Multiple sequence alignment - TraesCS6A01G187400

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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 TraesCS6A01G187400 chr6A 100.000 6349 0 0 1 6349 223554427 223560775 0.000000e+00 11725.0
1 TraesCS6A01G187400 chr6A 98.400 1500 23 1 4088 5586 221349737 221348238 0.000000e+00 2636.0
2 TraesCS6A01G187400 chr6A 97.730 1498 26 2 4088 5584 362227318 362228808 0.000000e+00 2571.0
3 TraesCS6A01G187400 chr6A 96.611 1505 42 3 4088 5585 324279881 324281383 0.000000e+00 2488.0
4 TraesCS6A01G187400 chr6A 95.901 1415 51 2 4176 5583 324277993 324279407 0.000000e+00 2285.0
5 TraesCS6A01G187400 chr6A 92.270 1423 87 16 4088 5495 17930661 17932075 0.000000e+00 1997.0
6 TraesCS6A01G187400 chr6A 90.921 1476 104 20 4088 5542 412377778 412379244 0.000000e+00 1956.0
7 TraesCS6A01G187400 chr6A 91.603 1429 91 17 4088 5495 598074062 598072642 0.000000e+00 1947.0
8 TraesCS6A01G187400 chr6A 87.508 1505 167 12 861 2349 591024693 591023194 0.000000e+00 1718.0
9 TraesCS6A01G187400 chr6A 92.041 980 67 5 2345 3318 591021544 591020570 0.000000e+00 1367.0
10 TraesCS6A01G187400 chr6A 100.000 733 0 0 6444 7176 223560870 223561602 0.000000e+00 1354.0
11 TraesCS6A01G187400 chr6A 97.933 774 15 1 3315 4087 221350540 221349767 0.000000e+00 1339.0
12 TraesCS6A01G187400 chr6A 97.665 771 17 1 3318 4087 362226518 362227288 0.000000e+00 1323.0
13 TraesCS6A01G187400 chr6A 96.654 777 25 1 3312 4087 324267024 324267800 0.000000e+00 1290.0
14 TraesCS6A01G187400 chr6A 96.887 771 23 1 3318 4087 324279081 324279851 0.000000e+00 1290.0
15 TraesCS6A01G187400 chr6A 92.980 755 46 5 3335 4087 576233336 576232587 0.000000e+00 1094.0
16 TraesCS6A01G187400 chr6A 92.857 700 44 4 5584 6281 591020574 591019879 0.000000e+00 1011.0
17 TraesCS6A01G187400 chr6D 95.396 2411 89 7 909 3318 163334909 163337298 0.000000e+00 3818.0
18 TraesCS6A01G187400 chr6D 91.065 2328 195 8 861 3186 441769889 441767573 0.000000e+00 3134.0
19 TraesCS6A01G187400 chr6D 95.515 758 15 8 5584 6322 163337294 163338051 0.000000e+00 1194.0
20 TraesCS6A01G187400 chr6D 94.472 597 19 7 6580 7174 163338069 163338653 0.000000e+00 907.0
21 TraesCS6A01G187400 chr6D 95.093 428 21 0 5772 6199 441759830 441759403 0.000000e+00 675.0
22 TraesCS6A01G187400 chr6D 96.034 353 12 1 1 351 163333955 163334307 2.250000e-159 573.0
23 TraesCS6A01G187400 chr6D 94.265 279 15 1 644 922 163334591 163334868 6.650000e-115 425.0
24 TraesCS6A01G187400 chr6D 88.889 261 15 7 337 583 163334325 163334585 6.990000e-80 309.0
25 TraesCS6A01G187400 chr6D 91.837 196 16 0 5584 5779 441765174 441764979 2.550000e-69 274.0
26 TraesCS6A01G187400 chr6D 82.450 302 29 10 6866 7165 441752015 441751736 7.190000e-60 243.0
27 TraesCS6A01G187400 chr6D 94.161 137 8 0 3182 3318 441765306 441765170 7.290000e-50 209.0
28 TraesCS6A01G187400 chr6D 95.918 49 2 0 6536 6584 468830567 468830519 5.970000e-11 80.5
29 TraesCS6A01G187400 chr6D 92.308 52 4 0 495 546 446091685 446091634 2.780000e-09 75.0
30 TraesCS6A01G187400 chr6B 91.626 2460 200 5 861 3318 667781381 667778926 0.000000e+00 3397.0
31 TraesCS6A01G187400 chr6B 92.144 1502 114 3 861 2361 298824018 298822520 0.000000e+00 2117.0
32 TraesCS6A01G187400 chr6B 98.047 973 18 1 2347 3318 298822172 298821200 0.000000e+00 1690.0
33 TraesCS6A01G187400 chr6B 97.813 686 15 0 5584 6269 298821204 298820519 0.000000e+00 1184.0
34 TraesCS6A01G187400 chr6B 91.931 694 49 3 5584 6273 667778930 667778240 0.000000e+00 965.0
35 TraesCS6A01G187400 chr6B 93.689 618 18 10 6580 7176 298820426 298819809 0.000000e+00 905.0
36 TraesCS6A01G187400 chr6B 98.039 51 1 0 6272 6322 298820494 298820444 9.920000e-14 89.8
37 TraesCS6A01G187400 chr3A 94.884 1505 52 7 4088 5583 83737142 83735654 0.000000e+00 2329.0
38 TraesCS6A01G187400 chr3A 96.883 770 20 2 3319 4087 83737938 83737172 0.000000e+00 1286.0
39 TraesCS6A01G187400 chr3A 91.288 792 43 8 3314 4082 83232547 83233335 0.000000e+00 1057.0
40 TraesCS6A01G187400 chr3A 77.678 887 144 25 3632 4476 385757245 385758119 6.470000e-135 492.0
41 TraesCS6A01G187400 chr3A 83.410 217 28 6 3882 4093 306863668 306863881 2.040000e-45 195.0
42 TraesCS6A01G187400 chr3A 76.590 346 57 20 5225 5558 535187335 535187668 1.240000e-37 169.0
43 TraesCS6A01G187400 chr3A 75.710 317 47 23 5257 5558 535185076 535185377 1.620000e-26 132.0
44 TraesCS6A01G187400 chr3A 89.394 66 6 1 6520 6584 336620399 336620334 1.660000e-11 82.4
45 TraesCS6A01G187400 chr3A 90.164 61 5 1 6525 6584 728367155 728367095 2.150000e-10 78.7
46 TraesCS6A01G187400 chr4A 89.706 1428 124 12 4088 5495 18296134 18297558 0.000000e+00 1801.0
