Multiple sequence alignment - TraesCS7A01G325600

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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 TraesCS7A01G325600 chr7A 100.000 4967 0 0 1 4967 473894154 473899120 0.000000e+00 9173.0
1 TraesCS7A01G325600 chr7A 96.457 875 22 3 1 866 634880355 634881229 0.000000e+00 1435.0
2 TraesCS7A01G325600 chr7A 89.785 186 13 5 906 1089 473886864 473887045 2.990000e-57 233.0
3 TraesCS7A01G325600 chr7A 81.467 259 27 7 2864 3122 610458939 610458702 5.070000e-45 193.0
4 TraesCS7A01G325600 chr7A 79.795 292 38 8 2387 2672 610491153 610490877 5.070000e-45 193.0
5 TraesCS7A01G325600 chr7A 88.889 54 5 1 879 931 422209507 422209560 1.150000e-06 65.8
6 TraesCS7A01G325600 chr7B 95.292 2379 97 9 966 3341 426857468 426859834 0.000000e+00 3759.0
7 TraesCS7A01G325600 chr7B 93.646 661 15 4 4312 4945 355799865 355800525 0.000000e+00 963.0
8 TraesCS7A01G325600 chr7B 93.671 395 22 3 3422 3813 426859832 426860226 5.540000e-164 588.0
9 TraesCS7A01G325600 chr7B 85.672 335 43 4 2788 3122 568773076 568772747 1.020000e-91 348.0
10 TraesCS7A01G325600 chr7B 83.791 364 32 13 2387 2742 568774211 568773867 2.230000e-83 320.0
11 TraesCS7A01G325600 chr7B 88.136 59 6 1 874 931 621621671 621621729 8.920000e-08 69.4
12 TraesCS7A01G325600 chr7D 93.179 2419 136 7 940 3340 412646049 412648456 0.000000e+00 3526.0
13 TraesCS7A01G325600 chr7D 94.133 767 42 3 2575 3341 412652943 412653706 0.000000e+00 1164.0
14 TraesCS7A01G325600 chr7D 86.377 668 68 14 3422 4071 412648455 412649117 0.000000e+00 708.0
15 TraesCS7A01G325600 chr7D 85.237 359 31 14 3422 3777 412653704 412654043 2.850000e-92 350.0
16 TraesCS7A01G325600 chr7D 78.912 294 34 11 2387 2673 530337689 530337417 1.840000e-39 174.0
17 TraesCS7A01G325600 chr7D 97.849 93 2 0 3331 3423 221585389 221585297 1.430000e-35 161.0
18 TraesCS7A01G325600 chr7D 90.833 120 9 1 2669 2788 530336892 530336775 5.150000e-35 159.0
19 TraesCS7A01G325600 chr5A 97.807 912 12 2 1 904 649789852 649790763 0.000000e+00 1567.0
20 TraesCS7A01G325600 chr3B 94.182 911 29 4 1 903 633294584 633295478 0.000000e+00 1367.0
21 TraesCS7A01G325600 chr3B 94.799 596 22 3 1 588 707908044 707908638 0.000000e+00 920.0
22 TraesCS7A01G325600 chr3B 91.250 640 26 6 4312 4945 96747096 96747711 0.000000e+00 845.0
23 TraesCS7A01G325600 chr3B 85.081 248 33 4 4308 4553 609851790 609852035 2.970000e-62 250.0
24 TraesCS7A01G325600 chr3B 88.889 54 5 1 879 931 330598284 330598337 1.150000e-06 65.8
25 TraesCS7A01G325600 chr4B 92.234 940 41 14 1 931 104936418 104935502 0.000000e+00 1303.0
26 TraesCS7A01G325600 chr4B 98.936 94 1 0 3338 3431 592354519 592354426 8.550000e-38 169.0
27 TraesCS7A01G325600 chr2A 97.826 644 7 2 4309 4945 608781239 608781882 0.000000e+00 1105.0
28 TraesCS7A01G325600 chr4A 95.833 648 16 4 4309 4945 241660901 241660254 0.000000e+00 1037.0
29 TraesCS7A01G325600 chr4A 95.098 102 2 3 3333 3433 608987154 608987055 1.850000e-34 158.0
30 TraesCS7A01G325600 chr3D 95.490 643 17 6 4310 4945 229365596 229366233 0.000000e+00 1016.0
31 TraesCS7A01G325600 chr3D 95.146 103 4 1 3334 3435 23941563 23941461 1.430000e-35 161.0
32 TraesCS7A01G325600 chr3D 95.146 103 3 1 3338 3438 561754052 561753950 1.430000e-35 161.0
33 TraesCS7A01G325600 chr3D 87.931 58 7 0 874 931 135170922 135170865 8.920000e-08 69.4
34 TraesCS7A01G325600 chr1A 93.495 661 16 4 4312 4945 516632516 516631856 0.000000e+00 957.0
35 TraesCS7A01G325600 chr5B 90.923 661 29 8 4309 4945 46616011 46616664 0.000000e+00 859.0
36 TraesCS7A01G325600 chr5B 89.599 548 52 3 348 894 634276669 634276126 0.000000e+00 691.0
37 TraesCS7A01G325600 chr5B 91.724 290 15 3 1 282 634276957 634276669 1.300000e-105 394.0
38 TraesCS7A01G325600 chr2D 89.051 548 45 7 348 894 288159245 288158712 0.000000e+00 665.0
39 TraesCS7A01G325600 chr2B 88.869 548 49 8 348 894 738505980 738506516 0.000000e+00 664.0
40 TraesCS7A01G325600 chr2B 93.750 256 14 2 1 255 738505690 738505944 2.810000e-102 383.0
41 TraesCS7A01G325600 chr4D 88.686 548 47 7 348 894 188966843 188967376 0.000000e+00 654.0
42 TraesCS7A01G325600 chr4D 89.655 290 22 2 1 282 188966554 188966843 3.650000e-96 363.0
