Multiple sequence alignment - TraesCS1A01G332600

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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 TraesCS1A01G332600 chr1A 100.000 4786 0 0 1 4786 520937227 520942012 0.000000e+00 8839
1 TraesCS1A01G332600 chr1A 81.765 170 26 5 4436 4602 97157431 97157264 2.320000e-28 137
2 TraesCS1A01G332600 chr1A 100.000 64 0 0 1 64 405459861 405459924 8.410000e-23 119
3 TraesCS1A01G332600 chr1A 95.775 71 2 1 1 71 306705037 306705106 3.910000e-21 113
4 TraesCS1A01G332600 chr1A 95.775 71 2 1 1 71 344291098 344291029 3.910000e-21 113
5 TraesCS1A01G332600 chr1B 90.256 3982 222 78 627 4531 575439649 575443541 0.000000e+00 5051
6 TraesCS1A01G332600 chr1B 91.375 371 16 7 60 414 575438037 575438407 1.200000e-135 494
7 TraesCS1A01G332600 chr1B 85.938 128 14 3 4659 4783 575443908 575444034 3.000000e-27 134
8 TraesCS1A01G332600 chr1D 93.223 2169 92 20 2264 4413 425299717 425301849 0.000000e+00 3140
9 TraesCS1A01G332600 chr1D 87.410 1525 106 40 779 2239 425298223 425299725 0.000000e+00 1674
10 TraesCS1A01G332600 chr1D 90.244 328 25 6 60 382 425296820 425297145 5.730000e-114 422
11 TraesCS1A01G332600 chr1D 85.818 275 25 4 415 688 425297287 425297548 3.650000e-71 279
12 TraesCS1A01G332600 chr1D 88.889 171 13 5 4622 4786 425301865 425302035 6.280000e-49 206
13 TraesCS1A01G332600 chr1D 91.262 103 2 2 764 859 425298120 425298222 3.000000e-27 134
14 TraesCS1A01G332600 chr2A 94.444 486 19 4 2341 2820 746931081 746930598 0.000000e+00 741
15 TraesCS1A01G332600 chr2A 89.171 591 44 13 4048 4622 746927445 746926859 0.000000e+00 719
16 TraesCS1A01G332600 chr2A 96.751 277 7 1 2842 3118 746927718 746927444 1.210000e-125 460
17 TraesCS1A01G332600 chr2A 94.161 137 5 3 4653 4786 746926744 746926608 6.280000e-49 206
18 TraesCS1A01G332600 chr2A 81.765 170 26 5 4436 4602 22594708 22594875 2.320000e-28 137
19 TraesCS1A01G332600 chr2A 95.775 71 2 1 2 72 158065681 158065750 3.910000e-21 113
20 TraesCS1A01G332600 chr3A 90.031 321 27 5 4303 4622 11635106 11635422 1.240000e-110 411
21 TraesCS1A01G332600 chr3A 86.780 295 36 2 2254 2545 536896501 536896795 4.620000e-85 326
22 TraesCS1A01G332600 chr3A 91.566 166 10 2 4622 4783 11635783 11635948 4.820000e-55 226
23 TraesCS1A01G332600 chr3A 82.840 169 25 4 4436 4602 136523130 136522964 1.070000e-31 148
24 TraesCS1A01G332600 chr3D 86.913 298 36 2 2254 2548 413677201 413676904 9.930000e-87 331
25 TraesCS1A01G332600 chr3D 82.803 157 24 3 4443 4599 157359455 157359608 2.320000e-28 137
26 TraesCS1A01G332600 chr3B 86.913 298 36 2 2254 2548 539943428 539943131 9.930000e-87 331
27 TraesCS1A01G332600 chr2D 95.050 101 4 1 2189 2289 532435019 532435118 1.780000e-34 158
28 TraesCS1A01G332600 chr5A 80.723 166 28 4 4439 4602 383833801 383833964 5.030000e-25 126
29 TraesCS1A01G332600 chr4A 98.551 69 1 0 1 69 585664281 585664213 6.500000e-24 122
30 TraesCS1A01G332600 chr4A 97.101 69 2 0 1 69 171217337 171217269 3.030000e-22 117
31 TraesCS1A01G332600 chr4A 94.595 74 2 1 1 74 329073539 329073468 3.910000e-21 113
32 TraesCS1A01G332600 chr4A 92.500 80 3 3 1 78 170275818 170275896 1.410000e-20 111
33 TraesCS1A01G332600 chrUn 100.000 64 0 0 1 64 38015031 38014968 8.410000e-23 119


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 TraesCS1A01G332600 chr1A 520937227 520942012 4785 False 8839.000000 8839 100.000000 1 4786 1 chr1A.!!$F3 4785
1 TraesCS1A01G332600 chr1B 575438037 575444034 5997 False 1893.000000 5051 89.189667 60 4783 3 chr1B.!!$F1 4723
2 TraesCS1A01G332600 chr1D 425296820 425302035 5215 False 975.833333 3140 89.474333 60 4786 6 chr1D.!!$F1 4726
3 TraesCS1A01G332600 chr2A 746926608 746931081 4473 True 531.500000 741 93.631750 2341 4786 4 chr2A.!!$R1 2445
4 TraesCS1A01G332600 chr3A 11635106 11635948 842 False 318.500000 411 90.798500 4303 4783 2 chr3A.!!$F2 480

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
53 54 1.695242 TGCAGAGTAAAAAGGACCGGA 59.305 47.619 9.46 0.00 0.00 5.14 F
1017 2737 0.102481 AATGGAGTAGCACGTAGGCG 59.898 55.000 0.00 0.00 44.93 5.52 F
1539 3286 0.323360 TAATCAGCCAGGGTTGCACC 60.323 55.000 0.00 0.00 37.60 5.01 F
1728 3498 0.325296 ATGAGTGTAAGCGAGGGGGA 60.325 55.000 0.00 0.00 0.00 4.81 F
