Multiple sequence alignment - TraesCS4A01G207400

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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 TraesCS4A01G207400 chr4A 100.000 3505 0 0 1 3505 500638009 500634505 0.000000e+00 6473.0
1 TraesCS4A01G207400 chr4A 79.641 167 23 6 2923 3079 68464422 68464587 3.700000e-20 110.0
2 TraesCS4A01G207400 chr4B 95.958 866 31 3 1679 2544 124503293 124502432 0.000000e+00 1402.0
3 TraesCS4A01G207400 chr4B 91.863 934 42 12 707 1615 124504237 124503313 0.000000e+00 1273.0
4 TraesCS4A01G207400 chr4B 91.722 302 21 2 3206 3505 124501373 124501074 1.950000e-112 416.0
5 TraesCS4A01G207400 chr4B 89.844 256 21 3 2657 2907 124502447 124502192 1.210000e-84 324.0
6 TraesCS4A01G207400 chr4B 83.962 106 15 1 2994 3099 644586420 644586317 2.230000e-17 100.0
7 TraesCS4A01G207400 chr4D 95.949 864 34 1 1679 2542 87954867 87954005 0.000000e+00 1400.0
8 TraesCS4A01G207400 chr4D 92.688 930 39 7 707 1615 87955814 87954893 0.000000e+00 1314.0
9 TraesCS4A01G207400 chr4D 88.372 301 33 1 3207 3505 87952419 87952119 9.250000e-96 361.0
10 TraesCS4A01G207400 chr4D 92.952 227 16 0 2703 2929 87954004 87953778 7.250000e-87 331.0
11 TraesCS4A01G207400 chr4D 89.474 209 15 2 2728 2929 87953127 87952919 1.250000e-64 257.0
12 TraesCS4A01G207400 chr2A 95.056 708 32 3 1 706 740014362 740013656 0.000000e+00 1110.0
13 TraesCS4A01G207400 chr2A 93.952 711 38 3 1 707 11259432 11258723 0.000000e+00 1070.0
14 TraesCS4A01G207400 chr2A 85.593 118 13 4 2545 2660 15029192 15029077 1.710000e-23 121.0
15 TraesCS4A01G207400 chr2A 74.205 283 54 14 1268 1545 762590676 762590944 2.230000e-17 100.0
16 TraesCS4A01G207400 chr5A 94.625 707 35 2 1 707 573059236 573059939 0.000000e+00 1092.0
17 TraesCS4A01G207400 chr5A 94.618 706 37 1 1 706 641577093 641576389 0.000000e+00 1092.0
18 TraesCS4A01G207400 chr5A 77.612 268 37 16 2841 3100 476075794 476075542 1.310000e-29 141.0
19 TraesCS4A01G207400 chr5A 87.500 56 2 2 2885 2939 421855787 421855838 3.780000e-05 60.2
20 TraesCS4A01G207400 chr3A 94.413 716 30 5 1 706 613364268 613364983 0.000000e+00 1092.0
21 TraesCS4A01G207400 chr3A 94.258 714 36 3 1 709 748203524 748204237 0.000000e+00 1086.0
22 TraesCS4A01G207400 chr3A 93.838 714 36 6 1 707 705576920 705576208 0.000000e+00 1068.0
23 TraesCS4A01G207400 chr5D 93.994 716 33 4 1 707 424890378 424889664 0.000000e+00 1075.0
24 TraesCS4A01G207400 chr5D 81.395 129 20 4 3002 3128 482561656 482561530 6.190000e-18 102.0
25 TraesCS4A01G207400 chr5D 92.000 50 4 0 2975 3024 306791207 306791256 1.750000e-08 71.3
26 TraesCS4A01G207400 chr7A 93.952 711 36 4 4 707 110870798 110870088 0.000000e+00 1068.0
27 TraesCS4A01G207400 chr7A 80.198 202 28 5 2899 3100 6609012 6608823 1.310000e-29 141.0
28 TraesCS4A01G207400 chr6D 75.451 554 110 21 1017 1560 14239482 14240019 2.700000e-61 246.0
29 TraesCS4A01G207400 chr1D 78.187 353 52 17 2847 3196 389598263 389597933 5.930000e-48 202.0
30 TraesCS4A01G207400 chr1D 74.638 414 78 18 2037 2444 345376032 345376424 1.300000e-34 158.0
31 TraesCS4A01G207400 chr1D 85.714 119 15 2 2545 2662 324754091 324754208 1.320000e-24 124.0
32 TraesCS4A01G207400 chr1D 77.253 233 33 9 2923 3142 141898406 141898631 6.150000e-23 119.0
33 TraesCS4A01G207400 chr1D 85.000 60 4 4 2881 2939 61326976 61327031 4.890000e-04 56.5
34 TraesCS4A01G207400 chr1B 74.584 421 78 19 2037 2450 465388357 465387959 1.300000e-34 158.0
35 TraesCS4A01G207400 chr1B 89.423 104 8 2 2548 2650 595691991 595691890 1.020000e-25 128.0
36 TraesCS4A01G207400 chr1B 89.706 68 6 1 2930 2997 662014725 662014791 6.230000e-13 86.1
37 TraesCS4A01G207400 chr1A 74.699 415 76 19 2037 2444 445503549 445503941 1.300000e-34 158.0
38 TraesCS4A01G207400 chr7D 77.860 271 42 13 2833 3100 626440409 626440154 6.060000e-33 152.0
39 TraesCS4A01G207400 chr3D 82.386 176 19 8 2932 3095 36572711 36572886 3.650000e-30 143.0
40 TraesCS4A01G207400 chr3D 86.066 122 12 4 2545 2665 540276052 540276169 3.670000e-25 126.0
41 TraesCS4A01G207400 chr2D 79.710 207 29 10 2973 3172 57257055 57257255 1.700000e-28 137.0
42 TraesCS4A01G207400 chr2D 73.050 282 59 11 1268 1545 381190200 381190468 2.240000e-12 84.2
43 TraesCS4A01G207400 chr7B 78.261 207 31 9 2923 3118 581317055 581316852 1.710000e-23 121.0
44 TraesCS4A01G207400 chr7B 94.286 35 2 0 2841 2875 565576171 565576137 2.000000e-03 54.7
45 TraesCS4A01G207400 chr5B 85.124 121 15 3 2545 2665 705849874 705849757 1.710000e-23 121.0
46 TraesCS4A01G207400 chr3B 75.746 268 36 19 2866 3119 167058399 167058651 1.330000e-19 108.0
47 TraesCS4A01G207400 chr6A 77.222 180 27 13 2998 3174 535981452 535981284 3.730000e-15 93.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G207400 chr4A 500634505 500638009 3504 True 6473.00 6473 100.00000 1 3505 1 chr4A.!!$R1 3504
1 TraesCS4A01G207400 chr4B 124501074 124504237 3163 True 853.75 1402 92.34675 707 3505 4 chr4B.!!$R2 2798
2 TraesCS4A01G207400 chr4D 87952119 87955814 3695 True 732.60 1400 91.88700 707 3505 5 chr4D.!!$R1 2798
3 TraesCS4A01G207400 chr2A 740013656 740014362 706 True 1110.00 1110 95.05600 1 706 1 chr2A.!!$R3 705
