Multiple sequence alignment - TraesCS5B01G261800

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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 TraesCS5B01G261800 chr5B 100.000 2155 0 0 2466 4620 446412932 446415086 0.000000e+00 3980.0
1 TraesCS5B01G261800 chr5B 100.000 2031 0 0 1 2031 446410467 446412497 0.000000e+00 3751.0
2 TraesCS5B01G261800 chr5B 93.822 1214 53 11 830 2031 446010403 446009200 0.000000e+00 1807.0
3 TraesCS5B01G261800 chr5B 93.380 1133 45 8 903 2031 447207183 447206077 0.000000e+00 1650.0
4 TraesCS5B01G261800 chr5B 92.664 1036 49 13 2502 3521 447205744 447204720 0.000000e+00 1467.0
5 TraesCS5B01G261800 chr5B 86.888 1083 69 46 2468 3523 446009197 446008161 0.000000e+00 1146.0
6 TraesCS5B01G261800 chr5B 88.363 739 82 4 2 738 394008117 394008853 0.000000e+00 885.0
7 TraesCS5B01G261800 chr5B 96.584 322 10 1 4300 4620 447204001 447203680 2.450000e-147 532.0
8 TraesCS5B01G261800 chr5B 81.192 537 59 13 4124 4619 446829884 446830419 1.200000e-105 394.0
9 TraesCS5B01G261800 chr5B 94.413 179 9 1 4104 4282 447204254 447204077 1.640000e-69 274.0
10 TraesCS5B01G261800 chr5B 78.414 227 26 12 3567 3773 446008088 446007865 4.850000e-25 126.0
11 TraesCS5B01G261800 chr5D 94.938 1284 55 4 746 2019 374295174 374296457 0.000000e+00 2002.0
12 TraesCS5B01G261800 chr5D 90.526 950 49 19 2587 3522 374296578 374297500 0.000000e+00 1218.0
13 TraesCS5B01G261800 chr5D 92.879 323 23 0 4297 4619 374312932 374313254 1.950000e-128 470.0
14 TraesCS5B01G261800 chr5D 88.797 241 13 5 4071 4300 374297961 374298198 2.720000e-72 283.0
15 TraesCS5B01G261800 chr5D 100.000 33 0 0 2493 2525 374296491 374296523 1.390000e-05 62.1
16 TraesCS5B01G261800 chr5A 91.923 1300 72 12 746 2019 476072604 476073896 0.000000e+00 1788.0
17 TraesCS5B01G261800 chr5A 92.287 739 55 2 1 738 635563221 635563958 0.000000e+00 1048.0
18 TraesCS5B01G261800 chr5A 90.993 755 52 10 2773 3519 476074129 476074875 0.000000e+00 1003.0
19 TraesCS5B01G261800 chr5A 98.485 132 1 1 3904 4034 857821 857690 1.000000e-56 231.0
20 TraesCS5B01G261800 chr5A 96.970 132 4 0 3902 4033 385545885 385546016 6.020000e-54 222.0
21 TraesCS5B01G261800 chr5A 76.877 333 46 15 3566 3877 476075031 476075353 4.780000e-35 159.0
22 TraesCS5B01G261800 chr7B 94.723 739 37 2 1 738 443325159 443325896 0.000000e+00 1147.0
23 TraesCS5B01G261800 chr7B 98.450 129 2 0 3905 4033 89765776 89765904 1.290000e-55 228.0
24 TraesCS5B01G261800 chr6A 94.378 747 37 5 1 746 604447252 604446510 0.000000e+00 1142.0
25 TraesCS5B01G261800 chr3D 92.308 741 54 3 1 740 284850136 284849398 0.000000e+00 1050.0
26 TraesCS5B01G261800 chr3D 84.336 1047 125 26 996 2019 174455356 174456386 0.000000e+00 989.0
27 TraesCS5B01G261800 chr3D 94.590 573 29 2 1459 2031 584112541 584111971 0.000000e+00 885.0
28 TraesCS5B01G261800 chr3D 83.747 726 98 18 2806 3518 174456666 174457384 0.000000e+00 669.0
29 TraesCS5B01G261800 chr3D 95.620 137 6 0 3897 4033 7920981 7921117 2.160000e-53 220.0
30 TraesCS5B01G261800 chr6B 91.643 694 56 2 46 738 43244118 43243426 0.000000e+00 959.0
31 TraesCS5B01G261800 chr3B 88.753 738 81 2 2 738 816087151 816087887 0.000000e+00 902.0
32 TraesCS5B01G261800 chr3B 83.679 723 99 17 2808 3518 252958232 252958947 0.000000e+00 664.0
33 TraesCS5B01G261800 chr3B 87.402 508 56 6 1520 2019 252957445 252957952 1.110000e-160 577.0
34 TraesCS5B01G261800 chr3B 84.713 471 57 11 996 1464 252956910 252957367 1.520000e-124 457.0
35 TraesCS5B01G261800 chr2B 88.140 742 84 4 2 741 245813119 245812380 0.000000e+00 880.0
36 TraesCS5B01G261800 chr1B 88.054 745 86 3 2 745 288443633 288442891 0.000000e+00 880.0
37 TraesCS5B01G261800 chr7A 82.085 921 129 30 1130 2020 221741695 221740781 0.000000e+00 754.0
38 TraesCS5B01G261800 chr7A 93.103 145 10 0 3889 4033 603025196 603025340 3.620000e-51 213.0
39 TraesCS5B01G261800 chr3A 88.780 508 49 5 1520 2019 213256900 213257407 2.360000e-172 616.0
40 TraesCS5B01G261800 chr3A 86.564 521 70 0 2998 3518 213257901 213258421 4.010000e-160 575.0
