Multiple sequence alignment - TraesCS5B01G175500

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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 TraesCS5B01G175500 chr5B 100.000 5244 0 0 1 5244 321534522 321529279 0.000000e+00 9684.0
1 TraesCS5B01G175500 chr5B 99.626 535 1 1 3494 4027 321471439 321470905 0.000000e+00 976.0
2 TraesCS5B01G175500 chr5B 89.206 806 54 17 2705 3493 321472183 321471394 0.000000e+00 976.0
3 TraesCS5B01G175500 chr5B 95.547 539 20 3 1 538 678968896 678968361 0.000000e+00 859.0
4 TraesCS5B01G175500 chr5B 98.718 234 3 0 3567 3800 321467926 321467693 2.920000e-112 416.0
5 TraesCS5B01G175500 chr5B 91.481 270 15 3 1720 1989 321474269 321474008 1.070000e-96 364.0
6 TraesCS5B01G175500 chr5B 97.633 169 0 1 4023 4187 321470487 321470319 2.390000e-73 287.0
7 TraesCS5B01G175500 chr5B 94.355 124 7 0 3838 3961 249075194 249075071 1.930000e-44 191.0
8 TraesCS5B01G175500 chr5B 94.400 125 5 2 2484 2607 321474004 321473881 1.930000e-44 191.0
9 TraesCS5B01G175500 chr5B 90.210 143 12 1 4574 4714 321465018 321464876 8.970000e-43 185.0
10 TraesCS5B01G175500 chr5B 79.661 295 23 11 4839 5104 321440942 321440656 1.500000e-40 178.0
11 TraesCS5B01G175500 chr5B 89.855 138 7 4 1437 1573 321474404 321474273 2.510000e-38 171.0
12 TraesCS5B01G175500 chr5B 100.000 45 0 0 3449 3493 321531029 321530985 3.370000e-12 84.2
13 TraesCS5B01G175500 chr5B 100.000 45 0 0 3494 3538 321531074 321531030 3.370000e-12 84.2
14 TraesCS5B01G175500 chr5B 97.436 39 1 0 2596 2634 321472221 321472183 3.390000e-07 67.6
15 TraesCS5B01G175500 chr5A 93.632 1743 72 10 1764 3491 375552055 375550337 0.000000e+00 2567.0
16 TraesCS5B01G175500 chr5A 92.921 1229 53 8 3494 4718 375550380 375549182 0.000000e+00 1757.0
17 TraesCS5B01G175500 chr5A 94.087 964 46 5 667 1621 375553012 375552051 0.000000e+00 1454.0
18 TraesCS5B01G175500 chr5A 95.620 548 22 2 1 547 662733579 662733033 0.000000e+00 878.0
19 TraesCS5B01G175500 chr5A 90.323 155 5 5 1374 1528 375377034 375376890 1.490000e-45 195.0
20 TraesCS5B01G175500 chr5A 82.292 192 24 6 4926 5108 613739826 613740016 1.950000e-34 158.0
21 TraesCS5B01G175500 chr5A 91.549 71 6 0 4167 4237 296301821 296301891 1.200000e-16 99.0
22 TraesCS5B01G175500 chr5D 93.372 1554 64 13 658 2198 283345056 283343529 0.000000e+00 2263.0
23 TraesCS5B01G175500 chr5D 94.021 1338 38 11 3494 4818 283342511 283341203 0.000000e+00 1989.0
24 TraesCS5B01G175500 chr5D 90.670 1104 50 23 2405 3493 283343532 283342467 0.000000e+00 1419.0
25 TraesCS5B01G175500 chr5D 87.253 659 37 25 4302 4953 283107815 283107197 0.000000e+00 708.0
26 TraesCS5B01G175500 chr5D 91.022 323 13 7 2899 3213 283108212 283107898 6.280000e-114 422.0
27 TraesCS5B01G175500 chr5D 88.554 166 18 1 3796 3961 223647536 223647700 3.200000e-47 200.0
28 TraesCS5B01G175500 chr5D 91.429 140 10 2 4843 4982 283340987 283340850 1.930000e-44 191.0
29 TraesCS5B01G175500 chr5D 89.922 129 10 3 4978 5105 283104410 283104284 4.200000e-36 163.0
30 TraesCS5B01G175500 chr5D 94.318 88 5 0 3870 3957 505561061 505561148 9.160000e-28 135.0
31 TraesCS5B01G175500 chr5D 97.297 74 2 0 3292 3365 283107891 283107818 5.510000e-25 126.0
32 TraesCS5B01G175500 chr5D 82.114 123 9 4 4167 4289 223647808 223647917 5.590000e-15 93.5
33 TraesCS5B01G175500 chr6B 95.430 547 21 3 1 545 164824750 164824206 0.000000e+00 869.0
34 TraesCS5B01G175500 chr6B 96.075 535 15 2 1 534 560645397 560644868 0.000000e+00 867.0
35 TraesCS5B01G175500 chr6B 84.127 189 19 6 4924 5102 217169202 217169015 6.980000e-39 172.0
36 TraesCS5B01G175500 chr7B 95.896 536 21 1 1 535 731968128 731968663 0.000000e+00 867.0
37 TraesCS5B01G175500 chr6A 95.247 547 25 1 1 546 57686601 57686055 0.000000e+00 865.0
38 TraesCS5B01G175500 chr6A 81.218 197 18 9 4924 5109 157963844 157964032 1.970000e-29 141.0
39 TraesCS5B01G175500 chr3B 95.572 542 21 2 9 547 188866563 188866022 0.000000e+00 865.0
40 TraesCS5B01G175500 chr3B 79.500 200 31 3 4925 5115 243239384 243239582 3.290000e-27 134.0
41 TraesCS5B01G175500 chr2B 95.880 534 21 1 1 533 360852566 360853099 0.000000e+00 863.0
42 TraesCS5B01G175500 chr4A 94.918 551 25 3 1 548 13294672 13295222 0.000000e+00 859.0
43 TraesCS5B01G175500 chr3D 84.293 191 22 3 4926 5109 110218704 110218515 4.170000e-41 180.0
44 TraesCS5B01G175500 chr6D 83.756 197 20 7 4924 5109 123159176 123158981 5.400000e-40 176.0
45 TraesCS5B01G175500 chr1D 82.524 206 26 9 4926 5121 328898758 328898553 6.980000e-39 172.0
46 TraesCS5B01G175500 chr1D 81.592 201 25 6 4925 5115 367846180 367846378 7.030000e-34 156.0
47 TraesCS5B01G175500 chr1D 80.319 188 29 6 4926 5105 433402285 433402098 9.160000e-28 135.0
