Multiple sequence alignment - TraesCS1A01G204600

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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 TraesCS1A01G204600 chr1A 100.000 2354 0 0 1 2354 366366520 366368873 0.000000e+00 4348
1 TraesCS1A01G204600 chr1A 92.000 400 28 2 1242 1640 366299426 366299822 2.040000e-155 558
2 TraesCS1A01G204600 chr1A 81.818 506 63 19 182 673 366296148 366296638 4.710000e-107 398
3 TraesCS1A01G204600 chr1A 76.198 647 147 6 935 1579 366276869 366277510 3.750000e-88 335
4 TraesCS1A01G204600 chr1A 98.165 109 2 0 674 782 385269113 385269221 8.590000e-45 191
5 TraesCS1A01G204600 chr1A 99.038 104 1 0 674 777 558592180 558592077 1.110000e-43 187
6 TraesCS1A01G204600 chr1A 99.038 104 1 0 674 777 585628430 585628327 1.110000e-43 187
7 TraesCS1A01G204600 chr1A 94.118 85 4 1 63 147 565296911 565296994 6.830000e-26 128
8 TraesCS1A01G204600 chr1B 93.410 865 48 6 778 1640 395309913 395310770 0.000000e+00 1273
9 TraesCS1A01G204600 chr1B 88.050 887 77 16 778 1640 395276699 395277580 0.000000e+00 1024
10 TraesCS1A01G204600 chr1B 93.991 466 16 1 220 673 395309456 395309921 0.000000e+00 695
11 TraesCS1A01G204600 chr1B 82.087 508 62 20 181 673 395276214 395276707 7.830000e-110 407
12 TraesCS1A01G204600 chr1B 76.579 649 137 13 935 1577 395259576 395260215 2.240000e-90 342
13 TraesCS1A01G204600 chr1B 93.103 87 5 1 1613 1699 395307402 395307487 2.460000e-25 126
14 TraesCS1A01G204600 chr1D 92.857 868 47 8 778 1640 293949207 293950064 0.000000e+00 1245
15 TraesCS1A01G204600 chr1D 88.383 878 79 14 778 1640 293933622 293934491 0.000000e+00 1035
16 TraesCS1A01G204600 chr1D 91.653 599 38 6 1768 2354 255182188 255182786 0.000000e+00 819
17 TraesCS1A01G204600 chr1D 92.401 579 34 5 1786 2354 429956643 429956065 0.000000e+00 817
18 TraesCS1A01G204600 chr1D 92.969 512 22 3 175 673 293948705 293949215 0.000000e+00 734
19 TraesCS1A01G204600 chr1D 82.222 495 61 18 192 673 293933150 293933630 3.640000e-108 401
20 TraesCS1A01G204600 chr1D 77.006 648 136 11 935 1577 293914641 293915280 2.220000e-95 359
21 TraesCS1A01G204600 chr5D 93.080 578 31 5 1786 2354 371395087 371394510 0.000000e+00 837
22 TraesCS1A01G204600 chr5D 91.833 600 36 7 1768 2354 358045818 358046417 0.000000e+00 824
23 TraesCS1A01G204600 chr5D 83.882 304 49 0 1224 1527 506949634 506949937 8.230000e-75 291
24 TraesCS1A01G204600 chr7D 91.472 598 39 8 1768 2354 483345686 483346282 0.000000e+00 811
25 TraesCS1A01G204600 chr6D 91.472 598 40 6 1768 2354 318494392 318494989 0.000000e+00 811
26 TraesCS1A01G204600 chr3D 91.457 597 38 6 1771 2354 341417788 341417192 0.000000e+00 808
27 TraesCS1A01G204600 chr2D 92.096 582 33 6 1786 2354 143785119 143784538 0.000000e+00 808
28 TraesCS1A01G204600 chr2D 92.096 582 32 7 1786 2354 159273812 159273232 0.000000e+00 808
29 TraesCS1A01G204600 chr2D 91.765 85 6 1 63 147 606423203 606423120 1.480000e-22 117
30 TraesCS1A01G204600 chr5A 97.279 147 3 1 1 147 100765270 100765415 5.020000e-62 248
31 TraesCS1A01G204600 chr5A 99.038 104 1 0 674 777 480125000 480124897 1.110000e-43 187
32 TraesCS1A01G204600 chr5A 99.038 104 1 0 674 777 531614580 531614683 1.110000e-43 187
33 TraesCS1A01G204600 chr2B 90.184 163 12 4 1 162 46739364 46739523 2.370000e-50 209
34 TraesCS1A01G204600 chr2B 99.057 106 1 0 674 779 259029446 259029341 8.590000e-45 191
35 TraesCS1A01G204600 chr2B 93.103 116 7 1 47 162 46738759 46738873 4.020000e-38 169
36 TraesCS1A01G204600 chr5B 95.763 118 3 2 673 788 688104332 688104215 3.090000e-44 189
37 TraesCS1A01G204600 chr3A 99.048 105 1 0 673 777 13241599 13241703 3.090000e-44 189
38 TraesCS1A01G204600 chr3A 89.474 95 8 2 104 198 61243067 61243159 4.110000e-23 119
39 TraesCS1A01G204600 chr7B 98.113 106 2 0 672 777 275706900 275706795 4.000000e-43 185
40 TraesCS1A01G204600 chr2A 88.281 128 13 2 63 190 706905511 706905386 4.050000e-33 152
41 TraesCS1A01G204600 chr3B 87.407 135 9 7 63 190 459780157 459780024 5.240000e-32 148
42 TraesCS1A01G204600 chr6A 82.895 152 20 5 42 190 591099186 591099334 5.280000e-27 132
43 TraesCS1A01G204600 chr7A 83.704 135 14 7 63 190 658988189 658988056 1.140000e-23 121


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 TraesCS1A01G204600 chr1A 366366520 366368873 2353 False 4348.0 4348 100.000000 1 2354 1 chr1A.!!$F2 2353
1 TraesCS1A01G204600 chr1A 366296148 366299822 3674 False 478.0 558 86.909000 182 1640 2 chr1A.!!$F5 1458
