Multiple sequence alignment - TraesCS6A01G358100

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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 TraesCS6A01G358100 chr6A 100.000 3978 0 0 1 3978 588229429 588233406 0.000000e+00 7347.0
1 TraesCS6A01G358100 chr6A 85.171 263 36 1 308 567 558192472 558192210 2.360000e-67 267.0
2 TraesCS6A01G358100 chr6D 93.897 1491 64 14 647 2127 439805333 439806806 0.000000e+00 2224.0
3 TraesCS6A01G358100 chr6D 91.932 1475 73 18 2127 3588 439807180 439808621 0.000000e+00 2023.0
4 TraesCS6A01G358100 chr6D 91.542 402 26 7 3584 3978 439808893 439809293 7.520000e-152 547.0
5 TraesCS6A01G358100 chr6D 84.270 267 27 8 23 275 42046046 42045781 3.070000e-61 246.0
6 TraesCS6A01G358100 chr6B 92.351 1059 47 11 647 1692 664834077 664835114 0.000000e+00 1476.0
7 TraesCS6A01G358100 chr6B 94.670 394 13 2 2811 3202 664836111 664836498 4.400000e-169 604.0
8 TraesCS6A01G358100 chr6B 74.460 278 64 4 2261 2536 175523041 175523313 3.250000e-21 113.0
9 TraesCS6A01G358100 chr4B 80.416 577 97 11 23 589 599890221 599889651 3.670000e-115 425.0
10 TraesCS6A01G358100 chr1D 79.646 565 98 10 29 586 280043667 280043113 1.340000e-104 390.0
11 TraesCS6A01G358100 chr1D 83.509 285 38 5 1101 1382 160177121 160176843 1.420000e-64 257.0
12 TraesCS6A01G358100 chr5D 80.337 534 83 12 23 541 73503025 73503551 6.240000e-103 385.0
13 TraesCS6A01G358100 chr5D 100.000 33 0 0 3471 3503 118173736 118173768 1.190000e-05 62.1
14 TraesCS6A01G358100 chr7A 78.462 585 88 17 23 595 106924283 106923725 8.180000e-92 348.0
15 TraesCS6A01G358100 chr7A 77.160 486 82 12 42 524 724306687 724306228 5.100000e-64 255.0
16 TraesCS6A01G358100 chr2A 78.996 538 74 22 23 552 763794415 763794921 8.240000e-87 331.0
17 TraesCS6A01G358100 chr3D 84.566 311 39 1 251 552 47350302 47350612 2.320000e-77 300.0
18 TraesCS6A01G358100 chr2D 77.486 533 90 16 23 544 11029311 11028798 3.890000e-75 292.0
19 TraesCS6A01G358100 chr3A 78.541 466 71 14 23 484 168831396 168830956 3.030000e-71 279.0
20 TraesCS6A01G358100 chr4D 80.332 361 62 8 231 589 465572302 465571949 8.480000e-67 265.0
21 TraesCS6A01G358100 chrUn 85.246 244 33 1 327 567 138455365 138455608 8.540000e-62 248.0
22 TraesCS6A01G358100 chr7B 81.545 233 30 8 23 247 103068467 103068240 3.160000e-41 180.0
23 TraesCS6A01G358100 chr7B 100.000 33 0 0 3471 3503 559640277 559640245 1.190000e-05 62.1
24 TraesCS6A01G358100 chr4A 79.358 218 41 4 23 238 654112927 654113142 2.480000e-32 150.0
25 TraesCS6A01G358100 chr5B 97.059 34 1 0 3470 3503 128680519 128680486 1.540000e-04 58.4
26 TraesCS6A01G358100 chr5B 97.059 34 1 0 3470 3503 128701083 128701050 1.540000e-04 58.4
27 TraesCS6A01G358100 chr5B 97.059 34 1 0 3471 3504 584173890 584173923 1.540000e-04 58.4
28 TraesCS6A01G358100 chr5B 87.755 49 4 2 3457 3504 540345415 540345462 5.550000e-04 56.5
29 TraesCS6A01G358100 chr2B 97.059 34 1 0 3471 3504 191088100 191088133 1.540000e-04 58.4
30 TraesCS6A01G358100 chr1B 97.059 34 1 0 3471 3504 34197173 34197206 1.540000e-04 58.4


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 TraesCS6A01G358100 chr6A 588229429 588233406 3977 False 7347 7347 100.0000 1 3978 1 chr6A.!!$F1 3977
1 TraesCS6A01G358100 chr6D 439805333 439809293 3960 False 1598 2224 92.4570 647 3978 3 chr6D.!!$F1 3331
2 TraesCS6A01G358100 chr6B 664834077 664836498 2421 False 1040 1476 93.5105 647 3202 2 chr6B.!!$F2 2555
3 TraesCS6A01G358100 chr4B 599889651 599890221 570 True 425 425 80.4160 23 589 1 chr4B.!!$R1 566
4 TraesCS6A01G358100 chr1D 280043113 280043667 554 True 390 390 79.6460 29 586 1 chr1D.!!$R2 557
5 TraesCS6A01G358100 chr5D 73503025 73503551 526 False 385 385 80.3370 23 541 1 chr5D.!!$F1 518
6 TraesCS6A01G358100 chr7A 106923725 106924283 558 True 348 348 78.4620 23 595 1 chr7A.!!$R1 572
7 TraesCS6A01G358100 chr2A 763794415 763794921 506 False 331 331 78.9960 23 552 1 chr2A.!!$F1 529
8 TraesCS6A01G358100 chr2D 11028798 11029311 513 True 292 292 77.4860 23 544 1 chr2D.!!$R1 521

