Multiple sequence alignment - TraesCS4A01G206900

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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 TraesCS4A01G206900 chr4A 100.000 4025 0 0 1 4025 500348681 500352705 0.000000e+00 7433.0
1 TraesCS4A01G206900 chr4A 94.872 39 1 1 3237 3275 494006933 494006896 4.340000e-05 60.2
2 TraesCS4A01G206900 chr4D 91.481 2606 100 44 701 3265 87713931 87716455 0.000000e+00 3470.0
3 TraesCS4A01G206900 chr4D 90.988 688 40 7 3354 4025 87716619 87717300 0.000000e+00 907.0
4 TraesCS4A01G206900 chr4D 81.849 292 30 12 259 535 408579882 408579599 1.460000e-54 224.0
5 TraesCS4A01G206900 chr4D 84.426 122 15 1 531 648 487380168 487380289 2.540000e-22 117.0
6 TraesCS4A01G206900 chr4D 87.302 63 6 2 590 652 442439137 442439077 2.010000e-08 71.3
7 TraesCS4A01G206900 chr4B 91.705 1314 65 23 703 1989 124017517 124018813 0.000000e+00 1783.0
8 TraesCS4A01G206900 chr4B 91.000 1200 69 17 1987 3173 124018916 124020089 0.000000e+00 1581.0
9 TraesCS4A01G206900 chr4B 89.897 871 50 14 3175 4023 124020149 124021003 0.000000e+00 1086.0
10 TraesCS4A01G206900 chr4B 87.558 217 24 3 14 229 124017006 124017220 8.640000e-62 248.0
11 TraesCS4A01G206900 chr1D 92.517 294 22 0 1347 1640 7921310 7921017 4.810000e-114 422.0
12 TraesCS4A01G206900 chr1D 83.505 291 30 10 255 527 39864312 39864602 5.160000e-64 255.0
13 TraesCS4A01G206900 chr1D 88.462 52 4 2 515 564 47945321 47945270 1.210000e-05 62.1
14 TraesCS4A01G206900 chr1B 92.517 294 22 0 1347 1640 10113708 10113415 4.810000e-114 422.0
15 TraesCS4A01G206900 chr1B 85.057 87 12 1 563 648 475487881 475487967 1.990000e-13 87.9
16 TraesCS4A01G206900 chr1B 92.982 57 4 0 1052 1108 10114115 10114059 2.580000e-12 84.2
17 TraesCS4A01G206900 chr5B 91.892 296 24 0 1346 1641 207577667 207577962 8.050000e-112 414.0
18 TraesCS4A01G206900 chr5B 84.825 257 24 5 1347 1603 11061134 11061375 1.120000e-60 244.0
19 TraesCS4A01G206900 chr5B 91.429 105 6 2 1030 1134 207577347 207577448 1.510000e-29 141.0
20 TraesCS4A01G206900 chr5B 100.000 31 0 0 3245 3275 218214628 218214598 1.560000e-04 58.4
21 TraesCS4A01G206900 chr1A 92.150 293 23 0 1348 1640 9589136 9588844 8.050000e-112 414.0
22 TraesCS4A01G206900 chr1A 87.356 87 11 0 570 656 28924818 28924732 2.560000e-17 100.0
23 TraesCS4A01G206900 chr1A 91.429 70 6 0 1052 1121 9589279 9589210 3.310000e-16 97.1
24 TraesCS4A01G206900 chr1A 100.000 31 0 0 3245 3275 9174055 9174025 1.560000e-04 58.4
25 TraesCS4A01G206900 chr1A 100.000 31 0 0 3245 3275 9201449 9201419 1.560000e-04 58.4
26 TraesCS4A01G206900 chr5A 91.216 296 26 0 1346 1641 244450135 244449840 1.740000e-108 403.0
27 TraesCS4A01G206900 chr5A 91.429 105 6 2 1030 1134 244450455 244450354 1.510000e-29 141.0
28 TraesCS4A01G206900 chr5A 84.416 77 11 1 573 648 654099182 654099258 1.550000e-09 75.0
29 TraesCS4A01G206900 chr5A 92.857 42 2 1 523 564 345772758 345772718 4.340000e-05 60.2
30 TraesCS4A01G206900 chr5A 100.000 31 0 0 3245 3275 231302129 231302099 1.560000e-04 58.4
31 TraesCS4A01G206900 chr5D 90.878 296 27 0 1346 1641 204871866 204871571 8.110000e-107 398.0
32 TraesCS4A01G206900 chr5D 94.624 93 5 0 1031 1123 204872185 204872093 1.170000e-30 145.0
33 TraesCS4A01G206900 chr3D 84.354 294 29 8 259 539 58397917 58397628 5.130000e-69 272.0
34 TraesCS4A01G206900 chr3D 80.537 298 32 10 256 533 170555753 170556044 5.270000e-49 206.0
35 TraesCS4A01G206900 chr3D 100.000 30 0 0 3246 3275 67480967 67480996 5.620000e-04 56.5
36 TraesCS4A01G206900 chr6B 82.192 292 32 13 259 532 157609880 157610169 2.420000e-57 233.0
37 TraesCS4A01G206900 chr6B 80.567 247 30 15 302 534 157644153 157644395 1.490000e-39 174.0
38 TraesCS4A01G206900 chr7D 81.818 297 31 7 252 533 520343099 520343387 1.130000e-55 228.0
39 TraesCS4A01G206900 chr7D 80.623 289 37 10 261 533 509828437 509828152 5.270000e-49 206.0
40 TraesCS4A01G206900 chr3B 81.507 292 33 12 256 527 606379170 606379460 1.880000e-53 220.0
41 TraesCS4A01G206900 chr3B 85.345 116 14 2 537 649 719859987 719859872 2.540000e-22 117.0
42 TraesCS4A01G206900 chr6A 80.936 299 32 12 259 534 99211940 99212236 3.150000e-51 213.0
43 TraesCS4A01G206900 chr6A 82.203 236 29 8 309 534 99213119 99213351 1.480000e-44 191.0
44 TraesCS4A01G206900 chr6A 90.000 50 2 3 516 564 6375361 6375314 1.210000e-05 62.1
45 TraesCS4A01G206900 chr6A 90.698 43 2 2 3286 3326 143976591 143976549 5.620000e-04 56.5
46 TraesCS4A01G206900 chr2A 80.783 281 38 12 259 533 550578796 550579066 5.270000e-49 206.0
47 TraesCS4A01G206900 chr2A 79.110 292 29 14 260 533 524147684 524147961 5.350000e-39 172.0
48 TraesCS4A01G206900 chr2A 83.516 91 14 1 563 652 649629214 649629304 2.580000e-12 84.2
49 TraesCS4A01G206900 chr2A 91.111 45 4 0 520 564 743327474 743327518 1.210000e-05 62.1
50 TraesCS4A01G206900 chr3A 80.420 286 41 8 256 527 157036180 157036464 1.900000e-48 204.0
51 TraesCS4A01G206900 chr3A 84.615 91 13 1 563 652 13962749 13962659 5.540000e-14 89.8
