Multiple sequence alignment - TraesCS3B01G403600

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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 TraesCS3B01G403600 chr3B 100.000 4724 0 0 1 4724 637644231 637648954 0.000000e+00 8724.0
1 TraesCS3B01G403600 chr3B 95.039 907 42 3 1 906 1633923 1633019 0.000000e+00 1423.0
2 TraesCS3B01G403600 chr3B 90.516 1065 58 22 1509 2550 637898892 637899936 0.000000e+00 1367.0
3 TraesCS3B01G403600 chr3B 84.990 1026 112 23 2729 3718 637900182 637901201 0.000000e+00 1003.0
4 TraesCS3B01G403600 chr3B 88.172 465 45 4 4040 4502 637901544 637902000 3.590000e-151 545.0
5 TraesCS3B01G403600 chr3B 88.802 384 39 4 1006 1388 637898520 637898900 7.990000e-128 468.0
6 TraesCS3B01G403600 chr3B 100.000 238 0 0 5035 5272 637649265 637649502 1.740000e-119 440.0
7 TraesCS3B01G403600 chr3B 87.111 225 27 2 5049 5272 157382323 157382546 2.440000e-63 254.0
8 TraesCS3B01G403600 chr3B 85.169 236 33 2 5039 5272 245264522 245264757 1.900000e-59 241.0
9 TraesCS3B01G403600 chr3B 91.860 86 6 1 2645 2730 637899934 637900018 9.270000e-23 119.0
10 TraesCS3B01G403600 chr3A 92.362 1702 89 15 920 2600 621662813 621664494 0.000000e+00 2385.0
11 TraesCS3B01G403600 chr3A 88.763 1949 147 33 2595 4493 621664595 621666521 0.000000e+00 2320.0
12 TraesCS3B01G403600 chr3A 86.758 219 26 3 5039 5256 749232638 749232854 1.900000e-59 241.0
13 TraesCS3B01G403600 chr5B 95.480 907 39 2 1 906 701869899 701870804 0.000000e+00 1447.0
14 TraesCS3B01G403600 chr5B 95.374 908 40 2 1 907 115872803 115871897 0.000000e+00 1443.0
15 TraesCS3B01G403600 chr5B 83.024 754 98 10 1457 2209 637399453 637400177 0.000000e+00 656.0
16 TraesCS3B01G403600 chr2B 94.846 912 44 3 1 911 731625676 731626585 0.000000e+00 1421.0
17 TraesCS3B01G403600 chr2B 91.531 921 52 13 1 906 611697421 611698330 0.000000e+00 1245.0
18 TraesCS3B01G403600 chr2B 87.051 919 72 20 19 906 98450029 98450931 0.000000e+00 994.0
19 TraesCS3B01G403600 chr2B 85.477 241 28 5 5037 5272 688214057 688214295 1.470000e-60 244.0
20 TraesCS3B01G403600 chrUn 95.857 869 34 2 1 869 8325366 8326232 0.000000e+00 1404.0
21 TraesCS3B01G403600 chrUn 80.388 877 123 23 1231 2096 340515290 340516128 5.800000e-174 621.0
22 TraesCS3B01G403600 chrUn 80.388 877 123 23 1231 2096 371116777 371117615 5.800000e-174 621.0
23 TraesCS3B01G403600 chr3D 92.797 944 48 13 1594 2529 478356766 478357697 0.000000e+00 1349.0
24 TraesCS3B01G403600 chr3D 84.637 1061 107 31 2676 3721 478357730 478358749 0.000000e+00 1005.0
25 TraesCS3B01G403600 chr3D 92.918 706 19 7 3799 4502 478358825 478359501 0.000000e+00 998.0
26 TraesCS3B01G403600 chr3D 94.814 617 30 2 922 1538 478356149 478356763 0.000000e+00 961.0
27 TraesCS3B01G403600 chr3D 83.123 1108 115 35 2645 3721 478437369 478438435 0.000000e+00 944.0
28 TraesCS3B01G403600 chr3D 83.308 659 70 19 3851 4493 478438540 478439174 5.920000e-159 571.0
29 TraesCS3B01G403600 chr3D 95.135 185 8 1 4538 4721 478361195 478361379 1.860000e-74 291.0
30 TraesCS3B01G403600 chr3D 87.764 237 28 1 5037 5272 306662766 306662530 5.200000e-70 276.0
31 TraesCS3B01G403600 chr3D 85.841 226 30 2 5049 5272 423019816 423019591 6.820000e-59 239.0
32 TraesCS3B01G403600 chr3D 83.173 208 13 13 2365 2550 478437164 478437371 2.520000e-38 171.0
33 TraesCS3B01G403600 chr3D 100.000 45 0 0 4502 4546 478359647 478359691 3.380000e-12 84.2
34 TraesCS3B01G403600 chr7B 91.848 920 48 14 1 906 465821812 465820906 0.000000e+00 1258.0
35 TraesCS3B01G403600 chr7B 83.533 753 95 8 1457 2209 677887461 677888184 0.000000e+00 676.0
36 TraesCS3B01G403600 chr1B 91.008 923 63 13 1 909 39832859 39831943 0.000000e+00 1227.0
37 TraesCS3B01G403600 chr1B 90.552 942 56 13 1 914 603223742 603222806 0.000000e+00 1216.0
38 TraesCS3B01G403600 chr4D 81.345 922 121 26 1186 2096 65469988 65469107 0.000000e+00 702.0
39 TraesCS3B01G403600 chr4B 83.687 754 93 7 1457 2209 117025532 117024808 0.000000e+00 684.0
40 TraesCS3B01G403600 chr2A 81.023 880 118 22 1228 2096 66017410 66018251 0.000000e+00 654.0
41 TraesCS3B01G403600 chr4A 84.035 689 80 14 1418 2096 540911958 540912626 2.070000e-178 636.0
42 TraesCS3B01G403600 chr5A 80.341 880 124 23 1228 2096 699745089 699745930 5.800000e-174 621.0
43 TraesCS3B01G403600 chr5A 82.278 79 13 1 4633 4710 20645955 20645877 3.410000e-07 67.6
44 TraesCS3B01G403600 chr1D 86.695 233 28 3 5042 5272 448234692 448234461 6.780000e-64 255.0
45 TraesCS3B01G403600 chr6D 88.517 209 22 2 5065 5272 438272470 438272263 8.760000e-63 252.0
46 TraesCS3B01G403600 chr5D 86.937 222 24 4 5054 5272 58122517 58122298 1.470000e-60 244.0


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 TraesCS3B01G403600 chr3B 637644231 637649502 5271 False 4582.000000 8724 100.000000 1 5272 2 chr3B.!!$F3 5271
1 TraesCS3B01G403600 chr3B 1633019 1633923 904 True 1423.000000 1423 95.039000 1 906 1 chr3B.!!$R1 905
2 TraesCS3B01G403600 chr3B 637898520 637902000 3480 False 700.400000 1367 88.868000 1006 4502 5 chr3B.!!$F4 3496
3 TraesCS3B01G403600 chr3A 621662813 621666521 3708 False 2352.500000 2385 90.562500 920 4493 2 chr3A.!!$F2 3573
4 TraesCS3B01G403600 chr5B 701869899 701870804 905 False 1447.000000 1447 95.480000 1 906 1 chr5B.!!$F2 905
5 TraesCS3B01G403600 chr5B 115871897 115872803 906 True 1443.000000 1443 95.374000 1 907 1 chr5B.!!$R1 906
6 TraesCS3B01G403600 chr5B 637399453 637400177 724 False 656.000000 656 83.024000 1457 2209 1 chr5B.!!$F1 752
7 TraesCS3B01G403600 chr2B 731625676 731626585 909 False 1421.000000 1421 94.846000 1 911 1 chr2B.!!$F4 910
