Multiple sequence alignment - TraesCS7B01G011900

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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 TraesCS7B01G011900 chr7B 100.000 3950 0 0 1 3950 7561665 7557716 0.000000e+00 7295.0
1 TraesCS7B01G011900 chr7B 94.693 1451 55 6 831 2274 10581887 10583322 0.000000e+00 2233.0
2 TraesCS7B01G011900 chr7B 93.983 349 21 0 1174 1522 622577178 622577526 2.700000e-146 529.0
3 TraesCS7B01G011900 chr7B 93.410 349 23 0 1174 1522 702697177 702697525 5.850000e-143 518.0
4 TraesCS7B01G011900 chr7B 91.691 349 29 0 1174 1522 154311556 154311208 5.930000e-133 484.0
5 TraesCS7B01G011900 chr7B 89.389 311 28 5 3473 3779 10584540 10584849 1.720000e-103 387.0
6 TraesCS7B01G011900 chr7B 94.089 203 11 1 1995 2196 154310240 154310038 1.380000e-79 307.0
7 TraesCS7B01G011900 chr7B 93.689 206 11 2 1992 2196 702698485 702698689 1.380000e-79 307.0
8 TraesCS7B01G011900 chr7B 81.229 293 37 6 2753 3043 10103450 10103726 1.850000e-53 220.0
9 TraesCS7B01G011900 chr7B 90.361 166 8 5 4 168 10577738 10577896 1.110000e-50 211.0
10 TraesCS7B01G011900 chr7B 84.177 158 19 4 3775 3932 10603801 10603952 8.840000e-32 148.0
11 TraesCS7B01G011900 chr7B 90.588 85 5 2 2499 2580 154309908 154309824 4.170000e-20 110.0
12 TraesCS7B01G011900 chr7B 88.636 88 7 2 2496 2580 622578822 622578909 1.940000e-18 104.0
13 TraesCS7B01G011900 chr7B 97.059 34 1 0 2593 2626 7558990 7558957 1.530000e-04 58.4
14 TraesCS7B01G011900 chr7B 97.059 34 1 0 2676 2709 7559073 7559040 1.530000e-04 58.4
15 TraesCS7B01G011900 chr7A 89.746 1141 58 18 834 1925 70806038 70804908 0.000000e+00 1404.0
16 TraesCS7B01G011900 chr7A 88.560 979 70 16 985 1945 74668984 74669938 0.000000e+00 1149.0
17 TraesCS7B01G011900 chr7A 85.967 734 57 18 2397 3121 74670493 74671189 0.000000e+00 743.0
18 TraesCS7B01G011900 chr7A 84.245 768 59 31 2400 3123 70781473 70780724 0.000000e+00 691.0
19 TraesCS7B01G011900 chr7A 81.426 603 47 25 2402 2968 645738567 645737994 2.180000e-117 433.0
20 TraesCS7B01G011900 chr7A 78.168 655 111 12 836 1471 74883350 74883991 4.790000e-104 388.0
21 TraesCS7B01G011900 chr7A 91.844 282 13 4 1917 2196 70451057 70450784 6.190000e-103 385.0
22 TraesCS7B01G011900 chr7A 91.815 281 15 2 1917 2196 95468374 95468647 6.190000e-103 385.0
23 TraesCS7B01G011900 chr7A 81.538 325 48 9 2758 3076 74602794 74603112 1.410000e-64 257.0
24 TraesCS7B01G011900 chr7A 84.556 259 28 8 2870 3121 74595135 74595388 3.050000e-61 246.0
25 TraesCS7B01G011900 chr7A 79.300 343 58 9 2771 3111 71120054 71119723 1.100000e-55 228.0
26 TraesCS7B01G011900 chr7A 95.902 122 5 0 2272 2393 74670235 74670356 8.660000e-47 198.0
27 TraesCS7B01G011900 chr7A 85.263 190 10 4 1973 2154 645738955 645738776 3.140000e-41 180.0
28 TraesCS7B01G011900 chr7A 82.039 206 36 1 2750 2954 70896009 70895804 1.460000e-39 174.0
29 TraesCS7B01G011900 chr7A 85.526 152 18 4 3775 3926 74671589 74671736 5.280000e-34 156.0
30 TraesCS7B01G011900 chr7A 86.466 133 14 3 3800 3932 70778971 70778843 4.110000e-30 143.0
31 TraesCS7B01G011900 chr7A 92.045 88 6 1 3179 3266 74671212 74671298 5.360000e-24 122.0
32 TraesCS7B01G011900 chr7A 93.333 45 3 0 1783 1827 74593334 74593378 2.550000e-07 67.6
33 TraesCS7B01G011900 chr7A 94.595 37 1 1 2590 2626 74670737 74670772 5.510000e-04 56.5
34 TraesCS7B01G011900 chr7A 100.000 28 0 0 3263 3290 634352458 634352431 7.000000e-03 52.8
35 TraesCS7B01G011900 chr7D 87.303 1016 54 24 734 1735 69012703 69013657 0.000000e+00 1092.0
36 TraesCS7B01G011900 chr7D 88.659 917 36 14 628 1523 66376295 66375426 0.000000e+00 1055.0
37 TraesCS7B01G011900 chr7D 96.501 343 12 0 1606 1948 66375350 66375008 5.730000e-158 568.0
38 TraesCS7B01G011900 chr7D 79.173 653 106 13 836 1471 69055303 69055942 3.650000e-115 425.0
39 TraesCS7B01G011900 chr7D 85.028 354 42 8 2771 3121 66514550 66514205 2.260000e-92 350.0
40 TraesCS7B01G011900 chr7D 80.077 517 39 22 2272 2755 66374796 66374311 3.810000e-85 326.0
41 TraesCS7B01G011900 chr7D 91.416 233 13 5 2046 2273 69013652 69013882 2.960000e-81 313.0
42 TraesCS7B01G011900 chr7D 78.431 561 62 21 3223 3780 69014634 69015138 1.070000e-80 311.0
43 TraesCS7B01G011900 chr7D 83.025 324 43 7 2758 3076 66515682 66515366 2.320000e-72 283.0
44 TraesCS7B01G011900 chr7D 80.952 378 48 15 2709 3076 68921471 68921834 1.080000e-70 278.0
45 TraesCS7B01G011900 chr7D 85.938 256 29 4 2869 3121 68911256 68911507 2.340000e-67 267.0
46 TraesCS7B01G011900 chr7D 89.189 185 17 1 216 400 69012473 69012654 1.100000e-55 228.0
47 TraesCS7B01G011900 chr7D 82.061 262 24 7 3521 3779 66373532 66373291 6.690000e-48 202.0
48 TraesCS7B01G011900 chr7D 87.975 158 15 3 3775 3932 66370067 66369914 2.420000e-42 183.0
