Multiple sequence alignment - TraesCS5B01G176200

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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 TraesCS5B01G176200 chr5B 100.000 6623 0 0 837 7459 322199928 322206550 0.000000e+00 12231.0
1 TraesCS5B01G176200 chr5B 100.000 514 0 0 1 514 322199092 322199605 0.000000e+00 950.0
2 TraesCS5B01G176200 chr5B 90.566 106 10 0 4942 5047 422699572 422699467 2.810000e-29 141.0
3 TraesCS5B01G176200 chr5D 95.735 5182 141 26 837 5945 284893412 284898586 0.000000e+00 8272.0
4 TraesCS5B01G176200 chr5D 92.237 1198 44 12 6068 7231 284898605 284899787 0.000000e+00 1652.0
5 TraesCS5B01G176200 chr5D 93.137 408 17 3 4 403 284892889 284893293 8.340000e-164 588.0
6 TraesCS5B01G176200 chr5D 91.011 178 11 4 7241 7416 284900939 284901113 1.250000e-57 235.0
7 TraesCS5B01G176200 chr5D 94.340 106 3 3 5956 6060 252117417 252117314 7.750000e-35 159.0
8 TraesCS5B01G176200 chr5D 88.034 117 13 1 398 514 284893233 284893348 3.630000e-28 137.0
9 TraesCS5B01G176200 chr5A 92.178 2902 158 31 3059 5921 376466599 376469470 0.000000e+00 4037.0
10 TraesCS5B01G176200 chr5A 87.230 1527 116 28 837 2336 376464175 376465649 0.000000e+00 1666.0
11 TraesCS5B01G176200 chr5A 93.654 1040 51 10 6071 7100 376469575 376470609 0.000000e+00 1541.0
12 TraesCS5B01G176200 chr5A 91.971 411 22 5 5 405 376463643 376464052 3.910000e-157 566.0
13 TraesCS5B01G176200 chr5A 85.714 322 23 7 2673 2989 376465965 376466268 1.210000e-82 318.0
14 TraesCS5B01G176200 chr5A 89.806 206 21 0 2470 2675 376465678 376465883 1.600000e-66 265.0
15 TraesCS5B01G176200 chr5A 96.939 98 3 0 5970 6067 676906 677003 1.660000e-36 165.0
16 TraesCS5B01G176200 chr5A 93.548 93 5 1 422 514 376464014 376464105 3.630000e-28 137.0
17 TraesCS5B01G176200 chr5A 84.783 92 9 4 6869 6959 678203657 678203570 3.710000e-13 87.9
18 TraesCS5B01G176200 chr5A 91.525 59 4 1 7402 7459 680971265 680971207 6.200000e-11 80.5
19 TraesCS5B01G176200 chr6D 95.862 145 4 2 2333 2477 267532942 267532800 4.500000e-57 233.0
20 TraesCS5B01G176200 chr6D 97.000 100 2 1 5971 6070 95714148 95714246 4.630000e-37 167.0
21 TraesCS5B01G176200 chr6D 88.119 101 12 0 1080 1180 115772136 115772236 3.660000e-23 121.0
22 TraesCS5B01G176200 chr6D 91.228 57 3 2 7400 7456 438321721 438321775 8.030000e-10 76.8
23 TraesCS5B01G176200 chr1A 93.464 153 7 3 2333 2482 287698579 287698731 2.710000e-54 224.0
24 TraesCS5B01G176200 chr1A 92.593 81 6 0 4955 5035 157150663 157150743 4.730000e-22 117.0
25 TraesCS5B01G176200 chr3A 91.304 161 11 3 2333 2492 375018127 375018285 4.530000e-52 217.0
26 TraesCS5B01G176200 chr3A 94.286 105 4 2 5973 6077 68289881 68289779 7.750000e-35 159.0
27 TraesCS5B01G176200 chr3A 92.661 109 7 1 5957 6065 659039403 659039510 1.000000e-33 156.0
28 TraesCS5B01G176200 chr3A 97.959 49 1 0 7411 7459 659527395 659527347 1.330000e-12 86.1
29 TraesCS5B01G176200 chr3D 90.000 170 12 5 2318 2483 603750504 603750336 1.630000e-51 215.0
30 TraesCS5B01G176200 chr3D 96.040 101 3 1 5972 6072 65607314 65607215 5.990000e-36 163.0
31 TraesCS5B01G176200 chr3D 91.262 103 9 0 4947 5049 204235125 204235023 2.810000e-29 141.0
32 TraesCS5B01G176200 chr3D 93.258 89 6 0 4947 5035 234500894 234500982 1.690000e-26 132.0
33 TraesCS5B01G176200 chr3D 91.011 89 8 0 4947 5035 222940376 222940464 3.660000e-23 121.0
34 TraesCS5B01G176200 chr3D 97.917 48 1 0 7412 7459 555801725 555801678 4.800000e-12 84.2
35 TraesCS5B01G176200 chr3B 91.304 161 9 5 2336 2495 398842515 398842359 1.630000e-51 215.0
36 TraesCS5B01G176200 chr3B 90.196 102 10 0 4942 5043 158404808 158404707 4.700000e-27 134.0
37 TraesCS5B01G176200 chr2A 91.772 158 7 5 2336 2492 524833379 524833227 1.630000e-51 215.0
38 TraesCS5B01G176200 chr2A 94.393 107 4 2 5973 6079 629644074 629643970 5.990000e-36 163.0
39 TraesCS5B01G176200 chr2A 88.679 106 12 0 4942 5047 522231166 522231271 6.070000e-26 130.0
40 TraesCS5B01G176200 chr1B 91.720 157 10 3 2333 2489 537649131 537649284 1.630000e-51 215.0
41 TraesCS5B01G176200 chr1B 91.667 96 6 1 4942 5035 201956966 201957061 1.690000e-26 132.0
42 TraesCS5B01G176200 chr1B 97.917 48 1 0 7412 7459 409702539 409702586 4.800000e-12 84.2
43 TraesCS5B01G176200 chr6B 88.571 175 15 5 2318 2489 343030804 343030976 2.730000e-49 207.0
44 TraesCS5B01G176200 chr6B 95.146 103 2 3 5958 6060 423189610 423189511 7.750000e-35 159.0
45 TraesCS5B01G176200 chr6B 88.119 101 12 0 1080 1180 205234742 205234842 3.660000e-23 121.0
46 TraesCS5B01G176200 chr6B 97.959 49 1 0 7411 7459 178029932 178029884 1.330000e-12 86.1
47 TraesCS5B01G176200 chr4D 94.495 109 3 3 5970 6077 5081573 5081679 1.660000e-36 165.0
48 TraesCS5B01G176200 chr4D 88.298 94 11 0 4942 5035 162795102 162795195 6.120000e-21 113.0
49 TraesCS5B01G176200 chr4D 84.906 106 9 3 4942 5047 24569975 24570073 4.760000e-17 100.0
50 TraesCS5B01G176200 chr4D 84.906 106 9 2 4942 5047 417247630 417247532 4.760000e-17 100.0