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
583 611 0.029433 TCGGCGAGATCGATGACAAG 59.971 55.0 4.99 0.0 43.02 3.16 F
605 633 0.247814 GGACGTCGCTGCAATGATTG 60.248 55.0 9.92 0.0 0.00 2.67 F
1180 1214 0.250252 TGCATGCGACCTTCAACTGA 60.250 50.0 14.09 0.0 0.00 3.41 F
2809 3368 0.723459 GCGGTAAGAAAACGCCGTTG 60.723 55.0 1.95 0.0 46.92 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1507 1547 2.507471 ACCAGATTCAGACCATTCCTCC 59.493 50.000 0.00 0.0 0.0 4.30 R
2276 2746 3.892588 TGAGTTTTTAGAACCCCGCAAAT 59.107 39.130 0.00 0.0 0.0 2.32 R
2868 3427 0.792640 CGTTCCTGCATGCGGATATC 59.207 55.000 28.32 18.5 0.0 1.63 R
3935 5054 6.887545 TCAGAATGTATAAAATGTCCCCGTTT 59.112 34.615 0.00 0.0 37.4 3.60 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
46 47 1.685180 CGATCCCTCTCCACACCACTA 60.685 57.143 0.00 0.00 0.00 2.74
73 75 1.000145 GATTCCTCCCCCGCCAAAA 60.000 57.895 0.00 0.00 0.00 2.44
82 84 1.073199 CCCGCCAAAACTCTCTGGT 59.927 57.895 0.00 0.00 34.97 4.00
91 93 1.258445 AACTCTCTGGTACGGGCTGG 61.258 60.000 0.00 0.00 33.92 4.85
159 161 2.679716 GGCAGGCAACAGGAGGAT 59.320 61.111 0.00 0.00 41.41 3.24
165 167 0.179000 GGCAACAGGAGGATGACGAT 59.821 55.000 0.00 0.00 0.00 3.73
174 176 2.632996 GGAGGATGACGATGTCCCAATA 59.367 50.000 0.00 0.00 35.00 1.90
177 179 4.163427 AGGATGACGATGTCCCAATAGAT 58.837 43.478 0.00 0.00 35.00 1.98
221 226 2.362369 CGCCACCATCCTCCTCAGT 61.362 63.158 0.00 0.00 0.00 3.41
227 232 3.893763 ATCCTCCTCAGTCGCGCG 61.894 66.667 26.76 26.76 0.00 6.86
261 274 3.560251 ACCCTCGCTGGTGCACTT 61.560 61.111 17.98 0.00 37.20 3.16
295 308 1.445942 CGAGTCCCGTGCCCATTAT 59.554 57.895 0.00 0.00 0.00 1.28
296 309 0.880278 CGAGTCCCGTGCCCATTATG 60.880 60.000 0.00 0.00 0.00 1.90
322 344 4.699522 GTGCGGGAGGAGCGGTTT 62.700 66.667 0.00 0.00 37.44 3.27
325 347 4.065281 CGGGAGGAGCGGTTTCGT 62.065 66.667 0.00 0.00 38.89 3.85
328 350 1.218316 GGAGGAGCGGTTTCGTGAT 59.782 57.895 0.00 0.00 38.89 3.06
334 356 2.202171 CGGTTTCGTGATGCGCAC 60.202 61.111 14.90 7.75 44.21 5.34
358 383 0.618458 ATGTCGCCTACAACCACCAT 59.382 50.000 0.00 0.00 42.70 3.55
368 393 1.279496 CAACCACCATCTCCTCCAGA 58.721 55.000 0.00 0.00 34.78 3.86
391 416 4.399395 CTGCAGGCGGAGGAGCAA 62.399 66.667 5.57 0.00 39.27 3.91
478 506 2.123854 TCCGCCCGCTAGATCTGT 60.124 61.111 5.18 0.00 0.00 3.41
545 573 2.355837 GCAAGGAGTGCGACGACA 60.356 61.111 0.00 0.00 45.10 4.35
549 577 3.112709 GGAGTGCGACGACAAGGC 61.113 66.667 0.00 0.00 0.00 4.35
556 584 2.504244 GACGACAAGGCGGACGAG 60.504 66.667 0.00 0.00 35.12 4.18
557 585 4.719369 ACGACAAGGCGGACGAGC 62.719 66.667 0.00 0.00 35.12 5.03
575 603 2.949678 CGGTGTTCGGCGAGATCG 60.950 66.667 10.46 9.53 43.27 3.69
576 604 2.488355 GGTGTTCGGCGAGATCGA 59.512 61.111 10.46 0.00 43.02 3.59
577 605 1.065928 GGTGTTCGGCGAGATCGAT 59.934 57.895 10.46 0.00 43.02 3.59
578 606 1.209275 GGTGTTCGGCGAGATCGATG 61.209 60.000 10.46 0.00 43.02 3.84
579 607 0.248498 GTGTTCGGCGAGATCGATGA 60.248 55.000 10.46 0.00 43.02 2.92
580 608 0.248498 TGTTCGGCGAGATCGATGAC 60.248 55.000 10.46 3.16 43.02 3.06
581 609 0.248498 GTTCGGCGAGATCGATGACA 60.248 55.000 10.46 0.00 43.02 3.58
582 610 0.454196 TTCGGCGAGATCGATGACAA 59.546 50.000 10.46 0.00 43.02 3.18
583 611 0.029433 TCGGCGAGATCGATGACAAG 59.971 55.000 4.99 0.00 43.02 3.16
584 612 0.936764 CGGCGAGATCGATGACAAGG 60.937 60.000 0.54 0.00 43.02 3.61
585 613 0.385751 GGCGAGATCGATGACAAGGA 59.614 55.000 0.54 0.00 43.02 3.36
586 614 1.601663 GGCGAGATCGATGACAAGGAG 60.602 57.143 0.54 0.00 43.02 3.69
587 615 1.601663 GCGAGATCGATGACAAGGAGG 60.602 57.143 0.54 0.00 43.02 4.30
588 616 1.950216 CGAGATCGATGACAAGGAGGA 59.050 52.381 0.54 0.00 43.02 3.71
589 617 2.287308 CGAGATCGATGACAAGGAGGAC 60.287 54.545 0.54 0.00 43.02 3.85
590 618 1.678627 AGATCGATGACAAGGAGGACG 59.321 52.381 0.54 0.00 0.00 4.79
591 619 1.405821 GATCGATGACAAGGAGGACGT 59.594 52.381 0.54 0.00 0.00 4.34
592 620 0.809385 TCGATGACAAGGAGGACGTC 59.191 55.000 7.13 7.13 0.00 4.34
593 621 0.523546 CGATGACAAGGAGGACGTCG 60.524 60.000 9.92 0.00 35.93 5.12
594 622 0.802607 GATGACAAGGAGGACGTCGC 60.803 60.000 9.92 3.87 32.17 5.19
