Multiple sequence alignment - TraesCS2D01G285600

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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 TraesCS2D01G285600 chr2D 100.000 4812 0 0 1 4812 363968234 363973045 0.000000e+00 8887.0
1 TraesCS2D01G285600 chr2D 89.320 206 18 4 3837 4038 240791202 240790997 6.180000e-64 255.0
2 TraesCS2D01G285600 chr2D 84.259 108 14 3 4102 4206 37254772 37254665 8.520000e-18 102.0
3 TraesCS2D01G285600 chr2A 93.905 2182 55 28 1688 3848 489839568 489841692 0.000000e+00 3221.0
4 TraesCS2D01G285600 chr2A 90.760 671 39 7 1 668 489834140 489834790 0.000000e+00 874.0
5 TraesCS2D01G285600 chr2A 93.714 525 15 7 852 1366 489838231 489838747 0.000000e+00 771.0
6 TraesCS2D01G285600 chr2A 88.268 358 26 12 4019 4373 489841694 489842038 9.640000e-112 414.0
7 TraesCS2D01G285600 chr2A 88.545 323 12 7 557 856 489834835 489835155 7.610000e-98 368.0
8 TraesCS2D01G285600 chr2A 95.853 217 9 0 1396 1612 489839009 489839225 7.660000e-93 351.0
9 TraesCS2D01G285600 chr2A 85.207 338 30 6 4466 4802 489842197 489842515 3.590000e-86 329.0
10 TraesCS2D01G285600 chr2A 85.437 103 13 2 4098 4199 310408903 310409004 6.590000e-19 106.0
11 TraesCS2D01G285600 chr2A 95.161 62 3 0 495 556 489834790 489834851 1.100000e-16 99.0
12 TraesCS2D01G285600 chr2B 94.096 1660 63 16 1645 3296 432126993 432128625 0.000000e+00 2490.0
13 TraesCS2D01G285600 chr2B 91.950 1031 42 18 606 1603 432125614 432126636 0.000000e+00 1406.0
14 TraesCS2D01G285600 chr2B 95.596 545 6 7 3323 3854 432128615 432129154 0.000000e+00 857.0
15 TraesCS2D01G285600 chr2B 91.667 456 34 2 1 454 432124723 432125176 3.160000e-176 628.0
16 TraesCS2D01G285600 chr2B 86.617 538 54 6 4019 4544 432129159 432129690 3.230000e-161 579.0
17 TraesCS2D01G285600 chr2B 86.561 253 24 4 4561 4812 432129678 432129921 2.210000e-68 270.0
18 TraesCS2D01G285600 chr5D 98.214 168 2 1 3852 4019 60140928 60140762 4.710000e-75 292.0
19 TraesCS2D01G285600 chr3D 96.491 171 6 0 3849 4019 300567780 300567950 2.840000e-72 283.0
20 TraesCS2D01G285600 chr3D 93.333 180 10 2 3837 4015 577904062 577904240 1.030000e-66 265.0
21 TraesCS2D01G285600 chr3D 94.220 173 8 2 3853 4023 526507070 526506898 3.690000e-66 263.0
22 TraesCS2D01G285600 chr1D 95.808 167 6 1 3853 4019 20054876 20055041 7.940000e-68 268.0
23 TraesCS2D01G285600 chr1D 80.745 161 24 6 4098 4257 156133339 156133493 8.460000e-23 119.0
24 TraesCS2D01G285600 chr1D 84.466 103 16 0 4098 4200 493498542 493498440 8.520000e-18 102.0
25 TraesCS2D01G285600 chr6D 95.238 168 8 0 3851 4018 359354943 359354776 2.860000e-67 267.0
26 TraesCS2D01G285600 chr7D 94.767 172 6 2 3849 4020 535594485 535594317 1.030000e-66 265.0
27 TraesCS2D01G285600 chr7D 85.000 100 13 2 4114 4211 193400933 193400834 3.060000e-17 100.0
28 TraesCS2D01G285600 chr7B 94.048 168 10 0 3850 4017 620131418 620131585 6.180000e-64 255.0
29 TraesCS2D01G285600 chr1B 85.586 111 16 0 4109 4219 250423703 250423813 3.040000e-22 117.0
30 TraesCS2D01G285600 chr3A 79.375 160 27 4 4098 4257 509865253 509865406 1.830000e-19 108.0
31 TraesCS2D01G285600 chr1A 85.294 102 15 0 4109 4210 171456540 171456439 6.590000e-19 106.0
32 TraesCS2D01G285600 chr1A 85.859 99 8 4 4117 4213 546020481 546020575 3.060000e-17 100.0
33 TraesCS2D01G285600 chr4A 83.186 113 18 1 4107 4219 75348937 75349048 8.520000e-18 102.0
34 TraesCS2D01G285600 chr4A 80.165 121 22 2 4093 4213 96018828 96018710 6.630000e-14 89.8


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 TraesCS2D01G285600 chr2D 363968234 363973045 4811 False 8887.000000 8887 100.000000 1 4812 1 chr2D.!!$F1 4811
1 TraesCS2D01G285600 chr2A 489834140 489842515 8375 False 803.375000 3221 91.426625 1 4802 8 chr2A.!!$F2 4801
2 TraesCS2D01G285600 chr2B 432124723 432129921 5198 False 1038.333333 2490 91.081167 1 4812 6 chr2B.!!$F1 4811

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
499 850 0.108207 TTGGTCCGACCGGCTAAAAA 59.892 50.0 13.02 0.0 42.58 1.94 F
1245 4851 0.175989 CCCTCGTCCTCTGGCTAAAC 59.824 60.0 0.00 0.0 0.00 2.01 F
1636 5494 0.686112 ATTAATGTTGGGGGCGGTGG 60.686 55.0 0.00 0.0 0.00 4.61 F
2431 6611 0.733566 CGCAGCGCATGGTTGAATTT 60.734 50.0 11.47 0.0 0.00 1.82 F
3389 7575 0.531974 TGTGCTCGTGGGTGTTTCTC 60.532 55.0 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 6052 0.251787 AGGACCAATCAAAGGCACCC 60.252 55.0 0.0 0.0 0.0 4.61 R
2431 6611 1.040646 ACAGCTTCTCCTTGTCGTCA 58.959 50.0 0.0 0.0 0.0 4.35 R
3322 7507 0.385390 CCTTGCTGTGGCGAGTTTTT 59.615 50.0 4.8 0.0 45.9 1.94 R
3567 7758 0.681733 TTGACAGGAGTGGAGTGAGC 59.318 55.0 0.0 0.0 0.0 4.26 R
4345 8544 1.255667 TTCTGGACAGCGGGAGTACC 61.256 60.0 0.0 0.0 0.0 3.34 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
61 67 1.296715 GGTGCTGGAACCAGTCGAT 59.703 57.895 19.97 0.00 45.24 3.59
201 207 2.402388 CGACGACGACGCTACCAT 59.598 61.111 7.30 0.00 43.96 3.55
203 209 2.202570 ACGACGACGCTACCATGC 60.203 61.111 7.30 0.00 43.96 4.06
224 230 2.032030 CCTGAACGACGTTGCTGAAAAT 60.032 45.455 19.60 0.00 0.00 1.82
316 322 1.787847 CAAGGCATCGACCGTCAAC 59.212 57.895 0.00 0.00 33.69 3.18
469 817 3.430374 GGAGAAGCGGCTAGTATTTCACA 60.430 47.826 1.35 0.00 0.00 3.58
