Multiple sequence alignment - TraesCS2A01G521000

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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 TraesCS2A01G521000 chr2A 100.000 6919 0 0 1 6919 743579603 743572685 0.000000e+00 12778.0
1 TraesCS2A01G521000 chr2A 82.669 2158 255 58 1564 3664 743566243 743564148 0.000000e+00 1803.0
2 TraesCS2A01G521000 chr2A 86.918 1246 152 9 4256 5496 743562622 743561383 0.000000e+00 1387.0
3 TraesCS2A01G521000 chr2A 83.863 818 115 12 4256 5064 561024453 561025262 0.000000e+00 763.0
4 TraesCS2A01G521000 chr2A 82.176 763 105 19 5199 5932 561025384 561026144 1.640000e-175 627.0
5 TraesCS2A01G521000 chr2A 86.632 576 66 7 5488 6060 743551890 743551323 1.640000e-175 627.0
6 TraesCS2A01G521000 chr2A 85.294 578 57 18 3049 3614 561023869 561024430 7.790000e-159 571.0
7 TraesCS2A01G521000 chr2A 90.794 315 19 6 914 1220 743568162 743567850 4.990000e-111 412.0
8 TraesCS2A01G521000 chr2A 84.980 253 34 3 935 1186 561022508 561022757 3.200000e-63 254.0
9 TraesCS2A01G521000 chr2A 87.560 209 25 1 2599 2807 561023666 561023873 2.490000e-59 241.0
10 TraesCS2A01G521000 chr2D 94.755 2669 116 16 4256 6919 611233818 611231169 0.000000e+00 4132.0
11 TraesCS2A01G521000 chr2D 89.070 1784 142 31 2135 3886 611235577 611233815 0.000000e+00 2165.0
12 TraesCS2A01G521000 chr2D 87.742 1811 203 14 4256 6060 611223909 611222112 0.000000e+00 2097.0
13 TraesCS2A01G521000 chr2D 94.886 919 42 4 1 915 20651188 20652105 0.000000e+00 1432.0
14 TraesCS2A01G521000 chr2D 94.777 919 42 5 1 915 205593397 205592481 0.000000e+00 1426.0
15 TraesCS2A01G521000 chr2D 86.190 1231 111 37 915 2121 611236755 611235560 0.000000e+00 1277.0
16 TraesCS2A01G521000 chr2D 84.217 849 86 28 3055 3886 611224723 611223906 0.000000e+00 782.0
17 TraesCS2A01G521000 chr2D 81.693 945 131 23 2135 3053 611225942 611225014 0.000000e+00 749.0
18 TraesCS2A01G521000 chr2D 83.313 809 124 10 4256 5059 427444327 427443525 0.000000e+00 736.0
19 TraesCS2A01G521000 chr2D 85.540 574 62 14 3055 3620 427444904 427444344 1.290000e-161 580.0
20 TraesCS2A01G521000 chr2D 82.276 615 97 11 5328 5932 427442992 427442380 7.950000e-144 521.0
21 TraesCS2A01G521000 chr2D 80.414 725 94 31 1422 2119 611226630 611225927 6.190000e-140 508.0
22 TraesCS2A01G521000 chr2D 87.898 314 25 6 914 1216 611227151 611226840 2.370000e-94 357.0
23 TraesCS2A01G521000 chr2D 83.500 400 34 16 3886 4261 90313373 90312982 1.850000e-90 344.0
24 TraesCS2A01G521000 chr2D 74.538 703 122 41 5215 5885 427329180 427328503 3.200000e-63 254.0
25 TraesCS2A01G521000 chr2D 88.038 209 23 2 2599 2807 427445112 427444906 5.360000e-61 246.0
26 TraesCS2A01G521000 chr2D 84.274 248 36 2 917 1164 427446217 427445973 8.970000e-59 239.0
27 TraesCS2A01G521000 chr2D 78.287 327 53 12 3282 3593 427330951 427330628 1.970000e-45 195.0
28 TraesCS2A01G521000 chr2D 85.938 192 16 5 1697 1884 427445545 427445361 1.970000e-45 195.0
29 TraesCS2A01G521000 chr2D 87.500 160 13 7 1697 1853 427335885 427335730 1.980000e-40 178.0
30 TraesCS2A01G521000 chr2D 96.296 54 2 0 5199 5252 427443471 427443418 9.560000e-14 89.8
31 TraesCS2A01G521000 chr2B 92.691 2668 135 24 4256 6919 746138397 746135786 0.000000e+00 3792.0
32 TraesCS2A01G521000 chr2B 88.304 1787 151 38 2139 3886 746140161 746138394 0.000000e+00 2089.0
33 TraesCS2A01G521000 chr2B 87.587 1724 195 14 4256 5973 746110447 746108737 0.000000e+00 1980.0
34 TraesCS2A01G521000 chr2B 85.275 1202 130 35 945 2119 746141332 746140151 0.000000e+00 1195.0
35 TraesCS2A01G521000 chr2B 85.932 853 88 23 3055 3886 746111285 746110444 0.000000e+00 881.0
36 TraesCS2A01G521000 chr2B 81.847 942 129 21 2135 3053 746112497 746111575 0.000000e+00 754.0
37 TraesCS2A01G521000 chr2B 81.481 756 117 16 5199 5932 504320604 504319850 3.570000e-167 599.0
38 TraesCS2A01G521000 chr2B 86.715 557 52 14 3055 3605 504322092 504321552 3.570000e-167 599.0
39 TraesCS2A01G521000 chr2B 89.145 433 28 9 912 1330 746115962 746115535 7.950000e-144 521.0
40 TraesCS2A01G521000 chr2B 80.000 725 99 30 1422 2119 746113187 746112482 1.730000e-135 494.0
41 TraesCS2A01G521000 chr2B 84.974 193 17 6 1697 1884 504324416 504324231 1.190000e-42 185.0
42 TraesCS2A01G521000 chr2B 87.500 160 13 7 1697 1853 504206238 504206083 1.980000e-40 178.0
43 TraesCS2A01G521000 chr2B 82.162 185 25 4 2599 2782 504323886 504323709 1.200000e-32 152.0
44 TraesCS2A01G521000 chr1D 95.000 920 40 5 1 915 460551695 460550777 0.000000e+00 1439.0
45 TraesCS2A01G521000 chr1D 94.771 918 43 4 1 915 468557451 468556536 0.000000e+00 1424.0
46 TraesCS2A01G521000 chr7D 94.897 921 40 6 1 917 374567471 374568388 0.000000e+00 1434.0
