Multiple sequence alignment - TraesCS3A01G028600

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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 TraesCS3A01G028600 chr3A 100.000 5119 0 0 1 5119 15298873 15293755 0.000000e+00 9454.0
1 TraesCS3A01G028600 chr3A 87.083 929 108 6 3194 4119 15291461 15292380 0.000000e+00 1040.0
2 TraesCS3A01G028600 chr3A 85.561 838 120 1 1290 2127 15289522 15290358 0.000000e+00 876.0
3 TraesCS3A01G028600 chr3A 83.410 868 110 17 1273 2140 15287856 15288689 0.000000e+00 774.0
4 TraesCS3A01G028600 chr3A 81.116 842 140 14 3194 4030 15065112 15064285 0.000000e+00 656.0
5 TraesCS3A01G028600 chr3A 87.591 411 43 7 2146 2555 15288806 15289209 2.160000e-128 470.0
6 TraesCS3A01G028600 chr3A 87.198 414 41 8 2135 2547 15290473 15290875 1.300000e-125 460.0
7 TraesCS3A01G028600 chr3A 77.315 745 128 24 3393 4121 14925533 14924814 7.980000e-108 401.0
8 TraesCS3A01G028600 chr3A 79.290 507 85 12 1609 2097 15066931 15066427 2.280000e-88 337.0
9 TraesCS3A01G028600 chr3A 82.843 204 20 10 2616 2815 15290911 15291103 8.810000e-38 169.0
10 TraesCS3A01G028600 chr3A 92.000 75 3 1 2974 3045 15291235 15291309 9.070000e-18 102.0
11 TraesCS3A01G028600 chr3A 89.286 56 2 3 604 656 533623243 533623297 3.310000e-07 67.6
12 TraesCS3A01G028600 chrUn 91.603 3549 190 46 1250 4724 244505808 244509322 0.000000e+00 4804.0
13 TraesCS3A01G028600 chrUn 84.607 929 130 7 3194 4119 244512638 244511720 0.000000e+00 911.0
14 TraesCS3A01G028600 chrUn 85.680 838 119 1 1290 2127 244514968 244514132 0.000000e+00 881.0
15 TraesCS3A01G028600 chrUn 85.444 845 100 18 1285 2127 244516637 244515814 0.000000e+00 857.0
16 TraesCS3A01G028600 chrUn 89.687 543 34 7 653 1173 244505244 244505786 0.000000e+00 673.0
17 TraesCS3A01G028600 chrUn 84.412 417 52 9 2146 2555 244515691 244515281 1.030000e-106 398.0
18 TraesCS3A01G028600 chrUn 89.531 277 25 4 4845 5119 244509882 244510156 1.050000e-91 348.0
19 TraesCS3A01G028600 chrUn 92.174 115 7 2 2619 2731 244513181 244513067 1.480000e-35 161.0
20 TraesCS3A01G028600 chrUn 87.838 74 3 3 2974 3044 244512861 244512791 1.180000e-11 82.4
21 TraesCS3A01G028600 chr3D 93.785 2478 118 10 653 3105 5869618 5872084 0.000000e+00 3690.0
22 TraesCS3A01G028600 chr3D 87.926 1673 94 36 3109 4724 5872117 5873738 0.000000e+00 1871.0
23 TraesCS3A01G028600 chr3D 85.699 930 111 12 3194 4119 5876697 5875786 0.000000e+00 961.0
24 TraesCS3A01G028600 chr3D 86.277 838 114 1 1290 2127 5878645 5877809 0.000000e+00 909.0
25 TraesCS3A01G028600 chr3D 85.900 844 98 16 1285 2127 5880311 5879488 0.000000e+00 880.0
26 TraesCS3A01G028600 chr3D 79.812 852 136 21 3194 4031 6033166 6033995 5.710000e-164 588.0
27 TraesCS3A01G028600 chr3D 88.862 413 33 5 4718 5119 5873761 5874171 3.560000e-136 496.0
28 TraesCS3A01G028600 chr3D 88.293 410 41 6 2147 2555 5879361 5878958 7.710000e-133 484.0
29 TraesCS3A01G028600 chr3D 86.553 409 46 7 2146 2553 5877678 5877278 4.700000e-120 442.0
30 TraesCS3A01G028600 chr3D 77.477 777 129 31 3362 4121 6067827 6068574 1.700000e-114 424.0
31 TraesCS3A01G028600 chr3D 83.085 201 19 10 2619 2815 5877245 5877056 8.810000e-38 169.0
32 TraesCS3A01G028600 chr3D 93.636 110 7 0 1 110 5868225 5868334 1.140000e-36 165.0
33 TraesCS3A01G028600 chr3D 90.909 55 1 4 605 656 313101808 313101861 2.560000e-08 71.3
34 TraesCS3A01G028600 chr3B 80.963 914 139 17 3225 4121 7595510 7594615 0.000000e+00 691.0
35 TraesCS3A01G028600 chr3B 77.992 777 128 25 3362 4121 7482963 7482213 1.010000e-121 448.0
36 TraesCS3A01G028600 chr3B 77.215 158 29 3 2903 3055 7595874 7595719 9.130000e-13 86.1
37 TraesCS3A01G028600 chr3B 80.851 94 16 1 5028 5119 420720177 420720270 7.110000e-09 73.1
38 TraesCS3A01G028600 chr3B 87.931 58 3 3 602 656 678629094 678629150 1.190000e-06 65.8
39 TraesCS3A01G028600 chr7A 87.000 100 12 1 4625 4724 729442706 729442608 1.510000e-20 111.0
40 TraesCS3A01G028600 chr7A 87.000 100 12 1 4625 4724 729489594 729489496 1.510000e-20 111.0
41 TraesCS3A01G028600 chr5A 86.000 100 13 1 4625 4724 678622516 678622418 7.010000e-19 106.0
42 TraesCS3A01G028600 chr1D 80.000 145 24 5 4377 4520 119263354 119263494 9.070000e-18 102.0
43 TraesCS3A01G028600 chr4B 80.800 125 18 6 4377 4499 122633167 122633287 5.460000e-15 93.5
44 TraesCS3A01G028600 chr6B 82.222 90 15 1 357 446 476338677 476338589 5.500000e-10 76.8
45 TraesCS3A01G028600 chr7B 95.556 45 0 2 613 656 66320630 66320587 2.560000e-08 71.3
46 TraesCS3A01G028600 chr2D 92.000 50 3 1 608 656 511922691 511922642 9.200000e-08 69.4
47 TraesCS3A01G028600 chr5B 87.931 58 3 3 602 656 182745422 182745366 1.190000e-06 65.8
