Multiple sequence alignment - TraesCS3D01G418100

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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 TraesCS3D01G418100 chr3D 100.000 5726 0 0 1 5726 530414470 530420195 0.000000e+00 10575.0
1 TraesCS3D01G418100 chr3D 80.179 1115 136 29 3420 4453 529903404 529904514 0.000000e+00 756.0
2 TraesCS3D01G418100 chr3D 81.170 786 95 23 1018 1788 529898572 529899319 2.970000e-162 582.0
3 TraesCS3D01G418100 chr3D 85.714 147 14 7 5297 5442 530275278 530275418 1.290000e-31 148.0
4 TraesCS3D01G418100 chr3D 97.059 34 0 1 2259 2292 530416681 530416713 8.010000e-04 56.5
5 TraesCS3D01G418100 chr3D 97.059 34 0 1 2212 2244 530416728 530416761 8.010000e-04 56.5
6 TraesCS3D01G418100 chr3A 94.182 1461 52 9 769 2211 664136865 664138310 0.000000e+00 2196.0
7 TraesCS3D01G418100 chr3A 94.628 1117 38 5 3367 4477 664139539 664140639 0.000000e+00 1711.0
8 TraesCS3D01G418100 chr3A 90.746 1167 60 22 2240 3372 664138357 664139509 0.000000e+00 1513.0
9 TraesCS3D01G418100 chr3A 94.085 710 22 9 4579 5281 664140636 664141332 0.000000e+00 1061.0
10 TraesCS3D01G418100 chr3A 79.570 1116 140 34 3420 4453 664102306 664103415 0.000000e+00 717.0
11 TraesCS3D01G418100 chr3A 83.000 500 70 7 1019 1518 664098877 664099361 6.810000e-119 438.0
12 TraesCS3D01G418100 chr3A 94.872 234 11 1 5278 5510 664143064 664143297 1.170000e-96 364.0
13 TraesCS3D01G418100 chr3A 97.653 213 3 2 5515 5726 664143389 664143600 1.170000e-96 364.0
14 TraesCS3D01G418100 chr3A 86.344 227 7 6 564 782 664136346 664136556 5.770000e-55 226.0
15 TraesCS3D01G418100 chr3A 90.551 127 11 1 4474 4599 620765531 620765657 3.550000e-37 167.0
16 TraesCS3D01G418100 chr3A 97.059 34 0 1 2212 2244 664138376 664138409 8.010000e-04 56.5
17 TraesCS3D01G418100 chr3B 91.667 576 44 3 1 574 809340726 809340153 0.000000e+00 795.0
18 TraesCS3D01G418100 chr3B 90.718 571 34 10 1 564 783144163 783143605 0.000000e+00 743.0
19 TraesCS3D01G418100 chr3B 80.510 785 97 30 1018 1785 700926917 700927662 8.390000e-153 551.0
20 TraesCS3D01G418100 chr5A 92.049 566 41 3 1 564 336952173 336951610 0.000000e+00 793.0
21 TraesCS3D01G418100 chr5A 90.476 567 49 4 1 564 336643537 336644101 0.000000e+00 743.0
22 TraesCS3D01G418100 chr5A 74.115 1186 187 65 3367 4454 696477226 696478389 4.190000e-101 379.0
23 TraesCS3D01G418100 chr5A 81.400 457 62 12 1056 1499 683656739 683657185 9.130000e-93 351.0
24 TraesCS3D01G418100 chr5A 80.380 474 58 20 1035 1504 687366557 687366115 1.540000e-85 327.0
25 TraesCS3D01G418100 chr5A 81.579 418 54 12 1056 1460 681872451 681872044 1.990000e-84 324.0
26 TraesCS3D01G418100 chr5A 78.189 486 66 14 3531 3987 687362670 687362196 2.030000e-69 274.0
27 TraesCS3D01G418100 chr5A 76.891 476 63 25 1039 1501 696475907 696476348 5.770000e-55 226.0
28 TraesCS3D01G418100 chr5A 97.222 108 3 0 4473 4580 654382299 654382192 3.520000e-42 183.0
29 TraesCS3D01G418100 chr5A 91.200 125 9 2 4474 4597 392583823 392583700 9.870000e-38 169.0
30 TraesCS3D01G418100 chr2A 90.973 565 39 8 1 562 13404593 13405148 0.000000e+00 750.0
31 TraesCS3D01G418100 chr2A 90.317 568 41 8 1 564 587907165 587906608 0.000000e+00 732.0
32 TraesCS3D01G418100 chr2A 90.018 571 45 9 1 564 644843849 644843284 0.000000e+00 728.0
33 TraesCS3D01G418100 chr2A 97.196 107 3 0 4474 4580 767559912 767560018 1.270000e-41 182.0
34 TraesCS3D01G418100 chr2A 91.406 128 9 2 4477 4603 79166798 79166924 2.120000e-39 174.0
35 TraesCS3D01G418100 chr2A 93.966 116 6 1 4473 4588 96153219 96153105 2.120000e-39 174.0
36 TraesCS3D01G418100 chr6B 89.369 555 34 12 1 549 6618524 6617989 0.000000e+00 675.0
37 TraesCS3D01G418100 chr4D 77.078 1095 154 45 3435 4457 500680296 500679227 5.050000e-150 542.0
38 TraesCS3D01G418100 chr4D 81.917 459 62 14 1056 1499 500682606 500682154 9.060000e-98 368.0
39 TraesCS3D01G418100 chr4D 81.489 470 54 20 1035 1501 503140323 503140762 7.060000e-94 355.0
40 TraesCS3D01G418100 chr4D 74.111 1012 145 52 3531 4465 503144895 503145866 5.570000e-80 309.0
41 TraesCS3D01G418100 chr4D 76.123 423 67 19 4079 4470 500551507 500551088 2.110000e-44 191.0
42 TraesCS3D01G418100 chr4D 87.156 109 14 0 4347 4455 508938831 508938939 2.170000e-24 124.0
43 TraesCS3D01G418100 chr5B 83.929 504 67 10 67 564 495440607 495441102 2.420000e-128 470.0
44 TraesCS3D01G418100 chrUn 80.833 480 68 11 1030 1494 377122401 377122871 7.060000e-94 355.0
45 TraesCS3D01G418100 chrUn 80.833 480 68 11 1030 1494 377129665 377130135 7.060000e-94 355.0
46 TraesCS3D01G418100 chrUn 80.417 480 70 11 1030 1494 10166045 10165575 1.530000e-90 344.0
47 TraesCS3D01G418100 chrUn 75.113 221 25 9 3367 3580 359681386 359681583 6.150000e-10 76.8
48 TraesCS3D01G418100 chrUn 75.113 221 25 13 3367 3580 446001076 446001273 6.150000e-10 76.8
49 TraesCS3D01G418100 chr4B 81.410 468 56 18 1039 1504 647763344 647762906 2.540000e-93 353.0