499 850 0.108207 TTGGTCCGACCGGCTAAAAA 59.892 50.000 13.02 0.00 42.58 1.94
608 1098 4.925646 GTGTAGTAGTGGTTACCTTTTCCG 59.074 45.833 2.07 0.00 32.37 4.30
611 1101 3.647590 AGTAGTGGTTACCTTTTCCGGAA 59.352 43.478 14.35 14.35 32.37 4.30
686 1176 1.757682 TCCAGACACACAAACCCAAC 58.242 50.000 0.00 0.00 0.00 3.77
769 1261 9.185192 CCATTTAAAGACAGTCAAGTCAAAATC 57.815 33.333 2.66 0.00 40.98 2.17
822 1338 4.631131 AGCAATGCCCAAAAACTAAAGAC 58.369 39.130 0.00 0.00 0.00 3.01
824 1340 4.314961 CAATGCCCAAAAACTAAAGACCC 58.685 43.478 0.00 0.00 0.00 4.46
861 4457 5.469479 TGCTTTTGCCTAACTAAGCAATTC 58.531 37.500 5.95 0.00 46.98 2.17
879 4475 2.034879 CCCACACCTCGTCACATGC 61.035 63.158 0.00 0.00 0.00 4.06
1042 4648 4.988598 CGGTGGTCTGTGCGGCTT 62.989 66.667 0.00 0.00 0.00 4.35
1101 4707 0.608130 TGGTGGAGGACAAGATCACG 59.392 55.000 0.00 0.00 0.00 4.35
1245 4851 0.175989 CCCTCGTCCTCTGGCTAAAC 59.824 60.000 0.00 0.00 0.00 2.01
1287 4893 2.023673 CACAAGCTTCCCACTGTTTCA 58.976 47.619 0.00 0.00 0.00 2.69
1314 4920 7.451255 TCTTATTGCATTATTGGTATTGGGGAG 59.549 37.037 0.00 0.00 0.00 4.30
1318 4924 4.396166 GCATTATTGGTATTGGGGAGATCG 59.604 45.833 0.00 0.00 0.00 3.69
1528 5386 2.293399 GTGTCCCAACTGTTGATGGAAC 59.707 50.000 21.49 15.00 38.26 3.62
1603 5461 7.414436 TGTTTTGTTAGAACTGACTGCATAAC 58.586 34.615 0.00 0.00 0.00 1.89
1612 5470 3.244078 ACTGACTGCATAACCTCGTGAAA 60.244 43.478 0.00 0.00 0.00 2.69
1613 5471 3.935203 CTGACTGCATAACCTCGTGAAAT 59.065 43.478 0.00 0.00 0.00 2.17
1614 5472 3.684305 TGACTGCATAACCTCGTGAAATG 59.316 43.478 0.00 0.00 0.00 2.32
1615 5473 3.009723 ACTGCATAACCTCGTGAAATGG 58.990 45.455 0.00 0.00 0.00 3.16
1616 5474 3.009723 CTGCATAACCTCGTGAAATGGT 58.990 45.455 0.00 0.00 35.29 3.55
1617 5475 4.188462 CTGCATAACCTCGTGAAATGGTA 58.812 43.478 0.00 0.00 33.17 3.25
1618 5476 4.776349 TGCATAACCTCGTGAAATGGTAT 58.224 39.130 0.00 0.00 33.17 2.73
1619 5477 5.189928 TGCATAACCTCGTGAAATGGTATT 58.810 37.500 0.00 0.00 33.17 1.89
1620 5478 6.350103 TGCATAACCTCGTGAAATGGTATTA 58.650 36.000 0.00 0.00 33.17 0.98
1621 5479 6.824196 TGCATAACCTCGTGAAATGGTATTAA 59.176 34.615 0.00 0.00 33.17 1.40
1622 5480 7.500892 TGCATAACCTCGTGAAATGGTATTAAT 59.499 33.333 0.00 0.00 33.17 1.40
1623 5481 7.803189 GCATAACCTCGTGAAATGGTATTAATG 59.197 37.037 0.00 0.00 33.17 1.90
1624 5482 8.836413 CATAACCTCGTGAAATGGTATTAATGT 58.164 33.333 0.00 0.00 33.17 2.71
1625 5483 7.696992 AACCTCGTGAAATGGTATTAATGTT 57.303 32.000 0.00 0.00 33.17 2.71
1626 5484 7.083875 ACCTCGTGAAATGGTATTAATGTTG 57.916 36.000 0.00 0.00 31.50 3.33
1627 5485 6.094881 ACCTCGTGAAATGGTATTAATGTTGG 59.905 38.462 0.00 0.00 31.50 3.77
1628 5486 6.443934 TCGTGAAATGGTATTAATGTTGGG 57.556 37.500 0.00 0.00 0.00 4.12
1629 5487 5.358442 TCGTGAAATGGTATTAATGTTGGGG 59.642 40.000 0.00 0.00 0.00 4.96
1630 5488 5.451242 CGTGAAATGGTATTAATGTTGGGGG 60.451 44.000 0.00 0.00 0.00 5.40
1631 5489 4.407296 TGAAATGGTATTAATGTTGGGGGC 59.593 41.667 0.00 0.00 0.00 5.80
1632 5490 2.060050 TGGTATTAATGTTGGGGGCG 57.940 50.000 0.00 0.00 0.00 6.13
1633 5491 1.324383 GGTATTAATGTTGGGGGCGG 58.676 55.000 0.00 0.00 0.00 6.13
1634 5492 1.410507 GGTATTAATGTTGGGGGCGGT 60.411 52.381 0.00 0.00 0.00 5.68
1635 5493 1.679153 GTATTAATGTTGGGGGCGGTG 59.321 52.381 0.00 0.00 0.00 4.94
1636 5494 0.686112 ATTAATGTTGGGGGCGGTGG 60.686 55.000 0.00 0.00 0.00 4.61
1637 5495 1.790635 TTAATGTTGGGGGCGGTGGA 61.791 55.000 0.00 0.00 0.00 4.02
1638 5496 1.576368 TAATGTTGGGGGCGGTGGAT 61.576 55.000 0.00 0.00 0.00 3.41
1639 5497 2.854300 AATGTTGGGGGCGGTGGATC 62.854 60.000 0.00 0.00 0.00 3.36
1640 5498 3.728373 GTTGGGGGCGGTGGATCT 61.728 66.667 0.00 0.00 0.00 2.75
1641 5499 3.407967 TTGGGGGCGGTGGATCTC 61.408 66.667 0.00 0.00 0.00 2.75
1642 5500 4.731853 TGGGGGCGGTGGATCTCA 62.732 66.667 0.00 0.00 0.00 3.27
1643 5501 4.176752 GGGGGCGGTGGATCTCAC 62.177 72.222 5.94 5.94 45.34 3.51
1834 6008 3.844211 AGTATAGCTGGAACAAAGGTGGA 59.156 43.478 0.00 0.00 38.70 4.02
1878 6052 2.608752 GCATCCACAAAAGCAACCTCTG 60.609 50.000 0.00 0.00 0.00 3.35
2298 6478 2.130272 TGTACATCGCAGGAGAGAGT 57.870 50.000 0.00 0.00 0.00 3.24
2329 6509 0.877071 AGCCATTCTGCTTGTTCACG 59.123 50.000 0.00 0.00 38.85 4.35
2343 6523 4.974368 TGTTCACGTCCTTGTTCAATTT 57.026 36.364 0.00 0.00 0.00 1.82
2392 6572 9.520515 AACTACAATGATGATCACTTTTAAGGT 57.479 29.630 0.00 0.00 0.00 3.50
2431 6611 0.733566 CGCAGCGCATGGTTGAATTT 60.734 50.000 11.47 0.00 0.00 1.82
2513 6693 9.545611 CAAAGCTTACCAAAAATATGAATTTGC 57.454 29.630 0.00 0.00 35.46 3.68
2514 6694 8.845413 AAGCTTACCAAAAATATGAATTTGCA 57.155 26.923 0.00 0.00 35.46 4.08
2515 6695 8.483307 AGCTTACCAAAAATATGAATTTGCAG 57.517 30.769 0.00 2.43 35.46 4.41
2516 6696 8.313292 AGCTTACCAAAAATATGAATTTGCAGA 58.687 29.630 0.00 0.00 35.46 4.26
2517 6697 8.598075 GCTTACCAAAAATATGAATTTGCAGAG 58.402 33.333 0.00 3.35 35.46 3.35
2518 6698 6.973229 ACCAAAAATATGAATTTGCAGAGC 57.027 33.333 0.00 0.00 35.46 4.09
2519 6699 5.577945 ACCAAAAATATGAATTTGCAGAGCG 59.422 36.000 0.00 0.00 35.46 5.03
2520 6700 5.577945 CCAAAAATATGAATTTGCAGAGCGT 59.422 36.000 0.00 0.00 35.46 5.07
2521 6701 6.454583 CCAAAAATATGAATTTGCAGAGCGTG 60.455 38.462 0.00 0.00 35.46 5.34
2522 6702 4.970662 AATATGAATTTGCAGAGCGTGT 57.029 36.364 0.00 0.00 0.00 4.49