2 TraesCS1A01G204600 chr1A 366276869 366277510 641 False 335.0 335 76.198000 935 1579 1 chr1A.!!$F1 644
3 TraesCS1A01G204600 chr1B 395276214 395277580 1366 False 715.5 1024 85.068500 181 1640 2 chr1B.!!$F2 1459
4 TraesCS1A01G204600 chr1B 395307402 395310770 3368 False 698.0 1273 93.501333 220 1699 3 chr1B.!!$F3 1479
5 TraesCS1A01G204600 chr1B 395259576 395260215 639 False 342.0 342 76.579000 935 1577 1 chr1B.!!$F1 642
6 TraesCS1A01G204600 chr1D 293948705 293950064 1359 False 989.5 1245 92.913000 175 1640 2 chr1D.!!$F4 1465
7 TraesCS1A01G204600 chr1D 255182188 255182786 598 False 819.0 819 91.653000 1768 2354 1 chr1D.!!$F1 586
8 TraesCS1A01G204600 chr1D 429956065 429956643 578 True 817.0 817 92.401000 1786 2354 1 chr1D.!!$R1 568
9 TraesCS1A01G204600 chr1D 293933150 293934491 1341 False 718.0 1035 85.302500 192 1640 2 chr1D.!!$F3 1448
10 TraesCS1A01G204600 chr1D 293914641 293915280 639 False 359.0 359 77.006000 935 1577 1 chr1D.!!$F2 642
11 TraesCS1A01G204600 chr5D 371394510 371395087 577 True 837.0 837 93.080000 1786 2354 1 chr5D.!!$R1 568
12 TraesCS1A01G204600 chr5D 358045818 358046417 599 False 824.0 824 91.833000 1768 2354 1 chr5D.!!$F1 586
13 TraesCS1A01G204600 chr7D 483345686 483346282 596 False 811.0 811 91.472000 1768 2354 1 chr7D.!!$F1 586
14 TraesCS1A01G204600 chr6D 318494392 318494989 597 False 811.0 811 91.472000 1768 2354 1 chr6D.!!$F1 586
15 TraesCS1A01G204600 chr3D 341417192 341417788 596 True 808.0 808 91.457000 1771 2354 1 chr3D.!!$R1 583
16 TraesCS1A01G204600 chr2D 143784538 143785119 581 True 808.0 808 92.096000 1786 2354 1 chr2D.!!$R1 568
17 TraesCS1A01G204600 chr2D 159273232 159273812 580 True 808.0 808 92.096000 1786 2354 1 chr2D.!!$R2 568

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
67 68 0.10852 CTTGGCTCCGCGGTTTAGTA 60.109 55.0 27.15 2.82 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 6150 0.606096 GTGCGGGGGCTAAAAACAAT 59.394 50.0 0.0 0.0 0.0 2.71 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.712057 GTACGACCCAAAGAGAACGA 57.288 50.000 0.00 0.00 0.00 3.85
20 21 3.017265 GTACGACCCAAAGAGAACGAA 57.983 47.619 0.00 0.00 0.00 3.85
21 22 1.861971 ACGACCCAAAGAGAACGAAC 58.138 50.000 0.00 0.00 0.00 3.95
22 23 1.137479 ACGACCCAAAGAGAACGAACA 59.863 47.619 0.00 0.00 0.00 3.18
23 24 1.525619 CGACCCAAAGAGAACGAACAC 59.474 52.381 0.00 0.00 0.00 3.32
24 25 2.557317 GACCCAAAGAGAACGAACACA 58.443 47.619 0.00 0.00 0.00 3.72
25 26 2.544267 GACCCAAAGAGAACGAACACAG 59.456 50.000 0.00 0.00 0.00 3.66
26 27 1.873591 CCCAAAGAGAACGAACACAGG 59.126 52.381 0.00 0.00 0.00 4.00
27 28 1.264288 CCAAAGAGAACGAACACAGGC 59.736 52.381 0.00 0.00 0.00 4.85
29 30 0.250338 AAGAGAACGAACACAGGCCC 60.250 55.000 0.00 0.00 0.00 5.80
31 32 3.047877 GAACGAACACAGGCCCGG 61.048 66.667 0.00 0.00 0.00 5.73
32 33 3.524648 GAACGAACACAGGCCCGGA 62.525 63.158 0.73 0.00 0.00 5.14
33 34 2.999739 GAACGAACACAGGCCCGGAA 63.000 60.000 0.73 0.00 0.00 4.30
34 35 3.047877 CGAACACAGGCCCGGAAC 61.048 66.667 0.73 0.00 0.00 3.62
35 36 2.430367 GAACACAGGCCCGGAACT 59.570 61.111 0.73 0.00 0.00 3.01
36 37 1.228154 GAACACAGGCCCGGAACTT 60.228 57.895 0.73 0.00 0.00 2.66
37 38 0.822121 GAACACAGGCCCGGAACTTT 60.822 55.000 0.73 0.00 0.00 2.66
39 40 0.396556 ACACAGGCCCGGAACTTTTT 60.397 50.000 0.73 0.00 0.00 1.94
57 58 3.612472 TTTTAACGAAACTTGGCTCCG 57.388 42.857 0.00 0.00 0.00 4.63
58 59 0.869730 TTAACGAAACTTGGCTCCGC 59.130 50.000 0.00 0.00 0.00 5.54
59 60 1.286354 TAACGAAACTTGGCTCCGCG 61.286 55.000 0.00 0.00 0.00 6.46
60 61 3.788766 CGAAACTTGGCTCCGCGG 61.789 66.667 22.12 22.12 0.00 6.46
62 63 2.203294 AAACTTGGCTCCGCGGTT 60.203 55.556 27.15 7.12 0.00 4.44
63 64 1.792118 GAAACTTGGCTCCGCGGTTT 61.792 55.000 27.15 16.28 32.69 3.27
64 65 0.535553 AAACTTGGCTCCGCGGTTTA 60.536 50.000 27.15 4.62 30.15 2.01
65 66 0.953960 AACTTGGCTCCGCGGTTTAG 60.954 55.000 27.15 16.89 0.00 1.85
66 67 1.375523 CTTGGCTCCGCGGTTTAGT 60.376 57.895 27.15 0.00 0.00 2.24
67 68 0.108520 CTTGGCTCCGCGGTTTAGTA 60.109 55.000 27.15 2.82 0.00 1.82
83 84 7.137490 GGTTTAGTACCACCTTGTGTATTTC 57.863 40.000 0.00 0.00 46.92 2.17
84 85 6.711645 GGTTTAGTACCACCTTGTGTATTTCA 59.288 38.462 0.00 0.00 46.92 2.69
86 87 7.915293 TTAGTACCACCTTGTGTATTTCATG 57.085 36.000 0.00 0.00 0.00 3.07
88 89 7.011499 AGTACCACCTTGTGTATTTCATGTA 57.989 36.000 0.00 0.00 0.00 2.29
