Multiple sequence alignment - TraesCS5A01G321900

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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 TraesCS5A01G321900 chr5A 100.000 5411 0 0 1 5411 534568838 534574248 0.000000e+00 9993.0
1 TraesCS5A01G321900 chr5A 82.759 638 90 13 1348 1972 534464181 534464811 7.920000e-153 551.0
2 TraesCS5A01G321900 chr5A 75.311 563 111 23 3291 3842 534372788 534373333 1.510000e-60 244.0
3 TraesCS5A01G321900 chr5A 87.500 160 20 0 1106 1265 534625623 534625782 9.260000e-43 185.0
4 TraesCS5A01G321900 chr5A 84.127 126 15 3 2722 2847 64376737 64376617 3.420000e-22 117.0
5 TraesCS5A01G321900 chr5A 81.667 120 21 1 2418 2536 534627002 534627121 1.240000e-16 99.0
6 TraesCS5A01G321900 chr5B 90.836 1866 143 16 2843 4695 507372659 507374509 0.000000e+00 2473.0
7 TraesCS5A01G321900 chr5B 91.678 1442 81 14 832 2250 507370708 507372133 0.000000e+00 1962.0
8 TraesCS5A01G321900 chr5B 85.497 593 55 16 4680 5255 507374555 507375133 1.680000e-164 590.0
9 TraesCS5A01G321900 chr5B 84.106 604 79 12 1381 1971 507585293 507585892 7.870000e-158 568.0
10 TraesCS5A01G321900 chr5B 83.361 607 82 13 1380 1972 507059186 507059787 1.330000e-150 544.0
11 TraesCS5A01G321900 chr5B 83.333 606 76 16 928 1513 507590097 507590697 2.220000e-148 536.0
12 TraesCS5A01G321900 chr5B 77.099 917 154 37 1089 1972 507187588 507188481 3.790000e-131 479.0
13 TraesCS5A01G321900 chr5B 86.932 352 30 7 2385 2725 507372316 507372662 1.100000e-101 381.0
14 TraesCS5A01G321900 chr5B 89.683 252 26 0 2952 3203 507189922 507190173 6.760000e-84 322.0
15 TraesCS5A01G321900 chr5B 85.500 200 27 1 3291 3488 507190291 507190490 1.980000e-49 207.0
16 TraesCS5A01G321900 chr5B 94.872 78 1 3 5336 5411 316603112 316603188 9.520000e-23 119.0
17 TraesCS5A01G321900 chr5B 93.590 78 3 2 5336 5411 649421629 649421552 1.230000e-21 115.0
18 TraesCS5A01G321900 chr5B 73.090 301 63 16 3713 4007 507061368 507061656 2.080000e-14 91.6
19 TraesCS5A01G321900 chr5D 93.591 1685 55 23 596 2253 421090550 421088892 0.000000e+00 2464.0
20 TraesCS5A01G321900 chr5D 89.376 1826 162 18 2843 4649 420964257 420962445 0.000000e+00 2268.0
21 TraesCS5A01G321900 chr5D 92.287 1491 84 11 2257 3743 421087484 421086021 0.000000e+00 2087.0
22 TraesCS5A01G321900 chr5D 90.031 1304 91 12 3987 5266 421085099 421083811 0.000000e+00 1652.0
23 TraesCS5A01G321900 chr5D 90.223 583 53 3 7 585 470046457 470045875 0.000000e+00 758.0
24 TraesCS5A01G321900 chr5D 89.134 589 59 4 1 585 360902436 360903023 0.000000e+00 728.0
25 TraesCS5A01G321900 chr5D 79.847 918 141 30 1092 1975 421138848 421137941 9.890000e-177 630.0
26 TraesCS5A01G321900 chr5D 80.135 886 135 32 1115 1975 421163469 421162600 1.660000e-174 623.0
27 TraesCS5A01G321900 chr5D 86.879 564 59 11 4758 5315 420962279 420961725 7.700000e-173 617.0
28 TraesCS5A01G321900 chr5D 85.050 301 33 6 2392 2685 420964650 420964355 4.100000e-76 296.0
29 TraesCS5A01G321900 chr5D 82.840 338 48 9 2954 3285 420969729 420969396 1.470000e-75 294.0
30 TraesCS5A01G321900 chr5D 87.649 251 29 2 2954 3203 421136415 421136166 1.910000e-74 291.0
31 TraesCS5A01G321900 chr5D 75.395 569 109 25 3291 3845 421172723 421172172 4.190000e-61 246.0
32 TraesCS5A01G321900 chr5D 86.758 219 17 6 2053 2265 420964911 420964699 3.260000e-57 233.0
33 TraesCS5A01G321900 chr5D 86.207 232 10 3 3764 3995 421085491 421085282 1.170000e-56 231.0
34 TraesCS5A01G321900 chr4A 91.081 583 48 3 7 585 690120415 690120997 0.000000e+00 785.0
35 TraesCS5A01G321900 chr2D 89.679 591 56 3 1 587 589887546 589888135 0.000000e+00 749.0
36 TraesCS5A01G321900 chr2D 89.041 584 58 4 7 585 448192157 448191575 0.000000e+00 719.0
37 TraesCS5A01G321900 chr2D 74.548 609 119 23 1382 1969 7877204 7877797 3.260000e-57 233.0
38 TraesCS5A01G321900 chr6D 89.555 584 56 3 7 585 54233357 54232774 0.000000e+00 736.0
39 TraesCS5A01G321900 chr6D 94.737 76 3 1 5337 5411 325696546 325696621 3.420000e-22 117.0
40 TraesCS5A01G321900 chr6D 82.308 130 17 2 2722 2851 367751207 367751330 2.060000e-19 108.0
41 TraesCS5A01G321900 chr7D 89.519 582 56 3 9 585 550995874 550996455 0.000000e+00 732.0
42 TraesCS5A01G321900 chr7B 89.537 583 53 5 7 585 577304028 577303450 0.000000e+00 732.0
43 TraesCS5A01G321900 chr7B 93.506 77 4 1 5336 5411 591331795 591331871 4.430000e-21 113.0
44 TraesCS5A01G321900 chr7A 89.078 586 59 3 8 588 722581422 722580837 0.000000e+00 723.0
45 TraesCS5A01G321900 chrUn 80.135 886 135 32 1115 1975 270061096 270060227 1.660000e-174 623.0
46 TraesCS5A01G321900 chrUn 83.031 607 84 13 1380 1972 325468858 325468257 2.870000e-147 532.0
47 TraesCS5A01G321900 chrUn 93.506 77 3 2 5337 5411 90109931 90109855 4.430000e-21 113.0
48 TraesCS5A01G321900 chrUn 79.104 134 23 4 3713 3845 466887369 466887240 2.680000e-13 87.9
49 TraesCS5A01G321900 chr1B 83.748 603 85 9 1378 1969 632659649 632659049 4.730000e-155 558.0
50 TraesCS5A01G321900 chr1B 80.328 366 64 5 2843 3203 632657508 632657146 2.480000e-68 270.0
51 TraesCS5A01G321900 chr1B 94.667 75 3 1 5337 5411 98240753 98240826 1.230000e-21 115.0
52 TraesCS5A01G321900 chr2B 74.860 537 102 20 1453 1971 4503404 4503925 4.250000e-51 213.0
53 TraesCS5A01G321900 chr2B 84.496 129 12 4 2718 2844 550043587 550043465 2.650000e-23 121.0
54 TraesCS5A01G321900 chr4B 84.677 124 14 1 2722 2845 564869585 564869467 9.520000e-23 119.0