2523 6703 6.435430 AAATATGAATTTGCAGAGCGTGTA 57.565 33.333 0.00 0.00 33.97 2.90
2524 6704 6.624352 AATATGAATTTGCAGAGCGTGTAT 57.376 33.333 0.00 0.00 0.00 2.29
2525 6705 3.745332 TGAATTTGCAGAGCGTGTATG 57.255 42.857 0.00 0.00 0.00 2.39
2532 6712 2.993220 TGCAGAGCGTGTATGTTTACAG 59.007 45.455 0.00 0.00 38.98 2.74
2535 6715 4.201628 GCAGAGCGTGTATGTTTACAGAAG 60.202 45.833 0.00 0.00 38.98 2.85
2537 6717 3.000727 AGCGTGTATGTTTACAGAAGCC 58.999 45.455 0.00 0.00 38.98 4.35
2542 6722 4.326548 GTGTATGTTTACAGAAGCCTCGTC 59.673 45.833 0.00 0.00 38.98 4.20
2555 6735 5.812642 AGAAGCCTCGTCAATTTATAGTGTG 59.187 40.000 0.00 0.00 0.00 3.82
2557 6737 3.002348 GCCTCGTCAATTTATAGTGTGCC 59.998 47.826 0.00 0.00 0.00 5.01
2575 6756 1.731720 CCTGCTCTCTTTTTCCCTCG 58.268 55.000 0.00 0.00 0.00 4.63
2585 6766 4.662278 TCTTTTTCCCTCGTTGATCCAAT 58.338 39.130 0.00 0.00 0.00 3.16
2674 6855 1.270358 GGGCTGATATCGGACTCAACC 60.270 57.143 17.12 6.25 0.00 3.77
2778 6959 1.545428 GGTGATGAGCCAAGTGACCAA 60.545 52.381 0.00 0.00 0.00 3.67
2921 7102 6.136857 TCTGCTAAGGAGATGTATGTAACCT 58.863 40.000 0.00 0.00 0.00 3.50
2938 7119 1.217882 CCTTGTCACTGACGGACAAC 58.782 55.000 4.71 0.00 46.95 3.32
3084 7265 2.646175 GGACGGTCTGCAGCAGGTA 61.646 63.158 22.62 0.44 31.51 3.08
3108 7289 5.674525 TGGATTTGCCTATCTGTTAGAGTG 58.325 41.667 0.00 0.00 37.63 3.51
3121 7306 8.630054 ATCTGTTAGAGTGTCTATCTGTATCC 57.370 38.462 0.00 0.00 0.00 2.59
3128 7313 3.440872 GTGTCTATCTGTATCCGCTAGGG 59.559 52.174 0.00 0.00 38.33 3.53
3135 7320 4.338879 TCTGTATCCGCTAGGGGTATTAC 58.661 47.826 23.98 21.31 32.79 1.89
3138 7323 1.335145 TCCGCTAGGGGTATTACAGC 58.665 55.000 23.98 0.00 38.33 4.40
3153 7338 2.574006 ACAGCTGCATTTCCTTCAGA 57.426 45.000 15.27 0.00 0.00 3.27
3307 7492 5.163923 GGTAAAGAACCGCATACAGTTGTAC 60.164 44.000 0.00 0.00 38.88 2.90
3308 7493 3.955650 AGAACCGCATACAGTTGTACT 57.044 42.857 0.00 0.00 32.72 2.73
3309 7494 9.199421 GGTAAAGAACCGCATACAGTTGTACTG 62.199 44.444 5.33 5.33 44.54 2.74
3323 7508 7.806149 CAGTTGTACTGTACGTATCAATGAA 57.194 36.000 12.87 0.00 41.19 2.57
3342 7527 1.455383 AAAACTCGCCACAGCAAGGG 61.455 55.000 0.00 0.00 39.83 3.95
3389 7575 0.531974 TGTGCTCGTGGGTGTTTCTC 60.532 55.000 0.00 0.00 0.00 2.87
3390 7576 1.070786 TGCTCGTGGGTGTTTCTCC 59.929 57.895 0.00 0.00 0.00 3.71
3391 7577 2.027625 GCTCGTGGGTGTTTCTCCG 61.028 63.158 0.00 0.00 0.00 4.63
3392 7578 2.027625 CTCGTGGGTGTTTCTCCGC 61.028 63.158 0.00 0.00 0.00 5.54
3393 7579 2.280524 CGTGGGTGTTTCTCCGCA 60.281 61.111 0.00 0.00 33.43 5.69
3567 7758 1.497991 ATTGGCCATCGTTATCGTCG 58.502 50.000 6.09 0.00 38.33 5.12
3568 7759 1.149361 TTGGCCATCGTTATCGTCGC 61.149 55.000 6.09 0.00 38.33 5.19
3569 7760 1.299926 GGCCATCGTTATCGTCGCT 60.300 57.895 0.00 0.00 38.33 4.93
3570 7761 1.276145 GGCCATCGTTATCGTCGCTC 61.276 60.000 0.00 0.00 38.33 5.03
3571 7762 0.594028 GCCATCGTTATCGTCGCTCA 60.594 55.000 0.00 0.00 38.33 4.26
3611 7804 1.978617 GCCATGGTGGGTGGTGAAG 60.979 63.158 14.67 0.00 38.19 3.02
3830 8028 2.036475 TGACCTCAACTCAAGAGACAGC 59.964 50.000 3.73 0.00 35.09 4.40
3854 8052 7.011295 AGCTCGTGTTCTTGTACTACTATCTAC 59.989 40.741 0.00 0.00 0.00 2.59
3855 8053 7.011295 GCTCGTGTTCTTGTACTACTATCTACT 59.989 40.741 0.00 0.00 0.00 2.57
3856 8054 8.417780 TCGTGTTCTTGTACTACTATCTACTC 57.582 38.462 0.00 0.00 0.00 2.59
3857 8055 7.493971 TCGTGTTCTTGTACTACTATCTACTCC 59.506 40.741 0.00 0.00 0.00 3.85
3858 8056 7.254727 CGTGTTCTTGTACTACTATCTACTCCC 60.255 44.444 0.00 0.00 0.00 4.30
3859 8057 7.774625 GTGTTCTTGTACTACTATCTACTCCCT 59.225 40.741 0.00 0.00 0.00 4.20
3860 8058 7.992033 TGTTCTTGTACTACTATCTACTCCCTC 59.008 40.741 0.00 0.00 0.00 4.30
3861 8059 7.077050 TCTTGTACTACTATCTACTCCCTCC 57.923 44.000 0.00 0.00 0.00 4.30
3862 8060 5.480642 TGTACTACTATCTACTCCCTCCG 57.519 47.826 0.00 0.00 0.00 4.63
3863 8061 4.904251 TGTACTACTATCTACTCCCTCCGT 59.096 45.833 0.00 0.00 0.00 4.69
3864 8062 5.367937 TGTACTACTATCTACTCCCTCCGTT 59.632 44.000 0.00 0.00 0.00 4.44
3865 8063 4.971939 ACTACTATCTACTCCCTCCGTTC 58.028 47.826 0.00 0.00 0.00 3.95
3866 8064 3.226682 ACTATCTACTCCCTCCGTTCC 57.773 52.381 0.00 0.00 0.00 3.62
3867 8065 2.784682 ACTATCTACTCCCTCCGTTCCT 59.215 50.000 0.00 0.00 0.00 3.36
3868 8066 3.979347 ACTATCTACTCCCTCCGTTCCTA 59.021 47.826 0.00 0.00 0.00 2.94
3869 8067 3.967467 ATCTACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
3870 8068 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
3871 8069 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
3872 8070 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
3873 8071 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
3874 8072 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
3875 8073 7.706674 TCTACTCCCTCCGTTCCTAAATATAT 58.293 38.462 0.00 0.00 0.00 0.86
3876 8074 6.854091 ACTCCCTCCGTTCCTAAATATATC 57.146 41.667 0.00 0.00 0.00 1.63
3877 8075 6.563163 ACTCCCTCCGTTCCTAAATATATCT 58.437 40.000 0.00 0.00 0.00 1.98
3878 8076 6.664384 ACTCCCTCCGTTCCTAAATATATCTC 59.336 42.308 0.00 0.00 0.00 2.75
3879 8077 6.801953 TCCCTCCGTTCCTAAATATATCTCT 58.198 40.000 0.00 0.00 0.00 3.10
3880 8078 7.246763 TCCCTCCGTTCCTAAATATATCTCTT 58.753 38.462 0.00 0.00 0.00 2.85
3881 8079 7.733501 TCCCTCCGTTCCTAAATATATCTCTTT 59.266 37.037 0.00 0.00 0.00 2.52