41 TraesCS5B01G261800 chr3A 86.047 473 49 9 996 1465 213256373 213256831 4.150000e-135 492.0
42 TraesCS5B01G261800 chrUn 85.030 501 72 3 1523 2020 86286135 86286635 1.480000e-139 507.0
43 TraesCS5B01G261800 chr7D 86.982 338 35 7 1130 1461 208656645 208656311 5.650000e-99 372.0
44 TraesCS5B01G261800 chr4B 97.692 130 3 0 3905 4034 82019250 82019121 1.670000e-54 224.0
45 TraesCS5B01G261800 chr2A 97.692 130 3 0 3906 4035 194169802 194169673 1.670000e-54 224.0
46 TraesCS5B01G261800 chr2A 95.620 137 5 1 3899 4035 753531292 753531427 7.780000e-53 219.0
47 TraesCS5B01G261800 chr2D 95.620 137 4 2 3907 4043 645613178 645613044 7.780000e-53 219.0


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 TraesCS5B01G261800 chr5B 446410467 446415086 4619 False 3865.500000 3980 100.000000 1 4620 2 chr5B.!!$F3 4619
1 TraesCS5B01G261800 chr5B 446007865 446010403 2538 True 1026.333333 1807 86.374667 830 3773 3 chr5B.!!$R1 2943
2 TraesCS5B01G261800 chr5B 447203680 447207183 3503 True 980.750000 1650 94.260250 903 4620 4 chr5B.!!$R2 3717
3 TraesCS5B01G261800 chr5B 394008117 394008853 736 False 885.000000 885 88.363000 2 738 1 chr5B.!!$F1 736
4 TraesCS5B01G261800 chr5B 446829884 446830419 535 False 394.000000 394 81.192000 4124 4619 1 chr5B.!!$F2 495
5 TraesCS5B01G261800 chr5D 374295174 374298198 3024 False 891.275000 2002 93.565250 746 4300 4 chr5D.!!$F2 3554
6 TraesCS5B01G261800 chr5A 635563221 635563958 737 False 1048.000000 1048 92.287000 1 738 1 chr5A.!!$F2 737
7 TraesCS5B01G261800 chr5A 476072604 476075353 2749 False 983.333333 1788 86.597667 746 3877 3 chr5A.!!$F3 3131
8 TraesCS5B01G261800 chr7B 443325159 443325896 737 False 1147.000000 1147 94.723000 1 738 1 chr7B.!!$F2 737
9 TraesCS5B01G261800 chr6A 604446510 604447252 742 True 1142.000000 1142 94.378000 1 746 1 chr6A.!!$R1 745
10 TraesCS5B01G261800 chr3D 284849398 284850136 738 True 1050.000000 1050 92.308000 1 740 1 chr3D.!!$R1 739
11 TraesCS5B01G261800 chr3D 584111971 584112541 570 True 885.000000 885 94.590000 1459 2031 1 chr3D.!!$R2 572
12 TraesCS5B01G261800 chr3D 174455356 174457384 2028 False 829.000000 989 84.041500 996 3518 2 chr3D.!!$F2 2522
13 TraesCS5B01G261800 chr6B 43243426 43244118 692 True 959.000000 959 91.643000 46 738 1 chr6B.!!$R1 692
14 TraesCS5B01G261800 chr3B 816087151 816087887 736 False 902.000000 902 88.753000 2 738 1 chr3B.!!$F1 736
15 TraesCS5B01G261800 chr3B 252956910 252958947 2037 False 566.000000 664 85.264667 996 3518 3 chr3B.!!$F2 2522
16 TraesCS5B01G261800 chr2B 245812380 245813119 739 True 880.000000 880 88.140000 2 741 1 chr2B.!!$R1 739
17 TraesCS5B01G261800 chr1B 288442891 288443633 742 True 880.000000 880 88.054000 2 745 1 chr1B.!!$R1 743
18 TraesCS5B01G261800 chr7A 221740781 221741695 914 True 754.000000 754 82.085000 1130 2020 1 chr7A.!!$R1 890
19 TraesCS5B01G261800 chr3A 213256373 213258421 2048 False 561.000000 616 87.130333 996 3518 3 chr3A.!!$F1 2522
20 TraesCS5B01G261800 chrUn 86286135 86286635 500 False 507.000000 507 85.030000 1523 2020 1 chrUn.!!$F1 497

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
796 798 0.179119 GCTGTCTGGCCATGCATTTC 60.179 55.0 5.51 0.00 0.00 2.17 F
1474 1510 0.453950 CGTACGCACGTGCTCTTAGT 60.454 55.0 35.27 26.75 43.31 2.24 F
2023 2131 0.618458 CAGCTTGCTTGGTACCCCTA 59.382 55.0 10.07 0.00 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2650 3180 1.205417 CCATTGGACCTGGCACAAATC 59.795 52.381 0.00 0.0 38.70 2.17 R
2876 3419 0.389817 CGACATTGCCGTGGAAGAGA 60.390 55.000 0.00 0.0 0.00 3.10 R
4010 4751 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 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
52 53 1.895798 GGATCAGGGATGTAGATCGCA 59.104 52.381 17.59 0.17 42.66 5.10
148 149 3.046390 CCAACAGTCGCGATTAGATCTC 58.954 50.000 14.06 0.00 0.00 2.75
223 225 2.769621 TCATGGATGGAGGCCGCT 60.770 61.111 6.40 0.00 0.00 5.52
231 233 1.971505 ATGGAGGCCGCTCGAATCAA 61.972 55.000 6.40 0.00 0.00 2.57
