Multiple sequence alignment - TraesCS7B01G135800

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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 TraesCS7B01G135800 chr7B 100.000 4557 0 0 1 4557 167009766 167005210 0.000000e+00 8416.0
1 TraesCS7B01G135800 chr7B 87.283 920 106 7 15 927 266013245 266012330 0.000000e+00 1040.0
2 TraesCS7B01G135800 chr7A 96.546 1303 40 2 922 2224 215192875 215191578 0.000000e+00 2152.0
3 TraesCS7B01G135800 chr7A 93.909 1379 55 5 2214 3592 215191534 215190185 0.000000e+00 2054.0
4 TraesCS7B01G135800 chr7A 89.128 929 96 3 1 925 288872601 288873528 0.000000e+00 1151.0
5 TraesCS7B01G135800 chr7A 88.293 914 99 6 18 925 163624927 163625838 0.000000e+00 1088.0
6 TraesCS7B01G135800 chr7A 85.991 928 126 3 1 926 286946228 286945303 0.000000e+00 990.0
7 TraesCS7B01G135800 chr7A 96.522 115 4 0 3665 3779 704910746 704910632 1.670000e-44 191.0
8 TraesCS7B01G135800 chr7A 92.857 112 7 1 3779 3890 493632797 493632687 1.310000e-35 161.0
9 TraesCS7B01G135800 chr7A 91.935 62 4 1 3884 3944 215189560 215189499 8.120000e-13 86.1
10 TraesCS7B01G135800 chr7D 92.339 1475 64 15 2214 3665 203406110 203404662 0.000000e+00 2052.0
11 TraesCS7B01G135800 chr7D 94.041 1309 40 7 922 2224 203407430 203406154 0.000000e+00 1951.0
12 TraesCS7B01G135800 chr7D 85.874 538 56 7 4024 4557 203404512 203403991 5.150000e-154 555.0
13 TraesCS7B01G135800 chr3B 89.644 927 89 5 1 925 495699607 495698686 0.000000e+00 1173.0
14 TraesCS7B01G135800 chr3B 82.699 578 84 10 3985 4557 794589509 794590075 2.450000e-137 499.0
15 TraesCS7B01G135800 chr4A 87.863 931 106 5 1 926 547048213 547047285 0.000000e+00 1086.0
16 TraesCS7B01G135800 chr1A 84.946 930 134 6 1 926 527689080 527690007 0.000000e+00 937.0
17 TraesCS7B01G135800 chr1A 86.631 187 21 3 3695 3878 10710027 10710212 2.150000e-48 204.0
18 TraesCS7B01G135800 chr6A 84.466 927 137 6 1 923 2162729 2163652 0.000000e+00 907.0
19 TraesCS7B01G135800 chr5A 78.349 933 184 16 1 923 300158762 300157838 5.080000e-164 588.0
20 TraesCS7B01G135800 chr5A 83.361 607 84 9 3957 4557 37642582 37643177 3.100000e-151 545.0
21 TraesCS7B01G135800 chr6B 84.433 591 74 11 3974 4557 127311887 127311308 2.380000e-157 566.0
22 TraesCS7B01G135800 chr6B 82.010 617 95 9 3947 4557 146669562 146670168 1.130000e-140 510.0
23 TraesCS7B01G135800 chr5D 82.982 617 89 11 3950 4557 380519736 380520345 1.110000e-150 544.0
24 TraesCS7B01G135800 chr5D 95.833 120 4 1 3660 3779 91413452 91413334 4.650000e-45 193.0
25 TraesCS7B01G135800 chr5D 92.308 117 7 2 3779 3894 418294186 418294301 1.010000e-36 165.0
26 TraesCS7B01G135800 chr5B 82.658 617 90 10 3948 4557 48913389 48913995 8.680000e-147 531.0
27 TraesCS7B01G135800 chr5B 96.040 101 4 0 3779 3879 535055979 535056079 1.010000e-36 165.0
28 TraesCS7B01G135800 chr2A 83.333 564 78 10 3996 4554 747329292 747329844 1.460000e-139 507.0
29 TraesCS7B01G135800 chr2A 96.552 116 4 0 3664 3779 516889603 516889488 4.650000e-45 193.0
30 TraesCS7B01G135800 chr2A 93.233 133 6 3 3647 3779 693265545 693265674 4.650000e-45 193.0
31 TraesCS7B01G135800 chr2A 93.103 116 7 1 3779 3894 169355668 169355554 7.840000e-38 169.0
32 TraesCS7B01G135800 chr1D 81.138 615 103 7 3948 4557 67387180 67387786 8.870000e-132 481.0
33 TraesCS7B01G135800 chr1D 96.522 115 4 0 3665 3779 200346112 200346226 1.670000e-44 191.0
34 TraesCS7B01G135800 chr1D 94.355 124 7 0 3656 3779 448103128 448103251 1.670000e-44 191.0
35 TraesCS7B01G135800 chr1D 81.641 256 18 10 3664 3891 420948253 420947999 7.790000e-43 185.0
36 TraesCS7B01G135800 chr6D 81.724 580 90 12 3985 4557 266323346 266322776 1.920000e-128 470.0
37 TraesCS7B01G135800 chr3A 80.395 607 96 15 3947 4544 724015727 724016319 1.500000e-119 440.0
38 TraesCS7B01G135800 chr4B 83.794 253 17 6 3664 3892 621866066 621866318 7.680000e-53 219.0
39 TraesCS7B01G135800 chr2D 96.522 115 4 0 3665 3779 123571159 123571045 1.670000e-44 191.0
40 TraesCS7B01G135800 chr2D 93.805 113 6 1 3779 3891 541547431 541547542 7.840000e-38 169.0
41 TraesCS7B01G135800 chr1B 92.913 127 7 2 3653 3779 326918505 326918629 2.800000e-42 183.0
42 TraesCS7B01G135800 chr3D 93.043 115 7 1 3779 3893 563449041 563448928 2.820000e-37 167.0


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 TraesCS7B01G135800 chr7B 167005210 167009766 4556 True 8416.000000 8416 100.000000 1 4557 1 chr7B.!!$R1 4556
1 TraesCS7B01G135800 chr7B 266012330 266013245 915 True 1040.000000 1040 87.283000 15 927 1 chr7B.!!$R2 912
2 TraesCS7B01G135800 chr7A 215189499 215192875 3376 True 1430.700000 2152 94.130000 922 3944 3 chr7A.!!$R4 3022
3 TraesCS7B01G135800 chr7A 288872601 288873528 927 False 1151.000000 1151 89.128000 1 925 1 chr7A.!!$F2 924
