Multiple sequence alignment - TraesCS7A01G136600

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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 TraesCS7A01G136600 chr7A 100.000 4131 0 0 1 4131 89075696 89071566 0.000000e+00 7629.0
1 TraesCS7A01G136600 chr7A 100.000 29 0 0 2 30 567573940 567573912 2.000000e-03 54.7
2 TraesCS7A01G136600 chr7B 96.222 1694 59 1 1689 3382 36508264 36506576 0.000000e+00 2769.0
3 TraesCS7A01G136600 chr7B 91.076 1255 51 23 402 1597 36509582 36508330 0.000000e+00 1640.0
4 TraesCS7A01G136600 chr7B 92.769 567 28 6 3568 4131 36506583 36506027 0.000000e+00 808.0
5 TraesCS7A01G136600 chr7B 91.092 348 29 2 2949 3296 36505074 36504729 1.740000e-128 470.0
6 TraesCS7A01G136600 chr7D 95.352 1678 53 9 1688 3359 87749661 87751319 0.000000e+00 2643.0
7 TraesCS7A01G136600 chr7D 95.257 1476 52 7 131 1597 87748140 87749606 0.000000e+00 2322.0
8 TraesCS7A01G136600 chr7D 89.888 534 31 12 138 666 87769819 87769304 0.000000e+00 665.0
9 TraesCS7A01G136600 chr7D 88.473 347 34 4 2945 3290 87689471 87689130 8.260000e-112 414.0
10 TraesCS7A01G136600 chr7D 96.429 140 1 2 3 140 87770046 87769909 1.160000e-55 228.0
11 TraesCS7A01G136600 chr7D 88.235 187 18 1 3383 3569 368587379 368587197 1.930000e-53 220.0
12 TraesCS7A01G136600 chr7D 96.154 104 4 0 3678 3781 87769182 87769285 1.970000e-38 171.0
13 TraesCS7A01G136600 chr7D 100.000 29 0 0 2 30 501084376 501084348 2.000000e-03 54.7
14 TraesCS7A01G136600 chr2D 89.418 189 14 2 3380 3566 23725338 23725522 2.480000e-57 233.0
15 TraesCS7A01G136600 chr3D 87.027 185 23 1 3383 3566 465178836 465179020 1.510000e-49 207.0
16 TraesCS7A01G136600 chr6D 79.208 303 47 11 188 486 453470529 453470239 3.260000e-46 196.0
17 TraesCS7A01G136600 chr2A 77.580 281 46 14 198 472 564615495 564615764 1.990000e-33 154.0
18 TraesCS7A01G136600 chr2B 77.455 275 42 15 208 472 501014087 501013823 3.330000e-31 147.0
19 TraesCS7A01G136600 chr6B 77.122 271 46 14 208 472 701069504 701069244 4.300000e-30 143.0
20 TraesCS7A01G136600 chr6B 77.206 272 44 16 208 472 701071309 701071049 4.300000e-30 143.0
21 TraesCS7A01G136600 chr5B 76.727 275 52 12 205 472 599185340 599185609 4.300000e-30 143.0
22 TraesCS7A01G136600 chr5A 76.895 277 48 10 201 472 23590543 23590808 4.300000e-30 143.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G136600 chr7A 89071566 89075696 4130 True 7629.00 7629 100.00000 1 4131 1 chr7A.!!$R1 4130
1 TraesCS7A01G136600 chr7B 36504729 36509582 4853 True 1421.75 2769 92.78975 402 4131 4 chr7B.!!$R1 3729
2 TraesCS7A01G136600 chr7D 87748140 87751319 3179 False 2482.50 2643 95.30450 131 3359 2 chr7D.!!$F2 3228
3 TraesCS7A01G136600 chr7D 87769304 87770046 742 True 446.50 665 93.15850 3 666 2 chr7D.!!$R4 663

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
237 332 0.320697 AGCTCGGGTGAACAGTAACC 59.679 55.0 0.00 0.00 35.59 2.85 F
1204 1363 0.246757 GTACACGTTCATTGAGCGCG 60.247 55.0 20.74 14.86 39.75 6.86 F
1963 2129 0.459237 CCTACACGCTGCTCAAGGAG 60.459 60.0 0.00 0.00 36.50 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1852 0.305922 GCTATCTGCACGCACATTCC 59.694 55.0 0.0 0.0 42.31 3.01 R
2713 2879 0.512952 CGGCGAACCAGTTCTTGAAG 59.487 55.0 0.0 0.0 37.44 3.02 R
3474 3646 0.183492 TGATGATTAGTGGCTGGGGC 59.817 55.0 0.0 0.0 37.82 5.80 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
36 37 5.032846 ACCCATCTTTTACATGGAGAGAGA 58.967 41.667 0.00 0.00 43.32 3.10
37 38 5.130145 ACCCATCTTTTACATGGAGAGAGAG 59.870 44.000 0.00 0.00 43.32 3.20
56 57 1.822990 AGGCATGCAATTGTCCTTCTG 59.177 47.619 21.36 0.00 0.00 3.02
189 284 6.006449 CCTATAAAGCTAGCACAAATGGGAT 58.994 40.000 18.83 0.00 0.00 3.85
237 332 0.320697 AGCTCGGGTGAACAGTAACC 59.679 55.000 0.00 0.00 35.59 2.85
311 406 7.547019 TGTGAAACATTGACAAAATGCTTGTTA 59.453 29.630 3.67 0.00 45.67 2.41
330 425 6.007936 TGTTAGCTTGCAAAATTACATCGT 57.992 33.333 0.00 0.00 0.00 3.73
358 453 1.198867 CATTCGTGGAAATCGTGGCAA 59.801 47.619 0.00 0.00 0.00 4.52
359 454 0.871722 TTCGTGGAAATCGTGGCAAG 59.128 50.000 0.00 0.00 0.00 4.01
360 455 0.953471 TCGTGGAAATCGTGGCAAGG 60.953 55.000 0.00 0.00 0.00 3.61
364 459 1.611491 TGGAAATCGTGGCAAGGAAAC 59.389 47.619 0.00 0.00 0.00 2.78
377 472 5.884792 TGGCAAGGAAACAAACAAATCAATT 59.115 32.000 0.00 0.00 0.00 2.32
468 572 5.345472 TGTCATTTCATGCTGTAATTTTGCG 59.655 36.000 0.00 0.00 0.00 4.85
793 952 2.482374 GCAGCCATCAACGCAGTC 59.518 61.111 0.00 0.00 45.00 3.51