440 442 4.002982 GCCTATCGCATGTGATAATGGAA 58.997 43.478 26.89 11.30 37.47 3.53
496 498 0.450482 CGCCACAATTCACGTTCGAC 60.450 55.000 0.00 0.00 0.00 4.20
513 515 2.092049 TCGACTGTGGCTCCTATCCTAA 60.092 50.000 0.00 0.00 0.00 2.69
706 708 0.249280 GCGGGGAACACTTTTGTTGG 60.249 55.000 0.00 0.00 46.43 3.77
724 726 7.765695 TTGTTGGATAAAGCTCTCTGATTTT 57.234 32.000 0.00 0.00 35.69 1.82
777 779 5.220024 GCATTATTTGCTTTCGTTTCCGAAG 60.220 40.000 0.00 0.00 46.67 3.79
778 780 8.541344 GCATTATTTGCTTTCGTTTCCGAAGC 62.541 42.308 0.00 0.00 46.67 3.86
796 798 0.179119 GCTGTCTGGCCATGCATTTC 60.179 55.000 5.51 0.00 0.00 2.17
854 859 0.874390 TTCCAATCGAACAGCAGTGC 59.126 50.000 7.13 7.13 0.00 4.40
876 881 1.949631 GTTCCCGCGCCGATAAGAG 60.950 63.158 0.00 0.00 0.00 2.85
983 999 0.460284 AAGCAGCCCGTAACGATCTG 60.460 55.000 0.00 0.00 32.52 2.90
1059 1079 2.338015 GGACGTGACCAGGTCGCTA 61.338 63.158 27.14 2.74 44.55 4.26
1077 1097 1.836999 TACTGCCCCTGCACGACATT 61.837 55.000 0.00 0.00 44.23 2.71
1474 1510 0.453950 CGTACGCACGTGCTCTTAGT 60.454 55.000 35.27 26.75 43.31 2.24
2021 2129 0.678048 CTCAGCTTGCTTGGTACCCC 60.678 60.000 10.07 0.00 0.00 4.95
2022 2130 1.133809 TCAGCTTGCTTGGTACCCCT 61.134 55.000 10.07 0.00 0.00 4.79
2023 2131 0.618458 CAGCTTGCTTGGTACCCCTA 59.382 55.000 10.07 0.00 0.00 3.53
2026 2134 1.490910 GCTTGCTTGGTACCCCTATCT 59.509 52.381 10.07 0.00 0.00 1.98
2027 2135 2.485657 GCTTGCTTGGTACCCCTATCTC 60.486 54.545 10.07 0.00 0.00 2.75
2028 2136 2.868964 TGCTTGGTACCCCTATCTCT 57.131 50.000 10.07 0.00 0.00 3.10
2029 2137 2.679082 TGCTTGGTACCCCTATCTCTC 58.321 52.381 10.07 0.00 0.00 3.20
2030 2138 2.247635 TGCTTGGTACCCCTATCTCTCT 59.752 50.000 10.07 0.00 0.00 3.10
2487 2601 2.101415 TCTCTCTCTCTCTCTCTCTGCG 59.899 54.545 0.00 0.00 0.00 5.18
2525 2972 7.497249 AGGAAAATGACTGCTGTAGTATTCATC 59.503 37.037 0.00 0.00 40.53 2.92
2534 2981 8.140628 ACTGCTGTAGTATTCATCTATGTTCTG 58.859 37.037 0.00 0.00 38.04 3.02
2547 2994 0.770499 TGTTCTGGTGATCTGGCCAA 59.230 50.000 7.01 0.00 33.93 4.52
2618 3120 0.894835 GGCACCCGTTGAAATTCCAT 59.105 50.000 0.00 0.00 0.00 3.41
2650 3180 9.790344 AGTTATCTGATAGGGATCTTCATTTTG 57.210 33.333 0.00 0.00 32.79 2.44
2651 3181 9.784531 GTTATCTGATAGGGATCTTCATTTTGA 57.215 33.333 0.00 0.00 32.79 2.69
2741 3279 8.908678 CACATTGTCAATCAGTACAATTTTCTG 58.091 33.333 0.00 0.00 42.22 3.02
2745 3283 5.048083 GTCAATCAGTACAATTTTCTGGCCA 60.048 40.000 4.71 4.71 0.00 5.36
2749 3288 6.418057 TCAGTACAATTTTCTGGCCATTTT 57.582 33.333 5.51 0.00 0.00 1.82
2774 3313 3.330267 CCTGAACCTAGAAACAGAGTGC 58.670 50.000 10.15 0.00 32.90 4.40
2777 3316 5.392767 TGAACCTAGAAACAGAGTGCTAG 57.607 43.478 0.00 0.00 0.00 3.42
2804 3343 6.509656 CAACATAACTGAATGGATCAATGGG 58.490 40.000 0.00 0.00 37.67 4.00
2876 3419 2.204090 ATCCCTGGGTGGTCGGTT 60.204 61.111 13.56 0.00 0.00 4.44
2920 3463 3.928727 TGGAACAGTCACCGTAAGTAG 57.071 47.619 0.00 0.00 0.00 2.57
2923 3466 3.505293 GGAACAGTCACCGTAAGTAGACT 59.495 47.826 0.00 0.00 37.34 3.24
2924 3467 4.379290 GGAACAGTCACCGTAAGTAGACTC 60.379 50.000 0.00 0.00 35.79 3.36
2927 3470 3.080319 AGTCACCGTAAGTAGACTCCAC 58.920 50.000 0.00 0.00 34.02 4.02
2930 3473 3.890756 TCACCGTAAGTAGACTCCACAAA 59.109 43.478 0.00 0.00 0.00 2.83
2931 3474 4.525487 TCACCGTAAGTAGACTCCACAAAT 59.475 41.667 0.00 0.00 0.00 2.32
2934 3483 5.011329 ACCGTAAGTAGACTCCACAAATTCA 59.989 40.000 0.00 0.00 0.00 2.57
2952 3510 6.770746 AATTCAATCATTTCTCAGGGACAG 57.229 37.500 0.00 0.00 0.00 3.51
2970 3528 0.689055 AGTCTGCCACATGAGCTCAA 59.311 50.000 22.50 4.23 0.00 3.02
3484 4046 0.718904 CATCAAAATCGTCGGCGTCA 59.281 50.000 10.18 0.00 39.49 4.35
3526 4120 3.251571 CCAACGCTAGGTAAGTTCAGAC 58.748 50.000 0.00 0.00 0.00 3.51
3537 4131 5.836358 AGGTAAGTTCAGACTTCAGACTCTT 59.164 40.000 0.00 0.00 44.75 2.85
3546 4140 6.045318 CAGACTTCAGACTCTTGAACAAGAA 58.955 40.000 16.29 1.22 45.75 2.52
3557 4151 6.319658 ACTCTTGAACAAGAAAATCTGCAGAA 59.680 34.615 22.50 4.23 45.75 3.02
3559 4153 7.365741 TCTTGAACAAGAAAATCTGCAGAATC 58.634 34.615 22.50 18.41 43.79 2.52
