Multiple sequence alignment - TraesCS3B01G353900

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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 TraesCS3B01G353900 chr3B 100.000 6943 0 0 1 6943 564253866 564246924 0.000000e+00 12785
1 TraesCS3B01G353900 chr3B 98.485 264 4 0 3669 3932 786512813 786512550 3.790000e-127 466
2 TraesCS3B01G353900 chr3B 95.522 268 12 0 3668 3935 782679904 782679637 4.980000e-116 429
3 TraesCS3B01G353900 chr3D 93.463 3702 116 30 18 3671 432035847 432032224 0.000000e+00 5398
4 TraesCS3B01G353900 chr3D 96.578 3039 63 13 3931 6943 432032225 432029202 0.000000e+00 4998
5 TraesCS3B01G353900 chr3A 97.096 2996 64 5 3931 6919 569426328 569423349 0.000000e+00 5029
6 TraesCS3B01G353900 chr3A 94.471 2930 113 20 433 3346 569429657 569426761 0.000000e+00 4468
7 TraesCS3B01G353900 chr3A 88.957 326 5 7 38 361 569429973 569429677 2.360000e-99 374
8 TraesCS3B01G353900 chr3A 90.850 153 11 1 3422 3574 569426698 569426549 1.180000e-47 202
9 TraesCS3B01G353900 chr3A 96.040 101 4 0 3571 3671 569426427 569426327 1.550000e-36 165
10 TraesCS3B01G353900 chr6A 98.864 264 3 0 3669 3932 57708277 57708540 8.150000e-129 472
11 TraesCS3B01G353900 chr7B 98.859 263 3 0 3670 3932 304933182 304933444 2.930000e-128 470
12 TraesCS3B01G353900 chr1B 98.106 264 5 0 3670 3933 395981903 395982166 1.760000e-125 460
13 TraesCS3B01G353900 chr4A 97.378 267 6 1 3670 3936 717962620 717962885 2.950000e-123 453
14 TraesCS3B01G353900 chr4A 95.911 269 10 1 3669 3937 90433901 90433634 1.070000e-117 435
15 TraesCS3B01G353900 chr5A 96.591 264 9 0 3670 3933 436890853 436890590 8.270000e-119 438
16 TraesCS3B01G353900 chr2B 96.591 264 9 0 3669 3932 478891793 478891530 8.270000e-119 438


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 TraesCS3B01G353900 chr3B 564246924 564253866 6942 True 12785.0 12785 100.0000 1 6943 1 chr3B.!!$R1 6942
1 TraesCS3B01G353900 chr3D 432029202 432035847 6645 True 5198.0 5398 95.0205 18 6943 2 chr3D.!!$R1 6925
2 TraesCS3B01G353900 chr3A 569423349 569429973 6624 True 2047.6 5029 93.4828 38 6919 5 chr3A.!!$R1 6881

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
164 167 0.110147 GACCACACGACACGAGAGAG 60.110 60.0 0.00 0.00 0.00 3.20 F
166 169 0.167033 CCACACGACACGAGAGAGAG 59.833 60.0 0.00 0.00 0.00 3.20 F
949 971 0.246910 GAAGAGGAGGAACGGTGGTC 59.753 60.0 0.00 0.00 0.00 4.02 F
1598 1641 0.445436 CAAGACAAGCGGCAGATGTC 59.555 55.0 19.43 19.43 42.91 3.06 F
2271 2319 2.231215 AGCCGATGATGTAAGACAGC 57.769 50.0 0.00 0.00 34.60 4.40 F
3694 3888 0.179145 CTCCGTCCGCGAATAAGTGT 60.179 55.0 8.23 0.00 41.33 3.55 F
3930 4124 0.033796 TATTCGTGGACGGAGGGAGT 60.034 55.0 0.00 0.00 40.29 3.85 F
5282 5479 0.823356 GCCCAGGTGCACTTTCAAGA 60.823 55.0 17.98 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 1621 0.035317 ACATCTGCCGCTTGTCTTGA 59.965 50.000 0.00 0.0 0.00 3.02 R
1579 1622 0.445436 GACATCTGCCGCTTGTCTTG 59.555 55.000 11.87 0.0 37.40 3.02 R
2429 2477 0.322456 TTCCATTGAAGACAGGGCCG 60.322 55.000 0.00 0.0 0.00 6.13 R
2852 2900 0.470341 GGAACTATGGGAGACAGGCC 59.530 60.000 0.00 0.0 0.00 5.19 R
3911 4105 0.033796 ACTCCCTCCGTCCACGAATA 60.034 55.000 0.00 0.0 43.02 1.75 R
5282 5479 3.371965 TCTAAGGTGTCGCTCCCTATTT 58.628 45.455 0.00 0.0 0.00 1.40 R
5616 5820 6.605471 TCTGTTACTATCAGGTGTGTTCAT 57.395 37.500 0.00 0.0 34.15 2.57 R
6187 6397 0.601841 ACCCTAAAACGACACCAGCG 60.602 55.000 0.00 0.0 0.00 5.18 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
34 35 8.511321 ACGATACAGATGCATACTTTTTCAAAA 58.489 29.630 0.00 0.00 0.00 2.44
35 36 9.340695 CGATACAGATGCATACTTTTTCAAAAA 57.659 29.630 0.00 0.00 0.00 1.94
71 74 1.097547 CATGACAGACCGGGCCAATC 61.098 60.000 1.76 0.00 0.00 2.67
158 161 1.081376 GAGAGGACCACACGACACG 60.081 63.158 0.00 0.00 0.00 4.49
159 162 1.512996 GAGAGGACCACACGACACGA 61.513 60.000 0.00 0.00 0.00 4.35
160 163 1.081376 GAGGACCACACGACACGAG 60.081 63.158 0.00 0.00 0.00 4.18
161 164 1.512996 GAGGACCACACGACACGAGA 61.513 60.000 0.00 0.00 0.00 4.04
162 165 1.081376 GGACCACACGACACGAGAG 60.081 63.158 0.00 0.00 0.00 3.20
163 166 1.512996 GGACCACACGACACGAGAGA 61.513 60.000 0.00 0.00 0.00 3.10
164 167 0.110147 GACCACACGACACGAGAGAG 60.110 60.000 0.00 0.00 0.00 3.20
165 168 0.534427 ACCACACGACACGAGAGAGA 60.534 55.000 0.00 0.00 0.00 3.10
166 169 0.167033 CCACACGACACGAGAGAGAG 59.833 60.000 0.00 0.00 0.00 3.20
167 170 1.149148 CACACGACACGAGAGAGAGA 58.851 55.000 0.00 0.00 0.00 3.10
168 171 1.127766 CACACGACACGAGAGAGAGAG 59.872 57.143 0.00 0.00 0.00 3.20
