Multiple sequence alignment - TraesCS5A01G417500

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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 TraesCS5A01G417500 chr5A 100.000 5213 0 0 1 5213 605772605 605767393 0.000000e+00 9627.0
1 TraesCS5A01G417500 chr5A 84.279 1304 126 43 3278 4567 605758955 605757717 0.000000e+00 1199.0
2 TraesCS5A01G417500 chr5A 84.567 635 64 12 1 605 708753007 708752377 2.690000e-167 599.0
3 TraesCS5A01G417500 chr5A 86.116 569 54 9 53 599 451928102 451928667 1.620000e-164 590.0
4 TraesCS5A01G417500 chr5A 81.250 432 50 15 1792 2205 605740629 605740211 2.340000e-83 320.0
5 TraesCS5A01G417500 chr5A 93.333 90 6 0 686 775 708752067 708751978 3.270000e-27 134.0
6 TraesCS5A01G417500 chr5A 91.579 95 7 1 686 780 451928983 451929076 4.240000e-26 130.0
7 TraesCS5A01G417500 chr5A 94.286 70 4 0 2229 2298 605716028 605715959 1.990000e-19 108.0
8 TraesCS5A01G417500 chr5A 88.571 70 8 0 2229 2298 605740139 605740070 9.300000e-13 86.1
9 TraesCS5A01G417500 chr5D 88.442 2336 150 34 2229 4543 484293001 484290765 0.000000e+00 2708.0
10 TraesCS5A01G417500 chr5D 89.727 1431 85 23 823 2212 484294475 484293066 0.000000e+00 1772.0
11 TraesCS5A01G417500 chr5D 86.439 1320 129 27 3279 4567 484229321 484228021 0.000000e+00 1400.0
12 TraesCS5A01G417500 chr5D 92.344 640 41 6 4577 5213 484219320 484218686 0.000000e+00 904.0
13 TraesCS5A01G417500 chr5D 86.836 828 73 10 3718 4538 484220245 484219447 0.000000e+00 893.0
14 TraesCS5A01G417500 chr5D 84.580 655 66 17 1 623 443247405 443248056 7.420000e-173 617.0
15 TraesCS5A01G417500 chr5D 83.871 310 30 13 135 438 373942561 373942266 1.430000e-70 278.0
16 TraesCS5A01G417500 chr5D 94.444 90 5 0 686 775 443248430 443248519 7.040000e-29 139.0
17 TraesCS5A01G417500 chr5D 98.148 54 1 0 4525 4578 484219429 484219376 1.550000e-15 95.3
18 TraesCS5A01G417500 chr5B 93.191 1454 58 15 3762 5213 595339136 595337722 0.000000e+00 2098.0
19 TraesCS5A01G417500 chr5B 90.909 1353 75 20 882 2203 595344143 595342808 0.000000e+00 1773.0
20 TraesCS5A01G417500 chr5B 93.624 894 37 7 2845 3726 595340021 595339136 0.000000e+00 1317.0
21 TraesCS5A01G417500 chr5B 85.451 543 46 11 2285 2819 595340535 595340018 7.680000e-148 534.0
22 TraesCS5A01G417500 chr5B 85.437 309 25 9 135 438 373058403 373058110 2.360000e-78 303.0
23 TraesCS5A01G417500 chr5B 85.161 310 26 10 135 438 605327147 605326852 3.050000e-77 300.0
24 TraesCS5A01G417500 chr5B 95.714 70 3 0 2229 2298 595342734 595342665 4.270000e-21 113.0
25 TraesCS5A01G417500 chr1A 96.782 777 24 1 1 776 25963833 25964609 0.000000e+00 1295.0
26 TraesCS5A01G417500 chr1A 79.167 480 64 17 166 623 556831474 556831939 3.050000e-77 300.0
27 TraesCS5A01G417500 chr1A 78.947 475 63 18 175 626 555946780 555946320 6.600000e-74 289.0
28 TraesCS5A01G417500 chr1A 78.947 475 63 18 175 626 556822607 556822147 6.600000e-74 289.0
29 TraesCS5A01G417500 chr1A 90.722 97 6 2 686 780 556834486 556834581 5.480000e-25 126.0
30 TraesCS5A01G417500 chrUn 92.344 640 39 6 4577 5213 244093540 244092908 0.000000e+00 902.0
31 TraesCS5A01G417500 chrUn 92.344 640 39 6 4577 5213 244106183 244105551 0.000000e+00 902.0
32 TraesCS5A01G417500 chrUn 92.344 640 39 6 4577 5213 262358780 262359412 0.000000e+00 902.0
33 TraesCS5A01G417500 chrUn 85.352 867 77 20 3718 4578 244094418 244093596 0.000000e+00 852.0
34 TraesCS5A01G417500 chrUn 85.352 867 77 20 3718 4578 244107061 244106239 0.000000e+00 852.0
35 TraesCS5A01G417500 chrUn 85.352 867 77 20 3718 4578 262357902 262358724 0.000000e+00 852.0
36 TraesCS5A01G417500 chrUn 79.515 454 67 17 184 623 22790582 22791023 3.050000e-77 300.0
37 TraesCS5A01G417500 chrUn 85.802 162 14 7 1 153 22790420 22790581 4.180000e-36 163.0
38 TraesCS5A01G417500 chrUn 93.333 90 6 0 686 775 22791395 22791484 3.270000e-27 134.0
39 TraesCS5A01G417500 chr1D 85.321 654 66 9 1 626 442783788 442783137 0.000000e+00 649.0
40 TraesCS5A01G417500 chr2B 84.592 662 54 14 1 626 98778561 98777912 9.590000e-172 614.0
41 TraesCS5A01G417500 chr2B 93.103 87 6 0 689 775 98777553 98777467 1.520000e-25 128.0
42 TraesCS5A01G417500 chr7A 79.325 474 62 17 175 626 589767473 589767014 3.050000e-77 300.0
43 TraesCS5A01G417500 chr7A 78.346 508 70 23 152 628 457443583 457443085 5.110000e-75 292.0
44 TraesCS5A01G417500 chr2D 96.667 90 3 0 686 775 376947932 376947843 3.250000e-32 150.0
45 TraesCS5A01G417500 chr2A 81.319 182 32 2 443 623 766840040 766840220 4.210000e-31 147.0
46 TraesCS5A01G417500 chr3B 94.565 92 5 0 686 777 215889513 215889604 5.440000e-30 143.0


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 TraesCS5A01G417500 chr5A 605767393 605772605 5212 True 9627.000000 9627 100.000000 1 5213 1 chr5A.!!$R3 5212