8 TraesCS3B01G403600 chr2B 611697421 611698330 909 False 1245.000000 1245 91.531000 1 906 1 chr2B.!!$F2 905
9 TraesCS3B01G403600 chr2B 98450029 98450931 902 False 994.000000 994 87.051000 19 906 1 chr2B.!!$F1 887
10 TraesCS3B01G403600 chrUn 8325366 8326232 866 False 1404.000000 1404 95.857000 1 869 1 chrUn.!!$F1 868
11 TraesCS3B01G403600 chrUn 340515290 340516128 838 False 621.000000 621 80.388000 1231 2096 1 chrUn.!!$F2 865
12 TraesCS3B01G403600 chrUn 371116777 371117615 838 False 621.000000 621 80.388000 1231 2096 1 chrUn.!!$F3 865
13 TraesCS3B01G403600 chr3D 478356149 478361379 5230 False 781.366667 1349 93.383500 922 4721 6 chr3D.!!$F1 3799
14 TraesCS3B01G403600 chr3D 478437164 478439174 2010 False 562.000000 944 83.201333 2365 4493 3 chr3D.!!$F2 2128
15 TraesCS3B01G403600 chr7B 465820906 465821812 906 True 1258.000000 1258 91.848000 1 906 1 chr7B.!!$R1 905
16 TraesCS3B01G403600 chr7B 677887461 677888184 723 False 676.000000 676 83.533000 1457 2209 1 chr7B.!!$F1 752
17 TraesCS3B01G403600 chr1B 39831943 39832859 916 True 1227.000000 1227 91.008000 1 909 1 chr1B.!!$R1 908
18 TraesCS3B01G403600 chr1B 603222806 603223742 936 True 1216.000000 1216 90.552000 1 914 1 chr1B.!!$R2 913
19 TraesCS3B01G403600 chr4D 65469107 65469988 881 True 702.000000 702 81.345000 1186 2096 1 chr4D.!!$R1 910
20 TraesCS3B01G403600 chr4B 117024808 117025532 724 True 684.000000 684 83.687000 1457 2209 1 chr4B.!!$R1 752
21 TraesCS3B01G403600 chr2A 66017410 66018251 841 False 654.000000 654 81.023000 1228 2096 1 chr2A.!!$F1 868
22 TraesCS3B01G403600 chr4A 540911958 540912626 668 False 636.000000 636 84.035000 1418 2096 1 chr4A.!!$F1 678
23 TraesCS3B01G403600 chr5A 699745089 699745930 841 False 621.000000 621 80.341000 1228 2096 1 chr5A.!!$F1 868

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
280 311 0.107897 CACTACAACCTATGGGCGCA 60.108 55.0 10.83 5.7 35.63 6.09 F
428 460 0.902984 ACACTAGGCCATCGGACACA 60.903 55.0 5.01 0.0 29.21 3.72 F
1254 1324 0.409876 TCCACCTGTACCAGCTCTCT 59.590 55.0 0.00 0.0 0.00 3.10 F
1329 1399 0.320421 CCCACAACCTGTTCGACGAT 60.320 55.0 0.00 0.0 0.00 3.73 F
2563 2692 0.468400 AGCTACTCCCTCCGATCCAC 60.468 60.0 0.00 0.0 0.00 4.02 F
3379 3812 0.035056 ATGTCGCTGAGGGAAAAGGG 60.035 55.0 0.00 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1086 1156 1.008424 CGCGTCGTAGGCAGATGAT 60.008 57.895 0.00 0.0 0.00 2.45 R
1311 1381 1.508632 AATCGTCGAACAGGTTGTGG 58.491 50.000 0.00 0.0 0.00 4.17 R
2967 3368 2.688446 ACGACGCCAGAAGATTATGAGA 59.312 45.455 0.00 0.0 0.00 3.27 R
3060 3467 4.092091 GCTGATCCTTGTTTCACGAGTTAG 59.908 45.833 0.00 0.0 0.00 2.34 R
4205 4854 1.074405 TGGTTGAAATGCTGGAGCTCT 59.926 47.619 14.64 0.0 42.66 4.09 R
5092 7412 0.098552 TGCATGCGGCTATTTGAACG 59.901 50.000 14.09 0.0 45.15 3.95 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
187 204 1.805869 GAGAACTGACAGCACAGCAT 58.194 50.000 1.25 0.00 41.06 3.79
204 221 1.462616 CATCAAATCCCTCACGGCAA 58.537 50.000 0.00 0.00 0.00 4.52
280 311 0.107897 CACTACAACCTATGGGCGCA 60.108 55.000 10.83 5.70 35.63 6.09
338 369 1.937191 AAATCCAAACCCTCCGCAAT 58.063 45.000 0.00 0.00 0.00 3.56
387 419 1.152963 GGCGATGGGTGCATACCTT 60.153 57.895 11.15 5.40 46.66 3.50
428 460 0.902984 ACACTAGGCCATCGGACACA 60.903 55.000 5.01 0.00 29.21 3.72
460 492 1.148273 GACCTTCAGCACACACCCA 59.852 57.895 0.00 0.00 0.00 4.51
585 618 4.803426 CACGCCCTCCGCTCTCAC 62.803 72.222 0.00 0.00 41.76 3.51
667 712 0.938926 AGGGAGGGAGAGAAGGGGAT 60.939 60.000 0.00 0.00 0.00 3.85
722 777 1.214367 GTCTCGGCAGTTTCGAACAA 58.786 50.000 0.00 0.00 36.15 2.83
911 981 9.045223 AGTTGCTTTTTAGCATTTAGGAAAAAG 57.955 29.630 12.21 12.21 45.36 2.27
914 984 9.777297 TGCTTTTTAGCATTTAGGAAAAAGAAT 57.223 25.926 18.14 0.00 45.40 2.40
937 1007 1.227823 TGACAACCAAGTCCCTGCG 60.228 57.895 0.00 0.00 37.73 5.18
944 1014 1.172180 CCAAGTCCCTGCGCTTTCAA 61.172 55.000 9.73 0.00 0.00 2.69
1254 1324 0.409876 TCCACCTGTACCAGCTCTCT 59.590 55.000 0.00 0.00 0.00 3.10
1268 1338 1.002544 GCTCTCTGTGCAGGTAACCTT 59.997 52.381 0.00 0.00 37.17 3.50
1281 1351 2.290071 GGTAACCTTGCTAGCTTCCACA 60.290 50.000 17.23 0.00 0.00 4.17
1293 1363 1.270839 GCTTCCACAGTAGCTTGGACA 60.271 52.381 4.28 0.00 41.79 4.02
1302 1372 3.077359 AGTAGCTTGGACATGTGAAAGC 58.923 45.455 24.73 24.73 44.24 3.51
1311 1381 1.675641 ATGTGAAAGCCTCCGTGCC 60.676 57.895 0.00 0.00 0.00 5.01
1329 1399 0.320421 CCCACAACCTGTTCGACGAT 60.320 55.000 0.00 0.00 0.00 3.73
1330 1400 1.508632 CCACAACCTGTTCGACGATT 58.491 50.000 0.00 0.00 0.00 3.34
1399 1470 3.817647 CAGCTACCTGCAGAAGTTCTTTT 59.182 43.478 17.39 0.00 45.94 2.27
1410 1481 6.183360 TGCAGAAGTTCTTTTTGATGTACGTT 60.183 34.615 1.56 0.00 0.00 3.99
1476 1548 1.329171 CCCTCCTCAGGTCAGAGCAG 61.329 65.000 1.66 0.00 38.30 4.24
1527 1610 4.851639 ATCTACCCTGCTGTCAATTTCT 57.148 40.909 0.00 0.00 0.00 2.52
1592 1675 8.065627 TCTCAGGAGTCCCATTAGTAAGAAATA 58.934 37.037 5.25 0.00 33.88 1.40
1681 1770 5.790593 TGGAGTACTTTGGTCAGTATTCAC 58.209 41.667 0.00 0.00 37.60 3.18
1968 2063 8.385267 TTGTCAAGCAAAAGATCAGTGATCTCA 61.385 37.037 31.00 19.67 39.03 3.27
2017 2118 3.026630 TGGCTCTACTGAAACGAACAG 57.973 47.619 0.00 0.00 40.68 3.16
2020 2121 3.060602 GCTCTACTGAAACGAACAGCTT 58.939 45.455 0.00 0.00 38.74 3.74
2138 2239 3.006323 ACAGTTGTTGTTGCCTTCACAAA 59.994 39.130 0.00 0.00 36.31 2.83
2324 2426 2.894387 GCAGCACATCGAGGCCTC 60.894 66.667 23.79 23.79 0.00 4.70
2563 2692 0.468400 AGCTACTCCCTCCGATCCAC 60.468 60.000 0.00 0.00 0.00 4.02
