Multiple sequence alignment - TraesCS6D01G263900

Loading Multiple Alignment...

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 TraesCS6D01G263900 chr6D 100.000 3401 0 0 1 3401 372767283 372770683 0.000000e+00 6281
1 TraesCS6D01G263900 chr6D 92.500 600 33 5 2751 3339 414263340 414263938 0.000000e+00 848
2 TraesCS6D01G263900 chr6D 78.812 1246 222 33 1170 2402 372785916 372784700 0.000000e+00 800
3 TraesCS6D01G263900 chr6D 90.500 600 39 11 2750 3340 388335903 388335313 0.000000e+00 776
4 TraesCS6D01G263900 chr6D 76.917 1252 233 37 1179 2399 372821564 372820338 0.000000e+00 660
5 TraesCS6D01G263900 chr6B 94.536 1995 87 9 510 2486 559462208 559464198 0.000000e+00 3061
6 TraesCS6D01G263900 chr6B 77.608 1246 225 36 1170 2402 559408400 559409604 0.000000e+00 706
7 TraesCS6D01G263900 chr6B 91.232 479 41 1 26 504 559461477 559461954 0.000000e+00 651
8 TraesCS6D01G263900 chr6B 76.111 1260 251 34 1168 2399 559355693 559356930 6.240000e-172 614
9 TraesCS6D01G263900 chr6B 91.892 111 3 2 2539 2645 559468901 559469009 2.110000e-32 150
10 TraesCS6D01G263900 chr2D 94.416 591 31 1 2751 3339 544581458 544580868 0.000000e+00 907
11 TraesCS6D01G263900 chr2D 91.528 602 36 8 2750 3339 306336422 306337020 0.000000e+00 815
12 TraesCS6D01G263900 chr2D 76.972 938 181 27 1360 2281 637375626 637374708 1.410000e-138 503
13 TraesCS6D01G263900 chr3D 94.378 587 30 2 2753 3339 170800757 170801340 0.000000e+00 898
14 TraesCS6D01G263900 chr3D 86.928 306 17 3 3117 3401 281007397 281007094 4.230000e-84 322
15 TraesCS6D01G263900 chr3D 84.740 308 25 4 3113 3399 338544524 338544830 4.290000e-74 289
16 TraesCS6D01G263900 chr5B 93.888 589 33 3 2752 3339 639224008 639224594 0.000000e+00 885
17 TraesCS6D01G263900 chr5D 90.342 673 43 4 2750 3401 428668054 428668725 0.000000e+00 863
18 TraesCS6D01G263900 chr5D 92.228 579 33 8 2772 3339 400367754 400367177 0.000000e+00 809
19 TraesCS6D01G263900 chr5D 85.484 310 23 7 3113 3401 366735230 366735538 1.530000e-78 303
20 TraesCS6D01G263900 chr5D 84.984 313 22 5 3113 3401 532238942 532239253 9.230000e-76 294
21 TraesCS6D01G263900 chr1D 92.359 602 33 6 2750 3340 447062028 447062627 0.000000e+00 845
22 TraesCS6D01G263900 chr1D 84.013 319 28 8 3105 3401 231457108 231456791 5.550000e-73 285
23 TraesCS6D01G263900 chr6A 77.814 1235 224 31 1190 2402 514493626 514492420 0.000000e+00 717
24 TraesCS6D01G263900 chr6A 76.442 1231 244 30 1179 2383 514679206 514677996 2.880000e-175 625
25 TraesCS6D01G263900 chr6A 87.042 409 36 1 26 417 514402636 514402228 2.410000e-121 446
26 TraesCS6D01G263900 chr6A 82.781 302 29 5 3121 3401 167669717 167669418 7.290000e-62 248
27 TraesCS6D01G263900 chr6A 91.176 102 3 2 2547 2644 514402050 514401951 2.130000e-27 134
28 TraesCS6D01G263900 chr4D 87.097 310 17 5 3113 3401 151997930 151997623 2.530000e-86 329
29 TraesCS6D01G263900 chr7A 72.186 1244 262 54 1213 2402 679531617 679530404 1.530000e-78 303
30 TraesCS6D01G263900 chr7A 71.880 1234 271 50 1216 2402 679594637 679593433 1.540000e-73 287
31 TraesCS6D01G263900 chr7D 71.967 1220 252 63 1199 2364 587302185 587303368 3.340000e-70 276
32 TraesCS6D01G263900 chr7B 75.377 398 71 16 1213 1588 658895531 658895139 2.100000e-37 167


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 TraesCS6D01G263900 chr6D 372767283 372770683 3400 False 6281 6281 100.000 1 3401 1 chr6D.!!$F1 3400
1 TraesCS6D01G263900 chr6D 414263340 414263938 598 False 848 848 92.500 2751 3339 1 chr6D.!!$F2 588
2 TraesCS6D01G263900 chr6D 372784700 372785916 1216 True 800 800 78.812 1170 2402 1 chr6D.!!$R1 1232
3 TraesCS6D01G263900 chr6D 388335313 388335903 590 True 776 776 90.500 2750 3340 1 chr6D.!!$R3 590
4 TraesCS6D01G263900 chr6D 372820338 372821564 1226 True 660 660 76.917 1179 2399 1 chr6D.!!$R2 1220
5 TraesCS6D01G263900 chr6B 559461477 559464198 2721 False 1856 3061 92.884 26 2486 2 chr6B.!!$F4 2460
6 TraesCS6D01G263900 chr6B 559408400 559409604 1204 False 706 706 77.608 1170 2402 1 chr6B.!!$F2 1232
7 TraesCS6D01G263900 chr6B 559355693 559356930 1237 False 614 614 76.111 1168 2399 1 chr6B.!!$F1 1231
8 TraesCS6D01G263900 chr2D 544580868 544581458 590 True 907 907 94.416 2751 3339 1 chr2D.!!$R1 588
9 TraesCS6D01G263900 chr2D 306336422 306337020 598 False 815 815 91.528 2750 3339 1 chr2D.!!$F1 589
10 TraesCS6D01G263900 chr2D 637374708 637375626 918 True 503 503 76.972 1360 2281 1 chr2D.!!$R2 921