48 TraesCS3A01G028600 chr5B 90.000 50 4 1 608 656 679686676 679686627 4.280000e-06 63.9
49 TraesCS3A01G028600 chr5B 89.796 49 4 1 609 656 69131972 69131924 1.540000e-05 62.1
50 TraesCS3A01G028600 chr1B 87.719 57 5 2 602 656 56271358 56271302 1.190000e-06 65.8
51 TraesCS3A01G028600 chr4D 92.500 40 3 0 316 355 463702383 463702344 1.990000e-04 58.4


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 TraesCS3A01G028600 chr3A 15293755 15298873 5118 True 9454.000000 9454 100.000000 1 5119 1 chr3A.!!$R2 5118
1 TraesCS3A01G028600 chr3A 15287856 15292380 4524 False 555.857143 1040 86.526571 1273 4119 7 chr3A.!!$F2 2846
2 TraesCS3A01G028600 chr3A 15064285 15066931 2646 True 496.500000 656 80.203000 1609 4030 2 chr3A.!!$R3 2421
3 TraesCS3A01G028600 chr3A 14924814 14925533 719 True 401.000000 401 77.315000 3393 4121 1 chr3A.!!$R1 728
4 TraesCS3A01G028600 chrUn 244505244 244510156 4912 False 1941.666667 4804 90.273667 653 5119 3 chrUn.!!$F1 4466
5 TraesCS3A01G028600 chrUn 244511720 244516637 4917 True 548.400000 911 86.692500 1285 4119 6 chrUn.!!$R1 2834
6 TraesCS3A01G028600 chr3D 5868225 5874171 5946 False 1555.500000 3690 91.052250 1 5119 4 chr3D.!!$F4 5118
7 TraesCS3A01G028600 chr3D 5875786 5880311 4525 True 640.833333 961 85.967833 1285 4119 6 chr3D.!!$R1 2834
8 TraesCS3A01G028600 chr3D 6033166 6033995 829 False 588.000000 588 79.812000 3194 4031 1 chr3D.!!$F1 837
9 TraesCS3A01G028600 chr3D 6067827 6068574 747 False 424.000000 424 77.477000 3362 4121 1 chr3D.!!$F2 759
10 TraesCS3A01G028600 chr3B 7482213 7482963 750 True 448.000000 448 77.992000 3362 4121 1 chr3B.!!$R1 759
11 TraesCS3A01G028600 chr3B 7594615 7595874 1259 True 388.550000 691 79.089000 2903 4121 2 chr3B.!!$R2 1218

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
404 748 0.108992 GTACCATCGAAGGTGTGCGA 60.109 55.0 22.16 0.00 43.14 5.10 F
1147 1976 0.036388 TGGACCGGATTCAGTTCAGC 60.036 55.0 9.46 0.00 0.00 4.26 F
1379 2208 0.106819 GCCTGCTGTCCATGGAAGAT 60.107 55.0 18.20 0.00 0.00 2.40 F
2742 6028 0.471591 AATTGGCAAGGCTTGTCCCA 60.472 50.0 27.49 22.86 33.37 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 2208 0.039618 GGGCCCTGTCCATCTCAAAA 59.960 55.000 17.04 0.0 0.0 2.44 R
2454 5716 0.537143 TCAGCACATGTTCCGCCTTT 60.537 50.000 0.00 0.0 0.0 3.11 R
3117 6505 1.067354 CAATCTGCAAAGGAACCAGGC 60.067 52.381 0.00 0.0 0.0 4.85 R
4380 7868 0.317770 CACTCGCGCCAAAACACAAT 60.318 50.000 0.00 0.0 0.0 2.71 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
41 42 9.209175 GATATAAGTTAAGGACCTAAGTGCATG 57.791 37.037 0.00 0.00 36.65 4.06
60 61 5.983118 TGCATGAGTACAACTCCATATTACG 59.017 40.000 0.00 0.00 44.44 3.18
61 62 6.183360 TGCATGAGTACAACTCCATATTACGA 60.183 38.462 0.00 0.00 44.44 3.43
63 64 8.027189 GCATGAGTACAACTCCATATTACGATA 58.973 37.037 0.00 0.00 44.44 2.92
68 69 8.298140 AGTACAACTCCATATTACGATAGAAGC 58.702 37.037 0.00 0.00 41.38 3.86
227 529 5.754406 TCTGGAAATGCACACAAATTTTGAG 59.246 36.000 15.81 10.28 0.00 3.02
344 688 6.003234 GTTTAGGAACCTTCTGAAAGCTTC 57.997 41.667 0.00 0.00 0.00 3.86
345 689 3.147553 AGGAACCTTCTGAAAGCTTCC 57.852 47.619 0.00 10.37 43.40 3.46
346 690 2.163509 GGAACCTTCTGAAAGCTTCCC 58.836 52.381 0.00 0.00 39.72 3.97
348 692 3.222603 GAACCTTCTGAAAGCTTCCCAA 58.777 45.455 0.00 0.00 0.00 4.12
350 694 3.642141 ACCTTCTGAAAGCTTCCCAAAA 58.358 40.909 0.00 0.00 0.00 2.44
351 695 3.384789 ACCTTCTGAAAGCTTCCCAAAAC 59.615 43.478 0.00 0.00 0.00 2.43
352 696 3.243873 CCTTCTGAAAGCTTCCCAAAACC 60.244 47.826 0.00 0.00 0.00 3.27
354 698 1.000274 CTGAAAGCTTCCCAAAACCGG 60.000 52.381 0.00 0.00 0.00 5.28
355 699 1.037493 GAAAGCTTCCCAAAACCGGT 58.963 50.000 0.00 0.00 0.00 5.28
357 701 2.368311 AAGCTTCCCAAAACCGGTAA 57.632 45.000 8.00 0.00 0.00 2.85
359 703 2.668625 AGCTTCCCAAAACCGGTAAAA 58.331 42.857 8.00 0.00 0.00 1.52
360 704 3.032459 AGCTTCCCAAAACCGGTAAAAA 58.968 40.909 8.00 0.00 0.00 1.94
380 724 0.668535 AAAAGACAAAGTGAGCCGGC 59.331 50.000 21.89 21.89 0.00 6.13
381 725 1.172812 AAAGACAAAGTGAGCCGGCC 61.173 55.000 26.15 15.80 0.00 6.13
382 726 3.056328 GACAAAGTGAGCCGGCCC 61.056 66.667 26.15 13.59 0.00 5.80
383 727 3.842925 GACAAAGTGAGCCGGCCCA 62.843 63.158 26.15 17.08 0.00 5.36
384 728 2.361610 CAAAGTGAGCCGGCCCAT 60.362 61.111 26.15 3.93 0.00 4.00
385 729 2.361610 AAAGTGAGCCGGCCCATG 60.362 61.111 26.15 0.00 0.00 3.66
386 730 3.210012 AAAGTGAGCCGGCCCATGT 62.210 57.895 26.15 6.35 0.00 3.21
387 731 1.847798 AAAGTGAGCCGGCCCATGTA 61.848 55.000 26.15 0.00 0.00 2.29
388 732 2.513897 GTGAGCCGGCCCATGTAC 60.514 66.667 26.15 9.67 0.00 2.90