794 953 3.044059 GCAGCCATCAACGCAGTCC 62.044 63.158 0.00 0.00 45.00 3.85
1113 1272 1.263217 CGGGCGCAGGATTACAATAAC 59.737 52.381 10.83 0.00 0.00 1.89
1122 1281 4.690748 CAGGATTACAATAACGGCGATGAT 59.309 41.667 16.62 0.00 0.00 2.45
1204 1363 0.246757 GTACACGTTCATTGAGCGCG 60.247 55.000 20.74 14.86 39.75 6.86
1389 1548 4.329545 GGCACTGACTTCCCCGCA 62.330 66.667 0.00 0.00 0.00 5.69
1612 1771 2.836944 GGTGGAGTACCTTGTTCGC 58.163 57.895 0.00 0.00 46.51 4.70
1615 1774 2.098831 GGAGTACCTTGTTCGCCGC 61.099 63.158 0.00 0.00 0.00 6.53
1617 1776 3.122971 GTACCTTGTTCGCCGCCC 61.123 66.667 0.00 0.00 0.00 6.13
1619 1778 3.305177 TACCTTGTTCGCCGCCCTC 62.305 63.158 0.00 0.00 0.00 4.30
1620 1779 4.697756 CCTTGTTCGCCGCCCTCA 62.698 66.667 0.00 0.00 0.00 3.86
1628 1787 4.760047 GCCGCCCTCACGACATGT 62.760 66.667 0.00 0.00 34.06 3.21
1629 1788 2.047274 CCGCCCTCACGACATGTT 60.047 61.111 0.00 0.00 34.06 2.71
1630 1789 1.671054 CCGCCCTCACGACATGTTT 60.671 57.895 0.00 0.00 34.06 2.83
1666 1832 3.909776 CATTTCTTGCTTGCTCTGTCA 57.090 42.857 0.00 0.00 0.00 3.58
1667 1833 3.822996 CATTTCTTGCTTGCTCTGTCAG 58.177 45.455 0.00 0.00 0.00 3.51
1668 1834 2.916702 TTCTTGCTTGCTCTGTCAGA 57.083 45.000 1.78 1.78 0.00 3.27
1669 1835 2.916702 TCTTGCTTGCTCTGTCAGAA 57.083 45.000 3.67 0.00 0.00 3.02
1670 1836 3.198409 TCTTGCTTGCTCTGTCAGAAA 57.802 42.857 3.67 0.00 0.00 2.52
1671 1837 3.544684 TCTTGCTTGCTCTGTCAGAAAA 58.455 40.909 3.67 1.13 0.00 2.29
1672 1838 3.947196 TCTTGCTTGCTCTGTCAGAAAAA 59.053 39.130 3.67 0.78 0.00 1.94
1694 1860 3.940209 TTGATCAAGGTTGGAATGTGC 57.060 42.857 3.38 0.00 0.00 4.57
1726 1892 0.598942 TGATGTACGTGTGCTGCGTT 60.599 50.000 0.00 0.00 42.85 4.84
1729 1895 1.568606 TGTACGTGTGCTGCGTTAAA 58.431 45.000 0.00 0.00 42.85 1.52
1746 1912 4.760204 CGTTAAAGATCCCAAGTTCAAGGT 59.240 41.667 0.00 0.00 0.00 3.50
1816 1982 1.878522 CATGGCCTACGACGTGCTC 60.879 63.158 11.56 1.71 0.00 4.26
1963 2129 0.459237 CCTACACGCTGCTCAAGGAG 60.459 60.000 0.00 0.00 36.50 3.69
1969 2135 4.479993 CTGCTCAAGGAGGGCCCG 62.480 72.222 18.44 0.58 40.87 6.13
2042 2208 1.335597 CCGTGTACAACTGCGAGAAGA 60.336 52.381 0.00 0.00 0.00 2.87
2179 2345 1.452833 GGCCATCTTCCAGCTCACC 60.453 63.158 0.00 0.00 0.00 4.02
2182 2348 0.460987 CCATCTTCCAGCTCACCGTC 60.461 60.000 0.00 0.00 0.00 4.79
2184 2350 1.751351 CATCTTCCAGCTCACCGTCTA 59.249 52.381 0.00 0.00 0.00 2.59
2308 2474 3.023735 AGCCCCATGGAGTTCCCC 61.024 66.667 15.22 0.00 34.29 4.81
2332 2498 3.458163 TCGGGGCTCATGTCGACC 61.458 66.667 14.12 0.00 0.00 4.79
2443 2609 3.542676 AACGACTCCACGGTGCCA 61.543 61.111 1.68 0.00 37.61 4.92
2554 2720 3.047877 CCCTTCGACAACCGCACC 61.048 66.667 0.00 0.00 38.37 5.01
2713 2879 0.685097 TCAACTGGCAGGACTACACC 59.315 55.000 20.34 0.00 0.00 4.16
2756 2922 1.164411 CAAAATGGGCGAGCACTACA 58.836 50.000 0.00 0.00 0.00 2.74
2785 2951 3.490399 CGAGAACGTCTACTCCTTCAAC 58.510 50.000 10.30 0.00 34.56 3.18
2792 2958 2.165234 GTCTACTCCTTCAACGGTACCC 59.835 54.545 6.25 0.00 0.00 3.69
2850 3016 3.546543 CCTGCCGGGGCTCGAATA 61.547 66.667 9.18 0.00 42.43 1.75
2857 3023 1.446366 GGGGCTCGAATACCTGGAC 59.554 63.158 0.00 0.00 0.00 4.02
3146 3312 7.516470 CGTGCTTATGATCTGTGAAAATCTCTC 60.516 40.741 0.00 0.00 0.00 3.20
3220 3386 4.413851 ACATTTTTATTTGGTGGTTGGGGT 59.586 37.500 0.00 0.00 0.00 4.95
3225 3391 7.425224 TTTTATTTGGTGGTTGGGGTATATG 57.575 36.000 0.00 0.00 0.00 1.78
3227 3393 3.655615 TTGGTGGTTGGGGTATATGTC 57.344 47.619 0.00 0.00 0.00 3.06
3231 3397 3.463944 GTGGTTGGGGTATATGTCTTCG 58.536 50.000 0.00 0.00 0.00 3.79
3296 3462 3.024547 TCTCGAGCAACTACAGGCTTAT 58.975 45.455 7.81 0.00 41.22 1.73
3381 3553 3.228878 GTGCACACACACGTAAACTAC 57.771 47.619 13.17 0.00 46.61 2.73
3382 3554 2.033492 GTGCACACACACGTAAACTACC 60.033 50.000 13.17 0.00 46.61 3.18
3383 3555 1.190763 GCACACACACGTAAACTACCG 59.809 52.381 0.00 0.00 0.00 4.02
3384 3556 2.730069 CACACACACGTAAACTACCGA 58.270 47.619 0.00 0.00 0.00 4.69
3385 3557 3.311106 CACACACACGTAAACTACCGAT 58.689 45.455 0.00 0.00 0.00 4.18
3386 3558 4.475028 CACACACACGTAAACTACCGATA 58.525 43.478 0.00 0.00 0.00 2.92
3387 3559 4.916831 CACACACACGTAAACTACCGATAA 59.083 41.667 0.00 0.00 0.00 1.75
3388 3560 5.574055 CACACACACGTAAACTACCGATAAT 59.426 40.000 0.00 0.00 0.00 1.28
3389 3561 5.574055 ACACACACGTAAACTACCGATAATG 59.426 40.000 0.00 0.00 0.00 1.90
3390 3562 4.563976 ACACACGTAAACTACCGATAATGC 59.436 41.667 0.00 0.00 0.00 3.56
3391 3563 4.802039 CACACGTAAACTACCGATAATGCT 59.198 41.667 0.00 0.00 0.00 3.79
