Multiple sequence alignment - TraesCS4A01G111700

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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 TraesCS4A01G111700 chr4A 100.000 8001 0 0 1 8001 136760832 136752832 0.000000e+00 14776.0
1 TraesCS4A01G111700 chr4A 94.382 267 15 0 7585 7851 593281642 593281908 2.080000e-110 411.0
2 TraesCS4A01G111700 chr4D 96.261 7461 187 38 184 7599 336657051 336664464 0.000000e+00 12148.0
3 TraesCS4A01G111700 chr4D 80.441 363 42 20 1325 1673 145529178 145528831 4.790000e-62 250.0
4 TraesCS4A01G111700 chr4D 80.460 348 42 13 1325 1660 145494151 145493818 8.020000e-60 243.0
5 TraesCS4A01G111700 chr4D 89.103 156 16 1 7847 8001 336664454 336664609 8.190000e-45 193.0
6 TraesCS4A01G111700 chr4B 96.022 5304 133 28 2318 7591 414860847 414866102 0.000000e+00 8554.0
7 TraesCS4A01G111700 chr4B 94.858 1653 61 10 505 2135 414858874 414860524 0.000000e+00 2560.0
8 TraesCS4A01G111700 chr4B 89.796 196 10 8 2132 2324 414860559 414860747 8.020000e-60 243.0
9 TraesCS4A01G111700 chr4B 84.615 156 23 1 7847 8001 414866099 414866254 3.870000e-33 154.0
10 TraesCS4A01G111700 chr1A 90.301 1495 80 28 4496 5974 35507257 35508702 0.000000e+00 1897.0
11 TraesCS4A01G111700 chr1A 96.424 783 27 1 4291 5073 35532925 35533706 0.000000e+00 1290.0
12 TraesCS4A01G111700 chr1A 91.558 616 43 8 6242 6852 35513044 35513655 0.000000e+00 841.0
13 TraesCS4A01G111700 chr1A 91.136 361 27 5 6495 6852 35483745 35484103 1.210000e-132 484.0
14 TraesCS4A01G111700 chr1A 98.068 207 4 0 4291 4497 35500635 35500841 2.120000e-95 361.0
15 TraesCS4A01G111700 chr1A 83.024 377 47 12 6118 6493 35438751 35439111 7.740000e-85 326.0
16 TraesCS4A01G111700 chr1A 82.620 397 32 17 6895 7285 35484105 35484470 4.660000e-82 316.0
17 TraesCS4A01G111700 chr1A 89.565 230 18 4 6895 7122 35513657 35513882 3.650000e-73 287.0
18 TraesCS4A01G111700 chr1A 87.444 223 17 3 5981 6194 35512809 35513029 6.200000e-61 246.0
19 TraesCS4A01G111700 chr1A 87.970 133 12 4 7121 7253 35534721 35534849 3.870000e-33 154.0
20 TraesCS4A01G111700 chr1A 98.701 77 1 0 6472 6548 35534358 35534434 3.890000e-28 137.0
21 TraesCS4A01G111700 chr1A 88.462 104 8 4 7154 7257 35513885 35513984 1.090000e-23 122.0
22 TraesCS4A01G111700 chr1A 88.710 62 7 0 7904 7965 415642769 415642830 8.610000e-10 76.8
23 TraesCS4A01G111700 chr1B 90.420 1451 89 21 4494 5940 55971373 55972777 0.000000e+00 1864.0
24 TraesCS4A01G111700 chr1B 91.377 1322 92 10 4638 5954 55953601 55954905 0.000000e+00 1790.0
25 TraesCS4A01G111700 chr1B 91.081 1323 95 11 4638 5954 55942347 55943652 0.000000e+00 1768.0
26 TraesCS4A01G111700 chr1B 91.452 1205 63 17 4479 5679 56014322 56015490 0.000000e+00 1618.0
27 TraesCS4A01G111700 chr1B 90.044 1125 76 14 4820 5940 55993410 55994502 0.000000e+00 1424.0
28 TraesCS4A01G111700 chr1B 84.501 471 64 8 4 470 134579700 134580165 2.630000e-124 457.0
29 TraesCS4A01G111700 chr1B 97.283 184 5 0 4291 4474 56014094 56014277 6.030000e-81 313.0
30 TraesCS4A01G111700 chr1B 96.739 184 6 0 4291 4474 55970923 55971106 2.800000e-79 307.0
31 TraesCS4A01G111700 chr1B 84.810 158 13 4 5957 6103 55943739 55943896 1.800000e-31 148.0
32 TraesCS4A01G111700 chr1B 84.810 158 13 4 5957 6103 55954992 55955149 1.800000e-31 148.0
33 TraesCS4A01G111700 chr1B 91.919 99 8 0 5957 6055 56015889 56015987 1.080000e-28 139.0
34 TraesCS4A01G111700 chr1B 97.959 49 1 0 7028 7076 55943894 55943942 1.430000e-12 86.1
35 TraesCS4A01G111700 chr1B 97.959 49 1 0 7028 7076 55955147 55955195 1.430000e-12 86.1
36 TraesCS4A01G111700 chr1D 93.371 1252 57 7 4291 5535 36312649 36313881 0.000000e+00 1829.0
37 TraesCS4A01G111700 chr1D 83.636 495 64 11 1 491 75935208 75934727 4.400000e-122 449.0
38 TraesCS4A01G111700 chr1D 93.865 163 9 1 6913 7075 36314338 36314499 2.230000e-60 244.0
39 TraesCS4A01G111700 chr1D 88.889 126 10 4 7121 7246 36314501 36314622 1.390000e-32 152.0
40 TraesCS4A01G111700 chr1D 97.403 77 1 1 6472 6548 36314134 36314209 6.520000e-26 130.0
41 TraesCS4A01G111700 chr2B 81.679 1763 300 23 3375 5126 64995724 64993974 0.000000e+00 1445.0
42 TraesCS4A01G111700 chr2B 85.600 500 58 10 1 491 697672131 697672625 5.540000e-141 512.0
43 TraesCS4A01G111700 chr2B 84.472 483 59 10 1 472 787149646 787150123 5.660000e-126 462.0
44 TraesCS4A01G111700 chr2B 80.208 192 33 4 1077 1266 64997075 64996887 1.080000e-28 139.0
45 TraesCS4A01G111700 chr2D 81.576 1764 300 22 3375 5126 37259302 37257552 0.000000e+00 1434.0
46 TraesCS4A01G111700 chr2D 88.600 500 46 7 1 492 325807804 325807308 1.490000e-166 597.0
47 TraesCS4A01G111700 chr2D 83.694 509 60 20 1 499 372172292 372171797 7.320000e-125 459.0
48 TraesCS4A01G111700 chr2D 83.217 143 22 2 1125 1266 37260911 37260770 6.520000e-26 130.0
49 TraesCS4A01G111700 chr2A 81.566 1763 301 20 3375 5126 42160234 42158485 0.000000e+00 1434.0