50 TraesCS3D01G418100 chr4B 76.899 632 91 31 3435 4037 644347333 644347938 2.000000e-79 307.0
51 TraesCS3D01G418100 chr4B 75.676 592 97 26 3699 4268 647759376 647758810 9.520000e-63 252.0
52 TraesCS3D01G418100 chr4B 75.507 592 98 25 3699 4268 648066573 648067139 4.430000e-61 246.0
53 TraesCS3D01G418100 chr4B 84.615 130 19 1 4336 4465 647758715 647758587 1.670000e-25 128.0
54 TraesCS3D01G418100 chr4B 80.303 132 20 4 4330 4458 658612732 658612604 1.700000e-15 95.3
55 TraesCS3D01G418100 chr4B 80.303 132 20 4 4330 4458 658643707 658643579 1.700000e-15 95.3
56 TraesCS3D01G418100 chr1A 94.118 119 7 0 4472 4590 499985464 499985346 1.270000e-41 182.0
57 TraesCS3D01G418100 chr6A 93.220 118 8 0 4473 4590 74530455 74530572 2.120000e-39 174.0
58 TraesCS3D01G418100 chr4A 93.103 116 7 1 4466 4580 343923576 343923691 9.870000e-38 169.0


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 TraesCS3D01G418100 chr3D 530414470 530420195 5725 False 3562.666667 10575 98.039333 1 5726 3 chr3D.!!$F4 5725
1 TraesCS3D01G418100 chr3D 529903404 529904514 1110 False 756.000000 756 80.179000 3420 4453 1 chr3D.!!$F2 1033
2 TraesCS3D01G418100 chr3D 529898572 529899319 747 False 582.000000 582 81.170000 1018 1788 1 chr3D.!!$F1 770
3 TraesCS3D01G418100 chr3A 664136346 664143600 7254 False 936.437500 2196 93.696125 564 5726 8 chr3A.!!$F3 5162
4 TraesCS3D01G418100 chr3A 664098877 664103415 4538 False 577.500000 717 81.285000 1019 4453 2 chr3A.!!$F2 3434
5 TraesCS3D01G418100 chr3B 809340153 809340726 573 True 795.000000 795 91.667000 1 574 1 chr3B.!!$R2 573
6 TraesCS3D01G418100 chr3B 783143605 783144163 558 True 743.000000 743 90.718000 1 564 1 chr3B.!!$R1 563
7 TraesCS3D01G418100 chr3B 700926917 700927662 745 False 551.000000 551 80.510000 1018 1785 1 chr3B.!!$F1 767
8 TraesCS3D01G418100 chr5A 336951610 336952173 563 True 793.000000 793 92.049000 1 564 1 chr5A.!!$R1 563
9 TraesCS3D01G418100 chr5A 336643537 336644101 564 False 743.000000 743 90.476000 1 564 1 chr5A.!!$F1 563
10 TraesCS3D01G418100 chr5A 696475907 696478389 2482 False 302.500000 379 75.503000 1039 4454 2 chr5A.!!$F3 3415
11 TraesCS3D01G418100 chr5A 687362196 687366557 4361 True 300.500000 327 79.284500 1035 3987 2 chr5A.!!$R5 2952
12 TraesCS3D01G418100 chr2A 13404593 13405148 555 False 750.000000 750 90.973000 1 562 1 chr2A.!!$F1 561
13 TraesCS3D01G418100 chr2A 587906608 587907165 557 True 732.000000 732 90.317000 1 564 1 chr2A.!!$R2 563
14 TraesCS3D01G418100 chr2A 644843284 644843849 565 True 728.000000 728 90.018000 1 564 1 chr2A.!!$R3 563
15 TraesCS3D01G418100 chr6B 6617989 6618524 535 True 675.000000 675 89.369000 1 549 1 chr6B.!!$R1 548
16 TraesCS3D01G418100 chr4D 500679227 500682606 3379 True 455.000000 542 79.497500 1056 4457 2 chr4D.!!$R2 3401
17 TraesCS3D01G418100 chr4D 503144895 503145866 971 False 309.000000 309 74.111000 3531 4465 1 chr4D.!!$F2 934
18 TraesCS3D01G418100 chr4B 644347333 644347938 605 False 307.000000 307 76.899000 3435 4037 1 chr4B.!!$F1 602
19 TraesCS3D01G418100 chr4B 648066573 648067139 566 False 246.000000 246 75.507000 3699 4268 1 chr4B.!!$F2 569
20 TraesCS3D01G418100 chr4B 647758587 647763344 4757 True 244.333333 353 80.567000 1039 4465 3 chr4B.!!$R3 3426

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
703 723 0.530870 GGTGGCCTCTGCTTATCGTC 60.531 60.0 3.32 0.00 37.74 4.20 F
1891 2689 0.037326 TCTTGGCATCACGTCTCCAC 60.037 55.0 0.00 0.00 0.00 4.02 F
3372 6839 0.590195 GTGAACACAGGAAGCAGCTG 59.410 55.0 10.11 10.11 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2655 5918 0.701310 AACCCATGATACCCCCTCCC 60.701 60.0 0.0 0.0 0.0 4.30 R
3786 9216 0.752743 ATGATGTTCCCATGCCACGG 60.753 55.0 0.0 0.0 0.0 4.94 R
5290 12565 0.343372 AGTCAGGGATTGGGCTAGGA 59.657 55.0 0.0 0.0 0.0 2.94 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 27 8.593945 TTTTAGAAAATGGGATAACATCTGCT 57.406 30.769 0.00 0.00 0.00 4.24
60 62 3.120546 GCATACACGCTAGCCACAATATG 60.121 47.826 9.66 11.05 0.00 1.78
154 158 4.429854 AGTCAGAAAGATTATGAGGGCC 57.570 45.455 0.00 0.00 0.00 5.80
241 247 1.133325 AGGGAGTAGCTCACGGATGAT 60.133 52.381 0.00 0.00 39.19 2.45
334 346 6.331369 TGAATGATAGTGAGTCATGCGATA 57.669 37.500 0.00 0.00 34.86 2.92
393 406 3.131755 GGTGTTCCTATTAGGCGTACACT 59.868 47.826 25.20 0.00 39.55 3.55
442 455 5.928839 AGGACGATAAGCAATGATACATGTC 59.071 40.000 0.00 0.00 0.00 3.06
443 456 5.120830 GGACGATAAGCAATGATACATGTCC 59.879 44.000 0.00 0.00 34.84 4.02
450 463 3.246226 GCAATGATACATGTCCGACACTC 59.754 47.826 0.00 0.00 0.00 3.51
455 469 2.154854 ACATGTCCGACACTCTGTTG 57.845 50.000 2.57 0.00 0.00 3.33
578 594 7.836842 TGTTTGCTAGTGAATACTGATGACTA 58.163 34.615 0.00 0.00 37.78 2.59
579 595 7.759886 TGTTTGCTAGTGAATACTGATGACTAC 59.240 37.037 0.00 0.00 37.78 2.73
