Multiple sequence alignment - TraesCS1D01G213600

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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 TraesCS1D01G213600 chr1D 100.000 3579 0 0 1 3579 298691454 298687876 0.000000e+00 6610.0
1 TraesCS1D01G213600 chr1D 100.000 2891 0 0 4070 6960 298687385 298684495 0.000000e+00 5339.0
2 TraesCS1D01G213600 chr1D 87.660 470 29 8 6489 6936 301252631 301252169 2.880000e-143 520.0
3 TraesCS1D01G213600 chr1D 81.818 319 38 12 6493 6795 405013077 405012763 4.170000e-62 250.0
4 TraesCS1D01G213600 chr1B 96.958 2893 69 9 695 3579 402145953 402143072 0.000000e+00 4837.0
5 TraesCS1D01G213600 chr1B 94.504 1765 48 7 4782 6498 402141345 402139582 0.000000e+00 2676.0
6 TraesCS1D01G213600 chr1B 93.412 592 35 4 70 660 402146546 402145958 0.000000e+00 874.0
7 TraesCS1D01G213600 chr1B 96.407 501 14 2 4070 4566 402142329 402141829 0.000000e+00 822.0
8 TraesCS1D01G213600 chr1B 92.237 219 8 1 4565 4783 402141586 402141377 1.130000e-77 302.0
9 TraesCS1D01G213600 chr1B 80.074 271 41 8 4487 4756 271293270 271293528 9.220000e-44 189.0
10 TraesCS1D01G213600 chr1A 95.966 1785 47 6 1802 3579 372632919 372631153 0.000000e+00 2874.0
11 TraesCS1D01G213600 chr1A 94.146 1879 53 9 4560 6391 372629747 372627879 0.000000e+00 2808.0
12 TraesCS1D01G213600 chr1A 93.887 1783 86 13 32 1802 372638076 372636305 0.000000e+00 2667.0
13 TraesCS1D01G213600 chr1A 92.029 1242 65 10 5269 6493 372625475 372624251 0.000000e+00 1714.0
14 TraesCS1D01G213600 chr1A 96.407 501 9 5 4070 4563 372630701 372630203 0.000000e+00 817.0
15 TraesCS1D01G213600 chr1A 83.491 424 43 12 6491 6891 53462749 53462330 3.070000e-98 370.0
16 TraesCS1D01G213600 chr7A 86.318 497 33 10 6493 6957 538984602 538985095 6.230000e-140 508.0
17 TraesCS1D01G213600 chr7A 88.889 90 9 1 6792 6880 68202077 68202166 7.380000e-20 110.0
18 TraesCS1D01G213600 chr2A 87.500 456 22 12 6491 6924 744952954 744953396 1.740000e-135 494.0
19 TraesCS1D01G213600 chr2A 86.567 268 26 7 6579 6845 391862688 391862430 3.180000e-73 287.0
20 TraesCS1D01G213600 chr2A 86.598 97 11 2 6792 6887 505416569 505416664 9.550000e-19 106.0
21 TraesCS1D01G213600 chr3A 87.651 413 28 14 6491 6891 72419854 72419453 6.360000e-125 459.0
22 TraesCS1D01G213600 chr3D 88.060 402 27 3 6491 6880 468742668 468743060 2.290000e-124 457.0
23 TraesCS1D01G213600 chr3D 85.294 68 8 2 537 603 556609614 556609680 1.250000e-07 69.4
24 TraesCS1D01G213600 chr3B 88.366 361 28 3 6492 6840 687751395 687751753 8.350000e-114 422.0
25 TraesCS1D01G213600 chr3B 89.846 325 18 8 6491 6802 790491235 790491557 3.020000e-108 403.0
26 TraesCS1D01G213600 chr3B 84.865 185 27 1 6491 6674 589532547 589532731 1.190000e-42 185.0
27 TraesCS1D01G213600 chr4A 85.791 373 29 13 6486 6845 616240791 616241152 2.370000e-99 374.0
28 TraesCS1D01G213600 chr5B 81.348 445 60 11 6518 6945 338502630 338502192 2.400000e-89 340.0
29 TraesCS1D01G213600 chr5B 82.692 312 38 10 6491 6789 300125283 300125591 5.350000e-66 263.0
30 TraesCS1D01G213600 chr5B 76.718 262 44 8 4502 4758 702423878 702424127 5.670000e-26 130.0
31 TraesCS1D01G213600 chr6D 83.861 316 35 9 6493 6795 22991038 22990726 3.180000e-73 287.0
32 TraesCS1D01G213600 chr6D 76.265 257 46 13 4503 4756 380795656 380795412 9.480000e-24 122.0
33 TraesCS1D01G213600 chr5D 77.256 277 39 16 4492 4758 175768200 175767938 2.620000e-29 141.0
34 TraesCS1D01G213600 chr5D 85.938 64 9 0 548 611 490163121 490163058 1.250000e-07 69.4
35 TraesCS1D01G213600 chr5D 100.000 28 0 0 6364 6391 521675727 521675700 1.300000e-02 52.8
36 TraesCS1D01G213600 chr7D 83.333 66 9 2 568 631 615875638 615875573 7.540000e-05 60.2
37 TraesCS1D01G213600 chr2D 100.000 29 0 0 575 603 14859572 14859544 4.000000e-03 54.7


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 TraesCS1D01G213600 chr1D 298684495 298691454 6959 True 5974.5 6610 100.0000 1 6960 2 chr1D.!!$R3 6959
1 TraesCS1D01G213600 chr1B 402139582 402146546 6964 True 1902.2 4837 94.7036 70 6498 5 chr1B.!!$R1 6428
2 TraesCS1D01G213600 chr1A 372624251 372638076 13825 True 2176.0 2874 94.4870 32 6493 5 chr1A.!!$R2 6461

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
930 942 1.153168 CGTCCCATTTCGGCATCCT 60.153 57.895 0.0 0.00 0.00 3.24 F
1740 1755 0.394938 TGTACAAGTGTCATGCCCGT 59.605 50.000 0.0 0.00 0.00 5.28 F
2730 6135 0.370273 GCGTTGCCACTGATAGAACG 59.630 55.000 0.0 0.00 41.72 3.95 F
3391 6799 1.094785 CTTCCCTTGCACAATACGGG 58.905 55.000 0.0 0.75 36.21 5.28 F
5262 9703 2.874086 GTTAGCCACTTTAACACCGTGT 59.126 45.455 0.0 0.00 32.56 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 5289 5.462530 TCGACTAAAAGTCAGAACCATGA 57.537 39.130 7.75 0.0 45.30 3.07 R
3210 6618 6.524101 AAAAATACATGGTTTAGTCGGCAT 57.476 33.333 0.00 0.0 0.00 4.40 R
4692 9069 3.921677 TGATCTTCCACGTACCACTTTC 58.078 45.455 0.00 0.0 0.00 2.62 R
5330 9771 3.191888 AGAGAAGAGGTCCTTAAGCCA 57.808 47.619 0.00 0.0 34.68 4.75 R
6540 11417 0.174617 CGTTGGGCCAACTTTTGTGT 59.825 50.000 38.24 0.0 41.62 3.72 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
