Multiple sequence alignment - TraesCS2A01G304900

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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 TraesCS2A01G304900 chr2A 100.000 9869 0 0 1 9869 524337996 524328128 0.000000e+00 18225
1 TraesCS2A01G304900 chr2D 95.917 6466 206 24 1 6433 387744494 387738054 0.000000e+00 10425
2 TraesCS2A01G304900 chr2D 96.696 2603 63 9 6447 9044 387737780 387735196 0.000000e+00 4309
3 TraesCS2A01G304900 chr2D 95.710 746 21 6 9124 9869 387735030 387734296 0.000000e+00 1190
4 TraesCS2A01G304900 chr2D 97.436 78 2 0 9046 9123 387735078 387735001 6.220000e-27 134
5 TraesCS2A01G304900 chr2D 88.889 90 10 0 4504 4593 306487754 306487665 2.910000e-20 111
6 TraesCS2A01G304900 chr2B 95.887 5398 165 24 1 5368 458858507 458853137 0.000000e+00 8685
7 TraesCS2A01G304900 chr2B 92.071 2018 80 42 7886 9869 458850593 458848622 0.000000e+00 2767
8 TraesCS2A01G304900 chr2B 96.813 1255 34 3 6447 7696 458851847 458850594 0.000000e+00 2091
9 TraesCS2A01G304900 chr2B 95.885 972 35 3 5465 6434 458853098 458852130 0.000000e+00 1568
10 TraesCS2A01G304900 chr1D 93.023 86 6 0 4508 4593 279101461 279101376 1.040000e-24 126
11 TraesCS2A01G304900 chr6D 92.045 88 7 0 4506 4593 90111904 90111817 3.740000e-24 124
12 TraesCS2A01G304900 chr5D 91.860 86 7 0 4508 4593 442203812 442203727 4.840000e-23 121
13 TraesCS2A01G304900 chr7D 90.698 86 8 0 4509 4594 234807771 234807856 2.250000e-21 115
14 TraesCS2A01G304900 chr3A 90.000 90 8 1 4505 4594 114570395 114570307 2.250000e-21 115
15 TraesCS2A01G304900 chr7B 88.764 89 4 4 4506 4593 450642113 450642196 4.880000e-18 104


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 TraesCS2A01G304900 chr2A 524328128 524337996 9868 True 18225.00 18225 100.00000 1 9869 1 chr2A.!!$R1 9868
1 TraesCS2A01G304900 chr2D 387734296 387744494 10198 True 4014.50 10425 96.43975 1 9869 4 chr2D.!!$R2 9868
2 TraesCS2A01G304900 chr2B 458848622 458858507 9885 True 3777.75 8685 95.16400 1 9869 4 chr2B.!!$R1 9868

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
307 310 0.172803 GGCTGACTGTACGGTTCGAT 59.827 55.000 9.15 0.00 0.00 3.59 F
547 550 0.530744 TAGAACCGCTGCGATTGACT 59.469 50.000 25.45 9.69 0.00 3.41 F
1422 1443 0.033504 TCACTTCGACCTGGCTTGTC 59.966 55.000 0.00 0.00 0.00 3.18 F
1423 1444 0.034059 CACTTCGACCTGGCTTGTCT 59.966 55.000 0.00 0.00 0.00 3.41 F
1424 1445 0.759346 ACTTCGACCTGGCTTGTCTT 59.241 50.000 0.00 0.00 0.00 3.01 F
1425 1446 1.141053 ACTTCGACCTGGCTTGTCTTT 59.859 47.619 0.00 0.00 0.00 2.52 F
2009 2030 1.574428 CAAGCACCTGTACAACGGC 59.426 57.895 0.00 0.37 0.00 5.68 F
3375 3396 4.588528 TGCTTCTACAAATTTCTGCCCTTT 59.411 37.500 0.00 0.00 0.00 3.11 F
4739 4769 0.401738 TTGTGCAAGCTCTAGGCCTT 59.598 50.000 12.58 0.00 43.05 4.35 F
5366 5397 0.038343 GGTGTGCGCCATCAACAATT 60.038 50.000 4.18 0.00 0.00 2.32 F
5368 5399 0.243365 TGTGCGCCATCAACAATTCC 59.757 50.000 4.18 0.00 0.00 3.01 F
6331 6366 0.247736 GCTCTTCGTCCTCACATGGT 59.752 55.000 0.00 0.00 0.00 3.55 F
6434 6469 1.280710 TGGAAGCCGTCATAACCATGT 59.719 47.619 0.00 0.00 33.57 3.21 F
6807 7112 1.533625 TGCCATTCTGCTAAACGCTT 58.466 45.000 0.00 0.00 40.11 4.68 F
6868 7177 1.682854 ACCGGTGTCAACTTTCTACGA 59.317 47.619 6.12 0.00 0.00 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1164 0.038343 CCGGATTTGCCCTTTGTGTG 60.038 55.000 0.00 0.0 0.00 3.82 R
1920 1941 0.251634 GCAGACTTTCCTGAGAGGGG 59.748 60.000 0.00 0.0 35.59 4.79 R
2946 2967 3.246880 AACCACCGTCCCAGGGTC 61.247 66.667 5.01 0.0 33.44 4.46 R
3584 3605 1.755179 AATTCCCTGCAAGACCATCG 58.245 50.000 0.00 0.0 34.07 3.84 R
3585 3606 5.047377 TGTTTTAATTCCCTGCAAGACCATC 60.047 40.000 0.00 0.0 34.07 3.51 R
3640 3665 7.707624 TGAGGAAATAAAATCTTGCAGATGT 57.292 32.000 0.00 0.0 34.65 3.06 R
3829 3854 2.222027 CAGGAGGTGAGTGGTCAAAAC 58.778 52.381 0.00 0.0 33.27 2.43 R
5350 5381 0.527565 AGGAATTGTTGATGGCGCAC 59.472 50.000 10.83 0.0 0.00 5.34 R
6719 7024 0.166814 GAACATGACTGCCTTGTCGC 59.833 55.000 0.00 0.0 39.64 5.19 R
7060 7369 2.579873 TCCTCGGTAAGTATTCCCTCG 58.420 52.381 0.00 0.0 0.00 4.63 R
7211 7520 7.884354 AGGAAGGAAAACGTATGTATAAAACCA 59.116 33.333 0.00 0.0 0.00 3.67 R
7752 8062 5.233988 AGTGCATTCAACTAAGTCTCAGTC 58.766 41.667 0.00 0.0 0.00 3.51 R
8417 8727 5.710567 ACCCTGAAAGAAAGTATGTAAAGCC 59.289 40.000 0.00 0.0 34.07 4.35 R
8779 9089 0.404426 AAAACCCTACCAGAGGCCAC 59.596 55.000 5.01 0.0 45.17 5.01 R
9044 9355 0.741915 CTCTCGGCAGGTAGTTCTCC 59.258 60.000 0.00 0.0 0.00 3.71 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
162 163 3.382832 CCAGTCGCCTCCCGTCTT 61.383 66.667 0.00 0.00 38.35 3.01