48 TraesCS5B01G175500 chr2A 82.065 184 29 4 4926 5107 575686829 575686648 2.530000e-33 154.0
49 TraesCS5B01G175500 chr1B 86.458 96 9 4 5028 5121 70184088 70183995 9.290000e-18 102.0


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 TraesCS5B01G175500 chr5B 321529279 321534522 5243 True 3284.133333 9684 100.000000 1 5244 3 chr5B.!!$R5 5243
1 TraesCS5B01G175500 chr5B 678968361 678968896 535 True 859.000000 859 95.547000 1 538 1 chr5B.!!$R3 537
2 TraesCS5B01G175500 chr5B 321464876 321474404 9528 True 403.733333 976 94.285000 1437 4714 9 chr5B.!!$R4 3277
3 TraesCS5B01G175500 chr5A 375549182 375553012 3830 True 1926.000000 2567 93.546667 667 4718 3 chr5A.!!$R3 4051
4 TraesCS5B01G175500 chr5A 662733033 662733579 546 True 878.000000 878 95.620000 1 547 1 chr5A.!!$R2 546
5 TraesCS5B01G175500 chr5D 283340850 283345056 4206 True 1465.500000 2263 92.373000 658 4982 4 chr5D.!!$R2 4324
6 TraesCS5B01G175500 chr5D 283104284 283108212 3928 True 354.750000 708 91.373500 2899 5105 4 chr5D.!!$R1 2206
7 TraesCS5B01G175500 chr6B 164824206 164824750 544 True 869.000000 869 95.430000 1 545 1 chr6B.!!$R1 544
8 TraesCS5B01G175500 chr6B 560644868 560645397 529 True 867.000000 867 96.075000 1 534 1 chr6B.!!$R3 533
9 TraesCS5B01G175500 chr7B 731968128 731968663 535 False 867.000000 867 95.896000 1 535 1 chr7B.!!$F1 534
10 TraesCS5B01G175500 chr6A 57686055 57686601 546 True 865.000000 865 95.247000 1 546 1 chr6A.!!$R1 545
11 TraesCS5B01G175500 chr3B 188866022 188866563 541 True 865.000000 865 95.572000 9 547 1 chr3B.!!$R1 538
12 TraesCS5B01G175500 chr2B 360852566 360853099 533 False 863.000000 863 95.880000 1 533 1 chr2B.!!$F1 532
13 TraesCS5B01G175500 chr4A 13294672 13295222 550 False 859.000000 859 94.918000 1 548 1 chr4A.!!$F1 547

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
625 633 0.031449 TGCGCCAACAAAAGCTTACC 59.969 50.0 4.18 0.0 0.0 2.85 F
1084 1095 0.589708 GCGCTACCTTCCGTTTTGTT 59.410 50.0 0.00 0.0 0.0 2.83 F
1685 1709 0.616111 AGAGACCGTGGAGCTGGATT 60.616 55.0 0.00 0.0 0.0 3.01 F
2311 2336 0.888619 CTTCCACACTACTCTGGCGA 59.111 55.0 0.00 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1619 0.110486 ACAATTCACCACTTCGGGCT 59.890 50.0 0.00 0.0 40.22 5.19 R
2353 2378 0.460811 GCATCCTCGTCATCAGCACA 60.461 55.0 0.00 0.0 0.00 4.57 R
2965 4664 0.537828 TTTTGGTACCAGGGAACGGC 60.538 55.0 15.65 0.0 0.00 5.68 R
4257 8559 0.038166 GTTGGAACTGGAGATGGGCA 59.962 55.0 0.00 0.0 0.00 5.36 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
237 240 6.245408 TGGCATGTCAGATTTAAAGTTAGGT 58.755 36.000 0.00 0.00 0.00 3.08
334 337 1.095600 CTCTAGCGCAGTAGGTCACA 58.904 55.000 11.47 0.00 0.00 3.58
476 482 7.451877 TGGTGGGTAATTATTTGCAACTTTAGA 59.548 33.333 0.00 0.00 0.00 2.10
552 560 9.974750 GTAAAGATAAAGATAAAGATATGCGGC 57.025 33.333 0.00 0.00 0.00 6.53
553 561 6.893958 AGATAAAGATAAAGATATGCGGCG 57.106 37.500 0.51 0.51 0.00 6.46
554 562 6.398918 AGATAAAGATAAAGATATGCGGCGT 58.601 36.000 9.37 0.00 0.00 5.68
555 563 6.874134 AGATAAAGATAAAGATATGCGGCGTT 59.126 34.615 9.37 0.00 0.00 4.84
556 564 8.033038 AGATAAAGATAAAGATATGCGGCGTTA 58.967 33.333 9.37 0.93 0.00 3.18
557 565 8.718102 ATAAAGATAAAGATATGCGGCGTTAT 57.282 30.769 9.37 6.48 0.00 1.89
558 566 6.408858 AAGATAAAGATATGCGGCGTTATG 57.591 37.500 9.37 0.00 0.00 1.90
559 567 2.969443 AAAGATATGCGGCGTTATGC 57.031 45.000 9.37 1.35 45.38 3.14
568 576 2.967615 GCGTTATGCGGGAGGCTC 60.968 66.667 5.78 5.78 44.05 4.70
569 577 2.499205 CGTTATGCGGGAGGCTCA 59.501 61.111 17.69 0.00 44.05 4.26
570 578 1.883084 CGTTATGCGGGAGGCTCAC 60.883 63.158 17.69 12.63 44.05 3.51
577 585 3.063084 GGGAGGCTCACGAGTCGT 61.063 66.667 13.56 13.56 42.36 4.34
578 586 2.486042 GGAGGCTCACGAGTCGTC 59.514 66.667 16.86 4.61 38.32 4.20
579 587 2.486042 GAGGCTCACGAGTCGTCC 59.514 66.667 16.86 14.43 38.32 4.79
580 588 3.053849 GAGGCTCACGAGTCGTCCC 62.054 68.421 16.86 15.87 38.32 4.46
581 589 3.371063 GGCTCACGAGTCGTCCCA 61.371 66.667 16.86 1.56 38.32 4.37
582 590 2.126424 GCTCACGAGTCGTCCCAC 60.126 66.667 16.86 1.82 38.32 4.61
583 591 2.627737 GCTCACGAGTCGTCCCACT 61.628 63.158 16.86 0.00 38.32 4.00
584 592 1.957562 CTCACGAGTCGTCCCACTT 59.042 57.895 16.86 0.00 38.32 3.16
585 593 0.387367 CTCACGAGTCGTCCCACTTG 60.387 60.000 16.86 2.70 38.32 3.16
586 594 2.022129 CACGAGTCGTCCCACTTGC 61.022 63.158 16.86 0.00 38.32 4.01
587 595 2.338620 CGAGTCGTCCCACTTGCA 59.661 61.111 3.82 0.00 0.00 4.08
588 596 1.734477 CGAGTCGTCCCACTTGCAG 60.734 63.158 3.82 0.00 0.00 4.41
589 597 2.029844 GAGTCGTCCCACTTGCAGC 61.030 63.158 0.00 0.00 0.00 5.25
590 598 2.280797 GTCGTCCCACTTGCAGCA 60.281 61.111 0.00 0.00 0.00 4.41