4 TraesCS7B01G135800 chr7A 163624927 163625838 911 False 1088.000000 1088 88.293000 18 925 1 chr7A.!!$F1 907
5 TraesCS7B01G135800 chr7A 286945303 286946228 925 True 990.000000 990 85.991000 1 926 1 chr7A.!!$R1 925
6 TraesCS7B01G135800 chr7D 203403991 203407430 3439 True 1519.333333 2052 90.751333 922 4557 3 chr7D.!!$R1 3635
7 TraesCS7B01G135800 chr3B 495698686 495699607 921 True 1173.000000 1173 89.644000 1 925 1 chr3B.!!$R1 924
8 TraesCS7B01G135800 chr3B 794589509 794590075 566 False 499.000000 499 82.699000 3985 4557 1 chr3B.!!$F1 572
9 TraesCS7B01G135800 chr4A 547047285 547048213 928 True 1086.000000 1086 87.863000 1 926 1 chr4A.!!$R1 925
10 TraesCS7B01G135800 chr1A 527689080 527690007 927 False 937.000000 937 84.946000 1 926 1 chr1A.!!$F2 925
11 TraesCS7B01G135800 chr6A 2162729 2163652 923 False 907.000000 907 84.466000 1 923 1 chr6A.!!$F1 922
12 TraesCS7B01G135800 chr5A 300157838 300158762 924 True 588.000000 588 78.349000 1 923 1 chr5A.!!$R1 922
13 TraesCS7B01G135800 chr5A 37642582 37643177 595 False 545.000000 545 83.361000 3957 4557 1 chr5A.!!$F1 600
14 TraesCS7B01G135800 chr6B 127311308 127311887 579 True 566.000000 566 84.433000 3974 4557 1 chr6B.!!$R1 583
15 TraesCS7B01G135800 chr6B 146669562 146670168 606 False 510.000000 510 82.010000 3947 4557 1 chr6B.!!$F1 610
16 TraesCS7B01G135800 chr5D 380519736 380520345 609 False 544.000000 544 82.982000 3950 4557 1 chr5D.!!$F1 607
17 TraesCS7B01G135800 chr5B 48913389 48913995 606 False 531.000000 531 82.658000 3948 4557 1 chr5B.!!$F1 609
18 TraesCS7B01G135800 chr2A 747329292 747329844 552 False 507.000000 507 83.333000 3996 4554 1 chr2A.!!$F2 558
19 TraesCS7B01G135800 chr1D 67387180 67387786 606 False 481.000000 481 81.138000 3948 4557 1 chr1D.!!$F1 609
20 TraesCS7B01G135800 chr6D 266322776 266323346 570 True 470.000000 470 81.724000 3985 4557 1 chr6D.!!$R1 572
21 TraesCS7B01G135800 chr3A 724015727 724016319 592 False 440.000000 440 80.395000 3947 4544 1 chr3A.!!$F1 597

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
446 450 0.191064 TCCACCTCTTCTGGGAGTGT 59.809 55.000 0.0 0.0 0.00 3.55 F
822 840 1.608283 GCTCCCAGACACCTGTTGTAC 60.608 57.143 0.0 0.0 39.17 2.90 F
1627 1656 1.739562 GCTCACACAGCCTTCTCCG 60.740 63.158 0.0 0.0 43.17 4.63 F
1935 1964 0.035439 TTGTTGGGAAGGGCGAGATC 60.035 55.000 0.0 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1552 1581 0.546747 TTCTTCCCGTGGATGGAGGT 60.547 55.0 6.15 0.00 32.37 3.85 R
1823 1852 1.089920 CACATTACTGCCACTCTGCC 58.910 55.0 0.00 0.00 0.00 4.85 R
3122 3205 0.436531 CGCAGTTTGAGTTCGAGCTC 59.563 55.0 21.09 21.09 36.12 4.09 R
3772 4441 0.249826 TCAATATCGAGCGCATGCCA 60.250 50.0 13.15 0.00 44.31 4.92 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
44 45 5.024133 CCATCAGGAAAAACCGATCGGTG 62.024 52.174 38.73 24.11 42.58 4.94
62 63 1.474077 GTGTATGAAGCTTTGCAGGGG 59.526 52.381 0.00 0.00 0.00 4.79
103 104 2.051345 GCACGCCAACAGAAACGG 60.051 61.111 0.00 0.00 0.00 4.44
161 165 4.179579 GGCGCCGGCATTGTCTTC 62.180 66.667 28.98 3.90 42.47 2.87
162 166 4.179579 GCGCCGGCATTGTCTTCC 62.180 66.667 28.98 0.00 39.62 3.46
182 186 0.745845 ATGCACAGACGCCTGATTCC 60.746 55.000 5.48 0.00 43.02 3.01
230 234 0.400213 TGTTCTCCACCAAATCGGCT 59.600 50.000 0.00 0.00 39.03 5.52
235 239 2.039216 TCTCCACCAAATCGGCTTACAA 59.961 45.455 0.00 0.00 39.03 2.41
246 250 1.464355 CGGCTTACAACGCGCAATTTA 60.464 47.619 5.73 0.00 0.00 1.40
265 269 0.546122 ACAGAGGGTCAACACAGCAA 59.454 50.000 0.00 0.00 0.00 3.91
278 282 4.170292 ACACAGCAATTTCAGAAGCATC 57.830 40.909 0.00 0.00 0.00 3.91
329 333 4.425772 TCAAGATGTTCCTCTGGTTCCTA 58.574 43.478 0.00 0.00 0.00 2.94
353 357 2.095059 CCAAGACAAGCTATGGTGCAAC 60.095 50.000 0.00 0.00 34.99 4.17
446 450 0.191064 TCCACCTCTTCTGGGAGTGT 59.809 55.000 0.00 0.00 0.00 3.55
455 459 2.630889 TCTGGGAGTGTCCAATCTCT 57.369 50.000 0.00 0.00 38.64 3.10
456 460 2.182827 TCTGGGAGTGTCCAATCTCTG 58.817 52.381 0.00 0.00 38.64 3.35
506 510 2.031097 GCTGATTGCCAGGCCCTAAAT 61.031 52.381 9.64 0.99 43.13 1.40
600 604 1.880340 CGAGAGGGCATCAAGTCGC 60.880 63.158 0.58 0.00 0.00 5.19
615 619 4.172512 CGCTGCTGGCCCTCATCT 62.173 66.667 0.00 0.00 37.74 2.90
669 673 3.214328 GTCTTCAGAGGAAAACAAGCCA 58.786 45.455 0.00 0.00 31.35 4.75
710 714 3.030168 ATGCCGCCGAGACATGGAA 62.030 57.895 0.00 0.00 0.00 3.53
787 794 2.094757 TATCGCCATAGCCACACCCG 62.095 60.000 0.00 0.00 34.57 5.28
822 840 1.608283 GCTCCCAGACACCTGTTGTAC 60.608 57.143 0.00 0.00 39.17 2.90
831 850 4.163458 AGACACCTGTTGTACTTTTCTCCA 59.837 41.667 0.00 0.00 39.17 3.86
842 861 5.872617 TGTACTTTTCTCCACATTCATACGG 59.127 40.000 0.00 0.00 0.00 4.02
