Multiple sequence alignment - TraesCS5D01G071900

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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 TraesCS5D01G071900 chr5D 100.000 3411 0 0 2473 5883 70639948 70636538 0.000000e+00 6300.0
1 TraesCS5D01G071900 chr5D 100.000 2219 0 0 1 2219 70642420 70640202 0.000000e+00 4098.0
2 TraesCS5D01G071900 chr5D 79.968 624 99 15 211 823 94347161 94346553 2.520000e-118 436.0
3 TraesCS5D01G071900 chr5A 96.484 2588 77 8 2473 5052 60528606 60526025 0.000000e+00 4263.0
4 TraesCS5D01G071900 chr5A 94.126 698 22 7 1155 1833 60529624 60528927 0.000000e+00 1044.0
5 TraesCS5D01G071900 chr5A 92.833 293 11 3 1936 2219 60528930 60528639 3.280000e-112 416.0
6 TraesCS5D01G071900 chr5A 91.667 240 11 3 983 1215 60529895 60529658 2.040000e-84 324.0
7 TraesCS5D01G071900 chr5A 75.281 623 107 32 204 816 457534229 457533644 2.720000e-63 254.0
8 TraesCS5D01G071900 chr5A 81.138 334 35 21 484 811 536992809 536993120 5.890000e-60 243.0
9 TraesCS5D01G071900 chr5A 80.838 334 36 21 484 811 537000752 537001063 2.740000e-58 237.0
10 TraesCS5D01G071900 chr5A 97.436 117 3 0 1828 1944 9649939 9649823 3.600000e-47 200.0
11 TraesCS5D01G071900 chr5A 93.443 61 4 0 1155 1215 60529671 60529611 2.260000e-14 91.6
12 TraesCS5D01G071900 chr5B 96.560 1628 46 7 2473 4097 75906950 75905330 0.000000e+00 2687.0
13 TraesCS5D01G071900 chr5B 93.600 875 50 5 4180 5052 75902909 75902039 0.000000e+00 1301.0
14 TraesCS5D01G071900 chr5B 90.186 968 83 5 4 969 75953513 75952556 0.000000e+00 1251.0
15 TraesCS5D01G071900 chr5B 96.139 518 7 5 1002 1508 75908064 75907549 0.000000e+00 833.0
16 TraesCS5D01G071900 chr5B 81.613 620 88 18 210 823 101828011 101827412 1.910000e-134 490.0
17 TraesCS5D01G071900 chr5B 97.778 270 5 1 1565 1833 75907553 75907284 1.150000e-126 464.0
18 TraesCS5D01G071900 chr5B 91.743 218 10 3 1936 2145 75907287 75907070 4.460000e-76 296.0
19 TraesCS5D01G071900 chr5B 97.143 140 4 0 4047 4186 75905334 75905195 2.740000e-58 237.0
20 TraesCS5D01G071900 chr5B 74.227 582 115 20 216 788 231264620 231265175 1.660000e-50 211.0
21 TraesCS5D01G071900 chr5B 99.130 115 1 0 1826 1940 622393556 622393442 2.150000e-49 207.0
22 TraesCS5D01G071900 chr5B 80.159 252 36 11 566 816 394271217 394271455 6.060000e-40 176.0
23 TraesCS5D01G071900 chr5B 94.000 50 3 0 957 1006 75908395 75908346 6.320000e-10 76.8
24 TraesCS5D01G071900 chr5B 96.875 32 1 0 2521 2552 421644707 421644738 3.000000e-03 54.7
25 TraesCS5D01G071900 chr2D 93.489 814 46 2 5076 5883 469774276 469773464 0.000000e+00 1203.0
26 TraesCS5D01G071900 chr2D 80.573 628 95 18 204 823 420980374 420979766 5.370000e-125 459.0
27 TraesCS5D01G071900 chr2D 80.000 620 102 17 204 816 305953079 305953683 7.000000e-119 438.0
28 TraesCS5D01G071900 chr2D 86.893 206 25 2 1 205 204106318 204106522 4.590000e-56 230.0
29 TraesCS5D01G071900 chr2D 95.833 120 3 2 1825 1944 43919057 43918940 6.020000e-45 193.0
30 TraesCS5D01G071900 chr2B 93.243 814 47 5 5076 5883 650398990 650398179 0.000000e+00 1192.0
31 TraesCS5D01G071900 chr2B 88.500 200 22 1 1 199 398159974 398159775 2.120000e-59 241.0
32 TraesCS5D01G071900 chr2A 92.901 817 50 5 5073 5883 591742389 591743203 0.000000e+00 1181.0
33 TraesCS5D01G071900 chr2A 99.115 113 1 0 1825 1937 650256705 650256593 2.780000e-48 204.0
34 TraesCS5D01G071900 chr7B 92.794 791 48 6 5100 5883 730195135 730195923 0.000000e+00 1136.0
35 TraesCS5D01G071900 chr6B 92.025 815 55 4 5075 5883 185563186 185563996 0.000000e+00 1136.0
36 TraesCS5D01G071900 chr6B 92.366 131 9 1 1820 1949 640393822 640393952 1.010000e-42 185.0
37 TraesCS5D01G071900 chr3A 92.739 785 50 4 5105 5883 26013432 26014215 0.000000e+00 1127.0
38 TraesCS5D01G071900 chr3A 99.115 113 1 0 1830 1942 614468532 614468420 2.780000e-48 204.0
39 TraesCS5D01G071900 chrUn 91.523 814 61 5 5076 5883 91138665 91139476 0.000000e+00 1114.0
40 TraesCS5D01G071900 chr7A 90.720 819 63 9 5076 5883 126187575 126188391 0.000000e+00 1079.0
41 TraesCS5D01G071900 chr7A 90.541 666 59 2 5218 5883 36406584 36407245 0.000000e+00 878.0
42 TraesCS5D01G071900 chr7A 87.440 207 24 2 1 206 232883547 232883342 2.740000e-58 237.0
43 TraesCS5D01G071900 chr7A 88.384 198 19 4 8 203 310739066 310739261 9.860000e-58 235.0
44 TraesCS5D01G071900 chr7A 95.122 123 5 1 1830 1952 267276159 267276038 6.020000e-45 193.0
45 TraesCS5D01G071900 chr7D 81.695 590 86 16 224 806 193492415 193492989 6.900000e-129 472.0
46 TraesCS5D01G071900 chr7D 80.452 619 102 16 204 816 54185525 54186130 6.950000e-124 455.0
47 TraesCS5D01G071900 chr7D 86.957 207 24 3 1 206 223054866 223054662 4.590000e-56 230.0
48 TraesCS5D01G071900 chr3D 82.600 500 82 3 204 699 588129813 588130311 2.520000e-118 436.0
49 TraesCS5D01G071900 chr4D 81.107 524 88 6 204 724 88051002 88050487 5.490000e-110 409.0
