Multiple sequence alignment - TraesCS4A01G097900

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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 TraesCS4A01G097900 chr4A 100.000 5102 0 0 1 5102 109422673 109427774 0.000000e+00 9422.0
1 TraesCS4A01G097900 chr4A 86.023 1760 234 9 1395 3145 110638837 110637081 0.000000e+00 1877.0
2 TraesCS4A01G097900 chr4A 95.473 243 9 2 3288 3530 99024490 99024250 2.230000e-103 387.0
3 TraesCS4A01G097900 chr4A 83.659 410 28 22 4267 4653 591849053 591849446 2.920000e-92 350.0
4 TraesCS4A01G097900 chr4A 88.830 188 11 7 3953 4131 591848664 591848850 6.650000e-54 222.0
5 TraesCS4A01G097900 chr4B 97.365 2695 55 5 605 3289 439322837 439320149 0.000000e+00 4569.0
6 TraesCS4A01G097900 chr4B 87.130 1655 209 4 1396 3048 437949441 437951093 0.000000e+00 1873.0
7 TraesCS4A01G097900 chr4B 93.407 819 32 11 3870 4677 439319296 439318489 0.000000e+00 1194.0
8 TraesCS4A01G097900 chr4B 91.105 371 15 8 3518 3872 439319711 439319343 2.140000e-133 486.0
9 TraesCS4A01G097900 chr4B 91.036 357 15 9 3518 3858 439320150 439319795 2.780000e-127 466.0
10 TraesCS4A01G097900 chr4B 84.314 459 31 17 4267 4698 20720059 20720503 1.320000e-110 411.0
11 TraesCS4A01G097900 chr4B 94.262 244 12 1 4861 5102 439317133 439317376 6.240000e-99 372.0
12 TraesCS4A01G097900 chr4B 94.581 203 10 1 1084 1285 437949114 437949316 3.840000e-81 313.0
13 TraesCS4A01G097900 chr4B 87.895 190 11 8 3953 4131 20719628 20719816 4.000000e-51 213.0
14 TraesCS4A01G097900 chr4B 92.667 150 8 3 4694 4842 439317600 439317453 4.000000e-51 213.0
15 TraesCS4A01G097900 chr4B 96.341 82 3 0 3208 3289 439319791 439319710 8.910000e-28 135.0
16 TraesCS4A01G097900 chr4D 96.784 2705 63 10 605 3289 355861035 355858335 0.000000e+00 4492.0
17 TraesCS4A01G097900 chr4D 87.311 1655 208 2 1395 3048 354136403 354138056 0.000000e+00 1892.0
18 TraesCS4A01G097900 chr4D 91.379 638 28 6 4207 4843 355855892 355855281 0.000000e+00 848.0
19 TraesCS4A01G097900 chr4D 90.785 586 49 5 2 584 41721822 41722405 0.000000e+00 778.0
20 TraesCS4A01G097900 chr4D 90.614 586 47 8 1 582 381095975 381095394 0.000000e+00 771.0
21 TraesCS4A01G097900 chr4D 92.798 361 15 5 3518 3873 355858342 355857988 3.520000e-141 512.0
22 TraesCS4A01G097900 chr4D 92.033 364 11 9 3868 4218 355857915 355857557 3.550000e-136 496.0
23 TraesCS4A01G097900 chr4D 83.921 454 33 16 4271 4698 10970965 10971404 1.030000e-106 398.0
24 TraesCS4A01G097900 chr4D 93.333 255 14 3 4851 5102 355854950 355855204 1.730000e-99 374.0
25 TraesCS4A01G097900 chr4D 85.375 253 31 6 4853 5102 500053895 500054144 1.820000e-64 257.0
26 TraesCS4A01G097900 chr4D 93.220 59 4 0 4778 4836 10971586 10971644 2.530000e-13 87.9
27 TraesCS4A01G097900 chr3D 87.155 1666 210 4 1394 3057 462851023 462852686 0.000000e+00 1888.0
28 TraesCS4A01G097900 chr3D 86.729 1703 216 6 1394 3091 463191627 463189930 0.000000e+00 1884.0
29 TraesCS4A01G097900 chr3D 90.492 589 51 3 1 584 522088083 522087495 0.000000e+00 773.0
30 TraesCS4A01G097900 chr3D 96.250 240 8 1 3288 3527 83889610 83889372 4.790000e-105 392.0
31 TraesCS4A01G097900 chr3D 96.186 236 9 0 3288 3523 83888682 83888447 2.230000e-103 387.0
32 TraesCS4A01G097900 chr3A 86.098 1748 225 12 1396 3141 606436003 606434272 0.000000e+00 1866.0
33 TraesCS4A01G097900 chr3B 86.839 1664 214 5 1396 3057 616310978 616309318 0.000000e+00 1855.0
34 TraesCS4A01G097900 chr3B 85.433 254 27 5 4851 5102 382709058 382709303 6.560000e-64 255.0
35 TraesCS4A01G097900 chr3B 86.316 190 26 0 4913 5102 441483890 441483701 1.860000e-49 207.0
36 TraesCS4A01G097900 chr3B 97.059 34 1 0 4778 4811 172008047 172008080 1.980000e-04 58.4
37 TraesCS4A01G097900 chr2D 90.339 590 50 6 1 584 127265975 127265387 0.000000e+00 767.0
38 TraesCS4A01G097900 chr2D 91.455 550 45 2 1 549 306311259 306311807 0.000000e+00 754.0
39 TraesCS4A01G097900 chr6D 90.273 586 55 2 1 584 452836631 452837216 0.000000e+00 765.0
40 TraesCS4A01G097900 chr6D 89.597 596 50 5 1 584 87469431 87468836 0.000000e+00 747.0
41 TraesCS4A01G097900 chr6D 88.737 586 57 6 1 580 427341761 427342343 0.000000e+00 708.0
42 TraesCS4A01G097900 chr6D 90.308 227 21 1 1059 1285 426118845 426118620 3.860000e-76 296.0
43 TraesCS4A01G097900 chr2B 89.358 592 53 5 1 582 210704487 210703896 0.000000e+00 736.0
44 TraesCS4A01G097900 chr7A 96.596 235 8 0 3288 3522 721097171 721097405 1.720000e-104 390.0
45 TraesCS4A01G097900 chr7A 84.677 248 32 5 4860 5102 422486719 422486473 5.100000e-60 243.0
46 TraesCS4A01G097900 chr7A 84.524 252 32 7 4851 5100 729611507 729611753 5.100000e-60 243.0
47 TraesCS4A01G097900 chr5D 96.596 235 8 0 3288 3522 129481345 129481579 1.720000e-104 390.0
48 TraesCS4A01G097900 chr5D 94.000 250 12 3 3273 3522 489769835 489770081 4.820000e-100 375.0
49 TraesCS4A01G097900 chr7D 96.186 236 9 0 3288 3523 45145491 45145726 2.230000e-103 387.0
50 TraesCS4A01G097900 chr7D 84.646 254 29 10 4851 5100 636666748 636666501 1.420000e-60 244.0
51 TraesCS4A01G097900 chr7D 91.111 45 4 0 4772 4816 506006987 506006943 1.530000e-05 62.1
52 TraesCS4A01G097900 chr5B 95.436 241 11 0 3285 3525 711718975 711718735 8.010000e-103 385.0
53 TraesCS4A01G097900 chr5B 91.760 267 17 5 3257 3522 341533394 341533656 2.900000e-97 366.0
54 TraesCS4A01G097900 chr5B 88.889 54 5 1 4763 4816 331618745 331618797 1.190000e-06 65.8
55 TraesCS4A01G097900 chr1B 83.784 444 32 16 4267 4684 35130808 35131237 8.010000e-103 385.0