4 TraesCS4A01G207400 chr2A 11258723 11259432 709 True 1070.00 1070 93.95200 1 707 1 chr2A.!!$R1 706
5 TraesCS4A01G207400 chr5A 573059236 573059939 703 False 1092.00 1092 94.62500 1 707 1 chr5A.!!$F2 706
6 TraesCS4A01G207400 chr5A 641576389 641577093 704 True 1092.00 1092 94.61800 1 706 1 chr5A.!!$R2 705
7 TraesCS4A01G207400 chr3A 613364268 613364983 715 False 1092.00 1092 94.41300 1 706 1 chr3A.!!$F1 705
8 TraesCS4A01G207400 chr3A 748203524 748204237 713 False 1086.00 1086 94.25800 1 709 1 chr3A.!!$F2 708
9 TraesCS4A01G207400 chr3A 705576208 705576920 712 True 1068.00 1068 93.83800 1 707 1 chr3A.!!$R1 706
10 TraesCS4A01G207400 chr5D 424889664 424890378 714 True 1075.00 1075 93.99400 1 707 1 chr5D.!!$R1 706
11 TraesCS4A01G207400 chr7A 110870088 110870798 710 True 1068.00 1068 93.95200 4 707 1 chr7A.!!$R2 703
12 TraesCS4A01G207400 chr6D 14239482 14240019 537 False 246.00 246 75.45100 1017 1560 1 chr6D.!!$F1 543

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
593 609 0.178944 TCTCTCAACTTCCGGGGTGA 60.179 55.0 0.0 0.0 0.0 4.02 F
1040 1083 0.244178 GTGGAGGACGTGGAGAAGAC 59.756 60.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 1703 0.034186 CCCATGGAGGCACTTTGCTA 60.034 55.0 15.22 0.0 44.28 3.49 R
2618 2673 0.179084 CCGGATGTACACGCAGGATT 60.179 55.0 10.08 0.0 0.00 3.01 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
130 131 2.043248 GCCCCTCTCCCGTACAGA 60.043 66.667 0.00 0.00 0.00 3.41
302 303 0.251474 ACTATATAGTGCGGGCCGGA 60.251 55.000 29.48 24.64 34.72 5.14
315 316 2.428925 GCCGGATAGGTCGTGGGAA 61.429 63.158 5.05 0.00 43.70 3.97
330 331 0.328926 GGGAATAAACCCCACGTCCA 59.671 55.000 0.00 0.00 43.81 4.02
354 355 3.678072 GTCGTCACGATCCAAAAGAATCA 59.322 43.478 1.61 0.00 38.42 2.57
562 578 7.180408 AGTGGTAGAAGAGCTCACCTTATAAAA 59.820 37.037 17.77 0.00 32.04 1.52
565 581 8.258708 GGTAGAAGAGCTCACCTTATAAAAAGA 58.741 37.037 17.77 0.00 0.00 2.52
593 609 0.178944 TCTCTCAACTTCCGGGGTGA 60.179 55.000 0.00 0.00 0.00 4.02
601 617 2.547990 ACTTCCGGGGTGAGACTAAAT 58.452 47.619 0.00 0.00 0.00 1.40
632 648 3.005791 CACTCACTCCACTCACATGTGTA 59.994 47.826 24.63 11.15 36.30 2.90
683 700 1.290134 AGTTGGGTTTTGGGCCAAAA 58.710 45.000 34.51 34.51 40.41 2.44
726 743 9.743057 CCAACAAGTTCAATTCATAAACACTTA 57.257 29.630 0.00 0.00 0.00 2.24
746 763 6.144402 CACTTACAAAACCAAGCATCAACATC 59.856 38.462 0.00 0.00 0.00 3.06
773 793 4.094887 CCGATGTCCAAAATCAACCAGTAG 59.905 45.833 0.00 0.00 0.00 2.57
787 822 1.609555 CCAGTAGACCTATCGTGCTCC 59.390 57.143 0.00 0.00 0.00 4.70
873 909 0.951040 GCCAGACTGTAAAGCACGCT 60.951 55.000 0.93 0.00 0.00 5.07
888 924 2.919387 GCACGCTAGTAAACTGACACGA 60.919 50.000 0.00 0.00 0.00 4.35
938 981 5.476599 CCTCTTCTGCTGCTCTACATATACT 59.523 44.000 0.00 0.00 0.00 2.12
939 982 6.349280 CCTCTTCTGCTGCTCTACATATACTC 60.349 46.154 0.00 0.00 0.00 2.59
940 983 5.475220 TCTTCTGCTGCTCTACATATACTCC 59.525 44.000 0.00 0.00 0.00 3.85
981 1024 4.919168 CCATCAGTGCACAACAAATTACTG 59.081 41.667 21.04 4.26 37.47 2.74
982 1025 5.507817 CCATCAGTGCACAACAAATTACTGT 60.508 40.000 21.04 0.00 37.42 3.55
983 1026 6.293900 CCATCAGTGCACAACAAATTACTGTA 60.294 38.462 21.04 0.00 37.42 2.74
984 1027 6.055231 TCAGTGCACAACAAATTACTGTAC 57.945 37.500 21.04 0.00 37.42 2.90
1040 1083 0.244178 GTGGAGGACGTGGAGAAGAC 59.756 60.000 0.00 0.00 0.00 3.01
1444 1499 1.520787 CGGAGGTATGCCGTTCACC 60.521 63.158 0.00 0.00 43.66 4.02
1548 1603 2.270527 GAGAACCAGCTGCCCCTC 59.729 66.667 8.66 9.73 0.00 4.30
1604 1659 4.154737 GGGTGGAAAAACATCGGTAAGTAC 59.845 45.833 0.00 0.00 0.00 2.73
1615 1670 3.634504 TCGGTAAGTACAGAGCCCAATA 58.365 45.455 0.00 0.00 0.00 1.90
1616 1671 4.220724 TCGGTAAGTACAGAGCCCAATAT 58.779 43.478 0.00 0.00 0.00 1.28
1617 1672 5.387788 TCGGTAAGTACAGAGCCCAATATA 58.612 41.667 0.00 0.00 0.00 0.86
1618 1673 5.834742 TCGGTAAGTACAGAGCCCAATATAA 59.165 40.000 0.00 0.00 0.00 0.98
1619 1674 6.495872 TCGGTAAGTACAGAGCCCAATATAAT 59.504 38.462 0.00 0.00 0.00 1.28
1620 1675 6.590292 CGGTAAGTACAGAGCCCAATATAATG 59.410 42.308 0.00 0.00 0.00 1.90
1621 1676 6.879458 GGTAAGTACAGAGCCCAATATAATGG 59.121 42.308 0.00 0.00 40.35 3.16
1622 1677 6.763715 AAGTACAGAGCCCAATATAATGGA 57.236 37.500 8.51 0.00 43.54 3.41
1623 1678 6.959606 AGTACAGAGCCCAATATAATGGAT 57.040 37.500 8.51 0.00 43.54 3.41
1625 1680 7.170965 AGTACAGAGCCCAATATAATGGATTG 58.829 38.462 8.51 3.91 43.54 2.67
1627 1682 6.797707 ACAGAGCCCAATATAATGGATTGAT 58.202 36.000 8.51 0.00 43.54 2.57
1629 1684 8.563502 ACAGAGCCCAATATAATGGATTGATAT 58.436 33.333 8.51 0.00 43.54 1.63
1630 1685 9.064706 CAGAGCCCAATATAATGGATTGATATC 57.935 37.037 8.51 0.00 43.54 1.63
1632 1687 9.282569 GAGCCCAATATAATGGATTGATATCTC 57.717 37.037 8.51 0.00 43.54 2.75
1633 1688 8.784880 AGCCCAATATAATGGATTGATATCTCA 58.215 33.333 8.51 0.00 43.54 3.27
1634 1689 8.844244 GCCCAATATAATGGATTGATATCTCAC 58.156 37.037 8.51 0.00 43.54 3.51
1635 1690 9.910267 CCCAATATAATGGATTGATATCTCACA 57.090 33.333 8.51 0.00 43.54 3.58
1660 1715 6.648879 TTTTTAACTGATAGCAAAGTGCCT 57.351 33.333 0.00 0.00 46.52 4.75
1661 1716 5.880054 TTTAACTGATAGCAAAGTGCCTC 57.120 39.130 0.00 0.00 46.52 4.70
1662 1717 2.409948 ACTGATAGCAAAGTGCCTCC 57.590 50.000 0.00 0.00 46.52 4.30