50 TraesCS5D01G071900 chr1D 88.835 206 21 2 1 205 147900345 147900549 9.790000e-63 252.0
51 TraesCS5D01G071900 chr4B 87.019 208 24 3 1 206 88157749 88157543 1.270000e-56 231.0
52 TraesCS5D01G071900 chr4B 86.893 206 25 2 1 205 351883044 351882840 4.590000e-56 230.0
53 TraesCS5D01G071900 chr6A 99.107 112 1 0 1826 1937 64543179 64543068 1.000000e-47 202.0
54 TraesCS5D01G071900 chr1A 99.107 112 1 0 1827 1938 384334445 384334556 1.000000e-47 202.0


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 TraesCS5D01G071900 chr5D 70636538 70642420 5882 True 5199.000000 6300 100.000000 1 5883 2 chr5D.!!$R2 5882
1 TraesCS5D01G071900 chr5D 94346553 94347161 608 True 436.000000 436 79.968000 211 823 1 chr5D.!!$R1 612
2 TraesCS5D01G071900 chr5A 60526025 60529895 3870 True 1227.720000 4263 93.710600 983 5052 5 chr5A.!!$R3 4069
3 TraesCS5D01G071900 chr5A 457533644 457534229 585 True 254.000000 254 75.281000 204 816 1 chr5A.!!$R2 612
4 TraesCS5D01G071900 chr5B 75952556 75953513 957 True 1251.000000 1251 90.186000 4 969 1 chr5B.!!$R1 965
5 TraesCS5D01G071900 chr5B 75902039 75908395 6356 True 842.114286 2687 95.280429 957 5052 7 chr5B.!!$R4 4095
6 TraesCS5D01G071900 chr5B 101827412 101828011 599 True 490.000000 490 81.613000 210 823 1 chr5B.!!$R2 613
7 TraesCS5D01G071900 chr5B 231264620 231265175 555 False 211.000000 211 74.227000 216 788 1 chr5B.!!$F1 572
8 TraesCS5D01G071900 chr2D 469773464 469774276 812 True 1203.000000 1203 93.489000 5076 5883 1 chr2D.!!$R3 807
9 TraesCS5D01G071900 chr2D 420979766 420980374 608 True 459.000000 459 80.573000 204 823 1 chr2D.!!$R2 619
10 TraesCS5D01G071900 chr2D 305953079 305953683 604 False 438.000000 438 80.000000 204 816 1 chr2D.!!$F2 612
11 TraesCS5D01G071900 chr2B 650398179 650398990 811 True 1192.000000 1192 93.243000 5076 5883 1 chr2B.!!$R2 807
12 TraesCS5D01G071900 chr2A 591742389 591743203 814 False 1181.000000 1181 92.901000 5073 5883 1 chr2A.!!$F1 810
13 TraesCS5D01G071900 chr7B 730195135 730195923 788 False 1136.000000 1136 92.794000 5100 5883 1 chr7B.!!$F1 783
14 TraesCS5D01G071900 chr6B 185563186 185563996 810 False 1136.000000 1136 92.025000 5075 5883 1 chr6B.!!$F1 808
15 TraesCS5D01G071900 chr3A 26013432 26014215 783 False 1127.000000 1127 92.739000 5105 5883 1 chr3A.!!$F1 778
16 TraesCS5D01G071900 chrUn 91138665 91139476 811 False 1114.000000 1114 91.523000 5076 5883 1 chrUn.!!$F1 807
17 TraesCS5D01G071900 chr7A 126187575 126188391 816 False 1079.000000 1079 90.720000 5076 5883 1 chr7A.!!$F2 807
18 TraesCS5D01G071900 chr7A 36406584 36407245 661 False 878.000000 878 90.541000 5218 5883 1 chr7A.!!$F1 665
19 TraesCS5D01G071900 chr7D 193492415 193492989 574 False 472.000000 472 81.695000 224 806 1 chr7D.!!$F2 582
20 TraesCS5D01G071900 chr7D 54185525 54186130 605 False 455.000000 455 80.452000 204 816 1 chr7D.!!$F1 612
21 TraesCS5D01G071900 chr4D 88050487 88051002 515 True 409.000000 409 81.107000 204 724 1 chr4D.!!$R1 520

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
30 31 0.107165 GAGCCGGGGTTAAGCAATCT 60.107 55.000 2.18 0.0 0.00 2.40 F
138 139 0.319405 ACACCTAGTGTTACACCCGC 59.681 55.000 12.28 0.0 45.08 6.13 F
989 1016 0.734942 CGGCGGTGTCGAGTATGTTT 60.735 55.000 0.00 0.0 39.00 2.83 F
1503 1934 1.268335 ACGAACGACCACAACATTTGC 60.268 47.619 0.14 0.0 0.00 3.68 F
2751 3197 0.602562 TTTTGCAGGAATTCAGCCCG 59.397 50.000 16.50 0.0 0.00 6.13 F
4419 7209 0.250553 TCCCAACATGACCAACGTCC 60.251 55.000 0.00 0.0 38.32 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1830 0.390860 CGGGGACAGAGCAGGATTAG 59.609 60.000 0.00 0.0 0.00 1.73 R
1915 2348 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.0 0.00 2.83 R
1916 2349 2.256117 ACTCCCTCCGTTCACTTTTG 57.744 50.000 0.00 0.0 0.00 2.44 R
3189 3635 1.067354 CCTTGCTTTGAATGGGCAGAC 60.067 52.381 0.00 0.0 37.28 3.51 R
4661 7451 0.603707 CACGGTGGCATCAGTCAACT 60.604 55.000 0.00 0.0 34.00 3.16 R
5298 8102 2.106332 CGGATGACTACCGGGTGC 59.894 66.667 10.66 0.0 45.65 5.01 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
30 31 0.107165 GAGCCGGGGTTAAGCAATCT 60.107 55.000 2.18 0.00 0.00 2.40
31 32 1.140252 GAGCCGGGGTTAAGCAATCTA 59.860 52.381 2.18 0.00 0.00 1.98
57 58 7.861629 TGTAACCATATCCATCAAGAAAGACT 58.138 34.615 0.00 0.00 0.00 3.24
64 65 5.505181 TCCATCAAGAAAGACTAAGCCTT 57.495 39.130 0.00 0.00 0.00 4.35
94 95 0.819582 TCGTAGGGCTTTTACCTCCG 59.180 55.000 0.00 0.00 38.61 4.63
96 97 0.463295 GTAGGGCTTTTACCTCCGCC 60.463 60.000 0.00 0.00 39.54 6.13
114 115 2.896443 GAGAGGGGCCTGAACTCG 59.104 66.667 0.84 0.00 36.40 4.18
124 125 2.490991 GCCTGAACTCGTTAAACACCT 58.509 47.619 0.00 0.00 0.00 4.00
138 139 0.319405 ACACCTAGTGTTACACCCGC 59.681 55.000 12.28 0.00 45.08 6.13
140 141 1.808390 CCTAGTGTTACACCCGCGC 60.808 63.158 12.28 0.00 34.49 6.86
152 153 4.625781 CCGCGCCGTAGCTAGGTC 62.626 72.222 12.21 0.00 36.60 3.85
