Multiple sequence alignment - TraesCS2B01G422000

Loading Multiple Alignment...

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 TraesCS2B01G422000 chr2B 100.000 3620 0 0 1 3620 607249091 607245472 0.000000e+00 6685.0
1 TraesCS2B01G422000 chr2B 84.337 830 75 26 1 785 745780258 745779439 0.000000e+00 761.0
2 TraesCS2B01G422000 chr2B 90.291 103 9 1 2860 2961 798196674 798196776 2.270000e-27 134.0
3 TraesCS2B01G422000 chr2B 96.000 50 2 0 737 786 18318953 18319002 8.330000e-12 82.4
4 TraesCS2B01G422000 chr2D 93.040 2112 87 26 786 2864 515829358 515827274 0.000000e+00 3031.0
5 TraesCS2B01G422000 chr2D 94.167 240 12 1 3383 3620 515826931 515826692 7.390000e-97 364.0
6 TraesCS2B01G422000 chr2D 94.643 168 8 1 3078 3245 515827089 515826923 3.590000e-65 259.0
7 TraesCS2B01G422000 chr2D 89.167 120 10 3 2946 3063 515827275 515827157 2.910000e-31 147.0
8 TraesCS2B01G422000 chr2D 81.319 91 15 2 693 782 391849561 391849650 5.010000e-09 73.1
9 TraesCS2B01G422000 chr2D 100.000 29 0 0 3355 3383 538052855 538052827 2.000000e-03 54.7
10 TraesCS2B01G422000 chr2A 92.268 1927 82 20 786 2677 659651771 659649877 0.000000e+00 2671.0
11 TraesCS2B01G422000 chr2A 92.946 241 10 3 3383 3620 659649438 659649202 9.620000e-91 344.0
12 TraesCS2B01G422000 chr2A 84.868 304 24 14 2948 3245 659649717 659649430 1.640000e-73 287.0
13 TraesCS2B01G422000 chr6B 88.265 801 71 13 1 787 653860333 653859542 0.000000e+00 937.0
14 TraesCS2B01G422000 chr6B 87.417 151 6 10 3245 3382 564215914 564216064 1.040000e-35 161.0
15 TraesCS2B01G422000 chr6B 86.364 154 7 11 3242 3382 648253170 648253018 4.840000e-34 156.0
16 TraesCS2B01G422000 chr6B 83.444 151 5 11 3246 3383 107881575 107881718 4.910000e-24 122.0
17 TraesCS2B01G422000 chr7B 99.138 116 1 0 3243 3358 395244282 395244397 3.660000e-50 209.0
18 TraesCS2B01G422000 chr7B 87.500 64 8 0 722 785 625972523 625972460 1.390000e-09 75.0
19 TraesCS2B01G422000 chr4B 100.000 113 0 0 3246 3358 596938927 596939039 3.660000e-50 209.0
20 TraesCS2B01G422000 chr4B 94.690 113 6 0 3246 3358 6087189 6087077 3.710000e-40 176.0
21 TraesCS2B01G422000 chr4B 87.417 151 6 10 3246 3383 81924610 81924460 1.040000e-35 161.0
22 TraesCS2B01G422000 chr4B 91.176 102 6 3 2848 2947 519259020 519258920 6.300000e-28 135.0
23 TraesCS2B01G422000 chr4B 100.000 28 0 0 3356 3383 596939051 596939078 7.000000e-03 52.8
24 TraesCS2B01G422000 chr3B 100.000 112 0 0 3247 3358 650647105 650646994 1.320000e-49 207.0
25 TraesCS2B01G422000 chr3B 93.750 96 5 1 2860 2955 334313155 334313061 3.770000e-30 143.0
26 TraesCS2B01G422000 chr1A 96.460 113 4 0 3246 3358 390384100 390383988 1.720000e-43 187.0
27 TraesCS2B01G422000 chr1A 94.690 113 6 0 3246 3358 14111098 14110986 3.710000e-40 176.0
28 TraesCS2B01G422000 chr1A 100.000 31 0 0 3355 3385 14110976 14110946 1.400000e-04 58.4
29 TraesCS2B01G422000 chr4D 95.575 113 5 0 3246 3358 336119594 336119706 7.980000e-42 182.0
30 TraesCS2B01G422000 chr4D 86.667 150 7 10 3246 3382 319326006 319326155 1.740000e-33 154.0
31 TraesCS2B01G422000 chr3A 95.575 113 5 0 3246 3358 747611588 747611476 7.980000e-42 182.0
32 TraesCS2B01G422000 chr6D 94.690 113 6 0 3246 3358 1947567 1947679 3.710000e-40 176.0
33 TraesCS2B01G422000 chr6D 87.586 145 14 4 645 785 7155584 7155440 8.040000e-37 165.0
34 TraesCS2B01G422000 chr7D 88.276 145 13 4 645 785 602209032 602209176 1.730000e-38 171.0
35 TraesCS2B01G422000 chr7D 84.286 70 6 5 664 729 415392380 415392312 3.020000e-06 63.9
36 TraesCS2B01G422000 chr1B 87.417 151 6 10 3246 3383 648992672 648992522 1.040000e-35 161.0
37 TraesCS2B01G422000 chr1B 91.489 94 8 0 2854 2947 616907443 616907536 2.930000e-26 130.0
38 TraesCS2B01G422000 chr4A 87.324 142 14 4 645 782 374328881 374329022 3.740000e-35 159.0
39 TraesCS2B01G422000 chr1D 86.897 145 15 4 645 785 478176864 478176720 3.740000e-35 159.0
40 TraesCS2B01G422000 chr5B 93.814 97 6 0 2851 2947 72255095 72255191 2.910000e-31 147.0
41 TraesCS2B01G422000 chr5B 92.233 103 8 0 2851 2953 72824568 72824466 2.910000e-31 147.0
42 TraesCS2B01G422000 chr5B 92.553 94 7 0 2862 2955 496801841 496801934 6.300000e-28 135.0
43 TraesCS2B01G422000 chr5A 95.556 90 4 0 2858 2947 90623750 90623661 1.050000e-30 145.0
44 TraesCS2B01G422000 chr5A 94.505 91 5 0 2862 2952 38014620 38014710 1.360000e-29 141.0


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 TraesCS2B01G422000 chr2B 607245472 607249091 3619 True 6685.000000 6685 100.000000 1 3620 1 chr2B.!!$R1 3619
1 TraesCS2B01G422000 chr2B 745779439 745780258 819 True 761.000000 761 84.337000 1 785 1 chr2B.!!$R2 784
2 TraesCS2B01G422000 chr2D 515826692 515829358 2666 True 950.250000 3031 92.754250 786 3620 4 chr2D.!!$R2 2834
3 TraesCS2B01G422000 chr2A 659649202 659651771 2569 True 1100.666667 2671 90.027333 786 3620 3 chr2A.!!$R1 2834
4 TraesCS2B01G422000 chr6B 653859542 653860333 791 True 937.000000 937 88.265000 1 787 1 chr6B.!!$R2 786

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
441 470 0.034059 CTGCCACCGAAGTCAAGAGT 59.966 55.0 0.00 0.00 0.00 3.24 F
509 539 0.035343 GGGGTCAAGCTCCAAGGTAC 60.035 60.0 0.00 0.00 37.78 3.34 F
1061 1127 1.177256 AGACACCGCGTAAGTCACCT 61.177 55.0 20.04 2.58 41.68 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1747 0.100146 GCGACAACCTAGTACTCCGG 59.900 60.0 0.00 3.92 0.00 5.14 R
