Multiple sequence alignment - TraesCS3D01G155500

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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 TraesCS3D01G155500 chr3D 100.000 6063 0 0 1 6063 122589052 122595114 0.000000e+00 11197.0
1 TraesCS3D01G155500 chr3D 89.110 854 37 18 1 841 123291119 123290309 0.000000e+00 1011.0
2 TraesCS3D01G155500 chr3D 94.521 365 17 3 5701 6063 136563571 136563934 1.480000e-155 560.0
3 TraesCS3D01G155500 chr3D 90.716 377 20 8 5701 6063 583369023 583369398 7.060000e-134 488.0
4 TraesCS3D01G155500 chr3D 93.103 87 6 0 3453 3539 122592417 122592503 1.770000e-25 128.0
5 TraesCS3D01G155500 chr3D 93.103 87 6 0 3366 3452 122592504 122592590 1.770000e-25 128.0
6 TraesCS3D01G155500 chr3D 94.000 50 3 0 4445 4494 122593403 122593452 6.520000e-10 76.8
7 TraesCS3D01G155500 chr3D 94.000 50 3 0 4352 4401 122593496 122593545 6.520000e-10 76.8
8 TraesCS3D01G155500 chr3A 95.882 2501 84 10 1162 3655 128302776 128305264 0.000000e+00 4030.0
9 TraesCS3D01G155500 chr3A 92.139 1870 62 24 3647 5453 128307293 128309140 0.000000e+00 2560.0
10 TraesCS3D01G155500 chr3A 97.377 305 7 1 842 1145 128302168 128302472 9.010000e-143 518.0
11 TraesCS3D01G155500 chr3A 91.525 236 18 2 5472 5705 128309195 128309430 2.110000e-84 324.0
12 TraesCS3D01G155500 chr3A 94.253 87 4 1 3453 3539 128304976 128305061 1.370000e-26 132.0
13 TraesCS3D01G155500 chr3A 94.000 50 3 0 4445 4494 128308035 128308084 6.520000e-10 76.8
14 TraesCS3D01G155500 chr3B 96.462 2431 79 5 1191 3615 174247794 174250223 0.000000e+00 4006.0
15 TraesCS3D01G155500 chr3B 93.589 1903 63 24 3603 5453 174250268 174252163 0.000000e+00 2784.0
16 TraesCS3D01G155500 chr3B 91.117 349 27 4 5704 6050 595427098 595426752 2.560000e-128 470.0
17 TraesCS3D01G155500 chr3B 96.094 256 10 0 842 1097 174247222 174247477 9.400000e-113 418.0
18 TraesCS3D01G155500 chr3B 94.624 186 8 2 5522 5705 174252184 174252369 2.770000e-73 287.0
19 TraesCS3D01G155500 chr3B 88.412 233 16 5 5704 5925 550022241 550022473 2.790000e-68 270.0
20 TraesCS3D01G155500 chr3B 93.103 87 6 0 3453 3539 174249974 174250060 1.770000e-25 128.0
21 TraesCS3D01G155500 chr3B 93.976 83 5 0 3366 3448 174250061 174250143 6.380000e-25 126.0
22 TraesCS3D01G155500 chr3B 94.000 50 3 0 4445 4494 174251052 174251101 6.520000e-10 76.8
23 TraesCS3D01G155500 chr7A 96.044 2174 58 10 3388 5536 594698075 594700245 0.000000e+00 3513.0
24 TraesCS3D01G155500 chr7A 96.007 1102 33 7 2299 3400 594675823 594676913 0.000000e+00 1781.0
25 TraesCS3D01G155500 chr7A 96.884 1059 32 1 1245 2302 594667807 594668865 0.000000e+00 1772.0
26 TraesCS3D01G155500 chr7A 97.810 274 6 0 850 1123 594667227 594667500 1.980000e-129 473.0
27 TraesCS3D01G155500 chr7A 96.571 175 5 1 5537 5710 594701599 594701773 7.690000e-74 289.0
28 TraesCS3D01G155500 chr7A 85.556 270 36 3 155 423 63474723 63474456 4.630000e-71 279.0
29 TraesCS3D01G155500 chr7A 97.143 35 1 0 3453 3487 594676879 594676913 6.560000e-05 60.2
30 TraesCS3D01G155500 chr4B 86.907 611 57 11 79 668 228459944 228460552 0.000000e+00 664.0
31 TraesCS3D01G155500 chr5A 88.376 542 41 13 79 601 365138457 365138995 3.080000e-177 632.0
32 TraesCS3D01G155500 chr6D 91.170 453 24 4 397 839 119509371 119509817 8.700000e-168 601.0
33 TraesCS3D01G155500 chr6D 92.182 307 18 1 2 302 119508722 119509028 4.340000e-116 429.0
34 TraesCS3D01G155500 chr1D 94.247 365 19 2 5701 6063 291490521 291490157 1.910000e-154 556.0
35 TraesCS3D01G155500 chr7B 91.094 393 27 5 5679 6063 89426812 89427204 5.380000e-145 525.0
36 TraesCS3D01G155500 chr6B 92.412 369 22 4 5701 6063 695475068 695474700 6.960000e-144 521.0
37 TraesCS3D01G155500 chr6B 91.057 369 24 7 5702 6062 33631788 33632155 1.960000e-134 490.0
38 TraesCS3D01G155500 chr6B 86.701 391 44 8 33 420 322065608 322065223 1.560000e-115 427.0
39 TraesCS3D01G155500 chr2B 91.826 367 27 3 5699 6063 77484430 77484795 5.420000e-140 508.0
40 TraesCS3D01G155500 chr2B 92.281 285 19 3 5705 5988 607317779 607317497 9.470000e-108 401.0
41 TraesCS3D01G155500 chr6A 85.606 264 33 5 155 417 189427469 189427728 7.740000e-69 272.0
42 TraesCS3D01G155500 chr1A 84.815 270 39 2 155 423 522884546 522884278 2.790000e-68 270.0
43 TraesCS3D01G155500 chr2A 85.227 264 35 4 155 417 554450208 554450468 1.000000e-67 268.0
44 TraesCS3D01G155500 chrUn 94.845 97 5 0 5967 6063 68202601 68202505 1.050000e-32 152.0


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 TraesCS3D01G155500 chr3D 122589052 122595114 6062 False 2321.320000 11197 94.841200 1 6063 5 chr3D.!!$F3 6062
1 TraesCS3D01G155500 chr3D 123290309 123291119 810 True 1011.000000 1011 89.110000 1 841 1 chr3D.!!$R1 840
2 TraesCS3D01G155500 chr3A 128302168 128309430 7262 False 1273.466667 4030 94.196000 842 5705 6 chr3A.!!$F1 4863
3 TraesCS3D01G155500 chr3B 174247222 174252369 5147 False 1117.971429 4006 94.549714 842 5705 7 chr3B.!!$F2 4863
4 TraesCS3D01G155500 chr7A 594698075 594701773 3698 False 1901.000000 3513 96.307500 3388 5710 2 chr7A.!!$F3 2322
5 TraesCS3D01G155500 chr7A 594667227 594668865 1638 False 1122.500000 1772 97.347000 850 2302 2 chr7A.!!$F1 1452
6 TraesCS3D01G155500 chr7A 594675823 594676913 1090 False 920.600000 1781 96.575000 2299 3487 2 chr7A.!!$F2 1188
