Multiple sequence alignment - TraesCS4A01G101300

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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 TraesCS4A01G101300 chr4A 100.000 3241 0 0 1 3241 113607604 113610844 0.000000e+00 5986.0
1 TraesCS4A01G101300 chr4A 83.250 400 60 5 2846 3241 570407091 570407487 8.550000e-96 361.0
2 TraesCS4A01G101300 chr4D 95.188 956 33 5 1261 2209 351659452 351658503 0.000000e+00 1498.0
3 TraesCS4A01G101300 chr4D 89.821 560 36 10 621 1165 351660154 351659601 0.000000e+00 699.0
4 TraesCS4A01G101300 chr4D 83.293 413 64 4 2829 3239 241499686 241499277 3.050000e-100 375.0
5 TraesCS4A01G101300 chr4B 94.027 971 34 10 1261 2210 434587142 434586175 0.000000e+00 1450.0
6 TraesCS4A01G101300 chr4B 90.632 427 26 6 749 1164 434587710 434587287 3.650000e-154 555.0
7 TraesCS4A01G101300 chr4B 82.970 505 75 10 2260 2761 102501427 102501923 2.290000e-121 446.0
8 TraesCS4A01G101300 chr4B 92.453 212 11 5 532 740 434589694 434589485 6.800000e-77 298.0
9 TraesCS4A01G101300 chr4B 97.391 115 3 0 3 117 434591451 434591337 2.550000e-46 196.0
10 TraesCS4A01G101300 chr2D 83.480 569 84 6 2260 2826 427652830 427653390 3.710000e-144 521.0
11 TraesCS4A01G101300 chr2D 81.038 559 89 14 2260 2814 340428096 340427551 2.310000e-116 429.0
12 TraesCS4A01G101300 chr2D 81.340 418 68 9 2829 3241 427653421 427653833 6.700000e-87 331.0
13 TraesCS4A01G101300 chr6A 81.803 588 87 17 2251 2826 478117836 478117257 2.930000e-130 475.0
14 TraesCS4A01G101300 chr3D 86.473 414 54 1 2829 3240 129526424 129526837 1.370000e-123 453.0
15 TraesCS4A01G101300 chr3D 81.501 573 70 27 2260 2826 129525851 129526393 3.840000e-119 438.0
16 TraesCS4A01G101300 chr2A 81.379 580 87 16 2260 2826 519960394 519960965 1.370000e-123 453.0
17 TraesCS4A01G101300 chr2A 79.553 582 100 17 2251 2821 104643693 104643120 6.520000e-107 398.0
18 TraesCS4A01G101300 chr2B 81.593 565 86 12 2264 2826 253514056 253513508 4.930000e-123 451.0
19 TraesCS4A01G101300 chr2B 81.928 415 70 4 2830 3241 538079791 538079379 2.390000e-91 346.0
20 TraesCS4A01G101300 chr1D 82.966 499 78 6 2261 2756 133577762 133578256 8.250000e-121 444.0
21 TraesCS4A01G101300 chr1D 89.231 65 5 2 532 596 387796238 387796300 2.680000e-11 80.5
22 TraesCS4A01G101300 chr5A 82.012 517 77 14 2264 2772 284314142 284314650 2.990000e-115 425.0
23 TraesCS4A01G101300 chr6B 85.678 398 51 5 2848 3241 450397706 450397311 6.470000e-112 414.0
24 TraesCS4A01G101300 chr3B 83.453 417 62 5 2829 3241 431865351 431865764 6.560000e-102 381.0
25 TraesCS4A01G101300 chr3B 73.669 338 61 17 153 486 570962101 570961788 4.420000e-19 106.0
26 TraesCS4A01G101300 chr7D 83.838 396 59 4 2849 3241 250491264 250490871 3.950000e-99 372.0
27 TraesCS4A01G101300 chr7D 82.775 418 63 5 2829 3241 258891266 258890853 6.610000e-97 364.0


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 TraesCS4A01G101300 chr4A 113607604 113610844 3240 False 5986.00 5986 100.00000 1 3241 1 chr4A.!!$F1 3240
1 TraesCS4A01G101300 chr4D 351658503 351660154 1651 True 1098.50 1498 92.50450 621 2209 2 chr4D.!!$R2 1588
2 TraesCS4A01G101300 chr4B 434586175 434591451 5276 True 624.75 1450 93.62575 3 2210 4 chr4B.!!$R1 2207
3 TraesCS4A01G101300 chr2D 340427551 340428096 545 True 429.00 429 81.03800 2260 2814 1 chr2D.!!$R1 554
4 TraesCS4A01G101300 chr2D 427652830 427653833 1003 False 426.00 521 82.41000 2260 3241 2 chr2D.!!$F1 981
5 TraesCS4A01G101300 chr6A 478117257 478117836 579 True 475.00 475 81.80300 2251 2826 1 chr6A.!!$R1 575
6 TraesCS4A01G101300 chr3D 129525851 129526837 986 False 445.50 453 83.98700 2260 3240 2 chr3D.!!$F1 980
7 TraesCS4A01G101300 chr2A 519960394 519960965 571 False 453.00 453 81.37900 2260 2826 1 chr2A.!!$F1 566
8 TraesCS4A01G101300 chr2A 104643120 104643693 573 True 398.00 398 79.55300 2251 2821 1 chr2A.!!$R1 570
9 TraesCS4A01G101300 chr2B 253513508 253514056 548 True 451.00 451 81.59300 2264 2826 1 chr2B.!!$R1 562
10 TraesCS4A01G101300 chr5A 284314142 284314650 508 False 425.00 425 82.01200 2264 2772 1 chr5A.!!$F1 508

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
504 1818 0.037303 ACAATGGAGAGGCTGGTGTG 59.963 55.000 0.00 0.0 0.00 3.82 F
510 1824 0.246086 GAGAGGCTGGTGTGAGACTG 59.754 60.000 0.00 0.0 28.27 3.51 F
746 2076 1.065998 GTGGGGCCAAGTTATGACGTA 60.066 52.381 4.39 0.0 0.00 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 5404 0.033503 AATAAAACTCCCCTGCCCCG 60.034 55.000 0.0 0.0 0.00 5.73 R
2212 5406 1.006639 TGGAATAAAACTCCCCTGCCC 59.993 52.381 0.0 0.0 31.32 5.36 R
2714 5936 0.755698 GCCCGTCTATCAGTGGGAGA 60.756 60.000 0.0 0.0 44.88 3.71 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
91 92 7.801716 TGATGCAAACTAAGTTGAGTTTACT 57.198 32.000 0.00 0.00 45.70 2.24
117 118 6.678857 ACCTAGTCCTCTTAAAATGGGAGAAT 59.321 38.462 0.00 0.00 0.00 2.40
119 120 8.055790 CCTAGTCCTCTTAAAATGGGAGAATTT 58.944 37.037 0.00 0.00 0.00 1.82
120 121 7.946381 AGTCCTCTTAAAATGGGAGAATTTC 57.054 36.000 0.00 0.00 0.00 2.17
121 122 6.599638 AGTCCTCTTAAAATGGGAGAATTTCG 59.400 38.462 0.00 0.00 0.00 3.46
122 123 6.598064 GTCCTCTTAAAATGGGAGAATTTCGA 59.402 38.462 0.00 0.00 0.00 3.71
123 124 7.120726 GTCCTCTTAAAATGGGAGAATTTCGAA 59.879 37.037 0.00 0.00 0.00 3.71
124 125 7.668052 TCCTCTTAAAATGGGAGAATTTCGAAA 59.332 33.333 13.91 13.91 0.00 3.46
125 126 8.303876 CCTCTTAAAATGGGAGAATTTCGAAAA 58.696 33.333 15.66 0.00 0.00 2.29