50 TraesCS4A01G111700 chr2A 84.244 476 66 8 1 472 675390339 675390809 9.470000e-124 455.0
51 TraesCS4A01G111700 chr2A 95.094 265 12 1 7588 7851 615337365 615337629 4.470000e-112 416.0
52 TraesCS4A01G111700 chr2A 94.677 263 12 2 7588 7849 49842244 49842505 2.690000e-109 407.0
53 TraesCS4A01G111700 chr2A 85.903 227 32 0 2599 2825 42160614 42160388 8.020000e-60 243.0
54 TraesCS4A01G111700 chr2A 83.221 149 22 3 1119 1266 42161807 42161661 5.040000e-27 134.0
55 TraesCS4A01G111700 chrUn 90.044 1125 76 14 4820 5940 319316023 319317115 0.000000e+00 1424.0
56 TraesCS4A01G111700 chrUn 83.055 779 71 36 1185 1937 178689254 178688511 0.000000e+00 651.0
57 TraesCS4A01G111700 chrUn 84.810 158 13 4 5957 6103 480727093 480726936 1.800000e-31 148.0
58 TraesCS4A01G111700 chrUn 97.959 49 1 0 7028 7076 480726938 480726890 1.430000e-12 86.1
59 TraesCS4A01G111700 chr5A 85.084 476 61 9 1 472 40615831 40616300 2.020000e-130 477.0
60 TraesCS4A01G111700 chr5A 84.211 494 64 13 1 487 40616392 40616878 1.220000e-127 468.0
61 TraesCS4A01G111700 chr5A 94.139 273 14 2 7587 7858 104621189 104620918 1.610000e-111 414.0
62 TraesCS4A01G111700 chr5A 95.057 263 13 0 7588 7850 631743434 631743696 1.610000e-111 414.0
63 TraesCS4A01G111700 chr5A 80.902 377 42 14 1325 1690 268024658 268024301 3.680000e-68 270.0
64 TraesCS4A01G111700 chr3A 95.076 264 13 0 7585 7848 474832558 474832821 4.470000e-112 416.0
65 TraesCS4A01G111700 chr7A 95.057 263 13 0 7587 7849 643222334 643222596 1.610000e-111 414.0
66 TraesCS4A01G111700 chr6A 95.038 262 12 1 7587 7848 448411313 448411573 2.080000e-110 411.0
67 TraesCS4A01G111700 chr5B 94.074 270 16 0 7580 7849 8966826 8967095 2.080000e-110 411.0


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 TraesCS4A01G111700 chr4A 136752832 136760832 8000 True 14776.000000 14776 100.000000 1 8001 1 chr4A.!!$R1 8000
1 TraesCS4A01G111700 chr4D 336657051 336664609 7558 False 6170.500000 12148 92.682000 184 8001 2 chr4D.!!$F1 7817
2 TraesCS4A01G111700 chr4B 414858874 414866254 7380 False 2877.750000 8554 91.322750 505 8001 4 chr4B.!!$F1 7496
3 TraesCS4A01G111700 chr1A 35507257 35508702 1445 False 1897.000000 1897 90.301000 4496 5974 1 chr1A.!!$F3 1478
4 TraesCS4A01G111700 chr1A 35532925 35534849 1924 False 527.000000 1290 94.365000 4291 7253 3 chr1A.!!$F7 2962
5 TraesCS4A01G111700 chr1A 35483745 35484470 725 False 400.000000 484 86.878000 6495 7285 2 chr1A.!!$F5 790
6 TraesCS4A01G111700 chr1A 35512809 35513984 1175 False 374.000000 841 89.257250 5981 7257 4 chr1A.!!$F6 1276
7 TraesCS4A01G111700 chr1B 55993410 55994502 1092 False 1424.000000 1424 90.044000 4820 5940 1 chr1B.!!$F1 1120
8 TraesCS4A01G111700 chr1B 55970923 55972777 1854 False 1085.500000 1864 93.579500 4291 5940 2 chr1B.!!$F5 1649
9 TraesCS4A01G111700 chr1B 56014094 56015987 1893 False 690.000000 1618 93.551333 4291 6055 3 chr1B.!!$F6 1764
10 TraesCS4A01G111700 chr1B 55953601 55955195 1594 False 674.700000 1790 91.382000 4638 7076 3 chr1B.!!$F4 2438
11 TraesCS4A01G111700 chr1B 55942347 55943942 1595 False 667.366667 1768 91.283333 4638 7076 3 chr1B.!!$F3 2438
12 TraesCS4A01G111700 chr1D 36312649 36314622 1973 False 588.750000 1829 93.382000 4291 7246 4 chr1D.!!$F1 2955
13 TraesCS4A01G111700 chr2B 64993974 64997075 3101 True 792.000000 1445 80.943500 1077 5126 2 chr2B.!!$R1 4049
14 TraesCS4A01G111700 chr2D 37257552 37260911 3359 True 782.000000 1434 82.396500 1125 5126 2 chr2D.!!$R3 4001
15 TraesCS4A01G111700 chr2A 42158485 42161807 3322 True 603.666667 1434 83.563333 1119 5126 3 chr2A.!!$R1 4007
16 TraesCS4A01G111700 chrUn 319316023 319317115 1092 False 1424.000000 1424 90.044000 4820 5940 1 chrUn.!!$F1 1120
17 TraesCS4A01G111700 chrUn 178688511 178689254 743 True 651.000000 651 83.055000 1185 1937 1 chrUn.!!$R1 752
18 TraesCS4A01G111700 chr5A 40615831 40616878 1047 False 472.500000 477 84.647500 1 487 2 chr5A.!!$F2 486

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
215 503 0.604243 AGAACAATGCCCGTGCGTTA 60.604 50.000 0.00 0.00 44.83 3.18 F
431 721 1.686741 GGTTGAACAAAGGGGTGGTGA 60.687 52.381 0.00 0.00 0.00 4.02 F
638 939 1.745489 AACGGCCAAGATTCCTCGC 60.745 57.895 2.24 0.00 0.00 5.03 F
670 977 2.612115 CCCACCCCAAGCCTCTCT 60.612 66.667 0.00 0.00 0.00 3.10 F
2053 2759 2.683152 GCATGGATCTCTTGCAAGTCCT 60.683 50.000 26.26 14.10 43.52 3.85 F
2078 2784 2.930562 GGGGAGTGAGCACCCAGT 60.931 66.667 0.00 0.00 45.89 4.00 F
3554 4668 2.290896 TGTTGATGGTGAAGATCCCCAC 60.291 50.000 6.55 6.55 0.00 4.61 F
3734 4848 4.321378 GCAAGGCCATTTTCATTTTGCATT 60.321 37.500 5.01 0.00 39.25 3.56 F
5126 6499 2.269940 ACCTGGGCAAGACTGAAGTAT 58.730 47.619 0.00 0.00 0.00 2.12 F
5652 7066 0.946221 CCAGTGCCTCAGTTGACGAC 60.946 60.000 0.00 0.00 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1690 0.993746 GAGCAGCAAAACAGAACGCG 60.994 55.000 3.53 3.53 0.00 6.01 R
2382 3234 1.537397 TGGGCTGAGCAGGAGAAGT 60.537 57.895 6.82 0.00 0.00 3.01 R
