Multiple sequence alignment - TraesCS1A01G230800

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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 TraesCS1A01G230800 chr1A 100.000 2599 0 0 1 2599 403609997 403612595 0.000000e+00 4800.0
1 TraesCS1A01G230800 chr1A 84.694 588 81 9 2016 2599 513531576 513530994 1.730000e-161 579.0
2 TraesCS1A01G230800 chr1A 88.889 54 5 1 570 623 574532764 574532712 6.000000e-07 65.8
3 TraesCS1A01G230800 chr1B 87.160 1324 112 29 666 1979 432560776 432559501 0.000000e+00 1450.0
4 TraesCS1A01G230800 chr1B 94.382 623 34 1 1978 2599 198649949 198650571 0.000000e+00 955.0
5 TraesCS1A01G230800 chr1B 91.214 626 47 3 1980 2599 622139239 622138616 0.000000e+00 845.0
6 TraesCS1A01G230800 chr1B 93.593 437 28 0 2139 2575 622095329 622094893 0.000000e+00 652.0
7 TraesCS1A01G230800 chr1D 89.961 1036 74 12 666 1689 319642983 319641966 0.000000e+00 1310.0
8 TraesCS1A01G230800 chr1D 85.531 311 28 3 1671 1981 319630305 319630012 2.510000e-80 309.0
9 TraesCS1A01G230800 chr1D 100.000 28 0 0 357 384 472293537 472293564 5.000000e-03 52.8
10 TraesCS1A01G230800 chr6D 95.146 618 29 1 1982 2599 444505920 444505304 0.000000e+00 974.0
11 TraesCS1A01G230800 chr6D 100.000 28 0 0 357 384 89154594 89154567 5.000000e-03 52.8
12 TraesCS1A01G230800 chr4D 94.855 622 32 0 1978 2599 507050594 507051215 0.000000e+00 972.0
13 TraesCS1A01G230800 chr5A 94.023 619 37 0 1981 2599 590401279 590401897 0.000000e+00 939.0
14 TraesCS1A01G230800 chr5A 90.179 112 9 2 1747 1857 602964561 602964671 7.500000e-31 145.0
15 TraesCS1A01G230800 chr6B 91.424 618 47 4 1982 2599 669903483 669902872 0.000000e+00 843.0
16 TraesCS1A01G230800 chr6B 100.000 28 0 0 357 384 660703574 660703601 5.000000e-03 52.8
17 TraesCS1A01G230800 chr7B 91.424 618 36 7 1982 2599 682973090 682973690 0.000000e+00 832.0
18 TraesCS1A01G230800 chr7B 87.129 101 9 4 313 411 314274265 314274363 7.600000e-21 111.0
19 TraesCS1A01G230800 chr2D 86.957 483 48 8 49 519 600323744 600323265 1.770000e-146 529.0
20 TraesCS1A01G230800 chr2D 83.871 527 64 9 2 522 602726190 602725679 1.400000e-132 483.0
21 TraesCS1A01G230800 chr2D 96.503 143 4 1 1982 2124 84785305 84785164 4.320000e-58 235.0
22 TraesCS1A01G230800 chr2D 77.186 263 37 18 273 520 53995037 53995291 5.840000e-27 132.0
23 TraesCS1A01G230800 chr5B 82.068 619 107 4 1983 2599 273192641 273193257 2.290000e-145 525.0
24 TraesCS1A01G230800 chr5B 85.535 159 23 0 1 159 15358435 15358593 1.600000e-37 167.0
25 TraesCS1A01G230800 chr3D 86.920 237 21 7 1749 1984 560157699 560157472 9.230000e-65 257.0
26 TraesCS1A01G230800 chr3D 94.737 38 1 1 463 500 600530551 600530515 1.000000e-04 58.4
27 TraesCS1A01G230800 chr5D 100.000 29 0 0 357 385 423328363 423328335 1.000000e-03 54.7
28 TraesCS1A01G230800 chr5D 100.000 28 0 0 357 384 301100411 301100438 5.000000e-03 52.8
29 TraesCS1A01G230800 chr3A 100.000 29 0 0 356 384 696237776 696237804 1.000000e-03 54.7
30 TraesCS1A01G230800 chr7D 100.000 28 0 0 357 384 625766889 625766862 5.000000e-03 52.8
31 TraesCS1A01G230800 chr2B 100.000 28 0 0 357 384 649683903 649683930 5.000000e-03 52.8


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 TraesCS1A01G230800 chr1A 403609997 403612595 2598 False 4800 4800 100.000 1 2599 1 chr1A.!!$F1 2598
1 TraesCS1A01G230800 chr1A 513530994 513531576 582 True 579 579 84.694 2016 2599 1 chr1A.!!$R1 583
2 TraesCS1A01G230800 chr1B 432559501 432560776 1275 True 1450 1450 87.160 666 1979 1 chr1B.!!$R1 1313
3 TraesCS1A01G230800 chr1B 198649949 198650571 622 False 955 955 94.382 1978 2599 1 chr1B.!!$F1 621
4 TraesCS1A01G230800 chr1B 622138616 622139239 623 True 845 845 91.214 1980 2599 1 chr1B.!!$R3 619
5 TraesCS1A01G230800 chr1D 319641966 319642983 1017 True 1310 1310 89.961 666 1689 1 chr1D.!!$R2 1023
6 TraesCS1A01G230800 chr6D 444505304 444505920 616 True 974 974 95.146 1982 2599 1 chr6D.!!$R2 617
7 TraesCS1A01G230800 chr4D 507050594 507051215 621 False 972 972 94.855 1978 2599 1 chr4D.!!$F1 621
8 TraesCS1A01G230800 chr5A 590401279 590401897 618 False 939 939 94.023 1981 2599 1 chr5A.!!$F1 618
