Multiple sequence alignment - TraesCS2B01G553300

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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 TraesCS2B01G553300 chr2B 100.000 4702 0 0 1 4702 748970703 748975404 0.000000e+00 8684.0
1 TraesCS2B01G553300 chr2B 82.516 469 64 9 2985 3451 564975693 564976145 3.410000e-106 396.0
2 TraesCS2B01G553300 chr2A 93.826 3223 113 24 1492 4702 745025020 745028168 0.000000e+00 4771.0
3 TraesCS2B01G553300 chr2A 84.268 731 40 26 730 1453 745023877 745024539 1.100000e-180 643.0
4 TraesCS2B01G553300 chr2A 100.000 32 0 0 684 715 745023849 745023880 5.080000e-05 60.2
5 TraesCS2B01G553300 chr2D 95.108 1983 71 12 2741 4702 613434447 613436424 0.000000e+00 3101.0
6 TraesCS2B01G553300 chr2D 89.955 896 79 8 1491 2382 613433182 613434070 0.000000e+00 1146.0
7 TraesCS2B01G553300 chr2D 90.798 815 33 24 634 1421 613431753 613432552 0.000000e+00 1051.0
8 TraesCS2B01G553300 chr2D 82.051 468 69 6 2985 3451 454714006 454714459 7.380000e-103 385.0
9 TraesCS2B01G553300 chr6D 94.474 742 37 4 1800 2538 75851423 75852163 0.000000e+00 1140.0
10 TraesCS2B01G553300 chr6D 94.205 742 39 4 1800 2538 313699973 313699233 0.000000e+00 1129.0
11 TraesCS2B01G553300 chr6D 94.205 742 38 5 1800 2538 118382551 118381812 0.000000e+00 1127.0
12 TraesCS2B01G553300 chr6D 93.943 743 40 5 1800 2538 408615630 408614889 0.000000e+00 1118.0
13 TraesCS2B01G553300 chr6D 89.947 189 17 2 3813 3999 337746036 337745848 4.700000e-60 243.0
14 TraesCS2B01G553300 chr3D 94.340 742 38 4 1800 2538 219539454 219540194 0.000000e+00 1134.0
15 TraesCS2B01G553300 chr3D 86.424 523 51 11 3813 4329 342127030 342126522 5.320000e-154 555.0
16 TraesCS2B01G553300 chr3D 91.139 79 4 2 4358 4433 342126523 342126445 2.310000e-18 104.0
17 TraesCS2B01G553300 chr1B 94.070 742 40 4 1800 2538 27121473 27122213 0.000000e+00 1123.0
18 TraesCS2B01G553300 chr1D 93.809 743 41 5 1800 2538 117993004 117992263 0.000000e+00 1112.0
19 TraesCS2B01G553300 chr4B 92.427 515 30 4 1 514 596331057 596330551 0.000000e+00 726.0
20 TraesCS2B01G553300 chr3B 90.840 524 39 5 1 523 592687949 592687434 0.000000e+00 693.0
21 TraesCS2B01G553300 chr3B 86.486 629 71 10 3814 4433 314207217 314207840 0.000000e+00 678.0
22 TraesCS2B01G553300 chr3B 90.019 521 43 5 1 520 670538357 670538869 0.000000e+00 665.0
23 TraesCS2B01G553300 chr3B 92.308 65 3 2 457 520 21613932 21613869 1.800000e-14 91.6
24 TraesCS2B01G553300 chr3B 92.188 64 3 2 457 519 606223310 606223372 6.480000e-14 89.8
25 TraesCS2B01G553300 chr6A 86.465 628 73 8 3813 4432 204935614 204934991 0.000000e+00 678.0
26 TraesCS2B01G553300 chr6A 86.878 442 48 6 3585 4018 301800409 301799970 1.970000e-133 486.0
27 TraesCS2B01G553300 chr6A 79.648 511 73 16 3033 3532 301800897 301800407 5.830000e-89 339.0
28 TraesCS2B01G553300 chr6A 83.750 320 39 10 4020 4331 301790206 301789892 1.660000e-74 291.0
29 TraesCS2B01G553300 chr5D 89.464 541 38 6 1 523 470549402 470548863 0.000000e+00 665.0
30 TraesCS2B01G553300 chr5D 88.931 524 46 7 1 514 416433577 416433056 1.850000e-178 636.0
31 TraesCS2B01G553300 chr5D 85.689 566 63 5 3824 4388 520995442 520994894 8.770000e-162 580.0
32 TraesCS2B01G553300 chr7D 89.905 525 40 7 1 520 363043508 363044024 0.000000e+00 664.0
33 TraesCS2B01G553300 chr7D 90.177 509 40 8 4 511 265174537 265174038 0.000000e+00 654.0
34 TraesCS2B01G553300 chr7B 89.827 521 39 9 1 520 334789799 334790306 0.000000e+00 656.0
35 TraesCS2B01G553300 chr5B 89.695 524 41 9 1 523 658540096 658539585 0.000000e+00 656.0
36 TraesCS2B01G553300 chr1A 82.479 468 66 7 2985 3451 335108155 335108607 3.410000e-106 396.0
37 TraesCS2B01G553300 chr6B 81.838 468 69 7 2985 3451 250783291 250782839 3.430000e-101 379.0
38 TraesCS2B01G553300 chr4A 89.384 292 28 2 4142 4431 377614529 377614239 9.620000e-97 364.0
39 TraesCS2B01G553300 chr7A 87.797 295 33 2 4139 4431 133419282 133419575 4.510000e-90 342.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G553300 chr2B 748970703 748975404 4701 False 8684.000000 8684 100.000000 1 4702 1 chr2B.!!$F2 4701
1 TraesCS2B01G553300 chr2A 745023849 745028168 4319 False 1824.733333 4771 92.698000 684 4702 3 chr2A.!!$F1 4018
2 TraesCS2B01G553300 chr2D 613431753 613436424 4671 False 1766.000000 3101 91.953667 634 4702 3 chr2D.!!$F2 4068
3 TraesCS2B01G553300 chr6D 75851423 75852163 740 False 1140.000000 1140 94.474000 1800 2538 1 chr6D.!!$F1 738
4 TraesCS2B01G553300 chr6D 313699233 313699973 740 True 1129.000000 1129 94.205000 1800 2538 1 chr6D.!!$R2 738