55 TraesCS5A01G321900 chr3B 94.737 76 3 1 5337 5411 737704206 737704131 3.420000e-22 117.0
56 TraesCS5A01G321900 chr3B 84.167 120 14 1 2728 2847 661840403 661840289 1.590000e-20 111.0
57 TraesCS5A01G321900 chr6A 93.506 77 3 2 5337 5411 564113669 564113745 4.430000e-21 113.0
58 TraesCS5A01G321900 chr2A 93.506 77 3 2 5337 5411 709581323 709581247 4.430000e-21 113.0
59 TraesCS5A01G321900 chr3A 82.171 129 17 3 2722 2850 155427669 155427547 7.410000e-19 106.0
60 TraesCS5A01G321900 chr1D 82.927 123 16 1 2722 2844 20995887 20996004 7.410000e-19 106.0
61 TraesCS5A01G321900 chr1D 82.927 123 16 1 2722 2844 365841139 365841256 7.410000e-19 106.0


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 TraesCS5A01G321900 chr5A 534568838 534574248 5410 False 9993.0 9993 100.00000 1 5411 1 chr5A.!!$F3 5410
1 TraesCS5A01G321900 chr5A 534464181 534464811 630 False 551.0 551 82.75900 1348 1972 1 chr5A.!!$F2 624
2 TraesCS5A01G321900 chr5A 534372788 534373333 545 False 244.0 244 75.31100 3291 3842 1 chr5A.!!$F1 551
3 TraesCS5A01G321900 chr5B 507370708 507375133 4425 False 1351.5 2473 88.73575 832 5255 4 chr5B.!!$F6 4423
4 TraesCS5A01G321900 chr5B 507585293 507585892 599 False 568.0 568 84.10600 1381 1971 1 chr5B.!!$F2 590
5 TraesCS5A01G321900 chr5B 507590097 507590697 600 False 536.0 536 83.33300 928 1513 1 chr5B.!!$F3 585
6 TraesCS5A01G321900 chr5B 507187588 507190490 2902 False 336.0 479 84.09400 1089 3488 3 chr5B.!!$F5 2399
7 TraesCS5A01G321900 chr5B 507059186 507061656 2470 False 317.8 544 78.22550 1380 4007 2 chr5B.!!$F4 2627
8 TraesCS5A01G321900 chr5D 421083811 421090550 6739 True 1608.5 2464 90.52900 596 5266 4 chr5D.!!$R6 4670
9 TraesCS5A01G321900 chr5D 420961725 420964911 3186 True 853.5 2268 87.01575 2053 5315 4 chr5D.!!$R5 3262
10 TraesCS5A01G321900 chr5D 470045875 470046457 582 True 758.0 758 90.22300 7 585 1 chr5D.!!$R4 578
11 TraesCS5A01G321900 chr5D 360902436 360903023 587 False 728.0 728 89.13400 1 585 1 chr5D.!!$F1 584
12 TraesCS5A01G321900 chr5D 421162600 421163469 869 True 623.0 623 80.13500 1115 1975 1 chr5D.!!$R2 860
13 TraesCS5A01G321900 chr5D 421136166 421138848 2682 True 460.5 630 83.74800 1092 3203 2 chr5D.!!$R7 2111
14 TraesCS5A01G321900 chr5D 421172172 421172723 551 True 246.0 246 75.39500 3291 3845 1 chr5D.!!$R3 554
15 TraesCS5A01G321900 chr4A 690120415 690120997 582 False 785.0 785 91.08100 7 585 1 chr4A.!!$F1 578
16 TraesCS5A01G321900 chr2D 589887546 589888135 589 False 749.0 749 89.67900 1 587 1 chr2D.!!$F2 586
17 TraesCS5A01G321900 chr2D 448191575 448192157 582 True 719.0 719 89.04100 7 585 1 chr2D.!!$R1 578
18 TraesCS5A01G321900 chr2D 7877204 7877797 593 False 233.0 233 74.54800 1382 1969 1 chr2D.!!$F1 587
19 TraesCS5A01G321900 chr6D 54232774 54233357 583 True 736.0 736 89.55500 7 585 1 chr6D.!!$R1 578
20 TraesCS5A01G321900 chr7D 550995874 550996455 581 False 732.0 732 89.51900 9 585 1 chr7D.!!$F1 576
21 TraesCS5A01G321900 chr7B 577303450 577304028 578 True 732.0 732 89.53700 7 585 1 chr7B.!!$R1 578
22 TraesCS5A01G321900 chr7A 722580837 722581422 585 True 723.0 723 89.07800 8 588 1 chr7A.!!$R1 580
23 TraesCS5A01G321900 chrUn 270060227 270061096 869 True 623.0 623 80.13500 1115 1975 1 chrUn.!!$R2 860
24 TraesCS5A01G321900 chrUn 325468257 325468858 601 True 532.0 532 83.03100 1380 1972 1 chrUn.!!$R3 592
25 TraesCS5A01G321900 chr1B 632657146 632659649 2503 True 414.0 558 82.03800 1378 3203 2 chr1B.!!$R1 1825
26 TraesCS5A01G321900 chr2B 4503404 4503925 521 False 213.0 213 74.86000 1453 1971 1 chr2B.!!$F1 518

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
70 71 0.039074 CACTGGAGACGTTTCGAGCT 60.039 55.0 16.44 3.38 0.0 4.09 F
593 601 0.314935 CCAAACACGCCTTGCTGATT 59.685 50.0 0.00 0.00 0.0 2.57 F
686 694 0.533755 GCTGCCGCTTAGATCCATGT 60.534 55.0 0.00 0.00 0.0 3.21 F
1324 1371 1.027357 TCGGCGAAGGTAGGTGATAC 58.973 55.0 7.35 0.00 0.0 2.24 F
2741 5990 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.0 0.00 0.00 0.0 2.27 F
3918 7814 1.318576 GTGTGAACTTGAACCCAGGG 58.681 55.0 2.85 2.85 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2029 1.156736 ACTTACGCAGTTCATGGCAC 58.843 50.000 0.00 0.0 37.78 5.01 R
2089 3165 1.955080 GGCTGCACGTAGTACCTAGAT 59.045 52.381 0.50 0.0 41.61 1.98 R
2366 5398 5.080337 AGATAAGTGCTCTTCATCCCGATA 58.920 41.667 3.91 0.0 35.36 2.92 R
2823 6072 0.908180 ACTCCCTCCGTCCGGAAAAT 60.908 55.000 5.23 0.0 44.66 1.82 R
4356 8445 0.261402 CCCCATCCTTAATGTGCCCA 59.739 55.000 0.00 0.0 33.13 5.36 R
5318 9575 0.104855 CCAAGCGCATGACCTAGCTA 59.895 55.000 15.31 0.0 39.25 3.32 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
37 38 1.415659 CGATCATCTTGGCCTCCTCTT 59.584 52.381 3.32 0.00 0.00 2.85
59 60 0.622136 TCGCCCTACTACACTGGAGA 59.378 55.000 0.00 0.00 0.00 3.71
66 67 2.701073 ACTACACTGGAGACGTTTCG 57.299 50.000 0.00 0.00 0.00 3.46
67 68 2.224606 ACTACACTGGAGACGTTTCGA 58.775 47.619 0.00 0.00 0.00 3.71
70 71 0.039074 CACTGGAGACGTTTCGAGCT 60.039 55.000 16.44 3.38 0.00 4.09
101 102 1.679305 GCCTCCTCTCTCGTCCACA 60.679 63.158 0.00 0.00 0.00 4.17
143 144 0.990374 AGCACTGCATTCTCCTCCTT 59.010 50.000 3.30 0.00 0.00 3.36
154 155 5.665459 CATTCTCCTCCTTTATCGACTGTT 58.335 41.667 0.00 0.00 0.00 3.16
315 317 4.380867 CGCATACTGCATTTCTTTTTCCCT 60.381 41.667 0.00 0.00 45.36 4.20