89 90 7.455058 AGTACCACCTTGTGTATTTCATGTAA 58.545 34.615 0.00 0.00 0.00 2.41
90 91 6.569179 ACCACCTTGTGTATTTCATGTAAC 57.431 37.500 0.00 0.00 0.00 2.50
91 92 5.180492 ACCACCTTGTGTATTTCATGTAACG 59.820 40.000 0.00 0.00 0.00 3.18
92 93 5.180492 CCACCTTGTGTATTTCATGTAACGT 59.820 40.000 0.00 0.00 0.00 3.99
93 94 6.369340 CCACCTTGTGTATTTCATGTAACGTA 59.631 38.462 0.00 0.00 0.00 3.57
95 96 7.329962 CACCTTGTGTATTTCATGTAACGTAGA 59.670 37.037 0.00 0.00 0.00 2.59
96 97 7.874016 ACCTTGTGTATTTCATGTAACGTAGAA 59.126 33.333 0.00 0.00 0.00 2.10
106 107 5.918576 TCATGTAACGTAGAATTAGATGCGG 59.081 40.000 0.00 0.00 34.74 5.69
107 108 4.613944 TGTAACGTAGAATTAGATGCGGG 58.386 43.478 0.00 0.00 0.00 6.13
108 109 4.338964 TGTAACGTAGAATTAGATGCGGGA 59.661 41.667 0.00 0.00 0.00 5.14
109 110 3.366440 ACGTAGAATTAGATGCGGGAC 57.634 47.619 0.00 0.00 0.00 4.46
128 129 5.915175 GGGACGAAACTAAGAATATCACCT 58.085 41.667 0.00 0.00 0.00 4.00
130 131 6.258068 GGGACGAAACTAAGAATATCACCTTG 59.742 42.308 0.00 0.00 0.00 3.61
131 132 6.238130 GGACGAAACTAAGAATATCACCTTGC 60.238 42.308 0.00 0.00 0.00 4.01
133 134 6.879458 ACGAAACTAAGAATATCACCTTGCTT 59.121 34.615 0.00 0.00 0.00 3.91
135 136 8.879759 CGAAACTAAGAATATCACCTTGCTTTA 58.120 33.333 0.00 0.00 0.00 1.85
224 225 1.679153 ACGGACAATTCCCAACAACAC 59.321 47.619 0.00 0.00 38.99 3.32
226 2062 2.031157 CGGACAATTCCCAACAACACTC 60.031 50.000 0.00 0.00 38.99 3.51
379 2215 5.182570 TGATGTACGGATAGGAACGAATAGG 59.817 44.000 0.00 0.00 0.00 2.57
381 2217 2.954792 ACGGATAGGAACGAATAGGGT 58.045 47.619 0.00 0.00 0.00 4.34
527 2363 4.142752 ACAACATTGAGAGCACAATCATCG 60.143 41.667 0.00 0.00 38.25 3.84
554 2390 1.301244 GATCGCATCCTGCATCGGT 60.301 57.895 0.00 0.00 45.36 4.69
590 2426 2.750301 TCCATCTATCAACGTCGTCG 57.250 50.000 0.00 0.00 43.34 5.12
636 2484 2.015227 AACCGTGCAAACCAAGCAGG 62.015 55.000 0.00 0.00 43.63 4.85
669 2517 3.806949 TGGTCTCACCAGGCTTAAATT 57.193 42.857 0.00 0.00 44.79 1.82
670 2518 3.686016 TGGTCTCACCAGGCTTAAATTC 58.314 45.455 0.00 0.00 44.79 2.17
671 2519 3.017442 GGTCTCACCAGGCTTAAATTCC 58.983 50.000 0.00 0.00 38.42 3.01
672 2520 3.017442 GTCTCACCAGGCTTAAATTCCC 58.983 50.000 0.00 0.00 0.00 3.97
673 2521 2.017049 CTCACCAGGCTTAAATTCCCG 58.983 52.381 0.00 0.00 0.00 5.14
674 2522 1.102978 CACCAGGCTTAAATTCCCGG 58.897 55.000 0.00 0.00 0.00 5.73
675 2523 0.996583 ACCAGGCTTAAATTCCCGGA 59.003 50.000 0.73 0.00 0.00 5.14
676 2524 1.064685 ACCAGGCTTAAATTCCCGGAG 60.065 52.381 0.73 0.00 0.00 4.63
677 2525 1.025041 CAGGCTTAAATTCCCGGAGC 58.975 55.000 0.73 0.61 0.00 4.70
678 2526 2.415825 GGCTTAAATTCCCGGAGCC 58.584 57.895 11.87 11.87 45.21 4.70
679 2527 1.444917 GGCTTAAATTCCCGGAGCCG 61.445 60.000 11.87 1.06 42.91 5.52
690 2538 3.551407 GGAGCCGGATCCCCTGAC 61.551 72.222 28.96 0.78 32.79 3.51
691 2539 3.917760 GAGCCGGATCCCCTGACG 61.918 72.222 9.02 0.00 0.00 4.35
692 2540 4.779733 AGCCGGATCCCCTGACGT 62.780 66.667 5.05 0.00 0.00 4.34
693 2541 2.836360 GCCGGATCCCCTGACGTA 60.836 66.667 5.05 0.00 0.00 3.57
694 2542 3.126528 CCGGATCCCCTGACGTAC 58.873 66.667 6.06 0.00 0.00 3.67
695 2543 2.719979 CGGATCCCCTGACGTACG 59.280 66.667 15.01 15.01 0.00 3.67
696 2544 2.842256 CGGATCCCCTGACGTACGG 61.842 68.421 21.06 1.19 0.00 4.02
697 2545 2.416260 GATCCCCTGACGTACGGC 59.584 66.667 21.06 18.72 0.00 5.68
698 2546 3.148031 GATCCCCTGACGTACGGCC 62.148 68.421 20.48 10.81 0.00 6.13
699 2547 3.968837 ATCCCCTGACGTACGGCCA 62.969 63.158 20.48 14.99 0.00 5.36
700 2548 4.446413 CCCCTGACGTACGGCCAC 62.446 72.222 20.48 7.80 0.00 5.01
701 2549 4.446413 CCCTGACGTACGGCCACC 62.446 72.222 20.48 2.90 0.00 4.61
702 2550 3.379445 CCTGACGTACGGCCACCT 61.379 66.667 20.48 0.00 0.00 4.00
703 2551 2.126071 CTGACGTACGGCCACCTG 60.126 66.667 20.48 0.00 0.00 4.00
704 2552 2.598099 TGACGTACGGCCACCTGA 60.598 61.111 20.48 0.00 0.00 3.86
705 2553 2.126189 GACGTACGGCCACCTGAC 60.126 66.667 21.06 0.00 0.00 3.51
706 2554 3.958822 GACGTACGGCCACCTGACG 62.959 68.421 21.06 6.95 36.05 4.35
707 2555 4.047059 CGTACGGCCACCTGACGT 62.047 66.667 7.57 0.00 43.88 4.34
708 2556 2.341176 GTACGGCCACCTGACGTT 59.659 61.111 2.24 0.00 41.53 3.99
709 2557 2.025418 GTACGGCCACCTGACGTTG 61.025 63.158 2.24 0.00 41.53 4.10
710 2558 3.229156 TACGGCCACCTGACGTTGG 62.229 63.158 2.24 6.95 41.53 3.77
714 2562 4.263572 CCACCTGACGTTGGGCCA 62.264 66.667 0.00 0.00 0.00 5.36
715 2563 2.978010 CACCTGACGTTGGGCCAC 60.978 66.667 5.23 0.00 0.00 5.01
