 12.39 46.25 1.85
7446 8365 5.621197 TGTCTTGCGTAAACATGCTTAAT 57.379 34.783 0.00 0.00 0.00 1.40
7447 8366 6.729391 TGTCTTGCGTAAACATGCTTAATA 57.271 33.333 0.00 0.00 0.00 0.98
7448 8367 7.135089 TGTCTTGCGTAAACATGCTTAATAA 57.865 32.000 0.00 0.00 0.00 1.40
7449 8368 7.757526 TGTCTTGCGTAAACATGCTTAATAAT 58.242 30.769 0.00 0.00 0.00 1.28
7450 8369 8.240682 TGTCTTGCGTAAACATGCTTAATAATT 58.759 29.630 0.00 0.00 0.00 1.40
7451 8370 8.523464 GTCTTGCGTAAACATGCTTAATAATTG 58.477 33.333 0.00 0.00 0.00 2.32
7452 8371 6.804534 TGCGTAAACATGCTTAATAATTGC 57.195 33.333 0.00 0.00 0.00 3.56
7453 8372 6.325596 TGCGTAAACATGCTTAATAATTGCA 58.674 32.000 0.00 0.00 41.13 4.08
7454 8373 6.977502 TGCGTAAACATGCTTAATAATTGCAT 59.022 30.769 0.00 0.00 46.74 3.96
7455 8374 8.131731 TGCGTAAACATGCTTAATAATTGCATA 58.868 29.630 0.00 0.00 44.39 3.14
7456 8375 9.128107 GCGTAAACATGCTTAATAATTGCATAT 57.872 29.630 0.00 0.00 44.39 1.78
7500 8419 4.537135 TCACCTCCTACAACATGTCTTC 57.463 45.455 0.00 0.00 0.00 2.87
7557 8476 5.615289 AGCACATAATGGATAGTTCCTGAC 58.385 41.667 0.00 0.00 43.07 3.51
7680 8620 5.122396 GTCCCTGCAGATGTGTTTTAGTTAG 59.878 44.000 17.39 0.00 0.00 2.34
7757 8697 4.627035 GGCCTGATATGCAAAACTGAAAAC 59.373 41.667 0.00 0.00 0.00 2.43
7759 8699 5.346822 GCCTGATATGCAAAACTGAAAACAG 59.653 40.000 0.00 0.00 0.00 3.16
7760 8700 6.449698 CCTGATATGCAAAACTGAAAACAGT 58.550 36.000 0.00 0.00 36.92 3.55
7791 8731 6.336842 AGAATCAAAGCACATAAGCTGTTT 57.663 33.333 0.00 0.00 45.89 2.83
7928 8868 2.094545 CCTACAATGCCTTTGCTGGAAC 60.095 50.000 0.00 0.00 39.03 3.62
7935 8875 1.269448 GCCTTTGCTGGAACGAAATGA 59.731 47.619 0.00 0.00 33.53 2.57
7936 8876 2.288152 GCCTTTGCTGGAACGAAATGAA 60.288 45.455 0.00 0.00 33.53 2.57
7937 8877 3.798548 GCCTTTGCTGGAACGAAATGAAA 60.799 43.478 0.00 0.00 33.53 2.69
7938 8878 4.559153 CCTTTGCTGGAACGAAATGAAAT 58.441 39.130 0.00 0.00 0.00 2.17
7939 8879 4.990426 CCTTTGCTGGAACGAAATGAAATT 59.010 37.500 0.00 0.00 38.98 1.82
7940 8880 5.107375 CCTTTGCTGGAACGAAATGAAATTG 60.107 40.000 0.00 0.00 36.10 2.32
7941 8881 3.316283 TGCTGGAACGAAATGAAATTGC 58.684 40.909 0.00 0.00 36.10 3.56
7950 8890 4.828291 GAAATGAAATTGCGGTCACATG 57.172 40.909 0.00 0.00 36.10 3.21
7951 8891 2.945447 ATGAAATTGCGGTCACATGG 57.055 45.000 0.00 0.00 0.00 3.66
7952 8892 0.243365 TGAAATTGCGGTCACATGGC 59.757 50.000 0.00 0.00 0.00 4.40
7953 8893 0.243365 GAAATTGCGGTCACATGGCA 59.757 50.000 0.00 0.00 34.35 4.92
7954 8894 0.244450 AAATTGCGGTCACATGGCAG 59.756 50.000 0.00 0.00 38.04 4.85
7955 8895 0.895100 AATTGCGGTCACATGGCAGT 60.895 50.000 0.00 0.00 38.04 4.40
7956 8896 0.895100 ATTGCGGTCACATGGCAGTT 60.895 50.000 0.00 0.00 38.04 3.16
