Multiple sequence alignment - TraesCS4B01G123100

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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 TraesCS4B01G123100 chr4B 100.000 5678 0 0 1 5678 146499491 146493814 0.000000e+00 10486.0
1 TraesCS4B01G123100 chr4B 100.000 34 0 0 1 34 111708386 111708353 4.750000e-06 63.9
2 TraesCS4B01G123100 chr4A 95.252 3896 123 26 903 4783 472917736 472921584 0.000000e+00 6113.0
3 TraesCS4B01G123100 chr4A 85.623 779 93 13 4914 5678 472921592 472922365 0.000000e+00 800.0
4 TraesCS4B01G123100 chr4D 94.802 2270 83 10 1653 3897 102168179 102165920 0.000000e+00 3506.0
5 TraesCS4B01G123100 chr4D 94.420 1577 66 12 30 1600 102169750 102168190 0.000000e+00 2405.0
6 TraesCS4B01G123100 chr4D 97.126 835 19 3 3949 4783 102165920 102165091 0.000000e+00 1404.0
7 TraesCS4B01G123100 chr4D 86.585 328 35 6 4914 5237 102165083 102164761 2.520000e-93 353.0
8 TraesCS4B01G123100 chr4D 91.429 140 6 3 4780 4914 50424248 50424386 2.700000e-43 187.0
9 TraesCS4B01G123100 chr4D 89.706 136 13 1 4780 4914 122727269 122727134 7.560000e-39 172.0
10 TraesCS4B01G123100 chr4D 87.333 150 14 2 4779 4923 87959700 87959551 3.520000e-37 167.0
11 TraesCS4B01G123100 chr4D 87.692 130 12 2 4780 4905 66503911 66503782 1.270000e-31 148.0
12 TraesCS4B01G123100 chr4D 86.029 136 14 3 4779 4914 455701440 455701310 2.130000e-29 141.0
13 TraesCS4B01G123100 chr5D 94.529 658 24 6 1075 1721 320921299 320920643 0.000000e+00 1005.0
14 TraesCS4B01G123100 chr5D 92.705 658 36 4 1075 1721 531913270 531913926 0.000000e+00 939.0
15 TraesCS4B01G123100 chr5D 86.027 365 36 7 1162 1526 233508454 233508105 1.490000e-100 377.0
16 TraesCS4B01G123100 chr5D 98.148 162 3 0 1833 1994 531913924 531914085 3.350000e-72 283.0
17 TraesCS4B01G123100 chr5D 96.894 161 5 0 1834 1994 320920644 320920484 2.610000e-68 270.0
18 TraesCS4B01G123100 chr5D 100.000 35 0 0 1 35 313088213 313088247 1.320000e-06 65.8
19 TraesCS4B01G123100 chr3A 92.553 658 37 7 1075 1721 645742465 645741809 0.000000e+00 933.0
20 TraesCS4B01G123100 chr3A 94.059 606 10 2 1833 2437 645741811 645741231 0.000000e+00 896.0
21 TraesCS4B01G123100 chr3A 94.050 605 11 1 1833 2437 260680717 260680138 0.000000e+00 894.0
22 TraesCS4B01G123100 chr3A 90.122 658 53 6 1075 1721 260681371 260680715 0.000000e+00 845.0
23 TraesCS4B01G123100 chr3A 92.562 605 18 3 1833 2437 36857536 36856959 0.000000e+00 843.0
24 TraesCS4B01G123100 chr3D 93.554 605 14 1 1833 2437 418847430 418848009 0.000000e+00 878.0
25 TraesCS4B01G123100 chr3D 92.991 428 23 5 1300 1721 418847006 418847432 8.080000e-173 617.0
26 TraesCS4B01G123100 chr3D 93.151 219 9 2 1091 1303 418834780 418834998 3.300000e-82 316.0
27 TraesCS4B01G123100 chr3D 89.437 142 9 3 4778 4914 506878912 506878772 2.100000e-39 174.0
28 TraesCS4B01G123100 chr3D 87.586 145 14 4 4771 4914 395037683 395037542 1.270000e-36 165.0
29 TraesCS4B01G123100 chr3D 88.028 142 14 2 4776 4914 581542815 581542674 1.270000e-36 165.0
30 TraesCS4B01G123100 chrUn 93.399 606 13 3 1833 2437 74792526 74793105 0.000000e+00 872.0
31 TraesCS4B01G123100 chrUn 91.373 255 15 4 1473 1721 74792275 74792528 5.450000e-90 342.0
32 TraesCS4B01G123100 chr2A 93.234 606 13 4 1833 2437 575784110 575783532 0.000000e+00 867.0
33 TraesCS4B01G123100 chr2A 90.588 255 17 4 1473 1721 303688567 303688314 1.180000e-86 331.0
34 TraesCS4B01G123100 chr2A 90.588 255 17 4 1473 1721 575784361 575784108 1.180000e-86 331.0
35 TraesCS4B01G123100 chr2A 97.531 162 3 1 1833 1994 303688316 303688156 5.600000e-70 276.0
36 TraesCS4B01G123100 chr7A 93.223 605 14 3 1833 2437 627185446 627186023 0.000000e+00 865.0
37 TraesCS4B01G123100 chr7A 80.658 517 90 9 38 552 188664373 188663865 5.330000e-105 392.0
38 TraesCS4B01G123100 chr5A 83.015 524 84 5 30 550 685010635 685011156 2.390000e-128 470.0
39 TraesCS4B01G123100 chr5A 85.205 365 39 7 1162 1526 321720935 321720586 1.500000e-95 361.0
40 TraesCS4B01G123100 chr5A 89.362 141 12 3 4776 4914 74676071 74676210 2.100000e-39 174.0
41 TraesCS4B01G123100 chr6A 81.107 524 90 9 30 551 470409246 470408730 1.470000e-110 411.0
42 TraesCS4B01G123100 chr2D 81.179 526 86 11 32 552 342557198 342556681 1.470000e-110 411.0
43 TraesCS4B01G123100 chr2D 90.714 140 10 1 4778 4914 540163587 540163726 3.490000e-42 183.0
44 TraesCS4B01G123100 chr2D 100.000 34 0 0 1 34 369098486 369098453 4.750000e-06 63.9
45 TraesCS4B01G123100 chr5B 86.301 365 35 7 1162 1526 271300572 271300921 3.210000e-102 383.0
46 TraesCS4B01G123100 chr7D 81.304 460 76 10 95 551 420624715 420624263 1.160000e-96 364.0
47 TraesCS4B01G123100 chr7D 81.292 449 72 11 109 555 483690593 483691031 2.520000e-93 353.0
48 TraesCS4B01G123100 chr7D 90.000 140 12 2 4776 4914 54659631 54659493 4.520000e-41 180.0
49 TraesCS4B01G123100 chr7D 80.729 192 35 2 1173 1363 217937234 217937424 1.270000e-31 148.0
50 TraesCS4B01G123100 chr7D 92.857 42 2 1 1 42 190914545 190914505 6.140000e-05 60.2
51 TraesCS4B01G123100 chr3B 79.513 493 75 25 29 512 19424746 19425221 1.530000e-85 327.0
52 TraesCS4B01G123100 chr3B 89.209 139 13 2 4778 4914 195365547 195365685 7.560000e-39 172.0
53 TraesCS4B01G123100 chr3B 100.000 34 0 0 1 34 660777692 660777725 4.750000e-06 63.9
54 TraesCS4B01G123100 chr3B 97.222 36 0 1 1 36 496768627 496768593 6.140000e-05 60.2
55 TraesCS4B01G123100 chr6D 80.397 403 73 6 153 552 1368134 1367735 9.250000e-78 302.0