171 172 1.402852 GCCTCCCGTCTTTGCAATTTC 60.403 52.381 0.00 0.00 0.00 2.17
172 173 2.162681 CCTCCCGTCTTTGCAATTTCT 58.837 47.619 0.00 0.00 0.00 2.52
307 310 0.172803 GGCTGACTGTACGGTTCGAT 59.827 55.000 9.15 0.00 0.00 3.59
389 392 1.268845 CCAAAACGTAACCCTGTGTGC 60.269 52.381 0.00 0.00 0.00 4.57
396 399 0.978151 TAACCCTGTGTGCGTATGGT 59.022 50.000 0.00 0.00 0.00 3.55
399 402 2.390696 ACCCTGTGTGCGTATGGTATA 58.609 47.619 0.00 0.00 0.00 1.47
429 432 5.048573 GGCCAAAAATGCATTGATTTTCAGT 60.049 36.000 13.82 0.00 35.01 3.41
430 433 5.854338 GCCAAAAATGCATTGATTTTCAGTG 59.146 36.000 13.82 0.09 37.20 3.66
440 443 7.604714 CATTGATTTTCAGTGCTATCGATTG 57.395 36.000 1.71 2.00 27.55 2.67
460 463 6.568271 CGATTGTTTGAACAGAATCATGTCCA 60.568 38.462 8.46 0.00 40.50 4.02
463 466 5.008911 TGTTTGAACAGAATCATGTCCACAG 59.991 40.000 0.00 0.00 34.30 3.66
465 468 3.327464 TGAACAGAATCATGTCCACAGGA 59.673 43.478 0.00 0.00 41.13 3.86
511 514 4.485024 TCTCATACTCTATTTCGTCGCC 57.515 45.455 0.00 0.00 0.00 5.54
512 515 3.252701 TCTCATACTCTATTTCGTCGCCC 59.747 47.826 0.00 0.00 0.00 6.13
543 546 0.727398 GCTTTAGAACCGCTGCGATT 59.273 50.000 25.45 14.07 0.00 3.34
547 550 0.530744 TAGAACCGCTGCGATTGACT 59.469 50.000 25.45 9.69 0.00 3.41
567 570 6.017192 TGACTGGATAACTGGACTTAGTCTT 58.983 40.000 12.41 1.67 35.54 3.01
568 571 6.071334 TGACTGGATAACTGGACTTAGTCTTG 60.071 42.308 12.41 7.79 35.54 3.02
576 579 4.162509 ACTGGACTTAGTCTTGCCTTATCC 59.837 45.833 12.41 0.00 32.47 2.59
585 588 4.583073 AGTCTTGCCTTATCCGTTTGTTTT 59.417 37.500 0.00 0.00 0.00 2.43
589 592 2.858839 CCTTATCCGTTTGTTTTCGCC 58.141 47.619 0.00 0.00 0.00 5.54
595 598 1.515221 CCGTTTGTTTTCGCCTTTTCG 59.485 47.619 0.00 0.00 0.00 3.46
649 652 9.892130 CCCTAATATGGATAACATCTTTAGGTC 57.108 37.037 18.09 0.00 44.46 3.85
695 698 9.371136 TCAGTTATTTATAGCTTGTCTTCAGTG 57.629 33.333 0.00 0.00 0.00 3.66
700 703 8.854614 ATTTATAGCTTGTCTTCAGTGAAGTT 57.145 30.769 27.83 7.90 40.24 2.66
725 728 4.897670 TGAGCTTCTGATATGATCTCACCA 59.102 41.667 0.00 0.00 0.00 4.17
727 730 6.040209 AGCTTCTGATATGATCTCACCATC 57.960 41.667 0.00 0.00 0.00 3.51
739 742 2.093500 TCTCACCATCGCAGTTGCTAAT 60.093 45.455 2.29 0.00 39.32 1.73
741 744 1.739466 CACCATCGCAGTTGCTAATGT 59.261 47.619 2.29 0.00 39.32 2.71
749 752 2.291741 GCAGTTGCTAATGTAGGCATCC 59.708 50.000 0.00 0.00 38.30 3.51
764 767 6.780522 TGTAGGCATCCTTAGTGATGTATACA 59.219 38.462 8.27 8.27 43.28 2.29
765 768 6.352016 AGGCATCCTTAGTGATGTATACAG 57.648 41.667 11.91 0.00 43.28 2.74
767 770 5.482908 GCATCCTTAGTGATGTATACAGGG 58.517 45.833 11.91 5.04 43.28 4.45
768 771 5.482908 CATCCTTAGTGATGTATACAGGGC 58.517 45.833 11.91 4.20 37.85 5.19
785 788 1.483415 GGGCTCACCATCATTTGCATT 59.517 47.619 0.00 0.00 39.85 3.56
808 826 9.443283 CATTCTTGTTTCTTACTCTGTTTCTTG 57.557 33.333 0.00 0.00 0.00 3.02
865 886 7.092079 TCTATCACACAATTTGAGGCATTTTG 58.908 34.615 2.79 0.00 0.00 2.44
925 946 5.106673 GCTATTTACACACCTCAGTTTGGTC 60.107 44.000 0.00 0.00 35.28 4.02
932 953 1.202818 ACCTCAGTTTGGTCTTGGCTC 60.203 52.381 0.00 0.00 31.03 4.70
1050 1071 1.154093 CAGCTGCAATGACAAGCCG 60.154 57.895 0.00 0.00 0.00 5.52
1116 1137 6.620877 TCCCTTAGCAAAGATGACTTTCTA 57.379 37.500 0.00 0.00 43.41 2.10
1143 1164 5.063880 TCAAGCTTTCTGTTCTCTTTACCC 58.936 41.667 0.00 0.00 0.00 3.69
1161 1182 0.038343 CCACACAAAGGGCAAATCCG 60.038 55.000 0.00 0.00 34.94 4.18
1249 1270 2.953648 TCGTAGAGACAGTTGTTCACCA 59.046 45.455 0.00 0.00 0.00 4.17
1419 1440 3.842869 GATCACTTCGACCTGGCTT 57.157 52.632 0.00 0.00 0.00 4.35
1420 1441 1.363744 GATCACTTCGACCTGGCTTG 58.636 55.000 0.00 0.00 0.00 4.01
1422 1443 0.033504 TCACTTCGACCTGGCTTGTC 59.966 55.000 0.00 0.00 0.00 3.18
1423 1444 0.034059 CACTTCGACCTGGCTTGTCT 59.966 55.000 0.00 0.00 0.00 3.41
1424 1445 0.759346 ACTTCGACCTGGCTTGTCTT 59.241 50.000 0.00 0.00 0.00 3.01
1425 1446 1.141053 ACTTCGACCTGGCTTGTCTTT 59.859 47.619 0.00 0.00 0.00 2.52
1426 1447 2.222027 CTTCGACCTGGCTTGTCTTTT 58.778 47.619 0.00 0.00 0.00 2.27
1427 1448 3.181458 ACTTCGACCTGGCTTGTCTTTTA 60.181 43.478 0.00 0.00 0.00 1.52
1428 1449 2.762745 TCGACCTGGCTTGTCTTTTAC 58.237 47.619 0.00 0.00 0.00 2.01
1429 1450 2.367567 TCGACCTGGCTTGTCTTTTACT 59.632 45.455 0.00 0.00 0.00 2.24
1430 1451 3.139077 CGACCTGGCTTGTCTTTTACTT 58.861 45.455 0.00 0.00 0.00 2.24
1431 1452 3.186613 CGACCTGGCTTGTCTTTTACTTC 59.813 47.826 0.00 0.00 0.00 3.01
1432 1453 3.487372 ACCTGGCTTGTCTTTTACTTCC 58.513 45.455 0.00 0.00 0.00 3.46
1433 1454 3.117663 ACCTGGCTTGTCTTTTACTTCCA 60.118 43.478 0.00 0.00 0.00 3.53
1437 1458 3.367395 GGCTTGTCTTTTACTTCCATGCC 60.367 47.826 0.00 0.00 38.59 4.40