1797 3569 0.391927 TCCTTAATTGACACCGGCCG 60.392 55.000 21.04 21.04 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1163 2893 0.179006 GCTAGCTGGATGGGAAAGGG 60.179 60.000 7.70 0.00 0.00 3.95 R
2018 3793 0.321122 CTGAGCCACTGAGGAACACC 60.321 60.000 0.00 0.00 41.22 4.16 R
3298 7957 0.595588 AACGAATTGCATTGCACGGA 59.404 45.000 19.92 4.75 38.71 4.69 R
3300 7959 1.407434 ACAACGAATTGCATTGCACG 58.593 45.000 11.66 14.22 38.71 5.34 R
3790 8460 1.564818 TCCCGTTTATATTGGGTGGCA 59.435 47.619 4.81 0.00 43.75 4.92 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
35 36 9.928236 GTTTGACTTCAGAGAATTCTAATATGC 57.072 33.333 8.25 0.00 30.73 3.14
36 37 9.671279 TTTGACTTCAGAGAATTCTAATATGCA 57.329 29.630 8.25 0.00 30.73 3.96
37 38 8.883954 TGACTTCAGAGAATTCTAATATGCAG 57.116 34.615 8.25 7.58 30.73 4.41
38 39 8.699130 TGACTTCAGAGAATTCTAATATGCAGA 58.301 33.333 8.25 0.00 30.73 4.26
39 40 9.195411 GACTTCAGAGAATTCTAATATGCAGAG 57.805 37.037 8.25 6.79 30.73 3.35
40 41 8.703743 ACTTCAGAGAATTCTAATATGCAGAGT 58.296 33.333 8.25 7.29 30.73 3.24
50 51 8.732746 TTCTAATATGCAGAGTAAAAAGGACC 57.267 34.615 0.00 0.00 0.00 4.46
51 52 6.984474 TCTAATATGCAGAGTAAAAAGGACCG 59.016 38.462 0.00 0.00 0.00 4.79
52 53 2.178912 TGCAGAGTAAAAAGGACCGG 57.821 50.000 0.00 0.00 0.00 5.28
53 54 1.695242 TGCAGAGTAAAAAGGACCGGA 59.305 47.619 9.46 0.00 0.00 5.14
54 55 2.289444 TGCAGAGTAAAAAGGACCGGAG 60.289 50.000 9.46 0.00 0.00 4.63
122 123 3.507162 TGGGTGCTGATCAAAAGAAGA 57.493 42.857 0.00 0.00 0.00 2.87
184 185 4.022329 GTGGTGGAGGATTTGTAAAGGTTG 60.022 45.833 0.00 0.00 0.00 3.77
208 209 7.754624 TGTATGTATGTTGGTGATATTGGGAT 58.245 34.615 0.00 0.00 0.00 3.85
295 322 5.407407 ACTAACACAGTCTCATAACCTGG 57.593 43.478 0.00 0.00 28.33 4.45
297 324 1.909302 ACACAGTCTCATAACCTGGGG 59.091 52.381 0.00 0.00 33.87 4.96
382 425 5.369699 AGGGTATGCTGTAAATCAGTGGTAT 59.630 40.000 0.00 0.00 45.23 2.73
386 429 4.191544 TGCTGTAAATCAGTGGTATCTGC 58.808 43.478 0.00 0.00 45.23 4.26
396 490 2.546494 GGTATCTGCATGTGCGGCC 61.546 63.158 8.93 0.00 46.62 6.13
400 494 2.867793 ATCTGCATGTGCGGCCGTAA 62.868 55.000 28.70 13.31 46.62 3.18
437 591 8.859517 TTAAAATAACTTGGTTCAAAGTTCGG 57.140 30.769 8.38 0.00 45.10 4.30
449 603 6.338937 GTTCAAAGTTCGGACACTATCCTAT 58.661 40.000 0.00 0.00 46.69 2.57
461 616 7.254455 CGGACACTATCCTATGCAAAGTAAAAG 60.254 40.741 0.00 0.00 46.69 2.27
464 619 9.379791 ACACTATCCTATGCAAAGTAAAAGTAC 57.620 33.333 0.00 0.00 0.00 2.73
521 677 6.421801 CCTTTCCAGTAATTGCTCAACAAAAG 59.578 38.462 0.00 0.56 42.86 2.27
536 692 8.006027 GCTCAACAAAAGCATTAAACAATCTTC 58.994 33.333 0.00 0.00 39.61 2.87
636 792 3.950078 GCATCTTGCAGTCTTATTGAGC 58.050 45.455 0.00 0.00 44.26 4.26
667 1793 4.578928 ACTGTTGTGTTAACCCTAGCTTTG 59.421 41.667 2.48 0.00 0.00 2.77
726 2091 4.948621 AGCTAGTACGGAGTAGTTGTCAAT 59.051 41.667 11.21 0.00 45.54 2.57
728 2093 5.515626 GCTAGTACGGAGTAGTTGTCAATTG 59.484 44.000 11.21 0.00 45.54 2.32
730 2095 6.282199 AGTACGGAGTAGTTGTCAATTGAT 57.718 37.500 12.12 0.00 45.54 2.57
749 2114 2.122783 TTAAGCTGGTGGCGCTTTAT 57.877 45.000 7.64 0.00 44.76 1.40
889 2603 7.148440 CCGGTCTAGCATTGACTACTATACTAC 60.148 44.444 0.00 0.00 35.04 2.73
890 2604 7.603404 CGGTCTAGCATTGACTACTATACTACT 59.397 40.741 0.00 0.00 35.04 2.57
935 2654 2.106683 ACCGAGCTTTACCATGCGC 61.107 57.895 0.00 0.00 0.00 6.09
976 2695 3.106827 TCACAGTGAATATCTCTGCCCA 58.893 45.455 0.00 0.00 40.54 5.36
1016 2736 1.854227 GAATGGAGTAGCACGTAGGC 58.146 55.000 0.00 0.00 0.00 3.93
1017 2737 0.102481 AATGGAGTAGCACGTAGGCG 59.898 55.000 0.00 0.00 44.93 5.52
1080 2800 3.349927 TGCTCATCATTTAGTTGCTGCT 58.650 40.909 0.00 0.00 0.00 4.24
1135 2855 4.135153 CGAGCGACCTCCCAGTGG 62.135 72.222 0.63 0.63 34.49 4.00
1147 2877 2.042464 TCCCAGTGGAGCTATCATCAC 58.958 52.381 11.95 0.00 35.03 3.06
1177 2907 0.624500 TCCCTCCCTTTCCCATCCAG 60.625 60.000 0.00 0.00 0.00 3.86
1178 2908 1.228510 CCTCCCTTTCCCATCCAGC 59.771 63.158 0.00 0.00 0.00 4.85
1179 2909 1.284841 CCTCCCTTTCCCATCCAGCT 61.285 60.000 0.00 0.00 0.00 4.24
1180 2910 1.511613 CTCCCTTTCCCATCCAGCTA 58.488 55.000 0.00 0.00 0.00 3.32
1181 2911 1.419387 CTCCCTTTCCCATCCAGCTAG 59.581 57.143 0.00 0.00 0.00 3.42
1210 2940 4.625972 TTACACGCAGATTATCAGTCGA 57.374 40.909 7.94 0.00 0.00 4.20
1214 2944 1.268589 CGCAGATTATCAGTCGACGGT 60.269 52.381 15.37 6.97 0.00 4.83
1217 2947 1.602851 AGATTATCAGTCGACGGTCGG 59.397 52.381 28.07 13.94 40.88 4.79
