Multiple sequence alignment - TraesCS5D01G289900

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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 TraesCS5D01G289900 chr5D 100.000 4382 0 0 1 4382 388339118 388334737 0.000000e+00 8093.0
1 TraesCS5D01G289900 chr5D 86.520 408 34 12 3634 4032 388591233 388590838 3.130000e-116 429.0
2 TraesCS5D01G289900 chr5D 83.513 279 20 12 2730 2990 388591506 388591236 2.040000e-58 237.0
3 TraesCS5D01G289900 chr5A 94.674 2422 71 19 1981 4381 491374234 491371850 0.000000e+00 3705.0
4 TraesCS5D01G289900 chr5A 88.970 961 56 25 652 1603 491376214 491375295 0.000000e+00 1142.0
5 TraesCS5D01G289900 chr5A 88.753 489 41 4 3081 3563 491532676 491532196 1.760000e-163 586.0
6 TraesCS5D01G289900 chr5A 85.751 386 49 5 3999 4381 491525709 491525327 1.900000e-108 403.0
7 TraesCS5D01G289900 chr5A 86.494 348 23 12 1641 1988 491375299 491374976 1.160000e-95 361.0
8 TraesCS5D01G289900 chr5A 81.704 399 53 7 3621 4011 491532137 491531751 9.150000e-82 315.0
9 TraesCS5D01G289900 chr5A 88.750 240 22 4 1 238 491376488 491376252 5.550000e-74 289.0
10 TraesCS5D01G289900 chr6D 86.667 765 76 12 3628 4381 106896003 106895254 0.000000e+00 824.0
11 TraesCS5D01G289900 chr6D 89.198 324 28 1 3240 3563 106896385 106896069 8.830000e-107 398.0
12 TraesCS5D01G289900 chr6D 86.517 267 19 4 2996 3246 106945421 106945156 1.200000e-70 278.0
13 TraesCS5D01G289900 chr5B 88.654 661 44 15 1512 2169 466985152 466984520 0.000000e+00 776.0
14 TraesCS5D01G289900 chr5B 83.607 488 59 10 32 511 466991627 466991153 5.200000e-119 438.0
15 TraesCS5D01G289900 chr5B 88.679 106 11 1 1195 1299 466985256 466985151 1.280000e-25 128.0
16 TraesCS5D01G289900 chr5B 98.276 58 1 0 2164 2221 466975899 466975842 7.750000e-18 102.0
17 TraesCS5D01G289900 chr5B 93.333 45 2 1 7 51 466991835 466991792 1.020000e-06 65.8
18 TraesCS5D01G289900 chr7B 76.812 1449 231 60 1240 2671 44255879 44257239 0.000000e+00 717.0
19 TraesCS5D01G289900 chr7D 74.331 1644 303 66 1239 2819 91665127 91663540 4.880000e-164 588.0
20 TraesCS5D01G289900 chr7D 78.058 556 96 17 2129 2671 92227971 92228513 1.180000e-85 327.0
21 TraesCS5D01G289900 chr6A 84.175 594 66 15 3799 4381 130409090 130408514 6.410000e-153 551.0
22 TraesCS5D01G289900 chr6A 87.500 224 15 4 2996 3208 130409312 130409091 3.380000e-61 246.0
23 TraesCS5D01G289900 chr4D 85.138 545 64 8 3648 4186 20434108 20434641 3.860000e-150 542.0
24 TraesCS5D01G289900 chr7A 83.135 421 62 9 1138 1553 94395397 94395813 4.140000e-100 375.0
25 TraesCS5D01G289900 chr7A 88.889 72 6 2 617 687 469383318 469383388 2.170000e-13 87.9
26 TraesCS5D01G289900 chr4B 79.633 545 57 20 3648 4186 32423272 32423768 4.200000e-90 342.0
27 TraesCS5D01G289900 chr4A 91.209 182 12 1 3650 3827 581199619 581199800 1.220000e-60 244.0
28 TraesCS5D01G289900 chr2B 91.045 67 6 0 621 687 87422354 87422420 1.680000e-14 91.6
29 TraesCS5D01G289900 chr2B 91.379 58 5 0 622 679 514342247 514342190 3.630000e-11 80.5
30 TraesCS5D01G289900 chr2B 84.337 83 9 4 620 698 657271189 657271271 1.310000e-10 78.7
31 TraesCS5D01G289900 chr1D 92.063 63 5 0 617 679 318885403 318885465 6.040000e-14 89.8
32 TraesCS5D01G289900 chr1B 90.769 65 6 0 623 687 18112404 18112468 2.170000e-13 87.9
33 TraesCS5D01G289900 chr2A 90.164 61 5 1 619 679 55949893 55949952 1.310000e-10 78.7
34 TraesCS5D01G289900 chr3B 87.692 65 8 0 623 687 486470315 486470251 4.700000e-10 76.8


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 TraesCS5D01G289900 chr5D 388334737 388339118 4381 True 8093.00 8093 100.0000 1 4382 1 chr5D.!!$R1 4381
1 TraesCS5D01G289900 chr5D 388590838 388591506 668 True 333.00 429 85.0165 2730 4032 2 chr5D.!!$R2 1302
2 TraesCS5D01G289900 chr5A 491371850 491376488 4638 True 1374.25 3705 89.7220 1 4381 4 chr5A.!!$R2 4380
3 TraesCS5D01G289900 chr5A 491531751 491532676 925 True 450.50 586 85.2285 3081 4011 2 chr5A.!!$R3 930
4 TraesCS5D01G289900 chr6D 106895254 106896385 1131 True 611.00 824 87.9325 3240 4381 2 chr6D.!!$R2 1141
5 TraesCS5D01G289900 chr5B 466984520 466985256 736 True 452.00 776 88.6665 1195 2169 2 chr5B.!!$R2 974
6 TraesCS5D01G289900 chr5B 466991153 466991835 682 True 251.90 438 88.4700 7 511 2 chr5B.!!$R3 504
7 TraesCS5D01G289900 chr7B 44255879 44257239 1360 False 717.00 717 76.8120 1240 2671 1 chr7B.!!$F1 1431
8 TraesCS5D01G289900 chr7D 91663540 91665127 1587 True 588.00 588 74.3310 1239 2819 1 chr7D.!!$R1 1580
9 TraesCS5D01G289900 chr7D 92227971 92228513 542 False 327.00 327 78.0580 2129 2671 1 chr7D.!!$F1 542
10 TraesCS5D01G289900 chr6A 130408514 130409312 798 True 398.50 551 85.8375 2996 4381 2 chr6A.!!$R1 1385
11 TraesCS5D01G289900 chr4D 20434108 20434641 533 False 542.00 542 85.1380 3648 4186 1 chr4D.!!$F1 538

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
469 662 0.109342 GATGGCTAGGACCCACATGG 59.891 60.000 0.0 0.0 41.37 3.66 F
1459 1659 0.118144 AGAGCTGGGAGAAGGAAGGT 59.882 55.000 0.0 0.0 0.00 3.50 F
1863 2128 0.174162 GCAACATGGATGACCTTGGC 59.826 55.000 0.0 0.0 43.06 4.52 F