420 426 0.532640 TATGCGCCGAGACAATGCAT 60.533 50.000 4.18 0.00 46.94 3.96
424 430 1.731700 GCCGAGACAATGCATGCAT 59.268 52.632 27.46 27.46 38.46 3.96
430 436 3.490249 CGAGACAATGCATGCATCCAAAT 60.490 43.478 32.25 17.60 35.31 2.32
434 440 4.444536 ACAATGCATGCATCCAAATAACC 58.555 39.130 32.25 0.00 35.31 2.85
442 448 5.798125 TGCATCCAAATAACCTGTCAAAA 57.202 34.783 0.00 0.00 0.00 2.44
459 467 5.483231 TGTCAAAATTGATCCCCTAATGCAA 59.517 36.000 0.00 0.00 39.73 4.08
490 498 2.103373 TGCAGGCAACCAAACAACTTA 58.897 42.857 0.00 0.00 37.17 2.24
498 506 6.493458 AGGCAACCAAACAACTTACAGATATT 59.507 34.615 0.00 0.00 37.17 1.28
567 575 2.810274 ACAATGCAGCTACTGTTCACTG 59.190 45.455 0.00 0.00 33.43 3.66
587 595 0.871163 CTGCAACCAAACACGCCTTG 60.871 55.000 0.00 0.00 0.00 3.61
588 596 2.237066 GCAACCAAACACGCCTTGC 61.237 57.895 0.00 0.00 0.00 4.01
589 597 1.437160 CAACCAAACACGCCTTGCT 59.563 52.632 0.00 0.00 0.00 3.91
590 598 0.871163 CAACCAAACACGCCTTGCTG 60.871 55.000 0.00 0.00 0.00 4.41
591 599 1.034838 AACCAAACACGCCTTGCTGA 61.035 50.000 0.00 0.00 0.00 4.26
592 600 0.823356 ACCAAACACGCCTTGCTGAT 60.823 50.000 0.00 0.00 0.00 2.90
593 601 0.314935 CCAAACACGCCTTGCTGATT 59.685 50.000 0.00 0.00 0.00 2.57
594 602 1.269726 CCAAACACGCCTTGCTGATTT 60.270 47.619 0.00 0.00 0.00 2.17
595 603 2.030363 CCAAACACGCCTTGCTGATTTA 60.030 45.455 0.00 0.00 0.00 1.40
596 604 3.367292 CCAAACACGCCTTGCTGATTTAT 60.367 43.478 0.00 0.00 0.00 1.40
597 605 3.492421 AACACGCCTTGCTGATTTATG 57.508 42.857 0.00 0.00 0.00 1.90
598 606 1.745087 ACACGCCTTGCTGATTTATGG 59.255 47.619 0.00 0.00 0.00 2.74
599 607 1.745087 CACGCCTTGCTGATTTATGGT 59.255 47.619 0.00 0.00 0.00 3.55
609 617 4.141733 TGCTGATTTATGGTCGATTCCAGA 60.142 41.667 0.93 0.00 41.05 3.86
614 622 1.207791 ATGGTCGATTCCAGAAGCCT 58.792 50.000 0.93 0.00 41.05 4.58
642 650 2.032681 GCAGGAAGACGCCAGGTT 59.967 61.111 0.00 0.00 0.00 3.50
643 651 1.600916 GCAGGAAGACGCCAGGTTT 60.601 57.895 0.00 0.00 0.00 3.27
645 653 1.880646 GCAGGAAGACGCCAGGTTTAA 60.881 52.381 0.00 0.00 0.00 1.52
646 654 2.500229 CAGGAAGACGCCAGGTTTAAA 58.500 47.619 0.00 0.00 0.00 1.52
647 655 2.882137 CAGGAAGACGCCAGGTTTAAAA 59.118 45.455 0.00 0.00 0.00 1.52
648 656 2.882761 AGGAAGACGCCAGGTTTAAAAC 59.117 45.455 0.00 0.00 0.00 2.43
685 693 1.233285 GGCTGCCGCTTAGATCCATG 61.233 60.000 1.35 0.00 36.09 3.66
686 694 0.533755 GCTGCCGCTTAGATCCATGT 60.534 55.000 0.00 0.00 0.00 3.21
687 695 1.959042 CTGCCGCTTAGATCCATGTT 58.041 50.000 0.00 0.00 0.00 2.71
688 696 2.806745 GCTGCCGCTTAGATCCATGTTA 60.807 50.000 0.00 0.00 0.00 2.41
689 697 3.668447 CTGCCGCTTAGATCCATGTTAT 58.332 45.455 0.00 0.00 0.00 1.89
690 698 4.067896 CTGCCGCTTAGATCCATGTTATT 58.932 43.478 0.00 0.00 0.00 1.40
691 699 3.814842 TGCCGCTTAGATCCATGTTATTG 59.185 43.478 0.00 0.00 0.00 1.90
714 722 2.036731 TCGACCTGGACGGATGGT 59.963 61.111 17.79 0.00 36.70 3.55
716 724 2.125106 GACCTGGACGGATGGTGC 60.125 66.667 0.00 0.00 37.52 5.01
742 750 2.487805 GGGGAACACCGGAGTTACTTTT 60.488 50.000 23.91 0.00 41.60 2.27
751 759 7.047271 ACACCGGAGTTACTTTTGTTAACTTA 58.953 34.615 9.46 0.00 34.55 2.24
810 818 1.892474 GTGGAGTGCTTCTCTGTCTCT 59.108 52.381 8.78 0.00 42.40 3.10
814 822 3.119495 GGAGTGCTTCTCTGTCTCTTCTC 60.119 52.174 8.78 0.00 42.40 2.87
908 931 5.573380 AGCTAGCAATCCTCATCCATTAA 57.427 39.130 18.83 0.00 0.00 1.40
939 962 3.711086 TCGAGCTGATCACTTCATAAGC 58.289 45.455 0.00 0.00 32.72 3.09
944 967 3.193263 CTGATCACTTCATAAGCGCAGT 58.807 45.455 11.47 0.00 32.72 4.40
1137 1170 2.893398 GTCACCCCTACTGCGAGG 59.107 66.667 0.00 0.00 36.23 4.63
1293 1340 8.711457 CGCTCTTAGTACTACCTAGAATCTTAC 58.289 40.741 0.91 0.00 0.00 2.34
1308 1355 6.946165 AGAATCTTACGTATATCGCTATCGG 58.054 40.000 0.00 0.00 44.19 4.18
1323 1370 1.991121 ATCGGCGAAGGTAGGTGATA 58.009 50.000 15.93 0.00 0.00 2.15
1324 1371 1.027357 TCGGCGAAGGTAGGTGATAC 58.973 55.000 7.35 0.00 0.00 2.24
1328 1375 2.628657 GGCGAAGGTAGGTGATACTGAT 59.371 50.000 0.00 0.00 34.56 2.90
1329 1376 3.825014 GGCGAAGGTAGGTGATACTGATA 59.175 47.826 0.00 0.00 34.56 2.15
1342 1397 7.399191 AGGTGATACTGATACTAGTTTTGGTCA 59.601 37.037 0.00 0.00 32.19 4.02
1485 1544 2.582978 GGGCCGTGGAAGACTACC 59.417 66.667 0.00 0.00 0.00 3.18
1948 2029 3.919216 AGGACGTCAAGTTCATCAAGAG 58.081 45.455 18.91 0.00 0.00 2.85
2001 2793 3.242969 CCATTTCGATCATGCCACTCTTG 60.243 47.826 0.00 0.00 0.00 3.02
2077 2869 5.418840 AGCCAGGTAAAAATGGTCATACAAG 59.581 40.000 0.00 0.00 38.91 3.16
2082 3158 9.620660 CAGGTAAAAATGGTCATACAAGTTAAC 57.379 33.333 0.00 0.00 0.00 2.01
2083 3159 8.799367 AGGTAAAAATGGTCATACAAGTTAACC 58.201 33.333 0.88 0.00 0.00 2.85
2084 3160 8.030692 GGTAAAAATGGTCATACAAGTTAACCC 58.969 37.037 0.88 0.00 0.00 4.11
2085 3161 7.849322 AAAAATGGTCATACAAGTTAACCCT 57.151 32.000 0.88 0.00 0.00 4.34
2086 3162 7.849322 AAAATGGTCATACAAGTTAACCCTT 57.151 32.000 0.88 0.00 0.00 3.95
2088 3164 4.571919 TGGTCATACAAGTTAACCCTTCG 58.428 43.478 0.88 0.00 0.00 3.79
2089 3165 4.283978 TGGTCATACAAGTTAACCCTTCGA 59.716 41.667 0.88 0.00 0.00 3.71
2212 3823 7.507829 ACTTCTGCTGCTCTATCAAGATATTT 58.492 34.615 0.00 0.00 0.00 1.40
2322 5354 8.037382 ACTTGTCACAGACATGAATTTATCTG 57.963 34.615 16.73 3.24 42.40 2.90
2328 5360 7.281549 TCACAGACATGAATTTATCTGGACATG 59.718 37.037 11.97 0.00 42.39 3.21
2363 5395 9.047371 TCTAAATATATTCATTTCCGCGACAAA 57.953 29.630 8.23 6.67 30.84 2.83