49 TraesCS7B01G011900 chr7D 88.387 155 14 3 3775 3929 69016221 69016371 2.420000e-42 183.0
50 TraesCS7B01G011900 chr7D 86.792 159 13 6 3775 3932 69017567 69017718 1.890000e-38 171.0
51 TraesCS7B01G011900 chr7D 85.217 115 8 2 3335 3449 66373787 66373682 4.170000e-20 110.0
52 TraesCS7B01G011900 chr7D 92.424 66 5 0 3225 3290 66373924 66373859 1.170000e-15 95.3
53 TraesCS7B01G011900 chr7D 98.077 52 1 0 1562 1613 66375427 66375376 1.510000e-14 91.6
54 TraesCS7B01G011900 chr7D 94.915 59 2 1 2397 2455 69014057 69014114 1.510000e-14 91.6
55 TraesCS7B01G011900 chr7D 93.333 45 3 0 1783 1827 68902745 68902789 2.550000e-07 67.6
56 TraesCS7B01G011900 chr7D 80.723 83 12 4 3210 3290 548816644 548816564 1.190000e-05 62.1
57 TraesCS7B01G011900 chr7D 97.059 34 0 1 2593 2626 66374389 66374357 5.510000e-04 56.5
58 TraesCS7B01G011900 chr2A 82.687 670 89 11 835 1477 84748933 84749602 1.590000e-158 569.0
59 TraesCS7B01G011900 chr2B 83.497 612 71 14 835 1417 135794763 135795373 9.650000e-151 544.0
60 TraesCS7B01G011900 chr6B 93.696 349 22 0 1174 1522 521450234 521450582 1.260000e-144 523.0
61 TraesCS7B01G011900 chr6B 82.629 213 22 4 1948 2160 135303849 135304046 1.460000e-39 174.0
62 TraesCS7B01G011900 chr6B 90.226 133 9 3 2145 2273 135304062 135304194 1.890000e-38 171.0
63 TraesCS7B01G011900 chr6B 88.636 88 7 2 2496 2580 521451880 521451967 1.940000e-18 104.0
64 TraesCS7B01G011900 chr1A 92.958 355 25 0 1174 1528 61237132 61236778 5.850000e-143 518.0
65 TraesCS7B01G011900 chr1A 91.103 281 15 3 1917 2196 424484572 424484301 4.820000e-99 372.0
66 TraesCS7B01G011900 chr1A 90.747 281 18 2 1917 2196 61236250 61235977 6.240000e-98 368.0
67 TraesCS7B01G011900 chr1A 97.500 40 1 0 2235 2274 61235979 61235940 7.080000e-08 69.4
68 TraesCS7B01G011900 chr1B 91.691 349 29 0 1174 1522 72054271 72054619 5.930000e-133 484.0
69 TraesCS7B01G011900 chr1D 79.787 658 83 23 836 1472 486926547 486925919 2.180000e-117 433.0
70 TraesCS7B01G011900 chr3A 91.459 281 16 3 1917 2196 129249215 129248942 2.880000e-101 379.0
71 TraesCS7B01G011900 chr3A 85.915 213 15 6 1948 2160 36518024 36517827 3.090000e-51 213.0
72 TraesCS7B01G011900 chr3A 86.000 150 14 5 2145 2287 36517812 36517663 1.900000e-33 154.0
73 TraesCS7B01G011900 chrUn 79.298 570 63 19 3223 3779 84525305 84525832 8.120000e-92 348.0
74 TraesCS7B01G011900 chrUn 96.341 164 5 1 1782 1945 84524072 84524234 6.510000e-68 268.0
75 TraesCS7B01G011900 chrUn 88.608 158 14 3 3775 3932 84526850 84527003 5.210000e-44 189.0
76 TraesCS7B01G011900 chrUn 83.902 205 13 13 2397 2590 84524675 84524870 1.130000e-40 178.0
77 TraesCS7B01G011900 chr2D 83.612 299 22 15 1979 2273 260140225 260140500 5.070000e-64 255.0
78 TraesCS7B01G011900 chr4B 80.449 312 50 7 2770 3076 258794359 258794054 1.100000e-55 228.0
79 TraesCS7B01G011900 chr4B 88.966 145 9 5 2145 2282 155552270 155552414 5.250000e-39 172.0
80 TraesCS7B01G011900 chr4B 88.060 134 11 3 2145 2273 661349016 661349149 1.900000e-33 154.0
81 TraesCS7B01G011900 chr6A 83.505 194 13 12 2397 2580 76580507 76580691 3.160000e-36 163.0
82 TraesCS7B01G011900 chr5B 83.505 194 13 11 2397 2580 89069967 89069783 3.160000e-36 163.0


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 TraesCS7B01G011900 chr7B 7557716 7561665 3949 True 2470.600000 7295 98.039333 1 3950 3 chr7B.!!$R1 3949
1 TraesCS7B01G011900 chr7B 10577738 10584849 7111 False 943.666667 2233 91.481000 4 3779 3 chr7B.!!$F3 3775
2 TraesCS7B01G011900 chr7B 702697177 702698689 1512 False 412.500000 518 93.549500 1174 2196 2 chr7B.!!$F5 1022
3 TraesCS7B01G011900 chr7B 622577178 622578909 1731 False 316.500000 529 91.309500 1174 2580 2 chr7B.!!$F4 1406
4 TraesCS7B01G011900 chr7B 154309824 154311556 1732 True 300.333333 484 92.122667 1174 2580 3 chr7B.!!$R2 1406
5 TraesCS7B01G011900 chr7A 70804908 70806038 1130 True 1404.000000 1404 89.746000 834 1925 1 chr7A.!!$R2 1091
6 TraesCS7B01G011900 chr7A 70778843 70781473 2630 True 417.000000 691 85.355500 2400 3932 2 chr7A.!!$R6 1532
7 TraesCS7B01G011900 chr7A 74668984 74671736 2752 False 404.083333 1149 90.432500 985 3926 6 chr7A.!!$F5 2941
8 TraesCS7B01G011900 chr7A 74883350 74883991 641 False 388.000000 388 78.168000 836 1471 1 chr7A.!!$F2 635
9 TraesCS7B01G011900 chr7A 645737994 645738955 961 True 306.500000 433 83.344500 1973 2968 2 chr7A.!!$R7 995
10 TraesCS7B01G011900 chr7D 69055303 69055942 639 False 425.000000 425 79.173000 836 1471 1 chr7D.!!$F4 635
11 TraesCS7B01G011900 chr7D 69012473 69017718 5245 False 341.371429 1092 88.061857 216 3932 7 chr7D.!!$F5 3716
12 TraesCS7B01G011900 chr7D 66514205 66515682 1477 True 316.500000 350 84.026500 2758 3121 2 chr7D.!!$R3 363
