Multiple sequence alignment - TraesCS2B01G239400

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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 TraesCS2B01G239400 chr2B 100.000 3713 0 0 1 3713 243572100 243568388 0.000000e+00 6857
1 TraesCS2B01G239400 chr2D 96.770 3468 93 12 1 3461 187532498 187529043 0.000000e+00 5766
2 TraesCS2B01G239400 chr2A 97.253 3240 81 4 1 3235 200181960 200178724 0.000000e+00 5483
3 TraesCS2B01G239400 chr2A 89.362 141 7 4 3323 3461 200178729 200178595 1.770000e-38 171


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 TraesCS2B01G239400 chr2B 243568388 243572100 3712 True 6857 6857 100.0000 1 3713 1 chr2B.!!$R1 3712
1 TraesCS2B01G239400 chr2D 187529043 187532498 3455 True 5766 5766 96.7700 1 3461 1 chr2D.!!$R1 3460
2 TraesCS2B01G239400 chr2A 200178595 200181960 3365 True 2827 5483 93.3075 1 3461 2 chr2A.!!$R1 3460

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
105 106 2.683867 CCACTGTAGTCCTCTAGTTCCG 59.316 54.545 0.0 0.0 0.00 4.30 F
813 814 3.211045 GCTCTGTAGTGTTGGGTTTTGA 58.789 45.455 0.0 0.0 0.00 2.69 F
1767 1772 0.179034 CTAGGCATGGGAACTCTGGC 60.179 60.000 0.0 0.0 38.77 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 1739 0.251165 GCCTAGCAACCAAACCCTCA 60.251 55.0 0.00 0.0 0.00 3.86 R
1781 1786 0.465097 CTCCCGGCATTTCAGAGCAT 60.465 55.0 0.00 0.0 0.00 3.79 R
3672 3680 0.031585 ACTCACTACTTGAACGCGCA 59.968 50.0 5.73 0.0 32.21 6.09 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
105 106 2.683867 CCACTGTAGTCCTCTAGTTCCG 59.316 54.545 0.00 0.00 0.00 4.30
340 341 6.479990 AGCAGACAAATTAAAGAAAACTTGCC 59.520 34.615 0.00 0.00 0.00 4.52
551 552 7.260603 ACCATCTTGATGCAAAATTTACTAGC 58.739 34.615 5.16 0.00 0.00 3.42
560 561 9.405587 GATGCAAAATTTACTAGCACTGTTAAA 57.594 29.630 8.93 0.00 38.12 1.52
583 584 4.367039 TTTCCAAGGGAAAGGTAGAGTG 57.633 45.455 6.35 0.00 45.42 3.51
813 814 3.211045 GCTCTGTAGTGTTGGGTTTTGA 58.789 45.455 0.00 0.00 0.00 2.69
1620 1625 5.472137 TGTGAAGGAACTATTAACCAAGTGC 59.528 40.000 0.00 0.00 38.49 4.40
1734 1739 2.426381 GCGTCTAGGTGCTTACCTACTT 59.574 50.000 2.17 0.00 41.12 2.24
1767 1772 0.179034 CTAGGCATGGGAACTCTGGC 60.179 60.000 0.00 0.00 38.77 4.85
1781 1786 2.371841 ACTCTGGCACAAACATCTACCA 59.628 45.455 0.00 0.00 38.70 3.25
2137 2142 5.224821 ACCTTTGGAGTTTACACCTCTAC 57.775 43.478 0.00 0.00 0.00 2.59
2151 2156 4.079672 ACACCTCTACCTGTCTATGCTACT 60.080 45.833 0.00 0.00 0.00 2.57
2161 2166 5.336770 CCTGTCTATGCTACTCAAGTCACAA 60.337 44.000 0.00 0.00 0.00 3.33
2676 2681 0.815734 CAATGCTCTTGGGCTGGAAG 59.184 55.000 0.00 0.00 0.00 3.46
2678 2683 0.255318 ATGCTCTTGGGCTGGAAGAG 59.745 55.000 13.66 13.66 46.31 2.85
2757 2763 6.969828 AAAGAAAACAGAGGTTATAGAGCG 57.030 37.500 0.00 0.00 35.82 5.03
2843 2850 5.450818 TGCCTAAATGTAGACCAGGAATT 57.549 39.130 0.00 0.00 0.00 2.17
2844 2851 5.192927 TGCCTAAATGTAGACCAGGAATTG 58.807 41.667 0.00 0.00 0.00 2.32
2848 2855 2.672961 TGTAGACCAGGAATTGAGCG 57.327 50.000 0.00 0.00 0.00 5.03
2903 2910 1.603739 AGTTTTCCTGCGCTTCCCC 60.604 57.895 9.73 0.00 0.00 4.81
2909 2916 2.512515 CTGCGCTTCCCCTGTAGC 60.513 66.667 9.73 0.00 0.00 3.58
3088 3095 3.743911 CGTTACATGAGCAAGTGGTGTAA 59.256 43.478 0.00 0.00 34.08 2.41
3135 3142 0.322546 ATTGGGCTTTGGGTCGAGAC 60.323 55.000 0.00 0.00 0.00 3.36
3178 3185 3.790820 GTGTTGTACGTTCGTTCTACACA 59.209 43.478 27.71 15.17 39.62 3.72
3179 3186 3.790820 TGTTGTACGTTCGTTCTACACAC 59.209 43.478 12.64 8.78 0.00 3.82
3251 3258 2.781945 GATGCCATCGTCCCAAAATC 57.218 50.000 0.00 0.00 0.00 2.17
3252 3259 1.338020 GATGCCATCGTCCCAAAATCC 59.662 52.381 0.00 0.00 0.00 3.01
3253 3260 0.038890 TGCCATCGTCCCAAAATCCA 59.961 50.000 0.00 0.00 0.00 3.41
3254 3261 1.181786 GCCATCGTCCCAAAATCCAA 58.818 50.000 0.00 0.00 0.00 3.53
3255 3262 1.548269 GCCATCGTCCCAAAATCCAAA 59.452 47.619 0.00 0.00 0.00 3.28
3256 3263 2.168313 GCCATCGTCCCAAAATCCAAAT 59.832 45.455 0.00 0.00 0.00 2.32
3275 3282 4.370364 AATGCTCGGCGACAATATTTTT 57.630 36.364 4.99 0.00 0.00 1.94
3296 3303 0.112218 TGGGCAATGATATTCCGGGG 59.888 55.000 0.00 0.00 0.00 5.73
3411 3419 1.202651 ACGTCCAAACTCCCAAGTCTG 60.203 52.381 0.00 0.00 33.48 3.51
3430 3438 3.193479 TCTGAGCTAGCGACATTTTCAGA 59.807 43.478 20.56 20.56 37.74 3.27
3433 3441 4.115516 GAGCTAGCGACATTTTCAGATCA 58.884 43.478 9.55 0.00 0.00 2.92
3439 3447 3.302092 GCGACATTTTCAGATCAGCGTAG 60.302 47.826 0.00 0.00 0.00 3.51
3440 3448 4.105486 CGACATTTTCAGATCAGCGTAGA 58.895 43.478 0.00 0.00 0.00 2.59
3442 3450 5.330455 ACATTTTCAGATCAGCGTAGAGA 57.670 39.130 0.00 0.00 0.00 3.10
3455 3463 1.540407 GTAGAGAAGCGAACTGAGCG 58.460 55.000 0.00 0.00 40.04 5.03
3456 3464 1.135632 GTAGAGAAGCGAACTGAGCGT 60.136 52.381 0.00 0.00 40.04 5.07
3457 3465 0.387878 AGAGAAGCGAACTGAGCGTG 60.388 55.000 0.00 0.00 40.04 5.34
3459 3467 1.664965 GAAGCGAACTGAGCGTGGT 60.665 57.895 0.00 0.00 40.04 4.16
3461 3469 1.222115 AAGCGAACTGAGCGTGGTTC 61.222 55.000 8.09 8.09 40.04 3.62
3463 3471 3.550656 GAACTGAGCGTGGTTCGG 58.449 61.111 3.77 0.00 40.26 4.30
3464 3472 1.006571 GAACTGAGCGTGGTTCGGA 60.007 57.895 0.00 0.00 40.26 4.55