2689 3748 1.475682 GCCAAAGAAAGCCAGATCAGG 59.524 52.381 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 2124 0.037447 TCGGTCATCCATGTTGCCAA 59.963 50.000 0.00 0.00 0.00 4.52 R
2873 3941 0.726827 ACAACTTGATATGCCACGCG 59.273 50.000 3.53 3.53 0.00 6.01 R
3369 4474 1.694150 AGGCAGTGAAGTGTAAGCTCA 59.306 47.619 0.00 0.00 0.00 4.26 R
3901 5012 3.646162 ACCATCTGTCTGGACAAACTACA 59.354 43.478 4.94 0.00 41.33 2.74 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 4.082787 TGAATGCTAGCAGTTAACTTTGGC 60.083 41.667 23.89 11.27 0.00 4.52
120 305 7.360113 ACCACATTAAACAACTTTTCATCCT 57.640 32.000 0.00 0.00 0.00 3.24
124 309 9.965824 CACATTAAACAACTTTTCATCCTTAGT 57.034 29.630 0.00 0.00 0.00 2.24
131 316 9.503399 AACAACTTTTCATCCTTAGTACCTAAG 57.497 33.333 4.39 4.39 42.00 2.18
135 320 8.033626 ACTTTTCATCCTTAGTACCTAAGTTCG 58.966 37.037 9.49 0.00 41.09 3.95
137 322 4.951715 TCATCCTTAGTACCTAAGTTCGCA 59.048 41.667 9.49 0.00 41.09 5.10
147 332 8.212317 AGTACCTAAGTTCGCAAAAAGTTTTA 57.788 30.769 0.24 0.00 0.00 1.52
180 366 8.812513 TTACCCCTTCTAAAGTATTTTAAGCC 57.187 34.615 0.00 0.00 40.09 4.35
267 453 2.996621 GCACTATCGAGAAGCAAGTGTT 59.003 45.455 0.00 0.00 39.74 3.32
270 456 3.990469 ACTATCGAGAAGCAAGTGTTGTG 59.010 43.478 0.00 0.00 0.00 3.33
284 470 3.392616 AGTGTTGTGGAGAAGAATGAGGT 59.607 43.478 0.00 0.00 0.00 3.85
286 472 3.077359 GTTGTGGAGAAGAATGAGGTGG 58.923 50.000 0.00 0.00 0.00 4.61
310 496 2.159476 CCAATGAACTCGGAGTTGCATG 60.159 50.000 26.87 19.52 38.80 4.06
313 499 0.716108 GAACTCGGAGTTGCATGACG 59.284 55.000 26.87 0.00 38.80 4.35
322 508 2.146342 AGTTGCATGACGTCAAGAAGG 58.854 47.619 24.13 10.82 0.00 3.46
339 525 5.324832 AGAAGGAACCCATCAAGAAAGAA 57.675 39.130 0.00 0.00 0.00 2.52
346 532 4.536765 ACCCATCAAGAAAGAAGTTGTGT 58.463 39.130 0.00 0.00 0.00 3.72
347 533 4.339247 ACCCATCAAGAAAGAAGTTGTGTG 59.661 41.667 0.00 0.00 0.00 3.82
348 534 4.293415 CCATCAAGAAAGAAGTTGTGTGC 58.707 43.478 0.00 0.00 0.00 4.57
364 550 4.647291 GTGTGCACATACACTTGACTAC 57.353 45.455 24.69 0.68 45.70 2.73
366 552 3.070302 TGTGCACATACACTTGACTACCA 59.930 43.478 17.42 0.00 41.30 3.25
383 570 7.054124 TGACTACCATGAGAAAAAGAAGTGTT 58.946 34.615 0.00 0.00 0.00 3.32
392 579 2.922740 AAAGAAGTGTTCGGCTACCA 57.077 45.000 0.00 0.00 34.02 3.25
400 587 0.243095 GTTCGGCTACCAGTTCGAGT 59.757 55.000 0.00 0.00 33.11 4.18
403 590 1.805945 GGCTACCAGTTCGAGTGCG 60.806 63.158 0.00 0.00 39.35 5.34
404 591 1.805945 GCTACCAGTTCGAGTGCGG 60.806 63.158 0.00 0.00 38.28 5.69
419 607 1.200020 GTGCGGGAAAAATGTCTGGAG 59.800 52.381 0.00 0.00 0.00 3.86
423 611 3.005367 GCGGGAAAAATGTCTGGAGAAAA 59.995 43.478 0.00 0.00 0.00 2.29
446 639 4.388080 CACCGCATGCCACGTGTG 62.388 66.667 15.65 7.57 0.00 3.82
469 662 0.109342 GATGGCTAGGACCCACATGG 59.891 60.000 0.00 0.00 41.37 3.66
482 675 3.631250 CCCACATGGTAGGTTGCTAAAT 58.369 45.455 0.00 0.00 0.00 1.40
488 681 4.765813 TGGTAGGTTGCTAAATAGGGTC 57.234 45.455 0.00 0.00 0.00 4.46
496 689 5.336451 GGTTGCTAAATAGGGTCAAAACTGG 60.336 44.000 0.00 0.00 0.00 4.00
497 690 3.761752 TGCTAAATAGGGTCAAAACTGGC 59.238 43.478 0.00 0.00 0.00 4.85
511 704 6.756542 GTCAAAACTGGCAAAACTTTCACTAT 59.243 34.615 0.00 0.00 0.00 2.12
512 705 7.918562 GTCAAAACTGGCAAAACTTTCACTATA 59.081 33.333 0.00 0.00 0.00 1.31
513 706 8.470805 TCAAAACTGGCAAAACTTTCACTATAA 58.529 29.630 0.00 0.00 0.00 0.98
514 707 9.092876 CAAAACTGGCAAAACTTTCACTATAAA 57.907 29.630 0.00 0.00 0.00 1.40
515 708 8.642908 AAACTGGCAAAACTTTCACTATAAAC 57.357 30.769 0.00 0.00 0.00 2.01
516 709 7.341445 ACTGGCAAAACTTTCACTATAAACA 57.659 32.000 0.00 0.00 0.00 2.83
517 710 7.425606 ACTGGCAAAACTTTCACTATAAACAG 58.574 34.615 0.00 0.00 0.00 3.16
518 711 6.744112 TGGCAAAACTTTCACTATAAACAGG 58.256 36.000 0.00 0.00 0.00 4.00
519 712 6.322712 TGGCAAAACTTTCACTATAAACAGGT 59.677 34.615 0.00 0.00 0.00 4.00
520 713 6.640907 GGCAAAACTTTCACTATAAACAGGTG 59.359 38.462 0.00 0.00 0.00 4.00
521 714 7.422399 GCAAAACTTTCACTATAAACAGGTGA 58.578 34.615 0.00 0.00 38.07 4.02
522 715 7.918562 GCAAAACTTTCACTATAAACAGGTGAA 59.081 33.333 0.00 0.00 44.69 3.18
539 732 5.500645 GGTGAAAGCTGACAAGTAAAACT 57.499 39.130 0.00 0.00 0.00 2.66
540 733 5.891451 GGTGAAAGCTGACAAGTAAAACTT 58.109 37.500 0.00 0.00 39.39 2.66
541 734 6.330278 GGTGAAAGCTGACAAGTAAAACTTT 58.670 36.000 0.00 0.00 36.03 2.66
542 735 6.472486 GGTGAAAGCTGACAAGTAAAACTTTC 59.528 38.462 0.00 0.00 36.03 2.62
543 736 7.027161 GTGAAAGCTGACAAGTAAAACTTTCA 58.973 34.615 10.32 10.32 45.37 2.69
544 737 7.027161 TGAAAGCTGACAAGTAAAACTTTCAC 58.973 34.615 10.32 0.00 43.74 3.18
545 738 6.759497 AAGCTGACAAGTAAAACTTTCACT 57.241 33.333 0.00 0.00 36.03 3.41
546 739 7.859325 AAGCTGACAAGTAAAACTTTCACTA 57.141 32.000 0.00 0.00 36.03 2.74
547 740 7.859325 AGCTGACAAGTAAAACTTTCACTAA 57.141 32.000 0.00 0.00 36.03 2.24
548 741 8.276252 AGCTGACAAGTAAAACTTTCACTAAA 57.724 30.769 0.00 0.00 36.03 1.85
549 742 8.903820 AGCTGACAAGTAAAACTTTCACTAAAT 58.096 29.630 0.00 0.00 36.03 1.40
550 743 9.170584 GCTGACAAGTAAAACTTTCACTAAATC 57.829 33.333 0.00 0.00 36.03 2.17
551 744 9.370126 CTGACAAGTAAAACTTTCACTAAATCG 57.630 33.333 0.00 0.00 36.03 3.34
552 745 8.339714 TGACAAGTAAAACTTTCACTAAATCGG 58.660 33.333 0.00 0.00 36.03 4.18