11 TraesCS6D01G263900 chr3D 170800757 170801340 583 False 898 898 94.378 2753 3339 1 chr3D.!!$F1 586
12 TraesCS6D01G263900 chr5B 639224008 639224594 586 False 885 885 93.888 2752 3339 1 chr5B.!!$F1 587
13 TraesCS6D01G263900 chr5D 428668054 428668725 671 False 863 863 90.342 2750 3401 1 chr5D.!!$F2 651
14 TraesCS6D01G263900 chr5D 400367177 400367754 577 True 809 809 92.228 2772 3339 1 chr5D.!!$R1 567
15 TraesCS6D01G263900 chr1D 447062028 447062627 599 False 845 845 92.359 2750 3340 1 chr1D.!!$F1 590
16 TraesCS6D01G263900 chr6A 514492420 514493626 1206 True 717 717 77.814 1190 2402 1 chr6A.!!$R2 1212
17 TraesCS6D01G263900 chr6A 514677996 514679206 1210 True 625 625 76.442 1179 2383 1 chr6A.!!$R3 1204
18 TraesCS6D01G263900 chr6A 514401951 514402636 685 True 290 446 89.109 26 2644 2 chr6A.!!$R4 2618
19 TraesCS6D01G263900 chr7A 679530404 679531617 1213 True 303 303 72.186 1213 2402 1 chr7A.!!$R1 1189
20 TraesCS6D01G263900 chr7A 679593433 679594637 1204 True 287 287 71.880 1216 2402 1 chr7A.!!$R2 1186
21 TraesCS6D01G263900 chr7D 587302185 587303368 1183 False 276 276 71.967 1199 2364 1 chr7D.!!$F1 1165

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
205 206 0.037697 ATAGCGACAACGAACAGGCA 60.038 50.0 0.00 0.0 42.66 4.75 F
858 1124 0.040425 CGTACACTTGCCAAGTTGCC 60.040 55.0 7.51 0.0 40.46 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1142 1426 0.037326 ACGGCGATCATCACAACTGT 60.037 50.000 16.62 0.0 0.00 3.55 R
2492 2844 1.425066 AGCCAGGTCAATCCAAAGTCA 59.575 47.619 0.00 0.0 39.02 3.41 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
40 41 1.890876 TTGAAACATCTGTGTCCCCG 58.109 50.000 0.00 0.00 37.67 5.73
50 51 1.070786 GTGTCCCCGCTGACTTTGA 59.929 57.895 4.51 0.00 36.21 2.69
62 63 3.152341 CTGACTTTGAGCCTCCATTTGT 58.848 45.455 0.00 0.00 0.00 2.83
183 184 4.485163 GGACTTCATTCCGTCCAAAATTG 58.515 43.478 3.72 0.00 46.98 2.32
192 193 4.004314 TCCGTCCAAAATTGAAATAGCGA 58.996 39.130 0.00 0.00 0.00 4.93
205 206 0.037697 ATAGCGACAACGAACAGGCA 60.038 50.000 0.00 0.00 42.66 4.75
268 286 4.201871 CCAAAGCATTTTTGCTGCCATATG 60.202 41.667 0.55 0.00 45.54 1.78
398 416 9.900264 CTTTTCTATTTTCTTCAAAACAAACGG 57.100 29.630 0.00 0.00 34.24 4.44
417 435 4.082125 ACGGAAAAGATTTGGCTCATCTT 58.918 39.130 6.06 6.06 41.84 2.40
443 461 5.610429 AATAAAGGAGGGGTAAACAAGGT 57.390 39.130 0.00 0.00 0.00 3.50
465 483 6.500751 AGGTTCATAGTTTAGAGAGGTCCAAA 59.499 38.462 0.00 0.00 0.00 3.28
482 500 3.567585 TCCAAAACGCATCTCATCAACAA 59.432 39.130 0.00 0.00 0.00 2.83
491 509 5.159209 GCATCTCATCAACAAGACAAAAGG 58.841 41.667 0.00 0.00 0.00 3.11
504 522 3.958147 AGACAAAAGGGGTAAACAAGGTG 59.042 43.478 0.00 0.00 0.00 4.00
507 525 2.694616 AAGGGGTAAACAAGGTGCAT 57.305 45.000 0.00 0.00 0.00 3.96
569 835 4.210120 GCAAGATGTGAAGGTATAAGCGAG 59.790 45.833 0.00 0.00 0.00 5.03
570 836 5.592054 CAAGATGTGAAGGTATAAGCGAGA 58.408 41.667 0.00 0.00 0.00 4.04
617 883 5.848406 AGACTAAATCCATGAATCGTCTCC 58.152 41.667 0.00 0.00 0.00 3.71
620 886 1.806496 ATCCATGAATCGTCTCCCCA 58.194 50.000 0.00 0.00 0.00 4.96
623 889 1.544093 CCATGAATCGTCTCCCCATGG 60.544 57.143 4.14 4.14 45.38 3.66
633 899 1.484653 TCTCCCCATGGACAACGTATG 59.515 52.381 15.22 0.00 35.03 2.39
667 933 6.202954 CCAGGTCGATCCACTAATAACAATTC 59.797 42.308 0.00 0.00 39.02 2.17
685 951 5.163723 ACAATTCACGTAAGGCATCAGATTG 60.164 40.000 0.00 0.00 46.39 2.67
717 983 7.642071 AAAATCCAAAAATCTCATGTCAACG 57.358 32.000 0.00 0.00 0.00 4.10
723 989 4.749245 AAATCTCATGTCAACGAACCAC 57.251 40.909 0.00 0.00 0.00 4.16
741 1007 3.062763 CCACTCAATACCATCGCAGATC 58.937 50.000 0.00 0.00 45.12 2.75
743 1009 3.739810 CACTCAATACCATCGCAGATCAG 59.260 47.826 0.00 0.00 45.12 2.90
759 1025 5.445275 GCAGATCAGCGTAGAAGAGAAAAAC 60.445 44.000 0.00 0.00 0.00 2.43
788 1054 7.094075 CCCATTACTGAGCAATACCTACGTATA 60.094 40.741 0.00 0.00 33.90 1.47
818 1084 3.248602 GCATCACGAACTGGATAATCCAC 59.751 47.826 0.00 0.00 42.67 4.02
827 1093 3.152341 CTGGATAATCCACCCTGCATTC 58.848 50.000 0.00 0.00 42.67 2.67
828 1094 2.513317 TGGATAATCCACCCTGCATTCA 59.487 45.455 0.00 0.00 42.67 2.57
831 1097 2.610438 AATCCACCCTGCATTCAAGT 57.390 45.000 0.00 0.00 0.00 3.16
858 1124 0.040425 CGTACACTTGCCAAGTTGCC 60.040 55.000 7.51 0.00 40.46 4.52
910 1185 4.776322 CCAGGCGGCGTTGATCCA 62.776 66.667 9.37 0.00 0.00 3.41