3882 8080 7.819900 CCCTCCGTTCCTAAATATATCTCTTTG 59.180 40.741 0.00 0.00 0.00 2.77
3883 8081 8.368668 CCTCCGTTCCTAAATATATCTCTTTGT 58.631 37.037 0.00 0.00 0.00 2.83
3915 8113 4.982916 CACTAAATGGACTACATACGGAGC 59.017 45.833 0.00 0.00 39.40 4.70
3916 8114 4.647853 ACTAAATGGACTACATACGGAGCA 59.352 41.667 0.00 0.00 39.40 4.26
3917 8115 4.481368 AAATGGACTACATACGGAGCAA 57.519 40.909 0.00 0.00 39.40 3.91
3918 8116 4.481368 AATGGACTACATACGGAGCAAA 57.519 40.909 0.00 0.00 39.40 3.68
3919 8117 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
3920 8118 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
3921 8119 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
3922 8120 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
3923 8121 4.873827 GGACTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.00 0.00 2.57
3924 8122 5.527582 GGACTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
3925 8123 6.363577 ACTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
3926 8124 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
3927 8125 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
3928 8126 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
3929 8127 6.498304 ACATACGGAGCAAAATGAATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
3930 8128 6.319658 ACATACGGAGCAAAATGAATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
3931 8129 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
3932 8130 6.124088 ACGGAGCAAAATGAATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
3933 8131 5.647658 ACGGAGCAAAATGAATGAATCTACA 59.352 36.000 0.00 0.00 0.00 2.74
3934 8132 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
3935 8133 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
3936 8134 7.542025 GGAGCAAAATGAATGAATCTACACTT 58.458 34.615 0.00 0.00 0.00 3.16
3937 8135 8.677300 GGAGCAAAATGAATGAATCTACACTTA 58.323 33.333 0.00 0.00 0.00 2.24
3959 8157 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
3962 8160 7.987268 AAATGCATCTATATACATCCGTACG 57.013 36.000 8.69 8.69 0.00 3.67
3963 8161 6.694877 ATGCATCTATATACATCCGTACGT 57.305 37.500 15.21 0.00 0.00 3.57
3964 8162 5.875930 TGCATCTATATACATCCGTACGTG 58.124 41.667 15.21 9.44 0.00 4.49
3965 8163 5.163693 TGCATCTATATACATCCGTACGTGG 60.164 44.000 15.21 5.54 0.00 4.94
3966 8164 5.163683 GCATCTATATACATCCGTACGTGGT 60.164 44.000 15.21 11.27 0.00 4.16
3967 8165 6.624423 GCATCTATATACATCCGTACGTGGTT 60.624 42.308 15.21 1.80 0.00 3.67
3968 8166 6.882610 TCTATATACATCCGTACGTGGTTT 57.117 37.500 15.21 6.91 0.00 3.27
3969 8167 7.977789 TCTATATACATCCGTACGTGGTTTA 57.022 36.000 15.21 8.75 0.00 2.01
3970 8168 8.565896 TCTATATACATCCGTACGTGGTTTAT 57.434 34.615 15.21 14.35 0.00 1.40
3971 8169 9.665719 TCTATATACATCCGTACGTGGTTTATA 57.334 33.333 15.21 14.65 0.00 0.98
3972 8170 9.926751 CTATATACATCCGTACGTGGTTTATAG 57.073 37.037 15.21 18.75 0.00 1.31
3973 8171 4.989279 ACATCCGTACGTGGTTTATAGT 57.011 40.909 15.21 0.00 0.00 2.12
3974 8172 4.675510 ACATCCGTACGTGGTTTATAGTG 58.324 43.478 15.21 0.00 0.00 2.74
3975 8173 3.781079 TCCGTACGTGGTTTATAGTGG 57.219 47.619 15.21 0.00 0.00 4.00
3976 8174 3.351740 TCCGTACGTGGTTTATAGTGGA 58.648 45.455 15.21 0.00 0.00 4.02
3977 8175 3.761218 TCCGTACGTGGTTTATAGTGGAA 59.239 43.478 15.21 0.00 0.00 3.53
3978 8176 4.402155 TCCGTACGTGGTTTATAGTGGAAT 59.598 41.667 15.21 0.00 0.00 3.01
3979 8177 4.741676 CCGTACGTGGTTTATAGTGGAATC 59.258 45.833 15.21 0.00 0.00 2.52
3980 8178 5.450965 CCGTACGTGGTTTATAGTGGAATCT 60.451 44.000 15.21 0.00 0.00 2.40
3981 8179 5.684626 CGTACGTGGTTTATAGTGGAATCTC 59.315 44.000 7.22 0.00 0.00 2.75
3982 8180 5.934402 ACGTGGTTTATAGTGGAATCTCT 57.066 39.130 0.00 0.00 0.00 3.10
3983 8181 7.254898 CGTACGTGGTTTATAGTGGAATCTCTA 60.255 40.741 7.22 0.00 0.00 2.43
3984 8182 7.598759 ACGTGGTTTATAGTGGAATCTCTAT 57.401 36.000 0.00 0.00 34.95 1.98
3985 8183 8.701908 ACGTGGTTTATAGTGGAATCTCTATA 57.298 34.615 0.00 0.00 33.37 1.31
3986 8184 9.139734 ACGTGGTTTATAGTGGAATCTCTATAA 57.860 33.333 11.26 11.26 38.81 0.98
3987 8185 9.976511 CGTGGTTTATAGTGGAATCTCTATAAA 57.023 33.333 17.61 17.61 42.89 1.40
4010 8208 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
4011 8209 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
4012 8210 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
4013 8211 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
4014 8212 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
4015 8213 7.450944 ACTTATATTTAGGAACGGAGGGAGTAG 59.549 40.741 0.00 0.00 0.00 2.57
4016 8214 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
4017 8215 4.591321 TTTAGGAACGGAGGGAGTAGTA 57.409 45.455 0.00 0.00 0.00 1.82
4034 8232 7.107542 GGAGTAGTATAGTAGCTAGAGTGCAT 58.892 42.308 0.00 0.00 34.99 3.96
4082 8280 6.326064 TGGAAATCCAATCAAAAAGGTCTTCA 59.674 34.615 0.00 0.00 44.35 3.02
4105 8303 6.042781 TCACAAGTGTAATCAGTTACTCCCTT 59.957 38.462 0.00 0.00 40.66 3.95
4106 8304 6.147821 CACAAGTGTAATCAGTTACTCCCTTG 59.852 42.308 15.74 15.74 41.28 3.61
4191 8390 3.252400 ACGAACACACTAAAACACGTCA 58.748 40.909 0.00 0.00 0.00 4.35
4201 8400 7.642194 CACACTAAAACACGTCAACATACATTT 59.358 33.333 0.00 0.00 0.00 2.32