553 746 7.645402 ACAAGTAAAACTTTCACTAAATCGGG 58.355 34.615 0.00 0.00 36.03 5.14
554 747 7.283807 ACAAGTAAAACTTTCACTAAATCGGGT 59.716 33.333 0.00 0.00 36.03 5.28
555 748 8.776470 CAAGTAAAACTTTCACTAAATCGGGTA 58.224 33.333 0.00 0.00 36.03 3.69
556 749 8.907222 AGTAAAACTTTCACTAAATCGGGTAA 57.093 30.769 0.00 0.00 0.00 2.85
557 750 9.511272 AGTAAAACTTTCACTAAATCGGGTAAT 57.489 29.630 0.00 0.00 0.00 1.89
558 751 9.764870 GTAAAACTTTCACTAAATCGGGTAATC 57.235 33.333 0.00 0.00 0.00 1.75
559 752 6.997239 AACTTTCACTAAATCGGGTAATCC 57.003 37.500 0.00 0.00 0.00 3.01
560 753 6.057321 ACTTTCACTAAATCGGGTAATCCA 57.943 37.500 0.00 0.00 34.36 3.41
561 754 6.113411 ACTTTCACTAAATCGGGTAATCCAG 58.887 40.000 0.00 0.00 34.36 3.86
562 755 5.943349 TTCACTAAATCGGGTAATCCAGA 57.057 39.130 0.00 0.00 41.69 3.86
564 757 5.853936 TCACTAAATCGGGTAATCCAGATG 58.146 41.667 1.20 0.00 45.29 2.90
565 758 5.600898 TCACTAAATCGGGTAATCCAGATGA 59.399 40.000 1.20 0.00 45.29 2.92
566 759 6.099125 TCACTAAATCGGGTAATCCAGATGAA 59.901 38.462 1.20 0.00 45.29 2.57
567 760 6.202954 CACTAAATCGGGTAATCCAGATGAAC 59.797 42.308 1.20 0.00 45.29 3.18
568 761 4.771114 AATCGGGTAATCCAGATGAACA 57.229 40.909 1.20 0.00 45.29 3.18
569 762 4.771114 ATCGGGTAATCCAGATGAACAA 57.229 40.909 0.00 0.00 44.58 2.83
570 763 4.771114 TCGGGTAATCCAGATGAACAAT 57.229 40.909 0.00 0.00 33.27 2.71
571 764 5.110814 TCGGGTAATCCAGATGAACAATT 57.889 39.130 0.00 0.00 33.27 2.32
572 765 4.881273 TCGGGTAATCCAGATGAACAATTG 59.119 41.667 3.24 3.24 33.27 2.32
573 766 4.640201 CGGGTAATCCAGATGAACAATTGT 59.360 41.667 4.92 4.92 34.36 2.71
574 767 5.125417 CGGGTAATCCAGATGAACAATTGTT 59.875 40.000 23.49 23.49 36.72 2.83
575 768 6.317642 CGGGTAATCCAGATGAACAATTGTTA 59.682 38.462 23.33 12.30 35.03 2.41
576 769 7.148154 CGGGTAATCCAGATGAACAATTGTTAA 60.148 37.037 23.33 17.22 35.03 2.01
577 770 8.527810 GGGTAATCCAGATGAACAATTGTTAAA 58.472 33.333 23.33 15.07 35.28 1.52
581 774 9.865321 AATCCAGATGAACAATTGTTAAATGAG 57.135 29.630 23.33 11.63 38.56 2.90
582 775 7.829725 TCCAGATGAACAATTGTTAAATGAGG 58.170 34.615 23.33 18.96 38.56 3.86
583 776 7.451255 TCCAGATGAACAATTGTTAAATGAGGT 59.549 33.333 23.33 0.21 38.56 3.85
584 777 8.739039 CCAGATGAACAATTGTTAAATGAGGTA 58.261 33.333 23.33 3.20 38.56 3.08
614 807 9.667107 TGTGTAAAAGAAATATCAAGGTAGGAG 57.333 33.333 0.00 0.00 0.00 3.69
615 808 9.110502 GTGTAAAAGAAATATCAAGGTAGGAGG 57.889 37.037 0.00 0.00 0.00 4.30
616 809 8.832735 TGTAAAAGAAATATCAAGGTAGGAGGT 58.167 33.333 0.00 0.00 0.00 3.85
622 815 9.682465 AGAAATATCAAGGTAGGAGGTAAAAAC 57.318 33.333 0.00 0.00 0.00 2.43
623 816 9.682465 GAAATATCAAGGTAGGAGGTAAAAACT 57.318 33.333 0.00 0.00 0.00 2.66
626 819 7.809880 ATCAAGGTAGGAGGTAAAAACTACT 57.190 36.000 0.00 0.00 36.81 2.57
627 820 7.237209 TCAAGGTAGGAGGTAAAAACTACTC 57.763 40.000 0.00 0.00 36.81 2.59
633 826 5.087391 GGAGGTAAAAACTACTCCCTCTG 57.913 47.826 0.00 0.00 42.87 3.35
634 827 4.531339 GGAGGTAAAAACTACTCCCTCTGT 59.469 45.833 0.00 0.00 42.87 3.41
635 828 5.337410 GGAGGTAAAAACTACTCCCTCTGTC 60.337 48.000 0.00 0.00 42.87 3.51
636 829 5.404395 AGGTAAAAACTACTCCCTCTGTCT 58.596 41.667 0.00 0.00 0.00 3.41
637 830 5.481122 AGGTAAAAACTACTCCCTCTGTCTC 59.519 44.000 0.00 0.00 0.00 3.36
638 831 5.245526 GGTAAAAACTACTCCCTCTGTCTCA 59.754 44.000 0.00 0.00 0.00 3.27
639 832 6.070710 GGTAAAAACTACTCCCTCTGTCTCAT 60.071 42.308 0.00 0.00 0.00 2.90
640 833 7.123847 GGTAAAAACTACTCCCTCTGTCTCATA 59.876 40.741 0.00 0.00 0.00 2.15
641 834 7.554959 AAAAACTACTCCCTCTGTCTCATAA 57.445 36.000 0.00 0.00 0.00 1.90
642 835 7.741554 AAAACTACTCCCTCTGTCTCATAAT 57.258 36.000 0.00 0.00 0.00 1.28
643 836 6.723298 AACTACTCCCTCTGTCTCATAATG 57.277 41.667 0.00 0.00 0.00 1.90
644 837 5.772004 ACTACTCCCTCTGTCTCATAATGT 58.228 41.667 0.00 0.00 0.00 2.71
645 838 6.912426 ACTACTCCCTCTGTCTCATAATGTA 58.088 40.000 0.00 0.00 0.00 2.29
646 839 7.355101 ACTACTCCCTCTGTCTCATAATGTAA 58.645 38.462 0.00 0.00 0.00 2.41
647 840 6.723298 ACTCCCTCTGTCTCATAATGTAAG 57.277 41.667 0.00 0.00 0.00 2.34
648 841 6.436027 ACTCCCTCTGTCTCATAATGTAAGA 58.564 40.000 0.00 0.00 0.00 2.10
649 842 6.322712 ACTCCCTCTGTCTCATAATGTAAGAC 59.677 42.308 0.00 0.00 39.87 3.01
650 843 5.598830 TCCCTCTGTCTCATAATGTAAGACC 59.401 44.000 0.00 0.00 38.91 3.85
681 874 9.554395 TTGAATCTAGTGTAGTGTCAAAAATCA 57.446 29.630 0.00 0.00 31.59 2.57
741 935 1.091537 TTCGGAATCGTCATTTGGCC 58.908 50.000 0.00 0.00 37.69 5.36
745 939 2.483013 CGGAATCGTCATTTGGCCTCTA 60.483 50.000 3.32 0.00 0.00 2.43
801 995 3.053455 CTCCGTTTGACTTGTCTCTGAC 58.947 50.000 2.35 0.00 0.00 3.51
806 1000 4.200092 GTTTGACTTGTCTCTGACCCTTT 58.800 43.478 2.35 0.00 0.00 3.11
807 1001 3.753294 TGACTTGTCTCTGACCCTTTC 57.247 47.619 2.35 0.00 0.00 2.62
808 1002 3.309296 TGACTTGTCTCTGACCCTTTCT 58.691 45.455 2.35 0.00 0.00 2.52
809 1003 4.480115 TGACTTGTCTCTGACCCTTTCTA 58.520 43.478 2.35 0.00 0.00 2.10
810 1004 4.281182 TGACTTGTCTCTGACCCTTTCTAC 59.719 45.833 2.35 0.00 0.00 2.59
832 1026 2.222819 CGTGATAGCGGCAAAAACTCTC 60.223 50.000 1.45 0.00 0.00 3.20
833 1027 3.003480 GTGATAGCGGCAAAAACTCTCT 58.997 45.455 1.45 0.00 0.00 3.10