1365 3101 1.604693 CGCCTCGCCCTATTAATTCGT 60.605 52.381 0.00 0.00 0.00 3.85
1374 3115 4.619863 GCCCTATTAATTCGTGGCGATCTA 60.620 45.833 0.00 0.00 35.23 1.98
1391 3132 2.303549 CTACGGGGAGAAGCTGGCTG 62.304 65.000 0.00 0.00 0.00 4.85
1451 3192 5.861787 GCGTTTATAATTGCTTTCTTGGTGT 59.138 36.000 3.00 0.00 0.00 4.16
1452 3193 7.024768 GCGTTTATAATTGCTTTCTTGGTGTA 58.975 34.615 3.00 0.00 0.00 2.90
1460 3201 3.244526 TGCTTTCTTGGTGTAGATCTGCA 60.245 43.478 9.69 9.69 0.00 4.41
1472 3213 3.465990 ATCTGCACAGATTCCGTGG 57.534 52.632 7.34 0.00 45.31 4.94
1477 3218 1.234821 GCACAGATTCCGTGGTTTCA 58.765 50.000 2.38 0.00 34.85 2.69
1478 3219 1.197721 GCACAGATTCCGTGGTTTCAG 59.802 52.381 2.38 0.00 34.85 3.02
1479 3220 2.494059 CACAGATTCCGTGGTTTCAGT 58.506 47.619 0.00 0.00 0.00 3.41
1505 3246 3.753294 TTTCGAGCTCCTTCTTGAGTT 57.247 42.857 8.47 0.00 34.74 3.01
1516 3257 4.399618 TCCTTCTTGAGTTGTAGATCCTCG 59.600 45.833 0.00 0.00 0.00 4.63
1524 3265 6.982852 TGAGTTGTAGATCCTCGGATTAATC 58.017 40.000 6.93 6.93 34.60 1.75
1528 3269 3.971245 AGATCCTCGGATTAATCAGCC 57.029 47.619 17.07 0.00 34.60 4.85
1539 3286 0.323360 TAATCAGCCAGGGTTGCACC 60.323 55.000 0.00 0.00 37.60 5.01
1555 3302 0.475906 CACCTGGAATCCTGGATCCC 59.524 60.000 28.69 7.44 44.09 3.85
1568 3315 1.421268 TGGATCCCCATGGAAATCTCG 59.579 52.381 15.22 0.00 45.98 4.04
1584 3331 0.595588 CTCGGATGGTCTCGATCTGG 59.404 60.000 0.00 0.00 34.77 3.86
1587 3334 1.269309 CGGATGGTCTCGATCTGGTTC 60.269 57.143 0.00 0.00 0.00 3.62
1591 3338 2.739943 TGGTCTCGATCTGGTTCTGAT 58.260 47.619 0.00 0.00 0.00 2.90
1596 3343 2.100418 CTCGATCTGGTTCTGATGCTCA 59.900 50.000 0.00 0.00 0.00 4.26
1597 3344 2.697229 TCGATCTGGTTCTGATGCTCAT 59.303 45.455 0.00 0.00 0.00 2.90
1598 3345 3.058450 CGATCTGGTTCTGATGCTCATC 58.942 50.000 3.03 3.03 38.29 2.92
1599 3346 2.996249 TCTGGTTCTGATGCTCATCC 57.004 50.000 7.34 0.00 37.02 3.51
1600 3347 1.487976 TCTGGTTCTGATGCTCATCCC 59.512 52.381 7.34 2.48 37.02 3.85
1601 3348 1.211212 CTGGTTCTGATGCTCATCCCA 59.789 52.381 7.34 6.45 37.02 4.37
1603 3350 2.228059 GGTTCTGATGCTCATCCCATG 58.772 52.381 7.34 0.00 37.02 3.66
1604 3351 2.228059 GTTCTGATGCTCATCCCATGG 58.772 52.381 4.14 4.14 37.02 3.66
1609 3363 3.025978 TGATGCTCATCCCATGGTTTTC 58.974 45.455 11.73 0.00 37.02 2.29
1634 3389 3.588210 TTTTTCCCTTTTCCCTCTCGT 57.412 42.857 0.00 0.00 0.00 4.18
1635 3390 2.853235 TTTCCCTTTTCCCTCTCGTC 57.147 50.000 0.00 0.00 0.00 4.20
1646 3416 1.540267 CCTCTCGTCTCCTGTCACTT 58.460 55.000 0.00 0.00 0.00 3.16
1653 3423 3.887110 TCGTCTCCTGTCACTTTTCACTA 59.113 43.478 0.00 0.00 0.00 2.74
1668 3438 3.111853 TCACTAGCTATTTCCGGCATG 57.888 47.619 0.00 0.00 0.00 4.06
1670 3440 1.768870 ACTAGCTATTTCCGGCATGGT 59.231 47.619 0.00 0.00 39.52 3.55
1671 3441 2.969950 ACTAGCTATTTCCGGCATGGTA 59.030 45.455 0.00 0.00 39.52 3.25
1672 3442 3.583086 ACTAGCTATTTCCGGCATGGTAT 59.417 43.478 0.00 0.00 39.52 2.73
1677 3447 2.208132 TTTCCGGCATGGTATGTTGT 57.792 45.000 0.00 0.00 39.52 3.32
1683 3453 4.097135 TCCGGCATGGTATGTTGTTAATTG 59.903 41.667 0.00 0.00 39.52 2.32
1690 3460 7.148154 GCATGGTATGTTGTTAATTGTCTACCA 60.148 37.037 9.98 9.98 40.98 3.25
1692 3462 7.681679 TGGTATGTTGTTAATTGTCTACCAGA 58.318 34.615 0.00 0.00 34.09 3.86
1725 3495 4.124851 ACTAAATGAGTGTAAGCGAGGG 57.875 45.455 0.00 0.00 36.87 4.30
1727 3497 0.541863 AATGAGTGTAAGCGAGGGGG 59.458 55.000 0.00 0.00 0.00 5.40
1728 3498 0.325296 ATGAGTGTAAGCGAGGGGGA 60.325 55.000 0.00 0.00 0.00 4.81
1729 3499 0.325296 TGAGTGTAAGCGAGGGGGAT 60.325 55.000 0.00 0.00 0.00 3.85
1731 3501 0.617820 AGTGTAAGCGAGGGGGATGT 60.618 55.000 0.00 0.00 0.00 3.06
1738 3509 2.249139 AGCGAGGGGGATGTAGTAATC 58.751 52.381 0.00 0.00 0.00 1.75
1794 3566 8.391075 ACATATATTTCCTTAATTGACACCGG 57.609 34.615 0.00 0.00 0.00 5.28
1795 3567 5.767816 ATATTTCCTTAATTGACACCGGC 57.232 39.130 0.00 0.00 0.00 6.13
1796 3568 1.828979 TTCCTTAATTGACACCGGCC 58.171 50.000 0.00 0.00 0.00 6.13
1797 3569 0.391927 TCCTTAATTGACACCGGCCG 60.392 55.000 21.04 21.04 0.00 6.13
1816 3588 2.143122 CGGCAAGCTCACTAAACTCAA 58.857 47.619 0.00 0.00 0.00 3.02
1820 3592 4.216257 GGCAAGCTCACTAAACTCAATCAA 59.784 41.667 0.00 0.00 0.00 2.57
1838 3610 2.153645 CAATTAGTGCAGGTGTGAGCA 58.846 47.619 0.00 0.00 38.65 4.26
1851 3623 1.065998 TGTGAGCATGTGATAGCAGCA 60.066 47.619 0.00 0.00 0.00 4.41
1860 3632 3.930336 TGTGATAGCAGCATATGTAGGC 58.070 45.455 4.29 5.98 0.00 3.93