580 596 7.404671 TTGCTAGTGAATACTGATGACTACA 57.595 36.000 0.00 0.00 37.78 2.74
600 616 4.028131 ACATGAGTACGAAATAGGACCCA 58.972 43.478 0.00 0.00 0.00 4.51
601 617 4.142004 ACATGAGTACGAAATAGGACCCAC 60.142 45.833 0.00 0.00 0.00 4.61
602 618 3.433343 TGAGTACGAAATAGGACCCACA 58.567 45.455 0.00 0.00 0.00 4.17
603 619 4.028131 TGAGTACGAAATAGGACCCACAT 58.972 43.478 0.00 0.00 0.00 3.21
604 620 5.202765 TGAGTACGAAATAGGACCCACATA 58.797 41.667 0.00 0.00 0.00 2.29
690 710 4.754667 GTCGTCCTTCCGGTGGCC 62.755 72.222 0.00 0.00 0.00 5.36
697 717 3.249189 TTCCGGTGGCCTCTGCTT 61.249 61.111 3.32 0.00 37.74 3.91
698 718 1.899437 CTTCCGGTGGCCTCTGCTTA 61.899 60.000 3.32 0.00 37.74 3.09
699 719 1.271840 TTCCGGTGGCCTCTGCTTAT 61.272 55.000 3.32 0.00 37.74 1.73
700 720 1.227674 CCGGTGGCCTCTGCTTATC 60.228 63.158 3.32 0.00 37.74 1.75
701 721 1.592669 CGGTGGCCTCTGCTTATCG 60.593 63.158 3.32 0.00 37.74 2.92
702 722 1.522569 GGTGGCCTCTGCTTATCGT 59.477 57.895 3.32 0.00 37.74 3.73
703 723 0.530870 GGTGGCCTCTGCTTATCGTC 60.531 60.000 3.32 0.00 37.74 4.20
704 724 0.530870 GTGGCCTCTGCTTATCGTCC 60.531 60.000 3.32 0.00 37.74 4.79
720 740 4.330944 TCGTCCTAATTTCCATACGCAT 57.669 40.909 0.00 0.00 0.00 4.73
743 767 1.486726 GGACAGGCACTAGCTAACCAT 59.513 52.381 9.20 0.00 41.70 3.55
756 780 6.954684 ACTAGCTAACCATATATAGCCACACT 59.045 38.462 0.00 0.00 44.42 3.55
761 785 7.063074 GCTAACCATATATAGCCACACTAAACG 59.937 40.741 3.96 0.00 38.85 3.60
767 791 8.912658 CATATATAGCCACACTAAACGTTACAG 58.087 37.037 0.00 4.65 33.57 2.74
938 1289 1.200483 CATAAATCTCTGCGTCGCGT 58.800 50.000 13.38 0.00 0.00 6.01
1006 1357 1.370172 CGACTATAGCGCCGTGGTC 60.370 63.158 2.29 9.96 0.00 4.02
1114 1465 4.021925 GGTGAGCTTGGCGAGGGT 62.022 66.667 3.44 0.00 0.00 4.34
1115 1466 2.743928 GTGAGCTTGGCGAGGGTG 60.744 66.667 3.44 0.00 0.00 4.61
1116 1467 2.922503 TGAGCTTGGCGAGGGTGA 60.923 61.111 3.44 0.00 0.00 4.02
1126 1485 2.283676 GAGGGTGAGGGGTCACGA 60.284 66.667 0.00 0.00 41.26 4.35
1648 2117 4.768968 AGACGGAAGGTAGTTTGCTAGTTA 59.231 41.667 0.00 0.00 0.00 2.24
1649 2118 5.421374 AGACGGAAGGTAGTTTGCTAGTTAT 59.579 40.000 0.00 0.00 0.00 1.89
1650 2119 6.604795 AGACGGAAGGTAGTTTGCTAGTTATA 59.395 38.462 0.00 0.00 0.00 0.98
1651 2120 6.803642 ACGGAAGGTAGTTTGCTAGTTATAG 58.196 40.000 0.00 0.00 0.00 1.31
1652 2121 6.604795 ACGGAAGGTAGTTTGCTAGTTATAGA 59.395 38.462 0.00 0.00 0.00 1.98
1653 2122 7.123247 ACGGAAGGTAGTTTGCTAGTTATAGAA 59.877 37.037 0.00 0.00 0.00 2.10
1654 2123 8.142551 CGGAAGGTAGTTTGCTAGTTATAGAAT 58.857 37.037 0.00 0.00 0.00 2.40
1655 2124 9.262358 GGAAGGTAGTTTGCTAGTTATAGAATG 57.738 37.037 0.00 0.00 0.00 2.67
1656 2125 9.819267 GAAGGTAGTTTGCTAGTTATAGAATGT 57.181 33.333 0.00 0.00 0.00 2.71
1657 2126 9.601217 AAGGTAGTTTGCTAGTTATAGAATGTG 57.399 33.333 0.00 0.00 0.00 3.21
1658 2127 8.978472 AGGTAGTTTGCTAGTTATAGAATGTGA 58.022 33.333 0.00 0.00 0.00 3.58
1659 2128 9.032420 GGTAGTTTGCTAGTTATAGAATGTGAC 57.968 37.037 0.00 0.00 0.00 3.67
1660 2129 7.757097 AGTTTGCTAGTTATAGAATGTGACG 57.243 36.000 0.00 0.00 0.00 4.35
1663 2132 6.203808 TGCTAGTTATAGAATGTGACGTGT 57.796 37.500 0.00 0.00 0.00 4.49
1664 2133 6.033966 TGCTAGTTATAGAATGTGACGTGTG 58.966 40.000 0.00 0.00 0.00 3.82
1665 2134 5.051641 GCTAGTTATAGAATGTGACGTGTGC 60.052 44.000 0.00 0.00 0.00 4.57
1767 2540 1.824230 GCTTTGGACACCATAATGGCA 59.176 47.619 0.00 0.00 42.67 4.92
1828 2624 4.861210 TCACACAACTGTCGTTTGTTTTT 58.139 34.783 0.00 0.00 0.00 1.94
1839 2635 7.062956 ACTGTCGTTTGTTTTTCAAAAATCTCC 59.937 33.333 0.00 0.00 45.84 3.71
1847 2643 8.661352 TGTTTTTCAAAAATCTCCATTTCTCC 57.339 30.769 0.00 0.00 30.37 3.71
1858 2654 6.952605 TCTCCATTTCTCCTTTTCCTCTTA 57.047 37.500 0.00 0.00 0.00 2.10
1859 2655 6.951971 TCTCCATTTCTCCTTTTCCTCTTAG 58.048 40.000 0.00 0.00 0.00 2.18
1861 2657 7.678598 TCTCCATTTCTCCTTTTCCTCTTAGTA 59.321 37.037 0.00 0.00 0.00 1.82
1891 2689 0.037326 TCTTGGCATCACGTCTCCAC 60.037 55.000 0.00 0.00 0.00 4.02
1900 2698 2.025727 CGTCTCCACCGGTATCGC 59.974 66.667 6.87 0.00 34.56 4.58
1921 2719 3.758300 CCGTTGATGACTTATGGTTTGC 58.242 45.455 0.00 0.00 0.00 3.68
2059 2867 1.609208 GCTCCTTCCTTGCAGTTCAA 58.391 50.000 0.00 0.00 0.00 2.69
2061 2869 2.856222 CTCCTTCCTTGCAGTTCAACT 58.144 47.619 0.00 0.00 0.00 3.16
2071 2879 1.570813 CAGTTCAACTGCGTGAGTGA 58.429 50.000 4.15 0.00 39.62 3.41
2162 3304 6.478588 GTGACGATATTTTGACATGGTCTTC 58.521 40.000 0.00 0.00 32.82 2.87
2211 3425 3.890756 TGCATAATTTAGAGCCACCATGG 59.109 43.478 11.19 11.19 41.55 3.66
2213 3427 4.261741 GCATAATTTAGAGCCACCATGGTG 60.262 45.833 34.08 34.08 45.02 4.17
2215 3429 4.584638 AATTTAGAGCCACCATGGTGTA 57.415 40.909 36.62 22.87 44.02 2.90
2228 3442 2.198827 TGGTGTAGCCAGTGGATTTG 57.801 50.000 15.20 0.00 43.61 2.32
2229 3443 1.702401 TGGTGTAGCCAGTGGATTTGA 59.298 47.619 15.20 0.00 43.61 2.69
2230 3444 2.107378 TGGTGTAGCCAGTGGATTTGAA 59.893 45.455 15.20 0.00 43.61 2.69