591 599 1.672356 GTCGTCCCACTTGCAGCAT 60.672 57.895 0.00 0.00 0.00 3.79
592 600 1.672030 TCGTCCCACTTGCAGCATG 60.672 57.895 6.74 6.74 40.87 4.06
593 601 1.672030 CGTCCCACTTGCAGCATGA 60.672 57.895 14.99 0.00 39.69 3.07
594 602 1.028330 CGTCCCACTTGCAGCATGAT 61.028 55.000 14.99 0.00 39.69 2.45
595 603 0.454600 GTCCCACTTGCAGCATGATG 59.545 55.000 14.99 6.59 39.69 3.07
596 604 0.038599 TCCCACTTGCAGCATGATGT 59.961 50.000 13.32 0.57 39.69 3.06
597 605 0.892755 CCCACTTGCAGCATGATGTT 59.107 50.000 13.32 0.00 39.69 2.71
598 606 1.135199 CCCACTTGCAGCATGATGTTC 60.135 52.381 13.32 0.00 39.69 3.18
599 607 1.816835 CCACTTGCAGCATGATGTTCT 59.183 47.619 13.32 0.00 39.69 3.01
600 608 2.415491 CCACTTGCAGCATGATGTTCTG 60.415 50.000 13.32 2.84 39.69 3.02
603 611 1.063649 GCAGCATGATGTTCTGCCG 59.936 57.895 13.32 0.00 45.34 5.69
604 612 1.725665 CAGCATGATGTTCTGCCGG 59.274 57.895 1.88 0.00 39.69 6.13
605 613 0.745486 CAGCATGATGTTCTGCCGGA 60.745 55.000 5.05 0.00 39.69 5.14
606 614 0.182061 AGCATGATGTTCTGCCGGAT 59.818 50.000 5.05 0.00 39.22 4.18
607 615 0.309922 GCATGATGTTCTGCCGGATG 59.690 55.000 5.05 0.00 32.15 3.51
608 616 0.309922 CATGATGTTCTGCCGGATGC 59.690 55.000 5.05 0.00 41.77 3.91
609 617 1.162181 ATGATGTTCTGCCGGATGCG 61.162 55.000 5.05 0.00 45.60 4.73
610 618 3.173390 GATGTTCTGCCGGATGCGC 62.173 63.158 5.05 0.00 45.60 6.09
613 621 4.713735 TTCTGCCGGATGCGCCAA 62.714 61.111 5.05 0.00 45.60 4.52
617 625 4.049640 GCCGGATGCGCCAACAAA 62.050 61.111 5.05 0.00 35.94 2.83
618 626 2.647875 CCGGATGCGCCAACAAAA 59.352 55.556 4.18 0.00 35.94 2.44
619 627 1.444212 CCGGATGCGCCAACAAAAG 60.444 57.895 4.18 0.00 35.94 2.27
620 628 2.088178 CGGATGCGCCAACAAAAGC 61.088 57.895 4.18 0.00 35.94 3.51
621 629 1.290009 GGATGCGCCAACAAAAGCT 59.710 52.632 4.18 0.00 36.34 3.74
622 630 0.319813 GGATGCGCCAACAAAAGCTT 60.320 50.000 4.18 0.00 36.34 3.74
623 631 1.067915 GGATGCGCCAACAAAAGCTTA 60.068 47.619 4.18 0.00 36.34 3.09
624 632 1.985684 GATGCGCCAACAAAAGCTTAC 59.014 47.619 4.18 0.00 0.00 2.34
625 633 0.031449 TGCGCCAACAAAAGCTTACC 59.969 50.000 4.18 0.00 0.00 2.85
626 634 1.001745 GCGCCAACAAAAGCTTACCG 61.002 55.000 0.00 0.00 0.00 4.02
627 635 1.001745 CGCCAACAAAAGCTTACCGC 61.002 55.000 0.00 0.00 39.57 5.68
699 707 7.032580 CCAAACGACTGCCATTAAAAATCATA 58.967 34.615 0.00 0.00 0.00 2.15
708 716 7.725251 TGCCATTAAAAATCATAGGTGAATCC 58.275 34.615 0.00 0.00 38.01 3.01
910 921 2.361230 CTTCCCTTTCCCCACGCC 60.361 66.667 0.00 0.00 0.00 5.68
939 950 2.354729 CTCAAATCCCCCGCACCA 59.645 61.111 0.00 0.00 0.00 4.17
1051 1062 1.215647 GTCGTCGGTGAGCAATCCT 59.784 57.895 0.00 0.00 0.00 3.24
1082 1093 1.131826 CGCGCTACCTTCCGTTTTG 59.868 57.895 5.56 0.00 0.00 2.44
1084 1095 0.589708 GCGCTACCTTCCGTTTTGTT 59.410 50.000 0.00 0.00 0.00 2.83
1092 1103 4.884247 ACCTTCCGTTTTGTTTTTGTTCA 58.116 34.783 0.00 0.00 0.00 3.18
1178 1191 1.992667 GTTGTTCACGATCTGATGCGA 59.007 47.619 13.66 0.00 0.00 5.10
1186 1199 1.194098 CGATCTGATGCGATTTGAGGC 59.806 52.381 0.00 0.00 0.00 4.70
1187 1200 2.216046 GATCTGATGCGATTTGAGGCA 58.784 47.619 0.00 0.00 44.29 4.75
1312 1325 7.200455 CGCACGATTGGATACCATATAAGATA 58.800 38.462 0.00 0.00 31.53 1.98
1330 1343 8.824159 ATAAGATATTCCTGTTCAAGTGATCG 57.176 34.615 0.00 0.00 0.00 3.69
1345 1364 2.540101 GTGATCGATCTTTGTTAGGCGG 59.460 50.000 25.02 0.00 0.00 6.13
1400 1419 1.889170 CTGCCGTCCTGCTGATAGATA 59.111 52.381 0.00 0.00 32.50 1.98
1401 1420 1.889170 TGCCGTCCTGCTGATAGATAG 59.111 52.381 0.00 0.00 0.00 2.08
1402 1421 2.163509 GCCGTCCTGCTGATAGATAGA 58.836 52.381 0.00 0.00 0.00 1.98
1403 1422 2.558795 GCCGTCCTGCTGATAGATAGAA 59.441 50.000 0.00 0.00 0.00 2.10
1453 1476 4.996758 TGACTGTGATGTAGTGTTGGATTG 59.003 41.667 0.00 0.00 0.00 2.67
1477 1500 6.538742 TGTCTCTTTTCTGTTTCACCAACTAG 59.461 38.462 0.00 0.00 36.21 2.57
1578 1601 1.403780 GGACTTGTGTAGCGGTAGGTG 60.404 57.143 0.00 0.00 0.00 4.00
1595 1619 1.383386 TGCGGGAGTGGGGCTTATA 60.383 57.895 0.00 0.00 0.00 0.98
1608 1632 1.583054 GCTTATAGCCCGAAGTGGTG 58.417 55.000 0.00 0.00 34.48 4.17
1638 1662 3.262660 AGCAGATCACAATCCTCACTTGA 59.737 43.478 0.00 0.00 31.78 3.02
1671 1695 4.336153 GCCTAGTTACCTGTAGACAGAGAC 59.664 50.000 11.31 6.59 46.59 3.36
1673 1697 3.345414 AGTTACCTGTAGACAGAGACCG 58.655 50.000 11.31 0.00 46.59 4.79
1685 1709 0.616111 AGAGACCGTGGAGCTGGATT 60.616 55.000 0.00 0.00 0.00 3.01
1787 1811 3.057386 CAGCAAATTGTATGTGTCCAGCA 60.057 43.478 0.00 0.00 0.00 4.41
1867 1891 8.438676 AATGCTGTGTAAATTGTAGATAGGTC 57.561 34.615 0.00 0.00 0.00 3.85
1935 1959 7.856145 ATCAGATGTTGGAAATACTGAGAAC 57.144 36.000 0.00 0.00 36.31 3.01
2034 2058 3.056250 ACAAGTGGCACATGTTTTGTTGA 60.056 39.130 21.64 0.00 44.52 3.18