43 TraesCS7A01G325600 chr5D 91.247 457 39 1 348 803 560626937 560626481 5.460000e-174 621.0
44 TraesCS7A01G325600 chr5D 90.378 291 17 4 1 282 560627225 560626937 6.070000e-99 372.0
45 TraesCS7A01G325600 chrUn 95.288 382 11 2 4571 4945 384000846 384000465 2.560000e-167 599.0
46 TraesCS7A01G325600 chr1D 95.946 296 9 1 4312 4607 92968375 92968667 1.250000e-130 477.0
47 TraesCS7A01G325600 chr1D 93.750 320 8 1 4638 4945 92968982 92969301 2.090000e-128 470.0
48 TraesCS7A01G325600 chr6A 94.393 107 4 2 3331 3435 201248385 201248491 3.980000e-36 163.0
49 TraesCS7A01G325600 chr6D 98.876 89 1 0 3339 3427 85039235 85039147 5.150000e-35 159.0
50 TraesCS7A01G325600 chr6D 95.000 100 4 1 3335 3434 413065935 413065837 6.660000e-34 156.0
51 TraesCS7A01G325600 chr6D 88.889 54 5 1 879 931 184474632 184474579 1.150000e-06 65.8
52 TraesCS7A01G325600 chr3A 94.231 104 3 3 3322 3423 738131473 738131575 6.660000e-34 156.0
53 TraesCS7A01G325600 chr3A 88.889 54 5 1 879 931 378573363 378573310 1.150000e-06 65.8
54 TraesCS7A01G325600 chr1B 87.719 57 4 3 874 930 650046402 650046349 4.150000e-06 63.9


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 TraesCS7A01G325600 chr7A 473894154 473899120 4966 False 9173.0 9173 100.0000 1 4967 1 chr7A.!!$F3 4966
1 TraesCS7A01G325600 chr7A 634880355 634881229 874 False 1435.0 1435 96.4570 1 866 1 chr7A.!!$F4 865
2 TraesCS7A01G325600 chr7B 426857468 426860226 2758 False 2173.5 3759 94.4815 966 3813 2 chr7B.!!$F3 2847
3 TraesCS7A01G325600 chr7B 355799865 355800525 660 False 963.0 963 93.6460 4312 4945 1 chr7B.!!$F1 633
4 TraesCS7A01G325600 chr7B 568772747 568774211 1464 True 334.0 348 84.7315 2387 3122 2 chr7B.!!$R1 735
5 TraesCS7A01G325600 chr7D 412646049 412654043 7994 False 1437.0 3526 89.7315 940 4071 4 chr7D.!!$F1 3131
6 TraesCS7A01G325600 chr5A 649789852 649790763 911 False 1567.0 1567 97.8070 1 904 1 chr5A.!!$F1 903
7 TraesCS7A01G325600 chr3B 633294584 633295478 894 False 1367.0 1367 94.1820 1 903 1 chr3B.!!$F4 902
8 TraesCS7A01G325600 chr3B 707908044 707908638 594 False 920.0 920 94.7990 1 588 1 chr3B.!!$F5 587
9 TraesCS7A01G325600 chr3B 96747096 96747711 615 False 845.0 845 91.2500 4312 4945 1 chr3B.!!$F1 633
10 TraesCS7A01G325600 chr4B 104935502 104936418 916 True 1303.0 1303 92.2340 1 931 1 chr4B.!!$R1 930
11 TraesCS7A01G325600 chr2A 608781239 608781882 643 False 1105.0 1105 97.8260 4309 4945 1 chr2A.!!$F1 636
12 TraesCS7A01G325600 chr4A 241660254 241660901 647 True 1037.0 1037 95.8330 4309 4945 1 chr4A.!!$R1 636
13 TraesCS7A01G325600 chr3D 229365596 229366233 637 False 1016.0 1016 95.4900 4310 4945 1 chr3D.!!$F1 635
14 TraesCS7A01G325600 chr1A 516631856 516632516 660 True 957.0 957 93.4950 4312 4945 1 chr1A.!!$R1 633
15 TraesCS7A01G325600 chr5B 46616011 46616664 653 False 859.0 859 90.9230 4309 4945 1 chr5B.!!$F1 636
16 TraesCS7A01G325600 chr5B 634276126 634276957 831 True 542.5 691 90.6615 1 894 2 chr5B.!!$R1 893
17 TraesCS7A01G325600 chr2D 288158712 288159245 533 True 665.0 665 89.0510 348 894 1 chr2D.!!$R1 546
18 TraesCS7A01G325600 chr2B 738505690 738506516 826 False 523.5 664 91.3095 1 894 2 chr2B.!!$F1 893
19 TraesCS7A01G325600 chr4D 188966554 188967376 822 False 508.5 654 89.1705 1 894 2 chr4D.!!$F1 893
20 TraesCS7A01G325600 chr5D 560626481 560627225 744 True 496.5 621 90.8125 1 803 2 chr5D.!!$R1 802
21 TraesCS7A01G325600 chr1D 92968375 92969301 926 False 473.5 477 94.8480 4312 4945 2 chr1D.!!$F1 633

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
946 963 0.178903 TATAGAGGCCCCGGAGCATT 60.179 55.000 11.18 0.0 0.00 3.56 F
1543 1581 0.818445 CTGCATGAGGAGGCATGACC 60.818 60.000 8.40 0.0 46.64 4.02 F
2319 2357 1.066215 TGTGTTATCGACATGCTGGCT 60.066 47.619 0.00 0.0 41.10 4.75 F
2981 3771 0.467290 AACGGGGCTTGTTCATGTGT 60.467 50.000 0.00 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2303 0.392060 ACGTCGGTTTTATGCCCTCC 60.392 55.000 0.00 0.0 0.00 4.30 R
2964 3754 0.039256 CAACACATGAACAAGCCCCG 60.039 55.000 0.00 0.0 0.00 5.73 R
3406 4196 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.0 0.00 4.12 R
4429 5407 1.940613 GCCTAGGCCAAGTTTACATCG 59.059 52.381 24.19 0.0 34.56 3.84 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
454 466 7.367285 TGAAATACATGTTAAAGCAGAACCAC 58.633 34.615 2.30 0.00 0.00 4.16