51 TraesCS5B01G176200 chr2D 91.509 106 9 0 4942 5047 159383560 159383455 6.030000e-31 147.0
52 TraesCS5B01G176200 chr2D 90.426 94 9 0 4942 5035 197291862 197291955 2.830000e-24 124.0
53 TraesCS5B01G176200 chr2D 86.792 106 7 3 4942 5047 501242377 501242279 2.200000e-20 111.0
54 TraesCS5B01G176200 chr7A 88.679 106 12 0 4942 5047 143261666 143261771 6.070000e-26 130.0
55 TraesCS5B01G176200 chr6A 88.119 101 12 0 1080 1180 144247530 144247630 3.660000e-23 121.0
56 TraesCS5B01G176200 chr4B 85.577 104 10 5 6860 6959 124737678 124737576 3.680000e-18 104.0
57 TraesCS5B01G176200 chr4B 97.917 48 1 0 7412 7459 579627061 579627014 4.800000e-12 84.2
58 TraesCS5B01G176200 chr4B 82.474 97 12 4 6863 6958 471155302 471155210 6.200000e-11 80.5
59 TraesCS5B01G176200 chr4B 81.915 94 12 5 6867 6959 654443092 654443181 2.890000e-09 75.0
60 TraesCS5B01G176200 chr1D 98.000 50 1 0 7410 7459 450202220 450202171 3.710000e-13 87.9
61 TraesCS5B01G176200 chr7D 82.474 97 13 4 6862 6958 156686591 156686499 1.720000e-11 82.4
62 TraesCS5B01G176200 chr2B 96.000 50 2 0 7410 7459 196539992 196539943 1.720000e-11 82.4
63 TraesCS5B01G176200 chr2B 80.412 97 14 3 6863 6958 118604621 118604713 1.340000e-07 69.4
64 TraesCS5B01G176200 chr7B 80.851 94 13 4 6868 6960 32896673 32896584 1.340000e-07 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G176200 chr5B 322199092 322206550 7458 False 6590.500000 12231 100.000000 1 7459 2 chr5B.!!$F1 7458
1 TraesCS5B01G176200 chr5D 284892889 284901113 8224 False 2176.800000 8272 92.030800 4 7416 5 chr5D.!!$F1 7412
2 TraesCS5B01G176200 chr5A 376463643 376470609 6966 False 1218.571429 4037 90.585857 5 7100 7 chr5A.!!$F2 7095

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
997 1015 1.217747 TGGAGAGGAGCAGGAGGAGA 61.218 60.000 0.00 0.0 0.00 3.71 F
1574 1596 0.908198 AGCTGGGAAGAGATGTGTCC 59.092 55.000 0.00 0.0 0.00 4.02 F
3230 3644 0.712380 AATCTTGGTTCCTGGGGCAT 59.288 50.000 0.00 0.0 0.00 4.40 F
3868 4298 0.609681 AGAGAGTGGGGACTGACGAC 60.610 60.000 0.00 0.0 0.00 4.34 F
4768 5205 1.000843 CATGCTATACGGCACTGGCTA 59.999 52.381 0.52 0.0 45.36 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2680 2743 1.133606 TGCATCATGACTGGCCATCAT 60.134 47.619 19.14 19.14 37.27 2.45 R
3280 3696 3.433306 TCAGGTTCTAACATGGTTGGG 57.567 47.619 7.56 0.00 40.78 4.12 R
4750 5187 1.338107 ATAGCCAGTGCCGTATAGCA 58.662 50.000 0.00 0.00 41.46 3.49 R
4983 5420 4.819769 TGCAATTTCTACCTTTGATTGGC 58.180 39.130 0.00 0.00 0.00 4.52 R
6739 7255 0.038709 GGCAAGGCACGCATTTGTAA 60.039 50.000 0.51 0.00 0.00 2.41 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
33 34 2.268920 GCATCGCAGAAGTGGGGA 59.731 61.111 0.00 0.00 43.58 4.81
88 89 3.562232 TTCCGGCGTTGGGTCCTT 61.562 61.111 6.01 0.00 0.00 3.36
278 284 3.177884 ACCAGCAGCAACCAGGGA 61.178 61.111 0.00 0.00 0.00 4.20
372 378 7.553881 TTCAATCGGTGAAGAAAGGATTATC 57.446 36.000 0.00 0.00 41.47 1.75
373 379 6.889198 TCAATCGGTGAAGAAAGGATTATCT 58.111 36.000 0.00 0.00 31.51 1.98
374 380 6.763135 TCAATCGGTGAAGAAAGGATTATCTG 59.237 38.462 0.00 0.00 31.51 2.90
375 381 5.932619 TCGGTGAAGAAAGGATTATCTGA 57.067 39.130 0.00 0.00 0.00 3.27
376 382 5.907207 TCGGTGAAGAAAGGATTATCTGAG 58.093 41.667 0.00 0.00 0.00 3.35
377 383 5.656859 TCGGTGAAGAAAGGATTATCTGAGA 59.343 40.000 0.00 0.00 0.00 3.27
378 384 6.325028 TCGGTGAAGAAAGGATTATCTGAGAT 59.675 38.462 0.00 0.00 0.00 2.75
379 385 7.505923 TCGGTGAAGAAAGGATTATCTGAGATA 59.494 37.037 0.00 0.00 0.00 1.98
380 386 8.144478 CGGTGAAGAAAGGATTATCTGAGATAA 58.856 37.037 16.46 16.46 0.00 1.75
403 409 9.802039 ATAATTTAACAGTGGAAGTAAGTTGGA 57.198 29.630 0.00 0.00 0.00 3.53
404 410 8.706322 AATTTAACAGTGGAAGTAAGTTGGAT 57.294 30.769 0.00 0.00 0.00 3.41
405 411 8.706322 ATTTAACAGTGGAAGTAAGTTGGATT 57.294 30.769 0.00 0.00 0.00 3.01
406 412 7.504924 TTAACAGTGGAAGTAAGTTGGATTG 57.495 36.000 0.00 0.00 0.00 2.67
407 413 4.398319 ACAGTGGAAGTAAGTTGGATTGG 58.602 43.478 0.00 0.00 0.00 3.16
408 414 4.141251 ACAGTGGAAGTAAGTTGGATTGGT 60.141 41.667 0.00 0.00 0.00 3.67
409 415 5.072600 ACAGTGGAAGTAAGTTGGATTGGTA 59.927 40.000 0.00 0.00 0.00 3.25
410 416 6.001460 CAGTGGAAGTAAGTTGGATTGGTAA 58.999 40.000 0.00 0.00 0.00 2.85
411 417 6.488683 CAGTGGAAGTAAGTTGGATTGGTAAA 59.511 38.462 0.00 0.00 0.00 2.01
412 418 6.489022 AGTGGAAGTAAGTTGGATTGGTAAAC 59.511 38.462 0.00 0.00 0.00 2.01
413 419 6.263617 GTGGAAGTAAGTTGGATTGGTAAACA 59.736 38.462 0.00 0.00 0.00 2.83
414 420 6.834451 TGGAAGTAAGTTGGATTGGTAAACAA 59.166 34.615 0.00 0.00 44.54 2.83
415 421 7.342284 TGGAAGTAAGTTGGATTGGTAAACAAA 59.658 33.333 0.00 0.00 43.46 2.83
416 422 7.865889 GGAAGTAAGTTGGATTGGTAAACAAAG 59.134 37.037 0.00 0.00 43.46 2.77
417 423 7.284919 AGTAAGTTGGATTGGTAAACAAAGG 57.715 36.000 0.00 0.00 43.46 3.11
418 424 7.064229 AGTAAGTTGGATTGGTAAACAAAGGA 58.936 34.615 0.00 0.00 43.46 3.36
419 425 6.994421 AAGTTGGATTGGTAAACAAAGGAT 57.006 33.333 0.00 0.00 43.46 3.24
420 426 9.016438 GTAAGTTGGATTGGTAAACAAAGGATA 57.984 33.333 0.00 0.00 43.46 2.59
