Multiple sequence alignment - TraesCS6A01G230000

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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 TraesCS6A01G230000 chr6A 100.000 7858 0 0 1 7858 432540264 432532407 0.000000e+00 14512.0
1 TraesCS6A01G230000 chr6A 91.127 834 68 6 1 833 442469263 442468435 0.000000e+00 1125.0
2 TraesCS6A01G230000 chr6D 95.490 1907 57 10 5977 7858 290902530 290904432 0.000000e+00 3018.0
3 TraesCS6A01G230000 chr6D 95.996 1823 50 8 916 2718 290900711 290902530 0.000000e+00 2940.0
4 TraesCS6A01G230000 chr6D 90.875 1348 110 7 3066 4407 73895 72555 0.000000e+00 1796.0
5 TraesCS6A01G230000 chr6D 90.663 1071 82 7 2745 3805 421048041 421049103 0.000000e+00 1408.0
6 TraesCS6A01G230000 chr6D 91.463 410 29 1 5545 5954 421049833 421050236 6.890000e-155 558.0
7 TraesCS6A01G230000 chr6D 91.197 284 20 4 5675 5954 452116544 452116826 1.600000e-101 381.0
8 TraesCS6A01G230000 chr6D 87.349 332 32 6 5182 5503 71247 70916 9.630000e-99 372.0
9 TraesCS6A01G230000 chr6B 95.779 1753 62 5 923 2670 451671933 451673678 0.000000e+00 2817.0
10 TraesCS6A01G230000 chr6B 94.041 1544 66 22 6013 7543 451673714 451675244 0.000000e+00 2318.0
11 TraesCS6A01G230000 chr6B 89.134 1362 122 18 3066 4407 48355711 48357066 0.000000e+00 1672.0
12 TraesCS6A01G230000 chr6B 93.636 660 36 5 4410 5064 48357820 48358478 0.000000e+00 981.0
13 TraesCS6A01G230000 chr6B 92.492 666 42 5 4405 5064 3810188 3810851 0.000000e+00 946.0
14 TraesCS6A01G230000 chr6B 92.145 331 18 3 7530 7858 451676774 451677098 2.000000e-125 460.0
15 TraesCS6A01G230000 chr6B 89.667 300 24 4 5657 5954 704458333 704458627 7.440000e-100 375.0
16 TraesCS6A01G230000 chr6B 79.787 282 24 11 5382 5663 704458133 704458381 2.910000e-39 174.0
17 TraesCS6A01G230000 chr7A 92.983 1696 106 7 2719 4404 656907333 656909025 0.000000e+00 2460.0
18 TraesCS6A01G230000 chr7A 90.419 835 72 4 1 834 201170200 201169373 0.000000e+00 1092.0
19 TraesCS6A01G230000 chr7A 92.587 661 45 2 4408 5064 338087566 338086906 0.000000e+00 946.0
20 TraesCS6A01G230000 chr7A 89.268 410 37 2 5545 5954 656910019 656910421 2.530000e-139 507.0
21 TraesCS6A01G230000 chr3B 92.878 1699 109 6 2719 4407 8048161 8046465 0.000000e+00 2457.0
22 TraesCS6A01G230000 chr3B 93.981 648 37 1 4408 5053 800269385 800270032 0.000000e+00 979.0
23 TraesCS6A01G230000 chr3B 91.224 433 30 3 5545 5976 8044869 8044444 4.090000e-162 582.0
24 TraesCS6A01G230000 chr3B 86.047 301 26 10 6937 7232 507516676 507516387 7.660000e-80 309.0
25 TraesCS6A01G230000 chr3D 92.819 1699 109 7 2719 4407 418491087 418489392 0.000000e+00 2449.0
26 TraesCS6A01G230000 chr3D 92.819 1699 109 7 2719 4407 534674272 534672577 0.000000e+00 2449.0
27 TraesCS6A01G230000 chr3D 90.767 834 73 3 1 833 173591331 173590501 0.000000e+00 1110.0
28 TraesCS6A01G230000 chr3D 92.769 567 35 3 4408 4970 418488628 418488064 0.000000e+00 815.0
29 TraesCS6A01G230000 chr3D 90.308 454 27 4 5501 5954 534671007 534670571 5.290000e-161 579.0
30 TraesCS6A01G230000 chr3D 89.868 454 29 4 5501 5954 418487822 418487386 1.140000e-157 568.0
31 TraesCS6A01G230000 chr3D 95.755 212 8 1 2719 2929 434022125 434022336 2.720000e-89 340.0
32 TraesCS6A01G230000 chr5A 95.247 1115 46 5 4794 5902 633147994 633149107 0.000000e+00 1759.0
33 TraesCS6A01G230000 chr5A 85.742 1017 64 22 4529 5504 40104542 40103566 0.000000e+00 1000.0
34 TraesCS6A01G230000 chr5A 92.556 403 28 2 1 403 702694343 702694743 1.900000e-160 577.0
35 TraesCS6A01G230000 chr5A 80.326 798 96 39 969 1720 634061206 634061988 1.490000e-151 547.0
36 TraesCS6A01G230000 chr5A 87.583 451 51 4 384 833 88063782 88064228 1.170000e-142 518.0
37 TraesCS6A01G230000 chr5A 87.594 266 29 3 569 833 702694791 702695053 9.910000e-79 305.0
38 TraesCS6A01G230000 chr2D 89.068 1363 122 17 3066 4407 283139510 283140866 0.000000e+00 1666.0
39 TraesCS6A01G230000 chr2D 93.524 664 38 3 4405 5064 283141614 283142276 0.000000e+00 983.0
40 TraesCS6A01G230000 chr4A 90.617 1247 99 11 3068 4305 599733559 599734796 0.000000e+00 1639.0
41 TraesCS6A01G230000 chr4A 90.166 783 55 8 4408 5185 643425258 643424493 0.000000e+00 1000.0
42 TraesCS6A01G230000 chr4A 90.000 330 29 3 5179 5504 643423288 643422959 2.620000e-114 424.0
43 TraesCS6A01G230000 chr4A 100.000 28 0 0 6950 6977 488112561 488112588 1.400000e-02 52.8
44 TraesCS6A01G230000 chr2B 91.148 1028 83 6 3386 4407 689133304 689132279 0.000000e+00 1387.0
45 TraesCS6A01G230000 chr2B 94.737 285 15 0 4997 5281 532470293 532470009 2.010000e-120 444.0
46 TraesCS6A01G230000 chr2B 83.918 342 32 17 6987 7311 47420816 47421151 9.910000e-79 305.0
47 TraesCS6A01G230000 chr2B 92.784 97 4 2 5318 5411 532470008 532469912 3.820000e-28 137.0
48 TraesCS6A01G230000 chr2A 91.881 973 68 7 2723 3690 44843786 44844752 0.000000e+00 1349.0
49 TraesCS6A01G230000 chr2A 92.620 664 44 3 4405 5064 103913436 103914098 0.000000e+00 950.0