910 927 6.371548 ACGGGCATTTGTGCTAGTATATTATG 59.628 38.462 0.07 0.00 34.73 1.90
936 953 9.862371 GTATGTACATATGCATATATAGAGGCC 57.138 37.037 18.70 0.00 36.05 5.19
937 954 7.303182 TGTACATATGCATATATAGAGGCCC 57.697 40.000 18.70 0.60 0.00 5.80
938 955 5.832539 ACATATGCATATATAGAGGCCCC 57.167 43.478 18.70 0.00 0.00 5.80
946 963 0.178903 TATAGAGGCCCCGGAGCATT 60.179 55.000 11.18 0.00 0.00 3.56
948 965 4.115199 GAGGCCCCGGAGCATTGT 62.115 66.667 11.18 0.00 0.00 2.71
955 972 0.880278 CCCGGAGCATTGTATCACCG 60.880 60.000 0.73 0.00 40.03 4.94
964 981 2.125269 GTATCACCGCACGGGCTT 60.125 61.111 8.62 0.00 40.62 4.35
967 984 1.966901 TATCACCGCACGGGCTTGAT 61.967 55.000 22.59 22.59 41.02 2.57
973 990 3.044059 GCACGGGCTTGATCACTGC 62.044 63.158 0.00 10.48 36.96 4.40
981 998 4.614946 GGGCTTGATCACTGCATATTTTC 58.385 43.478 18.07 3.08 0.00 2.29
990 1007 1.531149 CTGCATATTTTCCCCGTAGCG 59.469 52.381 0.00 0.00 0.00 4.26
1063 1083 1.476085 CTTCACCAATGCCGCCAATTA 59.524 47.619 0.00 0.00 0.00 1.40
1099 1119 3.127533 GCGCTGCCAATTCGACCT 61.128 61.111 0.00 0.00 0.00 3.85
1103 1123 1.604378 CTGCCAATTCGACCTCCCT 59.396 57.895 0.00 0.00 0.00 4.20
1172 1192 4.170062 CCAACGCTGCCGCATCAG 62.170 66.667 0.00 0.00 38.22 2.90
1173 1193 3.425713 CAACGCTGCCGCATCAGT 61.426 61.111 0.00 0.00 38.22 3.41
1174 1194 3.425713 AACGCTGCCGCATCAGTG 61.426 61.111 12.51 12.51 46.79 3.66
1176 1196 3.857854 CGCTGCCGCATCAGTGTC 61.858 66.667 0.00 0.00 39.16 3.67
1177 1197 2.743538 GCTGCCGCATCAGTGTCA 60.744 61.111 0.00 0.00 36.49 3.58
1183 1203 2.382746 CGCATCAGTGTCACCACCG 61.383 63.158 0.00 0.00 42.88 4.94
1197 1217 1.874019 CACCGCGTCCTCTTCATCG 60.874 63.158 4.92 0.00 0.00 3.84
1292 1312 2.628465 ATCCTCCTCCCCCTCCCA 60.628 66.667 0.00 0.00 0.00 4.37
1536 1574 1.817099 GTTCCGCTGCATGAGGAGG 60.817 63.158 0.00 0.00 45.21 4.30
1539 1577 2.203167 CGCTGCATGAGGAGGCAT 60.203 61.111 0.00 0.00 38.43 4.40
1543 1581 0.818445 CTGCATGAGGAGGCATGACC 60.818 60.000 8.40 0.00 46.64 4.02
1610 1648 4.619227 CAGGAACCGTGGTGGCGT 62.619 66.667 0.00 0.00 43.94 5.68
1677 1715 2.597903 GGGCTGGACAAGGATCCC 59.402 66.667 8.55 0.00 38.06 3.85
2050 2088 3.453353 TGATGATGCATGGAGAGTCTTCA 59.547 43.478 2.46 2.85 0.00 3.02
2062 2100 3.235195 AGAGTCTTCAATTCGAACGACG 58.765 45.455 0.00 0.00 44.09 5.12
2067 2105 2.914816 TCAATTCGAACGACGTTGTG 57.085 45.000 19.60 10.49 43.13 3.33
2088 2126 9.337396 GTTGTGGATGTAATATCCTACAATTCA 57.663 33.333 18.07 1.24 39.24 2.57
2307 2345 7.042051 ACGTATCAACATTATGCCTGTGTTATC 60.042 37.037 0.00 0.00 34.55 1.75
2319 2357 1.066215 TGTGTTATCGACATGCTGGCT 60.066 47.619 0.00 0.00 41.10 4.75
2385 2423 2.353109 GCCCTTTGAAGCTGAAACATCC 60.353 50.000 0.00 0.00 0.00 3.51
2436 2474 2.748461 AACACGGTGACATTGAAACG 57.252 45.000 16.29 0.00 0.00 3.60
2442 2480 1.135402 GGTGACATTGAAACGGGCATC 60.135 52.381 0.00 0.00 0.00 3.91
2796 3586 4.619760 TCACTACGTTATCACTGCGAAAAG 59.380 41.667 0.00 0.00 0.00 2.27
2964 3754 8.281212 ACCACAGGTTTCATCATTTCTATAAC 57.719 34.615 0.00 0.00 27.29 1.89
2981 3771 0.467290 AACGGGGCTTGTTCATGTGT 60.467 50.000 0.00 0.00 0.00 3.72
3186 3976 7.660030 ACATATTTATCCCTTTGACCCTTTG 57.340 36.000 0.00 0.00 0.00 2.77
3329 4119 6.365247 GTGTATACGATAGGTTTGGTATGCTG 59.635 42.308 0.00 0.00 43.77 4.41
3341 4131 7.888546 AGGTTTGGTATGCTGTTAGAAATTACT 59.111 33.333 0.00 0.00 0.00 2.24
3342 4132 8.182227 GGTTTGGTATGCTGTTAGAAATTACTC 58.818 37.037 0.00 0.00 0.00 2.59
3343 4133 7.859325 TTGGTATGCTGTTAGAAATTACTCC 57.141 36.000 0.00 0.00 0.00 3.85
3344 4134 6.354130 TGGTATGCTGTTAGAAATTACTCCC 58.646 40.000 0.00 0.00 0.00 4.30
3345 4135 6.157994 TGGTATGCTGTTAGAAATTACTCCCT 59.842 38.462 0.00 0.00 0.00 4.20
3346 4136 6.706716 GGTATGCTGTTAGAAATTACTCCCTC 59.293 42.308 0.00 0.00 0.00 4.30
3347 4137 6.567602 ATGCTGTTAGAAATTACTCCCTCT 57.432 37.500 0.00 0.00 0.00 3.69
3348 4138 5.734720 TGCTGTTAGAAATTACTCCCTCTG 58.265 41.667 0.00 0.00 0.00 3.35
3349 4139 5.248477 TGCTGTTAGAAATTACTCCCTCTGT 59.752 40.000 0.00 0.00 0.00 3.41
3350 4140 5.813157 GCTGTTAGAAATTACTCCCTCTGTC 59.187 44.000 0.00 0.00 0.00 3.51
3351 4141 6.295719 TGTTAGAAATTACTCCCTCTGTCC 57.704 41.667 0.00 0.00 0.00 4.02
3352 4142 5.189145 TGTTAGAAATTACTCCCTCTGTCCC 59.811 44.000 0.00 0.00 0.00 4.46