56 TraesCS4A01G097900 chr1B 81.659 458 40 19 4267 4698 35700284 35699845 1.760000e-89 340.0
57 TraesCS4A01G097900 chr1B 95.477 199 9 0 1084 1282 512175815 512175617 8.240000e-83 318.0
58 TraesCS4A01G097900 chr1B 85.475 179 16 6 3954 4131 35700656 35700487 1.460000e-40 178.0
59 TraesCS4A01G097900 chr1B 91.667 48 4 0 4764 4811 668281290 668281337 3.300000e-07 67.6
60 TraesCS4A01G097900 chr1B 100.000 28 0 0 3868 3895 35130167 35130194 9.000000e-03 52.8
61 TraesCS4A01G097900 chr1D 82.314 458 40 17 4267 4698 21455693 21455251 4.860000e-95 359.0
62 TraesCS4A01G097900 chr1D 95.980 199 8 0 1084 1282 382237625 382237427 1.770000e-84 324.0
63 TraesCS4A01G097900 chr1D 88.770 187 11 7 3954 4131 21456081 21455896 2.390000e-53 220.0
64 TraesCS4A01G097900 chr1A 81.878 458 38 21 4267 4698 23006055 23005617 1.360000e-90 344.0
65 TraesCS4A01G097900 chr1A 94.975 199 10 0 1084 1282 482338963 482338765 3.840000e-81 313.0
66 TraesCS4A01G097900 chrUn 81.659 458 40 19 4267 4698 328887183 328887622 1.760000e-89 340.0
67 TraesCS4A01G097900 chrUn 85.475 179 16 6 3954 4131 328886811 328886980 1.460000e-40 178.0
68 TraesCS4A01G097900 chrUn 97.436 39 0 1 4778 4815 336469327 336469289 1.190000e-06 65.8
69 TraesCS4A01G097900 chrUn 97.436 39 0 1 4778 4815 397152002 397151964 1.190000e-06 65.8
70 TraesCS4A01G097900 chr6A 91.189 227 19 1 1059 1285 571033773 571033548 1.780000e-79 307.0
71 TraesCS4A01G097900 chr6B 90.749 227 20 1 1059 1285 641412899 641412674 8.300000e-78 302.0
72 TraesCS4A01G097900 chr6B 83.465 254 34 6 4851 5099 15864832 15865082 3.970000e-56 230.0
73 TraesCS4A01G097900 chr5A 90.857 175 11 3 4528 4698 622203850 622203677 3.970000e-56 230.0
74 TraesCS4A01G097900 chr5A 88.750 160 8 7 3982 4131 622204584 622204425 2.430000e-43 187.0
75 TraesCS4A01G097900 chr5A 100.000 28 0 0 3868 3895 622204882 622204855 9.000000e-03 52.8


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 TraesCS4A01G097900 chr4A 109422673 109427774 5101 False 9422.000000 9422 100.0000 1 5102 1 chr4A.!!$F1 5101
1 TraesCS4A01G097900 chr4A 110637081 110638837 1756 True 1877.000000 1877 86.0230 1395 3145 1 chr4A.!!$R2 1750
2 TraesCS4A01G097900 chr4A 591848664 591849446 782 False 286.000000 350 86.2445 3953 4653 2 chr4A.!!$F2 700
3 TraesCS4A01G097900 chr4B 439317453 439322837 5384 True 1177.166667 4569 93.6535 605 4842 6 chr4B.!!$R1 4237
4 TraesCS4A01G097900 chr4B 437949114 437951093 1979 False 1093.000000 1873 90.8555 1084 3048 2 chr4B.!!$F3 1964
5 TraesCS4A01G097900 chr4B 20719628 20720503 875 False 312.000000 411 86.1045 3953 4698 2 chr4B.!!$F2 745
6 TraesCS4A01G097900 chr4D 354136403 354138056 1653 False 1892.000000 1892 87.3110 1395 3048 1 chr4D.!!$F2 1653
7 TraesCS4A01G097900 chr4D 355855281 355861035 5754 True 1587.000000 4492 93.2485 605 4843 4 chr4D.!!$R2 4238
8 TraesCS4A01G097900 chr4D 41721822 41722405 583 False 778.000000 778 90.7850 2 584 1 chr4D.!!$F1 582
9 TraesCS4A01G097900 chr4D 381095394 381095975 581 True 771.000000 771 90.6140 1 582 1 chr4D.!!$R1 581
10 TraesCS4A01G097900 chr4D 10970965 10971644 679 False 242.950000 398 88.5705 4271 4836 2 chr4D.!!$F5 565
11 TraesCS4A01G097900 chr3D 462851023 462852686 1663 False 1888.000000 1888 87.1550 1394 3057 1 chr3D.!!$F1 1663
12 TraesCS4A01G097900 chr3D 463189930 463191627 1697 True 1884.000000 1884 86.7290 1394 3091 1 chr3D.!!$R1 1697
13 TraesCS4A01G097900 chr3D 522087495 522088083 588 True 773.000000 773 90.4920 1 584 1 chr3D.!!$R2 583
14 TraesCS4A01G097900 chr3D 83888447 83889610 1163 True 389.500000 392 96.2180 3288 3527 2 chr3D.!!$R3 239
15 TraesCS4A01G097900 chr3A 606434272 606436003 1731 True 1866.000000 1866 86.0980 1396 3141 1 chr3A.!!$R1 1745
16 TraesCS4A01G097900 chr3B 616309318 616310978 1660 True 1855.000000 1855 86.8390 1396 3057 1 chr3B.!!$R2 1661
17 TraesCS4A01G097900 chr2D 127265387 127265975 588 True 767.000000 767 90.3390 1 584 1 chr2D.!!$R1 583
18 TraesCS4A01G097900 chr2D 306311259 306311807 548 False 754.000000 754 91.4550 1 549 1 chr2D.!!$F1 548
19 TraesCS4A01G097900 chr6D 452836631 452837216 585 False 765.000000 765 90.2730 1 584 1 chr6D.!!$F2 583
20 TraesCS4A01G097900 chr6D 87468836 87469431 595 True 747.000000 747 89.5970 1 584 1 chr6D.!!$R1 583
21 TraesCS4A01G097900 chr6D 427341761 427342343 582 False 708.000000 708 88.7370 1 580 1 chr6D.!!$F1 579
22 TraesCS4A01G097900 chr2B 210703896 210704487 591 True 736.000000 736 89.3580 1 582 1 chr2B.!!$R1 581
23 TraesCS4A01G097900 chr1B 35699845 35700656 811 True 259.000000 340 83.5670 3954 4698 2 chr1B.!!$R2 744
24 TraesCS4A01G097900 chr1B 35130167 35131237 1070 False 218.900000 385 91.8920 3868 4684 2 chr1B.!!$F2 816
25 TraesCS4A01G097900 chr1D 21455251 21456081 830 True 289.500000 359 85.5420 3954 4698 2 chr1D.!!$R2 744
26 TraesCS4A01G097900 chrUn 328886811 328887622 811 False 259.000000 340 83.5670 3954 4698 2 chrUn.!!$F1 744

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
601 622 0.478507 AAGTCCTTCACCCCAACCTG 59.521 55.000 0.00 0.0 0.0 4.00 F
662 683 0.768622 CTGGAAACCTGTACACCCCA 59.231 55.000 0.00 0.0 0.0 4.96 F
695 716 1.004745 ACCAATCGATGCCTTCCAACT 59.995 47.619 0.00 0.0 0.0 3.16 F
2588 2670 1.214062 CGGCAAGTTCGAGCTCTCT 59.786 57.895 12.85 4.7 0.0 3.10 F
2888 2971 0.326264 ACAAGATCGCCTCCAAGCTT 59.674 50.000 0.00 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2687 2770 2.106338 TGTGATCTTGTTCTTCTGCCCA 59.894 45.455 0.00 0.0 0.00 5.36 R