126 127 9.691362 CTCTTAAAATGGGAGAATTTCGAAAAA 57.309 29.630 15.66 0.00 0.00 1.94
166 167 6.371809 AAATTAGTTGAGTTTGCTCGAACA 57.628 33.333 3.14 0.00 44.48 3.18
169 170 3.466836 AGTTGAGTTTGCTCGAACATGA 58.533 40.909 0.00 0.00 44.48 3.07
175 176 3.369147 AGTTTGCTCGAACATGATCTTCG 59.631 43.478 9.90 9.90 41.55 3.79
187 1501 0.446616 GATCTTCGGCGTGAAAACCC 59.553 55.000 6.85 0.00 35.79 4.11
190 1504 1.440938 CTTCGGCGTGAAAACCCACA 61.441 55.000 6.85 0.00 35.79 4.17
195 1509 1.335872 GGCGTGAAAACCCACAATCTG 60.336 52.381 0.00 0.00 36.89 2.90
199 1513 2.031157 GTGAAAACCCACAATCTGACCG 60.031 50.000 0.00 0.00 37.04 4.79
201 1515 1.892209 AAACCCACAATCTGACCGTC 58.108 50.000 0.00 0.00 0.00 4.79
219 1533 2.357952 CGTCGATAGTTGGATCTGGTGA 59.642 50.000 0.00 0.00 37.40 4.02
221 1535 2.357952 TCGATAGTTGGATCTGGTGACG 59.642 50.000 0.00 0.00 37.40 4.35
225 1539 3.309436 TTGGATCTGGTGACGGCGG 62.309 63.158 13.24 0.00 36.33 6.13
226 1540 4.530857 GGATCTGGTGACGGCGGG 62.531 72.222 13.24 0.00 36.33 6.13
227 1541 4.530857 GATCTGGTGACGGCGGGG 62.531 72.222 13.24 0.00 36.33 5.73
249 1563 0.588252 CACGTGTTGCTCCCTTCTTG 59.412 55.000 7.58 0.00 0.00 3.02
250 1564 0.468226 ACGTGTTGCTCCCTTCTTGA 59.532 50.000 0.00 0.00 0.00 3.02
255 1569 0.478072 TTGCTCCCTTCTTGAAGGCA 59.522 50.000 20.71 14.03 38.63 4.75
257 1571 1.340405 TGCTCCCTTCTTGAAGGCATC 60.340 52.381 20.71 12.61 38.63 3.91
258 1572 1.340405 GCTCCCTTCTTGAAGGCATCA 60.340 52.381 20.71 6.26 38.63 3.07
260 1574 1.704628 TCCCTTCTTGAAGGCATCACA 59.295 47.619 20.71 1.13 37.92 3.58
270 1584 5.988310 TGAAGGCATCACATTTGAAGAAT 57.012 34.783 0.00 0.00 34.61 2.40
271 1585 6.349243 TGAAGGCATCACATTTGAAGAATT 57.651 33.333 0.00 0.00 34.61 2.17
308 1622 0.958822 GCCGTCAAAAGATGGTTGGT 59.041 50.000 5.70 0.00 33.84 3.67
317 1631 0.180406 AGATGGTTGGTACGGATGGC 59.820 55.000 0.00 0.00 0.00 4.40
320 1634 1.226262 GGTTGGTACGGATGGCCAT 59.774 57.895 20.96 20.96 31.71 4.40
326 1640 0.180406 GTACGGATGGCCATTGAGGT 59.820 55.000 21.84 16.85 40.61 3.85
338 1652 5.053145 GGCCATTGAGGTATATCATCGATC 58.947 45.833 0.00 0.00 40.61 3.69
340 1654 5.521735 GCCATTGAGGTATATCATCGATCAC 59.478 44.000 0.00 0.00 40.61 3.06
341 1655 6.629068 GCCATTGAGGTATATCATCGATCACT 60.629 42.308 0.00 0.00 40.61 3.41
342 1656 6.755607 CCATTGAGGTATATCATCGATCACTG 59.244 42.308 0.00 0.00 29.67 3.66
343 1657 5.316327 TGAGGTATATCATCGATCACTGC 57.684 43.478 0.00 0.00 0.00 4.40
359 1673 4.707105 TCACTGCTTTGATCACTTGAGAA 58.293 39.130 0.00 0.00 0.00 2.87
360 1674 5.125356 TCACTGCTTTGATCACTTGAGAAA 58.875 37.500 0.00 0.00 0.00 2.52
362 1676 6.263842 TCACTGCTTTGATCACTTGAGAAATT 59.736 34.615 0.00 0.00 0.00 1.82
387 1701 9.898152 TTTTCTTCTTCTTCTTCTTCTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
388 1702 9.898152 TTTCTTCTTCTTCTTCTTCTTCTTCTT 57.102 29.630 0.00 0.00 0.00 2.52
389 1703 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
390 1704 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
391 1705 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
392 1706 9.898152 TTCTTCTTCTTCTTCTTCTTCTTCTTT 57.102 29.630 0.00 0.00 0.00 2.52
393 1707 9.898152 TCTTCTTCTTCTTCTTCTTCTTCTTTT 57.102 29.630 0.00 0.00 0.00 2.27
396 1710 9.672673 TCTTCTTCTTCTTCTTCTTCTTTTTCA 57.327 29.630 0.00 0.00 0.00 2.69
418 1732 9.534565 TTTCATTATGTGTCTAGACATAGCTTC 57.465 33.333 27.54 14.38 43.97 3.86
429 1743 7.380065 GTCTAGACATAGCTTCGGTCTTATTTG 59.620 40.741 18.20 6.33 41.74 2.32
432 1746 5.978814 ACATAGCTTCGGTCTTATTTGACT 58.021 37.500 0.00 0.00 37.16 3.41
435 1749 7.390718 ACATAGCTTCGGTCTTATTTGACTTTT 59.609 33.333 0.00 0.00 37.16 2.27
436 1750 6.002062 AGCTTCGGTCTTATTTGACTTTTG 57.998 37.500 0.00 0.00 37.16 2.44
437 1751 4.617223 GCTTCGGTCTTATTTGACTTTTGC 59.383 41.667 0.00 0.00 37.16 3.68
438 1752 5.562890 GCTTCGGTCTTATTTGACTTTTGCT 60.563 40.000 0.00 0.00 37.16 3.91
439 1753 6.348213 GCTTCGGTCTTATTTGACTTTTGCTA 60.348 38.462 0.00 0.00 37.16 3.49
442 1756 8.106247 TCGGTCTTATTTGACTTTTGCTATTT 57.894 30.769 0.00 0.00 37.16 1.40
443 1757 8.573035 TCGGTCTTATTTGACTTTTGCTATTTT 58.427 29.630 0.00 0.00 37.16 1.82
444 1758 8.638565 CGGTCTTATTTGACTTTTGCTATTTTG 58.361 33.333 0.00 0.00 37.16 2.44
445 1759 8.435430 GGTCTTATTTGACTTTTGCTATTTTGC 58.565 33.333 0.00 0.00 37.16 3.68
446 1760 8.435430 GTCTTATTTGACTTTTGCTATTTTGCC 58.565 33.333 0.00 0.00 34.39 4.52
447 1761 8.147058 TCTTATTTGACTTTTGCTATTTTGCCA 58.853 29.630 0.00 0.00 0.00 4.92
448 1762 6.790285 ATTTGACTTTTGCTATTTTGCCAG 57.210 33.333 0.00 0.00 0.00 4.85
449 1763 3.652274 TGACTTTTGCTATTTTGCCAGC 58.348 40.909 0.00 0.00 38.31 4.85
450 1764 3.069300 TGACTTTTGCTATTTTGCCAGCA 59.931 39.130 0.00 0.00 45.72 4.41
451 1765 4.248058 GACTTTTGCTATTTTGCCAGCAT 58.752 39.130 0.00 0.00 46.56 3.79
452 1766 3.998341 ACTTTTGCTATTTTGCCAGCATG 59.002 39.130 0.00 0.00 46.56 4.06
453 1767 3.957591 TTTGCTATTTTGCCAGCATGA 57.042 38.095 0.00 0.00 46.56 3.07
454 1768 4.475051 TTTGCTATTTTGCCAGCATGAT 57.525 36.364 0.00 0.00 46.56 2.45
455 1769 4.475051 TTGCTATTTTGCCAGCATGATT 57.525 36.364 0.00 0.00 46.56 2.57
457 1771 4.834534 TGCTATTTTGCCAGCATGATTTT 58.165 34.783 0.00 0.00 42.68 1.82
459 1773 5.114081 GCTATTTTGCCAGCATGATTTTCT 58.886 37.500 0.00 0.00 39.69 2.52
461 1775 4.339872 TTTTGCCAGCATGATTTTCTGT 57.660 36.364 0.00 0.00 39.69 3.41
462 1776 3.306917 TTGCCAGCATGATTTTCTGTG 57.693 42.857 0.00 0.00 39.69 3.66
463 1777 2.241160 TGCCAGCATGATTTTCTGTGT 58.759 42.857 0.00 0.00 39.69 3.72