2470 3322 0.317160 GGCAAACGGGAAAAGGGAAG 59.683 55.000 0.00 0.00 0.00 3.46 R
2652 3755 4.170468 AGGTCCCACATATCCACATTTC 57.830 45.455 0.00 0.00 0.00 2.17 R
3172 4286 0.792640 GACATGCAGGTCACTTGACG 59.207 55.000 25.58 0.00 45.65 4.35 R
3734 4848 4.081862 CCAAAGTTACGTGTATCCTCCTCA 60.082 45.833 0.00 0.00 0.00 3.86 R
4889 6259 6.690530 ACAATGGTCAATATTGTGTGGAAAG 58.309 36.000 14.97 3.42 44.57 2.62 R
5652 7066 0.924090 GGTCTTCGATAACAGCAGCG 59.076 55.000 0.00 0.00 0.00 5.18 R
6234 7822 0.110678 CCTCATGCCTCATGCCTCAT 59.889 55.000 2.12 0.00 41.18 2.90 R
7461 9334 1.002430 CTAGAACTGCCAGCTGACCAA 59.998 52.381 17.39 0.00 0.00 3.67 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
29 30 8.931385 AATAAATGTTCATCAAATTCTTCCCG 57.069 30.769 0.00 0.00 0.00 5.14
31 32 4.764679 TGTTCATCAAATTCTTCCCGTG 57.235 40.909 0.00 0.00 0.00 4.94
143 422 7.106890 TCATATACATGAAAGGTTGGACGAAA 58.893 34.615 0.00 0.00 38.25 3.46
145 424 3.815809 ACATGAAAGGTTGGACGAAAGA 58.184 40.909 0.00 0.00 0.00 2.52
154 433 0.761323 TGGACGAAAGAGTGGTGGGA 60.761 55.000 0.00 0.00 0.00 4.37
160 439 3.181443 ACGAAAGAGTGGTGGGAAGAAAT 60.181 43.478 0.00 0.00 0.00 2.17
177 457 7.093333 GGGAAGAAATGTGAAATGGAACCTTAT 60.093 37.037 0.00 0.00 0.00 1.73
212 500 1.019278 ACTAGAACAATGCCCGTGCG 61.019 55.000 0.00 0.00 41.78 5.34
215 503 0.604243 AGAACAATGCCCGTGCGTTA 60.604 50.000 0.00 0.00 44.83 3.18
257 545 8.679288 TTCTACTACGTTAGCTTGTGATTTAC 57.321 34.615 0.00 0.00 0.00 2.01
431 721 1.686741 GGTTGAACAAAGGGGTGGTGA 60.687 52.381 0.00 0.00 0.00 4.02
432 722 2.104170 GTTGAACAAAGGGGTGGTGAA 58.896 47.619 0.00 0.00 0.00 3.18
438 728 3.653164 ACAAAGGGGTGGTGAAAAGAAT 58.347 40.909 0.00 0.00 0.00 2.40
439 729 3.387699 ACAAAGGGGTGGTGAAAAGAATG 59.612 43.478 0.00 0.00 0.00 2.67
440 730 2.309136 AGGGGTGGTGAAAAGAATGG 57.691 50.000 0.00 0.00 0.00 3.16
448 738 4.990426 GTGGTGAAAAGAATGGTGAAATGG 59.010 41.667 0.00 0.00 0.00 3.16
449 739 4.898265 TGGTGAAAAGAATGGTGAAATGGA 59.102 37.500 0.00 0.00 0.00 3.41
453 743 6.986231 GTGAAAAGAATGGTGAAATGGAAACT 59.014 34.615 0.00 0.00 0.00 2.66
457 747 9.546428 AAAAGAATGGTGAAATGGAAACTTTAG 57.454 29.630 0.00 0.00 0.00 1.85
458 748 7.232118 AGAATGGTGAAATGGAAACTTTAGG 57.768 36.000 0.00 0.00 0.00 2.69
461 751 6.399639 TGGTGAAATGGAAACTTTAGGTTC 57.600 37.500 0.00 0.00 37.12 3.62
466 756 9.378551 GTGAAATGGAAACTTTAGGTTCTTTTT 57.621 29.630 7.41 7.45 37.12 1.94
526 827 8.767478 AGGAATGCAAAGAAACAATGAATTAG 57.233 30.769 0.00 0.00 0.00 1.73
545 846 9.577110 TGAATTAGCTTTAATCAATGCTTTCAG 57.423 29.630 0.00 0.00 41.09 3.02
638 939 1.745489 AACGGCCAAGATTCCTCGC 60.745 57.895 2.24 0.00 0.00 5.03
670 977 2.612115 CCCACCCCAAGCCTCTCT 60.612 66.667 0.00 0.00 0.00 3.10
913 1234 4.427394 GATGCTTCGATCCGTGCT 57.573 55.556 0.00 0.00 0.00 4.40
969 1290 3.004944 GGTTTTGGCGTCTGATTTGGTTA 59.995 43.478 0.00 0.00 0.00 2.85
975 1296 4.814234 TGGCGTCTGATTTGGTTATATGTC 59.186 41.667 0.00 0.00 0.00 3.06
1248 1573 2.811317 GTGCTCGTCTCCGGCTTG 60.811 66.667 0.00 0.00 33.31 4.01
1354 1690 3.488090 GCTGGCGGCGTTACTGTC 61.488 66.667 9.37 0.00 0.00 3.51
1455 1928 5.465390 TCTGCGATTACTTCAATTTATCCCG 59.535 40.000 0.00 0.00 0.00 5.14
1752 2449 8.484214 AGGCTGATTACTTCTATTCACTATGA 57.516 34.615 0.00 0.00 0.00 2.15
1955 2661 6.814146 GCTGCAGTTACTAGTTCTGACTTATT 59.186 38.462 23.07 0.00 37.33 1.40
1959 2665 7.008447 GCAGTTACTAGTTCTGACTTATTGACG 59.992 40.741 23.07 0.00 37.33 4.35
2007 2713 3.555168 GGGTGTTAGAATGATCTAGCCCG 60.555 52.174 0.00 0.00 39.29 6.13
2020 2726 5.527214 TGATCTAGCCCGACATGTATTTTTG 59.473 40.000 0.00 0.00 0.00 2.44
2053 2759 2.683152 GCATGGATCTCTTGCAAGTCCT 60.683 50.000 26.26 14.10 43.52 3.85
2078 2784 2.930562 GGGGAGTGAGCACCCAGT 60.931 66.667 0.00 0.00 45.89 4.00
2102 2808 4.982241 TTCTGAGGAATCAAACCTGAGT 57.018 40.909 0.00 0.00 39.23 3.41
2207 2951 2.965147 CCTGGAAAAGGGAACACACAAT 59.035 45.455 0.00 0.00 43.15 2.71
2209 2953 3.891366 CTGGAAAAGGGAACACACAATCT 59.109 43.478 0.00 0.00 0.00 2.40
2213 2957 5.458041 AAAAGGGAACACACAATCTGATG 57.542 39.130 0.00 0.00 0.00 3.07
2338 3190 7.041508 GCTATGTAGCTAGCATTTTCATGTCTT 60.042 37.037 18.83 0.00 45.62 3.01
2457 3309 6.463995 TTGGGCAAAGTAATATGGTCATTC 57.536 37.500 0.00 0.00 0.00 2.67
2458 3310 4.892934 TGGGCAAAGTAATATGGTCATTCC 59.107 41.667 0.00 0.00 0.00 3.01
2777 3880 4.155462 ACAATGCTGTTCTTGTATCTGCTG 59.845 41.667 0.00 0.00 33.96 4.41
2989 4094 8.680001 GTTTTGGATGGTAATAAGTAAATCCGT 58.320 33.333 0.00 0.00 37.07 4.69
3430 4544 7.816031 AGACAAGGCAGTTGAATTTAATGATTG 59.184 33.333 5.12 0.00 38.60 2.67
3554 4668 2.290896 TGTTGATGGTGAAGATCCCCAC 60.291 50.000 6.55 6.55 0.00 4.61
3734 4848 4.321378 GCAAGGCCATTTTCATTTTGCATT 60.321 37.500 5.01 0.00 39.25 3.56
4199 5315 9.760660 GTCTGTGTCATGAACTGTAAAATATTC 57.239 33.333 0.00 0.00 0.00 1.75
4223 5339 4.451557 CGTTTATGACGTTCTGTTGGTTC 58.548 43.478 0.00 0.00 46.49 3.62