13 TraesCS7B01G011900 chr7D 66369914 66376295 6381 True 298.600000 1055 89.783333 628 3932 9 chr7D.!!$R2 3304
14 TraesCS7B01G011900 chr2A 84748933 84749602 669 False 569.000000 569 82.687000 835 1477 1 chr2A.!!$F1 642
15 TraesCS7B01G011900 chr2B 135794763 135795373 610 False 544.000000 544 83.497000 835 1417 1 chr2B.!!$F1 582
16 TraesCS7B01G011900 chr6B 521450234 521451967 1733 False 313.500000 523 91.166000 1174 2580 2 chr6B.!!$F2 1406
17 TraesCS7B01G011900 chr1A 61235940 61237132 1192 True 318.466667 518 93.735000 1174 2274 3 chr1A.!!$R2 1100
18 TraesCS7B01G011900 chr1D 486925919 486926547 628 True 433.000000 433 79.787000 836 1472 1 chr1D.!!$R1 636
19 TraesCS7B01G011900 chrUn 84524072 84527003 2931 False 245.750000 348 87.037250 1782 3932 4 chrUn.!!$F1 2150

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
828 4165 0.036952 CCACAGGCCCATATAGCTCG 60.037 60.0 0.0 0.0 0.0 5.03 F
1540 5015 0.804989 GGTTCTGTTCTTGGCATCCG 59.195 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2627 7395 2.658325 GCATGACTTGACAAATTGACGC 59.342 45.455 0.0 0.0 0.0 5.19 R
3519 9670 0.590195 GCTGGTCTTTGTGTGCTCTG 59.410 55.000 0.0 0.0 0.0 3.35 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
18 19 1.537397 TCAGCTTGTCCTGCTCCCT 60.537 57.895 0.00 0.00 38.92 4.20
26 27 0.326264 GTCCTGCTCCCTTCATGTGT 59.674 55.000 0.00 0.00 0.00 3.72
27 28 0.325933 TCCTGCTCCCTTCATGTGTG 59.674 55.000 0.00 0.00 0.00 3.82
42 43 2.098614 TGTGTGGTCTTGCACATTGTT 58.901 42.857 0.00 0.00 40.24 2.83
60 61 8.394877 CACATTGTTGTTAGTGAACTGTCTTTA 58.605 33.333 0.00 0.00 36.45 1.85
137 138 3.558931 TTATGACCGATGCCATGAAGT 57.441 42.857 0.00 0.00 0.00 3.01
138 139 1.959042 ATGACCGATGCCATGAAGTC 58.041 50.000 0.00 0.00 0.00 3.01
139 140 0.612744 TGACCGATGCCATGAAGTCA 59.387 50.000 0.00 0.00 32.15 3.41
140 141 1.293924 GACCGATGCCATGAAGTCAG 58.706 55.000 0.00 0.00 0.00 3.51
141 142 0.107508 ACCGATGCCATGAAGTCAGG 60.108 55.000 0.00 0.00 0.00 3.86
142 143 0.178767 CCGATGCCATGAAGTCAGGA 59.821 55.000 0.00 0.00 0.00 3.86
143 144 1.202734 CCGATGCCATGAAGTCAGGAT 60.203 52.381 0.00 0.00 0.00 3.24
180 181 3.807553 TCAGCATGACAACAACTTCTGA 58.192 40.909 0.00 0.00 42.56 3.27
181 182 3.811497 TCAGCATGACAACAACTTCTGAG 59.189 43.478 0.00 0.00 42.56 3.35
186 219 4.937201 TGACAACAACTTCTGAGAGCTA 57.063 40.909 0.00 0.00 0.00 3.32
192 225 7.217200 ACAACAACTTCTGAGAGCTAACAATA 58.783 34.615 0.00 0.00 0.00 1.90
218 251 8.579863 ACAGAGCATTTTATACTCTTGCTTTTT 58.420 29.630 0.00 0.00 43.29 1.94
258 291 8.410141 TGTTCAGTTTAGGAAAATCGAAAATGT 58.590 29.630 0.00 0.00 30.95 2.71
261 294 8.792633 TCAGTTTAGGAAAATCGAAAATGTCAT 58.207 29.630 0.00 0.00 30.95 3.06
274 307 6.145534 TCGAAAATGTCATGTAGAGTTGTCAC 59.854 38.462 0.00 0.00 0.00 3.67
288 321 1.464734 TGTCACTCTCTTAGAGGCGG 58.535 55.000 9.58 3.25 46.45 6.13
290 323 1.064946 CACTCTCTTAGAGGCGGCG 59.935 63.158 9.58 0.51 46.45 6.46
291 324 2.122167 ACTCTCTTAGAGGCGGCGG 61.122 63.158 9.78 0.00 46.45 6.13
338 2728 3.254654 CGCGTTGACATCGGCGAT 61.255 61.111 18.14 18.14 32.91 4.58
375 2765 2.169832 TGAAGCTCCTTCGACTTTGG 57.830 50.000 0.00 0.00 42.78 3.28
400 2790 0.813821 GACAATCTTGCTTGCCTCCC 59.186 55.000 0.00 0.00 0.00 4.30
403 2793 0.112995 AATCTTGCTTGCCTCCCACA 59.887 50.000 0.00 0.00 0.00 4.17
406 2796 0.245539 CTTGCTTGCCTCCCACATTG 59.754 55.000 0.00 0.00 0.00 2.82
433 2823 8.114331 ACATGTGACTTTGTTGTCATCATTAT 57.886 30.769 0.00 0.00 46.77 1.28
434 2824 8.239314 ACATGTGACTTTGTTGTCATCATTATC 58.761 33.333 0.00 0.00 46.77 1.75
436 2826 7.584108 TGTGACTTTGTTGTCATCATTATCAC 58.416 34.615 0.64 11.44 46.77 3.06
447 2837 1.760613 TCATTATCACCCCTCACCGTC 59.239 52.381 0.00 0.00 0.00 4.79
461 2851 1.811266 CCGTCCACAAGCAGGATCG 60.811 63.158 0.00 0.00 37.52 3.69
463 2853 0.389817 CGTCCACAAGCAGGATCGAA 60.390 55.000 0.00 0.00 37.52 3.71
473 2863 0.755079 CAGGATCGAAGCTCCATGGA 59.245 55.000 15.27 15.27 35.08 3.41
474 2864 0.755686 AGGATCGAAGCTCCATGGAC 59.244 55.000 11.44 8.29 35.08 4.02
475 2865 0.755686 GGATCGAAGCTCCATGGACT 59.244 55.000 11.44 10.61 32.72 3.85
476 2866 1.539929 GGATCGAAGCTCCATGGACTG 60.540 57.143 11.44 3.05 32.72 3.51
488 2878 0.616111 ATGGACTGAAGCGAGAGGGT 60.616 55.000 0.00 0.00 0.00 4.34
517 2907 1.847328 TCTCCGATGACAGCTTGGTA 58.153 50.000 0.00 0.00 0.00 3.25
521 2911 2.236146 TCCGATGACAGCTTGGTATGTT 59.764 45.455 0.00 0.00 0.00 2.71
548 2938 5.324409 TGCTATGATTTCCAGTGGTTTTCT 58.676 37.500 9.54 0.00 0.00 2.52
567 2985 4.015872 TCTAAGAAGGCACGGTTTCATT 57.984 40.909 0.00 0.00 0.00 2.57
570 2988 4.400529 AAGAAGGCACGGTTTCATTTTT 57.599 36.364 0.00 0.00 0.00 1.94
572 2990 5.121221 AGAAGGCACGGTTTCATTTTTAG 57.879 39.130 0.00 0.00 0.00 1.85