389 733 3.792736 TGAGCCGGCCCATGTACC 61.793 66.667 26.15 2.77 0.00 3.34
390 734 3.792736 GAGCCGGCCCATGTACCA 61.793 66.667 26.15 0.00 0.00 3.25
391 735 3.096495 AGCCGGCCCATGTACCAT 61.096 61.111 26.15 0.00 0.00 3.55
392 736 2.594592 GCCGGCCCATGTACCATC 60.595 66.667 18.11 0.00 0.00 3.51
393 737 2.280797 CCGGCCCATGTACCATCG 60.281 66.667 0.00 0.00 0.00 3.84
394 738 2.802724 CCGGCCCATGTACCATCGA 61.803 63.158 0.00 0.00 0.00 3.59
395 739 1.145156 CGGCCCATGTACCATCGAA 59.855 57.895 0.00 0.00 0.00 3.71
396 740 0.880278 CGGCCCATGTACCATCGAAG 60.880 60.000 0.00 0.00 0.00 3.79
397 741 0.535102 GGCCCATGTACCATCGAAGG 60.535 60.000 4.85 4.85 0.00 3.46
398 742 0.180406 GCCCATGTACCATCGAAGGT 59.820 55.000 17.60 17.60 45.72 3.50
399 743 1.953559 CCCATGTACCATCGAAGGTG 58.046 55.000 22.16 5.35 43.14 4.00
400 744 1.209504 CCCATGTACCATCGAAGGTGT 59.790 52.381 22.16 5.56 43.14 4.16
401 745 2.279741 CCATGTACCATCGAAGGTGTG 58.720 52.381 22.16 16.22 43.14 3.82
402 746 1.665679 CATGTACCATCGAAGGTGTGC 59.334 52.381 22.16 12.20 43.14 4.57
403 747 0.389296 TGTACCATCGAAGGTGTGCG 60.389 55.000 22.16 0.00 43.14 5.34
404 748 0.108992 GTACCATCGAAGGTGTGCGA 60.109 55.000 22.16 0.00 43.14 5.10
406 750 0.821517 ACCATCGAAGGTGTGCGATA 59.178 50.000 12.35 0.00 44.56 2.92
407 751 1.412710 ACCATCGAAGGTGTGCGATAT 59.587 47.619 12.35 0.00 44.56 1.63
408 752 1.794701 CCATCGAAGGTGTGCGATATG 59.205 52.381 0.00 0.00 44.56 1.78
409 753 2.473816 CATCGAAGGTGTGCGATATGT 58.526 47.619 0.00 0.00 44.56 2.29
410 754 2.203800 TCGAAGGTGTGCGATATGTC 57.796 50.000 0.00 0.00 0.00 3.06
449 793 9.061435 CAAAATGTGGTAATTATGGTTTTTGGT 57.939 29.630 11.65 0.00 31.36 3.67
450 794 8.614469 AAATGTGGTAATTATGGTTTTTGGTG 57.386 30.769 0.00 0.00 0.00 4.17
457 801 4.775058 TTATGGTTTTTGGTGACCGATG 57.225 40.909 0.00 0.00 38.81 3.84
459 803 1.950909 TGGTTTTTGGTGACCGATGAC 59.049 47.619 0.00 0.00 38.81 3.06
461 805 3.181453 TGGTTTTTGGTGACCGATGACTA 60.181 43.478 0.00 0.00 38.81 2.59
462 806 3.187842 GGTTTTTGGTGACCGATGACTAC 59.812 47.826 0.00 0.00 0.00 2.73
464 808 1.634960 TTGGTGACCGATGACTACCA 58.365 50.000 0.00 0.00 39.49 3.25
468 812 1.135083 GTGACCGATGACTACCAGTGG 60.135 57.143 7.91 7.91 0.00 4.00
505 850 2.154462 CTGTGGGTGTTTAAGAGGCTG 58.846 52.381 0.00 0.00 0.00 4.85
511 856 4.200092 GGGTGTTTAAGAGGCTGGATTAG 58.800 47.826 0.00 0.00 0.00 1.73
523 868 2.588620 CTGGATTAGCTAGGTCCGACT 58.411 52.381 17.52 0.00 34.72 4.18
524 869 2.554893 CTGGATTAGCTAGGTCCGACTC 59.445 54.545 17.52 0.00 34.72 3.36
525 870 1.887854 GGATTAGCTAGGTCCGACTCC 59.112 57.143 10.44 0.00 0.00 3.85
526 871 1.536331 GATTAGCTAGGTCCGACTCCG 59.464 57.143 0.00 0.00 0.00 4.63
527 872 0.543277 TTAGCTAGGTCCGACTCCGA 59.457 55.000 0.00 0.00 38.22 4.55
528 873 0.179062 TAGCTAGGTCCGACTCCGAC 60.179 60.000 0.00 0.00 38.22 4.79
540 885 3.551890 CCGACTCCGACATGTAAATTCTG 59.448 47.826 0.00 0.00 38.22 3.02
549 894 8.047911 TCCGACATGTAAATTCTGGGTTTATAA 58.952 33.333 0.00 0.00 0.00 0.98
550 895 8.126700 CCGACATGTAAATTCTGGGTTTATAAC 58.873 37.037 0.00 0.00 0.00 1.89
566 911 7.951591 GGTTTATAACCCATCATTATGCTTGT 58.048 34.615 0.00 0.00 46.12 3.16
575 920 1.135315 CATTATGCTTGTGCGCAACCT 60.135 47.619 14.00 2.55 44.06 3.50
576 921 0.240678 TTATGCTTGTGCGCAACCTG 59.759 50.000 14.00 3.89 44.06 4.00
604 949 2.371841 TGTGCTCCAGTATCCACAGTTT 59.628 45.455 0.00 0.00 33.66 2.66
606 951 4.184629 GTGCTCCAGTATCCACAGTTTAG 58.815 47.826 0.00 0.00 0.00 1.85
607 952 3.838317 TGCTCCAGTATCCACAGTTTAGT 59.162 43.478 0.00 0.00 0.00 2.24
608 953 4.286032 TGCTCCAGTATCCACAGTTTAGTT 59.714 41.667 0.00 0.00 0.00 2.24
610 955 5.337652 GCTCCAGTATCCACAGTTTAGTTCT 60.338 44.000 0.00 0.00 0.00 3.01
612 957 4.631813 CCAGTATCCACAGTTTAGTTCTGC 59.368 45.833 0.00 0.00 36.50 4.26
613 958 5.482908 CAGTATCCACAGTTTAGTTCTGCT 58.517 41.667 0.00 0.00 36.50 4.24
614 959 5.578727 CAGTATCCACAGTTTAGTTCTGCTC 59.421 44.000 0.00 0.00 36.50 4.26
615 960 3.402628 TCCACAGTTTAGTTCTGCTCC 57.597 47.619 0.00 0.00 36.50 4.70
616 961 2.038557 TCCACAGTTTAGTTCTGCTCCC 59.961 50.000 0.00 0.00 36.50 4.30
617 962 2.039084 CCACAGTTTAGTTCTGCTCCCT 59.961 50.000 0.00 0.00 36.50 4.20
619 964 2.303311 ACAGTTTAGTTCTGCTCCCTCC 59.697 50.000 0.00 0.00 36.50 4.30
620 965 1.550976 AGTTTAGTTCTGCTCCCTCCG 59.449 52.381 0.00 0.00 0.00 4.63
622 967 1.183549 TTAGTTCTGCTCCCTCCGTC 58.816 55.000 0.00 0.00 0.00 4.79
623 968 0.683504 TAGTTCTGCTCCCTCCGTCC 60.684 60.000 0.00 0.00 0.00 4.79
624 969 2.683933 TTCTGCTCCCTCCGTCCC 60.684 66.667 0.00 0.00 0.00 4.46
626 971 2.765807 CTGCTCCCTCCGTCCCAT 60.766 66.667 0.00 0.00 0.00 4.00
