Multiple sequence alignment - TraesCS5A01G106500

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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 TraesCS5A01G106500 chr5A 100.000 4076 0 0 1 4076 176445923 176449998 0.000000e+00 7528.0
1 TraesCS5A01G106500 chr5D 96.156 3590 93 16 1 3575 170317653 170314094 0.000000e+00 5823.0
2 TraesCS5A01G106500 chr5D 89.937 159 13 1 3914 4072 170314037 170313882 6.910000e-48 202.0
3 TraesCS5A01G106500 chr5D 100.000 32 0 0 4041 4072 228261077 228261108 4.400000e-05 60.2
4 TraesCS5A01G106500 chr5B 95.359 3598 110 23 1 3575 162494410 162490847 0.000000e+00 5666.0
5 TraesCS5A01G106500 chr5B 85.106 235 31 4 3576 3809 477556964 477556733 1.890000e-58 237.0
6 TraesCS5A01G106500 chr5B 95.082 61 3 0 3809 3869 162490846 162490786 3.350000e-16 97.1
7 TraesCS5A01G106500 chr6A 84.848 231 28 7 3576 3804 520435029 520435254 4.100000e-55 226.0
8 TraesCS5A01G106500 chr7B 84.052 232 35 2 3576 3807 170961993 170961764 5.300000e-54 222.0
9 TraesCS5A01G106500 chr7B 83.691 233 30 4 3576 3808 516266760 516266984 3.190000e-51 213.0
10 TraesCS5A01G106500 chr6B 84.416 231 30 6 3576 3804 81024229 81024455 5.300000e-54 222.0
11 TraesCS5A01G106500 chr4B 83.265 245 34 6 3576 3818 139756008 139756247 6.860000e-53 219.0
12 TraesCS5A01G106500 chr7A 83.913 230 34 3 3576 3804 424628708 424628935 2.470000e-52 217.0
13 TraesCS5A01G106500 chr1B 83.621 232 34 4 3578 3808 654441267 654441039 8.870000e-52 215.0
14 TraesCS5A01G106500 chr4A 82.969 229 37 2 3576 3804 730792290 730792516 5.340000e-49 206.0
15 TraesCS5A01G106500 chr3A 95.000 40 2 0 4033 4072 727269941 727269980 3.400000e-06 63.9
16 TraesCS5A01G106500 chr7D 100.000 31 0 0 4041 4071 169413727 169413697 1.580000e-04 58.4


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 TraesCS5A01G106500 chr5A 176445923 176449998 4075 False 7528.00 7528 100.0000 1 4076 1 chr5A.!!$F1 4075
1 TraesCS5A01G106500 chr5D 170313882 170317653 3771 True 3012.50 5823 93.0465 1 4072 2 chr5D.!!$R1 4071
2 TraesCS5A01G106500 chr5B 162490786 162494410 3624 True 2881.55 5666 95.2205 1 3869 2 chr5B.!!$R2 3868

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
640 642 0.174845 GCCGTGTATACTGCCTGTGA 59.825 55.000 4.17 0.00 31.67 3.58 F
1355 1360 1.623811 GACCTGCCTCTAGTGGTTTCA 59.376 52.381 12.31 1.69 32.30 2.69 F
2152 2161 2.846193 TGCCTGGTTCTGTTGAGTTAC 58.154 47.619 0.00 0.00 0.00 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1820 0.459899 CTCACTACCGTATGCTGGCA 59.540 55.0 0.0 0.0 0.00 4.92 R
2475 2484 0.545646 GCTCAGCCCTCTTCCTCAAT 59.454 55.0 0.0 0.0 0.00 2.57 R
3895 3922 0.105964 TGGGTTTAGCAAGGTGCCAA 60.106 50.0 0.0 0.0 46.52 4.52 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.198696 TTTCCCCTCTTTCCCCTCCT 59.801 55.000 0.00 0.00 0.00 3.69
49 50 6.093357 CCTCGATCTGATCTCGATTCATCTAA 59.907 42.308 15.16 0.00 43.53 2.10
117 118 1.953017 CGAGGCCTCTCTATCGGTG 59.047 63.158 29.73 7.64 37.86 4.94
153 154 4.488731 CGTATCGTTGATTCTGTGTGTTCG 60.489 45.833 0.00 0.00 0.00 3.95
363 364 1.068741 CCCCTCATCGCCAGTAAGTAC 59.931 57.143 0.00 0.00 0.00 2.73
374 376 2.558974 CAGTAAGTACCCCTCCCCTTT 58.441 52.381 0.00 0.00 0.00 3.11
424 426 8.293867 CGAGAAAGATAGATCTAAAATCGACCT 58.706 37.037 6.52 1.53 35.76 3.85
437 439 0.250234 TCGACCTGGCTTGGATTCAG 59.750 55.000 0.00 0.00 0.00 3.02
560 562 5.982890 AACCTGATTTGAATTGACCGATT 57.017 34.783 0.00 0.00 0.00 3.34
561 563 5.314923 ACCTGATTTGAATTGACCGATTG 57.685 39.130 0.00 0.00 0.00 2.67
562 564 5.009631 ACCTGATTTGAATTGACCGATTGA 58.990 37.500 0.00 0.00 0.00 2.57
563 565 5.653769 ACCTGATTTGAATTGACCGATTGAT 59.346 36.000 0.00 0.00 0.00 2.57
564 566 6.183360 ACCTGATTTGAATTGACCGATTGATC 60.183 38.462 0.00 0.00 0.00 2.92
565 567 6.135290 TGATTTGAATTGACCGATTGATCC 57.865 37.500 0.00 0.00 0.00 3.36
566 568 5.651576 TGATTTGAATTGACCGATTGATCCA 59.348 36.000 0.00 0.00 0.00 3.41
569 571 4.525996 TGAATTGACCGATTGATCCATGT 58.474 39.130 0.00 0.00 0.00 3.21
583 585 0.664761 CCATGTTCCATGGATGTCGC 59.335 55.000 17.06 4.68 41.64 5.19
640 642 0.174845 GCCGTGTATACTGCCTGTGA 59.825 55.000 4.17 0.00 31.67 3.58
711 713 7.363617 CCTTCTATAGTTTAGTGGGAGAACGTT 60.364 40.741 0.00 0.00 0.00 3.99
819 821 4.164843 AGGTTTGTACATCAGTGTGGTT 57.835 40.909 0.00 0.00 39.39 3.67
822 824 1.890876 TGTACATCAGTGTGGTTGGC 58.109 50.000 0.00 0.00 39.39 4.52
856 858 6.766944 TCAACTTGGATGTTCATTTGCAATTT 59.233 30.769 0.00 0.00 0.00 1.82
1131 1136 8.766994 AGAAATACCATATTGCAACAGGTAAT 57.233 30.769 22.68 15.59 38.25 1.89
1180 1185 2.092538 AGCATGCCTAGATTCTTGTGCT 60.093 45.455 15.66 6.08 36.91 4.40