716 2564 3.168528 ACCTGACGTTGGGCCACT 61.169 61.111 5.23 0.00 0.00 4.00
717 2565 2.358737 CCTGACGTTGGGCCACTC 60.359 66.667 5.23 1.32 0.00 3.51
718 2566 2.425592 CTGACGTTGGGCCACTCA 59.574 61.111 5.23 6.65 0.00 3.41
719 2567 1.961277 CTGACGTTGGGCCACTCAC 60.961 63.158 5.23 0.00 0.00 3.51
720 2568 3.041940 GACGTTGGGCCACTCACG 61.042 66.667 23.66 23.66 0.00 4.35
742 2590 4.368543 GGTCCGGGTCCACACGTC 62.369 72.222 0.00 0.00 42.08 4.34
743 2591 3.608662 GTCCGGGTCCACACGTCA 61.609 66.667 0.00 0.00 42.08 4.35
744 2592 3.299977 TCCGGGTCCACACGTCAG 61.300 66.667 0.00 0.00 42.08 3.51
747 2595 3.986006 GGGTCCACACGTCAGCGA 61.986 66.667 0.00 0.00 42.00 4.93
748 2596 2.430921 GGTCCACACGTCAGCGAG 60.431 66.667 0.00 0.00 42.00 5.03
749 2597 2.335369 GTCCACACGTCAGCGAGT 59.665 61.111 0.00 0.00 42.28 4.18
762 2610 4.746951 CGAGTGCGCCGTACGTCA 62.747 66.667 15.21 6.28 46.11 4.35
763 2611 2.874780 GAGTGCGCCGTACGTCAG 60.875 66.667 15.21 6.03 46.11 3.51
764 2612 3.318539 GAGTGCGCCGTACGTCAGA 62.319 63.158 15.21 0.00 46.11 3.27
765 2613 2.874780 GTGCGCCGTACGTCAGAG 60.875 66.667 15.21 1.85 46.11 3.35
766 2614 4.111016 TGCGCCGTACGTCAGAGG 62.111 66.667 15.21 0.00 46.11 3.69
767 2615 3.807538 GCGCCGTACGTCAGAGGA 61.808 66.667 15.21 0.00 46.11 3.71
768 2616 2.403987 CGCCGTACGTCAGAGGAG 59.596 66.667 15.21 0.00 36.87 3.69
769 2617 2.102553 GCCGTACGTCAGAGGAGC 59.897 66.667 15.21 3.74 0.00 4.70
770 2618 2.408241 GCCGTACGTCAGAGGAGCT 61.408 63.158 15.21 0.00 0.00 4.09
771 2619 1.429825 CCGTACGTCAGAGGAGCTG 59.570 63.158 15.21 0.00 46.31 4.24
772 2620 1.226435 CGTACGTCAGAGGAGCTGC 60.226 63.158 7.22 0.00 44.52 5.25
773 2621 1.226435 GTACGTCAGAGGAGCTGCG 60.226 63.158 0.00 0.00 44.52 5.18
774 2622 2.986413 ACGTCAGAGGAGCTGCGT 60.986 61.111 0.00 0.00 45.57 5.24
775 2623 1.645704 TACGTCAGAGGAGCTGCGTC 61.646 60.000 14.59 0.00 46.59 5.19
776 2624 2.183046 GTCAGAGGAGCTGCGTCC 59.817 66.667 0.00 9.30 44.52 4.79
828 2676 3.003275 GGCGGATTGATTTGCGAGAATTA 59.997 43.478 0.00 0.00 31.44 1.40
838 2686 2.526077 TGCGAGAATTACAGTGTAGCG 58.474 47.619 2.68 5.40 0.00 4.26
885 2733 6.189677 TCCGCTTGTAAATGTCCAATAAAG 57.810 37.500 0.00 0.00 0.00 1.85
923 2771 3.940852 TGTACCATCATGATTGCAGTGAC 59.059 43.478 5.16 0.00 0.00 3.67
959 2816 0.877743 GAAAACCTGCCACTCTCTGC 59.122 55.000 0.00 0.00 0.00 4.26
1013 2870 1.815613 ACTCGTCATGACAGACAGAGG 59.184 52.381 24.93 12.52 40.31 3.69
1026 2883 2.048127 AGAGGCAACGCGGAACTC 60.048 61.111 12.47 12.44 43.56 3.01
1046 2903 1.372087 CCCGTGGCATTCTTCAGAGC 61.372 60.000 0.00 0.00 0.00 4.09
1073 2930 0.385974 GTGGAACTCAACGTGCATGC 60.386 55.000 11.82 11.82 0.00 4.06
1405 5588 2.813474 CGGAATGCAGGCGACGAA 60.813 61.111 0.00 0.00 0.00 3.85
1551 5734 3.559384 GGTGACGGGGATTTCTTCTTCTT 60.559 47.826 0.00 0.00 0.00 2.52
1552 5735 3.685272 GTGACGGGGATTTCTTCTTCTTC 59.315 47.826 0.00 0.00 0.00 2.87
1553 5736 3.583086 TGACGGGGATTTCTTCTTCTTCT 59.417 43.478 0.00 0.00 0.00 2.85
1554 5737 4.041691 TGACGGGGATTTCTTCTTCTTCTT 59.958 41.667 0.00 0.00 0.00 2.52
1555 5738 4.580868 ACGGGGATTTCTTCTTCTTCTTC 58.419 43.478 0.00 0.00 0.00 2.87
1556 5739 3.619038 CGGGGATTTCTTCTTCTTCTTCG 59.381 47.826 0.00 0.00 0.00 3.79
1557 5740 3.942115 GGGGATTTCTTCTTCTTCTTCGG 59.058 47.826 0.00 0.00 0.00 4.30
1558 5741 4.323562 GGGGATTTCTTCTTCTTCTTCGGA 60.324 45.833 0.00 0.00 0.00 4.55
1559 5742 4.873259 GGGATTTCTTCTTCTTCTTCGGAG 59.127 45.833 0.00 0.00 0.00 4.63
1649 5857 2.300533 CCGTTTTATCGGCGTACCC 58.699 57.895 6.85 0.00 43.96 3.69
1650 5858 0.179103 CCGTTTTATCGGCGTACCCT 60.179 55.000 6.85 0.00 43.96 4.34
1651 5859 1.203065 CGTTTTATCGGCGTACCCTC 58.797 55.000 6.85 0.00 0.00 4.30
1652 5860 1.575244 GTTTTATCGGCGTACCCTCC 58.425 55.000 6.85 0.00 0.00 4.30
1653 5861 0.465287 TTTTATCGGCGTACCCTCCC 59.535 55.000 6.85 0.00 0.00 4.30
1654 5862 1.737355 TTTATCGGCGTACCCTCCCG 61.737 60.000 6.85 0.00 43.21 5.14
1672 5880 3.506096 CGCGCCTCGTCCTCTGTA 61.506 66.667 0.00 0.00 0.00 2.74
1673 5881 2.835705 CGCGCCTCGTCCTCTGTAT 61.836 63.158 0.00 0.00 0.00 2.29
1674 5882 1.299468 GCGCCTCGTCCTCTGTATG 60.299 63.158 0.00 0.00 0.00 2.39
1675 5883 1.360551 CGCCTCGTCCTCTGTATGG 59.639 63.158 0.00 0.00 0.00 2.74
1676 5884 1.742768 GCCTCGTCCTCTGTATGGG 59.257 63.158 0.00 0.00 0.00 4.00
1677 5885 1.742768 CCTCGTCCTCTGTATGGGC 59.257 63.158 0.00 0.00 0.00 5.36
1678 5886 1.742768 CTCGTCCTCTGTATGGGCC 59.257 63.158 0.00 0.00 0.00 5.80