1 TraesCS5A01G417500 chr5A 605757717 605758955 1238 True 1199.000000 1199 84.279000 3278 4567 1 chr5A.!!$R2 1289
2 TraesCS5A01G417500 chr5A 708751978 708753007 1029 True 366.500000 599 88.950000 1 775 2 chr5A.!!$R5 774
3 TraesCS5A01G417500 chr5A 451928102 451929076 974 False 360.000000 590 88.847500 53 780 2 chr5A.!!$F1 727
4 TraesCS5A01G417500 chr5A 605740070 605740629 559 True 203.050000 320 84.910500 1792 2298 2 chr5A.!!$R4 506
5 TraesCS5A01G417500 chr5D 484290765 484294475 3710 True 2240.000000 2708 89.084500 823 4543 2 chr5D.!!$R4 3720
6 TraesCS5A01G417500 chr5D 484228021 484229321 1300 True 1400.000000 1400 86.439000 3279 4567 1 chr5D.!!$R2 1288
7 TraesCS5A01G417500 chr5D 484218686 484220245 1559 True 630.766667 904 92.442667 3718 5213 3 chr5D.!!$R3 1495
8 TraesCS5A01G417500 chr5D 443247405 443248519 1114 False 378.000000 617 89.512000 1 775 2 chr5D.!!$F1 774
9 TraesCS5A01G417500 chr5B 595337722 595344143 6421 True 1167.000000 2098 91.777800 882 5213 5 chr5B.!!$R3 4331
10 TraesCS5A01G417500 chr1A 25963833 25964609 776 False 1295.000000 1295 96.782000 1 776 1 chr1A.!!$F1 775
11 TraesCS5A01G417500 chr1A 556831474 556834581 3107 False 213.000000 300 84.944500 166 780 2 chr1A.!!$F2 614
12 TraesCS5A01G417500 chrUn 244092908 244094418 1510 True 877.000000 902 88.848000 3718 5213 2 chrUn.!!$R1 1495
13 TraesCS5A01G417500 chrUn 244105551 244107061 1510 True 877.000000 902 88.848000 3718 5213 2 chrUn.!!$R2 1495
14 TraesCS5A01G417500 chrUn 262357902 262359412 1510 False 877.000000 902 88.848000 3718 5213 2 chrUn.!!$F2 1495
15 TraesCS5A01G417500 chr1D 442783137 442783788 651 True 649.000000 649 85.321000 1 626 1 chr1D.!!$R1 625
16 TraesCS5A01G417500 chr2B 98777467 98778561 1094 True 371.000000 614 88.847500 1 775 2 chr2B.!!$R1 774

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
787 3382 0.258774 GGCCCTGCCTCTTAATCCAA 59.741 55.000 0.00 0.0 46.69 3.53 F
789 3384 1.064389 GCCCTGCCTCTTAATCCAAGT 60.064 52.381 0.00 0.0 35.58 3.16 F
1626 4230 0.183492 AGCTCACCTTCTGCAAACCA 59.817 50.000 0.00 0.0 0.00 3.67 F
2065 4699 0.384309 TAGCACGGATACAGGAAGCG 59.616 55.000 0.00 0.0 0.00 4.68 F
3179 8040 0.677098 GGAAGCTTTCGGACCTTCCC 60.677 60.000 15.33 0.0 45.62 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 4230 0.110486 AGGACGGCATGAACTTTGGT 59.890 50.0 0.00 0.00 0.00 3.67 R
2444 7287 0.331278 CAATGAGTGGGCCCTTACCA 59.669 55.0 25.70 15.75 35.14 3.25 R
2873 7723 1.360820 TGTCGCACTTGAACGTTTCA 58.639 45.0 0.46 0.00 38.04 2.69 R
3734 8607 3.265791 GAGTCATGACATTGGAGTGTCC 58.734 50.0 27.02 0.00 46.17 4.02 R
4891 9881 0.249197 TGCCGATGCAGAGAGAATCG 60.249 55.0 0.00 0.00 44.23 3.34 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
30 31 1.740285 CTGTCCCTAATCCCGTCCG 59.260 63.158 0.00 0.00 0.00 4.79
96 114 3.309296 CTCCCCTGCATAGGTCTTCTTA 58.691 50.000 2.33 0.00 42.96 2.10
189 211 3.050619 GTCATCTTCTCGTTCGTGTTGT 58.949 45.455 0.00 0.00 0.00 3.32
221 243 1.664017 CGGATCTGCTGATCTGGCG 60.664 63.158 26.68 19.86 46.90 5.69
224 246 0.388659 GATCTGCTGATCTGGCGACT 59.611 55.000 22.39 0.00 44.19 4.18
240 262 3.627577 GGCGACTTACATCCACATCAATT 59.372 43.478 0.00 0.00 0.00 2.32
551 599 3.127548 CACCAAATTCTGAATCACCGAGG 59.872 47.826 2.92 2.99 0.00 4.63
552 600 3.244911 ACCAAATTCTGAATCACCGAGGT 60.245 43.478 2.92 3.55 0.00 3.85
607 655 4.541973 TCGATCCATGACATTGGGATAG 57.458 45.455 7.18 7.62 41.39 2.08
609 657 5.083821 TCGATCCATGACATTGGGATAGTA 58.916 41.667 7.18 0.00 41.39 1.82
785 3380 4.909678 GGCCCTGCCTCTTAATCC 57.090 61.111 0.00 0.00 46.69 3.01
786 3381 1.922821 GGCCCTGCCTCTTAATCCA 59.077 57.895 0.00 0.00 46.69 3.41
787 3382 0.258774 GGCCCTGCCTCTTAATCCAA 59.741 55.000 0.00 0.00 46.69 3.53
788 3383 1.685148 GCCCTGCCTCTTAATCCAAG 58.315 55.000 0.00 0.00 35.38 3.61
789 3384 1.064389 GCCCTGCCTCTTAATCCAAGT 60.064 52.381 0.00 0.00 35.58 3.16
790 3385 2.648059 CCCTGCCTCTTAATCCAAGTG 58.352 52.381 0.00 0.00 35.58 3.16
791 3386 2.239654 CCCTGCCTCTTAATCCAAGTGA 59.760 50.000 0.00 0.00 35.58 3.41
792 3387 3.117738 CCCTGCCTCTTAATCCAAGTGAT 60.118 47.826 0.00 0.00 35.58 3.06
793 3388 4.530875 CCTGCCTCTTAATCCAAGTGATT 58.469 43.478 0.00 0.00 45.64 2.57
794 3389 4.578105 CCTGCCTCTTAATCCAAGTGATTC 59.422 45.833 0.00 0.00 42.75 2.52
795 3390 4.191544 TGCCTCTTAATCCAAGTGATTCG 58.808 43.478 0.00 0.00 42.75 3.34
796 3391 4.081142 TGCCTCTTAATCCAAGTGATTCGA 60.081 41.667 0.00 0.00 42.75 3.71
797 3392 4.271291 GCCTCTTAATCCAAGTGATTCGAC 59.729 45.833 0.00 0.00 42.75 4.20
798 3393 4.504461 CCTCTTAATCCAAGTGATTCGACG 59.496 45.833 0.00 0.00 42.75 5.12