47 TraesCS2A01G521000 chr7D 87.539 321 29 4 3944 4264 205494219 205494528 1.830000e-95 361.0
48 TraesCS2A01G521000 chr4D 94.880 918 40 6 1 915 22937581 22936668 0.000000e+00 1428.0
49 TraesCS2A01G521000 chr4D 94.691 923 43 5 1 919 306791822 306790902 0.000000e+00 1428.0
50 TraesCS2A01G521000 chr4D 84.635 384 37 11 3886 4262 496412013 496411645 5.100000e-96 363.0
51 TraesCS2A01G521000 chr7A 94.218 934 47 6 1 929 497684810 497683879 0.000000e+00 1419.0
52 TraesCS2A01G521000 chr7A 90.881 318 20 6 3944 4260 188573897 188573588 1.070000e-112 418.0
53 TraesCS2A01G521000 chr7A 83.099 71 12 0 2844 2914 717980078 717980008 1.610000e-06 65.8
54 TraesCS2A01G521000 chr3A 94.553 918 45 4 1 915 738074125 738075040 0.000000e+00 1413.0
55 TraesCS2A01G521000 chr6B 87.651 332 27 7 3932 4262 637093336 637093654 2.360000e-99 374.0
56 TraesCS2A01G521000 chr6B 96.429 56 2 0 6371 6426 264943603 264943548 7.390000e-15 93.5
57 TraesCS2A01G521000 chr3D 83.663 404 33 16 3872 4261 463218704 463219088 3.970000e-92 350.0
58 TraesCS2A01G521000 chr5B 89.130 276 24 3 3949 4223 394626073 394625803 8.600000e-89 339.0
59 TraesCS2A01G521000 chr5B 87.415 294 30 4 3969 4261 394625804 394625517 1.440000e-86 331.0
60 TraesCS2A01G521000 chr7B 83.113 379 42 12 3884 4249 602083101 602083470 6.690000e-85 326.0
61 TraesCS2A01G521000 chr4A 87.500 128 14 2 3055 3181 37901727 37901601 5.590000e-31 147.0
62 TraesCS2A01G521000 chr5A 83.529 85 13 1 1578 1661 382073125 382073209 2.070000e-10 78.7
63 TraesCS2A01G521000 chr5D 81.250 96 16 2 1528 1622 288550331 288550425 7.440000e-10 76.8
64 TraesCS2A01G521000 chrUn 83.784 74 12 0 2841 2914 87049788 87049861 3.460000e-08 71.3
65 TraesCS2A01G521000 chr3B 100.000 32 0 0 1274 1305 162711318 162711287 7.490000e-05 60.2


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 TraesCS2A01G521000 chr2A 743572685 743579603 6918 True 12778.000000 12778 100.000000 1 6919 1 chr2A.!!$R2 6918
1 TraesCS2A01G521000 chr2A 743561383 743568162 6779 True 1200.666667 1803 86.793667 914 5496 3 chr2A.!!$R3 4582
2 TraesCS2A01G521000 chr2A 743551323 743551890 567 True 627.000000 627 86.632000 5488 6060 1 chr2A.!!$R1 572
3 TraesCS2A01G521000 chr2A 561022508 561026144 3636 False 491.200000 763 84.774600 935 5932 5 chr2A.!!$F1 4997
4 TraesCS2A01G521000 chr2D 611231169 611236755 5586 True 2524.666667 4132 90.005000 915 6919 3 chr2D.!!$R7 6004
5 TraesCS2A01G521000 chr2D 20651188 20652105 917 False 1432.000000 1432 94.886000 1 915 1 chr2D.!!$F1 914
6 TraesCS2A01G521000 chr2D 205592481 205593397 916 True 1426.000000 1426 94.777000 1 915 1 chr2D.!!$R2 914
7 TraesCS2A01G521000 chr2D 611222112 611227151 5039 True 898.600000 2097 84.392800 914 6060 5 chr2D.!!$R6 5146
8 TraesCS2A01G521000 chr2D 427442380 427446217 3837 True 372.400000 736 86.525000 917 5932 7 chr2D.!!$R5 5015
9 TraesCS2A01G521000 chr2D 427328503 427330951 2448 True 224.500000 254 76.412500 3282 5885 2 chr2D.!!$R4 2603
10 TraesCS2A01G521000 chr2B 746135786 746141332 5546 True 2358.666667 3792 88.756667 945 6919 3 chr2B.!!$R4 5974
11 TraesCS2A01G521000 chr2B 746108737 746115962 7225 True 926.000000 1980 84.902200 912 5973 5 chr2B.!!$R3 5061
12 TraesCS2A01G521000 chr2B 504319850 504324416 4566 True 383.750000 599 83.833000 1697 5932 4 chr2B.!!$R2 4235
13 TraesCS2A01G521000 chr1D 460550777 460551695 918 True 1439.000000 1439 95.000000 1 915 1 chr1D.!!$R1 914
14 TraesCS2A01G521000 chr1D 468556536 468557451 915 True 1424.000000 1424 94.771000 1 915 1 chr1D.!!$R2 914
15 TraesCS2A01G521000 chr7D 374567471 374568388 917 False 1434.000000 1434 94.897000 1 917 1 chr7D.!!$F2 916
16 TraesCS2A01G521000 chr4D 22936668 22937581 913 True 1428.000000 1428 94.880000 1 915 1 chr4D.!!$R1 914
17 TraesCS2A01G521000 chr4D 306790902 306791822 920 True 1428.000000 1428 94.691000 1 919 1 chr4D.!!$R2 918
18 TraesCS2A01G521000 chr7A 497683879 497684810 931 True 1419.000000 1419 94.218000 1 929 1 chr7A.!!$R2 928
19 TraesCS2A01G521000 chr3A 738074125 738075040 915 False 1413.000000 1413 94.553000 1 915 1 chr3A.!!$F1 914
20 TraesCS2A01G521000 chr5B 394625517 394626073 556 True 335.000000 339 88.272500 3949 4261 2 chr5B.!!$R1 312

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
802 811 0.321653 GAGGTTGCGAAGATGGTGGT 60.322 55.000 0.00 0.0 0.00 4.16 F
985 1004 0.533491 ACGCTGAAACATAGCCGGTA 59.467 50.000 1.90 0.0 37.90 4.02 F
1567 4031 0.645868 GTCTTTTCCGCCTCGAATCG 59.354 55.000 0.00 0.0 0.00 3.34 F
1576 5240 1.635663 GCCTCGAATCGGTGTTGGTG 61.636 60.000 1.76 0.0 0.00 4.17 F
2815 8366 2.830293 AGAAACTAGGTACACCCTCCC 58.170 52.381 0.00 0.0 44.81 4.30 F
3379 9241 3.428045 GCTGTTGTCCAAAGGTATGATGC 60.428 47.826 0.00 0.0 0.00 3.91 F