4889 6259 2.297033 ACCAATGTGCACAGTTCATTCC 59.703 45.455 25.84 0.00 30.74 3.01
4952 6324 3.259374 CAGAGTTTGAGGGTCTGCTAGAA 59.741 47.826 0.00 0.00 31.83 2.10
5126 6499 2.269940 ACCTGGGCAAGACTGAAGTAT 58.730 47.619 0.00 0.00 0.00 2.12
5134 6507 7.389232 TGGGCAAGACTGAAGTATGATATATG 58.611 38.462 0.00 0.00 0.00 1.78
5206 6580 5.671493 TCTTCCACTTTCTTTTCGTCTTCT 58.329 37.500 0.00 0.00 0.00 2.85
5224 6598 8.280497 TCGTCTTCTGCTATTTGAAGTTAAAAC 58.720 33.333 0.00 0.00 40.20 2.43
5225 6599 8.283291 CGTCTTCTGCTATTTGAAGTTAAAACT 58.717 33.333 0.00 0.00 42.04 2.66
5652 7066 0.946221 CCAGTGCCTCAGTTGACGAC 60.946 60.000 0.00 0.00 0.00 4.34
5683 7097 6.993902 TGTTATCGAAGACCTTTTAACCAAGT 59.006 34.615 0.00 0.00 42.51 3.16
5774 7188 8.554835 AGCCTCTTTTTAACTACTTCTGATTC 57.445 34.615 0.00 0.00 0.00 2.52
5775 7189 8.379331 AGCCTCTTTTTAACTACTTCTGATTCT 58.621 33.333 0.00 0.00 0.00 2.40
5776 7190 8.447053 GCCTCTTTTTAACTACTTCTGATTCTG 58.553 37.037 0.00 0.00 0.00 3.02
5777 7191 9.712305 CCTCTTTTTAACTACTTCTGATTCTGA 57.288 33.333 0.00 0.00 0.00 3.27
5858 7273 4.728608 CGTTTCACACTAGAAAGCAAACAC 59.271 41.667 0.00 0.00 38.11 3.32
5896 7311 5.532406 ACATAGGTGCATATTTGGTAAGCAG 59.468 40.000 0.00 0.00 37.65 4.24
5950 7365 7.062605 GTCACATTTCTTTCTGTTATGCATTGG 59.937 37.037 3.54 0.00 0.00 3.16
6165 7753 7.744715 CCGTAAAGATGTTTTCAATACTGTGAC 59.255 37.037 0.00 0.00 0.00 3.67
6186 7774 3.007940 ACTGCCTGTGTCAAATAGCTGTA 59.992 43.478 0.00 0.00 31.78 2.74
6228 7816 9.700831 AATAACTTACTTCCTTATTTCTGGCAT 57.299 29.630 0.00 0.00 0.00 4.40
6229 7817 7.396540 AACTTACTTCCTTATTTCTGGCATG 57.603 36.000 0.00 0.00 0.00 4.06
6230 7818 5.358160 ACTTACTTCCTTATTTCTGGCATGC 59.642 40.000 9.90 9.90 0.00 4.06
6231 7819 3.026694 ACTTCCTTATTTCTGGCATGCC 58.973 45.455 30.54 30.54 0.00 4.40
6232 7820 1.679139 TCCTTATTTCTGGCATGCCG 58.321 50.000 30.87 24.20 39.42 5.69
6233 7821 0.031178 CCTTATTTCTGGCATGCCGC 59.969 55.000 30.87 9.72 39.42 6.53
6234 7822 0.740149 CTTATTTCTGGCATGCCGCA 59.260 50.000 30.87 17.56 45.17 5.69
6235 7823 1.338973 CTTATTTCTGGCATGCCGCAT 59.661 47.619 30.87 20.63 45.17 4.73
6236 7824 0.669619 TATTTCTGGCATGCCGCATG 59.330 50.000 30.87 26.13 45.17 4.06
6237 7825 1.038681 ATTTCTGGCATGCCGCATGA 61.039 50.000 32.83 21.79 43.81 3.07
6294 7882 6.857777 TGGGCATTTGTTTAATTTCAGTTG 57.142 33.333 0.00 0.00 0.00 3.16
6698 8554 3.557228 AGGAGATGAAGCATCAAGACC 57.443 47.619 9.77 0.00 42.72 3.85
7183 9045 1.746322 TTGTGTGGGTCGTTCCGCTA 61.746 55.000 10.56 0.15 38.11 4.26
7316 9184 4.513442 TGCATATGGTAGTTCAGTTGTCC 58.487 43.478 4.56 0.00 0.00 4.02
7410 9283 4.320202 GCATTTGTCCTCGCAACTCTTTAA 60.320 41.667 0.00 0.00 0.00 1.52
7415 9288 3.813724 GTCCTCGCAACTCTTTAACCTTT 59.186 43.478 0.00 0.00 0.00 3.11
7461 9334 6.082031 TGTGCATAGATAGGTTAGGGTACAT 58.918 40.000 0.00 0.00 0.00 2.29
7478 9351 0.524862 CATTGGTCAGCTGGCAGTTC 59.475 55.000 21.89 2.63 0.00 3.01
7581 9457 4.263243 CCTGAAAGTGAGGTCAATTCTCCT 60.263 45.833 0.00 0.00 32.55 3.69
7587 9463 6.821616 AGTGAGGTCAATTCTCCTGAATAT 57.178 37.500 3.03 0.00 41.62 1.28
7588 9464 7.921041 AGTGAGGTCAATTCTCCTGAATATA 57.079 36.000 3.03 0.00 41.62 0.86
7589 9465 7.731054 AGTGAGGTCAATTCTCCTGAATATAC 58.269 38.462 3.03 0.00 41.62 1.47
7590 9466 7.566879 AGTGAGGTCAATTCTCCTGAATATACT 59.433 37.037 3.03 0.00 41.62 2.12
7591 9467 7.870445 GTGAGGTCAATTCTCCTGAATATACTC 59.130 40.741 3.03 0.00 41.62 2.59
7592 9468 7.015682 TGAGGTCAATTCTCCTGAATATACTCC 59.984 40.741 3.03 0.00 41.62 3.85
7593 9469 6.271159 AGGTCAATTCTCCTGAATATACTCCC 59.729 42.308 0.00 0.00 41.62 4.30
7594 9470 6.271159 GGTCAATTCTCCTGAATATACTCCCT 59.729 42.308 0.00 0.00 41.62 4.20
7595 9471 7.382898 GTCAATTCTCCTGAATATACTCCCTC 58.617 42.308 0.00 0.00 41.62 4.30
7596 9472 6.498651 TCAATTCTCCTGAATATACTCCCTCC 59.501 42.308 0.00 0.00 41.62 4.30
7597 9473 4.035612 TCTCCTGAATATACTCCCTCCG 57.964 50.000 0.00 0.00 0.00 4.63
7598 9474 3.093057 CTCCTGAATATACTCCCTCCGG 58.907 54.545 0.00 0.00 0.00 5.14
7599 9475 2.449730 TCCTGAATATACTCCCTCCGGT 59.550 50.000 0.00 0.00 0.00 5.28
7600 9476 2.826725 CCTGAATATACTCCCTCCGGTC 59.173 54.545 0.00 0.00 0.00 4.79
7601 9477 2.826725 CTGAATATACTCCCTCCGGTCC 59.173 54.545 0.00 0.00 0.00 4.46
7602 9478 2.449730 TGAATATACTCCCTCCGGTCCT 59.550 50.000 0.00 0.00 0.00 3.85
7603 9479 3.116862 TGAATATACTCCCTCCGGTCCTT 60.117 47.826 0.00 0.00 0.00 3.36
7604 9480 3.632420 ATATACTCCCTCCGGTCCTTT 57.368 47.619 0.00 0.00 0.00 3.11
7605 9481 2.265526 ATACTCCCTCCGGTCCTTTT 57.734 50.000 0.00 0.00 0.00 2.27
7606 9482 2.034436 TACTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.00 0.00 1.94
7607 9483 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
7608 9484 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
7609 9485 1.907255 CTCCCTCCGGTCCTTTTTACT 59.093 52.381 0.00 0.00 0.00 2.24
7610 9486 1.904537 TCCCTCCGGTCCTTTTTACTC 59.095 52.381 0.00 0.00 0.00 2.59
7611 9487 1.907255 CCCTCCGGTCCTTTTTACTCT 59.093 52.381 0.00 0.00 0.00 3.24