4202 8401 7.642194 ACACTAAAACACGTCAACATACATTTG 59.358 33.333 0.00 0.00 0.00 2.32
4206 8405 8.641499 AAAACACGTCAACATACATTTGATTT 57.359 26.923 0.00 0.00 35.47 2.17
4208 8407 8.948853 AACACGTCAACATACATTTGATTTAG 57.051 30.769 0.00 0.00 35.47 1.85
4310 8509 9.801873 ATGTATGGGAATTTCGAAAATTTACTG 57.198 29.630 15.66 0.00 0.00 2.74
4345 8544 4.651778 TGGTCTGTCATACTGGGAAAAAG 58.348 43.478 0.00 0.00 0.00 2.27
4362 8561 1.258445 AAGGTACTCCCGCTGTCCAG 61.258 60.000 0.00 0.00 38.49 3.86
4370 8569 3.709653 ACTCCCGCTGTCCAGAATTAATA 59.290 43.478 0.00 0.00 0.00 0.98
4371 8570 4.058817 CTCCCGCTGTCCAGAATTAATAC 58.941 47.826 0.00 0.00 0.00 1.89
4372 8571 3.452990 TCCCGCTGTCCAGAATTAATACA 59.547 43.478 0.00 0.00 0.00 2.29
4373 8572 4.102524 TCCCGCTGTCCAGAATTAATACAT 59.897 41.667 0.00 0.00 0.00 2.29
4374 8573 4.452455 CCCGCTGTCCAGAATTAATACATC 59.548 45.833 0.00 0.00 0.00 3.06
4375 8574 4.452455 CCGCTGTCCAGAATTAATACATCC 59.548 45.833 0.00 0.00 0.00 3.51
4376 8575 4.150627 CGCTGTCCAGAATTAATACATCCG 59.849 45.833 0.00 0.00 0.00 4.18
4384 8583 8.967918 TCCAGAATTAATACATCCGTATCTAGG 58.032 37.037 0.00 0.00 37.34 3.02
4395 8594 6.267928 ACATCCGTATCTAGGCAAATCTAAGT 59.732 38.462 0.00 0.00 0.00 2.24
4405 8604 9.959721 TCTAGGCAAATCTAAGTCAAGTAATTT 57.040 29.630 0.00 0.00 0.00 1.82
4486 8777 4.142902 GCTGTGTACAATCAAATGCGTACT 60.143 41.667 0.00 0.00 36.14 2.73
4505 8796 2.806244 ACTTGTAGATTCACGTTGCCAC 59.194 45.455 0.00 0.00 0.00 5.01
4528 8821 0.462581 ACATATGCAGGGCGTGACTG 60.463 55.000 12.03 4.53 38.95 3.51
4530 8823 0.179073 ATATGCAGGGCGTGACTGTC 60.179 55.000 12.03 0.00 38.22 3.51
4544 8837 5.457148 GCGTGACTGTCACTAAGATTATCTG 59.543 44.000 31.34 16.30 44.85 2.90
4546 8839 6.470556 CGTGACTGTCACTAAGATTATCTGTG 59.529 42.308 31.34 12.27 44.85 3.66
4557 8850 8.082242 ACTAAGATTATCTGTGTTTTGTTTGGC 58.918 33.333 0.00 0.00 0.00 4.52
4573 8866 9.474920 TTTTGTTTGGCAAACTAAGATTATCTG 57.525 29.630 35.03 0.00 45.70 2.90
4613 8906 7.282332 TCCAAAACATGTTATGTCATTCACA 57.718 32.000 12.39 0.00 44.07 3.58
4700 8994 2.025727 GACTACGATGCCCCGACG 59.974 66.667 1.78 0.00 0.00 5.12
4718 9012 3.243816 TGCTGCTCTGCTCCACCA 61.244 61.111 0.00 0.00 0.00 4.17
4750 9044 1.153568 CTGCACCCGACGATGATGT 60.154 57.895 0.00 0.00 0.00 3.06
4797 9091 2.611800 TCCACATGGAGCAGGCCT 60.612 61.111 0.00 0.00 39.78 5.19
4802 9096 1.227883 CATGGAGCAGGCCTAGCTG 60.228 63.158 27.52 14.31 43.58 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 67 1.610967 TGGTAGCACCATCCGGTCA 60.611 57.895 0.00 0.00 44.71 4.02
201 207 2.108157 AGCAACGTCGTTCAGGCA 59.892 55.556 17.81 0.00 0.00 4.75
203 209 0.934496 TTTCAGCAACGTCGTTCAGG 59.066 50.000 7.86 0.00 0.00 3.86
224 230 3.547054 AAACAGGTCACGGTAGAAACA 57.453 42.857 0.00 0.00 0.00 2.83
316 322 2.463589 TACCCTGGCTTGCCTTGTCG 62.464 60.000 13.18 0.00 0.00 4.35
340 346 1.032114 GGCCAACAGCTCGCCTAATT 61.032 55.000 0.00 0.00 43.05 1.40
372 378 3.410628 ATGACGGATGCCCTGCCA 61.411 61.111 0.00 0.00 0.00 4.92
375 381 2.910360 TCCATGACGGATGCCCTG 59.090 61.111 0.00 0.00 39.64 4.45
399 405 3.202906 CACTTTCACTCCGTTCTCCAAA 58.797 45.455 0.00 0.00 0.00 3.28
400 406 2.484770 CCACTTTCACTCCGTTCTCCAA 60.485 50.000 0.00 0.00 0.00 3.53
401 407 1.070134 CCACTTTCACTCCGTTCTCCA 59.930 52.381 0.00 0.00 0.00 3.86
577 1067 6.012157 AGGTAACCACTACTACACCTCTCTTA 60.012 42.308 0.00 0.00 30.59 2.10
608 1098 3.006940 TGTATGTGTCGGAGCATTTTCC 58.993 45.455 1.17 0.00 0.00 3.13
611 1101 4.517285 AGAATGTATGTGTCGGAGCATTT 58.483 39.130 1.17 0.00 0.00 2.32
625 1115 5.016051 ACGCAGTGATCTTGAGAATGTAT 57.984 39.130 0.00 0.00 42.51 2.29
675 1165 0.383949 CAAGGGACGTTGGGTTTGTG 59.616 55.000 0.00 0.00 0.00 3.33
676 1166 0.256464 TCAAGGGACGTTGGGTTTGT 59.744 50.000 5.09 0.00 0.00 2.83
686 1176 3.129638 TGTTTGGTCTTTTTCAAGGGACG 59.870 43.478 0.00 0.00 0.00 4.79
769 1261 7.378181 AGGCAAAAACATGAATAGGTTTAGTG 58.622 34.615 0.00 0.00 39.63 2.74
806 1322 2.299013 CAGGGGTCTTTAGTTTTTGGGC 59.701 50.000 0.00 0.00 0.00 5.36
808 1324 4.038763 GGTTCAGGGGTCTTTAGTTTTTGG 59.961 45.833 0.00 0.00 0.00 3.28
861 4457 2.034879 GCATGTGACGAGGTGTGGG 61.035 63.158 0.00 0.00 0.00 4.61
879 4475 7.120579 TGGCAATAAATAGGTTTGACAGTACTG 59.879 37.037 21.44 21.44 33.56 2.74
1245 4851 2.354821 GCAGCCACTAAATTTACCTCCG 59.645 50.000 0.00 0.00 0.00 4.63
1287 4893 7.955185 TCCCCAATACCAATAATGCAATAAGAT 59.045 33.333 0.00 0.00 0.00 2.40
1314 4920 1.205893 ACTGTTCCTTCTCCTGCGATC 59.794 52.381 0.00 0.00 0.00 3.69
1318 4924 1.070758 TCACACTGTTCCTTCTCCTGC 59.929 52.381 0.00 0.00 0.00 4.85
1492 5350 6.832384 AGTTGGGACACTTCGTATATCTTCTA 59.168 38.462 0.00 0.00 39.29 2.10
1528 5386 8.874744 TCAAAATTTAAAGGTAAAAAGTCCCG 57.125 30.769 0.00 0.00 32.98 5.14
1603 5461 6.459573 CCCAACATTAATACCATTTCACGAGG 60.460 42.308 0.00 0.00 0.00 4.63
1612 5470 2.593026 CGCCCCCAACATTAATACCAT 58.407 47.619 0.00 0.00 0.00 3.55
1613 5471 1.410365 CCGCCCCCAACATTAATACCA 60.410 52.381 0.00 0.00 0.00 3.25
1614 5472 1.324383 CCGCCCCCAACATTAATACC 58.676 55.000 0.00 0.00 0.00 2.73
1615 5473 1.679153 CACCGCCCCCAACATTAATAC 59.321 52.381 0.00 0.00 0.00 1.89
1616 5474 1.410365 CCACCGCCCCCAACATTAATA 60.410 52.381 0.00 0.00 0.00 0.98
1617 5475 0.686112 CCACCGCCCCCAACATTAAT 60.686 55.000 0.00 0.00 0.00 1.40