2233 3447 4.546570 GTGTAGCCAGTGGATTTGAAAAC 58.453 43.478 15.20 0.28 0.00 2.43
2236 3450 2.293399 AGCCAGTGGATTTGAAAACGTC 59.707 45.455 15.20 0.00 0.00 4.34
2237 3451 2.034053 GCCAGTGGATTTGAAAACGTCA 59.966 45.455 15.20 0.00 0.00 4.35
2238 3452 3.490078 GCCAGTGGATTTGAAAACGTCAA 60.490 43.478 15.20 0.00 44.74 3.18
2362 5379 7.589395 TGCACCAGTTTACTTACACAATATTG 58.411 34.615 14.01 14.01 0.00 1.90
2436 5489 8.538409 AATAGATGTTCTTTTTGCCATTTGAC 57.462 30.769 0.00 0.00 0.00 3.18
2773 6066 1.416030 GAAATTGTGCCAAACAGGGGT 59.584 47.619 0.00 0.00 40.74 4.95
2848 6217 2.054232 TGTCGCCCAAACACCTAAAA 57.946 45.000 0.00 0.00 0.00 1.52
2879 6248 2.685106 TGGCCAACCCAGTAATTTCA 57.315 45.000 0.61 0.00 39.18 2.69
2980 6356 8.845793 ACATAAATGGGCTAATCCTATATTGGA 58.154 33.333 8.40 8.40 34.60 3.53
3362 6829 5.006153 TGAATAGGATACGGTGAACACAG 57.994 43.478 7.25 5.49 46.39 3.66
3372 6839 0.590195 GTGAACACAGGAAGCAGCTG 59.410 55.000 10.11 10.11 0.00 4.24
3452 8799 6.304356 TGCACACTTATTTTCTCTGTTCTG 57.696 37.500 0.00 0.00 0.00 3.02
3629 9019 7.389884 AGACGTACGTATAACACATCCAGATAT 59.610 37.037 22.87 0.00 0.00 1.63
3795 9225 3.499737 GGAGCGTTCCGTGGCATG 61.500 66.667 1.31 0.00 32.79 4.06
3796 9226 3.499737 GAGCGTTCCGTGGCATGG 61.500 66.667 20.02 20.02 0.00 3.66
3799 9229 2.359354 CGTTCCGTGGCATGGGAA 60.359 61.111 25.01 20.18 39.92 3.97
3981 9428 2.501223 TAGGCTCGTGTTTGGCTCCG 62.501 60.000 0.00 0.00 39.76 4.63
4154 9646 3.923614 CGACTGGATCGCGATTCC 58.076 61.111 24.33 23.41 45.52 3.01
4388 9922 0.836400 TGTGTGGGGAAGAGGAGGAC 60.836 60.000 0.00 0.00 0.00 3.85
4476 10010 8.470002 AGCACAGAAATTTTCCTTCATTATACC 58.530 33.333 5.52 0.00 0.00 2.73
4477 10011 7.706607 GCACAGAAATTTTCCTTCATTATACCC 59.293 37.037 5.52 0.00 0.00 3.69
4478 10012 8.197439 CACAGAAATTTTCCTTCATTATACCCC 58.803 37.037 5.52 0.00 0.00 4.95
4479 10013 7.344612 ACAGAAATTTTCCTTCATTATACCCCC 59.655 37.037 5.52 0.00 0.00 5.40
4480 10014 7.565029 CAGAAATTTTCCTTCATTATACCCCCT 59.435 37.037 5.52 0.00 0.00 4.79
4481 10015 7.785028 AGAAATTTTCCTTCATTATACCCCCTC 59.215 37.037 5.52 0.00 0.00 4.30
4482 10016 5.397553 TTTTCCTTCATTATACCCCCTCC 57.602 43.478 0.00 0.00 0.00 4.30
4483 10017 2.616524 TCCTTCATTATACCCCCTCCG 58.383 52.381 0.00 0.00 0.00 4.63
4484 10018 2.090380 TCCTTCATTATACCCCCTCCGT 60.090 50.000 0.00 0.00 0.00 4.69
4485 10019 2.709397 CCTTCATTATACCCCCTCCGTT 59.291 50.000 0.00 0.00 0.00 4.44
4486 10020 3.137728 CCTTCATTATACCCCCTCCGTTT 59.862 47.826 0.00 0.00 0.00 3.60
4487 10021 4.386711 CTTCATTATACCCCCTCCGTTTC 58.613 47.826 0.00 0.00 0.00 2.78
4488 10022 3.386063 TCATTATACCCCCTCCGTTTCA 58.614 45.455 0.00 0.00 0.00 2.69
4489 10023 3.781407 TCATTATACCCCCTCCGTTTCAA 59.219 43.478 0.00 0.00 0.00 2.69
4490 10024 4.227754 TCATTATACCCCCTCCGTTTCAAA 59.772 41.667 0.00 0.00 0.00 2.69
4491 10025 4.866327 TTATACCCCCTCCGTTTCAAAT 57.134 40.909 0.00 0.00 0.00 2.32
4492 10026 3.750501 ATACCCCCTCCGTTTCAAATT 57.249 42.857 0.00 0.00 0.00 1.82
4493 10027 4.866327 ATACCCCCTCCGTTTCAAATTA 57.134 40.909 0.00 0.00 0.00 1.40
4494 10028 2.799017 ACCCCCTCCGTTTCAAATTAC 58.201 47.619 0.00 0.00 0.00 1.89
4495 10029 2.377531 ACCCCCTCCGTTTCAAATTACT 59.622 45.455 0.00 0.00 0.00 2.24
4496 10030 3.181426 ACCCCCTCCGTTTCAAATTACTT 60.181 43.478 0.00 0.00 0.00 2.24
4497 10031 3.192633 CCCCCTCCGTTTCAAATTACTTG 59.807 47.826 0.00 0.00 36.25 3.16
4498 10032 3.824443 CCCCTCCGTTTCAAATTACTTGT 59.176 43.478 0.00 0.00 36.34 3.16
4499 10033 4.082949 CCCCTCCGTTTCAAATTACTTGTC 60.083 45.833 0.00 0.00 36.34 3.18
4500 10034 4.378046 CCCTCCGTTTCAAATTACTTGTCG 60.378 45.833 0.00 0.00 36.34 4.35
4501 10035 4.212636 CCTCCGTTTCAAATTACTTGTCGT 59.787 41.667 0.00 0.00 36.34 4.34
4502 10036 5.406175 CCTCCGTTTCAAATTACTTGTCGTA 59.594 40.000 0.00 0.00 36.34 3.43
4503 10037 6.400727 CCTCCGTTTCAAATTACTTGTCGTAG 60.401 42.308 0.00 0.00 36.34 3.51
4504 10038 6.215121 TCCGTTTCAAATTACTTGTCGTAGA 58.785 36.000 0.00 0.00 36.34 2.59
4505 10039 6.700960 TCCGTTTCAAATTACTTGTCGTAGAA 59.299 34.615 0.00 0.00 39.69 2.10
4506 10040 7.224362 TCCGTTTCAAATTACTTGTCGTAGAAA 59.776 33.333 0.00 0.00 39.69 2.52
4507 10041 8.013378 CCGTTTCAAATTACTTGTCGTAGAAAT 58.987 33.333 0.00 0.00 39.69 2.17
4508 10042 8.827599 CGTTTCAAATTACTTGTCGTAGAAATG 58.172 33.333 0.00 0.00 39.69 2.32
4509 10043 9.113876 GTTTCAAATTACTTGTCGTAGAAATGG 57.886 33.333 0.00 0.00 39.69 3.16
4510 10044 8.610248 TTCAAATTACTTGTCGTAGAAATGGA 57.390 30.769 0.00 0.00 39.69 3.41
4511 10045 8.786826 TCAAATTACTTGTCGTAGAAATGGAT 57.213 30.769 0.00 0.00 39.69 3.41
4512 10046 8.664798 TCAAATTACTTGTCGTAGAAATGGATG 58.335 33.333 0.00 0.00 39.69 3.51
4513 10047 8.450964 CAAATTACTTGTCGTAGAAATGGATGT 58.549 33.333 0.00 0.00 39.69 3.06
4514 10048 9.661563 AAATTACTTGTCGTAGAAATGGATGTA 57.338 29.630 0.00 0.00 39.69 2.29
4515 10049 9.832445 AATTACTTGTCGTAGAAATGGATGTAT 57.168 29.630 0.00 0.00 39.69 2.29