2056 2080 6.179756 TGAGCAAGCCATGTTCTTAGAATAA 58.820 36.000 0.00 0.00 39.76 1.40
2216 2241 3.290710 GTCATGTTGGCCTCATTATGGT 58.709 45.455 3.32 0.00 0.00 3.55
2246 2271 2.432628 CACCCTCGTCCTTGCGTC 60.433 66.667 0.00 0.00 0.00 5.19
2256 2281 1.275573 GTCCTTGCGTCTTCCTAAGGT 59.724 52.381 0.00 0.00 40.39 3.50
2257 2282 1.549170 TCCTTGCGTCTTCCTAAGGTC 59.451 52.381 0.00 0.00 40.39 3.85
2264 2289 1.559682 GTCTTCCTAAGGTCCATGGCA 59.440 52.381 6.96 0.00 0.00 4.92
2311 2336 0.888619 CTTCCACACTACTCTGGCGA 59.111 55.000 0.00 0.00 0.00 5.54
2331 2356 3.378399 GAGGAGGGAGAGGCGTTGC 62.378 68.421 0.00 0.00 0.00 4.17
2345 2370 1.304381 GTTGCCAGCAATGGGGAGA 60.304 57.895 8.52 0.00 38.28 3.71
2353 2378 2.568509 CAGCAATGGGGAGAAAATGGTT 59.431 45.455 0.00 0.00 0.00 3.67
2423 2448 2.462456 TGTCTCTGCTGTCCATGTTC 57.538 50.000 0.00 0.00 0.00 3.18
2634 4331 6.888632 ACCAATTCTTCATGATGGATATAGGC 59.111 38.462 17.29 0.00 35.16 3.93
2684 4381 8.675705 TTGGTTGTCAGATAATGTATGTATGG 57.324 34.615 0.00 0.00 0.00 2.74
2685 4382 7.801104 TGGTTGTCAGATAATGTATGTATGGT 58.199 34.615 0.00 0.00 0.00 3.55
2686 4383 8.929487 TGGTTGTCAGATAATGTATGTATGGTA 58.071 33.333 0.00 0.00 0.00 3.25
2687 4384 9.772973 GGTTGTCAGATAATGTATGTATGGTAA 57.227 33.333 0.00 0.00 0.00 2.85
2726 4423 1.001181 GCACAGGTTACCTTACCGTGA 59.999 52.381 19.56 0.00 43.21 4.35
2728 4425 1.274447 ACAGGTTACCTTACCGTGAGC 59.726 52.381 0.00 0.00 43.21 4.26
2810 4507 5.997746 TGCCTCTACAGGTAATTGAATATGC 59.002 40.000 0.00 0.00 42.74 3.14
2998 4699 7.540474 TGGTACCAAAACCATATTGCTTTAA 57.460 32.000 13.60 0.00 44.68 1.52
3112 4821 9.592720 GTTTGTTTCAATTGTGTAATTTATGCC 57.407 29.630 5.13 0.00 34.34 4.40
3295 5011 7.323420 TGAAGGATCACAGAGTGTATTAACAG 58.677 38.462 0.00 0.00 35.91 3.16
3459 5182 5.187186 AGGATTGCTGCTGATTCTTTGATTT 59.813 36.000 0.00 0.00 0.00 2.17
3460 5183 5.873164 GGATTGCTGCTGATTCTTTGATTTT 59.127 36.000 0.00 0.00 0.00 1.82
3461 5184 6.370718 GGATTGCTGCTGATTCTTTGATTTTT 59.629 34.615 0.00 0.00 0.00 1.94
3489 5212 5.726980 TTCCATCTTGGGAAAATGAACTG 57.273 39.130 0.00 0.00 43.77 3.16
3490 5213 4.996793 TCCATCTTGGGAAAATGAACTGA 58.003 39.130 0.00 0.00 38.32 3.41
3491 5214 4.766891 TCCATCTTGGGAAAATGAACTGAC 59.233 41.667 0.00 0.00 38.32 3.51
3492 5215 4.082026 CCATCTTGGGAAAATGAACTGACC 60.082 45.833 0.00 0.00 32.67 4.02
3493 5216 4.177537 TCTTGGGAAAATGAACTGACCA 57.822 40.909 0.00 0.00 0.00 4.02
3494 5217 4.739793 TCTTGGGAAAATGAACTGACCAT 58.260 39.130 0.00 0.00 0.00 3.55
3495 5218 5.147032 TCTTGGGAAAATGAACTGACCATT 58.853 37.500 0.00 0.00 35.92 3.16
3496 5219 5.243730 TCTTGGGAAAATGAACTGACCATTC 59.756 40.000 0.00 0.00 33.51 2.67
3497 5220 4.739793 TGGGAAAATGAACTGACCATTCT 58.260 39.130 0.00 0.00 33.51 2.40
3498 5221 5.147032 TGGGAAAATGAACTGACCATTCTT 58.853 37.500 0.00 0.00 33.51 2.52
3499 5222 5.602145 TGGGAAAATGAACTGACCATTCTTT 59.398 36.000 0.00 0.00 33.51 2.52
3500 5223 5.928264 GGGAAAATGAACTGACCATTCTTTG 59.072 40.000 0.00 0.00 33.51 2.77
3501 5224 6.239289 GGGAAAATGAACTGACCATTCTTTGA 60.239 38.462 0.00 0.00 33.51 2.69
3502 5225 7.381323 GGAAAATGAACTGACCATTCTTTGAT 58.619 34.615 0.00 0.00 33.51 2.57
3503 5226 7.874528 GGAAAATGAACTGACCATTCTTTGATT 59.125 33.333 0.00 0.00 33.51 2.57
4254 8556 2.943036 TTCTTCTAGCGGGGTGTTTT 57.057 45.000 0.00 0.00 0.00 2.43
4256 8558 1.002773 TCTTCTAGCGGGGTGTTTTCC 59.997 52.381 0.00 0.00 0.00 3.13
4257 8559 1.003233 CTTCTAGCGGGGTGTTTTCCT 59.997 52.381 0.00 0.00 0.00 3.36
4321 9768 6.324512 CCCATGGGATTTGAAATGTAGATTCA 59.675 38.462 28.27 0.00 37.50 2.57
4566 11158 2.489722 TGTGTTGCAGCAACTGTTTACA 59.510 40.909 32.99 25.84 43.85 2.41
4697 11767 2.370281 TGCTACTAGCTGACTGCAAC 57.630 50.000 9.49 0.00 45.94 4.17
4713 11783 2.198406 GCAACCCCGTTTCTTGTTTTC 58.802 47.619 0.00 0.00 0.00 2.29
4717 11787 4.811969 ACCCCGTTTCTTGTTTTCTTTT 57.188 36.364 0.00 0.00 0.00 2.27
4718 11788 5.155278 ACCCCGTTTCTTGTTTTCTTTTT 57.845 34.783 0.00 0.00 0.00 1.94
4722 11792 5.867174 CCCGTTTCTTGTTTTCTTTTTCTGT 59.133 36.000 0.00 0.00 0.00 3.41
4731 11801 8.614469 TTGTTTTCTTTTTCTGTCACCAAAAT 57.386 26.923 0.00 0.00 0.00 1.82
4761 11832 4.771590 TCGTTCCACACTACGAGTAATT 57.228 40.909 0.00 0.00 41.38 1.40
4764 11835 5.984926 TCGTTCCACACTACGAGTAATTTTT 59.015 36.000 0.00 0.00 41.38 1.94
4809 11880 3.244911 ACTGAATCGAATCCAAACCCTGT 60.245 43.478 0.00 0.00 0.00 4.00
4835 11919 3.732212 TCCAATTCCAGAGATGCGTATG 58.268 45.455 0.00 0.00 0.00 2.39
5014 15057 9.489084 AATATTGATTTCATGATGCATCAAAGG 57.511 29.630 31.79 22.86 38.73 3.11
5035 15078 7.630242 AAGGACATTGATTTCGTGTTGATAT 57.370 32.000 0.00 0.00 0.00 1.63
5036 15079 7.630242 AGGACATTGATTTCGTGTTGATATT 57.370 32.000 0.00 0.00 0.00 1.28