1222 1227 9.868277 AAAGTTTGTCAAATGAATGTAAACTGA 57.132 25.926 0.40 0.00 38.04 3.41
1236 1241 7.621428 ATGTAAACTGACCAATCTGATGAAG 57.379 36.000 0.00 0.00 0.00 3.02
1328 1333 6.586463 TGTTAAAGAAGTGACAGTCGATCATC 59.414 38.462 0.00 0.00 0.00 2.92
1355 1360 1.623811 GACCTGCCTCTAGTGGTTTCA 59.376 52.381 12.31 1.69 32.30 2.69
1412 1417 7.885399 AGGAAGAGCAAAGTAAGACATGTTAAT 59.115 33.333 0.00 0.00 0.00 1.40
1435 1440 4.394729 TCGCAACCTTTTATGGAAGTTCT 58.605 39.130 2.25 0.00 0.00 3.01
1442 1447 9.720769 CAACCTTTTATGGAAGTTCTTACTCTA 57.279 33.333 2.25 0.00 31.99 2.43
1514 1519 3.695830 TCCATACACTTGACACTTCCC 57.304 47.619 0.00 0.00 0.00 3.97
2152 2161 2.846193 TGCCTGGTTCTGTTGAGTTAC 58.154 47.619 0.00 0.00 0.00 2.50
2261 2270 6.169800 AGGAAGCAAGAGAAAGACTAATGAC 58.830 40.000 0.00 0.00 0.00 3.06
2475 2484 9.534565 GTGAGCTACTATTTCAATGTCTTCATA 57.465 33.333 0.00 0.00 33.49 2.15
2505 2514 1.211457 AGGGCTGAGCAGAATAGGTTG 59.789 52.381 6.82 0.00 0.00 3.77
2652 2661 1.272092 TGCAATCAAGTTCCCCTCCAG 60.272 52.381 0.00 0.00 0.00 3.86
2704 2716 3.251004 GGATGAGTTTGACTGTTGTGGTC 59.749 47.826 0.00 0.00 0.00 4.02
2778 2790 2.689983 CAATAACCAGGAGGCAACCATC 59.310 50.000 0.00 0.00 39.06 3.51
2782 2794 1.147817 ACCAGGAGGCAACCATCTTTT 59.852 47.619 0.00 0.00 39.06 2.27
2805 2817 1.889170 ACAGATGCTCAAGACGACTCA 59.111 47.619 0.00 0.00 0.00 3.41
2840 2852 1.094785 GCTCCGCATGTTTGTACCAT 58.905 50.000 0.00 0.00 0.00 3.55
2967 2979 4.406326 TGGGATATTGGTTTCAGTAGCGTA 59.594 41.667 0.00 0.00 0.00 4.42
3038 3050 5.188751 TGTTTGGAAAGGGTTCTTGTGAAAT 59.811 36.000 0.00 0.00 33.52 2.17
3137 3149 6.127479 ACCTGCTTTTGAAATTTGTACAGTGA 60.127 34.615 0.00 0.00 0.00 3.41
3274 3286 9.133627 CTGTCTATTTGTAGTTATCCATCATCG 57.866 37.037 0.00 0.00 0.00 3.84
3299 3311 3.551863 CGATGATCTCCTGTAGCCTGTTC 60.552 52.174 0.00 0.00 0.00 3.18
3300 3312 2.111384 TGATCTCCTGTAGCCTGTTCC 58.889 52.381 0.00 0.00 0.00 3.62
3301 3313 1.414550 GATCTCCTGTAGCCTGTTCCC 59.585 57.143 0.00 0.00 0.00 3.97
3302 3314 0.413832 TCTCCTGTAGCCTGTTCCCT 59.586 55.000 0.00 0.00 0.00 4.20
3303 3315 0.539051 CTCCTGTAGCCTGTTCCCTG 59.461 60.000 0.00 0.00 0.00 4.45
3304 3316 0.178903 TCCTGTAGCCTGTTCCCTGT 60.179 55.000 0.00 0.00 0.00 4.00
3305 3317 0.693049 CCTGTAGCCTGTTCCCTGTT 59.307 55.000 0.00 0.00 0.00 3.16
3315 3327 1.347707 TGTTCCCTGTTGTAGCCTCTG 59.652 52.381 0.00 0.00 0.00 3.35
3426 3442 8.627208 ATGACAAATCATATCGCTTTCCTTAT 57.373 30.769 0.00 0.00 44.11 1.73
3427 3443 8.450578 TGACAAATCATATCGCTTTCCTTATT 57.549 30.769 0.00 0.00 0.00 1.40
3486 3507 3.055094 AGCAGGGTTGTGTTACTATGAGG 60.055 47.826 0.00 0.00 0.00 3.86
3494 3515 4.552355 TGTGTTACTATGAGGTGTCAACG 58.448 43.478 0.00 0.00 35.88 4.10
3515 3536 2.338500 GATGGTCAACCGTGAAGTCTC 58.662 52.381 0.00 0.00 39.43 3.36
3555 3582 4.387559 ACAAGTTTTCGTGGCAAGTTTTTC 59.612 37.500 0.00 0.00 33.76 2.29
3575 3602 2.289547 TCTTTTGCTACGCCTGACAAAC 59.710 45.455 0.00 0.00 32.12 2.93
3576 3603 0.584396 TTTGCTACGCCTGACAAACG 59.416 50.000 0.00 0.00 0.00 3.60
3577 3604 0.531090 TTGCTACGCCTGACAAACGT 60.531 50.000 7.47 7.47 43.45 3.99
3578 3605 0.942410 TGCTACGCCTGACAAACGTC 60.942 55.000 5.75 0.00 40.99 4.34
3579 3606 1.623973 GCTACGCCTGACAAACGTCC 61.624 60.000 5.75 0.00 40.99 4.79
3580 3607 0.038526 CTACGCCTGACAAACGTCCT 60.039 55.000 5.75 0.00 40.99 3.85
3581 3608 1.200716 CTACGCCTGACAAACGTCCTA 59.799 52.381 5.75 0.00 40.99 2.94
3582 3609 0.038526 ACGCCTGACAAACGTCCTAG 60.039 55.000 0.00 0.00 34.35 3.02
3583 3610 0.038526 CGCCTGACAAACGTCCTAGT 60.039 55.000 0.00 0.00 32.01 2.57
3584 3611 1.604693 CGCCTGACAAACGTCCTAGTT 60.605 52.381 0.00 0.00 35.59 2.24
3585 3612 2.490991 GCCTGACAAACGTCCTAGTTT 58.509 47.619 0.00 0.00 44.27 2.66
3586 3613 3.656559 GCCTGACAAACGTCCTAGTTTA 58.343 45.455 0.00 0.00 41.84 2.01
3587 3614 4.251268 GCCTGACAAACGTCCTAGTTTAT 58.749 43.478 0.00 0.00 41.84 1.40
3588 3615 4.694037 GCCTGACAAACGTCCTAGTTTATT 59.306 41.667 0.00 0.00 41.84 1.40
3589 3616 5.390567 GCCTGACAAACGTCCTAGTTTATTG 60.391 44.000 0.00 0.00 41.84 1.90
3590 3617 5.121768 CCTGACAAACGTCCTAGTTTATTGG 59.878 44.000 0.00 0.00 41.84 3.16
3591 3618 5.613329 TGACAAACGTCCTAGTTTATTGGT 58.387 37.500 0.00 0.00 41.84 3.67
3592 3619 5.697633 TGACAAACGTCCTAGTTTATTGGTC 59.302 40.000 0.00 0.68 41.84 4.02
3593 3620 5.861727 ACAAACGTCCTAGTTTATTGGTCT 58.138 37.500 0.00 0.00 41.84 3.85
3594 3621 5.930569 ACAAACGTCCTAGTTTATTGGTCTC 59.069 40.000 0.00 0.00 41.84 3.36
3595 3622 4.732672 ACGTCCTAGTTTATTGGTCTCC 57.267 45.455 0.00 0.00 0.00 3.71
3596 3623 4.351127 ACGTCCTAGTTTATTGGTCTCCT 58.649 43.478 0.00 0.00 0.00 3.69
3597 3624 4.776308 ACGTCCTAGTTTATTGGTCTCCTT 59.224 41.667 0.00 0.00 0.00 3.36