466 1780 3.571571 CCAGCATGATTTTCTGTGTGTG 58.428 45.455 0.00 0.00 39.69 3.82
467 1781 3.005050 CCAGCATGATTTTCTGTGTGTGT 59.995 43.478 0.00 0.00 39.69 3.72
468 1782 4.500205 CCAGCATGATTTTCTGTGTGTGTT 60.500 41.667 0.00 0.00 39.69 3.32
469 1783 4.443063 CAGCATGATTTTCTGTGTGTGTTG 59.557 41.667 0.00 0.00 39.69 3.33
471 1785 4.737352 GCATGATTTTCTGTGTGTGTTGGT 60.737 41.667 0.00 0.00 0.00 3.67
472 1786 5.350633 CATGATTTTCTGTGTGTGTTGGTT 58.649 37.500 0.00 0.00 0.00 3.67
476 1790 2.192664 TCTGTGTGTGTTGGTTGTGT 57.807 45.000 0.00 0.00 0.00 3.72
477 1791 1.809547 TCTGTGTGTGTTGGTTGTGTG 59.190 47.619 0.00 0.00 0.00 3.82
478 1792 0.242286 TGTGTGTGTTGGTTGTGTGC 59.758 50.000 0.00 0.00 0.00 4.57
479 1793 0.457681 GTGTGTGTTGGTTGTGTGCC 60.458 55.000 0.00 0.00 0.00 5.01
480 1794 0.610509 TGTGTGTTGGTTGTGTGCCT 60.611 50.000 0.00 0.00 0.00 4.75
481 1795 0.100503 GTGTGTTGGTTGTGTGCCTC 59.899 55.000 0.00 0.00 0.00 4.70
482 1796 1.034838 TGTGTTGGTTGTGTGCCTCC 61.035 55.000 0.00 0.00 0.00 4.30
483 1797 0.751643 GTGTTGGTTGTGTGCCTCCT 60.752 55.000 0.00 0.00 0.00 3.69
484 1798 0.840617 TGTTGGTTGTGTGCCTCCTA 59.159 50.000 0.00 0.00 0.00 2.94
485 1799 1.213182 TGTTGGTTGTGTGCCTCCTAA 59.787 47.619 0.00 0.00 0.00 2.69
486 1800 1.607148 GTTGGTTGTGTGCCTCCTAAC 59.393 52.381 0.00 0.00 0.00 2.34
487 1801 0.840617 TGGTTGTGTGCCTCCTAACA 59.159 50.000 0.00 0.00 0.00 2.41
488 1802 1.213182 TGGTTGTGTGCCTCCTAACAA 59.787 47.619 0.00 0.00 0.00 2.83
489 1803 2.158534 TGGTTGTGTGCCTCCTAACAAT 60.159 45.455 0.00 0.00 35.20 2.71
490 1804 2.228822 GGTTGTGTGCCTCCTAACAATG 59.771 50.000 0.00 0.00 35.20 2.82
491 1805 2.198827 TGTGTGCCTCCTAACAATGG 57.801 50.000 0.00 0.00 0.00 3.16
492 1806 1.702401 TGTGTGCCTCCTAACAATGGA 59.298 47.619 0.00 0.00 0.00 3.41
500 1814 1.839994 TCCTAACAATGGAGAGGCTGG 59.160 52.381 0.00 0.00 0.00 4.85
501 1815 1.561542 CCTAACAATGGAGAGGCTGGT 59.438 52.381 0.00 0.00 0.00 4.00
502 1816 2.636830 CTAACAATGGAGAGGCTGGTG 58.363 52.381 0.00 0.00 0.00 4.17
503 1817 0.773644 AACAATGGAGAGGCTGGTGT 59.226 50.000 0.00 0.00 0.00 4.16
504 1818 0.037303 ACAATGGAGAGGCTGGTGTG 59.963 55.000 0.00 0.00 0.00 3.82
505 1819 0.325933 CAATGGAGAGGCTGGTGTGA 59.674 55.000 0.00 0.00 0.00 3.58
506 1820 0.617413 AATGGAGAGGCTGGTGTGAG 59.383 55.000 0.00 0.00 0.00 3.51
507 1821 0.252421 ATGGAGAGGCTGGTGTGAGA 60.252 55.000 0.00 0.00 0.00 3.27
508 1822 1.188219 TGGAGAGGCTGGTGTGAGAC 61.188 60.000 0.00 0.00 0.00 3.36
509 1823 0.902516 GGAGAGGCTGGTGTGAGACT 60.903 60.000 0.00 0.00 32.17 3.24
510 1824 0.246086 GAGAGGCTGGTGTGAGACTG 59.754 60.000 0.00 0.00 28.27 3.51
511 1825 1.190833 AGAGGCTGGTGTGAGACTGG 61.191 60.000 0.00 0.00 28.27 4.00
512 1826 2.177594 GAGGCTGGTGTGAGACTGGG 62.178 65.000 0.00 0.00 28.27 4.45
513 1827 2.359230 GCTGGTGTGAGACTGGGC 60.359 66.667 0.00 0.00 0.00 5.36
516 1830 1.762522 CTGGTGTGAGACTGGGCTGT 61.763 60.000 0.00 0.00 0.00 4.40
521 1835 1.838396 TGAGACTGGGCTGTGCTCA 60.838 57.895 0.00 0.00 36.30 4.26
528 1842 2.174210 ACTGGGCTGTGCTCATTATGAT 59.826 45.455 0.00 0.00 38.82 2.45
529 1843 3.220110 CTGGGCTGTGCTCATTATGATT 58.780 45.455 0.00 0.00 38.82 2.57
530 1844 2.953648 TGGGCTGTGCTCATTATGATTG 59.046 45.455 0.00 0.00 32.27 2.67
531 1845 2.954318 GGGCTGTGCTCATTATGATTGT 59.046 45.455 0.00 0.00 0.00 2.71
532 1846 4.136796 GGGCTGTGCTCATTATGATTGTA 58.863 43.478 0.00 0.00 0.00 2.41
533 1847 4.763793 GGGCTGTGCTCATTATGATTGTAT 59.236 41.667 0.00 0.00 0.00 2.29
534 1848 5.335426 GGGCTGTGCTCATTATGATTGTATG 60.335 44.000 0.00 0.00 0.00 2.39
535 1849 5.471116 GGCTGTGCTCATTATGATTGTATGA 59.529 40.000 0.00 0.00 0.00 2.15
536 1850 6.150641 GGCTGTGCTCATTATGATTGTATGAT 59.849 38.462 0.00 0.00 0.00 2.45
540 1854 9.558396 TGTGCTCATTATGATTGTATGATTGTA 57.442 29.630 0.00 0.00 0.00 2.41
570 1884 6.865205 TCGATGCTACATCATGAGTCAATAAG 59.135 38.462 0.09 0.00 0.00 1.73
578 1892 8.682936 ACATCATGAGTCAATAAGAATTACCC 57.317 34.615 0.09 0.00 30.46 3.69
579 1893 8.274322 ACATCATGAGTCAATAAGAATTACCCA 58.726 33.333 0.09 0.00 30.46 4.51
582 1896 9.699410 TCATGAGTCAATAAGAATTACCCATTT 57.301 29.630 0.00 0.00 30.46 2.32
583 1897 9.740239 CATGAGTCAATAAGAATTACCCATTTG 57.260 33.333 0.00 0.00 30.46 2.32
584 1898 8.877864 TGAGTCAATAAGAATTACCCATTTGT 57.122 30.769 0.00 0.00 30.46 2.83
585 1899 8.956426 TGAGTCAATAAGAATTACCCATTTGTC 58.044 33.333 0.00 0.00 30.46 3.18
586 1900 8.877864 AGTCAATAAGAATTACCCATTTGTCA 57.122 30.769 0.00 0.00 30.46 3.58
603 1917 8.382875 CCATTTGTCAAAAGAAAGTTGAGTTTC 58.617 33.333 1.31 3.63 35.71 2.78
713 2043 1.803943 CGAGAGGAGACGACAAGGG 59.196 63.158 0.00 0.00 0.00 3.95
746 2076 1.065998 GTGGGGCCAAGTTATGACGTA 60.066 52.381 4.39 0.00 0.00 3.57
816 3920 3.118454 ATCCGCGTCCGTTGCAAG 61.118 61.111 4.92 0.00 0.00 4.01
877 3981 1.865340 GCGATCTCGTTTTCCATACCC 59.135 52.381 1.14 0.00 42.22 3.69
938 4042 3.431725 CGCCGGCAAAGGAAGGTC 61.432 66.667 28.98 0.00 0.00 3.85
997 4101 2.625314 CGGACAGCTTCTCATAGATGGA 59.375 50.000 0.00 0.00 35.90 3.41
998 4102 3.257873 CGGACAGCTTCTCATAGATGGAT 59.742 47.826 0.00 0.00 35.90 3.41
999 4103 4.617995 CGGACAGCTTCTCATAGATGGATC 60.618 50.000 0.00 0.00 35.90 3.36
1083 4187 1.669265 CTCGCGGGAAAAGGTAAATCC 59.331 52.381 0.00 0.00 0.00 3.01
1135 4244 1.831652 CTCCCTTCTTCTGCACCGGT 61.832 60.000 0.00 0.00 0.00 5.28
1138 4247 1.230635 CCTTCTTCTGCACCGGTGTG 61.231 60.000 33.92 25.81 45.65 3.82
1139 4248 1.227823 TTCTTCTGCACCGGTGTGG 60.228 57.895 33.92 25.34 42.99 4.17
1186 4318 5.861787 CGTGGGATCTTTTTGGTCAAATAAC 59.138 40.000 0.00 0.00 0.00 1.89