858 877 3.814577 CGGTCACTTGATCGGAACT 57.185 52.632 3.87 0.00 44.34 3.01
1412 1441 2.676016 GATCTCGGCCTGCTCGTCTG 62.676 65.000 0.00 0.00 0.00 3.51
1627 1656 1.739562 GCTCACACAGCCTTCTCCG 60.740 63.158 0.00 0.00 43.17 4.63
1693 1722 2.514592 GCCGCAGCTCTAATGCCA 60.515 61.111 0.00 0.00 40.67 4.92
1733 1762 3.204119 CGGCAGCATCGGCAATGA 61.204 61.111 0.00 0.00 44.61 2.57
1833 1862 1.003355 TTACTGCAGGCAGAGTGGC 60.003 57.895 26.63 0.00 46.30 5.01
1838 1867 1.003355 GCAGGCAGAGTGGCAGTAA 60.003 57.895 0.00 0.00 46.46 2.24
1901 1930 2.429478 TGCTGATGTTGAGGACACATG 58.571 47.619 0.00 0.00 42.04 3.21
1905 1934 4.067192 CTGATGTTGAGGACACATGTGAA 58.933 43.478 31.94 12.63 42.04 3.18
1929 1958 2.207229 GGGTGTTGTTGGGAAGGGC 61.207 63.158 0.00 0.00 0.00 5.19
1935 1964 0.035439 TTGTTGGGAAGGGCGAGATC 60.035 55.000 0.00 0.00 0.00 2.75
2404 2485 7.831690 TGGTTAGTGTTTCAATTATATGGCTGA 59.168 33.333 0.00 0.00 0.00 4.26
2539 2620 6.079424 TCCTTGTTGTAAGTACAAATTGGC 57.921 37.500 5.49 0.00 46.54 4.52
2558 2639 2.162408 GGCTGTCTGCTAACCATGTTTC 59.838 50.000 1.44 0.00 42.39 2.78
2662 2743 5.343325 CACAATCAGTACGATCGTGATATGG 59.657 44.000 30.23 16.77 40.89 2.74
2773 2856 0.234106 CCGATGATCTTGATGCACGC 59.766 55.000 0.00 0.00 0.00 5.34
2774 2857 0.932399 CGATGATCTTGATGCACGCA 59.068 50.000 0.00 0.00 0.00 5.24
3058 3141 0.035915 GAGCCTCTCAAACCTGGACC 60.036 60.000 0.00 0.00 0.00 4.46
3060 3143 1.492993 GCCTCTCAAACCTGGACCCT 61.493 60.000 0.00 0.00 0.00 4.34
3087 3170 2.507339 GAGGATCGGAAAGCTCTCTG 57.493 55.000 0.00 0.00 0.00 3.35
3122 3205 2.224281 TGTCTGCTTGGTGACTACAAGG 60.224 50.000 7.22 0.00 44.16 3.61
3265 3348 2.159272 GAACAAGCACCGCGTCACTC 62.159 60.000 4.92 0.00 0.00 3.51
3276 3359 2.345641 CCGCGTCACTCTTATGTTTCAG 59.654 50.000 4.92 0.00 0.00 3.02
3302 3385 4.273480 AGTTTATACTGCTGCTTATTGCCG 59.727 41.667 0.00 0.00 35.27 5.69
3346 3429 1.721664 CGCCATCCTCGACCGAGTTA 61.722 60.000 16.86 6.46 40.44 2.24
3430 3528 7.565398 AGCTTAGAAGAATATACCAGACAAGGA 59.435 37.037 0.00 0.00 0.00 3.36
3484 3582 9.575783 TTTCAAATTTCGTTTGTAACTAAGCTT 57.424 25.926 3.48 3.48 45.87 3.74
3528 3626 4.012374 TCTGATGGTCCAAGATTTTCTGC 58.988 43.478 0.00 0.00 0.00 4.26
3569 3667 5.780984 TGCTATCATCAGCTAATCACTGAG 58.219 41.667 0.00 0.00 46.71 3.35
3570 3668 5.537674 TGCTATCATCAGCTAATCACTGAGA 59.462 40.000 0.00 0.00 46.71 3.27
3571 3669 6.041296 TGCTATCATCAGCTAATCACTGAGAA 59.959 38.462 0.00 0.00 46.71 2.87
3572 3670 6.365789 GCTATCATCAGCTAATCACTGAGAAC 59.634 42.308 0.00 0.00 46.71 3.01
3573 3671 5.016051 TCATCAGCTAATCACTGAGAACC 57.984 43.478 0.00 0.00 46.71 3.62
3574 3672 4.713814 TCATCAGCTAATCACTGAGAACCT 59.286 41.667 0.00 0.00 46.71 3.50
3575 3673 5.188555 TCATCAGCTAATCACTGAGAACCTT 59.811 40.000 0.00 0.00 46.71 3.50
3576 3674 5.078411 TCAGCTAATCACTGAGAACCTTC 57.922 43.478 0.00 0.00 39.21 3.46
3577 3675 4.774726 TCAGCTAATCACTGAGAACCTTCT 59.225 41.667 0.00 0.00 39.21 2.85
3578 3676 5.952347 TCAGCTAATCACTGAGAACCTTCTA 59.048 40.000 0.00 0.00 39.21 2.10
3579 3677 6.039616 CAGCTAATCACTGAGAACCTTCTAC 58.960 44.000 0.00 0.00 37.73 2.59
3580 3678 5.955355 AGCTAATCACTGAGAACCTTCTACT 59.045 40.000 0.00 0.00 37.73 2.57
3581 3679 6.096282 AGCTAATCACTGAGAACCTTCTACTC 59.904 42.308 0.00 0.00 37.73 2.59
3616 3867 7.504238 TGTGTACTGAGTTTTATTGGAAATGGT 59.496 33.333 0.00 0.00 0.00 3.55
3617 3868 8.357402 GTGTACTGAGTTTTATTGGAAATGGTT 58.643 33.333 0.00 0.00 0.00 3.67
3665 4334 9.862371 ACTCTGCTATGCTATGTTATATACAAC 57.138 33.333 0.00 0.00 40.89 3.32
3685 4354 7.737972 ACAACTAGTTAATGTGTACATGCAA 57.262 32.000 8.04 0.00 36.56 4.08
3686 4355 8.335532 ACAACTAGTTAATGTGTACATGCAAT 57.664 30.769 8.04 0.00 36.56 3.56
3704 4373 5.549347 TGCAATGCATGTTAATTTGGAAGT 58.451 33.333 2.72 0.00 31.71 3.01
3705 4374 6.695429 TGCAATGCATGTTAATTTGGAAGTA 58.305 32.000 2.72 0.00 31.71 2.24
3706 4375 7.329499 TGCAATGCATGTTAATTTGGAAGTAT 58.671 30.769 2.72 0.00 31.71 2.12
3707 4376 8.473219 TGCAATGCATGTTAATTTGGAAGTATA 58.527 29.630 2.72 0.00 31.71 1.47
3708 4377 9.480053 GCAATGCATGTTAATTTGGAAGTATAT 57.520 29.630 0.00 0.00 0.00 0.86
3721 4390 7.956420 TTGGAAGTATATTAAGTGCATACGG 57.044 36.000 0.00 0.00 31.76 4.02
3722 4391 7.292713 TGGAAGTATATTAAGTGCATACGGA 57.707 36.000 0.00 0.00 31.76 4.69
3723 4392 7.903145 TGGAAGTATATTAAGTGCATACGGAT 58.097 34.615 0.00 0.00 31.76 4.18
3724 4393 9.027202 TGGAAGTATATTAAGTGCATACGGATA 57.973 33.333 0.00 0.00 31.76 2.59
3733 4402 9.871238 ATTAAGTGCATACGGATATTAAGTAGG 57.129 33.333 0.00 0.00 0.00 3.18
3734 4403 7.534723 AAGTGCATACGGATATTAAGTAGGA 57.465 36.000 0.00 0.00 0.00 2.94
3735 4404 7.719871 AGTGCATACGGATATTAAGTAGGAT 57.280 36.000 0.00 0.00 0.00 3.24
3736 4405 8.818622 AGTGCATACGGATATTAAGTAGGATA 57.181 34.615 0.00 0.00 0.00 2.59