595 623 1.251527 ATGACAAGGAGGACGTCGCT 61.252 55.000 9.92 7.88 32.17 4.93
596 624 1.444553 GACAAGGAGGACGTCGCTG 60.445 63.158 9.92 4.61 0.00 5.18
597 625 2.811317 CAAGGAGGACGTCGCTGC 60.811 66.667 9.92 12.81 0.00 5.25
598 626 3.303135 AAGGAGGACGTCGCTGCA 61.303 61.111 21.23 0.00 0.00 4.41
599 627 2.867855 AAGGAGGACGTCGCTGCAA 61.868 57.895 21.23 0.00 0.00 4.08
600 628 2.125512 GGAGGACGTCGCTGCAAT 60.126 61.111 16.66 0.00 0.00 3.56
601 629 2.456119 GGAGGACGTCGCTGCAATG 61.456 63.158 16.66 0.00 0.00 2.82
602 630 1.446099 GAGGACGTCGCTGCAATGA 60.446 57.895 9.92 0.00 0.00 2.57
603 631 0.807667 GAGGACGTCGCTGCAATGAT 60.808 55.000 9.92 0.00 0.00 2.45
604 632 0.391661 AGGACGTCGCTGCAATGATT 60.392 50.000 9.92 0.00 0.00 2.57
605 633 0.247814 GGACGTCGCTGCAATGATTG 60.248 55.000 9.92 0.00 0.00 2.67
606 634 0.721154 GACGTCGCTGCAATGATTGA 59.279 50.000 9.76 0.00 0.00 2.57
607 635 1.128507 GACGTCGCTGCAATGATTGAA 59.871 47.619 9.76 0.00 0.00 2.69
608 636 1.535028 ACGTCGCTGCAATGATTGAAA 59.465 42.857 9.76 0.00 0.00 2.69
609 637 2.031245 ACGTCGCTGCAATGATTGAAAA 60.031 40.909 9.76 0.00 0.00 2.29
610 638 2.339400 CGTCGCTGCAATGATTGAAAAC 59.661 45.455 9.76 0.00 0.00 2.43
611 639 2.339400 GTCGCTGCAATGATTGAAAACG 59.661 45.455 9.76 5.66 0.00 3.60
612 640 2.225255 TCGCTGCAATGATTGAAAACGA 59.775 40.909 9.76 8.02 0.00 3.85
613 641 2.979151 CGCTGCAATGATTGAAAACGAA 59.021 40.909 9.76 0.00 0.00 3.85
614 642 3.181550 CGCTGCAATGATTGAAAACGAAC 60.182 43.478 9.76 0.00 0.00 3.95
615 643 3.735240 GCTGCAATGATTGAAAACGAACA 59.265 39.130 9.76 0.00 0.00 3.18
616 644 4.143473 GCTGCAATGATTGAAAACGAACAG 60.143 41.667 9.76 5.22 0.00 3.16
617 645 5.180367 TGCAATGATTGAAAACGAACAGA 57.820 34.783 9.76 0.00 0.00 3.41
618 646 5.771469 TGCAATGATTGAAAACGAACAGAT 58.229 33.333 9.76 0.00 0.00 2.90
619 647 6.215121 TGCAATGATTGAAAACGAACAGATT 58.785 32.000 9.76 0.00 0.00 2.40
620 648 7.366513 TGCAATGATTGAAAACGAACAGATTA 58.633 30.769 9.76 0.00 0.00 1.75
621 649 7.864882 TGCAATGATTGAAAACGAACAGATTAA 59.135 29.630 9.76 0.00 0.00 1.40
622 650 8.698854 GCAATGATTGAAAACGAACAGATTAAA 58.301 29.630 9.76 0.00 0.00 1.52
625 653 9.965824 ATGATTGAAAACGAACAGATTAAAAGT 57.034 25.926 0.00 0.00 0.00 2.66
626 654 9.796120 TGATTGAAAACGAACAGATTAAAAGTT 57.204 25.926 0.00 0.00 0.00 2.66
632 660 9.849166 AAAACGAACAGATTAAAAGTTTTCTCA 57.151 25.926 3.60 0.00 36.09 3.27
634 662 9.450807 AACGAACAGATTAAAAGTTTTCTCATG 57.549 29.630 3.60 3.45 0.00 3.07
635 663 8.836413 ACGAACAGATTAAAAGTTTTCTCATGA 58.164 29.630 3.60 0.00 0.00 3.07
636 664 9.663904 CGAACAGATTAAAAGTTTTCTCATGAA 57.336 29.630 3.60 0.00 0.00 2.57
671 699 1.284982 CCTTCGTCACAGTGCCTTCG 61.285 60.000 0.00 0.00 0.00 3.79
683 711 2.744768 GCCTTCGTAGCAGCAGCAC 61.745 63.158 3.17 0.00 45.49 4.40
701 734 2.028476 GCACAGTACCACCACATGTAGA 60.028 50.000 0.00 0.00 0.00 2.59
713 746 0.582960 CATGTAGATGATTGCGCGCA 59.417 50.000 33.09 33.09 0.00 6.09
737 770 3.678529 GCAGTCACCACCACAAACATTTT 60.679 43.478 0.00 0.00 0.00 1.82
759 793 5.699097 TCTTTGTTCCCGGTTAGAAATTG 57.301 39.130 0.00 0.00 0.00 2.32
760 794 5.134661 TCTTTGTTCCCGGTTAGAAATTGT 58.865 37.500 0.00 0.00 0.00 2.71
762 796 6.428771 TCTTTGTTCCCGGTTAGAAATTGTAG 59.571 38.462 0.00 0.00 0.00 2.74
763 797 5.231702 TGTTCCCGGTTAGAAATTGTAGT 57.768 39.130 0.00 0.00 0.00 2.73
764 798 6.357579 TGTTCCCGGTTAGAAATTGTAGTA 57.642 37.500 0.00 0.00 0.00 1.82
765 799 6.400568 TGTTCCCGGTTAGAAATTGTAGTAG 58.599 40.000 0.00 0.00 0.00 2.57
766 800 6.211184 TGTTCCCGGTTAGAAATTGTAGTAGA 59.789 38.462 0.00 0.00 0.00 2.59
767 801 7.093201 TGTTCCCGGTTAGAAATTGTAGTAGAT 60.093 37.037 0.00 0.00 0.00 1.98
772 806 7.762615 CCGGTTAGAAATTGTAGTAGATGAACA 59.237 37.037 0.00 0.00 0.00 3.18
961 995 1.534595 CTTCAGACAGAGTTGGCAAGC 59.465 52.381 0.00 0.00 33.45 4.01
962 996 0.469494 TCAGACAGAGTTGGCAAGCA 59.531 50.000 0.00 0.00 33.45 3.91
963 997 1.134128 TCAGACAGAGTTGGCAAGCAA 60.134 47.619 0.00 0.00 33.45 3.91
964 998 1.266175 CAGACAGAGTTGGCAAGCAAG 59.734 52.381 0.00 0.00 33.45 4.01
