Multiple sequence alignment - TraesCS5D01G151300

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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 TraesCS5D01G151300 chr5D 100.000 5582 0 0 1 5582 240512148 240506567 0.000000e+00 10309.0
1 TraesCS5D01G151300 chr5A 96.584 3279 107 3 1761 5036 313306632 313309908 0.000000e+00 5430.0
2 TraesCS5D01G151300 chr5A 93.458 856 28 11 775 1618 313305688 313306527 0.000000e+00 1245.0
3 TraesCS5D01G151300 chr5A 90.537 708 39 13 1 689 313302090 313302788 0.000000e+00 911.0
4 TraesCS5D01G151300 chr5A 96.964 494 12 3 5036 5528 313309947 313310438 0.000000e+00 826.0
5 TraesCS5D01G151300 chr5A 98.571 70 1 0 5513 5582 313310456 313310525 2.110000e-24 124.0
6 TraesCS5D01G151300 chr5A 92.683 82 4 2 1667 1747 495049870 495049950 3.530000e-22 117.0
7 TraesCS5D01G151300 chr5A 89.130 92 8 2 1644 1734 158685914 158685824 4.570000e-21 113.0
8 TraesCS5D01G151300 chr5A 96.970 66 2 0 697 762 313305301 313305366 1.640000e-20 111.0
9 TraesCS5D01G151300 chr5B 93.638 3285 171 15 1761 5036 263215132 263218387 0.000000e+00 4874.0
10 TraesCS5D01G151300 chr5B 92.958 1633 60 24 1 1618 263213455 263215047 0.000000e+00 2327.0
11 TraesCS5D01G151300 chr5B 90.934 364 29 4 5220 5582 263218742 263219102 2.340000e-133 486.0
12 TraesCS5D01G151300 chr5B 86.567 134 17 1 5083 5215 263218568 263218701 4.510000e-31 147.0
13 TraesCS5D01G151300 chr2D 83.696 368 50 10 5219 5579 645934699 645935063 6.930000e-89 339.0
14 TraesCS5D01G151300 chr2D 96.053 76 2 1 1673 1747 446347777 446347852 7.590000e-24 122.0
15 TraesCS5D01G151300 chr2D 94.872 78 3 1 1671 1747 315978068 315978145 2.730000e-23 121.0
16 TraesCS5D01G151300 chr2A 81.744 367 57 10 5220 5579 771680672 771681035 1.180000e-76 298.0
17 TraesCS5D01G151300 chr2A 84.848 66 8 2 4960 5024 183792825 183792761 1.300000e-06 65.8
18 TraesCS5D01G151300 chr2B 82.371 329 48 10 5220 5541 789615537 789615212 1.530000e-70 278.0
19 TraesCS5D01G151300 chr2B 87.218 133 16 1 5039 5170 449826976 449826844 3.480000e-32 150.0
20 TraesCS5D01G151300 chr2B 87.692 130 15 1 5039 5167 493711708 493711579 3.480000e-32 150.0
21 TraesCS5D01G151300 chr2B 97.260 73 2 0 1671 1743 638822394 638822466 2.110000e-24 124.0
22 TraesCS5D01G151300 chr2B 94.872 78 3 1 1671 1747 383639988 383640065 2.730000e-23 121.0
23 TraesCS5D01G151300 chr2B 83.544 79 9 3 4960 5036 272109584 272109660 2.790000e-08 71.3
24 TraesCS5D01G151300 chr3B 90.299 134 12 1 5036 5168 556288601 556288468 2.070000e-39 174.0
25 TraesCS5D01G151300 chr3B 83.333 78 11 2 4960 5036 413085114 413085190 2.790000e-08 71.3
26 TraesCS5D01G151300 chr1D 90.299 134 11 2 5034 5166 89134797 89134929 2.070000e-39 174.0
27 TraesCS5D01G151300 chr1D 83.333 66 9 2 4960 5024 72296672 72296736 6.040000e-05 60.2
28 TraesCS5D01G151300 chr6B 89.474 133 13 1 5036 5167 650791039 650790907 3.460000e-37 167.0
29 TraesCS5D01G151300 chr6B 94.872 78 3 1 1671 1747 662167404 662167327 2.730000e-23 121.0
30 TraesCS5D01G151300 chr1A 86.667 135 16 2 5034 5167 85313691 85313824 1.250000e-31 148.0
31 TraesCS5D01G151300 chr4B 85.211 142 20 1 5027 5167 183525083 183525224 1.620000e-30 145.0
32 TraesCS5D01G151300 chr7B 93.750 80 4 1 1670 1748 222731917 222731996 9.820000e-23 119.0
33 TraesCS5D01G151300 chr1B 89.655 87 9 0 1673 1759 557408747 557408661 1.640000e-20 111.0
34 TraesCS5D01G151300 chr7D 82.051 78 12 2 4960 5036 379120474 379120398 1.300000e-06 65.8
35 TraesCS5D01G151300 chr7A 83.582 67 9 2 4959 5024 495300563 495300628 1.680000e-05 62.1
36 TraesCS5D01G151300 chr4D 83.333 66 9 2 4960 5024 160231806 160231870 6.040000e-05 60.2
37 TraesCS5D01G151300 chr4D 83.333 66 9 2 4960 5024 218939498 218939562 6.040000e-05 60.2


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 TraesCS5D01G151300 chr5D 240506567 240512148 5581 True 10309.000000 10309 100.00000 1 5582 1 chr5D.!!$R1 5581
1 TraesCS5D01G151300 chr5A 313302090 313310525 8435 False 1441.166667 5430 95.51400 1 5582 6 chr5A.!!$F2 5581
2 TraesCS5D01G151300 chr5B 263213455 263219102 5647 False 1958.500000 4874 91.02425 1 5582 4 chr5B.!!$F1 5581

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
258 260 0.110373 GGTGCTGTTTTTACCGAGCG 60.110 55.0 0.00 0.00 33.97 5.03 F