1663 1718 1.630369 ACTGATAGCAAAGTGCCTCCA 59.370 47.619 0.00 0.00 46.52 3.86
1664 1719 2.240667 ACTGATAGCAAAGTGCCTCCAT 59.759 45.455 0.00 0.00 46.52 3.41
1665 1720 2.617308 CTGATAGCAAAGTGCCTCCATG 59.383 50.000 0.00 0.00 46.52 3.66
1666 1721 1.952296 GATAGCAAAGTGCCTCCATGG 59.048 52.381 4.97 4.97 46.52 3.66
1667 1722 0.034186 TAGCAAAGTGCCTCCATGGG 60.034 55.000 13.02 2.26 46.52 4.00
1668 1723 1.304381 GCAAAGTGCCTCCATGGGA 60.304 57.895 13.02 0.00 37.42 4.37
1669 1724 3.687509 AGCAAAGTGCCTCCATGGGAG 62.688 57.143 13.02 8.02 46.52 4.30
1677 1732 3.902515 CTCCATGGGAGCATACGAG 57.097 57.895 13.02 0.00 43.29 4.18
1688 1743 3.192422 GGAGCATACGAGCTACATGATCT 59.808 47.826 15.44 0.00 46.75 2.75
1693 1748 3.090952 ACGAGCTACATGATCTTGAGC 57.909 47.619 15.03 16.58 0.00 4.26
1716 1771 4.423732 CTTTGTGCTAACCATTATGTGCC 58.576 43.478 0.00 0.00 0.00 5.01
1723 1778 2.442236 ACCATTATGTGCCTCTTGGG 57.558 50.000 0.00 0.00 38.36 4.12
1741 1796 1.619332 GGGTGGCTAGACCTATGCTAC 59.381 57.143 0.00 0.00 40.22 3.58
1847 1902 1.170919 TAGACATCTACCGCCGGAGC 61.171 60.000 11.71 0.00 0.00 4.70
2444 2499 1.478510 GTCACCGACATCATCCAGACT 59.521 52.381 0.00 0.00 32.09 3.24
2447 2502 1.205655 ACCGACATCATCCAGACTGTG 59.794 52.381 0.93 0.00 0.00 3.66
2456 2511 3.513912 TCATCCAGACTGTGTATTCCGTT 59.486 43.478 0.93 0.00 0.00 4.44
2492 2547 4.870991 GTGCAGGGAAAGAGACAGTATTAC 59.129 45.833 0.00 0.00 0.00 1.89
2499 2554 5.755861 GGAAAGAGACAGTATTACAGCCATC 59.244 44.000 0.00 0.00 0.00 3.51
2501 2556 5.269505 AGAGACAGTATTACAGCCATCAC 57.730 43.478 0.00 0.00 0.00 3.06
2512 2567 2.109799 CCATCACTAGCGGGGCTG 59.890 66.667 0.00 0.00 40.10 4.85
2514 2569 1.068753 CATCACTAGCGGGGCTGAG 59.931 63.158 0.00 0.00 40.10 3.35
2531 2586 2.055042 AGCGTACCTGAGCTCCCAG 61.055 63.158 12.15 3.04 39.98 4.45
2551 2606 3.183237 GCTGTTAGCGTTACACTTTGG 57.817 47.619 0.00 0.00 0.00 3.28
2552 2607 2.664698 GCTGTTAGCGTTACACTTTGGC 60.665 50.000 0.00 0.00 0.00 4.52
2553 2608 2.806244 CTGTTAGCGTTACACTTTGGCT 59.194 45.455 0.00 0.00 37.73 4.75
2554 2609 3.207778 TGTTAGCGTTACACTTTGGCTT 58.792 40.909 0.00 0.00 35.28 4.35
2555 2610 4.378774 TGTTAGCGTTACACTTTGGCTTA 58.621 39.130 0.00 0.00 35.28 3.09
2556 2611 4.998672 TGTTAGCGTTACACTTTGGCTTAT 59.001 37.500 0.00 0.00 35.28 1.73
2557 2612 6.164876 TGTTAGCGTTACACTTTGGCTTATA 58.835 36.000 0.00 0.00 35.28 0.98
2558 2613 6.311935 TGTTAGCGTTACACTTTGGCTTATAG 59.688 38.462 0.00 0.00 35.28 1.31
2559 2614 4.189231 AGCGTTACACTTTGGCTTATAGG 58.811 43.478 0.00 0.00 0.00 2.57
2560 2615 3.937079 GCGTTACACTTTGGCTTATAGGT 59.063 43.478 0.00 0.00 0.00 3.08
2561 2616 4.201783 GCGTTACACTTTGGCTTATAGGTG 60.202 45.833 0.00 0.00 0.00 4.00
2562 2617 4.933400 CGTTACACTTTGGCTTATAGGTGT 59.067 41.667 0.00 0.00 40.34 4.16
2563 2618 6.101332 CGTTACACTTTGGCTTATAGGTGTA 58.899 40.000 0.00 0.00 38.56 2.90
2564 2619 6.255020 CGTTACACTTTGGCTTATAGGTGTAG 59.745 42.308 0.00 0.00 39.93 2.74
2565 2620 7.325694 GTTACACTTTGGCTTATAGGTGTAGA 58.674 38.462 0.00 0.00 39.93 2.59
2566 2621 6.561519 ACACTTTGGCTTATAGGTGTAGAT 57.438 37.500 0.00 0.00 36.37 1.98
2567 2622 6.349300 ACACTTTGGCTTATAGGTGTAGATG 58.651 40.000 0.00 0.00 36.37 2.90
2568 2623 5.237344 CACTTTGGCTTATAGGTGTAGATGC 59.763 44.000 0.00 0.00 0.00 3.91
2569 2624 5.104527 ACTTTGGCTTATAGGTGTAGATGCA 60.105 40.000 0.00 0.00 0.00 3.96
2570 2625 4.336889 TGGCTTATAGGTGTAGATGCAC 57.663 45.455 0.00 0.00 38.56 4.57
2579 2634 2.991250 GTGTAGATGCACCCATTGTCT 58.009 47.619 0.00 0.00 33.53 3.41
2580 2635 4.137116 GTGTAGATGCACCCATTGTCTA 57.863 45.455 0.00 0.00 33.53 2.59
2581 2636 4.513442 GTGTAGATGCACCCATTGTCTAA 58.487 43.478 0.00 0.00 33.53 2.10
2582 2637 4.941263 GTGTAGATGCACCCATTGTCTAAA 59.059 41.667 0.00 0.00 33.53 1.85
2583 2638 5.590259 GTGTAGATGCACCCATTGTCTAAAT 59.410 40.000 0.00 0.00 33.53 1.40
2584 2639 6.765989 GTGTAGATGCACCCATTGTCTAAATA 59.234 38.462 0.00 0.00 33.53 1.40
2585 2640 6.765989 TGTAGATGCACCCATTGTCTAAATAC 59.234 38.462 0.00 0.00 0.00 1.89
2586 2641 5.754782 AGATGCACCCATTGTCTAAATACA 58.245 37.500 0.00 0.00 0.00 2.29
2587 2642 6.186957 AGATGCACCCATTGTCTAAATACAA 58.813 36.000 0.00 0.00 43.16 2.41
2588 2643 6.663093 AGATGCACCCATTGTCTAAATACAAA 59.337 34.615 0.00 0.00 42.33 2.83
2589 2644 6.849085 TGCACCCATTGTCTAAATACAAAT 57.151 33.333 0.00 0.00 42.33 2.32
2590 2645 7.238486 TGCACCCATTGTCTAAATACAAATT 57.762 32.000 0.00 0.00 42.33 1.82
2591 2646 7.675062 TGCACCCATTGTCTAAATACAAATTT 58.325 30.769 0.00 0.00 42.33 1.82
2592 2647 8.153550 TGCACCCATTGTCTAAATACAAATTTT 58.846 29.630 0.00 0.00 42.33 1.82
2593 2648 9.646427 GCACCCATTGTCTAAATACAAATTTTA 57.354 29.630 0.00 0.00 42.33 1.52
2636 2691 1.651987 AAATCCTGCGTGTACATCCG 58.348 50.000 0.00 0.00 0.00 4.18
2637 2692 0.179084 AATCCTGCGTGTACATCCGG 60.179 55.000 0.00 0.00 0.00 5.14
2638 2693 1.040893 ATCCTGCGTGTACATCCGGA 61.041 55.000 6.61 6.61 0.00 5.14
2639 2694 1.518572 CCTGCGTGTACATCCGGAC 60.519 63.158 6.12 0.00 0.00 4.79
2640 2695 1.214325 CTGCGTGTACATCCGGACA 59.786 57.895 6.12 0.00 0.00 4.02
2641 2696 0.179111 CTGCGTGTACATCCGGACAT 60.179 55.000 6.12 0.00 0.00 3.06
2642 2697 0.248012 TGCGTGTACATCCGGACATT 59.752 50.000 6.12 0.00 0.00 2.71