3905 11113 0.035881 CTAGATGATGGCCCGCACAT 59.964 55.000 0.00 0.0 0.00 3.21 F
4171 11627 0.117541 TAGGTTAGTGGGAGTGGGCA 59.882 55.000 0.00 0.0 0.00 5.36 F
4445 12055 0.324943 GGAGGAGGCAAACTGTAGCA 59.675 55.000 7.34 0.0 0.00 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 5664 1.061424 TCCCAGATGCTTGATCCCCTA 60.061 52.381 0.00 0.0 0.00 3.53 R
2607 6564 2.270352 TGCTCCTGTCGGTGATTTTT 57.730 45.000 0.00 0.0 0.00 1.94 R
3077 8920 1.078848 AGGCGCACATCTTCCTGTC 60.079 57.895 10.83 0.0 0.00 3.51 R
3351 9213 2.107204 ACCTTTGGACAACAGCTCATCT 59.893 45.455 0.00 0.0 0.00 2.90 R
3886 11094 0.035881 ATGTGCGGGCCATCATCTAG 59.964 55.000 4.39 0.0 0.00 2.43 R
4478 12088 0.390860 GCGAGTATCTGATGGTGGCT 59.609 55.000 0.00 0.0 0.00 4.75 R
5582 13894 1.064240 TGGTAGTCTATCCTGGCGTCA 60.064 52.381 0.00 0.0 0.00 4.35 R
5887 14219 3.433306 TGGTTTCCAGGTTATCTGTGG 57.567 47.619 0.00 0.0 41.83 4.17 R
6421 14760 0.767375 AGCTTTCAGAGACTTGCCCA 59.233 50.000 0.00 0.0 0.00 5.36 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
56 59 1.216990 CTGGAGGTATTGCCCCTTCT 58.783 55.000 0.00 0.00 38.26 2.85
130 133 2.281484 CCGGTGTGTTCTGGTGGG 60.281 66.667 0.00 0.00 0.00 4.61
592 600 3.244009 ACTCTGAAGATGGATATGTGGCG 60.244 47.826 0.00 0.00 0.00 5.69
618 626 4.175337 TGGCAGCCTCATACCCGC 62.175 66.667 14.15 0.00 0.00 6.13
661 669 4.704833 CAGACTGGTGGGTGCCCG 62.705 72.222 2.44 0.00 39.42 6.13
729 737 0.966179 TAGCTGCGAGGTCTGTTTGA 59.034 50.000 0.00 0.00 0.00 2.69
737 745 4.161565 TGCGAGGTCTGTTTGATATTAGGT 59.838 41.667 0.00 0.00 0.00 3.08
743 752 6.098982 AGGTCTGTTTGATATTAGGTCCAGAG 59.901 42.308 0.00 0.00 0.00 3.35
802 811 0.321653 GAGGTTGCGAAGATGGTGGT 60.322 55.000 0.00 0.00 0.00 4.16
807 816 1.974265 TGCGAAGATGGTGGTTTTGA 58.026 45.000 0.00 0.00 0.00 2.69
828 837 9.531942 TTTTGATCTTACTGTTGTACGACTTTA 57.468 29.630 14.38 3.01 31.24 1.85
840 849 8.575589 TGTTGTACGACTTTATAAGGTCTTGTA 58.424 33.333 21.32 15.18 0.00 2.41
952 970 0.973632 TGCCTATATAGGTGGTGCCG 59.026 55.000 26.27 2.84 45.42 5.69
985 1004 0.533491 ACGCTGAAACATAGCCGGTA 59.467 50.000 1.90 0.00 37.90 4.02
987 1006 2.210116 CGCTGAAACATAGCCGGTATT 58.790 47.619 1.90 0.00 37.90 1.89
990 1009 4.091509 CGCTGAAACATAGCCGGTATTATC 59.908 45.833 1.90 0.00 37.90 1.75
991 1010 4.994852 GCTGAAACATAGCCGGTATTATCA 59.005 41.667 1.90 0.00 35.15 2.15
1181 1286 5.182001 CCACTCGTTTTTCCTTCATTGATCT 59.818 40.000 0.00 0.00 0.00 2.75
1227 1382 7.811236 CAGCAAAATCTGTTGACAAGTATGAAT 59.189 33.333 0.00 0.00 38.47 2.57
1268 1423 1.474879 TGCGTGATAGTCATTCACCGA 59.525 47.619 0.00 0.00 40.29 4.69
1280 1436 0.682852 TTCACCGACCGGACTCAAAT 59.317 50.000 16.07 0.00 38.96 2.32
1355 3772 5.818136 AAACTGTACGCTGCATTTCATAT 57.182 34.783 0.00 0.00 0.00 1.78
1367 3784 7.253420 CGCTGCATTTCATATACAAACAACTTC 60.253 37.037 0.00 0.00 0.00 3.01
1370 3787 9.571810 TGCATTTCATATACAAACAACTTCATC 57.428 29.630 0.00 0.00 0.00 2.92
1381 3798 7.651808 ACAAACAACTTCATCTTCTAATGGTG 58.348 34.615 0.00 0.00 0.00 4.17
1382 3799 6.824305 AACAACTTCATCTTCTAATGGTGG 57.176 37.500 0.00 0.00 0.00 4.61
1442 3904 7.457024 TCAGATTTTCATCAGAATCAAAGCA 57.543 32.000 0.00 0.00 35.28 3.91
1448 3910 7.661127 TTTCATCAGAATCAAAGCAATTTGG 57.339 32.000 0.00 0.00 32.89 3.28
1464 3926 5.066505 GCAATTTGGTAATCGGATCAGACTT 59.933 40.000 0.00 0.00 0.00 3.01
1474 3937 4.637276 TCGGATCAGACTTTGCTGTTTTA 58.363 39.130 0.00 0.00 37.20 1.52
1484 3948 5.487433 ACTTTGCTGTTTTACAAAAAGCCT 58.513 33.333 8.59 0.00 36.27 4.58
1561 4025 3.125573 GGCCGTCTTTTCCGCCTC 61.126 66.667 0.00 0.00 0.00 4.70
1567 4031 0.645868 GTCTTTTCCGCCTCGAATCG 59.354 55.000 0.00 0.00 0.00 3.34
1576 5240 1.635663 GCCTCGAATCGGTGTTGGTG 61.636 60.000 1.76 0.00 0.00 4.17
1629 5487 9.436957 GACCTAAATCTGATCACTTTTCAAGTA 57.563 33.333 0.00 0.00 40.46 2.24
1677 5540 7.174946 AGTTTGAATTCATGGACTAACGACATT 59.825 33.333 9.40 0.00 0.00 2.71
1687 5550 6.751157 TGGACTAACGACATTTTTCACTCTA 58.249 36.000 0.00 0.00 0.00 2.43
1728 5597 9.023962 ACATTATGAATTCTTTTTGGTCTAGCA 57.976 29.630 7.05 0.00 0.00 3.49
1842 5719 3.066190 CCAGCACCCAGGCATGTG 61.066 66.667 0.00 0.00 35.83 3.21
1861 5738 8.783093 GGCATGTGCAGTATATACATCTTTTAA 58.217 33.333 15.18 0.00 44.36 1.52
1878 5755 9.035607 CATCTTTTAAACGCAGTGTATCTATCT 57.964 33.333 0.00 0.00 45.00 1.98
1879 5756 8.630278 TCTTTTAAACGCAGTGTATCTATCTC 57.370 34.615 0.00 0.00 45.00 2.75
1880 5757 8.467598 TCTTTTAAACGCAGTGTATCTATCTCT 58.532 33.333 0.00 0.00 45.00 3.10
1971 5873 9.639601 GGTCAAGAAATCACCTTTTTATTTAGG 57.360 33.333 0.00 0.00 37.56 2.69
1972 5874 9.140286 GTCAAGAAATCACCTTTTTATTTAGGC 57.860 33.333 0.00 0.00 34.79 3.93
1973 5875 8.865090 TCAAGAAATCACCTTTTTATTTAGGCA 58.135 29.630 0.00 0.00 34.79 4.75
1974 5876 9.487790 CAAGAAATCACCTTTTTATTTAGGCAA 57.512 29.630 0.00 0.00 34.79 4.52