20 21 3.949842 TGAGTCTGACTCCAAGTGATG 57.050 47.619 29.42 0.00 44.44 3.07
38 39 7.630242 AGTGATGGTAAACAAACTATCATGG 57.370 36.000 6.36 0.00 45.43 3.66
52 53 3.577649 ATCATGGTCTATCCGCTTACG 57.422 47.619 0.00 0.00 39.52 3.18
82 83 2.036733 TGTCGACGAGATGAAGGGTTTT 59.963 45.455 11.62 0.00 0.00 2.43
95 96 8.390921 AGATGAAGGGTTTTCTTCTAACCATAA 58.609 33.333 7.04 0.00 45.51 1.90
106 107 7.914427 TCTTCTAACCATAAAGGAGCATAGA 57.086 36.000 0.00 0.00 41.22 1.98
182 183 5.183904 GGAAGTTTGCAGGAATGAACTATGT 59.816 40.000 0.00 0.00 32.44 2.29
207 208 3.045634 ACATGGTTCCATATCCCTTCGA 58.954 45.455 3.88 0.00 0.00 3.71
236 237 1.459450 TGGATGCTTTAAACTCGGGC 58.541 50.000 0.00 0.00 0.00 6.13
262 264 4.821805 ACCCGATATCCTTAAACAATGCAG 59.178 41.667 0.00 0.00 0.00 4.41
273 275 1.401761 ACAATGCAGCACTTCCAACA 58.598 45.000 0.00 0.00 0.00 3.33
564 572 7.284716 TGGACTACACTATAAATCTGACGTCAT 59.715 37.037 20.40 6.67 0.00 3.06
585 593 7.319646 GTCATACTTTTTACCATGGCAAATCA 58.680 34.615 13.04 0.66 0.00 2.57
635 643 2.289820 CGAGGATGTCAAATGAGCATGG 59.710 50.000 0.00 0.00 0.00 3.66
752 763 8.674607 ACGTCAGATTTTTCTTTTAGTGTTTCT 58.325 29.630 0.00 0.00 0.00 2.52
808 820 3.589288 AGGAAAACAGAGGCTATTGGACT 59.411 43.478 0.00 0.00 34.86 3.85
930 942 1.153168 CGTCCCATTTCGGCATCCT 60.153 57.895 0.00 0.00 0.00 3.24
962 974 4.520492 CCACATAACTGCTCACTTCCTTTT 59.480 41.667 0.00 0.00 0.00 2.27
1341 1356 3.414269 TGGTACGTTCCCCTTTCATTTC 58.586 45.455 8.91 0.00 0.00 2.17
1507 1522 2.437518 TTAGCGGCCGTGCACAACTA 62.438 55.000 28.70 14.52 37.31 2.24
1618 1633 1.838112 TTGATTGGATGTCTGTGGGC 58.162 50.000 0.00 0.00 0.00 5.36
1678 1693 4.403113 TGCATATTCAGGACATGTTGCATT 59.597 37.500 12.31 0.00 34.24 3.56
1712 1727 3.957497 TGATTATGGGTGTATGGTTTGCC 59.043 43.478 0.00 0.00 0.00 4.52
1740 1755 0.394938 TGTACAAGTGTCATGCCCGT 59.605 50.000 0.00 0.00 0.00 5.28
1761 1776 6.368516 CCCGTTGTAATTTCTGCATTTTCATT 59.631 34.615 0.00 0.00 0.00 2.57
1766 1781 9.491675 TTGTAATTTCTGCATTTTCATTCACAT 57.508 25.926 0.00 0.00 0.00 3.21
1777 1792 5.867903 TTTCATTCACATTGTTCCAACCT 57.132 34.783 0.00 0.00 0.00 3.50
1778 1793 5.867903 TTCATTCACATTGTTCCAACCTT 57.132 34.783 0.00 0.00 0.00 3.50
1887 5289 6.114187 TCTGACTGTTACATGATCTTGGTT 57.886 37.500 12.76 0.00 0.00 3.67
2161 5563 2.538333 GCAGACGCTGTGCATCATTTAG 60.538 50.000 8.32 0.00 40.86 1.85
2260 5665 8.550376 ACGTTTACATTAGAAAAGTAAAAGCGA 58.450 29.630 12.94 0.00 39.29 4.93
2277 5682 4.258702 AGCGATTATGATAGCGGAACTT 57.741 40.909 0.00 0.00 38.71 2.66
2435 5840 7.226720 CGATAACCTGTTTTAGTCATATGCCTT 59.773 37.037 0.00 0.00 0.00 4.35
2436 5841 6.515272 AACCTGTTTTAGTCATATGCCTTG 57.485 37.500 0.00 0.00 0.00 3.61
2730 6135 0.370273 GCGTTGCCACTGATAGAACG 59.630 55.000 0.00 0.00 41.72 3.95
2840 6248 6.687105 AGACGCTTCATTTTAATTATGCGTTC 59.313 34.615 17.69 12.94 44.17 3.95
3056 6464 2.900546 TGTTGTCCCTGGTTTGTGTTTT 59.099 40.909 0.00 0.00 0.00 2.43
3210 6618 8.200120 CACTATTCAATGAGTGAGGTAAGATCA 58.800 37.037 0.00 0.00 44.88 2.92
3391 6799 1.094785 CTTCCCTTGCACAATACGGG 58.905 55.000 0.00 0.75 36.21 5.28
4598 8974 6.842437 ATGGATCTAGCATGTATAAGTCGT 57.158 37.500 0.00 0.00 0.00 4.34
4599 8975 7.939784 ATGGATCTAGCATGTATAAGTCGTA 57.060 36.000 0.00 0.00 0.00 3.43
4600 8976 7.939784 TGGATCTAGCATGTATAAGTCGTAT 57.060 36.000 0.00 0.00 0.00 3.06
4601 8977 9.628500 ATGGATCTAGCATGTATAAGTCGTATA 57.372 33.333 0.00 0.00 0.00 1.47
4602 8978 9.457436 TGGATCTAGCATGTATAAGTCGTATAA 57.543 33.333 0.00 0.00 0.00 0.98
4603 8979 9.938670 GGATCTAGCATGTATAAGTCGTATAAG 57.061 37.037 0.00 0.00 0.00 1.73
4692 9069 8.839343 TGCATACCATAAGTGAAAATCATAGTG 58.161 33.333 0.00 0.00 0.00 2.74
4698 9075 9.778993 CCATAAGTGAAAATCATAGTGAAAGTG 57.221 33.333 0.00 0.00 0.00 3.16
4723 9100 5.424121 ACGTGGAAGATCAAAAAGAGTTG 57.576 39.130 0.00 0.00 0.00 3.16
4800 9210 9.614792 AACTTTACATCTTAAAGACTGTCAGTT 57.385 29.630 7.00 6.30 37.80 3.16
5182 9623 5.122869 TGACATGCTTATTGCTTGACTTCTC 59.877 40.000 9.85 0.00 46.07 2.87
5215 9656 6.073314 AGCCTATATCCATGAAATGCACTTT 58.927 36.000 0.00 0.00 44.97 2.66
5216 9657 6.208204 AGCCTATATCCATGAAATGCACTTTC 59.792 38.462 12.10 12.10 44.97 2.62
5234 9675 8.303876 TGCACTTTCCTCTTTGATAATTTTACC 58.696 33.333 0.00 0.00 0.00 2.85
5256 9697 5.172934 CCGTATGAGTTAGCCACTTTAACA 58.827 41.667 0.00 0.00 35.01 2.41
5262 9703 2.874086 GTTAGCCACTTTAACACCGTGT 59.126 45.455 0.00 0.00 32.56 4.49
5299 9740 8.690203 TCAAGGTTTTGATTCTAATGACAGAA 57.310 30.769 0.00 0.00 38.37 3.02
5301 9742 8.571336 CAAGGTTTTGATTCTAATGACAGAACT 58.429 33.333 0.00 0.00 37.37 3.01
5398 9839 5.408299 TCAGTTGAATGAAGAATGGTGTACG 59.592 40.000 0.00 0.00 0.00 3.67
5515 9956 2.558359 GTTTATGCTGGTTGCTGAGGTT 59.442 45.455 0.00 0.00 43.37 3.50
5655 10096 9.952030 TTTGTGAGGTATGTATTATCTGTTGAA 57.048 29.630 0.00 0.00 0.00 2.69
5694 10135 6.210385 ACCAAGTGGACATAATGCAAAATGTA 59.790 34.615 15.08 1.37 36.48 2.29
5869 10311 1.004277 CTGCGCTCGAGTTCGTTTCT 61.004 55.000 15.13 0.00 40.80 2.52