3465 3473 0.599204 GAACTGAGCGTGGTTCGGAA 60.599 55.000 0.00 0.00 40.26 4.30
3466 3474 0.034896 AACTGAGCGTGGTTCGGAAT 59.965 50.000 0.00 0.00 40.26 3.01
3467 3475 0.670546 ACTGAGCGTGGTTCGGAATG 60.671 55.000 0.00 0.00 40.26 2.67
3468 3476 1.361668 CTGAGCGTGGTTCGGAATGG 61.362 60.000 0.00 0.00 40.26 3.16
3469 3477 1.375523 GAGCGTGGTTCGGAATGGT 60.376 57.895 0.00 0.00 40.26 3.55
3470 3478 0.108520 GAGCGTGGTTCGGAATGGTA 60.109 55.000 0.00 0.00 40.26 3.25
3471 3479 0.390735 AGCGTGGTTCGGAATGGTAC 60.391 55.000 0.00 0.00 40.26 3.34
3472 3480 1.363885 GCGTGGTTCGGAATGGTACC 61.364 60.000 4.43 4.43 40.26 3.34
3473 3481 0.037139 CGTGGTTCGGAATGGTACCA 60.037 55.000 18.99 18.99 38.29 3.25
3474 3482 1.608542 CGTGGTTCGGAATGGTACCAA 60.609 52.381 20.76 0.00 41.95 3.67
3475 3483 1.808343 GTGGTTCGGAATGGTACCAAC 59.192 52.381 20.76 15.66 41.95 3.77
3476 3484 1.271488 TGGTTCGGAATGGTACCAACC 60.271 52.381 20.76 22.48 46.98 3.77
3477 3485 1.456296 GTTCGGAATGGTACCAACCC 58.544 55.000 25.71 23.16 46.16 4.11
3478 3486 1.065647 TTCGGAATGGTACCAACCCA 58.934 50.000 26.18 16.76 46.16 4.51
3479 3487 0.325602 TCGGAATGGTACCAACCCAC 59.674 55.000 26.18 14.29 46.16 4.61
3480 3488 0.326927 CGGAATGGTACCAACCCACT 59.673 55.000 26.18 7.10 46.16 4.00
3481 3489 1.555992 CGGAATGGTACCAACCCACTA 59.444 52.381 26.18 2.27 46.16 2.74
3482 3490 2.419574 CGGAATGGTACCAACCCACTAG 60.420 54.545 26.18 14.08 46.16 2.57
3483 3491 2.092592 GGAATGGTACCAACCCACTAGG 60.093 54.545 20.76 0.00 46.16 3.02
3499 3507 6.295719 CCACTAGGGTTTAAGTCATACACT 57.704 41.667 0.00 0.00 36.64 3.55
3501 3509 6.594159 CCACTAGGGTTTAAGTCATACACTTG 59.406 42.308 0.00 0.00 45.60 3.16
3502 3510 6.594159 CACTAGGGTTTAAGTCATACACTTGG 59.406 42.308 0.00 0.00 45.60 3.61
3503 3511 4.332828 AGGGTTTAAGTCATACACTTGGC 58.667 43.478 0.00 0.00 45.60 4.52
3504 3512 4.076394 GGGTTTAAGTCATACACTTGGCA 58.924 43.478 0.00 0.00 45.60 4.92
3505 3513 4.082949 GGGTTTAAGTCATACACTTGGCAC 60.083 45.833 0.00 0.00 45.60 5.01
3506 3514 4.760204 GGTTTAAGTCATACACTTGGCACT 59.240 41.667 0.00 0.00 45.60 4.40
3507 3515 5.334879 GGTTTAAGTCATACACTTGGCACTG 60.335 44.000 0.00 0.00 45.60 3.66
3508 3516 2.479566 AGTCATACACTTGGCACTGG 57.520 50.000 0.00 0.00 26.56 4.00
3509 3517 1.699634 AGTCATACACTTGGCACTGGT 59.300 47.619 0.00 0.00 26.56 4.00
3510 3518 1.806542 GTCATACACTTGGCACTGGTG 59.193 52.381 11.28 11.28 37.48 4.17
3511 3519 1.419762 TCATACACTTGGCACTGGTGT 59.580 47.619 19.04 19.04 43.70 4.16
3512 3520 2.158682 TCATACACTTGGCACTGGTGTT 60.159 45.455 19.87 9.43 42.21 3.32
3513 3521 1.961793 TACACTTGGCACTGGTGTTC 58.038 50.000 19.87 0.00 42.21 3.18
3514 3522 1.095228 ACACTTGGCACTGGTGTTCG 61.095 55.000 12.33 0.00 40.30 3.95
3515 3523 2.186826 ACTTGGCACTGGTGTTCGC 61.187 57.895 2.64 0.00 0.00 4.70
3516 3524 2.124529 TTGGCACTGGTGTTCGCA 60.125 55.556 2.64 0.00 0.00 5.10
3517 3525 1.723608 CTTGGCACTGGTGTTCGCAA 61.724 55.000 2.64 0.00 0.00 4.85
3518 3526 1.106351 TTGGCACTGGTGTTCGCAAT 61.106 50.000 2.64 0.00 0.00 3.56
3519 3527 1.106351 TGGCACTGGTGTTCGCAATT 61.106 50.000 2.64 0.00 0.00 2.32
3520 3528 0.031994 GGCACTGGTGTTCGCAATTT 59.968 50.000 2.64 0.00 0.00 1.82
3521 3529 1.537990 GGCACTGGTGTTCGCAATTTT 60.538 47.619 2.64 0.00 0.00 1.82
3522 3530 1.786579 GCACTGGTGTTCGCAATTTTC 59.213 47.619 2.64 0.00 0.00 2.29
3523 3531 2.543653 GCACTGGTGTTCGCAATTTTCT 60.544 45.455 2.64 0.00 0.00 2.52
3524 3532 3.044986 CACTGGTGTTCGCAATTTTCTG 58.955 45.455 0.00 0.00 0.00 3.02
3525 3533 2.948979 ACTGGTGTTCGCAATTTTCTGA 59.051 40.909 0.00 0.00 0.00 3.27
3526 3534 3.380004 ACTGGTGTTCGCAATTTTCTGAA 59.620 39.130 0.00 0.00 0.00 3.02
3527 3535 4.037923 ACTGGTGTTCGCAATTTTCTGAAT 59.962 37.500 0.00 0.00 0.00 2.57
3528 3536 4.942852 TGGTGTTCGCAATTTTCTGAATT 58.057 34.783 0.00 0.00 0.00 2.17
3529 3537 5.355596 TGGTGTTCGCAATTTTCTGAATTT 58.644 33.333 0.00 0.00 0.00 1.82
3530 3538 5.233902 TGGTGTTCGCAATTTTCTGAATTTG 59.766 36.000 8.45 8.45 32.15 2.32
3531 3539 5.234116 GGTGTTCGCAATTTTCTGAATTTGT 59.766 36.000 12.38 0.00 31.81 2.83
3532 3540 6.238076 GGTGTTCGCAATTTTCTGAATTTGTT 60.238 34.615 12.38 0.00 31.81 2.83
3533 3541 7.179410 GTGTTCGCAATTTTCTGAATTTGTTT 58.821 30.769 12.38 0.00 31.81 2.83
3534 3542 7.370576 GTGTTCGCAATTTTCTGAATTTGTTTC 59.629 33.333 12.38 0.00 31.81 2.78
3535 3543 7.063898 TGTTCGCAATTTTCTGAATTTGTTTCA 59.936 29.630 12.38 0.00 42.09 2.69
3536 3544 7.531280 TCGCAATTTTCTGAATTTGTTTCAA 57.469 28.000 12.38 0.00 43.64 2.69
3537 3545 7.620215 TCGCAATTTTCTGAATTTGTTTCAAG 58.380 30.769 12.38 0.00 43.64 3.02
3538 3546 6.355144 CGCAATTTTCTGAATTTGTTTCAAGC 59.645 34.615 12.38 0.00 43.64 4.01
3539 3547 7.412063 GCAATTTTCTGAATTTGTTTCAAGCT 58.588 30.769 12.38 0.00 43.64 3.74
3540 3548 7.585210 GCAATTTTCTGAATTTGTTTCAAGCTC 59.415 33.333 12.38 0.00 43.64 4.09
3541 3549 8.823818 CAATTTTCTGAATTTGTTTCAAGCTCT 58.176 29.630 0.00 0.00 43.64 4.09
3542 3550 7.992180 TTTTCTGAATTTGTTTCAAGCTCTC 57.008 32.000 0.00 0.00 43.64 3.20
3543 3551 5.348418 TCTGAATTTGTTTCAAGCTCTCG 57.652 39.130 0.00 0.00 43.64 4.04
3544 3552 4.214119 TCTGAATTTGTTTCAAGCTCTCGG 59.786 41.667 0.00 0.00 43.64 4.63