2564 2693 0.755698 GCTACTCCCTCCGATCCACA 60.756 60.000 0.00 0.00 0.00 4.17
2575 2704 6.003950 CCCTCCGATCCACATATTAATTGTT 58.996 40.000 0.00 0.00 0.00 2.83
2580 2709 6.238731 CCGATCCACATATTAATTGTTGCTGT 60.239 38.462 0.00 0.00 0.00 4.40
2626 2861 3.366724 TCGTACTAAAGCAGCGACAATTG 59.633 43.478 3.24 3.24 0.00 2.32
2627 2862 3.366724 CGTACTAAAGCAGCGACAATTGA 59.633 43.478 13.59 0.00 0.00 2.57
2636 2871 5.299949 AGCAGCGACAATTGATATGTATCA 58.700 37.500 13.59 0.00 40.69 2.15
2641 2876 5.349817 GCGACAATTGATATGTATCAGAGGG 59.650 44.000 13.59 0.00 42.99 4.30
2643 2878 6.810676 CGACAATTGATATGTATCAGAGGGAG 59.189 42.308 13.59 0.00 42.99 4.30
2847 3247 8.032952 TGATGATTCAGTACACAAAGATTGTC 57.967 34.615 0.00 0.00 43.23 3.18
2856 3256 7.225538 CAGTACACAAAGATTGTCATATCTCCC 59.774 40.741 0.00 0.00 43.23 4.30
2878 3279 4.460382 CCATGTATTTGTTGACAGAGCCTT 59.540 41.667 0.00 0.00 0.00 4.35
2921 3322 9.151471 CATATAATTTCCACCCTTGTATAGTCG 57.849 37.037 0.00 0.00 0.00 4.18
2922 3323 2.973694 TTCCACCCTTGTATAGTCGC 57.026 50.000 0.00 0.00 0.00 5.19
2963 3364 5.561725 GCAATCTGCAGTAGCTTTATTAGCC 60.562 44.000 14.67 0.00 46.71 3.93
2998 3402 6.102006 TCTTCTGGCGTCGTATTAAATTTG 57.898 37.500 0.00 0.00 0.00 2.32
3001 3405 6.102006 TCTGGCGTCGTATTAAATTTGAAG 57.898 37.500 0.00 0.00 0.00 3.02
3060 3467 4.819088 GGGAGCAAGAAGAGTTTGATATCC 59.181 45.833 0.00 0.00 0.00 2.59
3153 3560 0.171007 CCATTGGCGCCTGTAAGTTG 59.829 55.000 29.70 13.41 0.00 3.16
3155 3562 0.893270 ATTGGCGCCTGTAAGTTGCA 60.893 50.000 29.70 0.00 34.28 4.08
3167 3574 7.042051 CGCCTGTAAGTTGCATATACATTACTT 60.042 37.037 7.07 4.73 0.00 2.24
3168 3575 8.070171 GCCTGTAAGTTGCATATACATTACTTG 58.930 37.037 6.44 2.64 0.00 3.16
3346 3779 0.251916 CGGCAGTAGGGATGGTTGAA 59.748 55.000 0.00 0.00 0.00 2.69
3379 3812 0.035056 ATGTCGCTGAGGGAAAAGGG 60.035 55.000 0.00 0.00 0.00 3.95
3382 3815 2.766660 GCTGAGGGAAAAGGGGCT 59.233 61.111 0.00 0.00 0.00 5.19
3386 3819 0.326927 TGAGGGAAAAGGGGCTTACG 59.673 55.000 0.00 0.00 0.00 3.18
3440 3884 8.906867 AGAGAGAAATGTTTCTGTTGAATCAAA 58.093 29.630 12.39 0.00 46.84 2.69
3564 4011 3.434940 ACCAAACCAGATCCTGTAACC 57.565 47.619 0.00 0.00 0.00 2.85
3572 4019 4.656112 ACCAGATCCTGTAACCCAAGATAG 59.344 45.833 0.00 0.00 0.00 2.08
3573 4020 4.901849 CCAGATCCTGTAACCCAAGATAGA 59.098 45.833 0.00 0.00 0.00 1.98
3574 4021 5.545723 CCAGATCCTGTAACCCAAGATAGAT 59.454 44.000 0.00 0.00 0.00 1.98
3575 4022 6.462500 CAGATCCTGTAACCCAAGATAGATG 58.538 44.000 0.00 0.00 0.00 2.90
3650 4099 1.000938 CAACAGACTTTGGCCTCTTGC 60.001 52.381 3.32 0.00 40.16 4.01
3701 4150 6.769341 AGCTGTCATACTTTGATGATAATGCA 59.231 34.615 0.00 0.00 38.11 3.96
3742 4217 1.102978 CAAGGCGGAATAAGGTTGGG 58.897 55.000 0.00 0.00 0.00 4.12
3743 4218 0.702316 AAGGCGGAATAAGGTTGGGT 59.298 50.000 0.00 0.00 0.00 4.51
3747 4222 3.090790 GGCGGAATAAGGTTGGGTTTTA 58.909 45.455 0.00 0.00 0.00 1.52
3818 4293 2.101415 CTGATACGATTGGTGCCAGAGA 59.899 50.000 0.00 0.00 33.76 3.10
3819 4294 2.101415 TGATACGATTGGTGCCAGAGAG 59.899 50.000 0.00 0.00 0.00 3.20
3826 4301 1.072159 GGTGCCAGAGAGTTGCTGT 59.928 57.895 0.00 0.00 0.00 4.40
3828 4303 0.250038 GTGCCAGAGAGTTGCTGTGA 60.250 55.000 0.00 0.00 40.17 3.58
3833 4308 2.740981 CCAGAGAGTTGCTGTGATTGTC 59.259 50.000 0.00 0.00 40.17 3.18
3841 4316 4.692625 AGTTGCTGTGATTGTCTATGTGTC 59.307 41.667 0.00 0.00 0.00 3.67
3860 4342 4.094294 GTGTCAGCAATACGCATTTTCCTA 59.906 41.667 0.00 0.00 46.13 2.94
3880 4362 6.724351 TCCTATATGCCGTATCCTTGTACTA 58.276 40.000 0.00 0.00 0.00 1.82
4056 4705 7.558161 TCTTCAGAATTGCAATTCATATCGT 57.442 32.000 39.58 23.42 45.59 3.73
4293 4944 1.477553 TGAAATGATCCTTGCTGCCC 58.522 50.000 0.00 0.00 0.00 5.36
4305 4956 2.914289 CTGCCCCCTGCTAGGAAG 59.086 66.667 4.00 0.00 37.67 3.46
4309 4960 1.348775 GCCCCCTGCTAGGAAGATGT 61.349 60.000 4.00 0.00 37.67 3.06
4325 4976 2.162681 GATGTGGTGGAAAGTTGGGAG 58.837 52.381 0.00 0.00 0.00 4.30
4395 5046 4.575973 GGATGCTCGCCCATGCCT 62.576 66.667 0.00 0.00 0.00 4.75
4400 5051 0.395586 TGCTCGCCCATGCCTTATTT 60.396 50.000 0.00 0.00 0.00 1.40
4563 6882 5.884792 TGTAATAATGTGTGTGCATGGATGA 59.115 36.000 0.00 0.00 0.00 2.92
4601 6920 0.525668 GTAGATGGTGGAGTGCGTCG 60.526 60.000 0.00 0.00 0.00 5.12
4650 6969 1.742880 CTCCTGGTGGACATGTGCG 60.743 63.158 13.03 0.00 37.46 5.34
4721 7041 1.689273 CGCTAGGAGTTAGGGCATCTT 59.311 52.381 0.00 0.00 35.80 2.40
4722 7042 2.288518 CGCTAGGAGTTAGGGCATCTTC 60.289 54.545 0.00 0.00 35.80 2.87
4723 7043 2.700897 GCTAGGAGTTAGGGCATCTTCA 59.299 50.000 0.00 0.00 0.00 3.02
5055 7375 4.473477 CCGTCTCCCTCATCTTTTAAGT 57.527 45.455 0.00 0.00 0.00 2.24
5056 7376 4.434520 CCGTCTCCCTCATCTTTTAAGTC 58.565 47.826 0.00 0.00 0.00 3.01
5057 7377 4.434520 CGTCTCCCTCATCTTTTAAGTCC 58.565 47.826 0.00 0.00 0.00 3.85
5058 7378 4.081642 CGTCTCCCTCATCTTTTAAGTCCA 60.082 45.833 0.00 0.00 0.00 4.02
5059 7379 5.179533 GTCTCCCTCATCTTTTAAGTCCAC 58.820 45.833 0.00 0.00 0.00 4.02
5060 7380 4.844085 TCTCCCTCATCTTTTAAGTCCACA 59.156 41.667 0.00 0.00 0.00 4.17
5061 7381 4.906618 TCCCTCATCTTTTAAGTCCACAC 58.093 43.478 0.00 0.00 0.00 3.82
5062 7382 3.684788 CCCTCATCTTTTAAGTCCACACG 59.315 47.826 0.00 0.00 0.00 4.49
5063 7383 4.562757 CCCTCATCTTTTAAGTCCACACGA 60.563 45.833 0.00 0.00 0.00 4.35
5064 7384 5.178797 CCTCATCTTTTAAGTCCACACGAT 58.821 41.667 0.00 0.00 0.00 3.73
5065 7385 5.292101 CCTCATCTTTTAAGTCCACACGATC 59.708 44.000 0.00 0.00 0.00 3.69
5066 7386 5.789521 TCATCTTTTAAGTCCACACGATCA 58.210 37.500 0.00 0.00 0.00 2.92