3353 4143 3.803340 AGAAATTACTCCCTCTGTCCCA 58.197 45.455 0.00 0.00 0.00 4.37
3354 4144 3.777522 AGAAATTACTCCCTCTGTCCCAG 59.222 47.826 0.00 0.00 0.00 4.45
3355 4145 3.491766 AATTACTCCCTCTGTCCCAGA 57.508 47.619 0.00 0.00 38.25 3.86
3356 4146 3.491766 ATTACTCCCTCTGTCCCAGAA 57.508 47.619 0.00 0.00 40.18 3.02
3357 4147 3.491766 TTACTCCCTCTGTCCCAGAAT 57.508 47.619 0.00 0.00 40.18 2.40
3358 4148 4.620086 TTACTCCCTCTGTCCCAGAATA 57.380 45.455 0.00 0.00 40.18 1.75
3359 4149 3.715648 ACTCCCTCTGTCCCAGAATAT 57.284 47.619 0.00 0.00 40.18 1.28
3360 4150 4.834406 ACTCCCTCTGTCCCAGAATATA 57.166 45.455 0.00 0.00 40.18 0.86
3361 4151 5.157770 ACTCCCTCTGTCCCAGAATATAA 57.842 43.478 0.00 0.00 40.18 0.98
3362 4152 5.151454 ACTCCCTCTGTCCCAGAATATAAG 58.849 45.833 0.00 0.00 40.18 1.73
3363 4153 5.103043 ACTCCCTCTGTCCCAGAATATAAGA 60.103 44.000 0.00 0.00 40.18 2.10
3364 4154 5.788430 TCCCTCTGTCCCAGAATATAAGAA 58.212 41.667 0.00 0.00 40.18 2.52
3365 4155 5.602978 TCCCTCTGTCCCAGAATATAAGAAC 59.397 44.000 0.00 0.00 40.18 3.01
3366 4156 5.509840 CCCTCTGTCCCAGAATATAAGAACG 60.510 48.000 0.00 0.00 40.18 3.95
3367 4157 5.069251 CCTCTGTCCCAGAATATAAGAACGT 59.931 44.000 0.00 0.00 40.18 3.99
3368 4158 6.407074 CCTCTGTCCCAGAATATAAGAACGTT 60.407 42.308 0.00 0.00 40.18 3.99
3369 4159 6.942976 TCTGTCCCAGAATATAAGAACGTTT 58.057 36.000 0.46 0.00 37.57 3.60
3370 4160 7.391620 TCTGTCCCAGAATATAAGAACGTTTT 58.608 34.615 0.46 0.00 37.57 2.43
3371 4161 7.881232 TCTGTCCCAGAATATAAGAACGTTTTT 59.119 33.333 9.22 9.22 37.57 1.94
3372 4162 7.812648 TGTCCCAGAATATAAGAACGTTTTTG 58.187 34.615 13.87 0.00 0.00 2.44
3373 4163 7.662258 TGTCCCAGAATATAAGAACGTTTTTGA 59.338 33.333 13.87 2.81 0.00 2.69
3374 4164 7.961283 GTCCCAGAATATAAGAACGTTTTTGAC 59.039 37.037 13.87 5.89 0.00 3.18
3375 4165 7.662258 TCCCAGAATATAAGAACGTTTTTGACA 59.338 33.333 13.87 0.01 0.00 3.58
3376 4166 7.749126 CCCAGAATATAAGAACGTTTTTGACAC 59.251 37.037 13.87 2.84 0.00 3.67
3377 4167 8.504005 CCAGAATATAAGAACGTTTTTGACACT 58.496 33.333 13.87 4.79 0.00 3.55
3381 4171 9.769093 AATATAAGAACGTTTTTGACACTATGC 57.231 29.630 13.87 0.00 0.00 3.14
3382 4172 5.751243 AAGAACGTTTTTGACACTATGCT 57.249 34.783 0.46 0.00 0.00 3.79
3383 4173 6.854496 AAGAACGTTTTTGACACTATGCTA 57.146 33.333 0.46 0.00 0.00 3.49
3384 4174 6.467723 AGAACGTTTTTGACACTATGCTAG 57.532 37.500 0.46 0.00 0.00 3.42
3385 4175 5.989777 AGAACGTTTTTGACACTATGCTAGT 59.010 36.000 0.46 0.00 40.28 2.57
3399 4189 7.958053 ACTATGCTAGTGTTAAAAACGTTCT 57.042 32.000 0.00 0.00 37.69 3.01
3400 4190 8.374327 ACTATGCTAGTGTTAAAAACGTTCTT 57.626 30.769 0.00 0.00 37.69 2.52
3401 4191 9.480053 ACTATGCTAGTGTTAAAAACGTTCTTA 57.520 29.630 0.00 0.00 37.69 2.10
3413 4203 9.609950 TTAAAAACGTTCTTATATTTTGGGACG 57.390 29.630 0.00 0.00 0.00 4.79
3414 4204 5.806366 AACGTTCTTATATTTTGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
3415 4205 5.088680 ACGTTCTTATATTTTGGGACGGA 57.911 39.130 0.00 0.00 0.00 4.69
3416 4206 5.114081 ACGTTCTTATATTTTGGGACGGAG 58.886 41.667 0.00 0.00 0.00 4.63
3417 4207 4.510340 CGTTCTTATATTTTGGGACGGAGG 59.490 45.833 0.00 0.00 0.00 4.30
3418 4208 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
3419 4209 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
3420 4210 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
3421 4211 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3422 4212 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3423 4213 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
3424 4214 0.178926 TTTGGGACGGAGGGAGTACA 60.179 55.000 0.00 0.00 0.00 2.90
3425 4215 0.042131 TTGGGACGGAGGGAGTACAT 59.958 55.000 0.00 0.00 0.00 2.29
3426 4216 0.686441 TGGGACGGAGGGAGTACATG 60.686 60.000 0.00 0.00 0.00 3.21
3454 4244 2.567615 TGGGTCTAAGCTCTTCCAAGAC 59.432 50.000 0.00 3.58 36.64 3.01
3523 4313 9.528018 TTGACAAAACTGGAAATAACAATCTTC 57.472 29.630 0.00 0.00 0.00 2.87
3532 4322 6.853872 TGGAAATAACAATCTTCGTTGTTTCG 59.146 34.615 9.88 0.00 46.96 3.46
3557 4347 6.131961 AGGGCAACATAATTCTTTGCTAGAT 58.868 36.000 14.70 1.61 44.18 1.98
3570 4360 7.928307 TCTTTGCTAGATTTGAAAGTATGCT 57.072 32.000 0.00 0.00 0.00 3.79
3571 4361 7.755591 TCTTTGCTAGATTTGAAAGTATGCTG 58.244 34.615 0.00 0.00 0.00 4.41