627 972 1.457643 CTGCTCCCTCCGTCCCATA 60.458 63.158 0.00 0.00 0.00 2.74
628 973 1.002403 TGCTCCCTCCGTCCCATAA 59.998 57.895 0.00 0.00 0.00 1.90
629 974 0.399949 TGCTCCCTCCGTCCCATAAT 60.400 55.000 0.00 0.00 0.00 1.28
631 976 1.424638 CTCCCTCCGTCCCATAATGT 58.575 55.000 0.00 0.00 0.00 2.71
632 977 2.605257 CTCCCTCCGTCCCATAATGTA 58.395 52.381 0.00 0.00 0.00 2.29
633 978 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
634 979 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
636 981 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
639 984 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
641 986 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
642 987 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
643 988 6.313411 CCGTCCCATAATGTAAGACGTTTTTA 59.687 38.462 9.63 0.00 46.62 1.52
645 990 7.148606 CGTCCCATAATGTAAGACGTTTTTACA 60.149 37.037 21.30 21.30 43.89 2.41
646 991 8.505625 GTCCCATAATGTAAGACGTTTTTACAA 58.494 33.333 22.27 12.62 42.40 2.41
648 993 8.508875 CCCATAATGTAAGACGTTTTTACAACT 58.491 33.333 22.27 16.86 42.40 3.16
707 1503 2.703409 GCCTAATCGTGCAGTGCG 59.297 61.111 11.20 0.00 0.00 5.34
790 1586 4.749245 TTTCGAGACAAGGCAATTTCTC 57.251 40.909 0.00 0.00 0.00 2.87
912 1727 1.507141 CGGCGGATCCATTAACTGGC 61.507 60.000 13.41 3.90 45.52 4.85
969 1784 3.758931 GTTGGCCGCCCACAATCC 61.759 66.667 7.03 0.00 41.97 3.01
1106 1925 2.585900 AGGTAAATCCCTCCCCTTTTCC 59.414 50.000 0.00 0.00 36.75 3.13
1125 1944 1.683011 CCTCTTCCCGCATCCAAATGT 60.683 52.381 0.00 0.00 35.18 2.71
1133 1952 0.174162 GCATCCAAATGTGCTGGACC 59.826 55.000 0.00 0.00 45.67 4.46
1147 1976 0.036388 TGGACCGGATTCAGTTCAGC 60.036 55.000 9.46 0.00 0.00 4.26
1178 2007 4.934001 TCTGCTTTATTCAGTTCAGCTCAG 59.066 41.667 0.00 0.00 33.48 3.35
1179 2008 4.645535 TGCTTTATTCAGTTCAGCTCAGT 58.354 39.130 0.00 0.00 0.00 3.41
1182 2011 5.180117 GCTTTATTCAGTTCAGCTCAGTTCA 59.820 40.000 0.00 0.00 0.00 3.18
1183 2012 6.620303 GCTTTATTCAGTTCAGCTCAGTTCAG 60.620 42.308 0.00 0.00 0.00 3.02
1184 2013 3.827008 TTCAGTTCAGCTCAGTTCAGT 57.173 42.857 0.00 0.00 0.00 3.41
1185 2014 3.827008 TCAGTTCAGCTCAGTTCAGTT 57.173 42.857 0.00 0.00 0.00 3.16
1186 2015 3.722147 TCAGTTCAGCTCAGTTCAGTTC 58.278 45.455 0.00 0.00 0.00 3.01
1216 2045 8.059461 TCACATCTAGAGTAAATCCCTTCAGTA 58.941 37.037 0.00 0.00 0.00 2.74
1220 2049 8.896722 TCTAGAGTAAATCCCTTCAGTAAGTT 57.103 34.615 0.00 0.00 0.00 2.66
1358 2187 4.177537 TGTCAGAAAGATTGGGTTTGGA 57.822 40.909 0.00 0.00 0.00 3.53
1375 2204 1.300963 GAAGCCTGCTGTCCATGGA 59.699 57.895 11.44 11.44 0.00 3.41
1379 2208 0.106819 GCCTGCTGTCCATGGAAGAT 60.107 55.000 18.20 0.00 0.00 2.40
1382 2211 3.094572 CCTGCTGTCCATGGAAGATTTT 58.905 45.455 18.20 0.00 0.00 1.82
1721 4220 3.283751 TGTCAACAGGTACTTGTTTGGG 58.716 45.455 19.71 9.96 34.60 4.12
1730 4229 2.597217 TTGTTTGGGGCCGCTCAG 60.597 61.111 21.80 0.00 0.00 3.35
2105 4624 3.546815 GCTTGCTGGTAATTACTCATGCG 60.547 47.826 15.05 2.65 0.00 4.73
2140 4771 6.596703 CAATCAAACTGACTGTGATACACTG 58.403 40.000 0.00 0.00 38.85 3.66
2141 4772 4.058124 TCAAACTGACTGTGATACACTGC 58.942 43.478 8.28 3.63 36.91 4.40
2370 5632 7.040478 TGTTTGCTCAATCAGTAACTTTATGCT 60.040 33.333 0.00 0.00 0.00 3.79
2454 5716 5.268387 ACATGGGAAATGGTAGCATTGTTA 58.732 37.500 20.22 8.40 0.00 2.41
2543 5805 2.232452 CACCCATCAAAATAACCCGCAA 59.768 45.455 0.00 0.00 0.00 4.85
2550 5812 2.920490 CAAAATAACCCGCAACCGATTG 59.080 45.455 0.00 0.00 38.99 2.67
2742 6028 0.471591 AATTGGCAAGGCTTGTCCCA 60.472 50.000 27.49 22.86 33.37 4.37
2797 6090 7.660208 TCTGTATTCTTCAACTTTGTTACCCTC 59.340 37.037 0.00 0.00 0.00 4.30
2832 6156 9.045223 TCTCTACATATTCATGAAATGGAAACG 57.955 33.333 22.95 11.48 46.73 3.60
2966 6295 3.154710 GGGTCCGTTTTCTTGGAAGAAT 58.845 45.455 2.71 0.00 43.92 2.40
3100 6459 7.083875 ACACTATGTTATGGTTTCCAATTCG 57.916 36.000 0.00 0.00 36.95 3.34
3105 6464 5.067273 TGTTATGGTTTCCAATTCGACACT 58.933 37.500 0.00 0.00 36.95 3.55
3122 6510 1.672356 CTTCTGTGTTCCCGCCTGG 60.672 63.158 0.00 0.00 0.00 4.45
3255 6668 1.680735 CAACAGTGGGCAAGTAAAGCA 59.319 47.619 0.00 0.00 0.00 3.91
3602 7029 0.828343 GCCAGAGCTACGTCCCCTAT 60.828 60.000 0.00 0.00 35.50 2.57
3796 7229 3.640407 ACGGTGCCTGCTCCATGT 61.640 61.111 10.51 0.00 0.00 3.21
3812 7245 1.273606 CATGTGGAAGAGGACGACAGT 59.726 52.381 0.00 0.00 30.57 3.55
3827 7260 1.056700 ACAGTGTGTTCCTCCTGGCT 61.057 55.000 0.00 0.00 0.00 4.75
3828 7261 0.604780 CAGTGTGTTCCTCCTGGCTG 60.605 60.000 0.00 0.00 0.00 4.85
3829 7262 1.056700 AGTGTGTTCCTCCTGGCTGT 61.057 55.000 0.00 0.00 0.00 4.40
3830 7263 0.886490 GTGTGTTCCTCCTGGCTGTG 60.886 60.000 0.00 0.00 0.00 3.66