1672 1752 0.457337 CGGGTGCGACAACCTAGTAC 60.457 60.0 11.34 0.00 39.46 2.73 R
2753 2847 0.037877 AGTGCAGCAGGAGAAGCAAT 59.962 50.0 0.00 0.00 38.91 3.56 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
119 120 0.247736 GATCTCCCAGCACTTGTCGT 59.752 55.000 0.00 0.00 0.00 4.34
135 136 0.319211 TCGTCGTGGTTTCAAGCGAT 60.319 50.000 0.00 0.00 35.78 4.58
206 207 2.124067 CCGGTGGGTGTTGGTTGT 60.124 61.111 0.00 0.00 0.00 3.32
208 209 0.465824 CCGGTGGGTGTTGGTTGTAA 60.466 55.000 0.00 0.00 0.00 2.41
297 304 2.110627 GCCATCGGATGCAGCTCT 59.889 61.111 12.54 0.00 0.00 4.09
351 380 1.327303 GTTGCATCTCCACCAAACCA 58.673 50.000 0.00 0.00 0.00 3.67
367 396 1.194781 ACCAAGTCTGCAGATCCCGT 61.195 55.000 21.47 11.35 0.00 5.28
430 459 4.410400 GGAACCTCCCTGCCACCG 62.410 72.222 0.00 0.00 0.00 4.94
433 462 2.804828 GAACCTCCCTGCCACCGAAG 62.805 65.000 0.00 0.00 0.00 3.79
434 463 3.322466 CCTCCCTGCCACCGAAGT 61.322 66.667 0.00 0.00 0.00 3.01
436 465 2.525629 TCCCTGCCACCGAAGTCA 60.526 61.111 0.00 0.00 0.00 3.41
439 468 1.371183 CCTGCCACCGAAGTCAAGA 59.629 57.895 0.00 0.00 0.00 3.02
440 469 0.671781 CCTGCCACCGAAGTCAAGAG 60.672 60.000 0.00 0.00 0.00 2.85
441 470 0.034059 CTGCCACCGAAGTCAAGAGT 59.966 55.000 0.00 0.00 0.00 3.24
442 471 0.249868 TGCCACCGAAGTCAAGAGTG 60.250 55.000 0.00 0.00 0.00 3.51
443 472 1.569479 GCCACCGAAGTCAAGAGTGC 61.569 60.000 0.00 0.00 0.00 4.40
444 473 0.249868 CCACCGAAGTCAAGAGTGCA 60.250 55.000 0.00 0.00 0.00 4.57
446 475 1.261619 CACCGAAGTCAAGAGTGCAAC 59.738 52.381 0.00 0.00 0.00 4.17
447 476 0.868406 CCGAAGTCAAGAGTGCAACC 59.132 55.000 0.00 0.00 37.80 3.77
448 477 1.581934 CGAAGTCAAGAGTGCAACCA 58.418 50.000 0.00 0.00 37.80 3.67
449 478 1.528586 CGAAGTCAAGAGTGCAACCAG 59.471 52.381 0.00 0.00 37.80 4.00
450 479 1.876156 GAAGTCAAGAGTGCAACCAGG 59.124 52.381 0.00 0.00 37.80 4.45
451 480 0.109342 AGTCAAGAGTGCAACCAGGG 59.891 55.000 0.00 0.00 37.80 4.45
452 481 0.179018 GTCAAGAGTGCAACCAGGGT 60.179 55.000 0.00 0.00 37.80 4.34
497 527 0.038166 GCCTGAGTCAATGGGGTCAA 59.962 55.000 0.00 0.00 0.00 3.18
509 539 0.035343 GGGGTCAAGCTCCAAGGTAC 60.035 60.000 0.00 0.00 37.78 3.34
554 585 4.845580 CGCGAGGCTGAGGGCATT 62.846 66.667 0.00 0.00 44.01 3.56
601 632 6.725834 GGAAGATCTGGATAGAAGAGGAAGAT 59.274 42.308 0.00 0.00 36.32 2.40
619 650 4.998671 AGATGCGAGAGAAAGAGATGAA 57.001 40.909 0.00 0.00 0.00 2.57
633 664 4.763073 AGAGATGAAATGAGATGCGTCAA 58.237 39.130 8.99 0.00 0.00 3.18
690 737 1.841103 TGAGTGGGCCAGTGCTACA 60.841 57.895 20.91 7.55 37.74 2.74
798 854 4.089361 ACATTTCCCATCTTGAAACCCTC 58.911 43.478 0.00 0.00 34.77 4.30
803 859 1.885887 CCATCTTGAAACCCTCGCAAA 59.114 47.619 0.00 0.00 0.00 3.68
851 907 1.604593 CCAGTGCCCAGGTTTCCAG 60.605 63.158 0.00 0.00 0.00 3.86
948 1008 2.998949 GTCCCATTCCCTCCGCTT 59.001 61.111 0.00 0.00 0.00 4.68
976 1036 3.923864 AGCAGTTCCGCACCGACA 61.924 61.111 0.00 0.00 0.00 4.35
1061 1127 1.177256 AGACACCGCGTAAGTCACCT 61.177 55.000 20.04 2.58 41.68 4.00
1091 1169 3.393970 CCGCCTCCTCTTCCTGCA 61.394 66.667 0.00 0.00 0.00 4.41
1267 1346 1.899437 CGCCTTCCTGTAAGCCCTCA 61.899 60.000 0.00 0.00 33.49 3.86
1292 1371 2.750657 GCCACCTCCCCCAGATCTG 61.751 68.421 16.24 16.24 0.00 2.90
1313 1392 6.286758 TCTGTTCGTCTCCGTACTCTAATAT 58.713 40.000 0.00 0.00 35.64 1.28
1314 1393 6.202379 TCTGTTCGTCTCCGTACTCTAATATG 59.798 42.308 0.00 0.00 35.64 1.78
1318 1397 7.325660 TCGTCTCCGTACTCTAATATGTTTT 57.674 36.000 0.00 0.00 35.01 2.43
1406 1485 2.997897 GGCCGTGAGTCTCCCACT 60.998 66.667 0.00 0.00 38.45 4.00
1434 1513 1.247567 TTGCCAGTTTGCTTCTAGGC 58.752 50.000 0.00 0.00 42.32 3.93
1585 1664 1.275291 TCGGATGAGGTTTGTCTGGTC 59.725 52.381 0.00 0.00 0.00 4.02
1631 1711 1.896660 TGGAAACTTGCTCCGGTGC 60.897 57.895 21.41 21.41 35.55 5.01
1667 1747 5.699839 CCACAACTTGCCAAAATACTACTC 58.300 41.667 0.00 0.00 0.00 2.59
1668 1748 5.335661 CCACAACTTGCCAAAATACTACTCC 60.336 44.000 0.00 0.00 0.00 3.85
1669 1749 4.454504 ACAACTTGCCAAAATACTACTCCG 59.545 41.667 0.00 0.00 0.00 4.63
1670 1750 3.606687 ACTTGCCAAAATACTACTCCGG 58.393 45.455 0.00 0.00 0.00 5.14
1671 1751 3.262405 ACTTGCCAAAATACTACTCCGGA 59.738 43.478 2.93 2.93 0.00 5.14
1672 1752 3.536956 TGCCAAAATACTACTCCGGAG 57.463 47.619 30.11 30.11 0.00 4.63
1673 1753 2.835764 TGCCAAAATACTACTCCGGAGT 59.164 45.455 37.59 37.59 45.02 3.85
1674 1754 4.025360 TGCCAAAATACTACTCCGGAGTA 58.975 43.478 35.93 35.93 42.54 2.59
1675 1755 4.142093 TGCCAAAATACTACTCCGGAGTAC 60.142 45.833 35.34 23.37 42.54 2.73
1676 1756 4.099113 GCCAAAATACTACTCCGGAGTACT 59.901 45.833 35.34 28.24 42.54 2.73
1686 1766 0.100146 CCGGAGTACTAGGTTGTCGC 59.900 60.000 0.00 0.00 0.00 5.19
1690 1770 0.893447 AGTACTAGGTTGTCGCACCC 59.107 55.000 0.00 0.00 37.58 4.61
1695 1775 2.030490 TAGGTTGTCGCACCCGTTGT 62.030 55.000 0.00 0.00 37.58 3.32
1712 1792 9.465985 CACCCGTTGTGTTAAATAACTAATTTT 57.534 29.630 5.05 0.00 40.26 1.82
1750 1830 2.544480 TGATAACACAGCGAGTCTCG 57.456 50.000 18.08 18.08 43.89 4.04
1776 1856 7.360101 GGTTACAATGTCAGTGTGTCAGAATAC 60.360 40.741 15.91 2.00 0.00 1.89
1800 1880 8.327941 ACGGATGATGTTTATATGATCTTTGG 57.672 34.615 0.00 0.00 0.00 3.28
1826 1906 9.840427 GAGTGCTTGTGTAATTAATAATGTTGT 57.160 29.630 0.00 0.00 0.00 3.32
1910 1993 7.592885 TCTATTACCCTTAACTGATAACGCT 57.407 36.000 0.00 0.00 0.00 5.07