7 TraesCS3D01G155500 chr4B 228459944 228460552 608 False 664.000000 664 86.907000 79 668 1 chr4B.!!$F1 589
8 TraesCS3D01G155500 chr5A 365138457 365138995 538 False 632.000000 632 88.376000 79 601 1 chr5A.!!$F1 522
9 TraesCS3D01G155500 chr6D 119508722 119509817 1095 False 515.000000 601 91.676000 2 839 2 chr6D.!!$F1 837

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
381 401 0.036388 TGATGGAGCTTGACGGAACC 60.036 55.000 0.00 0.00 0.00 3.62 F
385 405 0.175989 GGAGCTTGACGGAACCCTAG 59.824 60.000 0.00 0.00 0.00 3.02 F
449 755 0.248949 GAACCCTAGATGACGCCGAC 60.249 60.000 0.00 0.00 0.00 4.79 F
638 946 0.327964 ATGAAGAGGGAGGAAGGGGG 60.328 60.000 0.00 0.00 0.00 5.40 F
1050 1368 0.617413 TAGTCCTCCTCGTCGACCTT 59.383 55.000 10.58 0.00 0.00 3.50 F
2593 3199 1.383664 TCAGAGGAGGATGGGGCTG 60.384 63.158 0.00 0.00 0.00 4.85 F
3234 3849 0.610232 CTTGGCCCAGACTTTGAGGG 60.610 60.000 0.00 0.00 45.68 4.30 F
4078 6806 0.728542 TGCTGACATTGTAGCGCATG 59.271 50.000 11.47 7.08 42.74 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 2328 0.252650 CCCCCACACCCAAATCCAAT 60.253 55.000 0.0 0.0 0.00 3.16 R
1981 2586 0.683973 CTGTCCACAGCTCCTTCACT 59.316 55.000 0.0 0.0 37.15 3.41 R
2201 2807 1.728971 CAGTGCCATTCTTCTCGACAC 59.271 52.381 0.0 0.0 0.00 3.67 R
2593 3199 1.195448 CACCGAACAGTTGACATGAGC 59.805 52.381 0.0 0.0 0.00 4.26 R
2808 3414 1.021202 CGACAGACAAGCCAACCAAA 58.979 50.000 0.0 0.0 0.00 3.28 R
3641 4313 2.676632 TGCATGATCAATTTGTGGGC 57.323 45.000 0.0 0.0 0.00 5.36 R
5050 7823 0.304705 CTTTCGTTCACACGCTGCTT 59.695 50.000 0.0 0.0 46.70 3.91 R
5822 10002 0.107831 CTCCGTTTGTGGGAGTCCAA 59.892 55.000 12.3 0.0 46.04 3.53 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
116 123 3.584848 ACCCTCCTACCATCATTATGCTC 59.415 47.826 0.00 0.00 0.00 4.26
157 164 3.532641 ATTCTGAAGGCAACCCTCTTT 57.467 42.857 0.00 0.00 41.90 2.52
180 187 2.206576 AGCCTCAGATTCACCCAAAC 57.793 50.000 0.00 0.00 0.00 2.93
181 188 1.707427 AGCCTCAGATTCACCCAAACT 59.293 47.619 0.00 0.00 0.00 2.66
285 292 2.107366 TCGCCTTGATCTGGTGATACA 58.893 47.619 14.57 0.00 38.95 2.29
293 300 4.967036 TGATCTGGTGATACAACACACAA 58.033 39.130 0.00 0.00 41.88 3.33
306 326 3.740044 ACACACAAAGAACACGAACAG 57.260 42.857 0.00 0.00 0.00 3.16
307 327 2.159572 ACACACAAAGAACACGAACAGC 60.160 45.455 0.00 0.00 0.00 4.40
328 348 2.594592 ACAAGAACACAGCGGGGC 60.595 61.111 0.00 0.00 0.00 5.80
365 385 4.899502 ACCTTGAAGATGACGAACTTGAT 58.100 39.130 0.00 0.00 0.00 2.57
376 396 1.391485 CGAACTTGATGGAGCTTGACG 59.609 52.381 0.00 0.00 0.00 4.35
377 397 1.734465 GAACTTGATGGAGCTTGACGG 59.266 52.381 0.00 0.00 0.00 4.79
378 398 0.976641 ACTTGATGGAGCTTGACGGA 59.023 50.000 0.00 0.00 0.00 4.69
379 399 1.347707 ACTTGATGGAGCTTGACGGAA 59.652 47.619 0.00 0.00 0.00 4.30
380 400 1.734465 CTTGATGGAGCTTGACGGAAC 59.266 52.381 0.00 0.00 0.00 3.62
381 401 0.036388 TGATGGAGCTTGACGGAACC 60.036 55.000 0.00 0.00 0.00 3.62
382 402 0.744771 GATGGAGCTTGACGGAACCC 60.745 60.000 0.00 0.00 0.00 4.11
383 403 1.201429 ATGGAGCTTGACGGAACCCT 61.201 55.000 0.00 0.00 0.00 4.34
384 404 0.543410 TGGAGCTTGACGGAACCCTA 60.543 55.000 0.00 0.00 0.00 3.53
385 405 0.175989 GGAGCTTGACGGAACCCTAG 59.824 60.000 0.00 0.00 0.00 3.02
386 406 1.183549 GAGCTTGACGGAACCCTAGA 58.816 55.000 0.00 0.00 0.00 2.43
387 407 0.896226 AGCTTGACGGAACCCTAGAC 59.104 55.000 0.00 0.00 0.00 2.59
388 408 0.458025 GCTTGACGGAACCCTAGACG 60.458 60.000 0.00 0.00 0.00 4.18
389 409 0.458025 CTTGACGGAACCCTAGACGC 60.458 60.000 0.00 0.00 0.00 5.19
390 410 2.101770 GACGGAACCCTAGACGCG 59.898 66.667 3.53 3.53 0.00 6.01
391 411 2.674380 ACGGAACCCTAGACGCGT 60.674 61.111 13.85 13.85 0.00 6.01
392 412 2.202570 CGGAACCCTAGACGCGTG 60.203 66.667 20.70 3.63 0.00 5.34
393 413 2.183555 GGAACCCTAGACGCGTGG 59.816 66.667 20.70 15.12 0.00 4.94
394 414 2.183555 GAACCCTAGACGCGTGGG 59.816 66.667 26.75 26.75 46.07 4.61
395 415 4.078516 AACCCTAGACGCGTGGGC 62.079 66.667 27.91 10.54 44.56 5.36
444 750 3.430929 CCTTGAAGGAACCCTAGATGACG 60.431 52.174 4.95 0.00 37.67 4.35
445 751 1.480954 TGAAGGAACCCTAGATGACGC 59.519 52.381 0.00 0.00 31.13 5.19
446 752 0.831307 AAGGAACCCTAGATGACGCC 59.169 55.000 0.00 0.00 31.13 5.68
447 753 1.067582 GGAACCCTAGATGACGCCG 59.932 63.158 0.00 0.00 0.00 6.46
448 754 1.389609 GGAACCCTAGATGACGCCGA 61.390 60.000 0.00 0.00 0.00 5.54
449 755 0.248949 GAACCCTAGATGACGCCGAC 60.249 60.000 0.00 0.00 0.00 4.79
468 774 3.744719 CCGACGCCAACGAGGAGA 61.745 66.667 9.03 0.00 43.93 3.71
516 824 1.719709 CGACGACGTCAGCCAGATA 59.280 57.895 26.26 0.00 32.09 1.98
638 946 0.327964 ATGAAGAGGGAGGAAGGGGG 60.328 60.000 0.00 0.00 0.00 5.40
699 1007 2.689034 AAGAGGAAGGGGGAGGCG 60.689 66.667 0.00 0.00 0.00 5.52
721 1029 2.035449 TCTCTGGAGCGACGAAAGAAAA 59.965 45.455 0.00 0.00 0.00 2.29
781 1089 1.701292 ACAGGTAGTAAAAAGGCCGGT 59.299 47.619 1.90 0.00 0.00 5.28
1050 1368 0.617413 TAGTCCTCCTCGTCGACCTT 59.383 55.000 10.58 0.00 0.00 3.50
1593 2198 1.685224 CAGGGGCATACAGGTGTGT 59.315 57.895 0.00 0.00 41.06 3.72
1723 2328 2.043248 GGCTCGTCTGGGGAGGTA 60.043 66.667 0.00 0.00 32.10 3.08
1834 2439 2.289382 TGCGAGGTTGAGATTGTTAGCA 60.289 45.455 0.00 0.00 0.00 3.49