936 1211 8.954729 AGAGCTCCCATCTATCTATATAAGCTA 58.045 37.037 10.93 0.00 36.56 3.32
937 1212 9.581289 GAGCTCCCATCTATCTATATAAGCTAA 57.419 37.037 0.87 0.00 36.56 3.09
953 1228 3.462021 AGCTAAGGAATTTAGAGCTGCG 58.538 45.455 0.00 0.00 41.10 5.18
974 1249 6.686630 TGCGATTAACCAGTTCAATTCAATT 58.313 32.000 0.00 0.00 0.00 2.32
1043 1318 1.465777 CATGTCATCTGTTTCGCAGCA 59.534 47.619 0.00 0.00 44.66 4.41
1061 1336 0.605860 CAGCTGCTTCTCCTGCTGTT 60.606 55.000 0.00 0.00 46.38 3.16
1063 1338 0.321475 GCTGCTTCTCCTGCTGTTCT 60.321 55.000 0.00 0.00 0.00 3.01
1079 1354 1.861575 GTTCTGCTACTATTCTGCCGC 59.138 52.381 0.00 0.00 0.00 6.53
1083 1358 0.249657 GCTACTATTCTGCCGCTGCT 60.250 55.000 0.70 0.00 38.71 4.24
1124 1399 1.135199 CGAGCAACCAGGTACGTACAT 60.135 52.381 26.02 17.76 0.00 2.29
1125 1400 2.537401 GAGCAACCAGGTACGTACATC 58.463 52.381 26.02 10.66 0.00 3.06
1126 1401 1.897133 AGCAACCAGGTACGTACATCA 59.103 47.619 26.02 0.00 0.00 3.07
1127 1402 1.997606 GCAACCAGGTACGTACATCAC 59.002 52.381 26.02 9.59 0.00 3.06
1128 1403 2.610976 GCAACCAGGTACGTACATCACA 60.611 50.000 26.02 0.00 0.00 3.58
1129 1404 2.991190 CAACCAGGTACGTACATCACAC 59.009 50.000 26.02 8.52 0.00 3.82
1130 1405 1.547372 ACCAGGTACGTACATCACACC 59.453 52.381 26.02 10.60 0.00 4.16
1131 1406 1.546923 CCAGGTACGTACATCACACCA 59.453 52.381 26.02 0.00 0.00 4.17
1132 1407 2.167693 CCAGGTACGTACATCACACCAT 59.832 50.000 26.02 0.00 0.00 3.55
1142 1426 3.173151 ACATCACACCATCTGTCCAGTA 58.827 45.455 0.00 0.00 0.00 2.74
1158 1442 2.604914 CCAGTACAGTTGTGATGATCGC 59.395 50.000 0.00 0.00 0.00 4.58
1159 1443 2.604914 CAGTACAGTTGTGATGATCGCC 59.395 50.000 3.23 0.00 0.00 5.54
1164 1448 1.732259 AGTTGTGATGATCGCCGTTTC 59.268 47.619 3.23 0.00 0.00 2.78
1166 1450 2.022764 TGTGATGATCGCCGTTTCAT 57.977 45.000 3.23 5.27 35.33 2.57
1172 1456 1.392168 TGATCGCCGTTTCATTTCGTC 59.608 47.619 0.00 0.00 0.00 4.20
1869 2207 2.047274 CCGACCAATGCCACGTCT 60.047 61.111 0.00 0.00 0.00 4.18
1872 2210 1.003839 GACCAATGCCACGTCTGGA 60.004 57.895 0.00 0.00 40.55 3.86
2250 2588 0.603707 TCGTCAACCTCGACCGTAGT 60.604 55.000 0.00 0.00 31.91 2.73
2402 2754 4.266070 GCCAGGCGCATGCTGATG 62.266 66.667 18.18 10.71 42.25 3.07
2404 2756 1.897137 CCAGGCGCATGCTGATGAT 60.897 57.895 18.18 0.00 42.25 2.45
2425 2777 4.884668 TTCATTTCCGGTGACTACTTCT 57.115 40.909 0.00 0.00 0.00 2.85
2457 2809 0.808755 GTGAATTGTGCGGTAAGGGG 59.191 55.000 0.00 0.00 0.00 4.79
2465 2817 2.666098 GCGGTAAGGGGCAGGAAGA 61.666 63.158 0.00 0.00 0.00 2.87
2470 2822 2.025321 GGTAAGGGGCAGGAAGATCAAA 60.025 50.000 0.00 0.00 0.00 2.69
2471 2823 2.222227 AAGGGGCAGGAAGATCAAAC 57.778 50.000 0.00 0.00 0.00 2.93
2495 2847 7.687005 CTCGTTCAGAGGAATAATAGTTGAC 57.313 40.000 0.00 0.00 43.20 3.18
2496 2848 7.406031 TCGTTCAGAGGAATAATAGTTGACT 57.594 36.000 0.00 0.00 35.05 3.41
2497 2849 7.837863 TCGTTCAGAGGAATAATAGTTGACTT 58.162 34.615 0.00 0.00 35.05 3.01
2498 2850 8.311836 TCGTTCAGAGGAATAATAGTTGACTTT 58.688 33.333 0.00 0.00 35.05 2.66
2499 2851 8.383619 CGTTCAGAGGAATAATAGTTGACTTTG 58.616 37.037 0.00 0.00 35.05 2.77
2500 2852 8.669243 GTTCAGAGGAATAATAGTTGACTTTGG 58.331 37.037 0.00 0.00 35.05 3.28
2501 2853 8.146053 TCAGAGGAATAATAGTTGACTTTGGA 57.854 34.615 0.00 0.00 0.00 3.53
2502 2854 8.772250 TCAGAGGAATAATAGTTGACTTTGGAT 58.228 33.333 0.00 0.00 0.00 3.41
2503 2855 9.401058 CAGAGGAATAATAGTTGACTTTGGATT 57.599 33.333 0.00 0.00 0.00 3.01
2504 2856 9.401058 AGAGGAATAATAGTTGACTTTGGATTG 57.599 33.333 0.00 0.00 0.00 2.67
2505 2857 9.396022 GAGGAATAATAGTTGACTTTGGATTGA 57.604 33.333 0.00 0.00 0.00 2.57
2506 2858 9.178758 AGGAATAATAGTTGACTTTGGATTGAC 57.821 33.333 0.00 0.00 0.00 3.18
2507 2859 8.406297 GGAATAATAGTTGACTTTGGATTGACC 58.594 37.037 0.00 0.00 39.54 4.02
2508 2860 9.178758 GAATAATAGTTGACTTTGGATTGACCT 57.821 33.333 0.00 0.00 39.86 3.85
2509 2861 6.824305 AATAGTTGACTTTGGATTGACCTG 57.176 37.500 0.00 0.00 39.86 4.00
2510 2862 3.490348 AGTTGACTTTGGATTGACCTGG 58.510 45.455 0.00 0.00 39.86 4.45
2511 2863 1.909700 TGACTTTGGATTGACCTGGC 58.090 50.000 0.00 0.00 39.86 4.85
2512 2864 1.425066 TGACTTTGGATTGACCTGGCT 59.575 47.619 0.00 0.00 39.86 4.75
2513 2865 2.158475 TGACTTTGGATTGACCTGGCTT 60.158 45.455 0.00 0.00 39.86 4.35
2514 2866 2.893489 GACTTTGGATTGACCTGGCTTT 59.107 45.455 0.00 0.00 39.86 3.51
2515 2867 3.308401 ACTTTGGATTGACCTGGCTTTT 58.692 40.909 0.00 0.00 39.86 2.27
2516 2868 3.070015 ACTTTGGATTGACCTGGCTTTTG 59.930 43.478 0.00 0.00 39.86 2.44