3392 3564 5.039333 ACACGTAAACTACCGATAATGCTC 58.961 41.667 0.00 0.00 0.00 4.26
3393 3565 4.443394 CACGTAAACTACCGATAATGCTCC 59.557 45.833 0.00 0.00 0.00 4.70
3394 3566 4.098349 ACGTAAACTACCGATAATGCTCCA 59.902 41.667 0.00 0.00 0.00 3.86
3395 3567 5.221382 ACGTAAACTACCGATAATGCTCCAT 60.221 40.000 0.00 0.00 0.00 3.41
3396 3568 5.345202 CGTAAACTACCGATAATGCTCCATC 59.655 44.000 0.00 0.00 0.00 3.51
3397 3569 5.552870 AAACTACCGATAATGCTCCATCT 57.447 39.130 0.00 0.00 0.00 2.90
3398 3570 6.665992 AAACTACCGATAATGCTCCATCTA 57.334 37.500 0.00 0.00 0.00 1.98
3399 3571 5.646577 ACTACCGATAATGCTCCATCTAC 57.353 43.478 0.00 0.00 0.00 2.59
3400 3572 3.577649 ACCGATAATGCTCCATCTACG 57.422 47.619 0.00 0.00 0.00 3.51
3401 3573 3.154710 ACCGATAATGCTCCATCTACGA 58.845 45.455 0.00 0.00 0.00 3.43
3402 3574 3.572682 ACCGATAATGCTCCATCTACGAA 59.427 43.478 0.00 0.00 0.00 3.85
3403 3575 3.921021 CCGATAATGCTCCATCTACGAAC 59.079 47.826 0.00 0.00 0.00 3.95
3404 3576 4.546570 CGATAATGCTCCATCTACGAACA 58.453 43.478 0.00 0.00 0.00 3.18
3405 3577 4.618912 CGATAATGCTCCATCTACGAACAG 59.381 45.833 0.00 0.00 0.00 3.16
3406 3578 2.231215 ATGCTCCATCTACGAACAGC 57.769 50.000 0.00 0.00 0.00 4.40
3407 3579 1.186200 TGCTCCATCTACGAACAGCT 58.814 50.000 0.00 0.00 0.00 4.24
3408 3580 2.375146 TGCTCCATCTACGAACAGCTA 58.625 47.619 0.00 0.00 0.00 3.32
3409 3581 2.359214 TGCTCCATCTACGAACAGCTAG 59.641 50.000 0.00 0.00 0.00 3.42
3410 3582 2.860582 GCTCCATCTACGAACAGCTAGC 60.861 54.545 6.62 6.62 0.00 3.42
3411 3583 1.681793 TCCATCTACGAACAGCTAGCC 59.318 52.381 12.13 0.00 0.00 3.93
3412 3584 1.683917 CCATCTACGAACAGCTAGCCT 59.316 52.381 12.13 0.00 0.00 4.58
3413 3585 2.885266 CCATCTACGAACAGCTAGCCTA 59.115 50.000 12.13 0.00 0.00 3.93
3414 3586 3.304794 CCATCTACGAACAGCTAGCCTAC 60.305 52.174 12.13 0.00 0.00 3.18
3415 3587 1.938577 TCTACGAACAGCTAGCCTACG 59.061 52.381 12.13 14.43 0.00 3.51
3416 3588 0.379669 TACGAACAGCTAGCCTACGC 59.620 55.000 12.13 0.00 0.00 4.42
3417 3589 1.138883 CGAACAGCTAGCCTACGCA 59.861 57.895 12.13 0.00 37.52 5.24
3418 3590 0.457853 CGAACAGCTAGCCTACGCAA 60.458 55.000 12.13 0.00 37.52 4.85
3419 3591 1.722011 GAACAGCTAGCCTACGCAAA 58.278 50.000 12.13 0.00 37.52 3.68
3420 3592 1.661112 GAACAGCTAGCCTACGCAAAG 59.339 52.381 12.13 0.00 37.52 2.77
3421 3593 0.608640 ACAGCTAGCCTACGCAAAGT 59.391 50.000 12.13 0.00 37.52 2.66
3422 3594 1.822990 ACAGCTAGCCTACGCAAAGTA 59.177 47.619 12.13 0.00 37.52 2.24
3423 3595 2.232941 ACAGCTAGCCTACGCAAAGTAA 59.767 45.455 12.13 0.00 37.52 2.24
3424 3596 2.603560 CAGCTAGCCTACGCAAAGTAAC 59.396 50.000 12.13 0.00 37.52 2.50
3425 3597 1.587034 GCTAGCCTACGCAAAGTAACG 59.413 52.381 2.29 0.00 37.52 3.18
3426 3598 2.872370 CTAGCCTACGCAAAGTAACGT 58.128 47.619 0.00 0.00 45.85 3.99
3427 3599 3.731867 GCTAGCCTACGCAAAGTAACGTA 60.732 47.826 2.29 0.00 43.35 3.57
3428 3600 3.302365 AGCCTACGCAAAGTAACGTAA 57.698 42.857 0.00 0.00 43.48 3.18
3429 3601 3.853475 AGCCTACGCAAAGTAACGTAAT 58.147 40.909 0.00 0.00 43.48 1.89
3430 3602 4.997565 AGCCTACGCAAAGTAACGTAATA 58.002 39.130 0.00 0.00 43.48 0.98
3431 3603 5.594926 AGCCTACGCAAAGTAACGTAATAT 58.405 37.500 0.00 0.00 43.48 1.28
3432 3604 6.044682 AGCCTACGCAAAGTAACGTAATATT 58.955 36.000 0.00 0.00 43.48 1.28
3433 3605 6.536224 AGCCTACGCAAAGTAACGTAATATTT 59.464 34.615 0.00 0.00 43.48 1.40
3434 3606 6.842780 GCCTACGCAAAGTAACGTAATATTTC 59.157 38.462 0.00 0.00 43.48 2.17
3435 3607 7.254218 GCCTACGCAAAGTAACGTAATATTTCT 60.254 37.037 0.00 0.00 43.48 2.52
3436 3608 9.236691 CCTACGCAAAGTAACGTAATATTTCTA 57.763 33.333 0.00 0.00 43.48 2.10
3439 3611 9.143631 ACGCAAAGTAACGTAATATTTCTAACT 57.856 29.630 0.00 0.00 41.48 2.24
3454 3626 7.816300 ATTTCTAACTATAATCCTCTCCCCC 57.184 40.000 0.00 0.00 0.00 5.40
3469 3641 3.288099 CCCCCTGATTTCAAGTGGG 57.712 57.895 0.00 0.00 37.68 4.61
3470 3642 0.704076 CCCCCTGATTTCAAGTGGGA 59.296 55.000 9.81 0.00 40.23 4.37
3471 3643 1.288932 CCCCCTGATTTCAAGTGGGAT 59.711 52.381 9.81 0.00 40.23 3.85
3472 3644 2.381911 CCCCTGATTTCAAGTGGGATG 58.618 52.381 5.21 0.00 40.23 3.51
3473 3645 2.381911 CCCTGATTTCAAGTGGGATGG 58.618 52.381 0.00 0.00 40.23 3.51
3474 3646 2.381911 CCTGATTTCAAGTGGGATGGG 58.618 52.381 0.00 0.00 0.00 4.00
3475 3647 1.753073 CTGATTTCAAGTGGGATGGGC 59.247 52.381 0.00 0.00 0.00 5.36
3476 3648 1.114627 GATTTCAAGTGGGATGGGCC 58.885 55.000 0.00 0.00 0.00 5.80
3492 3664 3.027419 GCCCCAGCCACTAATCATC 57.973 57.895 0.00 0.00 0.00 2.92
3493 3665 0.183492 GCCCCAGCCACTAATCATCA 59.817 55.000 0.00 0.00 0.00 3.07