839 1033 1.266989 CGGCAAAAACTCTCTGTTCCC 59.733 52.381 0.00 0.00 38.03 3.97
857 1051 0.673437 CCAAACAGGGCACGAATTGT 59.327 50.000 0.00 0.00 0.00 2.71
858 1052 1.068434 CCAAACAGGGCACGAATTGTT 59.932 47.619 0.00 0.00 35.43 2.83
860 1054 3.194062 CAAACAGGGCACGAATTGTTTT 58.806 40.909 1.56 0.00 40.62 2.43
891 1086 6.377327 AAATGAAGTTGTATTATGGGCTCG 57.623 37.500 0.00 0.00 0.00 5.03
974 1169 4.436998 GCGGTCTACTGCGCCACT 62.437 66.667 4.18 0.00 38.61 4.00
976 1171 2.701780 CGGTCTACTGCGCCACTCT 61.702 63.158 4.18 0.00 0.00 3.24
977 1172 1.592223 GGTCTACTGCGCCACTCTT 59.408 57.895 4.18 0.00 0.00 2.85
978 1173 0.458716 GGTCTACTGCGCCACTCTTC 60.459 60.000 4.18 0.00 0.00 2.87
979 1174 0.798771 GTCTACTGCGCCACTCTTCG 60.799 60.000 4.18 0.00 0.00 3.79
980 1175 1.213013 CTACTGCGCCACTCTTCGT 59.787 57.895 4.18 0.00 0.00 3.85
981 1176 0.798771 CTACTGCGCCACTCTTCGTC 60.799 60.000 4.18 0.00 0.00 4.20
982 1177 2.209064 TACTGCGCCACTCTTCGTCC 62.209 60.000 4.18 0.00 0.00 4.79
983 1178 3.288308 CTGCGCCACTCTTCGTCCT 62.288 63.158 4.18 0.00 0.00 3.85
984 1179 2.507324 GCGCCACTCTTCGTCCTC 60.507 66.667 0.00 0.00 0.00 3.71
985 1180 2.202492 CGCCACTCTTCGTCCTCG 60.202 66.667 0.00 0.00 38.55 4.63
986 1181 2.507324 GCCACTCTTCGTCCTCGC 60.507 66.667 0.00 0.00 36.96 5.03
987 1182 2.182030 CCACTCTTCGTCCTCGCC 59.818 66.667 0.00 0.00 36.96 5.54
988 1183 2.182030 CACTCTTCGTCCTCGCCC 59.818 66.667 0.00 0.00 36.96 6.13
1006 1201 1.589414 CCTCATCCTCAACCCCTCTT 58.411 55.000 0.00 0.00 0.00 2.85
1007 1202 2.629639 CCCTCATCCTCAACCCCTCTTA 60.630 54.545 0.00 0.00 0.00 2.10
1014 1209 3.077695 TCCTCAACCCCTCTTACTCTTCT 59.922 47.826 0.00 0.00 0.00 2.85
1015 1210 3.196685 CCTCAACCCCTCTTACTCTTCTG 59.803 52.174 0.00 0.00 0.00 3.02
1016 1211 3.835395 CTCAACCCCTCTTACTCTTCTGT 59.165 47.826 0.00 0.00 0.00 3.41
1018 1213 2.822697 ACCCCTCTTACTCTTCTGTCC 58.177 52.381 0.00 0.00 0.00 4.02
1019 1214 2.111972 ACCCCTCTTACTCTTCTGTCCA 59.888 50.000 0.00 0.00 0.00 4.02
1020 1215 2.763448 CCCCTCTTACTCTTCTGTCCAG 59.237 54.545 0.00 0.00 0.00 3.86
1022 1217 2.828520 CCTCTTACTCTTCTGTCCAGCA 59.171 50.000 0.00 0.00 0.00 4.41
1023 1218 3.119173 CCTCTTACTCTTCTGTCCAGCAG 60.119 52.174 0.00 0.00 46.34 4.24
1025 1220 1.930251 TACTCTTCTGTCCAGCAGCT 58.070 50.000 0.00 0.00 44.66 4.24
1067 1265 6.473455 CACTCAGAAAGACAAAATCAACCAAC 59.527 38.462 0.00 0.00 0.00 3.77
1098 1298 1.452833 GAGATGGGTCCAGCAAGGC 60.453 63.158 8.03 0.00 37.29 4.35
1099 1299 2.825836 GATGGGTCCAGCAAGGCG 60.826 66.667 0.00 0.00 37.29 5.52
1100 1300 3.628646 GATGGGTCCAGCAAGGCGT 62.629 63.158 0.00 0.00 37.29 5.68
1101 1301 3.210012 ATGGGTCCAGCAAGGCGTT 62.210 57.895 0.00 0.00 37.29 4.84
1102 1302 3.365265 GGGTCCAGCAAGGCGTTG 61.365 66.667 14.70 14.70 37.29 4.10
1111 1311 1.208614 CAAGGCGTTGCTCTTGAGC 59.791 57.895 15.01 15.01 38.29 4.26
1112 1312 2.320587 AAGGCGTTGCTCTTGAGCG 61.321 57.895 16.48 5.13 37.69 5.03
1113 1313 3.793144 GGCGTTGCTCTTGAGCGG 61.793 66.667 16.48 10.05 37.69 5.52
1114 1314 2.738521 GCGTTGCTCTTGAGCGGA 60.739 61.111 16.48 6.32 37.69 5.54
1115 1315 2.734673 GCGTTGCTCTTGAGCGGAG 61.735 63.158 16.48 11.09 37.69 4.63
1275 1475 2.750657 GGGAGCTGGGGGAGATGTG 61.751 68.421 0.00 0.00 0.00 3.21
1283 1483 2.725312 GGGGAGATGTGCGAGCTCA 61.725 63.158 15.40 2.24 39.01 4.26
1426 1626 1.993956 TCCACAAAACACCTCCCATG 58.006 50.000 0.00 0.00 0.00 3.66
1428 1628 0.318120 CACAAAACACCTCCCATGCC 59.682 55.000 0.00 0.00 0.00 4.40
1429 1629 0.188342 ACAAAACACCTCCCATGCCT 59.812 50.000 0.00 0.00 0.00 4.75
1451 1651 1.962402 GCTTCCTACAGAGCTGGGAGA 60.962 57.143 0.00 0.00 34.19 3.71
1459 1659 0.118144 AGAGCTGGGAGAAGGAAGGT 59.882 55.000 0.00 0.00 0.00 3.50
1462 1662 0.693049 GCTGGGAGAAGGAAGGTCAA 59.307 55.000 0.00 0.00 0.00 3.18
1463 1663 1.073923 GCTGGGAGAAGGAAGGTCAAA 59.926 52.381 0.00 0.00 0.00 2.69
1600 1816 1.255882 CGGATGAGGATGAGGAGGAG 58.744 60.000 0.00 0.00 0.00 3.69
1603 1819 2.427002 GGATGAGGATGAGGAGGAGGAA 60.427 54.545 0.00 0.00 0.00 3.36
1610 1826 3.261390 GGATGAGGAGGAGGAAGATGATG 59.739 52.174 0.00 0.00 0.00 3.07
1611 1827 3.695357 TGAGGAGGAGGAAGATGATGA 57.305 47.619 0.00 0.00 0.00 2.92
1612 1828 3.303938 TGAGGAGGAGGAAGATGATGAC 58.696 50.000 0.00 0.00 0.00 3.06
1741 1978 0.331278 TCTTCAACCCCCGCATCAAT 59.669 50.000 0.00 0.00 0.00 2.57
1831 2074 2.047370 GCCCCATTTTTGGTGGCG 60.047 61.111 8.21 0.00 36.23 5.69
1845 2088 2.251371 GGCGTTTGTCGTCCTTGC 59.749 61.111 0.00 0.00 42.13 4.01
1846 2089 2.539338 GGCGTTTGTCGTCCTTGCA 61.539 57.895 0.00 0.00 42.13 4.08
1850 2094 1.002900 CGTTTGTCGTCCTTGCAACAT 60.003 47.619 0.00 0.00 34.52 2.71
1859 2124 1.355381 TCCTTGCAACATGGATGACCT 59.645 47.619 0.00 0.00 33.63 3.85
1863 2128 0.174162 GCAACATGGATGACCTTGGC 59.826 55.000 0.00 0.00 43.06 4.52
1864 2129 1.548081 CAACATGGATGACCTTGGCA 58.452 50.000 0.00 0.00 43.06 4.92
1865 2130 1.894466 CAACATGGATGACCTTGGCAA 59.106 47.619 0.00 0.00 43.06 4.52
1866 2131 1.549203 ACATGGATGACCTTGGCAAC 58.451 50.000 0.00 0.00 43.06 4.17
1891 2156 4.355925 ACCGAAAGAAGGTCGTGC 57.644 55.556 0.00 0.00 37.44 5.34
1983 2998 2.361610 CTTGGAGCCGGCATGGTT 60.362 61.111 31.54 7.13 41.21 3.67