153 154 3.584052 CGCGCCGTAGCTAGGTCT 61.584 66.667 12.21 0.00 36.60 3.85
154 155 2.249535 CGCGCCGTAGCTAGGTCTA 61.250 63.158 12.21 0.00 36.60 2.59
199 201 3.639094 CTCATTCTCAGGATCGTAACCCT 59.361 47.826 0.00 0.00 0.00 4.34
200 202 3.637229 TCATTCTCAGGATCGTAACCCTC 59.363 47.826 0.00 0.00 0.00 4.30
201 203 1.676746 TCTCAGGATCGTAACCCTCG 58.323 55.000 0.00 0.00 0.00 4.63
202 204 1.211212 TCTCAGGATCGTAACCCTCGA 59.789 52.381 0.00 0.00 41.45 4.04
287 289 4.133820 CAATGACCACCACTACAACAAGA 58.866 43.478 0.00 0.00 0.00 3.02
359 362 5.098663 ACATAATCCATAACCCGGTAGGAT 58.901 41.667 11.51 11.51 40.66 3.24
417 428 7.126733 AGTACTAGGAAGGATGTAGAATGTGT 58.873 38.462 0.00 0.00 0.00 3.72
598 616 3.632145 GGGTGAAAATGTTGTGTCTGAGT 59.368 43.478 0.00 0.00 0.00 3.41
607 625 5.139435 TGTTGTGTCTGAGTATGAAGGAG 57.861 43.478 0.00 0.00 0.00 3.69
608 626 3.876274 TGTGTCTGAGTATGAAGGAGC 57.124 47.619 0.00 0.00 0.00 4.70
609 627 2.164422 TGTGTCTGAGTATGAAGGAGCG 59.836 50.000 0.00 0.00 0.00 5.03
643 664 6.319911 TGCACGATTCACCCAATTTTATCATA 59.680 34.615 0.00 0.00 0.00 2.15
651 672 6.983307 TCACCCAATTTTATCATAAAATGCGG 59.017 34.615 14.85 17.13 30.94 5.69
666 687 1.377202 GCGGGATTGAGCAACTCCA 60.377 57.895 11.23 0.00 0.00 3.86
843 870 9.434420 TTCTGATTTAAACTTTGGGCAATATTG 57.566 29.630 11.27 11.27 0.00 1.90
866 893 5.348164 GCACCCGCAAAATACATAATCTTT 58.652 37.500 0.00 0.00 38.36 2.52
894 921 9.695526 GGCAATATTTGATATGTATGCAGAAAA 57.304 29.630 0.00 0.00 31.37 2.29
926 953 3.725485 TGGTTATACTGACCACGCG 57.275 52.632 3.53 3.53 42.06 6.01
930 957 2.124903 GTTATACTGACCACGCGGATG 58.875 52.381 12.47 0.00 35.59 3.51
987 1014 2.488355 CGGCGGTGTCGAGTATGT 59.512 61.111 0.00 0.00 39.00 2.29
988 1015 1.153901 CGGCGGTGTCGAGTATGTT 60.154 57.895 0.00 0.00 39.00 2.71
989 1016 0.734942 CGGCGGTGTCGAGTATGTTT 60.735 55.000 0.00 0.00 39.00 2.83
1408 1830 4.814294 CACCTCCGTGCCGTAGCC 62.814 72.222 0.00 0.00 38.69 3.93
1503 1934 1.268335 ACGAACGACCACAACATTTGC 60.268 47.619 0.14 0.00 0.00 3.68
1554 1986 2.742372 CCCGGCTTCTCAACACCG 60.742 66.667 0.00 0.00 45.21 4.94
1563 1995 3.426695 GCTTCTCAACACCGGATTTGATG 60.427 47.826 9.46 0.60 31.41 3.07
1690 2123 8.752187 CATTATATGTTGGATAGAAATTGGGGG 58.248 37.037 0.00 0.00 0.00 5.40
1829 2262 8.037758 CCAGATGCGATAGATAGGAACTTTATT 58.962 37.037 0.00 0.00 38.25 1.40
1834 2267 8.521176 TGCGATAGATAGGAACTTTATTACTCC 58.479 37.037 0.00 0.00 38.25 3.85
1835 2268 7.975058 GCGATAGATAGGAACTTTATTACTCCC 59.025 40.741 0.00 0.00 38.25 4.30
1836 2269 9.245481 CGATAGATAGGAACTTTATTACTCCCT 57.755 37.037 0.00 0.00 38.25 4.20
1839 2272 8.485578 AGATAGGAACTTTATTACTCCCTCTG 57.514 38.462 0.00 0.00 41.75 3.35
1840 2273 8.068733 AGATAGGAACTTTATTACTCCCTCTGT 58.931 37.037 0.00 0.00 41.75 3.41
1841 2274 6.954352 AGGAACTTTATTACTCCCTCTGTT 57.046 37.500 0.00 0.00 27.25 3.16
1842 2275 6.948589 AGGAACTTTATTACTCCCTCTGTTC 58.051 40.000 0.00 0.00 27.25 3.18
1843 2276 6.500751 AGGAACTTTATTACTCCCTCTGTTCA 59.499 38.462 0.00 0.00 27.25 3.18
1844 2277 6.594547 GGAACTTTATTACTCCCTCTGTTCAC 59.405 42.308 0.00 0.00 34.70 3.18
1845 2278 6.936968 ACTTTATTACTCCCTCTGTTCACT 57.063 37.500 0.00 0.00 0.00 3.41
1846 2279 7.317722 ACTTTATTACTCCCTCTGTTCACTT 57.682 36.000 0.00 0.00 0.00 3.16
1847 2280 7.746703 ACTTTATTACTCCCTCTGTTCACTTT 58.253 34.615 0.00 0.00 0.00 2.66
1848 2281 8.218488 ACTTTATTACTCCCTCTGTTCACTTTT 58.782 33.333 0.00 0.00 0.00 2.27
1849 2282 9.720769 CTTTATTACTCCCTCTGTTCACTTTTA 57.279 33.333 0.00 0.00 0.00 1.52
1853 2286 9.892130 ATTACTCCCTCTGTTCACTTTTATAAG 57.108 33.333 0.00 0.00 37.40 1.73
1854 2287 7.554959 ACTCCCTCTGTTCACTTTTATAAGA 57.445 36.000 0.00 0.00 35.30 2.10
1855 2288 7.387643 ACTCCCTCTGTTCACTTTTATAAGAC 58.612 38.462 0.00 0.00 35.30 3.01
1856 2289 6.708285 TCCCTCTGTTCACTTTTATAAGACC 58.292 40.000 0.00 0.00 35.30 3.85
1857 2290 6.500751 TCCCTCTGTTCACTTTTATAAGACCT 59.499 38.462 0.00 0.00 35.30 3.85
1858 2291 7.017254 TCCCTCTGTTCACTTTTATAAGACCTT 59.983 37.037 0.00 0.00 35.30 3.50
1859 2292 7.119846 CCCTCTGTTCACTTTTATAAGACCTTG 59.880 40.741 0.00 0.00 35.30 3.61
1860 2293 7.878127 CCTCTGTTCACTTTTATAAGACCTTGA 59.122 37.037 0.00 0.00 35.30 3.02
1861 2294 9.273016 CTCTGTTCACTTTTATAAGACCTTGAA 57.727 33.333 0.00 0.00 35.30 2.69
1862 2295 9.273016 TCTGTTCACTTTTATAAGACCTTGAAG 57.727 33.333 0.00 0.00 35.30 3.02
1863 2296 9.273016 CTGTTCACTTTTATAAGACCTTGAAGA 57.727 33.333 0.00 0.00 35.30 2.87
1864 2297 9.052759 TGTTCACTTTTATAAGACCTTGAAGAC 57.947 33.333 0.00 0.00 35.30 3.01
1865 2298 9.052759 GTTCACTTTTATAAGACCTTGAAGACA 57.947 33.333 0.00 0.00 35.30 3.41
1866 2299 9.793259 TTCACTTTTATAAGACCTTGAAGACAT 57.207 29.630 0.00 0.00 35.30 3.06
1867 2300 9.793259 TCACTTTTATAAGACCTTGAAGACATT 57.207 29.630 0.00 0.00 35.30 2.71
1873 2306 7.913674 ATAAGACCTTGAAGACATTTCAGAC 57.086 36.000 0.00 0.00 0.00 3.51
1874 2307 5.296151 AGACCTTGAAGACATTTCAGACA 57.704 39.130 0.00 0.00 0.00 3.41