1679 5887 2.076622 CTCGTCCTCTGTATGGGCCG 62.077 65.000 0.00 0.00 0.00 6.13
1680 5888 2.822399 GTCCTCTGTATGGGCCGG 59.178 66.667 0.00 0.00 0.00 6.13
1681 5889 3.161450 TCCTCTGTATGGGCCGGC 61.161 66.667 21.18 21.18 0.00 6.13
1682 5890 4.256180 CCTCTGTATGGGCCGGCC 62.256 72.222 38.57 38.57 0.00 6.13
1693 5901 3.310307 GCCGGCCCATTGTTGGTT 61.310 61.111 18.11 0.00 41.91 3.67
1694 5902 2.878089 GCCGGCCCATTGTTGGTTT 61.878 57.895 18.11 0.00 41.91 3.27
1695 5903 1.751563 CCGGCCCATTGTTGGTTTT 59.248 52.632 0.00 0.00 41.91 2.43
1696 5904 0.107643 CCGGCCCATTGTTGGTTTTT 59.892 50.000 0.00 0.00 41.91 1.94
1697 5905 1.507562 CGGCCCATTGTTGGTTTTTC 58.492 50.000 0.00 0.00 41.91 2.29
1698 5906 1.069978 CGGCCCATTGTTGGTTTTTCT 59.930 47.619 0.00 0.00 41.91 2.52
1699 5907 2.297597 CGGCCCATTGTTGGTTTTTCTA 59.702 45.455 0.00 0.00 41.91 2.10
1700 5908 3.056179 CGGCCCATTGTTGGTTTTTCTAT 60.056 43.478 0.00 0.00 41.91 1.98
1701 5909 4.562552 CGGCCCATTGTTGGTTTTTCTATT 60.563 41.667 0.00 0.00 41.91 1.73
1702 5910 4.694982 GGCCCATTGTTGGTTTTTCTATTG 59.305 41.667 0.00 0.00 41.91 1.90
1703 5911 5.512232 GGCCCATTGTTGGTTTTTCTATTGA 60.512 40.000 0.00 0.00 41.91 2.57
1704 5912 5.639082 GCCCATTGTTGGTTTTTCTATTGAG 59.361 40.000 0.00 0.00 41.91 3.02
1705 5913 6.518200 GCCCATTGTTGGTTTTTCTATTGAGA 60.518 38.462 0.00 0.00 41.91 3.27
1706 5914 7.441017 CCCATTGTTGGTTTTTCTATTGAGAA 58.559 34.615 0.00 0.00 41.91 2.87
1707 5915 7.930865 CCCATTGTTGGTTTTTCTATTGAGAAA 59.069 33.333 0.00 0.00 43.94 2.52
1708 5916 9.323985 CCATTGTTGGTTTTTCTATTGAGAAAA 57.676 29.630 8.43 8.43 45.60 2.29
1720 5928 8.704849 TTCTATTGAGAAAACTTTTGGATGGA 57.295 30.769 0.00 0.00 38.80 3.41
1721 5929 8.884124 TCTATTGAGAAAACTTTTGGATGGAT 57.116 30.769 0.00 0.00 0.00 3.41
1722 5930 9.312904 TCTATTGAGAAAACTTTTGGATGGATT 57.687 29.630 0.00 0.00 0.00 3.01
1723 5931 9.933723 CTATTGAGAAAACTTTTGGATGGATTT 57.066 29.630 0.00 0.00 0.00 2.17
1725 5933 9.631257 ATTGAGAAAACTTTTGGATGGATTTTT 57.369 25.926 0.00 0.00 0.00 1.94
1753 5961 7.845066 AAAAGGTTTCTCAATATACGACCTC 57.155 36.000 0.00 0.00 35.11 3.85
1754 5962 6.793505 AAGGTTTCTCAATATACGACCTCT 57.206 37.500 0.00 0.00 35.11 3.69
1755 5963 6.394025 AGGTTTCTCAATATACGACCTCTC 57.606 41.667 0.00 0.00 30.59 3.20
1756 5964 5.302313 AGGTTTCTCAATATACGACCTCTCC 59.698 44.000 0.00 0.00 30.59 3.71
1757 5965 5.302313 GGTTTCTCAATATACGACCTCTCCT 59.698 44.000 0.00 0.00 0.00 3.69
1758 5966 6.440436 GTTTCTCAATATACGACCTCTCCTC 58.560 44.000 0.00 0.00 0.00 3.71
1759 5967 5.306114 TCTCAATATACGACCTCTCCTCA 57.694 43.478 0.00 0.00 0.00 3.86
1760 5968 5.691896 TCTCAATATACGACCTCTCCTCAA 58.308 41.667 0.00 0.00 0.00 3.02
1761 5969 6.127101 TCTCAATATACGACCTCTCCTCAAA 58.873 40.000 0.00 0.00 0.00 2.69
1762 5970 6.778069 TCTCAATATACGACCTCTCCTCAAAT 59.222 38.462 0.00 0.00 0.00 2.32
1763 5971 7.287927 TCTCAATATACGACCTCTCCTCAAATT 59.712 37.037 0.00 0.00 0.00 1.82
1764 5972 7.792032 TCAATATACGACCTCTCCTCAAATTT 58.208 34.615 0.00 0.00 0.00 1.82
1765 5973 8.265055 TCAATATACGACCTCTCCTCAAATTTT 58.735 33.333 0.00 0.00 0.00 1.82
1766 5974 8.893727 CAATATACGACCTCTCCTCAAATTTTT 58.106 33.333 0.00 0.00 0.00 1.94
1830 6038 8.895737 AGTCAATGTTAACTTTTCGAAACCTAA 58.104 29.630 10.79 5.83 0.00 2.69
1886 6095 5.446473 GCATGGACTCAGTTCAAATCTTACG 60.446 44.000 0.00 0.00 0.00 3.18
1978 6195 2.929161 GCACACACGCTACATACTTCCA 60.929 50.000 0.00 0.00 0.00 3.53
1979 6196 3.322369 CACACACGCTACATACTTCCAA 58.678 45.455 0.00 0.00 0.00 3.53
1980 6197 3.367932 CACACACGCTACATACTTCCAAG 59.632 47.826 0.00 0.00 0.00 3.61
1985 6202 3.630769 ACGCTACATACTTCCAAGATCGA 59.369 43.478 0.00 0.00 0.00 3.59
2000 6217 5.010922 CCAAGATCGATCAATCTTCCTCTCT 59.989 44.000 26.47 0.00 42.68 3.10
2037 6257 4.460263 AGCTATCAGTTTCCAACACACAA 58.540 39.130 0.00 0.00 0.00 3.33
2051 6271 5.163519 CCAACACACAACCATTCTTTCTCTT 60.164 40.000 0.00 0.00 0.00 2.85
2055 6275 6.998074 ACACACAACCATTCTTTCTCTTCATA 59.002 34.615 0.00 0.00 0.00 2.15
2084 6306 9.175312 TCGATCTCTAACTCTAAACTACACAAT 57.825 33.333 0.00 0.00 0.00 2.71
2088 6310 9.742144 TCTCTAACTCTAAACTACACAATCTCT 57.258 33.333 0.00 0.00 0.00 3.10
2137 6362 2.985282 CACACCCGCCATTGCACT 60.985 61.111 0.00 0.00 37.32 4.40
2268 6508 0.322636 TCACTCCCTCGAGACTGTCC 60.323 60.000 15.71 0.00 38.52 4.02
2286 6526 0.250295 CCCACTCTTTCTTCCGCACA 60.250 55.000 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.525619 GTGTTCGTTCTCTTTGGGTCG 59.474 52.381 0.00 0.00 0.00 4.79