2020 3035 1.831389 CGTTGGACAAGCACTCCACG 61.831 60.000 0.00 2.13 37.54 4.94
2107 3131 2.846206 TCAGTTATTGATCTGCCAGGGT 59.154 45.455 0.00 0.00 0.00 4.34
2125 3149 1.604755 GGTTGTGTGTGTTTATGCGGA 59.395 47.619 0.00 0.00 0.00 5.54
2126 3150 2.033550 GGTTGTGTGTGTTTATGCGGAA 59.966 45.455 0.00 0.00 0.00 4.30
2223 3247 3.371063 TCGGTGGAGGTGAGCGTC 61.371 66.667 0.00 0.00 35.82 5.19
2303 3335 3.565307 ACCAGGAGCTCAGATTCTCTAG 58.435 50.000 17.19 0.00 0.00 2.43
2374 3406 7.332430 ACAAATATTGGTGCATTCACAATTGAG 59.668 33.333 13.59 4.14 44.87 3.02
2398 3430 2.106511 CAAGTCCTTGAGGTGGAGGAAA 59.893 50.000 0.61 0.00 43.35 3.13
2435 3475 6.127535 GCCGTATAAGGACATATACTTGGCTA 60.128 42.308 9.10 0.00 39.56 3.93
2438 3478 9.302345 CGTATAAGGACATATACTTGGCTAATG 57.698 37.037 4.00 0.00 36.86 1.90
2445 3485 7.333528 ACATATACTTGGCTAATGTGTTTGG 57.666 36.000 0.00 0.00 29.93 3.28
2488 3528 3.763897 GCTTCAACAATCCACCTGGTATT 59.236 43.478 0.00 0.00 36.34 1.89
2490 3530 5.279456 GCTTCAACAATCCACCTGGTATTTT 60.279 40.000 0.00 0.00 36.34 1.82
2555 3596 3.149981 TGATGCGTTTTATTCACCACCA 58.850 40.909 0.00 0.00 0.00 4.17
2689 3748 1.475682 GCCAAAGAAAGCCAGATCAGG 59.524 52.381 0.00 0.00 0.00 3.86
2772 3831 6.831353 TGGAAGTTCAGTTTGATCTTTTGGTA 59.169 34.615 5.01 0.00 36.76 3.25
2873 3941 3.750652 AGTTGCTTAGCTTGCTCTTCTTC 59.249 43.478 5.60 0.00 0.00 2.87
3189 4292 4.091509 GTCACTGTAACACCTTTAGCATCG 59.908 45.833 0.00 0.00 0.00 3.84
3340 4445 4.148079 TGCATTGGTGGAATAACTGACAA 58.852 39.130 0.00 0.00 0.00 3.18
3341 4446 4.586421 TGCATTGGTGGAATAACTGACAAA 59.414 37.500 0.00 0.00 0.00 2.83
3364 4469 3.950395 GGATAGCTGGCACTTTTCAAGAT 59.050 43.478 0.00 0.00 0.00 2.40
3369 4474 6.350629 AGCTGGCACTTTTCAAGATAAATT 57.649 33.333 0.00 0.00 0.00 1.82
3387 4492 4.756084 AATTGAGCTTACACTTCACTGC 57.244 40.909 0.00 0.00 0.00 4.40
3812 4920 4.440826 ACGTAGTCATGGGAGTATCTCT 57.559 45.455 0.00 0.00 29.74 3.10
3827 4938 8.629158 GGGAGTATCTCTGATCATATGTATGTC 58.371 40.741 1.90 0.00 33.26 3.06
3828 4939 9.407380 GGAGTATCTCTGATCATATGTATGTCT 57.593 37.037 1.90 0.00 33.26 3.41
3860 4971 1.830587 ATCAGCCGAACTGCTCCACA 61.831 55.000 0.94 0.00 46.76 4.17
3894 5005 2.725275 TTAGGCAGCGCGTTTGTTGC 62.725 55.000 8.43 8.41 35.87 4.17
3895 5006 4.921847 GGCAGCGCGTTTGTTGCA 62.922 61.111 17.32 0.00 38.27 4.08
3896 5007 2.730604 GCAGCGCGTTTGTTGCAT 60.731 55.556 8.43 0.00 36.59 3.96
3897 5008 2.302230 GCAGCGCGTTTGTTGCATT 61.302 52.632 8.43 0.00 36.59 3.56
3898 5009 1.820233 GCAGCGCGTTTGTTGCATTT 61.820 50.000 8.43 0.00 36.59 2.32
3899 5010 0.111617 CAGCGCGTTTGTTGCATTTG 60.112 50.000 8.43 0.00 0.00 2.32
3900 5011 0.527385 AGCGCGTTTGTTGCATTTGT 60.527 45.000 8.43 0.00 0.00 2.83
3901 5012 0.300193 GCGCGTTTGTTGCATTTGTT 59.700 45.000 8.43 0.00 0.00 2.83
3902 5013 1.910863 GCGCGTTTGTTGCATTTGTTG 60.911 47.619 8.43 0.00 0.00 3.33
4110 5232 5.774498 ATGGTTTTTCCTCTCTGTTTGAC 57.226 39.130 0.00 0.00 37.07 3.18
4118 5240 5.477607 TCCTCTCTGTTTGACGGAAAATA 57.522 39.130 0.00 0.00 32.26 1.40
4163 5285 9.753674 ACTTTCCCATTTCTCTATTTACATCAA 57.246 29.630 0.00 0.00 0.00 2.57
4381 5512 8.469309 AGATAAATGAAAACTGATATGGGTGG 57.531 34.615 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.138692 AGTTAACTGCTAGCATTCAGAAAAG 57.861 36.000 19.72 5.53 34.57 2.27
65 250 9.920946 AGCATTGAAAATACTAAAATAGGGAGA 57.079 29.630 0.00 0.00 0.00 3.71
124 309 9.453325 CAATAAAACTTTTTGCGAACTTAGGTA 57.547 29.630 0.00 0.00 0.00 3.08
131 316 6.822073 AGACCAATAAAACTTTTTGCGAAC 57.178 33.333 0.00 0.00 0.00 3.95
195 381 0.521735 GTCCGGCAAAAGAATCGCTT 59.478 50.000 0.00 0.00 38.88 4.68
267 453 2.619931 TCCACCTCATTCTTCTCCACA 58.380 47.619 0.00 0.00 0.00 4.17
270 456 2.305927 TGGTTCCACCTCATTCTTCTCC 59.694 50.000 0.00 0.00 39.58 3.71
284 470 1.697432 ACTCCGAGTTCATTGGTTCCA 59.303 47.619 0.00 0.00 33.54 3.53
286 472 2.095718 GCAACTCCGAGTTCATTGGTTC 60.096 50.000 10.98 0.00 36.03 3.62
295 481 0.033504 ACGTCATGCAACTCCGAGTT 59.966 50.000 8.03 8.03 39.39 3.01
298 484 0.032815 TTGACGTCATGCAACTCCGA 59.967 50.000 20.80 0.00 0.00 4.55
310 496 2.289444 TGATGGGTTCCTTCTTGACGTC 60.289 50.000 9.11 9.11 0.00 4.34
313 499 4.021102 TCTTGATGGGTTCCTTCTTGAC 57.979 45.455 0.00 0.00 0.00 3.18
322 508 5.067805 ACACAACTTCTTTCTTGATGGGTTC 59.932 40.000 0.00 0.00 0.00 3.62
346 532 4.020662 TCATGGTAGTCAAGTGTATGTGCA 60.021 41.667 0.00 0.00 0.00 4.57
347 533 4.503910 TCATGGTAGTCAAGTGTATGTGC 58.496 43.478 0.00 0.00 0.00 4.57
348 534 5.965922 TCTCATGGTAGTCAAGTGTATGTG 58.034 41.667 0.00 0.00 0.00 3.21
362 548 5.468746 CCGAACACTTCTTTTTCTCATGGTA 59.531 40.000 0.00 0.00 0.00 3.25
364 550 4.787598 CCGAACACTTCTTTTTCTCATGG 58.212 43.478 0.00 0.00 0.00 3.66
366 552 4.137543 AGCCGAACACTTCTTTTTCTCAT 58.862 39.130 0.00 0.00 0.00 2.90
383 570 1.880894 CACTCGAACTGGTAGCCGA 59.119 57.895 0.00 0.00 0.00 5.54
392 579 1.535462 CATTTTTCCCGCACTCGAACT 59.465 47.619 0.00 0.00 38.10 3.01
400 587 1.073125 TCTCCAGACATTTTTCCCGCA 59.927 47.619 0.00 0.00 0.00 5.69
469 662 6.657966 AGTTTTGACCCTATTTAGCAACCTAC 59.342 38.462 0.00 0.00 0.00 3.18
482 675 3.637769 AGTTTTGCCAGTTTTGACCCTA 58.362 40.909 0.00 0.00 0.00 3.53
