Multiple sequence alignment - TraesCS2D01G173900

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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 TraesCS2D01G173900 chr2D 100.000 4982 0 0 1 4982 117395240 117390259 0.000000e+00 9201.0
1 TraesCS2D01G173900 chr2D 79.061 277 48 8 1 274 480128853 480129122 1.100000e-41 182.0
2 TraesCS2D01G173900 chr2B 90.846 2021 116 30 329 2314 167863092 167861106 0.000000e+00 2643.0
3 TraesCS2D01G173900 chr2B 94.399 982 47 4 2447 3422 256324900 256325879 0.000000e+00 1502.0
4 TraesCS2D01G173900 chr2B 94.141 990 51 3 2446 3429 117072609 117071621 0.000000e+00 1500.0
5 TraesCS2D01G173900 chr2B 83.749 843 91 27 3422 4233 167860840 167860013 0.000000e+00 756.0
6 TraesCS2D01G173900 chr2B 89.235 353 26 10 1 350 167864063 167863720 9.910000e-117 431.0
7 TraesCS2D01G173900 chr2B 83.065 372 49 10 3703 4061 650056370 650056740 4.810000e-85 326.0
8 TraesCS2D01G173900 chr2B 94.595 37 1 1 701 737 27537160 27537125 6.970000e-04 56.5
9 TraesCS2D01G173900 chr2A 90.774 1756 105 22 588 2323 119013597 119011879 0.000000e+00 2292.0
10 TraesCS2D01G173900 chr2A 90.539 909 50 12 3422 4313 119011646 119010757 0.000000e+00 1170.0
11 TraesCS2D01G173900 chr2A 84.720 517 29 13 4504 4982 119010519 119010015 5.840000e-129 472.0
12 TraesCS2D01G173900 chr2A 95.489 133 4 1 2319 2451 119011769 119011639 1.410000e-50 211.0
13 TraesCS2D01G173900 chr2A 93.805 113 5 2 4396 4508 119010754 119010644 8.580000e-38 169.0
14 TraesCS2D01G173900 chr2A 100.000 33 0 0 704 736 102894629 102894661 1.500000e-05 62.1
15 TraesCS2D01G173900 chr2A 92.500 40 0 3 705 744 756943550 756943586 3.000000e-03 54.7
16 TraesCS2D01G173900 chr3D 95.603 978 35 5 2452 3422 583586484 583585508 0.000000e+00 1561.0
17 TraesCS2D01G173900 chr3D 82.424 165 28 1 312 475 143174641 143174477 5.200000e-30 143.0
18 TraesCS2D01G173900 chr5D 95.394 977 39 2 2452 3422 128585708 128586684 0.000000e+00 1550.0
19 TraesCS2D01G173900 chr5D 94.990 978 41 3 2451 3422 488166743 488165768 0.000000e+00 1528.0
20 TraesCS2D01G173900 chr5D 94.595 37 0 2 708 744 460447910 460447944 6.970000e-04 56.5
21 TraesCS2D01G173900 chr7A 94.893 979 42 3 2452 3422 14668339 14667361 0.000000e+00 1524.0
22 TraesCS2D01G173900 chr1A 94.877 976 44 2 2452 3422 482775783 482776757 0.000000e+00 1520.0
23 TraesCS2D01G173900 chr1A 83.110 373 50 8 3703 4062 428307282 428306910 1.340000e-85 327.0
24 TraesCS2D01G173900 chr1A 89.130 46 2 3 699 744 573386331 573386373 3.000000e-03 54.7
25 TraesCS2D01G173900 chr1D 94.672 976 45 3 2451 3421 108827249 108828222 0.000000e+00 1507.0
26 TraesCS2D01G173900 chr1D 75.265 283 58 11 7 283 288935369 288935093 1.880000e-24 124.0
27 TraesCS2D01G173900 chr6A 94.016 986 52 3 2452 3431 77787208 77788192 0.000000e+00 1487.0
28 TraesCS2D01G173900 chr6B 83.914 373 46 10 3703 4062 30988113 30988484 1.330000e-90 344.0
29 TraesCS2D01G173900 chr6B 94.595 37 0 2 708 744 703402209 703402243 6.970000e-04 56.5
30 TraesCS2D01G173900 chr6B 94.595 37 0 2 708 744 703475902 703475936 6.970000e-04 56.5
31 TraesCS2D01G173900 chr1B 83.333 372 50 8 3703 4062 360321540 360321169 2.870000e-87 333.0
32 TraesCS2D01G173900 chr5A 83.019 371 51 8 3703 4061 323092166 323092536 4.810000e-85 326.0
33 TraesCS2D01G173900 chr5A 93.182 44 0 2 701 744 139894292 139894252 1.500000e-05 62.1
34 TraesCS2D01G173900 chr5A 100.000 28 0 0 3705 3732 323084863 323084836 9.000000e-03 52.8
35 TraesCS2D01G173900 chr3B 82.574 373 51 10 3703 4062 590309878 590310249 2.890000e-82 316.0
36 TraesCS2D01G173900 chr5B 81.618 272 44 5 6 274 520045721 520045989 2.330000e-53 220.0
37 TraesCS2D01G173900 chr5B 81.250 272 45 5 6 274 520036055 520036323 1.090000e-51 215.0
38 TraesCS2D01G173900 chr5B 75.887 282 56 11 1 279 433539408 433539136 3.130000e-27 134.0
39 TraesCS2D01G173900 chr4A 82.427 239 34 6 312 543 590203485 590203248 8.460000e-48 202.0
40 TraesCS2D01G173900 chr4A 81.463 205 26 9 88 283 9461023 9461224 1.860000e-34 158.0
41 TraesCS2D01G173900 chr4A 95.000 40 0 2 705 744 556378546 556378509 1.500000e-05 62.1
42 TraesCS2D01G173900 chr4B 81.116 233 36 2 318 543 611008188 611007957 3.960000e-41 180.0
43 TraesCS2D01G173900 chr4B 89.320 103 8 2 3764 3863 307895969 307896071 5.240000e-25 126.0
44 TraesCS2D01G173900 chr4B 89.320 103 8 2 3764 3863 307898760 307898862 5.240000e-25 126.0
45 TraesCS2D01G173900 chr4B 75.362 276 60 6 1 274 546571428 546571159 5.240000e-25 126.0
46 TraesCS2D01G173900 chr6D 80.672 238 39 5 312 543 456277838 456278074 1.430000e-40 178.0
47 TraesCS2D01G173900 chr7D 78.846 260 44 9 21 277 587763815 587763564 1.110000e-36 165.0
48 TraesCS2D01G173900 chr4D 83.152 184 25 4 312 492 25155139 25154959 3.990000e-36 163.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G173900 chr2D 117390259 117395240 4981 True 9201.000000 9201 100.000000 1 4982 1 chr2D.!!$R1 4981
1 TraesCS2D01G173900 chr2B 256324900 256325879 979 False 1502.000000 1502 94.399000 2447 3422 1 chr2B.!!$F1 975
2 TraesCS2D01G173900 chr2B 117071621 117072609 988 True 1500.000000 1500 94.141000 2446 3429 1 chr2B.!!$R2 983
3 TraesCS2D01G173900 chr2B 167860013 167864063 4050 True 1276.666667 2643 87.943333 1 4233 3 chr2B.!!$R3 4232
4 TraesCS2D01G173900 chr2A 119010015 119013597 3582 True 862.800000 2292 91.065400 588 4982 5 chr2A.!!$R1 4394
5 TraesCS2D01G173900 chr3D 583585508 583586484 976 True 1561.000000 1561 95.603000 2452 3422 1 chr3D.!!$R2 970