1870 1891 7.922811 GGGATTTTTCTCCTATTTATGCAACAG 59.077 37.037 0.00 0.00 35.50 3.16
1920 1941 6.183360 TGGATAATGTGCCGAAAAGTACAATC 60.183 38.462 0.00 0.00 0.00 2.67
2009 2030 1.574428 CAAGCACCTGTACAACGGC 59.426 57.895 0.00 0.37 0.00 5.68
2482 2503 5.886992 TGAATCATCATTCATGCTGTTCAC 58.113 37.500 0.00 0.00 42.99 3.18
3375 3396 4.588528 TGCTTCTACAAATTTCTGCCCTTT 59.411 37.500 0.00 0.00 0.00 3.11
3584 3605 8.929746 TGATCAGATGAGCGTTATGAATTAATC 58.070 33.333 0.00 0.00 32.18 1.75
3585 3606 7.338440 TCAGATGAGCGTTATGAATTAATCG 57.662 36.000 0.00 0.00 0.00 3.34
3682 3707 5.376625 TCCTCAAATTAGCACTGAACACTT 58.623 37.500 0.00 0.00 0.00 3.16
3704 3729 5.484173 TGTCTATTAATTTGCAGCTTCCG 57.516 39.130 0.00 0.00 0.00 4.30
3791 3816 8.021396 CAGATCATGCATTTATCACAGGTAATG 58.979 37.037 17.13 0.00 0.00 1.90
4007 4032 8.581253 AAAAATAGCTAAGTAAGTGGAATGCT 57.419 30.769 0.00 0.00 0.00 3.79
4051 4076 9.668497 GGTCTGAAGTAGTTATATTTGGACTTT 57.332 33.333 0.00 0.00 0.00 2.66
4066 4091 2.355132 GGACTTTGCTGCATCATCTCTG 59.645 50.000 1.84 0.00 0.00 3.35
4187 4212 7.885399 AGATCAAAATTAGCTGTTACAGTTCCT 59.115 33.333 14.23 5.32 33.43 3.36
4363 4393 1.137872 GGGTACAGGAGTGATGCTCTG 59.862 57.143 0.00 0.00 43.62 3.35
4485 4515 7.125792 CTGATTACCAGGTACTTTCTACCAT 57.874 40.000 0.00 0.00 39.99 3.55
4582 4612 9.354544 GTCGAAAAGCGTCTTATATTTTGATAC 57.645 33.333 0.00 0.00 41.80 2.24
4606 4636 5.395768 CGGAGGGAGTAAGAGACAATCATTT 60.396 44.000 0.00 0.00 0.00 2.32
4739 4769 0.401738 TTGTGCAAGCTCTAGGCCTT 59.598 50.000 12.58 0.00 43.05 4.35
4790 4820 5.943349 TTAATCGTCCCAATCTGAGGTAA 57.057 39.130 0.00 0.00 0.00 2.85
4805 4835 9.647918 AATCTGAGGTAAGTCTGTCAGAATATA 57.352 33.333 3.51 0.00 46.39 0.86
4987 5017 4.158025 TGTGAAAAAGTGGCCGAAAAACTA 59.842 37.500 0.00 0.00 0.00 2.24
5045 5075 2.283145 AGCATGCTGTGTTCTCCTTT 57.717 45.000 21.98 0.00 0.00 3.11
5103 5133 9.232473 GTCCTTACCAATCTTTTCAGTATTCTT 57.768 33.333 0.00 0.00 0.00 2.52
5254 5285 2.107204 ACATGTCAGTGAAAAGGGCTCT 59.893 45.455 0.00 0.00 0.00 4.09
5261 5292 5.938125 GTCAGTGAAAAGGGCTCTATGTTTA 59.062 40.000 0.00 0.00 0.00 2.01
5301 5332 4.953579 GCCCCATATTTGTAAAAGGAGTCA 59.046 41.667 0.00 0.00 0.00 3.41
5322 5353 2.876550 ACACTTTGGTTTTAGTCTCCGC 59.123 45.455 0.00 0.00 0.00 5.54
5350 5381 8.353684 TGGTAAAATTAGTTACACATGTTGGTG 58.646 33.333 0.00 0.00 44.35 4.17
5366 5397 0.038343 GGTGTGCGCCATCAACAATT 60.038 50.000 4.18 0.00 0.00 2.32
5368 5399 0.243365 TGTGCGCCATCAACAATTCC 59.757 50.000 4.18 0.00 0.00 3.01
5376 5407 4.016444 GCCATCAACAATTCCTACCTGAA 58.984 43.478 0.00 0.00 0.00 3.02
5426 5457 7.951347 AGATGCACCAAATCTTAGAAATCTT 57.049 32.000 0.00 0.00 29.94 2.40
5449 5480 8.282592 TCTTGTGAGATGTTTCGAAAGTTAATG 58.717 33.333 11.66 0.00 0.00 1.90
5491 5524 4.072131 TGGTCTCTTAACTCAAACATGCC 58.928 43.478 0.00 0.00 0.00 4.40
5492 5525 4.072131 GGTCTCTTAACTCAAACATGCCA 58.928 43.478 0.00 0.00 0.00 4.92
5500 5533 4.148128 ACTCAAACATGCCAGATAGAGG 57.852 45.455 0.00 0.00 0.00 3.69
5516 5549 1.705186 AGAGGGTTTGGTAGTGCACAT 59.295 47.619 21.04 6.83 0.00 3.21
5560 5593 8.759641 CAGATTTACATGTAGCAGTCTCATTAC 58.240 37.037 5.56 0.00 0.00 1.89
5609 5642 5.431765 ACCTGATGGTTTTAGAGTGCATAG 58.568 41.667 0.00 0.00 46.05 2.23
5726 5759 3.307674 TGCAAATTTGAAGTGCTTAGCG 58.692 40.909 22.31 0.00 39.09 4.26
5952 5985 7.862372 TCTTCAAATGAATTATTTATCTGCGCC 59.138 33.333 4.18 0.00 36.87 6.53
6095 6128 6.071784 TGCATGATTTAAGCTGTTTCATGACT 60.072 34.615 23.02 0.00 43.99 3.41
6247 6282 8.268738 GTCATCACAAACAAGTAATTTTCTTGC 58.731 33.333 13.72 0.00 43.97 4.01
6331 6366 0.247736 GCTCTTCGTCCTCACATGGT 59.752 55.000 0.00 0.00 0.00 3.55
6381 6416 9.494271 GAATCTCTTGTGCATGGTATAGATAAA 57.506 33.333 0.00 0.00 0.00 1.40
6422 6457 1.439679 GAGGTGTAGTTTGGAAGCCG 58.560 55.000 0.00 0.00 0.00 5.52
6434 6469 1.280710 TGGAAGCCGTCATAACCATGT 59.719 47.619 0.00 0.00 33.57 3.21
6435 6470 2.502130 TGGAAGCCGTCATAACCATGTA 59.498 45.455 0.00 0.00 33.57 2.29
6436 6471 3.135712 TGGAAGCCGTCATAACCATGTAT 59.864 43.478 0.00 0.00 33.57 2.29
6437 6472 4.134563 GGAAGCCGTCATAACCATGTATT 58.865 43.478 0.00 0.00 33.57 1.89
6438 6473 4.578928 GGAAGCCGTCATAACCATGTATTT 59.421 41.667 0.00 0.00 33.57 1.40
6439 6474 5.067283 GGAAGCCGTCATAACCATGTATTTT 59.933 40.000 0.00 0.00 33.57 1.82
6440 6475 5.751243 AGCCGTCATAACCATGTATTTTC 57.249 39.130 0.00 0.00 33.57 2.29
6441 6476 4.578928 AGCCGTCATAACCATGTATTTTCC 59.421 41.667 0.00 0.00 33.57 3.13
6442 6477 4.261447 GCCGTCATAACCATGTATTTTCCC 60.261 45.833 0.00 0.00 33.57 3.97
6443 6478 4.277423 CCGTCATAACCATGTATTTTCCCC 59.723 45.833 0.00 0.00 33.57 4.81