3545 3553 3.882888 TGAATTTGTTTCAAGCTCTCGGT 59.117 39.130 0.00 0.00 41.38 4.69
3546 3554 3.904136 ATTTGTTTCAAGCTCTCGGTG 57.096 42.857 0.00 0.00 0.00 4.94
3547 3555 2.613026 TTGTTTCAAGCTCTCGGTGA 57.387 45.000 0.00 0.00 0.00 4.02
3548 3556 2.839486 TGTTTCAAGCTCTCGGTGAT 57.161 45.000 0.00 0.00 0.00 3.06
3549 3557 2.416747 TGTTTCAAGCTCTCGGTGATG 58.583 47.619 0.00 0.00 0.00 3.07
3550 3558 1.129437 GTTTCAAGCTCTCGGTGATGC 59.871 52.381 0.00 0.00 0.00 3.91
3551 3559 0.610174 TTCAAGCTCTCGGTGATGCT 59.390 50.000 0.00 0.00 37.37 3.79
3552 3560 0.174389 TCAAGCTCTCGGTGATGCTC 59.826 55.000 0.00 0.00 34.38 4.26
3553 3561 0.108472 CAAGCTCTCGGTGATGCTCA 60.108 55.000 0.00 0.00 34.38 4.26
3554 3562 0.829333 AAGCTCTCGGTGATGCTCAT 59.171 50.000 0.00 0.00 34.38 2.90
3555 3563 0.829333 AGCTCTCGGTGATGCTCATT 59.171 50.000 0.00 0.00 0.00 2.57
3556 3564 1.202510 AGCTCTCGGTGATGCTCATTC 60.203 52.381 0.00 0.00 0.00 2.67
3557 3565 1.472201 GCTCTCGGTGATGCTCATTCA 60.472 52.381 0.00 0.00 0.00 2.57
3558 3566 2.471818 CTCTCGGTGATGCTCATTCAG 58.528 52.381 0.00 0.00 0.00 3.02
3559 3567 1.827344 TCTCGGTGATGCTCATTCAGT 59.173 47.619 0.00 0.00 0.00 3.41
3560 3568 1.931841 CTCGGTGATGCTCATTCAGTG 59.068 52.381 0.00 0.00 0.00 3.66
3561 3569 1.012086 CGGTGATGCTCATTCAGTGG 58.988 55.000 0.00 0.00 0.00 4.00
3562 3570 1.386533 GGTGATGCTCATTCAGTGGG 58.613 55.000 0.00 0.00 0.00 4.61
3563 3571 1.065199 GGTGATGCTCATTCAGTGGGA 60.065 52.381 0.00 0.00 0.00 4.37
3564 3572 2.286872 GTGATGCTCATTCAGTGGGAG 58.713 52.381 0.00 0.00 0.00 4.30
3565 3573 1.211212 TGATGCTCATTCAGTGGGAGG 59.789 52.381 8.70 0.00 0.00 4.30
3566 3574 1.487976 GATGCTCATTCAGTGGGAGGA 59.512 52.381 8.70 6.73 33.48 3.71
3567 3575 1.588239 TGCTCATTCAGTGGGAGGAT 58.412 50.000 8.70 0.00 0.00 3.24
3568 3576 2.763039 TGCTCATTCAGTGGGAGGATA 58.237 47.619 8.70 0.00 0.00 2.59
3569 3577 2.435805 TGCTCATTCAGTGGGAGGATAC 59.564 50.000 8.70 0.00 0.00 2.24
3570 3578 2.435805 GCTCATTCAGTGGGAGGATACA 59.564 50.000 8.70 0.00 41.41 2.29
3571 3579 3.072184 GCTCATTCAGTGGGAGGATACAT 59.928 47.826 8.70 0.00 41.41 2.29
3572 3580 4.445448 GCTCATTCAGTGGGAGGATACATT 60.445 45.833 8.70 0.00 41.41 2.71
3573 3581 5.688807 CTCATTCAGTGGGAGGATACATTT 58.311 41.667 0.00 0.00 41.41 2.32
3574 3582 6.078456 TCATTCAGTGGGAGGATACATTTT 57.922 37.500 0.00 0.00 41.41 1.82
3575 3583 6.122277 TCATTCAGTGGGAGGATACATTTTC 58.878 40.000 0.00 0.00 41.41 2.29
3576 3584 4.137116 TCAGTGGGAGGATACATTTTCG 57.863 45.455 0.00 0.00 41.41 3.46
3577 3585 3.517901 TCAGTGGGAGGATACATTTTCGT 59.482 43.478 0.00 0.00 41.41 3.85
3578 3586 3.871594 CAGTGGGAGGATACATTTTCGTC 59.128 47.826 0.00 0.00 41.41 4.20
3579 3587 2.864343 GTGGGAGGATACATTTTCGTCG 59.136 50.000 0.00 0.00 41.41 5.12
3580 3588 2.761767 TGGGAGGATACATTTTCGTCGA 59.238 45.455 0.00 0.00 41.41 4.20
3581 3589 3.121544 GGGAGGATACATTTTCGTCGAC 58.878 50.000 5.18 5.18 41.41 4.20
3582 3590 3.181478 GGGAGGATACATTTTCGTCGACT 60.181 47.826 14.70 0.00 41.41 4.18
3583 3591 4.037208 GGGAGGATACATTTTCGTCGACTA 59.963 45.833 14.70 0.00 41.41 2.59
3584 3592 5.450965 GGGAGGATACATTTTCGTCGACTAA 60.451 44.000 14.70 6.16 41.41 2.24
3585 3593 5.686397 GGAGGATACATTTTCGTCGACTAAG 59.314 44.000 14.70 0.00 41.41 2.18
3586 3594 6.446781 AGGATACATTTTCGTCGACTAAGA 57.553 37.500 14.70 4.64 41.41 2.10
3587 3595 6.860080 AGGATACATTTTCGTCGACTAAGAA 58.140 36.000 14.70 7.13 41.41 2.52
3588 3596 6.973474 AGGATACATTTTCGTCGACTAAGAAG 59.027 38.462 14.70 4.09 41.41 2.85
3589 3597 6.971184 GGATACATTTTCGTCGACTAAGAAGA 59.029 38.462 14.70 5.73 0.00 2.87
3590 3598 7.044183 GGATACATTTTCGTCGACTAAGAAGAC 60.044 40.741 14.70 0.00 0.00 3.01
3596 3604 3.967203 GTCGACTAAGAAGACGCCTAT 57.033 47.619 8.70 0.00 40.10 2.57
3598 3606 5.021120 GTCGACTAAGAAGACGCCTATAG 57.979 47.826 8.70 0.00 40.10 1.31
3599 3607 4.511082 GTCGACTAAGAAGACGCCTATAGT 59.489 45.833 8.70 0.00 40.10 2.12
3600 3608 4.510711 TCGACTAAGAAGACGCCTATAGTG 59.489 45.833 0.00 0.00 40.10 2.74
3601 3609 4.319622 CGACTAAGAAGACGCCTATAGTGG 60.320 50.000 0.00 0.00 34.36 4.00
3606 3614 1.776662 AGACGCCTATAGTGGCTTCA 58.223 50.000 13.13 0.00 44.04 3.02
3607 3615 2.320781 AGACGCCTATAGTGGCTTCAT 58.679 47.619 13.13 0.00 44.04 2.57
3608 3616 2.297597 AGACGCCTATAGTGGCTTCATC 59.702 50.000 13.13 2.50 44.04 2.92
3609 3617 5.160821 AGACGCCTATAGTGGCTTCATCG 62.161 52.174 13.13 0.00 44.04 3.84
3614 3622 4.992688 CCTATAGTGGCTTCATCGATCTC 58.007 47.826 0.00 0.00 0.00 2.75
3615 3623 4.460731 CCTATAGTGGCTTCATCGATCTCA 59.539 45.833 0.00 0.00 0.00 3.27
3616 3624 4.944619 ATAGTGGCTTCATCGATCTCAA 57.055 40.909 0.00 0.00 0.00 3.02
3617 3625 3.616956 AGTGGCTTCATCGATCTCAAA 57.383 42.857 0.00 0.00 0.00 2.69
3618 3626 3.529533 AGTGGCTTCATCGATCTCAAAG 58.470 45.455 0.00 0.00 0.00 2.77
3619 3627 3.196469 AGTGGCTTCATCGATCTCAAAGA 59.804 43.478 0.00 0.00 0.00 2.52
3620 3628 4.125703 GTGGCTTCATCGATCTCAAAGAT 58.874 43.478 0.00 0.00 37.73 2.40
3621 3629 4.025061 GTGGCTTCATCGATCTCAAAGATG 60.025 45.833 0.00 2.17 42.11 2.90
3622 3630 4.141869 TGGCTTCATCGATCTCAAAGATGA 60.142 41.667 0.00 6.24 46.05 2.92