2378 5410 5.456192 GCGACAAATATATCGGGATGAAG 57.544 43.478 6.20 0.00 38.78 3.02
2380 5412 5.289675 GCGACAAATATATCGGGATGAAGAG 59.710 44.000 6.20 0.00 38.78 2.85
2741 5990 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
2742 5991 0.320697 CTCCCTCCGTCCGAAAAAGT 59.679 55.000 0.00 0.00 0.00 2.66
2757 6006 5.451242 CCGAAAAAGTTTGTCCCTCAAATGA 60.451 40.000 0.00 0.00 45.88 2.57
2758 6007 5.458779 CGAAAAAGTTTGTCCCTCAAATGAC 59.541 40.000 0.00 0.00 45.88 3.06
2762 6011 3.885297 AGTTTGTCCCTCAAATGACTGTG 59.115 43.478 0.00 0.00 45.88 3.66
2796 6045 8.877779 CCAAATTAGTGCTATGCTAGATACATC 58.122 37.037 0.00 0.00 0.00 3.06
2802 6051 8.138928 AGTGCTATGCTAGATACATCCATTTA 57.861 34.615 0.00 0.00 0.00 1.40
2806 6055 9.658799 GCTATGCTAGATACATCCATTTAAGAA 57.341 33.333 0.00 0.00 0.00 2.52
2835 6084 1.519408 ACACAAGATTTTCCGGACGG 58.481 50.000 1.83 3.96 0.00 4.79
2845 6094 2.832201 CCGGACGGAGGGAGTACC 60.832 72.222 4.40 0.00 37.50 3.34
2857 6106 4.654262 GGAGGGAGTACCAGTCAATATTGA 59.346 45.833 14.23 14.23 43.89 2.57
3048 6302 6.126863 TGGGGAAATCAACTAGGCTATATG 57.873 41.667 0.00 0.00 0.00 1.78
3391 6692 6.126409 TGGACCAAGTGAACAAATAGAGTTT 58.874 36.000 0.00 0.00 0.00 2.66
3439 6740 2.803492 GCCTAGTGTTTATGGAGCTCCG 60.803 54.545 27.43 9.70 39.43 4.63
3497 6800 5.318630 TCAACCTTAATCCACCTTTGTACC 58.681 41.667 0.00 0.00 0.00 3.34
3521 6825 7.499232 ACCCTTTTTCAACCTAATCATCTATCG 59.501 37.037 0.00 0.00 0.00 2.92
3523 6827 7.041098 CCTTTTTCAACCTAATCATCTATCGGG 60.041 40.741 0.00 0.00 0.00 5.14
3642 6958 6.134535 TCTAGGTTATTGGAGCAAAAAGGA 57.865 37.500 0.00 0.00 0.00 3.36
3653 6969 7.722949 TGGAGCAAAAAGGAAAGAATATGAT 57.277 32.000 0.00 0.00 0.00 2.45
3842 7717 9.337396 TCTCGCCAATAGTGTTTATGAAATAAT 57.663 29.630 0.00 0.00 38.83 1.28
3916 7812 3.189287 GCTATGTGTGAACTTGAACCCAG 59.811 47.826 0.00 0.00 0.00 4.45
3918 7814 1.318576 GTGTGAACTTGAACCCAGGG 58.681 55.000 2.85 2.85 0.00 4.45
3980 7878 5.056480 TGATATTCTGTCAGTAAATGGCCG 58.944 41.667 0.00 0.00 29.99 6.13
4115 8203 2.337359 TCCTACCAACCAAGCTAGGT 57.663 50.000 0.00 0.00 45.91 3.08
4356 8445 6.966534 ATGGATGACTTTGTTGAGTCTTTT 57.033 33.333 6.59 0.00 44.99 2.27
4392 8481 1.266989 GGGGCTTCAAGACTTTCAACG 59.733 52.381 0.00 0.00 0.00 4.10
4416 8505 5.967674 GTCCGTCAAGCAAGAATAATCAATG 59.032 40.000 0.00 0.00 0.00 2.82
4439 8528 6.406370 TGTGCAGTTATATTAGTGTGCTTCT 58.594 36.000 0.00 0.00 0.00 2.85
4527 8625 8.893727 ACATAGTAATTAAGAACCAGAACATGC 58.106 33.333 0.00 0.00 0.00 4.06
4745 8904 6.002653 AGAAAACATACTAACTCCATCCCC 57.997 41.667 0.00 0.00 0.00 4.81
4746 8905 5.491078 AGAAAACATACTAACTCCATCCCCA 59.509 40.000 0.00 0.00 0.00 4.96
4747 8906 5.994416 AAACATACTAACTCCATCCCCAT 57.006 39.130 0.00 0.00 0.00 4.00
4748 8907 7.349859 AGAAAACATACTAACTCCATCCCCATA 59.650 37.037 0.00 0.00 0.00 2.74
4777 9025 0.186386 ATGGGACGGAGGGAGTAGAG 59.814 60.000 0.00 0.00 0.00 2.43
4807 9057 6.707161 CGGTAAACAATATAGATTTTCCCCGA 59.293 38.462 0.00 0.00 0.00 5.14
4953 9203 1.134220 AGCCTTGTTCGGAGTTTCACA 60.134 47.619 0.00 0.00 0.00 3.58
4967 9217 1.896220 TTCACAGCCCATCACAGAAC 58.104 50.000 0.00 0.00 0.00 3.01
4998 9248 1.486211 TCATTCCCCTCTCGTTCCTC 58.514 55.000 0.00 0.00 0.00 3.71
5030 9281 5.867903 ATTCATCCTTCTCAGTCTCGAAT 57.132 39.130 0.00 0.00 0.00 3.34
5066 9317 2.743718 CCGCCGCCTATGGAGAAT 59.256 61.111 0.00 0.00 0.00 2.40
5077 9328 4.141846 GCCTATGGAGAATGAAGACAGTCA 60.142 45.833 2.66 0.00 42.55 3.41
5165 9417 0.249120 ACGATGACGATGCCTCCAAA 59.751 50.000 0.00 0.00 42.66 3.28
5180 9432 1.007238 TCCAAAGACGAGGAGGAGGAT 59.993 52.381 0.00 0.00 0.00 3.24
5191 9446 3.148279 GGAGGATGCCGACGACCT 61.148 66.667 0.00 0.00 35.29 3.85
5194 9449 3.515286 GGATGCCGACGACCTCGA 61.515 66.667 0.78 0.00 46.14 4.04
5275 9532 3.620300 GACGTCGACATCCGCACCA 62.620 63.158 17.16 0.00 38.37 4.17
5288 9545 2.668212 CACCAACGCCACGACCAT 60.668 61.111 0.00 0.00 0.00 3.55
5291 9548 1.216977 CCAACGCCACGACCATCTA 59.783 57.895 0.00 0.00 0.00 1.98
5294 9551 2.954868 CGCCACGACCATCTACGC 60.955 66.667 0.00 0.00 0.00 4.42
5295 9552 2.183300 GCCACGACCATCTACGCA 59.817 61.111 0.00 0.00 0.00 5.24
5301 9558 2.588877 ACCATCTACGCATGCCGC 60.589 61.111 13.15 0.00 41.76 6.53
5307 9564 1.065764 CTACGCATGCCGCTCTACA 59.934 57.895 13.15 0.00 41.76 2.74
5315 9572 3.298958 CCGCTCTACAGGCTTGGA 58.701 61.111 0.00 0.00 0.00 3.53
5316 9573 1.826024 CCGCTCTACAGGCTTGGAT 59.174 57.895 0.00 0.00 0.00 3.41
5317 9574 0.249657 CCGCTCTACAGGCTTGGATC 60.250 60.000 0.00 0.00 0.00 3.36
5318 9575 0.749649 CGCTCTACAGGCTTGGATCT 59.250 55.000 0.00 0.00 0.00 2.75
5319 9576 1.957177 CGCTCTACAGGCTTGGATCTA 59.043 52.381 0.00 0.00 0.00 1.98
5320 9577 2.030363 CGCTCTACAGGCTTGGATCTAG 60.030 54.545 0.00 0.00 0.00 2.43
5321 9578 2.288763 GCTCTACAGGCTTGGATCTAGC 60.289 54.545 0.00 10.67 37.91 3.42
5322 9579 3.230134 CTCTACAGGCTTGGATCTAGCT 58.770 50.000 16.33 0.00 38.67 3.32
5323 9580 4.402829 CTCTACAGGCTTGGATCTAGCTA 58.597 47.826 16.33 0.00 38.67 3.32
5324 9581 4.402829 TCTACAGGCTTGGATCTAGCTAG 58.597 47.826 15.01 15.01 38.67 3.42
5325 9582 2.324541 ACAGGCTTGGATCTAGCTAGG 58.675 52.381 20.58 4.57 38.67 3.02
5326 9583 2.324541 CAGGCTTGGATCTAGCTAGGT 58.675 52.381 20.58 14.33 38.67 3.08
5327 9584 2.298729 CAGGCTTGGATCTAGCTAGGTC 59.701 54.545 23.59 23.59 38.67 3.85
5328 9585 2.091055 AGGCTTGGATCTAGCTAGGTCA 60.091 50.000 30.39 18.30 38.67 4.02