52 TraesCS4A01G206900 chr7A 81.053 190 25 6 252 430 596659324 596659135 1.510000e-29 141.0
53 TraesCS4A01G206900 chr7A 95.455 44 1 1 521 564 167525858 167525900 7.220000e-08 69.4
54 TraesCS4A01G206900 chrUn 80.208 192 25 7 252 430 347888199 347888008 9.080000e-27 132.0
55 TraesCS4A01G206900 chrUn 100.000 31 0 0 3245 3275 278887167 278887197 1.560000e-04 58.4
56 TraesCS4A01G206900 chrUn 100.000 31 0 0 3245 3275 395191349 395191379 1.560000e-04 58.4
57 TraesCS4A01G206900 chr2B 90.000 90 9 0 563 652 775365829 775365740 2.540000e-22 117.0
58 TraesCS4A01G206900 chr6D 84.444 90 13 1 563 651 434786127 434786216 1.990000e-13 87.9


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 TraesCS4A01G206900 chr4A 500348681 500352705 4024 False 7433.0 7433 100.0000 1 4025 1 chr4A.!!$F1 4024
1 TraesCS4A01G206900 chr4D 87713931 87717300 3369 False 2188.5 3470 91.2345 701 4025 2 chr4D.!!$F2 3324
2 TraesCS4A01G206900 chr4B 124017006 124021003 3997 False 1174.5 1783 90.0400 14 4023 4 chr4B.!!$F1 4009
3 TraesCS4A01G206900 chr1B 10113415 10114115 700 True 253.1 422 92.7495 1052 1640 2 chr1B.!!$R1 588
4 TraesCS4A01G206900 chr5B 207577347 207577962 615 False 277.5 414 91.6605 1030 1641 2 chr5B.!!$F2 611
5 TraesCS4A01G206900 chr5A 244449840 244450455 615 True 272.0 403 91.3225 1030 1641 2 chr5A.!!$R3 611
6 TraesCS4A01G206900 chr5D 204871571 204872185 614 True 271.5 398 92.7510 1031 1641 2 chr5D.!!$R1 610
7 TraesCS4A01G206900 chr6A 99211940 99213351 1411 False 202.0 213 81.5695 259 534 2 chr6A.!!$F1 275

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
215 216 0.244721 TCGGCGATGCTCATATGAGG 59.755 55.000 29.43 16.3 42.29 3.86 F
488 512 0.396435 AGCACTGTCATCCCGTTTCA 59.604 50.000 0.00 0.0 0.00 2.69 F
566 590 0.623723 TGGTTGGATGGTTAGAGCCC 59.376 55.000 0.00 0.0 0.00 5.19 F
567 591 0.623723 GGTTGGATGGTTAGAGCCCA 59.376 55.000 0.00 0.0 36.16 5.36 F
1163 1416 0.863538 CTCCTTGATCGAGCGACACG 60.864 60.000 4.21 0.0 0.00 4.49 F
1211 1473 1.758906 GGTTCCTCTCCCCTCTCCG 60.759 68.421 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1141 1385 0.030101 GTCGCTCGATCAAGGAGGAG 59.970 60.000 0.0 0.0 32.1 3.69 R
1460 1981 1.141019 GCCGTAGATTCCGAGCACA 59.859 57.895 0.0 0.0 0.0 4.57 R
2074 2703 2.031682 AGTCACTTGCGATGTTTTCTGC 60.032 45.455 0.0 0.0 0.0 4.26 R
2497 3528 5.323371 TGAAACTGAAAAACTGTGAAGGG 57.677 39.130 0.0 0.0 0.0 3.95 R
2611 3643 2.026014 AGCTTTGGTTGTTGCGCG 59.974 55.556 0.0 0.0 0.0 6.86 R
3168 4204 2.033801 GCCATGCTACACATAAGCCAAG 59.966 50.000 0.0 0.0 39.3 3.61 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
43 44 1.537889 ATCACCCTGACGAACCCCA 60.538 57.895 0.00 0.00 0.00 4.96
45 46 3.622826 ACCCTGACGAACCCCACG 61.623 66.667 0.00 0.00 0.00 4.94
64 65 1.526225 GGAGGTGGCGAAATAGGGC 60.526 63.158 0.00 0.00 0.00 5.19
87 88 2.233431 TGGCTTCACCATTAATGTTGGC 59.767 45.455 12.47 8.92 46.36 4.52
88 89 2.497273 GGCTTCACCATTAATGTTGGCT 59.503 45.455 12.47 0.00 37.81 4.75
119 120 8.762481 TCTACCACTAGAAACTAGATGCATAA 57.238 34.615 0.00 0.00 0.00 1.90
125 126 4.950050 AGAAACTAGATGCATAACCCTCG 58.050 43.478 0.00 0.00 0.00 4.63
156 157 1.241990 GGGTCAAAGCCTTTCCGGAC 61.242 60.000 1.83 0.00 31.81 4.79
158 159 1.302192 TCAAAGCCTTTCCGGACGG 60.302 57.895 1.83 9.44 33.16 4.79
162 163 4.772687 GCCTTTCCGGACGGGGAC 62.773 72.222 19.72 8.77 35.32 4.46
180 181 4.450053 GGGACCTCTTTCTCAAGATGATG 58.550 47.826 0.00 0.00 38.42 3.07
182 183 4.450053 GACCTCTTTCTCAAGATGATGGG 58.550 47.826 0.00 0.00 38.42 4.00
187 188 1.135094 TCTCAAGATGATGGGAGGGC 58.865 55.000 0.00 0.00 0.00 5.19
198 199 2.124693 GGGAGGGCTCAGTCTCTCG 61.125 68.421 0.00 0.00 0.00 4.04
199 200 2.124693 GGAGGGCTCAGTCTCTCGG 61.125 68.421 0.00 0.00 0.00 4.63
200 201 2.757917 AGGGCTCAGTCTCTCGGC 60.758 66.667 0.00 0.00 0.00 5.54
201 202 4.200283 GGGCTCAGTCTCTCGGCG 62.200 72.222 0.00 0.00 0.00 6.46
202 203 3.134792 GGCTCAGTCTCTCGGCGA 61.135 66.667 10.14 10.14 0.00 5.54
215 216 0.244721 TCGGCGATGCTCATATGAGG 59.755 55.000 29.43 16.30 42.29 3.86
229 230 2.434359 GAGGTAGGGCGTGTGTGC 60.434 66.667 0.00 0.00 0.00 4.57
230 231 4.373116 AGGTAGGGCGTGTGTGCG 62.373 66.667 0.00 0.00 35.06 5.34
231 232 4.675029 GGTAGGGCGTGTGTGCGT 62.675 66.667 0.00 0.00 35.06 5.24
232 233 3.411351 GTAGGGCGTGTGTGCGTG 61.411 66.667 0.00 0.00 35.06 5.34
233 234 3.918977 TAGGGCGTGTGTGCGTGT 61.919 61.111 0.00 0.00 35.06 4.49
238 239 2.323105 CGTGTGTGCGTGTGTTCC 59.677 61.111 0.00 0.00 0.00 3.62
239 240 2.713154 GTGTGTGCGTGTGTTCCC 59.287 61.111 0.00 0.00 0.00 3.97
240 241 1.817941 GTGTGTGCGTGTGTTCCCT 60.818 57.895 0.00 0.00 0.00 4.20
242 243 2.203139 TGTGCGTGTGTTCCCTGG 60.203 61.111 0.00 0.00 0.00 4.45
244 245 3.164977 TGCGTGTGTTCCCTGGGA 61.165 61.111 12.53 12.53 0.00 4.37
245 246 2.668550 GCGTGTGTTCCCTGGGAC 60.669 66.667 16.85 11.43 0.00 4.46
255 256 1.144057 CCCTGGGACGAGTGTATGC 59.856 63.158 7.01 0.00 0.00 3.14
257 258 1.663379 CCTGGGACGAGTGTATGCGA 61.663 60.000 0.00 0.00 0.00 5.10
259 260 0.604073 TGGGACGAGTGTATGCGAAA 59.396 50.000 0.00 0.00 0.00 3.46