2643 2698 1.477295 TGCGTGTACATCCGGACATTA 59.523 47.619 6.12 0.00 0.00 1.90
2644 2699 2.101750 TGCGTGTACATCCGGACATTAT 59.898 45.455 6.12 0.00 0.00 1.28
2645 2700 3.318557 TGCGTGTACATCCGGACATTATA 59.681 43.478 6.12 0.00 0.00 0.98
2646 2701 4.021807 TGCGTGTACATCCGGACATTATAT 60.022 41.667 6.12 0.00 0.00 0.86
2647 2702 5.183522 TGCGTGTACATCCGGACATTATATA 59.816 40.000 6.12 0.00 0.00 0.86
2648 2703 6.127563 TGCGTGTACATCCGGACATTATATAT 60.128 38.462 6.12 0.00 0.00 0.86
2649 2704 6.755141 GCGTGTACATCCGGACATTATATATT 59.245 38.462 6.12 0.00 0.00 1.28
2650 2705 7.277098 GCGTGTACATCCGGACATTATATATTT 59.723 37.037 6.12 0.00 0.00 1.40
2651 2706 8.592155 CGTGTACATCCGGACATTATATATTTG 58.408 37.037 6.12 0.00 0.00 2.32
2652 2707 9.431887 GTGTACATCCGGACATTATATATTTGT 57.568 33.333 6.12 5.09 0.00 2.83
2653 2708 9.430623 TGTACATCCGGACATTATATATTTGTG 57.569 33.333 6.12 0.00 0.00 3.33
2654 2709 7.377766 ACATCCGGACATTATATATTTGTGC 57.622 36.000 6.12 7.51 0.00 4.57
2655 2710 6.939730 ACATCCGGACATTATATATTTGTGCA 59.060 34.615 6.12 0.00 31.97 4.57
2656 2711 6.795098 TCCGGACATTATATATTTGTGCAC 57.205 37.500 10.75 10.75 31.97 4.57
2657 2712 5.703592 TCCGGACATTATATATTTGTGCACC 59.296 40.000 15.69 0.00 31.97 5.01
2658 2713 5.471797 CCGGACATTATATATTTGTGCACCA 59.528 40.000 15.69 0.00 31.97 4.17
2659 2714 6.016693 CCGGACATTATATATTTGTGCACCAA 60.017 38.462 15.69 10.55 31.97 3.67
2660 2715 7.421599 CGGACATTATATATTTGTGCACCAAA 58.578 34.615 15.69 14.70 46.59 3.28
2668 2723 2.414058 TTGTGCACCAAATGTTAGCG 57.586 45.000 15.69 0.00 0.00 4.26
2669 2724 1.313772 TGTGCACCAAATGTTAGCGT 58.686 45.000 15.69 0.00 0.00 5.07
2674 2729 4.147479 GTGCACCAAATGTTAGCGTTAAAC 59.853 41.667 5.22 0.00 0.00 2.01
2680 2735 6.875195 ACCAAATGTTAGCGTTAAACTAGCTA 59.125 34.615 0.00 0.00 41.88 3.32
2695 2750 7.703058 AAACTAGCTAAAATACCTGTGCATT 57.297 32.000 0.00 0.00 0.00 3.56
2696 2751 6.683974 ACTAGCTAAAATACCTGTGCATTG 57.316 37.500 0.00 0.00 0.00 2.82
2697 2752 4.376340 AGCTAAAATACCTGTGCATTGC 57.624 40.909 0.46 0.46 0.00 3.56
2698 2753 3.131046 AGCTAAAATACCTGTGCATTGCC 59.869 43.478 6.12 0.00 0.00 4.52
2699 2754 3.119173 GCTAAAATACCTGTGCATTGCCA 60.119 43.478 6.12 3.05 0.00 4.92
2700 2755 3.317603 AAAATACCTGTGCATTGCCAC 57.682 42.857 6.12 5.33 36.28 5.01
2701 2756 0.810648 AATACCTGTGCATTGCCACG 59.189 50.000 6.12 1.13 38.55 4.94
2702 2757 0.035534 ATACCTGTGCATTGCCACGA 60.036 50.000 6.12 0.00 38.55 4.35
2704 2759 1.106351 ACCTGTGCATTGCCACGAAA 61.106 50.000 6.12 0.00 38.55 3.46
2750 2810 8.768397 ACCAGGTTATTGTATATCTTGTCAGAA 58.232 33.333 0.00 0.00 30.76 3.02
2807 2867 7.642082 ATGATTCAGCAAAATTCTAGAGCTT 57.358 32.000 0.89 0.00 32.35 3.74
2875 2935 4.883083 TGTCAATCGACTGACTTTAGCTT 58.117 39.130 25.48 0.00 45.03 3.74
2878 2938 6.074005 GTCAATCGACTGACTTTAGCTTTTG 58.926 40.000 19.18 0.00 42.11 2.44
2882 2942 3.607078 CGACTGACTTTAGCTTTTGTGGC 60.607 47.826 0.00 0.00 0.00 5.01
2897 2957 1.606668 TGTGGCCAGTCGATTTTGAAC 59.393 47.619 5.11 0.00 0.00 3.18
2898 2958 1.606668 GTGGCCAGTCGATTTTGAACA 59.393 47.619 5.11 0.00 0.00 3.18
2911 2971 6.320164 TCGATTTTGAACAAAGGAAGGAGAAA 59.680 34.615 0.46 0.00 0.00 2.52
2918 2978 2.822561 CAAAGGAAGGAGAAAGAAGGGC 59.177 50.000 0.00 0.00 0.00 5.19
2933 2993 4.214327 GGCCTCGCCGGAGAGAAG 62.214 72.222 33.72 20.00 43.27 2.85
2934 2994 4.214327 GCCTCGCCGGAGAGAAGG 62.214 72.222 33.72 20.60 43.27 3.46
2935 2995 2.440430 CCTCGCCGGAGAGAAGGA 60.440 66.667 33.72 0.00 43.27 3.36
2936 2996 2.052690 CCTCGCCGGAGAGAAGGAA 61.053 63.158 33.72 0.00 43.27 3.36
2937 2997 1.435515 CTCGCCGGAGAGAAGGAAG 59.564 63.158 29.23 1.24 43.27 3.46
2938 2998 2.010582 CTCGCCGGAGAGAAGGAAGG 62.011 65.000 29.23 0.42 43.27 3.46
2939 2999 2.052690 CGCCGGAGAGAAGGAAGGA 61.053 63.158 5.05 0.00 0.00 3.36
2940 3000 1.819905 GCCGGAGAGAAGGAAGGAG 59.180 63.158 5.05 0.00 0.00 3.69
2941 3001 0.684805 GCCGGAGAGAAGGAAGGAGA 60.685 60.000 5.05 0.00 0.00 3.71
2942 3002 1.853963 CCGGAGAGAAGGAAGGAGAA 58.146 55.000 0.00 0.00 0.00 2.87
2943 3003 2.180276 CCGGAGAGAAGGAAGGAGAAA 58.820 52.381 0.00 0.00 0.00 2.52
2944 3004 2.769095 CCGGAGAGAAGGAAGGAGAAAT 59.231 50.000 0.00 0.00 0.00 2.17
2945 3005 3.961408 CCGGAGAGAAGGAAGGAGAAATA 59.039 47.826 0.00 0.00 0.00 1.40
2946 3006 4.406003 CCGGAGAGAAGGAAGGAGAAATAA 59.594 45.833 0.00 0.00 0.00 1.40
2947 3007 5.452636 CCGGAGAGAAGGAAGGAGAAATAAG 60.453 48.000 0.00 0.00 0.00 1.73
2948 3008 5.452636 CGGAGAGAAGGAAGGAGAAATAAGG 60.453 48.000 0.00 0.00 0.00 2.69
2949 3009 5.163248 GGAGAGAAGGAAGGAGAAATAAGGG 60.163 48.000 0.00 0.00 0.00 3.95
2950 3010 4.724293 AGAGAAGGAAGGAGAAATAAGGGG 59.276 45.833 0.00 0.00 0.00 4.79
2951 3011 3.203263 AGAAGGAAGGAGAAATAAGGGGC 59.797 47.826 0.00 0.00 0.00 5.80
2952 3012 2.865199 AGGAAGGAGAAATAAGGGGCT 58.135 47.619 0.00 0.00 0.00 5.19
2953 3013 2.780592 AGGAAGGAGAAATAAGGGGCTC 59.219 50.000 0.00 0.00 0.00 4.70
2954 3014 2.509964 GGAAGGAGAAATAAGGGGCTCA 59.490 50.000 0.00 0.00 0.00 4.26
2955 3015 3.546724 GAAGGAGAAATAAGGGGCTCAC 58.453 50.000 0.00 0.00 0.00 3.51
2956 3016 2.852130 AGGAGAAATAAGGGGCTCACT 58.148 47.619 0.00 0.00 0.00 3.41
2957 3017 2.507471 AGGAGAAATAAGGGGCTCACTG 59.493 50.000 0.00 0.00 0.00 3.66
