Multiple sequence alignment - TraesCS1A01G179500

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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 TraesCS1A01G179500 chr1A 100.000 5802 0 0 1 5802 324499360 324493559 0.000000e+00 10715.0
1 TraesCS1A01G179500 chr1A 94.495 109 4 2 3530 3638 357777918 357777812 3.600000e-37 167.0
2 TraesCS1A01G179500 chr1A 92.308 104 7 1 5217 5320 176451820 176451718 4.680000e-31 147.0
3 TraesCS1A01G179500 chr1D 94.102 3018 109 32 543 3533 252921315 252918340 0.000000e+00 4523.0
4 TraesCS1A01G179500 chr1D 96.784 1648 45 3 4162 5802 252917768 252916122 0.000000e+00 2743.0
5 TraesCS1A01G179500 chr1D 94.659 543 25 2 3626 4164 252918342 252917800 0.000000e+00 839.0
6 TraesCS1A01G179500 chr1D 93.501 477 15 5 1 477 252922022 252921562 0.000000e+00 695.0
7 TraesCS1A01G179500 chr1D 93.269 104 6 1 5217 5320 181629192 181629090 1.010000e-32 152.0
8 TraesCS1A01G179500 chr1D 89.130 92 9 1 30 120 252922042 252921951 4.750000e-21 113.0
9 TraesCS1A01G179500 chr1B 95.394 2019 63 13 2164 4164 359900670 359902676 0.000000e+00 3186.0
10 TraesCS1A01G179500 chr1B 96.527 1641 49 4 4162 5801 359902709 359904342 0.000000e+00 2708.0
11 TraesCS1A01G179500 chr1B 88.530 1517 94 21 693 2181 359899156 359900620 0.000000e+00 1764.0
12 TraesCS1A01G179500 chr1B 95.323 449 17 1 3 447 359896666 359897114 0.000000e+00 710.0
13 TraesCS1A01G179500 chr1B 90.000 80 7 1 30 108 359896644 359896723 1.030000e-17 102.0
14 TraesCS1A01G179500 chr1B 92.188 64 5 0 9 72 359896724 359896787 2.230000e-14 91.6
15 TraesCS1A01G179500 chr7D 95.370 108 5 0 3530 3637 119737451 119737344 7.730000e-39 172.0
16 TraesCS1A01G179500 chr7A 93.913 115 3 3 3533 3644 164447345 164447458 2.780000e-38 171.0
17 TraesCS1A01G179500 chr5B 94.595 111 5 1 3523 3632 254944499 254944389 2.780000e-38 171.0
18 TraesCS1A01G179500 chr6D 97.000 100 3 0 3530 3629 73831590 73831491 1.000000e-37 169.0
19 TraesCS1A01G179500 chr5A 95.327 107 4 1 3528 3633 667712556 667712450 1.000000e-37 169.0
20 TraesCS1A01G179500 chr2B 95.238 105 4 1 3529 3633 518046829 518046932 1.290000e-36 165.0
21 TraesCS1A01G179500 chr3B 91.057 123 7 4 3531 3651 12406770 12406650 4.650000e-36 163.0
22 TraesCS1A01G179500 chr4D 93.137 102 6 1 5207 5307 479956918 479957019 1.300000e-31 148.0
23 TraesCS1A01G179500 chr4D 96.591 88 3 0 5220 5307 117425317 117425230 4.680000e-31 147.0
24 TraesCS1A01G179500 chr4D 97.647 85 2 0 5223 5307 502760762 502760678 4.680000e-31 147.0
25 TraesCS1A01G179500 chr4A 96.591 88 3 0 5225 5312 458238545 458238632 4.680000e-31 147.0
26 TraesCS1A01G179500 chr4A 94.737 38 1 1 619 656 603494410 603494374 2.260000e-04 58.4
27 TraesCS1A01G179500 chr4B 91.176 102 8 1 5207 5307 607282391 607282492 2.820000e-28 137.0


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 TraesCS1A01G179500 chr1A 324493559 324499360 5801 True 10715.000000 10715 100.000000 1 5802 1 chr1A.!!$R2 5801
1 TraesCS1A01G179500 chr1D 252916122 252922042 5920 True 1782.600000 4523 93.635200 1 5802 5 chr1D.!!$R2 5801
2 TraesCS1A01G179500 chr1B 359896644 359904342 7698 False 1426.933333 3186 92.993667 3 5801 6 chr1B.!!$F1 5798

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
484 2424 0.482446 TCCCAATGGCCAGTTTGACT 59.518 50.0 18.76 0.00 0.00 3.41 F
485 2425 0.604578 CCCAATGGCCAGTTTGACTG 59.395 55.0 18.76 4.19 45.53 3.51 F
1597 3662 0.701147 TCTCTCTCTCTGCCTGTCCA 59.299 55.0 0.00 0.00 0.00 4.02 F
2048 4129 0.394938 TTGCGCCAGAACAGGTCTTA 59.605 50.0 4.18 0.00 32.70 2.10 F
3548 5710 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.0 0.00 0.00 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 3648 0.534412 AATCGTGGACAGGCAGAGAG 59.466 55.000 0.00 0.0 0.00 3.20 R
2022 4103 0.591170 TGTTCTGGCGCAAAGTTAGC 59.409 50.000 10.83 0.0 0.00 3.09 R
3281 5443 0.596577 ATGCTGCTGAACAAGTGCTG 59.403 50.000 0.00 0.0 0.00 4.41 R
