Multiple sequence alignment - TraesCS7D01G314100

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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 TraesCS7D01G314100 chr7D 100.000 2875 0 0 1 2875 399425744 399428618 0.000000e+00 5310.0
1 TraesCS7D01G314100 chr7D 84.043 470 52 17 116 576 229270463 229270918 5.690000e-117 431.0
2 TraesCS7D01G314100 chr7D 80.282 355 51 17 38 376 629182498 629182849 1.710000e-62 250.0
3 TraesCS7D01G314100 chr7D 77.778 405 66 21 175 564 64546774 64547169 8.010000e-56 228.0
4 TraesCS7D01G314100 chr7D 82.812 128 21 1 607 733 18778840 18778713 2.340000e-21 113.0
5 TraesCS7D01G314100 chr7A 94.253 1305 50 13 747 2048 456194220 456195502 0.000000e+00 1971.0
6 TraesCS7D01G314100 chr7B 95.297 978 39 3 1072 2044 403416052 403417027 0.000000e+00 1544.0
7 TraesCS7D01G314100 chr7B 88.632 475 30 4 583 1057 403408986 403409436 9.000000e-155 556.0
8 TraesCS7D01G314100 chr7B 96.121 232 9 0 815 1046 403415825 403416056 2.090000e-101 379.0
9 TraesCS7D01G314100 chr7B 76.181 487 85 24 36 505 600451701 600452173 8.010000e-56 228.0
10 TraesCS7D01G314100 chr4D 93.160 848 40 5 2033 2865 469071841 469070997 0.000000e+00 1229.0
11 TraesCS7D01G314100 chr4D 82.500 200 18 6 2043 2228 302691435 302691239 2.970000e-35 159.0
12 TraesCS7D01G314100 chr2B 93.510 832 38 4 2045 2863 158437644 158438472 0.000000e+00 1223.0
13 TraesCS7D01G314100 chr2B 85.217 115 17 0 613 727 495712542 495712656 5.030000e-23 119.0
14 TraesCS7D01G314100 chr1B 93.214 840 41 4 2035 2861 115774430 115775266 0.000000e+00 1221.0
15 TraesCS7D01G314100 chr1B 87.277 841 90 9 2039 2863 121848564 121847725 0.000000e+00 944.0
16 TraesCS7D01G314100 chr5B 95.434 679 30 1 2185 2863 614986297 614986974 0.000000e+00 1081.0
17 TraesCS7D01G314100 chr5B 94.624 93 3 2 2038 2129 54826406 54826497 2.990000e-30 143.0
18 TraesCS7D01G314100 chr6A 88.494 817 86 4 2045 2861 563195951 563196759 0.000000e+00 981.0
19 TraesCS7D01G314100 chr1D 88.087 831 79 11 2045 2861 345404397 345403573 0.000000e+00 968.0
20 TraesCS7D01G314100 chr1D 81.240 597 78 30 1 575 260888333 260887749 4.370000e-123 451.0
21 TraesCS7D01G314100 chr5D 87.879 825 85 6 2056 2865 448446089 448446913 0.000000e+00 955.0
22 TraesCS7D01G314100 chr5D 87.545 827 83 14 2057 2865 368574695 368575519 0.000000e+00 939.0
23 TraesCS7D01G314100 chr6D 94.959 615 18 1 2050 2651 140221754 140221140 0.000000e+00 952.0
24 TraesCS7D01G314100 chr6D 86.699 827 89 14 2054 2863 9200554 9201376 0.000000e+00 898.0
25 TraesCS7D01G314100 chr6D 86.643 569 52 16 2045 2597 434181785 434181225 2.450000e-170 608.0
26 TraesCS7D01G314100 chr6D 88.991 109 11 1 2037 2144 447057189 447057297 1.800000e-27 134.0
27 TraesCS7D01G314100 chr4B 87.893 826 79 12 2045 2863 1866063 1866874 0.000000e+00 952.0
28 TraesCS7D01G314100 chr2A 86.449 856 78 11 2046 2863 535734277 535735132 0.000000e+00 904.0
29 TraesCS7D01G314100 chr4A 86.435 833 96 11 2045 2863 29499502 29498673 0.000000e+00 896.0
30 TraesCS7D01G314100 chr4A 78.512 363 52 23 22 366 485391690 485392044 6.240000e-52 215.0
31 TraesCS7D01G314100 chr4A 88.991 109 12 0 2036 2144 157875996 157876104 5.000000e-28 135.0
32 TraesCS7D01G314100 chr4A 80.992 121 15 6 613 732 626779120 626779007 3.950000e-14 89.8
33 TraesCS7D01G314100 chr4A 95.349 43 2 0 613 655 626779264 626779222 5.140000e-08 69.4
34 TraesCS7D01G314100 chr3D 81.818 319 42 14 40 347 44219192 44219505 1.320000e-63 254.0
35 TraesCS7D01G314100 chr3D 79.155 355 50 21 29 365 613826898 613827246 1.040000e-54 224.0
36 TraesCS7D01G314100 chr3A 80.352 341 45 20 22 347 534321607 534321940 3.700000e-59 239.0
37 TraesCS7D01G314100 chr3B 78.919 370 52 22 17 369 60638435 60638075 8.010000e-56 228.0
38 TraesCS7D01G314100 chr5A 82.237 152 27 0 586 737 6251207 6251056 6.460000e-27 132.0


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 TraesCS7D01G314100 chr7D 399425744 399428618 2874 False 5310.0 5310 100.000 1 2875 1 chr7D.!!$F3 2874
1 TraesCS7D01G314100 chr7A 456194220 456195502 1282 False 1971.0 1971 94.253 747 2048 1 chr7A.!!$F1 1301
2 TraesCS7D01G314100 chr7B 403415825 403417027 1202 False 961.5 1544 95.709 815 2044 2 chr7B.!!$F3 1229
3 TraesCS7D01G314100 chr4D 469070997 469071841 844 True 1229.0 1229 93.160 2033 2865 1 chr4D.!!$R2 832
4 TraesCS7D01G314100 chr2B 158437644 158438472 828 False 1223.0 1223 93.510 2045 2863 1 chr2B.!!$F1 818
5 TraesCS7D01G314100 chr1B 115774430 115775266 836 False 1221.0 1221 93.214 2035 2861 1 chr1B.!!$F1 826
6 TraesCS7D01G314100 chr1B 121847725 121848564 839 True 944.0 944 87.277 2039 2863 1 chr1B.!!$R1 824
7 TraesCS7D01G314100 chr5B 614986297 614986974 677 False 1081.0 1081 95.434 2185 2863 1 chr5B.!!$F2 678