4516 10050 9.832445 ATTACTTGTCGTAGAAATGGATGTATT 57.168 29.630 0.00 0.00 39.69 1.89
4517 10051 9.661563 TTACTTGTCGTAGAAATGGATGTATTT 57.338 29.630 0.00 0.00 39.69 1.40
4519 10053 9.314321 ACTTGTCGTAGAAATGGATGTATTTAG 57.686 33.333 0.00 0.00 39.69 1.85
4520 10054 9.529325 CTTGTCGTAGAAATGGATGTATTTAGA 57.471 33.333 0.00 0.00 39.69 2.10
4521 10055 9.878667 TTGTCGTAGAAATGGATGTATTTAGAA 57.121 29.630 0.00 0.00 39.69 2.10
4522 10056 9.309516 TGTCGTAGAAATGGATGTATTTAGAAC 57.690 33.333 0.00 0.00 39.69 3.01
4523 10057 9.530633 GTCGTAGAAATGGATGTATTTAGAACT 57.469 33.333 0.00 0.00 39.69 3.01
4553 10087 7.867305 ACATCTAGATACATCCATACCTACG 57.133 40.000 4.54 0.00 0.00 3.51
4554 10088 7.631007 ACATCTAGATACATCCATACCTACGA 58.369 38.462 4.54 0.00 0.00 3.43
4555 10089 7.553402 ACATCTAGATACATCCATACCTACGAC 59.447 40.741 4.54 0.00 0.00 4.34
4556 10090 7.012661 TCTAGATACATCCATACCTACGACA 57.987 40.000 0.00 0.00 0.00 4.35
4557 10091 7.455891 TCTAGATACATCCATACCTACGACAA 58.544 38.462 0.00 0.00 0.00 3.18
4558 10092 6.576662 AGATACATCCATACCTACGACAAG 57.423 41.667 0.00 0.00 0.00 3.16
4559 10093 6.069331 AGATACATCCATACCTACGACAAGT 58.931 40.000 0.00 0.00 0.00 3.16
4560 10094 7.229308 AGATACATCCATACCTACGACAAGTA 58.771 38.462 0.00 0.00 0.00 2.24
4561 10095 7.722728 AGATACATCCATACCTACGACAAGTAA 59.277 37.037 0.00 0.00 34.45 2.24
4562 10096 6.726490 ACATCCATACCTACGACAAGTAAT 57.274 37.500 0.00 0.00 34.45 1.89
4563 10097 7.120923 ACATCCATACCTACGACAAGTAATT 57.879 36.000 0.00 0.00 34.45 1.40
4564 10098 7.208080 ACATCCATACCTACGACAAGTAATTC 58.792 38.462 0.00 0.00 34.45 2.17
4565 10099 5.824429 TCCATACCTACGACAAGTAATTCG 58.176 41.667 0.00 0.00 41.14 3.34
4566 10100 4.980434 CCATACCTACGACAAGTAATTCGG 59.020 45.833 0.00 0.00 39.63 4.30
4567 10101 5.221106 CCATACCTACGACAAGTAATTCGGA 60.221 44.000 0.00 0.00 39.63 4.55
4568 10102 4.789012 ACCTACGACAAGTAATTCGGAA 57.211 40.909 0.00 0.00 39.63 4.30
4569 10103 4.488879 ACCTACGACAAGTAATTCGGAAC 58.511 43.478 0.00 0.00 39.63 3.62
4570 10104 3.545078 CCTACGACAAGTAATTCGGAACG 59.455 47.826 0.00 0.00 44.64 3.95
4571 10105 3.500982 TACGACAAGTAATTCGGAACGG 58.499 45.455 0.00 0.00 42.34 4.44
4602 10136 8.316214 AGTACCATTCTAGGTATTTTGAACGAA 58.684 33.333 0.00 0.00 45.32 3.85
4603 10137 7.373778 ACCATTCTAGGTATTTTGAACGAAC 57.626 36.000 0.00 0.00 40.98 3.95
4609 10143 9.940166 TTCTAGGTATTTTGAACGAACTTTTTC 57.060 29.630 0.00 0.00 0.00 2.29
4626 10160 5.912955 ACTTTTTCGGTGATTTTGAACGATC 59.087 36.000 0.00 0.00 33.26 3.69
4693 10227 9.751542 AGTATCGAAGTTTAAATCCTACATGAG 57.248 33.333 0.00 0.00 0.00 2.90
4694 10228 9.530633 GTATCGAAGTTTAAATCCTACATGAGT 57.469 33.333 0.00 0.00 0.00 3.41
4696 10230 8.842358 TCGAAGTTTAAATCCTACATGAGTTT 57.158 30.769 0.00 0.00 0.00 2.66
4820 10354 6.150976 CAGGTAAATCATGAGCAAACCAACTA 59.849 38.462 16.95 0.00 0.00 2.24
4841 10375 0.033601 AAAACTATGCCCCCATCGCA 60.034 50.000 0.00 0.00 41.28 5.10
5020 10557 2.557059 TAGCATCAGGACACGGCGTG 62.557 60.000 35.89 35.89 39.75 5.34
5113 10653 3.654414 CTCTGGTTCCACTAGTTCACAC 58.346 50.000 0.00 0.00 0.00 3.82
5215 10755 0.036952 CAACGAGCTGGAGGACACAT 60.037 55.000 1.44 0.00 0.00 3.21
5269 10809 5.981088 ATAATGTTGATCAAGTTGCCACA 57.019 34.783 8.80 2.18 0.00 4.17
5281 10821 2.423538 AGTTGCCACAGTGAAAACTCAC 59.576 45.455 12.64 0.00 40.69 3.51
5282 10822 1.388547 TGCCACAGTGAAAACTCACC 58.611 50.000 0.62 0.00 41.26 4.02
5283 10823 1.340502 TGCCACAGTGAAAACTCACCA 60.341 47.619 0.62 0.00 41.26 4.17
5284 10824 1.956477 GCCACAGTGAAAACTCACCAT 59.044 47.619 0.62 0.00 41.26 3.55
5290 12565 3.567164 CAGTGAAAACTCACCATTGCTCT 59.433 43.478 1.71 0.00 41.26 4.09
5293 12568 3.181440 TGAAAACTCACCATTGCTCTCCT 60.181 43.478 0.00 0.00 0.00 3.69
5352 12627 1.341209 AGATCGATCAGCATTGCGGTA 59.659 47.619 26.47 0.00 0.00 4.02
5357 12632 1.532868 GATCAGCATTGCGGTACATCC 59.467 52.381 8.63 0.00 0.00 3.51
5382 12657 1.811558 CGGCCAGTCCCATCACTAATG 60.812 57.143 2.24 0.00 34.93 1.90
5384 12659 2.438021 GGCCAGTCCCATCACTAATGTA 59.562 50.000 0.00 0.00 33.13 2.29
5446 12721 1.395954 CGATCTTGCTGTGTGGTGATG 59.604 52.381 0.00 0.00 0.00 3.07
5488 12764 3.570638 CTGCCCTGATCAAGCGCG 61.571 66.667 0.00 0.00 31.90 6.86
5510 12786 2.736081 CGCCCGCATGTACTTTGTACTA 60.736 50.000 8.94 0.00 0.00 1.82
5512 12788 3.677976 GCCCGCATGTACTTTGTACTACT 60.678 47.826 8.94 0.00 0.00 2.57
5514 12790 5.653507 CCCGCATGTACTTTGTACTACTTA 58.346 41.667 8.94 0.00 0.00 2.24
5650 13014 4.520492 ACAAGATGGTGATTTGGAGTGTTC 59.480 41.667 0.00 0.00 0.00 3.18
5712 13076 6.515832 ACTGATACAGAATCGTGCATATTCA 58.484 36.000 20.49 6.61 37.42 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 158 6.543465 TGTTTCATCCTATTACTCATTGGCTG 59.457 38.462 0.00 0.00 0.00 4.85
195 200 2.260822 CAGTGAAAGGAGAGGAAGGGA 58.739 52.381 0.00 0.00 0.00 4.20
334 346 9.968870 GGTTAATCTAAGATAATGAGTTCGTCT 57.031 33.333 0.00 0.00 0.00 4.18