1920 2003 3.773860 CTGATAACGCTGTCAGTCTCT 57.226 47.619 4.56 0.00 36.36 3.10
1956 2039 5.806286 TGGCTTTCTAAAATATTTCGCTCG 58.194 37.500 0.10 0.00 0.00 5.03
2028 2111 6.147821 TGTCTTGCTGAGCTGTTTAATAACTC 59.852 38.462 5.83 0.00 35.24 3.01
2029 2112 5.643777 TCTTGCTGAGCTGTTTAATAACTCC 59.356 40.000 5.83 0.00 35.24 3.85
2030 2113 4.905429 TGCTGAGCTGTTTAATAACTCCA 58.095 39.130 5.83 0.00 35.24 3.86
2066 2149 5.928264 GGTGAAGGAAAGATGAATTGTTTGG 59.072 40.000 0.00 0.00 0.00 3.28
2190 2273 1.469703 CGCTGCCATGAATCTTGTGAA 59.530 47.619 0.00 0.00 0.00 3.18
2193 2276 3.691118 GCTGCCATGAATCTTGTGAAGTA 59.309 43.478 0.00 0.00 0.00 2.24
2295 2378 3.259374 CAGCTCCAAGAAGACCAAGACTA 59.741 47.826 0.00 0.00 0.00 2.59
2369 2455 2.294074 GCATCGGTTAAGGTGGCATAA 58.706 47.619 0.00 0.00 0.00 1.90
2436 2522 2.224161 GCTTGTCTTATCGCAGGAGGAT 60.224 50.000 0.00 0.00 0.00 3.24
2502 2588 3.071479 CGTTTGCTGCTTAGGGTTTAGA 58.929 45.455 0.00 0.00 0.00 2.10
2591 2677 0.622136 TGGCATGCTGGAGATGTCTT 59.378 50.000 18.92 0.00 0.00 3.01
2640 2734 3.476552 TGACTGCTTTTCTTTCGTGGAT 58.523 40.909 0.00 0.00 0.00 3.41
2711 2805 1.208052 GATGACTAGCCTGCTGTTGGA 59.792 52.381 0.97 0.00 0.00 3.53
2753 2847 3.558418 GTCTTGTGTTCGCCTTTCACTTA 59.442 43.478 0.00 0.00 33.82 2.24
2754 2848 4.213482 GTCTTGTGTTCGCCTTTCACTTAT 59.787 41.667 0.00 0.00 33.82 1.73
2757 2864 3.234386 GTGTTCGCCTTTCACTTATTGC 58.766 45.455 0.00 0.00 0.00 3.56
2794 2903 2.270047 GCTTGAGTTTTGTGCAGCAAA 58.730 42.857 0.00 9.46 44.52 3.68
2800 2910 6.343226 TGAGTTTTGTGCAGCAAATTTTAC 57.657 33.333 12.95 9.37 45.38 2.01
2830 2940 9.995003 TTATTAAGATTGTGTCCAATTGCTTTT 57.005 25.926 0.00 0.00 41.37 2.27
2853 2963 2.359900 CTCTGTAGTTGACCAATGGCC 58.640 52.381 0.00 0.00 0.00 5.36
2854 2964 1.702401 TCTGTAGTTGACCAATGGCCA 59.298 47.619 8.56 8.56 0.00 5.36
2863 2973 2.575735 TGACCAATGGCCATCTGTTCTA 59.424 45.455 21.08 7.26 0.00 2.10
2864 2974 2.945668 GACCAATGGCCATCTGTTCTAC 59.054 50.000 21.08 3.67 0.00 2.59
2865 2975 2.578021 ACCAATGGCCATCTGTTCTACT 59.422 45.455 21.08 0.00 0.00 2.57
2866 2976 3.209410 CCAATGGCCATCTGTTCTACTC 58.791 50.000 21.08 0.00 0.00 2.59
2867 2977 3.209410 CAATGGCCATCTGTTCTACTCC 58.791 50.000 21.08 0.00 0.00 3.85
2868 2978 1.204146 TGGCCATCTGTTCTACTCCC 58.796 55.000 0.00 0.00 0.00 4.30
2869 2979 1.273838 TGGCCATCTGTTCTACTCCCT 60.274 52.381 0.00 0.00 0.00 4.20
2870 2980 1.414550 GGCCATCTGTTCTACTCCCTC 59.585 57.143 0.00 0.00 0.00 4.30
2871 2981 1.414550 GCCATCTGTTCTACTCCCTCC 59.585 57.143 0.00 0.00 0.00 4.30
2872 2982 1.683917 CCATCTGTTCTACTCCCTCCG 59.316 57.143 0.00 0.00 0.00 4.63
2873 2983 2.379972 CATCTGTTCTACTCCCTCCGT 58.620 52.381 0.00 0.00 0.00 4.69
2874 2984 2.125773 TCTGTTCTACTCCCTCCGTC 57.874 55.000 0.00 0.00 0.00 4.79
2875 2985 1.634459 TCTGTTCTACTCCCTCCGTCT 59.366 52.381 0.00 0.00 0.00 4.18
2876 2986 2.018515 CTGTTCTACTCCCTCCGTCTC 58.981 57.143 0.00 0.00 0.00 3.36
2877 2987 1.353358 TGTTCTACTCCCTCCGTCTCA 59.647 52.381 0.00 0.00 0.00 3.27
2878 2988 2.025226 TGTTCTACTCCCTCCGTCTCAT 60.025 50.000 0.00 0.00 0.00 2.90
2879 2989 3.201487 TGTTCTACTCCCTCCGTCTCATA 59.799 47.826 0.00 0.00 0.00 2.15
2880 2990 4.205587 GTTCTACTCCCTCCGTCTCATAA 58.794 47.826 0.00 0.00 0.00 1.90
2881 2991 4.726035 TCTACTCCCTCCGTCTCATAAT 57.274 45.455 0.00 0.00 0.00 1.28
2882 2992 4.399219 TCTACTCCCTCCGTCTCATAATG 58.601 47.826 0.00 0.00 0.00 1.90
2883 2993 3.033659 ACTCCCTCCGTCTCATAATGT 57.966 47.619 0.00 0.00 0.00 2.71
2884 2994 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
2885 2995 4.543689 ACTCCCTCCGTCTCATAATGTAA 58.456 43.478 0.00 0.00 0.00 2.41
2886 2996 4.585162 ACTCCCTCCGTCTCATAATGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
2887 2997 4.800023 TCCCTCCGTCTCATAATGTAAGA 58.200 43.478 0.00 0.00 0.00 2.10
2888 2998 5.394738 TCCCTCCGTCTCATAATGTAAGAT 58.605 41.667 0.00 0.00 0.00 2.40
2889 2999 5.243954 TCCCTCCGTCTCATAATGTAAGATG 59.756 44.000 0.00 0.00 0.00 2.90
2890 3000 5.011125 CCCTCCGTCTCATAATGTAAGATGT 59.989 44.000 0.00 0.00 0.00 3.06
2891 3001 6.463049 CCCTCCGTCTCATAATGTAAGATGTT 60.463 42.308 0.00 0.00 0.00 2.71
2892 3002 6.986817 CCTCCGTCTCATAATGTAAGATGTTT 59.013 38.462 0.00 0.00 0.00 2.83
2893 3003 7.495934 CCTCCGTCTCATAATGTAAGATGTTTT 59.504 37.037 0.00 0.00 0.00 2.43
2894 3004 8.786826 TCCGTCTCATAATGTAAGATGTTTTT 57.213 30.769 0.00 0.00 0.00 1.94
2939 3049 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2940 3050 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2941 3051 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2942 3052 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2943 3053 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2944 3054 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2945 3055 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2964 3074 4.518970 GGAGTAACATTTTGCAGTCAGGAA 59.481 41.667 0.00 0.00 0.00 3.36
2965 3075 5.438761 AGTAACATTTTGCAGTCAGGAAC 57.561 39.130 0.00 0.00 0.00 3.62
2966 3076 3.354089 AACATTTTGCAGTCAGGAACG 57.646 42.857 0.00 0.00 0.00 3.95
2967 3077 1.608590 ACATTTTGCAGTCAGGAACGG 59.391 47.619 0.00 0.00 0.00 4.44
2969 3079 2.045561 TTTTGCAGTCAGGAACGGAA 57.954 45.000 0.00 0.00 32.22 4.30
2970 3080 1.593196 TTTGCAGTCAGGAACGGAAG 58.407 50.000 0.00 0.00 32.22 3.46
3079 3199 1.382522 CAGCCATGAAGCGTGGTATT 58.617 50.000 7.44 0.00 42.15 1.89
