Multiple sequence alignment - TraesCS5B01G414400

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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 TraesCS5B01G414400 chr5B 100.000 3893 0 0 1 3893 588833584 588829692 0.000000e+00 7190.0
1 TraesCS5B01G414400 chr5B 87.006 2101 175 53 879 2934 588778408 588776361 0.000000e+00 2278.0
2 TraesCS5B01G414400 chr5B 87.163 779 62 11 39 786 588779378 588778607 0.000000e+00 850.0
3 TraesCS5B01G414400 chr5B 80.177 565 89 19 3336 3893 70559730 70560278 6.060000e-108 401.0
4 TraesCS5B01G414400 chr5A 90.051 2342 153 38 889 3174 599449157 599446840 0.000000e+00 2961.0
5 TraesCS5B01G414400 chr5A 87.291 1975 166 37 985 2934 599390503 599388589 0.000000e+00 2178.0
6 TraesCS5B01G414400 chr5A 92.803 792 29 15 2 786 599452008 599451238 0.000000e+00 1122.0
7 TraesCS5B01G414400 chr5A 86.649 749 58 18 45 786 599391527 599390814 0.000000e+00 791.0
8 TraesCS5B01G414400 chr5A 88.790 562 55 7 3336 3893 547539295 547538738 0.000000e+00 682.0
9 TraesCS5B01G414400 chr5A 89.333 75 3 2 790 859 599390784 599390710 5.360000e-14 89.8
10 TraesCS5B01G414400 chr5A 92.982 57 2 2 829 883 599451217 599451161 8.960000e-12 82.4
11 TraesCS5B01G414400 chrUn 78.345 1450 200 64 1000 2359 177132905 177131480 0.000000e+00 833.0
12 TraesCS5B01G414400 chrUn 78.345 1450 200 64 1000 2359 306187850 306186425 0.000000e+00 833.0
13 TraesCS5B01G414400 chrUn 80.530 642 93 23 2442 3078 364582554 364583168 7.620000e-127 464.0
14 TraesCS5B01G414400 chrUn 87.850 107 10 2 3172 3275 361756082 361756188 5.280000e-24 122.0
15 TraesCS5B01G414400 chr2B 78.345 1450 200 64 1000 2359 3787559 3788984 0.000000e+00 833.0
16 TraesCS5B01G414400 chr2B 78.319 1416 193 64 1034 2359 1317977 1316586 0.000000e+00 809.0
17 TraesCS5B01G414400 chr2B 79.435 992 152 36 999 1954 3906186 3907161 0.000000e+00 654.0
18 TraesCS5B01G414400 chr2B 79.456 993 151 35 999 1954 4185191 4186167 0.000000e+00 654.0
19 TraesCS5B01G414400 chr2B 79.810 946 137 25 1974 2885 4186320 4187245 1.180000e-179 640.0
20 TraesCS5B01G414400 chr2B 79.406 942 148 23 1974 2885 3907314 3908239 1.190000e-174 623.0
21 TraesCS5B01G414400 chr2B 82.465 576 79 17 3328 3893 159096116 159096679 5.850000e-133 484.0
22 TraesCS5B01G414400 chr2B 80.530 642 93 23 2442 3078 1315348 1314734 7.620000e-127 464.0
23 TraesCS5B01G414400 chr2B 80.530 642 93 23 2442 3078 3789586 3790200 7.620000e-127 464.0
24 TraesCS5B01G414400 chr2B 95.161 62 3 0 3165 3226 135918310 135918371 8.900000e-17 99.0
25 TraesCS5B01G414400 chr2B 92.537 67 5 0 3162 3228 172985068 172985134 3.200000e-16 97.1
26 TraesCS5B01G414400 chr1B 90.941 563 39 8 3333 3891 16179030 16178476 0.000000e+00 747.0
27 TraesCS5B01G414400 chr1B 81.338 568 87 17 3336 3893 15657243 15656685 9.930000e-121 444.0
28 TraesCS5B01G414400 chr1A 88.948 561 56 5 3336 3893 19703193 19702636 0.000000e+00 688.0
29 TraesCS5B01G414400 chr6B 87.389 563 58 8 3336 3893 117537132 117537686 5.490000e-178 634.0
30 TraesCS5B01G414400 chr6B 79.114 158 33 0 389 546 691783470 691783627 4.110000e-20 110.0
31 TraesCS5B01G414400 chr6B 85.437 103 15 0 634 736 692016686 692016788 1.480000e-19 108.0
32 TraesCS5B01G414400 chr6B 84.466 103 16 0 634 736 691795101 691795203 6.880000e-18 102.0
33 TraesCS5B01G414400 chr7B 86.165 571 60 11 3327 3893 1816437 1816992 2.000000e-167 599.0
34 TraesCS5B01G414400 chr3B 85.146 478 47 15 3336 3803 125782049 125782512 5.890000e-128 468.0
35 TraesCS5B01G414400 chr3B 76.040 601 108 31 1685 2261 177493744 177493156 2.960000e-71 279.0
36 TraesCS5B01G414400 chr3B 92.647 68 5 0 3160 3227 808639487 808639420 8.900000e-17 99.0
37 TraesCS5B01G414400 chr2A 85.034 441 65 1 2442 2881 5783790 5783350 7.670000e-122 448.0
38 TraesCS5B01G414400 chr2A 81.951 410 47 7 1975 2366 5784450 5784050 4.850000e-84 322.0
39 TraesCS5B01G414400 chr6A 80.742 566 89 16 3336 3892 277286355 277285801 1.290000e-114 424.0
40 TraesCS5B01G414400 chr6A 80.488 123 24 0 637 759 600978013 600978135 1.150000e-15 95.3
41 TraesCS5B01G414400 chr6A 78.740 127 27 0 633 759 601032944 601033070 6.930000e-13 86.1
42 TraesCS5B01G414400 chr6A 82.292 96 16 1 642 736 601166202 601166297 8.960000e-12 82.4
43 TraesCS5B01G414400 chr2D 77.959 490 77 15 1132 1611 7719168 7718700 1.070000e-70 278.0
44 TraesCS5B01G414400 chr4B 95.455 66 3 0 3166 3231 81985243 81985178 5.320000e-19 106.0
45 TraesCS5B01G414400 chr6D 85.000 100 15 0 637 736 454734390 454734291 6.880000e-18 102.0
46 TraesCS5B01G414400 chr6D 81.553 103 19 0 634 736 454926747 454926849 6.930000e-13 86.1