402 415 4.796231 CTTCCTGTCCCGCCGACG 62.796 72.222 0.00 0.00 45.23 5.12
414 427 4.696479 ATCATTGCTTATCGTCCTTCCT 57.304 40.909 0.00 0.00 0.00 3.36
442 455 1.872952 TGCATTTCAACAGAGTGTCGG 59.127 47.619 0.00 0.00 0.00 4.79
443 456 2.660094 CGTGCATTTCAACAGAGTGTCG 60.660 50.000 0.00 0.00 0.00 4.35
540 556 1.576920 CAAACATGCCCGTGCGTTA 59.423 52.632 0.00 0.00 41.78 3.18
578 594 4.028131 TGGGTCCTATTTCGTACTCATGT 58.972 43.478 0.00 0.00 0.00 3.21
579 595 4.142026 TGTGGGTCCTATTTCGTACTCATG 60.142 45.833 0.00 0.00 0.00 3.07
580 596 4.028131 TGTGGGTCCTATTTCGTACTCAT 58.972 43.478 0.00 0.00 0.00 2.90
603 619 9.502091 GGCCATGTATGTAAATAATGAAGTCTA 57.498 33.333 0.00 0.00 0.00 2.59
604 620 7.448469 GGGCCATGTATGTAAATAATGAAGTCT 59.552 37.037 4.39 0.00 0.00 3.24
690 710 5.601662 TGGAAATTAGGACGATAAGCAGAG 58.398 41.667 0.00 0.00 0.00 3.35
697 717 5.456548 TGCGTATGGAAATTAGGACGATA 57.543 39.130 0.00 0.00 32.20 2.92
698 718 4.330944 TGCGTATGGAAATTAGGACGAT 57.669 40.909 0.00 0.00 32.20 3.73
699 719 3.804786 TGCGTATGGAAATTAGGACGA 57.195 42.857 0.00 0.00 32.20 4.20
700 720 3.363970 GCATGCGTATGGAAATTAGGACG 60.364 47.826 15.54 0.00 34.79 4.79
701 721 3.363970 CGCATGCGTATGGAAATTAGGAC 60.364 47.826 31.33 0.00 34.79 3.85
702 722 2.805671 CGCATGCGTATGGAAATTAGGA 59.194 45.455 31.33 0.00 34.79 2.94
703 723 2.095768 CCGCATGCGTATGGAAATTAGG 60.096 50.000 35.55 13.92 37.81 2.69
704 724 2.805671 TCCGCATGCGTATGGAAATTAG 59.194 45.455 35.55 17.37 37.81 1.73
720 740 1.254975 TTAGCTAGTGCCTGTCCGCA 61.255 55.000 0.00 0.00 40.80 5.69
735 756 7.063074 CGTTTAGTGTGGCTATATATGGTTAGC 59.937 40.741 0.00 0.00 40.07 3.09
743 767 6.919662 GCTGTAACGTTTAGTGTGGCTATATA 59.080 38.462 5.91 0.00 0.00 0.86
756 780 3.125316 GACCACACTGCTGTAACGTTTA 58.875 45.455 5.91 0.00 0.00 2.01
761 785 1.797025 GAGGACCACACTGCTGTAAC 58.203 55.000 0.00 0.00 0.00 2.50
767 791 0.179124 GATCTCGAGGACCACACTGC 60.179 60.000 13.56 0.00 0.00 4.40
804 1150 1.580704 GTCGTACGTGATGGTTTAGCG 59.419 52.381 16.05 0.00 0.00 4.26
869 1220 3.319198 GTCCTCCCCTGGACGCAA 61.319 66.667 0.00 0.00 45.69 4.85
938 1289 1.071699 CGGTTTCTTGTTCCAGGGAGA 59.928 52.381 0.00 0.00 0.00 3.71
1006 1357 2.523015 CCAACCTAGCTAACACGTACG 58.477 52.381 15.01 15.01 0.00 3.67
1109 1460 2.283676 TCGTGACCCCTCACCCTC 60.284 66.667 0.00 0.00 43.64 4.30
1110 1461 2.283966 CTCGTGACCCCTCACCCT 60.284 66.667 0.00 0.00 43.64 4.34
1111 1462 4.083862 GCTCGTGACCCCTCACCC 62.084 72.222 0.00 0.00 43.64 4.61
1112 1463 3.302347 CTGCTCGTGACCCCTCACC 62.302 68.421 0.00 0.00 43.64 4.02
1113 1464 2.262915 CTGCTCGTGACCCCTCAC 59.737 66.667 0.00 0.00 43.17 3.51
1114 1465 2.997315 CCTGCTCGTGACCCCTCA 60.997 66.667 0.00 0.00 0.00 3.86
1115 1466 2.997897 ACCTGCTCGTGACCCCTC 60.998 66.667 0.00 0.00 0.00 4.30
1116 1467 3.314331 CACCTGCTCGTGACCCCT 61.314 66.667 0.00 0.00 35.68 4.79
1126 1485 2.111878 GCAGTGGTGTCACCTGCT 59.888 61.111 22.79 17.55 44.64 4.24
1236 1604 2.058595 GGCCTAGGCAGAGGTCGAA 61.059 63.158 34.09 0.00 44.11 3.71
1660 2129 4.455124 GAGTCAAACAGATAAACGCACAC 58.545 43.478 0.00 0.00 0.00 3.82
1663 2132 3.386486 ACGAGTCAAACAGATAAACGCA 58.614 40.909 0.00 0.00 0.00 5.24
1664 2133 4.385244 AACGAGTCAAACAGATAAACGC 57.615 40.909 0.00 0.00 0.00 4.84
1702 2177 9.443323 AGTTAAGAAGAGAGGAAGCTAAAAATC 57.557 33.333 0.00 0.00 0.00 2.17
1767 2540 6.732896 ATAATCTAGGAAGTGACATTCGGT 57.267 37.500 0.00 0.00 0.00 4.69
1804 2600 1.396996 ACAAACGACAGTTGTGTGAGC 59.603 47.619 17.12 0.00 41.05 4.26
1828 2624 7.510343 AGGAAAAGGAGAAATGGAGATTTTTGA 59.490 33.333 0.00 0.00 31.58 2.69
1839 2635 9.898152 AGATTACTAAGAGGAAAAGGAGAAATG 57.102 33.333 0.00 0.00 0.00 2.32
1858 2654 6.541641 GTGATGCCAAGATCAAGAAGATTACT 59.458 38.462 0.00 0.00 37.00 2.24
1859 2655 6.510799 CGTGATGCCAAGATCAAGAAGATTAC 60.511 42.308 0.00 0.00 37.00 1.89
1861 2657 4.334759 CGTGATGCCAAGATCAAGAAGATT 59.665 41.667 0.00 0.00 37.00 2.40
1900 2698 3.427503 GGCAAACCATAAGTCATCAACGG 60.428 47.826 0.00 0.00 35.26 4.44
2071 2879 5.656416 TCCAGATGGTTTGACAAAGAGTTTT 59.344 36.000 0.00 0.00 36.34 2.43
2162 3304 7.251704 AGTTGACATCTGACAAAGTTTACTG 57.748 36.000 0.00 0.00 32.18 2.74
2211 3425 4.546570 GTTTTCAAATCCACTGGCTACAC 58.453 43.478 0.00 0.00 0.00 2.90
2213 3427 3.252458 ACGTTTTCAAATCCACTGGCTAC 59.748 43.478 0.00 0.00 0.00 3.58
2215 3429 2.293399 GACGTTTTCAAATCCACTGGCT 59.707 45.455 0.00 0.00 0.00 4.75
2222 3436 6.142320 GTCATCTTGTTGACGTTTTCAAATCC 59.858 38.462 0.00 0.00 46.09 3.01
2224 3438 6.559810 TGTCATCTTGTTGACGTTTTCAAAT 58.440 32.000 0.00 0.00 46.09 2.32
2225 3439 5.944013 TGTCATCTTGTTGACGTTTTCAAA 58.056 33.333 0.00 0.00 46.09 2.69
2233 3447 7.729187 ACAAATAGTGTTGTCATCTTGTTGACG 60.729 37.037 7.16 0.00 40.08 4.35
2236 3450 7.613247 CACAAATAGTGTTGTCATCTTGTTG 57.387 36.000 0.00 0.00 43.40 3.33
2398 5451 7.348080 AGAACATCTATTTACGGATGAGTGA 57.652 36.000 9.47 0.00 41.05 3.41
