Multiple sequence alignment - TraesCS4B01G250500

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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 TraesCS4B01G250500 chr4B 100.000 5376 0 0 1 5376 516973637 516968262 0.000000e+00 9928.0
1 TraesCS4B01G250500 chr4D 93.480 1319 53 15 1584 2893 419201303 419200009 0.000000e+00 1929.0
2 TraesCS4B01G250500 chr4D 89.352 1559 70 42 61 1574 419202906 419201399 0.000000e+00 1871.0
3 TraesCS4B01G250500 chr4D 94.927 749 36 1 3646 4392 419198733 419197985 0.000000e+00 1171.0
4 TraesCS4B01G250500 chr4D 93.426 791 25 8 2894 3660 419199539 419198752 0.000000e+00 1147.0
5 TraesCS4B01G250500 chr4D 93.578 109 7 0 4656 4764 419197884 419197776 4.310000e-36 163.0
6 TraesCS4B01G250500 chr4D 97.222 36 0 1 5040 5074 509476209 509476174 5.810000e-05 60.2
7 TraesCS4B01G250500 chr4A 89.612 1521 98 36 1568 3056 45747348 45748840 0.000000e+00 1879.0
8 TraesCS4B01G250500 chr4A 92.573 1306 74 11 3133 4416 45748879 45750183 0.000000e+00 1853.0
9 TraesCS4B01G250500 chr4A 86.472 1545 92 53 58 1574 45745843 45747298 0.000000e+00 1587.0
10 TraesCS4B01G250500 chr4A 80.936 299 26 15 4490 4758 45750187 45750484 1.960000e-49 207.0
11 TraesCS4B01G250500 chr2B 99.196 622 4 1 4755 5376 460483602 460482982 0.000000e+00 1120.0
12 TraesCS4B01G250500 chr2B 89.720 107 10 1 4659 4764 238259539 238259433 9.390000e-28 135.0
13 TraesCS4B01G250500 chr2B 86.441 118 14 2 4648 4764 154490805 154490689 1.570000e-25 128.0
14 TraesCS4B01G250500 chr2B 87.736 106 10 3 4660 4764 154500278 154500175 2.630000e-23 121.0
15 TraesCS4B01G250500 chr2B 98.361 61 1 0 1 61 100658555 100658615 2.050000e-19 108.0
16 TraesCS4B01G250500 chr5A 98.873 621 7 0 4756 5376 368104490 368105110 0.000000e+00 1109.0
17 TraesCS4B01G250500 chr3D 83.282 975 124 22 3440 4392 382002573 382003530 0.000000e+00 861.0
18 TraesCS4B01G250500 chr5D 82.985 958 128 16 3453 4392 6107710 6106770 0.000000e+00 833.0
19 TraesCS4B01G250500 chr5D 98.305 59 1 0 1 59 240093137 240093195 2.650000e-18 104.0
20 TraesCS4B01G250500 chr5D 89.041 73 5 2 4756 4828 142561265 142561334 2.670000e-13 87.9
21 TraesCS4B01G250500 chr5B 89.095 431 28 11 355 783 548215977 548215564 7.980000e-143 518.0
22 TraesCS4B01G250500 chr1A 86.131 274 25 5 3440 3702 590837970 590837699 3.170000e-72 283.0
23 TraesCS4B01G250500 chr1A 98.361 61 1 0 1 61 179030221 179030161 2.050000e-19 108.0
24 TraesCS4B01G250500 chr1A 92.593 54 3 1 4751 4804 64900394 64900446 5.770000e-10 76.8
25 TraesCS4B01G250500 chr1A 95.745 47 2 0 4756 4802 426928849 426928803 5.770000e-10 76.8
26 TraesCS4B01G250500 chr1A 92.453 53 3 1 4752 4804 144635754 144635703 2.080000e-09 75.0
27 TraesCS4B01G250500 chr7A 76.923 559 64 43 4752 5299 692484764 692485268 1.920000e-64 257.0
28 TraesCS4B01G250500 chr7A 92.857 70 2 3 1 68 142528116 142528048 1.230000e-16 99.0
29 TraesCS4B01G250500 chr7A 92.000 50 4 0 5300 5349 692485323 692485372 2.690000e-08 71.3
30 TraesCS4B01G250500 chr6D 85.792 183 19 6 5158 5337 15382126 15381948 2.560000e-43 187.0
31 TraesCS4B01G250500 chr6D 95.918 49 2 0 5300 5348 15381931 15381883 4.460000e-11 80.5
32 TraesCS4B01G250500 chr2A 90.099 101 8 2 4660 4758 102325240 102325340 4.370000e-26 130.0
33 TraesCS4B01G250500 chr2A 98.361 61 1 0 1 61 196117915 196117975 2.050000e-19 108.0
34 TraesCS4B01G250500 chr2A 94.030 67 2 2 1 67 606517644 606517580 3.430000e-17 100.0
35 TraesCS4B01G250500 chr2A 95.918 49 2 0 5300 5348 678727464 678727416 4.460000e-11 80.5
36 TraesCS4B01G250500 chr2D 89.320 103 10 1 4657 4758 103129907 103130009 1.570000e-25 128.0
37 TraesCS4B01G250500 chr2D 87.611 113 11 3 4647 4758 106265361 106265471 1.570000e-25 128.0
38 TraesCS4B01G250500 chr2D 87.736 106 12 1 4660 4764 181440613 181440508 7.310000e-24 122.0
39 TraesCS4B01G250500 chr2D 87.500 64 8 0 4756 4819 16061708 16061645 2.080000e-09 75.0
40 TraesCS4B01G250500 chr1B 98.361 61 1 0 1 61 362541893 362541953 2.050000e-19 108.0
41 TraesCS4B01G250500 chr6B 98.305 59 1 0 1 59 12533232 12533174 2.650000e-18 104.0
42 TraesCS4B01G250500 chr7B 98.276 58 1 0 1 58 255065396 255065453 9.530000e-18 102.0
43 TraesCS4B01G250500 chrUn 84.000 100 10 6 4429 4527 31917579 31917673 2.060000e-14 91.6
44 TraesCS4B01G250500 chr3A 94.444 54 3 0 4756 4809 25905967 25905914 3.450000e-12 84.2
45 TraesCS4B01G250500 chr7D 85.000 80 10 2 4756 4834 590131831 590131909 4.460000e-11 80.5


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 TraesCS4B01G250500 chr4B 516968262 516973637 5375 True 9928.0 9928 100.00000 1 5376 1 chr4B.!!$R1 5375
1 TraesCS4B01G250500 chr4D 419197776 419202906 5130 True 1256.2 1929 92.95260 61 4764 5 chr4D.!!$R2 4703
2 TraesCS4B01G250500 chr4A 45745843 45750484 4641 False 1381.5 1879 87.39825 58 4758 4 chr4A.!!$F1 4700
3 TraesCS4B01G250500 chr2B 460482982 460483602 620 True 1120.0 1120 99.19600 4755 5376 1 chr2B.!!$R4 621
4 TraesCS4B01G250500 chr5A 368104490 368105110 620 False 1109.0 1109 98.87300 4756 5376 1 chr5A.!!$F1 620
5 TraesCS4B01G250500 chr3D 382002573 382003530 957 False 861.0 861 83.28200 3440 4392 1 chr3D.!!$F1 952
