Multiple sequence alignment - TraesCS1A01G275000

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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 TraesCS1A01G275000 chr1A 100.000 2951 0 0 1 2951 469308705 469311655 0.000000e+00 5450.0
1 TraesCS1A01G275000 chr1D 90.909 2387 115 47 268 2609 370341280 370343609 0.000000e+00 3112.0
2 TraesCS1A01G275000 chr1D 92.857 252 15 3 1 251 370339910 370340159 2.160000e-96 363.0
3 TraesCS1A01G275000 chr1D 75.661 189 30 8 399 578 469827927 469828108 2.440000e-11 80.5
4 TraesCS1A01G275000 chr1B 93.384 1829 74 20 789 2609 493857535 493859324 0.000000e+00 2663.0
5 TraesCS1A01G275000 chr1B 84.856 799 68 23 1 764 493856632 493857412 0.000000e+00 756.0
6 TraesCS1A01G275000 chr1B 97.727 88 2 0 2610 2697 602735739 602735826 5.090000e-33 152.0
7 TraesCS1A01G275000 chr1B 84.298 121 18 1 2816 2936 493859371 493859490 1.860000e-22 117.0
8 TraesCS1A01G275000 chr4A 87.587 572 51 13 1189 1758 590441757 590442310 0.000000e+00 645.0
9 TraesCS1A01G275000 chr3B 84.740 308 38 8 1097 1401 646003140 646002839 1.720000e-77 300.0
10 TraesCS1A01G275000 chr3D 83.183 333 41 9 1075 1401 483177355 483177032 1.030000e-74 291.0
11 TraesCS1A01G275000 chr3D 97.619 84 2 0 2611 2694 518565721 518565804 8.520000e-31 145.0
12 TraesCS1A01G275000 chr3A 84.194 310 36 11 1097 1401 626016528 626016227 3.720000e-74 289.0
13 TraesCS1A01G275000 chr6D 91.925 161 13 0 1104 1264 358326165 358326005 2.960000e-55 226.0
14 TraesCS1A01G275000 chr6A 91.925 161 13 0 1104 1264 500083784 500083624 2.960000e-55 226.0
15 TraesCS1A01G275000 chr6B 91.304 161 14 0 1104 1264 539727709 539727549 1.380000e-53 220.0
16 TraesCS1A01G275000 chr6B 95.294 85 4 0 2613 2697 28816001 28816085 5.130000e-28 135.0
17 TraesCS1A01G275000 chr2D 91.558 154 11 2 1112 1264 32763270 32763422 8.290000e-51 211.0
18 TraesCS1A01G275000 chr2B 96.591 88 3 0 2610 2697 441881257 441881170 2.370000e-31 147.0
19 TraesCS1A01G275000 chr5D 96.552 87 3 0 2611 2697 514028719 514028633 8.520000e-31 145.0
20 TraesCS1A01G275000 chr5D 75.000 228 42 12 358 578 254826144 254825925 1.130000e-14 91.6
21 TraesCS1A01G275000 chr5D 85.294 68 6 3 399 465 480503310 480503246 1.900000e-07 67.6
22 TraesCS1A01G275000 chr5A 78.571 238 37 8 358 583 338221696 338221461 8.520000e-31 145.0
23 TraesCS1A01G275000 chr5B 95.455 88 4 0 2610 2697 492249828 492249915 1.100000e-29 141.0
24 TraesCS1A01G275000 chr4D 95.402 87 2 1 2611 2697 426797544 426797460 1.430000e-28 137.0
25 TraesCS1A01G275000 chr4B 95.349 86 2 1 2612 2697 436498871 436498788 5.130000e-28 135.0
26 TraesCS1A01G275000 chr4B 93.258 89 5 1 2610 2697 465747426 465747338 2.390000e-26 130.0


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 TraesCS1A01G275000 chr1A 469308705 469311655 2950 False 5450.000000 5450 100.000000 1 2951 1 chr1A.!!$F1 2950
1 TraesCS1A01G275000 chr1D 370339910 370343609 3699 False 1737.500000 3112 91.883000 1 2609 2 chr1D.!!$F2 2608
2 TraesCS1A01G275000 chr1B 493856632 493859490 2858 False 1178.666667 2663 87.512667 1 2936 3 chr1B.!!$F2 2935
3 TraesCS1A01G275000 chr4A 590441757 590442310 553 False 645.000000 645 87.587000 1189 1758 1 chr4A.!!$F1 569

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
181 183 0.530288 GGTTGTTATGGCGCCATTGT 59.470 50.0 44.18 26.3 37.82 2.71 F
1719 2977 0.111089 GCGAGTTCAACTTCAGCGTG 60.111 55.0 0.00 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 3021 1.006805 GGGAGCATCGTCAGATCGG 60.007 63.158 0.00 0.0 34.23 4.18 R
2762 4022 0.037303 TGGACGTCGAAGGGAGTACT 59.963 55.000 9.92 0.0 0.00 2.73 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
36 37 4.388499 TCCTCCCCAAAGTCGCGC 62.388 66.667 0.00 0.00 0.00 6.86
38 39 4.735132 CTCCCCAAAGTCGCGCGA 62.735 66.667 31.40 31.40 0.00 5.87
89 90 5.277857 TCCTGTCTTAGTGCTAATTAGGC 57.722 43.478 14.28 7.20 0.00 3.93
126 127 3.187637 CGTGAAATTTTCTCTACGGCCAA 59.812 43.478 2.24 0.00 0.00 4.52
181 183 0.530288 GGTTGTTATGGCGCCATTGT 59.470 50.000 44.18 26.30 37.82 2.71
183 185 1.201181 GTTGTTATGGCGCCATTGTGA 59.799 47.619 44.18 25.83 37.82 3.58
260 262 2.041081 CCATGGTACCTCCTGGTTTGAA 59.959 50.000 14.36 0.00 46.05 2.69
269 271 6.200878 ACCTCCTGGTTTGAATTCTTCTTA 57.799 37.500 7.05 0.00 46.05 2.10
276 278 7.079451 TGGTTTGAATTCTTCTTACCTCTCT 57.921 36.000 7.05 0.00 35.91 3.10
288 1408 5.734720 TCTTACCTCTCTTTAACCATGCAG 58.265 41.667 0.00 0.00 0.00 4.41
291 1411 2.618816 CCTCTCTTTAACCATGCAGGCA 60.619 50.000 0.00 0.00 43.14 4.75
303 1427 2.048444 TGCAGGCATGGATCTTCTTC 57.952 50.000 0.00 0.00 0.00 2.87
346 1470 2.933260 GCCGTGGTCATGTTTTGTTTTT 59.067 40.909 0.00 0.00 0.00 1.94
348 1472 4.177026 CCGTGGTCATGTTTTGTTTTTCA 58.823 39.130 0.00 0.00 0.00 2.69
349 1473 4.267452 CCGTGGTCATGTTTTGTTTTTCAG 59.733 41.667 0.00 0.00 0.00 3.02
350 1474 4.862018 CGTGGTCATGTTTTGTTTTTCAGT 59.138 37.500 0.00 0.00 0.00 3.41