47 TraesCS6A01G187400 chr4A 81.132 212 28 12 5275 5480 242890052 242890257 7.450000e-35 159.0
48 TraesCS6A01G187400 chr4A 79.717 212 31 11 5275 5480 242892122 242892327 7.500000e-30 143.0
49 TraesCS6A01G187400 chr5A 94.430 772 24 9 3318 4087 672037205 672037959 0.000000e+00 1170.0
50 TraesCS6A01G187400 chr5A 90.468 577 23 6 3631 4177 4208011 4207437 0.000000e+00 732.0
51 TraesCS6A01G187400 chr5A 91.176 68 5 1 5492 5558 36824757 36824690 2.760000e-14 91.6
52 TraesCS6A01G187400 chr3B 91.000 800 46 14 3318 4093 246154254 246155051 0.000000e+00 1055.0
53 TraesCS6A01G187400 chr3B 94.340 53 3 0 6532 6584 313810736 313810788 1.660000e-11 82.4
54 TraesCS6A01G187400 chr7D 94.231 52 3 0 6533 6584 18921864 18921915 5.970000e-11 80.5
55 TraesCS6A01G187400 chr1D 94.231 52 3 0 6533 6584 84051119 84051170 5.970000e-11 80.5
56 TraesCS6A01G187400 chr1D 95.918 49 2 0 6536 6584 480524961 480524913 5.970000e-11 80.5
57 TraesCS6A01G187400 chr2A 93.878 49 3 0 500 548 504359755 504359707 2.780000e-09 75.0
58 TraesCS6A01G187400 chr1A 97.436 39 0 1 510 547 562738883 562738845 1.670000e-06 65.8
59 TraesCS6A01G187400 chr4B 92.857 42 3 0 505 546 97353799 97353758 2.160000e-05 62.1


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 TraesCS6A01G187400 chr6A 223554427 223561602 7175 False 6539.500000 11725 100.000000 1 7176 2 chr6A.!!$F4 7175
1 TraesCS6A01G187400 chr6A 324277993 324281383 3390 False 2021.000000 2488 96.466333 3318 5585 3 chr6A.!!$F5 2267
2 TraesCS6A01G187400 chr6A 17930661 17932075 1414 False 1997.000000 1997 92.270000 4088 5495 1 chr6A.!!$F1 1407
3 TraesCS6A01G187400 chr6A 221348238 221350540 2302 True 1987.500000 2636 98.166500 3315 5586 2 chr6A.!!$R3 2271
4 TraesCS6A01G187400 chr6A 412377778 412379244 1466 False 1956.000000 1956 90.921000 4088 5542 1 chr6A.!!$F3 1454
5 TraesCS6A01G187400 chr6A 362226518 362228808 2290 False 1947.000000 2571 97.697500 3318 5584 2 chr6A.!!$F6 2266
6 TraesCS6A01G187400 chr6A 598072642 598074062 1420 True 1947.000000 1947 91.603000 4088 5495 1 chr6A.!!$R2 1407
7 TraesCS6A01G187400 chr6A 591019879 591024693 4814 True 1365.333333 1718 90.802000 861 6281 3 chr6A.!!$R4 5420
8 TraesCS6A01G187400 chr6A 324267024 324267800 776 False 1290.000000 1290 96.654000 3312 4087 1 chr6A.!!$F2 775
9 TraesCS6A01G187400 chr6A 576232587 576233336 749 True 1094.000000 1094 92.980000 3335 4087 1 chr6A.!!$R1 752
10 TraesCS6A01G187400 chr6D 441764979 441769889 4910 True 1205.666667 3134 92.354333 861 5779 3 chr6D.!!$R5 4918
11 TraesCS6A01G187400 chr6D 163333955 163338653 4698 False 1204.333333 3818 94.095167 1 7174 6 chr6D.!!$F1 7173
12 TraesCS6A01G187400 chr6B 667778240 667781381 3141 True 2181.000000 3397 91.778500 861 6273 2 chr6B.!!$R2 5412
13 TraesCS6A01G187400 chr6B 298819809 298824018 4209 True 1197.160000 2117 95.946400 861 7176 5 chr6B.!!$R1 6315
14 TraesCS6A01G187400 chr3A 83735654 83737938 2284 True 1807.500000 2329 95.883500 3319 5583 2 chr3A.!!$R3 2264
15 TraesCS6A01G187400 chr3A 83232547 83233335 788 False 1057.000000 1057 91.288000 3314 4082 1 chr3A.!!$F1 768
16 TraesCS6A01G187400 chr3A 385757245 385758119 874 False 492.000000 492 77.678000 3632 4476 1 chr3A.!!$F3 844
17 TraesCS6A01G187400 chr4A 18296134 18297558 1424 False 1801.000000 1801 89.706000 4088 5495 1 chr4A.!!$F1 1407
18 TraesCS6A01G187400 chr5A 672037205 672037959 754 False 1170.000000 1170 94.430000 3318 4087 1 chr5A.!!$F1 769
19 TraesCS6A01G187400 chr5A 4207437 4208011 574 True 732.000000 732 90.468000 3631 4177 1 chr5A.!!$R1 546
20 TraesCS6A01G187400 chr3B 246154254 246155051 797 False 1055.000000 1055 91.000000 3318 4093 1 chr3B.!!$F1 775

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
698 747 0.905337 CCCCGTGAGTTCCTCTTCCT 60.905 60.0 0.0 0.0 0.00 3.36 F
2332 2452 0.111446 TTGTGGCGAAATTCCCTGGA 59.889 50.0 0.0 0.0 0.00 3.86 F
3035 5173 0.535102 AACGCCCAGAACCTTGACAG 60.535 55.0 0.0 0.0 0.00 3.51 F
4202 8681 0.107643 TGCACCGTGGATGTGAAAGA 59.892 50.0 0.0 0.0 35.74 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 4623 0.541863 AAGGATGGTTAGCCCTGACG 59.458 55.000 0.00 0.0 30.80 4.35 R
3654 8070 0.880278 GGACGAGCTGTTTGTGCAGA 60.880 55.000 0.00 0.0 38.70 4.26 R
5513 10023 7.054751 AGCCCACAAGTTATCTTAGGTTAATC 58.945 38.462 4.43 0.0 32.07 1.75 R
6556 11094 0.106318 TAGGGACGAGTTAGGCCTCC 60.106 60.000 9.68 1.4 39.91 4.30 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
51 52 1.679139 CGGCATCCTTCTGGCATTTA 58.321 50.000 0.00 0.00 41.51 1.40
121 122 3.967987 AGAGGAAATAATACCAGGCGAGT 59.032 43.478 0.00 0.00 0.00 4.18
147 148 5.807520 CGACGGATATCCATGAAAGAATAGG 59.192 44.000 21.70 3.00 35.14 2.57