3494 3666 1.202976 GCCCCAGCCACTAATCATCAT 60.203 52.381 0.00 0.00 0.00 2.45
3495 3667 2.787994 CCCCAGCCACTAATCATCATC 58.212 52.381 0.00 0.00 0.00 2.92
3496 3668 2.553904 CCCCAGCCACTAATCATCATCC 60.554 54.545 0.00 0.00 0.00 3.51
3497 3669 2.107031 CCCAGCCACTAATCATCATCCA 59.893 50.000 0.00 0.00 0.00 3.41
3498 3670 3.435457 CCCAGCCACTAATCATCATCCAA 60.435 47.826 0.00 0.00 0.00 3.53
3499 3671 4.404640 CCAGCCACTAATCATCATCCAAT 58.595 43.478 0.00 0.00 0.00 3.16
3500 3672 4.831155 CCAGCCACTAATCATCATCCAATT 59.169 41.667 0.00 0.00 0.00 2.32
3501 3673 6.005823 CCAGCCACTAATCATCATCCAATTA 58.994 40.000 0.00 0.00 0.00 1.40
3502 3674 6.072286 CCAGCCACTAATCATCATCCAATTAC 60.072 42.308 0.00 0.00 0.00 1.89
3503 3675 6.006449 AGCCACTAATCATCATCCAATTACC 58.994 40.000 0.00 0.00 0.00 2.85
3504 3676 6.006449 GCCACTAATCATCATCCAATTACCT 58.994 40.000 0.00 0.00 0.00 3.08
3505 3677 7.017551 AGCCACTAATCATCATCCAATTACCTA 59.982 37.037 0.00 0.00 0.00 3.08
3506 3678 7.119846 GCCACTAATCATCATCCAATTACCTAC 59.880 40.741 0.00 0.00 0.00 3.18
3507 3679 7.607991 CCACTAATCATCATCCAATTACCTACC 59.392 40.741 0.00 0.00 0.00 3.18
3508 3680 8.378565 CACTAATCATCATCCAATTACCTACCT 58.621 37.037 0.00 0.00 0.00 3.08
3509 3681 8.598041 ACTAATCATCATCCAATTACCTACCTC 58.402 37.037 0.00 0.00 0.00 3.85
3510 3682 5.825593 TCATCATCCAATTACCTACCTCC 57.174 43.478 0.00 0.00 0.00 4.30
3511 3683 5.223655 TCATCATCCAATTACCTACCTCCA 58.776 41.667 0.00 0.00 0.00 3.86
3512 3684 5.071788 TCATCATCCAATTACCTACCTCCAC 59.928 44.000 0.00 0.00 0.00 4.02
3513 3685 4.367166 TCATCCAATTACCTACCTCCACA 58.633 43.478 0.00 0.00 0.00 4.17
3514 3686 4.975147 TCATCCAATTACCTACCTCCACAT 59.025 41.667 0.00 0.00 0.00 3.21
3515 3687 5.071788 TCATCCAATTACCTACCTCCACATC 59.928 44.000 0.00 0.00 0.00 3.06
3516 3688 4.367166 TCCAATTACCTACCTCCACATCA 58.633 43.478 0.00 0.00 0.00 3.07
3517 3689 4.785914 TCCAATTACCTACCTCCACATCAA 59.214 41.667 0.00 0.00 0.00 2.57
3518 3690 4.881850 CCAATTACCTACCTCCACATCAAC 59.118 45.833 0.00 0.00 0.00 3.18
3519 3691 5.339200 CCAATTACCTACCTCCACATCAACT 60.339 44.000 0.00 0.00 0.00 3.16
3520 3692 6.180472 CAATTACCTACCTCCACATCAACTT 58.820 40.000 0.00 0.00 0.00 2.66
3521 3693 5.836024 TTACCTACCTCCACATCAACTTT 57.164 39.130 0.00 0.00 0.00 2.66
3522 3694 4.724279 ACCTACCTCCACATCAACTTTT 57.276 40.909 0.00 0.00 0.00 2.27
3523 3695 5.836024 ACCTACCTCCACATCAACTTTTA 57.164 39.130 0.00 0.00 0.00 1.52
3524 3696 5.557866 ACCTACCTCCACATCAACTTTTAC 58.442 41.667 0.00 0.00 0.00 2.01
3525 3697 5.309806 ACCTACCTCCACATCAACTTTTACT 59.690 40.000 0.00 0.00 0.00 2.24
3526 3698 6.183361 ACCTACCTCCACATCAACTTTTACTT 60.183 38.462 0.00 0.00 0.00 2.24
3527 3699 7.016858 ACCTACCTCCACATCAACTTTTACTTA 59.983 37.037 0.00 0.00 0.00 2.24
3528 3700 7.881232 CCTACCTCCACATCAACTTTTACTTAA 59.119 37.037 0.00 0.00 0.00 1.85
3529 3701 9.280174 CTACCTCCACATCAACTTTTACTTAAA 57.720 33.333 0.00 0.00 0.00 1.52
3530 3702 8.528044 ACCTCCACATCAACTTTTACTTAAAA 57.472 30.769 0.00 0.00 34.35 1.52
3531 3703 8.973182 ACCTCCACATCAACTTTTACTTAAAAA 58.027 29.630 0.00 0.00 35.04 1.94
3532 3704 9.244799 CCTCCACATCAACTTTTACTTAAAAAC 57.755 33.333 0.00 0.00 35.04 2.43
3552 3724 6.894339 AAACTTCACATAAGTTTACCTGGG 57.106 37.500 12.79 0.00 45.51 4.45
3553 3725 5.578157 ACTTCACATAAGTTTACCTGGGT 57.422 39.130 0.00 0.00 0.00 4.51
3554 3726 5.557866 ACTTCACATAAGTTTACCTGGGTC 58.442 41.667 0.00 0.00 0.00 4.46
3555 3727 5.309806 ACTTCACATAAGTTTACCTGGGTCT 59.690 40.000 0.00 0.00 0.00 3.85
3556 3728 6.499350 ACTTCACATAAGTTTACCTGGGTCTA 59.501 38.462 0.00 0.00 0.00 2.59
3557 3729 6.540438 TCACATAAGTTTACCTGGGTCTAG 57.460 41.667 0.00 0.00 0.00 2.43
3558 3730 5.105064 TCACATAAGTTTACCTGGGTCTAGC 60.105 44.000 0.00 0.00 0.00 3.42
3559 3731 4.781087 ACATAAGTTTACCTGGGTCTAGCA 59.219 41.667 0.00 0.00 0.00 3.49
3560 3732 5.428783 ACATAAGTTTACCTGGGTCTAGCAT 59.571 40.000 0.00 0.00 0.00 3.79
3561 3733 4.929146 AAGTTTACCTGGGTCTAGCATT 57.071 40.909 0.00 0.00 0.00 3.56
3562 3734 4.222124 AGTTTACCTGGGTCTAGCATTG 57.778 45.455 0.00 0.00 0.00 2.82
3563 3735 2.683362 GTTTACCTGGGTCTAGCATTGC 59.317 50.000 0.00 0.00 0.00 3.56
3564 3736 1.879575 TACCTGGGTCTAGCATTGCT 58.120 50.000 16.63 16.63 43.41 3.91
3565 3737 0.543749 ACCTGGGTCTAGCATTGCTC 59.456 55.000 15.81 0.36 40.44 4.26
3566 3738 0.543277 CCTGGGTCTAGCATTGCTCA 59.457 55.000 15.81 5.62 40.44 4.26
3567 3739 1.142465 CCTGGGTCTAGCATTGCTCAT 59.858 52.381 15.81 0.00 40.44 2.90