2517 2869 2.673775 TGGATTGACCTGGCTTTTGA 57.326 45.000 0.00 0.00 39.86 2.69
2518 2870 2.517959 TGGATTGACCTGGCTTTTGAG 58.482 47.619 0.00 0.00 39.86 3.02
2519 2871 2.158475 TGGATTGACCTGGCTTTTGAGT 60.158 45.455 0.00 0.00 39.86 3.41
2520 2872 2.893489 GGATTGACCTGGCTTTTGAGTT 59.107 45.455 0.00 0.00 35.41 3.01
2521 2873 3.321968 GGATTGACCTGGCTTTTGAGTTT 59.678 43.478 0.00 0.00 35.41 2.66
2522 2874 4.202253 GGATTGACCTGGCTTTTGAGTTTT 60.202 41.667 0.00 0.00 35.41 2.43
2523 2875 5.010617 GGATTGACCTGGCTTTTGAGTTTTA 59.989 40.000 0.00 0.00 35.41 1.52
2524 2876 6.295292 GGATTGACCTGGCTTTTGAGTTTTAT 60.295 38.462 0.00 0.00 35.41 1.40
2525 2877 7.093945 GGATTGACCTGGCTTTTGAGTTTTATA 60.094 37.037 0.00 0.00 35.41 0.98
2526 2878 7.589958 TTGACCTGGCTTTTGAGTTTTATAA 57.410 32.000 0.00 0.00 0.00 0.98
2527 2879 7.589958 TGACCTGGCTTTTGAGTTTTATAAA 57.410 32.000 0.00 0.00 0.00 1.40
2528 2880 7.430441 TGACCTGGCTTTTGAGTTTTATAAAC 58.570 34.615 0.00 0.00 0.00 2.01
2529 2881 7.286775 TGACCTGGCTTTTGAGTTTTATAAACT 59.713 33.333 4.59 4.59 0.00 2.66
2530 2882 7.658261 ACCTGGCTTTTGAGTTTTATAAACTC 58.342 34.615 20.07 20.07 45.12 3.01
2546 2898 9.974980 TTTATAAACTCAAAAACCCTTTAGCTG 57.025 29.630 0.00 0.00 0.00 4.24
2547 2899 4.937201 AACTCAAAAACCCTTTAGCTGG 57.063 40.909 0.00 0.00 0.00 4.85
2594 2950 4.022416 GGGATGTTTTGTGACAGCAACATA 60.022 41.667 19.21 0.59 39.43 2.29
2595 2951 5.336690 GGGATGTTTTGTGACAGCAACATAT 60.337 40.000 19.21 5.69 39.43 1.78
2596 2952 5.574055 GGATGTTTTGTGACAGCAACATATG 59.426 40.000 19.21 0.00 39.43 1.78
2597 2953 5.764487 TGTTTTGTGACAGCAACATATGA 57.236 34.783 10.38 0.00 0.00 2.15
2598 2954 6.330004 TGTTTTGTGACAGCAACATATGAT 57.670 33.333 10.38 0.00 0.00 2.45
2599 2955 6.380995 TGTTTTGTGACAGCAACATATGATC 58.619 36.000 10.38 0.00 0.00 2.92
2604 2960 3.495753 TGACAGCAACATATGATCGATGC 59.504 43.478 10.38 11.05 0.00 3.91
2641 2997 8.539674 GCTGGTTAAGTTTGTTTGTAATTTCAG 58.460 33.333 0.00 0.00 0.00 3.02
2644 3000 9.738832 GGTTAAGTTTGTTTGTAATTTCAGCTA 57.261 29.630 0.00 0.00 0.00 3.32
2648 3004 9.646427 AAGTTTGTTTGTAATTTCAGCTACAAA 57.354 25.926 6.20 6.20 42.71 2.83
2649 3005 9.646427 AGTTTGTTTGTAATTTCAGCTACAAAA 57.354 25.926 10.89 1.89 45.03 2.44
2653 3009 8.547069 TGTTTGTAATTTCAGCTACAAAAATGC 58.453 29.630 10.89 1.79 45.03 3.56
2654 3010 8.764287 GTTTGTAATTTCAGCTACAAAAATGCT 58.236 29.630 10.89 0.00 45.03 3.79
2655 3011 9.973450 TTTGTAATTTCAGCTACAAAAATGCTA 57.027 25.926 7.58 0.00 42.25 3.49
2656 3012 9.624697 TTGTAATTTCAGCTACAAAAATGCTAG 57.375 29.630 0.00 0.00 35.59 3.42
2657 3013 9.008965 TGTAATTTCAGCTACAAAAATGCTAGA 57.991 29.630 0.00 0.00 35.05 2.43
2658 3014 9.278734 GTAATTTCAGCTACAAAAATGCTAGAC 57.721 33.333 0.00 0.00 35.05 2.59
2659 3015 5.880054 TTCAGCTACAAAAATGCTAGACC 57.120 39.130 0.00 0.00 35.05 3.85
2660 3016 5.165961 TCAGCTACAAAAATGCTAGACCT 57.834 39.130 0.00 0.00 35.05 3.85
2661 3017 6.294361 TCAGCTACAAAAATGCTAGACCTA 57.706 37.500 0.00 0.00 35.05 3.08
2662 3018 6.106673 TCAGCTACAAAAATGCTAGACCTAC 58.893 40.000 0.00 0.00 35.05 3.18
2663 3019 5.005779 CAGCTACAAAAATGCTAGACCTACG 59.994 44.000 0.00 0.00 35.05 3.51
2664 3020 4.868734 GCTACAAAAATGCTAGACCTACGT 59.131 41.667 0.00 0.00 0.00 3.57
2665 3021 6.038356 GCTACAAAAATGCTAGACCTACGTA 58.962 40.000 0.00 0.00 0.00 3.57
2666 3022 6.532657 GCTACAAAAATGCTAGACCTACGTAA 59.467 38.462 0.00 0.00 0.00 3.18
2700 3056 7.283633 CGTAACCTACGTAAACTTTCTTTTCC 58.716 38.462 0.00 0.00 46.41 3.13
2701 3057 7.042791 CGTAACCTACGTAAACTTTCTTTTCCA 60.043 37.037 0.00 0.00 46.41 3.53
2702 3058 6.609237 ACCTACGTAAACTTTCTTTTCCAC 57.391 37.500 0.00 0.00 0.00 4.02
2703 3059 6.351711 ACCTACGTAAACTTTCTTTTCCACT 58.648 36.000 0.00 0.00 0.00 4.00
2704 3060 7.500141 ACCTACGTAAACTTTCTTTTCCACTA 58.500 34.615 0.00 0.00 0.00 2.74
2705 3061 7.986889 ACCTACGTAAACTTTCTTTTCCACTAA 59.013 33.333 0.00 0.00 0.00 2.24
2706 3062 8.278408 CCTACGTAAACTTTCTTTTCCACTAAC 58.722 37.037 0.00 0.00 0.00 2.34
2707 3063 7.854557 ACGTAAACTTTCTTTTCCACTAACT 57.145 32.000 0.00 0.00 0.00 2.24
2708 3064 7.691158 ACGTAAACTTTCTTTTCCACTAACTG 58.309 34.615 0.00 0.00 0.00 3.16
2709 3065 7.550196 ACGTAAACTTTCTTTTCCACTAACTGA 59.450 33.333 0.00 0.00 0.00 3.41
2710 3066 8.392612 CGTAAACTTTCTTTTCCACTAACTGAA 58.607 33.333 0.00 0.00 0.00 3.02
2711 3067 9.499585 GTAAACTTTCTTTTCCACTAACTGAAC 57.500 33.333 0.00 0.00 0.00 3.18