1618 5476 1.304547 CCACCGCCCCCAACATTAA 60.305 57.895 0.00 0.00 0.00 1.40
1619 5477 1.576368 ATCCACCGCCCCCAACATTA 61.576 55.000 0.00 0.00 0.00 1.90
1620 5478 2.854300 GATCCACCGCCCCCAACATT 62.854 60.000 0.00 0.00 0.00 2.71
1621 5479 3.346734 ATCCACCGCCCCCAACAT 61.347 61.111 0.00 0.00 0.00 2.71
1622 5480 4.041762 GATCCACCGCCCCCAACA 62.042 66.667 0.00 0.00 0.00 3.33
1623 5481 3.699134 GAGATCCACCGCCCCCAAC 62.699 68.421 0.00 0.00 0.00 3.77
1624 5482 3.407967 GAGATCCACCGCCCCCAA 61.408 66.667 0.00 0.00 0.00 4.12
1625 5483 4.731853 TGAGATCCACCGCCCCCA 62.732 66.667 0.00 0.00 0.00 4.96
1626 5484 4.176752 GTGAGATCCACCGCCCCC 62.177 72.222 3.65 0.00 39.86 5.40
1633 5491 5.923204 AGTGATAAATCAGGTGAGATCCAC 58.077 41.667 5.94 5.94 44.95 4.02
1634 5492 6.042093 GGTAGTGATAAATCAGGTGAGATCCA 59.958 42.308 0.00 0.00 37.51 3.41
1635 5493 6.042093 TGGTAGTGATAAATCAGGTGAGATCC 59.958 42.308 0.00 0.00 37.51 3.36
1636 5494 7.055667 TGGTAGTGATAAATCAGGTGAGATC 57.944 40.000 0.00 0.00 37.51 2.75
1637 5495 7.345653 TCTTGGTAGTGATAAATCAGGTGAGAT 59.654 37.037 0.00 0.00 37.51 2.75
1638 5496 6.667848 TCTTGGTAGTGATAAATCAGGTGAGA 59.332 38.462 0.00 0.00 37.51 3.27
1639 5497 6.878317 TCTTGGTAGTGATAAATCAGGTGAG 58.122 40.000 0.00 0.00 37.51 3.51
1640 5498 6.867519 TCTTGGTAGTGATAAATCAGGTGA 57.132 37.500 0.00 0.00 37.51 4.02
1641 5499 7.227512 GGAATCTTGGTAGTGATAAATCAGGTG 59.772 40.741 0.00 0.00 37.51 4.00
1642 5500 7.127955 AGGAATCTTGGTAGTGATAAATCAGGT 59.872 37.037 0.00 0.00 37.51 4.00
1643 5501 7.512992 AGGAATCTTGGTAGTGATAAATCAGG 58.487 38.462 0.00 0.00 37.51 3.86
1653 5826 5.799213 AGAGACAAAGGAATCTTGGTAGTG 58.201 41.667 0.00 0.00 37.28 2.74
1802 5976 5.163269 TGTTCCAGCTATACTCATTGCTCAT 60.163 40.000 0.00 0.00 40.62 2.90
1834 6008 7.319646 TGCAACTTTTACAAGAGACAAAATGT 58.680 30.769 0.00 0.00 33.72 2.71
1878 6052 0.251787 AGGACCAATCAAAGGCACCC 60.252 55.000 0.00 0.00 0.00 4.61
2323 6503 5.336744 TCAAAATTGAACAAGGACGTGAAC 58.663 37.500 0.00 0.00 33.55 3.18
2343 6523 4.739793 AGAACACCAAGGGATGAATTCAA 58.260 39.130 13.09 0.00 0.00 2.69
2392 6572 2.888594 GCTAGTTGCGGAACATAGTGA 58.111 47.619 22.29 0.00 34.17 3.41
2431 6611 1.040646 ACAGCTTCTCCTTGTCGTCA 58.959 50.000 0.00 0.00 0.00 4.35
2507 6687 4.503741 AAACATACACGCTCTGCAAATT 57.496 36.364 0.00 0.00 0.00 1.82
2508 6688 4.454161 TGTAAACATACACGCTCTGCAAAT 59.546 37.500 0.00 0.00 0.00 2.32
2509 6689 3.810386 TGTAAACATACACGCTCTGCAAA 59.190 39.130 0.00 0.00 0.00 3.68
2510 6690 3.394719 TGTAAACATACACGCTCTGCAA 58.605 40.909 0.00 0.00 0.00 4.08
2511 6691 2.993220 CTGTAAACATACACGCTCTGCA 59.007 45.455 0.00 0.00 0.00 4.41
2512 6692 3.250744 TCTGTAAACATACACGCTCTGC 58.749 45.455 0.00 0.00 0.00 4.26
2513 6693 4.201628 GCTTCTGTAAACATACACGCTCTG 60.202 45.833 0.00 0.00 0.00 3.35
2514 6694 3.927142 GCTTCTGTAAACATACACGCTCT 59.073 43.478 0.00 0.00 0.00 4.09
2515 6695 3.062234 GGCTTCTGTAAACATACACGCTC 59.938 47.826 0.00 0.00 0.00 5.03
2516 6696 3.000727 GGCTTCTGTAAACATACACGCT 58.999 45.455 0.00 0.00 0.00 5.07
2517 6697 3.000727 AGGCTTCTGTAAACATACACGC 58.999 45.455 0.00 0.00 0.00 5.34
2518 6698 3.303495 CGAGGCTTCTGTAAACATACACG 59.697 47.826 0.00 0.00 0.00 4.49
2519 6699 4.243270 ACGAGGCTTCTGTAAACATACAC 58.757 43.478 0.00 0.00 0.00 2.90
2520 6700 4.021807 TGACGAGGCTTCTGTAAACATACA 60.022 41.667 0.00 0.00 0.00 2.29
2521 6701 4.491676 TGACGAGGCTTCTGTAAACATAC 58.508 43.478 0.00 0.00 0.00 2.39
2522 6702 4.794278 TGACGAGGCTTCTGTAAACATA 57.206 40.909 0.00 0.00 0.00 2.29
2523 6703 3.678056 TGACGAGGCTTCTGTAAACAT 57.322 42.857 0.00 0.00 0.00 2.71
2524 6704 3.462483 TTGACGAGGCTTCTGTAAACA 57.538 42.857 0.00 0.00 0.00 2.83
2525 6705 5.358298 AAATTGACGAGGCTTCTGTAAAC 57.642 39.130 0.00 0.00 0.00 2.01
2532 6712 5.502544 GCACACTATAAATTGACGAGGCTTC 60.503 44.000 0.00 0.00 0.00 3.86
2535 6715 3.002348 GGCACACTATAAATTGACGAGGC 59.998 47.826 0.00 0.00 0.00 4.70
2537 6717 4.260375 GCAGGCACACTATAAATTGACGAG 60.260 45.833 0.00 0.00 0.00 4.18
2542 6722 5.121811 AGAGAGCAGGCACACTATAAATTG 58.878 41.667 0.00 0.00 0.00 2.32
2555 6735 1.458398 GAGGGAAAAAGAGAGCAGGC 58.542 55.000 0.00 0.00 0.00 4.85
2557 6737 2.464157 ACGAGGGAAAAAGAGAGCAG 57.536 50.000 0.00 0.00 0.00 4.24
2585 6766 2.354704 CGAGAACAGGATTGCCCAACTA 60.355 50.000 0.00 0.00 37.41 2.24
2674 6855 2.942710 ACCGTCGTGAAGATGTTGTAG 58.057 47.619 0.00 0.00 34.06 2.74
2744 6925 2.107041 ATCACCCTGTCGCAAACCGA 62.107 55.000 0.00 0.00 45.15 4.69
2938 7119 2.143122 TGCTCGGTAGACTGCAAAAAG 58.857 47.619 0.00 0.00 32.12 2.27
3084 7265 6.126652 ACACTCTAACAGATAGGCAAATCCAT 60.127 38.462 0.00 0.00 37.29 3.41
3108 7289 3.018149 CCCCTAGCGGATACAGATAGAC 58.982 54.545 0.00 0.00 33.12 2.59
3121 7306 1.605712 GCAGCTGTAATACCCCTAGCG 60.606 57.143 16.64 0.00 39.27 4.26
3128 7313 4.640201 TGAAGGAAATGCAGCTGTAATACC 59.360 41.667 16.64 14.68 0.00 2.73
3135 7320 3.834610 CTTTCTGAAGGAAATGCAGCTG 58.165 45.455 10.11 10.11 42.25 4.24
3153 7338 1.535462 CTCGGTGAAATCGCAACCTTT 59.465 47.619 0.00 0.00 0.00 3.11
3307 7492 5.952064 GCGAGTTTTTCATTGATACGTACAG 59.048 40.000 0.00 0.00 0.00 2.74
3308 7493 5.163933 GGCGAGTTTTTCATTGATACGTACA 60.164 40.000 0.00 0.00 0.00 2.90
3309 7494 5.163933 TGGCGAGTTTTTCATTGATACGTAC 60.164 40.000 0.00 0.00 0.00 3.67