3623 3631 4.996122 GGCTTCATCGATCTCAAAGATGAT 59.004 41.667 9.99 0.00 46.65 2.45
3624 3632 6.162079 GGCTTCATCGATCTCAAAGATGATA 58.838 40.000 9.99 3.30 46.65 2.15
3625 3633 6.817641 GGCTTCATCGATCTCAAAGATGATAT 59.182 38.462 9.99 0.00 46.65 1.63
3626 3634 7.201539 GGCTTCATCGATCTCAAAGATGATATG 60.202 40.741 9.99 6.35 46.65 1.78
3627 3635 7.331440 GCTTCATCGATCTCAAAGATGATATGT 59.669 37.037 9.99 0.00 46.65 2.29
3628 3636 8.754230 TTCATCGATCTCAAAGATGATATGTC 57.246 34.615 9.99 0.00 46.65 3.06
3629 3637 7.025963 TCATCGATCTCAAAGATGATATGTCG 58.974 38.462 0.00 0.00 43.81 4.35
3630 3638 5.703876 TCGATCTCAAAGATGATATGTCGG 58.296 41.667 0.00 0.00 34.53 4.79
3631 3639 4.325741 CGATCTCAAAGATGATATGTCGGC 59.674 45.833 0.00 0.00 34.53 5.54
3632 3640 3.995199 TCTCAAAGATGATATGTCGGCC 58.005 45.455 0.00 0.00 34.37 6.13
3633 3641 3.070018 CTCAAAGATGATATGTCGGCCC 58.930 50.000 0.00 0.00 34.37 5.80
3634 3642 2.437651 TCAAAGATGATATGTCGGCCCA 59.562 45.455 0.00 0.00 0.00 5.36
3635 3643 2.810274 CAAAGATGATATGTCGGCCCAG 59.190 50.000 0.00 0.00 0.00 4.45
3636 3644 1.722034 AGATGATATGTCGGCCCAGT 58.278 50.000 0.00 0.00 0.00 4.00
3637 3645 2.050144 AGATGATATGTCGGCCCAGTT 58.950 47.619 0.00 0.00 0.00 3.16
3638 3646 2.439507 AGATGATATGTCGGCCCAGTTT 59.560 45.455 0.00 0.00 0.00 2.66
3639 3647 2.799126 TGATATGTCGGCCCAGTTTT 57.201 45.000 0.00 0.00 0.00 2.43
3640 3648 3.080300 TGATATGTCGGCCCAGTTTTT 57.920 42.857 0.00 0.00 0.00 1.94
3641 3649 3.013921 TGATATGTCGGCCCAGTTTTTC 58.986 45.455 0.00 0.00 0.00 2.29
3642 3650 1.444836 TATGTCGGCCCAGTTTTTCG 58.555 50.000 0.00 0.00 0.00 3.46
3643 3651 0.250553 ATGTCGGCCCAGTTTTTCGA 60.251 50.000 0.00 0.00 0.00 3.71
3644 3652 0.464013 TGTCGGCCCAGTTTTTCGAA 60.464 50.000 0.00 0.00 0.00 3.71
3645 3653 0.879090 GTCGGCCCAGTTTTTCGAAT 59.121 50.000 0.00 0.00 0.00 3.34
3646 3654 0.878416 TCGGCCCAGTTTTTCGAATG 59.122 50.000 0.00 0.00 0.00 2.67
3647 3655 0.596082 CGGCCCAGTTTTTCGAATGT 59.404 50.000 0.00 0.00 0.00 2.71
3648 3656 1.665735 CGGCCCAGTTTTTCGAATGTG 60.666 52.381 0.00 0.00 0.00 3.21
3649 3657 1.418373 GCCCAGTTTTTCGAATGTGC 58.582 50.000 0.00 0.00 0.00 4.57
3650 3658 1.000274 GCCCAGTTTTTCGAATGTGCT 60.000 47.619 0.00 0.00 0.00 4.40
3651 3659 2.922335 GCCCAGTTTTTCGAATGTGCTC 60.922 50.000 0.00 0.00 0.00 4.26
3652 3660 2.293122 CCCAGTTTTTCGAATGTGCTCA 59.707 45.455 0.00 0.00 0.00 4.26
3653 3661 3.057315 CCCAGTTTTTCGAATGTGCTCAT 60.057 43.478 0.00 0.00 35.59 2.90
3654 3662 4.155826 CCCAGTTTTTCGAATGTGCTCATA 59.844 41.667 0.00 0.00 33.49 2.15
3655 3663 5.163622 CCCAGTTTTTCGAATGTGCTCATAT 60.164 40.000 0.00 0.00 33.49 1.78
3656 3664 5.740569 CCAGTTTTTCGAATGTGCTCATATG 59.259 40.000 0.00 0.00 33.49 1.78
3657 3665 5.740569 CAGTTTTTCGAATGTGCTCATATGG 59.259 40.000 0.00 0.00 33.49 2.74
3658 3666 5.647658 AGTTTTTCGAATGTGCTCATATGGA 59.352 36.000 0.00 0.00 33.49 3.41
3659 3667 6.319658 AGTTTTTCGAATGTGCTCATATGGAT 59.680 34.615 0.00 0.00 33.49 3.41
3660 3668 7.498900 AGTTTTTCGAATGTGCTCATATGGATA 59.501 33.333 0.00 0.00 33.49 2.59
3661 3669 7.425577 TTTTCGAATGTGCTCATATGGATAG 57.574 36.000 0.00 0.00 33.49 2.08
3662 3670 5.982890 TCGAATGTGCTCATATGGATAGA 57.017 39.130 2.13 0.00 33.49 1.98
3663 3671 6.345096 TCGAATGTGCTCATATGGATAGAA 57.655 37.500 2.13 0.00 33.49 2.10
3664 3672 6.758254 TCGAATGTGCTCATATGGATAGAAA 58.242 36.000 2.13 0.00 33.49 2.52
3665 3673 7.216494 TCGAATGTGCTCATATGGATAGAAAA 58.784 34.615 2.13 0.00 33.49 2.29
3666 3674 7.879677 TCGAATGTGCTCATATGGATAGAAAAT 59.120 33.333 2.13 0.00 33.49 1.82
3667 3675 7.961283 CGAATGTGCTCATATGGATAGAAAATG 59.039 37.037 2.13 0.00 33.49 2.32
3668 3676 8.701908 AATGTGCTCATATGGATAGAAAATGT 57.298 30.769 2.13 0.00 33.49 2.71
3669 3677 7.500720 TGTGCTCATATGGATAGAAAATGTG 57.499 36.000 2.13 0.00 0.00 3.21
3670 3678 7.056006 TGTGCTCATATGGATAGAAAATGTGT 58.944 34.615 2.13 0.00 0.00 3.72
3671 3679 7.012610 TGTGCTCATATGGATAGAAAATGTGTG 59.987 37.037 2.13 0.00 0.00 3.82
3672 3680 7.012704 GTGCTCATATGGATAGAAAATGTGTGT 59.987 37.037 2.13 0.00 0.00 3.72
3673 3681 7.012610 TGCTCATATGGATAGAAAATGTGTGTG 59.987 37.037 2.13 0.00 0.00 3.82
3674 3682 7.263100 TCATATGGATAGAAAATGTGTGTGC 57.737 36.000 2.13 0.00 0.00 4.57
3675 3683 4.621068 ATGGATAGAAAATGTGTGTGCG 57.379 40.909 0.00 0.00 0.00 5.34
3676 3684 2.161410 TGGATAGAAAATGTGTGTGCGC 59.839 45.455 0.00 0.00 0.00 6.09
3677 3685 2.430956 GATAGAAAATGTGTGTGCGCG 58.569 47.619 0.00 0.00 0.00 6.86
3678 3686 1.222300 TAGAAAATGTGTGTGCGCGT 58.778 45.000 8.43 0.00 0.00 6.01
3679 3687 0.380378 AGAAAATGTGTGTGCGCGTT 59.620 45.000 8.43 0.00 36.03 4.84
3680 3688 0.770008 GAAAATGTGTGTGCGCGTTC 59.230 50.000 8.43 1.34 33.64 3.95
3681 3689 0.099613 AAAATGTGTGTGCGCGTTCA 59.900 45.000 8.43 4.43 33.64 3.18
3682 3690 0.099613 AAATGTGTGTGCGCGTTCAA 59.900 45.000 8.43 0.00 33.64 2.69
3683 3691 0.316937 AATGTGTGTGCGCGTTCAAG 60.317 50.000 8.43 0.00 29.11 3.02
3684 3692 1.436195 ATGTGTGTGCGCGTTCAAGT 61.436 50.000 8.43 0.00 0.00 3.16
3685 3693 0.806492 TGTGTGTGCGCGTTCAAGTA 60.806 50.000 8.43 0.00 0.00 2.24
3686 3694 0.111266 GTGTGTGCGCGTTCAAGTAG 60.111 55.000 8.43 0.00 0.00 2.57
3687 3695 0.528901 TGTGTGCGCGTTCAAGTAGT 60.529 50.000 8.43 0.00 0.00 2.73