3562 4156 7.088272 TGAACAAGAAAATCTGCAGAATCATG 58.912 34.615 22.50 21.71 0.00 3.07
3563 4157 6.829229 ACAAGAAAATCTGCAGAATCATGA 57.171 33.333 26.02 0.00 0.00 3.07
3601 4272 2.671130 CAGGTGTTGCTGTTTTTGGT 57.329 45.000 0.00 0.00 0.00 3.67
3624 4298 6.070710 GGTATGGATCAGAAGGTATAGGAACC 60.071 46.154 0.00 0.00 40.06 3.62
3659 4349 8.724229 TGTTGAACATTTCATCAATCTGTAGAG 58.276 33.333 0.00 0.00 39.84 2.43
3666 4356 9.247126 CATTTCATCAATCTGTAGAGTGTAGAG 57.753 37.037 8.90 0.00 40.61 2.43
3675 4375 6.540995 TCTGTAGAGTGTAGAGTGTAGGTTT 58.459 40.000 0.00 0.00 0.00 3.27
3676 4376 7.683578 TCTGTAGAGTGTAGAGTGTAGGTTTA 58.316 38.462 0.00 0.00 0.00 2.01
3705 4409 4.888239 TGTCTAGTAGTAGGATGTTGAGGC 59.112 45.833 4.74 0.00 0.00 4.70
3737 4444 2.175878 AGTCAGTGTCATTGCCTCAC 57.824 50.000 0.00 0.00 0.00 3.51
3765 4475 7.518188 ACGATATGGGGTCATATTCTTTTCTT 58.482 34.615 0.00 0.00 44.20 2.52
3773 4483 8.557029 GGGGTCATATTCTTTTCTTTATGTACG 58.443 37.037 0.00 0.00 0.00 3.67
3774 4484 9.321562 GGGTCATATTCTTTTCTTTATGTACGA 57.678 33.333 0.00 0.00 0.00 3.43
3780 4490 4.860907 TCTTTTCTTTATGTACGAGACGGC 59.139 41.667 0.00 0.00 0.00 5.68
3810 4532 4.468765 TTTGTATCGAACGGTTCCCATA 57.531 40.909 14.83 8.75 0.00 2.74
3834 4556 6.060028 TGAATATACCGAAATTTGCAGCTC 57.940 37.500 0.00 0.00 0.00 4.09
3885 4626 5.364157 AGTTGGGTATAGATCAACTGGAGAC 59.636 44.000 11.96 0.00 46.17 3.36
3888 4629 4.262249 GGGTATAGATCAACTGGAGACTGC 60.262 50.000 0.00 0.00 0.00 4.40
3894 4635 2.771089 TCAACTGGAGACTGCACAATC 58.229 47.619 0.00 0.00 0.00 2.67
3897 4638 1.364626 CTGGAGACTGCACAATCGCC 61.365 60.000 0.00 0.00 35.52 5.54
3903 4644 2.169352 AGACTGCACAATCGCCTTATCT 59.831 45.455 0.00 0.00 0.00 1.98
3904 4645 2.939103 GACTGCACAATCGCCTTATCTT 59.061 45.455 0.00 0.00 0.00 2.40
3905 4646 4.119862 GACTGCACAATCGCCTTATCTTA 58.880 43.478 0.00 0.00 0.00 2.10
3906 4647 4.708177 ACTGCACAATCGCCTTATCTTAT 58.292 39.130 0.00 0.00 0.00 1.73
3907 4648 5.853936 ACTGCACAATCGCCTTATCTTATA 58.146 37.500 0.00 0.00 0.00 0.98
3908 4649 5.696724 ACTGCACAATCGCCTTATCTTATAC 59.303 40.000 0.00 0.00 0.00 1.47
3909 4650 5.853936 TGCACAATCGCCTTATCTTATACT 58.146 37.500 0.00 0.00 0.00 2.12
3911 4652 5.348997 GCACAATCGCCTTATCTTATACTCC 59.651 44.000 0.00 0.00 0.00 3.85
3912 4653 5.869888 CACAATCGCCTTATCTTATACTCCC 59.130 44.000 0.00 0.00 0.00 4.30
3913 4654 5.780793 ACAATCGCCTTATCTTATACTCCCT 59.219 40.000 0.00 0.00 0.00 4.20
3914 4655 6.071278 ACAATCGCCTTATCTTATACTCCCTC 60.071 42.308 0.00 0.00 0.00 4.30
3915 4656 4.342359 TCGCCTTATCTTATACTCCCTCC 58.658 47.826 0.00 0.00 0.00 4.30
3917 4658 4.087907 GCCTTATCTTATACTCCCTCCGT 58.912 47.826 0.00 0.00 0.00 4.69
3918 4659 4.158209 GCCTTATCTTATACTCCCTCCGTC 59.842 50.000 0.00 0.00 0.00 4.79
3919 4660 4.705991 CCTTATCTTATACTCCCTCCGTCC 59.294 50.000 0.00 0.00 0.00 4.79
3920 4661 2.267174 TCTTATACTCCCTCCGTCCG 57.733 55.000 0.00 0.00 0.00 4.79
3921 4662 1.770658 TCTTATACTCCCTCCGTCCGA 59.229 52.381 0.00 0.00 0.00 4.55
3922 4663 2.173356 TCTTATACTCCCTCCGTCCGAA 59.827 50.000 0.00 0.00 0.00 4.30
3924 4665 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
3925 4666 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
3927 4668 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
3928 4669 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
3930 4671 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3931 4672 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3932 4673 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3933 4674 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3934 4675 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
3935 4676 4.571919 TCCGTCCGAAAATACTTGTCATT 58.428 39.130 0.00 0.00 0.00 2.57
3936 4677 5.722263 TCCGTCCGAAAATACTTGTCATTA 58.278 37.500 0.00 0.00 0.00 1.90
3937 4678 6.164876 TCCGTCCGAAAATACTTGTCATTAA 58.835 36.000 0.00 0.00 0.00 1.40
3938 4679 6.649973 TCCGTCCGAAAATACTTGTCATTAAA 59.350 34.615 0.00 0.00 0.00 1.52
3940 4681 7.966204 CCGTCCGAAAATACTTGTCATTAAAAT 59.034 33.333 0.00 0.00 0.00 1.82