1194 4326 8.870160 TCTTTTTGGTCAAATAACTGTTGATG 57.130 30.769 2.69 0.00 37.34 3.07
1236 4369 3.220507 ACGAACATGAACATGCATTGG 57.779 42.857 13.71 6.64 42.39 3.16
1240 4373 1.066716 ACATGAACATGCATTGGCCAC 60.067 47.619 3.88 0.00 42.39 5.01
1241 4374 1.066787 CATGAACATGCATTGGCCACA 60.067 47.619 3.88 0.00 40.13 4.17
1242 4375 1.268066 TGAACATGCATTGGCCACAT 58.732 45.000 3.88 2.42 40.13 3.21
1243 4376 2.454538 TGAACATGCATTGGCCACATA 58.545 42.857 3.88 0.00 40.13 2.29
1244 4377 3.032459 TGAACATGCATTGGCCACATAT 58.968 40.909 3.88 0.00 40.13 1.78
1245 4378 3.181474 TGAACATGCATTGGCCACATATG 60.181 43.478 3.88 8.48 40.13 1.78
1246 4379 1.069513 ACATGCATTGGCCACATATGC 59.930 47.619 27.08 27.08 39.44 3.14
1247 4380 1.069358 CATGCATTGGCCACATATGCA 59.931 47.619 34.33 34.33 45.69 3.96
1279 4448 8.443898 AAGAAGTTTAACAGACGTTTTGTTTC 57.556 30.769 19.92 13.01 39.36 2.78
1862 5046 1.078918 TGGCTGAACAGATGCTCCG 60.079 57.895 5.97 0.00 0.00 4.63
1935 5119 2.315386 GGCGTCGGTTGAGGTTGTC 61.315 63.158 0.00 0.00 32.59 3.18
2047 5231 1.225745 GGCAAGAAACGCGATGACG 60.226 57.895 15.93 0.00 42.93 4.35
2078 5262 1.270550 CAGGGTTCTGTCCATTGTTGC 59.729 52.381 0.00 0.00 36.30 4.17
2097 5281 1.471676 GCCGAGGTCGAGTGATTTCAT 60.472 52.381 0.00 0.00 43.02 2.57
2108 5292 4.849926 CGAGTGATTTCATGAGTGCAAAAG 59.150 41.667 0.00 0.00 0.00 2.27
2154 5342 6.203723 CCCTCTTTATCTTCGATGAATGTTCC 59.796 42.308 4.98 0.00 0.00 3.62
2157 5345 8.201554 TCTTTATCTTCGATGAATGTTCCAAG 57.798 34.615 4.98 1.55 0.00 3.61
2177 5365 1.856629 CAATGTGCCCTTTCCTGGAT 58.143 50.000 0.00 0.00 0.00 3.41
2213 5407 2.343101 CACAGTGTGTGTTATACCGGG 58.657 52.381 15.43 0.00 43.08 5.73
2214 5408 1.276989 ACAGTGTGTGTTATACCGGGG 59.723 52.381 6.32 0.00 34.94 5.73
2215 5409 0.251073 AGTGTGTGTTATACCGGGGC 59.749 55.000 6.32 0.00 0.00 5.80
2216 5410 0.036199 GTGTGTGTTATACCGGGGCA 60.036 55.000 6.32 0.00 0.00 5.36
2217 5411 0.250793 TGTGTGTTATACCGGGGCAG 59.749 55.000 6.32 0.00 0.00 4.85
2218 5412 0.463116 GTGTGTTATACCGGGGCAGG 60.463 60.000 6.32 0.00 37.30 4.85
2219 5413 1.147600 GTGTTATACCGGGGCAGGG 59.852 63.158 6.32 0.00 35.02 4.45
2220 5414 2.073716 TGTTATACCGGGGCAGGGG 61.074 63.158 6.32 0.00 35.02 4.79
2221 5415 1.767268 GTTATACCGGGGCAGGGGA 60.767 63.158 6.32 0.00 35.02 4.81
2222 5416 1.460689 TTATACCGGGGCAGGGGAG 60.461 63.158 6.32 0.00 35.02 4.30
2223 5417 2.260316 TTATACCGGGGCAGGGGAGT 62.260 60.000 6.32 0.00 35.02 3.85
2224 5418 2.260316 TATACCGGGGCAGGGGAGTT 62.260 60.000 6.32 0.00 35.02 3.01
2225 5419 3.749679 TATACCGGGGCAGGGGAGTTT 62.750 57.143 6.32 0.00 35.02 2.66
2226 5420 3.979497 CCGGGGCAGGGGAGTTTT 61.979 66.667 0.00 0.00 0.00 2.43
2227 5421 2.608550 CCGGGGCAGGGGAGTTTTA 61.609 63.158 0.00 0.00 0.00 1.52
2228 5422 1.613061 CGGGGCAGGGGAGTTTTAT 59.387 57.895 0.00 0.00 0.00 1.40
2229 5423 0.033503 CGGGGCAGGGGAGTTTTATT 60.034 55.000 0.00 0.00 0.00 1.40
2230 5424 1.776662 GGGGCAGGGGAGTTTTATTC 58.223 55.000 0.00 0.00 0.00 1.75
2231 5425 1.688311 GGGGCAGGGGAGTTTTATTCC 60.688 57.143 0.00 0.00 0.00 3.01
2232 5426 1.006639 GGGCAGGGGAGTTTTATTCCA 59.993 52.381 0.00 0.00 36.40 3.53
2233 5427 2.359249 GGGCAGGGGAGTTTTATTCCAT 60.359 50.000 0.00 0.00 36.40 3.41
2234 5428 2.959030 GGCAGGGGAGTTTTATTCCATC 59.041 50.000 0.00 0.00 36.40 3.51
2235 5429 3.627237 GGCAGGGGAGTTTTATTCCATCA 60.627 47.826 0.00 0.00 36.40 3.07
2236 5430 4.023291 GCAGGGGAGTTTTATTCCATCAA 58.977 43.478 0.00 0.00 36.40 2.57
2237 5431 4.651045 GCAGGGGAGTTTTATTCCATCAAT 59.349 41.667 0.00 0.00 36.40 2.57
2238 5432 5.833131 GCAGGGGAGTTTTATTCCATCAATA 59.167 40.000 0.00 0.00 36.40 1.90
2239 5433 6.323739 GCAGGGGAGTTTTATTCCATCAATAA 59.676 38.462 0.00 0.00 35.49 1.40
2240 5434 7.470563 GCAGGGGAGTTTTATTCCATCAATAAG 60.471 40.741 0.00 0.00 38.06 1.73
2241 5435 7.014615 CAGGGGAGTTTTATTCCATCAATAAGG 59.985 40.741 0.00 0.00 38.06 2.69
2242 5436 6.239317 GGGGAGTTTTATTCCATCAATAAGGC 60.239 42.308 0.00 0.00 38.06 4.35
2243 5437 6.323739 GGGAGTTTTATTCCATCAATAAGGCA 59.676 38.462 0.00 0.00 38.06 4.75
2244 5438 7.015584 GGGAGTTTTATTCCATCAATAAGGCAT 59.984 37.037 0.00 0.00 38.06 4.40
2245 5439 9.077885 GGAGTTTTATTCCATCAATAAGGCATA 57.922 33.333 0.00 0.00 38.06 3.14
2246 5440 9.899226 GAGTTTTATTCCATCAATAAGGCATAC 57.101 33.333 0.00 0.00 38.06 2.39
2247 5441 8.567948 AGTTTTATTCCATCAATAAGGCATACG 58.432 33.333 0.00 0.00 38.06 3.06
2248 5442 8.564574 GTTTTATTCCATCAATAAGGCATACGA 58.435 33.333 0.00 0.00 38.06 3.43
2249 5443 7.905604 TTATTCCATCAATAAGGCATACGAG 57.094 36.000 0.00 0.00 32.81 4.18
2250 5444 5.545063 TTCCATCAATAAGGCATACGAGA 57.455 39.130 0.00 0.00 0.00 4.04
2251 5445 5.139435 TCCATCAATAAGGCATACGAGAG 57.861 43.478 0.00 0.00 0.00 3.20
2252 5446 4.832823 TCCATCAATAAGGCATACGAGAGA 59.167 41.667 0.00 0.00 0.00 3.10
2253 5447 5.304357 TCCATCAATAAGGCATACGAGAGAA 59.696 40.000 0.00 0.00 0.00 2.87
2254 5448 6.014242 TCCATCAATAAGGCATACGAGAGAAT 60.014 38.462 0.00 0.00 0.00 2.40
2255 5449 6.652481 CCATCAATAAGGCATACGAGAGAATT 59.348 38.462 0.00 0.00 0.00 2.17
2258 5452 9.778741 ATCAATAAGGCATACGAGAGAATTAAA 57.221 29.630 0.00 0.00 0.00 1.52
2356 5567 6.869695 AGAAAAACAATTTACACGGGAAAGT 58.130 32.000 0.00 0.00 0.00 2.66
2379 5595 7.616313 AGTTCCCAACAAACAAAAGAATAACA 58.384 30.769 0.00 0.00 0.00 2.41
2380 5596 7.763985 AGTTCCCAACAAACAAAAGAATAACAG 59.236 33.333 0.00 0.00 0.00 3.16
2456 5676 8.655970 AGAAAAACCAAAAAGAAACGAGAAATG 58.344 29.630 0.00 0.00 0.00 2.32