5920 10362 2.955660 ACTAGGAGAATTCGAGCCTGAG 59.044 50.000 20.76 16.55 32.04 3.35
6004 10446 4.215399 TGTCAGCACATAAAACAACTAGGC 59.785 41.667 0.00 0.00 0.00 3.93
6275 10717 8.097662 TCACAGTATGGTTGATACATGTGTTAA 58.902 33.333 9.11 1.53 43.62 2.01
6370 10828 1.559682 TGATTGTAACCTGCTCCCTCC 59.440 52.381 0.00 0.00 0.00 4.30
6384 10842 3.967987 GCTCCCTCCGTCCCATAATATAT 59.032 47.826 0.00 0.00 0.00 0.86
6494 11371 9.803507 AAATAATGATCCTCATCTGCATTTAGA 57.196 29.630 0.00 0.00 35.76 2.10
6495 11372 9.451002 AATAATGATCCTCATCTGCATTTAGAG 57.549 33.333 0.00 0.00 35.76 2.43
6496 11373 4.639334 TGATCCTCATCTGCATTTAGAGC 58.361 43.478 0.00 0.00 0.00 4.09
6497 11374 4.102054 TGATCCTCATCTGCATTTAGAGCA 59.898 41.667 0.00 0.00 40.19 4.26
6499 11376 4.194640 TCCTCATCTGCATTTAGAGCAAC 58.805 43.478 0.00 0.00 42.17 4.17
6501 11378 4.272991 CCTCATCTGCATTTAGAGCAACTC 59.727 45.833 0.00 0.00 42.17 3.01
6502 11379 4.194640 TCATCTGCATTTAGAGCAACTCC 58.805 43.478 0.00 0.00 42.17 3.85
6503 11380 3.701205 TCTGCATTTAGAGCAACTCCA 57.299 42.857 0.00 0.00 42.17 3.86
6504 11381 4.019792 TCTGCATTTAGAGCAACTCCAA 57.980 40.909 0.00 0.00 42.17 3.53
6507 11384 3.444742 TGCATTTAGAGCAACTCCAATGG 59.555 43.478 14.39 0.00 39.39 3.16
6508 11385 3.181483 GCATTTAGAGCAACTCCAATGGG 60.181 47.826 0.00 0.00 34.69 4.00
6509 11386 2.806945 TTAGAGCAACTCCAATGGGG 57.193 50.000 0.00 0.00 38.37 4.96
6510 11387 0.255890 TAGAGCAACTCCAATGGGGC 59.744 55.000 0.00 0.00 36.21 5.80
6511 11388 2.361610 AGCAACTCCAATGGGGCG 60.362 61.111 0.00 0.00 36.21 6.13
6525 11402 2.874751 GGCGACCCATTTTGTCCG 59.125 61.111 0.00 0.00 0.00 4.79
6526 11403 1.969589 GGCGACCCATTTTGTCCGT 60.970 57.895 0.00 0.00 0.00 4.69
6527 11404 1.520600 GGCGACCCATTTTGTCCGTT 61.521 55.000 0.00 0.00 0.00 4.44
6529 11406 1.928595 GCGACCCATTTTGTCCGTTTG 60.929 52.381 0.00 0.00 0.00 2.93
6531 11408 3.904586 CCCATTTTGTCCGTTTGGG 57.095 52.632 0.00 0.00 41.02 4.12
6532 11409 1.044611 CCCATTTTGTCCGTTTGGGT 58.955 50.000 0.00 0.00 41.78 4.51
6534 11411 2.628657 CCCATTTTGTCCGTTTGGGTTA 59.371 45.455 0.00 0.00 41.78 2.85
6535 11412 3.259625 CCCATTTTGTCCGTTTGGGTTAT 59.740 43.478 0.00 0.00 41.78 1.89
6536 11413 4.490743 CCATTTTGTCCGTTTGGGTTATC 58.509 43.478 0.00 0.00 37.00 1.75
6537 11414 4.490743 CATTTTGTCCGTTTGGGTTATCC 58.509 43.478 0.00 0.00 37.00 2.59
6538 11415 2.953284 TTGTCCGTTTGGGTTATCCA 57.047 45.000 0.00 0.00 45.43 3.41
6548 11425 5.782893 TTTGGGTTATCCAGACACAAAAG 57.217 39.130 2.47 0.00 44.75 2.27
6549 11426 4.447138 TGGGTTATCCAGACACAAAAGT 57.553 40.909 0.00 0.00 41.46 2.66
6550 11427 4.798882 TGGGTTATCCAGACACAAAAGTT 58.201 39.130 0.00 0.00 41.46 2.66
6551 11428 4.582656 TGGGTTATCCAGACACAAAAGTTG 59.417 41.667 0.00 0.00 41.46 3.16
6552 11429 4.022329 GGGTTATCCAGACACAAAAGTTGG 60.022 45.833 0.00 0.00 35.00 3.77
6553 11430 4.546570 GTTATCCAGACACAAAAGTTGGC 58.453 43.478 0.00 0.00 34.12 4.52
6555 11432 0.389025 CCAGACACAAAAGTTGGCCC 59.611 55.000 0.00 0.00 34.12 5.80
6556 11433 1.110442 CAGACACAAAAGTTGGCCCA 58.890 50.000 0.00 0.00 34.12 5.36
6557 11434 1.480137 CAGACACAAAAGTTGGCCCAA 59.520 47.619 0.00 0.00 34.12 4.12
6558 11435 1.480545 AGACACAAAAGTTGGCCCAAC 59.519 47.619 19.12 19.12 43.83 3.77
6578 11455 3.351416 GGCGACCCAAACGGACAC 61.351 66.667 0.00 0.00 34.64 3.67
6579 11456 2.589442 GCGACCCAAACGGACACA 60.589 61.111 0.00 0.00 34.64 3.72
6580 11457 2.604174 GCGACCCAAACGGACACAG 61.604 63.158 0.00 0.00 34.64 3.66
6581 11458 2.604174 CGACCCAAACGGACACAGC 61.604 63.158 0.00 0.00 34.64 4.40
6600 11477 3.993584 TCCGCCCGCTGTACGTTT 61.994 61.111 0.00 0.00 41.42 3.60
6602 11479 3.834373 CGCCCGCTGTACGTTTCG 61.834 66.667 0.00 0.00 41.42 3.46
6604 11481 3.007070 GCCCGCTGTACGTTTCGTG 62.007 63.158 0.00 0.00 41.39 4.35
6605 11482 1.662446 CCCGCTGTACGTTTCGTGT 60.662 57.895 0.00 0.00 41.39 4.49
6606 11483 1.611592 CCCGCTGTACGTTTCGTGTC 61.612 60.000 0.00 0.00 41.39 3.67
6607 11484 1.611592 CCGCTGTACGTTTCGTGTCC 61.612 60.000 0.00 0.00 41.39 4.02
6619 11496 2.186903 GTGTCCACGCGGATCCAT 59.813 61.111 12.47 0.00 45.33 3.41
6620 11497 1.449601 GTGTCCACGCGGATCCATT 60.450 57.895 12.47 0.00 45.33 3.16
6621 11498 1.024579 GTGTCCACGCGGATCCATTT 61.025 55.000 12.47 0.00 45.33 2.32
6622 11499 0.742990 TGTCCACGCGGATCCATTTC 60.743 55.000 12.47 0.00 45.33 2.17
6634 11511 4.925068 GGATCCATTTCCGTCTCAAATTG 58.075 43.478 6.95 0.00 0.00 2.32
6639 11516 5.767665 TCCATTTCCGTCTCAAATTGAAGAA 59.232 36.000 0.00 0.00 0.00 2.52
6641 11518 6.922957 CCATTTCCGTCTCAAATTGAAGAAAA 59.077 34.615 11.46 3.96 0.00 2.29
6642 11519 7.599998 CCATTTCCGTCTCAAATTGAAGAAAAT 59.400 33.333 11.46 5.53 0.00 1.82
6644 11521 8.940768 TTTCCGTCTCAAATTGAAGAAAATTT 57.059 26.923 0.00 0.00 39.71 1.82
6655 11532 6.676237 TTGAAGAAAATTTGGGTCAAAAGC 57.324 33.333 7.75 0.00 36.90 3.51
6656 11533 4.808364 TGAAGAAAATTTGGGTCAAAAGCG 59.192 37.500 0.00 0.00 36.90 4.68
6657 11534 3.727726 AGAAAATTTGGGTCAAAAGCGG 58.272 40.909 0.00 0.00 36.90 5.52
6658 11535 1.877637 AAATTTGGGTCAAAAGCGGC 58.122 45.000 0.00 0.00 36.90 6.53