460 466 3.782656 ACACCGGAAGTAAGTTGGATT 57.217 42.857 9.46 0.00 0.00 3.01
462 468 4.466827 ACACCGGAAGTAAGTTGGATTTT 58.533 39.130 9.46 0.00 0.00 1.82
463 469 4.277423 ACACCGGAAGTAAGTTGGATTTTG 59.723 41.667 9.46 0.00 0.00 2.44
465 471 4.891168 ACCGGAAGTAAGTTGGATTTTGTT 59.109 37.500 9.46 0.00 0.00 2.83
468 474 7.231925 ACCGGAAGTAAGTTGGATTTTGTTATT 59.768 33.333 9.46 0.00 0.00 1.40
469 475 8.732531 CCGGAAGTAAGTTGGATTTTGTTATTA 58.267 33.333 0.00 0.00 0.00 0.98
997 1015 1.217747 TGGAGAGGAGCAGGAGGAGA 61.218 60.000 0.00 0.00 0.00 3.71
1005 1023 2.238395 GGAGCAGGAGGAGAAGATGTTT 59.762 50.000 0.00 0.00 0.00 2.83
1323 1341 2.665185 ACCGTGCGCTTTGACTCC 60.665 61.111 9.73 0.00 0.00 3.85
1391 1409 3.925630 ATTGGGGGCGTCTGTGCTG 62.926 63.158 0.00 0.00 34.52 4.41
1395 1414 2.343758 GGGCGTCTGTGCTGAAGA 59.656 61.111 0.00 0.00 34.52 2.87
1402 1421 3.849911 CGTCTGTGCTGAAGATTTAGGA 58.150 45.455 0.00 0.00 0.00 2.94
1407 1426 6.205658 GTCTGTGCTGAAGATTTAGGAAAGTT 59.794 38.462 0.00 0.00 0.00 2.66
1418 1437 7.606349 AGATTTAGGAAAGTTTGGATCAAAGC 58.394 34.615 0.00 0.00 33.82 3.51
1423 1442 4.309933 GAAAGTTTGGATCAAAGCTTGGG 58.690 43.478 12.21 0.00 33.82 4.12
1438 1457 2.514803 CTTGGGTCTTTGTTACCTGGG 58.485 52.381 0.00 0.00 37.18 4.45
1478 1500 1.215382 CGATGTTGGACGAGGAGCA 59.785 57.895 0.00 0.00 0.00 4.26
1482 1504 1.367840 GTTGGACGAGGAGCAGTGT 59.632 57.895 0.00 0.00 0.00 3.55
1501 1523 4.941263 AGTGTATTTGCGCTTAGGATTCAA 59.059 37.500 9.73 0.00 0.00 2.69
1520 1542 1.178534 ACACGCCCTTGGATTTGGTG 61.179 55.000 0.00 0.00 35.76 4.17
1523 1545 1.202952 ACGCCCTTGGATTTGGTGTTA 60.203 47.619 0.00 0.00 39.79 2.41
1574 1596 0.908198 AGCTGGGAAGAGATGTGTCC 59.092 55.000 0.00 0.00 0.00 4.02
1673 1695 1.740380 CGATCTTGGATTCCAGCACGT 60.740 52.381 5.36 0.00 33.81 4.49
1727 1749 4.599047 AGAGAGAAATGTCGATGATCCC 57.401 45.455 0.00 0.00 0.00 3.85
1771 1793 1.973812 GCACTCAGGGGCTGGTTTC 60.974 63.158 0.00 0.00 31.51 2.78
1772 1794 1.672356 CACTCAGGGGCTGGTTTCG 60.672 63.158 0.00 0.00 31.51 3.46
1833 1871 7.274033 ACTTTTGCTTTTCTTTAACGGTGTTAC 59.726 33.333 0.00 0.00 0.00 2.50
1848 1886 7.324354 ACGGTGTTACTTCAGTTTATTTGTT 57.676 32.000 0.00 0.00 0.00 2.83
1899 1938 5.118203 GCATCAGCTCAGAATTTGAACAAAC 59.882 40.000 2.03 0.00 34.81 2.93
1916 1955 2.756760 CAAACAGGCAGCTATGGACAAT 59.243 45.455 0.00 0.00 0.00 2.71
1921 1960 1.869767 GGCAGCTATGGACAATCTTCG 59.130 52.381 0.00 0.00 0.00 3.79
1944 1983 5.232202 CGAAATATCGGATATCGGGTTCATG 59.768 44.000 10.77 0.00 45.32 3.07
1962 2001 3.065306 TCGGTTCGACCTTGGCAT 58.935 55.556 0.00 0.00 35.66 4.40
1967 2006 2.639065 GGTTCGACCTTGGCATTATCA 58.361 47.619 0.00 0.00 34.73 2.15
2020 2061 5.525199 AGGCGTATCGAAACAAAAATGTTT 58.475 33.333 6.65 6.65 43.77 2.83
2073 2114 5.904984 TGCCACTCCCACATAAATAGTAT 57.095 39.130 0.00 0.00 0.00 2.12
2143 2185 2.352323 GGTGGTTTGCGTAAGAAATGGG 60.352 50.000 0.00 0.00 43.02 4.00
2289 2349 3.512329 TGACCTGTCACGTACATATTGGT 59.488 43.478 0.00 0.00 37.50 3.67
2359 2419 1.308216 AGGGGTGCCTGGAAGCTAT 60.308 57.895 3.45 0.00 0.00 2.97
2680 2743 7.857456 AGTCATGGTGGTAAATTGTAGTCATA 58.143 34.615 0.00 0.00 0.00 2.15
2784 2934 5.235850 TGTGTGGAAATAGCAGAAAGGTA 57.764 39.130 0.00 0.00 34.18 3.08
2792 2942 6.036844 GGAAATAGCAGAAAGGTAGTTTACGG 59.963 42.308 0.00 0.00 38.46 4.02
2981 3192 9.511272 TTTACCCTTTTCTTCTAAATACTGACC 57.489 33.333 0.00 0.00 0.00 4.02
3230 3644 0.712380 AATCTTGGTTCCTGGGGCAT 59.288 50.000 0.00 0.00 0.00 4.40
3280 3696 7.951530 ATGCTTGTAAATGCCAAATTATAGC 57.048 32.000 0.00 0.00 0.00 2.97
3298 3714 1.710809 AGCCCAACCATGTTAGAACCT 59.289 47.619 0.00 0.00 0.00 3.50
3830 4260 3.317603 TGATGCACATCTCTTCGTTGA 57.682 42.857 11.66 0.00 38.60 3.18
3868 4298 0.609681 AGAGAGTGGGGACTGACGAC 60.610 60.000 0.00 0.00 0.00 4.34
3875 4305 2.352032 GGGACTGACGACTGAGGGG 61.352 68.421 0.00 0.00 0.00 4.79
3930 4360 3.679502 TCACTTGACACAGTATTGCATCG 59.320 43.478 0.00 0.00 0.00 3.84
4106 4536 9.368674 CTTTAATATGAATTGGTTGTGAATGCA 57.631 29.630 0.00 0.00 0.00 3.96
4396 4826 2.162681 GCACTTTCCCACTGCAGTTAT 58.837 47.619 18.94 0.00 0.00 1.89
4768 5205 1.000843 CATGCTATACGGCACTGGCTA 59.999 52.381 0.52 0.00 45.36 3.93
4925 5362 5.181811 TCACGGATGTTTCTAGAACGACTTA 59.818 40.000 16.53 0.00 0.00 2.24
4992 5429 2.042686 CTCGGATGAGGCCAATCAAA 57.957 50.000 17.48 6.38 38.65 2.69
5519 5985 6.894103 AGGTCTTGCCATTTCTGATAGAAAAT 59.106 34.615 7.95 0.00 40.18 1.82
5603 6069 0.486879 TTCCCCAATTTGCAGGGTCT 59.513 50.000 7.78 0.00 43.89 3.85
5876 6350 3.146066 GCATGAACAAGTGGAGGTAACA 58.854 45.455 0.00 0.00 41.41 2.41
5882 6356 3.751518 ACAAGTGGAGGTAACATTGACC 58.248 45.455 0.00 0.00 41.41 4.02
5883 6357 3.137544 ACAAGTGGAGGTAACATTGACCA 59.862 43.478 0.00 0.00 39.65 4.02
5912 6392 9.025041 TCTTCTGTCATATTCTTAGTTGTCTCA 57.975 33.333 0.00 0.00 0.00 3.27
5945 6425 4.746611 CCAGACAAGAAGAATTTGTTTGCC 59.253 41.667 3.85 0.00 38.56 4.52
5947 6427 5.811613 CAGACAAGAAGAATTTGTTTGCCAA 59.188 36.000 0.00 0.00 38.78 4.52