3683 4476 9.021807 AGTTACTAGCTGAATAGTTTACAGTGA 57.978 33.333 0.00 0.00 37.24 3.41
3703 4496 7.663081 ACAGTGATCTCAAGCTCTATTTTTCAA 59.337 33.333 0.00 0.00 0.00 2.69
3738 4532 4.082300 CAGTGCTATATTTGTTGTTGCCCA 60.082 41.667 0.00 0.00 0.00 5.36
3799 4597 8.814235 CGATTTCTTTACACGAAGGTACATAAT 58.186 33.333 0.00 0.00 0.00 1.28
3898 4702 1.808945 GCTTGATGTCTTCCACACTGG 59.191 52.381 0.00 0.00 38.04 4.00
3924 4732 7.246674 ACAAAGTATTCTGCAACCATATACG 57.753 36.000 0.00 0.00 0.00 3.06
3925 4733 5.924475 AAGTATTCTGCAACCATATACGC 57.076 39.130 0.00 0.00 0.00 4.42
3947 4755 5.343058 CGCAGTGTAAACAATCATTGGAAAG 59.657 40.000 1.58 0.00 34.12 2.62
3948 4756 5.634859 GCAGTGTAAACAATCATTGGAAAGG 59.365 40.000 1.58 0.00 34.12 3.11
3949 4757 5.634859 CAGTGTAAACAATCATTGGAAAGGC 59.365 40.000 1.58 0.00 34.12 4.35
3957 4765 1.559219 TCATTGGAAAGGCGGATGAGA 59.441 47.619 0.00 0.00 0.00 3.27
3964 4772 3.282885 GAAAGGCGGATGAGAGGAAAAT 58.717 45.455 0.00 0.00 0.00 1.82
3979 4787 9.605275 TGAGAGGAAAATAAGATGAACATACAG 57.395 33.333 0.00 0.00 0.00 2.74
3991 4799 7.177878 AGATGAACATACAGAAGTTTGGGATT 58.822 34.615 0.00 0.00 31.88 3.01
4000 4809 4.584325 CAGAAGTTTGGGATTTGTTGAGGA 59.416 41.667 0.00 0.00 0.00 3.71
4005 4814 1.780309 TGGGATTTGTTGAGGACTGGT 59.220 47.619 0.00 0.00 0.00 4.00
4035 4844 8.713737 AACATATAATGGATCTGTGATCGATG 57.286 34.615 0.54 0.00 33.60 3.84
4036 4845 7.845037 ACATATAATGGATCTGTGATCGATGT 58.155 34.615 0.54 0.00 33.60 3.06
4037 4846 8.316946 ACATATAATGGATCTGTGATCGATGTT 58.683 33.333 0.54 0.00 33.60 2.71
4040 4849 3.524541 TGGATCTGTGATCGATGTTGTG 58.475 45.455 0.54 0.00 0.00 3.33
4055 4865 6.204688 TCGATGTTGTGCTAGAGAAAATTGTT 59.795 34.615 0.00 0.00 0.00 2.83
4058 4868 9.846248 GATGTTGTGCTAGAGAAAATTGTTTAT 57.154 29.630 0.00 0.00 0.00 1.40
4077 4887 9.509956 TTGTTTATATGTAGCTGTTTACAAGGT 57.490 29.630 0.00 0.00 37.13 3.50
4090 4955 8.137437 GCTGTTTACAAGGTGAATAATATGCAT 58.863 33.333 3.79 3.79 0.00 3.96
4102 4967 9.958285 GTGAATAATATGCATACAGTATTCACG 57.042 33.333 32.92 0.00 42.08 4.35
4158 5032 5.574891 TTGTATTTCACAAGTGCACTGTT 57.425 34.783 22.49 7.46 42.29 3.16
4175 5049 6.559042 CACTGTTGCAAAAGTAAGTTTCTG 57.441 37.500 21.83 3.70 0.00 3.02
4177 5051 6.806249 CACTGTTGCAAAAGTAAGTTTCTGAA 59.194 34.615 21.83 0.00 0.00 3.02
4179 5053 6.096695 TGTTGCAAAAGTAAGTTTCTGAACC 58.903 36.000 0.00 0.00 36.39 3.62
4180 5054 6.071616 TGTTGCAAAAGTAAGTTTCTGAACCT 60.072 34.615 0.00 0.00 36.39 3.50
4181 5055 7.121463 TGTTGCAAAAGTAAGTTTCTGAACCTA 59.879 33.333 0.00 0.00 36.39 3.08
4182 5056 7.259290 TGCAAAAGTAAGTTTCTGAACCTAG 57.741 36.000 0.00 0.00 36.39 3.02
4184 5058 7.719633 TGCAAAAGTAAGTTTCTGAACCTAGAT 59.280 33.333 0.00 0.00 36.39 1.98
4185 5059 8.568794 GCAAAAGTAAGTTTCTGAACCTAGATT 58.431 33.333 0.00 0.00 36.39 2.40
4229 5103 8.929260 ATTTCATATTTGAGGCAGATACATGA 57.071 30.769 0.00 0.00 32.27 3.07
4277 5152 9.479549 AAATTCACATCATCTATTGGGTAAAGT 57.520 29.630 0.00 0.00 0.00 2.66
4281 5156 6.974622 CACATCATCTATTGGGTAAAGTTTGC 59.025 38.462 0.00 0.00 0.00 3.68
4301 5176 6.875948 TTGCTAGTTTCAGTAAAAGATGCA 57.124 33.333 0.00 0.00 0.00 3.96
4303 5178 6.845302 TGCTAGTTTCAGTAAAAGATGCATG 58.155 36.000 2.46 0.00 0.00 4.06
4306 5181 7.905493 GCTAGTTTCAGTAAAAGATGCATGTAC 59.095 37.037 2.46 1.05 0.00 2.90
4429 5407 7.012799 GGTGGATTTCATTCTAAGATTCCAGAC 59.987 40.741 0.00 0.00 31.97 3.51
4912 9536 1.594833 CACACCCCGGAAGATCGAA 59.405 57.895 0.73 0.00 0.00 3.71
4935 9559 0.533308 TTTGTGGTACGTGGTCAGCC 60.533 55.000 0.00 0.00 0.00 4.85
4945 9569 2.740055 GGTCAGCCTGTCTGCGTG 60.740 66.667 0.00 0.00 42.56 5.34
4946 9570 3.418068 GTCAGCCTGTCTGCGTGC 61.418 66.667 0.00 0.00 42.56 5.34
4947 9571 3.927548 TCAGCCTGTCTGCGTGCA 61.928 61.111 0.00 0.00 42.56 4.57
4948 9572 2.974148 CAGCCTGTCTGCGTGCAA 60.974 61.111 0.00 0.00 35.78 4.08
4949 9573 2.667536 AGCCTGTCTGCGTGCAAG 60.668 61.111 0.00 0.00 36.02 4.01
4950 9574 2.666190 GCCTGTCTGCGTGCAAGA 60.666 61.111 2.99 0.00 0.00 3.02
4951 9575 2.959357 GCCTGTCTGCGTGCAAGAC 61.959 63.158 9.64 9.64 0.00 3.01
4952 9576 1.301244 CCTGTCTGCGTGCAAGACT 60.301 57.895 16.02 0.00 34.03 3.24
4953 9577 0.038251 CCTGTCTGCGTGCAAGACTA 60.038 55.000 16.02 4.49 34.03 2.59
4954 9578 1.404717 CCTGTCTGCGTGCAAGACTAT 60.405 52.381 16.02 0.00 34.03 2.12
