Multiple sequence alignment - TraesCS4D01G246400

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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 TraesCS4D01G246400 chr4D 100.000 8624 0 0 1 8624 415005847 414997224 0.000000e+00 15926.0
1 TraesCS4D01G246400 chr4D 97.872 47 1 0 1376 1422 415004418 415004372 2.000000e-11 82.4
2 TraesCS4D01G246400 chr4D 97.872 47 1 0 1430 1476 415004472 415004426 2.000000e-11 82.4
3 TraesCS4D01G246400 chr4B 94.477 3549 155 16 1678 5211 511168350 511164828 0.000000e+00 5430.0
4 TraesCS4D01G246400 chr4B 93.434 1995 46 12 5192 7155 511164814 511162874 0.000000e+00 2880.0
5 TraesCS4D01G246400 chr4B 88.896 1675 93 43 14 1649 511169967 511168347 0.000000e+00 1977.0
6 TraesCS4D01G246400 chr4B 90.022 1373 76 26 7151 8494 511162785 511161445 0.000000e+00 1720.0
7 TraesCS4D01G246400 chr4B 91.111 90 5 3 7764 7851 510844512 510844600 1.520000e-22 119.0
8 TraesCS4D01G246400 chr4B 80.124 161 29 3 6347 6506 535298755 535298913 5.470000e-22 117.0
9 TraesCS4D01G246400 chr4B 97.872 47 1 0 1376 1422 511168572 511168526 2.000000e-11 82.4
10 TraesCS4D01G246400 chr4B 91.489 47 4 0 1430 1476 511168626 511168580 2.010000e-06 65.8
11 TraesCS4D01G246400 chr4A 91.349 3306 209 38 1678 4955 48522903 48526159 0.000000e+00 4449.0
12 TraesCS4D01G246400 chr4A 94.259 1376 52 8 6868 8228 48528084 48529447 0.000000e+00 2078.0
13 TraesCS4D01G246400 chr4A 90.890 1449 68 29 215 1635 48521482 48522894 0.000000e+00 1886.0
14 TraesCS4D01G246400 chr4A 91.345 1063 56 11 5106 6162 48526616 48527648 0.000000e+00 1421.0
15 TraesCS4D01G246400 chr4A 89.474 399 24 4 6277 6657 48527652 48528050 1.010000e-133 488.0
16 TraesCS4D01G246400 chr4A 84.389 442 18 22 8223 8624 48529474 48529904 3.780000e-103 387.0
17 TraesCS4D01G246400 chr4A 79.431 457 65 19 7410 7851 48891808 48891366 6.550000e-76 296.0
18 TraesCS4D01G246400 chr4A 91.324 219 14 3 1 218 48520973 48521187 2.350000e-75 294.0
19 TraesCS4D01G246400 chr4A 81.728 301 35 12 5476 5764 48894726 48894434 5.210000e-57 233.0
20 TraesCS4D01G246400 chr4A 90.341 176 14 2 4947 5121 48526405 48526578 2.420000e-55 228.0
21 TraesCS4D01G246400 chr4A 94.565 92 4 1 6082 6172 36535280 36535371 3.250000e-29 141.0
22 TraesCS4D01G246400 chr4A 76.642 274 36 13 7043 7316 48892099 48891854 9.090000e-25 126.0
23 TraesCS4D01G246400 chr4A 97.872 47 1 0 1430 1476 48522622 48522668 2.000000e-11 82.4
24 TraesCS4D01G246400 chr4A 97.727 44 1 0 1376 1419 48522676 48522719 9.280000e-10 76.8
25 TraesCS4D01G246400 chr3B 80.679 383 55 10 3172 3540 64302082 64301705 6.590000e-71 279.0
26 TraesCS4D01G246400 chr3B 83.111 225 30 2 5240 5464 64300315 64300099 1.900000e-46 198.0
27 TraesCS4D01G246400 chr3B 77.607 326 34 25 434 750 817517158 817517453 2.490000e-35 161.0
28 TraesCS4D01G246400 chr3B 97.222 36 0 1 6129 6163 810565544 810565509 9.350000e-05 60.2
29 TraesCS4D01G246400 chr5B 76.568 606 82 37 620 1201 5123601 5124170 2.370000e-70 278.0
30 TraesCS4D01G246400 chr5B 96.040 101 3 1 6186 6286 166379083 166379182 6.930000e-36 163.0
31 TraesCS4D01G246400 chr5D 73.798 603 95 45 635 1212 3792793 3793357 6.880000e-41 180.0
32 TraesCS4D01G246400 chr5D 94.495 109 5 1 6178 6286 139441023 139440916 5.350000e-37 167.0
33 TraesCS4D01G246400 chr3A 93.913 115 4 3 6181 6295 470095675 470095786 4.140000e-38 171.0
34 TraesCS4D01G246400 chr3A 82.105 190 24 7 5463 5642 740192410 740192221 4.170000e-33 154.0
35 TraesCS4D01G246400 chr3A 83.969 131 13 6 654 782 740157706 740157582 1.520000e-22 119.0
36 TraesCS4D01G246400 chr7B 94.495 109 4 2 6189 6296 162120908 162120801 5.350000e-37 167.0
37 TraesCS4D01G246400 chr5A 94.286 105 5 1 6178 6282 174594014 174594117 8.960000e-35 159.0
38 TraesCS4D01G246400 chr3D 92.661 109 6 2 6178 6285 168584880 168584773 1.160000e-33 156.0
39 TraesCS4D01G246400 chr3D 75.186 403 56 34 660 1053 607985395 607985028 5.390000e-32 150.0
40 TraesCS4D01G246400 chr3D 89.091 55 4 2 6110 6163 332801467 332801414 5.590000e-07 67.6
41 TraesCS4D01G246400 chr2D 93.396 106 5 2 6189 6293 120106052 120105948 1.160000e-33 156.0