6 TraesCS2D01G173900 chr5D 128585708 128586684 976 False 1550.000000 1550 95.394000 2452 3422 1 chr5D.!!$F1 970
7 TraesCS2D01G173900 chr5D 488165768 488166743 975 True 1528.000000 1528 94.990000 2451 3422 1 chr5D.!!$R1 971
8 TraesCS2D01G173900 chr7A 14667361 14668339 978 True 1524.000000 1524 94.893000 2452 3422 1 chr7A.!!$R1 970
9 TraesCS2D01G173900 chr1A 482775783 482776757 974 False 1520.000000 1520 94.877000 2452 3422 1 chr1A.!!$F1 970
10 TraesCS2D01G173900 chr1D 108827249 108828222 973 False 1507.000000 1507 94.672000 2451 3421 1 chr1D.!!$F1 970
11 TraesCS2D01G173900 chr6A 77787208 77788192 984 False 1487.000000 1487 94.016000 2452 3431 1 chr6A.!!$F1 979

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
883 1537 0.038159 CGTCAAAGCTCCTCCTTCGT 60.038 55.0 0.0 0.0 0.00 3.85 F
1037 1691 1.080927 TCCCCTCCCTCTAGATCCCC 61.081 65.0 0.0 0.0 0.00 4.81 F
2659 3483 0.102300 GTGTGGGCGAACTGCTTTTT 59.898 50.0 0.0 0.0 45.43 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2500 3324 1.416401 ACAGTGAACAACGATCCAGGT 59.584 47.619 0.00 0.00 0.00 4.00 R
2717 3541 1.640917 TCCACAAGGTAGGAGTGTCC 58.359 55.000 0.00 0.00 34.52 4.02 R
4028 4900 0.029700 GGCAAACACACGGTGGTTAC 59.970 55.000 13.48 9.18 41.92 2.50 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 1.757682 TTTTGCCGAGGAAACAGTGT 58.242 45.000 0.00 0.00 0.00 3.55
32 33 1.227853 GCCGAGGAAACAGTGTGGT 60.228 57.895 0.00 0.00 0.00 4.16
40 41 3.199071 AGGAAACAGTGTGGTCAACTACA 59.801 43.478 0.00 0.00 34.90 2.74
73 74 1.135112 CCGCCTTAGTTTTTGATGGGC 60.135 52.381 0.00 0.00 35.33 5.36
93 95 2.413142 GGGGTGTCGGAGTCCTACG 61.413 68.421 7.77 0.00 38.52 3.51
94 96 1.676967 GGGTGTCGGAGTCCTACGT 60.677 63.158 7.77 0.00 38.28 3.57
130 132 3.997952 GGCAAAGCCCCCTTCCCT 61.998 66.667 0.00 0.00 44.06 4.20
149 151 3.377172 CCCTCAGTTTGTTTCGACTTTGT 59.623 43.478 0.00 0.00 0.00 2.83
150 152 4.342772 CCTCAGTTTGTTTCGACTTTGTG 58.657 43.478 0.00 0.00 0.00 3.33
156 158 4.785511 TTGTTTCGACTTTGTGGGAAAA 57.214 36.364 0.00 0.00 30.96 2.29
183 185 4.415332 GGACTGCTCCGCGAACGA 62.415 66.667 8.23 0.00 43.93 3.85
216 218 1.792757 TTGGATGGCTTGCAGGGTCT 61.793 55.000 0.00 0.00 0.00 3.85
217 219 1.751927 GGATGGCTTGCAGGGTCTG 60.752 63.158 0.00 0.00 34.12 3.51
220 222 2.360475 GGCTTGCAGGGTCTGGAC 60.360 66.667 0.00 0.00 30.08 4.02
231 233 1.372683 GTCTGGACAGCTGCTTCCA 59.627 57.895 21.33 21.33 39.72 3.53
242 244 1.804372 GCTGCTTCCAGACGGATACAG 60.804 57.143 0.00 6.83 42.41 2.74
285 287 1.886861 GATGCCCTTACGCGCATACG 61.887 60.000 5.73 0.00 45.52 3.06
298 300 1.268032 CGCATACGCTCCATCCAAAAC 60.268 52.381 0.00 0.00 35.30 2.43
308 310 4.749476 GCTCCATCCAAAACCCCAAAATTT 60.749 41.667 0.00 0.00 0.00 1.82
309 311 4.979335 TCCATCCAAAACCCCAAAATTTC 58.021 39.130 0.00 0.00 0.00 2.17
310 312 4.413520 TCCATCCAAAACCCCAAAATTTCA 59.586 37.500 0.00 0.00 0.00 2.69
358 1004 9.804758 TTTGATTAAACAAACGGATTACAAACT 57.195 25.926 6.79 0.00 35.29 2.66
365 1011 7.368480 ACAAACGGATTACAAACTGTATACC 57.632 36.000 0.00 0.00 32.20 2.73
385 1031 8.969267 GTATACCTGTGATCATTAAAAGAGACG 58.031 37.037 0.00 0.00 0.00 4.18
390 1036 5.643348 TGTGATCATTAAAAGAGACGTGCAT 59.357 36.000 0.00 0.00 0.00 3.96
416 1062 8.407832 TGGATGACTTGCAATATTACATCAAAG 58.592 33.333 21.09 3.73 35.75 2.77
446 1092 9.956797 CCGTATGAAGCAAAATTAAAATTTCAG 57.043 29.630 1.36 0.15 37.62 3.02
496 1142 1.134401 GTCATCCACCATCACCGTCAT 60.134 52.381 0.00 0.00 0.00 3.06
501 1147 1.066215 CCACCATCACCGTCATCAAGA 60.066 52.381 0.00 0.00 0.00 3.02
512 1158 3.878086 GTCATCAAGACAACGCTGAAA 57.122 42.857 0.00 0.00 46.77 2.69
555 1201 6.428771 GTCATACCTAGATGTAGACTCTGACC 59.571 46.154 0.00 0.00 0.00 4.02
621 1271 3.580895 TCCCAAAATTTCTTAGTTGCCCC 59.419 43.478 0.00 0.00 0.00 5.80
622 1272 3.326297 CCCAAAATTTCTTAGTTGCCCCA 59.674 43.478 0.00 0.00 0.00 4.96
623 1273 4.202409 CCCAAAATTTCTTAGTTGCCCCAA 60.202 41.667 0.00 0.00 0.00 4.12
714 1364 7.412137 TTTGCTTTTCTTACTACGTACTTCC 57.588 36.000 0.00 0.00 0.00 3.46
716 1366 6.385033 TGCTTTTCTTACTACGTACTTCCTC 58.615 40.000 0.00 0.00 0.00 3.71
717 1367 5.804473 GCTTTTCTTACTACGTACTTCCTCC 59.196 44.000 0.00 0.00 0.00 4.30
718 1368 5.551760 TTTCTTACTACGTACTTCCTCCG 57.448 43.478 0.00 0.00 0.00 4.63
719 1369 4.207891 TCTTACTACGTACTTCCTCCGT 57.792 45.455 0.00 0.00 38.53 4.69
720 1370 4.579869 TCTTACTACGTACTTCCTCCGTT 58.420 43.478 0.00 0.00 36.12 4.44
723 1373 3.149196 ACTACGTACTTCCTCCGTTTCA 58.851 45.455 0.00 0.00 36.12 2.69
724 1374 3.569701 ACTACGTACTTCCTCCGTTTCAA 59.430 43.478 0.00 0.00 36.12 2.69
725 1375 3.457610 ACGTACTTCCTCCGTTTCAAA 57.542 42.857 0.00 0.00 0.00 2.69
726 1376 3.999046 ACGTACTTCCTCCGTTTCAAAT 58.001 40.909 0.00 0.00 0.00 2.32
727 1377 4.383173 ACGTACTTCCTCCGTTTCAAATT 58.617 39.130 0.00 0.00 0.00 1.82
728 1378 5.540911 ACGTACTTCCTCCGTTTCAAATTA 58.459 37.500 0.00 0.00 0.00 1.40
729 1379 5.406477 ACGTACTTCCTCCGTTTCAAATTAC 59.594 40.000 0.00 0.00 0.00 1.89
730 1380 5.636543 CGTACTTCCTCCGTTTCAAATTACT 59.363 40.000 0.00 0.00 0.00 2.24
731 1381 6.183360 CGTACTTCCTCCGTTTCAAATTACTC 60.183 42.308 0.00 0.00 0.00 2.59
732 1382 4.689345 ACTTCCTCCGTTTCAAATTACTCG 59.311 41.667 0.00 0.00 0.00 4.18
733 1383 4.261578 TCCTCCGTTTCAAATTACTCGT 57.738 40.909 0.00 0.00 0.00 4.18
734 1384 4.240096 TCCTCCGTTTCAAATTACTCGTC 58.760 43.478 0.00 0.00 0.00 4.20
735 1385 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
736 1386 3.641648 TCCGTTTCAAATTACTCGTCGT 58.358 40.909 0.00 0.00 0.00 4.34