351 1475 5.347364 CGTGGTCATGTTTTGTTTTTCAGTT 59.653 36.000 0.00 0.00 0.00 3.16
352 1476 6.128688 CGTGGTCATGTTTTGTTTTTCAGTTT 60.129 34.615 0.00 0.00 0.00 2.66
353 1477 7.570324 CGTGGTCATGTTTTGTTTTTCAGTTTT 60.570 33.333 0.00 0.00 0.00 2.43
354 1478 7.533561 GTGGTCATGTTTTGTTTTTCAGTTTTG 59.466 33.333 0.00 0.00 0.00 2.44
355 1479 6.522855 GGTCATGTTTTGTTTTTCAGTTTTGC 59.477 34.615 0.00 0.00 0.00 3.68
356 1480 7.297391 GTCATGTTTTGTTTTTCAGTTTTGCT 58.703 30.769 0.00 0.00 0.00 3.91
364 1488 7.769272 TGTTTTTCAGTTTTGCTAAATGAGG 57.231 32.000 0.00 0.00 0.00 3.86
372 1496 6.006449 AGTTTTGCTAAATGAGGAGTGACAT 58.994 36.000 0.00 0.00 0.00 3.06
375 1499 4.682787 TGCTAAATGAGGAGTGACATACG 58.317 43.478 0.00 0.00 0.00 3.06
376 1500 4.159693 TGCTAAATGAGGAGTGACATACGT 59.840 41.667 0.00 0.00 0.00 3.57
395 1519 1.279840 GTGGCACGAAACACTCTGC 59.720 57.895 0.00 0.00 34.84 4.26
401 1525 2.146342 CACGAAACACTCTGCCTTGAT 58.854 47.619 0.00 0.00 0.00 2.57
402 1526 2.096069 CACGAAACACTCTGCCTTGATG 60.096 50.000 0.00 0.00 0.00 3.07
471 1595 8.538409 AAAATTTGAACTTGCCATCTGAATAC 57.462 30.769 0.00 0.00 0.00 1.89
480 1613 2.874701 GCCATCTGAATACGTGCTTGAT 59.125 45.455 0.00 0.00 0.00 2.57
485 1618 6.292542 CCATCTGAATACGTGCTTGATAACTG 60.293 42.308 0.00 0.00 0.00 3.16
491 1624 7.815549 TGAATACGTGCTTGATAACTGAAGTTA 59.184 33.333 0.00 5.43 43.71 2.24
514 1647 6.620877 ATCATCCTGGTGTCACTAAACTTA 57.379 37.500 2.35 0.00 0.00 2.24
515 1648 6.620877 TCATCCTGGTGTCACTAAACTTAT 57.379 37.500 2.35 0.00 0.00 1.73
521 1654 8.038944 TCCTGGTGTCACTAAACTTATCATAAC 58.961 37.037 2.35 0.00 0.00 1.89
578 1711 1.282157 GTGGCACTTATCAGGGTCCTT 59.718 52.381 11.13 0.00 0.00 3.36
579 1712 1.992557 TGGCACTTATCAGGGTCCTTT 59.007 47.619 0.00 0.00 0.00 3.11
580 1713 3.054655 GTGGCACTTATCAGGGTCCTTTA 60.055 47.826 11.13 0.00 0.00 1.85
581 1714 3.589735 TGGCACTTATCAGGGTCCTTTAA 59.410 43.478 0.00 0.00 0.00 1.52
582 1715 4.229582 TGGCACTTATCAGGGTCCTTTAAT 59.770 41.667 0.00 0.00 0.00 1.40
591 1724 9.771534 TTATCAGGGTCCTTTAATTTGTTTTTG 57.228 29.630 0.00 0.00 0.00 2.44
698 1839 9.237846 GCTAAATGGATTTTAGAATACACAAGC 57.762 33.333 8.82 0.21 46.59 4.01
764 1919 4.683334 GCAACAACTCGCCACGGC 62.683 66.667 0.00 0.00 37.85 5.68
769 1924 3.307906 AACTCGCCACGGCCACTA 61.308 61.111 2.24 0.00 37.98 2.74
778 2023 2.884827 CCACGGCCACTAACTAACTAC 58.115 52.381 2.24 0.00 0.00 2.73
780 2025 3.508762 CACGGCCACTAACTAACTACTG 58.491 50.000 2.24 0.00 0.00 2.74
781 2026 3.057033 CACGGCCACTAACTAACTACTGT 60.057 47.826 2.24 0.00 0.00 3.55
782 2027 4.156556 CACGGCCACTAACTAACTACTGTA 59.843 45.833 2.24 0.00 0.00 2.74
783 2028 4.766891 ACGGCCACTAACTAACTACTGTAA 59.233 41.667 2.24 0.00 0.00 2.41
784 2029 5.420104 ACGGCCACTAACTAACTACTGTAAT 59.580 40.000 2.24 0.00 0.00 1.89
785 2030 6.071165 ACGGCCACTAACTAACTACTGTAATT 60.071 38.462 2.24 0.00 0.00 1.40
786 2031 7.122650 ACGGCCACTAACTAACTACTGTAATTA 59.877 37.037 2.24 0.00 0.00 1.40
787 2032 7.433425 CGGCCACTAACTAACTACTGTAATTAC 59.567 40.741 8.75 8.75 0.00 1.89
790 2035 9.798994 CCACTAACTAACTACTGTAATTACCAG 57.201 37.037 13.01 11.99 0.00 4.00
969 2224 3.123620 GTCTCCTGCCTGCTTGCG 61.124 66.667 0.00 0.00 0.00 4.85
982 2237 1.398958 GCTTGCGGATCTCCTCCTCT 61.399 60.000 0.00 0.00 42.47 3.69
983 2238 0.673437 CTTGCGGATCTCCTCCTCTC 59.327 60.000 0.00 0.00 42.47 3.20
984 2239 0.757188 TTGCGGATCTCCTCCTCTCC 60.757 60.000 0.00 0.00 42.47 3.71
985 2240 4.073052 CGGATCTCCTCCTCTCCG 57.927 66.667 0.00 0.00 43.98 4.63
1503 2761 3.646162 TCTACTCCAAGTTCTTGAGCCAA 59.354 43.478 13.29 0.00 0.00 4.52
1719 2977 0.111089 GCGAGTTCAACTTCAGCGTG 60.111 55.000 0.00 0.00 0.00 5.34
1783 3041 1.663074 GATCTGACGATGCTCCCGC 60.663 63.158 0.00 0.00 0.00 6.13
1830 3088 2.677979 GCCGTTCAGTTCGCTTCCC 61.678 63.158 0.00 0.00 0.00 3.97
1832 3090 1.372499 CGTTCAGTTCGCTTCCCGA 60.372 57.895 0.00 0.00 45.77 5.14
1833 3091 0.736325 CGTTCAGTTCGCTTCCCGAT 60.736 55.000 0.00 0.00 46.81 4.18
1834 3092 1.000145 GTTCAGTTCGCTTCCCGATC 59.000 55.000 0.00 0.00 46.81 3.69
1860 3118 2.512515 GCCATGAGCCTCCACGAC 60.513 66.667 0.00 0.00 34.35 4.34
1862 3120 2.887568 CATGAGCCTCCACGACGC 60.888 66.667 0.00 0.00 0.00 5.19
1973 3231 4.094212 GCTCATTTTCAAGCTCGTTGATC 58.906 43.478 0.00 0.00 44.89 2.92
1980 3238 3.195698 GCTCGTTGATCCGTGGCC 61.196 66.667 0.00 0.00 0.00 5.36
2004 3262 2.029728 CGCTGTCCTCGTGATTGATTTC 59.970 50.000 0.00 0.00 0.00 2.17
2005 3263 3.002791 GCTGTCCTCGTGATTGATTTCA 58.997 45.455 0.00 0.00 0.00 2.69
2042 3301 5.191124 TCCTCTCCCTATTTTTACCCTTGTC 59.809 44.000 0.00 0.00 0.00 3.18
2054 3313 7.721409 TTTTACCCTTGTCCAAAAGTAACTT 57.279 32.000 2.66 0.00 0.00 2.66
2055 3314 8.820153 TTTTACCCTTGTCCAAAAGTAACTTA 57.180 30.769 0.00 0.00 0.00 2.24
2093 3352 1.800586 CGTGTTCATGGTCAAGGAGTG 59.199 52.381 0.00 0.00 0.00 3.51
2094 3353 2.806745 CGTGTTCATGGTCAAGGAGTGT 60.807 50.000 0.00 0.00 0.00 3.55
2102 3361 4.137116 TGGTCAAGGAGTGTATACATGC 57.863 45.455 9.18 4.21 0.00 4.06
