Multiple sequence alignment - TraesCS5A01G529900

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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 TraesCS5A01G529900 chr5A 100.000 4047 0 0 1 4047 688972615 688976661 0.000000e+00 7474.0
1 TraesCS5A01G529900 chr4B 92.834 3084 133 43 540 3575 650960320 650963363 0.000000e+00 4390.0
2 TraesCS5A01G529900 chr4B 90.316 475 30 10 22 486 650959564 650960032 3.460000e-170 608.0
3 TraesCS5A01G529900 chr4B 88.274 307 24 5 3677 3982 650963363 650963658 1.380000e-94 357.0
4 TraesCS5A01G529900 chr4B 78.652 267 53 4 2764 3027 602448976 602448711 1.500000e-39 174.0
5 TraesCS5A01G529900 chr4B 81.967 122 8 6 3558 3676 551263501 551263611 1.550000e-14 91.6
6 TraesCS5A01G529900 chr4D 94.951 1644 40 13 553 2183 504328418 504330031 0.000000e+00 2536.0
7 TraesCS5A01G529900 chr4D 89.644 1236 65 24 2379 3576 504330133 504331343 0.000000e+00 1515.0
8 TraesCS5A01G529900 chr4D 91.971 411 25 5 22 430 504327495 504327899 1.630000e-158 569.0
9 TraesCS5A01G529900 chr4D 80.496 564 96 9 1020 1576 477508637 477508081 1.740000e-113 420.0
10 TraesCS5A01G529900 chr4D 85.437 309 24 9 3678 3982 504331339 504331630 6.570000e-78 302.0
11 TraesCS5A01G529900 chr4D 77.470 253 55 2 2776 3027 477507107 477506856 2.520000e-32 150.0
12 TraesCS5A01G529900 chr1B 83.445 1190 162 22 1000 2158 398005998 398007183 0.000000e+00 1074.0
13 TraesCS5A01G529900 chr1B 85.606 264 38 0 2774 3037 398007499 398007762 1.110000e-70 278.0
14 TraesCS5A01G529900 chr1B 82.000 100 16 2 3584 3683 217691147 217691244 2.590000e-12 84.2
15 TraesCS5A01G529900 chr1D 83.277 1190 164 27 1000 2158 296489213 296490398 0.000000e+00 1062.0
16 TraesCS5A01G529900 chr1D 87.121 264 34 0 2774 3037 296490704 296490967 2.360000e-77 300.0
17 TraesCS5A01G529900 chr1A 82.762 1195 161 34 1000 2158 369322660 369323845 0.000000e+00 1024.0
18 TraesCS5A01G529900 chr1A 86.590 261 35 0 2774 3034 369324164 369324424 5.120000e-74 289.0
19 TraesCS5A01G529900 chr1A 81.529 157 25 3 2862 3016 243161183 243161029 4.250000e-25 126.0
20 TraesCS5A01G529900 chr1A 90.244 41 3 1 3622 3662 72498592 72498553 7.000000e-03 52.8
21 TraesCS5A01G529900 chr6D 82.487 571 92 7 1046 1612 463549388 463548822 1.010000e-135 494.0
22 TraesCS5A01G529900 chr6A 81.675 573 99 5 1043 1612 610203873 610204442 4.730000e-129 472.0
23 TraesCS5A01G529900 chr6A 77.385 283 55 9 2762 3038 610205963 610206242 4.190000e-35 159.0
24 TraesCS5A01G529900 chr6B 81.533 574 98 7 1043 1612 706910991 706911560 2.200000e-127 466.0
25 TraesCS5A01G529900 chr3D 87.500 104 7 4 3573 3676 433322220 433322123 9.190000e-22 115.0
26 TraesCS5A01G529900 chr3D 90.909 77 4 1 3574 3650 608466386 608466459 2.570000e-17 100.0
27 TraesCS5A01G529900 chr2B 94.737 57 3 0 3564 3620 16197266 16197322 5.570000e-14 89.8
28 TraesCS5A01G529900 chr7D 91.935 62 4 1 3559 3619 237270822 237270761 7.210000e-13 86.1
29 TraesCS5A01G529900 chr7B 86.250 80 6 5 3572 3648 509568417 509568340 9.320000e-12 82.4
30 TraesCS5A01G529900 chr3B 81.553 103 13 6 3577 3676 449805827 449805926 3.350000e-11 80.5
31 TraesCS5A01G529900 chr5D 81.443 97 15 3 3587 3683 183389455 183389362 4.340000e-10 76.8
32 TraesCS5A01G529900 chr7A 96.875 32 1 0 3622 3653 475977254 475977223 2.000000e-03 54.7
33 TraesCS5A01G529900 chr5B 100.000 29 0 0 3620 3648 20727621 20727593 2.000000e-03 54.7


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 TraesCS5A01G529900 chr5A 688972615 688976661 4046 False 7474.0 7474 100.000000 1 4047 1 chr5A.!!$F1 4046
1 TraesCS5A01G529900 chr4B 650959564 650963658 4094 False 1785.0 4390 90.474667 22 3982 3 chr4B.!!$F2 3960
2 TraesCS5A01G529900 chr4D 504327495 504331630 4135 False 1230.5 2536 90.500750 22 3982 4 chr4D.!!$F1 3960
3 TraesCS5A01G529900 chr4D 477506856 477508637 1781 True 285.0 420 78.983000 1020 3027 2 chr4D.!!$R1 2007
4 TraesCS5A01G529900 chr1B 398005998 398007762 1764 False 676.0 1074 84.525500 1000 3037 2 chr1B.!!$F2 2037
5 TraesCS5A01G529900 chr1D 296489213 296490967 1754 False 681.0 1062 85.199000 1000 3037 2 chr1D.!!$F1 2037
6 TraesCS5A01G529900 chr1A 369322660 369324424 1764 False 656.5 1024 84.676000 1000 3034 2 chr1A.!!$F1 2034
7 TraesCS5A01G529900 chr6D 463548822 463549388 566 True 494.0 494 82.487000 1046 1612 1 chr6D.!!$R1 566
8 TraesCS5A01G529900 chr6A 610203873 610206242 2369 False 315.5 472 79.530000 1043 3038 2 chr6A.!!$F1 1995
9 TraesCS5A01G529900 chr6B 706910991 706911560 569 False 466.0 466 81.533000 1043 1612 1 chr6B.!!$F1 569

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