151 152 6.248433 GGATATCCATGAAAGAATAGGGCAA 58.752 40.000 17.34 0.00 35.64 4.52
305 308 1.909700 AAAATTCAGCTTCGGCAGGA 58.090 45.000 0.00 0.00 44.74 3.86
351 354 3.118408 CCGGATGAGTCCAGGAATAACAA 60.118 47.826 0.00 0.00 45.37 2.83
363 399 7.329471 GTCCAGGAATAACAAAAAGCTTTCATC 59.671 37.037 13.10 3.65 0.00 2.92
399 435 7.504924 AGGAATCTCGACTAGTCTTATGAAG 57.495 40.000 20.34 8.21 0.00 3.02
473 509 1.205417 CTCCAAAATGTGTGGATGCCC 59.795 52.381 0.00 0.00 44.19 5.36
499 543 2.671070 CACCGTGGCCCATCTTCT 59.329 61.111 0.00 0.00 0.00 2.85
502 546 0.988832 ACCGTGGCCCATCTTCTTTA 59.011 50.000 0.00 0.00 0.00 1.85
506 550 3.278574 CGTGGCCCATCTTCTTTATTGA 58.721 45.455 0.00 0.00 0.00 2.57
507 551 3.065371 CGTGGCCCATCTTCTTTATTGAC 59.935 47.826 0.00 0.00 0.00 3.18
509 553 2.033424 GGCCCATCTTCTTTATTGACGC 59.967 50.000 0.00 0.00 0.00 5.19
544 592 4.569943 CTTACGCCTGCCTGAACATATAT 58.430 43.478 0.00 0.00 0.00 0.86
583 632 7.928706 GCCAATTAGAAAAGCAGAGTAGAGATA 59.071 37.037 0.00 0.00 0.00 1.98
584 633 9.255304 CCAATTAGAAAAGCAGAGTAGAGATAC 57.745 37.037 0.00 0.00 0.00 2.24
585 634 9.809096 CAATTAGAAAAGCAGAGTAGAGATACA 57.191 33.333 0.00 0.00 0.00 2.29
593 642 4.038642 GCAGAGTAGAGATACAAAGAGGGG 59.961 50.000 0.00 0.00 0.00 4.79
608 657 3.097162 GGGGGAGGGGGCTACAAG 61.097 72.222 0.00 0.00 0.00 3.16
612 661 1.615424 GGAGGGGGCTACAAGGACA 60.615 63.158 0.00 0.00 0.00 4.02
616 665 1.923909 GGGGCTACAAGGACAGGGT 60.924 63.158 0.00 0.00 0.00 4.34
618 667 1.198759 GGGCTACAAGGACAGGGTGA 61.199 60.000 0.00 0.00 0.00 4.02
619 668 0.912486 GGCTACAAGGACAGGGTGAT 59.088 55.000 0.00 0.00 0.00 3.06
620 669 2.116238 GGCTACAAGGACAGGGTGATA 58.884 52.381 0.00 0.00 0.00 2.15
621 670 2.504175 GGCTACAAGGACAGGGTGATAA 59.496 50.000 0.00 0.00 0.00 1.75
622 671 3.136626 GGCTACAAGGACAGGGTGATAAT 59.863 47.826 0.00 0.00 0.00 1.28
623 672 4.385310 GGCTACAAGGACAGGGTGATAATT 60.385 45.833 0.00 0.00 0.00 1.40
625 674 6.354130 GCTACAAGGACAGGGTGATAATTAA 58.646 40.000 0.00 0.00 0.00 1.40
628 677 5.044846 ACAAGGACAGGGTGATAATTAAGCT 60.045 40.000 0.00 0.00 0.00 3.74
629 678 6.157994 ACAAGGACAGGGTGATAATTAAGCTA 59.842 38.462 0.00 0.00 0.00 3.32
630 679 6.824958 AGGACAGGGTGATAATTAAGCTAA 57.175 37.500 0.00 0.00 0.00 3.09
632 681 7.639378 AGGACAGGGTGATAATTAAGCTAAAA 58.361 34.615 0.00 0.00 0.00 1.52
634 683 8.568794 GGACAGGGTGATAATTAAGCTAAAATC 58.431 37.037 0.00 0.00 0.00 2.17
635 684 9.343539 GACAGGGTGATAATTAAGCTAAAATCT 57.656 33.333 0.00 0.00 0.00 2.40
637 686 8.499162 CAGGGTGATAATTAAGCTAAAATCTCG 58.501 37.037 0.00 0.00 0.00 4.04
641 690 8.552034 GTGATAATTAAGCTAAAATCTCGCAGT 58.448 33.333 0.00 0.00 0.00 4.40
698 747 0.905337 CCCCGTGAGTTCCTCTTCCT 60.905 60.000 0.00 0.00 0.00 3.36
699 748 0.977395 CCCGTGAGTTCCTCTTCCTT 59.023 55.000 0.00 0.00 0.00 3.36
705 754 2.372172 TGAGTTCCTCTTCCTTCCAACC 59.628 50.000 0.00 0.00 0.00 3.77
707 756 2.783510 AGTTCCTCTTCCTTCCAACCAA 59.216 45.455 0.00 0.00 0.00 3.67
708 757 3.204382 AGTTCCTCTTCCTTCCAACCAAA 59.796 43.478 0.00 0.00 0.00 3.28
709 758 3.958147 GTTCCTCTTCCTTCCAACCAAAA 59.042 43.478 0.00 0.00 0.00 2.44
712 761 3.511540 CCTCTTCCTTCCAACCAAAATCC 59.488 47.826 0.00 0.00 0.00 3.01
747 796 9.010029 CCTGTTCTTTACAACAATACTGGTATT 57.990 33.333 0.66 0.66 35.83 1.89
765 814 3.604875 ATTTCTGCTGCCCAAATCTTG 57.395 42.857 0.00 0.00 0.00 3.02
778 827 3.947196 CCAAATCTTGCCTATACAGTGCA 59.053 43.478 0.00 0.00 0.00 4.57
786 835 2.817258 GCCTATACAGTGCACAAACCAA 59.183 45.455 21.04 0.00 0.00 3.67
887 936 6.985188 TCTTCCTGTTATTCACAATACTGC 57.015 37.500 0.00 0.00 33.87 4.40
982 1085 2.447429 ACTCGAGAGATATTGGGGGAGA 59.553 50.000 21.68 0.00 40.84 3.71
1082 1188 0.609131 ACTGCCATTTCCCTTCCACG 60.609 55.000 0.00 0.00 0.00 4.94
1359 1479 1.946768 TGGTTTCCAAAGCTCAAGTCG 59.053 47.619 3.12 0.00 37.31 4.18
1475 1595 2.291209 TTTCTGCCAGCTCCATTTCA 57.709 45.000 0.00 0.00 0.00 2.69
1483 1603 2.094854 CCAGCTCCATTTCAAGTTGAGC 60.095 50.000 5.56 5.11 46.74 4.26
1666 1786 6.545504 AGCTTCAGTACTTGTACATGTTTG 57.454 37.500 18.38 16.17 0.00 2.93
1692 1812 2.160417 CAGTTTCACAGGCGAGATTTCC 59.840 50.000 0.00 0.00 0.00 3.13
1719 1839 0.678395 TCACCGCCGTAAACTTGGTA 59.322 50.000 0.00 0.00 0.00 3.25
1746 1866 5.694231 TTGATGTGTCCTCAAACAATCTG 57.306 39.130 0.00 0.00 29.96 2.90
1792 1912 2.504175 GGTAGGCTCATCAACCTTACCA 59.496 50.000 0.00 0.00 37.50 3.25
1866 1986 1.593750 GCTGCCGAATCTCAGCGAT 60.594 57.895 8.20 0.00 44.94 4.58
1869 1989 2.416027 GCTGCCGAATCTCAGCGATATA 60.416 50.000 8.20 0.00 44.94 0.86
2208 2328 0.992695 GGACCTTTCCTACCCAGCTT 59.007 55.000 0.00 0.00 39.13 3.74
2241 2361 3.325293 ACACGTCTTGAGATGAGCAAT 57.675 42.857 7.20 0.00 35.16 3.56