2113 3372 6.430000 GGAGTGTATACATGCGGGATAAAAAT 59.570 38.462 9.18 0.00 0.00 1.82
2116 3375 6.205853 GTGTATACATGCGGGATAAAAATGGA 59.794 38.462 9.18 0.00 0.00 3.41
2117 3376 6.945435 TGTATACATGCGGGATAAAAATGGAT 59.055 34.615 0.08 0.00 0.00 3.41
2119 3378 5.612725 ACATGCGGGATAAAAATGGATTT 57.387 34.783 0.00 0.00 0.00 2.17
2120 3379 5.358922 ACATGCGGGATAAAAATGGATTTG 58.641 37.500 0.00 0.00 0.00 2.32
2122 3381 6.097554 ACATGCGGGATAAAAATGGATTTGTA 59.902 34.615 0.00 0.00 0.00 2.41
2123 3382 5.897050 TGCGGGATAAAAATGGATTTGTAC 58.103 37.500 0.00 0.00 0.00 2.90
2124 3383 5.654650 TGCGGGATAAAAATGGATTTGTACT 59.345 36.000 0.00 0.00 0.00 2.73
2125 3384 5.977129 GCGGGATAAAAATGGATTTGTACTG 59.023 40.000 0.00 0.00 0.00 2.74
2127 3386 7.201750 GCGGGATAAAAATGGATTTGTACTGTA 60.202 37.037 0.00 0.00 0.00 2.74
2178 3437 9.489084 TGGCAATATACTTACTATTAACAGCTG 57.511 33.333 13.48 13.48 0.00 4.24
2219 3478 4.321082 GCTACACGTTCACTTCTTCCTAGT 60.321 45.833 0.00 0.00 0.00 2.57
2276 3535 4.394712 CCTGACCTGGGCGTGGAC 62.395 72.222 5.56 0.00 0.00 4.02
2286 3545 4.856801 GCGTGGACGGATGGGCAT 62.857 66.667 0.71 0.00 40.23 4.40
2287 3546 2.896854 CGTGGACGGATGGGCATG 60.897 66.667 0.00 0.00 35.37 4.06
2292 3551 2.751436 ACGGATGGGCATGCACAC 60.751 61.111 28.07 18.67 29.15 3.82
2293 3552 2.751036 CGGATGGGCATGCACACA 60.751 61.111 28.07 17.96 29.15 3.72
2294 3553 2.887360 GGATGGGCATGCACACAC 59.113 61.111 28.07 21.58 29.15 3.82
2295 3554 1.978080 GGATGGGCATGCACACACA 60.978 57.895 28.07 12.56 29.15 3.72
2296 3555 1.324740 GGATGGGCATGCACACACAT 61.325 55.000 28.07 16.80 29.15 3.21
2301 3560 3.265955 CATGCACACACATGCCGA 58.734 55.556 0.00 0.00 45.50 5.54
2433 3692 0.802607 CCACTAGTCGCTCGAAAGGC 60.803 60.000 0.00 0.00 0.00 4.35
2594 3854 3.832171 CGAGCGAGCGTTCACTGC 61.832 66.667 7.46 0.00 0.00 4.40
2609 3869 2.079158 CACTGCCATCGTCTTCAACAT 58.921 47.619 0.00 0.00 0.00 2.71
2610 3870 2.485426 CACTGCCATCGTCTTCAACATT 59.515 45.455 0.00 0.00 0.00 2.71
2613 3873 4.037923 ACTGCCATCGTCTTCAACATTTTT 59.962 37.500 0.00 0.00 0.00 1.94
2634 3894 2.943036 TTTTGCGGGGTAAAGAGAGT 57.057 45.000 0.00 0.00 0.00 3.24
2635 3895 2.943036 TTTGCGGGGTAAAGAGAGTT 57.057 45.000 0.00 0.00 0.00 3.01
2636 3896 2.943036 TTGCGGGGTAAAGAGAGTTT 57.057 45.000 0.00 0.00 0.00 2.66
2637 3897 2.943036 TGCGGGGTAAAGAGAGTTTT 57.057 45.000 0.00 0.00 0.00 2.43
2638 3898 3.217681 TGCGGGGTAAAGAGAGTTTTT 57.782 42.857 0.00 0.00 0.00 1.94
2639 3899 4.354893 TGCGGGGTAAAGAGAGTTTTTA 57.645 40.909 0.00 0.00 0.00 1.52
2640 3900 4.913784 TGCGGGGTAAAGAGAGTTTTTAT 58.086 39.130 0.00 0.00 0.00 1.40
2641 3901 5.318630 TGCGGGGTAAAGAGAGTTTTTATT 58.681 37.500 0.00 0.00 0.00 1.40
2642 3902 5.182380 TGCGGGGTAAAGAGAGTTTTTATTG 59.818 40.000 0.00 0.00 0.00 1.90
2643 3903 5.637809 CGGGGTAAAGAGAGTTTTTATTGC 58.362 41.667 0.00 0.00 0.00 3.56
2644 3904 5.182380 CGGGGTAAAGAGAGTTTTTATTGCA 59.818 40.000 0.00 0.00 0.00 4.08
2645 3905 6.294286 CGGGGTAAAGAGAGTTTTTATTGCAA 60.294 38.462 0.00 0.00 0.00 4.08
2646 3906 7.576856 CGGGGTAAAGAGAGTTTTTATTGCAAT 60.577 37.037 17.56 17.56 0.00 3.56
2647 3907 7.545615 GGGGTAAAGAGAGTTTTTATTGCAATG 59.454 37.037 22.27 0.00 0.00 2.82
2648 3908 8.088365 GGGTAAAGAGAGTTTTTATTGCAATGT 58.912 33.333 22.27 0.00 0.00 2.71
2666 3926 9.838975 TTGCAATGTAATAGTGTTACAATCAAG 57.161 29.630 15.34 6.34 38.26 3.02
2667 3927 9.225436 TGCAATGTAATAGTGTTACAATCAAGA 57.775 29.630 15.34 0.00 38.26 3.02
2668 3928 9.708222 GCAATGTAATAGTGTTACAATCAAGAG 57.292 33.333 15.34 0.00 38.26 2.85
2670 3930 7.843490 TGTAATAGTGTTACAATCAAGAGGC 57.157 36.000 9.77 0.00 32.53 4.70
2671 3931 6.821665 TGTAATAGTGTTACAATCAAGAGGCC 59.178 38.462 9.77 0.00 32.53 5.19
2672 3932 3.788227 AGTGTTACAATCAAGAGGCCA 57.212 42.857 5.01 0.00 0.00 5.36
2673 3933 3.412386 AGTGTTACAATCAAGAGGCCAC 58.588 45.455 5.01 0.00 0.00 5.01
2674 3934 3.146066 GTGTTACAATCAAGAGGCCACA 58.854 45.455 5.01 0.00 0.00 4.17
2675 3935 3.568007 GTGTTACAATCAAGAGGCCACAA 59.432 43.478 5.01 0.00 0.00 3.33
2676 3936 3.568007 TGTTACAATCAAGAGGCCACAAC 59.432 43.478 5.01 0.00 0.00 3.32
2677 3937 2.664402 ACAATCAAGAGGCCACAACT 57.336 45.000 5.01 0.00 0.00 3.16
2678 3938 2.508526 ACAATCAAGAGGCCACAACTC 58.491 47.619 5.01 0.00 35.20 3.01
2679 3939 1.815003 CAATCAAGAGGCCACAACTCC 59.185 52.381 5.01 0.00 35.58 3.85
2680 3940 1.366319 ATCAAGAGGCCACAACTCCT 58.634 50.000 5.01 0.00 35.58 3.69
2684 3944 3.965888 GAGGCCACAACTCCTCAAT 57.034 52.632 5.01 0.00 46.24 2.57
2686 3946 2.633488 GAGGCCACAACTCCTCAATAC 58.367 52.381 5.01 0.00 46.24 1.89
2687 3947 1.985159 AGGCCACAACTCCTCAATACA 59.015 47.619 5.01 0.00 0.00 2.29
2688 3948 2.375174 AGGCCACAACTCCTCAATACAA 59.625 45.455 5.01 0.00 0.00 2.41
2689 3949 2.749621 GGCCACAACTCCTCAATACAAG 59.250 50.000 0.00 0.00 0.00 3.16
2690 3950 2.749621 GCCACAACTCCTCAATACAAGG 59.250 50.000 0.00 0.00 35.05 3.61