3310 7495 4.930405 TGGCGAGTTTTTCATTGATACGTA 59.070 37.500 0.00 0.00 0.00 3.57
3311 7496 3.749088 TGGCGAGTTTTTCATTGATACGT 59.251 39.130 0.00 0.00 0.00 3.57
3313 7498 5.041951 TGTGGCGAGTTTTTCATTGATAC 57.958 39.130 0.00 0.00 0.00 2.24
3314 7499 4.379394 GCTGTGGCGAGTTTTTCATTGATA 60.379 41.667 0.00 0.00 0.00 2.15
3315 7500 3.612479 GCTGTGGCGAGTTTTTCATTGAT 60.612 43.478 0.00 0.00 0.00 2.57
3316 7501 2.287547 GCTGTGGCGAGTTTTTCATTGA 60.288 45.455 0.00 0.00 0.00 2.57
3317 7502 2.053627 GCTGTGGCGAGTTTTTCATTG 58.946 47.619 0.00 0.00 0.00 2.82
3318 7503 1.680735 TGCTGTGGCGAGTTTTTCATT 59.319 42.857 0.00 0.00 42.25 2.57
3319 7504 1.317613 TGCTGTGGCGAGTTTTTCAT 58.682 45.000 0.00 0.00 42.25 2.57
3320 7505 1.065401 CTTGCTGTGGCGAGTTTTTCA 59.935 47.619 0.00 0.00 43.20 2.69
3321 7506 1.600413 CCTTGCTGTGGCGAGTTTTTC 60.600 52.381 4.80 0.00 45.90 2.29
3322 7507 0.385390 CCTTGCTGTGGCGAGTTTTT 59.615 50.000 4.80 0.00 45.90 1.94
3323 7508 1.455383 CCCTTGCTGTGGCGAGTTTT 61.455 55.000 4.80 0.00 45.90 2.43
3342 7527 1.529865 GGCCACGTTCTAAACTGACAC 59.470 52.381 0.00 0.00 0.00 3.67
3567 7758 0.681733 TTGACAGGAGTGGAGTGAGC 59.318 55.000 0.00 0.00 0.00 4.26
3568 7759 1.337635 GCTTGACAGGAGTGGAGTGAG 60.338 57.143 0.00 0.00 0.00 3.51
3569 7760 0.681733 GCTTGACAGGAGTGGAGTGA 59.318 55.000 0.00 0.00 0.00 3.41
3570 7761 0.683973 AGCTTGACAGGAGTGGAGTG 59.316 55.000 0.00 0.00 0.00 3.51
3571 7762 0.972883 GAGCTTGACAGGAGTGGAGT 59.027 55.000 0.00 0.00 0.00 3.85
3830 8028 8.422973 AGTAGATAGTAGTACAAGAACACGAG 57.577 38.462 2.52 0.00 0.00 4.18
3854 8052 6.893005 AGAGATATATTTAGGAACGGAGGGAG 59.107 42.308 0.00 0.00 0.00 4.30
3855 8053 6.801953 AGAGATATATTTAGGAACGGAGGGA 58.198 40.000 0.00 0.00 0.00 4.20
3856 8054 7.483580 AAGAGATATATTTAGGAACGGAGGG 57.516 40.000 0.00 0.00 0.00 4.30
3857 8055 8.368668 ACAAAGAGATATATTTAGGAACGGAGG 58.631 37.037 0.00 0.00 0.00 4.30
3892 8090 4.982916 GCTCCGTATGTAGTCCATTTAGTG 59.017 45.833 0.00 0.00 34.86 2.74
3893 8091 4.647853 TGCTCCGTATGTAGTCCATTTAGT 59.352 41.667 0.00 0.00 34.86 2.24
3894 8092 5.196341 TGCTCCGTATGTAGTCCATTTAG 57.804 43.478 0.00 0.00 34.86 1.85
3895 8093 5.601583 TTGCTCCGTATGTAGTCCATTTA 57.398 39.130 0.00 0.00 34.86 1.40
3896 8094 4.481368 TTGCTCCGTATGTAGTCCATTT 57.519 40.909 0.00 0.00 34.86 2.32
3897 8095 4.481368 TTTGCTCCGTATGTAGTCCATT 57.519 40.909 0.00 0.00 34.86 3.16
3898 8096 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
3899 8097 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
3900 8098 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
3901 8099 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
3902 8100 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
3903 8101 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
3904 8102 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
3905 8103 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
3906 8104 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
3907 8105 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
3908 8106 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
3909 8107 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
3910 8108 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
3911 8109 7.093322 AGTGTAGATTCATTCATTTTGCTCC 57.907 36.000 0.00 0.00 0.00 4.70
3933 8131 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
3936 8134 9.511144 CGTACGGATGTATATAGATGCATTTTA 57.489 33.333 7.57 0.00 38.38 1.52
3937 8135 8.033038 ACGTACGGATGTATATAGATGCATTTT 58.967 33.333 21.06 0.00 38.38 1.82
3938 8136 7.488150 CACGTACGGATGTATATAGATGCATTT 59.512 37.037 21.06 0.00 38.38 2.32
3939 8137 6.972901 CACGTACGGATGTATATAGATGCATT 59.027 38.462 21.06 1.23 38.38 3.56
3940 8138 6.459710 CCACGTACGGATGTATATAGATGCAT 60.460 42.308 21.06 0.00 40.68 3.96
3941 8139 5.163693 CCACGTACGGATGTATATAGATGCA 60.164 44.000 21.06 0.00 32.11 3.96
3942 8140 5.163683 ACCACGTACGGATGTATATAGATGC 60.164 44.000 21.06 0.00 32.11 3.91
3943 8141 6.432607 ACCACGTACGGATGTATATAGATG 57.567 41.667 21.06 3.48 32.11 2.90
3944 8142 7.458409 AAACCACGTACGGATGTATATAGAT 57.542 36.000 21.06 0.00 32.11 1.98
3945 8143 6.882610 AAACCACGTACGGATGTATATAGA 57.117 37.500 21.06 0.00 32.11 1.98
3946 8144 9.926751 CTATAAACCACGTACGGATGTATATAG 57.073 37.037 21.06 17.33 32.11 1.31
3947 8145 9.448438 ACTATAAACCACGTACGGATGTATATA 57.552 33.333 21.06 12.77 32.11 0.86
3948 8146 8.239314 CACTATAAACCACGTACGGATGTATAT 58.761 37.037 21.06 12.35 32.11 0.86
3949 8147 7.308529 CCACTATAAACCACGTACGGATGTATA 60.309 40.741 21.06 11.65 32.11 1.47
3950 8148 6.441274 CACTATAAACCACGTACGGATGTAT 58.559 40.000 21.06 11.15 32.11 2.29
3951 8149 5.221028 CCACTATAAACCACGTACGGATGTA 60.221 44.000 21.06 4.19 0.00 2.29
3952 8150 4.440525 CCACTATAAACCACGTACGGATGT 60.441 45.833 21.06 10.36 0.00 3.06
3953 8151 4.046462 CCACTATAAACCACGTACGGATG 58.954 47.826 21.06 9.60 0.00 3.51
3954 8152 3.953612 TCCACTATAAACCACGTACGGAT 59.046 43.478 21.06 0.82 0.00 4.18
3955 8153 3.351740 TCCACTATAAACCACGTACGGA 58.648 45.455 21.06 0.00 0.00 4.69
3956 8154 3.781079 TCCACTATAAACCACGTACGG 57.219 47.619 21.06 8.46 0.00 4.02
3957 8155 5.585390 AGATTCCACTATAAACCACGTACG 58.415 41.667 15.01 15.01 0.00 3.67