2712 3068 7.696992 AACTTTCTTTTCCACTAACTGAACA 57.303 32.000 0.00 0.00 0.00 3.18
2713 3069 7.881775 ACTTTCTTTTCCACTAACTGAACAT 57.118 32.000 0.00 0.00 0.00 2.71
2714 3070 7.931275 ACTTTCTTTTCCACTAACTGAACATC 58.069 34.615 0.00 0.00 0.00 3.06
2715 3071 7.775561 ACTTTCTTTTCCACTAACTGAACATCT 59.224 33.333 0.00 0.00 0.00 2.90
2716 3072 9.273016 CTTTCTTTTCCACTAACTGAACATCTA 57.727 33.333 0.00 0.00 0.00 1.98
2717 3073 9.793259 TTTCTTTTCCACTAACTGAACATCTAT 57.207 29.630 0.00 0.00 0.00 1.98
2718 3074 9.793259 TTCTTTTCCACTAACTGAACATCTATT 57.207 29.630 0.00 0.00 0.00 1.73
2719 3075 9.436957 TCTTTTCCACTAACTGAACATCTATTC 57.563 33.333 0.00 0.00 0.00 1.75
2720 3076 9.219603 CTTTTCCACTAACTGAACATCTATTCA 57.780 33.333 0.00 0.00 37.08 2.57
2721 3077 8.547967 TTTCCACTAACTGAACATCTATTCAC 57.452 34.615 0.00 0.00 34.84 3.18
2722 3078 7.239763 TCCACTAACTGAACATCTATTCACA 57.760 36.000 0.00 0.00 34.84 3.58
2723 3079 7.676004 TCCACTAACTGAACATCTATTCACAA 58.324 34.615 0.00 0.00 34.84 3.33
2724 3080 7.819415 TCCACTAACTGAACATCTATTCACAAG 59.181 37.037 0.00 0.00 34.84 3.16
2725 3081 7.413438 CCACTAACTGAACATCTATTCACAAGC 60.413 40.741 0.00 0.00 34.84 4.01
2726 3082 7.118245 CACTAACTGAACATCTATTCACAAGCA 59.882 37.037 0.00 0.00 34.84 3.91
2727 3083 7.826252 ACTAACTGAACATCTATTCACAAGCAT 59.174 33.333 0.00 0.00 34.84 3.79
2728 3084 9.317936 CTAACTGAACATCTATTCACAAGCATA 57.682 33.333 0.00 0.00 34.84 3.14
2729 3085 8.565896 AACTGAACATCTATTCACAAGCATAA 57.434 30.769 0.00 0.00 34.84 1.90
2730 3086 7.978982 ACTGAACATCTATTCACAAGCATAAC 58.021 34.615 0.00 0.00 34.84 1.89
2731 3087 7.066284 ACTGAACATCTATTCACAAGCATAACC 59.934 37.037 0.00 0.00 34.84 2.85
2732 3088 6.883756 TGAACATCTATTCACAAGCATAACCA 59.116 34.615 0.00 0.00 33.62 3.67
2733 3089 7.557358 TGAACATCTATTCACAAGCATAACCAT 59.443 33.333 0.00 0.00 33.62 3.55
2734 3090 7.886629 ACATCTATTCACAAGCATAACCATT 57.113 32.000 0.00 0.00 0.00 3.16
2735 3091 8.297470 ACATCTATTCACAAGCATAACCATTT 57.703 30.769 0.00 0.00 0.00 2.32
2736 3092 8.752187 ACATCTATTCACAAGCATAACCATTTT 58.248 29.630 0.00 0.00 0.00 1.82
2737 3093 9.590451 CATCTATTCACAAGCATAACCATTTTT 57.410 29.630 0.00 0.00 0.00 1.94
2768 3124 4.574674 ACATAAGAGCAACTCCAATGGA 57.425 40.909 0.48 0.48 31.53 3.41
2803 3159 2.593436 CCGCTGTCCGTTTGGGTT 60.593 61.111 0.00 0.00 37.00 4.11
2887 3244 4.115199 GGCGACCCATTCCTGGCT 62.115 66.667 0.00 0.00 41.64 4.75
2931 3291 2.649034 GCGGACACGAGAAGGACA 59.351 61.111 0.00 0.00 44.60 4.02
2934 3294 1.658673 GGACACGAGAAGGACACGT 59.341 57.895 0.00 0.00 45.50 4.49
3355 3761 3.496870 CCTCCTTTGCTTGTAGAACTGGT 60.497 47.826 0.00 0.00 0.00 4.00
3377 3783 2.497092 CGTCGACGATGTCTTGCGG 61.497 63.158 33.35 0.00 43.02 5.69
3395 3801 2.539338 GGAAGCGTTCGCACCACAA 61.539 57.895 18.95 0.00 32.97 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.906660 GACACAGATGTTTCAATTAATAAACCA 57.093 29.630 10.08 0.00 39.95 3.67
11 12 9.353999 GGACACAGATGTTTCAATTAATAAACC 57.646 33.333 10.08 0.00 39.95 3.27
12 13 9.353999 GGGACACAGATGTTTCAATTAATAAAC 57.646 33.333 6.82 6.82 39.95 2.01
13 14 8.527810 GGGGACACAGATGTTTCAATTAATAAA 58.472 33.333 1.91 0.00 39.95 1.40
14 15 7.148154 CGGGGACACAGATGTTTCAATTAATAA 60.148 37.037 1.91 0.00 39.95 1.40
15 16 6.317642 CGGGGACACAGATGTTTCAATTAATA 59.682 38.462 1.91 0.00 39.95 0.98
16 17 5.125417 CGGGGACACAGATGTTTCAATTAAT 59.875 40.000 1.91 0.00 39.95 1.40
17 18 4.457603 CGGGGACACAGATGTTTCAATTAA 59.542 41.667 1.91 0.00 39.95 1.40
18 19 4.006989 CGGGGACACAGATGTTTCAATTA 58.993 43.478 1.91 0.00 39.95 1.40
19 20 2.819608 CGGGGACACAGATGTTTCAATT 59.180 45.455 1.91 0.00 39.95 2.32
20 21 2.436417 CGGGGACACAGATGTTTCAAT 58.564 47.619 1.91 0.00 39.95 2.57
21 22 1.890876 CGGGGACACAGATGTTTCAA 58.109 50.000 1.91 0.00 39.95 2.69
22 23 0.605319 GCGGGGACACAGATGTTTCA 60.605 55.000 1.91 0.00 39.95 2.69
23 24 0.321653 AGCGGGGACACAGATGTTTC 60.322 55.000 0.00 0.00 39.95 2.78
24 25 0.606401 CAGCGGGGACACAGATGTTT 60.606 55.000 0.00 0.00 39.95 2.83
40 41 1.831580 AATGGAGGCTCAAAGTCAGC 58.168 50.000 17.69 0.00 36.02 4.26
50 51 2.634453 CCCAAAAAGACAAATGGAGGCT 59.366 45.455 0.00 0.00 34.82 4.58
62 63 1.110518 GCGGACCCAACCCAAAAAGA 61.111 55.000 0.00 0.00 0.00 2.52
136 137 7.254522 CCCAAAATCTGTGTTTTGAACATCTTG 60.255 37.037 16.64 0.00 46.78 3.02
183 184 2.474032 GCCTGTTCGTTGTCGCTATTTC 60.474 50.000 0.00 0.00 36.96 2.17
192 193 1.674359 TCAACATGCCTGTTCGTTGT 58.326 45.000 4.20 0.00 43.76 3.32