3688 3696 0.111266 GTGTGCGCGTTCAAGTAGTG 60.111 55.000 8.43 0.00 0.00 2.74
3689 3697 0.249114 TGTGCGCGTTCAAGTAGTGA 60.249 50.000 8.43 0.00 0.00 3.41
3690 3698 0.435008 GTGCGCGTTCAAGTAGTGAG 59.565 55.000 8.43 0.00 37.61 3.51
3691 3699 0.031585 TGCGCGTTCAAGTAGTGAGT 59.968 50.000 8.43 0.00 37.61 3.41
3692 3700 0.435008 GCGCGTTCAAGTAGTGAGTG 59.565 55.000 8.43 0.00 37.61 3.51
3693 3701 1.767289 CGCGTTCAAGTAGTGAGTGT 58.233 50.000 0.00 0.00 37.61 3.55
3694 3702 2.919387 GCGCGTTCAAGTAGTGAGTGTA 60.919 50.000 8.43 0.00 37.61 2.90
3695 3703 3.499048 CGCGTTCAAGTAGTGAGTGTAT 58.501 45.455 0.00 0.00 37.61 2.29
3696 3704 3.300853 CGCGTTCAAGTAGTGAGTGTATG 59.699 47.826 0.00 0.00 37.61 2.39
3697 3705 4.235360 GCGTTCAAGTAGTGAGTGTATGT 58.765 43.478 0.00 0.00 37.61 2.29
3698 3706 4.090066 GCGTTCAAGTAGTGAGTGTATGTG 59.910 45.833 0.00 0.00 37.61 3.21
3699 3707 4.090066 CGTTCAAGTAGTGAGTGTATGTGC 59.910 45.833 0.00 0.00 37.61 4.57
3700 3708 3.833442 TCAAGTAGTGAGTGTATGTGCG 58.167 45.455 0.00 0.00 0.00 5.34
3701 3709 3.254903 TCAAGTAGTGAGTGTATGTGCGT 59.745 43.478 0.00 0.00 0.00 5.24
3702 3710 4.456566 TCAAGTAGTGAGTGTATGTGCGTA 59.543 41.667 0.00 0.00 0.00 4.42
3703 3711 5.124936 TCAAGTAGTGAGTGTATGTGCGTAT 59.875 40.000 0.00 0.00 0.00 3.06
3704 3712 6.316890 TCAAGTAGTGAGTGTATGTGCGTATA 59.683 38.462 0.00 0.00 0.00 1.47
3705 3713 6.879276 AGTAGTGAGTGTATGTGCGTATAT 57.121 37.500 0.00 0.00 0.00 0.86
3706 3714 7.974482 AGTAGTGAGTGTATGTGCGTATATA 57.026 36.000 0.00 0.00 0.00 0.86
3707 3715 7.804712 AGTAGTGAGTGTATGTGCGTATATAC 58.195 38.462 12.38 12.38 33.09 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 3.943381 TCAATCATGATGAGTCTGCCAAC 59.057 43.478 9.46 0.00 0.00 3.77
222 223 2.093500 TCTCTGTCAAATGTCCCCATCG 60.093 50.000 0.00 0.00 0.00 3.84
300 301 1.977854 TCTGCTTGCCTTTCCTCTACA 59.022 47.619 0.00 0.00 0.00 2.74
301 302 2.289694 TGTCTGCTTGCCTTTCCTCTAC 60.290 50.000 0.00 0.00 0.00 2.59
340 341 5.334569 CGGACCAAACACTAAATACACAAGG 60.335 44.000 0.00 0.00 0.00 3.61
449 450 9.425577 GATGAGAGTTTTAAGTTGTAAGTAGCT 57.574 33.333 0.00 0.00 0.00 3.32
517 518 7.887996 TTTGCATCAAGATGGTAATTTGAAC 57.112 32.000 11.66 0.00 39.16 3.18
518 519 9.504708 AATTTTGCATCAAGATGGTAATTTGAA 57.495 25.926 11.66 0.00 39.16 2.69
610 611 7.915293 AACGTGACATTCCAATTCATTAGTA 57.085 32.000 0.00 0.00 0.00 1.82
611 612 6.817765 AACGTGACATTCCAATTCATTAGT 57.182 33.333 0.00 0.00 0.00 2.24
612 613 8.450964 ACTTAACGTGACATTCCAATTCATTAG 58.549 33.333 0.00 0.00 0.00 1.73
705 706 9.104713 TCTGGTGATATGTAGGATAACATGAAT 57.895 33.333 0.00 0.00 40.29 2.57
766 767 7.859377 CAAATGCAATTCTATATCGCAAGAACT 59.141 33.333 0.00 0.00 44.60 3.01
774 775 6.895898 ACAGAGCAAATGCAATTCTATATCG 58.104 36.000 8.28 0.00 45.16 2.92
813 814 4.236935 CAGGCGACAAAGCATAAACATTT 58.763 39.130 0.00 0.00 39.27 2.32
1604 1609 3.670625 TCAGCGCACTTGGTTAATAGTT 58.329 40.909 11.47 0.00 0.00 2.24
1605 1610 3.262420 CTCAGCGCACTTGGTTAATAGT 58.738 45.455 11.47 0.00 0.00 2.12
1620 1625 1.134699 TCCTCACTTAATGCCTCAGCG 60.135 52.381 0.00 0.00 44.31 5.18
1707 1712 0.905357 AAGCACCTAGACGCTGGATT 59.095 50.000 6.63 0.00 38.82 3.01
1734 1739 0.251165 GCCTAGCAACCAAACCCTCA 60.251 55.000 0.00 0.00 0.00 3.86
1767 1772 4.256110 TCAGAGCATGGTAGATGTTTGTG 58.744 43.478 0.00 0.00 0.00 3.33
1781 1786 0.465097 CTCCCGGCATTTCAGAGCAT 60.465 55.000 0.00 0.00 0.00 3.79
2137 2142 4.158579 TGTGACTTGAGTAGCATAGACAGG 59.841 45.833 0.00 0.00 0.00 4.00
2151 2156 6.545666 TCTTAAGCATTTCCTTTGTGACTTGA 59.454 34.615 0.00 0.00 0.00 3.02
2161 2166 5.819991 TGGTCTGATCTTAAGCATTTCCTT 58.180 37.500 0.00 0.00 0.00 3.36
2241 2246 1.686355 GTGGGTTGTTGACATCCACA 58.314 50.000 21.68 12.08 43.60 4.17
2247 2252 1.153127 GTCCCGTGGGTTGTTGACA 60.153 57.895 4.53 0.00 36.47 3.58
2676 2681 3.137533 GGCAGATATCAACTTCCTGCTC 58.862 50.000 5.32 0.40 46.65 4.26
2678 2683 3.137533 GAGGCAGATATCAACTTCCTGC 58.862 50.000 5.32 0.00 46.71 4.85
2757 2763 2.261729 AGAAAGGAGACCAGGGACTTC 58.738 52.381 0.00 0.00 34.60 3.01
2903 2910 4.811024 ACATAATCACCACGAATGCTACAG 59.189 41.667 0.00 0.00 0.00 2.74
2909 2916 5.066375 ACATCCAACATAATCACCACGAATG 59.934 40.000 0.00 0.00 0.00 2.67
3088 3095 2.136878 CCTAGGCACGCCCTGATCT 61.137 63.158 3.95 0.00 45.91 2.75
3114 3121 0.322456 CTCGACCCAAAGCCCAATCA 60.322 55.000 0.00 0.00 0.00 2.57
3135 3142 1.942657 CTTCGGGTACATGCATCCAAG 59.057 52.381 0.00 0.00 0.00 3.61
3178 3185 2.512896 AGAATTGCCCATCATCCTCAGT 59.487 45.455 0.00 0.00 0.00 3.41
3179 3186 2.885266 CAGAATTGCCCATCATCCTCAG 59.115 50.000 0.00 0.00 0.00 3.35
3234 3241 0.038890 TGGATTTTGGGACGATGGCA 59.961 50.000 0.00 0.00 0.00 4.92
3235 3242 1.181786 TTGGATTTTGGGACGATGGC 58.818 50.000 0.00 0.00 0.00 4.40
3249 3256 0.676466 TTGTCGCCGAGCATTTGGAT 60.676 50.000 0.00 0.00 0.00 3.41
3250 3257 0.676466 ATTGTCGCCGAGCATTTGGA 60.676 50.000 0.00 0.00 0.00 3.53
3251 3258 1.013596 TATTGTCGCCGAGCATTTGG 58.986 50.000 0.00 0.00 0.00 3.28
3252 3259 3.338818 AATATTGTCGCCGAGCATTTG 57.661 42.857 0.00 0.00 0.00 2.32
3253 3260 4.370364 AAAATATTGTCGCCGAGCATTT 57.630 36.364 0.00 0.00 0.00 2.32