262 263 2.284417 GGGACGAGTGTATGCGAAAATC 59.716 50.000 0.00 0.00 0.00 2.17
263 264 2.927477 GGACGAGTGTATGCGAAAATCA 59.073 45.455 0.00 0.00 0.00 2.57
287 288 1.089920 CGGCTATTGGGAGCATATGC 58.910 55.000 20.36 20.36 44.76 3.14
307 321 2.027837 GCTCCTGCCCATCAAAAATGTT 60.028 45.455 0.00 0.00 0.00 2.71
355 369 1.066303 TCATTGTCACACCAAAACGCC 59.934 47.619 0.00 0.00 0.00 5.68
361 375 1.379309 ACACCAAAACGCCACCTGT 60.379 52.632 0.00 0.00 0.00 4.00
365 379 1.406180 ACCAAAACGCCACCTGTAAAC 59.594 47.619 0.00 0.00 0.00 2.01
381 395 6.004574 CCTGTAAACTTTTAGGAGGAAAGCT 58.995 40.000 0.00 0.00 37.57 3.74
385 399 9.063615 TGTAAACTTTTAGGAGGAAAGCTTAAG 57.936 33.333 0.00 0.00 37.57 1.85
388 402 8.618702 AACTTTTAGGAGGAAAGCTTAAGTAC 57.381 34.615 0.00 0.00 37.57 2.73
390 404 7.878644 ACTTTTAGGAGGAAAGCTTAAGTACTG 59.121 37.037 0.00 0.00 37.57 2.74
392 406 8.426569 TTTAGGAGGAAAGCTTAAGTACTGTA 57.573 34.615 0.00 0.00 0.00 2.74
406 420 9.599322 CTTAAGTACTGTAATCTGTGCAAAAAG 57.401 33.333 0.00 0.00 32.57 2.27
421 442 3.239712 GCAAAAAGAAACAAGTCGAACGG 59.760 43.478 0.00 0.00 0.00 4.44
422 443 3.685836 AAAAGAAACAAGTCGAACGGG 57.314 42.857 0.00 0.00 0.00 5.28
427 448 4.634199 AGAAACAAGTCGAACGGGAAATA 58.366 39.130 0.00 0.00 0.00 1.40
434 455 5.349061 AGTCGAACGGGAAATATTACCTT 57.651 39.130 7.33 0.00 0.00 3.50
487 511 1.464997 GAAGCACTGTCATCCCGTTTC 59.535 52.381 0.00 0.00 0.00 2.78
488 512 0.396435 AGCACTGTCATCCCGTTTCA 59.604 50.000 0.00 0.00 0.00 2.69
492 516 3.595173 CACTGTCATCCCGTTTCACATA 58.405 45.455 0.00 0.00 0.00 2.29
493 517 3.618594 CACTGTCATCCCGTTTCACATAG 59.381 47.826 0.00 0.00 0.00 2.23
498 522 6.645306 TGTCATCCCGTTTCACATAGAATTA 58.355 36.000 0.00 0.00 35.83 1.40
503 527 5.584649 TCCCGTTTCACATAGAATTAGCAAG 59.415 40.000 0.00 0.00 35.83 4.01
540 564 9.601217 ACACTAACAAGAATATCTATGTGAACC 57.399 33.333 0.00 0.00 0.00 3.62
541 565 9.599866 CACTAACAAGAATATCTATGTGAACCA 57.400 33.333 0.00 0.00 0.00 3.67
544 568 7.865706 ACAAGAATATCTATGTGAACCAACC 57.134 36.000 0.00 0.00 0.00 3.77
545 569 7.633789 ACAAGAATATCTATGTGAACCAACCT 58.366 34.615 0.00 0.00 0.00 3.50
546 570 7.554118 ACAAGAATATCTATGTGAACCAACCTG 59.446 37.037 0.00 0.00 0.00 4.00
548 572 7.050377 AGAATATCTATGTGAACCAACCTGTG 58.950 38.462 0.00 0.00 0.00 3.66
561 585 2.879103 ACCTGTGGTTGGATGGTTAG 57.121 50.000 0.00 0.00 27.29 2.34
562 586 2.344592 ACCTGTGGTTGGATGGTTAGA 58.655 47.619 0.00 0.00 27.29 2.10
563 587 2.305927 ACCTGTGGTTGGATGGTTAGAG 59.694 50.000 0.00 0.00 27.29 2.43
564 588 2.359900 CTGTGGTTGGATGGTTAGAGC 58.640 52.381 0.00 0.00 0.00 4.09
565 589 1.004277 TGTGGTTGGATGGTTAGAGCC 59.996 52.381 0.00 0.00 0.00 4.70
566 590 0.623723 TGGTTGGATGGTTAGAGCCC 59.376 55.000 0.00 0.00 0.00 5.19
567 591 0.623723 GGTTGGATGGTTAGAGCCCA 59.376 55.000 0.00 0.00 36.16 5.36
568 592 1.215423 GGTTGGATGGTTAGAGCCCAT 59.785 52.381 0.00 0.00 45.37 4.00
583 607 2.702093 CCATCAGGGGTCAAGTCCT 58.298 57.895 0.00 0.00 0.00 3.85
589 613 2.950990 AGGGGTCAAGTCCTGATACT 57.049 50.000 0.00 0.00 36.14 2.12
590 614 2.753247 AGGGGTCAAGTCCTGATACTC 58.247 52.381 0.00 0.00 36.14 2.59
591 615 1.409427 GGGGTCAAGTCCTGATACTCG 59.591 57.143 0.00 0.00 36.14 4.18
592 616 1.202428 GGGTCAAGTCCTGATACTCGC 60.202 57.143 0.00 0.00 36.14 5.03
593 617 1.476891 GGTCAAGTCCTGATACTCGCA 59.523 52.381 0.00 0.00 36.14 5.10
594 618 2.101582 GGTCAAGTCCTGATACTCGCAT 59.898 50.000 0.00 0.00 36.14 4.73
595 619 3.430929 GGTCAAGTCCTGATACTCGCATT 60.431 47.826 0.00 0.00 36.14 3.56
596 620 4.202121 GGTCAAGTCCTGATACTCGCATTA 60.202 45.833 0.00 0.00 36.14 1.90
597 621 5.509840 GGTCAAGTCCTGATACTCGCATTAT 60.510 44.000 0.00 0.00 36.14 1.28
598 622 5.986135 GTCAAGTCCTGATACTCGCATTATT 59.014 40.000 0.00 0.00 36.14 1.40
599 623 6.144724 GTCAAGTCCTGATACTCGCATTATTC 59.855 42.308 0.00 0.00 36.14 1.75
600 624 5.791336 AGTCCTGATACTCGCATTATTCA 57.209 39.130 0.00 0.00 0.00 2.57
601 625 6.352016 AGTCCTGATACTCGCATTATTCAT 57.648 37.500 0.00 0.00 0.00 2.57
602 626 6.162079 AGTCCTGATACTCGCATTATTCATG 58.838 40.000 0.00 0.00 35.73 3.07
603 627 5.928839 GTCCTGATACTCGCATTATTCATGT 59.071 40.000 0.00 0.00 34.98 3.21
604 628 7.039714 AGTCCTGATACTCGCATTATTCATGTA 60.040 37.037 0.00 0.00 34.98 2.29
605 629 7.761704 GTCCTGATACTCGCATTATTCATGTAT 59.238 37.037 0.00 0.00 34.98 2.29
606 630 8.314021 TCCTGATACTCGCATTATTCATGTATT 58.686 33.333 0.00 0.00 34.98 1.89
607 631 8.939929 CCTGATACTCGCATTATTCATGTATTT 58.060 33.333 0.00 0.00 34.98 1.40
624 648 9.184523 TCATGTATTTATTTCAGGATTTTCGGT 57.815 29.630 0.00 0.00 0.00 4.69
625 649 9.236691 CATGTATTTATTTCAGGATTTTCGGTG 57.763 33.333 0.00 0.00 0.00 4.94
626 650 8.568676 TGTATTTATTTCAGGATTTTCGGTGA 57.431 30.769 0.00 0.00 0.00 4.02
627 651 9.184523 TGTATTTATTTCAGGATTTTCGGTGAT 57.815 29.630 0.00 0.00 0.00 3.06
628 652 9.450807 GTATTTATTTCAGGATTTTCGGTGATG 57.549 33.333 0.00 0.00 0.00 3.07
629 653 7.461182 TTTATTTCAGGATTTTCGGTGATGT 57.539 32.000 0.00 0.00 0.00 3.06
630 654 8.568676 TTTATTTCAGGATTTTCGGTGATGTA 57.431 30.769 0.00 0.00 0.00 2.29