9 TraesCS1A01G230800 chr6B 669902872 669903483 611 True 843 843 91.424 1982 2599 1 chr6B.!!$R1 617
10 TraesCS1A01G230800 chr7B 682973090 682973690 600 False 832 832 91.424 1982 2599 1 chr7B.!!$F2 617
11 TraesCS1A01G230800 chr2D 602725679 602726190 511 True 483 483 83.871 2 522 1 chr2D.!!$R3 520
12 TraesCS1A01G230800 chr5B 273192641 273193257 616 False 525 525 82.068 1983 2599 1 chr5B.!!$F2 616

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
159 160 0.031994 GGCCTTGCATTGTTGTTCGT 59.968 50.0 0.0 0.0 0.00 3.85 F
668 674 0.041312 AACACGCAGCAAACGTCATC 60.041 50.0 0.0 0.0 42.96 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1404 0.110486 ACTTCTTTGGTGCCGGTCAT 59.890 50.0 1.9 0.0 0.0 3.06 R
1707 1726 0.249031 GCTACAATGGCAATTCCCGC 60.249 55.0 0.0 0.0 0.0 6.13 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.504647 CGAGCTCCGCCGTATGTAGA 61.505 60.000 8.47 0.00 0.00 2.59
21 22 0.040246 GAGCTCCGCCGTATGTAGAC 60.040 60.000 0.87 0.00 0.00 2.59
22 23 0.465824 AGCTCCGCCGTATGTAGACT 60.466 55.000 0.00 0.00 0.00 3.24
24 25 1.022735 CTCCGCCGTATGTAGACTGT 58.977 55.000 0.00 0.00 0.00 3.55
31 32 3.790123 GCCGTATGTAGACTGTCGTTACC 60.790 52.174 1.52 0.00 0.00 2.85
53 54 0.815734 GCACATCCATGCTTGCTCTT 59.184 50.000 0.00 0.00 42.62 2.85
56 57 1.203994 ACATCCATGCTTGCTCTTTGC 59.796 47.619 0.00 0.00 43.25 3.68
64 65 0.037975 CTTGCTCTTTGCCGCCAAAT 60.038 50.000 0.00 0.00 39.98 2.32
119 120 2.506217 ACAGCACCGCGATGTACG 60.506 61.111 8.23 0.00 45.66 3.67
159 160 0.031994 GGCCTTGCATTGTTGTTCGT 59.968 50.000 0.00 0.00 0.00 3.85
160 161 1.130955 GCCTTGCATTGTTGTTCGTG 58.869 50.000 0.00 0.00 0.00 4.35
162 163 2.797792 GCCTTGCATTGTTGTTCGTGAA 60.798 45.455 0.00 0.00 0.00 3.18
185 186 2.956333 TCACCTCTGAGACAAGTTTCGA 59.044 45.455 6.17 0.00 0.00 3.71
192 193 4.328983 TCTGAGACAAGTTTCGACAACAAC 59.671 41.667 11.33 2.19 0.00 3.32
227 228 2.458629 GCGACAACGAACGACGAC 59.541 61.111 0.00 0.00 45.77 4.34
244 245 1.136057 CGACTATGCTAGTGCGCGATA 60.136 52.381 12.10 0.00 43.34 2.92
247 248 0.109919 TATGCTAGTGCGCGATACGG 60.110 55.000 12.10 7.83 43.93 4.02
280 281 7.881516 GCTTTTGCAATTTTTACAACAAGAG 57.118 32.000 0.00 0.00 46.58 2.85
281 282 7.463544 GCTTTTGCAATTTTTACAACAAGAGT 58.536 30.769 0.00 0.00 46.58 3.24
282 283 7.635973 GCTTTTGCAATTTTTACAACAAGAGTC 59.364 33.333 0.00 0.00 46.58 3.36
285 286 7.754069 TGCAATTTTTACAACAAGAGTCTTG 57.246 32.000 27.66 27.66 0.00 3.02
286 287 7.319646 TGCAATTTTTACAACAAGAGTCTTGT 58.680 30.769 28.97 28.97 34.89 3.16
287 288 7.816995 TGCAATTTTTACAACAAGAGTCTTGTT 59.183 29.630 35.15 35.15 42.75 2.83
288 289 9.296400 GCAATTTTTACAACAAGAGTCTTGTTA 57.704 29.630 38.04 26.64 40.30 2.41
292 293 8.780846 TTTTACAACAAGAGTCTTGTTACAGA 57.219 30.769 38.04 25.04 40.30 3.41
293 294 8.780846 TTTACAACAAGAGTCTTGTTACAGAA 57.219 30.769 38.04 28.12 40.30 3.02
294 295 8.780846 TTACAACAAGAGTCTTGTTACAGAAA 57.219 30.769 38.04 26.47 40.30 2.52
295 296 7.681939 ACAACAAGAGTCTTGTTACAGAAAA 57.318 32.000 38.04 0.00 40.30 2.29
296 297 8.281212 ACAACAAGAGTCTTGTTACAGAAAAT 57.719 30.769 38.04 19.40 40.30 1.82
297 298 8.739972 ACAACAAGAGTCTTGTTACAGAAAATT 58.260 29.630 38.04 18.77 40.30 1.82
344 345 6.980397 ACAGGAGTTTTGTTGCAGAAAATTAG 59.020 34.615 8.47 3.06 0.00 1.73
350 351 8.686334 AGTTTTGTTGCAGAAAATTAGAGAAGA 58.314 29.630 8.47 0.00 0.00 2.87
356 357 6.681777 TGCAGAAAATTAGAGAAGAAAAGGC 58.318 36.000 0.00 0.00 0.00 4.35
367 368 4.831107 AGAAGAAAAGGCTTTGCAACAAA 58.169 34.783 19.92 0.00 0.00 2.83
369 370 4.470334 AGAAAAGGCTTTGCAACAAAGA 57.530 36.364 19.92 0.00 0.00 2.52
373 374 2.110578 AGGCTTTGCAACAAAGACCTT 58.889 42.857 19.64 2.54 35.91 3.50
394 395 7.781056 ACCTTGTTGCAGAAATTAAAGAAGAA 58.219 30.769 0.00 0.00 0.00 2.52
398 399 9.868277 TTGTTGCAGAAATTAAAGAAGAAGAAA 57.132 25.926 0.00 0.00 0.00 2.52
441 446 7.421599 TGTTGCAAAAATTAGAAACTGATCGA 58.578 30.769 0.00 0.00 0.00 3.59
445 450 6.462949 GCAAAAATTAGAAACTGATCGACTCG 59.537 38.462 0.00 0.00 0.00 4.18
447 452 8.644619 CAAAAATTAGAAACTGATCGACTCGTA 58.355 33.333 0.00 0.00 0.00 3.43