1873 3645 5.651139 GCATATGTAGGCTCATTCATCCATT 59.349 40.000 4.29 0.00 0.00 3.16
1875 3647 7.012138 GCATATGTAGGCTCATTCATCCATTAG 59.988 40.741 4.29 0.00 0.00 1.73
1876 3648 4.645535 TGTAGGCTCATTCATCCATTAGC 58.354 43.478 0.00 0.00 0.00 3.09
1877 3649 4.349048 TGTAGGCTCATTCATCCATTAGCT 59.651 41.667 0.00 0.00 0.00 3.32
1879 3651 3.393609 AGGCTCATTCATCCATTAGCTCA 59.606 43.478 0.00 0.00 0.00 4.26
1880 3652 3.501445 GGCTCATTCATCCATTAGCTCAC 59.499 47.826 0.00 0.00 0.00 3.51
1881 3653 4.387598 GCTCATTCATCCATTAGCTCACT 58.612 43.478 0.00 0.00 0.00 3.41
1882 3654 5.512060 GGCTCATTCATCCATTAGCTCACTA 60.512 44.000 0.00 0.00 0.00 2.74
1884 3656 6.484643 GCTCATTCATCCATTAGCTCACTAAA 59.515 38.462 0.00 0.00 41.62 1.85
1885 3657 7.519649 GCTCATTCATCCATTAGCTCACTAAAC 60.520 40.741 0.00 0.00 41.62 2.01
1886 3658 7.568349 TCATTCATCCATTAGCTCACTAAACT 58.432 34.615 0.00 0.00 41.62 2.66
2018 3793 0.804364 TGTGGCGAATAAAGCTGCAG 59.196 50.000 10.11 10.11 34.52 4.41
2174 3968 2.169789 GTGCATGCGACGATGAGCT 61.170 57.895 14.09 0.00 0.00 4.09
2853 7511 1.597797 ATGGCGGCAACAATGTCCAG 61.598 55.000 18.31 0.00 0.00 3.86
3236 7894 7.341805 AGGTAAGTCATGCTGTGATTTAAGAT 58.658 34.615 8.43 0.00 39.70 2.40
3245 7903 8.886719 CATGCTGTGATTTAAGATTACTTGAGA 58.113 33.333 0.00 0.00 37.53 3.27
3264 7922 4.658901 TGAGAGGGGATTATTTGGGAGTAC 59.341 45.833 0.00 0.00 0.00 2.73
3298 7957 3.295973 TCAAGTTAAGGTTTTGCAGCCT 58.704 40.909 1.32 1.32 36.51 4.58
3300 7959 2.239400 AGTTAAGGTTTTGCAGCCTCC 58.761 47.619 6.96 0.09 33.24 4.30
3319 7978 1.407434 CGTGCAATGCAATTCGTTGT 58.593 45.000 10.44 0.00 41.47 3.32
3407 8069 2.027745 TGCTTGGGAGTCTCTGCTTAAG 60.028 50.000 0.00 0.00 0.00 1.85
3415 8078 2.094442 AGTCTCTGCTTAAGAAGTCGGC 60.094 50.000 10.41 4.90 33.37 5.54
3446 8109 9.739276 TCTTGTGAGTTTTGTATCTCCATTAAT 57.261 29.630 0.00 0.00 0.00 1.40
3447 8110 9.994432 CTTGTGAGTTTTGTATCTCCATTAATC 57.006 33.333 0.00 0.00 0.00 1.75
3448 8111 9.513906 TTGTGAGTTTTGTATCTCCATTAATCA 57.486 29.630 0.00 0.00 0.00 2.57
3502 8166 3.633525 TGCAACTCTTTCATGTTCTTGCT 59.366 39.130 0.00 0.00 0.00 3.91
3537 8201 6.522625 TGTTGTTGGGGTTATACATGATTG 57.477 37.500 0.00 0.00 0.00 2.67
3580 8246 6.826231 TGTATGACTCTTTCACAAGGACAAAA 59.174 34.615 0.00 0.00 36.92 2.44
3790 8460 4.574674 TGAAAGCATGGTTCACTCCTAT 57.425 40.909 11.16 0.00 30.08 2.57
3812 8482 2.578786 CCACCCAATATAAACGGGACC 58.421 52.381 10.61 0.00 43.21 4.46
3876 8550 1.681780 CCACAGTTGGGACACACACTT 60.682 52.381 0.00 0.00 39.29 3.16
3944 8618 8.996024 TTTAAAATTGTAGCTGAATAAAGGCC 57.004 30.769 0.00 0.00 0.00 5.19
3952 8626 5.695851 AGCTGAATAAAGGCCATAATTCG 57.304 39.130 5.01 8.14 32.23 3.34
3974 8648 8.880878 TTCGTATAAGCAATTAAGCATAGTGA 57.119 30.769 0.00 0.00 36.85 3.41
4026 8705 6.500041 GCAAATTGCATGATTTAATTGGCAT 58.500 32.000 13.73 0.00 44.26 4.40
4043 8722 3.577848 TGGCATGCCAATTTTACTGAACT 59.422 39.130 36.95 0.00 44.12 3.01
4061 8740 6.209391 ACTGAACTTTTTGCCTATACAATGCT 59.791 34.615 0.00 0.00 0.00 3.79
4062 8741 6.991938 TGAACTTTTTGCCTATACAATGCTT 58.008 32.000 0.00 0.00 0.00 3.91
4063 8742 7.441017 TGAACTTTTTGCCTATACAATGCTTT 58.559 30.769 0.00 0.00 0.00 3.51
4064 8743 7.930865 TGAACTTTTTGCCTATACAATGCTTTT 59.069 29.630 0.00 0.00 0.00 2.27
4065 8744 8.675705 AACTTTTTGCCTATACAATGCTTTTT 57.324 26.923 0.00 0.00 0.00 1.94
4082 8761 2.201921 TTTTTGCGGGTGCCTATACA 57.798 45.000 0.00 0.00 41.78 2.29
4083 8762 2.201921 TTTTGCGGGTGCCTATACAA 57.798 45.000 0.00 0.00 41.78 2.41
4084 8763 2.428544 TTTGCGGGTGCCTATACAAT 57.571 45.000 0.00 0.00 41.78 2.71
4085 8764 1.674359 TTGCGGGTGCCTATACAATG 58.326 50.000 0.00 0.00 41.78 2.82
4086 8765 0.833949 TGCGGGTGCCTATACAATGA 59.166 50.000 0.00 0.00 41.78 2.57
4097 8776 5.359576 TGCCTATACAATGATTGTTTGACCC 59.640 40.000 16.75 2.46 42.22 4.46
4124 8803 5.376854 AGATGTTACAAAGTGCACAATCC 57.623 39.130 21.04 0.32 0.00 3.01
4134 8813 6.153340 ACAAAGTGCACAATCCATTATTAGCT 59.847 34.615 21.04 0.00 32.07 3.32
4135 8814 7.339212 ACAAAGTGCACAATCCATTATTAGCTA 59.661 33.333 21.04 0.00 32.07 3.32
4193 8872 1.790623 CGAGGTAAAACAGTGTCACCG 59.209 52.381 13.20 0.00 34.36 4.94
4199 8878 4.035909 GGTAAAACAGTGTCACCGATGTTT 59.964 41.667 13.32 13.32 45.21 2.83
4205 8884 6.385649 ACAGTGTCACCGATGTTTAAAAAT 57.614 33.333 0.00 0.00 0.00 1.82