47 TraesCS5B01G414400 chr5D 96.721 61 2 0 3168 3228 386126307 386126367 6.880000e-18 102.0
48 TraesCS5B01G414400 chr4A 93.750 64 4 0 3164 3227 650851806 650851869 3.200000e-16 97.1
49 TraesCS5B01G414400 chr4A 93.750 64 4 0 3164 3227 650861970 650862033 3.200000e-16 97.1
50 TraesCS5B01G414400 chr3A 95.082 61 3 0 3168 3228 750495539 750495599 3.200000e-16 97.1


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 TraesCS5B01G414400 chr5B 588829692 588833584 3892 True 7190.000000 7190 100.000000 1 3893 1 chr5B.!!$R1 3892
1 TraesCS5B01G414400 chr5B 588776361 588779378 3017 True 1564.000000 2278 87.084500 39 2934 2 chr5B.!!$R2 2895
2 TraesCS5B01G414400 chr5B 70559730 70560278 548 False 401.000000 401 80.177000 3336 3893 1 chr5B.!!$F1 557
3 TraesCS5B01G414400 chr5A 599446840 599452008 5168 True 1388.466667 2961 91.945333 2 3174 3 chr5A.!!$R3 3172
4 TraesCS5B01G414400 chr5A 599388589 599391527 2938 True 1019.600000 2178 87.757667 45 2934 3 chr5A.!!$R2 2889
5 TraesCS5B01G414400 chr5A 547538738 547539295 557 True 682.000000 682 88.790000 3336 3893 1 chr5A.!!$R1 557
6 TraesCS5B01G414400 chrUn 177131480 177132905 1425 True 833.000000 833 78.345000 1000 2359 1 chrUn.!!$R1 1359
7 TraesCS5B01G414400 chrUn 306186425 306187850 1425 True 833.000000 833 78.345000 1000 2359 1 chrUn.!!$R2 1359
8 TraesCS5B01G414400 chrUn 364582554 364583168 614 False 464.000000 464 80.530000 2442 3078 1 chrUn.!!$F2 636
9 TraesCS5B01G414400 chr2B 3787559 3790200 2641 False 648.500000 833 79.437500 1000 3078 2 chr2B.!!$F4 2078
10 TraesCS5B01G414400 chr2B 4185191 4187245 2054 False 647.000000 654 79.633000 999 2885 2 chr2B.!!$F6 1886
11 TraesCS5B01G414400 chr2B 3906186 3908239 2053 False 638.500000 654 79.420500 999 2885 2 chr2B.!!$F5 1886
12 TraesCS5B01G414400 chr2B 1314734 1317977 3243 True 636.500000 809 79.424500 1034 3078 2 chr2B.!!$R1 2044
13 TraesCS5B01G414400 chr2B 159096116 159096679 563 False 484.000000 484 82.465000 3328 3893 1 chr2B.!!$F2 565
14 TraesCS5B01G414400 chr1B 16178476 16179030 554 True 747.000000 747 90.941000 3333 3891 1 chr1B.!!$R2 558
15 TraesCS5B01G414400 chr1B 15656685 15657243 558 True 444.000000 444 81.338000 3336 3893 1 chr1B.!!$R1 557
16 TraesCS5B01G414400 chr1A 19702636 19703193 557 True 688.000000 688 88.948000 3336 3893 1 chr1A.!!$R1 557
17 TraesCS5B01G414400 chr6B 117537132 117537686 554 False 634.000000 634 87.389000 3336 3893 1 chr6B.!!$F1 557
18 TraesCS5B01G414400 chr7B 1816437 1816992 555 False 599.000000 599 86.165000 3327 3893 1 chr7B.!!$F1 566
19 TraesCS5B01G414400 chr3B 177493156 177493744 588 True 279.000000 279 76.040000 1685 2261 1 chr3B.!!$R1 576
20 TraesCS5B01G414400 chr2A 5783350 5784450 1100 True 385.000000 448 83.492500 1975 2881 2 chr2A.!!$R1 906
21 TraesCS5B01G414400 chr6A 277285801 277286355 554 True 424.000000 424 80.742000 3336 3892 1 chr6A.!!$R1 556

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
566 599 0.316442 GATTGATGCACGACGCCATG 60.316 55.0 6.35 0.00 41.33 3.66 F
740 777 0.753867 TCCCGTCACACAAACTAGCA 59.246 50.0 0.00 0.00 0.00 3.49 F
2437 6003 0.032952 TAAGTGTCTGCCGTGGTGAC 59.967 55.0 7.07 7.07 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2432 5998 0.536006 AAGCTGCAAGTGGAGTCACC 60.536 55.0 1.02 0.0 44.64 4.02 R
2562 6128 0.745486 TCAGCAGCGGGATTGACATG 60.745 55.0 0.00 0.0 0.00 3.21 R
3813 7409 0.462047 CCGAATTGAGCCCGCTAAGT 60.462 55.0 0.00 0.0 0.00 2.24 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
167 168 1.112315 TGTTGGGGTTCATGTGCACC 61.112 55.000 15.69 0.00 0.00 5.01
198 199 2.052782 AGAAGTGAAAACAAGGCGGT 57.947 45.000 0.00 0.00 0.00 5.68
244 245 1.350310 ACCACGTTTCTGGTCCCCTT 61.350 55.000 0.00 0.00 40.91 3.95
295 300 2.282958 AGTCGGCCGAGAACAGGA 60.283 61.111 31.97 0.00 0.00 3.86
474 507 2.981302 CAGTCCAGGACATCGGCA 59.019 61.111 22.31 0.00 34.60 5.69
497 530 2.158696 GGTGCAAGGATAGCCTCTCATT 60.159 50.000 0.00 0.00 46.28 2.57
566 599 0.316442 GATTGATGCACGACGCCATG 60.316 55.000 6.35 0.00 41.33 3.66
602 639 6.441222 TGGATTAGAAAAGGTAGCTAGGAGA 58.559 40.000 0.00 0.00 0.00 3.71
615 652 9.362151 AGGTAGCTAGGAGATATAATTAGATGC 57.638 37.037 0.00 0.00 0.00 3.91
616 653 9.137459 GGTAGCTAGGAGATATAATTAGATGCA 57.863 37.037 0.00 0.00 0.00 3.96
619 656 8.649591 AGCTAGGAGATATAATTAGATGCATGG 58.350 37.037 2.46 0.00 0.00 3.66
624 661 8.680903 GGAGATATAATTAGATGCATGGTTTGG 58.319 37.037 2.46 0.00 0.00 3.28
626 663 9.017509 AGATATAATTAGATGCATGGTTTGGTG 57.982 33.333 2.46 0.00 0.00 4.17
627 664 3.806625 ATTAGATGCATGGTTTGGTGC 57.193 42.857 2.46 0.00 41.61 5.01
633 670 1.717194 GCATGGTTTGGTGCAAGATG 58.283 50.000 0.00 0.00 40.94 2.90