50 TraesCS6A01G230000 chr2A 89.521 334 29 1 5545 5878 44845733 44846060 1.220000e-112 418.0
51 TraesCS6A01G230000 chr2A 91.824 159 7 3 2719 2871 698154080 698154238 4.770000e-52 217.0
52 TraesCS6A01G230000 chr3A 90.288 834 74 4 1 833 488106560 488107387 0.000000e+00 1085.0
53 TraesCS6A01G230000 chr3A 88.708 859 68 13 1 833 602493747 602494602 0.000000e+00 1022.0
54 TraesCS6A01G230000 chr3A 88.849 834 85 6 1 833 428611866 428612692 0.000000e+00 1018.0
55 TraesCS6A01G230000 chr3A 86.582 395 46 5 3066 3458 594035015 594034626 5.630000e-116 429.0
56 TraesCS6A01G230000 chr1D 88.969 834 66 8 1 833 214486298 214485490 0.000000e+00 1007.0
57 TraesCS6A01G230000 chr1D 84.343 396 34 18 6931 7310 463343223 463343606 5.800000e-96 363.0
58 TraesCS6A01G230000 chr1D 85.044 341 25 16 6984 7311 487170749 487171076 2.730000e-84 324.0
59 TraesCS6A01G230000 chr1B 93.534 665 38 4 4405 5064 653800537 653801201 0.000000e+00 985.0
60 TraesCS6A01G230000 chr1B 93.333 285 19 0 4997 5281 32760441 32760157 9.430000e-114 422.0
61 TraesCS6A01G230000 chr1B 89.577 307 28 3 5179 5482 483376260 483376565 3.440000e-103 387.0
62 TraesCS6A01G230000 chr1B 82.581 310 27 18 6931 7228 596944267 596943973 1.690000e-61 248.0
63 TraesCS6A01G230000 chrUn 91.702 699 39 6 4934 5629 323279403 323278721 0.000000e+00 952.0
64 TraesCS6A01G230000 chrUn 96.167 287 9 2 2719 3004 323279675 323279390 1.190000e-127 468.0
65 TraesCS6A01G230000 chrUn 90.244 41 4 0 7572 7612 18405702 18405742 4.000000e-03 54.7
66 TraesCS6A01G230000 chr5D 94.330 582 30 2 4910 5488 443658648 443659229 0.000000e+00 889.0
67 TraesCS6A01G230000 chr5D 88.987 454 32 5 5501 5954 80299062 80299497 5.360000e-151 545.0
68 TraesCS6A01G230000 chr5D 78.272 787 101 41 970 1720 506246136 506246888 7.240000e-120 442.0
69 TraesCS6A01G230000 chr5B 77.910 756 86 39 1010 1720 637126180 637126899 5.710000e-106 396.0
70 TraesCS6A01G230000 chr7B 83.548 389 48 13 6935 7315 656425413 656425033 4.510000e-92 350.0
71 TraesCS6A01G230000 chr1A 82.821 390 39 12 6931 7310 555535842 555536213 2.730000e-84 324.0
72 TraesCS6A01G230000 chr1A 82.443 393 39 13 6931 7310 555535341 555535716 4.580000e-82 316.0


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 TraesCS6A01G230000 chr6A 432532407 432540264 7857 True 14512.000000 14512 100.000000 1 7858 1 chr6A.!!$R1 7857
1 TraesCS6A01G230000 chr6A 442468435 442469263 828 True 1125.000000 1125 91.127000 1 833 1 chr6A.!!$R2 832
2 TraesCS6A01G230000 chr6D 290900711 290904432 3721 False 2979.000000 3018 95.743000 916 7858 2 chr6D.!!$F2 6942
3 TraesCS6A01G230000 chr6D 70916 73895 2979 True 1084.000000 1796 89.112000 3066 5503 2 chr6D.!!$R1 2437
4 TraesCS6A01G230000 chr6D 421048041 421050236 2195 False 983.000000 1408 91.063000 2745 5954 2 chr6D.!!$F3 3209
5 TraesCS6A01G230000 chr6B 451671933 451677098 5165 False 1865.000000 2817 93.988333 923 7858 3 chr6B.!!$F3 6935
6 TraesCS6A01G230000 chr6B 48355711 48358478 2767 False 1326.500000 1672 91.385000 3066 5064 2 chr6B.!!$F2 1998
7 TraesCS6A01G230000 chr6B 3810188 3810851 663 False 946.000000 946 92.492000 4405 5064 1 chr6B.!!$F1 659
8 TraesCS6A01G230000 chr7A 656907333 656910421 3088 False 1483.500000 2460 91.125500 2719 5954 2 chr7A.!!$F1 3235
9 TraesCS6A01G230000 chr7A 201169373 201170200 827 True 1092.000000 1092 90.419000 1 834 1 chr7A.!!$R1 833
10 TraesCS6A01G230000 chr7A 338086906 338087566 660 True 946.000000 946 92.587000 4408 5064 1 chr7A.!!$R2 656
11 TraesCS6A01G230000 chr3B 8044444 8048161 3717 True 1519.500000 2457 92.051000 2719 5976 2 chr3B.!!$R2 3257
12 TraesCS6A01G230000 chr3B 800269385 800270032 647 False 979.000000 979 93.981000 4408 5053 1 chr3B.!!$F1 645
13 TraesCS6A01G230000 chr3D 534670571 534674272 3701 True 1514.000000 2449 91.563500 2719 5954 2 chr3D.!!$R3 3235
14 TraesCS6A01G230000 chr3D 418487386 418491087 3701 True 1277.333333 2449 91.818667 2719 5954 3 chr3D.!!$R2 3235
15 TraesCS6A01G230000 chr3D 173590501 173591331 830 True 1110.000000 1110 90.767000 1 833 1 chr3D.!!$R1 832
16 TraesCS6A01G230000 chr5A 633147994 633149107 1113 False 1759.000000 1759 95.247000 4794 5902 1 chr5A.!!$F2 1108
17 TraesCS6A01G230000 chr5A 40103566 40104542 976 True 1000.000000 1000 85.742000 4529 5504 1 chr5A.!!$R1 975
18 TraesCS6A01G230000 chr5A 634061206 634061988 782 False 547.000000 547 80.326000 969 1720 1 chr5A.!!$F3 751
19 TraesCS6A01G230000 chr5A 702694343 702695053 710 False 441.000000 577 90.075000 1 833 2 chr5A.!!$F4 832
20 TraesCS6A01G230000 chr2D 283139510 283142276 2766 False 1324.500000 1666 91.296000 3066 5064 2 chr2D.!!$F1 1998
21 TraesCS6A01G230000 chr4A 599733559 599734796 1237 False 1639.000000 1639 90.617000 3068 4305 1 chr4A.!!$F2 1237
22 TraesCS6A01G230000 chr4A 643422959 643425258 2299 True 712.000000 1000 90.083000 4408 5504 2 chr4A.!!$R1 1096
23 TraesCS6A01G230000 chr2B 689132279 689133304 1025 True 1387.000000 1387 91.148000 3386 4407 1 chr2B.!!$R1 1021