3831 7264 1.302832 GTGTTCCTCCTGGCTGTGG 60.303 63.158 0.00 0.00 0.00 4.17
3832 7265 2.352805 GTTCCTCCTGGCTGTGGG 59.647 66.667 0.00 0.00 0.00 4.61
3833 7266 2.935481 TTCCTCCTGGCTGTGGGG 60.935 66.667 0.00 0.00 0.00 4.96
3978 7420 0.681175 GGGCAGCATTTTGTTGGACT 59.319 50.000 0.00 0.00 0.00 3.85
4075 7517 4.284490 GCCTACATATCTGGTTGGATCTGA 59.716 45.833 0.00 0.00 33.72 3.27
4147 7613 7.346698 TGGGGCATAATTTCTTCATGGAAAATA 59.653 33.333 1.91 0.00 38.46 1.40
4269 7754 8.015185 AGGGAAATTCACCATGAAATATCTTG 57.985 34.615 0.00 0.00 40.12 3.02
4335 7823 3.358707 GCGCGCCACCCAAAACTA 61.359 61.111 23.24 0.00 0.00 2.24
4343 7831 0.178947 CACCCAAAACTAAGCCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
4380 7868 3.075432 CCTTCTCCCCCTTTTAGGAACAA 59.925 47.826 0.00 0.00 37.67 2.83
4398 7886 0.383949 AATTGTGTTTTGGCGCGAGT 59.616 45.000 12.10 0.00 0.00 4.18
4413 7908 0.978146 CGAGTGTCCCCTCCAGGAAT 60.978 60.000 0.00 0.00 37.78 3.01
4423 7918 2.039084 CCCTCCAGGAATATTTCGGGAG 59.961 54.545 27.56 27.56 44.75 4.30
4430 7925 3.136626 AGGAATATTTCGGGAGGTTCCAG 59.863 47.826 10.77 0.00 38.64 3.86
4456 7951 2.397044 TTTGGCACCCCTCTGAAAAT 57.603 45.000 0.00 0.00 0.00 1.82
4458 7953 1.923356 TGGCACCCCTCTGAAAATTC 58.077 50.000 0.00 0.00 0.00 2.17
4471 7966 2.554462 TGAAAATTCCGGACGCATTTCA 59.446 40.909 20.57 20.57 35.20 2.69
4483 7978 4.209080 GGACGCATTTCAAAACTTTTCTGG 59.791 41.667 0.00 0.00 0.00 3.86
4499 7994 4.640771 TTCTGGCTTGATGGTTTACTCT 57.359 40.909 0.00 0.00 0.00 3.24
4501 7996 3.012518 CTGGCTTGATGGTTTACTCTGG 58.987 50.000 0.00 0.00 0.00 3.86
4503 7998 3.274288 GGCTTGATGGTTTACTCTGGAG 58.726 50.000 0.00 0.00 0.00 3.86
4505 8000 3.869912 GCTTGATGGTTTACTCTGGAGCA 60.870 47.826 0.00 0.00 0.00 4.26
4544 8065 4.878971 TCTGAAACATTTTCGGTGTCTTCA 59.121 37.500 7.24 0.00 31.87 3.02
4566 8087 6.090129 TCAAAACTTTTCCGTTGACTTTCTG 58.910 36.000 0.00 0.00 0.00 3.02
4567 8088 4.632538 AACTTTTCCGTTGACTTTCTGG 57.367 40.909 0.00 0.00 0.00 3.86
4568 8089 3.881220 ACTTTTCCGTTGACTTTCTGGA 58.119 40.909 0.00 0.00 0.00 3.86
4569 8090 3.626217 ACTTTTCCGTTGACTTTCTGGAC 59.374 43.478 0.00 0.00 0.00 4.02
4570 8091 3.553828 TTTCCGTTGACTTTCTGGACT 57.446 42.857 0.00 0.00 0.00 3.85
4571 8092 3.553828 TTCCGTTGACTTTCTGGACTT 57.446 42.857 0.00 0.00 0.00 3.01
4572 8093 3.553828 TCCGTTGACTTTCTGGACTTT 57.446 42.857 0.00 0.00 0.00 2.66
4573 8094 3.463944 TCCGTTGACTTTCTGGACTTTC 58.536 45.455 0.00 0.00 0.00 2.62
4574 8095 3.134081 TCCGTTGACTTTCTGGACTTTCT 59.866 43.478 0.00 0.00 0.00 2.52
4575 8096 3.495001 CCGTTGACTTTCTGGACTTTCTC 59.505 47.826 0.00 0.00 0.00 2.87
4576 8097 4.372656 CGTTGACTTTCTGGACTTTCTCT 58.627 43.478 0.00 0.00 0.00 3.10
4577 8098 4.446051 CGTTGACTTTCTGGACTTTCTCTC 59.554 45.833 0.00 0.00 0.00 3.20
4578 8099 5.360591 GTTGACTTTCTGGACTTTCTCTCA 58.639 41.667 0.00 0.00 0.00 3.27
4642 8168 3.347216 CTGTGTTCGGATCAAAGGGATT 58.653 45.455 0.00 0.00 36.00 3.01
4643 8169 3.081061 TGTGTTCGGATCAAAGGGATTG 58.919 45.455 0.00 0.00 40.58 2.67
4751 8307 3.074412 ACCCACGAAATCAACAGATGTC 58.926 45.455 0.00 0.00 0.00 3.06
4764 8320 0.398522 AGATGTCGGTCCCCTGCATA 60.399 55.000 0.00 0.00 0.00 3.14
4820 8815 2.860735 GCCTCGATGTGTACAGATCAAC 59.139 50.000 27.02 12.73 31.23 3.18
4882 8886 2.513026 CTTCCACTGTCTCGGGCCTG 62.513 65.000 4.71 4.71 0.00 4.85
4981 8985 2.507471 AGGGAGCAGTTCCTTAGGAATG 59.493 50.000 17.42 15.73 44.04 2.67
5045 9049 1.138266 GGCCTTAAGCGTGTGATCCTA 59.862 52.381 0.00 0.00 45.17 2.94
5056 9060 4.318332 CGTGTGATCCTATAGGTACGGTA 58.682 47.826 18.51 0.00 36.34 4.02
5086 9092 8.867112 ATAGATACGAGCGAAACTTTTTGATA 57.133 30.769 0.00 0.00 0.00 2.15
5087 9093 7.223058 AGATACGAGCGAAACTTTTTGATAG 57.777 36.000 0.00 0.00 0.00 2.08
5089 9095 5.265407 ACGAGCGAAACTTTTTGATAGAC 57.735 39.130 0.00 0.00 0.00 2.59
5105 9111 6.961360 TGATAGACGATCAATAGTGGAACT 57.039 37.500 0.00 0.00 46.16 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.532521 ACTCATGCACTTAGGTCCTTAACT 59.467 41.667 0.00 0.00 0.00 2.24
41 42 9.828852 CTTCTATCGTAATATGGAGTTGTACTC 57.171 37.037 0.00 0.00 44.32 2.59
140 440 5.625921 ATTGTGTTTTGCAAAAGCTGTTT 57.374 30.435 24.46 6.17 0.00 2.83
141 441 5.625921 AATTGTGTTTTGCAAAAGCTGTT 57.374 30.435 24.46 12.82 0.00 3.16
202 504 6.111382 TCAAAATTTGTGTGCATTTCCAGAA 58.889 32.000 5.56 0.00 0.00 3.02
204 506 5.524646 ACTCAAAATTTGTGTGCATTTCCAG 59.475 36.000 11.94 0.00 36.17 3.86
360 704 1.067060 GCCGGCTCACTTTGTCTTTTT 59.933 47.619 22.15 0.00 0.00 1.94
361 705 0.668535 GCCGGCTCACTTTGTCTTTT 59.331 50.000 22.15 0.00 0.00 2.27
362 706 1.172812 GGCCGGCTCACTTTGTCTTT 61.173 55.000 28.56 0.00 0.00 2.52