616 634 0.319083 TGTACCGAATGCGTTCCTGT 59.681 50.0 13.02 12.33 35.23 4.00 F
1270 4110 0.666577 CTGCAGCTTCCTTGCTTTGC 60.667 55.0 0.00 0.00 41.98 3.68 F
2057 4963 0.037326 ATTCCTCTTTCGCAGTCGCA 60.037 50.0 0.00 0.00 38.40 5.10 F
2371 5277 0.610687 AGAACTGGCAGTACAGGAGC 59.389 55.0 22.37 4.78 42.75 4.70 F
4040 6949 0.179032 TGTGACGCTTGGGATGTTGT 60.179 50.0 0.00 0.00 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1099 3938 0.108207 CCCTGTCCTGGAGATCATGC 59.892 60.000 0.00 0.0 0.00 4.06 R
1541 4391 0.534203 TCCAGTTTGCGGAACAGACC 60.534 55.000 5.69 0.0 40.84 3.85 R
2951 5860 0.179702 GCAGCTCCATCAGACCATCA 59.820 55.000 0.00 0.0 0.00 3.07 R
3010 5919 1.251251 GGTTTGCAAGTCCATCAGCT 58.749 50.000 14.99 0.0 0.00 4.24 R
4144 7053 1.744014 CTGCAAGCTGCTGGGTTTT 59.256 52.632 1.35 0.0 45.31 2.43 R
5142 8195 1.553704 ACCTCCGTCTGGGTTATTGAC 59.446 52.381 0.00 0.0 37.00 3.18 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
202 203 6.154445 CACAGTTTTGAATTTCTGAGGGATG 58.846 40.000 0.00 0.00 0.00 3.51
203 204 6.016024 CACAGTTTTGAATTTCTGAGGGATGA 60.016 38.462 0.00 0.00 0.00 2.92
204 205 6.723052 ACAGTTTTGAATTTCTGAGGGATGAT 59.277 34.615 0.00 0.00 0.00 2.45
205 206 7.890127 ACAGTTTTGAATTTCTGAGGGATGATA 59.110 33.333 0.00 0.00 0.00 2.15
206 207 8.910944 CAGTTTTGAATTTCTGAGGGATGATAT 58.089 33.333 0.00 0.00 0.00 1.63
252 254 4.337274 AGTGTAACCTGGTGCTGTTTTTAC 59.663 41.667 0.00 0.00 37.80 2.01
258 260 0.110373 GGTGCTGTTTTTACCGAGCG 60.110 55.000 0.00 0.00 33.97 5.03
369 371 3.745975 CGTTGTCACTTGGATGTGTACAT 59.254 43.478 0.00 0.00 38.90 2.29
417 419 4.757149 AGTTGTAGTGCAGAAAATCTCACC 59.243 41.667 0.00 0.00 30.28 4.02
433 435 0.591170 CACCGCTTGTTGTTACCAGG 59.409 55.000 0.00 0.00 0.00 4.45
457 459 4.190772 CTGTGGTTGCTTGTTTTCCAAAT 58.809 39.130 0.00 0.00 31.20 2.32
463 465 6.825721 TGGTTGCTTGTTTTCCAAATGTTATT 59.174 30.769 0.00 0.00 31.20 1.40
490 492 2.689471 GCATCCATTTGGTGATAGTGCA 59.311 45.455 0.00 0.00 36.34 4.57
512 514 2.416162 CCGAGGTCAGAGCTGTTAAGAC 60.416 54.545 6.92 0.00 0.00 3.01
533 550 5.011125 AGACAAAAGACTTGATCTCTTCCGA 59.989 40.000 0.00 0.00 36.27 4.55
613 631 1.659098 CTTCTGTACCGAATGCGTTCC 59.341 52.381 13.02 0.00 35.23 3.62
616 634 0.319083 TGTACCGAATGCGTTCCTGT 59.681 50.000 13.02 12.33 35.23 4.00
632 650 1.474879 CCTGTGCATGCATGATGAACA 59.525 47.619 30.64 22.95 46.97 3.18
762 3291 2.608752 GGAGCCGAGTCGTTTACTTTCA 60.609 50.000 12.31 0.00 39.07 2.69
771 3300 7.488471 CCGAGTCGTTTACTTTCATTATCTCTT 59.512 37.037 12.31 0.00 39.07 2.85
832 3667 5.647658 CCATTGTAGTTTGTGGATCTAGCAA 59.352 40.000 0.00 0.00 33.53 3.91
844 3679 5.049129 GTGGATCTAGCAAAGCAATGATACC 60.049 44.000 0.00 0.00 0.00 2.73
992 3831 2.008242 AAGCCGAGATCTCCTAGCAT 57.992 50.000 22.19 12.32 0.00 3.79
1033 3872 3.140623 GGTAGGAGATCGACCTCTGTAC 58.859 54.545 6.78 8.78 38.02 2.90
1034 3873 3.181452 GGTAGGAGATCGACCTCTGTACT 60.181 52.174 6.78 0.00 38.02 2.73
1035 3874 4.040217 GGTAGGAGATCGACCTCTGTACTA 59.960 50.000 6.78 0.00 38.02 1.82
1099 3938 3.256136 ACCTGAGTAACTTTCTCCTCACG 59.744 47.826 0.00 0.00 31.11 4.35
1192 4032 2.987547 CCAAGGGTGGTGCTGCTG 60.988 66.667 0.00 0.00 40.42 4.41
1193 4033 3.677648 CAAGGGTGGTGCTGCTGC 61.678 66.667 8.89 8.89 40.20 5.25
1247 4087 2.689034 AGCCTCCCTAGTGCACCC 60.689 66.667 14.63 0.00 0.00 4.61
1264 4104 2.559840 CGCACTGCAGCTTCCTTG 59.440 61.111 15.27 4.32 0.00 3.61
1268 4108 0.672342 CACTGCAGCTTCCTTGCTTT 59.328 50.000 15.27 0.00 41.98 3.51
1269 4109 0.672342 ACTGCAGCTTCCTTGCTTTG 59.328 50.000 15.27 0.00 41.98 2.77
1270 4110 0.666577 CTGCAGCTTCCTTGCTTTGC 60.667 55.000 0.00 0.00 41.98 3.68
1495 4343 4.332819 GCTATTGTTCGGTGAAAGCACTAT 59.667 41.667 0.00 0.00 44.52 2.12
1541 4391 2.972625 TCCTTCTGTGTAATTCTGCCG 58.027 47.619 0.00 0.00 0.00 5.69
1569 4419 1.266989 CCGCAAACTGGAGTTTCTTCC 59.733 52.381 1.66 0.00 45.54 3.46
1603 4453 2.264813 GTCGGCGCTTGTAGACATTTA 58.735 47.619 7.64 0.00 34.09 1.40
1618 4468 6.259550 AGACATTTACAAGCCAAGAATGAC 57.740 37.500 0.00 0.00 33.24 3.06
1622 4528 5.947228 TTTACAAGCCAAGAATGACTCAG 57.053 39.130 0.00 0.00 0.00 3.35
1626 4532 5.075493 ACAAGCCAAGAATGACTCAGAAAT 58.925 37.500 0.00 0.00 0.00 2.17
1627 4533 5.182760 ACAAGCCAAGAATGACTCAGAAATC 59.817 40.000 0.00 0.00 0.00 2.17
1632 4538 6.294397 GCCAAGAATGACTCAGAAATCTTGTT 60.294 38.462 17.04 0.00 41.18 2.83