452 457 6.621316 AGAAACTGATCGACTCGTACATAT 57.379 37.500 0.00 0.00 0.00 1.78
453 458 6.660722 AGAAACTGATCGACTCGTACATATC 58.339 40.000 0.00 0.00 0.00 1.63
458 463 5.699839 TGATCGACTCGTACATATCCAATG 58.300 41.667 0.00 0.00 0.00 2.82
459 464 4.499037 TCGACTCGTACATATCCAATGG 57.501 45.455 0.00 0.00 0.00 3.16
491 496 1.202256 GCCCGGCCGATCTTTTAAAAG 60.202 52.381 30.73 19.91 37.36 2.27
559 565 2.715536 AAAAACTGGGTGACGCTCC 58.284 52.632 0.31 0.00 0.00 4.70
560 566 1.164041 AAAAACTGGGTGACGCTCCG 61.164 55.000 0.31 0.00 0.00 4.63
561 567 3.530910 AAACTGGGTGACGCTCCGG 62.531 63.158 0.00 0.00 35.60 5.14
563 569 4.003788 CTGGGTGACGCTCCGGTT 62.004 66.667 0.00 0.00 0.00 4.44
564 570 3.934391 CTGGGTGACGCTCCGGTTC 62.934 68.421 0.00 0.00 0.00 3.62
567 573 4.719369 GTGACGCTCCGGTTCGCT 62.719 66.667 15.74 5.73 0.00 4.93
568 574 4.717629 TGACGCTCCGGTTCGCTG 62.718 66.667 15.74 9.54 0.00 5.18
569 575 4.415332 GACGCTCCGGTTCGCTGA 62.415 66.667 15.74 0.00 0.00 4.26
570 576 4.421479 ACGCTCCGGTTCGCTGAG 62.421 66.667 15.74 0.00 0.00 3.35
572 578 4.821589 GCTCCGGTTCGCTGAGGG 62.822 72.222 0.00 0.00 0.00 4.30
573 579 4.821589 CTCCGGTTCGCTGAGGGC 62.822 72.222 0.00 0.00 37.64 5.19
582 588 3.224324 GCTGAGGGCGTATCGGGA 61.224 66.667 0.00 0.00 0.00 5.14
583 589 3.043419 CTGAGGGCGTATCGGGAG 58.957 66.667 0.00 0.00 0.00 4.30
584 590 2.520982 TGAGGGCGTATCGGGAGG 60.521 66.667 0.00 0.00 0.00 4.30
585 591 3.303928 GAGGGCGTATCGGGAGGG 61.304 72.222 0.00 0.00 0.00 4.30
586 592 4.936081 AGGGCGTATCGGGAGGGG 62.936 72.222 0.00 0.00 0.00 4.79
587 593 4.928140 GGGCGTATCGGGAGGGGA 62.928 72.222 0.00 0.00 0.00 4.81
588 594 3.303928 GGCGTATCGGGAGGGGAG 61.304 72.222 0.00 0.00 0.00 4.30
589 595 3.303928 GCGTATCGGGAGGGGAGG 61.304 72.222 0.00 0.00 0.00 4.30
590 596 2.519441 CGTATCGGGAGGGGAGGA 59.481 66.667 0.00 0.00 0.00 3.71
591 597 1.902432 CGTATCGGGAGGGGAGGAC 60.902 68.421 0.00 0.00 0.00 3.85
592 598 1.902432 GTATCGGGAGGGGAGGACG 60.902 68.421 0.00 0.00 0.00 4.79
593 599 2.389449 TATCGGGAGGGGAGGACGT 61.389 63.158 0.00 0.00 0.00 4.34
594 600 2.635787 TATCGGGAGGGGAGGACGTG 62.636 65.000 0.00 0.00 0.00 4.49
620 626 4.430423 CTCGTTTGCCAGCGCGTC 62.430 66.667 8.43 0.00 38.08 5.19
623 629 4.683334 GTTTGCCAGCGCGTCACC 62.683 66.667 8.43 0.00 38.08 4.02
632 638 3.049674 CGCGTCACCCAGCACATT 61.050 61.111 0.00 0.00 0.00 2.71
633 639 2.616330 CGCGTCACCCAGCACATTT 61.616 57.895 0.00 0.00 0.00 2.32
634 640 1.081242 GCGTCACCCAGCACATTTG 60.081 57.895 0.00 0.00 0.00 2.32
635 641 1.795170 GCGTCACCCAGCACATTTGT 61.795 55.000 0.00 0.00 0.00 2.83
648 654 3.047796 CACATTTGTGCAAACTCTCAGC 58.952 45.455 0.00 0.00 39.39 4.26
649 655 2.689471 ACATTTGTGCAAACTCTCAGCA 59.311 40.909 0.00 0.00 35.63 4.41
650 656 3.130869 ACATTTGTGCAAACTCTCAGCAA 59.869 39.130 0.00 0.00 40.35 3.91
651 657 2.849880 TTGTGCAAACTCTCAGCAAC 57.150 45.000 0.00 0.00 40.35 4.17
652 658 1.748950 TGTGCAAACTCTCAGCAACA 58.251 45.000 0.00 0.00 40.35 3.33
653 659 1.401552 TGTGCAAACTCTCAGCAACAC 59.598 47.619 0.00 0.00 40.35 3.32
654 660 0.657312 TGCAAACTCTCAGCAACACG 59.343 50.000 0.00 0.00 34.97 4.49
655 661 0.658536 GCAAACTCTCAGCAACACGC 60.659 55.000 0.00 0.00 42.91 5.34
656 662 0.657312 CAAACTCTCAGCAACACGCA 59.343 50.000 0.00 0.00 46.13 5.24
657 663 0.940126 AAACTCTCAGCAACACGCAG 59.060 50.000 0.00 0.00 46.13 5.18
658 664 1.502163 AACTCTCAGCAACACGCAGC 61.502 55.000 0.00 0.00 46.13 5.25
659 665 1.957695 CTCTCAGCAACACGCAGCA 60.958 57.895 0.00 0.00 46.13 4.41
660 666 1.501337 CTCTCAGCAACACGCAGCAA 61.501 55.000 0.00 0.00 46.13 3.91
661 667 1.094650 TCTCAGCAACACGCAGCAAA 61.095 50.000 0.00 0.00 46.13 3.68
662 668 0.931662 CTCAGCAACACGCAGCAAAC 60.932 55.000 0.00 0.00 46.13 2.93
663 669 2.024588 AGCAACACGCAGCAAACG 59.975 55.556 0.00 0.00 46.13 3.60
664 670 2.277884 GCAACACGCAGCAAACGT 60.278 55.556 0.00 0.00 46.42 3.99
668 674 0.041312 AACACGCAGCAAACGTCATC 60.041 50.000 0.00 0.00 42.96 2.92
717 723 0.249031 GTGCAAACTCCCAGCAACAC 60.249 55.000 0.00 0.00 40.35 3.32
739 745 2.159421 GCAGCACATGGAAGATTGACAG 60.159 50.000 0.00 0.00 0.00 3.51