8 TraesCS7D01G314100 chr6A 563195951 563196759 808 False 981.0 981 88.494 2045 2861 1 chr6A.!!$F1 816
9 TraesCS7D01G314100 chr1D 345403573 345404397 824 True 968.0 968 88.087 2045 2861 1 chr1D.!!$R2 816
10 TraesCS7D01G314100 chr1D 260887749 260888333 584 True 451.0 451 81.240 1 575 1 chr1D.!!$R1 574
11 TraesCS7D01G314100 chr5D 448446089 448446913 824 False 955.0 955 87.879 2056 2865 1 chr5D.!!$F2 809
12 TraesCS7D01G314100 chr5D 368574695 368575519 824 False 939.0 939 87.545 2057 2865 1 chr5D.!!$F1 808
13 TraesCS7D01G314100 chr6D 140221140 140221754 614 True 952.0 952 94.959 2050 2651 1 chr6D.!!$R1 601
14 TraesCS7D01G314100 chr6D 9200554 9201376 822 False 898.0 898 86.699 2054 2863 1 chr6D.!!$F1 809
15 TraesCS7D01G314100 chr6D 434181225 434181785 560 True 608.0 608 86.643 2045 2597 1 chr6D.!!$R2 552
16 TraesCS7D01G314100 chr4B 1866063 1866874 811 False 952.0 952 87.893 2045 2863 1 chr4B.!!$F1 818
17 TraesCS7D01G314100 chr2A 535734277 535735132 855 False 904.0 904 86.449 2046 2863 1 chr2A.!!$F1 817
18 TraesCS7D01G314100 chr4A 29498673 29499502 829 True 896.0 896 86.435 2045 2863 1 chr4A.!!$R1 818

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
615 664 0.107831 CCTGTTTGGGAACGTCCTCA 59.892 55.0 0.0 0.0 38.65 3.86 F
1067 1145 0.107945 GTGCTGATCCTGGTCTGGTC 60.108 60.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1805 0.531532 CATGTCCGTCCCAGATCTGC 60.532 60.000 17.76 2.95 0.00 4.26 R
2080 2166 1.808343 GGCTGCATGCATCGATTGATA 59.192 47.619 22.97 0.00 45.15 2.15 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
39 40 7.190871 ACGTGAACTTTTACAAATTCGTGAAT 58.809 30.769 0.00 0.00 0.00 2.57
40 41 8.336806 ACGTGAACTTTTACAAATTCGTGAATA 58.663 29.630 0.00 0.00 0.00 1.75
120 144 9.840427 CGATGAACTATTTTAAACCAATGAACT 57.160 29.630 0.00 0.00 0.00 3.01
146 171 8.541133 TTTTTCAAAACCGATGAACTCTTTTT 57.459 26.923 0.00 0.00 36.57 1.94
153 178 6.451064 ACCGATGAACTCTTTTTCAAAACT 57.549 33.333 0.00 0.00 38.95 2.66
161 186 9.874205 TGAACTCTTTTTCAAAACTGAATGAAT 57.126 25.926 0.00 0.00 35.63 2.57
235 281 6.961576 TCGATGAACTTTTTACAAAACCGAT 58.038 32.000 0.00 0.00 0.00 4.18
239 285 7.743520 TGAACTTTTTACAAAACCGATGAAC 57.256 32.000 0.00 0.00 0.00 3.18
291 337 8.477984 TTTCTGATTTTGTGAACTTCTTTTGG 57.522 30.769 0.00 0.00 0.00 3.28
292 338 6.572519 TCTGATTTTGTGAACTTCTTTTGGG 58.427 36.000 0.00 0.00 0.00 4.12
295 341 6.816140 TGATTTTGTGAACTTCTTTTGGGAAC 59.184 34.615 0.00 0.00 0.00 3.62
353 399 7.830217 TGAATTCGTGAACTTTTTGAATACG 57.170 32.000 0.04 0.00 0.00 3.06
412 460 5.126222 TGTGGAGTTTTGAATTTAGTGCACA 59.874 36.000 21.04 1.84 39.98 4.57
415 463 6.922957 TGGAGTTTTGAATTTAGTGCACATTC 59.077 34.615 21.04 18.75 0.00 2.67
417 465 7.653311 GGAGTTTTGAATTTAGTGCACATTCTT 59.347 33.333 21.04 7.03 0.00 2.52
418 466 8.356533 AGTTTTGAATTTAGTGCACATTCTTG 57.643 30.769 21.04 0.00 0.00 3.02
419 467 7.981225 AGTTTTGAATTTAGTGCACATTCTTGT 59.019 29.630 21.04 0.00 36.15 3.16
420 468 7.928908 TTTGAATTTAGTGCACATTCTTGTC 57.071 32.000 21.04 7.72 32.34 3.18
424 472 7.978414 TGAATTTAGTGCACATTCTTGTCAAAA 59.022 29.630 21.04 3.95 32.34 2.44
492 541 5.510671 AGCAATGTACGTGCAATAAATAGC 58.489 37.500 19.92 1.52 44.74 2.97
493 542 5.065859 AGCAATGTACGTGCAATAAATAGCA 59.934 36.000 19.92 0.00 44.74 3.49
502 551 5.455392 GTGCAATAAATAGCATGGCTACAG 58.545 41.667 0.00 0.00 44.24 2.74
508 557 7.736447 ATAAATAGCATGGCTACAGTTCTTC 57.264 36.000 0.00 0.00 44.24 2.87
520 569 8.562892 TGGCTACAGTTCTTCGTACTTATATAC 58.437 37.037 0.00 0.00 0.00 1.47
527 576 6.849588 TCTTCGTACTTATATACTGTCGCA 57.150 37.500 0.00 0.00 0.00 5.10
533 582 8.864024 TCGTACTTATATACTGTCGCACTATAC 58.136 37.037 0.00 0.00 0.00 1.47
543 592 6.806751 ACTGTCGCACTATACTATTTCACAT 58.193 36.000 0.00 0.00 0.00 3.21
546 595 6.475402 TGTCGCACTATACTATTTCACATGTG 59.525 38.462 20.18 20.18 0.00 3.21
578 627 2.835431 TGGCCAACAAACCACCGG 60.835 61.111 0.61 0.00 0.00 5.28
579 628 4.293648 GGCCAACAAACCACCGGC 62.294 66.667 0.00 0.00 42.21 6.13
580 629 4.639171 GCCAACAAACCACCGGCG 62.639 66.667 0.00 0.00 32.14 6.46
581 630 4.639171 CCAACAAACCACCGGCGC 62.639 66.667 0.00 0.00 0.00 6.53
582 631 3.591835 CAACAAACCACCGGCGCT 61.592 61.111 7.64 0.00 0.00 5.92
583 632 3.284449 AACAAACCACCGGCGCTC 61.284 61.111 7.64 0.00 0.00 5.03
584 633 3.767630 AACAAACCACCGGCGCTCT 62.768 57.895 7.64 0.00 0.00 4.09
585 634 3.423154 CAAACCACCGGCGCTCTC 61.423 66.667 7.64 0.00 0.00 3.20
590 639 4.717629 CACCGGCGCTCTCGTCAA 62.718 66.667 7.64 0.00 41.03 3.18
591 640 3.760035 ACCGGCGCTCTCGTCAAT 61.760 61.111 7.64 0.00 41.03 2.57
592 641 2.411701 CCGGCGCTCTCGTCAATA 59.588 61.111 7.64 0.00 41.03 1.90
593 642 1.226859 CCGGCGCTCTCGTCAATAA 60.227 57.895 7.64 0.00 41.03 1.40
594 643 0.597637 CCGGCGCTCTCGTCAATAAT 60.598 55.000 7.64 0.00 41.03 1.28