2958 3018 2.422093 GGAGAAATAAGGGGCTCACTGG 60.422 54.545 0.00 0.00 0.00 4.00
2959 3019 2.505819 GAGAAATAAGGGGCTCACTGGA 59.494 50.000 0.00 0.00 0.00 3.86
2960 3020 2.507471 AGAAATAAGGGGCTCACTGGAG 59.493 50.000 0.00 0.00 44.33 3.86
2961 3021 1.216990 AATAAGGGGCTCACTGGAGG 58.783 55.000 0.00 0.00 41.67 4.30
2962 3022 0.695803 ATAAGGGGCTCACTGGAGGG 60.696 60.000 0.00 0.00 41.67 4.30
2965 3025 2.365635 GGGCTCACTGGAGGGCTA 60.366 66.667 0.00 0.00 41.67 3.93
2966 3026 2.736826 GGGCTCACTGGAGGGCTAC 61.737 68.421 0.00 0.00 41.67 3.58
2967 3027 2.736826 GGCTCACTGGAGGGCTACC 61.737 68.421 0.00 0.00 41.67 3.18
2984 3044 7.129425 AGGGCTACCTCATTATCTATCTTAGG 58.871 42.308 0.00 0.00 46.95 2.69
2991 3051 9.327731 ACCTCATTATCTATCTTAGGGTTTAGG 57.672 37.037 0.00 0.00 0.00 2.69
2992 3052 8.261522 CCTCATTATCTATCTTAGGGTTTAGGC 58.738 40.741 0.00 0.00 0.00 3.93
2993 3053 8.974292 TCATTATCTATCTTAGGGTTTAGGCT 57.026 34.615 0.00 0.00 0.00 4.58
2999 3059 1.577291 TTAGGGTTTAGGCTGGGGGC 61.577 60.000 0.00 0.00 40.90 5.80
3000 3060 4.815108 GGGTTTAGGCTGGGGGCG 62.815 72.222 0.00 0.00 42.94 6.13
3001 3061 4.815108 GGTTTAGGCTGGGGGCGG 62.815 72.222 0.00 0.00 42.94 6.13
3002 3062 4.043100 GTTTAGGCTGGGGGCGGT 62.043 66.667 0.00 0.00 42.94 5.68
3003 3063 4.041762 TTTAGGCTGGGGGCGGTG 62.042 66.667 0.00 0.00 42.94 4.94
3030 3354 3.948719 GGTGGTGGGGCTTCGTCA 61.949 66.667 0.00 0.00 0.00 4.35
3073 3397 3.631046 GCTAGAGGGATGGCCGGG 61.631 72.222 2.18 0.00 33.83 5.73
3099 3423 4.388499 CAAGACCGACGGTGGGGG 62.388 72.222 27.26 7.23 35.25 5.40
3100 3424 4.626402 AAGACCGACGGTGGGGGA 62.626 66.667 27.26 0.00 35.25 4.81
3106 3430 3.396570 GACGGTGGGGGACGGATT 61.397 66.667 0.00 0.00 0.00 3.01
3108 3432 2.024590 GACGGTGGGGGACGGATTAG 62.025 65.000 0.00 0.00 0.00 1.73
3113 4147 0.105658 TGGGGGACGGATTAGAGGAG 60.106 60.000 0.00 0.00 0.00 3.69
3116 4150 1.473497 GGGACGGATTAGAGGAGGGC 61.473 65.000 0.00 0.00 0.00 5.19
3118 4152 1.807495 GACGGATTAGAGGAGGGCGG 61.807 65.000 0.00 0.00 0.00 6.13
3188 4300 3.046870 GCATGTTTGCCGGTGGAA 58.953 55.556 1.90 0.00 43.38 3.53
3189 4301 1.080569 GCATGTTTGCCGGTGGAAG 60.081 57.895 1.90 0.00 43.38 3.46
3191 4303 0.958091 CATGTTTGCCGGTGGAAGAA 59.042 50.000 1.90 0.00 0.00 2.52
3192 4304 1.068333 CATGTTTGCCGGTGGAAGAAG 60.068 52.381 1.90 0.00 0.00 2.85
3193 4305 0.181587 TGTTTGCCGGTGGAAGAAGA 59.818 50.000 1.90 0.00 0.00 2.87
3194 4306 1.314730 GTTTGCCGGTGGAAGAAGAA 58.685 50.000 1.90 0.00 0.00 2.52
3197 4309 0.762418 TGCCGGTGGAAGAAGAAGAA 59.238 50.000 1.90 0.00 0.00 2.52
3199 4311 1.270893 GCCGGTGGAAGAAGAAGAAGT 60.271 52.381 1.90 0.00 0.00 3.01
3200 4312 2.689646 CCGGTGGAAGAAGAAGAAGTC 58.310 52.381 0.00 0.00 0.00 3.01
3201 4313 2.300437 CCGGTGGAAGAAGAAGAAGTCT 59.700 50.000 0.00 0.00 38.69 3.24
3203 4315 4.381079 CCGGTGGAAGAAGAAGAAGTCTAG 60.381 50.000 0.00 0.00 34.56 2.43
3204 4316 4.459685 CGGTGGAAGAAGAAGAAGTCTAGA 59.540 45.833 0.00 0.00 34.56 2.43
3235 4691 1.298859 CTTTCTTCCCGCCACTTCCG 61.299 60.000 0.00 0.00 0.00 4.30
3236 4692 1.760479 TTTCTTCCCGCCACTTCCGA 61.760 55.000 0.00 0.00 0.00 4.55
3264 4720 2.362369 CCCCTGCTCATCTGACGGT 61.362 63.158 0.00 0.00 0.00 4.83
3271 4727 4.457496 CATCTGACGGTGCCGCCT 62.457 66.667 10.87 0.00 44.19 5.52
3272 4728 3.706373 ATCTGACGGTGCCGCCTT 61.706 61.111 10.87 0.00 44.19 4.35
3273 4729 3.665675 ATCTGACGGTGCCGCCTTC 62.666 63.158 10.87 1.75 44.19 3.46
3343 4799 3.853330 CCGATTGTGACTGCGGCG 61.853 66.667 0.51 0.51 37.08 6.46
3386 4842 0.474184 GCAATGCCTTCCCTAGCCTA 59.526 55.000 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 0.613777 GAACCCCACCTCTCGTGATT 59.386 55.000 0.00 0.00 46.20 2.57
266 267 2.569183 GTCAGGCAGACGTCTACCT 58.431 57.895 28.51 28.51 40.34 3.08
302 303 3.851458 GGGTTTATTCCCACGACCTAT 57.149 47.619 0.00 0.00 46.30 2.57
315 316 1.338389 CGACTTGGACGTGGGGTTTAT 60.338 52.381 0.00 0.00 0.00 1.40
330 331 3.380479 TCTTTTGGATCGTGACGACTT 57.620 42.857 10.91 0.00 39.18 3.01
354 355 4.905295 CGCGTTAATTACTGAACCGTTTTT 59.095 37.500 0.00 0.00 0.00 1.94
562 578 6.349777 CGGAAGTTGAGAGAGAGTTGTATCTT 60.350 42.308 0.00 0.00 0.00 2.40
565 581 4.158764 CCGGAAGTTGAGAGAGAGTTGTAT 59.841 45.833 0.00 0.00 0.00 2.29
567 583 2.297597 CCGGAAGTTGAGAGAGAGTTGT 59.702 50.000 0.00 0.00 0.00 3.32
593 609 7.010339 AGTGAGTGAGGCTAAAATTTAGTCT 57.990 36.000 18.58 18.58 31.26 3.24
601 617 2.972713 AGTGGAGTGAGTGAGGCTAAAA 59.027 45.455 0.00 0.00 0.00 1.52
632 648 2.905415 TTCTCTTGGCCCATTCATGT 57.095 45.000 0.00 0.00 0.00 3.21
683 700 4.662278 TGTTGGAATTTTGCTAGTAGGCT 58.338 39.130 0.00 0.00 0.00 4.58
726 743 4.669206 TGATGTTGATGCTTGGTTTTGT 57.331 36.364 0.00 0.00 0.00 2.83
727 744 4.211794 GGTTGATGTTGATGCTTGGTTTTG 59.788 41.667 0.00 0.00 0.00 2.44
746 763 3.574614 GTTGATTTTGGACATCGGGTTG 58.425 45.455 0.00 0.00 0.00 3.77
787 822 4.884247 AGGAAGAGAAAAGTGGAGTAACG 58.116 43.478 0.00 0.00 0.00 3.18
873 909 5.575606 GCTTGCTTATCGTGTCAGTTTACTA 59.424 40.000 0.00 0.00 0.00 1.82
938 981 1.517361 CGCATGGCACTGTAGAGGA 59.483 57.895 0.00 0.00 0.00 3.71
939 982 2.176273 GCGCATGGCACTGTAGAGG 61.176 63.158 0.30 0.00 42.87 3.69