2265 2385 1.765314 AGATTCTCTGGTCCCATTCCG 59.235 52.381 0.00 0.00 0.00 4.30
2283 2403 2.747446 TCCGACTTTAGCAGGCAAAATC 59.253 45.455 0.00 0.00 0.00 2.17
2332 2452 0.111446 TTGTGGCGAAATTCCCTGGA 59.889 50.000 0.00 0.00 0.00 3.86
2427 4563 4.768968 ACAATTGGAGTGCTAAAGCTCAAT 59.231 37.500 10.83 5.78 42.66 2.57
2486 4623 1.539827 ACCTGCAGCGTTTGGATTTAC 59.460 47.619 8.66 0.00 0.00 2.01
2962 5099 2.568062 TCTGGCAAGGTGTACCGAATTA 59.432 45.455 0.00 0.00 42.08 1.40
3035 5173 0.535102 AACGCCCAGAACCTTGACAG 60.535 55.000 0.00 0.00 0.00 3.51
3092 5230 1.561769 TTGGGTGAGATCCGGCACAT 61.562 55.000 11.37 0.00 36.76 3.21
3186 7595 1.137282 GGTAGCTTAGACAGGTGGCTC 59.863 57.143 0.00 0.00 33.72 4.70
3316 7731 0.654160 CGCCATAGTGCACTGTGATG 59.346 55.000 36.53 26.97 37.28 3.07
3542 7957 6.597280 GCCTGATCTGAAAAGAGTCTTACAAT 59.403 38.462 5.65 6.60 0.00 2.71
3591 8007 6.314400 TGCACACGAATTAACCTAAGATAACC 59.686 38.462 0.00 0.00 0.00 2.85
3654 8070 1.553704 GGACATAACACTTCTCCCCGT 59.446 52.381 0.00 0.00 0.00 5.28
3744 8160 1.581934 CAGCGTCAAACACCTTCTCA 58.418 50.000 0.00 0.00 0.00 3.27
3851 8267 1.004200 CGGGCTTGTAGGGTTCGTT 60.004 57.895 0.00 0.00 0.00 3.85
3900 8317 1.252175 GCTCGATATCTCAGCTGGGA 58.748 55.000 20.89 20.89 0.00 4.37
4202 8681 0.107643 TGCACCGTGGATGTGAAAGA 59.892 50.000 0.00 0.00 35.74 2.52
4324 8803 1.077930 TGCTCGAGGGCGTAGTACT 60.078 57.895 15.58 0.00 38.98 2.73
4478 8957 2.151202 GAAGTCCAGTTTGGCGAATCA 58.849 47.619 0.00 0.00 37.47 2.57
5481 9970 6.597280 GCCTGATCTGAAAAGAGTCTTACAAT 59.403 38.462 5.65 6.60 0.00 2.71
5513 10023 3.247006 ACCTAGATAACTTGCACACGG 57.753 47.619 0.00 0.00 0.00 4.94
5743 10253 6.678900 GCACCAGGTAAGAAATAGAAATGCAG 60.679 42.308 0.00 0.00 0.00 4.41
5786 10296 2.480419 GGATGTACCATGTGCTAATCGC 59.520 50.000 0.00 0.00 38.79 4.58
5863 10373 1.272769 GTCTACAGCTTCGGAGTGGTT 59.727 52.381 0.00 0.00 0.00 3.67
6156 10666 4.082895 GCAGCATGTTGTCTCTGAAGAAAT 60.083 41.667 11.44 0.00 39.31 2.17
6341 10879 0.965439 TTTTTGACCGGAATGGCAGG 59.035 50.000 9.46 0.00 43.94 4.85
6343 10881 0.893270 TTTGACCGGAATGGCAGGTG 60.893 55.000 9.46 0.00 45.59 4.00
6344 10882 3.134127 GACCGGAATGGCAGGTGC 61.134 66.667 9.46 0.00 45.59 5.01
6345 10883 3.628646 GACCGGAATGGCAGGTGCT 62.629 63.158 9.46 0.00 45.59 4.40
6346 10884 2.825836 CCGGAATGGCAGGTGCTC 60.826 66.667 0.00 0.00 41.70 4.26
6347 10885 2.270205 CGGAATGGCAGGTGCTCT 59.730 61.111 1.26 0.00 41.70 4.09
6348 10886 2.110967 CGGAATGGCAGGTGCTCTG 61.111 63.158 1.26 3.74 46.03 3.35
6470 11008 3.897325 GTTGAGAAATCAACCGGGAAAC 58.103 45.455 6.32 0.00 42.88 2.78
6471 11009 3.305131 GTTGAGAAATCAACCGGGAAACC 60.305 47.826 6.32 0.00 42.88 3.27
6472 11010 5.525987 GTTGAGAAATCAACCGGGAAACCT 61.526 45.833 6.32 0.00 44.59 3.50
6473 11011 6.263148 GTTGAGAAATCAACCGGGAAACCTA 61.263 44.000 6.32 0.00 44.59 3.08
6474 11012 7.523394 GTTGAGAAATCAACCGGGAAACCTAT 61.523 42.308 6.32 0.00 44.59 2.57
6475 11013 9.222581 GTTGAGAAATCAACCGGGAAACCTATC 62.223 44.444 6.32 0.00 44.59 2.08
6491 11029 8.635328 GGAAACCTATCTAAAGAACCAAAAACA 58.365 33.333 0.00 0.00 0.00 2.83
6494 11032 8.178313 ACCTATCTAAAGAACCAAAAACAAGG 57.822 34.615 0.00 0.00 0.00 3.61
6495 11033 7.783119 ACCTATCTAAAGAACCAAAAACAAGGT 59.217 33.333 0.00 0.00 40.61 3.50
6496 11034 9.292195 CCTATCTAAAGAACCAAAAACAAGGTA 57.708 33.333 0.00 0.00 37.07 3.08
6499 11037 7.485810 TCTAAAGAACCAAAAACAAGGTAAGC 58.514 34.615 0.00 0.00 37.07 3.09
6500 11038 4.665833 AGAACCAAAAACAAGGTAAGCC 57.334 40.909 0.00 0.00 37.07 4.35
6501 11039 4.027437 AGAACCAAAAACAAGGTAAGCCA 58.973 39.130 0.00 0.00 37.07 4.75
6502 11040 4.099419 AGAACCAAAAACAAGGTAAGCCAG 59.901 41.667 0.00 0.00 37.07 4.85
6503 11041 2.698274 ACCAAAAACAAGGTAAGCCAGG 59.302 45.455 0.00 0.00 36.07 4.45
6504 11042 2.547855 CCAAAAACAAGGTAAGCCAGGC 60.548 50.000 1.84 1.84 37.19 4.85
6505 11043 1.338107 AAAACAAGGTAAGCCAGGCC 58.662 50.000 8.22 0.00 37.19 5.19
6506 11044 0.893727 AAACAAGGTAAGCCAGGCCG 60.894 55.000 8.22 0.00 37.19 6.13
6507 11045 3.134127 CAAGGTAAGCCAGGCCGC 61.134 66.667 8.22 0.00 37.19 6.53
6508 11046 4.426313 AAGGTAAGCCAGGCCGCC 62.426 66.667 8.22 8.18 37.19 6.13
6510 11048 4.733542 GGTAAGCCAGGCCGCCAA 62.734 66.667 13.15 0.00 34.09 4.52
6511 11049 2.675075 GTAAGCCAGGCCGCCAAA 60.675 61.111 13.15 0.00 0.00 3.28
6512 11050 2.116340 TAAGCCAGGCCGCCAAAA 59.884 55.556 13.15 0.00 0.00 2.44
6513 11051 1.531840 TAAGCCAGGCCGCCAAAAA 60.532 52.632 13.15 0.00 0.00 1.94
6514 11052 1.811645 TAAGCCAGGCCGCCAAAAAC 61.812 55.000 13.15 0.00 0.00 2.43
6515 11053 3.922640 GCCAGGCCGCCAAAAACA 61.923 61.111 13.15 0.00 0.00 2.83