169 172 1.001068 ACACGACACGAGAGAGAGAGA 59.999 52.381 0.00 0.00 0.00 3.10
170 173 1.658596 CACGACACGAGAGAGAGAGAG 59.341 57.143 0.00 0.00 0.00 3.20
171 174 1.546923 ACGACACGAGAGAGAGAGAGA 59.453 52.381 0.00 0.00 0.00 3.10
172 175 2.193447 CGACACGAGAGAGAGAGAGAG 58.807 57.143 0.00 0.00 0.00 3.20
173 176 2.159296 CGACACGAGAGAGAGAGAGAGA 60.159 54.545 0.00 0.00 0.00 3.10
174 177 3.448686 GACACGAGAGAGAGAGAGAGAG 58.551 54.545 0.00 0.00 0.00 3.20
175 178 3.096852 ACACGAGAGAGAGAGAGAGAGA 58.903 50.000 0.00 0.00 0.00 3.10
176 179 3.131223 ACACGAGAGAGAGAGAGAGAGAG 59.869 52.174 0.00 0.00 0.00 3.20
177 180 3.381590 CACGAGAGAGAGAGAGAGAGAGA 59.618 52.174 0.00 0.00 0.00 3.10
279 282 2.528673 ACTACTCCTTAACCTCGGCT 57.471 50.000 0.00 0.00 0.00 5.52
280 283 2.377073 ACTACTCCTTAACCTCGGCTC 58.623 52.381 0.00 0.00 0.00 4.70
281 284 1.682323 CTACTCCTTAACCTCGGCTCC 59.318 57.143 0.00 0.00 0.00 4.70
282 285 0.976590 ACTCCTTAACCTCGGCTCCC 60.977 60.000 0.00 0.00 0.00 4.30
283 286 0.688087 CTCCTTAACCTCGGCTCCCT 60.688 60.000 0.00 0.00 0.00 4.20
358 361 1.200020 CGAAGCCAAGCAAAACTAGGG 59.800 52.381 0.00 0.00 0.00 3.53
422 428 1.321743 CGATTCGAAAACTCAGCGGAG 59.678 52.381 12.66 12.66 46.96 4.63
445 461 4.421058 GCAGGAACCGATTTTTCAATACC 58.579 43.478 0.00 0.00 0.00 2.73
543 560 1.362355 CTTTCCCACACGGCCAAAC 59.638 57.895 2.24 0.00 0.00 2.93
651 668 3.314331 CACCACCAGTCCTCGCCT 61.314 66.667 0.00 0.00 0.00 5.52
661 678 3.089874 CCTCGCCTCCCCATCCAA 61.090 66.667 0.00 0.00 0.00 3.53
941 963 2.114616 GCATCTGAGGAAGAGGAGGAA 58.885 52.381 0.00 0.00 39.10 3.36
949 971 0.246910 GAAGAGGAGGAACGGTGGTC 59.753 60.000 0.00 0.00 0.00 4.02
1240 1278 6.150396 TCTTTTTGAATTTTTCCGCTGGTA 57.850 33.333 0.00 0.00 0.00 3.25
1290 1328 8.345565 GGTTAGATTGCTAATAATTGGACACTG 58.654 37.037 0.00 0.00 38.74 3.66
1291 1329 6.382869 AGATTGCTAATAATTGGACACTGC 57.617 37.500 0.00 0.00 0.00 4.40
1427 1466 2.862512 CACAACCGTATGTGGCAATTC 58.137 47.619 9.33 0.00 45.47 2.17
1480 1519 3.134458 GCTGAGCACCATATACTCAACC 58.866 50.000 0.00 0.00 39.79 3.77
1494 1534 3.937814 ACTCAACCGCTGATGTTTGATA 58.062 40.909 0.00 0.00 32.14 2.15
1521 1564 5.473066 ACTGCTCTTTTGGCATGTTATTT 57.527 34.783 0.00 0.00 39.07 1.40
1532 1575 9.849166 TTTTGGCATGTTATTTTAGTAGCTAAC 57.151 29.630 0.00 0.00 0.00 2.34
1533 1576 7.241663 TGGCATGTTATTTTAGTAGCTAACG 57.758 36.000 0.00 0.00 0.00 3.18
1561 1604 4.482386 CAGAAATGCAAAGTGTCTGATGG 58.518 43.478 0.30 0.00 38.37 3.51
1562 1605 4.022589 CAGAAATGCAAAGTGTCTGATGGT 60.023 41.667 0.30 0.00 38.37 3.55
1564 1607 5.769662 AGAAATGCAAAGTGTCTGATGGTTA 59.230 36.000 0.00 0.00 0.00 2.85
1565 1608 5.633830 AATGCAAAGTGTCTGATGGTTAG 57.366 39.130 0.00 0.00 0.00 2.34
1566 1609 4.350368 TGCAAAGTGTCTGATGGTTAGA 57.650 40.909 0.00 0.00 0.00 2.10
1567 1610 4.713553 TGCAAAGTGTCTGATGGTTAGAA 58.286 39.130 0.00 0.00 0.00 2.10
1568 1611 5.316167 TGCAAAGTGTCTGATGGTTAGAAT 58.684 37.500 0.00 0.00 0.00 2.40
1569 1612 5.181811 TGCAAAGTGTCTGATGGTTAGAATG 59.818 40.000 0.00 0.00 0.00 2.67
1570 1613 5.182001 GCAAAGTGTCTGATGGTTAGAATGT 59.818 40.000 0.00 0.00 0.00 2.71
1571 1614 6.371548 GCAAAGTGTCTGATGGTTAGAATGTA 59.628 38.462 0.00 0.00 0.00 2.29
1572 1615 7.066284 GCAAAGTGTCTGATGGTTAGAATGTAT 59.934 37.037 0.00 0.00 0.00 2.29
1573 1616 8.950210 CAAAGTGTCTGATGGTTAGAATGTATT 58.050 33.333 0.00 0.00 0.00 1.89
1574 1617 8.498054 AAGTGTCTGATGGTTAGAATGTATTG 57.502 34.615 0.00 0.00 0.00 1.90
1575 1618 7.624549 AGTGTCTGATGGTTAGAATGTATTGT 58.375 34.615 0.00 0.00 0.00 2.71
1576 1619 8.103305 AGTGTCTGATGGTTAGAATGTATTGTT 58.897 33.333 0.00 0.00 0.00 2.83
1577 1620 8.730680 GTGTCTGATGGTTAGAATGTATTGTTT 58.269 33.333 0.00 0.00 0.00 2.83
1578 1621 9.295825 TGTCTGATGGTTAGAATGTATTGTTTT 57.704 29.630 0.00 0.00 0.00 2.43
1579 1622 9.774742 GTCTGATGGTTAGAATGTATTGTTTTC 57.225 33.333 0.00 0.00 0.00 2.29
1580 1623 9.513906 TCTGATGGTTAGAATGTATTGTTTTCA 57.486 29.630 0.00 0.00 0.00 2.69
1598 1641 0.445436 CAAGACAAGCGGCAGATGTC 59.555 55.000 19.43 19.43 42.91 3.06
1671 1714 4.079844 TCTGGTTGCAATTATCTGGATCCA 60.080 41.667 15.27 15.27 35.03 3.41
1680 1723 6.418819 GCAATTATCTGGATCCAAAATGTTCG 59.581 38.462 17.00 1.11 0.00 3.95
1745 1789 3.955771 TTCCTTGTGCGTGTAAAGTTC 57.044 42.857 0.00 0.00 0.00 3.01
1828 1872 9.543018 GTATTCTGATTTCTTAACCTTTTGACG 57.457 33.333 0.00 0.00 0.00 4.35
1856 1903 8.666573 TGTAACACGACATTTCTTGTAAAAAGA 58.333 29.630 0.00 0.00 39.18 2.52
1865 1913 8.999431 ACATTTCTTGTAAAAAGAGCTAATCGA 58.001 29.630 0.00 0.00 36.57 3.59
1970 2018 6.768483 TGATCTTGAAACTGATGGTTAGTGA 58.232 36.000 0.00 0.00 37.12 3.41