961 1386 0.036875 GAGCACTAACCAGCCACCTT 59.963 55.000 0.00 0.00 0.00 3.50 F
962 1387 1.278127 GAGCACTAACCAGCCACCTTA 59.722 52.381 0.00 0.00 0.00 2.69 F
1626 2063 2.095438 ACTGGAAGGACCTCGAGGGT 62.095 60.000 34.04 20.04 45.39 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2567 0.106708 TCTTGAGGAACAGCTTGCGT 59.893 50.0 0.00 0.0 0.0 5.24 R
2728 4534 0.535553 TTACACCGCCGGAGCTTTTT 60.536 50.0 11.71 0.0 36.6 1.94 R
3055 4861 0.535102 GGGCGATGTTGGTAGATGGG 60.535 60.0 0.00 0.0 0.0 4.00 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
26 27 7.831753 AGCACACACTCCATATACAGATATAC 58.168 38.462 0.00 0.00 0.00 1.47
79 82 2.125350 GGAGTGAAGGCTCAGGCG 60.125 66.667 0.00 0.00 39.81 5.52
144 153 5.011023 ACACCCTTTTTGACAGAATTGATCC 59.989 40.000 0.00 0.00 0.00 3.36
152 161 4.631131 TGACAGAATTGATCCGCGATATT 58.369 39.130 8.23 0.00 0.00 1.28
159 168 7.276438 CAGAATTGATCCGCGATATTTGATAGA 59.724 37.037 8.23 0.00 0.00 1.98
170 179 7.513968 GCGATATTTGATAGACTTTTAGCCAG 58.486 38.462 0.00 0.00 0.00 4.85
181 190 5.814705 AGACTTTTAGCCAGATCATTTCGAG 59.185 40.000 0.00 0.00 0.00 4.04
186 195 3.474600 AGCCAGATCATTTCGAGGATTG 58.525 45.455 0.00 0.00 0.00 2.67
210 219 6.931281 TGCTTAGTTTATCACTAGGATGCATC 59.069 38.462 18.81 18.81 39.28 3.91
239 249 2.927477 CTGCATCTTTACCGCGTTTCTA 59.073 45.455 4.92 0.00 0.00 2.10
243 253 5.581479 TGCATCTTTACCGCGTTTCTAAATA 59.419 36.000 4.92 0.00 0.00 1.40
532 542 5.880887 GGTACCCTAATTAAGCCTATGATGC 59.119 44.000 0.00 0.00 0.00 3.91
533 543 4.579869 ACCCTAATTAAGCCTATGATGCG 58.420 43.478 0.00 0.00 0.00 4.73
534 544 3.375299 CCCTAATTAAGCCTATGATGCGC 59.625 47.826 0.00 0.00 0.00 6.09
535 545 3.375299 CCTAATTAAGCCTATGATGCGCC 59.625 47.826 4.18 0.00 0.00 6.53
536 546 1.442769 ATTAAGCCTATGATGCGCCG 58.557 50.000 4.18 0.00 0.00 6.46
537 547 0.105964 TTAAGCCTATGATGCGCCGT 59.894 50.000 4.18 0.00 0.00 5.68
538 548 0.963225 TAAGCCTATGATGCGCCGTA 59.037 50.000 4.18 0.00 0.00 4.02
550 796 1.534811 GCGCCGTACGTACATAGTGC 61.535 60.000 24.50 23.16 46.11 4.40
569 975 3.063997 GTGCTGTCCAAGTGCATACATAC 59.936 47.826 0.00 0.00 39.00 2.39
570 976 3.270027 GCTGTCCAAGTGCATACATACA 58.730 45.455 0.00 0.00 0.00 2.29
665 1077 9.740710 GTAGATAGTTTTGGGCCAATAATATCT 57.259 33.333 37.51 37.51 41.52 1.98
673 1085 4.202599 TGGGCCAATAATATCTCAGTGCAT 60.203 41.667 2.13 0.00 0.00 3.96
689 1101 0.812412 GCATACGTACATTGGGCGGT 60.812 55.000 0.00 0.00 0.00 5.68
815 1231 2.409870 CCGCTCCAACCTTCCATGC 61.410 63.158 0.00 0.00 0.00 4.06
817 1233 1.304381 GCTCCAACCTTCCATGCCA 60.304 57.895 0.00 0.00 0.00 4.92
907 1327 4.041917 CCACACCGGTGCATGCAC 62.042 66.667 37.29 37.29 43.88 4.57
915 1335 3.045142 GTGCATGCACACTGCCTT 58.955 55.556 39.12 0.00 44.23 4.35
916 1336 1.080974 GTGCATGCACACTGCCTTC 60.081 57.895 39.12 14.13 44.23 3.46
918 1338 2.327343 GCATGCACACTGCCTTCGA 61.327 57.895 14.21 0.00 44.23 3.71
919 1339 1.792301 CATGCACACTGCCTTCGAG 59.208 57.895 0.00 0.00 44.23 4.04
920 1340 1.376424 ATGCACACTGCCTTCGAGG 60.376 57.895 0.00 0.00 44.23 4.63
921 1341 2.031163 GCACACTGCCTTCGAGGT 59.969 61.111 0.00 0.00 37.80 3.85
926 1351 3.123620 CTGCCTTCGAGGTGCAGC 61.124 66.667 19.49 8.11 45.09 5.25
961 1386 0.036875 GAGCACTAACCAGCCACCTT 59.963 55.000 0.00 0.00 0.00 3.50
962 1387 1.278127 GAGCACTAACCAGCCACCTTA 59.722 52.381 0.00 0.00 0.00 2.69
965 1390 2.552373 GCACTAACCAGCCACCTTAACT 60.552 50.000 0.00 0.00 0.00 2.24
966 1391 3.307199 GCACTAACCAGCCACCTTAACTA 60.307 47.826 0.00 0.00 0.00 2.24
968 1393 4.222145 CACTAACCAGCCACCTTAACTAGA 59.778 45.833 0.00 0.00 0.00 2.43
969 1394 5.030820 ACTAACCAGCCACCTTAACTAGAT 58.969 41.667 0.00 0.00 0.00 1.98
970 1395 6.097839 CACTAACCAGCCACCTTAACTAGATA 59.902 42.308 0.00 0.00 0.00 1.98
971 1396 5.615925 AACCAGCCACCTTAACTAGATAG 57.384 43.478 0.00 0.00 0.00 2.08
973 1398 3.643792 CCAGCCACCTTAACTAGATAGCT 59.356 47.826 0.00 0.00 0.00 3.32
974 1399 4.262249 CCAGCCACCTTAACTAGATAGCTC 60.262 50.000 0.00 0.00 0.00 4.09
975 1400 3.898741 AGCCACCTTAACTAGATAGCTCC 59.101 47.826 0.00 0.00 0.00 4.70
976 1401 3.641906 GCCACCTTAACTAGATAGCTCCA 59.358 47.826 0.00 0.00 0.00 3.86
977 1402 4.284746 GCCACCTTAACTAGATAGCTCCAT 59.715 45.833 0.00 0.00 0.00 3.41
978 1403 5.567823 GCCACCTTAACTAGATAGCTCCATC 60.568 48.000 0.00 0.00 0.00 3.51
979 1404 5.777732 CCACCTTAACTAGATAGCTCCATCT 59.222 44.000 4.45 4.45 38.76 2.90
980 1405 6.071616 CCACCTTAACTAGATAGCTCCATCTC 60.072 46.154 2.16 0.00 36.63 2.75
981 1406 6.014012 ACCTTAACTAGATAGCTCCATCTCC 58.986 44.000 2.16 0.00 36.63 3.71
982 1407 5.420739 CCTTAACTAGATAGCTCCATCTCCC 59.579 48.000 2.16 0.00 36.63 4.30
983 1408 4.477536 AACTAGATAGCTCCATCTCCCA 57.522 45.455 2.16 0.00 36.63 4.37