1653 4559 2.027192 TGCCCAGTTCATCTTGTAGGAC 60.027 50.000 0.00 0.00 0.00 3.85
1654 4560 2.237392 GCCCAGTTCATCTTGTAGGACT 59.763 50.000 0.00 0.00 0.00 3.85
1655 4561 3.866651 CCCAGTTCATCTTGTAGGACTG 58.133 50.000 0.00 0.00 0.00 3.51
1656 4562 3.261897 CCCAGTTCATCTTGTAGGACTGT 59.738 47.826 0.00 0.00 0.00 3.55
1657 4563 4.248859 CCAGTTCATCTTGTAGGACTGTG 58.751 47.826 0.00 0.00 0.00 3.66
1658 4564 3.681897 CAGTTCATCTTGTAGGACTGTGC 59.318 47.826 0.00 0.00 0.00 4.57
1659 4565 3.580458 AGTTCATCTTGTAGGACTGTGCT 59.420 43.478 7.10 7.10 0.00 4.40
1660 4566 3.876274 TCATCTTGTAGGACTGTGCTC 57.124 47.619 4.68 0.00 0.00 4.26
1663 4569 4.284490 TCATCTTGTAGGACTGTGCTCTTT 59.716 41.667 4.68 0.00 0.00 2.52
1664 4570 4.258702 TCTTGTAGGACTGTGCTCTTTC 57.741 45.455 4.68 0.00 0.00 2.62
1666 4572 4.345257 TCTTGTAGGACTGTGCTCTTTCTT 59.655 41.667 4.68 0.00 0.00 2.52
1667 4573 5.538813 TCTTGTAGGACTGTGCTCTTTCTTA 59.461 40.000 4.68 0.00 0.00 2.10
1668 4574 6.211584 TCTTGTAGGACTGTGCTCTTTCTTAT 59.788 38.462 4.68 0.00 0.00 1.73
1669 4575 5.967088 TGTAGGACTGTGCTCTTTCTTATC 58.033 41.667 4.68 0.00 0.00 1.75
1670 4576 5.480422 TGTAGGACTGTGCTCTTTCTTATCA 59.520 40.000 4.68 0.00 0.00 2.15
1671 4577 5.083533 AGGACTGTGCTCTTTCTTATCAG 57.916 43.478 0.00 0.00 0.00 2.90
1672 4578 4.530161 AGGACTGTGCTCTTTCTTATCAGT 59.470 41.667 0.00 0.00 37.37 3.41
1673 4579 4.629200 GGACTGTGCTCTTTCTTATCAGTG 59.371 45.833 0.00 0.00 35.32 3.66
1674 4580 5.220710 ACTGTGCTCTTTCTTATCAGTGT 57.779 39.130 0.00 0.00 34.18 3.55
1675 4581 6.346477 ACTGTGCTCTTTCTTATCAGTGTA 57.654 37.500 0.00 0.00 34.18 2.90
1676 4582 6.393990 ACTGTGCTCTTTCTTATCAGTGTAG 58.606 40.000 0.00 0.00 34.18 2.74
1677 4583 6.209589 ACTGTGCTCTTTCTTATCAGTGTAGA 59.790 38.462 0.00 0.00 34.18 2.59
1678 4584 6.993079 TGTGCTCTTTCTTATCAGTGTAGAA 58.007 36.000 0.00 0.00 0.00 2.10
1679 4585 7.093354 TGTGCTCTTTCTTATCAGTGTAGAAG 58.907 38.462 0.00 0.00 30.32 2.85
1680 4586 7.093992 GTGCTCTTTCTTATCAGTGTAGAAGT 58.906 38.462 0.00 0.00 30.32 3.01
1681 4587 7.062839 GTGCTCTTTCTTATCAGTGTAGAAGTG 59.937 40.741 0.00 0.00 30.32 3.16
1682 4588 6.035542 GCTCTTTCTTATCAGTGTAGAAGTGC 59.964 42.308 0.00 0.00 30.32 4.40
1683 4589 6.993079 TCTTTCTTATCAGTGTAGAAGTGCA 58.007 36.000 0.00 0.00 30.32 4.57
1684 4590 7.615403 TCTTTCTTATCAGTGTAGAAGTGCAT 58.385 34.615 0.00 0.00 30.32 3.96
1685 4591 7.547019 TCTTTCTTATCAGTGTAGAAGTGCATG 59.453 37.037 0.00 0.00 30.32 4.06
1686 4592 5.111989 TCTTATCAGTGTAGAAGTGCATGC 58.888 41.667 11.82 11.82 0.00 4.06
1687 4593 3.623906 ATCAGTGTAGAAGTGCATGCT 57.376 42.857 20.33 0.00 0.00 3.79
1688 4594 2.964740 TCAGTGTAGAAGTGCATGCTC 58.035 47.619 20.33 15.94 0.00 4.26
1689 4595 2.564504 TCAGTGTAGAAGTGCATGCTCT 59.435 45.455 20.33 18.23 0.00 4.09
1690 4596 3.763897 TCAGTGTAGAAGTGCATGCTCTA 59.236 43.478 21.70 15.62 0.00 2.43
1691 4597 4.111198 CAGTGTAGAAGTGCATGCTCTAG 58.889 47.826 21.70 4.30 0.00 2.43
1692 4598 3.766591 AGTGTAGAAGTGCATGCTCTAGT 59.233 43.478 21.70 14.24 0.00 2.57
1693 4599 4.109050 GTGTAGAAGTGCATGCTCTAGTC 58.891 47.826 21.70 16.19 0.00 2.59
1694 4600 3.763897 TGTAGAAGTGCATGCTCTAGTCA 59.236 43.478 21.70 15.00 0.00 3.41
1695 4601 3.969287 AGAAGTGCATGCTCTAGTCAA 57.031 42.857 21.70 0.00 0.00 3.18
1696 4602 4.484537 AGAAGTGCATGCTCTAGTCAAT 57.515 40.909 21.70 5.92 0.00 2.57
1697 4603 4.190001 AGAAGTGCATGCTCTAGTCAATG 58.810 43.478 21.70 0.00 0.00 2.82
1698 4604 2.286872 AGTGCATGCTCTAGTCAATGC 58.713 47.619 20.22 15.01 35.77 3.56
1699 4605 2.011947 GTGCATGCTCTAGTCAATGCA 58.988 47.619 20.33 18.49 41.91 3.96
1700 4606 2.421073 GTGCATGCTCTAGTCAATGCAA 59.579 45.455 20.33 10.22 44.98 4.08
1701 4607 2.421073 TGCATGCTCTAGTCAATGCAAC 59.579 45.455 20.33 8.82 41.32 4.17
1702 4608 2.223433 GCATGCTCTAGTCAATGCAACC 60.223 50.000 11.37 3.46 38.96 3.77
1703 4609 2.857186 TGCTCTAGTCAATGCAACCA 57.143 45.000 0.00 0.00 32.12 3.67
1704 4610 3.138884 TGCTCTAGTCAATGCAACCAA 57.861 42.857 0.00 0.00 32.12 3.67
1705 4611 3.485394 TGCTCTAGTCAATGCAACCAAA 58.515 40.909 0.00 0.00 32.12 3.28
1706 4612 3.888323 TGCTCTAGTCAATGCAACCAAAA 59.112 39.130 0.00 0.00 32.12 2.44
1707 4613 4.022935 TGCTCTAGTCAATGCAACCAAAAG 60.023 41.667 0.00 0.00 32.12 2.27
1708 4614 4.216257 GCTCTAGTCAATGCAACCAAAAGA 59.784 41.667 0.00 0.00 0.00 2.52