1981 2029 6.042093 ACTGATGGTTAGTGATTCATACCGAT 59.958 38.462 9.56 6.02 0.00 4.18
2047 2095 5.366482 TCCATGCAAAGTGTATAGCCTTA 57.634 39.130 0.00 0.00 0.00 2.69
2271 2319 2.231215 AGCCGATGATGTAAGACAGC 57.769 50.000 0.00 0.00 34.60 4.40
2872 2920 1.204146 GCCTGTCTCCCATAGTTCCA 58.796 55.000 0.00 0.00 0.00 3.53
2950 2998 0.539207 TGGCTGCTGGCATTGTAACA 60.539 50.000 16.03 0.00 44.10 2.41
3101 3149 4.141711 ACAGTGAATATGCTGGAACGGTAT 60.142 41.667 0.00 0.00 43.85 2.73
3116 3164 7.557724 TGGAACGGTATGTTATTTATCACAGA 58.442 34.615 0.00 0.00 42.09 3.41
3193 3248 5.704354 TGGCATATGGGATTATGTTGTCTT 58.296 37.500 4.56 0.00 33.07 3.01
3200 3255 5.569355 TGGGATTATGTTGTCTTCACATGT 58.431 37.500 0.00 0.00 30.55 3.21
3237 3292 7.863666 ACAATGACGAATTTTAAGACCGTTAA 58.136 30.769 0.00 0.00 33.32 2.01
3298 3353 4.202567 ACAATGTGGTTGGTATTCCTCACT 60.203 41.667 9.82 0.00 42.28 3.41
3307 3362 3.889538 TGGTATTCCTCACTGAGTATCGG 59.110 47.826 5.32 0.00 40.24 4.18
3363 3418 4.724074 AACTCATGGTTGTGGCATATTG 57.276 40.909 0.00 0.00 36.70 1.90
3455 3523 9.784531 TCAGAAGATTATGAGAAGTTCTGTTTT 57.215 29.630 10.90 0.00 41.02 2.43
3563 3632 1.922135 CTTTGGTCGGCGTGGGAATG 61.922 60.000 6.85 0.00 0.00 2.67
3583 3777 7.038017 GGGAATGAAAGATAGTAGATGGATGGA 60.038 40.741 0.00 0.00 0.00 3.41
3621 3815 4.695928 ACTTTGCCCTCTTCGATTAAGTTC 59.304 41.667 0.00 0.00 36.51 3.01
3674 3868 9.601217 ACATGTGTCTTTCTACAATTATACTCC 57.399 33.333 0.00 0.00 0.00 3.85
3675 3869 9.046296 CATGTGTCTTTCTACAATTATACTCCC 57.954 37.037 0.00 0.00 0.00 4.30
3676 3870 8.375493 TGTGTCTTTCTACAATTATACTCCCT 57.625 34.615 0.00 0.00 0.00 4.20
3677 3871 8.475639 TGTGTCTTTCTACAATTATACTCCCTC 58.524 37.037 0.00 0.00 0.00 4.30
3678 3872 7.927092 GTGTCTTTCTACAATTATACTCCCTCC 59.073 40.741 0.00 0.00 0.00 4.30
3679 3873 7.146648 GTCTTTCTACAATTATACTCCCTCCG 58.853 42.308 0.00 0.00 0.00 4.63
3680 3874 6.837568 TCTTTCTACAATTATACTCCCTCCGT 59.162 38.462 0.00 0.00 0.00 4.69
3681 3875 6.645790 TTCTACAATTATACTCCCTCCGTC 57.354 41.667 0.00 0.00 0.00 4.79
3682 3876 5.075493 TCTACAATTATACTCCCTCCGTCC 58.925 45.833 0.00 0.00 0.00 4.79
3683 3877 2.626743 ACAATTATACTCCCTCCGTCCG 59.373 50.000 0.00 0.00 0.00 4.79
3684 3878 1.254954 ATTATACTCCCTCCGTCCGC 58.745 55.000 0.00 0.00 0.00 5.54
3685 3879 1.168407 TTATACTCCCTCCGTCCGCG 61.168 60.000 0.00 0.00 37.95 6.46
3686 3880 2.043604 TATACTCCCTCCGTCCGCGA 62.044 60.000 8.23 0.00 41.33 5.87
3687 3881 2.898920 ATACTCCCTCCGTCCGCGAA 62.899 60.000 8.23 0.00 41.33 4.70
3688 3882 2.898920 TACTCCCTCCGTCCGCGAAT 62.899 60.000 8.23 0.00 41.33 3.34
3689 3883 2.124193 TCCCTCCGTCCGCGAATA 60.124 61.111 8.23 0.00 41.33 1.75
3690 3884 1.731433 CTCCCTCCGTCCGCGAATAA 61.731 60.000 8.23 0.00 41.33 1.40
3691 3885 1.299926 CCCTCCGTCCGCGAATAAG 60.300 63.158 8.23 0.00 41.33 1.73
3692 3886 1.436336 CCTCCGTCCGCGAATAAGT 59.564 57.895 8.23 0.00 41.33 2.24
3693 3887 0.870307 CCTCCGTCCGCGAATAAGTG 60.870 60.000 8.23 0.00 41.33 3.16
3694 3888 0.179145 CTCCGTCCGCGAATAAGTGT 60.179 55.000 8.23 0.00 41.33 3.55
3695 3889 1.064505 CTCCGTCCGCGAATAAGTGTA 59.935 52.381 8.23 0.00 41.33 2.90
3696 3890 1.194495 CCGTCCGCGAATAAGTGTAC 58.806 55.000 8.23 0.00 41.33 2.90
3697 3891 1.202222 CCGTCCGCGAATAAGTGTACT 60.202 52.381 8.23 0.00 41.33 2.73
3698 3892 2.523015 CGTCCGCGAATAAGTGTACTT 58.477 47.619 8.23 2.51 41.33 2.24
3699 3893 2.529090 CGTCCGCGAATAAGTGTACTTC 59.471 50.000 8.23 0.00 41.33 3.01
3700 3894 3.730061 CGTCCGCGAATAAGTGTACTTCT 60.730 47.826 8.23 0.00 41.33 2.85
3701 3895 4.494690 CGTCCGCGAATAAGTGTACTTCTA 60.495 45.833 8.23 0.00 41.33 2.10
3702 3896 4.968788 GTCCGCGAATAAGTGTACTTCTAG 59.031 45.833 8.23 0.00 37.40 2.43
3703 3897 3.729716 CCGCGAATAAGTGTACTTCTAGC 59.270 47.826 8.23 3.15 37.40 3.42
3704 3898 4.497674 CCGCGAATAAGTGTACTTCTAGCT 60.498 45.833 8.23 0.00 37.40 3.32
3705 3899 5.035443 CGCGAATAAGTGTACTTCTAGCTT 58.965 41.667 0.00 0.00 37.40 3.74
3706 3900 5.515626 CGCGAATAAGTGTACTTCTAGCTTT 59.484 40.000 0.00 0.00 37.40 3.51
3707 3901 6.034683 CGCGAATAAGTGTACTTCTAGCTTTT 59.965 38.462 0.00 0.00 37.40 2.27
3708 3902 7.174082 GCGAATAAGTGTACTTCTAGCTTTTG 58.826 38.462 0.00 0.00 37.40 2.44
3709 3903 7.148623 GCGAATAAGTGTACTTCTAGCTTTTGT 60.149 37.037 0.00 0.00 37.40 2.83
3710 3904 8.373992 CGAATAAGTGTACTTCTAGCTTTTGTC 58.626 37.037 0.00 0.00 37.40 3.18
3711 3905 8.549338 AATAAGTGTACTTCTAGCTTTTGTCC 57.451 34.615 0.00 0.00 37.40 4.02
3712 3906 5.810080 AGTGTACTTCTAGCTTTTGTCCT 57.190 39.130 0.00 0.00 0.00 3.85
3713 3907 6.912951 AGTGTACTTCTAGCTTTTGTCCTA 57.087 37.500 0.00 0.00 0.00 2.94