6516 11054 2.339712 CCAGGCCGCCAAAAACAG 59.660 61.111 13.15 0.00 0.00 3.16
6517 11055 2.356194 CAGGCCGCCAAAAACAGC 60.356 61.111 13.15 0.00 0.00 4.40
6518 11056 2.837291 AGGCCGCCAAAAACAGCA 60.837 55.556 13.15 0.00 0.00 4.41
6519 11057 2.209315 AGGCCGCCAAAAACAGCAT 61.209 52.632 13.15 0.00 0.00 3.79
6520 11058 2.028733 GGCCGCCAAAAACAGCATG 61.029 57.895 3.91 0.00 46.00 4.06
6521 11059 2.028733 GCCGCCAAAAACAGCATGG 61.029 57.895 0.00 0.00 43.62 3.66
6527 11065 2.836262 CCAAAAACAGCATGGCAAAGA 58.164 42.857 0.00 0.00 43.62 2.52
6528 11066 2.545106 CCAAAAACAGCATGGCAAAGAC 59.455 45.455 0.00 0.00 43.62 3.01
6529 11067 3.196463 CAAAAACAGCATGGCAAAGACA 58.804 40.909 0.00 0.00 43.62 3.41
6530 11068 2.806608 AAACAGCATGGCAAAGACAG 57.193 45.000 0.00 0.00 43.62 3.51
6531 11069 1.985473 AACAGCATGGCAAAGACAGA 58.015 45.000 0.00 0.00 43.62 3.41
6532 11070 1.531423 ACAGCATGGCAAAGACAGAG 58.469 50.000 0.00 0.00 43.62 3.35
6533 11071 0.809385 CAGCATGGCAAAGACAGAGG 59.191 55.000 0.00 0.00 0.00 3.69
6534 11072 0.323178 AGCATGGCAAAGACAGAGGG 60.323 55.000 0.00 0.00 0.00 4.30
6535 11073 0.322816 GCATGGCAAAGACAGAGGGA 60.323 55.000 0.00 0.00 0.00 4.20
6536 11074 1.457346 CATGGCAAAGACAGAGGGAC 58.543 55.000 0.00 0.00 0.00 4.46
6538 11076 2.024176 TGGCAAAGACAGAGGGACTA 57.976 50.000 0.00 0.00 41.55 2.59
6539 11077 1.623811 TGGCAAAGACAGAGGGACTAC 59.376 52.381 0.00 0.00 41.55 2.73
6540 11078 1.903183 GGCAAAGACAGAGGGACTACT 59.097 52.381 0.00 0.00 41.55 2.57
6541 11079 2.093921 GGCAAAGACAGAGGGACTACTC 60.094 54.545 0.00 0.00 41.55 2.59
6542 11080 2.093921 GCAAAGACAGAGGGACTACTCC 60.094 54.545 0.00 0.00 41.55 3.85
6551 11089 2.137692 GGACTACTCCCATGCCTCC 58.862 63.158 0.00 0.00 0.00 4.30
6552 11090 0.399233 GGACTACTCCCATGCCTCCT 60.399 60.000 0.00 0.00 0.00 3.69
6553 11091 1.501582 GACTACTCCCATGCCTCCTT 58.498 55.000 0.00 0.00 0.00 3.36
6554 11092 1.414550 GACTACTCCCATGCCTCCTTC 59.585 57.143 0.00 0.00 0.00 3.46
6555 11093 1.273838 ACTACTCCCATGCCTCCTTCA 60.274 52.381 0.00 0.00 0.00 3.02
6556 11094 1.415659 CTACTCCCATGCCTCCTTCAG 59.584 57.143 0.00 0.00 0.00 3.02
6557 11095 1.277580 ACTCCCATGCCTCCTTCAGG 61.278 60.000 0.00 0.00 46.82 3.86
6568 11106 1.867363 TCCTTCAGGAGGCCTAACTC 58.133 55.000 4.42 0.00 45.87 3.01
6569 11107 0.461961 CCTTCAGGAGGCCTAACTCG 59.538 60.000 4.42 2.80 39.09 4.18
6570 11108 1.187087 CTTCAGGAGGCCTAACTCGT 58.813 55.000 4.42 0.00 38.39 4.18
6571 11109 1.135333 CTTCAGGAGGCCTAACTCGTC 59.865 57.143 4.42 0.00 38.39 4.20
6572 11110 0.683504 TCAGGAGGCCTAACTCGTCC 60.684 60.000 4.42 0.00 38.39 4.79
6573 11111 1.381463 AGGAGGCCTAACTCGTCCC 60.381 63.158 4.42 0.00 38.81 4.46
6574 11112 1.381463 GGAGGCCTAACTCGTCCCT 60.381 63.158 4.42 0.00 38.39 4.20
6575 11113 0.106318 GGAGGCCTAACTCGTCCCTA 60.106 60.000 4.42 0.00 38.39 3.53
6576 11114 1.687368 GGAGGCCTAACTCGTCCCTAA 60.687 57.143 4.42 0.00 38.39 2.69
6577 11115 2.317973 GAGGCCTAACTCGTCCCTAAT 58.682 52.381 4.42 0.00 0.00 1.73
6578 11116 2.296752 GAGGCCTAACTCGTCCCTAATC 59.703 54.545 4.42 0.00 0.00 1.75
6585 11123 5.127356 CCTAACTCGTCCCTAATCAAAGACT 59.873 44.000 0.00 0.00 0.00 3.24
6697 11237 8.927675 ATGTTGGACTACAAAATTACTGGTTA 57.072 30.769 0.00 0.00 41.58 2.85
6733 11273 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
6884 11442 1.731613 CCACGACGCTTGCTTACGA 60.732 57.895 0.00 0.00 0.00 3.43
7169 11729 2.158652 ACATGGCAGGATCTGATTCTGG 60.159 50.000 23.87 11.88 32.44 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 6.838382 ACTAGGTGGAAGAAACTGTGTAATT 58.162 36.000 0.00 0.00 0.00 1.40
121 122 4.929819 TCTTTCATGGATATCCGTCGAA 57.070 40.909 13.91 16.34 39.43 3.71
147 148 7.205297 AGAATCACATTAGCAATAATGTTGCC 58.795 34.615 11.06 0.00 45.36 4.52
305 308 3.323775 TCTTCCTTCAAACAGTAGGGGT 58.676 45.455 0.00 0.00 35.61 4.95
351 354 6.469782 TTCAAACAGGAGATGAAAGCTTTT 57.530 33.333 14.05 0.00 22.26 2.27
363 399 4.390297 GTCGAGATTCCTTTCAAACAGGAG 59.610 45.833 0.00 0.00 41.66 3.69
399 435 4.081917 CACTACTCAAGGTTTCCTCCTCTC 60.082 50.000 0.00 0.00 36.74 3.20
509 553 2.808958 CGTAAGCCCGCCATTGACG 61.809 63.158 0.00 0.00 0.00 4.35
570 619 4.038642 CCCCTCTTTGTATCTCTACTCTGC 59.961 50.000 0.00 0.00 0.00 4.26
593 642 2.042261 TCCTTGTAGCCCCCTCCC 59.958 66.667 0.00 0.00 0.00 4.30
596 645 1.616628 CCTGTCCTTGTAGCCCCCT 60.617 63.158 0.00 0.00 0.00 4.79
601 650 3.906720 TTATCACCCTGTCCTTGTAGC 57.093 47.619 0.00 0.00 0.00 3.58
602 651 6.483640 GCTTAATTATCACCCTGTCCTTGTAG 59.516 42.308 0.00 0.00 0.00 2.74
603 652 6.157994 AGCTTAATTATCACCCTGTCCTTGTA 59.842 38.462 0.00 0.00 0.00 2.41
606 655 5.717119 AGCTTAATTATCACCCTGTCCTT 57.283 39.130 0.00 0.00 0.00 3.36
608 657 7.875327 TTTTAGCTTAATTATCACCCTGTCC 57.125 36.000 0.00 0.00 0.00 4.02