488 681 8.641499 TTATAGTGAAAGTTTTGCCAGTTTTG 57.359 30.769 0.00 0.00 0.00 2.44
496 689 7.422399 TCACCTGTTTATAGTGAAAGTTTTGC 58.578 34.615 0.00 0.00 37.58 3.68
511 704 4.523083 ACTTGTCAGCTTTCACCTGTTTA 58.477 39.130 0.00 0.00 0.00 2.01
512 705 3.356290 ACTTGTCAGCTTTCACCTGTTT 58.644 40.909 0.00 0.00 0.00 2.83
513 706 3.004752 ACTTGTCAGCTTTCACCTGTT 57.995 42.857 0.00 0.00 0.00 3.16
514 707 2.717639 ACTTGTCAGCTTTCACCTGT 57.282 45.000 0.00 0.00 0.00 4.00
515 708 5.066505 AGTTTTACTTGTCAGCTTTCACCTG 59.933 40.000 0.00 0.00 0.00 4.00
516 709 5.193679 AGTTTTACTTGTCAGCTTTCACCT 58.806 37.500 0.00 0.00 0.00 4.00
517 710 5.500645 AGTTTTACTTGTCAGCTTTCACC 57.499 39.130 0.00 0.00 0.00 4.02
518 711 7.027161 TGAAAGTTTTACTTGTCAGCTTTCAC 58.973 34.615 14.77 0.00 42.65 3.18
519 712 7.027161 GTGAAAGTTTTACTTGTCAGCTTTCA 58.973 34.615 14.77 14.77 44.17 2.69
520 713 7.251281 AGTGAAAGTTTTACTTGTCAGCTTTC 58.749 34.615 7.20 0.00 38.66 2.62
521 714 7.158099 AGTGAAAGTTTTACTTGTCAGCTTT 57.842 32.000 7.20 0.00 38.66 3.51
522 715 6.759497 AGTGAAAGTTTTACTTGTCAGCTT 57.241 33.333 7.20 0.00 38.66 3.74
523 716 7.859325 TTAGTGAAAGTTTTACTTGTCAGCT 57.141 32.000 17.14 0.00 38.66 4.24
524 717 9.170584 GATTTAGTGAAAGTTTTACTTGTCAGC 57.829 33.333 17.14 0.77 38.66 4.26
525 718 9.370126 CGATTTAGTGAAAGTTTTACTTGTCAG 57.630 33.333 17.14 4.94 38.66 3.51
526 719 8.339714 CCGATTTAGTGAAAGTTTTACTTGTCA 58.660 33.333 17.14 0.00 38.66 3.58
527 720 7.801783 CCCGATTTAGTGAAAGTTTTACTTGTC 59.198 37.037 17.14 11.85 38.66 3.18
528 721 7.283807 ACCCGATTTAGTGAAAGTTTTACTTGT 59.716 33.333 17.14 5.32 38.66 3.16
529 722 7.645402 ACCCGATTTAGTGAAAGTTTTACTTG 58.355 34.615 17.14 4.54 38.66 3.16
530 723 7.812690 ACCCGATTTAGTGAAAGTTTTACTT 57.187 32.000 17.14 1.01 40.80 2.24
531 724 8.907222 TTACCCGATTTAGTGAAAGTTTTACT 57.093 30.769 16.30 16.30 0.00 2.24
532 725 9.764870 GATTACCCGATTTAGTGAAAGTTTTAC 57.235 33.333 2.38 2.38 0.00 2.01
533 726 8.949177 GGATTACCCGATTTAGTGAAAGTTTTA 58.051 33.333 0.00 0.00 0.00 1.52
534 727 7.449086 TGGATTACCCGATTTAGTGAAAGTTTT 59.551 33.333 0.00 0.00 37.93 2.43
535 728 6.943718 TGGATTACCCGATTTAGTGAAAGTTT 59.056 34.615 0.00 0.00 37.93 2.66
536 729 6.478129 TGGATTACCCGATTTAGTGAAAGTT 58.522 36.000 0.00 0.00 37.93 2.66
537 730 6.057321 TGGATTACCCGATTTAGTGAAAGT 57.943 37.500 0.00 0.00 37.93 2.66
538 731 6.346096 TCTGGATTACCCGATTTAGTGAAAG 58.654 40.000 0.00 0.00 37.93 2.62
539 732 6.302535 TCTGGATTACCCGATTTAGTGAAA 57.697 37.500 0.00 0.00 37.93 2.69
540 733 5.943349 TCTGGATTACCCGATTTAGTGAA 57.057 39.130 0.00 0.00 37.93 3.18
541 734 5.600898 TCATCTGGATTACCCGATTTAGTGA 59.399 40.000 0.00 0.00 37.89 3.41
542 735 5.853936 TCATCTGGATTACCCGATTTAGTG 58.146 41.667 0.00 0.00 37.89 2.74
543 736 6.126883 TGTTCATCTGGATTACCCGATTTAGT 60.127 38.462 0.00 0.00 37.89 2.24
544 737 6.288294 TGTTCATCTGGATTACCCGATTTAG 58.712 40.000 0.00 0.00 37.89 1.85
545 738 6.241882 TGTTCATCTGGATTACCCGATTTA 57.758 37.500 0.00 0.00 37.89 1.40
546 739 5.110814 TGTTCATCTGGATTACCCGATTT 57.889 39.130 0.00 0.00 37.89 2.17
547 740 4.771114 TGTTCATCTGGATTACCCGATT 57.229 40.909 0.00 0.00 37.89 3.34
548 741 4.771114 TTGTTCATCTGGATTACCCGAT 57.229 40.909 0.00 0.00 39.99 4.18
549 742 4.771114 ATTGTTCATCTGGATTACCCGA 57.229 40.909 0.00 0.00 37.93 5.14
550 743 4.640201 ACAATTGTTCATCTGGATTACCCG 59.360 41.667 4.92 0.00 37.93 5.28
551 744 6.530019 AACAATTGTTCATCTGGATTACCC 57.470 37.500 18.13 0.00 31.64 3.69
555 748 9.865321 CTCATTTAACAATTGTTCATCTGGATT 57.135 29.630 26.46 2.22 39.31 3.01
556 749 8.472413 CCTCATTTAACAATTGTTCATCTGGAT 58.528 33.333 26.46 4.16 39.31 3.41
557 750 7.451255 ACCTCATTTAACAATTGTTCATCTGGA 59.549 33.333 26.46 15.80 39.31 3.86
558 751 7.605449 ACCTCATTTAACAATTGTTCATCTGG 58.395 34.615 26.46 21.72 39.31 3.86
588 781 9.667107 CTCCTACCTTGATATTTCTTTTACACA 57.333 33.333 0.00 0.00 0.00 3.72
589 782 9.110502 CCTCCTACCTTGATATTTCTTTTACAC 57.889 37.037 0.00 0.00 0.00 2.90
590 783 8.832735 ACCTCCTACCTTGATATTTCTTTTACA 58.167 33.333 0.00 0.00 0.00 2.41
596 789 9.682465 GTTTTTACCTCCTACCTTGATATTTCT 57.318 33.333 0.00 0.00 0.00 2.52
597 790 9.682465 AGTTTTTACCTCCTACCTTGATATTTC 57.318 33.333 0.00 0.00 0.00 2.17
600 793 9.503369 AGTAGTTTTTACCTCCTACCTTGATAT 57.497 33.333 0.00 0.00 32.12 1.63
601 794 8.906238 AGTAGTTTTTACCTCCTACCTTGATA 57.094 34.615 0.00 0.00 32.12 2.15
602 795 7.092979 GGAGTAGTTTTTACCTCCTACCTTGAT 60.093 40.741 0.00 0.00 32.12 2.57
603 796 6.212187 GGAGTAGTTTTTACCTCCTACCTTGA 59.788 42.308 0.00 0.00 32.12 3.02
604 797 6.404708 GGAGTAGTTTTTACCTCCTACCTTG 58.595 44.000 0.00 0.00 32.12 3.61
605 798 5.486775 GGGAGTAGTTTTTACCTCCTACCTT 59.513 44.000 0.00 0.00 32.12 3.50
606 799 5.028802 GGGAGTAGTTTTTACCTCCTACCT 58.971 45.833 0.00 0.00 32.12 3.08
607 800 5.028802 AGGGAGTAGTTTTTACCTCCTACC 58.971 45.833 0.00 0.00 32.12 3.18
608 801 5.957168 AGAGGGAGTAGTTTTTACCTCCTAC 59.043 44.000 0.00 0.00 44.24 3.18
609 802 5.956563 CAGAGGGAGTAGTTTTTACCTCCTA 59.043 44.000 0.00 0.00 44.24 2.94
610 803 4.778427 CAGAGGGAGTAGTTTTTACCTCCT 59.222 45.833 0.00 0.00 44.24 3.69
611 804 4.531339 ACAGAGGGAGTAGTTTTTACCTCC 59.469 45.833 0.00 0.00 44.24 4.30