6444 6479 4.277423 CGTCATAACCATGTATTTTCCCCC 59.723 45.833 0.00 0.00 33.57 5.40
6445 6480 5.454966 GTCATAACCATGTATTTTCCCCCT 58.545 41.667 0.00 0.00 33.57 4.79
6493 6798 2.226200 TGATGTGGATTGCAGACGTTTG 59.774 45.455 0.86 0.86 0.00 2.93
6627 6932 2.092375 AGCAATTGGTAGGTCCCTAAGC 60.092 50.000 8.73 0.00 34.77 3.09
6636 6941 6.946323 TGGTAGGTCCCTAAGCAGATAGCTA 61.946 48.000 0.00 0.00 44.50 3.32
6719 7024 2.859165 TTAGGTTGAGCTGGTCTTGG 57.141 50.000 8.47 0.00 0.00 3.61
6807 7112 1.533625 TGCCATTCTGCTAAACGCTT 58.466 45.000 0.00 0.00 40.11 4.68
6851 7156 7.534085 TCATTAATTCTGTTACTTGCTACCG 57.466 36.000 0.00 0.00 0.00 4.02
6867 7176 2.144482 ACCGGTGTCAACTTTCTACG 57.856 50.000 6.12 0.00 0.00 3.51
6868 7177 1.682854 ACCGGTGTCAACTTTCTACGA 59.317 47.619 6.12 0.00 0.00 3.43
6890 7199 4.508551 TCTGGATATTGTGCATCTTGGT 57.491 40.909 0.00 0.00 0.00 3.67
6955 7264 8.604890 GCCTAGATTGTAAATCTTGTCAACTAC 58.395 37.037 7.74 0.00 0.00 2.73
7060 7369 2.361438 AGTACTGCGGCATCTAGTAACC 59.639 50.000 1.75 0.00 0.00 2.85
7098 7407 6.051717 CCGAGGATGTCAAAAAGAGTGATAT 58.948 40.000 0.00 0.00 30.40 1.63
7211 7520 2.887152 CAACCTTCTTGTAGCTGCCTTT 59.113 45.455 0.00 0.00 0.00 3.11
7236 7546 8.042944 TGGTTTTATACATACGTTTTCCTTCC 57.957 34.615 0.00 0.00 0.00 3.46
7237 7547 7.884354 TGGTTTTATACATACGTTTTCCTTCCT 59.116 33.333 0.00 0.00 0.00 3.36
7466 7776 4.858935 TGAGTTCGCCAAAAATCTTTCTG 58.141 39.130 0.00 0.00 0.00 3.02
7640 7950 6.952935 AATTGAGACTTCGTTGAGTATGAC 57.047 37.500 0.00 0.00 0.00 3.06
7777 8087 5.698545 ACTGAGACTTAGTTGAATGCACTTC 59.301 40.000 0.00 0.00 0.00 3.01
7826 8136 9.386122 AGTTAAATCAGGATATCACATACTCCT 57.614 33.333 4.83 0.00 38.68 3.69
7829 8139 8.964533 AAATCAGGATATCACATACTCCTACT 57.035 34.615 4.83 0.00 35.95 2.57
8030 8340 8.692710 TGAGGTAGTTGGTCATTAGTTATAGTG 58.307 37.037 0.00 0.00 0.00 2.74
8045 8355 6.109359 AGTTATAGTGAATCCTCTTGTGTGC 58.891 40.000 0.00 0.00 0.00 4.57
8055 8365 8.149647 TGAATCCTCTTGTGTGCATTTATTTTT 58.850 29.630 0.00 0.00 0.00 1.94
8405 8715 3.149196 CAGCTCTGGGAACTAAAGCAAA 58.851 45.455 0.00 0.00 35.42 3.68
8414 8724 5.538433 TGGGAACTAAAGCAAAGCATTACTT 59.462 36.000 0.00 0.00 41.70 2.24
8417 8727 6.741358 GGAACTAAAGCAAAGCATTACTTACG 59.259 38.462 0.00 0.00 37.75 3.18
8419 8729 3.487563 AAGCAAAGCATTACTTACGGC 57.512 42.857 0.00 0.00 37.75 5.68
8779 9089 3.730761 GCAGCGTCCAACAGCCTG 61.731 66.667 0.00 0.00 0.00 4.85
8811 9121 1.362355 GGTTTTGCCCAAGTGGACG 59.638 57.895 0.00 0.00 37.39 4.79
8814 9124 2.920076 TTTTGCCCAAGTGGACGGCT 62.920 55.000 0.00 0.00 43.42 5.52
9015 9326 5.932619 ATGTACCACACTGCAGTAATAGA 57.067 39.130 21.20 8.43 0.00 1.98
9016 9327 5.068234 TGTACCACACTGCAGTAATAGAC 57.932 43.478 21.20 15.15 0.00 2.59
9017 9328 4.770531 TGTACCACACTGCAGTAATAGACT 59.229 41.667 21.20 1.03 39.82 3.24
9121 9548 1.298340 CCGGGTGTGGATTGTAGCA 59.702 57.895 0.00 0.00 0.00 3.49
9122 9549 0.744414 CCGGGTGTGGATTGTAGCAG 60.744 60.000 0.00 0.00 0.00 4.24
9123 9550 1.369091 CGGGTGTGGATTGTAGCAGC 61.369 60.000 0.00 0.00 0.00 5.25
9124 9551 0.035056 GGGTGTGGATTGTAGCAGCT 60.035 55.000 0.00 0.00 0.00 4.24
9125 9552 1.614317 GGGTGTGGATTGTAGCAGCTT 60.614 52.381 0.00 0.00 0.00 3.74
9126 9553 1.470098 GGTGTGGATTGTAGCAGCTTG 59.530 52.381 0.00 0.00 0.00 4.01
9127 9554 1.470098 GTGTGGATTGTAGCAGCTTGG 59.530 52.381 0.00 0.00 0.00 3.61
9128 9555 1.073763 TGTGGATTGTAGCAGCTTGGT 59.926 47.619 0.00 0.00 0.00 3.67
9129 9556 1.470098 GTGGATTGTAGCAGCTTGGTG 59.530 52.381 0.00 0.00 0.00 4.17
9130 9557 1.073763 TGGATTGTAGCAGCTTGGTGT 59.926 47.619 0.00 0.00 0.00 4.16
9131 9558 2.304470 TGGATTGTAGCAGCTTGGTGTA 59.696 45.455 0.00 0.00 0.00 2.90
9132 9559 2.678336 GGATTGTAGCAGCTTGGTGTAC 59.322 50.000 0.00 0.00 0.00 2.90
9133 9560 2.178912 TTGTAGCAGCTTGGTGTACC 57.821 50.000 0.00 0.00 0.00 3.34
9134 9561 0.323629 TGTAGCAGCTTGGTGTACCC 59.676 55.000 0.00 0.00 34.29 3.69
9135 9562 0.739813 GTAGCAGCTTGGTGTACCCG 60.740 60.000 0.00 0.00 35.15 5.28
9136 9563 1.895020 TAGCAGCTTGGTGTACCCGG 61.895 60.000 0.00 0.00 35.15 5.73
9137 9564 2.046314 CAGCTTGGTGTACCCGGG 60.046 66.667 22.25 22.25 35.15 5.73
9138 9565 2.528378 AGCTTGGTGTACCCGGGT 60.528 61.111 32.66 32.66 35.15 5.28
9139 9566 2.359478 GCTTGGTGTACCCGGGTG 60.359 66.667 36.97 18.53 35.15 4.61
9140 9567 3.153825 CTTGGTGTACCCGGGTGT 58.846 61.111 36.97 13.43 35.15 4.16
9141 9568 1.302192 CTTGGTGTACCCGGGTGTG 60.302 63.158 36.97 13.36 35.15 3.82
9142 9569 2.741486 CTTGGTGTACCCGGGTGTGG 62.741 65.000 36.97 14.35 35.15 4.17
9143 9570 2.924101 GGTGTACCCGGGTGTGGA 60.924 66.667 36.97 14.03 0.00 4.02