6659 11536 0.319469 AATTTGGGTCAAAAGCGGCG 60.319 50.000 0.51 0.51 36.90 6.46
6660 11537 2.763627 ATTTGGGTCAAAAGCGGCGC 62.764 55.000 26.86 26.86 36.90 6.53
6661 11538 4.947147 TGGGTCAAAAGCGGCGCT 62.947 61.111 31.35 31.35 42.56 5.92
6664 11541 2.476499 GTCAAAAGCGGCGCTCTC 59.524 61.111 36.44 18.68 38.25 3.20
6665 11542 2.029844 GTCAAAAGCGGCGCTCTCT 61.030 57.895 36.44 17.88 38.25 3.10
6666 11543 2.029288 TCAAAAGCGGCGCTCTCTG 61.029 57.895 36.44 28.75 38.25 3.35
6667 11544 2.031163 AAAAGCGGCGCTCTCTGT 59.969 55.556 36.44 17.00 38.25 3.41
6668 11545 2.320587 AAAAGCGGCGCTCTCTGTG 61.321 57.895 36.44 0.00 38.25 3.66
6674 11551 4.828925 GCGCTCTCTGTGCCCTCC 62.829 72.222 0.00 0.00 45.73 4.30
6675 11552 4.154347 CGCTCTCTGTGCCCTCCC 62.154 72.222 0.00 0.00 0.00 4.30
6676 11553 3.791586 GCTCTCTGTGCCCTCCCC 61.792 72.222 0.00 0.00 0.00 4.81
6677 11554 3.465403 CTCTCTGTGCCCTCCCCG 61.465 72.222 0.00 0.00 0.00 5.73
6678 11555 4.316823 TCTCTGTGCCCTCCCCGT 62.317 66.667 0.00 0.00 0.00 5.28
6679 11556 3.775654 CTCTGTGCCCTCCCCGTC 61.776 72.222 0.00 0.00 0.00 4.79
6699 11576 3.790437 CCTCTGTCCGGGCTGCAT 61.790 66.667 7.97 0.00 0.00 3.96
6717 11594 4.982701 GTGCTGCCTGCCCCACTT 62.983 66.667 0.00 0.00 42.00 3.16
6718 11595 4.980702 TGCTGCCTGCCCCACTTG 62.981 66.667 0.00 0.00 42.00 3.16
6723 11600 2.757099 CCTGCCCCACTTGCCATC 60.757 66.667 0.00 0.00 0.00 3.51
6724 11601 2.757099 CTGCCCCACTTGCCATCC 60.757 66.667 0.00 0.00 0.00 3.51
6726 11603 3.070576 GCCCCACTTGCCATCCAC 61.071 66.667 0.00 0.00 0.00 4.02
6729 11606 2.440147 CCACTTGCCATCCACCCA 59.560 61.111 0.00 0.00 0.00 4.51
6730 11607 1.000739 CCACTTGCCATCCACCCAT 59.999 57.895 0.00 0.00 0.00 4.00
6731 11608 1.039233 CCACTTGCCATCCACCCATC 61.039 60.000 0.00 0.00 0.00 3.51
6732 11609 1.039233 CACTTGCCATCCACCCATCC 61.039 60.000 0.00 0.00 0.00 3.51
6733 11610 1.825191 CTTGCCATCCACCCATCCG 60.825 63.158 0.00 0.00 0.00 4.18
6735 11612 2.203209 GCCATCCACCCATCCGTC 60.203 66.667 0.00 0.00 0.00 4.79
6736 11613 2.510906 CCATCCACCCATCCGTCC 59.489 66.667 0.00 0.00 0.00 4.79
6739 11616 1.385915 ATCCACCCATCCGTCCCAT 60.386 57.895 0.00 0.00 0.00 4.00
6740 11617 1.418908 ATCCACCCATCCGTCCCATC 61.419 60.000 0.00 0.00 0.00 3.51
6741 11618 2.510906 CACCCATCCGTCCCATCC 59.489 66.667 0.00 0.00 0.00 3.51
6742 11619 3.161450 ACCCATCCGTCCCATCCG 61.161 66.667 0.00 0.00 0.00 4.18
6743 11620 3.941188 CCCATCCGTCCCATCCGG 61.941 72.222 0.00 0.00 46.83 5.14
6745 11622 2.421739 CATCCGTCCCATCCGGTC 59.578 66.667 0.00 0.00 45.63 4.79
6747 11624 1.833049 ATCCGTCCCATCCGGTCTC 60.833 63.158 0.00 0.00 45.63 3.36
6749 11626 2.491022 CCGTCCCATCCGGTCTCTC 61.491 68.421 0.00 0.00 40.59 3.20
6750 11627 1.454111 CGTCCCATCCGGTCTCTCT 60.454 63.158 0.00 0.00 0.00 3.10
6751 11628 1.448922 CGTCCCATCCGGTCTCTCTC 61.449 65.000 0.00 0.00 0.00 3.20
6752 11629 1.110518 GTCCCATCCGGTCTCTCTCC 61.111 65.000 0.00 0.00 0.00 3.71
6753 11630 1.231641 CCCATCCGGTCTCTCTCCT 59.768 63.158 0.00 0.00 0.00 3.69
6756 11633 0.184933 CATCCGGTCTCTCTCCTCCT 59.815 60.000 0.00 0.00 0.00 3.69
6757 11634 0.930726 ATCCGGTCTCTCTCCTCCTT 59.069 55.000 0.00 0.00 0.00 3.36
6760 11637 1.903183 CCGGTCTCTCTCCTCCTTTTT 59.097 52.381 0.00 0.00 0.00 1.94
6761 11638 2.093921 CCGGTCTCTCTCCTCCTTTTTC 60.094 54.545 0.00 0.00 0.00 2.29
6762 11639 2.829120 CGGTCTCTCTCCTCCTTTTTCT 59.171 50.000 0.00 0.00 0.00 2.52
6763 11640 3.259625 CGGTCTCTCTCCTCCTTTTTCTT 59.740 47.826 0.00 0.00 0.00 2.52
6764 11641 4.619628 CGGTCTCTCTCCTCCTTTTTCTTC 60.620 50.000 0.00 0.00 0.00 2.87
6765 11642 4.530553 GGTCTCTCTCCTCCTTTTTCTTCT 59.469 45.833 0.00 0.00 0.00 2.85
6766 11643 5.337250 GGTCTCTCTCCTCCTTTTTCTTCTC 60.337 48.000 0.00 0.00 0.00 2.87
6768 11645 3.841255 TCTCTCCTCCTTTTTCTTCTCCC 59.159 47.826 0.00 0.00 0.00 4.30
6770 11647 3.328050 TCTCCTCCTTTTTCTTCTCCCAC 59.672 47.826 0.00 0.00 0.00 4.61
6771 11648 2.375509 TCCTCCTTTTTCTTCTCCCACC 59.624 50.000 0.00 0.00 0.00 4.61
6772 11649 2.555448 CCTCCTTTTTCTTCTCCCACCC 60.555 54.545 0.00 0.00 0.00 4.61
6773 11650 2.108250 CTCCTTTTTCTTCTCCCACCCA 59.892 50.000 0.00 0.00 0.00 4.51
6775 11652 2.158460 CCTTTTTCTTCTCCCACCCACT 60.158 50.000 0.00 0.00 0.00 4.00
6776 11653 2.951229 TTTTCTTCTCCCACCCACTC 57.049 50.000 0.00 0.00 0.00 3.51
6777 11654 1.814429 TTTCTTCTCCCACCCACTCA 58.186 50.000 0.00 0.00 0.00 3.41
6778 11655 1.056660 TTCTTCTCCCACCCACTCAC 58.943 55.000 0.00 0.00 0.00 3.51
6779 11656 0.836400 TCTTCTCCCACCCACTCACC 60.836 60.000 0.00 0.00 0.00 4.02
6780 11657 1.842381 CTTCTCCCACCCACTCACCC 61.842 65.000 0.00 0.00 0.00 4.61
6781 11658 2.529136 CTCCCACCCACTCACCCA 60.529 66.667 0.00 0.00 0.00 4.51
6783 11660 3.966543 CCCACCCACTCACCCACC 61.967 72.222 0.00 0.00 0.00 4.61
6784 11661 3.966543 CCACCCACTCACCCACCC 61.967 72.222 0.00 0.00 0.00 4.61
6785 11662 3.174987 CACCCACTCACCCACCCA 61.175 66.667 0.00 0.00 0.00 4.51
6786 11663 3.175710 ACCCACTCACCCACCCAC 61.176 66.667 0.00 0.00 0.00 4.61
6789 11666 3.174987 CACTCACCCACCCACCCA 61.175 66.667 0.00 0.00 0.00 4.51
6790 11667 2.854032 ACTCACCCACCCACCCAG 60.854 66.667 0.00 0.00 0.00 4.45