5067 7387 6.227522 TCATCTTTTAAGTCCACACGATCAA 58.772 36.000 0.00 0.00 0.00 2.57
5068 7388 6.708502 TCATCTTTTAAGTCCACACGATCAAA 59.291 34.615 0.00 0.00 0.00 2.69
5069 7389 7.390440 TCATCTTTTAAGTCCACACGATCAAAT 59.610 33.333 0.00 0.00 0.00 2.32
5070 7390 8.664798 CATCTTTTAAGTCCACACGATCAAATA 58.335 33.333 0.00 0.00 0.00 1.40
5071 7391 8.251750 TCTTTTAAGTCCACACGATCAAATAG 57.748 34.615 0.00 0.00 0.00 1.73
5072 7392 6.417191 TTTAAGTCCACACGATCAAATAGC 57.583 37.500 0.00 0.00 0.00 2.97
5073 7393 2.906354 AGTCCACACGATCAAATAGCC 58.094 47.619 0.00 0.00 0.00 3.93
5074 7394 2.236146 AGTCCACACGATCAAATAGCCA 59.764 45.455 0.00 0.00 0.00 4.75
5075 7395 3.118261 AGTCCACACGATCAAATAGCCAT 60.118 43.478 0.00 0.00 0.00 4.40
5076 7396 4.100963 AGTCCACACGATCAAATAGCCATA 59.899 41.667 0.00 0.00 0.00 2.74
5077 7397 4.997395 GTCCACACGATCAAATAGCCATAT 59.003 41.667 0.00 0.00 0.00 1.78
5078 7398 6.014584 AGTCCACACGATCAAATAGCCATATA 60.015 38.462 0.00 0.00 0.00 0.86
5079 7399 6.090898 GTCCACACGATCAAATAGCCATATAC 59.909 42.308 0.00 0.00 0.00 1.47
5080 7400 5.931724 CCACACGATCAAATAGCCATATACA 59.068 40.000 0.00 0.00 0.00 2.29
5081 7401 6.595326 CCACACGATCAAATAGCCATATACAT 59.405 38.462 0.00 0.00 0.00 2.29
5082 7402 7.763985 CCACACGATCAAATAGCCATATACATA 59.236 37.037 0.00 0.00 0.00 2.29
5083 7403 8.811378 CACACGATCAAATAGCCATATACATAG 58.189 37.037 0.00 0.00 0.00 2.23
5084 7404 8.749354 ACACGATCAAATAGCCATATACATAGA 58.251 33.333 0.00 0.00 0.00 1.98
5085 7405 9.242477 CACGATCAAATAGCCATATACATAGAG 57.758 37.037 0.00 0.00 0.00 2.43
5086 7406 8.972127 ACGATCAAATAGCCATATACATAGAGT 58.028 33.333 0.00 0.00 0.00 3.24
5097 7417 9.850628 GCCATATACATAGAGTATAAACGTTCA 57.149 33.333 0.00 0.00 45.97 3.18
5104 7424 9.257651 ACATAGAGTATAAACGTTCAAATAGCC 57.742 33.333 0.00 0.00 0.00 3.93
5105 7425 6.823678 AGAGTATAAACGTTCAAATAGCCG 57.176 37.500 0.00 0.00 0.00 5.52
5106 7426 5.233689 AGAGTATAAACGTTCAAATAGCCGC 59.766 40.000 0.00 0.00 0.00 6.53
5107 7427 4.871557 AGTATAAACGTTCAAATAGCCGCA 59.128 37.500 0.00 0.00 0.00 5.69
5108 7428 4.893424 ATAAACGTTCAAATAGCCGCAT 57.107 36.364 0.00 0.00 0.00 4.73
5109 7429 2.542766 AACGTTCAAATAGCCGCATG 57.457 45.000 0.00 0.00 0.00 4.06
5110 7430 0.098728 ACGTTCAAATAGCCGCATGC 59.901 50.000 7.91 7.91 41.71 4.06
5111 7431 0.098552 CGTTCAAATAGCCGCATGCA 59.901 50.000 19.57 0.00 44.83 3.96
5112 7432 1.268692 CGTTCAAATAGCCGCATGCAT 60.269 47.619 19.57 5.35 44.83 3.96
5113 7433 2.388121 GTTCAAATAGCCGCATGCATC 58.612 47.619 19.57 8.33 44.83 3.91
5114 7434 1.677942 TCAAATAGCCGCATGCATCA 58.322 45.000 19.57 0.00 44.83 3.07
5115 7435 1.334556 TCAAATAGCCGCATGCATCAC 59.665 47.619 19.57 3.20 44.83 3.06
5116 7436 1.335810 CAAATAGCCGCATGCATCACT 59.664 47.619 19.57 10.94 44.83 3.41
5117 7437 2.549064 AATAGCCGCATGCATCACTA 57.451 45.000 19.57 12.78 44.83 2.74
5118 7438 2.090400 ATAGCCGCATGCATCACTAG 57.910 50.000 19.57 0.00 44.83 2.57
5119 7439 0.752658 TAGCCGCATGCATCACTAGT 59.247 50.000 19.57 0.00 44.83 2.57
5120 7440 0.107508 AGCCGCATGCATCACTAGTT 60.108 50.000 19.57 0.00 44.83 2.24
5121 7441 0.734889 GCCGCATGCATCACTAGTTT 59.265 50.000 19.57 0.00 40.77 2.66
5122 7442 1.939934 GCCGCATGCATCACTAGTTTA 59.060 47.619 19.57 0.00 40.77 2.01
5123 7443 2.354510 GCCGCATGCATCACTAGTTTAA 59.645 45.455 19.57 0.00 40.77 1.52
5124 7444 3.181501 GCCGCATGCATCACTAGTTTAAA 60.182 43.478 19.57 0.00 40.77 1.52
5125 7445 4.498009 GCCGCATGCATCACTAGTTTAAAT 60.498 41.667 19.57 0.00 40.77 1.40
5126 7446 5.581605 CCGCATGCATCACTAGTTTAAATT 58.418 37.500 19.57 0.00 0.00 1.82
5127 7447 6.035843 CCGCATGCATCACTAGTTTAAATTT 58.964 36.000 19.57 0.00 0.00 1.82
5128 7448 6.531240 CCGCATGCATCACTAGTTTAAATTTT 59.469 34.615 19.57 0.00 0.00 1.82
5129 7449 7.700234 CCGCATGCATCACTAGTTTAAATTTTA 59.300 33.333 19.57 0.00 0.00 1.52
5130 7450 9.071221 CGCATGCATCACTAGTTTAAATTTTAA 57.929 29.630 19.57 0.00 0.00 1.52
5168 7488 9.920946 ATTACATCCTAACATTGTTGTATCCTT 57.079 29.630 12.30 0.00 34.06 3.36
5169 7489 9.747898 TTACATCCTAACATTGTTGTATCCTTT 57.252 29.630 12.30 0.00 34.06 3.11
5171 7491 9.747898 ACATCCTAACATTGTTGTATCCTTTAA 57.252 29.630 12.30 0.00 34.06 1.52
5173 7493 8.570068 TCCTAACATTGTTGTATCCTTTAACC 57.430 34.615 12.30 0.00 34.06 2.85
5174 7494 7.334921 TCCTAACATTGTTGTATCCTTTAACCG 59.665 37.037 12.30 0.00 34.06 4.44
5175 7495 5.305139 ACATTGTTGTATCCTTTAACCGC 57.695 39.130 0.00 0.00 33.16 5.68
5176 7496 4.762765 ACATTGTTGTATCCTTTAACCGCA 59.237 37.500 0.00 0.00 33.16 5.69
5177 7497 4.752661 TTGTTGTATCCTTTAACCGCAC 57.247 40.909 0.00 0.00 0.00 5.34
5178 7498 3.741249 TGTTGTATCCTTTAACCGCACA 58.259 40.909 0.00 0.00 0.00 4.57
5179 7499 3.499157 TGTTGTATCCTTTAACCGCACAC 59.501 43.478 0.00 0.00 0.00 3.82
5180 7500 3.688694 TGTATCCTTTAACCGCACACT 57.311 42.857 0.00 0.00 0.00 3.55
5181 7501 3.331150 TGTATCCTTTAACCGCACACTG 58.669 45.455 0.00 0.00 0.00 3.66
5182 7502 2.851263 ATCCTTTAACCGCACACTGA 57.149 45.000 0.00 0.00 0.00 3.41
5183 7503 2.851263 TCCTTTAACCGCACACTGAT 57.149 45.000 0.00 0.00 0.00 2.90
5184 7504 2.422597 TCCTTTAACCGCACACTGATG 58.577 47.619 0.00 0.00 0.00 3.07
5185 7505 1.135689 CCTTTAACCGCACACTGATGC 60.136 52.381 0.00 0.00 42.48 3.91
5186 7506 1.806542 CTTTAACCGCACACTGATGCT 59.193 47.619 6.99 0.00 43.80 3.79
5187 7507 1.438651 TTAACCGCACACTGATGCTC 58.561 50.000 6.99 0.00 43.80 4.26
5188 7508 0.320050 TAACCGCACACTGATGCTCA 59.680 50.000 6.99 0.00 43.80 4.26
5189 7509 0.534877 AACCGCACACTGATGCTCAA 60.535 50.000 6.99 0.00 43.80 3.02
5190 7510 0.321919 ACCGCACACTGATGCTCAAT 60.322 50.000 6.99 0.00 43.80 2.57