7957 8897 1.794151 TTGCGGTCACATGGCAGTTG 61.794 55.000 0.00 0.00 38.04 3.16
7958 8898 2.562912 CGGTCACATGGCAGTTGC 59.437 61.111 0.00 0.00 41.14 4.17
7959 8899 1.968017 CGGTCACATGGCAGTTGCT 60.968 57.895 3.88 0.00 41.70 3.91
7960 8900 1.582968 GGTCACATGGCAGTTGCTG 59.417 57.895 3.88 0.00 41.70 4.41
7961 8901 0.890542 GGTCACATGGCAGTTGCTGA 60.891 55.000 3.88 0.00 41.70 4.26
7962 8902 0.953727 GTCACATGGCAGTTGCTGAA 59.046 50.000 3.88 0.00 41.70 3.02
7963 8903 0.953727 TCACATGGCAGTTGCTGAAC 59.046 50.000 3.88 0.00 41.70 3.18
7964 8904 0.669619 CACATGGCAGTTGCTGAACA 59.330 50.000 3.88 0.00 41.70 3.18
7965 8905 1.067364 CACATGGCAGTTGCTGAACAA 59.933 47.619 3.88 0.00 41.70 2.83
7966 8906 1.338973 ACATGGCAGTTGCTGAACAAG 59.661 47.619 3.88 0.00 39.50 3.16
7967 8907 1.610038 CATGGCAGTTGCTGAACAAGA 59.390 47.619 3.88 0.00 39.50 3.02
7968 8908 1.024271 TGGCAGTTGCTGAACAAGAC 58.976 50.000 3.88 0.00 39.50 3.01
7969 8909 0.040958 GGCAGTTGCTGAACAAGACG 60.041 55.000 3.88 0.00 39.50 4.18
7970 8910 0.040958 GCAGTTGCTGAACAAGACGG 60.041 55.000 0.00 0.00 39.50 4.79
7971 8911 1.581934 CAGTTGCTGAACAAGACGGA 58.418 50.000 0.00 0.00 39.50 4.69
7972 8912 1.528586 CAGTTGCTGAACAAGACGGAG 59.471 52.381 0.00 0.00 39.50 4.63
7973 8913 1.412710 AGTTGCTGAACAAGACGGAGA 59.587 47.619 0.00 0.00 39.50 3.71
7974 8914 1.527311 GTTGCTGAACAAGACGGAGAC 59.473 52.381 0.00 0.00 39.50 3.36
8007 8987 3.050089 TGGTCACCTTCCCTAGTTTGAA 58.950 45.455 0.00 0.00 0.00 2.69
8080 9060 4.041049 CAGCAAAGCACAACGAACATAAA 58.959 39.130 0.00 0.00 0.00 1.40
8094 9074 8.599774 CAACGAACATAAACAAAAATGGACTTT 58.400 29.630 0.00 0.00 0.00 2.66
8099 9079 2.415697 ACAAAAATGGACTTTCCGCG 57.584 45.000 0.00 0.00 40.17 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 76 9.601217 CATGCATTAACTTTTACTAGGAGTACT 57.399 33.333 0.00 0.00 28.93 2.73
75 77 9.379791 ACATGCATTAACTTTTACTAGGAGTAC 57.620 33.333 0.00 0.00 28.93 2.73
76 78 9.595823 GACATGCATTAACTTTTACTAGGAGTA 57.404 33.333 0.00 0.00 0.00 2.59
77 79 8.100791 TGACATGCATTAACTTTTACTAGGAGT 58.899 33.333 0.00 0.00 0.00 3.85
78 80 8.492673 TGACATGCATTAACTTTTACTAGGAG 57.507 34.615 0.00 0.00 0.00 3.69
140 144 6.746745 AGCAAAAATAATGCCATTGGAAAG 57.253 33.333 6.95 0.00 44.91 2.62
178 182 9.084533 AGGTCTTATATCTAGAAACAGATGGAC 57.915 37.037 0.00 0.00 35.99 4.02
208 212 7.861372 CCGTATGTAGTTCGTATTGAAATCTCT 59.139 37.037 0.00 0.00 38.60 3.10
260 278 5.039480 ACGAAGCAAAATGAGTGAATCTG 57.961 39.130 0.00 0.00 0.00 2.90
284 302 2.579684 CTTACTGCCTCCGTCCTGCC 62.580 65.000 0.00 0.00 0.00 4.85
314 453 4.673441 CTGCTAAGTAGTACATCAAGCGT 58.327 43.478 2.52 0.00 0.00 5.07