595 644 0.778815 CGGCGCTCTCGTCAATAATC 59.221 55.000 7.64 0.00 41.03 1.75
596 645 1.140816 GGCGCTCTCGTCAATAATCC 58.859 55.000 7.64 0.00 40.61 3.01
597 646 1.140816 GCGCTCTCGTCAATAATCCC 58.859 55.000 0.00 0.00 38.14 3.85
598 647 1.269831 GCGCTCTCGTCAATAATCCCT 60.270 52.381 0.00 0.00 38.14 4.20
599 648 2.398498 CGCTCTCGTCAATAATCCCTG 58.602 52.381 0.00 0.00 0.00 4.45
600 649 2.223829 CGCTCTCGTCAATAATCCCTGT 60.224 50.000 0.00 0.00 0.00 4.00
601 650 3.738281 CGCTCTCGTCAATAATCCCTGTT 60.738 47.826 0.00 0.00 0.00 3.16
602 651 4.192317 GCTCTCGTCAATAATCCCTGTTT 58.808 43.478 0.00 0.00 0.00 2.83
603 652 4.034510 GCTCTCGTCAATAATCCCTGTTTG 59.965 45.833 0.00 0.00 0.00 2.93
604 653 4.513442 TCTCGTCAATAATCCCTGTTTGG 58.487 43.478 0.00 0.00 0.00 3.28
614 663 2.928416 CCTGTTTGGGAACGTCCTC 58.072 57.895 0.00 0.00 38.65 3.71
615 664 0.107831 CCTGTTTGGGAACGTCCTCA 59.892 55.000 0.00 0.00 38.65 3.86
616 665 1.476110 CCTGTTTGGGAACGTCCTCAA 60.476 52.381 0.00 0.00 38.65 3.02
617 666 1.873591 CTGTTTGGGAACGTCCTCAAG 59.126 52.381 0.00 0.00 38.65 3.02
618 667 1.235724 GTTTGGGAACGTCCTCAAGG 58.764 55.000 0.00 0.00 36.57 3.61
619 668 0.841289 TTTGGGAACGTCCTCAAGGT 59.159 50.000 0.00 0.00 36.57 3.50
620 669 0.841289 TTGGGAACGTCCTCAAGGTT 59.159 50.000 0.00 0.00 38.63 3.50
621 670 0.841289 TGGGAACGTCCTCAAGGTTT 59.159 50.000 0.00 0.00 36.15 3.27
622 671 2.048601 TGGGAACGTCCTCAAGGTTTA 58.951 47.619 0.00 0.00 36.15 2.01
623 672 2.438763 TGGGAACGTCCTCAAGGTTTAA 59.561 45.455 0.00 0.00 36.15 1.52
624 673 3.117963 TGGGAACGTCCTCAAGGTTTAAA 60.118 43.478 0.00 0.00 36.15 1.52
625 674 3.884693 GGGAACGTCCTCAAGGTTTAAAA 59.115 43.478 0.00 0.00 36.15 1.52
626 675 4.521639 GGGAACGTCCTCAAGGTTTAAAAT 59.478 41.667 0.00 0.00 36.15 1.82
627 676 5.706833 GGGAACGTCCTCAAGGTTTAAAATA 59.293 40.000 0.00 0.00 36.15 1.40
628 677 6.128090 GGGAACGTCCTCAAGGTTTAAAATAG 60.128 42.308 0.00 0.00 36.15 1.73
629 678 6.652062 GGAACGTCCTCAAGGTTTAAAATAGA 59.348 38.462 0.00 0.00 36.15 1.98
630 679 7.360691 GGAACGTCCTCAAGGTTTAAAATAGAC 60.361 40.741 0.00 0.00 36.15 2.59
631 680 5.936372 ACGTCCTCAAGGTTTAAAATAGACC 59.064 40.000 0.00 0.00 36.34 3.85
632 681 5.063060 CGTCCTCAAGGTTTAAAATAGACCG 59.937 44.000 0.00 0.00 38.48 4.79
633 682 5.353400 GTCCTCAAGGTTTAAAATAGACCGG 59.647 44.000 0.00 0.00 38.48 5.28
634 683 5.248934 TCCTCAAGGTTTAAAATAGACCGGA 59.751 40.000 9.46 0.00 38.48 5.14
635 684 5.941647 CCTCAAGGTTTAAAATAGACCGGAA 59.058 40.000 9.46 0.00 38.48 4.30
636 685 6.602009 CCTCAAGGTTTAAAATAGACCGGAAT 59.398 38.462 9.46 0.00 38.48 3.01
637 686 7.201705 CCTCAAGGTTTAAAATAGACCGGAATC 60.202 40.741 9.46 0.00 38.48 2.52
638 687 7.169591 TCAAGGTTTAAAATAGACCGGAATCA 58.830 34.615 9.46 0.00 38.48 2.57
639 688 7.666388 TCAAGGTTTAAAATAGACCGGAATCAA 59.334 33.333 9.46 0.00 38.48 2.57
640 689 8.301002 CAAGGTTTAAAATAGACCGGAATCAAA 58.699 33.333 9.46 0.00 38.48 2.69
641 690 8.051901 AGGTTTAAAATAGACCGGAATCAAAG 57.948 34.615 9.46 0.00 38.48 2.77
642 691 7.886446 AGGTTTAAAATAGACCGGAATCAAAGA 59.114 33.333 9.46 0.00 38.48 2.52
643 692 8.517056 GGTTTAAAATAGACCGGAATCAAAGAA 58.483 33.333 9.46 0.00 0.00 2.52
647 696 6.604735 AATAGACCGGAATCAAAGAATTCG 57.395 37.500 9.46 0.00 36.66 3.34
648 697 3.270877 AGACCGGAATCAAAGAATTCGG 58.729 45.455 9.46 0.37 36.66 4.30
649 698 3.007635 GACCGGAATCAAAGAATTCGGT 58.992 45.455 9.46 7.14 41.19 4.69
650 699 2.747446 ACCGGAATCAAAGAATTCGGTG 59.253 45.455 9.46 2.53 39.18 4.94
651 700 2.747446 CCGGAATCAAAGAATTCGGTGT 59.253 45.455 0.00 0.00 36.66 4.16
652 701 3.426159 CCGGAATCAAAGAATTCGGTGTG 60.426 47.826 0.00 0.00 36.66 3.82
653 702 3.501950 GGAATCAAAGAATTCGGTGTGC 58.498 45.455 0.00 0.00 36.66 4.57
654 703 3.191371 GGAATCAAAGAATTCGGTGTGCT 59.809 43.478 0.00 0.00 36.66 4.40
655 704 4.394920 GGAATCAAAGAATTCGGTGTGCTA 59.605 41.667 0.00 0.00 36.66 3.49
656 705 5.106317 GGAATCAAAGAATTCGGTGTGCTAA 60.106 40.000 0.00 0.00 36.66 3.09
657 706 6.404734 GGAATCAAAGAATTCGGTGTGCTAAT 60.405 38.462 0.00 0.00 36.66 1.73
658 707 5.957842 TCAAAGAATTCGGTGTGCTAATT 57.042 34.783 0.00 0.00 0.00 1.40
659 708 6.325919 TCAAAGAATTCGGTGTGCTAATTT 57.674 33.333 0.00 0.00 0.00 1.82
660 709 6.378582 TCAAAGAATTCGGTGTGCTAATTTC 58.621 36.000 0.00 0.00 0.00 2.17
661 710 4.965119 AGAATTCGGTGTGCTAATTTCC 57.035 40.909 0.00 0.00 0.00 3.13
662 711 4.331968 AGAATTCGGTGTGCTAATTTCCA 58.668 39.130 0.00 0.00 0.00 3.53
663 712 4.764823 AGAATTCGGTGTGCTAATTTCCAA 59.235 37.500 0.00 0.00 0.00 3.53
664 713 4.701956 ATTCGGTGTGCTAATTTCCAAG 57.298 40.909 0.00 0.00 0.00 3.61
665 714 3.410631 TCGGTGTGCTAATTTCCAAGA 57.589 42.857 0.00 0.00 0.00 3.02
666 715 3.950397 TCGGTGTGCTAATTTCCAAGAT 58.050 40.909 0.00 0.00 0.00 2.40
667 716 4.331968 TCGGTGTGCTAATTTCCAAGATT 58.668 39.130 0.00 0.00 0.00 2.40
668 717 5.492895 TCGGTGTGCTAATTTCCAAGATTA 58.507 37.500 0.00 0.00 0.00 1.75