9144 9571 2.295602 GGTGTACCCGGGTGTGGAT 61.296 63.158 36.97 10.79 0.00 3.41
9145 9572 1.681076 GTGTACCCGGGTGTGGATT 59.319 57.895 36.97 9.93 0.00 3.01
9146 9573 0.675522 GTGTACCCGGGTGTGGATTG 60.676 60.000 36.97 0.88 0.00 2.67
9147 9574 1.128809 TGTACCCGGGTGTGGATTGT 61.129 55.000 36.97 8.21 0.00 2.71
9148 9575 0.903942 GTACCCGGGTGTGGATTGTA 59.096 55.000 36.97 10.03 0.00 2.41
9149 9576 1.134610 GTACCCGGGTGTGGATTGTAG 60.135 57.143 36.97 0.00 0.00 2.74
9150 9577 1.451387 CCCGGGTGTGGATTGTAGC 60.451 63.158 14.18 0.00 0.00 3.58
9191 9618 1.983972 CCGTCAGTTAGCTGTCTGTC 58.016 55.000 15.92 11.38 43.05 3.51
9227 9654 0.740149 CTGTTGCTGTTGGCTGTTGA 59.260 50.000 0.00 0.00 42.39 3.18
9387 9814 4.715520 ACATGCTCGCTTTAATATGACG 57.284 40.909 0.00 0.00 0.00 4.35
9401 9828 1.330655 ATGACGGCGATCTCCAGGTT 61.331 55.000 16.62 0.00 0.00 3.50
9540 9967 4.236527 AGGGAGATATTGGTCGCTTTTT 57.763 40.909 0.00 0.00 32.36 1.94
9579 10006 3.119849 AGCTGCGCATTTATTTTTCTCGT 60.120 39.130 12.24 0.00 0.00 4.18
9591 10018 1.872388 TTTCTCGTGTCATTTCGGCA 58.128 45.000 0.00 0.00 0.00 5.69
9601 10028 0.609131 CATTTCGGCAACAGGTCCCT 60.609 55.000 0.00 0.00 0.00 4.20
9647 10074 4.023279 TGAAATCACCAAAGTCAACCGATG 60.023 41.667 0.00 0.00 0.00 3.84
9658 10085 0.813184 CAACCGATGCAAAGGCTCAT 59.187 50.000 10.35 0.00 41.91 2.90
9672 10099 8.740906 TGCAAAGGCTCATATACTACTCTATAC 58.259 37.037 0.00 0.00 41.91 1.47
9673 10100 8.962679 GCAAAGGCTCATATACTACTCTATACT 58.037 37.037 0.00 0.00 36.96 2.12
9715 10142 0.168128 CGCCTCCGGTTGATTTGTTC 59.832 55.000 0.00 0.00 0.00 3.18
9739 10198 2.783828 AGTGACGCGAGATTGGATAG 57.216 50.000 15.93 0.00 0.00 2.08
9762 10221 3.015677 CGCGAACCACCGAACAAA 58.984 55.556 0.00 0.00 0.00 2.83
9807 10266 4.152625 CCGCTTGCTCGCTTTCCG 62.153 66.667 0.00 0.00 38.61 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 4.083862 GACTGGGTCGGGGACAGC 62.084 72.222 0.00 0.00 35.70 4.40
162 163 3.712187 GGGAAAACACGAGAAATTGCAA 58.288 40.909 0.00 0.00 0.00 4.08
171 172 1.670083 GTCCCCGGGAAAACACGAG 60.670 63.158 26.32 0.57 31.38 4.18
172 173 2.426887 GTCCCCGGGAAAACACGA 59.573 61.111 26.32 5.47 31.38 4.35
191 192 2.600388 CGTGAACTCGCACCAGAAA 58.400 52.632 0.00 0.00 35.37 2.52
307 310 1.548081 TTCCGTCGAACACCCTATCA 58.452 50.000 0.00 0.00 0.00 2.15
339 342 0.251608 ATTGAACAAACCCCTCCCCG 60.252 55.000 0.00 0.00 0.00 5.73
389 392 1.337354 TGGCCGTGCATATACCATACG 60.337 52.381 0.00 0.00 34.78 3.06
396 399 2.428530 TGCATTTTTGGCCGTGCATATA 59.571 40.909 13.31 0.00 42.13 0.86
399 402 1.370437 TGCATTTTTGGCCGTGCAT 59.630 47.368 13.31 0.00 42.13 3.96
429 432 6.371271 TGATTCTGTTCAAACAATCGATAGCA 59.629 34.615 0.00 0.00 38.66 3.49
430 433 6.775088 TGATTCTGTTCAAACAATCGATAGC 58.225 36.000 0.00 0.00 38.66 2.97
433 436 7.149569 ACATGATTCTGTTCAAACAATCGAT 57.850 32.000 0.00 0.00 38.66 3.59
439 442 4.886489 TGTGGACATGATTCTGTTCAAACA 59.114 37.500 0.00 0.00 36.41 2.83
440 443 5.437289 TGTGGACATGATTCTGTTCAAAC 57.563 39.130 0.00 0.00 36.41 2.93
460 463 2.040813 ACTCCATCAATTGCAGTCCTGT 59.959 45.455 0.00 0.00 0.00 4.00
463 466 3.567164 CCATACTCCATCAATTGCAGTCC 59.433 47.826 0.00 0.00 0.00 3.85
465 468 2.954318 GCCATACTCCATCAATTGCAGT 59.046 45.455 0.00 2.84 0.00 4.40
480 483 7.700234 CGAAATAGAGTATGAGATGAGCCATAC 59.300 40.741 0.00 0.00 43.16 2.39
499 502 0.739462 TGTGCTGGGCGACGAAATAG 60.739 55.000 0.00 0.00 0.00 1.73
525 528 1.999735 TCAATCGCAGCGGTTCTAAAG 59.000 47.619 11.27 0.00 0.00 1.85
543 546 5.580998 AGACTAAGTCCAGTTATCCAGTCA 58.419 41.667 0.00 0.00 34.89 3.41
547 550 4.081087 GGCAAGACTAAGTCCAGTTATCCA 60.081 45.833 0.00 0.00 32.18 3.41
567 570 2.350964 GCGAAAACAAACGGATAAGGCA 60.351 45.455 0.00 0.00 0.00 4.75
568 571 2.247637 GCGAAAACAAACGGATAAGGC 58.752 47.619 0.00 0.00 0.00 4.35
576 579 1.515221 CCGAAAAGGCGAAAACAAACG 59.485 47.619 0.00 0.00 0.00 3.60
585 588 1.374252 GAGCTCACCGAAAAGGCGA 60.374 57.895 9.40 0.00 46.52 5.54
589 592 2.964740 TCATCAGAGCTCACCGAAAAG 58.035 47.619 17.77 4.59 0.00 2.27
595 598 2.286872 CAACCATCATCAGAGCTCACC 58.713 52.381 17.77 0.00 0.00 4.02
663 666 9.454859 AGACAAGCTATAAATAACTGAAAGCTT 57.545 29.630 0.00 0.00 46.63 3.74
670 673 9.371136 TCACTGAAGACAAGCTATAAATAACTG 57.629 33.333 0.00 0.00 0.00 3.16
679 682 6.767902 TCAAAACTTCACTGAAGACAAGCTAT 59.232 34.615 23.08 0.00 41.71 2.97
695 698 8.436046 AGATCATATCAGAAGCTCAAAACTTC 57.564 34.615 0.00 0.00 43.16 3.01
700 703 6.126968 TGGTGAGATCATATCAGAAGCTCAAA 60.127 38.462 0.00 0.00 35.90 2.69
725 728 3.745480 ATGCCTACATTAGCAACTGCGAT 60.745 43.478 0.00 0.00 43.36 4.58
727 730 1.942657 ATGCCTACATTAGCAACTGCG 59.057 47.619 0.00 0.00 43.36 5.18