677 714 1.597797 CCTTACACGGTAGCCACGGA 61.598 60.000 0.00 0.00 35.23 4.69
699 736 2.266055 GAGCTCCTTCACCACCCG 59.734 66.667 0.87 0.00 0.00 5.28
740 777 0.753867 TCCCGTCACACAAACTAGCA 59.246 50.000 0.00 0.00 0.00 3.49
743 780 0.865769 CGTCACACAAACTAGCACCC 59.134 55.000 0.00 0.00 0.00 4.61
786 823 3.890756 CTGCTGTTATTGGCCATGGAATA 59.109 43.478 18.40 8.91 0.00 1.75
787 824 3.636300 TGCTGTTATTGGCCATGGAATAC 59.364 43.478 18.40 2.31 0.00 1.89
788 825 3.891366 GCTGTTATTGGCCATGGAATACT 59.109 43.478 18.40 0.00 0.00 2.12
803 866 7.443575 CCATGGAATACTGAGAGACTAAATTGG 59.556 40.741 5.56 0.00 0.00 3.16
814 877 7.079451 AGAGACTAAATTGGTTCTCTTTCCA 57.921 36.000 7.01 0.00 31.35 3.53
815 878 6.937465 AGAGACTAAATTGGTTCTCTTTCCAC 59.063 38.462 7.01 0.00 31.35 4.02
825 893 4.879545 GGTTCTCTTTCCACTACACAAACA 59.120 41.667 0.00 0.00 0.00 2.83
826 894 5.355910 GGTTCTCTTTCCACTACACAAACAA 59.644 40.000 0.00 0.00 0.00 2.83
870 943 9.003658 GTATTTATAATGCAAGCTCATACCTGT 57.996 33.333 0.00 0.00 0.00 4.00
874 947 1.625315 TGCAAGCTCATACCTGTGTCT 59.375 47.619 0.00 0.00 0.00 3.41
885 1083 7.013846 GCTCATACCTGTGTCTCTATCTAACTT 59.986 40.741 0.00 0.00 0.00 2.66
914 2986 1.687123 AGCTAGGCAAGTGGGTATACG 59.313 52.381 0.00 0.00 0.00 3.06
945 3019 4.527038 TCCAGTGCTGCTATATAAGTACCC 59.473 45.833 0.00 0.00 30.18 3.69
958 3035 2.467566 AGTACCCCAAAACTGCTACG 57.532 50.000 0.00 0.00 0.00 3.51
1012 3104 2.393646 GGAGAGTCATGGAGCCTAACT 58.606 52.381 0.00 0.00 0.00 2.24
1059 3151 1.091771 CGCTGCTGGTGACCATAAGG 61.092 60.000 4.03 0.00 42.21 2.69
1161 3253 2.520458 CTTGTTGGGTCCCTGCCA 59.480 61.111 10.00 0.00 0.00 4.92
1456 3563 2.774439 GTGAAGCAAATGTTCACCGT 57.226 45.000 13.30 0.00 45.42 4.83
1466 3573 1.338107 TGTTCACCGTCAGGACAGAT 58.662 50.000 0.00 0.00 41.02 2.90
1475 3582 2.693069 GTCAGGACAGATGTGTTCCAG 58.307 52.381 12.00 6.09 36.88 3.86
1478 3585 3.007290 TCAGGACAGATGTGTTCCAGAAG 59.993 47.826 12.00 2.62 36.88 2.85
1490 3597 4.750598 GTGTTCCAGAAGGACTACTTGAAC 59.249 45.833 0.00 0.00 45.73 3.18
1509 3616 1.280457 CCCTAGCCTGGACTCAGTTT 58.720 55.000 0.00 0.00 39.31 2.66
1511 3618 2.040412 CCCTAGCCTGGACTCAGTTTTT 59.960 50.000 0.00 0.00 39.31 1.94
1541 3648 3.057174 GGGTCATATTTGCAAACGGACAA 60.057 43.478 27.12 4.95 0.00 3.18
1577 3684 2.360726 AAATTCGTCCACCCGGCC 60.361 61.111 0.00 0.00 0.00 6.13
1610 3717 6.543100 AGGAGACGATCAAGGTTACTACTTAG 59.457 42.308 0.00 0.00 0.00 2.18
1614 3721 6.850555 ACGATCAAGGTTACTACTTAGTCAC 58.149 40.000 0.00 0.00 37.73 3.67
1616 3723 7.826252 ACGATCAAGGTTACTACTTAGTCACTA 59.174 37.037 0.00 0.00 37.73 2.74
1617 3724 8.121708 CGATCAAGGTTACTACTTAGTCACTAC 58.878 40.741 0.00 0.00 37.73 2.73
1618 3725 9.176460 GATCAAGGTTACTACTTAGTCACTACT 57.824 37.037 0.00 0.00 37.73 2.57
1620 3727 9.442047 TCAAGGTTACTACTTAGTCACTACTAC 57.558 37.037 0.00 0.00 37.94 2.73
1621 3728 9.447157 CAAGGTTACTACTTAGTCACTACTACT 57.553 37.037 0.00 0.00 37.94 2.57
1743 3919 2.358247 GATGGAACGGTGGTGCGT 60.358 61.111 0.00 0.00 0.00 5.24
2065 4390 2.771089 TGTGACAAGCAAGATCTCACC 58.229 47.619 0.00 0.00 31.94 4.02
2072 4397 3.210232 AGCAAGATCTCACCCATCATG 57.790 47.619 0.00 0.00 0.00 3.07
2102 4427 3.923614 GCCAGCAGCGTATACGAG 58.076 61.111 28.66 19.53 43.02 4.18
2210 4547 2.029844 GTGCAGGACTCTGTTCGCC 61.030 63.158 0.00 0.00 42.78 5.54
2297 4651 4.547367 GGAGGTCGCCCGGGAATG 62.547 72.222 29.31 13.71 35.12 2.67
2363 4726 5.105351 TCAAGCTGGTACGCTATGCATATAT 60.105 40.000 6.92 0.00 37.23 0.86
2367 4730 7.821652 AGCTGGTACGCTATGCATATATATAG 58.178 38.462 6.92 0.00 36.56 1.31
2369 4732 8.727910 GCTGGTACGCTATGCATATATATAGTA 58.272 37.037 6.92 3.50 31.16 1.82
2375 5906 9.788889 ACGCTATGCATATATATAGTACCAGTA 57.211 33.333 6.92 0.00 31.16 2.74
2394 5925 7.062322 ACCAGTAAAATCTCATCCATGCATTA 58.938 34.615 0.00 0.00 0.00 1.90
2431 5997 4.737855 ACATCTAATAAGTGTCTGCCGT 57.262 40.909 0.00 0.00 0.00 5.68
2432 5998 4.433615 ACATCTAATAAGTGTCTGCCGTG 58.566 43.478 0.00 0.00 0.00 4.94
2433 5999 3.520290 TCTAATAAGTGTCTGCCGTGG 57.480 47.619 0.00 0.00 0.00 4.94
2434 6000 2.829720 TCTAATAAGTGTCTGCCGTGGT 59.170 45.455 0.00 0.00 0.00 4.16
2435 6001 1.808411 AATAAGTGTCTGCCGTGGTG 58.192 50.000 0.00 0.00 0.00 4.17
2436 6002 0.973632 ATAAGTGTCTGCCGTGGTGA 59.026 50.000 0.00 0.00 0.00 4.02
2437 6003 0.032952 TAAGTGTCTGCCGTGGTGAC 59.967 55.000 7.07 7.07 0.00 3.67
2439 6005 1.664965 GTGTCTGCCGTGGTGACTC 60.665 63.158 12.72 7.63 0.00 3.36
2440 6006 2.048127 GTCTGCCGTGGTGACTCC 60.048 66.667 6.84 0.00 0.00 3.85
2481 6047 0.323451 TCTTGGAGACGCTGAGGCTA 60.323 55.000 0.00 0.00 39.26 3.93
2485 6051 2.598565 TGGAGACGCTGAGGCTATATT 58.401 47.619 0.00 0.00 39.26 1.28