3737 4406 9.422681 AGTGCATACGGATATTAAGTAGGATAT 57.577 33.333 0.00 0.00 0.00 1.63
3765 4434 9.825972 ATTTGCGTGTTATTATATGATTAGCAC 57.174 29.630 0.00 0.00 0.00 4.40
3766 4435 8.601845 TTGCGTGTTATTATATGATTAGCACT 57.398 30.769 0.00 0.00 0.00 4.40
3767 4436 9.699703 TTGCGTGTTATTATATGATTAGCACTA 57.300 29.630 0.00 0.00 0.00 2.74
3768 4437 9.869757 TGCGTGTTATTATATGATTAGCACTAT 57.130 29.630 0.00 0.00 0.00 2.12
3779 4448 6.258230 TGATTAGCACTATATTTGGCATGC 57.742 37.500 9.90 9.90 0.00 4.06
3780 4449 4.747540 TTAGCACTATATTTGGCATGCG 57.252 40.909 12.44 0.00 38.12 4.73
3781 4450 1.267806 AGCACTATATTTGGCATGCGC 59.732 47.619 12.44 0.00 38.12 6.09
3782 4451 1.267806 GCACTATATTTGGCATGCGCT 59.732 47.619 12.44 0.00 38.60 5.92
3783 4452 2.666619 GCACTATATTTGGCATGCGCTC 60.667 50.000 12.44 0.00 38.60 5.03
3784 4453 1.800586 ACTATATTTGGCATGCGCTCG 59.199 47.619 12.44 0.00 38.60 5.03
3785 4454 2.068519 CTATATTTGGCATGCGCTCGA 58.931 47.619 12.44 0.00 38.60 4.04
3786 4455 1.527034 ATATTTGGCATGCGCTCGAT 58.473 45.000 12.44 3.94 38.60 3.59
3787 4456 2.162319 TATTTGGCATGCGCTCGATA 57.838 45.000 12.44 2.98 38.60 2.92
3788 4457 1.527034 ATTTGGCATGCGCTCGATAT 58.473 45.000 12.44 0.00 38.60 1.63
3789 4458 1.308047 TTTGGCATGCGCTCGATATT 58.692 45.000 12.44 0.00 38.60 1.28
3790 4459 0.587768 TTGGCATGCGCTCGATATTG 59.412 50.000 12.44 0.00 38.60 1.90
3791 4460 0.249826 TGGCATGCGCTCGATATTGA 60.250 50.000 12.44 0.00 38.60 2.57
3792 4461 0.867746 GGCATGCGCTCGATATTGAA 59.132 50.000 12.44 0.00 38.60 2.69
3793 4462 1.136141 GGCATGCGCTCGATATTGAAG 60.136 52.381 12.44 0.00 38.60 3.02
3794 4463 1.136141 GCATGCGCTCGATATTGAAGG 60.136 52.381 9.73 0.00 34.30 3.46
3795 4464 2.407090 CATGCGCTCGATATTGAAGGA 58.593 47.619 9.73 0.00 0.00 3.36
3796 4465 2.595124 TGCGCTCGATATTGAAGGAA 57.405 45.000 9.73 0.00 0.00 3.36
3797 4466 3.111853 TGCGCTCGATATTGAAGGAAT 57.888 42.857 9.73 0.00 0.00 3.01
3798 4467 3.059884 TGCGCTCGATATTGAAGGAATC 58.940 45.455 9.73 0.00 0.00 2.52
3799 4468 3.243873 TGCGCTCGATATTGAAGGAATCT 60.244 43.478 9.73 0.00 0.00 2.40
3800 4469 4.022329 TGCGCTCGATATTGAAGGAATCTA 60.022 41.667 9.73 0.00 0.00 1.98
3801 4470 4.560819 GCGCTCGATATTGAAGGAATCTAG 59.439 45.833 0.00 0.00 0.00 2.43
3802 4471 5.098893 CGCTCGATATTGAAGGAATCTAGG 58.901 45.833 0.00 0.00 0.00 3.02
3803 4472 5.336055 CGCTCGATATTGAAGGAATCTAGGT 60.336 44.000 0.00 0.00 0.00 3.08
3804 4473 6.096695 GCTCGATATTGAAGGAATCTAGGTC 58.903 44.000 0.00 0.00 0.00 3.85
3805 4474 6.255596 TCGATATTGAAGGAATCTAGGTCG 57.744 41.667 0.00 0.00 0.00 4.79
3806 4475 5.768662 TCGATATTGAAGGAATCTAGGTCGT 59.231 40.000 0.00 0.00 31.07 4.34
3807 4476 6.264744 TCGATATTGAAGGAATCTAGGTCGTT 59.735 38.462 0.00 0.00 31.07 3.85
3808 4477 7.446319 TCGATATTGAAGGAATCTAGGTCGTTA 59.554 37.037 0.00 0.00 31.07 3.18
3809 4478 7.751348 CGATATTGAAGGAATCTAGGTCGTTAG 59.249 40.741 0.00 0.00 0.00 2.34
3810 4479 8.707796 ATATTGAAGGAATCTAGGTCGTTAGA 57.292 34.615 0.00 0.00 34.38 2.10
3811 4480 7.604657 ATTGAAGGAATCTAGGTCGTTAGAT 57.395 36.000 0.00 2.49 41.09 1.98
3813 4482 6.806751 TGAAGGAATCTAGGTCGTTAGATTG 58.193 40.000 17.75 0.00 45.67 2.67
3814 4483 6.605995 TGAAGGAATCTAGGTCGTTAGATTGA 59.394 38.462 17.75 0.00 45.67 2.57
3815 4484 6.394025 AGGAATCTAGGTCGTTAGATTGAC 57.606 41.667 17.75 12.72 45.67 3.18
3816 4485 5.892119 AGGAATCTAGGTCGTTAGATTGACA 59.108 40.000 17.75 0.00 45.67 3.58
3817 4486 6.551601 AGGAATCTAGGTCGTTAGATTGACAT 59.448 38.462 17.75 6.06 45.67 3.06
3818 4487 6.642950 GGAATCTAGGTCGTTAGATTGACATG 59.357 42.308 17.75 0.00 45.67 3.21
3819 4488 6.961360 ATCTAGGTCGTTAGATTGACATGA 57.039 37.500 0.00 0.00 37.13 3.07
3820 4489 6.961360 TCTAGGTCGTTAGATTGACATGAT 57.039 37.500 0.00 0.00 36.83 2.45
3821 4490 7.348080 TCTAGGTCGTTAGATTGACATGATT 57.652 36.000 0.00 0.00 36.83 2.57
3822 4491 7.782049 TCTAGGTCGTTAGATTGACATGATTT 58.218 34.615 0.00 0.00 36.83 2.17
3823 4492 6.668541 AGGTCGTTAGATTGACATGATTTG 57.331 37.500 0.00 0.00 36.83 2.32
3824 4493 6.406370 AGGTCGTTAGATTGACATGATTTGA 58.594 36.000 0.00 0.00 36.83 2.69
3825 4494 7.050377 AGGTCGTTAGATTGACATGATTTGAT 58.950 34.615 0.00 0.00 36.83 2.57
3826 4495 7.011763 AGGTCGTTAGATTGACATGATTTGATG 59.988 37.037 0.00 0.00 36.83 3.07
3827 4496 7.128331 GTCGTTAGATTGACATGATTTGATGG 58.872 38.462 0.00 0.00 35.20 3.51
3828 4497 5.911280 CGTTAGATTGACATGATTTGATGGC 59.089 40.000 0.00 0.00 0.00 4.40
3829 4498 4.931661 AGATTGACATGATTTGATGGCC 57.068 40.909 0.00 0.00 29.16 5.36
3830 4499 3.317149 AGATTGACATGATTTGATGGCCG 59.683 43.478 0.00 0.00 29.16 6.13
3831 4500 2.416680 TGACATGATTTGATGGCCGA 57.583 45.000 0.00 0.00 29.16 5.54
3832 4501 2.291365 TGACATGATTTGATGGCCGAG 58.709 47.619 0.00 0.00 29.16 4.63