3568 3740 2.369860 CCTGGGTCTAGCATTGCTCATA 59.630 50.000 15.81 0.00 40.44 2.15
3598 3770 2.157421 GCATGCGGCATAGCTAGTC 58.843 57.895 16.21 0.00 43.97 2.59
3605 3777 1.334779 CGGCATAGCTAGTCCGTACAC 60.335 57.143 21.64 0.00 37.33 2.90
3676 3848 1.276421 AGATCAACCCAACGACCTCAG 59.724 52.381 0.00 0.00 0.00 3.35
3750 3922 3.130340 ACGTGCAAGTCCAAATGTTTTCT 59.870 39.130 0.00 0.00 0.00 2.52
3769 3941 8.956426 TGTTTTCTATGTCTTTTCTTTGTGTCT 58.044 29.630 0.00 0.00 0.00 3.41
3774 3946 7.993183 TCTATGTCTTTTCTTTGTGTCTCCTTT 59.007 33.333 0.00 0.00 0.00 3.11
3775 3947 9.273016 CTATGTCTTTTCTTTGTGTCTCCTTTA 57.727 33.333 0.00 0.00 0.00 1.85
3777 3949 8.519799 TGTCTTTTCTTTGTGTCTCCTTTATT 57.480 30.769 0.00 0.00 0.00 1.40
3779 3951 9.803315 GTCTTTTCTTTGTGTCTCCTTTATTTT 57.197 29.630 0.00 0.00 0.00 1.82
3834 4008 1.813753 ACAGGCGTGTGTGTGTGTC 60.814 57.895 11.97 0.00 34.75 3.67
3849 4023 4.059459 GTCTGTTGTGTCGCGCGG 62.059 66.667 31.69 11.31 0.00 6.46
3875 4049 0.806241 GGGTGTGTTGTGTCAACGTT 59.194 50.000 0.00 0.00 0.00 3.99
3885 4059 3.864243 TGTGTCAACGTTAAGGTCAACT 58.136 40.909 0.00 0.00 0.00 3.16
3930 4104 5.881447 ACGTTACACACTTATTTTTGCACA 58.119 33.333 0.00 0.00 0.00 4.57
4027 4201 5.937975 TTAAGGGTAATACTAACGCCACT 57.062 39.130 0.00 0.00 0.00 4.00
4035 4209 7.117379 GGGTAATACTAACGCCACTAATTCATC 59.883 40.741 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.822990 CAGAAGGACAATTGCATGCCT 59.177 47.619 16.68 4.70 0.00 4.75
37 38 1.547372 ACAGAAGGACAATTGCATGCC 59.453 47.619 16.68 2.28 0.00 4.40
56 57 2.277084 GAGAGAGTCGAGAGAGTGGAC 58.723 57.143 0.00 0.00 45.54 4.02
185 280 5.869579 TCAGGATTAGAATAGTTGCATCCC 58.130 41.667 0.00 0.00 32.03 3.85
189 284 5.129320 TGAGCTCAGGATTAGAATAGTTGCA 59.871 40.000 13.74 0.00 0.00 4.08
305 400 6.582295 ACGATGTAATTTTGCAAGCTAACAAG 59.418 34.615 0.00 5.57 0.00 3.16
311 406 4.764679 TGACGATGTAATTTTGCAAGCT 57.235 36.364 0.00 0.00 0.00 3.74
330 425 5.234116 CACGATTTCCACGAATGTCATATGA 59.766 40.000 0.00 0.00 34.70 2.15
358 453 7.123355 TGGAGAATTGATTTGTTTGTTTCCT 57.877 32.000 0.00 0.00 0.00 3.36
359 454 7.784633 TTGGAGAATTGATTTGTTTGTTTCC 57.215 32.000 0.00 0.00 0.00 3.13
364 459 9.654417 GAACATTTTGGAGAATTGATTTGTTTG 57.346 29.630 0.00 0.00 0.00 2.93
377 472 7.382110 TGTGTTTGAAAAGAACATTTTGGAGA 58.618 30.769 0.00 0.00 39.03 3.71
468 572 8.563732 CCTAGCTTTCAAATATTTTCCTAGCTC 58.436 37.037 19.23 0.36 37.58 4.09
590 721 5.474189 CGTTCCCAGTTCCATAACCTAAAAA 59.526 40.000 0.00 0.00 36.15 1.94
602 733 4.939439 ACACATTATAACGTTCCCAGTTCC 59.061 41.667 2.82 0.00 33.42 3.62
803 962 1.339291 GGCATGCAGAATTTAGGAGGC 59.661 52.381 21.36 1.65 32.01 4.70
1113 1272 1.175347 TCTCCTCCTCATCATCGCCG 61.175 60.000 0.00 0.00 0.00 6.46
1122 1281 1.490574 GCTTAGGCTTCTCCTCCTCA 58.509 55.000 0.00 0.00 43.20 3.86
1204 1363 3.056328 GTGCGGGAACTCCTTGGC 61.056 66.667 0.00 0.00 35.95 4.52
1377 1536 1.595929 GACGTTTGCGGGGAAGTCA 60.596 57.895 0.00 0.00 43.45 3.41
1597 1756 2.098831 GCGGCGAACAAGGTACTCC 61.099 63.158 12.98 0.00 38.49 3.85
1598 1757 2.098831 GGCGGCGAACAAGGTACTC 61.099 63.158 12.98 0.00 38.49 2.59
1600 1759 3.122971 GGGCGGCGAACAAGGTAC 61.123 66.667 12.98 0.00 0.00 3.34
1601 1760 3.305177 GAGGGCGGCGAACAAGGTA 62.305 63.158 12.98 0.00 0.00 3.08
1602 1761 4.699522 GAGGGCGGCGAACAAGGT 62.700 66.667 12.98 0.00 0.00 3.50
1603 1762 4.697756 TGAGGGCGGCGAACAAGG 62.698 66.667 12.98 0.00 0.00 3.61
1604 1763 3.423154 GTGAGGGCGGCGAACAAG 61.423 66.667 12.98 0.00 0.00 3.16
1611 1770 4.760047 ACATGTCGTGAGGGCGGC 62.760 66.667 0.00 0.00 36.96 6.53
1612 1771 1.635663 GAAACATGTCGTGAGGGCGG 61.636 60.000 0.00 0.00 0.00 6.13
1615 1774 0.798776 GCAGAAACATGTCGTGAGGG 59.201 55.000 0.00 0.00 0.00 4.30
1617 1776 3.113325 CATGCAGAAACATGTCGTGAG 57.887 47.619 0.00 0.00 42.05 3.51
1646 1812 3.501062 TCTGACAGAGCAAGCAAGAAATG 59.499 43.478 0.00 0.00 0.00 2.32
1648 1814 3.198409 TCTGACAGAGCAAGCAAGAAA 57.802 42.857 0.00 0.00 0.00 2.52
1651 1817 3.976793 TTTTCTGACAGAGCAAGCAAG 57.023 42.857 5.10 0.00 0.00 4.01
1669 1835 6.205270 GCACATTCCAACCTTGATCAATTTTT 59.795 34.615 8.96 0.00 0.00 1.94
1670 1836 5.702209 GCACATTCCAACCTTGATCAATTTT 59.298 36.000 8.96 2.24 0.00 1.82
1671 1837 5.240121 GCACATTCCAACCTTGATCAATTT 58.760 37.500 8.96 2.62 0.00 1.82
1672 1838 4.618927 CGCACATTCCAACCTTGATCAATT 60.619 41.667 8.96 0.00 0.00 2.32
1673 1839 3.119388 CGCACATTCCAACCTTGATCAAT 60.119 43.478 8.96 0.00 0.00 2.57
1674 1840 2.228582 CGCACATTCCAACCTTGATCAA 59.771 45.455 8.12 8.12 0.00 2.57