1227 1652 2.602267 TCCACCATGGTCGTCGGT 60.602 61.111 16.53 0.00 39.03 4.69
1626 2063 2.095438 ACTGGAAGGACCTCGAGGGT 62.095 60.000 34.04 20.04 45.39 4.34
2274 3995 4.256920 CTGGCTAGCTAATTTGTCACACT 58.743 43.478 15.72 0.00 0.00 3.55
2471 4259 9.153721 GATGCATGGATTTTCTTTTGAATACAA 57.846 29.630 2.46 0.00 38.37 2.41
2522 4311 6.653020 ACCAAATTGCTATCTAGTCATCACA 58.347 36.000 0.00 0.00 0.00 3.58
2529 4318 5.067023 TGCTATCTAGTCATCACACACTCAG 59.933 44.000 0.00 0.00 0.00 3.35
2615 4404 4.503643 CCAGCATCAAAAGACCCACAAATT 60.504 41.667 0.00 0.00 0.00 1.82
2736 4542 4.442038 CCCCCTCCCAAAAAGCTC 57.558 61.111 0.00 0.00 0.00 4.09
2884 4690 3.628646 GAGCACGGTGGCAGGGAAT 62.629 63.158 10.60 0.00 35.83 3.01
2887 4693 1.450312 CACGGTGGCAGGGAATCTC 60.450 63.158 0.00 0.00 0.00 2.75
2923 4729 1.374252 GGCGAACCTGATCGTGTGT 60.374 57.895 0.00 0.00 44.49 3.72
2986 4792 3.245052 CCTTCTGGAACCACCTCATCTTT 60.245 47.826 0.00 0.00 39.86 2.52
3055 4861 2.483188 CGGAAAGATGTAGCCACCCTAC 60.483 54.545 0.00 0.00 45.44 3.18
3303 5120 2.600731 GAGGGAGATGATTATCACGCG 58.399 52.381 3.53 3.53 40.22 6.01
3309 5126 1.831389 ATGATTATCACGCGCGGTGC 61.831 55.000 35.22 15.51 46.56 5.01
3512 5344 2.288666 GTATGTATGTGGCAGGTGGTG 58.711 52.381 0.00 0.00 0.00 4.17
3548 5380 2.833631 ACGAAATCTCCTGTCGGTTT 57.166 45.000 0.00 0.00 39.07 3.27
3568 5403 9.144298 TCGGTTTCTCTCCTAATTAATCACTAT 57.856 33.333 0.00 0.00 0.00 2.12
3586 5421 7.934855 TCACTATATAATACTCCCTTCGTCC 57.065 40.000 0.00 0.00 0.00 4.79
3587 5422 6.888632 TCACTATATAATACTCCCTTCGTCCC 59.111 42.308 0.00 0.00 0.00 4.46
3588 5423 6.662234 CACTATATAATACTCCCTTCGTCCCA 59.338 42.308 0.00 0.00 0.00 4.37
3589 5424 7.177921 CACTATATAATACTCCCTTCGTCCCAA 59.822 40.741 0.00 0.00 0.00 4.12
3590 5425 7.731688 ACTATATAATACTCCCTTCGTCCCAAA 59.268 37.037 0.00 0.00 0.00 3.28
3591 5426 5.703730 ATAATACTCCCTTCGTCCCAAAA 57.296 39.130 0.00 0.00 0.00 2.44
3592 5427 4.586306 AATACTCCCTTCGTCCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
3593 5428 5.703730 AATACTCCCTTCGTCCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
3594 5429 5.703730 ATACTCCCTTCGTCCCAAAATAA 57.296 39.130 0.00 0.00 0.00 1.40
3595 5430 3.951663 ACTCCCTTCGTCCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
3596 5431 3.329814 ACTCCCTTCGTCCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
3597 5432 3.681593 TCCCTTCGTCCCAAAATAAGTG 58.318 45.455 0.00 0.00 0.00 3.16
3598 5433 3.073356 TCCCTTCGTCCCAAAATAAGTGT 59.927 43.478 0.00 0.00 0.00 3.55
3599 5434 3.439129 CCCTTCGTCCCAAAATAAGTGTC 59.561 47.826 0.00 0.00 0.00 3.67
3600 5435 4.324267 CCTTCGTCCCAAAATAAGTGTCT 58.676 43.478 0.00 0.00 0.00 3.41
3601 5436 4.392138 CCTTCGTCCCAAAATAAGTGTCTC 59.608 45.833 0.00 0.00 0.00 3.36
3602 5437 4.610605 TCGTCCCAAAATAAGTGTCTCA 57.389 40.909 0.00 0.00 0.00 3.27
3603 5438 4.963373 TCGTCCCAAAATAAGTGTCTCAA 58.037 39.130 0.00 0.00 0.00 3.02
3604 5439 4.753107 TCGTCCCAAAATAAGTGTCTCAAC 59.247 41.667 0.00 0.00 0.00 3.18
3605 5440 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3606 5441 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3607 5442 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3608 5443 7.041644 CGTCCCAAAATAAGTGTCTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
3609 5444 8.290325 GTCCCAAAATAAGTGTCTCAACTTTAG 58.710 37.037 0.00 0.00 40.77 1.85
3610 5445 7.996644 TCCCAAAATAAGTGTCTCAACTTTAGT 59.003 33.333 0.00 0.00 40.77 2.24
3611 5446 9.280174 CCCAAAATAAGTGTCTCAACTTTAGTA 57.720 33.333 0.00 0.00 40.77 1.82
3618 5453 8.788325 AAGTGTCTCAACTTTAGTACAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
3619 5454 9.880157 AAGTGTCTCAACTTTAGTACAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
3652 5487 9.490379 AAGTGTCTCAACTTTAGTATAAAGGTG 57.510 33.333 17.37 17.37 44.18 4.00
3657 5492 7.011499 TCAACTTTAGTATAAAGGTGAGGCA 57.989 36.000 20.62 4.70 45.82 4.75
3658 5493 6.877322 TCAACTTTAGTATAAAGGTGAGGCAC 59.123 38.462 20.62 0.00 45.82 5.01
3659 5494 6.879458 CAACTTTAGTATAAAGGTGAGGCACT 59.121 38.462 18.26 0.00 45.30 4.40
3660 5495 7.017319 ACTTTAGTATAAAGGTGAGGCACTT 57.983 36.000 12.53 0.00 41.55 3.16
3661 5496 8.142485 ACTTTAGTATAAAGGTGAGGCACTTA 57.858 34.615 12.53 0.00 41.55 2.24
3662 5497 8.769359 ACTTTAGTATAAAGGTGAGGCACTTAT 58.231 33.333 12.53 0.00 41.55 1.73
3663 5498 9.614792 CTTTAGTATAAAGGTGAGGCACTTATT 57.385 33.333 0.00 0.00 41.55 1.40
3664 5499 9.969001 TTTAGTATAAAGGTGAGGCACTTATTT 57.031 29.630 0.00 0.00 41.55 1.40
3665 5500 9.969001 TTAGTATAAAGGTGAGGCACTTATTTT 57.031 29.630 0.00 0.00 41.55 1.82
3666 5501 8.281212 AGTATAAAGGTGAGGCACTTATTTTG 57.719 34.615 0.00 0.00 41.55 2.44