2691 3951 3.810743 GCCACAACTCCTCAATACAAGGT 60.811 47.826 0.00 0.00 35.29 3.50
2692 3952 3.753272 CCACAACTCCTCAATACAAGGTG 59.247 47.826 0.00 0.00 35.29 4.00
2693 3953 3.753272 CACAACTCCTCAATACAAGGTGG 59.247 47.826 0.00 0.00 35.29 4.61
2694 3954 3.650942 ACAACTCCTCAATACAAGGTGGA 59.349 43.478 0.00 0.00 35.29 4.02
2695 3955 4.256920 CAACTCCTCAATACAAGGTGGAG 58.743 47.826 0.00 0.00 44.61 3.86
2696 3956 2.237392 ACTCCTCAATACAAGGTGGAGC 59.763 50.000 9.06 0.00 43.34 4.70
2697 3957 2.237143 CTCCTCAATACAAGGTGGAGCA 59.763 50.000 0.00 0.00 35.35 4.26
2698 3958 2.846206 TCCTCAATACAAGGTGGAGCAT 59.154 45.455 0.00 0.00 35.29 3.79
2699 3959 3.118261 TCCTCAATACAAGGTGGAGCATC 60.118 47.826 0.00 0.00 35.29 3.91
2700 3960 3.118112 CCTCAATACAAGGTGGAGCATCT 60.118 47.826 0.00 0.00 33.73 2.90
2701 3961 4.521146 CTCAATACAAGGTGGAGCATCTT 58.479 43.478 0.00 0.00 34.88 2.40
2702 3962 4.517285 TCAATACAAGGTGGAGCATCTTC 58.483 43.478 0.00 0.00 31.84 2.87
2703 3963 4.019411 TCAATACAAGGTGGAGCATCTTCA 60.019 41.667 0.00 0.00 31.84 3.02
2704 3964 2.957402 ACAAGGTGGAGCATCTTCAA 57.043 45.000 0.00 0.00 31.84 2.69
2705 3965 2.508526 ACAAGGTGGAGCATCTTCAAC 58.491 47.619 0.00 0.00 31.84 3.18
2706 3966 2.158623 ACAAGGTGGAGCATCTTCAACA 60.159 45.455 0.00 0.00 31.84 3.33
2707 3967 2.886523 CAAGGTGGAGCATCTTCAACAA 59.113 45.455 0.00 0.00 31.84 2.83
2708 3968 3.228188 AGGTGGAGCATCTTCAACAAA 57.772 42.857 0.00 0.00 26.81 2.83
2709 3969 3.565307 AGGTGGAGCATCTTCAACAAAA 58.435 40.909 0.00 0.00 26.81 2.44
2710 3970 4.154942 AGGTGGAGCATCTTCAACAAAAT 58.845 39.130 0.00 0.00 26.81 1.82
2711 3971 4.590222 AGGTGGAGCATCTTCAACAAAATT 59.410 37.500 0.00 0.00 26.81 1.82
2712 3972 5.774690 AGGTGGAGCATCTTCAACAAAATTA 59.225 36.000 0.00 0.00 26.81 1.40
2713 3973 6.071728 AGGTGGAGCATCTTCAACAAAATTAG 60.072 38.462 0.00 0.00 26.81 1.73
2714 3974 5.574443 GTGGAGCATCTTCAACAAAATTAGC 59.426 40.000 0.00 0.00 33.73 3.09
2715 3975 5.243507 TGGAGCATCTTCAACAAAATTAGCA 59.756 36.000 0.00 0.00 33.73 3.49
2716 3976 5.803967 GGAGCATCTTCAACAAAATTAGCAG 59.196 40.000 0.00 0.00 33.73 4.24
2717 3977 5.166398 AGCATCTTCAACAAAATTAGCAGC 58.834 37.500 0.00 0.00 0.00 5.25
2718 3978 4.030977 GCATCTTCAACAAAATTAGCAGCG 59.969 41.667 0.00 0.00 0.00 5.18
2719 3979 4.829064 TCTTCAACAAAATTAGCAGCGT 57.171 36.364 0.00 0.00 0.00 5.07
2751 4011 8.934023 ACTATGGTTATTTTCAAGAACAAGGA 57.066 30.769 0.00 0.00 0.00 3.36
2778 4038 3.740631 AAAAAGTACTCCCTTCGACGT 57.259 42.857 0.00 0.00 0.00 4.34
2779 4039 3.294816 AAAAGTACTCCCTTCGACGTC 57.705 47.619 5.18 5.18 0.00 4.34
2780 4040 1.172175 AAGTACTCCCTTCGACGTCC 58.828 55.000 10.58 0.00 0.00 4.79
2781 4041 0.037303 AGTACTCCCTTCGACGTCCA 59.963 55.000 10.58 0.00 0.00 4.02
2782 4042 0.169894 GTACTCCCTTCGACGTCCAC 59.830 60.000 10.58 0.00 0.00 4.02
2783 4043 0.037303 TACTCCCTTCGACGTCCACT 59.963 55.000 10.58 0.00 0.00 4.00
2784 4044 0.826672 ACTCCCTTCGACGTCCACTT 60.827 55.000 10.58 0.00 0.00 3.16
2785 4045 0.317479 CTCCCTTCGACGTCCACTTT 59.683 55.000 10.58 0.00 0.00 2.66
2786 4046 1.542915 CTCCCTTCGACGTCCACTTTA 59.457 52.381 10.58 0.00 0.00 1.85
2787 4047 1.542915 TCCCTTCGACGTCCACTTTAG 59.457 52.381 10.58 0.00 0.00 1.85
2788 4048 1.271656 CCCTTCGACGTCCACTTTAGT 59.728 52.381 10.58 0.00 0.00 2.24
2789 4049 2.489329 CCCTTCGACGTCCACTTTAGTA 59.511 50.000 10.58 0.00 0.00 1.82
2790 4050 3.496155 CCTTCGACGTCCACTTTAGTAC 58.504 50.000 10.58 0.00 0.00 2.73
2791 4051 3.058016 CCTTCGACGTCCACTTTAGTACA 60.058 47.826 10.58 0.00 0.00 2.90
2792 4052 4.539870 CTTCGACGTCCACTTTAGTACAA 58.460 43.478 10.58 0.00 0.00 2.41
2793 4053 3.888934 TCGACGTCCACTTTAGTACAAC 58.111 45.455 10.58 0.00 0.00 3.32
2794 4054 3.565482 TCGACGTCCACTTTAGTACAACT 59.435 43.478 10.58 0.00 0.00 3.16
2795 4055 4.036734 TCGACGTCCACTTTAGTACAACTT 59.963 41.667 10.58 0.00 0.00 2.66
2796 4056 4.741676 CGACGTCCACTTTAGTACAACTTT 59.258 41.667 10.58 0.00 0.00 2.66
2797 4057 5.332055 CGACGTCCACTTTAGTACAACTTTG 60.332 44.000 10.58 0.00 0.00 2.77
2798 4058 5.422145 ACGTCCACTTTAGTACAACTTTGT 58.578 37.500 0.00 0.00 44.86 2.83
2799 4059 6.572519 ACGTCCACTTTAGTACAACTTTGTA 58.427 36.000 0.00 0.00 42.35 2.41
2800 4060 7.212274 ACGTCCACTTTAGTACAACTTTGTAT 58.788 34.615 5.16 0.00 44.59 2.29
2801 4061 8.359642 ACGTCCACTTTAGTACAACTTTGTATA 58.640 33.333 5.16 0.00 44.59 1.47
2802 4062 9.195411 CGTCCACTTTAGTACAACTTTGTATAA 57.805 33.333 5.16 3.53 44.59 0.98
2814 4074 8.924511 ACAACTTTGTATAATATGGATCAGGG 57.075 34.615 0.00 0.00 40.16 4.45
2822 4082 4.891992 AATATGGATCAGGGGAGTAACG 57.108 45.455 0.00 0.00 0.00 3.18
2830 4090 1.053424 AGGGGAGTAACGACTTGCAA 58.947 50.000 0.00 0.00 35.45 4.08
2832 4092 0.788391 GGGAGTAACGACTTGCAACG 59.212 55.000 7.81 7.81 35.45 4.10
2833 4093 0.788391 GGAGTAACGACTTGCAACGG 59.212 55.000 13.23 0.00 35.45 4.44
2839 4099 2.325082 CGACTTGCAACGGAAGGGG 61.325 63.158 0.00 0.00 0.00 4.79
2846 4106 1.600107 CAACGGAAGGGGAATCGGA 59.400 57.895 0.00 0.00 0.00 4.55