5191 7511 0.376152 CCGCACACTGATGCTCAATC 59.624 55.000 6.99 0.00 43.80 2.67
5192 7512 1.081094 CGCACACTGATGCTCAATCA 58.919 50.000 6.99 0.00 43.80 2.57
5202 7522 5.369409 TGATGCTCAATCAGATCTTCCTT 57.631 39.130 0.00 0.00 40.50 3.36
5203 7523 5.366460 TGATGCTCAATCAGATCTTCCTTC 58.634 41.667 0.00 0.00 40.50 3.46
5204 7524 4.831674 TGCTCAATCAGATCTTCCTTCA 57.168 40.909 0.00 0.00 0.00 3.02
5205 7525 5.169992 TGCTCAATCAGATCTTCCTTCAA 57.830 39.130 0.00 0.00 0.00 2.69
5206 7526 5.752650 TGCTCAATCAGATCTTCCTTCAAT 58.247 37.500 0.00 0.00 0.00 2.57
5207 7527 6.185511 TGCTCAATCAGATCTTCCTTCAATT 58.814 36.000 0.00 0.00 0.00 2.32
5208 7528 6.095021 TGCTCAATCAGATCTTCCTTCAATTG 59.905 38.462 0.00 0.00 0.00 2.32
5209 7529 6.446781 TCAATCAGATCTTCCTTCAATTGC 57.553 37.500 0.00 0.00 0.00 3.56
5210 7530 6.185511 TCAATCAGATCTTCCTTCAATTGCT 58.814 36.000 0.00 0.00 0.00 3.91
5211 7531 6.662234 TCAATCAGATCTTCCTTCAATTGCTT 59.338 34.615 0.00 0.00 0.00 3.91
5212 7532 5.892160 TCAGATCTTCCTTCAATTGCTTG 57.108 39.130 0.00 0.00 0.00 4.01
5213 7533 5.319453 TCAGATCTTCCTTCAATTGCTTGT 58.681 37.500 0.00 0.00 33.87 3.16
5214 7534 5.182570 TCAGATCTTCCTTCAATTGCTTGTG 59.817 40.000 0.00 0.00 33.87 3.33
5215 7535 5.182570 CAGATCTTCCTTCAATTGCTTGTGA 59.817 40.000 0.00 0.00 33.87 3.58
5216 7536 5.415077 AGATCTTCCTTCAATTGCTTGTGAG 59.585 40.000 0.00 0.00 33.87 3.51
5217 7537 4.464008 TCTTCCTTCAATTGCTTGTGAGT 58.536 39.130 0.00 0.00 33.87 3.41
5218 7538 4.889409 TCTTCCTTCAATTGCTTGTGAGTT 59.111 37.500 0.00 0.00 33.87 3.01
5219 7539 4.572985 TCCTTCAATTGCTTGTGAGTTG 57.427 40.909 0.00 0.00 33.87 3.16
5220 7540 3.318839 TCCTTCAATTGCTTGTGAGTTGG 59.681 43.478 0.00 0.00 33.87 3.77
5221 7541 3.068590 CCTTCAATTGCTTGTGAGTTGGT 59.931 43.478 0.00 0.00 33.87 3.67
5222 7542 3.988379 TCAATTGCTTGTGAGTTGGTC 57.012 42.857 0.00 0.00 33.87 4.02
5223 7543 2.290367 TCAATTGCTTGTGAGTTGGTCG 59.710 45.455 0.00 0.00 33.87 4.79
5224 7544 2.254546 ATTGCTTGTGAGTTGGTCGA 57.745 45.000 0.00 0.00 0.00 4.20
5225 7545 2.254546 TTGCTTGTGAGTTGGTCGAT 57.745 45.000 0.00 0.00 0.00 3.59
5226 7546 1.511850 TGCTTGTGAGTTGGTCGATG 58.488 50.000 0.00 0.00 0.00 3.84
5227 7547 0.166814 GCTTGTGAGTTGGTCGATGC 59.833 55.000 0.00 0.00 0.00 3.91
5228 7548 0.798776 CTTGTGAGTTGGTCGATGCC 59.201 55.000 0.00 0.00 0.00 4.40
5229 7549 0.948623 TTGTGAGTTGGTCGATGCCG 60.949 55.000 0.00 0.00 37.07 5.69
5230 7550 1.080093 GTGAGTTGGTCGATGCCGA 60.080 57.895 0.00 0.00 43.35 5.54
5242 7562 4.145876 TCGATGCCGAATTAATTGATGC 57.854 40.909 5.17 5.90 42.51 3.91
5243 7563 3.563390 TCGATGCCGAATTAATTGATGCA 59.437 39.130 5.17 11.21 42.51 3.96
5244 7564 4.216042 TCGATGCCGAATTAATTGATGCAT 59.784 37.500 20.26 20.26 42.51 3.96
5245 7565 4.919168 CGATGCCGAATTAATTGATGCATT 59.081 37.500 20.74 10.98 38.02 3.56
5246 7566 5.060077 CGATGCCGAATTAATTGATGCATTC 59.940 40.000 20.74 15.36 38.02 2.67
5247 7567 4.289342 TGCCGAATTAATTGATGCATTCG 58.711 39.130 5.17 4.11 44.89 3.34
5259 7579 8.847444 AATTGATGCATTCGAATAAACTCTTC 57.153 30.769 10.97 6.45 0.00 2.87
5260 7580 6.983474 TGATGCATTCGAATAAACTCTTCA 57.017 33.333 10.97 8.58 0.00 3.02
5261 7581 7.376435 TGATGCATTCGAATAAACTCTTCAA 57.624 32.000 10.97 0.00 0.00 2.69
5262 7582 7.988737 TGATGCATTCGAATAAACTCTTCAAT 58.011 30.769 10.97 0.00 0.00 2.57
5263 7583 7.911727 TGATGCATTCGAATAAACTCTTCAATG 59.088 33.333 10.97 0.00 31.58 2.82
5264 7584 7.144722 TGCATTCGAATAAACTCTTCAATGT 57.855 32.000 10.97 0.00 31.35 2.71
5265 7585 7.022979 TGCATTCGAATAAACTCTTCAATGTG 58.977 34.615 10.97 0.00 31.35 3.21
5266 7586 6.470235 GCATTCGAATAAACTCTTCAATGTGG 59.530 38.462 10.97 0.00 31.35 4.17
5267 7587 5.545658 TCGAATAAACTCTTCAATGTGGC 57.454 39.130 0.00 0.00 0.00 5.01
5268 7588 4.394920 TCGAATAAACTCTTCAATGTGGCC 59.605 41.667 0.00 0.00 0.00 5.36
5269 7589 4.662145 GAATAAACTCTTCAATGTGGCCG 58.338 43.478 0.00 0.00 0.00 6.13
5270 7590 1.247567 AAACTCTTCAATGTGGCCGG 58.752 50.000 0.00 0.00 0.00 6.13
5271 7591 0.400213 AACTCTTCAATGTGGCCGGA 59.600 50.000 5.05 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.447586 AGTTGGCGAAATAGAGCTGTCTA 59.552 43.478 0.00 0.00 39.70 2.59
204 221 2.124085 TGGGGAATCACGGGGTCT 59.876 61.111 0.00 0.00 0.00 3.85
280 311 5.532406 CGAACATGGAGGTGGATTTAATCAT 59.468 40.000 7.29 0.00 0.00 2.45
338 369 2.310233 GCTTTCTGCGTGTGCTCGA 61.310 57.895 0.00 0.00 43.34 4.04
667 712 0.764890 CCAATCCGCTCCCCATTCTA 59.235 55.000 0.00 0.00 0.00 2.10
722 777 4.096003 CCCCGTCCGTTGGCTCAT 62.096 66.667 0.00 0.00 0.00 2.90
911 981 5.817816 CAGGGACTTGGTTGTCAGTATATTC 59.182 44.000 0.00 0.00 34.60 1.75
914 984 3.055385 GCAGGGACTTGGTTGTCAGTATA 60.055 47.826 0.00 0.00 34.60 1.47
916 986 1.071699 GCAGGGACTTGGTTGTCAGTA 59.928 52.381 0.00 0.00 34.60 2.74
917 987 0.179018 GCAGGGACTTGGTTGTCAGT 60.179 55.000 0.00 0.00 34.60 3.41
918 988 1.230635 CGCAGGGACTTGGTTGTCAG 61.231 60.000 0.00 0.00 34.60 3.51
937 1007 2.851195 TGGAACAGGAGAGTTGAAAGC 58.149 47.619 0.00 0.00 0.00 3.51
944 1014 0.771755 GGGGTTTGGAACAGGAGAGT 59.228 55.000 0.00 0.00 42.39 3.24
1086 1156 1.008424 CGCGTCGTAGGCAGATGAT 60.008 57.895 0.00 0.00 0.00 2.45
1143 1213 3.513768 TTCCGCTGCTGCTTCGTCA 62.514 57.895 14.03 0.00 36.97 4.35
1254 1324 1.610624 GCTAGCAAGGTTACCTGCACA 60.611 52.381 21.37 11.65 32.13 4.57
1281 1351 3.077359 GCTTTCACATGTCCAAGCTACT 58.923 45.455 23.03 0.00 38.89 2.57
1293 1363 1.675641 GGCACGGAGGCTTTCACAT 60.676 57.895 0.00 0.00 40.24 3.21
1302 1372 3.953775 AGGTTGTGGGCACGGAGG 61.954 66.667 0.00 0.00 0.00 4.30
1311 1381 1.508632 AATCGTCGAACAGGTTGTGG 58.491 50.000 0.00 0.00 0.00 4.17