1875 2308 5.684704 AGACCTTGAAGACATTTCAGACAA 58.315 37.500 0.00 0.00 0.00 3.18
1876 2309 6.302269 AGACCTTGAAGACATTTCAGACAAT 58.698 36.000 0.00 0.00 0.00 2.71
1877 2310 6.206243 AGACCTTGAAGACATTTCAGACAATG 59.794 38.462 0.00 0.00 39.67 2.82
1879 2312 6.147581 CCTTGAAGACATTTCAGACAATGTG 58.852 40.000 12.82 2.31 45.55 3.21
1880 2313 5.112220 TGAAGACATTTCAGACAATGTGC 57.888 39.130 12.82 7.29 45.55 4.57
1881 2314 4.579753 TGAAGACATTTCAGACAATGTGCA 59.420 37.500 12.82 0.00 45.55 4.57
1882 2315 5.067544 TGAAGACATTTCAGACAATGTGCAA 59.932 36.000 12.82 0.00 45.55 4.08
1883 2316 5.518848 AGACATTTCAGACAATGTGCAAA 57.481 34.783 12.82 0.00 45.55 3.68
1884 2317 5.904941 AGACATTTCAGACAATGTGCAAAA 58.095 33.333 12.82 0.00 45.55 2.44
1885 2318 5.750067 AGACATTTCAGACAATGTGCAAAAC 59.250 36.000 12.82 2.36 45.55 2.43
1886 2319 5.417811 ACATTTCAGACAATGTGCAAAACA 58.582 33.333 0.00 0.00 44.19 2.83
1887 2320 5.521010 ACATTTCAGACAATGTGCAAAACAG 59.479 36.000 0.00 0.00 44.19 3.16
1888 2321 3.082698 TCAGACAATGTGCAAAACAGC 57.917 42.857 0.00 0.00 43.64 4.40
1889 2322 2.129607 CAGACAATGTGCAAAACAGCC 58.870 47.619 0.00 0.00 43.64 4.85
1890 2323 2.034124 AGACAATGTGCAAAACAGCCT 58.966 42.857 0.00 0.00 43.64 4.58
1891 2324 3.004629 CAGACAATGTGCAAAACAGCCTA 59.995 43.478 0.00 0.00 43.64 3.93
1892 2325 3.828451 AGACAATGTGCAAAACAGCCTAT 59.172 39.130 0.00 0.00 43.64 2.57
1893 2326 4.281688 AGACAATGTGCAAAACAGCCTATT 59.718 37.500 0.00 0.00 43.64 1.73
1894 2327 4.959723 ACAATGTGCAAAACAGCCTATTT 58.040 34.783 0.00 0.00 43.64 1.40
1895 2328 5.367302 ACAATGTGCAAAACAGCCTATTTT 58.633 33.333 0.00 0.00 43.64 1.82
1896 2329 5.236911 ACAATGTGCAAAACAGCCTATTTTG 59.763 36.000 3.83 3.83 45.68 2.44
1897 2330 4.662468 TGTGCAAAACAGCCTATTTTGA 57.338 36.364 12.19 0.00 45.75 2.69
1898 2331 4.619973 TGTGCAAAACAGCCTATTTTGAG 58.380 39.130 12.19 0.00 45.75 3.02
1899 2332 4.099266 TGTGCAAAACAGCCTATTTTGAGT 59.901 37.500 12.19 0.00 45.75 3.41
1900 2333 5.049828 GTGCAAAACAGCCTATTTTGAGTT 58.950 37.500 12.19 0.00 45.75 3.01
1901 2334 5.049167 TGCAAAACAGCCTATTTTGAGTTG 58.951 37.500 12.19 4.12 45.75 3.16
1902 2335 5.049828 GCAAAACAGCCTATTTTGAGTTGT 58.950 37.500 12.19 0.00 45.75 3.32
1903 2336 5.175673 GCAAAACAGCCTATTTTGAGTTGTC 59.824 40.000 12.19 0.00 45.75 3.18
1904 2337 6.507023 CAAAACAGCCTATTTTGAGTTGTCT 58.493 36.000 1.96 0.00 45.75 3.41
1905 2338 5.695851 AACAGCCTATTTTGAGTTGTCTG 57.304 39.130 0.00 0.00 0.00 3.51
1906 2339 4.973168 ACAGCCTATTTTGAGTTGTCTGA 58.027 39.130 0.00 0.00 0.00 3.27
1907 2340 5.376625 ACAGCCTATTTTGAGTTGTCTGAA 58.623 37.500 0.00 0.00 0.00 3.02
1908 2341 5.827797 ACAGCCTATTTTGAGTTGTCTGAAA 59.172 36.000 0.00 0.00 0.00 2.69
1909 2342 6.145535 CAGCCTATTTTGAGTTGTCTGAAAC 58.854 40.000 0.00 0.00 0.00 2.78
1910 2343 5.049405 AGCCTATTTTGAGTTGTCTGAAACG 60.049 40.000 0.00 0.00 35.13 3.60
1911 2344 5.049680 GCCTATTTTGAGTTGTCTGAAACGA 60.050 40.000 0.00 0.00 35.13 3.85
1912 2345 6.363473 CCTATTTTGAGTTGTCTGAAACGAC 58.637 40.000 0.00 0.00 41.93 4.34
1923 2356 6.102006 TGTCTGAAACGACTTACAAAAGTG 57.898 37.500 0.00 0.00 46.09 3.16
1924 2357 5.870433 TGTCTGAAACGACTTACAAAAGTGA 59.130 36.000 0.00 0.00 46.09 3.41
1925 2358 6.369340 TGTCTGAAACGACTTACAAAAGTGAA 59.631 34.615 0.00 0.00 46.09 3.18
1926 2359 6.681599 GTCTGAAACGACTTACAAAAGTGAAC 59.318 38.462 0.00 0.00 46.09 3.18
1927 2360 5.552807 TGAAACGACTTACAAAAGTGAACG 58.447 37.500 0.00 0.00 46.09 3.95
1928 2361 4.525411 AACGACTTACAAAAGTGAACGG 57.475 40.909 0.00 0.00 46.09 4.44
1929 2362 3.784338 ACGACTTACAAAAGTGAACGGA 58.216 40.909 0.00 0.00 46.09 4.69
1930 2363 3.800506 ACGACTTACAAAAGTGAACGGAG 59.199 43.478 0.00 0.00 46.09 4.63
1931 2364 3.183775 CGACTTACAAAAGTGAACGGAGG 59.816 47.826 0.00 0.00 46.09 4.30
1932 2365 3.473625 ACTTACAAAAGTGAACGGAGGG 58.526 45.455 0.00 0.00 44.40 4.30
1933 2366 3.135167 ACTTACAAAAGTGAACGGAGGGA 59.865 43.478 0.00 0.00 44.40 4.20
1934 2367 2.256117 ACAAAAGTGAACGGAGGGAG 57.744 50.000 0.00 0.00 0.00 4.30
2053 2495 7.140083 TTGTTTGACAATCAAGGACTAGCCTT 61.140 38.462 11.36 11.36 44.81 4.35
2075 2517 6.769822 CCTTGAGATGCTCTTACATTGGTAAT 59.230 38.462 0.00 0.00 38.72 1.89
2209 2652 0.685097 TCAGACAGTGTTAGTGGGGC 59.315 55.000 0.00 0.00 0.00 5.80
2216 2659 2.746277 GTTAGTGGGGCGCACCAG 60.746 66.667 36.48 0.00 42.20 4.00
2751 3197 0.602562 TTTTGCAGGAATTCAGCCCG 59.397 50.000 16.50 0.00 0.00 6.13
2865 3311 4.633565 CAGACTATTGAAGGTGAAGAAGGC 59.366 45.833 0.00 0.00 0.00 4.35
2990 3436 5.188327 AGGTGAAAGCTTTTTCTTACAGC 57.812 39.130 14.05 14.21 46.63 4.40
3189 3635 0.665835 TTGTTGCGGTAAAGGTGCTG 59.334 50.000 0.00 0.00 0.00 4.41
3369 3815 5.422331 ACATACACTGCTAGGTGACATACTT 59.578 40.000 6.18 0.00 40.13 2.24
3377 3823 3.073274 AGGTGACATACTTTTCTGCCC 57.927 47.619 0.00 0.00 0.00 5.36
3389 3835 3.806949 TTTCTGCCCTATGTGTCCTTT 57.193 42.857 0.00 0.00 0.00 3.11