1907 2512 1.480498 GGTGTGTGAGGTGGGGAATTT 60.480 52.381 0.00 0.00 0.00 1.82
1921 2526 3.009723 GGGAATTTCGAGCAGTTGATGA 58.990 45.455 0.00 0.00 0.00 2.92
1980 2585 2.053244 CAGGATAGGAGCAAGGGTGAT 58.947 52.381 0.00 0.00 0.00 3.06
1981 2586 3.242867 CAGGATAGGAGCAAGGGTGATA 58.757 50.000 0.00 0.00 0.00 2.15
2180 2786 1.975680 TGGCCTTCTCGTACCTTTCTT 59.024 47.619 3.32 0.00 0.00 2.52
2201 2807 7.677041 TTTCTTGATGAACTATGCATTACTGCG 60.677 37.037 3.54 0.00 41.98 5.18
2261 2867 2.744202 CGAAGAGTCCTGAAACATTGGG 59.256 50.000 0.00 0.00 0.00 4.12
2505 3111 5.940470 AGTGAAATTGTCATCTCTTGGTACC 59.060 40.000 4.43 4.43 38.90 3.34
2509 3115 5.762179 ATTGTCATCTCTTGGTACCTCAA 57.238 39.130 14.36 0.00 0.00 3.02
2522 3128 3.118884 GGTACCTCAACGAGCCTTCATAA 60.119 47.826 4.06 0.00 0.00 1.90
2593 3199 1.383664 TCAGAGGAGGATGGGGCTG 60.384 63.158 0.00 0.00 0.00 4.85
2808 3414 3.695830 TTGGGAAATCTAGCTGAACGT 57.304 42.857 0.00 0.00 0.00 3.99
2884 3490 7.121759 CAGTGAGATATTTTGAACACAGGGAAT 59.878 37.037 0.00 0.00 0.00 3.01
2940 3546 5.582269 CGAAGCTTCCATTATTCTGTTGAGA 59.418 40.000 20.62 0.00 0.00 3.27
2990 3596 5.068198 ACAAAGACAACAATTCAGCATCTGT 59.932 36.000 0.00 0.00 32.61 3.41
3017 3623 7.040478 TGGATCAGAACAAACCTCAAAATACAG 60.040 37.037 0.00 0.00 0.00 2.74
3093 3701 4.828939 CAGCCCTGCAATTATTTCCTATGA 59.171 41.667 0.00 0.00 0.00 2.15
3234 3849 0.610232 CTTGGCCCAGACTTTGAGGG 60.610 60.000 0.00 0.00 45.68 4.30
3310 3925 3.577805 ATAAACCTCCAAGGGGATTCG 57.422 47.619 0.00 0.00 43.91 3.34
3343 3958 7.497579 TCTGACAGTATTGTTAAGTTTGCTGAA 59.502 33.333 1.59 0.00 37.76 3.02
3439 4054 2.089980 GGCTCTGTTGATGCTTGTGAT 58.910 47.619 0.00 0.00 0.00 3.06
3523 4138 4.574013 ACTATTAGCTCTGTTGATGCTTGC 59.426 41.667 0.00 0.00 38.15 4.01
3569 4184 9.702494 ATAAGTAGTTTTGTAAGGTACAGTGAC 57.298 33.333 0.00 0.00 40.24 3.67
3572 4187 5.663456 AGTTTTGTAAGGTACAGTGACGAA 58.337 37.500 0.00 0.00 40.24 3.85
3641 4313 8.870160 TTCAAGAAAATTGTACAAGGAACATG 57.130 30.769 14.65 9.15 0.00 3.21
3952 6666 5.244402 TGCTTCAGTTCCAATCATGTGAAAT 59.756 36.000 0.00 0.00 0.00 2.17
4073 6798 3.498927 AAGCATTGCTGACATTGTAGC 57.501 42.857 12.82 9.80 39.62 3.58
4078 6806 0.728542 TGCTGACATTGTAGCGCATG 59.271 50.000 11.47 7.08 42.74 4.06
4079 6807 0.729116 GCTGACATTGTAGCGCATGT 59.271 50.000 11.47 10.91 0.00 3.21
4080 6808 1.131126 GCTGACATTGTAGCGCATGTT 59.869 47.619 11.47 0.00 0.00 2.71
4438 7211 7.215789 TCTACGGTGACACAAAGGTTTAAATA 58.784 34.615 8.08 0.00 0.00 1.40
4666 7439 1.676384 GAGCAGCCAGAGGAACTGT 59.324 57.895 0.00 0.00 44.40 3.55
5269 8043 0.831307 GTATGTCCTGTCACCCCTCC 59.169 60.000 0.00 0.00 0.00 4.30
5278 8062 3.499563 CCTGTCACCCCTCCAAAAATGTA 60.500 47.826 0.00 0.00 0.00 2.29
5279 8063 4.344104 CTGTCACCCCTCCAAAAATGTAT 58.656 43.478 0.00 0.00 0.00 2.29
5296 8080 9.715121 AAAAATGTATTGTCTTCTTCTACGGTA 57.285 29.630 0.00 0.00 0.00 4.02
5300 8084 7.833786 TGTATTGTCTTCTTCTACGGTAATGT 58.166 34.615 0.00 0.00 0.00 2.71
5325 8109 4.282703 ACTTCTTTTCGGCTGACTACCTTA 59.717 41.667 0.00 0.00 0.00 2.69
5334 8118 2.034812 GCTGACTACCTTATGCTAGCGT 59.965 50.000 15.08 15.08 0.00 5.07
5335 8119 3.491104 GCTGACTACCTTATGCTAGCGTT 60.491 47.826 16.03 4.88 0.00 4.84
5705 9885 5.939764 TCCTTATTGCAGAAGCTCTAAGA 57.060 39.130 5.18 0.00 42.74 2.10
5721 9901 4.625800 GAGCATCTCCAGCCGTTT 57.374 55.556 0.00 0.00 0.00 3.60
5722 9902 2.093216 GAGCATCTCCAGCCGTTTG 58.907 57.895 0.00 0.00 0.00 2.93
5723 9903 1.986575 GAGCATCTCCAGCCGTTTGC 61.987 60.000 0.00 0.00 41.71 3.68
5724 9904 3.056313 GCATCTCCAGCCGTTTGCC 62.056 63.158 0.00 0.00 42.71 4.52
5725 9905 2.044946 ATCTCCAGCCGTTTGCCC 60.045 61.111 0.00 0.00 42.71 5.36
5726 9906 2.606587 ATCTCCAGCCGTTTGCCCT 61.607 57.895 0.00 0.00 42.71 5.19
5727 9907 2.142292 ATCTCCAGCCGTTTGCCCTT 62.142 55.000 0.00 0.00 42.71 3.95
5728 9908 1.903404 CTCCAGCCGTTTGCCCTTT 60.903 57.895 0.00 0.00 42.71 3.11
5729 9909 1.866853 CTCCAGCCGTTTGCCCTTTC 61.867 60.000 0.00 0.00 42.71 2.62
5730 9910 2.199652 CCAGCCGTTTGCCCTTTCA 61.200 57.895 0.00 0.00 42.71 2.69
5731 9911 1.535204 CCAGCCGTTTGCCCTTTCAT 61.535 55.000 0.00 0.00 42.71 2.57
5732 9912 0.388907 CAGCCGTTTGCCCTTTCATG 60.389 55.000 0.00 0.00 42.71 3.07
5733 9913 0.539438 AGCCGTTTGCCCTTTCATGA 60.539 50.000 0.00 0.00 42.71 3.07
5734 9914 0.109132 GCCGTTTGCCCTTTCATGAG 60.109 55.000 0.00 0.00 0.00 2.90
5735 9915 0.527565 CCGTTTGCCCTTTCATGAGG 59.472 55.000 0.00 0.00 36.52 3.86
5742 9922 3.339253 GCCCTTTCATGAGGCATTTTT 57.661 42.857 17.28 0.00 46.34 1.94
5758 9938 1.301954 TTTTTCGCCTCCTAGGGGC 59.698 57.895 24.19 24.19 46.84 5.80
5759 9939 1.205460 TTTTTCGCCTCCTAGGGGCT 61.205 55.000 28.30 0.00 46.84 5.19
5760 9940 1.910580 TTTTCGCCTCCTAGGGGCTG 61.911 60.000 28.30 22.94 46.84 4.85
5763 9943 3.871395 GCCTCCTAGGGGCTGCTG 61.871 72.222 25.84 5.85 45.57 4.41
5764 9944 3.167105 CCTCCTAGGGGCTGCTGG 61.167 72.222 9.46 0.00 0.00 4.85
5765 9945 3.871395 CTCCTAGGGGCTGCTGGC 61.871 72.222 9.46 8.77 40.90 4.85
5768 9948 4.232878 CTAGGGGCTGCTGGCGAG 62.233 72.222 11.02 4.76 42.94 5.03
5769 9949 4.777854 TAGGGGCTGCTGGCGAGA 62.778 66.667 11.02 0.00 42.94 4.04
5772 9952 4.400961 GGGCTGCTGGCGAGAACT 62.401 66.667 11.02 0.00 42.94 3.01
5773 9953 2.359230 GGCTGCTGGCGAGAACTT 60.359 61.111 0.00 0.00 42.94 2.66