7612 9488 2.354805 CCCTCCGGTCCTTTTTACTCTG 60.355 54.545 0.00 0.00 0.00 3.35
7613 9489 2.347731 CTCCGGTCCTTTTTACTCTGC 58.652 52.381 0.00 0.00 0.00 4.26
7614 9490 1.695242 TCCGGTCCTTTTTACTCTGCA 59.305 47.619 0.00 0.00 0.00 4.41
7615 9491 2.304761 TCCGGTCCTTTTTACTCTGCAT 59.695 45.455 0.00 0.00 0.00 3.96
7616 9492 3.516300 TCCGGTCCTTTTTACTCTGCATA 59.484 43.478 0.00 0.00 0.00 3.14
7617 9493 4.163458 TCCGGTCCTTTTTACTCTGCATAT 59.837 41.667 0.00 0.00 0.00 1.78
7618 9494 4.881850 CCGGTCCTTTTTACTCTGCATATT 59.118 41.667 0.00 0.00 0.00 1.28
7619 9495 6.053005 CCGGTCCTTTTTACTCTGCATATTA 58.947 40.000 0.00 0.00 0.00 0.98
7620 9496 6.202954 CCGGTCCTTTTTACTCTGCATATTAG 59.797 42.308 0.00 0.00 0.00 1.73
7621 9497 6.984474 CGGTCCTTTTTACTCTGCATATTAGA 59.016 38.462 0.00 0.00 0.00 2.10
7622 9498 7.494625 CGGTCCTTTTTACTCTGCATATTAGAA 59.505 37.037 0.00 0.00 0.00 2.10
7623 9499 9.343539 GGTCCTTTTTACTCTGCATATTAGAAT 57.656 33.333 0.00 0.00 0.00 2.40
7629 9505 8.818141 TTTACTCTGCATATTAGAATTCTCCG 57.182 34.615 12.24 0.00 0.00 4.63
7630 9506 6.656632 ACTCTGCATATTAGAATTCTCCGA 57.343 37.500 12.24 0.00 0.00 4.55
7631 9507 7.055667 ACTCTGCATATTAGAATTCTCCGAA 57.944 36.000 12.24 0.95 0.00 4.30
7632 9508 7.151308 ACTCTGCATATTAGAATTCTCCGAAG 58.849 38.462 12.24 2.14 0.00 3.79
7633 9509 7.055667 TCTGCATATTAGAATTCTCCGAAGT 57.944 36.000 12.24 0.00 0.00 3.01
7634 9510 7.148641 TCTGCATATTAGAATTCTCCGAAGTC 58.851 38.462 12.24 0.00 0.00 3.01
7635 9511 6.816136 TGCATATTAGAATTCTCCGAAGTCA 58.184 36.000 12.24 0.99 0.00 3.41
7636 9512 7.272244 TGCATATTAGAATTCTCCGAAGTCAA 58.728 34.615 12.24 0.00 0.00 3.18
7637 9513 7.768582 TGCATATTAGAATTCTCCGAAGTCAAA 59.231 33.333 12.24 0.00 0.00 2.69
7638 9514 8.064814 GCATATTAGAATTCTCCGAAGTCAAAC 58.935 37.037 12.24 0.00 0.00 2.93
7639 9515 9.319143 CATATTAGAATTCTCCGAAGTCAAACT 57.681 33.333 12.24 0.00 0.00 2.66
7640 9516 9.892130 ATATTAGAATTCTCCGAAGTCAAACTT 57.108 29.630 12.24 0.00 41.95 2.66
7660 9536 6.445357 ACTTCACAAAGTTTGACCGTATTT 57.555 33.333 22.23 0.00 43.28 1.40
7661 9537 7.556733 ACTTCACAAAGTTTGACCGTATTTA 57.443 32.000 22.23 0.00 43.28 1.40
7662 9538 8.161699 ACTTCACAAAGTTTGACCGTATTTAT 57.838 30.769 22.23 0.00 43.28 1.40
7663 9539 9.275398 ACTTCACAAAGTTTGACCGTATTTATA 57.725 29.630 22.23 0.00 43.28 0.98
7666 9542 9.438228 TCACAAAGTTTGACCGTATTTATATGA 57.562 29.630 22.23 7.49 0.00 2.15
7763 9639 9.462174 TTGATTTTAGATTGTGAATGTTGACAC 57.538 29.630 0.00 0.00 37.51 3.67
7764 9640 8.849168 TGATTTTAGATTGTGAATGTTGACACT 58.151 29.630 0.00 0.00 37.81 3.55
7765 9641 9.683069 GATTTTAGATTGTGAATGTTGACACTT 57.317 29.630 0.00 0.00 37.81 3.16
7767 9643 9.868277 TTTTAGATTGTGAATGTTGACACTTTT 57.132 25.926 0.00 0.00 37.81 2.27
7768 9644 9.868277 TTTAGATTGTGAATGTTGACACTTTTT 57.132 25.926 0.00 0.00 37.81 1.94
7797 9673 3.263602 GTTGGTCAAACTTTACGAGGC 57.736 47.619 0.00 0.00 35.75 4.70
7798 9674 2.876550 GTTGGTCAAACTTTACGAGGCT 59.123 45.455 0.00 0.00 35.75 4.58
7799 9675 3.202829 TGGTCAAACTTTACGAGGCTT 57.797 42.857 0.00 0.00 0.00 4.35
7800 9676 2.875933 TGGTCAAACTTTACGAGGCTTG 59.124 45.455 0.00 0.00 0.00 4.01
7801 9677 3.135994 GGTCAAACTTTACGAGGCTTGA 58.864 45.455 9.20 0.00 32.24 3.02
7802 9678 3.059120 GGTCAAACTTTACGAGGCTTGAC 60.059 47.826 9.20 5.19 44.00 3.18
7803 9679 3.808174 GTCAAACTTTACGAGGCTTGACT 59.192 43.478 9.20 0.00 42.80 3.41
7804 9680 4.272748 GTCAAACTTTACGAGGCTTGACTT 59.727 41.667 9.20 0.00 42.80 3.01
7805 9681 4.879545 TCAAACTTTACGAGGCTTGACTTT 59.120 37.500 9.20 0.00 30.70 2.66
7806 9682 6.018507 GTCAAACTTTACGAGGCTTGACTTTA 60.019 38.462 9.20 0.00 42.80 1.85
7807 9683 6.202188 TCAAACTTTACGAGGCTTGACTTTAG 59.798 38.462 9.20 1.25 30.70 1.85
7808 9684 5.211174 ACTTTACGAGGCTTGACTTTAGT 57.789 39.130 9.20 1.85 0.00 2.24
7809 9685 5.608449 ACTTTACGAGGCTTGACTTTAGTT 58.392 37.500 9.20 0.00 0.00 2.24
7810 9686 6.752168 ACTTTACGAGGCTTGACTTTAGTTA 58.248 36.000 9.20 0.00 0.00 2.24
7811 9687 7.212274 ACTTTACGAGGCTTGACTTTAGTTAA 58.788 34.615 9.20 0.00 0.00 2.01
7812 9688 7.712205 ACTTTACGAGGCTTGACTTTAGTTAAA 59.288 33.333 9.20 0.00 0.00 1.52
7813 9689 8.611654 TTTACGAGGCTTGACTTTAGTTAAAT 57.388 30.769 9.20 0.00 0.00 1.40
7814 9690 8.611654 TTACGAGGCTTGACTTTAGTTAAATT 57.388 30.769 9.20 0.00 0.00 1.82
7815 9691 7.506328 ACGAGGCTTGACTTTAGTTAAATTT 57.494 32.000 9.20 0.00 0.00 1.82
7816 9692 7.937649 ACGAGGCTTGACTTTAGTTAAATTTT 58.062 30.769 9.20 0.00 0.00 1.82
7817 9693 9.059260 ACGAGGCTTGACTTTAGTTAAATTTTA 57.941 29.630 9.20 0.00 0.00 1.52
7838 9714 8.883789 TTTTATATGCGAACTAAAAAGAACCG 57.116 30.769 0.00 0.00 0.00 4.44
7839 9715 3.824414 ATGCGAACTAAAAAGAACCGG 57.176 42.857 0.00 0.00 0.00 5.28
7840 9716 2.836262 TGCGAACTAAAAAGAACCGGA 58.164 42.857 9.46 0.00 0.00 5.14
7841 9717 2.803956 TGCGAACTAAAAAGAACCGGAG 59.196 45.455 9.46 0.00 0.00 4.63
7889 9766 4.350245 AGTAAAAGTTTTGCCCCCTATCC 58.650 43.478 11.18 0.00 0.00 2.59