3667 5502 4.871933 AAAGGTGAGGCACTTATTTTGG 57.128 40.909 0.00 0.00 41.55 3.28
3668 5503 2.807676 AGGTGAGGCACTTATTTTGGG 58.192 47.619 0.00 0.00 41.55 4.12
3669 5504 2.378547 AGGTGAGGCACTTATTTTGGGA 59.621 45.455 0.00 0.00 41.55 4.37
3670 5505 3.011708 AGGTGAGGCACTTATTTTGGGAT 59.988 43.478 0.00 0.00 41.55 3.85
3671 5506 3.131046 GGTGAGGCACTTATTTTGGGATG 59.869 47.826 0.00 0.00 41.55 3.51
3672 5507 3.131046 GTGAGGCACTTATTTTGGGATGG 59.869 47.826 0.00 0.00 41.55 3.51
3673 5508 3.011144 TGAGGCACTTATTTTGGGATGGA 59.989 43.478 0.00 0.00 41.55 3.41
3674 5509 3.633986 GAGGCACTTATTTTGGGATGGAG 59.366 47.826 0.00 0.00 41.55 3.86
3675 5510 2.695147 GGCACTTATTTTGGGATGGAGG 59.305 50.000 0.00 0.00 0.00 4.30
3676 5511 3.627237 GGCACTTATTTTGGGATGGAGGA 60.627 47.826 0.00 0.00 0.00 3.71
3677 5512 4.023291 GCACTTATTTTGGGATGGAGGAA 58.977 43.478 0.00 0.00 0.00 3.36
3678 5513 4.466015 GCACTTATTTTGGGATGGAGGAAA 59.534 41.667 0.00 0.00 0.00 3.13
3684 5519 5.993748 TTTTGGGATGGAGGAAATACAAC 57.006 39.130 0.00 0.00 0.00 3.32
3756 5591 0.476338 TTGTTAGGCAGCTGTTGGGA 59.524 50.000 16.64 0.00 0.00 4.37
3757 5592 0.476338 TGTTAGGCAGCTGTTGGGAA 59.524 50.000 16.64 0.16 0.00 3.97
3850 5686 2.827322 TCCAAATGGCAAATCTCACTGG 59.173 45.455 0.00 0.00 34.44 4.00
3865 5704 4.755123 TCTCACTGGCTTTAGTTTTGTAGC 59.245 41.667 0.00 0.00 0.00 3.58
3870 5709 7.229707 TCACTGGCTTTAGTTTTGTAGCATAAA 59.770 33.333 0.00 0.00 35.36 1.40
3896 5735 6.327626 AGGCAATCATAGTATCTAACACCTGT 59.672 38.462 0.00 0.00 0.00 4.00
3905 5744 6.491383 AGTATCTAACACCTGTTCTACTGGA 58.509 40.000 9.37 0.00 39.29 3.86
3914 5753 8.235359 ACACCTGTTCTACTGGAATAGTATAC 57.765 38.462 9.37 0.00 40.94 1.47
3938 5777 8.344446 ACTAACAATAAATTAACCTCACACCC 57.656 34.615 0.00 0.00 0.00 4.61
3947 5786 5.633655 TTAACCTCACACCCTTTGTCTTA 57.366 39.130 0.00 0.00 35.67 2.10
3949 5788 3.046374 ACCTCACACCCTTTGTCTTACT 58.954 45.455 0.00 0.00 35.67 2.24
3950 5789 4.228824 ACCTCACACCCTTTGTCTTACTA 58.771 43.478 0.00 0.00 35.67 1.82
3951 5790 4.040095 ACCTCACACCCTTTGTCTTACTAC 59.960 45.833 0.00 0.00 35.67 2.73
3960 5799 6.014755 ACCCTTTGTCTTACTACTACCAAGAC 60.015 42.308 6.73 6.73 45.41 3.01
3966 5805 4.158025 TCTTACTACTACCAAGACAGCAGC 59.842 45.833 0.00 0.00 0.00 5.25
3968 5807 0.902531 TACTACCAAGACAGCAGCCC 59.097 55.000 0.00 0.00 0.00 5.19
3982 5821 1.755179 CAGCCCACCCAACAGAATAG 58.245 55.000 0.00 0.00 0.00 1.73
3983 5822 1.281867 CAGCCCACCCAACAGAATAGA 59.718 52.381 0.00 0.00 0.00 1.98
3984 5823 1.282157 AGCCCACCCAACAGAATAGAC 59.718 52.381 0.00 0.00 0.00 2.59
3985 5824 1.004277 GCCCACCCAACAGAATAGACA 59.996 52.381 0.00 0.00 0.00 3.41
3986 5825 2.711542 CCCACCCAACAGAATAGACAC 58.288 52.381 0.00 0.00 0.00 3.67
3987 5826 2.305927 CCCACCCAACAGAATAGACACT 59.694 50.000 0.00 0.00 0.00 3.55
3988 5827 3.600388 CCACCCAACAGAATAGACACTC 58.400 50.000 0.00 0.00 0.00 3.51
3989 5828 3.007940 CCACCCAACAGAATAGACACTCA 59.992 47.826 0.00 0.00 0.00 3.41
3990 5829 4.323792 CCACCCAACAGAATAGACACTCAT 60.324 45.833 0.00 0.00 0.00 2.90
3991 5830 4.633126 CACCCAACAGAATAGACACTCATG 59.367 45.833 0.00 0.00 0.00 3.07
3992 5831 4.287067 ACCCAACAGAATAGACACTCATGT 59.713 41.667 0.00 0.00 43.71 3.21
4006 5845 6.169557 ACACTCATGTCCTACTTGTAAACA 57.830 37.500 0.00 0.00 31.55 2.83
4007 5846 6.588204 ACACTCATGTCCTACTTGTAAACAA 58.412 36.000 0.00 0.00 31.55 2.83
4008 5847 7.051623 ACACTCATGTCCTACTTGTAAACAAA 58.948 34.615 0.00 0.00 31.55 2.83
4009 5848 7.554835 ACACTCATGTCCTACTTGTAAACAAAA 59.445 33.333 0.00 0.00 31.55 2.44
4010 5849 8.070171 CACTCATGTCCTACTTGTAAACAAAAG 58.930 37.037 0.00 0.00 35.15 2.27
4011 5850 6.966021 TCATGTCCTACTTGTAAACAAAAGC 58.034 36.000 0.00 0.00 35.15 3.51
4012 5851 6.544197 TCATGTCCTACTTGTAAACAAAAGCA 59.456 34.615 0.00 0.00 35.15 3.91
4013 5852 6.761099 TGTCCTACTTGTAAACAAAAGCAA 57.239 33.333 0.00 0.00 35.15 3.91
4014 5853 7.159322 TGTCCTACTTGTAAACAAAAGCAAA 57.841 32.000 0.00 0.00 35.15 3.68
4015 5854 7.777095 TGTCCTACTTGTAAACAAAAGCAAAT 58.223 30.769 0.00 0.00 35.15 2.32
4016 5855 8.904834 TGTCCTACTTGTAAACAAAAGCAAATA 58.095 29.630 0.00 0.00 35.15 1.40
4017 5856 9.394477 GTCCTACTTGTAAACAAAAGCAAATAG 57.606 33.333 0.00 0.00 35.15 1.73
4018 5857 8.079809 TCCTACTTGTAAACAAAAGCAAATAGC 58.920 33.333 0.00 0.00 38.37 2.97
4019 5858 7.865385 CCTACTTGTAAACAAAAGCAAATAGCA 59.135 33.333 0.00 0.00 39.73 3.49
4020 5859 9.410556 CTACTTGTAAACAAAAGCAAATAGCAT 57.589 29.630 0.00 0.00 39.73 3.79
4021 5860 8.298030 ACTTGTAAACAAAAGCAAATAGCATC 57.702 30.769 0.00 0.00 39.73 3.91
4022 5861 7.925483 ACTTGTAAACAAAAGCAAATAGCATCA 59.075 29.630 0.00 0.00 39.73 3.07