1709 4615 5.689383 TCTAGTCAATGCAACCAAAAGAC 57.311 39.130 0.00 0.00 0.00 3.01
1710 4616 3.733443 AGTCAATGCAACCAAAAGACC 57.267 42.857 0.00 0.00 0.00 3.85
1711 4617 2.034558 AGTCAATGCAACCAAAAGACCG 59.965 45.455 0.00 0.00 0.00 4.79
1712 4618 2.034053 GTCAATGCAACCAAAAGACCGA 59.966 45.455 0.00 0.00 0.00 4.69
1713 4619 2.890311 TCAATGCAACCAAAAGACCGAT 59.110 40.909 0.00 0.00 0.00 4.18
1714 4620 3.057596 TCAATGCAACCAAAAGACCGATC 60.058 43.478 0.00 0.00 0.00 3.69
1715 4621 2.270352 TGCAACCAAAAGACCGATCT 57.730 45.000 0.00 0.00 36.42 2.75
1716 4622 1.879380 TGCAACCAAAAGACCGATCTG 59.121 47.619 0.00 0.00 34.48 2.90
1717 4623 2.151202 GCAACCAAAAGACCGATCTGA 58.849 47.619 0.00 0.00 34.48 3.27
1718 4624 2.749621 GCAACCAAAAGACCGATCTGAT 59.250 45.455 0.00 0.00 34.48 2.90
1719 4625 3.426695 GCAACCAAAAGACCGATCTGATG 60.427 47.826 0.00 0.00 34.48 3.07
1720 4626 2.991250 ACCAAAAGACCGATCTGATGG 58.009 47.619 9.14 9.14 34.48 3.51
1721 4627 2.571653 ACCAAAAGACCGATCTGATGGA 59.428 45.455 16.17 0.00 34.48 3.41
1722 4628 3.009033 ACCAAAAGACCGATCTGATGGAA 59.991 43.478 16.17 0.00 34.48 3.53
1723 4629 3.624861 CCAAAAGACCGATCTGATGGAAG 59.375 47.826 5.34 0.00 34.48 3.46
1724 4630 4.507710 CAAAAGACCGATCTGATGGAAGA 58.492 43.478 11.46 0.00 34.48 2.87
1725 4631 4.399004 AAAGACCGATCTGATGGAAGAG 57.601 45.455 11.46 0.00 34.48 2.85
1726 4632 3.304911 AGACCGATCTGATGGAAGAGA 57.695 47.619 11.46 0.00 32.29 3.10
1727 4633 2.955660 AGACCGATCTGATGGAAGAGAC 59.044 50.000 11.46 0.00 32.29 3.36
1728 4634 2.955660 GACCGATCTGATGGAAGAGACT 59.044 50.000 11.46 0.00 0.00 3.24
1729 4635 4.138290 GACCGATCTGATGGAAGAGACTA 58.862 47.826 11.46 0.00 0.00 2.59
1730 4636 4.141287 ACCGATCTGATGGAAGAGACTAG 58.859 47.826 11.46 0.00 0.00 2.57
1731 4637 4.141367 ACCGATCTGATGGAAGAGACTAGA 60.141 45.833 0.00 0.00 0.00 2.43
1732 4638 4.215399 CCGATCTGATGGAAGAGACTAGAC 59.785 50.000 0.00 0.00 0.00 2.59
1733 4639 4.819088 CGATCTGATGGAAGAGACTAGACA 59.181 45.833 0.00 0.00 0.00 3.41
1734 4640 5.298026 CGATCTGATGGAAGAGACTAGACAA 59.702 44.000 0.00 0.00 0.00 3.18
1735 4641 6.016360 CGATCTGATGGAAGAGACTAGACAAT 60.016 42.308 0.00 0.00 0.00 2.71
1736 4642 7.174080 CGATCTGATGGAAGAGACTAGACAATA 59.826 40.741 0.00 0.00 0.00 1.90
1737 4643 7.575414 TCTGATGGAAGAGACTAGACAATAC 57.425 40.000 0.00 0.00 0.00 1.89
1738 4644 6.261158 TCTGATGGAAGAGACTAGACAATACG 59.739 42.308 0.00 0.00 0.00 3.06
1739 4645 5.886474 TGATGGAAGAGACTAGACAATACGT 59.114 40.000 0.00 0.00 0.00 3.57
1740 4646 6.377429 TGATGGAAGAGACTAGACAATACGTT 59.623 38.462 0.00 0.00 0.00 3.99
1741 4647 6.585695 TGGAAGAGACTAGACAATACGTTT 57.414 37.500 0.00 0.00 0.00 3.60
1742 4648 7.692460 TGGAAGAGACTAGACAATACGTTTA 57.308 36.000 0.00 0.00 0.00 2.01
1743 4649 8.114331 TGGAAGAGACTAGACAATACGTTTAA 57.886 34.615 0.00 0.00 0.00 1.52
1744 4650 8.025445 TGGAAGAGACTAGACAATACGTTTAAC 58.975 37.037 0.00 0.00 0.00 2.01
1791 4697 9.992910 TGTTCATTGTTAGTGTACTAGTATACG 57.007 33.333 20.15 7.82 33.21 3.06
1823 4729 2.057137 ACAATAGGCATCACCGCATT 57.943 45.000 0.00 0.00 46.52 3.56
1873 4779 4.273724 CACAGGATCATGAGCTCAATTCAG 59.726 45.833 22.50 8.95 0.00 3.02
1929 4835 1.123077 ACCGAGGCTAATGATCTGCA 58.877 50.000 0.00 0.00 0.00 4.41
1941 4847 3.361281 TGATCTGCATCTTGCTTCCTT 57.639 42.857 0.75 0.00 45.31 3.36
1961 4867 4.365723 CTTTTATCATGCCAGGAATGTGC 58.634 43.478 7.37 0.00 0.00 4.57
1970 4876 2.760092 GCCAGGAATGTGCTTAATGGAA 59.240 45.455 0.00 0.00 0.00 3.53
2005 4911 1.067821 GACTAAGGATCTCGGCACAGG 59.932 57.143 0.00 0.00 0.00 4.00
2057 4963 0.037326 ATTCCTCTTTCGCAGTCGCA 60.037 50.000 0.00 0.00 38.40 5.10
2136 5042 4.047883 ACTACATAGGATTTGCCCTCCTT 58.952 43.478 4.36 0.00 40.29 3.36
2150 5056 3.084786 CCCTCCTTTACTTGCTTTCCTG 58.915 50.000 0.00 0.00 0.00 3.86
2239 5145 1.584724 AATACCCCCTCAGTGACTGG 58.415 55.000 13.33 3.47 31.51 4.00
2248 5154 1.204467 CTCAGTGACTGGAGAAGGAGC 59.796 57.143 13.33 0.00 31.51 4.70
2281 5187 1.064240 ACAAACTTTGTCCCCGGAGTT 60.064 47.619 0.73 0.00 40.56 3.01
2282 5188 1.336755 CAAACTTTGTCCCCGGAGTTG 59.663 52.381 0.73 0.00 33.02 3.16
2296 5202 4.021544 CCCGGAGTTGAAAAATTCCATTGA 60.022 41.667 0.73 0.00 32.89 2.57
2306 5212 5.988310 AAAATTCCATTGATGACTGCTCA 57.012 34.783 0.00 0.00 0.00 4.26
2310 5216 2.040145 TCCATTGATGACTGCTCAACCA 59.960 45.455 0.00 0.00 35.57 3.67