772 778 0.107557 TGTCACGCTCCATGATGCAT 60.108 50.000 0.00 0.00 0.00 3.96
782 788 2.138320 CCATGATGCATCACTCGTACC 58.862 52.381 30.92 0.00 40.03 3.34
784 790 1.190643 TGATGCATCACTCGTACCCA 58.809 50.000 25.42 0.00 0.00 4.51
792 800 4.302455 CATCACTCGTACCCAAGATGATC 58.698 47.826 7.03 0.00 35.98 2.92
904 917 2.034221 AGGCTGCCTCCCGTTTTC 59.966 61.111 17.22 0.00 0.00 2.29
923 936 3.868757 TCACCTCCGACATGTTCTAAG 57.131 47.619 0.00 0.00 0.00 2.18
1003 1016 4.338879 CATTTTCTGTTCCTCTGTCCCAT 58.661 43.478 0.00 0.00 0.00 4.00
1028 1041 6.366604 TCTGAAACCGAAAACCAAAAGAAAAC 59.633 34.615 0.00 0.00 0.00 2.43
1046 1059 4.391405 AAACAAAGGGAGAGCAAACAAG 57.609 40.909 0.00 0.00 0.00 3.16
1047 1060 2.310538 ACAAAGGGAGAGCAAACAAGG 58.689 47.619 0.00 0.00 0.00 3.61
1050 1063 1.302511 GGGAGAGCAAACAAGGCGA 60.303 57.895 0.00 0.00 36.08 5.54
1083 1096 1.404391 GGCTAGAATCGTCTCCGTTCA 59.596 52.381 0.00 0.00 35.12 3.18
1171 1185 3.242478 CCGAAACTTTGCAAACGTACAGA 60.242 43.478 8.05 0.00 0.00 3.41
1174 1188 5.493133 AAACTTTGCAAACGTACAGATCA 57.507 34.783 8.05 0.00 0.00 2.92
1176 1190 6.795098 AACTTTGCAAACGTACAGATCATA 57.205 33.333 8.05 0.00 0.00 2.15
1196 1210 2.309528 TCATTTCGATCCAACCCGAG 57.690 50.000 0.00 0.00 36.11 4.63
1198 1212 0.909623 ATTTCGATCCAACCCGAGGT 59.090 50.000 0.00 0.00 37.65 3.85
1199 1213 7.146642 TATCATTTCGATCCAACCCGAGGTT 62.147 44.000 2.81 2.81 40.00 3.50
1211 1225 1.278238 CCGAGGTTGAACTGATACGC 58.722 55.000 0.00 0.00 0.00 4.42
1216 1231 1.389106 GGTTGAACTGATACGCGTGAC 59.611 52.381 24.59 15.95 0.00 3.67
1217 1232 2.055838 GTTGAACTGATACGCGTGACA 58.944 47.619 24.59 19.68 0.00 3.58
1218 1233 2.425578 TGAACTGATACGCGTGACAA 57.574 45.000 24.59 0.62 0.00 3.18
1226 1241 4.922719 TGATACGCGTGACAATGTATGTA 58.077 39.130 24.59 0.00 44.12 2.29
1243 1258 1.061735 TGTATGGTGCAGGAGGGGATA 60.062 52.381 0.00 0.00 0.00 2.59
1248 1263 1.439543 GTGCAGGAGGGGATATTCCT 58.560 55.000 0.00 0.00 44.59 3.36
1286 1301 0.319641 GAGTGTCCGCGAAGAAGGTT 60.320 55.000 8.23 0.00 0.00 3.50
1356 1371 1.006571 GACAAGACGGCGTTCTGGA 60.007 57.895 16.19 0.00 0.00 3.86
1403 1418 2.282816 CCCATGACCGGCACCAAA 60.283 61.111 0.00 0.00 0.00 3.28
1406 1421 0.893270 CCATGACCGGCACCAAAGAA 60.893 55.000 0.00 0.00 0.00 2.52
1442 1457 3.918220 CGCGCCGAGATGCTCAAC 61.918 66.667 0.00 0.00 0.00 3.18
1444 1459 2.125552 CGCCGAGATGCTCAACCA 60.126 61.111 0.00 0.00 0.00 3.67
1527 1544 2.050691 GCCATGTACAGCAAAACGTTG 58.949 47.619 0.00 0.00 37.83 4.10
1616 1633 8.362464 TCCTGTATCACTGTATGTAAGTCTTT 57.638 34.615 0.00 0.00 0.00 2.52
1618 1635 9.737427 CCTGTATCACTGTATGTAAGTCTTTAG 57.263 37.037 0.00 0.00 0.00 1.85
1621 1638 9.582431 GTATCACTGTATGTAAGTCTTTAGCAA 57.418 33.333 0.00 0.00 0.00 3.91
1636 1653 7.915397 AGTCTTTAGCAAACACTTACACATTTG 59.085 33.333 0.00 0.00 35.57 2.32
1638 1655 3.751570 GCAAACACTTACACATTTGCG 57.248 42.857 4.94 0.00 45.13 4.85
1680 1699 3.648339 AATTTCAGTGACTTTGCGCAT 57.352 38.095 12.75 0.00 0.00 4.73
1683 1702 1.812235 TCAGTGACTTTGCGCATCAT 58.188 45.000 12.75 0.00 0.00 2.45
1689 1708 2.292845 TGACTTTGCGCATCATGACAAA 59.707 40.909 12.75 3.23 0.00 2.83
1702 1721 6.400727 GCATCATGACAAAATTTCAGCAGTTC 60.401 38.462 0.00 0.00 0.00 3.01
1703 1722 6.146601 TCATGACAAAATTTCAGCAGTTCA 57.853 33.333 0.00 0.00 0.00 3.18
1707 1726 7.236674 TGACAAAATTTCAGCAGTTCAATTG 57.763 32.000 0.00 0.00 0.00 2.32
1737 1756 3.244526 TGCCATTGTAGCAACTTCTGAGA 60.245 43.478 0.00 0.00 37.28 3.27
1742 1761 2.095008 TGTAGCAACTTCTGAGAGCTCG 60.095 50.000 8.37 0.00 38.25 5.03
1743 1762 0.389687 AGCAACTTCTGAGAGCTCGC 60.390 55.000 10.93 10.93 34.42 5.03
1764 1783 1.108776 CATGGGGTGCTTTCCATCTG 58.891 55.000 2.99 0.00 41.43 2.90
1772 1791 1.074405 TGCTTTCCATCTGACAGCCTT 59.926 47.619 0.00 0.00 44.55 4.35
1777 1796 3.334583 TCCATCTGACAGCCTTGTAAC 57.665 47.619 0.00 0.00 37.76 2.50
1788 1807 6.072508 TGACAGCCTTGTAACTGAATTCAATC 60.073 38.462 9.88 1.37 37.76 2.67
1806 1825 9.893634 AATTCAATCCAAATTCATTTGCTATGA 57.106 25.926 6.73 7.17 44.32 2.15
1846 1865 2.359461 GGAGGCCCCTACTCTCTTTACT 60.359 54.545 0.00 0.00 35.34 2.24
1847 1866 2.696187 GAGGCCCCTACTCTCTTTACTG 59.304 54.545 0.00 0.00 32.28 2.74
