Multiple sequence alignment - TraesCS7D01G466000

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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 TraesCS7D01G466000 chr7D 100.000 4935 0 0 4783 9717 579827748 579822814 0.000000e+00 9114.0
1 TraesCS7D01G466000 chr7D 100.000 4440 0 0 1 4440 579832530 579828091 0.000000e+00 8200.0
2 TraesCS7D01G466000 chr7A 91.998 4174 188 57 262 4352 671476894 671472784 0.000000e+00 5723.0
3 TraesCS7D01G466000 chr7A 95.372 3090 87 23 4783 7857 671470966 671467918 0.000000e+00 4863.0
4 TraesCS7D01G466000 chr7A 90.006 1541 79 33 8216 9717 671467500 671465996 0.000000e+00 1923.0
5 TraesCS7D01G466000 chr7A 96.677 331 9 2 7890 8219 671467921 671467592 5.130000e-152 549.0
6 TraesCS7D01G466000 chr7A 93.561 264 16 1 1 264 671477185 671476923 9.150000e-105 392.0
7 TraesCS7D01G466000 chr7B 94.810 3179 121 19 5117 8278 646067470 646064319 0.000000e+00 4916.0
8 TraesCS7D01G466000 chr7B 91.075 1535 80 25 2912 4420 646072131 646070628 0.000000e+00 2023.0
9 TraesCS7D01G466000 chr7B 89.892 1019 68 22 883 1889 646074385 646073390 0.000000e+00 1279.0
10 TraesCS7D01G466000 chr7B 94.944 712 27 3 5579 6283 221550240 221549531 0.000000e+00 1107.0
11 TraesCS7D01G466000 chr7B 94.944 712 27 3 5579 6283 248068605 248069314 0.000000e+00 1107.0
12 TraesCS7D01G466000 chr7B 95.315 619 21 3 8404 9021 646064281 646063670 0.000000e+00 976.0
13 TraesCS7D01G466000 chr7B 88.177 609 39 3 2309 2917 646072730 646072155 0.000000e+00 695.0
14 TraesCS7D01G466000 chr7B 85.449 646 60 16 262 887 646078431 646077800 8.230000e-180 641.0
15 TraesCS7D01G466000 chr7B 95.549 337 14 1 4783 5119 646068059 646067724 1.110000e-148 538.0
16 TraesCS7D01G466000 chr7B 83.415 609 30 25 9013 9579 646063002 646062423 5.240000e-137 499.0
17 TraesCS7D01G466000 chr7B 96.651 209 7 0 56 264 646078667 646078459 2.010000e-91 348.0
18 TraesCS7D01G466000 chr7B 84.384 333 43 7 1952 2278 646073394 646073065 1.570000e-82 318.0
19 TraesCS7D01G466000 chr7B 93.162 117 6 2 9602 9717 646062439 646062324 4.670000e-38 171.0
20 TraesCS7D01G466000 chr7B 93.519 108 6 1 2187 2294 646073119 646073013 1.010000e-34 159.0
21 TraesCS7D01G466000 chr7B 82.075 106 10 8 346 449 145779614 145779712 2.250000e-11 82.4
22 TraesCS7D01G466000 chr7B 88.372 43 5 0 8296 8338 646064319 646064277 1.800000e-02 52.8
23 TraesCS7D01G466000 chr2D 88.816 1073 74 9 2309 3350 45942306 45941249 0.000000e+00 1275.0
24 TraesCS7D01G466000 chr2D 88.827 1074 73 10 2309 3350 46006065 46005007 0.000000e+00 1275.0
25 TraesCS7D01G466000 chr2D 91.639 610 36 6 2309 2917 45961042 45960447 0.000000e+00 830.0
26 TraesCS7D01G466000 chr2D 90.820 610 42 5 2309 2918 46024798 46024203 0.000000e+00 804.0
27 TraesCS7D01G466000 chr2D 91.304 437 33 5 2917 3350 45960418 45959984 8.400000e-165 592.0
28 TraesCS7D01G466000 chr2D 90.698 430 37 3 2923 3350 46024169 46023741 3.940000e-158 569.0
29 TraesCS7D01G466000 chr2D 80.000 110 20 2 336 445 498279354 498279247 8.090000e-11 80.5
30 TraesCS7D01G466000 chrUn 88.734 1074 74 10 2309 3350 271715056 271716114 0.000000e+00 1269.0
31 TraesCS7D01G466000 chrUn 88.734 1074 74 10 2309 3350 320489056 320490114 0.000000e+00 1269.0
32 TraesCS7D01G466000 chrUn 95.084 712 26 3 5579 6283 407577706 407576997 0.000000e+00 1112.0
33 TraesCS7D01G466000 chrUn 94.951 713 26 4 5579 6283 436838254 436838964 0.000000e+00 1109.0
34 TraesCS7D01G466000 chrUn 94.944 712 27 3 5579 6283 259192071 259192780 0.000000e+00 1107.0
35 TraesCS7D01G466000 chrUn 88.060 603 40 4 2779 3350 402512081 402512682 0.000000e+00 686.0
36 TraesCS7D01G466000 chr4B 94.944 712 27 3 5579 6283 60935171 60934462 0.000000e+00 1107.0
37 TraesCS7D01G466000 chr4B 94.944 712 27 3 5579 6283 651859461 651860170 0.000000e+00 1107.0
38 TraesCS7D01G466000 chr4B 86.111 72 10 0 1178 1249 609406843 609406914 2.910000e-10 78.7
39 TraesCS7D01G466000 chr1B 81.852 270 43 4 3931 4196 455206672 455206939 1.270000e-53 222.0
40 TraesCS7D01G466000 chr6B 84.496 129 14 6 512 636 171463823 171463949 1.330000e-23 122.0
41 TraesCS7D01G466000 chr4D 87.500 72 9 0 1178 1249 481036637 481036708 6.250000e-12 84.2
42 TraesCS7D01G466000 chr4D 84.722 72 8 2 437 507 482519849 482519780 1.750000e-07 69.4
43 TraesCS7D01G466000 chr3B 81.373 102 12 6 346 444 64413553 64413650 1.050000e-09 76.8
44 TraesCS7D01G466000 chr4A 75.155 161 36 4 284 443 703881239 703881396 1.350000e-08 73.1
45 TraesCS7D01G466000 chr6D 85.294 68 10 0 569 636 395716631 395716564 4.870000e-08 71.3


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 TraesCS7D01G466000 chr7D 579822814 579832530 9716 True 8657.000000 9114 100.000000 1 9717 2 chr7D.!!$R1 9716
1 TraesCS7D01G466000 chr7A 671465996 671477185 11189 True 2690.000000 5723 93.522800 1 9717 5 chr7A.!!$R1 9716
2 TraesCS7D01G466000 chr7B 221549531 221550240 709 True 1107.000000 1107 94.944000 5579 6283 1 chr7B.!!$R1 704
3 TraesCS7D01G466000 chr7B 248068605 248069314 709 False 1107.000000 1107 94.944000 5579 6283 1 chr7B.!!$F2 704
4 TraesCS7D01G466000 chr7B 646062324 646078667 16343 True 970.446154 4916 90.751538 56 9717 13 chr7B.!!$R2 9661
5 TraesCS7D01G466000 chr2D 45941249 45942306 1057 True 1275.000000 1275 88.816000 2309 3350 1 chr2D.!!$R1 1041