3080 3200 2.560504 CAGCCATGAAGCGTGGTATTA 58.439 47.619 7.44 0.00 42.15 0.98
3081 3201 3.141398 CAGCCATGAAGCGTGGTATTAT 58.859 45.455 7.44 0.00 42.15 1.28
3123 3288 5.475564 ACGTTAAGTTTGCCCATGTATTCTT 59.524 36.000 0.00 0.00 0.00 2.52
3210 3375 2.857592 ATCATTTTAAGGCAGCGCTG 57.142 45.000 32.83 32.83 0.00 5.18
3226 3391 1.529622 CGCTGCATAATGTTCCACACG 60.530 52.381 0.00 0.00 0.00 4.49
3236 3401 2.787567 TTCCACACGCGTGAGGTGA 61.788 57.895 41.24 31.45 46.80 4.02
3237 3402 2.279851 CCACACGCGTGAGGTGAA 60.280 61.111 42.94 0.00 46.80 3.18
3238 3403 2.594962 CCACACGCGTGAGGTGAAC 61.595 63.158 42.94 0.00 46.80 3.18
3239 3404 1.591594 CACACGCGTGAGGTGAACT 60.592 57.895 42.94 17.58 46.80 3.01
3240 3405 1.143183 ACACGCGTGAGGTGAACTT 59.857 52.632 42.94 16.79 38.73 2.66
3241 3406 1.151777 ACACGCGTGAGGTGAACTTG 61.152 55.000 42.94 14.73 38.73 3.16
3242 3407 0.874175 CACGCGTGAGGTGAACTTGA 60.874 55.000 34.93 0.00 37.60 3.02
3243 3408 0.179094 ACGCGTGAGGTGAACTTGAA 60.179 50.000 12.93 0.00 0.00 2.69
3244 3409 0.232303 CGCGTGAGGTGAACTTGAAC 59.768 55.000 0.00 0.00 0.00 3.18
3245 3410 0.586802 GCGTGAGGTGAACTTGAACC 59.413 55.000 0.00 0.00 36.66 3.62
3246 3411 0.859232 CGTGAGGTGAACTTGAACCG 59.141 55.000 0.00 0.00 41.61 4.44
3247 3412 1.226746 GTGAGGTGAACTTGAACCGG 58.773 55.000 0.00 0.00 41.61 5.28
3248 3413 1.124780 TGAGGTGAACTTGAACCGGA 58.875 50.000 9.46 0.00 41.61 5.14
3249 3414 1.487142 TGAGGTGAACTTGAACCGGAA 59.513 47.619 9.46 0.00 41.61 4.30
3250 3415 1.871676 GAGGTGAACTTGAACCGGAAC 59.128 52.381 9.46 1.34 41.61 3.62
3251 3416 1.489230 AGGTGAACTTGAACCGGAACT 59.511 47.619 9.46 0.00 41.61 3.01
3252 3417 2.701951 AGGTGAACTTGAACCGGAACTA 59.298 45.455 9.46 0.00 41.61 2.24
3253 3418 2.804527 GGTGAACTTGAACCGGAACTAC 59.195 50.000 9.46 0.00 0.00 2.73
3254 3419 3.493873 GGTGAACTTGAACCGGAACTACT 60.494 47.826 9.46 0.00 0.00 2.57
3255 3420 4.124970 GTGAACTTGAACCGGAACTACTT 58.875 43.478 9.46 0.00 0.00 2.24
3256 3421 4.025145 GTGAACTTGAACCGGAACTACTTG 60.025 45.833 9.46 0.00 0.00 3.16
3257 3422 4.141892 TGAACTTGAACCGGAACTACTTGA 60.142 41.667 9.46 0.00 0.00 3.02
3258 3423 3.725490 ACTTGAACCGGAACTACTTGAC 58.275 45.455 9.46 0.00 0.00 3.18
3259 3424 2.427232 TGAACCGGAACTACTTGACG 57.573 50.000 9.46 0.00 0.00 4.35
3263 3428 3.011513 CGGAACTACTTGACGGACG 57.988 57.895 0.00 0.00 0.00 4.79
3264 3429 0.518636 CGGAACTACTTGACGGACGA 59.481 55.000 0.00 0.00 0.00 4.20
3265 3430 1.131883 CGGAACTACTTGACGGACGAT 59.868 52.381 0.00 0.00 0.00 3.73
3266 3431 2.415090 CGGAACTACTTGACGGACGATT 60.415 50.000 0.00 0.00 0.00 3.34
3267 3432 3.582780 GGAACTACTTGACGGACGATTT 58.417 45.455 0.00 0.00 0.00 2.17
3268 3433 3.992427 GGAACTACTTGACGGACGATTTT 59.008 43.478 0.00 0.00 0.00 1.82
3269 3434 4.450080 GGAACTACTTGACGGACGATTTTT 59.550 41.667 0.00 0.00 0.00 1.94
3286 3451 1.471964 TTTTGTTGAACGACGCATGC 58.528 45.000 7.91 7.91 0.00 4.06
3287 3452 0.378610 TTTGTTGAACGACGCATGCA 59.621 45.000 19.57 0.00 0.00 3.96
3288 3453 0.316607 TTGTTGAACGACGCATGCAC 60.317 50.000 19.57 10.09 0.00 4.57
3289 3454 1.788203 GTTGAACGACGCATGCACG 60.788 57.895 25.27 25.27 39.50 5.34
3290 3455 1.951631 TTGAACGACGCATGCACGA 60.952 52.632 30.81 13.42 36.70 4.35
3291 3456 1.288419 TTGAACGACGCATGCACGAT 61.288 50.000 30.81 23.10 36.70 3.73
3292 3457 0.456995 TGAACGACGCATGCACGATA 60.457 50.000 30.81 17.77 36.70 2.92
3293 3458 0.227234 GAACGACGCATGCACGATAG 59.773 55.000 30.81 12.78 46.19 2.08
3294 3459 1.752501 AACGACGCATGCACGATAGC 61.753 55.000 30.81 7.94 42.67 2.97
3295 3460 1.946156 CGACGCATGCACGATAGCT 60.946 57.895 23.55 0.00 42.67 3.32
3296 3461 1.561730 GACGCATGCACGATAGCTG 59.438 57.895 19.57 0.00 42.67 4.24
3297 3462 0.871592 GACGCATGCACGATAGCTGA 60.872 55.000 19.57 0.00 42.67 4.26
3298 3463 0.249615 ACGCATGCACGATAGCTGAT 60.250 50.000 19.57 0.00 42.67 2.90
3299 3464 0.437678 CGCATGCACGATAGCTGATC 59.562 55.000 19.57 0.00 42.67 2.92
3300 3465 0.795085 GCATGCACGATAGCTGATCC 59.205 55.000 14.21 0.00 42.67 3.36
3301 3466 1.875157 GCATGCACGATAGCTGATCCA 60.875 52.381 14.21 0.00 42.67 3.41
3302 3467 2.486918 CATGCACGATAGCTGATCCAA 58.513 47.619 0.00 0.00 42.67 3.53
3303 3468 2.229675 TGCACGATAGCTGATCCAAG 57.770 50.000 0.00 0.00 42.67 3.61
3304 3469 0.864455 GCACGATAGCTGATCCAAGC 59.136 55.000 0.00 0.00 43.88 4.01
3310 3475 3.724494 GCTGATCCAAGCGCCTAC 58.276 61.111 2.29 0.00 32.56 3.18
3311 3476 2.240500 GCTGATCCAAGCGCCTACG 61.241 63.158 2.29 0.00 44.07 3.51
3312 3477 1.592669 CTGATCCAAGCGCCTACGG 60.593 63.158 2.29 0.00 40.57 4.02
3313 3478 2.967615 GATCCAAGCGCCTACGGC 60.968 66.667 2.29 0.00 46.75 5.68
3322 3487 2.202810 GCCTACGGCTGCTCAGAC 60.203 66.667 0.00 0.00 46.69 3.51
3323 3488 2.716017 GCCTACGGCTGCTCAGACT 61.716 63.158 0.00 0.00 46.69 3.24
3324 3489 1.893786 CCTACGGCTGCTCAGACTT 59.106 57.895 0.00 0.00 33.16 3.01
3325 3490 0.459237 CCTACGGCTGCTCAGACTTG 60.459 60.000 0.00 0.00 33.16 3.16
3326 3491 1.079819 TACGGCTGCTCAGACTTGC 60.080 57.895 0.00 0.00 33.16 4.01
3327 3492 2.507110 TACGGCTGCTCAGACTTGCC 62.507 60.000 0.00 0.00 40.14 4.52
3328 3493 2.033141 GGCTGCTCAGACTTGCCA 59.967 61.111 0.00 0.00 42.79 4.92
3329 3494 2.039405 GGCTGCTCAGACTTGCCAG 61.039 63.158 0.00 0.00 42.79 4.85
3330 3495 1.302351 GCTGCTCAGACTTGCCAGT 60.302 57.895 0.29 0.00 35.17 4.00