669 718 5.353123 TCGGTGTGCTAATTTCCAAGATTAC 59.647 40.000 0.00 0.00 0.00 1.89
670 719 5.123186 CGGTGTGCTAATTTCCAAGATTACA 59.877 40.000 0.00 0.00 0.00 2.41
671 720 6.348950 CGGTGTGCTAATTTCCAAGATTACAA 60.349 38.462 0.00 0.00 0.00 2.41
672 721 7.029563 GGTGTGCTAATTTCCAAGATTACAAG 58.970 38.462 0.00 0.00 0.00 3.16
673 722 7.309194 GGTGTGCTAATTTCCAAGATTACAAGT 60.309 37.037 0.00 0.00 0.00 3.16
674 723 8.082242 GTGTGCTAATTTCCAAGATTACAAGTT 58.918 33.333 0.00 0.00 0.00 2.66
675 724 8.296713 TGTGCTAATTTCCAAGATTACAAGTTC 58.703 33.333 0.00 0.00 0.00 3.01
676 725 8.296713 GTGCTAATTTCCAAGATTACAAGTTCA 58.703 33.333 0.00 0.00 0.00 3.18
677 726 8.514594 TGCTAATTTCCAAGATTACAAGTTCAG 58.485 33.333 0.00 0.00 0.00 3.02
678 727 7.970614 GCTAATTTCCAAGATTACAAGTTCAGG 59.029 37.037 0.00 0.00 0.00 3.86
679 728 9.231297 CTAATTTCCAAGATTACAAGTTCAGGA 57.769 33.333 0.00 0.00 0.00 3.86
680 729 8.477419 AATTTCCAAGATTACAAGTTCAGGAA 57.523 30.769 0.00 0.00 30.97 3.36
681 730 8.655935 ATTTCCAAGATTACAAGTTCAGGAAT 57.344 30.769 0.00 0.00 32.19 3.01
682 731 7.687941 TTCCAAGATTACAAGTTCAGGAATC 57.312 36.000 0.00 0.00 0.00 2.52
683 732 5.874810 TCCAAGATTACAAGTTCAGGAATCG 59.125 40.000 0.00 0.00 32.85 3.34
684 733 5.874810 CCAAGATTACAAGTTCAGGAATCGA 59.125 40.000 0.00 0.00 32.85 3.59
685 734 6.540189 CCAAGATTACAAGTTCAGGAATCGAT 59.460 38.462 0.00 0.00 32.85 3.59
686 735 7.066284 CCAAGATTACAAGTTCAGGAATCGATT 59.934 37.037 11.20 11.20 32.85 3.34
687 736 8.454106 CAAGATTACAAGTTCAGGAATCGATTT 58.546 33.333 12.81 0.00 32.85 2.17
688 737 9.667107 AAGATTACAAGTTCAGGAATCGATTTA 57.333 29.630 12.81 0.00 32.85 1.40
689 738 9.319143 AGATTACAAGTTCAGGAATCGATTTAG 57.681 33.333 12.81 5.66 32.85 1.85
690 739 5.803020 ACAAGTTCAGGAATCGATTTAGC 57.197 39.130 12.81 0.00 0.00 3.09
691 740 5.491982 ACAAGTTCAGGAATCGATTTAGCT 58.508 37.500 12.81 3.57 0.00 3.32
692 741 5.940470 ACAAGTTCAGGAATCGATTTAGCTT 59.060 36.000 12.81 9.02 0.00 3.74
693 742 6.431234 ACAAGTTCAGGAATCGATTTAGCTTT 59.569 34.615 12.81 0.00 0.00 3.51
694 743 6.670077 AGTTCAGGAATCGATTTAGCTTTC 57.330 37.500 12.81 0.00 0.00 2.62
695 744 5.292101 AGTTCAGGAATCGATTTAGCTTTCG 59.708 40.000 12.81 0.00 36.72 3.46
696 745 4.755411 TCAGGAATCGATTTAGCTTTCGT 58.245 39.130 12.81 0.00 36.74 3.85
697 746 4.804139 TCAGGAATCGATTTAGCTTTCGTC 59.196 41.667 12.81 0.00 36.74 4.20
698 747 4.806247 CAGGAATCGATTTAGCTTTCGTCT 59.194 41.667 12.81 2.92 36.74 4.18
699 748 5.977725 CAGGAATCGATTTAGCTTTCGTCTA 59.022 40.000 12.81 0.00 36.74 2.59
700 749 6.642950 CAGGAATCGATTTAGCTTTCGTCTAT 59.357 38.462 12.81 0.00 36.74 1.98
701 750 7.808381 CAGGAATCGATTTAGCTTTCGTCTATA 59.192 37.037 12.81 0.00 36.74 1.31
702 751 8.358148 AGGAATCGATTTAGCTTTCGTCTATAA 58.642 33.333 12.81 0.00 36.74 0.98
703 752 8.640291 GGAATCGATTTAGCTTTCGTCTATAAG 58.360 37.037 12.81 0.00 36.74 1.73
704 753 9.182933 GAATCGATTTAGCTTTCGTCTATAAGT 57.817 33.333 12.81 0.00 36.74 2.24
705 754 9.530633 AATCGATTTAGCTTTCGTCTATAAGTT 57.469 29.630 4.39 0.00 36.74 2.66
706 755 8.557869 TCGATTTAGCTTTCGTCTATAAGTTC 57.442 34.615 11.56 0.00 36.74 3.01
707 756 8.186163 TCGATTTAGCTTTCGTCTATAAGTTCA 58.814 33.333 11.56 0.00 36.74 3.18
708 757 8.804743 CGATTTAGCTTTCGTCTATAAGTTCAA 58.195 33.333 0.00 0.00 0.00 2.69
710 759 9.871238 ATTTAGCTTTCGTCTATAAGTTCAAGA 57.129 29.630 0.00 0.00 0.00 3.02
711 760 9.871238 TTTAGCTTTCGTCTATAAGTTCAAGAT 57.129 29.630 0.00 0.00 0.00 2.40
712 761 9.871238 TTAGCTTTCGTCTATAAGTTCAAGATT 57.129 29.630 0.00 0.00 0.00 2.40
713 762 8.779354 AGCTTTCGTCTATAAGTTCAAGATTT 57.221 30.769 0.00 0.00 0.00 2.17
714 763 9.871238 AGCTTTCGTCTATAAGTTCAAGATTTA 57.129 29.630 0.00 0.00 0.00 1.40
739 788 6.720012 TTTGAACTTTTTCCTTTGTTGAGC 57.280 33.333 0.00 0.00 0.00 4.26
740 789 4.754322 TGAACTTTTTCCTTTGTTGAGCC 58.246 39.130 0.00 0.00 0.00 4.70
741 790 3.436700 ACTTTTTCCTTTGTTGAGCCG 57.563 42.857 0.00 0.00 0.00 5.52
742 791 2.127251 CTTTTTCCTTTGTTGAGCCGC 58.873 47.619 0.00 0.00 0.00 6.53
743 792 1.107114 TTTTCCTTTGTTGAGCCGCA 58.893 45.000 0.00 0.00 0.00 5.69
744 793 1.327303 TTTCCTTTGTTGAGCCGCAT 58.673 45.000 0.00 0.00 0.00 4.73
745 794 0.881118 TTCCTTTGTTGAGCCGCATC 59.119 50.000 0.00 0.00 0.00 3.91
755 804 6.060028 TGTTGAGCCGCATCTTAAAATATC 57.940 37.500 0.00 0.00 0.00 1.63
809 858 1.814394 TCATGGACAAATGCAGTCTGC 59.186 47.619 18.32 18.32 45.29 4.26
832 881 2.639065 CCACCGGCAGCTTAAAGATAA 58.361 47.619 0.00 0.00 0.00 1.75
1058 1136 4.101448 GGCGGTGGTGCTGATCCT 62.101 66.667 0.00 0.00 34.52 3.24
1059 1137 2.821366 GCGGTGGTGCTGATCCTG 60.821 66.667 0.00 0.00 0.00 3.86
1060 1138 2.124983 CGGTGGTGCTGATCCTGG 60.125 66.667 0.00 0.00 0.00 4.45
1061 1139 2.959484 CGGTGGTGCTGATCCTGGT 61.959 63.158 0.00 0.00 0.00 4.00
1062 1140 1.078143 GGTGGTGCTGATCCTGGTC 60.078 63.158 0.00 0.00 0.00 4.02