3611 5773 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.0 0.00 3.28 R
5239 7536 1.133356 GGAAAGGGCTAGGCAATCCAT 60.133 52.381 19.14 0.0 33.74 3.41 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
26 47 4.037923 AGCAAAGCTCTCTGTAGATCTAGC 59.962 45.833 1.64 3.59 30.62 3.42
102 127 1.671054 ACCATCTGCGGTCCAAACG 60.671 57.895 0.00 0.00 32.11 3.60
314 339 4.640771 TCTTTGAATGCCTACAGGTTCT 57.359 40.909 0.00 0.00 37.57 3.01
383 408 2.618045 GGTTACAGTGCTGGGTGCTTAT 60.618 50.000 4.11 0.00 43.37 1.73
419 444 2.734492 GCACTTCATGGATCTTGCTTGC 60.734 50.000 0.00 0.00 0.00 4.01
472 2201 7.661027 ACAGTTGTTTAAATTTGGATCCCAATG 59.339 33.333 11.65 6.99 43.55 2.82
482 2422 1.619432 GGATCCCAATGGCCAGTTTGA 60.619 52.381 18.76 11.66 0.00 2.69
483 2423 1.478105 GATCCCAATGGCCAGTTTGAC 59.522 52.381 18.76 5.54 0.00 3.18
484 2424 0.482446 TCCCAATGGCCAGTTTGACT 59.518 50.000 18.76 0.00 0.00 3.41
485 2425 0.604578 CCCAATGGCCAGTTTGACTG 59.395 55.000 18.76 4.19 45.53 3.51
486 2426 1.331214 CCAATGGCCAGTTTGACTGT 58.669 50.000 18.76 0.00 44.50 3.55
487 2427 1.688197 CCAATGGCCAGTTTGACTGTT 59.312 47.619 18.76 0.00 44.50 3.16
488 2428 2.102925 CCAATGGCCAGTTTGACTGTTT 59.897 45.455 18.76 0.00 44.50 2.83
489 2429 3.125316 CAATGGCCAGTTTGACTGTTTG 58.875 45.455 13.05 2.43 44.50 2.93
490 2430 2.136298 TGGCCAGTTTGACTGTTTGA 57.864 45.000 0.00 0.00 44.50 2.69
508 2448 7.439056 ACTGTTTGAGAACATTTTTATGCCAAG 59.561 33.333 0.00 0.00 44.30 3.61
535 2476 4.511527 ACAAAACACACATGGCAATTTCA 58.488 34.783 0.00 0.00 0.00 2.69
546 2487 6.645827 CACATGGCAATTTCATTAGAAACACA 59.354 34.615 0.00 0.00 45.79 3.72
556 2497 9.941325 ATTTCATTAGAAACACATGGCAATTTA 57.059 25.926 0.00 0.00 45.79 1.40
557 2498 8.984891 TTCATTAGAAACACATGGCAATTTAG 57.015 30.769 0.00 0.00 0.00 1.85
558 2499 7.035004 TCATTAGAAACACATGGCAATTTAGC 58.965 34.615 0.00 0.00 0.00 3.09
559 2500 4.870123 AGAAACACATGGCAATTTAGCA 57.130 36.364 0.00 0.00 35.83 3.49
560 2501 5.212532 AGAAACACATGGCAATTTAGCAA 57.787 34.783 0.00 0.00 35.83 3.91
561 2502 4.990426 AGAAACACATGGCAATTTAGCAAC 59.010 37.500 0.00 0.00 35.83 4.17
563 2504 4.333913 ACACATGGCAATTTAGCAACAA 57.666 36.364 0.00 0.00 35.83 2.83
564 2505 4.057432 ACACATGGCAATTTAGCAACAAC 58.943 39.130 0.00 0.00 35.83 3.32
566 2507 4.150980 CACATGGCAATTTAGCAACAACAG 59.849 41.667 0.00 0.00 35.83 3.16
567 2508 4.039004 ACATGGCAATTTAGCAACAACAGA 59.961 37.500 0.00 0.00 35.83 3.41
586 2529 8.981647 ACAACAGATTTTGCTATGAAAATTGTC 58.018 29.630 0.00 0.00 36.00 3.18
591 2534 6.746104 TTTTGCTATGAAAATTGTCGTGTG 57.254 33.333 0.17 0.00 0.00 3.82
605 2548 3.064207 GTCGTGTGTGCTTGAAGGAATA 58.936 45.455 0.00 0.00 0.00 1.75
644 2587 9.771915 CAACTAAAATTGCTGTGAAAAATGTTT 57.228 25.926 0.00 0.00 0.00 2.83
664 2607 1.962807 TGTTTTGCCATCCACCTTCAG 59.037 47.619 0.00 0.00 0.00 3.02
668 2611 1.817099 GCCATCCACCTTCAGCGAG 60.817 63.158 0.00 0.00 0.00 5.03
720 2760 5.801350 TTAATGTGGAATTTCTGCGAGAG 57.199 39.130 0.00 0.00 0.00 3.20
734 2774 2.202566 GCGAGAGGTTACATGCCTAAC 58.797 52.381 0.00 0.00 36.29 2.34
735 2775 2.159085 GCGAGAGGTTACATGCCTAACT 60.159 50.000 6.27 0.00 36.29 2.24
736 2776 3.448686 CGAGAGGTTACATGCCTAACTG 58.551 50.000 6.27 0.00 36.29 3.16
737 2777 3.130516 CGAGAGGTTACATGCCTAACTGA 59.869 47.826 6.27 0.00 36.29 3.41
738 2778 4.381612 CGAGAGGTTACATGCCTAACTGAA 60.382 45.833 6.27 0.00 36.29 3.02
739 2779 5.488341 GAGAGGTTACATGCCTAACTGAAA 58.512 41.667 6.27 0.00 36.29 2.69
740 2780 5.491982 AGAGGTTACATGCCTAACTGAAAG 58.508 41.667 6.27 0.00 36.29 2.62
741 2781 5.013183 AGAGGTTACATGCCTAACTGAAAGT 59.987 40.000 6.27 0.00 43.33 2.66
773 2813 0.969409 GGATGGAAAGCTTGGCTGCT 60.969 55.000 0.00 0.01 46.40 4.24
811 2851 4.570772 TGCTACACGCAGGAAGAATAAATC 59.429 41.667 0.00 0.00 45.47 2.17
812 2852 4.318121 GCTACACGCAGGAAGAATAAATCG 60.318 45.833 0.00 0.00 38.92 3.34