2340 5246 6.457257 GGTTGAGAGTGTTACTATCGAGACTC 60.457 46.154 0.00 0.00 39.19 3.36
2364 5270 2.889512 TGGAGAAGAGAACTGGCAGTA 58.110 47.619 22.37 0.00 0.00 2.74
2371 5277 0.610687 AGAACTGGCAGTACAGGAGC 59.389 55.000 22.37 4.78 42.75 4.70
2415 5321 3.510719 GCCAATAACACGCATGACAATT 58.489 40.909 0.00 0.00 0.00 2.32
2438 5344 5.895636 ACTGTGAAGAAACAAATGTCACA 57.104 34.783 4.86 4.86 44.64 3.58
2491 5397 5.301555 GGAGTCTTCTAAATATGCCCAGAC 58.698 45.833 0.00 0.00 0.00 3.51
2500 5406 2.418368 TATGCCCAGACCAATGTCAC 57.582 50.000 0.00 0.00 44.33 3.67
2514 5420 4.330250 CAATGTCACTGTGGGAAGAGAAT 58.670 43.478 8.11 0.00 0.00 2.40
2516 5422 2.038952 TGTCACTGTGGGAAGAGAATGG 59.961 50.000 8.11 0.00 0.00 3.16
2525 5431 3.849574 TGGGAAGAGAATGGTATGGTGAA 59.150 43.478 0.00 0.00 0.00 3.18
2531 5437 7.093771 GGAAGAGAATGGTATGGTGAACAAATT 60.094 37.037 0.00 0.00 0.00 1.82
2534 5440 8.109634 AGAGAATGGTATGGTGAACAAATTAGT 58.890 33.333 0.00 0.00 0.00 2.24
2541 5447 6.824305 ATGGTGAACAAATTAGTGAGAAGG 57.176 37.500 0.00 0.00 0.00 3.46
2545 5451 4.761739 TGAACAAATTAGTGAGAAGGCTGG 59.238 41.667 0.00 0.00 0.00 4.85
2768 5674 3.788672 CCCACTGATAGACTTGGGC 57.211 57.895 0.00 0.00 42.40 5.36
2843 5749 2.948979 AGATGACGATGAGAGTGACCTC 59.051 50.000 0.00 0.00 38.04 3.85
2859 5765 2.781911 CTCGAGGAGGATGACGACA 58.218 57.895 3.91 0.00 0.00 4.35
2873 5782 3.014623 TGACGACAACAGTATCTCGGAT 58.985 45.455 0.00 0.00 0.00 4.18
2881 5790 4.250116 ACAGTATCTCGGATGATGAAGC 57.750 45.455 0.00 0.00 0.00 3.86
2909 5818 4.099419 GGAGAGGAAGAGGAGAAAGATGAC 59.901 50.000 0.00 0.00 0.00 3.06
2951 5860 4.103311 GTCATAGGAAAGAATGGTAGGGCT 59.897 45.833 0.00 0.00 0.00 5.19
3010 5919 4.119862 CTGAAGTTTGAACTCGACCAGAA 58.880 43.478 0.00 0.00 38.57 3.02
3014 5923 2.154854 TTGAACTCGACCAGAAGCTG 57.845 50.000 0.00 0.00 0.00 4.24
3030 5939 0.961019 GCTGATGGACTTGCAAACCA 59.039 50.000 21.75 21.75 38.09 3.67
3144 6053 2.238701 GCCTCAGGGGAAGGGGAAA 61.239 63.158 0.00 0.00 37.23 3.13
3193 6102 1.985614 CACCATCTGTCCTCCTGCA 59.014 57.895 0.00 0.00 0.00 4.41
3232 6141 5.933617 TGATCTTCCTTCTGACCATATTGG 58.066 41.667 0.00 0.00 45.02 3.16
3556 6465 4.804868 TGCATGAAGGCAATAACAATGT 57.195 36.364 0.00 0.00 41.65 2.71
3651 6560 6.980593 TCAGTTCATCCAGGTAAATTTGTTG 58.019 36.000 0.00 0.00 0.00 3.33
3807 6716 2.159352 TGTCGTCGAAGCGAATTCCATA 60.159 45.455 0.00 0.00 42.82 2.74
4040 6949 0.179032 TGTGACGCTTGGGATGTTGT 60.179 50.000 0.00 0.00 0.00 3.32
4065 6974 4.260784 CCGGTTCAAGAAAAGTCAAGTGAG 60.261 45.833 0.00 0.00 0.00 3.51
4144 7053 2.103771 AGAGAGCTGTCAACTGCAGAAA 59.896 45.455 23.35 1.59 42.33 2.52
4235 7144 5.599999 AGGCTATTCAATACACTCGAAGT 57.400 39.130 0.00 0.00 0.00 3.01
4267 7176 3.896272 TCAGATGCATCATAGCTCAGAGT 59.104 43.478 27.81 0.00 34.99 3.24
4371 7280 4.499183 CTTTCGAGCAGTTAATCTCTGGT 58.501 43.478 0.00 0.00 44.58 4.00
4420 7329 1.078567 GAGGTGGAGCTGAAGCCAG 60.079 63.158 0.00 0.00 43.38 4.85
4790 7708 9.692749 GTTCCCCTTTCTTTAATTTTTAGACAG 57.307 33.333 0.00 0.00 0.00 3.51
4906 7824 5.553290 GCTTCAAAGCCTACTAAAAGGAG 57.447 43.478 3.27 0.00 46.20 3.69
5121 8174 9.491675 TTGTTAGTCAAATCTACGACCAAAATA 57.508 29.630 0.00 0.00 32.64 1.40
5142 8195 2.785562 TGACACAAAATACGAAGGGGG 58.214 47.619 0.00 0.00 0.00 5.40
5215 8270 3.458779 TTTGTAGCGGCGAAACATTAC 57.541 42.857 12.98 3.27 0.00 1.89
5249 8341 7.819644 TGTGACATTCAATCGATTCTCATTTT 58.180 30.769 7.92 0.00 0.00 1.82
5266 8358 6.656693 TCTCATTTTCCCTTTTTGCACAAAAA 59.343 30.769 17.64 17.64 44.98 1.94
5296 8388 7.174413 TCCTTTTCCAATGTCTATCAATGTGA 58.826 34.615 0.00 0.00 0.00 3.58
5435 8527 7.112984 CCTTGTTGCGAAGTAAGACAATAAAAC 59.887 37.037 0.00 0.00 29.05 2.43
5445 8537 3.956744 AGACAATAAAACAGCTCCCTCC 58.043 45.455 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
252 254 2.399356 GGAAAGGAAAGGCGCTCGG 61.399 63.158 7.64 0.00 0.00 4.63
433 435 1.570813 GAAAACAAGCAACCACAGCC 58.429 50.000 0.00 0.00 0.00 4.85
457 459 5.187381 ACCAAATGGATGCATGTCAATAACA 59.813 36.000 2.46 0.00 39.60 2.41
463 465 2.805194 TCACCAAATGGATGCATGTCA 58.195 42.857 2.46 2.37 38.94 3.58
490 492 1.546476 CTTAACAGCTCTGACCTCGGT 59.454 52.381 3.60 0.00 0.00 4.69
492 494 2.229062 TGTCTTAACAGCTCTGACCTCG 59.771 50.000 3.60 0.00 0.00 4.63
533 550 3.168292 CCCAGGAAAATTCTTCAAGGCT 58.832 45.455 0.00 0.00 0.00 4.58