7891 9768 1.393468 AAGTTTTGCCCCCTATCCCT 58.607 50.000 0.00 0.00 0.00 4.20
7892 9769 1.393468 AGTTTTGCCCCCTATCCCTT 58.607 50.000 0.00 0.00 0.00 3.95
7896 9773 1.988539 TTGCCCCCTATCCCTTGTTA 58.011 50.000 0.00 0.00 0.00 2.41
7909 9786 0.392998 CTTGTTAGAGCGGCCACCAT 60.393 55.000 2.24 0.00 0.00 3.55
7925 9802 1.672356 CATCGATGCCCCCGATTCC 60.672 63.158 13.37 0.00 43.33 3.01
7926 9803 2.146724 ATCGATGCCCCCGATTCCA 61.147 57.895 0.00 0.00 43.33 3.53
7929 9806 3.099170 ATGCCCCCGATTCCAGCT 61.099 61.111 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.095440 AGGTAATTCACGGGAAGAATTTGATG 59.905 38.462 6.16 0.00 41.54 3.07
16 17 5.566469 AGGTAATTCACGGGAAGAATTTGA 58.434 37.500 6.16 0.00 41.54 2.69
20 21 9.862149 AAATATAAGGTAATTCACGGGAAGAAT 57.138 29.630 6.16 0.00 36.25 2.40
123 402 4.963373 TCTTTCGTCCAACCTTTCATGTA 58.037 39.130 0.00 0.00 0.00 2.29
125 404 3.815401 ACTCTTTCGTCCAACCTTTCATG 59.185 43.478 0.00 0.00 0.00 3.07
126 405 3.815401 CACTCTTTCGTCCAACCTTTCAT 59.185 43.478 0.00 0.00 0.00 2.57
127 406 3.202906 CACTCTTTCGTCCAACCTTTCA 58.797 45.455 0.00 0.00 0.00 2.69
129 408 2.092592 ACCACTCTTTCGTCCAACCTTT 60.093 45.455 0.00 0.00 0.00 3.11
143 422 2.711009 TCACATTTCTTCCCACCACTCT 59.289 45.455 0.00 0.00 0.00 3.24
145 424 3.593442 TTCACATTTCTTCCCACCACT 57.407 42.857 0.00 0.00 0.00 4.00
154 433 8.193953 ACATAAGGTTCCATTTCACATTTCTT 57.806 30.769 0.00 0.00 0.00 2.52
190 470 2.699954 CACGGGCATTGTTCTAGTCTT 58.300 47.619 0.00 0.00 0.00 3.01
237 525 5.867716 ACAGGTAAATCACAAGCTAACGTAG 59.132 40.000 0.00 0.00 0.00 3.51
250 538 8.669946 TCGCATTATTATTGACAGGTAAATCA 57.330 30.769 0.00 0.00 0.00 2.57
252 540 9.897744 CAATCGCATTATTATTGACAGGTAAAT 57.102 29.630 0.00 0.00 33.38 1.40
254 542 8.341903 CACAATCGCATTATTATTGACAGGTAA 58.658 33.333 0.00 0.00 35.18 2.85
256 544 6.318648 ACACAATCGCATTATTATTGACAGGT 59.681 34.615 0.00 0.00 35.18 4.00
257 545 6.728200 ACACAATCGCATTATTATTGACAGG 58.272 36.000 0.00 0.00 35.18 4.00
409 699 1.007842 ACCACCCCTTTGTTCAACCTT 59.992 47.619 0.00 0.00 0.00 3.50
410 700 0.634465 ACCACCCCTTTGTTCAACCT 59.366 50.000 0.00 0.00 0.00 3.50
411 701 0.750249 CACCACCCCTTTGTTCAACC 59.250 55.000 0.00 0.00 0.00 3.77
412 702 1.770294 TCACCACCCCTTTGTTCAAC 58.230 50.000 0.00 0.00 0.00 3.18
413 703 2.534042 TTCACCACCCCTTTGTTCAA 57.466 45.000 0.00 0.00 0.00 2.69
414 704 2.534042 TTTCACCACCCCTTTGTTCA 57.466 45.000 0.00 0.00 0.00 3.18
415 705 3.028130 TCTTTTCACCACCCCTTTGTTC 58.972 45.455 0.00 0.00 0.00 3.18
416 706 3.108847 TCTTTTCACCACCCCTTTGTT 57.891 42.857 0.00 0.00 0.00 2.83
419 709 2.972021 CCATTCTTTTCACCACCCCTTT 59.028 45.455 0.00 0.00 0.00 3.11
431 721 9.546428 CTAAAGTTTCCATTTCACCATTCTTTT 57.454 29.630 0.00 0.00 0.00 2.27
432 722 8.150296 CCTAAAGTTTCCATTTCACCATTCTTT 58.850 33.333 0.00 0.00 0.00 2.52
438 728 6.133356 AGAACCTAAAGTTTCCATTTCACCA 58.867 36.000 0.00 0.00 39.40 4.17
439 729 6.650427 AGAACCTAAAGTTTCCATTTCACC 57.350 37.500 0.00 0.00 39.40 4.02
440 730 8.942338 AAAAGAACCTAAAGTTTCCATTTCAC 57.058 30.769 0.00 0.00 39.40 3.18
482 772 8.987890 GCATTCCTTGTCTTATCTTCTTATCTC 58.012 37.037 0.00 0.00 0.00 2.75
499 799 6.847956 TTCATTGTTTCTTTGCATTCCTTG 57.152 33.333 0.00 0.00 0.00 3.61
526 827 5.220098 GCGAACTGAAAGCATTGATTAAAGC 60.220 40.000 0.00 0.00 37.60 3.51
653 954 1.306997 TAGAGAGGCTTGGGGTGGG 60.307 63.158 0.00 0.00 0.00 4.61
913 1234 1.146041 CAGAAATGGCGATCGGGGA 59.854 57.895 18.30 0.00 0.00 4.81
969 1290 2.023771 CCTGCATCGCGCGACATAT 61.024 57.895 37.37 17.50 46.97 1.78
1248 1573 4.344865 TCAGCCCCAAGCCCGTTC 62.345 66.667 0.00 0.00 45.47 3.95
1354 1690 0.993746 GAGCAGCAAAACAGAACGCG 60.994 55.000 3.53 3.53 0.00 6.01
1455 1928 2.103094 TCAGCCCTGTCTGCACATATAC 59.897 50.000 0.00 0.00 34.19 1.47
1572 2048 6.238676 GCAAACAATCTGATGATCATAGCAGT 60.239 38.462 18.82 7.80 31.51 4.40
1752 2449 8.641541 AGTAGGATCACAAAACAATCAACAATT 58.358 29.630 0.00 0.00 0.00 2.32
1955 2661 4.545208 TTTCCATAATGTCAGTCCGTCA 57.455 40.909 0.00 0.00 0.00 4.35
1959 2665 7.814264 AATCTGATTTCCATAATGTCAGTCC 57.186 36.000 0.00 0.00 37.96 3.85
2007 2713 6.586082 CCTAAAGTGCCACAAAAATACATGTC 59.414 38.462 0.00 0.00 0.00 3.06
2020 2726 1.678101 GATCCATGCCTAAAGTGCCAC 59.322 52.381 0.00 0.00 0.00 5.01
2053 2759 2.039879 GGTGCTCACTCCCCTCTAAAAA 59.960 50.000 0.00 0.00 0.00 1.94
2102 2808 4.308458 CGTGTGCCCCTCGGACAA 62.308 66.667 0.00 0.00 0.00 3.18
2200 2944 2.093075 AGGAGGCTCATCAGATTGTGTG 60.093 50.000 17.69 0.00 0.00 3.82
2201 2945 2.093075 CAGGAGGCTCATCAGATTGTGT 60.093 50.000 17.69 0.00 0.00 3.72
2207 2951 1.956869 TTTCCAGGAGGCTCATCAGA 58.043 50.000 17.69 5.56 33.74 3.27
2209 2953 2.795231 CTTTTCCAGGAGGCTCATCA 57.205 50.000 17.69 0.00 33.74 3.07
2247 2992 8.472007 ACAATCCACTAATTTTACCAACTCAA 57.528 30.769 0.00 0.00 0.00 3.02
2382 3234 1.537397 TGGGCTGAGCAGGAGAAGT 60.537 57.895 6.82 0.00 0.00 3.01
2457 3309 5.068329 GGAAAAGGGAAGATAATTGCTCAGG 59.932 44.000 0.00 0.00 0.00 3.86