916 2963 3.058160 CCAACGGCAGGCAAGAGG 61.058 66.667 0.00 0.00 0.00 3.69
917 2964 3.741476 CAACGGCAGGCAAGAGGC 61.741 66.667 0.00 0.00 43.74 4.70
1112 3160 2.022129 CTCAGAACCCACGTCGCAC 61.022 63.158 0.00 0.00 0.00 5.34
1348 3396 2.152016 TCGAGGATGCCATCGTACTAG 58.848 52.381 0.00 0.00 39.86 2.57
1349 3397 2.152016 CGAGGATGCCATCGTACTAGA 58.848 52.381 0.00 0.00 34.30 2.43
1583 3648 1.042559 CCCTCTCCTGCAGGTCTCTC 61.043 65.000 31.58 0.00 36.34 3.20
1595 3660 1.102978 GGTCTCTCTCTCTGCCTGTC 58.897 60.000 0.00 0.00 0.00 3.51
1597 3662 0.701147 TCTCTCTCTCTGCCTGTCCA 59.299 55.000 0.00 0.00 0.00 4.02
1638 3704 6.312141 TCATGAGAATCCCATGACAGTTAA 57.688 37.500 3.21 0.00 43.67 2.01
1642 3708 6.303054 TGAGAATCCCATGACAGTTAACAAA 58.697 36.000 8.61 0.00 0.00 2.83
1643 3709 6.947733 TGAGAATCCCATGACAGTTAACAAAT 59.052 34.615 8.61 0.00 0.00 2.32
1645 3711 8.511604 AGAATCCCATGACAGTTAACAAATAG 57.488 34.615 8.61 0.00 0.00 1.73
1646 3712 8.109634 AGAATCCCATGACAGTTAACAAATAGT 58.890 33.333 8.61 0.00 0.00 2.12
1648 3714 8.964476 ATCCCATGACAGTTAACAAATAGTAG 57.036 34.615 8.61 0.00 0.00 2.57
1734 3805 6.143915 TCTATGGAAACCTGGAGCTATTAGT 58.856 40.000 0.00 0.00 0.00 2.24
1823 3904 6.276847 TGTTTGATAAATTTGCGGAAAGTGT 58.723 32.000 8.41 0.00 0.00 3.55
1839 3920 5.488341 GAAAGTGTAGGAAGCCTTATGTCA 58.512 41.667 0.00 0.00 34.61 3.58
1965 4046 2.457598 TCGAGAACTTGCTGGAGGTAT 58.542 47.619 0.00 0.00 0.00 2.73
2022 4103 8.996024 TTTCTTGGAGGTTTTGTTCTTTTAAG 57.004 30.769 0.00 0.00 0.00 1.85
2037 4118 3.552604 TTTAAGCTAACTTTGCGCCAG 57.447 42.857 4.18 3.01 37.33 4.85
2048 4129 0.394938 TTGCGCCAGAACAGGTCTTA 59.605 50.000 4.18 0.00 32.70 2.10
2058 4139 7.521585 CGCCAGAACAGGTCTTATTTAGTTTTT 60.522 37.037 0.00 0.00 32.70 1.94
2376 4526 2.504367 TGTGCTTTTCTGCCCTTCTAC 58.496 47.619 0.00 0.00 0.00 2.59
2379 4529 2.371841 TGCTTTTCTGCCCTTCTACTGA 59.628 45.455 0.00 0.00 0.00 3.41
2408 4558 4.641094 ACATGACTTGGTTGTTTCCGTTTA 59.359 37.500 0.00 0.00 0.00 2.01
2741 4893 7.227512 CACTTCTGTCTTTAACTCTCATTTGGT 59.772 37.037 0.00 0.00 0.00 3.67
2836 4988 7.939782 TGCAAAATTTGATGTTCTGTCTAAGA 58.060 30.769 10.26 0.00 0.00 2.10
2900 5052 8.931385 TTGAAAATATCTTTGCCTGCTTATTC 57.069 30.769 0.00 0.00 0.00 1.75
2977 5129 8.273780 AGACATTTTTCTCCATACAAGCTTAG 57.726 34.615 0.00 0.00 0.00 2.18
2981 5133 2.108168 TCTCCATACAAGCTTAGGCGT 58.892 47.619 0.00 0.00 44.37 5.68
3064 5217 1.138859 GCTGTTCCAAAGGGTTTTGCT 59.861 47.619 0.00 0.00 41.87 3.91
3139 5300 6.089249 AGCAATCAAGGTTACTGAAAAAGG 57.911 37.500 0.00 0.00 0.00 3.11
3163 5324 2.738846 CGACACTTACAGCAGCTCAAAT 59.261 45.455 0.00 0.00 0.00 2.32
3176 5337 1.994779 GCTCAAATGGATGCCAAAACG 59.005 47.619 0.00 0.00 36.95 3.60
3341 5503 0.610174 CAGCAGCACCTTCCTGTCTA 59.390 55.000 0.00 0.00 32.93 2.59
3518 5680 2.163509 TGCTCTATGAGGTATCTCCGC 58.836 52.381 0.00 0.00 41.99 5.54
3534 5696 1.202417 TCCGCATCTGCAGCTAAGTAC 60.202 52.381 9.47 0.00 42.21 2.73
3535 5697 1.202463 CCGCATCTGCAGCTAAGTACT 60.202 52.381 9.47 0.00 42.21 2.73
3536 5698 2.123342 CGCATCTGCAGCTAAGTACTC 58.877 52.381 9.47 0.00 42.21 2.59
3537 5699 2.478831 GCATCTGCAGCTAAGTACTCC 58.521 52.381 9.47 0.00 41.59 3.85
3538 5700 2.804933 GCATCTGCAGCTAAGTACTCCC 60.805 54.545 9.47 0.00 41.59 4.30
3539 5701 2.534042 TCTGCAGCTAAGTACTCCCT 57.466 50.000 9.47 0.00 0.00 4.20
3540 5702 2.379972 TCTGCAGCTAAGTACTCCCTC 58.620 52.381 9.47 0.00 0.00 4.30
3541 5703 1.410882 CTGCAGCTAAGTACTCCCTCC 59.589 57.143 0.00 0.00 0.00 4.30
3542 5704 0.386113 GCAGCTAAGTACTCCCTCCG 59.614 60.000 0.00 0.00 0.00 4.63
3543 5705 1.765230 CAGCTAAGTACTCCCTCCGT 58.235 55.000 0.00 0.00 0.00 4.69
3544 5706 1.677052 CAGCTAAGTACTCCCTCCGTC 59.323 57.143 0.00 0.00 0.00 4.79
3545 5707 1.031235 GCTAAGTACTCCCTCCGTCC 58.969 60.000 0.00 0.00 0.00 4.79
3546 5708 1.689984 CTAAGTACTCCCTCCGTCCC 58.310 60.000 0.00 0.00 0.00 4.46