1063 1141 1.557269 GGTGGTGCTGATCCTGGTCT 61.557 60.000 0.00 0.00 0.00 3.85
1064 1142 0.392193 GTGGTGCTGATCCTGGTCTG 60.392 60.000 0.00 0.00 0.00 3.51
1065 1143 1.222936 GGTGCTGATCCTGGTCTGG 59.777 63.158 0.00 0.00 0.00 3.86
1066 1144 1.557269 GGTGCTGATCCTGGTCTGGT 61.557 60.000 0.00 0.00 0.00 4.00
1067 1145 0.107945 GTGCTGATCCTGGTCTGGTC 60.108 60.000 0.00 0.00 0.00 4.02
1068 1146 1.142748 GCTGATCCTGGTCTGGTCG 59.857 63.158 0.00 0.00 0.00 4.79
1069 1147 1.142748 CTGATCCTGGTCTGGTCGC 59.857 63.158 0.00 0.00 0.00 5.19
1070 1148 2.303549 CTGATCCTGGTCTGGTCGCC 62.304 65.000 0.00 0.00 0.00 5.54
1071 1149 3.432051 GATCCTGGTCTGGTCGCCG 62.432 68.421 0.00 0.00 0.00 6.46
1116 1194 4.429212 ATGGACGCGCACGCTACA 62.429 61.111 13.70 9.26 45.53 2.74
1125 1203 0.524816 CGCACGCTACATTCTACGGT 60.525 55.000 0.00 0.00 0.00 4.83
1177 1255 3.746492 GCAAACCAACTACTCTGATTCGT 59.254 43.478 0.00 0.00 0.00 3.85
1188 1266 1.143838 TGATTCGTCCCCGCATCAG 59.856 57.895 0.00 0.00 40.86 2.90
1199 1277 2.397252 GCATCAGCACGCGAAGTC 59.603 61.111 15.93 1.39 41.58 3.01
1228 1309 6.328148 ACCTAATTAACATTCTCCACGGGATA 59.672 38.462 0.00 0.00 0.00 2.59
1230 1311 5.623956 ATTAACATTCTCCACGGGATACA 57.376 39.130 0.00 0.00 39.74 2.29
1231 1312 5.623956 TTAACATTCTCCACGGGATACAT 57.376 39.130 0.00 0.00 39.74 2.29
1232 1313 6.734502 TTAACATTCTCCACGGGATACATA 57.265 37.500 0.00 0.00 39.74 2.29
1454 1535 1.490910 GCCAACTACTCCAAGCCCTAT 59.509 52.381 0.00 0.00 0.00 2.57
1590 1671 2.045045 CCAAGAAGGGCGGCATCA 60.045 61.111 12.47 0.00 0.00 3.07
1649 1730 2.049802 GTCTTCAACGTCGCCGGA 60.050 61.111 5.05 0.00 38.78 5.14
1666 1747 3.236003 GACCCGGCGAAGTCAAGGT 62.236 63.158 20.37 12.36 33.08 3.50
1724 1805 0.995024 ACATGAAGAGGAACTGGGGG 59.005 55.000 0.00 0.00 41.55 5.40
1760 1841 2.289444 ACATGTCCAAAATCTCGTCGGT 60.289 45.455 0.00 0.00 0.00 4.69
1957 2041 1.594862 GTTTCTGCATCCTTCGATCGG 59.405 52.381 16.41 0.00 0.00 4.18
1958 2042 0.824109 TTCTGCATCCTTCGATCGGT 59.176 50.000 16.41 0.00 0.00 4.69
1968 2052 3.382227 TCCTTCGATCGGTATTTGCTACA 59.618 43.478 16.41 0.00 31.44 2.74
2001 2085 0.390340 CTATGGTGCTGCGTGAGTGT 60.390 55.000 0.00 0.00 0.00 3.55
2080 2166 2.203788 TTGACCTCCGGCCTCTGT 60.204 61.111 0.00 0.00 0.00 3.41
2120 2207 8.356657 TGCAGCCATATTATTAAAAAGCGTAAT 58.643 29.630 0.00 0.00 0.00 1.89
2178 2285 2.898729 ATCTCTAAGGTGCCACATCG 57.101 50.000 0.00 0.00 0.00 3.84
2454 2582 8.494433 TCTAGTGTTTCATATAGCCCAGAAAAT 58.506 33.333 0.00 0.00 32.44 1.82
2478 2606 6.161855 TGCACATATCCCTATCCGAATATC 57.838 41.667 0.00 0.00 0.00 1.63
2840 2971 5.156355 CAGAGAAAATTCCATTCGTGGTTG 58.844 41.667 0.00 0.00 32.04 3.77
2867 2998 5.998454 CCAACTAATGGTATCTGCTGAAG 57.002 43.478 0.00 0.00 44.85 3.02
2868 2999 4.818546 CCAACTAATGGTATCTGCTGAAGG 59.181 45.833 0.00 0.00 44.85 3.46
2869 3000 5.396772 CCAACTAATGGTATCTGCTGAAGGA 60.397 44.000 0.00 0.00 44.85 3.36
2870 3001 5.957771 ACTAATGGTATCTGCTGAAGGAA 57.042 39.130 0.00 0.00 0.00 3.36
2871 3002 6.313519 ACTAATGGTATCTGCTGAAGGAAA 57.686 37.500 0.00 0.00 0.00 3.13
2872 3003 6.904626 ACTAATGGTATCTGCTGAAGGAAAT 58.095 36.000 0.00 0.00 0.00 2.17
2873 3004 6.769822 ACTAATGGTATCTGCTGAAGGAAATG 59.230 38.462 0.00 0.00 0.00 2.32
2874 3005 4.574674 TGGTATCTGCTGAAGGAAATGT 57.425 40.909 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.231705 TCACGAATTTGTAAAAGTTCACGTA 57.768 32.000 0.00 0.00 0.00 3.57
14 15 6.109320 TCACGAATTTGTAAAAGTTCACGT 57.891 33.333 0.00 0.00 0.00 4.49
94 115 9.840427 AGTTCATTGGTTTAAAATAGTTCATCG 57.160 29.630 0.00 0.00 0.00 3.84
269 315 6.572519 TCCCAAAAGAAGTTCACAAAATCAG 58.427 36.000 5.50 0.00 0.00 2.90
270 316 6.537453 TCCCAAAAGAAGTTCACAAAATCA 57.463 33.333 5.50 0.00 0.00 2.57
279 325 3.818773 TCATCGGTTCCCAAAAGAAGTTC 59.181 43.478 0.00 0.00 0.00 3.01
283 329 3.827722 AGTTCATCGGTTCCCAAAAGAA 58.172 40.909 0.00 0.00 0.00 2.52
285 331 4.584327 AAAGTTCATCGGTTCCCAAAAG 57.416 40.909 0.00 0.00 0.00 2.27
327 373 8.738554 CGTATTCAAAAAGTTCACGAATTCAAA 58.261 29.630 6.22 0.00 0.00 2.69
328 374 7.911205 ACGTATTCAAAAAGTTCACGAATTCAA 59.089 29.630 6.22 0.00 0.00 2.69
329 375 7.374754 CACGTATTCAAAAAGTTCACGAATTCA 59.625 33.333 6.22 0.00 0.00 2.57
330 376 7.584847 TCACGTATTCAAAAAGTTCACGAATTC 59.415 33.333 0.00 0.00 0.00 2.17
331 377 7.411274 TCACGTATTCAAAAAGTTCACGAATT 58.589 30.769 0.00 0.00 0.00 2.17
332 378 6.950545 TCACGTATTCAAAAAGTTCACGAAT 58.049 32.000 0.00 0.00 0.00 3.34
333 379 6.347270 TCACGTATTCAAAAAGTTCACGAA 57.653 33.333 0.00 0.00 0.00 3.85
334 380 5.970140 TCACGTATTCAAAAAGTTCACGA 57.030 34.783 0.00 0.00 0.00 4.35
335 381 6.189567 AGTTCACGTATTCAAAAAGTTCACG 58.810 36.000 0.00 0.00 0.00 4.35
336 382 7.964545 AAGTTCACGTATTCAAAAAGTTCAC 57.035 32.000 0.00 0.00 0.00 3.18