5948 6428 5.812127 AGACAAGAAGAATTTGTTTGCCAAC 59.188 36.000 0.00 0.00 38.78 3.77
5949 6429 5.733676 ACAAGAAGAATTTGTTTGCCAACT 58.266 33.333 2.01 0.00 35.32 3.16
5950 6430 6.172630 ACAAGAAGAATTTGTTTGCCAACTT 58.827 32.000 2.01 0.00 35.32 2.66
5951 6431 6.313658 ACAAGAAGAATTTGTTTGCCAACTTC 59.686 34.615 2.01 0.00 40.93 3.01
5952 6432 5.976458 AGAAGAATTTGTTTGCCAACTTCA 58.024 33.333 0.00 0.00 42.26 3.02
5953 6433 6.044682 AGAAGAATTTGTTTGCCAACTTCAG 58.955 36.000 0.00 0.00 42.26 3.02
5954 6434 5.343307 AGAATTTGTTTGCCAACTTCAGT 57.657 34.783 2.01 0.00 42.26 3.41
5955 6435 6.463995 AGAATTTGTTTGCCAACTTCAGTA 57.536 33.333 2.01 0.00 42.26 2.74
5956 6436 7.054491 AGAATTTGTTTGCCAACTTCAGTAT 57.946 32.000 2.01 0.00 42.26 2.12
5957 6437 7.500141 AGAATTTGTTTGCCAACTTCAGTATT 58.500 30.769 2.01 0.00 42.26 1.89
5963 6443 3.754965 TGCCAACTTCAGTATTTGCTCT 58.245 40.909 0.00 0.00 0.00 4.09
5981 6461 3.887110 GCTCTCTAGTTTCTACTCCCTCC 59.113 52.174 0.00 0.00 35.78 4.30
5984 6464 4.018597 TCTCTAGTTTCTACTCCCTCCGTT 60.019 45.833 0.00 0.00 35.78 4.44
5985 6465 4.268359 TCTAGTTTCTACTCCCTCCGTTC 58.732 47.826 0.00 0.00 35.78 3.95
5986 6466 2.177734 AGTTTCTACTCCCTCCGTTCC 58.822 52.381 0.00 0.00 0.00 3.62
5987 6467 1.897802 GTTTCTACTCCCTCCGTTCCA 59.102 52.381 0.00 0.00 0.00 3.53
5990 6470 2.829023 TCTACTCCCTCCGTTCCAAAT 58.171 47.619 0.00 0.00 0.00 2.32
5993 6473 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
5994 6474 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
5995 6475 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
5997 6477 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
5998 6478 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
5999 6479 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
6000 6480 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
6001 6481 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
6002 6482 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
6004 6484 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
6005 6485 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
6006 6486 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
6007 6487 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
6008 6488 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
6009 6489 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
6010 6490 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
6011 6491 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
6015 6495 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
6018 6498 6.553524 TCGTCGTGGTTTTAGTTCAAATTTT 58.446 32.000 0.00 0.00 0.00 1.82
6019 6499 6.469595 TCGTCGTGGTTTTAGTTCAAATTTTG 59.530 34.615 2.59 2.59 0.00 2.44
6021 6501 7.008447 CGTCGTGGTTTTAGTTCAAATTTTGAA 59.992 33.333 18.29 18.29 46.68 2.69
6034 6514 7.743520 TCAAATTTTGAACTAAAACCACGAC 57.256 32.000 9.36 0.00 40.80 4.34
6040 6520 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
6041 6521 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
6042 6522 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
6043 6523 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
6044 6524 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
6045 6525 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
6046 6526 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
6047 6527 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
6048 6528 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
6049 6529 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
6050 6530 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
6051 6531 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
6052 6532 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
6053 6533 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
6054 6534 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
6055 6535 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
6099 6590 7.637229 CATTGAAGTATGAATGAGATGTCCAC 58.363 38.462 0.00 0.00 32.24 4.02
6105 6597 1.394917 GAATGAGATGTCCACACACGC 59.605 52.381 0.00 0.00 34.48 5.34
6106 6598 0.610174 ATGAGATGTCCACACACGCT 59.390 50.000 0.00 0.00 34.48 5.07
6107 6599 0.319813 TGAGATGTCCACACACGCTG 60.320 55.000 0.00 0.00 34.48 5.18
6266 6762 2.034376 AGCGTCTCCGACCAGAGT 59.966 61.111 0.00 0.00 35.28 3.24
6392 6888 4.803908 GGGGGCAAGCCTTCTCCG 62.804 72.222 11.40 0.00 36.10 4.63
6476 6972 3.623203 GCTGAGATCCAAATTCTGGGTGA 60.623 47.826 6.77 0.00 46.44 4.02
6522 7018 1.951130 CCATGTCGAATCTCGGCCG 60.951 63.158 22.12 22.12 45.07 6.13
6739 7255 7.537596 TTTACCACATTTCCAAGATCACATT 57.462 32.000 0.00 0.00 0.00 2.71
6871 7387 2.364647 ACTTGCGGGCTAATCTACTACC 59.635 50.000 0.00 0.00 0.00 3.18
6957 7474 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.00 0.00 2.73
6962 7479 1.204231 GGACGGAGGGAGTAGTTGAAC 59.796 57.143 0.00 0.00 0.00 3.18
6963 7480 1.891150 GACGGAGGGAGTAGTTGAACA 59.109 52.381 0.00 0.00 0.00 3.18
7076 7593 5.717119 AATGCTAGGAGGTAGAACCAATT 57.283 39.130 0.00 0.00 41.95 2.32