6791 11668 4.351054 CTCACCCACCCACCCAGC 62.351 72.222 0.00 0.00 0.00 4.85
6792 11669 4.918360 TCACCCACCCACCCAGCT 62.918 66.667 0.00 0.00 0.00 4.24
6793 11670 4.351054 CACCCACCCACCCAGCTC 62.351 72.222 0.00 0.00 0.00 4.09
6796 11673 4.394712 CCACCCACCCAGCTCGTC 62.395 72.222 0.00 0.00 0.00 4.20
6797 11674 4.394712 CACCCACCCAGCTCGTCC 62.395 72.222 0.00 0.00 0.00 4.79
6799 11676 3.775654 CCCACCCAGCTCGTCCTC 61.776 72.222 0.00 0.00 0.00 3.71
6800 11677 3.775654 CCACCCAGCTCGTCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
6801 11678 2.681778 CACCCAGCTCGTCCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
6804 11681 2.492090 CCAGCTCGTCCTCCTTCG 59.508 66.667 0.00 0.00 0.00 3.79
6805 11682 2.492090 CAGCTCGTCCTCCTTCGG 59.508 66.667 0.00 0.00 0.00 4.30
6806 11683 3.453679 AGCTCGTCCTCCTTCGGC 61.454 66.667 0.00 0.00 0.00 5.54
6807 11684 4.856607 GCTCGTCCTCCTTCGGCG 62.857 72.222 0.00 0.00 0.00 6.46
6808 11685 4.856607 CTCGTCCTCCTTCGGCGC 62.857 72.222 0.00 0.00 0.00 6.53
6826 11703 2.880879 CGATGCTCCGACGTGGTG 60.881 66.667 0.00 0.00 39.52 4.17
6827 11704 2.509336 GATGCTCCGACGTGGTGG 60.509 66.667 0.00 0.00 39.52 4.61
6828 11705 4.082523 ATGCTCCGACGTGGTGGG 62.083 66.667 0.00 0.00 39.52 4.61
6831 11708 4.436998 CTCCGACGTGGTGGGCTC 62.437 72.222 0.00 0.00 39.52 4.70
6840 11717 4.459089 GGTGGGCTCGTGCTCCTC 62.459 72.222 6.92 8.37 39.40 3.71
6841 11718 4.459089 GTGGGCTCGTGCTCCTCC 62.459 72.222 6.92 1.17 39.40 4.30
6898 11775 3.566853 CTGGCCGCGCACATACTG 61.567 66.667 8.75 0.00 0.00 2.74
6908 11785 1.798735 CACATACTGCTGGTGCTGC 59.201 57.895 0.00 0.00 41.07 5.25
6910 11787 0.675837 ACATACTGCTGGTGCTGCTG 60.676 55.000 0.00 0.00 41.07 4.41
6911 11788 1.748122 ATACTGCTGGTGCTGCTGC 60.748 57.895 8.89 8.89 41.07 5.25
6916 11793 4.129737 CTGGTGCTGCTGCCATGC 62.130 66.667 13.47 0.00 38.71 4.06
6925 11802 3.498834 CTGCCATGCGCGTGCTTA 61.499 61.111 24.29 10.83 43.34 3.09
6926 11803 3.444717 CTGCCATGCGCGTGCTTAG 62.445 63.158 24.29 16.15 43.34 2.18
6929 11806 1.882625 CCATGCGCGTGCTTAGCTA 60.883 57.895 24.29 0.00 43.34 3.32
6930 11807 1.561730 CATGCGCGTGCTTAGCTAG 59.438 57.895 23.16 0.19 43.34 3.42
6945 11822 2.090400 GCTAGCTAGCTATGCATGCA 57.910 50.000 33.71 25.04 45.62 3.96
6947 11824 2.352034 GCTAGCTAGCTATGCATGCATG 59.648 50.000 37.43 27.54 45.62 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.949842 CATCACTTGGAGTCAGACTCA 57.050 47.619 28.26 14.09 46.79 3.41
12 13 7.970061 CCATGATAGTTTGTTTACCATCACTTG 59.030 37.037 0.00 0.00 30.80 3.16
13 14 7.669722 ACCATGATAGTTTGTTTACCATCACTT 59.330 33.333 0.00 0.00 30.80 3.16
14 15 7.175104 ACCATGATAGTTTGTTTACCATCACT 58.825 34.615 0.00 0.00 30.80 3.41
15 16 7.336931 AGACCATGATAGTTTGTTTACCATCAC 59.663 37.037 0.00 0.00 30.80 3.06
16 17 7.402054 AGACCATGATAGTTTGTTTACCATCA 58.598 34.615 0.00 0.00 32.20 3.07
17 18 7.865706 AGACCATGATAGTTTGTTTACCATC 57.134 36.000 0.00 0.00 0.00 3.51
18 19 9.561069 GATAGACCATGATAGTTTGTTTACCAT 57.439 33.333 0.00 0.00 0.00 3.55
19 20 7.990886 GGATAGACCATGATAGTTTGTTTACCA 59.009 37.037 0.00 0.00 38.79 3.25
20 21 7.170998 CGGATAGACCATGATAGTTTGTTTACC 59.829 40.741 0.00 0.00 38.90 2.85
21 22 7.307219 GCGGATAGACCATGATAGTTTGTTTAC 60.307 40.741 0.00 0.00 38.90 2.01
22 23 6.704493 GCGGATAGACCATGATAGTTTGTTTA 59.296 38.462 0.00 0.00 38.90 2.01
23 24 5.527582 GCGGATAGACCATGATAGTTTGTTT 59.472 40.000 0.00 0.00 38.90 2.83
24 25 5.057149 GCGGATAGACCATGATAGTTTGTT 58.943 41.667 0.00 0.00 38.90 2.83
25 26 4.345257 AGCGGATAGACCATGATAGTTTGT 59.655 41.667 0.00 0.00 38.90 2.83
26 27 4.887748 AGCGGATAGACCATGATAGTTTG 58.112 43.478 0.00 0.00 38.90 2.93
27 28 5.552870 AAGCGGATAGACCATGATAGTTT 57.447 39.130 0.00 0.00 38.90 2.66
28 29 5.335740 CGTAAGCGGATAGACCATGATAGTT 60.336 44.000 0.00 0.00 38.90 2.24
29 30 4.156190 CGTAAGCGGATAGACCATGATAGT 59.844 45.833 0.00 0.00 38.90 2.12
30 31 4.663166 CGTAAGCGGATAGACCATGATAG 58.337 47.826 0.00 0.00 38.90 2.08
52 53 0.313043 TCTCGTCGACAAAGTGGACC 59.687 55.000 17.16 0.00 37.87 4.46
54 55 1.883926 TCATCTCGTCGACAAAGTGGA 59.116 47.619 17.16 10.75 0.00 4.02
82 83 7.785028 TCTCTATGCTCCTTTATGGTTAGAAGA 59.215 37.037 0.00 0.00 37.07 2.87
95 96 3.181461 CCCACGAAATCTCTATGCTCCTT 60.181 47.826 0.00 0.00 0.00 3.36
106 107 4.023980 TGATAGTCTCACCCACGAAATCT 58.976 43.478 0.00 0.00 0.00 2.40
182 183 5.221641 CGAAGGGATATGGAACCATGTTCTA 60.222 44.000 15.59 1.45 37.82 2.10
207 208 8.184192 CGAGTTTAAAGCATCCAAGATACAATT 58.816 33.333 0.00 0.00 0.00 2.32
236 237 6.485313 TGCATTGTTTAAGGATATCGGGTAAG 59.515 38.462 0.00 0.00 0.00 2.34
255 256 2.512485 TTGTTGGAAGTGCTGCATTG 57.488 45.000 5.27 0.00 0.00 2.82
364 366 1.405463 GGAAGAAACATTCCATCCGCC 59.595 52.381 0.64 0.00 46.77 6.13
564 572 8.153550 ACATTTGATTTGCCATGGTAAAAAGTA 58.846 29.630 28.47 16.18 33.78 2.24
585 593 7.513371 ACATGATTTGCCATGAAAAACATTT 57.487 28.000 10.42 5.80 44.98 2.32
665 673 5.523438 TTAGTTTGCAAGGTCCGATTTTT 57.477 34.783 0.00 0.00 0.00 1.94
667 675 5.523438 TTTTAGTTTGCAAGGTCCGATTT 57.477 34.783 0.00 0.00 0.00 2.17