2500 6066 5.076873 GGCTATATTGCCCCATAACTTTCA 58.923 41.667 16.42 0.00 46.82 2.69
2541 6107 1.718757 GCACCATCCTCGCCAACATC 61.719 60.000 0.00 0.00 0.00 3.06
2542 6108 1.153369 ACCATCCTCGCCAACATCG 60.153 57.895 0.00 0.00 0.00 3.84
2562 6128 1.468914 GAGGTGCCAAAAGGAACGATC 59.531 52.381 0.00 0.00 0.00 3.69
2604 6170 4.379174 CACCGGGACAAAGAGGTG 57.621 61.111 6.32 0.00 46.52 4.00
2869 6435 1.006043 TCCCTCTCATCGTCAGGAACT 59.994 52.381 0.00 0.00 43.88 3.01
2871 6437 3.024547 CCCTCTCATCGTCAGGAACTTA 58.975 50.000 0.00 0.00 34.60 2.24
2969 6543 5.923114 GCCCGCCTACTAGTAGTAAATAAAC 59.077 44.000 24.84 6.44 29.00 2.01
3032 6606 6.890979 TGATTATGTCACCATTGTTGTTCA 57.109 33.333 0.00 0.00 32.29 3.18
3050 6624 9.056005 TGTTGTTCATCCAAAGCTACATATATC 57.944 33.333 0.00 0.00 0.00 1.63
3084 6658 5.347012 TGTGATATGTATGCAATGCGAAG 57.653 39.130 0.00 0.00 0.00 3.79
3106 6680 7.959651 CGAAGCTTTGGAATATACTTATGATGC 59.040 37.037 5.72 0.00 0.00 3.91
3157 6734 9.807386 GTACACATGATTACAACTCTTTACAAC 57.193 33.333 0.00 0.00 0.00 3.32
3174 6751 8.380099 TCTTTACAACAACCTCAACCATATACT 58.620 33.333 0.00 0.00 0.00 2.12
3175 6752 8.556213 TTTACAACAACCTCAACCATATACTC 57.444 34.615 0.00 0.00 0.00 2.59
3176 6753 5.497474 ACAACAACCTCAACCATATACTCC 58.503 41.667 0.00 0.00 0.00 3.85
3177 6754 4.772886 ACAACCTCAACCATATACTCCC 57.227 45.455 0.00 0.00 0.00 4.30
3178 6755 4.371681 ACAACCTCAACCATATACTCCCT 58.628 43.478 0.00 0.00 0.00 4.20
3179 6756 4.409247 ACAACCTCAACCATATACTCCCTC 59.591 45.833 0.00 0.00 0.00 4.30
3180 6757 4.561254 ACCTCAACCATATACTCCCTCT 57.439 45.455 0.00 0.00 0.00 3.69
3181 6758 4.227197 ACCTCAACCATATACTCCCTCTG 58.773 47.826 0.00 0.00 0.00 3.35
3182 6759 4.227197 CCTCAACCATATACTCCCTCTGT 58.773 47.826 0.00 0.00 0.00 3.41
3183 6760 4.282195 CCTCAACCATATACTCCCTCTGTC 59.718 50.000 0.00 0.00 0.00 3.51
3184 6761 4.223953 TCAACCATATACTCCCTCTGTCC 58.776 47.826 0.00 0.00 0.00 4.02
3185 6762 2.877866 ACCATATACTCCCTCTGTCCG 58.122 52.381 0.00 0.00 0.00 4.79
3186 6763 2.445905 ACCATATACTCCCTCTGTCCGA 59.554 50.000 0.00 0.00 0.00 4.55
3187 6764 3.117246 ACCATATACTCCCTCTGTCCGAA 60.117 47.826 0.00 0.00 0.00 4.30
3188 6765 3.895656 CCATATACTCCCTCTGTCCGAAA 59.104 47.826 0.00 0.00 0.00 3.46
3189 6766 4.344102 CCATATACTCCCTCTGTCCGAAAA 59.656 45.833 0.00 0.00 0.00 2.29
3190 6767 5.012148 CCATATACTCCCTCTGTCCGAAAAT 59.988 44.000 0.00 0.00 0.00 1.82
3191 6768 6.210784 CCATATACTCCCTCTGTCCGAAAATA 59.789 42.308 0.00 0.00 0.00 1.40
3192 6769 3.889520 ACTCCCTCTGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
3193 6770 3.442076 ACTCCCTCTGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
3194 6771 3.838903 ACTCCCTCTGTCCGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
3195 6772 4.184629 CTCCCTCTGTCCGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
3196 6773 3.581332 TCCCTCTGTCCGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
3197 6774 3.933332 CCCTCTGTCCGAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
3198 6775 3.612860 CCTCTGTCCGAAAATACTTGTCG 59.387 47.826 0.00 0.00 34.58 4.35
3207 6784 6.403333 CGAAAATACTTGTCGGAGAAATGA 57.597 37.500 0.00 0.00 39.69 2.57
3208 6785 6.827641 CGAAAATACTTGTCGGAGAAATGAA 58.172 36.000 0.00 0.00 39.69 2.57
3209 6786 7.464358 CGAAAATACTTGTCGGAGAAATGAAT 58.536 34.615 0.00 0.00 39.69 2.57
3210 6787 8.600625 CGAAAATACTTGTCGGAGAAATGAATA 58.399 33.333 0.00 0.00 39.69 1.75
3216 6793 8.970691 ACTTGTCGGAGAAATGAATAAAAATG 57.029 30.769 0.00 0.00 39.69 2.32
3217 6794 8.028938 ACTTGTCGGAGAAATGAATAAAAATGG 58.971 33.333 0.00 0.00 39.69 3.16
3218 6795 7.695480 TGTCGGAGAAATGAATAAAAATGGA 57.305 32.000 0.00 0.00 39.69 3.41
3219 6796 8.292444 TGTCGGAGAAATGAATAAAAATGGAT 57.708 30.769 0.00 0.00 39.69 3.41
3220 6797 8.190122 TGTCGGAGAAATGAATAAAAATGGATG 58.810 33.333 0.00 0.00 39.69 3.51
3221 6798 8.190784 GTCGGAGAAATGAATAAAAATGGATGT 58.809 33.333 0.00 0.00 39.69 3.06
3222 6799 9.402320 TCGGAGAAATGAATAAAAATGGATGTA 57.598 29.630 0.00 0.00 0.00 2.29
3235 6812 8.732746 AAAAATGGATGTATCTAGTACCACAC 57.267 34.615 0.00 0.00 32.03 3.82
3236 6813 7.432148 AAATGGATGTATCTAGTACCACACA 57.568 36.000 0.00 0.00 32.03 3.72
3237 6814 7.618019 AATGGATGTATCTAGTACCACACAT 57.382 36.000 0.00 0.00 32.03 3.21
3238 6815 6.650427 TGGATGTATCTAGTACCACACATC 57.350 41.667 12.01 12.01 40.84 3.06
3240 6817 6.650427 GATGTATCTAGTACCACACATCCA 57.350 41.667 10.36 0.00 37.41 3.41
3241 6818 7.233389 GATGTATCTAGTACCACACATCCAT 57.767 40.000 10.36 0.00 37.41 3.41
3242 6819 7.618019 ATGTATCTAGTACCACACATCCATT 57.382 36.000 0.00 0.00 32.03 3.16