4206 8885 7.499321 ACAGTGTCACCGATGTTTAAAAATA 57.501 32.000 0.00 0.00 0.00 1.40
4207 8886 8.106247 ACAGTGTCACCGATGTTTAAAAATAT 57.894 30.769 0.00 0.00 0.00 1.28
4356 9093 8.514136 TTGATTTTAATCGGTGCTTTAACAAG 57.486 30.769 0.00 0.00 38.26 3.16
4409 9146 6.518208 TCGTTTTTAATTGGTTCCCCATAG 57.482 37.500 0.00 0.00 41.49 2.23
4472 9209 3.103080 TGGTCCCTCTTACCTTCTCTC 57.897 52.381 0.00 0.00 37.91 3.20
4493 9230 4.906618 TCTTTCACATGGGAGGTAAGAAC 58.093 43.478 7.91 0.00 0.00 3.01
4500 9237 5.646360 CACATGGGAGGTAAGAACGTAAAAT 59.354 40.000 0.00 0.00 0.00 1.82
4504 9241 7.910441 TGGGAGGTAAGAACGTAAAATTTAG 57.090 36.000 0.00 0.00 0.00 1.85
4553 9290 5.548406 ACGGCCCAAATCTGTTATATACTC 58.452 41.667 0.00 0.00 0.00 2.59
4575 9312 7.963532 ACTCTTACCTCTTATGTGAAAACAGA 58.036 34.615 0.00 0.00 0.00 3.41
4583 9320 7.361286 CCTCTTATGTGAAAACAGAAGGTAAGC 60.361 40.741 11.94 0.00 38.88 3.09
4588 9325 3.244770 TGAAAACAGAAGGTAAGCGGGAT 60.245 43.478 0.00 0.00 0.00 3.85
4629 9740 5.009010 CCAAAATGGATGCTATACTGGTCAC 59.991 44.000 0.00 0.00 40.96 3.67
4642 9753 9.032420 GCTATACTGGTCACTAAAACAAGATAC 57.968 37.037 0.00 0.00 0.00 2.24
4783 9902 8.186821 TGCAAAAAGGAAAACACCATTTATTTG 58.813 29.630 0.00 0.00 31.88 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.928236 GCATATTAGAATTCTCTGAAGTCAAAC 57.072 33.333 12.24 0.00 32.70 2.93
10 11 9.671279 TGCATATTAGAATTCTCTGAAGTCAAA 57.329 29.630 12.24 0.00 32.70 2.69
11 12 9.322773 CTGCATATTAGAATTCTCTGAAGTCAA 57.677 33.333 12.24 0.00 32.70 3.18
12 13 8.699130 TCTGCATATTAGAATTCTCTGAAGTCA 58.301 33.333 12.24 3.02 32.70 3.41
13 14 9.195411 CTCTGCATATTAGAATTCTCTGAAGTC 57.805 37.037 12.24 0.25 32.70 3.01
14 15 8.703743 ACTCTGCATATTAGAATTCTCTGAAGT 58.296 33.333 12.24 7.56 32.70 3.01
24 25 9.343539 GGTCCTTTTTACTCTGCATATTAGAAT 57.656 33.333 0.00 0.00 0.00 2.40
25 26 7.494625 CGGTCCTTTTTACTCTGCATATTAGAA 59.505 37.037 0.00 0.00 0.00 2.10
26 27 6.984474 CGGTCCTTTTTACTCTGCATATTAGA 59.016 38.462 0.00 0.00 0.00 2.10
27 28 6.202954 CCGGTCCTTTTTACTCTGCATATTAG 59.797 42.308 0.00 0.00 0.00 1.73
28 29 6.053005 CCGGTCCTTTTTACTCTGCATATTA 58.947 40.000 0.00 0.00 0.00 0.98
29 30 4.881850 CCGGTCCTTTTTACTCTGCATATT 59.118 41.667 0.00 0.00 0.00 1.28
30 31 4.163458 TCCGGTCCTTTTTACTCTGCATAT 59.837 41.667 0.00 0.00 0.00 1.78
31 32 3.516300 TCCGGTCCTTTTTACTCTGCATA 59.484 43.478 0.00 0.00 0.00 3.14
32 33 2.304761 TCCGGTCCTTTTTACTCTGCAT 59.695 45.455 0.00 0.00 0.00 3.96
33 34 1.695242 TCCGGTCCTTTTTACTCTGCA 59.305 47.619 0.00 0.00 0.00 4.41
34 35 2.347731 CTCCGGTCCTTTTTACTCTGC 58.652 52.381 0.00 0.00 0.00 4.26
35 36 2.354805 CCCTCCGGTCCTTTTTACTCTG 60.355 54.545 0.00 0.00 0.00 3.35
36 37 1.907255 CCCTCCGGTCCTTTTTACTCT 59.093 52.381 0.00 0.00 0.00 3.24
37 38 1.904537 TCCCTCCGGTCCTTTTTACTC 59.095 52.381 0.00 0.00 0.00 2.59
38 39 1.907255 CTCCCTCCGGTCCTTTTTACT 59.093 52.381 0.00 0.00 0.00 2.24
39 40 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
40 41 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
41 42 1.627329 GTACTCCCTCCGGTCCTTTTT 59.373 52.381 0.00 0.00 0.00 1.94
42 43 1.203275 AGTACTCCCTCCGGTCCTTTT 60.203 52.381 0.00 0.00 0.00 2.27
43 44 0.412640 AGTACTCCCTCCGGTCCTTT 59.587 55.000 0.00 0.00 0.00 3.11
44 45 1.302907 TAGTACTCCCTCCGGTCCTT 58.697 55.000 0.00 0.00 0.00 3.36
45 46 1.532038 ATAGTACTCCCTCCGGTCCT 58.468 55.000 0.00 0.00 0.00 3.85
46 47 2.789213 GTATAGTACTCCCTCCGGTCC 58.211 57.143 0.00 0.00 0.00 4.46
47 48 2.037772 TCGTATAGTACTCCCTCCGGTC 59.962 54.545 0.00 0.00 0.00 4.79
48 49 2.050144 TCGTATAGTACTCCCTCCGGT 58.950 52.381 0.00 0.00 0.00 5.28
49 50 2.847327 TCGTATAGTACTCCCTCCGG 57.153 55.000 0.00 0.00 0.00 5.14
50 51 3.072944 CCTTCGTATAGTACTCCCTCCG 58.927 54.545 0.00 0.00 0.00 4.63
51 52 4.363991 TCCTTCGTATAGTACTCCCTCC 57.636 50.000 0.00 0.00 0.00 4.30
52 53 7.992754 TTTATCCTTCGTATAGTACTCCCTC 57.007 40.000 0.00 0.00 0.00 4.30
53 54 8.773033 TTTTTATCCTTCGTATAGTACTCCCT 57.227 34.615 0.00 0.00 0.00 4.20
54 55 8.087136 CCTTTTTATCCTTCGTATAGTACTCCC 58.913 40.741 0.00 0.00 0.00 4.30
55 56 7.598118 GCCTTTTTATCCTTCGTATAGTACTCC 59.402 40.741 0.00 0.00 0.00 3.85
56 57 8.139989 TGCCTTTTTATCCTTCGTATAGTACTC 58.860 37.037 0.00 0.00 0.00 2.59
57 58 8.015185 TGCCTTTTTATCCTTCGTATAGTACT 57.985 34.615 0.00 0.00 0.00 2.73
58 59 8.709646 CATGCCTTTTTATCCTTCGTATAGTAC 58.290 37.037 0.00 0.00 0.00 2.73