2059 5978 4.178545 ACGCTTGGGAAATCAATTCTTG 57.821 40.909 0.00 0.00 38.18 3.02
2167 6097 8.674263 ACTATATACTACTCACGTACAAAGCT 57.326 34.615 0.00 0.00 0.00 3.74
2181 6111 9.440784 CACGTACAAAGCTTAAAATCAAACTTA 57.559 29.630 0.00 0.00 0.00 2.24
2324 6262 5.710099 AGAGTCAAAGTTTTGTGTTGGAGAA 59.290 36.000 4.67 0.00 39.18 2.87
2329 6267 7.757624 GTCAAAGTTTTGTGTTGGAGAATGTAA 59.242 33.333 4.67 0.00 39.18 2.41
2398 6336 6.052840 TGTATGTCCGAGTATCTTACGAAC 57.947 41.667 0.00 0.00 0.00 3.95
2416 6354 8.682128 TTACGAACTTTCAATGCCAATATTTC 57.318 30.769 0.00 0.00 0.00 2.17
2508 6450 6.375377 GTGTGATCGCCAACAAAGTAATTTA 58.625 36.000 3.31 0.00 0.00 1.40
2589 6545 7.553044 GCCCTTTTTAATAAAGCTCTACTGAGA 59.447 37.037 0.00 0.00 42.73 3.27
2607 6564 7.333528 ACTGAGAAAGTAATGTTTTGCAGAA 57.666 32.000 0.00 0.00 37.36 3.02
2707 6668 8.993121 TGTCTTGCTTTTCAACTAGATCTTTAG 58.007 33.333 0.00 0.00 0.00 1.85
2755 6716 2.998670 AGTTGCTGATCAAGATCACACG 59.001 45.455 8.61 1.68 42.42 4.49
2808 8359 9.280174 CAATCCTACAAAAAGAAACTAGGTACA 57.720 33.333 0.00 0.00 0.00 2.90
2815 8366 2.830293 AGAAACTAGGTACACCCTCCC 58.170 52.381 0.00 0.00 44.81 4.30
2884 8437 9.412460 TGATAAAATCTACAGGAAAATCAGCAT 57.588 29.630 0.00 0.00 0.00 3.79
2968 8522 5.286082 GCAAATTTAGCGTTGTAGATGTTGG 59.714 40.000 0.00 0.00 0.00 3.77
3053 8607 7.753309 TTCAATTATCTTCGAACAAAGGGAA 57.247 32.000 0.00 0.00 0.00 3.97
3069 8912 7.123383 ACAAAGGGAATACCGATCCTAATTTT 58.877 34.615 0.00 0.00 46.96 1.82
3077 8920 9.516314 GAATACCGATCCTAATTTTCCAAAAAG 57.484 33.333 0.00 0.00 0.00 2.27
3335 9197 3.751698 GTCAACCGAGAAGGCATTAAGTT 59.248 43.478 0.00 0.00 46.52 2.66
3351 9213 8.726988 GGCATTAAGTTCTACAACAACTTGATA 58.273 33.333 7.86 0.00 42.73 2.15
3379 9241 3.428045 GCTGTTGTCCAAAGGTATGATGC 60.428 47.826 0.00 0.00 0.00 3.91
3628 9512 8.617290 TTGTTTTCTAAGAACATAACTCCCTC 57.383 34.615 0.00 0.00 36.92 4.30
3629 9513 7.741785 TGTTTTCTAAGAACATAACTCCCTCA 58.258 34.615 0.00 0.00 32.44 3.86
3630 9514 7.878127 TGTTTTCTAAGAACATAACTCCCTCAG 59.122 37.037 0.00 0.00 32.44 3.35
3631 9515 7.554959 TTTCTAAGAACATAACTCCCTCAGT 57.445 36.000 0.00 0.00 36.64 3.41
3664 9551 6.231258 AGACATGAGAATGCAACTCTATCA 57.769 37.500 19.77 8.85 0.00 2.15
3674 10836 6.808321 ATGCAACTCTATCAGGGTAACTTA 57.192 37.500 0.00 0.00 0.00 2.24
3683 10845 9.646427 CTCTATCAGGGTAACTTATGAATAAGC 57.354 37.037 9.50 0.00 42.66 3.09
3687 10852 7.054124 TCAGGGTAACTTATGAATAAGCAAGG 58.946 38.462 9.50 0.00 42.66 3.61
3750 10917 4.093556 GTCAAACGGAAGCATTTCTCCTAG 59.906 45.833 0.00 0.00 33.68 3.02
3813 10980 5.592282 TGAAGATTGAAAAAGTGTGGCTACA 59.408 36.000 0.00 0.00 0.00 2.74
3838 11036 8.963130 CACGCTTTGTAAAACTATTTCATTTCA 58.037 29.630 0.00 0.00 0.00 2.69
3840 11038 8.638565 CGCTTTGTAAAACTATTTCATTTCAGG 58.361 33.333 0.00 0.00 0.00 3.86
3859 11057 5.023452 TCAGGTGAAGGTAGTATCATGTGT 58.977 41.667 0.00 0.00 0.00 3.72
3897 11105 9.294030 CATTAACTTTCAAAACTAGATGATGGC 57.706 33.333 0.00 0.00 0.00 4.40
3898 11106 5.904362 ACTTTCAAAACTAGATGATGGCC 57.096 39.130 0.00 0.00 0.00 5.36
3899 11107 4.706962 ACTTTCAAAACTAGATGATGGCCC 59.293 41.667 0.00 0.00 0.00 5.80
3900 11108 2.917933 TCAAAACTAGATGATGGCCCG 58.082 47.619 0.00 0.00 0.00 6.13
3901 11109 1.334869 CAAAACTAGATGATGGCCCGC 59.665 52.381 0.00 0.00 0.00 6.13
3902 11110 0.546122 AAACTAGATGATGGCCCGCA 59.454 50.000 0.00 0.00 0.00 5.69
3903 11111 0.179045 AACTAGATGATGGCCCGCAC 60.179 55.000 0.00 0.00 0.00 5.34
3904 11112 1.337384 ACTAGATGATGGCCCGCACA 61.337 55.000 0.00 0.00 0.00 4.57
3905 11113 0.035881 CTAGATGATGGCCCGCACAT 59.964 55.000 0.00 0.00 0.00 3.21
3906 11114 0.473755 TAGATGATGGCCCGCACATT 59.526 50.000 0.00 0.00 0.00 2.71
3907 11115 1.105167 AGATGATGGCCCGCACATTG 61.105 55.000 0.00 0.00 0.00 2.82
3908 11116 1.380246 ATGATGGCCCGCACATTGT 60.380 52.632 0.00 0.00 0.00 2.71
3909 11117 0.971959 ATGATGGCCCGCACATTGTT 60.972 50.000 0.00 0.00 0.00 2.83
3910 11118 1.153784 GATGGCCCGCACATTGTTG 60.154 57.895 0.00 0.00 0.00 3.33
3911 11119 3.299524 ATGGCCCGCACATTGTTGC 62.300 57.895 0.00 0.00 39.28 4.17
3912 11120 3.988525 GGCCCGCACATTGTTGCA 61.989 61.111 0.00 0.00 43.15 4.08
3913 11121 2.431260 GCCCGCACATTGTTGCAG 60.431 61.111 10.41 1.52 43.15 4.41
3914 11122 3.041701 CCCGCACATTGTTGCAGT 58.958 55.556 10.41 0.00 43.15 4.40
3915 11123 1.861542 GCCCGCACATTGTTGCAGTA 61.862 55.000 10.41 0.00 43.15 2.74
3916 11124 0.810648 CCCGCACATTGTTGCAGTAT 59.189 50.000 10.41 0.00 43.15 2.12
3917 11125 2.013400 CCCGCACATTGTTGCAGTATA 58.987 47.619 10.41 0.00 43.15 1.47
3918 11126 2.618241 CCCGCACATTGTTGCAGTATAT 59.382 45.455 10.41 0.00 43.15 0.86
3919 11127 3.066621 CCCGCACATTGTTGCAGTATATT 59.933 43.478 10.41 0.00 43.15 1.28