799 3394 5.068234 TCTTAATCCAAGTGATTCGACGT 57.932 39.130 0.00 0.00 42.75 4.34
800 3395 5.475719 TCTTAATCCAAGTGATTCGACGTT 58.524 37.500 0.00 0.00 42.75 3.99
801 3396 5.929992 TCTTAATCCAAGTGATTCGACGTTT 59.070 36.000 0.00 0.00 42.75 3.60
802 3397 6.425721 TCTTAATCCAAGTGATTCGACGTTTT 59.574 34.615 0.00 0.00 42.75 2.43
803 3398 5.432885 AATCCAAGTGATTCGACGTTTTT 57.567 34.783 0.00 0.00 39.56 1.94
838 3433 3.803021 GCACATTGGCAGGAAAATTGTGA 60.803 43.478 4.47 0.00 0.00 3.58
844 3439 4.410099 TGGCAGGAAAATTGTGAGAAGAT 58.590 39.130 0.00 0.00 0.00 2.40
846 3441 4.171754 GCAGGAAAATTGTGAGAAGATGC 58.828 43.478 0.00 0.00 0.00 3.91
865 3460 9.638300 GAAGATGCTGTAATAATCGTGTAAAAG 57.362 33.333 0.00 0.00 0.00 2.27
870 3465 9.767684 TGCTGTAATAATCGTGTAAAAGAAATG 57.232 29.630 0.00 0.00 0.00 2.32
871 3466 9.982291 GCTGTAATAATCGTGTAAAAGAAATGA 57.018 29.630 0.00 0.00 0.00 2.57
878 3473 7.703058 ATCGTGTAAAAGAAATGAATTCCCT 57.297 32.000 2.27 0.00 38.94 4.20
1431 4035 4.493747 AGCTACGGCGGCTTCGTC 62.494 66.667 13.24 0.00 44.37 4.20
1626 4230 0.183492 AGCTCACCTTCTGCAAACCA 59.817 50.000 0.00 0.00 0.00 3.67
1679 4283 5.163332 GGGACTACATCAGGGTAGGTAAAAG 60.163 48.000 5.45 0.00 43.99 2.27
1742 4362 7.679400 GCGATTGAGATTGTTCACCATGATTAA 60.679 37.037 0.00 0.00 0.00 1.40
1746 4366 7.167535 TGAGATTGTTCACCATGATTAACTCA 58.832 34.615 0.00 0.00 38.53 3.41
1754 4374 3.264193 ACCATGATTAACTCAGGTGCTGA 59.736 43.478 0.00 0.00 38.25 4.26
1772 4392 4.881273 TGCTGAAGCTTAGAACTTGTGAAA 59.119 37.500 0.00 0.00 42.66 2.69
1773 4393 5.532406 TGCTGAAGCTTAGAACTTGTGAAAT 59.468 36.000 0.00 0.00 42.66 2.17
1777 4397 9.766277 CTGAAGCTTAGAACTTGTGAAATAATC 57.234 33.333 0.00 0.00 0.00 1.75
1781 4401 8.680903 AGCTTAGAACTTGTGAAATAATCCATG 58.319 33.333 0.00 0.00 0.00 3.66
1811 4432 4.516698 ACCTGCGGCTCTATAAATCAAATG 59.483 41.667 0.00 0.00 0.00 2.32
1866 4487 7.981225 ACCTATATTGGTTGAATTGTTGAATGC 59.019 33.333 2.68 0.00 36.89 3.56
1867 4488 6.890663 ATATTGGTTGAATTGTTGAATGCG 57.109 33.333 0.00 0.00 0.00 4.73
1869 4490 4.517952 TGGTTGAATTGTTGAATGCGAT 57.482 36.364 0.00 0.00 0.00 4.58
1878 4499 3.598299 TGTTGAATGCGATGTGATCTCA 58.402 40.909 0.00 0.00 0.00 3.27
1879 4500 3.619929 TGTTGAATGCGATGTGATCTCAG 59.380 43.478 3.58 0.00 0.00 3.35
1882 4503 4.256110 TGAATGCGATGTGATCTCAGTTT 58.744 39.130 3.58 0.00 0.00 2.66
1887 4508 3.425359 GCGATGTGATCTCAGTTTGTTGG 60.425 47.826 3.58 0.00 0.00 3.77
1890 4511 5.615544 CGATGTGATCTCAGTTTGTTGGAAC 60.616 44.000 3.58 0.00 0.00 3.62
1891 4512 3.559655 TGTGATCTCAGTTTGTTGGAACG 59.440 43.478 0.00 0.00 34.74 3.95
1901 4522 4.022676 AGTTTGTTGGAACGTTTGACAGTT 60.023 37.500 0.46 0.00 34.74 3.16
1905 4526 5.120399 TGTTGGAACGTTTGACAGTTAGAT 58.880 37.500 0.46 0.00 0.00 1.98
1922 4543 9.236006 ACAGTTAGATGAATTCAGCAATTAGTT 57.764 29.630 24.50 5.61 34.14 2.24
1946 4567 5.903010 TGGTGTAAGCTCCTTAGGATATGAA 59.097 40.000 0.00 0.00 33.76 2.57
1947 4568 6.558775 TGGTGTAAGCTCCTTAGGATATGAAT 59.441 38.462 0.00 0.00 33.76 2.57
1948 4569 7.733047 TGGTGTAAGCTCCTTAGGATATGAATA 59.267 37.037 0.00 0.00 33.76 1.75
1949 4570 8.763601 GGTGTAAGCTCCTTAGGATATGAATAT 58.236 37.037 0.00 0.00 0.00 1.28
1950 4571 9.593134 GTGTAAGCTCCTTAGGATATGAATATG 57.407 37.037 0.00 0.00 0.00 1.78
1951 4572 8.762645 TGTAAGCTCCTTAGGATATGAATATGG 58.237 37.037 0.00 0.00 0.00 2.74
1959 4586 7.989741 CCTTAGGATATGAATATGGTGCTTAGG 59.010 40.741 0.00 0.00 0.00 2.69
1972 4606 6.249035 TGGTGCTTAGGTTTTTCTAATTCG 57.751 37.500 0.00 0.00 0.00 3.34
1975 4609 7.118680 TGGTGCTTAGGTTTTTCTAATTCGTAG 59.881 37.037 0.00 0.00 0.00 3.51
1976 4610 7.118825 GGTGCTTAGGTTTTTCTAATTCGTAGT 59.881 37.037 0.00 0.00 0.00 2.73
1999 4633 3.011595 ACATCAAATGATTCTCCCCCACA 59.988 43.478 0.00 0.00 31.21 4.17
2013 4647 0.404040 CCCACACTTTTCCCAGCCTA 59.596 55.000 0.00 0.00 0.00 3.93
2031 4665 4.825085 AGCCTAATGGAAAACGAAAACAGA 59.175 37.500 0.00 0.00 34.57 3.41
2034 4668 6.074516 GCCTAATGGAAAACGAAAACAGAAAC 60.075 38.462 0.00 0.00 34.57 2.78
2035 4669 6.975772 CCTAATGGAAAACGAAAACAGAAACA 59.024 34.615 0.00 0.00 34.57 2.83
2065 4699 0.384309 TAGCACGGATACAGGAAGCG 59.616 55.000 0.00 0.00 0.00 4.68
2067 4701 1.515954 CACGGATACAGGAAGCGGT 59.484 57.895 0.00 0.00 0.00 5.68
2082 4716 2.225068 GCGGTCTCTGCTGCTAAATA 57.775 50.000 0.00 0.00 37.74 1.40
2085 4719 3.800261 GCGGTCTCTGCTGCTAAATATCA 60.800 47.826 0.00 0.00 37.74 2.15
2099 4733 6.214208 TGCTAAATATCACAGCCCAGAGATAT 59.786 38.462 0.00 0.00 34.60 1.63
2104 4738 7.805083 ATATCACAGCCCAGAGATATAACTT 57.195 36.000 0.00 0.00 32.43 2.66
2105 4739 5.957771 TCACAGCCCAGAGATATAACTTT 57.042 39.130 0.00 0.00 0.00 2.66
2113 4747 5.998363 CCCAGAGATATAACTTTTAGGCCAC 59.002 44.000 5.01 0.00 0.00 5.01