737 1387 3.670055 TCCGTTTCAAATTACTCGTCGTC 59.330 43.478 0.00 0.00 0.00 4.20
738 1388 3.671928 CCGTTTCAAATTACTCGTCGTCT 59.328 43.478 0.00 0.00 0.00 4.18
752 1402 7.143514 ACTCGTCGTCTAGAAAAATAGTCTT 57.856 36.000 0.00 0.00 0.00 3.01
785 1435 3.118542 ACGCGGTAAAGATACGAATTCC 58.881 45.455 12.47 0.00 32.51 3.01
883 1537 0.038159 CGTCAAAGCTCCTCCTTCGT 60.038 55.000 0.00 0.00 0.00 3.85
898 1552 1.239296 TTCGTGACCAGATCGACGGT 61.239 55.000 2.77 2.77 38.56 4.83
981 1635 3.384532 TCGGCGGTTCACCCTACC 61.385 66.667 7.21 0.00 0.00 3.18
990 1644 4.189188 CACCCTACCCGACGCTCG 62.189 72.222 0.00 1.17 40.07 5.03
996 1650 1.367599 CTACCCGACGCTCGTCTCTT 61.368 60.000 18.51 6.37 42.54 2.85
1037 1691 1.080927 TCCCCTCCCTCTAGATCCCC 61.081 65.000 0.00 0.00 0.00 4.81
1132 1786 2.356665 TAGGTGGCAGCTGTTTTGAA 57.643 45.000 28.23 4.10 0.00 2.69
1135 1790 1.953686 GGTGGCAGCTGTTTTGAACTA 59.046 47.619 16.64 0.00 0.00 2.24
1156 1811 7.516198 ACTATTGATATTGAATTCCTGTGGC 57.484 36.000 2.27 0.00 0.00 5.01
1297 1973 2.094762 ACAACATCCGCTTCTGGTAC 57.905 50.000 0.00 0.00 0.00 3.34
1454 2130 5.253330 TGGTAATGAATCTGTTCCTTCACC 58.747 41.667 0.00 0.00 34.43 4.02
1494 2171 4.861196 TGCAATATTGGTTAGTTGGGCTA 58.139 39.130 17.02 0.00 0.00 3.93
1497 2174 6.382570 TGCAATATTGGTTAGTTGGGCTAATT 59.617 34.615 17.02 0.00 41.25 1.40
1502 2179 7.823745 ATTGGTTAGTTGGGCTAATTATCTG 57.176 36.000 0.00 0.00 41.25 2.90
1507 2184 7.556635 GGTTAGTTGGGCTAATTATCTGAAACT 59.443 37.037 0.00 0.00 41.25 2.66
1510 2187 5.835113 TGGGCTAATTATCTGAAACTTGC 57.165 39.130 0.00 0.00 0.00 4.01
1553 2230 1.250328 CCAAGGAGCTGAATGTTGCA 58.750 50.000 0.00 0.00 0.00 4.08
1616 2293 3.181497 CCATTTTCCCGTGTCAGCAATAG 60.181 47.826 0.00 0.00 0.00 1.73
1617 2294 2.851263 TTTCCCGTGTCAGCAATAGT 57.149 45.000 0.00 0.00 0.00 2.12
1656 2333 2.286365 TTGTTTGTAGAGCCTTGGGG 57.714 50.000 0.00 0.00 0.00 4.96
1693 2370 6.443849 AGAAGAGGTACAATTCATCCACCTTA 59.556 38.462 0.00 0.00 39.71 2.69
1694 2371 5.990668 AGAGGTACAATTCATCCACCTTAC 58.009 41.667 0.00 0.00 39.71 2.34
1695 2372 5.726793 AGAGGTACAATTCATCCACCTTACT 59.273 40.000 0.00 0.00 39.71 2.24
1696 2373 6.901300 AGAGGTACAATTCATCCACCTTACTA 59.099 38.462 0.00 0.00 39.71 1.82
1699 2376 6.761714 GGTACAATTCATCCACCTTACTACAG 59.238 42.308 0.00 0.00 0.00 2.74
1706 2383 5.356190 TCATCCACCTTACTACAGTAGTTCG 59.644 44.000 18.56 9.71 40.14 3.95
1721 2398 5.518487 CAGTAGTTCGTTGGTTTTGCATTTT 59.482 36.000 0.00 0.00 0.00 1.82
1724 2401 5.175127 AGTTCGTTGGTTTTGCATTTTCTT 58.825 33.333 0.00 0.00 0.00 2.52
1735 2412 7.228507 GGTTTTGCATTTTCTTCCACCTTATTT 59.771 33.333 0.00 0.00 0.00 1.40
1751 2428 7.065923 CCACCTTATTTTAAGGAGAGCTTGTAC 59.934 40.741 17.93 0.00 39.81 2.90
1768 2445 4.948341 TGTACTTGTCTTGCTCCTGTAA 57.052 40.909 0.00 0.00 0.00 2.41
1776 2453 4.461431 TGTCTTGCTCCTGTAAGATCGTAA 59.539 41.667 0.49 0.00 44.39 3.18
1801 2478 9.582431 AAAAATGATCAAACATCTATTGCAGAG 57.418 29.630 0.00 0.00 36.48 3.35
1820 2497 5.177511 GCAGAGAAAGTGGTTAAATTTTGCC 59.822 40.000 0.00 0.00 0.00 4.52
1824 2501 6.749139 AGAAAGTGGTTAAATTTTGCCTCTC 58.251 36.000 12.55 5.50 0.00 3.20
1831 2508 7.973944 GTGGTTAAATTTTGCCTCTCGAATAAT 59.026 33.333 0.00 0.00 0.00 1.28
1849 2527 8.556194 TCGAATAATTAATGCAATACTGGTGAC 58.444 33.333 0.00 0.00 0.00 3.67
1858 2536 3.877508 GCAATACTGGTGACCATTCCTAC 59.122 47.826 4.03 0.00 30.82 3.18
1879 2557 6.765036 CCTACAATGATAGACAATTGAGCTGT 59.235 38.462 13.59 7.21 0.00 4.40
1891 2569 7.337689 AGACAATTGAGCTGTATTGCAATTCTA 59.662 33.333 18.75 5.98 38.49 2.10
2359 3178 8.827177 TGAGTCACAATCTAAGTCGTTTTAAT 57.173 30.769 0.00 0.00 0.00 1.40
2500 3324 1.697082 TTACCCAACTCGCCCACACA 61.697 55.000 0.00 0.00 0.00 3.72
2511 3335 1.374947 CCCACACACCTGGATCGTT 59.625 57.895 0.00 0.00 32.30 3.85
2530 3354 4.104776 CGTTGTTCACTGTCTTTTGCATT 58.895 39.130 0.00 0.00 0.00 3.56
2659 3483 0.102300 GTGTGGGCGAACTGCTTTTT 59.898 50.000 0.00 0.00 45.43 1.94
2681 3505 1.480212 CCACACAGCCACCACCTAGA 61.480 60.000 0.00 0.00 0.00 2.43
2717 3541 0.040067 GAACTGCTTTTCGCCCACAG 60.040 55.000 0.00 0.00 38.05 3.66
2963 3794 2.241880 GGTTGGACCACACGTGACG 61.242 63.158 25.01 13.69 38.42 4.35
3026 3858 5.312895 TGTGGCAAGTAGTTAATCACACAT 58.687 37.500 0.00 0.00 32.12 3.21
3067 3899 3.615496 ACACGCGACAACTACCATAAATC 59.385 43.478 15.93 0.00 0.00 2.17
3146 3979 2.368875 ACTTGCCATCCCGGATAACTAG 59.631 50.000 0.73 4.46 36.56 2.57
3179 4012 3.063997 CAGGATGGCAACTAAATCGTCAC 59.936 47.826 0.00 0.00 37.61 3.67
3324 4161 2.026729 TGTGGGCAATTCTAATGTCCGA 60.027 45.455 0.00 0.00 45.71 4.55
3355 4192 3.958860 GTGTGGGCTGCCTCCTGT 61.959 66.667 19.68 0.00 0.00 4.00
3422 4259 0.172578 TGGCAGTTATCGTCGTCCTG 59.827 55.000 0.00 0.00 0.00 3.86
3426 4263 3.043586 GCAGTTATCGTCGTCCTGTATG 58.956 50.000 0.00 0.00 0.00 2.39
3511 4362 8.953313 CCTTGGAAAACCGTATTAGTCTAAAAT 58.047 33.333 0.00 0.00 0.00 1.82
3592 4445 9.316730 GCAATTTGATATCTTTTCTAATGCCAA 57.683 29.630 3.98 0.00 0.00 4.52
3598 4451 7.768582 TGATATCTTTTCTAATGCCAACTCGAA 59.231 33.333 3.98 0.00 0.00 3.71
3599 4452 8.682936 ATATCTTTTCTAATGCCAACTCGAAT 57.317 30.769 0.00 0.00 0.00 3.34
3601 4454 7.915293 TCTTTTCTAATGCCAACTCGAATTA 57.085 32.000 0.00 0.00 0.00 1.40
3604 4460 8.780846 TTTTCTAATGCCAACTCGAATTAGTA 57.219 30.769 10.54 1.54 35.21 1.82
3612 4468 6.479990 TGCCAACTCGAATTAGTATGAATGAG 59.520 38.462 0.00 0.00 0.00 2.90
3656 4518 4.102524 TCCACCATGTTCTAACAGACTGTT 59.897 41.667 23.61 23.61 43.04 3.16