5 TraesCS2B01G553300 chr6D 118381812 118382551 739 True 1127.000000 1127 94.205000 1800 2538 1 chr6D.!!$R1 738
6 TraesCS2B01G553300 chr6D 408614889 408615630 741 True 1118.000000 1118 93.943000 1800 2538 1 chr6D.!!$R4 738
7 TraesCS2B01G553300 chr3D 219539454 219540194 740 False 1134.000000 1134 94.340000 1800 2538 1 chr3D.!!$F1 738
8 TraesCS2B01G553300 chr3D 342126445 342127030 585 True 329.500000 555 88.781500 3813 4433 2 chr3D.!!$R1 620
9 TraesCS2B01G553300 chr1B 27121473 27122213 740 False 1123.000000 1123 94.070000 1800 2538 1 chr1B.!!$F1 738
10 TraesCS2B01G553300 chr1D 117992263 117993004 741 True 1112.000000 1112 93.809000 1800 2538 1 chr1D.!!$R1 738
11 TraesCS2B01G553300 chr4B 596330551 596331057 506 True 726.000000 726 92.427000 1 514 1 chr4B.!!$R1 513
12 TraesCS2B01G553300 chr3B 592687434 592687949 515 True 693.000000 693 90.840000 1 523 1 chr3B.!!$R2 522
13 TraesCS2B01G553300 chr3B 314207217 314207840 623 False 678.000000 678 86.486000 3814 4433 1 chr3B.!!$F1 619
14 TraesCS2B01G553300 chr3B 670538357 670538869 512 False 665.000000 665 90.019000 1 520 1 chr3B.!!$F3 519
15 TraesCS2B01G553300 chr6A 204934991 204935614 623 True 678.000000 678 86.465000 3813 4432 1 chr6A.!!$R1 619
16 TraesCS2B01G553300 chr6A 301799970 301800897 927 True 412.500000 486 83.263000 3033 4018 2 chr6A.!!$R3 985
17 TraesCS2B01G553300 chr5D 470548863 470549402 539 True 665.000000 665 89.464000 1 523 1 chr5D.!!$R2 522
18 TraesCS2B01G553300 chr5D 416433056 416433577 521 True 636.000000 636 88.931000 1 514 1 chr5D.!!$R1 513
19 TraesCS2B01G553300 chr5D 520994894 520995442 548 True 580.000000 580 85.689000 3824 4388 1 chr5D.!!$R3 564
20 TraesCS2B01G553300 chr7D 363043508 363044024 516 False 664.000000 664 89.905000 1 520 1 chr7D.!!$F1 519
21 TraesCS2B01G553300 chr7B 334789799 334790306 507 False 656.000000 656 89.827000 1 520 1 chr7B.!!$F1 519
22 TraesCS2B01G553300 chr5B 658539585 658540096 511 True 656.000000 656 89.695000 1 523 1 chr5B.!!$R1 522

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
809 843 0.252558 TCTCCCAACCACCCCTCTAC 60.253 60.0 0.0 0.0 0.0 2.59 F
1422 1482 0.101219 TGATCTCATCTGCGTGTCGG 59.899 55.0 0.0 0.0 0.0 4.79 F
1461 1521 0.107945 CTTGTCAGCTACCCCTCTGC 60.108 60.0 0.0 0.0 0.0 4.26 F
1520 2225 0.108138 GCCAGCCTGAGATTGTACGT 60.108 55.0 0.0 0.0 0.0 3.57 F
3118 3891 0.883833 CAAGAAGGATTGCTGCGGTT 59.116 50.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 2340 0.321830 GCCATGCAACAAAGGCCATT 60.322 50.000 5.01 0.0 41.25 3.16 R
3091 3864 0.171903 CAATCCTTCTTGCAAGGGCG 59.828 55.000 25.73 13.8 45.35 6.13 R
3407 4191 2.289565 GACCATGTAGGCCTTTGTAGC 58.710 52.381 12.58 0.0 43.14 3.58 R
3612 4397 2.420687 GGTAGAATTCCCAGTCAGGCAG 60.421 54.545 0.65 0.0 35.39 4.85 R
4054 4854 1.278127 AGCCTTACCATGCTGTAACGT 59.722 47.619 0.00 0.0 36.23 3.99 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
105 106 2.135139 CTGAAGCACGCAGAAACTGTA 58.865 47.619 0.00 0.00 35.39 2.74
106 107 2.738846 CTGAAGCACGCAGAAACTGTAT 59.261 45.455 0.00 0.00 35.39 2.29
195 196 2.806244 ACGATCAAGGGTTTCAGTTTCG 59.194 45.455 0.00 0.00 0.00 3.46
213 214 0.606401 CGGGGTGAGAATGTTGTGCT 60.606 55.000 0.00 0.00 0.00 4.40
261 266 2.991250 AGAGTTCACCCAATTCCATCG 58.009 47.619 0.00 0.00 0.00 3.84
288 293 1.069227 GCGTGATTGGGAAACTCACAC 60.069 52.381 0.00 0.00 39.36 3.82
311 316 4.447054 CGCAACTGCAAAATGATTTGGTTA 59.553 37.500 2.12 0.00 44.93 2.85
318 323 7.331687 ACTGCAAAATGATTTGGTTAAGCATAC 59.668 33.333 8.40 4.06 41.79 2.39
321 326 7.486551 GCAAAATGATTTGGTTAAGCATACGTA 59.513 33.333 8.40 0.00 41.79 3.57
374 379 6.601741 TTCTTTATTTGGCTTGCAAAACTG 57.398 33.333 0.00 0.00 0.00 3.16
400 406 9.944663 GTGTGAGACATTTTTACTTGTATTCAA 57.055 29.630 0.00 0.00 0.00 2.69
497 527 6.837992 AGCAATGCAAAAATGAGCTATTTTG 58.162 32.000 19.73 19.73 45.74 2.44
499 529 7.040961 AGCAATGCAAAAATGAGCTATTTTGTT 60.041 29.630 22.53 13.31 45.74 2.83
500 530 7.060174 GCAATGCAAAAATGAGCTATTTTGTTG 59.940 33.333 22.53 20.44 45.74 3.33
502 532 7.410800 TGCAAAAATGAGCTATTTTGTTGAG 57.589 32.000 22.53 7.33 45.74 3.02
528 558 4.235731 CCAACCGGCTACCAATCC 57.764 61.111 0.00 0.00 0.00 3.01
529 559 1.301623 CCAACCGGCTACCAATCCA 59.698 57.895 0.00 0.00 0.00 3.41
530 560 0.322997 CCAACCGGCTACCAATCCAA 60.323 55.000 0.00 0.00 0.00 3.53
531 561 1.540267 CAACCGGCTACCAATCCAAA 58.460 50.000 0.00 0.00 0.00 3.28
532 562 2.099405 CAACCGGCTACCAATCCAAAT 58.901 47.619 0.00 0.00 0.00 2.32
533 563 2.052782 ACCGGCTACCAATCCAAATC 57.947 50.000 0.00 0.00 0.00 2.17
534 564 1.564348 ACCGGCTACCAATCCAAATCT 59.436 47.619 0.00 0.00 0.00 2.40