56 TraesCS4B01G123100 chr6D 89.855 138 13 1 4777 4914 436407571 436407707 5.850000e-40 176.0
57 TraesCS4B01G123100 chr2B 90.977 133 10 2 4783 4914 118465813 118465682 1.630000e-40 178.0
58 TraesCS4B01G123100 chr2B 80.110 181 31 5 30 208 433134901 433135078 4.620000e-26 130.0
59 TraesCS4B01G123100 chr1A 89.630 135 14 0 4780 4914 390701119 390700985 7.560000e-39 172.0
60 TraesCS4B01G123100 chr1A 88.148 135 14 2 4783 4916 505748038 505747905 5.890000e-35 159.0
61 TraesCS4B01G123100 chr1A 87.770 139 11 4 4779 4914 573384398 573384533 2.120000e-34 158.0
62 TraesCS4B01G123100 chr7B 89.209 139 12 3 4777 4914 130896546 130896410 2.720000e-38 171.0
63 TraesCS4B01G123100 chr7B 100.000 35 0 0 1 35 315987894 315987928 1.320000e-06 65.8
64 TraesCS4B01G123100 chr7B 100.000 34 0 0 1 34 128296689 128296722 4.750000e-06 63.9
65 TraesCS4B01G123100 chr7B 89.362 47 1 4 1 46 19229683 19229640 7.950000e-04 56.5
66 TraesCS4B01G123100 chr1B 87.770 139 13 2 4780 4914 566027738 566027876 5.890000e-35 159.0


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 TraesCS4B01G123100 chr4B 146493814 146499491 5677 True 10486.0 10486 100.00000 1 5678 1 chr4B.!!$R2 5677
1 TraesCS4B01G123100 chr4A 472917736 472922365 4629 False 3456.5 6113 90.43750 903 5678 2 chr4A.!!$F1 4775
2 TraesCS4B01G123100 chr4D 102164761 102169750 4989 True 1917.0 3506 93.23325 30 5237 4 chr4D.!!$R5 5207
3 TraesCS4B01G123100 chr5D 320920484 320921299 815 True 637.5 1005 95.71150 1075 1994 2 chr5D.!!$R2 919
4 TraesCS4B01G123100 chr5D 531913270 531914085 815 False 611.0 939 95.42650 1075 1994 2 chr5D.!!$F2 919
5 TraesCS4B01G123100 chr3A 645741231 645742465 1234 True 914.5 933 93.30600 1075 2437 2 chr3A.!!$R3 1362
6 TraesCS4B01G123100 chr3A 260680138 260681371 1233 True 869.5 894 92.08600 1075 2437 2 chr3A.!!$R2 1362
7 TraesCS4B01G123100 chr3A 36856959 36857536 577 True 843.0 843 92.56200 1833 2437 1 chr3A.!!$R1 604
8 TraesCS4B01G123100 chr3D 418847006 418848009 1003 False 747.5 878 93.27250 1300 2437 2 chr3D.!!$F2 1137
9 TraesCS4B01G123100 chrUn 74792275 74793105 830 False 607.0 872 92.38600 1473 2437 2 chrUn.!!$F1 964
10 TraesCS4B01G123100 chr2A 575783532 575784361 829 True 599.0 867 91.91100 1473 2437 2 chr2A.!!$R2 964
11 TraesCS4B01G123100 chr7A 627185446 627186023 577 False 865.0 865 93.22300 1833 2437 1 chr7A.!!$F1 604
12 TraesCS4B01G123100 chr7A 188663865 188664373 508 True 392.0 392 80.65800 38 552 1 chr7A.!!$R1 514
13 TraesCS4B01G123100 chr5A 685010635 685011156 521 False 470.0 470 83.01500 30 550 1 chr5A.!!$F2 520
14 TraesCS4B01G123100 chr6A 470408730 470409246 516 True 411.0 411 81.10700 30 551 1 chr6A.!!$R1 521
15 TraesCS4B01G123100 chr2D 342556681 342557198 517 True 411.0 411 81.17900 32 552 1 chr2D.!!$R1 520

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
782 788 0.108396 TGCAGCACTACAAAGGAGCA 59.892 50.0 0.00 0.0 32.2 4.26 F
828 834 0.622665 AATGGGGGAGAAGACAGCAG 59.377 55.0 0.00 0.0 0.0 4.24 F
2725 2913 0.847373 TGGACTGGTTTACAAGCCCA 59.153 50.0 0.00 0.0 0.0 5.36 F
3188 3377 0.254059 TGATTGAATCCCCCTCCCCA 60.254 55.0 2.26 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2697 2885 0.398318 AAACCAGTCCAGAGGCAGTC 59.602 55.000 0.00 0.00 0.0 3.51 R
2780 2968 4.637483 ATGGTGTACTGTTTATGCATGC 57.363 40.909 11.82 11.82 0.0 4.06 R
4601 4812 0.394192 CCTCTCACCACTTCACAGCA 59.606 55.000 0.00 0.00 0.0 4.41 R
5126 5347 0.363512 CTGTGATTTCTGTCGACGCG 59.636 55.000 11.62 3.53 0.0 6.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.466714 CCCCCTCTAGGTCCATCTC 57.533 63.158 0.00 0.00 0.00 2.75
19 20 0.540830 CCCCCTCTAGGTCCATCTCG 60.541 65.000 0.00 0.00 0.00 4.04
20 21 0.478942 CCCCTCTAGGTCCATCTCGA 59.521 60.000 0.00 0.00 0.00 4.04
21 22 1.076350 CCCCTCTAGGTCCATCTCGAT 59.924 57.143 0.00 0.00 0.00 3.59
22 23 2.442413 CCCTCTAGGTCCATCTCGATC 58.558 57.143 0.00 0.00 0.00 3.69
23 24 2.442413 CCTCTAGGTCCATCTCGATCC 58.558 57.143 0.00 0.00 0.00 3.36
24 25 2.041081 CCTCTAGGTCCATCTCGATCCT 59.959 54.545 0.00 0.00 0.00 3.24
25 26 3.499563 CCTCTAGGTCCATCTCGATCCTT 60.500 52.174 0.00 0.00 0.00 3.36
26 27 4.148838 CTCTAGGTCCATCTCGATCCTTT 58.851 47.826 0.00 0.00 0.00 3.11
27 28 4.145807 TCTAGGTCCATCTCGATCCTTTC 58.854 47.826 0.00 0.00 0.00 2.62
28 29 2.752030 AGGTCCATCTCGATCCTTTCA 58.248 47.619 0.00 0.00 0.00 2.69
64 65 4.950205 AGAAACCTAAACCTGAGTTCGA 57.050 40.909 0.00 0.00 34.19 3.71
126 128 3.824443 GTGCTATGGTTGTGGTTTACCTT 59.176 43.478 0.00 0.00 35.41 3.50
130 132 6.151985 TGCTATGGTTGTGGTTTACCTTAATG 59.848 38.462 0.00 0.00 35.41 1.90
131 133 6.376018 GCTATGGTTGTGGTTTACCTTAATGA 59.624 38.462 0.00 0.00 35.41 2.57
132 134 7.094118 GCTATGGTTGTGGTTTACCTTAATGAA 60.094 37.037 0.00 0.00 35.41 2.57
134 136 7.222000 TGGTTGTGGTTTACCTTAATGAATC 57.778 36.000 0.00 0.00 35.41 2.52
135 137 7.007723 TGGTTGTGGTTTACCTTAATGAATCT 58.992 34.615 0.00 0.00 35.41 2.40
136 138 7.507616 TGGTTGTGGTTTACCTTAATGAATCTT 59.492 33.333 0.00 0.00 35.41 2.40
137 139 8.364894 GGTTGTGGTTTACCTTAATGAATCTTT 58.635 33.333 0.00 0.00 36.82 2.52
143 145 9.447040 GGTTTACCTTAATGAATCTTTATTCGC 57.553 33.333 0.00 0.00 43.84 4.70
146 148 7.865706 ACCTTAATGAATCTTTATTCGCTGT 57.134 32.000 0.00 0.00 43.84 4.40
192 194 9.706691 AATATAAGAACATATGACCCAAGTACG 57.293 33.333 10.38 0.00 0.00 3.67
201 203 7.494625 ACATATGACCCAAGTACGAAAAGTATG 59.505 37.037 10.38 0.00 37.69 2.39
269 271 8.473358 TCGTTTCATATTCAGTTATCTAGGGA 57.527 34.615 0.00 0.00 0.00 4.20