3658 4520 4.452455 CACCATGTTCTAACAGACTGTTCC 59.548 45.833 23.79 11.21 43.04 3.62
3662 4524 6.263168 CCATGTTCTAACAGACTGTTCCTTTT 59.737 38.462 23.79 2.18 43.04 2.27
3663 4525 6.677781 TGTTCTAACAGACTGTTCCTTTTG 57.322 37.500 23.79 8.97 40.22 2.44
3664 4526 6.411376 TGTTCTAACAGACTGTTCCTTTTGA 58.589 36.000 23.79 10.86 40.22 2.69
3813 4675 4.834496 TCAAGAGGCAGATCAAAATGGTTT 59.166 37.500 0.00 0.00 0.00 3.27
3816 4678 2.901839 AGGCAGATCAAAATGGTTTGCT 59.098 40.909 6.16 0.00 43.30 3.91
3817 4679 2.997986 GGCAGATCAAAATGGTTTGCTG 59.002 45.455 6.16 0.00 43.30 4.41
3818 4680 3.555586 GGCAGATCAAAATGGTTTGCTGT 60.556 43.478 6.16 0.00 43.30 4.40
3819 4681 4.060205 GCAGATCAAAATGGTTTGCTGTT 58.940 39.130 0.00 0.00 43.30 3.16
3822 4684 6.202570 GCAGATCAAAATGGTTTGCTGTTTTA 59.797 34.615 0.00 0.00 43.30 1.52
3864 4735 6.742109 TGGAAGAGCTTCATTTTTCTGAAAG 58.258 36.000 11.90 0.00 41.20 2.62
3895 4766 4.533919 CTGGAGAATCAAGTGACTGAGT 57.466 45.455 0.00 0.00 36.25 3.41
3898 4769 5.059161 TGGAGAATCAAGTGACTGAGTTTG 58.941 41.667 0.00 0.00 36.25 2.93
4009 4881 1.807165 GCATCTGCGAGCGTCTGAA 60.807 57.895 0.00 0.00 0.00 3.02
4028 4900 4.923893 TGAATCTTTGTGCAGTTGTTCAG 58.076 39.130 0.00 0.00 0.00 3.02
4038 4910 2.557317 CAGTTGTTCAGTAACCACCGT 58.443 47.619 0.00 0.00 32.90 4.83
4062 4934 5.767665 TGTGTTTGCCTGATGTATTTACTGT 59.232 36.000 0.00 0.00 0.00 3.55
4078 4950 2.040178 ACTGTTCTGTTTCCTCCGAGT 58.960 47.619 0.00 0.00 0.00 4.18
4248 5128 1.808945 CTGACATTTCGCTGCCTCTTT 59.191 47.619 0.00 0.00 0.00 2.52
4251 5131 2.421424 GACATTTCGCTGCCTCTTTGAT 59.579 45.455 0.00 0.00 0.00 2.57
4254 5134 1.159285 TTCGCTGCCTCTTTGATGTG 58.841 50.000 0.00 0.00 0.00 3.21
4267 5147 0.035317 TGATGTGGGCAGTGTGAGTC 59.965 55.000 0.00 0.00 0.00 3.36
4297 5177 0.480690 ATGGGTGGTTTGGCACTACA 59.519 50.000 0.00 0.00 38.64 2.74
4320 5200 2.732094 GTGCTCGCACGTAACGGT 60.732 61.111 6.25 0.00 37.19 4.83
4321 5201 1.442520 GTGCTCGCACGTAACGGTA 60.443 57.895 6.25 0.00 37.19 4.02
4322 5202 1.154169 TGCTCGCACGTAACGGTAG 60.154 57.895 9.90 3.10 0.00 3.18
4323 5203 1.135315 GCTCGCACGTAACGGTAGA 59.865 57.895 9.90 0.00 0.00 2.59
4324 5204 1.130458 GCTCGCACGTAACGGTAGAC 61.130 60.000 9.90 0.00 0.00 2.59
4325 5205 0.522076 CTCGCACGTAACGGTAGACC 60.522 60.000 9.90 0.00 0.00 3.85
4326 5206 1.209898 CGCACGTAACGGTAGACCA 59.790 57.895 0.00 0.00 35.14 4.02
4327 5207 0.179156 CGCACGTAACGGTAGACCAT 60.179 55.000 0.00 0.00 35.14 3.55
4328 5208 1.063912 CGCACGTAACGGTAGACCATA 59.936 52.381 0.00 0.00 35.14 2.74
4329 5209 2.724349 GCACGTAACGGTAGACCATAG 58.276 52.381 0.00 0.00 35.14 2.23
4330 5210 2.098117 GCACGTAACGGTAGACCATAGT 59.902 50.000 0.00 0.00 35.14 2.12
4331 5211 3.428045 GCACGTAACGGTAGACCATAGTT 60.428 47.826 0.00 0.00 35.14 2.24
4332 5212 4.737054 CACGTAACGGTAGACCATAGTTT 58.263 43.478 0.00 0.00 35.14 2.66
4333 5213 4.560035 CACGTAACGGTAGACCATAGTTTG 59.440 45.833 0.00 0.00 35.14 2.93
4334 5214 4.218417 ACGTAACGGTAGACCATAGTTTGT 59.782 41.667 0.00 0.00 35.14 2.83
4335 5215 5.414454 ACGTAACGGTAGACCATAGTTTGTA 59.586 40.000 0.00 0.00 35.14 2.41
4336 5216 5.739161 CGTAACGGTAGACCATAGTTTGTAC 59.261 44.000 0.00 0.00 35.14 2.90
4337 5217 5.990120 AACGGTAGACCATAGTTTGTACT 57.010 39.130 0.00 0.00 35.52 2.73
4338 5218 5.573337 ACGGTAGACCATAGTTTGTACTC 57.427 43.478 0.00 0.00 33.97 2.59
4339 5219 5.259632 ACGGTAGACCATAGTTTGTACTCT 58.740 41.667 0.00 0.00 33.97 3.24
4340 5220 5.713861 ACGGTAGACCATAGTTTGTACTCTT 59.286 40.000 0.00 0.00 33.97 2.85
4341 5221 6.210185 ACGGTAGACCATAGTTTGTACTCTTT 59.790 38.462 0.00 0.00 33.97 2.52
4342 5222 7.095270 CGGTAGACCATAGTTTGTACTCTTTT 58.905 38.462 0.00 0.00 33.97 2.27
4343 5223 7.275123 CGGTAGACCATAGTTTGTACTCTTTTC 59.725 40.741 0.00 0.00 33.97 2.29
4344 5224 8.312564 GGTAGACCATAGTTTGTACTCTTTTCT 58.687 37.037 0.00 0.00 34.28 2.52
4345 5225 9.708092 GTAGACCATAGTTTGTACTCTTTTCTT 57.292 33.333 0.00 0.00 35.78 2.52
4358 5238 9.996554 TGTACTCTTTTCTTATTTGATGAGTGA 57.003 29.630 0.00 0.00 35.52 3.41
4360 5240 8.908786 ACTCTTTTCTTATTTGATGAGTGACA 57.091 30.769 0.00 0.00 33.09 3.58
4361 5241 8.778358 ACTCTTTTCTTATTTGATGAGTGACAC 58.222 33.333 0.00 0.00 33.09 3.67
4362 5242 8.675705 TCTTTTCTTATTTGATGAGTGACACA 57.324 30.769 8.59 0.00 0.00 3.72
4363 5243 8.777413 TCTTTTCTTATTTGATGAGTGACACAG 58.223 33.333 8.59 0.00 0.00 3.66
4364 5244 7.439157 TTTCTTATTTGATGAGTGACACAGG 57.561 36.000 8.59 0.00 0.00 4.00
4365 5245 6.358974 TCTTATTTGATGAGTGACACAGGA 57.641 37.500 8.59 0.00 0.00 3.86
4366 5246 6.401394 TCTTATTTGATGAGTGACACAGGAG 58.599 40.000 8.59 0.00 0.00 3.69
4367 5247 4.897509 ATTTGATGAGTGACACAGGAGA 57.102 40.909 8.59 0.00 0.00 3.71
4368 5248 4.687901 TTTGATGAGTGACACAGGAGAA 57.312 40.909 8.59 0.00 0.00 2.87
4369 5249 3.949842 TGATGAGTGACACAGGAGAAG 57.050 47.619 8.59 0.00 0.00 2.85
4370 5250 3.234353 TGATGAGTGACACAGGAGAAGT 58.766 45.455 8.59 0.00 0.00 3.01
4371 5251 3.006217 TGATGAGTGACACAGGAGAAGTG 59.994 47.826 8.59 0.00 42.56 3.16
4379 5259 3.951979 CACAGGAGAAGTGTTGTGTTC 57.048 47.619 0.00 0.00 36.92 3.18
4380 5260 3.270027 CACAGGAGAAGTGTTGTGTTCA 58.730 45.455 0.00 0.00 36.92 3.18
4381 5261 3.879295 CACAGGAGAAGTGTTGTGTTCAT 59.121 43.478 0.00 0.00 36.92 2.57
4382 5262 4.336433 CACAGGAGAAGTGTTGTGTTCATT 59.664 41.667 0.00 0.00 36.92 2.57
4383 5263 4.336433 ACAGGAGAAGTGTTGTGTTCATTG 59.664 41.667 0.00 0.00 0.00 2.82
4384 5264 3.316308 AGGAGAAGTGTTGTGTTCATTGC 59.684 43.478 0.00 0.00 0.00 3.56