2729 2812 0.820226 CGATGTCCTCCTTGCTCAGA 59.180 55.000 0.00 0.0 0.00 3.27 R
2888 2971 2.602267 TTCTTGTCGGCCTCGGGA 60.602 61.111 0.00 0.0 36.95 5.14 R
3704 4244 0.037160 ATACCCAGCCCGAACGTTTT 59.963 50.000 0.46 0.0 0.00 2.43 R
4475 7358 0.111089 CGAGTTGAGCAGACAAACGC 60.111 55.000 0.00 0.0 0.00 4.84 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
49 50 0.538516 ATGCTAGAGATCGAGGCCGT 60.539 55.000 0.00 0.00 37.05 5.68
78 79 2.919228 AGACAAAGGCGAAAGAAGTGT 58.081 42.857 0.00 0.00 0.00 3.55
110 111 0.620410 TGATGACCGGGGTGGAGATT 60.620 55.000 6.32 0.00 42.00 2.40
211 212 1.268589 CGACGAGTGATCTATGGCGTT 60.269 52.381 0.00 0.00 31.58 4.84
217 219 1.412710 GTGATCTATGGCGTTGAGGGA 59.587 52.381 0.00 0.00 0.00 4.20
463 483 2.565647 CATGAAATGGGTCGGCACA 58.434 52.632 0.00 0.00 41.79 4.57
495 516 1.339610 CCGACCCAAATGCAAAACTGA 59.660 47.619 0.00 0.00 0.00 3.41
501 522 3.007182 CCCAAATGCAAAACTGAGTGGAT 59.993 43.478 0.00 0.00 0.00 3.41
584 605 3.065371 CGCCCCATTAAAGTTGCTCTAAG 59.935 47.826 0.00 0.00 0.00 2.18
585 606 4.017126 GCCCCATTAAAGTTGCTCTAAGT 58.983 43.478 0.00 0.00 0.00 2.24
586 607 4.096532 GCCCCATTAAAGTTGCTCTAAGTC 59.903 45.833 0.00 0.00 0.00 3.01
587 608 4.640647 CCCCATTAAAGTTGCTCTAAGTCC 59.359 45.833 0.00 0.00 0.00 3.85
588 609 5.501156 CCCATTAAAGTTGCTCTAAGTCCT 58.499 41.667 0.00 0.00 0.00 3.85
589 610 5.946377 CCCATTAAAGTTGCTCTAAGTCCTT 59.054 40.000 0.00 0.00 0.00 3.36
590 611 6.094186 CCCATTAAAGTTGCTCTAAGTCCTTC 59.906 42.308 0.00 0.00 0.00 3.46
591 612 6.655003 CCATTAAAGTTGCTCTAAGTCCTTCA 59.345 38.462 0.00 0.00 0.00 3.02
592 613 7.361286 CCATTAAAGTTGCTCTAAGTCCTTCAC 60.361 40.741 0.00 0.00 0.00 3.18
593 614 3.686916 AGTTGCTCTAAGTCCTTCACC 57.313 47.619 0.00 0.00 0.00 4.02
594 615 2.303311 AGTTGCTCTAAGTCCTTCACCC 59.697 50.000 0.00 0.00 0.00 4.61
595 616 1.276622 TGCTCTAAGTCCTTCACCCC 58.723 55.000 0.00 0.00 0.00 4.95
596 617 1.276622 GCTCTAAGTCCTTCACCCCA 58.723 55.000 0.00 0.00 0.00 4.96
597 618 1.628846 GCTCTAAGTCCTTCACCCCAA 59.371 52.381 0.00 0.00 0.00 4.12
598 619 2.615747 GCTCTAAGTCCTTCACCCCAAC 60.616 54.545 0.00 0.00 0.00 3.77
599 620 1.982958 TCTAAGTCCTTCACCCCAACC 59.017 52.381 0.00 0.00 0.00 3.77
600 621 1.985895 CTAAGTCCTTCACCCCAACCT 59.014 52.381 0.00 0.00 0.00 3.50
601 622 0.478507 AAGTCCTTCACCCCAACCTG 59.521 55.000 0.00 0.00 0.00 4.00
602 623 1.603739 GTCCTTCACCCCAACCTGC 60.604 63.158 0.00 0.00 0.00 4.85
603 624 1.774217 TCCTTCACCCCAACCTGCT 60.774 57.895 0.00 0.00 0.00 4.24
662 683 0.768622 CTGGAAACCTGTACACCCCA 59.231 55.000 0.00 0.00 0.00 4.96
695 716 1.004745 ACCAATCGATGCCTTCCAACT 59.995 47.619 0.00 0.00 0.00 3.16
696 717 2.238646 ACCAATCGATGCCTTCCAACTA 59.761 45.455 0.00 0.00 0.00 2.24
723 749 4.275936 CCACAAGTCTGGAACAAAAGGTAG 59.724 45.833 0.00 0.00 38.70 3.18
793 819 3.146828 AAACCCCACACCCTGGAGC 62.147 63.158 0.00 0.00 43.95 4.70
804 830 2.286523 CCTGGAGCCGAGTCCAACT 61.287 63.158 7.09 0.00 46.29 3.16
939 976 4.202172 ACCACAACCTTTTAAATCCAACCG 60.202 41.667 0.00 0.00 0.00 4.44
943 980 2.030628 ACCTTTTAAATCCAACCGCGTG 60.031 45.455 4.92 0.00 0.00 5.34
1311 1350 3.387374 CCCTCTGTTATGCTCTGATCTGT 59.613 47.826 0.00 0.00 0.00 3.41
2588 2670 1.214062 CGGCAAGTTCGAGCTCTCT 59.786 57.895 12.85 4.70 0.00 3.10
2687 2770 2.584391 GGCGGAGGACAAGACCACT 61.584 63.158 0.00 0.00 0.00 4.00
2729 2812 2.042404 TTACCAACGACAAGGGGCGT 62.042 55.000 0.00 0.00 43.39 5.68
2888 2971 0.326264 ACAAGATCGCCTCCAAGCTT 59.674 50.000 0.00 0.00 0.00 3.74
2963 3046 1.956170 CGACAACAACCAGCTCGCT 60.956 57.895 0.00 0.00 0.00 4.93
3041 3124 1.153168 CGCCAAGATGTACCAGGGG 60.153 63.158 0.00 0.00 0.00 4.79
3065 3148 1.973281 CGCTGAAATGCCTGGTGGT 60.973 57.895 0.00 0.00 35.27 4.16
3176 3274 6.882656 AGATCGCCTACTATTCTATACCGTA 58.117 40.000 0.00 0.00 0.00 4.02
3181 3279 7.493971 TCGCCTACTATTCTATACCGTATCTTC 59.506 40.741 0.00 0.00 0.00 2.87
3214 3312 5.348986 GTGGATTCTAGTATCGTTCTGCAA 58.651 41.667 3.56 0.00 0.00 4.08
3225 3762 4.280101 TCGTTCTGCAATTTTTCGTTCA 57.720 36.364 0.00 0.00 0.00 3.18
3317 3854 2.476619 CGTCACAGTTTAGAAGGCACAG 59.523 50.000 0.00 0.00 0.00 3.66
3365 3902 0.887933 CAAGGTTTAGGGCGCATTGT 59.112 50.000 10.83 0.00 0.00 2.71
3465 4002 6.939163 AGCCCATCTCACAATCAATAGATAAC 59.061 38.462 0.00 0.00 33.08 1.89
3488 4025 5.212745 CCACCTAGGTCCTAGAGAATTTCT 58.787 45.833 25.27 0.00 36.26 2.52
3594 4131 4.508461 TTGATTGAATGTCTGGTTGCTG 57.492 40.909 0.00 0.00 0.00 4.41
3601 4138 4.756642 TGAATGTCTGGTTGCTGAACTTAG 59.243 41.667 0.00 0.00 32.15 2.18
3638 4176 6.095021 TCTCTAGTTGCTACAATCGCTTTAGA 59.905 38.462 0.13 0.00 0.00 2.10
3647 4185 5.864628 ACAATCGCTTTAGAAGAGGTTTC 57.135 39.130 0.00 0.00 28.65 2.78
3660 4198 6.769512 AGAAGAGGTTTCATTGCAACTAGTA 58.230 36.000 0.00 0.00 0.00 1.82
3704 4244 9.113838 GTTTCTAGATGATCAAATGCCTTTCTA 57.886 33.333 0.00 0.00 0.00 2.10
3709 4249 7.253422 AGATGATCAAATGCCTTTCTAAAACG 58.747 34.615 0.00 0.00 0.00 3.60
3769 4322 9.522804 TTCATTATTTATTATTGGCCGTTTGAC 57.477 29.630 0.00 0.00 0.00 3.18
3841 4409 7.543172 ACATTTGTCATGTGAAATAGATGTTGC 59.457 33.333 0.00 0.00 32.20 4.17
3858 4426 1.965935 TGCAAGTTTAGCTCAGCACA 58.034 45.000 0.00 0.00 34.59 4.57
3860 4428 2.886523 TGCAAGTTTAGCTCAGCACATT 59.113 40.909 0.00 0.00 34.59 2.71
3861 4429 4.071423 TGCAAGTTTAGCTCAGCACATTA 58.929 39.130 0.00 0.00 34.59 1.90
3862 4430 4.083324 TGCAAGTTTAGCTCAGCACATTAC 60.083 41.667 0.00 0.00 34.59 1.89