5159 15202 8.871686 AAAACTTGTTCCTCAAATGAATGTAC 57.128 30.769 0.00 0.00 35.48 2.90
5160 15203 6.575162 ACTTGTTCCTCAAATGAATGTACC 57.425 37.500 0.00 0.00 35.48 3.34
5161 15204 5.476945 ACTTGTTCCTCAAATGAATGTACCC 59.523 40.000 0.00 0.00 35.48 3.69
5162 15205 4.991776 TGTTCCTCAAATGAATGTACCCA 58.008 39.130 0.00 0.00 0.00 4.51
5163 15206 5.009631 TGTTCCTCAAATGAATGTACCCAG 58.990 41.667 0.00 0.00 0.00 4.45
5164 15207 3.620488 TCCTCAAATGAATGTACCCAGC 58.380 45.455 0.00 0.00 0.00 4.85
5165 15208 3.010027 TCCTCAAATGAATGTACCCAGCA 59.990 43.478 0.00 0.00 0.00 4.41
5166 15209 3.129287 CCTCAAATGAATGTACCCAGCAC 59.871 47.826 0.00 0.00 0.00 4.40
5167 15210 3.758023 CTCAAATGAATGTACCCAGCACA 59.242 43.478 0.00 0.00 0.00 4.57
5168 15211 4.148079 TCAAATGAATGTACCCAGCACAA 58.852 39.130 0.00 0.00 0.00 3.33
5169 15212 4.586421 TCAAATGAATGTACCCAGCACAAA 59.414 37.500 0.00 0.00 0.00 2.83
5170 15213 5.069648 TCAAATGAATGTACCCAGCACAAAA 59.930 36.000 0.00 0.00 0.00 2.44
5171 15214 5.743636 AATGAATGTACCCAGCACAAAAT 57.256 34.783 0.00 0.00 0.00 1.82
5172 15215 5.743636 ATGAATGTACCCAGCACAAAATT 57.256 34.783 0.00 0.00 0.00 1.82
5173 15216 6.849085 ATGAATGTACCCAGCACAAAATTA 57.151 33.333 0.00 0.00 0.00 1.40
5174 15217 6.266168 TGAATGTACCCAGCACAAAATTAG 57.734 37.500 0.00 0.00 0.00 1.73
5175 15218 5.772672 TGAATGTACCCAGCACAAAATTAGT 59.227 36.000 0.00 0.00 0.00 2.24
5176 15219 5.643379 ATGTACCCAGCACAAAATTAGTG 57.357 39.130 6.59 6.59 39.92 2.74
5177 15220 4.465886 TGTACCCAGCACAAAATTAGTGT 58.534 39.130 11.28 1.63 39.17 3.55
5178 15221 4.890581 TGTACCCAGCACAAAATTAGTGTT 59.109 37.500 11.28 4.22 39.17 3.32
5179 15222 6.062749 TGTACCCAGCACAAAATTAGTGTTA 58.937 36.000 11.28 0.00 39.17 2.41
5180 15223 5.705609 ACCCAGCACAAAATTAGTGTTAG 57.294 39.130 11.28 4.89 39.17 2.34
5181 15224 5.381757 ACCCAGCACAAAATTAGTGTTAGA 58.618 37.500 11.28 0.00 39.17 2.10
5182 15225 6.010219 ACCCAGCACAAAATTAGTGTTAGAT 58.990 36.000 11.28 0.00 39.17 1.98
5183 15226 7.172342 ACCCAGCACAAAATTAGTGTTAGATA 58.828 34.615 11.28 0.00 39.17 1.98
5184 15227 7.834181 ACCCAGCACAAAATTAGTGTTAGATAT 59.166 33.333 11.28 0.00 39.17 1.63
5185 15228 9.337396 CCCAGCACAAAATTAGTGTTAGATATA 57.663 33.333 11.28 0.00 39.17 0.86
5224 15267 1.670791 TGGGACAACTTGTTTCGGAC 58.329 50.000 0.00 0.00 31.92 4.79
5225 15268 0.584876 GGGACAACTTGTTTCGGACG 59.415 55.000 0.00 0.00 0.00 4.79
5226 15269 1.574134 GGACAACTTGTTTCGGACGA 58.426 50.000 0.00 0.00 0.00 4.20
5227 15270 1.259770 GGACAACTTGTTTCGGACGAC 59.740 52.381 0.00 0.00 0.00 4.34
5228 15271 2.199236 GACAACTTGTTTCGGACGACT 58.801 47.619 0.00 0.00 0.00 4.18
5229 15272 2.606272 GACAACTTGTTTCGGACGACTT 59.394 45.455 0.00 0.00 0.00 3.01
5230 15273 3.784338 ACAACTTGTTTCGGACGACTTA 58.216 40.909 0.00 0.00 0.00 2.24
5231 15274 4.183101 ACAACTTGTTTCGGACGACTTAA 58.817 39.130 0.00 0.00 0.00 1.85
5232 15275 4.812626 ACAACTTGTTTCGGACGACTTAAT 59.187 37.500 0.00 0.00 0.00 1.40
5233 15276 5.295045 ACAACTTGTTTCGGACGACTTAATT 59.705 36.000 0.00 0.00 0.00 1.40
5234 15277 5.996669 ACTTGTTTCGGACGACTTAATTT 57.003 34.783 0.00 0.00 0.00 1.82
5235 15278 6.367686 ACTTGTTTCGGACGACTTAATTTT 57.632 33.333 0.00 0.00 0.00 1.82
5236 15279 6.788243 ACTTGTTTCGGACGACTTAATTTTT 58.212 32.000 0.00 0.00 0.00 1.94
5237 15280 6.908820 ACTTGTTTCGGACGACTTAATTTTTC 59.091 34.615 0.00 0.00 0.00 2.29
5238 15281 5.750650 TGTTTCGGACGACTTAATTTTTCC 58.249 37.500 0.00 0.00 0.00 3.13
5239 15282 5.528320 TGTTTCGGACGACTTAATTTTTCCT 59.472 36.000 0.00 0.00 0.00 3.36
5240 15283 6.038492 TGTTTCGGACGACTTAATTTTTCCTT 59.962 34.615 0.00 0.00 0.00 3.36
5241 15284 6.622833 TTCGGACGACTTAATTTTTCCTTT 57.377 33.333 0.00 0.00 0.00 3.11
5242 15285 6.622833 TCGGACGACTTAATTTTTCCTTTT 57.377 33.333 0.00 0.00 0.00 2.27
5243 15286 7.030075 TCGGACGACTTAATTTTTCCTTTTT 57.970 32.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 196 9.788960 CATGCCATATATGAAAATTCATCAGAG 57.211 33.333 14.54 2.71 44.17 3.35
334 337 0.879839 GCAGCGCATTGGTTGGTTTT 60.880 50.000 11.47 0.00 0.00 2.43
361 364 6.380079 GGAGATCCCCTCATATACAACAAT 57.620 41.667 0.00 0.00 43.76 2.71
416 422 7.219344 CGGTAAATGAGAAGAACGTTTTGTTTT 59.781 33.333 0.46 0.12 42.09 2.43
417 423 6.689669 CGGTAAATGAGAAGAACGTTTTGTTT 59.310 34.615 0.46 0.00 42.09 2.83
436 442 0.896019 CCACCAATGCCACCGGTAAA 60.896 55.000 6.87 0.00 0.00 2.01
476 482 5.221843 TGCCTGTCTGTCATTAAAACTACCT 60.222 40.000 0.00 0.00 0.00 3.08
550 558 4.547367 AGCCTCCCGCATAACGCC 62.547 66.667 0.00 0.00 41.76 5.68
551 559 2.967615 GAGCCTCCCGCATAACGC 60.968 66.667 0.00 0.00 41.76 4.84
552 560 1.883084 GTGAGCCTCCCGCATAACG 60.883 63.158 0.00 0.00 41.38 3.18
553 561 1.883084 CGTGAGCCTCCCGCATAAC 60.883 63.158 0.00 0.00 41.38 1.89