6 TraesCS7D01G466000 chr2D 46005007 46006065 1058 True 1275.000000 1275 88.827000 2309 3350 1 chr2D.!!$R2 1041
7 TraesCS7D01G466000 chr2D 45959984 45961042 1058 True 711.000000 830 91.471500 2309 3350 2 chr2D.!!$R4 1041
8 TraesCS7D01G466000 chr2D 46023741 46024798 1057 True 686.500000 804 90.759000 2309 3350 2 chr2D.!!$R5 1041
9 TraesCS7D01G466000 chrUn 271715056 271716114 1058 False 1269.000000 1269 88.734000 2309 3350 1 chrUn.!!$F2 1041
10 TraesCS7D01G466000 chrUn 320489056 320490114 1058 False 1269.000000 1269 88.734000 2309 3350 1 chrUn.!!$F3 1041
11 TraesCS7D01G466000 chrUn 407576997 407577706 709 True 1112.000000 1112 95.084000 5579 6283 1 chrUn.!!$R1 704
12 TraesCS7D01G466000 chrUn 436838254 436838964 710 False 1109.000000 1109 94.951000 5579 6283 1 chrUn.!!$F5 704
13 TraesCS7D01G466000 chrUn 259192071 259192780 709 False 1107.000000 1107 94.944000 5579 6283 1 chrUn.!!$F1 704
14 TraesCS7D01G466000 chrUn 402512081 402512682 601 False 686.000000 686 88.060000 2779 3350 1 chrUn.!!$F4 571
15 TraesCS7D01G466000 chr4B 60934462 60935171 709 True 1107.000000 1107 94.944000 5579 6283 1 chr4B.!!$R1 704
16 TraesCS7D01G466000 chr4B 651859461 651860170 709 False 1107.000000 1107 94.944000 5579 6283 1 chr4B.!!$F2 704

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
785 843 0.168568 TGCTTCGCGTCACACGTATA 59.831 50.000 5.77 0.0 44.73 1.47 F
1701 5225 0.179181 CGCCGTAGCTAGTGTTCGAA 60.179 55.000 0.00 0.0 36.60 3.71 F
1977 5502 0.452184 TCGAGTTTCTAGCTCAGGCG 59.548 55.000 0.00 0.0 44.37 5.52 F
3631 7531 0.181114 CCCATTGCTGTAGCTGCCTA 59.819 55.000 5.38 0.0 42.66 3.93 F
4411 8343 4.092821 TGCACATACGCTTGTACATTCTTC 59.907 41.667 0.00 0.0 0.00 2.87 F
6184 12748 1.202651 ACGCCAGTTAGTGCTGTTTCT 60.203 47.619 0.00 0.0 34.84 2.52 F
6287 12851 2.552315 GCTCGAATTTTTGGAGTGTCCA 59.448 45.455 0.00 0.0 46.61 4.02 F
7080 13649 1.281656 GGCCAACTTGTGCACGTAC 59.718 57.895 13.13 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2358 6199 1.133915 ACCAACTATACCAATGGGGCG 60.134 52.381 3.55 0.0 42.05 6.13 R
3260 7153 3.137544 TCAAGTCCCAACATACAACACCT 59.862 43.478 0.00 0.0 0.00 4.00 R
3748 7649 0.734889 AATTACTGCATGAGCCGTGC 59.265 50.000 11.20 11.2 45.53 5.34 R
4991 11278 1.067495 AGCTTCTTCGGCAGTCTACAC 60.067 52.381 0.00 0.0 0.00 2.90 R
6409 12974 2.118679 ACAGCAGCCATATGACTACCA 58.881 47.619 3.65 0.0 0.00 3.25 R
7058 13627 0.109781 CGTGCACAAGTTGGCCATAC 60.110 55.000 18.64 8.2 0.00 2.39 R
8112 14733 1.202698 ACTTGCCGGAAGCCTATCATC 60.203 52.381 5.05 0.0 42.71 2.92 R
9058 16457 0.314935 ACTTTGACAGCAAATGGGCG 59.685 50.000 0.00 0.0 42.66 6.13 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
19 20 2.467566 GGTAAACGACAGTGGTGGAT 57.532 50.000 0.00 0.00 0.00 3.41
44 45 1.522355 CAGCAGGTGTGATAGCCCG 60.522 63.158 0.00 0.00 0.00 6.13
114 115 2.101582 ACTGACGAATCCATACTCTGCC 59.898 50.000 0.00 0.00 0.00 4.85
115 116 2.101415 CTGACGAATCCATACTCTGCCA 59.899 50.000 0.00 0.00 0.00 4.92
181 182 4.225042 AGAACTGGCAGTATGTGACCATTA 59.775 41.667 22.37 0.00 39.31 1.90
257 258 5.187186 TGGGGAGTTTAGTATTCAGAGTGAC 59.813 44.000 0.00 0.00 0.00 3.67
270 302 2.952310 CAGAGTGACCAGATCCGACATA 59.048 50.000 0.00 0.00 0.00 2.29
420 452 7.554835 ACCGTCTTATTATTGAATAAAGTGCCA 59.445 33.333 1.27 0.00 37.13 4.92
426 458 9.693739 TTATTATTGAATAAAGTGCCAAGAGGA 57.306 29.630 1.27 0.00 35.11 3.71
432 464 2.683211 AAGTGCCAAGAGGATGGTTT 57.317 45.000 0.00 0.00 42.75 3.27
435 467 4.322057 AGTGCCAAGAGGATGGTTTTAT 57.678 40.909 0.00 0.00 42.75 1.40
490 523 2.543653 GCACGAACATATGGCAATTCCC 60.544 50.000 7.80 0.00 0.00 3.97
522 556 3.987745 TGGCAATTTAGGGGCTATTTGA 58.012 40.909 0.00 0.00 0.00 2.69
542 576 5.759506 TGATTCGCTTCCACAAAAACTAA 57.240 34.783 0.00 0.00 0.00 2.24
543 577 5.516090 TGATTCGCTTCCACAAAAACTAAC 58.484 37.500 0.00 0.00 0.00 2.34
564 598 2.702478 CCCTGAGTGAGGCATGAATCTA 59.298 50.000 0.00 0.00 41.19 1.98
569 603 2.507058 AGTGAGGCATGAATCTAAGGCA 59.493 45.455 0.00 0.00 0.00 4.75
615 653 2.032681 GCCCGACAAAGGAGCTGT 59.967 61.111 0.00 0.00 0.00 4.40
636 674 3.073650 GTCTGATAGGCCTCCATCCAAAT 59.926 47.826 9.68 0.00 0.00 2.32
640 678 1.527457 AGGCCTCCATCCAAATAGCT 58.473 50.000 0.00 0.00 0.00 3.32
642 680 1.143684 GGCCTCCATCCAAATAGCTCA 59.856 52.381 0.00 0.00 0.00 4.26
774 832 2.537792 TAAGACCGGAGTGCTTCGCG 62.538 60.000 9.46 0.00 0.00 5.87
775 833 4.719369 GACCGGAGTGCTTCGCGT 62.719 66.667 9.46 0.00 0.00 6.01
783 841 2.012414 GTGCTTCGCGTCACACGTA 61.012 57.895 18.49 0.00 44.73 3.57
785 843 0.168568 TGCTTCGCGTCACACGTATA 59.831 50.000 5.77 0.00 44.73 1.47
788 846 2.244251 CTTCGCGTCACACGTATAACA 58.756 47.619 5.77 0.00 44.73 2.41
789 847 1.605500 TCGCGTCACACGTATAACAC 58.394 50.000 5.77 0.00 44.73 3.32
790 848 1.197492 TCGCGTCACACGTATAACACT 59.803 47.619 5.77 0.00 44.73 3.55
791 849 1.980844 CGCGTCACACGTATAACACTT 59.019 47.619 0.00 0.00 44.73 3.16
792 850 3.120373 TCGCGTCACACGTATAACACTTA 60.120 43.478 5.77 0.00 44.73 2.24
794 852 4.086427 CGCGTCACACGTATAACACTTATC 60.086 45.833 0.00 0.00 44.73 1.75
796 854 5.457799 GCGTCACACGTATAACACTTATCAT 59.542 40.000 0.00 0.00 44.73 2.45
797 855 6.020121 GCGTCACACGTATAACACTTATCATT 60.020 38.462 0.00 0.00 44.73 2.57
798 856 7.544596 CGTCACACGTATAACACTTATCATTC 58.455 38.462 0.00 0.00 36.74 2.67