315 454 3.487574 GCTGCTAAGTAGTACATCAAGCG 59.512 47.826 2.52 4.17 0.00 4.68
316 455 3.487574 CGCTGCTAAGTAGTACATCAAGC 59.512 47.826 2.52 6.22 0.00 4.01
317 456 4.921547 TCGCTGCTAAGTAGTACATCAAG 58.078 43.478 2.52 0.00 0.00 3.02
319 458 4.638865 TCTTCGCTGCTAAGTAGTACATCA 59.361 41.667 12.82 0.00 0.00 3.07
320 459 5.171147 TCTTCGCTGCTAAGTAGTACATC 57.829 43.478 12.82 0.00 0.00 3.06
321 460 4.641094 ACTCTTCGCTGCTAAGTAGTACAT 59.359 41.667 12.82 0.00 0.00 2.29
322 461 4.008330 ACTCTTCGCTGCTAAGTAGTACA 58.992 43.478 12.82 0.00 0.00 2.90
323 462 4.094590 TGACTCTTCGCTGCTAAGTAGTAC 59.905 45.833 12.82 0.00 0.00 2.73
324 463 4.259356 TGACTCTTCGCTGCTAAGTAGTA 58.741 43.478 12.82 0.00 0.00 1.82
325 464 3.082548 TGACTCTTCGCTGCTAAGTAGT 58.917 45.455 12.82 13.63 0.00 2.73
326 465 3.766676 TGACTCTTCGCTGCTAAGTAG 57.233 47.619 12.82 11.13 0.00 2.57
327 466 4.514781 TTTGACTCTTCGCTGCTAAGTA 57.485 40.909 12.82 1.13 0.00 2.24
328 467 3.386768 TTTGACTCTTCGCTGCTAAGT 57.613 42.857 12.82 3.74 0.00 2.24
329 468 3.494626 TGTTTTGACTCTTCGCTGCTAAG 59.505 43.478 7.53 7.53 0.00 2.18
330 469 3.247648 GTGTTTTGACTCTTCGCTGCTAA 59.752 43.478 0.00 0.00 0.00 3.09
335 474 5.758296 TCATTTAGTGTTTTGACTCTTCGCT 59.242 36.000 0.00 0.00 0.00 4.93
395 538 6.602803 TCCACAGCTTTGAATTAATCATGCTA 59.397 34.615 0.17 0.00 42.50 3.49
399 542 6.183360 CGAGTCCACAGCTTTGAATTAATCAT 60.183 38.462 0.17 0.00 38.03 2.45
415 558 1.829096 TCCAACGGTCGAGTCCACA 60.829 57.895 0.00 0.00 0.00 4.17
421 564 2.138656 AACGAGGTCCAACGGTCGAG 62.139 60.000 11.93 0.00 36.30 4.04
456 600 1.992277 CTCCTAGGTGCCAGCCACT 60.992 63.158 9.08 0.00 44.08 4.00
465 609 0.625849 ATGGGGTTTGCTCCTAGGTG 59.374 55.000 9.08 7.68 35.83 4.00
585 734 0.900182 CACTTTGGGAAGGGAAGGGC 60.900 60.000 0.00 0.00 38.64 5.19
586 735 0.900182 GCACTTTGGGAAGGGAAGGG 60.900 60.000 0.00 0.00 38.64 3.95
991 1141 2.344203 CGAGGACGAGGAGGCTTGT 61.344 63.158 0.00 0.00 42.66 3.16
992 1142 2.492090 CGAGGACGAGGAGGCTTG 59.508 66.667 0.00 0.00 42.66 4.01
993 1143 2.756283 CCGAGGACGAGGAGGCTT 60.756 66.667 0.00 0.00 42.66 4.35
996 1146 4.824515 AGGCCGAGGACGAGGAGG 62.825 72.222 0.00 0.00 42.66 4.30
1061 1211 0.034059 AGAAACCACTCACCAGAGCG 59.966 55.000 0.00 0.00 46.09 5.03
1083 1233 4.208686 CTCCGCCACGAGGGTAGC 62.209 72.222 0.00 0.00 39.65 3.58
1084 1234 4.208686 GCTCCGCCACGAGGGTAG 62.209 72.222 0.00 0.00 39.65 3.18
1337 1510 3.698029 TGCAGAAACAGAAAAGCACTC 57.302 42.857 0.00 0.00 0.00 3.51
1356 1529 8.697067 ACGTACTAATTAATAGCAACGCTTATG 58.303 33.333 11.14 0.00 43.12 1.90
1378 1558 0.036590 CCGGGGGAAAAGGAAACGTA 59.963 55.000 0.00 0.00 0.00 3.57
1379 1559 1.228337 CCGGGGGAAAAGGAAACGT 60.228 57.895 0.00 0.00 0.00 3.99