4023 5862 8.654230 TTGTAAACAAAAGCAAATAGCATCAA 57.346 26.923 0.00 0.00 38.20 2.57
4024 5863 8.763356 TTGTAAACAAAAGCAAATAGCATCAAG 58.237 29.630 0.00 0.00 38.20 3.02
4032 5871 5.399604 GCAAATAGCATCAAGGATTTTGC 57.600 39.130 9.14 9.14 44.79 3.68
4033 5872 5.114081 GCAAATAGCATCAAGGATTTTGCT 58.886 37.500 14.27 7.92 44.42 3.91
4034 5873 5.583457 GCAAATAGCATCAAGGATTTTGCTT 59.417 36.000 14.27 0.00 40.84 3.91
4035 5874 6.238022 GCAAATAGCATCAAGGATTTTGCTTC 60.238 38.462 14.27 0.00 40.84 3.86
4036 5875 6.534475 AATAGCATCAAGGATTTTGCTTCA 57.466 33.333 1.22 0.00 40.84 3.02
4037 5876 4.877378 AGCATCAAGGATTTTGCTTCAA 57.123 36.364 0.00 0.00 40.84 2.69
4038 5877 4.817517 AGCATCAAGGATTTTGCTTCAAG 58.182 39.130 0.00 0.00 40.84 3.02
4039 5878 4.282703 AGCATCAAGGATTTTGCTTCAAGT 59.717 37.500 0.00 0.00 40.84 3.16
4040 5879 4.387862 GCATCAAGGATTTTGCTTCAAGTG 59.612 41.667 0.00 0.00 33.23 3.16
4041 5880 5.775686 CATCAAGGATTTTGCTTCAAGTGA 58.224 37.500 0.00 0.00 0.00 3.41
4042 5881 6.395629 CATCAAGGATTTTGCTTCAAGTGAT 58.604 36.000 0.00 0.00 0.00 3.06
4043 5882 6.409524 TCAAGGATTTTGCTTCAAGTGATT 57.590 33.333 0.00 0.00 0.00 2.57
4044 5883 7.523293 TCAAGGATTTTGCTTCAAGTGATTA 57.477 32.000 0.00 0.00 0.00 1.75
4045 5884 7.950512 TCAAGGATTTTGCTTCAAGTGATTAA 58.049 30.769 0.00 0.00 0.00 1.40
4046 5885 7.867403 TCAAGGATTTTGCTTCAAGTGATTAAC 59.133 33.333 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.620738 ATCTGTATATGGAGTGTGTGCTT 57.379 39.130 0.00 0.00 0.00 3.91
1 2 6.924913 ATATCTGTATATGGAGTGTGTGCT 57.075 37.500 0.00 0.00 0.00 4.40
2 3 7.757173 CAGTATATCTGTATATGGAGTGTGTGC 59.243 40.741 0.00 0.00 39.17 4.57
19 20 7.576666 GCTCGATCATCTCCAAACAGTATATCT 60.577 40.741 0.00 0.00 0.00 1.98
20 21 6.529829 GCTCGATCATCTCCAAACAGTATATC 59.470 42.308 0.00 0.00 0.00 1.63
26 27 1.857217 CGCTCGATCATCTCCAAACAG 59.143 52.381 0.00 0.00 0.00 3.16
38 39 4.560856 AGCTGCCGACGCTCGATC 62.561 66.667 8.63 0.00 43.74 3.69
39 40 4.560856 GAGCTGCCGACGCTCGAT 62.561 66.667 0.00 0.00 43.74 3.59
62 65 2.125350 CGCCTGAGCCTTCACTCC 60.125 66.667 0.00 0.00 35.72 3.85
85 88 1.341080 CCCTTGACATTGGGCAAAGT 58.659 50.000 1.65 0.00 36.61 2.66
144 153 6.145534 TGGCTAAAAGTCTATCAAATATCGCG 59.854 38.462 0.00 0.00 0.00 5.87
152 161 9.113838 GAAATGATCTGGCTAAAAGTCTATCAA 57.886 33.333 0.00 0.00 30.75 2.57
159 168 4.878397 CCTCGAAATGATCTGGCTAAAAGT 59.122 41.667 0.00 0.00 0.00 2.66
170 179 6.610741 AACTAAGCAATCCTCGAAATGATC 57.389 37.500 0.00 0.00 0.00 2.92
181 190 7.095017 GCATCCTAGTGATAAACTAAGCAATCC 60.095 40.741 0.00 0.00 40.92 3.01
186 195 7.117523 CAGATGCATCCTAGTGATAAACTAAGC 59.882 40.741 23.06 0.00 40.92 3.09
210 219 2.012673 GGTAAAGATGCAGGCACTCAG 58.987 52.381 0.00 0.00 34.60 3.35
239 249 8.322091 AGTTGTTCATAGCTAGGTCACTTATTT 58.678 33.333 5.15 0.00 0.00 1.40
243 253 5.482908 CAGTTGTTCATAGCTAGGTCACTT 58.517 41.667 5.15 0.00 0.00 3.16
312 322 1.065551 GGCGACCCAATAAAGCATCAC 59.934 52.381 0.00 0.00 0.00 3.06
342 352 2.487532 CCCGCCACCGAGGTAGTAG 61.488 68.421 0.00 0.00 40.61 2.57
343 353 2.440796 CCCGCCACCGAGGTAGTA 60.441 66.667 0.00 0.00 40.61 1.82
376 386 2.940158 TGATCATGCCATTTCCCTCTG 58.060 47.619 0.00 0.00 0.00 3.35
419 429 0.179124 CTCTCTTTTCTCCTCGCGGG 60.179 60.000 6.13 0.59 0.00 6.13
509 519 5.581085 CGCATCATAGGCTTAATTAGGGTAC 59.419 44.000 0.00 0.00 0.00 3.34
510 520 5.730550 CGCATCATAGGCTTAATTAGGGTA 58.269 41.667 0.00 0.00 0.00 3.69
511 521 4.579869 CGCATCATAGGCTTAATTAGGGT 58.420 43.478 0.00 0.00 0.00 4.34
512 522 3.375299 GCGCATCATAGGCTTAATTAGGG 59.625 47.826 0.30 0.00 0.00 3.53
513 523 3.375299 GGCGCATCATAGGCTTAATTAGG 59.625 47.826 10.83 0.00 0.00 2.69
514 524 3.062639 CGGCGCATCATAGGCTTAATTAG 59.937 47.826 10.83 0.00 0.00 1.73
515 525 3.000041 CGGCGCATCATAGGCTTAATTA 59.000 45.455 10.83 0.00 0.00 1.40
516 526 1.806542 CGGCGCATCATAGGCTTAATT 59.193 47.619 10.83 0.00 0.00 1.40
517 527 1.270839 ACGGCGCATCATAGGCTTAAT 60.271 47.619 10.83 0.00 0.00 1.40
518 528 0.105964 ACGGCGCATCATAGGCTTAA 59.894 50.000 10.83 0.00 0.00 1.85
519 529 0.963225 TACGGCGCATCATAGGCTTA 59.037 50.000 10.83 0.00 0.00 3.09
520 530 0.600255 GTACGGCGCATCATAGGCTT 60.600 55.000 10.83 0.00 0.00 4.35
521 531 1.006102 GTACGGCGCATCATAGGCT 60.006 57.895 10.83 0.00 0.00 4.58
522 532 2.372690 CGTACGGCGCATCATAGGC 61.373 63.158 10.83 0.00 0.00 3.93
523 533 0.239082 TACGTACGGCGCATCATAGG 59.761 55.000 21.06 3.74 46.11 2.57
524 534 1.324718 GTACGTACGGCGCATCATAG 58.675 55.000 21.06 0.00 46.11 2.23
525 535 0.662085 TGTACGTACGGCGCATCATA 59.338 50.000 21.06 0.00 46.11 2.15
526 536 0.031585 ATGTACGTACGGCGCATCAT 59.968 50.000 21.06 10.88 46.11 2.45