3254 3261 4.370364 AAAAATATTGTCGCCGAGCATT 57.630 36.364 0.00 0.00 0.00 3.56
3275 3282 2.315176 CCCGGAATATCATTGCCCAAA 58.685 47.619 0.73 0.00 0.00 3.28
3276 3283 1.480312 CCCCGGAATATCATTGCCCAA 60.480 52.381 0.73 0.00 0.00 4.12
3317 3324 2.541120 GCTTGCCTATCCTGCAGCG 61.541 63.158 8.66 1.56 40.35 5.18
3320 3327 0.744414 GTTCGCTTGCCTATCCTGCA 60.744 55.000 0.00 0.00 36.84 4.41
3321 3328 0.744414 TGTTCGCTTGCCTATCCTGC 60.744 55.000 0.00 0.00 0.00 4.85
3411 3419 4.115516 TGATCTGAAAATGTCGCTAGCTC 58.884 43.478 13.93 6.50 0.00 4.09
3430 3438 1.746220 AGTTCGCTTCTCTACGCTGAT 59.254 47.619 0.00 0.00 0.00 2.90
3433 3441 1.131504 CTCAGTTCGCTTCTCTACGCT 59.868 52.381 0.00 0.00 0.00 5.07
3439 3447 1.347817 CCACGCTCAGTTCGCTTCTC 61.348 60.000 0.00 0.00 0.00 2.87
3440 3448 1.373497 CCACGCTCAGTTCGCTTCT 60.373 57.895 0.00 0.00 0.00 2.85
3442 3450 1.222115 GAACCACGCTCAGTTCGCTT 61.222 55.000 0.00 0.00 33.65 4.68
3455 3463 1.808343 GTTGGTACCATTCCGAACCAC 59.192 52.381 17.17 3.41 41.58 4.16
3456 3464 1.271488 GGTTGGTACCATTCCGAACCA 60.271 52.381 21.40 0.04 44.36 3.67
3457 3465 1.456296 GGTTGGTACCATTCCGAACC 58.544 55.000 17.17 15.31 44.36 3.62
3459 3467 1.065647 TGGGTTGGTACCATTCCGAA 58.934 50.000 17.17 10.33 46.96 4.30
3461 3469 0.326927 AGTGGGTTGGTACCATTCCG 59.673 55.000 17.17 0.00 46.96 4.30
3462 3470 2.092592 CCTAGTGGGTTGGTACCATTCC 60.093 54.545 17.17 19.93 46.96 3.01
3463 3471 3.277142 CCTAGTGGGTTGGTACCATTC 57.723 52.381 17.17 11.97 46.96 2.67
3476 3484 6.295719 AGTGTATGACTTAAACCCTAGTGG 57.704 41.667 0.00 0.00 41.37 4.00
3477 3485 6.594159 CCAAGTGTATGACTTAAACCCTAGTG 59.406 42.308 0.00 0.00 43.52 2.74
3478 3486 6.708285 CCAAGTGTATGACTTAAACCCTAGT 58.292 40.000 0.00 0.00 43.52 2.57
3479 3487 5.585047 GCCAAGTGTATGACTTAAACCCTAG 59.415 44.000 0.00 0.00 43.52 3.02
3480 3488 5.013287 TGCCAAGTGTATGACTTAAACCCTA 59.987 40.000 0.00 0.00 43.52 3.53
3481 3489 4.202524 TGCCAAGTGTATGACTTAAACCCT 60.203 41.667 0.00 0.00 43.52 4.34
3482 3490 4.076394 TGCCAAGTGTATGACTTAAACCC 58.924 43.478 0.00 0.00 43.52 4.11
3483 3491 4.760204 AGTGCCAAGTGTATGACTTAAACC 59.240 41.667 0.00 0.00 43.52 3.27
3484 3492 5.334879 CCAGTGCCAAGTGTATGACTTAAAC 60.335 44.000 0.00 0.00 43.52 2.01
3485 3493 4.759693 CCAGTGCCAAGTGTATGACTTAAA 59.240 41.667 0.00 0.00 43.52 1.52
3486 3494 4.202419 ACCAGTGCCAAGTGTATGACTTAA 60.202 41.667 0.00 0.00 43.52 1.85
3487 3495 3.326588 ACCAGTGCCAAGTGTATGACTTA 59.673 43.478 0.00 0.00 43.52 2.24
3488 3496 2.106511 ACCAGTGCCAAGTGTATGACTT 59.893 45.455 0.00 0.00 46.52 3.01
3489 3497 1.699634 ACCAGTGCCAAGTGTATGACT 59.300 47.619 0.00 0.00 35.94 3.41
3490 3498 1.806542 CACCAGTGCCAAGTGTATGAC 59.193 52.381 0.00 0.00 0.00 3.06
3491 3499 1.419762 ACACCAGTGCCAAGTGTATGA 59.580 47.619 1.55 0.00 42.71 2.15
3492 3500 1.896220 ACACCAGTGCCAAGTGTATG 58.104 50.000 1.55 0.00 42.71 2.39
3493 3501 2.504367 GAACACCAGTGCCAAGTGTAT 58.496 47.619 3.71 0.00 43.69 2.29
3494 3502 1.808512 CGAACACCAGTGCCAAGTGTA 60.809 52.381 3.71 0.00 43.69 2.90
3495 3503 1.095228 CGAACACCAGTGCCAAGTGT 61.095 55.000 0.00 0.00 46.33 3.55
3496 3504 1.648720 CGAACACCAGTGCCAAGTG 59.351 57.895 0.00 0.00 37.53 3.16
3497 3505 2.186826 GCGAACACCAGTGCCAAGT 61.187 57.895 0.00 0.00 0.00 3.16
3498 3506 1.723608 TTGCGAACACCAGTGCCAAG 61.724 55.000 0.00 0.00 0.00 3.61
3499 3507 1.106351 ATTGCGAACACCAGTGCCAA 61.106 50.000 0.00 0.00 0.00 4.52
3500 3508 1.106351 AATTGCGAACACCAGTGCCA 61.106 50.000 0.00 0.00 0.00 4.92
3501 3509 0.031994 AAATTGCGAACACCAGTGCC 59.968 50.000 0.00 0.00 0.00 5.01
3502 3510 1.786579 GAAAATTGCGAACACCAGTGC 59.213 47.619 0.00 0.00 0.00 4.40
3503 3511 3.044986 CAGAAAATTGCGAACACCAGTG 58.955 45.455 0.00 0.00 0.00 3.66
3504 3512 2.948979 TCAGAAAATTGCGAACACCAGT 59.051 40.909 0.00 0.00 0.00 4.00
3505 3513 3.624326 TCAGAAAATTGCGAACACCAG 57.376 42.857 0.00 0.00 0.00 4.00
3506 3514 4.582701 ATTCAGAAAATTGCGAACACCA 57.417 36.364 0.00 0.00 0.00 4.17
3507 3515 5.234116 ACAAATTCAGAAAATTGCGAACACC 59.766 36.000 10.50 0.00 29.87 4.16
3508 3516 6.272698 ACAAATTCAGAAAATTGCGAACAC 57.727 33.333 10.50 0.00 29.87 3.32
3509 3517 6.900568 AACAAATTCAGAAAATTGCGAACA 57.099 29.167 10.50 0.00 29.87 3.18
3510 3518 7.397970 TGAAACAAATTCAGAAAATTGCGAAC 58.602 30.769 10.50 3.69 43.08 3.95
3511 3519 7.531280 TGAAACAAATTCAGAAAATTGCGAA 57.469 28.000 10.50 0.00 43.08 4.70
3523 3531 3.882888 ACCGAGAGCTTGAAACAAATTCA 59.117 39.130 0.00 0.00 46.22 2.57
3524 3532 4.024048 TCACCGAGAGCTTGAAACAAATTC 60.024 41.667 0.00 0.00 38.60 2.17
3525 3533 3.882888 TCACCGAGAGCTTGAAACAAATT 59.117 39.130 0.00 0.00 0.00 1.82
3526 3534 3.476552 TCACCGAGAGCTTGAAACAAAT 58.523 40.909 0.00 0.00 0.00 2.32
3527 3535 2.912771 TCACCGAGAGCTTGAAACAAA 58.087 42.857 0.00 0.00 0.00 2.83
3528 3536 2.613026 TCACCGAGAGCTTGAAACAA 57.387 45.000 0.00 0.00 0.00 2.83
3529 3537 2.416747 CATCACCGAGAGCTTGAAACA 58.583 47.619 0.00 0.00 0.00 2.83
3530 3538 1.129437 GCATCACCGAGAGCTTGAAAC 59.871 52.381 0.00 0.00 0.00 2.78
3531 3539 1.002430 AGCATCACCGAGAGCTTGAAA 59.998 47.619 0.00 0.00 32.52 2.69
3532 3540 0.610174 AGCATCACCGAGAGCTTGAA 59.390 50.000 0.00 0.00 32.52 2.69