3990 4731 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
3998 4739 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
4004 4745 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
4007 4748 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
4008 4749 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
4009 4750 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
4010 4751 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
4011 4752 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
4012 4753 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
4020 4761 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
4022 4763 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
4023 4764 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
4027 4768 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4028 4769 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4029 4770 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4032 4773 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
4038 4779 0.686769 GGACGGAGGGAGTACACCAT 60.687 60.000 11.69 3.58 0.00 3.55
4041 4782 2.557490 GACGGAGGGAGTACACCATATC 59.443 54.545 11.69 5.89 0.00 1.63
4044 4785 3.005897 CGGAGGGAGTACACCATATCAAG 59.994 52.174 11.69 1.54 0.00 3.02
4047 4788 3.967987 AGGGAGTACACCATATCAAGACC 59.032 47.826 11.69 0.00 0.00 3.85
4048 4789 3.967987 GGGAGTACACCATATCAAGACCT 59.032 47.826 11.69 0.00 0.00 3.85
4049 4790 4.202264 GGGAGTACACCATATCAAGACCTG 60.202 50.000 11.69 0.00 0.00 4.00
4051 4792 5.305644 GGAGTACACCATATCAAGACCTGAT 59.694 44.000 4.24 0.00 46.86 2.90
4058 4799 2.926778 ATCAAGACCTGATAGCAGCC 57.073 50.000 1.39 0.00 43.32 4.85
4059 4800 1.571955 TCAAGACCTGATAGCAGCCA 58.428 50.000 1.39 0.00 40.91 4.75
4060 4801 2.121948 TCAAGACCTGATAGCAGCCAT 58.878 47.619 1.39 0.00 40.91 4.40
4063 4804 1.415659 AGACCTGATAGCAGCCATGTC 59.584 52.381 1.39 4.78 40.91 3.06
4064 4805 1.415659 GACCTGATAGCAGCCATGTCT 59.584 52.381 1.39 0.00 40.91 3.41
4065 4806 1.415659 ACCTGATAGCAGCCATGTCTC 59.584 52.381 1.39 0.00 40.91 3.36
4066 4807 1.693062 CCTGATAGCAGCCATGTCTCT 59.307 52.381 1.39 0.00 40.91 3.10
4067 4808 2.548280 CCTGATAGCAGCCATGTCTCTG 60.548 54.545 1.39 0.00 40.91 3.35
4069 4906 3.299503 TGATAGCAGCCATGTCTCTGTA 58.700 45.455 8.15 2.35 33.09 2.74
4075 4912 4.835056 AGCAGCCATGTCTCTGTATGTATA 59.165 41.667 8.15 0.00 33.09 1.47
4082 4919 6.697455 CCATGTCTCTGTATGTATACACACAC 59.303 42.308 12.91 9.50 38.28 3.82
4085 4922 7.662897 TGTCTCTGTATGTATACACACACAAA 58.337 34.615 12.91 2.06 41.37 2.83
4093 4930 7.843490 ATGTATACACACACAAATCCACTAC 57.157 36.000 7.96 0.00 37.54 2.73
4094 4931 6.999950 TGTATACACACACAAATCCACTACT 58.000 36.000 0.08 0.00 0.00 2.57
4096 4933 8.755028 TGTATACACACACAAATCCACTACTAT 58.245 33.333 0.08 0.00 0.00 2.12
4099 4936 6.530120 ACACACACAAATCCACTACTATGAA 58.470 36.000 0.00 0.00 0.00 2.57
4100 4937 6.650807 ACACACACAAATCCACTACTATGAAG 59.349 38.462 0.00 0.00 0.00 3.02
4101 4938 6.873605 CACACACAAATCCACTACTATGAAGA 59.126 38.462 0.00 0.00 0.00 2.87
4102 4939 7.550551 CACACACAAATCCACTACTATGAAGAT 59.449 37.037 0.00 0.00 0.00 2.40
4180 5017 1.213537 CGTCCCAAGCAATGCCTTG 59.786 57.895 0.00 6.05 41.40 3.61
4191 5034 5.864418 AGCAATGCCTTGATTATTGACAT 57.136 34.783 0.00 0.00 34.55 3.06
4214 5057 4.162320 TCTTTCCCTGTCATCTTATCGCTT 59.838 41.667 0.00 0.00 0.00 4.68
4277 5146 5.727791 GCATTGTGATCGTGGTTGATAAGAC 60.728 44.000 0.00 0.00 0.00 3.01
4319 5224 6.926630 AACATACTAATCTCTCATCCCCTC 57.073 41.667 0.00 0.00 0.00 4.30
4370 5276 4.142609 TGCTTGGGACTCATAAGTGATC 57.857 45.455 0.00 0.00 35.28 2.92
4492 5414 6.703607 ACGAAATATCTCCTGAATCATGTGTC 59.296 38.462 0.00 0.00 0.00 3.67
4539 5461 2.809446 CATTCGCCACGTTGAGATCTA 58.191 47.619 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 5.726397 CCACATGATGGTGATGATTTTTGT 58.274 37.500 0.00 0.00 44.46 2.83
78 79 1.322538 GGTTGCGGGAATGCCAGATT 61.323 55.000 0.00 0.00 35.15 2.40
134 135 1.241990 CCGGGGAGATCTAATCGCGA 61.242 60.000 13.09 13.09 37.69 5.87