613 631 2.931512 TGTTCATCATGCATGCACAG 57.068 45.000 25.37 18.84 34.14 3.66
640 665 6.983984 TGTTCATCTGCATCAATCAAAGAAA 58.016 32.000 0.00 0.00 0.00 2.52
641 666 6.578163 TGTTCATCTGCATCAATCAAAGAA 57.422 33.333 0.00 0.00 0.00 2.52
642 667 6.578163 TTGTTCATCTGCATCAATCAAAGA 57.422 33.333 0.00 0.00 0.00 2.52
643 668 7.010183 GGAATTGTTCATCTGCATCAATCAAAG 59.990 37.037 0.00 0.00 0.00 2.77
644 669 6.814644 GGAATTGTTCATCTGCATCAATCAAA 59.185 34.615 0.00 0.00 0.00 2.69
645 670 6.153851 AGGAATTGTTCATCTGCATCAATCAA 59.846 34.615 0.00 0.00 0.00 2.57
646 671 5.655090 AGGAATTGTTCATCTGCATCAATCA 59.345 36.000 0.00 0.00 0.00 2.57
647 672 5.977725 CAGGAATTGTTCATCTGCATCAATC 59.022 40.000 0.00 0.00 0.00 2.67
690 715 2.260844 TCCTGCCAAAGAGTCTTGTG 57.739 50.000 6.06 7.06 0.00 3.33
811 3646 5.181245 GCTTTGCTAGATCCACAAACTACAA 59.819 40.000 0.00 0.00 0.00 2.41
832 3667 2.091720 TGCTGGATGGGTATCATTGCTT 60.092 45.455 0.00 0.00 35.97 3.91
992 3831 3.896888 ACCTTTGTCCATCATGAAGCAAA 59.103 39.130 0.00 8.10 0.00 3.68
1033 3872 8.683615 TGACATGTCCAAATGTACTAGTAGTAG 58.316 37.037 22.85 2.87 40.87 2.57
1034 3873 8.584063 TGACATGTCCAAATGTACTAGTAGTA 57.416 34.615 22.85 5.90 40.87 1.82
1035 3874 7.476540 TGACATGTCCAAATGTACTAGTAGT 57.523 36.000 22.85 8.14 40.87 2.73
1099 3938 0.108207 CCCTGTCCTGGAGATCATGC 59.892 60.000 0.00 0.00 0.00 4.06
1192 4032 0.319405 ATCCCTTGCTTTGCACTTGC 59.681 50.000 0.00 0.00 38.71 4.01
1193 4033 1.067354 GGATCCCTTGCTTTGCACTTG 60.067 52.381 0.00 0.00 38.71 3.16
1247 4087 2.559840 CAAGGAAGCTGCAGTGCG 59.440 61.111 16.64 6.61 38.13 5.34
1270 4110 4.227538 TCGAACAAGTAAAGAAGCGAGAG 58.772 43.478 0.00 0.00 0.00 3.20
1495 4343 3.851458 AGATTCATCACAGCATAGGCA 57.149 42.857 0.67 0.00 44.61 4.75
1541 4391 0.534203 TCCAGTTTGCGGAACAGACC 60.534 55.000 5.69 0.00 40.84 3.85
1603 4453 3.777106 TCTGAGTCATTCTTGGCTTGT 57.223 42.857 0.00 0.00 38.12 3.16
1609 4459 6.581542 GCAACAAGATTTCTGAGTCATTCTTG 59.418 38.462 21.55 21.55 43.45 3.02
1612 4462 5.397326 GGCAACAAGATTTCTGAGTCATTC 58.603 41.667 0.00 0.00 0.00 2.67
1618 4468 3.152341 ACTGGGCAACAAGATTTCTGAG 58.848 45.455 0.00 0.00 39.74 3.35
1622 4528 4.219288 AGATGAACTGGGCAACAAGATTTC 59.781 41.667 0.00 0.00 39.74 2.17
1626 4532 2.886523 CAAGATGAACTGGGCAACAAGA 59.113 45.455 0.00 0.00 39.74 3.02
1627 4533 2.624838 ACAAGATGAACTGGGCAACAAG 59.375 45.455 0.00 0.00 39.74 3.16
1632 4538 2.027192 GTCCTACAAGATGAACTGGGCA 60.027 50.000 0.00 0.00 0.00 5.36
1653 4559 6.625362 TCTACACTGATAAGAAAGAGCACAG 58.375 40.000 0.00 0.00 0.00 3.66
1654 4560 6.590234 TCTACACTGATAAGAAAGAGCACA 57.410 37.500 0.00 0.00 0.00 4.57
1655 4561 7.062839 CACTTCTACACTGATAAGAAAGAGCAC 59.937 40.741 0.00 0.00 0.00 4.40
1656 4562 7.093354 CACTTCTACACTGATAAGAAAGAGCA 58.907 38.462 0.00 0.00 0.00 4.26
1657 4563 6.035542 GCACTTCTACACTGATAAGAAAGAGC 59.964 42.308 0.00 0.00 0.00 4.09
1658 4564 7.093354 TGCACTTCTACACTGATAAGAAAGAG 58.907 38.462 0.00 0.00 0.00 2.85
1659 4565 6.993079 TGCACTTCTACACTGATAAGAAAGA 58.007 36.000 0.00 0.00 0.00 2.52
1660 4566 7.675870 GCATGCACTTCTACACTGATAAGAAAG 60.676 40.741 14.21 0.00 0.00 2.62
1663 4569 5.105187 AGCATGCACTTCTACACTGATAAGA 60.105 40.000 21.98 0.00 0.00 2.10
1664 4570 5.114780 AGCATGCACTTCTACACTGATAAG 58.885 41.667 21.98 0.00 0.00 1.73
1666 4572 4.403752 AGAGCATGCACTTCTACACTGATA 59.596 41.667 21.98 0.00 0.00 2.15
1667 4573 3.197333 AGAGCATGCACTTCTACACTGAT 59.803 43.478 21.98 0.00 0.00 2.90
1668 4574 2.564504 AGAGCATGCACTTCTACACTGA 59.435 45.455 21.98 0.00 0.00 3.41
1669 4575 2.969990 AGAGCATGCACTTCTACACTG 58.030 47.619 21.98 0.00 0.00 3.66
1670 4576 3.766591 ACTAGAGCATGCACTTCTACACT 59.233 43.478 22.83 7.97 0.00 3.55
1671 4577 4.109050 GACTAGAGCATGCACTTCTACAC 58.891 47.826 22.83 9.76 0.00 2.90
1672 4578 3.763897 TGACTAGAGCATGCACTTCTACA 59.236 43.478 22.83 14.35 0.00 2.74
1673 4579 4.377839 TGACTAGAGCATGCACTTCTAC 57.622 45.455 22.83 12.21 0.00 2.59
1674 4580 5.354767 CATTGACTAGAGCATGCACTTCTA 58.645 41.667 22.83 17.21 0.00 2.10
1675 4581 3.969287 TTGACTAGAGCATGCACTTCT 57.031 42.857 22.83 17.00 0.00 2.85
1676 4582 3.242673 GCATTGACTAGAGCATGCACTTC 60.243 47.826 22.83 15.25 35.35 3.01
1677 4583 2.681848 GCATTGACTAGAGCATGCACTT 59.318 45.455 22.83 5.97 35.35 3.16