1380 1560 2.632544 GCCGGGGGAAAAGGAAACG 61.633 63.158 2.18 0.00 0.00 3.60
1398 1579 2.534019 CGGACCGCCCAATCAATCG 61.534 63.158 0.00 0.00 34.14 3.34
1505 1705 4.151867 GCGAATCCAAAGAAACGAACTAGT 59.848 41.667 0.00 0.00 0.00 2.57
1506 1706 4.389077 AGCGAATCCAAAGAAACGAACTAG 59.611 41.667 0.00 0.00 0.00 2.57
1507 1707 4.312443 AGCGAATCCAAAGAAACGAACTA 58.688 39.130 0.00 0.00 0.00 2.24
1508 1708 3.139077 AGCGAATCCAAAGAAACGAACT 58.861 40.909 0.00 0.00 0.00 3.01
1509 1709 3.537793 AGCGAATCCAAAGAAACGAAC 57.462 42.857 0.00 0.00 0.00 3.95
1510 1710 3.562141 TGAAGCGAATCCAAAGAAACGAA 59.438 39.130 0.00 0.00 0.00 3.85
1536 1736 2.123342 CCATTTCAGAGAGCGACGATC 58.877 52.381 4.63 4.63 0.00 3.69
1548 1748 2.436417 TCCGGCTTTTCTCCATTTCAG 58.564 47.619 0.00 0.00 0.00 3.02
1580 1780 2.245096 CAAATTCAACTACGCAGCAGC 58.755 47.619 0.00 0.00 37.42 5.25
1587 1787 3.058501 AGGAAACGCCAAATTCAACTACG 60.059 43.478 0.00 0.00 40.02 3.51
1598 1798 0.382515 CGTTGGAAAGGAAACGCCAA 59.617 50.000 0.00 0.00 42.17 4.52
1606 1806 4.545208 TGTGTATGATCGTTGGAAAGGA 57.455 40.909 0.00 0.00 45.59 3.36
1613 1813 8.279695 TGTTTCAAAAATGTGTATGATCGTTG 57.720 30.769 0.00 0.00 0.00 4.10
1637 1840 2.537625 GCTAGCTAACAGCAGTTCGATG 59.462 50.000 7.70 0.00 45.56 3.84
1745 1949 9.373603 CACCATTCATTCATCATAAACACAAAT 57.626 29.630 0.00 0.00 0.00 2.32
1758 1962 3.635373 GCAGGTCATCACCATTCATTCAT 59.365 43.478 0.00 0.00 46.68 2.57
1759 1963 3.018856 GCAGGTCATCACCATTCATTCA 58.981 45.455 0.00 0.00 46.68 2.57
1760 1964 2.360165 GGCAGGTCATCACCATTCATTC 59.640 50.000 0.00 0.00 46.68 2.67
1761 1965 2.291735 TGGCAGGTCATCACCATTCATT 60.292 45.455 0.00 0.00 46.68 2.57
1769 1973 2.119801 ATGAAGTGGCAGGTCATCAC 57.880 50.000 6.95 0.00 0.00 3.06
1771 1975 5.841957 ATAAAATGAAGTGGCAGGTCATC 57.158 39.130 11.99 0.00 30.76 2.92
1841 2047 1.802508 CGCGGTGATCTGCTACAATGA 60.803 52.381 0.00 0.00 43.19 2.57
1857 2063 3.702048 TTCTGGGAAGGGACGCGG 61.702 66.667 12.47 0.00 0.00 6.46
1858 2064 2.434359 GTTCTGGGAAGGGACGCG 60.434 66.667 3.53 3.53 0.00 6.01
1949 2156 3.579151 GGTCTGTGGAAAACTAGAGGTCT 59.421 47.826 0.00 0.00 0.00 3.85
1966 2175 8.571336 ACTCATTTTGTAAAATCTCAAGGTCTG 58.429 33.333 0.00 0.00 36.52 3.51
1968 2177 9.827411 GTACTCATTTTGTAAAATCTCAAGGTC 57.173 33.333 0.00 0.00 36.52 3.85
1973 2182 9.430623 TCGATGTACTCATTTTGTAAAATCTCA 57.569 29.630 0.00 0.00 36.52 3.27
2130 2346 1.002069 TCTGGTCCTTCATGGCCAAT 58.998 50.000 10.96 0.00 40.01 3.16
2199 2415 2.045926 GCTGCCCGATCCTGTTGT 60.046 61.111 0.00 0.00 0.00 3.32
2201 2417 2.045926 GTGCTGCCCGATCCTGTT 60.046 61.111 0.00 0.00 0.00 3.16