3533 3541 0.174389 GAGCATCACCGAGAGCTTGA 59.826 55.000 0.00 0.00 37.48 3.02
3534 3542 0.108472 TGAGCATCACCGAGAGCTTG 60.108 55.000 0.00 0.00 42.56 4.01
3535 3543 2.280835 TGAGCATCACCGAGAGCTT 58.719 52.632 0.00 0.00 42.56 3.74
3536 3544 4.024717 TGAGCATCACCGAGAGCT 57.975 55.556 0.00 0.00 42.56 4.09
3546 3554 1.487976 TCCTCCCACTGAATGAGCATC 59.512 52.381 0.00 0.00 0.00 3.91
3547 3555 1.588239 TCCTCCCACTGAATGAGCAT 58.412 50.000 0.00 0.00 0.00 3.79
3548 3556 1.588239 ATCCTCCCACTGAATGAGCA 58.412 50.000 0.00 0.00 0.00 4.26
3549 3557 2.435805 TGTATCCTCCCACTGAATGAGC 59.564 50.000 0.00 0.00 0.00 4.26
3550 3558 4.970860 ATGTATCCTCCCACTGAATGAG 57.029 45.455 0.00 0.00 0.00 2.90
3551 3559 5.715439 AAATGTATCCTCCCACTGAATGA 57.285 39.130 0.00 0.00 0.00 2.57
3552 3560 5.008019 CGAAAATGTATCCTCCCACTGAATG 59.992 44.000 0.00 0.00 0.00 2.67
3553 3561 5.126067 CGAAAATGTATCCTCCCACTGAAT 58.874 41.667 0.00 0.00 0.00 2.57
3554 3562 4.019681 ACGAAAATGTATCCTCCCACTGAA 60.020 41.667 0.00 0.00 0.00 3.02
3555 3563 3.517901 ACGAAAATGTATCCTCCCACTGA 59.482 43.478 0.00 0.00 0.00 3.41
3556 3564 3.871594 GACGAAAATGTATCCTCCCACTG 59.128 47.826 0.00 0.00 0.00 3.66
3557 3565 3.430374 CGACGAAAATGTATCCTCCCACT 60.430 47.826 0.00 0.00 0.00 4.00
3558 3566 2.864343 CGACGAAAATGTATCCTCCCAC 59.136 50.000 0.00 0.00 0.00 4.61
3559 3567 2.761767 TCGACGAAAATGTATCCTCCCA 59.238 45.455 0.00 0.00 0.00 4.37
3560 3568 3.121544 GTCGACGAAAATGTATCCTCCC 58.878 50.000 0.00 0.00 0.00 4.30
3561 3569 4.043037 AGTCGACGAAAATGTATCCTCC 57.957 45.455 10.46 0.00 0.00 4.30
3562 3570 6.493116 TCTTAGTCGACGAAAATGTATCCTC 58.507 40.000 12.27 0.00 0.00 3.71
3563 3571 6.446781 TCTTAGTCGACGAAAATGTATCCT 57.553 37.500 12.27 0.00 0.00 3.24
3564 3572 6.971184 TCTTCTTAGTCGACGAAAATGTATCC 59.029 38.462 12.27 0.00 0.00 2.59
3565 3573 7.819781 GTCTTCTTAGTCGACGAAAATGTATC 58.180 38.462 12.27 0.00 0.00 2.24
3566 3574 7.737525 GTCTTCTTAGTCGACGAAAATGTAT 57.262 36.000 12.27 0.00 0.00 2.29
3576 3584 3.967203 ATAGGCGTCTTCTTAGTCGAC 57.033 47.619 7.70 7.70 40.61 4.20
3577 3585 4.510711 CACTATAGGCGTCTTCTTAGTCGA 59.489 45.833 0.00 0.00 35.38 4.20
3578 3586 4.319622 CCACTATAGGCGTCTTCTTAGTCG 60.320 50.000 0.00 0.00 36.27 4.18
3579 3587 4.557097 GCCACTATAGGCGTCTTCTTAGTC 60.557 50.000 0.00 0.00 46.12 2.59
3580 3588 3.318557 GCCACTATAGGCGTCTTCTTAGT 59.681 47.826 0.00 0.00 46.12 2.24
3581 3589 3.903360 GCCACTATAGGCGTCTTCTTAG 58.097 50.000 0.00 0.00 46.12 2.18
3583 3591 2.892784 GCCACTATAGGCGTCTTCTT 57.107 50.000 0.00 0.00 46.12 2.52
3592 3600 4.460731 TGAGATCGATGAAGCCACTATAGG 59.539 45.833 0.54 0.00 0.00 2.57
3593 3601 5.635417 TGAGATCGATGAAGCCACTATAG 57.365 43.478 0.54 0.00 0.00 1.31
3594 3602 6.265422 TCTTTGAGATCGATGAAGCCACTATA 59.735 38.462 0.54 0.00 0.00 1.31
3595 3603 4.944619 TTGAGATCGATGAAGCCACTAT 57.055 40.909 0.54 0.00 0.00 2.12
3596 3604 4.402474 TCTTTGAGATCGATGAAGCCACTA 59.598 41.667 0.54 0.00 0.00 2.74
3597 3605 3.196469 TCTTTGAGATCGATGAAGCCACT 59.804 43.478 0.54 0.00 0.00 4.00
3598 3606 3.525537 TCTTTGAGATCGATGAAGCCAC 58.474 45.455 0.54 0.00 0.00 5.01
3599 3607 3.893326 TCTTTGAGATCGATGAAGCCA 57.107 42.857 0.54 0.00 0.00 4.75
3600 3608 4.375272 TCATCTTTGAGATCGATGAAGCC 58.625 43.478 0.54 0.00 40.20 4.35
3601 3609 7.331440 ACATATCATCTTTGAGATCGATGAAGC 59.669 37.037 0.54 0.00 44.51 3.86
3602 3610 8.760103 ACATATCATCTTTGAGATCGATGAAG 57.240 34.615 0.54 1.95 44.51 3.02
3603 3611 7.540055 CGACATATCATCTTTGAGATCGATGAA 59.460 37.037 0.54 5.25 44.51 2.57
3604 3612 7.025963 CGACATATCATCTTTGAGATCGATGA 58.974 38.462 0.54 11.20 45.16 2.92
3605 3613 6.253083 CCGACATATCATCTTTGAGATCGATG 59.747 42.308 0.54 2.17 31.48 3.84
3606 3614 6.328714 CCGACATATCATCTTTGAGATCGAT 58.671 40.000 0.00 0.00 31.48 3.59
3607 3615 5.703876 CCGACATATCATCTTTGAGATCGA 58.296 41.667 0.00 0.00 31.48 3.59
3608 3616 4.325741 GCCGACATATCATCTTTGAGATCG 59.674 45.833 0.00 0.00 31.48 3.69
3609 3617 4.629200 GGCCGACATATCATCTTTGAGATC 59.371 45.833 0.00 0.00 31.48 2.75
3610 3618 4.564406 GGGCCGACATATCATCTTTGAGAT 60.564 45.833 0.00 0.00 34.13 2.75
3611 3619 3.244215 GGGCCGACATATCATCTTTGAGA 60.244 47.826 0.00 0.00 34.73 3.27
3612 3620 3.070018 GGGCCGACATATCATCTTTGAG 58.930 50.000 0.00 0.00 34.73 3.02
3613 3621 2.437651 TGGGCCGACATATCATCTTTGA 59.562 45.455 0.00 0.00 36.00 2.69
3614 3622 2.810274 CTGGGCCGACATATCATCTTTG 59.190 50.000 0.00 0.00 0.00 2.77
3615 3623 2.439507 ACTGGGCCGACATATCATCTTT 59.560 45.455 0.00 0.00 0.00 2.52
3616 3624 2.050144 ACTGGGCCGACATATCATCTT 58.950 47.619 0.00 0.00 0.00 2.40
3617 3625 1.722034 ACTGGGCCGACATATCATCT 58.278 50.000 0.00 0.00 0.00 2.90
3618 3626 2.550830 AACTGGGCCGACATATCATC 57.449 50.000 0.00 0.00 0.00 2.92
3619 3627 3.297134 AAAACTGGGCCGACATATCAT 57.703 42.857 0.00 0.00 0.00 2.45
3620 3628 2.799126 AAAACTGGGCCGACATATCA 57.201 45.000 0.00 0.00 0.00 2.15
3621 3629 2.031683 CGAAAAACTGGGCCGACATATC 59.968 50.000 0.00 0.00 0.00 1.63
3622 3630 2.014128 CGAAAAACTGGGCCGACATAT 58.986 47.619 0.00 0.00 0.00 1.78
3623 3631 1.002201 TCGAAAAACTGGGCCGACATA 59.998 47.619 0.00 0.00 0.00 2.29