2125 4759 2.590793 TAGGCCACATAAAGGGGGTA 57.409 50.000 5.01 0.00 42.99 3.69
2127 4761 1.499007 AGGCCACATAAAGGGGGTATG 59.501 52.381 5.01 0.00 42.99 2.39
2151 4796 4.276926 GGACATAAGAATCCATGAGTTGCC 59.723 45.833 0.00 0.00 34.87 4.52
2167 4812 1.076777 GCCCAGCCTTGCCTTCATA 60.077 57.895 0.00 0.00 0.00 2.15
2178 4823 9.598517 CAGCCTTGCCTTCATAAAAATAAATAA 57.401 29.630 0.00 0.00 0.00 1.40
2205 4855 6.703607 ACATTTCTCTTCGCTAATACTCCATG 59.296 38.462 0.00 0.00 0.00 3.66
2207 4857 5.440234 TCTCTTCGCTAATACTCCATGTC 57.560 43.478 0.00 0.00 0.00 3.06
2219 4895 9.959749 CTAATACTCCATGTCTTCTAAGTCTTC 57.040 37.037 0.00 0.00 0.00 2.87
2235 4933 4.489810 AGTCTTCAAGATGCTACTTCACG 58.510 43.478 0.00 0.00 0.00 4.35
2268 4966 7.913789 TGTAAATATACTGGTGGTGAAGTTCT 58.086 34.615 4.17 0.00 32.98 3.01
2273 4971 3.545703 ACTGGTGGTGAAGTTCTGAAAG 58.454 45.455 4.17 0.00 0.00 2.62
2314 7155 5.550232 TGGATGTCAAGTGAAAATGATCG 57.450 39.130 0.00 0.00 0.00 3.69
2317 7158 5.297776 GGATGTCAAGTGAAAATGATCGGAT 59.702 40.000 0.00 0.00 0.00 4.18
2318 7159 5.550232 TGTCAAGTGAAAATGATCGGATG 57.450 39.130 0.00 0.00 0.00 3.51
2326 7167 5.065218 GTGAAAATGATCGGATGTAGCAGTT 59.935 40.000 0.00 0.00 0.00 3.16
2327 7168 6.257849 GTGAAAATGATCGGATGTAGCAGTTA 59.742 38.462 0.00 0.00 0.00 2.24
2328 7169 6.821160 TGAAAATGATCGGATGTAGCAGTTAA 59.179 34.615 0.00 0.00 0.00 2.01
2329 7170 6.851222 AAATGATCGGATGTAGCAGTTAAG 57.149 37.500 0.00 0.00 0.00 1.85
2330 7171 5.791336 ATGATCGGATGTAGCAGTTAAGA 57.209 39.130 0.00 0.00 0.00 2.10
2331 7172 5.791336 TGATCGGATGTAGCAGTTAAGAT 57.209 39.130 0.00 0.00 0.00 2.40
2332 7173 5.773575 TGATCGGATGTAGCAGTTAAGATC 58.226 41.667 0.00 0.00 34.33 2.75
2350 7191 9.494271 GTTAAGATCTAAGATCAATGGTGCATA 57.506 33.333 0.00 0.00 0.00 3.14
2363 7204 9.797642 ATCAATGGTGCATAGAAAATATCAGTA 57.202 29.630 0.00 0.00 0.00 2.74
2365 7206 7.658179 ATGGTGCATAGAAAATATCAGTACG 57.342 36.000 0.00 0.00 0.00 3.67
2366 7207 5.989168 TGGTGCATAGAAAATATCAGTACGG 59.011 40.000 0.00 0.00 0.00 4.02
2367 7208 5.107065 GGTGCATAGAAAATATCAGTACGGC 60.107 44.000 0.00 0.00 0.00 5.68
2371 7212 6.128526 GCATAGAAAATATCAGTACGGCCTTC 60.129 42.308 0.00 0.00 0.00 3.46
2372 7213 4.704965 AGAAAATATCAGTACGGCCTTCC 58.295 43.478 0.00 0.00 0.00 3.46
2373 7214 4.163458 AGAAAATATCAGTACGGCCTTCCA 59.837 41.667 0.00 0.00 0.00 3.53
2374 7215 4.706842 AAATATCAGTACGGCCTTCCAT 57.293 40.909 0.00 0.00 0.00 3.41
2375 7216 3.685139 ATATCAGTACGGCCTTCCATG 57.315 47.619 0.00 0.00 0.00 3.66
2376 7217 1.496060 ATCAGTACGGCCTTCCATGA 58.504 50.000 0.00 0.00 0.00 3.07
2377 7218 1.496060 TCAGTACGGCCTTCCATGAT 58.504 50.000 0.00 0.00 0.00 2.45
2386 7227 4.956075 ACGGCCTTCCATGATTTTTAATCT 59.044 37.500 0.00 0.00 0.00 2.40
2388 7229 5.507985 CGGCCTTCCATGATTTTTAATCTCC 60.508 44.000 0.00 0.00 0.00 3.71
2391 7232 7.287696 GGCCTTCCATGATTTTTAATCTCCTTA 59.712 37.037 0.00 0.00 0.00 2.69
2392 7233 8.355913 GCCTTCCATGATTTTTAATCTCCTTAG 58.644 37.037 0.00 0.00 0.00 2.18
2440 7283 8.422566 AGTTACTCTATGATTTTACCCACTAGC 58.577 37.037 0.00 0.00 0.00 3.42
2441 7284 6.176014 ACTCTATGATTTTACCCACTAGCC 57.824 41.667 0.00 0.00 0.00 3.93
2442 7285 5.665812 ACTCTATGATTTTACCCACTAGCCA 59.334 40.000 0.00 0.00 0.00 4.75
2443 7286 5.925509 TCTATGATTTTACCCACTAGCCAC 58.074 41.667 0.00 0.00 0.00 5.01
2444 7287 4.862641 ATGATTTTACCCACTAGCCACT 57.137 40.909 0.00 0.00 0.00 4.00
2457 7300 2.355115 CCACTGGTAAGGGCCCAC 59.645 66.667 27.56 14.95 0.00 4.61
2459 7302 1.299976 CACTGGTAAGGGCCCACTC 59.700 63.158 27.56 13.13 0.00 3.51
2460 7303 1.151899 ACTGGTAAGGGCCCACTCA 60.152 57.895 27.56 15.30 0.00 3.41
2487 7330 4.392921 ACGGAACCTCATCAGTTATCAG 57.607 45.455 0.00 0.00 0.00 2.90
2504 7347 9.755804 CAGTTATCAGTTATCACACATACAGAT 57.244 33.333 0.00 0.00 0.00 2.90
2609 7458 5.120208 ACAACAATTTTGAGACGATACTCCG 59.880 40.000 0.00 0.00 36.22 4.63
2623 7472 4.201930 CGATACTCCGATATCTAGGTTGCC 60.202 50.000 0.34 0.00 30.54 4.52
2628 7477 4.641396 TCCGATATCTAGGTTGCCAATTG 58.359 43.478 0.00 0.00 0.00 2.32
2631 7480 5.707298 CCGATATCTAGGTTGCCAATTGATT 59.293 40.000 7.12 0.00 0.00 2.57
2671 7520 9.408069 CTATCAAACTAACTATTAAGCCCTACG 57.592 37.037 0.00 0.00 0.00 3.51
2703 7552 5.934625 AGCAATTAAGAGAGACAACGACATT 59.065 36.000 0.00 0.00 0.00 2.71
2745 7594 2.846206 TGGCAGTCTTAGACCCATCATT 59.154 45.455 8.96 0.00 32.18 2.57
2763 7612 7.063898 CCCATCATTATATCGATCTTGTGTCAC 59.936 40.741 0.00 0.00 0.00 3.67
2777 7626 7.332213 TCTTGTGTCACAATGAGAAATGAAA 57.668 32.000 18.49 0.00 37.48 2.69
2792 7641 6.799512 AGAAATGAAACTCACAGAACCAAAG 58.200 36.000 0.00 0.00 0.00 2.77
2794 7643 2.687935 TGAAACTCACAGAACCAAAGCC 59.312 45.455 0.00 0.00 0.00 4.35