3863 4431 4.083324 GCAAGTTTAGCTCAGCACATTACA 60.083 41.667 0.00 0.00 0.00 2.41
3864 4432 5.385617 CAAGTTTAGCTCAGCACATTACAC 58.614 41.667 0.00 0.00 0.00 2.90
3865 4433 3.679980 AGTTTAGCTCAGCACATTACACG 59.320 43.478 0.00 0.00 0.00 4.49
3866 4434 3.586100 TTAGCTCAGCACATTACACGA 57.414 42.857 0.00 0.00 0.00 4.35
3900 4675 5.315348 ACTATGCAAATGCCCACAATTTTT 58.685 33.333 2.46 0.00 41.18 1.94
4033 4847 5.238214 GCAGACAATGAGAACTGAGAAGTTT 59.762 40.000 0.00 0.00 32.90 2.66
4080 4904 5.235305 ACTTGTGTTGCTGTCTGTAAAAG 57.765 39.130 0.00 0.00 0.00 2.27
4342 7217 3.815401 CCTCACAACTTCGGTGATTTCTT 59.185 43.478 0.00 0.00 43.72 2.52
4407 7282 6.040054 ACGTTATGTTTCTTTTGTAGGGCTTT 59.960 34.615 0.00 0.00 0.00 3.51
4468 7344 8.664669 TCTTCTATACATGATGGTTAGGCATA 57.335 34.615 0.00 0.00 0.00 3.14
4475 7358 5.300034 ACATGATGGTTAGGCATATGTGTTG 59.700 40.000 0.00 0.00 0.00 3.33
4476 7359 3.631686 TGATGGTTAGGCATATGTGTTGC 59.368 43.478 4.29 0.00 39.41 4.17
4477 7360 2.013400 TGGTTAGGCATATGTGTTGCG 58.987 47.619 4.29 0.00 41.07 4.85
4478 7361 2.014128 GGTTAGGCATATGTGTTGCGT 58.986 47.619 4.29 0.00 41.07 5.24
4479 7362 2.422127 GGTTAGGCATATGTGTTGCGTT 59.578 45.455 4.29 0.00 41.07 4.84
4494 7377 0.111089 GCGTTTGTCTGCTCAACTCG 60.111 55.000 0.00 0.00 0.00 4.18
4512 7395 6.588756 TCAACTCGTTTATCAGTTCACCATAC 59.411 38.462 0.00 0.00 30.06 2.39
4563 7472 8.698973 TGTTTCATCTTCCCAAACACTTATTA 57.301 30.769 0.00 0.00 35.57 0.98
4734 8588 1.500474 TAGCTGCAGAGGCCTTATGT 58.500 50.000 20.43 0.00 40.13 2.29
4737 8591 1.407989 GCTGCAGAGGCCTTATGTTCT 60.408 52.381 20.43 0.00 40.13 3.01
4774 8628 3.470709 ACTCCCGAGCATATTGAATGTG 58.529 45.455 0.00 0.00 0.00 3.21
4782 8666 6.292865 CCGAGCATATTGAATGTGATAACGTT 60.293 38.462 5.88 5.88 0.00 3.99
4818 8702 3.665190 GGAGGGAGTATTTGCTTATCGG 58.335 50.000 0.00 0.00 0.00 4.18
4843 8727 8.186163 GGTCTACAATAACTTTTATTTTCGGGG 58.814 37.037 0.00 0.00 0.00 5.73
4844 8728 8.949177 GTCTACAATAACTTTTATTTTCGGGGA 58.051 33.333 0.00 0.00 0.00 4.81
4845 8729 9.689501 TCTACAATAACTTTTATTTTCGGGGAT 57.310 29.630 0.00 0.00 0.00 3.85
4846 8730 9.730420 CTACAATAACTTTTATTTTCGGGGATG 57.270 33.333 0.00 0.00 0.00 3.51
4847 8731 7.039270 ACAATAACTTTTATTTTCGGGGATGC 58.961 34.615 0.00 0.00 0.00 3.91
4848 8732 3.775661 ACTTTTATTTTCGGGGATGCG 57.224 42.857 0.00 0.00 0.00 4.73
4849 8733 2.425668 ACTTTTATTTTCGGGGATGCGG 59.574 45.455 0.00 0.00 0.00 5.69
4850 8734 2.131776 TTTATTTTCGGGGATGCGGT 57.868 45.000 0.00 0.00 0.00 5.68
4851 8735 1.670791 TTATTTTCGGGGATGCGGTC 58.329 50.000 0.00 0.00 0.00 4.79
4852 8736 0.834612 TATTTTCGGGGATGCGGTCT 59.165 50.000 0.00 0.00 0.00 3.85
4853 8737 0.748005 ATTTTCGGGGATGCGGTCTG 60.748 55.000 0.00 0.00 0.00 3.51
4854 8738 3.969250 TTTCGGGGATGCGGTCTGC 62.969 63.158 0.00 0.00 46.70 4.26
4876 8760 4.138487 ACCCGAGGTGATCAGTAAATTC 57.862 45.455 0.00 0.00 32.98 2.17
4877 8761 3.123804 CCCGAGGTGATCAGTAAATTCG 58.876 50.000 0.00 0.00 0.00 3.34
4878 8762 3.430374 CCCGAGGTGATCAGTAAATTCGT 60.430 47.826 0.00 0.00 0.00 3.85
4879 8763 4.181578 CCGAGGTGATCAGTAAATTCGTT 58.818 43.478 0.00 0.00 0.00 3.85
4880 8764 4.630069 CCGAGGTGATCAGTAAATTCGTTT 59.370 41.667 0.00 0.00 0.00 3.60
4881 8765 5.808540 CCGAGGTGATCAGTAAATTCGTTTA 59.191 40.000 0.00 0.00 0.00 2.01
4882 8766 6.311935 CCGAGGTGATCAGTAAATTCGTTTAA 59.688 38.462 0.00 0.00 0.00 1.52
4883 8767 7.148540 CCGAGGTGATCAGTAAATTCGTTTAAA 60.149 37.037 0.00 0.00 0.00 1.52
4884 8768 8.225107 CGAGGTGATCAGTAAATTCGTTTAAAA 58.775 33.333 0.00 0.00 0.00 1.52
4936 8820 7.395190 TTTTTGTGATGCTAGATGCTTATGT 57.605 32.000 0.00 0.00 43.37 2.29
4937 8821 5.996669 TTGTGATGCTAGATGCTTATGTG 57.003 39.130 0.00 0.00 43.37 3.21
4938 8822 3.811497 TGTGATGCTAGATGCTTATGTGC 59.189 43.478 0.00 0.00 43.37 4.57
4939 8823 3.062042 TGATGCTAGATGCTTATGTGCG 58.938 45.455 0.00 0.00 43.37 5.34
4940 8824 1.220529 TGCTAGATGCTTATGTGCGC 58.779 50.000 0.00 0.00 43.37 6.09
4941 8825 0.162507 GCTAGATGCTTATGTGCGCG 59.837 55.000 0.00 0.00 38.95 6.86
4942 8826 1.770957 CTAGATGCTTATGTGCGCGA 58.229 50.000 12.10 0.00 35.36 5.87
4943 8827 2.127251 CTAGATGCTTATGTGCGCGAA 58.873 47.619 12.10 0.00 35.36 4.70
4944 8828 0.933097 AGATGCTTATGTGCGCGAAG 59.067 50.000 12.10 4.99 35.36 3.79
4960 8844 2.486128 CGAAGCTCGTGTCAAATTTCG 58.514 47.619 0.00 0.00 34.72 3.46
4961 8845 2.096909 CGAAGCTCGTGTCAAATTTCGT 60.097 45.455 0.00 0.00 34.72 3.85
4962 8846 2.949714 AGCTCGTGTCAAATTTCGTG 57.050 45.000 0.00 0.00 0.00 4.35
4963 8847 1.531149 AGCTCGTGTCAAATTTCGTGG 59.469 47.619 0.00 0.00 0.00 4.94
4964 8848 1.529438 GCTCGTGTCAAATTTCGTGGA 59.471 47.619 0.00 0.00 0.00 4.02
4965 8849 2.411547 GCTCGTGTCAAATTTCGTGGAG 60.412 50.000 0.00 0.00 0.00 3.86
4966 8850 2.800544 CTCGTGTCAAATTTCGTGGAGT 59.199 45.455 0.00 0.00 0.00 3.85
4967 8851 3.199677 TCGTGTCAAATTTCGTGGAGTT 58.800 40.909 0.00 0.00 0.00 3.01
4968 8852 3.623960 TCGTGTCAAATTTCGTGGAGTTT 59.376 39.130 0.00 0.00 0.00 2.66
4969 8853 3.723764 CGTGTCAAATTTCGTGGAGTTTG 59.276 43.478 0.00 0.00 33.91 2.93
4970 8854 4.041723 GTGTCAAATTTCGTGGAGTTTGG 58.958 43.478 0.00 0.00 33.55 3.28
4971 8855 3.948473 TGTCAAATTTCGTGGAGTTTGGA 59.052 39.130 0.00 0.00 33.55 3.53
4972 8856 4.201970 TGTCAAATTTCGTGGAGTTTGGAC 60.202 41.667 0.00 0.00 33.55 4.02
4973 8857 3.948473 TCAAATTTCGTGGAGTTTGGACA 59.052 39.130 0.00 0.00 33.55 4.02
4974 8858 4.582656 TCAAATTTCGTGGAGTTTGGACAT 59.417 37.500 0.00 0.00 33.55 3.06
4975 8859 5.068460 TCAAATTTCGTGGAGTTTGGACATT 59.932 36.000 0.00 0.00 33.55 2.71