5329 9586 2.903135 GGCTTGGATCTAGCTAGGTCAT 59.097 50.000 30.39 13.83 38.67 3.06
5330 9587 3.306641 GGCTTGGATCTAGCTAGGTCATG 60.307 52.174 30.39 20.83 38.67 3.07
5331 9588 3.864160 GCTTGGATCTAGCTAGGTCATGC 60.864 52.174 30.39 25.17 35.12 4.06
5332 9589 1.889170 TGGATCTAGCTAGGTCATGCG 59.111 52.381 30.39 1.32 35.12 4.73
5333 9590 1.403514 GGATCTAGCTAGGTCATGCGC 60.404 57.143 30.39 12.78 35.12 6.09
5334 9591 1.543802 GATCTAGCTAGGTCATGCGCT 59.456 52.381 26.06 0.00 33.63 5.92
5335 9592 1.403814 TCTAGCTAGGTCATGCGCTT 58.596 50.000 20.58 0.00 34.14 4.68
5336 9593 1.067669 TCTAGCTAGGTCATGCGCTTG 59.932 52.381 20.58 16.66 34.14 4.01
5337 9594 0.104855 TAGCTAGGTCATGCGCTTGG 59.895 55.000 21.59 7.64 34.14 3.61
5338 9595 1.153369 GCTAGGTCATGCGCTTGGA 60.153 57.895 21.59 7.72 0.00 3.53
5339 9596 0.533755 GCTAGGTCATGCGCTTGGAT 60.534 55.000 21.59 11.15 0.00 3.41
5340 9597 1.506493 CTAGGTCATGCGCTTGGATC 58.494 55.000 21.59 10.58 0.00 3.36
5341 9598 0.106708 TAGGTCATGCGCTTGGATCC 59.893 55.000 21.59 19.39 0.00 3.36
5342 9599 2.537560 GGTCATGCGCTTGGATCCG 61.538 63.158 21.59 0.00 0.00 4.18
5343 9600 2.203056 TCATGCGCTTGGATCCGG 60.203 61.111 21.59 0.00 0.00 5.14
5344 9601 3.957535 CATGCGCTTGGATCCGGC 61.958 66.667 15.12 16.61 0.00 6.13
5345 9602 4.181010 ATGCGCTTGGATCCGGCT 62.181 61.111 21.74 6.09 0.00 5.52
5346 9603 2.807107 ATGCGCTTGGATCCGGCTA 61.807 57.895 21.74 13.74 0.00 3.93
5347 9604 2.663188 GCGCTTGGATCCGGCTAG 60.663 66.667 21.74 11.67 0.00 3.42
5348 9605 2.663188 CGCTTGGATCCGGCTAGC 60.663 66.667 21.74 18.13 0.00 3.42
5349 9606 2.281139 GCTTGGATCCGGCTAGCC 60.281 66.667 24.75 24.75 0.00 3.93
5350 9607 2.812619 GCTTGGATCCGGCTAGCCT 61.813 63.158 30.55 13.30 0.00 4.58
5351 9608 1.070445 CTTGGATCCGGCTAGCCTG 59.930 63.158 30.55 24.64 0.00 4.85
5352 9609 3.106986 TTGGATCCGGCTAGCCTGC 62.107 63.158 30.55 18.16 0.00 4.85
5353 9610 3.237741 GGATCCGGCTAGCCTGCT 61.238 66.667 30.55 16.86 0.00 4.24
5354 9611 2.341911 GATCCGGCTAGCCTGCTC 59.658 66.667 30.55 21.19 0.00 4.26
5355 9612 3.233259 GATCCGGCTAGCCTGCTCC 62.233 68.421 30.55 12.76 0.00 4.70
5358 9615 3.922640 CGGCTAGCCTGCTCCCTC 61.923 72.222 30.55 1.87 0.00 4.30
5359 9616 3.555324 GGCTAGCCTGCTCCCTCC 61.555 72.222 27.17 0.00 0.00 4.30
5360 9617 2.445654 GCTAGCCTGCTCCCTCCT 60.446 66.667 2.29 0.00 0.00 3.69
5361 9618 2.506957 GCTAGCCTGCTCCCTCCTC 61.507 68.421 2.29 0.00 0.00 3.71
5362 9619 1.075674 CTAGCCTGCTCCCTCCTCA 60.076 63.158 0.00 0.00 0.00 3.86
5363 9620 0.471591 CTAGCCTGCTCCCTCCTCAT 60.472 60.000 0.00 0.00 0.00 2.90
5364 9621 0.762082 TAGCCTGCTCCCTCCTCATG 60.762 60.000 0.00 0.00 0.00 3.07
5365 9622 2.509916 CCTGCTCCCTCCTCATGC 59.490 66.667 0.00 0.00 0.00 4.06
5366 9623 2.071262 CCTGCTCCCTCCTCATGCT 61.071 63.158 0.00 0.00 0.00 3.79
5367 9624 1.446791 CTGCTCCCTCCTCATGCTC 59.553 63.158 0.00 0.00 0.00 4.26
5368 9625 2.042404 CTGCTCCCTCCTCATGCTCC 62.042 65.000 0.00 0.00 0.00 4.70
5369 9626 2.817056 GCTCCCTCCTCATGCTCCC 61.817 68.421 0.00 0.00 0.00 4.30
5370 9627 1.383664 CTCCCTCCTCATGCTCCCA 60.384 63.158 0.00 0.00 0.00 4.37
5371 9628 0.767446 CTCCCTCCTCATGCTCCCAT 60.767 60.000 0.00 0.00 0.00 4.00
5372 9629 0.765903 TCCCTCCTCATGCTCCCATC 60.766 60.000 0.00 0.00 0.00 3.51
5373 9630 1.759881 CCTCCTCATGCTCCCATCC 59.240 63.158 0.00 0.00 0.00 3.51
5374 9631 1.058428 CCTCCTCATGCTCCCATCCA 61.058 60.000 0.00 0.00 0.00 3.41
5375 9632 1.065647 CTCCTCATGCTCCCATCCAT 58.934 55.000 0.00 0.00 0.00 3.41
5376 9633 0.769247 TCCTCATGCTCCCATCCATG 59.231 55.000 0.00 0.00 40.05 3.66
5377 9634 0.894184 CCTCATGCTCCCATCCATGC 60.894 60.000 0.00 0.00 38.89 4.06
5378 9635 0.110678 CTCATGCTCCCATCCATGCT 59.889 55.000 0.00 0.00 38.89 3.79
5379 9636 0.109913 TCATGCTCCCATCCATGCTC 59.890 55.000 0.00 0.00 38.89 4.26
5380 9637 0.894184 CATGCTCCCATCCATGCTCC 60.894 60.000 0.00 0.00 33.27 4.70
5381 9638 2.077842 ATGCTCCCATCCATGCTCCC 62.078 60.000 0.00 0.00 0.00 4.30
5382 9639 2.760378 GCTCCCATCCATGCTCCCA 61.760 63.158 0.00 0.00 0.00 4.37
5383 9640 1.150081 CTCCCATCCATGCTCCCAC 59.850 63.158 0.00 0.00 0.00 4.61
5384 9641 1.308128 TCCCATCCATGCTCCCACT 60.308 57.895 0.00 0.00 0.00 4.00
5385 9642 0.920763 TCCCATCCATGCTCCCACTT 60.921 55.000 0.00 0.00 0.00 3.16
5386 9643 0.466922 CCCATCCATGCTCCCACTTC 60.467 60.000 0.00 0.00 0.00 3.01
5387 9644 0.256752 CCATCCATGCTCCCACTTCA 59.743 55.000 0.00 0.00 0.00 3.02
5388 9645 1.133575 CCATCCATGCTCCCACTTCAT 60.134 52.381 0.00 0.00 0.00 2.57
5389 9646 2.228059 CATCCATGCTCCCACTTCATC 58.772 52.381 0.00 0.00 0.00 2.92
5390 9647 0.548031 TCCATGCTCCCACTTCATCC 59.452 55.000 0.00 0.00 0.00 3.51
5391 9648 0.549950 CCATGCTCCCACTTCATCCT 59.450 55.000 0.00 0.00 0.00 3.24
5392 9649 1.770658 CCATGCTCCCACTTCATCCTA 59.229 52.381 0.00 0.00 0.00 2.94
5393 9650 2.486191 CCATGCTCCCACTTCATCCTAC 60.486 54.545 0.00 0.00 0.00 3.18
5394 9651 0.824109 TGCTCCCACTTCATCCTACG 59.176 55.000 0.00 0.00 0.00 3.51
5395 9652 0.105039 GCTCCCACTTCATCCTACGG 59.895 60.000 0.00 0.00 0.00 4.02
5396 9653 0.105039 CTCCCACTTCATCCTACGGC 59.895 60.000 0.00 0.00 0.00 5.68
5397 9654 0.325296 TCCCACTTCATCCTACGGCT 60.325 55.000 0.00 0.00 0.00 5.52
5398 9655 0.179073 CCCACTTCATCCTACGGCTG 60.179 60.000 0.00 0.00 0.00 4.85
5399 9656 0.537188 CCACTTCATCCTACGGCTGT 59.463 55.000 2.42 2.42 0.00 4.40