42 TraesCS4D01G246400 chr1A 93.333 105 6 1 6182 6286 293720640 293720537 4.170000e-33 154.0
43 TraesCS4D01G246400 chr6B 76.023 171 24 12 184 354 130896053 130895900 1.200000e-08 73.1


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 TraesCS4D01G246400 chr4D 414997224 415005847 8623 True 5363.600000 15926 98.581333 1 8624 3 chr4D.!!$R1 8623
1 TraesCS4D01G246400 chr4B 511161445 511169967 8522 True 2025.866667 5430 92.698333 14 8494 6 chr4B.!!$R1 8480
2 TraesCS4D01G246400 chr4A 48520973 48529904 8931 False 1139.020000 4449 91.897000 1 8624 10 chr4A.!!$F2 8623
3 TraesCS4D01G246400 chr4A 48891366 48894726 3360 True 218.333333 296 79.267000 5476 7851 3 chr4A.!!$R1 2375
4 TraesCS4D01G246400 chr3B 64300099 64302082 1983 True 238.500000 279 81.895000 3172 5464 2 chr3B.!!$R2 2292
5 TraesCS4D01G246400 chr5B 5123601 5124170 569 False 278.000000 278 76.568000 620 1201 1 chr5B.!!$F1 581

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
85 88 0.762418 TGTTCGACAAGTGGATGGGT 59.238 50.000 0.00 0.00 0.00 4.51 F
717 1055 1.739562 GAGCAGACCGGAACAGCAG 60.740 63.158 9.46 0.00 0.00 4.24 F
2345 2744 0.035056 CTCCTGGGGAAATTGACGCT 60.035 55.000 0.00 0.00 0.00 5.07 F
3436 3855 0.388263 GAGGAACGAGTCGAACACCC 60.388 60.000 21.50 11.71 0.00 4.61 F
3781 4203 0.099436 GTGCGGATGCTTGTCATTCC 59.901 55.000 0.00 0.00 43.34 3.01 F
5051 5786 0.179000 CGGCCTCATAGTTCTGGCTT 59.821 55.000 0.00 0.00 44.36 4.35 F
6480 7609 0.108138 CCAACGCTTCTGTAGGGGAG 60.108 60.000 3.60 0.00 40.94 4.30 F
7062 9984 0.515564 CCAACCCTCGTTGTAAAGCG 59.484 55.000 2.61 0.00 46.71 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 1845 0.706729 GACAAAGACGTACCTTCGCG 59.293 55.0 0.00 0.00 0.00 5.87 R
2632 3031 0.319555 CGCTTCGTCTCTTGGTCCAA 60.320 55.0 3.76 3.76 0.00 3.53 R
3603 4022 0.250166 AGGCACAAGAACCGTGTACC 60.250 55.0 0.00 0.00 36.71 3.34 R
4360 4785 0.179108 GCGTCGGAACTAGGATTGCT 60.179 55.0 0.00 0.00 0.00 3.91 R
5525 6580 0.969149 TGTGATGTCTCTTGCCGACT 59.031 50.0 0.00 0.00 32.70 4.18 R
6750 7884 0.811616 GAAGGTACCATGCCTGCGAG 60.812 60.0 15.94 0.00 36.30 5.03 R
7587 10602 0.246360 TGACGACGATGTGCCTCATT 59.754 50.0 0.00 0.00 36.83 2.57 R
8403 11477 0.468029 AAGTTGGTTGCTGGGAGGTG 60.468 55.0 0.00 0.00 0.00 4.00 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
84 87 1.890876 TTGTTCGACAAGTGGATGGG 58.109 50.000 0.00 0.00 32.34 4.00
85 88 0.762418 TGTTCGACAAGTGGATGGGT 59.238 50.000 0.00 0.00 0.00 4.51
128 132 5.416947 CCTGCCGTGTAGTAGAATAGTTTT 58.583 41.667 0.00 0.00 0.00 2.43
131 135 6.694447 TGCCGTGTAGTAGAATAGTTTTTCT 58.306 36.000 0.00 0.00 39.28 2.52
132 136 6.810182 TGCCGTGTAGTAGAATAGTTTTTCTC 59.190 38.462 0.00 0.00 37.20 2.87
134 138 7.318141 CCGTGTAGTAGAATAGTTTTTCTCCA 58.682 38.462 0.00 0.00 37.20 3.86
180 184 7.049799 ACTTGAAAGCATTAAAAAGTAGCCA 57.950 32.000 0.00 0.00 0.00 4.75
190 194 6.576551 TTAAAAAGTAGCCAAAAACAAGCG 57.423 33.333 0.00 0.00 0.00 4.68
211 215 1.823169 TAGACAGAAAACGGCCGCCT 61.823 55.000 28.58 14.69 0.00 5.52
234 540 6.071616 CCTTTTAAGCGGCTAGAGAGATAGAT 60.072 42.308 1.35 0.00 0.00 1.98
236 542 7.997773 TTTAAGCGGCTAGAGAGATAGATAA 57.002 36.000 1.35 0.00 0.00 1.75
240 546 6.423182 AGCGGCTAGAGAGATAGATAAAGAT 58.577 40.000 0.00 0.00 0.00 2.40
242 548 6.459573 GCGGCTAGAGAGATAGATAAAGATGG 60.460 46.154 0.00 0.00 0.00 3.51
243 549 6.826231 CGGCTAGAGAGATAGATAAAGATGGA 59.174 42.308 0.00 0.00 0.00 3.41
259 565 6.558488 AAGATGGAAGATAGATGGATAGGC 57.442 41.667 0.00 0.00 0.00 3.93
263 569 4.774726 TGGAAGATAGATGGATAGGCAGAC 59.225 45.833 0.00 0.00 0.00 3.51
264 570 4.161377 GGAAGATAGATGGATAGGCAGACC 59.839 50.000 0.00 0.00 0.00 3.85
265 571 4.410481 AGATAGATGGATAGGCAGACCA 57.590 45.455 0.00 0.00 39.06 4.02
266 572 4.093011 AGATAGATGGATAGGCAGACCAC 58.907 47.826 0.00 0.00 39.06 4.16
267 573 2.180946 AGATGGATAGGCAGACCACA 57.819 50.000 0.00 0.00 39.06 4.17
288 604 2.089854 GGCGAGTTGCATCGTCATT 58.910 52.632 9.33 0.00 46.31 2.57
314 630 3.995669 GTCGCGCACGCAGTTTCA 61.996 61.111 16.04 0.00 41.61 2.69
571 908 1.794222 GTGTCCGCGATTCCCAAAG 59.206 57.895 8.23 0.00 0.00 2.77
608 945 2.872245 CTCACACCTCGAAAGCAAAAGA 59.128 45.455 0.00 0.00 0.00 2.52