4385 5265 3.316308 GGAGAAGTGTTGTGTTCATTGCT 59.684 43.478 0.00 0.00 0.00 3.91
4386 5266 4.531332 GAGAAGTGTTGTGTTCATTGCTC 58.469 43.478 0.00 0.00 0.00 4.26
4387 5267 3.947196 AGAAGTGTTGTGTTCATTGCTCA 59.053 39.130 0.00 0.00 0.00 4.26
4388 5268 4.398988 AGAAGTGTTGTGTTCATTGCTCAA 59.601 37.500 0.00 0.00 0.00 3.02
4389 5269 4.924305 AGTGTTGTGTTCATTGCTCAAT 57.076 36.364 0.00 0.00 0.00 2.57
4390 5270 6.262944 AGAAGTGTTGTGTTCATTGCTCAATA 59.737 34.615 0.00 0.00 0.00 1.90
4391 5271 6.005583 AGTGTTGTGTTCATTGCTCAATAG 57.994 37.500 0.00 0.00 0.00 1.73
4392 5272 5.764686 AGTGTTGTGTTCATTGCTCAATAGA 59.235 36.000 0.00 0.00 0.00 1.98
4393 5273 6.262944 AGTGTTGTGTTCATTGCTCAATAGAA 59.737 34.615 0.00 0.48 0.00 2.10
4394 5274 6.917477 GTGTTGTGTTCATTGCTCAATAGAAA 59.083 34.615 0.00 0.00 0.00 2.52
4409 5289 7.923344 GCTCAATAGAAATAGTACAAGAGAGCA 59.077 37.037 0.00 0.00 41.19 4.26
4433 5313 2.808543 GCTCGGTTTATCAATAGCCCTG 59.191 50.000 0.00 0.00 0.00 4.45
4446 5326 4.404691 CCCTGAGGCACCAAGAAC 57.595 61.111 0.00 0.00 0.00 3.01
4476 5356 1.269723 GGTGGCTGGCTAGAAACAAAC 59.730 52.381 0.00 0.00 0.00 2.93
4480 5360 4.072131 TGGCTGGCTAGAAACAAACTTAG 58.928 43.478 0.00 0.00 0.00 2.18
4502 5382 3.402628 ACTGGCGAGAAGAAGCTTAAA 57.597 42.857 1.44 0.00 0.00 1.52
4534 5542 1.419012 TGATGATCCATGTGAGGAGGC 59.581 52.381 0.00 0.00 41.90 4.70
4605 5614 0.541392 CTGTACACATAGCCTGGGCA 59.459 55.000 14.39 0.56 44.88 5.36
4606 5615 0.988063 TGTACACATAGCCTGGGCAA 59.012 50.000 14.39 0.00 44.88 4.52
4607 5616 1.339631 TGTACACATAGCCTGGGCAAC 60.340 52.381 14.39 1.49 44.88 4.17
4624 5633 2.773487 CAACCCCGGCGAATGATATTA 58.227 47.619 9.30 0.00 0.00 0.98
4666 5675 2.097825 GCTTCATGCCTGATGGAAAGT 58.902 47.619 6.94 0.00 35.15 2.66
4667 5676 2.494870 GCTTCATGCCTGATGGAAAGTT 59.505 45.455 6.94 0.00 35.15 2.66
4669 5678 4.562143 GCTTCATGCCTGATGGAAAGTTTT 60.562 41.667 6.94 0.00 35.15 2.43
4670 5679 5.336690 GCTTCATGCCTGATGGAAAGTTTTA 60.337 40.000 6.94 0.00 35.15 1.52
4671 5680 6.628844 GCTTCATGCCTGATGGAAAGTTTTAT 60.629 38.462 6.94 0.00 35.15 1.40
4672 5681 6.455360 TCATGCCTGATGGAAAGTTTTATC 57.545 37.500 6.78 6.78 34.57 1.75
4673 5682 5.951148 TCATGCCTGATGGAAAGTTTTATCA 59.049 36.000 12.90 12.90 34.57 2.15
4674 5683 6.608405 TCATGCCTGATGGAAAGTTTTATCAT 59.392 34.615 13.57 7.85 34.57 2.45
4675 5684 6.455360 TGCCTGATGGAAAGTTTTATCATC 57.545 37.500 13.57 14.31 34.41 2.92
4676 5685 5.951148 TGCCTGATGGAAAGTTTTATCATCA 59.049 36.000 19.59 19.59 37.96 3.07
4682 5691 9.117183 TGATGGAAAGTTTTATCATCAGAGATG 57.883 33.333 18.12 0.62 36.70 2.90
4683 5692 9.334947 GATGGAAAGTTTTATCATCAGAGATGA 57.665 33.333 11.65 11.65 34.19 2.92
4684 5693 8.728337 TGGAAAGTTTTATCATCAGAGATGAG 57.272 34.615 14.23 0.00 0.00 2.90
4762 5777 4.177026 CTGCAATCTTTACTAGCTGACGT 58.823 43.478 0.00 0.00 0.00 4.34
4788 5803 0.389037 TTGTTGTGCTGCGTTGCAAA 60.389 45.000 0.00 0.00 45.12 3.68
4825 5843 0.324614 ATGACACGCATCACCTTGGA 59.675 50.000 0.00 0.00 28.85 3.53
4828 5846 0.951558 ACACGCATCACCTTGGAAAC 59.048 50.000 0.00 0.00 0.00 2.78
4916 5961 4.608948 TTGTGGGTTTGAACTTTGTTGT 57.391 36.364 0.00 0.00 0.00 3.32
4977 6022 6.564328 AGTAAGTTTAATAAGGTACGGTCCG 58.436 40.000 10.48 10.48 0.00 4.79
4978 6023 3.785486 AGTTTAATAAGGTACGGTCCGC 58.215 45.455 12.28 0.00 0.00 5.54
4979 6024 3.195396 AGTTTAATAAGGTACGGTCCGCA 59.805 43.478 12.28 0.00 0.00 5.69
4980 6025 3.883830 TTAATAAGGTACGGTCCGCAA 57.116 42.857 12.28 0.00 0.00 4.85
4981 6026 2.304751 AATAAGGTACGGTCCGCAAG 57.695 50.000 12.28 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.530744 GTTTCCTCGGCAAAATCCCC 59.469 55.000 0.00 0.00 0.00 4.81
9 10 2.034558 CACACTGTTTCCTCGGCAAAAT 59.965 45.455 0.00 0.00 0.00 1.82
13 14 1.227823 CCACACTGTTTCCTCGGCA 60.228 57.895 0.00 0.00 0.00 5.69
15 16 0.105964 TGACCACACTGTTTCCTCGG 59.894 55.000 0.00 0.00 0.00 4.63
18 19 3.199071 TGTAGTTGACCACACTGTTTCCT 59.801 43.478 0.00 0.00 0.00 3.36
29 30 1.944024 CCGCACTTTTGTAGTTGACCA 59.056 47.619 0.00 0.00 33.85 4.02
32 33 0.948678 GCCCGCACTTTTGTAGTTGA 59.051 50.000 0.00 0.00 33.85 3.18
59 60 0.323908 CCCCGGCCCATCAAAAACTA 60.324 55.000 0.00 0.00 0.00 2.24
83 85 2.799371 CGAGCCACGTAGGACTCC 59.201 66.667 8.04 0.00 41.22 3.85
93 95 3.628280 GAGTCCGGACACGAGCCAC 62.628 68.421 35.00 6.70 44.60 5.01
94 96 3.371063 GAGTCCGGACACGAGCCA 61.371 66.667 35.00 0.00 44.60 4.75
120 122 0.482887 AACAAACTGAGGGAAGGGGG 59.517 55.000 0.00 0.00 0.00 5.40
130 132 3.127895 CCCACAAAGTCGAAACAAACTGA 59.872 43.478 0.00 0.00 0.00 3.41
149 151 2.578940 AGTCCGGACCATAATTTTCCCA 59.421 45.455 30.82 0.00 0.00 4.37
150 152 2.949644 CAGTCCGGACCATAATTTTCCC 59.050 50.000 30.82 0.86 0.00 3.97
156 158 0.759346 GGAGCAGTCCGGACCATAAT 59.241 55.000 30.82 12.81 31.37 1.28
181 183 1.095228 CCAACATCGACCCCCATTCG 61.095 60.000 0.00 0.00 37.85 3.34
183 185 0.926293 ATCCAACATCGACCCCCATT 59.074 50.000 0.00 0.00 0.00 3.16
216 218 1.372683 GTCTGGAAGCAGCTGTCCA 59.627 57.895 21.33 21.33 41.72 4.02
217 219 1.739562 CGTCTGGAAGCAGCTGTCC 60.740 63.158 16.64 15.68 0.00 4.02
220 222 2.659016 TCCGTCTGGAAGCAGCTG 59.341 61.111 10.11 10.11 42.85 4.24
231 233 2.163815 CTCAAACCGTCTGTATCCGTCT 59.836 50.000 0.00 0.00 0.00 4.18
242 244 2.741211 GCCGACCCTCAAACCGTC 60.741 66.667 0.00 0.00 0.00 4.79
285 287 1.347062 TTTGGGGTTTTGGATGGAGC 58.653 50.000 0.00 0.00 0.00 4.70
345 991 6.071221 TCACAGGTATACAGTTTGTAATCCGT 60.071 38.462 5.01 1.10 36.31 4.69