1146 1180 0.457337 GTACGTCCGTCATCACCCAC 60.457 60.000 0.00 0.00 0.00 4.61
1152 1186 2.677228 GTCATCACCCACCCCCTG 59.323 66.667 0.00 0.00 0.00 4.45
1153 1187 3.338250 TCATCACCCACCCCCTGC 61.338 66.667 0.00 0.00 0.00 4.85
1154 1188 3.660571 CATCACCCACCCCCTGCA 61.661 66.667 0.00 0.00 0.00 4.41
1155 1189 2.618185 ATCACCCACCCCCTGCAT 60.618 61.111 0.00 0.00 0.00 3.96
1156 1190 3.000099 ATCACCCACCCCCTGCATG 62.000 63.158 0.00 0.00 0.00 4.06
1159 1193 4.468769 CCCACCCCCTGCATGCAT 62.469 66.667 22.97 2.13 0.00 3.96
1180 1214 0.250252 TGCATGCGACCTTCAACTGA 60.250 50.000 14.09 0.00 0.00 3.41
1391 1431 2.238898 GGCTACAGGTAACCCAACAGAT 59.761 50.000 0.00 0.00 37.17 2.90
1392 1432 3.270877 GCTACAGGTAACCCAACAGATG 58.729 50.000 0.00 0.00 37.17 2.90
1454 1494 1.586578 CGATTGGTGACGTGATTACCG 59.413 52.381 0.00 0.00 37.29 4.02
1487 1527 5.840940 ACAGTTACTCACGTTGCTAATTC 57.159 39.130 0.00 0.00 0.00 2.17
1507 1547 2.173669 CAGCCCAATCTACACGCCG 61.174 63.158 0.00 0.00 0.00 6.46
1656 1700 3.475575 ACAGTTGTGATACATGCACACA 58.524 40.909 13.54 13.54 45.10 3.72
1672 1716 3.064820 GCACACATGTACCCGATTAAAGG 59.935 47.826 0.00 0.00 0.00 3.11
1768 1817 4.582240 AGCTGCAAATCTAAGCTTATTCCC 59.418 41.667 6.64 0.00 44.79 3.97
1769 1818 4.261783 GCTGCAAATCTAAGCTTATTCCCC 60.262 45.833 6.64 0.00 34.05 4.81
1771 1820 6.260700 TGCAAATCTAAGCTTATTCCCCTA 57.739 37.500 6.64 0.00 0.00 3.53
1801 1850 6.806751 AGTCTAAGCTTATTCAATCGTAGCA 58.193 36.000 6.64 0.00 34.37 3.49
1894 1944 9.599866 CAGAACCACAATTATATACTCAACTGA 57.400 33.333 0.00 0.00 0.00 3.41
1997 2080 7.573968 ATTTGATTTACTATCTCTGTTGGGC 57.426 36.000 0.00 0.00 0.00 5.36
2015 2098 6.183360 TGTTGGGCATATTAGCTCATTTTCTG 60.183 38.462 0.00 0.00 45.94 3.02
2168 2628 7.517320 TGCATGTGATAGTATTTACTTCCCAT 58.483 34.615 0.00 0.00 37.73 4.00
2205 2672 2.550208 GCATAAGTAACGGATGGAGGGG 60.550 54.545 0.00 0.00 0.00 4.79
2237 2704 4.765339 TGGTATACCAGAGACATGTATCGG 59.235 45.833 21.05 21.70 42.01 4.18
2238 2705 5.008331 GGTATACCAGAGACATGTATCGGA 58.992 45.833 26.83 16.11 35.64 4.55
2239 2706 5.652891 GGTATACCAGAGACATGTATCGGAT 59.347 44.000 26.83 13.89 35.64 4.18
2240 2707 5.651387 ATACCAGAGACATGTATCGGATG 57.349 43.478 26.83 16.09 0.00 3.51
2241 2708 3.300388 ACCAGAGACATGTATCGGATGT 58.700 45.455 26.83 14.40 36.73 3.06
2276 2746 3.853207 ACCCGTATATAGGCTCCTTTGA 58.147 45.455 0.00 0.00 0.00 2.69
2285 2755 1.512694 GCTCCTTTGATTTGCGGGG 59.487 57.895 0.00 0.00 0.00 5.73
2307 2777 7.173032 GGGGTTCTAAAAACTCAAGAATAGGA 58.827 38.462 0.00 0.00 32.26 2.94
2324 2794 9.601810 AAGAATAGGAAAAACAAAGGAATAGGT 57.398 29.630 0.00 0.00 0.00 3.08
2325 2795 9.601810 AGAATAGGAAAAACAAAGGAATAGGTT 57.398 29.630 0.00 0.00 0.00 3.50
2454 2927 6.854091 TGGTAAAACTAAAAACAACCCACT 57.146 33.333 0.00 0.00 0.00 4.00
2536 3009 8.060689 TCATCCATATGAATTTGAAAAGGAGGA 58.939 33.333 3.65 0.00 39.20 3.71
2546 3019 3.751518 TGAAAAGGAGGACAAAGTAGGC 58.248 45.455 0.00 0.00 0.00 3.93
2596 3069 6.821160 TGAAACTGGGTTCAAAGGAAAATTTC 59.179 34.615 0.00 0.00 34.59 2.17
2632 3105 3.509442 TGCCTCATTCCTTTGAACCAAT 58.491 40.909 0.00 0.00 32.13 3.16
2634 3107 3.511146 GCCTCATTCCTTTGAACCAATGA 59.489 43.478 0.00 0.00 34.74 2.57
2766 3325 0.914551 CTTCAGACCGATACGCGTTG 59.085 55.000 20.78 7.97 38.67 4.10
2776 3335 2.410730 CGATACGCGTTGTTTTTCCTCT 59.589 45.455 20.78 0.00 34.64 3.69
2778 3337 4.609783 CGATACGCGTTGTTTTTCCTCTTT 60.610 41.667 20.78 0.00 34.64 2.52
2779 3338 3.497297 ACGCGTTGTTTTTCCTCTTTT 57.503 38.095 5.58 0.00 0.00 2.27
2780 3339 3.840468 ACGCGTTGTTTTTCCTCTTTTT 58.160 36.364 5.58 0.00 0.00 1.94
2807 3366 3.247046 GCGGTAAGAAAACGCCGT 58.753 55.556 0.00 0.00 46.92 5.68
2808 3367 1.570967 GCGGTAAGAAAACGCCGTT 59.429 52.632 0.00 0.00 46.92 4.44
2809 3368 0.723459 GCGGTAAGAAAACGCCGTTG 60.723 55.000 1.95 0.00 46.92 4.10
2866 3425 1.478510 CAGTAAGCTGATCCACGTCCT 59.521 52.381 0.00 0.00 45.28 3.85
2868 3427 2.093973 AGTAAGCTGATCCACGTCCTTG 60.094 50.000 0.00 0.00 0.00 3.61
2873 3432 3.006323 AGCTGATCCACGTCCTTGATATC 59.994 47.826 0.00 0.00 0.00 1.63