4956 9580 2.068519 TGTCTGCGTGCAAGACTATTG 58.931 47.619 16.02 0.00 34.03 1.90
4957 9581 2.288763 TGTCTGCGTGCAAGACTATTGA 60.289 45.455 16.02 0.00 34.03 2.57
4959 9583 4.112634 GTCTGCGTGCAAGACTATTGATA 58.887 43.478 2.99 0.00 0.00 2.15
4960 9584 4.208047 GTCTGCGTGCAAGACTATTGATAG 59.792 45.833 2.99 0.00 36.46 2.08
4961 9585 4.097892 TCTGCGTGCAAGACTATTGATAGA 59.902 41.667 2.99 0.00 34.50 1.98
4962 9586 4.112634 TGCGTGCAAGACTATTGATAGAC 58.887 43.478 2.99 0.00 34.50 2.59
4963 9587 4.112634 GCGTGCAAGACTATTGATAGACA 58.887 43.478 2.99 0.00 34.50 3.41
4964 9588 4.026475 GCGTGCAAGACTATTGATAGACAC 60.026 45.833 2.99 4.69 34.50 3.67
4965 9589 5.344066 CGTGCAAGACTATTGATAGACACT 58.656 41.667 5.08 0.00 34.50 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
431 443 7.370383 CAGTGGTTCTGCTTTAACATGTATTT 58.630 34.615 0.00 0.00 37.36 1.40
520 532 2.187958 TCAGACTCCAATACCAGGTGG 58.812 52.381 0.76 0.00 42.17 4.61
858 874 6.225318 GTTGCCACGGATATAGGTTACAATA 58.775 40.000 0.00 0.00 0.00 1.90
910 927 9.862371 GGCCTCTATATATGCATATGTACATAC 57.138 37.037 26.21 12.30 31.87 2.39
914 931 6.572509 CGGGGCCTCTATATATGCATATGTAC 60.573 46.154 26.21 12.97 0.00 2.90
917 934 4.323028 CCGGGGCCTCTATATATGCATATG 60.323 50.000 26.21 11.98 0.00 1.78
922 939 1.689273 CTCCGGGGCCTCTATATATGC 59.311 57.143 0.00 0.00 0.00 3.14
923 940 1.689273 GCTCCGGGGCCTCTATATATG 59.311 57.143 18.17 0.00 0.00 1.78
931 948 2.056906 ATACAATGCTCCGGGGCCTC 62.057 60.000 26.97 0.00 0.00 4.70
932 949 2.056906 GATACAATGCTCCGGGGCCT 62.057 60.000 26.97 12.35 0.00 5.19
933 950 1.600916 GATACAATGCTCCGGGGCC 60.601 63.158 26.97 6.29 0.00 5.80
934 951 1.148273 TGATACAATGCTCCGGGGC 59.852 57.895 22.87 22.87 0.00 5.80
935 952 0.535102 GGTGATACAATGCTCCGGGG 60.535 60.000 0.00 0.00 0.00 5.73
936 953 0.880278 CGGTGATACAATGCTCCGGG 60.880 60.000 0.00 0.00 37.47 5.73
937 954 1.498865 GCGGTGATACAATGCTCCGG 61.499 60.000 0.00 0.00 40.42 5.14
938 955 0.809636 TGCGGTGATACAATGCTCCG 60.810 55.000 0.00 0.00 42.29 4.63
946 963 2.949909 AAGCCCGTGCGGTGATACA 61.950 57.895 9.90 0.00 44.33 2.29
948 965 1.966901 ATCAAGCCCGTGCGGTGATA 61.967 55.000 11.75 0.00 42.02 2.15
955 972 3.044059 GCAGTGATCAAGCCCGTGC 62.044 63.158 9.64 3.59 37.95 5.34
964 981 3.213506 CGGGGAAAATATGCAGTGATCA 58.786 45.455 0.00 0.00 0.00 2.92
967 984 2.799126 ACGGGGAAAATATGCAGTGA 57.201 45.000 0.00 0.00 0.00 3.41
973 990 3.463944 AGTTCGCTACGGGGAAAATATG 58.536 45.455 0.00 0.00 44.06 1.78
981 998 3.186047 CGCAAGTTCGCTACGGGG 61.186 66.667 0.00 0.00 0.00 5.73
990 1007 3.485743 GTGGACAAAACATTCGCAAGTTC 59.514 43.478 0.00 0.00 39.48 3.01
1032 1049 0.323629 TTGGTGAAGGAAGGCTACCG 59.676 55.000 0.00 0.00 34.16 4.02
1063 1083 0.328258 CACGGGGTTGGAGGAAGAAT 59.672 55.000 0.00 0.00 0.00 2.40
1090 1110 2.064581 CGGGGAGGGAGGTCGAATT 61.065 63.158 0.00 0.00 0.00 2.17
1173 1193 3.986006 GAGGACGCGGTGGTGACA 61.986 66.667 12.47 0.00 38.70 3.58
1174 1194 3.222354 AAGAGGACGCGGTGGTGAC 62.222 63.158 12.47 0.00 0.00 3.67
1175 1195 2.915659 AAGAGGACGCGGTGGTGA 60.916 61.111 12.47 0.00 0.00 4.02
1176 1196 2.432628 GAAGAGGACGCGGTGGTG 60.433 66.667 12.47 0.00 0.00 4.17
1177 1197 2.227089 GATGAAGAGGACGCGGTGGT 62.227 60.000 12.47 0.00 0.00 4.16
1183 1203 2.579684 AAGGCCGATGAAGAGGACGC 62.580 60.000 0.00 0.00 41.45 5.19
1419 1457 0.391661 CCATCCTGTCGAACACCTGG 60.392 60.000 0.00 0.00 0.00 4.45
1421 1459 1.296715 GCCATCCTGTCGAACACCT 59.703 57.895 0.00 0.00 0.00 4.00
1610 1648 1.664649 CCGAGTTCTTGCACGCAGA 60.665 57.895 0.00 0.00 0.00 4.26
1650 1688 3.820425 TCCAGCCCGGATTTGACT 58.180 55.556 0.73 0.00 39.64 3.41
2050 2088 1.855513 TCCACAACGTCGTTCGAATT 58.144 45.000 7.86 0.00 42.86 2.17
2062 2100 9.337396 TGAATTGTAGGATATTACATCCACAAC 57.663 33.333 16.44 8.75 39.52 3.32
2088 2126 2.235402 CTGCCCAAGAGCCAAAATCATT 59.765 45.455 0.00 0.00 0.00 2.57
2117 2155 0.951558 TTCAACTGCTTCTTTCGGGC 59.048 50.000 0.00 0.00 0.00 6.13
2224 2262 7.546358 TCGAATAAATGCAAACCTTCATGAAT 58.454 30.769 8.96 0.00 0.00 2.57
2265 2303 0.392060 ACGTCGGTTTTATGCCCTCC 60.392 55.000 0.00 0.00 0.00 4.30
2268 2306 2.553086 TGATACGTCGGTTTTATGCCC 58.447 47.619 0.00 0.00 0.00 5.36
2307 2345 1.213733 CTGATCGAGCCAGCATGTCG 61.214 60.000 0.00 0.00 34.98 4.35