2499 5720 9.226345 GTTTCTCAAATACACAAGAAGAAAGTG 57.774 33.333 0.00 0.00 39.12 3.16
2500 5721 7.496529 TCTCAAATACACAAGAAGAAAGTGG 57.503 36.000 0.00 0.00 37.58 4.00
2504 5725 8.912988 TCAAATACACAAGAAGAAAGTGGAAAT 58.087 29.630 0.00 0.00 37.58 2.17
2562 5784 5.760743 TGAACACCGACAACTGAAATGAATA 59.239 36.000 0.00 0.00 0.00 1.75
2569 5791 6.908820 CCGACAACTGAAATGAATATGTGATG 59.091 38.462 0.00 0.00 0.00 3.07
2604 5826 6.961360 TGTCGATGAGAAATACATACTCCT 57.039 37.500 0.00 0.00 0.00 3.69
2674 5896 2.320681 TCCCCCTCCAGGATAATACG 57.679 55.000 0.00 0.00 38.24 3.06
2683 5905 1.550976 CAGGATAATACGGAGGCTCCC 59.449 57.143 27.36 11.34 31.13 4.30
2697 5919 4.715130 TCCCGAGGGTCCCACTGG 62.715 72.222 11.55 10.24 36.47 4.00
2714 5936 2.421399 GGTAAGCGGGCTCCTACGT 61.421 63.158 0.00 0.00 0.00 3.57
2775 5997 4.074526 GCTGGCTCTGGCTCGTCA 62.075 66.667 0.00 0.00 38.73 4.35
2815 6037 3.129638 GCCCCAATAAGCGTAAATGTCAA 59.870 43.478 0.00 0.00 0.00 3.18
2826 6048 4.732355 GCGTAAATGTCAACCGGCATAATT 60.732 41.667 0.00 0.00 0.00 1.40
2838 6088 2.223340 CGGCATAATTGAGAAGGTGCAC 60.223 50.000 8.80 8.80 34.45 4.57
2839 6089 2.754552 GGCATAATTGAGAAGGTGCACA 59.245 45.455 20.43 0.00 34.45 4.57
2842 6092 4.726416 CATAATTGAGAAGGTGCACACAC 58.274 43.478 20.43 8.66 46.66 3.82
2864 6114 3.243771 CCATAATAGTCTCACGGGTGTCC 60.244 52.174 0.00 0.00 0.00 4.02
2868 6118 0.251832 AGTCTCACGGGTGTCCTGAT 60.252 55.000 1.33 0.00 33.36 2.90
2873 6123 1.628340 TCACGGGTGTCCTGATTGAAT 59.372 47.619 1.33 0.00 33.36 2.57
2900 6150 5.854010 AGTTATACTGAAATCGCCTCAGA 57.146 39.130 13.14 1.14 42.51 3.27
2905 6155 0.036388 TGAAATCGCCTCAGACCACC 60.036 55.000 0.00 0.00 0.00 4.61
2906 6156 0.036388 GAAATCGCCTCAGACCACCA 60.036 55.000 0.00 0.00 0.00 4.17
2915 6165 3.629398 GCCTCAGACCACCATCAATAAAG 59.371 47.826 0.00 0.00 0.00 1.85
2946 6198 5.068198 CCAAATGCTAGCATAATCAAGGTGT 59.932 40.000 29.77 7.99 35.31 4.16
2948 6200 3.808728 TGCTAGCATAATCAAGGTGTCC 58.191 45.455 14.93 0.00 0.00 4.02
2953 6205 4.406456 AGCATAATCAAGGTGTCCAACAA 58.594 39.130 0.00 0.00 0.00 2.83
2972 6224 6.881602 CCAACAAGTAAAAGCTTCTCCTCTAT 59.118 38.462 0.00 0.00 0.00 1.98
2983 6235 3.500448 TCTCCTCTATCTCATCGTGCT 57.500 47.619 0.00 0.00 0.00 4.40
2985 6237 3.567585 TCTCCTCTATCTCATCGTGCTTG 59.432 47.826 0.00 0.00 0.00 4.01
3013 6265 4.744795 ATCTCAAAATGTCTAGCGAGGT 57.255 40.909 0.00 0.00 0.00 3.85
3039 6291 7.015098 TGGGAAGCATAAATACCACCATAAATG 59.985 37.037 0.00 0.00 0.00 2.32
3042 6294 7.524717 AGCATAAATACCACCATAAATGACC 57.475 36.000 0.00 0.00 0.00 4.02
3064 6316 1.060713 CTTCGAGCGGTTAGTGTGTG 58.939 55.000 0.00 0.00 0.00 3.82
3067 6319 0.039437 CGAGCGGTTAGTGTGTGACT 60.039 55.000 0.00 0.00 38.88 3.41
3069 6321 0.600255 AGCGGTTAGTGTGTGACTGC 60.600 55.000 0.00 0.00 44.09 4.40
3070 6322 0.600255 GCGGTTAGTGTGTGACTGCT 60.600 55.000 0.00 0.00 41.33 4.24
3107 6359 7.122204 AGCACCCAAACTAAAAGTTATATCACC 59.878 37.037 0.00 0.00 37.47 4.02
3130 6382 7.935338 CCATAAAGATCATGGTGCAAAATAC 57.065 36.000 0.00 0.00 38.53 1.89
3141 6393 1.892474 TGCAAAATACCAAGGTCAGGC 59.108 47.619 0.00 0.00 0.00 4.85
3152 6404 2.813042 GTCAGGCGAGCTGAGTGC 60.813 66.667 0.00 0.00 43.29 4.40
3205 6457 6.700520 CCTCCCGACAAATAATGAGTAGTAAC 59.299 42.308 0.00 0.00 0.00 2.50
3211 6463 9.282247 CGACAAATAATGAGTAGTAACGTAACT 57.718 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 7.240167 AGAGGACTAGGTAGTAAACTCAACTT 58.760 38.462 13.88 0.00 36.50 2.66
91 92 6.748969 TCTCCCATTTTAAGAGGACTAGGTA 58.251 40.000 0.00 0.00 0.00 3.08
141 142 7.254852 TGTTCGAGCAAACTCAACTAATTTTT 58.745 30.769 0.00 0.00 43.66 1.94
142 143 6.791303 TGTTCGAGCAAACTCAACTAATTTT 58.209 32.000 0.00 0.00 43.66 1.82
143 144 6.371809 TGTTCGAGCAAACTCAACTAATTT 57.628 33.333 0.00 0.00 43.66 1.82
144 145 6.204688 TCATGTTCGAGCAAACTCAACTAATT 59.795 34.615 5.91 0.00 43.66 1.40
145 146 5.700832 TCATGTTCGAGCAAACTCAACTAAT 59.299 36.000 5.91 0.00 43.66 1.73
149 150 3.878086 TCATGTTCGAGCAAACTCAAC 57.122 42.857 5.91 0.00 43.66 3.18
166 167 1.737793 GGTTTTCACGCCGAAGATCAT 59.262 47.619 0.00 0.00 34.32 2.45
169 170 0.250553 TGGGTTTTCACGCCGAAGAT 60.251 50.000 0.00 0.00 34.32 2.40
175 176 0.958822 AGATTGTGGGTTTTCACGCC 59.041 50.000 0.00 0.00 40.31 5.68
187 1501 3.422417 ACTATCGACGGTCAGATTGTG 57.578 47.619 19.66 13.43 33.09 3.33
190 1504 3.021695 TCCAACTATCGACGGTCAGATT 58.978 45.455 16.46 2.60 0.00 2.40
195 1509 2.287668 CCAGATCCAACTATCGACGGTC 60.288 54.545 0.00 0.00 0.00 4.79
199 1513 3.707793 GTCACCAGATCCAACTATCGAC 58.292 50.000 0.00 0.00 0.00 4.20
201 1515 2.543861 CCGTCACCAGATCCAACTATCG 60.544 54.545 0.00 0.00 0.00 2.92
241 1555 8.192401 TTCAAATGTGATGCCTTCAAGAAGGG 62.192 42.308 25.67 11.16 44.66 3.95
249 1563 7.662604 AAAATTCTTCAAATGTGATGCCTTC 57.337 32.000 0.00 0.00 32.48 3.46
250 1564 7.935210 AGAAAAATTCTTCAAATGTGATGCCTT 59.065 29.630 0.00 0.00 36.36 4.35
270 1584 7.324935 TGACGGCACATAGACTATAAGAAAAA 58.675 34.615 0.00 0.00 0.00 1.94
271 1585 6.869695 TGACGGCACATAGACTATAAGAAAA 58.130 36.000 0.00 0.00 0.00 2.29
278 1592 5.339008 TCTTTTGACGGCACATAGACTAT 57.661 39.130 0.00 0.00 0.00 2.12
290 1604 2.158841 CGTACCAACCATCTTTTGACGG 59.841 50.000 0.00 0.00 37.88 4.79
291 1605 2.158841 CCGTACCAACCATCTTTTGACG 59.841 50.000 0.00 0.00 0.00 4.35
308 1622 1.796017 TACCTCAATGGCCATCCGTA 58.204 50.000 21.08 13.56 40.22 4.02
317 1631 6.755607 CAGTGATCGATGATATACCTCAATGG 59.244 42.308 0.54 0.00 42.93 3.16