3243 6820 7.432148 TGTATCTAGTACCACACATCCATTT 57.568 36.000 0.00 0.00 32.03 2.32
3244 6821 7.857456 TGTATCTAGTACCACACATCCATTTT 58.143 34.615 0.00 0.00 32.03 1.82
3245 6822 7.985184 TGTATCTAGTACCACACATCCATTTTC 59.015 37.037 0.00 0.00 32.03 2.29
3246 6823 5.741011 TCTAGTACCACACATCCATTTTCC 58.259 41.667 0.00 0.00 0.00 3.13
3247 6824 3.697166 AGTACCACACATCCATTTTCCC 58.303 45.455 0.00 0.00 0.00 3.97
3248 6825 1.544724 ACCACACATCCATTTTCCCG 58.455 50.000 0.00 0.00 0.00 5.14
3249 6826 0.817013 CCACACATCCATTTTCCCGG 59.183 55.000 0.00 0.00 0.00 5.73
3250 6827 0.173255 CACACATCCATTTTCCCGGC 59.827 55.000 0.00 0.00 0.00 6.13
3251 6828 0.251564 ACACATCCATTTTCCCGGCA 60.252 50.000 0.00 0.00 0.00 5.69
3252 6829 0.894141 CACATCCATTTTCCCGGCAA 59.106 50.000 0.00 0.00 0.00 4.52
3253 6830 1.135024 CACATCCATTTTCCCGGCAAG 60.135 52.381 0.00 0.00 0.00 4.01
3254 6831 1.185315 CATCCATTTTCCCGGCAAGT 58.815 50.000 0.00 0.00 0.00 3.16
3255 6832 2.291282 ACATCCATTTTCCCGGCAAGTA 60.291 45.455 0.00 0.00 0.00 2.24
3256 6833 2.818751 TCCATTTTCCCGGCAAGTAT 57.181 45.000 0.00 0.00 0.00 2.12
3257 6834 3.094484 TCCATTTTCCCGGCAAGTATT 57.906 42.857 0.00 0.00 0.00 1.89
3258 6835 3.436243 TCCATTTTCCCGGCAAGTATTT 58.564 40.909 0.00 0.00 0.00 1.40
3259 6836 3.445805 TCCATTTTCCCGGCAAGTATTTC 59.554 43.478 0.00 0.00 0.00 2.17
3260 6837 3.430236 CCATTTTCCCGGCAAGTATTTCC 60.430 47.826 0.00 0.00 0.00 3.13
3261 6838 1.455248 TTTCCCGGCAAGTATTTCCG 58.545 50.000 0.00 0.00 42.58 4.30
3264 6841 3.107447 CGGCAAGTATTTCCGGGC 58.893 61.111 0.00 0.00 39.52 6.13
3265 6842 2.478033 CGGCAAGTATTTCCGGGCC 61.478 63.158 0.00 2.22 39.52 5.80
3266 6843 2.478033 GGCAAGTATTTCCGGGCCG 61.478 63.158 21.46 21.46 0.00 6.13
3267 6844 1.450669 GCAAGTATTTCCGGGCCGA 60.451 57.895 30.79 8.18 0.00 5.54
3268 6845 1.436983 GCAAGTATTTCCGGGCCGAG 61.437 60.000 30.79 17.99 0.00 4.63
3269 6846 0.814010 CAAGTATTTCCGGGCCGAGG 60.814 60.000 30.79 12.35 0.00 4.63
3270 6847 1.979619 AAGTATTTCCGGGCCGAGGG 61.980 60.000 30.79 11.48 0.00 4.30
3271 6848 2.041715 TATTTCCGGGCCGAGGGA 60.042 61.111 30.79 14.08 0.00 4.20
3272 6849 2.138179 TATTTCCGGGCCGAGGGAG 61.138 63.158 30.79 10.59 33.01 4.30
3273 6850 2.884179 TATTTCCGGGCCGAGGGAGT 62.884 60.000 30.79 5.51 33.01 3.85
3274 6851 2.884179 ATTTCCGGGCCGAGGGAGTA 62.884 60.000 30.79 8.64 33.01 2.59
3275 6852 4.828296 TCCGGGCCGAGGGAGTAC 62.828 72.222 30.79 0.00 0.00 2.73
3277 6854 3.072468 CGGGCCGAGGGAGTACAA 61.072 66.667 24.41 0.00 0.00 2.41
3278 6855 2.901042 GGGCCGAGGGAGTACAAG 59.099 66.667 0.00 0.00 0.00 3.16
3279 6856 1.684734 GGGCCGAGGGAGTACAAGA 60.685 63.158 0.00 0.00 0.00 3.02
3280 6857 1.049289 GGGCCGAGGGAGTACAAGAT 61.049 60.000 0.00 0.00 0.00 2.40
3281 6858 1.700955 GGCCGAGGGAGTACAAGATA 58.299 55.000 0.00 0.00 0.00 1.98
3282 6859 2.037144 GGCCGAGGGAGTACAAGATAA 58.963 52.381 0.00 0.00 0.00 1.75
3283 6860 2.223994 GGCCGAGGGAGTACAAGATAAC 60.224 54.545 0.00 0.00 0.00 1.89
3284 6861 2.429610 GCCGAGGGAGTACAAGATAACA 59.570 50.000 0.00 0.00 0.00 2.41
3285 6862 3.118884 GCCGAGGGAGTACAAGATAACAA 60.119 47.826 0.00 0.00 0.00 2.83
3286 6863 4.443034 GCCGAGGGAGTACAAGATAACAAT 60.443 45.833 0.00 0.00 0.00 2.71
3287 6864 5.050490 CCGAGGGAGTACAAGATAACAATG 58.950 45.833 0.00 0.00 0.00 2.82
3288 6865 5.395324 CCGAGGGAGTACAAGATAACAATGT 60.395 44.000 0.00 0.00 0.00 2.71
3289 6866 6.183360 CCGAGGGAGTACAAGATAACAATGTA 60.183 42.308 0.00 0.00 0.00 2.29
3290 6867 6.696148 CGAGGGAGTACAAGATAACAATGTAC 59.304 42.308 7.10 7.10 46.11 2.90
3328 6905 7.981102 AAAGAATAAGTACTGAGTTGTTCCC 57.019 36.000 0.00 0.00 37.00 3.97
3329 6906 6.051179 AGAATAAGTACTGAGTTGTTCCCC 57.949 41.667 0.00 0.00 37.00 4.81
3330 6907 5.785940 AGAATAAGTACTGAGTTGTTCCCCT 59.214 40.000 0.00 0.00 37.00 4.79
3331 6908 6.272558 AGAATAAGTACTGAGTTGTTCCCCTT 59.727 38.462 0.00 0.00 37.00 3.95
3332 6909 4.353383 AAGTACTGAGTTGTTCCCCTTC 57.647 45.455 0.00 0.00 0.00 3.46
3333 6910 3.588569 AGTACTGAGTTGTTCCCCTTCT 58.411 45.455 0.00 0.00 0.00 2.85
3334 6911 3.579151 AGTACTGAGTTGTTCCCCTTCTC 59.421 47.826 0.00 0.00 0.00 2.87
3417 6998 1.598856 CCTCTCCCTCTCTCCCCCTT 61.599 65.000 0.00 0.00 0.00 3.95
3604 7190 1.945354 GCGGGAGATCAACTGGACGA 61.945 60.000 0.00 0.00 0.00 4.20
3751 7338 4.332543 TTCCAGGAGGCGGGGAGT 62.333 66.667 0.00 0.00 33.74 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.386010 ACAAAAGGGTAAATTAAGGTGAAAAAC 57.614 29.630 0.00 0.00 0.00 2.43
43 44 6.258160 AGCGACTTAACATTCATTGCAATAC 58.742 36.000 12.53 0.00 0.00 1.89
140 141 1.152830 GAACCCCAACAGAAGCCCA 59.847 57.895 0.00 0.00 0.00 5.36
167 168 0.800683 TCACTTCTTCGTATGGCGCG 60.801 55.000 0.00 0.00 41.07 6.86