6 TraesCS4B01G250500 chr5D 6106770 6107710 940 True 833.0 833 82.98500 3453 4392 1 chr5D.!!$R1 939

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
368 390 0.034337 TACCCACCAGCTTGTTCGTC 59.966 55.000 0.00 0.0 0.00 4.20 F
664 700 0.456995 GGTCTCGTCTCGCTTCCTTG 60.457 60.000 0.00 0.0 0.00 3.61 F
1295 1363 0.040425 GCACATTGTGGTTCGTGGAC 60.040 55.000 18.05 0.0 33.64 4.02 F
1300 1368 0.462937 TTGTGGTTCGTGGACAGTGG 60.463 55.000 0.00 0.0 0.00 4.00 F
2541 2709 1.001641 GCTGAGTGGGCATGGAACT 60.002 57.895 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1276 1344 0.040425 GTCCACGAACCACAATGTGC 60.040 55.000 8.05 0.00 31.34 4.57 R
2402 2566 0.324943 ATTCCCACGAGTCAACTGGG 59.675 55.000 10.22 10.22 45.58 4.45 R
2544 2712 1.267806 AGTTTGGCATCAACTCTTGCG 59.732 47.619 0.00 0.00 39.78 4.85 R
2631 2799 1.645710 CAGGACCTAACAGGAGTGGT 58.354 55.000 0.00 0.00 37.67 4.16 R
4452 5193 0.037326 ATGCTCTCAACGGCGAAGAA 60.037 50.000 16.62 0.00 0.00 2.52 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 2.210424 CTGAGAGAAGCTGGGGAGG 58.790 63.158 0.00 0.00 0.00 4.30
19 20 1.306482 TGAGAGAAGCTGGGGAGGG 60.306 63.158 0.00 0.00 0.00 4.30
20 21 2.041928 AGAGAAGCTGGGGAGGGG 59.958 66.667 0.00 0.00 0.00 4.79
21 22 3.093172 GAGAAGCTGGGGAGGGGG 61.093 72.222 0.00 0.00 0.00 5.40
22 23 3.952799 GAGAAGCTGGGGAGGGGGT 62.953 68.421 0.00 0.00 0.00 4.95
23 24 3.412408 GAAGCTGGGGAGGGGGTC 61.412 72.222 0.00 0.00 0.00 4.46
24 25 4.285790 AAGCTGGGGAGGGGGTCA 62.286 66.667 0.00 0.00 0.00 4.02
25 26 3.829311 AAGCTGGGGAGGGGGTCAA 62.829 63.158 0.00 0.00 0.00 3.18
26 27 3.023735 GCTGGGGAGGGGGTCAAT 61.024 66.667 0.00 0.00 0.00 2.57
27 28 2.626467 GCTGGGGAGGGGGTCAATT 61.626 63.158 0.00 0.00 0.00 2.32
28 29 1.615262 CTGGGGAGGGGGTCAATTC 59.385 63.158 0.00 0.00 0.00 2.17
29 30 0.921256 CTGGGGAGGGGGTCAATTCT 60.921 60.000 0.00 0.00 0.00 2.40
30 31 1.214305 TGGGGAGGGGGTCAATTCTG 61.214 60.000 0.00 0.00 0.00 3.02
31 32 1.615262 GGGAGGGGGTCAATTCTGG 59.385 63.158 0.00 0.00 0.00 3.86
32 33 1.615262 GGAGGGGGTCAATTCTGGG 59.385 63.158 0.00 0.00 0.00 4.45
33 34 0.919289 GGAGGGGGTCAATTCTGGGA 60.919 60.000 0.00 0.00 0.00 4.37
34 35 0.548510 GAGGGGGTCAATTCTGGGAG 59.451 60.000 0.00 0.00 0.00 4.30
35 36 0.121197 AGGGGGTCAATTCTGGGAGA 59.879 55.000 0.00 0.00 0.00 3.71
36 37 0.999712 GGGGGTCAATTCTGGGAGAA 59.000 55.000 0.00 0.00 38.78 2.87
37 38 1.570979 GGGGGTCAATTCTGGGAGAAT 59.429 52.381 0.00 0.00 46.22 2.40
50 51 3.319137 GGGAGAATTGCCCAAAAGAAC 57.681 47.619 7.89 0.00 45.31 3.01
51 52 2.899900 GGGAGAATTGCCCAAAAGAACT 59.100 45.455 7.89 0.00 45.31 3.01
52 53 3.306294 GGGAGAATTGCCCAAAAGAACTG 60.306 47.826 7.89 0.00 45.31 3.16
53 54 3.306294 GGAGAATTGCCCAAAAGAACTGG 60.306 47.826 0.00 0.00 0.00 4.00
54 55 2.037641 AGAATTGCCCAAAAGAACTGGC 59.962 45.455 0.00 0.00 44.27 4.85
55 56 0.686789 ATTGCCCAAAAGAACTGGCC 59.313 50.000 0.00 0.00 43.35 5.36
56 57 1.406860 TTGCCCAAAAGAACTGGCCC 61.407 55.000 0.00 0.00 43.35 5.80
57 58 1.533994 GCCCAAAAGAACTGGCCCT 60.534 57.895 0.00 0.00 37.94 5.19
58 59 1.536073 GCCCAAAAGAACTGGCCCTC 61.536 60.000 0.00 0.00 37.94 4.30
59 60 0.178964 CCCAAAAGAACTGGCCCTCA 60.179 55.000 0.00 0.00 32.10 3.86
150 151 5.237127 TGACTGTGAAGTGTATCAGCAAAAG 59.763 40.000 0.00 0.00 0.00 2.27
169 170 6.656003 CAAAAGTCCGTAGAAACTAAACAGG 58.344 40.000 0.00 0.00 0.00 4.00
170 171 5.541953 AAGTCCGTAGAAACTAAACAGGT 57.458 39.130 0.00 0.00 0.00 4.00
172 173 6.018589 AGTCCGTAGAAACTAAACAGGTAC 57.981 41.667 0.00 0.00 0.00 3.34
184 191 4.929819 AAACAGGTACCACCATTTGAAC 57.070 40.909 15.94 0.00 41.95 3.18
202 209 0.506932 ACGCGACAAACTCGTTCATG 59.493 50.000 15.93 0.00 44.92 3.07
218 225 0.164217 CATGCACAAAAATGGCGCAC 59.836 50.000 10.83 0.00 35.02 5.34
236 243 3.554692 CGATTGGTCCAGCGCGAC 61.555 66.667 12.10 4.00 0.00 5.19
248 261 1.512926 AGCGCGACTGAACATCTTTT 58.487 45.000 12.10 0.00 0.00 2.27
328 350 5.930837 AATCTACCACAGAAGAGAGAAGG 57.069 43.478 0.00 0.00 36.67 3.46
329 351 3.093057 TCTACCACAGAAGAGAGAAGGC 58.907 50.000 0.00 0.00 0.00 4.35
348 370 0.179089 CAGGCACGGATCTCCAGAAG 60.179 60.000 0.00 0.00 35.14 2.85
366 388 0.034896 AGTACCCACCAGCTTGTTCG 59.965 55.000 0.00 0.00 0.00 3.95
368 390 0.034337 TACCCACCAGCTTGTTCGTC 59.966 55.000 0.00 0.00 0.00 4.20
613 644 4.436998 CGCCTGACGGGGACAGAC 62.437 72.222 1.55 0.00 45.63 3.51
614 645 3.311110 GCCTGACGGGGACAGACA 61.311 66.667 1.55 0.00 37.54 3.41
615 646 2.879233 GCCTGACGGGGACAGACAA 61.879 63.158 1.55 0.00 37.54 3.18
664 700 0.456995 GGTCTCGTCTCGCTTCCTTG 60.457 60.000 0.00 0.00 0.00 3.61
670 706 1.433534 GTCTCGCTTCCTTGTTCCTG 58.566 55.000 0.00 0.00 0.00 3.86
729 765 4.955811 TCTTTGCCTCTTCTAACAGACA 57.044 40.909 0.00 0.00 0.00 3.41
748 784 0.990374 AGCAGCATTTCCAGACCTCT 59.010 50.000 0.00 0.00 0.00 3.69
765 803 6.773200 CAGACCTCTTGTGTATGATCCTAGTA 59.227 42.308 0.00 0.00 0.00 1.82
777 815 5.306114 TGATCCTAGTAACTGATCCGAGA 57.694 43.478 4.19 0.00 35.18 4.04
778 816 5.309638 TGATCCTAGTAACTGATCCGAGAG 58.690 45.833 4.19 0.00 35.18 3.20
829 867 2.360767 GCAATTGCCTGCCCCATGA 61.361 57.895 20.06 0.00 36.25 3.07
875 913 2.224137 TGCATTGTTTGGGCGAATTCAA 60.224 40.909 6.22 3.81 0.00 2.69