3598 3625 5.247792 ACGTCCTAGTTTATTGGTCTCCTTT 59.752 40.000 0.00 0.00 0.00 3.11
3599 3626 5.581085 CGTCCTAGTTTATTGGTCTCCTTTG 59.419 44.000 0.00 0.00 0.00 2.77
3600 3627 6.573680 CGTCCTAGTTTATTGGTCTCCTTTGA 60.574 42.308 0.00 0.00 0.00 2.69
3601 3628 7.166167 GTCCTAGTTTATTGGTCTCCTTTGAA 58.834 38.462 0.00 0.00 0.00 2.69
3602 3629 7.664318 GTCCTAGTTTATTGGTCTCCTTTGAAA 59.336 37.037 0.00 0.00 0.00 2.69
3603 3630 8.390921 TCCTAGTTTATTGGTCTCCTTTGAAAT 58.609 33.333 0.00 0.00 0.00 2.17
3604 3631 9.025041 CCTAGTTTATTGGTCTCCTTTGAAATT 57.975 33.333 0.00 0.00 0.00 1.82
3607 3634 8.704668 AGTTTATTGGTCTCCTTTGAAATTTGT 58.295 29.630 0.00 0.00 0.00 2.83
3608 3635 8.764287 GTTTATTGGTCTCCTTTGAAATTTGTG 58.236 33.333 0.00 0.00 0.00 3.33
3609 3636 4.320608 TGGTCTCCTTTGAAATTTGTGC 57.679 40.909 0.00 0.00 0.00 4.57
3610 3637 3.960102 TGGTCTCCTTTGAAATTTGTGCT 59.040 39.130 0.00 0.00 0.00 4.40
3611 3638 5.136828 TGGTCTCCTTTGAAATTTGTGCTA 58.863 37.500 0.00 0.00 0.00 3.49
3612 3639 5.596361 TGGTCTCCTTTGAAATTTGTGCTAA 59.404 36.000 0.00 0.00 0.00 3.09
3613 3640 6.097554 TGGTCTCCTTTGAAATTTGTGCTAAA 59.902 34.615 0.00 0.00 0.00 1.85
3614 3641 7.154656 GGTCTCCTTTGAAATTTGTGCTAAAT 58.845 34.615 0.00 0.00 0.00 1.40
3615 3642 7.657354 GGTCTCCTTTGAAATTTGTGCTAAATT 59.343 33.333 0.00 6.47 0.00 1.82
3616 3643 9.045223 GTCTCCTTTGAAATTTGTGCTAAATTT 57.955 29.630 18.46 18.46 41.11 1.82
3617 3644 9.612066 TCTCCTTTGAAATTTGTGCTAAATTTT 57.388 25.926 19.04 8.24 39.23 1.82
3618 3645 9.654417 CTCCTTTGAAATTTGTGCTAAATTTTG 57.346 29.630 19.04 0.00 39.23 2.44
3619 3646 9.171877 TCCTTTGAAATTTGTGCTAAATTTTGT 57.828 25.926 19.04 5.00 39.23 2.83
3620 3647 9.786105 CCTTTGAAATTTGTGCTAAATTTTGTT 57.214 25.926 19.04 4.74 39.23 2.83
3624 3651 9.985318 TGAAATTTGTGCTAAATTTTGTTCAAG 57.015 25.926 19.04 0.00 39.23 3.02
3625 3652 9.986833 GAAATTTGTGCTAAATTTTGTTCAAGT 57.013 25.926 19.04 0.00 39.23 3.16
3673 3700 9.855361 TGCATGTTAACAAAATTTATTTCGTTG 57.145 25.926 13.23 2.18 0.00 4.10
3674 3701 9.312146 GCATGTTAACAAAATTTATTTCGTTGG 57.688 29.630 13.23 0.00 0.00 3.77
3717 3744 9.927668 AGTTTCCAAATGATATAGTTTTTGGTG 57.072 29.630 16.55 1.35 45.32 4.17
3718 3745 9.921637 GTTTCCAAATGATATAGTTTTTGGTGA 57.078 29.630 16.55 8.84 45.32 4.02
3719 3746 9.921637 TTTCCAAATGATATAGTTTTTGGTGAC 57.078 29.630 16.55 0.00 45.32 3.67
3720 3747 8.642935 TCCAAATGATATAGTTTTTGGTGACA 57.357 30.769 16.55 0.00 45.32 3.58
3721 3748 9.253832 TCCAAATGATATAGTTTTTGGTGACAT 57.746 29.630 16.55 0.00 45.32 3.06
3722 3749 9.304731 CCAAATGATATAGTTTTTGGTGACATG 57.695 33.333 11.96 0.00 41.94 3.21
3723 3750 8.810427 CAAATGATATAGTTTTTGGTGACATGC 58.190 33.333 0.00 0.00 42.32 4.06
3724 3751 7.643569 ATGATATAGTTTTTGGTGACATGCA 57.356 32.000 0.00 0.00 42.32 3.96
3725 3752 7.459795 TGATATAGTTTTTGGTGACATGCAA 57.540 32.000 0.00 0.00 42.32 4.08
3726 3753 7.537715 TGATATAGTTTTTGGTGACATGCAAG 58.462 34.615 0.00 0.00 42.32 4.01
3727 3754 7.392953 TGATATAGTTTTTGGTGACATGCAAGA 59.607 33.333 0.00 0.00 42.32 3.02
3728 3755 4.734398 AGTTTTTGGTGACATGCAAGAA 57.266 36.364 0.00 0.00 42.32 2.52
3729 3756 4.432712 AGTTTTTGGTGACATGCAAGAAC 58.567 39.130 0.00 8.30 42.32 3.01
3730 3757 4.081752 AGTTTTTGGTGACATGCAAGAACA 60.082 37.500 14.93 0.00 42.32 3.18
3731 3758 4.669206 TTTTGGTGACATGCAAGAACAT 57.331 36.364 0.00 0.00 42.32 2.71
3732 3759 4.669206 TTTGGTGACATGCAAGAACATT 57.331 36.364 0.00 0.00 42.32 2.71
3733 3760 4.669206 TTGGTGACATGCAAGAACATTT 57.331 36.364 0.00 0.00 42.32 2.32
3734 3761 4.669206 TGGTGACATGCAAGAACATTTT 57.331 36.364 0.00 0.00 33.40 1.82
3735 3762 5.021033 TGGTGACATGCAAGAACATTTTT 57.979 34.783 0.00 0.00 33.40 1.94
3736 3763 4.809958 TGGTGACATGCAAGAACATTTTTG 59.190 37.500 0.00 0.00 33.40 2.44
3737 3764 4.810491 GGTGACATGCAAGAACATTTTTGT 59.190 37.500 0.00 0.00 0.00 2.83
3738 3765 5.294060 GGTGACATGCAAGAACATTTTTGTT 59.706 36.000 0.00 0.00 34.29 2.83
3739 3766 6.478344 GGTGACATGCAAGAACATTTTTGTTA 59.522 34.615 0.00 0.00 31.35 2.41
3740 3767 7.306749 GGTGACATGCAAGAACATTTTTGTTAG 60.307 37.037 0.00 0.00 31.35 2.34
3741 3768 7.222611 GTGACATGCAAGAACATTTTTGTTAGT 59.777 33.333 0.00 0.00 31.35 2.24
3742 3769 7.763528 TGACATGCAAGAACATTTTTGTTAGTT 59.236 29.630 0.00 0.00 31.35 2.24
3743 3770 9.243637 GACATGCAAGAACATTTTTGTTAGTTA 57.756 29.630 0.00 0.00 31.35 2.24
3744 3771 9.593134 ACATGCAAGAACATTTTTGTTAGTTAA 57.407 25.926 0.00 0.00 31.35 2.01
3766 3793 9.209297 GTTAAATTTATGATCAAAATTTGGCGC 57.791 29.630 28.48 19.60 43.10 6.53
3767 3794 6.981762 AATTTATGATCAAAATTTGGCGCA 57.018 29.167 10.83 2.69 33.78 6.09
3768 3795 6.981762 ATTTATGATCAAAATTTGGCGCAA 57.018 29.167 10.83 0.00 0.00 4.85