612 661 7.173390 GCGAGATTTTAGCTTAATTATCACCCT 59.827 37.037 0.00 0.00 0.00 4.34
616 665 8.551205 CACTGCGAGATTTTAGCTTAATTATCA 58.449 33.333 0.00 0.00 0.00 2.15
618 667 8.662781 TCACTGCGAGATTTTAGCTTAATTAT 57.337 30.769 0.00 0.00 0.00 1.28
619 668 8.662781 ATCACTGCGAGATTTTAGCTTAATTA 57.337 30.769 0.00 0.00 0.00 1.40
620 669 6.985188 TCACTGCGAGATTTTAGCTTAATT 57.015 33.333 0.00 0.00 0.00 1.40
621 670 7.710907 TGTATCACTGCGAGATTTTAGCTTAAT 59.289 33.333 0.00 0.00 0.00 1.40
622 671 7.039270 TGTATCACTGCGAGATTTTAGCTTAA 58.961 34.615 0.00 0.00 0.00 1.85
623 672 6.569780 TGTATCACTGCGAGATTTTAGCTTA 58.430 36.000 0.00 0.00 0.00 3.09
625 674 5.011090 TGTATCACTGCGAGATTTTAGCT 57.989 39.130 0.00 0.00 0.00 3.32
628 677 6.037062 CCATGTTGTATCACTGCGAGATTTTA 59.963 38.462 0.00 0.00 0.00 1.52
629 678 5.163723 CCATGTTGTATCACTGCGAGATTTT 60.164 40.000 0.00 0.00 0.00 1.82
630 679 4.333649 CCATGTTGTATCACTGCGAGATTT 59.666 41.667 0.00 0.00 0.00 2.17
632 681 3.132824 TCCATGTTGTATCACTGCGAGAT 59.867 43.478 0.00 0.00 0.00 2.75
634 683 2.862536 CTCCATGTTGTATCACTGCGAG 59.137 50.000 0.00 0.00 0.00 5.03
635 684 2.892374 CTCCATGTTGTATCACTGCGA 58.108 47.619 0.00 0.00 0.00 5.10
637 686 1.672881 GGCTCCATGTTGTATCACTGC 59.327 52.381 0.00 0.00 0.00 4.40
641 690 1.138859 CTCGGGCTCCATGTTGTATCA 59.861 52.381 0.00 0.00 0.00 2.15
698 747 3.575805 AGAAGCTGGATTTTGGTTGGAA 58.424 40.909 0.00 0.00 0.00 3.53
699 748 3.243359 AGAAGCTGGATTTTGGTTGGA 57.757 42.857 0.00 0.00 0.00 3.53
705 754 4.522022 AGAACAGGAAGAAGCTGGATTTTG 59.478 41.667 0.00 0.00 0.00 2.44
707 756 4.379302 AGAACAGGAAGAAGCTGGATTT 57.621 40.909 0.00 0.00 0.00 2.17
708 757 4.379302 AAGAACAGGAAGAAGCTGGATT 57.621 40.909 0.00 0.00 0.00 3.01
709 758 4.379302 AAAGAACAGGAAGAAGCTGGAT 57.621 40.909 0.00 0.00 0.00 3.41
712 761 5.296780 TGTTGTAAAGAACAGGAAGAAGCTG 59.703 40.000 0.00 0.00 39.87 4.24
747 796 0.604578 GCAAGATTTGGGCAGCAGAA 59.395 50.000 0.00 0.00 0.00 3.02
765 814 2.432444 TGGTTTGTGCACTGTATAGGC 58.568 47.619 19.41 0.00 0.00 3.93
786 835 4.229123 AGGATTTGGAGTTCATCACCAGAT 59.771 41.667 0.00 0.00 38.01 2.90
887 936 0.179078 GATCTGGGCAGCAGAGACAG 60.179 60.000 0.00 0.00 31.61 3.51
982 1085 0.330604 ATCTGCCAAGCACAGGTGAT 59.669 50.000 3.10 0.00 35.78 3.06
1082 1188 4.562757 GGATTGGTTTCCTAAAGGTTTGCC 60.563 45.833 0.00 0.00 36.34 4.52
1359 1479 2.029844 GTTGGTGTCGAGGAGCAGC 61.030 63.158 0.00 0.00 0.00 5.25
1475 1595 2.099756 GTCAACTTGCCAAGCTCAACTT 59.900 45.455 3.88 0.00 40.05 2.66
1483 1603 1.008538 GGCGTGTCAACTTGCCAAG 60.009 57.895 2.11 2.11 46.76 3.61
1581 1701 6.470235 GCAGCATATTATTTGACACACTCAAC 59.530 38.462 0.00 0.00 38.70 3.18
1666 1786 1.008538 CGCCTGTGAAACTGTTGGC 60.009 57.895 8.36 8.36 38.04 4.52
1672 1792 2.039084 AGGAAATCTCGCCTGTGAAACT 59.961 45.455 0.00 0.00 38.04 2.66
1692 1812 2.149803 TTACGGCGGTGACACTGGAG 62.150 60.000 16.14 3.72 0.00 3.86
1719 1839 3.181451 TGTTTGAGGACACATCAAGCTCT 60.181 43.478 12.25 0.00 38.33 4.09
1746 1866 3.452627 AGTCATCTGGTATTGTCCCTGTC 59.547 47.826 0.00 0.00 0.00 3.51
1863 1983 6.586463 ACATGTTCTCAAATAGCCGTATATCG 59.414 38.462 0.00 0.00 39.52 2.92
1866 1986 9.419297 GATAACATGTTCTCAAATAGCCGTATA 57.581 33.333 15.85 0.00 0.00 1.47
1869 1989 6.258727 CAGATAACATGTTCTCAAATAGCCGT 59.741 38.462 21.81 0.12 0.00 5.68
2208 2328 4.062293 CAAGACGTGTAAAGTTCCATGGA 58.938 43.478 11.44 11.44 0.00 3.41
2265 2385 4.083271 ACTTCGATTTTGCCTGCTAAAGTC 60.083 41.667 5.14 3.38 0.00 3.01
2283 2403 1.737838 TTGCTGCCCTGAATACTTCG 58.262 50.000 0.00 0.00 0.00 3.79
2332 2452 7.453126 TGTTACCTGTGAAATACCCATCAAATT 59.547 33.333 0.00 0.00 0.00 1.82
2486 4623 0.541863 AAGGATGGTTAGCCCTGACG 59.458 55.000 0.00 0.00 30.80 4.35
2721 4858 6.688922 GCCTCCTGGAGATATCATTGTTGTTA 60.689 42.308 25.18 0.00 34.57 2.41
2761 4898 3.693085 AGCATGATACTGGCAAGAACAAG 59.307 43.478 0.00 0.00 0.00 3.16
2962 5099 2.057922 ACCTTCTCCATCCACAACACT 58.942 47.619 0.00 0.00 0.00 3.55
3035 5173 1.355005 GAAGTCCTTCTCGAGCTTGC 58.645 55.000 7.81 0.00 36.69 4.01
3092 5230 3.058016 GCAGAGCAGCTTGACAATGTTTA 60.058 43.478 0.00 0.00 0.00 2.01
3186 7595 3.312890 ACCAACTCTATCCCTCTGATGG 58.687 50.000 0.00 0.00 34.76 3.51
3654 8070 0.880278 GGACGAGCTGTTTGTGCAGA 60.880 55.000 0.00 0.00 38.70 4.26
3679 8095 1.302993 GCGCTTCCCCACCTTACAA 60.303 57.895 0.00 0.00 0.00 2.41
5513 10023 7.054751 AGCCCACAAGTTATCTTAGGTTAATC 58.945 38.462 4.43 0.00 32.07 1.75
5551 10061 1.143813 CCTGTCATATGGAAGGCCCT 58.856 55.000 0.00 0.00 35.38 5.19
5863 10373 0.249868 CCGTTGTGAGCTCCAACAGA 60.250 55.000 30.46 13.27 41.76 3.41
6227 10737 6.068010 TCATTTGCACCCGGAAATTCTATAT 58.932 36.000 0.73 0.00 40.78 0.86