3064 3899 4.033709 AGCTACCTCCTGTGAATGTATGT 58.966 43.478 0.00 0.00 0.00 2.29
3065 3900 4.100189 AGCTACCTCCTGTGAATGTATGTC 59.900 45.833 0.00 0.00 0.00 3.06
3089 3924 7.485913 GTCATCAACGATGCAAAGTAATTGATT 59.514 33.333 0.00 0.00 38.73 2.57
3121 3958 5.405797 TGGTTTATGTATGTACGTAACGCA 58.594 37.500 0.00 0.00 37.39 5.24
3226 4063 1.040646 TAGGCGCATCTGTTCCTAGG 58.959 55.000 10.83 0.82 0.00 3.02
3227 4064 0.978146 AGGCGCATCTGTTCCTAGGT 60.978 55.000 10.83 0.00 0.00 3.08
3228 4065 0.750850 GGCGCATCTGTTCCTAGGTA 59.249 55.000 10.83 0.00 0.00 3.08
3233 4070 4.799678 CGCATCTGTTCCTAGGTAGTATG 58.200 47.826 9.08 8.73 0.00 2.39
3253 4090 3.807538 GGACGCGCCTGACTCGTA 61.808 66.667 5.73 0.00 40.43 3.43
3267 4104 1.107114 CTCGTATCACAGAGTGCCCT 58.893 55.000 0.00 0.00 32.98 5.19
3268 4105 1.066303 CTCGTATCACAGAGTGCCCTC 59.934 57.143 0.00 0.00 38.04 4.30
3335 4172 0.179094 TCGATCGAATTGAACCCCCG 60.179 55.000 16.99 0.00 0.00 5.73
3404 4241 2.586648 AGAAATTGGGTGTGGGAGAC 57.413 50.000 0.00 0.00 0.00 3.36
3420 4257 1.371635 GACATGTTGTTGCCGGTGC 60.372 57.895 1.90 0.00 38.26 5.01
3449 4286 1.338864 GGGGAGGAGACGAAAAGGAAC 60.339 57.143 0.00 0.00 0.00 3.62
3466 4303 4.606071 CTGTAAAGCAGCGCCTCT 57.394 55.556 2.29 0.00 38.52 3.69
3494 4331 4.346129 GAGCTCCTATTTGACGCATTTTG 58.654 43.478 0.87 0.00 0.00 2.44
3524 4361 1.467734 CTGGATCTGCTGCTTGACAAC 59.532 52.381 0.00 0.00 0.00 3.32
3614 4727 2.158900 ACTACAATGGAGAATCTGGGCG 60.159 50.000 0.00 0.00 33.73 6.13
3618 4731 3.117888 ACAATGGAGAATCTGGGCGTATT 60.118 43.478 0.00 0.00 33.73 1.89
3619 4732 4.102524 ACAATGGAGAATCTGGGCGTATTA 59.897 41.667 0.00 0.00 33.73 0.98
3622 4735 2.028020 GGAGAATCTGGGCGTATTAGGG 60.028 54.545 0.00 0.00 33.73 3.53
3623 4736 1.978580 AGAATCTGGGCGTATTAGGGG 59.021 52.381 0.00 0.00 0.00 4.79
3697 4811 9.495572 GGGTAACATTTGAAAATTGGACAATTA 57.504 29.630 10.38 0.00 38.07 1.40
3877 4992 5.755330 TCCGAATAAATTTTCAAAAGCGC 57.245 34.783 0.00 0.00 0.00 5.92
3878 4993 4.623595 TCCGAATAAATTTTCAAAAGCGCC 59.376 37.500 2.29 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.619227 AACCTGCGGACACACGGG 62.619 66.667 0.00 0.00 0.00 5.28
1 2 3.345808 CAACCTGCGGACACACGG 61.346 66.667 0.00 0.00 0.00 4.94
4 5 1.003839 GATCCAACCTGCGGACACA 60.004 57.895 0.00 0.00 34.69 3.72
5 6 1.745489 GGATCCAACCTGCGGACAC 60.745 63.158 6.95 0.00 34.69 3.67
6 7 1.899437 GAGGATCCAACCTGCGGACA 61.899 60.000 15.82 0.00 40.73 4.02
7 8 1.153349 GAGGATCCAACCTGCGGAC 60.153 63.158 15.82 0.00 40.73 4.79
19 20 0.113385 TGGAGAGGGATCGGAGGATC 59.887 60.000 0.00 0.00 46.85 3.36
20 21 0.178947 GTGGAGAGGGATCGGAGGAT 60.179 60.000 0.00 0.00 34.96 3.24
21 22 1.230497 GTGGAGAGGGATCGGAGGA 59.770 63.158 0.00 0.00 0.00 3.71
46 47 1.699257 GGGGGAGGAATCCATGGTAGT 60.699 57.143 12.58 0.00 0.00 2.73
73 75 1.682684 CCAGCCCGTACCAGAGAGT 60.683 63.158 0.00 0.00 0.00 3.24
91 93 2.815647 CTTCTTCTGGTCCGGCGC 60.816 66.667 0.00 0.00 0.00 6.53
150 152 1.115467 GGACATCGTCATCCTCCTGT 58.885 55.000 0.00 0.00 33.68 4.00
159 161 3.243401 CGTCATCTATTGGGACATCGTCA 60.243 47.826 0.00 0.00 39.30 4.35
165 167 0.104120 CCGCGTCATCTATTGGGACA 59.896 55.000 4.92 0.00 0.00 4.02
174 176 3.122971 TCGTCGACCGCGTCATCT 61.123 61.111 10.58 0.00 38.98 2.90
227 232 4.779733 TGGCGGAGGAGGAGGGTC 62.780 72.222 0.00 0.00 0.00 4.46
261 274 2.225791 CTCGCCGATGGTCAAGGTGA 62.226 60.000 10.18 10.18 41.66 4.02
266 279 2.577059 GGACTCGCCGATGGTCAA 59.423 61.111 8.49 0.00 0.00 3.18
295 308 3.245346 TCCCGCACCATGTCCACA 61.245 61.111 0.00 0.00 0.00 4.17
296 309 2.436646 CTCCCGCACCATGTCCAC 60.437 66.667 0.00 0.00 0.00 4.02
325 347 2.126110 ACATCGTCGTGCGCATCA 60.126 55.556 15.91 0.00 41.07 3.07
336 358 0.389426 GTGGTTGTAGGCGACATCGT 60.389 55.000 0.07 0.00 42.22 3.73
342 364 0.535335 GAGATGGTGGTTGTAGGCGA 59.465 55.000 0.00 0.00 0.00 5.54
368 393 2.124819 CTCCGCCTGCAGATGCTT 60.125 61.111 17.39 0.00 42.66 3.91
442 470 3.077519 GCGGTATGACTCGGGCAGT 62.078 63.158 0.00 0.00 38.45 4.40
443 471 2.279517 GCGGTATGACTCGGGCAG 60.280 66.667 0.00 0.00 0.00 4.85
447 475 2.331805 CGGAGCGGTATGACTCGG 59.668 66.667 0.00 0.00 33.55 4.63