535 565 2.775384 ACCGGCTACCAATCCAAATCTA 59.225 45.455 0.00 0.00 0.00 1.98
536 566 3.201266 ACCGGCTACCAATCCAAATCTAA 59.799 43.478 0.00 0.00 0.00 2.10
537 567 4.204012 CCGGCTACCAATCCAAATCTAAA 58.796 43.478 0.00 0.00 0.00 1.85
538 568 4.642885 CCGGCTACCAATCCAAATCTAAAA 59.357 41.667 0.00 0.00 0.00 1.52
539 569 5.449999 CCGGCTACCAATCCAAATCTAAAAC 60.450 44.000 0.00 0.00 0.00 2.43
540 570 5.124776 CGGCTACCAATCCAAATCTAAAACA 59.875 40.000 0.00 0.00 0.00 2.83
541 571 6.564328 GGCTACCAATCCAAATCTAAAACAG 58.436 40.000 0.00 0.00 0.00 3.16
542 572 6.405842 GGCTACCAATCCAAATCTAAAACAGG 60.406 42.308 0.00 0.00 0.00 4.00
543 573 6.405842 GCTACCAATCCAAATCTAAAACAGGG 60.406 42.308 0.00 0.00 0.00 4.45
544 574 4.222810 ACCAATCCAAATCTAAAACAGGGC 59.777 41.667 0.00 0.00 0.00 5.19
545 575 4.423732 CAATCCAAATCTAAAACAGGGCG 58.576 43.478 0.00 0.00 0.00 6.13
546 576 2.442413 TCCAAATCTAAAACAGGGCGG 58.558 47.619 0.00 0.00 0.00 6.13
547 577 1.476488 CCAAATCTAAAACAGGGCGGG 59.524 52.381 0.00 0.00 0.00 6.13
548 578 1.135112 CAAATCTAAAACAGGGCGGGC 60.135 52.381 0.00 0.00 0.00 6.13
549 579 0.683179 AATCTAAAACAGGGCGGGCC 60.683 55.000 13.58 13.58 0.00 5.80
550 580 1.571773 ATCTAAAACAGGGCGGGCCT 61.572 55.000 18.71 18.71 36.10 5.19
551 581 1.749258 CTAAAACAGGGCGGGCCTC 60.749 63.158 21.75 0.69 36.10 4.70
552 582 3.615509 TAAAACAGGGCGGGCCTCG 62.616 63.158 21.75 17.72 42.76 4.63
571 601 3.936203 GTGGGCGGCCGATCCATA 61.936 66.667 32.94 16.14 32.71 2.74
572 602 3.936203 TGGGCGGCCGATCCATAC 61.936 66.667 33.48 9.05 34.01 2.39
597 627 2.303163 AAAAAGCGGACAAAACCACC 57.697 45.000 0.00 0.00 0.00 4.61
599 629 1.033202 AAAGCGGACAAAACCACCGT 61.033 50.000 0.00 0.00 46.95 4.83
600 630 1.033202 AAGCGGACAAAACCACCGTT 61.033 50.000 0.00 0.00 46.95 4.44
601 631 1.009335 GCGGACAAAACCACCGTTC 60.009 57.895 0.00 0.00 46.95 3.95
602 632 1.277440 CGGACAAAACCACCGTTCG 59.723 57.895 0.00 0.00 41.47 3.95
603 633 1.430707 CGGACAAAACCACCGTTCGT 61.431 55.000 0.00 0.00 41.47 3.85
604 634 0.734309 GGACAAAACCACCGTTCGTT 59.266 50.000 0.00 0.00 0.00 3.85
605 635 1.132834 GGACAAAACCACCGTTCGTTT 59.867 47.619 0.00 0.00 33.69 3.60
606 636 2.178783 GACAAAACCACCGTTCGTTTG 58.821 47.619 0.00 0.00 32.65 2.93
607 637 1.135344 ACAAAACCACCGTTCGTTTGG 60.135 47.619 8.05 8.05 32.65 3.28
608 638 1.132643 CAAAACCACCGTTCGTTTGGA 59.867 47.619 14.23 0.00 32.65 3.53
609 639 1.682740 AAACCACCGTTCGTTTGGAT 58.317 45.000 14.23 3.11 34.24 3.41
610 640 1.232119 AACCACCGTTCGTTTGGATC 58.768 50.000 14.23 0.00 34.24 3.36
611 641 0.947180 ACCACCGTTCGTTTGGATCG 60.947 55.000 14.23 0.00 37.55 3.69
612 642 0.668096 CCACCGTTCGTTTGGATCGA 60.668 55.000 0.00 0.00 39.62 3.59
613 643 0.437295 CACCGTTCGTTTGGATCGAC 59.563 55.000 0.00 0.00 39.62 4.20
614 644 0.668401 ACCGTTCGTTTGGATCGACC 60.668 55.000 0.00 0.00 39.62 4.79
615 645 1.356527 CCGTTCGTTTGGATCGACCC 61.357 60.000 0.00 0.00 39.62 4.46
616 646 0.389426 CGTTCGTTTGGATCGACCCT 60.389 55.000 0.00 0.00 39.62 4.34
617 647 1.135315 CGTTCGTTTGGATCGACCCTA 60.135 52.381 0.00 0.00 39.62 3.53
618 648 2.480759 CGTTCGTTTGGATCGACCCTAT 60.481 50.000 0.00 0.00 39.62 2.57
619 649 2.864343 GTTCGTTTGGATCGACCCTATG 59.136 50.000 0.00 0.00 37.05 2.23
620 650 2.380941 TCGTTTGGATCGACCCTATGA 58.619 47.619 0.00 0.00 38.00 2.15
621 651 2.761767 TCGTTTGGATCGACCCTATGAA 59.238 45.455 0.00 0.00 38.00 2.57
622 652 3.123804 CGTTTGGATCGACCCTATGAAG 58.876 50.000 0.00 0.00 38.00 3.02
623 653 3.430374 CGTTTGGATCGACCCTATGAAGT 60.430 47.826 0.00 0.00 38.00 3.01
624 654 4.514401 GTTTGGATCGACCCTATGAAGTT 58.486 43.478 0.00 0.00 38.00 2.66
625 655 3.819564 TGGATCGACCCTATGAAGTTG 57.180 47.619 0.00 0.00 38.00 3.16
626 656 2.158957 TGGATCGACCCTATGAAGTTGC 60.159 50.000 0.00 0.00 38.00 4.17
627 657 2.103263 GGATCGACCCTATGAAGTTGCT 59.897 50.000 0.00 0.00 0.00 3.91
628 658 2.961526 TCGACCCTATGAAGTTGCTC 57.038 50.000 0.00 0.00 0.00 4.26
629 659 2.457598 TCGACCCTATGAAGTTGCTCT 58.542 47.619 0.00 0.00 0.00 4.09
630 660 2.427453 TCGACCCTATGAAGTTGCTCTC 59.573 50.000 0.00 0.00 0.00 3.20
631 661 2.166459 CGACCCTATGAAGTTGCTCTCA 59.834 50.000 0.00 0.00 0.00 3.27
632 662 3.181471 CGACCCTATGAAGTTGCTCTCAT 60.181 47.826 0.00 0.00 0.00 2.90
679 709 4.202243 CCTTTTCTTGGGATTTTGTGCTGA 60.202 41.667 0.00 0.00 0.00 4.26
800 834 3.781307 CCGGCGATCTCCCAACCA 61.781 66.667 9.30 0.00 0.00 3.67
801 835 2.511600 CGGCGATCTCCCAACCAC 60.512 66.667 0.00 0.00 0.00 4.16
803 837 2.124695 GCGATCTCCCAACCACCC 60.125 66.667 0.00 0.00 0.00 4.61
804 838 2.590092 CGATCTCCCAACCACCCC 59.410 66.667 0.00 0.00 0.00 4.95
806 840 1.915983 GATCTCCCAACCACCCCTC 59.084 63.158 0.00 0.00 0.00 4.30
