Multiple sequence alignment - TraesCS2A01G214600

Loading Multiple Alignment...

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 TraesCS2A01G214600 chr2A 100.000 2662 0 0 1 2662 200628162 200625501 0.000000e+00 4916.0
1 TraesCS2A01G214600 chr2A 88.205 195 23 0 1001 1195 200920151 200919957 1.590000e-57 233.0
2 TraesCS2A01G214600 chr2D 89.757 1972 105 34 702 2662 187648845 187646960 0.000000e+00 2433.0
3 TraesCS2A01G214600 chr2D 88.205 195 23 0 1001 1195 187969805 187969611 1.590000e-57 233.0
4 TraesCS2A01G214600 chr2B 89.108 1625 90 42 702 2318 243791128 243789583 0.000000e+00 1940.0
5 TraesCS2A01G214600 chr2B 89.565 230 24 0 2 231 243793659 243793430 2.590000e-75 292.0
6 TraesCS2A01G214600 chr2B 88.718 195 22 0 1001 1195 243830778 243830584 3.420000e-59 239.0
7 TraesCS2A01G214600 chr2B 85.909 220 8 3 2444 2662 243789535 243789338 2.080000e-51 213.0
8 TraesCS2A01G214600 chr2B 100.000 30 0 0 2356 2385 243789586 243789557 3.700000e-04 56.5
9 TraesCS2A01G214600 chr5A 84.073 383 50 6 241 620 168418223 168418597 2.520000e-95 359.0
10 TraesCS2A01G214600 chr5D 82.632 380 58 4 245 623 136493365 136492993 1.980000e-86 329.0
11 TraesCS2A01G214600 chr5B 82.474 388 54 10 244 626 149581236 149580858 7.110000e-86 327.0
12 TraesCS2A01G214600 chr6D 86.364 176 24 0 1450 1625 463478762 463478587 2.700000e-45 193.0
13 TraesCS2A01G214600 chr6D 82.418 182 32 0 1443 1624 24001851 24002032 2.740000e-35 159.0
14 TraesCS2A01G214600 chr6B 86.364 176 24 0 1450 1625 706746999 706746824 2.700000e-45 193.0
15 TraesCS2A01G214600 chr6A 85.795 176 25 0 1450 1625 609983186 609983011 1.260000e-43 187.0
16 TraesCS2A01G214600 chr6A 82.682 179 29 2 1443 1620 22522968 22523145 9.860000e-35 158.0
17 TraesCS2A01G214600 chr4B 83.784 185 30 0 47 231 315632668 315632484 2.720000e-40 176.0
18 TraesCS2A01G214600 chr7B 87.313 134 17 0 1061 1194 677538701 677538568 1.280000e-33 154.0
19 TraesCS2A01G214600 chr7B 85.821 134 19 0 1061 1194 677667863 677667730 2.760000e-30 143.0
20 TraesCS2A01G214600 chr7A 86.232 138 17 1 1061 1196 690918422 690918285 5.940000e-32 148.0
21 TraesCS2A01G214600 chr7A 86.232 138 17 1 1061 1196 690930192 690930055 5.940000e-32 148.0
22 TraesCS2A01G214600 chr1A 81.026 195 30 6 1433 1624 21023090 21023280 5.940000e-32 148.0
23 TraesCS2A01G214600 chr3A 81.319 182 32 2 1443 1623 746261686 746261866 2.140000e-31 147.0


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 TraesCS2A01G214600 chr2A 200625501 200628162 2661 True 4916.000 4916 100.0000 1 2662 1 chr2A.!!$R1 2661
1 TraesCS2A01G214600 chr2D 187646960 187648845 1885 True 2433.000 2433 89.7570 702 2662 1 chr2D.!!$R1 1960
2 TraesCS2A01G214600 chr2B 243789338 243793659 4321 True 625.375 1940 91.1455 2 2662 4 chr2B.!!$R2 2660