122 123 2.303022 CTCCATATAGCACGGGACCATT 59.697 50.000 0.00 0.00 0.00 3.16
184 185 9.383519 CTATCCCAATATCACCAACATACATAC 57.616 37.037 0.00 0.00 0.00 2.39
208 209 0.596577 GCCCATATGCGACGTCTCTA 59.403 55.000 14.70 2.64 0.00 2.43
282 309 4.855340 TCATTTTCCCCAGGTTATGAGAC 58.145 43.478 0.00 0.00 0.00 3.36
283 310 5.732331 ATCATTTTCCCCAGGTTATGAGA 57.268 39.130 0.00 0.00 0.00 3.27
284 311 6.796785 AAATCATTTTCCCCAGGTTATGAG 57.203 37.500 0.00 0.00 0.00 2.90
382 425 3.597675 TTACGGCCGCACATGCAGA 62.598 57.895 28.58 0.00 42.21 4.26
386 429 2.834574 TTTATTTACGGCCGCACATG 57.165 45.000 28.58 0.00 0.00 3.21
437 591 8.494016 ACTTTTACTTTGCATAGGATAGTGTC 57.506 34.615 9.08 0.00 0.00 3.67
510 666 7.412137 AGATTGTTTAATGCTTTTGTTGAGC 57.588 32.000 0.00 0.00 40.53 4.26
561 717 8.792633 TCAGTCCTTCAAAACATTATACTTTGG 58.207 33.333 0.00 0.00 32.17 3.28
569 725 8.359642 CCAATCTTTCAGTCCTTCAAAACATTA 58.640 33.333 0.00 0.00 0.00 1.90
578 734 3.679389 TGCTCCAATCTTTCAGTCCTTC 58.321 45.455 0.00 0.00 0.00 3.46
583 739 3.319122 GTGGTTTGCTCCAATCTTTCAGT 59.681 43.478 0.00 0.00 39.34 3.41
636 792 7.272037 AGGGTTAACACAACAGTGAATTTAG 57.728 36.000 11.16 0.00 37.04 1.85
667 1793 5.744666 ATTAATTGCCGTACATGTACACC 57.255 39.130 30.17 21.34 35.87 4.16
726 2091 0.322456 AGCGCCACCAGCTTAATCAA 60.322 50.000 2.29 0.00 43.24 2.57
728 2093 4.225497 AGCGCCACCAGCTTAATC 57.775 55.556 2.29 0.00 43.24 1.75
749 2114 5.241949 AGACGGGTTAATACATTGCAAAACA 59.758 36.000 1.71 0.00 0.00 2.83
889 2603 2.141535 GCCGGTAGCAGAAGTGATAG 57.858 55.000 1.90 0.00 42.97 2.08
926 2645 3.445687 ACGAGACGGCGCATGGTA 61.446 61.111 10.83 0.00 33.86 3.25
946 2665 0.036952 ATTCACTGTGAGTGGCCTCG 60.037 55.000 10.77 0.00 45.94 4.63
976 2695 1.204941 GTCGAATATATCCAGCCGGCT 59.795 52.381 27.08 27.08 0.00 5.52
991 2711 1.466866 CGTGCTACTCCATTCGTCGAA 60.467 52.381 10.61 10.61 0.00 3.71
993 2713 0.179171 ACGTGCTACTCCATTCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
1016 2736 2.761392 TTACCATGGATCGTACGACG 57.239 50.000 22.14 6.79 44.19 5.12
1017 2737 4.269363 CCTTTTTACCATGGATCGTACGAC 59.731 45.833 22.14 14.10 0.00 4.34
1080 2800 4.523083 AGAAGAACTTGTGGTGCTTGTTA 58.477 39.130 0.00 0.00 43.49 2.41
1135 2855 1.690893 TGCTCCTGGTGATGATAGCTC 59.309 52.381 0.00 0.00 0.00 4.09
1160 2890 1.228510 GCTGGATGGGAAAGGGAGG 59.771 63.158 0.00 0.00 0.00 4.30
1161 2891 1.419387 CTAGCTGGATGGGAAAGGGAG 59.581 57.143 0.00 0.00 0.00 4.30
1162 2892 1.511613 CTAGCTGGATGGGAAAGGGA 58.488 55.000 0.00 0.00 0.00 4.20
1163 2893 0.179006 GCTAGCTGGATGGGAAAGGG 60.179 60.000 7.70 0.00 0.00 3.95
1164 2894 0.842635 AGCTAGCTGGATGGGAAAGG 59.157 55.000 18.57 0.00 0.00 3.11
1165 2895 2.038295 CCTAGCTAGCTGGATGGGAAAG 59.962 54.545 28.01 13.30 0.00 2.62
1166 2896 2.050144 CCTAGCTAGCTGGATGGGAAA 58.950 52.381 28.01 3.74 0.00 3.13
1177 2907 1.134907 TGCGTGTAAACCCTAGCTAGC 60.135 52.381 15.74 6.62 0.00 3.42
1178 2908 2.426024 TCTGCGTGTAAACCCTAGCTAG 59.574 50.000 14.20 14.20 0.00 3.42
1179 2909 2.449464 TCTGCGTGTAAACCCTAGCTA 58.551 47.619 0.00 0.00 0.00 3.32
1180 2910 1.263356 TCTGCGTGTAAACCCTAGCT 58.737 50.000 0.00 0.00 0.00 3.32
1181 2911 2.311124 ATCTGCGTGTAAACCCTAGC 57.689 50.000 0.00 0.00 0.00 3.42
1319 3055 1.372683 GAGCTGAAGTGACCCTGCA 59.627 57.895 0.00 0.00 0.00 4.41
1320 3056 0.673022 CTGAGCTGAAGTGACCCTGC 60.673 60.000 0.00 0.00 0.00 4.85
1365 3101 1.076559 TTCTCCCCGTAGATCGCCA 60.077 57.895 0.00 0.00 38.35 5.69
1374 3115 3.710722 CAGCCAGCTTCTCCCCGT 61.711 66.667 0.00 0.00 0.00 5.28
1403 3144 5.536554 ACTTACAAGCATGAGAAATCGTG 57.463 39.130 0.00 0.00 0.00 4.35
1451 3192 2.101415 CCACGGAATCTGTGCAGATCTA 59.899 50.000 16.37 0.00 46.75 1.98
1452 3193 1.134580 CCACGGAATCTGTGCAGATCT 60.135 52.381 16.37 6.01 46.75 2.75
1460 3201 2.104111 TCACTGAAACCACGGAATCTGT 59.896 45.455 0.00 0.00 0.00 3.41
1468 3209 3.985279 TCGAAATACTCACTGAAACCACG 59.015 43.478 0.00 0.00 0.00 4.94
1472 3213 4.327627 GGAGCTCGAAATACTCACTGAAAC 59.672 45.833 7.83 0.00 31.88 2.78
1477 3218 4.020543 AGAAGGAGCTCGAAATACTCACT 58.979 43.478 7.83 0.00 31.88 3.41
1478 3219 4.379339 AGAAGGAGCTCGAAATACTCAC 57.621 45.455 7.83 0.00 31.88 3.51
1479 3220 4.462834 TCAAGAAGGAGCTCGAAATACTCA 59.537 41.667 7.83 0.00 31.88 3.41
1505 3246 4.220821 GGCTGATTAATCCGAGGATCTACA 59.779 45.833 12.90 3.74 33.08 2.74
1516 3257 1.683385 GCAACCCTGGCTGATTAATCC 59.317 52.381 12.90 0.00 0.00 3.01