2385 2423 4.096984 GCACCAAGAACAATCCTCCATAAG 59.903 45.833 0.00 0.00 0.00 1.73
2436 2474 3.454375 CATTTCTGCAATCTTGATGCCC 58.546 45.455 0.00 0.00 43.16 5.36
2796 3586 1.301953 CCCAAAAGCAAAGGCCAGC 60.302 57.895 5.01 6.06 42.56 4.85
2964 3754 0.039256 CAACACATGAACAAGCCCCG 60.039 55.000 0.00 0.00 0.00 5.73
2981 3771 9.645128 ATTTACTGATCCATCACCAATAATCAA 57.355 29.630 0.00 0.00 32.50 2.57
3186 3976 8.863049 CAGCAAGAAAATATTGACCAAATGTAC 58.137 33.333 0.00 0.00 0.00 2.90
3283 4073 6.265577 ACACGACCTTCTCAAGAAAATTTTG 58.734 36.000 8.47 0.00 33.07 2.44
3284 4074 6.451064 ACACGACCTTCTCAAGAAAATTTT 57.549 33.333 2.28 2.28 33.07 1.82
3323 4113 7.125811 ACAGAGGGAGTAATTTCTAACAGCATA 59.874 37.037 0.00 0.00 0.00 3.14
3329 4119 5.189145 TGGGACAGAGGGAGTAATTTCTAAC 59.811 44.000 0.00 0.00 0.00 2.34
3347 4137 7.662258 TCAAAAACGTTCTTATATTCTGGGACA 59.338 33.333 0.00 0.00 0.00 4.02
3348 4138 7.961283 GTCAAAAACGTTCTTATATTCTGGGAC 59.039 37.037 0.00 0.00 0.00 4.46
3349 4139 7.662258 TGTCAAAAACGTTCTTATATTCTGGGA 59.338 33.333 0.00 0.00 0.00 4.37
3350 4140 7.749126 GTGTCAAAAACGTTCTTATATTCTGGG 59.251 37.037 0.00 0.00 0.00 4.45
3351 4141 8.504005 AGTGTCAAAAACGTTCTTATATTCTGG 58.496 33.333 0.00 0.00 0.00 3.86
3355 4145 9.769093 GCATAGTGTCAAAAACGTTCTTATATT 57.231 29.630 0.00 0.00 0.00 1.28
3356 4146 9.162764 AGCATAGTGTCAAAAACGTTCTTATAT 57.837 29.630 0.00 0.00 0.00 0.86
3357 4147 8.542497 AGCATAGTGTCAAAAACGTTCTTATA 57.458 30.769 0.00 0.00 0.00 0.98
3358 4148 7.435068 AGCATAGTGTCAAAAACGTTCTTAT 57.565 32.000 0.00 0.00 0.00 1.73
3359 4149 6.854496 AGCATAGTGTCAAAAACGTTCTTA 57.146 33.333 0.00 0.00 0.00 2.10
3360 4150 5.751243 AGCATAGTGTCAAAAACGTTCTT 57.249 34.783 0.00 0.00 0.00 2.52
3361 4151 6.467723 CTAGCATAGTGTCAAAAACGTTCT 57.532 37.500 0.00 0.00 32.85 3.01
3387 4177 9.609950 CGTCCCAAAATATAAGAACGTTTTTAA 57.390 29.630 14.41 5.85 0.00 1.52
3388 4178 8.235905 CCGTCCCAAAATATAAGAACGTTTTTA 58.764 33.333 13.02 13.02 0.00 1.52
3389 4179 7.040548 TCCGTCCCAAAATATAAGAACGTTTTT 60.041 33.333 9.22 9.22 0.00 1.94
3390 4180 6.430616 TCCGTCCCAAAATATAAGAACGTTTT 59.569 34.615 0.46 0.00 0.00 2.43
3391 4181 5.939296 TCCGTCCCAAAATATAAGAACGTTT 59.061 36.000 0.46 0.00 0.00 3.60
3392 4182 5.490159 TCCGTCCCAAAATATAAGAACGTT 58.510 37.500 0.00 0.00 0.00 3.99
3393 4183 5.088680 TCCGTCCCAAAATATAAGAACGT 57.911 39.130 0.00 0.00 0.00 3.99
3394 4184 4.510340 CCTCCGTCCCAAAATATAAGAACG 59.490 45.833 0.00 0.00 0.00 3.95
3395 4185 4.820173 CCCTCCGTCCCAAAATATAAGAAC 59.180 45.833 0.00 0.00 0.00 3.01
3396 4186 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
3397 4187 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
3398 4188 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
3399 4189 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
3400 4190 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
3401 4191 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
3402 4192 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3403 4193 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3404 4194 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3405 4195 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
3406 4196 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
3407 4197 0.686441 CATGTACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
3408 4198 0.396695 TCATGTACTCCCTCCGTCCC 60.397 60.000 0.00 0.00 0.00 4.46
3409 4199 1.705873 ATCATGTACTCCCTCCGTCC 58.294 55.000 0.00 0.00 0.00 4.79
3410 4200 4.337145 AGATATCATGTACTCCCTCCGTC 58.663 47.826 5.32 0.00 0.00 4.79
3411 4201 4.390129 AGATATCATGTACTCCCTCCGT 57.610 45.455 5.32 0.00 0.00 4.69
3412 4202 4.081972 CCAAGATATCATGTACTCCCTCCG 60.082 50.000 5.32 0.00 0.00 4.63
3413 4203 4.223923 CCCAAGATATCATGTACTCCCTCC 59.776 50.000 5.32 0.00 0.00 4.30
3414 4204 4.841246 ACCCAAGATATCATGTACTCCCTC 59.159 45.833 5.32 0.00 0.00 4.30
3415 4205 4.832492 ACCCAAGATATCATGTACTCCCT 58.168 43.478 5.32 0.00 0.00 4.20
3416 4206 4.841246 AGACCCAAGATATCATGTACTCCC 59.159 45.833 5.32 0.00 0.00 4.30
3417 4207 7.540474 TTAGACCCAAGATATCATGTACTCC 57.460 40.000 5.32 0.00 0.00 3.85
3418 4208 7.039363 AGCTTAGACCCAAGATATCATGTACTC 60.039 40.741 5.32 0.00 0.00 2.59