3833 4502 2.093021 TGACATGATTTGATGGCCGAGA 60.093 45.455 0.00 0.00 29.16 4.04
3834 4503 3.144506 GACATGATTTGATGGCCGAGAT 58.855 45.455 0.00 0.00 0.00 2.75
3835 4504 3.559069 ACATGATTTGATGGCCGAGATT 58.441 40.909 0.00 0.00 0.00 2.40
3836 4505 4.717877 ACATGATTTGATGGCCGAGATTA 58.282 39.130 0.00 0.00 0.00 1.75
3837 4506 5.132502 ACATGATTTGATGGCCGAGATTAA 58.867 37.500 0.00 0.00 0.00 1.40
3838 4507 5.771666 ACATGATTTGATGGCCGAGATTAAT 59.228 36.000 0.00 0.00 0.00 1.40
3839 4508 6.266103 ACATGATTTGATGGCCGAGATTAATT 59.734 34.615 0.00 0.00 0.00 1.40
3840 4509 6.075762 TGATTTGATGGCCGAGATTAATTG 57.924 37.500 0.00 0.00 0.00 2.32
3841 4510 5.827267 TGATTTGATGGCCGAGATTAATTGA 59.173 36.000 0.00 0.00 0.00 2.57
3842 4511 6.320926 TGATTTGATGGCCGAGATTAATTGAA 59.679 34.615 0.00 0.00 0.00 2.69
3843 4512 6.713762 TTTGATGGCCGAGATTAATTGAAT 57.286 33.333 0.00 0.00 0.00 2.57
3844 4513 5.947228 TGATGGCCGAGATTAATTGAATC 57.053 39.130 0.00 0.00 43.89 2.52
3855 4524 5.604565 GATTAATTGAATCTGCCCCTTTGG 58.395 41.667 0.00 0.00 40.84 3.28
3856 4525 5.453762 GATTAATTGAATCTGCCCCTTTGGG 60.454 44.000 0.00 0.00 46.29 4.12
3857 4526 7.821224 GATTAATTGAATCTGCCCCTTTGGGT 61.821 42.308 1.64 0.00 45.81 4.51
3858 4527 9.513780 GATTAATTGAATCTGCCCCTTTGGGTC 62.514 44.444 1.64 0.00 45.81 4.46
3944 4613 7.385478 GTGCTTTATCTAAACTAGGCAGGATAC 59.615 40.741 0.00 0.00 0.00 2.24
3993 4702 4.290093 TGGCCTCTACAGTAGAATGATGT 58.710 43.478 11.57 0.00 33.75 3.06
4052 4765 7.507829 AGTCTATGATTCAGAAGCTTGCTTAT 58.492 34.615 2.10 1.95 0.00 1.73
4122 4845 6.980416 ATAGGACTAGATGACTAAACACCC 57.020 41.667 0.00 0.00 0.00 4.61
4127 4850 6.550108 GGACTAGATGACTAAACACCCATCTA 59.450 42.308 0.00 0.00 42.57 1.98
4128 4851 7.233757 GGACTAGATGACTAAACACCCATCTAT 59.766 40.741 0.00 0.00 43.49 1.98
4129 4852 8.554490 ACTAGATGACTAAACACCCATCTATT 57.446 34.615 0.00 0.00 43.49 1.73
4130 4853 8.643324 ACTAGATGACTAAACACCCATCTATTC 58.357 37.037 0.00 0.00 43.49 1.75
4195 4918 5.602978 AGTTACCATCTTTCATCGGGTAGAT 59.397 40.000 0.00 0.00 41.01 1.98
4212 4935 5.130643 GGGTAGATCTAGTAACCAAAGGCTT 59.869 44.000 13.25 0.00 33.46 4.35
4217 4940 5.562298 TCTAGTAACCAAAGGCTTTCTGT 57.438 39.130 10.08 7.66 0.00 3.41
4224 4947 3.160269 CCAAAGGCTTTCTGTCTTCCAT 58.840 45.455 10.08 0.00 40.13 3.41
4238 4961 6.719829 TCTGTCTTCCATAAGAGTGAGTAACA 59.280 38.462 0.00 0.00 42.40 2.41
4252 4975 4.445385 GTGAGTAACAACCACGTACGAATT 59.555 41.667 24.41 9.83 0.00 2.17
4253 4976 5.049167 TGAGTAACAACCACGTACGAATTT 58.951 37.500 24.41 8.19 0.00 1.82
4284 5007 3.633986 GCCCTGTAGATAAGCTGCAAAAT 59.366 43.478 1.02 0.00 38.80 1.82
4421 5145 1.076332 AGCCACGTCTCAAATAACGC 58.924 50.000 0.00 0.00 42.47 4.84
4548 5273 4.278170 TGATCACAAAAGCTACACCTTTGG 59.722 41.667 11.46 2.69 35.36 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.106285 CCCCCTGCAAAGCTTCATAC 58.894 55.000 0.00 0.00 0.00 2.39
45 46 0.998928 TCCCCCTGCAAAGCTTCATA 59.001 50.000 0.00 0.00 0.00 2.15
50 51 4.351054 CGGTCCCCCTGCAAAGCT 62.351 66.667 0.00 0.00 0.00 3.74
103 104 0.582005 GATTACTTGGCCGACGATGC 59.418 55.000 0.00 0.00 0.00 3.91
111 115 1.440145 GCGAGCTGGATTACTTGGCC 61.440 60.000 0.00 0.00 0.00 5.36
144 148 4.179579 GAAGACAATGCCGGCGCC 62.180 66.667 23.90 19.07 0.00 6.53
161 165 1.028330 AATCAGGCGTCTGTGCATGG 61.028 55.000 18.04 0.00 46.02 3.66
197 201 2.616510 GGAGAACATTCCTGAGGTGTGG 60.617 54.545 0.00 0.00 34.27 4.17
230 234 3.120477 CCTCTGTAAATTGCGCGTTGTAA 60.120 43.478 8.43 0.00 0.00 2.41
235 239 0.321298 ACCCTCTGTAAATTGCGCGT 60.321 50.000 8.43 0.00 0.00 6.01
246 250 0.546122 TTGCTGTGTTGACCCTCTGT 59.454 50.000 0.00 0.00 0.00 3.41
265 269 6.845758 TCTTCCAAATGATGCTTCTGAAAT 57.154 33.333 0.88 0.00 0.00 2.17
278 282 1.643880 GCGCCCAAATCTTCCAAATG 58.356 50.000 0.00 0.00 0.00 2.32
353 357 2.671177 CCTTCGTTGCAGCCTGTCG 61.671 63.158 0.00 0.00 0.00 4.35
446 450 3.394274 TCCAAACCTTCACAGAGATTGGA 59.606 43.478 0.00 0.00 38.73 3.53
474 478 3.650298 AATCAGCCCATGCCGCAGT 62.650 57.895 0.00 0.00 38.69 4.40
490 494 0.936691 AGGATTTAGGGCCTGGCAAT 59.063 50.000 22.05 11.35 32.06 3.56
545 549 1.490693 CGGTGATGATCCTTTCGGCG 61.491 60.000 0.00 0.00 0.00 6.46
584 588 1.220206 CAGCGACTTGATGCCCTCT 59.780 57.895 0.00 0.00 0.00 3.69
600 604 1.030488 CACAAGATGAGGGCCAGCAG 61.030 60.000 6.18 0.00 32.59 4.24
615 619 2.040947 TCTCCAACCATATGTGCCACAA 59.959 45.455 0.00 0.00 0.00 3.33
669 673 2.167219 CGATGATGTGGCGCTCGTT 61.167 57.895 7.64 0.00 0.00 3.85
701 705 0.322816 AGCGCCATTGTTCCATGTCT 60.323 50.000 2.29 0.00 0.00 3.41
710 714 3.376078 CCTGCCAAGCGCCATTGT 61.376 61.111 2.29 0.00 36.24 2.71
810 828 4.196971 GTGGAGAAAAGTACAACAGGTGT 58.803 43.478 0.00 0.00 44.82 4.16
822 840 4.935205 TGACCGTATGAATGTGGAGAAAAG 59.065 41.667 0.00 0.00 0.00 2.27