470 498 1.152943 AGCGGGCGAGACAGATCTA 60.153 57.895 0.00 0.00 34.34 1.98
558 586 2.663630 ATCGATCTCGCCGAACACCG 62.664 60.000 0.00 0.00 39.62 4.94
559 587 1.065928 ATCGATCTCGCCGAACACC 59.934 57.895 0.00 0.00 39.62 4.16
560 588 0.248498 TCATCGATCTCGCCGAACAC 60.248 55.000 0.00 0.00 39.62 3.32
561 589 0.248498 GTCATCGATCTCGCCGAACA 60.248 55.000 0.00 0.00 39.62 3.18
562 590 0.248498 TGTCATCGATCTCGCCGAAC 60.248 55.000 0.00 0.00 39.62 3.95
563 591 0.454196 TTGTCATCGATCTCGCCGAA 59.546 50.000 0.00 0.00 39.62 4.30
564 592 0.029433 CTTGTCATCGATCTCGCCGA 59.971 55.000 0.00 0.00 40.53 5.54
565 593 0.936764 CCTTGTCATCGATCTCGCCG 60.937 60.000 0.00 0.00 39.60 6.46
566 594 0.385751 TCCTTGTCATCGATCTCGCC 59.614 55.000 0.00 0.00 39.60 5.54
567 595 1.601663 CCTCCTTGTCATCGATCTCGC 60.602 57.143 0.00 0.00 39.60 5.03
568 596 1.950216 TCCTCCTTGTCATCGATCTCG 59.050 52.381 0.00 0.00 41.45 4.04
569 597 2.287308 CGTCCTCCTTGTCATCGATCTC 60.287 54.545 0.00 0.00 0.00 2.75
570 598 1.678627 CGTCCTCCTTGTCATCGATCT 59.321 52.381 0.00 0.00 0.00 2.75
571 599 1.405821 ACGTCCTCCTTGTCATCGATC 59.594 52.381 0.00 0.00 0.00 3.69
572 600 1.405821 GACGTCCTCCTTGTCATCGAT 59.594 52.381 3.51 0.00 32.91 3.59
573 601 0.809385 GACGTCCTCCTTGTCATCGA 59.191 55.000 3.51 0.00 32.91 3.59
574 602 0.523546 CGACGTCCTCCTTGTCATCG 60.524 60.000 10.58 0.00 32.91 3.84
575 603 0.802607 GCGACGTCCTCCTTGTCATC 60.803 60.000 10.58 0.00 32.91 2.92
576 604 1.215647 GCGACGTCCTCCTTGTCAT 59.784 57.895 10.58 0.00 32.91 3.06
577 605 1.901948 AGCGACGTCCTCCTTGTCA 60.902 57.895 10.58 0.00 32.91 3.58
578 606 1.444553 CAGCGACGTCCTCCTTGTC 60.445 63.158 10.58 0.00 0.00 3.18
579 607 2.651361 CAGCGACGTCCTCCTTGT 59.349 61.111 10.58 0.00 0.00 3.16
580 608 2.811317 GCAGCGACGTCCTCCTTG 60.811 66.667 10.58 2.75 0.00 3.61
581 609 2.172483 ATTGCAGCGACGTCCTCCTT 62.172 55.000 10.58 0.00 0.00 3.36
582 610 2.650116 ATTGCAGCGACGTCCTCCT 61.650 57.895 10.58 0.84 0.00 3.69
583 611 2.125512 ATTGCAGCGACGTCCTCC 60.126 61.111 10.58 0.00 0.00 4.30
584 612 0.807667 ATCATTGCAGCGACGTCCTC 60.808 55.000 10.58 1.88 0.00 3.71
585 613 0.391661 AATCATTGCAGCGACGTCCT 60.392 50.000 10.58 5.32 0.00 3.85
586 614 0.247814 CAATCATTGCAGCGACGTCC 60.248 55.000 10.58 2.76 0.00 4.79
587 615 0.721154 TCAATCATTGCAGCGACGTC 59.279 50.000 5.18 5.18 0.00 4.34
588 616 1.155889 TTCAATCATTGCAGCGACGT 58.844 45.000 0.00 0.00 0.00 4.34
589 617 2.245795 TTTCAATCATTGCAGCGACG 57.754 45.000 0.00 0.00 0.00 5.12
590 618 2.339400 CGTTTTCAATCATTGCAGCGAC 59.661 45.455 0.00 0.00 0.00 5.19
591 619 2.225255 TCGTTTTCAATCATTGCAGCGA 59.775 40.909 4.81 4.81 0.00 4.93
592 620 2.583739 TCGTTTTCAATCATTGCAGCG 58.416 42.857 0.00 0.00 0.00 5.18
593 621 3.735240 TGTTCGTTTTCAATCATTGCAGC 59.265 39.130 0.00 0.00 0.00 5.25
594 622 5.214417 TCTGTTCGTTTTCAATCATTGCAG 58.786 37.500 0.00 0.00 0.00 4.41
595 623 5.180367 TCTGTTCGTTTTCAATCATTGCA 57.820 34.783 0.00 0.00 0.00 4.08
596 624 6.695292 AATCTGTTCGTTTTCAATCATTGC 57.305 33.333 0.00 0.00 0.00 3.56
599 627 9.965824 ACTTTTAATCTGTTCGTTTTCAATCAT 57.034 25.926 0.00 0.00 0.00 2.45
600 628 9.796120 AACTTTTAATCTGTTCGTTTTCAATCA 57.204 25.926 0.00 0.00 0.00 2.57
604 632 9.849166 AGAAAACTTTTAATCTGTTCGTTTTCA 57.151 25.926 20.06 0.00 45.24 2.69
606 634 9.849166 TGAGAAAACTTTTAATCTGTTCGTTTT 57.151 25.926 0.00 0.00 36.26 2.43
608 636 9.450807 CATGAGAAAACTTTTAATCTGTTCGTT 57.549 29.630 0.00 0.00 0.00 3.85
609 637 8.836413 TCATGAGAAAACTTTTAATCTGTTCGT 58.164 29.630 0.00 0.00 0.00 3.85
610 638 9.663904 TTCATGAGAAAACTTTTAATCTGTTCG 57.336 29.630 0.00 0.00 0.00 3.95
649 677 2.421877 AGGCACTGTGACGAAGGACG 62.422 60.000 12.86 0.00 43.32 4.79
650 678 0.249911 AAGGCACTGTGACGAAGGAC 60.250 55.000 12.86 0.00 40.86 3.85
651 679 0.033504 GAAGGCACTGTGACGAAGGA 59.966 55.000 12.86 0.00 40.86 3.36
652 680 1.284982 CGAAGGCACTGTGACGAAGG 61.285 60.000 12.86 0.00 40.86 3.46
653 681 0.597637 ACGAAGGCACTGTGACGAAG 60.598 55.000 12.86 7.81 40.86 3.79
654 682 0.669619 TACGAAGGCACTGTGACGAA 59.330 50.000 12.86 0.00 40.86 3.85