618 955 2.672996 GCAAAAGAGCAGGGCGGA 60.673 61.111 0.00 0.00 0.00 5.54
717 1055 1.739562 GAGCAGACCGGAACAGCAG 60.740 63.158 9.46 0.00 0.00 4.24
718 1056 3.426568 GCAGACCGGAACAGCAGC 61.427 66.667 9.46 0.00 0.00 5.25
719 1057 2.031012 CAGACCGGAACAGCAGCA 59.969 61.111 9.46 0.00 0.00 4.41
724 1062 2.591429 CGGAACAGCAGCACACCA 60.591 61.111 0.00 0.00 0.00 4.17
727 1065 2.896801 GAACAGCAGCACACCACCG 61.897 63.158 0.00 0.00 0.00 4.94
728 1066 4.935495 ACAGCAGCACACCACCGG 62.935 66.667 0.00 0.00 0.00 5.28
729 1067 4.624364 CAGCAGCACACCACCGGA 62.624 66.667 9.46 0.00 0.00 5.14
730 1068 4.626081 AGCAGCACACCACCGGAC 62.626 66.667 9.46 0.00 0.00 4.79
731 1069 4.927782 GCAGCACACCACCGGACA 62.928 66.667 9.46 0.00 0.00 4.02
831 1181 2.115595 CTATGCGCTCGTTTCTCTCTG 58.884 52.381 9.73 0.00 0.00 3.35
1301 1678 2.682494 TTCCCTTAGGAGCGGCGT 60.682 61.111 9.37 0.00 45.19 5.68
1302 1679 2.630592 CTTCCCTTAGGAGCGGCGTC 62.631 65.000 9.37 4.77 45.19 5.19
1468 1845 4.436998 CCACAGGCTCGTCGGACC 62.437 72.222 1.91 0.00 0.00 4.46
1588 1973 6.984474 GCTCAGCAATGTGGTAGTATTAGTAA 59.016 38.462 0.00 0.00 0.00 2.24
1642 2035 2.574006 ATGCACACATCTCACTGGTT 57.426 45.000 0.00 0.00 0.00 3.67
1645 2038 4.019792 TGCACACATCTCACTGGTTATT 57.980 40.909 0.00 0.00 0.00 1.40
1646 2039 5.159273 TGCACACATCTCACTGGTTATTA 57.841 39.130 0.00 0.00 0.00 0.98
1647 2040 5.744171 TGCACACATCTCACTGGTTATTAT 58.256 37.500 0.00 0.00 0.00 1.28
1648 2041 6.179756 TGCACACATCTCACTGGTTATTATT 58.820 36.000 0.00 0.00 0.00 1.40
1649 2042 6.658816 TGCACACATCTCACTGGTTATTATTT 59.341 34.615 0.00 0.00 0.00 1.40
1650 2043 7.148255 TGCACACATCTCACTGGTTATTATTTC 60.148 37.037 0.00 0.00 0.00 2.17
1651 2044 7.679638 GCACACATCTCACTGGTTATTATTTCC 60.680 40.741 0.00 0.00 0.00 3.13
1652 2045 7.336679 CACACATCTCACTGGTTATTATTTCCA 59.663 37.037 0.00 0.00 0.00 3.53
1653 2046 7.888021 ACACATCTCACTGGTTATTATTTCCAA 59.112 33.333 0.00 0.00 0.00 3.53
1654 2047 8.739039 CACATCTCACTGGTTATTATTTCCAAA 58.261 33.333 0.00 0.00 0.00 3.28
1655 2048 9.308000 ACATCTCACTGGTTATTATTTCCAAAA 57.692 29.630 0.00 0.00 0.00 2.44
1809 2203 6.757897 TGCACATTAGGAAAGTGGAATTAG 57.242 37.500 0.00 0.00 33.98 1.73
1825 2220 1.603236 TTAGGGCTTGCCATTTGCCG 61.603 55.000 14.04 0.00 46.97 5.69
1952 2347 2.095059 GGCAAGCTAAGGTGATGTGTTG 60.095 50.000 0.00 0.00 0.00 3.33
1978 2373 0.248866 GTGTTTCCTTGTTGGCACCG 60.249 55.000 0.00 0.00 35.26 4.94
2218 2614 1.875963 CCGCCGAGACAAGCAATTT 59.124 52.632 0.00 0.00 0.00 1.82
2343 2742 1.032114 GGCTCCTGGGGAAATTGACG 61.032 60.000 0.00 0.00 0.00 4.35
2345 2744 0.035056 CTCCTGGGGAAATTGACGCT 60.035 55.000 0.00 0.00 0.00 5.07
2448 2847 4.218200 CCAAGGAATGTTGTTGATGTAGCA 59.782 41.667 0.00 0.00 0.00 3.49
2587 2986 2.770232 CCTAACCTCATTAGTTCCCGGT 59.230 50.000 0.00 0.00 39.01 5.28
2594 2993 1.134788 CATTAGTTCCCGGTCGAAGCT 60.135 52.381 0.00 1.35 0.00 3.74
2632 3031 0.909610 TCGTTTGGAGGAGGAGGCAT 60.910 55.000 0.00 0.00 0.00 4.40
2768 3167 1.901591 CCACACACCAGAAGAGCAAT 58.098 50.000 0.00 0.00 0.00 3.56
2872 3274 2.813908 GTCGTCGCCACCACATCC 60.814 66.667 0.00 0.00 0.00 3.51
3013 3416 5.606749 AGGTGGTACATGATTTCTATGCCTA 59.393 40.000 0.00 0.00 44.52 3.93
3101 3505 4.383850 CAACAATCAAAGTTGGACACCA 57.616 40.909 0.00 0.00 41.92 4.17
3107 3511 2.093394 TCAAAGTTGGACACCAGTCGAA 60.093 45.455 0.00 0.00 45.92 3.71
3161 3565 5.449553 TGTCTATCCTAGTTCTGATGCTCA 58.550 41.667 0.00 0.00 0.00 4.26
3365 3784 4.606961 GGACACGACATCAACACAAATTT 58.393 39.130 0.00 0.00 0.00 1.82
3416 3835 3.113260 AGCACATTAAGGTCTATCGCC 57.887 47.619 0.00 0.00 0.00 5.54
3436 3855 0.388263 GAGGAACGAGTCGAACACCC 60.388 60.000 21.50 11.71 0.00 4.61
3451 3870 1.457831 ACCCTCGGCCATCCTAGTC 60.458 63.158 2.24 0.00 0.00 2.59
3475 3894 6.606796 TCCATATGTTTGTTGTTCCAGCATAT 59.393 34.615 1.24 0.00 31.18 1.78
3479 3898 7.701539 ATGTTTGTTGTTCCAGCATATCTTA 57.298 32.000 0.00 0.00 0.00 2.10
3532 3951 8.851145 TGTAACATTTACTCATTTGGCAAAGTA 58.149 29.630 18.61 11.95 0.00 2.24
3541 3960 4.280425 TCATTTGGCAAAGTAGCATGAACA 59.720 37.500 18.61 0.00 35.83 3.18
3587 4006 5.588568 GAAGCATATGATCCTTCGTCAAG 57.411 43.478 6.97 0.00 0.00 3.02
3602 4021 2.613977 CGTCAAGCATCTCTTTGGAGGT 60.614 50.000 0.00 0.00 39.86 3.85