363 707 1.600916 GGCCGGCTCACTTTGTCTT 60.601 57.895 28.56 0.00 0.00 3.01
364 708 2.032681 GGCCGGCTCACTTTGTCT 59.967 61.111 28.56 0.00 0.00 3.41
365 709 3.056328 GGGCCGGCTCACTTTGTC 61.056 66.667 28.56 5.59 0.00 3.18
366 710 3.210012 ATGGGCCGGCTCACTTTGT 62.210 57.895 35.86 13.67 0.00 2.83
367 711 2.361610 ATGGGCCGGCTCACTTTG 60.362 61.111 35.86 0.00 0.00 2.77
368 712 1.847798 TACATGGGCCGGCTCACTTT 61.848 55.000 35.86 21.37 0.00 2.66
369 713 2.297895 TACATGGGCCGGCTCACTT 61.298 57.895 35.86 24.24 0.00 3.16
370 714 2.687200 TACATGGGCCGGCTCACT 60.687 61.111 35.86 22.73 0.00 3.41
371 715 2.513897 GTACATGGGCCGGCTCAC 60.514 66.667 35.86 16.28 0.00 3.51
372 716 3.792736 GGTACATGGGCCGGCTCA 61.793 66.667 35.14 35.14 0.00 4.26
373 717 3.792736 TGGTACATGGGCCGGCTC 61.793 66.667 28.56 25.91 0.00 4.70
384 728 4.739683 TATCGCACACCTTCGATGGTACA 61.740 47.826 21.46 5.74 44.10 2.90
385 729 0.108992 TCGCACACCTTCGATGGTAC 60.109 55.000 21.46 13.29 38.45 3.34
386 730 0.821517 ATCGCACACCTTCGATGGTA 59.178 50.000 21.46 7.45 42.95 3.25
387 731 0.821517 TATCGCACACCTTCGATGGT 59.178 50.000 16.84 16.84 44.10 3.55
388 732 1.794701 CATATCGCACACCTTCGATGG 59.205 52.381 15.45 15.45 44.10 3.51
389 733 2.472861 GACATATCGCACACCTTCGATG 59.527 50.000 7.30 0.00 44.10 3.84
390 734 2.743938 GACATATCGCACACCTTCGAT 58.256 47.619 2.72 2.72 45.87 3.59
391 735 1.533129 CGACATATCGCACACCTTCGA 60.533 52.381 0.00 0.00 42.43 3.71
392 736 0.846401 CGACATATCGCACACCTTCG 59.154 55.000 0.00 0.00 42.43 3.79
398 742 9.898797 TGTGATAAGTTGTCGACATATCGCACA 62.899 40.741 31.11 27.63 46.30 4.57
399 743 7.649635 TGTGATAAGTTGTCGACATATCGCAC 61.650 42.308 31.11 26.17 46.30 5.34
403 747 9.425893 CATTTTGTGATAAGTTGTCGACATATC 57.574 33.333 20.80 21.78 38.70 1.63
404 748 8.946085 ACATTTTGTGATAAGTTGTCGACATAT 58.054 29.630 20.80 14.26 0.00 1.78
405 749 8.317891 ACATTTTGTGATAAGTTGTCGACATA 57.682 30.769 20.80 9.56 0.00 2.29
406 750 7.202016 ACATTTTGTGATAAGTTGTCGACAT 57.798 32.000 20.80 7.28 0.00 3.06
407 751 6.612247 ACATTTTGTGATAAGTTGTCGACA 57.388 33.333 15.76 15.76 0.00 4.35
422 766 9.061435 CCAAAAACCATAATTACCACATTTTGT 57.939 29.630 16.11 0.00 34.89 2.83
425 769 8.432805 TCACCAAAAACCATAATTACCACATTT 58.567 29.630 0.00 0.00 0.00 2.32
431 775 5.183522 TCGGTCACCAAAAACCATAATTACC 59.816 40.000 0.00 0.00 35.13 2.85
433 777 6.659668 TCATCGGTCACCAAAAACCATAATTA 59.340 34.615 0.00 0.00 35.13 1.40
445 789 1.548719 CTGGTAGTCATCGGTCACCAA 59.451 52.381 0.00 0.00 38.74 3.67
449 793 1.182667 CCACTGGTAGTCATCGGTCA 58.817 55.000 0.00 0.00 0.00 4.02
450 794 1.134560 GTCCACTGGTAGTCATCGGTC 59.865 57.143 0.00 0.00 0.00 4.79
457 801 3.788775 GACGTGTCCACTGGTAGTC 57.211 57.895 0.00 0.00 0.00 2.59
484 828 1.073923 AGCCTCTTAAACACCCACAGG 59.926 52.381 0.00 0.00 40.04 4.00
486 830 1.202879 CCAGCCTCTTAAACACCCACA 60.203 52.381 0.00 0.00 0.00 4.17
491 835 4.884458 GCTAATCCAGCCTCTTAAACAC 57.116 45.455 0.00 0.00 45.23 3.32
505 850 1.887854 GGAGTCGGACCTAGCTAATCC 59.112 57.143 12.06 12.06 0.00 3.01
511 856 1.102222 ATGTCGGAGTCGGACCTAGC 61.102 60.000 23.51 3.84 36.95 3.42
512 857 0.663688 CATGTCGGAGTCGGACCTAG 59.336 60.000 23.51 12.22 36.95 3.02
516 861 2.642139 TTTACATGTCGGAGTCGGAC 57.358 50.000 20.71 20.71 36.95 4.79
519 864 3.551890 CCAGAATTTACATGTCGGAGTCG 59.448 47.826 0.00 0.00 37.82 4.18
522 867 3.873910 ACCCAGAATTTACATGTCGGAG 58.126 45.455 0.00 0.00 0.00 4.63
523 868 3.992943 ACCCAGAATTTACATGTCGGA 57.007 42.857 0.00 0.00 0.00 4.55
524 869 6.693315 ATAAACCCAGAATTTACATGTCGG 57.307 37.500 0.00 0.00 0.00 4.79
525 870 8.126700 GGTTATAAACCCAGAATTTACATGTCG 58.873 37.037 0.00 0.00 46.12 4.35
549 894 1.677576 CGCACAAGCATAATGATGGGT 59.322 47.619 0.00 0.00 42.27 4.51
550 895 1.601162 GCGCACAAGCATAATGATGGG 60.601 52.381 0.30 0.00 42.27 4.00
566 911 2.670789 GCACATTAATTCAGGTTGCGCA 60.671 45.455 5.66 5.66 0.00 6.09
575 920 5.822519 GTGGATACTGGAGCACATTAATTCA 59.177 40.000 0.00 0.00 37.61 2.57
576 921 5.822519 TGTGGATACTGGAGCACATTAATTC 59.177 40.000 0.00 0.00 37.61 2.17
604 949 0.683504 GGACGGAGGGAGCAGAACTA 60.684 60.000 0.00 0.00 0.00 2.24
606 951 2.579738 GGACGGAGGGAGCAGAAC 59.420 66.667 0.00 0.00 0.00 3.01
607 952 2.683933 GGGACGGAGGGAGCAGAA 60.684 66.667 0.00 0.00 0.00 3.02
608 953 1.944896 TATGGGACGGAGGGAGCAGA 61.945 60.000 0.00 0.00 0.00 4.26
610 955 0.399949 ATTATGGGACGGAGGGAGCA 60.400 55.000 0.00 0.00 0.00 4.26
612 957 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
613 958 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
614 959 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