275 277 8.816894 TCATATTCAGTTATCTAGGGACAATCC 58.183 37.037 0.00 0.00 35.23 3.01
309 311 9.562408 TTTTGTTCTTTCAAAACCCTTTACTTT 57.438 25.926 0.00 0.00 40.73 2.66
429 431 5.689383 AGCAAACATTTAGTGTGTGTAGG 57.311 39.130 0.18 0.00 46.05 3.18
540 542 4.631813 GCTACAACTGATCCCTTACACTTG 59.368 45.833 0.00 0.00 0.00 3.16
561 563 2.499685 GTTATCACGGCGGCTCCT 59.500 61.111 13.24 0.00 0.00 3.69
562 564 1.153429 GTTATCACGGCGGCTCCTT 60.153 57.895 13.24 0.00 0.00 3.36
587 592 8.091385 TCTCAAATATCACATCATCCAAATCG 57.909 34.615 0.00 0.00 0.00 3.34
592 597 5.936686 ATCACATCATCCAAATCGTCATC 57.063 39.130 0.00 0.00 0.00 2.92
607 612 2.357777 CGTCATCCCCCAACCCTATTTT 60.358 50.000 0.00 0.00 0.00 1.82
629 634 3.067320 TCTCCATCATCTCTGTTACTGCG 59.933 47.826 0.00 0.00 0.00 5.18
630 635 1.863454 CCATCATCTCTGTTACTGCGC 59.137 52.381 0.00 0.00 0.00 6.09
631 636 1.863454 CATCATCTCTGTTACTGCGCC 59.137 52.381 4.18 0.00 0.00 6.53
664 669 2.094854 GCACCTTTGATCCAGAAGCTTG 60.095 50.000 2.10 0.00 0.00 4.01
665 670 3.152341 CACCTTTGATCCAGAAGCTTGT 58.848 45.455 2.10 0.00 0.00 3.16
667 672 3.571401 ACCTTTGATCCAGAAGCTTGTTG 59.429 43.478 2.10 1.66 0.00 3.33
714 720 5.233689 CGAACTTGAACCTACGAGTTTTTCT 59.766 40.000 0.00 0.00 42.40 2.52
723 729 1.226746 CGAGTTTTTCTGCGGAACCT 58.773 50.000 7.69 4.22 0.00 3.50
745 751 1.843851 AGATTTCCCTATGCCCGTCAA 59.156 47.619 0.00 0.00 0.00 3.18
760 766 1.960689 CGTCAAAACCCCAACCAAGAT 59.039 47.619 0.00 0.00 0.00 2.40
777 783 4.438336 CCAAGATCATGCAGCACTACAAAG 60.438 45.833 0.00 0.00 0.00 2.77
782 788 0.108396 TGCAGCACTACAAAGGAGCA 59.892 50.000 0.00 0.00 32.20 4.26
802 808 1.707427 ACCCCTTGATCAGTTTGAGCT 59.293 47.619 0.00 0.00 33.24 4.09
825 831 3.107601 TGTAGAATGGGGGAGAAGACAG 58.892 50.000 0.00 0.00 0.00 3.51
826 832 0.915364 AGAATGGGGGAGAAGACAGC 59.085 55.000 0.00 0.00 0.00 4.40
828 834 0.622665 AATGGGGGAGAAGACAGCAG 59.377 55.000 0.00 0.00 0.00 4.24
833 839 1.201429 GGGAGAAGACAGCAGGGGAA 61.201 60.000 0.00 0.00 0.00 3.97
843 849 2.292521 ACAGCAGGGGAAGATAGTCTCA 60.293 50.000 0.00 0.00 0.00 3.27
845 851 2.769095 AGCAGGGGAAGATAGTCTCAAC 59.231 50.000 0.00 0.00 0.00 3.18
903 910 4.576330 ACTCGAGGGGATTGATTCTTTT 57.424 40.909 18.41 0.00 0.00 2.27
904 911 4.923415 ACTCGAGGGGATTGATTCTTTTT 58.077 39.130 18.41 0.00 0.00 1.94
1023 1034 2.049156 CGCAGACTCGCTTCACCA 60.049 61.111 0.00 0.00 0.00 4.17
1033 1044 3.134458 CTCGCTTCACCAGTTTCTTTCT 58.866 45.455 0.00 0.00 0.00 2.52
1546 1570 7.758495 AGGTAGCGATTTTAATTCGTTTTGAT 58.242 30.769 10.26 0.00 0.00 2.57
1548 1572 7.483691 GGTAGCGATTTTAATTCGTTTTGATGT 59.516 33.333 10.26 0.00 0.00 3.06
1551 1575 6.458284 GCGATTTTAATTCGTTTTGATGTTGC 59.542 34.615 10.26 0.00 0.00 4.17
1565 1596 0.949397 TGTTGCTTTGCTCTGCTCAG 59.051 50.000 0.00 0.00 0.00 3.35
1630 1661 2.613977 CGATCTGAGGACTTGGCACTTT 60.614 50.000 0.00 0.00 0.00 2.66
1647 1678 5.244626 GGCACTTTCTCATATATGCCCATTT 59.755 40.000 7.92 0.00 45.59 2.32
1648 1679 6.385033 GCACTTTCTCATATATGCCCATTTC 58.615 40.000 7.92 0.00 0.00 2.17
1710 1741 1.629013 TGCAATCAGAGCGAACTACG 58.371 50.000 0.00 0.00 45.66 3.51
1894 2073 3.970842 ACTACTCTAGCCTAGTTGCAGT 58.029 45.455 0.00 0.00 0.00 4.40
2077 2263 6.128486 TGCCTTTATTTTGAGGATGCTATCA 58.872 36.000 0.00 0.00 34.91 2.15
2093 2279 9.415544 GGATGCTATCATTAATTTTCATTGGAC 57.584 33.333 0.00 0.00 31.96 4.02
2427 2614 6.370994 GGTTAAGTAGAGCTTTTACTGTTCCC 59.629 42.308 11.30 7.02 38.57 3.97
2487 2674 8.664798 CGTCTATTCATCTGTAAAATTGGACAA 58.335 33.333 0.00 0.00 0.00 3.18
2536 2723 4.271049 CAGCATGGTTTAGTATGTTCCTCG 59.729 45.833 0.00 0.00 0.00 4.63
2624 2812 2.159627 GGAGCAACACATTACTCAACCG 59.840 50.000 0.00 0.00 30.66 4.44
2697 2885 9.793252 CCTTAATTTTGGTCTATGTCATTGAAG 57.207 33.333 0.00 0.00 0.00 3.02
2725 2913 0.847373 TGGACTGGTTTACAAGCCCA 59.153 50.000 0.00 0.00 0.00 5.36
2998 3186 4.334443 CATTTGCTCGAACGAAGGTATTG 58.666 43.478 0.00 0.00 0.00 1.90
3080 3269 5.355350 ACCAAGATCTTAAGCTCCAATTTCG 59.645 40.000 7.86 0.00 0.00 3.46
3136 3325 4.536765 TCCTTCAGTTTTTCCTTGCTCTT 58.463 39.130 0.00 0.00 0.00 2.85
3188 3377 0.254059 TGATTGAATCCCCCTCCCCA 60.254 55.000 2.26 0.00 0.00 4.96
3308 3497 6.012658 TGCTTCACATGTTCAAGTATTTCC 57.987 37.500 13.49 0.59 0.00 3.13
3427 3638 6.818644 TCATGCTAGTACTTTCAGAACAATCC 59.181 38.462 0.00 0.00 0.00 3.01
3486 3697 0.622136 TCCATGAGGTGATGCTTGCT 59.378 50.000 0.00 0.00 35.89 3.91
3607 3818 5.592104 TCTGATTCGAATTAGCACCAGTA 57.408 39.130 21.68 3.58 0.00 2.74
3680 3891 8.848948 TTTTATATTGTACATGCATTGAACCG 57.151 30.769 0.00 0.00 0.00 4.44
3847 4058 3.904339 AGGAATTGACCTGCTATCGGTAT 59.096 43.478 0.00 0.00 39.01 2.73
3873 4084 6.039382 GCTAAAAAGCTTAAATGCTAGCCCTA 59.961 38.462 13.29 0.00 43.24 3.53
3963 4174 5.913137 TGTTGTTTCTCCAACTCAACAAT 57.087 34.783 6.57 0.00 44.01 2.71
4003 4214 3.525609 TGCTTAACCATCCATTCCCTGTA 59.474 43.478 0.00 0.00 0.00 2.74
4450 4661 8.356657 CCTTGAGAATTATCGACTGAAGATACT 58.643 37.037 1.62 0.00 31.07 2.12
4451 4662 9.743057 CTTGAGAATTATCGACTGAAGATACTT 57.257 33.333 0.00 0.00 31.07 2.24
4452 4663 9.521503 TTGAGAATTATCGACTGAAGATACTTG 57.478 33.333 0.00 0.00 31.07 3.16
4472 4683 6.533730 ACTTGTTGTTCAGATCATGTAGGAA 58.466 36.000 0.00 0.00 0.00 3.36
4601 4812 3.678056 TGACAAGTGAAGCTATTCGGT 57.322 42.857 0.00 0.00 38.34 4.69
4606 4817 1.276421 AGTGAAGCTATTCGGTGCTGT 59.724 47.619 0.00 0.00 39.71 4.40
4767 4984 1.613836 CCATTTCTATGAGCTGGCCC 58.386 55.000 0.00 0.00 33.37 5.80
4779 4996 1.584495 CTGGCCCGGTTTAGCAAAC 59.416 57.895 0.00 3.93 40.65 2.93