24 TraesCS6A01G230000 chr2A 103913436 103914098 662 False 950.000000 950 92.620000 4405 5064 1 chr2A.!!$F1 659
25 TraesCS6A01G230000 chr2A 44843786 44846060 2274 False 883.500000 1349 90.701000 2723 5878 2 chr2A.!!$F3 3155
26 TraesCS6A01G230000 chr3A 488106560 488107387 827 False 1085.000000 1085 90.288000 1 833 1 chr3A.!!$F2 832
27 TraesCS6A01G230000 chr3A 602493747 602494602 855 False 1022.000000 1022 88.708000 1 833 1 chr3A.!!$F3 832
28 TraesCS6A01G230000 chr3A 428611866 428612692 826 False 1018.000000 1018 88.849000 1 833 1 chr3A.!!$F1 832
29 TraesCS6A01G230000 chr1D 214485490 214486298 808 True 1007.000000 1007 88.969000 1 833 1 chr1D.!!$R1 832
30 TraesCS6A01G230000 chr1B 653800537 653801201 664 False 985.000000 985 93.534000 4405 5064 1 chr1B.!!$F2 659
31 TraesCS6A01G230000 chrUn 323278721 323279675 954 True 710.000000 952 93.934500 2719 5629 2 chrUn.!!$R1 2910
32 TraesCS6A01G230000 chr5D 443658648 443659229 581 False 889.000000 889 94.330000 4910 5488 1 chr5D.!!$F2 578
33 TraesCS6A01G230000 chr5D 506246136 506246888 752 False 442.000000 442 78.272000 970 1720 1 chr5D.!!$F3 750
34 TraesCS6A01G230000 chr5B 637126180 637126899 719 False 396.000000 396 77.910000 1010 1720 1 chr5B.!!$F1 710
35 TraesCS6A01G230000 chr1A 555535341 555536213 872 False 320.000000 324 82.632000 6931 7310 2 chr1A.!!$F1 379

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
33 34 0.036010 ATTTGGAGCAGGGTGACGAG 60.036 55.000 0.00 0.0 0.00 4.18 F
418 448 0.970427 TCATGCCACTGTAGAGCGGA 60.970 55.000 0.00 0.0 0.00 5.54 F
1553 1635 1.077716 AGGCCGGTTGGTATTCAGC 60.078 57.895 1.90 0.0 37.67 4.26 F
2605 2713 1.169577 TCACTCCGAGCAGAGACTTC 58.830 55.000 5.54 0.0 37.33 3.01 F
3422 3561 0.313043 CTTGCACTTGAGGTTGCTGG 59.687 55.000 0.00 0.0 0.00 4.85 F
4261 4411 0.668401 GCTTGCTTGCACCAACATCC 60.668 55.000 0.00 0.0 0.00 3.51 F
5289 7464 2.034376 TTGTACGCCCGGCCAATT 59.966 55.556 2.24 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1322 1393 1.198094 TTCAGTCGATGGGAAGGGCA 61.198 55.000 0.00 0.00 0.00 5.36 R
1872 1980 1.531423 AGTTTGCTCAGCATGGTCAG 58.469 50.000 0.00 0.00 38.76 3.51 R
2824 2944 1.136695 CTGCAAAACTGGCCAAGTGAA 59.863 47.619 7.01 0.00 39.81 3.18 R
3780 3930 0.443869 AATGTCGTTTGCTGCTAGCG 59.556 50.000 13.27 13.27 46.26 4.26 R
4749 5667 0.584876 GTTTGTTCCAACGAGGGTCG 59.415 55.000 0.00 0.00 46.93 4.79 R
5379 7561 0.677731 TGCCGCCATTGAAGGAGAAG 60.678 55.000 2.21 0.00 0.00 2.85 R
7154 9872 0.108585 ACATTGGAGCAAGTCGTGGT 59.891 50.000 0.00 0.00 41.89 4.16 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
33 34 0.036010 ATTTGGAGCAGGGTGACGAG 60.036 55.000 0.00 0.00 0.00 4.18
44 45 3.949754 CAGGGTGACGAGGTAACATACTA 59.050 47.826 0.00 0.00 41.41 1.82
141 144 5.244785 AGATGTGATGACAATGATGCAAC 57.755 39.130 0.00 0.00 35.11 4.17
142 145 4.703093 AGATGTGATGACAATGATGCAACA 59.297 37.500 0.00 0.00 35.11 3.33
147 150 4.687018 TGATGACAATGATGCAACAAAAGC 59.313 37.500 0.00 0.00 0.00 3.51
206 209 1.946984 ACCCTCCGGATGTGTTCTTA 58.053 50.000 3.57 0.00 0.00 2.10
307 315 2.431260 TTTGCGAGCGTACGGACC 60.431 61.111 18.39 0.00 32.82 4.46
320 328 3.480133 GGACCGCTACCATGCCCT 61.480 66.667 0.00 0.00 0.00 5.19
387 395 4.668118 GTTCCCGACGGACGCCAA 62.668 66.667 17.49 0.00 38.14 4.52
418 448 0.970427 TCATGCCACTGTAGAGCGGA 60.970 55.000 0.00 0.00 0.00 5.54
486 541 2.278142 GACATTGGAATGGCGCGC 60.278 61.111 25.94 25.94 40.70 6.86
487 542 3.050166 GACATTGGAATGGCGCGCA 62.050 57.895 34.42 19.50 40.70 6.09
512 567 3.140707 TCATTTCATGTCCATATGCCCCT 59.859 43.478 0.00 0.00 0.00 4.79
521 576 4.953579 TGTCCATATGCCCCTTTTTCTTAC 59.046 41.667 0.00 0.00 0.00 2.34
553 608 3.936461 ACAGTGGGGTGCCTTATATCTA 58.064 45.455 0.00 0.00 0.00 1.98
555 610 4.913968 ACAGTGGGGTGCCTTATATCTAAT 59.086 41.667 0.00 0.00 0.00 1.73
584 639 8.449251 TTTTATGGTGTTTTACTTTAGACGGT 57.551 30.769 0.00 0.00 0.00 4.83
610 665 8.297426 TGTACATAGTAAGAGTGAGACAACAAG 58.703 37.037 0.00 0.00 0.00 3.16
626 681 7.619050 AGACAACAAGATGATGACATAGAAGT 58.381 34.615 0.00 0.00 36.82 3.01
643 698 9.244292 ACATAGAAGTTACATGTAGAGTCAAGA 57.756 33.333 5.56 0.00 31.26 3.02
649 704 7.952671 AGTTACATGTAGAGTCAAGAAGAACA 58.047 34.615 5.56 0.00 0.00 3.18
678 733 7.639062 AGAGGATAAATGATGTATGGGAAGT 57.361 36.000 0.00 0.00 0.00 3.01
713 768 9.734984 ATGATTGAGATGCTAAATGATGTATGA 57.265 29.630 0.00 0.00 0.00 2.15
714 769 9.563748 TGATTGAGATGCTAAATGATGTATGAA 57.436 29.630 0.00 0.00 0.00 2.57
733 788 4.641396 TGAAAAGAGAATGTGATGGACGT 58.359 39.130 0.00 0.00 0.00 4.34
747 802 4.452114 TGATGGACGTCAAGTTCAATGAAG 59.548 41.667 18.91 0.00 42.62 3.02
748 803 2.548057 TGGACGTCAAGTTCAATGAAGC 59.452 45.455 18.91 0.00 34.85 3.86
749 804 2.095718 GGACGTCAAGTTCAATGAAGCC 60.096 50.000 18.91 0.00 30.69 4.35
750 805 2.548057 GACGTCAAGTTCAATGAAGCCA 59.452 45.455 11.55 0.00 30.69 4.75
754 809 4.498009 CGTCAAGTTCAATGAAGCCAAGTT 60.498 41.667 0.00 0.00 0.00 2.66
755 810 4.978580 GTCAAGTTCAATGAAGCCAAGTTC 59.021 41.667 0.00 0.00 0.00 3.01