940 983 2.176273 GGCGCATGGCACTGTAGAG 61.176 63.158 10.83 0.00 46.16 2.43
981 1024 4.634443 ACCATGGCGATTTCAACTAAGTAC 59.366 41.667 13.04 0.00 0.00 2.73
982 1025 4.839121 ACCATGGCGATTTCAACTAAGTA 58.161 39.130 13.04 0.00 0.00 2.24
983 1026 3.686016 ACCATGGCGATTTCAACTAAGT 58.314 40.909 13.04 0.00 0.00 2.24
984 1027 4.155826 TCAACCATGGCGATTTCAACTAAG 59.844 41.667 13.04 0.00 0.00 2.18
995 1038 1.003839 GTCACCTCAACCATGGCGA 60.004 57.895 13.04 8.06 0.00 5.54
1440 1495 3.755628 GGCGCGTAGTCTGGGTGA 61.756 66.667 8.43 0.00 0.00 4.02
1444 1499 2.813908 GTTGGGCGCGTAGTCTGG 60.814 66.667 8.43 0.00 0.00 3.86
1548 1603 1.142748 GATCCTGTGGAGCACGAGG 59.857 63.158 0.00 0.00 38.12 4.63
1581 1636 3.151554 ACTTACCGATGTTTTTCCACCC 58.848 45.455 0.00 0.00 0.00 4.61
1604 1659 8.991783 ATATCAATCCATTATATTGGGCTCTG 57.008 34.615 12.61 6.42 37.37 3.35
1639 1694 4.700213 GGAGGCACTTTGCTATCAGTTAAA 59.300 41.667 0.00 0.00 44.28 1.52
1640 1695 4.261801 GGAGGCACTTTGCTATCAGTTAA 58.738 43.478 0.00 0.00 44.28 2.01
1641 1696 3.263170 TGGAGGCACTTTGCTATCAGTTA 59.737 43.478 0.00 0.00 44.28 2.24
1642 1697 2.040278 TGGAGGCACTTTGCTATCAGTT 59.960 45.455 0.00 0.00 44.28 3.16
1643 1698 1.630369 TGGAGGCACTTTGCTATCAGT 59.370 47.619 0.00 0.00 44.28 3.41
1644 1699 2.408271 TGGAGGCACTTTGCTATCAG 57.592 50.000 0.00 0.00 44.28 2.90
1645 1700 2.646930 CATGGAGGCACTTTGCTATCA 58.353 47.619 0.00 0.00 44.28 2.15
1646 1701 1.952296 CCATGGAGGCACTTTGCTATC 59.048 52.381 5.56 0.00 44.28 2.08
1647 1702 1.410648 CCCATGGAGGCACTTTGCTAT 60.411 52.381 15.22 0.00 44.28 2.97
1648 1703 0.034186 CCCATGGAGGCACTTTGCTA 60.034 55.000 15.22 0.00 44.28 3.49
1649 1704 1.304713 CCCATGGAGGCACTTTGCT 60.305 57.895 15.22 0.00 44.28 3.91
1650 1705 1.304381 TCCCATGGAGGCACTTTGC 60.304 57.895 15.22 0.00 41.55 3.68
1651 1706 2.877975 CTCCCATGGAGGCACTTTG 58.122 57.895 15.22 0.00 45.43 2.77
1660 1715 0.760567 AGCTCGTATGCTCCCATGGA 60.761 55.000 15.22 0.00 39.34 3.41
1661 1716 0.969149 TAGCTCGTATGCTCCCATGG 59.031 55.000 4.14 4.14 42.97 3.66
1662 1717 1.341209 TGTAGCTCGTATGCTCCCATG 59.659 52.381 0.00 0.00 42.97 3.66
1663 1718 1.704641 TGTAGCTCGTATGCTCCCAT 58.295 50.000 0.00 0.00 42.97 4.00
1664 1719 1.341209 CATGTAGCTCGTATGCTCCCA 59.659 52.381 0.00 3.98 42.97 4.37
1665 1720 1.613925 TCATGTAGCTCGTATGCTCCC 59.386 52.381 0.00 0.00 42.97 4.30
1666 1721 3.192422 AGATCATGTAGCTCGTATGCTCC 59.808 47.826 0.00 0.00 42.97 4.70
1667 1722 4.433186 AGATCATGTAGCTCGTATGCTC 57.567 45.455 0.00 0.00 42.97 4.26
1668 1723 4.279420 TCAAGATCATGTAGCTCGTATGCT 59.721 41.667 0.00 5.77 46.11 3.79
1669 1724 4.550422 TCAAGATCATGTAGCTCGTATGC 58.450 43.478 0.00 0.00 0.00 3.14
1670 1725 4.620609 GCTCAAGATCATGTAGCTCGTATG 59.379 45.833 12.25 0.00 0.00 2.39
1671 1726 4.321601 GGCTCAAGATCATGTAGCTCGTAT 60.322 45.833 16.42 0.00 33.67 3.06
1672 1727 3.004839 GGCTCAAGATCATGTAGCTCGTA 59.995 47.826 16.42 0.00 33.67 3.43
1673 1728 2.223923 GGCTCAAGATCATGTAGCTCGT 60.224 50.000 16.42 0.00 33.67 4.18
1674 1729 2.035704 AGGCTCAAGATCATGTAGCTCG 59.964 50.000 16.42 0.00 33.67 5.03
1675 1730 3.749665 AGGCTCAAGATCATGTAGCTC 57.250 47.619 16.42 10.15 33.67 4.09
1676 1731 4.197750 CAAAGGCTCAAGATCATGTAGCT 58.802 43.478 16.42 0.00 33.67 3.32
1677 1732 3.944015 ACAAAGGCTCAAGATCATGTAGC 59.056 43.478 11.50 11.50 0.00 3.58
1688 1743 2.356665 TGGTTAGCACAAAGGCTCAA 57.643 45.000 0.00 0.00 44.54 3.02
1693 1748 4.423732 GCACATAATGGTTAGCACAAAGG 58.576 43.478 0.00 0.00 0.00 3.11
1716 1771 2.160721 TAGGTCTAGCCACCCAAGAG 57.839 55.000 6.07 0.00 40.61 2.85
1723 1778 2.228059 TCGTAGCATAGGTCTAGCCAC 58.772 52.381 6.07 0.00 40.61 5.01
1741 1796 1.293924 GAGCACCATCCTGTTGATCG 58.706 55.000 0.00 0.00 0.00 3.69
1760 1815 2.133742 CTGCCACGCCAAGGAAGTTG 62.134 60.000 0.00 0.00 35.71 3.16
1829 1884 2.491022 GCTCCGGCGGTAGATGTCT 61.491 63.158 27.32 0.00 0.00 3.41
1847 1902 0.815734 CGGTGGTGTGGAGTAGTAGG 59.184 60.000 0.00 0.00 0.00 3.18
1859 1914 3.596066 CTCTGTCCTGCCGGTGGTG 62.596 68.421 1.90 2.10 0.00 4.17
2126 2181 1.746727 CGACGCTCCGCATGAAGAAG 61.747 60.000 0.00 0.00 0.00 2.85
2178 2233 4.891727 CCGGACGATCCCCTTGCG 62.892 72.222 0.00 0.00 31.13 4.85
2492 2547 2.109799 CCCCGCTAGTGATGGCTG 59.890 66.667 4.44 0.00 0.00 4.85
2499 2554 4.880537 CGCTCAGCCCCGCTAGTG 62.881 72.222 0.00 0.00 36.40 2.74
2501 2556 3.217017 TACGCTCAGCCCCGCTAG 61.217 66.667 0.00 0.00 36.40 3.42
2514 2569 2.496817 CTGGGAGCTCAGGTACGC 59.503 66.667 17.19 0.00 0.00 4.42
2531 2586 2.664698 GCCAAAGTGTAACGCTAACAGC 60.665 50.000 0.00 0.00 45.86 4.40
2542 2597 7.497595 CATCTACACCTATAAGCCAAAGTGTA 58.502 38.462 0.00 0.00 39.12 2.90
2543 2598 6.349300 CATCTACACCTATAAGCCAAAGTGT 58.651 40.000 0.00 0.00 41.12 3.55
2544 2599 5.237344 GCATCTACACCTATAAGCCAAAGTG 59.763 44.000 0.00 0.00 0.00 3.16
2545 2600 5.104527 TGCATCTACACCTATAAGCCAAAGT 60.105 40.000 0.00 0.00 0.00 2.66
2546 2601 5.237344 GTGCATCTACACCTATAAGCCAAAG 59.763 44.000 0.00 0.00 34.35 2.77
2547 2602 5.123227 GTGCATCTACACCTATAAGCCAAA 58.877 41.667 0.00 0.00 34.35 3.28
2548 2603 4.703897 GTGCATCTACACCTATAAGCCAA 58.296 43.478 0.00 0.00 34.35 4.52
2549 2604 4.336889 GTGCATCTACACCTATAAGCCA 57.663 45.455 0.00 0.00 34.35 4.75