631 655 5.873179 TTTCAGGATTTTCGGTGATGTAC 57.127 39.130 0.00 0.00 0.00 2.90
632 656 4.819105 TCAGGATTTTCGGTGATGTACT 57.181 40.909 0.00 0.00 0.00 2.73
633 657 5.160607 TCAGGATTTTCGGTGATGTACTT 57.839 39.130 0.00 0.00 0.00 2.24
634 658 5.556915 TCAGGATTTTCGGTGATGTACTTT 58.443 37.500 0.00 0.00 0.00 2.66
635 659 5.642063 TCAGGATTTTCGGTGATGTACTTTC 59.358 40.000 0.00 0.00 0.00 2.62
636 660 5.411361 CAGGATTTTCGGTGATGTACTTTCA 59.589 40.000 0.00 0.00 0.00 2.69
637 661 5.643777 AGGATTTTCGGTGATGTACTTTCAG 59.356 40.000 0.00 0.00 0.00 3.02
638 662 5.411669 GGATTTTCGGTGATGTACTTTCAGT 59.588 40.000 0.00 0.00 0.00 3.41
639 663 5.666969 TTTTCGGTGATGTACTTTCAGTG 57.333 39.130 0.00 0.00 0.00 3.66
640 664 3.313012 TCGGTGATGTACTTTCAGTGG 57.687 47.619 0.00 0.00 0.00 4.00
641 665 2.028476 TCGGTGATGTACTTTCAGTGGG 60.028 50.000 0.00 0.00 0.00 4.61
642 666 2.028476 CGGTGATGTACTTTCAGTGGGA 60.028 50.000 0.00 0.00 0.00 4.37
643 667 3.600388 GGTGATGTACTTTCAGTGGGAG 58.400 50.000 0.00 0.00 0.00 4.30
644 668 3.600388 GTGATGTACTTTCAGTGGGAGG 58.400 50.000 0.00 0.00 0.00 4.30
645 669 3.260884 GTGATGTACTTTCAGTGGGAGGA 59.739 47.826 0.00 0.00 0.00 3.71
646 670 3.515502 TGATGTACTTTCAGTGGGAGGAG 59.484 47.826 0.00 0.00 0.00 3.69
647 671 3.254093 TGTACTTTCAGTGGGAGGAGA 57.746 47.619 0.00 0.00 0.00 3.71
648 672 2.897969 TGTACTTTCAGTGGGAGGAGAC 59.102 50.000 0.00 0.00 0.00 3.36
649 673 0.969894 ACTTTCAGTGGGAGGAGACG 59.030 55.000 0.00 0.00 0.00 4.18
650 674 0.969894 CTTTCAGTGGGAGGAGACGT 59.030 55.000 0.00 0.00 0.00 4.34
651 675 1.344763 CTTTCAGTGGGAGGAGACGTT 59.655 52.381 0.00 0.00 0.00 3.99
652 676 1.420430 TTCAGTGGGAGGAGACGTTT 58.580 50.000 0.00 0.00 0.00 3.60
653 677 1.420430 TCAGTGGGAGGAGACGTTTT 58.580 50.000 0.00 0.00 0.00 2.43
654 678 1.343465 TCAGTGGGAGGAGACGTTTTC 59.657 52.381 0.00 0.00 0.00 2.29
723 967 2.557490 AGTATTAAGTCGCCCGGAGATC 59.443 50.000 0.73 0.00 0.00 2.75
837 1081 1.338020 GTGCAAAACCAAGGAGTCCAG 59.662 52.381 12.86 3.08 0.00 3.86
938 1182 6.986250 AGAAAATAAAAGCAAACTGGAGAGG 58.014 36.000 0.00 0.00 0.00 3.69
1141 1385 3.460478 ATCGCCTCTCCTCCCTCCC 62.460 68.421 0.00 0.00 0.00 4.30
1142 1386 4.150454 CGCCTCTCCTCCCTCCCT 62.150 72.222 0.00 0.00 0.00 4.20
1144 1388 2.612251 CCTCTCCTCCCTCCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1145 1389 2.018086 CCTCTCCTCCCTCCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1148 1392 2.018086 CTCCTCCCTCCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1149 1393 1.550374 TCCTCCCTCCCTCCTCCTT 60.550 63.158 0.00 0.00 0.00 3.36
1159 1412 1.103987 CCTCCTCCTTGATCGAGCGA 61.104 60.000 4.21 3.10 0.00 4.93
1163 1416 0.863538 CTCCTTGATCGAGCGACACG 60.864 60.000 4.21 0.00 0.00 4.49
1178 1431 3.829948 CGACACGCTAGGAAGAAAACTA 58.170 45.455 0.00 0.00 0.00 2.24
1179 1432 3.852536 CGACACGCTAGGAAGAAAACTAG 59.147 47.826 0.00 0.00 39.68 2.57
1189 1449 8.251721 GCTAGGAAGAAAACTAGTTAGATGTCA 58.748 37.037 8.92 0.00 39.07 3.58
1195 1455 6.726764 AGAAAACTAGTTAGATGTCAGAGGGT 59.273 38.462 8.92 0.00 0.00 4.34
1211 1473 1.758906 GGTTCCTCTCCCCTCTCCG 60.759 68.421 0.00 0.00 0.00 4.63
1325 1845 2.925262 CGCTGGATCCGGCTAGAGG 61.925 68.421 36.58 20.91 45.52 3.69
1648 2169 3.265791 CTGGAGTCAGGTAAAGATGCAC 58.734 50.000 0.00 0.00 37.36 4.57
1707 2228 5.761234 TCTTTGACTTTTAAGCGGTATGTGT 59.239 36.000 0.00 0.00 0.00 3.72
1758 2279 8.837059 GCATTACGGTTTGATTAATAATTAGCG 58.163 33.333 11.07 11.07 0.00 4.26
1759 2280 8.837059 CATTACGGTTTGATTAATAATTAGCGC 58.163 33.333 0.00 0.00 0.00 5.92
1816 2337 2.570442 TTTTCCAAAACAGACGTGGC 57.430 45.000 0.00 0.00 32.10 5.01
1841 2362 9.609346 GCTACTCCCTTTGTGATTAGTTTATTA 57.391 33.333 0.00 0.00 0.00 0.98
1869 2390 9.845740 TGTTGATATTGGTAGTAGCATGTATTT 57.154 29.630 2.28 0.00 0.00 1.40
1895 2416 8.380644 TCTACAAAGCGAGAATTATTTCTTTCG 58.619 33.333 1.60 3.68 42.34 3.46
1899 2420 9.490663 CAAAGCGAGAATTATTTCTTTCGTTAT 57.509 29.630 1.60 0.00 42.34 1.89
1910 2431 9.849166 TTATTTCTTTCGTTATTTTTAGCCTGG 57.151 29.630 0.00 0.00 0.00 4.45
1974 2497 6.038714 GTGGATCCTTCTGTTTGTAATCCATC 59.961 42.308 14.23 0.00 42.14 3.51
2026 2655 7.484007 CAGTTATGTGTTTGAATGATCTTGCTC 59.516 37.037 0.00 0.00 0.00 4.26
2047 2676 6.127563 TGCTCGTACTTGTGACTATGGAATTA 60.128 38.462 0.00 0.00 0.00 1.40
2090 2719 6.636666 ATTTAATGCAGAAAACATCGCAAG 57.363 33.333 0.00 0.00 39.65 4.01
2205 2835 2.424557 AGTTCTGATGTGAGCAGCAAG 58.575 47.619 0.00 0.00 40.78 4.01
2316 2955 7.444792 AGACATTTTGCCTGCAATATTTTGAAA 59.555 29.630 5.25 0.00 35.70 2.69
2362 3001 6.313905 CGAAAGTACATGTTCTTGGATAAGCT 59.686 38.462 17.24 0.57 33.82 3.74
2497 3528 6.108687 TCTATGATGTGGTTGATCAGTGTTC 58.891 40.000 0.00 0.00 33.38 3.18
2611 3643 3.195396 TGGATTTTGATTGCAGGGCTAAC 59.805 43.478 0.00 0.00 0.00 2.34
2638 3670 0.395173 AACCAAAGCTGTTCGTGGGT 60.395 50.000 0.00 0.00 35.32 4.51
2704 3736 0.107268 TCATCGTGGGCATCATCCTG 59.893 55.000 0.00 0.00 0.00 3.86
2876 3908 2.473984 GACACTTCCAGTACCGTTTTCG 59.526 50.000 0.00 0.00 43.67 3.46