756 811 4.644234 TCAAGTTCAATGAAGCCAAGTTCA 59.356 37.500 0.00 0.00 40.68 3.18
757 812 5.126869 TCAAGTTCAATGAAGCCAAGTTCAA 59.873 36.000 0.00 0.00 39.84 2.69
758 813 5.796424 AGTTCAATGAAGCCAAGTTCAAT 57.204 34.783 0.00 0.00 39.84 2.57
759 814 5.535333 AGTTCAATGAAGCCAAGTTCAATG 58.465 37.500 0.00 0.00 39.84 2.82
761 816 5.787953 TCAATGAAGCCAAGTTCAATGAA 57.212 34.783 2.60 0.00 41.34 2.57
762 817 6.159299 TCAATGAAGCCAAGTTCAATGAAA 57.841 33.333 0.00 0.00 41.34 2.69
763 818 6.580788 TCAATGAAGCCAAGTTCAATGAAAA 58.419 32.000 0.00 0.00 41.34 2.29
764 819 6.702723 TCAATGAAGCCAAGTTCAATGAAAAG 59.297 34.615 0.00 0.00 41.34 2.27
765 820 4.947645 TGAAGCCAAGTTCAATGAAAAGG 58.052 39.130 0.00 1.32 33.41 3.11
766 821 4.648762 TGAAGCCAAGTTCAATGAAAAGGA 59.351 37.500 12.02 0.00 33.41 3.36
834 889 2.210116 ACAACACACGGACAGTCAATC 58.790 47.619 2.17 0.00 0.00 2.67
835 890 2.209273 CAACACACGGACAGTCAATCA 58.791 47.619 2.17 0.00 0.00 2.57
836 891 2.611751 CAACACACGGACAGTCAATCAA 59.388 45.455 2.17 0.00 0.00 2.57
837 892 2.210116 ACACACGGACAGTCAATCAAC 58.790 47.619 2.17 0.00 0.00 3.18
838 893 2.158957 ACACACGGACAGTCAATCAACT 60.159 45.455 2.17 0.00 0.00 3.16
839 894 3.069016 ACACACGGACAGTCAATCAACTA 59.931 43.478 2.17 0.00 0.00 2.24
840 895 4.055360 CACACGGACAGTCAATCAACTAA 58.945 43.478 2.17 0.00 0.00 2.24
841 896 4.690748 CACACGGACAGTCAATCAACTAAT 59.309 41.667 2.17 0.00 0.00 1.73
842 897 5.179368 CACACGGACAGTCAATCAACTAATT 59.821 40.000 2.17 0.00 0.00 1.40
843 898 6.367695 CACACGGACAGTCAATCAACTAATTA 59.632 38.462 2.17 0.00 0.00 1.40
844 899 6.932400 ACACGGACAGTCAATCAACTAATTAA 59.068 34.615 2.17 0.00 0.00 1.40
845 900 7.442969 ACACGGACAGTCAATCAACTAATTAAA 59.557 33.333 2.17 0.00 0.00 1.52
846 901 8.286800 CACGGACAGTCAATCAACTAATTAAAA 58.713 33.333 2.17 0.00 0.00 1.52
847 902 8.842280 ACGGACAGTCAATCAACTAATTAAAAA 58.158 29.630 2.17 0.00 0.00 1.94
848 903 9.840427 CGGACAGTCAATCAACTAATTAAAAAT 57.160 29.630 2.17 0.00 0.00 1.82
879 934 9.742144 ATTAGGAATAGAGATGTCATACTACGT 57.258 33.333 0.00 0.00 0.00 3.57
882 937 9.168451 AGGAATAGAGATGTCATACTACGTATG 57.832 37.037 0.00 7.51 44.93 2.39
883 938 8.948145 GGAATAGAGATGTCATACTACGTATGT 58.052 37.037 12.25 0.00 44.21 2.29
887 942 8.537049 AGAGATGTCATACTACGTATGTACTC 57.463 38.462 12.25 14.08 44.21 2.59
888 943 7.603404 AGAGATGTCATACTACGTATGTACTCC 59.397 40.741 12.25 7.02 44.21 3.85
889 944 6.654161 AGATGTCATACTACGTATGTACTCCC 59.346 42.308 12.25 5.42 44.21 4.30
890 945 5.933617 TGTCATACTACGTATGTACTCCCT 58.066 41.667 12.25 0.00 44.21 4.20
891 946 5.761726 TGTCATACTACGTATGTACTCCCTG 59.238 44.000 12.25 0.00 44.21 4.45
892 947 5.762218 GTCATACTACGTATGTACTCCCTGT 59.238 44.000 12.25 0.00 44.21 4.00
893 948 5.761726 TCATACTACGTATGTACTCCCTGTG 59.238 44.000 12.25 0.00 44.21 3.66
894 949 3.960571 ACTACGTATGTACTCCCTGTGT 58.039 45.455 0.00 0.00 0.00 3.72
895 950 3.944015 ACTACGTATGTACTCCCTGTGTC 59.056 47.826 0.00 0.00 0.00 3.67
896 951 2.799017 ACGTATGTACTCCCTGTGTCA 58.201 47.619 0.00 0.00 0.00 3.58
897 952 3.159472 ACGTATGTACTCCCTGTGTCAA 58.841 45.455 0.00 0.00 0.00 3.18
898 953 3.575256 ACGTATGTACTCCCTGTGTCAAA 59.425 43.478 0.00 0.00 0.00 2.69
899 954 4.039488 ACGTATGTACTCCCTGTGTCAAAA 59.961 41.667 0.00 0.00 0.00 2.44
900 955 4.992319 CGTATGTACTCCCTGTGTCAAAAA 59.008 41.667 0.00 0.00 0.00 1.94
901 956 5.642063 CGTATGTACTCCCTGTGTCAAAAAT 59.358 40.000 0.00 0.00 0.00 1.82
902 957 5.964958 ATGTACTCCCTGTGTCAAAAATG 57.035 39.130 0.00 0.00 0.00 2.32
903 958 3.568007 TGTACTCCCTGTGTCAAAAATGC 59.432 43.478 0.00 0.00 0.00 3.56
904 959 2.949447 ACTCCCTGTGTCAAAAATGCT 58.051 42.857 0.00 0.00 0.00 3.79
905 960 4.098914 ACTCCCTGTGTCAAAAATGCTA 57.901 40.909 0.00 0.00 0.00 3.49
906 961 4.666512 ACTCCCTGTGTCAAAAATGCTAT 58.333 39.130 0.00 0.00 0.00 2.97
907 962 5.079643 ACTCCCTGTGTCAAAAATGCTATT 58.920 37.500 0.00 0.00 0.00 1.73
908 963 6.245408 ACTCCCTGTGTCAAAAATGCTATTA 58.755 36.000 0.00 0.00 0.00 0.98
909 964 6.891908 ACTCCCTGTGTCAAAAATGCTATTAT 59.108 34.615 0.00 0.00 0.00 1.28
910 965 7.099266 TCCCTGTGTCAAAAATGCTATTATG 57.901 36.000 0.00 0.00 0.00 1.90
911 966 6.096705 TCCCTGTGTCAAAAATGCTATTATGG 59.903 38.462 0.00 0.00 0.00 2.74
912 967 5.750067 CCTGTGTCAAAAATGCTATTATGGC 59.250 40.000 0.00 0.00 0.00 4.40
913 968 6.278172 TGTGTCAAAAATGCTATTATGGCA 57.722 33.333 5.58 5.58 44.05 4.92
914 969 6.098679 TGTGTCAAAAATGCTATTATGGCAC 58.901 36.000 5.17 16.41 42.69 5.01
916 971 8.053664 TGTGTCAAAAATGCTATTATGGCACAG 61.054 37.037 19.16 0.00 45.26 3.66
1039 1098 1.288439 CTCTCATCGCTATGCCGCT 59.712 57.895 0.00 0.00 32.76 5.52
1263 1334 3.518998 GCTCTACAGGCTCGCCGA 61.519 66.667 1.69 0.00 41.95 5.54
1322 1393 1.525535 CCGACCTCCGTACGATCCT 60.526 63.158 18.76 0.00 36.31 3.24
1452 1534 2.505498 CGATTCGCCTCGTGAACGG 61.505 63.158 2.59 0.00 40.29 4.44
1531 1613 6.827762 AGAAGATAATTTTCAAGGCTGAGAGG 59.172 38.462 0.00 0.00 31.69 3.69
1553 1635 1.077716 AGGCCGGTTGGTATTCAGC 60.078 57.895 1.90 0.00 37.67 4.26