590 3008 4.595762 TTAGTCAGTAGTTTCGGTTGCT 57.404 40.909 0.00 0.00 0.00 3.91
593 3011 3.069729 AGTCAGTAGTTTCGGTTGCTTCT 59.930 43.478 0.00 0.00 0.00 2.85
594 3012 3.808174 GTCAGTAGTTTCGGTTGCTTCTT 59.192 43.478 0.00 0.00 0.00 2.52
610 3028 7.418025 GGTTGCTTCTTAGTGAGGTATGACTAT 60.418 40.741 0.00 0.00 0.00 2.12
612 3030 7.717568 TGCTTCTTAGTGAGGTATGACTATTC 58.282 38.462 0.00 0.00 0.00 1.75
613 3031 7.561722 TGCTTCTTAGTGAGGTATGACTATTCT 59.438 37.037 0.00 0.00 0.00 2.40
688 3110 3.636679 TCAAATTGGGTGAGGTTTGACA 58.363 40.909 0.00 0.00 36.11 3.58
709 3131 6.041637 TGACAACTCCTATACTCTTGTTGTGT 59.958 38.462 12.92 0.00 44.96 3.72
710 3132 6.827727 ACAACTCCTATACTCTTGTTGTGTT 58.172 36.000 8.24 0.00 43.85 3.32
712 3134 7.773690 ACAACTCCTATACTCTTGTTGTGTTTT 59.226 33.333 8.24 0.00 43.85 2.43
751 3173 4.464069 TGTTGTTTTGGGAAGGAAACAG 57.536 40.909 0.00 0.00 36.63 3.16
784 3209 4.087892 GCAGGAGGCGCTCAGGAA 62.088 66.667 7.64 0.00 31.08 3.36
807 4144 2.555123 GGCTGTGCCGAGAAAATCA 58.445 52.632 0.00 0.00 39.62 2.57
821 4158 1.006813 AAATCACCCACAGGCCCATA 58.993 50.000 0.00 0.00 36.11 2.74
823 4160 2.132303 ATCACCCACAGGCCCATATA 57.868 50.000 0.00 0.00 36.11 0.86
824 4161 1.434188 TCACCCACAGGCCCATATAG 58.566 55.000 0.00 0.00 36.11 1.31
825 4162 0.250901 CACCCACAGGCCCATATAGC 60.251 60.000 0.00 0.00 36.11 2.97
826 4163 0.401979 ACCCACAGGCCCATATAGCT 60.402 55.000 0.00 0.00 36.11 3.32
827 4164 0.326264 CCCACAGGCCCATATAGCTC 59.674 60.000 0.00 0.00 0.00 4.09
828 4165 0.036952 CCACAGGCCCATATAGCTCG 60.037 60.000 0.00 0.00 0.00 5.03
1159 4565 0.953960 GTTCCAAGGCGATGACGGTT 60.954 55.000 0.00 0.00 40.15 4.44
1287 4693 1.075151 GGAACGGGAGGAGGAGGAT 60.075 63.158 0.00 0.00 0.00 3.24
1538 5013 4.525912 ATTTGGTTCTGTTCTTGGCATC 57.474 40.909 0.00 0.00 0.00 3.91
1540 5015 0.804989 GGTTCTGTTCTTGGCATCCG 59.195 55.000 0.00 0.00 0.00 4.18
1542 5017 2.151202 GTTCTGTTCTTGGCATCCGAA 58.849 47.619 0.00 0.00 0.00 4.30
1543 5018 2.099141 TCTGTTCTTGGCATCCGAAG 57.901 50.000 0.00 0.00 0.00 3.79
1544 5019 1.347707 TCTGTTCTTGGCATCCGAAGT 59.652 47.619 0.00 0.00 0.00 3.01
1560 5035 3.719144 GTTCCGAACCCAACCGCG 61.719 66.667 0.00 0.00 0.00 6.46
1620 5129 2.730183 TTGCGTTTCTTGACGTCTTG 57.270 45.000 17.92 9.44 44.50 3.02
1737 5259 4.047059 CGGTGGGTCGTGTACGCT 62.047 66.667 4.67 0.00 41.50 5.07
2012 6436 3.223674 TCCTACTGGTCGATGCATCTA 57.776 47.619 23.73 11.14 34.23 1.98
2015 6439 3.507622 CCTACTGGTCGATGCATCTATGA 59.492 47.826 23.73 11.51 0.00 2.15
2025 6449 7.043854 GGTCGATGCATCTATGATTTTGTTTTG 60.044 37.037 23.73 3.22 0.00 2.44
2283 6782 4.954875 TGTCCATGATTTGAAAACCCAAC 58.045 39.130 0.00 0.00 0.00 3.77
2293 6792 3.702792 TGAAAACCCAACTCTGGTTCAA 58.297 40.909 0.00 0.00 45.23 2.69
2393 6918 2.438021 TCCCACAGCACTACTTGAAAGT 59.562 45.455 0.71 0.71 42.91 2.66
2394 6919 3.644265 TCCCACAGCACTACTTGAAAGTA 59.356 43.478 3.06 3.06 40.37 2.24
2395 6920 3.746492 CCCACAGCACTACTTGAAAGTAC 59.254 47.826 0.00 0.00 40.37 2.73
2446 7161 8.303156 TCAGATTTCTTCAGAGAGACACTAAAG 58.697 37.037 0.00 0.00 32.44 1.85
2542 7289 8.840321 GCACATATTCACACTAAACCTTGATAT 58.160 33.333 0.00 0.00 0.00 1.63
2601 7369 9.612620 AGATAATTTAGTTTCGCTTTCTGTTTG 57.387 29.630 0.00 0.00 0.00 2.93
2606 7374 9.959749 ATTTAGTTTCGCTTTCTGTTTGATTTA 57.040 25.926 0.00 0.00 0.00 1.40
2607 7375 9.445786 TTTAGTTTCGCTTTCTGTTTGATTTAG 57.554 29.630 0.00 0.00 0.00 1.85
2610 7378 5.627499 TCGCTTTCTGTTTGATTTAGCAT 57.373 34.783 0.00 0.00 0.00 3.79
2611 7379 6.735678 TCGCTTTCTGTTTGATTTAGCATA 57.264 33.333 0.00 0.00 0.00 3.14
2612 7380 7.320443 TCGCTTTCTGTTTGATTTAGCATAT 57.680 32.000 0.00 0.00 0.00 1.78
2613 7381 7.761409 TCGCTTTCTGTTTGATTTAGCATATT 58.239 30.769 0.00 0.00 0.00 1.28
2614 7382 7.697710 TCGCTTTCTGTTTGATTTAGCATATTG 59.302 33.333 0.00 0.00 0.00 1.90
2615 7383 7.485913 CGCTTTCTGTTTGATTTAGCATATTGT 59.514 33.333 0.00 0.00 0.00 2.71
2616 7384 9.787532 GCTTTCTGTTTGATTTAGCATATTGTA 57.212 29.630 0.00 0.00 0.00 2.41
2629 7397 9.509855 TTTAGCATATTGTAAATGGTTTTAGCG 57.490 29.630 0.00 0.00 36.52 4.26
2631 7399 7.193595 AGCATATTGTAAATGGTTTTAGCGTC 58.806 34.615 0.00 0.00 31.22 5.19
2636 7412 8.825667 ATTGTAAATGGTTTTAGCGTCAATTT 57.174 26.923 0.00 0.00 0.00 1.82
2659 7436 3.433615 GTCAAGTCATGCTTTTAGCGTCT 59.566 43.478 0.37 0.00 46.26 4.18
2669 7446 7.979537 TCATGCTTTTAGCGTCTTAGATAAGAA 59.020 33.333 3.92 0.00 46.26 2.52
2737 7533 9.832445 ACCAAATTCAGGTTGTATACTATAGTG 57.168 33.333 15.90 0.00 35.33 2.74
2755 7551 9.819267 ACTATAGTGTTCCATAAAAGCTAGTTC 57.181 33.333 4.10 0.00 0.00 3.01
2795 8710 6.654793 TGTTTTTCAGGTTTTGTGCATAAC 57.345 33.333 0.00 0.00 0.00 1.89
2857 8772 7.660208 TCAAGTTATTAGTCTTTTCCAGTGGTC 59.340 37.037 9.54 0.00 0.00 4.02