2285 2501 7.540474 AGTCAATTAGAAGGTCACTCTTACA 57.460 36.000 0.00 0.00 0.00 2.41
2290 2506 9.606631 ATCAATTAGTCAATTAGAAGGTCACTC 57.393 33.333 0.00 0.00 32.96 3.51
2302 2518 7.446625 GGAGATACAGGCATCAATTAGTCAATT 59.553 37.037 0.00 0.00 34.60 2.32
2405 2622 3.368248 ACCATTAATGCCTGTCAATGCT 58.632 40.909 10.11 0.00 0.00 3.79
2624 2841 8.100508 AGCTTAAAAGAAGACAGATGGTAAAC 57.899 34.615 0.00 0.00 0.00 2.01
2640 2857 4.291540 TGTGCACAACTGAGCTTAAAAG 57.708 40.909 19.28 0.00 32.76 2.27
2644 2861 3.069289 CTGATGTGCACAACTGAGCTTA 58.931 45.455 25.72 2.11 32.76 3.09
2664 2884 5.603596 TGCTCAAAATGATTTGCTTCAACT 58.396 33.333 0.00 0.00 44.52 3.16
2667 2887 5.204409 ACTGCTCAAAATGATTTGCTTCA 57.796 34.783 0.00 0.00 44.52 3.02
2725 2945 5.596836 ACAAAAGCAAGAAAAGGTCATGA 57.403 34.783 0.00 0.00 0.00 3.07
3576 3849 5.516339 CCAATGATGTACAAGCGGAAATTTC 59.484 40.000 9.83 9.83 0.00 2.17
3696 3970 9.056005 GCTACATATCCAACAGATAACAAATGA 57.944 33.333 0.00 0.00 40.86 2.57
4113 4868 2.566279 TCTCTTCTCTGAGCTGCAATGT 59.434 45.455 1.02 0.00 34.29 2.71
4194 4949 0.597568 TGGCTGTTCTTGCATTTCCG 59.402 50.000 0.00 0.00 0.00 4.30
4299 5054 9.341899 CTTACCATGTTAACTTTTGCAGTATTC 57.658 33.333 7.22 0.00 32.94 1.75
4330 5085 5.858381 AGACAAAGAAATGCAGTCTCACTA 58.142 37.500 3.32 0.00 34.71 2.74
4376 5133 2.917713 ATGGGCAATGGAGTGGTAAA 57.082 45.000 0.00 0.00 0.00 2.01
4883 5711 2.427453 TGATTGTCTAACCGAGCTCCTC 59.573 50.000 8.47 0.00 0.00 3.71
4928 5756 3.829948 CTCAAGCTTGCGAATTTCATGT 58.170 40.909 21.99 0.00 0.00 3.21
5246 6074 3.005554 CTCAGCATTCGGAAGTGACATT 58.994 45.455 0.00 0.00 0.00 2.71
5258 6086 3.129638 ACTTCGGAGTAGTCTCAGCATTC 59.870 47.826 0.00 0.00 42.05 2.67
5333 6176 5.045286 AGGTGCTCTTATCAGATTTGGTCTT 60.045 40.000 0.00 0.00 34.00 3.01
5361 6210 1.621072 CCTGCTAGAAGAGTGGGGAGT 60.621 57.143 0.00 0.00 0.00 3.85
5677 6529 1.948834 TGTGTGTGCAAGATCAAGTGG 59.051 47.619 0.00 0.00 0.00 4.00
6094 6949 8.271458 TGTTGGCTCATCATAATCTTTACCTTA 58.729 33.333 0.00 0.00 0.00 2.69
6128 6983 4.666512 AGCAATATGACCAAAGGACACTT 58.333 39.130 0.00 0.00 38.99 3.16
6142 6998 2.838736 ACGAAGCAGGGTAGCAATATG 58.161 47.619 0.00 0.00 36.85 1.78
6160 7018 6.274001 ACGAGTTGAATAATGCAGATAACG 57.726 37.500 0.00 0.00 0.00 3.18
6172 7030 4.028131 ACCTACATGGGACGAGTTGAATA 58.972 43.478 0.00 0.00 41.11 1.75
6235 7098 1.341852 ACTGCAGCAATGCACAAATGA 59.658 42.857 15.27 0.00 40.23 2.57
6468 7331 1.073763 CTGATGTTCCCACCCTCACAA 59.926 52.381 0.00 0.00 0.00 3.33
6620 7483 6.426328 CCAGTATGAAATGTATCAGCTCCTTC 59.574 42.308 0.00 0.00 39.69 3.46
6652 7515 1.963515 GCCAGTTCACCTTGGTGAATT 59.036 47.619 30.26 25.23 43.99 2.17