2797 7646 3.857157 ACTCACAGAACCAAAGCCTTA 57.143 42.857 0.00 0.00 0.00 2.69
2798 7647 4.164843 ACTCACAGAACCAAAGCCTTAA 57.835 40.909 0.00 0.00 0.00 1.85
2799 7648 4.532834 ACTCACAGAACCAAAGCCTTAAA 58.467 39.130 0.00 0.00 0.00 1.52
2808 7657 7.756722 CAGAACCAAAGCCTTAAAACATCATAG 59.243 37.037 0.00 0.00 0.00 2.23
2815 7664 7.814264 AGCCTTAAAACATCATAGATCCAAG 57.186 36.000 0.00 0.00 0.00 3.61
2816 7665 6.774656 AGCCTTAAAACATCATAGATCCAAGG 59.225 38.462 0.00 0.00 33.52 3.61
2817 7666 6.547510 GCCTTAAAACATCATAGATCCAAGGT 59.452 38.462 0.00 0.00 33.06 3.50
2818 7667 7.719633 GCCTTAAAACATCATAGATCCAAGGTA 59.280 37.037 0.00 0.00 33.06 3.08
2819 7668 9.799106 CCTTAAAACATCATAGATCCAAGGTAT 57.201 33.333 0.00 0.00 0.00 2.73
2897 7747 4.539509 AACGTTCAAGTGCGACATTTTA 57.460 36.364 0.00 0.00 0.00 1.52
2903 7753 6.575572 CGTTCAAGTGCGACATTTTAAATGTA 59.424 34.615 21.34 5.59 31.52 2.29
2975 7825 5.242393 ACTTCTTGCTGTAATTCTGTTGCAT 59.758 36.000 0.00 0.00 0.00 3.96
2989 7839 3.987547 TGTTGCATGGTTGTATTGGTTG 58.012 40.909 0.00 0.00 0.00 3.77
3004 7854 7.206687 TGTATTGGTTGAGTTTTGGAAATCAC 58.793 34.615 0.00 0.00 39.34 3.06
3080 7930 6.615088 ACACTTATTTAATTCTGCTGTGCTG 58.385 36.000 0.00 0.00 0.00 4.41
3131 7992 8.956426 TGTACTGAAAATGTGAAAGAAAAGACT 58.044 29.630 0.00 0.00 0.00 3.24
3179 8040 0.677098 GGAAGCTTTCGGACCTTCCC 60.677 60.000 15.33 0.00 45.62 3.97
3237 8098 5.749596 TGTGTTGTTCAATGGAAGTACAG 57.250 39.130 0.00 0.00 31.77 2.74
3252 8113 4.357918 AGTACAGAACTTGATGCCTGTT 57.642 40.909 0.00 0.00 40.07 3.16
3253 8114 4.718961 AGTACAGAACTTGATGCCTGTTT 58.281 39.130 0.00 0.00 40.07 2.83
3620 8484 1.889105 CCGGGATGATCGCAAGGTG 60.889 63.158 10.19 0.00 38.47 4.00
3643 8507 4.558697 GCCAACCCTGCTTTAACTAAACAG 60.559 45.833 0.00 0.00 0.00 3.16
3734 8607 5.907207 ACTAGTAATGGCATACTGACTGTG 58.093 41.667 0.00 3.46 36.78 3.66
3944 8818 6.053632 TGTGGATGAGTCATCACATAGTTT 57.946 37.500 29.56 0.00 42.13 2.66
3958 8832 9.643693 CATCACATAGTTTTAATGCTCCTTTTT 57.356 29.630 0.00 0.00 0.00 1.94
4194 9082 1.893786 CCTGAGGAAGGTGGACTCG 59.106 63.158 0.00 0.00 41.74 4.18
4257 9150 8.262227 TGTATACCATGTAAGAAATTCCGACTT 58.738 33.333 0.00 0.00 0.00 3.01
4275 9170 5.461526 CGACTTTCATCTGTGTCTGTCTTA 58.538 41.667 0.00 0.00 0.00 2.10
4289 9184 7.931407 TGTGTCTGTCTTAACATTGATAACTGT 59.069 33.333 0.00 0.00 34.13 3.55
4329 9224 2.169832 TCCTAAAGTCTGCAGTGTGC 57.830 50.000 14.67 3.05 45.29 4.57
4375 9273 2.714250 TGAACCTTAAGGGCCTCTTTGA 59.286 45.455 25.31 0.92 40.27 2.69
4638 9626 9.695155 AACTAGTTTATATATTTGGTTGCTGGT 57.305 29.630 1.12 0.00 0.00 4.00
4721 9710 8.940952 GGATTTGATATATTTGTAGTCCTCTGC 58.059 37.037 0.00 0.00 0.00 4.26
4791 9781 0.755698 TGTAGGAGGGCGATCCAGAC 60.756 60.000 9.72 7.54 42.26 3.51
4823 9813 8.567878 TAGTGTTTGACTCCAGTGTGTACACC 62.568 46.154 22.91 13.98 40.73 4.16
4891 9881 0.598419 GACAAGGCTTGCCAAGTTGC 60.598 55.000 26.45 3.15 0.00 4.17
4926 9916 4.280436 TCGGCAGGAAAGAATTGTTAGA 57.720 40.909 0.00 0.00 0.00 2.10
5132 10125 3.561097 CCATCACATCCAAACTACCACCA 60.561 47.826 0.00 0.00 0.00 4.17
5170 10163 5.573282 CACGAGTAGTTAACACTCAAGGATG 59.427 44.000 24.81 15.79 42.12 3.51
5171 10164 4.563184 CGAGTAGTTAACACTCAAGGATGC 59.437 45.833 24.81 3.46 42.12 3.91
5172 10165 5.622460 CGAGTAGTTAACACTCAAGGATGCT 60.622 44.000 24.81 7.26 42.12 3.79
5173 10166 5.725362 AGTAGTTAACACTCAAGGATGCTC 58.275 41.667 8.61 0.00 34.06 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.823045 TCTTTCAAAGGACAAAGAAGAGGAC 59.177 40.000 0.00 0.00 36.02 3.85
221 243 6.741992 TGTGAATTGATGTGGATGTAAGTC 57.258 37.500 0.00 0.00 0.00 3.01
224 246 7.148035 CCTGAATGTGAATTGATGTGGATGTAA 60.148 37.037 0.00 0.00 0.00 2.41
240 262 3.068024 GGAACAAAAGCACCTGAATGTGA 59.932 43.478 0.00 0.00 38.55 3.58
505 553 7.140705 TGAATGAGTTACTTTTTCATGCACAG 58.859 34.615 6.77 0.00 33.09 3.66
551 599 7.971722 ACAGTTAGTGGTTGTTGTTTATTGAAC 59.028 33.333 0.00 0.00 38.78 3.18
552 600 8.057536 ACAGTTAGTGGTTGTTGTTTATTGAA 57.942 30.769 0.00 0.00 0.00 2.69
607 655 2.863809 CCCTTGCCTTACCATCCATAC 58.136 52.381 0.00 0.00 0.00 2.39
609 657 0.106015 GCCCTTGCCTTACCATCCAT 60.106 55.000 0.00 0.00 0.00 3.41
636 684 9.003658 ACAGGACTATTTCTCAACTGTTATTTG 57.996 33.333 0.00 0.00 34.36 2.32
780 3375 6.548441 AAAAACGTCGAATCACTTGGATTA 57.452 33.333 0.00 0.00 46.17 1.75
809 3404 2.768698 TCCTGCCAATGTGCAAAATTG 58.231 42.857 13.88 13.88 41.34 2.32
810 3405 3.488778 TTCCTGCCAATGTGCAAAATT 57.511 38.095 0.00 0.00 41.51 1.82
811 3406 3.488778 TTTCCTGCCAATGTGCAAAAT 57.511 38.095 0.00 0.00 41.51 1.82
812 3407 2.996249 TTTCCTGCCAATGTGCAAAA 57.004 40.000 0.00 0.00 41.51 2.44
813 3408 2.996249 TTTTCCTGCCAATGTGCAAA 57.004 40.000 0.00 0.00 41.51 3.68