205 206 1.145738 AGGCCAGAACCTGTTCAACAT 59.854 47.619 5.01 0.00 41.84 2.71
215 216 1.111277 AAACAACACAGGCCAGAACC 58.889 50.000 5.01 0.00 0.00 3.62
268 286 2.877168 CCTCAGAGCATTTGATAGGCAC 59.123 50.000 0.00 0.00 0.00 5.01
394 412 4.082125 AGATGAGCCAAATCTTTTCCGTT 58.918 39.130 0.00 0.00 29.94 4.44
396 414 4.708726 AAGATGAGCCAAATCTTTTCCG 57.291 40.909 1.35 0.00 40.65 4.30
417 435 8.848830 ACCTTGTTTACCCCTCCTTTATTAATA 58.151 33.333 0.00 0.00 0.00 0.98
443 461 6.872020 CGTTTTGGACCTCTCTAAACTATGAA 59.128 38.462 0.00 0.00 0.00 2.57
465 483 3.402110 TGTCTTGTTGATGAGATGCGTT 58.598 40.909 0.00 0.00 0.00 4.84
482 500 3.958147 CACCTTGTTTACCCCTTTTGTCT 59.042 43.478 0.00 0.00 0.00 3.41
491 509 8.459911 AAACTATATATGCACCTTGTTTACCC 57.540 34.615 0.00 0.00 0.00 3.69
544 810 4.332543 CGCTTATACCTTCACATCTTGCAA 59.667 41.667 0.00 0.00 0.00 4.08
550 816 5.047660 AGGATCTCGCTTATACCTTCACATC 60.048 44.000 0.00 0.00 0.00 3.06
569 835 5.712152 AACCAAACATGACAAAGAGGATC 57.288 39.130 0.00 0.00 0.00 3.36
570 836 7.505585 TCTTTAACCAAACATGACAAAGAGGAT 59.494 33.333 0.00 0.00 0.00 3.24
617 883 1.209504 AGTCCATACGTTGTCCATGGG 59.790 52.381 13.02 0.00 39.79 4.00
620 886 2.304761 ACCAAGTCCATACGTTGTCCAT 59.695 45.455 0.00 0.00 0.00 3.41
667 933 2.223112 GCACAATCTGATGCCTTACGTG 60.223 50.000 0.00 0.00 35.73 4.49
685 951 5.990996 TGAGATTTTTGGATTTTTCTGGCAC 59.009 36.000 0.00 0.00 0.00 5.01
717 983 2.609459 CTGCGATGGTATTGAGTGGTTC 59.391 50.000 0.00 0.00 0.00 3.62
723 989 2.735663 GCTGATCTGCGATGGTATTGAG 59.264 50.000 8.95 0.00 0.00 3.02
741 1007 4.319549 GGGTTGTTTTTCTCTTCTACGCTG 60.320 45.833 0.00 0.00 0.00 5.18
743 1009 3.562557 TGGGTTGTTTTTCTCTTCTACGC 59.437 43.478 0.00 0.00 0.00 4.42
759 1025 4.526970 AGGTATTGCTCAGTAATGGGTTG 58.473 43.478 0.00 0.00 0.00 3.77
827 1093 1.865865 AGTGTACGAACTGGCACTTG 58.134 50.000 0.00 0.00 38.86 3.16
828 1094 2.614829 AAGTGTACGAACTGGCACTT 57.385 45.000 0.00 0.00 44.36 3.16
831 1097 2.612200 GCAAGTGTACGAACTGGCA 58.388 52.632 7.65 0.00 45.09 4.92
858 1124 6.283161 CAGTTGACTCTGCACATATGTATG 57.717 41.667 8.32 0.00 39.55 2.39
910 1185 7.825709 AGCTTATATAGATAGATGGGAGCTCT 58.174 38.462 14.64 0.00 31.71 4.09
936 1211 5.297029 GGTTAATCGCAGCTCTAAATTCCTT 59.703 40.000 0.00 0.00 0.00 3.36
937 1212 4.816925 GGTTAATCGCAGCTCTAAATTCCT 59.183 41.667 0.00 0.00 0.00 3.36
951 1226 6.806249 TGAATTGAATTGAACTGGTTAATCGC 59.194 34.615 0.00 0.00 0.00 4.58
953 1228 7.814107 TGCTGAATTGAATTGAACTGGTTAATC 59.186 33.333 0.00 0.00 0.00 1.75
1043 1318 0.321475 GAACAGCAGGAGAAGCAGCT 60.321 55.000 0.00 0.00 37.95 4.24
1061 1336 1.067669 CAGCGGCAGAATAGTAGCAGA 59.932 52.381 1.45 0.00 0.00 4.26
1063 1338 0.530650 GCAGCGGCAGAATAGTAGCA 60.531 55.000 3.18 0.00 40.72 3.49
1079 1354 3.485431 CGGCTTCAGCACGAGCAG 61.485 66.667 7.77 0.00 45.49 4.24
1083 1358 2.049156 CAGACGGCTTCAGCACGA 60.049 61.111 14.17 0.00 44.36 4.35
1124 1399 2.604139 TGTACTGGACAGATGGTGTGA 58.396 47.619 6.29 0.00 40.56 3.58
1142 1426 0.037326 ACGGCGATCATCACAACTGT 60.037 50.000 16.62 0.00 0.00 3.55
1158 1442 7.617533 AAAATTTACAGACGAAATGAAACGG 57.382 32.000 0.00 0.00 0.00 4.44
1164 1448 9.144085 GTCGCTATAAAATTTACAGACGAAATG 57.856 33.333 10.37 0.00 0.00 2.32
1166 1450 8.470040 AGTCGCTATAAAATTTACAGACGAAA 57.530 30.769 10.37 0.00 0.00 3.46
1172 1456 6.823678 ACGGAGTCGCTATAAAATTTACAG 57.176 37.500 0.00 0.00 29.74 2.74
1684 2004 1.683707 TGTCGGAGGAGCTCAGCAT 60.684 57.895 17.19 0.00 31.08 3.79
1869 2207 1.447838 GCCGAGCGTGAGAAATCCA 60.448 57.895 0.00 0.00 0.00 3.41
2250 2588 3.315140 TTGCCGATGACGACCCCA 61.315 61.111 0.00 0.00 42.66 4.96
2305 2643 4.241555 GCCGATGACGCTGGGGAT 62.242 66.667 0.00 0.00 38.29 3.85
2402 2754 5.420409 AGAAGTAGTCACCGGAAATGAATC 58.580 41.667 9.46 0.00 0.00 2.52
2404 2756 4.884668 AGAAGTAGTCACCGGAAATGAA 57.115 40.909 9.46 0.00 0.00 2.57
2425 2777 4.502282 GCACAATTCACAATCACAAACGAA 59.498 37.500 0.00 0.00 0.00 3.85
2457 2809 3.067106 TGAACGAGTTTGATCTTCCTGC 58.933 45.455 0.00 0.00 0.00 4.85
2465 2817 8.478877 ACTATTATTCCTCTGAACGAGTTTGAT 58.521 33.333 0.00 0.00 38.11 2.57
2470 2822 7.122948 AGTCAACTATTATTCCTCTGAACGAGT 59.877 37.037 0.00 0.00 38.11 4.18
2471 2823 7.484975 AGTCAACTATTATTCCTCTGAACGAG 58.515 38.462 0.00 0.00 39.57 4.18
2481 2833 8.406297 GGTCAATCCAAAGTCAACTATTATTCC 58.594 37.037 0.00 0.00 35.97 3.01
2486 2838 5.711976 CCAGGTCAATCCAAAGTCAACTATT 59.288 40.000 0.00 0.00 39.02 1.73