2950 3982 1.302285 CTGGATTGCTGCTCCTGGT 59.698 57.895 9.08 0.00 33.69 4.00
2951 3983 0.323178 CTGGATTGCTGCTCCTGGTT 60.323 55.000 9.08 0.00 33.69 3.67
3068 4101 8.742777 CCACTCTAATTCCTTGATTCAAATTCA 58.257 33.333 0.01 0.00 0.00 2.57
3165 4201 7.339212 ACAAACTTGCAATTCATATAGGCTACA 59.661 33.333 0.00 0.00 0.00 2.74
3168 4204 7.707104 ACTTGCAATTCATATAGGCTACAAAC 58.293 34.615 0.00 0.00 0.00 2.93
3173 4209 6.884280 ATTCATATAGGCTACAAACTTGGC 57.116 37.500 0.00 0.00 0.00 4.52
3174 4210 5.630415 TCATATAGGCTACAAACTTGGCT 57.370 39.130 0.00 0.00 39.84 4.75
3175 4211 6.001449 TCATATAGGCTACAAACTTGGCTT 57.999 37.500 0.00 0.00 37.73 4.35
3176 4212 7.131907 TCATATAGGCTACAAACTTGGCTTA 57.868 36.000 0.00 0.00 37.73 3.09
3177 4213 7.745717 TCATATAGGCTACAAACTTGGCTTAT 58.254 34.615 0.00 0.00 37.73 1.73
3251 4344 4.337555 TCACTGTTCTAATACGCTACTCCC 59.662 45.833 0.00 0.00 0.00 4.30
3273 4366 6.055588 CCCTCCGTTCACAATTATAAGATGT 58.944 40.000 1.82 1.82 0.00 3.06
3275 4368 7.713507 CCCTCCGTTCACAATTATAAGATGTTA 59.286 37.037 4.41 0.00 0.00 2.41
3276 4369 8.548721 CCTCCGTTCACAATTATAAGATGTTAC 58.451 37.037 4.41 5.55 0.00 2.50
3296 4389 6.811665 TGTTACACTCTGAGATTAATTGTCGG 59.188 38.462 12.44 0.00 0.00 4.79
3297 4390 4.184629 ACACTCTGAGATTAATTGTCGGC 58.815 43.478 12.44 0.00 0.00 5.54
3403 4810 6.208599 ACATTTTATAACAGTGAACAGTGGGG 59.791 38.462 13.14 0.00 36.10 4.96
3439 4846 7.858052 AAGCTGATGTTTCAAAGAATTTACG 57.142 32.000 0.00 0.00 35.03 3.18
3490 4897 4.820897 TCCTTGTGTAGCAGTAACTCATG 58.179 43.478 0.00 0.00 0.00 3.07
3550 4959 7.067496 TGAGAAGTTTAACTGAGGAGAACAT 57.933 36.000 0.00 0.00 0.00 2.71
3555 4964 7.251321 AGTTTAACTGAGGAGAACATGATCT 57.749 36.000 4.99 4.99 0.00 2.75
3567 4976 7.508636 AGGAGAACATGATCTCTAGCTGAAATA 59.491 37.037 26.42 0.00 44.30 1.40
3571 4980 8.430801 AACATGATCTCTAGCTGAAATACAAC 57.569 34.615 0.00 0.00 0.00 3.32
3592 5001 6.653320 ACAACGGTAAATCATCAAGTACACAT 59.347 34.615 0.00 0.00 0.00 3.21
3595 5004 7.553334 ACGGTAAATCATCAAGTACACATACT 58.447 34.615 0.00 0.00 43.91 2.12
3596 5005 8.689061 ACGGTAAATCATCAAGTACACATACTA 58.311 33.333 0.00 0.00 41.00 1.82
3597 5006 9.181805 CGGTAAATCATCAAGTACACATACTAG 57.818 37.037 0.00 0.00 41.00 2.57
3719 5142 5.008911 TGAAACACAACACAGATGAGGAATG 59.991 40.000 0.00 0.00 0.00 2.67
3915 5339 2.185004 TTGCTTACCAGCCTGAAGAC 57.815 50.000 0.00 0.00 46.74 3.01
3930 5354 4.142816 CCTGAAGACCAATTTAGAGCAACG 60.143 45.833 0.00 0.00 0.00 4.10
3936 5360 2.414559 CCAATTTAGAGCAACGGCACAG 60.415 50.000 0.00 0.00 44.61 3.66
3973 5398 0.584876 GCAACGGTTAGCAAACGACT 59.415 50.000 12.23 0.00 36.39 4.18
4000 5425 2.171003 TCGATCAGAGTGCAGGAGAAA 58.829 47.619 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.778750 TCCCCTACTACCACTATTAGAATGC 59.221 44.000 0.00 0.00 0.00 3.56
2 3 7.674348 TGATCCCCTACTACCACTATTAGAATG 59.326 40.741 0.00 0.00 0.00 2.67
3 4 7.674772 GTGATCCCCTACTACCACTATTAGAAT 59.325 40.741 0.00 0.00 0.00 2.40
4 5 7.008941 GTGATCCCCTACTACCACTATTAGAA 58.991 42.308 0.00 0.00 0.00 2.10
5 6 6.468359 GGTGATCCCCTACTACCACTATTAGA 60.468 46.154 0.00 0.00 0.00 2.10
6 7 5.715753 GGTGATCCCCTACTACCACTATTAG 59.284 48.000 0.00 0.00 0.00 1.73
7 8 5.648247 GGTGATCCCCTACTACCACTATTA 58.352 45.833 0.00 0.00 0.00 0.98
8 9 4.490706 GGTGATCCCCTACTACCACTATT 58.509 47.826 0.00 0.00 0.00 1.73
9 10 4.129317 GGTGATCCCCTACTACCACTAT 57.871 50.000 0.00 0.00 0.00 2.12
10 11 3.607490 GGTGATCCCCTACTACCACTA 57.393 52.381 0.00 0.00 0.00 2.74
11 12 2.473576 GGTGATCCCCTACTACCACT 57.526 55.000 0.00 0.00 0.00 4.00
33 34 4.078516 CCTCCCGTGGGGTTCGTC 62.079 72.222 4.81 0.00 44.74 4.20
34 35 4.948080 ACCTCCCGTGGGGTTCGT 62.948 66.667 4.81 0.00 44.74 3.85
43 44 1.520666 CTATTTCGCCACCTCCCGT 59.479 57.895 0.00 0.00 0.00 5.28
45 46 1.148498 CCCTATTTCGCCACCTCCC 59.852 63.158 0.00 0.00 0.00 4.30
57 58 1.214305 TGGTGAAGCCAGGCCCTATT 61.214 55.000 8.22 0.00 43.61 1.73
86 87 3.594603 TTCTAGTGGTAGAACTGCAGC 57.405 47.619 15.27 0.00 39.86 5.25
87 88 5.140747 AGTTTCTAGTGGTAGAACTGCAG 57.859 43.478 13.48 13.48 43.63 4.41
88 89 6.008331 TCTAGTTTCTAGTGGTAGAACTGCA 58.992 40.000 4.13 0.00 43.63 4.41
119 120 1.076777 CCCAATGGATTGCGAGGGT 60.077 57.895 0.00 0.00 36.48 4.34
125 126 1.207811 CTTTGACCCCCAATGGATTGC 59.792 52.381 0.00 0.00 36.48 3.56
156 157 1.267121 TCTTGAGAAAGAGGTCCCCG 58.733 55.000 0.00 0.00 0.00 5.73
158 159 4.450053 CATCATCTTGAGAAAGAGGTCCC 58.550 47.826 0.69 0.00 32.85 4.46
162 163 4.444591 CCTCCCATCATCTTGAGAAAGAGG 60.445 50.000 0.00 0.00 31.48 3.69
167 168 1.492176 GCCCTCCCATCATCTTGAGAA 59.508 52.381 0.00 0.00 0.00 2.87
180 181 2.124693 CGAGAGACTGAGCCCTCCC 61.125 68.421 0.00 0.00 0.00 4.30
182 183 2.781158 GCCGAGAGACTGAGCCCTC 61.781 68.421 0.00 0.00 0.00 4.30
187 188 1.299014 GCATCGCCGAGAGACTGAG 60.299 63.158 0.00 0.00 0.00 3.35
198 199 2.417924 CCTACCTCATATGAGCATCGCC 60.418 54.545 24.81 0.00 40.75 5.54
199 200 2.417924 CCCTACCTCATATGAGCATCGC 60.418 54.545 24.81 0.00 40.75 4.58
200 201 2.417924 GCCCTACCTCATATGAGCATCG 60.418 54.545 24.81 14.61 40.75 3.84