814 3409 3.139850 CAATTTTCCTGCCAATGTGCAA 58.860 40.909 0.00 0.00 41.51 4.08
815 3410 2.104451 ACAATTTTCCTGCCAATGTGCA 59.896 40.909 0.00 0.00 39.37 4.57
816 3411 2.481185 CACAATTTTCCTGCCAATGTGC 59.519 45.455 0.00 0.00 0.00 4.57
817 3412 3.991773 CTCACAATTTTCCTGCCAATGTG 59.008 43.478 0.00 0.00 0.00 3.21
818 3413 3.896888 TCTCACAATTTTCCTGCCAATGT 59.103 39.130 0.00 0.00 0.00 2.71
819 3414 4.524316 TCTCACAATTTTCCTGCCAATG 57.476 40.909 0.00 0.00 0.00 2.82
820 3415 4.834496 TCTTCTCACAATTTTCCTGCCAAT 59.166 37.500 0.00 0.00 0.00 3.16
821 3416 4.214310 TCTTCTCACAATTTTCCTGCCAA 58.786 39.130 0.00 0.00 0.00 4.52
838 3433 8.942338 TTTACACGATTATTACAGCATCTTCT 57.058 30.769 0.00 0.00 0.00 2.85
844 3439 9.767684 CATTTCTTTTACACGATTATTACAGCA 57.232 29.630 0.00 0.00 0.00 4.41
894 3489 2.124109 TGCGGGCAACAACTTCCA 60.124 55.556 0.00 0.00 39.74 3.53
1317 3921 4.530857 GGGGATCTGTCGGCGGTG 62.531 72.222 7.21 0.00 0.00 4.94
1431 4035 3.536917 TGGGCGAGGTGATAGGCG 61.537 66.667 0.00 0.00 0.00 5.52
1626 4230 0.110486 AGGACGGCATGAACTTTGGT 59.890 50.000 0.00 0.00 0.00 3.67
1659 4263 6.154706 ACTGACTTTTACCTACCCTGATGTAG 59.845 42.308 0.00 0.00 38.34 2.74
1717 4336 5.746307 ATCATGGTGAACAATCTCAATCG 57.254 39.130 0.00 0.00 0.00 3.34
1742 4362 2.251818 TCTAAGCTTCAGCACCTGAGT 58.748 47.619 0.00 0.00 41.75 3.41
1746 4366 3.181450 ACAAGTTCTAAGCTTCAGCACCT 60.181 43.478 0.00 0.00 45.16 4.00
1754 4374 8.635765 TGGATTATTTCACAAGTTCTAAGCTT 57.364 30.769 3.48 3.48 0.00 3.74
1824 4445 8.139350 CCAATATAGGTACGTCAATGTGACTTA 58.861 37.037 6.80 0.00 44.85 2.24
1825 4446 6.984474 CCAATATAGGTACGTCAATGTGACTT 59.016 38.462 6.80 0.12 44.85 3.01
1826 4447 6.097839 ACCAATATAGGTACGTCAATGTGACT 59.902 38.462 6.80 0.00 41.78 3.41
1828 4449 6.474140 ACCAATATAGGTACGTCAATGTGA 57.526 37.500 0.00 0.00 40.98 3.58
1832 4453 8.836413 CAATTCAACCAATATAGGTACGTCAAT 58.164 33.333 0.00 0.00 42.25 2.57
1833 4454 7.825270 ACAATTCAACCAATATAGGTACGTCAA 59.175 33.333 0.00 0.00 42.25 3.18
1834 4455 7.332557 ACAATTCAACCAATATAGGTACGTCA 58.667 34.615 0.00 0.00 42.25 4.35
1835 4456 7.781548 ACAATTCAACCAATATAGGTACGTC 57.218 36.000 0.00 0.00 42.25 4.34
1836 4457 7.825270 TCAACAATTCAACCAATATAGGTACGT 59.175 33.333 0.00 0.00 42.25 3.57
1837 4458 8.203937 TCAACAATTCAACCAATATAGGTACG 57.796 34.615 0.00 0.00 42.25 3.67
1840 4461 7.981225 GCATTCAACAATTCAACCAATATAGGT 59.019 33.333 0.00 0.00 45.91 3.08
1841 4462 7.167968 CGCATTCAACAATTCAACCAATATAGG 59.832 37.037 0.00 0.00 0.00 2.57
1842 4463 7.914871 TCGCATTCAACAATTCAACCAATATAG 59.085 33.333 0.00 0.00 0.00 1.31
1843 4464 7.766283 TCGCATTCAACAATTCAACCAATATA 58.234 30.769 0.00 0.00 0.00 0.86
1844 4465 6.629128 TCGCATTCAACAATTCAACCAATAT 58.371 32.000 0.00 0.00 0.00 1.28
1866 4487 3.996363 TCCAACAAACTGAGATCACATCG 59.004 43.478 0.00 0.00 0.00 3.84
1867 4488 5.615544 CGTTCCAACAAACTGAGATCACATC 60.616 44.000 0.00 0.00 0.00 3.06
1869 4490 3.559655 CGTTCCAACAAACTGAGATCACA 59.440 43.478 0.00 0.00 0.00 3.58
1878 4499 3.504520 ACTGTCAAACGTTCCAACAAACT 59.495 39.130 0.00 0.00 0.00 2.66
1879 4500 3.828786 ACTGTCAAACGTTCCAACAAAC 58.171 40.909 0.00 0.00 0.00 2.93
1882 4503 4.505808 TCTAACTGTCAAACGTTCCAACA 58.494 39.130 0.00 5.74 0.00 3.33
1887 4508 7.572759 TGAATTCATCTAACTGTCAAACGTTC 58.427 34.615 3.38 0.00 0.00 3.95
1890 4511 6.017933 GCTGAATTCATCTAACTGTCAAACG 58.982 40.000 8.96 0.00 0.00 3.60
1891 4512 6.902341 TGCTGAATTCATCTAACTGTCAAAC 58.098 36.000 8.96 0.00 0.00 2.93
1901 4522 7.611467 ACACCAACTAATTGCTGAATTCATCTA 59.389 33.333 8.96 1.94 33.63 1.98
1905 4526 7.517614 TTACACCAACTAATTGCTGAATTCA 57.482 32.000 8.12 8.12 33.63 2.57
1922 4543 5.464069 TCATATCCTAAGGAGCTTACACCA 58.536 41.667 0.00 0.00 34.05 4.17
1946 4567 8.621286 CGAATTAGAAAAACCTAAGCACCATAT 58.379 33.333 0.00 0.00 32.75 1.78
1947 4568 7.608761 ACGAATTAGAAAAACCTAAGCACCATA 59.391 33.333 0.00 0.00 32.75 2.74
1948 4569 6.433093 ACGAATTAGAAAAACCTAAGCACCAT 59.567 34.615 0.00 0.00 32.75 3.55
1949 4570 5.766174 ACGAATTAGAAAAACCTAAGCACCA 59.234 36.000 0.00 0.00 32.75 4.17
1950 4571 6.250344 ACGAATTAGAAAAACCTAAGCACC 57.750 37.500 0.00 0.00 32.75 5.01
1951 4572 8.026341 ACTACGAATTAGAAAAACCTAAGCAC 57.974 34.615 0.00 0.00 32.75 4.40
1972 4606 5.998363 GGGGGAGAATCATTTGATGTACTAC 59.002 44.000 0.00 0.00 36.25 2.73
1975 4609 4.580580 GTGGGGGAGAATCATTTGATGTAC 59.419 45.833 0.00 0.00 36.25 2.90
1976 4610 4.229353 TGTGGGGGAGAATCATTTGATGTA 59.771 41.667 0.00 0.00 36.25 2.29
1999 4633 3.825908 TTCCATTAGGCTGGGAAAAGT 57.174 42.857 12.79 0.00 37.74 2.66
2013 4647 6.090223 GTGTGTTTCTGTTTTCGTTTTCCATT 59.910 34.615 0.00 0.00 0.00 3.16
2034 4668 3.617540 TCCGTGCTAAAACAATGTGTG 57.382 42.857 0.00 0.00 0.00 3.82