1678 4584 2.286872 GCATTGACTAGAGCATGCACT 58.713 47.619 21.45 21.45 35.35 4.40
1679 4585 2.011947 TGCATTGACTAGAGCATGCAC 58.988 47.619 21.98 14.59 39.69 4.57
1680 4586 2.406596 TGCATTGACTAGAGCATGCA 57.593 45.000 21.98 17.72 41.91 3.96
1681 4587 2.223433 GGTTGCATTGACTAGAGCATGC 60.223 50.000 10.51 10.51 36.80 4.06
1682 4588 3.011818 TGGTTGCATTGACTAGAGCATG 58.988 45.455 0.00 0.00 36.80 4.06
1683 4589 3.354948 TGGTTGCATTGACTAGAGCAT 57.645 42.857 0.00 0.00 36.80 3.79
1684 4590 2.857186 TGGTTGCATTGACTAGAGCA 57.143 45.000 0.00 0.00 34.79 4.26
1685 4591 4.216257 TCTTTTGGTTGCATTGACTAGAGC 59.784 41.667 0.00 0.00 0.00 4.09
1686 4592 5.335191 GGTCTTTTGGTTGCATTGACTAGAG 60.335 44.000 0.00 0.00 0.00 2.43
1687 4593 4.518970 GGTCTTTTGGTTGCATTGACTAGA 59.481 41.667 0.00 0.00 0.00 2.43
1688 4594 4.613622 CGGTCTTTTGGTTGCATTGACTAG 60.614 45.833 0.00 0.00 0.00 2.57
1689 4595 3.252215 CGGTCTTTTGGTTGCATTGACTA 59.748 43.478 0.00 0.00 0.00 2.59
1690 4596 2.034558 CGGTCTTTTGGTTGCATTGACT 59.965 45.455 0.00 0.00 0.00 3.41
1691 4597 2.034053 TCGGTCTTTTGGTTGCATTGAC 59.966 45.455 0.00 0.00 0.00 3.18
1692 4598 2.302260 TCGGTCTTTTGGTTGCATTGA 58.698 42.857 0.00 0.00 0.00 2.57
1693 4599 2.791383 TCGGTCTTTTGGTTGCATTG 57.209 45.000 0.00 0.00 0.00 2.82
1694 4600 3.057315 CAGATCGGTCTTTTGGTTGCATT 60.057 43.478 0.00 0.00 30.42 3.56
1695 4601 2.489329 CAGATCGGTCTTTTGGTTGCAT 59.511 45.455 0.00 0.00 30.42 3.96
1696 4602 1.879380 CAGATCGGTCTTTTGGTTGCA 59.121 47.619 0.00 0.00 30.42 4.08
1697 4603 2.151202 TCAGATCGGTCTTTTGGTTGC 58.849 47.619 0.00 0.00 30.42 4.17
1698 4604 3.127548 CCATCAGATCGGTCTTTTGGTTG 59.872 47.826 13.38 1.42 32.74 3.77
1699 4605 3.009033 TCCATCAGATCGGTCTTTTGGTT 59.991 43.478 18.67 0.00 36.21 3.67
1700 4606 2.571653 TCCATCAGATCGGTCTTTTGGT 59.428 45.455 18.67 0.00 36.21 3.67
1701 4607 3.266510 TCCATCAGATCGGTCTTTTGG 57.733 47.619 14.89 14.89 36.16 3.28
1702 4608 4.507710 TCTTCCATCAGATCGGTCTTTTG 58.492 43.478 0.00 0.00 30.42 2.44
1703 4609 4.467795 TCTCTTCCATCAGATCGGTCTTTT 59.532 41.667 0.00 0.00 30.42 2.27
1704 4610 4.026744 TCTCTTCCATCAGATCGGTCTTT 58.973 43.478 0.00 0.00 30.42 2.52
1705 4611 3.383185 GTCTCTTCCATCAGATCGGTCTT 59.617 47.826 0.00 0.00 30.42 3.01
1706 4612 2.955660 GTCTCTTCCATCAGATCGGTCT 59.044 50.000 0.00 0.00 34.14 3.85
1707 4613 2.955660 AGTCTCTTCCATCAGATCGGTC 59.044 50.000 0.00 0.00 0.00 4.79
1708 4614 3.025322 AGTCTCTTCCATCAGATCGGT 57.975 47.619 0.00 0.00 0.00 4.69
1709 4615 4.215399 GTCTAGTCTCTTCCATCAGATCGG 59.785 50.000 0.00 0.00 0.00 4.18
1710 4616 4.819088 TGTCTAGTCTCTTCCATCAGATCG 59.181 45.833 0.00 0.00 0.00 3.69
1711 4617 6.707440 TTGTCTAGTCTCTTCCATCAGATC 57.293 41.667 0.00 0.00 0.00 2.75
1712 4618 7.040755 CGTATTGTCTAGTCTCTTCCATCAGAT 60.041 40.741 0.00 0.00 0.00 2.90
1713 4619 6.261158 CGTATTGTCTAGTCTCTTCCATCAGA 59.739 42.308 0.00 0.00 0.00 3.27
1714 4620 6.038825 ACGTATTGTCTAGTCTCTTCCATCAG 59.961 42.308 0.00 0.00 0.00 2.90
1715 4621 5.886474 ACGTATTGTCTAGTCTCTTCCATCA 59.114 40.000 0.00 0.00 0.00 3.07
1716 4622 6.380095 ACGTATTGTCTAGTCTCTTCCATC 57.620 41.667 0.00 0.00 0.00 3.51
1717 4623 6.777213 AACGTATTGTCTAGTCTCTTCCAT 57.223 37.500 0.00 0.00 0.00 3.41
1718 4624 6.585695 AAACGTATTGTCTAGTCTCTTCCA 57.414 37.500 0.00 0.00 0.00 3.53
1719 4625 7.217825 CGTTAAACGTATTGTCTAGTCTCTTCC 59.782 40.741 0.00 0.00 36.74 3.46
1720 4626 8.090845 CGTTAAACGTATTGTCTAGTCTCTTC 57.909 38.462 0.00 0.00 36.74 2.87
1744 4650 6.148270 ACACTGATTGTTGACGTATAAACG 57.852 37.500 0.00 0.00 45.54 3.60
1757 4663 6.942532 ACACTAACAATGAACACTGATTGT 57.057 33.333 0.00 0.00 43.16 2.71
1758 4664 8.087982 AGTACACTAACAATGAACACTGATTG 57.912 34.615 0.00 0.00 35.95 2.67
1759 4665 9.424319 CTAGTACACTAACAATGAACACTGATT 57.576 33.333 0.00 0.00 0.00 2.57
1765 4671 9.992910 CGTATACTAGTACACTAACAATGAACA 57.007 33.333 9.54 0.00 0.00 3.18
1791 4697 4.072131 TGCCTATTGTTGAAGAACACTCC 58.928 43.478 0.00 0.00 41.92 3.85
1913 4819 3.188873 GCAAGATGCAGATCATTAGCCTC 59.811 47.826 0.00 0.00 44.26 4.70
1929 4835 4.957954 TGGCATGATAAAAGGAAGCAAGAT 59.042 37.500 0.00 0.00 0.00 2.40
1941 4847 3.634504 AGCACATTCCTGGCATGATAAA 58.365 40.909 13.35 0.00 0.00 1.40
1970 4876 9.692325 AGATCCTTAGTCATCTGCTTAAATTTT 57.308 29.630 0.00 0.00 0.00 1.82
2136 5042 3.857157 AGACACCAGGAAAGCAAGTAA 57.143 42.857 0.00 0.00 0.00 2.24