5400 9657 1.066143 CCACTTCATCCTACGGCTGTT 60.066 52.381 1.99 0.00 0.00 3.16
5401 9658 2.615493 CCACTTCATCCTACGGCTGTTT 60.615 50.000 1.99 0.00 0.00 2.83
5402 9659 3.074412 CACTTCATCCTACGGCTGTTTT 58.926 45.455 1.99 0.00 0.00 2.43
5403 9660 3.502211 CACTTCATCCTACGGCTGTTTTT 59.498 43.478 1.99 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.005097 TCCAGTGTAGTAGGGCGAGAA 59.995 52.381 0.00 0.00 0.00 2.87
101 102 2.564771 CACCATGGTATCGTCAATGCT 58.435 47.619 19.28 0.00 0.00 3.79
143 144 3.363575 GCTCGTGCAAAAACAGTCGATAA 60.364 43.478 4.26 0.00 39.41 1.75
257 259 2.788640 GCGGTGGATAGTGGCCGTA 61.789 63.158 0.00 0.00 45.30 4.02
296 298 5.838521 AGGAAAGGGAAAAAGAAATGCAGTA 59.161 36.000 0.00 0.00 0.00 2.74
315 317 3.307480 GGGTTAACAGCTAGCAGAGGAAA 60.307 47.826 18.83 0.30 0.00 3.13
420 426 5.798125 TTTTGACAGGTTATTTGGATGCA 57.202 34.783 0.00 0.00 0.00 3.96
424 430 7.310361 GGGATCAATTTTGACAGGTTATTTGGA 60.310 37.037 0.00 0.00 40.49 3.53
430 436 5.269554 AGGGGATCAATTTTGACAGGTTA 57.730 39.130 0.00 0.00 40.49 2.85
434 440 5.127519 TGCATTAGGGGATCAATTTTGACAG 59.872 40.000 0.00 0.00 40.49 3.51
442 448 5.134725 ACTTCTTGCATTAGGGGATCAAT 57.865 39.130 0.00 0.00 0.00 2.57
459 467 2.648059 GTTGCCTGCATATGGACTTCT 58.352 47.619 4.56 0.00 0.00 2.85
490 498 8.743085 AAAACAGTCTCATATGCAATATCTGT 57.257 30.769 0.00 4.35 40.34 3.41
522 530 8.432013 TGTATACACATCTCAATTCAGCCTAAT 58.568 33.333 0.08 0.00 0.00 1.73
531 539 6.544931 AGCTGCATTGTATACACATCTCAATT 59.455 34.615 4.68 0.00 33.76 2.32
532 540 6.060136 AGCTGCATTGTATACACATCTCAAT 58.940 36.000 4.68 0.00 33.76 2.57
567 575 2.627510 AAGGCGTGTTTGGTTGCAGC 62.628 55.000 0.00 0.00 0.00 5.25
587 595 4.380531 TCTGGAATCGACCATAAATCAGC 58.619 43.478 0.00 0.00 39.34 4.26
588 596 5.049818 GCTTCTGGAATCGACCATAAATCAG 60.050 44.000 0.00 0.00 39.34 2.90
589 597 4.816385 GCTTCTGGAATCGACCATAAATCA 59.184 41.667 0.00 0.00 39.34 2.57
590 598 4.214332 GGCTTCTGGAATCGACCATAAATC 59.786 45.833 0.00 0.00 39.34 2.17
591 599 4.137543 GGCTTCTGGAATCGACCATAAAT 58.862 43.478 0.00 0.00 39.34 1.40
592 600 3.199946 AGGCTTCTGGAATCGACCATAAA 59.800 43.478 0.00 0.00 39.34 1.40
593 601 2.771943 AGGCTTCTGGAATCGACCATAA 59.228 45.455 0.00 0.00 39.34 1.90
594 602 2.103094 CAGGCTTCTGGAATCGACCATA 59.897 50.000 0.00 0.00 39.34 2.74
595 603 1.134280 CAGGCTTCTGGAATCGACCAT 60.134 52.381 0.00 0.00 39.34 3.55
596 604 0.250234 CAGGCTTCTGGAATCGACCA 59.750 55.000 0.00 0.00 38.33 4.02
597 605 1.092345 GCAGGCTTCTGGAATCGACC 61.092 60.000 0.00 0.00 38.87 4.79
598 606 0.391661 TGCAGGCTTCTGGAATCGAC 60.392 55.000 0.00 0.00 35.89 4.20
599 607 0.107993 CTGCAGGCTTCTGGAATCGA 60.108 55.000 5.57 0.00 38.37 3.59
625 633 0.321298 TAAACCTGGCGTCTTCCTGC 60.321 55.000 0.00 0.00 0.00 4.85
626 634 2.178912 TTAAACCTGGCGTCTTCCTG 57.821 50.000 0.00 0.00 0.00 3.86
642 650 2.955660 CAGGTGAAGCACAGGGTTTTAA 59.044 45.455 0.00 0.00 35.86 1.52
643 651 2.582052 CAGGTGAAGCACAGGGTTTTA 58.418 47.619 0.00 0.00 35.86 1.52
645 653 1.109323 GCAGGTGAAGCACAGGGTTT 61.109 55.000 0.00 0.00 35.86 3.27
646 654 1.529244 GCAGGTGAAGCACAGGGTT 60.529 57.895 0.00 0.00 35.86 4.11
647 655 2.113986 GCAGGTGAAGCACAGGGT 59.886 61.111 0.00 0.00 35.86 4.34
648 656 1.970114 CAGCAGGTGAAGCACAGGG 60.970 63.158 0.00 0.00 35.86 4.45
685 693 4.738740 CGTCCAGGTCGAGATAACAATAAC 59.261 45.833 0.00 0.00 0.00 1.89
686 694 4.202080 CCGTCCAGGTCGAGATAACAATAA 60.202 45.833 7.77 0.00 34.51 1.40
687 695 3.317149 CCGTCCAGGTCGAGATAACAATA 59.683 47.826 7.77 0.00 34.51 1.90
688 696 2.100916 CCGTCCAGGTCGAGATAACAAT 59.899 50.000 7.77 0.00 34.51 2.71
689 697 1.475280 CCGTCCAGGTCGAGATAACAA 59.525 52.381 7.77 0.00 34.51 2.83
690 698 1.100510 CCGTCCAGGTCGAGATAACA 58.899 55.000 7.77 0.00 34.51 2.41
691 699 1.386533 TCCGTCCAGGTCGAGATAAC 58.613 55.000 7.77 0.00 41.99 1.89
742 750 5.345702 CAGGCGTATACAGCTAAGTTAACA 58.654 41.667 8.61 0.00 34.52 2.41
751 759 1.227380 GCAGCAGGCGTATACAGCT 60.227 57.895 15.76 10.22 35.63 4.24
810 818 1.251527 GGGCTCAGTCGACAGGAGAA 61.252 60.000 30.04 4.52 0.00 2.87
814 822 4.135153 CCGGGCTCAGTCGACAGG 62.135 72.222 19.50 9.68 0.00 4.00
939 962 1.661743 GCTAGCTACTCGATCACTGCG 60.662 57.143 7.70 0.00 0.00 5.18
944 967 0.869068 GCTCGCTAGCTACTCGATCA 59.131 55.000 13.93 0.00 45.85 2.92
1137 1170 3.935203 CGATGTATATGGGTTCCATGAGC 59.065 47.826 9.50 0.91 44.84 4.26
1308 1355 4.519730 AGTATCAGTATCACCTACCTTCGC 59.480 45.833 0.00 0.00 0.00 4.70
1323 1370 7.719633 ACACAAATGACCAAAACTAGTATCAGT 59.280 33.333 0.00 0.00 0.00 3.41
1324 1371 8.099364 ACACAAATGACCAAAACTAGTATCAG 57.901 34.615 0.00 0.00 0.00 2.90
1328 1375 6.485313 CCTGACACAAATGACCAAAACTAGTA 59.515 38.462 0.00 0.00 0.00 1.82
1329 1376 5.299279 CCTGACACAAATGACCAAAACTAGT 59.701 40.000 0.00 0.00 0.00 2.57
1583 1643 3.490759 GAGTGGTGCACGCGGATG 61.491 66.667 12.47 0.56 39.64 3.51
1948 2029 1.156736 ACTTACGCAGTTCATGGCAC 58.843 50.000 0.00 0.00 37.78 5.01
2001 2793 6.154203 TCACATCACAGATGAGGATTCTAC 57.846 41.667 13.46 0.00 39.01 2.59
2077 2869 6.293135 CGTAGTACCTAGATCGAAGGGTTAAC 60.293 46.154 18.14 0.00 38.54 2.01
2082 3158 3.497640 CACGTAGTACCTAGATCGAAGGG 59.502 52.174 18.14 8.04 41.61 3.95
2083 3159 3.059051 GCACGTAGTACCTAGATCGAAGG 60.059 52.174 13.82 13.82 41.61 3.46
2084 3160 3.558829 TGCACGTAGTACCTAGATCGAAG 59.441 47.826 0.00 0.00 41.61 3.79
2085 3161 3.534554 TGCACGTAGTACCTAGATCGAA 58.465 45.455 0.00 0.00 41.61 3.71