3920 11128 4.439974 CCCGCACATTGTTGCAGTATATTT 60.440 41.667 10.41 0.00 43.15 1.40
3921 11129 5.101628 CCGCACATTGTTGCAGTATATTTT 58.898 37.500 10.41 0.00 43.15 1.82
3922 11130 5.004630 CCGCACATTGTTGCAGTATATTTTG 59.995 40.000 10.41 0.00 43.15 2.44
3923 11131 5.499017 CGCACATTGTTGCAGTATATTTTGC 60.499 40.000 10.41 4.63 43.15 3.68
4087 11543 9.491675 AAATTCTCATGTATTTTTGCATGTTCA 57.508 25.926 0.00 0.00 42.09 3.18
4095 11551 3.988379 TTTTGCATGTTCAGGTGAGTC 57.012 42.857 0.00 0.00 0.00 3.36
4099 11555 3.554934 TGCATGTTCAGGTGAGTCTTTT 58.445 40.909 0.00 0.00 0.00 2.27
4101 11557 3.057946 GCATGTTCAGGTGAGTCTTTTCC 60.058 47.826 0.00 0.00 0.00 3.13
4132 11588 2.595124 CATGATGTTGTGGCATGCAT 57.405 45.000 21.36 2.33 33.81 3.96
4133 11589 2.200899 CATGATGTTGTGGCATGCATG 58.799 47.619 22.70 22.70 33.81 4.06
4134 11590 1.258676 TGATGTTGTGGCATGCATGT 58.741 45.000 26.79 5.18 0.00 3.21
4155 11611 7.735500 CATGTTTGCATGTTGAAAGAAATAGG 58.264 34.615 0.00 0.00 45.48 2.57
4163 11619 7.538575 CATGTTGAAAGAAATAGGTTAGTGGG 58.461 38.462 0.00 0.00 0.00 4.61
4169 11625 3.780850 AGAAATAGGTTAGTGGGAGTGGG 59.219 47.826 0.00 0.00 0.00 4.61
4171 11627 0.117541 TAGGTTAGTGGGAGTGGGCA 59.882 55.000 0.00 0.00 0.00 5.36
4178 11634 1.133199 AGTGGGAGTGGGCATTTTTCA 60.133 47.619 0.00 0.00 0.00 2.69
4180 11636 1.901159 TGGGAGTGGGCATTTTTCATG 59.099 47.619 0.00 0.00 0.00 3.07
4208 11665 1.281577 TGTGATGAGGTGGCATGCTTA 59.718 47.619 18.92 4.21 0.00 3.09
4236 11693 8.331931 TGTTGAGAGAAATATATTAGTGGGGT 57.668 34.615 0.00 0.00 0.00 4.95
4239 11696 9.892444 TTGAGAGAAATATATTAGTGGGGTCTA 57.108 33.333 0.00 0.00 0.00 2.59
4255 11712 9.839185 AGTGGGGTCTAAGCTATTTAGATATAA 57.161 33.333 0.00 0.00 46.99 0.98
4445 12055 0.324943 GGAGGAGGCAAACTGTAGCA 59.675 55.000 7.34 0.00 0.00 3.49
4478 12088 1.490490 GGAGGGAGCCATACATTGTCA 59.510 52.381 0.00 0.00 0.00 3.58
4572 12190 3.129988 GCCCTTTATCATATCATGCAGCC 59.870 47.826 0.00 0.00 0.00 4.85
4669 12290 2.659428 AGCTTTGGTCTCATATTGGGC 58.341 47.619 0.00 0.00 0.00 5.36
4715 12336 5.404096 TCTAGTATTGTTGCGATGAAACGA 58.596 37.500 0.00 0.00 35.09 3.85
4744 12365 6.461110 AGAATTCATGCTTGGATGGTAAAG 57.539 37.500 8.44 0.00 0.00 1.85
4753 12374 4.436986 GCTTGGATGGTAAAGTCTTTACGC 60.437 45.833 23.07 16.82 44.96 4.42
4756 12377 5.310451 TGGATGGTAAAGTCTTTACGCTTT 58.690 37.500 23.07 11.56 44.96 3.51
4884 12505 2.961526 TCCCGAGAGCATGAAAGTAC 57.038 50.000 0.00 0.00 0.00 2.73
5000 12621 4.868067 ACTACGTTTATAGCATTCCTCCG 58.132 43.478 0.00 0.00 0.00 4.63
5220 13174 4.687483 GCATGCTAACATTGCCCAATTATC 59.313 41.667 11.37 0.00 32.87 1.75
5315 13271 4.461198 TCCTTCAGTTTTCTCCCAACTTC 58.539 43.478 0.00 0.00 31.83 3.01
5410 13714 6.533730 TGATCTGCTACTTTTTCTCAAGGAA 58.466 36.000 0.00 0.00 0.00 3.36
5582 13894 4.530875 CACTAAATGAAGCCCTCAAGGAT 58.469 43.478 0.00 0.00 37.67 3.24
5605 13917 0.674534 GCCAGGATAGACTACCACCG 59.325 60.000 0.00 0.00 0.00 4.94
5606 13918 2.027949 GCCAGGATAGACTACCACCGT 61.028 57.143 0.00 0.00 0.00 4.83
5834 14165 3.392947 TGGACTACAACCATGGTCTGAAA 59.607 43.478 20.07 11.02 32.03 2.69
5887 14219 9.298774 GTTCAAGAATTTTCTCAATGATGATCC 57.701 33.333 0.00 0.00 36.28 3.36
5933 14265 4.328536 ACAAATAATGGAGGCGTTGTACA 58.671 39.130 0.00 0.00 0.00 2.90
5935 14267 6.116806 ACAAATAATGGAGGCGTTGTACATA 58.883 36.000 0.00 0.00 0.00 2.29
6026 14358 4.851639 AGATCAATGTAACAGGAGGCTT 57.148 40.909 0.00 0.00 0.00 4.35
6166 14505 9.846248 AATGTTTAATTCAACATACTGCTCTTC 57.154 29.630 16.34 0.00 44.95 2.87
6266 14605 5.407387 TCGTTAAGTCATCCAACTAACTTGC 59.593 40.000 0.00 0.00 34.09 4.01
6279 14618 6.449698 CAACTAACTTGCCAAAGACATTCAT 58.550 36.000 0.00 0.00 36.84 2.57
6356 14695 6.749118 GTGCCTACATTTGAATTCACAATCTC 59.251 38.462 7.89 0.00 0.00 2.75
6402 14741 0.043032 TAGCCGGTTTCCTCCCCTTA 59.957 55.000 1.90 0.00 0.00 2.69
6404 14743 1.844544 GCCGGTTTCCTCCCCTTACA 61.845 60.000 1.90 0.00 0.00 2.41
6421 14760 5.513267 CCCTTACACTCAAGCTAAAGGTTCT 60.513 44.000 0.00 0.00 33.20 3.01
6501 14842 8.994429 AAGTCACAGAAGTCAAGTCTATAATG 57.006 34.615 0.00 0.00 0.00 1.90
6524 14865 8.644318 ATGTAATAGTACCAGCTTAAGTTTCG 57.356 34.615 4.02 0.00 0.00 3.46
6525 14866 7.605449 TGTAATAGTACCAGCTTAAGTTTCGT 58.395 34.615 4.02 0.00 0.00 3.85
6526 14867 8.090214 TGTAATAGTACCAGCTTAAGTTTCGTT 58.910 33.333 4.02 0.00 0.00 3.85
6527 14868 7.592439 AATAGTACCAGCTTAAGTTTCGTTC 57.408 36.000 4.02 0.00 0.00 3.95
6528 14869 4.313282 AGTACCAGCTTAAGTTTCGTTCC 58.687 43.478 4.02 0.00 0.00 3.62
6529 14870 2.501261 ACCAGCTTAAGTTTCGTTCCC 58.499 47.619 4.02 0.00 0.00 3.97
6530 14871 2.105993 ACCAGCTTAAGTTTCGTTCCCT 59.894 45.455 4.02 0.00 0.00 4.20
6531 14872 3.325716 ACCAGCTTAAGTTTCGTTCCCTA 59.674 43.478 4.02 0.00 0.00 3.53
6532 14873 4.019591 ACCAGCTTAAGTTTCGTTCCCTAT 60.020 41.667 4.02 0.00 0.00 2.57