4976 8860 5.529581 AATTTCGTGGAGTTTGGACATTT 57.470 34.783 0.00 0.00 0.00 2.32
4977 8861 4.561735 TTTCGTGGAGTTTGGACATTTC 57.438 40.909 0.00 0.00 0.00 2.17
4978 8862 3.201353 TCGTGGAGTTTGGACATTTCA 57.799 42.857 0.00 0.00 0.00 2.69
4979 8863 3.138304 TCGTGGAGTTTGGACATTTCAG 58.862 45.455 0.00 0.00 0.00 3.02
4980 8864 2.878406 CGTGGAGTTTGGACATTTCAGT 59.122 45.455 0.00 0.00 0.00 3.41
4981 8865 3.303990 CGTGGAGTTTGGACATTTCAGTG 60.304 47.826 0.00 0.00 0.00 3.66
4982 8866 3.004734 GTGGAGTTTGGACATTTCAGTGG 59.995 47.826 0.00 0.00 0.00 4.00
4983 8867 2.029918 GGAGTTTGGACATTTCAGTGGC 60.030 50.000 0.00 0.00 0.00 5.01
4984 8868 2.887152 GAGTTTGGACATTTCAGTGGCT 59.113 45.455 0.00 0.00 0.00 4.75
4985 8869 2.887152 AGTTTGGACATTTCAGTGGCTC 59.113 45.455 0.00 0.00 0.00 4.70
4986 8870 2.887152 GTTTGGACATTTCAGTGGCTCT 59.113 45.455 0.00 0.00 0.00 4.09
4987 8871 2.479566 TGGACATTTCAGTGGCTCTC 57.520 50.000 0.00 0.00 0.00 3.20
4988 8872 1.699083 TGGACATTTCAGTGGCTCTCA 59.301 47.619 0.00 0.00 0.00 3.27
4989 8873 2.289882 TGGACATTTCAGTGGCTCTCAG 60.290 50.000 0.00 0.00 0.00 3.35
4990 8874 1.736681 GACATTTCAGTGGCTCTCAGC 59.263 52.381 0.00 0.00 41.46 4.26
4991 8875 1.072806 ACATTTCAGTGGCTCTCAGCA 59.927 47.619 0.00 0.00 44.75 4.41
4992 8876 2.156917 CATTTCAGTGGCTCTCAGCAA 58.843 47.619 0.00 0.00 44.75 3.91
4993 8877 2.346766 TTTCAGTGGCTCTCAGCAAA 57.653 45.000 0.00 0.00 44.75 3.68
4994 8878 2.346766 TTCAGTGGCTCTCAGCAAAA 57.653 45.000 0.00 0.00 44.75 2.44
4995 8879 2.346766 TCAGTGGCTCTCAGCAAAAA 57.653 45.000 0.00 0.00 44.75 1.94
5017 8901 8.887036 AAAAAGACAAATTTTAGGGCAGTAAG 57.113 30.769 0.00 0.00 32.20 2.34
5018 8902 7.833285 AAAGACAAATTTTAGGGCAGTAAGA 57.167 32.000 0.00 0.00 0.00 2.10
5019 8903 7.833285 AAGACAAATTTTAGGGCAGTAAGAA 57.167 32.000 0.00 0.00 0.00 2.52
5020 8904 7.833285 AGACAAATTTTAGGGCAGTAAGAAA 57.167 32.000 0.00 0.00 0.00 2.52
5021 8905 7.886338 AGACAAATTTTAGGGCAGTAAGAAAG 58.114 34.615 0.00 0.00 0.00 2.62
5022 8906 7.505923 AGACAAATTTTAGGGCAGTAAGAAAGT 59.494 33.333 0.00 0.00 0.00 2.66
5023 8907 8.018537 ACAAATTTTAGGGCAGTAAGAAAGTT 57.981 30.769 0.00 0.00 0.00 2.66
5024 8908 8.482943 ACAAATTTTAGGGCAGTAAGAAAGTTT 58.517 29.630 0.00 0.00 0.00 2.66
5025 8909 9.974980 CAAATTTTAGGGCAGTAAGAAAGTTTA 57.025 29.630 0.00 0.00 0.00 2.01
5026 8910 9.976511 AAATTTTAGGGCAGTAAGAAAGTTTAC 57.023 29.630 0.00 0.00 34.48 2.01
5027 8911 8.935614 ATTTTAGGGCAGTAAGAAAGTTTACT 57.064 30.769 0.00 0.00 42.94 2.24
5038 8922 9.538508 AGTAAGAAAGTTTACTGTTCACGTATT 57.461 29.630 0.00 0.00 41.17 1.89
5039 8923 9.577003 GTAAGAAAGTTTACTGTTCACGTATTG 57.423 33.333 0.00 0.00 32.15 1.90
5040 8924 7.781548 AGAAAGTTTACTGTTCACGTATTGT 57.218 32.000 0.00 0.00 0.00 2.71
5041 8925 8.205131 AGAAAGTTTACTGTTCACGTATTGTT 57.795 30.769 0.00 0.00 0.00 2.83
5042 8926 8.671028 AGAAAGTTTACTGTTCACGTATTGTTT 58.329 29.630 0.00 0.00 0.00 2.83
5043 8927 9.281075 GAAAGTTTACTGTTCACGTATTGTTTT 57.719 29.630 0.00 0.00 0.00 2.43
5044 8928 8.609478 AAGTTTACTGTTCACGTATTGTTTTG 57.391 30.769 0.00 0.00 0.00 2.44
5045 8929 7.976826 AGTTTACTGTTCACGTATTGTTTTGA 58.023 30.769 0.00 0.00 0.00 2.69
5046 8930 7.906527 AGTTTACTGTTCACGTATTGTTTTGAC 59.093 33.333 0.00 0.00 0.00 3.18
5047 8931 5.164606 ACTGTTCACGTATTGTTTTGACC 57.835 39.130 0.00 0.00 0.00 4.02
5048 8932 4.198473 TGTTCACGTATTGTTTTGACCG 57.802 40.909 0.00 0.00 0.00 4.79
5049 8933 3.869832 TGTTCACGTATTGTTTTGACCGA 59.130 39.130 0.00 0.00 0.00 4.69
5050 8934 4.512198 TGTTCACGTATTGTTTTGACCGAT 59.488 37.500 0.00 0.00 0.00 4.18
5051 8935 5.007823 TGTTCACGTATTGTTTTGACCGATT 59.992 36.000 0.00 0.00 0.00 3.34
5052 8936 5.676532 TCACGTATTGTTTTGACCGATTT 57.323 34.783 0.00 0.00 0.00 2.17
5053 8937 6.062434 TCACGTATTGTTTTGACCGATTTT 57.938 33.333 0.00 0.00 0.00 1.82
5054 8938 5.910166 TCACGTATTGTTTTGACCGATTTTG 59.090 36.000 0.00 0.00 0.00 2.44
5055 8939 5.683743 CACGTATTGTTTTGACCGATTTTGT 59.316 36.000 0.00 0.00 0.00 2.83
5056 8940 5.910723 ACGTATTGTTTTGACCGATTTTGTC 59.089 36.000 0.00 0.00 0.00 3.18
5057 8941 6.140110 CGTATTGTTTTGACCGATTTTGTCT 58.860 36.000 0.00 0.00 33.83 3.41
5058 8942 6.635239 CGTATTGTTTTGACCGATTTTGTCTT 59.365 34.615 0.00 0.00 33.83 3.01
5059 8943 7.166804 CGTATTGTTTTGACCGATTTTGTCTTT 59.833 33.333 0.00 0.00 33.83 2.52
5060 8944 7.841915 ATTGTTTTGACCGATTTTGTCTTTT 57.158 28.000 0.00 0.00 33.83 2.27
5061 8945 7.659652 TTGTTTTGACCGATTTTGTCTTTTT 57.340 28.000 0.00 0.00 33.83 1.94
5081 8965 6.748333 TTTTTGCTATGAACTCCTCAGATG 57.252 37.500 0.00 0.00 37.52 2.90
5082 8966 5.426689 TTTGCTATGAACTCCTCAGATGT 57.573 39.130 0.00 0.00 37.52 3.06
5083 8967 4.662468 TGCTATGAACTCCTCAGATGTC 57.338 45.455 0.00 0.00 37.52 3.06
5084 8968 3.386078 TGCTATGAACTCCTCAGATGTCC 59.614 47.826 0.00 0.00 37.52 4.02
5085 8969 3.244044 GCTATGAACTCCTCAGATGTCCC 60.244 52.174 0.00 0.00 37.52 4.46
5086 8970 2.325661 TGAACTCCTCAGATGTCCCA 57.674 50.000 0.00 0.00 0.00 4.37
5087 8971 2.619931 TGAACTCCTCAGATGTCCCAA 58.380 47.619 0.00 0.00 0.00 4.12
5088 8972 2.303022 TGAACTCCTCAGATGTCCCAAC 59.697 50.000 0.00 0.00 0.00 3.77
5089 8973 2.030027 ACTCCTCAGATGTCCCAACA 57.970 50.000 0.00 0.00 40.38 3.33
5090 8974 2.338809 ACTCCTCAGATGTCCCAACAA 58.661 47.619 0.00 0.00 39.30 2.83
5091 8975 2.304180 ACTCCTCAGATGTCCCAACAAG 59.696 50.000 0.00 0.00 39.30 3.16
5092 8976 1.003580 TCCTCAGATGTCCCAACAAGC 59.996 52.381 0.00 0.00 39.30 4.01
5093 8977 1.004044 CCTCAGATGTCCCAACAAGCT 59.996 52.381 0.00 0.00 39.30 3.74