6798 7661 3.942829 CCTGCAGAAGGTAGATGACAAA 58.057 45.455 17.39 0.00 41.74 2.83
6900 7764 4.342092 CCTGATTGAACAAGTCCAAAACCT 59.658 41.667 0.00 0.00 0.00 3.50
6901 7765 4.099419 ACCTGATTGAACAAGTCCAAAACC 59.901 41.667 0.00 0.00 0.00 3.27
6902 7766 5.043248 CACCTGATTGAACAAGTCCAAAAC 58.957 41.667 0.00 0.00 0.00 2.43
6937 7804 3.139077 CTGAACCTGAAACGTTAAGCCT 58.861 45.455 0.00 0.00 0.00 4.58
6983 7850 6.813649 GCAGAAGTTCCAAGGATAAAAATTCC 59.186 38.462 0.00 0.00 0.00 3.01
6995 7862 3.655276 AGCAAATGCAGAAGTTCCAAG 57.345 42.857 8.28 0.00 45.16 3.61
7030 7897 3.073062 ACACTCCACTCTGCCAAAATAGT 59.927 43.478 0.00 0.00 0.00 2.12
7031 7898 3.438087 CACACTCCACTCTGCCAAAATAG 59.562 47.826 0.00 0.00 0.00 1.73
7032 7899 3.181445 ACACACTCCACTCTGCCAAAATA 60.181 43.478 0.00 0.00 0.00 1.40
7033 7900 2.233271 CACACTCCACTCTGCCAAAAT 58.767 47.619 0.00 0.00 0.00 1.82
7056 7937 5.116084 TCACTCTAATTTTAGGCTGGCAT 57.884 39.130 3.38 0.00 0.00 4.40
7079 7960 8.347004 TGAAGCAATCCACAAAATAGTCATTA 57.653 30.769 0.00 0.00 0.00 1.90
7148 8029 8.188139 TCAGTACCTTTTCAAAGTCATTTTCAC 58.812 33.333 0.00 0.00 34.20 3.18
7172 8068 2.715749 ATTCCGCATCTGATGGTTCA 57.284 45.000 18.60 0.00 0.00 3.18
7173 8069 4.335315 TGTTTATTCCGCATCTGATGGTTC 59.665 41.667 18.60 2.12 0.00 3.62
7174 8070 4.096382 GTGTTTATTCCGCATCTGATGGTT 59.904 41.667 18.60 0.04 0.00 3.67
7177 8073 4.571984 TCAGTGTTTATTCCGCATCTGATG 59.428 41.667 13.26 13.26 0.00 3.07
7178 8074 4.769688 TCAGTGTTTATTCCGCATCTGAT 58.230 39.130 0.00 0.00 0.00 2.90
7179 8075 4.200838 TCAGTGTTTATTCCGCATCTGA 57.799 40.909 0.00 0.00 0.00 3.27
7180 8076 4.728882 GCTTCAGTGTTTATTCCGCATCTG 60.729 45.833 0.00 0.00 0.00 2.90
7181 8077 3.375299 GCTTCAGTGTTTATTCCGCATCT 59.625 43.478 0.00 0.00 0.00 2.90
7182 8078 3.126858 TGCTTCAGTGTTTATTCCGCATC 59.873 43.478 0.00 0.00 0.00 3.91
7183 8079 3.081061 TGCTTCAGTGTTTATTCCGCAT 58.919 40.909 0.00 0.00 0.00 4.73
7184 8080 2.499197 TGCTTCAGTGTTTATTCCGCA 58.501 42.857 0.00 0.00 0.00 5.69
7185 8081 3.552604 TTGCTTCAGTGTTTATTCCGC 57.447 42.857 0.00 0.00 0.00 5.54
7186 8082 8.424731 GTTATTTTTGCTTCAGTGTTTATTCCG 58.575 33.333 0.00 0.00 0.00 4.30
7187 8083 9.476202 AGTTATTTTTGCTTCAGTGTTTATTCC 57.524 29.630 0.00 0.00 0.00 3.01
7239 8145 2.030540 CGCCATGTTCATCCATCATTCC 60.031 50.000 0.00 0.00 0.00 3.01
7240 8146 2.880268 TCGCCATGTTCATCCATCATTC 59.120 45.455 0.00 0.00 0.00 2.67
7241 8147 2.882761 CTCGCCATGTTCATCCATCATT 59.117 45.455 0.00 0.00 0.00 2.57
7245 8159 0.107066 TGCTCGCCATGTTCATCCAT 60.107 50.000 0.00 0.00 0.00 3.41
7266 8180 2.736400 GCCACAAAGAATATGCTGTGCC 60.736 50.000 0.07 0.00 38.26 5.01
7270 8184 2.164827 TGCAGCCACAAAGAATATGCTG 59.835 45.455 5.01 5.01 46.70 4.41