554 562 2.016393 CTCGTGAGCCTCCCGCATAA 62.016 60.000 0.00 0.00 41.38 1.90
555 563 2.441348 TCGTGAGCCTCCCGCATA 60.441 61.111 0.00 0.00 41.38 3.14
556 564 3.842923 CTCGTGAGCCTCCCGCAT 61.843 66.667 0.00 0.00 41.38 4.73
558 566 4.500116 GACTCGTGAGCCTCCCGC 62.500 72.222 0.00 0.00 37.98 6.13
559 567 4.180946 CGACTCGTGAGCCTCCCG 62.181 72.222 0.00 0.00 0.00 5.14
560 568 3.053849 GACGACTCGTGAGCCTCCC 62.054 68.421 9.27 0.00 41.37 4.30
561 569 2.486042 GACGACTCGTGAGCCTCC 59.514 66.667 9.27 0.00 41.37 4.30
562 570 2.486042 GGACGACTCGTGAGCCTC 59.514 66.667 9.27 0.00 41.37 4.70
563 571 3.063084 GGGACGACTCGTGAGCCT 61.063 66.667 9.27 0.00 41.37 4.58
564 572 3.371063 TGGGACGACTCGTGAGCC 61.371 66.667 9.27 3.99 41.37 4.70
565 573 2.126424 GTGGGACGACTCGTGAGC 60.126 66.667 9.27 0.00 41.37 4.26
566 574 0.387367 CAAGTGGGACGACTCGTGAG 60.387 60.000 9.27 0.00 41.37 3.51
567 575 1.658114 CAAGTGGGACGACTCGTGA 59.342 57.895 9.27 0.00 41.37 4.35
568 576 2.022129 GCAAGTGGGACGACTCGTG 61.022 63.158 9.27 0.00 41.37 4.35
569 577 2.338984 GCAAGTGGGACGACTCGT 59.661 61.111 3.08 3.08 45.10 4.18
570 578 1.734477 CTGCAAGTGGGACGACTCG 60.734 63.158 0.00 0.00 0.00 4.18
571 579 2.029844 GCTGCAAGTGGGACGACTC 61.030 63.158 0.00 0.00 35.30 3.36
572 580 2.031163 GCTGCAAGTGGGACGACT 59.969 61.111 0.00 0.00 35.30 4.18
573 581 1.672356 ATGCTGCAAGTGGGACGAC 60.672 57.895 6.36 0.00 35.30 4.34
574 582 1.672030 CATGCTGCAAGTGGGACGA 60.672 57.895 6.36 0.00 35.30 4.20
575 583 1.028330 ATCATGCTGCAAGTGGGACG 61.028 55.000 6.36 0.00 35.30 4.79
576 584 0.454600 CATCATGCTGCAAGTGGGAC 59.545 55.000 6.36 0.00 35.30 4.46
577 585 0.038599 ACATCATGCTGCAAGTGGGA 59.961 50.000 6.36 0.00 35.30 4.37
578 586 0.892755 AACATCATGCTGCAAGTGGG 59.107 50.000 6.36 0.63 35.30 4.61
579 587 1.816835 AGAACATCATGCTGCAAGTGG 59.183 47.619 6.36 1.71 35.30 4.00
580 588 2.863739 CAGAACATCATGCTGCAAGTG 58.136 47.619 6.36 8.51 35.30 3.16
586 594 0.745486 TCCGGCAGAACATCATGCTG 60.745 55.000 0.00 0.00 46.28 4.41
587 595 0.182061 ATCCGGCAGAACATCATGCT 59.818 50.000 0.00 0.00 42.19 3.79
588 596 0.309922 CATCCGGCAGAACATCATGC 59.690 55.000 0.00 0.00 41.80 4.06
589 597 0.309922 GCATCCGGCAGAACATCATG 59.690 55.000 0.00 0.00 43.97 3.07
590 598 1.162181 CGCATCCGGCAGAACATCAT 61.162 55.000 0.00 0.00 45.17 2.45
591 599 1.815003 CGCATCCGGCAGAACATCA 60.815 57.895 0.00 0.00 45.17 3.07
592 600 3.017323 CGCATCCGGCAGAACATC 58.983 61.111 0.00 0.00 45.17 3.06
593 601 3.204827 GCGCATCCGGCAGAACAT 61.205 61.111 0.30 0.00 45.17 2.71
601 609 1.444212 CTTTTGTTGGCGCATCCGG 60.444 57.895 10.83 0.00 37.80 5.14
602 610 2.088178 GCTTTTGTTGGCGCATCCG 61.088 57.895 10.83 0.00 37.80 4.18
603 611 0.319813 AAGCTTTTGTTGGCGCATCC 60.320 50.000 10.83 0.00 0.00 3.51
604 612 1.985684 GTAAGCTTTTGTTGGCGCATC 59.014 47.619 10.83 0.00 0.00 3.91
605 613 1.336795 GGTAAGCTTTTGTTGGCGCAT 60.337 47.619 10.83 0.00 0.00 4.73
606 614 0.031449 GGTAAGCTTTTGTTGGCGCA 59.969 50.000 10.83 0.00 0.00 6.09
607 615 1.001745 CGGTAAGCTTTTGTTGGCGC 61.002 55.000 3.20 0.00 0.00 6.53
608 616 1.001745 GCGGTAAGCTTTTGTTGGCG 61.002 55.000 3.20 0.00 44.04 5.69
609 617 2.809181 GCGGTAAGCTTTTGTTGGC 58.191 52.632 3.20 0.00 44.04 4.52
680 688 7.333528 TCACCTATGATTTTTAATGGCAGTC 57.666 36.000 0.00 0.00 0.00 3.51
910 921 0.536006 GATTTGAGGGGATCGCCTGG 60.536 60.000 34.05 0.00 0.00 4.45
939 950 0.540830 CGATCGAAGGAGAGGGGGAT 60.541 60.000 10.26 0.00 0.00 3.85
1046 1057 1.817209 GCGAAGGAGGACGAGGATT 59.183 57.895 0.00 0.00 0.00 3.01
1082 1093 5.212934 GTCGAGGGAAGAATGAACAAAAAC 58.787 41.667 0.00 0.00 0.00 2.43
1084 1095 3.818773 GGTCGAGGGAAGAATGAACAAAA 59.181 43.478 0.00 0.00 0.00 2.44
1092 1103 2.494918 CGCGGTCGAGGGAAGAAT 59.505 61.111 0.00 0.00 38.10 2.40
1186 1199 3.377485 CCTTTCCAGAGATGCATGTTCTG 59.623 47.826 22.33 22.33 38.41 3.02
1187 1200 3.618351 CCTTTCCAGAGATGCATGTTCT 58.382 45.455 2.46 3.98 0.00 3.01
1201 1214 0.034186 ATTCCTCGCATGCCTTTCCA 60.034 50.000 13.15 0.00 0.00 3.53
1312 1325 5.350504 AGATCGATCACTTGAACAGGAAT 57.649 39.130 26.47 0.00 0.00 3.01
1330 1343 2.695359 TCACACCGCCTAACAAAGATC 58.305 47.619 0.00 0.00 0.00 2.75
1345 1364 2.264813 GTGGCATGCAATCAATCACAC 58.735 47.619 21.36 10.89 0.00 3.82
1400 1419 4.346730 TCATGGCTTCATCAACCATTTCT 58.653 39.130 0.00 0.00 42.31 2.52
1401 1420 4.724074 TCATGGCTTCATCAACCATTTC 57.276 40.909 0.00 0.00 42.31 2.17
1402 1421 6.551975 TCATATCATGGCTTCATCAACCATTT 59.448 34.615 0.00 0.00 42.31 2.32
1403 1422 6.072649 TCATATCATGGCTTCATCAACCATT 58.927 36.000 0.00 0.00 42.31 3.16
1453 1476 5.819825 AGTTGGTGAAACAGAAAAGAGAC 57.180 39.130 0.00 0.00 41.61 3.36
1477 1500 3.613299 GCTGTTACGCCTTTCTCTAGAAC 59.387 47.826 0.00 0.00 33.13 3.01