2436 5489 9.689976 AGTTCAAGATACATCTCGAAGATAATG 57.310 33.333 0.00 0.00 31.07 1.90
2655 5918 0.701310 AACCCATGATACCCCCTCCC 60.701 60.000 0.00 0.00 0.00 4.30
3292 6711 9.384682 CGCCTAAACGAGTTTCTTTTATTTTTA 57.615 29.630 4.32 0.00 34.23 1.52
3362 6829 4.701956 TTAAATTAGTGCAGCTGCTTCC 57.298 40.909 36.61 24.23 42.66 3.46
3452 8799 1.303309 AGCTTGACACTCACTGCAAC 58.697 50.000 0.00 0.00 31.33 4.17
3629 9019 6.239036 GGTGAGATGCTGTAGACACATGTATA 60.239 42.308 0.00 0.00 33.14 1.47
3671 9072 4.467084 TCACGGCCGGGCAATCTC 62.467 66.667 31.76 1.27 0.00 2.75
3672 9073 4.473520 CTCACGGCCGGGCAATCT 62.474 66.667 31.76 2.42 0.00 2.40
3786 9216 0.752743 ATGATGTTCCCATGCCACGG 60.753 55.000 0.00 0.00 0.00 4.94
3787 9217 1.066002 GAATGATGTTCCCATGCCACG 59.934 52.381 0.00 0.00 0.00 4.94
3788 9218 1.410153 GGAATGATGTTCCCATGCCAC 59.590 52.381 0.00 0.00 39.16 5.01
3789 9219 1.779221 GGAATGATGTTCCCATGCCA 58.221 50.000 0.00 0.00 39.16 4.92
3796 9226 2.270352 TATGCCGGGAATGATGTTCC 57.730 50.000 0.00 0.00 37.86 3.62
3797 9227 3.149196 ACATATGCCGGGAATGATGTTC 58.851 45.455 19.51 0.00 0.00 3.18
3798 9228 3.228188 ACATATGCCGGGAATGATGTT 57.772 42.857 19.51 0.00 0.00 2.71
3799 9229 2.957402 ACATATGCCGGGAATGATGT 57.043 45.000 19.51 16.63 0.00 3.06
3959 9406 1.671054 GCCAAACACGAGCCTAGCA 60.671 57.895 0.00 0.00 0.00 3.49
3981 9428 2.355837 TGCAGTGAAGTCGGCGTC 60.356 61.111 6.85 0.00 0.00 5.19
4043 9514 3.129502 TCGTTCTCCGGCGATCGT 61.130 61.111 20.79 0.00 37.11 3.73
4154 9646 1.267732 GCGTCCTTGATGCAAATCTCG 60.268 52.381 3.51 0.00 43.32 4.04
4208 9700 1.068417 CAAACCGACCACGTCTCCA 59.932 57.895 0.00 0.00 37.88 3.86
4388 9922 2.034879 AGCATCAGCCAAACCGTCG 61.035 57.895 0.00 0.00 43.56 5.12
4473 10007 3.588396 AGTAATTTGAAACGGAGGGGGTA 59.412 43.478 0.00 0.00 0.00 3.69
4474 10008 2.377531 AGTAATTTGAAACGGAGGGGGT 59.622 45.455 0.00 0.00 0.00 4.95
4475 10009 3.081710 AGTAATTTGAAACGGAGGGGG 57.918 47.619 0.00 0.00 0.00 5.40
4476 10010 3.824443 ACAAGTAATTTGAAACGGAGGGG 59.176 43.478 0.00 0.00 39.21 4.79
4477 10011 4.378046 CGACAAGTAATTTGAAACGGAGGG 60.378 45.833 0.00 0.00 39.21 4.30
4478 10012 4.212636 ACGACAAGTAATTTGAAACGGAGG 59.787 41.667 0.00 0.00 39.21 4.30
4479 10013 5.338614 ACGACAAGTAATTTGAAACGGAG 57.661 39.130 0.00 0.00 39.21 4.63
4480 10014 6.215121 TCTACGACAAGTAATTTGAAACGGA 58.785 36.000 0.00 0.00 39.21 4.69
4481 10015 6.456447 TCTACGACAAGTAATTTGAAACGG 57.544 37.500 0.00 0.00 39.21 4.44
4482 10016 8.827599 CATTTCTACGACAAGTAATTTGAAACG 58.172 33.333 0.00 0.00 39.21 3.60
4483 10017 9.113876 CCATTTCTACGACAAGTAATTTGAAAC 57.886 33.333 0.00 0.00 39.21 2.78
4484 10018 9.058174 TCCATTTCTACGACAAGTAATTTGAAA 57.942 29.630 0.00 0.00 39.21 2.69
4485 10019 8.610248 TCCATTTCTACGACAAGTAATTTGAA 57.390 30.769 0.00 0.00 39.21 2.69
4486 10020 8.664798 CATCCATTTCTACGACAAGTAATTTGA 58.335 33.333 0.00 0.00 39.21 2.69
4487 10021 8.450964 ACATCCATTTCTACGACAAGTAATTTG 58.549 33.333 0.00 0.00 42.68 2.32
4488 10022 8.561738 ACATCCATTTCTACGACAAGTAATTT 57.438 30.769 0.00 0.00 34.45 1.82
4489 10023 9.832445 ATACATCCATTTCTACGACAAGTAATT 57.168 29.630 0.00 0.00 34.45 1.40
4490 10024 9.832445 AATACATCCATTTCTACGACAAGTAAT 57.168 29.630 0.00 0.00 34.45 1.89
4491 10025 9.661563 AAATACATCCATTTCTACGACAAGTAA 57.338 29.630 0.00 0.00 34.45 2.24
4493 10027 9.314321 CTAAATACATCCATTTCTACGACAAGT 57.686 33.333 0.00 0.00 30.84 3.16
4494 10028 9.529325 TCTAAATACATCCATTTCTACGACAAG 57.471 33.333 0.00 0.00 30.84 3.16
4495 10029 9.878667 TTCTAAATACATCCATTTCTACGACAA 57.121 29.630 0.00 0.00 30.84 3.18
4496 10030 9.309516 GTTCTAAATACATCCATTTCTACGACA 57.690 33.333 0.00 0.00 30.84 4.35
4497 10031 9.530633 AGTTCTAAATACATCCATTTCTACGAC 57.469 33.333 0.00 0.00 30.84 4.34
4527 10061 9.562408 CGTAGGTATGGATGTATCTAGATGTAT 57.438 37.037 15.79 9.11 0.00 2.29
4528 10062 8.765517 TCGTAGGTATGGATGTATCTAGATGTA 58.234 37.037 15.79 4.44 0.00 2.29
4529 10063 7.553402 GTCGTAGGTATGGATGTATCTAGATGT 59.447 40.741 15.79 1.25 0.00 3.06
4530 10064 7.553044 TGTCGTAGGTATGGATGTATCTAGATG 59.447 40.741 15.79 0.00 0.00 2.90
4531 10065 7.631007 TGTCGTAGGTATGGATGTATCTAGAT 58.369 38.462 10.73 10.73 0.00 1.98
4532 10066 7.012661 TGTCGTAGGTATGGATGTATCTAGA 57.987 40.000 0.00 0.00 0.00 2.43
4533 10067 7.390996 ACTTGTCGTAGGTATGGATGTATCTAG 59.609 40.741 0.00 0.00 0.00 2.43
4534 10068 7.229308 ACTTGTCGTAGGTATGGATGTATCTA 58.771 38.462 0.00 0.00 0.00 1.98
4535 10069 6.069331 ACTTGTCGTAGGTATGGATGTATCT 58.931 40.000 0.00 0.00 0.00 1.98
4536 10070 6.328641 ACTTGTCGTAGGTATGGATGTATC 57.671 41.667 0.00 0.00 0.00 2.24
4537 10071 7.828508 TTACTTGTCGTAGGTATGGATGTAT 57.171 36.000 0.00 0.00 0.00 2.29
4538 10072 7.828508 ATTACTTGTCGTAGGTATGGATGTA 57.171 36.000 0.00 0.00 0.00 2.29
4539 10073 6.726490 ATTACTTGTCGTAGGTATGGATGT 57.274 37.500 0.00 0.00 0.00 3.06
4540 10074 6.362551 CGAATTACTTGTCGTAGGTATGGATG 59.637 42.308 0.00 0.00 32.61 3.51