807 841 0.621862 GATCTCCCAACCACCCCTCT 60.622 60.000 0.00 0.00 0.00 3.69
808 842 0.722676 ATCTCCCAACCACCCCTCTA 59.277 55.000 0.00 0.00 0.00 2.43
809 843 0.252558 TCTCCCAACCACCCCTCTAC 60.253 60.000 0.00 0.00 0.00 2.59
812 846 1.272554 CCCAACCACCCCTCTACCTC 61.273 65.000 0.00 0.00 0.00 3.85
833 884 3.169099 CTTCTGTCTCTTCTTCCCTCCA 58.831 50.000 0.00 0.00 0.00 3.86
871 923 2.818841 CCACCCGCGTATCCATCA 59.181 61.111 4.92 0.00 0.00 3.07
917 969 0.620556 CATACTCAACACCCAGCCCT 59.379 55.000 0.00 0.00 0.00 5.19
946 998 3.243168 GCTAACCACGGATGATACACGTA 60.243 47.826 0.00 0.00 39.02 3.57
952 1004 1.607148 CGGATGATACACGTAGCTCCA 59.393 52.381 0.00 0.00 0.00 3.86
970 1022 3.869065 TCCAGTTAATAACTTCCTGCCG 58.131 45.455 2.41 0.00 40.46 5.69
1048 1103 4.108299 CCGGTACTGCATGGGCCA 62.108 66.667 9.61 9.61 40.13 5.36
1049 1104 2.045438 CGGTACTGCATGGGCCAA 60.045 61.111 11.89 0.00 40.13 4.52
1262 1321 3.128764 TCTGTCGCATGTCAACTAGTAGG 59.871 47.826 0.00 0.00 0.00 3.18
1329 1389 4.277672 TGCTAGTACACCGGATAAGATGAC 59.722 45.833 9.46 0.00 0.00 3.06
1352 1412 1.001860 TGCCATGTCAATGACGACTCA 59.998 47.619 9.00 1.92 35.67 3.41
1353 1413 2.283298 GCCATGTCAATGACGACTCAT 58.717 47.619 9.00 0.00 38.94 2.90
1354 1414 2.679837 GCCATGTCAATGACGACTCATT 59.320 45.455 9.00 0.00 46.36 2.57
1360 1420 2.479566 AATGACGACTCATTGCCACT 57.520 45.000 0.80 0.00 44.16 4.00
1361 1421 2.015736 ATGACGACTCATTGCCACTC 57.984 50.000 0.00 0.00 32.79 3.51
1367 1427 1.133790 GACTCATTGCCACTCATTGCC 59.866 52.381 0.00 0.00 0.00 4.52
1378 1438 1.408702 ACTCATTGCCACGCTTTGTTT 59.591 42.857 0.00 0.00 0.00 2.83
1381 1441 4.236935 CTCATTGCCACGCTTTGTTTAAT 58.763 39.130 0.00 0.00 0.00 1.40
1382 1442 4.626042 TCATTGCCACGCTTTGTTTAATT 58.374 34.783 0.00 0.00 0.00 1.40
1383 1443 5.773575 TCATTGCCACGCTTTGTTTAATTA 58.226 33.333 0.00 0.00 0.00 1.40
1384 1444 5.861251 TCATTGCCACGCTTTGTTTAATTAG 59.139 36.000 0.00 0.00 0.00 1.73
1385 1445 3.570559 TGCCACGCTTTGTTTAATTAGC 58.429 40.909 0.00 0.00 0.00 3.09
1402 1462 0.396435 AGCGTTCAAGTGGACCATGA 59.604 50.000 0.00 0.00 0.00 3.07
1421 1481 2.049959 GATGATCTCATCTGCGTGTCG 58.950 52.381 11.99 0.00 46.88 4.35
1422 1482 0.101219 TGATCTCATCTGCGTGTCGG 59.899 55.000 0.00 0.00 0.00 4.79
1423 1483 1.211818 GATCTCATCTGCGTGTCGGC 61.212 60.000 0.00 0.00 0.00 5.54
1432 1492 4.675029 CGTGTCGGCCCGTTCCTT 62.675 66.667 1.63 0.00 0.00 3.36
1440 1500 1.545841 GGCCCGTTCCTTTGATCTTT 58.454 50.000 0.00 0.00 0.00 2.52
1443 1503 3.344515 GCCCGTTCCTTTGATCTTTACT 58.655 45.455 0.00 0.00 0.00 2.24
1453 1513 6.874134 TCCTTTGATCTTTACTTGTCAGCTAC 59.126 38.462 0.00 0.00 0.00 3.58
1455 1515 5.086104 TGATCTTTACTTGTCAGCTACCC 57.914 43.478 0.00 0.00 0.00 3.69
1456 1516 3.975168 TCTTTACTTGTCAGCTACCCC 57.025 47.619 0.00 0.00 0.00 4.95
1457 1517 3.517612 TCTTTACTTGTCAGCTACCCCT 58.482 45.455 0.00 0.00 0.00 4.79
1458 1518 3.514309 TCTTTACTTGTCAGCTACCCCTC 59.486 47.826 0.00 0.00 0.00 4.30
1459 1519 2.921834 TACTTGTCAGCTACCCCTCT 57.078 50.000 0.00 0.00 0.00 3.69
1460 1520 1.270907 ACTTGTCAGCTACCCCTCTG 58.729 55.000 0.00 0.00 0.00 3.35
1461 1521 0.107945 CTTGTCAGCTACCCCTCTGC 60.108 60.000 0.00 0.00 0.00 4.26
1462 1522 0.835971 TTGTCAGCTACCCCTCTGCA 60.836 55.000 0.00 0.00 0.00 4.41
1463 1523 0.618680 TGTCAGCTACCCCTCTGCAT 60.619 55.000 0.00 0.00 0.00 3.96
1465 1525 1.342819 GTCAGCTACCCCTCTGCATAG 59.657 57.143 0.00 0.00 0.00 2.23
1466 1526 0.683973 CAGCTACCCCTCTGCATAGG 59.316 60.000 11.17 11.17 36.30 2.57
1472 1532 4.547859 CCTCTGCATAGGGTGTGC 57.452 61.111 10.29 0.00 42.81 4.57
1473 1533 1.522355 CCTCTGCATAGGGTGTGCG 60.522 63.158 10.29 0.00 45.37 5.34
1475 1535 1.079197 TCTGCATAGGGTGTGCGTG 60.079 57.895 0.00 0.00 45.37 5.34
1476 1536 2.046411 TGCATAGGGTGTGCGTGG 60.046 61.111 0.00 0.00 45.37 4.94
1477 1537 2.824041 GCATAGGGTGTGCGTGGG 60.824 66.667 0.00 0.00 32.29 4.61
1478 1538 2.824041 CATAGGGTGTGCGTGGGC 60.824 66.667 0.00 0.00 40.52 5.36
1479 1539 3.009115 ATAGGGTGTGCGTGGGCT 61.009 61.111 0.00 0.00 40.82 5.19
1481 1541 2.536997 ATAGGGTGTGCGTGGGCTTC 62.537 60.000 0.00 0.00 40.82 3.86
1482 1542 4.643387 GGGTGTGCGTGGGCTTCT 62.643 66.667 0.00 0.00 40.82 2.85
1484 1544 1.741770 GGTGTGCGTGGGCTTCTAG 60.742 63.158 0.00 0.00 40.82 2.43
1485 1545 1.741770 GTGTGCGTGGGCTTCTAGG 60.742 63.158 0.00 0.00 40.82 3.02
1487 1547 1.003718 GTGCGTGGGCTTCTAGGTT 60.004 57.895 0.00 0.00 40.82 3.50
1488 1548 1.003839 TGCGTGGGCTTCTAGGTTG 60.004 57.895 0.00 0.00 40.82 3.77
1489 1549 1.745489 GCGTGGGCTTCTAGGTTGG 60.745 63.158 0.00 0.00 35.83 3.77
1519 2224 1.148157 CGCCAGCCTGAGATTGTACG 61.148 60.000 0.00 0.00 0.00 3.67