3769 3796 6.791887 TTTATGATCAAAATTTGGCGCAAA 57.208 29.167 10.83 0.00 37.75 3.68
3770 3797 6.791887 TTATGATCAAAATTTGGCGCAAAA 57.208 29.167 13.33 13.33 36.90 2.44
3771 3798 5.883503 ATGATCAAAATTTGGCGCAAAAT 57.116 30.435 17.16 17.16 36.90 1.82
3772 3799 6.981762 ATGATCAAAATTTGGCGCAAAATA 57.018 29.167 22.68 8.00 36.90 1.40
3773 3800 6.163159 TGATCAAAATTTGGCGCAAAATAC 57.837 33.333 22.68 10.64 36.90 1.89
3774 3801 5.698089 TGATCAAAATTTGGCGCAAAATACA 59.302 32.000 22.68 12.72 36.90 2.29
3775 3802 5.991328 TCAAAATTTGGCGCAAAATACAA 57.009 30.435 22.68 6.80 36.90 2.41
3776 3803 6.551385 TCAAAATTTGGCGCAAAATACAAT 57.449 29.167 22.68 4.75 36.90 2.71
3777 3804 7.658179 TCAAAATTTGGCGCAAAATACAATA 57.342 28.000 22.68 5.76 36.90 1.90
3778 3805 7.737395 TCAAAATTTGGCGCAAAATACAATAG 58.263 30.769 22.68 10.12 36.90 1.73
3779 3806 6.660887 AAATTTGGCGCAAAATACAATAGG 57.339 33.333 22.68 0.00 36.90 2.57
3780 3807 5.590530 ATTTGGCGCAAAATACAATAGGA 57.409 34.783 21.19 0.00 36.90 2.94
3781 3808 4.364415 TTGGCGCAAAATACAATAGGAC 57.636 40.909 10.83 0.00 0.00 3.85
3782 3809 2.685897 TGGCGCAAAATACAATAGGACC 59.314 45.455 10.83 0.00 0.00 4.46
3783 3810 2.034179 GGCGCAAAATACAATAGGACCC 59.966 50.000 10.83 0.00 0.00 4.46
3784 3811 2.685897 GCGCAAAATACAATAGGACCCA 59.314 45.455 0.30 0.00 0.00 4.51
3785 3812 3.129638 GCGCAAAATACAATAGGACCCAA 59.870 43.478 0.30 0.00 0.00 4.12
3786 3813 4.668289 CGCAAAATACAATAGGACCCAAC 58.332 43.478 0.00 0.00 0.00 3.77
3787 3814 4.156922 CGCAAAATACAATAGGACCCAACA 59.843 41.667 0.00 0.00 0.00 3.33
3788 3815 5.336055 CGCAAAATACAATAGGACCCAACAA 60.336 40.000 0.00 0.00 0.00 2.83
3789 3816 6.459923 GCAAAATACAATAGGACCCAACAAA 58.540 36.000 0.00 0.00 0.00 2.83
3790 3817 6.367695 GCAAAATACAATAGGACCCAACAAAC 59.632 38.462 0.00 0.00 0.00 2.93
3791 3818 6.599356 AAATACAATAGGACCCAACAAACC 57.401 37.500 0.00 0.00 0.00 3.27
3792 3819 3.603965 ACAATAGGACCCAACAAACCA 57.396 42.857 0.00 0.00 0.00 3.67
3793 3820 3.496331 ACAATAGGACCCAACAAACCAG 58.504 45.455 0.00 0.00 0.00 4.00
3794 3821 2.825532 CAATAGGACCCAACAAACCAGG 59.174 50.000 0.00 0.00 0.00 4.45
3795 3822 1.822425 TAGGACCCAACAAACCAGGA 58.178 50.000 0.00 0.00 0.00 3.86
3796 3823 1.158007 AGGACCCAACAAACCAGGAT 58.842 50.000 0.00 0.00 0.00 3.24
3797 3824 1.203050 AGGACCCAACAAACCAGGATG 60.203 52.381 0.00 0.00 0.00 3.51
3857 3884 7.125659 TCCACTTATCTAACCATCAGATGTCAA 59.874 37.037 9.64 0.00 34.58 3.18
3869 3896 7.014134 ACCATCAGATGTCAAGTACTAGATCTG 59.986 40.741 19.67 19.67 37.43 2.90
3870 3897 7.230309 CCATCAGATGTCAAGTACTAGATCTGA 59.770 40.741 25.88 25.88 43.64 3.27
3871 3898 7.800155 TCAGATGTCAAGTACTAGATCTGAG 57.200 40.000 22.48 7.29 38.91 3.35
3872 3899 7.569240 TCAGATGTCAAGTACTAGATCTGAGA 58.431 38.462 22.48 11.14 38.91 3.27
3873 3900 8.217111 TCAGATGTCAAGTACTAGATCTGAGAT 58.783 37.037 22.48 14.56 38.91 2.75
3874 3901 8.291740 CAGATGTCAAGTACTAGATCTGAGATG 58.708 40.741 20.54 2.98 37.92 2.90
3875 3902 6.384258 TGTCAAGTACTAGATCTGAGATGC 57.616 41.667 5.18 0.00 0.00 3.91
3876 3903 5.300539 TGTCAAGTACTAGATCTGAGATGCC 59.699 44.000 5.18 0.00 0.00 4.40
3877 3904 5.300539 GTCAAGTACTAGATCTGAGATGCCA 59.699 44.000 5.18 0.00 0.00 4.92
3878 3905 5.300539 TCAAGTACTAGATCTGAGATGCCAC 59.699 44.000 5.18 0.00 0.00 5.01
3879 3906 4.797743 AGTACTAGATCTGAGATGCCACA 58.202 43.478 5.18 0.00 0.00 4.17
3880 3907 5.392995 AGTACTAGATCTGAGATGCCACAT 58.607 41.667 5.18 0.00 0.00 3.21
3881 3908 6.547402 AGTACTAGATCTGAGATGCCACATA 58.453 40.000 5.18 0.00 0.00 2.29
3882 3909 7.181361 AGTACTAGATCTGAGATGCCACATAT 58.819 38.462 5.18 0.00 0.00 1.78
3883 3910 6.528537 ACTAGATCTGAGATGCCACATATC 57.471 41.667 5.18 0.00 0.00 1.63
3884 3911 6.255287 ACTAGATCTGAGATGCCACATATCT 58.745 40.000 5.18 0.00 37.59 1.98
3885 3912 6.725369 ACTAGATCTGAGATGCCACATATCTT 59.275 38.462 5.18 0.00 35.14 2.40
3886 3913 6.040209 AGATCTGAGATGCCACATATCTTC 57.960 41.667 0.00 0.05 35.14 2.87
3887 3914 4.613925 TCTGAGATGCCACATATCTTCC 57.386 45.455 4.10 0.00 35.14 3.46
3888 3915 4.229639 TCTGAGATGCCACATATCTTCCT 58.770 43.478 4.10 0.00 35.14 3.36
3889 3916 4.657504 TCTGAGATGCCACATATCTTCCTT 59.342 41.667 4.10 0.00 35.14 3.36
3890 3917 5.840693 TCTGAGATGCCACATATCTTCCTTA 59.159 40.000 4.10 0.00 35.14 2.69
3891 3918 6.014755 TCTGAGATGCCACATATCTTCCTTAG 60.015 42.308 4.10 0.00 35.14 2.18
3892 3919 5.012458 TGAGATGCCACATATCTTCCTTAGG 59.988 44.000 4.10 0.00 35.14 2.69
3893 3920 4.910304 AGATGCCACATATCTTCCTTAGGT 59.090 41.667 0.00 0.00 30.98 3.08
3894 3921 5.370880 AGATGCCACATATCTTCCTTAGGTT 59.629 40.000 0.00 0.00 30.98 3.50
3895 3922 5.450818 TGCCACATATCTTCCTTAGGTTT 57.549 39.130 0.00 0.00 0.00 3.27