2559 2614 2.991250 AGACAATGGGTGCATCTACAC 58.009 47.619 0.00 0.00 39.94 2.90
2560 2615 4.835284 TTAGACAATGGGTGCATCTACA 57.165 40.909 0.00 0.00 0.00 2.74
2561 2616 6.765989 TGTATTTAGACAATGGGTGCATCTAC 59.234 38.462 0.00 0.00 0.00 2.59
2562 2617 6.894682 TGTATTTAGACAATGGGTGCATCTA 58.105 36.000 0.00 0.00 0.00 1.98
2563 2618 5.754782 TGTATTTAGACAATGGGTGCATCT 58.245 37.500 0.00 0.00 0.00 2.90
2564 2619 6.449635 TTGTATTTAGACAATGGGTGCATC 57.550 37.500 0.00 0.00 34.40 3.91
2565 2620 6.849085 TTTGTATTTAGACAATGGGTGCAT 57.151 33.333 0.00 0.00 39.04 3.96
2566 2621 6.849085 ATTTGTATTTAGACAATGGGTGCA 57.151 33.333 0.00 0.00 39.04 4.57
2567 2622 8.546597 AAAATTTGTATTTAGACAATGGGTGC 57.453 30.769 0.00 0.00 39.04 5.01
2615 2670 2.418628 CGGATGTACACGCAGGATTTTT 59.581 45.455 0.00 0.00 0.00 1.94
2616 2671 2.006888 CGGATGTACACGCAGGATTTT 58.993 47.619 0.00 0.00 0.00 1.82
2617 2672 1.651987 CGGATGTACACGCAGGATTT 58.348 50.000 0.00 0.00 0.00 2.17
2618 2673 0.179084 CCGGATGTACACGCAGGATT 60.179 55.000 10.08 0.00 0.00 3.01
2619 2674 1.040893 TCCGGATGTACACGCAGGAT 61.041 55.000 13.13 0.00 0.00 3.24
2620 2675 1.679641 TCCGGATGTACACGCAGGA 60.680 57.895 13.13 13.13 0.00 3.86
2621 2676 1.518572 GTCCGGATGTACACGCAGG 60.519 63.158 7.81 3.96 0.00 4.85
2622 2677 0.179111 ATGTCCGGATGTACACGCAG 60.179 55.000 7.81 0.00 0.00 5.18
2623 2678 0.248012 AATGTCCGGATGTACACGCA 59.752 50.000 7.81 0.00 0.00 5.24
2624 2679 2.212869 TAATGTCCGGATGTACACGC 57.787 50.000 7.81 0.00 0.00 5.34
2625 2680 8.592155 CAAATATATAATGTCCGGATGTACACG 58.408 37.037 7.81 0.00 0.00 4.49
2626 2681 9.431887 ACAAATATATAATGTCCGGATGTACAC 57.568 33.333 7.81 0.00 0.00 2.90
2627 2682 9.430623 CACAAATATATAATGTCCGGATGTACA 57.569 33.333 7.81 0.55 0.00 2.90
2628 2683 8.388103 GCACAAATATATAATGTCCGGATGTAC 58.612 37.037 7.81 0.00 0.00 2.90
2629 2684 8.097662 TGCACAAATATATAATGTCCGGATGTA 58.902 33.333 7.81 0.08 0.00 2.29
2630 2685 6.939730 TGCACAAATATATAATGTCCGGATGT 59.060 34.615 7.81 0.00 0.00 3.06
2631 2686 7.243487 GTGCACAAATATATAATGTCCGGATG 58.757 38.462 13.17 0.00 0.00 3.51
2632 2687 6.374333 GGTGCACAAATATATAATGTCCGGAT 59.626 38.462 20.43 0.00 0.00 4.18
2633 2688 5.703592 GGTGCACAAATATATAATGTCCGGA 59.296 40.000 20.43 0.00 0.00 5.14
2634 2689 5.471797 TGGTGCACAAATATATAATGTCCGG 59.528 40.000 20.43 0.00 0.00 5.14
2635 2690 6.552859 TGGTGCACAAATATATAATGTCCG 57.447 37.500 20.43 0.00 0.00 4.79
2649 2704 1.678627 ACGCTAACATTTGGTGCACAA 59.321 42.857 20.43 3.78 37.28 3.33
2650 2705 1.313772 ACGCTAACATTTGGTGCACA 58.686 45.000 20.43 1.62 0.00 4.57
2651 2706 2.415697 AACGCTAACATTTGGTGCAC 57.584 45.000 8.80 8.80 0.00 4.57
2652 2707 4.036971 AGTTTAACGCTAACATTTGGTGCA 59.963 37.500 0.00 0.00 0.00 4.57
2653 2708 4.542735 AGTTTAACGCTAACATTTGGTGC 58.457 39.130 0.00 0.00 0.00 5.01
2654 2709 5.793457 GCTAGTTTAACGCTAACATTTGGTG 59.207 40.000 0.00 0.00 0.00 4.17
2655 2710 5.704053 AGCTAGTTTAACGCTAACATTTGGT 59.296 36.000 0.00 0.00 31.12 3.67
2656 2711 6.178239 AGCTAGTTTAACGCTAACATTTGG 57.822 37.500 0.00 0.00 31.12 3.28
2657 2712 9.601971 TTTTAGCTAGTTTAACGCTAACATTTG 57.398 29.630 13.99 0.00 43.55 2.32
2661 2716 8.872845 GGTATTTTAGCTAGTTTAACGCTAACA 58.127 33.333 13.99 10.04 43.55 2.41
2662 2717 9.091784 AGGTATTTTAGCTAGTTTAACGCTAAC 57.908 33.333 13.99 6.52 43.55 2.34
2663 2718 9.090692 CAGGTATTTTAGCTAGTTTAACGCTAA 57.909 33.333 11.47 11.47 42.55 3.09
2664 2719 8.253113 ACAGGTATTTTAGCTAGTTTAACGCTA 58.747 33.333 0.00 1.57 34.67 4.26
2665 2720 7.064253 CACAGGTATTTTAGCTAGTTTAACGCT 59.936 37.037 3.30 3.30 34.67 5.07
2666 2721 7.178074 CACAGGTATTTTAGCTAGTTTAACGC 58.822 38.462 0.00 0.00 34.67 4.84
2667 2722 7.148540 TGCACAGGTATTTTAGCTAGTTTAACG 60.149 37.037 0.00 0.00 34.67 3.18
2668 2723 8.036273 TGCACAGGTATTTTAGCTAGTTTAAC 57.964 34.615 0.00 0.00 34.67 2.01
2669 2724 8.801882 ATGCACAGGTATTTTAGCTAGTTTAA 57.198 30.769 0.00 0.00 34.67 1.52
2674 2729 5.506317 GGCAATGCACAGGTATTTTAGCTAG 60.506 44.000 7.79 0.00 34.67 3.42
2680 2735 2.352617 CGTGGCAATGCACAGGTATTTT 60.353 45.455 7.79 0.00 0.00 1.82
2687 2742 2.095314 TGTATTTCGTGGCAATGCACAG 60.095 45.455 7.79 0.00 0.00 3.66
2695 2750 3.472652 ACTTCACTTGTATTTCGTGGCA 58.527 40.909 0.00 0.00 0.00 4.92
2696 2751 4.433805 CGTACTTCACTTGTATTTCGTGGC 60.434 45.833 0.00 0.00 0.00 5.01
2697 2752 4.919168 TCGTACTTCACTTGTATTTCGTGG 59.081 41.667 0.00 0.00 0.00 4.94
2698 2753 5.854866 TCTCGTACTTCACTTGTATTTCGTG 59.145 40.000 0.00 0.00 0.00 4.35
2699 2754 5.855395 GTCTCGTACTTCACTTGTATTTCGT 59.145 40.000 0.00 0.00 0.00 3.85
2700 2755 5.854866 TGTCTCGTACTTCACTTGTATTTCG 59.145 40.000 0.00 0.00 0.00 3.46
2701 2756 6.089150 GGTGTCTCGTACTTCACTTGTATTTC 59.911 42.308 0.00 0.00 0.00 2.17
2702 2757 5.924825 GGTGTCTCGTACTTCACTTGTATTT 59.075 40.000 0.00 0.00 0.00 1.40
2704 2759 4.521639 TGGTGTCTCGTACTTCACTTGTAT 59.478 41.667 0.00 0.00 0.00 2.29
2750 2810 4.928661 GTTGTGATCAACGCATCTAAGT 57.071 40.909 0.00 0.00 43.23 2.24
2781 2841 7.705214 AGCTCTAGAATTTTGCTGAATCATTC 58.295 34.615 2.83 0.00 32.32 2.67
2807 2867 3.141398 CCTTGTTTGTAAGCTCTCTGCA 58.859 45.455 0.00 0.00 45.94 4.41
2875 2935 2.302260 TCAAAATCGACTGGCCACAAA 58.698 42.857 0.00 0.00 0.00 2.83