7111 7628 0.824759 AGATACTTGGACAGGCGGTC 59.175 55.000 9.42 9.42 46.20 4.79
7121 7638 2.836154 AGGCGGTCCTGAGCAAAA 59.164 55.556 0.00 0.00 42.34 2.44
7143 7660 4.481368 AAATGTGACTACGGCCTGAATA 57.519 40.909 0.00 0.00 0.00 1.75
7145 7662 3.241067 TGTGACTACGGCCTGAATAAC 57.759 47.619 0.00 0.00 0.00 1.89
7153 7676 1.780503 GGCCTGAATAACCCAGCATT 58.219 50.000 0.00 0.00 0.00 3.56
7158 7681 4.445735 GCCTGAATAACCCAGCATTACCTA 60.446 45.833 0.00 0.00 0.00 3.08
7164 7687 3.214696 ACCCAGCATTACCTAATCTGC 57.785 47.619 0.00 0.00 0.00 4.26
7165 7688 2.780010 ACCCAGCATTACCTAATCTGCT 59.220 45.455 0.00 0.00 0.00 4.24
7175 7699 3.679389 ACCTAATCTGCTTGACAACCAG 58.321 45.455 4.38 4.38 0.00 4.00
7231 7755 2.486966 GCATTCAGCGGGTTCAGC 59.513 61.111 0.00 0.00 0.00 4.26
7233 7757 1.986575 GCATTCAGCGGGTTCAGCTC 61.987 60.000 0.00 0.00 44.06 4.09
7235 7759 2.543067 ATTCAGCGGGTTCAGCTCCC 62.543 60.000 0.00 0.00 44.06 4.30
7236 7760 3.710722 CAGCGGGTTCAGCTCCCT 61.711 66.667 7.35 0.00 44.06 4.20
7237 7761 3.394836 AGCGGGTTCAGCTCCCTC 61.395 66.667 7.35 0.00 41.83 4.30
7238 7762 4.475135 GCGGGTTCAGCTCCCTCC 62.475 72.222 7.35 0.00 42.56 4.30
7239 7763 3.003173 CGGGTTCAGCTCCCTCCA 61.003 66.667 7.35 0.00 42.56 3.86
7240 7764 2.592993 CGGGTTCAGCTCCCTCCAA 61.593 63.158 7.35 0.00 42.56 3.53
7241 7765 1.915078 CGGGTTCAGCTCCCTCCAAT 61.915 60.000 7.35 0.00 42.56 3.16
7242 7766 0.394899 GGGTTCAGCTCCCTCCAATG 60.395 60.000 1.59 0.00 41.58 2.82
7244 7768 1.559682 GGTTCAGCTCCCTCCAATGTA 59.440 52.381 0.00 0.00 0.00 2.29
7251 8919 0.468226 TCCCTCCAATGTACCGCATC 59.532 55.000 0.00 0.00 36.67 3.91
7279 8947 2.345641 CAGAATCTCAACGTGTTAGCCG 59.654 50.000 0.00 0.00 0.00 5.52
7305 8973 0.754217 ATTGTGGGCAGCTGCATAGG 60.754 55.000 37.63 0.81 44.36 2.57
7306 8974 2.141011 TTGTGGGCAGCTGCATAGGT 62.141 55.000 37.63 0.00 44.36 3.08
7317 8985 0.403655 TGCATAGGTTTGGTGCTCCA 59.596 50.000 2.64 2.64 42.66 3.86
7319 8987 1.886222 GCATAGGTTTGGTGCTCCACA 60.886 52.381 7.09 0.00 44.22 4.17
7320 8988 2.086869 CATAGGTTTGGTGCTCCACAG 58.913 52.381 7.09 0.00 44.22 3.66
7343 9011 2.343426 TGTTTGGTTGCGTGCACCA 61.343 52.632 12.15 7.62 0.00 4.17
7344 9012 1.067250 GTTTGGTTGCGTGCACCAT 59.933 52.632 12.15 0.00 33.06 3.55
7374 9042 1.741706 CATGTGTGACTCAATGGAGCC 59.258 52.381 0.00 0.00 45.42 4.70
7380 9048 0.833287 GACTCAATGGAGCCTGGCTA 59.167 55.000 23.44 7.53 45.42 3.93
7390 9058 1.599542 GAGCCTGGCTAAGTAAATGCG 59.400 52.381 23.44 0.00 39.88 4.73
7391 9059 0.663153 GCCTGGCTAAGTAAATGCGG 59.337 55.000 12.43 0.00 0.00 5.69
7400 9068 6.376018 TGGCTAAGTAAATGCGGACTAAAAAT 59.624 34.615 0.00 0.00 0.00 1.82
7423 9091 3.266510 TGTTCTGCATGTACTCCATCC 57.733 47.619 0.00 0.00 0.00 3.51
7424 9092 2.205074 GTTCTGCATGTACTCCATCCG 58.795 52.381 0.00 0.00 0.00 4.18
7425 9093 1.485124 TCTGCATGTACTCCATCCGT 58.515 50.000 0.00 0.00 0.00 4.69
7426 9094 1.831106 TCTGCATGTACTCCATCCGTT 59.169 47.619 0.00 0.00 0.00 4.44
7427 9095 2.159099 TCTGCATGTACTCCATCCGTTC 60.159 50.000 0.00 0.00 0.00 3.95
7428 9096 1.134521 TGCATGTACTCCATCCGTTCC 60.135 52.381 0.00 0.00 0.00 3.62
7429 9097 1.139058 GCATGTACTCCATCCGTTCCT 59.861 52.381 0.00 0.00 0.00 3.36
7430 9098 2.364324 GCATGTACTCCATCCGTTCCTA 59.636 50.000 0.00 0.00 0.00 2.94
7431 9099 3.181469 GCATGTACTCCATCCGTTCCTAA 60.181 47.826 0.00 0.00 0.00 2.69
7432 9100 4.682320 GCATGTACTCCATCCGTTCCTAAA 60.682 45.833 0.00 0.00 0.00 1.85
7433 9101 5.611374 CATGTACTCCATCCGTTCCTAAAT 58.389 41.667 0.00 0.00 0.00 1.40
7434 9102 6.740401 GCATGTACTCCATCCGTTCCTAAATA 60.740 42.308 0.00 0.00 0.00 1.40
7435 9103 6.989155 TGTACTCCATCCGTTCCTAAATAT 57.011 37.500 0.00 0.00 0.00 1.28
7436 9104 8.528643 CATGTACTCCATCCGTTCCTAAATATA 58.471 37.037 0.00 0.00 0.00 0.86
7437 9105 8.481492 TGTACTCCATCCGTTCCTAAATATAA 57.519 34.615 0.00 0.00 0.00 0.98
7438 9106 8.582437 TGTACTCCATCCGTTCCTAAATATAAG 58.418 37.037 0.00 0.00 0.00 1.73
7439 9107 7.613551 ACTCCATCCGTTCCTAAATATAAGT 57.386 36.000 0.00 0.00 0.00 2.24
7440 9108 7.668492 ACTCCATCCGTTCCTAAATATAAGTC 58.332 38.462 0.00 0.00 0.00 3.01
7441 9109 7.509659 ACTCCATCCGTTCCTAAATATAAGTCT 59.490 37.037 0.00 0.00 0.00 3.24
7442 9110 8.258850 TCCATCCGTTCCTAAATATAAGTCTT 57.741 34.615 0.00 0.00 0.00 3.01
7443 9111 8.711170 TCCATCCGTTCCTAAATATAAGTCTTT 58.289 33.333 0.00 0.00 0.00 2.52
7444 9112 9.991906 CCATCCGTTCCTAAATATAAGTCTTTA 57.008 33.333 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.208463 TGTTTATTTTTCCCCACTTCTGC 57.792 39.130 0.00 0.00 0.00 4.26
33 34 6.935771 TGCATCTGCTCCATTTGTTTATTTTT 59.064 30.769 3.53 0.00 42.66 1.94
88 89 4.484639 GCTAGCTAGCTCTGCTCATGCA 62.485 54.545 33.71 0.00 45.48 3.96
258 264 2.596631 CTGGTTGCTGCTGGTGCT 60.597 61.111 0.00 0.00 40.48 4.40
278 284 3.710677 CAGGAGAAGAAGGGATGATGAGT 59.289 47.826 0.00 0.00 0.00 3.41
289 295 4.836825 TCATTTACTGCCAGGAGAAGAAG 58.163 43.478 0.00 0.00 0.00 2.85
377 383 9.802039 TCCAACTTACTTCCACTGTTAAATTAT 57.198 29.630 0.00 0.00 0.00 1.28