1850 1869 1.763545 CCCCTACTCTCTTTACTGGGC 59.236 57.143 0.00 0.00 32.26 5.36
1851 1870 2.467880 CCCTACTCTCTTTACTGGGCA 58.532 52.381 0.00 0.00 0.00 5.36
1852 1871 2.432510 CCCTACTCTCTTTACTGGGCAG 59.567 54.545 0.00 0.00 0.00 4.85
1853 1872 3.366396 CCTACTCTCTTTACTGGGCAGA 58.634 50.000 0.00 0.00 0.00 4.26
1870 1889 3.254166 GGCAGAAGAAGATGCAAGTTTCA 59.746 43.478 0.00 0.00 44.37 2.69
1872 1891 4.678742 GCAGAAGAAGATGCAAGTTTCAAC 59.321 41.667 0.00 0.00 42.11 3.18
1874 1893 3.904136 AGAAGATGCAAGTTTCAACCG 57.096 42.857 0.00 0.00 0.00 4.44
1875 1894 2.554032 AGAAGATGCAAGTTTCAACCGG 59.446 45.455 0.00 0.00 0.00 5.28
1877 1896 0.313672 GATGCAAGTTTCAACCGGCA 59.686 50.000 0.00 7.95 40.92 5.69
1895 1914 2.468831 GCAATTTTGAACGAACAGCCA 58.531 42.857 0.00 0.00 0.00 4.75
1897 1916 4.233789 GCAATTTTGAACGAACAGCCATA 58.766 39.130 0.00 0.00 0.00 2.74
1908 1927 3.726607 GAACAGCCATAGACATCTCCAG 58.273 50.000 0.00 0.00 0.00 3.86
1910 1929 1.055040 AGCCATAGACATCTCCAGGC 58.945 55.000 9.84 9.84 37.47 4.85
1917 1936 1.415659 AGACATCTCCAGGCTGTATGC 59.584 52.381 14.43 9.87 41.94 3.14
1923 1942 0.538584 TCCAGGCTGTATGCTGTCTG 59.461 55.000 14.43 14.02 43.19 3.51
1933 1952 2.235845 ATGCTGTCTGTGATCCGATG 57.764 50.000 0.00 0.00 0.00 3.84
1945 1964 4.541482 CCGATGCGCACATGCCAC 62.541 66.667 14.90 0.00 36.35 5.01
1969 1988 2.927477 ACACACTCAATACGGCAATACG 59.073 45.455 0.00 0.00 40.31 3.06
2176 2207 2.130272 TGAGACTGGAGCGTATGTCT 57.870 50.000 5.44 5.44 41.76 3.41
2210 2241 1.494721 TGAGAAGCCCTTTGGTGAAGT 59.505 47.619 0.00 0.00 33.29 3.01
2298 2329 9.307121 CTCACGAACAAAGTGAATATCTATCTT 57.693 33.333 0.00 0.00 46.43 2.40
2392 2423 2.881352 GTAGCACGCTCGAGTGGC 60.881 66.667 28.30 25.59 42.09 5.01
2474 2505 1.609072 CCCGATACTCAGATTCAGCGA 59.391 52.381 0.00 0.00 0.00 4.93
2504 2535 5.083122 TGGAAATTGTATCCTGCCTTTTCA 58.917 37.500 0.00 0.00 37.85 2.69
2507 2538 6.934083 GGAAATTGTATCCTGCCTTTTCAAAA 59.066 34.615 0.00 0.00 33.98 2.44
2568 2599 1.135083 GGATGTGGATCGACGAGTGTT 60.135 52.381 3.01 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.945179 GGTAACGACAGTCTACATACGG 58.055 50.000 0.00 0.00 0.00 4.02
53 54 3.381136 GGAGGCATTTGGCGGCAA 61.381 61.111 21.79 21.79 46.16 4.52
82 83 2.330393 CGTACCGGATGCGTCGAT 59.670 61.111 9.46 0.00 0.00 3.59
88 89 2.890474 CTGTGGCGTACCGGATGC 60.890 66.667 9.46 8.83 39.70 3.91
89 90 2.890474 GCTGTGGCGTACCGGATG 60.890 66.667 9.46 0.00 39.70 3.51
105 106 3.252484 GGACGTACATCGCGGTGC 61.252 66.667 21.49 6.39 44.19 5.01
109 110 3.604202 GCGTGGACGTACATCGCG 61.604 66.667 24.55 16.22 44.19 5.87
113 114 2.263540 GTGGGCGTGGACGTACAT 59.736 61.111 2.42 0.00 42.22 2.29
114 115 3.993584 GGTGGGCGTGGACGTACA 61.994 66.667 0.00 0.00 42.22 2.90
134 135 3.434319 CAATGCAAGGCCGAGCGT 61.434 61.111 16.07 13.57 0.00 5.07
144 145 4.502282 GTGATTTCACGAACAACAATGCAA 59.498 37.500 0.00 0.00 37.10 4.08
159 160 4.963318 ACTTGTCTCAGAGGTGATTTCA 57.037 40.909 0.00 0.00 30.18 2.69
160 161 5.107298 CGAAACTTGTCTCAGAGGTGATTTC 60.107 44.000 0.00 2.13 30.18 2.17
162 163 4.039245 TCGAAACTTGTCTCAGAGGTGATT 59.961 41.667 0.00 0.00 30.18 2.57
192 193 2.128274 CGTTCCGCAACAACGTCG 60.128 61.111 0.00 0.00 41.39 5.12
227 228 1.251355 CGTATCGCGCACTAGCATAG 58.749 55.000 8.75 0.00 46.50 2.23
244 245 1.959085 CAAAAGCATGTCCAGCCGT 59.041 52.632 0.00 0.00 0.00 5.68
247 248 2.088950 ATTGCAAAAGCATGTCCAGC 57.911 45.000 1.71 0.00 0.00 4.85
271 272 7.681939 TTTTCTGTAACAAGACTCTTGTTGT 57.318 32.000 33.51 19.41 42.05 3.32
305 306 2.301346 CTCCTGTTGCACAACCTCTTT 58.699 47.619 10.82 0.00 40.46 2.52
322 323 7.425606 TCTCTAATTTTCTGCAACAAAACTCC 58.574 34.615 5.56 0.00 0.00 3.85
324 325 8.686334 TCTTCTCTAATTTTCTGCAACAAAACT 58.314 29.630 5.56 0.00 0.00 2.66
325 326 8.856490 TCTTCTCTAATTTTCTGCAACAAAAC 57.144 30.769 5.56 0.00 0.00 2.43
344 345 4.045636 TGTTGCAAAGCCTTTTCTTCTC 57.954 40.909 0.00 0.00 0.00 2.87
350 351 3.055167 AGGTCTTTGTTGCAAAGCCTTTT 60.055 39.130 20.85 8.99 33.26 2.27
367 368 6.959639 TCTTTAATTTCTGCAACAAGGTCT 57.040 33.333 0.00 0.00 0.00 3.85