2957 8875 2.029290 TCGGTGCAGAGTAGAAAAGGAC 60.029 50.000 0.00 0.00 0.00 3.85
3077 9015 7.693132 TGCATTGAGATATAGGCTTAGGAAAT 58.307 34.615 0.00 0.00 0.00 2.17
3123 9061 7.758076 TCTGCTAGCTGAAATTGATTCATTTTG 59.242 33.333 20.65 0.88 46.62 2.44
3124 9062 7.604549 TGCTAGCTGAAATTGATTCATTTTGA 58.395 30.769 17.23 2.97 46.62 2.69
3129 9067 9.280174 AGCTGAAATTGATTCATTTTGAATTGT 57.720 25.926 10.41 0.00 46.20 2.71
3157 9112 2.554344 GGCCCATGTGGTTCTGAACTTA 60.554 50.000 19.05 7.14 36.04 2.24
3162 9117 5.534654 CCCATGTGGTTCTGAACTTAAGAAA 59.465 40.000 19.05 0.91 35.50 2.52
3172 9132 8.665685 GTTCTGAACTTAAGAAACTCTGTGAAA 58.334 33.333 10.09 0.00 35.50 2.69
3181 9194 4.646492 AGAAACTCTGTGAAAATTGGTGCT 59.354 37.500 0.00 0.00 0.00 4.40
3232 9245 4.404073 TGTGGTGGTTCTTGCAGTTAATTT 59.596 37.500 0.00 0.00 0.00 1.82
3243 9256 4.311606 TGCAGTTAATTTAGCACTCGACA 58.688 39.130 0.00 0.00 31.05 4.35
3252 9265 4.976224 TTAGCACTCGACATTAGCTGTA 57.024 40.909 0.00 0.00 38.54 2.74
3290 9303 6.885918 TCAGTCCATCAGCAGAAAATGAATTA 59.114 34.615 0.00 0.00 0.00 1.40
3291 9304 7.394077 TCAGTCCATCAGCAGAAAATGAATTAA 59.606 33.333 0.00 0.00 0.00 1.40
3322 9425 8.340443 CACATATTCAGGATAACATGTGAACAG 58.660 37.037 0.00 0.00 40.14 3.16
3327 9430 7.615582 TCAGGATAACATGTGAACAGAATTC 57.384 36.000 0.00 0.00 0.00 2.17
3328 9431 7.167535 TCAGGATAACATGTGAACAGAATTCA 58.832 34.615 8.44 0.00 0.00 2.57
3329 9432 7.335171 TCAGGATAACATGTGAACAGAATTCAG 59.665 37.037 8.44 1.65 0.00 3.02
3330 9433 6.600822 AGGATAACATGTGAACAGAATTCAGG 59.399 38.462 8.44 1.79 0.00 3.86
3331 9434 6.599244 GGATAACATGTGAACAGAATTCAGGA 59.401 38.462 8.44 0.00 0.00 3.86
3332 9435 7.284034 GGATAACATGTGAACAGAATTCAGGAT 59.716 37.037 8.44 0.00 0.00 3.24
3335 9438 7.563888 ACATGTGAACAGAATTCAGGATATG 57.436 36.000 8.44 6.02 0.00 1.78
3372 9475 4.150098 CCGTAAGAACACTAGTTTCTGCAC 59.850 45.833 16.17 15.27 38.30 4.57
3377 9480 7.986085 AAGAACACTAGTTTCTGCACATTAT 57.014 32.000 16.17 2.04 38.30 1.28
3390 9493 6.653020 TCTGCACATTATATTGTTCTCAGGT 58.347 36.000 14.71 0.00 0.00 4.00
3391 9494 7.112122 TCTGCACATTATATTGTTCTCAGGTT 58.888 34.615 14.71 0.00 0.00 3.50
3392 9495 8.264347 TCTGCACATTATATTGTTCTCAGGTTA 58.736 33.333 14.71 2.47 0.00 2.85
3393 9496 8.978874 TGCACATTATATTGTTCTCAGGTTAT 57.021 30.769 0.00 0.00 0.00 1.89
3452 9591 6.877668 TGGTATTAACTATCAGGTCCACAA 57.122 37.500 0.00 0.00 0.00 3.33
3494 9645 4.024048 AGGCTAGACAAATCAACAAACACG 60.024 41.667 0.00 0.00 0.00 4.49
3500 9651 6.791303 AGACAAATCAACAAACACGTTACAT 58.209 32.000 0.00 0.00 0.00 2.29
3519 9670 1.227999 TGCACAGCACGGCTAAGAAC 61.228 55.000 0.00 0.00 36.40 3.01
3533 9720 3.809832 GCTAAGAACAGAGCACACAAAGA 59.190 43.478 0.00 0.00 38.62 2.52
3544 9731 2.653890 CACACAAAGACCAGCGATTTG 58.346 47.619 0.00 0.00 39.32 2.32
3572 9760 1.276138 CTTTCAATGGGGTTGCCTTCC 59.724 52.381 0.00 0.00 37.74 3.46
3583 9771 3.368427 GGGTTGCCTTCCTTTTGCTTATC 60.368 47.826 0.00 0.00 0.00 1.75
3586 9774 3.505386 TGCCTTCCTTTTGCTTATCCAA 58.495 40.909 0.00 0.00 0.00 3.53
3595 9783 5.893824 CCTTTTGCTTATCCAATACCTCCTT 59.106 40.000 0.00 0.00 0.00 3.36
3633 9821 7.287696 ACAGAGAAAATTACACATTTGGTCCTT 59.712 33.333 0.00 0.00 0.00 3.36
3643 9831 5.304101 ACACATTTGGTCCTTGAATTTGCTA 59.696 36.000 0.00 0.00 0.00 3.49
3651 9839 4.095036 GTCCTTGAATTTGCTAGCACCTAC 59.905 45.833 19.17 10.30 0.00 3.18
3666 9857 3.680475 GCACCTACCACCATATCGAAACA 60.680 47.826 0.00 0.00 0.00 2.83
3699 9890 7.062322 TGCTTCAATATGGTCCTTGAATACAT 58.938 34.615 5.49 0.00 39.79 2.29
3732 9923 7.502060 AACATCTAGAGAAGGAGGAAATGAA 57.498 36.000 0.00 0.00 0.00 2.57
3745 9936 4.536765 AGGAAATGAAAATATCACCGCCT 58.463 39.130 0.00 0.00 41.93 5.52
3785 13348 2.417239 GCATGCCACAAAACCATCAATG 59.583 45.455 6.36 0.00 0.00 2.82
3786 13349 2.166821 TGCCACAAAACCATCAATGC 57.833 45.000 0.00 0.00 0.00 3.56
3788 13351 2.896044 TGCCACAAAACCATCAATGCTA 59.104 40.909 0.00 0.00 0.00 3.49
3813 13376 6.145338 TCGTTGGTATCCTCAATCTAACTC 57.855 41.667 0.00 0.00 0.00 3.01
3831 13394 3.601443 CTCTTGAGAGTGTCGGGATTT 57.399 47.619 0.00 0.00 37.40 2.17
3839 13402 2.487762 GAGTGTCGGGATTTGCATGAAA 59.512 45.455 0.00 0.00 0.00 2.69
3848 13411 5.394005 CGGGATTTGCATGAAAAGTATCCAA 60.394 40.000 16.06 0.00 0.00 3.53
3849 13412 5.812127 GGGATTTGCATGAAAAGTATCCAAC 59.188 40.000 16.06 0.54 0.00 3.77
3850 13413 6.397272 GGATTTGCATGAAAAGTATCCAACA 58.603 36.000 11.13 0.00 0.00 3.33
3851 13414 6.532657 GGATTTGCATGAAAAGTATCCAACAG 59.467 38.462 11.13 0.00 0.00 3.16
3852 13415 4.439305 TGCATGAAAAGTATCCAACAGC 57.561 40.909 0.00 0.00 0.00 4.40
3939 13502 2.423446 CCTCCTAGGCCATGTCGC 59.577 66.667 5.01 0.00 0.00 5.19