337 383 8.973835 AAAAGTTCACGTATTCAAAAAGTTCA 57.026 26.923 0.00 0.00 0.00 3.18
394 442 8.130307 ACAAGAATGTGCACTAAATTCAAAAC 57.870 30.769 22.98 4.34 38.69 2.43
462 511 4.131649 TGCACGTACATTGCTAGGTAAT 57.868 40.909 15.48 0.00 40.86 1.89
473 522 5.562696 GCCATGCTATTTATTGCACGTACAT 60.563 40.000 1.10 0.00 40.99 2.29
492 541 4.111375 AGTACGAAGAACTGTAGCCATG 57.889 45.455 0.00 0.00 0.00 3.66
493 542 4.803098 AAGTACGAAGAACTGTAGCCAT 57.197 40.909 0.00 0.00 0.00 4.40
502 551 7.111317 GTGCGACAGTATATAAGTACGAAGAAC 59.889 40.741 0.00 0.00 0.00 3.01
508 557 8.867935 AGTATAGTGCGACAGTATATAAGTACG 58.132 37.037 13.74 0.00 35.53 3.67
520 569 6.697455 ACATGTGAAATAGTATAGTGCGACAG 59.303 38.462 0.00 0.00 0.00 3.51
527 576 6.126768 ACTGGGCACATGTGAAATAGTATAGT 60.127 38.462 29.80 14.56 0.00 2.12
533 582 3.119388 CCAACTGGGCACATGTGAAATAG 60.119 47.826 29.80 20.54 0.00 1.73
543 592 0.179032 CACTACACCAACTGGGCACA 60.179 55.000 0.00 0.00 42.05 4.57
546 595 1.971695 GCCACTACACCAACTGGGC 60.972 63.158 0.00 0.00 42.05 5.36
575 624 0.597637 ATTATTGACGAGAGCGCCGG 60.598 55.000 2.29 0.00 42.48 6.13
576 625 0.778815 GATTATTGACGAGAGCGCCG 59.221 55.000 2.29 2.67 42.48 6.46
577 626 1.140816 GGATTATTGACGAGAGCGCC 58.859 55.000 2.29 0.00 42.48 6.53
578 627 1.140816 GGGATTATTGACGAGAGCGC 58.859 55.000 0.00 0.00 42.48 5.92
579 628 2.223829 ACAGGGATTATTGACGAGAGCG 60.224 50.000 0.00 0.00 44.79 5.03
580 629 3.460857 ACAGGGATTATTGACGAGAGC 57.539 47.619 0.00 0.00 0.00 4.09
581 630 4.572389 CCAAACAGGGATTATTGACGAGAG 59.428 45.833 0.00 0.00 0.00 3.20
582 631 4.513442 CCAAACAGGGATTATTGACGAGA 58.487 43.478 0.00 0.00 0.00 4.04
583 632 4.882671 CCAAACAGGGATTATTGACGAG 57.117 45.455 0.00 0.00 0.00 4.18
596 645 0.107831 TGAGGACGTTCCCAAACAGG 59.892 55.000 0.00 0.00 37.19 4.00
597 646 1.873591 CTTGAGGACGTTCCCAAACAG 59.126 52.381 0.00 0.00 37.19 3.16
598 647 1.476110 CCTTGAGGACGTTCCCAAACA 60.476 52.381 0.00 0.00 37.19 2.83
599 648 1.235724 CCTTGAGGACGTTCCCAAAC 58.764 55.000 0.00 0.00 37.19 2.93
600 649 0.841289 ACCTTGAGGACGTTCCCAAA 59.159 50.000 3.59 0.00 37.19 3.28
601 650 0.841289 AACCTTGAGGACGTTCCCAA 59.159 50.000 3.59 0.00 37.19 4.12
602 651 0.841289 AAACCTTGAGGACGTTCCCA 59.159 50.000 3.59 0.00 37.19 4.37
603 652 2.845363 TAAACCTTGAGGACGTTCCC 57.155 50.000 3.59 0.00 37.19 3.97
604 653 5.700722 ATTTTAAACCTTGAGGACGTTCC 57.299 39.130 3.59 0.00 38.94 3.62
605 654 7.360691 GGTCTATTTTAAACCTTGAGGACGTTC 60.361 40.741 3.59 0.00 38.94 3.95
606 655 6.429078 GGTCTATTTTAAACCTTGAGGACGTT 59.571 38.462 3.59 0.00 38.94 3.99
607 656 5.936372 GGTCTATTTTAAACCTTGAGGACGT 59.064 40.000 3.59 0.00 38.94 4.34
608 657 5.063060 CGGTCTATTTTAAACCTTGAGGACG 59.937 44.000 3.59 0.00 38.94 4.79
609 658 5.353400 CCGGTCTATTTTAAACCTTGAGGAC 59.647 44.000 3.59 0.00 38.94 3.85
610 659 5.248934 TCCGGTCTATTTTAAACCTTGAGGA 59.751 40.000 0.00 0.00 38.94 3.71
611 660 5.493809 TCCGGTCTATTTTAAACCTTGAGG 58.506 41.667 0.00 0.00 42.17 3.86
612 661 7.335924 TGATTCCGGTCTATTTTAAACCTTGAG 59.664 37.037 0.00 0.00 0.00 3.02
613 662 7.169591 TGATTCCGGTCTATTTTAAACCTTGA 58.830 34.615 0.00 0.00 0.00 3.02
614 663 7.385778 TGATTCCGGTCTATTTTAAACCTTG 57.614 36.000 0.00 0.00 0.00 3.61
615 664 8.411991 TTTGATTCCGGTCTATTTTAAACCTT 57.588 30.769 0.00 0.00 0.00 3.50
616 665 7.886446 TCTTTGATTCCGGTCTATTTTAAACCT 59.114 33.333 0.00 0.00 0.00 3.50
617 666 8.047413 TCTTTGATTCCGGTCTATTTTAAACC 57.953 34.615 0.00 0.00 0.00 3.27
621 670 8.609176 CGAATTCTTTGATTCCGGTCTATTTTA 58.391 33.333 0.00 0.00 33.45 1.52
622 671 7.415206 CCGAATTCTTTGATTCCGGTCTATTTT 60.415 37.037 0.00 0.00 33.45 1.82
623 672 6.038271 CCGAATTCTTTGATTCCGGTCTATTT 59.962 38.462 0.00 0.00 33.45 1.40
624 673 5.527582 CCGAATTCTTTGATTCCGGTCTATT 59.472 40.000 0.00 0.00 33.45 1.73
625 674 5.057149 CCGAATTCTTTGATTCCGGTCTAT 58.943 41.667 0.00 0.00 33.45 1.98
626 675 4.081309 ACCGAATTCTTTGATTCCGGTCTA 60.081 41.667 0.00 0.00 37.88 2.59
627 676 3.270877 CCGAATTCTTTGATTCCGGTCT 58.729 45.455 0.00 0.00 33.45 3.85
628 677 3.007635 ACCGAATTCTTTGATTCCGGTC 58.992 45.455 0.00 0.00 37.88 4.79
629 678 2.747446 CACCGAATTCTTTGATTCCGGT 59.253 45.455 0.00 0.00 40.33 5.28
630 679 2.747446 ACACCGAATTCTTTGATTCCGG 59.253 45.455 3.52 0.00 36.58 5.14
631 680 3.747193 CACACCGAATTCTTTGATTCCG 58.253 45.455 3.52 0.00 33.45 4.30
632 681 3.191371 AGCACACCGAATTCTTTGATTCC 59.809 43.478 3.52 0.00 33.45 3.01
633 682 4.425577 AGCACACCGAATTCTTTGATTC 57.574 40.909 3.52 0.00 33.64 2.52
634 683 5.957842 TTAGCACACCGAATTCTTTGATT 57.042 34.783 3.52 0.00 0.00 2.57
635 684 6.515272 AATTAGCACACCGAATTCTTTGAT 57.485 33.333 3.52 0.00 0.00 2.57
636 685 5.957842 AATTAGCACACCGAATTCTTTGA 57.042 34.783 3.52 0.00 0.00 2.69
637 686 5.572896 GGAAATTAGCACACCGAATTCTTTG 59.427 40.000 3.52 2.91 29.90 2.77