1329 1399 3.446873 AGAAGCACAACACCAATGTCAAA 59.553 39.130 0.00 0.00 38.45 2.69
1330 1400 3.023119 AGAAGCACAACACCAATGTCAA 58.977 40.909 0.00 0.00 38.45 3.18
1399 1470 2.036006 GCCCGCCAACGTACATCAA 61.036 57.895 0.00 0.00 37.70 2.57
1527 1610 2.124109 TGCGCCCAAGGTGTTTGA 60.124 55.556 4.18 0.00 39.21 2.69
1592 1675 7.663905 TGTGTTAAGTGTAATGTTAGAGCCATT 59.336 33.333 0.00 0.00 36.53 3.16
1681 1770 6.401394 TCTGATGTTGAACACCTCTGAATAG 58.599 40.000 0.00 0.00 29.04 1.73
1747 1836 7.031975 GCCAACAGAAAGAAAAGAGATTATGG 58.968 38.462 0.00 0.00 0.00 2.74
2017 2118 3.750130 TGAAGAATCTGACTGCTCAAAGC 59.250 43.478 0.00 0.00 42.82 3.51
2020 2121 6.936335 TGTAAATGAAGAATCTGACTGCTCAA 59.064 34.615 0.00 0.00 0.00 3.02
2138 2239 8.073467 TGAAATACAAAACCAAGTCCTTTCTT 57.927 30.769 0.00 0.00 0.00 2.52
2324 2426 9.930693 ATGTTTCTAACTGGTACTTTAGAAGAG 57.069 33.333 17.01 6.12 41.25 2.85
2475 2598 9.855021 ATACAACAACTGCCAAATATTTCTAAC 57.145 29.630 0.00 0.00 0.00 2.34
2605 2840 3.366724 TCAATTGTCGCTGCTTTAGTACG 59.633 43.478 5.13 0.00 0.00 3.67
2697 2932 7.979444 ACTGAATTGCTAAGTTTAAGCTGTA 57.021 32.000 0.00 0.00 40.73 2.74
2847 3247 7.716560 TCTGTCAACAAATACATGGGAGATATG 59.283 37.037 0.00 0.00 0.00 1.78
2856 3256 5.633830 AAGGCTCTGTCAACAAATACATG 57.366 39.130 0.00 0.00 0.00 3.21
2921 3322 4.439305 TTGCAGTTCATATCAACTTGGC 57.561 40.909 0.00 0.00 34.17 4.52
2922 3323 6.263344 CAGATTGCAGTTCATATCAACTTGG 58.737 40.000 0.00 0.00 34.17 3.61
2963 3364 4.880759 ACGCCAGAAGATTATGAGATCAG 58.119 43.478 0.00 0.00 0.00 2.90
2967 3368 2.688446 ACGACGCCAGAAGATTATGAGA 59.312 45.455 0.00 0.00 0.00 3.27
3060 3467 4.092091 GCTGATCCTTGTTTCACGAGTTAG 59.908 45.833 0.00 0.00 0.00 2.34
3153 3560 7.026631 TGCCTTGAACAAGTAATGTATATGC 57.973 36.000 12.54 6.14 42.99 3.14
3167 3574 5.376625 AGTCTGAACTTAATGCCTTGAACA 58.623 37.500 0.00 0.00 28.74 3.18
3168 3575 5.948992 AGTCTGAACTTAATGCCTTGAAC 57.051 39.130 0.00 0.00 28.74 3.18
3242 3658 9.093458 ACAAATTATTCTGATTGGAAAAGTCCT 57.907 29.630 0.00 0.00 45.22 3.85
3346 3779 2.610859 ACATTGGTCGCCCTCCCT 60.611 61.111 0.00 0.00 0.00 4.20
3363 3796 3.077907 CCCCTTTTCCCTCAGCGA 58.922 61.111 0.00 0.00 0.00 4.93
3379 3812 4.164294 CCTATCTATAACGCACGTAAGCC 58.836 47.826 0.00 0.00 45.62 4.35
3382 3815 3.507233 CCCCCTATCTATAACGCACGTAA 59.493 47.826 0.00 0.00 0.00 3.18
3386 3819 5.416947 CAATACCCCCTATCTATAACGCAC 58.583 45.833 0.00 0.00 0.00 5.34
3440 3884 1.708993 ATGACGCCAGGCATATGGGT 61.709 55.000 13.30 0.00 46.15 4.51
3564 4011 9.730705 TTAAAGATAAGCATCCATCTATCTTGG 57.269 33.333 4.43 0.00 35.31 3.61
3572 4019 8.897752 AGAACAGTTTAAAGATAAGCATCCATC 58.102 33.333 0.00 0.00 0.00 3.51
3573 4020 8.680903 CAGAACAGTTTAAAGATAAGCATCCAT 58.319 33.333 0.00 0.00 0.00 3.41
3574 4021 7.362056 GCAGAACAGTTTAAAGATAAGCATCCA 60.362 37.037 0.00 0.00 0.00 3.41
3575 4022 6.969473 GCAGAACAGTTTAAAGATAAGCATCC 59.031 38.462 0.00 0.00 0.00 3.51
3652 4101 2.557869 TGTTGGAACCTACCAGCCTAT 58.442 47.619 0.00 0.00 41.19 2.57
3701 4150 2.923121 AGCATGATAACAACCGCAGAT 58.077 42.857 0.00 0.00 0.00 2.90
3742 4217 6.071560 CCTTTGGTTTCCCTGGACTATAAAAC 60.072 42.308 0.00 0.00 0.00 2.43
3743 4218 6.014012 CCTTTGGTTTCCCTGGACTATAAAA 58.986 40.000 0.00 0.00 0.00 1.52
3747 4222 2.291605 GCCTTTGGTTTCCCTGGACTAT 60.292 50.000 0.00 0.00 0.00 2.12
3818 4293 4.645535 ACACATAGACAATCACAGCAACT 58.354 39.130 0.00 0.00 0.00 3.16
3819 4294 4.452114 TGACACATAGACAATCACAGCAAC 59.548 41.667 0.00 0.00 0.00 4.17
3826 4301 5.519927 CGTATTGCTGACACATAGACAATCA 59.480 40.000 0.00 0.00 0.00 2.57
3828 4303 4.271049 GCGTATTGCTGACACATAGACAAT 59.729 41.667 0.00 0.00 41.73 2.71
3833 4308 4.801147 AATGCGTATTGCTGACACATAG 57.199 40.909 0.00 0.00 46.63 2.23
3841 4316 5.796935 GCATATAGGAAAATGCGTATTGCTG 59.203 40.000 0.00 0.00 46.63 4.41
3860 4342 7.476540 TGAATAGTACAAGGATACGGCATAT 57.523 36.000 0.00 0.00 46.39 1.78
3950 4435 5.181245 CAGAAACCAATATAGTATTGCCGGG 59.819 44.000 2.18 0.00 0.00 5.73
4056 4705 2.270352 ATCGACCACCTGCAAAAGAA 57.730 45.000 0.00 0.00 0.00 2.52
4175 4824 3.445687 TCGCGGTCGGCAGTGTAT 61.446 61.111 6.13 0.00 43.84 2.29
4205 4854 1.074405 TGGTTGAAATGCTGGAGCTCT 59.926 47.619 14.64 0.00 42.66 4.09
4293 4944 1.134280 CACCACATCTTCCTAGCAGGG 60.134 57.143 2.86 0.00 35.59 4.45
4305 4956 2.162681 CTCCCAACTTTCCACCACATC 58.837 52.381 0.00 0.00 0.00 3.06
4309 4960 1.152830 GGCTCCCAACTTTCCACCA 59.847 57.895 0.00 0.00 0.00 4.17
4325 4976 1.186200 GGAAGGGGAAATTGTCAGGC 58.814 55.000 0.00 0.00 0.00 4.85
4391 5042 1.996898 CAGCGTCGTGTAAATAAGGCA 59.003 47.619 0.00 0.00 0.00 4.75
4395 5046 2.280445 CGATGCAGCGTCGTGTAAATAA 59.720 45.455 26.05 0.00 37.99 1.40
4400 5051 2.878991 GCGATGCAGCGTCGTGTA 60.879 61.111 32.16 0.00 43.73 2.90
4582 6901 0.525668 CGACGCACTCCACCATCTAC 60.526 60.000 0.00 0.00 0.00 2.59
5034 7354 4.434520 GACTTAAAAGATGAGGGAGACGG 58.565 47.826 0.00 0.00 0.00 4.79
5035 7355 4.081642 TGGACTTAAAAGATGAGGGAGACG 60.082 45.833 0.00 0.00 0.00 4.18
5036 7356 5.179533 GTGGACTTAAAAGATGAGGGAGAC 58.820 45.833 0.00 0.00 0.00 3.36
5037 7357 4.844085 TGTGGACTTAAAAGATGAGGGAGA 59.156 41.667 0.00 0.00 0.00 3.71
5038 7358 4.938226 GTGTGGACTTAAAAGATGAGGGAG 59.062 45.833 0.00 0.00 0.00 4.30
5039 7359 4.562757 CGTGTGGACTTAAAAGATGAGGGA 60.563 45.833 0.00 0.00 0.00 4.20
5040 7360 3.684788 CGTGTGGACTTAAAAGATGAGGG 59.315 47.826 0.00 0.00 0.00 4.30
5041 7361 4.566004 TCGTGTGGACTTAAAAGATGAGG 58.434 43.478 0.00 0.00 0.00 3.86
5042 7362 5.869344 TGATCGTGTGGACTTAAAAGATGAG 59.131 40.000 0.00 0.00 0.00 2.90