3662 4084 0.304705 GACATGGCCAATAACGCTCG 59.695 55.000 10.96 0.00 0.00 5.03
3781 4203 0.099436 GTGCGGATGCTTGTCATTCC 59.901 55.000 0.00 0.00 43.34 3.01
3921 4343 5.508153 CCAAACATTTTGTCGGATGTGGTAA 60.508 40.000 0.00 0.00 36.65 2.85
4027 4451 1.883275 CCGGTTGTTGTGCCTTATTCA 59.117 47.619 0.00 0.00 0.00 2.57
4033 4457 4.987408 TGTTGTGCCTTATTCATCATGG 57.013 40.909 0.00 0.00 0.00 3.66
4118 4542 1.029681 AAAGTTGGAACCCGTTGAGC 58.970 50.000 0.00 0.00 0.00 4.26
4171 4595 1.051812 CCATCCTAGTCCCGATGCTT 58.948 55.000 2.18 0.00 35.55 3.91
4211 4635 1.985447 ATCGCCGATGTGCTTGCTTG 61.985 55.000 0.00 0.00 0.00 4.01
4220 4644 3.071874 TGTGCTTGCTTGCCTAGTATT 57.928 42.857 0.00 0.00 0.00 1.89
4358 4783 1.172812 AGGAACAAGTTGGAAGCCGC 61.173 55.000 7.96 0.00 0.00 6.53
4360 4785 1.519408 GAACAAGTTGGAAGCCGCTA 58.481 50.000 7.96 0.00 0.00 4.26
4463 4913 6.491745 TGTTGGCCATTTCTTTGTATCTTACA 59.508 34.615 6.09 0.00 36.79 2.41
4489 4939 4.497006 GCACATGATAGCTGGTCAAACATC 60.497 45.833 0.00 0.00 0.00 3.06
4556 5013 4.955925 TTGTTGGACACGGCATAAATAG 57.044 40.909 0.00 0.00 0.00 1.73
4606 5065 1.735018 CATATTCGGCAACCAACGTCA 59.265 47.619 0.00 0.00 0.00 4.35
4650 5109 2.717809 GGAACAACTCGAGCGTCGC 61.718 63.158 13.61 9.80 40.21 5.19
4695 5154 4.776795 TTCTGTGTATCTTGTGACGCTA 57.223 40.909 0.00 0.00 0.00 4.26
4737 5196 3.695830 ACATTTACTCGGACATGGTGT 57.304 42.857 0.00 0.00 0.00 4.16
4883 5352 5.979288 ACGAGTCTAACACTTACCAAGAT 57.021 39.130 0.00 0.00 34.41 2.40
5051 5786 0.179000 CGGCCTCATAGTTCTGGCTT 59.821 55.000 0.00 0.00 44.36 4.35
5071 5806 4.772434 CTTGACATTCCGTTGTACAACTG 58.228 43.478 30.47 25.55 39.08 3.16
5113 5848 7.635441 GTGTAAAACACTGACTCAAACGCAAG 61.635 42.308 2.97 0.00 45.27 4.01
5117 5905 3.248602 ACACTGACTCAAACGCAAGATTC 59.751 43.478 0.00 0.00 43.62 2.52
5196 6017 1.742761 CAAGGATGTCCGAGCAATGT 58.257 50.000 0.00 0.00 42.08 2.71
5250 6304 2.845784 TGGTGCACCAAGGATGCT 59.154 55.556 36.10 0.00 44.35 3.79
5294 6348 0.458025 AAGCCTACGTGCTCGCTTAC 60.458 55.000 8.29 0.00 41.80 2.34
5525 6580 1.001520 CCGTCATGACCACCACTTGTA 59.998 52.381 20.03 0.00 0.00 2.41
5596 6663 1.152096 AACCCTCCACCTTCTCCGT 60.152 57.895 0.00 0.00 0.00 4.69
5652 6724 3.390639 TGCACATTTTCCCCTTTCATTGT 59.609 39.130 0.00 0.00 0.00 2.71
5951 7025 1.140312 TGGGAGTCTGCTGGTTTCTT 58.860 50.000 0.00 0.00 0.00 2.52
6230 7341 5.554822 AAGTGTCGCAGTTTTGAACTAAA 57.445 34.783 0.00 0.00 40.46 1.85
6273 7384 5.277825 CAAAACTGCGACACTTATTTTGGA 58.722 37.500 0.00 0.00 34.77 3.53
6296 7407 6.267242 GGATCGGAGGGAGTATTAGTTTAAGT 59.733 42.308 0.00 0.00 0.00 2.24
6467 7596 1.734465 CAGGATGAACTCTTCCAACGC 59.266 52.381 12.70 0.00 41.25 4.84
6480 7609 0.108138 CCAACGCTTCTGTAGGGGAG 60.108 60.000 3.60 0.00 40.94 4.30
6648 7777 7.724061 AGGAATTCAGCTTTGAAAGGTAAAGTA 59.276 33.333 9.51 0.00 37.49 2.24
6657 7786 9.639601 GCTTTGAAAGGTAAAGTAATTTGCTAT 57.360 29.630 7.09 0.00 37.44 2.97
6749 7883 5.356882 ACATAACAAATTCCGTGTCACAG 57.643 39.130 3.42 0.00 0.00 3.66
6750 7884 2.774439 AACAAATTCCGTGTCACAGC 57.226 45.000 3.42 0.00 0.00 4.40
6756 7890 3.108289 CCGTGTCACAGCTCGCAG 61.108 66.667 3.42 0.00 0.00 5.18
6766 7900 2.897350 GCTCGCAGGCATGGTACC 60.897 66.667 4.43 4.43 0.00 3.34
6795 7929 4.890088 TGACAATGCTACGTTCCTACTTT 58.110 39.130 0.00 0.00 0.00 2.66
6857 7991 8.849168 TGCCATTTTAATCATGTAGTTATCTGG 58.151 33.333 0.00 0.00 0.00 3.86
6858 7992 9.066892 GCCATTTTAATCATGTAGTTATCTGGA 57.933 33.333 0.00 0.00 0.00 3.86
6914 8048 2.315176 ACCAAGCCAAGCAACATACAA 58.685 42.857 0.00 0.00 0.00 2.41
6929 8063 6.364976 GCAACATACAACCACCAAATTAAGTC 59.635 38.462 0.00 0.00 0.00 3.01
7062 9984 0.515564 CCAACCCTCGTTGTAAAGCG 59.484 55.000 2.61 0.00 46.71 4.68
7108 10030 9.146984 TGTTCTATACATGCTGTTGTTTAGTAC 57.853 33.333 0.00 11.24 34.80 2.73
7109 10031 9.146984 GTTCTATACATGCTGTTGTTTAGTACA 57.853 33.333 0.00 0.00 34.59 2.90
7139 10061 8.547967 TTAGTAGCAGTTGGTTCTTATTTCAG 57.452 34.615 0.00 0.00 0.00 3.02
7156 10171 9.319143 CTTATTTCAGTGTTCCTACCTTCTATG 57.681 37.037 0.00 0.00 0.00 2.23
7180 10195 3.988379 TTTGCTTCTGTTGATCACCAC 57.012 42.857 0.00 0.00 0.00 4.16