3958 8156 6.803642 AGAGATTCCACTATAAACCACGTAC 58.196 40.000 0.00 0.00 0.00 3.67
3959 8157 8.701908 ATAGAGATTCCACTATAAACCACGTA 57.298 34.615 0.00 0.00 0.00 3.57
3960 8158 5.934402 AGAGATTCCACTATAAACCACGT 57.066 39.130 0.00 0.00 0.00 4.49
3961 8159 9.976511 TTTATAGAGATTCCACTATAAACCACG 57.023 33.333 18.88 0.00 41.95 4.94
3984 8182 8.645110 CCCTCCGTTCCTAAATATAAGTCTTTA 58.355 37.037 0.00 0.00 0.00 1.85
3985 8183 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3986 8184 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3987 8185 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3988 8186 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3989 8187 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3990 8188 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3991 8189 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
3992 8190 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
3993 8191 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
3994 8192 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3995 8193 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3996 8194 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3997 8195 4.803329 ATACTACTCCCTCCGTTCCTAA 57.197 45.455 0.00 0.00 0.00 2.69
3998 8196 4.910304 ACTATACTACTCCCTCCGTTCCTA 59.090 45.833 0.00 0.00 0.00 2.94
3999 8197 3.721050 ACTATACTACTCCCTCCGTTCCT 59.279 47.826 0.00 0.00 0.00 3.36
4000 8198 4.097551 ACTATACTACTCCCTCCGTTCC 57.902 50.000 0.00 0.00 0.00 3.62
4001 8199 4.694982 GCTACTATACTACTCCCTCCGTTC 59.305 50.000 0.00 0.00 0.00 3.95
4002 8200 4.350520 AGCTACTATACTACTCCCTCCGTT 59.649 45.833 0.00 0.00 0.00 4.44
4003 8201 3.909364 AGCTACTATACTACTCCCTCCGT 59.091 47.826 0.00 0.00 0.00 4.69
4004 8202 4.556592 AGCTACTATACTACTCCCTCCG 57.443 50.000 0.00 0.00 0.00 4.63
4005 8203 6.441604 ACTCTAGCTACTATACTACTCCCTCC 59.558 46.154 0.00 0.00 0.00 4.30
4006 8204 7.325694 CACTCTAGCTACTATACTACTCCCTC 58.674 46.154 0.00 0.00 0.00 4.30
4007 8205 6.296030 GCACTCTAGCTACTATACTACTCCCT 60.296 46.154 0.00 0.00 0.00 4.20
4008 8206 5.876460 GCACTCTAGCTACTATACTACTCCC 59.124 48.000 0.00 0.00 0.00 4.30
4009 8207 6.465948 TGCACTCTAGCTACTATACTACTCC 58.534 44.000 0.00 0.00 34.99 3.85
4010 8208 8.447833 CAATGCACTCTAGCTACTATACTACTC 58.552 40.741 0.00 0.00 34.99 2.59
4011 8209 7.094549 GCAATGCACTCTAGCTACTATACTACT 60.095 40.741 0.00 0.00 34.99 2.57
4012 8210 7.024768 GCAATGCACTCTAGCTACTATACTAC 58.975 42.308 0.00 0.00 34.99 2.73
4013 8211 6.128254 CGCAATGCACTCTAGCTACTATACTA 60.128 42.308 5.91 0.00 34.99 1.82
4014 8212 5.335269 CGCAATGCACTCTAGCTACTATACT 60.335 44.000 5.91 0.00 34.99 2.12
4015 8213 4.854291 CGCAATGCACTCTAGCTACTATAC 59.146 45.833 5.91 0.00 34.99 1.47
4016 8214 4.519350 ACGCAATGCACTCTAGCTACTATA 59.481 41.667 5.91 0.00 34.99 1.31
4017 8215 3.319405 ACGCAATGCACTCTAGCTACTAT 59.681 43.478 5.91 0.00 34.99 2.12
4034 8232 2.293122 CCTTGAAAGGTGATTGACGCAA 59.707 45.455 0.57 0.00 41.41 4.85
4082 8280 6.183361 ACAAGGGAGTAACTGATTACACTTGT 60.183 38.462 18.63 18.63 45.59 3.16
4148 8347 6.586463 TCGTTCACTCATTTCAGTCTGTATTC 59.414 38.462 0.00 0.00 0.00 1.75
4245 8444 4.193826 GCCTTGCGATATATTCTCTCCA 57.806 45.455 0.00 0.00 0.00 3.86
4310 8509 3.067833 GACAGACCAAAGGTAACAGCTC 58.932 50.000 0.00 0.00 35.25 4.09
4345 8544 1.255667 TTCTGGACAGCGGGAGTACC 61.256 60.000 0.00 0.00 0.00 3.34
4350 8549 3.452990 TGTATTAATTCTGGACAGCGGGA 59.547 43.478 0.00 0.00 0.00 5.14
4362 8561 8.997621 TTGCCTAGATACGGATGTATTAATTC 57.002 34.615 0.00 0.00 41.37 2.17
4370 8569 6.267928 ACTTAGATTTGCCTAGATACGGATGT 59.732 38.462 0.00 0.00 0.00 3.06
4371 8570 6.692486 ACTTAGATTTGCCTAGATACGGATG 58.308 40.000 0.00 0.00 0.00 3.51
4372 8571 6.493802 TGACTTAGATTTGCCTAGATACGGAT 59.506 38.462 0.00 0.00 0.00 4.18
4373 8572 5.831525 TGACTTAGATTTGCCTAGATACGGA 59.168 40.000 0.00 0.00 0.00 4.69
4374 8573 6.085555 TGACTTAGATTTGCCTAGATACGG 57.914 41.667 0.00 0.00 0.00 4.02
4375 8574 7.203910 ACTTGACTTAGATTTGCCTAGATACG 58.796 38.462 0.00 0.00 0.00 3.06
4442 8641 6.940298 ACAGCTCCTAGTAAATTTTAGTTGCA 59.060 34.615 0.00 0.00 0.00 4.08
4486 8777 2.839975 TGTGGCAACGTGAATCTACAA 58.160 42.857 0.00 0.00 42.51 2.41
4505 8796 1.472082 TCACGCCCTGCATATGTTTTG 59.528 47.619 4.29 0.00 0.00 2.44
4530 8823 9.398170 CCAAACAAAACACAGATAATCTTAGTG 57.602 33.333 0.00 0.00 36.34 2.74
4557 8850 6.039047 AGTGCCATGCAGATAATCTTAGTTTG 59.961 38.462 0.00 0.00 40.08 2.93
4573 8866 4.454728 TTTGGATAAAAGAGTGCCATGC 57.545 40.909 0.00 0.00 0.00 4.06
4650 8943 7.786943 TGTCATCTGATCTAGAGGAGGTTTTAT 59.213 37.037 8.96 0.00 45.94 1.40
4651 8944 7.126061 TGTCATCTGATCTAGAGGAGGTTTTA 58.874 38.462 8.96 0.00 45.94 1.52
4652 8945 5.960811 TGTCATCTGATCTAGAGGAGGTTTT 59.039 40.000 8.96 0.00 45.94 2.43
4700 8994 2.745492 GGTGGAGCAGAGCAGCAC 60.745 66.667 0.00 0.00 36.85 4.40
4741 9035 2.027929 TCAAACGGGGTTACATCATCGT 60.028 45.455 0.00 0.00 0.00 3.73
4742 9036 2.350498 GTCAAACGGGGTTACATCATCG 59.650 50.000 0.00 0.00 0.00 3.84
4745 9039 1.798283 CGTCAAACGGGGTTACATCA 58.202 50.000 0.00 0.00 38.08 3.07
4750 9044 1.597578 GGCACGTCAAACGGGGTTA 60.598 57.895 3.70 0.00 46.78 2.85


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

AutoCloner maintained by Alex Coulton.