1520 2225 0.108138 GCCAGCCTGAGATTGTACGT 60.108 55.000 0.00 0.00 0.00 3.57
1521 2226 1.136305 GCCAGCCTGAGATTGTACGTA 59.864 52.381 0.00 0.00 0.00 3.57
1523 2228 2.481449 CCAGCCTGAGATTGTACGTACC 60.481 54.545 22.43 7.75 0.00 3.34
1558 2264 3.992427 CAGGAAACACCCGAGTAACTAAC 59.008 47.826 0.00 0.00 40.05 2.34
1565 2271 2.365293 ACCCGAGTAACTAACGTTTGGT 59.635 45.455 5.91 5.65 34.59 3.67
1580 2286 4.538917 CGTTTGGTACGGCTGTAATTTTT 58.461 39.130 7.05 0.00 46.42 1.94
1605 2311 3.435890 CCAGTTTTGGTCTTAAGGGGTGA 60.436 47.826 1.85 0.00 39.79 4.02
1631 2337 4.348461 TGTGTGGGAAGATAACTGTACCAA 59.652 41.667 0.00 0.00 0.00 3.67
1632 2338 5.163184 TGTGTGGGAAGATAACTGTACCAAA 60.163 40.000 0.00 0.00 0.00 3.28
1634 2340 7.107542 GTGTGGGAAGATAACTGTACCAAATA 58.892 38.462 0.00 0.00 0.00 1.40
1635 2341 7.608761 GTGTGGGAAGATAACTGTACCAAATAA 59.391 37.037 0.00 0.00 0.00 1.40
1731 2437 2.753055 GGATTTCCTAGAGGATCCGC 57.247 55.000 7.52 7.52 44.98 5.54
1742 2448 4.383931 AGAGGATCCGCTAATAGTGGTA 57.616 45.455 17.38 7.04 45.85 3.25
1882 2588 8.482943 TGAGCTATTTAGATTTTAGTGCCTACA 58.517 33.333 0.00 0.00 0.00 2.74
1883 2589 9.495572 GAGCTATTTAGATTTTAGTGCCTACAT 57.504 33.333 0.00 0.00 0.00 2.29
1914 2621 9.956720 CTGAAAAATTAAGGGATGTATCATGAC 57.043 33.333 0.00 0.00 0.00 3.06
1924 2631 4.818546 GGATGTATCATGACACTCCAAAGG 59.181 45.833 14.19 0.00 32.09 3.11
2137 2844 7.283127 AGGTTAGTAGATAATGCAATGGTGTTG 59.717 37.037 0.00 0.00 0.00 3.33
2143 2850 1.058284 ATGCAATGGTGTTGGCCTTT 58.942 45.000 3.32 0.00 0.00 3.11
2462 3215 7.645058 TCTTTGACAGGTTTGAATTTCTCTT 57.355 32.000 0.00 0.00 0.00 2.85
2463 3216 7.707104 TCTTTGACAGGTTTGAATTTCTCTTC 58.293 34.615 0.00 0.00 0.00 2.87
2522 3277 8.234546 TGTTCTTTGAACTAACTTTTGAGTGAC 58.765 33.333 11.06 0.00 0.00 3.67
2541 3296 7.385752 TGAGTGACCACGGTTTAATAACTTTAG 59.614 37.037 0.00 0.00 34.59 1.85
2600 3357 1.358725 CTGTTGGCATACCGTCGGTG 61.359 60.000 27.20 12.34 39.70 4.94
2679 3436 9.748100 GCGCTTATTTTTCTTAGAGATAATAGC 57.252 33.333 0.00 0.00 0.00 2.97
2741 3498 4.762251 ACTCAAAAATCCTACAGGCAGTTC 59.238 41.667 0.00 0.00 34.44 3.01
2746 3503 6.731292 AAAATCCTACAGGCAGTTCTTTTT 57.269 33.333 0.00 0.00 34.44 1.94
2747 3504 7.833285 AAAATCCTACAGGCAGTTCTTTTTA 57.167 32.000 0.00 0.00 34.44 1.52
2799 3558 6.511767 CGTCCACCTTAAATATTCATGCTGTC 60.512 42.308 0.00 0.00 0.00 3.51
2855 3628 8.231161 GTCTAACCTTTAATCAAGCTTTCTGAC 58.769 37.037 0.00 0.00 0.00 3.51
2982 3755 7.923888 CAATCAATTGGTACTGGAAGTGATAG 58.076 38.462 5.42 0.00 40.07 2.08
3002 3775 2.422127 AGACTAGCTCGAGTTGCTCTTC 59.578 50.000 15.13 6.12 41.46 2.87
3091 3864 5.975693 TTTGGTTAGATGTTCCATTGGAC 57.024 39.130 4.45 1.74 0.00 4.02
3118 3891 0.883833 CAAGAAGGATTGCTGCGGTT 59.116 50.000 0.00 0.00 0.00 4.44
3233 4006 2.746362 GAGTTTGGAATGCAGACAGAGG 59.254 50.000 0.00 0.00 0.00 3.69
3407 4191 9.347934 CTTGTTTCATTCTAGTACTCTGTACTG 57.652 37.037 17.52 9.58 0.00 2.74
3430 4214 1.640670 ACAAAGGCCTACATGGTCCAT 59.359 47.619 5.16 0.00 42.71 3.41
3487 4271 4.700213 ACACCATTGCTGACTGTAAATACC 59.300 41.667 0.00 0.00 0.00 2.73
3612 4397 6.834168 TGGTTAAGATGATCTTTTGAACCC 57.166 37.500 24.73 13.78 39.85 4.11
3644 4429 3.939592 GGGAATTCTACCTTCCGTTCTTG 59.060 47.826 5.23 0.00 42.63 3.02
3720 4505 1.192428 ACCAGATCTCGGTGGTTACC 58.808 55.000 13.91 0.00 45.17 2.85
3972 4770 5.522097 CCCTTGTACATTTTGAAACAACCAC 59.478 40.000 0.00 0.00 0.00 4.16
4067 4867 4.868171 ACAAGTATGTACGTTACAGCATGG 59.132 41.667 0.00 0.00 42.77 3.66
4073 4873 1.734163 ACGTTACAGCATGGTAAGGC 58.266 50.000 0.00 0.00 43.62 4.35
4113 4913 8.171164 TCGAGATATGTACATGTTCTCTCAAT 57.829 34.615 29.12 12.73 33.18 2.57
4179 4981 4.592485 AGCCAATAGTTAGATCTGACCG 57.408 45.455 13.65 1.31 0.00 4.79
4200 5002 6.817184 ACCGATTTGATAATGCTACTGTACT 58.183 36.000 0.00 0.00 0.00 2.73
4274 5076 3.015327 ACATTGCAGGAAGCTGAGATTC 58.985 45.455 1.05 1.05 45.94 2.52
4472 5280 8.151596 TCTGGATTTATAAATACACGCCACATA 58.848 33.333 17.58 2.69 34.38 2.29
4627 5435 3.308402 CCTTTCTCCCCAGTGCTTTCATA 60.308 47.826 0.00 0.00 0.00 2.15
4633 5441 2.173356 CCCCAGTGCTTTCATATCCAGA 59.827 50.000 0.00 0.00 0.00 3.86
4655 5463 3.921677 AGCCTGCAAAACTTGAATGATG 58.078 40.909 0.00 0.00 0.00 3.07
4673 5481 2.495155 TGAATGCAGGCTACACACAT 57.505 45.000 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.153745 GCACGCTCGACATCCTTCT 60.154 57.895 0.00 0.00 0.00 2.85
105 106 2.039480 ACACAAGCAGTCATCACCTCAT 59.961 45.455 0.00 0.00 0.00 2.90
106 107 1.417517 ACACAAGCAGTCATCACCTCA 59.582 47.619 0.00 0.00 0.00 3.86
171 172 2.955614 ACTGAAACCCTTGATCGTACG 58.044 47.619 9.53 9.53 0.00 3.67