4780 4997 1.152735 TGGCCCGGTTTAGCAAACA 60.153 52.632 0.00 0.00 43.15 2.83
4781 4998 1.175983 TGGCCCGGTTTAGCAAACAG 61.176 55.000 0.00 8.66 43.15 3.16
4782 4999 1.176619 GGCCCGGTTTAGCAAACAGT 61.177 55.000 0.00 0.00 43.15 3.55
4783 5000 0.671796 GCCCGGTTTAGCAAACAGTT 59.328 50.000 0.00 0.00 43.15 3.16
4798 5015 6.695292 CAAACAGTTTGCCTAATTCACATC 57.305 37.500 13.11 0.00 33.36 3.06
4799 5016 6.449698 CAAACAGTTTGCCTAATTCACATCT 58.550 36.000 13.11 0.00 33.36 2.90
4800 5017 7.592938 CAAACAGTTTGCCTAATTCACATCTA 58.407 34.615 13.11 0.00 33.36 1.98
4801 5018 6.992063 ACAGTTTGCCTAATTCACATCTAG 57.008 37.500 0.00 0.00 0.00 2.43
4802 5019 6.711277 ACAGTTTGCCTAATTCACATCTAGA 58.289 36.000 0.00 0.00 0.00 2.43
4803 5020 7.341805 ACAGTTTGCCTAATTCACATCTAGAT 58.658 34.615 0.00 0.00 0.00 1.98
4804 5021 7.281774 ACAGTTTGCCTAATTCACATCTAGATG 59.718 37.037 27.63 27.63 44.15 2.90
4805 5022 6.261826 AGTTTGCCTAATTCACATCTAGATGC 59.738 38.462 28.86 14.31 42.39 3.91
4806 5023 5.557576 TGCCTAATTCACATCTAGATGCT 57.442 39.130 28.86 15.38 42.39 3.79
4807 5024 5.933617 TGCCTAATTCACATCTAGATGCTT 58.066 37.500 28.86 19.36 42.39 3.91
4808 5025 6.359804 TGCCTAATTCACATCTAGATGCTTT 58.640 36.000 28.86 19.20 42.39 3.51
4809 5026 6.830324 TGCCTAATTCACATCTAGATGCTTTT 59.170 34.615 28.86 19.48 42.39 2.27
4810 5027 7.340232 TGCCTAATTCACATCTAGATGCTTTTT 59.660 33.333 28.86 19.78 42.39 1.94
4811 5028 8.840321 GCCTAATTCACATCTAGATGCTTTTTA 58.160 33.333 28.86 19.82 42.39 1.52
4819 5036 9.713740 CACATCTAGATGCTTTTTAAAGATGTC 57.286 33.333 28.86 1.37 45.35 3.06
4820 5037 9.453572 ACATCTAGATGCTTTTTAAAGATGTCA 57.546 29.630 28.86 0.00 45.35 3.58
4821 5038 9.713740 CATCTAGATGCTTTTTAAAGATGTCAC 57.286 33.333 19.47 0.00 38.28 3.67
4822 5039 8.846943 TCTAGATGCTTTTTAAAGATGTCACA 57.153 30.769 6.41 0.00 38.28 3.58
4823 5040 9.453572 TCTAGATGCTTTTTAAAGATGTCACAT 57.546 29.630 6.41 0.00 38.28 3.21
4824 5041 9.713740 CTAGATGCTTTTTAAAGATGTCACATC 57.286 33.333 10.05 10.05 38.28 3.06
4825 5042 8.345724 AGATGCTTTTTAAAGATGTCACATCT 57.654 30.769 15.05 15.05 38.28 2.90
4826 5043 9.453572 AGATGCTTTTTAAAGATGTCACATCTA 57.546 29.630 20.94 3.25 36.99 1.98
4829 5046 8.023128 TGCTTTTTAAAGATGTCACATCTAAGC 58.977 33.333 29.69 29.69 38.28 3.09
4830 5047 8.239998 GCTTTTTAAAGATGTCACATCTAAGCT 58.760 33.333 29.37 16.10 38.28 3.74
4833 5050 7.849804 TTAAAGATGTCACATCTAAGCTTCC 57.150 36.000 20.94 0.00 0.00 3.46
4834 5051 5.426689 AAGATGTCACATCTAAGCTTCCA 57.573 39.130 20.94 0.00 0.00 3.53
4835 5052 4.764172 AGATGTCACATCTAAGCTTCCAC 58.236 43.478 19.29 0.00 0.00 4.02
4836 5053 4.223700 AGATGTCACATCTAAGCTTCCACA 59.776 41.667 19.29 0.00 0.00 4.17
4837 5054 4.350368 TGTCACATCTAAGCTTCCACAA 57.650 40.909 0.00 0.00 0.00 3.33
4838 5055 4.713553 TGTCACATCTAAGCTTCCACAAA 58.286 39.130 0.00 0.00 0.00 2.83
4839 5056 5.316167 TGTCACATCTAAGCTTCCACAAAT 58.684 37.500 0.00 0.00 0.00 2.32
4840 5057 6.472016 TGTCACATCTAAGCTTCCACAAATA 58.528 36.000 0.00 0.00 0.00 1.40
4841 5058 7.112122 TGTCACATCTAAGCTTCCACAAATAT 58.888 34.615 0.00 0.00 0.00 1.28
4842 5059 8.264347 TGTCACATCTAAGCTTCCACAAATATA 58.736 33.333 0.00 0.00 0.00 0.86
4843 5060 9.277783 GTCACATCTAAGCTTCCACAAATATAT 57.722 33.333 0.00 0.00 0.00 0.86
4849 5066 9.791801 TCTAAGCTTCCACAAATATATAATGCA 57.208 29.630 0.00 0.00 0.00 3.96
4852 5069 8.640063 AGCTTCCACAAATATATAATGCATCA 57.360 30.769 0.00 0.00 0.00 3.07
4853 5070 9.081204 AGCTTCCACAAATATATAATGCATCAA 57.919 29.630 0.00 0.00 0.00 2.57
4854 5071 9.132521 GCTTCCACAAATATATAATGCATCAAC 57.867 33.333 0.00 0.00 0.00 3.18
4895 5112 8.567285 AGGATAAAGAAATAGACCACAAACAG 57.433 34.615 0.00 0.00 0.00 3.16
4896 5113 8.383175 AGGATAAAGAAATAGACCACAAACAGA 58.617 33.333 0.00 0.00 0.00 3.41
4897 5114 9.010029 GGATAAAGAAATAGACCACAAACAGAA 57.990 33.333 0.00 0.00 0.00 3.02
4900 5117 6.824305 AGAAATAGACCACAAACAGAATGG 57.176 37.500 0.00 0.00 43.62 3.16
4901 5118 6.542821 AGAAATAGACCACAAACAGAATGGA 58.457 36.000 0.00 0.00 43.62 3.41
4902 5119 7.177878 AGAAATAGACCACAAACAGAATGGAT 58.822 34.615 0.00 0.00 43.62 3.41
4903 5120 8.328758 AGAAATAGACCACAAACAGAATGGATA 58.671 33.333 0.00 0.00 43.62 2.59
4904 5121 9.125026 GAAATAGACCACAAACAGAATGGATAT 57.875 33.333 0.00 0.00 43.62 1.63
4905 5122 8.682936 AATAGACCACAAACAGAATGGATATC 57.317 34.615 0.00 0.00 43.62 1.63
4906 5123 6.065976 AGACCACAAACAGAATGGATATCA 57.934 37.500 4.83 0.00 43.62 2.15
4907 5124 6.118170 AGACCACAAACAGAATGGATATCAG 58.882 40.000 4.83 0.00 43.62 2.90
4908 5125 4.641989 ACCACAAACAGAATGGATATCAGC 59.358 41.667 4.83 0.00 43.62 4.26
4909 5126 4.885907 CCACAAACAGAATGGATATCAGCT 59.114 41.667 4.83 0.00 43.62 4.24
4910 5127 5.359009 CCACAAACAGAATGGATATCAGCTT 59.641 40.000 4.83 0.00 43.62 3.74
4911 5128 6.543465 CCACAAACAGAATGGATATCAGCTTA 59.457 38.462 4.83 0.00 43.62 3.09
4912 5129 7.255035 CCACAAACAGAATGGATATCAGCTTAG 60.255 40.741 4.83 0.00 43.62 2.18
4935 5152 4.953940 AATTACACACCACTTTGCCAAT 57.046 36.364 0.00 0.00 0.00 3.16
4971 5191 7.693969 AAAAGGACTATGAACTTTCATCTGG 57.306 36.000 7.74 3.57 44.17 3.86
4983 5203 3.507162 TTCATCTGGCTTGTTTGAGGA 57.493 42.857 0.00 0.00 0.00 3.71
5016 5236 1.133790 GCCAGCTCATGACCAAATGTC 59.866 52.381 0.00 0.00 44.72 3.06
5051 5272 3.433031 GGACATATCCGTGGACATTTGGA 60.433 47.826 0.00 0.00 34.48 3.53
5069 5290 2.025793 TGGAGTCTTGTTTGGTGAACCA 60.026 45.455 0.00 0.00 45.94 3.67
5073 5294 4.398319 AGTCTTGTTTGGTGAACCATAGG 58.602 43.478 2.34 0.00 46.97 2.57