638 687 5.242838 TGGAAATTAGCACACCGAATTCTTT 59.757 36.000 3.52 0.00 29.90 2.52
639 688 4.764823 TGGAAATTAGCACACCGAATTCTT 59.235 37.500 3.52 0.00 29.90 2.52
640 689 4.331968 TGGAAATTAGCACACCGAATTCT 58.668 39.130 3.52 0.00 29.90 2.40
641 690 4.695217 TGGAAATTAGCACACCGAATTC 57.305 40.909 0.00 0.00 29.90 2.17
642 691 4.764823 TCTTGGAAATTAGCACACCGAATT 59.235 37.500 0.00 0.00 31.22 2.17
643 692 4.331968 TCTTGGAAATTAGCACACCGAAT 58.668 39.130 0.00 0.00 0.00 3.34
644 693 3.745799 TCTTGGAAATTAGCACACCGAA 58.254 40.909 0.00 0.00 0.00 4.30
645 694 3.410631 TCTTGGAAATTAGCACACCGA 57.589 42.857 0.00 0.00 0.00 4.69
646 695 4.701956 AATCTTGGAAATTAGCACACCG 57.298 40.909 0.00 0.00 0.00 4.94
647 696 6.509418 TGTAATCTTGGAAATTAGCACACC 57.491 37.500 0.00 0.00 0.00 4.16
648 697 7.593825 ACTTGTAATCTTGGAAATTAGCACAC 58.406 34.615 0.00 0.00 0.00 3.82
649 698 7.759489 ACTTGTAATCTTGGAAATTAGCACA 57.241 32.000 0.00 0.00 0.00 4.57
650 699 8.296713 TGAACTTGTAATCTTGGAAATTAGCAC 58.703 33.333 0.00 0.00 0.00 4.40
651 700 8.402798 TGAACTTGTAATCTTGGAAATTAGCA 57.597 30.769 0.00 0.00 0.00 3.49
652 701 7.970614 CCTGAACTTGTAATCTTGGAAATTAGC 59.029 37.037 0.00 0.00 0.00 3.09
653 702 9.231297 TCCTGAACTTGTAATCTTGGAAATTAG 57.769 33.333 0.00 0.00 0.00 1.73
654 703 9.581289 TTCCTGAACTTGTAATCTTGGAAATTA 57.419 29.630 0.00 0.00 31.30 1.40
655 704 8.477419 TTCCTGAACTTGTAATCTTGGAAATT 57.523 30.769 0.00 0.00 31.30 1.82
656 705 8.655935 ATTCCTGAACTTGTAATCTTGGAAAT 57.344 30.769 0.00 0.00 34.85 2.17
657 706 7.094805 CGATTCCTGAACTTGTAATCTTGGAAA 60.095 37.037 0.00 0.00 34.85 3.13
658 707 6.371548 CGATTCCTGAACTTGTAATCTTGGAA 59.628 38.462 0.00 0.00 35.28 3.53
659 708 5.874810 CGATTCCTGAACTTGTAATCTTGGA 59.125 40.000 0.00 0.00 0.00 3.53
660 709 5.874810 TCGATTCCTGAACTTGTAATCTTGG 59.125 40.000 0.00 0.00 0.00 3.61
661 710 6.968131 TCGATTCCTGAACTTGTAATCTTG 57.032 37.500 0.00 0.00 0.00 3.02
662 711 8.567285 AAATCGATTCCTGAACTTGTAATCTT 57.433 30.769 11.83 0.00 0.00 2.40
663 712 9.319143 CTAAATCGATTCCTGAACTTGTAATCT 57.681 33.333 11.83 0.00 0.00 2.40
664 713 8.064814 GCTAAATCGATTCCTGAACTTGTAATC 58.935 37.037 11.83 0.00 0.00 1.75
665 714 7.770897 AGCTAAATCGATTCCTGAACTTGTAAT 59.229 33.333 11.83 0.00 0.00 1.89
666 715 7.103641 AGCTAAATCGATTCCTGAACTTGTAA 58.896 34.615 11.83 0.00 0.00 2.41
667 716 6.640518 AGCTAAATCGATTCCTGAACTTGTA 58.359 36.000 11.83 0.00 0.00 2.41
668 717 5.491982 AGCTAAATCGATTCCTGAACTTGT 58.508 37.500 11.83 0.00 0.00 3.16
669 718 6.428385 AAGCTAAATCGATTCCTGAACTTG 57.572 37.500 11.83 0.00 0.00 3.16
670 719 6.183360 CGAAAGCTAAATCGATTCCTGAACTT 60.183 38.462 11.83 6.98 41.43 2.66
671 720 5.292101 CGAAAGCTAAATCGATTCCTGAACT 59.708 40.000 11.83 1.05 41.43 3.01
672 721 5.063564 ACGAAAGCTAAATCGATTCCTGAAC 59.936 40.000 19.45 0.00 41.43 3.18
673 722 5.175859 ACGAAAGCTAAATCGATTCCTGAA 58.824 37.500 19.45 0.00 41.43 3.02
674 723 4.755411 ACGAAAGCTAAATCGATTCCTGA 58.245 39.130 19.45 0.00 41.43 3.86
675 724 4.806247 AGACGAAAGCTAAATCGATTCCTG 59.194 41.667 19.45 5.93 41.43 3.86
676 725 5.012328 AGACGAAAGCTAAATCGATTCCT 57.988 39.130 19.45 5.66 41.43 3.36
677 726 8.516811 TTATAGACGAAAGCTAAATCGATTCC 57.483 34.615 19.45 3.33 41.43 3.01
678 727 9.182933 ACTTATAGACGAAAGCTAAATCGATTC 57.817 33.333 19.45 9.97 41.43 2.52
679 728 9.530633 AACTTATAGACGAAAGCTAAATCGATT 57.469 29.630 19.45 4.39 41.43 3.34
680 729 9.182933 GAACTTATAGACGAAAGCTAAATCGAT 57.817 33.333 19.45 11.59 41.43 3.59
681 730 8.186163 TGAACTTATAGACGAAAGCTAAATCGA 58.814 33.333 19.45 0.00 41.43 3.59
682 731 8.336498 TGAACTTATAGACGAAAGCTAAATCG 57.664 34.615 13.11 13.11 44.33 3.34
684 733 9.871238 TCTTGAACTTATAGACGAAAGCTAAAT 57.129 29.630 0.00 0.00 0.00 1.40
685 734 9.871238 ATCTTGAACTTATAGACGAAAGCTAAA 57.129 29.630 0.00 0.00 0.00 1.85
686 735 9.871238 AATCTTGAACTTATAGACGAAAGCTAA 57.129 29.630 0.00 0.00 0.00 3.09
687 736 9.871238 AAATCTTGAACTTATAGACGAAAGCTA 57.129 29.630 0.00 0.00 0.00 3.32
688 737 8.779354 AAATCTTGAACTTATAGACGAAAGCT 57.221 30.769 0.00 0.00 0.00 3.74
713 762 8.878769 GCTCAACAAAGGAAAAAGTTCAAAATA 58.121 29.630 0.00 0.00 35.25 1.40
714 763 7.148255 GGCTCAACAAAGGAAAAAGTTCAAAAT 60.148 33.333 0.00 0.00 35.25 1.82
715 764 6.148645 GGCTCAACAAAGGAAAAAGTTCAAAA 59.851 34.615 0.00 0.00 35.25 2.44
716 765 5.641636 GGCTCAACAAAGGAAAAAGTTCAAA 59.358 36.000 0.00 0.00 35.25 2.69
717 766 5.175127 GGCTCAACAAAGGAAAAAGTTCAA 58.825 37.500 0.00 0.00 35.25 2.69
718 767 4.676723 CGGCTCAACAAAGGAAAAAGTTCA 60.677 41.667 0.00 0.00 35.25 3.18
719 768 3.796717 CGGCTCAACAAAGGAAAAAGTTC 59.203 43.478 0.00 0.00 0.00 3.01
720 769 3.780902 CGGCTCAACAAAGGAAAAAGTT 58.219 40.909 0.00 0.00 0.00 2.66
721 770 2.481276 GCGGCTCAACAAAGGAAAAAGT 60.481 45.455 0.00 0.00 0.00 2.66
722 771 2.127251 GCGGCTCAACAAAGGAAAAAG 58.873 47.619 0.00 0.00 0.00 2.27