320 1634 5.478332 AGCAGTGATCGATGATATACCTCAA 59.522 40.000 0.54 0.00 0.00 3.02
338 1652 5.428496 TTTCTCAAGTGATCAAAGCAGTG 57.572 39.130 0.00 0.00 0.00 3.66
340 1654 7.866393 AGAAAATTTCTCAAGTGATCAAAGCAG 59.134 33.333 1.80 0.00 34.07 4.24
341 1655 7.719483 AGAAAATTTCTCAAGTGATCAAAGCA 58.281 30.769 1.80 0.00 34.07 3.91
342 1656 8.585189 AAGAAAATTTCTCAAGTGATCAAAGC 57.415 30.769 8.86 0.00 39.61 3.51
343 1657 9.962783 AGAAGAAAATTTCTCAAGTGATCAAAG 57.037 29.630 8.86 0.00 39.61 2.77
362 1676 9.898152 AAGAAGAAGAAGAAGAAGAAGAAGAAA 57.102 29.630 0.00 0.00 0.00 2.52
385 1699 9.996554 TGTCTAGACACATAATGAAAAAGAAGA 57.003 29.630 21.74 0.00 36.21 2.87
390 1704 9.890629 AGCTATGTCTAGACACATAATGAAAAA 57.109 29.630 27.41 0.23 45.05 1.94
391 1705 9.890629 AAGCTATGTCTAGACACATAATGAAAA 57.109 29.630 27.41 0.45 45.05 2.29
392 1706 9.534565 GAAGCTATGTCTAGACACATAATGAAA 57.465 33.333 27.41 1.00 45.05 2.69
393 1707 7.862873 CGAAGCTATGTCTAGACACATAATGAA 59.137 37.037 27.41 1.78 45.05 2.57
394 1708 7.363431 CGAAGCTATGTCTAGACACATAATGA 58.637 38.462 27.41 2.56 45.05 2.57
395 1709 6.584184 CCGAAGCTATGTCTAGACACATAATG 59.416 42.308 27.41 14.12 45.05 1.90
396 1710 6.265649 ACCGAAGCTATGTCTAGACACATAAT 59.734 38.462 27.41 13.91 45.05 1.28
397 1711 5.593095 ACCGAAGCTATGTCTAGACACATAA 59.407 40.000 27.41 12.35 45.05 1.90
401 1715 3.628487 AGACCGAAGCTATGTCTAGACAC 59.372 47.826 27.41 15.06 45.05 3.67
402 1716 3.887352 AGACCGAAGCTATGTCTAGACA 58.113 45.455 27.07 27.07 46.44 3.41
404 1718 7.284716 TCAAATAAGACCGAAGCTATGTCTAGA 59.715 37.037 11.71 0.00 38.36 2.43
409 1723 5.978814 AGTCAAATAAGACCGAAGCTATGT 58.021 37.500 0.00 0.00 39.34 2.29
418 1732 8.638565 CAAAATAGCAAAAGTCAAATAAGACCG 58.361 33.333 0.00 0.00 39.34 4.79
429 1743 3.652274 TGCTGGCAAAATAGCAAAAGTC 58.348 40.909 0.00 0.00 46.06 3.01
436 1750 5.006358 CAGAAAATCATGCTGGCAAAATAGC 59.994 40.000 0.00 0.00 40.29 2.97
437 1751 6.035650 CACAGAAAATCATGCTGGCAAAATAG 59.964 38.462 0.00 0.00 34.05 1.73
438 1752 5.870433 CACAGAAAATCATGCTGGCAAAATA 59.130 36.000 0.00 0.00 34.05 1.40
439 1753 4.693566 CACAGAAAATCATGCTGGCAAAAT 59.306 37.500 0.00 0.00 34.05 1.82
442 1756 2.629137 ACACAGAAAATCATGCTGGCAA 59.371 40.909 0.00 0.00 34.05 4.52
443 1757 2.029739 CACACAGAAAATCATGCTGGCA 60.030 45.455 0.00 0.00 34.05 4.92
444 1758 2.029649 ACACACAGAAAATCATGCTGGC 60.030 45.455 0.00 0.00 34.05 4.85
445 1759 3.005050 ACACACACAGAAAATCATGCTGG 59.995 43.478 0.00 0.00 34.05 4.85
446 1760 4.233123 ACACACACAGAAAATCATGCTG 57.767 40.909 0.00 0.00 35.81 4.41
447 1761 4.500205 CCAACACACACAGAAAATCATGCT 60.500 41.667 0.00 0.00 0.00 3.79
448 1762 3.737266 CCAACACACACAGAAAATCATGC 59.263 43.478 0.00 0.00 0.00 4.06
449 1763 4.935702 ACCAACACACACAGAAAATCATG 58.064 39.130 0.00 0.00 0.00 3.07
450 1764 5.105392 ACAACCAACACACACAGAAAATCAT 60.105 36.000 0.00 0.00 0.00 2.45
451 1765 4.219507 ACAACCAACACACACAGAAAATCA 59.780 37.500 0.00 0.00 0.00 2.57
452 1766 4.562394 CACAACCAACACACACAGAAAATC 59.438 41.667 0.00 0.00 0.00 2.17
453 1767 4.021544 ACACAACCAACACACACAGAAAAT 60.022 37.500 0.00 0.00 0.00 1.82
454 1768 3.319405 ACACAACCAACACACACAGAAAA 59.681 39.130 0.00 0.00 0.00 2.29
455 1769 2.887783 ACACAACCAACACACACAGAAA 59.112 40.909 0.00 0.00 0.00 2.52
457 1771 1.809547 CACACAACCAACACACACAGA 59.190 47.619 0.00 0.00 0.00 3.41
459 1773 0.242286 GCACACAACCAACACACACA 59.758 50.000 0.00 0.00 0.00 3.72
461 1775 0.610509 AGGCACACAACCAACACACA 60.611 50.000 0.00 0.00 0.00 3.72
462 1776 0.100503 GAGGCACACAACCAACACAC 59.899 55.000 0.00 0.00 0.00 3.82
463 1777 1.034838 GGAGGCACACAACCAACACA 61.035 55.000 0.00 0.00 0.00 3.72
466 1780 1.607148 GTTAGGAGGCACACAACCAAC 59.393 52.381 0.00 0.00 0.00 3.77
467 1781 1.213182 TGTTAGGAGGCACACAACCAA 59.787 47.619 0.00 0.00 0.00 3.67
468 1782 0.840617 TGTTAGGAGGCACACAACCA 59.159 50.000 0.00 0.00 0.00 3.67
469 1783 1.975660 TTGTTAGGAGGCACACAACC 58.024 50.000 0.00 0.00 0.00 3.77
471 1785 2.107378 TCCATTGTTAGGAGGCACACAA 59.893 45.455 0.00 0.00 33.78 3.33
472 1786 1.702401 TCCATTGTTAGGAGGCACACA 59.298 47.619 0.00 0.00 0.00 3.72
480 1794 1.839994 CCAGCCTCTCCATTGTTAGGA 59.160 52.381 0.00 0.00 0.00 2.94
481 1795 1.561542 ACCAGCCTCTCCATTGTTAGG 59.438 52.381 0.00 0.00 0.00 2.69
482 1796 2.026822 ACACCAGCCTCTCCATTGTTAG 60.027 50.000 0.00 0.00 0.00 2.34
483 1797 1.985159 ACACCAGCCTCTCCATTGTTA 59.015 47.619 0.00 0.00 0.00 2.41
484 1798 0.773644 ACACCAGCCTCTCCATTGTT 59.226 50.000 0.00 0.00 0.00 2.83
485 1799 0.037303 CACACCAGCCTCTCCATTGT 59.963 55.000 0.00 0.00 0.00 2.71
486 1800 0.325933 TCACACCAGCCTCTCCATTG 59.674 55.000 0.00 0.00 0.00 2.82
487 1801 0.617413 CTCACACCAGCCTCTCCATT 59.383 55.000 0.00 0.00 0.00 3.16
488 1802 0.252421 TCTCACACCAGCCTCTCCAT 60.252 55.000 0.00 0.00 0.00 3.41
489 1803 1.156095 TCTCACACCAGCCTCTCCA 59.844 57.895 0.00 0.00 0.00 3.86
490 1804 0.902516 AGTCTCACACCAGCCTCTCC 60.903 60.000 0.00 0.00 0.00 3.71
491 1805 0.246086 CAGTCTCACACCAGCCTCTC 59.754 60.000 0.00 0.00 0.00 3.20
492 1806 1.190833 CCAGTCTCACACCAGCCTCT 61.191 60.000 0.00 0.00 0.00 3.69
493 1807 1.294780 CCAGTCTCACACCAGCCTC 59.705 63.158 0.00 0.00 0.00 4.70
494 1808 2.219875 CCCAGTCTCACACCAGCCT 61.220 63.158 0.00 0.00 0.00 4.58
495 1809 2.348998 CCCAGTCTCACACCAGCC 59.651 66.667 0.00 0.00 0.00 4.85
496 1810 2.359230 GCCCAGTCTCACACCAGC 60.359 66.667 0.00 0.00 0.00 4.85
497 1811 1.004080 CAGCCCAGTCTCACACCAG 60.004 63.158 0.00 0.00 0.00 4.00
498 1812 1.766059 ACAGCCCAGTCTCACACCA 60.766 57.895 0.00 0.00 0.00 4.17