670 678 4.794655 GCAATTTTAGTTTGCAAGGTCCGA 60.795 41.667 0.00 0.00 46.78 4.55
671 679 3.428534 GCAATTTTAGTTTGCAAGGTCCG 59.571 43.478 0.00 0.00 46.78 4.79
717 728 5.752712 AGAAAAATCTGACGTTTTCTCTGC 58.247 37.500 18.31 2.48 46.23 4.26
722 733 9.285770 ACACTAAAAGAAAAATCTGACGTTTTC 57.714 29.630 15.50 15.50 41.83 2.29
930 942 1.339055 GCAGTTATGTGGCCTGTGAGA 60.339 52.381 3.32 0.00 0.00 3.27
962 974 1.338136 GGAGGCGGAGAAGAATGGGA 61.338 60.000 0.00 0.00 0.00 4.37
1341 1356 4.786575 GGCGCAGAAACTATTTTACGAAAG 59.213 41.667 10.83 0.00 0.00 2.62
1678 1693 4.021456 CACCCATAATCAGGTACGCATCTA 60.021 45.833 0.00 0.00 33.52 1.98
1712 1727 6.017934 GGCATGACACTTGTACAACCATATAG 60.018 42.308 3.59 0.00 0.00 1.31
1740 1755 8.883954 TGTGAATGAAAATGCAGAAATTACAA 57.116 26.923 0.00 0.00 0.00 2.41
1830 5231 6.828502 ACATGTAGTCAGCATAAATACACG 57.171 37.500 0.00 0.00 0.00 4.49
1887 5289 5.462530 TCGACTAAAAGTCAGAACCATGA 57.537 39.130 7.75 0.00 45.30 3.07
2435 5840 9.369672 ACAAGGTTAACATTAAAGGAAATACCA 57.630 29.630 5.01 0.00 42.04 3.25
2436 5841 9.850628 GACAAGGTTAACATTAAAGGAAATACC 57.149 33.333 5.01 0.00 39.35 2.73
2594 5999 7.933577 AGCTGATTATCCAAAAATATCGAGACA 59.066 33.333 0.00 0.00 0.00 3.41
2626 6031 7.515643 GCAACCTATATTGCGATATAAACGTT 58.484 34.615 13.57 12.38 45.08 3.99
2730 6135 7.656707 ATCAAGCAAAAACAATTGACATACC 57.343 32.000 13.59 0.00 34.71 2.73
2840 6248 6.649973 TCAATACCCAACTTTGCAATTTCATG 59.350 34.615 0.00 0.00 0.00 3.07
3210 6618 6.524101 AAAAATACATGGTTTAGTCGGCAT 57.476 33.333 0.00 0.00 0.00 4.40
3391 6799 6.650120 TGTCTTATCTGGATAAACAAGGTCC 58.350 40.000 4.85 0.00 33.34 4.46
4343 8012 6.662755 AGTCTGACTGAATATATGGCCAAAA 58.337 36.000 10.96 0.12 0.00 2.44
4500 8170 4.013728 TCAAGCACGCCTTATATTTTGGT 58.986 39.130 0.00 0.00 31.00 3.67
4601 8977 8.970020 TGCAAGAAAAATATGATGATACCACTT 58.030 29.630 0.00 0.00 0.00 3.16
4602 8978 8.523915 TGCAAGAAAAATATGATGATACCACT 57.476 30.769 0.00 0.00 0.00 4.00
4603 8979 9.585099 TTTGCAAGAAAAATATGATGATACCAC 57.415 29.630 0.00 0.00 0.00 4.16
4673 9050 9.778993 CCACTTTCACTATGATTTTCACTTATG 57.221 33.333 0.00 0.00 0.00 1.90
4692 9069 3.921677 TGATCTTCCACGTACCACTTTC 58.078 45.455 0.00 0.00 0.00 2.62
4698 9075 4.995487 ACTCTTTTTGATCTTCCACGTACC 59.005 41.667 0.00 0.00 0.00 3.34
4723 9100 5.179555 CCTTCCTAAAATATAAGGCGCAGTC 59.820 44.000 10.83 0.00 32.66 3.51
4770 9147 8.958119 ACAGTCTTTAAGATGTAAAGTTGACA 57.042 30.769 0.00 0.00 36.30 3.58
5182 9623 5.250982 TCATGGATATAGGCTTGCATCAAG 58.749 41.667 0.00 2.40 43.57 3.02
5215 9656 9.542462 CTCATACGGTAAAATTATCAAAGAGGA 57.458 33.333 0.00 0.00 0.00 3.71
5216 9657 9.326413 ACTCATACGGTAAAATTATCAAAGAGG 57.674 33.333 0.00 0.00 0.00 3.69
5234 9675 5.063060 GGTGTTAAAGTGGCTAACTCATACG 59.937 44.000 0.00 0.00 38.56 3.06
5256 9697 4.202111 CCTTGAATTCCAGAAAAACACGGT 60.202 41.667 8.09 0.00 0.00 4.83
5262 9703 9.108284 GAATCAAAACCTTGAATTCCAGAAAAA 57.892 29.630 8.09 0.00 44.64 1.94
5330 9771 3.191888 AGAGAAGAGGTCCTTAAGCCA 57.808 47.619 0.00 0.00 34.68 4.75
5398 9839 5.591099 TCTTTCAATCTTTTCAGTGCCAAC 58.409 37.500 0.00 0.00 0.00 3.77
5515 9956 0.324614 CTACAGGATGGGCACACACA 59.675 55.000 0.00 0.00 43.62 3.72
5655 10096 1.771255 ACTTGGTCACTCTTTCTGCCT 59.229 47.619 0.00 0.00 0.00 4.75
5694 10135 4.996758 GCAAAACAAGCCCATCATTACTTT 59.003 37.500 0.00 0.00 0.00 2.66
5869 10311 7.331026 CAAAGTAAGAATCTACCATGTCCTCA 58.669 38.462 0.00 0.00 0.00 3.86
5920 10362 1.082690 GTTCTGTAGGCAGCTTCAGC 58.917 55.000 0.00 0.00 42.29 4.26
6004 10446 0.324645 ATAGGTTGCCCTTTGCCCAG 60.325 55.000 0.00 0.00 42.66 4.45
6275 10717 0.941542 CCGGACACACACAAATTCGT 59.058 50.000 0.00 0.00 0.00 3.85
6494 11371 2.361610 CGCCCCATTGGAGTTGCT 60.362 61.111 3.62 0.00 35.39 3.91
6495 11372 2.361104 TCGCCCCATTGGAGTTGC 60.361 61.111 3.62 0.53 35.07 4.17
6496 11373 2.046285 GGTCGCCCCATTGGAGTTG 61.046 63.158 3.62 0.00 35.07 3.16
6497 11374 2.355115 GGTCGCCCCATTGGAGTT 59.645 61.111 3.62 0.00 35.07 3.01
6507 11384 2.696759 CGGACAAAATGGGTCGCCC 61.697 63.158 7.87 7.87 45.71 6.13
6508 11385 1.520600 AACGGACAAAATGGGTCGCC 61.521 55.000 0.00 0.00 36.12 5.54
6509 11386 0.312729 AAACGGACAAAATGGGTCGC 59.687 50.000 0.00 0.00 36.12 5.19
6510 11387 1.335506 CCAAACGGACAAAATGGGTCG 60.336 52.381 0.00 0.00 36.12 4.79
6511 11388 1.000394 CCCAAACGGACAAAATGGGTC 60.000 52.381 0.90 0.00 44.67 4.46
6514 11391 2.900716 AACCCAAACGGACAAAATGG 57.099 45.000 0.00 0.00 34.64 3.16
6515 11392 4.021894 TGGATAACCCAAACGGACAAAATG 60.022 41.667 0.00 0.00 43.29 2.32
6516 11393 4.153411 TGGATAACCCAAACGGACAAAAT 58.847 39.130 0.00 0.00 43.29 1.82
6518 11395 3.150767 CTGGATAACCCAAACGGACAAA 58.849 45.455 0.00 0.00 46.07 2.83
6519 11396 2.372504 TCTGGATAACCCAAACGGACAA 59.627 45.455 0.00 0.00 46.07 3.18
6520 11397 1.979308 TCTGGATAACCCAAACGGACA 59.021 47.619 0.00 0.00 46.07 4.02
6521 11398 2.289819 TGTCTGGATAACCCAAACGGAC 60.290 50.000 0.00 0.00 46.07 4.79
6522 11399 1.979308 TGTCTGGATAACCCAAACGGA 59.021 47.619 0.00 0.00 46.07 4.69
6524 11401 2.773487 TGTGTCTGGATAACCCAAACG 58.227 47.619 0.00 0.00 46.07 3.60