6322 10860 0.965439 CCTGCCATTCCGGTCAAAAA 59.035 50.000 0.00 0.00 36.97 1.94
6323 10861 0.178975 ACCTGCCATTCCGGTCAAAA 60.179 50.000 0.00 0.00 36.97 2.44
6324 10862 0.893270 CACCTGCCATTCCGGTCAAA 60.893 55.000 0.00 0.00 36.97 2.69
6325 10863 1.303236 CACCTGCCATTCCGGTCAA 60.303 57.895 0.00 0.00 36.97 3.18
6326 10864 2.350895 CACCTGCCATTCCGGTCA 59.649 61.111 0.00 0.00 36.97 4.02
6327 10865 3.134127 GCACCTGCCATTCCGGTC 61.134 66.667 0.00 0.00 36.97 4.79
6330 10868 2.110967 CAGAGCACCTGCCATTCCG 61.111 63.158 0.00 0.00 43.38 4.30
6331 10869 3.915575 CAGAGCACCTGCCATTCC 58.084 61.111 0.00 0.00 43.38 3.01
6450 10988 2.888414 GGTTTCCCGGTTGATTTCTCAA 59.112 45.455 0.00 0.00 39.07 3.02
6451 10989 2.107552 AGGTTTCCCGGTTGATTTCTCA 59.892 45.455 0.00 0.00 35.12 3.27
6452 10990 2.791655 AGGTTTCCCGGTTGATTTCTC 58.208 47.619 0.00 0.00 35.12 2.87
6453 10991 2.971901 AGGTTTCCCGGTTGATTTCT 57.028 45.000 0.00 0.00 35.12 2.52
6454 10992 4.524053 AGATAGGTTTCCCGGTTGATTTC 58.476 43.478 0.00 0.00 35.12 2.17
6455 10993 4.586306 AGATAGGTTTCCCGGTTGATTT 57.414 40.909 0.00 0.00 35.12 2.17
6456 10994 5.703730 TTAGATAGGTTTCCCGGTTGATT 57.296 39.130 0.00 0.00 35.12 2.57
6457 10995 5.427481 TCTTTAGATAGGTTTCCCGGTTGAT 59.573 40.000 0.00 0.00 35.12 2.57
6458 10996 4.778958 TCTTTAGATAGGTTTCCCGGTTGA 59.221 41.667 0.00 0.00 35.12 3.18
6459 10997 5.093849 TCTTTAGATAGGTTTCCCGGTTG 57.906 43.478 0.00 0.00 35.12 3.77
6460 10998 5.494724 GTTCTTTAGATAGGTTTCCCGGTT 58.505 41.667 0.00 0.00 35.12 4.44
6461 10999 4.080695 GGTTCTTTAGATAGGTTTCCCGGT 60.081 45.833 0.00 0.00 35.12 5.28
6462 11000 4.080751 TGGTTCTTTAGATAGGTTTCCCGG 60.081 45.833 0.00 0.00 35.12 5.73
6463 11001 5.093849 TGGTTCTTTAGATAGGTTTCCCG 57.906 43.478 0.00 0.00 35.12 5.14
6464 11002 7.770366 TTTTGGTTCTTTAGATAGGTTTCCC 57.230 36.000 0.00 0.00 0.00 3.97
6465 11003 8.635328 TGTTTTTGGTTCTTTAGATAGGTTTCC 58.365 33.333 0.00 0.00 0.00 3.13
6468 11006 8.638873 CCTTGTTTTTGGTTCTTTAGATAGGTT 58.361 33.333 0.00 0.00 0.00 3.50
6469 11007 7.783119 ACCTTGTTTTTGGTTCTTTAGATAGGT 59.217 33.333 0.00 0.00 31.62 3.08
6470 11008 8.178313 ACCTTGTTTTTGGTTCTTTAGATAGG 57.822 34.615 0.00 0.00 31.62 2.57
6473 11011 8.141909 GCTTACCTTGTTTTTGGTTCTTTAGAT 58.858 33.333 0.00 0.00 37.74 1.98
6474 11012 7.417003 GGCTTACCTTGTTTTTGGTTCTTTAGA 60.417 37.037 0.00 0.00 37.74 2.10
6475 11013 6.700081 GGCTTACCTTGTTTTTGGTTCTTTAG 59.300 38.462 0.00 0.00 37.74 1.85
6476 11014 6.154706 TGGCTTACCTTGTTTTTGGTTCTTTA 59.845 34.615 0.00 0.00 37.74 1.85
6477 11015 5.046231 TGGCTTACCTTGTTTTTGGTTCTTT 60.046 36.000 0.00 0.00 37.74 2.52
6478 11016 4.468153 TGGCTTACCTTGTTTTTGGTTCTT 59.532 37.500 0.00 0.00 37.74 2.52
6479 11017 4.027437 TGGCTTACCTTGTTTTTGGTTCT 58.973 39.130 0.00 0.00 37.74 3.01
6480 11018 4.368315 CTGGCTTACCTTGTTTTTGGTTC 58.632 43.478 0.00 0.00 37.74 3.62
6481 11019 3.133901 CCTGGCTTACCTTGTTTTTGGTT 59.866 43.478 0.00 0.00 37.74 3.67
6482 11020 2.698274 CCTGGCTTACCTTGTTTTTGGT 59.302 45.455 0.00 0.00 40.12 3.67
6483 11021 2.547855 GCCTGGCTTACCTTGTTTTTGG 60.548 50.000 12.43 0.00 36.63 3.28
6484 11022 2.547855 GGCCTGGCTTACCTTGTTTTTG 60.548 50.000 19.68 0.00 36.63 2.44
6485 11023 1.691976 GGCCTGGCTTACCTTGTTTTT 59.308 47.619 19.68 0.00 36.63 1.94
6486 11024 1.338107 GGCCTGGCTTACCTTGTTTT 58.662 50.000 19.68 0.00 36.63 2.43
6487 11025 0.893727 CGGCCTGGCTTACCTTGTTT 60.894 55.000 19.68 0.00 36.63 2.83
6488 11026 1.303317 CGGCCTGGCTTACCTTGTT 60.303 57.895 19.68 0.00 36.63 2.83
6489 11027 2.351276 CGGCCTGGCTTACCTTGT 59.649 61.111 19.68 0.00 36.63 3.16
6490 11028 3.134127 GCGGCCTGGCTTACCTTG 61.134 66.667 19.68 1.44 36.63 3.61
6491 11029 4.426313 GGCGGCCTGGCTTACCTT 62.426 66.667 19.68 0.00 40.72 3.50
6493 11031 4.733542 TTGGCGGCCTGGCTTACC 62.734 66.667 21.46 17.10 45.14 2.85
6494 11032 1.811645 TTTTTGGCGGCCTGGCTTAC 61.812 55.000 21.46 9.21 45.14 2.34
6495 11033 1.531840 TTTTTGGCGGCCTGGCTTA 60.532 52.632 21.46 0.00 45.14 3.09
6496 11034 2.841988 TTTTTGGCGGCCTGGCTT 60.842 55.556 21.46 0.00 45.14 4.35
6497 11035 3.615709 GTTTTTGGCGGCCTGGCT 61.616 61.111 21.46 0.00 45.14 4.75
6498 11036 3.864160 CTGTTTTTGGCGGCCTGGC 62.864 63.158 21.46 11.05 45.12 4.85
6499 11037 2.339712 CTGTTTTTGGCGGCCTGG 59.660 61.111 21.46 0.00 0.00 4.45
6500 11038 2.356194 GCTGTTTTTGGCGGCCTG 60.356 61.111 21.46 0.00 32.41 4.85
6501 11039 2.209315 ATGCTGTTTTTGGCGGCCT 61.209 52.632 21.46 0.00 37.43 5.19
6502 11040 2.028733 CATGCTGTTTTTGGCGGCC 61.029 57.895 13.32 13.32 37.43 6.13
6503 11041 2.028733 CCATGCTGTTTTTGGCGGC 61.029 57.895 0.00 0.00 38.62 6.53
6504 11042 2.028733 GCCATGCTGTTTTTGGCGG 61.029 57.895 0.00 0.00 45.75 6.13