3452 3898 3.380393 TGCAGGTAAGGGTTATAGCAGA 58.620 45.455 0.00 0.00 0.00 4.26
3489 3935 4.142881 GGAGAGTCCGTGTTAAAATTGCTC 60.143 45.833 0.00 0.00 0.00 4.26
3742 4194 7.572523 TTTCATTCTGATCTCTCTCTCTCTC 57.427 40.000 0.00 0.00 0.00 3.20
3743 4195 6.505048 TCATTCTGATCTCTCTCTCTCTCT 57.495 41.667 0.00 0.00 0.00 3.10
3744 4196 6.528321 TCATTCTGATCTCTCTCTCTCTCTC 58.472 44.000 0.00 0.00 0.00 3.20
3745 4197 6.328410 TCATTCTGATCTCTCTCTCTCTCTCT 59.672 42.308 0.00 0.00 0.00 3.10
3746 4198 5.798125 TCTGATCTCTCTCTCTCTCTCTC 57.202 47.826 0.00 0.00 0.00 3.20
3747 4199 5.462240 TCTGATCTCTCTCTCTCTCTCTCT 58.538 45.833 0.00 0.00 0.00 3.10
3997 4449 6.302269 ACTGAGTTGTGATTCTTCTTCCATT 58.698 36.000 0.00 0.00 0.00 3.16
4144 4642 0.455972 CCACAATTAGCAAACCGCCG 60.456 55.000 0.00 0.00 44.04 6.46
4172 4670 9.364989 GTGTAAGAATATCTCAAGAGCCATATC 57.635 37.037 0.00 0.00 0.00 1.63
4311 7101 5.645929 GGACAGCTCGAGAAGATGATAGATA 59.354 44.000 18.75 0.00 44.41 1.98
4419 7209 0.250553 TCCCAACATGACCAACGTCC 60.251 55.000 0.00 0.00 38.32 4.79
4442 7232 1.373570 GGATGCTGACCGGAGAAAAG 58.626 55.000 9.46 0.00 0.00 2.27
4606 7396 4.623167 GCCGTGAGCAGTACAGAATATATG 59.377 45.833 0.00 0.00 42.97 1.78
4643 7433 4.881273 TGTTGTACATTATCATGCTGGGTC 59.119 41.667 0.00 0.00 33.05 4.46
4696 7486 2.038033 ACCGTGGTGTTACTATGCAGTT 59.962 45.455 0.00 0.00 36.14 3.16
4805 7598 2.677524 GCCTCACTTGCCATGCCA 60.678 61.111 0.00 0.00 0.00 4.92
4823 7616 6.456718 CCATGCCAAAATAACTAAATTTGCCG 60.457 38.462 0.00 0.00 33.72 5.69
4829 7622 0.453782 AACTAAATTTGCCGCGCGTC 60.454 50.000 29.95 18.43 0.00 5.19
4855 7648 0.729140 CGAAATGCCCTGTGCGAAAC 60.729 55.000 0.00 0.00 45.60 2.78
4914 7708 9.515020 GCGATTTTATAGAAAAATTGTCATCCA 57.485 29.630 0.00 0.00 38.04 3.41
4947 7741 1.335872 CCAATGTCTTTGTGGGCGTTC 60.336 52.381 0.00 0.00 33.15 3.95
4993 7790 2.490115 GTTTGCCCATTAACATGTCCGA 59.510 45.455 0.00 0.00 0.00 4.55
5004 7801 7.066284 CCATTAACATGTCCGAGAGAGAAAAAT 59.934 37.037 0.00 0.00 0.00 1.82
5018 7816 1.872952 GAAAAATGGTGTTTGGGCTGC 59.127 47.619 0.00 0.00 0.00 5.25
5034 7832 1.596727 GCTGCATGGATTCTTCTCGAC 59.403 52.381 0.00 0.00 0.00 4.20
5055 7853 2.535984 CGTAAGTTGATCGTCATGGAGC 59.464 50.000 0.00 0.00 0.00 4.70
5056 7854 2.029838 AAGTTGATCGTCATGGAGCC 57.970 50.000 0.00 0.00 0.00 4.70
5057 7855 0.179100 AGTTGATCGTCATGGAGCCG 60.179 55.000 0.00 0.00 0.00 5.52
5058 7856 1.521457 TTGATCGTCATGGAGCCGC 60.521 57.895 0.00 0.00 0.00 6.53
5059 7857 1.960040 TTGATCGTCATGGAGCCGCT 61.960 55.000 0.00 0.00 0.00 5.52
5060 7858 1.227380 GATCGTCATGGAGCCGCTT 60.227 57.895 0.00 0.00 0.00 4.68
5061 7859 1.218230 GATCGTCATGGAGCCGCTTC 61.218 60.000 0.00 0.00 0.00 3.86
5062 7860 2.650813 ATCGTCATGGAGCCGCTTCC 62.651 60.000 0.00 0.00 37.77 3.46
5063 7861 2.586792 GTCATGGAGCCGCTTCCT 59.413 61.111 0.00 0.00 38.12 3.36
5064 7862 1.823295 GTCATGGAGCCGCTTCCTA 59.177 57.895 0.00 0.00 38.12 2.94
5065 7863 0.178068 GTCATGGAGCCGCTTCCTAA 59.822 55.000 0.00 0.00 38.12 2.69
5066 7864 1.131638 TCATGGAGCCGCTTCCTAAT 58.868 50.000 0.00 0.00 38.12 1.73
5067 7865 2.037251 GTCATGGAGCCGCTTCCTAATA 59.963 50.000 0.00 0.00 38.12 0.98
5068 7866 2.703536 TCATGGAGCCGCTTCCTAATAA 59.296 45.455 0.00 0.00 38.12 1.40
5069 7867 3.327757 TCATGGAGCCGCTTCCTAATAAT 59.672 43.478 0.00 0.00 38.12 1.28
5070 7868 4.530553 TCATGGAGCCGCTTCCTAATAATA 59.469 41.667 0.00 0.00 38.12 0.98
5071 7869 4.967084 TGGAGCCGCTTCCTAATAATAA 57.033 40.909 0.00 0.00 38.12 1.40
5074 7872 4.876679 GGAGCCGCTTCCTAATAATAATCC 59.123 45.833 0.00 0.00 34.27 3.01
5168 7966 1.111277 GGTTTATCATGCCACACCCC 58.889 55.000 0.00 0.00 0.00 4.95
5180 7978 1.352352 CCACACCCCTTGACTCTTGAT 59.648 52.381 0.00 0.00 0.00 2.57
5275 8079 3.919216 AGAACTCATCAACCTTCGACAG 58.081 45.455 0.00 0.00 0.00 3.51
5293 8097 3.429085 ACAGTCGTTAGTAATTACCGCG 58.571 45.455 12.05 13.29 0.00 6.46
5298 8102 2.034339 CGTTAGTAATTACCGCGCTTGG 60.034 50.000 12.05 2.00 0.00 3.61
5300 8104 0.391927 AGTAATTACCGCGCTTGGCA 60.392 50.000 12.05 0.00 43.84 4.92
5403 8212 1.557099 TCAGCAAGTCGTAGTCCCAT 58.443 50.000 0.00 0.00 0.00 4.00
5485 8294 1.138859 GCAGCAACAAAACCTCCCTTT 59.861 47.619 0.00 0.00 0.00 3.11
5507 8316 4.744570 TGAGTCTCGTAAAATAGCACCAG 58.255 43.478 0.00 0.00 0.00 4.00
5564 8373 8.511604 AGCATCAACATTAAGCTTTATACAGT 57.488 30.769 3.20 0.00 29.98 3.55
5571 8381 9.672673 AACATTAAGCTTTATACAGTCTGATGT 57.327 29.630 3.20 0.00 37.19 3.06
5583 8393 5.516768 TACAGTCTGATGTTGGTCTAGACCT 60.517 44.000 35.83 20.43 42.01 3.85
5629 8439 3.570125 GCTTCTTTTCTGCTACCCAGTTT 59.430 43.478 0.00 0.00 42.38 2.66
5668 8479 0.733729 GTAGAGACGATCGTGCTGGT 59.266 55.000 28.12 13.25 0.00 4.00
5778 8589 1.625315 CTGGAATGAGACACCACCAGA 59.375 52.381 0.00 0.00 45.02 3.86
5827 8638 4.899457 AGTATCAATGAACCGGACCTATGA 59.101 41.667 9.46 7.50 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.880027 CATAGATTGCTTAACCCCGGC 59.120 52.381 0.00 0.00 0.00 6.13