499 1813 1.302033 CACAGCCCAGTCTCACACC 60.302 63.158 0.00 0.00 0.00 4.16
500 1814 1.963338 GCACAGCCCAGTCTCACAC 60.963 63.158 0.00 0.00 0.00 3.82
501 1815 2.104572 GAGCACAGCCCAGTCTCACA 62.105 60.000 0.00 0.00 0.00 3.58
502 1816 1.375268 GAGCACAGCCCAGTCTCAC 60.375 63.158 0.00 0.00 0.00 3.51
503 1817 1.196766 ATGAGCACAGCCCAGTCTCA 61.197 55.000 0.00 0.00 38.05 3.27
504 1818 0.035630 AATGAGCACAGCCCAGTCTC 60.036 55.000 0.00 0.00 0.00 3.36
505 1819 1.279496 TAATGAGCACAGCCCAGTCT 58.721 50.000 0.00 0.00 0.00 3.24
506 1820 1.945394 CATAATGAGCACAGCCCAGTC 59.055 52.381 0.00 0.00 0.00 3.51
507 1821 1.561076 TCATAATGAGCACAGCCCAGT 59.439 47.619 0.00 0.00 0.00 4.00
508 1822 2.336945 TCATAATGAGCACAGCCCAG 57.663 50.000 0.00 0.00 0.00 4.45
509 1823 2.953648 CAATCATAATGAGCACAGCCCA 59.046 45.455 0.00 0.00 0.00 5.36
510 1824 2.954318 ACAATCATAATGAGCACAGCCC 59.046 45.455 0.00 0.00 0.00 5.19
511 1825 5.471116 TCATACAATCATAATGAGCACAGCC 59.529 40.000 0.00 0.00 0.00 4.85
512 1826 6.549912 TCATACAATCATAATGAGCACAGC 57.450 37.500 0.00 0.00 0.00 4.40
513 1827 8.565416 ACAATCATACAATCATAATGAGCACAG 58.435 33.333 0.00 0.00 33.40 3.66
521 1835 9.605275 CGAGGGATACAATCATACAATCATAAT 57.395 33.333 0.00 0.00 39.74 1.28
528 1842 5.012046 AGCATCGAGGGATACAATCATACAA 59.988 40.000 0.00 0.00 39.74 2.41
529 1843 4.528206 AGCATCGAGGGATACAATCATACA 59.472 41.667 0.00 0.00 39.74 2.29
530 1844 5.078411 AGCATCGAGGGATACAATCATAC 57.922 43.478 0.00 0.00 39.74 2.39
531 1845 5.714806 TGTAGCATCGAGGGATACAATCATA 59.285 40.000 13.53 0.00 34.53 2.15
532 1846 4.528206 TGTAGCATCGAGGGATACAATCAT 59.472 41.667 13.53 0.00 34.53 2.45
533 1847 3.895041 TGTAGCATCGAGGGATACAATCA 59.105 43.478 13.53 0.00 34.53 2.57
534 1848 4.521130 TGTAGCATCGAGGGATACAATC 57.479 45.455 13.53 0.00 34.53 2.67
535 1849 4.528206 TGATGTAGCATCGAGGGATACAAT 59.472 41.667 18.06 9.61 40.12 2.71
536 1850 3.895041 TGATGTAGCATCGAGGGATACAA 59.105 43.478 18.06 4.46 40.12 2.41
540 1854 3.168292 TCATGATGTAGCATCGAGGGAT 58.832 45.455 0.00 0.00 0.00 3.85
546 1860 6.865205 TCTTATTGACTCATGATGTAGCATCG 59.135 38.462 0.00 0.00 0.00 3.84
570 1884 8.887036 ACTTTCTTTTGACAAATGGGTAATTC 57.113 30.769 12.42 0.00 0.00 2.17
578 1892 8.382875 GGAAACTCAACTTTCTTTTGACAAATG 58.617 33.333 0.50 4.48 31.76 2.32
579 1893 8.093927 TGGAAACTCAACTTTCTTTTGACAAAT 58.906 29.630 0.50 0.00 31.76 2.32
582 1896 6.582677 TGGAAACTCAACTTTCTTTTGACA 57.417 33.333 0.00 0.00 31.76 3.58
583 1897 7.883229 TTTGGAAACTCAACTTTCTTTTGAC 57.117 32.000 0.00 0.00 31.76 3.18
584 1898 8.894768 TTTTTGGAAACTCAACTTTCTTTTGA 57.105 26.923 0.00 0.00 31.76 2.69
713 2043 1.677552 CCCCACCTCTGTGTACCAC 59.322 63.158 0.00 0.00 41.09 4.16
721 2051 0.625849 ATAACTTGGCCCCACCTCTG 59.374 55.000 0.00 0.00 40.22 3.35
746 2076 4.725790 GCAGATTGGTTTGCCTTCTAAT 57.274 40.909 0.00 0.00 34.28 1.73
805 3903 0.447801 CTGCCATACTTGCAACGGAC 59.552 55.000 0.00 0.00 38.46 4.79
816 3920 0.825010 CCATGAAGCCCCTGCCATAC 60.825 60.000 0.00 0.00 38.69 2.39
877 3981 1.258982 GCAAGGAATGTATCAGCGTCG 59.741 52.381 0.00 0.00 0.00 5.12
997 4101 2.336891 CCTGTCTCCTGGGATGATGAT 58.663 52.381 0.00 0.00 0.00 2.45
998 4102 1.798626 CCTGTCTCCTGGGATGATGA 58.201 55.000 0.00 0.00 0.00 2.92
1012 4116 1.990614 GACACCTCCCTCCCCTGTC 60.991 68.421 0.00 0.00 0.00 3.51
1097 4201 3.202097 GAGCTAACCTCTTCATCTTGGC 58.798 50.000 0.00 0.00 37.60 4.52
1135 4244 4.061131 TCCATCTTAAGAGGAGACCACA 57.939 45.455 18.40 0.00 0.00 4.17
1144 4253 2.543012 CACGCATGCTCCATCTTAAGAG 59.457 50.000 17.13 3.45 0.00 2.85
1186 4318 1.605232 TGCTGTGCAACTCATCAACAG 59.395 47.619 0.00 0.00 38.04 3.16
1194 4326 4.691860 ATCATAACTTGCTGTGCAACTC 57.308 40.909 0.45 0.00 43.99 3.01
1236 4369 4.906065 TCTTTTCATCTGCATATGTGGC 57.094 40.909 11.42 0.00 0.00 5.01
1240 4373 9.844790 TGTTAAACTTCTTTTCATCTGCATATG 57.155 29.630 5.74 5.74 0.00 1.78
1242 4375 9.283768 TCTGTTAAACTTCTTTTCATCTGCATA 57.716 29.630 0.00 0.00 0.00 3.14
1243 4376 8.078596 GTCTGTTAAACTTCTTTTCATCTGCAT 58.921 33.333 0.00 0.00 0.00 3.96
1244 4377 7.417612 GTCTGTTAAACTTCTTTTCATCTGCA 58.582 34.615 0.00 0.00 0.00 4.41
1245 4378 6.575201 CGTCTGTTAAACTTCTTTTCATCTGC 59.425 38.462 0.00 0.00 0.00 4.26
1246 4379 7.630924 ACGTCTGTTAAACTTCTTTTCATCTG 58.369 34.615 0.00 0.00 0.00 2.90
1247 4380 7.787725 ACGTCTGTTAAACTTCTTTTCATCT 57.212 32.000 0.00 0.00 0.00 2.90
1671 4849 2.597510 AAGAACAGCCCGTTGCCC 60.598 61.111 0.00 0.00 42.71 5.36
1767 4945 2.262915 GTGGTGGCCGAGACAGAG 59.737 66.667 0.00 0.00 0.00 3.35
1824 5008 1.009449 GAGATCGAGTTCGCTCCCG 60.009 63.158 2.14 0.00 41.09 5.14
1862 5046 1.912371 CTTCCCTTTCTTCCGCGTGC 61.912 60.000 4.92 0.00 0.00 5.34
2041 5225 2.500509 CTGACCTAGGAAGCGTCATC 57.499 55.000 17.98 0.00 34.49 2.92
2078 5262 2.159240 TCATGAAATCACTCGACCTCGG 60.159 50.000 0.00 0.00 40.29 4.63
2097 5281 1.004398 CGCACGTTACTTTTGCACTCA 60.004 47.619 0.00 0.00 35.93 3.41
2108 5292 2.159881 GGAGTCATCAAACGCACGTTAC 60.160 50.000 9.08 3.39 37.35 2.50
2154 5342 0.971386 AGGAAAGGGCACATTGCTTG 59.029 50.000 0.00 0.00 44.28 4.01
2157 5345 0.899717 TCCAGGAAAGGGCACATTGC 60.900 55.000 0.00 0.00 44.08 3.56
2177 5365 3.469564 GTGACACCACACACCTTGA 57.530 52.632 0.00 0.00 42.72 3.02
2196 5390 0.251073 GCCCCGGTATAACACACACT 59.749 55.000 0.00 0.00 0.00 3.55
2210 5404 0.033503 AATAAAACTCCCCTGCCCCG 60.034 55.000 0.00 0.00 0.00 5.73
2211 5405 1.688311 GGAATAAAACTCCCCTGCCCC 60.688 57.143 0.00 0.00 0.00 5.80