1054 1119 1.279496 TGTCTGCCTACATGCTCCTT 58.721 50.000 0.00 0.00 0.00 3.36
1055 1120 1.208052 TGTCTGCCTACATGCTCCTTC 59.792 52.381 0.00 0.00 0.00 3.46
1056 1121 1.484240 GTCTGCCTACATGCTCCTTCT 59.516 52.381 0.00 0.00 0.00 2.85
1239 1304 5.353123 TCTGAATTTGGTACGCTTATGTTCC 59.647 40.000 0.00 0.00 0.00 3.62
1294 1362 0.179032 AGCACATTGTGGTTCGTGGA 60.179 50.000 15.45 0.00 41.72 4.02
1295 1363 0.040425 GCACATTGTGGTTCGTGGAC 60.040 55.000 18.05 0.00 33.64 4.02
1296 1364 1.304254 CACATTGTGGTTCGTGGACA 58.696 50.000 9.00 0.00 0.00 4.02
1297 1365 1.264020 CACATTGTGGTTCGTGGACAG 59.736 52.381 9.00 0.00 0.00 3.51
1298 1366 1.134220 ACATTGTGGTTCGTGGACAGT 60.134 47.619 0.00 0.00 0.00 3.55
1299 1367 1.264020 CATTGTGGTTCGTGGACAGTG 59.736 52.381 0.00 0.00 0.00 3.66
1300 1368 0.462937 TTGTGGTTCGTGGACAGTGG 60.463 55.000 0.00 0.00 0.00 4.00
1309 1377 1.611977 CGTGGACAGTGGACTGACTTA 59.388 52.381 13.74 0.00 46.59 2.24
1341 1409 2.129607 CATGCTGTTTCCAACAACTGC 58.870 47.619 8.11 8.11 46.42 4.40
1422 1490 8.677148 TTTTAGTCTTCATTCAGTAGTTGCTT 57.323 30.769 0.00 0.00 0.00 3.91
1430 1498 1.623811 TCAGTAGTTGCTTCTGGGTCC 59.376 52.381 3.59 0.00 31.32 4.46
1484 1556 3.111853 TCTATGCTCATAGTTTGCCCG 57.888 47.619 14.48 0.00 41.12 6.13
1487 1559 2.481471 GCTCATAGTTTGCCCGCCC 61.481 63.158 0.00 0.00 0.00 6.13
1510 1582 5.118510 CCACTGCGAATTTTGTATTCCAAAC 59.881 40.000 0.00 0.00 42.63 2.93
1569 1641 6.327934 TGTTACGGTCTCTAGTTTATCAAGC 58.672 40.000 0.00 0.00 0.00 4.01
1887 2045 2.414750 AAAAACAGGGTGAGGCGTG 58.585 52.632 0.00 0.00 0.00 5.34
1894 2052 2.504175 ACAGGGTGAGGCGTGTAATATT 59.496 45.455 0.00 0.00 0.00 1.28
1946 2104 7.750229 ACTTGTGTCAGATGTTCACATATTT 57.250 32.000 11.74 0.00 40.85 1.40
1996 2154 9.134055 TGATATTGCATTTCCATCATTGTTCTA 57.866 29.630 0.00 0.00 0.00 2.10
2001 2159 6.604396 TGCATTTCCATCATTGTTCTAGATGT 59.396 34.615 0.00 0.00 37.93 3.06
2035 2193 8.543774 ACCTACTCATAGTTGATGAAAATCACT 58.456 33.333 0.00 0.00 44.14 3.41
2106 2266 6.056236 GGGAGGAGATATGGTAAAAGTGAAC 58.944 44.000 0.00 0.00 0.00 3.18
2128 2288 3.881688 CCCAAGCCAGATGAAGTTATCAG 59.118 47.826 0.00 0.00 42.53 2.90
2159 2323 9.747898 ACCAAGTGAAATATATGTACAAGGAAA 57.252 29.630 0.00 0.00 0.00 3.13
2179 2343 1.825090 TGATGTGCACAATGAGGGAC 58.175 50.000 25.72 8.37 0.00 4.46
2204 2368 1.913778 ATGGAGTTGCATGTGCTTGA 58.086 45.000 6.55 0.00 42.66 3.02
2253 2417 4.281941 ACACTCAACAGAACTAGCTCATGA 59.718 41.667 0.00 0.00 0.00 3.07
2254 2418 5.221521 ACACTCAACAGAACTAGCTCATGAA 60.222 40.000 0.00 0.00 0.00 2.57
2261 2425 6.233434 ACAGAACTAGCTCATGAATGAACAA 58.767 36.000 0.00 0.00 36.18 2.83
2318 2482 2.717639 ATGCACTCCATGGAAGGTAC 57.282 50.000 17.00 6.65 31.48 3.34
2402 2566 9.774742 GTCAAATACACAATCTCAAAAGGATAC 57.225 33.333 0.00 0.00 0.00 2.24
2432 2596 3.123804 CTCGTGGGAATTCGGTAATCTG 58.876 50.000 0.00 0.00 0.00 2.90
2471 2639 4.020751 TCTGTGCTCAGCTCTTCTATGTTT 60.021 41.667 10.95 0.00 41.10 2.83
2483 2651 7.126421 AGCTCTTCTATGTTTATCCCTTCTGAA 59.874 37.037 0.00 0.00 0.00 3.02
2541 2709 1.001641 GCTGAGTGGGCATGGAACT 60.002 57.895 0.00 0.00 0.00 3.01
2544 2712 2.036256 AGTGGGCATGGAACTGGC 59.964 61.111 0.00 0.00 40.76 4.85
2617 2785 1.120530 ACTCCGGCAGTTGTATAGGG 58.879 55.000 0.00 0.00 26.56 3.53
2645 2813 1.279271 CTCCCAACCACTCCTGTTAGG 59.721 57.143 0.00 0.00 36.46 2.69
2646 2814 1.064825 CCCAACCACTCCTGTTAGGT 58.935 55.000 0.00 0.00 36.53 3.08
2838 3006 8.735692 TCATATCTTGATGTTTTGCATGACTA 57.264 30.769 0.00 0.00 38.06 2.59
2839 3007 9.346005 TCATATCTTGATGTTTTGCATGACTAT 57.654 29.630 0.00 0.00 38.06 2.12
2840 3008 9.608617 CATATCTTGATGTTTTGCATGACTATC 57.391 33.333 0.00 0.00 38.06 2.08
2851 3033 6.688637 TTGCATGACTATCAGAAGAAATGG 57.311 37.500 0.00 0.00 0.00 3.16
2934 3585 7.147811 TGGTTGTCCCCTGCAATAAAATAATAC 60.148 37.037 0.00 0.00 0.00 1.89
2954 3613 3.574614 ACATTGCCGTGCTGTTTTAATC 58.425 40.909 0.00 0.00 0.00 1.75
3129 3797 8.768019 TGATTAATATATAGAATGCATCAGCGC 58.232 33.333 0.00 0.00 46.23 5.92
3131 3799 9.987272 ATTAATATATAGAATGCATCAGCGCTA 57.013 29.630 10.99 0.00 46.23 4.26
3400 4068 8.635765 ACAACATTGGTGTAGATGTATCTTTT 57.364 30.769 5.31 0.00 37.67 2.27
3446 4123 5.588246 TGTATCTTGTGTGAGCAAAAAGTCA 59.412 36.000 0.00 0.00 0.00 3.41
3610 4287 1.550524 CTACAGGCAAGCCTCACACTA 59.449 52.381 11.38 0.00 46.28 2.74
3627 4313 0.108992 CTAGTAAACTGCGGTCGCCA 60.109 55.000 12.94 0.60 41.09 5.69
3636 4322 2.935955 CGGTCGCCACAGTGTTTC 59.064 61.111 0.00 0.00 0.00 2.78
3690 4409 1.875009 TTGTTCTCAGTGCTCTGCTG 58.125 50.000 10.95 6.59 41.10 4.41
3944 4665 6.488344 TCAACTACCATTGAAACATGTGCTAA 59.512 34.615 0.00 0.00 35.65 3.09
3956 4677 8.363390 TGAAACATGTGCTAATTCAACCATTTA 58.637 29.630 0.00 0.00 0.00 1.40
3959 4680 7.839907 ACATGTGCTAATTCAACCATTTATGT 58.160 30.769 0.00 0.00 0.00 2.29
3960 4681 7.975616 ACATGTGCTAATTCAACCATTTATGTC 59.024 33.333 0.00 0.00 0.00 3.06
4057 4779 1.121378 TGTACAACGTGACCCTCCAA 58.879 50.000 0.00 0.00 0.00 3.53
4384 5120 2.487265 GGCCTGTTCTTGAGTGGAGAAA 60.487 50.000 0.00 0.00 35.11 2.52
4401 5142 6.710744 GTGGAGAAAGTTCTTTATCACAAGGA 59.289 38.462 17.59 0.00 37.73 3.36