1585 1669 1.662629 CAGATCTGTTGTTAGGCTGCG 59.337 52.381 14.95 0.00 0.00 5.18
1587 1671 2.169352 AGATCTGTTGTTAGGCTGCGAT 59.831 45.455 0.00 0.00 0.00 4.58
1614 1722 8.801715 ATGATTTTACAATGTCTGTTTGTGAC 57.198 30.769 0.00 0.00 39.64 3.67
1722 1830 5.312895 TGTTCAACATTGGTATGCTAGTGT 58.687 37.500 0.00 0.00 35.03 3.55
1889 1997 2.224499 TGTACTGACCATGCTGAGCAAA 60.224 45.455 12.69 0.00 43.62 3.68
1901 2009 4.905429 TGCTGAGCAAACTTACCATTAGA 58.095 39.130 3.81 0.00 34.76 2.10
1926 2034 4.251268 GGTCTGGTATGTAGTTTGGTCAC 58.749 47.826 0.00 0.00 0.00 3.67
2195 2303 9.630098 CAATGCACACTGTCTCTTTATTTATTT 57.370 29.630 0.00 0.00 0.00 1.40
2200 2308 9.398170 CACACTGTCTCTTTATTTATTTGTTGG 57.602 33.333 0.00 0.00 0.00 3.77
2321 2429 3.761752 GGAAATAAACCCTGTGCTTAGCA 59.238 43.478 1.39 1.39 35.60 3.49
2371 2479 2.614057 CACACACTCCCACAAGAACTTC 59.386 50.000 0.00 0.00 0.00 3.01
2598 2706 6.479990 TCATTTGTTATAATCACTCCGAGCAG 59.520 38.462 0.00 0.00 0.00 4.24
2605 2713 1.169577 TCACTCCGAGCAGAGACTTC 58.830 55.000 5.54 0.00 37.33 3.01
2633 2741 6.870965 GTGAAGGATAGCCTGACATACTAATG 59.129 42.308 0.00 0.00 46.28 1.90
2711 2831 9.970395 CTGCAGCCTGAAAATTTAAATGATATA 57.030 29.630 0.00 0.00 0.00 0.86
2824 2944 5.304101 TCCATATCACACAAAGGCAAAAAGT 59.696 36.000 0.00 0.00 0.00 2.66
3003 3127 4.802918 GCTGTACCTTCCACTTAGCTGAAA 60.803 45.833 0.00 0.00 0.00 2.69
3008 3132 8.107095 TGTACCTTCCACTTAGCTGAAATAAAT 58.893 33.333 0.00 0.00 0.00 1.40
3204 3330 5.887754 AGGCCAAAAGAGACTATGGTTAAA 58.112 37.500 5.01 0.00 35.34 1.52
3248 3374 6.070366 AGTCCTGTCCAAAATACTACCTAACC 60.070 42.308 0.00 0.00 0.00 2.85
3416 3555 1.131638 TCTCCACTTGCACTTGAGGT 58.868 50.000 0.00 0.00 0.00 3.85
3420 3559 1.027357 CACTTGCACTTGAGGTTGCT 58.973 50.000 0.00 0.00 0.00 3.91
3421 3560 1.027357 ACTTGCACTTGAGGTTGCTG 58.973 50.000 0.00 0.00 0.00 4.41
3422 3561 0.313043 CTTGCACTTGAGGTTGCTGG 59.687 55.000 0.00 0.00 0.00 4.85
3465 3608 2.164827 TGCTGCTGCCAATGTAAATGAG 59.835 45.455 13.47 0.00 38.71 2.90
3605 3750 6.378710 AACTTCTCAAACCAAGTTAGCTTC 57.621 37.500 0.00 0.00 40.35 3.86
3608 3753 5.048846 TCTCAAACCAAGTTAGCTTCCTT 57.951 39.130 0.00 0.00 31.49 3.36
3650 3795 3.134458 CTCCTTTTTCTTCAGTCGTGCT 58.866 45.455 0.00 0.00 0.00 4.40
3719 3864 4.283978 TCTTGGTCATTGGAACATGCATTT 59.716 37.500 0.00 0.00 41.24 2.32
3728 3873 3.191162 TGGAACATGCATTTGTAGCACTC 59.809 43.478 0.00 0.00 45.95 3.51
3769 3914 2.561478 TCCTCTAGTTGTGGCCAAAC 57.439 50.000 7.24 14.58 30.94 2.93
3780 3930 1.799994 GTGGCCAAACACAATGCATTC 59.200 47.619 7.24 0.00 40.99 2.67
3781 3931 1.070038 GGCCAAACACAATGCATTCG 58.930 50.000 9.53 6.39 0.00 3.34
3788 3938 1.399440 ACACAATGCATTCGCTAGCAG 59.601 47.619 16.45 7.87 44.94 4.24
3849 3999 9.569167 GCCATATCATGAAATTTATGAGACATG 57.431 33.333 13.35 8.80 37.91 3.21
3927 4077 7.667219 CCTTGCCTATCATGTATACTTCCATTT 59.333 37.037 4.17 0.00 0.00 2.32
3965 4115 5.363868 TCCATCTCTTTAGGACATAGTGTGG 59.636 44.000 0.00 0.00 0.00 4.17
4029 4179 1.280710 TGTCCACACAATATTCCCGCT 59.719 47.619 0.00 0.00 0.00 5.52
4034 4184 3.748048 CCACACAATATTCCCGCTCTATG 59.252 47.826 0.00 0.00 0.00 2.23
4057 4207 7.340122 TGGAACATTTGACAACTACATGAAA 57.660 32.000 0.00 0.00 0.00 2.69
4060 4210 7.591426 GGAACATTTGACAACTACATGAAACTC 59.409 37.037 0.00 0.00 0.00 3.01
4082 4232 4.340950 TCTTTGGTTCAAAGGATCACCAAC 59.659 41.667 17.08 0.00 46.64 3.77
4132 4282 2.821969 GTCAAATCACCATGCAACCTCT 59.178 45.455 0.00 0.00 0.00 3.69
4139 4289 3.264193 TCACCATGCAACCTCTCAATAGT 59.736 43.478 0.00 0.00 0.00 2.12
4220 4370 7.596494 TCATATTCACTTTGGAAAGCTTCAAG 58.404 34.615 0.00 2.86 39.63 3.02
4227 4377 7.041098 TCACTTTGGAAAGCTTCAAGAATAGTC 60.041 37.037 0.00 0.00 39.63 2.59
4261 4411 0.668401 GCTTGCTTGCACCAACATCC 60.668 55.000 0.00 0.00 0.00 3.51
4268 4418 4.063529 CACCAACATCCGTGTGCT 57.936 55.556 0.00 0.00 38.92 4.40
4646 5563 6.542852 CACAACCTCGGTTACTTCATAATTG 58.457 40.000 0.21 0.00 36.46 2.32
4725 5643 2.650608 CTCTAAAACGCTTTGGTGCAC 58.349 47.619 8.80 8.80 0.00 4.57
4749 5667 6.017357 ACGATCAGTTTACCCTTTTCTTTGAC 60.017 38.462 0.00 0.00 0.00 3.18
4971 5894 2.158449 GTGAGGCACAACAGAATTCTCG 59.842 50.000 4.57 4.27 34.08 4.04
5237 7412 6.942576 AGTTTGCTTATGTACTGAACCTGATT 59.057 34.615 0.00 0.00 0.00 2.57
5272 7447 4.157246 TGGACCTGTACATGTACTGAACT 58.843 43.478 32.63 19.64 37.23 3.01
5289 7464 2.034376 TTGTACGCCCGGCCAATT 59.966 55.556 2.24 0.00 0.00 2.32
5411 7596 2.892425 CGGCAGCGATGGACTTCC 60.892 66.667 1.46 0.00 0.00 3.46
5464 7649 1.647334 CCCTACTCCTCTCCTCCGGT 61.647 65.000 0.00 0.00 0.00 5.28
5489 7674 3.011517 GCCCCTGCTCTCCTCCAA 61.012 66.667 0.00 0.00 33.53 3.53
5496 7681 2.637383 GCTCTCCTCCAACGACGGT 61.637 63.158 0.00 0.00 0.00 4.83
5533 7718 2.514824 GAATGGCAGAGGTCCCGC 60.515 66.667 0.00 0.00 0.00 6.13
5733 7918 0.967380 TCTCTCTCCGTGATGCTGCA 60.967 55.000 4.13 4.13 0.00 4.41
5848 8033 1.597663 CGGCGAAGTGTTTTCTTCAGT 59.402 47.619 0.00 0.00 42.53 3.41
5907 8092 1.670811 GCCTTTGTGTGATATGGACCG 59.329 52.381 0.00 0.00 0.00 4.79