739 742 6.780522 TGTATACATCACTAAGGATGCCTACA 59.219 38.462 0.08 11.31 46.81 2.74
741 744 6.437477 CCTGTATACATCACTAAGGATGCCTA 59.563 42.308 5.91 0.00 46.81 3.93
749 752 5.509840 GGTGAGCCCTGTATACATCACTAAG 60.510 48.000 25.45 7.80 37.71 2.18
764 767 0.040058 TGCAAATGATGGTGAGCCCT 59.960 50.000 0.00 0.00 0.00 5.19
765 768 1.117150 ATGCAAATGATGGTGAGCCC 58.883 50.000 0.00 0.00 0.00 5.19
767 770 3.795623 AGAATGCAAATGATGGTGAGC 57.204 42.857 0.00 0.00 0.00 4.26
768 771 5.068234 ACAAGAATGCAAATGATGGTGAG 57.932 39.130 0.00 0.00 0.00 3.51
785 788 6.597672 TGCAAGAAACAGAGTAAGAAACAAGA 59.402 34.615 0.00 0.00 0.00 3.02
808 826 3.243035 TGCACGCCTACAAAATATGATGC 60.243 43.478 0.00 0.00 0.00 3.91
865 886 3.503363 GCATGTGCGGGCAGTCTC 61.503 66.667 0.00 0.00 0.00 3.36
925 946 2.149578 CTCACAAAGTCAGGAGCCAAG 58.850 52.381 0.00 0.00 0.00 3.61
932 953 4.869297 GTGATGAGATCTCACAAAGTCAGG 59.131 45.833 27.37 0.00 43.11 3.86
1116 1137 6.765915 AAAGAGAACAGAAAGCTTGAACTT 57.234 33.333 0.00 0.00 0.00 2.66
1143 1164 0.038343 CCGGATTTGCCCTTTGTGTG 60.038 55.000 0.00 0.00 0.00 3.82
1161 1182 3.429085 CATTGTATTGCAGTTCGCTTCC 58.571 45.455 0.00 0.00 43.06 3.46
1230 1251 4.054780 TGTGGTGAACAACTGTCTCTAC 57.945 45.455 0.00 0.00 35.24 2.59
1249 1270 6.350445 GGGAATATGAGTTTTGTTGCTGATGT 60.350 38.462 0.00 0.00 0.00 3.06
1416 1437 3.255642 TGGCATGGAAGTAAAAGACAAGC 59.744 43.478 0.00 0.00 0.00 4.01
1417 1438 5.452078 TTGGCATGGAAGTAAAAGACAAG 57.548 39.130 0.00 0.00 0.00 3.16
1418 1439 5.774690 AGATTGGCATGGAAGTAAAAGACAA 59.225 36.000 0.00 0.00 0.00 3.18
1419 1440 5.324409 AGATTGGCATGGAAGTAAAAGACA 58.676 37.500 0.00 0.00 0.00 3.41
1420 1441 5.904362 AGATTGGCATGGAAGTAAAAGAC 57.096 39.130 0.00 0.00 0.00 3.01
1422 1443 7.094205 ACAGTAAGATTGGCATGGAAGTAAAAG 60.094 37.037 0.00 0.00 0.00 2.27
1423 1444 6.719370 ACAGTAAGATTGGCATGGAAGTAAAA 59.281 34.615 0.00 0.00 0.00 1.52
1424 1445 6.245408 ACAGTAAGATTGGCATGGAAGTAAA 58.755 36.000 0.00 0.00 0.00 2.01
1425 1446 5.815581 ACAGTAAGATTGGCATGGAAGTAA 58.184 37.500 0.00 0.00 0.00 2.24
1426 1447 5.435686 ACAGTAAGATTGGCATGGAAGTA 57.564 39.130 0.00 0.00 0.00 2.24
1427 1448 4.307032 ACAGTAAGATTGGCATGGAAGT 57.693 40.909 0.00 0.00 0.00 3.01
1428 1449 6.115446 TCTTACAGTAAGATTGGCATGGAAG 58.885 40.000 17.71 1.38 39.73 3.46
1429 1450 6.061022 TCTTACAGTAAGATTGGCATGGAA 57.939 37.500 17.71 0.00 39.73 3.53
1430 1451 5.692115 TCTTACAGTAAGATTGGCATGGA 57.308 39.130 17.71 0.00 39.73 3.41
1431 1452 5.220931 GCTTCTTACAGTAAGATTGGCATGG 60.221 44.000 21.41 7.78 43.72 3.66
1432 1453 5.355071 TGCTTCTTACAGTAAGATTGGCATG 59.645 40.000 25.72 13.59 43.72 4.06
1433 1454 5.500234 TGCTTCTTACAGTAAGATTGGCAT 58.500 37.500 25.72 0.00 43.72 4.40
1539 1560 5.049405 CCTTTAGTGGACAGCTAACAAGTTG 60.049 44.000 0.00 0.00 0.00 3.16
1920 1941 0.251634 GCAGACTTTCCTGAGAGGGG 59.748 60.000 0.00 0.00 35.59 4.79
2009 2030 3.541632 ACCACATAATTGCTCCGGTAAG 58.458 45.455 0.00 0.00 0.00 2.34
2015 2036 3.509575 TGTTCCAACCACATAATTGCTCC 59.490 43.478 0.00 0.00 0.00 4.70
2022 2043 7.171653 TCTGATATGTTGTTCCAACCACATAA 58.828 34.615 16.22 4.92 45.06 1.90
2023 2044 6.716284 TCTGATATGTTGTTCCAACCACATA 58.284 36.000 15.15 15.15 45.59 2.29
2946 2967 3.246880 AACCACCGTCCCAGGGTC 61.247 66.667 5.01 0.00 33.44 4.46
3584 3605 1.755179 AATTCCCTGCAAGACCATCG 58.245 50.000 0.00 0.00 34.07 3.84
3585 3606 5.047377 TGTTTTAATTCCCTGCAAGACCATC 60.047 40.000 0.00 0.00 34.07 3.51
3640 3665 7.707624 TGAGGAAATAAAATCTTGCAGATGT 57.292 32.000 0.00 0.00 34.65 3.06
3682 3707 4.335315 CCGGAAGCTGCAAATTAATAGACA 59.665 41.667 0.00 0.00 0.00 3.41
3728 3753 7.069578 AGTGAAACAAGAGGACAAACTACTAGA 59.930 37.037 0.00 0.00 41.43 2.43
3822 3847 3.380004 GGTGAGTGGTCAAAACAACATCA 59.620 43.478 0.00 0.00 33.27 3.07
3829 3854 2.222027 CAGGAGGTGAGTGGTCAAAAC 58.778 52.381 0.00 0.00 33.27 2.43
4006 4031 5.122869 CAGACCTGTGATGTGGAATTTACAG 59.877 44.000 0.00 0.00 36.27 2.74
4007 4032 5.003160 CAGACCTGTGATGTGGAATTTACA 58.997 41.667 0.00 0.00 0.00 2.41
4051 4076 2.629051 CAGTTCAGAGATGATGCAGCA 58.371 47.619 7.31 7.31 0.00 4.41
4203 4228 6.436847 TGCATTCAGGGATTTCAAATGTAGAA 59.563 34.615 0.00 0.00 31.52 2.10
4582 4612 3.024547 TGATTGTCTCTTACTCCCTCCG 58.975 50.000 0.00 0.00 0.00 4.63
4739 4769 4.811024 TGTTTGAAAACAACACAGTTTGCA 59.189 33.333 6.15 0.00 45.17 4.08
4805 4835 9.772973 TTTGTACAGTAGAAGTTGTATGTCAAT 57.227 29.630 0.00 0.00 38.38 2.57
4821 4851 4.112634 GCGCTGAGATGATTTGTACAGTA 58.887 43.478 0.00 0.00 0.00 2.74
4861 4891 2.957402 TCTTTGTCTTGGGCATCACT 57.043 45.000 0.00 0.00 0.00 3.41
4888 4918 7.178451 TCACGGATAAAGCAATCTATATCCTCA 59.822 37.037 8.55 0.00 40.99 3.86