1539 3286 1.075050 CATGGGGATCCAGGATTCCAG 59.925 57.143 26.49 12.89 46.99 3.86
1555 3302 2.105477 AGACCATCCGAGATTTCCATGG 59.895 50.000 4.97 4.97 36.76 3.66
1568 3315 2.035632 AGAACCAGATCGAGACCATCC 58.964 52.381 0.00 0.00 0.00 3.51
1587 3334 6.677105 ATGAAAACCATGGGATGAGCATCAG 61.677 44.000 18.09 0.07 41.05 2.90
1591 3338 2.601240 TGAAAACCATGGGATGAGCA 57.399 45.000 18.09 3.45 0.00 4.26
1634 3389 3.898123 AGCTAGTGAAAAGTGACAGGAGA 59.102 43.478 0.00 0.00 0.00 3.71
1635 3390 4.264460 AGCTAGTGAAAAGTGACAGGAG 57.736 45.455 0.00 0.00 0.00 3.69
1646 3416 3.620427 TGCCGGAAATAGCTAGTGAAA 57.380 42.857 5.05 0.00 0.00 2.69
1653 3423 2.106511 ACATACCATGCCGGAAATAGCT 59.893 45.455 5.05 0.00 38.63 3.32
1668 3438 8.556213 TTCTGGTAGACAATTAACAACATACC 57.444 34.615 0.00 0.00 33.56 2.73
1671 3441 9.912634 CAAATTCTGGTAGACAATTAACAACAT 57.087 29.630 0.00 0.00 0.00 2.71
1672 3442 9.126151 TCAAATTCTGGTAGACAATTAACAACA 57.874 29.630 0.00 0.00 0.00 3.33
1677 3447 8.877864 ACCATCAAATTCTGGTAGACAATTAA 57.122 30.769 5.70 0.00 43.91 1.40
1683 3453 9.444600 TTTAGTAACCATCAAATTCTGGTAGAC 57.555 33.333 7.50 8.67 44.97 2.59
1690 3460 9.520515 ACACTCATTTAGTAACCATCAAATTCT 57.479 29.630 0.00 0.00 35.76 2.40
1718 3488 2.249139 GATTACTACATCCCCCTCGCT 58.751 52.381 0.00 0.00 0.00 4.93
1725 3495 7.981102 GGATTTAGTTGGATTACTACATCCC 57.019 40.000 14.01 2.39 44.68 3.85
1727 3497 9.832445 TGAAGGATTTAGTTGGATTACTACATC 57.168 33.333 0.00 0.00 37.20 3.06
1728 3498 9.838339 CTGAAGGATTTAGTTGGATTACTACAT 57.162 33.333 0.00 0.00 30.62 2.29
1729 3499 7.769044 GCTGAAGGATTTAGTTGGATTACTACA 59.231 37.037 0.00 0.00 33.69 2.74
1731 3501 7.857456 TGCTGAAGGATTTAGTTGGATTACTA 58.143 34.615 0.00 0.00 33.69 1.82
1792 3564 3.950794 TTAGTGAGCTTGCCGGCCG 62.951 63.158 26.77 21.04 0.00 6.13
1793 3565 1.674322 TTTAGTGAGCTTGCCGGCC 60.674 57.895 26.77 8.84 0.00 6.13
1794 3566 0.955919 AGTTTAGTGAGCTTGCCGGC 60.956 55.000 22.73 22.73 0.00 6.13
1795 3567 1.079503 GAGTTTAGTGAGCTTGCCGG 58.920 55.000 0.00 0.00 0.00 6.13
1796 3568 1.795768 TGAGTTTAGTGAGCTTGCCG 58.204 50.000 0.00 0.00 0.00 5.69
1797 3569 3.753272 TGATTGAGTTTAGTGAGCTTGCC 59.247 43.478 0.00 0.00 0.00 4.52
1816 3588 3.012518 GCTCACACCTGCACTAATTGAT 58.987 45.455 0.00 0.00 0.00 2.57
1820 3592 2.290514 ACATGCTCACACCTGCACTAAT 60.291 45.455 0.00 0.00 42.26 1.73
1838 3610 4.224594 AGCCTACATATGCTGCTATCACAT 59.775 41.667 11.30 0.00 36.23 3.21
1851 3623 7.052873 GCTAATGGATGAATGAGCCTACATAT 58.947 38.462 0.00 0.00 28.75 1.78
1860 3632 7.714377 AGTTTAGTGAGCTAATGGATGAATGAG 59.286 37.037 0.00 0.00 37.09 2.90
1873 3645 7.286215 ACAACTACTGAAGTTTAGTGAGCTA 57.714 36.000 10.41 0.00 46.61 3.32
1875 3647 7.326547 GTCTACAACTACTGAAGTTTAGTGAGC 59.673 40.741 10.41 0.00 46.61 4.26
1876 3648 8.569641 AGTCTACAACTACTGAAGTTTAGTGAG 58.430 37.037 10.41 6.64 46.61 3.51
1877 3649 8.350722 CAGTCTACAACTACTGAAGTTTAGTGA 58.649 37.037 10.41 0.00 46.61 3.41
1879 3651 8.235359 ACAGTCTACAACTACTGAAGTTTAGT 57.765 34.615 9.30 5.55 46.61 2.24
1880 3652 9.828852 CTACAGTCTACAACTACTGAAGTTTAG 57.171 37.037 9.30 0.00 46.61 1.85
1881 3653 8.295288 GCTACAGTCTACAACTACTGAAGTTTA 58.705 37.037 9.30 0.00 46.61 2.01
1882 3654 7.146648 GCTACAGTCTACAACTACTGAAGTTT 58.853 38.462 9.30 0.00 46.61 2.66
1884 3656 5.768662 TGCTACAGTCTACAACTACTGAAGT 59.231 40.000 9.30 0.00 44.79 3.01
1885 3657 6.087522 GTGCTACAGTCTACAACTACTGAAG 58.912 44.000 9.30 0.00 44.79 3.02
1886 3658 5.334646 CGTGCTACAGTCTACAACTACTGAA 60.335 44.000 9.30 0.00 44.79 3.02
2018 3793 0.321122 CTGAGCCACTGAGGAACACC 60.321 60.000 0.00 0.00 41.22 4.16
2174 3968 1.269778 CGGCGCTTATCATCTCAAGGA 60.270 52.381 7.64 0.00 0.00 3.36
3219 7877 8.886719 TCTCAAGTAATCTTAAATCACAGCATG 58.113 33.333 0.00 0.00 35.48 4.06
3236 7894 5.734140 TCCCAAATAATCCCCTCTCAAGTAA 59.266 40.000 0.00 0.00 0.00 2.24
3245 7903 3.722101 CCAGTACTCCCAAATAATCCCCT 59.278 47.826 0.00 0.00 0.00 4.79
3264 7922 4.637534 CCTTAACTTGATCATCACACCCAG 59.362 45.833 0.00 0.00 0.00 4.45
3298 7957 0.595588 AACGAATTGCATTGCACGGA 59.404 45.000 19.92 4.75 38.71 4.69
3300 7959 1.407434 ACAACGAATTGCATTGCACG 58.593 45.000 11.66 14.22 38.71 5.34
3407 8069 2.734079 CTCACAAGAGAAAGCCGACTTC 59.266 50.000 0.00 0.00 44.98 3.01
3415 8078 7.442364 TGGAGATACAAAACTCACAAGAGAAAG 59.558 37.037 0.00 0.00 44.98 2.62