7272 10287 3.305709 CTCGTCTGAGGGTGCAAAA 57.694 52.632 0.00 0.00 38.65 2.44
7310 10325 1.134280 CCCTTCATCTTCAGCATCGGT 60.134 52.381 0.00 0.00 0.00 4.69
7474 10489 2.410466 GAGAGGATCGACGGCTTCT 58.590 57.895 0.00 0.00 42.67 2.85
7579 10594 4.069232 CCGGAGGCAGCGAAGTCA 62.069 66.667 0.00 0.00 46.14 3.41
7587 10602 2.847234 AGCGAAGTCACCCACCCA 60.847 61.111 0.00 0.00 0.00 4.51
7763 10789 8.888579 ACTGCACATTACAGTACTTATTATCC 57.111 34.615 0.00 0.00 46.32 2.59
7764 10790 8.705594 ACTGCACATTACAGTACTTATTATCCT 58.294 33.333 0.00 0.00 46.32 3.24
7765 10791 8.887036 TGCACATTACAGTACTTATTATCCTG 57.113 34.615 0.00 0.00 0.00 3.86
7839 10870 9.850628 CAAACATATGACAGATTGAACATTCTT 57.149 29.630 10.38 0.00 0.00 2.52
7854 10885 3.885297 ACATTCTTGTTCTTCTGGTGGTG 59.115 43.478 0.00 0.00 29.55 4.17
7855 10886 2.638480 TCTTGTTCTTCTGGTGGTGG 57.362 50.000 0.00 0.00 0.00 4.61
7868 10899 1.029681 GTGGTGGTCACTTGTTTCCC 58.970 55.000 0.93 0.00 42.86 3.97
7875 10906 2.099098 GGTCACTTGTTTCCCACTGTTG 59.901 50.000 0.00 0.00 0.00 3.33
7885 10916 1.203523 TCCCACTGTTGTTGTTGTTGC 59.796 47.619 0.00 0.00 0.00 4.17
7886 10917 1.639280 CCACTGTTGTTGTTGTTGCC 58.361 50.000 0.00 0.00 0.00 4.52
7889 10920 1.135517 ACTGTTGTTGTTGTTGCCGTC 60.136 47.619 0.00 0.00 0.00 4.79
7891 10922 1.226435 TTGTTGTTGTTGCCGTCGC 60.226 52.632 0.00 0.00 0.00 5.19
7896 10927 4.595538 TTGTTGCCGTCGCCGTCT 62.596 61.111 0.00 0.00 0.00 4.18
7898 10929 2.431260 GTTGCCGTCGCCGTCTTA 60.431 61.111 0.00 0.00 0.00 2.10
7900 10931 3.636313 TTGCCGTCGCCGTCTTAGG 62.636 63.158 0.00 0.00 0.00 2.69
7901 10932 3.818787 GCCGTCGCCGTCTTAGGA 61.819 66.667 0.00 0.00 0.00 2.94
7906 10944 1.787012 GTCGCCGTCTTAGGACAAAA 58.213 50.000 5.77 0.00 42.21 2.44
7916 10954 3.391296 TCTTAGGACAAAAGGTCTGCAGT 59.609 43.478 14.67 0.00 46.16 4.40
8129 11168 5.990120 TCTTCATCACATCTTCAGAGTCA 57.010 39.130 0.00 0.00 0.00 3.41
8137 11176 3.834813 ACATCTTCAGAGTCAGTGGCTTA 59.165 43.478 0.00 0.00 0.00 3.09
8138 11177 3.944055 TCTTCAGAGTCAGTGGCTTAC 57.056 47.619 0.00 0.00 0.00 2.34
8139 11178 3.501349 TCTTCAGAGTCAGTGGCTTACT 58.499 45.455 0.00 0.00 41.36 2.24
8265 11337 1.349026 ACACCCAGTCAGAAGTGATGG 59.651 52.381 0.00 0.00 34.36 3.51
8286 11358 3.585862 GAACATCTTAGTCGCACCTTCA 58.414 45.455 0.00 0.00 0.00 3.02
8306 11378 5.957771 TCAGAGTTGGTAGCTTTCCATAT 57.042 39.130 10.42 3.77 34.75 1.78
8308 11380 7.055667 TCAGAGTTGGTAGCTTTCCATATAG 57.944 40.000 10.42 2.72 34.75 1.31
8309 11381 6.611642 TCAGAGTTGGTAGCTTTCCATATAGT 59.388 38.462 10.42 0.88 34.75 2.12
8441 11516 6.263168 CCAACTTACTCAATCCACTTTCAACT 59.737 38.462 0.00 0.00 0.00 3.16
8539 11644 3.243068 GGTGAAAGTGATGCTCAACGTTT 60.243 43.478 0.00 0.00 0.00 3.60
8540 11645 4.024387 GGTGAAAGTGATGCTCAACGTTTA 60.024 41.667 0.00 0.00 0.00 2.01
8544 11649 4.732285 AGTGATGCTCAACGTTTAACAG 57.268 40.909 0.00 0.00 0.00 3.16
8571 11680 3.625764 GCTTACACCACTCAAAACACAGA 59.374 43.478 0.00 0.00 0.00 3.41
8581 11690 6.473455 CCACTCAAAACACAGAAGAAAACATC 59.527 38.462 0.00 0.00 0.00 3.06
8617 11728 8.886719 CATAAAGAATAGTGCAGTGATTCTTGA 58.113 33.333 24.26 20.78 45.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.338800 TCGATTACGATAGGAAGTTTTACCT 57.661 36.000 0.00 0.00 46.15 3.08
83 86 3.764972 GGGCTAGAGTATGGATCTACACC 59.235 52.174 0.00 0.00 0.00 4.16
84 87 3.764972 GGGGCTAGAGTATGGATCTACAC 59.235 52.174 0.00 0.00 0.00 2.90
85 88 3.663136 AGGGGCTAGAGTATGGATCTACA 59.337 47.826 0.00 0.00 0.00 2.74
128 132 9.770097 GAATAACATGTATCTTCAGATGGAGAA 57.230 33.333 0.00 0.00 36.05 2.87
180 184 5.510323 CGTTTTCTGTCTAACGCTTGTTTTT 59.490 36.000 0.00 0.00 40.33 1.94
190 194 0.165295 GCGGCCGTTTTCTGTCTAAC 59.835 55.000 28.70 0.08 0.00 2.34
211 215 6.902771 ATCTATCTCTCTAGCCGCTTAAAA 57.097 37.500 0.00 0.00 0.00 1.52
234 540 7.679881 TGCCTATCCATCTATCTTCCATCTTTA 59.320 37.037 0.00 0.00 0.00 1.85
236 542 6.028131 TGCCTATCCATCTATCTTCCATCTT 58.972 40.000 0.00 0.00 0.00 2.40
240 546 4.774726 GTCTGCCTATCCATCTATCTTCCA 59.225 45.833 0.00 0.00 0.00 3.53
242 548 4.774726 TGGTCTGCCTATCCATCTATCTTC 59.225 45.833 0.00 0.00 35.27 2.87
243 549 4.530161 GTGGTCTGCCTATCCATCTATCTT 59.470 45.833 0.00 0.00 33.68 2.40