474 507 0.978146 AGAGGCTATCCTTGCACCGT 60.978 55.000 0.00 0.00 44.46 4.83
478 511 2.158711 CCAATGAGAGGCTATCCTTGCA 60.159 50.000 18.11 0.00 44.46 4.08
497 530 2.785389 AAACCTTGGAGGGGGCCA 60.785 61.111 4.39 0.00 40.58 5.36
566 599 3.845781 TCTAATCCATCACCTGCTTCC 57.154 47.619 0.00 0.00 0.00 3.46
602 639 7.233144 TGCACCAAACCATGCATCTAATTATAT 59.767 33.333 0.00 0.00 46.63 0.86
607 644 3.098377 TGCACCAAACCATGCATCTAAT 58.902 40.909 0.00 0.00 46.63 1.73
608 645 2.523245 TGCACCAAACCATGCATCTAA 58.477 42.857 0.00 0.00 46.63 2.10
610 647 3.054679 TGCACCAAACCATGCATCT 57.945 47.368 0.00 0.00 46.63 2.90
615 652 1.717194 GCATCTTGCACCAAACCATG 58.283 50.000 0.00 0.00 44.26 3.66
616 653 0.244450 CGCATCTTGCACCAAACCAT 59.756 50.000 0.00 0.00 45.36 3.55
617 654 1.106351 ACGCATCTTGCACCAAACCA 61.106 50.000 0.00 0.00 45.36 3.67
618 655 0.878416 TACGCATCTTGCACCAAACC 59.122 50.000 0.00 0.00 45.36 3.27
619 656 1.401018 GGTACGCATCTTGCACCAAAC 60.401 52.381 4.60 0.00 45.36 2.93
621 658 0.036164 AGGTACGCATCTTGCACCAA 59.964 50.000 10.50 0.00 45.36 3.67
624 661 1.369091 CCCAGGTACGCATCTTGCAC 61.369 60.000 0.00 0.00 45.36 4.57
626 663 1.078426 ACCCAGGTACGCATCTTGC 60.078 57.895 0.00 0.00 40.69 4.01
627 664 0.537188 AGACCCAGGTACGCATCTTG 59.463 55.000 0.00 0.00 0.00 3.02
628 665 0.824759 GAGACCCAGGTACGCATCTT 59.175 55.000 0.00 0.00 0.00 2.40
630 667 1.609555 CTAGAGACCCAGGTACGCATC 59.390 57.143 0.00 0.00 0.00 3.91
631 668 1.693627 CTAGAGACCCAGGTACGCAT 58.306 55.000 0.00 0.00 0.00 4.73
632 669 1.035932 GCTAGAGACCCAGGTACGCA 61.036 60.000 0.00 0.00 0.00 5.24
633 670 1.734748 GCTAGAGACCCAGGTACGC 59.265 63.158 0.00 0.00 0.00 4.42
699 736 1.682344 GGGGGCTTCATTGGGTCAC 60.682 63.158 0.00 0.00 0.00 3.67
786 823 6.926630 AGAGAACCAATTTAGTCTCTCAGT 57.073 37.500 5.94 0.00 33.31 3.41
787 824 7.333174 GGAAAGAGAACCAATTTAGTCTCTCAG 59.667 40.741 10.49 0.00 33.97 3.35
788 825 7.162082 GGAAAGAGAACCAATTTAGTCTCTCA 58.838 38.462 10.49 0.00 33.97 3.27
803 866 6.431198 TTGTTTGTGTAGTGGAAAGAGAAC 57.569 37.500 0.00 0.00 0.00 3.01
825 893 1.152830 ACGGCAACCCACAAGGATT 59.847 52.632 0.00 0.00 39.89 3.01
826 894 1.603455 CACGGCAACCCACAAGGAT 60.603 57.895 0.00 0.00 39.89 3.24
885 1083 5.045140 ACCCACTTGCCTAGCTTCTTTATAA 60.045 40.000 0.00 0.00 0.00 0.98
888 1086 2.642807 ACCCACTTGCCTAGCTTCTTTA 59.357 45.455 0.00 0.00 0.00 1.85
914 2986 1.968540 GCAGCACTGGACCAAGACC 60.969 63.158 0.00 0.00 0.00 3.85
945 3019 1.804748 GTTCTCCCGTAGCAGTTTTGG 59.195 52.381 0.00 0.00 0.00 3.28
958 3035 5.437060 TGCTTAACCTATGATTGTTCTCCC 58.563 41.667 0.00 0.00 0.00 4.30
991 3083 1.414550 GTTAGGCTCCATGACTCTCCC 59.585 57.143 0.00 0.00 34.56 4.30
1012 3104 4.060667 GGCCAGGGCTTGCCCTAA 62.061 66.667 30.31 0.00 41.97 2.69
1059 3151 4.973168 TCCAAATCAGATACCATACTGCC 58.027 43.478 0.00 0.00 34.57 4.85
1161 3253 1.842562 ACAAGCATCCTATGGCACTCT 59.157 47.619 0.00 0.00 0.00 3.24
1456 3563 2.608623 TCTGGAACACATCTGTCCTGA 58.391 47.619 0.00 0.00 0.00 3.86
1466 3573 3.964688 TCAAGTAGTCCTTCTGGAACACA 59.035 43.478 0.00 0.00 45.18 3.72
1475 3582 3.118702 GGCTAGGGTTCAAGTAGTCCTTC 60.119 52.174 0.00 0.00 0.00 3.46
1478 3585 2.168728 CAGGCTAGGGTTCAAGTAGTCC 59.831 54.545 0.00 0.00 0.00 3.85
1490 3597 1.280457 AAACTGAGTCCAGGCTAGGG 58.720 55.000 0.00 0.00 44.60 3.53
1509 3616 3.093057 CAAATATGACCCCGTTCCCAAA 58.907 45.455 0.00 0.00 0.00 3.28
1511 3618 1.683629 GCAAATATGACCCCGTTCCCA 60.684 52.381 0.00 0.00 0.00 4.37
1541 3648 4.421479 CGGCGTCGCTTCCAGTCT 62.421 66.667 18.11 0.00 0.00 3.24
1577 3684 3.257393 CTTGATCGTCTCCTGGTTGAAG 58.743 50.000 0.00 0.00 0.00 3.02
1679 3837 1.872952 TGCTGACATGGACTGAAAACG 59.127 47.619 0.00 0.00 0.00 3.60
1719 3877 2.100631 CACCGTTCCATCGTCTGCC 61.101 63.158 0.00 0.00 0.00 4.85
1992 4317 1.814527 GTGTCGGCAGGTACCTAGG 59.185 63.158 15.80 7.41 0.00 3.02
2065 4390 1.091771 AAGTCGCGCCTTCATGATGG 61.092 55.000 20.70 20.70 0.00 3.51
2096 4421 1.437772 CGAGCAGGTCGTCCTCGTAT 61.438 60.000 14.02 0.00 44.20 3.06
2131 4456 2.745100 CACTGCGACATGCCTGCT 60.745 61.111 0.00 0.00 45.60 4.24
2235 4572 2.487265 GGAACATCGCCCAGGTAATGAT 60.487 50.000 7.24 0.00 0.00 2.45
2367 4730 5.822519 TGCATGGATGAGATTTTACTGGTAC 59.177 40.000 0.00 0.00 0.00 3.34
2369 4732 4.858850 TGCATGGATGAGATTTTACTGGT 58.141 39.130 0.00 0.00 0.00 4.00
2407 5973 7.368059 CACGGCAGACACTTATTAGATGTATA 58.632 38.462 0.00 0.00 0.00 1.47
2424 5990 2.523168 TGGAGTCACCACGGCAGA 60.523 61.111 0.00 0.00 44.64 4.26
2432 5998 0.536006 AAGCTGCAAGTGGAGTCACC 60.536 55.000 1.02 0.00 44.64 4.02
2433 5999 2.169832 TAAGCTGCAAGTGGAGTCAC 57.830 50.000 1.02 0.00 43.93 3.67