201 202 2.417924 CGCCCTACCTCATATGAGCATC 60.418 54.545 24.81 10.25 40.75 3.91
202 203 1.552337 CGCCCTACCTCATATGAGCAT 59.448 52.381 24.81 17.43 40.75 3.79
215 216 3.411351 CACGCACACACGCCCTAC 61.411 66.667 0.00 0.00 36.19 3.18
229 230 2.357034 CGTCCCAGGGAACACACG 60.357 66.667 10.89 5.94 31.38 4.49
230 231 1.004918 CTCGTCCCAGGGAACACAC 60.005 63.158 10.89 0.00 31.38 3.82
231 232 1.458777 ACTCGTCCCAGGGAACACA 60.459 57.895 10.89 0.00 31.38 3.72
232 233 1.004918 CACTCGTCCCAGGGAACAC 60.005 63.158 10.89 0.00 31.38 3.32
233 234 0.178955 TACACTCGTCCCAGGGAACA 60.179 55.000 10.89 0.00 31.38 3.18
238 239 1.226974 CGCATACACTCGTCCCAGG 60.227 63.158 0.00 0.00 0.00 4.45
239 240 0.172578 TTCGCATACACTCGTCCCAG 59.827 55.000 0.00 0.00 0.00 4.45
240 241 0.604073 TTTCGCATACACTCGTCCCA 59.396 50.000 0.00 0.00 0.00 4.37
242 243 2.927477 TGATTTTCGCATACACTCGTCC 59.073 45.455 0.00 0.00 0.00 4.79
244 245 5.545658 ATTTGATTTTCGCATACACTCGT 57.454 34.783 0.00 0.00 0.00 4.18
245 246 5.167803 CGAATTTGATTTTCGCATACACTCG 59.832 40.000 0.00 0.00 39.43 4.18
255 256 4.739716 CCCAATAGCCGAATTTGATTTTCG 59.260 41.667 0.00 0.00 44.17 3.46
257 258 5.682212 GCTCCCAATAGCCGAATTTGATTTT 60.682 40.000 0.00 0.00 36.45 1.82
259 260 3.319122 GCTCCCAATAGCCGAATTTGATT 59.681 43.478 0.00 0.00 36.45 2.57
262 263 2.023673 TGCTCCCAATAGCCGAATTTG 58.976 47.619 0.00 0.00 42.05 2.32
263 264 2.435372 TGCTCCCAATAGCCGAATTT 57.565 45.000 0.00 0.00 42.05 1.82
287 288 3.967332 AACATTTTTGATGGGCAGGAG 57.033 42.857 0.00 0.00 0.00 3.69
326 340 9.853555 GTTTTGGTGTGACAATGATCATATTTA 57.146 29.630 9.04 0.00 0.00 1.40
327 341 7.541783 CGTTTTGGTGTGACAATGATCATATTT 59.458 33.333 9.04 0.00 0.00 1.40
328 342 7.028962 CGTTTTGGTGTGACAATGATCATATT 58.971 34.615 9.04 0.00 0.00 1.28
329 343 6.554419 CGTTTTGGTGTGACAATGATCATAT 58.446 36.000 9.04 0.00 0.00 1.78
330 344 5.618863 GCGTTTTGGTGTGACAATGATCATA 60.619 40.000 9.04 0.00 0.00 2.15
331 345 4.797471 CGTTTTGGTGTGACAATGATCAT 58.203 39.130 1.18 1.18 0.00 2.45
333 347 2.979813 GCGTTTTGGTGTGACAATGATC 59.020 45.455 0.00 0.00 0.00 2.92
334 348 2.288152 GGCGTTTTGGTGTGACAATGAT 60.288 45.455 0.00 0.00 0.00 2.45
346 360 1.679153 AGTTTACAGGTGGCGTTTTGG 59.321 47.619 0.00 0.00 0.00 3.28
350 364 3.566742 CCTAAAAGTTTACAGGTGGCGTT 59.433 43.478 7.67 0.00 0.00 4.84
355 369 6.294010 GCTTTCCTCCTAAAAGTTTACAGGTG 60.294 42.308 13.30 11.41 36.36 4.00
365 379 7.878644 ACAGTACTTAAGCTTTCCTCCTAAAAG 59.121 37.037 3.20 0.90 36.91 2.27
381 395 9.332502 TCTTTTTGCACAGATTACAGTACTTAA 57.667 29.630 0.00 0.00 0.00 1.85
385 399 7.913297 TGTTTCTTTTTGCACAGATTACAGTAC 59.087 33.333 0.00 0.00 0.00 2.73
388 402 7.489113 ACTTGTTTCTTTTTGCACAGATTACAG 59.511 33.333 0.00 0.00 0.00 2.74
390 404 7.305418 CGACTTGTTTCTTTTTGCACAGATTAC 60.305 37.037 0.00 0.00 0.00 1.89
392 406 5.516339 CGACTTGTTTCTTTTTGCACAGATT 59.484 36.000 0.00 0.00 0.00 2.40
406 420 3.891056 ATTTCCCGTTCGACTTGTTTC 57.109 42.857 0.00 0.00 0.00 2.78
460 484 2.223502 GGATGACAGTGCTTCGTCGATA 60.224 50.000 0.00 0.00 34.78 2.92
462 486 0.109272 GGATGACAGTGCTTCGTCGA 60.109 55.000 0.00 0.00 34.78 4.20
463 487 1.078759 GGGATGACAGTGCTTCGTCG 61.079 60.000 0.00 0.00 34.78 5.12
476 500 5.758296 GCTAATTCTATGTGAAACGGGATGA 59.242 40.000 0.00 0.00 42.39 2.92
487 511 5.808042 AGTGTGCTTGCTAATTCTATGTG 57.192 39.130 0.00 0.00 0.00 3.21
488 512 6.187125 CAAGTGTGCTTGCTAATTCTATGT 57.813 37.500 0.00 0.00 44.54 2.29
542 566 2.305927 CTCTAACCATCCAACCACAGGT 59.694 50.000 0.00 0.00 37.65 4.00
543 567 2.941415 GCTCTAACCATCCAACCACAGG 60.941 54.545 0.00 0.00 0.00 4.00
544 568 2.359900 GCTCTAACCATCCAACCACAG 58.640 52.381 0.00 0.00 0.00 3.66
545 569 1.004277 GGCTCTAACCATCCAACCACA 59.996 52.381 0.00 0.00 0.00 4.17
546 570 1.682087 GGGCTCTAACCATCCAACCAC 60.682 57.143 0.00 0.00 0.00 4.16
548 572 0.623723 TGGGCTCTAACCATCCAACC 59.376 55.000 0.00 0.00 31.83 3.77
549 573 2.736670 ATGGGCTCTAACCATCCAAC 57.263 50.000 0.00 0.00 45.33 3.77
565 589 2.702093 AGGACTTGACCCCTGATGG 58.298 57.895 0.00 0.00 0.00 3.51
570 594 2.753247 GAGTATCAGGACTTGACCCCT 58.247 52.381 0.00 0.00 38.99 4.79
571 595 1.409427 CGAGTATCAGGACTTGACCCC 59.591 57.143 0.00 0.00 38.99 4.95
572 596 1.202428 GCGAGTATCAGGACTTGACCC 60.202 57.143 0.00 0.00 38.99 4.46
573 597 1.476891 TGCGAGTATCAGGACTTGACC 59.523 52.381 0.00 0.00 38.99 4.02
574 598 2.941453 TGCGAGTATCAGGACTTGAC 57.059 50.000 0.00 0.00 38.99 3.18
575 599 5.791336 ATAATGCGAGTATCAGGACTTGA 57.209 39.130 0.00 0.00 40.85 3.02
576 600 5.985530 TGAATAATGCGAGTATCAGGACTTG 59.014 40.000 0.00 0.00 34.39 3.16
577 601 6.161855 TGAATAATGCGAGTATCAGGACTT 57.838 37.500 0.00 0.00 33.17 3.01
578 602 5.791336 TGAATAATGCGAGTATCAGGACT 57.209 39.130 0.00 0.00 33.17 3.85
579 603 5.928839 ACATGAATAATGCGAGTATCAGGAC 59.071 40.000 0.00 0.00 40.22 3.85
580 604 6.101650 ACATGAATAATGCGAGTATCAGGA 57.898 37.500 0.00 0.00 40.22 3.86
581 605 8.484641 AATACATGAATAATGCGAGTATCAGG 57.515 34.615 0.00 0.00 40.22 3.86
598 622 9.184523 ACCGAAAATCCTGAAATAAATACATGA 57.815 29.630 0.00 0.00 0.00 3.07