252 558 0.462047 CCGTTGTGGTCTGCCTATCC 60.462 60.000 0.00 0.00 35.27 2.59
259 565 1.594293 AACTCGCCGTTGTGGTCTG 60.594 57.895 0.00 0.00 41.21 3.51
267 573 2.357034 ACGATGCAACTCGCCGTT 60.357 55.556 9.55 0.00 42.35 4.44
348 664 2.019951 GCGCTTCAGTTTCGACCGA 61.020 57.895 0.00 0.00 0.00 4.69
562 899 1.305886 GGGAGGGGTACTTTGGGAAT 58.694 55.000 0.00 0.00 0.00 3.01
571 908 1.233659 GAGAGAGGGGGAGGGGTAC 59.766 68.421 0.00 0.00 0.00 3.34
629 966 6.002911 CGCAACAAAAATAATTTGCTTCTCG 58.997 36.000 3.88 0.00 41.80 4.04
633 970 5.179182 CCCTCGCAACAAAAATAATTTGCTT 59.821 36.000 3.88 0.00 41.80 3.91
717 1055 1.852067 GATGTTGTCCGGTGGTGTGC 61.852 60.000 0.00 0.00 0.00 4.57
718 1056 0.533978 TGATGTTGTCCGGTGGTGTG 60.534 55.000 0.00 0.00 0.00 3.82
719 1057 0.181587 TTGATGTTGTCCGGTGGTGT 59.818 50.000 0.00 0.00 0.00 4.16
724 1062 1.305219 CGCCATTGATGTTGTCCGGT 61.305 55.000 0.00 0.00 0.00 5.28
727 1065 0.451783 GGACGCCATTGATGTTGTCC 59.548 55.000 12.96 12.96 40.52 4.02
728 1066 1.135689 GTGGACGCCATTGATGTTGTC 60.136 52.381 1.90 4.97 35.28 3.18
729 1067 0.881118 GTGGACGCCATTGATGTTGT 59.119 50.000 1.90 0.00 35.28 3.32
730 1068 0.171007 GGTGGACGCCATTGATGTTG 59.829 55.000 1.90 0.00 35.28 3.33
731 1069 0.038166 AGGTGGACGCCATTGATGTT 59.962 50.000 4.54 0.00 35.28 2.71
831 1181 0.035630 AGCTCATGACACAGGAAGCC 60.036 55.000 0.00 0.00 0.00 4.35
971 1334 2.607892 GCCACGAACTGGTCACTGC 61.608 63.158 0.00 0.00 42.99 4.40
1228 1605 2.045536 CAGGGAGCTTGTCCTGGC 60.046 66.667 18.42 0.00 46.06 4.85
1277 1654 4.157120 TCCTAAGGGAAGCGGCGC 62.157 66.667 26.86 26.86 38.93 6.53
1289 1666 3.515286 CCTCGACGCCGCTCCTAA 61.515 66.667 0.00 0.00 35.37 2.69
1325 1702 4.752879 TAAGAGCGGCACCGGCAC 62.753 66.667 11.65 0.00 43.71 5.01
1326 1703 4.010224 TTAAGAGCGGCACCGGCA 62.010 61.111 11.65 0.00 43.71 5.69
1327 1704 3.497031 GTTAAGAGCGGCACCGGC 61.497 66.667 11.65 3.34 40.19 6.13
1328 1705 3.186047 CGTTAAGAGCGGCACCGG 61.186 66.667 11.65 0.00 40.19 5.28
1329 1706 3.186047 CCGTTAAGAGCGGCACCG 61.186 66.667 4.30 4.30 42.82 4.94
1468 1845 0.706729 GACAAAGACGTACCTTCGCG 59.293 55.000 0.00 0.00 0.00 5.87
1555 1940 1.068055 CACATTGCTGAGCTTGGGAAC 60.068 52.381 5.83 0.00 0.00 3.62
1559 1944 1.741706 CTACCACATTGCTGAGCTTGG 59.258 52.381 5.83 9.49 0.00 3.61
1658 2051 9.231297 ACACAATAGACTATTATTTGTGCAGTT 57.769 29.630 19.59 4.92 32.03 3.16
1659 2052 8.792830 ACACAATAGACTATTATTTGTGCAGT 57.207 30.769 19.59 5.37 32.03 4.40
1673 2066 8.031277 CGTTAAACCTACCTAACACAATAGACT 58.969 37.037 0.00 0.00 0.00 3.24
1674 2067 7.276438 CCGTTAAACCTACCTAACACAATAGAC 59.724 40.741 0.00 0.00 0.00 2.59
1675 2068 7.178274 TCCGTTAAACCTACCTAACACAATAGA 59.822 37.037 0.00 0.00 0.00 1.98
1676 2069 7.276438 GTCCGTTAAACCTACCTAACACAATAG 59.724 40.741 0.00 0.00 0.00 1.73
1860 2255 3.391049 GGCGCCTTTTACTCCATACTAG 58.609 50.000 22.15 0.00 0.00 2.57
1952 2347 2.288395 CCAACAAGGAAACACAGATGGC 60.288 50.000 0.00 0.00 41.22 4.40
1978 2373 2.280628 CGAGCTGTAAGACAATTCCCC 58.719 52.381 0.00 0.00 34.07 4.81
2343 2742 0.390998 GAGTGCAGGAGGAAGACAGC 60.391 60.000 0.00 0.00 0.00 4.40
2345 2744 1.967535 CGAGTGCAGGAGGAAGACA 59.032 57.895 0.00 0.00 0.00 3.41
2448 2847 1.006102 CACCGACGACTTCTTGGCT 60.006 57.895 0.00 0.00 0.00 4.75
2601 3000 1.156736 CCAAACGATGAAGTTCGGCT 58.843 50.000 0.00 0.00 43.33 5.52
2632 3031 0.319555 CGCTTCGTCTCTTGGTCCAA 60.320 55.000 3.76 3.76 0.00 3.53
2702 3101 1.009389 CAGGTTGTCGTCGAAGGCTC 61.009 60.000 4.26 0.00 0.00 4.70
2768 3167 4.219115 GAGGATGGAGGATTGTCTAGTCA 58.781 47.826 0.00 0.00 0.00 3.41
2819 3218 2.557056 GAGTAAGGTTTCCCCAACTTGC 59.443 50.000 0.00 0.00 33.24 4.01
3101 3505 0.104304 ACCAGCGACAAACTTCGACT 59.896 50.000 0.00 0.00 41.78 4.18
3107 3511 1.670811 CTTGTTCACCAGCGACAAACT 59.329 47.619 0.00 0.00 33.37 2.66
3183 3587 1.028905 GGTAAGCAAACACACTGGCA 58.971 50.000 0.00 0.00 0.00 4.92
3233 3638 2.094597 TGAAATGGCAAGCCTTTGATCG 60.095 45.455 12.96 0.00 36.36 3.69
3234 3639 3.598019 TGAAATGGCAAGCCTTTGATC 57.402 42.857 12.96 8.25 36.36 2.92
3279 3684 6.477688 CACATCCAGATAAATGTTTGAATGGC 59.522 38.462 0.00 0.00 33.92 4.40
3416 3835 0.728466 GGTGTTCGACTCGTTCCTCG 60.728 60.000 0.00 0.00 41.41 4.63