2847 4107 0.462047 CAACGGAAGGGGAATCGGAG 60.462 60.000 0.00 0.00 0.00 4.63
2864 4124 4.704833 GAACCAGCTGCGCCCTGA 62.705 66.667 22.24 0.00 32.03 3.86
2891 4151 2.215196 GCCTTCCGTATAATTCCGCAA 58.785 47.619 0.00 0.00 0.00 4.85
2892 4152 2.032290 GCCTTCCGTATAATTCCGCAAC 60.032 50.000 0.00 0.00 0.00 4.17
2898 4158 6.197364 TCCGTATAATTCCGCAACAAAATT 57.803 33.333 0.00 0.00 0.00 1.82
2901 4161 6.237437 CCGTATAATTCCGCAACAAAATTGTG 60.237 38.462 0.00 0.00 41.31 3.33
2903 4163 2.299993 TTCCGCAACAAAATTGTGCA 57.700 40.000 15.69 0.00 41.31 4.57
2939 4199 3.620061 ACTGTGGAGTGATGCACTG 57.380 52.632 4.60 5.48 45.44 3.66
2940 4200 0.035881 ACTGTGGAGTGATGCACTGG 59.964 55.000 4.60 3.00 45.44 4.00
2941 4201 0.035881 CTGTGGAGTGATGCACTGGT 59.964 55.000 4.60 0.00 45.44 4.00
2942 4202 0.250424 TGTGGAGTGATGCACTGGTG 60.250 55.000 4.60 0.00 45.44 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.970610 ACGATCACGGACGTTTAATATCG 59.029 43.478 16.73 16.73 44.46 2.92
38 39 4.736793 GTCACGATCACGGACGTTTAATAT 59.263 41.667 0.00 0.00 44.46 1.28
89 90 3.699894 ACGCCACTGAGCTGGAGG 61.700 66.667 0.00 0.00 35.51 4.30
151 153 1.196808 CATAACAACCGCAGTCCACAC 59.803 52.381 0.00 0.00 0.00 3.82
181 183 1.068264 CAGTAGCGTGTTGAGCTCTCA 60.068 52.381 16.19 11.37 44.79 3.27
183 185 0.962489 ACAGTAGCGTGTTGAGCTCT 59.038 50.000 16.19 0.00 44.79 4.09
260 262 7.554476 GCATGGTTAAAGAGAGGTAAGAAGAAT 59.446 37.037 0.00 0.00 0.00 2.40
269 271 2.619074 GCCTGCATGGTTAAAGAGAGGT 60.619 50.000 0.00 0.00 38.35 3.85
288 1408 5.028549 TCACTAAGAAGAAGATCCATGCC 57.971 43.478 0.00 0.00 0.00 4.40
291 1411 9.206690 TGACTAATCACTAAGAAGAAGATCCAT 57.793 33.333 0.00 0.00 0.00 3.41
346 1470 5.470098 GTCACTCCTCATTTAGCAAAACTGA 59.530 40.000 0.00 0.00 0.00 3.41
348 1472 5.376625 TGTCACTCCTCATTTAGCAAAACT 58.623 37.500 0.00 0.00 0.00 2.66
349 1473 5.689383 TGTCACTCCTCATTTAGCAAAAC 57.311 39.130 0.00 0.00 0.00 2.43
350 1474 6.092122 CGTATGTCACTCCTCATTTAGCAAAA 59.908 38.462 0.00 0.00 0.00 2.44
351 1475 5.580691 CGTATGTCACTCCTCATTTAGCAAA 59.419 40.000 0.00 0.00 0.00 3.68
352 1476 5.109210 CGTATGTCACTCCTCATTTAGCAA 58.891 41.667 0.00 0.00 0.00 3.91
353 1477 4.159693 ACGTATGTCACTCCTCATTTAGCA 59.840 41.667 0.00 0.00 0.00 3.49
354 1478 4.504461 CACGTATGTCACTCCTCATTTAGC 59.496 45.833 0.00 0.00 0.00 3.09
355 1479 5.516696 CACACGTATGTCACTCCTCATTTAG 59.483 44.000 0.00 0.00 36.72 1.85
356 1480 5.407502 CACACGTATGTCACTCCTCATTTA 58.592 41.667 0.00 0.00 36.72 1.40
363 1487 0.037697 TGCCACACGTATGTCACTCC 60.038 55.000 0.00 0.00 36.72 3.85
364 1488 1.068474 GTGCCACACGTATGTCACTC 58.932 55.000 0.00 0.00 36.72 3.51
375 1499 0.304705 CAGAGTGTTTCGTGCCACAC 59.695 55.000 0.00 0.00 43.17 3.82
376 1500 1.436195 GCAGAGTGTTTCGTGCCACA 61.436 55.000 0.00 0.00 33.99 4.17
450 1574 4.759693 ACGTATTCAGATGGCAAGTTCAAA 59.240 37.500 0.00 0.00 0.00 2.69
452 1576 3.684305 CACGTATTCAGATGGCAAGTTCA 59.316 43.478 0.00 0.00 0.00 3.18
453 1577 3.485877 GCACGTATTCAGATGGCAAGTTC 60.486 47.826 0.00 0.00 0.00 3.01
465 1589 6.163476 ACTTCAGTTATCAAGCACGTATTCA 58.837 36.000 0.00 0.00 0.00 2.57
480 1613 6.212589 TGACACCAGGATGATAACTTCAGTTA 59.787 38.462 1.89 1.89 43.71 2.24
485 1618 5.091261 AGTGACACCAGGATGATAACTTC 57.909 43.478 0.84 0.00 39.69 3.01
491 1624 5.505181 AAGTTTAGTGACACCAGGATGAT 57.495 39.130 0.84 0.00 39.69 2.45
499 1632 9.821662 GTTTGTTATGATAAGTTTAGTGACACC 57.178 33.333 0.84 0.00 0.00 4.16
501 1634 9.478768 TCGTTTGTTATGATAAGTTTAGTGACA 57.521 29.630 0.00 0.00 0.00 3.58
514 1647 5.447279 GGCAACTTCGATCGTTTGTTATGAT 60.447 40.000 15.94 0.00 35.15 2.45
515 1648 4.142988 GGCAACTTCGATCGTTTGTTATGA 60.143 41.667 15.94 0.00 0.00 2.15
521 1654 2.095768 ACATGGCAACTTCGATCGTTTG 60.096 45.455 15.94 16.64 37.61 2.93
533 1666 1.371635 GGCACGAACACATGGCAAC 60.372 57.895 0.00 0.00 40.91 4.17
591 1724 6.900568 ACGAGTTCAATCTTCATGAGAATC 57.099 37.500 0.00 0.00 38.06 2.52
690 1831 4.322725 CCAGTGTCTCCTTATGCTTGTGTA 60.323 45.833 0.00 0.00 0.00 2.90
697 1838 4.082733 GGTTTTTCCAGTGTCTCCTTATGC 60.083 45.833 0.00 0.00 35.97 3.14
698 1839 5.316987 AGGTTTTTCCAGTGTCTCCTTATG 58.683 41.667 0.00 0.00 39.02 1.90
699 1840 5.310857 AGAGGTTTTTCCAGTGTCTCCTTAT 59.689 40.000 0.00 0.00 39.02 1.73
700 1841 4.658901 AGAGGTTTTTCCAGTGTCTCCTTA 59.341 41.667 0.00 0.00 39.02 2.69
764 1919 9.798994 CTGGTAATTACAGTAGTTAGTTAGTGG 57.201 37.037 17.16 0.00 0.00 4.00
778 2023 4.694982 TGTGCATGTGACTGGTAATTACAG 59.305 41.667 17.16 13.76 41.64 2.74
780 2025 5.572211 CATGTGCATGTGACTGGTAATTAC 58.428 41.667 7.09 7.09 34.23 1.89
781 2026 4.096231 GCATGTGCATGTGACTGGTAATTA 59.904 41.667 12.96 0.00 40.80 1.40
782 2027 3.119388 GCATGTGCATGTGACTGGTAATT 60.119 43.478 12.96 0.00 40.80 1.40
783 2028 2.424601 GCATGTGCATGTGACTGGTAAT 59.575 45.455 12.96 0.00 40.80 1.89
784 2029 1.811965 GCATGTGCATGTGACTGGTAA 59.188 47.619 12.96 0.00 40.80 2.85
785 2030 1.452110 GCATGTGCATGTGACTGGTA 58.548 50.000 12.96 0.00 40.80 3.25