3714 3908 7.299246 AGTGTACTTCTAGCTTTTGTCCTAA 57.701 36.000 0.00 0.00 0.00 2.69
3715 3909 7.379750 AGTGTACTTCTAGCTTTTGTCCTAAG 58.620 38.462 0.00 0.00 0.00 2.18
3716 3910 7.015389 AGTGTACTTCTAGCTTTTGTCCTAAGT 59.985 37.037 0.00 0.00 0.00 2.24
3717 3911 7.328982 GTGTACTTCTAGCTTTTGTCCTAAGTC 59.671 40.741 0.00 0.00 0.00 3.01
3718 3912 6.420913 ACTTCTAGCTTTTGTCCTAAGTCA 57.579 37.500 0.00 0.00 0.00 3.41
3719 3913 6.827727 ACTTCTAGCTTTTGTCCTAAGTCAA 58.172 36.000 0.00 0.00 0.00 3.18
3720 3914 7.280356 ACTTCTAGCTTTTGTCCTAAGTCAAA 58.720 34.615 0.00 0.00 30.64 2.69
3721 3915 7.442666 ACTTCTAGCTTTTGTCCTAAGTCAAAG 59.557 37.037 0.00 0.00 33.54 2.77
3722 3916 6.827727 TCTAGCTTTTGTCCTAAGTCAAAGT 58.172 36.000 0.00 0.00 33.54 2.66
3723 3917 7.280356 TCTAGCTTTTGTCCTAAGTCAAAGTT 58.720 34.615 0.00 0.00 33.54 2.66
3724 3918 6.775594 AGCTTTTGTCCTAAGTCAAAGTTT 57.224 33.333 0.00 0.00 33.54 2.66
3725 3919 7.170393 AGCTTTTGTCCTAAGTCAAAGTTTT 57.830 32.000 0.00 0.00 33.54 2.43
3726 3920 8.288689 AGCTTTTGTCCTAAGTCAAAGTTTTA 57.711 30.769 0.00 0.00 33.54 1.52
3727 3921 8.745590 AGCTTTTGTCCTAAGTCAAAGTTTTAA 58.254 29.630 0.00 0.00 33.54 1.52
3728 3922 9.361315 GCTTTTGTCCTAAGTCAAAGTTTTAAA 57.639 29.630 0.00 0.00 33.54 1.52
3821 4015 9.950496 ACATTTCAAAACAGATCTAGTGATACT 57.050 29.630 0.00 0.00 32.19 2.12
3844 4038 8.511604 ACTAATTTAGTGTCATAAATGCTGCT 57.488 30.769 8.27 0.00 37.69 4.24
3845 4039 9.613428 ACTAATTTAGTGTCATAAATGCTGCTA 57.387 29.630 8.27 0.00 37.69 3.49
3846 4040 9.869844 CTAATTTAGTGTCATAAATGCTGCTAC 57.130 33.333 0.00 0.00 35.91 3.58
3847 4041 8.511604 AATTTAGTGTCATAAATGCTGCTACT 57.488 30.769 0.00 0.00 35.91 2.57
3848 4042 7.921786 TTTAGTGTCATAAATGCTGCTACTT 57.078 32.000 0.00 0.00 0.00 2.24
3849 4043 7.921786 TTAGTGTCATAAATGCTGCTACTTT 57.078 32.000 0.00 1.23 0.00 2.66
3850 4044 6.824305 AGTGTCATAAATGCTGCTACTTTT 57.176 33.333 0.00 0.00 0.00 2.27
3851 4045 7.219484 AGTGTCATAAATGCTGCTACTTTTT 57.781 32.000 0.00 0.00 0.00 1.94
3901 4095 9.788960 AAAACTTTGACTTAAGACAAAAGCTAG 57.211 29.630 25.68 18.71 38.68 3.42
3902 4096 8.732746 AACTTTGACTTAAGACAAAAGCTAGA 57.267 30.769 25.68 9.24 38.68 2.43
3903 4097 8.732746 ACTTTGACTTAAGACAAAAGCTAGAA 57.267 30.769 25.68 8.67 38.68 2.10
3904 4098 8.831550 ACTTTGACTTAAGACAAAAGCTAGAAG 58.168 33.333 25.68 17.12 38.68 2.85
3905 4099 8.732746 TTTGACTTAAGACAAAAGCTAGAAGT 57.267 30.769 24.34 0.00 36.92 3.01
3906 4100 9.826574 TTTGACTTAAGACAAAAGCTAGAAGTA 57.173 29.630 24.34 4.07 36.92 2.24
3907 4101 8.813643 TGACTTAAGACAAAAGCTAGAAGTAC 57.186 34.615 10.09 0.00 0.00 2.73
3908 4102 8.418662 TGACTTAAGACAAAAGCTAGAAGTACA 58.581 33.333 10.09 0.00 0.00 2.90
3909 4103 8.590719 ACTTAAGACAAAAGCTAGAAGTACAC 57.409 34.615 10.09 0.00 0.00 2.90
3910 4104 8.422566 ACTTAAGACAAAAGCTAGAAGTACACT 58.577 33.333 10.09 0.00 0.00 3.55
3911 4105 9.262358 CTTAAGACAAAAGCTAGAAGTACACTT 57.738 33.333 0.00 0.00 39.23 3.16
3914 4108 9.780186 AAGACAAAAGCTAGAAGTACACTTATT 57.220 29.630 0.00 0.00 36.11 1.40
3915 4109 9.425577 AGACAAAAGCTAGAAGTACACTTATTC 57.574 33.333 0.00 0.00 36.11 1.75
3916 4110 8.240883 ACAAAAGCTAGAAGTACACTTATTCG 57.759 34.615 0.00 0.00 36.11 3.34
3917 4111 7.871463 ACAAAAGCTAGAAGTACACTTATTCGT 59.129 33.333 0.00 0.00 36.11 3.85
3918 4112 7.813852 AAAGCTAGAAGTACACTTATTCGTG 57.186 36.000 0.00 0.00 40.67 4.35
3919 4113 5.892568 AGCTAGAAGTACACTTATTCGTGG 58.107 41.667 0.00 0.00 39.19 4.94
3920 4114 5.651139 AGCTAGAAGTACACTTATTCGTGGA 59.349 40.000 0.00 0.00 39.19 4.02
3921 4115 5.742926 GCTAGAAGTACACTTATTCGTGGAC 59.257 44.000 0.00 0.00 46.77 4.02
3924 4118 3.492421 GTACACTTATTCGTGGACGGA 57.508 47.619 0.00 0.00 38.82 4.69
3925 4119 2.649331 ACACTTATTCGTGGACGGAG 57.351 50.000 0.00 0.00 39.19 4.63
3926 4120 1.203994 ACACTTATTCGTGGACGGAGG 59.796 52.381 0.00 0.00 39.19 4.30
3927 4121 0.822164 ACTTATTCGTGGACGGAGGG 59.178 55.000 0.00 0.00 40.29 4.30
3928 4122 1.108776 CTTATTCGTGGACGGAGGGA 58.891 55.000 0.00 0.00 40.29 4.20
3929 4123 1.067212 CTTATTCGTGGACGGAGGGAG 59.933 57.143 0.00 0.00 40.29 4.30
3930 4124 0.033796 TATTCGTGGACGGAGGGAGT 60.034 55.000 0.00 0.00 40.29 3.85
3931 4125 0.033796 ATTCGTGGACGGAGGGAGTA 60.034 55.000 0.00 0.00 40.29 2.59
3948 4142 4.382470 GGGAGTATGTGCTATCTGCTATGG 60.382 50.000 0.00 0.00 43.37 2.74
3957 4151 5.463724 GTGCTATCTGCTATGGTTGTCTTAC 59.536 44.000 0.00 0.00 43.37 2.34
3984 4178 7.563888 ACTTCATGAAATGTGACATAGATGG 57.436 36.000 9.88 0.00 46.80 3.51
4296 4490 7.529519 GCTAAATGCATTCGTATTACTTAACCG 59.470 37.037 13.38 0.00 42.31 4.44