223 225 8.183104 AGATATCTTGGTCATACTTGATTCGA 57.817 34.615 0.00 0.00 33.56 3.71
440 442 3.243907 GCACTAACTCCTGACAGTCAGTT 60.244 47.826 25.88 17.83 42.80 3.16
496 498 4.963318 TCATTTAGGATAGGAGCCACAG 57.037 45.455 0.00 0.00 0.00 3.66
513 515 7.918076 TCACAACTAAGGTCTCCTATTTCATT 58.082 34.615 0.00 0.00 31.13 2.57
527 529 9.364989 TCAAAAACAGAAAAATCACAACTAAGG 57.635 29.630 0.00 0.00 0.00 2.69
574 576 1.130561 GATGTGCCGGTAAGTTTGCTC 59.869 52.381 1.90 0.00 0.00 4.26
628 630 0.173481 CTCCTCGAGCCAACATTCGA 59.827 55.000 6.99 0.00 42.91 3.71
669 671 1.446618 CGCAATCAGCCAAAAGGCC 60.447 57.895 2.33 0.00 41.38 5.19
706 708 4.260948 CGGGCAAAATCAGAGAGCTTTATC 60.261 45.833 0.00 0.00 0.00 1.75
772 774 2.110967 CATGGCCAGACAGCTTCGG 61.111 63.158 13.05 0.00 0.00 4.30
777 779 0.179119 GAAATGCATGGCCAGACAGC 60.179 55.000 13.05 13.32 0.00 4.40
778 780 0.458669 GGAAATGCATGGCCAGACAG 59.541 55.000 13.05 1.84 0.00 3.51
796 798 4.513692 TCACCTCGTGATTTACAGTTTTGG 59.486 41.667 0.00 0.00 37.67 3.28
869 874 6.420903 GTCCAAAAAGTTTGGTTGCTCTTATC 59.579 38.462 17.12 0.00 40.40 1.75
876 881 2.675844 GGTGTCCAAAAAGTTTGGTTGC 59.324 45.455 17.12 10.57 40.40 4.17
936 947 1.663379 TTCCGCCGTCGATGATCTGT 61.663 55.000 6.11 0.00 38.10 3.41
983 999 1.451387 ATGGCCGGTCGAATCCAAC 60.451 57.895 0.00 0.00 31.66 3.77
1050 1070 3.077556 AGGGGCAGTAGCGACCTG 61.078 66.667 0.00 0.00 44.14 4.00
1470 1506 6.411376 TCAAGCCGGAAGAATCAATTACTAA 58.589 36.000 5.05 0.00 0.00 2.24
1474 1510 5.436175 TGATCAAGCCGGAAGAATCAATTA 58.564 37.500 5.05 0.00 0.00 1.40
2487 2601 3.676646 GTCATTTTCCTCAAGTGCAATGC 59.323 43.478 0.00 0.00 0.00 3.56
2525 2972 2.171237 TGGCCAGATCACCAGAACATAG 59.829 50.000 0.00 0.00 0.00 2.23
2534 2981 5.537674 AGATATTCAAATTGGCCAGATCACC 59.462 40.000 5.11 0.00 0.00 4.02
2547 2994 9.357652 CGAAATGTTTGACCAAGATATTCAAAT 57.642 29.630 3.50 0.00 40.42 2.32
2618 3120 8.707796 AAGATCCCTATCAGATAACTAAACGA 57.292 34.615 0.00 0.00 34.28 3.85
2635 3152 5.337813 GGCACAAATCAAAATGAAGATCCCT 60.338 40.000 0.00 0.00 0.00 4.20
2648 3178 2.079170 TTGGACCTGGCACAAATCAA 57.921 45.000 0.00 0.00 38.70 2.57
2649 3179 1.894466 CATTGGACCTGGCACAAATCA 59.106 47.619 7.59 0.00 38.70 2.57
2650 3180 1.205417 CCATTGGACCTGGCACAAATC 59.795 52.381 0.00 0.00 38.70 2.17
2651 3181 1.269012 CCATTGGACCTGGCACAAAT 58.731 50.000 0.00 0.00 38.70 2.32
2653 3183 4.517663 CCATTGGACCTGGCACAA 57.482 55.556 0.00 6.17 38.70 3.33
2672 3202 4.615452 GCAAGAACCATCTTCTCTGCAAAG 60.615 45.833 0.00 0.00 44.11 2.77
2749 3288 4.658901 ACTCTGTTTCTAGGTTCAGGGAAA 59.341 41.667 13.03 0.00 33.25 3.13
2774 3313 6.539826 TGATCCATTCAGTTATGTTGCACTAG 59.460 38.462 0.00 0.00 0.00 2.57
2777 3316 5.565592 TGATCCATTCAGTTATGTTGCAC 57.434 39.130 0.00 0.00 0.00 4.57
2785 3324 5.449297 TCACCCATTGATCCATTCAGTTA 57.551 39.130 0.00 0.00 35.27 2.24
2804 3343 0.394762 TCAGGCCCTGCATGAATCAC 60.395 55.000 5.66 0.00 46.20 3.06
2876 3419 0.389817 CGACATTGCCGTGGAAGAGA 60.390 55.000 0.00 0.00 0.00 3.10
2920 3463 7.596494 TGAGAAATGATTGAATTTGTGGAGTC 58.404 34.615 0.00 0.00 29.89 3.36
2923 3466 6.071221 CCCTGAGAAATGATTGAATTTGTGGA 60.071 38.462 0.00 0.00 29.89 4.02
2924 3467 6.071221 TCCCTGAGAAATGATTGAATTTGTGG 60.071 38.462 0.00 0.00 29.89 4.17
2927 3470 6.927416 TGTCCCTGAGAAATGATTGAATTTG 58.073 36.000 0.00 0.00 29.89 2.32
2930 3473 5.824421 ACTGTCCCTGAGAAATGATTGAAT 58.176 37.500 0.00 0.00 0.00 2.57
2931 3474 5.013495 AGACTGTCCCTGAGAAATGATTGAA 59.987 40.000 3.76 0.00 0.00 2.69
2934 3483 4.841422 CAGACTGTCCCTGAGAAATGATT 58.159 43.478 3.76 0.00 33.65 2.57
2952 3510 1.085091 CTTGAGCTCATGTGGCAGAC 58.915 55.000 19.04 7.05 0.00 3.51
3526 4120 8.068977 CAGATTTTCTTGTTCAAGAGTCTGAAG 58.931 37.037 27.11 14.70 37.10 3.02
3537 4131 6.638096 TGATTCTGCAGATTTTCTTGTTCA 57.362 33.333 19.04 6.93 0.00 3.18
3546 4140 5.507637 AGAAGGTCATGATTCTGCAGATTT 58.492 37.500 19.04 8.43 34.52 2.17
3557 4151 6.039493 GCATCAAATCAAGAGAAGGTCATGAT 59.961 38.462 0.00 0.00 43.89 2.45
3559 4153 5.124936 TGCATCAAATCAAGAGAAGGTCATG 59.875 40.000 0.00 0.00 0.00 3.07