5094 8978 2.082231 CTCAGATGTCCCAACAAGCTG 58.918 52.381 0.00 0.00 40.47 4.24
5095 8979 1.699083 TCAGATGTCCCAACAAGCTGA 59.301 47.619 9.17 9.17 43.11 4.26
5096 8980 2.106338 TCAGATGTCCCAACAAGCTGAA 59.894 45.455 10.25 0.00 42.74 3.02
5097 8981 2.886523 CAGATGTCCCAACAAGCTGAAA 59.113 45.455 0.00 0.00 41.07 2.69
5098 8982 3.508793 CAGATGTCCCAACAAGCTGAAAT 59.491 43.478 0.00 0.00 41.07 2.17
5099 8983 4.021719 CAGATGTCCCAACAAGCTGAAATT 60.022 41.667 0.00 0.00 41.07 1.82
5100 8984 4.590222 AGATGTCCCAACAAGCTGAAATTT 59.410 37.500 0.00 0.00 39.30 1.82
5101 8985 4.057406 TGTCCCAACAAGCTGAAATTTG 57.943 40.909 0.00 0.00 30.70 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.029743 GCCTTTGTCTTGGCGTTGA 58.970 52.632 0.00 0.00 39.71 3.18
78 79 2.362736 GGTCATCATGCTTGCAAGAGA 58.637 47.619 30.39 22.01 0.00 3.10
110 111 4.487714 GGTGTTGAGATCCACCTTCATA 57.512 45.455 10.62 0.00 46.17 2.15
343 345 6.374333 GGCTTCAGAAAATACCACAGTTCATA 59.626 38.462 0.00 0.00 0.00 2.15
380 399 1.028330 CAGCGGCCATGTCTCATGTT 61.028 55.000 2.24 0.00 0.00 2.71
381 400 1.450848 CAGCGGCCATGTCTCATGT 60.451 57.895 2.24 0.00 0.00 3.21
433 452 6.357579 ACCCATTTCATGTCTGCATTTAAA 57.642 33.333 0.00 0.00 31.99 1.52
571 592 4.390264 GGTGAAGGACTTAGAGCAACTTT 58.610 43.478 0.00 0.00 0.00 2.66
584 605 1.603739 GCAGGTTGGGGTGAAGGAC 60.604 63.158 0.00 0.00 0.00 3.85
585 606 1.774217 AGCAGGTTGGGGTGAAGGA 60.774 57.895 0.00 0.00 0.00 3.36
586 607 1.303643 GAGCAGGTTGGGGTGAAGG 60.304 63.158 0.00 0.00 0.00 3.46
587 608 0.607489 CTGAGCAGGTTGGGGTGAAG 60.607 60.000 0.00 0.00 0.00 3.02
588 609 1.455849 CTGAGCAGGTTGGGGTGAA 59.544 57.895 0.00 0.00 0.00 3.18
589 610 2.528818 CCTGAGCAGGTTGGGGTGA 61.529 63.158 8.38 0.00 43.61 4.02
590 611 2.034687 CCTGAGCAGGTTGGGGTG 59.965 66.667 8.38 0.00 43.61 4.61
599 620 1.401931 CGCCAATTTTGACCTGAGCAG 60.402 52.381 0.00 0.00 0.00 4.24
600 621 0.597568 CGCCAATTTTGACCTGAGCA 59.402 50.000 0.00 0.00 0.00 4.26
601 622 0.109132 CCGCCAATTTTGACCTGAGC 60.109 55.000 0.00 0.00 0.00 4.26
602 623 0.109132 GCCGCCAATTTTGACCTGAG 60.109 55.000 0.00 0.00 0.00 3.35
603 624 0.825425 TGCCGCCAATTTTGACCTGA 60.825 50.000 0.00 0.00 0.00 3.86
643 664 0.768622 TGGGGTGTACAGGTTTCCAG 59.231 55.000 0.00 0.00 0.00 3.86
662 683 2.006888 CGATTGGTTCGTGGCTACAAT 58.993 47.619 0.00 0.00 43.01 2.71
695 716 1.771854 TGTTCCAGACTTGTGGCCTTA 59.228 47.619 3.32 0.00 37.53 2.69
696 717 0.550914 TGTTCCAGACTTGTGGCCTT 59.449 50.000 3.32 0.00 37.53 4.35
723 749 0.393537 CTGGCAGGTGGAGACATTCC 60.394 60.000 6.61 0.00 46.14 3.01
793 819 3.691342 TGGCGGAGTTGGACTCGG 61.691 66.667 10.26 10.26 45.96 4.63
829 855 4.778143 CAGGAGGAAACCGCGGGG 62.778 72.222 31.76 18.33 40.11 5.73
874 911 0.779997 AGAATGTTCCTTGGGTGGCT 59.220 50.000 0.00 0.00 0.00 4.75
879 916 2.422093 GGGCTCTAGAATGTTCCTTGGG 60.422 54.545 0.00 0.00 0.00 4.12
1311 1350 5.010719 ACGACATGAAAACAGAGGACTAGAA 59.989 40.000 0.00 0.00 0.00 2.10
1383 1465 2.159324 TCGCATCTGCAAACAAACAACA 60.159 40.909 2.72 0.00 42.21 3.33
1384 1466 2.458951 TCGCATCTGCAAACAAACAAC 58.541 42.857 2.72 0.00 42.21 3.32
1385 1467 2.859526 TCGCATCTGCAAACAAACAA 57.140 40.000 2.72 0.00 42.21 2.83
2687 2770 2.106338 TGTGATCTTGTTCTTCTGCCCA 59.894 45.455 0.00 0.00 0.00 5.36
2729 2812 0.820226 CGATGTCCTCCTTGCTCAGA 59.180 55.000 0.00 0.00 0.00 3.27
2888 2971 2.602267 TTCTTGTCGGCCTCGGGA 60.602 61.111 0.00 0.00 36.95 5.14
2963 3046 3.071457 TGTCATCAAACTCTTCAGCCTCA 59.929 43.478 0.00 0.00 0.00 3.86
3173 3265 3.120792 CCACCGTACAATGGAAGATACG 58.879 50.000 6.55 0.00 38.34 3.06
3181 3279 4.402056 ACTAGAATCCACCGTACAATGG 57.598 45.455 0.00 6.11 37.32 3.16
3214 3312 9.897744 CAATGTATATATGCCTGAACGAAAAAT 57.102 29.630 0.00 0.00 0.00 1.82
3317 3854 2.789893 TGGAAACGCACGCAAATTTAAC 59.210 40.909 0.00 0.00 0.00 2.01
3465 4002 5.212745 AGAAATTCTCTAGGACCTAGGTGG 58.787 45.833 25.35 16.41 35.03 4.61
3488 4025 1.079875 CGGTTTAGAAGGCGCGCTTA 61.080 55.000 32.29 15.27 0.00 3.09
3514 4051 9.835389 CAAGTATACTGTCTTCTAGTACTACCT 57.165 37.037 6.06 0.00 33.80 3.08
3594 4131 5.669477 AGAGATTCATGACAGGCTAAGTTC 58.331 41.667 0.00 0.00 0.00 3.01
3601 4138 3.559242 GCAACTAGAGATTCATGACAGGC 59.441 47.826 0.00 0.00 0.00 4.85
3638 4176 6.375455 CCATACTAGTTGCAATGAAACCTCTT 59.625 38.462 0.59 0.00 0.00 2.85
3647 4185 4.333649 CCACAGTCCATACTAGTTGCAATG 59.666 45.833 0.59 0.00 33.48 2.82
3660 4198 2.592102 ACAATTGCTCCACAGTCCAT 57.408 45.000 5.05 0.00 0.00 3.41
3704 4244 0.037160 ATACCCAGCCCGAACGTTTT 59.963 50.000 0.46 0.00 0.00 2.43
3758 4311 1.034838 AACAGCTTGTCAAACGGCCA 61.035 50.000 2.24 0.00 0.00 5.36
3769 4322 6.417044 GCAATGCTAGAATAATGAACAGCTTG 59.583 38.462 0.00 0.00 0.00 4.01
3841 4409 5.385617 GTGTAATGTGCTGAGCTAAACTTG 58.614 41.667 5.83 0.00 0.00 3.16
3858 4426 7.929245 TGCATAGTTATGTGGTAATCGTGTAAT 59.071 33.333 1.49 0.00 36.11 1.89
3860 4428 6.807789 TGCATAGTTATGTGGTAATCGTGTA 58.192 36.000 1.49 0.00 36.11 2.90
3861 4429 5.666462 TGCATAGTTATGTGGTAATCGTGT 58.334 37.500 1.49 0.00 36.11 4.49
3862 4430 6.597262 TTGCATAGTTATGTGGTAATCGTG 57.403 37.500 0.00 0.00 36.11 4.35
3863 4431 7.639039 CATTTGCATAGTTATGTGGTAATCGT 58.361 34.615 0.00 0.00 36.11 3.73
3864 4432 6.578545 GCATTTGCATAGTTATGTGGTAATCG 59.421 38.462 0.00 0.00 41.59 3.34
3865 4433 6.863126 GGCATTTGCATAGTTATGTGGTAATC 59.137 38.462 4.74 0.00 44.36 1.75
3866 4434 6.239289 GGGCATTTGCATAGTTATGTGGTAAT 60.239 38.462 4.74 0.00 44.36 1.89