5075 5296 5.010282 GTCTTGTTTGGTGAACCATAGGAT 58.990 41.667 2.34 0.00 46.97 3.24
5088 5309 6.906901 TGAACCATAGGATAAGTCTTAAGGGT 59.093 38.462 1.85 0.00 31.25 4.34
5101 5322 3.262405 TCTTAAGGGTAACTCCAACGCAT 59.738 43.478 1.85 0.00 38.11 4.73
5113 5334 1.791785 CCAACGCATGAACGCATTTTT 59.208 42.857 0.00 0.00 36.19 1.94
5166 5387 2.543653 GCCCAATGCACGGACATAAATC 60.544 50.000 5.55 0.00 40.77 2.17
5167 5388 2.951642 CCCAATGCACGGACATAAATCT 59.048 45.455 5.55 0.00 0.00 2.40
5185 5407 2.305928 TCTGTTTTGTGTCCATGTGGG 58.694 47.619 0.00 0.00 35.41 4.61
5224 5477 1.379843 GGGTCGGGTTTGCATCCAT 60.380 57.895 10.02 0.00 0.00 3.41
5232 5485 2.687935 GGGTTTGCATCCATACGAACAT 59.312 45.455 10.02 0.00 32.72 2.71
5237 5490 3.457234 TGCATCCATACGAACATGAGAC 58.543 45.455 0.00 0.00 0.00 3.36
5238 5491 2.472861 GCATCCATACGAACATGAGACG 59.527 50.000 0.00 4.55 0.00 4.18
5239 5492 3.795488 GCATCCATACGAACATGAGACGA 60.795 47.826 0.00 0.00 0.00 4.20
5240 5493 3.416119 TCCATACGAACATGAGACGAC 57.584 47.619 0.00 0.00 0.00 4.34
5242 5495 2.109463 CATACGAACATGAGACGACCG 58.891 52.381 0.00 0.00 0.00 4.79
5244 5497 2.497092 CGAACATGAGACGACCGCG 61.497 63.158 0.00 0.00 44.79 6.46
5287 5540 3.741388 CGCCCTACAGTCCTTTTAGATGG 60.741 52.174 0.00 0.00 0.00 3.51
5290 5543 3.199946 CCTACAGTCCTTTTAGATGGGCA 59.800 47.826 0.00 0.00 0.00 5.36
5291 5544 3.356529 ACAGTCCTTTTAGATGGGCAG 57.643 47.619 0.00 0.00 0.00 4.85
5293 5546 1.566231 AGTCCTTTTAGATGGGCAGGG 59.434 52.381 0.00 0.00 0.00 4.45
5295 5548 0.756815 CCTTTTAGATGGGCAGGGGC 60.757 60.000 0.00 0.00 40.13 5.80
5323 5580 1.899438 GCCCACTCTTCTCCCTCTCTT 60.899 57.143 0.00 0.00 0.00 2.85
5333 5590 0.850883 TCCCTCTCTTTGCCCCCAAT 60.851 55.000 0.00 0.00 0.00 3.16
5365 5622 1.185315 CCCAACCCTAGCCATTGTTG 58.815 55.000 0.00 0.00 38.20 3.33
5367 5624 1.549203 CAACCCTAGCCATTGTTGCT 58.451 50.000 0.00 0.00 42.81 3.91
5369 5626 0.405585 ACCCTAGCCATTGTTGCTGT 59.594 50.000 0.00 0.00 39.91 4.40
5370 5627 1.203050 ACCCTAGCCATTGTTGCTGTT 60.203 47.619 0.00 0.00 39.91 3.16
5373 5630 3.955775 GCCATTGTTGCTGTTGGC 58.044 55.556 0.00 0.00 46.94 4.52
5391 5648 2.434359 CGGAGAGGGTTTCGGTGC 60.434 66.667 0.00 0.00 0.00 5.01
5393 5650 2.747686 GAGAGGGTTTCGGTGCCA 59.252 61.111 0.00 0.00 0.00 4.92
5400 5657 2.361104 TTTCGGTGCCAGCCATCC 60.361 61.111 0.00 0.00 0.00 3.51
5437 5694 1.534175 CGACGAGCTCAAGATACACCC 60.534 57.143 15.40 0.00 0.00 4.61
5441 5698 1.523938 GCTCAAGATACACCCCCGC 60.524 63.158 0.00 0.00 0.00 6.13
5442 5699 1.227263 CTCAAGATACACCCCCGCG 60.227 63.158 0.00 0.00 0.00 6.46
5460 5720 0.106918 CGGAGCTCTCCCTGTAGACT 60.107 60.000 14.64 0.00 46.96 3.24
5471 5731 1.473278 CCTGTAGACTTCCTCCACGAC 59.527 57.143 0.00 0.00 0.00 4.34
5483 5743 2.106332 CACGACCCGGCATAGGAC 59.894 66.667 0.00 0.00 0.00 3.85
5486 5746 2.416260 GACCCGGCATAGGACGTC 59.584 66.667 7.13 7.13 46.78 4.34
5491 5751 1.432251 CGGCATAGGACGTCGACTT 59.568 57.895 14.70 3.52 41.88 3.01
5494 5754 0.179134 GCATAGGACGTCGACTTGCT 60.179 55.000 19.46 19.46 0.00 3.91
5498 5758 0.603569 AGGACGTCGACTTGCTGAAT 59.396 50.000 15.23 0.00 0.00 2.57
5500 5760 1.126846 GGACGTCGACTTGCTGAATTG 59.873 52.381 14.70 0.00 0.00 2.32
5505 5765 1.071542 TCGACTTGCTGAATTGGGACA 59.928 47.619 0.00 0.00 0.00 4.02
5513 5773 2.162681 CTGAATTGGGACACCTGGTTC 58.837 52.381 0.00 0.00 39.29 3.62
5529 5789 4.034258 TCGTGGACGAGCACGACC 62.034 66.667 16.99 16.99 46.91 4.79
5574 5834 1.372997 CGTGTGCGTGCTCCTAGTT 60.373 57.895 0.00 0.00 0.00 2.24
5591 5851 2.379634 TTCACGTGCGGCGATTGAG 61.380 57.895 12.98 0.00 44.77 3.02
5610 5870 2.760385 GGGAGACCGGTGAGGAGG 60.760 72.222 14.63 0.00 45.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.540830 CGAGATGGACCTAGAGGGGG 60.541 65.000 0.00 0.00 40.27 5.40
1 2 0.478942 TCGAGATGGACCTAGAGGGG 59.521 60.000 0.00 0.00 40.27 4.79
3 4 2.041081 AGGATCGAGATGGACCTAGAGG 59.959 54.545 0.00 0.00 42.17 3.69
4 5 3.433306 AGGATCGAGATGGACCTAGAG 57.567 52.381 0.00 0.00 0.00 2.43
5 6 3.885976 AAGGATCGAGATGGACCTAGA 57.114 47.619 0.00 0.00 0.00 2.43
6 7 3.891977 TGAAAGGATCGAGATGGACCTAG 59.108 47.826 0.00 0.00 0.00 3.02
7 8 3.891977 CTGAAAGGATCGAGATGGACCTA 59.108 47.826 0.00 0.00 0.00 3.08
8 9 2.697751 CTGAAAGGATCGAGATGGACCT 59.302 50.000 0.00 0.00 0.00 3.85
9 10 2.432510 ACTGAAAGGATCGAGATGGACC 59.567 50.000 0.00 0.00 39.30 4.46
10 11 3.810310 ACTGAAAGGATCGAGATGGAC 57.190 47.619 0.00 0.00 39.30 4.02
11 12 3.679917 GCAACTGAAAGGATCGAGATGGA 60.680 47.826 0.00 0.00 39.30 3.41
12 13 2.611292 GCAACTGAAAGGATCGAGATGG 59.389 50.000 0.00 0.00 39.30 3.51
13 14 2.283617 CGCAACTGAAAGGATCGAGATG 59.716 50.000 0.00 0.00 39.30 2.90
14 15 2.544685 CGCAACTGAAAGGATCGAGAT 58.455 47.619 0.00 0.00 39.30 2.75
15 16 1.404181 CCGCAACTGAAAGGATCGAGA 60.404 52.381 0.00 0.00 39.30 4.04
16 17 1.002366 CCGCAACTGAAAGGATCGAG 58.998 55.000 0.00 0.00 39.30 4.04
17 18 0.391130 CCCGCAACTGAAAGGATCGA 60.391 55.000 0.00 0.00 39.30 3.59
18 19 0.391130 TCCCGCAACTGAAAGGATCG 60.391 55.000 0.00 0.00 39.30 3.69
19 20 1.339151 ACTCCCGCAACTGAAAGGATC 60.339 52.381 0.00 0.00 39.30 3.36
20 21 0.693049 ACTCCCGCAACTGAAAGGAT 59.307 50.000 0.00 0.00 39.30 3.24
21 22 0.250295 CACTCCCGCAACTGAAAGGA 60.250 55.000 0.00 0.00 39.30 3.36
22 23 0.250295 TCACTCCCGCAACTGAAAGG 60.250 55.000 0.00 0.00 39.30 3.11
23 24 1.813513 ATCACTCCCGCAACTGAAAG 58.186 50.000 0.00 0.00 42.29 2.62
24 25 2.565391 TCTATCACTCCCGCAACTGAAA 59.435 45.455 0.00 0.00 0.00 2.69
25 26 2.176045 TCTATCACTCCCGCAACTGAA 58.824 47.619 0.00 0.00 0.00 3.02