3331 3496 1.575576 GCTGCTCAGACTTGCCAGTG 61.576 60.000 0.00 0.00 31.22 3.66
3332 3497 0.954449 CTGCTCAGACTTGCCAGTGG 60.954 60.000 4.20 4.20 31.22 4.00
3333 3498 1.372683 GCTCAGACTTGCCAGTGGA 59.627 57.895 15.20 0.00 31.22 4.02
3334 3499 0.035630 GCTCAGACTTGCCAGTGGAT 60.036 55.000 15.20 0.00 31.22 3.41
3335 3500 1.735386 CTCAGACTTGCCAGTGGATG 58.265 55.000 15.20 4.05 31.22 3.51
3346 3511 1.203052 CCAGTGGATGGTTTGTGATGC 59.797 52.381 1.68 0.00 44.91 3.91
3347 3512 1.887854 CAGTGGATGGTTTGTGATGCA 59.112 47.619 0.00 0.00 0.00 3.96
3348 3513 2.094906 CAGTGGATGGTTTGTGATGCAG 60.095 50.000 0.00 0.00 0.00 4.41
3349 3514 1.888512 GTGGATGGTTTGTGATGCAGT 59.111 47.619 0.00 0.00 0.00 4.40
3350 3515 1.887854 TGGATGGTTTGTGATGCAGTG 59.112 47.619 0.00 0.00 0.00 3.66
3351 3516 1.888512 GGATGGTTTGTGATGCAGTGT 59.111 47.619 0.00 0.00 0.00 3.55
3352 3517 2.095059 GGATGGTTTGTGATGCAGTGTC 60.095 50.000 0.00 0.00 0.00 3.67
3353 3518 0.943673 TGGTTTGTGATGCAGTGTCG 59.056 50.000 0.00 0.00 0.00 4.35
3354 3519 0.944386 GGTTTGTGATGCAGTGTCGT 59.056 50.000 0.00 0.00 0.00 4.34
3355 3520 1.334059 GGTTTGTGATGCAGTGTCGTG 60.334 52.381 0.00 0.00 0.00 4.35
3356 3521 0.307453 TTTGTGATGCAGTGTCGTGC 59.693 50.000 0.00 0.00 44.27 5.34
3362 3527 3.640000 GCAGTGTCGTGCAAGCGT 61.640 61.111 0.00 0.00 43.41 5.07
3363 3528 2.546321 CAGTGTCGTGCAAGCGTC 59.454 61.111 0.00 0.00 0.00 5.19
3364 3529 3.030308 AGTGTCGTGCAAGCGTCG 61.030 61.111 0.00 0.00 0.00 5.12
3365 3530 3.327754 GTGTCGTGCAAGCGTCGT 61.328 61.111 0.00 0.00 0.00 4.34
3366 3531 3.326981 TGTCGTGCAAGCGTCGTG 61.327 61.111 0.00 0.00 0.00 4.35
3367 3532 3.327754 GTCGTGCAAGCGTCGTGT 61.328 61.111 0.00 0.00 0.00 4.49
3368 3533 3.326981 TCGTGCAAGCGTCGTGTG 61.327 61.111 0.00 0.00 0.00 3.82
3369 3534 3.626244 CGTGCAAGCGTCGTGTGT 61.626 61.111 0.00 0.00 0.00 3.72
3370 3535 2.053116 GTGCAAGCGTCGTGTGTG 60.053 61.111 0.00 0.00 0.00 3.82
3371 3536 2.510464 TGCAAGCGTCGTGTGTGT 60.510 55.556 0.00 0.00 0.00 3.72
3372 3537 1.227002 TGCAAGCGTCGTGTGTGTA 60.227 52.632 0.00 0.00 0.00 2.90
3373 3538 1.212455 TGCAAGCGTCGTGTGTGTAG 61.212 55.000 0.00 0.00 0.00 2.74
3374 3539 1.487231 CAAGCGTCGTGTGTGTAGC 59.513 57.895 0.00 0.00 0.00 3.58
3375 3540 1.066752 AAGCGTCGTGTGTGTAGCA 59.933 52.632 0.00 0.00 0.00 3.49
3396 3561 1.610038 CTGCTCAACTTGAACATGGCA 59.390 47.619 0.00 0.00 0.00 4.92
3419 3584 3.857157 AACCTGTCAAGAACCTTAGCA 57.143 42.857 0.00 0.00 0.00 3.49
3458 3623 5.946377 TGAAGAAGACTATCTACAGCTGACA 59.054 40.000 23.35 6.67 0.00 3.58
3540 3708 3.705043 AAAGCAACTGCATATAGCTGC 57.295 42.857 4.22 0.00 45.14 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 3.249799 GCAGCCCCAATTTTTGTTACAAC 59.750 43.478 0.00 0.00 0.00 3.32
119 120 0.320374 AGGATCGCTTGAAACCACGA 59.680 50.000 0.00 0.00 39.11 4.35
162 163 1.335810 AGACAACGACGACAAGTGCTA 59.664 47.619 0.00 0.00 0.00 3.49
199 200 1.671845 GGCGACAAGTGTTACAACCAA 59.328 47.619 0.00 0.00 0.00 3.67
206 207 2.623878 TTTGGAGGCGACAAGTGTTA 57.376 45.000 0.00 0.00 0.00 2.41
208 209 1.072331 AGATTTGGAGGCGACAAGTGT 59.928 47.619 0.00 0.00 0.00 3.55
261 268 3.699894 CTGCCTGGTGCTCGGACT 61.700 66.667 0.00 0.00 42.00 3.85
297 304 2.437002 GCAACCGGCCGTGGATTA 60.437 61.111 26.12 0.00 36.11 1.75
351 380 1.513158 CGACGGGATCTGCAGACTT 59.487 57.895 20.97 3.44 0.00 3.01
390 419 0.321653 GGCTGTTCTGTCCAATCCGT 60.322 55.000 0.00 0.00 0.00 4.69
428 457 0.868406 GGTTGCACTCTTGACTTCGG 59.132 55.000 0.00 0.00 0.00 4.30
430 459 1.876156 CCTGGTTGCACTCTTGACTTC 59.124 52.381 0.00 0.00 0.00 3.01
433 462 0.179018 ACCCTGGTTGCACTCTTGAC 60.179 55.000 0.00 0.00 0.00 3.18
434 463 0.108585 GACCCTGGTTGCACTCTTGA 59.891 55.000 0.00 0.00 0.00 3.02
436 465 1.352622 TGGACCCTGGTTGCACTCTT 61.353 55.000 0.00 0.00 0.00 2.85
439 468 2.833913 CCTGGACCCTGGTTGCACT 61.834 63.158 4.02 0.00 0.00 4.40
440 469 2.282462 CCTGGACCCTGGTTGCAC 60.282 66.667 4.02 0.00 0.00 4.57
441 470 3.579302 CCCTGGACCCTGGTTGCA 61.579 66.667 10.50 0.00 33.83 4.08
442 471 3.580319 ACCCTGGACCCTGGTTGC 61.580 66.667 10.50 0.00 33.83 4.17
443 472 2.436109 CACCCTGGACCCTGGTTG 59.564 66.667 10.50 3.54 33.83 3.77
444 473 3.580319 GCACCCTGGACCCTGGTT 61.580 66.667 10.50 0.00 33.83 3.67
446 475 4.039092 CTGCACCCTGGACCCTGG 62.039 72.222 0.00 5.11 35.20 4.45
447 476 4.729918 GCTGCACCCTGGACCCTG 62.730 72.222 0.00 0.00 0.00 4.45
474 503 2.110967 CCCATTGACTCAGGCAGCG 61.111 63.158 0.00 0.00 0.00 5.18
487 516 0.040204 CCTTGGAGCTTGACCCCATT 59.960 55.000 0.00 0.00 0.00 3.16
497 527 1.258445 CCCGTCTGTACCTTGGAGCT 61.258 60.000 0.00 0.00 0.00 4.09
571 602 2.155279 TCTATCCAGATCTTCCTCGCG 58.845 52.381 0.00 0.00 0.00 5.87
601 632 5.077134 TCATTTCATCTCTTTCTCTCGCA 57.923 39.130 0.00 0.00 0.00 5.10
619 650 0.035152 TGCCCTTGACGCATCTCATT 60.035 50.000 0.00 0.00 0.00 2.57
643 674 2.656085 CAGCTACCTTATCTCTTCGCG 58.344 52.381 0.00 0.00 0.00 5.87
690 737 2.215451 ATCGCCCCTGCTTGTTCCAT 62.215 55.000 0.00 0.00 34.43 3.41
771 827 6.239458 GGGTTTCAAGATGGGAAATGTTTGTA 60.239 38.462 0.00 0.00 36.71 2.41
811 867 1.079057 GAGAGAAACTGGACCGGCC 60.079 63.158 0.00 4.32 37.10 6.13
851 907 1.590525 TGGTATCGGTTGCGATCGC 60.591 57.895 32.48 32.48 42.35 4.58
948 1008 3.240134 GAACTGCTGCGGACTGGGA 62.240 63.158 16.72 0.00 0.00 4.37
976 1036 1.852626 CTTTGGGGAGGGTGAGGGT 60.853 63.158 0.00 0.00 0.00 4.34