4987 5017 6.711194 GCTTAAAGTCTGAAGAAGTAACCCTT 59.289 38.462 0.00 0.00 35.59 3.95
5103 5133 4.935352 AGCAAAAGCTGGAAAACACATA 57.065 36.364 0.00 0.00 0.00 2.29
5271 5302 6.394345 TTTTACAAATATGGGGCCCAAATT 57.606 33.333 32.57 21.26 36.95 1.82
5301 5332 2.876550 GCGGAGACTAAAACCAAAGTGT 59.123 45.455 0.00 0.00 0.00 3.55
5322 5353 9.405587 CCAACATGTGTAACTAATTTTACCAAG 57.594 33.333 0.00 0.00 38.04 3.61
5350 5381 0.527565 AGGAATTGTTGATGGCGCAC 59.472 50.000 10.83 0.00 0.00 5.34
5419 5450 7.355778 ACTTTCGAAACATCTCACAAGATTTC 58.644 34.615 6.47 0.00 40.38 2.17
5422 5453 6.867662 AACTTTCGAAACATCTCACAAGAT 57.132 33.333 6.47 0.00 43.24 2.40
5426 5457 6.017523 TGCATTAACTTTCGAAACATCTCACA 60.018 34.615 6.47 0.00 0.00 3.58
5449 5480 4.236935 CCAACTATTCAACATGGTTGTGC 58.763 43.478 8.75 0.00 38.36 4.57
5491 5524 3.197766 TGCACTACCAAACCCTCTATCTG 59.802 47.826 0.00 0.00 0.00 2.90
5492 5525 3.197983 GTGCACTACCAAACCCTCTATCT 59.802 47.826 10.32 0.00 0.00 1.98
5500 5533 2.778299 TGAGATGTGCACTACCAAACC 58.222 47.619 19.41 0.06 0.00 3.27
5516 5549 7.664552 AAATCTGGGCAAAAATATCATGAGA 57.335 32.000 0.09 0.00 0.00 3.27
5628 5661 4.752146 TCACATCATCAGACTAGCACAAG 58.248 43.478 0.00 0.00 0.00 3.16
5695 5728 4.467082 ACTTCAAATTTGCATAGCCCATCA 59.533 37.500 13.54 0.00 0.00 3.07
5726 5759 4.745620 GTCAGACAGGTCAGTAGTTCAAAC 59.254 45.833 1.84 0.00 0.00 2.93
5786 5819 1.076412 TGTCTTGCTTGGTGCCCAA 60.076 52.632 6.50 6.50 41.69 4.12
5816 5849 2.871236 GCTCTATCAGAAGGCTCCATGC 60.871 54.545 0.00 0.00 41.94 4.06
5952 5985 5.243981 TGCAAATTGGAACATTAACATGGG 58.756 37.500 0.00 0.00 39.30 4.00
6095 6128 5.820947 GTCCACACTCCTAAAAGAAAACTCA 59.179 40.000 0.00 0.00 0.00 3.41
6192 6225 3.057969 TGACAGGCTGACAATAAGGTG 57.942 47.619 23.66 0.00 0.00 4.00
6247 6282 7.330946 TGTTTGACACGAATCTAGATAGTTTGG 59.669 37.037 5.46 1.40 0.00 3.28
6283 6318 0.733729 CTTGCTCTGCAGATCCTTGC 59.266 55.000 18.63 17.00 40.61 4.01
6331 6366 1.172175 TGTGTGTTGCAAGTGCTTGA 58.828 45.000 15.31 0.00 42.93 3.02
6381 6416 6.146184 CCTCGACGAACAAAATGCATATAGAT 59.854 38.462 0.00 0.00 0.00 1.98
6388 6423 1.262950 CACCTCGACGAACAAAATGCA 59.737 47.619 0.00 0.00 0.00 3.96
6397 6432 1.955778 TCCAAACTACACCTCGACGAA 59.044 47.619 0.00 0.00 0.00 3.85
6422 6457 5.454966 AGGGGGAAAATACATGGTTATGAC 58.545 41.667 0.00 0.00 37.73 3.06
6434 6469 4.706616 ACCTGTAGAAGAGGGGGAAAATA 58.293 43.478 0.00 0.00 34.56 1.40
6435 6470 3.542604 ACCTGTAGAAGAGGGGGAAAAT 58.457 45.455 0.00 0.00 34.56 1.82
6436 6471 2.999928 ACCTGTAGAAGAGGGGGAAAA 58.000 47.619 0.00 0.00 34.56 2.29
6437 6472 2.735259 ACCTGTAGAAGAGGGGGAAA 57.265 50.000 0.00 0.00 34.56 3.13
6438 6473 2.735259 AACCTGTAGAAGAGGGGGAA 57.265 50.000 0.00 0.00 34.56 3.97
6439 6474 2.658489 ACTAACCTGTAGAAGAGGGGGA 59.342 50.000 0.00 0.00 34.56 4.81
6440 6475 3.117552 ACTAACCTGTAGAAGAGGGGG 57.882 52.381 0.00 0.00 34.56 5.40
6441 6476 5.127356 CAGTAACTAACCTGTAGAAGAGGGG 59.873 48.000 0.00 0.00 34.56 4.79
6442 6477 5.394333 GCAGTAACTAACCTGTAGAAGAGGG 60.394 48.000 0.00 0.00 34.56 4.30
6443 6478 5.652518 GCAGTAACTAACCTGTAGAAGAGG 58.347 45.833 0.00 0.00 36.57 3.69
6444 6479 5.123502 TCGCAGTAACTAACCTGTAGAAGAG 59.876 44.000 0.00 0.00 0.00 2.85
6445 6480 5.005740 TCGCAGTAACTAACCTGTAGAAGA 58.994 41.667 0.00 0.00 0.00 2.87
6493 6798 3.674997 TCCAAAGTGGATCAGTTGTAGC 58.325 45.455 0.00 0.00 42.67 3.58
6627 6932 0.982704 AGGCAGGGCATAGCTATCTG 59.017 55.000 13.90 13.90 0.00 2.90
6636 6941 2.233566 TGTTCAGGAGGCAGGGCAT 61.234 57.895 0.00 0.00 0.00 4.40
6719 7024 0.166814 GAACATGACTGCCTTGTCGC 59.833 55.000 0.00 0.00 39.64 5.19
6851 7156 3.927142 CCAGATCGTAGAAAGTTGACACC 59.073 47.826 0.00 0.00 43.58 4.16
6867 7176 5.068636 ACCAAGATGCACAATATCCAGATC 58.931 41.667 0.00 0.00 0.00 2.75
6868 7177 5.057843 ACCAAGATGCACAATATCCAGAT 57.942 39.130 0.00 0.00 0.00 2.90
6890 7199 4.219070 CACCATGATTTCTCCAGCAAGAAA 59.781 41.667 10.23 10.23 46.31 2.52
6955 7264 4.142816 CGGTTCTTCTTGACCTAAATGCAG 60.143 45.833 0.00 0.00 0.00 4.41
7060 7369 2.579873 TCCTCGGTAAGTATTCCCTCG 58.420 52.381 0.00 0.00 0.00 4.63
7211 7520 7.884354 AGGAAGGAAAACGTATGTATAAAACCA 59.116 33.333 0.00 0.00 0.00 3.67
7466 7776 8.164070 AGACATTATTAGTTAATGATGGACCCC 58.836 37.037 16.32 0.00 46.88 4.95
7742 8052 6.570672 ACTAAGTCTCAGTCGATAACAACA 57.429 37.500 0.00 0.00 0.00 3.33
7743 8053 7.082602 TCAACTAAGTCTCAGTCGATAACAAC 58.917 38.462 0.00 0.00 0.00 3.32
7744 8054 7.210718 TCAACTAAGTCTCAGTCGATAACAA 57.789 36.000 0.00 0.00 0.00 2.83
7752 8062 5.233988 AGTGCATTCAACTAAGTCTCAGTC 58.766 41.667 0.00 0.00 0.00 3.51