195 196 1.270550 CAAGCACAACATTCTCACCCC 59.729 52.381 0.00 0.00 0.00 4.95
213 214 2.586245 CCGCTCCTCCATGCTCAA 59.414 61.111 0.00 0.00 0.00 3.02
242 247 2.420022 CACGATGGAATTGGGTGAACTC 59.580 50.000 0.00 0.00 29.54 3.01
261 266 1.164411 TTCCCAATCACGCATGTCAC 58.836 50.000 0.00 0.00 0.00 3.67
288 293 2.801679 ACCAAATCATTTTGCAGTTGCG 59.198 40.909 0.00 0.00 45.83 4.85
311 316 3.198068 CAACATGAGCCTACGTATGCTT 58.802 45.455 23.53 8.73 38.11 3.91
318 323 0.447801 GTTGCCAACATGAGCCTACG 59.552 55.000 1.91 0.00 0.00 3.51
321 326 0.469705 TTGGTTGCCAACATGAGCCT 60.470 50.000 10.18 0.00 38.75 4.58
350 355 6.767423 ACAGTTTTGCAAGCCAAATAAAGAAT 59.233 30.769 0.00 0.00 42.63 2.40
374 379 9.944663 TTGAATACAAGTAAAAATGTCTCACAC 57.055 29.630 0.00 0.00 0.00 3.82
450 467 8.597662 GCTTTTGCATTCAAACATATGGATAT 57.402 30.769 7.80 0.00 46.58 1.63
452 469 6.913873 GCTTTTGCATTCAAACATATGGAT 57.086 33.333 7.80 0.00 46.58 3.41
496 526 2.521451 TTGGCCGCCCTACTCAACA 61.521 57.895 7.03 0.00 0.00 3.33
497 527 2.038837 GTTGGCCGCCCTACTCAAC 61.039 63.158 7.03 0.00 34.54 3.18
499 529 3.712907 GGTTGGCCGCCCTACTCA 61.713 66.667 7.03 0.00 37.10 3.41
520 550 5.420739 GCCCTGTTTTAGATTTGGATTGGTA 59.579 40.000 0.00 0.00 0.00 3.25
523 553 4.423732 CGCCCTGTTTTAGATTTGGATTG 58.576 43.478 0.00 0.00 0.00 2.67
524 554 3.447229 CCGCCCTGTTTTAGATTTGGATT 59.553 43.478 0.00 0.00 0.00 3.01
525 555 3.023832 CCGCCCTGTTTTAGATTTGGAT 58.976 45.455 0.00 0.00 0.00 3.41
526 556 2.442413 CCGCCCTGTTTTAGATTTGGA 58.558 47.619 0.00 0.00 0.00 3.53
527 557 1.476488 CCCGCCCTGTTTTAGATTTGG 59.524 52.381 0.00 0.00 0.00 3.28
528 558 1.135112 GCCCGCCCTGTTTTAGATTTG 60.135 52.381 0.00 0.00 0.00 2.32
529 559 1.182667 GCCCGCCCTGTTTTAGATTT 58.817 50.000 0.00 0.00 0.00 2.17
530 560 0.683179 GGCCCGCCCTGTTTTAGATT 60.683 55.000 0.00 0.00 0.00 2.40
531 561 1.076995 GGCCCGCCCTGTTTTAGAT 60.077 57.895 0.00 0.00 0.00 1.98
532 562 2.193087 GAGGCCCGCCCTGTTTTAGA 62.193 60.000 0.00 0.00 46.60 2.10
533 563 1.749258 GAGGCCCGCCCTGTTTTAG 60.749 63.158 0.00 0.00 46.60 1.85
534 564 2.353573 GAGGCCCGCCCTGTTTTA 59.646 61.111 0.00 0.00 46.60 1.52
554 584 3.936203 TATGGATCGGCCGCCCAC 61.936 66.667 31.85 18.46 40.66 4.61
555 585 3.936203 GTATGGATCGGCCGCCCA 61.936 66.667 31.49 31.49 40.66 5.36
558 588 3.986006 TCCGTATGGATCGGCCGC 61.986 66.667 23.51 7.37 46.49 6.53
578 608 1.470112 CGGTGGTTTTGTCCGCTTTTT 60.470 47.619 0.00 0.00 37.90 1.94
579 609 0.101579 CGGTGGTTTTGTCCGCTTTT 59.898 50.000 0.00 0.00 37.90 2.27
580 610 1.033202 ACGGTGGTTTTGTCCGCTTT 61.033 50.000 2.72 0.00 46.92 3.51
581 611 1.033202 AACGGTGGTTTTGTCCGCTT 61.033 50.000 2.72 0.00 46.92 4.68
582 612 1.441732 GAACGGTGGTTTTGTCCGCT 61.442 55.000 2.72 0.00 46.92 5.52
583 613 1.009335 GAACGGTGGTTTTGTCCGC 60.009 57.895 2.72 0.00 46.92 5.54
585 615 0.734309 AACGAACGGTGGTTTTGTCC 59.266 50.000 0.00 0.00 36.24 4.02
586 616 2.178783 CAAACGAACGGTGGTTTTGTC 58.821 47.619 11.16 0.00 33.86 3.18
587 617 1.135344 CCAAACGAACGGTGGTTTTGT 60.135 47.619 11.16 0.00 33.86 2.83
588 618 1.132643 TCCAAACGAACGGTGGTTTTG 59.867 47.619 11.16 8.30 33.86 2.44
589 619 1.461559 TCCAAACGAACGGTGGTTTT 58.538 45.000 11.16 0.00 33.86 2.43
590 620 1.605232 GATCCAAACGAACGGTGGTTT 59.395 47.619 7.86 7.86 36.24 3.27
591 621 1.232119 GATCCAAACGAACGGTGGTT 58.768 50.000 15.12 0.00 39.63 3.67
592 622 0.947180 CGATCCAAACGAACGGTGGT 60.947 55.000 15.12 0.00 33.43 4.16
593 623 0.668096 TCGATCCAAACGAACGGTGG 60.668 55.000 11.22 11.22 37.37 4.61
594 624 0.437295 GTCGATCCAAACGAACGGTG 59.563 55.000 0.00 0.00 41.31 4.94
595 625 0.668401 GGTCGATCCAAACGAACGGT 60.668 55.000 0.00 0.00 41.31 4.83
596 626 1.356527 GGGTCGATCCAAACGAACGG 61.357 60.000 10.69 0.00 46.52 4.44
597 627 0.389426 AGGGTCGATCCAAACGAACG 60.389 55.000 19.03 0.00 46.52 3.95
598 628 2.660189 TAGGGTCGATCCAAACGAAC 57.340 50.000 19.03 0.00 45.13 3.95
599 629 2.761767 TCATAGGGTCGATCCAAACGAA 59.238 45.455 19.03 0.00 41.31 3.85
600 630 2.380941 TCATAGGGTCGATCCAAACGA 58.619 47.619 19.03 4.71 38.11 3.85
601 631 2.882927 TCATAGGGTCGATCCAAACG 57.117 50.000 19.03 2.07 38.11 3.60
602 632 4.138487 ACTTCATAGGGTCGATCCAAAC 57.862 45.455 19.03 0.00 38.11 2.93
603 633 4.513442 CAACTTCATAGGGTCGATCCAAA 58.487 43.478 19.03 4.65 38.11 3.28
604 634 3.681594 GCAACTTCATAGGGTCGATCCAA 60.682 47.826 19.03 0.69 38.11 3.53
605 635 2.158957 GCAACTTCATAGGGTCGATCCA 60.159 50.000 19.03 3.12 38.11 3.41
606 636 2.103263 AGCAACTTCATAGGGTCGATCC 59.897 50.000 6.61 6.61 0.00 3.36
607 637 3.068873 AGAGCAACTTCATAGGGTCGATC 59.931 47.826 0.00 0.00 33.29 3.69
608 638 3.034635 AGAGCAACTTCATAGGGTCGAT 58.965 45.455 0.00 0.00 33.29 3.59