4403 5144 6.710744 GGAGAAAGTTCTTTATCACAAGGACA 59.289 38.462 17.59 0.00 34.97 4.02
4412 5153 8.463930 TCTTTATCACAAGGACATTTTCACTT 57.536 30.769 0.00 0.00 0.00 3.16
4416 5157 9.513906 TTATCACAAGGACATTTTCACTTATCA 57.486 29.630 0.00 0.00 0.00 2.15
4417 5158 7.202016 TCACAAGGACATTTTCACTTATCAC 57.798 36.000 0.00 0.00 0.00 3.06
4418 5159 6.206634 TCACAAGGACATTTTCACTTATCACC 59.793 38.462 0.00 0.00 0.00 4.02
4419 5160 6.207417 CACAAGGACATTTTCACTTATCACCT 59.793 38.462 0.00 0.00 0.00 4.00
4420 5161 6.777580 ACAAGGACATTTTCACTTATCACCTT 59.222 34.615 0.00 0.00 34.92 3.50
4421 5162 6.824305 AGGACATTTTCACTTATCACCTTG 57.176 37.500 0.00 0.00 0.00 3.61
4423 5164 7.004086 AGGACATTTTCACTTATCACCTTGAA 58.996 34.615 0.00 0.00 0.00 2.69
4424 5165 7.671398 AGGACATTTTCACTTATCACCTTGAAT 59.329 33.333 0.00 0.00 0.00 2.57
4425 5166 7.970614 GGACATTTTCACTTATCACCTTGAATC 59.029 37.037 0.00 0.00 0.00 2.52
4427 5168 6.494893 TTTTCACTTATCACCTTGAATCGG 57.505 37.500 0.00 0.00 0.00 4.18
4428 5169 3.531538 TCACTTATCACCTTGAATCGGC 58.468 45.455 0.00 0.00 0.00 5.54
4430 5171 3.879295 CACTTATCACCTTGAATCGGCAT 59.121 43.478 0.00 0.00 0.00 4.40
4431 5172 4.336433 CACTTATCACCTTGAATCGGCATT 59.664 41.667 0.00 0.00 0.00 3.56
4432 5173 4.949856 ACTTATCACCTTGAATCGGCATTT 59.050 37.500 0.00 0.00 0.00 2.32
4433 5174 5.418840 ACTTATCACCTTGAATCGGCATTTT 59.581 36.000 0.00 0.00 0.00 1.82
4434 5175 3.848272 TCACCTTGAATCGGCATTTTC 57.152 42.857 0.00 0.00 0.00 2.29
4435 5176 3.153130 TCACCTTGAATCGGCATTTTCA 58.847 40.909 0.00 0.00 0.00 2.69
4436 5177 3.057596 TCACCTTGAATCGGCATTTTCAC 60.058 43.478 0.00 0.00 31.87 3.18
4437 5178 3.057315 CACCTTGAATCGGCATTTTCACT 60.057 43.478 0.00 0.00 31.87 3.41
4438 5179 3.573967 ACCTTGAATCGGCATTTTCACTT 59.426 39.130 0.00 0.00 31.87 3.16
4440 5181 5.418840 ACCTTGAATCGGCATTTTCACTTAT 59.581 36.000 0.00 0.00 31.87 1.73
4441 5182 5.973565 CCTTGAATCGGCATTTTCACTTATC 59.026 40.000 0.00 0.00 31.87 1.75
4444 5185 6.728200 TGAATCGGCATTTTCACTTATCATC 58.272 36.000 0.00 0.00 0.00 2.92
4445 5186 5.695851 ATCGGCATTTTCACTTATCATCC 57.304 39.130 0.00 0.00 0.00 3.51
4446 5187 4.780815 TCGGCATTTTCACTTATCATCCT 58.219 39.130 0.00 0.00 0.00 3.24
4447 5188 4.576053 TCGGCATTTTCACTTATCATCCTG 59.424 41.667 0.00 0.00 0.00 3.86
4449 5190 5.066375 CGGCATTTTCACTTATCATCCTGAA 59.934 40.000 0.00 0.00 0.00 3.02
4450 5191 6.238842 CGGCATTTTCACTTATCATCCTGAAT 60.239 38.462 0.00 0.00 0.00 2.57
4452 5193 7.014038 GGCATTTTCACTTATCATCCTGAATCT 59.986 37.037 0.00 0.00 0.00 2.40
4453 5194 8.411683 GCATTTTCACTTATCATCCTGAATCTT 58.588 33.333 0.00 0.00 0.00 2.40
4454 5195 9.947669 CATTTTCACTTATCATCCTGAATCTTC 57.052 33.333 0.00 0.00 0.00 2.87
4455 5196 9.917887 ATTTTCACTTATCATCCTGAATCTTCT 57.082 29.630 0.00 0.00 0.00 2.85
4456 5197 9.745018 TTTTCACTTATCATCCTGAATCTTCTT 57.255 29.630 0.00 0.00 0.00 2.52
4457 5198 8.954950 TTCACTTATCATCCTGAATCTTCTTC 57.045 34.615 0.00 0.00 0.00 2.87
4458 5199 7.205992 TCACTTATCATCCTGAATCTTCTTCG 58.794 38.462 0.00 0.00 0.00 3.79
4460 5201 3.185246 TCATCCTGAATCTTCTTCGCC 57.815 47.619 0.00 0.00 0.00 5.54
4461 5202 1.863454 CATCCTGAATCTTCTTCGCCG 59.137 52.381 0.00 0.00 0.00 6.46
4462 5203 0.895530 TCCTGAATCTTCTTCGCCGT 59.104 50.000 0.00 0.00 0.00 5.68
4463 5204 1.275291 TCCTGAATCTTCTTCGCCGTT 59.725 47.619 0.00 0.00 0.00 4.44
4464 5205 1.394917 CCTGAATCTTCTTCGCCGTTG 59.605 52.381 0.00 0.00 0.00 4.10
4465 5206 2.337583 CTGAATCTTCTTCGCCGTTGA 58.662 47.619 0.00 0.00 0.00 3.18
4466 5207 2.337583 TGAATCTTCTTCGCCGTTGAG 58.662 47.619 0.00 0.00 0.00 3.02
4467 5208 2.029380 TGAATCTTCTTCGCCGTTGAGA 60.029 45.455 0.00 0.00 0.00 3.27
4468 5209 2.285827 ATCTTCTTCGCCGTTGAGAG 57.714 50.000 0.00 0.00 0.00 3.20
4469 5210 0.388649 TCTTCTTCGCCGTTGAGAGC 60.389 55.000 0.00 0.00 0.00 4.09
4470 5211 0.667487 CTTCTTCGCCGTTGAGAGCA 60.667 55.000 0.00 0.00 0.00 4.26
4471 5212 0.037326 TTCTTCGCCGTTGAGAGCAT 60.037 50.000 0.00 0.00 0.00 3.79
4472 5213 0.458543 TCTTCGCCGTTGAGAGCATC 60.459 55.000 0.00 0.00 0.00 3.91
4473 5214 1.424493 CTTCGCCGTTGAGAGCATCC 61.424 60.000 0.00 0.00 33.66 3.51
4474 5215 1.888436 TTCGCCGTTGAGAGCATCCT 61.888 55.000 0.00 0.00 33.66 3.24
4475 5216 1.035385 TCGCCGTTGAGAGCATCCTA 61.035 55.000 0.00 0.00 33.66 2.94
4476 5217 0.179111 CGCCGTTGAGAGCATCCTAA 60.179 55.000 0.00 0.00 33.66 2.69
4477 5218 1.291132 GCCGTTGAGAGCATCCTAAC 58.709 55.000 0.00 0.00 33.66 2.34
4480 5221 3.190874 CCGTTGAGAGCATCCTAACTTC 58.809 50.000 0.00 0.00 33.66 3.01
4481 5222 3.368427 CCGTTGAGAGCATCCTAACTTCA 60.368 47.826 0.00 0.00 33.66 3.02
4482 5223 4.245660 CGTTGAGAGCATCCTAACTTCAA 58.754 43.478 0.00 0.00 33.66 2.69
4483 5224 4.690748 CGTTGAGAGCATCCTAACTTCAAA 59.309 41.667 0.00 0.00 33.66 2.69
4484 5225 5.389935 CGTTGAGAGCATCCTAACTTCAAAC 60.390 44.000 0.00 0.00 33.66 2.93
4487 5228 7.004555 TGAGAGCATCCTAACTTCAAACTAA 57.995 36.000 0.00 0.00 33.66 2.24
4488 5229 6.874134 TGAGAGCATCCTAACTTCAAACTAAC 59.126 38.462 0.00 0.00 33.66 2.34
4498 5239 5.592104 ACTTCAAACTAACAACAAAGGGG 57.408 39.130 0.00 0.00 0.00 4.79
4502 5243 6.607004 TCAAACTAACAACAAAGGGGAAAA 57.393 33.333 0.00 0.00 0.00 2.29
4509 5250 3.699538 ACAACAAAGGGGAAAAGTCTCAC 59.300 43.478 0.00 0.00 0.00 3.51