1091 1169 2.579410 AAGCCATGAACGTTAACCCT 57.421 45.000 0.00 0.00 0.00 4.34
1277 1356 0.978146 CGAACAGATCTGGGGGAGGT 60.978 60.000 26.08 0.53 34.19 3.85
1313 1392 0.248702 GCCGCCGAAGTTTCAAAACA 60.249 50.000 8.23 0.00 41.30 2.83
1314 1393 0.248702 TGCCGCCGAAGTTTCAAAAC 60.249 50.000 0.00 0.00 39.17 2.43
1318 1397 2.668212 CCTGCCGCCGAAGTTTCA 60.668 61.111 0.00 0.00 0.00 2.69
1406 1485 3.290710 AGCAAACTGGCAAAAGAGAAGA 58.709 40.909 0.00 0.00 35.83 2.87
1412 1491 3.858503 GCCTAGAAGCAAACTGGCAAAAG 60.859 47.826 0.00 0.00 40.04 2.27
1413 1492 2.035832 GCCTAGAAGCAAACTGGCAAAA 59.964 45.455 0.00 0.00 40.04 2.44
1414 1493 1.613437 GCCTAGAAGCAAACTGGCAAA 59.387 47.619 0.00 0.00 40.04 3.68
1415 1494 1.202927 AGCCTAGAAGCAAACTGGCAA 60.203 47.619 11.51 0.00 42.46 4.52
1434 1513 5.759763 AGATGCAAAACCCTAAAAGCAAAAG 59.240 36.000 0.00 0.00 35.45 2.27
1513 1592 4.090090 TGGTGACCTAAAAGGAGAGAGAG 58.910 47.826 2.11 0.00 37.67 3.20
1515 1594 4.323104 CCTTGGTGACCTAAAAGGAGAGAG 60.323 50.000 12.57 0.00 41.49 3.20
1631 1711 2.706890 AGTTGTGGCAAGTATAACGGG 58.293 47.619 0.00 0.00 0.00 5.28
1667 1747 0.100146 GCGACAACCTAGTACTCCGG 59.900 60.000 0.00 3.92 0.00 5.14
1668 1748 0.806868 TGCGACAACCTAGTACTCCG 59.193 55.000 0.00 0.00 0.00 4.63
1669 1749 1.135170 GGTGCGACAACCTAGTACTCC 60.135 57.143 0.00 0.00 37.24 3.85
1670 1750 1.135170 GGGTGCGACAACCTAGTACTC 60.135 57.143 0.00 0.00 38.38 2.59
1671 1751 0.893447 GGGTGCGACAACCTAGTACT 59.107 55.000 0.00 0.00 38.38 2.73
1672 1752 0.457337 CGGGTGCGACAACCTAGTAC 60.457 60.000 11.34 0.00 39.46 2.73
1673 1753 0.895100 ACGGGTGCGACAACCTAGTA 60.895 55.000 11.34 0.00 39.46 1.82
1674 1754 1.751349 AACGGGTGCGACAACCTAGT 61.751 55.000 11.34 5.61 39.46 2.57
1675 1755 1.005394 AACGGGTGCGACAACCTAG 60.005 57.895 11.34 5.11 39.46 3.02
1676 1756 1.301087 CAACGGGTGCGACAACCTA 60.301 57.895 11.34 0.00 39.46 3.08
1686 1766 9.465985 AAAATTAGTTATTTAACACAACGGGTG 57.534 29.630 7.80 7.80 43.18 4.61
1702 1782 4.456566 GGGCAACGGACTGAAAATTAGTTA 59.543 41.667 0.00 0.00 37.60 2.24
1712 1792 1.488705 ATCTTGGGGCAACGGACTGA 61.489 55.000 0.00 0.00 37.60 3.41
1750 1830 4.377021 TCTGACACACTGACATTGTAACC 58.623 43.478 0.00 0.00 0.00 2.85
1776 1856 8.552083 TCCAAAGATCATATAAACATCATCCG 57.448 34.615 0.00 0.00 0.00 4.18
1800 1880 9.840427 ACAACATTATTAATTACACAAGCACTC 57.160 29.630 0.00 0.00 0.00 3.51
1910 1993 5.985530 CAGAACATTGTAACAGAGACTGACA 59.014 40.000 5.76 0.00 35.18 3.58
1920 2003 7.575414 TTTAGAAAGCCAGAACATTGTAACA 57.425 32.000 0.00 0.00 0.00 2.41
1956 2039 2.228103 CCGTTTTCCCTTTGCTAACCTC 59.772 50.000 0.00 0.00 0.00 3.85
2028 2111 1.002468 CTTCACCAAACAGACGCTTGG 60.002 52.381 0.00 0.00 46.36 3.61
2029 2112 1.002468 CCTTCACCAAACAGACGCTTG 60.002 52.381 0.00 0.00 0.00 4.01
2030 2113 1.134220 TCCTTCACCAAACAGACGCTT 60.134 47.619 0.00 0.00 0.00 4.68
2066 2149 3.066760 GGCATGCATTAACCAGTTAGGAC 59.933 47.826 21.36 0.00 41.22 3.85
2190 2273 8.682936 AATGCATAGCAGTATAAGCTTTTACT 57.317 30.769 20.04 20.04 43.65 2.24
2193 2276 9.956720 CTTAAATGCATAGCAGTATAAGCTTTT 57.043 29.630 3.20 0.00 43.65 2.27
2286 2369 0.956633 TCGTCAGCGTTAGTCTTGGT 59.043 50.000 0.00 0.00 39.49 3.67
2295 2378 1.068741 AGAACCTTCTTCGTCAGCGTT 59.931 47.619 0.00 0.00 39.49 4.84
2369 2455 4.546829 AAATTCCATCAGCACTGCAATT 57.453 36.364 3.30 0.00 0.00 2.32
2416 2502 3.068732 TCATCCTCCTGCGATAAGACAAG 59.931 47.826 0.00 0.00 0.00 3.16
2436 2522 7.162973 TCCCTCATCTACTATTTACTCCTCA 57.837 40.000 0.00 0.00 0.00 3.86
2502 2588 0.815213 CCGGACATCGACATGGCAAT 60.815 55.000 0.00 0.00 40.32 3.56
2591 2677 7.118535 GGGTTTTAAGCTTTTCTTGTCAAACAA 59.881 33.333 3.20 0.00 35.00 2.83
2753 2847 0.037877 AGTGCAGCAGGAGAAGCAAT 59.962 50.000 0.00 0.00 38.91 3.56
2754 2848 0.179009 AAGTGCAGCAGGAGAAGCAA 60.179 50.000 0.00 0.00 38.91 3.91
2757 2864 0.605860 AGCAAGTGCAGCAGGAGAAG 60.606 55.000 6.00 0.00 45.16 2.85
2818 2928 5.385198 ACTACAGAGGAAAAAGCAATTGGA 58.615 37.500 7.72 0.00 0.00 3.53
2830 2940 3.559171 GCCATTGGTCAACTACAGAGGAA 60.559 47.826 4.26 0.00 0.00 3.36
2853 2963 2.359531 GACGGAGGGAGTAGAACAGATG 59.640 54.545 0.00 0.00 0.00 2.90
2854 2964 2.242708 AGACGGAGGGAGTAGAACAGAT 59.757 50.000 0.00 0.00 0.00 2.90
2863 2973 3.033659 ACATTATGAGACGGAGGGAGT 57.966 47.619 0.00 0.00 0.00 3.85
2864 2974 4.827835 TCTTACATTATGAGACGGAGGGAG 59.172 45.833 0.00 0.00 0.00 4.30
2865 2975 4.800023 TCTTACATTATGAGACGGAGGGA 58.200 43.478 0.00 0.00 0.00 4.20
2866 2976 5.011125 ACATCTTACATTATGAGACGGAGGG 59.989 44.000 0.00 0.00 0.00 4.30
2867 2977 6.090483 ACATCTTACATTATGAGACGGAGG 57.910 41.667 0.00 0.00 0.00 4.30
2868 2978 8.425577 AAAACATCTTACATTATGAGACGGAG 57.574 34.615 0.00 0.00 0.00 4.63
2869 2979 8.786826 AAAAACATCTTACATTATGAGACGGA 57.213 30.769 0.00 0.00 0.00 4.69
2914 3024 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2915 3025 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2916 3026 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2917 3027 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2918 3028 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2920 3030 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2921 3031 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2922 3032 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2923 3033 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2924 3034 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2925 3035 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2926 3036 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2927 3037 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