5912 8097 1.065782 TGTGTGATATGGACCGTTGGG 60.066 52.381 0.00 0.00 40.11 4.12
5928 8113 2.962421 GTTGGGTCTGTTTTGGATGGAA 59.038 45.455 0.00 0.00 0.00 3.53
6146 8332 8.821686 TGGAAATATCTAAAATTGGCTCTTGA 57.178 30.769 0.00 0.00 0.00 3.02
6214 8400 2.721425 TTCCTCGTTTTTGTCCTGGT 57.279 45.000 0.00 0.00 0.00 4.00
6389 8583 3.317430 TCTGAGACCATCTGATGACATCG 59.683 47.826 18.92 4.42 31.52 3.84
6393 8587 5.048434 TGAGACCATCTGATGACATCGATAC 60.048 44.000 18.92 12.94 0.00 2.24
6397 8591 5.240844 ACCATCTGATGACATCGATACGTAA 59.759 40.000 18.92 0.00 0.00 3.18
6477 8671 1.627864 TTCACCGTCCTCATCTCACA 58.372 50.000 0.00 0.00 0.00 3.58
6762 8957 4.316645 TGCAGCATTAATTTGCATTGTGT 58.683 34.783 16.54 0.00 45.23 3.72
6869 9064 2.952310 GCTTTCCTGATAAGGCCGAAAT 59.048 45.455 0.00 0.00 0.00 2.17
6949 9144 6.770785 TGTACAGATGTGGAGTTTTTAAGCTT 59.229 34.615 3.48 3.48 0.00 3.74
7180 9898 3.189080 CGACTTGCTCCAATGTGATTTCA 59.811 43.478 0.00 0.00 0.00 2.69
7187 9905 5.067283 TGCTCCAATGTGATTTCATGATGAG 59.933 40.000 0.00 0.00 0.00 2.90
7417 10140 7.792374 TCAGCACTAGATAATTTTTGGCTAG 57.208 36.000 0.00 0.00 35.76 3.42
7461 10184 1.696884 GGCAAACCTCCAAATTTCCCA 59.303 47.619 0.00 0.00 0.00 4.37
7640 11908 1.065126 AGCCATACCTTCCTGCACTTC 60.065 52.381 0.00 0.00 0.00 3.01
7767 12035 2.161855 TGGCATGCCACACTTTCTTAG 58.838 47.619 35.59 0.00 41.89 2.18
7829 12097 1.244019 GCCACCAATTTCACCGAGCT 61.244 55.000 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.036010 CGTCACCCTGCTCCAAATCT 60.036 55.000 0.00 0.00 0.00 2.40
33 34 6.534079 GGTCATTGTGTCACTAGTATGTTACC 59.466 42.308 4.27 0.00 0.00 2.85
44 45 3.480470 CCTCTTTGGTCATTGTGTCACT 58.520 45.455 4.27 0.00 0.00 3.41
141 144 6.539103 GTGTTAGAGATACCCTAAGGCTTTTG 59.461 42.308 4.45 0.00 36.11 2.44
142 145 6.352823 GGTGTTAGAGATACCCTAAGGCTTTT 60.353 42.308 4.45 0.00 33.65 2.27
147 150 4.277921 GTCGGTGTTAGAGATACCCTAAGG 59.722 50.000 0.00 0.00 36.23 2.69
244 247 0.759959 TGTGGGGAAAAGCGTGTCTA 59.240 50.000 0.00 0.00 0.00 2.59
307 315 2.590007 GAGCAGGGCATGGTAGCG 60.590 66.667 2.95 0.00 40.53 4.26
320 328 2.171840 GAGTCAGGGTAGTCAAGAGCA 58.828 52.381 0.00 0.00 0.00 4.26
452 482 3.736100 CGGCGCCAGTGAAATGCA 61.736 61.111 28.98 0.00 0.00 3.96
521 576 4.638865 GGCACCCCACTGTACTAAAAATAG 59.361 45.833 0.00 0.00 0.00 1.73
572 627 9.102757 CTCTTACTATGTACACCGTCTAAAGTA 57.897 37.037 0.00 0.00 0.00 2.24
584 639 7.754851 TGTTGTCTCACTCTTACTATGTACA 57.245 36.000 0.00 0.00 0.00 2.90
626 681 9.778741 AATTGTTCTTCTTGACTCTACATGTAA 57.221 29.630 7.06 0.00 0.00 2.41
678 733 3.117398 AGCATCTCAATCATTGCCCCTTA 60.117 43.478 0.00 0.00 35.71 2.69
713 768 4.641396 TGACGTCCATCACATTCTCTTTT 58.359 39.130 14.12 0.00 0.00 2.27
714 769 4.271696 TGACGTCCATCACATTCTCTTT 57.728 40.909 14.12 0.00 0.00 2.52
733 788 4.644234 TGAACTTGGCTTCATTGAACTTGA 59.356 37.500 0.00 0.00 0.00 3.02
747 802 3.243839 TGCTCCTTTTCATTGAACTTGGC 60.244 43.478 0.00 1.86 0.00 4.52
748 803 4.589216 TGCTCCTTTTCATTGAACTTGG 57.411 40.909 0.00 2.35 0.00 3.61
749 804 5.775686 TCATGCTCCTTTTCATTGAACTTG 58.224 37.500 0.00 0.00 0.00 3.16
750 805 6.014840 ACATCATGCTCCTTTTCATTGAACTT 60.015 34.615 0.00 0.00 0.00 2.66
754 809 5.988310 AACATCATGCTCCTTTTCATTGA 57.012 34.783 0.00 0.00 0.00 2.57
755 810 5.929992 ACAAACATCATGCTCCTTTTCATTG 59.070 36.000 0.00 0.00 0.00 2.82
756 811 6.105397 ACAAACATCATGCTCCTTTTCATT 57.895 33.333 0.00 0.00 0.00 2.57
757 812 5.733620 ACAAACATCATGCTCCTTTTCAT 57.266 34.783 0.00 0.00 0.00 2.57
758 813 5.534207 AACAAACATCATGCTCCTTTTCA 57.466 34.783 0.00 0.00 0.00 2.69
759 814 6.913170 TCTAACAAACATCATGCTCCTTTTC 58.087 36.000 0.00 0.00 0.00 2.29
761 816 6.899393 TTCTAACAAACATCATGCTCCTTT 57.101 33.333 0.00 0.00 0.00 3.11
762 817 8.049117 TCTATTCTAACAAACATCATGCTCCTT 58.951 33.333 0.00 0.00 0.00 3.36
763 818 7.568349 TCTATTCTAACAAACATCATGCTCCT 58.432 34.615 0.00 0.00 0.00 3.69
764 819 7.712639 TCTCTATTCTAACAAACATCATGCTCC 59.287 37.037 0.00 0.00 0.00 4.70
765 820 8.654230 TCTCTATTCTAACAAACATCATGCTC 57.346 34.615 0.00 0.00 0.00 4.26
766 821 8.481314 TCTCTCTATTCTAACAAACATCATGCT 58.519 33.333 0.00 0.00 0.00 3.79
794 849 3.322254 TGTCACGGGCCAACAATTATTTT 59.678 39.130 4.39 0.00 0.00 1.82
799 854 0.387565 GTTGTCACGGGCCAACAATT 59.612 50.000 6.71 0.00 40.46 2.32
853 908 9.742144 ACGTAGTATGACATCTCTATTCCTAAT 57.258 33.333 0.00 0.00 41.94 1.73
874 929 3.943381 TGACACAGGGAGTACATACGTAG 59.057 47.826 0.08 0.00 0.00 3.51
875 930 3.954200 TGACACAGGGAGTACATACGTA 58.046 45.455 0.00 0.00 0.00 3.57
876 931 2.799017 TGACACAGGGAGTACATACGT 58.201 47.619 0.00 0.00 0.00 3.57
877 932 3.861276 TTGACACAGGGAGTACATACG 57.139 47.619 0.00 0.00 0.00 3.06
878 933 6.622896 GCATTTTTGACACAGGGAGTACATAC 60.623 42.308 0.00 0.00 0.00 2.39
879 934 5.414454 GCATTTTTGACACAGGGAGTACATA 59.586 40.000 0.00 0.00 0.00 2.29
880 935 4.218417 GCATTTTTGACACAGGGAGTACAT 59.782 41.667 0.00 0.00 0.00 2.29
881 936 3.568007 GCATTTTTGACACAGGGAGTACA 59.432 43.478 0.00 0.00 0.00 2.90