3547 5709 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3548 5710 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
3549 5711 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3550 5712 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3551 5713 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3552 5714 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3553 5715 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3554 5716 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3555 5717 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3556 5718 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3557 5719 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
3558 5720 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
3559 5721 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
3560 5722 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
3561 5723 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
3562 5724 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3563 5725 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3564 5726 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3565 5727 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3566 5728 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3567 5729 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
3568 5730 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3569 5731 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3570 5732 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3571 5733 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
3577 5739 8.788325 AAGTGACTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
3578 5740 8.197988 AGTGACTCAACTTTGTACTAACTTTG 57.802 34.615 0.00 0.00 0.00 2.77
3579 5741 7.822822 AGTGACTCAACTTTGTACTAACTTTGT 59.177 33.333 0.00 0.00 0.00 2.83
3580 5742 9.090692 GTGACTCAACTTTGTACTAACTTTGTA 57.909 33.333 0.00 0.00 0.00 2.41
3581 5743 9.090692 TGACTCAACTTTGTACTAACTTTGTAC 57.909 33.333 6.58 6.58 40.27 2.90
3582 5744 9.310716 GACTCAACTTTGTACTAACTTTGTACT 57.689 33.333 12.73 0.00 40.44 2.73
3583 5745 9.095065 ACTCAACTTTGTACTAACTTTGTACTG 57.905 33.333 12.73 4.94 40.44 2.74
3584 5746 9.309516 CTCAACTTTGTACTAACTTTGTACTGA 57.690 33.333 12.73 7.97 40.44 3.41
3585 5747 9.656040 TCAACTTTGTACTAACTTTGTACTGAA 57.344 29.630 12.73 8.09 40.44 3.02
3586 5748 9.916397 CAACTTTGTACTAACTTTGTACTGAAG 57.084 33.333 17.70 17.70 40.44 3.02
3587 5749 8.139521 ACTTTGTACTAACTTTGTACTGAAGC 57.860 34.615 18.42 0.00 40.44 3.86
3588 5750 7.985752 ACTTTGTACTAACTTTGTACTGAAGCT 59.014 33.333 18.42 0.00 40.44 3.74
3589 5751 9.472361 CTTTGTACTAACTTTGTACTGAAGCTA 57.528 33.333 12.73 2.49 40.44 3.32
3590 5752 9.472361 TTTGTACTAACTTTGTACTGAAGCTAG 57.528 33.333 12.73 13.64 40.44 3.42
3591 5753 8.174733 TGTACTAACTTTGTACTGAAGCTAGT 57.825 34.615 19.76 19.76 40.44 2.57
3592 5754 9.288576 TGTACTAACTTTGTACTGAAGCTAGTA 57.711 33.333 18.50 18.50 40.44 1.82
3602 5764 9.856488 TTGTACTGAAGCTAGTATAAAGTTGAG 57.144 33.333 3.99 0.00 35.75 3.02
3603 5765 9.021807 TGTACTGAAGCTAGTATAAAGTTGAGT 57.978 33.333 0.00 0.00 35.75 3.41
3604 5766 9.505995 GTACTGAAGCTAGTATAAAGTTGAGTC 57.494 37.037 0.00 0.00 35.75 3.36
3605 5767 8.123639 ACTGAAGCTAGTATAAAGTTGAGTCA 57.876 34.615 0.00 0.00 0.00 3.41
3606 5768 8.030106 ACTGAAGCTAGTATAAAGTTGAGTCAC 58.970 37.037 0.00 0.00 0.00 3.67
3607 5769 8.123639 TGAAGCTAGTATAAAGTTGAGTCACT 57.876 34.615 0.00 0.00 0.00 3.41
3608 5770 8.585881 TGAAGCTAGTATAAAGTTGAGTCACTT 58.414 33.333 0.00 0.00 38.74 3.16
3617 5779 8.934023 ATAAAGTTGAGTCACTTATTTTGGGA 57.066 30.769 0.00 0.00 35.87 4.37
3618 5780 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3619 5781 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
3620 5782 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
3621 5783 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