4866 5060 6.294397 GGAATTGATTATCCTTCAGATGCCAC 60.294 42.308 6.85 0.00 36.33 5.01
4867 5061 5.378230 TTGATTATCCTTCAGATGCCACT 57.622 39.130 0.00 0.00 36.33 4.00
4868 5062 5.378230 TGATTATCCTTCAGATGCCACTT 57.622 39.130 0.00 0.00 36.33 3.16
5193 5390 6.321945 GGGGTACTTCTTTTTACCTGTTTTCA 59.678 38.462 0.00 0.00 38.30 2.69
5194 5391 7.198390 GGGTACTTCTTTTTACCTGTTTTCAC 58.802 38.462 0.00 0.00 38.30 3.18
5282 5479 0.823356 GCCCAGGTGCACTTTCAAGA 60.823 55.000 17.98 0.00 0.00 3.02
5582 5786 7.809331 GTGTGTTGATGTTATTGATCATTGTGT 59.191 33.333 0.00 0.00 29.96 3.72
6055 6259 4.438472 GCATCTGAAGAATTGAGCTTGGAC 60.438 45.833 0.00 0.00 0.00 4.02
6065 6269 2.844946 TGAGCTTGGACGATGTTTTGA 58.155 42.857 0.00 0.00 0.00 2.69
6187 6397 6.149474 GGGGTGCTCAACATATATTGTATGTC 59.851 42.308 6.53 0.00 37.68 3.06
6191 6401 6.146021 TGCTCAACATATATTGTATGTCGCTG 59.854 38.462 6.53 2.89 37.68 5.18
6228 6439 5.106987 GGTGCTAAAATTGCTTGAACCATTG 60.107 40.000 0.00 0.00 0.00 2.82
6242 6453 4.098044 TGAACCATTGCGTTTGGAAGTAAA 59.902 37.500 6.41 0.00 37.69 2.01
6461 6672 0.393077 AGGGAGGTCGAATTATGGCG 59.607 55.000 0.00 0.00 0.00 5.69
6620 6831 3.386402 GGTGGCAGCTACTAGAGATTTCT 59.614 47.826 9.90 0.00 37.46 2.52
6666 6877 1.451387 CTGGACCAATACCACCGGC 60.451 63.158 0.00 0.00 33.57 6.13
6708 6919 2.654863 ACTCACCAAGTCAAACAAGGG 58.345 47.619 0.00 0.00 30.02 3.95
6740 6951 4.825422 TCCTGATGAAGTCTAAGTTGCTG 58.175 43.478 0.00 0.00 0.00 4.41
6898 7122 4.335037 TGCAAAAATTGAAAGCCAACCTTC 59.665 37.500 0.00 0.00 37.63 3.46
6906 7130 5.767816 TGAAAGCCAACCTTCTTAAGTTC 57.232 39.130 1.63 0.00 31.99 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.775939 AAGTATGCATCTGTATCGTTGATG 57.224 37.500 0.19 0.00 40.16 3.07
4 5 7.792374 AAAAGTATGCATCTGTATCGTTGAT 57.208 32.000 0.19 0.00 0.00 2.57
5 6 7.333174 TGAAAAAGTATGCATCTGTATCGTTGA 59.667 33.333 0.19 0.00 0.00 3.18
6 7 7.463544 TGAAAAAGTATGCATCTGTATCGTTG 58.536 34.615 0.19 0.00 0.00 4.10
7 8 7.609760 TGAAAAAGTATGCATCTGTATCGTT 57.390 32.000 0.19 0.00 0.00 3.85
8 9 7.609760 TTGAAAAAGTATGCATCTGTATCGT 57.390 32.000 0.19 0.00 0.00 3.73
9 10 8.894409 TTTTGAAAAAGTATGCATCTGTATCG 57.106 30.769 0.19 0.00 0.00 2.92
93 96 2.260743 GTCGGGTTCGGTGAGTCC 59.739 66.667 0.00 0.00 36.95 3.85
158 161 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
159 162 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
160 163 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
161 164 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
162 165 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
163 166 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
164 167 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
165 168 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
166 169 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
167 170 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
168 171 3.640967 AGCTCTCTCTCTCTCTCTCTCTC 59.359 52.174 0.00 0.00 0.00 3.20
169 172 3.387374 CAGCTCTCTCTCTCTCTCTCTCT 59.613 52.174 0.00 0.00 0.00 3.10
170 173 3.494048 CCAGCTCTCTCTCTCTCTCTCTC 60.494 56.522 0.00 0.00 0.00 3.20
171 174 2.437281 CCAGCTCTCTCTCTCTCTCTCT 59.563 54.545 0.00 0.00 0.00 3.10
172 175 2.486191 CCCAGCTCTCTCTCTCTCTCTC 60.486 59.091 0.00 0.00 0.00 3.20
173 176 1.492176 CCCAGCTCTCTCTCTCTCTCT 59.508 57.143 0.00 0.00 0.00 3.10
174 177 1.490490 TCCCAGCTCTCTCTCTCTCTC 59.510 57.143 0.00 0.00 0.00 3.20
175 178 1.595311 TCCCAGCTCTCTCTCTCTCT 58.405 55.000 0.00 0.00 0.00 3.10
176 179 2.427095 GTTTCCCAGCTCTCTCTCTCTC 59.573 54.545 0.00 0.00 0.00 3.20
177 180 2.456577 GTTTCCCAGCTCTCTCTCTCT 58.543 52.381 0.00 0.00 0.00 3.10
279 282 2.238701 GGCCAAGGAAGGGAAGGGA 61.239 63.158 0.00 0.00 0.00 4.20
280 283 2.360585 GGCCAAGGAAGGGAAGGG 59.639 66.667 0.00 0.00 0.00 3.95
281 284 2.044946 CGGCCAAGGAAGGGAAGG 60.045 66.667 2.24 0.00 0.00 3.46
282 285 2.751837 GCGGCCAAGGAAGGGAAG 60.752 66.667 2.24 0.00 0.00 3.46
283 286 4.360405 GGCGGCCAAGGAAGGGAA 62.360 66.667 15.62 0.00 0.00 3.97
380 383 9.559958 AATCGAATCGGAAAATAATAATGATGC 57.440 29.630 1.76 0.00 0.00 3.91
422 428 3.592898 ATTGAAAAATCGGTTCCTGCC 57.407 42.857 0.00 0.00 0.00 4.85
651 668 2.696125 GGGAGGCTTGGATGGGGA 60.696 66.667 0.00 0.00 0.00 4.81
730 747 0.611896 TCCTCAGGTGAGCGACATGA 60.612 55.000 0.00 6.19 43.02 3.07
861 881 3.314388 GAACGCTCGCTTGGCTTGG 62.314 63.158 0.00 0.00 0.00 3.61
862 882 2.174349 GAACGCTCGCTTGGCTTG 59.826 61.111 0.00 0.00 0.00 4.01
863 883 3.050275 GGAACGCTCGCTTGGCTT 61.050 61.111 0.00 0.00 0.00 4.35