26 27 1.847328 TCTATCACTCCCGCAACTGA 58.153 50.000 0.00 0.00 0.00 3.41
27 28 2.672961 TTCTATCACTCCCGCAACTG 57.327 50.000 0.00 0.00 0.00 3.16
28 29 2.354805 GGTTTCTATCACTCCCGCAACT 60.355 50.000 0.00 0.00 0.00 3.16
64 65 7.202029 CCCTTTAATCCCATATGCAACAATTCT 60.202 37.037 0.00 0.00 0.00 2.40
126 128 8.712363 GCATCTACAGCGAATAAAGATTCATTA 58.288 33.333 0.00 0.00 41.48 1.90
130 132 6.777526 AGCATCTACAGCGAATAAAGATTC 57.222 37.500 0.00 0.00 38.51 2.52
131 133 6.512415 GCAAGCATCTACAGCGAATAAAGATT 60.512 38.462 0.00 0.00 37.01 2.40
132 134 5.049818 GCAAGCATCTACAGCGAATAAAGAT 60.050 40.000 0.00 0.00 37.01 2.40
134 136 4.272018 AGCAAGCATCTACAGCGAATAAAG 59.728 41.667 0.00 0.00 37.01 1.85
135 137 4.191544 AGCAAGCATCTACAGCGAATAAA 58.808 39.130 0.00 0.00 37.01 1.40
136 138 3.797039 AGCAAGCATCTACAGCGAATAA 58.203 40.909 0.00 0.00 37.01 1.40
137 139 3.459232 AGCAAGCATCTACAGCGAATA 57.541 42.857 0.00 0.00 37.01 1.75
138 140 2.322355 AGCAAGCATCTACAGCGAAT 57.678 45.000 0.00 0.00 37.01 3.34
139 141 2.427095 TCTAGCAAGCATCTACAGCGAA 59.573 45.455 0.00 0.00 37.01 4.70
140 142 2.024414 TCTAGCAAGCATCTACAGCGA 58.976 47.619 0.00 0.00 37.01 4.93
141 143 2.223688 ACTCTAGCAAGCATCTACAGCG 60.224 50.000 0.00 0.00 37.01 5.18
142 144 3.451141 ACTCTAGCAAGCATCTACAGC 57.549 47.619 0.00 0.00 0.00 4.40
143 145 4.142071 TGGAACTCTAGCAAGCATCTACAG 60.142 45.833 0.00 0.00 0.00 2.74
144 146 3.769300 TGGAACTCTAGCAAGCATCTACA 59.231 43.478 0.00 0.00 0.00 2.74
145 147 4.392921 TGGAACTCTAGCAAGCATCTAC 57.607 45.455 0.00 0.00 0.00 2.59
146 148 5.620738 ATTGGAACTCTAGCAAGCATCTA 57.379 39.130 0.00 0.00 0.00 1.98
184 186 6.963049 AGCTAACATACTTTTCGTACTTGG 57.037 37.500 0.00 0.00 0.00 3.61
255 257 7.403231 AGAAAAGGATTGTCCCTAGATAACTGA 59.597 37.037 0.00 0.00 37.19 3.41
383 385 8.799367 GCTTTACCTAGAACAAAGGGATAAAAA 58.201 33.333 10.66 0.00 38.54 1.94
470 472 5.606348 ACTCAATGAGGAGCTAAAGGTAG 57.394 43.478 15.38 0.00 38.50 3.18
540 542 3.199891 GCCGCCGTGATAACCCAC 61.200 66.667 0.00 0.00 0.00 4.61
561 563 8.562052 CGATTTGGATGATGTGATATTTGAGAA 58.438 33.333 0.00 0.00 0.00 2.87
562 564 7.716560 ACGATTTGGATGATGTGATATTTGAGA 59.283 33.333 0.00 0.00 0.00 3.27
587 592 3.052869 AGAAAATAGGGTTGGGGGATGAC 60.053 47.826 0.00 0.00 0.00 3.06
592 597 1.643811 TGGAGAAAATAGGGTTGGGGG 59.356 52.381 0.00 0.00 0.00 5.40
607 612 3.067320 CGCAGTAACAGAGATGATGGAGA 59.933 47.826 0.00 0.00 0.00 3.71
631 636 0.529378 AAAGGTGCCGGTAGAGTACG 59.471 55.000 1.90 0.00 0.00 3.67
645 650 3.515602 ACAAGCTTCTGGATCAAAGGT 57.484 42.857 0.00 0.00 34.86 3.50
664 669 1.599419 GGTTTGTCACGCATGTCCAAC 60.599 52.381 0.00 0.00 0.00 3.77
665 670 0.665835 GGTTTGTCACGCATGTCCAA 59.334 50.000 0.00 0.00 0.00 3.53
667 672 1.206578 CGGTTTGTCACGCATGTCC 59.793 57.895 0.00 0.00 0.00 4.02
714 720 1.913419 AGGGAAATCTAAGGTTCCGCA 59.087 47.619 0.00 0.00 43.68 5.69
723 729 3.042682 TGACGGGCATAGGGAAATCTAA 58.957 45.455 0.00 0.00 0.00 2.10
745 751 1.901833 GCATGATCTTGGTTGGGGTTT 59.098 47.619 10.35 0.00 0.00 3.27
760 766 2.703416 CTCCTTTGTAGTGCTGCATGA 58.297 47.619 5.27 0.00 0.00 3.07
777 783 0.329596 AACTGATCAAGGGGTGCTCC 59.670 55.000 0.00 0.00 0.00 4.70
782 788 1.707427 AGCTCAAACTGATCAAGGGGT 59.293 47.619 0.00 0.00 0.00 4.95
802 808 2.838202 GTCTTCTCCCCCATTCTACACA 59.162 50.000 0.00 0.00 0.00 3.72
825 831 2.482142 CGTTGAGACTATCTTCCCCTGC 60.482 54.545 0.00 0.00 0.00 4.85
826 832 2.761208 ACGTTGAGACTATCTTCCCCTG 59.239 50.000 0.00 0.00 0.00 4.45
828 834 2.223525 CGACGTTGAGACTATCTTCCCC 60.224 54.545 0.00 0.00 0.00 4.81
833 839 3.118482 TCCTACCGACGTTGAGACTATCT 60.118 47.826 3.74 0.00 0.00 1.98
1013 1024 3.194005 AGAAAGAAACTGGTGAAGCGA 57.806 42.857 0.00 0.00 0.00 4.93
1152 1165 0.745845 CTTCTCCATGGTGCTTCCGG 60.746 60.000 12.58 0.00 39.52 5.14
1309 1332 0.183971 GGAGGAGGGAGATCTCACGA 59.816 60.000 23.85 0.00 38.25 4.35
1546 1570 0.949397 CTGAGCAGAGCAAAGCAACA 59.051 50.000 0.00 0.00 0.00 3.33
1548 1572 1.335810 CAACTGAGCAGAGCAAAGCAA 59.664 47.619 4.21 0.00 0.00 3.91
1551 1575 0.240411 GCCAACTGAGCAGAGCAAAG 59.760 55.000 4.21 0.00 0.00 2.77
1591 1622 3.147553 TCGATGGATAGGAGACTCAGG 57.852 52.381 4.53 0.00 43.67 3.86
1630 1661 6.014242 AGAGTTCGAAATGGGCATATATGAGA 60.014 38.462 17.10 0.00 0.00 3.27
1647 1678 2.731451 CGATGCAAAACTCAGAGTTCGA 59.269 45.455 16.44 1.61 37.47 3.71
1648 1679 2.159787 CCGATGCAAAACTCAGAGTTCG 60.160 50.000 16.44 13.66 37.47 3.95
1686 1717 4.063998 AGTTCGCTCTGATTGCATATCA 57.936 40.909 10.01 10.01 0.00 2.15
2077 2263 7.270047 CCATCTGCTGTCCAATGAAAATTAAT 58.730 34.615 0.00 0.00 0.00 1.40
2093 2279 0.462225 CTGGACTCTGCCATCTGCTG 60.462 60.000 0.00 0.00 42.00 4.41
2427 2614 3.379372 CCTCATGGGTGTAGCTTTTCATG 59.621 47.826 0.00 0.17 34.89 3.07
2536 2723 6.436218 ACAACACAAAAATAGGGAATAGGACC 59.564 38.462 0.00 0.00 0.00 4.46
2624 2812 3.315191 CCGATGGACCAAATATCAACACC 59.685 47.826 0.00 0.00 0.00 4.16
2690 2878 2.027377 AGTCCAGAGGCAGTCTTCAATG 60.027 50.000 0.00 0.00 30.64 2.82
2697 2885 0.398318 AAACCAGTCCAGAGGCAGTC 59.602 55.000 0.00 0.00 0.00 3.51
2725 2913 5.662674 AAGTTAGGCTCAAAGTACGAGAT 57.337 39.130 0.00 0.00 31.84 2.75
2780 2968 4.637483 ATGGTGTACTGTTTATGCATGC 57.363 40.909 11.82 11.82 0.00 4.06
2791 2979 5.902613 AATGTGAATCCAATGGTGTACTG 57.097 39.130 0.00 0.00 0.00 2.74
2793 2981 6.266168 TCAAATGTGAATCCAATGGTGTAC 57.734 37.500 0.00 0.00 0.00 2.90
2998 3186 3.551659 GGCTTTAGAATTGCTGCTATGGC 60.552 47.826 0.00 0.00 39.26 4.40