6533 14874 5.188359 ACCAGCTTAAGTTTCGTTCCCTATA 59.812 40.000 4.02 0.00 0.00 1.31
6534 14875 6.110707 CCAGCTTAAGTTTCGTTCCCTATAA 58.889 40.000 4.02 0.00 0.00 0.98
6535 14876 6.258068 CCAGCTTAAGTTTCGTTCCCTATAAG 59.742 42.308 4.02 0.00 0.00 1.73
6536 14877 6.817140 CAGCTTAAGTTTCGTTCCCTATAAGT 59.183 38.462 4.02 0.00 0.00 2.24
6537 14878 7.333672 CAGCTTAAGTTTCGTTCCCTATAAGTT 59.666 37.037 4.02 0.00 0.00 2.66
6538 14879 8.534496 AGCTTAAGTTTCGTTCCCTATAAGTTA 58.466 33.333 4.02 0.00 0.00 2.24
6539 14880 9.154847 GCTTAAGTTTCGTTCCCTATAAGTTAA 57.845 33.333 4.02 0.00 0.00 2.01
6711 15078 4.037208 ACATCCAAAGTTTCTCAGTGCAAG 59.963 41.667 0.00 0.00 0.00 4.01
6716 15083 6.321181 TCCAAAGTTTCTCAGTGCAAGTATTT 59.679 34.615 0.00 0.00 0.00 1.40
6719 15086 8.958043 CAAAGTTTCTCAGTGCAAGTATTTAAC 58.042 33.333 0.00 0.00 0.00 2.01
6728 15095 8.081633 TCAGTGCAAGTATTTAACAATTCCAAG 58.918 33.333 0.00 0.00 0.00 3.61
6781 15148 6.924060 AGTACAAGCACTGTAACTTAACTCAG 59.076 38.462 0.00 0.00 42.23 3.35
6830 15197 6.533819 TTTCTGTAACTAACATGGTCGTTG 57.466 37.500 10.73 0.00 37.50 4.10
6874 15242 5.764131 TCGGACAAACACATTTTACATTCC 58.236 37.500 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 59 0.552848 GGGAAGGGATGCATGGAAGA 59.447 55.000 2.46 0.00 0.00 2.87
148 151 1.903404 CAAGGCGGCCAAGGTTTCT 60.903 57.895 23.09 0.00 0.00 2.52
312 318 0.250770 GTCGCCTCCAGGAAGGTTTT 60.251 55.000 0.00 0.00 38.79 2.43
313 319 1.128188 AGTCGCCTCCAGGAAGGTTT 61.128 55.000 0.00 0.00 38.79 3.27
332 338 1.912731 TCCGATCCCAATGTTCTTGGA 59.087 47.619 5.57 0.00 42.06 3.53
338 344 2.423373 CCTTCCATCCGATCCCAATGTT 60.423 50.000 0.00 0.00 0.00 2.71
605 613 3.164269 CCTGGCGGGTATGAGGCT 61.164 66.667 3.48 0.00 0.00 4.58
729 737 3.056250 CGCTGATGCTCTGGACCTAATAT 60.056 47.826 0.00 0.00 36.97 1.28
737 745 4.166888 GGGCGCTGATGCTCTGGA 62.167 66.667 7.64 0.00 36.97 3.86
743 752 2.517875 ATGAAGGGGCGCTGATGC 60.518 61.111 7.64 0.00 0.00 3.91
802 811 8.428186 AAAGTCGTACAACAGTAAGATCAAAA 57.572 30.769 0.00 0.00 30.88 2.44
807 816 9.798994 CCTTATAAAGTCGTACAACAGTAAGAT 57.201 33.333 0.00 0.00 30.88 2.40
985 1004 3.822735 GCAGCCATATGGTGTGTGATAAT 59.177 43.478 22.79 0.00 44.44 1.28
987 1006 2.172293 TGCAGCCATATGGTGTGTGATA 59.828 45.455 22.79 6.96 44.44 2.15
990 1009 1.133598 CTTGCAGCCATATGGTGTGTG 59.866 52.381 22.79 15.30 44.44 3.82
991 1010 1.004628 TCTTGCAGCCATATGGTGTGT 59.995 47.619 22.79 3.11 44.44 3.72
1181 1286 6.539173 TGCTGAACTAAGAAAGGAAACCATA 58.461 36.000 0.00 0.00 0.00 2.74
1268 1423 2.513753 TGCAATCAATTTGAGTCCGGT 58.486 42.857 0.00 0.00 37.53 5.28
1280 1436 4.202295 TGTTGGCCTAAAACATGCAATCAA 60.202 37.500 3.32 0.00 32.71 2.57
1331 1529 4.661993 TGAAATGCAGCGTACAGTTTAG 57.338 40.909 0.00 0.00 0.00 1.85
1332 1530 6.918892 ATATGAAATGCAGCGTACAGTTTA 57.081 33.333 0.00 0.00 0.00 2.01
1333 1531 5.818136 ATATGAAATGCAGCGTACAGTTT 57.182 34.783 0.00 0.00 0.00 2.66
1334 1532 5.815222 TGTATATGAAATGCAGCGTACAGTT 59.185 36.000 0.00 0.00 0.00 3.16
1355 3772 8.783093 CACCATTAGAAGATGAAGTTGTTTGTA 58.217 33.333 0.00 0.00 0.00 2.41
1367 3784 2.360165 GCTTGCCCACCATTAGAAGATG 59.640 50.000 0.00 0.00 0.00 2.90
1370 3787 1.106285 GGCTTGCCCACCATTAGAAG 58.894 55.000 0.00 0.00 0.00 2.85
1406 3862 9.817809 CTGATGAAAATCTGAATTGATGGATTT 57.182 29.630 0.00 0.00 39.22 2.17
1407 3863 9.197306 TCTGATGAAAATCTGAATTGATGGATT 57.803 29.630 0.00 0.00 0.00 3.01
1418 3876 7.457024 TGCTTTGATTCTGATGAAAATCTGA 57.543 32.000 0.00 0.00 35.63 3.27
1420 3878 9.720769 AAATTGCTTTGATTCTGATGAAAATCT 57.279 25.926 0.00 0.00 35.63 2.40
1429 3887 7.028962 CGATTACCAAATTGCTTTGATTCTGA 58.971 34.615 0.22 0.00 43.71 3.27
1442 3904 6.404734 GCAAAGTCTGATCCGATTACCAAATT 60.405 38.462 0.00 0.00 0.00 1.82
1448 3910 4.184629 ACAGCAAAGTCTGATCCGATTAC 58.815 43.478 0.00 0.00 37.51 1.89
1464 3926 5.337578 AGAGGCTTTTTGTAAAACAGCAA 57.662 34.783 11.67 0.00 35.59 3.91
1474 3937 8.919777 ACTAGTATTTACAAGAGGCTTTTTGT 57.080 30.769 18.28 18.28 40.39 2.83
1484 3948 6.376299 TCAAGAGCGGACTAGTATTTACAAGA 59.624 38.462 0.00 0.00 0.00 3.02
1561 4025 4.083749 TCAAATAACACCAACACCGATTCG 60.084 41.667 0.00 0.00 0.00 3.34
1567 4031 9.482627 TTTATTTGATCAAATAACACCAACACC 57.517 29.630 36.42 0.00 46.71 4.16
1629 5487 3.568007 TGATTTCACGCTTTAAGCCAACT 59.432 39.130 11.64 0.00 38.18 3.16
1719 5588 9.725019 CCATATTTGTAATAAGATGCTAGACCA 57.275 33.333 0.00 0.00 0.00 4.02
1720 5589 9.726438 ACCATATTTGTAATAAGATGCTAGACC 57.274 33.333 0.00 0.00 0.00 3.85
1722 5591 9.639601 CGACCATATTTGTAATAAGATGCTAGA 57.360 33.333 0.00 0.00 0.00 2.43
1723 5592 9.639601 TCGACCATATTTGTAATAAGATGCTAG 57.360 33.333 0.00 0.00 0.00 3.42
1747 5618 4.687483 TCATACTGCAGCATGTGAATATCG 59.313 41.667 23.24 0.00 39.31 2.92