358 1004 9.817809 GTCTCTTTTAATGATCACAGGTATACA 57.182 33.333 5.01 0.00 0.00 2.29
365 1011 5.120674 TGCACGTCTCTTTTAATGATCACAG 59.879 40.000 0.00 0.00 0.00 3.66
377 1023 2.027745 AGTCATCCATGCACGTCTCTTT 60.028 45.455 0.00 0.00 0.00 2.52
390 1036 7.878547 TTGATGTAATATTGCAAGTCATCCA 57.121 32.000 10.40 11.93 32.17 3.41
408 1054 3.684788 GCTTCATACGGTGTCTTTGATGT 59.315 43.478 0.00 0.00 0.00 3.06
416 1062 7.861176 TTTTAATTTTGCTTCATACGGTGTC 57.139 32.000 0.00 0.00 0.00 3.67
512 1158 3.881220 TGACGACAGGTTTCCTTCTTTT 58.119 40.909 0.00 0.00 0.00 2.27
523 1169 3.899726 ACATCTAGGTATGACGACAGGT 58.100 45.455 0.00 0.00 0.00 4.00
524 1170 5.179742 GTCTACATCTAGGTATGACGACAGG 59.820 48.000 0.00 0.00 33.70 4.00
555 1201 0.684805 AGAGCGTTCCCCTACAGAGG 60.685 60.000 0.00 0.00 43.33 3.69
575 1221 8.043710 GGATTTTGGATGAAGAAGAGACTAGAA 58.956 37.037 0.00 0.00 0.00 2.10
621 1271 3.057736 CCTGATGCAGACTCCTTTTGTTG 60.058 47.826 0.00 0.00 32.44 3.33
622 1272 3.152341 CCTGATGCAGACTCCTTTTGTT 58.848 45.455 0.00 0.00 32.44 2.83
623 1273 2.787994 CCTGATGCAGACTCCTTTTGT 58.212 47.619 0.00 0.00 32.44 2.83
710 1360 4.689345 ACGAGTAATTTGAAACGGAGGAAG 59.311 41.667 0.00 0.00 0.00 3.46
712 1362 4.240096 GACGAGTAATTTGAAACGGAGGA 58.760 43.478 0.00 0.00 0.00 3.71
713 1363 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
714 1364 3.671928 ACGACGAGTAATTTGAAACGGAG 59.328 43.478 0.00 0.00 0.00 4.63
716 1366 3.671928 AGACGACGAGTAATTTGAAACGG 59.328 43.478 0.00 0.00 0.00 4.44
717 1367 4.880760 AGACGACGAGTAATTTGAAACG 57.119 40.909 0.00 0.00 0.00 3.60
718 1368 7.558435 TTCTAGACGACGAGTAATTTGAAAC 57.442 36.000 0.00 0.00 0.00 2.78
719 1369 8.578308 TTTTCTAGACGACGAGTAATTTGAAA 57.422 30.769 0.00 0.00 0.00 2.69
720 1370 8.578308 TTTTTCTAGACGACGAGTAATTTGAA 57.422 30.769 0.00 0.00 0.00 2.69
723 1373 9.852091 ACTATTTTTCTAGACGACGAGTAATTT 57.148 29.630 0.00 0.00 0.00 1.82
724 1374 9.500864 GACTATTTTTCTAGACGACGAGTAATT 57.499 33.333 0.00 0.00 0.00 1.40
725 1375 8.891720 AGACTATTTTTCTAGACGACGAGTAAT 58.108 33.333 0.00 0.00 0.00 1.89
726 1376 8.261492 AGACTATTTTTCTAGACGACGAGTAA 57.739 34.615 0.00 0.00 0.00 2.24
727 1377 7.840342 AGACTATTTTTCTAGACGACGAGTA 57.160 36.000 0.00 0.00 0.00 2.59
728 1378 6.740411 AGACTATTTTTCTAGACGACGAGT 57.260 37.500 0.00 0.00 0.00 4.18
729 1379 6.469595 CCAAGACTATTTTTCTAGACGACGAG 59.530 42.308 0.00 0.00 0.00 4.18
730 1380 6.149973 TCCAAGACTATTTTTCTAGACGACGA 59.850 38.462 0.00 0.00 0.00 4.20
731 1381 6.250951 GTCCAAGACTATTTTTCTAGACGACG 59.749 42.308 0.00 0.00 0.00 5.12
732 1382 7.062022 GTGTCCAAGACTATTTTTCTAGACGAC 59.938 40.741 0.00 0.00 32.73 4.34
733 1383 7.088905 GTGTCCAAGACTATTTTTCTAGACGA 58.911 38.462 0.00 0.00 32.73 4.20
734 1384 6.033619 CGTGTCCAAGACTATTTTTCTAGACG 59.966 42.308 0.00 0.00 32.73 4.18
735 1385 6.867293 ACGTGTCCAAGACTATTTTTCTAGAC 59.133 38.462 0.00 0.00 33.15 2.59
736 1386 6.989659 ACGTGTCCAAGACTATTTTTCTAGA 58.010 36.000 0.00 0.00 33.15 2.43
737 1387 6.866770 TGACGTGTCCAAGACTATTTTTCTAG 59.133 38.462 0.00 0.00 33.15 2.43
738 1388 6.751157 TGACGTGTCCAAGACTATTTTTCTA 58.249 36.000 0.00 0.00 33.15 2.10
785 1435 4.873129 CGCGTCCGGTGGGAGATG 62.873 72.222 0.00 0.00 44.97 2.90
971 1625 2.283388 AGCGTCGGGTAGGGTGAA 60.283 61.111 0.00 0.00 0.00 3.18
990 1644 0.035630 AGCTCACCATGGCAAGAGAC 60.036 55.000 25.39 18.16 0.00 3.36
996 1650 1.001764 CAAGGAGCTCACCATGGCA 60.002 57.895 17.19 0.00 0.00 4.92
1037 1691 0.602905 ACGGTTCGCAAGGAAGAAGG 60.603 55.000 0.00 0.00 34.69 3.46
1109 1763 0.251297 AAACAGCTGCCACCTATGCA 60.251 50.000 15.27 0.00 37.17 3.96
1132 1786 7.062322 TGCCACAGGAATTCAATATCAATAGT 58.938 34.615 7.93 0.00 0.00 2.12
1135 1790 6.795144 TTGCCACAGGAATTCAATATCAAT 57.205 33.333 7.93 0.00 0.00 2.57
1156 1811 7.633621 TCTTCAAAGATCGCTGCTTTATATTG 58.366 34.615 0.00 0.00 34.05 1.90
1281 1936 0.108804 CACGTACCAGAAGCGGATGT 60.109 55.000 0.00 0.00 0.00 3.06
1297 1973 5.158494 TGTAGACTACAATACAAGCACACG 58.842 41.667 12.99 0.00 35.38 4.49
1454 2130 0.884704 CATCGGGAATAACCAGGCCG 60.885 60.000 0.00 0.00 41.20 6.13
1494 2171 5.824904 ATGCGAGCAAGTTTCAGATAATT 57.175 34.783 0.57 0.00 0.00 1.40
1497 2174 3.181507 GCAATGCGAGCAAGTTTCAGATA 60.182 43.478 0.57 0.00 0.00 1.98
1502 2179 1.334054 CTGCAATGCGAGCAAGTTTC 58.666 50.000 0.57 0.00 42.17 2.78
1507 2184 1.580942 GTTCCTGCAATGCGAGCAA 59.419 52.632 0.57 0.00 42.17 3.91
1510 2187 0.379669 GATGGTTCCTGCAATGCGAG 59.620 55.000 0.00 0.00 0.00 5.03
1591 2268 0.240945 CTGACACGGGAAAATGGTGC 59.759 55.000 0.00 0.00 35.11 5.01
1616 2293 3.401033 AAGCAACAATTTTAGGGCCAC 57.599 42.857 6.18 0.00 0.00 5.01
1617 2294 4.133078 CAAAAGCAACAATTTTAGGGCCA 58.867 39.130 6.18 0.00 0.00 5.36
1656 2333 5.784177 TGTACCTCTTCTGTCATCTCAAAC 58.216 41.667 0.00 0.00 0.00 2.93
1693 2370 4.271776 GCAAAACCAACGAACTACTGTAGT 59.728 41.667 14.53 14.53 41.73 2.73
1694 2371 4.271533 TGCAAAACCAACGAACTACTGTAG 59.728 41.667 13.13 13.13 0.00 2.74
1695 2372 4.190001 TGCAAAACCAACGAACTACTGTA 58.810 39.130 0.00 0.00 0.00 2.74
1696 2373 3.011119 TGCAAAACCAACGAACTACTGT 58.989 40.909 0.00 0.00 0.00 3.55
1699 2376 5.746721 AGAAAATGCAAAACCAACGAACTAC 59.253 36.000 0.00 0.00 0.00 2.73
1706 2383 4.035091 GGTGGAAGAAAATGCAAAACCAAC 59.965 41.667 0.00 0.00 0.00 3.77
1721 2398 6.215636 AGCTCTCCTTAAAATAAGGTGGAAGA 59.784 38.462 14.18 9.50 38.55 2.87
1724 2401 6.180472 CAAGCTCTCCTTAAAATAAGGTGGA 58.820 40.000 14.18 12.41 38.55 4.02
1735 2412 6.223852 CAAGACAAGTACAAGCTCTCCTTAA 58.776 40.000 0.00 0.00 31.00 1.85