3624 3632 0.250553 TCGAAAAACTGGGCCGACAT 60.251 50.000 0.00 0.00 0.00 3.06
3625 3633 0.464013 TTCGAAAAACTGGGCCGACA 60.464 50.000 0.00 0.00 0.00 4.35
3626 3634 0.879090 ATTCGAAAAACTGGGCCGAC 59.121 50.000 0.00 0.00 0.00 4.79
3627 3635 0.878416 CATTCGAAAAACTGGGCCGA 59.122 50.000 0.00 0.00 0.00 5.54
3628 3636 0.596082 ACATTCGAAAAACTGGGCCG 59.404 50.000 0.00 0.00 0.00 6.13
3629 3637 1.934849 GCACATTCGAAAAACTGGGCC 60.935 52.381 11.78 0.00 31.83 5.80
3630 3638 1.000274 AGCACATTCGAAAAACTGGGC 60.000 47.619 14.42 14.42 38.31 5.36
3631 3639 2.293122 TGAGCACATTCGAAAAACTGGG 59.707 45.455 0.00 0.00 0.00 4.45
3632 3640 3.624326 TGAGCACATTCGAAAAACTGG 57.376 42.857 0.00 0.00 0.00 4.00
3633 3641 5.740569 CCATATGAGCACATTCGAAAAACTG 59.259 40.000 0.00 0.00 37.87 3.16
3634 3642 5.647658 TCCATATGAGCACATTCGAAAAACT 59.352 36.000 0.00 0.00 37.87 2.66
3635 3643 5.879237 TCCATATGAGCACATTCGAAAAAC 58.121 37.500 0.00 0.00 37.87 2.43
3636 3644 6.698008 ATCCATATGAGCACATTCGAAAAA 57.302 33.333 0.00 0.00 37.87 1.94
3637 3645 7.216494 TCTATCCATATGAGCACATTCGAAAA 58.784 34.615 0.00 0.00 37.87 2.29
3638 3646 6.758254 TCTATCCATATGAGCACATTCGAAA 58.242 36.000 0.00 0.00 37.87 3.46
3639 3647 6.345096 TCTATCCATATGAGCACATTCGAA 57.655 37.500 3.65 0.00 37.87 3.71
3640 3648 5.982890 TCTATCCATATGAGCACATTCGA 57.017 39.130 3.65 0.00 37.87 3.71
3641 3649 7.425577 TTTTCTATCCATATGAGCACATTCG 57.574 36.000 3.65 0.00 37.87 3.34
3642 3650 8.790718 ACATTTTCTATCCATATGAGCACATTC 58.209 33.333 3.65 0.00 37.87 2.67
3643 3651 8.573885 CACATTTTCTATCCATATGAGCACATT 58.426 33.333 3.65 0.00 37.87 2.71
3644 3652 7.722728 ACACATTTTCTATCCATATGAGCACAT 59.277 33.333 3.65 1.31 40.16 3.21
3645 3653 7.012610 CACACATTTTCTATCCATATGAGCACA 59.987 37.037 3.65 0.00 0.00 4.57
3646 3654 7.012704 ACACACATTTTCTATCCATATGAGCAC 59.987 37.037 3.65 0.00 0.00 4.40
3647 3655 7.012610 CACACACATTTTCTATCCATATGAGCA 59.987 37.037 3.65 0.00 0.00 4.26
3648 3656 7.358066 CACACACATTTTCTATCCATATGAGC 58.642 38.462 3.65 0.00 0.00 4.26
3649 3657 7.358066 GCACACACATTTTCTATCCATATGAG 58.642 38.462 3.65 0.00 0.00 2.90
3650 3658 6.018016 CGCACACACATTTTCTATCCATATGA 60.018 38.462 3.65 0.00 0.00 2.15
3651 3659 6.138088 CGCACACACATTTTCTATCCATATG 58.862 40.000 0.00 0.00 0.00 1.78
3652 3660 5.277974 GCGCACACACATTTTCTATCCATAT 60.278 40.000 0.30 0.00 0.00 1.78
3653 3661 4.035091 GCGCACACACATTTTCTATCCATA 59.965 41.667 0.30 0.00 0.00 2.74
3654 3662 3.181497 GCGCACACACATTTTCTATCCAT 60.181 43.478 0.30 0.00 0.00 3.41
3655 3663 2.161410 GCGCACACACATTTTCTATCCA 59.839 45.455 0.30 0.00 0.00 3.41
3656 3664 2.785679 GCGCACACACATTTTCTATCC 58.214 47.619 0.30 0.00 0.00 2.59
3657 3665 2.159707 ACGCGCACACACATTTTCTATC 60.160 45.455 5.73 0.00 0.00 2.08
3658 3666 1.804151 ACGCGCACACACATTTTCTAT 59.196 42.857 5.73 0.00 0.00 1.98
3659 3667 1.222300 ACGCGCACACACATTTTCTA 58.778 45.000 5.73 0.00 0.00 2.10
3660 3668 0.380378 AACGCGCACACACATTTTCT 59.620 45.000 5.73 0.00 0.00 2.52
3661 3669 0.770008 GAACGCGCACACACATTTTC 59.230 50.000 5.73 0.00 0.00 2.29
3662 3670 0.099613 TGAACGCGCACACACATTTT 59.900 45.000 5.73 0.00 0.00 1.82
3663 3671 0.099613 TTGAACGCGCACACACATTT 59.900 45.000 5.73 0.00 0.00 2.32
3664 3672 0.316937 CTTGAACGCGCACACACATT 60.317 50.000 5.73 0.00 0.00 2.71
3665 3673 1.279539 CTTGAACGCGCACACACAT 59.720 52.632 5.73 0.00 0.00 3.21
3666 3674 0.806492 TACTTGAACGCGCACACACA 60.806 50.000 5.73 0.00 0.00 3.72
3667 3675 0.111266 CTACTTGAACGCGCACACAC 60.111 55.000 5.73 0.00 0.00 3.82
3668 3676 0.528901 ACTACTTGAACGCGCACACA 60.529 50.000 5.73 0.00 0.00 3.72
3669 3677 0.111266 CACTACTTGAACGCGCACAC 60.111 55.000 5.73 0.00 0.00 3.82
3670 3678 0.249114 TCACTACTTGAACGCGCACA 60.249 50.000 5.73 3.35 0.00 4.57
3671 3679 0.435008 CTCACTACTTGAACGCGCAC 59.565 55.000 5.73 0.00 32.21 5.34
3672 3680 0.031585 ACTCACTACTTGAACGCGCA 59.968 50.000 5.73 0.00 32.21 6.09
3673 3681 0.435008 CACTCACTACTTGAACGCGC 59.565 55.000 5.73 0.00 32.21 6.86
3674 3682 1.767289 ACACTCACTACTTGAACGCG 58.233 50.000 3.53 3.53 32.21 6.01
3675 3683 4.090066 CACATACACTCACTACTTGAACGC 59.910 45.833 0.00 0.00 32.21 4.84
3676 3684 4.090066 GCACATACACTCACTACTTGAACG 59.910 45.833 0.00 0.00 32.21 3.95
3677 3685 4.090066 CGCACATACACTCACTACTTGAAC 59.910 45.833 0.00 0.00 32.21 3.18
3678 3686 4.234574 CGCACATACACTCACTACTTGAA 58.765 43.478 0.00 0.00 32.21 2.69
3679 3687 3.254903 ACGCACATACACTCACTACTTGA 59.745 43.478 0.00 0.00 0.00 3.02
3680 3688 3.575630 ACGCACATACACTCACTACTTG 58.424 45.455 0.00 0.00 0.00 3.16
3681 3689 3.936372 ACGCACATACACTCACTACTT 57.064 42.857 0.00 0.00 0.00 2.24
3682 3690 6.879276 ATATACGCACATACACTCACTACT 57.121 37.500 0.00 0.00 0.00 2.57
3683 3691 6.735510 CGTATATACGCACATACACTCACTAC 59.264 42.308 21.35 0.00 43.14 2.73
3684 3692 6.824557 CGTATATACGCACATACACTCACTA 58.175 40.000 21.35 0.00 43.14 2.74
3685 3693 5.686834 CGTATATACGCACATACACTCACT 58.313 41.667 21.35 0.00 43.14 3.41
3686 3694 5.969970 CGTATATACGCACATACACTCAC 57.030 43.478 21.35 0.00 43.14 3.51


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

AutoCloner maintained by Alex Coulton.