3622 5784 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
3623 5785 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3624 5786 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
3625 5787 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3626 5788 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3627 5789 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3628 5790 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3638 5895 5.262804 GGACGGAGGGAGTAGTATATGAAT 58.737 45.833 0.00 0.00 0.00 2.57
3714 5971 4.029520 AGCCAGACTCTGACATGTTATCT 58.970 43.478 7.69 0.00 32.44 1.98
3755 6012 1.804151 TCATGGCTACGAGTTGTTTGC 59.196 47.619 0.00 0.00 0.00 3.68
3761 6018 2.604373 GCTACGAGTTGTTTGCAATGCA 60.604 45.455 2.72 2.72 36.92 3.96
3870 6128 9.725019 TCATTGAGAAGAAAAGTGCTAAGATAA 57.275 29.630 0.00 0.00 0.00 1.75
3896 6154 7.922278 ACGCAACGACCAATATCTACTATTTTA 59.078 33.333 0.00 0.00 0.00 1.52
3920 6178 5.905480 ACTTAATTTTTGGCTTCGCTTTG 57.095 34.783 0.00 0.00 0.00 2.77
4031 6292 9.229784 CATGCATTTATATGTCTGTTTGAGAAC 57.770 33.333 0.00 0.00 34.12 3.01
4470 6766 8.723311 TCCAGAATACAACGGTTATTGTAAAAG 58.277 33.333 2.73 0.00 45.63 2.27
4550 6846 6.039717 ACAAGTGTTTCATTGCAGTGACTATT 59.960 34.615 11.95 0.54 0.00 1.73
4608 6904 2.280186 GTTCCTATCAGCGGCCCG 60.280 66.667 0.00 0.00 0.00 6.13
4660 6956 4.536765 TCCTTCTTTGCTTCCTTTGTTCT 58.463 39.130 0.00 0.00 0.00 3.01
4667 6963 7.480810 TCTTTGCTTCCTTTGTTCTTAAGTTC 58.519 34.615 1.63 0.00 0.00 3.01
4693 6989 8.217115 CCATACTGAATTTTTATCAGACGATCG 58.783 37.037 14.88 14.88 45.74 3.69
4943 7240 2.354510 CTGCTTCCGTGTGTCAAGAAAA 59.645 45.455 0.00 0.00 0.00 2.29
5166 7463 4.075682 AGACACATCGGATCGTATGAGAT 58.924 43.478 11.64 0.00 0.00 2.75
5168 7465 5.010112 AGACACATCGGATCGTATGAGATTT 59.990 40.000 11.64 0.00 0.00 2.17
5202 7499 4.924305 ATCATATGCAAAGCAATTCCGT 57.076 36.364 0.00 0.00 43.62 4.69
5321 7618 6.315091 AGCTTGACAATCATATCTGCATTC 57.685 37.500 0.00 0.00 0.00 2.67
5333 7630 6.976349 TCATATCTGCATTCTTTTCAATGTGC 59.024 34.615 0.00 0.00 36.32 4.57
5475 7772 3.358707 TTGCTGTCTGTGCAAATTCAG 57.641 42.857 0.00 0.00 45.81 3.02
5685 7988 5.049818 GCAAGCCTGTCACAGATGATATTAC 60.050 44.000 6.30 0.00 37.14 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.223423 TCTACAGAGAGCTTTGCTTCG 57.777 47.619 0.00 0.00 39.88 3.79
2 3 5.451798 GCTAGATCTACAGAGAGCTTTGCTT 60.452 44.000 0.00 0.00 46.42 3.91
4 5 4.037923 AGCTAGATCTACAGAGAGCTTTGC 59.962 45.833 9.22 4.36 46.42 3.68
6 7 5.445069 TCAGCTAGATCTACAGAGAGCTTT 58.555 41.667 11.86 0.00 46.42 3.51
26 47 1.683385 TCGCAGATGGTGGATACTCAG 59.317 52.381 0.00 0.00 37.61 3.35
102 127 7.099266 TCTCTTGAGATCTTCAGACATCTTC 57.901 40.000 0.00 0.00 37.07 2.87
314 339 7.403837 AATATCCTACTACTAGTCACAGGGA 57.596 40.000 0.00 2.85 0.00 4.20
407 432 2.373540 TTGCATTGCAAGCAAGATCC 57.626 45.000 23.52 2.48 46.13 3.36
485 2425 7.713764 ACTTGGCATAAAAATGTTCTCAAAC 57.286 32.000 0.00 0.00 35.85 2.93
486 2426 8.203485 AGAACTTGGCATAAAAATGTTCTCAAA 58.797 29.630 0.00 0.00 38.42 2.69
487 2427 7.725251 AGAACTTGGCATAAAAATGTTCTCAA 58.275 30.769 0.00 0.00 38.42 3.02
488 2428 7.288810 AGAACTTGGCATAAAAATGTTCTCA 57.711 32.000 0.00 0.00 38.42 3.27
489 2429 8.296713 TGTAGAACTTGGCATAAAAATGTTCTC 58.703 33.333 8.44 3.34 41.53 2.87
490 2430 8.177119 TGTAGAACTTGGCATAAAAATGTTCT 57.823 30.769 0.00 0.00 43.07 3.01
508 2448 4.300189 TGCCATGTGTGTTTTGTAGAAC 57.700 40.909 0.00 0.00 0.00 3.01
535 2476 6.934056 TGCTAAATTGCCATGTGTTTCTAAT 58.066 32.000 0.00 0.00 0.00 1.73
546 2487 4.870123 TCTGTTGTTGCTAAATTGCCAT 57.130 36.364 0.00 0.00 0.00 4.40
557 2498 6.768029 TTTCATAGCAAAATCTGTTGTTGC 57.232 33.333 5.64 5.64 46.35 4.17
558 2499 9.588774 CAATTTTCATAGCAAAATCTGTTGTTG 57.411 29.630 0.00 0.00 35.35 3.33
559 2500 9.328845 ACAATTTTCATAGCAAAATCTGTTGTT 57.671 25.926 0.00 0.00 35.35 2.83