2035 4669 4.757657 TGTATCCGTGCTAAAACAATGTGT 59.242 37.500 0.00 0.00 0.00 3.72
2065 4699 4.697514 TGTGATATTTAGCAGCAGAGACC 58.302 43.478 0.00 0.00 0.00 3.85
2082 4716 6.506538 AAAGTTATATCTCTGGGCTGTGAT 57.493 37.500 0.00 0.00 0.00 3.06
2085 4719 6.689177 GCCTAAAAGTTATATCTCTGGGCTGT 60.689 42.308 10.60 0.00 32.92 4.40
2090 4724 6.591935 TGTGGCCTAAAAGTTATATCTCTGG 58.408 40.000 3.32 0.00 0.00 3.86
2099 4733 5.265989 CCCCTTTATGTGGCCTAAAAGTTA 58.734 41.667 3.32 0.00 0.00 2.24
2104 4738 2.004589 ACCCCCTTTATGTGGCCTAAA 58.995 47.619 3.32 0.00 0.00 1.85
2105 4739 1.688750 ACCCCCTTTATGTGGCCTAA 58.311 50.000 3.32 0.00 0.00 2.69
2113 4747 5.312178 TCTTATGTCCCATACCCCCTTTATG 59.688 44.000 0.00 0.00 0.00 1.90
2119 4753 3.010250 GGATTCTTATGTCCCATACCCCC 59.990 52.174 0.00 0.00 0.00 5.40
2125 4759 5.919348 ACTCATGGATTCTTATGTCCCAT 57.081 39.130 0.00 0.00 38.07 4.00
2127 4761 4.276926 GCAACTCATGGATTCTTATGTCCC 59.723 45.833 0.00 0.00 33.45 4.46
2151 4796 3.959535 TTTTTATGAAGGCAAGGCTGG 57.040 42.857 0.00 0.00 0.00 4.85
2178 4823 7.952671 TGGAGTATTAGCGAAGAGAAATGTAT 58.047 34.615 0.00 0.00 0.00 2.29
2186 4836 5.446143 AGACATGGAGTATTAGCGAAGAG 57.554 43.478 0.00 0.00 0.00 2.85
2188 4838 5.837437 AGAAGACATGGAGTATTAGCGAAG 58.163 41.667 0.00 0.00 30.41 3.79
2205 4855 7.543756 AGTAGCATCTTGAAGACTTAGAAGAC 58.456 38.462 0.00 2.03 0.00 3.01
2207 4857 8.031864 TGAAGTAGCATCTTGAAGACTTAGAAG 58.968 37.037 0.00 0.00 0.00 2.85
2219 4895 0.647410 CGGCGTGAAGTAGCATCTTG 59.353 55.000 0.00 0.00 34.54 3.02
2235 4933 6.031471 CCACCAGTATATTTACAAAAACGGC 58.969 40.000 0.00 0.00 0.00 5.68
2268 4966 7.545265 CCAAGAATCTTTGTTGTCAAACTTTCA 59.455 33.333 0.00 0.00 38.44 2.69
2273 4971 6.980397 ACATCCAAGAATCTTTGTTGTCAAAC 59.020 34.615 5.32 0.00 38.44 2.93
2314 7155 8.580720 TGATCTTAGATCTTAACTGCTACATCC 58.419 37.037 21.08 0.00 0.00 3.51
2317 7158 9.755804 CATTGATCTTAGATCTTAACTGCTACA 57.244 33.333 21.08 0.00 0.00 2.74
2318 7159 9.202273 CCATTGATCTTAGATCTTAACTGCTAC 57.798 37.037 21.08 0.00 0.00 3.58
2326 7167 9.093458 TCTATGCACCATTGATCTTAGATCTTA 57.907 33.333 21.08 10.94 0.00 2.10
2327 7168 7.971201 TCTATGCACCATTGATCTTAGATCTT 58.029 34.615 21.08 7.87 0.00 2.40
2328 7169 7.550597 TCTATGCACCATTGATCTTAGATCT 57.449 36.000 21.08 0.00 0.00 2.75
2329 7170 8.613060 TTTCTATGCACCATTGATCTTAGATC 57.387 34.615 14.79 14.79 0.00 2.75
2330 7171 8.985315 TTTTCTATGCACCATTGATCTTAGAT 57.015 30.769 0.00 0.00 0.00 1.98
2331 7172 8.985315 ATTTTCTATGCACCATTGATCTTAGA 57.015 30.769 0.00 0.00 0.00 2.10
2350 7191 4.163458 TGGAAGGCCGTACTGATATTTTCT 59.837 41.667 1.49 0.00 36.79 2.52
2363 7204 4.956075 AGATTAAAAATCATGGAAGGCCGT 59.044 37.500 0.00 0.00 36.79 5.68
2365 7206 5.600069 AGGAGATTAAAAATCATGGAAGGCC 59.400 40.000 0.00 0.00 0.00 5.19
2366 7207 6.721704 AGGAGATTAAAAATCATGGAAGGC 57.278 37.500 0.00 0.00 0.00 4.35
2367 7208 9.413734 ACTAAGGAGATTAAAAATCATGGAAGG 57.586 33.333 0.00 0.00 0.00 3.46
2386 7227 8.062065 ACAAGTTTGTGAAATTCAACTAAGGA 57.938 30.769 0.00 0.00 40.49 3.36
2391 7232 9.705290 AACTAAACAAGTTTGTGAAATTCAACT 57.295 25.926 8.37 0.00 46.61 3.16
2421 7264 5.760253 CAGTGGCTAGTGGGTAAAATCATAG 59.240 44.000 0.00 0.00 0.00 2.23
2438 7281 3.339093 GGGCCCTTACCAGTGGCT 61.339 66.667 17.04 0.00 44.71 4.75
2439 7282 3.657350 TGGGCCCTTACCAGTGGC 61.657 66.667 25.70 0.00 44.59 5.01
2440 7283 2.198304 GAGTGGGCCCTTACCAGTGG 62.198 65.000 25.70 7.91 41.61 4.00
2441 7284 1.299976 GAGTGGGCCCTTACCAGTG 59.700 63.158 25.70 0.00 41.61 3.66
2442 7285 0.550147 ATGAGTGGGCCCTTACCAGT 60.550 55.000 25.70 4.34 44.15 4.00
2443 7286 0.625849 AATGAGTGGGCCCTTACCAG 59.374 55.000 25.70 0.00 39.00 4.00
2444 7287 0.331278 CAATGAGTGGGCCCTTACCA 59.669 55.000 25.70 15.75 35.14 3.25
2457 7300 2.472695 TGAGGTTCCGTTCCAATGAG 57.527 50.000 0.00 0.00 0.00 2.90
2459 7302 2.679837 CTGATGAGGTTCCGTTCCAATG 59.320 50.000 0.00 0.00 0.00 2.82
2460 7303 2.305927 ACTGATGAGGTTCCGTTCCAAT 59.694 45.455 0.00 0.00 0.00 3.16
2591 7440 7.455641 AGATATCGGAGTATCGTCTCAAAAT 57.544 36.000 0.00 1.89 36.44 1.82
2598 7447 5.447548 GCAACCTAGATATCGGAGTATCGTC 60.448 48.000 3.87 0.00 36.44 4.20
2609 7458 7.516198 ACAATCAATTGGCAACCTAGATATC 57.484 36.000 0.00 0.00 41.96 1.63
2666 7515 5.172934 TCTTAATTGCTTGGTGTACGTAGG 58.827 41.667 0.00 0.00 0.00 3.18
2668 7517 6.028146 TCTCTTAATTGCTTGGTGTACGTA 57.972 37.500 0.00 0.00 0.00 3.57
2669 7518 4.890088 TCTCTTAATTGCTTGGTGTACGT 58.110 39.130 0.00 0.00 0.00 3.57
2670 7519 5.062308 GTCTCTCTTAATTGCTTGGTGTACG 59.938 44.000 0.00 0.00 0.00 3.67
2671 7520 5.932303 TGTCTCTCTTAATTGCTTGGTGTAC 59.068 40.000 0.00 0.00 0.00 2.90
2703 7552 6.889177 TGCCACATCAGTTTCATTTAGGATTA 59.111 34.615 0.00 0.00 0.00 1.75