1675 1841 1.811965 CGCACATTCCAACCTTGATCA 59.188 47.619 0.00 0.00 0.00 2.92
1676 1842 1.812571 ACGCACATTCCAACCTTGATC 59.187 47.619 0.00 0.00 0.00 2.92
1677 1843 1.541147 CACGCACATTCCAACCTTGAT 59.459 47.619 0.00 0.00 0.00 2.57
1678 1844 0.950836 CACGCACATTCCAACCTTGA 59.049 50.000 0.00 0.00 0.00 3.02
1679 1845 0.664166 GCACGCACATTCCAACCTTG 60.664 55.000 0.00 0.00 0.00 3.61
1680 1846 1.106351 TGCACGCACATTCCAACCTT 61.106 50.000 0.00 0.00 0.00 3.50
1681 1847 1.518056 CTGCACGCACATTCCAACCT 61.518 55.000 0.00 0.00 0.00 3.50
1682 1848 1.081242 CTGCACGCACATTCCAACC 60.081 57.895 0.00 0.00 0.00 3.77
1683 1849 0.523072 ATCTGCACGCACATTCCAAC 59.477 50.000 0.00 0.00 0.00 3.77
1684 1850 2.009051 CTATCTGCACGCACATTCCAA 58.991 47.619 0.00 0.00 0.00 3.53
1685 1851 1.655484 CTATCTGCACGCACATTCCA 58.345 50.000 0.00 0.00 0.00 3.53
1686 1852 0.305922 GCTATCTGCACGCACATTCC 59.694 55.000 0.00 0.00 42.31 3.01
1694 1860 1.781429 GTACATCACGCTATCTGCACG 59.219 52.381 0.00 0.00 43.06 5.34
1726 1892 5.576563 TCACCTTGAACTTGGGATCTTTA 57.423 39.130 0.00 0.00 0.00 1.85
1729 1895 3.652869 TCTTCACCTTGAACTTGGGATCT 59.347 43.478 0.00 0.00 32.21 2.75
1746 1912 1.165907 CGTGCTGTTGGCCTTCTTCA 61.166 55.000 3.32 0.00 40.92 3.02
1816 1982 1.210545 ACTTGTTGCCGTACGACGTG 61.211 55.000 18.76 0.06 40.58 4.49
2042 2208 3.823330 GTCGACGATGACCGGCCT 61.823 66.667 0.00 0.00 45.44 5.19
2179 2345 2.230940 CGGCGGCATCTTGTAGACG 61.231 63.158 10.53 0.00 0.00 4.18
2182 2348 1.883084 GTCCGGCGGCATCTTGTAG 60.883 63.158 23.83 0.00 0.00 2.74
2184 2350 4.778143 GGTCCGGCGGCATCTTGT 62.778 66.667 23.83 0.00 0.00 3.16
2362 2528 3.443045 GGGCGGGTGATGTTGCAG 61.443 66.667 0.00 0.00 0.00 4.41
2686 2852 1.171308 CCTGCCAGTTGAAGATGGTG 58.829 55.000 0.00 0.00 38.91 4.17
2713 2879 0.512952 CGGCGAACCAGTTCTTGAAG 59.487 55.000 0.00 0.00 37.44 3.02
2850 3016 3.009115 CGGTGATGGGGTCCAGGT 61.009 66.667 0.00 0.00 36.75 4.00
2857 3023 4.838152 CTGCCGTCGGTGATGGGG 62.838 72.222 13.94 0.00 39.01 4.96
2986 3152 1.352404 CTCCTCGCCGTCGAAGTAG 59.648 63.158 0.00 0.00 44.98 2.57
3050 3216 2.596851 GCAAGAGACTGGGAGCCCA 61.597 63.158 8.20 8.20 45.02 5.36
3146 3312 9.658799 AAATCTCTATACAATGATACAATCCCG 57.341 33.333 0.00 0.00 0.00 5.14
3220 3386 7.928167 ACATCTGAATTGAAGCGAAGACATATA 59.072 33.333 0.00 0.00 0.00 0.86
3225 3391 4.935885 ACATCTGAATTGAAGCGAAGAC 57.064 40.909 0.00 0.00 0.00 3.01
3227 3393 6.128445 ACTGTAACATCTGAATTGAAGCGAAG 60.128 38.462 0.00 0.00 0.00 3.79
3231 3397 6.310197 GTCACTGTAACATCTGAATTGAAGC 58.690 40.000 0.00 0.00 0.00 3.86
3371 3543 4.098349 TGGAGCATTATCGGTAGTTTACGT 59.902 41.667 0.00 0.00 0.00 3.57
3376 3548 5.335740 CGTAGATGGAGCATTATCGGTAGTT 60.336 44.000 0.00 0.00 0.00 2.24
3377 3549 4.156190 CGTAGATGGAGCATTATCGGTAGT 59.844 45.833 0.00 0.00 0.00 2.73
3378 3550 4.395231 TCGTAGATGGAGCATTATCGGTAG 59.605 45.833 0.00 0.00 0.00 3.18
3379 3551 4.329392 TCGTAGATGGAGCATTATCGGTA 58.671 43.478 0.00 0.00 0.00 4.02
3380 3552 3.154710 TCGTAGATGGAGCATTATCGGT 58.845 45.455 0.00 0.00 0.00 4.69
3381 3553 3.850122 TCGTAGATGGAGCATTATCGG 57.150 47.619 0.00 0.00 0.00 4.18
3382 3554 4.546570 TGTTCGTAGATGGAGCATTATCG 58.453 43.478 0.00 0.00 35.04 2.92
3383 3555 4.387256 GCTGTTCGTAGATGGAGCATTATC 59.613 45.833 0.00 0.00 35.04 1.75
3384 3556 4.039730 AGCTGTTCGTAGATGGAGCATTAT 59.960 41.667 0.00 0.00 35.61 1.28
3385 3557 3.384789 AGCTGTTCGTAGATGGAGCATTA 59.615 43.478 0.00 0.00 35.61 1.90
3386 3558 2.169352 AGCTGTTCGTAGATGGAGCATT 59.831 45.455 0.00 0.00 35.61 3.56
3387 3559 1.759445 AGCTGTTCGTAGATGGAGCAT 59.241 47.619 0.00 0.00 35.61 3.79
3388 3560 1.186200 AGCTGTTCGTAGATGGAGCA 58.814 50.000 0.00 0.00 35.61 4.26
3389 3561 2.860582 GCTAGCTGTTCGTAGATGGAGC 60.861 54.545 7.70 0.00 35.04 4.70
3390 3562 2.287909 GGCTAGCTGTTCGTAGATGGAG 60.288 54.545 15.72 0.00 35.04 3.86
3391 3563 1.681793 GGCTAGCTGTTCGTAGATGGA 59.318 52.381 15.72 0.00 35.04 3.41
3392 3564 1.683917 AGGCTAGCTGTTCGTAGATGG 59.316 52.381 15.72 0.00 35.04 3.51
3393 3565 3.607310 CGTAGGCTAGCTGTTCGTAGATG 60.607 52.174 15.72 0.00 35.04 2.90
3394 3566 2.548904 CGTAGGCTAGCTGTTCGTAGAT 59.451 50.000 15.72 0.00 35.04 1.98
3395 3567 1.938577 CGTAGGCTAGCTGTTCGTAGA 59.061 52.381 15.72 0.00 0.00 2.59
3396 3568 1.597445 GCGTAGGCTAGCTGTTCGTAG 60.597 57.143 15.72 0.00 35.83 3.51
3397 3569 0.379669 GCGTAGGCTAGCTGTTCGTA 59.620 55.000 15.72 0.00 35.83 3.43
3398 3570 1.139095 GCGTAGGCTAGCTGTTCGT 59.861 57.895 15.72 0.00 35.83 3.85