560 2501 8.891671 ACAATTTTCATAGCAAAATCTGTTGT 57.108 26.923 0.00 0.00 35.35 3.32
561 2502 8.157813 CGACAATTTTCATAGCAAAATCTGTTG 58.842 33.333 0.00 0.00 35.35 3.33
563 2504 7.326789 CACGACAATTTTCATAGCAAAATCTGT 59.673 33.333 0.00 0.00 35.35 3.41
564 2505 7.326789 ACACGACAATTTTCATAGCAAAATCTG 59.673 33.333 0.00 0.00 35.35 2.90
566 2507 7.114811 ACACACGACAATTTTCATAGCAAAATC 59.885 33.333 0.00 0.00 35.35 2.17
567 2508 6.922957 ACACACGACAATTTTCATAGCAAAAT 59.077 30.769 0.00 0.00 37.53 1.82
575 2518 3.988379 AGCACACACGACAATTTTCAT 57.012 38.095 0.00 0.00 0.00 2.57
586 2529 2.159653 GCTATTCCTTCAAGCACACACG 60.160 50.000 0.00 0.00 36.26 4.49
591 2534 3.019564 ACATGGCTATTCCTTCAAGCAC 58.980 45.455 0.00 0.00 38.01 4.40
605 2548 2.584835 TTAGTTGCAGGAACATGGCT 57.415 45.000 7.64 0.00 36.98 4.75
644 2587 1.962807 CTGAAGGTGGATGGCAAAACA 59.037 47.619 0.00 0.00 0.00 2.83
720 2760 5.122396 CAGACTTTCAGTTAGGCATGTAACC 59.878 44.000 0.00 0.00 33.98 2.85
734 2774 1.457303 CTCGGCGTTTCAGACTTTCAG 59.543 52.381 6.85 0.00 0.00 3.02
735 2775 1.497991 CTCGGCGTTTCAGACTTTCA 58.502 50.000 6.85 0.00 0.00 2.69
736 2776 0.790814 CCTCGGCGTTTCAGACTTTC 59.209 55.000 6.85 0.00 0.00 2.62
737 2777 0.391597 TCCTCGGCGTTTCAGACTTT 59.608 50.000 6.85 0.00 0.00 2.66
738 2778 0.608640 ATCCTCGGCGTTTCAGACTT 59.391 50.000 6.85 0.00 0.00 3.01
739 2779 0.108615 CATCCTCGGCGTTTCAGACT 60.109 55.000 6.85 0.00 0.00 3.24
740 2780 1.084370 CCATCCTCGGCGTTTCAGAC 61.084 60.000 6.85 0.00 0.00 3.51
741 2781 1.218047 CCATCCTCGGCGTTTCAGA 59.782 57.895 6.85 0.00 0.00 3.27
801 2841 5.964758 TGGCAAAATGAGCGATTTATTCTT 58.035 33.333 0.00 0.00 32.76 2.52
881 2928 0.036022 GGCCAGAGATGCATACCCTC 59.964 60.000 0.00 2.01 0.00 4.30
882 2929 0.695462 TGGCCAGAGATGCATACCCT 60.695 55.000 0.00 0.00 0.00 4.34
964 3012 1.374758 GTGGCTGGAGTGGACGAAG 60.375 63.158 0.00 0.00 0.00 3.79
966 3014 2.523168 TGTGGCTGGAGTGGACGA 60.523 61.111 0.00 0.00 0.00 4.20
969 3017 1.053835 TTCTGTGTGGCTGGAGTGGA 61.054 55.000 0.00 0.00 0.00 4.02
1112 3160 2.726351 GCGAGGAGTGGAGAAGGGG 61.726 68.421 0.00 0.00 0.00 4.79
1335 3383 0.757935 GGGGGTCTAGTACGATGGCA 60.758 60.000 0.00 0.00 0.00 4.92
1583 3648 0.534412 AATCGTGGACAGGCAGAGAG 59.466 55.000 0.00 0.00 0.00 3.20
1595 3660 8.242085 TCATGATGAATTTTGAAAAATCGTGG 57.758 30.769 16.74 4.79 37.62 4.94
1597 3662 9.695526 TTCTCATGATGAATTTTGAAAAATCGT 57.304 25.926 0.00 0.34 37.62 3.73
1638 3704 8.792830 ACATGTGCATACTTTCTACTATTTGT 57.207 30.769 0.00 0.00 0.00 2.83
1642 3708 9.618890 ATCAAACATGTGCATACTTTCTACTAT 57.381 29.630 0.00 0.00 0.00 2.12
1645 3711 9.869844 GATATCAAACATGTGCATACTTTCTAC 57.130 33.333 0.00 0.00 0.00 2.59
1646 3712 8.764287 CGATATCAAACATGTGCATACTTTCTA 58.236 33.333 0.00 0.00 0.00 2.10
1648 3714 7.374228 CACGATATCAAACATGTGCATACTTTC 59.626 37.037 0.00 0.00 0.00 2.62
1659 3729 6.481134 CAGAGTTTCCACGATATCAAACATG 58.519 40.000 15.06 10.74 32.20 3.21
1734 3805 5.827267 TCAGAAAACAACTCATGATCAACCA 59.173 36.000 0.00 0.00 0.00 3.67
1823 3904 2.293586 ACCCCTGACATAAGGCTTCCTA 60.294 50.000 1.30 0.00 35.85 2.94
1839 3920 1.080638 TATCCAAAAGCACCACCCCT 58.919 50.000 0.00 0.00 0.00 4.79
1986 4067 3.264450 ACCTCCAAGAAAGGACACATAGG 59.736 47.826 0.00 0.00 37.35 2.57
2022 4103 0.591170 TGTTCTGGCGCAAAGTTAGC 59.409 50.000 10.83 0.00 0.00 3.09
2037 4118 8.865590 TTGCAAAAACTAAATAAGACCTGTTC 57.134 30.769 0.00 0.00 0.00 3.18
2066 4148 9.528018 ACCAACAGAAAAACATAACAACTAATG 57.472 29.630 0.00 0.00 0.00 1.90
2079 4161 2.096819 TCGACAGCACCAACAGAAAAAC 59.903 45.455 0.00 0.00 0.00 2.43
2376 4526 9.559958 GAAACAACCAAGTCATGTTTATATCAG 57.440 33.333 3.38 0.00 44.72 2.90
2379 4529 7.175990 ACGGAAACAACCAAGTCATGTTTATAT 59.824 33.333 3.38 0.00 44.72 0.86
2408 4558 1.834263 CTCTCCCCTCTTCGATTGGTT 59.166 52.381 0.00 0.00 0.00 3.67
2528 4678 9.793252 ACTATGAACATTCTGCAATCATTTTAC 57.207 29.630 0.00 0.00 33.17 2.01