2458 3310 5.068329 GGGAAAAGGGAAGATAATTGCTCAG 59.932 44.000 0.00 0.00 0.00 3.35
2470 3322 0.317160 GGCAAACGGGAAAAGGGAAG 59.683 55.000 0.00 0.00 0.00 3.46
2652 3755 4.170468 AGGTCCCACATATCCACATTTC 57.830 45.455 0.00 0.00 0.00 2.17
2777 3880 5.368256 TCAGTAGTCAGTTCTTCCGTTAC 57.632 43.478 0.00 0.00 0.00 2.50
3001 4106 7.500720 TCAGTATATTGACATCAAATGCAGG 57.499 36.000 0.00 0.00 39.55 4.85
3172 4286 0.792640 GACATGCAGGTCACTTGACG 59.207 55.000 25.58 0.00 45.65 4.35
3554 4668 5.335426 GCTGATGGATGCAATTATACCAGTG 60.335 44.000 0.00 0.00 34.08 3.66
3734 4848 4.081862 CCAAAGTTACGTGTATCCTCCTCA 60.082 45.833 0.00 0.00 0.00 3.86
4210 5326 3.194861 TCAGACAAGAACCAACAGAACG 58.805 45.455 0.00 0.00 0.00 3.95
4889 6259 6.690530 ACAATGGTCAATATTGTGTGGAAAG 58.309 36.000 14.97 3.42 44.57 2.62
4952 6324 7.169158 TGAGTTCACTTCATTTGGAGTTTTT 57.831 32.000 0.00 0.00 0.00 1.94
5085 6458 8.902806 CCAGGTTATGCAGTCTTCAAATTTATA 58.097 33.333 0.00 0.00 0.00 0.98
5652 7066 0.924090 GGTCTTCGATAACAGCAGCG 59.076 55.000 0.00 0.00 0.00 5.18
5683 7097 1.702182 TTCTTGGCACATGCTTCCAA 58.298 45.000 11.78 11.78 39.30 3.53
5773 7187 9.778741 AAAACAGTCTTATTCTAACACATCAGA 57.221 29.630 0.00 0.00 0.00 3.27
5858 7273 5.413969 CACCTATGTGCATTAGTGATGTG 57.586 43.478 0.00 0.00 38.07 3.21
5896 7311 9.736023 GAATTACATAATCCCTGTTGATGTTTC 57.264 33.333 0.00 0.00 33.05 2.78
5950 7365 8.468399 AGATACTAGCAACTAAGTTCTGTAACC 58.532 37.037 0.00 0.00 36.15 2.85
6165 7753 2.430465 ACAGCTATTTGACACAGGCAG 58.570 47.619 0.00 0.00 0.00 4.85
6230 7818 3.285215 GCCTCATGCCTCATGCGG 61.285 66.667 10.54 10.54 46.07 5.69
6231 7819 1.897137 ATGCCTCATGCCTCATGCG 60.897 57.895 2.12 0.00 45.60 4.73
6232 7820 0.822121 TCATGCCTCATGCCTCATGC 60.822 55.000 12.85 0.00 41.18 4.06
6233 7821 1.239347 CTCATGCCTCATGCCTCATG 58.761 55.000 11.96 11.96 41.18 3.07
6234 7822 0.110678 CCTCATGCCTCATGCCTCAT 59.889 55.000 2.12 0.00 41.18 2.90
6235 7823 1.530283 CCTCATGCCTCATGCCTCA 59.470 57.895 2.12 0.00 41.18 3.86
6236 7824 1.897615 GCCTCATGCCTCATGCCTC 60.898 63.158 2.12 0.00 41.18 4.70
6237 7825 2.008006 ATGCCTCATGCCTCATGCCT 62.008 55.000 2.12 0.00 41.18 4.75
6294 7882 6.812160 AGTGGTACGTCAGAAGATATTTTGAC 59.188 38.462 12.45 12.45 37.24 3.18
6358 8120 6.424207 GTGTAACCAGAACTAGTGAAGAAAGG 59.576 42.308 0.00 0.00 0.00 3.11
6698 8554 1.066573 GTCCCACACTGTCCATCTCAG 60.067 57.143 0.00 0.00 38.68 3.35
7183 9045 2.914695 AGTTGGCATGCAACAAACAT 57.085 40.000 24.86 9.04 35.18 2.71
7415 9288 5.047590 ACAACGACATATGACACCTCAACTA 60.048 40.000 10.38 0.00 0.00 2.24
7461 9334 1.002430 CTAGAACTGCCAGCTGACCAA 59.998 52.381 17.39 0.00 0.00 3.67
7478 9351 4.219033 CGCAAAGGTTGTAGCAAAACTAG 58.781 43.478 0.00 0.00 0.00 2.57
7518 9391 2.224450 CCTAACTGTTTGGGAGTTCGGT 60.224 50.000 12.40 0.00 35.30 4.69
7519 9392 2.038033 TCCTAACTGTTTGGGAGTTCGG 59.962 50.000 18.58 0.00 37.45 4.30
7520 9393 3.396260 TCCTAACTGTTTGGGAGTTCG 57.604 47.619 18.58 0.00 37.45 3.95
7593 9469 2.289444 TGCAGAGTAAAAAGGACCGGAG 60.289 50.000 9.46 0.00 0.00 4.63
7594 9470 1.695242 TGCAGAGTAAAAAGGACCGGA 59.305 47.619 9.46 0.00 0.00 5.14
7595 9471 2.178912 TGCAGAGTAAAAAGGACCGG 57.821 50.000 0.00 0.00 0.00 5.28
7596 9472 6.984474 TCTAATATGCAGAGTAAAAAGGACCG 59.016 38.462 0.00 0.00 0.00 4.79
7597 9473 8.732746 TTCTAATATGCAGAGTAAAAAGGACC 57.267 34.615 0.00 0.00 0.00 4.46
7603 9479 9.261180 CGGAGAATTCTAATATGCAGAGTAAAA 57.739 33.333 8.25 0.00 0.00 1.52
7604 9480 8.638873 TCGGAGAATTCTAATATGCAGAGTAAA 58.361 33.333 8.25 0.00 0.00 2.01
7605 9481 8.178313 TCGGAGAATTCTAATATGCAGAGTAA 57.822 34.615 8.25 0.00 0.00 2.24
7606 9482 7.761038 TCGGAGAATTCTAATATGCAGAGTA 57.239 36.000 8.25 0.00 0.00 2.59
7607 9483 6.656632 TCGGAGAATTCTAATATGCAGAGT 57.343 37.500 8.25 0.00 0.00 3.24
7608 9484 7.151308 ACTTCGGAGAATTCTAATATGCAGAG 58.849 38.462 8.25 0.58 45.90 3.35
7609 9485 7.055667 ACTTCGGAGAATTCTAATATGCAGA 57.944 36.000 8.25 0.00 45.90 4.26
7610 9486 6.925718 TGACTTCGGAGAATTCTAATATGCAG 59.074 38.462 8.25 1.45 45.90 4.41
7611 9487 6.816136 TGACTTCGGAGAATTCTAATATGCA 58.184 36.000 8.25 0.00 45.90 3.96
7612 9488 7.715265 TTGACTTCGGAGAATTCTAATATGC 57.285 36.000 8.25 0.00 45.90 3.14
7613 9489 9.319143 AGTTTGACTTCGGAGAATTCTAATATG 57.681 33.333 8.25 2.10 45.90 1.78
7614 9490 9.892130 AAGTTTGACTTCGGAGAATTCTAATAT 57.108 29.630 8.25 0.00 45.90 1.28
7615 9491 9.367444 GAAGTTTGACTTCGGAGAATTCTAATA 57.633 33.333 8.25 0.00 44.22 0.98
7616 9492 8.257830 GAAGTTTGACTTCGGAGAATTCTAAT 57.742 34.615 8.25 0.00 44.22 1.73
7617 9493 7.653767 GAAGTTTGACTTCGGAGAATTCTAA 57.346 36.000 8.25 0.00 44.22 2.10
7640 9516 9.438228 TCATATAAATACGGTCAAACTTTGTGA 57.562 29.630 1.44 0.00 0.00 3.58
7737 9613 9.462174 GTGTCAACATTCACAATCTAAAATCAA 57.538 29.630 0.00 0.00 35.04 2.57
7738 9614 8.849168 AGTGTCAACATTCACAATCTAAAATCA 58.151 29.630 0.00 0.00 37.07 2.57
7739 9615 9.683069 AAGTGTCAACATTCACAATCTAAAATC 57.317 29.630 0.00 0.00 37.07 2.17