723 772 1.478510 TGCGGCTCAACAAAGGAAAAA 59.521 42.857 0.00 0.00 0.00 1.94
724 773 1.107114 TGCGGCTCAACAAAGGAAAA 58.893 45.000 0.00 0.00 0.00 2.29
725 774 1.269448 GATGCGGCTCAACAAAGGAAA 59.731 47.619 0.00 0.00 0.00 3.13
726 775 0.881118 GATGCGGCTCAACAAAGGAA 59.119 50.000 0.00 0.00 0.00 3.36
727 776 0.036732 AGATGCGGCTCAACAAAGGA 59.963 50.000 0.00 0.00 0.00 3.36
728 777 0.883833 AAGATGCGGCTCAACAAAGG 59.116 50.000 0.00 0.00 0.00 3.11
729 778 3.829886 TTAAGATGCGGCTCAACAAAG 57.170 42.857 0.00 0.00 0.00 2.77
730 779 4.576216 TTTTAAGATGCGGCTCAACAAA 57.424 36.364 0.00 0.00 0.00 2.83
731 780 4.782019 ATTTTAAGATGCGGCTCAACAA 57.218 36.364 0.00 0.00 0.00 2.83
732 781 5.008613 GGATATTTTAAGATGCGGCTCAACA 59.991 40.000 0.00 0.00 0.00 3.33
733 782 5.239525 AGGATATTTTAAGATGCGGCTCAAC 59.760 40.000 0.00 0.00 0.00 3.18
734 783 5.376625 AGGATATTTTAAGATGCGGCTCAA 58.623 37.500 0.00 0.00 0.00 3.02
735 784 4.973168 AGGATATTTTAAGATGCGGCTCA 58.027 39.130 0.00 0.00 0.00 4.26
736 785 4.393371 GGAGGATATTTTAAGATGCGGCTC 59.607 45.833 0.00 0.00 0.00 4.70
737 786 4.202461 TGGAGGATATTTTAAGATGCGGCT 60.202 41.667 0.00 0.00 0.00 5.52
738 787 4.072131 TGGAGGATATTTTAAGATGCGGC 58.928 43.478 0.00 0.00 0.00 6.53
739 788 6.824305 AATGGAGGATATTTTAAGATGCGG 57.176 37.500 0.00 0.00 0.00 5.69
740 789 9.778993 CATTAATGGAGGATATTTTAAGATGCG 57.221 33.333 7.62 0.00 0.00 4.73
741 790 9.578439 GCATTAATGGAGGATATTTTAAGATGC 57.422 33.333 17.02 0.00 0.00 3.91
743 792 8.960591 CGGCATTAATGGAGGATATTTTAAGAT 58.039 33.333 17.02 0.00 0.00 2.40
744 793 7.094377 GCGGCATTAATGGAGGATATTTTAAGA 60.094 37.037 17.02 0.00 0.00 2.10
745 794 7.029563 GCGGCATTAATGGAGGATATTTTAAG 58.970 38.462 17.02 0.00 0.00 1.85
755 804 4.201950 GCTAATATGCGGCATTAATGGAGG 60.202 45.833 21.99 5.19 0.00 4.30
783 832 5.948162 AGACTGCATTTGTCCATGAGTAAAT 59.052 36.000 0.00 0.00 35.21 1.40
784 833 5.181811 CAGACTGCATTTGTCCATGAGTAAA 59.818 40.000 0.00 0.00 35.21 2.01
788 837 2.159421 GCAGACTGCATTTGTCCATGAG 60.159 50.000 22.62 0.00 44.26 2.90
816 865 6.128391 TGTTGTACTTTATCTTTAAGCTGCCG 60.128 38.462 0.00 0.00 0.00 5.69
832 881 4.102681 GGGCTAGGTCCATATGTTGTACTT 59.897 45.833 1.24 0.00 0.00 2.24
933 982 5.287752 CCAATTCAACTTTGCGATGATTGAG 59.712 40.000 0.00 0.00 31.34 3.02
1046 1124 1.556373 CCAGACCAGGATCAGCACCA 61.556 60.000 0.00 0.00 0.00 4.17
1047 1125 1.222936 CCAGACCAGGATCAGCACC 59.777 63.158 0.00 0.00 0.00 5.01
1048 1126 0.107945 GACCAGACCAGGATCAGCAC 60.108 60.000 0.00 0.00 0.00 4.40
1049 1127 1.607801 CGACCAGACCAGGATCAGCA 61.608 60.000 0.00 0.00 0.00 4.41
1050 1128 1.142748 CGACCAGACCAGGATCAGC 59.857 63.158 0.00 0.00 0.00 4.26
1051 1129 1.142748 GCGACCAGACCAGGATCAG 59.857 63.158 0.00 0.00 0.00 2.90
1052 1130 2.359169 GGCGACCAGACCAGGATCA 61.359 63.158 0.00 0.00 0.00 2.92
1053 1131 2.501610 GGCGACCAGACCAGGATC 59.498 66.667 0.00 0.00 0.00 3.36
1054 1132 3.461773 CGGCGACCAGACCAGGAT 61.462 66.667 0.00 0.00 0.00 3.24
1125 1203 0.034089 TCTCAGCTCCGGTCTCATCA 60.034 55.000 0.00 0.00 0.00 3.07
1161 1239 3.166489 GGGGACGAATCAGAGTAGTTG 57.834 52.381 0.00 0.00 0.00 3.16
1188 1266 1.986698 TAGGTAAAGACTTCGCGTGC 58.013 50.000 5.77 0.00 0.00 5.34
1199 1277 7.012044 CCCGTGGAGAATGTTAATTAGGTAAAG 59.988 40.741 0.00 0.00 0.00 1.85
1402 1483 1.885850 GTTGCCGTCACCGTCACTT 60.886 57.895 0.00 0.00 0.00 3.16
1454 1535 1.227823 CGGGTTGCACCAGTTCTCA 60.228 57.895 7.49 0.00 41.02 3.27
1590 1671 1.689273 GTTGCCCGTCATCTCTATCCT 59.311 52.381 0.00 0.00 0.00 3.24
1649 1730 3.239253 ACCTTGACTTCGCCGGGT 61.239 61.111 2.18 0.00 0.00 5.28
1666 1747 2.203422 CCCCTTTCACGGCCAACA 60.203 61.111 2.24 0.00 0.00 3.33
1724 1805 0.531532 CATGTCCGTCCCAGATCTGC 60.532 60.000 17.76 2.95 0.00 4.26
1740 1821 2.346803 ACCGACGAGATTTTGGACATG 58.653 47.619 0.00 0.00 0.00 3.21
1923 2007 6.484643 GGATGCAGAAACACATACATGACTAT 59.515 38.462 0.00 0.00 0.00 2.12
1957 2041 8.936864 AGTTTGATGACTTACTGTAGCAAATAC 58.063 33.333 0.00 0.00 31.06 1.89
1968 2052 5.877012 CAGCACCATAGTTTGATGACTTACT 59.123 40.000 0.00 0.00 30.45 2.24
2001 2085 2.549992 CCCCGAATCAGAAGTGAACACA 60.550 50.000 7.68 0.00 35.88 3.72
2080 2166 1.808343 GGCTGCATGCATCGATTGATA 59.192 47.619 22.97 0.00 45.15 2.15
2120 2207 4.019591 GCTTCCTTGGAACCTAAGACCTTA 60.020 45.833 0.00 0.00 0.00 2.69
2163 2270 4.540153 CCCGATGTGGCACCTTAG 57.460 61.111 16.26 3.06 35.87 2.18
2437 2565 5.199723 TGTGCAATTTTCTGGGCTATATGA 58.800 37.500 0.00 0.00 0.00 2.15
2454 2582 4.908601 ATTCGGATAGGGATATGTGCAA 57.091 40.909 0.00 0.00 0.00 4.08
2478 2606 6.043411 GGAGTGGACATACAAGTAGCTAAAG 58.957 44.000 0.00 0.00 0.00 1.85
2745 2876 7.968405 GGTCTTTGCACATACGAAAGATTAAAT 59.032 33.333 0.00 0.00 37.86 1.40
2757 2888 2.683968 TGTCGAGGTCTTTGCACATAC 58.316 47.619 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.