2606 4756 4.983671 ATCGTCATACTACAGACTGCAA 57.016 40.909 1.25 0.00 32.68 4.08
2741 4893 7.771183 ACAGAATCAAACACAAAAGAGCTAAA 58.229 30.769 0.00 0.00 0.00 1.85
2836 4988 5.352569 CCTCGAACTGAAGAAATATGTTGCT 59.647 40.000 0.00 0.00 0.00 3.91
2900 5052 6.395629 TCTTTCTTATTACAACACTCCCTCG 58.604 40.000 0.00 0.00 0.00 4.63
2977 5129 4.501071 TGAAAGATAGTGGAAACTACGCC 58.499 43.478 0.00 0.00 0.00 5.68
3045 5198 3.243737 GGTAGCAAAACCCTTTGGAACAG 60.244 47.826 0.23 0.00 41.96 3.16
3139 5300 1.721926 GAGCTGCTGTAAGTGTCGTTC 59.278 52.381 7.01 0.00 35.30 3.95
3163 5324 2.026729 TCTATGGTCGTTTTGGCATCCA 60.027 45.455 0.00 0.00 0.00 3.41
3176 5337 4.843728 TGTTCAGGGAATGTTCTATGGTC 58.156 43.478 0.00 0.00 0.00 4.02
3281 5443 0.596577 ATGCTGCTGAACAAGTGCTG 59.403 50.000 0.00 0.00 0.00 4.41
3371 5533 4.725790 AGTTTATGCATGCTCTTTTCCC 57.274 40.909 20.33 0.00 0.00 3.97
3447 5609 2.809696 TGCACACTGAACATCACATCAG 59.190 45.455 1.46 1.46 46.69 2.90
3518 5680 2.697751 AGGGAGTACTTAGCTGCAGATG 59.302 50.000 20.43 2.13 0.00 2.90
3534 5696 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3535 5697 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3536 5698 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
3537 5699 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3538 5700 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
3539 5701 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
3540 5702 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
3541 5703 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
3542 5704 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3543 5705 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
3544 5706 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
3545 5707 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
3551 5713 9.880157 AAAGTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 0.00 0.00 35.87 2.24
3552 5714 8.665685 CAAAGTTAGTACAAAGTTGAGTCACTT 58.334 33.333 0.00 0.00 38.74 3.16
3553 5715 7.822822 ACAAAGTTAGTACAAAGTTGAGTCACT 59.177 33.333 0.00 0.00 0.00 3.41
3554 5716 7.971455 ACAAAGTTAGTACAAAGTTGAGTCAC 58.029 34.615 0.00 0.00 0.00 3.67
3555 5717 9.090692 GTACAAAGTTAGTACAAAGTTGAGTCA 57.909 33.333 0.00 0.00 41.08 3.41
3556 5718 9.310716 AGTACAAAGTTAGTACAAAGTTGAGTC 57.689 33.333 6.30 0.00 43.24 3.36
3557 5719 9.095065 CAGTACAAAGTTAGTACAAAGTTGAGT 57.905 33.333 6.30 0.00 43.24 3.41
3558 5720 9.309516 TCAGTACAAAGTTAGTACAAAGTTGAG 57.690 33.333 6.30 0.00 43.24 3.02
3559 5721 9.656040 TTCAGTACAAAGTTAGTACAAAGTTGA 57.344 29.630 6.30 0.00 43.24 3.18
3560 5722 9.916397 CTTCAGTACAAAGTTAGTACAAAGTTG 57.084 33.333 6.30 0.00 43.24 3.16
3561 5723 8.610035 GCTTCAGTACAAAGTTAGTACAAAGTT 58.390 33.333 14.41 0.00 43.24 2.66
3562 5724 7.985752 AGCTTCAGTACAAAGTTAGTACAAAGT 59.014 33.333 14.41 0.00 43.24 2.66
3563 5725 8.366671 AGCTTCAGTACAAAGTTAGTACAAAG 57.633 34.615 6.30 9.20 43.24 2.77
3564 5726 9.472361 CTAGCTTCAGTACAAAGTTAGTACAAA 57.528 33.333 16.82 0.44 43.24 2.83
3565 5727 8.636213 ACTAGCTTCAGTACAAAGTTAGTACAA 58.364 33.333 23.65 1.56 44.13 2.41
3566 5728 8.174733 ACTAGCTTCAGTACAAAGTTAGTACA 57.825 34.615 23.65 2.06 44.13 2.90
3576 5738 9.856488 CTCAACTTTATACTAGCTTCAGTACAA 57.144 33.333 0.00 0.00 33.94 2.41
3577 5739 9.021807 ACTCAACTTTATACTAGCTTCAGTACA 57.978 33.333 0.00 0.00 33.94 2.90
3578 5740 9.505995 GACTCAACTTTATACTAGCTTCAGTAC 57.494 37.037 0.00 0.00 33.94 2.73
3579 5741 9.239551 TGACTCAACTTTATACTAGCTTCAGTA 57.760 33.333 0.00 0.00 35.54 2.74
3580 5742 8.030106 GTGACTCAACTTTATACTAGCTTCAGT 58.970 37.037 0.00 0.00 0.00 3.41
3581 5743 8.247562 AGTGACTCAACTTTATACTAGCTTCAG 58.752 37.037 0.00 0.00 0.00 3.02
3582 5744 8.123639 AGTGACTCAACTTTATACTAGCTTCA 57.876 34.615 0.00 0.00 0.00 3.02
3583 5745 8.989653 AAGTGACTCAACTTTATACTAGCTTC 57.010 34.615 0.00 0.00 37.05 3.86
3592 5754 8.793592 GTCCCAAAATAAGTGACTCAACTTTAT 58.206 33.333 0.00 0.00 40.77 1.40