7277 8191 2.893441 TGGTTGCAGCCACAAAGAA 58.107 47.368 19.51 0.00 32.81 2.52
7278 8192 4.674306 TGGTTGCAGCCACAAAGA 57.326 50.000 19.51 0.00 32.81 2.52
7323 8242 3.202595 ACACCCTAAACCTGTTTGTGGTA 59.797 43.478 14.00 0.00 36.37 3.25
7332 8251 4.003648 GAGAATGACACACCCTAAACCTG 58.996 47.826 0.00 0.00 0.00 4.00
7400 8319 7.546667 ACATGATGTTAGGCAAGCTTAATTTTG 59.453 33.333 0.00 0.00 0.00 2.44
7417 8336 5.627499 ATGTTTACGCAAGACATGATGTT 57.373 34.783 0.00 0.00 43.62 2.71
7418 8337 8.224965 AAGCATGTTTACGCAAGACATGATGT 62.225 38.462 19.89 0.00 46.15 3.06
7419 8338 5.900934 AAGCATGTTTACGCAAGACATGATG 60.901 40.000 19.89 0.00 46.15 3.07
7423 8342 5.621197 TTAAGCATGTTTACGCAAGACAT 57.379 34.783 0.96 0.00 43.62 3.06
7424 8343 5.621197 ATTAAGCATGTTTACGCAAGACA 57.379 34.783 0.96 0.00 43.62 3.41
7425 8344 8.523464 CAATTATTAAGCATGTTTACGCAAGAC 58.477 33.333 0.96 0.00 43.62 3.01
7426 8345 7.219917 GCAATTATTAAGCATGTTTACGCAAGA 59.780 33.333 0.96 0.00 43.62 3.02
7427 8346 7.009083 TGCAATTATTAAGCATGTTTACGCAAG 59.991 33.333 0.96 0.00 36.94 4.01
7428 8347 6.808704 TGCAATTATTAAGCATGTTTACGCAA 59.191 30.769 0.96 0.00 32.55 4.85
7429 8348 6.325596 TGCAATTATTAAGCATGTTTACGCA 58.674 32.000 0.96 2.47 32.55 5.24
7430 8349 6.804534 TGCAATTATTAAGCATGTTTACGC 57.195 33.333 0.96 0.13 32.55 4.42
7500 8419 2.953648 TCCATGTGCAGCATATTTCAGG 59.046 45.455 1.05 1.02 35.74 3.86
7557 8476 4.073293 ACTCGAGCCCTGGTATTATTTG 57.927 45.455 13.61 0.00 0.00 2.32
7680 8620 8.830580 TGCATATTGTGAGTTTCTTATTAGAGC 58.169 33.333 0.00 0.00 0.00 4.09
7760 8700 9.787532 GCTTATGTGCTTTGATTCTTTAATACA 57.212 29.630 0.00 0.00 0.00 2.29
7791 8731 5.560722 TGGACTCTTTGAAATAGTGACCA 57.439 39.130 0.40 0.98 31.78 4.02
7928 8868 2.927429 TGTGACCGCAATTTCATTTCG 58.073 42.857 0.00 0.00 0.00 3.46
7935 8875 0.244450 CTGCCATGTGACCGCAATTT 59.756 50.000 0.00 0.00 30.85 1.82
7936 8876 0.895100 ACTGCCATGTGACCGCAATT 60.895 50.000 0.00 0.00 30.85 2.32
7937 8877 0.895100 AACTGCCATGTGACCGCAAT 60.895 50.000 0.00 0.00 30.85 3.56
7938 8878 1.528076 AACTGCCATGTGACCGCAA 60.528 52.632 0.00 0.00 30.85 4.85
7939 8879 2.112928 AACTGCCATGTGACCGCA 59.887 55.556 0.00 0.00 0.00 5.69
7940 8880 2.562912 CAACTGCCATGTGACCGC 59.437 61.111 0.00 0.00 0.00 5.68
7941 8881 1.968017 AGCAACTGCCATGTGACCG 60.968 57.895 0.00 0.00 43.38 4.79
7942 8882 0.890542 TCAGCAACTGCCATGTGACC 60.891 55.000 0.00 0.00 43.38 4.02
7943 8883 0.953727 TTCAGCAACTGCCATGTGAC 59.046 50.000 0.00 0.00 43.38 3.67
7944 8884 0.953727 GTTCAGCAACTGCCATGTGA 59.046 50.000 0.00 0.00 43.38 3.58
7945 8885 0.669619 TGTTCAGCAACTGCCATGTG 59.330 50.000 0.00 0.00 43.38 3.21