5043 7363 5.789521 TGATCGTGTGGACTTAAAAGATGA 58.210 37.500 0.00 0.00 0.00 2.92
5044 7364 6.480524 TTGATCGTGTGGACTTAAAAGATG 57.519 37.500 0.00 0.00 0.00 2.90
5045 7365 7.687941 ATTTGATCGTGTGGACTTAAAAGAT 57.312 32.000 0.00 0.00 0.00 2.40
5046 7366 7.148474 GCTATTTGATCGTGTGGACTTAAAAGA 60.148 37.037 0.00 0.00 0.00 2.52
5047 7367 6.961554 GCTATTTGATCGTGTGGACTTAAAAG 59.038 38.462 0.00 0.00 0.00 2.27
5048 7368 6.128117 GGCTATTTGATCGTGTGGACTTAAAA 60.128 38.462 0.00 0.00 0.00 1.52
5049 7369 5.353123 GGCTATTTGATCGTGTGGACTTAAA 59.647 40.000 0.00 0.00 0.00 1.52
5050 7370 4.873827 GGCTATTTGATCGTGTGGACTTAA 59.126 41.667 0.00 0.00 0.00 1.85
5051 7371 4.081365 TGGCTATTTGATCGTGTGGACTTA 60.081 41.667 0.00 0.00 0.00 2.24
5052 7372 3.270877 GGCTATTTGATCGTGTGGACTT 58.729 45.455 0.00 0.00 0.00 3.01
5053 7373 2.236146 TGGCTATTTGATCGTGTGGACT 59.764 45.455 0.00 0.00 0.00 3.85
5054 7374 2.627945 TGGCTATTTGATCGTGTGGAC 58.372 47.619 0.00 0.00 0.00 4.02
5055 7375 3.558931 ATGGCTATTTGATCGTGTGGA 57.441 42.857 0.00 0.00 0.00 4.02
5056 7376 5.931724 TGTATATGGCTATTTGATCGTGTGG 59.068 40.000 0.00 0.00 0.00 4.17
5057 7377 7.601073 ATGTATATGGCTATTTGATCGTGTG 57.399 36.000 0.00 0.00 0.00 3.82
5058 7378 8.749354 TCTATGTATATGGCTATTTGATCGTGT 58.251 33.333 0.00 0.00 0.00 4.49
5059 7379 9.242477 CTCTATGTATATGGCTATTTGATCGTG 57.758 37.037 0.00 0.00 0.00 4.35
5060 7380 8.972127 ACTCTATGTATATGGCTATTTGATCGT 58.028 33.333 0.00 0.00 0.00 3.73
5071 7391 9.850628 TGAACGTTTATACTCTATGTATATGGC 57.149 33.333 0.46 0.00 41.95 4.40
5078 7398 9.257651 GGCTATTTGAACGTTTATACTCTATGT 57.742 33.333 0.46 0.00 0.00 2.29
5079 7399 8.425491 CGGCTATTTGAACGTTTATACTCTATG 58.575 37.037 0.46 0.00 0.00 2.23
5080 7400 7.115947 GCGGCTATTTGAACGTTTATACTCTAT 59.884 37.037 0.46 0.00 0.00 1.98
5081 7401 6.418819 GCGGCTATTTGAACGTTTATACTCTA 59.581 38.462 0.46 0.00 0.00 2.43
5082 7402 5.233689 GCGGCTATTTGAACGTTTATACTCT 59.766 40.000 0.46 0.00 0.00 3.24
5083 7403 5.005971 TGCGGCTATTTGAACGTTTATACTC 59.994 40.000 0.46 0.00 0.00 2.59
5084 7404 4.871557 TGCGGCTATTTGAACGTTTATACT 59.128 37.500 0.46 0.00 0.00 2.12
5085 7405 5.146482 TGCGGCTATTTGAACGTTTATAC 57.854 39.130 0.46 0.00 0.00 1.47
5086 7406 5.743467 CATGCGGCTATTTGAACGTTTATA 58.257 37.500 0.46 0.00 0.00 0.98
5087 7407 4.597079 CATGCGGCTATTTGAACGTTTAT 58.403 39.130 0.46 0.00 0.00 1.40
5088 7408 3.729462 GCATGCGGCTATTTGAACGTTTA 60.729 43.478 0.00 0.00 40.25 2.01
5089 7409 2.862512 CATGCGGCTATTTGAACGTTT 58.137 42.857 0.46 0.00 0.00 3.60
5090 7410 1.467374 GCATGCGGCTATTTGAACGTT 60.467 47.619 0.00 0.00 40.25 3.99
5091 7411 0.098728 GCATGCGGCTATTTGAACGT 59.901 50.000 0.00 0.00 40.25 3.99
5092 7412 0.098552 TGCATGCGGCTATTTGAACG 59.901 50.000 14.09 0.00 45.15 3.95
5093 7413 2.223548 TGATGCATGCGGCTATTTGAAC 60.224 45.455 14.09 0.00 45.15 3.18
5094 7414 2.022934 TGATGCATGCGGCTATTTGAA 58.977 42.857 14.09 0.00 45.15 2.69
5095 7415 1.334556 GTGATGCATGCGGCTATTTGA 59.665 47.619 14.09 0.00 45.15 2.69
5096 7416 1.335810 AGTGATGCATGCGGCTATTTG 59.664 47.619 14.09 0.00 45.15 2.32
5097 7417 1.683943 AGTGATGCATGCGGCTATTT 58.316 45.000 14.09 0.00 45.15 1.40
5098 7418 2.224378 ACTAGTGATGCATGCGGCTATT 60.224 45.455 14.09 4.27 45.15 1.73
5099 7419 1.345741 ACTAGTGATGCATGCGGCTAT 59.654 47.619 14.09 0.00 45.15 2.97
5100 7420 0.752658 ACTAGTGATGCATGCGGCTA 59.247 50.000 14.09 10.96 45.15 3.93
5101 7421 0.107508 AACTAGTGATGCATGCGGCT 60.108 50.000 14.09 10.39 45.15 5.52
5102 7422 0.734889 AAACTAGTGATGCATGCGGC 59.265 50.000 14.09 7.96 45.13 6.53
5103 7423 4.614555 TTTAAACTAGTGATGCATGCGG 57.385 40.909 14.09 0.00 0.00 5.69
5104 7424 7.510428 AAAATTTAAACTAGTGATGCATGCG 57.490 32.000 14.09 0.00 0.00 4.73
5142 7462 9.920946 AAGGATACAACAATGTTAGGATGTAAT 57.079 29.630 0.00 0.00 41.05 1.89
5143 7463 9.747898 AAAGGATACAACAATGTTAGGATGTAA 57.252 29.630 0.00 0.00 41.05 2.41
5145 7465 9.747898 TTAAAGGATACAACAATGTTAGGATGT 57.252 29.630 0.00 0.00 41.05 3.06
5147 7467 9.185680 GGTTAAAGGATACAACAATGTTAGGAT 57.814 33.333 0.00 0.00 41.05 3.24
5148 7468 7.334921 CGGTTAAAGGATACAACAATGTTAGGA 59.665 37.037 0.00 0.00 41.05 2.94
5149 7469 7.469260 CGGTTAAAGGATACAACAATGTTAGG 58.531 38.462 0.00 0.00 41.05 2.69
5150 7470 6.964934 GCGGTTAAAGGATACAACAATGTTAG 59.035 38.462 0.00 0.00 41.05 2.34
5151 7471 6.430308 TGCGGTTAAAGGATACAACAATGTTA 59.570 34.615 0.00 0.00 41.05 2.41
5152 7472 5.241949 TGCGGTTAAAGGATACAACAATGTT 59.758 36.000 0.00 0.00 41.05 2.71
5153 7473 4.762765 TGCGGTTAAAGGATACAACAATGT 59.237 37.500 0.00 0.00 43.74 2.71
5154 7474 5.092781 GTGCGGTTAAAGGATACAACAATG 58.907 41.667 0.00 0.00 41.41 2.82
5155 7475 4.762765 TGTGCGGTTAAAGGATACAACAAT 59.237 37.500 0.00 0.00 41.41 2.71
5156 7476 4.023878 GTGTGCGGTTAAAGGATACAACAA 60.024 41.667 0.00 0.00 41.41 2.83
5157 7477 3.499157 GTGTGCGGTTAAAGGATACAACA 59.501 43.478 0.00 0.00 41.41 3.33
5158 7478 3.749609 AGTGTGCGGTTAAAGGATACAAC 59.250 43.478 4.21 0.00 41.41 3.32
5159 7479 3.749088 CAGTGTGCGGTTAAAGGATACAA 59.251 43.478 4.21 0.00 41.41 2.41
5160 7480 3.007074 TCAGTGTGCGGTTAAAGGATACA 59.993 43.478 0.00 0.00 41.41 2.29
5161 7481 3.592059 TCAGTGTGCGGTTAAAGGATAC 58.408 45.455 0.00 0.00 0.00 2.24
5162 7482 3.965379 TCAGTGTGCGGTTAAAGGATA 57.035 42.857 0.00 0.00 0.00 2.59
5163 7483 2.851263 TCAGTGTGCGGTTAAAGGAT 57.149 45.000 0.00 0.00 0.00 3.24
5164 7484 2.422597 CATCAGTGTGCGGTTAAAGGA 58.577 47.619 0.00 0.00 0.00 3.36
5165 7485 1.135689 GCATCAGTGTGCGGTTAAAGG 60.136 52.381 2.63 0.00 35.10 3.11
5166 7486 2.247311 GCATCAGTGTGCGGTTAAAG 57.753 50.000 2.63 0.00 35.10 1.85