6 7 1.873591 CCTGTGTTCGTTCTCTTTGGG 59.126 52.381 0.00 0.00 0.00 4.12
7 8 1.264288 GCCTGTGTTCGTTCTCTTTGG 59.736 52.381 0.00 0.00 0.00 3.28
8 9 1.264288 GGCCTGTGTTCGTTCTCTTTG 59.736 52.381 0.00 0.00 0.00 2.77
10 11 0.250338 GGGCCTGTGTTCGTTCTCTT 60.250 55.000 0.84 0.00 0.00 2.85
12 13 2.027625 CGGGCCTGTGTTCGTTCTC 61.028 63.158 2.29 0.00 0.00 2.87
15 16 3.109592 TTCCGGGCCTGTGTTCGTT 62.110 57.895 11.58 0.00 0.00 3.85
16 17 3.552384 TTCCGGGCCTGTGTTCGT 61.552 61.111 11.58 0.00 0.00 3.85
17 18 3.047877 GTTCCGGGCCTGTGTTCG 61.048 66.667 11.58 0.00 0.00 3.95
18 19 0.822121 AAAGTTCCGGGCCTGTGTTC 60.822 55.000 11.58 0.00 0.00 3.18
19 20 0.396556 AAAAGTTCCGGGCCTGTGTT 60.397 50.000 11.58 0.00 0.00 3.32
20 21 0.396556 AAAAAGTTCCGGGCCTGTGT 60.397 50.000 11.58 0.00 0.00 3.72
21 22 2.425562 AAAAAGTTCCGGGCCTGTG 58.574 52.632 11.58 1.93 0.00 3.66
36 37 3.954999 CGGAGCCAAGTTTCGTTAAAAA 58.045 40.909 0.00 0.00 0.00 1.94
37 38 3.612472 CGGAGCCAAGTTTCGTTAAAA 57.388 42.857 0.00 0.00 0.00 1.52
60 61 7.733402 TGAAATACACAAGGTGGTACTAAAC 57.267 36.000 1.07 0.00 37.94 2.01
62 63 7.455058 ACATGAAATACACAAGGTGGTACTAA 58.545 34.615 0.00 0.00 37.94 2.24
63 64 7.011499 ACATGAAATACACAAGGTGGTACTA 57.989 36.000 0.00 0.00 37.94 1.82
64 65 5.876357 ACATGAAATACACAAGGTGGTACT 58.124 37.500 0.00 0.00 37.94 2.73
65 66 7.524065 GTTACATGAAATACACAAGGTGGTAC 58.476 38.462 0.00 0.00 37.94 3.34
66 67 6.369340 CGTTACATGAAATACACAAGGTGGTA 59.631 38.462 0.00 0.00 37.94 3.25
67 68 5.180492 CGTTACATGAAATACACAAGGTGGT 59.820 40.000 0.00 0.00 37.94 4.16
70 71 7.380536 TCTACGTTACATGAAATACACAAGGT 58.619 34.615 0.00 0.00 0.00 3.50
71 72 7.821595 TCTACGTTACATGAAATACACAAGG 57.178 36.000 0.00 0.00 0.00 3.61
79 80 8.487970 CGCATCTAATTCTACGTTACATGAAAT 58.512 33.333 0.00 0.00 0.00 2.17
83 84 5.118664 CCCGCATCTAATTCTACGTTACATG 59.881 44.000 0.00 0.00 0.00 3.21
84 85 5.010314 TCCCGCATCTAATTCTACGTTACAT 59.990 40.000 0.00 0.00 0.00 2.29
86 87 4.678742 GTCCCGCATCTAATTCTACGTTAC 59.321 45.833 0.00 0.00 0.00 2.50
88 89 3.714391 GTCCCGCATCTAATTCTACGTT 58.286 45.455 0.00 0.00 0.00 3.99
89 90 2.287427 CGTCCCGCATCTAATTCTACGT 60.287 50.000 0.00 0.00 0.00 3.57
90 91 2.031420 TCGTCCCGCATCTAATTCTACG 60.031 50.000 0.00 0.00 0.00 3.51
91 92 3.637998 TCGTCCCGCATCTAATTCTAC 57.362 47.619 0.00 0.00 0.00 2.59
92 93 4.098960 AGTTTCGTCCCGCATCTAATTCTA 59.901 41.667 0.00 0.00 0.00 2.10
93 94 3.118738 AGTTTCGTCCCGCATCTAATTCT 60.119 43.478 0.00 0.00 0.00 2.40
95 96 3.261981 AGTTTCGTCCCGCATCTAATT 57.738 42.857 0.00 0.00 0.00 1.40
96 97 2.981859 AGTTTCGTCCCGCATCTAAT 57.018 45.000 0.00 0.00 0.00 1.73
99 100 1.822990 TCTTAGTTTCGTCCCGCATCT 59.177 47.619 0.00 0.00 0.00 2.90
102 103 2.754946 ATTCTTAGTTTCGTCCCGCA 57.245 45.000 0.00 0.00 0.00 5.69
103 104 4.208666 GTGATATTCTTAGTTTCGTCCCGC 59.791 45.833 0.00 0.00 0.00 6.13
104 105 4.743644 GGTGATATTCTTAGTTTCGTCCCG 59.256 45.833 0.00 0.00 0.00 5.14
106 107 6.238130 GCAAGGTGATATTCTTAGTTTCGTCC 60.238 42.308 0.00 0.00 0.00 4.79
107 108 6.535508 AGCAAGGTGATATTCTTAGTTTCGTC 59.464 38.462 0.00 0.00 0.00 4.20
108 109 6.407202 AGCAAGGTGATATTCTTAGTTTCGT 58.593 36.000 0.00 0.00 0.00 3.85
109 110 6.910536 AGCAAGGTGATATTCTTAGTTTCG 57.089 37.500 0.00 0.00 0.00 3.46
181 182 9.706691 CCGTCATTTGTGTAACCTTATCTATAT 57.293 33.333 0.00 0.00 34.36 0.86
182 183 8.916062 TCCGTCATTTGTGTAACCTTATCTATA 58.084 33.333 0.00 0.00 34.36 1.31
184 185 7.037438 GTCCGTCATTTGTGTAACCTTATCTA 58.963 38.462 0.00 0.00 34.36 1.98
185 186 5.873164 GTCCGTCATTTGTGTAACCTTATCT 59.127 40.000 0.00 0.00 34.36 1.98
224 225 4.457834 AGAGTAAACCAAGATGTCCGAG 57.542 45.455 0.00 0.00 0.00 4.63
226 2062 5.921408 GCTATAGAGTAAACCAAGATGTCCG 59.079 44.000 3.21 0.00 0.00 4.79
329 2165 4.708177 CGTTCCCTCCTTCATTGATATGT 58.292 43.478 0.00 0.00 33.34 2.29
379 2215 1.612442 TGCCCTGTCACTCCCTACC 60.612 63.158 0.00 0.00 0.00 3.18
381 2217 0.324738 CTCTGCCCTGTCACTCCCTA 60.325 60.000 0.00 0.00 0.00 3.53
527 2363 0.179089 AGGATGCGATCACTCTGCAC 60.179 55.000 0.00 0.00 42.11 4.57
554 2390 9.206690 GATAGATGGATCCTGGATAAGACATTA 57.793 37.037 14.23 7.82 0.00 1.90
590 2426 1.635663 CGCTTGTTGTCCCGGATGAC 61.636 60.000 0.73 2.84 35.77 3.06
673 2521 3.551407 GTCAGGGGATCCGGCTCC 61.551 72.222 16.35 16.35 38.33 4.70
674 2522 3.917760 CGTCAGGGGATCCGGCTC 61.918 72.222 5.45 0.00 38.33 4.70