5774 9954 1.968540 GGCTGCTGGCGAGAACTTT 60.969 57.895 0.00 0.00 42.94 2.66
5775 9955 1.208614 GCTGCTGGCGAGAACTTTG 59.791 57.895 0.00 0.00 0.00 2.77
5776 9956 1.871772 CTGCTGGCGAGAACTTTGG 59.128 57.895 0.00 0.00 0.00 3.28
5777 9957 2.192608 CTGCTGGCGAGAACTTTGGC 62.193 60.000 0.00 0.00 36.29 4.52
5778 9958 2.982744 GCTGGCGAGAACTTTGGCC 61.983 63.158 0.00 0.00 45.76 5.36
5779 9959 2.282180 TGGCGAGAACTTTGGCCC 60.282 61.111 0.00 0.00 44.96 5.80
5780 9960 3.431725 GGCGAGAACTTTGGCCCG 61.432 66.667 0.00 0.00 39.67 6.13
5781 9961 3.431725 GCGAGAACTTTGGCCCGG 61.432 66.667 0.00 0.00 0.00 5.73
5782 9962 2.746277 CGAGAACTTTGGCCCGGG 60.746 66.667 19.09 19.09 0.00 5.73
5783 9963 2.361230 GAGAACTTTGGCCCGGGG 60.361 66.667 25.28 9.31 0.00 5.73
5784 9964 3.938637 GAGAACTTTGGCCCGGGGG 62.939 68.421 25.28 2.24 38.57 5.40
5794 9974 3.489636 CCCGGGGGCCAAAATTTT 58.510 55.556 14.71 0.00 0.00 1.82
5795 9975 1.298340 CCCGGGGGCCAAAATTTTC 59.702 57.895 14.71 0.00 0.00 2.29
5796 9976 1.298340 CCGGGGGCCAAAATTTTCC 59.702 57.895 4.39 0.09 0.00 3.13
5797 9977 1.484444 CCGGGGGCCAAAATTTTCCA 61.484 55.000 4.39 0.00 0.00 3.53
5798 9978 0.321210 CGGGGGCCAAAATTTTCCAC 60.321 55.000 4.39 1.24 0.00 4.02
5799 9979 1.064003 GGGGGCCAAAATTTTCCACT 58.936 50.000 4.39 0.00 0.00 4.00
5800 9980 1.003118 GGGGGCCAAAATTTTCCACTC 59.997 52.381 4.39 0.00 0.00 3.51
5801 9981 1.337728 GGGGCCAAAATTTTCCACTCG 60.338 52.381 4.39 0.00 0.00 4.18
5802 9982 1.428448 GGCCAAAATTTTCCACTCGC 58.572 50.000 0.00 0.00 0.00 5.03
5803 9983 1.000843 GGCCAAAATTTTCCACTCGCT 59.999 47.619 0.00 0.00 0.00 4.93
5804 9984 2.061028 GCCAAAATTTTCCACTCGCTG 58.939 47.619 0.00 0.00 0.00 5.18
5805 9985 2.061028 CCAAAATTTTCCACTCGCTGC 58.939 47.619 0.00 0.00 0.00 5.25
5806 9986 2.061028 CAAAATTTTCCACTCGCTGCC 58.939 47.619 0.00 0.00 0.00 4.85
5807 9987 1.620822 AAATTTTCCACTCGCTGCCT 58.379 45.000 0.00 0.00 0.00 4.75
5808 9988 1.620822 AATTTTCCACTCGCTGCCTT 58.379 45.000 0.00 0.00 0.00 4.35
5809 9989 1.168714 ATTTTCCACTCGCTGCCTTC 58.831 50.000 0.00 0.00 0.00 3.46
5810 9990 0.889186 TTTTCCACTCGCTGCCTTCC 60.889 55.000 0.00 0.00 0.00 3.46
5811 9991 2.748058 TTTCCACTCGCTGCCTTCCC 62.748 60.000 0.00 0.00 0.00 3.97
5812 9992 4.020617 CCACTCGCTGCCTTCCCA 62.021 66.667 0.00 0.00 0.00 4.37
5813 9993 2.743928 CACTCGCTGCCTTCCCAC 60.744 66.667 0.00 0.00 0.00 4.61
5814 9994 4.379243 ACTCGCTGCCTTCCCACG 62.379 66.667 0.00 0.00 0.00 4.94
5815 9995 4.069232 CTCGCTGCCTTCCCACGA 62.069 66.667 0.00 0.00 0.00 4.35
5816 9996 3.997064 CTCGCTGCCTTCCCACGAG 62.997 68.421 0.00 0.00 43.46 4.18
5818 9998 4.704833 GCTGCCTTCCCACGAGCA 62.705 66.667 0.00 0.00 0.00 4.26
5819 9999 2.435586 CTGCCTTCCCACGAGCAG 60.436 66.667 0.00 0.00 45.92 4.24
5820 10000 3.241530 TGCCTTCCCACGAGCAGT 61.242 61.111 0.00 0.00 0.00 4.40
5828 10008 4.758692 CACGAGCAGTGTTGGACT 57.241 55.556 4.42 0.00 45.51 3.85
5829 10009 2.522060 CACGAGCAGTGTTGGACTC 58.478 57.895 4.42 0.00 45.51 3.36
5830 10010 0.946221 CACGAGCAGTGTTGGACTCC 60.946 60.000 4.42 0.00 45.51 3.85
5831 10011 1.374758 CGAGCAGTGTTGGACTCCC 60.375 63.158 0.00 0.00 29.75 4.30
5832 10012 1.754745 GAGCAGTGTTGGACTCCCA 59.245 57.895 0.00 0.00 41.64 4.37
5833 10013 0.603975 GAGCAGTGTTGGACTCCCAC 60.604 60.000 0.00 0.00 43.41 4.61
5834 10014 1.148273 GCAGTGTTGGACTCCCACA 59.852 57.895 0.00 0.00 43.41 4.17
5835 10015 0.465460 GCAGTGTTGGACTCCCACAA 60.465 55.000 3.55 0.00 43.41 3.33
5836 10016 2.021723 GCAGTGTTGGACTCCCACAAA 61.022 52.381 3.55 0.00 43.41 2.83
5837 10017 1.676006 CAGTGTTGGACTCCCACAAAC 59.324 52.381 3.55 0.00 43.41 2.93
5838 10018 0.661020 GTGTTGGACTCCCACAAACG 59.339 55.000 3.55 0.00 43.41 3.60
5839 10019 0.464735 TGTTGGACTCCCACAAACGG 60.465 55.000 0.00 0.00 43.41 4.44
5840 10020 0.179040 GTTGGACTCCCACAAACGGA 60.179 55.000 0.00 0.00 43.41 4.69
5844 10024 2.742372 CTCCCACAAACGGAGCGG 60.742 66.667 0.00 0.00 40.55 5.52
5847 10027 3.055719 CCACAAACGGAGCGGCAT 61.056 61.111 1.45 0.00 0.00 4.40
5848 10028 2.625823 CCACAAACGGAGCGGCATT 61.626 57.895 1.45 0.00 0.00 3.56
5849 10029 1.285641 CACAAACGGAGCGGCATTT 59.714 52.632 1.45 0.00 0.00 2.32
5850 10030 0.729140 CACAAACGGAGCGGCATTTC 60.729 55.000 1.45 0.00 0.00 2.17
5851 10031 1.511887 CAAACGGAGCGGCATTTCG 60.512 57.895 1.45 2.78 0.00 3.46
5852 10032 1.964373 AAACGGAGCGGCATTTCGT 60.964 52.632 1.45 3.44 35.48 3.85
5853 10033 1.908066 AAACGGAGCGGCATTTCGTC 61.908 55.000 1.45 0.00 33.34 4.20
5860 10040 2.785258 GGCATTTCGTCGAGCACC 59.215 61.111 7.20 0.00 0.00 5.01
5861 10041 1.741770 GGCATTTCGTCGAGCACCT 60.742 57.895 7.20 0.00 0.00 4.00
5862 10042 1.298859 GGCATTTCGTCGAGCACCTT 61.299 55.000 7.20 0.00 0.00 3.50
5863 10043 0.179215 GCATTTCGTCGAGCACCTTG 60.179 55.000 0.00 0.00 0.00 3.61
5864 10044 1.428448 CATTTCGTCGAGCACCTTGA 58.572 50.000 0.00 0.00 0.00 3.02
5865 10045 1.126846 CATTTCGTCGAGCACCTTGAC 59.873 52.381 0.00 3.08 40.46 3.18
5866 10046 0.599204 TTTCGTCGAGCACCTTGACC 60.599 55.000 6.96 0.00 40.69 4.02
5867 10047 2.742710 TTCGTCGAGCACCTTGACCG 62.743 60.000 6.96 3.63 40.69 4.79
5868 10048 3.112709 GTCGAGCACCTTGACCGC 61.113 66.667 1.89 0.00 38.56 5.68
5869 10049 4.717629 TCGAGCACCTTGACCGCG 62.718 66.667 0.00 0.00 0.00 6.46
5889 10069 4.477975 GGCGTCGACGACCTCCAG 62.478 72.222 39.74 10.32 42.67 3.86