15 16 4.514066 GGTTACATAGATTGCTTAACCCCG 59.486 45.833 0.00 0.00 31.83 5.73
19 20 9.502091 TGGATATGGTTACATAGATTGCTTAAC 57.498 33.333 0.00 0.00 42.48 2.01
30 31 9.778741 GTCTTTCTTGATGGATATGGTTACATA 57.221 33.333 0.00 0.00 43.31 2.29
31 32 8.497745 AGTCTTTCTTGATGGATATGGTTACAT 58.502 33.333 0.00 0.00 41.13 2.29
64 65 1.452651 CCCTACGACTCGTGCCCTA 60.453 63.158 14.47 0.00 41.39 3.53
77 78 0.463295 GGCGGAGGTAAAAGCCCTAC 60.463 60.000 0.00 0.00 43.54 3.18
96 97 2.896443 GAGTTCAGGCCCCTCTCG 59.104 66.667 0.00 0.00 0.00 4.04
124 125 2.262292 GGCGCGGGTGTAACACTA 59.738 61.111 8.83 0.00 38.93 2.74
136 137 2.249535 TAGACCTAGCTACGGCGCG 61.250 63.158 6.90 0.00 44.37 6.86
137 138 1.282265 GTAGACCTAGCTACGGCGC 59.718 63.158 6.90 0.00 44.37 6.53
138 139 1.513836 GGGTAGACCTAGCTACGGCG 61.514 65.000 4.80 4.80 41.26 6.46
140 141 0.477638 AGGGGTAGACCTAGCTACGG 59.522 60.000 6.26 7.46 41.26 4.02
151 152 1.342374 GGGGTACGAAAGAGGGGTAGA 60.342 57.143 0.00 0.00 0.00 2.59
152 153 1.117994 GGGGTACGAAAGAGGGGTAG 58.882 60.000 0.00 0.00 0.00 3.18
153 154 0.712380 AGGGGTACGAAAGAGGGGTA 59.288 55.000 0.00 0.00 0.00 3.69
154 155 0.712380 TAGGGGTACGAAAGAGGGGT 59.288 55.000 0.00 0.00 0.00 4.95
199 201 1.285950 CACCAGAGAACGCTGTCGA 59.714 57.895 5.04 0.00 39.41 4.20
200 202 0.597637 AACACCAGAGAACGCTGTCG 60.598 55.000 5.04 0.00 42.43 4.35
201 203 1.140816 GAACACCAGAGAACGCTGTC 58.859 55.000 5.04 0.00 34.06 3.51
202 204 0.464036 TGAACACCAGAGAACGCTGT 59.536 50.000 5.04 0.00 34.06 4.40
413 424 3.667497 TTGAAGCACACCAAAAACACA 57.333 38.095 0.00 0.00 0.00 3.72
417 428 6.183360 CCATCAAAATTGAAGCACACCAAAAA 60.183 34.615 0.00 0.00 41.13 1.94
598 616 2.418368 AACATTGCCGCTCCTTCATA 57.582 45.000 0.00 0.00 0.00 2.15
643 664 1.895131 AGTTGCTCAATCCCGCATTTT 59.105 42.857 0.00 0.00 35.85 1.82
651 672 7.818930 TGAAATTAAATTGGAGTTGCTCAATCC 59.181 33.333 0.00 0.00 31.08 3.01
741 762 9.314321 GAATACATTGAATAGAAAAGGAGACGA 57.686 33.333 0.00 0.00 0.00 4.20
743 764 9.099454 ACGAATACATTGAATAGAAAAGGAGAC 57.901 33.333 0.00 0.00 0.00 3.36
843 870 4.568152 AGATTATGTATTTTGCGGGTGC 57.432 40.909 0.00 0.00 43.20 5.01
866 893 6.947158 TCTGCATACATATCAAATATTGCCCA 59.053 34.615 0.00 0.00 29.61 5.36
923 950 2.452813 CGACCCACTTTCATCCGCG 61.453 63.158 0.00 0.00 0.00 6.46
926 953 2.106683 CGCCGACCCACTTTCATCC 61.107 63.158 0.00 0.00 0.00 3.51
946 973 5.332355 GCGTGATACATACCTCAATCGAAAC 60.332 44.000 0.00 0.00 0.00 2.78
987 1014 3.315142 ATCAGCGCTGCGAGGGAAA 62.315 57.895 32.44 13.24 0.00 3.13
988 1015 3.774528 ATCAGCGCTGCGAGGGAA 61.775 61.111 32.44 14.05 0.00 3.97
989 1016 4.519437 CATCAGCGCTGCGAGGGA 62.519 66.667 32.44 18.65 0.00 4.20
1173 1493 4.162690 GAACCAGCCGGCGAGGAT 62.163 66.667 37.08 29.29 45.00 3.24
1328 1750 3.274288 GGTTAGAGCAAGAGATTGGTGG 58.726 50.000 0.00 0.00 32.16 4.61
1408 1830 0.390860 CGGGGACAGAGCAGGATTAG 59.609 60.000 0.00 0.00 0.00 1.73
1503 1934 2.765807 ACGCAGGATCCAGGGAGG 60.766 66.667 25.26 6.04 39.47 4.30
1535 1966 3.056328 GTGTTGAGAAGCCGGGGC 61.056 66.667 2.18 0.18 42.33 5.80
1554 1986 1.680207 GAAGCTGGAGCCATCAAATCC 59.320 52.381 0.00 0.00 43.38 3.01
1563 1995 2.202676 CTCGTCGAAGCTGGAGCC 60.203 66.667 0.00 0.00 43.38 4.70
1690 2123 8.004344 CGATCAATCTCGAACAAAATACATACC 58.996 37.037 0.00 0.00 41.12 2.73
1829 2262 8.529476 GTCTTATAAAAGTGAACAGAGGGAGTA 58.471 37.037 0.00 0.00 34.13 2.59
1830 2263 7.387643 GTCTTATAAAAGTGAACAGAGGGAGT 58.612 38.462 0.00 0.00 34.13 3.85
1831 2264 6.819146 GGTCTTATAAAAGTGAACAGAGGGAG 59.181 42.308 0.00 0.00 34.13 4.30
1832 2265 6.500751 AGGTCTTATAAAAGTGAACAGAGGGA 59.499 38.462 0.00 0.00 34.13 4.20
1833 2266 6.712276 AGGTCTTATAAAAGTGAACAGAGGG 58.288 40.000 0.00 0.00 34.13 4.30
1834 2267 7.878127 TCAAGGTCTTATAAAAGTGAACAGAGG 59.122 37.037 0.00 0.00 34.13 3.69
1835 2268 8.833231 TCAAGGTCTTATAAAAGTGAACAGAG 57.167 34.615 0.00 0.00 34.13 3.35
1836 2269 9.273016 CTTCAAGGTCTTATAAAAGTGAACAGA 57.727 33.333 0.00 0.00 34.13 3.41
1837 2270 9.273016 TCTTCAAGGTCTTATAAAAGTGAACAG 57.727 33.333 0.00 0.00 34.13 3.16
1838 2271 9.052759 GTCTTCAAGGTCTTATAAAAGTGAACA 57.947 33.333 0.00 0.00 34.13 3.18
1839 2272 9.052759 TGTCTTCAAGGTCTTATAAAAGTGAAC 57.947 33.333 0.00 0.00 34.13 3.18
1840 2273 9.793259 ATGTCTTCAAGGTCTTATAAAAGTGAA 57.207 29.630 0.00 0.00 34.13 3.18
1841 2274 9.793259 AATGTCTTCAAGGTCTTATAAAAGTGA 57.207 29.630 0.00 0.00 34.13 3.41
1847 2280 9.436957 GTCTGAAATGTCTTCAAGGTCTTATAA 57.563 33.333 0.00 0.00 0.00 0.98
1848 2281 8.593679 TGTCTGAAATGTCTTCAAGGTCTTATA 58.406 33.333 0.00 0.00 0.00 0.98
1849 2282 7.453393 TGTCTGAAATGTCTTCAAGGTCTTAT 58.547 34.615 0.00 0.00 0.00 1.73
1850 2283 6.826668 TGTCTGAAATGTCTTCAAGGTCTTA 58.173 36.000 0.00 0.00 0.00 2.10
1851 2284 5.684704 TGTCTGAAATGTCTTCAAGGTCTT 58.315 37.500 0.00 0.00 0.00 3.01
1852 2285 5.296151 TGTCTGAAATGTCTTCAAGGTCT 57.704 39.130 0.00 0.00 0.00 3.85