882 937 3.821033 AGCATTTTTGACACAGGGAGTAC 59.179 43.478 0.00 0.00 0.00 2.73
883 938 4.098914 AGCATTTTTGACACAGGGAGTA 57.901 40.909 0.00 0.00 0.00 2.59
884 939 2.949447 AGCATTTTTGACACAGGGAGT 58.051 42.857 0.00 0.00 0.00 3.85
885 940 5.649782 AATAGCATTTTTGACACAGGGAG 57.350 39.130 0.00 0.00 0.00 4.30
886 941 6.096705 CCATAATAGCATTTTTGACACAGGGA 59.903 38.462 0.00 0.00 0.00 4.20
887 942 6.275335 CCATAATAGCATTTTTGACACAGGG 58.725 40.000 0.00 0.00 0.00 4.45
888 943 5.750067 GCCATAATAGCATTTTTGACACAGG 59.250 40.000 0.00 0.00 0.00 4.00
889 944 6.254157 GTGCCATAATAGCATTTTTGACACAG 59.746 38.462 0.00 0.00 43.29 3.66
890 945 6.098679 GTGCCATAATAGCATTTTTGACACA 58.901 36.000 0.00 0.00 43.29 3.72
891 946 6.098679 TGTGCCATAATAGCATTTTTGACAC 58.901 36.000 0.00 0.00 43.29 3.67
892 947 6.152492 TCTGTGCCATAATAGCATTTTTGACA 59.848 34.615 0.00 0.00 43.29 3.58
893 948 6.473455 GTCTGTGCCATAATAGCATTTTTGAC 59.527 38.462 0.00 0.00 43.29 3.18
894 949 6.563422 GTCTGTGCCATAATAGCATTTTTGA 58.437 36.000 0.00 0.00 43.29 2.69
895 950 5.456497 CGTCTGTGCCATAATAGCATTTTTG 59.544 40.000 0.00 0.00 43.29 2.44
896 951 5.450412 CCGTCTGTGCCATAATAGCATTTTT 60.450 40.000 0.00 0.00 43.29 1.94
897 952 4.036734 CCGTCTGTGCCATAATAGCATTTT 59.963 41.667 0.00 0.00 43.29 1.82
898 953 3.565482 CCGTCTGTGCCATAATAGCATTT 59.435 43.478 0.00 0.00 43.29 2.32
899 954 3.141398 CCGTCTGTGCCATAATAGCATT 58.859 45.455 0.00 0.00 43.29 3.56
900 955 2.368548 TCCGTCTGTGCCATAATAGCAT 59.631 45.455 0.00 0.00 43.29 3.79
901 956 1.760029 TCCGTCTGTGCCATAATAGCA 59.240 47.619 0.00 0.00 38.08 3.49
902 957 2.224066 ACTCCGTCTGTGCCATAATAGC 60.224 50.000 0.00 0.00 0.00 2.97
903 958 3.735237 ACTCCGTCTGTGCCATAATAG 57.265 47.619 0.00 0.00 0.00 1.73
904 959 4.466827 TCTACTCCGTCTGTGCCATAATA 58.533 43.478 0.00 0.00 0.00 0.98
905 960 3.296854 TCTACTCCGTCTGTGCCATAAT 58.703 45.455 0.00 0.00 0.00 1.28
906 961 2.730382 TCTACTCCGTCTGTGCCATAA 58.270 47.619 0.00 0.00 0.00 1.90
907 962 2.430248 TCTACTCCGTCTGTGCCATA 57.570 50.000 0.00 0.00 0.00 2.74
908 963 1.478510 CTTCTACTCCGTCTGTGCCAT 59.521 52.381 0.00 0.00 0.00 4.40
909 964 0.888619 CTTCTACTCCGTCTGTGCCA 59.111 55.000 0.00 0.00 0.00 4.92
910 965 1.174783 TCTTCTACTCCGTCTGTGCC 58.825 55.000 0.00 0.00 0.00 5.01
911 966 3.512033 ATTCTTCTACTCCGTCTGTGC 57.488 47.619 0.00 0.00 0.00 4.57
912 967 7.759886 TGAATAAATTCTTCTACTCCGTCTGTG 59.240 37.037 4.45 0.00 37.67 3.66
913 968 7.837863 TGAATAAATTCTTCTACTCCGTCTGT 58.162 34.615 4.45 0.00 37.67 3.41
914 969 8.703604 TTGAATAAATTCTTCTACTCCGTCTG 57.296 34.615 4.45 0.00 37.67 3.51
1039 1098 1.842920 TCAGGAGGAAGCACAGGCA 60.843 57.895 0.00 0.00 44.61 4.75
1322 1393 1.198094 TTCAGTCGATGGGAAGGGCA 61.198 55.000 0.00 0.00 0.00 5.36
1452 1534 2.622064 ATCCTCAACGGCATTAGGAC 57.378 50.000 0.00 0.00 40.83 3.85
1553 1635 6.867662 ACAACAGATCTGGTTAAAGAGTTG 57.132 37.500 26.08 18.45 36.59 3.16
1585 1669 9.630098 ACAAACAGACATTGTAAAATCATCATC 57.370 29.630 0.00 0.00 39.73 2.92
1587 1671 8.628280 TCACAAACAGACATTGTAAAATCATCA 58.372 29.630 0.00 0.00 39.73 3.07
1614 1722 8.040716 ACAAGAACATAAACCTAAATTCTCGG 57.959 34.615 0.00 0.00 0.00 4.63
1722 1830 8.017418 AGGGAAAATGAACTGTAATGAAACAA 57.983 30.769 0.00 0.00 0.00 2.83
1872 1980 1.531423 AGTTTGCTCAGCATGGTCAG 58.469 50.000 0.00 0.00 38.76 3.51
1901 2009 5.013704 TGACCAAACTACATACCAGACCAAT 59.986 40.000 0.00 0.00 0.00 3.16
1926 2034 6.211587 TCATTCTATGGGATTGCACAAAAG 57.788 37.500 0.00 0.00 0.00 2.27
2321 2429 6.045072 TGTTAGTGGATATGGACGAGTTTT 57.955 37.500 0.00 0.00 0.00 2.43
2605 2713 3.616956 TGTCAGGCTATCCTTCACAAG 57.383 47.619 0.00 0.00 41.93 3.16
2753 2873 3.550820 TGAAGAGCCTAAAGTTGCAACA 58.449 40.909 30.11 10.05 0.00 3.33
2824 2944 1.136695 CTGCAAAACTGGCCAAGTGAA 59.863 47.619 7.01 0.00 39.81 3.18
2934 3058 8.424274 TGTATGTTGAAACAGCTATAGACATG 57.576 34.615 3.21 1.30 43.04 3.21
2936 3060 7.041721 CCTGTATGTTGAAACAGCTATAGACA 58.958 38.462 3.21 0.00 43.04 3.41
3064 3189 5.945784 AGCCTTTCAATGTCAAATGCTACTA 59.054 36.000 0.00 0.00 34.22 1.82
3204 3330 7.116736 CAGGACTAACTACAATATTTTGGGGT 58.883 38.462 0.89 0.00 37.15 4.95
3225 3351 5.786457 TGGTTAGGTAGTATTTTGGACAGGA 59.214 40.000 0.00 0.00 0.00 3.86
3446 3589 4.707030 TTCTCATTTACATTGGCAGCAG 57.293 40.909 0.00 0.00 0.00 4.24
3504 3647 8.651589 AAGGTAAGCTGCAGTATGTATCTATA 57.348 34.615 16.64 0.00 39.31 1.31
3505 3648 7.546250 AAGGTAAGCTGCAGTATGTATCTAT 57.454 36.000 16.64 0.00 39.31 1.98
3508 3651 5.277538 GCAAAGGTAAGCTGCAGTATGTATC 60.278 44.000 16.64 3.15 39.31 2.24
3587 3732 5.066593 AGAAGGAAGCTAACTTGGTTTGAG 58.933 41.667 7.48 0.00 35.82 3.02
3608 3753 9.822727 AAGGAGGTTCCATCTAAAAATTTAAGA 57.177 29.630 5.82 5.82 39.61 2.10
3625 3770 4.024809 CACGACTGAAGAAAAAGGAGGTTC 60.025 45.833 0.00 0.00 0.00 3.62
3650 3795 3.754965 AGCCAATGAGTTGCTTAGTTCA 58.245 40.909 0.00 0.00 33.90 3.18
3662 3807 0.530744 ATGTGCAGCAAGCCAATGAG 59.469 50.000 0.00 0.00 44.83 2.90