1751 2428 3.862267 CGATCTTACAGGAGCAAGACAAG 59.138 47.826 0.00 0.00 33.78 3.16
1776 2453 8.963725 TCTCTGCAATAGATGTTTGATCATTTT 58.036 29.630 0.00 0.00 34.21 1.82
1801 2478 5.629435 CGAGAGGCAAAATTTAACCACTTTC 59.371 40.000 10.99 1.75 0.00 2.62
1820 2497 8.993121 ACCAGTATTGCATTAATTATTCGAGAG 58.007 33.333 0.00 0.00 0.00 3.20
1824 2501 7.803189 GGTCACCAGTATTGCATTAATTATTCG 59.197 37.037 0.00 0.00 0.00 3.34
1831 2508 5.359576 GGAATGGTCACCAGTATTGCATTAA 59.640 40.000 1.19 0.00 36.75 1.40
1849 2527 8.681486 TCAATTGTCTATCATTGTAGGAATGG 57.319 34.615 5.13 0.00 0.00 3.16
1858 2536 7.590322 GCAATACAGCTCAATTGTCTATCATTG 59.410 37.037 15.53 10.59 35.86 2.82
1891 2569 7.716998 TGTTTGGGCAACACACATTATTTATTT 59.283 29.630 0.00 0.00 40.71 1.40
1899 2577 2.170187 ACATGTTTGGGCAACACACATT 59.830 40.909 9.01 1.44 45.61 2.71
2241 2927 7.120285 AGTGAACCAGACTCATATTCAACAATG 59.880 37.037 0.00 0.00 31.45 2.82
2500 3324 1.416401 ACAGTGAACAACGATCCAGGT 59.584 47.619 0.00 0.00 0.00 4.00
2511 3335 7.275888 AGATTAATGCAAAAGACAGTGAACA 57.724 32.000 0.00 0.00 0.00 3.18
2530 3354 4.963373 TCCACCTTTTCGTGTCAAGATTA 58.037 39.130 0.00 0.00 31.47 1.75
2659 3483 4.892965 GTGGTGGCTGTGTGGGCA 62.893 66.667 0.00 0.00 39.45 5.36
2717 3541 1.640917 TCCACAAGGTAGGAGTGTCC 58.359 55.000 0.00 0.00 34.52 4.02
2883 3714 2.443260 ATCTGGTTGCCACGTACGCA 62.443 55.000 16.72 1.93 0.00 5.24
2963 3794 3.670625 TGCCATGTGTGTTTACCTAGTC 58.329 45.455 0.00 0.00 0.00 2.59
3026 3858 4.155099 CGTGTAATCAAACCATAGTTGCCA 59.845 41.667 0.00 0.00 35.97 4.92
3067 3899 6.112734 TGGTTAACTATAGTTGCCATGTCTG 58.887 40.000 26.44 0.00 38.50 3.51
3146 3979 3.106738 CCATCCTGGTTGGCAGATC 57.893 57.895 10.74 0.00 35.26 2.75
3511 4362 6.374613 CAGTACTACTGTCACAATCTAGACCA 59.625 42.308 7.93 0.00 41.19 4.02
3592 4445 7.772166 TGTGTCTCATTCATACTAATTCGAGT 58.228 34.615 0.00 0.00 0.00 4.18
3593 4446 8.809159 ATGTGTCTCATTCATACTAATTCGAG 57.191 34.615 0.00 0.00 32.08 4.04
3595 4448 9.684448 AGTATGTGTCTCATTCATACTAATTCG 57.316 33.333 13.13 0.00 46.62 3.34
3612 4468 9.257651 GGTGGAGTTATAACATAAGTATGTGTC 57.742 37.037 17.65 2.06 45.55 3.67
3632 4488 4.248859 CAGTCTGTTAGAACATGGTGGAG 58.751 47.826 0.00 0.00 38.41 3.86
3635 4491 4.452455 GGAACAGTCTGTTAGAACATGGTG 59.548 45.833 18.17 0.00 41.28 4.17
3760 4622 4.840680 TCTTGGATCTCTTGGAGAGTGAAA 59.159 41.667 4.99 0.00 42.26 2.69
3813 4675 5.308014 TCAGCAAAGAGAGATAAAACAGCA 58.692 37.500 0.00 0.00 0.00 4.41
3816 4678 7.120285 CCATTCTCAGCAAAGAGAGATAAAACA 59.880 37.037 4.16 0.00 44.78 2.83
3817 4679 7.335422 TCCATTCTCAGCAAAGAGAGATAAAAC 59.665 37.037 4.16 0.00 44.78 2.43
3818 4680 7.397221 TCCATTCTCAGCAAAGAGAGATAAAA 58.603 34.615 4.16 0.00 44.78 1.52
3819 4681 6.950842 TCCATTCTCAGCAAAGAGAGATAAA 58.049 36.000 4.16 0.00 44.78 1.40
3822 4684 5.189342 TCTTCCATTCTCAGCAAAGAGAGAT 59.811 40.000 4.16 0.56 44.78 2.75
3864 4735 7.492994 GTCACTTGATTCTCCAGTAGGATAAAC 59.507 40.741 0.00 0.00 44.70 2.01
3895 4766 2.807967 CTGCGACAGGACAGAAATCAAA 59.192 45.455 0.00 0.00 35.90 2.69
3918 4789 2.158449 GCCAAAATCTATCTCGCCATCG 59.842 50.000 0.00 0.00 0.00 3.84
4009 4881 5.221048 GGTTACTGAACAACTGCACAAAGAT 60.221 40.000 0.00 0.00 37.29 2.40
4028 4900 0.029700 GGCAAACACACGGTGGTTAC 59.970 55.000 13.48 9.18 41.92 2.50
4038 4910 5.767665 ACAGTAAATACATCAGGCAAACACA 59.232 36.000 0.00 0.00 0.00 3.72
4062 4934 2.233922 GGATCACTCGGAGGAAACAGAA 59.766 50.000 10.23 0.00 0.00 3.02
4078 4950 4.588951 AGTACACAGAGTTCAACAGGATCA 59.411 41.667 0.00 0.00 0.00 2.92
4149 5025 4.385825 TGTGAAAACACAGGGTAGATGAC 58.614 43.478 0.00 0.00 0.00 3.06
4237 5117 1.651240 CCCACATCAAAGAGGCAGCG 61.651 60.000 0.00 0.00 0.00 5.18
4248 5128 0.035317 GACTCACACTGCCCACATCA 59.965 55.000 0.00 0.00 0.00 3.07
4251 5131 2.421314 CGACTCACACTGCCCACA 59.579 61.111 0.00 0.00 0.00 4.17
4254 5134 2.715532 TTCAGCGACTCACACTGCCC 62.716 60.000 0.00 0.00 0.00 5.36
4267 5147 1.176527 ACCACCCATTTCATTCAGCG 58.823 50.000 0.00 0.00 0.00 5.18
4297 5177 1.884075 TTACGTGCGAGCACCATCCT 61.884 55.000 20.79 3.15 43.49 3.24
4313 5193 6.856895 AGTACAAACTATGGTCTACCGTTAC 58.143 40.000 0.00 0.00 34.35 2.50
4315 5195 5.713861 AGAGTACAAACTATGGTCTACCGTT 59.286 40.000 0.00 0.00 35.69 4.44
4316 5196 5.259632 AGAGTACAAACTATGGTCTACCGT 58.740 41.667 0.00 0.00 35.69 4.83
4317 5197 5.831702 AGAGTACAAACTATGGTCTACCG 57.168 43.478 0.00 0.00 35.69 4.02
4318 5198 8.312564 AGAAAAGAGTACAAACTATGGTCTACC 58.687 37.037 0.00 0.00 35.56 3.18
4319 5199 9.708092 AAGAAAAGAGTACAAACTATGGTCTAC 57.292 33.333 0.00 0.00 35.56 2.59
4332 5212 9.996554 TCACTCATCAAATAAGAAAAGAGTACA 57.003 29.630 0.00 0.00 33.72 2.90
4334 5214 9.996554 TGTCACTCATCAAATAAGAAAAGAGTA 57.003 29.630 0.00 0.00 33.72 2.59
4335 5215 8.778358 GTGTCACTCATCAAATAAGAAAAGAGT 58.222 33.333 0.00 0.00 35.66 3.24
4336 5216 8.777413 TGTGTCACTCATCAAATAAGAAAAGAG 58.223 33.333 4.27 0.00 0.00 2.85
4337 5217 8.675705 TGTGTCACTCATCAAATAAGAAAAGA 57.324 30.769 4.27 0.00 0.00 2.52
4338 5218 8.019669 CCTGTGTCACTCATCAAATAAGAAAAG 58.980 37.037 4.27 0.00 0.00 2.27
4339 5219 7.719193 TCCTGTGTCACTCATCAAATAAGAAAA 59.281 33.333 4.27 0.00 0.00 2.29
4340 5220 7.223584 TCCTGTGTCACTCATCAAATAAGAAA 58.776 34.615 4.27 0.00 0.00 2.52
4341 5221 6.768483 TCCTGTGTCACTCATCAAATAAGAA 58.232 36.000 4.27 0.00 0.00 2.52
4342 5222 6.211384 TCTCCTGTGTCACTCATCAAATAAGA 59.789 38.462 4.27 0.00 0.00 2.10
4343 5223 6.401394 TCTCCTGTGTCACTCATCAAATAAG 58.599 40.000 4.27 0.00 0.00 1.73