1853 2286 6.016777 ACATTGTCTGAAATGTCTTCAAGGTC 60.017 38.462 10.41 0.00 45.47 3.85
1854 2287 5.829924 ACATTGTCTGAAATGTCTTCAAGGT 59.170 36.000 10.41 0.00 45.47 3.50
1855 2288 6.147581 CACATTGTCTGAAATGTCTTCAAGG 58.852 40.000 12.25 0.00 45.47 3.61
1856 2289 5.628193 GCACATTGTCTGAAATGTCTTCAAG 59.372 40.000 12.25 5.42 45.47 3.02
1857 2290 5.067544 TGCACATTGTCTGAAATGTCTTCAA 59.932 36.000 12.25 0.00 45.47 2.69
1858 2291 4.579753 TGCACATTGTCTGAAATGTCTTCA 59.420 37.500 12.25 9.40 45.47 3.02
1859 2292 5.112220 TGCACATTGTCTGAAATGTCTTC 57.888 39.130 12.25 7.82 45.47 2.87
1860 2293 5.518848 TTGCACATTGTCTGAAATGTCTT 57.481 34.783 12.25 0.00 45.47 3.01
1861 2294 5.518848 TTTGCACATTGTCTGAAATGTCT 57.481 34.783 12.25 0.00 45.47 3.41
1862 2295 5.519566 TGTTTTGCACATTGTCTGAAATGTC 59.480 36.000 12.25 9.51 45.47 3.06
1864 2297 5.557514 GCTGTTTTGCACATTGTCTGAAATG 60.558 40.000 0.00 9.50 42.21 2.32
1865 2298 4.508861 GCTGTTTTGCACATTGTCTGAAAT 59.491 37.500 0.00 0.00 33.76 2.17
1866 2299 3.864583 GCTGTTTTGCACATTGTCTGAAA 59.135 39.130 0.00 0.00 33.76 2.69
1867 2300 3.446799 GCTGTTTTGCACATTGTCTGAA 58.553 40.909 0.00 0.00 33.76 3.02
1868 2301 2.223782 GGCTGTTTTGCACATTGTCTGA 60.224 45.455 0.00 0.00 33.76 3.27
1869 2302 2.129607 GGCTGTTTTGCACATTGTCTG 58.870 47.619 0.00 0.00 33.76 3.51
1870 2303 2.034124 AGGCTGTTTTGCACATTGTCT 58.966 42.857 0.00 0.00 33.76 3.41
1871 2304 2.514205 AGGCTGTTTTGCACATTGTC 57.486 45.000 0.00 0.00 33.76 3.18
1872 2305 4.605640 AATAGGCTGTTTTGCACATTGT 57.394 36.364 0.00 0.00 33.76 2.71
1873 2306 5.466058 TCAAAATAGGCTGTTTTGCACATTG 59.534 36.000 32.24 16.60 43.04 2.82
1874 2307 5.609423 TCAAAATAGGCTGTTTTGCACATT 58.391 33.333 32.24 6.77 43.04 2.71
1875 2308 5.212532 TCAAAATAGGCTGTTTTGCACAT 57.787 34.783 32.24 7.40 43.04 3.21
1876 2309 4.099266 ACTCAAAATAGGCTGTTTTGCACA 59.901 37.500 32.24 20.43 43.04 4.57
1877 2310 4.620982 ACTCAAAATAGGCTGTTTTGCAC 58.379 39.130 32.24 0.00 43.04 4.57
1878 2311 4.935352 ACTCAAAATAGGCTGTTTTGCA 57.065 36.364 32.24 23.09 43.04 4.08
1879 2312 5.049828 ACAACTCAAAATAGGCTGTTTTGC 58.950 37.500 32.24 0.00 43.04 3.68
1880 2313 6.418819 CAGACAACTCAAAATAGGCTGTTTTG 59.581 38.462 31.63 31.63 44.10 2.44
1881 2314 6.321181 TCAGACAACTCAAAATAGGCTGTTTT 59.679 34.615 15.20 15.20 0.00 2.43
1882 2315 5.827797 TCAGACAACTCAAAATAGGCTGTTT 59.172 36.000 3.12 3.12 0.00 2.83
1883 2316 5.376625 TCAGACAACTCAAAATAGGCTGTT 58.623 37.500 0.00 0.00 0.00 3.16
1884 2317 4.973168 TCAGACAACTCAAAATAGGCTGT 58.027 39.130 0.00 0.00 0.00 4.40
1885 2318 5.947228 TTCAGACAACTCAAAATAGGCTG 57.053 39.130 0.00 0.00 0.00 4.85
1886 2319 5.049405 CGTTTCAGACAACTCAAAATAGGCT 60.049 40.000 0.00 0.00 0.00 4.58
1887 2320 5.049680 TCGTTTCAGACAACTCAAAATAGGC 60.050 40.000 0.00 0.00 0.00 3.93
1888 2321 6.202954 AGTCGTTTCAGACAACTCAAAATAGG 59.797 38.462 0.00 0.00 43.24 2.57
1889 2322 7.178712 AGTCGTTTCAGACAACTCAAAATAG 57.821 36.000 0.00 0.00 43.24 1.73
1890 2323 7.548196 AAGTCGTTTCAGACAACTCAAAATA 57.452 32.000 0.00 0.00 43.24 1.40
1891 2324 6.436843 AAGTCGTTTCAGACAACTCAAAAT 57.563 33.333 0.00 0.00 43.24 1.82
1892 2325 5.873179 AAGTCGTTTCAGACAACTCAAAA 57.127 34.783 0.00 0.00 43.24 2.44
1893 2326 5.870433 TGTAAGTCGTTTCAGACAACTCAAA 59.130 36.000 0.00 0.00 43.24 2.69
1894 2327 5.412640 TGTAAGTCGTTTCAGACAACTCAA 58.587 37.500 0.00 0.00 43.24 3.02
1895 2328 5.001237 TGTAAGTCGTTTCAGACAACTCA 57.999 39.130 0.00 0.00 43.24 3.41
1896 2329 5.961395 TTGTAAGTCGTTTCAGACAACTC 57.039 39.130 0.00 0.00 43.24 3.01
1897 2330 6.370718 ACTTTTGTAAGTCGTTTCAGACAACT 59.629 34.615 0.00 0.00 40.60 3.16
1898 2331 6.464834 CACTTTTGTAAGTCGTTTCAGACAAC 59.535 38.462 0.00 0.00 42.67 3.32
1899 2332 6.369340 TCACTTTTGTAAGTCGTTTCAGACAA 59.631 34.615 0.00 0.00 42.67 3.18
1900 2333 5.870433 TCACTTTTGTAAGTCGTTTCAGACA 59.130 36.000 0.00 0.00 42.67 3.41
1901 2334 6.340537 TCACTTTTGTAAGTCGTTTCAGAC 57.659 37.500 0.00 0.00 42.67 3.51
1902 2335 6.454583 CGTTCACTTTTGTAAGTCGTTTCAGA 60.455 38.462 0.00 0.00 42.67 3.27
1903 2336 5.671140 CGTTCACTTTTGTAAGTCGTTTCAG 59.329 40.000 0.00 0.00 42.67 3.02
1904 2337 5.446206 CCGTTCACTTTTGTAAGTCGTTTCA 60.446 40.000 0.00 0.00 42.67 2.69
1905 2338 4.959757 CCGTTCACTTTTGTAAGTCGTTTC 59.040 41.667 0.00 0.00 42.67 2.78
1906 2339 4.630940 TCCGTTCACTTTTGTAAGTCGTTT 59.369 37.500 0.00 0.00 42.67 3.60
1907 2340 4.183101 TCCGTTCACTTTTGTAAGTCGTT 58.817 39.130 0.00 0.00 42.67 3.85
1908 2341 3.784338 TCCGTTCACTTTTGTAAGTCGT 58.216 40.909 0.00 0.00 42.67 4.34
1909 2342 3.183775 CCTCCGTTCACTTTTGTAAGTCG 59.816 47.826 0.00 0.00 42.67 4.18
1910 2343 3.497262 CCCTCCGTTCACTTTTGTAAGTC 59.503 47.826 0.00 0.00 42.67 3.01
1911 2344 3.135167 TCCCTCCGTTCACTTTTGTAAGT 59.865 43.478 0.00 0.00 45.40 2.24
1912 2345 3.735591 TCCCTCCGTTCACTTTTGTAAG 58.264 45.455 0.00 0.00 37.40 2.34
1913 2346 3.135167 ACTCCCTCCGTTCACTTTTGTAA 59.865 43.478 0.00 0.00 0.00 2.41