1792 5664 1.061424 TCCCAGATGCTTGATCCCCTA 60.061 52.381 0.00 0.00 0.00 3.53
1842 5719 8.548721 ACTGCGTTTAAAAGATGTATATACTGC 58.451 33.333 13.89 6.03 0.00 4.40
1843 5720 9.849607 CACTGCGTTTAAAAGATGTATATACTG 57.150 33.333 13.89 0.00 0.00 2.74
1970 5872 4.588805 GCTTCATGCACTAAAATTTGCC 57.411 40.909 0.00 0.00 42.31 4.52
2151 6081 7.949903 TGATTTTAAGCTTTGTACGTGAGTA 57.050 32.000 3.20 0.00 46.88 2.59
2153 6083 7.855904 AGTTTGATTTTAAGCTTTGTACGTGAG 59.144 33.333 3.20 0.00 0.00 3.51
2154 6084 7.699566 AGTTTGATTTTAAGCTTTGTACGTGA 58.300 30.769 3.20 0.00 0.00 4.35
2607 6564 2.270352 TGCTCCTGTCGGTGATTTTT 57.730 45.000 0.00 0.00 0.00 1.94
2755 6716 9.399403 GAACTAAAATTCAAAGATCTTGTCACC 57.601 33.333 9.17 0.00 0.00 4.02
2861 8413 7.833682 TCCATGCTGATTTTCCTGTAGATTTTA 59.166 33.333 0.00 0.00 0.00 1.52
2870 8422 5.128205 TGTAGATCCATGCTGATTTTCCTG 58.872 41.667 0.00 0.00 0.00 3.86
2952 8506 2.543777 ACACCAACATCTACAACGCT 57.456 45.000 0.00 0.00 0.00 5.07
2954 8508 4.755411 AGGATACACCAACATCTACAACG 58.245 43.478 0.00 0.00 42.04 4.10
2968 8522 8.958119 TTGACCAAATCTATACAAGGATACAC 57.042 34.615 0.00 0.00 41.41 2.90
2999 8553 6.431198 TGTTTGTCCTAAGTCAAACTTCAC 57.569 37.500 17.37 0.00 46.02 3.18
3028 8582 7.938140 TCCCTTTGTTCGAAGATAATTGAAT 57.062 32.000 0.00 0.00 35.04 2.57
3053 8607 8.683615 GTCTTTTTGGAAAATTAGGATCGGTAT 58.316 33.333 0.00 0.00 0.00 2.73
3069 8912 3.569701 GCACATCTTCCTGTCTTTTTGGA 59.430 43.478 0.00 0.00 0.00 3.53
3077 8920 1.078848 AGGCGCACATCTTCCTGTC 60.079 57.895 10.83 0.00 0.00 3.51
3335 9197 7.038048 CAGCTCATCTATCAAGTTGTTGTAGA 58.962 38.462 2.11 9.62 34.07 2.59
3351 9213 2.107204 ACCTTTGGACAACAGCTCATCT 59.893 45.455 0.00 0.00 0.00 2.90
3479 9360 6.483640 GCACCCCTGTAGATATAGAAAAGTTG 59.516 42.308 0.00 0.00 0.00 3.16
3605 9489 7.878644 ACTGAGGGAGTTATGTTCTTAGAAAAC 59.121 37.037 0.00 0.00 0.00 2.43
3628 9512 6.525121 TTCTCATGTCTAAAACGTCAACTG 57.475 37.500 0.00 0.00 0.00 3.16
3629 9513 6.347725 GCATTCTCATGTCTAAAACGTCAACT 60.348 38.462 0.00 0.00 32.28 3.16
3630 9514 5.790495 GCATTCTCATGTCTAAAACGTCAAC 59.210 40.000 0.00 0.00 32.28 3.18
3631 9515 5.468409 TGCATTCTCATGTCTAAAACGTCAA 59.532 36.000 0.00 0.00 32.28 3.18
3664 9551 7.208064 TCCTTGCTTATTCATAAGTTACCCT 57.792 36.000 8.11 0.00 41.34 4.34
3767 10934 8.927675 TTCAACCACTAATGTGTAAAACCTAT 57.072 30.769 0.00 0.00 42.34 2.57
3786 10953 4.507756 GCCACACTTTTTCAATCTTCAACC 59.492 41.667 0.00 0.00 0.00 3.77
3813 10980 9.180678 CTGAAATGAAATAGTTTTACAAAGCGT 57.819 29.630 0.00 0.00 0.00 5.07
3838 11036 7.038587 TGTTTACACATGATACTACCTTCACCT 60.039 37.037 0.00 0.00 0.00 4.00
3840 11038 8.718102 ATGTTTACACATGATACTACCTTCAC 57.282 34.615 0.00 0.00 42.46 3.18
3882 11090 1.064758 TGCGGGCCATCATCTAGTTTT 60.065 47.619 4.39 0.00 0.00 2.43
3883 11091 0.546122 TGCGGGCCATCATCTAGTTT 59.454 50.000 4.39 0.00 0.00 2.66
3884 11092 0.179045 GTGCGGGCCATCATCTAGTT 60.179 55.000 4.39 0.00 0.00 2.24
3885 11093 1.337384 TGTGCGGGCCATCATCTAGT 61.337 55.000 4.39 0.00 0.00 2.57
3886 11094 0.035881 ATGTGCGGGCCATCATCTAG 59.964 55.000 4.39 0.00 0.00 2.43
3887 11095 0.473755 AATGTGCGGGCCATCATCTA 59.526 50.000 4.39 0.00 0.00 1.98
3888 11096 1.105167 CAATGTGCGGGCCATCATCT 61.105 55.000 4.39 0.00 0.00 2.90
3889 11097 1.361271 CAATGTGCGGGCCATCATC 59.639 57.895 4.39 0.00 0.00 2.92
3890 11098 0.971959 AACAATGTGCGGGCCATCAT 60.972 50.000 4.39 1.52 0.00 2.45
3891 11099 1.606025 AACAATGTGCGGGCCATCA 60.606 52.632 4.39 0.00 0.00 3.07
3892 11100 1.153784 CAACAATGTGCGGGCCATC 60.154 57.895 4.39 0.00 0.00 3.51
3893 11101 2.972267 CAACAATGTGCGGGCCAT 59.028 55.556 4.39 0.00 0.00 4.40
3894 11102 3.988525 GCAACAATGTGCGGGCCA 61.989 61.111 4.39 0.00 34.21 5.36
3900 11108 5.348179 TGCAAAATATACTGCAACAATGTGC 59.652 36.000 8.74 0.00 45.25 4.57
3901 11109 6.947903 TGCAAAATATACTGCAACAATGTG 57.052 33.333 8.74 0.00 45.25 3.21
3930 11138 9.955208 CAAAATATTCGATGGATCTCATGAAAA 57.045 29.630 0.00 0.00 35.97 2.29
3931 11139 9.341078 TCAAAATATTCGATGGATCTCATGAAA 57.659 29.630 0.00 0.00 35.97 2.69
3932 11140 8.907222 TCAAAATATTCGATGGATCTCATGAA 57.093 30.769 0.00 6.51 35.97 2.57
3933 11141 8.152898 ACTCAAAATATTCGATGGATCTCATGA 58.847 33.333 0.00 0.00 35.97 3.07
3934 11142 8.320396 ACTCAAAATATTCGATGGATCTCATG 57.680 34.615 1.91 0.00 35.97 3.07
4066 11522 6.309494 CACCTGAACATGCAAAAATACATGAG 59.691 38.462 9.77 0.00 45.23 2.90
4075 11531 3.554934 AGACTCACCTGAACATGCAAAA 58.445 40.909 0.00 0.00 0.00 2.44
4086 11542 4.286297 TGTATGGGAAAAGACTCACCTG 57.714 45.455 0.00 0.00 0.00 4.00
4087 11543 4.289672 ACATGTATGGGAAAAGACTCACCT 59.710 41.667 0.00 0.00 0.00 4.00
4095 11551 5.327616 TCATGCAACATGTATGGGAAAAG 57.672 39.130 0.00 0.00 40.25 2.27