3593 5755 7.041644 CGTCCCAAAATAAGTGACTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
3594 5756 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3595 5757 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3596 5758 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3597 5759 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3598 5760 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3599 5761 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
3600 5762 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
3601 5763 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
3602 5764 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
3603 5765 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
3604 5766 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3605 5767 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3606 5768 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3607 5769 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3608 5770 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3609 5771 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
3610 5772 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
3611 5773 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3612 5774 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
3613 5775 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
3614 5776 3.009916 TCATATACTACTCCCTCCGTCCC 59.990 52.174 0.00 0.00 0.00 4.46
3615 5777 4.298103 TCATATACTACTCCCTCCGTCC 57.702 50.000 0.00 0.00 0.00 4.79
3616 5778 5.944599 TGATTCATATACTACTCCCTCCGTC 59.055 44.000 0.00 0.00 0.00 4.79
3617 5779 5.711036 GTGATTCATATACTACTCCCTCCGT 59.289 44.000 0.00 0.00 0.00 4.69
3618 5780 5.710567 TGTGATTCATATACTACTCCCTCCG 59.289 44.000 0.00 0.00 0.00 4.63
3619 5781 7.726033 ATGTGATTCATATACTACTCCCTCC 57.274 40.000 0.00 0.00 34.67 4.30
3621 5783 8.754080 GCTAATGTGATTCATATACTACTCCCT 58.246 37.037 0.00 0.00 35.48 4.20
3622 5784 8.531982 TGCTAATGTGATTCATATACTACTCCC 58.468 37.037 0.00 0.00 35.48 4.30
3638 5895 8.873186 ATGAATCATGGATAATGCTAATGTGA 57.127 30.769 0.00 0.00 36.11 3.58
3714 5971 9.330063 CCATGAGCAGTAAGTTAGAAATATGAA 57.670 33.333 0.00 0.00 0.00 2.57
3755 6012 1.068333 GCAACTACCCTGTGTGCATTG 60.068 52.381 0.00 0.00 0.00 2.82
3761 6018 0.837272 ACTGTGCAACTACCCTGTGT 59.163 50.000 0.00 0.00 38.04 3.72
3870 6128 3.795623 AGTAGATATTGGTCGTTGCGT 57.204 42.857 0.00 0.00 0.00 5.24
3914 6172 5.746721 ACTAAGCTAAAACCAAAACAAAGCG 59.253 36.000 0.00 0.00 33.80 4.68
3920 6178 8.814235 GGAGAAAAACTAAGCTAAAACCAAAAC 58.186 33.333 0.00 0.00 0.00 2.43
3971 6229 4.855105 GGCACATAGATGGCGTGA 57.145 55.556 0.00 0.00 35.20 4.35
4031 6292 9.453325 AATTTCAGCATTGCAAATAACTTTTTG 57.547 25.926 11.91 0.00 39.16 2.44
4382 6678 9.638300 GCATTCTCAAAACTATTATAACTGTCG 57.362 33.333 0.00 0.00 0.00 4.35
4627 6923 6.763135 GGAAGCAAAGAAGGAAGATTGTTTTT 59.237 34.615 0.00 0.00 0.00 1.94
4667 6963 8.217115 CGATCGTCTGATAAAAATTCAGTATGG 58.783 37.037 7.03 0.00 41.13 2.74
4693 6989 6.014012 AGAAAGATAGTATAGTCCTCCAGGC 58.986 44.000 0.00 0.00 34.44 4.85
4943 7240 9.971922 CTTAGAAACCTGATGAACAAAAAGATT 57.028 29.630 0.00 0.00 0.00 2.40
4976 7273 7.362662 TGCACAGAATAAAAAGTCATCAAGTC 58.637 34.615 0.00 0.00 0.00 3.01
5168 7465 8.352201 GCTTTGCATATGATATTTTCAGGTACA 58.648 33.333 6.97 0.00 37.89 2.90
5181 7478 4.924305 ACGGAATTGCTTTGCATATGAT 57.076 36.364 6.97 0.00 38.76 2.45
5184 7481 5.700373 ACAAAAACGGAATTGCTTTGCATAT 59.300 32.000 9.21 0.00 38.76 1.78
5239 7536 1.133356 GGAAAGGGCTAGGCAATCCAT 60.133 52.381 19.14 0.00 33.74 3.41
5321 7618 7.281774 ACTGAGTGATATAGGCACATTGAAAAG 59.718 37.037 10.17 0.00 38.70 2.27
5475 7772 8.872845 CCCAAAAGATTAATGTTAACTGCATTC 58.127 33.333 7.22 0.00 37.65 2.67


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

AutoCloner maintained by Alex Coulton.