1578 1601 1.371558 CTATAAGCCCCACTCCCGC 59.628 63.158 0.00 0.00 0.00 6.13
1595 1619 0.110486 ACAATTCACCACTTCGGGCT 59.890 50.000 0.00 0.00 40.22 5.19
1608 1632 6.317140 TGAGGATTGTGATCTGCTTACAATTC 59.683 38.462 9.09 7.62 43.03 2.17
1638 1662 1.064685 GGTAACTAGGCAAGCCATGGT 60.065 52.381 14.67 6.50 38.92 3.55
1671 1695 0.804989 GAACAAATCCAGCTCCACGG 59.195 55.000 0.00 0.00 0.00 4.94
1685 1709 0.466543 ACGCCAGTGTACAGGAACAA 59.533 50.000 5.35 0.00 0.00 2.83
1708 1732 6.705302 ACATATATGATGCCTGTAGTGAAGG 58.295 40.000 19.63 0.00 37.91 3.46
1757 1781 4.556135 CACATACAATTTGCTGCTCTTTCG 59.444 41.667 0.00 0.00 0.00 3.46
1761 1785 3.441572 GGACACATACAATTTGCTGCTCT 59.558 43.478 0.00 0.00 0.00 4.09
1787 1811 9.231297 TCTGCTTAAGTAAAGAAAATGCAGTAT 57.769 29.630 4.02 0.00 43.73 2.12
1798 1822 6.659242 CCAAAATCCCTCTGCTTAAGTAAAGA 59.341 38.462 4.02 4.67 37.38 2.52
1867 1891 7.273164 TGCAAATTGCTCAATTAGTGAAATACG 59.727 33.333 19.34 0.00 45.31 3.06
1935 1959 5.700846 AGATGTTATATAGCACGAACCTCG 58.299 41.667 0.91 0.00 46.93 4.63
2015 2039 2.481795 GCTCAACAAAACATGTGCCACT 60.482 45.455 0.00 0.00 42.99 4.00
2034 2058 7.651027 AATTATTCTAAGAACATGGCTTGCT 57.349 32.000 11.89 0.00 0.00 3.91
2178 2203 2.751436 CACCATGGACCCAAGGCG 60.751 66.667 21.47 0.00 38.26 5.52
2246 2271 2.954318 CAATGCCATGGACCTTAGGAAG 59.046 50.000 18.40 0.00 0.00 3.46
2256 2281 1.983481 GCCACCACAATGCCATGGA 60.983 57.895 18.40 0.31 39.46 3.41
2257 2282 2.580276 GCCACCACAATGCCATGG 59.420 61.111 7.63 7.63 42.13 3.66
2264 2289 0.677731 CATCCTCACGCCACCACAAT 60.678 55.000 0.00 0.00 0.00 2.71
2311 2336 1.079438 AACGCCTCTCCCTCCTCTT 59.921 57.895 0.00 0.00 0.00 2.85
2331 2356 1.483415 CCATTTTCTCCCCATTGCTGG 59.517 52.381 0.00 0.00 42.73 4.85
2345 2370 2.884012 TCGTCATCAGCACAACCATTTT 59.116 40.909 0.00 0.00 0.00 1.82
2353 2378 0.460811 GCATCCTCGTCATCAGCACA 60.461 55.000 0.00 0.00 0.00 4.57
2423 2448 1.163420 TAACAGCACTGCCACCAACG 61.163 55.000 0.00 0.00 0.00 4.10
2667 4364 9.917129 TTACCGTTACCATACATACATTATCTG 57.083 33.333 0.00 0.00 0.00 2.90
2726 4423 1.395826 GGCGACCTCACCATCTAGCT 61.396 60.000 0.00 0.00 0.00 3.32
2728 4425 1.609555 GTAGGCGACCTCACCATCTAG 59.390 57.143 1.46 0.00 34.61 2.43
2965 4664 0.537828 TTTTGGTACCAGGGAACGGC 60.538 55.000 15.65 0.00 0.00 5.68
2968 4667 2.368311 TGGTTTTGGTACCAGGGAAC 57.632 50.000 15.65 18.97 43.14 3.62
3020 4721 7.776107 ACATCAAGAGATCTTACATTCGAGAA 58.224 34.615 0.00 0.00 34.28 2.87
3112 4821 8.687824 AAAACATATTAAATGAACTTCGGCAG 57.312 30.769 5.11 0.00 0.00 4.85
3295 5011 8.840321 AGTAATTAATCACAAGCATGATACCAC 58.160 33.333 0.00 0.00 38.40 4.16
3465 5188 5.010922 CAGTTCATTTTCCCAAGATGGAACA 59.989 40.000 0.00 0.00 43.97 3.18
3466 5189 5.243730 TCAGTTCATTTTCCCAAGATGGAAC 59.756 40.000 0.00 0.00 43.97 3.62
3467 5190 5.243730 GTCAGTTCATTTTCCCAAGATGGAA 59.756 40.000 0.00 0.00 40.96 3.53
3468 5191 4.766891 GTCAGTTCATTTTCCCAAGATGGA 59.233 41.667 0.00 0.00 40.96 3.41
3469 5192 4.082026 GGTCAGTTCATTTTCCCAAGATGG 60.082 45.833 0.00 0.00 37.25 3.51
3470 5193 4.523943 TGGTCAGTTCATTTTCCCAAGATG 59.476 41.667 0.00 0.00 0.00 2.90
3471 5194 4.739793 TGGTCAGTTCATTTTCCCAAGAT 58.260 39.130 0.00 0.00 0.00 2.40
3472 5195 4.177537 TGGTCAGTTCATTTTCCCAAGA 57.822 40.909 0.00 0.00 0.00 3.02
3473 5196 5.244626 AGAATGGTCAGTTCATTTTCCCAAG 59.755 40.000 0.00 0.00 35.26 3.61
3474 5197 5.147032 AGAATGGTCAGTTCATTTTCCCAA 58.853 37.500 0.00 0.00 35.26 4.12
3475 5198 4.739793 AGAATGGTCAGTTCATTTTCCCA 58.260 39.130 0.00 0.00 35.26 4.37
3476 5199 5.728637 AAGAATGGTCAGTTCATTTTCCC 57.271 39.130 0.00 0.00 35.26 3.97
3477 5200 6.748132 TCAAAGAATGGTCAGTTCATTTTCC 58.252 36.000 0.00 0.00 35.26 3.13
3478 5201 8.822652 AATCAAAGAATGGTCAGTTCATTTTC 57.177 30.769 0.00 0.00 35.26 2.29
3479 5202 9.617523 AAAATCAAAGAATGGTCAGTTCATTTT 57.382 25.926 0.00 0.00 35.26 1.82
3480 5203 9.617523 AAAAATCAAAGAATGGTCAGTTCATTT 57.382 25.926 0.00 0.00 35.26 2.32
4254 8556 1.274703 GGAACTGGAGATGGGCAGGA 61.275 60.000 0.00 0.00 0.00 3.86
4256 8558 0.329261 TTGGAACTGGAGATGGGCAG 59.671 55.000 0.00 0.00 0.00 4.85
4257 8559 0.038166 GTTGGAACTGGAGATGGGCA 59.962 55.000 0.00 0.00 0.00 5.36
4566 11158 3.233355 GGTGCGAGACCATCAAAGT 57.767 52.632 0.00 0.00 45.34 2.66
4673 11743 2.100584 GCAGTCAGCTAGTAGCATCAGT 59.899 50.000 23.77 7.16 45.56 3.41
4697 11767 5.290885 CAGAAAAAGAAAACAAGAAACGGGG 59.709 40.000 0.00 0.00 0.00 5.73
4713 11783 7.035004 TGAGACAATTTTGGTGACAGAAAAAG 58.965 34.615 0.00 0.00 44.54 2.27
4717 11787 6.513230 CGATTGAGACAATTTTGGTGACAGAA 60.513 38.462 0.00 0.00 44.54 3.02
4718 11788 5.049474 CGATTGAGACAATTTTGGTGACAGA 60.049 40.000 0.00 0.00 44.54 3.41