4344 5224 6.358974 TCTCCTGTGTCACTCATCAAATAA 57.641 37.500 4.27 0.00 0.00 1.40
4345 5225 6.014242 ACTTCTCCTGTGTCACTCATCAAATA 60.014 38.462 4.27 0.00 0.00 1.40
4346 5226 4.897509 TCTCCTGTGTCACTCATCAAAT 57.102 40.909 4.27 0.00 0.00 2.32
4347 5227 4.101585 ACTTCTCCTGTGTCACTCATCAAA 59.898 41.667 4.27 0.00 0.00 2.69
4348 5228 3.643320 ACTTCTCCTGTGTCACTCATCAA 59.357 43.478 4.27 0.00 0.00 2.57
4349 5229 3.006217 CACTTCTCCTGTGTCACTCATCA 59.994 47.826 4.27 0.00 0.00 3.07
4350 5230 3.006323 ACACTTCTCCTGTGTCACTCATC 59.994 47.826 4.27 0.00 44.24 2.92
4351 5231 2.968574 ACACTTCTCCTGTGTCACTCAT 59.031 45.455 4.27 0.00 44.24 2.90
4352 5232 2.388735 ACACTTCTCCTGTGTCACTCA 58.611 47.619 4.27 0.00 44.24 3.41
4353 5233 3.126831 CAACACTTCTCCTGTGTCACTC 58.873 50.000 4.27 0.00 46.46 3.51
4354 5234 2.501723 ACAACACTTCTCCTGTGTCACT 59.498 45.455 4.27 0.00 46.46 3.41
4355 5235 2.609459 CACAACACTTCTCCTGTGTCAC 59.391 50.000 0.00 0.00 46.46 3.67
4356 5236 2.905075 CACAACACTTCTCCTGTGTCA 58.095 47.619 0.00 0.00 46.46 3.58
4359 5239 3.270027 TGAACACAACACTTCTCCTGTG 58.730 45.455 0.00 0.00 43.81 3.66
4360 5240 3.627395 TGAACACAACACTTCTCCTGT 57.373 42.857 0.00 0.00 0.00 4.00
4361 5241 4.790766 GCAATGAACACAACACTTCTCCTG 60.791 45.833 0.00 0.00 0.00 3.86
4362 5242 3.316308 GCAATGAACACAACACTTCTCCT 59.684 43.478 0.00 0.00 0.00 3.69
4363 5243 3.316308 AGCAATGAACACAACACTTCTCC 59.684 43.478 0.00 0.00 0.00 3.71
4364 5244 4.035558 TGAGCAATGAACACAACACTTCTC 59.964 41.667 0.00 0.00 0.00 2.87
4365 5245 3.947196 TGAGCAATGAACACAACACTTCT 59.053 39.130 0.00 0.00 0.00 2.85
4366 5246 4.291540 TGAGCAATGAACACAACACTTC 57.708 40.909 0.00 0.00 0.00 3.01
4367 5247 4.717233 TTGAGCAATGAACACAACACTT 57.283 36.364 0.00 0.00 0.00 3.16
4368 5248 4.924305 ATTGAGCAATGAACACAACACT 57.076 36.364 0.00 0.00 0.00 3.55
4369 5249 6.000891 TCTATTGAGCAATGAACACAACAC 57.999 37.500 5.99 0.00 32.50 3.32
4370 5250 6.631971 TTCTATTGAGCAATGAACACAACA 57.368 33.333 5.99 0.00 32.50 3.33
4371 5251 9.282247 CTATTTCTATTGAGCAATGAACACAAC 57.718 33.333 5.99 0.00 32.50 3.32
4372 5252 9.013229 ACTATTTCTATTGAGCAATGAACACAA 57.987 29.630 5.99 0.00 32.50 3.33
4373 5253 8.565896 ACTATTTCTATTGAGCAATGAACACA 57.434 30.769 5.99 0.00 32.50 3.72
4374 5254 9.922305 GTACTATTTCTATTGAGCAATGAACAC 57.078 33.333 5.99 0.00 32.50 3.32
4375 5255 9.665719 TGTACTATTTCTATTGAGCAATGAACA 57.334 29.630 5.99 0.88 32.50 3.18
4381 5261 9.809096 CTCTCTTGTACTATTTCTATTGAGCAA 57.191 33.333 0.00 0.00 0.00 3.91
4382 5262 7.923344 GCTCTCTTGTACTATTTCTATTGAGCA 59.077 37.037 0.00 0.00 39.95 4.26
4383 5263 7.923344 TGCTCTCTTGTACTATTTCTATTGAGC 59.077 37.037 0.00 0.00 40.41 4.26
4384 5264 9.809096 TTGCTCTCTTGTACTATTTCTATTGAG 57.191 33.333 0.00 0.00 0.00 3.02
4387 5267 9.103861 GCTTTGCTCTCTTGTACTATTTCTATT 57.896 33.333 0.00 0.00 0.00 1.73
4388 5268 8.482128 AGCTTTGCTCTCTTGTACTATTTCTAT 58.518 33.333 0.00 0.00 30.62 1.98
4389 5269 7.841956 AGCTTTGCTCTCTTGTACTATTTCTA 58.158 34.615 0.00 0.00 30.62 2.10
4390 5270 6.706295 AGCTTTGCTCTCTTGTACTATTTCT 58.294 36.000 0.00 0.00 30.62 2.52
4391 5271 6.976636 AGCTTTGCTCTCTTGTACTATTTC 57.023 37.500 0.00 0.00 30.62 2.17
4409 5289 3.883489 GGGCTATTGATAAACCGAGCTTT 59.117 43.478 0.00 0.00 0.00 3.51
4433 5313 1.808411 TTCATCGTTCTTGGTGCCTC 58.192 50.000 0.00 0.00 0.00 4.70
4446 5326 1.926511 GCCAGCCACCAGTTTCATCG 61.927 60.000 0.00 0.00 0.00 3.84
4476 5356 3.129638 AGCTTCTTCTCGCCAGTACTAAG 59.870 47.826 0.00 0.00 0.00 2.18
4480 5360 2.371910 AAGCTTCTTCTCGCCAGTAC 57.628 50.000 0.00 0.00 0.00 2.73
4502 5382 3.724478 TGGATCATCACCTCCACTAAGT 58.276 45.455 0.00 0.00 36.63 2.24
4546 5554 3.991367 TCTTCAGGAAAAAGGTCTCGAC 58.009 45.455 0.00 0.00 0.00 4.20
4548 5556 4.023963 GGTTTCTTCAGGAAAAAGGTCTCG 60.024 45.833 0.00 0.00 44.34 4.04
4605 5614 3.008594 TCATAATATCATTCGCCGGGGTT 59.991 43.478 19.13 5.97 0.00 4.11
4606 5615 2.569853 TCATAATATCATTCGCCGGGGT 59.430 45.455 19.13 0.59 0.00 4.95
4607 5616 3.260475 TCATAATATCATTCGCCGGGG 57.740 47.619 13.31 13.31 0.00 5.73
4609 5618 4.253685 ACCTTCATAATATCATTCGCCGG 58.746 43.478 0.00 0.00 0.00 6.13
4624 5633 2.290641 TGCCATCCACGTTTACCTTCAT 60.291 45.455 0.00 0.00 0.00 2.57
4693 5702 3.321396 GTCTCCATCAGCATCATCTCTGA 59.679 47.826 0.00 0.00 42.72 3.27
4694 5703 3.655486 GTCTCCATCAGCATCATCTCTG 58.345 50.000 0.00 0.00 0.00 3.35
4695 5704 2.296752 CGTCTCCATCAGCATCATCTCT 59.703 50.000 0.00 0.00 0.00 3.10
4696 5705 2.674954 CGTCTCCATCAGCATCATCTC 58.325 52.381 0.00 0.00 0.00 2.75
4697 5706 1.270199 GCGTCTCCATCAGCATCATCT 60.270 52.381 0.00 0.00 0.00 2.90
4698 5707 1.146637 GCGTCTCCATCAGCATCATC 58.853 55.000 0.00 0.00 0.00 2.92
4699 5708 0.599466 CGCGTCTCCATCAGCATCAT 60.599 55.000 0.00 0.00 0.00 2.45
4700 5709 1.227060 CGCGTCTCCATCAGCATCA 60.227 57.895 0.00 0.00 0.00 3.07
4709 5718 3.138798 GCTCCTACCGCGTCTCCA 61.139 66.667 4.92 0.00 0.00 3.86
4744 5759 5.348997 GCTTCAACGTCAGCTAGTAAAGATT 59.651 40.000 7.01 0.00 32.87 2.40
4753 5768 2.526304 ACAAGCTTCAACGTCAGCTA 57.474 45.000 15.12 0.00 46.01 3.32
4762 5777 0.248580 CGCAGCACAACAAGCTTCAA 60.249 50.000 0.00 0.00 41.14 2.69
4825 5843 0.609131 CAGTTCCTGGGCATCCGTTT 60.609 55.000 0.00 0.00 35.24 3.60
4847 5866 4.701765 CATTACTACTTGAGATGGCAGCT 58.298 43.478 4.21 4.21 0.00 4.24
4951 5996 8.188139 CGGACCGTACCTTATTAAACTTACTTA 58.812 37.037 5.48 0.00 0.00 2.24
4952 5997 7.035612 CGGACCGTACCTTATTAAACTTACTT 58.964 38.462 5.48 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.