369 370 7.346751 TCTTCTTTAATTTCTGCAACAAGGT 57.653 32.000 0.00 0.00 0.00 3.50
394 395 9.771915 CAACAATGCTTTTGTTACAAAATTTCT 57.228 25.926 21.33 6.63 40.30 2.52
422 423 7.653767 ACGAGTCGATCAGTTTCTAATTTTT 57.346 32.000 21.50 0.00 0.00 1.94
423 424 7.811236 TGTACGAGTCGATCAGTTTCTAATTTT 59.189 33.333 21.50 0.00 0.00 1.82
437 442 4.082190 CCCATTGGATATGTACGAGTCGAT 60.082 45.833 21.50 4.89 0.00 3.59
441 446 3.005472 CGTCCCATTGGATATGTACGAGT 59.995 47.826 3.62 0.00 44.28 4.18
445 450 2.038557 AGCCGTCCCATTGGATATGTAC 59.961 50.000 3.62 0.00 44.28 2.90
447 452 1.072331 GAGCCGTCCCATTGGATATGT 59.928 52.381 3.62 0.00 44.28 2.29
452 457 2.668632 GTGAGCCGTCCCATTGGA 59.331 61.111 3.62 0.00 38.75 3.53
453 458 2.819595 CGTGAGCCGTCCCATTGG 60.820 66.667 0.00 0.00 0.00 3.16
470 475 1.033202 TTTAAAAGATCGGCCGGGCC 61.033 55.000 28.61 28.61 46.75 5.80
474 479 3.625764 TGATCCTTTTAAAAGATCGGCCG 59.374 43.478 26.11 22.12 38.28 6.13
541 547 1.164041 CGGAGCGTCACCCAGTTTTT 61.164 55.000 0.00 0.00 0.00 1.94
542 548 1.597027 CGGAGCGTCACCCAGTTTT 60.597 57.895 0.00 0.00 0.00 2.43
543 549 2.030562 CGGAGCGTCACCCAGTTT 59.969 61.111 0.00 0.00 0.00 2.66
544 550 4.003788 CCGGAGCGTCACCCAGTT 62.004 66.667 0.00 0.00 0.00 3.16
546 552 3.934391 GAACCGGAGCGTCACCCAG 62.934 68.421 9.46 0.00 0.00 4.45
547 553 3.998672 GAACCGGAGCGTCACCCA 61.999 66.667 9.46 0.00 0.00 4.51
550 556 4.719369 AGCGAACCGGAGCGTCAC 62.719 66.667 9.46 0.00 38.61 3.67
551 557 4.717629 CAGCGAACCGGAGCGTCA 62.718 66.667 9.46 0.00 38.61 4.35
552 558 4.415332 TCAGCGAACCGGAGCGTC 62.415 66.667 9.46 7.67 38.61 5.19
553 559 4.421479 CTCAGCGAACCGGAGCGT 62.421 66.667 9.46 0.00 38.61 5.07
555 561 4.821589 CCCTCAGCGAACCGGAGC 62.822 72.222 9.46 11.16 34.84 4.70
556 562 4.821589 GCCCTCAGCGAACCGGAG 62.822 72.222 9.46 0.00 35.78 4.63
565 571 3.214250 CTCCCGATACGCCCTCAGC 62.214 68.421 0.00 0.00 38.52 4.26
566 572 2.565645 CCTCCCGATACGCCCTCAG 61.566 68.421 0.00 0.00 0.00 3.35
567 573 2.520982 CCTCCCGATACGCCCTCA 60.521 66.667 0.00 0.00 0.00 3.86
568 574 3.303928 CCCTCCCGATACGCCCTC 61.304 72.222 0.00 0.00 0.00 4.30
569 575 4.936081 CCCCTCCCGATACGCCCT 62.936 72.222 0.00 0.00 0.00 5.19
570 576 4.928140 TCCCCTCCCGATACGCCC 62.928 72.222 0.00 0.00 0.00 6.13
571 577 3.303928 CTCCCCTCCCGATACGCC 61.304 72.222 0.00 0.00 0.00 5.68
572 578 3.303928 CCTCCCCTCCCGATACGC 61.304 72.222 0.00 0.00 0.00 4.42
573 579 1.902432 GTCCTCCCCTCCCGATACG 60.902 68.421 0.00 0.00 0.00 3.06
574 580 1.902432 CGTCCTCCCCTCCCGATAC 60.902 68.421 0.00 0.00 0.00 2.24
575 581 2.389449 ACGTCCTCCCCTCCCGATA 61.389 63.158 0.00 0.00 0.00 2.92
576 582 3.752167 ACGTCCTCCCCTCCCGAT 61.752 66.667 0.00 0.00 0.00 4.18
577 583 4.753662 CACGTCCTCCCCTCCCGA 62.754 72.222 0.00 0.00 0.00 5.14
603 609 4.430423 GACGCGCTGGCAAACGAG 62.430 66.667 5.73 11.94 39.92 4.18
606 612 4.683334 GGTGACGCGCTGGCAAAC 62.683 66.667 5.73 2.86 39.92 2.93
615 621 2.616330 AAATGTGCTGGGTGACGCG 61.616 57.895 3.53 3.53 0.00 6.01
616 622 1.081242 CAAATGTGCTGGGTGACGC 60.081 57.895 0.00 0.00 0.00 5.19
617 623 0.040157 CACAAATGTGCTGGGTGACG 60.040 55.000 0.00 0.00 39.39 4.35
618 624 3.871775 CACAAATGTGCTGGGTGAC 57.128 52.632 0.00 0.00 39.39 3.67
628 634 2.689471 TGCTGAGAGTTTGCACAAATGT 59.311 40.909 0.00 0.00 32.36 2.71
629 635 3.358707 TGCTGAGAGTTTGCACAAATG 57.641 42.857 0.00 0.00 32.36 2.32
630 636 3.130869 TGTTGCTGAGAGTTTGCACAAAT 59.869 39.130 0.00 0.00 36.37 2.32
631 637 2.491298 TGTTGCTGAGAGTTTGCACAAA 59.509 40.909 0.00 0.00 36.37 2.83
632 638 2.090760 TGTTGCTGAGAGTTTGCACAA 58.909 42.857 0.00 0.00 36.37 3.33
633 639 1.401552 GTGTTGCTGAGAGTTTGCACA 59.598 47.619 0.00 0.00 36.37 4.57
634 640 1.595489 CGTGTTGCTGAGAGTTTGCAC 60.595 52.381 0.00 0.00 36.37 4.57
635 641 0.657312 CGTGTTGCTGAGAGTTTGCA 59.343 50.000 0.00 0.00 34.69 4.08
636 642 0.658536 GCGTGTTGCTGAGAGTTTGC 60.659 55.000 0.00 0.00 41.73 3.68
637 643 0.657312 TGCGTGTTGCTGAGAGTTTG 59.343 50.000 0.00 0.00 46.63 2.93
638 644 0.940126 CTGCGTGTTGCTGAGAGTTT 59.060 50.000 0.00 0.00 46.63 2.66
639 645 1.502163 GCTGCGTGTTGCTGAGAGTT 61.502 55.000 0.00 0.00 46.63 3.01