831 850 4.112634 CGATCAAGTGACCGTATGAATGT 58.887 43.478 0.00 0.00 0.00 2.71
842 861 4.082679 ACAGAGTAGTTCCGATCAAGTGAC 60.083 45.833 0.00 0.00 0.00 3.67
858 877 1.740585 GCAGAAGAGAGCGACAGAGTA 59.259 52.381 0.00 0.00 0.00 2.59
1552 1581 0.546747 TTCTTCCCGTGGATGGAGGT 60.547 55.000 6.15 0.00 32.37 3.85
1693 1722 2.046314 CTGTTTCCGGCCGTGGAT 60.046 61.111 26.12 0.00 38.00 3.41
1733 1762 4.437682 TCAGAAAGTTCCTTGTGGATGT 57.562 40.909 0.00 0.00 42.81 3.06
1823 1852 1.089920 CACATTACTGCCACTCTGCC 58.910 55.000 0.00 0.00 0.00 4.85
1833 1862 4.322650 CCCAATTTTCCCACCACATTACTG 60.323 45.833 0.00 0.00 0.00 2.74
1838 1867 1.977129 CACCCAATTTTCCCACCACAT 59.023 47.619 0.00 0.00 0.00 3.21
1919 1948 2.731571 CCGATCTCGCCCTTCCCAA 61.732 63.158 0.00 0.00 38.18 4.12
1920 1949 2.946988 ATCCGATCTCGCCCTTCCCA 62.947 60.000 0.00 0.00 38.18 4.37
1921 1950 1.759459 AATCCGATCTCGCCCTTCCC 61.759 60.000 0.00 0.00 38.18 3.97
1929 1958 5.180304 TGAGTTCATCTCTAATCCGATCTCG 59.820 44.000 0.00 0.00 43.13 4.04
1935 1964 4.447054 GCACATGAGTTCATCTCTAATCCG 59.553 45.833 0.00 0.00 43.13 4.18
1959 1988 7.001674 ACAAAATAGATTCCGCATATGGGTTA 58.998 34.615 17.56 6.32 0.00 2.85
2092 2121 4.799419 ACAAATGCATCAACAAAAGCAC 57.201 36.364 0.00 0.00 40.14 4.40
2184 2213 7.807977 ACAATATCAAGATAACCGAGCAATT 57.192 32.000 0.00 0.00 0.00 2.32
2189 2218 9.599322 GCAAATAACAATATCAAGATAACCGAG 57.401 33.333 0.00 0.00 0.00 4.63
2404 2485 8.730680 GGTCATGTCAAACATAATCAACTACTT 58.269 33.333 0.00 0.00 36.53 2.24
2539 2620 3.325870 TCGAAACATGGTTAGCAGACAG 58.674 45.455 0.00 0.00 0.00 3.51
2662 2743 7.442666 TGAAAACCAAGGCATAAAATGGTAAAC 59.557 33.333 0.00 0.00 45.15 2.01
2752 2835 1.259770 CGTGCATCAAGATCATCGGTG 59.740 52.381 0.00 0.00 0.00 4.94
2773 2856 3.791122 GCGAGTTGCTCCATTCATCATTG 60.791 47.826 0.00 0.00 41.73 2.82
2774 2857 2.357009 GCGAGTTGCTCCATTCATCATT 59.643 45.455 0.00 0.00 41.73 2.57
2870 2953 3.557228 ATCCTTCTCCTTGATCAGTGC 57.443 47.619 0.00 0.00 0.00 4.40
2871 2954 5.095145 TGAATCCTTCTCCTTGATCAGTG 57.905 43.478 0.00 0.00 0.00 3.66
2932 3015 4.008330 CACTCTGAATTGCACTTCTCCAT 58.992 43.478 16.65 0.00 0.00 3.41
2981 3064 2.027745 TCTCCTGGAGCAGTTGATCAAC 60.028 50.000 27.69 27.69 41.45 3.18
3087 3170 1.005340 CAGACATTTCTGCTCCTCGC 58.995 55.000 0.00 0.00 42.99 5.03
3112 3195 2.488545 GAGTTCGAGCTCCTTGTAGTCA 59.511 50.000 17.67 0.00 0.00 3.41
3122 3205 0.436531 CGCAGTTTGAGTTCGAGCTC 59.563 55.000 21.09 21.09 36.12 4.09
3241 3324 0.666577 ACGCGGTGCTTGTTCTAGAC 60.667 55.000 12.47 0.00 0.00 2.59
3302 3385 2.673368 GGCGCATAACATAGATGCCTAC 59.327 50.000 10.83 0.00 45.69 3.18
3322 3405 2.725008 GTCGAGGATGGCGAGAGG 59.275 66.667 0.00 0.00 38.59 3.69
3346 3429 4.587891 ACTTCTAAGCTCACGTAGGTACT 58.412 43.478 0.00 0.00 46.37 2.73
3430 3528 3.005791 GCTGGCAAGTTTACACAAGGATT 59.994 43.478 0.00 0.00 0.00 3.01
3484 3582 5.548056 AGATACAGGAACCAGAAAGAAAGGA 59.452 40.000 0.00 0.00 0.00 3.36
3528 3626 3.786635 AGCAGCTCTTATTCCACTTACG 58.213 45.455 0.00 0.00 0.00 3.18
3569 3667 5.050295 CACAAACTTTCCGAGTAGAAGGTTC 60.050 44.000 2.79 0.00 43.02 3.62
3570 3668 4.814771 CACAAACTTTCCGAGTAGAAGGTT 59.185 41.667 0.00 0.00 44.96 3.50
3571 3669 4.141779 ACACAAACTTTCCGAGTAGAAGGT 60.142 41.667 0.00 0.00 37.72 3.50
3572 3670 4.377897 ACACAAACTTTCCGAGTAGAAGG 58.622 43.478 0.00 0.00 37.72 3.46
3573 3671 6.144080 CAGTACACAAACTTTCCGAGTAGAAG 59.856 42.308 0.00 0.00 37.72 2.85
3574 3672 5.981315 CAGTACACAAACTTTCCGAGTAGAA 59.019 40.000 0.00 0.00 37.72 2.10
3575 3673 5.300034 TCAGTACACAAACTTTCCGAGTAGA 59.700 40.000 0.00 0.00 37.72 2.59
3576 3674 5.526115 TCAGTACACAAACTTTCCGAGTAG 58.474 41.667 0.00 0.00 37.72 2.57
3577 3675 5.068198 ACTCAGTACACAAACTTTCCGAGTA 59.932 40.000 0.00 0.00 37.72 2.59
3578 3676 4.142004 ACTCAGTACACAAACTTTCCGAGT 60.142 41.667 0.00 0.00 41.47 4.18
3579 3677 4.369182 ACTCAGTACACAAACTTTCCGAG 58.631 43.478 0.00 0.00 0.00 4.63
3580 3678 4.395959 ACTCAGTACACAAACTTTCCGA 57.604 40.909 0.00 0.00 0.00 4.55
3581 3679 5.479716 AAACTCAGTACACAAACTTTCCG 57.520 39.130 0.00 0.00 0.00 4.30
3616 3867 9.255304 GAGTTTTAGCCAATTGTCAAACATTAA 57.745 29.630 4.43 0.00 0.00 1.40
3617 3868 8.637986 AGAGTTTTAGCCAATTGTCAAACATTA 58.362 29.630 4.43 0.00 0.00 1.90
3626 3877 5.393461 GCATAGCAGAGTTTTAGCCAATTGT 60.393 40.000 4.43 0.00 0.00 2.71
3665 4334 6.784176 TGCATTGCATGTACACATTAACTAG 58.216 36.000 7.38 0.00 33.61 2.57
3666 4335 6.749923 TGCATTGCATGTACACATTAACTA 57.250 33.333 7.38 0.00 33.61 2.24
3667 4336 5.641783 TGCATTGCATGTACACATTAACT 57.358 34.783 7.38 0.00 33.61 2.24
3681 4350 5.549347 ACTTCCAAATTAACATGCATTGCA 58.451 33.333 14.72 14.72 44.86 4.08
3682 4351 7.775397 ATACTTCCAAATTAACATGCATTGC 57.225 32.000 0.00 0.46 0.00 3.56