7777 8087 7.035612 ACTTTAAAGCTCAACTTTCCAACTTG 58.964 34.615 15.24 0.00 45.78 3.16
8030 8340 8.437742 CAAAAATAAATGCACACAAGAGGATTC 58.562 33.333 0.00 0.00 0.00 2.52
8055 8365 9.466497 AATTGAGAATAGCCTTTAGAATGAACA 57.534 29.630 0.00 0.00 0.00 3.18
8405 8715 6.579865 AGTATGTAAAGCCGTAAGTAATGCT 58.420 36.000 0.00 0.00 35.08 3.79
8414 8724 6.592607 CCTGAAAGAAAGTATGTAAAGCCGTA 59.407 38.462 0.00 0.00 34.07 4.02
8417 8727 5.710567 ACCCTGAAAGAAAGTATGTAAAGCC 59.289 40.000 0.00 0.00 34.07 4.35
8419 8729 7.979444 TCACCCTGAAAGAAAGTATGTAAAG 57.021 36.000 0.00 0.00 34.07 1.85
8779 9089 0.404426 AAAACCCTACCAGAGGCCAC 59.596 55.000 5.01 0.00 45.17 5.01
8903 9214 3.118519 ACAAGAACTACCCTGAAACACGT 60.119 43.478 0.00 0.00 0.00 4.49
9015 9326 8.104566 AGACAGTTCTGATAAGACACTAGTAGT 58.895 37.037 6.83 0.00 0.00 2.73
9016 9327 8.500753 AGACAGTTCTGATAAGACACTAGTAG 57.499 38.462 6.83 0.00 0.00 2.57
9032 9343 4.083565 GGTAGTTCTCCTCAGACAGTTCT 58.916 47.826 0.00 0.00 0.00 3.01
9044 9355 0.741915 CTCTCGGCAGGTAGTTCTCC 59.258 60.000 0.00 0.00 0.00 3.71
9121 9548 2.528378 ACCCGGGTACACCAAGCT 60.528 61.111 29.13 0.00 40.22 3.74
9122 9549 2.359478 CACCCGGGTACACCAAGC 60.359 66.667 29.72 0.00 40.22 4.01
9123 9550 1.302192 CACACCCGGGTACACCAAG 60.302 63.158 29.72 15.15 40.22 3.61
9124 9551 2.820400 CCACACCCGGGTACACCAA 61.820 63.158 29.72 0.00 40.22 3.67
9125 9552 3.243053 CCACACCCGGGTACACCA 61.243 66.667 29.72 0.00 40.22 4.17
9126 9553 1.844544 AATCCACACCCGGGTACACC 61.845 60.000 29.72 0.00 0.00 4.16
9127 9554 0.675522 CAATCCACACCCGGGTACAC 60.676 60.000 29.72 0.00 0.00 2.90
9128 9555 1.128809 ACAATCCACACCCGGGTACA 61.129 55.000 29.72 10.89 0.00 2.90
9129 9556 0.903942 TACAATCCACACCCGGGTAC 59.096 55.000 29.72 0.00 0.00 3.34
9130 9557 1.196911 CTACAATCCACACCCGGGTA 58.803 55.000 29.72 11.98 0.00 3.69
9131 9558 1.988015 CTACAATCCACACCCGGGT 59.012 57.895 24.16 24.16 0.00 5.28
9132 9559 1.451387 GCTACAATCCACACCCGGG 60.451 63.158 22.25 22.25 0.00 5.73
9133 9560 0.744414 CTGCTACAATCCACACCCGG 60.744 60.000 0.00 0.00 0.00 5.73
9134 9561 0.249120 TCTGCTACAATCCACACCCG 59.751 55.000 0.00 0.00 0.00 5.28
9135 9562 2.292267 CATCTGCTACAATCCACACCC 58.708 52.381 0.00 0.00 0.00 4.61
9136 9563 2.679837 CACATCTGCTACAATCCACACC 59.320 50.000 0.00 0.00 0.00 4.16
9137 9564 2.679837 CCACATCTGCTACAATCCACAC 59.320 50.000 0.00 0.00 0.00 3.82
9138 9565 2.940971 GCCACATCTGCTACAATCCACA 60.941 50.000 0.00 0.00 0.00 4.17
9139 9566 1.672881 GCCACATCTGCTACAATCCAC 59.327 52.381 0.00 0.00 0.00 4.02
9140 9567 1.561076 AGCCACATCTGCTACAATCCA 59.439 47.619 0.00 0.00 37.28 3.41
9141 9568 2.338577 AGCCACATCTGCTACAATCC 57.661 50.000 0.00 0.00 37.28 3.01
9142 9569 3.311871 CAGAAGCCACATCTGCTACAATC 59.688 47.826 0.00 0.00 38.34 2.67
9143 9570 3.276857 CAGAAGCCACATCTGCTACAAT 58.723 45.455 0.00 0.00 38.34 2.71
9144 9571 2.038952 ACAGAAGCCACATCTGCTACAA 59.961 45.455 3.57 0.00 46.56 2.41
9145 9572 1.625315 ACAGAAGCCACATCTGCTACA 59.375 47.619 3.57 0.00 46.56 2.74
9146 9573 2.393271 ACAGAAGCCACATCTGCTAC 57.607 50.000 3.57 0.00 46.56 3.58
9147 9574 3.076621 CAAACAGAAGCCACATCTGCTA 58.923 45.455 3.57 0.00 46.56 3.49
9148 9575 1.884579 CAAACAGAAGCCACATCTGCT 59.115 47.619 3.57 0.00 46.56 4.24
9149 9576 1.881973 TCAAACAGAAGCCACATCTGC 59.118 47.619 3.57 0.00 46.56 4.26
9150 9577 4.156664 CTTCAAACAGAAGCCACATCTG 57.843 45.455 2.17 2.17 46.54 2.90
9387 9814 1.200020 CAAACAAACCTGGAGATCGCC 59.800 52.381 8.81 8.81 0.00 5.54
9401 9828 5.694910 GCTAGTACTACTGCTTCACAAACAA 59.305 40.000 0.00 0.00 0.00 2.83
9437 9864 6.855914 CGAGGAAACGAGAATTTCAAATCAAA 59.144 34.615 0.00 0.00 39.85 2.69
9438 9865 6.203915 TCGAGGAAACGAGAATTTCAAATCAA 59.796 34.615 0.00 0.00 39.85 2.57
9454 9881 8.013378 TCAAACGATATTTTCTTTCGAGGAAAC 58.987 33.333 12.89 4.24 36.73 2.78
9540 9967 3.869065 CAGCTCCTGTTATCGGGTTAAA 58.131 45.455 0.00 0.00 40.77 1.52
9579 10006 1.234821 GACCTGTTGCCGAAATGACA 58.765 50.000 0.00 0.00 0.00 3.58
9591 10018 3.322466 CTCCGGCAGGGACCTGTT 61.322 66.667 18.86 0.00 45.24 3.16
9647 10074 8.962679 AGTATAGAGTAGTATATGAGCCTTTGC 58.037 37.037 0.00 0.00 37.95 3.68
9672 10099 3.189285 TGACATGTCGCATGTGTGATAG 58.811 45.455 23.80 0.00 36.88 2.08
9673 10100 3.244033 TGACATGTCGCATGTGTGATA 57.756 42.857 23.80 0.00 36.88 2.15
9715 10142 1.457738 CAATCTCGCGTCACTACTCG 58.542 55.000 5.77 0.00 35.17 4.18
9762 10221 3.911698 TGCAGACGACGTGCAGGT 61.912 61.111 12.68 12.68 45.96 4.00
9807 10266 1.344114 TGGAAGGAGCAAAAACCATGC 59.656 47.619 0.00 0.00 44.15 4.06


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

AutoCloner maintained by Alex Coulton.