3953 4752 6.053005 AGTTTTGACCATCGACTAACAGAAA 58.947 36.000 0.00 0.00 0.00 2.52
4080 4904 7.931948 TCCAACTATCTCGGGATTAAGAATTTC 59.068 37.037 1.42 0.00 33.71 2.17
4269 7144 9.494479 CAAGTTGCATATACAAATTCAGTACAG 57.506 33.333 0.00 0.00 35.81 2.74
4468 7344 1.002468 GAGCAGACAAACGCAACACAT 60.002 47.619 0.00 0.00 0.00 3.21
4475 7358 0.111089 CGAGTTGAGCAGACAAACGC 60.111 55.000 0.00 0.00 0.00 4.84
4476 7359 1.209128 ACGAGTTGAGCAGACAAACG 58.791 50.000 0.00 0.00 37.60 3.60
4477 7360 3.675467 AAACGAGTTGAGCAGACAAAC 57.325 42.857 0.00 0.00 0.00 2.93
4478 7361 5.053811 TGATAAACGAGTTGAGCAGACAAA 58.946 37.500 0.00 0.00 0.00 2.83
4479 7362 4.627058 TGATAAACGAGTTGAGCAGACAA 58.373 39.130 0.00 0.00 0.00 3.18
4494 7377 5.585047 GTCAGGGTATGGTGAACTGATAAAC 59.415 44.000 0.00 0.00 39.97 2.01
4512 7395 7.928706 AGTCAATAGAAATTATTCGAGTCAGGG 59.071 37.037 0.00 0.00 40.63 4.45
4563 7472 6.845908 AGCAATGAATAAGACTGGACCATAT 58.154 36.000 0.00 0.00 0.00 1.78
4628 7537 4.437682 AAAATTGGACCTCACTCTGACA 57.562 40.909 0.00 0.00 0.00 3.58
4734 8588 6.407202 GGGAGTAGATGCTAGTTCAAAAGAA 58.593 40.000 0.00 0.00 0.00 2.52
4737 8591 4.464951 TCGGGAGTAGATGCTAGTTCAAAA 59.535 41.667 0.00 0.00 0.00 2.44
4774 8628 8.761575 TCCGTCCCATAATATAAAACGTTATC 57.238 34.615 0.00 0.00 32.10 1.75
4782 8666 5.408824 ACTCCCTCCGTCCCATAATATAAA 58.591 41.667 0.00 0.00 0.00 1.40
4818 8702 8.949177 TCCCCGAAAATAAAAGTTATTGTAGAC 58.051 33.333 0.00 0.00 0.00 2.59
4855 8739 3.430374 CGAATTTACTGATCACCTCGGGT 60.430 47.826 0.00 0.00 35.62 5.28
4856 8740 3.123804 CGAATTTACTGATCACCTCGGG 58.876 50.000 0.00 0.00 34.24 5.14
4857 8741 3.782046 ACGAATTTACTGATCACCTCGG 58.218 45.455 0.00 0.00 36.23 4.63
4858 8742 5.779806 AAACGAATTTACTGATCACCTCG 57.220 39.130 0.00 0.00 0.00 4.63
4922 8806 0.162507 CGCGCACATAAGCATCTAGC 59.837 55.000 8.75 0.00 46.19 3.42
4923 8807 1.770957 TCGCGCACATAAGCATCTAG 58.229 50.000 8.75 0.00 0.00 2.43
4924 8808 2.127251 CTTCGCGCACATAAGCATCTA 58.873 47.619 8.75 0.00 0.00 1.98
4925 8809 0.933097 CTTCGCGCACATAAGCATCT 59.067 50.000 8.75 0.00 0.00 2.90
4926 8810 0.655626 GCTTCGCGCACATAAGCATC 60.656 55.000 20.60 0.00 43.98 3.91
4927 8811 1.091771 AGCTTCGCGCACATAAGCAT 61.092 50.000 25.31 11.93 46.35 3.79
4928 8812 1.695893 GAGCTTCGCGCACATAAGCA 61.696 55.000 25.31 0.00 46.35 3.91
4929 8813 1.011794 GAGCTTCGCGCACATAAGC 60.012 57.895 18.60 18.60 44.70 3.09
4930 8814 1.270968 CGAGCTTCGCGCACATAAG 59.729 57.895 8.75 6.32 42.61 1.73
4931 8815 1.445410 ACGAGCTTCGCGCACATAA 60.445 52.632 8.75 0.00 45.12 1.90
4932 8816 2.158330 CACGAGCTTCGCGCACATA 61.158 57.895 8.75 0.00 45.12 2.29
4933 8817 3.481903 CACGAGCTTCGCGCACAT 61.482 61.111 8.75 0.00 45.12 3.21
4934 8818 4.942481 ACACGAGCTTCGCGCACA 62.942 61.111 8.75 0.00 45.12 4.57
4935 8819 4.122515 GACACGAGCTTCGCGCAC 62.123 66.667 8.75 0.00 45.12 5.34
4936 8820 4.639171 TGACACGAGCTTCGCGCA 62.639 61.111 8.75 0.00 45.12 6.09
4937 8821 2.227968 ATTTGACACGAGCTTCGCGC 62.228 55.000 0.00 0.00 45.12 6.86
4938 8822 0.163788 AATTTGACACGAGCTTCGCG 59.836 50.000 0.00 0.00 45.12 5.87
4939 8823 2.234187 GAAATTTGACACGAGCTTCGC 58.766 47.619 0.00 0.00 45.12 4.70
4940 8824 2.096909 ACGAAATTTGACACGAGCTTCG 60.097 45.455 0.00 0.00 46.93 3.79
4941 8825 3.218398 CACGAAATTTGACACGAGCTTC 58.782 45.455 0.00 0.00 0.00 3.86
4942 8826 2.032030 CCACGAAATTTGACACGAGCTT 60.032 45.455 0.00 0.00 0.00 3.74
4943 8827 1.531149 CCACGAAATTTGACACGAGCT 59.469 47.619 0.00 0.00 0.00 4.09
4944 8828 1.529438 TCCACGAAATTTGACACGAGC 59.471 47.619 0.00 0.00 0.00 5.03
4945 8829 2.800544 ACTCCACGAAATTTGACACGAG 59.199 45.455 0.00 0.00 0.00 4.18
4946 8830 2.828877 ACTCCACGAAATTTGACACGA 58.171 42.857 0.00 0.00 0.00 4.35
4947 8831 3.602390 AACTCCACGAAATTTGACACG 57.398 42.857 0.00 0.00 0.00 4.49
4948 8832 4.041723 CCAAACTCCACGAAATTTGACAC 58.958 43.478 0.00 0.00 34.62 3.67
4949 8833 3.948473 TCCAAACTCCACGAAATTTGACA 59.052 39.130 0.00 0.00 34.62 3.58
4950 8834 4.201970 TGTCCAAACTCCACGAAATTTGAC 60.202 41.667 0.00 0.00 34.62 3.18
4951 8835 3.948473 TGTCCAAACTCCACGAAATTTGA 59.052 39.130 0.00 0.00 34.62 2.69
4952 8836 4.300189 TGTCCAAACTCCACGAAATTTG 57.700 40.909 0.00 0.00 32.89 2.32
4953 8837 5.529581 AATGTCCAAACTCCACGAAATTT 57.470 34.783 0.00 0.00 0.00 1.82
4954 8838 5.068460 TGAAATGTCCAAACTCCACGAAATT 59.932 36.000 0.00 0.00 0.00 1.82
4955 8839 4.582656 TGAAATGTCCAAACTCCACGAAAT 59.417 37.500 0.00 0.00 0.00 2.17
4956 8840 3.948473 TGAAATGTCCAAACTCCACGAAA 59.052 39.130 0.00 0.00 0.00 3.46
4957 8841 3.546724 TGAAATGTCCAAACTCCACGAA 58.453 40.909 0.00 0.00 0.00 3.85
4958 8842 3.138304 CTGAAATGTCCAAACTCCACGA 58.862 45.455 0.00 0.00 0.00 4.35
4959 8843 2.878406 ACTGAAATGTCCAAACTCCACG 59.122 45.455 0.00 0.00 0.00 4.94
4960 8844 3.004734 CCACTGAAATGTCCAAACTCCAC 59.995 47.826 0.00 0.00 0.00 4.02
4961 8845 3.221771 CCACTGAAATGTCCAAACTCCA 58.778 45.455 0.00 0.00 0.00 3.86
4962 8846 2.029918 GCCACTGAAATGTCCAAACTCC 60.030 50.000 0.00 0.00 0.00 3.85
4963 8847 2.887152 AGCCACTGAAATGTCCAAACTC 59.113 45.455 0.00 0.00 0.00 3.01
4964 8848 2.887152 GAGCCACTGAAATGTCCAAACT 59.113 45.455 0.00 0.00 0.00 2.66
4965 8849 2.887152 AGAGCCACTGAAATGTCCAAAC 59.113 45.455 0.00 0.00 0.00 2.93
4966 8850 3.149196 GAGAGCCACTGAAATGTCCAAA 58.851 45.455 0.00 0.00 0.00 3.28
4967 8851 2.106338 TGAGAGCCACTGAAATGTCCAA 59.894 45.455 0.00 0.00 0.00 3.53
4968 8852 1.699083 TGAGAGCCACTGAAATGTCCA 59.301 47.619 0.00 0.00 0.00 4.02
4969 8853 2.354259 CTGAGAGCCACTGAAATGTCC 58.646 52.381 0.00 0.00 0.00 4.02