2928 3038 2.292389 TGTTACTCCCTCCGTCCCATAA 60.292 50.000 0.00 0.00 0.00 1.90
2929 3039 1.288633 TGTTACTCCCTCCGTCCCATA 59.711 52.381 0.00 0.00 0.00 2.74
2930 3040 0.042131 TGTTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00
2931 3041 0.042131 ATGTTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
2932 3042 1.201424 AATGTTACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
2933 3043 3.007635 CAAAATGTTACTCCCTCCGTCC 58.992 50.000 0.00 0.00 0.00 4.79
2934 3044 2.418976 GCAAAATGTTACTCCCTCCGTC 59.581 50.000 0.00 0.00 0.00 4.79
2935 3045 2.224670 TGCAAAATGTTACTCCCTCCGT 60.225 45.455 0.00 0.00 0.00 4.69
2936 3046 2.420022 CTGCAAAATGTTACTCCCTCCG 59.580 50.000 0.00 0.00 0.00 4.63
2937 3047 3.421844 ACTGCAAAATGTTACTCCCTCC 58.578 45.455 0.00 0.00 0.00 4.30
2938 3048 4.072131 TGACTGCAAAATGTTACTCCCTC 58.928 43.478 0.00 0.00 0.00 4.30
2939 3049 4.074970 CTGACTGCAAAATGTTACTCCCT 58.925 43.478 0.00 0.00 0.00 4.20
2940 3050 3.191371 CCTGACTGCAAAATGTTACTCCC 59.809 47.826 0.00 0.00 0.00 4.30
2941 3051 4.072131 TCCTGACTGCAAAATGTTACTCC 58.928 43.478 0.00 0.00 0.00 3.85
2942 3052 5.452777 GTTCCTGACTGCAAAATGTTACTC 58.547 41.667 0.00 0.00 0.00 2.59
2943 3053 4.024048 CGTTCCTGACTGCAAAATGTTACT 60.024 41.667 0.00 0.00 0.00 2.24
2944 3054 4.219033 CGTTCCTGACTGCAAAATGTTAC 58.781 43.478 0.00 0.00 0.00 2.50
2945 3055 3.252215 CCGTTCCTGACTGCAAAATGTTA 59.748 43.478 0.00 0.00 0.00 2.41
2982 3095 9.751542 ATCGATTTTTACATCCTGTCTAAGTAG 57.248 33.333 0.00 0.00 0.00 2.57
2988 3101 4.576463 GGCATCGATTTTTACATCCTGTCT 59.424 41.667 0.00 0.00 0.00 3.41
3011 3124 4.712425 GCGGCAAGCCAGCAACTG 62.712 66.667 18.31 0.34 40.81 3.16
3079 3199 7.905604 AACGTGTTTGAATCTGATGAAGATA 57.094 32.000 0.00 0.00 45.37 1.98
3081 3201 7.441157 ACTTAACGTGTTTGAATCTGATGAAGA 59.559 33.333 0.00 0.00 39.94 2.87
3123 3288 4.933505 TCACTGCACAAATTTGGATTGA 57.066 36.364 21.74 12.92 0.00 2.57
3204 3369 0.734889 GTGGAACATTATGCAGCGCT 59.265 50.000 2.64 2.64 44.52 5.92
3226 3391 0.586802 GGTTCAAGTTCACCTCACGC 59.413 55.000 0.00 0.00 0.00 5.34
3236 3401 4.124970 GTCAAGTAGTTCCGGTTCAAGTT 58.875 43.478 0.00 0.00 0.00 2.66
3237 3402 3.725490 GTCAAGTAGTTCCGGTTCAAGT 58.275 45.455 0.00 0.00 0.00 3.16
3238 3403 2.729882 CGTCAAGTAGTTCCGGTTCAAG 59.270 50.000 0.00 0.00 0.00 3.02
3239 3404 2.546373 CCGTCAAGTAGTTCCGGTTCAA 60.546 50.000 0.00 0.00 34.10 2.69
3240 3405 1.000060 CCGTCAAGTAGTTCCGGTTCA 60.000 52.381 0.00 0.00 34.10 3.18
3241 3406 1.270550 TCCGTCAAGTAGTTCCGGTTC 59.729 52.381 14.49 0.00 39.62 3.62
3242 3407 1.000171 GTCCGTCAAGTAGTTCCGGTT 60.000 52.381 14.49 0.00 39.62 4.44
3243 3408 0.600057 GTCCGTCAAGTAGTTCCGGT 59.400 55.000 14.49 0.00 39.62 5.28
3244 3409 0.455633 CGTCCGTCAAGTAGTTCCGG 60.456 60.000 10.41 10.41 39.98 5.14
3245 3410 0.518636 TCGTCCGTCAAGTAGTTCCG 59.481 55.000 0.00 0.00 0.00 4.30
3246 3411 2.935481 ATCGTCCGTCAAGTAGTTCC 57.065 50.000 0.00 0.00 0.00 3.62
3247 3412 5.587033 AAAAATCGTCCGTCAAGTAGTTC 57.413 39.130 0.00 0.00 0.00 3.01
3266 3431 1.849219 GCATGCGTCGTTCAACAAAAA 59.151 42.857 0.00 0.00 0.00 1.94
3267 3432 1.202188 TGCATGCGTCGTTCAACAAAA 60.202 42.857 14.09 0.00 0.00 2.44
3268 3433 0.378610 TGCATGCGTCGTTCAACAAA 59.621 45.000 14.09 0.00 0.00 2.83
3269 3434 0.316607 GTGCATGCGTCGTTCAACAA 60.317 50.000 14.09 0.00 0.00 2.83
3270 3435 1.278337 GTGCATGCGTCGTTCAACA 59.722 52.632 14.09 0.00 0.00 3.33
3271 3436 1.788203 CGTGCATGCGTCGTTCAAC 60.788 57.895 21.32 8.34 0.00 3.18
3272 3437 1.288419 ATCGTGCATGCGTCGTTCAA 61.288 50.000 25.87 13.23 0.00 2.69
3273 3438 0.456995 TATCGTGCATGCGTCGTTCA 60.457 50.000 25.87 13.51 0.00 3.18
3274 3439 0.227234 CTATCGTGCATGCGTCGTTC 59.773 55.000 25.87 8.29 0.00 3.95
3275 3440 1.752501 GCTATCGTGCATGCGTCGTT 61.753 55.000 25.87 21.72 0.00 3.85
3276 3441 2.230940 GCTATCGTGCATGCGTCGT 61.231 57.895 25.87 18.38 0.00 4.34
3277 3442 1.946156 AGCTATCGTGCATGCGTCG 60.946 57.895 22.86 22.86 34.99 5.12
3278 3443 0.871592 TCAGCTATCGTGCATGCGTC 60.872 55.000 14.09 7.90 34.99 5.19
3279 3444 0.249615 ATCAGCTATCGTGCATGCGT 60.250 50.000 14.09 1.48 34.99 5.24
3280 3445 0.437678 GATCAGCTATCGTGCATGCG 59.562 55.000 14.09 0.00 34.99 4.73
3281 3446 0.795085 GGATCAGCTATCGTGCATGC 59.205 55.000 11.82 11.82 35.21 4.06
3282 3447 2.159327 TGGATCAGCTATCGTGCATG 57.841 50.000 0.00 0.00 35.21 4.06
3283 3448 2.763933 CTTGGATCAGCTATCGTGCAT 58.236 47.619 0.00 0.00 35.21 3.96
3284 3449 1.807755 GCTTGGATCAGCTATCGTGCA 60.808 52.381 0.00 0.00 36.79 4.57
3285 3450 0.864455 GCTTGGATCAGCTATCGTGC 59.136 55.000 0.00 0.00 36.79 5.34
3286 3451 1.135046 CGCTTGGATCAGCTATCGTG 58.865 55.000 3.79 0.00 37.68 4.35
3287 3452 0.598680 GCGCTTGGATCAGCTATCGT 60.599 55.000 0.00 0.00 37.68 3.73
3288 3453 1.287730 GGCGCTTGGATCAGCTATCG 61.288 60.000 7.64 0.00 37.68 2.92
3289 3454 0.034616 AGGCGCTTGGATCAGCTATC 59.965 55.000 7.64 0.00 37.68 2.08
3290 3455 1.001406 GTAGGCGCTTGGATCAGCTAT 59.999 52.381 7.64 0.00 37.68 2.97
3291 3456 0.389391 GTAGGCGCTTGGATCAGCTA 59.611 55.000 7.64 0.00 37.68 3.32