3446 8109 7.066887 ACGCACCAATCATATTACAAAGATTGA 59.933 33.333 13.75 0.00 46.27 2.57
3447 8110 7.195646 ACGCACCAATCATATTACAAAGATTG 58.804 34.615 0.00 0.00 44.18 2.67
3448 8111 7.333528 ACGCACCAATCATATTACAAAGATT 57.666 32.000 0.00 0.00 0.00 2.40
3502 8166 3.501385 CCCCAACAACAAAAGGGAGGATA 60.501 47.826 0.00 0.00 44.30 2.59
3537 8201 7.035612 GTCATACAAATTGAAACTCCCCAATC 58.964 38.462 0.00 0.00 32.36 2.67
3744 8411 9.342308 CAATTCTATGGGATGAGCTAAGTAAAA 57.658 33.333 0.00 0.00 0.00 1.52
3749 8419 7.308469 GCTTTCAATTCTATGGGATGAGCTAAG 60.308 40.741 0.00 0.00 0.00 2.18
3790 8460 1.564818 TCCCGTTTATATTGGGTGGCA 59.435 47.619 4.81 0.00 43.75 4.92
3812 8482 6.969366 TCCTGTTAAATGACAAATCACACTG 58.031 36.000 0.00 0.00 37.79 3.66
3876 8550 1.814793 TTGCAACCGATCGAATTGGA 58.185 45.000 24.39 21.29 37.26 3.53
3942 8616 8.020819 TGCTTAATTGCTTATACGAATTATGGC 58.979 33.333 0.00 0.00 0.00 4.40
3990 8664 7.188468 TCATGCAATTTGCTTTTAAACTTCC 57.812 32.000 21.19 0.00 45.31 3.46
4002 8676 5.881447 TGCCAATTAAATCATGCAATTTGC 58.119 33.333 14.49 14.49 45.29 3.68
4003 8677 7.906611 CATGCCAATTAAATCATGCAATTTG 57.093 32.000 6.62 0.00 31.34 2.32
4024 8703 6.852345 GCAAAAAGTTCAGTAAAATTGGCATG 59.148 34.615 0.00 0.00 0.00 4.06
4026 8705 5.295540 GGCAAAAAGTTCAGTAAAATTGGCA 59.704 36.000 0.00 0.00 40.51 4.92
4063 8742 2.201921 TGTATAGGCACCCGCAAAAA 57.798 45.000 0.00 0.00 41.24 1.94
4064 8743 2.201921 TTGTATAGGCACCCGCAAAA 57.798 45.000 0.00 0.00 41.24 2.44
4065 8744 2.020720 CATTGTATAGGCACCCGCAAA 58.979 47.619 0.00 0.00 41.24 3.68
4066 8745 1.210722 TCATTGTATAGGCACCCGCAA 59.789 47.619 0.00 0.00 41.24 4.85
4067 8746 0.833949 TCATTGTATAGGCACCCGCA 59.166 50.000 0.00 0.00 41.24 5.69
4068 8747 2.185004 ATCATTGTATAGGCACCCGC 57.815 50.000 0.00 0.00 37.44 6.13
4069 8748 3.476552 ACAATCATTGTATAGGCACCCG 58.523 45.455 0.00 0.00 43.27 5.28
4070 8749 5.359576 TCAAACAATCATTGTATAGGCACCC 59.640 40.000 2.67 0.00 44.59 4.61
4071 8750 6.265577 GTCAAACAATCATTGTATAGGCACC 58.734 40.000 2.67 0.00 44.59 5.01
4072 8751 6.265577 GGTCAAACAATCATTGTATAGGCAC 58.734 40.000 2.67 0.00 44.59 5.01
4073 8752 5.359576 GGGTCAAACAATCATTGTATAGGCA 59.640 40.000 2.67 0.00 44.59 4.75
4074 8753 5.359576 TGGGTCAAACAATCATTGTATAGGC 59.640 40.000 2.67 0.00 44.59 3.93
4075 8754 7.403312 TTGGGTCAAACAATCATTGTATAGG 57.597 36.000 2.67 0.00 44.59 2.57
4078 8757 9.253832 TCTATTTGGGTCAAACAATCATTGTAT 57.746 29.630 2.67 0.00 44.59 2.29
4079 8758 8.642935 TCTATTTGGGTCAAACAATCATTGTA 57.357 30.769 2.67 0.00 44.59 2.41
4081 8760 8.036575 ACATCTATTTGGGTCAAACAATCATTG 58.963 33.333 0.00 0.00 36.13 2.82
4082 8761 8.137745 ACATCTATTTGGGTCAAACAATCATT 57.862 30.769 0.00 0.00 36.13 2.57
4083 8762 7.722949 ACATCTATTTGGGTCAAACAATCAT 57.277 32.000 0.00 0.00 36.13 2.45
4084 8763 7.537596 AACATCTATTTGGGTCAAACAATCA 57.462 32.000 0.00 0.00 36.13 2.57
4085 8764 8.519526 TGTAACATCTATTTGGGTCAAACAATC 58.480 33.333 0.00 0.00 36.13 2.67
4086 8765 8.415950 TGTAACATCTATTTGGGTCAAACAAT 57.584 30.769 0.00 0.00 36.13 2.71
4097 8776 8.746922 ATTGTGCACTTTGTAACATCTATTTG 57.253 30.769 19.41 0.00 0.00 2.32
4124 8803 8.992073 TGTTATGTGCATCAGTAGCTAATAATG 58.008 33.333 0.00 0.00 0.00 1.90
4134 8813 5.656859 ACTCCTAGTGTTATGTGCATCAGTA 59.343 40.000 0.00 0.00 0.00 2.74
4135 8814 4.467795 ACTCCTAGTGTTATGTGCATCAGT 59.532 41.667 0.00 0.00 0.00 3.41
4165 8844 6.588756 TGACACTGTTTTACCTCGCTAAATAG 59.411 38.462 0.00 0.00 0.00 1.73
4303 9039 9.377312 CCATTTTCTTTCTCCAACACTTAAAAA 57.623 29.630 0.00 0.00 0.00 1.94
4311 9048 4.648762 TCAAGCCATTTTCTTTCTCCAACA 59.351 37.500 0.00 0.00 0.00 3.33
4409 9146 4.091509 CCAATGAGCACTCAGTACGTAAAC 59.908 45.833 6.50 0.00 43.61 2.01
4472 9209 3.684788 CGTTCTTACCTCCCATGTGAAAG 59.315 47.826 0.00 0.00 0.00 2.62
4493 9230 7.095270 AGTAGTGGGTCTGACTAAATTTTACG 58.905 38.462 7.85 0.00 0.00 3.18
4504 9241 9.444600 TTGATTTAATTAAGTAGTGGGTCTGAC 57.555 33.333 0.00 0.00 0.00 3.51
4553 9290 7.661847 ACCTTCTGTTTTCACATAAGAGGTAAG 59.338 37.037 2.88 0.00 38.72 2.34
4562 9299 4.693566 CCGCTTACCTTCTGTTTTCACATA 59.306 41.667 0.00 0.00 30.39 2.29
4575 9312 4.497291 TTAACATGATCCCGCTTACCTT 57.503 40.909 0.00 0.00 0.00 3.50
4583 9320 7.795482 TGGTAATAGTTTTAACATGATCCCG 57.205 36.000 0.00 0.00 0.00 5.14
4615 9352 6.999950 TCTTGTTTTAGTGACCAGTATAGCA 58.000 36.000 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.