4970 8854 1.736681 GCTGAGAGCCACTGAAATGTC 59.263 52.381 0.00 0.00 34.48 3.06
4971 8855 1.072806 TGCTGAGAGCCACTGAAATGT 59.927 47.619 0.00 0.00 41.51 2.71
4972 8856 1.817357 TGCTGAGAGCCACTGAAATG 58.183 50.000 0.00 0.00 41.51 2.32
4973 8857 2.574006 TTGCTGAGAGCCACTGAAAT 57.426 45.000 0.00 0.00 41.51 2.17
4974 8858 2.346766 TTTGCTGAGAGCCACTGAAA 57.653 45.000 0.00 0.00 41.51 2.69
4975 8859 2.346766 TTTTGCTGAGAGCCACTGAA 57.653 45.000 0.00 0.00 41.51 3.02
4976 8860 2.346766 TTTTTGCTGAGAGCCACTGA 57.653 45.000 0.00 0.00 41.51 3.41
4992 8876 8.700973 TCTTACTGCCCTAAAATTTGTCTTTTT 58.299 29.630 0.00 0.00 31.15 1.94
4993 8877 8.245195 TCTTACTGCCCTAAAATTTGTCTTTT 57.755 30.769 0.00 0.00 33.17 2.27
4994 8878 7.833285 TCTTACTGCCCTAAAATTTGTCTTT 57.167 32.000 0.00 0.00 0.00 2.52
4995 8879 7.833285 TTCTTACTGCCCTAAAATTTGTCTT 57.167 32.000 0.00 0.00 0.00 3.01
4996 8880 7.505923 ACTTTCTTACTGCCCTAAAATTTGTCT 59.494 33.333 0.00 0.00 0.00 3.41
4997 8881 7.658261 ACTTTCTTACTGCCCTAAAATTTGTC 58.342 34.615 0.00 0.00 0.00 3.18
4998 8882 7.597288 ACTTTCTTACTGCCCTAAAATTTGT 57.403 32.000 0.00 0.00 0.00 2.83
4999 8883 8.887036 AAACTTTCTTACTGCCCTAAAATTTG 57.113 30.769 0.00 0.00 0.00 2.32
5000 8884 9.976511 GTAAACTTTCTTACTGCCCTAAAATTT 57.023 29.630 0.00 0.00 0.00 1.82
5001 8885 9.363401 AGTAAACTTTCTTACTGCCCTAAAATT 57.637 29.630 0.00 0.00 39.98 1.82
5002 8886 8.935614 AGTAAACTTTCTTACTGCCCTAAAAT 57.064 30.769 0.00 0.00 39.98 1.82
5012 8896 9.538508 AATACGTGAACAGTAAACTTTCTTACT 57.461 29.630 0.00 0.00 41.75 2.24
5013 8897 9.577003 CAATACGTGAACAGTAAACTTTCTTAC 57.423 33.333 0.00 0.00 32.84 2.34
5014 8898 9.316730 ACAATACGTGAACAGTAAACTTTCTTA 57.683 29.630 0.00 0.00 0.00 2.10
5015 8899 8.205131 ACAATACGTGAACAGTAAACTTTCTT 57.795 30.769 0.00 0.00 0.00 2.52
5016 8900 7.781548 ACAATACGTGAACAGTAAACTTTCT 57.218 32.000 0.00 0.00 0.00 2.52
5017 8901 8.831000 AAACAATACGTGAACAGTAAACTTTC 57.169 30.769 0.00 0.00 0.00 2.62
5018 8902 9.068008 CAAAACAATACGTGAACAGTAAACTTT 57.932 29.630 0.00 0.00 0.00 2.66
5019 8903 8.452534 TCAAAACAATACGTGAACAGTAAACTT 58.547 29.630 0.00 0.00 0.00 2.66
5020 8904 7.906527 GTCAAAACAATACGTGAACAGTAAACT 59.093 33.333 0.00 0.00 0.00 2.66
5021 8905 7.164662 GGTCAAAACAATACGTGAACAGTAAAC 59.835 37.037 0.00 0.00 0.00 2.01
5022 8906 7.188157 GGTCAAAACAATACGTGAACAGTAAA 58.812 34.615 0.00 0.00 0.00 2.01
5023 8907 6.509837 CGGTCAAAACAATACGTGAACAGTAA 60.510 38.462 0.00 0.00 0.00 2.24
5024 8908 5.050904 CGGTCAAAACAATACGTGAACAGTA 60.051 40.000 0.00 0.00 0.00 2.74
5025 8909 4.260456 CGGTCAAAACAATACGTGAACAGT 60.260 41.667 0.00 0.00 0.00 3.55
5026 8910 4.025563 TCGGTCAAAACAATACGTGAACAG 60.026 41.667 0.00 0.00 0.00 3.16
5027 8911 3.869832 TCGGTCAAAACAATACGTGAACA 59.130 39.130 0.00 0.00 0.00 3.18
5028 8912 4.455917 TCGGTCAAAACAATACGTGAAC 57.544 40.909 0.00 0.00 0.00 3.18
5029 8913 5.676532 AATCGGTCAAAACAATACGTGAA 57.323 34.783 0.00 0.00 0.00 3.18
5030 8914 5.676532 AAATCGGTCAAAACAATACGTGA 57.323 34.783 0.00 0.00 0.00 4.35
5031 8915 5.683743 ACAAAATCGGTCAAAACAATACGTG 59.316 36.000 0.00 0.00 0.00 4.49
5032 8916 5.823353 ACAAAATCGGTCAAAACAATACGT 58.177 33.333 0.00 0.00 0.00 3.57
5033 8917 6.140110 AGACAAAATCGGTCAAAACAATACG 58.860 36.000 0.00 0.00 37.74 3.06
5034 8918 7.924103 AAGACAAAATCGGTCAAAACAATAC 57.076 32.000 0.00 0.00 37.74 1.89
5035 8919 8.934507 AAAAGACAAAATCGGTCAAAACAATA 57.065 26.923 0.00 0.00 37.74 1.90
5036 8920 7.841915 AAAAGACAAAATCGGTCAAAACAAT 57.158 28.000 0.00 0.00 37.74 2.71
5037 8921 7.659652 AAAAAGACAAAATCGGTCAAAACAA 57.340 28.000 0.00 0.00 37.74 2.83
5058 8942 6.240894 ACATCTGAGGAGTTCATAGCAAAAA 58.759 36.000 0.00 0.00 34.68 1.94
5059 8943 5.809001 ACATCTGAGGAGTTCATAGCAAAA 58.191 37.500 0.00 0.00 34.68 2.44
5060 8944 5.423015 GACATCTGAGGAGTTCATAGCAAA 58.577 41.667 0.00 0.00 34.68 3.68
5061 8945 4.141846 GGACATCTGAGGAGTTCATAGCAA 60.142 45.833 0.00 0.00 34.68 3.91
5062 8946 3.386078 GGACATCTGAGGAGTTCATAGCA 59.614 47.826 0.00 0.00 34.68 3.49
5063 8947 3.244044 GGGACATCTGAGGAGTTCATAGC 60.244 52.174 0.00 0.00 34.68 2.97
5064 8948 3.963374 TGGGACATCTGAGGAGTTCATAG 59.037 47.826 0.00 0.00 34.68 2.23
5065 8949 3.994317 TGGGACATCTGAGGAGTTCATA 58.006 45.455 0.00 0.00 34.68 2.15
5066 8950 2.837947 TGGGACATCTGAGGAGTTCAT 58.162 47.619 0.00 0.00 34.68 2.57
5067 8951 2.303022 GTTGGGACATCTGAGGAGTTCA 59.697 50.000 0.00 0.00 39.30 3.18
5068 8952 2.303022 TGTTGGGACATCTGAGGAGTTC 59.697 50.000 0.00 0.00 39.30 3.01
5069 8953 2.338809 TGTTGGGACATCTGAGGAGTT 58.661 47.619 0.00 0.00 39.30 3.01
5070 8954 2.030027 TGTTGGGACATCTGAGGAGT 57.970 50.000 0.00 0.00 39.30 3.85
5071 8955 2.938756 GCTTGTTGGGACATCTGAGGAG 60.939 54.545 0.00 0.00 39.30 3.69
5072 8956 1.003580 GCTTGTTGGGACATCTGAGGA 59.996 52.381 0.00 0.00 39.30 3.71
5073 8957 1.004044 AGCTTGTTGGGACATCTGAGG 59.996 52.381 0.00 0.00 39.30 3.86
5074 8958 2.082231 CAGCTTGTTGGGACATCTGAG 58.918 52.381 0.00 0.00 39.30 3.35
5075 8959 1.699083 TCAGCTTGTTGGGACATCTGA 59.301 47.619 7.48 7.48 40.40 3.27
5076 8960 2.189594 TCAGCTTGTTGGGACATCTG 57.810 50.000 0.00 0.00 39.30 2.90
5077 8961 2.957402 TTCAGCTTGTTGGGACATCT 57.043 45.000 0.00 0.00 39.30 2.90
5078 8962 4.525912 AATTTCAGCTTGTTGGGACATC 57.474 40.909 0.00 0.00 39.30 3.06
5079 8963 4.634199 CAAATTTCAGCTTGTTGGGACAT 58.366 39.130 0.00 0.00 39.30 3.06
5080 8964 4.057406 CAAATTTCAGCTTGTTGGGACA 57.943 40.909 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.