3695 4364 8.999431 CCGTATGCACTTAATATACTTCCAAAT 58.001 33.333 0.00 0.00 0.00 2.32
3696 4365 8.205512 TCCGTATGCACTTAATATACTTCCAAA 58.794 33.333 0.00 0.00 0.00 3.28
3697 4366 7.728148 TCCGTATGCACTTAATATACTTCCAA 58.272 34.615 0.00 0.00 0.00 3.53
3698 4367 7.292713 TCCGTATGCACTTAATATACTTCCA 57.707 36.000 0.00 0.00 0.00 3.53
3707 4376 9.871238 CCTACTTAATATCCGTATGCACTTAAT 57.129 33.333 0.00 0.00 0.00 1.40
3708 4377 9.081204 TCCTACTTAATATCCGTATGCACTTAA 57.919 33.333 0.00 0.00 0.00 1.85
3709 4378 8.640063 TCCTACTTAATATCCGTATGCACTTA 57.360 34.615 0.00 0.00 0.00 2.24
3710 4379 7.534723 TCCTACTTAATATCCGTATGCACTT 57.465 36.000 0.00 0.00 0.00 3.16
3711 4380 7.719871 ATCCTACTTAATATCCGTATGCACT 57.280 36.000 0.00 0.00 0.00 4.40
3739 4408 9.825972 GTGCTAATCATATAATAACACGCAAAT 57.174 29.630 0.00 0.00 0.00 2.32
3740 4409 9.051679 AGTGCTAATCATATAATAACACGCAAA 57.948 29.630 0.00 0.00 0.00 3.68
3741 4410 8.601845 AGTGCTAATCATATAATAACACGCAA 57.398 30.769 0.00 0.00 0.00 4.85
3742 4411 9.869757 ATAGTGCTAATCATATAATAACACGCA 57.130 29.630 0.00 0.00 0.00 5.24
3753 4422 8.627403 GCATGCCAAATATAGTGCTAATCATAT 58.373 33.333 6.36 0.00 0.00 1.78
3754 4423 7.201635 CGCATGCCAAATATAGTGCTAATCATA 60.202 37.037 13.15 0.00 0.00 2.15
3755 4424 6.403964 CGCATGCCAAATATAGTGCTAATCAT 60.404 38.462 13.15 0.00 0.00 2.45
3756 4425 5.106594 CGCATGCCAAATATAGTGCTAATCA 60.107 40.000 13.15 0.00 0.00 2.57
3757 4426 5.327091 CGCATGCCAAATATAGTGCTAATC 58.673 41.667 13.15 0.00 0.00 1.75
3758 4427 4.379813 GCGCATGCCAAATATAGTGCTAAT 60.380 41.667 13.15 0.00 33.98 1.73
3759 4428 3.058293 GCGCATGCCAAATATAGTGCTAA 60.058 43.478 13.15 0.00 33.98 3.09
3760 4429 2.483877 GCGCATGCCAAATATAGTGCTA 59.516 45.455 13.15 0.00 33.98 3.49
3761 4430 1.267806 GCGCATGCCAAATATAGTGCT 59.732 47.619 13.15 0.00 33.98 4.40
3762 4431 1.267806 AGCGCATGCCAAATATAGTGC 59.732 47.619 13.15 5.40 44.31 4.40
3763 4432 2.411935 CGAGCGCATGCCAAATATAGTG 60.412 50.000 13.15 0.00 44.31 2.74
3764 4433 1.800586 CGAGCGCATGCCAAATATAGT 59.199 47.619 13.15 0.00 44.31 2.12
3765 4434 2.068519 TCGAGCGCATGCCAAATATAG 58.931 47.619 13.15 0.00 44.31 1.31
3766 4435 2.162319 TCGAGCGCATGCCAAATATA 57.838 45.000 13.15 0.00 44.31 0.86
3767 4436 1.527034 ATCGAGCGCATGCCAAATAT 58.473 45.000 13.15 0.00 44.31 1.28
3768 4437 2.162319 TATCGAGCGCATGCCAAATA 57.838 45.000 13.15 0.70 44.31 1.40
3769 4438 1.527034 ATATCGAGCGCATGCCAAAT 58.473 45.000 13.15 1.68 44.31 2.32
3770 4439 1.002576 CAATATCGAGCGCATGCCAAA 60.003 47.619 13.15 0.00 44.31 3.28
3771 4440 0.587768 CAATATCGAGCGCATGCCAA 59.412 50.000 13.15 0.00 44.31 4.52
3772 4441 0.249826 TCAATATCGAGCGCATGCCA 60.250 50.000 13.15 0.00 44.31 4.92
3773 4442 0.867746 TTCAATATCGAGCGCATGCC 59.132 50.000 13.15 4.99 44.31 4.40
3774 4443 1.136141 CCTTCAATATCGAGCGCATGC 60.136 52.381 11.47 7.91 43.24 4.06
3775 4444 2.407090 TCCTTCAATATCGAGCGCATG 58.593 47.619 11.47 0.07 0.00 4.06
3776 4445 2.820059 TCCTTCAATATCGAGCGCAT 57.180 45.000 11.47 0.00 0.00 4.73
3777 4446 2.595124 TTCCTTCAATATCGAGCGCA 57.405 45.000 11.47 0.00 0.00 6.09
3778 4447 3.321497 AGATTCCTTCAATATCGAGCGC 58.679 45.455 0.00 0.00 0.00 5.92
3779 4448 5.098893 CCTAGATTCCTTCAATATCGAGCG 58.901 45.833 0.00 0.00 0.00 5.03
3780 4449 6.031751 ACCTAGATTCCTTCAATATCGAGC 57.968 41.667 0.00 0.00 0.00 5.03
3781 4450 6.072397 ACGACCTAGATTCCTTCAATATCGAG 60.072 42.308 0.00 0.00 0.00 4.04
3782 4451 5.768662 ACGACCTAGATTCCTTCAATATCGA 59.231 40.000 0.00 0.00 0.00 3.59
3783 4452 6.015027 ACGACCTAGATTCCTTCAATATCG 57.985 41.667 0.00 0.00 0.00 2.92
3784 4453 8.794553 TCTAACGACCTAGATTCCTTCAATATC 58.205 37.037 0.00 0.00 0.00 1.63
3785 4454 8.707796 TCTAACGACCTAGATTCCTTCAATAT 57.292 34.615 0.00 0.00 0.00 1.28
3786 4455 8.707796 ATCTAACGACCTAGATTCCTTCAATA 57.292 34.615 0.00 0.00 35.50 1.90
3787 4456 7.604657 ATCTAACGACCTAGATTCCTTCAAT 57.395 36.000 0.00 0.00 35.50 2.57
3788 4457 7.123697 TCAATCTAACGACCTAGATTCCTTCAA 59.876 37.037 12.89 0.00 43.62 2.69
3789 4458 6.605995 TCAATCTAACGACCTAGATTCCTTCA 59.394 38.462 12.89 0.00 43.62 3.02
3790 4459 6.919115 GTCAATCTAACGACCTAGATTCCTTC 59.081 42.308 12.89 4.91 43.62 3.46
3791 4460 6.380274 TGTCAATCTAACGACCTAGATTCCTT 59.620 38.462 12.89 0.00 43.62 3.36
3792 4461 5.892119 TGTCAATCTAACGACCTAGATTCCT 59.108 40.000 12.89 0.00 43.62 3.36
3793 4462 6.145338 TGTCAATCTAACGACCTAGATTCC 57.855 41.667 12.89 9.23 43.62 3.01
3794 4463 7.426410 TCATGTCAATCTAACGACCTAGATTC 58.574 38.462 12.89 7.05 43.62 2.52
3795 4464 7.348080 TCATGTCAATCTAACGACCTAGATT 57.652 36.000 11.06 11.06 45.43 2.40
3796 4465 6.961360 TCATGTCAATCTAACGACCTAGAT 57.039 37.500 0.00 0.00 39.79 1.98