2086 3162 3.129109 CTGCACGTAGTACCTAGATCGA 58.871 50.000 0.00 0.00 41.61 3.59
2088 3164 2.030981 GGCTGCACGTAGTACCTAGATC 60.031 54.545 0.50 0.00 41.61 2.75
2089 3165 1.955080 GGCTGCACGTAGTACCTAGAT 59.045 52.381 0.50 0.00 41.61 1.98
2212 3823 5.759506 TCACTTACCAGATTTGCGAAAAA 57.240 34.783 0.00 0.00 0.00 1.94
2254 3865 6.611642 TCCAGCAGGAGAAGTTATAACATACT 59.388 38.462 17.65 12.36 39.61 2.12
2345 5377 7.201487 CCGATATATTTGTCGCGGAAATGAATA 60.201 37.037 20.52 14.03 41.11 1.75
2363 5395 7.563188 AGATAAGTGCTCTTCATCCCGATATAT 59.437 37.037 3.91 0.00 35.36 0.86
2366 5398 5.080337 AGATAAGTGCTCTTCATCCCGATA 58.920 41.667 3.91 0.00 35.36 2.92
2374 5406 9.587772 GTATAGTTCAAAGATAAGTGCTCTTCA 57.412 33.333 3.91 0.00 35.36 3.02
2375 5407 9.587772 TGTATAGTTCAAAGATAAGTGCTCTTC 57.412 33.333 3.91 0.00 35.36 2.87
2376 5408 9.372369 GTGTATAGTTCAAAGATAAGTGCTCTT 57.628 33.333 6.25 6.25 37.65 2.85
2377 5409 7.702772 CGTGTATAGTTCAAAGATAAGTGCTCT 59.297 37.037 0.00 0.00 0.00 4.09
2378 5410 7.515371 GCGTGTATAGTTCAAAGATAAGTGCTC 60.515 40.741 0.00 0.00 0.00 4.26
2380 5412 6.411652 GCGTGTATAGTTCAAAGATAAGTGC 58.588 40.000 0.00 0.00 0.00 4.40
2586 5688 8.826710 TGAAAAGTAAAGATATGTATTCTGGCG 58.173 33.333 0.00 0.00 0.00 5.69
2718 5967 1.396653 TTCGGACGGAGGGAGTAATC 58.603 55.000 0.00 0.00 0.00 1.75
2729 5978 1.002142 GGGACAAACTTTTTCGGACGG 60.002 52.381 0.00 0.00 0.00 4.79
2770 6019 8.783833 ATGTATCTAGCATAGCACTAATTTGG 57.216 34.615 0.00 0.00 38.99 3.28
2811 6060 4.212636 CGTCCGGAAAATCTTGTGTTAACT 59.787 41.667 5.23 0.00 0.00 2.24
2815 6064 1.877443 CCGTCCGGAAAATCTTGTGTT 59.123 47.619 5.23 0.00 37.50 3.32
2817 6066 1.732259 CTCCGTCCGGAAAATCTTGTG 59.268 52.381 5.23 0.00 44.66 3.33
2823 6072 0.908180 ACTCCCTCCGTCCGGAAAAT 60.908 55.000 5.23 0.00 44.66 1.82
2828 6077 2.832201 GGTACTCCCTCCGTCCGG 60.832 72.222 0.00 0.00 0.00 5.14
2835 6084 5.871396 TCAATATTGACTGGTACTCCCTC 57.129 43.478 14.23 0.00 31.01 4.30
2845 6094 6.808008 AACTGACCACTTCAATATTGACTG 57.192 37.500 17.76 14.68 36.83 3.51
2857 6106 6.959639 AATGTGTAATCAAACTGACCACTT 57.040 33.333 0.00 0.00 0.00 3.16
3048 6302 2.736400 CGCCAAATGAAATGGAAGGAGC 60.736 50.000 0.00 0.00 40.56 4.70
3250 6505 5.825679 ACAAGGTGTTGCTTAAGTATGTGAA 59.174 36.000 4.02 0.00 37.14 3.18
3258 6514 7.544217 AGTTTGTTAAACAAGGTGTTGCTTAAG 59.456 33.333 0.00 0.00 40.14 1.85
3375 6676 6.806739 GTGCCCATAAAACTCTATTTGTTCAC 59.193 38.462 0.00 0.00 0.00 3.18
3391 6692 1.072266 AGACAACAGGGTGCCCATAA 58.928 50.000 10.26 0.00 38.92 1.90
3439 6740 5.447010 GCAAGATCATGAGTGACTTACTTGC 60.447 44.000 12.31 12.31 43.74 4.01
3497 6800 7.041098 CCCGATAGATGATTAGGTTGAAAAAGG 60.041 40.741 0.00 0.00 39.76 3.11
3521 6825 1.135939 GTGTCCGCGCATTTTACCC 59.864 57.895 8.75 0.00 0.00 3.69
3523 6827 1.997606 ACTAGTGTCCGCGCATTTTAC 59.002 47.619 8.75 0.00 0.00 2.01
3553 6862 3.885297 AGAGTGGTTTTGTGATCAAGTGG 59.115 43.478 0.00 0.00 34.88 4.00
3845 7720 8.257602 TGCATCTATGAAAATACTACCTACCA 57.742 34.615 0.00 0.00 0.00 3.25
3846 7721 9.726438 AATGCATCTATGAAAATACTACCTACC 57.274 33.333 0.00 0.00 0.00 3.18
3849 7724 9.851686 TGAAATGCATCTATGAAAATACTACCT 57.148 29.630 0.00 0.00 0.00 3.08
3890 7786 5.451242 GGGTTCAAGTTCACACATAGCAAAA 60.451 40.000 0.00 0.00 0.00 2.44
3891 7787 4.037446 GGGTTCAAGTTCACACATAGCAAA 59.963 41.667 0.00 0.00 0.00 3.68
3892 7788 3.568007 GGGTTCAAGTTCACACATAGCAA 59.432 43.478 0.00 0.00 0.00 3.91
3916 7812 1.477014 GCCTCTACCTATTGTTGGCCC 60.477 57.143 0.00 0.00 33.37 5.80
3918 7814 2.710096 TGCCTCTACCTATTGTTGGC 57.290 50.000 0.00 0.00 37.23 4.52
3997 8085 2.887151 ATTCCCACTGAAGGTCAAGG 57.113 50.000 0.00 0.00 36.14 3.61
4008 8096 0.973632 TGTGCTCGTGTATTCCCACT 59.026 50.000 0.00 0.00 33.07 4.00
4126 8214 9.549078 TGATGAAGTTTTACATGTGTAGTTACA 57.451 29.630 9.11 2.26 34.63 2.41
4356 8445 0.261402 CCCCATCCTTAATGTGCCCA 59.739 55.000 0.00 0.00 33.13 5.36
4392 8481 5.545658 TTGATTATTCTTGCTTGACGGAC 57.454 39.130 0.00 0.00 0.00 4.79
4416 8505 6.910536 AGAAGCACACTAATATAACTGCAC 57.089 37.500 0.00 0.00 0.00 4.57
4439 8528 9.715123 CATATTGCTGTCGTCATACAATTTTAA 57.285 29.630 13.34 1.13 34.43 1.52
4527 8625 6.687081 TTGACTTGTAACCTTAGTTTGGTG 57.313 37.500 0.00 0.00 37.93 4.17
4578 8676 3.668141 ATCCCTGTTGGTGCATCATTA 57.332 42.857 0.00 0.00 34.77 1.90
4671 8769 3.582647 GAGAATGGGGGTTGGTCAAAATT 59.417 43.478 0.00 0.00 0.00 1.82
4723 8882 5.751586 TGGGGATGGAGTTAGTATGTTTTC 58.248 41.667 0.00 0.00 0.00 2.29
4734 8893 3.519510 CGGATGTATATGGGGATGGAGTT 59.480 47.826 0.00 0.00 0.00 3.01
4735 8894 3.107601 CGGATGTATATGGGGATGGAGT 58.892 50.000 0.00 0.00 0.00 3.85
4953 9203 1.599047 CTCGGTTCTGTGATGGGCT 59.401 57.895 0.00 0.00 0.00 5.19
4967 9217 1.545651 GGGGAATGAAATAGGCCTCGG 60.546 57.143 9.68 0.00 0.00 4.63
5006 9256 5.255710 TCGAGACTGAGAAGGATGAATTC 57.744 43.478 0.00 0.00 0.00 2.17
5008 9258 5.599732 CATTCGAGACTGAGAAGGATGAAT 58.400 41.667 0.00 0.00 30.68 2.57
5010 9260 3.181482 GCATTCGAGACTGAGAAGGATGA 60.181 47.826 6.22 0.00 30.68 2.92
5011 9261 3.122297 GCATTCGAGACTGAGAAGGATG 58.878 50.000 6.22 0.00 30.68 3.51
5012 9262 2.223688 CGCATTCGAGACTGAGAAGGAT 60.224 50.000 6.22 0.00 38.10 3.24
5066 9317 5.645624 GAGAGATCGATTTGACTGTCTTCA 58.354 41.667 9.51 0.00 0.00 3.02
5077 9328 1.671328 TGAGCGACGAGAGATCGATTT 59.329 47.619 0.00 0.00 42.25 2.17