799 857 7.544596 GTCACACGTATAACACTTATCATTCG 58.455 38.462 0.00 0.00 0.00 3.34
803 861 9.309516 ACACGTATAACACTTATCATTCGAATT 57.690 29.630 8.21 0.00 0.00 2.17
906 4385 1.076339 CTTGTGGTGGTGGTTGGGT 60.076 57.895 0.00 0.00 0.00 4.51
907 4386 1.380515 TTGTGGTGGTGGTTGGGTG 60.381 57.895 0.00 0.00 0.00 4.61
908 4387 2.520741 GTGGTGGTGGTTGGGTGG 60.521 66.667 0.00 0.00 0.00 4.61
909 4388 3.826822 TGGTGGTGGTTGGGTGGG 61.827 66.667 0.00 0.00 0.00 4.61
910 4389 3.828023 GGTGGTGGTTGGGTGGGT 61.828 66.667 0.00 0.00 0.00 4.51
1179 4660 3.081409 GCCCTGTCCGCCTTCCTA 61.081 66.667 0.00 0.00 0.00 2.94
1304 4785 1.073706 AGGCCGGTAAGATCCCCAT 60.074 57.895 1.90 0.00 0.00 4.00
1309 4790 2.326428 CCGGTAAGATCCCCATACACT 58.674 52.381 0.00 0.00 0.00 3.55
1311 4792 2.299297 CGGTAAGATCCCCATACACTCC 59.701 54.545 0.00 0.00 0.00 3.85
1312 4793 3.588569 GGTAAGATCCCCATACACTCCT 58.411 50.000 0.00 0.00 0.00 3.69
1314 4795 2.407340 AGATCCCCATACACTCCTCC 57.593 55.000 0.00 0.00 0.00 4.30
1317 4798 1.770518 CCCCATACACTCCTCCCCC 60.771 68.421 0.00 0.00 0.00 5.40
1318 4799 2.140792 CCCATACACTCCTCCCCCG 61.141 68.421 0.00 0.00 0.00 5.73
1319 4800 2.808206 CCATACACTCCTCCCCCGC 61.808 68.421 0.00 0.00 0.00 6.13
1320 4801 1.762460 CATACACTCCTCCCCCGCT 60.762 63.158 0.00 0.00 0.00 5.52
1321 4802 1.457831 ATACACTCCTCCCCCGCTC 60.458 63.158 0.00 0.00 0.00 5.03
1392 4886 3.627237 GGCTGGTTAGGATTGGATTGGAA 60.627 47.826 0.00 0.00 0.00 3.53
1486 4995 1.618888 CCCTCCTCTTCCCGTTGTCTA 60.619 57.143 0.00 0.00 0.00 2.59
1491 5000 2.481449 CCTCTTCCCGTTGTCTATTCCG 60.481 54.545 0.00 0.00 0.00 4.30
1506 5016 6.990349 TGTCTATTCCGTAATTTCCATTCCTC 59.010 38.462 0.00 0.00 0.00 3.71
1507 5017 6.990349 GTCTATTCCGTAATTTCCATTCCTCA 59.010 38.462 0.00 0.00 0.00 3.86
1508 5018 7.171678 GTCTATTCCGTAATTTCCATTCCTCAG 59.828 40.741 0.00 0.00 0.00 3.35
1509 5019 4.837093 TCCGTAATTTCCATTCCTCAGT 57.163 40.909 0.00 0.00 0.00 3.41
1510 5020 4.513442 TCCGTAATTTCCATTCCTCAGTG 58.487 43.478 0.00 0.00 0.00 3.66
1511 5021 3.065371 CCGTAATTTCCATTCCTCAGTGC 59.935 47.826 0.00 0.00 0.00 4.40
1512 5022 3.941483 CGTAATTTCCATTCCTCAGTGCT 59.059 43.478 0.00 0.00 0.00 4.40
1641 5160 1.065273 GCAGCAATGATCCCGCTTG 59.935 57.895 0.00 0.00 32.48 4.01
1643 5162 0.813184 CAGCAATGATCCCGCTTGTT 59.187 50.000 0.00 0.00 32.48 2.83
1644 5163 0.813184 AGCAATGATCCCGCTTGTTG 59.187 50.000 0.00 0.00 29.87 3.33
1645 5164 0.810648 GCAATGATCCCGCTTGTTGA 59.189 50.000 0.00 0.00 0.00 3.18
1646 5165 1.468054 GCAATGATCCCGCTTGTTGAC 60.468 52.381 0.00 0.00 0.00 3.18
1647 5166 2.086869 CAATGATCCCGCTTGTTGACT 58.913 47.619 0.00 0.00 0.00 3.41
1648 5167 1.742761 ATGATCCCGCTTGTTGACTG 58.257 50.000 0.00 0.00 0.00 3.51
1654 5173 2.629137 TCCCGCTTGTTGACTGTTACTA 59.371 45.455 0.00 0.00 0.00 1.82
1655 5174 2.993899 CCCGCTTGTTGACTGTTACTAG 59.006 50.000 0.00 0.00 0.00 2.57
1701 5225 0.179181 CGCCGTAGCTAGTGTTCGAA 60.179 55.000 0.00 0.00 36.60 3.71
1712 5236 4.731961 GCTAGTGTTCGAATGATGCAAATG 59.268 41.667 0.00 0.00 0.00 2.32
1718 5242 4.762956 TCGAATGATGCAAATGAACACA 57.237 36.364 0.00 0.00 0.00 3.72
1735 5259 3.177228 ACACAGCTCATCTCCTTTACCT 58.823 45.455 0.00 0.00 0.00 3.08
1740 5264 5.055812 CAGCTCATCTCCTTTACCTGATTC 58.944 45.833 0.00 0.00 0.00 2.52
1778 5302 6.182507 TGTTCCTGTTTAGGTTACTGATGT 57.817 37.500 0.00 0.00 44.88 3.06
1889 5413 3.066203 CCATGGAGGTACGTAATTTTGGC 59.934 47.826 5.56 0.00 0.00 4.52
1890 5414 2.713877 TGGAGGTACGTAATTTTGGCC 58.286 47.619 0.00 0.00 0.00 5.36
1891 5415 2.040012 TGGAGGTACGTAATTTTGGCCA 59.960 45.455 0.00 0.00 0.00 5.36
1896 5420 4.525100 AGGTACGTAATTTTGGCCACATTT 59.475 37.500 3.88 4.32 0.00 2.32
1903 5427 2.791383 TTTGGCCACATTTTCTGACG 57.209 45.000 3.88 0.00 0.00 4.35
1909 5433 2.484264 GCCACATTTTCTGACGCTTACT 59.516 45.455 0.00 0.00 0.00 2.24
1916 5440 2.741759 TCTGACGCTTACTGCATTGA 57.258 45.000 0.00 0.00 43.06 2.57
1977 5502 0.452184 TCGAGTTTCTAGCTCAGGCG 59.548 55.000 0.00 0.00 44.37 5.52
1980 5505 0.610687 AGTTTCTAGCTCAGGCGCTT 59.389 50.000 7.64 0.00 44.37 4.68
1988 5513 2.477506 AGCTCAGGCGCTTGAAAAGTC 61.478 52.381 23.23 9.85 44.37 3.01
2042 5567 2.010145 ATTAAGTCACGTCGCTGCAT 57.990 45.000 0.00 0.00 0.00 3.96
2332 6173 4.627467 AGTGCTAACTGCTAAGTGATTTCG 59.373 41.667 0.00 0.00 43.37 3.46
2338 6179 5.840940 ACTGCTAAGTGATTTCGTAACAC 57.159 39.130 0.00 0.00 34.48 3.32
2358 6199 5.174395 ACACTCATGTCAGTATCTTTGCTC 58.826 41.667 0.00 0.00 31.55 4.26
2406 6247 6.544928 TCTGCACTATGGATCTTCAACTTA 57.455 37.500 0.00 0.00 0.00 2.24
2537 6381 6.871844 TGTAGACAGAGAATCCATTCTTCTG 58.128 40.000 17.94 17.94 46.47 3.02
2546 6390 4.543590 ATCCATTCTTCTGTCGTGTCTT 57.456 40.909 0.00 0.00 0.00 3.01
2547 6391 4.336889 TCCATTCTTCTGTCGTGTCTTT 57.663 40.909 0.00 0.00 0.00 2.52
2548 6392 4.703897 TCCATTCTTCTGTCGTGTCTTTT 58.296 39.130 0.00 0.00 0.00 2.27
2549 6393 5.123227 TCCATTCTTCTGTCGTGTCTTTTT 58.877 37.500 0.00 0.00 0.00 1.94
2697 6552 1.377690 TGCCTTTGGGGAGGTAATGA 58.622 50.000 0.00 0.00 39.11 2.57
3006 6890 3.052082 CACTGCTCCTTGGTGCCG 61.052 66.667 10.65 7.29 0.00 5.69
3205 7098 6.455360 CCTTGTTGGTTTGTATATGCTGAT 57.545 37.500 0.00 0.00 0.00 2.90
3490 7385 8.469309 TCAGAAAAATGAATCCTTCTGAAGTT 57.531 30.769 15.72 4.95 46.61 2.66
3492 7387 7.536622 CAGAAAAATGAATCCTTCTGAAGTTCG 59.463 37.037 15.72 1.66 44.93 3.95