3099 3288 2.224769 TGAAGGAGTCGGCCAGAAATTT 60.225 45.455 2.24 0.00 0.00 1.82
3188 3377 2.414250 AAACATCAAATGGTGGGGGT 57.586 45.000 0.00 0.00 33.60 4.95
3295 3484 6.379988 AGAGAGAGAGAGGGAAATACTTGAAC 59.620 42.308 0.00 0.00 0.00 3.18
3308 3497 2.486191 GCAGGAGAGAGAGAGAGAGAGG 60.486 59.091 0.00 0.00 0.00 3.69
3486 3697 7.759489 AGTTTTGCTATGTTTCCAGATTGTA 57.241 32.000 0.00 0.00 0.00 2.41
3655 3866 8.462811 ACGGTTCAATGCATGTACAATATAAAA 58.537 29.630 0.00 0.00 31.42 1.52
3680 3891 7.915923 GCCTGATAAGGAGCACTTTTAATTAAC 59.084 37.037 0.00 0.00 40.64 2.01
3847 4058 5.394115 GGGCTAGCATTTAAGCTTTTTAGCA 60.394 40.000 18.24 0.00 43.70 3.49
3873 4084 7.771927 AATGATTTTCCAGTGAAGAGAATGT 57.228 32.000 0.00 0.00 0.00 2.71
3963 4174 9.120538 GGTTAAGCATATCTCCATAACTTGAAA 57.879 33.333 0.00 0.00 0.00 2.69
4161 4372 1.667154 CTGAGATCCTGTTCGCCGGA 61.667 60.000 5.05 0.00 0.00 5.14
4450 4661 8.408043 AAATTCCTACATGATCTGAACAACAA 57.592 30.769 0.00 0.00 0.00 2.83
4451 4662 8.408043 AAAATTCCTACATGATCTGAACAACA 57.592 30.769 0.00 0.00 0.00 3.33
4472 4683 7.826690 ACAATTCCGTACAGAGCAAATAAAAT 58.173 30.769 0.00 0.00 0.00 1.82
4593 4804 2.002586 CCACTTCACAGCACCGAATAG 58.997 52.381 0.00 0.00 0.00 1.73
4598 4809 1.224069 CTCACCACTTCACAGCACCG 61.224 60.000 0.00 0.00 0.00 4.94
4601 4812 0.394192 CCTCTCACCACTTCACAGCA 59.606 55.000 0.00 0.00 0.00 4.41
4606 4817 1.367471 CACGCCTCTCACCACTTCA 59.633 57.895 0.00 0.00 0.00 3.02
4677 4893 0.541392 TGTCCCCGACAGAATCATGG 59.459 55.000 0.00 0.00 37.67 3.66
4688 4904 2.354729 CTGGCCAAATGTCCCCGA 59.645 61.111 7.01 0.00 0.00 5.14
4779 4996 7.637229 CATCTAGATGTGAATTAGGCAAACTG 58.363 38.462 22.42 0.00 34.23 3.16
4780 4997 6.261826 GCATCTAGATGTGAATTAGGCAAACT 59.738 38.462 28.92 0.00 40.80 2.66
4781 4998 6.261826 AGCATCTAGATGTGAATTAGGCAAAC 59.738 38.462 28.92 10.81 40.80 2.93
4782 4999 6.359804 AGCATCTAGATGTGAATTAGGCAAA 58.640 36.000 28.92 0.00 40.80 3.68
4783 5000 5.933617 AGCATCTAGATGTGAATTAGGCAA 58.066 37.500 28.92 0.00 40.80 4.52
4792 5009 9.453572 ACATCTTTAAAAAGCATCTAGATGTGA 57.546 29.630 28.92 15.17 45.20 3.58
4793 5010 9.713740 GACATCTTTAAAAAGCATCTAGATGTG 57.286 33.333 28.92 18.28 46.24 3.21
4795 5012 9.713740 GTGACATCTTTAAAAAGCATCTAGATG 57.286 33.333 25.64 25.64 41.84 2.90
4796 5013 9.453572 TGTGACATCTTTAAAAAGCATCTAGAT 57.546 29.630 0.00 0.00 35.99 1.98
4797 5014 8.846943 TGTGACATCTTTAAAAAGCATCTAGA 57.153 30.769 0.00 0.00 35.99 2.43
4798 5015 9.713740 GATGTGACATCTTTAAAAAGCATCTAG 57.286 33.333 17.84 0.00 35.99 2.43
4799 5016 9.453572 AGATGTGACATCTTTAAAAAGCATCTA 57.546 29.630 21.66 0.00 36.99 1.98
4800 5017 8.345724 AGATGTGACATCTTTAAAAAGCATCT 57.654 30.769 21.66 11.80 35.48 2.90
4803 5020 8.023128 GCTTAGATGTGACATCTTTAAAAAGCA 58.977 33.333 33.47 16.00 35.98 3.91
4804 5021 8.239998 AGCTTAGATGTGACATCTTTAAAAAGC 58.760 33.333 32.47 32.47 36.08 3.51
4807 5024 8.730680 GGAAGCTTAGATGTGACATCTTTAAAA 58.269 33.333 30.49 18.29 0.00 1.52
4808 5025 7.882791 TGGAAGCTTAGATGTGACATCTTTAAA 59.117 33.333 30.49 18.61 0.00 1.52
4809 5026 7.334421 GTGGAAGCTTAGATGTGACATCTTTAA 59.666 37.037 30.49 19.26 0.00 1.52
4810 5027 6.818644 GTGGAAGCTTAGATGTGACATCTTTA 59.181 38.462 30.49 18.53 0.00 1.85
4811 5028 5.645497 GTGGAAGCTTAGATGTGACATCTTT 59.355 40.000 30.49 19.45 0.00 2.52
4812 5029 5.181748 GTGGAAGCTTAGATGTGACATCTT 58.818 41.667 30.49 14.32 0.00 2.40
4813 5030 4.223700 TGTGGAAGCTTAGATGTGACATCT 59.776 41.667 28.69 28.69 0.00 2.90
4814 5031 4.507710 TGTGGAAGCTTAGATGTGACATC 58.492 43.478 17.46 17.46 0.00 3.06
4815 5032 4.558226 TGTGGAAGCTTAGATGTGACAT 57.442 40.909 0.00 0.00 0.00 3.06
4816 5033 4.350368 TTGTGGAAGCTTAGATGTGACA 57.650 40.909 0.00 0.00 0.00 3.58
4817 5034 5.886960 ATTTGTGGAAGCTTAGATGTGAC 57.113 39.130 0.00 0.00 0.00 3.67
4823 5040 9.791801 TGCATTATATATTTGTGGAAGCTTAGA 57.208 29.630 0.00 0.00 0.00 2.10
4826 5043 9.081204 TGATGCATTATATATTTGTGGAAGCTT 57.919 29.630 0.00 0.00 0.00 3.74
4827 5044 8.640063 TGATGCATTATATATTTGTGGAAGCT 57.360 30.769 0.00 0.00 0.00 3.74
4828 5045 9.132521 GTTGATGCATTATATATTTGTGGAAGC 57.867 33.333 0.00 0.00 0.00 3.86
4869 5086 9.667107 CTGTTTGTGGTCTATTTCTTTATCCTA 57.333 33.333 0.00 0.00 0.00 2.94
4870 5087 8.383175 TCTGTTTGTGGTCTATTTCTTTATCCT 58.617 33.333 0.00 0.00 0.00 3.24
4871 5088 8.561738 TCTGTTTGTGGTCTATTTCTTTATCC 57.438 34.615 0.00 0.00 0.00 2.59
4874 5091 8.792633 CCATTCTGTTTGTGGTCTATTTCTTTA 58.207 33.333 0.00 0.00 0.00 1.85
4875 5092 7.505585 TCCATTCTGTTTGTGGTCTATTTCTTT 59.494 33.333 0.00 0.00 34.61 2.52
4876 5093 7.004086 TCCATTCTGTTTGTGGTCTATTTCTT 58.996 34.615 0.00 0.00 34.61 2.52
4877 5094 6.542821 TCCATTCTGTTTGTGGTCTATTTCT 58.457 36.000 0.00 0.00 34.61 2.52
4878 5095 6.817765 TCCATTCTGTTTGTGGTCTATTTC 57.182 37.500 0.00 0.00 34.61 2.17
4879 5096 9.125026 GATATCCATTCTGTTTGTGGTCTATTT 57.875 33.333 0.00 0.00 34.61 1.40
4880 5097 8.274322 TGATATCCATTCTGTTTGTGGTCTATT 58.726 33.333 0.00 0.00 34.61 1.73
4881 5098 7.805163 TGATATCCATTCTGTTTGTGGTCTAT 58.195 34.615 0.00 0.00 34.61 1.98
4882 5099 7.194112 TGATATCCATTCTGTTTGTGGTCTA 57.806 36.000 0.00 0.00 34.61 2.59
4883 5100 6.065976 TGATATCCATTCTGTTTGTGGTCT 57.934 37.500 0.00 0.00 34.61 3.85
4884 5101 5.220931 GCTGATATCCATTCTGTTTGTGGTC 60.221 44.000 0.00 0.00 34.61 4.02
4885 5102 4.641989 GCTGATATCCATTCTGTTTGTGGT 59.358 41.667 0.00 0.00 34.61 4.16
4886 5103 4.885907 AGCTGATATCCATTCTGTTTGTGG 59.114 41.667 0.00 0.00 0.00 4.17
4887 5104 6.446781 AAGCTGATATCCATTCTGTTTGTG 57.553 37.500 0.00 0.00 0.00 3.33