6505 11043 3.553039 GCCATGCTGTTTTTGGCG 58.447 55.556 0.00 0.00 45.75 5.69
6507 11045 2.545106 GTCTTTGCCATGCTGTTTTTGG 59.455 45.455 0.00 0.00 0.00 3.28
6508 11046 3.196463 TGTCTTTGCCATGCTGTTTTTG 58.804 40.909 0.00 0.00 0.00 2.44
6509 11047 3.132646 TCTGTCTTTGCCATGCTGTTTTT 59.867 39.130 0.00 0.00 0.00 1.94
6510 11048 2.694628 TCTGTCTTTGCCATGCTGTTTT 59.305 40.909 0.00 0.00 0.00 2.43
6511 11049 2.295349 CTCTGTCTTTGCCATGCTGTTT 59.705 45.455 0.00 0.00 0.00 2.83
6512 11050 1.884579 CTCTGTCTTTGCCATGCTGTT 59.115 47.619 0.00 0.00 0.00 3.16
6513 11051 1.531423 CTCTGTCTTTGCCATGCTGT 58.469 50.000 0.00 0.00 0.00 4.40
6514 11052 0.809385 CCTCTGTCTTTGCCATGCTG 59.191 55.000 0.00 0.00 0.00 4.41
6515 11053 0.323178 CCCTCTGTCTTTGCCATGCT 60.323 55.000 0.00 0.00 0.00 3.79
6516 11054 0.322816 TCCCTCTGTCTTTGCCATGC 60.323 55.000 0.00 0.00 0.00 4.06
6517 11055 1.004044 AGTCCCTCTGTCTTTGCCATG 59.996 52.381 0.00 0.00 0.00 3.66
6518 11056 1.366319 AGTCCCTCTGTCTTTGCCAT 58.634 50.000 0.00 0.00 0.00 4.40
6519 11057 1.623811 GTAGTCCCTCTGTCTTTGCCA 59.376 52.381 0.00 0.00 0.00 4.92
6520 11058 1.903183 AGTAGTCCCTCTGTCTTTGCC 59.097 52.381 0.00 0.00 0.00 4.52
6521 11059 2.093921 GGAGTAGTCCCTCTGTCTTTGC 60.094 54.545 5.14 0.00 36.76 3.68
6522 11060 3.878160 GGAGTAGTCCCTCTGTCTTTG 57.122 52.381 5.14 0.00 36.76 2.77
6533 11071 0.399233 AGGAGGCATGGGAGTAGTCC 60.399 60.000 8.22 8.22 43.05 3.85
6534 11072 1.414550 GAAGGAGGCATGGGAGTAGTC 59.585 57.143 0.00 0.00 0.00 2.59
6535 11073 1.273838 TGAAGGAGGCATGGGAGTAGT 60.274 52.381 0.00 0.00 0.00 2.73
6536 11074 1.415659 CTGAAGGAGGCATGGGAGTAG 59.584 57.143 0.00 0.00 0.00 2.57
6537 11075 1.500474 CTGAAGGAGGCATGGGAGTA 58.500 55.000 0.00 0.00 0.00 2.59
6538 11076 1.277580 CCTGAAGGAGGCATGGGAGT 61.278 60.000 0.00 0.00 34.01 3.85
6539 11077 0.984961 TCCTGAAGGAGGCATGGGAG 60.985 60.000 0.00 0.00 42.47 4.30
6540 11078 1.082766 TCCTGAAGGAGGCATGGGA 59.917 57.895 0.00 0.00 42.47 4.37
6541 11079 3.745546 TCCTGAAGGAGGCATGGG 58.254 61.111 0.00 0.00 42.47 4.00
6551 11089 1.135333 GACGAGTTAGGCCTCCTGAAG 59.865 57.143 9.68 0.00 34.61 3.02
6552 11090 1.183549 GACGAGTTAGGCCTCCTGAA 58.816 55.000 9.68 0.00 34.61 3.02
6553 11091 0.683504 GGACGAGTTAGGCCTCCTGA 60.684 60.000 9.68 0.00 36.04 3.86
6554 11092 1.677637 GGGACGAGTTAGGCCTCCTG 61.678 65.000 9.68 4.52 39.91 3.86
6555 11093 1.381463 GGGACGAGTTAGGCCTCCT 60.381 63.158 9.68 6.54 39.91 3.69
6556 11094 0.106318 TAGGGACGAGTTAGGCCTCC 60.106 60.000 9.68 1.40 39.91 4.30
6557 11095 1.772836 TTAGGGACGAGTTAGGCCTC 58.227 55.000 9.68 0.00 39.91 4.70
6558 11096 2.317973 GATTAGGGACGAGTTAGGCCT 58.682 52.381 11.78 11.78 39.91 5.19
6559 11097 2.037144 TGATTAGGGACGAGTTAGGCC 58.963 52.381 0.00 0.00 39.05 5.19
6560 11098 3.814005 TTGATTAGGGACGAGTTAGGC 57.186 47.619 0.00 0.00 0.00 3.93
6561 11099 5.127356 AGTCTTTGATTAGGGACGAGTTAGG 59.873 44.000 0.00 0.00 34.34 2.69
6562 11100 6.210287 AGTCTTTGATTAGGGACGAGTTAG 57.790 41.667 0.00 0.00 34.34 2.34
6563 11101 7.707624 TTAGTCTTTGATTAGGGACGAGTTA 57.292 36.000 0.00 0.00 34.34 2.24
6564 11102 6.600882 TTAGTCTTTGATTAGGGACGAGTT 57.399 37.500 0.00 0.00 34.34 3.01
6565 11103 6.793505 ATTAGTCTTTGATTAGGGACGAGT 57.206 37.500 0.00 0.00 34.34 4.18
6566 11104 6.702282 GGAATTAGTCTTTGATTAGGGACGAG 59.298 42.308 0.00 0.00 34.34 4.18
6567 11105 6.579865 GGAATTAGTCTTTGATTAGGGACGA 58.420 40.000 0.00 0.00 34.34 4.20
6568 11106 5.462398 CGGAATTAGTCTTTGATTAGGGACG 59.538 44.000 0.00 0.00 34.34 4.79
6569 11107 5.758784 CCGGAATTAGTCTTTGATTAGGGAC 59.241 44.000 0.00 0.00 0.00 4.46
6570 11108 5.163237 CCCGGAATTAGTCTTTGATTAGGGA 60.163 44.000 0.73 0.00 34.95 4.20
6571 11109 5.063880 CCCGGAATTAGTCTTTGATTAGGG 58.936 45.833 0.73 0.00 0.00 3.53
6572 11110 4.515567 GCCCGGAATTAGTCTTTGATTAGG 59.484 45.833 0.73 0.00 0.00 2.69
6573 11111 5.368989 AGCCCGGAATTAGTCTTTGATTAG 58.631 41.667 0.73 0.00 0.00 1.73
6574 11112 5.367945 AGCCCGGAATTAGTCTTTGATTA 57.632 39.130 0.73 0.00 0.00 1.75
6575 11113 4.236527 AGCCCGGAATTAGTCTTTGATT 57.763 40.909 0.73 0.00 0.00 2.57
6576 11114 3.933861 AGCCCGGAATTAGTCTTTGAT 57.066 42.857 0.73 0.00 0.00 2.57
6577 11115 4.829872 TTAGCCCGGAATTAGTCTTTGA 57.170 40.909 0.73 0.00 0.00 2.69
6578 11116 5.733373 GCATTTAGCCCGGAATTAGTCTTTG 60.733 44.000 0.73 0.00 37.23 2.77
6697 11237 1.830477 ACACACACACAGGCCAAAAAT 59.170 42.857 5.01 0.00 0.00 1.82
6814 11372 3.538591 TCCTTTAGCACATCAGAGCATG 58.461 45.455 0.00 0.00 33.43 4.06
6963 11521 8.578308 TGAAGAAAGAGTTGCAATTTATGTTG 57.422 30.769 0.59 0.00 0.00 3.33
7140 11700 5.393866 TCAGATCCTGCCATGTGTAGTATA 58.606 41.667 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.