3896 3923 5.826643 TGCCACATATCTTCCTTAGGTTTT 58.173 37.500 0.00 0.00 0.00 2.43
3897 3924 5.652014 TGCCACATATCTTCCTTAGGTTTTG 59.348 40.000 0.00 0.00 0.00 2.44
3898 3925 5.067805 GCCACATATCTTCCTTAGGTTTTGG 59.932 44.000 0.00 0.00 0.00 3.28
3899 3926 5.067805 CCACATATCTTCCTTAGGTTTTGGC 59.932 44.000 0.00 0.00 0.00 4.52
3900 3927 5.652014 CACATATCTTCCTTAGGTTTTGGCA 59.348 40.000 0.00 0.00 0.00 4.92
3901 3928 5.652452 ACATATCTTCCTTAGGTTTTGGCAC 59.348 40.000 0.00 0.00 0.00 5.01
3902 3929 2.871453 TCTTCCTTAGGTTTTGGCACC 58.129 47.619 0.00 0.00 37.04 5.01
3904 3931 3.117284 TCTTCCTTAGGTTTTGGCACCTT 60.117 43.478 0.00 0.00 45.76 3.50
3905 3932 2.593026 TCCTTAGGTTTTGGCACCTTG 58.407 47.619 0.00 0.00 45.76 3.61
3906 3933 1.000843 CCTTAGGTTTTGGCACCTTGC 59.999 52.381 0.00 0.00 45.76 4.01
3907 3934 1.963515 CTTAGGTTTTGGCACCTTGCT 59.036 47.619 0.00 0.00 45.76 3.91
3908 3935 2.961531 TAGGTTTTGGCACCTTGCTA 57.038 45.000 0.00 0.00 45.76 3.49
3909 3936 2.080654 AGGTTTTGGCACCTTGCTAA 57.919 45.000 0.00 0.00 45.76 3.09
3918 3945 1.890573 GCACCTTGCTAAACCCATCCA 60.891 52.381 0.00 0.00 40.96 3.41
3947 3974 4.901197 TTTCTTTAAAAAGCCCATCCCC 57.099 40.909 0.00 0.00 35.99 4.81
3961 3988 2.244769 CCATCCCCACTTTTGATACCCT 59.755 50.000 0.00 0.00 0.00 4.34
3987 4014 5.922960 AAACCCATCCCTAGCAATATGTA 57.077 39.130 0.00 0.00 0.00 2.29
3988 4015 6.468972 AAACCCATCCCTAGCAATATGTAT 57.531 37.500 0.00 0.00 0.00 2.29
3989 4016 6.468972 AACCCATCCCTAGCAATATGTATT 57.531 37.500 0.00 0.00 0.00 1.89
4024 4051 3.243907 CCTGGATGGTTCGGAGAATAGTC 60.244 52.174 0.00 0.00 45.90 2.59
4027 4054 3.567164 GGATGGTTCGGAGAATAGTCGTA 59.433 47.826 0.00 0.00 45.90 3.43
4034 4061 4.467769 TCGGAGAATAGTCGTATCCCTTT 58.532 43.478 0.00 0.00 0.00 3.11
4037 4064 6.547141 TCGGAGAATAGTCGTATCCCTTTAAA 59.453 38.462 0.00 0.00 0.00 1.52
4039 4066 7.871463 CGGAGAATAGTCGTATCCCTTTAAATT 59.129 37.037 0.00 0.00 0.00 1.82
4069 4096 7.472543 ACTTGATATTGGTGCTCGTATTTTTC 58.527 34.615 0.00 0.00 0.00 2.29
4072 4099 4.701956 ATTGGTGCTCGTATTTTTCTGG 57.298 40.909 0.00 0.00 0.00 3.86
4073 4100 3.410631 TGGTGCTCGTATTTTTCTGGA 57.589 42.857 0.00 0.00 0.00 3.86
4074 4101 3.071479 TGGTGCTCGTATTTTTCTGGAC 58.929 45.455 0.00 0.00 0.00 4.02
4075 4102 3.244422 TGGTGCTCGTATTTTTCTGGACT 60.244 43.478 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.815795 CGAGATCAGATCGAGGGGTGA 60.816 57.143 4.67 0.00 42.76 4.02
49 50 0.105913 GAGGATTCGGGGAGGAGAGT 60.106 60.000 0.00 0.00 0.00 3.24
153 154 1.854227 CCTCGAAACCCTAATCTCGC 58.146 55.000 0.00 0.00 0.00 5.03
363 364 2.928036 AAATCAAGAAAGGGGAGGGG 57.072 50.000 0.00 0.00 0.00 4.79
424 426 2.045045 CCCGCTGAATCCAAGCCA 60.045 61.111 0.00 0.00 0.00 4.75
437 439 6.203808 AGTCAAATTAAATTAAGGTCCCGC 57.796 37.500 0.00 0.00 0.00 6.13
569 571 1.449423 CCACGCGACATCCATGGAA 60.449 57.895 20.67 1.96 31.69 3.53
583 585 0.883833 ATTTGGAAGCAAGCTCCACG 59.116 50.000 11.16 0.00 32.63 4.94
711 713 0.672889 ACATTGTTTCCGCACATGCA 59.327 45.000 4.49 0.00 42.21 3.96
789 791 4.203226 TGATGTACAAACCTTCAAGTGCA 58.797 39.130 0.00 0.00 0.00 4.57
819 821 1.588674 CAAGTTGAACACTACCGCCA 58.411 50.000 0.00 0.00 32.94 5.69
822 824 3.399330 ACATCCAAGTTGAACACTACCG 58.601 45.455 3.87 0.00 32.94 4.02
856 858 9.357652 GAGGAAACGTATTGTGTTACTTATACA 57.642 33.333 0.00 0.00 0.00 2.29
1056 1061 0.038166 TTCCCCTCAGATTGCCACAC 59.962 55.000 0.00 0.00 0.00 3.82
1131 1136 0.960364 GCGAAGGGAAATGGCAGTCA 60.960 55.000 0.00 0.00 0.00 3.41
1180 1185 6.868622 ACAAACTTTAATTGCACACAACCTA 58.131 32.000 0.00 0.00 38.99 3.08
1222 1227 4.566488 GGACCAACTCTTCATCAGATTGGT 60.566 45.833 6.17 6.17 45.98 3.67
1236 1241 7.666623 TGAAATTCCAAAATTAGGACCAACTC 58.333 34.615 0.00 0.00 33.93 3.01
1328 1333 3.320541 CCACTAGAGGCAGGTCTCTTATG 59.679 52.174 8.93 7.74 43.26 1.90
1355 1360 2.346766 TTGCAGTCCAACATGTCTGT 57.653 45.000 12.37 0.00 37.12 3.41
1412 1417 4.825085 AGAACTTCCATAAAAGGTTGCGAA 59.175 37.500 0.00 0.00 0.00 4.70
1473 1478 6.116806 TGGAAGCAAAGTGTAAAGTGTAGAA 58.883 36.000 0.00 0.00 0.00 2.10
1514 1519 1.473434 GGGAAACTAGTCCTCATGGCG 60.473 57.143 0.00 0.00 37.85 5.69
1811 1820 0.459899 CTCACTACCGTATGCTGGCA 59.540 55.000 0.00 0.00 0.00 4.92
1860 1869 7.354751 AGTTTGGGCTAGTGAAAAATTAACA 57.645 32.000 0.00 0.00 0.00 2.41
1919 1928 4.995487 ACGAGTAAATGTCTTCCCTTTGAC 59.005 41.667 0.00 0.00 0.00 3.18
2023 2032 4.125703 CCATCAACTGAGCTCCTACAATC 58.874 47.826 12.15 0.00 0.00 2.67
2169 2178 3.058983 TGCAATCTGTCTTACAGCAAACG 60.059 43.478 2.12 0.00 45.54 3.60
2261 2270 0.890996 GGTGTTCAGACCAAGGGCAG 60.891 60.000 0.00 0.00 35.88 4.85
2475 2484 0.545646 GCTCAGCCCTCTTCCTCAAT 59.454 55.000 0.00 0.00 0.00 2.57