527 537 0.662085 TATGTACGTACGGCGCATCA 59.338 50.000 21.06 9.12 46.11 3.07
528 538 1.324718 CTATGTACGTACGGCGCATC 58.675 55.000 21.06 3.74 46.11 3.91
529 539 0.664761 ACTATGTACGTACGGCGCAT 59.335 50.000 21.06 20.16 46.11 4.73
530 540 0.248175 CACTATGTACGTACGGCGCA 60.248 55.000 21.06 14.84 46.11 6.09
531 541 1.534811 GCACTATGTACGTACGGCGC 61.535 60.000 21.06 13.85 46.11 6.53
533 543 1.202222 ACAGCACTATGTACGTACGGC 60.202 52.381 21.06 16.77 0.00 5.68
534 544 2.540361 GGACAGCACTATGTACGTACGG 60.540 54.545 21.06 14.62 32.25 4.02
535 545 2.096335 TGGACAGCACTATGTACGTACG 59.904 50.000 20.18 15.01 36.77 3.67
536 546 3.770263 TGGACAGCACTATGTACGTAC 57.230 47.619 18.90 18.90 36.77 3.67
537 547 3.760151 ACTTGGACAGCACTATGTACGTA 59.240 43.478 0.00 0.00 36.77 3.57
538 548 2.561419 ACTTGGACAGCACTATGTACGT 59.439 45.455 0.00 0.00 36.77 3.57
550 796 4.252878 TGTGTATGTATGCACTTGGACAG 58.747 43.478 12.99 0.00 42.76 3.51
569 975 3.061563 CGTACGTATCACCAACCAATGTG 59.938 47.826 7.22 0.00 0.00 3.21
570 976 3.255725 CGTACGTATCACCAACCAATGT 58.744 45.455 7.22 0.00 0.00 2.71
665 1077 2.899976 CCCAATGTACGTATGCACTGA 58.100 47.619 0.00 0.00 0.00 3.41
673 1085 0.108709 GTCACCGCCCAATGTACGTA 60.109 55.000 0.00 0.00 0.00 3.57
761 1173 3.339093 AGGGTAGGGTGCAAGGGC 61.339 66.667 0.00 0.00 41.68 5.19
769 1181 1.757340 GTCGCTAGCAGGGTAGGGT 60.757 63.158 16.45 0.00 35.13 4.34
808 1224 1.000233 GGGTGGTGATGGCATGGAA 60.000 57.895 3.81 0.00 0.00 3.53
815 1231 4.358841 TTGGCGGGGTGGTGATGG 62.359 66.667 0.00 0.00 0.00 3.51
817 1233 4.740822 GCTTGGCGGGGTGGTGAT 62.741 66.667 0.00 0.00 0.00 3.06
907 1327 2.031012 TGCACCTCGAAGGCAGTG 59.969 61.111 1.61 0.00 39.63 3.66
916 1336 3.932580 TTAGTGGCGCTGCACCTCG 62.933 63.158 11.58 0.00 0.00 4.63
918 1338 2.358737 GTTAGTGGCGCTGCACCT 60.359 61.111 11.58 1.00 0.00 4.00
919 1339 3.431725 GGTTAGTGGCGCTGCACC 61.432 66.667 11.58 12.78 0.00 5.01
920 1340 2.187599 CTTGGTTAGTGGCGCTGCAC 62.188 60.000 11.58 8.18 0.00 4.57
921 1341 1.965930 CTTGGTTAGTGGCGCTGCA 60.966 57.895 11.58 0.00 0.00 4.41
926 1351 1.639298 GCTCTGCTTGGTTAGTGGCG 61.639 60.000 0.00 0.00 0.00 5.69
928 1353 1.160137 GTGCTCTGCTTGGTTAGTGG 58.840 55.000 0.00 0.00 0.00 4.00
961 1386 5.600669 TGGGAGATGGAGCTATCTAGTTA 57.399 43.478 0.00 0.00 37.53 2.24
962 1387 4.477536 TGGGAGATGGAGCTATCTAGTT 57.522 45.455 0.00 0.00 37.53 2.24
965 1390 3.898123 GTGTTGGGAGATGGAGCTATCTA 59.102 47.826 0.00 0.00 37.53 1.98
966 1391 2.703007 GTGTTGGGAGATGGAGCTATCT 59.297 50.000 0.00 0.00 40.02 1.98
968 1393 1.771255 GGTGTTGGGAGATGGAGCTAT 59.229 52.381 0.00 0.00 0.00 2.97
969 1394 1.204146 GGTGTTGGGAGATGGAGCTA 58.796 55.000 0.00 0.00 0.00 3.32
970 1395 1.903877 CGGTGTTGGGAGATGGAGCT 61.904 60.000 0.00 0.00 0.00 4.09
971 1396 1.450312 CGGTGTTGGGAGATGGAGC 60.450 63.158 0.00 0.00 0.00 4.70
973 1398 2.966732 GCCGGTGTTGGGAGATGGA 61.967 63.158 1.90 0.00 0.00 3.41
974 1399 2.438434 GCCGGTGTTGGGAGATGG 60.438 66.667 1.90 0.00 0.00 3.51
975 1400 2.819595 CGCCGGTGTTGGGAGATG 60.820 66.667 6.91 0.00 0.00 2.90
976 1401 4.096003 CCGCCGGTGTTGGGAGAT 62.096 66.667 15.14 0.00 0.00 2.75
1227 1652 1.295423 GGCGTTCTTGAGGTAGCCA 59.705 57.895 0.00 0.00 43.65 4.75
1812 2567 0.106708 TCTTGAGGAACAGCTTGCGT 59.893 50.000 0.00 0.00 0.00 5.24
1878 2767 1.302431 CCACGACATGTTGAGCCCA 60.302 57.895 20.26 0.00 0.00 5.36
2214 3934 9.214957 CATGTATGTGTGTTTTAAACTCCTAGA 57.785 33.333 9.33 0.00 0.00 2.43
2215 3935 8.450964 CCATGTATGTGTGTTTTAAACTCCTAG 58.549 37.037 9.33 0.00 0.00 3.02
2216 3936 8.158132 TCCATGTATGTGTGTTTTAAACTCCTA 58.842 33.333 9.33 0.00 0.00 2.94
2274 3995 3.035363 TGTCACAGTGTCACCCTTCTAA 58.965 45.455 0.00 0.00 0.00 2.10
2484 4272 6.988522 AGCAATTTGGTCCGTTTTATACTTT 58.011 32.000 0.00 0.00 0.00 2.66
2491 4279 5.944007 ACTAGATAGCAATTTGGTCCGTTTT 59.056 36.000 4.03 0.00 0.00 2.43
2492 4280 5.497474 ACTAGATAGCAATTTGGTCCGTTT 58.503 37.500 4.03 0.00 0.00 3.60
2529 4318 7.556733 TTTAAGCTAGCTAGAGTCTACTGAC 57.443 40.000 25.15 2.33 43.22 3.51
2728 4534 0.535553 TTACACCGCCGGAGCTTTTT 60.536 50.000 11.71 0.00 36.60 1.94
2736 4542 2.807895 CGTCACTTACACCGCCGG 60.808 66.667 0.00 0.00 0.00 6.13
2878 4684 1.684386 CCAGCAGCGAGAGATTCCCT 61.684 60.000 0.00 0.00 0.00 4.20
2884 4690 3.071206 GACCCCAGCAGCGAGAGA 61.071 66.667 0.00 0.00 0.00 3.10
2947 4753 1.776662 AGGTGAGCTCATAGGCGTTA 58.223 50.000 21.47 0.00 37.29 3.18
2956 4762 0.687354 GGTTCCAGAAGGTGAGCTCA 59.313 55.000 13.74 13.74 35.89 4.26
3055 4861 0.535102 GGGCGATGTTGGTAGATGGG 60.535 60.000 0.00 0.00 0.00 4.00
3123 4933 2.627515 ATGTACAGGCTGCTGGTATG 57.372 50.000 15.89 0.00 0.00 2.39
3281 5096 2.354203 GCGTGATAATCATCTCCCTCCC 60.354 54.545 0.00 0.00 31.93 4.30