2878 2938 1.606668 TGTTCAAAATCGACTGGCCAC 59.393 47.619 0.00 0.00 0.00 5.01
2882 2942 4.829064 TCCTTTGTTCAAAATCGACTGG 57.171 40.909 0.00 0.00 0.00 4.00
2897 2957 2.822561 GCCCTTCTTTCTCCTTCCTTTG 59.177 50.000 0.00 0.00 0.00 2.77
2898 2958 2.225142 GGCCCTTCTTTCTCCTTCCTTT 60.225 50.000 0.00 0.00 0.00 3.11
2918 2978 2.010582 CTTCCTTCTCTCCGGCGAGG 62.011 65.000 20.95 6.02 42.97 4.63
2929 2989 3.203263 GCCCCTTATTTCTCCTTCCTTCT 59.797 47.826 0.00 0.00 0.00 2.85
2931 2991 3.202211 AGCCCCTTATTTCTCCTTCCTT 58.798 45.455 0.00 0.00 0.00 3.36
2932 2992 2.780592 GAGCCCCTTATTTCTCCTTCCT 59.219 50.000 0.00 0.00 0.00 3.36
2933 2993 2.509964 TGAGCCCCTTATTTCTCCTTCC 59.490 50.000 0.00 0.00 0.00 3.46
2934 2994 3.201045 AGTGAGCCCCTTATTTCTCCTTC 59.799 47.826 0.00 0.00 0.00 3.46
2935 2995 3.054065 CAGTGAGCCCCTTATTTCTCCTT 60.054 47.826 0.00 0.00 0.00 3.36
2936 2996 2.507471 CAGTGAGCCCCTTATTTCTCCT 59.493 50.000 0.00 0.00 0.00 3.69
2937 2997 2.422093 CCAGTGAGCCCCTTATTTCTCC 60.422 54.545 0.00 0.00 0.00 3.71
2938 2998 2.505819 TCCAGTGAGCCCCTTATTTCTC 59.494 50.000 0.00 0.00 0.00 2.87
2939 2999 2.507471 CTCCAGTGAGCCCCTTATTTCT 59.493 50.000 0.00 0.00 0.00 2.52
2940 3000 2.422093 CCTCCAGTGAGCCCCTTATTTC 60.422 54.545 0.00 0.00 37.29 2.17
2941 3001 1.566231 CCTCCAGTGAGCCCCTTATTT 59.434 52.381 0.00 0.00 37.29 1.40
2942 3002 1.216990 CCTCCAGTGAGCCCCTTATT 58.783 55.000 0.00 0.00 37.29 1.40
2943 3003 0.695803 CCCTCCAGTGAGCCCCTTAT 60.696 60.000 0.00 0.00 37.29 1.73
2944 3004 1.306997 CCCTCCAGTGAGCCCCTTA 60.307 63.158 0.00 0.00 37.29 2.69
2945 3005 2.612115 CCCTCCAGTGAGCCCCTT 60.612 66.667 0.00 0.00 37.29 3.95
2948 3008 2.365635 TAGCCCTCCAGTGAGCCC 60.366 66.667 0.00 0.00 37.29 5.19
2949 3009 2.736826 GGTAGCCCTCCAGTGAGCC 61.737 68.421 0.00 0.00 37.29 4.70
2950 3010 1.687493 AGGTAGCCCTCCAGTGAGC 60.687 63.158 0.00 0.00 35.62 4.26
2951 3011 4.796408 AGGTAGCCCTCCAGTGAG 57.204 61.111 0.00 0.00 35.62 3.51
2959 3019 7.129425 CCTAAGATAGATAATGAGGTAGCCCT 58.871 42.308 0.00 0.00 46.66 5.19
2960 3020 6.325286 CCCTAAGATAGATAATGAGGTAGCCC 59.675 46.154 0.00 0.00 0.00 5.19
2961 3021 6.898521 ACCCTAAGATAGATAATGAGGTAGCC 59.101 42.308 0.00 0.00 0.00 3.93
2962 3022 7.964666 ACCCTAAGATAGATAATGAGGTAGC 57.035 40.000 0.00 0.00 0.00 3.58
2965 3025 9.327731 CCTAAACCCTAAGATAGATAATGAGGT 57.672 37.037 0.00 0.00 0.00 3.85
2966 3026 8.261522 GCCTAAACCCTAAGATAGATAATGAGG 58.738 40.741 0.00 0.00 0.00 3.86
2967 3027 9.041354 AGCCTAAACCCTAAGATAGATAATGAG 57.959 37.037 0.00 0.00 0.00 2.90
2968 3028 8.816894 CAGCCTAAACCCTAAGATAGATAATGA 58.183 37.037 0.00 0.00 0.00 2.57
2984 3044 4.815108 CCGCCCCCAGCCTAAACC 62.815 72.222 0.00 0.00 38.78 3.27
3092 3416 1.408453 CCTCTAATCCGTCCCCCACC 61.408 65.000 0.00 0.00 0.00 4.61
3094 3418 0.105658 CTCCTCTAATCCGTCCCCCA 60.106 60.000 0.00 0.00 0.00 4.96
3095 3419 0.832559 CCTCCTCTAATCCGTCCCCC 60.833 65.000 0.00 0.00 0.00 5.40
3096 3420 0.832559 CCCTCCTCTAATCCGTCCCC 60.833 65.000 0.00 0.00 0.00 4.81
3097 3421 1.473497 GCCCTCCTCTAATCCGTCCC 61.473 65.000 0.00 0.00 0.00 4.46
3099 3423 1.660917 CGCCCTCCTCTAATCCGTC 59.339 63.158 0.00 0.00 0.00 4.79
3100 3424 1.833049 CCGCCCTCCTCTAATCCGT 60.833 63.158 0.00 0.00 0.00 4.69
3101 3425 1.807495 GACCGCCCTCCTCTAATCCG 61.807 65.000 0.00 0.00 0.00 4.18
3102 3426 1.807495 CGACCGCCCTCCTCTAATCC 61.807 65.000 0.00 0.00 0.00 3.01
3103 3427 1.660917 CGACCGCCCTCCTCTAATC 59.339 63.158 0.00 0.00 0.00 1.75
3104 3428 2.499827 GCGACCGCCCTCCTCTAAT 61.500 63.158 2.55 0.00 34.56 1.73
3171 4283 1.080569 CTTCCACCGGCAAACATGC 60.081 57.895 0.00 0.00 0.00 4.06
3172 4284 0.958091 TTCTTCCACCGGCAAACATG 59.042 50.000 0.00 0.00 0.00 3.21
3174 4286 0.181587 TCTTCTTCCACCGGCAAACA 59.818 50.000 0.00 0.00 0.00 2.83
3175 4287 1.266989 CTTCTTCTTCCACCGGCAAAC 59.733 52.381 0.00 0.00 0.00 2.93
3176 4288 1.142060 TCTTCTTCTTCCACCGGCAAA 59.858 47.619 0.00 0.00 0.00 3.68
3177 4289 0.762418 TCTTCTTCTTCCACCGGCAA 59.238 50.000 0.00 0.00 0.00 4.52
3179 4291 1.270893 ACTTCTTCTTCTTCCACCGGC 60.271 52.381 0.00 0.00 0.00 6.13
3180 4292 2.300437 AGACTTCTTCTTCTTCCACCGG 59.700 50.000 0.00 0.00 0.00 5.28
3181 4293 3.669251 AGACTTCTTCTTCTTCCACCG 57.331 47.619 0.00 0.00 0.00 4.94
3182 4294 5.105513 CCTCTAGACTTCTTCTTCTTCCACC 60.106 48.000 0.00 0.00 35.55 4.61
3183 4295 5.105513 CCCTCTAGACTTCTTCTTCTTCCAC 60.106 48.000 0.00 0.00 35.55 4.02
3185 4297 5.020795 ACCCTCTAGACTTCTTCTTCTTCC 58.979 45.833 0.00 0.00 35.55 3.46
3186 4298 7.706100 TTACCCTCTAGACTTCTTCTTCTTC 57.294 40.000 0.00 0.00 35.55 2.87
3187 4299 8.673456 ATTTACCCTCTAGACTTCTTCTTCTT 57.327 34.615 0.00 0.00 35.55 2.52
3188 4300 7.343574 GGATTTACCCTCTAGACTTCTTCTTCT 59.656 40.741 0.00 0.00 35.55 2.85
3189 4301 7.494211 GGATTTACCCTCTAGACTTCTTCTTC 58.506 42.308 0.00 0.00 35.55 2.87
3235 4691 0.741221 GAGCAGGGGTTGACGTGATC 60.741 60.000 0.00 0.00 35.05 2.92
3236 4692 1.296715 GAGCAGGGGTTGACGTGAT 59.703 57.895 0.00 0.00 0.00 3.06
3276 4732 2.786495 GGAGATCGGGAGCAGCGAA 61.786 63.158 0.00 0.00 0.00 4.70
3310 4766 2.579738 GGGTTCGAGGGAGTCTGC 59.420 66.667 0.00 0.00 0.00 4.26
3366 4822 4.995594 GCTAGGGAAGGCATTGCT 57.004 55.556 8.82 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.