2505 2514 4.701651 TCACTGTCAACATTCATTGGATCC 59.298 41.667 4.20 4.20 0.00 3.36
2652 2661 4.518211 CCAGACTCTTCATGCATATTTCCC 59.482 45.833 0.00 0.00 0.00 3.97
2704 2716 1.796459 GCAGCAATTTTCTTGCCTGTG 59.204 47.619 6.34 0.71 45.98 3.66
2778 2790 4.686091 TCGTCTTGAGCATCTGTGTAAAAG 59.314 41.667 0.00 0.00 34.92 2.27
2782 2794 2.820197 AGTCGTCTTGAGCATCTGTGTA 59.180 45.455 0.00 0.00 34.92 2.90
2805 2817 2.029623 GGAGCCTCAAATGATGTGCAT 58.970 47.619 0.00 0.00 39.43 3.96
2840 2852 1.499913 ATCAGTGGGTGTGCCATCCA 61.500 55.000 3.30 3.30 43.05 3.41
3038 3050 4.565652 GGGCAGTAGAAGAGTCATTTCCAA 60.566 45.833 0.00 0.00 0.00 3.53
3072 3084 5.429681 TCAGAAACCCGGATCATCTTTAA 57.570 39.130 0.73 0.00 0.00 1.52
3274 3286 1.271102 GGCTACAGGAGATCATCGACC 59.729 57.143 0.00 0.00 0.00 4.79
3299 3311 0.687354 ACACAGAGGCTACAACAGGG 59.313 55.000 0.00 0.00 0.00 4.45
3300 3312 2.563179 AGTACACAGAGGCTACAACAGG 59.437 50.000 0.00 0.00 0.00 4.00
3301 3313 3.005897 ACAGTACACAGAGGCTACAACAG 59.994 47.826 0.00 0.00 0.00 3.16
3302 3314 2.963101 ACAGTACACAGAGGCTACAACA 59.037 45.455 0.00 0.00 0.00 3.33
3303 3315 3.662247 ACAGTACACAGAGGCTACAAC 57.338 47.619 0.00 0.00 0.00 3.32
3304 3316 3.386726 ACAACAGTACACAGAGGCTACAA 59.613 43.478 0.00 0.00 0.00 2.41
3305 3317 2.963101 ACAACAGTACACAGAGGCTACA 59.037 45.455 0.00 0.00 0.00 2.74
3315 3327 5.734855 AACTTGTCATGACAACAGTACAC 57.265 39.130 32.36 2.11 45.42 2.90
3410 3426 7.171508 TGCAAGTAGAATAAGGAAAGCGATATG 59.828 37.037 0.00 0.00 0.00 1.78
3415 3431 5.525378 AGATGCAAGTAGAATAAGGAAAGCG 59.475 40.000 0.00 0.00 0.00 4.68
3486 3507 0.872388 GGTTGACCATCCGTTGACAC 59.128 55.000 0.00 0.00 35.64 3.67
3494 3515 1.002087 AGACTTCACGGTTGACCATCC 59.998 52.381 0.51 0.00 35.14 3.51
3506 3527 0.241481 AACCGAGAGCGAGACTTCAC 59.759 55.000 0.00 0.00 40.82 3.18
3515 3536 2.733218 TGCAACGAACCGAGAGCG 60.733 61.111 0.00 0.00 37.24 5.03
3575 3602 5.340439 AAGGAGACCAATAAACTAGGACG 57.660 43.478 0.00 0.00 0.00 4.79
3576 3603 6.708285 TCAAAGGAGACCAATAAACTAGGAC 58.292 40.000 0.00 0.00 0.00 3.85
3577 3604 6.945636 TCAAAGGAGACCAATAAACTAGGA 57.054 37.500 0.00 0.00 0.00 2.94
3578 3605 7.996098 TTTCAAAGGAGACCAATAAACTAGG 57.004 36.000 0.00 0.00 0.00 3.02
3581 3608 8.704668 ACAAATTTCAAAGGAGACCAATAAACT 58.295 29.630 0.00 0.00 0.00 2.66
3582 3609 8.764287 CACAAATTTCAAAGGAGACCAATAAAC 58.236 33.333 0.00 0.00 0.00 2.01
3583 3610 7.440856 GCACAAATTTCAAAGGAGACCAATAAA 59.559 33.333 0.00 0.00 0.00 1.40
3584 3611 6.928492 GCACAAATTTCAAAGGAGACCAATAA 59.072 34.615 0.00 0.00 0.00 1.40
3585 3612 6.267471 AGCACAAATTTCAAAGGAGACCAATA 59.733 34.615 0.00 0.00 0.00 1.90
3586 3613 5.070847 AGCACAAATTTCAAAGGAGACCAAT 59.929 36.000 0.00 0.00 0.00 3.16
3587 3614 4.405358 AGCACAAATTTCAAAGGAGACCAA 59.595 37.500 0.00 0.00 0.00 3.67
3588 3615 3.960102 AGCACAAATTTCAAAGGAGACCA 59.040 39.130 0.00 0.00 0.00 4.02
3589 3616 4.590850 AGCACAAATTTCAAAGGAGACC 57.409 40.909 0.00 0.00 0.00 3.85
3590 3617 8.593492 AATTTAGCACAAATTTCAAAGGAGAC 57.407 30.769 3.84 0.00 0.00 3.36
3591 3618 9.612066 AAAATTTAGCACAAATTTCAAAGGAGA 57.388 25.926 17.17 0.00 38.47 3.71
3592 3619 9.654417 CAAAATTTAGCACAAATTTCAAAGGAG 57.346 29.630 17.17 4.36 38.47 3.69
3593 3620 9.171877 ACAAAATTTAGCACAAATTTCAAAGGA 57.828 25.926 17.17 0.00 38.47 3.36
3594 3621 9.786105 AACAAAATTTAGCACAAATTTCAAAGG 57.214 25.926 17.17 10.23 38.47 3.11
3598 3625 9.985318 CTTGAACAAAATTTAGCACAAATTTCA 57.015 25.926 17.17 11.02 38.47 2.69
3599 3626 9.986833 ACTTGAACAAAATTTAGCACAAATTTC 57.013 25.926 17.17 9.24 38.47 2.17
3647 3674 9.855361 CAACGAAATAAATTTTGTTAACATGCA 57.145 25.926 16.85 0.00 46.99 3.96
3648 3675 9.312146 CCAACGAAATAAATTTTGTTAACATGC 57.688 29.630 16.85 0.00 46.99 4.06
3697 3724 8.810427 GCATGTCACCAAAAACTATATCATTTG 58.190 33.333 0.00 0.00 33.62 2.32
3698 3725 8.530311 TGCATGTCACCAAAAACTATATCATTT 58.470 29.630 0.00 0.00 0.00 2.32
3699 3726 8.065473 TGCATGTCACCAAAAACTATATCATT 57.935 30.769 0.00 0.00 0.00 2.57
3700 3727 7.643569 TGCATGTCACCAAAAACTATATCAT 57.356 32.000 0.00 0.00 0.00 2.45
3701 3728 7.392953 TCTTGCATGTCACCAAAAACTATATCA 59.607 33.333 0.00 0.00 0.00 2.15
3702 3729 7.761409 TCTTGCATGTCACCAAAAACTATATC 58.239 34.615 0.00 0.00 0.00 1.63
3703 3730 7.701539 TCTTGCATGTCACCAAAAACTATAT 57.298 32.000 0.00 0.00 0.00 0.86
3704 3731 7.013750 TGTTCTTGCATGTCACCAAAAACTATA 59.986 33.333 0.00 0.00 0.00 1.31
3705 3732 6.183360 TGTTCTTGCATGTCACCAAAAACTAT 60.183 34.615 0.00 0.00 0.00 2.12
3706 3733 5.126222 TGTTCTTGCATGTCACCAAAAACTA 59.874 36.000 0.00 0.00 0.00 2.24
3707 3734 4.081752 TGTTCTTGCATGTCACCAAAAACT 60.082 37.500 0.00 0.00 0.00 2.66