7946 8886 1.338973 CTTGTTCAGCAACTGCCATGT 59.661 47.619 0.00 0.00 43.38 3.21
7947 8887 1.610038 TCTTGTTCAGCAACTGCCATG 59.390 47.619 0.00 0.00 43.38 3.66
7948 8888 1.610522 GTCTTGTTCAGCAACTGCCAT 59.389 47.619 0.00 0.00 43.38 4.40
7949 8889 1.024271 GTCTTGTTCAGCAACTGCCA 58.976 50.000 0.00 0.00 43.38 4.92
7950 8890 0.040958 CGTCTTGTTCAGCAACTGCC 60.041 55.000 0.00 0.00 43.38 4.85
7951 8891 0.040958 CCGTCTTGTTCAGCAACTGC 60.041 55.000 0.00 0.00 42.49 4.40
7952 8892 1.528586 CTCCGTCTTGTTCAGCAACTG 59.471 52.381 0.00 0.00 33.17 3.16
7953 8893 1.412710 TCTCCGTCTTGTTCAGCAACT 59.587 47.619 0.00 0.00 33.17 3.16
7954 8894 1.527311 GTCTCCGTCTTGTTCAGCAAC 59.473 52.381 0.00 0.00 32.90 4.17
7955 8895 1.138069 TGTCTCCGTCTTGTTCAGCAA 59.862 47.619 0.00 0.00 35.50 3.91
7956 8896 0.750249 TGTCTCCGTCTTGTTCAGCA 59.250 50.000 0.00 0.00 0.00 4.41
7957 8897 1.865865 TTGTCTCCGTCTTGTTCAGC 58.134 50.000 0.00 0.00 0.00 4.26
7958 8898 4.058124 TCATTTGTCTCCGTCTTGTTCAG 58.942 43.478 0.00 0.00 0.00 3.02
7959 8899 4.066646 TCATTTGTCTCCGTCTTGTTCA 57.933 40.909 0.00 0.00 0.00 3.18
7960 8900 5.418310 TTTCATTTGTCTCCGTCTTGTTC 57.582 39.130 0.00 0.00 0.00 3.18
7961 8901 5.530915 TGATTTCATTTGTCTCCGTCTTGTT 59.469 36.000 0.00 0.00 0.00 2.83
7962 8902 5.063204 TGATTTCATTTGTCTCCGTCTTGT 58.937 37.500 0.00 0.00 0.00 3.16
7963 8903 5.611796 TGATTTCATTTGTCTCCGTCTTG 57.388 39.130 0.00 0.00 0.00 3.02
7964 8904 5.124457 CCATGATTTCATTTGTCTCCGTCTT 59.876 40.000 0.00 0.00 33.61 3.01
7965 8905 4.637534 CCATGATTTCATTTGTCTCCGTCT 59.362 41.667 0.00 0.00 33.61 4.18
7966 8906 4.396166 ACCATGATTTCATTTGTCTCCGTC 59.604 41.667 0.00 0.00 33.61 4.79
7967 8907 4.335416 ACCATGATTTCATTTGTCTCCGT 58.665 39.130 0.00 0.00 33.61 4.69
7968 8908 4.395854 TGACCATGATTTCATTTGTCTCCG 59.604 41.667 15.56 0.00 36.89 4.63
7969 8909 5.393461 GGTGACCATGATTTCATTTGTCTCC 60.393 44.000 16.96 16.96 39.40 3.71
7970 8910 5.416952 AGGTGACCATGATTTCATTTGTCTC 59.583 40.000 3.63 13.04 36.89 3.36
7971 8911 5.327732 AGGTGACCATGATTTCATTTGTCT 58.672 37.500 3.63 0.97 36.89 3.41
7972 8912 5.649782 AGGTGACCATGATTTCATTTGTC 57.350 39.130 3.63 10.78 36.68 3.18
7973 8913 5.047092 GGAAGGTGACCATGATTTCATTTGT 60.047 40.000 3.63 0.00 33.61 2.83
7974 8914 5.413499 GGAAGGTGACCATGATTTCATTTG 58.587 41.667 3.63 0.00 33.61 2.32
8022 9002 7.686519 TCATGCAGCAAATTATTGTTTTATGC 58.313 30.769 0.00 0.00 38.85 3.14
8035 9015 5.047164 TGTCCTAATTGTTCATGCAGCAAAT 60.047 36.000 0.00 0.00 0.00 2.32
8080 9060 1.679153 ACGCGGAAAGTCCATTTTTGT 59.321 42.857 12.47 0.00 35.91 2.83


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

AutoCloner maintained by Alex Coulton.