4531 5272 1.293179 CGAGCCACAGATCACCACA 59.707 57.895 0.00 0.00 0.00 4.17
4563 5305 0.596600 GAATGATGCAAGCATGGCGG 60.597 55.000 12.94 0.00 45.83 6.13
4587 5329 8.356657 CGGAGATGAGATCAAAGTAGATAGTTT 58.643 37.037 0.00 0.00 0.00 2.66
4590 5332 9.829507 AGATGAGATCAAAGTAGATAGTTTTGG 57.170 33.333 0.00 0.00 33.70 3.28
4599 5341 9.382244 CAAAGTAGATAGTTTTGGAAAAAGTCG 57.618 33.333 0.00 0.00 0.00 4.18
4600 5342 7.130303 AGTAGATAGTTTTGGAAAAAGTCGC 57.870 36.000 0.00 0.00 0.00 5.19
4601 5343 6.935208 AGTAGATAGTTTTGGAAAAAGTCGCT 59.065 34.615 0.00 0.05 0.00 4.93
4602 5344 8.092687 AGTAGATAGTTTTGGAAAAAGTCGCTA 58.907 33.333 0.00 0.00 0.00 4.26
4603 5345 7.923414 AGATAGTTTTGGAAAAAGTCGCTAT 57.077 32.000 0.00 0.00 0.00 2.97
4604 5346 8.336801 AGATAGTTTTGGAAAAAGTCGCTATT 57.663 30.769 0.00 0.00 0.00 1.73
4605 5347 9.444600 AGATAGTTTTGGAAAAAGTCGCTATTA 57.555 29.630 0.00 0.00 0.00 0.98
4608 5350 8.965986 AGTTTTGGAAAAAGTCGCTATTATTC 57.034 30.769 0.00 0.00 0.00 1.75
4610 5352 9.187455 GTTTTGGAAAAAGTCGCTATTATTCAA 57.813 29.630 0.00 0.00 0.00 2.69
4611 5353 9.751542 TTTTGGAAAAAGTCGCTATTATTCAAA 57.248 25.926 0.00 0.00 0.00 2.69
4614 5356 8.020819 TGGAAAAAGTCGCTATTATTCAAACAG 58.979 33.333 0.00 0.00 0.00 3.16
4615 5357 7.008357 GGAAAAAGTCGCTATTATTCAAACAGC 59.992 37.037 0.00 0.00 0.00 4.40
4616 5358 6.743575 AAAGTCGCTATTATTCAAACAGCT 57.256 33.333 0.00 0.00 0.00 4.24
4617 5359 7.843490 AAAGTCGCTATTATTCAAACAGCTA 57.157 32.000 0.00 0.00 0.00 3.32
4618 5360 6.830114 AGTCGCTATTATTCAAACAGCTAC 57.170 37.500 0.00 0.00 0.00 3.58
4621 5390 4.084537 CGCTATTATTCAAACAGCTACCCG 60.085 45.833 0.00 0.00 0.00 5.28
4624 5393 1.453155 ATTCAAACAGCTACCCGCAG 58.547 50.000 0.00 0.00 42.61 5.18
4637 5406 5.298527 AGCTACCCGCAGATTTTAAATTACC 59.701 40.000 0.00 0.00 42.61 2.85
4639 5408 5.576447 ACCCGCAGATTTTAAATTACCAG 57.424 39.130 0.00 0.00 0.00 4.00
4642 5411 6.033966 CCCGCAGATTTTAAATTACCAGTTC 58.966 40.000 0.00 0.00 0.00 3.01
4643 5412 6.127730 CCCGCAGATTTTAAATTACCAGTTCT 60.128 38.462 0.00 0.00 0.00 3.01
4644 5413 6.747280 CCGCAGATTTTAAATTACCAGTTCTG 59.253 38.462 0.00 0.00 33.07 3.02
4647 5416 9.556030 GCAGATTTTAAATTACCAGTTCTGTAC 57.444 33.333 0.00 0.00 32.63 2.90
4789 5559 2.096980 AGCAGAATCGAACGTCGTGATA 59.903 45.455 0.00 0.00 41.35 2.15
4874 5644 0.110486 ATCCACGTTCAGCCCACTTT 59.890 50.000 0.00 0.00 0.00 2.66
5355 6126 2.746375 GGGACCGATGATGCCCTGT 61.746 63.158 0.00 0.00 37.59 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.336632 CCCTCCCCAGCTTCTCTCAG 61.337 65.000 0.00 0.00 0.00 3.35
1 2 1.306482 CCCTCCCCAGCTTCTCTCA 60.306 63.158 0.00 0.00 0.00 3.27
6 7 3.412408 GACCCCCTCCCCAGCTTC 61.412 72.222 0.00 0.00 0.00 3.86
7 8 3.829311 TTGACCCCCTCCCCAGCTT 62.829 63.158 0.00 0.00 0.00 3.74
8 9 3.603330 ATTGACCCCCTCCCCAGCT 62.603 63.158 0.00 0.00 0.00 4.24
9 10 2.573893 GAATTGACCCCCTCCCCAGC 62.574 65.000 0.00 0.00 0.00 4.85
10 11 0.921256 AGAATTGACCCCCTCCCCAG 60.921 60.000 0.00 0.00 0.00 4.45
11 12 1.165782 AGAATTGACCCCCTCCCCA 59.834 57.895 0.00 0.00 0.00 4.96
12 13 1.615262 CAGAATTGACCCCCTCCCC 59.385 63.158 0.00 0.00 0.00 4.81
13 14 1.615262 CCAGAATTGACCCCCTCCC 59.385 63.158 0.00 0.00 0.00 4.30
14 15 0.919289 TCCCAGAATTGACCCCCTCC 60.919 60.000 0.00 0.00 0.00 4.30
15 16 0.548510 CTCCCAGAATTGACCCCCTC 59.451 60.000 0.00 0.00 0.00 4.30
16 17 0.121197 TCTCCCAGAATTGACCCCCT 59.879 55.000 0.00 0.00 0.00 4.79
17 18 0.999712 TTCTCCCAGAATTGACCCCC 59.000 55.000 0.00 0.00 0.00 5.40
30 31 2.899900 AGTTCTTTTGGGCAATTCTCCC 59.100 45.455 5.52 5.52 44.17 4.30
31 32 3.306294 CCAGTTCTTTTGGGCAATTCTCC 60.306 47.826 0.00 0.00 31.87 3.71
32 33 3.862264 GCCAGTTCTTTTGGGCAATTCTC 60.862 47.826 0.00 0.00 45.70 2.87
33 34 2.037641 GCCAGTTCTTTTGGGCAATTCT 59.962 45.455 0.00 0.00 45.70 2.40
34 35 2.416747 GCCAGTTCTTTTGGGCAATTC 58.583 47.619 0.00 0.00 45.70 2.17
35 36 2.549064 GCCAGTTCTTTTGGGCAATT 57.451 45.000 0.00 0.00 45.70 2.32
40 41 0.178964 TGAGGGCCAGTTCTTTTGGG 60.179 55.000 6.18 0.00 36.19 4.12
41 42 1.202927 TCTGAGGGCCAGTTCTTTTGG 60.203 52.381 6.18 0.00 43.38 3.28
42 43 2.276732 TCTGAGGGCCAGTTCTTTTG 57.723 50.000 6.18 0.00 43.38 2.44
43 44 3.075134 AGATTCTGAGGGCCAGTTCTTTT 59.925 43.478 6.18 0.00 43.38 2.27
44 45 2.646798 AGATTCTGAGGGCCAGTTCTTT 59.353 45.455 6.18 0.00 43.38 2.52
45 46 2.273619 AGATTCTGAGGGCCAGTTCTT 58.726 47.619 6.18 0.00 43.38 2.52
46 47 1.963985 AGATTCTGAGGGCCAGTTCT 58.036 50.000 6.18 0.00 43.38 3.01
47 48 2.751806 CAAAGATTCTGAGGGCCAGTTC 59.248 50.000 6.18 0.00 43.38 3.01
48 49 2.800250 CAAAGATTCTGAGGGCCAGTT 58.200 47.619 6.18 0.00 43.38 3.16
49 50 1.615384 GCAAAGATTCTGAGGGCCAGT 60.615 52.381 6.18 0.00 43.38 4.00
50 51 1.101331 GCAAAGATTCTGAGGGCCAG 58.899 55.000 6.18 0.00 44.27 4.85
51 52 0.323725 GGCAAAGATTCTGAGGGCCA 60.324 55.000 6.18 0.00 39.66 5.36
52 53 0.033699 AGGCAAAGATTCTGAGGGCC 60.034 55.000 0.00 0.00 40.18 5.80
53 54 1.387539 GAGGCAAAGATTCTGAGGGC 58.612 55.000 0.00 0.00 0.00 5.19
54 55 1.283029 TGGAGGCAAAGATTCTGAGGG 59.717 52.381 0.00 0.00 0.00 4.30
55 56 2.641305 CTGGAGGCAAAGATTCTGAGG 58.359 52.381 0.00 0.00 0.00 3.86