599 623 9.236691 CACCGAAAATCCTGAAATAAATACATG 57.763 33.333 0.00 0.00 0.00 3.21
600 624 9.184523 TCACCGAAAATCCTGAAATAAATACAT 57.815 29.630 0.00 0.00 0.00 2.29
601 625 8.568676 TCACCGAAAATCCTGAAATAAATACA 57.431 30.769 0.00 0.00 0.00 2.29
602 626 9.450807 CATCACCGAAAATCCTGAAATAAATAC 57.549 33.333 0.00 0.00 0.00 1.89
603 627 9.184523 ACATCACCGAAAATCCTGAAATAAATA 57.815 29.630 0.00 0.00 0.00 1.40
604 628 8.066612 ACATCACCGAAAATCCTGAAATAAAT 57.933 30.769 0.00 0.00 0.00 1.40
605 629 7.461182 ACATCACCGAAAATCCTGAAATAAA 57.539 32.000 0.00 0.00 0.00 1.40
606 630 7.827236 AGTACATCACCGAAAATCCTGAAATAA 59.173 33.333 0.00 0.00 0.00 1.40
607 631 7.335627 AGTACATCACCGAAAATCCTGAAATA 58.664 34.615 0.00 0.00 0.00 1.40
608 632 6.180472 AGTACATCACCGAAAATCCTGAAAT 58.820 36.000 0.00 0.00 0.00 2.17
609 633 5.556915 AGTACATCACCGAAAATCCTGAAA 58.443 37.500 0.00 0.00 0.00 2.69
610 634 5.160607 AGTACATCACCGAAAATCCTGAA 57.839 39.130 0.00 0.00 0.00 3.02
611 635 4.819105 AGTACATCACCGAAAATCCTGA 57.181 40.909 0.00 0.00 0.00 3.86
612 636 5.411361 TGAAAGTACATCACCGAAAATCCTG 59.589 40.000 0.00 0.00 0.00 3.86
613 637 5.556915 TGAAAGTACATCACCGAAAATCCT 58.443 37.500 0.00 0.00 0.00 3.24
614 638 5.869350 CTGAAAGTACATCACCGAAAATCC 58.131 41.667 0.00 0.00 0.00 3.01
631 655 0.969894 ACGTCTCCTCCCACTGAAAG 59.030 55.000 0.00 0.00 42.29 2.62
632 656 1.420430 AACGTCTCCTCCCACTGAAA 58.580 50.000 0.00 0.00 0.00 2.69
633 657 1.420430 AAACGTCTCCTCCCACTGAA 58.580 50.000 0.00 0.00 0.00 3.02
634 658 1.343465 GAAAACGTCTCCTCCCACTGA 59.657 52.381 0.00 0.00 0.00 3.41
635 659 1.797025 GAAAACGTCTCCTCCCACTG 58.203 55.000 0.00 0.00 0.00 3.66
636 660 0.317479 CGAAAACGTCTCCTCCCACT 59.683 55.000 0.00 0.00 0.00 4.00
637 661 0.669625 CCGAAAACGTCTCCTCCCAC 60.670 60.000 0.00 0.00 0.00 4.61
638 662 1.117142 ACCGAAAACGTCTCCTCCCA 61.117 55.000 0.00 0.00 0.00 4.37
639 663 0.669625 CACCGAAAACGTCTCCTCCC 60.670 60.000 0.00 0.00 0.00 4.30
640 664 0.316204 TCACCGAAAACGTCTCCTCC 59.684 55.000 0.00 0.00 0.00 4.30
641 665 1.993370 CATCACCGAAAACGTCTCCTC 59.007 52.381 0.00 0.00 0.00 3.71
642 666 1.343465 ACATCACCGAAAACGTCTCCT 59.657 47.619 0.00 0.00 0.00 3.69
643 667 1.792006 ACATCACCGAAAACGTCTCC 58.208 50.000 0.00 0.00 0.00 3.71
644 668 3.572584 AGTACATCACCGAAAACGTCTC 58.427 45.455 0.00 0.00 0.00 3.36
645 669 3.255149 AGAGTACATCACCGAAAACGTCT 59.745 43.478 0.00 0.00 0.00 4.18
646 670 3.364023 CAGAGTACATCACCGAAAACGTC 59.636 47.826 0.00 0.00 0.00 4.34
647 671 3.243636 ACAGAGTACATCACCGAAAACGT 60.244 43.478 0.00 0.00 0.00 3.99
648 672 3.314553 ACAGAGTACATCACCGAAAACG 58.685 45.455 0.00 0.00 0.00 3.60
649 673 6.774354 TTAACAGAGTACATCACCGAAAAC 57.226 37.500 0.00 0.00 0.00 2.43
650 674 7.972832 AATTAACAGAGTACATCACCGAAAA 57.027 32.000 0.00 0.00 0.00 2.29
651 675 7.972832 AAATTAACAGAGTACATCACCGAAA 57.027 32.000 0.00 0.00 0.00 3.46
652 676 7.972832 AAAATTAACAGAGTACATCACCGAA 57.027 32.000 0.00 0.00 0.00 4.30
653 677 9.661563 AATAAAATTAACAGAGTACATCACCGA 57.338 29.630 0.00 0.00 0.00 4.69
689 713 8.784043 GGCGACTTAATACTTTGGATTTATGAT 58.216 33.333 0.00 0.00 0.00 2.45
690 714 7.227910 GGGCGACTTAATACTTTGGATTTATGA 59.772 37.037 0.00 0.00 0.00 2.15
710 949 3.154589 AAAAAGATCTCCGGGCGAC 57.845 52.632 0.00 0.00 0.00 5.19
744 988 1.882623 CCATCGGATCAGATCTCACGA 59.117 52.381 10.36 10.88 34.70 4.35
773 1017 2.855660 TTTATCGATCTCGCCGTTCA 57.144 45.000 0.00 0.00 39.60 3.18
837 1081 3.438297 AGTATACAGGTGTGACGATGC 57.562 47.619 5.50 0.00 0.00 3.91
877 1121 2.356844 CCCCGACCCGATCTGATCTATA 60.357 54.545 15.16 0.00 0.00 1.31
878 1122 1.617263 CCCCGACCCGATCTGATCTAT 60.617 57.143 15.16 1.01 0.00 1.98
879 1123 0.251209 CCCCGACCCGATCTGATCTA 60.251 60.000 15.16 0.00 0.00 1.98
938 1182 0.032017 TAGGGAGAGGAACAGAGGGC 60.032 60.000 0.00 0.00 0.00 5.19
989 1233 1.801178 GCTTCTTTCCTGTGGAACTCG 59.199 52.381 0.00 0.00 41.87 4.18
1020 1264 3.197549 ACATCTTGCTCCTCTTCTTCCTC 59.802 47.826 0.00 0.00 0.00 3.71
1022 1266 3.530535 GACATCTTGCTCCTCTTCTTCC 58.469 50.000 0.00 0.00 0.00 3.46
1141 1385 0.030101 GTCGCTCGATCAAGGAGGAG 59.970 60.000 0.00 0.00 32.10 3.69
1142 1386 0.679960 TGTCGCTCGATCAAGGAGGA 60.680 55.000 0.00 0.00 32.10 3.71
1144 1388 0.863538 CGTGTCGCTCGATCAAGGAG 60.864 60.000 0.00 0.00 34.62 3.69
1145 1389 1.136774 CGTGTCGCTCGATCAAGGA 59.863 57.895 0.00 0.00 0.00 3.36
1159 1412 4.868314 ACTAGTTTTCTTCCTAGCGTGT 57.132 40.909 0.00 0.00 35.17 4.49
1163 1416 8.251721 TGACATCTAACTAGTTTTCTTCCTAGC 58.748 37.037 14.49 0.00 35.17 3.42
1164 1417 9.796120 CTGACATCTAACTAGTTTTCTTCCTAG 57.204 37.037 14.49 2.39 37.32 3.02
1166 1419 8.423906 TCTGACATCTAACTAGTTTTCTTCCT 57.576 34.615 14.49 0.00 0.00 3.36
1167 1420 7.762159 CCTCTGACATCTAACTAGTTTTCTTCC 59.238 40.741 14.49 1.06 0.00 3.46
1168 1421 7.762159 CCCTCTGACATCTAACTAGTTTTCTTC 59.238 40.741 14.49 5.37 0.00 2.87
1169 1422 7.235812 ACCCTCTGACATCTAACTAGTTTTCTT 59.764 37.037 14.49 0.00 0.00 2.52
1170 1423 6.726764 ACCCTCTGACATCTAACTAGTTTTCT 59.273 38.462 14.49 0.00 0.00 2.52