3292 3457 1.144936 GTAGGCGCTTGGATCAGCT 59.855 57.895 7.64 0.00 37.68 4.24
3293 3458 2.240500 CGTAGGCGCTTGGATCAGC 61.241 63.158 7.64 0.00 36.33 4.26
3294 3459 1.592669 CCGTAGGCGCTTGGATCAG 60.593 63.158 7.64 0.00 46.14 2.90
3295 3460 2.499205 CCGTAGGCGCTTGGATCA 59.501 61.111 7.64 0.00 46.14 2.92
3307 3472 1.080995 GCAAGTCTGAGCAGCCGTAG 61.081 60.000 0.00 0.00 0.00 3.51
3308 3473 1.079819 GCAAGTCTGAGCAGCCGTA 60.080 57.895 0.00 0.00 0.00 4.02
3309 3474 2.358003 GCAAGTCTGAGCAGCCGT 60.358 61.111 0.00 0.00 0.00 5.68
3310 3475 3.123620 GGCAAGTCTGAGCAGCCG 61.124 66.667 0.00 0.00 35.42 5.52
3311 3476 2.033141 TGGCAAGTCTGAGCAGCC 59.967 61.111 7.11 7.11 45.41 4.85
3312 3477 1.302351 ACTGGCAAGTCTGAGCAGC 60.302 57.895 0.00 0.00 26.77 5.25
3313 3478 0.954449 CCACTGGCAAGTCTGAGCAG 60.954 60.000 0.00 0.00 32.98 4.24
3314 3479 1.071987 CCACTGGCAAGTCTGAGCA 59.928 57.895 0.00 0.00 32.98 4.26
3315 3480 0.035630 ATCCACTGGCAAGTCTGAGC 60.036 55.000 0.00 0.00 32.98 4.26
3316 3481 1.678123 CCATCCACTGGCAAGTCTGAG 60.678 57.143 0.00 0.00 38.47 3.35
3317 3482 0.325933 CCATCCACTGGCAAGTCTGA 59.674 55.000 0.00 0.00 38.47 3.27
3318 3483 2.864114 CCATCCACTGGCAAGTCTG 58.136 57.895 0.00 0.00 38.47 3.51
3327 3492 1.887854 TGCATCACAAACCATCCACTG 59.112 47.619 0.00 0.00 0.00 3.66
3328 3493 2.165167 CTGCATCACAAACCATCCACT 58.835 47.619 0.00 0.00 0.00 4.00
3329 3494 1.888512 ACTGCATCACAAACCATCCAC 59.111 47.619 0.00 0.00 0.00 4.02
3330 3495 1.887854 CACTGCATCACAAACCATCCA 59.112 47.619 0.00 0.00 0.00 3.41
3331 3496 1.888512 ACACTGCATCACAAACCATCC 59.111 47.619 0.00 0.00 0.00 3.51
3332 3497 2.413239 CGACACTGCATCACAAACCATC 60.413 50.000 0.00 0.00 0.00 3.51
3333 3498 1.536766 CGACACTGCATCACAAACCAT 59.463 47.619 0.00 0.00 0.00 3.55
3334 3499 0.943673 CGACACTGCATCACAAACCA 59.056 50.000 0.00 0.00 0.00 3.67
3335 3500 0.944386 ACGACACTGCATCACAAACC 59.056 50.000 0.00 0.00 0.00 3.27
3336 3501 1.921573 GCACGACACTGCATCACAAAC 60.922 52.381 0.00 0.00 37.11 2.93
3337 3502 0.307453 GCACGACACTGCATCACAAA 59.693 50.000 0.00 0.00 37.11 2.83
3338 3503 0.813210 TGCACGACACTGCATCACAA 60.813 50.000 0.00 0.00 42.36 3.33
3339 3504 0.813210 TTGCACGACACTGCATCACA 60.813 50.000 0.00 0.00 46.47 3.58
3340 3505 0.110509 CTTGCACGACACTGCATCAC 60.111 55.000 0.00 0.00 46.47 3.06
3341 3506 1.844771 GCTTGCACGACACTGCATCA 61.845 55.000 0.00 0.00 46.47 3.07
3342 3507 1.154338 GCTTGCACGACACTGCATC 60.154 57.895 0.00 0.00 46.47 3.91
3343 3508 2.949106 GCTTGCACGACACTGCAT 59.051 55.556 0.00 0.00 46.47 3.96
3344 3509 3.639008 CGCTTGCACGACACTGCA 61.639 61.111 0.00 0.00 45.59 4.41
3345 3510 3.564342 GACGCTTGCACGACACTGC 62.564 63.158 3.48 0.00 37.70 4.40
3346 3511 2.546321 GACGCTTGCACGACACTG 59.454 61.111 3.48 0.00 36.70 3.66
3347 3512 3.030308 CGACGCTTGCACGACACT 61.030 61.111 3.48 0.00 36.70 3.55
3348 3513 3.327754 ACGACGCTTGCACGACAC 61.328 61.111 3.48 0.00 36.70 3.67
3349 3514 3.326981 CACGACGCTTGCACGACA 61.327 61.111 3.48 0.00 36.70 4.35
3350 3515 3.327754 ACACGACGCTTGCACGAC 61.328 61.111 3.48 0.00 36.70 4.34
3351 3516 3.326981 CACACGACGCTTGCACGA 61.327 61.111 3.48 0.00 36.70 4.35
3352 3517 3.626244 ACACACGACGCTTGCACG 61.626 61.111 0.00 0.00 39.50 5.34
3353 3518 1.484227 TACACACACGACGCTTGCAC 61.484 55.000 0.00 0.00 0.00 4.57
3354 3519 1.212455 CTACACACACGACGCTTGCA 61.212 55.000 0.00 0.00 0.00 4.08
3355 3520 1.487231 CTACACACACGACGCTTGC 59.513 57.895 0.00 0.00 0.00 4.01
3356 3521 1.212455 TGCTACACACACGACGCTTG 61.212 55.000 0.00 0.00 0.00 4.01
3357 3522 1.066752 TGCTACACACACGACGCTT 59.933 52.632 0.00 0.00 0.00 4.68
3358 3523 2.725641 TGCTACACACACGACGCT 59.274 55.556 0.00 0.00 0.00 5.07
3367 3532 2.158971 TCAAGTTGAGCAGTGCTACACA 60.159 45.455 19.77 9.45 39.88 3.72
3368 3533 2.483876 TCAAGTTGAGCAGTGCTACAC 58.516 47.619 19.77 17.18 39.88 2.90
3369 3534 2.872245 GTTCAAGTTGAGCAGTGCTACA 59.128 45.455 19.77 14.84 39.88 2.74
3370 3535 2.872245 TGTTCAAGTTGAGCAGTGCTAC 59.128 45.455 19.77 14.00 39.88 3.58
3371 3536 3.192541 TGTTCAAGTTGAGCAGTGCTA 57.807 42.857 19.77 0.00 39.88 3.49
3372 3537 2.042686 TGTTCAAGTTGAGCAGTGCT 57.957 45.000 19.86 19.86 43.88 4.40
3373 3538 2.606308 CCATGTTCAAGTTGAGCAGTGC 60.606 50.000 23.98 7.13 40.81 4.40
3374 3539 2.606308 GCCATGTTCAAGTTGAGCAGTG 60.606 50.000 23.98 20.10 40.81 3.66
3375 3540 1.610522 GCCATGTTCAAGTTGAGCAGT 59.389 47.619 23.98 11.98 40.81 4.40
3376 3541 1.610038 TGCCATGTTCAAGTTGAGCAG 59.390 47.619 23.98 14.41 40.81 4.24
3377 3542 1.610038 CTGCCATGTTCAAGTTGAGCA 59.390 47.619 22.46 22.46 41.68 4.26
3378 3543 1.610522 ACTGCCATGTTCAAGTTGAGC 59.389 47.619 12.39 12.39 0.00 4.26
3379 3544 4.320494 GGTTACTGCCATGTTCAAGTTGAG 60.320 45.833 5.56 0.00 0.00 3.02
3380 3545 3.568007 GGTTACTGCCATGTTCAAGTTGA 59.432 43.478 0.08 0.08 0.00 3.18
3381 3546 3.569701 AGGTTACTGCCATGTTCAAGTTG 59.430 43.478 0.00 0.00 0.00 3.16
3396 3561 4.347000 TGCTAAGGTTCTTGACAGGTTACT 59.653 41.667 0.00 0.00 0.00 2.24
3419 3584 7.787028 AGTCTTCTTCACTTCTCTTTACACTT 58.213 34.615 0.00 0.00 0.00 3.16
3458 3623 1.466025 CCAACTGCACTTGCCATGGT 61.466 55.000 14.67 0.00 41.18 3.55
3509 3677 4.373527 TGCAGTTGCTTTTCGTCTAGTTA 58.626 39.130 5.62 0.00 42.66 2.24
3540 3708 4.643463 AGAAGAGCTCATCATAGCAATGG 58.357 43.478 20.28 0.00 45.30 3.16


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

AutoCloner maintained by Alex Coulton.