675 2523 3.369410 TACGTCAGGGGATCCGGCT 62.369 63.158 5.45 0.00 38.33 5.52
676 2524 2.836360 TACGTCAGGGGATCCGGC 60.836 66.667 5.45 0.00 38.33 6.13
677 2525 2.842256 CGTACGTCAGGGGATCCGG 61.842 68.421 7.22 0.00 38.33 5.14
678 2526 2.719979 CGTACGTCAGGGGATCCG 59.280 66.667 7.22 0.00 38.33 4.18
679 2527 3.126528 CCGTACGTCAGGGGATCC 58.873 66.667 15.21 1.92 0.00 3.36
680 2528 2.416260 GCCGTACGTCAGGGGATC 59.584 66.667 15.21 0.00 32.45 3.36
681 2529 3.152400 GGCCGTACGTCAGGGGAT 61.152 66.667 15.21 0.00 32.45 3.85
682 2530 4.682334 TGGCCGTACGTCAGGGGA 62.682 66.667 15.21 0.00 32.45 4.81
683 2531 4.446413 GTGGCCGTACGTCAGGGG 62.446 72.222 15.21 0.00 32.45 4.79
684 2532 4.446413 GGTGGCCGTACGTCAGGG 62.446 72.222 15.21 0.00 35.13 4.45
685 2533 3.379445 AGGTGGCCGTACGTCAGG 61.379 66.667 15.21 0.00 0.00 3.86
686 2534 2.126071 CAGGTGGCCGTACGTCAG 60.126 66.667 15.21 0.00 0.00 3.51
687 2535 2.598099 TCAGGTGGCCGTACGTCA 60.598 61.111 15.21 9.40 0.00 4.35
688 2536 2.126189 GTCAGGTGGCCGTACGTC 60.126 66.667 15.21 0.00 0.00 4.34
689 2537 4.047059 CGTCAGGTGGCCGTACGT 62.047 66.667 15.21 0.00 33.91 3.57
690 2538 3.562779 AACGTCAGGTGGCCGTACG 62.563 63.158 8.69 8.69 40.48 3.67
691 2539 2.025418 CAACGTCAGGTGGCCGTAC 61.025 63.158 0.00 0.00 33.88 3.67
692 2540 2.340809 CAACGTCAGGTGGCCGTA 59.659 61.111 0.00 0.00 33.88 4.02
698 2546 2.978010 GTGGCCCAACGTCAGGTG 60.978 66.667 0.00 0.00 34.07 4.00
699 2547 3.168528 AGTGGCCCAACGTCAGGT 61.169 61.111 0.00 0.00 0.00 4.00
700 2548 2.358737 GAGTGGCCCAACGTCAGG 60.359 66.667 0.00 0.00 0.00 3.86
701 2549 1.961277 GTGAGTGGCCCAACGTCAG 60.961 63.158 0.00 0.00 0.00 3.51
702 2550 2.110213 GTGAGTGGCCCAACGTCA 59.890 61.111 0.00 0.00 0.00 4.35
703 2551 3.041940 CGTGAGTGGCCCAACGTC 61.042 66.667 0.00 0.00 0.00 4.34
725 2573 4.368543 GACGTGTGGACCCGGACC 62.369 72.222 0.73 6.89 0.00 4.46
726 2574 3.569049 CTGACGTGTGGACCCGGAC 62.569 68.421 0.73 0.00 0.00 4.79
727 2575 3.299977 CTGACGTGTGGACCCGGA 61.300 66.667 0.73 0.00 0.00 5.14
730 2578 3.916392 CTCGCTGACGTGTGGACCC 62.916 68.421 0.00 0.00 41.18 4.46
731 2579 2.430921 CTCGCTGACGTGTGGACC 60.431 66.667 0.00 0.00 41.18 4.46
732 2580 2.335369 ACTCGCTGACGTGTGGAC 59.665 61.111 0.00 0.00 43.76 4.02
745 2593 4.746951 TGACGTACGGCGCACTCG 62.747 66.667 21.06 6.32 46.11 4.18
746 2594 2.874780 CTGACGTACGGCGCACTC 60.875 66.667 21.06 7.29 46.11 3.51
747 2595 3.324099 CTCTGACGTACGGCGCACT 62.324 63.158 21.06 0.00 46.11 4.40
748 2596 2.874780 CTCTGACGTACGGCGCAC 60.875 66.667 21.06 2.50 46.11 5.34
749 2597 4.111016 CCTCTGACGTACGGCGCA 62.111 66.667 21.06 13.22 46.11 6.09
750 2598 3.736482 CTCCTCTGACGTACGGCGC 62.736 68.421 21.06 0.00 46.11 6.53
752 2600 2.102553 GCTCCTCTGACGTACGGC 59.897 66.667 21.06 18.72 0.00 5.68
753 2601 1.429825 CAGCTCCTCTGACGTACGG 59.570 63.158 21.06 1.50 45.72 4.02
754 2602 1.226435 GCAGCTCCTCTGACGTACG 60.226 63.158 15.01 15.01 45.72 3.67
755 2603 1.226435 CGCAGCTCCTCTGACGTAC 60.226 63.158 0.00 0.00 45.72 3.67
756 2604 1.645704 GACGCAGCTCCTCTGACGTA 61.646 60.000 11.86 0.00 46.96 3.57
757 2605 2.986413 ACGCAGCTCCTCTGACGT 60.986 61.111 0.00 0.00 45.72 4.34
758 2606 2.202544 GACGCAGCTCCTCTGACG 60.203 66.667 0.00 2.37 45.72 4.35
759 2607 1.032657 TAGGACGCAGCTCCTCTGAC 61.033 60.000 14.62 0.00 45.72 3.51
760 2608 0.323451 TTAGGACGCAGCTCCTCTGA 60.323 55.000 14.62 3.28 45.72 3.27
761 2609 0.532573 TTTAGGACGCAGCTCCTCTG 59.467 55.000 14.62 0.00 45.62 3.35
762 2610 1.490574 ATTTAGGACGCAGCTCCTCT 58.509 50.000 14.62 0.00 38.57 3.69
763 2611 2.205911 GAATTTAGGACGCAGCTCCTC 58.794 52.381 14.62 0.71 38.57 3.71
764 2612 1.134371 GGAATTTAGGACGCAGCTCCT 60.134 52.381 15.31 15.31 40.23 3.69
765 2613 1.300481 GGAATTTAGGACGCAGCTCC 58.700 55.000 3.35 3.35 0.00 4.70
766 2614 1.300481 GGGAATTTAGGACGCAGCTC 58.700 55.000 0.00 0.00 0.00 4.09
767 2615 0.107165 GGGGAATTTAGGACGCAGCT 60.107 55.000 0.00 0.00 0.00 4.24
768 2616 0.107165 AGGGGAATTTAGGACGCAGC 60.107 55.000 0.00 0.00 0.00 5.25
769 2617 2.017049 CAAGGGGAATTTAGGACGCAG 58.983 52.381 0.00 0.00 0.00 5.18
770 2618 1.953311 GCAAGGGGAATTTAGGACGCA 60.953 52.381 0.00 0.00 0.00 5.24
771 2619 0.738975 GCAAGGGGAATTTAGGACGC 59.261 55.000 0.00 0.00 0.00 5.19
772 2620 1.389555 GGCAAGGGGAATTTAGGACG 58.610 55.000 0.00 0.00 0.00 4.79
773 2621 1.288037 AGGGCAAGGGGAATTTAGGAC 59.712 52.381 0.00 0.00 0.00 3.85
774 2622 1.693799 AGGGCAAGGGGAATTTAGGA 58.306 50.000 0.00 0.00 0.00 2.94