378 384 9.802039 ATCCAACTTACTTCCACTGTTAAATTA 57.198 29.630 0.00 0.00 0.00 1.40
379 385 8.706322 ATCCAACTTACTTCCACTGTTAAATT 57.294 30.769 0.00 0.00 0.00 1.82
380 386 8.576442 CAATCCAACTTACTTCCACTGTTAAAT 58.424 33.333 0.00 0.00 0.00 1.40
381 387 7.013846 CCAATCCAACTTACTTCCACTGTTAAA 59.986 37.037 0.00 0.00 0.00 1.52
382 388 6.488683 CCAATCCAACTTACTTCCACTGTTAA 59.511 38.462 0.00 0.00 0.00 2.01
383 389 6.001460 CCAATCCAACTTACTTCCACTGTTA 58.999 40.000 0.00 0.00 0.00 2.41
384 390 4.827284 CCAATCCAACTTACTTCCACTGTT 59.173 41.667 0.00 0.00 0.00 3.16
385 391 4.141251 ACCAATCCAACTTACTTCCACTGT 60.141 41.667 0.00 0.00 0.00 3.55
386 392 4.398319 ACCAATCCAACTTACTTCCACTG 58.602 43.478 0.00 0.00 0.00 3.66
387 393 4.724279 ACCAATCCAACTTACTTCCACT 57.276 40.909 0.00 0.00 0.00 4.00
388 394 6.263617 TGTTTACCAATCCAACTTACTTCCAC 59.736 38.462 0.00 0.00 0.00 4.02
389 395 6.366340 TGTTTACCAATCCAACTTACTTCCA 58.634 36.000 0.00 0.00 0.00 3.53
390 396 6.887626 TGTTTACCAATCCAACTTACTTCC 57.112 37.500 0.00 0.00 0.00 3.46
391 397 7.865889 CCTTTGTTTACCAATCCAACTTACTTC 59.134 37.037 0.00 0.00 31.81 3.01
392 398 7.562088 TCCTTTGTTTACCAATCCAACTTACTT 59.438 33.333 0.00 0.00 31.81 2.24
393 399 7.064229 TCCTTTGTTTACCAATCCAACTTACT 58.936 34.615 0.00 0.00 31.81 2.24
394 400 7.279750 TCCTTTGTTTACCAATCCAACTTAC 57.720 36.000 0.00 0.00 31.81 2.34
395 401 9.589461 TTATCCTTTGTTTACCAATCCAACTTA 57.411 29.630 0.00 0.00 31.81 2.24
396 402 6.994421 ATCCTTTGTTTACCAATCCAACTT 57.006 33.333 0.00 0.00 31.81 2.66
397 403 8.664669 ATTATCCTTTGTTTACCAATCCAACT 57.335 30.769 0.00 0.00 31.81 3.16
401 407 9.981114 CCAATATTATCCTTTGTTTACCAATCC 57.019 33.333 0.00 0.00 31.81 3.01
402 408 9.476202 GCCAATATTATCCTTTGTTTACCAATC 57.524 33.333 0.00 0.00 31.81 2.67
403 409 8.141268 CGCCAATATTATCCTTTGTTTACCAAT 58.859 33.333 0.00 0.00 31.81 3.16
404 410 7.339721 TCGCCAATATTATCCTTTGTTTACCAA 59.660 33.333 0.00 0.00 0.00 3.67
405 411 6.829298 TCGCCAATATTATCCTTTGTTTACCA 59.171 34.615 0.00 0.00 0.00 3.25
406 412 7.227910 TCTCGCCAATATTATCCTTTGTTTACC 59.772 37.037 0.00 0.00 0.00 2.85
407 413 8.149973 TCTCGCCAATATTATCCTTTGTTTAC 57.850 34.615 0.00 0.00 0.00 2.01
408 414 8.918202 ATCTCGCCAATATTATCCTTTGTTTA 57.082 30.769 0.00 0.00 0.00 2.01
409 415 7.823745 ATCTCGCCAATATTATCCTTTGTTT 57.176 32.000 0.00 0.00 0.00 2.83
410 416 8.918202 TTATCTCGCCAATATTATCCTTTGTT 57.082 30.769 0.00 0.00 0.00 2.83
411 417 9.520515 AATTATCTCGCCAATATTATCCTTTGT 57.479 29.630 0.00 0.00 0.00 2.83
419 425 8.714179 CGGTGTTAAATTATCTCGCCAATATTA 58.286 33.333 0.00 0.00 0.00 0.98
420 426 7.308348 CCGGTGTTAAATTATCTCGCCAATATT 60.308 37.037 0.00 0.00 0.00 1.28
468 474 9.863845 TCAACGTCATTTTCTACTGTTCATATA 57.136 29.630 0.00 0.00 0.00 0.86
469 475 8.771920 TCAACGTCATTTTCTACTGTTCATAT 57.228 30.769 0.00 0.00 0.00 1.78
470 476 8.771920 ATCAACGTCATTTTCTACTGTTCATA 57.228 30.769 0.00 0.00 0.00 2.15
472 478 6.929049 AGATCAACGTCATTTTCTACTGTTCA 59.071 34.615 0.00 0.00 0.00 3.18
997 1015 1.149133 AGGCCAGGGGGAAACATCTT 61.149 55.000 5.01 0.00 35.59 2.40
1005 1023 4.037413 TGGATCAGGCCAGGGGGA 62.037 66.667 5.01 0.00 35.59 4.81
1285 1303 1.532868 CGCACCAACCAAGAAAGAGAG 59.467 52.381 0.00 0.00 0.00 3.20
1323 1341 3.857854 GACTCACATGCCGCGCTG 61.858 66.667 5.56 0.00 0.00 5.18
1381 1399 3.849911 TCCTAAATCTTCAGCACAGACG 58.150 45.455 0.00 0.00 0.00 4.18
1391 1409 9.631452 CTTTGATCCAAACTTTCCTAAATCTTC 57.369 33.333 0.00 0.00 0.00 2.87
1395 1414 7.544804 AGCTTTGATCCAAACTTTCCTAAAT 57.455 32.000 0.00 0.00 0.00 1.40
1402 1421 3.711190 ACCCAAGCTTTGATCCAAACTTT 59.289 39.130 0.00 0.00 29.51 2.66
1407 1426 2.978156 AGACCCAAGCTTTGATCCAA 57.022 45.000 0.00 0.00 0.00 3.53
1418 1437 2.107552 TCCCAGGTAACAAAGACCCAAG 59.892 50.000 0.00 0.00 37.73 3.61
1423 1442 3.314357 GTGTTGTCCCAGGTAACAAAGAC 59.686 47.826 6.28 3.92 37.15 3.01
1438 1457 2.310577 GCATTTCAGCGAAGTGTTGTC 58.689 47.619 12.59 0.00 32.95 3.18
1478 1500 4.513442 TGAATCCTAAGCGCAAATACACT 58.487 39.130 11.47 0.00 0.00 3.55
1482 1504 4.201773 CGTGTTGAATCCTAAGCGCAAATA 60.202 41.667 11.47 0.00 0.00 1.40
1501 1523 1.152830 ACCAAATCCAAGGGCGTGT 59.847 52.632 0.00 0.00 0.00 4.49
1520 1542 6.457528 GCAAAATCTGCCATGAGTAGACTAAC 60.458 42.308 0.00 0.00 46.13 2.34
1523 1545 3.944015 GCAAAATCTGCCATGAGTAGACT 59.056 43.478 0.00 0.00 46.13 3.24
1574 1596 2.202932 ATAGCCCTCGCAACGCAG 60.203 61.111 0.00 0.00 37.52 5.18
1653 1675 0.933097 CGTGCTGGAATCCAAGATCG 59.067 55.000 2.61 2.66 30.80 3.69
1727 1749 7.272084 CGCAGAAACTTCTTTCCTTATTCAATG 59.728 37.037 0.00 0.00 37.12 2.82
1766 1788 1.595093 CCTTGCATCCCCACGAAACC 61.595 60.000 0.00 0.00 0.00 3.27
1771 1793 1.889105 CGATCCTTGCATCCCCACG 60.889 63.158 0.00 0.00 0.00 4.94
1772 1794 1.526917 CCGATCCTTGCATCCCCAC 60.527 63.158 0.00 0.00 0.00 4.61
1827 1849 7.797123 CCGAGAACAAATAAACTGAAGTAACAC 59.203 37.037 0.00 0.00 0.00 3.32
1833 1871 8.391106 CCTTATCCGAGAACAAATAAACTGAAG 58.609 37.037 0.00 0.00 0.00 3.02
1848 1886 5.758296 GCAACAAATATGACCTTATCCGAGA 59.242 40.000 0.00 0.00 0.00 4.04