2434 6000 2.158827 TGTTAAGCTGCAAGTGGAGTCA 60.159 45.455 1.02 0.00 35.78 3.41
2435 6001 2.494059 TGTTAAGCTGCAAGTGGAGTC 58.506 47.619 1.02 0.00 35.78 3.36
2436 6002 2.638480 TGTTAAGCTGCAAGTGGAGT 57.362 45.000 1.02 0.00 35.78 3.85
2437 6003 2.816087 ACATGTTAAGCTGCAAGTGGAG 59.184 45.455 1.02 0.00 35.30 3.86
2439 6005 3.648339 AACATGTTAAGCTGCAAGTGG 57.352 42.857 9.97 0.00 35.30 4.00
2440 6006 5.180117 AGAGTAACATGTTAAGCTGCAAGTG 59.820 40.000 19.63 0.00 35.30 3.16
2481 6047 7.526041 TCTGTATGAAAGTTATGGGGCAATAT 58.474 34.615 0.00 0.00 0.00 1.28
2485 6051 4.385199 CCTCTGTATGAAAGTTATGGGGCA 60.385 45.833 0.00 0.00 0.00 5.36
2522 6088 1.718757 GATGTTGGCGAGGATGGTGC 61.719 60.000 0.00 0.00 0.00 5.01
2541 6107 0.882927 TCGTTCCTTTTGGCACCTCG 60.883 55.000 0.00 0.00 40.12 4.63
2542 6108 1.468914 GATCGTTCCTTTTGGCACCTC 59.531 52.381 0.00 0.00 40.12 3.85
2562 6128 0.745486 TCAGCAGCGGGATTGACATG 60.745 55.000 0.00 0.00 0.00 3.21
2646 6212 1.375523 GTCCACCGAGACGCCATTT 60.376 57.895 0.00 0.00 0.00 2.32
3056 6630 7.496591 TCGCATTGCATACATATCACATCATAT 59.503 33.333 9.69 0.00 0.00 1.78
3084 6658 8.733458 TCATGCATCATAAGTATATTCCAAAGC 58.267 33.333 0.00 0.00 0.00 3.51
3106 6680 5.233225 AGGATGTCGTGCTGTATAATCATG 58.767 41.667 0.00 0.00 0.00 3.07
3112 6686 4.399934 TGTACAAGGATGTCGTGCTGTATA 59.600 41.667 0.00 0.00 41.05 1.47
3113 6687 3.194755 TGTACAAGGATGTCGTGCTGTAT 59.805 43.478 0.00 0.00 41.05 2.29
3115 6689 1.343142 TGTACAAGGATGTCGTGCTGT 59.657 47.619 0.00 0.00 41.05 4.40
3157 6734 4.656112 AGAGGGAGTATATGGTTGAGGTTG 59.344 45.833 0.00 0.00 0.00 3.77
3174 6751 3.581332 ACAAGTATTTTCGGACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
3175 6752 3.933332 GACAAGTATTTTCGGACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
3176 6753 3.612860 CGACAAGTATTTTCGGACAGAGG 59.387 47.826 0.00 0.00 0.00 3.69
3177 6754 4.824848 CGACAAGTATTTTCGGACAGAG 57.175 45.455 0.00 0.00 0.00 3.35
3184 6761 6.403333 TCATTTCTCCGACAAGTATTTTCG 57.597 37.500 0.00 0.00 0.00 3.46
3191 6768 8.028938 CCATTTTTATTCATTTCTCCGACAAGT 58.971 33.333 0.00 0.00 0.00 3.16
3192 6769 8.243426 TCCATTTTTATTCATTTCTCCGACAAG 58.757 33.333 0.00 0.00 0.00 3.16
3193 6770 8.116651 TCCATTTTTATTCATTTCTCCGACAA 57.883 30.769 0.00 0.00 0.00 3.18
3194 6771 7.695480 TCCATTTTTATTCATTTCTCCGACA 57.305 32.000 0.00 0.00 0.00 4.35
3195 6772 8.190784 ACATCCATTTTTATTCATTTCTCCGAC 58.809 33.333 0.00 0.00 0.00 4.79
3196 6773 8.292444 ACATCCATTTTTATTCATTTCTCCGA 57.708 30.769 0.00 0.00 0.00 4.55
3209 6786 9.826574 GTGTGGTACTAGATACATCCATTTTTA 57.173 33.333 0.00 0.00 35.23 1.52
3210 6787 8.325787 TGTGTGGTACTAGATACATCCATTTTT 58.674 33.333 0.00 0.00 35.23 1.94
3211 6788 7.857456 TGTGTGGTACTAGATACATCCATTTT 58.143 34.615 0.00 0.00 35.23 1.82
3212 6789 7.432148 TGTGTGGTACTAGATACATCCATTT 57.568 36.000 0.00 0.00 35.23 2.32
3213 6790 7.618019 ATGTGTGGTACTAGATACATCCATT 57.382 36.000 0.00 0.00 35.23 3.16
3214 6791 7.233389 GATGTGTGGTACTAGATACATCCAT 57.767 40.000 14.88 0.00 38.79 3.41
3215 6792 6.650427 GATGTGTGGTACTAGATACATCCA 57.350 41.667 14.88 0.00 38.79 3.41
3217 6794 6.650427 TGGATGTGTGGTACTAGATACATC 57.350 41.667 16.39 16.39 42.06 3.06
3218 6795 7.618019 AATGGATGTGTGGTACTAGATACAT 57.382 36.000 0.00 4.16 35.23 2.29
3219 6796 7.432148 AAATGGATGTGTGGTACTAGATACA 57.568 36.000 0.00 0.00 35.23 2.29
3220 6797 7.441458 GGAAAATGGATGTGTGGTACTAGATAC 59.559 40.741 0.00 0.00 0.00 2.24
3221 6798 7.419750 GGGAAAATGGATGTGTGGTACTAGATA 60.420 40.741 0.00 0.00 0.00 1.98
3222 6799 6.357367 GGAAAATGGATGTGTGGTACTAGAT 58.643 40.000 0.00 0.00 0.00 1.98
3223 6800 5.338871 GGGAAAATGGATGTGTGGTACTAGA 60.339 44.000 0.00 0.00 0.00 2.43
3224 6801 4.881850 GGGAAAATGGATGTGTGGTACTAG 59.118 45.833 0.00 0.00 0.00 2.57
3225 6802 4.624364 CGGGAAAATGGATGTGTGGTACTA 60.624 45.833 0.00 0.00 0.00 1.82
3226 6803 3.697166 GGGAAAATGGATGTGTGGTACT 58.303 45.455 0.00 0.00 0.00 2.73
3227 6804 2.422127 CGGGAAAATGGATGTGTGGTAC 59.578 50.000 0.00 0.00 0.00 3.34
3228 6805 2.619332 CCGGGAAAATGGATGTGTGGTA 60.619 50.000 0.00 0.00 0.00 3.25
3229 6806 1.544724 CGGGAAAATGGATGTGTGGT 58.455 50.000 0.00 0.00 0.00 4.16
3230 6807 0.817013 CCGGGAAAATGGATGTGTGG 59.183 55.000 0.00 0.00 0.00 4.17
3231 6808 0.173255 GCCGGGAAAATGGATGTGTG 59.827 55.000 2.18 0.00 0.00 3.82
3232 6809 0.251564 TGCCGGGAAAATGGATGTGT 60.252 50.000 2.18 0.00 0.00 3.72
3233 6810 0.894141 TTGCCGGGAAAATGGATGTG 59.106 50.000 5.67 0.00 0.00 3.21
3234 6811 1.185315 CTTGCCGGGAAAATGGATGT 58.815 50.000 10.50 0.00 0.00 3.06
3235 6812 1.185315 ACTTGCCGGGAAAATGGATG 58.815 50.000 10.50 0.00 0.00 3.51
3236 6813 2.818751 TACTTGCCGGGAAAATGGAT 57.181 45.000 10.50 0.00 0.00 3.41