56 57 2.026449 ACCTGGAGGCAAAGATTCTGAG 60.026 50.000 0.00 0.00 39.32 3.35
57 58 1.988107 ACCTGGAGGCAAAGATTCTGA 59.012 47.619 0.00 0.00 39.32 3.27
58 59 2.089980 CACCTGGAGGCAAAGATTCTG 58.910 52.381 0.00 0.00 39.32 3.02
59 60 1.005215 CCACCTGGAGGCAAAGATTCT 59.995 52.381 0.00 0.00 39.32 2.40
150 151 5.164233 GGTACCTGTTTAGTTTCTACGGAC 58.836 45.833 4.06 0.00 0.00 4.79
169 170 1.136169 GTCGCGTTCAAATGGTGGTAC 60.136 52.381 5.77 0.00 0.00 3.34
170 171 1.149987 GTCGCGTTCAAATGGTGGTA 58.850 50.000 5.77 0.00 0.00 3.25
172 173 0.309302 TTGTCGCGTTCAAATGGTGG 59.691 50.000 5.77 0.00 0.00 4.61
202 209 2.656807 CGGTGCGCCATTTTTGTGC 61.657 57.895 18.18 0.00 39.63 4.57
218 225 4.812476 TCGCGCTGGACCAATCGG 62.812 66.667 5.56 7.55 38.77 4.18
236 243 7.278424 TCCTTTGCAAAAAGAAAAGATGTTCAG 59.722 33.333 13.84 0.00 44.45 3.02
243 250 7.386059 ACTTCTTCCTTTGCAAAAAGAAAAGA 58.614 30.769 26.99 20.14 44.45 2.52
248 261 6.279513 TGAACTTCTTCCTTTGCAAAAAGA 57.720 33.333 21.54 19.89 31.58 2.52
288 304 9.859427 TGGTAGATTTATTCTTTGCTTTCATTG 57.141 29.630 0.00 0.00 35.79 2.82
289 305 9.860898 GTGGTAGATTTATTCTTTGCTTTCATT 57.139 29.630 0.00 0.00 35.79 2.57
293 309 8.635765 TCTGTGGTAGATTTATTCTTTGCTTT 57.364 30.769 0.00 0.00 35.79 3.51
313 333 1.675415 GCCTGCCTTCTCTCTTCTGTG 60.675 57.143 0.00 0.00 0.00 3.66
328 350 2.202987 CTGGAGATCCGTGCCTGC 60.203 66.667 0.00 0.00 39.43 4.85
329 351 0.179089 CTTCTGGAGATCCGTGCCTG 60.179 60.000 0.00 0.00 39.43 4.85
348 370 0.250166 ACGAACAAGCTGGTGGGTAC 60.250 55.000 0.00 0.00 0.00 3.34
430 456 2.925170 ACTCACTCGGCAGGGCTT 60.925 61.111 0.00 0.00 0.00 4.35
610 641 1.133792 CCTCCACCAACCACTTTGTCT 60.134 52.381 0.00 0.00 32.71 3.41
612 643 0.923358 TCCTCCACCAACCACTTTGT 59.077 50.000 0.00 0.00 32.71 2.83
613 644 1.956477 CTTCCTCCACCAACCACTTTG 59.044 52.381 0.00 0.00 34.63 2.77
614 645 1.133482 CCTTCCTCCACCAACCACTTT 60.133 52.381 0.00 0.00 0.00 2.66
615 646 0.478507 CCTTCCTCCACCAACCACTT 59.521 55.000 0.00 0.00 0.00 3.16
678 714 1.129251 CGACATGTGCGAGCAAAAGAT 59.871 47.619 1.15 0.00 0.00 2.40
692 728 3.426695 GCAAAGATCCCAAACTCGACATG 60.427 47.826 0.00 0.00 0.00 3.21
729 765 0.990374 AGAGGTCTGGAAATGCTGCT 59.010 50.000 0.00 0.00 0.00 4.24
748 784 7.255486 CGGATCAGTTACTAGGATCATACACAA 60.255 40.741 12.64 0.00 39.30 3.33
765 803 3.444388 GTCAGTAACCTCTCGGATCAGTT 59.556 47.826 0.00 0.00 0.00 3.16
777 815 6.070366 GGGATTAACCAGTAAGTCAGTAACCT 60.070 42.308 0.00 0.00 41.20 3.50
778 816 6.111382 GGGATTAACCAGTAAGTCAGTAACC 58.889 44.000 0.00 0.00 41.20 2.85
779 817 5.809051 CGGGATTAACCAGTAAGTCAGTAAC 59.191 44.000 0.00 0.00 41.20 2.50
780 818 5.481473 ACGGGATTAACCAGTAAGTCAGTAA 59.519 40.000 0.00 0.00 44.69 2.24
781 819 5.018809 ACGGGATTAACCAGTAAGTCAGTA 58.981 41.667 0.00 0.00 44.69 2.74
782 820 3.836562 ACGGGATTAACCAGTAAGTCAGT 59.163 43.478 0.00 0.00 44.69 3.41
783 821 4.467198 ACGGGATTAACCAGTAAGTCAG 57.533 45.455 0.00 0.00 44.69 3.51
784 822 4.895668 AACGGGATTAACCAGTAAGTCA 57.104 40.909 0.00 0.00 45.71 3.41
785 823 7.854557 AATTAACGGGATTAACCAGTAAGTC 57.145 36.000 0.00 0.00 45.71 3.01
786 824 7.362315 GCAAATTAACGGGATTAACCAGTAAGT 60.362 37.037 0.00 0.00 45.71 2.24
787 825 6.970613 GCAAATTAACGGGATTAACCAGTAAG 59.029 38.462 0.00 0.00 45.71 2.34
788 826 6.433404 TGCAAATTAACGGGATTAACCAGTAA 59.567 34.615 0.00 0.00 45.71 2.24
789 827 5.944599 TGCAAATTAACGGGATTAACCAGTA 59.055 36.000 0.00 0.00 45.71 2.74
791 829 5.317733 TGCAAATTAACGGGATTAACCAG 57.682 39.130 0.00 0.00 41.20 4.00
829 867 2.531672 TCATCAGCCCCGATGACAT 58.468 52.632 6.91 0.00 45.31 3.06
875 913 1.305297 TGAGACGATGCCCTGAGGT 60.305 57.895 0.00 0.00 34.57 3.85
1054 1119 2.676822 AGCCGAAGCCGAGTGAGA 60.677 61.111 0.00 0.00 41.25 3.27
1055 1120 2.202676 GAGCCGAAGCCGAGTGAG 60.203 66.667 0.00 0.00 41.25 3.51
1056 1121 2.989253 TGAGCCGAAGCCGAGTGA 60.989 61.111 0.00 0.00 41.25 3.41
1274 1342 0.667993 CCACGAACCACAATGTGCTT 59.332 50.000 8.05 0.00 31.34 3.91
1275 1343 0.179032 TCCACGAACCACAATGTGCT 60.179 50.000 8.05 0.00 31.34 4.40
1276 1344 0.040425 GTCCACGAACCACAATGTGC 60.040 55.000 8.05 0.00 31.34 4.57
1290 1358 2.628657 AGTAAGTCAGTCCACTGTCCAC 59.371 50.000 6.61 3.20 44.12 4.02
1294 1362 4.142004 ACGAAAAGTAAGTCAGTCCACTGT 60.142 41.667 6.61 0.00 44.12 3.55
1295 1363 4.209288 CACGAAAAGTAAGTCAGTCCACTG 59.791 45.833 0.00 0.00 45.08 3.66
1296 1364 4.142004 ACACGAAAAGTAAGTCAGTCCACT 60.142 41.667 0.00 0.00 0.00 4.00
1297 1365 4.117685 ACACGAAAAGTAAGTCAGTCCAC 58.882 43.478 0.00 0.00 0.00 4.02
1298 1366 4.395959 ACACGAAAAGTAAGTCAGTCCA 57.604 40.909 0.00 0.00 0.00 4.02
1299 1367 4.807304 TGAACACGAAAAGTAAGTCAGTCC 59.193 41.667 0.00 0.00 0.00 3.85
1300 1368 5.961395 TGAACACGAAAAGTAAGTCAGTC 57.039 39.130 0.00 0.00 0.00 3.51
1309 1377 4.351192 GAAACAGCATGAACACGAAAAGT 58.649 39.130 0.00 0.00 39.69 2.66
1341 1409 4.082026 GGGTGATCCAAATCCTGAACAAAG 60.082 45.833 0.00 0.00 35.00 2.77
1422 1490 6.553100 AGAAAAACAATTAACATGGACCCAGA 59.447 34.615 0.00 0.00 0.00 3.86
1484 1556 2.939460 ATACAAAATTCGCAGTGGGC 57.061 45.000 1.51 0.00 39.90 5.36
1510 1582 7.149569 TCATTGCAGAGAGAAAATAACCTTG 57.850 36.000 0.00 0.00 0.00 3.61