5891 10071 4.477975 CGTCGACGACCTCCAGCC 62.478 72.222 33.35 0.00 43.02 4.85
5892 10072 3.371063 GTCGACGACCTCCAGCCA 61.371 66.667 17.25 0.00 0.00 4.75
5893 10073 3.062466 TCGACGACCTCCAGCCAG 61.062 66.667 0.00 0.00 0.00 4.85
5894 10074 4.803426 CGACGACCTCCAGCCAGC 62.803 72.222 0.00 0.00 0.00 4.85
5895 10075 4.803426 GACGACCTCCAGCCAGCG 62.803 72.222 0.00 0.00 0.00 5.18
5901 10081 3.847602 CTCCAGCCAGCGGAGGAG 61.848 72.222 17.40 14.92 45.43 3.69
5921 10101 4.831307 CGAGCGTCGACGGGGAAG 62.831 72.222 36.13 10.72 43.74 3.46
5922 10102 4.493747 GAGCGTCGACGGGGAAGG 62.494 72.222 36.13 9.97 40.23 3.46
5924 10104 4.493747 GCGTCGACGGGGAAGGAG 62.494 72.222 36.13 8.46 40.23 3.69
5925 10105 2.749044 CGTCGACGGGGAAGGAGA 60.749 66.667 29.70 0.00 35.37 3.71
5926 10106 2.883621 GTCGACGGGGAAGGAGAC 59.116 66.667 0.00 0.00 0.00 3.36
5927 10107 2.749044 TCGACGGGGAAGGAGACG 60.749 66.667 0.00 0.00 0.00 4.18
5928 10108 4.493747 CGACGGGGAAGGAGACGC 62.494 72.222 0.00 0.00 0.00 5.19
5929 10109 4.493747 GACGGGGAAGGAGACGCG 62.494 72.222 3.53 3.53 46.61 6.01
5933 10113 4.516195 GGGAAGGAGACGCGCCTC 62.516 72.222 14.63 14.63 31.02 4.70
5939 10119 4.148825 GAGACGCGCCTCCACCAT 62.149 66.667 11.80 0.00 0.00 3.55
5940 10120 4.457496 AGACGCGCCTCCACCATG 62.457 66.667 5.73 0.00 0.00 3.66
5947 10127 4.489771 CCTCCACCATGCCGGGTC 62.490 72.222 2.18 0.00 39.79 4.46
5948 10128 4.489771 CTCCACCATGCCGGGTCC 62.490 72.222 2.18 0.00 39.79 4.46
5954 10134 4.873129 CATGCCGGGTCCGTCGAG 62.873 72.222 2.18 0.00 37.81 4.04
5957 10137 4.570663 GCCGGGTCCGTCGAGATG 62.571 72.222 2.18 0.00 37.81 2.90
5958 10138 4.570663 CCGGGTCCGTCGAGATGC 62.571 72.222 8.67 0.00 37.81 3.91
5959 10139 3.822192 CGGGTCCGTCGAGATGCA 61.822 66.667 0.55 0.00 34.35 3.96
5960 10140 2.202756 GGGTCCGTCGAGATGCAC 60.203 66.667 0.00 0.00 0.00 4.57
5961 10141 2.579787 GGTCCGTCGAGATGCACG 60.580 66.667 0.00 0.00 35.72 5.34
5965 10145 4.498520 CGTCGAGATGCACGGGCT 62.499 66.667 12.74 0.00 41.91 5.19
5966 10146 2.887568 GTCGAGATGCACGGGCTG 60.888 66.667 12.74 0.00 41.91 4.85
5967 10147 4.147449 TCGAGATGCACGGGCTGG 62.147 66.667 12.74 0.00 41.91 4.85
5968 10148 4.147449 CGAGATGCACGGGCTGGA 62.147 66.667 12.74 0.00 41.91 3.86
5969 10149 2.202987 GAGATGCACGGGCTGGAG 60.203 66.667 12.74 0.00 41.91 3.86
5970 10150 2.685017 AGATGCACGGGCTGGAGA 60.685 61.111 12.74 0.00 41.91 3.71
5971 10151 2.512515 GATGCACGGGCTGGAGAC 60.513 66.667 12.74 0.00 41.91 3.36
5972 10152 4.457496 ATGCACGGGCTGGAGACG 62.457 66.667 12.74 0.00 41.91 4.18
6007 10187 3.770040 CCACGTGCCGGAGATGGA 61.770 66.667 10.91 0.00 31.69 3.41
6008 10188 2.202797 CACGTGCCGGAGATGGAG 60.203 66.667 5.05 0.00 0.00 3.86
6009 10189 2.362503 ACGTGCCGGAGATGGAGA 60.363 61.111 5.05 0.00 0.00 3.71
6010 10190 1.758514 ACGTGCCGGAGATGGAGAT 60.759 57.895 5.05 0.00 0.00 2.75
6011 10191 1.300465 CGTGCCGGAGATGGAGATG 60.300 63.158 5.05 0.00 0.00 2.90
6012 10192 1.596477 GTGCCGGAGATGGAGATGC 60.596 63.158 5.05 0.00 0.00 3.91
6013 10193 2.065789 TGCCGGAGATGGAGATGCA 61.066 57.895 5.05 0.00 0.00 3.96
6014 10194 1.301558 GCCGGAGATGGAGATGCAG 60.302 63.158 5.05 0.00 0.00 4.41
6015 10195 1.301558 CCGGAGATGGAGATGCAGC 60.302 63.158 0.00 0.00 0.00 5.25
6016 10196 1.747145 CGGAGATGGAGATGCAGCT 59.253 57.895 2.90 2.90 0.00 4.24
6017 10197 0.319727 CGGAGATGGAGATGCAGCTC 60.320 60.000 23.68 23.68 0.00 4.09
6018 10198 0.319727 GGAGATGGAGATGCAGCTCG 60.320 60.000 24.58 0.00 35.74 5.03
6019 10199 0.945265 GAGATGGAGATGCAGCTCGC 60.945 60.000 24.58 17.67 42.89 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 164 2.832838 TGGGTGAATCTGAGGCTAGAA 58.167 47.619 0.00 0.00 0.00 2.10
213 220 5.494390 TTCTAGGGTTTGTAGGAGGTTTC 57.506 43.478 0.00 0.00 0.00 2.78
285 292 3.669557 GCTGTTCGTGTTCTTTGTGTGTT 60.670 43.478 0.00 0.00 0.00 3.32
306 326 1.083401 CGCTGTGTTCTTGTCACGC 60.083 57.895 0.00 0.00 38.48 5.34
307 327 1.564622 CCGCTGTGTTCTTGTCACG 59.435 57.895 0.00 0.00 38.48 4.35
308 328 1.507141 CCCCGCTGTGTTCTTGTCAC 61.507 60.000 0.00 0.00 36.48 3.67
309 329 1.227823 CCCCGCTGTGTTCTTGTCA 60.228 57.895 0.00 0.00 0.00 3.58
310 330 2.617274 GCCCCGCTGTGTTCTTGTC 61.617 63.158 0.00 0.00 0.00 3.18
311 331 2.594592 GCCCCGCTGTGTTCTTGT 60.595 61.111 0.00 0.00 0.00 3.16
312 332 3.726517 CGCCCCGCTGTGTTCTTG 61.727 66.667 0.00 0.00 0.00 3.02
313 333 2.748058 ATTCGCCCCGCTGTGTTCTT 62.748 55.000 0.00 0.00 0.00 2.52
314 334 2.748058 AATTCGCCCCGCTGTGTTCT 62.748 55.000 0.00 0.00 0.00 3.01
315 335 2.332654 AATTCGCCCCGCTGTGTTC 61.333 57.895 0.00 0.00 0.00 3.18
316 336 2.282180 AATTCGCCCCGCTGTGTT 60.282 55.556 0.00 0.00 0.00 3.32
328 348 1.408702 CAAGGTAATGCCCCCAATTCG 59.591 52.381 0.00 0.00 38.26 3.34
365 385 0.543410 TAGGGTTCCGTCAAGCTCCA 60.543 55.000 0.00 0.00 32.62 3.86
376 396 2.183555 CCACGCGTCTAGGGTTCC 59.816 66.667 9.86 0.00 44.10 3.62
377 397 2.183555 CCCACGCGTCTAGGGTTC 59.816 66.667 21.83 0.00 44.10 3.62
378 398 4.078516 GCCCACGCGTCTAGGGTT 62.079 66.667 28.04 0.00 44.10 4.11
381 401 3.771160 AAGGCCCACGCGTCTAGG 61.771 66.667 9.86 12.36 35.02 3.02
382 402 2.509336 CAAGGCCCACGCGTCTAG 60.509 66.667 9.86 1.20 35.02 2.43
383 403 2.992689 TCAAGGCCCACGCGTCTA 60.993 61.111 9.86 0.00 35.02 2.59