3708 3735 4.180057 TGTTCTTGCATGTCACCAAAAAC 58.820 39.130 0.00 0.00 0.00 2.43
3709 3736 4.462508 TGTTCTTGCATGTCACCAAAAA 57.537 36.364 0.00 0.00 0.00 1.94
3710 3737 4.669206 ATGTTCTTGCATGTCACCAAAA 57.331 36.364 0.00 0.00 0.00 2.44
3711 3738 4.669206 AATGTTCTTGCATGTCACCAAA 57.331 36.364 0.00 0.00 0.00 3.28
3712 3739 4.669206 AAATGTTCTTGCATGTCACCAA 57.331 36.364 0.00 0.00 0.00 3.67
3713 3740 4.669206 AAAATGTTCTTGCATGTCACCA 57.331 36.364 0.00 0.00 0.00 4.17
3714 3741 4.810491 ACAAAAATGTTCTTGCATGTCACC 59.190 37.500 0.00 0.00 0.00 4.02
3715 3742 5.971895 ACAAAAATGTTCTTGCATGTCAC 57.028 34.783 0.00 0.00 0.00 3.67
3716 3743 7.264221 ACTAACAAAAATGTTCTTGCATGTCA 58.736 30.769 0.00 1.80 33.59 3.58
3717 3744 7.698836 ACTAACAAAAATGTTCTTGCATGTC 57.301 32.000 0.00 0.00 33.59 3.06
3718 3745 9.593134 TTAACTAACAAAAATGTTCTTGCATGT 57.407 25.926 0.00 0.00 33.59 3.21
3740 3767 9.209297 GCGCCAAATTTTGATCATAAATTTAAC 57.791 29.630 24.66 20.63 41.03 2.01
3741 3768 8.939929 TGCGCCAAATTTTGATCATAAATTTAA 58.060 25.926 24.66 14.33 41.03 1.52
3742 3769 8.484641 TGCGCCAAATTTTGATCATAAATTTA 57.515 26.923 24.66 15.14 41.03 1.40
3743 3770 7.375106 TGCGCCAAATTTTGATCATAAATTT 57.625 28.000 22.18 22.18 42.72 1.82
3744 3771 6.981762 TGCGCCAAATTTTGATCATAAATT 57.018 29.167 4.18 16.33 36.91 1.82
3745 3772 6.981762 TTGCGCCAAATTTTGATCATAAAT 57.018 29.167 4.18 6.40 0.00 1.40
3746 3773 6.791887 TTTGCGCCAAATTTTGATCATAAA 57.208 29.167 4.18 4.46 0.00 1.40
3747 3774 6.791887 TTTTGCGCCAAATTTTGATCATAA 57.208 29.167 4.18 0.00 33.19 1.90
3748 3775 6.981762 ATTTTGCGCCAAATTTTGATCATA 57.018 29.167 13.27 0.00 33.19 2.15
3749 3776 5.883503 ATTTTGCGCCAAATTTTGATCAT 57.116 30.435 13.27 0.00 33.19 2.45
3750 3777 5.698089 TGTATTTTGCGCCAAATTTTGATCA 59.302 32.000 22.61 10.90 33.19 2.92
3751 3778 6.163159 TGTATTTTGCGCCAAATTTTGATC 57.837 33.333 22.61 8.95 33.19 2.92
3752 3779 6.551385 TTGTATTTTGCGCCAAATTTTGAT 57.449 29.167 22.61 3.03 33.19 2.57
3753 3780 5.991328 TTGTATTTTGCGCCAAATTTTGA 57.009 30.435 22.61 4.11 33.19 2.69
3754 3781 6.960431 CCTATTGTATTTTGCGCCAAATTTTG 59.040 34.615 22.61 1.99 33.19 2.44
3755 3782 6.876257 TCCTATTGTATTTTGCGCCAAATTTT 59.124 30.769 22.61 4.44 33.19 1.82
3756 3783 6.312672 GTCCTATTGTATTTTGCGCCAAATTT 59.687 34.615 22.61 5.14 33.19 1.82
3757 3784 5.810074 GTCCTATTGTATTTTGCGCCAAATT 59.190 36.000 22.61 9.03 33.19 1.82
3758 3785 5.348164 GTCCTATTGTATTTTGCGCCAAAT 58.652 37.500 21.39 21.39 33.19 2.32
3759 3786 4.381079 GGTCCTATTGTATTTTGCGCCAAA 60.381 41.667 9.27 9.27 0.00 3.28
3760 3787 3.129638 GGTCCTATTGTATTTTGCGCCAA 59.870 43.478 4.18 0.00 0.00 4.52
3761 3788 2.685897 GGTCCTATTGTATTTTGCGCCA 59.314 45.455 4.18 0.00 0.00 5.69
3762 3789 2.034179 GGGTCCTATTGTATTTTGCGCC 59.966 50.000 4.18 0.00 0.00 6.53
3763 3790 2.685897 TGGGTCCTATTGTATTTTGCGC 59.314 45.455 0.00 0.00 0.00 6.09
3764 3791 4.156922 TGTTGGGTCCTATTGTATTTTGCG 59.843 41.667 0.00 0.00 0.00 4.85
3765 3792 5.652994 TGTTGGGTCCTATTGTATTTTGC 57.347 39.130 0.00 0.00 0.00 3.68
3766 3793 6.871492 GGTTTGTTGGGTCCTATTGTATTTTG 59.129 38.462 0.00 0.00 0.00 2.44
3767 3794 6.555360 TGGTTTGTTGGGTCCTATTGTATTTT 59.445 34.615 0.00 0.00 0.00 1.82
3768 3795 6.078664 TGGTTTGTTGGGTCCTATTGTATTT 58.921 36.000 0.00 0.00 0.00 1.40
3769 3796 5.646215 TGGTTTGTTGGGTCCTATTGTATT 58.354 37.500 0.00 0.00 0.00 1.89
3770 3797 5.261216 CTGGTTTGTTGGGTCCTATTGTAT 58.739 41.667 0.00 0.00 0.00 2.29
3771 3798 4.507691 CCTGGTTTGTTGGGTCCTATTGTA 60.508 45.833 0.00 0.00 0.00 2.41
3772 3799 3.496331 CTGGTTTGTTGGGTCCTATTGT 58.504 45.455 0.00 0.00 0.00 2.71
3773 3800 2.825532 CCTGGTTTGTTGGGTCCTATTG 59.174 50.000 0.00 0.00 0.00 1.90
3774 3801 2.719705 TCCTGGTTTGTTGGGTCCTATT 59.280 45.455 0.00 0.00 0.00 1.73
3775 3802 2.354328 TCCTGGTTTGTTGGGTCCTAT 58.646 47.619 0.00 0.00 0.00 2.57
3776 3803 1.822425 TCCTGGTTTGTTGGGTCCTA 58.178 50.000 0.00 0.00 0.00 2.94
3777 3804 1.158007 ATCCTGGTTTGTTGGGTCCT 58.842 50.000 0.00 0.00 0.00 3.85
3778 3805 1.256812 CATCCTGGTTTGTTGGGTCC 58.743 55.000 0.00 0.00 0.00 4.46
3779 3806 1.203001 TCCATCCTGGTTTGTTGGGTC 60.203 52.381 0.00 0.00 39.03 4.46
3780 3807 0.856982 TCCATCCTGGTTTGTTGGGT 59.143 50.000 0.00 0.00 39.03 4.51
3781 3808 1.549203 CTCCATCCTGGTTTGTTGGG 58.451 55.000 0.00 0.00 39.03 4.12
3782 3809 1.203050 ACCTCCATCCTGGTTTGTTGG 60.203 52.381 0.00 0.96 39.03 3.77
3783 3810 2.292828 ACCTCCATCCTGGTTTGTTG 57.707 50.000 0.00 0.00 39.03 3.33
3784 3811 4.675063 ATTACCTCCATCCTGGTTTGTT 57.325 40.909 0.00 0.00 39.03 2.83
3785 3812 4.788617 ACTATTACCTCCATCCTGGTTTGT 59.211 41.667 0.00 0.00 39.03 2.83
3786 3813 5.373812 ACTATTACCTCCATCCTGGTTTG 57.626 43.478 0.00 0.00 39.03 2.93