3237 6814 2.818751 ATACTTGCCGGGAAAATGGA 57.181 45.000 10.50 0.00 0.00 3.41
3238 6815 3.430236 GGAAATACTTGCCGGGAAAATGG 60.430 47.826 10.50 0.00 0.00 3.16
3239 6816 3.733684 CGGAAATACTTGCCGGGAAAATG 60.734 47.826 10.50 0.17 41.29 2.32
3240 6817 2.425668 CGGAAATACTTGCCGGGAAAAT 59.574 45.455 10.50 3.48 41.29 1.82
3241 6818 1.813786 CGGAAATACTTGCCGGGAAAA 59.186 47.619 10.50 0.78 41.29 2.29
3242 6819 1.455248 CGGAAATACTTGCCGGGAAA 58.545 50.000 10.50 0.00 41.29 3.13
3243 6820 3.162448 CGGAAATACTTGCCGGGAA 57.838 52.632 8.57 8.57 41.29 3.97
3244 6821 4.946038 CGGAAATACTTGCCGGGA 57.054 55.556 2.18 0.00 41.29 5.14
3247 6824 2.478033 GGCCCGGAAATACTTGCCG 61.478 63.158 0.73 0.00 44.42 5.69
3248 6825 2.478033 CGGCCCGGAAATACTTGCC 61.478 63.158 0.73 2.94 35.55 4.52
3249 6826 1.436983 CTCGGCCCGGAAATACTTGC 61.437 60.000 0.73 0.00 0.00 4.01
3250 6827 0.814010 CCTCGGCCCGGAAATACTTG 60.814 60.000 0.73 0.00 0.00 3.16
3251 6828 1.525442 CCTCGGCCCGGAAATACTT 59.475 57.895 0.73 0.00 0.00 2.24
3252 6829 2.440817 CCCTCGGCCCGGAAATACT 61.441 63.158 0.73 0.00 0.00 2.12
3253 6830 2.110420 CCCTCGGCCCGGAAATAC 59.890 66.667 0.73 0.00 0.00 1.89
3254 6831 2.041715 TCCCTCGGCCCGGAAATA 60.042 61.111 0.73 0.00 0.00 1.40
3255 6832 2.884179 TACTCCCTCGGCCCGGAAAT 62.884 60.000 0.73 0.00 0.00 2.17
3256 6833 3.605412 TACTCCCTCGGCCCGGAAA 62.605 63.158 0.73 0.00 0.00 3.13
3257 6834 4.064768 TACTCCCTCGGCCCGGAA 62.065 66.667 0.73 0.00 0.00 4.30
3258 6835 4.828296 GTACTCCCTCGGCCCGGA 62.828 72.222 0.73 4.11 0.00 5.14
3260 6837 3.072468 TTGTACTCCCTCGGCCCG 61.072 66.667 0.00 0.00 0.00 6.13
3261 6838 1.049289 ATCTTGTACTCCCTCGGCCC 61.049 60.000 0.00 0.00 0.00 5.80
3262 6839 1.700955 TATCTTGTACTCCCTCGGCC 58.299 55.000 0.00 0.00 0.00 6.13
3263 6840 2.429610 TGTTATCTTGTACTCCCTCGGC 59.570 50.000 0.00 0.00 0.00 5.54
3264 6841 4.730949 TTGTTATCTTGTACTCCCTCGG 57.269 45.455 0.00 0.00 0.00 4.63
3265 6842 5.661458 ACATTGTTATCTTGTACTCCCTCG 58.339 41.667 0.00 0.00 0.00 4.63
3302 6879 9.498176 GGGAACAACTCAGTACTTATTCTTTTA 57.502 33.333 0.00 0.00 0.00 1.52
3303 6880 7.447545 GGGGAACAACTCAGTACTTATTCTTTT 59.552 37.037 0.00 0.00 0.00 2.27
3304 6881 6.940867 GGGGAACAACTCAGTACTTATTCTTT 59.059 38.462 0.00 0.00 0.00 2.52
3305 6882 6.272558 AGGGGAACAACTCAGTACTTATTCTT 59.727 38.462 0.00 0.00 0.00 2.52
3306 6883 5.785940 AGGGGAACAACTCAGTACTTATTCT 59.214 40.000 0.00 0.00 0.00 2.40
3307 6884 6.051179 AGGGGAACAACTCAGTACTTATTC 57.949 41.667 0.00 0.00 0.00 1.75
3308 6885 6.272558 AGAAGGGGAACAACTCAGTACTTATT 59.727 38.462 0.00 0.00 0.00 1.40
3309 6886 5.785940 AGAAGGGGAACAACTCAGTACTTAT 59.214 40.000 0.00 0.00 0.00 1.73
3310 6887 5.152934 AGAAGGGGAACAACTCAGTACTTA 58.847 41.667 0.00 0.00 0.00 2.24
3311 6888 3.974642 AGAAGGGGAACAACTCAGTACTT 59.025 43.478 0.00 0.00 0.00 2.24
3312 6889 3.579151 GAGAAGGGGAACAACTCAGTACT 59.421 47.826 0.00 0.00 0.00 2.73
3313 6890 3.306849 GGAGAAGGGGAACAACTCAGTAC 60.307 52.174 0.00 0.00 0.00 2.73
3314 6891 2.904434 GGAGAAGGGGAACAACTCAGTA 59.096 50.000 0.00 0.00 0.00 2.74
3315 6892 1.700186 GGAGAAGGGGAACAACTCAGT 59.300 52.381 0.00 0.00 0.00 3.41
3316 6893 1.981495 AGGAGAAGGGGAACAACTCAG 59.019 52.381 0.00 0.00 0.00 3.35
3317 6894 1.978580 GAGGAGAAGGGGAACAACTCA 59.021 52.381 0.00 0.00 0.00 3.41
3318 6895 2.235155 GAGAGGAGAAGGGGAACAACTC 59.765 54.545 0.00 0.00 0.00 3.01
3319 6896 2.261729 GAGAGGAGAAGGGGAACAACT 58.738 52.381 0.00 0.00 0.00 3.16
3320 6897 1.066787 CGAGAGGAGAAGGGGAACAAC 60.067 57.143 0.00 0.00 0.00 3.32
3321 6898 1.267121 CGAGAGGAGAAGGGGAACAA 58.733 55.000 0.00 0.00 0.00 2.83
3322 6899 1.258445 GCGAGAGGAGAAGGGGAACA 61.258 60.000 0.00 0.00 0.00 3.18
3323 6900 1.518302 GCGAGAGGAGAAGGGGAAC 59.482 63.158 0.00 0.00 0.00 3.62
3324 6901 2.052690 CGCGAGAGGAGAAGGGGAA 61.053 63.158 0.00 0.00 0.00 3.97
3325 6902 2.440430 CGCGAGAGGAGAAGGGGA 60.440 66.667 0.00 0.00 0.00 4.81
3326 6903 2.440430 TCGCGAGAGGAGAAGGGG 60.440 66.667 3.71 0.00 34.84 4.79
3327 6904 2.776913 GGTCGCGAGAGGAGAAGGG 61.777 68.421 10.24 0.00 43.49 3.95
3328 6905 2.802106 GGTCGCGAGAGGAGAAGG 59.198 66.667 10.24 0.00 43.49 3.46
3329 6906 2.405594 CGGTCGCGAGAGGAGAAG 59.594 66.667 10.24 0.00 43.49 2.85
3330 6907 3.812019 GCGGTCGCGAGAGGAGAA 61.812 66.667 10.24 0.00 43.49 2.87
3332 6909 3.815569 GATGCGGTCGCGAGAGGAG 62.816 68.421 10.24 0.00 45.51 3.69
3333 6910 3.889044 GATGCGGTCGCGAGAGGA 61.889 66.667 10.24 8.46 45.51 3.71
3584 7170 1.596934 GTCCAGTTGATCTCCCGCA 59.403 57.895 0.00 0.00 0.00 5.69
3813 7409 0.462047 CCGAATTGAGCCCGCTAAGT 60.462 55.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.