615 960 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
616 961 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
617 962 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
620 965 8.031848 TGTAAAAACGTCTTACATTATGGGAC 57.968 34.615 15.53 1.75 34.99 4.46
622 967 8.508875 AGTTGTAAAAACGTCTTACATTATGGG 58.491 33.333 18.58 0.00 38.65 4.00
631 976 9.979578 TCCTACATTAGTTGTAAAAACGTCTTA 57.020 29.630 0.00 0.00 40.27 2.10
632 977 8.891671 TCCTACATTAGTTGTAAAAACGTCTT 57.108 30.769 0.00 0.00 40.27 3.01
633 978 7.117379 GCTCCTACATTAGTTGTAAAAACGTCT 59.883 37.037 0.00 0.00 40.27 4.18
634 979 7.117379 AGCTCCTACATTAGTTGTAAAAACGTC 59.883 37.037 0.00 0.00 40.27 4.34
636 981 7.117236 TCAGCTCCTACATTAGTTGTAAAAACG 59.883 37.037 0.00 0.00 40.27 3.60
639 984 7.903145 TCTCAGCTCCTACATTAGTTGTAAAA 58.097 34.615 0.00 0.00 40.27 1.52
641 986 7.201920 GGATCTCAGCTCCTACATTAGTTGTAA 60.202 40.741 0.00 0.00 40.27 2.41
642 987 6.265649 GGATCTCAGCTCCTACATTAGTTGTA 59.734 42.308 0.00 0.00 39.87 2.41
643 988 5.069781 GGATCTCAGCTCCTACATTAGTTGT 59.930 44.000 0.00 0.00 42.62 3.32
645 990 5.211973 TGGATCTCAGCTCCTACATTAGTT 58.788 41.667 0.00 0.00 33.69 2.24
646 991 4.809193 TGGATCTCAGCTCCTACATTAGT 58.191 43.478 0.00 0.00 33.69 2.24
648 993 4.038042 CGTTGGATCTCAGCTCCTACATTA 59.962 45.833 9.40 0.00 38.09 1.90
651 996 1.751351 CGTTGGATCTCAGCTCCTACA 59.249 52.381 9.40 0.00 38.09 2.74
654 999 1.965754 GCCGTTGGATCTCAGCTCCT 61.966 60.000 0.00 0.00 33.69 3.69
684 1480 0.447801 CTGCACGATTAGGCCAACAC 59.552 55.000 5.01 0.00 0.00 3.32
707 1503 1.227497 CTCAGATCGGCCAGCTTCC 60.227 63.158 2.24 0.00 0.00 3.46
790 1586 3.952628 GAGGGTTCGTGGCGAAGGG 62.953 68.421 4.11 0.00 46.54 3.95
969 1784 0.465097 TAGCTAGGGTTCGAGGTCGG 60.465 60.000 0.00 0.00 40.29 4.79
1056 1875 2.161609 GGACTTGTTGGCGGAATTGTAG 59.838 50.000 0.00 0.00 0.00 2.74
1106 1925 1.402968 CACATTTGGATGCGGGAAGAG 59.597 52.381 0.00 0.00 36.72 2.85
1125 1944 0.036388 GAACTGAATCCGGTCCAGCA 60.036 55.000 16.35 3.59 0.00 4.41
1133 1952 2.098117 GGGATTTGCTGAACTGAATCCG 59.902 50.000 7.61 0.00 45.39 4.18
1147 1976 6.151648 TGAACTGAATAAAGCAGAGGGATTTG 59.848 38.462 0.00 0.00 35.54 2.32
1178 2007 5.065704 TCTAGATGTGAGCTGAACTGAAC 57.934 43.478 0.00 0.00 0.00 3.18
1179 2008 4.769488 ACTCTAGATGTGAGCTGAACTGAA 59.231 41.667 0.00 0.00 35.12 3.02
1182 2011 6.842437 TTTACTCTAGATGTGAGCTGAACT 57.158 37.500 0.00 0.00 35.12 3.01
1183 2012 6.699642 GGATTTACTCTAGATGTGAGCTGAAC 59.300 42.308 0.00 0.00 35.12 3.18
1184 2013 6.183360 GGGATTTACTCTAGATGTGAGCTGAA 60.183 42.308 0.00 0.00 35.12 3.02
1185 2014 5.303078 GGGATTTACTCTAGATGTGAGCTGA 59.697 44.000 0.00 0.00 35.12 4.26
1186 2015 5.304101 AGGGATTTACTCTAGATGTGAGCTG 59.696 44.000 0.00 0.00 35.12 4.24
1216 2045 5.594317 AGTGAGTGGATTAAACAAGCAACTT 59.406 36.000 0.00 0.00 0.00 2.66
1220 2049 4.713553 TGAGTGAGTGGATTAAACAAGCA 58.286 39.130 0.00 0.00 0.00 3.91
1322 2151 1.552337 CTGACAAAGCCTCTCTGCCTA 59.448 52.381 0.00 0.00 0.00 3.93
1323 2152 0.324285 CTGACAAAGCCTCTCTGCCT 59.676 55.000 0.00 0.00 0.00 4.75
1324 2153 0.322975 TCTGACAAAGCCTCTCTGCC 59.677 55.000 0.00 0.00 0.00 4.85
1358 2187 0.323178 CTTCCATGGACAGCAGGCTT 60.323 55.000 15.91 0.00 0.00 4.35
1375 2204 3.359950 GCCCTGTCCATCTCAAAATCTT 58.640 45.455 0.00 0.00 0.00 2.40
1379 2208 0.039618 GGGCCCTGTCCATCTCAAAA 59.960 55.000 17.04 0.00 0.00 2.44
1382 2211 0.044092 TAAGGGCCCTGTCCATCTCA 59.956 55.000 29.50 0.00 0.00 3.27
1747 4246 1.448540 CCGCACCAGTCCATCTGTC 60.449 63.158 0.00 0.00 42.19 3.51
1945 4461 5.716228 ACCTGCATTTCAAGGACAATGAATA 59.284 36.000 0.00 0.00 36.72 1.75
2105 4624 5.091431 GTCAGTTTGATTGCAGAATGTAGC 58.909 41.667 0.00 0.00 39.31 3.58
2162 4794 4.158394 AGCATGCCATTATTTCGAACAAGT 59.842 37.500 15.66 0.00 0.00 3.16
2199 4831 3.014623 GGGTTACAAGACTGGTAATGCC 58.985 50.000 5.72 3.69 33.68 4.40
2370 5632 3.313249 CGCACCTATTTGCATCAGAATGA 59.687 43.478 0.00 0.00 42.92 2.57
2454 5716 0.537143 TCAGCACATGTTCCGCCTTT 60.537 50.000 0.00 0.00 0.00 3.11
2543 5805 1.995626 AGGGTAGGCTGCAATCGGT 60.996 57.895 4.64 0.00 0.00 4.69
2797 6090 9.899226 TTCATGAATATGTAGAGATCTTGTACG 57.101 33.333 3.38 0.00 35.73 3.67
2966 6295 2.292292 GGCTTCTTGGAAAAACTACGCA 59.708 45.455 0.00 0.00 0.00 5.24
3090 6449 4.811555 CACAGAAGTGTCGAATTGGAAA 57.188 40.909 0.00 0.00 40.92 3.13
3105 6464 1.990160 AACCAGGCGGGAACACAGAA 61.990 55.000 11.67 0.00 41.15 3.02
3114 6502 3.373565 GCAAAGGAACCAGGCGGG 61.374 66.667 0.79 0.79 44.81 6.13
3117 6505 1.067354 CAATCTGCAAAGGAACCAGGC 60.067 52.381 0.00 0.00 0.00 4.85
3118 6506 2.029649 CACAATCTGCAAAGGAACCAGG 60.030 50.000 0.00 0.00 0.00 4.45