3436 3855 1.924731 TATGGACTAGGATGGCCGAG 58.075 55.000 0.00 0.00 42.10 4.63
3451 3870 4.517952 TGCTGGAACAACAAACATATGG 57.482 40.909 7.80 0.00 38.70 2.74
3475 3894 3.192939 CAAGCACATTGGCCTCGTAAGA 61.193 50.000 3.32 0.00 38.72 2.10
3479 3898 0.823356 AACAAGCACATTGGCCTCGT 60.823 50.000 3.32 0.00 43.68 4.18
3532 3951 5.068636 AGAGAAATGACAAGTGTTCATGCT 58.931 37.500 0.00 0.00 0.00 3.79
3541 3960 7.492524 TCGCAAGATATAGAGAAATGACAAGT 58.507 34.615 0.00 0.00 45.01 3.16
3581 4000 2.005451 CCTCCAAAGAGATGCTTGACG 58.995 52.381 0.00 0.00 43.39 4.35
3587 4006 2.027192 TGTACCACCTCCAAAGAGATGC 60.027 50.000 0.00 0.00 43.39 3.91
3602 4021 0.533308 GGCACAAGAACCGTGTACCA 60.533 55.000 0.00 0.00 33.28 3.25
3603 4022 0.250166 AGGCACAAGAACCGTGTACC 60.250 55.000 0.00 0.00 36.71 3.34
3604 4023 1.589803 AAGGCACAAGAACCGTGTAC 58.410 50.000 0.00 0.00 36.71 2.90
3662 4084 1.136057 GCCCGAAGTCGTGTTTCATTC 60.136 52.381 0.00 0.00 37.74 2.67
3781 4203 1.268032 GCGTCATCATAAGGTTTGCCG 60.268 52.381 0.00 0.00 40.50 5.69
3921 4343 2.285977 GAATAAGGCATCGGAACCGTT 58.714 47.619 12.93 2.01 40.74 4.44
4038 4462 8.465999 ACTTGAGTGTTATTTGTCATGTCAAAA 58.534 29.630 19.46 7.29 40.05 2.44
4111 4535 1.537776 CCTCAGCCATAGAGCTCAACG 60.538 57.143 17.77 2.74 42.61 4.10
4114 4538 2.311463 GTACCTCAGCCATAGAGCTCA 58.689 52.381 17.77 2.09 42.61 4.26
4118 4542 3.701542 TGACTTGTACCTCAGCCATAGAG 59.298 47.826 0.00 0.00 0.00 2.43
4171 4595 1.529226 CAAGGTACACGGAAATGGCA 58.471 50.000 0.00 0.00 0.00 4.92
4358 4783 2.859032 GCGTCGGAACTAGGATTGCTAG 60.859 54.545 10.37 10.37 0.00 3.42
4360 4785 0.179108 GCGTCGGAACTAGGATTGCT 60.179 55.000 0.00 0.00 0.00 3.91
4463 4913 3.354948 TGACCAGCTATCATGTGCTTT 57.645 42.857 7.63 0.31 37.44 3.51
4489 4939 7.848051 GCGAAATCATGTAACAAGTTCAGATAG 59.152 37.037 0.00 0.00 0.00 2.08
4556 5013 5.176223 CCAAATTTGTGTGAGATTTGAGTGC 59.824 40.000 16.73 0.00 41.14 4.40
4737 5196 4.083537 CCAAACTTCGATTGTCAAATCCGA 60.084 41.667 0.00 0.00 39.29 4.55
4836 5298 2.300433 GAGCATATGGCCATCACAACA 58.700 47.619 24.80 3.19 46.50 3.33
4883 5352 2.435805 GGCATCAAGATCCTCTACCACA 59.564 50.000 0.00 0.00 0.00 4.17
5051 5786 3.558006 CACAGTTGTACAACGGAATGTCA 59.442 43.478 35.32 0.00 45.50 3.58
5113 5848 3.243201 GGATCAGGCACCAAAATCGAATC 60.243 47.826 0.00 0.00 0.00 2.52
5117 5905 1.462616 TGGATCAGGCACCAAAATCG 58.537 50.000 0.00 0.00 32.93 3.34
5196 6017 1.336440 CCGTGCAACAAACATCTCCAA 59.664 47.619 0.00 0.00 35.74 3.53
5250 6304 8.744568 TCACACCATAAAACATGCTTGATATA 57.255 30.769 6.60 0.00 0.00 0.86
5268 6322 1.301401 GCACGTAGGCTTCACACCA 60.301 57.895 0.00 0.00 0.00 4.17
5525 6580 0.969149 TGTGATGTCTCTTGCCGACT 59.031 50.000 0.00 0.00 32.70 4.18
5951 7025 7.332557 TCAACAAGTAACTTAGAGGAACAACA 58.667 34.615 0.00 0.00 0.00 3.33
6273 7384 6.837568 TCACTTAAACTAATACTCCCTCCGAT 59.162 38.462 0.00 0.00 0.00 4.18
6296 7407 1.207089 CCTCGAAGTAATGCACCCTCA 59.793 52.381 0.00 0.00 0.00 3.86
6467 7596 1.834263 CTCCAACCTCCCCTACAGAAG 59.166 57.143 0.00 0.00 0.00 2.85
6480 7609 1.909302 TCATCTGGGTTCTCTCCAACC 59.091 52.381 0.00 0.00 44.71 3.77
6657 7786 8.477256 AGCCTTTCAAAGCTTAATTATGCAATA 58.523 29.630 21.45 5.28 35.22 1.90
6658 7787 7.279313 CAGCCTTTCAAAGCTTAATTATGCAAT 59.721 33.333 21.45 9.96 37.18 3.56
6659 7788 6.591062 CAGCCTTTCAAAGCTTAATTATGCAA 59.409 34.615 21.45 7.63 37.18 4.08
6660 7789 6.101332 CAGCCTTTCAAAGCTTAATTATGCA 58.899 36.000 21.45 0.00 37.18 3.96
6661 7790 5.006068 GCAGCCTTTCAAAGCTTAATTATGC 59.994 40.000 13.95 13.95 37.18 3.14
6749 7883 2.876368 AAGGTACCATGCCTGCGAGC 62.876 60.000 15.94 0.00 36.30 5.03
6750 7884 0.811616 GAAGGTACCATGCCTGCGAG 60.812 60.000 15.94 0.00 36.30 5.03
6756 7890 2.092968 TGTCAGATGAAGGTACCATGCC 60.093 50.000 15.94 0.20 0.00 4.40
6766 7900 4.033358 GGAACGTAGCATTGTCAGATGAAG 59.967 45.833 0.00 0.00 0.00 3.02
6795 7929 0.973632 ACACACGGAGGTAAGCATGA 59.026 50.000 0.00 0.00 0.00 3.07
6852 7986 9.740710 GCCAAGTACCTTAAAATATATCCAGAT 57.259 33.333 0.00 0.00 0.00 2.90
6853 7987 8.945193 AGCCAAGTACCTTAAAATATATCCAGA 58.055 33.333 0.00 0.00 0.00 3.86
6854 7988 9.574516 AAGCCAAGTACCTTAAAATATATCCAG 57.425 33.333 0.00 0.00 0.00 3.86