640 646 1.958205 GCTGCGTGTTGCTGAGAGT 60.958 57.895 0.00 0.00 46.63 3.24
641 647 1.501337 TTGCTGCGTGTTGCTGAGAG 61.501 55.000 0.00 0.00 46.63 3.20
642 648 1.094650 TTTGCTGCGTGTTGCTGAGA 61.095 50.000 0.00 0.00 46.63 3.27
643 649 0.931662 GTTTGCTGCGTGTTGCTGAG 60.932 55.000 0.00 0.00 46.63 3.35
644 650 1.063972 GTTTGCTGCGTGTTGCTGA 59.936 52.632 0.00 0.00 46.63 4.26
645 651 2.287965 CGTTTGCTGCGTGTTGCTG 61.288 57.895 0.00 0.00 46.63 4.41
646 652 2.024588 CGTTTGCTGCGTGTTGCT 59.975 55.556 0.00 0.00 46.63 3.91
647 653 2.277884 ACGTTTGCTGCGTGTTGC 60.278 55.556 0.00 0.00 41.33 4.17
648 654 0.316937 ATGACGTTTGCTGCGTGTTG 60.317 50.000 5.61 0.00 43.04 3.33
649 655 0.041312 GATGACGTTTGCTGCGTGTT 60.041 50.000 5.61 0.00 43.04 3.32
650 656 1.569493 GATGACGTTTGCTGCGTGT 59.431 52.632 5.61 0.00 43.04 4.49
651 657 1.154413 GGATGACGTTTGCTGCGTG 60.154 57.895 5.61 0.00 43.04 5.34
652 658 2.667318 CGGATGACGTTTGCTGCGT 61.667 57.895 0.00 0.90 45.86 5.24
653 659 2.096406 CGGATGACGTTTGCTGCG 59.904 61.111 0.00 0.00 37.93 5.18
654 660 2.480555 CCGGATGACGTTTGCTGC 59.519 61.111 0.00 0.00 42.24 5.25
655 661 2.480555 GCCGGATGACGTTTGCTG 59.519 61.111 5.05 0.00 42.24 4.41
656 662 2.852495 ATCGCCGGATGACGTTTGCT 62.852 55.000 5.05 0.00 42.24 3.91
657 663 1.149361 TATCGCCGGATGACGTTTGC 61.149 55.000 5.05 0.00 42.24 3.68
658 664 0.575390 GTATCGCCGGATGACGTTTG 59.425 55.000 5.05 0.00 42.24 2.93
659 665 0.868602 CGTATCGCCGGATGACGTTT 60.869 55.000 5.05 0.00 42.24 3.60
660 666 1.298863 CGTATCGCCGGATGACGTT 60.299 57.895 5.05 0.00 42.24 3.99
661 667 1.996786 AACGTATCGCCGGATGACGT 61.997 55.000 5.05 12.23 40.84 4.34
662 668 0.868602 AAACGTATCGCCGGATGACG 60.869 55.000 5.05 11.50 43.80 4.35
663 669 0.575390 CAAACGTATCGCCGGATGAC 59.425 55.000 5.05 0.00 34.00 3.06
664 670 0.528901 CCAAACGTATCGCCGGATGA 60.529 55.000 5.05 1.30 34.00 2.92
668 674 2.510691 AGCCAAACGTATCGCCGG 60.511 61.111 0.00 0.00 0.00 6.13
717 723 1.089112 TCAATCTTCCATGTGCTGCG 58.911 50.000 0.00 0.00 0.00 5.18
739 745 1.375908 TGACAAGGCTCACGGCATC 60.376 57.895 0.00 0.00 44.01 3.91
772 778 2.357952 CGATCATCTTGGGTACGAGTGA 59.642 50.000 0.00 0.00 0.00 3.41
782 788 5.804473 GCTGTGACTATATCGATCATCTTGG 59.196 44.000 0.00 0.00 0.00 3.61
784 790 6.432472 TGAGCTGTGACTATATCGATCATCTT 59.568 38.462 0.00 0.00 0.00 2.40
792 800 4.294232 CCTTGTGAGCTGTGACTATATCG 58.706 47.826 0.00 0.00 0.00 2.92
899 912 3.139077 AGAACATGTCGGAGGTGAAAAC 58.861 45.455 0.00 0.00 0.00 2.43
904 917 3.775202 CTCTTAGAACATGTCGGAGGTG 58.225 50.000 0.00 0.00 0.00 4.00
923 936 3.072944 GAGCAATGAGGATGTATGGCTC 58.927 50.000 0.00 0.00 41.62 4.70
1003 1016 5.646577 TTCTTTTGGTTTTCGGTTTCAGA 57.353 34.783 0.00 0.00 0.00 3.27
1028 1041 1.000171 GCCTTGTTTGCTCTCCCTTTG 60.000 52.381 0.00 0.00 0.00 2.77
1046 1059 1.446272 CCTTCACTTCCGTCTCGCC 60.446 63.158 0.00 0.00 0.00 5.54
1047 1060 2.095252 GCCTTCACTTCCGTCTCGC 61.095 63.158 0.00 0.00 0.00 5.03
1050 1063 2.217510 TCTAGCCTTCACTTCCGTCT 57.782 50.000 0.00 0.00 0.00 4.18
1171 1185 4.937620 CGGGTTGGATCGAAATGATATGAT 59.062 41.667 0.00 0.00 37.47 2.45
1174 1188 4.563580 CCTCGGGTTGGATCGAAATGATAT 60.564 45.833 0.00 0.00 37.47 1.63
1176 1190 2.485479 CCTCGGGTTGGATCGAAATGAT 60.485 50.000 0.00 0.00 41.06 2.45
1196 1210 1.389106 GTCACGCGTATCAGTTCAACC 59.611 52.381 13.44 0.00 0.00 3.77
1198 1212 2.425578 TGTCACGCGTATCAGTTCAA 57.574 45.000 13.44 0.00 0.00 2.69
1199 1213 2.425578 TTGTCACGCGTATCAGTTCA 57.574 45.000 13.44 0.65 0.00 3.18
1205 1219 5.164090 CCATACATACATTGTCACGCGTATC 60.164 44.000 13.44 8.81 39.87 2.24
1207 1221 4.045783 CCATACATACATTGTCACGCGTA 58.954 43.478 13.44 0.00 39.87 4.42
1211 1225 3.620821 TGCACCATACATACATTGTCACG 59.379 43.478 0.00 0.00 39.87 4.35
1216 1231 3.817084 CCTCCTGCACCATACATACATTG 59.183 47.826 0.00 0.00 0.00 2.82
1217 1232 3.181440 CCCTCCTGCACCATACATACATT 60.181 47.826 0.00 0.00 0.00 2.71
1218 1233 2.373169 CCCTCCTGCACCATACATACAT 59.627 50.000 0.00 0.00 0.00 2.29
1226 1241 1.707427 GAATATCCCCTCCTGCACCAT 59.293 52.381 0.00 0.00 0.00 3.55
1267 1282 0.319641 AACCTTCTTCGCGGACACTC 60.320 55.000 6.13 0.00 0.00 3.51