3503 7398 5.063944 CCTTCTGAAGTTCGTCCATGTTATG 59.936 44.000 15.72 0.00 0.00 1.90
3567 7463 4.832266 TGCTAATTTTCTTCTGGGAAAGCA 59.168 37.500 0.00 0.00 36.69 3.91
3571 7467 6.423776 AATTTTCTTCTGGGAAAGCAATCA 57.576 33.333 0.00 0.00 36.69 2.57
3615 7511 3.275617 AGCATATTTAGTGAACGCCCA 57.724 42.857 0.00 0.00 0.00 5.36
3627 7527 1.308069 AACGCCCATTGCTGTAGCTG 61.308 55.000 5.38 0.00 42.66 4.24
3628 7528 2.803479 GCCCATTGCTGTAGCTGC 59.197 61.111 5.38 0.00 42.66 5.25
3631 7531 0.181114 CCCATTGCTGTAGCTGCCTA 59.819 55.000 5.38 0.00 42.66 3.93
3748 7649 9.042632 CGTGATTGAAAAATTGCAATTAATGTG 57.957 29.630 24.35 8.71 35.05 3.21
4039 7962 8.846211 AGCGGTAATATGCTTTTAACATGTAAT 58.154 29.630 0.00 0.00 38.57 1.89
4305 8236 7.223584 TCTTTGACATATCAACCTCAGTTTGA 58.776 34.615 0.00 0.00 44.66 2.69
4411 8343 4.092821 TGCACATACGCTTGTACATTCTTC 59.907 41.667 0.00 0.00 0.00 2.87
4412 8344 4.092821 GCACATACGCTTGTACATTCTTCA 59.907 41.667 0.00 0.00 0.00 3.02
4413 8345 5.220662 GCACATACGCTTGTACATTCTTCAT 60.221 40.000 0.00 0.00 0.00 2.57
4414 8346 6.675486 GCACATACGCTTGTACATTCTTCATT 60.675 38.462 0.00 0.00 0.00 2.57
4415 8347 6.901887 CACATACGCTTGTACATTCTTCATTC 59.098 38.462 0.00 0.00 0.00 2.67
4416 8348 6.818644 ACATACGCTTGTACATTCTTCATTCT 59.181 34.615 0.00 0.00 0.00 2.40
4417 8349 7.334421 ACATACGCTTGTACATTCTTCATTCTT 59.666 33.333 0.00 0.00 0.00 2.52
4427 8359 9.213799 GTACATTCTTCATTCTTCTTGTTCTCT 57.786 33.333 0.00 0.00 0.00 3.10
4434 8366 5.785423 TCATTCTTCTTGTTCTCTTCCCCTA 59.215 40.000 0.00 0.00 0.00 3.53
4436 8368 7.623677 TCATTCTTCTTGTTCTCTTCCCCTATA 59.376 37.037 0.00 0.00 0.00 1.31
4438 8370 9.676129 ATTCTTCTTGTTCTCTTCCCCTATATA 57.324 33.333 0.00 0.00 0.00 0.86
4846 11133 7.067494 AGTCAACAATAGTGTGCTTCTTCTTTT 59.933 33.333 0.00 0.00 38.27 2.27
4847 11134 8.342634 GTCAACAATAGTGTGCTTCTTCTTTTA 58.657 33.333 0.00 0.00 38.27 1.52
4917 11204 7.272515 AGCAAATATTTTGGTTACGATTTCACG 59.727 33.333 0.00 0.00 39.31 4.35
4957 11244 9.655769 CTGTGAATCGGAACTCAATTTTATATG 57.344 33.333 0.00 0.00 0.00 1.78
4991 11278 6.129115 CGGCTGAAAACTCATTTTATTGTGTG 60.129 38.462 0.00 0.00 38.17 3.82
4999 11286 8.677148 AACTCATTTTATTGTGTGTGTAGACT 57.323 30.769 0.00 0.00 0.00 3.24
5091 11378 9.213799 GTAAAAATGCATTTCCATTTGGTAGAA 57.786 29.630 24.28 0.00 42.78 2.10
5204 11747 7.389232 TCATGCTAGATAAATACCCATGAGTG 58.611 38.462 0.00 0.00 34.44 3.51
5303 11846 1.620822 ACCAAGGTCCAAGAACATGC 58.379 50.000 0.00 0.00 0.00 4.06
5447 11991 6.667558 ACACTATAGATAGCTAACAACCCC 57.332 41.667 6.78 0.00 33.68 4.95
5448 11992 6.382925 ACACTATAGATAGCTAACAACCCCT 58.617 40.000 6.78 0.00 33.68 4.79
5589 12144 2.438868 TGTGACTGTGATTCTGGTCG 57.561 50.000 0.00 0.00 0.00 4.79
5734 12289 7.171337 TGCCATTTTCTGCTTCTAATTTTGTTC 59.829 33.333 0.00 0.00 0.00 3.18
5794 12349 8.455903 TGAATTCCCTTAGCATTTTCTCTATG 57.544 34.615 2.27 0.00 0.00 2.23
5883 12445 9.602568 GTGAATAGTATATATCGAGAGGACTCA 57.397 37.037 1.75 0.00 42.72 3.41
5887 12449 6.112734 AGTATATATCGAGAGGACTCAGCTG 58.887 44.000 7.63 7.63 42.72 4.24
5900 12462 2.357009 ACTCAGCTGTGCAACTTTTGAG 59.643 45.455 14.67 12.32 40.86 3.02
6184 12748 1.202651 ACGCCAGTTAGTGCTGTTTCT 60.203 47.619 0.00 0.00 34.84 2.52
6287 12851 2.552315 GCTCGAATTTTTGGAGTGTCCA 59.448 45.455 0.00 0.00 46.61 4.02
6732 13297 5.869579 TGAAGAACTCTTGCAGGTAAGATT 58.130 37.500 0.00 0.00 36.21 2.40
6777 13342 2.790433 TGGAAGGTAGTGTTGCCATTC 58.210 47.619 0.00 0.00 0.00 2.67
6832 13397 5.499139 TTTAGGAGCAGAAAAACACAGTG 57.501 39.130 0.00 0.00 0.00 3.66
6987 13552 9.989869 TGTTTTCGCGATAATTTACATAATTCA 57.010 25.926 10.88 0.00 0.00 2.57
7080 13649 1.281656 GGCCAACTTGTGCACGTAC 59.718 57.895 13.13 0.00 0.00 3.67
7106 13675 8.184192 CCACAAGTAAATATGAACCATGTTCTC 58.816 37.037 8.30 0.00 0.00 2.87
7107 13676 8.950210 CACAAGTAAATATGAACCATGTTCTCT 58.050 33.333 8.30 0.00 0.00 3.10
7119 13688 6.380079 ACCATGTTCTCTACTTCTTCCATT 57.620 37.500 0.00 0.00 0.00 3.16
7120 13689 6.784031 ACCATGTTCTCTACTTCTTCCATTT 58.216 36.000 0.00 0.00 0.00 2.32
7220 13789 9.918630 AAATCAATTTTGCTATGCATATACTCC 57.081 29.630 6.92 0.00 38.76 3.85
7356 13927 6.787085 ATCTACGCTAAGGTGATAAATTGC 57.213 37.500 0.00 0.00 0.00 3.56
7647 14228 3.254629 GCTCCTGGCATTCTTCACA 57.745 52.632 0.00 0.00 41.35 3.58
7648 14229 1.760192 GCTCCTGGCATTCTTCACAT 58.240 50.000 0.00 0.00 41.35 3.21
7649 14230 2.097825 GCTCCTGGCATTCTTCACATT 58.902 47.619 0.00 0.00 41.35 2.71
7650 14231 2.098770 GCTCCTGGCATTCTTCACATTC 59.901 50.000 0.00 0.00 41.35 2.67
7651 14232 3.618351 CTCCTGGCATTCTTCACATTCT 58.382 45.455 0.00 0.00 0.00 2.40
7652 14233 3.349927 TCCTGGCATTCTTCACATTCTG 58.650 45.455 0.00 0.00 0.00 3.02
7653 14234 2.159282 CCTGGCATTCTTCACATTCTGC 60.159 50.000 0.00 0.00 0.00 4.26
7654 14235 2.573941 GGCATTCTTCACATTCTGCC 57.426 50.000 0.00 0.00 42.00 4.85
7655 14236 1.820519 GGCATTCTTCACATTCTGCCA 59.179 47.619 6.50 0.00 46.54 4.92
7696 14277 2.293598 ATTCCCTCCCTCACAGGATT 57.706 50.000 0.00 0.00 37.67 3.01
7852 14433 7.170277 TGCATGATATGTTATCCTAGCACAAT 58.830 34.615 0.00 0.00 0.00 2.71
7854 14435 8.517878 GCATGATATGTTATCCTAGCACAATTT 58.482 33.333 0.00 0.00 0.00 1.82
7877 14458 6.935741 TTTTCTCGACTCTTGAAAATTGGA 57.064 33.333 5.65 0.00 35.57 3.53
7878 14459 6.545504 TTTCTCGACTCTTGAAAATTGGAG 57.454 37.500 0.00 0.00 0.00 3.86