1899 1938 2.634815 AGATTGTCCATAGCTGCCTG 57.365 50.000 0.00 0.00 0.00 4.85
1921 1960 6.106673 ACATGAACCCGATATCCGATATTTC 58.893 40.000 0.00 3.65 41.76 2.17
1962 2001 5.277828 CGATATATCGCCCGACATCTGATAA 60.278 44.000 21.28 0.00 43.84 1.75
1993 2033 5.866335 TTTTTGTTTCGATACGCCTACAT 57.134 34.783 1.52 0.00 0.00 2.29
2020 2061 6.389830 AACACAAATAACTCAACAGATGCA 57.610 33.333 0.00 0.00 0.00 3.96
2021 2062 8.970691 ATAAACACAAATAACTCAACAGATGC 57.029 30.769 0.00 0.00 0.00 3.91
2080 2121 4.588528 ACTCAATATGCCCAAGTGTGTTTT 59.411 37.500 0.00 0.00 0.00 2.43
2125 2167 1.271102 TGCCCATTTCTTACGCAAACC 59.729 47.619 0.00 0.00 0.00 3.27
2143 2185 3.375299 AGATTTGACGAGTGCCTATTTGC 59.625 43.478 0.00 0.00 0.00 3.68
2256 2298 5.253330 ACGTGACAGGTCATTTTTATCCAT 58.747 37.500 5.29 0.00 42.18 3.41
2289 2349 3.130633 CTGATATTTCGGTCGGCATTGA 58.869 45.455 0.00 0.00 0.00 2.57
2359 2419 2.195727 TGGTTCTGGCACATGGATAGA 58.804 47.619 0.00 0.00 38.20 1.98
2443 2503 3.183373 ACAACAACAACAACAACAAAGCG 59.817 39.130 0.00 0.00 0.00 4.68
2680 2743 1.133606 TGCATCATGACTGGCCATCAT 60.134 47.619 19.14 19.14 37.27 2.45
2784 2934 3.851458 AAAAGACCCACTCCGTAAACT 57.149 42.857 0.00 0.00 0.00 2.66
2792 2942 4.200092 ACAGTGAAGAAAAAGACCCACTC 58.800 43.478 0.00 0.00 33.17 3.51
2837 2987 7.962917 AGCAATTGAAACCAAATAAAATAGCG 58.037 30.769 10.34 0.00 0.00 4.26
3230 3644 5.221501 TGGATATCATGCAAAGAGATCGTCA 60.222 40.000 16.21 9.83 35.21 4.35
3280 3696 3.433306 TCAGGTTCTAACATGGTTGGG 57.567 47.619 7.56 0.00 40.78 4.12
3565 3983 4.809426 CCCATTCTGTATTTCTGGTCGTAC 59.191 45.833 0.00 0.00 0.00 3.67
3830 4260 5.090139 TCTCTTCCTTCCACAGATCTTTCT 58.910 41.667 0.00 0.00 0.00 2.52
3868 4298 6.491403 CCATCTATACAAAAATTCCCCCTCAG 59.509 42.308 0.00 0.00 0.00 3.35
3930 4360 9.855021 AATACACACCAAAATTTTGCTATAGTC 57.145 29.630 22.90 0.00 36.86 2.59
4106 4536 5.182001 GGCATTTTACCATCGCTCTATCAAT 59.818 40.000 0.00 0.00 0.00 2.57
4510 4940 4.933505 TGCACATTCTCCAAAAACATCA 57.066 36.364 0.00 0.00 0.00 3.07
4564 4994 4.275936 ACTCATGCGAACTTAACTTGCTTT 59.724 37.500 0.00 0.00 0.00 3.51
4750 5187 1.338107 ATAGCCAGTGCCGTATAGCA 58.662 50.000 0.00 0.00 41.46 3.49
4925 5362 5.163733 GCTACAGTAGTAAGCTCGTTTCTCT 60.164 44.000 9.42 0.00 0.00 3.10
4983 5420 4.819769 TGCAATTTCTACCTTTGATTGGC 58.180 39.130 0.00 0.00 0.00 4.52
4992 5429 7.318141 CAAACATCAGAATGCAATTTCTACCT 58.682 34.615 2.30 0.00 36.07 3.08
5434 5900 6.832520 ATAGATGTGCATACTAGTCCTGAG 57.167 41.667 0.00 0.00 0.00 3.35
5482 5948 5.705609 TGGCAAGACCTAACAGAATTTTC 57.294 39.130 0.00 0.00 40.22 2.29
5876 6350 7.628234 AGAATATGACAGAAGAAGTGGTCAAT 58.372 34.615 0.00 0.00 42.83 2.57
5882 6356 9.429359 ACAACTAAGAATATGACAGAAGAAGTG 57.571 33.333 0.00 0.00 0.00 3.16
5883 6357 9.646427 GACAACTAAGAATATGACAGAAGAAGT 57.354 33.333 0.00 0.00 0.00 3.01
5912 6392 0.109153 TCTTGTCTGGCAGCACACAT 59.891 50.000 10.34 0.00 0.00 3.21
5945 6425 7.897575 AACTAGAGAGCAAATACTGAAGTTG 57.102 36.000 0.00 0.00 0.00 3.16
5947 6427 7.902087 AGAAACTAGAGAGCAAATACTGAAGT 58.098 34.615 0.00 0.00 0.00 3.01
5948 6428 9.296400 GTAGAAACTAGAGAGCAAATACTGAAG 57.704 37.037 0.00 0.00 0.00 3.02
5949 6429 9.026121 AGTAGAAACTAGAGAGCAAATACTGAA 57.974 33.333 0.00 0.00 32.84 3.02
5950 6430 8.582657 AGTAGAAACTAGAGAGCAAATACTGA 57.417 34.615 0.00 0.00 32.84 3.41
5951 6431 7.918562 GGAGTAGAAACTAGAGAGCAAATACTG 59.081 40.741 0.00 0.00 35.56 2.74
5952 6432 7.068962 GGGAGTAGAAACTAGAGAGCAAATACT 59.931 40.741 0.00 0.00 35.56 2.12
5953 6433 7.068962 AGGGAGTAGAAACTAGAGAGCAAATAC 59.931 40.741 0.00 0.00 35.56 1.89
5954 6434 7.126733 AGGGAGTAGAAACTAGAGAGCAAATA 58.873 38.462 0.00 0.00 35.56 1.40
5955 6435 5.961421 AGGGAGTAGAAACTAGAGAGCAAAT 59.039 40.000 0.00 0.00 35.56 2.32
5956 6436 5.334421 AGGGAGTAGAAACTAGAGAGCAAA 58.666 41.667 0.00 0.00 35.56 3.68
5957 6437 4.936802 AGGGAGTAGAAACTAGAGAGCAA 58.063 43.478 0.00 0.00 35.56 3.91
5963 6443 4.268359 GAACGGAGGGAGTAGAAACTAGA 58.732 47.826 0.00 0.00 35.56 2.43
5981 6461 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
5984 6464 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
5985 6465 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
5986 6466 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
5987 6467 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
5990 6470 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
5993 6473 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
5994 6474 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
5995 6475 6.469595 TCAAAATTTGAACTAAAACCACGACG 59.530 34.615 5.87 0.00 36.59 5.12
6009 6489 7.008447 CGTCGTGGTTTTAGTTCAAAATTTGAA 59.992 33.333 16.28 16.28 46.68 2.69
6010 6490 6.469595 CGTCGTGGTTTTAGTTCAAAATTTGA 59.530 34.615 4.03 4.03 38.36 2.69
6011 6491 6.469595 TCGTCGTGGTTTTAGTTCAAAATTTG 59.530 34.615 0.00 0.00 38.36 2.32
6015 6495 4.630940 ACTCGTCGTGGTTTTAGTTCAAAA 59.369 37.500 0.00 0.00 33.66 2.44
6018 6498 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