786 2031 2.260247 GCATGTGCATGTGACTGGT 58.740 52.632 12.96 0.00 40.80 4.00
961 2216 1.227497 GGAGGAGATCCGCAAGCAG 60.227 63.158 4.95 0.00 38.67 4.24
985 2240 2.375766 GCATGGCGACGATCGGATC 61.376 63.158 20.98 7.95 40.84 3.36
986 2241 2.356313 GCATGGCGACGATCGGAT 60.356 61.111 20.98 0.00 40.84 4.18
1080 2335 3.659089 CTCCACGTTGGGCCGGTAG 62.659 68.421 1.90 0.00 38.32 3.18
1326 2581 4.268687 CGGTGAGAGAACACTGCC 57.731 61.111 0.00 0.00 39.70 4.85
1362 2617 3.846405 TTCCAGGAGCAGGTCGGGT 62.846 63.158 8.36 0.00 0.00 5.28
1420 2678 4.521062 CTTCTCAGCCTCGCCCGG 62.521 72.222 0.00 0.00 0.00 5.73
1719 2977 1.139947 GTCGTAGCAGCTCTGGTCC 59.860 63.158 0.00 0.00 41.96 4.46
1763 3021 1.006805 GGGAGCATCGTCAGATCGG 60.007 63.158 0.00 0.00 34.23 4.18
1830 3088 1.300465 CATGGCGTCCTCCTGATCG 60.300 63.158 0.00 0.00 0.00 3.69
1832 3090 2.037620 GCTCATGGCGTCCTCCTGAT 62.038 60.000 0.00 0.00 0.00 2.90
1833 3091 2.725312 GCTCATGGCGTCCTCCTGA 61.725 63.158 0.00 0.00 0.00 3.86
1834 3092 2.202987 GCTCATGGCGTCCTCCTG 60.203 66.667 0.00 0.00 0.00 3.86
1980 3238 3.989698 AATCACGAGGACAGCGGCG 62.990 63.158 0.51 0.51 0.00 6.46
1989 3247 5.808042 AAGACATGAAATCAATCACGAGG 57.192 39.130 0.00 0.00 30.82 4.63
2004 3262 5.320277 AGGGAGAGGAAAAGAAAAGACATG 58.680 41.667 0.00 0.00 0.00 3.21
2005 3263 5.590976 AGGGAGAGGAAAAGAAAAGACAT 57.409 39.130 0.00 0.00 0.00 3.06
2093 3352 6.811253 TCCATTTTTATCCCGCATGTATAC 57.189 37.500 0.00 0.00 0.00 1.47
2094 3353 8.303156 CAAATCCATTTTTATCCCGCATGTATA 58.697 33.333 0.00 0.00 0.00 1.47
2102 3361 7.095695 ACAGTACAAATCCATTTTTATCCCG 57.904 36.000 0.00 0.00 0.00 5.14
2178 3437 2.587522 AGCTCAGAACAGGAAAAACCC 58.412 47.619 0.00 0.00 40.05 4.11
2219 3478 4.454161 CAGGAACAACATTGATTGGTCGTA 59.546 41.667 0.00 0.00 45.62 3.43
2270 3529 2.896854 CATGCCCATCCGTCCACG 60.897 66.667 0.00 0.00 39.44 4.94
2276 3535 2.751036 TGTGTGCATGCCCATCCG 60.751 61.111 16.68 0.00 0.00 4.18
2286 3545 2.980378 GCATCGGCATGTGTGTGCA 61.980 57.895 9.38 0.00 46.81 4.57
2287 3546 2.202518 GCATCGGCATGTGTGTGC 60.203 61.111 0.00 0.00 44.31 4.57
2292 3551 2.635338 CATCGGCATCGGCATGTG 59.365 61.111 0.00 0.00 43.71 3.21
2293 3552 3.282157 GCATCGGCATCGGCATGT 61.282 61.111 0.00 0.00 43.71 3.21
2294 3553 4.034258 GGCATCGGCATCGGCATG 62.034 66.667 0.00 0.00 43.71 4.06
2298 3557 3.417224 CATCGGCATCGGCATCGG 61.417 66.667 0.00 0.00 43.71 4.18
2299 3558 3.417224 CCATCGGCATCGGCATCG 61.417 66.667 0.00 0.00 43.71 3.84
2300 3559 2.281070 ACCATCGGCATCGGCATC 60.281 61.111 0.00 0.00 43.71 3.91
2301 3560 2.592574 CACCATCGGCATCGGCAT 60.593 61.111 0.00 0.00 43.71 4.40
2395 3654 1.402456 GGCAGCTGCTTCAGATTGTTG 60.402 52.381 35.82 0.00 41.70 3.33
2433 3692 1.154205 CGAGCTAGGGCCAAATGTCG 61.154 60.000 6.18 3.04 39.73 4.35
2437 3696 3.901844 TCTATAACGAGCTAGGGCCAAAT 59.098 43.478 6.18 0.00 39.73 2.32
2614 3874 3.217681 ACTCTCTTTACCCCGCAAAAA 57.782 42.857 0.00 0.00 0.00 1.94
2615 3875 2.943036 ACTCTCTTTACCCCGCAAAA 57.057 45.000 0.00 0.00 0.00 2.44
2616 3876 2.943036 AACTCTCTTTACCCCGCAAA 57.057 45.000 0.00 0.00 0.00 3.68
2617 3877 2.943036 AAACTCTCTTTACCCCGCAA 57.057 45.000 0.00 0.00 0.00 4.85
2618 3878 2.943036 AAAACTCTCTTTACCCCGCA 57.057 45.000 0.00 0.00 0.00 5.69
2619 3879 5.637809 CAATAAAAACTCTCTTTACCCCGC 58.362 41.667 0.00 0.00 0.00 6.13
2620 3880 5.182380 TGCAATAAAAACTCTCTTTACCCCG 59.818 40.000 0.00 0.00 0.00 5.73
2621 3881 6.584185 TGCAATAAAAACTCTCTTTACCCC 57.416 37.500 0.00 0.00 0.00 4.95
2622 3882 8.088365 ACATTGCAATAAAAACTCTCTTTACCC 58.912 33.333 12.53 0.00 0.00 3.69
2640 3900 9.838975 CTTGATTGTAACACTATTACATTGCAA 57.161 29.630 0.00 0.00 35.15 4.08
2641 3901 9.225436 TCTTGATTGTAACACTATTACATTGCA 57.775 29.630 0.63 0.00 35.15 4.08
2642 3902 9.708222 CTCTTGATTGTAACACTATTACATTGC 57.292 33.333 0.63 0.00 35.15 3.56
2644 3904 8.893727 GCCTCTTGATTGTAACACTATTACATT 58.106 33.333 0.63 0.00 35.15 2.71
2645 3905 7.499232 GGCCTCTTGATTGTAACACTATTACAT 59.501 37.037 0.00 0.00 35.15 2.29
2646 3906 6.821665 GGCCTCTTGATTGTAACACTATTACA 59.178 38.462 0.00 0.00 33.51 2.41
2647 3907 6.821665 TGGCCTCTTGATTGTAACACTATTAC 59.178 38.462 3.32 0.00 0.00 1.89
2648 3908 6.821665 GTGGCCTCTTGATTGTAACACTATTA 59.178 38.462 3.32 0.00 0.00 0.98
2649 3909 5.648092 GTGGCCTCTTGATTGTAACACTATT 59.352 40.000 3.32 0.00 0.00 1.73
2650 3910 5.186198 GTGGCCTCTTGATTGTAACACTAT 58.814 41.667 3.32 0.00 0.00 2.12
2651 3911 4.041075 TGTGGCCTCTTGATTGTAACACTA 59.959 41.667 3.32 0.00 0.00 2.74
2652 3912 3.181445 TGTGGCCTCTTGATTGTAACACT 60.181 43.478 3.32 0.00 0.00 3.55
2653 3913 3.146066 TGTGGCCTCTTGATTGTAACAC 58.854 45.455 3.32 0.00 0.00 3.32
2654 3914 3.500448 TGTGGCCTCTTGATTGTAACA 57.500 42.857 3.32 0.00 0.00 2.41
2655 3915 3.821033 AGTTGTGGCCTCTTGATTGTAAC 59.179 43.478 3.32 0.00 0.00 2.50
2656 3916 4.072131 GAGTTGTGGCCTCTTGATTGTAA 58.928 43.478 3.32 0.00 0.00 2.41