7879 14460 5.215252 TCTCGACTCTTGAAAATTGGAGT 57.785 39.130 0.00 0.00 41.05 3.85
7880 14461 6.340962 TCTCGACTCTTGAAAATTGGAGTA 57.659 37.500 0.00 0.00 38.87 2.59
7881 14462 6.936279 TCTCGACTCTTGAAAATTGGAGTAT 58.064 36.000 0.00 0.00 38.87 2.12
7882 14463 6.813649 TCTCGACTCTTGAAAATTGGAGTATG 59.186 38.462 0.00 0.00 38.87 2.39
7883 14464 6.697395 TCGACTCTTGAAAATTGGAGTATGA 58.303 36.000 0.00 0.00 38.87 2.15
7884 14465 6.813649 TCGACTCTTGAAAATTGGAGTATGAG 59.186 38.462 0.00 0.00 38.87 2.90
7885 14466 6.591834 CGACTCTTGAAAATTGGAGTATGAGT 59.408 38.462 0.00 0.00 38.87 3.41
7886 14467 7.201478 CGACTCTTGAAAATTGGAGTATGAGTC 60.201 40.741 0.00 0.00 41.57 3.36
7887 14468 7.453393 ACTCTTGAAAATTGGAGTATGAGTCA 58.547 34.615 0.00 0.00 37.29 3.41
7888 14469 7.939039 ACTCTTGAAAATTGGAGTATGAGTCAA 59.061 33.333 0.00 0.00 37.29 3.18
8055 14676 7.859875 CAGAAAATCTCCTTCAGTTTGACTTTC 59.140 37.037 0.00 0.00 0.00 2.62
8171 14794 8.740123 TGATTATCTTTAAATCACCGCCTAAA 57.260 30.769 0.00 0.00 38.19 1.85
8192 14815 8.713271 CCTAAACTTGTTTTGCAACAGTTAAAA 58.287 29.630 0.00 0.00 43.92 1.52
8278 14996 2.951726 TCTTCTGAACAGATGCTGTCG 58.048 47.619 5.34 0.00 44.62 4.35
8292 15010 2.357034 GTCGTTCTTGCCTCGCCA 60.357 61.111 0.00 0.00 0.00 5.69
8331 15049 2.046285 CAAATGGTCGTGGGGGCTC 61.046 63.158 0.00 0.00 0.00 4.70
8334 15052 3.968837 ATGGTCGTGGGGGCTCGTA 62.969 63.158 0.00 0.00 0.00 3.43
8335 15053 3.834799 GGTCGTGGGGGCTCGTAG 61.835 72.222 0.00 0.00 0.00 3.51
8336 15054 3.066814 GTCGTGGGGGCTCGTAGT 61.067 66.667 0.00 0.00 0.00 2.73
8337 15055 2.753043 TCGTGGGGGCTCGTAGTC 60.753 66.667 0.00 0.00 0.00 2.59
8338 15056 4.189188 CGTGGGGGCTCGTAGTCG 62.189 72.222 0.00 0.00 38.55 4.18
8339 15057 3.066814 GTGGGGGCTCGTAGTCGT 61.067 66.667 0.00 0.00 38.33 4.34
8340 15058 1.750399 GTGGGGGCTCGTAGTCGTA 60.750 63.158 0.00 0.00 38.33 3.43
8366 15084 4.383552 CCAGTCCAATTCACCCTCTCTTAG 60.384 50.000 0.00 0.00 0.00 2.18
8369 15087 4.938226 GTCCAATTCACCCTCTCTTAGTTG 59.062 45.833 0.00 0.00 0.00 3.16
8412 15130 6.656632 TGTTGTCTAGAATTCAGTCTCACT 57.343 37.500 8.44 0.00 0.00 3.41
8447 15165 6.018589 TCCTGTATCTATCTCATCTTTGCG 57.981 41.667 0.00 0.00 0.00 4.85
8478 15196 7.552687 TGCTGGTTTTAGTCCAATCTGTATTAG 59.447 37.037 0.00 0.00 34.35 1.73
8524 15242 7.860373 TCTTGTTTTGAAGATTATGGTTGTTCG 59.140 33.333 0.00 0.00 0.00 3.95
8764 15482 7.854557 TCACATCAATGTAAAGATGGAAGAG 57.145 36.000 7.26 0.00 44.50 2.85
8771 15489 3.582647 TGTAAAGATGGAAGAGCACAGGA 59.417 43.478 0.00 0.00 0.00 3.86
8807 15525 4.909696 TTTTCCGTTCTTGCAATCTTCA 57.090 36.364 0.00 0.00 0.00 3.02
8821 15539 5.579119 TGCAATCTTCAGCAAGCAATAAATG 59.421 36.000 0.00 0.00 37.90 2.32
8845 15563 4.670227 AGCGAACTTGCTCTGTAAATTC 57.330 40.909 0.00 0.00 42.95 2.17
8998 15723 6.957984 TTTTCTTCTGAGATCAGTGAATCG 57.042 37.500 9.56 0.00 44.12 3.34
9022 15747 2.415843 GCGCATGCTGCATGGAAT 59.584 55.556 35.63 5.80 45.36 3.01
9140 16539 5.128827 GGTTTCTTCTTTCTGGGTTTTCCTT 59.871 40.000 0.00 0.00 40.46 3.36
9141 16540 6.351881 GGTTTCTTCTTTCTGGGTTTTCCTTT 60.352 38.462 0.00 0.00 40.46 3.11
9142 16541 7.147794 GGTTTCTTCTTTCTGGGTTTTCCTTTA 60.148 37.037 0.00 0.00 40.46 1.85
9143 16542 7.964666 TTCTTCTTTCTGGGTTTTCCTTTAA 57.035 32.000 0.00 0.00 40.46 1.52
9144 16543 7.342769 TCTTCTTTCTGGGTTTTCCTTTAAC 57.657 36.000 0.00 0.00 40.46 2.01
9148 16547 8.141298 TCTTTCTGGGTTTTCCTTTAACTTTT 57.859 30.769 0.00 0.00 40.46 2.27
9373 16785 9.689976 TCGATGAATGTTTTCAAAATGTGTTAT 57.310 25.926 0.00 0.00 44.70 1.89
9551 16999 3.125316 CAGGTTTGCTCGGAAGTCATAAC 59.875 47.826 0.00 0.00 0.00 1.89
9577 17025 5.091261 AGATCTCAACATGGTGGAGTAAC 57.909 43.478 11.68 0.00 35.29 2.50
9586 17034 6.723298 ACATGGTGGAGTAACAATTTCAAA 57.277 33.333 0.00 0.00 0.00 2.69
9587 17035 7.118496 ACATGGTGGAGTAACAATTTCAAAA 57.882 32.000 0.00 0.00 0.00 2.44
9588 17036 7.560368 ACATGGTGGAGTAACAATTTCAAAAA 58.440 30.769 0.00 0.00 0.00 1.94
9670 17123 1.335872 CCAGGCCGAAACATTTGTGAC 60.336 52.381 0.00 0.00 0.00 3.67
9712 17172 4.039004 TCTTTGACCCAACAAATCATGTGG 59.961 41.667 0.00 0.00 42.99 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.430374 GCTACATATCCACCACTGTCGTT 60.430 47.826 0.00 0.00 0.00 3.85
7 8 3.722147 CTGCTACATATCCACCACTGTC 58.278 50.000 0.00 0.00 0.00 3.51
11 12 2.487934 CTGCTGCTACATATCCACCAC 58.512 52.381 0.00 0.00 0.00 4.16
19 20 3.243873 GCTATCACACCTGCTGCTACATA 60.244 47.826 0.00 0.00 0.00 2.29
44 45 3.085952 TGAAACTTCCCACATGATCCC 57.914 47.619 0.00 0.00 0.00 3.85
270 302 2.290323 CCTCATTGGGTTCCTTTCGAGT 60.290 50.000 0.00 0.00 0.00 4.18
486 519 6.371595 AAATTGCCATCATAAAGTTGGGAA 57.628 33.333 0.00 0.00 46.94 3.97
490 523 6.282930 CCCCTAAATTGCCATCATAAAGTTG 58.717 40.000 0.00 0.00 0.00 3.16
522 556 4.261867 GGGTTAGTTTTTGTGGAAGCGAAT 60.262 41.667 0.00 0.00 0.00 3.34
542 576 1.211457 GATTCATGCCTCACTCAGGGT 59.789 52.381 0.00 0.00 43.70 4.34
543 577 1.489649 AGATTCATGCCTCACTCAGGG 59.510 52.381 0.00 0.00 43.70 4.45
569 603 2.982026 GCCTCAGGCCTCCAAAATT 58.018 52.632 3.37 0.00 44.06 1.82
615 653 2.494888 TTGGATGGAGGCCTATCAGA 57.505 50.000 4.42 0.00 0.00 3.27
636 674 3.617284 TCCTCGTGTCACTAATGAGCTA 58.383 45.455 0.65 0.00 34.75 3.32
640 678 3.761752 TGTCATCCTCGTGTCACTAATGA 59.238 43.478 0.65 2.53 0.00 2.57