1914 2347 2.701951 ACTCCCTCCGTTCACTTTTGTA 59.298 45.455 0.00 0.00 0.00 2.41
1915 2348 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.00 0.00 2.83
1916 2349 2.256117 ACTCCCTCCGTTCACTTTTG 57.744 50.000 0.00 0.00 0.00 2.44
1917 2350 2.970640 AGTACTCCCTCCGTTCACTTTT 59.029 45.455 0.00 0.00 0.00 2.27
1918 2351 2.606378 AGTACTCCCTCCGTTCACTTT 58.394 47.619 0.00 0.00 0.00 2.66
1919 2352 2.305858 AGTACTCCCTCCGTTCACTT 57.694 50.000 0.00 0.00 0.00 3.16
1920 2353 2.305858 AAGTACTCCCTCCGTTCACT 57.694 50.000 0.00 0.00 0.00 3.41
1921 2354 4.732672 ATAAAGTACTCCCTCCGTTCAC 57.267 45.455 0.00 0.00 0.00 3.18
1922 2355 5.954150 ACTAATAAAGTACTCCCTCCGTTCA 59.046 40.000 0.00 0.00 36.36 3.18
1923 2356 6.320926 AGACTAATAAAGTACTCCCTCCGTTC 59.679 42.308 0.00 0.00 39.07 3.95
1924 2357 6.193504 AGACTAATAAAGTACTCCCTCCGTT 58.806 40.000 0.00 0.00 39.07 4.44
1925 2358 5.764432 AGACTAATAAAGTACTCCCTCCGT 58.236 41.667 0.00 0.00 39.07 4.69
1926 2359 7.999450 ATAGACTAATAAAGTACTCCCTCCG 57.001 40.000 0.00 0.00 39.07 4.63
2075 2517 7.892778 TCACTAAACTTCACGCATTTATACA 57.107 32.000 0.00 0.00 0.00 2.29
2119 2561 4.999311 GCATTGTACTATCAGATCCATGCA 59.001 41.667 0.00 0.00 0.00 3.96
2186 2629 2.417379 CCCACTAACACTGTCTGATCCG 60.417 54.545 0.00 0.00 0.00 4.18
2491 2934 6.683974 TCAAAAGTCACAGAGGAAAAGAAG 57.316 37.500 0.00 0.00 0.00 2.85
2571 3015 4.405762 CGTTTATCGGCACCGCTA 57.594 55.556 3.66 0.00 39.59 4.26
2751 3197 6.970484 TCAACAAAGAGAACTGGCTAATTTC 58.030 36.000 0.00 0.00 0.00 2.17
3189 3635 1.067354 CCTTGCTTTGAATGGGCAGAC 60.067 52.381 0.00 0.00 37.28 3.51
3369 3815 3.420893 CAAAGGACACATAGGGCAGAAA 58.579 45.455 0.00 0.00 0.00 2.52
3377 3823 6.446781 AAATGATCAGCAAAGGACACATAG 57.553 37.500 0.09 0.00 0.00 2.23
3389 3835 9.748708 GGTTATTAAAGCATTAAATGATCAGCA 57.251 29.630 0.09 0.00 34.80 4.41
3421 3867 4.524053 ACCCTTACCTGCAATACTTAAGC 58.476 43.478 1.29 0.00 0.00 3.09
3452 3898 4.508662 GGACTCTCCAGTTGAATCGAATT 58.491 43.478 0.00 0.00 36.28 2.17
3489 3935 4.664062 CCCATGGGCAACACCTAG 57.336 61.111 20.41 0.00 39.10 3.02
3578 4024 0.608130 TGGGTGTGAGATCCTTGTCG 59.392 55.000 0.00 0.00 0.00 4.35
3757 4209 3.888930 GGTATCCTCTGACAGAAGGAGAG 59.111 52.174 20.96 5.36 33.55 3.20
3762 4214 2.102252 GCCAGGTATCCTCTGACAGAAG 59.898 54.545 6.61 0.02 34.36 2.85
3997 4449 1.937223 CACCTAAATGATAACCGCGCA 59.063 47.619 8.75 0.00 0.00 6.09
4144 4642 6.341316 TGGCTCTTGAGATATTCTTACACAC 58.659 40.000 1.30 0.00 0.00 3.82
4311 7101 7.149202 AGTCTAGGTCATCTTCTAGATCTGT 57.851 40.000 5.18 0.00 42.41 3.41
4606 7396 5.119931 TGTACAACAACAGGATTTGCATC 57.880 39.130 0.00 0.00 0.00 3.91
4643 7433 2.052237 GAACACGCACTTGTGCCG 60.052 61.111 18.48 15.41 43.74 5.69
4661 7451 0.603707 CACGGTGGCATCAGTCAACT 60.604 55.000 0.00 0.00 34.00 3.16
4736 7529 2.279741 TGTCAGATAAATGCGTCAGGC 58.720 47.619 0.00 0.00 43.96 4.85
4805 7598 3.302170 CGCGCGGCAAATTTAGTTATTTT 59.698 39.130 24.84 0.00 0.00 1.82
4855 7648 4.383850 TCATTTACATGGCAATTTCCCG 57.616 40.909 0.00 0.00 0.00 5.14
4914 7708 2.768527 AGACATTGGATCCAGATCACGT 59.231 45.455 15.53 6.98 39.54 4.49
4993 7790 3.321968 GCCCAAACACCATTTTTCTCTCT 59.678 43.478 0.00 0.00 0.00 3.10
5004 7801 2.208619 CCATGCAGCCCAAACACCA 61.209 57.895 0.00 0.00 0.00 4.17
5018 7816 4.673441 ACTTACGTCGAGAAGAATCCATG 58.327 43.478 15.38 0.00 0.00 3.66
5034 7832 2.535984 GCTCCATGACGATCAACTTACG 59.464 50.000 0.00 0.00 0.00 3.18
5052 7850 5.735766 AGGATTATTATTAGGAAGCGGCTC 58.264 41.667 1.45 0.00 0.00 4.70
5053 7851 5.763876 AGGATTATTATTAGGAAGCGGCT 57.236 39.130 0.00 0.00 0.00 5.52
5054 7852 6.819397 AAAGGATTATTATTAGGAAGCGGC 57.181 37.500 0.00 0.00 0.00 6.53
5123 7921 5.997746 CCTGATTTCCTGATTCCGCTTATTA 59.002 40.000 0.00 0.00 0.00 0.98
5180 7978 8.106247 ACTATTGCTCGTTTTAATTTCTTGGA 57.894 30.769 0.00 0.00 0.00 3.53
5189 7987 6.592220 TGTGCTCATACTATTGCTCGTTTTAA 59.408 34.615 0.00 0.00 0.00 1.52
5275 8079 2.454055 AGCGCGGTAATTACTAACGAC 58.546 47.619 10.12 14.91 43.86 4.34
5293 8097 2.436115 GACTACCGGGTGCCAAGC 60.436 66.667 10.66 0.00 0.00 4.01
5298 8102 2.106332 CGGATGACTACCGGGTGC 59.894 66.667 10.66 0.00 45.65 5.01
5403 8212 3.060736 TGGAGGCGTTTGCACTATTAA 57.939 42.857 0.00 0.00 45.35 1.40
5485 8294 4.219944 ACTGGTGCTATTTTACGAGACTCA 59.780 41.667 2.82 0.00 0.00 3.41
5507 8316 4.748144 CTCAGGGGCAGGGGCAAC 62.748 72.222 0.00 0.00 43.71 4.17
5518 8327 4.514441 GCTTCATATCATGTTGACTCAGGG 59.486 45.833 0.00 0.00 0.00 4.45
5583 8393 2.818432 GTTCCTCCACGACAGACTAGAA 59.182 50.000 0.00 0.00 0.00 2.10
5629 8439 2.769663 ACAGATTAGGGGTATCGTTGCA 59.230 45.455 0.00 0.00 0.00 4.08
5668 8479 6.157820 TGTCCCATGATAAAGAGATTGGTACA 59.842 38.462 0.00 0.00 0.00 2.90
5827 8638 3.580193 GCCGCGATTGCTGAGCAT 61.580 61.111 8.44 0.00 38.76 3.79


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

AutoCloner maintained by Alex Coulton.