4722 11792 5.278266 GGAACGATTGAGACAATTTTGGTGA 60.278 40.000 0.00 0.00 0.00 4.02
4731 11801 3.469008 AGTGTGGAACGATTGAGACAA 57.531 42.857 0.00 0.00 42.39 3.18
4783 11854 4.475944 GGTTTGGATTCGATTCAGTGTTG 58.524 43.478 9.36 0.00 0.00 3.33
4809 11880 4.129380 CGCATCTCTGGAATTGGAATACA 58.871 43.478 0.00 0.00 0.00 2.29
4988 14869 9.489084 CCTTTGATGCATCATGAAATCAATATT 57.511 29.630 29.13 0.00 36.56 1.28
4989 14870 8.866093 TCCTTTGATGCATCATGAAATCAATAT 58.134 29.630 29.13 4.85 36.56 1.28
4991 14872 6.984474 GTCCTTTGATGCATCATGAAATCAAT 59.016 34.615 29.13 6.20 36.56 2.57
4992 14873 6.071278 TGTCCTTTGATGCATCATGAAATCAA 60.071 34.615 29.13 17.12 36.56 2.57
4993 14874 5.419471 TGTCCTTTGATGCATCATGAAATCA 59.581 36.000 29.13 19.51 36.56 2.57
4994 14875 5.898174 TGTCCTTTGATGCATCATGAAATC 58.102 37.500 29.13 17.50 36.56 2.17
5010 15053 5.766150 TCAACACGAAATCAATGTCCTTT 57.234 34.783 0.00 0.00 0.00 3.11
5133 15176 9.313118 GTACATTCATTTGAGGAACAAGTTTTT 57.687 29.630 0.00 0.00 39.77 1.94
5134 15177 7.926018 GGTACATTCATTTGAGGAACAAGTTTT 59.074 33.333 0.00 0.00 39.77 2.43
5135 15178 7.433680 GGTACATTCATTTGAGGAACAAGTTT 58.566 34.615 0.00 0.00 39.77 2.66
5136 15179 6.015434 GGGTACATTCATTTGAGGAACAAGTT 60.015 38.462 0.00 0.00 39.77 2.66
5137 15180 5.476945 GGGTACATTCATTTGAGGAACAAGT 59.523 40.000 0.00 0.00 39.77 3.16
5138 15181 5.476599 TGGGTACATTCATTTGAGGAACAAG 59.523 40.000 0.00 0.00 39.77 3.16
5139 15182 5.389520 TGGGTACATTCATTTGAGGAACAA 58.610 37.500 0.00 0.00 36.65 2.83
5140 15183 4.991776 TGGGTACATTCATTTGAGGAACA 58.008 39.130 0.00 0.00 0.00 3.18
5141 15184 4.142381 GCTGGGTACATTCATTTGAGGAAC 60.142 45.833 0.00 0.00 0.00 3.62
5142 15185 4.016444 GCTGGGTACATTCATTTGAGGAA 58.984 43.478 0.00 0.00 0.00 3.36
5143 15186 3.010027 TGCTGGGTACATTCATTTGAGGA 59.990 43.478 0.00 0.00 0.00 3.71
5144 15187 3.129287 GTGCTGGGTACATTCATTTGAGG 59.871 47.826 0.00 0.00 0.00 3.86
5145 15188 3.758023 TGTGCTGGGTACATTCATTTGAG 59.242 43.478 0.00 0.00 0.00 3.02
5146 15189 3.760738 TGTGCTGGGTACATTCATTTGA 58.239 40.909 0.00 0.00 0.00 2.69
5147 15190 4.517952 TTGTGCTGGGTACATTCATTTG 57.482 40.909 0.00 0.00 0.00 2.32
5148 15191 5.543507 TTTTGTGCTGGGTACATTCATTT 57.456 34.783 0.00 0.00 0.00 2.32
5149 15192 5.743636 ATTTTGTGCTGGGTACATTCATT 57.256 34.783 0.00 0.00 0.00 2.57
5150 15193 5.743636 AATTTTGTGCTGGGTACATTCAT 57.256 34.783 0.00 0.00 0.00 2.57
5151 15194 5.772672 ACTAATTTTGTGCTGGGTACATTCA 59.227 36.000 0.00 0.00 0.00 2.57
5152 15195 6.092748 CACTAATTTTGTGCTGGGTACATTC 58.907 40.000 0.00 0.00 0.00 2.67
5153 15196 5.538433 ACACTAATTTTGTGCTGGGTACATT 59.462 36.000 10.31 0.00 38.86 2.71
5154 15197 5.076873 ACACTAATTTTGTGCTGGGTACAT 58.923 37.500 10.31 0.00 38.86 2.29
5155 15198 4.465886 ACACTAATTTTGTGCTGGGTACA 58.534 39.130 10.31 0.00 38.86 2.90
5156 15199 5.447624 AACACTAATTTTGTGCTGGGTAC 57.552 39.130 10.31 0.00 38.86 3.34
5157 15200 6.535540 TCTAACACTAATTTTGTGCTGGGTA 58.464 36.000 10.31 0.00 38.86 3.69
5158 15201 5.381757 TCTAACACTAATTTTGTGCTGGGT 58.618 37.500 10.31 0.00 38.86 4.51
5159 15202 5.957842 TCTAACACTAATTTTGTGCTGGG 57.042 39.130 10.31 0.95 38.86 4.45
5201 15244 2.425668 CCGAAACAAGTTGTCCCAAACT 59.574 45.455 9.40 0.00 42.21 2.66
5202 15245 2.424246 TCCGAAACAAGTTGTCCCAAAC 59.576 45.455 9.40 0.00 0.00 2.93
5203 15246 2.424246 GTCCGAAACAAGTTGTCCCAAA 59.576 45.455 9.40 0.00 0.00 3.28
5204 15247 2.018515 GTCCGAAACAAGTTGTCCCAA 58.981 47.619 9.40 0.00 0.00 4.12
5205 15248 1.670791 GTCCGAAACAAGTTGTCCCA 58.329 50.000 9.40 0.00 0.00 4.37
5206 15249 0.584876 CGTCCGAAACAAGTTGTCCC 59.415 55.000 9.40 3.37 0.00 4.46
5207 15250 1.259770 GTCGTCCGAAACAAGTTGTCC 59.740 52.381 9.40 3.74 0.00 4.02
5208 15251 2.199236 AGTCGTCCGAAACAAGTTGTC 58.801 47.619 9.40 0.00 0.00 3.18
5209 15252 2.304751 AGTCGTCCGAAACAAGTTGT 57.695 45.000 1.64 1.64 0.00 3.32
5210 15253 4.782252 TTAAGTCGTCCGAAACAAGTTG 57.218 40.909 0.00 0.00 0.00 3.16
5211 15254 5.996669 AATTAAGTCGTCCGAAACAAGTT 57.003 34.783 0.00 0.00 0.00 2.66
5212 15255 5.996669 AAATTAAGTCGTCCGAAACAAGT 57.003 34.783 0.00 0.00 0.00 3.16
5213 15256 6.358822 GGAAAAATTAAGTCGTCCGAAACAAG 59.641 38.462 0.00 0.00 0.00 3.16
5214 15257 6.038492 AGGAAAAATTAAGTCGTCCGAAACAA 59.962 34.615 0.00 0.00 0.00 2.83
5215 15258 5.528320 AGGAAAAATTAAGTCGTCCGAAACA 59.472 36.000 0.00 0.00 0.00 2.83
5216 15259 5.993891 AGGAAAAATTAAGTCGTCCGAAAC 58.006 37.500 0.00 0.00 0.00 2.78
5217 15260 6.622833 AAGGAAAAATTAAGTCGTCCGAAA 57.377 33.333 0.00 0.00 0.00 3.46
5218 15261 6.622833 AAAGGAAAAATTAAGTCGTCCGAA 57.377 33.333 0.00 0.00 0.00 4.30
5219 15262 6.622833 AAAAGGAAAAATTAAGTCGTCCGA 57.377 33.333 0.00 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.