671 699 0.037326 TGGTACTGTGCTGCTGCTAC 60.037 55.000 17.00 12.91 40.48 3.58
683 711 4.736126 TCATCTACATGTGGTGGTACTG 57.264 45.455 9.11 0.00 0.00 2.74
713 746 1.078072 TTTGTGGTGGTGACTGCGT 60.078 52.632 0.00 0.00 0.00 5.24
721 754 5.159273 ACAAAGAAAATGTTTGTGGTGGT 57.841 34.783 5.00 0.00 44.55 4.16
722 755 5.064579 GGAACAAAGAAAATGTTTGTGGTGG 59.935 40.000 6.41 0.00 45.30 4.61
723 756 5.064579 GGGAACAAAGAAAATGTTTGTGGTG 59.935 40.000 6.41 0.00 45.30 4.17
737 770 5.134661 ACAATTTCTAACCGGGAACAAAGA 58.865 37.500 6.32 0.00 0.00 2.52
759 793 4.579340 TCATCGGACCTGTTCATCTACTAC 59.421 45.833 0.00 0.00 0.00 2.73
760 794 4.788679 TCATCGGACCTGTTCATCTACTA 58.211 43.478 0.00 0.00 0.00 1.82
762 796 3.243569 CCTCATCGGACCTGTTCATCTAC 60.244 52.174 0.00 0.00 33.16 2.59
763 797 2.959030 CCTCATCGGACCTGTTCATCTA 59.041 50.000 0.00 0.00 33.16 1.98
764 798 1.759445 CCTCATCGGACCTGTTCATCT 59.241 52.381 0.00 0.00 33.16 2.90
765 799 1.757118 TCCTCATCGGACCTGTTCATC 59.243 52.381 0.00 0.00 36.69 2.92
766 800 1.866015 TCCTCATCGGACCTGTTCAT 58.134 50.000 0.00 0.00 36.69 2.57
767 801 1.866015 ATCCTCATCGGACCTGTTCA 58.134 50.000 0.00 0.00 46.80 3.18
772 806 2.068834 ACGTTATCCTCATCGGACCT 57.931 50.000 0.00 0.00 46.80 3.85
961 995 1.624865 GCTCTGTCTGTCTGCGCTTG 61.625 60.000 9.73 1.08 0.00 4.01
962 996 1.373999 GCTCTGTCTGTCTGCGCTT 60.374 57.895 9.73 0.00 0.00 4.68
963 997 1.814772 AAGCTCTGTCTGTCTGCGCT 61.815 55.000 9.73 0.00 37.59 5.92
964 998 1.373999 AAGCTCTGTCTGTCTGCGC 60.374 57.895 0.00 0.00 0.00 6.09
1142 1176 2.376225 ATATGCATGCAGGGGGTGGG 62.376 60.000 26.69 0.00 0.00 4.61
1157 1191 2.615447 AGTTGAAGGTCGCATGCATATG 59.385 45.455 19.57 0.00 37.36 1.78
1158 1192 2.615447 CAGTTGAAGGTCGCATGCATAT 59.385 45.455 19.57 0.00 0.00 1.78
1159 1193 2.009051 CAGTTGAAGGTCGCATGCATA 58.991 47.619 19.57 1.39 0.00 3.14
1247 1287 2.333926 TGCGGAGTAACACAGATTTCG 58.666 47.619 0.00 0.00 0.00 3.46
1391 1431 9.906660 GTTCTACCAAACAATATTTCATTCACA 57.093 29.630 0.00 0.00 0.00 3.58
1416 1456 3.134574 TCGATGCCAGTTTTACCAAGT 57.865 42.857 0.00 0.00 0.00 3.16
1454 1494 5.107065 ACGTGAGTAACTGTTAGGTACGTAC 60.107 44.000 22.90 17.56 43.03 3.67
1487 1527 2.813179 GCGTGTAGATTGGGCTGCG 61.813 63.158 0.00 0.00 0.00 5.18
1507 1547 2.507471 ACCAGATTCAGACCATTCCTCC 59.493 50.000 0.00 0.00 0.00 4.30
1656 1700 4.407945 AGTGCTACCTTTAATCGGGTACAT 59.592 41.667 0.00 0.00 37.07 2.29
1672 1716 6.839820 AACAACTTGTACAGTAAGTGCTAC 57.160 37.500 0.00 0.00 38.32 3.58
1797 1846 6.771267 TCTCTTCTCTATCGGTTATGTTGCTA 59.229 38.462 0.00 0.00 0.00 3.49
1801 1850 7.825331 TCATCTCTTCTCTATCGGTTATGTT 57.175 36.000 0.00 0.00 0.00 2.71
2030 2114 4.093514 GCATTGTCGTCATGATTCACTTG 58.906 43.478 0.00 1.61 0.00 3.16
2072 2158 5.485662 AAGCGTTTGGATCATTAGCTTAC 57.514 39.130 11.23 0.00 41.00 2.34
2161 2621 7.445121 TGCTTACTATCTGTGATAATGGGAAG 58.555 38.462 0.00 0.00 29.87 3.46
2164 2624 9.376075 CTTATGCTTACTATCTGTGATAATGGG 57.624 37.037 0.00 0.00 0.00 4.00
2222 2689 5.351458 TGAAACATCCGATACATGTCTCTG 58.649 41.667 0.00 0.00 33.12 3.35
2237 2704 6.861065 ACGGGTAATCACATATGAAACATC 57.139 37.500 10.38 0.00 38.69 3.06
2276 2746 3.892588 TGAGTTTTTAGAACCCCGCAAAT 59.107 39.130 0.00 0.00 0.00 2.32
2376 2846 6.824305 ATTCCTATGAACCAAACACTCAAG 57.176 37.500 0.00 0.00 32.13 3.02
2435 2905 8.678593 TTTTCAAGTGGGTTGTTTTTAGTTTT 57.321 26.923 0.00 0.00 37.43 2.43
2439 2909 7.841915 ACATTTTCAAGTGGGTTGTTTTTAG 57.158 32.000 0.00 0.00 37.43 1.85
2445 2915 7.833285 AACTATACATTTTCAAGTGGGTTGT 57.167 32.000 0.00 0.00 37.43 3.32
2483 2956 6.195600 ACAAGACTATAAAACCTTGGTGGA 57.804 37.500 0.00 0.00 40.02 4.02
2514 2987 7.408756 TGTCCTCCTTTTCAAATTCATATGG 57.591 36.000 2.13 0.00 0.00 2.74
2536 3009 6.016276 CACAGGAATTTTACTGCCTACTTTGT 60.016 38.462 2.35 0.00 43.10 2.83
2546 3019 9.410556 CAAAGGAATAACACAGGAATTTTACTG 57.589 33.333 0.85 0.85 44.88 2.74
2632 3105 6.066032 TCCTATGGTGATACTATTCACGTCA 58.934 40.000 0.00 0.00 45.63 4.35
2634 3107 7.540474 AATCCTATGGTGATACTATTCACGT 57.460 36.000 0.00 0.00 45.63 4.49