5181 7501 5.366460 TGAAGGAAGATCTGATTGAGCATC 58.634 41.667 0.00 0.00 32.67 3.91
5182 7502 5.369409 TGAAGGAAGATCTGATTGAGCAT 57.631 39.130 0.00 0.00 32.67 3.79
5183 7503 4.831674 TGAAGGAAGATCTGATTGAGCA 57.168 40.909 0.00 0.00 32.67 4.26
5184 7504 6.496571 CAATTGAAGGAAGATCTGATTGAGC 58.503 40.000 0.00 0.00 0.00 4.26
5185 7505 6.319152 AGCAATTGAAGGAAGATCTGATTGAG 59.681 38.462 10.34 0.00 0.00 3.02
5186 7506 6.185511 AGCAATTGAAGGAAGATCTGATTGA 58.814 36.000 10.34 0.00 0.00 2.57
5187 7507 6.452494 AGCAATTGAAGGAAGATCTGATTG 57.548 37.500 10.34 0.83 0.00 2.67
5188 7508 6.436532 ACAAGCAATTGAAGGAAGATCTGATT 59.563 34.615 10.34 0.00 0.00 2.57
5189 7509 5.950549 ACAAGCAATTGAAGGAAGATCTGAT 59.049 36.000 10.34 0.00 0.00 2.90
5190 7510 5.182570 CACAAGCAATTGAAGGAAGATCTGA 59.817 40.000 10.34 0.00 0.00 3.27
5191 7511 5.182570 TCACAAGCAATTGAAGGAAGATCTG 59.817 40.000 10.34 0.00 0.00 2.90
5192 7512 5.319453 TCACAAGCAATTGAAGGAAGATCT 58.681 37.500 10.34 0.00 0.00 2.75
5193 7513 5.182760 ACTCACAAGCAATTGAAGGAAGATC 59.817 40.000 10.34 0.00 0.00 2.75
5194 7514 5.075493 ACTCACAAGCAATTGAAGGAAGAT 58.925 37.500 10.34 0.00 0.00 2.40
5195 7515 4.464008 ACTCACAAGCAATTGAAGGAAGA 58.536 39.130 10.34 0.00 0.00 2.87
5196 7516 4.843220 ACTCACAAGCAATTGAAGGAAG 57.157 40.909 10.34 1.39 0.00 3.46
5197 7517 4.202141 CCAACTCACAAGCAATTGAAGGAA 60.202 41.667 10.34 0.00 0.00 3.36
5198 7518 3.318839 CCAACTCACAAGCAATTGAAGGA 59.681 43.478 10.34 0.00 0.00 3.36
5199 7519 3.068590 ACCAACTCACAAGCAATTGAAGG 59.931 43.478 10.34 0.00 0.00 3.46
5200 7520 4.293415 GACCAACTCACAAGCAATTGAAG 58.707 43.478 10.34 0.00 0.00 3.02
5201 7521 3.243035 CGACCAACTCACAAGCAATTGAA 60.243 43.478 10.34 0.00 0.00 2.69
5202 7522 2.290367 CGACCAACTCACAAGCAATTGA 59.710 45.455 10.34 0.00 0.00 2.57
5203 7523 2.290367 TCGACCAACTCACAAGCAATTG 59.710 45.455 0.00 0.00 0.00 2.32
5204 7524 2.571212 TCGACCAACTCACAAGCAATT 58.429 42.857 0.00 0.00 0.00 2.32
5205 7525 2.254546 TCGACCAACTCACAAGCAAT 57.745 45.000 0.00 0.00 0.00 3.56
5206 7526 1.872952 CATCGACCAACTCACAAGCAA 59.127 47.619 0.00 0.00 0.00 3.91
5207 7527 1.511850 CATCGACCAACTCACAAGCA 58.488 50.000 0.00 0.00 0.00 3.91
5208 7528 0.166814 GCATCGACCAACTCACAAGC 59.833 55.000 0.00 0.00 0.00 4.01
5209 7529 0.798776 GGCATCGACCAACTCACAAG 59.201 55.000 0.00 0.00 0.00 3.16
5210 7530 0.948623 CGGCATCGACCAACTCACAA 60.949 55.000 0.00 0.00 39.00 3.33
5211 7531 1.374125 CGGCATCGACCAACTCACA 60.374 57.895 0.00 0.00 39.00 3.58
5212 7532 0.669318 TTCGGCATCGACCAACTCAC 60.669 55.000 0.00 0.00 45.92 3.51
5213 7533 0.249120 ATTCGGCATCGACCAACTCA 59.751 50.000 0.00 0.00 45.92 3.41
5214 7534 1.369625 AATTCGGCATCGACCAACTC 58.630 50.000 0.00 0.00 45.92 3.01
5215 7535 2.684001 TAATTCGGCATCGACCAACT 57.316 45.000 0.00 0.00 45.92 3.16
5216 7536 3.963383 ATTAATTCGGCATCGACCAAC 57.037 42.857 0.00 0.00 45.92 3.77
5217 7537 3.942115 TCAATTAATTCGGCATCGACCAA 59.058 39.130 0.00 0.00 45.92 3.67
5218 7538 3.536570 TCAATTAATTCGGCATCGACCA 58.463 40.909 0.00 0.00 45.92 4.02
5219 7539 4.466828 CATCAATTAATTCGGCATCGACC 58.533 43.478 0.00 0.00 45.92 4.79
5220 7540 3.908382 GCATCAATTAATTCGGCATCGAC 59.092 43.478 0.00 0.00 45.92 4.20
5221 7541 3.563390 TGCATCAATTAATTCGGCATCGA 59.437 39.130 11.76 0.00 44.44 3.59
5222 7542 3.887741 TGCATCAATTAATTCGGCATCG 58.112 40.909 11.76 0.00 37.82 3.84
5223 7543 5.060077 CGAATGCATCAATTAATTCGGCATC 59.940 40.000 21.59 16.26 44.66 3.91
5224 7544 4.919168 CGAATGCATCAATTAATTCGGCAT 59.081 37.500 18.18 18.18 44.66 4.40
5225 7545 4.036144 TCGAATGCATCAATTAATTCGGCA 59.964 37.500 16.00 16.00 46.99 5.69
5226 7546 4.536065 TCGAATGCATCAATTAATTCGGC 58.464 39.130 13.11 3.29 46.99 5.54
5227 7547 8.726650 TTATTCGAATGCATCAATTAATTCGG 57.273 30.769 20.87 0.00 46.99 4.30
5233 7553 9.935682 GAAGAGTTTATTCGAATGCATCAATTA 57.064 29.630 20.87 0.00 0.00 1.40
5234 7554 8.461222 TGAAGAGTTTATTCGAATGCATCAATT 58.539 29.630 20.87 7.31 0.00 2.32
5235 7555 7.988737 TGAAGAGTTTATTCGAATGCATCAAT 58.011 30.769 20.87 1.68 0.00 2.57
5236 7556 7.376435 TGAAGAGTTTATTCGAATGCATCAA 57.624 32.000 20.87 3.52 0.00 2.57
5237 7557 6.983474 TGAAGAGTTTATTCGAATGCATCA 57.017 33.333 20.87 11.43 0.00 3.07
5238 7558 7.912250 ACATTGAAGAGTTTATTCGAATGCATC 59.088 33.333 20.87 12.41 33.41 3.91
5239 7559 7.699391 CACATTGAAGAGTTTATTCGAATGCAT 59.301 33.333 20.87 0.00 33.41 3.96
5240 7560 7.022979 CACATTGAAGAGTTTATTCGAATGCA 58.977 34.615 20.87 4.34 33.41 3.96
5241 7561 6.470235 CCACATTGAAGAGTTTATTCGAATGC 59.530 38.462 20.87 10.43 33.41 3.56
5242 7562 6.470235 GCCACATTGAAGAGTTTATTCGAATG 59.530 38.462 20.87 3.03 34.69 2.67
5243 7563 6.404734 GGCCACATTGAAGAGTTTATTCGAAT 60.405 38.462 16.15 16.15 0.00 3.34
5244 7564 5.106317 GGCCACATTGAAGAGTTTATTCGAA 60.106 40.000 0.00 0.00 0.00 3.71
5245 7565 4.394920 GGCCACATTGAAGAGTTTATTCGA 59.605 41.667 0.00 0.00 0.00 3.71
5246 7566 4.662145 GGCCACATTGAAGAGTTTATTCG 58.338 43.478 0.00 0.00 0.00 3.34
5247 7567 4.438744 CCGGCCACATTGAAGAGTTTATTC 60.439 45.833 2.24 0.00 0.00 1.75
5248 7568 3.443681 CCGGCCACATTGAAGAGTTTATT 59.556 43.478 2.24 0.00 0.00 1.40
5249 7569 3.016736 CCGGCCACATTGAAGAGTTTAT 58.983 45.455 2.24 0.00 0.00 1.40
5250 7570 2.039216 TCCGGCCACATTGAAGAGTTTA 59.961 45.455 2.24 0.00 0.00 2.01
5251 7571 1.202879 TCCGGCCACATTGAAGAGTTT 60.203 47.619 2.24 0.00 0.00 2.66
5252 7572 0.400213 TCCGGCCACATTGAAGAGTT 59.600 50.000 2.24 0.00 0.00 3.01
5253 7573 2.066340 TCCGGCCACATTGAAGAGT 58.934 52.632 2.24 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.