3419 4209 6.784969 AGCTTAGACCCAAGATATCATGTACT 59.215 38.462 5.32 5.07 0.00 2.73
3420 4210 6.998802 AGCTTAGACCCAAGATATCATGTAC 58.001 40.000 5.32 0.00 0.00 2.90
3421 4211 7.013220 AGAGCTTAGACCCAAGATATCATGTA 58.987 38.462 5.32 0.00 0.00 2.29
3422 4212 5.843421 AGAGCTTAGACCCAAGATATCATGT 59.157 40.000 5.32 0.00 0.00 3.21
3423 4213 6.357579 AGAGCTTAGACCCAAGATATCATG 57.642 41.667 5.32 2.94 0.00 3.07
3424 4214 6.013812 GGAAGAGCTTAGACCCAAGATATCAT 60.014 42.308 5.32 0.00 0.00 2.45
3425 4215 5.305644 GGAAGAGCTTAGACCCAAGATATCA 59.694 44.000 5.32 0.00 0.00 2.15
3426 4216 5.305644 TGGAAGAGCTTAGACCCAAGATATC 59.694 44.000 0.00 0.00 0.00 1.63
3454 4244 8.688747 ATATGCCTTCTCATTTTCTCCTAAAG 57.311 34.615 0.00 0.00 0.00 1.85
3523 4313 0.591170 ATGTTGCCCTCGAAACAACG 59.409 50.000 15.80 0.00 45.18 4.10
3656 4449 9.291664 CACTGTAAACTATTCAGCTAGTAACTC 57.708 37.037 0.00 0.00 31.70 3.01
3679 4472 8.804912 ATTGAAAAATAGAGCTTGAGATCACT 57.195 30.769 0.00 0.00 31.88 3.41
3728 4522 5.741510 GCTTTAAACATTTTTGGGCAACAAC 59.258 36.000 0.00 0.00 39.19 3.32
3855 4659 5.390991 GCTCGAAAAGACCTGAAACTAATGG 60.391 44.000 0.00 0.00 0.00 3.16
3898 4702 7.850982 CGTATATGGTTGCAGAATACTTTGTTC 59.149 37.037 0.00 0.00 0.00 3.18
3924 4732 5.634859 CCTTTCCAATGATTGTTTACACTGC 59.365 40.000 4.27 0.00 0.00 4.40
3925 4733 5.634859 GCCTTTCCAATGATTGTTTACACTG 59.365 40.000 4.27 0.00 0.00 3.66
3947 4755 4.073293 TCTTATTTTCCTCTCATCCGCC 57.927 45.455 0.00 0.00 0.00 6.13
3948 4756 5.300752 TCATCTTATTTTCCTCTCATCCGC 58.699 41.667 0.00 0.00 0.00 5.54
3949 4757 6.763135 TGTTCATCTTATTTTCCTCTCATCCG 59.237 38.462 0.00 0.00 0.00 4.18
3957 4765 9.965902 ACTTCTGTATGTTCATCTTATTTTCCT 57.034 29.630 0.00 0.00 0.00 3.36
3964 4772 7.685481 TCCCAAACTTCTGTATGTTCATCTTA 58.315 34.615 0.00 0.00 0.00 2.10
3977 4785 4.584325 TCCTCAACAAATCCCAAACTTCTG 59.416 41.667 0.00 0.00 0.00 3.02
3978 4786 4.584743 GTCCTCAACAAATCCCAAACTTCT 59.415 41.667 0.00 0.00 0.00 2.85
3979 4787 4.584743 AGTCCTCAACAAATCCCAAACTTC 59.415 41.667 0.00 0.00 0.00 3.01
4026 4835 4.033990 TCTCTAGCACAACATCGATCAC 57.966 45.455 0.00 0.00 0.00 3.06
4032 4841 9.846248 ATAAACAATTTTCTCTAGCACAACATC 57.154 29.630 0.00 0.00 0.00 3.06
4055 4865 9.899661 ATTCACCTTGTAAACAGCTACATATAA 57.100 29.630 0.00 0.00 31.96 0.98
4058 4868 9.899661 ATTATTCACCTTGTAAACAGCTACATA 57.100 29.630 0.00 0.00 31.96 2.29
4077 4887 9.921637 TCGTGAATACTGTATGCATATTATTCA 57.078 29.630 25.91 25.91 33.31 2.57
4097 4962 9.906660 AATGCAAAATATTTCTTAACTCGTGAA 57.093 25.926 0.10 0.00 0.00 3.18
4152 5026 6.321717 TCAGAAACTTACTTTTGCAACAGTG 58.678 36.000 24.95 13.57 0.00 3.66
4156 5030 6.330278 AGGTTCAGAAACTTACTTTTGCAAC 58.670 36.000 0.00 0.00 35.61 4.17
4157 5031 6.524101 AGGTTCAGAAACTTACTTTTGCAA 57.476 33.333 0.00 0.00 35.61 4.08
4158 5032 7.051623 TCTAGGTTCAGAAACTTACTTTTGCA 58.948 34.615 5.89 0.00 35.61 4.08
4194 5068 9.857656 TGCCTCAAATATGAAATTTCTAGATCT 57.142 29.630 18.64 0.00 34.49 2.75
4196 5070 9.857656 TCTGCCTCAAATATGAAATTTCTAGAT 57.142 29.630 18.64 7.16 34.49 1.98
4197 5071 9.857656 ATCTGCCTCAAATATGAAATTTCTAGA 57.142 29.630 18.64 4.94 34.49 2.43
4200 5074 9.412460 TGTATCTGCCTCAAATATGAAATTTCT 57.588 29.630 18.64 7.42 34.49 2.52
4202 5076 9.976511 CATGTATCTGCCTCAAATATGAAATTT 57.023 29.630 0.00 0.00 34.49 1.82
4203 5077 9.358406 TCATGTATCTGCCTCAAATATGAAATT 57.642 29.630 0.00 0.00 34.49 1.82
4204 5078 8.790718 GTCATGTATCTGCCTCAAATATGAAAT 58.209 33.333 0.00 0.00 34.49 2.17
4268 5142 5.442391 ACTGAAACTAGCAAACTTTACCCA 58.558 37.500 0.00 0.00 0.00 4.51
4269 5143 7.500720 TTACTGAAACTAGCAAACTTTACCC 57.499 36.000 0.00 0.00 0.00 3.69
4270 5144 9.447040 CTTTTACTGAAACTAGCAAACTTTACC 57.553 33.333 0.00 0.00 0.00 2.85
4277 5152 7.270757 TGCATCTTTTACTGAAACTAGCAAA 57.729 32.000 0.00 0.00 0.00 3.68
4281 5156 8.110612 CGTACATGCATCTTTTACTGAAACTAG 58.889 37.037 0.00 0.00 0.00 2.57
4429 5407 1.940613 GCCTAGGCCAAGTTTACATCG 59.059 52.381 24.19 0.00 34.56 3.84
4727 6014 3.265995 GGGAGAACCTACCAGGATTTGAA 59.734 47.826 0.00 0.00 37.67 2.69
4912 9536 2.940410 CTGACCACGTACCACAAAAAGT 59.060 45.455 0.00 0.00 0.00 2.66
4935 9559 2.001812 ATAGTCTTGCACGCAGACAG 57.998 50.000 17.14 0.00 35.23 3.51


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

AutoCloner maintained by Alex Coulton.