384 404 4.681978 GTCAAGGCCCACGCGTCT 62.682 66.667 9.86 0.00 35.02 4.18
389 409 3.047877 GTTCCGTCAAGGCCCACG 61.048 66.667 11.62 11.62 40.77 4.94
390 410 2.671963 GGTTCCGTCAAGGCCCAC 60.672 66.667 0.00 0.00 40.77 4.61
391 411 3.961414 GGGTTCCGTCAAGGCCCA 61.961 66.667 0.00 0.00 40.79 5.36
392 412 2.253403 CTAGGGTTCCGTCAAGGCCC 62.253 65.000 0.00 0.00 41.25 5.80
393 413 1.221021 CTAGGGTTCCGTCAAGGCC 59.779 63.158 0.00 0.00 40.77 5.19
394 414 0.108281 GTCTAGGGTTCCGTCAAGGC 60.108 60.000 0.00 0.00 40.77 4.35
395 415 0.172803 CGTCTAGGGTTCCGTCAAGG 59.827 60.000 0.00 0.00 42.97 3.61
446 752 4.986587 TCGTTGGCGTCGGTGTCG 62.987 66.667 0.00 0.00 39.49 4.35
447 753 3.103911 CTCGTTGGCGTCGGTGTC 61.104 66.667 0.00 0.00 39.49 3.67
448 754 4.657824 CCTCGTTGGCGTCGGTGT 62.658 66.667 0.00 0.00 39.49 4.16
449 755 4.351938 TCCTCGTTGGCGTCGGTG 62.352 66.667 0.00 0.00 39.49 4.94
459 765 0.674534 GTGGTCAGTGTCTCCTCGTT 59.325 55.000 0.00 0.00 0.00 3.85
468 774 1.846007 TTTTTGCAGGTGGTCAGTGT 58.154 45.000 0.00 0.00 0.00 3.55
533 841 0.255033 TCTCTCCCCTCGATTCGTCA 59.745 55.000 5.89 0.00 0.00 4.35
638 946 4.864334 CCTCCCTCATGGCGCACC 62.864 72.222 10.83 0.00 0.00 5.01
644 952 1.767681 CTTCCTCTTCCTCCCTCATGG 59.232 57.143 0.00 0.00 0.00 3.66
647 955 0.043334 CCCTTCCTCTTCCTCCCTCA 59.957 60.000 0.00 0.00 0.00 3.86
677 985 1.001760 TCCCCCTTCCTCTTCCTCG 59.998 63.158 0.00 0.00 0.00 4.63
699 1007 0.522180 TCTTTCGTCGCTCCAGAGAC 59.478 55.000 0.00 0.63 40.70 3.36
721 1029 2.542907 CCGTGCGGCTCACTGTTTT 61.543 57.895 6.02 0.00 43.46 2.43
781 1089 0.704076 CCCCCTTCACCTGATTTGGA 59.296 55.000 0.00 0.00 0.00 3.53
1050 1368 1.551964 AGAGGGGAGGAGGGGGTTA 60.552 63.158 0.00 0.00 0.00 2.85
1187 1792 1.226831 GAGGAGAAGAAGAGGCGCG 60.227 63.158 0.00 0.00 0.00 6.86
1593 2198 2.128507 GGAACCAACGGCAACCCAA 61.129 57.895 0.00 0.00 0.00 4.12
1641 2246 1.485480 GTAAACCTCCACCCTAGCTCC 59.515 57.143 0.00 0.00 0.00 4.70
1644 2249 1.134877 GTCGTAAACCTCCACCCTAGC 60.135 57.143 0.00 0.00 0.00 3.42
1723 2328 0.252650 CCCCCACACCCAAATCCAAT 60.253 55.000 0.00 0.00 0.00 3.16
1907 2512 0.890683 TCTGCTCATCAACTGCTCGA 59.109 50.000 0.00 0.00 0.00 4.04
1921 2526 1.220206 CAACCTCGCCATCTCTGCT 59.780 57.895 0.00 0.00 0.00 4.24
1980 2585 1.895798 CTGTCCACAGCTCCTTCACTA 59.104 52.381 0.00 0.00 37.15 2.74
1981 2586 0.683973 CTGTCCACAGCTCCTTCACT 59.316 55.000 0.00 0.00 37.15 3.41
2180 2786 4.270808 CACGCAGTAATGCATAGTTCATCA 59.729 41.667 16.30 0.00 41.61 3.07
2201 2807 1.728971 CAGTGCCATTCTTCTCGACAC 59.271 52.381 0.00 0.00 0.00 3.67
2208 2814 4.518970 TGTTCTAAACCAGTGCCATTCTTC 59.481 41.667 0.00 0.00 0.00 2.87
2261 2867 2.565841 GTGGATCAGGCATGGAACTAC 58.434 52.381 0.00 0.00 0.00 2.73
2522 3128 3.456317 AAGGACGTGTCTCGCCTT 58.544 55.556 13.61 13.61 44.52 4.35
2593 3199 1.195448 CACCGAACAGTTGACATGAGC 59.805 52.381 0.00 0.00 0.00 4.26
2808 3414 1.021202 CGACAGACAAGCCAACCAAA 58.979 50.000 0.00 0.00 0.00 3.28
2884 3490 6.762702 TTTTGCATCAGAAGCATCATCTAA 57.237 33.333 0.14 0.00 42.33 2.10
2940 3546 4.023291 TCAACAGAAGCTCTTTGGGTTTT 58.977 39.130 0.00 0.00 0.00 2.43
2990 3596 6.729690 ATTTTGAGGTTTGTTCTGATCCAA 57.270 33.333 0.00 0.00 0.00 3.53
3017 3623 3.753842 TCTCGGATTTTGTAATTTGCGC 58.246 40.909 0.00 0.00 0.00 6.09
3147 3762 3.947196 CCTGATACATGCTTGTTAAGGCA 59.053 43.478 10.85 0.00 42.80 4.75
3187 3802 4.204799 ACCGGATTATTTCCAACCTAAGC 58.795 43.478 9.46 0.00 45.78 3.09
3234 3849 9.617975 CTTTTATCATCTTCTGTTTTGAACCTC 57.382 33.333 0.00 0.00 0.00 3.85
3310 3925 8.366671 ACTTAACAATACTGTCAGACTGAAAC 57.633 34.615 14.03 0.00 33.45 2.78
3343 3958 4.289672 ACATACCTGGACTTGATGGTCTTT 59.710 41.667 0.00 0.00 36.55 2.52
3439 4054 5.590530 AAACACAGACCAATGCTAAACAA 57.409 34.783 0.00 0.00 0.00 2.83
3523 4138 3.181826 TGCTTCAACGCTAAACATTCG 57.818 42.857 0.00 0.00 0.00 3.34
3641 4313 2.676632 TGCATGATCAATTTGTGGGC 57.323 45.000 0.00 0.00 0.00 5.36
3952 6666 5.104817 TGTGATGCTCCTATCTCACAATTCA 60.105 40.000 1.99 0.00 43.54 2.57
4014 6739 4.365514 TCAAGGAAAATGAGCACCACTA 57.634 40.909 0.00 0.00 0.00 2.74
4073 6798 6.519761 GTCATTAGAAGTTACAACAACATGCG 59.480 38.462 0.00 0.00 0.00 4.73
4078 6806 9.944663 TCAATTGTCATTAGAAGTTACAACAAC 57.055 29.630 5.13 0.00 33.27 3.32
4141 6876 3.796717 ACAACGCATGTGTCATATACTCG 59.203 43.478 13.23 0.00 41.93 4.18
4903 7676 1.960763 GACCATGTCAGTGCACGCA 60.961 57.895 12.01 12.39 32.09 5.24
4912 7685 1.212751 CGTCTCGCAGACCATGTCA 59.787 57.895 9.71 0.00 42.12 3.58
5050 7823 0.304705 CTTTCGTTCACACGCTGCTT 59.695 50.000 0.00 0.00 46.70 3.91
5207 7981 4.747540 TCAACAACGGAATGAATGAGTG 57.252 40.909 0.00 0.00 0.00 3.51
5269 8043 8.504005 ACCGTAGAAGAAGACAATACATTTTTG 58.496 33.333 0.00 0.00 0.00 2.44
5278 8062 6.812160 GTGACATTACCGTAGAAGAAGACAAT 59.188 38.462 0.00 0.00 0.00 2.71
5279 8063 6.015688 AGTGACATTACCGTAGAAGAAGACAA 60.016 38.462 0.00 0.00 0.00 3.18
5296 8080 3.251004 GTCAGCCGAAAAGAAGTGACATT 59.749 43.478 0.00 0.00 35.45 2.71
5300 8084 2.910688 AGTCAGCCGAAAAGAAGTGA 57.089 45.000 0.00 0.00 0.00 3.41
5325 8109 2.548067 GCCCACTATGTAACGCTAGCAT 60.548 50.000 16.45 5.33 0.00 3.79
5334 8118 1.391577 TAGTCGCGCCCACTATGTAA 58.608 50.000 0.00 0.00 0.00 2.41
5335 8119 1.612676 ATAGTCGCGCCCACTATGTA 58.387 50.000 20.58 2.22 36.01 2.29