2487 2839 5.256474 CCAGGTCAATCCAAAGTCAACTAT 58.744 41.667 0.00 0.00 39.02 2.12
2488 2840 4.651778 CCAGGTCAATCCAAAGTCAACTA 58.348 43.478 0.00 0.00 39.02 2.24
2489 2841 3.490348 CCAGGTCAATCCAAAGTCAACT 58.510 45.455 0.00 0.00 39.02 3.16
2490 2842 2.029918 GCCAGGTCAATCCAAAGTCAAC 60.030 50.000 0.00 0.00 39.02 3.18
2491 2843 2.158475 AGCCAGGTCAATCCAAAGTCAA 60.158 45.455 0.00 0.00 39.02 3.18
2492 2844 1.425066 AGCCAGGTCAATCCAAAGTCA 59.575 47.619 0.00 0.00 39.02 3.41
2493 2845 2.206576 AGCCAGGTCAATCCAAAGTC 57.793 50.000 0.00 0.00 39.02 3.01
2494 2846 2.683211 AAGCCAGGTCAATCCAAAGT 57.317 45.000 0.00 0.00 39.02 2.66
2495 2847 3.321682 TCAAAAGCCAGGTCAATCCAAAG 59.678 43.478 0.00 0.00 39.02 2.77
2496 2848 3.303938 TCAAAAGCCAGGTCAATCCAAA 58.696 40.909 0.00 0.00 39.02 3.28
2497 2849 2.892852 CTCAAAAGCCAGGTCAATCCAA 59.107 45.455 0.00 0.00 39.02 3.53
2498 2850 2.158475 ACTCAAAAGCCAGGTCAATCCA 60.158 45.455 0.00 0.00 39.02 3.41
2499 2851 2.519013 ACTCAAAAGCCAGGTCAATCC 58.481 47.619 0.00 0.00 0.00 3.01
2500 2852 4.590850 AAACTCAAAAGCCAGGTCAATC 57.409 40.909 0.00 0.00 0.00 2.67
2501 2853 6.670695 ATAAAACTCAAAAGCCAGGTCAAT 57.329 33.333 0.00 0.00 0.00 2.57
2502 2854 7.589958 TTATAAAACTCAAAAGCCAGGTCAA 57.410 32.000 0.00 0.00 0.00 3.18
2503 2855 7.286775 AGTTTATAAAACTCAAAAGCCAGGTCA 59.713 33.333 0.00 0.00 0.00 4.02
2504 2856 7.658261 AGTTTATAAAACTCAAAAGCCAGGTC 58.342 34.615 0.00 0.00 0.00 3.85
2505 2857 7.597288 AGTTTATAAAACTCAAAAGCCAGGT 57.403 32.000 0.00 0.00 0.00 4.00
2520 2872 9.974980 CAGCTAAAGGGTTTTTGAGTTTATAAA 57.025 29.630 0.00 0.00 0.00 1.40
2521 2873 8.581578 CCAGCTAAAGGGTTTTTGAGTTTATAA 58.418 33.333 0.00 0.00 0.00 0.98
2522 2874 7.177744 CCCAGCTAAAGGGTTTTTGAGTTTATA 59.822 37.037 0.00 0.00 41.61 0.98
2523 2875 6.014584 CCCAGCTAAAGGGTTTTTGAGTTTAT 60.015 38.462 0.00 0.00 41.61 1.40
2524 2876 5.303333 CCCAGCTAAAGGGTTTTTGAGTTTA 59.697 40.000 0.00 0.00 41.61 2.01
2525 2877 4.100963 CCCAGCTAAAGGGTTTTTGAGTTT 59.899 41.667 0.00 0.00 41.61 2.66
2526 2878 3.641436 CCCAGCTAAAGGGTTTTTGAGTT 59.359 43.478 0.00 0.00 41.61 3.01
2527 2879 3.230976 CCCAGCTAAAGGGTTTTTGAGT 58.769 45.455 0.00 0.00 41.61 3.41
2528 2880 3.942130 CCCAGCTAAAGGGTTTTTGAG 57.058 47.619 0.00 0.00 41.61 3.02
2529 2881 4.693058 TTAGCCCAGCTAAAGGGTTTTTGA 60.693 41.667 9.27 0.00 46.30 2.69
2530 2882 3.576550 TTAGCCCAGCTAAAGGGTTTTTG 59.423 43.478 9.27 0.00 46.30 2.44
2531 2883 3.851979 TTAGCCCAGCTAAAGGGTTTTT 58.148 40.909 9.27 0.00 46.30 1.94
2532 2884 3.536075 TTAGCCCAGCTAAAGGGTTTT 57.464 42.857 9.27 0.00 46.30 2.43
2541 2893 5.693769 AGTAGACAAATTTAGCCCAGCTA 57.306 39.130 0.00 0.00 40.44 3.32
2542 2894 4.576330 AGTAGACAAATTTAGCCCAGCT 57.424 40.909 0.00 0.00 43.41 4.24
2543 2895 4.270325 CGTAGTAGACAAATTTAGCCCAGC 59.730 45.833 0.00 0.00 0.00 4.85
2544 2896 5.416947 ACGTAGTAGACAAATTTAGCCCAG 58.583 41.667 0.00 0.00 41.94 4.45
2545 2897 5.410355 ACGTAGTAGACAAATTTAGCCCA 57.590 39.130 0.00 0.00 41.94 5.36
2546 2898 6.732531 AAACGTAGTAGACAAATTTAGCCC 57.267 37.500 0.00 0.00 45.00 5.19
2547 2899 7.019418 CCAAAACGTAGTAGACAAATTTAGCC 58.981 38.462 0.00 0.00 45.00 3.93
2548 2900 7.019418 CCCAAAACGTAGTAGACAAATTTAGC 58.981 38.462 0.00 0.00 45.00 3.09
2594 2950 4.577693 AGCAAAACATACAGCATCGATCAT 59.422 37.500 0.00 0.00 0.00 2.45
2595 2951 3.940852 AGCAAAACATACAGCATCGATCA 59.059 39.130 0.00 0.00 0.00 2.92
2596 2952 4.277258 CAGCAAAACATACAGCATCGATC 58.723 43.478 0.00 0.00 0.00 3.69
2597 2953 3.065786 CCAGCAAAACATACAGCATCGAT 59.934 43.478 0.00 0.00 0.00 3.59
2598 2954 2.419673 CCAGCAAAACATACAGCATCGA 59.580 45.455 0.00 0.00 0.00 3.59
2599 2955 2.162208 ACCAGCAAAACATACAGCATCG 59.838 45.455 0.00 0.00 0.00 3.84
2604 2960 6.978080 ACAAACTTAACCAGCAAAACATACAG 59.022 34.615 0.00 0.00 0.00 2.74
2641 2997 4.868734 ACGTAGGTCTAGCATTTTTGTAGC 59.131 41.667 0.00 0.00 0.00 3.58
2644 3000 5.873164 CCTTACGTAGGTCTAGCATTTTTGT 59.127 40.000 3.84 0.00 39.39 2.83
2645 3001 6.345920 CCTTACGTAGGTCTAGCATTTTTG 57.654 41.667 3.84 0.00 39.39 2.44
2676 3032 8.064222 GTGGAAAAGAAAGTTTACGTAGGTTAC 58.936 37.037 0.00 0.00 0.00 2.50
2677 3033 7.986889 AGTGGAAAAGAAAGTTTACGTAGGTTA 59.013 33.333 0.00 0.00 0.00 2.85
2678 3034 6.825213 AGTGGAAAAGAAAGTTTACGTAGGTT 59.175 34.615 0.00 0.00 0.00 3.50
2679 3035 6.351711 AGTGGAAAAGAAAGTTTACGTAGGT 58.648 36.000 0.00 0.00 0.00 3.08