7741 9617 9.868277 AAAAGTGTCAACATTCACAATCTAAAA 57.132 25.926 0.00 0.00 37.07 1.52
7742 9618 9.868277 AAAAAGTGTCAACATTCACAATCTAAA 57.132 25.926 0.00 0.00 37.07 1.85
7777 9653 2.876550 AGCCTCGTAAAGTTTGACCAAC 59.123 45.455 0.00 0.00 35.32 3.77
7778 9654 3.202829 AGCCTCGTAAAGTTTGACCAA 57.797 42.857 0.00 0.00 0.00 3.67
7779 9655 2.875933 CAAGCCTCGTAAAGTTTGACCA 59.124 45.455 0.00 0.00 0.00 4.02
7780 9656 3.059120 GTCAAGCCTCGTAAAGTTTGACC 60.059 47.826 8.09 0.00 39.44 4.02
7781 9657 3.808174 AGTCAAGCCTCGTAAAGTTTGAC 59.192 43.478 10.54 10.54 42.37 3.18
7782 9658 4.067972 AGTCAAGCCTCGTAAAGTTTGA 57.932 40.909 0.00 0.00 0.00 2.69
7783 9659 4.813296 AAGTCAAGCCTCGTAAAGTTTG 57.187 40.909 0.00 0.00 0.00 2.93
7784 9660 6.053650 ACTAAAGTCAAGCCTCGTAAAGTTT 58.946 36.000 0.00 0.00 0.00 2.66
7785 9661 5.608449 ACTAAAGTCAAGCCTCGTAAAGTT 58.392 37.500 0.00 0.00 0.00 2.66
7786 9662 5.211174 ACTAAAGTCAAGCCTCGTAAAGT 57.789 39.130 0.00 0.00 0.00 2.66
7787 9663 7.647907 TTAACTAAAGTCAAGCCTCGTAAAG 57.352 36.000 0.00 0.00 0.00 1.85
7788 9664 8.611654 ATTTAACTAAAGTCAAGCCTCGTAAA 57.388 30.769 0.00 0.00 0.00 2.01
7789 9665 8.611654 AATTTAACTAAAGTCAAGCCTCGTAA 57.388 30.769 0.00 0.00 0.00 3.18
7790 9666 8.611654 AAATTTAACTAAAGTCAAGCCTCGTA 57.388 30.769 0.00 0.00 0.00 3.43
7791 9667 7.506328 AAATTTAACTAAAGTCAAGCCTCGT 57.494 32.000 0.00 0.00 0.00 4.18
7812 9688 9.498307 CGGTTCTTTTTAGTTCGCATATAAAAT 57.502 29.630 0.00 0.00 30.75 1.82
7813 9689 7.964011 CCGGTTCTTTTTAGTTCGCATATAAAA 59.036 33.333 0.00 0.00 0.00 1.52
7814 9690 7.333921 TCCGGTTCTTTTTAGTTCGCATATAAA 59.666 33.333 0.00 0.00 0.00 1.40
7815 9691 6.817641 TCCGGTTCTTTTTAGTTCGCATATAA 59.182 34.615 0.00 0.00 0.00 0.98
7816 9692 6.339730 TCCGGTTCTTTTTAGTTCGCATATA 58.660 36.000 0.00 0.00 0.00 0.86
7817 9693 5.180271 TCCGGTTCTTTTTAGTTCGCATAT 58.820 37.500 0.00 0.00 0.00 1.78
7818 9694 4.567971 TCCGGTTCTTTTTAGTTCGCATA 58.432 39.130 0.00 0.00 0.00 3.14
7819 9695 3.404899 TCCGGTTCTTTTTAGTTCGCAT 58.595 40.909 0.00 0.00 0.00 4.73
7820 9696 2.803956 CTCCGGTTCTTTTTAGTTCGCA 59.196 45.455 0.00 0.00 0.00 5.10
7821 9697 2.159037 CCTCCGGTTCTTTTTAGTTCGC 59.841 50.000 0.00 0.00 0.00 4.70
7822 9698 2.740447 CCCTCCGGTTCTTTTTAGTTCG 59.260 50.000 0.00 0.00 0.00 3.95
7823 9699 4.001652 CTCCCTCCGGTTCTTTTTAGTTC 58.998 47.826 0.00 0.00 0.00 3.01
7824 9700 3.393609 ACTCCCTCCGGTTCTTTTTAGTT 59.606 43.478 0.00 0.00 0.00 2.24
7825 9701 2.977580 ACTCCCTCCGGTTCTTTTTAGT 59.022 45.455 0.00 0.00 0.00 2.24
7826 9702 3.697619 ACTCCCTCCGGTTCTTTTTAG 57.302 47.619 0.00 0.00 0.00 1.85
7827 9703 4.162651 AGTACTCCCTCCGGTTCTTTTTA 58.837 43.478 0.00 0.00 0.00 1.52
7828 9704 2.977580 AGTACTCCCTCCGGTTCTTTTT 59.022 45.455 0.00 0.00 0.00 1.94
7829 9705 2.617658 AGTACTCCCTCCGGTTCTTTT 58.382 47.619 0.00 0.00 0.00 2.27
7830 9706 2.302157 CAAGTACTCCCTCCGGTTCTTT 59.698 50.000 0.00 0.00 0.00 2.52
7831 9707 1.900486 CAAGTACTCCCTCCGGTTCTT 59.100 52.381 0.00 0.00 0.00 2.52
7832 9708 1.558233 CAAGTACTCCCTCCGGTTCT 58.442 55.000 0.00 0.00 0.00 3.01
7833 9709 0.108281 GCAAGTACTCCCTCCGGTTC 60.108 60.000 0.00 0.00 0.00 3.62
7834 9710 1.551019 GGCAAGTACTCCCTCCGGTT 61.551 60.000 0.00 0.00 0.00 4.44
7835 9711 1.988406 GGCAAGTACTCCCTCCGGT 60.988 63.158 0.00 0.00 0.00 5.28
7836 9712 1.686110 AGGCAAGTACTCCCTCCGG 60.686 63.158 8.79 0.00 0.00 5.14
7837 9713 1.517832 CAGGCAAGTACTCCCTCCG 59.482 63.158 11.12 0.33 0.00 4.63
7838 9714 1.908483 CCAGGCAAGTACTCCCTCC 59.092 63.158 11.12 3.90 0.00 4.30
7839 9715 1.222113 GCCAGGCAAGTACTCCCTC 59.778 63.158 6.55 0.33 0.00 4.30
7840 9716 2.660064 CGCCAGGCAAGTACTCCCT 61.660 63.158 13.30 8.79 0.00 4.20
7841 9717 2.125106 CGCCAGGCAAGTACTCCC 60.125 66.667 13.30 0.00 0.00 4.30
7842 9718 2.820037 GCGCCAGGCAAGTACTCC 60.820 66.667 13.30 0.00 42.87 3.85
7843 9719 2.820037 GGCGCCAGGCAAGTACTC 60.820 66.667 24.80 0.00 46.16 2.59
7844 9720 3.316573 GAGGCGCCAGGCAAGTACT 62.317 63.158 31.54 2.38 46.16 2.73
7845 9721 2.820037 GAGGCGCCAGGCAAGTAC 60.820 66.667 31.54 4.12 46.16 2.73
7854 9730 0.249953 TTTTACTTCACGAGGCGCCA 60.250 50.000 31.54 3.61 0.00 5.69
7866 9742 4.775780 GGATAGGGGGCAAAACTTTTACTT 59.224 41.667 0.00 0.00 0.00 2.24
7889 9766 1.745489 GGTGGCCGCTCTAACAAGG 60.745 63.158 17.49 0.00 0.00 3.61
7891 9768 0.392461 GATGGTGGCCGCTCTAACAA 60.392 55.000 17.49 0.00 0.00 2.83
7892 9769 1.220749 GATGGTGGCCGCTCTAACA 59.779 57.895 17.49 5.36 0.00 2.41
7896 9773 3.157252 ATCGATGGTGGCCGCTCT 61.157 61.111 17.49 3.26 0.00 4.09
7909 9786 2.766229 TGGAATCGGGGGCATCGA 60.766 61.111 4.05 4.05 41.04 3.59
7925 9802 2.093288 TCTTGCCTCTCCATTACAGCTG 60.093 50.000 13.48 13.48 0.00 4.24
7926 9803 2.093235 GTCTTGCCTCTCCATTACAGCT 60.093 50.000 0.00 0.00 0.00 4.24
7929 9806 1.559682 GGGTCTTGCCTCTCCATTACA 59.440 52.381 0.00 0.00 37.43 2.41


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

AutoCloner maintained by Alex Coulton.