642 680 4.220821 AGTTGTCATCCTCGTGTCACTAAT 59.779 41.667 0.65 0.00 0.00 1.73
774 832 7.430211 TCGAATGATAAGTGTTATACGTGTGAC 59.570 37.037 0.00 0.00 0.00 3.67
775 833 7.474190 TCGAATGATAAGTGTTATACGTGTGA 58.526 34.615 0.00 0.00 0.00 3.58
799 857 7.295930 ACTCGTCTCCGAATAAAACAAAATTC 58.704 34.615 0.00 0.00 43.69 2.17
803 861 5.524646 ACAACTCGTCTCCGAATAAAACAAA 59.475 36.000 0.00 0.00 43.69 2.83
804 862 5.050634 CACAACTCGTCTCCGAATAAAACAA 60.051 40.000 0.00 0.00 43.69 2.83
805 863 4.446385 CACAACTCGTCTCCGAATAAAACA 59.554 41.667 0.00 0.00 43.69 2.83
906 4385 1.079197 CGCTGCACAGTCATACCCA 60.079 57.895 0.00 0.00 0.00 4.51
907 4386 0.807667 CTCGCTGCACAGTCATACCC 60.808 60.000 0.00 0.00 0.00 3.69
908 4387 0.807667 CCTCGCTGCACAGTCATACC 60.808 60.000 0.00 0.00 0.00 2.73
909 4388 0.173481 TCCTCGCTGCACAGTCATAC 59.827 55.000 0.00 0.00 0.00 2.39
910 4389 0.173481 GTCCTCGCTGCACAGTCATA 59.827 55.000 0.00 0.00 0.00 2.15
1165 4646 1.153549 GCACTAGGAAGGCGGACAG 60.154 63.158 0.00 0.00 0.00 3.51
1167 4648 1.153549 CAGCACTAGGAAGGCGGAC 60.154 63.158 0.00 0.00 0.00 4.79
1174 4655 2.671070 GGCCAGCAGCACTAGGAA 59.329 61.111 0.00 0.00 46.50 3.36
1284 4765 2.819284 GGGGATCTTACCGGCCTGG 61.819 68.421 0.00 11.48 46.41 4.45
1304 4785 2.043248 GAGCGGGGGAGGAGTGTA 60.043 66.667 0.00 0.00 0.00 2.90
1373 4854 5.898120 TCTTTTCCAATCCAATCCTAACCA 58.102 37.500 0.00 0.00 0.00 3.67
1392 4886 1.488393 GGGCAGCTGACTCCTATCTTT 59.512 52.381 21.42 0.00 0.00 2.52
1486 4995 5.590259 CACTGAGGAATGGAAATTACGGAAT 59.410 40.000 0.00 0.00 0.00 3.01
1491 5000 4.943705 TGAGCACTGAGGAATGGAAATTAC 59.056 41.667 0.00 0.00 0.00 1.89
1506 5016 3.194329 TCCTAATGTGAGACTGAGCACTG 59.806 47.826 0.00 0.00 36.05 3.66
1507 5017 3.194542 GTCCTAATGTGAGACTGAGCACT 59.805 47.826 0.00 0.00 36.05 4.40
1508 5018 3.056536 TGTCCTAATGTGAGACTGAGCAC 60.057 47.826 0.00 0.00 35.63 4.40
1509 5019 3.165071 TGTCCTAATGTGAGACTGAGCA 58.835 45.455 0.00 0.00 0.00 4.26
1510 5020 3.876274 TGTCCTAATGTGAGACTGAGC 57.124 47.619 0.00 0.00 0.00 4.26
1511 5021 5.991606 TGTTTTGTCCTAATGTGAGACTGAG 59.008 40.000 0.00 0.00 0.00 3.35
1512 5022 5.924356 TGTTTTGTCCTAATGTGAGACTGA 58.076 37.500 0.00 0.00 0.00 3.41
1643 5162 8.404000 GCATTTAGCTAGTACTAGTAACAGTCA 58.596 37.037 26.76 11.58 41.15 3.41
1644 5163 8.785468 GCATTTAGCTAGTACTAGTAACAGTC 57.215 38.462 26.76 11.44 41.15 3.51
1683 5205 1.852895 CATTCGAACACTAGCTACGGC 59.147 52.381 0.00 0.00 39.06 5.68
1701 5225 3.508402 TGAGCTGTGTTCATTTGCATCAT 59.492 39.130 0.00 0.00 0.00 2.45
1712 5236 3.935828 GGTAAAGGAGATGAGCTGTGTTC 59.064 47.826 0.00 0.00 0.00 3.18
1718 5242 4.202202 CGAATCAGGTAAAGGAGATGAGCT 60.202 45.833 0.00 0.00 0.00 4.09
1735 5259 3.004629 ACAGCAACAGAAAATGCGAATCA 59.995 39.130 0.00 0.00 46.98 2.57
1740 5264 2.053627 GGAACAGCAACAGAAAATGCG 58.946 47.619 0.00 0.00 46.98 4.73
1778 5302 4.035558 GCAGCTGCAGCAAACATAATAGTA 59.964 41.667 38.24 0.00 45.16 1.82
1889 5413 3.667960 GCAGTAAGCGTCAGAAAATGTGG 60.668 47.826 0.00 0.00 0.00 4.17
1890 5414 3.482786 GCAGTAAGCGTCAGAAAATGTG 58.517 45.455 0.00 0.00 0.00 3.21
1891 5415 3.813529 GCAGTAAGCGTCAGAAAATGT 57.186 42.857 0.00 0.00 0.00 2.71
1945 5469 4.618965 AGAAACTCGAAACGAAACTAGCT 58.381 39.130 0.00 0.00 34.74 3.32
1960 5485 2.671854 GCGCCTGAGCTAGAAACTC 58.328 57.895 0.00 0.00 36.60 3.01
1977 5502 3.498397 TCGAGGTCAATGACTTTTCAAGC 59.502 43.478 13.53 0.00 34.61 4.01
1980 5505 4.272504 GTGTTCGAGGTCAATGACTTTTCA 59.727 41.667 13.53 3.45 35.73 2.69
1988 5513 2.494059 ACAAGGTGTTCGAGGTCAATG 58.506 47.619 0.00 0.00 0.00 2.82
2332 6173 6.591834 AGCAAAGATACTGACATGAGTGTTAC 59.408 38.462 0.00 0.00 39.09 2.50
2338 6179 3.244814 GCGAGCAAAGATACTGACATGAG 59.755 47.826 0.00 0.00 0.00 2.90
2358 6199 1.133915 ACCAACTATACCAATGGGGCG 60.134 52.381 3.55 0.00 42.05 6.13
2406 6247 5.767665 GGTGGGGAAAAGTTTGCAAATATTT 59.232 36.000 16.21 18.00 0.00 1.40
2476 6318 7.941795 ATTCAGAAATGAAGCACAGAAAAAG 57.058 32.000 0.00 0.00 0.00 2.27
2486 6330 5.345202 CAGCTCAACAATTCAGAAATGAAGC 59.655 40.000 5.15 10.05 0.00 3.86
2548 6392 8.936864 CCACTGGTTAAAACAAAATAACACAAA 58.063 29.630 0.00 0.00 34.44 2.83
2549 6393 7.064728 GCCACTGGTTAAAACAAAATAACACAA 59.935 33.333 0.00 0.00 34.44 3.33
2550 6394 6.535508 GCCACTGGTTAAAACAAAATAACACA 59.464 34.615 0.00 0.00 34.44 3.72
2551 6395 6.759356 AGCCACTGGTTAAAACAAAATAACAC 59.241 34.615 0.00 0.00 34.44 3.32
2552 6396 6.879400 AGCCACTGGTTAAAACAAAATAACA 58.121 32.000 0.00 0.00 34.44 2.41
2553 6397 7.207383 AGAGCCACTGGTTAAAACAAAATAAC 58.793 34.615 0.00 0.00 0.00 1.89
2554 6398 7.354751 AGAGCCACTGGTTAAAACAAAATAA 57.645 32.000 0.00 0.00 0.00 1.40
2555 6399 6.969993 AGAGCCACTGGTTAAAACAAAATA 57.030 33.333 0.00 0.00 0.00 1.40
2556 6400 5.869649 AGAGCCACTGGTTAAAACAAAAT 57.130 34.783 0.00 0.00 0.00 1.82
3167 7060 3.733443 ACAAGGTTGCTGAAATGGAAC 57.267 42.857 0.00 0.00 37.51 3.62
3260 7153 3.137544 TCAAGTCCCAACATACAACACCT 59.862 43.478 0.00 0.00 0.00 4.00
3490 7385 8.190326 AGACCTAAATATCATAACATGGACGA 57.810 34.615 0.00 0.00 0.00 4.20
3567 7463 7.920682 GGACACAAAAGTTAACTGTTGATGATT 59.079 33.333 34.91 16.43 42.44 2.57
3571 7467 6.767524 TGGACACAAAAGTTAACTGTTGAT 57.232 33.333 34.91 24.87 42.44 2.57
3615 7511 3.393472 GCTAGGCAGCTACAGCAAT 57.607 52.632 3.70 0.00 44.93 3.56
3636 7536 6.034161 TCTTAGCTACAGAAACCTTGGTAC 57.966 41.667 0.00 0.00 0.00 3.34