6525 11402 5.068591 ACTTTTGTGTCTGGATAACCCAAAC 59.931 40.000 0.00 0.00 46.07 2.93
6526 11403 5.205056 ACTTTTGTGTCTGGATAACCCAAA 58.795 37.500 0.00 0.00 46.07 3.28
6527 11404 4.798882 ACTTTTGTGTCTGGATAACCCAA 58.201 39.130 0.00 0.00 46.07 4.12
6529 11406 4.022329 CCAACTTTTGTGTCTGGATAACCC 60.022 45.833 0.00 0.00 34.81 4.11
6531 11408 4.546570 GCCAACTTTTGTGTCTGGATAAC 58.453 43.478 0.00 0.00 0.00 1.89
6532 11409 3.572255 GGCCAACTTTTGTGTCTGGATAA 59.428 43.478 0.00 0.00 0.00 1.75
6534 11411 1.963515 GGCCAACTTTTGTGTCTGGAT 59.036 47.619 0.00 0.00 0.00 3.41
6535 11412 1.398692 GGCCAACTTTTGTGTCTGGA 58.601 50.000 0.00 0.00 0.00 3.86
6536 11413 0.389025 GGGCCAACTTTTGTGTCTGG 59.611 55.000 4.39 0.00 0.00 3.86
6537 11414 1.110442 TGGGCCAACTTTTGTGTCTG 58.890 50.000 2.13 0.00 0.00 3.51
6538 11415 1.480545 GTTGGGCCAACTTTTGTGTCT 59.519 47.619 36.16 0.00 40.73 3.41
6539 11416 1.801025 CGTTGGGCCAACTTTTGTGTC 60.801 52.381 38.24 16.11 41.62 3.67
6540 11417 0.174617 CGTTGGGCCAACTTTTGTGT 59.825 50.000 38.24 0.00 41.62 3.72
6543 11420 1.068921 CCCGTTGGGCCAACTTTTG 59.931 57.895 38.24 25.87 41.62 2.44
6560 11437 4.629523 TGTCCGTTTGGGTCGCCC 62.630 66.667 7.87 7.87 45.71 6.13
6563 11440 2.604174 GCTGTGTCCGTTTGGGTCG 61.604 63.158 0.00 0.00 37.00 4.79
6564 11441 2.604174 CGCTGTGTCCGTTTGGGTC 61.604 63.158 0.00 0.00 37.00 4.46
6565 11442 2.590575 CGCTGTGTCCGTTTGGGT 60.591 61.111 0.00 0.00 37.00 4.51
6566 11443 2.590575 ACGCTGTGTCCGTTTGGG 60.591 61.111 0.00 0.00 34.96 4.12
6586 11463 2.735857 ACGAAACGTACAGCGGGC 60.736 61.111 0.00 0.00 46.52 6.13
6587 11464 1.611592 GACACGAAACGTACAGCGGG 61.612 60.000 0.00 0.00 46.52 6.13
6590 11467 0.505655 GTGGACACGAAACGTACAGC 59.494 55.000 0.00 0.00 38.32 4.40
6606 11483 3.420943 GGAAATGGATCCGCGTGG 58.579 61.111 9.28 9.28 0.00 4.94
6612 11489 4.640201 TCAATTTGAGACGGAAATGGATCC 59.360 41.667 4.20 4.20 36.05 3.36
6613 11490 5.818136 TCAATTTGAGACGGAAATGGATC 57.182 39.130 0.00 0.00 0.00 3.36
6614 11491 5.945784 TCTTCAATTTGAGACGGAAATGGAT 59.054 36.000 0.00 0.00 0.00 3.41
6615 11492 5.312895 TCTTCAATTTGAGACGGAAATGGA 58.687 37.500 0.00 0.00 0.00 3.41
6616 11493 5.627499 TCTTCAATTTGAGACGGAAATGG 57.373 39.130 0.00 0.00 0.00 3.16
6617 11494 7.928908 TTTTCTTCAATTTGAGACGGAAATG 57.071 32.000 13.88 0.00 0.00 2.32
6618 11495 9.546428 AAATTTTCTTCAATTTGAGACGGAAAT 57.454 25.926 13.88 10.23 35.45 2.17
6619 11496 8.940768 AAATTTTCTTCAATTTGAGACGGAAA 57.059 26.923 0.00 6.91 35.45 3.13
6628 11505 9.505995 CTTTTGACCCAAATTTTCTTCAATTTG 57.494 29.630 10.61 10.61 46.87 2.32
6630 11507 7.467131 CGCTTTTGACCCAAATTTTCTTCAATT 60.467 33.333 6.13 0.00 33.19 2.32
6631 11508 6.018016 CGCTTTTGACCCAAATTTTCTTCAAT 60.018 34.615 6.13 0.00 33.19 2.57
6632 11509 5.293079 CGCTTTTGACCCAAATTTTCTTCAA 59.707 36.000 0.00 0.00 33.19 2.69
6634 11511 4.211164 CCGCTTTTGACCCAAATTTTCTTC 59.789 41.667 0.00 0.00 33.19 2.87
6639 11516 1.871822 CGCCGCTTTTGACCCAAATTT 60.872 47.619 0.00 0.00 33.19 1.82
6641 11518 1.288752 CGCCGCTTTTGACCCAAAT 59.711 52.632 0.00 0.00 33.19 2.32
6642 11519 2.725008 CGCCGCTTTTGACCCAAA 59.275 55.556 0.00 0.00 0.00 3.28
6644 11521 4.947147 AGCGCCGCTTTTGACCCA 62.947 61.111 5.39 0.00 33.89 4.51
6645 11522 4.103103 GAGCGCCGCTTTTGACCC 62.103 66.667 15.07 0.00 39.88 4.46
6646 11523 3.028366 GAGAGCGCCGCTTTTGACC 62.028 63.158 15.07 0.00 39.88 4.02
6647 11524 2.029844 AGAGAGCGCCGCTTTTGAC 61.030 57.895 15.07 0.00 39.88 3.18
6648 11525 2.029288 CAGAGAGCGCCGCTTTTGA 61.029 57.895 15.07 0.00 39.88 2.69
6649 11526 2.320587 ACAGAGAGCGCCGCTTTTG 61.321 57.895 15.07 14.49 39.88 2.44
6650 11527 2.031163 ACAGAGAGCGCCGCTTTT 59.969 55.556 15.07 4.62 39.88 2.27
6651 11528 2.740055 CACAGAGAGCGCCGCTTT 60.740 61.111 15.07 7.73 39.88 3.51
6656 11533 4.828925 GAGGGCACAGAGAGCGCC 62.829 72.222 2.29 0.00 44.98 6.53
6657 11534 4.828925 GGAGGGCACAGAGAGCGC 62.829 72.222 0.00 0.00 44.31 5.92
6658 11535 4.154347 GGGAGGGCACAGAGAGCG 62.154 72.222 0.00 0.00 0.00 5.03
6659 11536 3.791586 GGGGAGGGCACAGAGAGC 61.792 72.222 0.00 0.00 0.00 4.09
6660 11537 3.465403 CGGGGAGGGCACAGAGAG 61.465 72.222 0.00 0.00 0.00 3.20
6661 11538 4.316823 ACGGGGAGGGCACAGAGA 62.317 66.667 0.00 0.00 0.00 3.10
6682 11559 3.790437 ATGCAGCCCGGACAGAGG 61.790 66.667 0.73 0.00 0.00 3.69
6683 11560 2.513204 CATGCAGCCCGGACAGAG 60.513 66.667 0.73 0.00 0.00 3.35
6685 11562 3.129502 CACATGCAGCCCGGACAG 61.130 66.667 0.73 0.00 0.00 3.51
6709 11586 3.070576 GTGGATGGCAAGTGGGGC 61.071 66.667 0.00 0.00 0.00 5.80
6710 11587 2.362889 GGTGGATGGCAAGTGGGG 60.363 66.667 0.00 0.00 0.00 4.96
6711 11588 2.362889 GGGTGGATGGCAAGTGGG 60.363 66.667 0.00 0.00 0.00 4.61
6713 11590 1.039233 GGATGGGTGGATGGCAAGTG 61.039 60.000 0.00 0.00 0.00 3.16
6714 11591 1.307647 GGATGGGTGGATGGCAAGT 59.692 57.895 0.00 0.00 0.00 3.16
6715 11592 1.825191 CGGATGGGTGGATGGCAAG 60.825 63.158 0.00 0.00 0.00 4.01
6716 11593 2.275089 CGGATGGGTGGATGGCAA 59.725 61.111 0.00 0.00 0.00 4.52
6717 11594 3.014538 ACGGATGGGTGGATGGCA 61.015 61.111 0.00 0.00 0.00 4.92