3399 3571 0.457853 TTGCGTAGGCTAGCTGTTCG 60.458 55.000 15.72 14.68 40.82 3.95
3400 3572 1.661112 CTTTGCGTAGGCTAGCTGTTC 59.339 52.381 15.72 0.00 40.82 3.18
3401 3573 1.002087 ACTTTGCGTAGGCTAGCTGTT 59.998 47.619 15.72 3.45 40.82 3.16
3402 3574 0.608640 ACTTTGCGTAGGCTAGCTGT 59.391 50.000 15.72 4.98 40.82 4.40
3403 3575 2.579207 TACTTTGCGTAGGCTAGCTG 57.421 50.000 15.72 3.63 40.82 4.24
3404 3576 2.734492 CGTTACTTTGCGTAGGCTAGCT 60.734 50.000 15.72 3.22 40.82 3.32
3405 3577 1.587034 CGTTACTTTGCGTAGGCTAGC 59.413 52.381 6.04 6.04 40.82 3.42
3406 3578 2.872370 ACGTTACTTTGCGTAGGCTAG 58.128 47.619 9.11 8.49 39.72 3.42
3407 3579 4.433186 TTACGTTACTTTGCGTAGGCTA 57.567 40.909 9.11 0.00 43.12 3.93
3408 3580 3.302365 TTACGTTACTTTGCGTAGGCT 57.698 42.857 9.11 0.00 43.12 4.58
3409 3581 5.895216 ATATTACGTTACTTTGCGTAGGC 57.105 39.130 0.00 0.00 43.12 3.93
3410 3582 8.123445 AGAAATATTACGTTACTTTGCGTAGG 57.877 34.615 0.00 0.00 43.12 3.18
3413 3585 9.143631 AGTTAGAAATATTACGTTACTTTGCGT 57.856 29.630 0.00 0.00 44.02 5.24
3428 3600 9.508721 GGGGGAGAGGATTATAGTTAGAAATAT 57.491 37.037 0.00 0.00 0.00 1.28
3429 3601 8.912614 GGGGGAGAGGATTATAGTTAGAAATA 57.087 38.462 0.00 0.00 0.00 1.40
3430 3602 7.816300 GGGGGAGAGGATTATAGTTAGAAAT 57.184 40.000 0.00 0.00 0.00 2.17
3451 3623 0.704076 TCCCACTTGAAATCAGGGGG 59.296 55.000 6.84 6.84 45.21 5.40
3452 3624 2.381911 CATCCCACTTGAAATCAGGGG 58.618 52.381 6.42 8.00 40.02 4.79
3453 3625 2.381911 CCATCCCACTTGAAATCAGGG 58.618 52.381 0.00 0.00 40.98 4.45
3454 3626 2.381911 CCCATCCCACTTGAAATCAGG 58.618 52.381 0.00 0.00 0.00 3.86
3455 3627 1.753073 GCCCATCCCACTTGAAATCAG 59.247 52.381 0.00 0.00 0.00 2.90
3456 3628 1.619432 GGCCCATCCCACTTGAAATCA 60.619 52.381 0.00 0.00 0.00 2.57
3457 3629 1.114627 GGCCCATCCCACTTGAAATC 58.885 55.000 0.00 0.00 0.00 2.17
3458 3630 3.305181 GGCCCATCCCACTTGAAAT 57.695 52.632 0.00 0.00 0.00 2.17
3459 3631 4.863415 GGCCCATCCCACTTGAAA 57.137 55.556 0.00 0.00 0.00 2.69
3474 3646 0.183492 TGATGATTAGTGGCTGGGGC 59.817 55.000 0.00 0.00 37.82 5.80
3475 3647 2.553904 GGATGATGATTAGTGGCTGGGG 60.554 54.545 0.00 0.00 0.00 4.96
3476 3648 2.107031 TGGATGATGATTAGTGGCTGGG 59.893 50.000 0.00 0.00 0.00 4.45
3477 3649 3.497103 TGGATGATGATTAGTGGCTGG 57.503 47.619 0.00 0.00 0.00 4.85
3478 3650 6.072286 GGTAATTGGATGATGATTAGTGGCTG 60.072 42.308 0.00 0.00 0.00 4.85
3479 3651 6.006449 GGTAATTGGATGATGATTAGTGGCT 58.994 40.000 0.00 0.00 0.00 4.75
3480 3652 6.006449 AGGTAATTGGATGATGATTAGTGGC 58.994 40.000 0.00 0.00 0.00 5.01
3481 3653 7.607991 GGTAGGTAATTGGATGATGATTAGTGG 59.392 40.741 0.00 0.00 0.00 4.00
3482 3654 8.378565 AGGTAGGTAATTGGATGATGATTAGTG 58.621 37.037 0.00 0.00 0.00 2.74
3483 3655 8.511748 AGGTAGGTAATTGGATGATGATTAGT 57.488 34.615 0.00 0.00 0.00 2.24
3484 3656 8.043710 GGAGGTAGGTAATTGGATGATGATTAG 58.956 40.741 0.00 0.00 0.00 1.73
3485 3657 7.515861 TGGAGGTAGGTAATTGGATGATGATTA 59.484 37.037 0.00 0.00 0.00 1.75
3486 3658 6.332635 TGGAGGTAGGTAATTGGATGATGATT 59.667 38.462 0.00 0.00 0.00 2.57
3487 3659 5.851693 TGGAGGTAGGTAATTGGATGATGAT 59.148 40.000 0.00 0.00 0.00 2.45
3488 3660 5.071788 GTGGAGGTAGGTAATTGGATGATGA 59.928 44.000 0.00 0.00 0.00 2.92
3489 3661 5.163205 TGTGGAGGTAGGTAATTGGATGATG 60.163 44.000 0.00 0.00 0.00 3.07
3490 3662 4.975147 TGTGGAGGTAGGTAATTGGATGAT 59.025 41.667 0.00 0.00 0.00 2.45
3491 3663 4.367166 TGTGGAGGTAGGTAATTGGATGA 58.633 43.478 0.00 0.00 0.00 2.92
3492 3664 4.771114 TGTGGAGGTAGGTAATTGGATG 57.229 45.455 0.00 0.00 0.00 3.51
3493 3665 4.975147 TGATGTGGAGGTAGGTAATTGGAT 59.025 41.667 0.00 0.00 0.00 3.41
3494 3666 4.367166 TGATGTGGAGGTAGGTAATTGGA 58.633 43.478 0.00 0.00 0.00 3.53
3495 3667 4.771114 TGATGTGGAGGTAGGTAATTGG 57.229 45.455 0.00 0.00 0.00 3.16
3496 3668 5.745227 AGTTGATGTGGAGGTAGGTAATTG 58.255 41.667 0.00 0.00 0.00 2.32
3497 3669 6.388619 AAGTTGATGTGGAGGTAGGTAATT 57.611 37.500 0.00 0.00 0.00 1.40
3498 3670 6.388619 AAAGTTGATGTGGAGGTAGGTAAT 57.611 37.500 0.00 0.00 0.00 1.89
3499 3671 5.836024 AAAGTTGATGTGGAGGTAGGTAA 57.164 39.130 0.00 0.00 0.00 2.85
3500 3672 5.836024 AAAAGTTGATGTGGAGGTAGGTA 57.164 39.130 0.00 0.00 0.00 3.08
3501 3673 4.724279 AAAAGTTGATGTGGAGGTAGGT 57.276 40.909 0.00 0.00 0.00 3.08
3502 3674 5.805728 AGTAAAAGTTGATGTGGAGGTAGG 58.194 41.667 0.00 0.00 0.00 3.18
3503 3675 8.842358 TTAAGTAAAAGTTGATGTGGAGGTAG 57.158 34.615 0.00 0.00 0.00 3.18
3504 3676 9.629878 TTTTAAGTAAAAGTTGATGTGGAGGTA 57.370 29.630 0.00 0.00 32.00 3.08
3505 3677 8.528044 TTTTAAGTAAAAGTTGATGTGGAGGT 57.472 30.769 0.00 0.00 32.00 3.85