2680 3036 6.856135 AGTGGAAAAGAAAGTTTACGTAGG 57.144 37.500 0.00 0.00 0.00 3.18
2681 3037 9.038803 AGTTAGTGGAAAAGAAAGTTTACGTAG 57.961 33.333 0.00 0.00 0.00 3.51
2682 3038 8.819974 CAGTTAGTGGAAAAGAAAGTTTACGTA 58.180 33.333 0.00 0.00 0.00 3.57
2683 3039 7.550196 TCAGTTAGTGGAAAAGAAAGTTTACGT 59.450 33.333 0.00 0.00 0.00 3.57
2684 3040 7.912383 TCAGTTAGTGGAAAAGAAAGTTTACG 58.088 34.615 0.00 0.00 0.00 3.18
2685 3041 9.499585 GTTCAGTTAGTGGAAAAGAAAGTTTAC 57.500 33.333 0.00 0.00 0.00 2.01
2686 3042 9.233649 TGTTCAGTTAGTGGAAAAGAAAGTTTA 57.766 29.630 0.00 0.00 0.00 2.01
2687 3043 8.117813 TGTTCAGTTAGTGGAAAAGAAAGTTT 57.882 30.769 0.00 0.00 0.00 2.66
2688 3044 7.696992 TGTTCAGTTAGTGGAAAAGAAAGTT 57.303 32.000 0.00 0.00 0.00 2.66
2689 3045 7.775561 AGATGTTCAGTTAGTGGAAAAGAAAGT 59.224 33.333 0.00 0.00 0.00 2.66
2690 3046 8.159344 AGATGTTCAGTTAGTGGAAAAGAAAG 57.841 34.615 0.00 0.00 0.00 2.62
2691 3047 9.793259 ATAGATGTTCAGTTAGTGGAAAAGAAA 57.207 29.630 0.00 0.00 0.00 2.52
2692 3048 9.793259 AATAGATGTTCAGTTAGTGGAAAAGAA 57.207 29.630 0.00 0.00 0.00 2.52
2693 3049 9.436957 GAATAGATGTTCAGTTAGTGGAAAAGA 57.563 33.333 0.00 0.00 0.00 2.52
2694 3050 9.219603 TGAATAGATGTTCAGTTAGTGGAAAAG 57.780 33.333 0.00 0.00 33.41 2.27
2695 3051 8.999431 GTGAATAGATGTTCAGTTAGTGGAAAA 58.001 33.333 0.00 0.00 38.68 2.29
2696 3052 8.154203 TGTGAATAGATGTTCAGTTAGTGGAAA 58.846 33.333 0.00 0.00 38.68 3.13
2697 3053 7.676004 TGTGAATAGATGTTCAGTTAGTGGAA 58.324 34.615 0.00 0.00 38.68 3.53
2698 3054 7.239763 TGTGAATAGATGTTCAGTTAGTGGA 57.760 36.000 0.00 0.00 38.68 4.02
2699 3055 7.413438 GCTTGTGAATAGATGTTCAGTTAGTGG 60.413 40.741 0.00 0.00 38.68 4.00
2700 3056 7.118245 TGCTTGTGAATAGATGTTCAGTTAGTG 59.882 37.037 0.00 0.00 38.68 2.74
2701 3057 7.161404 TGCTTGTGAATAGATGTTCAGTTAGT 58.839 34.615 0.00 0.00 38.68 2.24
2702 3058 7.601073 TGCTTGTGAATAGATGTTCAGTTAG 57.399 36.000 0.00 0.00 38.68 2.34
2703 3059 9.665719 TTATGCTTGTGAATAGATGTTCAGTTA 57.334 29.630 0.00 0.00 38.68 2.24
2704 3060 8.454106 GTTATGCTTGTGAATAGATGTTCAGTT 58.546 33.333 0.00 0.00 38.68 3.16
2705 3061 7.066284 GGTTATGCTTGTGAATAGATGTTCAGT 59.934 37.037 0.00 0.00 38.68 3.41
2706 3062 7.066163 TGGTTATGCTTGTGAATAGATGTTCAG 59.934 37.037 0.00 0.00 38.68 3.02
2707 3063 6.883756 TGGTTATGCTTGTGAATAGATGTTCA 59.116 34.615 0.00 0.00 35.84 3.18
2708 3064 7.320443 TGGTTATGCTTGTGAATAGATGTTC 57.680 36.000 0.00 0.00 0.00 3.18
2709 3065 7.886629 ATGGTTATGCTTGTGAATAGATGTT 57.113 32.000 0.00 0.00 0.00 2.71
2710 3066 7.886629 AATGGTTATGCTTGTGAATAGATGT 57.113 32.000 0.00 0.00 0.00 3.06
2711 3067 9.590451 AAAAATGGTTATGCTTGTGAATAGATG 57.410 29.630 0.00 0.00 0.00 2.90
2734 3090 7.821846 AGTTGCTCTTATGTTTTTCACCAAAAA 59.178 29.630 0.00 0.00 38.84 1.94
2735 3091 7.327214 AGTTGCTCTTATGTTTTTCACCAAAA 58.673 30.769 0.00 0.00 31.50 2.44
2736 3092 6.872920 AGTTGCTCTTATGTTTTTCACCAAA 58.127 32.000 0.00 0.00 0.00 3.28
2737 3093 6.460953 GGAGTTGCTCTTATGTTTTTCACCAA 60.461 38.462 0.00 0.00 0.00 3.67
2738 3094 5.009610 GGAGTTGCTCTTATGTTTTTCACCA 59.990 40.000 0.00 0.00 0.00 4.17
2739 3095 5.009610 TGGAGTTGCTCTTATGTTTTTCACC 59.990 40.000 0.00 0.00 0.00 4.02
2740 3096 6.072112 TGGAGTTGCTCTTATGTTTTTCAC 57.928 37.500 0.00 0.00 0.00 3.18
2741 3097 6.707440 TTGGAGTTGCTCTTATGTTTTTCA 57.293 33.333 0.00 0.00 0.00 2.69
2742 3098 6.587608 CCATTGGAGTTGCTCTTATGTTTTTC 59.412 38.462 0.00 0.00 0.00 2.29
2743 3099 6.267471 TCCATTGGAGTTGCTCTTATGTTTTT 59.733 34.615 0.00 0.00 0.00 1.94
2744 3100 5.774690 TCCATTGGAGTTGCTCTTATGTTTT 59.225 36.000 0.00 0.00 0.00 2.43
2745 3101 5.324409 TCCATTGGAGTTGCTCTTATGTTT 58.676 37.500 0.00 0.00 0.00 2.83
2746 3102 4.922206 TCCATTGGAGTTGCTCTTATGTT 58.078 39.130 0.00 0.00 0.00 2.71
2747 3103 4.521146 CTCCATTGGAGTTGCTCTTATGT 58.479 43.478 22.45 0.00 44.25 2.29
2768 3124 2.125673 CGGACGAAATGGGTCGCT 60.126 61.111 0.00 0.00 45.00 4.93
2790 3146 2.902846 CGCCAACCCAAACGGACA 60.903 61.111 0.00 0.00 34.64 4.02
2803 3159 3.283684 CCTTTTGTGTCCGCGCCA 61.284 61.111 0.00 0.00 0.00 5.69
2887 3244 2.670789 CGCAAATCCGGCTCAAAAATGA 60.671 45.455 0.00 0.00 0.00 2.57
3194 3579 1.095600 CATTCAGACGTCGGAGGAGA 58.904 55.000 17.70 4.46 0.00 3.71
3325 3710 1.768684 AAGCAAAGGAGGACGGAGCA 61.769 55.000 0.00 0.00 0.00 4.26
3377 3783 2.539338 TTGTGGTGCGAACGCTTCC 61.539 57.895 19.32 19.43 42.51 3.46


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

AutoCloner maintained by Alex Coulton.