3941 13504 3.506059 CTCCTAGGCCATGTCGCGG 62.506 68.421 6.13 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.676151 GAAGGGAGCAGGACAAGCTG 60.676 60.000 0.00 0.00 43.58 4.24
2 3 1.130054 TGAAGGGAGCAGGACAAGCT 61.130 55.000 0.00 0.00 46.82 3.74
18 19 2.049888 TGTGCAAGACCACACATGAA 57.950 45.000 0.00 0.00 41.67 2.57
26 27 3.951037 ACTAACAACAATGTGCAAGACCA 59.049 39.130 0.00 0.00 40.46 4.02
27 28 4.036262 TCACTAACAACAATGTGCAAGACC 59.964 41.667 0.00 0.00 40.46 3.85
101 102 6.382869 GGTCATAATTGAGACCCAGAAATG 57.617 41.667 16.29 0.00 46.79 2.32
137 138 5.104817 TGACTGTTGCTGATTGATATCCTGA 60.105 40.000 0.00 0.00 0.00 3.86
138 139 5.121105 TGACTGTTGCTGATTGATATCCTG 58.879 41.667 0.00 0.00 0.00 3.86
139 140 5.363562 TGACTGTTGCTGATTGATATCCT 57.636 39.130 0.00 0.00 0.00 3.24
140 141 4.024218 GCTGACTGTTGCTGATTGATATCC 60.024 45.833 0.00 0.00 0.00 2.59
141 142 4.573607 TGCTGACTGTTGCTGATTGATATC 59.426 41.667 0.00 0.00 0.00 1.63
142 143 4.520179 TGCTGACTGTTGCTGATTGATAT 58.480 39.130 7.91 0.00 0.00 1.63
143 144 3.941573 TGCTGACTGTTGCTGATTGATA 58.058 40.909 7.91 0.00 0.00 2.15
168 169 5.991328 TTGTTAGCTCTCAGAAGTTGTTG 57.009 39.130 0.00 0.00 0.00 3.33
171 172 7.093354 TCTGTATTGTTAGCTCTCAGAAGTTG 58.907 38.462 0.00 0.00 0.00 3.16
172 173 7.233389 TCTGTATTGTTAGCTCTCAGAAGTT 57.767 36.000 0.00 0.00 0.00 2.66
173 174 6.627065 GCTCTGTATTGTTAGCTCTCAGAAGT 60.627 42.308 0.00 0.00 31.63 3.01
174 175 5.748152 GCTCTGTATTGTTAGCTCTCAGAAG 59.252 44.000 0.00 0.00 31.63 2.85
179 180 6.917217 AAATGCTCTGTATTGTTAGCTCTC 57.083 37.500 0.00 0.00 35.95 3.20
180 181 8.970859 ATAAAATGCTCTGTATTGTTAGCTCT 57.029 30.769 0.00 0.00 35.95 4.09
218 251 5.895636 AACTGAACAGATGACACAAACAA 57.104 34.783 8.87 0.00 0.00 2.83
228 261 7.364522 TCGATTTTCCTAAACTGAACAGATG 57.635 36.000 8.87 0.00 0.00 2.90
274 307 2.725008 CCGCCGCCTCTAAGAGAG 59.275 66.667 1.62 1.62 41.96 3.20
288 321 2.427540 ATATCTGAGCTCCACGCCGC 62.428 60.000 12.15 0.00 40.39 6.53
290 323 0.965439 AGATATCTGAGCTCCACGCC 59.035 55.000 12.15 0.00 40.39 5.68
291 324 2.609244 GGAAGATATCTGAGCTCCACGC 60.609 54.545 12.15 0.00 39.57 5.34
304 2694 2.493713 GCGACACGACTGGAAGATAT 57.506 50.000 0.00 0.00 37.43 1.63
338 2728 6.779860 AGCTTCAAGTTAGGATCCAAGTTTA 58.220 36.000 15.82 4.68 0.00 2.01
375 2765 1.336240 GCAAGCAAGATTGTCCCACAC 60.336 52.381 0.00 0.00 32.56 3.82
403 2793 6.691754 TGACAACAAAGTCACATGTACAAT 57.308 33.333 0.00 0.00 43.18 2.71
416 2806 5.653769 AGGGGTGATAATGATGACAACAAAG 59.346 40.000 0.00 0.00 0.00 2.77
433 2823 2.920912 GTGGACGGTGAGGGGTGA 60.921 66.667 0.00 0.00 0.00 4.02
434 2824 2.731691 CTTGTGGACGGTGAGGGGTG 62.732 65.000 0.00 0.00 0.00 4.61
436 2826 2.347490 CTTGTGGACGGTGAGGGG 59.653 66.667 0.00 0.00 0.00 4.79
447 2837 0.392193 AGCTTCGATCCTGCTTGTGG 60.392 55.000 0.00 0.00 32.61 4.17
473 2863 1.324005 GGCTACCCTCTCGCTTCAGT 61.324 60.000 0.00 0.00 0.00 3.41
474 2864 1.439644 GGCTACCCTCTCGCTTCAG 59.560 63.158 0.00 0.00 0.00 3.02
475 2865 2.415608 CGGCTACCCTCTCGCTTCA 61.416 63.158 0.00 0.00 0.00 3.02
476 2866 2.413765 CGGCTACCCTCTCGCTTC 59.586 66.667 0.00 0.00 0.00 3.86
497 2887 0.976641 ACCAAGCTGTCATCGGAGAA 59.023 50.000 0.00 0.00 43.58 2.87
517 2907 6.183360 CCACTGGAAATCATAGCATTGAACAT 60.183 38.462 0.00 0.00 0.00 2.71
521 2911 4.858850 ACCACTGGAAATCATAGCATTGA 58.141 39.130 0.71 0.00 0.00 2.57
548 2938 5.523438 AAAAATGAAACCGTGCCTTCTTA 57.477 34.783 0.00 0.00 0.00 2.10
567 2985 5.362263 AGCAACCGAAACTACTGACTAAAA 58.638 37.500 0.00 0.00 0.00 1.52
570 2988 4.280174 AGAAGCAACCGAAACTACTGACTA 59.720 41.667 0.00 0.00 0.00 2.59
572 2990 3.391049 AGAAGCAACCGAAACTACTGAC 58.609 45.455 0.00 0.00 0.00 3.51
633 3051 9.784531 TGATGAGAAAACTCTCTTACAAAGAAT 57.215 29.630 3.95 0.00 37.02 2.40
664 3082 6.015918 TGTCAAACCTCACCCAATTTGATAT 58.984 36.000 0.00 0.00 41.64 1.63
674 3092 1.143073 AGGAGTTGTCAAACCTCACCC 59.857 52.381 6.72 0.00 36.94 4.61
677 3095 6.017192 AGAGTATAGGAGTTGTCAAACCTCA 58.983 40.000 13.63 4.04 36.94 3.86
688 3110 8.747538 AAAAACACAACAAGAGTATAGGAGTT 57.252 30.769 0.00 0.00 0.00 3.01
712 3134 8.999905 AAACAACAAGAGTATACCCCTAAAAA 57.000 30.769 0.00 0.00 0.00 1.94
714 3136 7.449086 CCAAAACAACAAGAGTATACCCCTAAA 59.551 37.037 0.00 0.00 0.00 1.85
715 3137 6.943718 CCAAAACAACAAGAGTATACCCCTAA 59.056 38.462 0.00 0.00 0.00 2.69
716 3138 6.478129 CCAAAACAACAAGAGTATACCCCTA 58.522 40.000 0.00 0.00 0.00 3.53
719 3141 5.318630 TCCCAAAACAACAAGAGTATACCC 58.681 41.667 0.00 0.00 0.00 3.69
720 3142 6.072119 CCTTCCCAAAACAACAAGAGTATACC 60.072 42.308 0.00 0.00 0.00 2.73
721 3143 6.713450 TCCTTCCCAAAACAACAAGAGTATAC 59.287 38.462 0.00 0.00 0.00 1.47
722 3144 6.843752 TCCTTCCCAAAACAACAAGAGTATA 58.156 36.000 0.00 0.00 0.00 1.47
723 3145 5.701224 TCCTTCCCAAAACAACAAGAGTAT 58.299 37.500 0.00 0.00 0.00 2.12