1519 1591 5.923114 GCGATAGTATCATTGCAGAGAGAAA 59.077 40.000 10.71 0.00 35.67 2.52
1569 1641 7.009907 CACTGACATGACTGTAACTACATGATG 59.990 40.741 11.85 0.00 41.45 3.07
1629 1787 9.509956 ACTAACCAACTAATGCTTACAATTACA 57.490 29.630 0.00 0.00 0.00 2.41
1904 2062 9.352784 GACACAAGTTATGCATGCTAAATTAAA 57.647 29.630 20.33 0.00 0.00 1.52
1905 2063 8.518702 TGACACAAGTTATGCATGCTAAATTAA 58.481 29.630 20.33 6.41 0.00 1.40
1906 2064 8.049655 TGACACAAGTTATGCATGCTAAATTA 57.950 30.769 20.33 0.00 0.00 1.40
1953 2111 6.151648 GCAATATCACATGGTTATGGCTATGT 59.848 38.462 0.00 0.00 40.43 2.29
2016 2174 7.130917 GCTGCTAGTGATTTTCATCAACTATG 58.869 38.462 0.00 0.00 41.30 2.23
2025 2183 1.992667 CGACGCTGCTAGTGATTTTCA 59.007 47.619 0.00 0.00 0.00 2.69
2106 2266 3.881688 CTGATAACTTCATCTGGCTTGGG 59.118 47.826 0.00 0.00 32.72 4.12
2159 2323 2.025605 AGTCCCTCATTGTGCACATCAT 60.026 45.455 22.39 9.52 0.00 2.45
2180 2344 2.025981 AGCACATGCAACTCCATTAGGA 60.026 45.455 6.64 0.00 45.16 2.94
2181 2345 2.372264 AGCACATGCAACTCCATTAGG 58.628 47.619 6.64 0.00 45.16 2.69
2182 2346 3.441222 TCAAGCACATGCAACTCCATTAG 59.559 43.478 6.64 0.00 45.16 1.73
2183 2347 3.419943 TCAAGCACATGCAACTCCATTA 58.580 40.909 6.64 0.00 45.16 1.90
2184 2348 2.241160 TCAAGCACATGCAACTCCATT 58.759 42.857 6.64 0.00 45.16 3.16
2185 2349 1.913778 TCAAGCACATGCAACTCCAT 58.086 45.000 6.64 0.00 45.16 3.41
2186 2350 1.913778 ATCAAGCACATGCAACTCCA 58.086 45.000 6.64 0.00 45.16 3.86
2187 2351 4.025015 CTAATCAAGCACATGCAACTCC 57.975 45.455 6.64 0.00 45.16 3.85
2230 2394 4.281941 TCATGAGCTAGTTCTGTTGAGTGT 59.718 41.667 8.15 0.00 0.00 3.55
2231 2395 4.814147 TCATGAGCTAGTTCTGTTGAGTG 58.186 43.478 8.15 0.00 0.00 3.51
2232 2396 5.474578 TTCATGAGCTAGTTCTGTTGAGT 57.525 39.130 8.15 0.00 0.00 3.41
2253 2417 7.094075 TGCTCTGCAGATAGATTTTTGTTCATT 60.094 33.333 18.63 0.00 33.32 2.57
2254 2418 6.376299 TGCTCTGCAGATAGATTTTTGTTCAT 59.624 34.615 18.63 0.00 33.32 2.57
2261 2425 8.566260 GTGATAATTGCTCTGCAGATAGATTTT 58.434 33.333 18.63 11.75 40.61 1.82
2318 2482 2.226437 CCAGAAGGAACGTTGGACATTG 59.774 50.000 5.00 0.00 36.89 2.82
2402 2566 0.324943 ATTCCCACGAGTCAACTGGG 59.675 55.000 10.22 10.22 45.58 4.45
2445 2609 1.690893 AGAAGAGCTGAGCACAGAACA 59.309 47.619 15.88 0.00 46.03 3.18
2483 2651 9.539194 AGAAAAGAATATTCAACCCTTCAGAAT 57.461 29.630 17.56 0.00 36.14 2.40
2541 2709 2.334946 GGCATCAACTCTTGCGCCA 61.335 57.895 4.18 0.00 43.92 5.69
2544 2712 1.267806 AGTTTGGCATCAACTCTTGCG 59.732 47.619 0.00 0.00 39.78 4.85
2617 2785 4.329545 TGGTTGGGAGAGCGGTGC 62.330 66.667 0.00 0.00 0.00 5.01
2631 2799 1.645710 CAGGACCTAACAGGAGTGGT 58.354 55.000 0.00 0.00 37.67 4.16
2811 2979 8.350722 AGTCATGCAAAACATCAAGATATGATC 58.649 33.333 0.00 0.00 45.91 2.92
2838 3006 5.432680 TTCTCAGAGCCATTTCTTCTGAT 57.567 39.130 4.12 0.00 36.92 2.90
2839 3007 4.897509 TTCTCAGAGCCATTTCTTCTGA 57.102 40.909 3.70 3.70 36.24 3.27
2840 3008 6.512342 AAATTCTCAGAGCCATTTCTTCTG 57.488 37.500 0.00 0.00 0.00 3.02
2851 3033 3.376546 CCTGCCTACAAAATTCTCAGAGC 59.623 47.826 0.00 0.00 0.00 4.09
2934 3585 3.609373 CAGATTAAAACAGCACGGCAATG 59.391 43.478 0.00 0.00 0.00 2.82
2954 3613 3.057969 TGTATCACAAGAAGCACCCAG 57.942 47.619 0.00 0.00 0.00 4.45
3129 3797 5.534654 TCATCCCCTGAAAACAAAGTGTTAG 59.465 40.000 0.00 0.00 40.14 2.34
3131 3799 4.285863 TCATCCCCTGAAAACAAAGTGTT 58.714 39.130 0.00 0.00 43.41 3.32
3400 4068 5.362430 ACATCTACACCCTTTGCAAGAAAAA 59.638 36.000 0.00 0.00 0.00 1.94
3404 4072 3.788227 ACATCTACACCCTTTGCAAGA 57.212 42.857 0.00 0.00 0.00 3.02
3405 4073 5.431765 AGATACATCTACACCCTTTGCAAG 58.568 41.667 0.00 0.00 34.85 4.01
3410 4087 6.013725 TCACACAAGATACATCTACACCCTTT 60.014 38.462 0.00 0.00 35.76 3.11
3446 4123 3.184783 TGTTTGCGTCGAAATTACGTCAT 59.815 39.130 0.00 0.00 42.26 3.06
3610 4287 1.666872 GTGGCGACCGCAGTTTACT 60.667 57.895 16.47 0.00 44.11 2.24
3627 4313 0.532862 CGTGCTCTGGGAAACACTGT 60.533 55.000 0.00 0.00 0.00 3.55
3690 4409 2.555547 GCCCATAAGCCGATGCCAC 61.556 63.158 0.00 0.00 38.69 5.01
3723 4442 1.201661 CGCGGTGCATTTATATCGACG 60.202 52.381 0.00 0.00 0.00 5.12
3770 4489 1.659098 GGATTCTTACGTGTCGCTTGG 59.341 52.381 0.00 0.00 0.00 3.61
3944 4665 7.040755 TGTTCAGAACGACATAAATGGTTGAAT 60.041 33.333 8.80 0.00 0.00 2.57
3956 4677 3.548818 GCAAGCTTTGTTCAGAACGACAT 60.549 43.478 8.80 0.00 0.00 3.06
3959 4680 2.288666 AGCAAGCTTTGTTCAGAACGA 58.711 42.857 8.80 3.82 0.00 3.85
3960 4681 2.763249 AGCAAGCTTTGTTCAGAACG 57.237 45.000 8.80 0.00 0.00 3.95
4057 4779 1.213094 CGCTCACGTTGAGGTCGTTT 61.213 55.000 14.19 0.00 44.43 3.60
4109 4842 2.999648 TGCTCTTCTGAGGCCGCT 61.000 61.111 8.34 0.00 40.53 5.52
4384 5120 8.352942 GTGAAAATGTCCTTGTGATAAAGAACT 58.647 33.333 0.00 0.00 0.00 3.01
4401 5142 7.362056 CCGATTCAAGGTGATAAGTGAAAATGT 60.362 37.037 0.00 0.00 33.93 2.71
4403 5144 6.404734 GCCGATTCAAGGTGATAAGTGAAAAT 60.405 38.462 0.00 0.00 33.93 1.82
4412 5153 4.946772 TGAAAATGCCGATTCAAGGTGATA 59.053 37.500 0.00 0.00 32.89 2.15
4416 5157 3.157087 AGTGAAAATGCCGATTCAAGGT 58.843 40.909 0.00 0.00 37.31 3.50
4417 5158 3.855689 AGTGAAAATGCCGATTCAAGG 57.144 42.857 0.00 0.00 37.31 3.61