609 639 2.427453 GAGAGCAACTTCATAGGGTCGA 59.573 50.000 0.00 0.00 33.29 4.20
610 640 2.166459 TGAGAGCAACTTCATAGGGTCG 59.834 50.000 0.00 0.00 33.29 4.79
611 641 3.895232 TGAGAGCAACTTCATAGGGTC 57.105 47.619 0.00 0.00 0.00 4.46
612 642 5.543507 CTATGAGAGCAACTTCATAGGGT 57.456 43.478 11.74 0.00 38.70 4.34
625 655 3.368843 TCAGTTTCCTGTGCTATGAGAGC 60.369 47.826 0.00 0.00 43.65 4.09
626 656 4.462508 TCAGTTTCCTGTGCTATGAGAG 57.537 45.455 0.00 0.00 39.82 3.20
627 657 4.440663 CGATCAGTTTCCTGTGCTATGAGA 60.441 45.833 0.00 0.00 39.82 3.27
628 658 3.801050 CGATCAGTTTCCTGTGCTATGAG 59.199 47.826 0.00 0.00 39.82 2.90
629 659 3.785486 CGATCAGTTTCCTGTGCTATGA 58.215 45.455 0.00 0.00 39.82 2.15
630 660 2.286294 GCGATCAGTTTCCTGTGCTATG 59.714 50.000 0.00 0.00 39.82 2.23
631 661 2.169352 AGCGATCAGTTTCCTGTGCTAT 59.831 45.455 0.00 0.00 39.30 2.97
632 662 1.550524 AGCGATCAGTTTCCTGTGCTA 59.449 47.619 0.00 0.00 39.30 3.49
652 682 5.588246 GCACAAAATCCCAAGAAAAGGAAAA 59.412 36.000 0.00 0.00 35.30 2.29
679 709 1.375326 GAGAAGCCCGGGACTGTTT 59.625 57.895 29.31 9.63 0.00 2.83
800 834 2.004589 AGACAGAAGAGGTAGAGGGGT 58.995 52.381 0.00 0.00 0.00 4.95
801 835 2.243736 AGAGACAGAAGAGGTAGAGGGG 59.756 54.545 0.00 0.00 0.00 4.79
803 837 4.855340 AGAAGAGACAGAAGAGGTAGAGG 58.145 47.826 0.00 0.00 0.00 3.69
804 838 5.357032 GGAAGAAGAGACAGAAGAGGTAGAG 59.643 48.000 0.00 0.00 0.00 2.43
806 840 4.401202 GGGAAGAAGAGACAGAAGAGGTAG 59.599 50.000 0.00 0.00 0.00 3.18
807 841 4.044825 AGGGAAGAAGAGACAGAAGAGGTA 59.955 45.833 0.00 0.00 0.00 3.08
808 842 3.169908 GGGAAGAAGAGACAGAAGAGGT 58.830 50.000 0.00 0.00 0.00 3.85
809 843 3.440127 AGGGAAGAAGAGACAGAAGAGG 58.560 50.000 0.00 0.00 0.00 3.69
812 846 3.056179 GTGGAGGGAAGAAGAGACAGAAG 60.056 52.174 0.00 0.00 0.00 2.85
917 969 1.264749 ATCCGTGGTTAGCAGAGGCA 61.265 55.000 1.71 0.00 44.61 4.75
946 998 4.518249 GCAGGAAGTTATTAACTGGAGCT 58.482 43.478 9.78 0.00 41.91 4.09
952 1004 3.532542 GAGCGGCAGGAAGTTATTAACT 58.467 45.455 1.45 3.16 45.46 2.24
1036 1091 2.115052 TCGTTTGGCCCATGCAGT 59.885 55.556 0.00 0.00 40.13 4.40
1094 1149 1.667154 CGGATTCTGGTCGAGCCTCA 61.667 60.000 12.85 0.00 38.35 3.86
1190 1245 1.588082 GATTTGTGGCAGCACAGGG 59.412 57.895 0.00 0.00 36.35 4.45
1262 1321 0.598065 AGTTGGCGGCAGAAATTGTC 59.402 50.000 12.87 0.00 0.00 3.18
1356 1416 0.387622 CAAAGCGTGGCAATGAGTGG 60.388 55.000 0.00 0.00 0.00 4.00
1357 1417 0.311790 ACAAAGCGTGGCAATGAGTG 59.688 50.000 0.00 0.00 0.00 3.51
1358 1418 1.032014 AACAAAGCGTGGCAATGAGT 58.968 45.000 0.00 0.00 0.00 3.41
1359 1419 2.138596 AAACAAAGCGTGGCAATGAG 57.861 45.000 0.00 0.00 0.00 2.90
1360 1420 3.717400 TTAAACAAAGCGTGGCAATGA 57.283 38.095 0.00 0.00 0.00 2.57
1361 1421 4.988708 AATTAAACAAAGCGTGGCAATG 57.011 36.364 0.00 0.00 0.00 2.82
1378 1438 4.274602 TGGTCCACTTGAACGCTAATTA 57.725 40.909 0.00 0.00 31.20 1.40
1381 1441 2.037902 TCATGGTCCACTTGAACGCTAA 59.962 45.455 0.00 0.00 31.20 3.09
1382 1442 1.621317 TCATGGTCCACTTGAACGCTA 59.379 47.619 0.00 0.00 31.20 4.26
1383 1443 0.396435 TCATGGTCCACTTGAACGCT 59.604 50.000 0.00 0.00 31.20 5.07
1384 1444 1.131126 CATCATGGTCCACTTGAACGC 59.869 52.381 0.00 0.00 36.90 4.84
1385 1445 2.698803 TCATCATGGTCCACTTGAACG 58.301 47.619 0.00 0.00 36.90 3.95
1386 1446 4.521146 AGATCATCATGGTCCACTTGAAC 58.479 43.478 0.00 0.00 36.90 3.18
1402 1462 1.269465 CCGACACGCAGATGAGATCAT 60.269 52.381 0.00 0.00 39.70 2.45
1421 1481 1.545841 AAAGATCAAAGGAACGGGCC 58.454 50.000 0.00 0.00 0.00 5.80
1422 1482 3.344515 AGTAAAGATCAAAGGAACGGGC 58.655 45.455 0.00 0.00 0.00 6.13
1423 1483 4.760204 ACAAGTAAAGATCAAAGGAACGGG 59.240 41.667 0.00 0.00 0.00 5.28
1427 1487 6.299141 AGCTGACAAGTAAAGATCAAAGGAA 58.701 36.000 0.00 0.00 0.00 3.36
1432 1492 5.488341 GGGTAGCTGACAAGTAAAGATCAA 58.512 41.667 0.00 0.00 0.00 2.57
1440 1500 2.457598 CAGAGGGGTAGCTGACAAGTA 58.542 52.381 0.00 0.00 0.00 2.24
1443 1503 0.835971 TGCAGAGGGGTAGCTGACAA 60.836 55.000 0.00 0.00 0.00 3.18
1455 1515 1.522355 CGCACACCCTATGCAGAGG 60.522 63.158 20.90 20.90 43.57 3.69
1456 1516 1.086067 CACGCACACCCTATGCAGAG 61.086 60.000 0.00 0.00 43.57 3.35
1457 1517 1.079197 CACGCACACCCTATGCAGA 60.079 57.895 0.00 0.00 43.57 4.26
1458 1518 2.108514 CCACGCACACCCTATGCAG 61.109 63.158 0.00 0.00 43.57 4.41
1459 1519 2.046411 CCACGCACACCCTATGCA 60.046 61.111 0.00 0.00 43.57 3.96
1460 1520 2.824041 CCCACGCACACCCTATGC 60.824 66.667 0.00 0.00 39.81 3.14
1461 1521 2.819984 AAGCCCACGCACACCCTATG 62.820 60.000 0.00 0.00 37.52 2.23
1462 1522 2.536997 GAAGCCCACGCACACCCTAT 62.537 60.000 0.00 0.00 37.52 2.57