1190 1225 1.064979 GGATCGAAAAAGGGGTAGGCA 60.065 52.381 0.00 0.00 0.00 4.75
1194 1229 4.921644 AAAGAGGATCGAAAAAGGGGTA 57.078 40.909 0.00 0.00 42.67 3.69
1195 1230 3.808834 AAAGAGGATCGAAAAAGGGGT 57.191 42.857 0.00 0.00 42.67 4.95
1197 1232 5.966742 AGAAAAAGAGGATCGAAAAAGGG 57.033 39.130 0.00 0.00 42.67 3.95
1199 1234 9.301153 TCAAAAAGAAAAAGAGGATCGAAAAAG 57.699 29.630 0.00 0.00 42.67 2.27
1200 1235 9.646427 TTCAAAAAGAAAAAGAGGATCGAAAAA 57.354 25.926 0.00 0.00 34.45 1.94
1201 1236 9.816354 ATTCAAAAAGAAAAAGAGGATCGAAAA 57.184 25.926 0.00 0.00 39.29 2.29
1290 1328 4.495844 GGGACAACTAAAATCGTGCATAGC 60.496 45.833 0.00 0.00 0.00 2.97
1291 1329 4.634004 TGGGACAACTAAAATCGTGCATAG 59.366 41.667 0.00 0.00 31.92 2.23
1369 1408 3.037549 ACAAAATTGGCAGTTCCTTCCA 58.962 40.909 0.00 0.00 35.26 3.53
1427 1466 6.507456 GCGTCGACACTAACAATAAATACCAG 60.507 42.308 17.16 0.00 0.00 4.00
1475 1514 3.684305 CACTATCAAACATCAGCGGTTGA 59.316 43.478 1.75 0.00 40.85 3.18
1480 1519 4.259970 GCAGTACACTATCAAACATCAGCG 60.260 45.833 0.00 0.00 0.00 5.18
1494 1534 2.638480 TGCCAAAAGAGCAGTACACT 57.362 45.000 0.00 0.00 34.69 3.55
1521 1564 6.748333 TTTCTGCTAGACGTTAGCTACTAA 57.252 37.500 21.86 12.56 40.95 2.24
1562 1605 9.677567 GCTTGTCTTGAAAACAATACATTCTAA 57.322 29.630 0.00 0.00 36.14 2.10
1564 1607 6.857964 CGCTTGTCTTGAAAACAATACATTCT 59.142 34.615 0.00 0.00 36.14 2.40
1565 1608 6.088085 CCGCTTGTCTTGAAAACAATACATTC 59.912 38.462 0.00 0.00 36.14 2.67
1566 1609 5.920273 CCGCTTGTCTTGAAAACAATACATT 59.080 36.000 0.00 0.00 36.14 2.71
1567 1610 5.460646 CCGCTTGTCTTGAAAACAATACAT 58.539 37.500 0.00 0.00 36.14 2.29
1568 1611 4.791411 GCCGCTTGTCTTGAAAACAATACA 60.791 41.667 0.00 0.00 36.14 2.29
1569 1612 3.668656 GCCGCTTGTCTTGAAAACAATAC 59.331 43.478 0.00 0.00 36.14 1.89
1570 1613 3.316588 TGCCGCTTGTCTTGAAAACAATA 59.683 39.130 0.00 0.00 36.14 1.90
1571 1614 2.100584 TGCCGCTTGTCTTGAAAACAAT 59.899 40.909 0.00 0.00 36.14 2.71
1572 1615 1.474478 TGCCGCTTGTCTTGAAAACAA 59.526 42.857 0.00 0.00 35.44 2.83
1573 1616 1.065401 CTGCCGCTTGTCTTGAAAACA 59.935 47.619 0.00 0.00 0.00 2.83
1574 1617 1.333619 TCTGCCGCTTGTCTTGAAAAC 59.666 47.619 0.00 0.00 0.00 2.43
1575 1618 1.674359 TCTGCCGCTTGTCTTGAAAA 58.326 45.000 0.00 0.00 0.00 2.29
1576 1619 1.536766 CATCTGCCGCTTGTCTTGAAA 59.463 47.619 0.00 0.00 0.00 2.69
1577 1620 1.159285 CATCTGCCGCTTGTCTTGAA 58.841 50.000 0.00 0.00 0.00 2.69
1578 1621 0.035317 ACATCTGCCGCTTGTCTTGA 59.965 50.000 0.00 0.00 0.00 3.02
1579 1622 0.445436 GACATCTGCCGCTTGTCTTG 59.555 55.000 11.87 0.00 37.40 3.02
1580 1623 1.016130 CGACATCTGCCGCTTGTCTT 61.016 55.000 15.12 0.00 38.06 3.01
1589 1632 3.046390 CTCTTACGATTCGACATCTGCC 58.954 50.000 13.95 0.00 0.00 4.85
1598 1641 8.507470 TGAATCATGATAACTCTTACGATTCG 57.493 34.615 9.04 4.14 40.07 3.34
1671 1714 1.068434 CCTGGCCAACACGAACATTTT 59.932 47.619 7.01 0.00 0.00 1.82
1680 1723 1.600916 GTCCTGACCTGGCCAACAC 60.601 63.158 7.01 0.87 0.00 3.32
1828 1872 8.603983 TTTTACAAGAAATGTCGTGTTACAAC 57.396 30.769 9.86 0.00 42.92 3.32
1856 1903 5.772521 ACACAGCAAAAATTTCGATTAGCT 58.227 33.333 0.00 0.00 0.00 3.32
1865 1913 7.768120 TCAAGGTTAATGACACAGCAAAAATTT 59.232 29.630 0.00 0.00 0.00 1.82
1868 1916 6.214191 TCAAGGTTAATGACACAGCAAAAA 57.786 33.333 0.00 0.00 0.00 1.94
1970 2018 9.778741 AACACAATGATACTTATCGGTATGAAT 57.221 29.630 0.00 0.00 35.48 2.57
2271 2319 5.236695 CAGCACCATCATGTCTTGATTCTAG 59.763 44.000 0.00 0.00 42.62 2.43
2429 2477 0.322456 TTCCATTGAAGACAGGGCCG 60.322 55.000 0.00 0.00 0.00 6.13
2437 2485 4.922206 AGTGCCATTAGTTCCATTGAAGA 58.078 39.130 0.00 0.00 0.00 2.87
2852 2900 0.470341 GGAACTATGGGAGACAGGCC 59.530 60.000 0.00 0.00 0.00 5.19
2947 2995 2.071778 AGCCAACATCACCAAGTGTT 57.928 45.000 0.00 0.00 39.00 3.32
2950 2998 5.435686 TCTTATAGCCAACATCACCAAGT 57.564 39.130 0.00 0.00 0.00 3.16
3193 3248 8.453320 GTCATTGTCTGAATAATTCACATGTGA 58.547 33.333 24.56 24.56 35.07 3.58
3208 3263 6.128661 CGGTCTTAAAATTCGTCATTGTCTGA 60.129 38.462 0.00 0.00 0.00 3.27
3211 3266 5.923665 ACGGTCTTAAAATTCGTCATTGTC 58.076 37.500 0.00 0.00 0.00 3.18
3237 3292 2.424956 GTCACGTCGGTTATTAGGTCCT 59.575 50.000 0.00 0.00 0.00 3.85
3298 3353 1.069204 GAATGGAGCAGCCGATACTCA 59.931 52.381 0.00 0.00 40.66 3.41
3307 3362 0.610232 ACAGGGTTGAATGGAGCAGC 60.610 55.000 0.00 0.00 0.00 5.25
3443 3511 5.652744 TCGCTACAAGAAAACAGAACTTC 57.347 39.130 0.00 0.00 0.00 3.01
3563 3632 6.334102 ACGTCCATCCATCTACTATCTTTC 57.666 41.667 0.00 0.00 0.00 2.62
3583 3777 3.443976 GCAAAGTTTTGTCATCCAACGT 58.556 40.909 6.48 0.00 40.24 3.99