6855 7989 9.930158 AAAGCCAAGTACCTTAAAATATATCCA 57.070 29.630 0.00 0.00 0.00 3.41
6857 7991 9.678941 GCAAAGCCAAGTACCTTAAAATATATC 57.321 33.333 0.00 0.00 0.00 1.63
6886 8020 1.168714 GCTTGGCTTGGTAGTTCAGG 58.831 55.000 0.00 0.00 0.00 3.86
7062 9984 6.261381 AGAACAGTCCGAATCTATCAGTAGTC 59.739 42.308 0.00 0.00 0.00 2.59
7108 10030 7.907214 AAGAACCAACTGCTACTAATTACTG 57.093 36.000 0.00 0.00 0.00 2.74
7139 10061 6.258947 GCAAATCTCATAGAAGGTAGGAACAC 59.741 42.308 0.00 0.00 0.00 3.32
7156 10171 4.456911 TGGTGATCAACAGAAGCAAATCTC 59.543 41.667 10.05 0.00 0.00 2.75
7180 10195 7.707464 TGTAAGATTACACACCAACATATACCG 59.293 37.037 1.30 0.00 38.64 4.02
7272 10287 3.649986 GTTGTCACGGCGCTGCTT 61.650 61.111 18.15 0.00 0.00 3.91
7310 10325 4.025858 GGGCTGCTGCTCTCACCA 62.026 66.667 15.64 0.00 36.57 4.17
7474 10489 2.248248 AGCTCTGCTGTACTGGTACAA 58.752 47.619 13.50 1.18 44.47 2.41
7570 10585 1.779061 ATTGGGTGGGTGACTTCGCT 61.779 55.000 0.00 0.00 0.00 4.93
7579 10594 1.803453 ATGTGCCTCATTGGGTGGGT 61.803 55.000 0.00 0.00 36.00 4.51
7587 10602 0.246360 TGACGACGATGTGCCTCATT 59.754 50.000 0.00 0.00 36.83 2.57
7761 10787 3.496692 CCACCATGTCTTCAGTTTCAGGA 60.497 47.826 0.00 0.00 0.00 3.86
7762 10788 2.816087 CCACCATGTCTTCAGTTTCAGG 59.184 50.000 0.00 0.00 0.00 3.86
7763 10789 2.816087 CCCACCATGTCTTCAGTTTCAG 59.184 50.000 0.00 0.00 0.00 3.02
7764 10790 2.441375 TCCCACCATGTCTTCAGTTTCA 59.559 45.455 0.00 0.00 0.00 2.69
7765 10791 3.077359 CTCCCACCATGTCTTCAGTTTC 58.923 50.000 0.00 0.00 0.00 2.78
7839 10870 1.134220 GTGACCACCACCAGAAGAACA 60.134 52.381 0.00 0.00 39.86 3.18
7843 10874 1.134098 ACAAGTGACCACCACCAGAAG 60.134 52.381 0.00 0.00 46.87 2.85
7854 10885 2.052782 ACAGTGGGAAACAAGTGACC 57.947 50.000 0.00 0.00 0.00 4.02
7855 10886 2.752903 ACAACAGTGGGAAACAAGTGAC 59.247 45.455 0.00 0.00 0.00 3.67
7868 10899 1.267365 CGGCAACAACAACAACAGTG 58.733 50.000 0.00 0.00 0.00 3.66
7875 10906 2.353030 GGCGACGGCAACAACAAC 60.353 61.111 17.49 0.00 42.47 3.32
7889 10920 1.076332 CCTTTTGTCCTAAGACGGCG 58.924 55.000 4.80 4.80 46.74 6.46
7891 10922 3.326747 CAGACCTTTTGTCCTAAGACGG 58.673 50.000 0.00 0.00 46.74 4.79
7896 10927 3.135712 TGACTGCAGACCTTTTGTCCTAA 59.864 43.478 23.35 0.00 45.68 2.69
7898 10929 1.490490 TGACTGCAGACCTTTTGTCCT 59.510 47.619 23.35 0.00 45.68 3.85
7900 10931 2.227388 CCATGACTGCAGACCTTTTGTC 59.773 50.000 23.35 6.09 44.82 3.18
7901 10932 2.233271 CCATGACTGCAGACCTTTTGT 58.767 47.619 23.35 0.00 0.00 2.83
7906 10944 1.002888 CAAGACCATGACTGCAGACCT 59.997 52.381 23.35 4.08 0.00 3.85
7916 10954 5.891551 TGCTACTGTATCTACAAGACCATGA 59.108 40.000 0.00 0.00 35.50 3.07
8129 11168 7.396623 ACAAAGTACTCTATACAGTAAGCCACT 59.603 37.037 0.00 0.00 38.32 4.00
8137 11176 7.147880 CCAGGCTAACAAAGTACTCTATACAGT 60.148 40.741 0.00 0.00 0.00 3.55
8138 11177 7.147880 ACCAGGCTAACAAAGTACTCTATACAG 60.148 40.741 0.00 0.00 0.00 2.74
8139 11178 6.666546 ACCAGGCTAACAAAGTACTCTATACA 59.333 38.462 0.00 0.00 0.00 2.29
8140 11179 7.110043 ACCAGGCTAACAAAGTACTCTATAC 57.890 40.000 0.00 0.00 0.00 1.47
8141 11180 6.893554 TGACCAGGCTAACAAAGTACTCTATA 59.106 38.462 0.00 0.00 0.00 1.31
8265 11337 3.585862 TGAAGGTGCGACTAAGATGTTC 58.414 45.455 0.00 0.00 0.00 3.18
8286 11358 7.785506 ACTACTATATGGAAAGCTACCAACTCT 59.214 37.037 14.98 3.52 40.93 3.24
8306 11378 9.170734 CTGTACCAGACTAACAATGTACTACTA 57.829 37.037 0.00 0.00 32.44 1.82
8308 11380 8.048534 TCTGTACCAGACTAACAATGTACTAC 57.951 38.462 0.00 0.00 35.39 2.73
8309 11381 8.818622 ATCTGTACCAGACTAACAATGTACTA 57.181 34.615 0.00 0.00 43.63 1.82
8330 11402 4.070716 ACTGAACAAGCCTTGAAGATCTG 58.929 43.478 12.25 9.70 0.00 2.90
8332 11404 5.934625 TCTAACTGAACAAGCCTTGAAGATC 59.065 40.000 12.25 4.64 0.00 2.75
8402 11476 1.903404 GTTGGTTGCTGGGAGGTGG 60.903 63.158 0.00 0.00 0.00 4.61
8403 11477 0.468029 AAGTTGGTTGCTGGGAGGTG 60.468 55.000 0.00 0.00 0.00 4.00
8571 11680 0.774908 TGTCCCGGGGATGTTTTCTT 59.225 50.000 23.50 0.00 32.73 2.52
8581 11690 2.729028 ATTCTTTATGTGTCCCGGGG 57.271 50.000 23.50 6.77 0.00 5.73


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

AutoCloner maintained by Alex Coulton.