2745 7594 7.940850 TCTCATTGTGACACAAGATCGATATA 58.059 34.615 24.25 0.00 41.94 0.86
2763 7612 6.860023 GGTTCTGTGAGTTTCATTTCTCATTG 59.140 38.462 0.00 0.00 41.67 2.82
2777 7626 2.736670 AAGGCTTTGGTTCTGTGAGT 57.263 45.000 0.00 0.00 0.00 3.41
2792 7641 6.547510 ACCTTGGATCTATGATGTTTTAAGGC 59.452 38.462 0.00 0.00 35.54 4.35
2824 7673 9.793259 ACTGAACCTTTTCATGTTCTTATTCTA 57.207 29.630 0.00 0.00 41.05 2.10
2825 7674 8.697507 ACTGAACCTTTTCATGTTCTTATTCT 57.302 30.769 0.00 0.00 41.05 2.40
2827 7676 8.515414 GCTACTGAACCTTTTCATGTTCTTATT 58.485 33.333 0.00 0.00 41.05 1.40
2828 7677 7.885399 AGCTACTGAACCTTTTCATGTTCTTAT 59.115 33.333 0.00 0.00 41.05 1.73
2829 7678 7.224297 AGCTACTGAACCTTTTCATGTTCTTA 58.776 34.615 0.00 0.00 41.05 2.10
2830 7679 6.064717 AGCTACTGAACCTTTTCATGTTCTT 58.935 36.000 0.00 0.00 41.05 2.52
2831 7680 5.625150 AGCTACTGAACCTTTTCATGTTCT 58.375 37.500 0.00 0.00 41.05 3.01
2832 7681 5.948992 AGCTACTGAACCTTTTCATGTTC 57.051 39.130 0.00 0.00 41.05 3.18
2833 7682 5.507985 GCAAGCTACTGAACCTTTTCATGTT 60.508 40.000 0.00 0.00 41.05 2.71
2834 7683 4.022849 GCAAGCTACTGAACCTTTTCATGT 60.023 41.667 0.00 0.00 41.05 3.21
2835 7684 4.479619 GCAAGCTACTGAACCTTTTCATG 58.520 43.478 0.00 0.00 41.05 3.07
2836 7685 3.507622 GGCAAGCTACTGAACCTTTTCAT 59.492 43.478 0.00 0.00 41.05 2.57
2837 7686 2.884639 GGCAAGCTACTGAACCTTTTCA 59.115 45.455 0.00 0.00 39.55 2.69
2838 7687 3.149981 AGGCAAGCTACTGAACCTTTTC 58.850 45.455 0.00 0.00 0.00 2.29
2839 7688 3.229697 AGGCAAGCTACTGAACCTTTT 57.770 42.857 0.00 0.00 0.00 2.27
2840 7689 2.959465 AGGCAAGCTACTGAACCTTT 57.041 45.000 0.00 0.00 0.00 3.11
2841 7690 4.367039 TTTAGGCAAGCTACTGAACCTT 57.633 40.909 0.00 0.00 0.00 3.50
2842 7691 4.576330 ATTTAGGCAAGCTACTGAACCT 57.424 40.909 0.00 0.00 0.00 3.50
2843 7692 6.944234 ATTATTTAGGCAAGCTACTGAACC 57.056 37.500 0.00 0.00 0.00 3.62
2873 7723 1.360820 TGTCGCACTTGAACGTTTCA 58.639 45.000 0.46 0.00 38.04 2.69
2916 7766 9.543783 AACTACGAAGTGAATCTAAGAAACTTT 57.456 29.630 0.00 0.00 45.73 2.66
2968 7818 3.638627 TCAACCAATACAACCATGCAACA 59.361 39.130 0.00 0.00 0.00 3.33
2975 7825 4.956700 TCCAAAACTCAACCAATACAACCA 59.043 37.500 0.00 0.00 0.00 3.67
2989 7839 6.389091 TGTATGCATGTGATTTCCAAAACTC 58.611 36.000 10.16 0.00 0.00 3.01
3037 7887 6.509418 AGTGTAAAAGCACTCACAAAAAGA 57.491 33.333 0.00 0.00 45.63 2.52
3131 7992 6.539826 CACTGATCAAGGCATATAACAACTCA 59.460 38.462 0.00 0.00 0.00 3.41
3179 8040 9.874205 ATGTGAATCAATACCTGGTTAATTTTG 57.126 29.630 3.84 2.56 0.00 2.44
3237 8098 4.874970 ACATGAAAACAGGCATCAAGTTC 58.125 39.130 0.00 0.00 0.00 3.01
3620 8484 3.319689 TGTTTAGTTAAAGCAGGGTTGGC 59.680 43.478 0.00 0.00 0.00 4.52
3734 8607 3.265791 GAGTCATGACATTGGAGTGTCC 58.734 50.000 27.02 0.00 46.17 4.02
3745 8618 9.904198 TTGATCCTAATTATTTGAGTCATGACA 57.096 29.630 27.02 7.35 0.00 3.58
3820 8694 4.413969 TGTATGAATTTCATGTGCTTGCG 58.586 39.130 19.81 0.00 37.70 4.85
3958 8832 5.305585 GTCTGGGTCTTGTTTATCAGACAA 58.694 41.667 14.09 0.00 45.89 3.18
3977 8859 8.578308 TGAAATATTGCTTTTTCAGTTGTCTG 57.422 30.769 0.00 0.00 37.03 3.51
4194 9082 2.350522 CATTATATCAGTGGCCGGCTC 58.649 52.381 28.56 19.53 0.00 4.70
4257 9150 7.216494 TCAATGTTAAGACAGACACAGATGAA 58.784 34.615 0.00 0.00 39.58 2.57
4275 9170 9.787435 TGGTAAGACTTAACAGTTATCAATGTT 57.213 29.630 8.94 0.00 42.15 2.71
4289 9184 5.481473 AGGATACGTTGGTGGTAAGACTTAA 59.519 40.000 0.00 0.00 46.39 1.85
4329 9224 1.267806 GACCAGCACTCCAACACAATG 59.732 52.381 0.00 0.00 0.00 2.82
4375 9273 4.745351 TGGATGAGGTAGCTGTCATAGAT 58.255 43.478 0.00 0.00 33.43 1.98
4467 9366 2.684881 GACGTCATGGCATTTGGAATCT 59.315 45.455 11.55 0.00 0.00 2.40
4638 9626 7.889600 AGTTTACCCCTTTTATCCGACATAAAA 59.110 33.333 10.20 10.20 33.83 1.52
4721 9710 0.250295 TTCTTGCTGAGTTGGGTCGG 60.250 55.000 0.00 0.00 0.00 4.79
4791 9781 5.178252 CACTGGAGTCAAACACTACAATCTG 59.822 44.000 0.00 0.00 46.19 2.90
4823 9813 1.003839 TGTTTGTCTAGGGGCTGCG 60.004 57.895 0.00 0.00 0.00 5.18
4891 9881 0.249197 TGCCGATGCAGAGAGAATCG 60.249 55.000 0.00 0.00 44.23 3.34
5051 10044 4.392138 GTCCTGTTCTTAATGGAAACGGAG 59.608 45.833 0.00 0.00 31.28 4.63
5055 10048 6.128254 GCTACTGTCCTGTTCTTAATGGAAAC 60.128 42.308 0.00 0.00 0.00 2.78
5170 10163 7.326305 CACCATAGTATAGTTCATACAACGAGC 59.674 40.741 0.00 0.00 41.84 5.03
5171 10164 8.350722 ACACCATAGTATAGTTCATACAACGAG 58.649 37.037 0.00 0.00 41.84 4.18
5172 10165 8.229253 ACACCATAGTATAGTTCATACAACGA 57.771 34.615 0.00 0.00 41.84 3.85
5173 10166 9.390795 GTACACCATAGTATAGTTCATACAACG 57.609 37.037 0.00 0.00 41.84 4.10


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

AutoCloner maintained by Alex Coulton.