3787 3814 6.099845 CAGTACTATTACCTCCATCCTGGTTT 59.900 42.308 0.00 0.00 39.03 3.27
3788 3815 5.602978 CAGTACTATTACCTCCATCCTGGTT 59.397 44.000 0.00 0.00 39.03 3.67
3789 3816 5.103215 TCAGTACTATTACCTCCATCCTGGT 60.103 44.000 0.00 0.00 39.03 4.00
3790 3817 5.394738 TCAGTACTATTACCTCCATCCTGG 58.605 45.833 0.00 0.00 39.43 4.45
3791 3818 6.551601 AGTTCAGTACTATTACCTCCATCCTG 59.448 42.308 0.00 0.00 34.56 3.86
3792 3819 6.551601 CAGTTCAGTACTATTACCTCCATCCT 59.448 42.308 0.00 0.00 34.56 3.24
3793 3820 6.739008 GCAGTTCAGTACTATTACCTCCATCC 60.739 46.154 0.00 0.00 34.56 3.51
3794 3821 6.183360 TGCAGTTCAGTACTATTACCTCCATC 60.183 42.308 0.00 0.00 34.56 3.51
3795 3822 5.661312 TGCAGTTCAGTACTATTACCTCCAT 59.339 40.000 0.00 0.00 34.56 3.41
3796 3823 5.020795 TGCAGTTCAGTACTATTACCTCCA 58.979 41.667 0.00 0.00 34.56 3.86
3797 3824 5.593679 TGCAGTTCAGTACTATTACCTCC 57.406 43.478 0.00 0.00 34.56 4.30
3798 3825 8.494016 AATTTGCAGTTCAGTACTATTACCTC 57.506 34.615 0.00 0.00 34.56 3.85
3799 3826 8.863872 AAATTTGCAGTTCAGTACTATTACCT 57.136 30.769 0.00 0.00 34.56 3.08
3807 3834 9.556030 GGAAGTAATAAATTTGCAGTTCAGTAC 57.444 33.333 0.00 0.00 0.00 2.73
3848 3875 7.800155 TCTCAGATCTAGTACTTGACATCTG 57.200 40.000 21.93 21.93 37.41 2.90
3849 3876 7.040478 GCATCTCAGATCTAGTACTTGACATCT 60.040 40.741 9.25 6.87 0.00 2.90
3857 3884 4.797743 TGTGGCATCTCAGATCTAGTACT 58.202 43.478 0.00 0.00 0.00 2.73
3869 3896 5.012561 ACCTAAGGAAGATATGTGGCATCTC 59.987 44.000 0.00 0.00 31.45 2.75
3870 3897 4.910304 ACCTAAGGAAGATATGTGGCATCT 59.090 41.667 0.00 0.00 34.15 2.90
3871 3898 5.234466 ACCTAAGGAAGATATGTGGCATC 57.766 43.478 0.00 0.00 0.00 3.91
3872 3899 5.653255 AACCTAAGGAAGATATGTGGCAT 57.347 39.130 0.00 0.00 0.00 4.40
3873 3900 5.450818 AAACCTAAGGAAGATATGTGGCA 57.549 39.130 0.00 0.00 0.00 4.92
3874 3901 5.067805 CCAAAACCTAAGGAAGATATGTGGC 59.932 44.000 0.00 0.00 0.00 5.01
3875 3902 5.067805 GCCAAAACCTAAGGAAGATATGTGG 59.932 44.000 0.00 0.00 0.00 4.17
3876 3903 5.652014 TGCCAAAACCTAAGGAAGATATGTG 59.348 40.000 0.00 0.00 0.00 3.21
3877 3904 5.652452 GTGCCAAAACCTAAGGAAGATATGT 59.348 40.000 0.00 0.00 0.00 2.29
3878 3905 5.067805 GGTGCCAAAACCTAAGGAAGATATG 59.932 44.000 0.00 0.00 37.24 1.78
3879 3906 5.201243 GGTGCCAAAACCTAAGGAAGATAT 58.799 41.667 0.00 0.00 37.24 1.63
3880 3907 4.595986 GGTGCCAAAACCTAAGGAAGATA 58.404 43.478 0.00 0.00 37.24 1.98
3881 3908 3.431415 GGTGCCAAAACCTAAGGAAGAT 58.569 45.455 0.00 0.00 37.24 2.40
3882 3909 2.871453 GGTGCCAAAACCTAAGGAAGA 58.129 47.619 0.00 0.00 37.24 2.87
3891 3918 2.479837 GTTTAGCAAGGTGCCAAAACC 58.520 47.619 13.70 0.00 46.52 3.27
3892 3919 2.479837 GGTTTAGCAAGGTGCCAAAAC 58.520 47.619 15.30 15.30 46.52 2.43
3893 3920 1.414550 GGGTTTAGCAAGGTGCCAAAA 59.585 47.619 0.00 0.00 46.52 2.44
3894 3921 1.044611 GGGTTTAGCAAGGTGCCAAA 58.955 50.000 0.00 0.00 46.52 3.28
3895 3922 0.105964 TGGGTTTAGCAAGGTGCCAA 60.106 50.000 0.00 0.00 46.52 4.52
3896 3923 0.114168 ATGGGTTTAGCAAGGTGCCA 59.886 50.000 0.00 0.00 46.52 4.92
3897 3924 0.817654 GATGGGTTTAGCAAGGTGCC 59.182 55.000 0.00 0.00 46.52 5.01
3898 3925 0.817654 GGATGGGTTTAGCAAGGTGC 59.182 55.000 0.00 0.00 45.46 5.01
3899 3926 2.214376 TGGATGGGTTTAGCAAGGTG 57.786 50.000 0.00 0.00 0.00 4.00
3900 3927 2.110011 AGTTGGATGGGTTTAGCAAGGT 59.890 45.455 0.00 0.00 0.00 3.50
3901 3928 2.807676 AGTTGGATGGGTTTAGCAAGG 58.192 47.619 0.00 0.00 0.00 3.61
3902 3929 4.871933 AAAGTTGGATGGGTTTAGCAAG 57.128 40.909 0.00 0.00 0.00 4.01
3903 3930 5.622346 AAAAAGTTGGATGGGTTTAGCAA 57.378 34.783 0.00 0.00 0.00 3.91
3933 3960 2.106338 CAAAAGTGGGGATGGGCTTTTT 59.894 45.455 0.00 0.00 0.00 1.94
3947 3974 4.157840 GGGTTTAGCAGGGTATCAAAAGTG 59.842 45.833 0.00 0.00 0.00 3.16
3961 3988 1.590591 TGCTAGGGATGGGTTTAGCA 58.409 50.000 1.25 1.25 44.36 3.49
3987 4014 1.202879 TCCAGGTTGGTTCGCTGAAAT 60.203 47.619 0.00 0.00 39.03 2.17
3988 4015 0.181587 TCCAGGTTGGTTCGCTGAAA 59.818 50.000 0.00 0.00 39.03 2.69
3989 4016 0.400213 ATCCAGGTTGGTTCGCTGAA 59.600 50.000 0.00 0.00 39.03 3.02
4020 4047 9.638176 AGTCTAGAATTTAAAGGGATACGACTA 57.362 33.333 0.00 0.00 37.60 2.59
4024 4051 9.765795 ATCAAGTCTAGAATTTAAAGGGATACG 57.234 33.333 1.94 0.00 37.60 3.06
4034 4061 9.547753 GAGCACCAATATCAAGTCTAGAATTTA 57.452 33.333 1.94 0.00 0.00 1.40
4037 4064 6.183360 ACGAGCACCAATATCAAGTCTAGAAT 60.183 38.462 0.00 0.00 0.00 2.40
4039 4066 4.645136 ACGAGCACCAATATCAAGTCTAGA 59.355 41.667 0.00 0.00 0.00 2.43
4044 4071 7.336931 AGAAAAATACGAGCACCAATATCAAGT 59.663 33.333 0.00 0.00 0.00 3.16
4045 4072 7.641411 CAGAAAAATACGAGCACCAATATCAAG 59.359 37.037 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.