3642 3836 8.856490 AATTGTAGAAAGACACATGTTTGAAC 57.144 30.769 0.00 0.00 0.00 3.18
3671 3865 1.731433 TTATTCGCGGACGGAGGGAG 61.731 60.000 6.13 0.00 40.63 4.30
3672 3866 1.731433 CTTATTCGCGGACGGAGGGA 61.731 60.000 6.13 0.00 40.63 4.20
3673 3867 1.299926 CTTATTCGCGGACGGAGGG 60.300 63.158 6.13 0.00 40.63 4.30
3674 3868 0.870307 CACTTATTCGCGGACGGAGG 60.870 60.000 6.13 0.00 40.63 4.30
3675 3869 0.179145 ACACTTATTCGCGGACGGAG 60.179 55.000 6.13 0.00 40.63 4.63
3676 3870 1.093972 TACACTTATTCGCGGACGGA 58.906 50.000 6.13 0.00 40.63 4.69
3677 3871 1.194495 GTACACTTATTCGCGGACGG 58.806 55.000 6.13 0.00 40.63 4.79
3678 3872 2.184385 AGTACACTTATTCGCGGACG 57.816 50.000 6.13 0.00 42.01 4.79
3679 3873 3.767278 AGAAGTACACTTATTCGCGGAC 58.233 45.455 6.13 0.00 36.11 4.79
3680 3874 4.497006 GCTAGAAGTACACTTATTCGCGGA 60.497 45.833 6.13 0.00 36.11 5.54
3681 3875 3.729716 GCTAGAAGTACACTTATTCGCGG 59.270 47.826 6.13 0.00 36.11 6.46
3682 3876 4.599047 AGCTAGAAGTACACTTATTCGCG 58.401 43.478 0.00 0.00 36.11 5.87
3683 3877 6.889019 AAAGCTAGAAGTACACTTATTCGC 57.111 37.500 0.00 0.00 36.11 4.70
3684 3878 8.240883 ACAAAAGCTAGAAGTACACTTATTCG 57.759 34.615 0.00 0.00 36.11 3.34
3685 3879 8.657729 GGACAAAAGCTAGAAGTACACTTATTC 58.342 37.037 0.00 0.00 36.11 1.75
3686 3880 8.376270 AGGACAAAAGCTAGAAGTACACTTATT 58.624 33.333 0.00 0.00 36.11 1.40
3687 3881 7.908453 AGGACAAAAGCTAGAAGTACACTTAT 58.092 34.615 0.00 0.00 36.11 1.73
3688 3882 7.299246 AGGACAAAAGCTAGAAGTACACTTA 57.701 36.000 0.00 0.00 36.11 2.24
3689 3883 6.176014 AGGACAAAAGCTAGAAGTACACTT 57.824 37.500 0.00 0.00 39.23 3.16
3690 3884 5.810080 AGGACAAAAGCTAGAAGTACACT 57.190 39.130 0.00 0.00 0.00 3.55
3691 3885 7.153315 ACTTAGGACAAAAGCTAGAAGTACAC 58.847 38.462 0.00 0.00 0.00 2.90
3692 3886 7.014905 TGACTTAGGACAAAAGCTAGAAGTACA 59.985 37.037 0.00 0.00 0.00 2.90
3693 3887 7.376615 TGACTTAGGACAAAAGCTAGAAGTAC 58.623 38.462 0.00 0.00 0.00 2.73
3694 3888 7.534723 TGACTTAGGACAAAAGCTAGAAGTA 57.465 36.000 0.00 0.00 0.00 2.24
3695 3889 6.420913 TGACTTAGGACAAAAGCTAGAAGT 57.579 37.500 0.00 0.00 0.00 3.01
3696 3890 7.442666 ACTTTGACTTAGGACAAAAGCTAGAAG 59.557 37.037 4.30 0.00 36.87 2.85
3697 3891 7.280356 ACTTTGACTTAGGACAAAAGCTAGAA 58.720 34.615 4.30 0.00 36.87 2.10
3698 3892 6.827727 ACTTTGACTTAGGACAAAAGCTAGA 58.172 36.000 4.30 0.00 36.87 2.43
3699 3893 7.497925 AACTTTGACTTAGGACAAAAGCTAG 57.502 36.000 4.30 0.00 36.87 3.42
3700 3894 7.875327 AAACTTTGACTTAGGACAAAAGCTA 57.125 32.000 4.30 0.00 36.87 3.32
3701 3895 6.775594 AAACTTTGACTTAGGACAAAAGCT 57.224 33.333 4.30 0.00 36.87 3.74
3702 3896 8.920509 TTAAAACTTTGACTTAGGACAAAAGC 57.079 30.769 4.30 0.00 36.87 3.51
3795 3989 9.950496 AGTATCACTAGATCTGTTTTGAAATGT 57.050 29.630 5.18 0.00 35.67 2.71
3818 4012 9.613428 AGCAGCATTTATGACACTAAATTAGTA 57.387 29.630 5.23 0.00 37.23 1.82
3819 4013 8.511604 AGCAGCATTTATGACACTAAATTAGT 57.488 30.769 0.00 0.00 40.28 2.24
3820 4014 9.869844 GTAGCAGCATTTATGACACTAAATTAG 57.130 33.333 0.00 0.00 30.68 1.73
3821 4015 9.613428 AGTAGCAGCATTTATGACACTAAATTA 57.387 29.630 0.00 0.00 30.68 1.40
3822 4016 8.511604 AGTAGCAGCATTTATGACACTAAATT 57.488 30.769 0.00 0.00 30.68 1.82
3823 4017 8.511604 AAGTAGCAGCATTTATGACACTAAAT 57.488 30.769 0.00 0.00 32.76 1.40
3824 4018 7.921786 AAGTAGCAGCATTTATGACACTAAA 57.078 32.000 0.00 0.00 0.00 1.85
3825 4019 7.921786 AAAGTAGCAGCATTTATGACACTAA 57.078 32.000 0.00 0.00 0.00 2.24
3826 4020 7.921786 AAAAGTAGCAGCATTTATGACACTA 57.078 32.000 0.00 0.00 0.00 2.74
3827 4021 6.824305 AAAAGTAGCAGCATTTATGACACT 57.176 33.333 0.00 0.00 0.00 3.55
3875 4069 9.788960 CTAGCTTTTGTCTTAAGTCAAAGTTTT 57.211 29.630 21.47 13.93 35.29 2.43
3876 4070 9.174166 TCTAGCTTTTGTCTTAAGTCAAAGTTT 57.826 29.630 21.47 15.16 35.29 2.66
3877 4071 8.732746 TCTAGCTTTTGTCTTAAGTCAAAGTT 57.267 30.769 21.47 17.02 35.29 2.66
3878 4072 8.732746 TTCTAGCTTTTGTCTTAAGTCAAAGT 57.267 30.769 21.47 15.13 35.29 2.66
3879 4073 8.831550 ACTTCTAGCTTTTGTCTTAAGTCAAAG 58.168 33.333 21.47 17.68 35.29 2.77
3880 4074 8.732746 ACTTCTAGCTTTTGTCTTAAGTCAAA 57.267 30.769 19.60 19.60 32.81 2.69
3881 4075 9.257651 GTACTTCTAGCTTTTGTCTTAAGTCAA 57.742 33.333 10.54 10.54 0.00 3.18
3882 4076 8.418662 TGTACTTCTAGCTTTTGTCTTAAGTCA 58.581 33.333 1.63 0.00 0.00 3.41
3883 4077 8.701540 GTGTACTTCTAGCTTTTGTCTTAAGTC 58.298 37.037 1.63 0.00 0.00 3.01
3884 4078 8.422566 AGTGTACTTCTAGCTTTTGTCTTAAGT 58.577 33.333 1.63 0.00 0.00 2.24
3885 4079 8.819643 AGTGTACTTCTAGCTTTTGTCTTAAG 57.180 34.615 0.00 0.00 0.00 1.85
3888 4082 9.780186 AATAAGTGTACTTCTAGCTTTTGTCTT 57.220 29.630 0.00 0.00 37.40 3.01