5118 9369 0.611062 TCCTCCGTGGTGTTCTCGAT 60.611 55.000 0.00 0.00 37.07 3.59
5165 9417 1.456705 GGCATCCTCCTCCTCGTCT 60.457 63.158 0.00 0.00 0.00 4.18
5191 9446 0.465097 GAGGTGGATAGGTCGGTCGA 60.465 60.000 0.00 0.00 0.00 4.20
5194 9449 0.750911 GTCGAGGTGGATAGGTCGGT 60.751 60.000 0.00 0.00 33.21 4.69
5238 9493 3.507009 CCGGACGTCGAGGAGGAC 61.507 72.222 20.09 0.00 42.43 3.85
5275 9532 1.153901 CGTAGATGGTCGTGGCGTT 60.154 57.895 0.00 0.00 0.00 4.84
5301 9558 3.230134 AGCTAGATCCAAGCCTGTAGAG 58.770 50.000 12.76 0.00 41.02 2.43
5307 9564 2.091055 TGACCTAGCTAGATCCAAGCCT 60.091 50.000 22.70 4.99 41.02 4.58
5312 9569 1.889170 CGCATGACCTAGCTAGATCCA 59.111 52.381 22.70 15.56 0.00 3.41
5313 9570 1.403514 GCGCATGACCTAGCTAGATCC 60.404 57.143 22.70 10.61 0.00 3.36
5315 9572 1.626686 AGCGCATGACCTAGCTAGAT 58.373 50.000 22.70 4.28 38.29 1.98
5316 9573 1.067669 CAAGCGCATGACCTAGCTAGA 59.932 52.381 22.70 2.39 39.25 2.43
5317 9574 1.495878 CAAGCGCATGACCTAGCTAG 58.504 55.000 14.20 14.20 39.25 3.42
5318 9575 0.104855 CCAAGCGCATGACCTAGCTA 59.895 55.000 15.31 0.00 39.25 3.32
5319 9576 1.153289 CCAAGCGCATGACCTAGCT 60.153 57.895 15.31 0.00 42.35 3.32
5320 9577 0.533755 ATCCAAGCGCATGACCTAGC 60.534 55.000 15.31 0.00 0.00 3.42
5321 9578 1.506493 GATCCAAGCGCATGACCTAG 58.494 55.000 15.31 0.00 0.00 3.02
5322 9579 0.106708 GGATCCAAGCGCATGACCTA 59.893 55.000 15.31 0.00 0.00 3.08
5323 9580 1.153086 GGATCCAAGCGCATGACCT 60.153 57.895 15.31 0.00 0.00 3.85
5324 9581 2.537560 CGGATCCAAGCGCATGACC 61.538 63.158 15.31 12.84 0.00 4.02
5325 9582 2.537560 CCGGATCCAAGCGCATGAC 61.538 63.158 15.31 5.14 0.00 3.06
5326 9583 2.203056 CCGGATCCAAGCGCATGA 60.203 61.111 15.31 4.98 0.00 3.07
5327 9584 2.994387 TAGCCGGATCCAAGCGCATG 62.994 60.000 11.47 8.27 0.00 4.06
5328 9585 2.721971 CTAGCCGGATCCAAGCGCAT 62.722 60.000 11.47 0.00 0.00 4.73
5329 9586 3.445518 CTAGCCGGATCCAAGCGCA 62.446 63.158 11.47 6.73 0.00 6.09
5330 9587 2.663188 CTAGCCGGATCCAAGCGC 60.663 66.667 13.41 0.00 0.00 5.92
5331 9588 2.663188 GCTAGCCGGATCCAAGCG 60.663 66.667 13.41 3.62 0.00 4.68
5332 9589 2.281139 GGCTAGCCGGATCCAAGC 60.281 66.667 20.16 14.07 0.00 4.01
5333 9590 1.070445 CAGGCTAGCCGGATCCAAG 59.930 63.158 27.83 7.91 41.95 3.61
5334 9591 3.106986 GCAGGCTAGCCGGATCCAA 62.107 63.158 34.48 0.00 41.95 3.53
5335 9592 3.550431 GCAGGCTAGCCGGATCCA 61.550 66.667 34.48 0.00 41.95 3.41
5336 9593 3.233259 GAGCAGGCTAGCCGGATCC 62.233 68.421 33.65 19.59 40.02 3.36
5337 9594 2.341911 GAGCAGGCTAGCCGGATC 59.658 66.667 34.48 32.86 39.23 3.36
5338 9595 3.237741 GGAGCAGGCTAGCCGGAT 61.238 66.667 34.48 30.10 41.95 4.18
5341 9598 3.922640 GAGGGAGCAGGCTAGCCG 61.923 72.222 27.83 22.20 41.95 5.52
5342 9599 3.555324 GGAGGGAGCAGGCTAGCC 61.555 72.222 27.19 27.19 34.23 3.93
5343 9600 2.445654 AGGAGGGAGCAGGCTAGC 60.446 66.667 6.04 6.04 0.00 3.42
5344 9601 0.471591 ATGAGGAGGGAGCAGGCTAG 60.472 60.000 0.00 0.00 0.00 3.42
5345 9602 0.762082 CATGAGGAGGGAGCAGGCTA 60.762 60.000 0.00 0.00 0.00 3.93
5346 9603 2.071262 CATGAGGAGGGAGCAGGCT 61.071 63.158 0.00 0.00 0.00 4.58
5347 9604 2.509916 CATGAGGAGGGAGCAGGC 59.490 66.667 0.00 0.00 0.00 4.85
5348 9605 2.042404 GAGCATGAGGAGGGAGCAGG 62.042 65.000 0.00 0.00 0.00 4.85
5349 9606 1.446791 GAGCATGAGGAGGGAGCAG 59.553 63.158 0.00 0.00 0.00 4.24
5350 9607 2.068821 GGAGCATGAGGAGGGAGCA 61.069 63.158 0.00 0.00 0.00 4.26
5351 9608 2.817056 GGGAGCATGAGGAGGGAGC 61.817 68.421 0.00 0.00 0.00 4.70
5352 9609 0.767446 ATGGGAGCATGAGGAGGGAG 60.767 60.000 0.00 0.00 0.00 4.30
5353 9610 0.765903 GATGGGAGCATGAGGAGGGA 60.766 60.000 0.00 0.00 0.00 4.20
5354 9611 1.759881 GATGGGAGCATGAGGAGGG 59.240 63.158 0.00 0.00 0.00 4.30
5355 9612 1.058428 TGGATGGGAGCATGAGGAGG 61.058 60.000 0.00 0.00 0.00 4.30
5356 9613 1.065647 ATGGATGGGAGCATGAGGAG 58.934 55.000 0.00 0.00 0.00 3.69
5357 9614 0.769247 CATGGATGGGAGCATGAGGA 59.231 55.000 0.00 0.00 0.00 3.71
5358 9615 0.894184 GCATGGATGGGAGCATGAGG 60.894 60.000 0.00 0.00 0.00 3.86
5359 9616 0.110678 AGCATGGATGGGAGCATGAG 59.889 55.000 0.00 0.00 0.00 2.90
5360 9617 0.109913 GAGCATGGATGGGAGCATGA 59.890 55.000 0.00 0.00 0.00 3.07
5361 9618 0.894184 GGAGCATGGATGGGAGCATG 60.894 60.000 0.00 0.00 0.00 4.06
5362 9619 1.459369 GGAGCATGGATGGGAGCAT 59.541 57.895 0.00 0.00 0.00 3.79
5363 9620 2.760378 GGGAGCATGGATGGGAGCA 61.760 63.158 0.00 0.00 0.00 4.26
5364 9621 2.114838 GGGAGCATGGATGGGAGC 59.885 66.667 0.00 0.00 0.00 4.70
5365 9622 1.150081 GTGGGAGCATGGATGGGAG 59.850 63.158 0.00 0.00 0.00 4.30
5366 9623 0.920763 AAGTGGGAGCATGGATGGGA 60.921 55.000 0.00 0.00 0.00 4.37
5367 9624 0.466922 GAAGTGGGAGCATGGATGGG 60.467 60.000 0.00 0.00 0.00 4.00
5368 9625 0.256752 TGAAGTGGGAGCATGGATGG 59.743 55.000 0.00 0.00 0.00 3.51
5369 9626 2.228059 GATGAAGTGGGAGCATGGATG 58.772 52.381 0.00 0.00 0.00 3.51
5370 9627 1.144503 GGATGAAGTGGGAGCATGGAT 59.855 52.381 0.00 0.00 0.00 3.41
5371 9628 0.548031 GGATGAAGTGGGAGCATGGA 59.452 55.000 0.00 0.00 0.00 3.41
5372 9629 0.549950 AGGATGAAGTGGGAGCATGG 59.450 55.000 0.00 0.00 0.00 3.66
5373 9630 2.804572 CGTAGGATGAAGTGGGAGCATG 60.805 54.545 0.00 0.00 0.00 4.06
5374 9631 1.414181 CGTAGGATGAAGTGGGAGCAT 59.586 52.381 0.00 0.00 0.00 3.79
5375 9632 0.824109 CGTAGGATGAAGTGGGAGCA 59.176 55.000 0.00 0.00 0.00 4.26
5376 9633 3.669354 CGTAGGATGAAGTGGGAGC 57.331 57.895 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.