3637 7537 5.337330 GCTCTTAGCTACAGAAACCTTGGTA 60.337 44.000 0.00 0.00 38.45 3.25
3638 7538 4.563786 GCTCTTAGCTACAGAAACCTTGGT 60.564 45.833 0.00 0.00 38.45 3.67
3639 7539 3.935828 GCTCTTAGCTACAGAAACCTTGG 59.064 47.826 0.00 0.00 38.45 3.61
3710 7611 9.906660 AATTTTTCAATCACGCATAAAGACTAA 57.093 25.926 0.00 0.00 0.00 2.24
3715 7616 6.819437 TGCAATTTTTCAATCACGCATAAAG 58.181 32.000 0.00 0.00 0.00 1.85
3718 7619 6.964741 ATTGCAATTTTTCAATCACGCATA 57.035 29.167 5.99 0.00 0.00 3.14
3748 7649 0.734889 AATTACTGCATGAGCCGTGC 59.265 50.000 11.20 11.20 45.53 5.34
4039 7962 7.398047 TGGTACAAGTGCCTACTTCTTATAAGA 59.602 37.037 11.24 11.24 45.12 2.10
4305 8236 4.156455 TGAAGAGAAAGAACCAAGTGCT 57.844 40.909 0.00 0.00 0.00 4.40
4370 8302 0.543277 CAAGGTGATCTAGGCCAGCA 59.457 55.000 5.01 0.00 33.61 4.41
4411 8343 4.916183 AGGGGAAGAGAACAAGAAGAATG 58.084 43.478 0.00 0.00 0.00 2.67
4412 8344 6.899892 ATAGGGGAAGAGAACAAGAAGAAT 57.100 37.500 0.00 0.00 0.00 2.40
4413 8345 7.996758 ATATAGGGGAAGAGAACAAGAAGAA 57.003 36.000 0.00 0.00 0.00 2.52
4414 8346 8.480133 GTATATAGGGGAAGAGAACAAGAAGA 57.520 38.462 0.00 0.00 0.00 2.87
4806 11092 1.949525 GTTGACTGCTCAAGCCTTTCA 59.050 47.619 0.00 0.00 37.06 2.69
4847 11134 8.416329 GCACCTAATCCTGAATTCAATACAAAT 58.584 33.333 9.88 0.00 0.00 2.32
4917 11204 2.526304 TCACAGTGAAGCACTACACC 57.474 50.000 0.00 0.00 43.43 4.16
4957 11244 1.947456 AGTTTTCAGCCGAAGTCAACC 59.053 47.619 0.00 0.00 31.28 3.77
4991 11278 1.067495 AGCTTCTTCGGCAGTCTACAC 60.067 52.381 0.00 0.00 0.00 2.90
4999 11286 1.405526 GGTGTCATAGCTTCTTCGGCA 60.406 52.381 0.00 0.00 0.00 5.69
5204 11747 8.198109 ACATAGTACATGTGTTTCTCCATAGAC 58.802 37.037 9.11 0.00 26.83 2.59
5303 11846 6.425114 AGGCATAGAAGCTCATAACAAATACG 59.575 38.462 0.00 0.00 34.17 3.06
5396 11940 8.307582 ACATAGCATGTTTACCTAGTTCTAGT 57.692 34.615 6.18 0.00 41.63 2.57
5432 11976 6.584185 TTTGAAAAGGGGTTGTTAGCTATC 57.416 37.500 0.00 0.00 0.00 2.08
5438 11982 5.071115 CCCTGATTTTGAAAAGGGGTTGTTA 59.929 40.000 14.09 0.00 44.94 2.41
5439 11983 4.141505 CCCTGATTTTGAAAAGGGGTTGTT 60.142 41.667 14.09 0.00 44.94 2.83
5440 11984 3.390967 CCCTGATTTTGAAAAGGGGTTGT 59.609 43.478 14.09 0.00 44.94 3.32
5441 11985 4.006780 CCCTGATTTTGAAAAGGGGTTG 57.993 45.455 14.09 0.00 44.94 3.77
5446 11990 6.015180 TCTGATTCACCCTGATTTTGAAAAGG 60.015 38.462 0.00 0.00 33.13 3.11
5447 11991 6.865205 GTCTGATTCACCCTGATTTTGAAAAG 59.135 38.462 0.00 0.00 33.13 2.27
5448 11992 6.323482 TGTCTGATTCACCCTGATTTTGAAAA 59.677 34.615 0.00 0.00 33.13 2.29
5589 12144 4.498009 GCCATCAATAAGCATACACACACC 60.498 45.833 0.00 0.00 0.00 4.16
5664 12219 5.534207 TCATTGCAACCTTTCAACTGAAT 57.466 34.783 0.00 0.00 33.54 2.57
5734 12289 4.811024 TGGAATATGCTTGCTAGAAGAACG 59.189 41.667 0.00 0.00 0.00 3.95
5794 12349 4.445452 TCACCGAAGTATAGAACCACAC 57.555 45.455 0.00 0.00 0.00 3.82
5883 12445 2.288030 GCATCTCAAAAGTTGCACAGCT 60.288 45.455 0.00 0.00 44.30 4.24
5887 12449 5.570589 GTGATAAGCATCTCAAAAGTTGCAC 59.429 40.000 10.20 0.00 46.33 4.57
6184 12748 9.725206 GGTATATACCTTGGAATCCTCCTAATA 57.275 37.037 22.56 0.00 41.71 0.98
6287 12851 9.629878 ACACTAGTACTACTAATAGAGCAACAT 57.370 33.333 0.00 0.00 29.00 2.71
6409 12974 2.118679 ACAGCAGCCATATGACTACCA 58.881 47.619 3.65 0.00 0.00 3.25
6451 13016 3.009723 AGTTTTATCATGAGGTGGTGCG 58.990 45.455 0.09 0.00 0.00 5.34
6732 13297 7.859325 AAGAAGAGCAACTTAGTGTGTTTAA 57.141 32.000 0.00 0.00 39.13 1.52
6777 13342 3.074412 GTTGTCCACCATACACCAGAAG 58.926 50.000 0.00 0.00 0.00 2.85
6832 13397 9.542462 TCTATTGTTACAGTTTACTCCATATGC 57.458 33.333 0.00 0.00 0.00 3.14
6859 13424 4.096382 AGGCTGAAATTTATGCACCTAACG 59.904 41.667 14.27 0.00 0.00 3.18
6987 13552 8.688747 TTCCAATTTGCCAAAATGATTAAACT 57.311 26.923 6.80 0.00 36.11 2.66
7044 13613 3.823873 TGGCCATACACAGAAACGAAATT 59.176 39.130 0.00 0.00 0.00 1.82
7057 13626 0.958091 GTGCACAAGTTGGCCATACA 59.042 50.000 13.17 0.00 0.00 2.29
7058 13627 0.109781 CGTGCACAAGTTGGCCATAC 60.110 55.000 18.64 8.20 0.00 2.39
7080 13649 8.055279 AGAACATGGTTCATATTTACTTGTGG 57.945 34.615 11.28 0.00 0.00 4.17
7120 13689 9.996554 TCATGACAGAGAAAGTTAAGAATGTTA 57.003 29.630 0.00 0.00 0.00 2.41
7220 13789 4.372656 GGTAAATGGACGAAGGAGATGAG 58.627 47.826 0.00 0.00 0.00 2.90
7356 13927 5.125097 AGAGGTGGTTATGTAGTACGTTGAG 59.875 44.000 0.00 0.00 0.00 3.02
7646 14227 5.277683 GCATACAGTATCACTTGGCAGAATG 60.278 44.000 0.00 0.00 40.87 2.67
7647 14228 4.818546 GCATACAGTATCACTTGGCAGAAT 59.181 41.667 0.00 0.00 0.00 2.40
7648 14229 4.191544 GCATACAGTATCACTTGGCAGAA 58.808 43.478 0.00 0.00 0.00 3.02
7649 14230 3.197549 TGCATACAGTATCACTTGGCAGA 59.802 43.478 0.00 0.00 0.00 4.26
7650 14231 3.534554 TGCATACAGTATCACTTGGCAG 58.465 45.455 0.00 0.00 0.00 4.85
7651 14232 3.625649 TGCATACAGTATCACTTGGCA 57.374 42.857 0.00 0.00 0.00 4.92
7652 14233 3.941483 AGTTGCATACAGTATCACTTGGC 59.059 43.478 0.00 0.00 0.00 4.52
7653 14234 7.609760 TTAAGTTGCATACAGTATCACTTGG 57.390 36.000 14.56 0.00 0.00 3.61
7654 14235 9.708222 GAATTAAGTTGCATACAGTATCACTTG 57.292 33.333 14.56 0.00 0.00 3.16
7655 14236 8.893727 GGAATTAAGTTGCATACAGTATCACTT 58.106 33.333 11.57 11.57 0.00 3.16
7696 14277 3.580100 GACTGCAGCAGCCACTCGA 62.580 63.158 23.05 0.00 41.13 4.04