724 3146 5.118729 TCCTTCCCAAAACAACAAGAGTA 57.881 39.130 0.00 0.00 0.00 2.59
725 3147 3.976015 TCCTTCCCAAAACAACAAGAGT 58.024 40.909 0.00 0.00 0.00 3.24
726 3148 5.109210 GTTTCCTTCCCAAAACAACAAGAG 58.891 41.667 0.00 0.00 35.83 2.85
727 3149 4.528596 TGTTTCCTTCCCAAAACAACAAGA 59.471 37.500 0.00 0.00 41.15 3.02
728 3150 4.826556 TGTTTCCTTCCCAAAACAACAAG 58.173 39.130 0.00 0.00 41.15 3.16
729 3151 4.323104 CCTGTTTCCTTCCCAAAACAACAA 60.323 41.667 2.73 0.00 42.86 2.83
730 3152 3.196685 CCTGTTTCCTTCCCAAAACAACA 59.803 43.478 2.73 0.00 42.86 3.33
731 3153 3.196901 ACCTGTTTCCTTCCCAAAACAAC 59.803 43.478 2.73 0.00 42.86 3.32
732 3154 3.445987 ACCTGTTTCCTTCCCAAAACAA 58.554 40.909 2.73 0.00 42.86 2.83
776 3198 2.743928 CAGCCCACGTTCCTGAGC 60.744 66.667 1.66 0.00 0.00 4.26
807 4144 0.401979 AGCTATATGGGCCTGTGGGT 60.402 55.000 4.53 0.00 34.45 4.51
821 4158 1.195115 TCAAGGAAGGTGCGAGCTAT 58.805 50.000 0.00 0.00 0.00 2.97
823 4160 0.108585 TTTCAAGGAAGGTGCGAGCT 59.891 50.000 0.00 0.00 0.00 4.09
824 4161 1.168714 ATTTCAAGGAAGGTGCGAGC 58.831 50.000 0.00 0.00 0.00 5.03
825 4162 3.600388 AGTATTTCAAGGAAGGTGCGAG 58.400 45.455 0.00 0.00 0.00 5.03
826 4163 3.596214 GAGTATTTCAAGGAAGGTGCGA 58.404 45.455 0.00 0.00 0.00 5.10
827 4164 2.678336 GGAGTATTTCAAGGAAGGTGCG 59.322 50.000 0.00 0.00 0.00 5.34
828 4165 3.017442 GGGAGTATTTCAAGGAAGGTGC 58.983 50.000 0.00 0.00 0.00 5.01
1103 4506 4.789075 CGTTCATCGACGCCCGGT 62.789 66.667 0.00 0.00 42.86 5.28
1159 4565 0.541063 TGGAGGAGCACGTACTGGAA 60.541 55.000 0.00 0.00 0.00 3.53
1473 4910 1.612442 AAGCGGGCTTACCTCAGGA 60.612 57.895 0.00 0.00 36.97 3.86
1482 4919 2.087646 GAAGAATCAAGAAGCGGGCTT 58.912 47.619 5.45 5.45 39.23 4.35
1538 5013 1.232621 GGTTGGGTTCGGAACTTCGG 61.233 60.000 19.40 0.00 0.00 4.30
1540 5015 1.848932 GCGGTTGGGTTCGGAACTTC 61.849 60.000 19.40 12.74 0.00 3.01
1542 5017 2.281276 GCGGTTGGGTTCGGAACT 60.281 61.111 19.40 0.00 0.00 3.01
1543 5018 3.719144 CGCGGTTGGGTTCGGAAC 61.719 66.667 12.41 12.41 0.00 3.62
1544 5019 4.992511 CCGCGGTTGGGTTCGGAA 62.993 66.667 19.50 0.00 44.23 4.30
1560 5035 1.753073 CAGAACCATGAATTGCTCCCC 59.247 52.381 0.00 0.00 0.00 4.81
1620 5129 1.135859 CCAAGTTGCGAACAGAGATGC 60.136 52.381 0.00 0.00 0.00 3.91
2012 6436 6.105397 AGCACTCCATCAAAACAAAATCAT 57.895 33.333 0.00 0.00 0.00 2.45
2015 6439 7.669427 TGAATAGCACTCCATCAAAACAAAAT 58.331 30.769 0.00 0.00 0.00 1.82
2154 6588 9.113838 AGACCACTTTATAGCATTCAATACTTG 57.886 33.333 0.00 0.00 0.00 3.16
2283 6782 6.481644 GCTAAACTAGGATGATTGAACCAGAG 59.518 42.308 0.00 0.00 0.00 3.35
2293 6792 8.540507 TCTCTGTAAAGCTAAACTAGGATGAT 57.459 34.615 0.00 0.00 0.00 2.45
2590 7341 8.693542 ACAATATGCTAAATCAAACAGAAAGC 57.306 30.769 0.00 0.00 33.56 3.51
2606 7374 7.095695 ACGCTAAAACCATTTACAATATGCT 57.904 32.000 0.00 0.00 0.00 3.79
2607 7375 6.970043 TGACGCTAAAACCATTTACAATATGC 59.030 34.615 0.00 0.00 0.00 3.14
2610 7378 9.915629 AAATTGACGCTAAAACCATTTACAATA 57.084 25.926 0.00 0.00 30.25 1.90
2611 7379 8.707839 CAAATTGACGCTAAAACCATTTACAAT 58.292 29.630 0.00 0.00 31.00 2.71
2612 7380 7.707035 ACAAATTGACGCTAAAACCATTTACAA 59.293 29.630 0.00 0.00 0.00 2.41
2613 7381 7.203910 ACAAATTGACGCTAAAACCATTTACA 58.796 30.769 0.00 0.00 0.00 2.41
2614 7382 7.380065 TGACAAATTGACGCTAAAACCATTTAC 59.620 33.333 0.00 0.00 0.00 2.01
2615 7383 7.426410 TGACAAATTGACGCTAAAACCATTTA 58.574 30.769 0.00 0.00 0.00 1.40
2616 7384 6.276847 TGACAAATTGACGCTAAAACCATTT 58.723 32.000 0.00 0.00 0.00 2.32
2619 7387 4.902443 TGACAAATTGACGCTAAAACCA 57.098 36.364 0.00 0.00 0.00 3.67
2620 7388 5.278604 ACTTGACAAATTGACGCTAAAACC 58.721 37.500 0.00 0.00 0.00 3.27
2621 7389 5.968848 TGACTTGACAAATTGACGCTAAAAC 59.031 36.000 0.00 0.00 0.00 2.43
2625 7393 4.378356 GCATGACTTGACAAATTGACGCTA 60.378 41.667 0.00 0.00 0.00 4.26
2627 7395 2.658325 GCATGACTTGACAAATTGACGC 59.342 45.455 0.00 0.00 0.00 5.19
2629 7397 6.833342 AAAAGCATGACTTGACAAATTGAC 57.167 33.333 0.00 0.00 39.09 3.18
2631 7399 6.399249 CGCTAAAAGCATGACTTGACAAATTG 60.399 38.462 0.00 0.00 42.58 2.32
2635 7411 3.563808 ACGCTAAAAGCATGACTTGACAA 59.436 39.130 0.00 0.00 42.58 3.18
2636 7412 3.138304 ACGCTAAAAGCATGACTTGACA 58.862 40.909 0.00 0.00 42.58 3.58
2669 7446 6.325919 TGCTAAATCAAACAGAAATCGGTT 57.674 33.333 0.00 0.00 35.85 4.44
2737 7533 4.700213 TGCAGGAACTAGCTTTTATGGAAC 59.300 41.667 0.00 0.00 36.02 3.62
2755 7551 8.531622 TGAAAAACAACAATATAATGTGCAGG 57.468 30.769 0.00 0.00 32.81 4.85
2795 8710 3.434984 GCAGAGCTAACAAAGAAGACTGG 59.565 47.826 0.00 0.00 0.00 4.00
2832 8747 7.360101 CGACCACTGGAAAAGACTAATAACTTG 60.360 40.741 0.71 0.00 0.00 3.16
2842 8757 1.949465 ACACGACCACTGGAAAAGAC 58.051 50.000 0.71 0.00 0.00 3.01