1171 1424 6.937392 ACCCTCTGACATCTAACTAGTTTTC 58.063 40.000 14.49 4.02 0.00 2.29
1175 1428 4.957327 GGAACCCTCTGACATCTAACTAGT 59.043 45.833 0.00 0.00 0.00 2.57
1178 1431 4.027437 GAGGAACCCTCTGACATCTAACT 58.973 47.826 5.78 0.00 46.41 2.24
1179 1432 4.394439 GAGGAACCCTCTGACATCTAAC 57.606 50.000 5.78 0.00 46.41 2.34
1195 1455 2.226149 GACCGGAGAGGGGAGAGGAA 62.226 65.000 9.46 0.00 46.96 3.36
1325 1845 1.804601 ACGAAACCGGTCAAATCTCC 58.195 50.000 8.04 0.00 0.00 3.71
1418 1939 1.550327 TGGACTTCATGACGAGCTCT 58.450 50.000 12.85 0.00 0.00 4.09
1460 1981 1.141019 GCCGTAGATTCCGAGCACA 59.859 57.895 0.00 0.00 0.00 4.57
1648 2169 5.291971 AGTCAAACAAATAAAAGCAGCAGG 58.708 37.500 0.00 0.00 0.00 4.85
1707 2228 4.023963 CAGCACTAACTAGCTACGAGCATA 60.024 45.833 9.09 0.15 45.56 3.14
1850 2371 9.899661 TTTGTAGAAATACATGCTACTACCAAT 57.100 29.630 8.35 0.00 36.38 3.16
1856 2377 6.338146 TCGCTTTGTAGAAATACATGCTACT 58.662 36.000 8.35 0.00 36.38 2.57
1869 2390 8.380644 CGAAAGAAATAATTCTCGCTTTGTAGA 58.619 33.333 0.00 0.00 45.19 2.59
1892 2413 7.706100 AATTACCCAGGCTAAAAATAACGAA 57.294 32.000 0.00 0.00 0.00 3.85
1899 2420 6.941436 TCGTTCTTAATTACCCAGGCTAAAAA 59.059 34.615 0.00 0.00 0.00 1.94
1900 2421 6.474630 TCGTTCTTAATTACCCAGGCTAAAA 58.525 36.000 0.00 0.00 0.00 1.52
1907 2428 7.048512 AGGAGATTTCGTTCTTAATTACCCAG 58.951 38.462 0.00 0.00 0.00 4.45
1910 2431 9.813446 TTCTAGGAGATTTCGTTCTTAATTACC 57.187 33.333 0.00 0.00 0.00 2.85
2026 2655 8.353684 AGAGATAATTCCATAGTCACAAGTACG 58.646 37.037 0.00 0.00 0.00 3.67
2074 2703 2.031682 AGTCACTTGCGATGTTTTCTGC 60.032 45.455 0.00 0.00 0.00 4.26
2205 2835 5.354842 ACTTAAGGTAGTGCCCTCAATAC 57.645 43.478 7.53 0.00 41.54 1.89
2217 2847 9.893305 CAAAGACCAAACAATAACTTAAGGTAG 57.107 33.333 6.37 0.00 0.00 3.18
2316 2955 9.507280 CTTTCGAATGTAAATCTGCAATATTGT 57.493 29.630 16.61 0.00 0.00 2.71
2438 3469 9.880157 GTAACTGTTCCAAATAGTAATACTCCA 57.120 33.333 0.00 0.00 32.16 3.86
2472 3503 5.668471 ACACTGATCAACCACATCATAGAG 58.332 41.667 0.00 0.00 29.78 2.43
2497 3528 5.323371 TGAAACTGAAAAACTGTGAAGGG 57.677 39.130 0.00 0.00 0.00 3.95
2611 3643 2.026014 AGCTTTGGTTGTTGCGCG 59.974 55.556 0.00 0.00 0.00 6.86
2638 3670 6.768483 TGCGAAAATGAGGATAAGGATCATA 58.232 36.000 0.00 0.00 33.27 2.15
2876 3908 2.419436 CCCACCACAACCCAAAAAGAAC 60.419 50.000 0.00 0.00 0.00 3.01
2950 3982 8.221944 CCACCAGTAGGATTAAAACCCATATAA 58.778 37.037 0.00 0.00 38.69 0.98
2951 3983 7.351454 ACCACCAGTAGGATTAAAACCCATATA 59.649 37.037 0.00 0.00 38.69 0.86
3068 4101 8.635765 TTTCTAACCATGCAGAAAAAGAGTAT 57.364 30.769 10.98 0.00 37.72 2.12
3165 4201 4.158394 CCATGCTACACATAAGCCAAGTTT 59.842 41.667 0.00 0.00 39.30 2.66
3168 4204 2.033801 GCCATGCTACACATAAGCCAAG 59.966 50.000 0.00 0.00 39.30 3.61
3251 4344 9.093970 TGTAACATCTTATAATTGTGAACGGAG 57.906 33.333 2.86 0.00 0.00 4.63
3273 4366 5.810587 GCCGACAATTAATCTCAGAGTGTAA 59.189 40.000 0.00 0.00 0.00 2.41
3275 4368 4.184629 GCCGACAATTAATCTCAGAGTGT 58.815 43.478 0.00 0.00 0.00 3.55
3276 4369 3.243877 CGCCGACAATTAATCTCAGAGTG 59.756 47.826 0.00 0.00 0.00 3.51
3282 4375 6.526566 ACTAAATCGCCGACAATTAATCTC 57.473 37.500 0.00 0.00 0.00 2.75
3296 4389 6.035758 CCCTCTACAACTTTGTACTAAATCGC 59.964 42.308 0.00 0.00 42.35 4.58
3297 4390 7.318141 TCCCTCTACAACTTTGTACTAAATCG 58.682 38.462 0.00 0.00 42.35 3.34
3374 4781 9.950680 CACTGTTCACTGTTATAAAATGTTTCT 57.049 29.630 0.00 0.00 0.00 2.52
3375 4782 9.180678 CCACTGTTCACTGTTATAAAATGTTTC 57.819 33.333 0.00 0.00 0.00 2.78
3403 4810 7.816640 TGAAACATCAGCTTTTAGAATGTACC 58.183 34.615 0.00 0.00 0.00 3.34
3439 4846 6.997942 AGGTTCTGGGTATTAGTTATCTCC 57.002 41.667 0.00 0.00 0.00 3.71
3490 4897 4.959596 ATCTTGCTGTCATGATTCACAC 57.040 40.909 0.00 0.00 34.56 3.82
3550 4959 5.127194 ACCGTTGTATTTCAGCTAGAGATCA 59.873 40.000 0.00 0.00 0.00 2.92
3555 4964 7.324935 TGATTTACCGTTGTATTTCAGCTAGA 58.675 34.615 0.00 0.00 0.00 2.43
3567 4976 5.992829 TGTGTACTTGATGATTTACCGTTGT 59.007 36.000 0.00 0.00 0.00 3.32
3571 4980 9.181805 CTAGTATGTGTACTTGATGATTTACCG 57.818 37.037 0.00 0.00 41.35 4.02
3595 5004 7.985752 TCGAGACAGACAGTATATTGAACTCTA 59.014 37.037 1.74 0.00 0.00 2.43
3596 5005 6.824196 TCGAGACAGACAGTATATTGAACTCT 59.176 38.462 1.74 0.00 0.00 3.24
3597 5006 7.017498 TCGAGACAGACAGTATATTGAACTC 57.983 40.000 1.74 0.00 0.00 3.01
3598 5007 7.255312 GGATCGAGACAGACAGTATATTGAACT 60.255 40.741 1.74 0.00 0.00 3.01
3915 5339 1.539388 TGTGCCGTTGCTCTAAATTGG 59.461 47.619 0.00 0.00 38.71 3.16
3930 5354 2.476185 GCGTGATTGATTGTACTGTGCC 60.476 50.000 0.00 0.00 0.00 5.01
3936 5360 1.127766 TGCACGCGTGATTGATTGTAC 59.872 47.619 41.19 19.88 0.00 2.90
3962 5387 5.407084 TGATCGAATTTTCAGTCGTTTGCTA 59.593 36.000 0.00 0.00 41.31 3.49
3963 5388 4.213270 TGATCGAATTTTCAGTCGTTTGCT 59.787 37.500 0.00 0.00 41.31 3.91
3973 5398 3.686241 CCTGCACTCTGATCGAATTTTCA 59.314 43.478 0.00 0.00 0.00 2.69
4000 5425 2.184167 CGTTGGCAAAGGTCCGTGT 61.184 57.895 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.