612 805 5.481122 AGACAGAGGGAGTAGTTTTTACCTC 59.519 44.000 0.00 0.00 43.67 3.85
613 806 5.404395 AGACAGAGGGAGTAGTTTTTACCT 58.596 41.667 0.00 0.00 0.00 3.08
614 807 5.245526 TGAGACAGAGGGAGTAGTTTTTACC 59.754 44.000 0.00 0.00 0.00 2.85
615 808 6.342338 TGAGACAGAGGGAGTAGTTTTTAC 57.658 41.667 0.00 0.00 0.00 2.01
616 809 8.660295 TTATGAGACAGAGGGAGTAGTTTTTA 57.340 34.615 0.00 0.00 0.00 1.52
617 810 7.554959 TTATGAGACAGAGGGAGTAGTTTTT 57.445 36.000 0.00 0.00 0.00 1.94
618 811 7.181125 ACATTATGAGACAGAGGGAGTAGTTTT 59.819 37.037 0.00 0.00 0.00 2.43
619 812 6.670027 ACATTATGAGACAGAGGGAGTAGTTT 59.330 38.462 0.00 0.00 0.00 2.66
620 813 6.198639 ACATTATGAGACAGAGGGAGTAGTT 58.801 40.000 0.00 0.00 0.00 2.24
621 814 5.772004 ACATTATGAGACAGAGGGAGTAGT 58.228 41.667 0.00 0.00 0.00 2.73
622 815 7.721842 TCTTACATTATGAGACAGAGGGAGTAG 59.278 40.741 0.00 0.00 0.00 2.57
623 816 7.502895 GTCTTACATTATGAGACAGAGGGAGTA 59.497 40.741 0.00 0.00 42.28 2.59
624 817 6.322712 GTCTTACATTATGAGACAGAGGGAGT 59.677 42.308 0.00 0.00 42.28 3.85
625 818 6.239176 GGTCTTACATTATGAGACAGAGGGAG 60.239 46.154 13.59 0.00 44.06 4.30
626 819 5.598830 GGTCTTACATTATGAGACAGAGGGA 59.401 44.000 13.59 0.00 44.06 4.20
627 820 5.600484 AGGTCTTACATTATGAGACAGAGGG 59.400 44.000 13.59 0.00 44.06 4.30
628 821 6.723298 AGGTCTTACATTATGAGACAGAGG 57.277 41.667 13.59 0.00 44.06 3.69
629 822 9.442047 AAAAAGGTCTTACATTATGAGACAGAG 57.558 33.333 13.59 0.00 44.06 3.35
659 852 9.950496 AAGATGATTTTTGACACTACACTAGAT 57.050 29.630 0.00 0.00 0.00 1.98
681 874 2.897823 ACACCCTCCATCCCTAAGAT 57.102 50.000 0.00 0.00 34.66 2.40
683 876 3.330126 TCTACACCCTCCATCCCTAAG 57.670 52.381 0.00 0.00 0.00 2.18
722 916 1.091537 GGCCAAATGACGATTCCGAA 58.908 50.000 0.00 0.00 39.50 4.30
723 917 0.251916 AGGCCAAATGACGATTCCGA 59.748 50.000 5.01 0.00 39.50 4.55
725 919 2.044123 AGAGGCCAAATGACGATTCC 57.956 50.000 5.01 0.00 0.00 3.01
730 924 6.093495 TCAAAAAGTATAGAGGCCAAATGACG 59.907 38.462 5.01 0.00 0.00 4.35
771 965 0.953960 GTCAAACGGAGGCCACGATT 60.954 55.000 24.06 16.47 34.93 3.34
801 995 2.135664 CGCTATCACGGTAGAAAGGG 57.864 55.000 0.00 0.00 0.00 3.95
839 1033 2.507339 AACAATTCGTGCCCTGTTTG 57.493 45.000 0.00 0.00 0.00 2.93
862 1056 8.691797 GCCCATAATACAACTTCATTTCCTAAA 58.308 33.333 0.00 0.00 0.00 1.85
863 1057 8.058847 AGCCCATAATACAACTTCATTTCCTAA 58.941 33.333 0.00 0.00 0.00 2.69
864 1058 7.582719 AGCCCATAATACAACTTCATTTCCTA 58.417 34.615 0.00 0.00 0.00 2.94
865 1059 6.435164 AGCCCATAATACAACTTCATTTCCT 58.565 36.000 0.00 0.00 0.00 3.36
866 1060 6.513393 CGAGCCCATAATACAACTTCATTTCC 60.513 42.308 0.00 0.00 0.00 3.13
891 1086 0.179936 CAGAAGACTGAGGCCCATCC 59.820 60.000 0.00 0.00 46.03 3.51
972 1167 2.035940 AGGGCGAGGACGAAGAGT 59.964 61.111 0.00 0.00 42.66 3.24
974 1169 1.379977 ATGAGGGCGAGGACGAAGA 60.380 57.895 0.00 0.00 42.66 2.87
976 1171 2.423898 GGATGAGGGCGAGGACGAA 61.424 63.158 0.00 0.00 42.66 3.85
977 1172 2.833582 GGATGAGGGCGAGGACGA 60.834 66.667 0.00 0.00 42.66 4.20
978 1173 2.835431 AGGATGAGGGCGAGGACG 60.835 66.667 0.00 0.00 42.93 4.79
979 1174 1.330655 TTGAGGATGAGGGCGAGGAC 61.331 60.000 0.00 0.00 0.00 3.85
980 1175 1.001631 TTGAGGATGAGGGCGAGGA 59.998 57.895 0.00 0.00 0.00 3.71
981 1176 1.144936 GTTGAGGATGAGGGCGAGG 59.855 63.158 0.00 0.00 0.00 4.63
982 1177 1.144936 GGTTGAGGATGAGGGCGAG 59.855 63.158 0.00 0.00 0.00 5.03
983 1178 2.367202 GGGTTGAGGATGAGGGCGA 61.367 63.158 0.00 0.00 0.00 5.54
984 1179 2.190578 GGGTTGAGGATGAGGGCG 59.809 66.667 0.00 0.00 0.00 6.13
985 1180 1.988982 GAGGGGTTGAGGATGAGGGC 61.989 65.000 0.00 0.00 0.00 5.19
986 1181 0.327000 AGAGGGGTTGAGGATGAGGG 60.327 60.000 0.00 0.00 0.00 4.30
987 1182 1.589414 AAGAGGGGTTGAGGATGAGG 58.411 55.000 0.00 0.00 0.00 3.86
988 1183 3.379452 AGTAAGAGGGGTTGAGGATGAG 58.621 50.000 0.00 0.00 0.00 2.90
1014 1209 4.025858 GGCTGGAGCTGCTGGACA 62.026 66.667 7.01 2.27 41.70 4.02
1015 1210 4.025858 TGGCTGGAGCTGCTGGAC 62.026 66.667 7.01 6.00 41.70 4.02
1016 1211 4.025858 GTGGCTGGAGCTGCTGGA 62.026 66.667 7.01 0.00 41.70 3.86
1020 1215 4.704833 TTCGGTGGCTGGAGCTGC 62.705 66.667 0.00 0.00 41.70 5.25
1022 1217 2.032681 GTTTCGGTGGCTGGAGCT 59.967 61.111 0.00 0.00 41.70 4.09
1023 1218 3.056328 GGTTTCGGTGGCTGGAGC 61.056 66.667 0.00 0.00 41.14 4.70
1025 1220 3.961414 GGGGTTTCGGTGGCTGGA 61.961 66.667 0.00 0.00 0.00 3.86
1077 1275 0.467384 CTTGCTGGACCCATCTCGAT 59.533 55.000 0.00 0.00 0.00 3.59
1103 1303 1.810441 CTGCTGCTCCGCTCAAGAG 60.810 63.158 0.00 0.00 0.00 2.85
1104 1304 2.263852 CTGCTGCTCCGCTCAAGA 59.736 61.111 0.00 0.00 0.00 3.02
1105 1305 3.497932 GCTGCTGCTCCGCTCAAG 61.498 66.667 8.53 0.00 36.03 3.02
1106 1306 4.318949 TGCTGCTGCTCCGCTCAA 62.319 61.111 17.00 0.00 40.48 3.02
1107 1307 4.754667 CTGCTGCTGCTCCGCTCA 62.755 66.667 17.00 0.00 40.48 4.26
1197 1397 1.617947 AACTCAGATCGGGAGGCCAC 61.618 60.000 17.95 0.00 36.70 5.01
1275 1475 0.038343 GATCTCCTCCATGAGCTCGC 60.038 60.000 9.64 0.00 32.22 5.03
1283 1483 1.935799 CGGATCAGGATCTCCTCCAT 58.064 55.000 9.01 0.00 46.65 3.41
1426 1626 1.153269 GCTCTGTAGGAAGCCAGGC 60.153 63.158 1.84 1.84 0.00 4.85