3506 3678 9.244799 GTTTTTAAGTAAAAGTTGATGTGGAGG 57.755 33.333 0.00 0.00 36.44 4.30
3526 3698 8.852135 CCCAGGTAAACTTATGTGAAGTTTTTA 58.148 33.333 17.74 2.00 45.20 1.52
3527 3699 7.343574 ACCCAGGTAAACTTATGTGAAGTTTTT 59.656 33.333 17.74 5.13 45.20 1.94
3528 3700 6.837048 ACCCAGGTAAACTTATGTGAAGTTTT 59.163 34.615 17.74 1.39 45.20 2.43
3530 3702 5.948842 ACCCAGGTAAACTTATGTGAAGTT 58.051 37.500 0.00 0.00 41.82 2.66
3531 3703 5.309806 AGACCCAGGTAAACTTATGTGAAGT 59.690 40.000 0.00 0.00 0.00 3.01
3532 3704 5.805728 AGACCCAGGTAAACTTATGTGAAG 58.194 41.667 0.00 0.00 0.00 3.02
3533 3705 5.836024 AGACCCAGGTAAACTTATGTGAA 57.164 39.130 0.00 0.00 0.00 3.18
3534 3706 5.105064 GCTAGACCCAGGTAAACTTATGTGA 60.105 44.000 0.00 0.00 0.00 3.58
3535 3707 5.116882 GCTAGACCCAGGTAAACTTATGTG 58.883 45.833 0.00 0.00 0.00 3.21
3536 3708 4.781087 TGCTAGACCCAGGTAAACTTATGT 59.219 41.667 0.00 0.00 0.00 2.29
3537 3709 5.353394 TGCTAGACCCAGGTAAACTTATG 57.647 43.478 0.00 0.00 0.00 1.90
3538 3710 6.357367 CAATGCTAGACCCAGGTAAACTTAT 58.643 40.000 0.00 0.00 0.00 1.73
3539 3711 5.741011 CAATGCTAGACCCAGGTAAACTTA 58.259 41.667 0.00 0.00 0.00 2.24
3540 3712 4.589908 CAATGCTAGACCCAGGTAAACTT 58.410 43.478 0.00 0.00 0.00 2.66
3541 3713 3.622455 GCAATGCTAGACCCAGGTAAACT 60.622 47.826 0.00 0.00 0.00 2.66
3542 3714 2.683362 GCAATGCTAGACCCAGGTAAAC 59.317 50.000 0.00 0.00 0.00 2.01
3543 3715 2.576191 AGCAATGCTAGACCCAGGTAAA 59.424 45.455 5.69 0.00 36.99 2.01
3544 3716 2.170607 GAGCAATGCTAGACCCAGGTAA 59.829 50.000 8.12 0.00 39.88 2.85
3545 3717 1.762957 GAGCAATGCTAGACCCAGGTA 59.237 52.381 8.12 0.00 39.88 3.08
3546 3718 0.543749 GAGCAATGCTAGACCCAGGT 59.456 55.000 8.12 0.00 39.88 4.00
3547 3719 0.543277 TGAGCAATGCTAGACCCAGG 59.457 55.000 8.12 0.00 39.88 4.45
3548 3720 2.634815 ATGAGCAATGCTAGACCCAG 57.365 50.000 8.12 0.00 39.88 4.45
3549 3721 2.771372 TGTATGAGCAATGCTAGACCCA 59.229 45.455 8.12 1.18 39.88 4.51
3550 3722 3.134458 GTGTATGAGCAATGCTAGACCC 58.866 50.000 8.12 0.00 39.88 4.46
3551 3723 4.065321 AGTGTATGAGCAATGCTAGACC 57.935 45.455 8.12 0.00 39.88 3.85
3552 3724 5.689514 CAGTAGTGTATGAGCAATGCTAGAC 59.310 44.000 8.12 7.21 39.88 2.59
3553 3725 5.737349 GCAGTAGTGTATGAGCAATGCTAGA 60.737 44.000 8.12 0.00 39.88 2.43
3554 3726 4.447054 GCAGTAGTGTATGAGCAATGCTAG 59.553 45.833 8.12 0.00 39.88 3.42
3555 3727 4.141959 TGCAGTAGTGTATGAGCAATGCTA 60.142 41.667 8.12 0.00 39.88 3.49
3556 3728 3.201290 GCAGTAGTGTATGAGCAATGCT 58.799 45.455 7.79 7.79 43.88 3.79
3557 3729 2.938451 TGCAGTAGTGTATGAGCAATGC 59.062 45.455 0.00 0.00 0.00 3.56
3558 3730 4.554134 GCATGCAGTAGTGTATGAGCAATG 60.554 45.833 26.96 5.92 46.67 2.82
3559 3731 3.562973 GCATGCAGTAGTGTATGAGCAAT 59.437 43.478 26.96 0.00 46.67 3.56
3560 3732 2.938451 GCATGCAGTAGTGTATGAGCAA 59.062 45.455 26.96 0.00 46.67 3.91
3561 3733 2.093553 TGCATGCAGTAGTGTATGAGCA 60.094 45.455 26.96 17.80 46.67 4.26
3562 3734 2.554142 TGCATGCAGTAGTGTATGAGC 58.446 47.619 26.96 15.75 46.67 4.26
3563 3735 4.727235 CATGCATGCAGTAGTGTATGAG 57.273 45.455 26.96 14.44 46.67 2.90
3586 3758 1.334779 CGTGTACGGACTAGCTATGCC 60.335 57.143 0.00 0.00 35.37 4.40
3590 3762 1.012086 CTGCGTGTACGGACTAGCTA 58.988 55.000 16.62 0.00 40.23 3.32
3598 3770 1.695893 CTCAATGGCTGCGTGTACGG 61.696 60.000 6.55 0.00 40.23 4.02
3605 3777 1.302366 TAATGCTCTCAATGGCTGCG 58.698 50.000 0.00 0.00 0.00 5.18
3750 3922 9.793259 ATAAAGGAGACACAAAGAAAAGACATA 57.207 29.630 0.00 0.00 0.00 2.29
3781 3953 9.898152 ACATTTAAAAATGAAAAGGAAAGGACA 57.102 25.926 19.53 0.00 46.72 4.02
3783 3955 9.898152 ACACATTTAAAAATGAAAAGGAAAGGA 57.102 25.926 19.53 0.00 46.72 3.36
3784 3956 9.934190 CACACATTTAAAAATGAAAAGGAAAGG 57.066 29.630 19.53 0.00 46.72 3.11
3819 3991 1.366111 AACAGACACACACACACGCC 61.366 55.000 0.00 0.00 0.00 5.68
3825 3997 1.355005 CGACACAACAGACACACACA 58.645 50.000 0.00 0.00 0.00 3.72
3831 4005 3.326981 CGCGCGACACAACAGACA 61.327 61.111 28.94 0.00 0.00 3.41
3849 4023 2.826738 ACAACACACCCACACGCC 60.827 61.111 0.00 0.00 0.00 5.68
3851 4025 1.021920 TGACACAACACACCCACACG 61.022 55.000 0.00 0.00 0.00 4.49
3911 4085 6.017026 TCGGAATGTGCAAAAATAAGTGTGTA 60.017 34.615 0.00 0.00 0.00 2.90
3930 4104 7.338800 ACATAGAATTGCATCTTTTCGGAAT 57.661 32.000 0.00 0.00 0.00 3.01
4011 4185 7.871463 AGGATGAATTAGTGGCGTTAGTATTAC 59.129 37.037 0.00 0.00 0.00 1.89
4022 4196 8.613482 GTTTTCTAAGTAGGATGAATTAGTGGC 58.387 37.037 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.