2783 3342 3.364946 GCGTTTTCTTACCGCTCAAAAA 58.635 40.909 0.00 0.00 43.81 1.94
2784 3343 2.287129 GGCGTTTTCTTACCGCTCAAAA 60.287 45.455 0.00 0.00 46.23 2.44
2785 3344 1.264826 GGCGTTTTCTTACCGCTCAAA 59.735 47.619 0.00 0.00 46.23 2.69
2786 3345 0.869730 GGCGTTTTCTTACCGCTCAA 59.130 50.000 0.00 0.00 46.23 3.02
2787 3346 1.286354 CGGCGTTTTCTTACCGCTCA 61.286 55.000 0.00 0.00 46.23 4.26
2792 3351 2.761392 AACAACGGCGTTTTCTTACC 57.239 45.000 24.49 0.00 0.00 2.85
2793 3352 5.081888 TCTAAACAACGGCGTTTTCTTAC 57.918 39.130 24.49 0.00 39.70 2.34
2794 3353 5.294060 ACTTCTAAACAACGGCGTTTTCTTA 59.706 36.000 24.49 17.77 39.70 2.10
2795 3354 4.095334 ACTTCTAAACAACGGCGTTTTCTT 59.905 37.500 24.49 17.60 39.70 2.52
2796 3355 3.624410 ACTTCTAAACAACGGCGTTTTCT 59.376 39.130 24.49 6.21 39.70 2.52
2797 3356 3.722289 CACTTCTAAACAACGGCGTTTTC 59.278 43.478 24.49 0.00 39.70 2.29
2798 3357 3.127376 ACACTTCTAAACAACGGCGTTTT 59.873 39.130 24.49 18.14 39.70 2.43
2799 3358 2.679336 ACACTTCTAAACAACGGCGTTT 59.321 40.909 24.49 11.83 41.78 3.60
2800 3359 2.282407 ACACTTCTAAACAACGGCGTT 58.718 42.857 21.19 21.19 0.00 4.84
2801 3360 1.944032 ACACTTCTAAACAACGGCGT 58.056 45.000 6.77 6.77 0.00 5.68
2802 3361 3.328237 AAACACTTCTAAACAACGGCG 57.672 42.857 4.80 4.80 0.00 6.46
2803 3362 3.722289 CGAAAACACTTCTAAACAACGGC 59.278 43.478 0.00 0.00 0.00 5.68
2804 3363 4.900664 ACGAAAACACTTCTAAACAACGG 58.099 39.130 0.00 0.00 0.00 4.44
2805 3364 6.016718 TGAACGAAAACACTTCTAAACAACG 58.983 36.000 0.00 0.00 0.00 4.10
2806 3365 7.784790 TTGAACGAAAACACTTCTAAACAAC 57.215 32.000 0.00 0.00 0.00 3.32
2807 3366 8.973835 ATTTGAACGAAAACACTTCTAAACAA 57.026 26.923 0.00 0.00 0.00 2.83
2808 3367 8.973835 AATTTGAACGAAAACACTTCTAAACA 57.026 26.923 0.00 0.00 0.00 2.83
2809 3368 9.285770 AGAATTTGAACGAAAACACTTCTAAAC 57.714 29.630 0.00 0.00 0.00 2.01
2866 3425 2.221169 GTTCCTGCATGCGGATATCAA 58.779 47.619 28.32 11.25 0.00 2.57
2868 3427 0.792640 CGTTCCTGCATGCGGATATC 59.207 55.000 28.32 18.50 0.00 1.63
2873 3432 3.499737 GGTCGTTCCTGCATGCGG 61.500 66.667 20.13 20.13 0.00 5.69
3064 3899 6.493449 TCAATTACTTTGCATCGTTGATGA 57.507 33.333 10.81 0.00 41.31 2.92
3065 3900 7.305019 CGAATCAATTACTTTGCATCGTTGATG 60.305 37.037 2.45 2.45 42.37 3.07
3089 3924 6.693978 CGTACATACATAAACCATCTGTTCGA 59.306 38.462 0.00 0.00 35.67 3.71
3121 3958 8.957926 AGTAGGAAGTAGGAGTATATGGTAACT 58.042 37.037 0.00 0.00 37.61 2.24
3127 3964 8.707796 TCCAAAGTAGGAAGTAGGAGTATATG 57.292 38.462 0.00 0.00 33.93 1.78
3226 4063 1.590792 GGCGCGTCCCACATACTAC 60.591 63.158 8.43 0.00 0.00 2.73
3227 4064 1.755395 AGGCGCGTCCCACATACTA 60.755 57.895 7.31 0.00 34.51 1.82
3228 4065 3.075005 AGGCGCGTCCCACATACT 61.075 61.111 7.31 0.00 34.51 2.12
3253 4090 1.649321 TCTTGAGGGCACTCTGTGAT 58.351 50.000 18.70 0.00 44.29 3.06
3267 4104 4.575885 GGCGGCCACTATATTAATCTTGA 58.424 43.478 15.62 0.00 0.00 3.02
3268 4105 3.370978 CGGCGGCCACTATATTAATCTTG 59.629 47.826 20.71 0.00 0.00 3.02
3335 4172 4.521062 ATCGGGCAGTCGCAGAGC 62.521 66.667 0.00 0.00 41.24 4.09
3381 4218 3.084786 CTCCCACACCCAATTTCTTCTC 58.915 50.000 0.00 0.00 0.00 2.87
3404 4241 2.049248 GGCACCGGCAACAACATG 60.049 61.111 0.00 0.00 43.71 3.21
3420 4257 1.692749 TCTCCTCCCCCAAATCCGG 60.693 63.158 0.00 0.00 0.00 5.14
3462 4299 1.799933 ATAGGAGCTCCCACAAGAGG 58.200 55.000 29.54 0.00 37.41 3.69
3466 4303 2.354704 CGTCAAATAGGAGCTCCCACAA 60.355 50.000 29.54 12.94 37.41 3.33
3494 4331 2.012673 AGCAGATCCAGAATTTGACGC 58.987 47.619 0.00 0.00 0.00 5.19
3524 4361 1.226717 GACTGGTTAGCCGCTCTCG 60.227 63.158 0.00 0.00 37.67 4.04
3544 4381 0.308993 GTCAGCAACACTTGTCAGGC 59.691 55.000 0.00 0.00 0.00 4.85
3604 4717 1.975680 TCCCCTAATACGCCCAGATTC 59.024 52.381 0.00 0.00 0.00 2.52
3639 4752 9.567776 TTACTAATGTCTTCACAATTTCAAGGA 57.432 29.630 0.00 0.00 35.64 3.36
3935 5054 6.887545 TCAGAATGTATAAAATGTCCCCGTTT 59.112 34.615 0.00 0.00 37.40 3.60
3939 5058 7.339466 ACTGTTCAGAATGTATAAAATGTCCCC 59.661 37.037 6.83 0.00 37.40 4.81


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

AutoCloner maintained by Alex Coulton.