1268 1283 0.600255 CAACCTTCTTCGCGGACACT 60.600 55.000 6.13 0.00 0.00 3.55
1274 1289 0.243907 TCTCCTCAACCTTCTTCGCG 59.756 55.000 0.00 0.00 0.00 5.87
1286 1301 1.975327 CTTCACCGCCTTCTCCTCA 59.025 57.895 0.00 0.00 0.00 3.86
1331 1346 2.432628 GCCGTCTTGTCCTCCGTG 60.433 66.667 0.00 0.00 0.00 4.94
1356 1371 3.647771 GGTCTTGGGGTCCGGCTT 61.648 66.667 0.00 0.00 0.00 4.35
1388 1403 0.523072 CTTCTTTGGTGCCGGTCATG 59.477 55.000 1.90 0.00 0.00 3.07
1389 1404 0.110486 ACTTCTTTGGTGCCGGTCAT 59.890 50.000 1.90 0.00 0.00 3.06
1403 1418 2.363795 TCGGCCGGATCCACTTCT 60.364 61.111 27.83 0.00 0.00 2.85
1406 1421 4.779733 AGGTCGGCCGGATCCACT 62.780 66.667 27.83 11.57 40.50 4.00
1499 1516 1.202521 TGCTGTACATGGCGGTATGAG 60.203 52.381 0.00 0.00 0.00 2.90
1527 1544 2.497107 TATAGTTTAGCACGCCCGTC 57.503 50.000 0.00 0.00 0.00 4.79
1598 1615 7.929245 TGTTTGCTAAAGACTTACATACAGTGA 59.071 33.333 0.00 0.00 0.00 3.41
1600 1617 7.931948 AGTGTTTGCTAAAGACTTACATACAGT 59.068 33.333 5.87 8.78 41.65 3.55
1680 1699 6.146601 TGAACTGCTGAAATTTTGTCATGA 57.853 33.333 0.00 0.00 0.00 3.07
1683 1702 6.238157 GCAATTGAACTGCTGAAATTTTGTCA 60.238 34.615 10.34 0.00 36.84 3.58
1689 1708 3.319755 CCGCAATTGAACTGCTGAAATT 58.680 40.909 10.34 0.00 37.67 1.82
1703 1722 1.278699 ACAATGGCAATTCCCGCAATT 59.721 42.857 0.00 0.00 33.12 2.32
1707 1726 0.249031 GCTACAATGGCAATTCCCGC 60.249 55.000 0.00 0.00 0.00 6.13
1755 1774 2.957402 ACAAGGCTGTCAGATGGAAA 57.043 45.000 3.32 0.00 0.00 3.13
1758 1777 3.005554 CAGTTACAAGGCTGTCAGATGG 58.994 50.000 3.32 0.00 36.96 3.51
1764 1783 5.689383 TTGAATTCAGTTACAAGGCTGTC 57.311 39.130 8.41 0.00 36.96 3.51
1806 1825 6.605194 GGCCTCCTCTTTGATTAGAAGATTTT 59.395 38.462 0.00 0.00 33.05 1.82
1810 1829 3.456277 GGGCCTCCTCTTTGATTAGAAGA 59.544 47.826 0.84 0.00 0.00 2.87
1814 1833 2.131023 AGGGGCCTCCTCTTTGATTAG 58.869 52.381 0.00 0.00 44.06 1.73
1846 1865 1.074405 ACTTGCATCTTCTTCTGCCCA 59.926 47.619 0.00 0.00 37.59 5.36
1847 1866 1.831580 ACTTGCATCTTCTTCTGCCC 58.168 50.000 0.00 0.00 37.59 5.36
1850 1869 5.218139 GGTTGAAACTTGCATCTTCTTCTG 58.782 41.667 0.00 0.00 0.00 3.02
1851 1870 4.023707 CGGTTGAAACTTGCATCTTCTTCT 60.024 41.667 0.00 0.00 0.00 2.85
1852 1871 4.222114 CGGTTGAAACTTGCATCTTCTTC 58.778 43.478 0.00 0.00 0.00 2.87
1853 1872 3.004734 CCGGTTGAAACTTGCATCTTCTT 59.995 43.478 0.00 0.00 0.00 2.52
1870 1889 2.159226 TGTTCGTTCAAAATTGCCGGTT 60.159 40.909 1.90 0.00 0.00 4.44
1872 1891 2.050691 CTGTTCGTTCAAAATTGCCGG 58.949 47.619 0.00 0.00 0.00 6.13
1874 1893 1.792367 GGCTGTTCGTTCAAAATTGCC 59.208 47.619 0.00 0.00 0.00 4.52
1875 1894 2.468831 TGGCTGTTCGTTCAAAATTGC 58.531 42.857 0.00 0.00 0.00 3.56
1877 1896 5.240623 TGTCTATGGCTGTTCGTTCAAAATT 59.759 36.000 0.00 0.00 0.00 1.82
1895 1914 3.260380 GCATACAGCCTGGAGATGTCTAT 59.740 47.826 0.00 0.00 37.23 1.98
1897 1916 1.415659 GCATACAGCCTGGAGATGTCT 59.584 52.381 0.00 0.00 37.23 3.41
1910 1929 2.099756 TCGGATCACAGACAGCATACAG 59.900 50.000 0.00 0.00 0.00 2.74
1917 1936 1.485838 GCGCATCGGATCACAGACAG 61.486 60.000 0.30 0.00 0.00 3.51
1923 1942 1.277739 CATGTGCGCATCGGATCAC 59.722 57.895 15.91 0.00 31.99 3.06
1933 1952 4.024143 TGTTCGTGGCATGTGCGC 62.024 61.111 0.00 0.00 43.26 6.09
1945 1964 1.424403 TGCCGTATTGAGTGTGTTCG 58.576 50.000 0.00 0.00 0.00 3.95
1969 1988 1.589716 AATCTTCACTTGCGCTGCCC 61.590 55.000 9.73 0.00 0.00 5.36
1976 1995 9.793252 ACACAATTATTATCAATCTTCACTTGC 57.207 29.630 0.00 0.00 0.00 4.01
2176 2207 2.751259 GCTTCTCAATGCATCCTTCACA 59.249 45.455 0.00 0.00 0.00 3.58
2210 2241 0.385029 AGTGCGCAATTTGCTGACAA 59.615 45.000 14.00 0.00 42.25 3.18
2258 2289 1.686587 TCGTGAGAAAGTGGCTCTTGA 59.313 47.619 2.09 0.00 36.40 3.02
2298 2329 2.066807 CGTCGCACGAAGCACATTA 58.933 52.632 0.00 0.00 46.05 1.90
2392 2423 1.227089 CCTCGTGGAGCTTCATCGG 60.227 63.158 14.38 5.27 34.57 4.18
2474 2505 4.860022 CAGGATACAATTTCCAGGTCCTT 58.140 43.478 0.00 0.00 41.41 3.36
2504 2535 7.497579 GGGTGATAATGTTGTTTCTTGGTTTTT 59.502 33.333 0.00 0.00 0.00 1.94
2507 2538 5.600484 TGGGTGATAATGTTGTTTCTTGGTT 59.400 36.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.