3889 4083 9.425577 GAATAAGTGTACTTCTAGCTTTTGTCT 57.574 33.333 0.00 0.00 37.40 3.41
3890 4084 8.373992 CGAATAAGTGTACTTCTAGCTTTTGTC 58.626 37.037 0.00 0.00 37.40 3.18
3891 4085 7.871463 ACGAATAAGTGTACTTCTAGCTTTTGT 59.129 33.333 0.00 0.00 37.40 2.83
3892 4086 8.162880 CACGAATAAGTGTACTTCTAGCTTTTG 58.837 37.037 0.00 0.00 37.40 2.44
3893 4087 7.331193 CCACGAATAAGTGTACTTCTAGCTTTT 59.669 37.037 0.00 0.00 40.33 2.27
3894 4088 6.812160 CCACGAATAAGTGTACTTCTAGCTTT 59.188 38.462 0.00 0.00 40.33 3.51
3895 4089 6.152323 TCCACGAATAAGTGTACTTCTAGCTT 59.848 38.462 0.00 0.00 40.33 3.74
3896 4090 5.651139 TCCACGAATAAGTGTACTTCTAGCT 59.349 40.000 0.00 0.00 40.33 3.32
3897 4091 5.742926 GTCCACGAATAAGTGTACTTCTAGC 59.257 44.000 0.00 0.00 40.33 3.42
3898 4092 5.964168 CGTCCACGAATAAGTGTACTTCTAG 59.036 44.000 0.00 0.00 43.02 2.43
3899 4093 5.163723 CCGTCCACGAATAAGTGTACTTCTA 60.164 44.000 0.00 0.00 43.02 2.10
3900 4094 4.380233 CCGTCCACGAATAAGTGTACTTCT 60.380 45.833 0.00 0.00 43.02 2.85
3901 4095 3.855950 CCGTCCACGAATAAGTGTACTTC 59.144 47.826 0.00 0.00 43.02 3.01
3902 4096 3.507233 TCCGTCCACGAATAAGTGTACTT 59.493 43.478 0.00 2.51 43.02 2.24
3903 4097 3.084039 TCCGTCCACGAATAAGTGTACT 58.916 45.455 0.00 0.00 43.02 2.73
3904 4098 3.432782 CTCCGTCCACGAATAAGTGTAC 58.567 50.000 0.00 0.00 43.02 2.90
3905 4099 2.424601 CCTCCGTCCACGAATAAGTGTA 59.575 50.000 0.00 0.00 43.02 2.90
3906 4100 1.203994 CCTCCGTCCACGAATAAGTGT 59.796 52.381 0.00 0.00 43.02 3.55
3907 4101 1.470979 CCCTCCGTCCACGAATAAGTG 60.471 57.143 0.00 0.00 43.02 3.16
3908 4102 0.822164 CCCTCCGTCCACGAATAAGT 59.178 55.000 0.00 0.00 43.02 2.24
3909 4103 1.067212 CTCCCTCCGTCCACGAATAAG 59.933 57.143 0.00 0.00 43.02 1.73
3910 4104 1.108776 CTCCCTCCGTCCACGAATAA 58.891 55.000 0.00 0.00 43.02 1.40
3911 4105 0.033796 ACTCCCTCCGTCCACGAATA 60.034 55.000 0.00 0.00 43.02 1.75
3912 4106 0.033796 TACTCCCTCCGTCCACGAAT 60.034 55.000 0.00 0.00 43.02 3.34
3913 4107 0.033796 ATACTCCCTCCGTCCACGAA 60.034 55.000 0.00 0.00 43.02 3.85
3914 4108 0.750546 CATACTCCCTCCGTCCACGA 60.751 60.000 0.00 0.00 43.02 4.35
3915 4109 1.035932 ACATACTCCCTCCGTCCACG 61.036 60.000 0.00 0.00 39.44 4.94
3916 4110 0.460311 CACATACTCCCTCCGTCCAC 59.540 60.000 0.00 0.00 0.00 4.02
3917 4111 1.327690 GCACATACTCCCTCCGTCCA 61.328 60.000 0.00 0.00 0.00 4.02
3918 4112 1.043673 AGCACATACTCCCTCCGTCC 61.044 60.000 0.00 0.00 0.00 4.79
3919 4113 1.688772 TAGCACATACTCCCTCCGTC 58.311 55.000 0.00 0.00 0.00 4.79
3920 4114 2.158445 AGATAGCACATACTCCCTCCGT 60.158 50.000 0.00 0.00 0.00 4.69
3921 4115 2.230025 CAGATAGCACATACTCCCTCCG 59.770 54.545 0.00 0.00 0.00 4.63
3922 4116 2.028567 GCAGATAGCACATACTCCCTCC 60.029 54.545 0.00 0.00 44.79 4.30
3923 4117 3.311486 GCAGATAGCACATACTCCCTC 57.689 52.381 0.00 0.00 44.79 4.30
3948 4142 7.740346 CACATTTCATGAAGTACGTAAGACAAC 59.260 37.037 8.41 0.00 43.62 3.32
3957 4151 7.755582 TCTATGTCACATTTCATGAAGTACG 57.244 36.000 8.41 0.72 0.00 3.67
3984 4178 1.273327 CCTGCCATTGAAAGGGAACAC 59.727 52.381 0.00 0.00 29.54 3.32
4866 5060 8.881743 CAGTTTCTCTTTGAGATCCATAAGAAG 58.118 37.037 0.00 0.00 38.56 2.85
4867 5061 8.597167 TCAGTTTCTCTTTGAGATCCATAAGAA 58.403 33.333 0.00 0.00 38.56 2.52
4868 5062 8.037758 GTCAGTTTCTCTTTGAGATCCATAAGA 58.962 37.037 0.00 0.00 38.56 2.10
5193 5390 7.285401 ACAGAAAAGACAAATGTGGTATTGAGT 59.715 33.333 0.00 0.00 0.00 3.41
5194 5391 7.651808 ACAGAAAAGACAAATGTGGTATTGAG 58.348 34.615 0.00 0.00 0.00 3.02
5282 5479 3.371965 TCTAAGGTGTCGCTCCCTATTT 58.628 45.455 0.00 0.00 0.00 1.40
5616 5820 6.605471 TCTGTTACTATCAGGTGTGTTCAT 57.395 37.500 0.00 0.00 34.15 2.57
6055 6259 8.961294 AAGAATTGAGAAGATTCAAAACATCG 57.039 30.769 0.00 0.00 40.21 3.84
6187 6397 0.601841 ACCCTAAAACGACACCAGCG 60.602 55.000 0.00 0.00 0.00 5.18
6191 6401 2.460757 TAGCACCCTAAAACGACACC 57.539 50.000 0.00 0.00 0.00 4.16
6228 6439 4.094442 CCTATGACCTTTACTTCCAAACGC 59.906 45.833 0.00 0.00 0.00 4.84
6242 6453 0.921896 ATGCCAACAGCCTATGACCT 59.078 50.000 0.00 0.00 42.71 3.85
6419 6630 6.946009 CCTTTCATCCTTTCCTTGGTAAACTA 59.054 38.462 0.00 0.00 0.00 2.24
6461 6672 2.472909 GGGCTTCCATACACGCAGC 61.473 63.158 0.00 0.00 0.00 5.25
6666 6877 7.435192 TGAGTATCGACAGCACAACATAATTAG 59.565 37.037 0.00 0.00 38.61 1.73
6708 6919 5.897050 AGACTTCATCAGGAACTAATCGTC 58.103 41.667 0.00 0.00 36.02 4.20
6724 6935 9.515226 AATAATTTACCAGCAACTTAGACTTCA 57.485 29.630 0.00 0.00 0.00 3.02
6906 7130 7.614494 ACATGGGTATTTTCAGAATCTTTTGG 58.386 34.615 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.