2657 3917 3.559171 GGAGTTGTGGCCTCTTGATTGTA 60.559 47.826 3.32 0.00 0.00 2.41
2658 3918 2.508526 GAGTTGTGGCCTCTTGATTGT 58.491 47.619 3.32 0.00 0.00 2.71
2659 3919 1.815003 GGAGTTGTGGCCTCTTGATTG 59.185 52.381 3.32 0.00 0.00 2.67
2660 3920 1.707427 AGGAGTTGTGGCCTCTTGATT 59.293 47.619 3.32 0.00 0.00 2.57
2661 3921 1.280421 GAGGAGTTGTGGCCTCTTGAT 59.720 52.381 3.32 0.00 45.72 2.57
2662 3922 0.687354 GAGGAGTTGTGGCCTCTTGA 59.313 55.000 3.32 0.00 45.72 3.02
2663 3923 3.239861 GAGGAGTTGTGGCCTCTTG 57.760 57.895 3.32 0.00 45.72 3.02
2667 3927 1.985159 TGTATTGAGGAGTTGTGGCCT 59.015 47.619 3.32 0.00 37.18 5.19
2668 3928 2.489938 TGTATTGAGGAGTTGTGGCC 57.510 50.000 0.00 0.00 0.00 5.36
2669 3929 2.749621 CCTTGTATTGAGGAGTTGTGGC 59.250 50.000 0.00 0.00 36.33 5.01
2670 3930 3.753272 CACCTTGTATTGAGGAGTTGTGG 59.247 47.826 0.00 0.00 37.72 4.17
2671 3931 3.753272 CCACCTTGTATTGAGGAGTTGTG 59.247 47.826 0.00 0.00 37.72 3.33
2672 3932 3.650942 TCCACCTTGTATTGAGGAGTTGT 59.349 43.478 0.00 0.00 37.72 3.32
2673 3933 4.256920 CTCCACCTTGTATTGAGGAGTTG 58.743 47.826 0.00 0.00 38.23 3.16
2674 3934 3.307762 GCTCCACCTTGTATTGAGGAGTT 60.308 47.826 0.00 0.00 43.47 3.01
2675 3935 2.237392 GCTCCACCTTGTATTGAGGAGT 59.763 50.000 0.00 0.00 43.47 3.85
2676 3936 2.237143 TGCTCCACCTTGTATTGAGGAG 59.763 50.000 0.00 0.00 44.19 3.69
2677 3937 2.265367 TGCTCCACCTTGTATTGAGGA 58.735 47.619 0.00 0.00 37.72 3.71
2678 3938 2.787473 TGCTCCACCTTGTATTGAGG 57.213 50.000 0.00 0.00 40.24 3.86
2679 3939 4.148128 AGATGCTCCACCTTGTATTGAG 57.852 45.455 0.00 0.00 0.00 3.02
2680 3940 4.019411 TGAAGATGCTCCACCTTGTATTGA 60.019 41.667 0.00 0.00 0.00 2.57
2681 3941 4.264253 TGAAGATGCTCCACCTTGTATTG 58.736 43.478 0.00 0.00 0.00 1.90
2682 3942 4.574674 TGAAGATGCTCCACCTTGTATT 57.425 40.909 0.00 0.00 0.00 1.89
2683 3943 4.263462 TGTTGAAGATGCTCCACCTTGTAT 60.263 41.667 0.00 0.00 0.00 2.29
2684 3944 3.072330 TGTTGAAGATGCTCCACCTTGTA 59.928 43.478 0.00 0.00 0.00 2.41
2685 3945 2.158623 TGTTGAAGATGCTCCACCTTGT 60.159 45.455 0.00 0.00 0.00 3.16
2686 3946 2.507484 TGTTGAAGATGCTCCACCTTG 58.493 47.619 0.00 0.00 0.00 3.61
2687 3947 2.957402 TGTTGAAGATGCTCCACCTT 57.043 45.000 0.00 0.00 0.00 3.50
2688 3948 2.957402 TTGTTGAAGATGCTCCACCT 57.043 45.000 0.00 0.00 0.00 4.00
2689 3949 4.525912 ATTTTGTTGAAGATGCTCCACC 57.474 40.909 0.00 0.00 0.00 4.61
2690 3950 5.574443 GCTAATTTTGTTGAAGATGCTCCAC 59.426 40.000 0.00 0.00 0.00 4.02
2691 3951 5.243507 TGCTAATTTTGTTGAAGATGCTCCA 59.756 36.000 0.00 0.00 0.00 3.86
2692 3952 5.713025 TGCTAATTTTGTTGAAGATGCTCC 58.287 37.500 0.00 0.00 0.00 4.70
2693 3953 5.287992 GCTGCTAATTTTGTTGAAGATGCTC 59.712 40.000 0.00 0.00 0.00 4.26
2694 3954 5.166398 GCTGCTAATTTTGTTGAAGATGCT 58.834 37.500 0.00 0.00 0.00 3.79
2695 3955 4.030977 CGCTGCTAATTTTGTTGAAGATGC 59.969 41.667 0.00 0.00 0.00 3.91
2696 3956 5.156355 ACGCTGCTAATTTTGTTGAAGATG 58.844 37.500 0.00 0.00 0.00 2.90
2697 3957 5.376854 ACGCTGCTAATTTTGTTGAAGAT 57.623 34.783 0.00 0.00 0.00 2.40
2698 3958 4.829064 ACGCTGCTAATTTTGTTGAAGA 57.171 36.364 0.00 0.00 0.00 2.87
2699 3959 4.554973 GCTACGCTGCTAATTTTGTTGAAG 59.445 41.667 0.00 0.00 0.00 3.02
2700 3960 4.023622 TGCTACGCTGCTAATTTTGTTGAA 60.024 37.500 0.00 0.00 0.00 2.69
2701 3961 3.500299 TGCTACGCTGCTAATTTTGTTGA 59.500 39.130 0.00 0.00 0.00 3.18
2702 3962 3.820689 TGCTACGCTGCTAATTTTGTTG 58.179 40.909 0.00 0.00 0.00 3.33
2703 3963 4.155826 TCATGCTACGCTGCTAATTTTGTT 59.844 37.500 0.00 0.00 0.00 2.83
2704 3964 3.689161 TCATGCTACGCTGCTAATTTTGT 59.311 39.130 0.00 0.00 0.00 2.83
2705 3965 4.031028 GTCATGCTACGCTGCTAATTTTG 58.969 43.478 0.00 0.00 0.00 2.44
2706 3966 3.941483 AGTCATGCTACGCTGCTAATTTT 59.059 39.130 0.00 0.00 0.00 1.82
2707 3967 3.535561 AGTCATGCTACGCTGCTAATTT 58.464 40.909 0.00 0.00 0.00 1.82
2708 3968 3.185246 AGTCATGCTACGCTGCTAATT 57.815 42.857 0.00 0.00 0.00 1.40
2709 3969 2.898729 AGTCATGCTACGCTGCTAAT 57.101 45.000 0.00 0.00 0.00 1.73
2710 3970 3.552890 CCATAGTCATGCTACGCTGCTAA 60.553 47.826 0.00 0.00 31.59 3.09
2711 3971 2.029918 CCATAGTCATGCTACGCTGCTA 60.030 50.000 0.00 0.00 31.59 3.49
2712 3972 1.269988 CCATAGTCATGCTACGCTGCT 60.270 52.381 0.00 0.00 31.59 4.24
2713 3973 1.143305 CCATAGTCATGCTACGCTGC 58.857 55.000 0.00 0.00 31.59 5.25
2714 3974 2.515926 ACCATAGTCATGCTACGCTG 57.484 50.000 0.00 0.00 31.59 5.18
2715 3975 4.873746 ATAACCATAGTCATGCTACGCT 57.126 40.909 0.00 0.00 31.59 5.07
2716 3976 5.924475 AAATAACCATAGTCATGCTACGC 57.076 39.130 0.00 0.00 31.59 4.42
2717 3977 7.477144 TGAAAATAACCATAGTCATGCTACG 57.523 36.000 0.00 0.00 31.59 3.51
2718 3978 9.109393 TCTTGAAAATAACCATAGTCATGCTAC 57.891 33.333 0.00 0.00 31.59 3.58
2719 3979 9.679661 TTCTTGAAAATAACCATAGTCATGCTA 57.320 29.630 0.00 0.00 0.00 3.49
2727 3987 9.626045 GTTCCTTGTTCTTGAAAATAACCATAG 57.374 33.333 0.00 0.00 32.54 2.23
2729 3989 8.017418 TGTTCCTTGTTCTTGAAAATAACCAT 57.983 30.769 0.00 0.00 32.54 3.55