4888 5105 7.568349 TCTAAGCTGATATCCATTCTGTTTGT 58.432 34.615 0.00 0.00 0.00 2.83
4889 5106 8.442632 TTCTAAGCTGATATCCATTCTGTTTG 57.557 34.615 0.00 0.00 0.00 2.93
4890 5107 9.638176 ATTTCTAAGCTGATATCCATTCTGTTT 57.362 29.630 0.00 0.00 0.00 2.83
4891 5108 9.638176 AATTTCTAAGCTGATATCCATTCTGTT 57.362 29.630 0.00 0.00 0.00 3.16
4896 5113 9.851686 TGTGTAATTTCTAAGCTGATATCCATT 57.148 29.630 0.00 0.00 0.00 3.16
4897 5114 9.277783 GTGTGTAATTTCTAAGCTGATATCCAT 57.722 33.333 0.00 0.00 0.00 3.41
4898 5115 7.715249 GGTGTGTAATTTCTAAGCTGATATCCA 59.285 37.037 0.00 0.00 0.00 3.41
4899 5116 7.715249 TGGTGTGTAATTTCTAAGCTGATATCC 59.285 37.037 0.00 0.00 0.00 2.59
4900 5117 8.552034 GTGGTGTGTAATTTCTAAGCTGATATC 58.448 37.037 0.00 0.00 0.00 1.63
4901 5118 8.267894 AGTGGTGTGTAATTTCTAAGCTGATAT 58.732 33.333 0.00 0.00 0.00 1.63
4902 5119 7.620880 AGTGGTGTGTAATTTCTAAGCTGATA 58.379 34.615 0.00 0.00 0.00 2.15
4903 5120 6.476378 AGTGGTGTGTAATTTCTAAGCTGAT 58.524 36.000 0.00 0.00 0.00 2.90
4904 5121 5.865085 AGTGGTGTGTAATTTCTAAGCTGA 58.135 37.500 0.00 0.00 0.00 4.26
4905 5122 6.560253 AAGTGGTGTGTAATTTCTAAGCTG 57.440 37.500 0.00 0.00 0.00 4.24
4906 5123 6.515035 GCAAAGTGGTGTGTAATTTCTAAGCT 60.515 38.462 0.00 0.00 0.00 3.74
4907 5124 5.629435 GCAAAGTGGTGTGTAATTTCTAAGC 59.371 40.000 0.00 0.00 0.00 3.09
4908 5125 6.149633 GGCAAAGTGGTGTGTAATTTCTAAG 58.850 40.000 0.00 0.00 0.00 2.18
4909 5126 5.594725 TGGCAAAGTGGTGTGTAATTTCTAA 59.405 36.000 0.00 0.00 0.00 2.10
4910 5127 5.133941 TGGCAAAGTGGTGTGTAATTTCTA 58.866 37.500 0.00 0.00 0.00 2.10
4911 5128 3.957497 TGGCAAAGTGGTGTGTAATTTCT 59.043 39.130 0.00 0.00 0.00 2.52
4912 5129 4.314740 TGGCAAAGTGGTGTGTAATTTC 57.685 40.909 0.00 0.00 0.00 2.17
4935 5152 7.994425 TCATAGTCCTTTTTAGCATGACAAA 57.006 32.000 0.00 0.00 0.00 2.83
4971 5191 3.193479 CCAACCCTATTCCTCAAACAAGC 59.807 47.826 0.00 0.00 0.00 4.01
4983 5203 0.929244 AGCTGGCATCCAACCCTATT 59.071 50.000 0.00 0.00 30.80 1.73
5016 5236 1.261938 TATGTCCGGGGTGTCCACAG 61.262 60.000 0.00 0.00 34.36 3.66
5069 5290 8.294690 TGGAGTTACCCTTAAGACTTATCCTAT 58.705 37.037 3.36 0.00 38.00 2.57
5073 5294 6.755607 CGTTGGAGTTACCCTTAAGACTTATC 59.244 42.308 3.36 0.00 38.00 1.75
5075 5296 5.567423 GCGTTGGAGTTACCCTTAAGACTTA 60.567 44.000 3.36 0.00 38.00 2.24
5088 5309 0.793861 GCGTTCATGCGTTGGAGTTA 59.206 50.000 0.00 0.00 0.00 2.24
5113 5334 1.469703 TCGACGCGGATCTAAACAGAA 59.530 47.619 12.47 0.00 0.00 3.02
5126 5347 0.363512 CTGTGATTTCTGTCGACGCG 59.636 55.000 11.62 3.53 0.00 6.01
5166 5387 1.269726 GCCCACATGGACACAAAACAG 60.270 52.381 0.00 0.00 37.39 3.16
5167 5388 0.749649 GCCCACATGGACACAAAACA 59.250 50.000 0.00 0.00 37.39 2.83
5185 5407 0.458370 AATTTGAGGCGGATTTGCGC 60.458 50.000 8.00 8.00 35.06 6.09
5224 5477 0.179181 GCGGTCGTCTCATGTTCGTA 60.179 55.000 0.00 0.00 0.00 3.43
5251 5504 3.255379 GGCGGACATCGAGCGAAC 61.255 66.667 0.00 0.00 42.43 3.95
5259 5512 1.043673 AGGACTGTAGGGCGGACATC 61.044 60.000 0.00 0.00 0.00 3.06
5260 5513 0.617820 AAGGACTGTAGGGCGGACAT 60.618 55.000 0.00 0.00 0.00 3.06
5300 5553 1.950973 GAGGGAGAAGAGTGGGCGTC 61.951 65.000 0.00 0.00 0.00 5.19
5301 5554 1.985116 GAGGGAGAAGAGTGGGCGT 60.985 63.158 0.00 0.00 0.00 5.68
5323 5580 1.691195 TATCGAGCGATTGGGGGCAA 61.691 55.000 10.89 0.00 36.17 4.52
5333 5590 1.141019 GTTGGGCACTATCGAGCGA 59.859 57.895 0.00 0.00 0.00 4.93
5365 5622 4.785453 CCCTCTCCGGCCAACAGC 62.785 72.222 2.24 0.00 42.60 4.40
5367 5624 2.406002 GAAACCCTCTCCGGCCAACA 62.406 60.000 2.24 0.00 0.00 3.33
5369 5626 2.754375 GAAACCCTCTCCGGCCAA 59.246 61.111 2.24 0.00 0.00 4.52
5370 5627 3.702048 CGAAACCCTCTCCGGCCA 61.702 66.667 2.24 0.00 0.00 5.36
5373 5630 2.264794 CACCGAAACCCTCTCCGG 59.735 66.667 0.00 0.00 46.65 5.14
5415 5672 0.100682 TGTATCTTGAGCTCGTCGGC 59.899 55.000 9.64 0.00 0.00 5.54
5416 5673 1.534175 GGTGTATCTTGAGCTCGTCGG 60.534 57.143 9.64 0.00 0.00 4.79
5417 5674 1.534175 GGGTGTATCTTGAGCTCGTCG 60.534 57.143 9.64 0.00 0.00 5.12
5418 5675 1.202428 GGGGTGTATCTTGAGCTCGTC 60.202 57.143 9.64 0.00 0.00 4.20
5419 5676 0.824759 GGGGTGTATCTTGAGCTCGT 59.175 55.000 9.64 0.00 0.00 4.18
5427 5684 2.364579 TCCGCGGGGGTGTATCTT 60.365 61.111 27.83 0.00 37.00 2.40
5453 5713 1.542492 GGTCGTGGAGGAAGTCTACA 58.458 55.000 0.00 0.00 36.44 2.74
5455 5715 0.679002 CGGGTCGTGGAGGAAGTCTA 60.679 60.000 0.00 0.00 0.00 2.59
5471 5731 3.214123 TCGACGTCCTATGCCGGG 61.214 66.667 10.58 0.00 0.00 5.73
5483 5743 0.443869 CCCAATTCAGCAAGTCGACG 59.556 55.000 10.46 0.00 0.00 5.12
5486 5746 1.197721 GTGTCCCAATTCAGCAAGTCG 59.802 52.381 0.00 0.00 0.00 4.18
5491 5751 0.251297 CCAGGTGTCCCAATTCAGCA 60.251 55.000 0.00 0.00 34.97 4.41
5494 5754 1.544537 CGAACCAGGTGTCCCAATTCA 60.545 52.381 0.00 0.00 0.00 2.57
5498 5758 1.147376 CACGAACCAGGTGTCCCAA 59.853 57.895 0.00 0.00 0.00 4.12
5500 5760 2.032071 CCACGAACCAGGTGTCCC 59.968 66.667 0.00 0.00 33.56 4.46
5536 5796 1.448717 GAGGCGAAGAAGGACTGGC 60.449 63.158 0.00 0.00 0.00 4.85
5539 5799 2.352032 CGGGAGGCGAAGAAGGACT 61.352 63.158 0.00 0.00 0.00 3.85
5570 5830 1.080366 AATCGCCGCACGTGAACTA 60.080 52.632 22.23 0.00 44.19 2.24
5574 5834 2.809174 CTCAATCGCCGCACGTGA 60.809 61.111 22.23 0.00 44.19 4.35
5585 5845 1.689582 ACCGGTCTCCCCCTCAATC 60.690 63.158 0.00 0.00 0.00 2.67
5591 5851 4.393778 TCCTCACCGGTCTCCCCC 62.394 72.222 2.59 0.00 0.00 5.40
5622 5882 0.609957 TCCTCGACGGCCTTCTTGTA 60.610 55.000 7.75 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.