5545 9724 3.812799 GTCAATGACATTCACGGGGACG 61.813 54.545 8.74 0.00 45.90 4.79
5656 9835 1.684983 GCATAACCAATCCAGCATGCT 59.315 47.619 16.30 16.30 36.66 3.79
5705 9885 2.042831 GCAAACGGCTGGAGATGCT 61.043 57.895 0.00 0.00 40.25 3.79
5710 9890 1.866853 GAAAGGGCAAACGGCTGGAG 61.867 60.000 0.00 0.00 44.01 3.86
5711 9891 1.901464 GAAAGGGCAAACGGCTGGA 60.901 57.895 0.00 0.00 44.01 3.86
5712 9892 1.535204 ATGAAAGGGCAAACGGCTGG 61.535 55.000 0.00 0.00 44.01 4.85
5713 9893 0.388907 CATGAAAGGGCAAACGGCTG 60.389 55.000 0.00 0.00 44.01 4.85
5714 9894 0.539438 TCATGAAAGGGCAAACGGCT 60.539 50.000 0.00 0.00 44.01 5.52
5715 9895 0.109132 CTCATGAAAGGGCAAACGGC 60.109 55.000 0.00 0.00 43.74 5.68
5716 9896 0.527565 CCTCATGAAAGGGCAAACGG 59.472 55.000 0.00 0.00 32.35 4.44
5717 9897 0.109132 GCCTCATGAAAGGGCAAACG 60.109 55.000 17.28 0.00 44.69 3.60
5718 9898 3.820595 GCCTCATGAAAGGGCAAAC 57.179 52.632 17.28 0.00 44.69 2.93
5722 9902 3.339253 AAAAATGCCTCATGAAAGGGC 57.661 42.857 15.74 15.74 45.45 5.19
5740 9920 1.301954 GCCCCTAGGAGGCGAAAAA 59.698 57.895 21.17 0.00 41.41 1.94
5741 9921 2.995547 GCCCCTAGGAGGCGAAAA 59.004 61.111 21.17 0.00 41.41 2.29
5747 9927 3.167105 CCAGCAGCCCCTAGGAGG 61.167 72.222 11.48 11.20 33.47 4.30
5748 9928 3.871395 GCCAGCAGCCCCTAGGAG 61.871 72.222 11.48 0.00 34.35 3.69
5751 9931 4.232878 CTCGCCAGCAGCCCCTAG 62.233 72.222 0.00 0.00 38.78 3.02
5752 9932 4.777854 TCTCGCCAGCAGCCCCTA 62.778 66.667 0.00 0.00 38.78 3.53
5755 9935 3.909086 AAGTTCTCGCCAGCAGCCC 62.909 63.158 0.00 0.00 38.78 5.19
5756 9936 1.968540 AAAGTTCTCGCCAGCAGCC 60.969 57.895 0.00 0.00 38.78 4.85
5757 9937 1.208614 CAAAGTTCTCGCCAGCAGC 59.791 57.895 0.00 0.00 38.52 5.25
5758 9938 1.871772 CCAAAGTTCTCGCCAGCAG 59.128 57.895 0.00 0.00 0.00 4.24
5759 9939 2.260869 GCCAAAGTTCTCGCCAGCA 61.261 57.895 0.00 0.00 0.00 4.41
5760 9940 2.563427 GCCAAAGTTCTCGCCAGC 59.437 61.111 0.00 0.00 0.00 4.85
5761 9941 2.335712 GGGCCAAAGTTCTCGCCAG 61.336 63.158 4.39 0.00 43.50 4.85
5762 9942 2.282180 GGGCCAAAGTTCTCGCCA 60.282 61.111 4.39 0.00 43.50 5.69
5763 9943 3.431725 CGGGCCAAAGTTCTCGCC 61.432 66.667 4.39 0.00 40.85 5.54
5764 9944 3.431725 CCGGGCCAAAGTTCTCGC 61.432 66.667 4.39 0.00 0.00 5.03
5765 9945 2.746277 CCCGGGCCAAAGTTCTCG 60.746 66.667 8.08 0.00 0.00 4.04
5766 9946 2.361230 CCCCGGGCCAAAGTTCTC 60.361 66.667 17.73 0.00 0.00 2.87
5767 9947 3.979497 CCCCCGGGCCAAAGTTCT 61.979 66.667 17.73 0.00 0.00 3.01
5777 9957 1.298340 GAAAATTTTGGCCCCCGGG 59.702 57.895 15.80 15.80 38.57 5.73
5778 9958 1.298340 GGAAAATTTTGGCCCCCGG 59.702 57.895 8.47 0.00 0.00 5.73
5779 9959 0.321210 GTGGAAAATTTTGGCCCCCG 60.321 55.000 8.47 0.00 0.00 5.73
5780 9960 1.003118 GAGTGGAAAATTTTGGCCCCC 59.997 52.381 8.47 3.42 0.00 5.40
5781 9961 1.337728 CGAGTGGAAAATTTTGGCCCC 60.338 52.381 8.47 3.80 0.00 5.80
5782 9962 1.939381 GCGAGTGGAAAATTTTGGCCC 60.939 52.381 8.47 4.18 0.00 5.80
5783 9963 1.000843 AGCGAGTGGAAAATTTTGGCC 59.999 47.619 8.47 4.93 0.00 5.36
5784 9964 2.061028 CAGCGAGTGGAAAATTTTGGC 58.939 47.619 8.47 0.00 0.00 4.52
5785 9965 2.061028 GCAGCGAGTGGAAAATTTTGG 58.939 47.619 8.47 0.00 0.00 3.28
5786 9966 2.061028 GGCAGCGAGTGGAAAATTTTG 58.939 47.619 8.47 0.00 0.00 2.44
5787 9967 1.963515 AGGCAGCGAGTGGAAAATTTT 59.036 42.857 2.28 2.28 0.00 1.82
5788 9968 1.620822 AGGCAGCGAGTGGAAAATTT 58.379 45.000 0.00 0.00 0.00 1.82
5789 9969 1.541588 GAAGGCAGCGAGTGGAAAATT 59.458 47.619 0.00 0.00 0.00 1.82
5790 9970 1.168714 GAAGGCAGCGAGTGGAAAAT 58.831 50.000 0.00 0.00 0.00 1.82
5791 9971 0.889186 GGAAGGCAGCGAGTGGAAAA 60.889 55.000 0.00 0.00 0.00 2.29
5792 9972 1.302511 GGAAGGCAGCGAGTGGAAA 60.303 57.895 0.00 0.00 0.00 3.13
5793 9973 2.347490 GGAAGGCAGCGAGTGGAA 59.653 61.111 0.00 0.00 0.00 3.53
5794 9974 3.706373 GGGAAGGCAGCGAGTGGA 61.706 66.667 0.00 0.00 0.00 4.02
5795 9975 4.020617 TGGGAAGGCAGCGAGTGG 62.021 66.667 0.00 0.00 0.00 4.00
5796 9976 2.743928 GTGGGAAGGCAGCGAGTG 60.744 66.667 0.00 0.00 0.00 3.51
5797 9977 4.379243 CGTGGGAAGGCAGCGAGT 62.379 66.667 0.00 0.00 0.00 4.18
5798 9978 3.997064 CTCGTGGGAAGGCAGCGAG 62.997 68.421 0.00 0.00 42.01 5.03
5799 9979 4.069232 CTCGTGGGAAGGCAGCGA 62.069 66.667 0.00 0.00 0.00 4.93
5801 9981 4.704833 TGCTCGTGGGAAGGCAGC 62.705 66.667 0.00 0.00 0.00 5.25
5802 9982 2.435586 CTGCTCGTGGGAAGGCAG 60.436 66.667 0.00 0.00 44.45 4.85
5803 9983 3.241530 ACTGCTCGTGGGAAGGCA 61.242 61.111 0.00 0.00 0.00 4.75
5804 9984 2.743928 CACTGCTCGTGGGAAGGC 60.744 66.667 0.00 0.00 40.02 4.35
5812 9992 1.367840 GGAGTCCAACACTGCTCGT 59.632 57.895 3.60 0.00 40.32 4.18
5813 9993 1.374758 GGGAGTCCAACACTGCTCG 60.375 63.158 12.30 0.00 43.04 5.03
5814 9994 0.603975 GTGGGAGTCCAACACTGCTC 60.604 60.000 12.23 0.00 46.04 4.26
5815 9995 1.344953 TGTGGGAGTCCAACACTGCT 61.345 55.000 15.98 0.00 46.04 4.24
5816 9996 0.465460 TTGTGGGAGTCCAACACTGC 60.465 55.000 19.66 0.00 46.04 4.40
5817 9997 1.676006 GTTTGTGGGAGTCCAACACTG 59.324 52.381 19.66 0.00 46.04 3.66
5818 9998 1.745827 CGTTTGTGGGAGTCCAACACT 60.746 52.381 19.66 0.00 46.04 3.55
5819 9999 0.661020 CGTTTGTGGGAGTCCAACAC 59.339 55.000 19.66 14.60 46.04 3.32
5820 10000 0.464735 CCGTTTGTGGGAGTCCAACA 60.465 55.000 15.98 15.98 46.04 3.33
5821 10001 0.179040 TCCGTTTGTGGGAGTCCAAC 60.179 55.000 10.08 10.08 46.04 3.77