6019 6499 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
6021 6501 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
6024 6504 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
6025 6505 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
6026 6506 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
6027 6507 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
6028 6508 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
6031 6511 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
6032 6512 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
6033 6513 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
6034 6514 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
6040 6520 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
6041 6521 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
6042 6522 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
6043 6523 2.832643 TATGTACTCCCTCCGTTCCA 57.167 50.000 0.00 0.00 0.00 3.53
6044 6524 4.684484 AAATATGTACTCCCTCCGTTCC 57.316 45.455 0.00 0.00 0.00 3.62
6045 6525 6.183360 ACCTTAAATATGTACTCCCTCCGTTC 60.183 42.308 0.00 0.00 0.00 3.95
6046 6526 5.664457 ACCTTAAATATGTACTCCCTCCGTT 59.336 40.000 0.00 0.00 0.00 4.44
6047 6527 5.214293 ACCTTAAATATGTACTCCCTCCGT 58.786 41.667 0.00 0.00 0.00 4.69
6048 6528 5.803237 ACCTTAAATATGTACTCCCTCCG 57.197 43.478 0.00 0.00 0.00 4.63
6049 6529 7.160049 GCTAACCTTAAATATGTACTCCCTCC 58.840 42.308 0.00 0.00 0.00 4.30
6050 6530 7.732996 TGCTAACCTTAAATATGTACTCCCTC 58.267 38.462 0.00 0.00 0.00 4.30
6051 6531 7.685849 TGCTAACCTTAAATATGTACTCCCT 57.314 36.000 0.00 0.00 0.00 4.20
6052 6532 8.784043 CAATGCTAACCTTAAATATGTACTCCC 58.216 37.037 0.00 0.00 0.00 4.30
6053 6533 9.555727 TCAATGCTAACCTTAAATATGTACTCC 57.444 33.333 0.00 0.00 0.00 3.85
6123 6615 3.181435 TGAACCTGATCATGGTGGAAACA 60.181 43.478 15.00 9.36 37.93 2.83
6266 6762 2.043852 GAGGACAGCTCCGGGAGA 60.044 66.667 27.95 0.00 42.22 3.71
6476 6972 6.204882 ACAGCAGACGATTAAGCTAACTTTTT 59.795 34.615 0.00 0.00 37.33 1.94
6522 7018 7.870445 AGAGAAACAAGAGTCAGTTTACAGATC 59.130 37.037 12.06 7.32 38.01 2.75
6706 7222 9.349713 TCTTGGAAATGTGGTAAATGGATATAC 57.650 33.333 0.00 0.00 0.00 1.47
6739 7255 0.038709 GGCAAGGCACGCATTTGTAA 60.039 50.000 0.51 0.00 0.00 2.41
6871 7387 6.663734 AGTCTTACATTTTGGAATAGAGGGG 58.336 40.000 0.00 0.00 0.00 4.79
6923 7440 5.918576 CCGTCCCAAAATGTAAGAAGTTTTC 59.081 40.000 0.00 0.00 0.00 2.29
6957 7474 0.313672 GCCAAAGCACGGATGTTCAA 59.686 50.000 0.00 0.00 39.53 2.69
6962 7479 2.480555 GACGCCAAAGCACGGATG 59.519 61.111 0.00 0.00 39.83 3.51
6963 7480 3.118454 CGACGCCAAAGCACGGAT 61.118 61.111 0.00 0.00 39.83 4.18
7076 7593 7.232737 TCCAAGTATCTGTTTTCTGAGAGTGTA 59.767 37.037 0.00 0.00 0.00 2.90
7121 7638 2.851263 TCAGGCCGTAGTCACATTTT 57.149 45.000 0.00 0.00 0.00 1.82
7143 7660 3.203040 AGCAGATTAGGTAATGCTGGGTT 59.797 43.478 0.00 0.00 0.00 4.11
7145 7662 3.498774 AGCAGATTAGGTAATGCTGGG 57.501 47.619 0.00 0.00 0.00 4.45
7153 7676 4.901197 TGGTTGTCAAGCAGATTAGGTA 57.099 40.909 13.35 0.00 34.36 3.08
7164 7687 2.908073 GCGGGCACTGGTTGTCAAG 61.908 63.158 0.00 0.00 33.56 3.02
7165 7688 2.904866 GCGGGCACTGGTTGTCAA 60.905 61.111 0.00 0.00 33.56 3.18
7227 7751 1.204146 GGTACATTGGAGGGAGCTGA 58.796 55.000 0.00 0.00 0.00 4.26
7231 7755 0.469917 ATGCGGTACATTGGAGGGAG 59.530 55.000 0.00 0.00 34.40 4.30
7233 7757 0.535102 GGATGCGGTACATTGGAGGG 60.535 60.000 0.00 0.00 39.84 4.30
7235 7759 1.138859 TGAGGATGCGGTACATTGGAG 59.861 52.381 0.00 0.00 39.84 3.86
7236 7760 1.134521 GTGAGGATGCGGTACATTGGA 60.135 52.381 0.00 0.00 39.84 3.53
7237 7761 1.134401 AGTGAGGATGCGGTACATTGG 60.134 52.381 0.00 0.00 39.84 3.16
7238 7762 2.205074 GAGTGAGGATGCGGTACATTG 58.795 52.381 0.00 0.00 39.84 2.82
7239 7763 1.831106 TGAGTGAGGATGCGGTACATT 59.169 47.619 0.00 0.00 39.84 2.71
7240 7764 1.410517 CTGAGTGAGGATGCGGTACAT 59.589 52.381 0.00 0.00 43.54 2.29
7241 7765 0.817654 CTGAGTGAGGATGCGGTACA 59.182 55.000 0.00 0.00 0.00 2.90
7242 7766 1.103803 TCTGAGTGAGGATGCGGTAC 58.896 55.000 0.00 0.00 0.00 3.34
7244 7768 1.137872 GATTCTGAGTGAGGATGCGGT 59.862 52.381 0.00 0.00 0.00 5.68
7251 8919 3.249091 CACGTTGAGATTCTGAGTGAGG 58.751 50.000 0.00 0.00 0.00 3.86
7279 8947 0.610232 AGCTGCCCACAATCCAAGTC 60.610 55.000 0.00 0.00 0.00 3.01
7317 8985 2.781158 GCAACCAAACACGCCCTGT 61.781 57.895 0.00 0.00 32.89 4.00
7319 8987 3.591835 CGCAACCAAACACGCCCT 61.592 61.111 0.00 0.00 0.00 5.19
7320 8988 3.894947 ACGCAACCAAACACGCCC 61.895 61.111 0.00 0.00 0.00 6.13
7374 9042 2.906354 AGTCCGCATTTACTTAGCCAG 58.094 47.619 0.00 0.00 0.00 4.85
7380 9048 7.826690 ACATGATTTTTAGTCCGCATTTACTT 58.173 30.769 0.00 0.00 0.00 2.24
7416 9084 7.897864 AGACTTATATTTAGGAACGGATGGAG 58.102 38.462 0.00 0.00 0.00 3.86
7417 9085 7.850935 AGACTTATATTTAGGAACGGATGGA 57.149 36.000 0.00 0.00 0.00 3.41
7418 9086 8.904099 AAAGACTTATATTTAGGAACGGATGG 57.096 34.615 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.