3309 5126 5.678483 CAGTGCACTGCTTAATTAATTAGCG 59.322 40.000 32.39 4.20 37.15 4.26
3343 5160 3.836365 TTAATCCATGCAGATCACCGA 57.164 42.857 0.00 0.00 0.00 4.69
3344 5161 4.067192 TCATTAATCCATGCAGATCACCG 58.933 43.478 0.00 0.00 0.00 4.94
3530 5362 2.924290 GAGAAACCGACAGGAGATTTCG 59.076 50.000 0.00 0.00 41.02 3.46
3568 5403 6.811634 TTTTGGGACGAAGGGAGTATTATA 57.188 37.500 0.00 0.00 0.00 0.98
3576 5411 3.073356 ACACTTATTTTGGGACGAAGGGA 59.927 43.478 0.00 0.00 0.00 4.20
3577 5412 3.418047 ACACTTATTTTGGGACGAAGGG 58.582 45.455 0.00 0.00 0.00 3.95
3578 5413 4.324267 AGACACTTATTTTGGGACGAAGG 58.676 43.478 0.00 0.00 0.00 3.46
3579 5414 4.994852 TGAGACACTTATTTTGGGACGAAG 59.005 41.667 0.00 0.00 0.00 3.79
3580 5415 4.963373 TGAGACACTTATTTTGGGACGAA 58.037 39.130 0.00 0.00 0.00 3.85
3581 5416 4.610605 TGAGACACTTATTTTGGGACGA 57.389 40.909 0.00 0.00 0.00 4.20
3582 5417 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
3583 5418 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3584 5419 7.996644 ACTAAAGTTGAGACACTTATTTTGGGA 59.003 33.333 0.00 0.00 35.87 4.37
3585 5420 8.166422 ACTAAAGTTGAGACACTTATTTTGGG 57.834 34.615 0.00 0.00 35.87 4.12
3592 5427 9.880157 AAAGTTGTACTAAAGTTGAGACACTTA 57.120 29.630 0.00 0.00 35.87 2.24
3593 5428 8.788325 AAAGTTGTACTAAAGTTGAGACACTT 57.212 30.769 0.00 0.00 38.74 3.16
3626 5461 9.490379 CACCTTTATACTAAAGTTGAGACACTT 57.510 33.333 0.00 0.00 38.74 3.16
3627 5462 8.867097 TCACCTTTATACTAAAGTTGAGACACT 58.133 33.333 0.00 0.00 27.84 3.55
3628 5463 9.141400 CTCACCTTTATACTAAAGTTGAGACAC 57.859 37.037 20.65 0.00 44.50 3.67
3629 5464 8.311836 CCTCACCTTTATACTAAAGTTGAGACA 58.688 37.037 24.22 1.63 44.50 3.41
3630 5465 7.278203 GCCTCACCTTTATACTAAAGTTGAGAC 59.722 40.741 24.22 15.45 44.50 3.36
3631 5466 7.038587 TGCCTCACCTTTATACTAAAGTTGAGA 60.039 37.037 24.22 11.08 44.50 3.27
3632 5467 7.064728 GTGCCTCACCTTTATACTAAAGTTGAG 59.935 40.741 19.31 19.31 42.67 3.02
3633 5468 6.877322 GTGCCTCACCTTTATACTAAAGTTGA 59.123 38.462 6.68 6.68 29.93 3.18
3634 5469 6.879458 AGTGCCTCACCTTTATACTAAAGTTG 59.121 38.462 6.04 2.82 34.49 3.16
3635 5470 7.017319 AGTGCCTCACCTTTATACTAAAGTT 57.983 36.000 6.04 0.00 34.49 2.66
3636 5471 6.622427 AGTGCCTCACCTTTATACTAAAGT 57.378 37.500 6.04 0.00 34.49 2.66
3637 5472 9.614792 AATAAGTGCCTCACCTTTATACTAAAG 57.385 33.333 0.61 0.61 34.49 1.85
3638 5473 9.969001 AAATAAGTGCCTCACCTTTATACTAAA 57.031 29.630 0.00 0.00 34.49 1.85
3639 5474 9.969001 AAAATAAGTGCCTCACCTTTATACTAA 57.031 29.630 0.00 0.00 34.49 2.24
3640 5475 9.391006 CAAAATAAGTGCCTCACCTTTATACTA 57.609 33.333 0.00 0.00 34.49 1.82
3641 5476 7.339466 CCAAAATAAGTGCCTCACCTTTATACT 59.661 37.037 0.00 0.00 34.49 2.12
3642 5477 7.416326 CCCAAAATAAGTGCCTCACCTTTATAC 60.416 40.741 0.00 0.00 34.49 1.47
3643 5478 6.605594 CCCAAAATAAGTGCCTCACCTTTATA 59.394 38.462 0.00 0.00 34.49 0.98
3644 5479 5.422012 CCCAAAATAAGTGCCTCACCTTTAT 59.578 40.000 0.00 0.00 34.49 1.40
3645 5480 4.770010 CCCAAAATAAGTGCCTCACCTTTA 59.230 41.667 0.00 0.00 34.49 1.85
3646 5481 3.578282 CCCAAAATAAGTGCCTCACCTTT 59.422 43.478 0.00 0.00 34.49 3.11
3647 5482 3.165071 CCCAAAATAAGTGCCTCACCTT 58.835 45.455 0.00 0.00 34.49 3.50
3648 5483 2.378547 TCCCAAAATAAGTGCCTCACCT 59.621 45.455 0.00 0.00 34.49 4.00
3649 5484 2.802719 TCCCAAAATAAGTGCCTCACC 58.197 47.619 0.00 0.00 34.49 4.02
3650 5485 3.131046 CCATCCCAAAATAAGTGCCTCAC 59.869 47.826 0.00 0.00 34.10 3.51
3651 5486 3.011144 TCCATCCCAAAATAAGTGCCTCA 59.989 43.478 0.00 0.00 0.00 3.86
3652 5487 3.631250 TCCATCCCAAAATAAGTGCCTC 58.369 45.455 0.00 0.00 0.00 4.70
3653 5488 3.628257 CCTCCATCCCAAAATAAGTGCCT 60.628 47.826 0.00 0.00 0.00 4.75
3654 5489 2.695147 CCTCCATCCCAAAATAAGTGCC 59.305 50.000 0.00 0.00 0.00 5.01
3655 5490 3.631250 TCCTCCATCCCAAAATAAGTGC 58.369 45.455 0.00 0.00 0.00 4.40
3656 5491 6.796785 ATTTCCTCCATCCCAAAATAAGTG 57.203 37.500 0.00 0.00 0.00 3.16
3657 5492 7.418378 TGTATTTCCTCCATCCCAAAATAAGT 58.582 34.615 0.00 0.00 0.00 2.24
3658 5493 7.896383 TGTATTTCCTCCATCCCAAAATAAG 57.104 36.000 0.00 0.00 0.00 1.73
3659 5494 7.125053 GGTTGTATTTCCTCCATCCCAAAATAA 59.875 37.037 0.00 0.00 0.00 1.40
3660 5495 6.609616 GGTTGTATTTCCTCCATCCCAAAATA 59.390 38.462 0.00 0.00 0.00 1.40
3661 5496 5.425217 GGTTGTATTTCCTCCATCCCAAAAT 59.575 40.000 0.00 0.00 0.00 1.82
3662 5497 4.775253 GGTTGTATTTCCTCCATCCCAAAA 59.225 41.667 0.00 0.00 0.00 2.44
3663 5498 4.202727 TGGTTGTATTTCCTCCATCCCAAA 60.203 41.667 0.00 0.00 0.00 3.28
3664 5499 3.335183 TGGTTGTATTTCCTCCATCCCAA 59.665 43.478 0.00 0.00 0.00 4.12
3665 5500 2.922955 TGGTTGTATTTCCTCCATCCCA 59.077 45.455 0.00 0.00 0.00 4.37