4418 5159 6.554419 TGATAAGTGAAAATGCCGATTCAAG 58.446 36.000 0.00 0.00 37.31 3.02
4419 5160 6.507958 TGATAAGTGAAAATGCCGATTCAA 57.492 33.333 0.00 0.00 37.31 2.69
4420 5161 6.238731 GGATGATAAGTGAAAATGCCGATTCA 60.239 38.462 0.00 0.00 33.37 2.57
4421 5162 6.016777 AGGATGATAAGTGAAAATGCCGATTC 60.017 38.462 0.00 0.00 0.00 2.52
4423 5164 5.240183 CAGGATGATAAGTGAAAATGCCGAT 59.760 40.000 0.00 0.00 39.69 4.18
4424 5165 4.576053 CAGGATGATAAGTGAAAATGCCGA 59.424 41.667 0.00 0.00 39.69 5.54
4425 5166 4.576053 TCAGGATGATAAGTGAAAATGCCG 59.424 41.667 0.00 0.00 42.56 5.69
4441 5182 1.863454 CGGCGAAGAAGATTCAGGATG 59.137 52.381 0.00 0.00 37.54 3.51
4444 5185 1.394917 CAACGGCGAAGAAGATTCAGG 59.605 52.381 16.62 0.00 0.00 3.86
4445 5186 2.337583 TCAACGGCGAAGAAGATTCAG 58.662 47.619 16.62 0.00 0.00 3.02
4446 5187 2.029380 TCTCAACGGCGAAGAAGATTCA 60.029 45.455 16.62 0.00 0.00 2.57
4447 5188 2.600867 CTCTCAACGGCGAAGAAGATTC 59.399 50.000 16.62 0.00 0.00 2.52
4449 5190 1.737363 GCTCTCAACGGCGAAGAAGAT 60.737 52.381 16.62 0.00 0.00 2.40
4450 5191 0.388649 GCTCTCAACGGCGAAGAAGA 60.389 55.000 16.62 9.73 0.00 2.87
4452 5193 0.037326 ATGCTCTCAACGGCGAAGAA 60.037 50.000 16.62 0.00 0.00 2.52
4453 5194 0.458543 GATGCTCTCAACGGCGAAGA 60.459 55.000 16.62 12.34 0.00 2.87
4454 5195 1.424493 GGATGCTCTCAACGGCGAAG 61.424 60.000 16.62 8.19 0.00 3.79
4455 5196 1.447838 GGATGCTCTCAACGGCGAA 60.448 57.895 16.62 0.00 0.00 4.70
4456 5197 1.035385 TAGGATGCTCTCAACGGCGA 61.035 55.000 16.62 0.00 0.00 5.54
4457 5198 0.179111 TTAGGATGCTCTCAACGGCG 60.179 55.000 4.80 4.80 0.00 6.46
4458 5199 1.134670 AGTTAGGATGCTCTCAACGGC 60.135 52.381 0.00 0.00 0.00 5.68
4460 5201 3.849911 TGAAGTTAGGATGCTCTCAACG 58.150 45.455 0.00 0.00 0.00 4.10
4461 5202 5.703130 AGTTTGAAGTTAGGATGCTCTCAAC 59.297 40.000 0.00 0.00 0.00 3.18
4462 5203 5.869579 AGTTTGAAGTTAGGATGCTCTCAA 58.130 37.500 0.00 0.00 0.00 3.02
4463 5204 5.489792 AGTTTGAAGTTAGGATGCTCTCA 57.510 39.130 0.00 0.00 0.00 3.27
4464 5205 6.874134 TGTTAGTTTGAAGTTAGGATGCTCTC 59.126 38.462 0.00 0.00 0.00 3.20
4465 5206 6.769512 TGTTAGTTTGAAGTTAGGATGCTCT 58.230 36.000 0.00 0.00 0.00 4.09
4466 5207 7.041372 TGTTGTTAGTTTGAAGTTAGGATGCTC 60.041 37.037 0.00 0.00 0.00 4.26
4467 5208 6.770785 TGTTGTTAGTTTGAAGTTAGGATGCT 59.229 34.615 0.00 0.00 0.00 3.79
4468 5209 6.966021 TGTTGTTAGTTTGAAGTTAGGATGC 58.034 36.000 0.00 0.00 0.00 3.91
4469 5210 9.450807 CTTTGTTGTTAGTTTGAAGTTAGGATG 57.549 33.333 0.00 0.00 0.00 3.51
4470 5211 8.630037 CCTTTGTTGTTAGTTTGAAGTTAGGAT 58.370 33.333 0.00 0.00 0.00 3.24
4471 5212 7.067737 CCCTTTGTTGTTAGTTTGAAGTTAGGA 59.932 37.037 0.00 0.00 0.00 2.94
4472 5213 7.200455 CCCTTTGTTGTTAGTTTGAAGTTAGG 58.800 38.462 0.00 0.00 0.00 2.69
4473 5214 7.067737 TCCCCTTTGTTGTTAGTTTGAAGTTAG 59.932 37.037 0.00 0.00 0.00 2.34
4474 5215 6.890814 TCCCCTTTGTTGTTAGTTTGAAGTTA 59.109 34.615 0.00 0.00 0.00 2.24
4475 5216 5.717654 TCCCCTTTGTTGTTAGTTTGAAGTT 59.282 36.000 0.00 0.00 0.00 2.66
4476 5217 5.265989 TCCCCTTTGTTGTTAGTTTGAAGT 58.734 37.500 0.00 0.00 0.00 3.01
4477 5218 5.845391 TCCCCTTTGTTGTTAGTTTGAAG 57.155 39.130 0.00 0.00 0.00 3.02
4480 5221 6.403049 ACTTTTCCCCTTTGTTGTTAGTTTG 58.597 36.000 0.00 0.00 0.00 2.93
4481 5222 6.439375 AGACTTTTCCCCTTTGTTGTTAGTTT 59.561 34.615 0.00 0.00 0.00 2.66
4482 5223 5.955959 AGACTTTTCCCCTTTGTTGTTAGTT 59.044 36.000 0.00 0.00 0.00 2.24
4483 5224 5.516044 AGACTTTTCCCCTTTGTTGTTAGT 58.484 37.500 0.00 0.00 0.00 2.24
4484 5225 5.592688 TGAGACTTTTCCCCTTTGTTGTTAG 59.407 40.000 0.00 0.00 0.00 2.34
4487 5228 3.699538 GTGAGACTTTTCCCCTTTGTTGT 59.300 43.478 0.00 0.00 0.00 3.32
4488 5229 3.243068 CGTGAGACTTTTCCCCTTTGTTG 60.243 47.826 0.00 0.00 0.00 3.33
4498 5239 1.627550 GCTCGGCCGTGAGACTTTTC 61.628 60.000 30.07 6.42 38.28 2.29
4553 5295 0.763652 ATCTCATCTCCGCCATGCTT 59.236 50.000 0.00 0.00 0.00 3.91
4587 5329 8.353684 TGTTTGAATAATAGCGACTTTTTCCAA 58.646 29.630 0.00 0.00 0.00 3.53
4590 5332 7.750903 AGCTGTTTGAATAATAGCGACTTTTTC 59.249 33.333 0.00 0.00 39.27 2.29
4593 5335 6.743575 AGCTGTTTGAATAATAGCGACTTT 57.256 33.333 0.00 0.00 39.27 2.66
4594 5336 6.258068 GGTAGCTGTTTGAATAATAGCGACTT 59.742 38.462 15.01 0.00 39.12 3.01
4595 5337 5.753921 GGTAGCTGTTTGAATAATAGCGACT 59.246 40.000 15.01 0.00 39.12 4.18
4596 5338 5.050295 GGGTAGCTGTTTGAATAATAGCGAC 60.050 44.000 0.00 9.71 39.27 5.19
4599 5341 4.319549 GCGGGTAGCTGTTTGAATAATAGC 60.320 45.833 0.00 0.00 44.04 2.97
4600 5342 5.344207 GCGGGTAGCTGTTTGAATAATAG 57.656 43.478 0.00 0.00 44.04 1.73
4615 5357 6.317893 ACTGGTAATTTAAAATCTGCGGGTAG 59.682 38.462 0.00 0.00 0.00 3.18
4616 5358 6.181908 ACTGGTAATTTAAAATCTGCGGGTA 58.818 36.000 0.00 0.00 0.00 3.69
4617 5359 5.014202 ACTGGTAATTTAAAATCTGCGGGT 58.986 37.500 0.00 0.00 0.00 5.28
4618 5360 5.576447 ACTGGTAATTTAAAATCTGCGGG 57.424 39.130 0.00 0.00 0.00 6.13
4621 5390 9.556030 GTACAGAACTGGTAATTTAAAATCTGC 57.444 33.333 6.76 0.00 36.19 4.26
4719 5489 2.434336 CCACACTAAGCAGCATACCCTA 59.566 50.000 0.00 0.00 0.00 3.53
4789 5559 1.358445 AGGTAAGGAGGAGGTCGAACT 59.642 52.381 0.34 0.34 0.00 3.01
5355 6126 4.020617 CAGCACGCCAGGGGAAGA 62.021 66.667 11.28 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.