3562 4156 4.096081 CCTGCATCAAATCAAGAGAAGGTC 59.904 45.833 0.00 0.00 0.00 3.85
3563 4157 4.015084 CCTGCATCAAATCAAGAGAAGGT 58.985 43.478 0.00 0.00 0.00 3.50
3592 4263 5.640147 ACCTTCTGATCCATACCAAAAACA 58.360 37.500 0.00 0.00 0.00 2.83
3601 4272 6.875469 AGGTTCCTATACCTTCTGATCCATA 58.125 40.000 0.00 0.00 46.39 2.74
3634 4324 8.725148 ACTCTACAGATTGATGAAATGTTCAAC 58.275 33.333 0.00 0.00 43.95 3.18
3692 4396 3.195610 CACTGTACAGCCTCAACATCCTA 59.804 47.826 22.90 0.00 0.00 2.94
3698 4402 5.105877 TGACTATACACTGTACAGCCTCAAC 60.106 44.000 22.90 8.36 0.00 3.18
3705 4409 6.496338 TGACACTGACTATACACTGTACAG 57.504 41.667 21.44 21.44 0.00 2.74
3737 4444 5.073311 AGAATATGACCCCATATCGTTCG 57.927 43.478 0.00 0.00 43.27 3.95
3765 4475 4.635833 TTACATGCCGTCTCGTACATAA 57.364 40.909 0.00 0.00 0.00 1.90
3769 4479 4.852609 AATTTTACATGCCGTCTCGTAC 57.147 40.909 0.00 0.00 0.00 3.67
3773 4483 5.901884 CGATACAAATTTTACATGCCGTCTC 59.098 40.000 0.00 0.00 0.00 3.36
3774 4484 5.583061 TCGATACAAATTTTACATGCCGTCT 59.417 36.000 0.00 0.00 0.00 4.18
3775 4485 5.802064 TCGATACAAATTTTACATGCCGTC 58.198 37.500 0.00 0.00 0.00 4.79
3776 4486 5.804692 TCGATACAAATTTTACATGCCGT 57.195 34.783 0.00 0.00 0.00 5.68
3777 4487 5.168856 CGTTCGATACAAATTTTACATGCCG 59.831 40.000 0.00 0.00 0.00 5.69
3778 4488 5.454232 CCGTTCGATACAAATTTTACATGCC 59.546 40.000 0.00 0.00 0.00 4.40
3780 4490 7.217447 GGAACCGTTCGATACAAATTTTACATG 59.783 37.037 5.19 0.00 0.00 3.21
3810 4532 6.294176 GGAGCTGCAAATTTCGGTATATTCAT 60.294 38.462 0.00 0.00 0.00 2.57
3834 4556 5.163416 ACCTTGTGGTTTCAGAAAATGAAGG 60.163 40.000 16.11 16.11 46.05 3.46
3858 4580 6.679542 TCCAGTTGATCTATACCCAACTCTA 58.320 40.000 0.00 0.00 45.93 2.43
3869 4610 3.771479 TGTGCAGTCTCCAGTTGATCTAT 59.229 43.478 0.00 0.00 0.00 1.98
3879 4620 1.375908 GGCGATTGTGCAGTCTCCA 60.376 57.895 0.00 0.00 36.28 3.86
3881 4622 2.010145 TAAGGCGATTGTGCAGTCTC 57.990 50.000 0.00 0.00 36.28 3.36
3885 4626 5.928839 AGTATAAGATAAGGCGATTGTGCAG 59.071 40.000 0.00 0.00 36.28 4.41
3888 4629 5.869888 GGGAGTATAAGATAAGGCGATTGTG 59.130 44.000 0.00 0.00 0.00 3.33
3894 4635 3.128938 CGGAGGGAGTATAAGATAAGGCG 59.871 52.174 0.00 0.00 0.00 5.52
3897 4638 4.395542 CGGACGGAGGGAGTATAAGATAAG 59.604 50.000 0.00 0.00 0.00 1.73
3903 4644 2.734755 TTCGGACGGAGGGAGTATAA 57.265 50.000 0.00 0.00 0.00 0.98
3904 4645 2.734755 TTTCGGACGGAGGGAGTATA 57.265 50.000 0.00 0.00 0.00 1.47
3905 4646 1.856629 TTTTCGGACGGAGGGAGTAT 58.143 50.000 0.00 0.00 0.00 2.12
3906 4647 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
3907 4648 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
3908 4649 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
3909 4650 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
3911 4652 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3912 4653 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
3913 4654 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
3914 4655 4.939509 AATGACAAGTATTTTCGGACGG 57.060 40.909 0.00 0.00 0.00 4.79
3915 4656 8.785101 CATTTTAATGACAAGTATTTTCGGACG 58.215 33.333 0.00 0.00 38.70 4.79
3964 4705 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
3972 4713 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
3978 4719 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
3981 4722 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
3982 4723 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
3983 4724 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
3984 4725 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
3985 4726 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
3986 4727 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
3994 4735 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
3995 4736 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
3996 4737 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
3997 4738 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