4099 11555 3.900971 ACATCATGCAACATGTATGGGA 58.099 40.909 11.25 0.00 40.25 4.37
4101 11557 4.801516 CACAACATCATGCAACATGTATGG 59.198 41.667 12.88 9.11 40.25 2.74
4131 11587 7.444299 ACCTATTTCTTTCAACATGCAAACAT 58.556 30.769 0.00 0.00 36.79 2.71
4132 11588 6.815089 ACCTATTTCTTTCAACATGCAAACA 58.185 32.000 0.00 0.00 0.00 2.83
4133 11589 7.713764 AACCTATTTCTTTCAACATGCAAAC 57.286 32.000 0.00 0.00 0.00 2.93
4134 11590 8.637986 ACTAACCTATTTCTTTCAACATGCAAA 58.362 29.630 0.00 0.00 0.00 3.68
4155 11611 2.215942 AAATGCCCACTCCCACTAAC 57.784 50.000 0.00 0.00 0.00 2.34
4163 11619 2.747396 TGCATGAAAAATGCCCACTC 57.253 45.000 7.78 0.00 43.94 3.51
4169 11625 4.211584 TCACACAACATGCATGAAAAATGC 59.788 37.500 32.75 3.37 44.76 3.56
4171 11627 6.224584 TCATCACACAACATGCATGAAAAAT 58.775 32.000 32.75 12.15 31.08 1.82
4178 11634 2.490509 CACCTCATCACACAACATGCAT 59.509 45.455 0.00 0.00 0.00 3.96
4180 11636 1.200716 CCACCTCATCACACAACATGC 59.799 52.381 0.00 0.00 0.00 4.06
4208 11665 9.784531 CCCACTAATATATTTCTCTCAACATGT 57.215 33.333 2.68 0.00 0.00 3.21
4225 11682 9.839185 ATCTAAATAGCTTAGACCCCACTAATA 57.161 33.333 0.00 0.00 46.96 0.98
4226 11683 8.743636 ATCTAAATAGCTTAGACCCCACTAAT 57.256 34.615 0.00 0.00 46.96 1.73
4255 11712 4.821805 CACCAGTGTCAGTTGGTTATCTTT 59.178 41.667 6.27 0.00 45.16 2.52
4445 12055 1.308216 CCCTCCCTGAATCCCCAGT 60.308 63.158 0.00 0.00 32.43 4.00
4478 12088 0.390860 GCGAGTATCTGATGGTGGCT 59.609 55.000 0.00 0.00 0.00 4.75
4543 12153 3.007940 TGATATGATAAAGGGCTGGGTCG 59.992 47.826 0.00 0.00 0.00 4.79
4572 12190 1.282248 ACGTTCATGGACGAACTGCG 61.282 55.000 32.59 4.86 45.47 5.18
4669 12290 1.843368 TGTACCGGACAAGGGAGTAG 58.157 55.000 9.46 0.00 34.15 2.57
4683 12304 7.298507 TCGCAACAATACTAGATTTTGTACC 57.701 36.000 0.00 0.00 33.44 3.34
4715 12336 5.944599 CCATCCAAGCATGAATTCTATAGCT 59.055 40.000 7.05 7.70 0.00 3.32
4744 12365 1.136336 CCAGCGTGAAAGCGTAAAGAC 60.136 52.381 0.00 0.00 43.00 3.01
4753 12374 3.100817 CGAAATTATGCCAGCGTGAAAG 58.899 45.455 0.00 0.00 0.00 2.62
4756 12377 1.663643 GACGAAATTATGCCAGCGTGA 59.336 47.619 0.00 0.00 31.58 4.35
4827 12448 2.578786 CGGGTCCAAAAACCTACAGTT 58.421 47.619 0.00 0.00 41.81 3.16
4992 12613 4.446371 CTCAAGCAATTAGACGGAGGAAT 58.554 43.478 0.00 0.00 0.00 3.01
5000 12621 4.006319 AGCTGTTCCTCAAGCAATTAGAC 58.994 43.478 0.00 0.00 0.00 2.59
5154 13094 5.587443 CAGTGGCAATGTCTCTATCATTCAA 59.413 40.000 6.80 0.00 33.92 2.69
5160 13100 6.283694 TGTAATCAGTGGCAATGTCTCTATC 58.716 40.000 15.19 1.88 0.00 2.08
5195 13135 1.264295 TGGGCAATGTTAGCATGCAA 58.736 45.000 21.98 9.44 35.15 4.08
5220 13174 2.480419 GACACCATTTCGAACACCTGAG 59.520 50.000 0.00 0.00 0.00 3.35
5321 13303 4.882671 ACATGCAGGTCATTTAATCGAC 57.117 40.909 0.00 0.00 31.79 4.20
5326 13630 3.947196 CAGCCTACATGCAGGTCATTTAA 59.053 43.478 7.56 0.00 38.05 1.52
5410 13714 4.998051 AGATGGTTGGATTGTGGTACTTT 58.002 39.130 0.00 0.00 0.00 2.66
5582 13894 1.064240 TGGTAGTCTATCCTGGCGTCA 60.064 52.381 0.00 0.00 0.00 4.35
5887 14219 3.433306 TGGTTTCCAGGTTATCTGTGG 57.567 47.619 0.00 0.00 41.83 4.17
6026 14358 4.776795 TCACTAGATACGTTCTTGCACA 57.223 40.909 0.00 0.00 35.79 4.57
6243 14582 5.390567 GGCAAGTTAGTTGGATGACTTAACG 60.391 44.000 1.75 0.00 36.56 3.18
6279 14618 9.604569 TTAATTAGGGTGCCACATAGTAGTATA 57.395 33.333 0.00 0.00 0.00 1.47
6356 14695 8.239681 TCGAACTAGCGGAAATGATTAATATG 57.760 34.615 0.00 0.00 0.00 1.78
6402 14741 3.496870 CCCAGAACCTTTAGCTTGAGTGT 60.497 47.826 0.00 0.00 0.00 3.55
6404 14743 2.553247 GCCCAGAACCTTTAGCTTGAGT 60.553 50.000 0.00 0.00 0.00 3.41
6421 14760 0.767375 AGCTTTCAGAGACTTGCCCA 59.233 50.000 0.00 0.00 0.00 5.36
6501 14842 8.471361 AACGAAACTTAAGCTGGTACTATTAC 57.529 34.615 1.29 0.00 0.00 1.89
6507 14848 3.434641 GGGAACGAAACTTAAGCTGGTAC 59.565 47.826 1.29 0.00 0.00 3.34
6520 14861 9.995003 TGTTAACTTAACTTATAGGGAACGAAA 57.005 29.630 7.22 0.00 39.38 3.46
6521 14862 9.423061 GTGTTAACTTAACTTATAGGGAACGAA 57.577 33.333 7.22 0.00 39.38 3.85
6522 14863 8.806146 AGTGTTAACTTAACTTATAGGGAACGA 58.194 33.333 7.22 0.00 39.38 3.85
6523 14864 8.992835 AGTGTTAACTTAACTTATAGGGAACG 57.007 34.615 7.22 0.00 39.38 3.95
6585 14952 6.586082 CGGAAACTTGGACAATTTTAATGAGG 59.414 38.462 1.14 0.00 0.00 3.86
6674 15041 8.964420 AACTTTGGATGTCAAATGTTATAACG 57.036 30.769 10.92 0.00 43.57 3.18
6711 15078 7.472543 AGTCGCATCTTGGAATTGTTAAATAC 58.527 34.615 0.00 0.00 0.00 1.89
6716 15083 5.245531 AGAAGTCGCATCTTGGAATTGTTA 58.754 37.500 0.00 0.00 0.00 2.41
6719 15086 4.409570 CAAGAAGTCGCATCTTGGAATTG 58.590 43.478 13.45 1.53 46.39 2.32
6728 15095 3.238108 TCTCTTCCAAGAAGTCGCATC 57.762 47.619 4.38 0.00 34.03 3.91
6830 15197 8.105742 GTCCGAAAAACAAACTTACACAATTTC 58.894 33.333 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.