2212 5406 1.006639 TGGAATAAAACTCCCCTGCCC 59.993 52.381 0.00 0.00 31.32 5.36
2213 5407 2.525105 TGGAATAAAACTCCCCTGCC 57.475 50.000 0.00 0.00 31.32 4.85
2214 5408 3.631250 TGATGGAATAAAACTCCCCTGC 58.369 45.455 0.00 0.00 31.32 4.85
2215 5409 7.014615 CCTTATTGATGGAATAAAACTCCCCTG 59.985 40.741 0.00 0.00 36.32 4.45
2216 5410 7.069344 CCTTATTGATGGAATAAAACTCCCCT 58.931 38.462 0.00 0.00 36.32 4.79
2217 5411 6.239317 GCCTTATTGATGGAATAAAACTCCCC 60.239 42.308 0.00 0.00 36.32 4.81
2218 5412 6.323739 TGCCTTATTGATGGAATAAAACTCCC 59.676 38.462 0.00 0.00 36.32 4.30
2219 5413 7.346751 TGCCTTATTGATGGAATAAAACTCC 57.653 36.000 0.00 0.00 36.32 3.85
2220 5414 9.899226 GTATGCCTTATTGATGGAATAAAACTC 57.101 33.333 0.00 0.00 36.32 3.01
2221 5415 8.567948 CGTATGCCTTATTGATGGAATAAAACT 58.432 33.333 0.00 0.00 36.32 2.66
2222 5416 8.564574 TCGTATGCCTTATTGATGGAATAAAAC 58.435 33.333 0.00 0.00 36.32 2.43
2223 5417 8.684386 TCGTATGCCTTATTGATGGAATAAAA 57.316 30.769 0.00 0.00 36.32 1.52
2224 5418 8.154203 TCTCGTATGCCTTATTGATGGAATAAA 58.846 33.333 0.00 0.00 36.32 1.40
2225 5419 7.676004 TCTCGTATGCCTTATTGATGGAATAA 58.324 34.615 0.00 0.00 35.58 1.40
2226 5420 7.178451 TCTCTCGTATGCCTTATTGATGGAATA 59.822 37.037 0.00 0.00 0.00 1.75
2227 5421 6.014242 TCTCTCGTATGCCTTATTGATGGAAT 60.014 38.462 0.00 0.00 0.00 3.01
2228 5422 5.304357 TCTCTCGTATGCCTTATTGATGGAA 59.696 40.000 0.00 0.00 0.00 3.53
2229 5423 4.832823 TCTCTCGTATGCCTTATTGATGGA 59.167 41.667 0.00 0.00 0.00 3.41
2230 5424 5.139435 TCTCTCGTATGCCTTATTGATGG 57.861 43.478 0.00 0.00 0.00 3.51
2231 5425 7.664082 AATTCTCTCGTATGCCTTATTGATG 57.336 36.000 0.00 0.00 0.00 3.07
2232 5426 9.778741 TTTAATTCTCTCGTATGCCTTATTGAT 57.221 29.630 0.00 0.00 0.00 2.57
2233 5427 9.607988 TTTTAATTCTCTCGTATGCCTTATTGA 57.392 29.630 0.00 0.00 0.00 2.57
2314 5510 9.203421 TGTTTTTCTCCTTTTTGTCTTTCTTTC 57.797 29.630 0.00 0.00 0.00 2.62
2322 5527 9.967245 GTGTAAATTGTTTTTCTCCTTTTTGTC 57.033 29.630 0.00 0.00 0.00 3.18
2330 5540 5.441709 TCCCGTGTAAATTGTTTTTCTCC 57.558 39.130 0.00 0.00 0.00 3.71
2356 5567 7.044798 CCTGTTATTCTTTTGTTTGTTGGGAA 58.955 34.615 0.00 0.00 0.00 3.97
2388 5604 9.871175 TTCCTAGTAGTAAAAGAAAACCCAAAT 57.129 29.630 0.00 0.00 0.00 2.32
2411 5630 9.811655 GTTTTTCTTGCTTGCTTAATTAATTCC 57.188 29.630 3.39 0.00 0.00 3.01
2419 5638 7.389053 TCTTTTTGGTTTTTCTTGCTTGCTTAA 59.611 29.630 0.00 0.00 0.00 1.85
2423 5643 5.544136 TCTTTTTGGTTTTTCTTGCTTGC 57.456 34.783 0.00 0.00 0.00 4.01
2428 5648 7.575332 TCTCGTTTCTTTTTGGTTTTTCTTG 57.425 32.000 0.00 0.00 0.00 3.02
2562 5784 5.528320 TCGACATTACATTCATGCATCACAT 59.472 36.000 0.00 0.00 40.66 3.21
2569 5791 5.912360 TCTCATCGACATTACATTCATGC 57.088 39.130 0.00 0.00 0.00 4.06
2683 5905 1.898154 CTTACCAGTGGGACCCTCG 59.102 63.158 15.21 4.88 38.05 4.63
2697 5919 1.065436 GACGTAGGAGCCCGCTTAC 59.935 63.158 0.00 0.00 0.00 2.34
2714 5936 0.755698 GCCCGTCTATCAGTGGGAGA 60.756 60.000 0.00 0.00 44.88 3.71
2815 6037 2.643551 CACCTTCTCAATTATGCCGGT 58.356 47.619 1.90 0.00 0.00 5.28
2838 6088 3.132289 ACCCGTGAGACTATTATGGTGTG 59.868 47.826 0.00 0.00 0.00 3.82
2839 6089 3.132289 CACCCGTGAGACTATTATGGTGT 59.868 47.826 0.00 0.00 37.74 4.16
2842 6092 3.243771 GGACACCCGTGAGACTATTATGG 60.244 52.174 0.96 0.00 0.00 2.74
2843 6093 3.637229 AGGACACCCGTGAGACTATTATG 59.363 47.826 0.96 0.00 37.58 1.90
2844 6094 3.637229 CAGGACACCCGTGAGACTATTAT 59.363 47.826 0.96 0.00 37.58 1.28
2868 6118 8.609176 GCGATTTCAGTATAACTTGGTATTCAA 58.391 33.333 0.00 0.00 0.00 2.69
2873 6123 6.127281 TGAGGCGATTTCAGTATAACTTGGTA 60.127 38.462 0.00 0.00 0.00 3.25
2900 6150 4.949856 GGACATGACTTTATTGATGGTGGT 59.050 41.667 0.00 0.00 0.00 4.16
2905 6155 7.262772 AGCATTTGGACATGACTTTATTGATG 58.737 34.615 0.00 0.00 0.00 3.07
2906 6156 7.414222 AGCATTTGGACATGACTTTATTGAT 57.586 32.000 0.00 0.00 0.00 2.57
2915 6165 5.756195 TTATGCTAGCATTTGGACATGAC 57.244 39.130 33.74 0.00 37.82 3.06
2946 6198 5.048846 AGGAGAAGCTTTTACTTGTTGGA 57.951 39.130 0.00 0.00 0.00 3.53
2948 6200 7.821846 AGATAGAGGAGAAGCTTTTACTTGTTG 59.178 37.037 2.73 0.00 0.00 3.33
2953 6205 7.255451 CGATGAGATAGAGGAGAAGCTTTTACT 60.255 40.741 0.26 0.26 0.00 2.24
2972 6224 4.586421 AGATTCCTATCAAGCACGATGAGA 59.414 41.667 0.00 0.00 32.95 3.27
2983 6235 7.439356 CGCTAGACATTTTGAGATTCCTATCAA 59.561 37.037 0.00 0.00 33.73 2.57
2985 6237 7.148641 TCGCTAGACATTTTGAGATTCCTATC 58.851 38.462 0.00 0.00 0.00 2.08
3013 6265 4.534647 ATGGTGGTATTTATGCTTCCCA 57.465 40.909 0.00 0.00 0.00 4.37
3032 6284 2.222027 GCTCGAAGGGGGTCATTTATG 58.778 52.381 0.00 0.00 0.00 1.90
3039 6291 2.294132 CTAACCGCTCGAAGGGGGTC 62.294 65.000 12.89 0.00 46.32 4.46
3064 6316 2.287373 GTGCTATGATTGCTCAGCAGTC 59.713 50.000 15.09 15.09 43.88 3.51
3067 6319 1.671979 GGTGCTATGATTGCTCAGCA 58.328 50.000 0.00 0.00 34.12 4.41
3069 6321 2.336945 TGGGTGCTATGATTGCTCAG 57.663 50.000 0.00 0.00 34.12 3.35
3070 6322 2.754552 GTTTGGGTGCTATGATTGCTCA 59.245 45.455 0.00 0.00 35.41 4.26
3107 6359 7.490840 TGGTATTTTGCACCATGATCTTTATG 58.509 34.615 0.00 0.00 41.17 1.90
3115 6367 3.505386 ACCTTGGTATTTTGCACCATGA 58.495 40.909 8.51 0.00 45.32 3.07
3130 6382 2.435586 CAGCTCGCCTGACCTTGG 60.436 66.667 0.00 0.00 44.64 3.61
3152 6404 2.352032 GGACGGTGGGAGAGTGGAG 61.352 68.421 0.00 0.00 0.00 3.86
3205 6457 7.536281 GCTAGTTTACATTTTTCCCAAGTTACG 59.464 37.037 0.00 0.00 0.00 3.18
3211 6463 7.286775 AGAGTTGCTAGTTTACATTTTTCCCAA 59.713 33.333 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.