2730 3990 7.411486 TGTTCCTTGTTCTTGAAAATAACCA 57.589 32.000 0.00 0.00 32.54 3.67
2759 4019 2.029560 GGACGTCGAAGGGAGTACTTTT 60.030 50.000 9.92 0.00 0.00 2.27
2760 4020 1.543358 GGACGTCGAAGGGAGTACTTT 59.457 52.381 9.92 0.00 0.00 2.66
2761 4021 1.172175 GGACGTCGAAGGGAGTACTT 58.828 55.000 9.92 0.00 0.00 2.24
2762 4022 0.037303 TGGACGTCGAAGGGAGTACT 59.963 55.000 9.92 0.00 0.00 2.73
2763 4023 0.169894 GTGGACGTCGAAGGGAGTAC 59.830 60.000 9.92 0.00 0.00 2.73
2764 4024 0.037303 AGTGGACGTCGAAGGGAGTA 59.963 55.000 9.92 0.00 0.00 2.59
2765 4025 0.826672 AAGTGGACGTCGAAGGGAGT 60.827 55.000 9.92 0.00 0.00 3.85
2766 4026 0.317479 AAAGTGGACGTCGAAGGGAG 59.683 55.000 9.92 0.00 0.00 4.30
2767 4027 1.542915 CTAAAGTGGACGTCGAAGGGA 59.457 52.381 9.92 0.00 0.00 4.20
2768 4028 1.271656 ACTAAAGTGGACGTCGAAGGG 59.728 52.381 9.92 0.00 0.00 3.95
2769 4029 2.719426 ACTAAAGTGGACGTCGAAGG 57.281 50.000 9.92 0.00 0.00 3.46
2770 4030 4.151258 TGTACTAAAGTGGACGTCGAAG 57.849 45.455 9.92 2.37 0.00 3.79
2771 4031 4.036734 AGTTGTACTAAAGTGGACGTCGAA 59.963 41.667 9.92 0.00 0.00 3.71
2772 4032 3.565482 AGTTGTACTAAAGTGGACGTCGA 59.435 43.478 9.92 1.86 0.00 4.20
2773 4033 3.893720 AGTTGTACTAAAGTGGACGTCG 58.106 45.455 9.92 0.00 0.00 5.12
2774 4034 5.521372 ACAAAGTTGTACTAAAGTGGACGTC 59.479 40.000 7.13 7.13 40.16 4.34
2775 4035 5.422145 ACAAAGTTGTACTAAAGTGGACGT 58.578 37.500 0.00 0.00 40.16 4.34
2776 4036 5.978934 ACAAAGTTGTACTAAAGTGGACG 57.021 39.130 0.00 0.00 40.16 4.79
2789 4049 7.944554 CCCCTGATCCATATTATACAAAGTTGT 59.055 37.037 1.75 1.75 44.86 3.32
2790 4050 8.163408 TCCCCTGATCCATATTATACAAAGTTG 58.837 37.037 0.00 0.00 0.00 3.16
2791 4051 8.287904 TCCCCTGATCCATATTATACAAAGTT 57.712 34.615 0.00 0.00 0.00 2.66
2792 4052 7.517604 ACTCCCCTGATCCATATTATACAAAGT 59.482 37.037 0.00 0.00 0.00 2.66
2793 4053 7.922382 ACTCCCCTGATCCATATTATACAAAG 58.078 38.462 0.00 0.00 0.00 2.77
2794 4054 7.888514 ACTCCCCTGATCCATATTATACAAA 57.111 36.000 0.00 0.00 0.00 2.83
2795 4055 8.822805 GTTACTCCCCTGATCCATATTATACAA 58.177 37.037 0.00 0.00 0.00 2.41
2796 4056 7.123697 CGTTACTCCCCTGATCCATATTATACA 59.876 40.741 0.00 0.00 0.00 2.29
2797 4057 7.341256 TCGTTACTCCCCTGATCCATATTATAC 59.659 40.741 0.00 0.00 0.00 1.47
2798 4058 7.341256 GTCGTTACTCCCCTGATCCATATTATA 59.659 40.741 0.00 0.00 0.00 0.98
2799 4059 6.154706 GTCGTTACTCCCCTGATCCATATTAT 59.845 42.308 0.00 0.00 0.00 1.28
2800 4060 5.479375 GTCGTTACTCCCCTGATCCATATTA 59.521 44.000 0.00 0.00 0.00 0.98
2801 4061 4.283722 GTCGTTACTCCCCTGATCCATATT 59.716 45.833 0.00 0.00 0.00 1.28
2802 4062 3.833070 GTCGTTACTCCCCTGATCCATAT 59.167 47.826 0.00 0.00 0.00 1.78
2803 4063 3.117246 AGTCGTTACTCCCCTGATCCATA 60.117 47.826 0.00 0.00 0.00 2.74
2804 4064 2.040178 GTCGTTACTCCCCTGATCCAT 58.960 52.381 0.00 0.00 0.00 3.41
2805 4065 1.006758 AGTCGTTACTCCCCTGATCCA 59.993 52.381 0.00 0.00 0.00 3.41
2806 4066 1.777941 AGTCGTTACTCCCCTGATCC 58.222 55.000 0.00 0.00 0.00 3.36
2807 4067 2.738964 GCAAGTCGTTACTCCCCTGATC 60.739 54.545 0.00 0.00 33.75 2.92
2808 4068 1.207329 GCAAGTCGTTACTCCCCTGAT 59.793 52.381 0.00 0.00 33.75 2.90
2809 4069 0.606604 GCAAGTCGTTACTCCCCTGA 59.393 55.000 0.00 0.00 33.75 3.86
2810 4070 0.320374 TGCAAGTCGTTACTCCCCTG 59.680 55.000 0.00 0.00 33.75 4.45
2811 4071 1.053424 TTGCAAGTCGTTACTCCCCT 58.947 50.000 0.00 0.00 33.75 4.79
2812 4072 1.154197 GTTGCAAGTCGTTACTCCCC 58.846 55.000 0.00 0.00 33.75 4.81
2813 4073 0.788391 CGTTGCAAGTCGTTACTCCC 59.212 55.000 0.00 0.00 33.75 4.30
2814 4074 0.788391 CCGTTGCAAGTCGTTACTCC 59.212 55.000 0.00 0.00 33.75 3.85
2822 4082 0.536460 TTCCCCTTCCGTTGCAAGTC 60.536 55.000 0.00 0.00 0.00 3.01
2830 4090 0.616679 TTCTCCGATTCCCCTTCCGT 60.617 55.000 0.00 0.00 0.00 4.69
2832 4092 0.180642 GGTTCTCCGATTCCCCTTCC 59.819 60.000 0.00 0.00 0.00 3.46
2833 4093 0.909623 TGGTTCTCCGATTCCCCTTC 59.090 55.000 0.00 0.00 36.30 3.46
2839 4099 1.424493 CGCAGCTGGTTCTCCGATTC 61.424 60.000 17.12 0.00 36.30 2.52
2858 4118 1.523938 GAAGGCGTATGGTCAGGGC 60.524 63.158 0.00 0.00 0.00 5.19
2864 4124 4.562143 GGAATTATACGGAAGGCGTATGGT 60.562 45.833 0.00 0.00 34.78 3.55
2865 4125 3.930848 GGAATTATACGGAAGGCGTATGG 59.069 47.826 0.00 0.00 34.78 2.74
2881 4141 4.371786 TGCACAATTTTGTTGCGGAATTA 58.628 34.783 0.00 0.00 39.91 1.40
2886 4146 1.932511 ACTTGCACAATTTTGTTGCGG 59.067 42.857 0.00 9.28 39.91 5.69
2888 4148 4.799419 ATCACTTGCACAATTTTGTTGC 57.201 36.364 0.00 9.46 39.91 4.17
2891 4151 8.603181 GTTTCTTTATCACTTGCACAATTTTGT 58.397 29.630 0.00 0.00 43.36 2.83
2892 4152 7.788846 CGTTTCTTTATCACTTGCACAATTTTG 59.211 33.333 0.00 0.00 0.00 2.44
2898 4158 4.572795 TGTCGTTTCTTTATCACTTGCACA 59.427 37.500 0.00 0.00 0.00 4.57
2901 4161 5.140177 CAGTGTCGTTTCTTTATCACTTGC 58.860 41.667 0.00 0.00 34.57 4.01
2903 4163 5.236478 CCACAGTGTCGTTTCTTTATCACTT 59.764 40.000 0.00 0.00 34.57 3.16


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

AutoCloner maintained by Alex Coulton.