3797 4466 6.961360 ATCATGTCAATCTAACGACCTAGA 57.039 37.500 0.00 0.00 32.53 2.43
3798 4467 7.706607 TCAAATCATGTCAATCTAACGACCTAG 59.293 37.037 0.00 0.00 0.00 3.02
3799 4468 7.552459 TCAAATCATGTCAATCTAACGACCTA 58.448 34.615 0.00 0.00 0.00 3.08
3800 4469 6.406370 TCAAATCATGTCAATCTAACGACCT 58.594 36.000 0.00 0.00 0.00 3.85
3801 4470 6.662414 TCAAATCATGTCAATCTAACGACC 57.338 37.500 0.00 0.00 0.00 4.79
3802 4471 7.128331 CCATCAAATCATGTCAATCTAACGAC 58.872 38.462 0.00 0.00 0.00 4.34
3803 4472 6.238456 GCCATCAAATCATGTCAATCTAACGA 60.238 38.462 0.00 0.00 0.00 3.85
3804 4473 5.911280 GCCATCAAATCATGTCAATCTAACG 59.089 40.000 0.00 0.00 0.00 3.18
3805 4474 6.211515 GGCCATCAAATCATGTCAATCTAAC 58.788 40.000 0.00 0.00 0.00 2.34
3806 4475 5.008911 CGGCCATCAAATCATGTCAATCTAA 59.991 40.000 2.24 0.00 0.00 2.10
3807 4476 4.516321 CGGCCATCAAATCATGTCAATCTA 59.484 41.667 2.24 0.00 0.00 1.98
3808 4477 3.317149 CGGCCATCAAATCATGTCAATCT 59.683 43.478 2.24 0.00 0.00 2.40
3809 4478 3.316029 TCGGCCATCAAATCATGTCAATC 59.684 43.478 2.24 0.00 0.00 2.67
3810 4479 3.289836 TCGGCCATCAAATCATGTCAAT 58.710 40.909 2.24 0.00 0.00 2.57
3811 4480 2.684374 CTCGGCCATCAAATCATGTCAA 59.316 45.455 2.24 0.00 0.00 3.18
3812 4481 2.093021 TCTCGGCCATCAAATCATGTCA 60.093 45.455 2.24 0.00 0.00 3.58
3813 4482 2.564771 TCTCGGCCATCAAATCATGTC 58.435 47.619 2.24 0.00 0.00 3.06
3814 4483 2.715749 TCTCGGCCATCAAATCATGT 57.284 45.000 2.24 0.00 0.00 3.21
3815 4484 5.694231 TTAATCTCGGCCATCAAATCATG 57.306 39.130 2.24 0.00 0.00 3.07
3816 4485 6.491062 TCAATTAATCTCGGCCATCAAATCAT 59.509 34.615 2.24 0.00 0.00 2.45
3817 4486 5.827267 TCAATTAATCTCGGCCATCAAATCA 59.173 36.000 2.24 0.00 0.00 2.57
3818 4487 6.317789 TCAATTAATCTCGGCCATCAAATC 57.682 37.500 2.24 0.00 0.00 2.17
3819 4488 6.713762 TTCAATTAATCTCGGCCATCAAAT 57.286 33.333 2.24 0.00 0.00 2.32
3820 4489 6.713762 ATTCAATTAATCTCGGCCATCAAA 57.286 33.333 2.24 0.00 0.00 2.69
3821 4490 6.317789 GATTCAATTAATCTCGGCCATCAA 57.682 37.500 2.24 0.00 40.82 2.57
3822 4491 5.947228 GATTCAATTAATCTCGGCCATCA 57.053 39.130 2.24 0.00 40.82 3.07
3832 4501 5.604565 CCAAAGGGGCAGATTCAATTAATC 58.395 41.667 0.00 0.00 43.81 1.75
3833 4502 5.619132 CCAAAGGGGCAGATTCAATTAAT 57.381 39.130 0.00 0.00 0.00 1.40
3874 4543 9.324008 CAGCCCCATCATCTATATCTATAATCT 57.676 37.037 0.00 0.00 0.00 2.40
3875 4544 8.040132 GCAGCCCCATCATCTATATCTATAATC 58.960 40.741 0.00 0.00 0.00 1.75
3876 4545 7.310299 CGCAGCCCCATCATCTATATCTATAAT 60.310 40.741 0.00 0.00 0.00 1.28
3877 4546 6.015095 CGCAGCCCCATCATCTATATCTATAA 60.015 42.308 0.00 0.00 0.00 0.98
3878 4547 5.478332 CGCAGCCCCATCATCTATATCTATA 59.522 44.000 0.00 0.00 0.00 1.31
3879 4548 4.282957 CGCAGCCCCATCATCTATATCTAT 59.717 45.833 0.00 0.00 0.00 1.98
3880 4549 3.638627 CGCAGCCCCATCATCTATATCTA 59.361 47.826 0.00 0.00 0.00 1.98
3881 4550 2.433604 CGCAGCCCCATCATCTATATCT 59.566 50.000 0.00 0.00 0.00 1.98
3882 4551 2.169352 ACGCAGCCCCATCATCTATATC 59.831 50.000 0.00 0.00 0.00 1.63
3883 4552 2.169352 GACGCAGCCCCATCATCTATAT 59.831 50.000 0.00 0.00 0.00 0.86
3884 4553 1.550524 GACGCAGCCCCATCATCTATA 59.449 52.381 0.00 0.00 0.00 1.31
3885 4554 0.322975 GACGCAGCCCCATCATCTAT 59.677 55.000 0.00 0.00 0.00 1.98
3886 4555 0.760567 AGACGCAGCCCCATCATCTA 60.761 55.000 0.00 0.00 0.00 1.98
3887 4556 2.068821 AGACGCAGCCCCATCATCT 61.069 57.895 0.00 0.00 0.00 2.90
3888 4557 1.890979 CAGACGCAGCCCCATCATC 60.891 63.158 0.00 0.00 0.00 2.92
3889 4558 2.191375 CAGACGCAGCCCCATCAT 59.809 61.111 0.00 0.00 0.00 2.45
3894 4563 2.044806 ATCATACCAGACGCAGCCCC 62.045 60.000 0.00 0.00 0.00 5.80
3898 4567 0.385751 ACCGATCATACCAGACGCAG 59.614 55.000 0.00 0.00 0.00 5.18
3954 4624 3.593780 AGGCCAGTAATCCTCTTTTTCCT 59.406 43.478 5.01 0.00 0.00 3.36
3955 4625 3.948473 GAGGCCAGTAATCCTCTTTTTCC 59.052 47.826 5.01 0.00 44.19 3.13
3971 4641 4.290093 ACATCATTCTACTGTAGAGGCCA 58.710 43.478 16.36 3.78 35.96 5.36
3979 4688 6.615726 AGGGGTTGTATACATCATTCTACTGT 59.384 38.462 6.36 0.00 0.00 3.55
4086 4807 1.544246 AGTCCTATTTTTGCCGGTTGC 59.456 47.619 1.90 0.00 41.77 4.17
4195 4918 5.307196 AGACAGAAAGCCTTTGGTTACTAGA 59.693 40.000 0.00 0.00 0.00 2.43
4212 4935 7.232737 TGTTACTCACTCTTATGGAAGACAGAA 59.767 37.037 0.00 0.00 36.75 3.02
4217 4940 6.269077 TGGTTGTTACTCACTCTTATGGAAGA 59.731 38.462 0.00 0.00 39.47 2.87
4224 4947 4.924305 ACGTGGTTGTTACTCACTCTTA 57.076 40.909 0.00 0.00 0.00 2.10
4238 4961 4.060205 ACTGCTTAAATTCGTACGTGGTT 58.940 39.130 16.05 9.82 0.00 3.67
4320 5043 8.871629 TTTGGGCTATATGAAACTGTAGAAAA 57.128 30.769 0.00 0.00 0.00 2.29
4396 5119 5.062934 CGTTATTTGAGACGTGGCTAAATGA 59.937 40.000 0.00 0.00 34.75 2.57
4421 5145 5.424757 TCACCCCTTCAAATAGTATTCACG 58.575 41.667 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.