2857 8772 2.094258 GCATCATGTCACAGGTAACACG 59.906 50.000 0.00 0.00 41.41 4.49
3068 9006 3.970640 AGAGCTACTGGGGATTTCCTAAG 59.029 47.826 0.00 0.00 35.95 2.18
3077 9015 2.254152 ATCACAAGAGCTACTGGGGA 57.746 50.000 0.00 0.00 36.28 4.81
3123 9061 0.970427 ATGGGCCGGGTTCACAATTC 60.970 55.000 2.18 0.00 0.00 2.17
3124 9062 1.078347 ATGGGCCGGGTTCACAATT 59.922 52.632 2.18 0.00 0.00 2.32
3126 9064 2.282816 CATGGGCCGGGTTCACAA 60.283 61.111 2.18 0.00 0.00 3.33
3127 9065 3.575247 ACATGGGCCGGGTTCACA 61.575 61.111 2.18 0.00 0.00 3.58
3128 9066 3.061848 CACATGGGCCGGGTTCAC 61.062 66.667 2.18 0.00 0.00 3.18
3129 9067 4.358841 CCACATGGGCCGGGTTCA 62.359 66.667 2.18 0.00 0.00 3.18
3131 9069 3.879180 GAACCACATGGGCCGGGTT 62.879 63.158 17.98 17.98 45.82 4.11
3157 9112 5.127682 AGCACCAATTTTCACAGAGTTTCTT 59.872 36.000 0.00 0.00 0.00 2.52
3162 9117 5.127682 AGAAAAGCACCAATTTTCACAGAGT 59.872 36.000 12.23 0.00 45.10 3.24
3172 9132 6.127196 TGACACCTAAAAGAAAAGCACCAATT 60.127 34.615 0.00 0.00 0.00 2.32
3181 9194 6.707440 TCATTGCTGACACCTAAAAGAAAA 57.293 33.333 0.00 0.00 0.00 2.29
3232 9245 3.066342 GGTACAGCTAATGTCGAGTGCTA 59.934 47.826 0.00 0.00 42.70 3.49
3243 9256 6.303839 TGAAACCTGAAAAGGTACAGCTAAT 58.696 36.000 0.00 0.00 42.20 1.73
3252 9265 3.662759 TGGACTGAAACCTGAAAAGGT 57.337 42.857 0.00 0.00 45.55 3.50
3297 9310 8.267183 TCTGTTCACATGTTATCCTGAATATGT 58.733 33.333 0.00 0.00 40.53 2.29
3298 9311 8.667076 TCTGTTCACATGTTATCCTGAATATG 57.333 34.615 0.00 0.00 34.92 1.78
3300 9313 9.685276 AATTCTGTTCACATGTTATCCTGAATA 57.315 29.630 0.00 0.00 0.00 1.75
3302 9315 7.665145 TGAATTCTGTTCACATGTTATCCTGAA 59.335 33.333 7.05 1.38 0.00 3.02
3303 9316 7.167535 TGAATTCTGTTCACATGTTATCCTGA 58.832 34.615 7.05 0.00 0.00 3.86
3304 9317 7.381766 TGAATTCTGTTCACATGTTATCCTG 57.618 36.000 7.05 0.00 0.00 3.86
3305 9318 6.600822 CCTGAATTCTGTTCACATGTTATCCT 59.399 38.462 7.05 0.00 0.00 3.24
3306 9319 6.599244 TCCTGAATTCTGTTCACATGTTATCC 59.401 38.462 7.05 0.00 0.00 2.59
3307 9320 7.615582 TCCTGAATTCTGTTCACATGTTATC 57.384 36.000 7.05 0.00 0.00 1.75
3358 9461 9.708222 GAACAATATAATGTGCAGAAACTAGTG 57.292 33.333 0.00 0.00 32.81 2.74
3426 9529 6.442564 TGTGGACCTGATAGTTAATACCAACT 59.557 38.462 0.00 0.00 41.56 3.16
3429 9532 6.213802 TGTTGTGGACCTGATAGTTAATACCA 59.786 38.462 0.00 0.00 0.00 3.25
3446 9585 4.466370 AGAATCGAGTCCTATTGTTGTGGA 59.534 41.667 9.63 0.00 0.00 4.02
3447 9586 4.759782 AGAATCGAGTCCTATTGTTGTGG 58.240 43.478 9.63 0.00 0.00 4.17
3452 9591 3.068873 GCCTGAGAATCGAGTCCTATTGT 59.931 47.826 9.63 0.00 38.61 2.71
3461 9600 4.377839 TTTGTCTAGCCTGAGAATCGAG 57.622 45.455 0.00 0.00 38.61 4.04
3463 9602 4.686972 TGATTTGTCTAGCCTGAGAATCG 58.313 43.478 0.00 0.00 38.61 3.34
3494 9645 1.154225 GCCGTGCTGTGCATGTAAC 60.154 57.895 10.32 0.00 43.26 2.50
3500 9651 1.070615 TTCTTAGCCGTGCTGTGCA 59.929 52.632 8.44 0.00 40.10 4.57
3519 9670 0.590195 GCTGGTCTTTGTGTGCTCTG 59.410 55.000 0.00 0.00 0.00 3.35
3544 9731 2.361567 CCCATTGAAAGGGGCCTGC 61.362 63.158 0.84 0.00 43.92 4.85
3572 9760 7.410120 AAAGGAGGTATTGGATAAGCAAAAG 57.590 36.000 0.00 0.00 0.00 2.27
3583 9771 3.055385 TGGACTCGAAAAGGAGGTATTGG 60.055 47.826 0.00 0.00 38.39 3.16
3586 9774 4.041198 TGTTTGGACTCGAAAAGGAGGTAT 59.959 41.667 0.00 0.00 38.39 2.73
3595 9783 6.693315 AATTTTCTCTGTTTGGACTCGAAA 57.307 33.333 0.00 0.00 0.00 3.46
3633 9821 3.343617 GTGGTAGGTGCTAGCAAATTCA 58.656 45.455 21.29 11.55 44.32 2.57
3643 9831 2.082140 TCGATATGGTGGTAGGTGCT 57.918 50.000 0.00 0.00 0.00 4.40
3651 9839 6.019640 GCATTTTTCATGTTTCGATATGGTGG 60.020 38.462 0.00 0.00 0.00 4.61
3666 9857 7.427989 AGGACCATATTGAAGCATTTTTCAT 57.572 32.000 0.00 0.00 36.97 2.57
3732 9923 3.100545 CCTGCAGGCGGTGATATTT 57.899 52.632 22.33 0.00 0.00 1.40
3745 9936 2.356278 GGAGGGTTGATGCCTGCA 59.644 61.111 0.00 0.00 0.00 4.41
3785 13348 5.542779 AGATTGAGGATACCAACGATTAGC 58.457 41.667 0.00 0.00 31.08 3.09
3786 13349 8.361139 AGTTAGATTGAGGATACCAACGATTAG 58.639 37.037 0.00 0.00 31.08 1.73
3788 13351 7.070074 AGAGTTAGATTGAGGATACCAACGATT 59.930 37.037 0.00 0.00 31.08 3.34
3813 13376 1.734465 GCAAATCCCGACACTCTCAAG 59.266 52.381 0.00 0.00 0.00 3.02
3821 13384 2.890311 ACTTTTCATGCAAATCCCGACA 59.110 40.909 0.00 0.00 0.00 4.35
3823 13386 4.338118 GGATACTTTTCATGCAAATCCCGA 59.662 41.667 0.00 0.00 0.00 5.14
3831 13394 4.081406 AGCTGTTGGATACTTTTCATGCA 58.919 39.130 0.00 0.00 37.61 3.96
3839 13402 4.329462 GCTAGCTAGCTGTTGGATACTT 57.671 45.455 33.71 0.00 45.62 2.24
3852 13415 3.131933 ACACATTGGAGACAGCTAGCTAG 59.868 47.826 18.86 16.84 44.54 3.42
3868 13431 4.894784 ACGTGATGGTTCTAGAACACATT 58.105 39.130 31.30 15.77 42.85 2.71


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

AutoCloner maintained by Alex Coulton.