7790 14371 7.919313 ATATTTTGTTAATCAGCTTGCATCG 57.081 32.000 0.00 0.00 0.00 3.84
7854 14435 6.542370 ACTCCAATTTTCAAGAGTCGAGAAAA 59.458 34.615 20.46 20.46 43.05 2.29
7855 14436 6.055588 ACTCCAATTTTCAAGAGTCGAGAAA 58.944 36.000 8.40 8.40 34.53 2.52
7856 14437 5.611374 ACTCCAATTTTCAAGAGTCGAGAA 58.389 37.500 0.00 0.00 34.53 2.87
7857 14438 5.215252 ACTCCAATTTTCAAGAGTCGAGA 57.785 39.130 0.00 0.00 34.53 4.04
7858 14439 6.813649 TCATACTCCAATTTTCAAGAGTCGAG 59.186 38.462 0.00 0.00 40.07 4.04
7859 14440 6.697395 TCATACTCCAATTTTCAAGAGTCGA 58.303 36.000 0.00 0.00 40.07 4.20
7860 14441 6.591834 ACTCATACTCCAATTTTCAAGAGTCG 59.408 38.462 0.00 0.00 40.07 4.18
7861 14442 7.604164 TGACTCATACTCCAATTTTCAAGAGTC 59.396 37.037 0.00 0.00 45.02 3.36
7862 14443 7.453393 TGACTCATACTCCAATTTTCAAGAGT 58.547 34.615 0.00 0.00 42.13 3.24
7863 14444 7.912056 TGACTCATACTCCAATTTTCAAGAG 57.088 36.000 0.00 0.00 0.00 2.85
7864 14445 8.868522 ATTGACTCATACTCCAATTTTCAAGA 57.131 30.769 0.00 0.00 0.00 3.02
7865 14446 9.918630 AAATTGACTCATACTCCAATTTTCAAG 57.081 29.630 0.00 0.00 42.87 3.02
8014 14632 7.117812 GGAGATTTTCTGTCTAAATCGTGTGAA 59.882 37.037 0.00 0.00 43.46 3.18
8020 14638 7.547370 ACTGAAGGAGATTTTCTGTCTAAATCG 59.453 37.037 0.00 0.00 43.46 3.34
8055 14676 2.080286 AGTTTGGGAATGTCGACGAG 57.920 50.000 11.62 0.00 0.00 4.18
8112 14733 1.202698 ACTTGCCGGAAGCCTATCATC 60.203 52.381 5.05 0.00 42.71 2.92
8171 14794 7.665561 ACATTTTAACTGTTGCAAAACAAGT 57.334 28.000 0.00 0.00 39.50 3.16
8192 14815 8.826293 ACTTCTTACTAAGCCTCTAACTACAT 57.174 34.615 0.00 0.00 0.00 2.29
8278 14996 2.035442 GGTCTGGCGAGGCAAGAAC 61.035 63.158 1.83 0.00 40.61 3.01
8292 15010 5.640158 TGGGATTTTATTACATCCGGTCT 57.360 39.130 0.00 0.00 40.13 3.85
8326 15044 2.720605 GCCTACGACTACGAGCCC 59.279 66.667 0.00 0.00 42.66 5.19
8331 15049 1.028330 TGGACTGGCCTACGACTACG 61.028 60.000 3.32 0.00 40.73 3.51
8333 15051 2.154567 ATTGGACTGGCCTACGACTA 57.845 50.000 3.32 0.00 37.63 2.59
8334 15052 1.207329 GAATTGGACTGGCCTACGACT 59.793 52.381 3.32 0.00 37.63 4.18
8335 15053 1.066430 TGAATTGGACTGGCCTACGAC 60.066 52.381 3.32 0.00 37.63 4.34
8336 15054 1.066430 GTGAATTGGACTGGCCTACGA 60.066 52.381 3.32 0.00 37.63 3.43
8337 15055 1.369625 GTGAATTGGACTGGCCTACG 58.630 55.000 3.32 0.00 37.63 3.51
8338 15056 1.682087 GGGTGAATTGGACTGGCCTAC 60.682 57.143 3.32 0.00 37.63 3.18
8339 15057 0.623723 GGGTGAATTGGACTGGCCTA 59.376 55.000 3.32 0.00 37.63 3.93
8340 15058 1.142688 AGGGTGAATTGGACTGGCCT 61.143 55.000 3.32 0.00 37.63 5.19
8366 15084 2.819608 TGGGCAAGTCTATCTTTGCAAC 59.180 45.455 0.00 4.41 34.40 4.17
8369 15087 3.445096 ACATTGGGCAAGTCTATCTTTGC 59.555 43.478 0.81 0.81 33.63 3.68
8412 15130 2.846206 AGATACAGGAGCATGGGTTTGA 59.154 45.455 0.00 0.00 0.00 2.69
8447 15165 3.350219 TGGACTAAAACCAGCATCTCC 57.650 47.619 0.00 0.00 33.22 3.71
8478 15196 1.602377 ACAAAAAGGCTACGTCACTGC 59.398 47.619 0.00 0.00 0.00 4.40
8764 15482 3.073274 AGTTTCCCAATACTCCTGTGC 57.927 47.619 0.00 0.00 0.00 4.57
8845 15563 5.156355 GTCATCAAATGTTGCTGTACTTGG 58.844 41.667 0.00 0.00 0.00 3.61
9022 15747 1.508667 AACCCTGCCCATGGTCATCA 61.509 55.000 11.73 2.17 32.40 3.07
9058 16457 0.314935 ACTTTGACAGCAAATGGGCG 59.685 50.000 0.00 0.00 42.66 6.13
9191 16590 5.298276 TGAGTTTCTAAAGATGTTTGCGGTT 59.702 36.000 0.00 0.00 0.00 4.44
9193 16592 5.356882 TGAGTTTCTAAAGATGTTTGCGG 57.643 39.130 0.00 0.00 0.00 5.69
9194 16593 6.602179 TCATGAGTTTCTAAAGATGTTTGCG 58.398 36.000 0.00 0.00 0.00 4.85
9195 16594 7.540055 CCTTCATGAGTTTCTAAAGATGTTTGC 59.460 37.037 0.00 0.00 0.00 3.68
9414 16841 6.358974 AACAGGGGGAAATAGTGAAAAATG 57.641 37.500 0.00 0.00 0.00 2.32
9415 16842 7.387265 AAAACAGGGGGAAATAGTGAAAAAT 57.613 32.000 0.00 0.00 0.00 1.82
9416 16843 6.816616 AAAACAGGGGGAAATAGTGAAAAA 57.183 33.333 0.00 0.00 0.00 1.94
9421 16848 7.297936 AGTTTTAAAACAGGGGGAAATAGTG 57.702 36.000 28.03 0.00 41.30 2.74
9422 16849 7.924358 AAGTTTTAAAACAGGGGGAAATAGT 57.076 32.000 28.03 4.65 41.30 2.12
9423 16850 9.085645 AGTAAGTTTTAAAACAGGGGGAAATAG 57.914 33.333 28.03 0.00 41.30 1.73
9504 16938 1.155042 CAGCTCAGCTCACCAGTTTC 58.845 55.000 0.00 0.00 36.40 2.78
9529 16963 1.813513 ATGACTTCCGAGCAAACCTG 58.186 50.000 0.00 0.00 0.00 4.00
9530 16964 3.244422 TGTTATGACTTCCGAGCAAACCT 60.244 43.478 0.00 0.00 0.00 3.50
9539 16978 5.895928 TGAGATCTTCTGTTATGACTTCCG 58.104 41.667 0.00 0.00 0.00 4.30
9541 16980 8.602328 CATGTTGAGATCTTCTGTTATGACTTC 58.398 37.037 0.00 0.00 0.00 3.01
9551 16999 4.190001 CTCCACCATGTTGAGATCTTCTG 58.810 47.826 0.00 0.00 28.31 3.02
9586 17034 8.572855 TCCACCATGTTTTCTTTTGAATTTTT 57.427 26.923 0.00 0.00 38.37 1.94
9587 17035 7.828717 ACTCCACCATGTTTTCTTTTGAATTTT 59.171 29.630 0.00 0.00 38.37 1.82
9588 17036 7.337938 ACTCCACCATGTTTTCTTTTGAATTT 58.662 30.769 0.00 0.00 38.37 1.82
9589 17037 6.888105 ACTCCACCATGTTTTCTTTTGAATT 58.112 32.000 0.00 0.00 38.37 2.17
9590 17038 6.484364 ACTCCACCATGTTTTCTTTTGAAT 57.516 33.333 0.00 0.00 38.37 2.57
9593 17041 6.475402 GTGTTACTCCACCATGTTTTCTTTTG 59.525 38.462 0.00 0.00 0.00 2.44
9597 17049 5.048846 AGTGTTACTCCACCATGTTTTCT 57.951 39.130 0.00 0.00 35.93 2.52
9684 17137 8.428063 ACATGATTTGTTGGGTCAAAGAAATAA 58.572 29.630 0.00 0.00 40.00 1.40


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

AutoCloner maintained by Alex Coulton.