6718 11595 2.203209 GACGGATGGGTGGATGGC 60.203 66.667 0.00 0.00 0.00 4.40
6719 11596 2.510906 GGACGGATGGGTGGATGG 59.489 66.667 0.00 0.00 0.00 3.51
6720 11597 1.708993 ATGGGACGGATGGGTGGATG 61.709 60.000 0.00 0.00 0.00 3.51
6721 11598 1.385915 ATGGGACGGATGGGTGGAT 60.386 57.895 0.00 0.00 0.00 3.41
6723 11600 2.510906 GATGGGACGGATGGGTGG 59.489 66.667 0.00 0.00 0.00 4.61
6724 11601 2.510906 GGATGGGACGGATGGGTG 59.489 66.667 0.00 0.00 0.00 4.61
6732 11609 1.448922 GAGAGAGACCGGATGGGACG 61.449 65.000 9.46 0.00 40.75 4.79
6733 11610 1.110518 GGAGAGAGACCGGATGGGAC 61.111 65.000 9.46 0.00 40.75 4.46
6735 11612 0.825840 GAGGAGAGAGACCGGATGGG 60.826 65.000 9.46 0.00 40.75 4.00
6736 11613 0.825840 GGAGGAGAGAGACCGGATGG 60.826 65.000 9.46 0.00 42.84 3.51
6739 11616 0.705253 AAAGGAGGAGAGAGACCGGA 59.295 55.000 9.46 0.00 0.00 5.14
6740 11617 1.562783 AAAAGGAGGAGAGAGACCGG 58.437 55.000 0.00 0.00 0.00 5.28
6741 11618 2.829120 AGAAAAAGGAGGAGAGAGACCG 59.171 50.000 0.00 0.00 0.00 4.79
6742 11619 4.530553 AGAAGAAAAAGGAGGAGAGAGACC 59.469 45.833 0.00 0.00 0.00 3.85
6743 11620 5.337250 GGAGAAGAAAAAGGAGGAGAGAGAC 60.337 48.000 0.00 0.00 0.00 3.36
6745 11622 4.081142 GGGAGAAGAAAAAGGAGGAGAGAG 60.081 50.000 0.00 0.00 0.00 3.20
6747 11624 3.584848 TGGGAGAAGAAAAAGGAGGAGAG 59.415 47.826 0.00 0.00 0.00 3.20
6749 11626 3.560239 GGTGGGAGAAGAAAAAGGAGGAG 60.560 52.174 0.00 0.00 0.00 3.69
6750 11627 2.375509 GGTGGGAGAAGAAAAAGGAGGA 59.624 50.000 0.00 0.00 0.00 3.71
6751 11628 2.555448 GGGTGGGAGAAGAAAAAGGAGG 60.555 54.545 0.00 0.00 0.00 4.30
6752 11629 2.108250 TGGGTGGGAGAAGAAAAAGGAG 59.892 50.000 0.00 0.00 0.00 3.69
6753 11630 2.140224 TGGGTGGGAGAAGAAAAAGGA 58.860 47.619 0.00 0.00 0.00 3.36
6756 11633 2.512056 TGAGTGGGTGGGAGAAGAAAAA 59.488 45.455 0.00 0.00 0.00 1.94
6757 11634 2.131854 TGAGTGGGTGGGAGAAGAAAA 58.868 47.619 0.00 0.00 0.00 2.29
6760 11637 0.836400 GGTGAGTGGGTGGGAGAAGA 60.836 60.000 0.00 0.00 0.00 2.87
6761 11638 1.679898 GGTGAGTGGGTGGGAGAAG 59.320 63.158 0.00 0.00 0.00 2.85
6762 11639 1.846124 GGGTGAGTGGGTGGGAGAA 60.846 63.158 0.00 0.00 0.00 2.87
6763 11640 2.203938 GGGTGAGTGGGTGGGAGA 60.204 66.667 0.00 0.00 0.00 3.71
6764 11641 2.529136 TGGGTGAGTGGGTGGGAG 60.529 66.667 0.00 0.00 0.00 4.30
6765 11642 2.852075 GTGGGTGAGTGGGTGGGA 60.852 66.667 0.00 0.00 0.00 4.37
6766 11643 3.966543 GGTGGGTGAGTGGGTGGG 61.967 72.222 0.00 0.00 0.00 4.61
6768 11645 3.174987 TGGGTGGGTGAGTGGGTG 61.175 66.667 0.00 0.00 0.00 4.61
6770 11647 3.966543 GGTGGGTGGGTGAGTGGG 61.967 72.222 0.00 0.00 0.00 4.61
6771 11648 3.966543 GGGTGGGTGGGTGAGTGG 61.967 72.222 0.00 0.00 0.00 4.00
6772 11649 3.174987 TGGGTGGGTGGGTGAGTG 61.175 66.667 0.00 0.00 0.00 3.51
6773 11650 2.854032 CTGGGTGGGTGGGTGAGT 60.854 66.667 0.00 0.00 0.00 3.41
6775 11652 4.918360 AGCTGGGTGGGTGGGTGA 62.918 66.667 0.00 0.00 0.00 4.02
6776 11653 4.351054 GAGCTGGGTGGGTGGGTG 62.351 72.222 0.00 0.00 0.00 4.61
6779 11656 4.394712 GACGAGCTGGGTGGGTGG 62.395 72.222 0.00 0.00 0.00 4.61
6780 11657 4.394712 GGACGAGCTGGGTGGGTG 62.395 72.222 0.00 0.00 0.00 4.61
6781 11658 4.640690 AGGACGAGCTGGGTGGGT 62.641 66.667 0.00 0.00 0.00 4.51
6783 11660 3.775654 GGAGGACGAGCTGGGTGG 61.776 72.222 0.00 0.00 0.00 4.61
6784 11661 2.232298 GAAGGAGGACGAGCTGGGTG 62.232 65.000 0.00 0.00 0.00 4.61
6785 11662 1.985116 GAAGGAGGACGAGCTGGGT 60.985 63.158 0.00 0.00 0.00 4.51
6786 11663 2.896443 GAAGGAGGACGAGCTGGG 59.104 66.667 0.00 0.00 0.00 4.45
6808 11685 4.129737 ACCACGTCGGAGCATCGG 62.130 66.667 10.46 0.00 38.63 4.18
6809 11686 2.880879 CACCACGTCGGAGCATCG 60.881 66.667 10.46 0.00 38.63 3.84
6810 11687 2.509336 CCACCACGTCGGAGCATC 60.509 66.667 10.46 0.00 38.63 3.91
6811 11688 4.082523 CCCACCACGTCGGAGCAT 62.083 66.667 10.46 0.00 38.63 3.79
6814 11691 4.436998 GAGCCCACCACGTCGGAG 62.437 72.222 10.46 3.34 38.63 4.63
6823 11700 4.459089 GAGGAGCACGAGCCCACC 62.459 72.222 13.09 9.38 43.56 4.61
6824 11701 4.459089 GGAGGAGCACGAGCCCAC 62.459 72.222 13.09 7.81 43.56 4.61
6881 11758 3.566853 CAGTATGTGCGCGGCCAG 61.567 66.667 8.83 0.00 0.00 4.85
6890 11767 0.675837 AGCAGCACCAGCAGTATGTG 60.676 55.000 0.00 0.00 45.49 3.21
6891 11768 0.675837 CAGCAGCACCAGCAGTATGT 60.676 55.000 0.00 0.00 45.49 2.29
6892 11769 1.989966 GCAGCAGCACCAGCAGTATG 61.990 60.000 0.00 0.00 45.49 2.39
6893 11770 1.748122 GCAGCAGCACCAGCAGTAT 60.748 57.895 0.00 0.00 45.49 2.12
6894 11771 2.359107 GCAGCAGCACCAGCAGTA 60.359 61.111 0.00 0.00 45.49 2.74
6897 11774 4.671590 ATGGCAGCAGCACCAGCA 62.672 61.111 12.35 0.00 45.49 4.41
6898 11775 4.129737 CATGGCAGCAGCACCAGC 62.130 66.667 12.35 2.43 44.61 4.85
6908 11785 3.444717 CTAAGCACGCGCATGGCAG 62.445 63.158 5.73 0.00 43.84 4.85
6910 11787 4.894203 GCTAAGCACGCGCATGGC 62.894 66.667 5.73 6.17 42.27 4.40
6911 11788 1.825285 CTAGCTAAGCACGCGCATGG 61.825 60.000 5.73 0.00 42.27 3.66
6926 11803 2.352034 CATGCATGCATAGCTAGCTAGC 59.648 50.000 33.96 33.96 41.09 3.42


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

AutoCloner maintained by Alex Coulton.