1463 1523 3.246112 AAGCCCACGCACACCCTA 61.246 61.111 0.00 0.00 37.52 3.53
1465 1525 3.248446 TAGAAGCCCACGCACACCC 62.248 63.158 0.00 0.00 37.52 4.61
1466 1526 1.741770 CTAGAAGCCCACGCACACC 60.742 63.158 0.00 0.00 37.52 4.16
1467 1527 1.741770 CCTAGAAGCCCACGCACAC 60.742 63.158 0.00 0.00 37.52 3.82
1469 1529 1.003718 AACCTAGAAGCCCACGCAC 60.004 57.895 0.00 0.00 37.52 5.34
1470 1530 1.003839 CAACCTAGAAGCCCACGCA 60.004 57.895 0.00 0.00 37.52 5.24
1471 1531 1.745489 CCAACCTAGAAGCCCACGC 60.745 63.158 0.00 0.00 0.00 5.34
1472 1532 0.899720 TACCAACCTAGAAGCCCACG 59.100 55.000 0.00 0.00 0.00 4.94
1473 1533 3.646736 ATTACCAACCTAGAAGCCCAC 57.353 47.619 0.00 0.00 0.00 4.61
1475 1535 4.579340 GCTTAATTACCAACCTAGAAGCCC 59.421 45.833 0.00 0.00 33.56 5.19
1476 1536 5.066117 GTGCTTAATTACCAACCTAGAAGCC 59.934 44.000 0.00 0.00 37.78 4.35
1477 1537 5.220605 CGTGCTTAATTACCAACCTAGAAGC 60.221 44.000 0.00 0.00 38.77 3.86
1478 1538 5.220605 GCGTGCTTAATTACCAACCTAGAAG 60.221 44.000 0.00 0.00 0.00 2.85
1479 1539 4.632688 GCGTGCTTAATTACCAACCTAGAA 59.367 41.667 0.00 0.00 0.00 2.10
1481 1541 3.311596 GGCGTGCTTAATTACCAACCTAG 59.688 47.826 0.00 0.00 0.00 3.02
1482 1542 3.272581 GGCGTGCTTAATTACCAACCTA 58.727 45.455 0.00 0.00 0.00 3.08
1484 1544 1.813786 TGGCGTGCTTAATTACCAACC 59.186 47.619 0.00 0.00 0.00 3.77
1485 1545 2.731027 GCTGGCGTGCTTAATTACCAAC 60.731 50.000 0.00 0.00 0.00 3.77
1487 1547 1.091537 GCTGGCGTGCTTAATTACCA 58.908 50.000 0.00 0.00 0.00 3.25
1488 1548 0.380733 GGCTGGCGTGCTTAATTACC 59.619 55.000 2.53 0.00 0.00 2.85
1489 1549 1.064060 CAGGCTGGCGTGCTTAATTAC 59.936 52.381 6.61 0.00 0.00 1.89
1580 2286 4.219919 CCCCTTAAGACCAAAACTGGAAA 58.780 43.478 3.36 0.00 0.00 3.13
1605 2311 4.706842 ACAGTTATCTTCCCACACAACT 57.293 40.909 0.00 0.00 0.00 3.16
1631 2337 3.876341 CCATGCAACAAAGGCCATTATT 58.124 40.909 5.01 0.00 0.00 1.40
1632 2338 2.420408 GCCATGCAACAAAGGCCATTAT 60.420 45.455 5.01 0.00 41.25 1.28
1634 2340 0.321830 GCCATGCAACAAAGGCCATT 60.322 50.000 5.01 0.00 41.25 3.16
1635 2341 1.297364 GCCATGCAACAAAGGCCAT 59.703 52.632 5.01 0.00 41.25 4.40
1742 2448 5.594317 GTCCCCAACTAATATTGCTGATTGT 59.406 40.000 0.00 0.00 0.00 2.71
1890 2597 9.736023 GTGTCATGATACATCCCTTAATTTTTC 57.264 33.333 16.86 0.00 0.00 2.29
1914 2621 5.410746 CGATCCATGATATTCCTTTGGAGTG 59.589 44.000 0.00 0.00 39.68 3.51
1924 2631 7.467623 GGACTTATTTGCGATCCATGATATTC 58.532 38.462 0.00 0.00 0.00 1.75
2143 2850 6.040278 TGTGAATTTCTCCATGTAAACTTGCA 59.960 34.615 0.00 0.00 0.00 4.08
2522 3277 4.392754 ACCGCTAAAGTTATTAAACCGTGG 59.607 41.667 0.00 0.00 36.15 4.94
2541 3296 0.951040 CTGTGAAGGGAGAACACCGC 60.951 60.000 0.00 0.00 34.18 5.68
2600 3357 2.489722 GTGGACCTGAAAAATCTCAGCC 59.510 50.000 0.00 0.00 41.36 4.85
2746 3503 6.038603 GGCAAACTACATCATGCAAGAGAATA 59.961 38.462 0.00 0.00 40.51 1.75
2747 3504 5.163581 GGCAAACTACATCATGCAAGAGAAT 60.164 40.000 0.00 0.00 40.51 2.40
2855 3628 9.091784 TGAGAAGTCGAATGAAATAAGAGAATG 57.908 33.333 0.00 0.00 0.00 2.67
2982 3755 2.478879 GGAAGAGCAACTCGAGCTAGTC 60.479 54.545 13.61 4.83 43.58 2.59
3002 3775 5.453567 AAACTTAGTAAGCTTTGCCTTGG 57.546 39.130 3.20 0.00 0.00 3.61
3091 3864 0.171903 CAATCCTTCTTGCAAGGGCG 59.828 55.000 25.73 13.80 45.35 6.13
3220 3993 7.472334 AAAAATCATTACCTCTGTCTGCATT 57.528 32.000 0.00 0.00 0.00 3.56
3407 4191 2.289565 GACCATGTAGGCCTTTGTAGC 58.710 52.381 12.58 0.00 43.14 3.58
3612 4397 2.420687 GGTAGAATTCCCAGTCAGGCAG 60.421 54.545 0.65 0.00 35.39 4.85
3626 4411 3.600388 CTGCAAGAACGGAAGGTAGAAT 58.400 45.455 0.00 0.00 34.07 2.40
3720 4505 3.315191 ACCGTTGGTTGTCATCTTTCTTG 59.685 43.478 0.00 0.00 27.29 3.02
4054 4854 1.278127 AGCCTTACCATGCTGTAACGT 59.722 47.619 0.00 0.00 36.23 3.99
4067 4867 4.613850 CGAAAGAAAAAGAGGCAGCCTTAC 60.614 45.833 17.46 3.23 31.76 2.34
4073 4873 6.314896 ACATATCTCGAAAGAAAAAGAGGCAG 59.685 38.462 0.00 0.00 41.32 4.85
4179 4981 8.662781 TTCCAGTACAGTAGCATTATCAAATC 57.337 34.615 0.00 0.00 0.00 2.17
4200 5002 7.451731 AGATGTATAGGGAGATTTGTTTCCA 57.548 36.000 0.00 0.00 35.09 3.53
4247 5049 2.298163 CAGCTTCCTGCAATGTTTTCCT 59.702 45.455 0.00 0.00 45.94 3.36
4274 5076 5.705609 AAAGCCTACATGTACAGGTTTTG 57.294 39.130 21.86 8.71 41.90 2.44
4525 5333 2.154854 TCTGCCAGTTCTTTCTGTCG 57.845 50.000 0.00 0.00 34.02 4.35
4627 5435 2.298163 CAAGTTTTGCAGGCTTCTGGAT 59.702 45.455 0.00 0.00 38.62 3.41
4633 5441 4.039488 TCATCATTCAAGTTTTGCAGGCTT 59.961 37.500 0.00 0.00 0.00 4.35
4655 5463 2.086869 ACATGTGTGTAGCCTGCATTC 58.913 47.619 0.00 0.00 36.63 2.67


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

AutoCloner maintained by Alex Coulton.