5822 10002 0.107831 CTCCGTTTGTGGGAGTCCAA 59.892 55.000 12.30 0.00 46.04 3.53
5823 10003 1.752198 CTCCGTTTGTGGGAGTCCA 59.248 57.895 12.30 0.00 44.92 4.02
5824 10004 4.695560 CTCCGTTTGTGGGAGTCC 57.304 61.111 0.00 0.00 44.92 3.85
5830 10010 2.141122 AAATGCCGCTCCGTTTGTGG 62.141 55.000 0.00 0.00 38.07 4.17
5831 10011 0.729140 GAAATGCCGCTCCGTTTGTG 60.729 55.000 0.00 0.00 0.00 3.33
5832 10012 1.579429 GAAATGCCGCTCCGTTTGT 59.421 52.632 0.00 0.00 0.00 2.83
5833 10013 1.511887 CGAAATGCCGCTCCGTTTG 60.512 57.895 0.00 0.00 0.00 2.93
5834 10014 1.908066 GACGAAATGCCGCTCCGTTT 61.908 55.000 0.00 0.00 33.32 3.60
5835 10015 2.358247 ACGAAATGCCGCTCCGTT 60.358 55.556 0.00 0.00 0.00 4.44
5836 10016 2.813908 GACGAAATGCCGCTCCGT 60.814 61.111 0.00 0.00 36.08 4.69
5837 10017 3.913573 CGACGAAATGCCGCTCCG 61.914 66.667 0.00 0.00 0.00 4.63
5838 10018 2.508439 TCGACGAAATGCCGCTCC 60.508 61.111 0.00 0.00 0.00 4.70
5839 10019 2.998667 CTCGACGAAATGCCGCTC 59.001 61.111 0.00 0.00 0.00 5.03
5840 10020 3.188786 GCTCGACGAAATGCCGCT 61.189 61.111 0.00 0.00 0.00 5.52
5841 10021 3.487202 TGCTCGACGAAATGCCGC 61.487 61.111 0.00 0.00 0.00 6.53
5842 10022 2.395690 GTGCTCGACGAAATGCCG 59.604 61.111 0.00 0.00 0.00 5.69
5843 10023 1.298859 AAGGTGCTCGACGAAATGCC 61.299 55.000 0.00 0.00 0.00 4.40
5844 10024 0.179215 CAAGGTGCTCGACGAAATGC 60.179 55.000 0.00 0.00 0.00 3.56
5845 10025 1.126846 GTCAAGGTGCTCGACGAAATG 59.873 52.381 0.00 0.00 0.00 2.32
5846 10026 1.429463 GTCAAGGTGCTCGACGAAAT 58.571 50.000 0.00 0.00 0.00 2.17
5847 10027 0.599204 GGTCAAGGTGCTCGACGAAA 60.599 55.000 0.00 0.00 0.00 3.46
5848 10028 1.006571 GGTCAAGGTGCTCGACGAA 60.007 57.895 0.00 0.00 0.00 3.85
5849 10029 2.649034 GGTCAAGGTGCTCGACGA 59.351 61.111 0.00 0.00 0.00 4.20
5850 10030 2.805353 CGGTCAAGGTGCTCGACG 60.805 66.667 0.00 0.00 0.00 5.12
5851 10031 3.112709 GCGGTCAAGGTGCTCGAC 61.113 66.667 0.00 0.00 0.00 4.20
5852 10032 4.717629 CGCGGTCAAGGTGCTCGA 62.718 66.667 0.00 0.00 0.00 4.04
5872 10052 4.477975 CTGGAGGTCGTCGACGCC 62.478 72.222 32.19 31.52 39.60 5.68
5874 10054 4.477975 GGCTGGAGGTCGTCGACG 62.478 72.222 31.30 31.30 41.45 5.12
5875 10055 3.343788 CTGGCTGGAGGTCGTCGAC 62.344 68.421 17.16 17.16 0.00 4.20
5876 10056 3.062466 CTGGCTGGAGGTCGTCGA 61.062 66.667 0.00 0.00 0.00 4.20
5877 10057 4.803426 GCTGGCTGGAGGTCGTCG 62.803 72.222 0.00 0.00 0.00 5.12
5878 10058 4.803426 CGCTGGCTGGAGGTCGTC 62.803 72.222 0.00 0.00 0.00 4.20
5904 10084 4.831307 CTTCCCCGTCGACGCTCG 62.831 72.222 31.73 19.68 42.10 5.03
5905 10085 4.493747 CCTTCCCCGTCGACGCTC 62.494 72.222 31.73 0.00 38.18 5.03
5907 10087 4.493747 CTCCTTCCCCGTCGACGC 62.494 72.222 31.73 0.00 38.18 5.19
5908 10088 2.749044 TCTCCTTCCCCGTCGACG 60.749 66.667 30.33 30.33 39.44 5.12
5909 10089 2.883621 GTCTCCTTCCCCGTCGAC 59.116 66.667 5.18 5.18 0.00 4.20
5910 10090 2.749044 CGTCTCCTTCCCCGTCGA 60.749 66.667 0.00 0.00 0.00 4.20
5911 10091 4.493747 GCGTCTCCTTCCCCGTCG 62.494 72.222 0.00 0.00 0.00 5.12
5912 10092 4.493747 CGCGTCTCCTTCCCCGTC 62.494 72.222 0.00 0.00 0.00 4.79
5916 10096 4.516195 GAGGCGCGTCTCCTTCCC 62.516 72.222 29.89 8.35 33.24 3.97
5922 10102 4.148825 ATGGTGGAGGCGCGTCTC 62.149 66.667 31.90 31.90 0.00 3.36
5923 10103 4.457496 CATGGTGGAGGCGCGTCT 62.457 66.667 27.24 15.91 0.00 4.18
5930 10110 4.489771 GACCCGGCATGGTGGAGG 62.490 72.222 0.00 0.00 39.24 4.30
5931 10111 4.489771 GGACCCGGCATGGTGGAG 62.490 72.222 0.00 0.00 39.24 3.86
5940 10120 4.570663 CATCTCGACGGACCCGGC 62.571 72.222 13.43 9.01 45.29 6.13
5941 10121 4.570663 GCATCTCGACGGACCCGG 62.571 72.222 13.43 0.00 44.69 5.73
5942 10122 3.822192 TGCATCTCGACGGACCCG 61.822 66.667 6.94 6.94 46.03 5.28
5943 10123 2.202756 GTGCATCTCGACGGACCC 60.203 66.667 0.00 0.00 0.00 4.46
5944 10124 2.579787 CGTGCATCTCGACGGACC 60.580 66.667 0.00 0.00 31.84 4.46
5948 10128 4.498520 AGCCCGTGCATCTCGACG 62.499 66.667 0.00 0.00 41.13 5.12
5949 10129 2.887568 CAGCCCGTGCATCTCGAC 60.888 66.667 0.00 0.00 41.13 4.20
5950 10130 4.147449 CCAGCCCGTGCATCTCGA 62.147 66.667 0.00 0.00 41.13 4.04
5951 10131 4.147449 TCCAGCCCGTGCATCTCG 62.147 66.667 0.00 0.00 41.13 4.04
5952 10132 2.202987 CTCCAGCCCGTGCATCTC 60.203 66.667 0.00 0.00 41.13 2.75
5953 10133 2.685017 TCTCCAGCCCGTGCATCT 60.685 61.111 0.00 0.00 41.13 2.90
5954 10134 2.512515 GTCTCCAGCCCGTGCATC 60.513 66.667 0.00 0.00 41.13 3.91
5955 10135 4.457496 CGTCTCCAGCCCGTGCAT 62.457 66.667 0.00 0.00 41.13 3.96
5994 10174 1.596477 GCATCTCCATCTCCGGCAC 60.596 63.158 0.00 0.00 0.00 5.01
5995 10175 2.036428 CTGCATCTCCATCTCCGGCA 62.036 60.000 0.00 0.00 0.00 5.69
5996 10176 1.301558 CTGCATCTCCATCTCCGGC 60.302 63.158 0.00 0.00 0.00 6.13
5997 10177 1.301558 GCTGCATCTCCATCTCCGG 60.302 63.158 0.00 0.00 0.00 5.14
5998 10178 0.319727 GAGCTGCATCTCCATCTCCG 60.320 60.000 6.27 0.00 0.00 4.63
5999 10179 0.319727 CGAGCTGCATCTCCATCTCC 60.320 60.000 11.80 0.00 0.00 3.71
6000 10180 0.945265 GCGAGCTGCATCTCCATCTC 60.945 60.000 11.80 0.00 45.45 2.75
6001 10181 1.069427 GCGAGCTGCATCTCCATCT 59.931 57.895 11.80 0.00 45.45 2.90
6002 10182 3.640231 GCGAGCTGCATCTCCATC 58.360 61.111 11.80 0.00 45.45 3.51


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

AutoCloner maintained by Alex Coulton.