4541 10075 6.444633 CGAATTACTTGTCGTAGGTATGGAT 58.555 40.000 0.00 0.00 32.61 3.41
4542 10076 5.221106 CCGAATTACTTGTCGTAGGTATGGA 60.221 44.000 0.00 0.00 35.48 3.41
4543 10077 4.980434 CCGAATTACTTGTCGTAGGTATGG 59.020 45.833 0.00 0.00 35.48 2.74
4544 10078 5.824429 TCCGAATTACTTGTCGTAGGTATG 58.176 41.667 0.00 0.00 35.48 2.39
4545 10079 6.268566 GTTCCGAATTACTTGTCGTAGGTAT 58.731 40.000 0.00 0.00 35.48 2.73
4546 10080 5.640732 GTTCCGAATTACTTGTCGTAGGTA 58.359 41.667 0.00 0.00 35.48 3.08
4547 10081 4.488879 GTTCCGAATTACTTGTCGTAGGT 58.511 43.478 0.00 0.00 35.48 3.08
4548 10082 3.545078 CGTTCCGAATTACTTGTCGTAGG 59.455 47.826 0.00 0.00 35.48 3.18
4549 10083 3.545078 CCGTTCCGAATTACTTGTCGTAG 59.455 47.826 0.00 0.00 35.48 3.51
4550 10084 3.190327 TCCGTTCCGAATTACTTGTCGTA 59.810 43.478 0.00 0.00 35.48 3.43
4551 10085 2.030007 TCCGTTCCGAATTACTTGTCGT 60.030 45.455 0.00 0.00 35.48 4.34
4552 10086 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
4553 10087 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4554 10088 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4555 10089 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4556 10090 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
4557 10091 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
4558 10092 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
4559 10093 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
4560 10094 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
4561 10095 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
4562 10096 0.967380 GGTACTCCCTCCGTTCCGAA 60.967 60.000 0.00 0.00 0.00 4.30
4563 10097 1.379044 GGTACTCCCTCCGTTCCGA 60.379 63.158 0.00 0.00 0.00 4.55
4564 10098 1.041447 ATGGTACTCCCTCCGTTCCG 61.041 60.000 0.00 0.00 0.00 4.30
4565 10099 1.138464 GAATGGTACTCCCTCCGTTCC 59.862 57.143 0.00 0.00 41.32 3.62
4566 10100 2.108970 AGAATGGTACTCCCTCCGTTC 58.891 52.381 7.75 7.75 45.07 3.95
4567 10101 2.249309 AGAATGGTACTCCCTCCGTT 57.751 50.000 0.00 0.00 35.89 4.44
4568 10102 2.424523 CCTAGAATGGTACTCCCTCCGT 60.425 54.545 0.00 0.00 0.00 4.69
4569 10103 2.240279 CCTAGAATGGTACTCCCTCCG 58.760 57.143 0.00 0.00 0.00 4.63
4570 10104 3.331718 ACCTAGAATGGTACTCCCTCC 57.668 52.381 0.00 0.00 38.79 4.30
4571 10105 6.997942 AAATACCTAGAATGGTACTCCCTC 57.002 41.667 0.00 0.00 44.34 4.30
4572 10106 6.906901 TCAAAATACCTAGAATGGTACTCCCT 59.093 38.462 0.00 0.00 44.34 4.20
4573 10107 7.133133 TCAAAATACCTAGAATGGTACTCCC 57.867 40.000 0.00 0.00 44.34 4.30
4574 10108 7.224167 CGTTCAAAATACCTAGAATGGTACTCC 59.776 40.741 0.00 0.00 44.34 3.85
4575 10109 7.977853 TCGTTCAAAATACCTAGAATGGTACTC 59.022 37.037 0.00 0.00 44.34 2.59
4576 10110 7.844009 TCGTTCAAAATACCTAGAATGGTACT 58.156 34.615 0.00 0.00 44.34 2.73
4577 10111 8.385858 GTTCGTTCAAAATACCTAGAATGGTAC 58.614 37.037 0.00 0.00 44.34 3.34
4602 10136 5.238006 TCGTTCAAAATCACCGAAAAAGT 57.762 34.783 0.00 0.00 0.00 2.66
4603 10137 6.142817 AGATCGTTCAAAATCACCGAAAAAG 58.857 36.000 0.00 0.00 0.00 2.27
4609 10143 9.158364 CATATTAAAGATCGTTCAAAATCACCG 57.842 33.333 0.00 0.00 0.00 4.94
4613 10147 8.134895 TGCCCATATTAAAGATCGTTCAAAATC 58.865 33.333 0.00 0.00 0.00 2.17
4626 10160 6.828785 ACTAACACCTTCTGCCCATATTAAAG 59.171 38.462 0.00 0.00 0.00 1.85
4664 10198 8.624701 TGTAGGATTTAAACTTCGATACTTCG 57.375 34.615 0.00 0.00 46.87 3.79
4770 10304 7.394641 TGGCCATATTAGTGTGATTGTGTAAAA 59.605 33.333 0.00 0.00 0.00 1.52
4771 10305 6.887002 TGGCCATATTAGTGTGATTGTGTAAA 59.113 34.615 0.00 0.00 0.00 2.01
4772 10306 6.418946 TGGCCATATTAGTGTGATTGTGTAA 58.581 36.000 0.00 0.00 0.00 2.41
4773 10307 5.995446 TGGCCATATTAGTGTGATTGTGTA 58.005 37.500 0.00 0.00 0.00 2.90
4911 10448 2.271800 CGAAGTCACCTGCTGGTAATC 58.728 52.381 15.70 9.92 46.60 1.75
5004 10541 0.802222 CTACACGCCGTGTCCTGATG 60.802 60.000 27.98 7.49 43.92 3.07
5020 10557 3.201290 AGCTTCACTATGTGCATGCTAC 58.799 45.455 20.33 15.34 32.98 3.58
5113 10653 7.560368 AGACAGTTGAATTATTACTCCCTGAG 58.440 38.462 0.00 0.00 35.52 3.35
5254 10794 2.636647 TCACTGTGGCAACTTGATCA 57.363 45.000 8.11 0.00 37.61 2.92
5290 12565 0.343372 AGTCAGGGATTGGGCTAGGA 59.657 55.000 0.00 0.00 0.00 2.94
5293 12568 0.621571 AGCAGTCAGGGATTGGGCTA 60.622 55.000 0.00 0.00 30.82 3.93
5382 12657 2.037144 ACCGTGGGTGGTGAGATATAC 58.963 52.381 0.00 0.00 41.85 1.47
5384 12659 1.580059 AACCGTGGGTGGTGAGATAT 58.420 50.000 0.00 0.00 42.89 1.63
5446 12721 0.387929 CACCCAGCCATCAATGCATC 59.612 55.000 0.00 0.00 0.00 3.91
5488 12764 1.363145 TACAAAGTACATGCGGGCGC 61.363 55.000 0.00 0.00 42.35 6.53
5510 12786 2.584143 GCCGTACGCGCCATAAGT 60.584 61.111 10.49 0.00 36.67 2.24
5512 12788 4.144703 TGGCCGTACGCGCCATAA 62.145 61.111 32.91 18.97 38.60 1.90
5634 12998 0.521735 GCGGAACACTCCAAATCACC 59.478 55.000 0.00 0.00 42.58 4.02


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

AutoCloner maintained by Alex Coulton.