775 2623 2.388735 GAAGGGCAAGGGGAATTTAGG 58.611 52.381 0.00 0.00 0.00 2.69
776 2624 2.292192 TGGAAGGGCAAGGGGAATTTAG 60.292 50.000 0.00 0.00 0.00 1.85
777 2625 1.719378 TGGAAGGGCAAGGGGAATTTA 59.281 47.619 0.00 0.00 0.00 1.40
778 2626 0.491371 TGGAAGGGCAAGGGGAATTT 59.509 50.000 0.00 0.00 0.00 1.82
828 2676 0.600255 GCTGAACACCGCTACACTGT 60.600 55.000 0.00 0.00 0.00 3.55
885 2733 3.829601 TGGTACAATGGTGAATGGGTTTC 59.170 43.478 0.00 0.00 31.92 2.78
923 2771 2.489938 TTCCCGTTTTCAGAGGATGG 57.510 50.000 0.00 0.00 0.00 3.51
959 2816 3.379240 CTGCCGTGTTCTCATCAGATAG 58.621 50.000 0.00 0.00 0.00 2.08
1026 2883 0.745845 CTCTGAAGAATGCCACGGGG 60.746 60.000 0.00 0.00 37.18 5.73
1046 2903 0.798776 GTTGAGTTCCACATGCTCGG 59.201 55.000 0.00 0.00 32.32 4.63
1073 2930 2.169789 CGGACAAGATCTGCAGCGG 61.170 63.158 9.47 0.00 0.00 5.52
1447 5630 4.377760 TCCCTCCCGAGCCTCGTT 62.378 66.667 13.83 0.00 38.40 3.85
1533 5716 4.580868 GAAGAAGAAGAAGAAATCCCCGT 58.419 43.478 0.00 0.00 0.00 5.28
1656 5864 1.299468 CATACAGAGGACGAGGCGC 60.299 63.158 0.00 0.00 0.00 6.53
1657 5865 1.360551 CCATACAGAGGACGAGGCG 59.639 63.158 0.00 0.00 0.00 5.52
1658 5866 1.742768 CCCATACAGAGGACGAGGC 59.257 63.158 0.00 0.00 0.00 4.70
1659 5867 1.742768 GCCCATACAGAGGACGAGG 59.257 63.158 0.00 0.00 0.00 4.63
1660 5868 1.742768 GGCCCATACAGAGGACGAG 59.257 63.158 0.00 0.00 0.00 4.18
1661 5869 3.950232 GGCCCATACAGAGGACGA 58.050 61.111 0.00 0.00 0.00 4.20
1663 5871 2.822399 CCGGCCCATACAGAGGAC 59.178 66.667 0.00 0.00 0.00 3.85
1664 5872 3.161450 GCCGGCCCATACAGAGGA 61.161 66.667 18.11 0.00 0.00 3.71
1665 5873 4.256180 GGCCGGCCCATACAGAGG 62.256 72.222 36.64 0.00 0.00 3.69
1680 5888 7.954305 TTCTCAATAGAAAAACCAACAATGGGC 60.954 37.037 0.00 0.00 43.86 5.36
1681 5889 7.441017 TTCTCAATAGAAAAACCAACAATGGG 58.559 34.615 0.00 0.00 43.86 4.00
1695 5903 8.704849 TCCATCCAAAAGTTTTCTCAATAGAA 57.295 30.769 0.00 0.00 40.03 2.10
1696 5904 8.884124 ATCCATCCAAAAGTTTTCTCAATAGA 57.116 30.769 0.00 0.00 0.00 1.98
1697 5905 9.933723 AAATCCATCCAAAAGTTTTCTCAATAG 57.066 29.630 0.00 0.00 0.00 1.73
1699 5907 9.631257 AAAAATCCATCCAAAAGTTTTCTCAAT 57.369 25.926 0.00 0.00 0.00 2.57
1728 5936 8.101419 AGAGGTCGTATATTGAGAAACCTTTTT 58.899 33.333 0.00 0.00 35.84 1.94
1729 5937 7.621796 AGAGGTCGTATATTGAGAAACCTTTT 58.378 34.615 0.00 0.00 35.84 2.27
1730 5938 7.184067 AGAGGTCGTATATTGAGAAACCTTT 57.816 36.000 0.00 0.00 35.84 3.11
1731 5939 6.183360 GGAGAGGTCGTATATTGAGAAACCTT 60.183 42.308 0.00 0.00 35.84 3.50
1732 5940 5.302313 GGAGAGGTCGTATATTGAGAAACCT 59.698 44.000 0.00 0.00 38.33 3.50
1733 5941 5.302313 AGGAGAGGTCGTATATTGAGAAACC 59.698 44.000 0.00 0.00 0.00 3.27
1734 5942 6.039493 TGAGGAGAGGTCGTATATTGAGAAAC 59.961 42.308 0.00 0.00 0.00 2.78
1735 5943 6.127101 TGAGGAGAGGTCGTATATTGAGAAA 58.873 40.000 0.00 0.00 0.00 2.52
1736 5944 5.691896 TGAGGAGAGGTCGTATATTGAGAA 58.308 41.667 0.00 0.00 0.00 2.87
1737 5945 5.306114 TGAGGAGAGGTCGTATATTGAGA 57.694 43.478 0.00 0.00 0.00 3.27
1738 5946 6.392625 TTTGAGGAGAGGTCGTATATTGAG 57.607 41.667 0.00 0.00 0.00 3.02
1739 5947 6.978674 ATTTGAGGAGAGGTCGTATATTGA 57.021 37.500 0.00 0.00 0.00 2.57
1740 5948 8.438676 AAAATTTGAGGAGAGGTCGTATATTG 57.561 34.615 0.00 0.00 0.00 1.90
1791 5999 8.999431 AGTTAACATTGACTCGATTTATTGTGT 58.001 29.630 8.61 0.00 0.00 3.72
1797 6005 8.980610 TCGAAAAGTTAACATTGACTCGATTTA 58.019 29.630 12.34 0.00 0.00 1.40
1813 6021 7.413219 CGTGCCATATTAGGTTTCGAAAAGTTA 60.413 37.037 13.10 2.84 0.00 2.24
1830 6038 8.234546 GGTAATTATTTCGAATTCGTGCCATAT 58.765 33.333 25.93 10.73 40.80 1.78
1941 6150 0.606096 GTGCGGGGGCTAAAAACAAT 59.394 50.000 0.00 0.00 0.00 2.71
1978 6195 6.729690 AAGAGAGGAAGATTGATCGATCTT 57.270 37.500 30.41 30.41 46.28 2.40
1979 6196 7.255801 GGTTAAGAGAGGAAGATTGATCGATCT 60.256 40.741 25.02 18.37 37.99 2.75
1980 6197 6.866248 GGTTAAGAGAGGAAGATTGATCGATC 59.134 42.308 18.72 18.72 0.00 3.69
1985 6202 5.728741 AGGTGGTTAAGAGAGGAAGATTGAT 59.271 40.000 0.00 0.00 0.00 2.57
2000 6217 5.724854 ACTGATAGCTTCCTAAGGTGGTTAA 59.275 40.000 0.00 0.00 39.97 2.01
2037 6257 8.970859 ATCGAAATATGAAGAGAAAGAATGGT 57.029 30.769 0.00 0.00 0.00 3.55
2095 6317 9.872721 TGTGAGGTAAATACATTTCGTAACATA 57.127 29.630 0.00 0.00 32.59 2.29
2137 6362 1.076412 AGAGAGAGCTCGGCATGGA 60.076 57.895 8.37 0.00 45.98 3.41
2268 6508 1.151668 CTGTGCGGAAGAAAGAGTGG 58.848 55.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.