3122 6510 3.149196 TCTCCACAATCTGCAAAGGAAC 58.851 45.455 0.00 0.00 0.00 3.62
3602 7029 3.611674 TGGCCGTCAAGCTCGTGA 61.612 61.111 0.00 0.00 0.00 4.35
3796 7229 0.673985 CACACTGTCGTCCTCTTCCA 59.326 55.000 0.00 0.00 0.00 3.53
3812 7245 1.451504 CACAGCCAGGAGGAACACA 59.548 57.895 0.00 0.00 36.89 3.72
3978 7420 0.878523 CTGTTCGTCACCGCCTTCAA 60.879 55.000 0.00 0.00 0.00 2.69
4147 7613 4.082787 GCAGCAATTACATTACACCAGTGT 60.083 41.667 8.71 8.71 46.87 3.55
4235 7720 1.068541 GTGAATTTCCCTTGCACCGAC 60.069 52.381 0.00 0.00 0.00 4.79
4270 7755 2.100197 GGCCCCATGGTTCTCTAAAAC 58.900 52.381 11.73 0.00 0.00 2.43
4335 7823 1.530655 CCTTTTCGTGTGGGGGCTT 60.531 57.895 0.00 0.00 0.00 4.35
4371 7859 4.363999 CGCCAAAACACAATTGTTCCTAA 58.636 39.130 8.77 0.00 45.69 2.69
4372 7860 3.797184 GCGCCAAAACACAATTGTTCCTA 60.797 43.478 8.77 0.00 45.69 2.94
4380 7868 0.317770 CACTCGCGCCAAAACACAAT 60.318 50.000 0.00 0.00 0.00 2.71
4398 7886 2.438021 CGAAATATTCCTGGAGGGGACA 59.562 50.000 0.00 0.00 34.78 4.02
4405 7900 2.771688 ACCTCCCGAAATATTCCTGGA 58.228 47.619 0.00 0.00 0.00 3.86
4406 7901 3.477530 GAACCTCCCGAAATATTCCTGG 58.522 50.000 0.00 0.00 0.00 4.45
4408 7903 3.120108 TGGAACCTCCCGAAATATTCCT 58.880 45.455 0.00 0.00 37.18 3.36
4413 7908 3.178865 AGTTCTGGAACCTCCCGAAATA 58.821 45.455 9.51 0.00 40.61 1.40
4441 7936 0.811281 CGGAATTTTCAGAGGGGTGC 59.189 55.000 0.00 0.00 0.00 5.01
4448 7943 2.107950 ATGCGTCCGGAATTTTCAGA 57.892 45.000 5.23 0.00 0.00 3.27
4450 7945 2.554462 TGAAATGCGTCCGGAATTTTCA 59.446 40.909 19.99 19.99 32.41 2.69
4451 7946 3.210358 TGAAATGCGTCCGGAATTTTC 57.790 42.857 5.23 13.41 0.00 2.29
4456 7951 1.950909 AGTTTTGAAATGCGTCCGGAA 59.049 42.857 5.23 0.00 0.00 4.30
4458 7953 2.415697 AAGTTTTGAAATGCGTCCGG 57.584 45.000 0.00 0.00 0.00 5.14
4471 7966 5.357742 AACCATCAAGCCAGAAAAGTTTT 57.642 34.783 0.00 0.00 0.00 2.43
4483 7978 2.680339 GCTCCAGAGTAAACCATCAAGC 59.320 50.000 0.00 0.00 0.00 4.01
4499 7994 3.457749 AGGGAAAACCAAAAATTGCTCCA 59.542 39.130 0.00 0.00 43.89 3.86
4501 7996 4.751600 CAGAGGGAAAACCAAAAATTGCTC 59.248 41.667 0.00 0.00 43.89 4.26
4503 7998 4.702831 TCAGAGGGAAAACCAAAAATTGC 58.297 39.130 0.00 0.00 43.89 3.56
4505 8000 6.716284 TGTTTCAGAGGGAAAACCAAAAATT 58.284 32.000 0.00 0.00 46.53 1.82
4544 8065 5.184287 TCCAGAAAGTCAACGGAAAAGTTTT 59.816 36.000 0.00 0.00 30.96 2.43
4566 8087 4.882842 AAGGAGTCTTGAGAGAAAGTCC 57.117 45.455 0.00 0.00 32.66 3.85
4567 8088 6.521162 AGAAAAGGAGTCTTGAGAGAAAGTC 58.479 40.000 0.00 0.00 32.66 3.01
4568 8089 6.493189 AGAAAAGGAGTCTTGAGAGAAAGT 57.507 37.500 0.00 0.00 32.66 2.66
4569 8090 7.666623 ACTAGAAAAGGAGTCTTGAGAGAAAG 58.333 38.462 0.00 0.00 32.66 2.62
4570 8091 7.604657 ACTAGAAAAGGAGTCTTGAGAGAAA 57.395 36.000 0.00 0.00 32.66 2.52
4571 8092 7.945664 AGTACTAGAAAAGGAGTCTTGAGAGAA 59.054 37.037 0.00 0.00 32.66 2.87
4572 8093 7.463431 AGTACTAGAAAAGGAGTCTTGAGAGA 58.537 38.462 0.00 0.00 32.75 3.10
4573 8094 7.392113 TGAGTACTAGAAAAGGAGTCTTGAGAG 59.608 40.741 0.00 0.00 39.08 3.20
4574 8095 7.232188 TGAGTACTAGAAAAGGAGTCTTGAGA 58.768 38.462 0.00 0.00 39.08 3.27
4575 8096 7.455641 TGAGTACTAGAAAAGGAGTCTTGAG 57.544 40.000 0.00 0.00 39.08 3.02
4576 8097 6.071840 GCTGAGTACTAGAAAAGGAGTCTTGA 60.072 42.308 0.00 0.00 39.08 3.02
4577 8098 6.096695 GCTGAGTACTAGAAAAGGAGTCTTG 58.903 44.000 0.00 0.00 39.08 3.02
4578 8099 5.775701 TGCTGAGTACTAGAAAAGGAGTCTT 59.224 40.000 0.00 0.00 39.08 3.01
4642 8168 4.873746 TTGTTCCAAACCTGTGTTTTCA 57.126 36.364 0.00 0.00 41.92 2.69
4643 8169 6.546972 TTTTTGTTCCAAACCTGTGTTTTC 57.453 33.333 0.00 0.00 41.92 2.29
4666 8192 4.544152 TCACTTCCTTTCCATTTCCCCTAT 59.456 41.667 0.00 0.00 0.00 2.57
4764 8320 8.447833 CAGCATGCATCAAACATTTAAAAATCT 58.552 29.630 21.98 0.00 0.00 2.40
4820 8815 6.207928 TGCATCACATCGGCTATAAAAATTG 58.792 36.000 0.00 0.00 0.00 2.32
4915 8919 2.768698 TCTTTTGTTACCGATCCGCAA 58.231 42.857 0.00 0.00 0.00 4.85
4981 8985 3.305131 CGTAGGAAAACCAAAGGAAAGCC 60.305 47.826 0.00 0.00 0.00 4.35
5015 9019 1.025113 GCTTAAGGCCTGTTCGGGAC 61.025 60.000 5.69 0.00 34.27 4.46
5029 9033 5.049198 CGTACCTATAGGATCACACGCTTAA 60.049 44.000 26.01 0.00 38.94 1.85
5066 9070 5.060077 CGTCTATCAAAAAGTTTCGCTCGTA 59.940 40.000 0.00 0.00 0.00 3.43
5068 9072 4.089493 TCGTCTATCAAAAAGTTTCGCTCG 59.911 41.667 0.00 0.00 0.00 5.03
5086 9092 4.382040 CCACAGTTCCACTATTGATCGTCT 60.382 45.833 0.00 0.00 0.00 4.18
5087 9093 3.865745 CCACAGTTCCACTATTGATCGTC 59.134 47.826 0.00 0.00 0.00 4.20
5089 9095 3.865745 GTCCACAGTTCCACTATTGATCG 59.134 47.826 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.