3998 4739 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
3999 4740 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
4000 4741 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
4001 4742 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
4002 4743 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
4003 4744 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
4004 4745 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
4005 4746 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4006 4747 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4007 4748 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4008 4749 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4009 4750 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4010 4751 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4011 4752 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4012 4753 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4013 4754 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4018 4759 2.413142 GGTGTACTCCCTCCGTCCG 61.413 68.421 2.33 0.00 0.00 4.79
4020 4761 2.062971 TATGGTGTACTCCCTCCGTC 57.937 55.000 11.36 0.00 0.00 4.79
4022 4763 2.594131 TGATATGGTGTACTCCCTCCG 58.406 52.381 11.36 0.00 0.00 4.63
4023 4764 4.039366 GTCTTGATATGGTGTACTCCCTCC 59.961 50.000 11.36 0.00 0.00 4.30
4027 4768 4.649674 TCAGGTCTTGATATGGTGTACTCC 59.350 45.833 7.03 7.03 0.00 3.85
4028 4769 5.854010 TCAGGTCTTGATATGGTGTACTC 57.146 43.478 0.00 0.00 0.00 2.59
4029 4770 6.015010 GCTATCAGGTCTTGATATGGTGTACT 60.015 42.308 5.22 0.00 45.36 2.73
4032 4773 4.655649 TGCTATCAGGTCTTGATATGGTGT 59.344 41.667 5.22 0.00 45.36 4.16
4038 4779 3.308401 TGGCTGCTATCAGGTCTTGATA 58.692 45.455 4.73 4.73 44.72 2.15
4041 4782 2.219458 CATGGCTGCTATCAGGTCTTG 58.781 52.381 0.00 0.00 40.65 3.02
4044 4785 1.415659 AGACATGGCTGCTATCAGGTC 59.584 52.381 0.00 12.21 42.71 3.85
4047 4788 2.102757 ACAGAGACATGGCTGCTATCAG 59.897 50.000 5.31 0.00 43.16 2.90
4048 4789 2.113807 ACAGAGACATGGCTGCTATCA 58.886 47.619 5.31 0.00 35.57 2.15
4049 4790 2.906691 ACAGAGACATGGCTGCTATC 57.093 50.000 5.31 0.00 35.57 2.08
4051 4792 3.033909 ACATACAGAGACATGGCTGCTA 58.966 45.455 5.31 0.00 35.57 3.49
4052 4793 1.836166 ACATACAGAGACATGGCTGCT 59.164 47.619 5.31 0.00 35.57 4.24
4053 4794 2.322355 ACATACAGAGACATGGCTGC 57.678 50.000 5.31 0.00 35.57 5.25
4054 4795 5.923114 GTGTATACATACAGAGACATGGCTG 59.077 44.000 5.31 8.44 43.32 4.85
4055 4796 5.598417 TGTGTATACATACAGAGACATGGCT 59.402 40.000 0.00 0.00 43.32 4.75
4056 4797 5.692204 GTGTGTATACATACAGAGACATGGC 59.308 44.000 23.33 0.00 43.32 4.40
4057 4798 6.697455 GTGTGTGTATACATACAGAGACATGG 59.303 42.308 29.17 0.00 46.14 3.66
4058 4799 7.685532 GTGTGTGTATACATACAGAGACATG 57.314 40.000 29.17 0.00 46.14 3.21
4067 4808 7.843490 AGTGGATTTGTGTGTGTATACATAC 57.157 36.000 21.98 21.98 45.77 2.39
4069 4906 7.620880 AGTAGTGGATTTGTGTGTGTATACAT 58.379 34.615 9.18 0.00 39.39 2.29
4075 4912 6.109156 TCATAGTAGTGGATTTGTGTGTGT 57.891 37.500 0.00 0.00 0.00 3.72
4082 4919 7.730084 TCCTGATCTTCATAGTAGTGGATTTG 58.270 38.462 0.00 0.00 0.00 2.32
4085 4922 6.376864 CGATCCTGATCTTCATAGTAGTGGAT 59.623 42.308 5.66 0.00 35.72 3.41
4093 4930 7.222417 GCAATCATACGATCCTGATCTTCATAG 59.778 40.741 5.66 0.00 35.72 2.23
4094 4931 7.038048 GCAATCATACGATCCTGATCTTCATA 58.962 38.462 5.66 0.00 35.72 2.15
4096 4933 5.221501 TGCAATCATACGATCCTGATCTTCA 60.222 40.000 5.66 0.00 35.72 3.02
4099 4936 4.562347 GGTGCAATCATACGATCCTGATCT 60.562 45.833 5.66 0.00 35.72 2.75
4100 4937 3.681897 GGTGCAATCATACGATCCTGATC 59.318 47.826 0.00 0.00 30.98 2.92
4101 4938 3.071457 TGGTGCAATCATACGATCCTGAT 59.929 43.478 0.00 0.00 33.59 2.90
4102 4939 2.433970 TGGTGCAATCATACGATCCTGA 59.566 45.455 0.00 0.00 0.00 3.86
4191 5034 3.706594 AGCGATAAGATGACAGGGAAAGA 59.293 43.478 0.00 0.00 0.00 2.52
4277 5146 6.569228 ATGTTAGTATCAAATCGTGTCGTG 57.431 37.500 0.00 0.00 0.00 4.35
4422 5344 3.333804 ACACAAACAAACCCAGCAAAAG 58.666 40.909 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.