3719 3864 1.202302 GCATCAGCTACGAGTGCTACA 60.202 52.381 0.00 0.00 38.92 2.74
3728 3873 5.333645 GGATAAACTCAATGCATCAGCTACG 60.334 44.000 0.00 0.00 42.74 3.51
3769 3914 1.858798 GCTGCTAGCGAATGCATTGTG 60.859 52.381 18.59 10.26 46.23 3.33
3780 3930 0.443869 AATGTCGTTTGCTGCTAGCG 59.556 50.000 13.27 13.27 46.26 4.26
3781 3931 1.527793 CGAATGTCGTTTGCTGCTAGC 60.528 52.381 8.10 8.10 37.09 3.42
3788 3938 0.721718 CTCTCCCGAATGTCGTTTGC 59.278 55.000 0.00 0.00 38.40 3.68
3927 4077 2.946329 GAGATGGACTAGAGAAGCACGA 59.054 50.000 0.00 0.00 0.00 4.35
3960 4110 2.621055 TGTAAAGACATTGCCACCACAC 59.379 45.455 0.00 0.00 0.00 3.82
4029 4179 8.100164 TCATGTAGTTGTCAAATGTTCCATAGA 58.900 33.333 0.00 0.00 0.00 1.98
4034 4184 7.425606 AGTTTCATGTAGTTGTCAAATGTTCC 58.574 34.615 0.00 0.00 0.00 3.62
4060 4210 4.935352 TTGGTGATCCTTTGAACCAAAG 57.065 40.909 9.90 11.35 46.83 2.77
4082 4232 1.365633 GAGGAGGAGCGCATAGTGG 59.634 63.158 11.47 0.00 0.00 4.00
4139 4289 8.300286 TGGATGAAAATAACAAATTCGCTGTTA 58.700 29.630 4.19 4.19 42.00 2.41
4220 4370 4.326548 GCAAAGTGTACACTCCGACTATTC 59.673 45.833 28.04 8.09 41.58 1.75
4227 4377 1.069906 GCAAGCAAAGTGTACACTCCG 60.070 52.381 28.04 21.50 41.58 4.63
4261 4411 4.324402 GCCAAGAATAAAAATGAGCACACG 59.676 41.667 0.00 0.00 0.00 4.49
4308 4458 9.129209 GTAAAAAGAAGAAAGGAATTGGAATCG 57.871 33.333 0.00 0.00 0.00 3.34
4341 4491 6.638096 TTCTTGATGCATTTTGAGAGAACA 57.362 33.333 0.00 0.00 0.00 3.18
4646 5563 2.666596 AATTGGATCGAGAGGCCGGC 62.667 60.000 21.18 21.18 0.00 6.13
4725 5643 6.371389 GTCAAAGAAAAGGGTAAACTGATCG 58.629 40.000 0.00 0.00 0.00 3.69
4749 5667 0.584876 GTTTGTTCCAACGAGGGTCG 59.415 55.000 0.00 0.00 46.93 4.79
4818 5738 1.338200 ACCGGCTTTGATGTGAGAGAC 60.338 52.381 0.00 0.00 0.00 3.36
4971 5894 3.332919 TGAGTGCTCTGCTCTGAAAATC 58.667 45.455 0.00 0.00 32.35 2.17
5237 7412 7.152942 TGTACAGGTCCATATACTAGTACCA 57.847 40.000 4.31 0.00 33.06 3.25
5272 7447 2.034376 AATTGGCCGGGCGTACAA 59.966 55.556 24.45 12.46 0.00 2.41
5296 7471 2.113860 TGTAGCTCATGAGGTTTGGC 57.886 50.000 30.69 18.48 40.09 4.52
5375 7557 1.339055 CGCCATTGAAGGAGAAGTCCA 60.339 52.381 0.00 0.00 46.80 4.02
5377 7559 1.373570 CCGCCATTGAAGGAGAAGTC 58.626 55.000 0.00 0.00 0.00 3.01
5378 7560 0.678048 GCCGCCATTGAAGGAGAAGT 60.678 55.000 2.21 0.00 0.00 3.01
5379 7561 0.677731 TGCCGCCATTGAAGGAGAAG 60.678 55.000 2.21 0.00 0.00 2.85
5411 7596 1.078426 AAGATCGTTCCGCCAAGGG 60.078 57.895 0.00 0.00 41.52 3.95
5489 7674 3.598715 TTGAGGTCGCACCGTCGT 61.599 61.111 0.00 0.00 44.90 4.34
5496 7681 1.375908 GCATCCAGTTGAGGTCGCA 60.376 57.895 0.00 0.00 0.00 5.10
5829 8014 2.031944 GGACTGAAGAAAACACTTCGCC 60.032 50.000 0.00 0.00 46.21 5.54
5848 8033 2.031465 GTTTTGGACGAGGGCGGA 59.969 61.111 0.00 0.00 43.17 5.54
5907 8092 2.593026 TCCATCCAAAACAGACCCAAC 58.407 47.619 0.00 0.00 0.00 3.77
5912 8097 6.331369 TCTTCATTTCCATCCAAAACAGAC 57.669 37.500 0.00 0.00 0.00 3.51
5928 8113 4.320494 CGTTGCAACTTTAGGCTCTTCATT 60.320 41.667 26.09 0.00 0.00 2.57
6146 8332 6.374417 AGGTCTGTGTATAGAACCAATGTT 57.626 37.500 0.00 0.00 34.91 2.71
6332 8526 5.221204 TGCACATTTCTGCTTTGTGAATACA 60.221 36.000 6.47 0.00 42.59 2.29
6389 8583 2.934553 GACAGGTTTGGGCTTACGTATC 59.065 50.000 0.00 0.00 0.00 2.24
6393 8587 1.156736 CAGACAGGTTTGGGCTTACG 58.843 55.000 0.00 0.00 0.00 3.18
6477 8671 9.723601 TGCTATGCAATTTTCTAAATTCCTTTT 57.276 25.926 0.00 0.00 34.76 2.27
6570 8764 1.001181 TGGCCAAGAGCAAAGAAATGC 59.999 47.619 0.61 0.00 46.50 3.56
6762 8957 5.010922 GGAAATATGGTGCTATTGATGCCAA 59.989 40.000 0.00 0.00 36.61 4.52
6811 9006 1.538512 TGCTCAATTCTGCAGCTTCAC 59.461 47.619 9.47 0.00 34.84 3.18
7154 9872 0.108585 ACATTGGAGCAAGTCGTGGT 59.891 50.000 0.00 0.00 41.89 4.16
7180 9898 5.339008 AAGTGCATGCAAATTCTCATCAT 57.661 34.783 24.58 0.00 0.00 2.45
7187 9905 3.307674 TGTTCGAAGTGCATGCAAATTC 58.692 40.909 24.58 25.55 0.00 2.17
7258 9981 7.180322 TGCTCCTGCCATGAAAAATATAAAA 57.820 32.000 0.00 0.00 38.71 1.52
7259 9982 6.788598 TGCTCCTGCCATGAAAAATATAAA 57.211 33.333 0.00 0.00 38.71 1.40
7262 9985 5.881923 AATGCTCCTGCCATGAAAAATAT 57.118 34.783 0.00 0.00 38.71 1.28
7267 9990 2.494471 CTCAAATGCTCCTGCCATGAAA 59.506 45.455 0.00 0.00 38.71 2.69
7338 10061 1.688735 AGCTGCGACTAATAGGATGCA 59.311 47.619 0.00 0.00 0.00 3.96
7339 10062 2.064762 CAGCTGCGACTAATAGGATGC 58.935 52.381 0.00 0.00 0.00 3.91
7340 10063 3.377346 ACAGCTGCGACTAATAGGATG 57.623 47.619 15.27 0.00 0.00 3.51
7341 10064 3.889538 TGTACAGCTGCGACTAATAGGAT 59.110 43.478 15.27 0.00 0.00 3.24
7343 10066 3.181490 TGTGTACAGCTGCGACTAATAGG 60.181 47.826 15.27 0.00 0.00 2.57
7640 11908 3.739519 GCATGGTAGAGTAAGAGGCTGTG 60.740 52.174 0.00 0.00 0.00 3.66
7754 12022 2.457366 AGCGACCTAAGAAAGTGTGG 57.543 50.000 0.00 0.00 0.00 4.17
7767 12035 1.421410 CTACGGCATGTGAAGCGACC 61.421 60.000 0.00 0.00 0.00 4.79
7829 12097 7.341445 ACTAAGTTGTCAAAAGCCACAAATA 57.659 32.000 0.00 0.00 34.33 1.40


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

AutoCloner maintained by Alex Coulton.