3666 5501 3.662759 TGGTTGTATTTCCTCCATCCC 57.337 47.619 0.00 0.00 0.00 3.85
3667 5502 7.839680 ATTTATGGTTGTATTTCCTCCATCC 57.160 36.000 0.00 0.00 39.28 3.51
3726 5561 4.995487 AGCTGCCTAACAACACTTTACTAC 59.005 41.667 0.00 0.00 0.00 2.73
3729 5564 3.564225 ACAGCTGCCTAACAACACTTTAC 59.436 43.478 15.27 0.00 0.00 2.01
3736 5571 0.598065 CCCAACAGCTGCCTAACAAC 59.402 55.000 15.27 0.00 0.00 3.32
3850 5686 6.866248 TGCCTTTTATGCTACAAAACTAAAGC 59.134 34.615 0.00 0.00 35.51 3.51
3870 5709 7.147479 ACAGGTGTTAGATACTATGATTGCCTT 60.147 37.037 0.00 0.00 0.00 4.35
3914 5753 8.575649 AGGGTGTGAGGTTAATTTATTGTTAG 57.424 34.615 0.00 0.00 0.00 2.34
3917 5756 7.289084 ACAAAGGGTGTGAGGTTAATTTATTGT 59.711 33.333 0.00 0.00 39.72 2.71
3918 5757 7.666623 ACAAAGGGTGTGAGGTTAATTTATTG 58.333 34.615 0.00 0.00 39.72 1.90
3919 5758 7.728532 AGACAAAGGGTGTGAGGTTAATTTATT 59.271 33.333 0.00 0.00 41.96 1.40
3920 5759 7.238710 AGACAAAGGGTGTGAGGTTAATTTAT 58.761 34.615 0.00 0.00 41.96 1.40
3921 5760 6.607019 AGACAAAGGGTGTGAGGTTAATTTA 58.393 36.000 0.00 0.00 41.96 1.40
3934 5773 5.733620 TGGTAGTAGTAAGACAAAGGGTG 57.266 43.478 0.00 0.00 0.00 4.61
3935 5774 6.014755 GTCTTGGTAGTAGTAAGACAAAGGGT 60.015 42.308 16.19 0.00 45.88 4.34
3947 5786 1.550976 GGCTGCTGTCTTGGTAGTAGT 59.449 52.381 0.00 0.00 0.00 2.73
3949 5788 0.902531 GGGCTGCTGTCTTGGTAGTA 59.097 55.000 0.00 0.00 0.00 1.82
3950 5789 1.127567 TGGGCTGCTGTCTTGGTAGT 61.128 55.000 0.00 0.00 0.00 2.73
3951 5790 0.674895 GTGGGCTGCTGTCTTGGTAG 60.675 60.000 0.00 0.00 0.00 3.18
3960 5799 2.981914 TTCTGTTGGGTGGGCTGCTG 62.982 60.000 0.00 0.00 0.00 4.41
3966 5805 2.305927 AGTGTCTATTCTGTTGGGTGGG 59.694 50.000 0.00 0.00 0.00 4.61
3968 5807 4.271696 TGAGTGTCTATTCTGTTGGGTG 57.728 45.455 0.00 0.00 0.00 4.61
3982 5821 7.225931 TTTGTTTACAAGTAGGACATGAGTGTC 59.774 37.037 0.00 0.05 43.94 3.67
3983 5822 6.169557 TGTTTACAAGTAGGACATGAGTGT 57.830 37.500 0.00 0.00 42.49 3.55
3984 5823 7.490962 TTTGTTTACAAGTAGGACATGAGTG 57.509 36.000 0.00 0.00 37.15 3.51
3985 5824 7.255139 GCTTTTGTTTACAAGTAGGACATGAGT 60.255 37.037 0.00 0.00 37.15 3.41
3986 5825 7.078228 GCTTTTGTTTACAAGTAGGACATGAG 58.922 38.462 0.00 0.00 37.15 2.90
3987 5826 6.544197 TGCTTTTGTTTACAAGTAGGACATGA 59.456 34.615 0.00 0.00 37.15 3.07
3988 5827 6.734137 TGCTTTTGTTTACAAGTAGGACATG 58.266 36.000 0.00 0.00 37.15 3.21
3989 5828 6.952773 TGCTTTTGTTTACAAGTAGGACAT 57.047 33.333 0.00 0.00 37.15 3.06
3990 5829 6.761099 TTGCTTTTGTTTACAAGTAGGACA 57.239 33.333 0.00 0.00 37.15 4.02
3991 5830 9.394477 CTATTTGCTTTTGTTTACAAGTAGGAC 57.606 33.333 0.00 0.00 37.15 3.85
3992 5831 8.079809 GCTATTTGCTTTTGTTTACAAGTAGGA 58.920 33.333 0.00 0.00 34.64 2.94
3993 5832 7.865385 TGCTATTTGCTTTTGTTTACAAGTAGG 59.135 33.333 0.00 0.00 43.37 3.18
3994 5833 8.795786 TGCTATTTGCTTTTGTTTACAAGTAG 57.204 30.769 0.00 0.00 43.37 2.57
3995 5834 9.405587 GATGCTATTTGCTTTTGTTTACAAGTA 57.594 29.630 0.00 0.00 43.37 2.24
3996 5835 7.925483 TGATGCTATTTGCTTTTGTTTACAAGT 59.075 29.630 0.00 0.00 43.37 3.16
3997 5836 8.296799 TGATGCTATTTGCTTTTGTTTACAAG 57.703 30.769 0.00 0.00 43.37 3.16
3998 5837 8.654230 TTGATGCTATTTGCTTTTGTTTACAA 57.346 26.923 0.00 0.00 43.37 2.41
3999 5838 7.384660 CCTTGATGCTATTTGCTTTTGTTTACA 59.615 33.333 0.00 0.00 43.37 2.41
4000 5839 7.598493 TCCTTGATGCTATTTGCTTTTGTTTAC 59.402 33.333 0.00 0.00 43.37 2.01
4001 5840 7.665690 TCCTTGATGCTATTTGCTTTTGTTTA 58.334 30.769 0.00 0.00 43.37 2.01
4002 5841 6.523840 TCCTTGATGCTATTTGCTTTTGTTT 58.476 32.000 0.00 0.00 43.37 2.83
4003 5842 6.100404 TCCTTGATGCTATTTGCTTTTGTT 57.900 33.333 0.00 0.00 43.37 2.83
4004 5843 5.726980 TCCTTGATGCTATTTGCTTTTGT 57.273 34.783 0.00 0.00 43.37 2.83
4005 5844 7.605410 AAATCCTTGATGCTATTTGCTTTTG 57.395 32.000 0.00 0.00 43.37 2.44
4006 5845 7.361457 GCAAAATCCTTGATGCTATTTGCTTTT 60.361 33.333 11.74 0.00 44.54 2.27
4007 5846 6.093082 GCAAAATCCTTGATGCTATTTGCTTT 59.907 34.615 11.74 0.00 44.54 3.51
4008 5847 5.583457 GCAAAATCCTTGATGCTATTTGCTT 59.417 36.000 11.74 0.00 44.54 3.91
4009 5848 5.114081 GCAAAATCCTTGATGCTATTTGCT 58.886 37.500 11.74 0.00 44.54 3.91
4010 5849 5.114081 AGCAAAATCCTTGATGCTATTTGC 58.886 37.500 11.22 11.22 46.61 3.68
4017 5856 4.387862 CACTTGAAGCAAAATCCTTGATGC 59.612 41.667 0.00 0.00 39.06 3.91
4018 5857 5.775686 TCACTTGAAGCAAAATCCTTGATG 58.224 37.500 0.00 0.00 0.00 3.07
4019 5858 6.600882 ATCACTTGAAGCAAAATCCTTGAT 57.399 33.333 0.00 0.00 0.00 2.57
4020 5859 6.409524 AATCACTTGAAGCAAAATCCTTGA 57.590 33.333 0.00 0.00 0.00 3.02
4021 5860 8.011067 GTTAATCACTTGAAGCAAAATCCTTG 57.989 34.615 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.