1428 1628 0.177604 CCAGCTCTGTAGGAAGCCAG 59.822 60.000 0.00 0.00 0.00 4.85
1429 1629 1.267574 CCCAGCTCTGTAGGAAGCCA 61.268 60.000 0.00 0.00 0.00 4.75
1451 1651 2.495084 GACGAAGCTTTGACCTTCCTT 58.505 47.619 20.86 0.00 36.26 3.36
1459 1659 1.072505 GGTGGGGACGAAGCTTTGA 59.927 57.895 20.86 0.00 0.00 2.69
1462 1662 1.990160 TTGTGGTGGGGACGAAGCTT 61.990 55.000 0.00 0.00 0.00 3.74
1463 1663 2.397413 CTTGTGGTGGGGACGAAGCT 62.397 60.000 0.00 0.00 0.00 3.74
1509 1709 1.251527 ATCGAGCACGGAACTGTCCT 61.252 55.000 3.11 0.00 42.44 3.85
1600 1816 3.305950 CCTCTCCATCGTCATCATCTTCC 60.306 52.174 0.00 0.00 0.00 3.46
1603 1819 3.156293 CTCCTCTCCATCGTCATCATCT 58.844 50.000 0.00 0.00 0.00 2.90
1610 1826 2.060050 TCTTCCTCCTCTCCATCGTC 57.940 55.000 0.00 0.00 0.00 4.20
1611 1827 2.765689 ATCTTCCTCCTCTCCATCGT 57.234 50.000 0.00 0.00 0.00 3.73
1612 1828 5.736951 AATAATCTTCCTCCTCTCCATCG 57.263 43.478 0.00 0.00 0.00 3.84
1831 2074 2.384382 CATGTTGCAAGGACGACAAAC 58.616 47.619 0.00 0.00 37.49 2.93
1845 2088 1.548081 TGCCAAGGTCATCCATGTTG 58.452 50.000 0.00 0.00 35.89 3.33
1846 2089 1.895131 GTTGCCAAGGTCATCCATGTT 59.105 47.619 0.00 0.00 35.89 2.71
1850 2094 1.548081 CATGTTGCCAAGGTCATCCA 58.452 50.000 0.00 0.00 35.89 3.41
1859 2124 0.037447 TCGGTCATCCATGTTGCCAA 59.963 50.000 0.00 0.00 0.00 4.52
1863 2128 3.127548 CCTTCTTTCGGTCATCCATGTTG 59.872 47.826 0.00 0.00 0.00 3.33
1864 2129 3.244911 ACCTTCTTTCGGTCATCCATGTT 60.245 43.478 0.00 0.00 0.00 2.71
1865 2130 2.305927 ACCTTCTTTCGGTCATCCATGT 59.694 45.455 0.00 0.00 0.00 3.21
1866 2131 2.991250 ACCTTCTTTCGGTCATCCATG 58.009 47.619 0.00 0.00 0.00 3.66
1891 2156 1.607148 TGATGAGTATACAGACGCCCG 59.393 52.381 5.50 0.00 0.00 6.13
1983 2998 2.121963 AGGACACCAGGCCTTCCA 60.122 61.111 20.96 0.00 33.74 3.53
2080 3104 4.349048 TGGCAGATCAATAACTGATAGGCT 59.651 41.667 0.00 0.00 45.23 4.58
2107 3131 4.371855 TTTTCCGCATAAACACACACAA 57.628 36.364 0.00 0.00 0.00 3.33
2125 3149 5.208121 TGACAAAATGAGGAGAGGGTTTTT 58.792 37.500 0.00 0.00 0.00 1.94
2126 3150 4.803452 TGACAAAATGAGGAGAGGGTTTT 58.197 39.130 0.00 0.00 0.00 2.43
2161 3185 4.922206 TCGTCTAAGTCTACAACCCCTAA 58.078 43.478 0.00 0.00 0.00 2.69
2223 3247 0.668535 TCCATGACGCTACTCCATCG 59.331 55.000 0.00 0.00 0.00 3.84
2303 3335 1.040339 TCCACACAGCCAACAAACCC 61.040 55.000 0.00 0.00 0.00 4.11
2351 3383 5.813672 GCTCAATTGTGAATGCACCAATATT 59.186 36.000 11.59 0.00 44.51 1.28
2391 3423 2.937149 GGCTTACTCGACAATTTCCTCC 59.063 50.000 0.00 0.00 0.00 4.30
2398 3430 4.581824 TCCTTATACGGCTTACTCGACAAT 59.418 41.667 0.00 0.00 0.00 2.71
2435 3475 5.053978 AGAAAGAGACTCCCAAACACATT 57.946 39.130 0.00 0.00 0.00 2.71
2438 3478 4.344359 AGAGAAAGAGACTCCCAAACAC 57.656 45.455 0.00 0.00 35.27 3.32
2526 3567 8.085296 TGGTGAATAAAACGCATCATAAAAACT 58.915 29.630 0.00 0.00 0.00 2.66
2539 3580 4.555262 AGCATTTGGTGGTGAATAAAACG 58.445 39.130 0.00 0.00 37.12 3.60
2689 3748 1.373570 GCCATGACCTACTTCACTGC 58.626 55.000 0.00 0.00 0.00 4.40
2772 3831 8.112183 AGGATAAGACTCAAAATGGAAATCAGT 58.888 33.333 0.00 0.00 0.00 3.41
2873 3941 0.726827 ACAACTTGATATGCCACGCG 59.273 50.000 3.53 3.53 0.00 6.01
3189 4292 3.245990 GCCTGTTTCTTGCATTTTGTGTC 59.754 43.478 0.00 0.00 0.00 3.67
3280 4383 7.375053 GTGATATCTCTCACATAGTTCTTCCC 58.625 42.308 3.98 0.00 44.03 3.97
3340 4445 3.439857 TGAAAAGTGCCAGCTATCCTT 57.560 42.857 0.00 0.00 0.00 3.36
3341 4446 3.009473 TCTTGAAAAGTGCCAGCTATCCT 59.991 43.478 0.00 0.00 46.34 3.24
3364 4469 5.181245 GGCAGTGAAGTGTAAGCTCAATTTA 59.819 40.000 0.00 0.00 0.00 1.40
3369 4474 1.694150 AGGCAGTGAAGTGTAAGCTCA 59.306 47.619 0.00 0.00 0.00 4.26
3387 4492 4.562347 CCCATCGATCTACAAGAATGGAGG 60.562 50.000 0.00 0.00 38.14 4.30
3483 4588 6.321181 TCAGGTAAAACATTGTTTTCTGCTCT 59.679 34.615 26.25 15.85 0.00 4.09
3487 4592 8.472683 TTTGTCAGGTAAAACATTGTTTTCTG 57.527 30.769 26.25 25.06 0.00 3.02
3589 4694 4.956075 AGTGAATGGGTTTCTTGTGTCTTT 59.044 37.500 0.00 0.00 35.23 2.52
3590 4695 4.536765 AGTGAATGGGTTTCTTGTGTCTT 58.463 39.130 0.00 0.00 35.23 3.01
3812 4920 8.186709 ACTGATGTGAGACATACATATGATCA 57.813 34.615 10.38 0.00 39.27 2.92
3827 4938 4.183865 TCGGCTGATAAAACTGATGTGAG 58.816 43.478 0.00 0.00 0.00 3.51
3828 4939 4.200838 TCGGCTGATAAAACTGATGTGA 57.799 40.909 0.00 0.00 0.00 3.58
3860 4971 4.519350 GCTGCCTAAGAAACTACCAAAACT 59.481 41.667 0.00 0.00 0.00 2.66
3894 5005 6.038161 TCTGTCTGGACAAACTACAACAAATG 59.962 38.462 4.94 0.00 41.33 2.32
3895 5006 6.119536 TCTGTCTGGACAAACTACAACAAAT 58.880 36.000 4.94 0.00 41.33 2.32
3896 5007 5.492895 TCTGTCTGGACAAACTACAACAAA 58.507 37.500 4.94 0.00 41.33 2.83
3897 5008 5.092554 TCTGTCTGGACAAACTACAACAA 57.907 39.130 4.94 0.00 41.33 2.83
3898 5009 4.746535 TCTGTCTGGACAAACTACAACA 57.253 40.909 4.94 0.00 41.33 3.33
3899 5010 4.452455 CCATCTGTCTGGACAAACTACAAC 59.548 45.833 4.94 0.00 41.33 3.32
3900 5011 4.102524 ACCATCTGTCTGGACAAACTACAA 59.897 41.667 4.94 0.00 41.33 2.41
3901 5012 3.646162 ACCATCTGTCTGGACAAACTACA 59.354 43.478 4.94 0.00 41.33 2.74
3902 5013 3.997021 CACCATCTGTCTGGACAAACTAC 59.003 47.826 4.94 0.00 41.33 2.73


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

AutoCloner maintained by Alex Coulton.