2150 5056 0.978667 GGAGGGGAGAGGAAGACACC 60.979 65.000 0.00 0.00 0.00 4.16
2239 5145 5.163364 TGTTGATTATCAGAGGCTCCTTCTC 60.163 44.000 11.71 1.91 0.00 2.87
2248 5154 7.308435 GGACAAAGTTTGTTGATTATCAGAGG 58.692 38.462 21.70 0.00 45.52 3.69
2281 5187 6.015265 TGAGCAGTCATCAATGGAATTTTTCA 60.015 34.615 0.00 0.00 31.22 2.69
2282 5188 6.392354 TGAGCAGTCATCAATGGAATTTTTC 58.608 36.000 0.00 0.00 31.22 2.29
2296 5202 1.004044 CCTCCTTGGTTGAGCAGTCAT 59.996 52.381 0.00 0.00 30.85 3.06
2310 5216 5.125739 CGATAGTAACACTCTCAACCTCCTT 59.874 44.000 0.00 0.00 0.00 3.36
2340 5246 1.719600 CCAGTTCTCTTCTCCAAGCG 58.280 55.000 0.00 0.00 0.00 4.68
2364 5270 1.959985 CTCCTCGACATATGCTCCTGT 59.040 52.381 1.58 0.00 0.00 4.00
2371 5277 1.543802 GGGCTCTCTCCTCGACATATG 59.456 57.143 0.00 0.00 0.00 1.78
2415 5321 6.993786 TGTGACATTTGTTTCTTCACAGTA 57.006 33.333 0.00 0.00 41.20 2.74
2438 5344 2.751259 CACAGTATCAGCTGCCACAAAT 59.249 45.455 9.47 0.00 39.96 2.32
2491 5397 2.038952 TCTCTTCCCACAGTGACATTGG 59.961 50.000 0.62 0.00 0.00 3.16
2500 5406 3.200825 ACCATACCATTCTCTTCCCACAG 59.799 47.826 0.00 0.00 0.00 3.66
2514 5420 6.774673 TCTCACTAATTTGTTCACCATACCA 58.225 36.000 0.00 0.00 0.00 3.25
2516 5422 7.626452 GCCTTCTCACTAATTTGTTCACCATAC 60.626 40.741 0.00 0.00 0.00 2.39
2525 5431 4.042187 AGACCAGCCTTCTCACTAATTTGT 59.958 41.667 0.00 0.00 0.00 2.83
2531 5437 0.898320 GCAGACCAGCCTTCTCACTA 59.102 55.000 0.00 0.00 0.00 2.74
2534 5440 1.881903 CTCGCAGACCAGCCTTCTCA 61.882 60.000 0.00 0.00 0.00 3.27
2541 5447 1.396301 CTCAAATTCTCGCAGACCAGC 59.604 52.381 0.00 0.00 0.00 4.85
2545 5451 2.341257 TGCTCTCAAATTCTCGCAGAC 58.659 47.619 0.00 0.00 0.00 3.51
2843 5749 0.526211 TGTTGTCGTCATCCTCCTCG 59.474 55.000 0.00 0.00 0.00 4.63
2858 5764 4.447054 GCTTCATCATCCGAGATACTGTTG 59.553 45.833 0.00 0.00 0.00 3.33
2859 5765 4.343526 AGCTTCATCATCCGAGATACTGTT 59.656 41.667 0.00 0.00 0.00 3.16
2873 5782 2.825223 TCCTCTCCTTCAGCTTCATCA 58.175 47.619 0.00 0.00 0.00 3.07
2881 5790 3.380471 TCTCCTCTTCCTCTCCTTCAG 57.620 52.381 0.00 0.00 0.00 3.02
2909 5818 3.181462 TGACATCCTCCTGATCATTTCCG 60.181 47.826 0.00 0.00 0.00 4.30
2951 5860 0.179702 GCAGCTCCATCAGACCATCA 59.820 55.000 0.00 0.00 0.00 3.07
2985 5894 2.801111 GGTCGAGTTCAAACTTCAGGAC 59.199 50.000 0.00 3.61 39.88 3.85
3010 5919 1.251251 GGTTTGCAAGTCCATCAGCT 58.749 50.000 14.99 0.00 0.00 4.24
3014 5923 2.229792 TCAGTGGTTTGCAAGTCCATC 58.770 47.619 22.14 16.79 33.68 3.51
3030 5939 5.508489 CCTTCAATTTCTGTGTTGCATCAGT 60.508 40.000 0.00 0.00 33.89 3.41
3144 6053 3.584848 GGTATCTGGGGCAACTCTATCAT 59.415 47.826 0.00 0.00 38.64 2.45
3193 6102 3.674477 AGATCAAATAGGCTTCCCCTCT 58.326 45.455 0.00 0.00 44.96 3.69
3232 6141 3.088532 TGCAATTGACTGTTATGGTCCC 58.911 45.455 10.34 0.00 33.22 4.46
3594 6503 5.633830 TCTGAAGTGCTGGATTCATTTTC 57.366 39.130 0.00 0.00 35.04 2.29
3651 6560 9.599322 CATTATATTTATTCGTCTGAAAGCCAC 57.401 33.333 0.00 0.00 37.71 5.01
3807 6716 7.837863 TCCTGAATAACGAGTTAACTTCATCT 58.162 34.615 10.02 0.00 29.21 2.90
4040 6949 2.045561 TGACTTTTCTTGAACCGGCA 57.954 45.000 0.00 0.00 0.00 5.69
4144 7053 1.744014 CTGCAAGCTGCTGGGTTTT 59.256 52.632 1.35 0.00 45.31 2.43
4235 7144 3.961582 TGCATCTGATCCTGCACAA 57.038 47.368 9.80 0.00 43.11 3.33
4267 7176 3.557054 CCTGTACCTTGAGCAAGCTTGTA 60.557 47.826 26.55 11.62 37.11 2.41
4371 7280 3.184628 AGACATCTTCCCCTTGTCATGA 58.815 45.455 0.00 0.00 41.71 3.07
4658 7567 8.691661 TTAATGGAACTTAGCTTCAGTTTCTT 57.308 30.769 14.79 8.20 34.49 2.52
4719 7637 8.623903 TCATAATTCAAATCCAGTATTCTGCAC 58.376 33.333 0.00 0.00 40.09 4.57
4790 7708 8.571336 TCGTTACAACCCTACTATTAGCTTATC 58.429 37.037 0.00 0.00 0.00 1.75
4906 7824 7.225931 TGCATTTGGATTACTCGAGTAAATACC 59.774 37.037 34.71 32.25 42.93 2.73
5121 8174 3.245122 ACCCCCTTCGTATTTTGTGTCAT 60.245 43.478 0.00 0.00 0.00 3.06
5142 8195 1.553704 ACCTCCGTCTGGGTTATTGAC 59.446 52.381 0.00 0.00 37.00 3.18
5215 8270 6.545508 TCGATTGAATGTCACAAAATAGCAG 58.454 36.000 0.00 0.00 0.00 4.24
5266 8358 8.884124 TTGATAGACATTGGAAAAGGAGAATT 57.116 30.769 0.00 0.00 0.00 2.17
5435 8527 3.638627 GGAAAATAAATGGGAGGGAGCTG 59.361 47.826 0.00 0.00 0.00 4.24
5445 8537 9.904198 ATGTTTTAGAATGGGGAAAATAAATGG 57.096 29.630 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.