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
476 527 0.034089 AAGCCACCATCCCTTGCTAC 60.034 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 4030 0.109723 TTCCCGCCTAAGCACTGTTT 59.89 50.0 0.0 0.0 39.83 2.83 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 1.053424 GCAACCTATCCGGGGTATGA 58.947 55.000 0.00 0.00 35.83 2.15
38 39 0.254747 CCGGGGTATGAAAGGCAAGA 59.745 55.000 0.00 0.00 0.00 3.02
72 73 9.578439 CCAAAATAAAAATCTTTTTGTGGCAAA 57.422 25.926 10.19 0.00 40.33 3.68
108 109 2.357517 CGAGTGGTGACCAGGTGC 60.358 66.667 3.58 0.00 32.34 5.01
110 111 1.302033 GAGTGGTGACCAGGTGCAG 60.302 63.158 3.58 0.00 32.34 4.41
122 123 2.546584 CCAGGTGCAGAAAAGAAAAGGC 60.547 50.000 0.00 0.00 0.00 4.35
124 125 1.270305 GGTGCAGAAAAGAAAAGGCCC 60.270 52.381 0.00 0.00 0.00 5.80
161 162 1.144691 TCTGGTGTGGGGAATGTGAA 58.855 50.000 0.00 0.00 0.00 3.18
166 167 2.009774 GTGTGGGGAATGTGAAGATCG 58.990 52.381 0.00 0.00 0.00 3.69
181 182 6.698766 TGTGAAGATCGTGATCACATCTTATG 59.301 38.462 31.40 16.32 46.11 1.90
184 185 5.456265 AGATCGTGATCACATCTTATGTCG 58.544 41.667 24.93 7.60 42.70 4.35
191 192 5.636543 TGATCACATCTTATGTCGATGCATC 59.363 40.000 17.10 17.10 42.70 3.91
199 200 2.281002 TCGATGCATCATGGCCCG 60.281 61.111 25.70 11.14 0.00 6.13
212 213 1.303317 GGCCCGATTTGTGTGGAGT 60.303 57.895 0.00 0.00 0.00 3.85
215 216 1.586154 CCCGATTTGTGTGGAGTGCC 61.586 60.000 0.00 0.00 0.00 5.01
225 226 2.201708 TGGAGTGCCGTACGGACAA 61.202 57.895 37.62 18.91 37.50 3.18
228 229 1.135024 GGAGTGCCGTACGGACAATAA 60.135 52.381 37.62 11.89 37.50 1.40
231 232 2.067766 GTGCCGTACGGACAATAACAA 58.932 47.619 37.62 8.34 37.50 2.83
232 233 2.479656 GTGCCGTACGGACAATAACAAA 59.520 45.455 37.62 7.64 37.50 2.83
234 235 2.479656 GCCGTACGGACAATAACAAACA 59.520 45.455 37.62 0.00 37.50 2.83
235 236 3.059051 GCCGTACGGACAATAACAAACAA 60.059 43.478 37.62 0.00 37.50 2.83
236 237 4.378666 GCCGTACGGACAATAACAAACAAT 60.379 41.667 37.62 0.00 37.50 2.71
237 238 5.318349 CCGTACGGACAATAACAAACAATC 58.682 41.667 30.64 0.00 37.50 2.67
238 239 5.121142 CCGTACGGACAATAACAAACAATCT 59.879 40.000 30.64 0.00 37.50 2.40
239 240 6.347888 CCGTACGGACAATAACAAACAATCTT 60.348 38.462 30.64 0.00 37.50 2.40
241 242 8.222433 CGTACGGACAATAACAAACAATCTTTA 58.778 33.333 7.57 0.00 0.00 1.85
242 243 9.321590 GTACGGACAATAACAAACAATCTTTAC 57.678 33.333 0.00 0.00 0.00 2.01
243 244 7.364970 ACGGACAATAACAAACAATCTTTACC 58.635 34.615 0.00 0.00 0.00 2.85
244 245 6.521821 CGGACAATAACAAACAATCTTTACCG 59.478 38.462 0.00 0.00 0.00 4.02
245 246 6.307077 GGACAATAACAAACAATCTTTACCGC 59.693 38.462 0.00 0.00 0.00 5.68
246 247 6.740110 ACAATAACAAACAATCTTTACCGCA 58.260 32.000 0.00 0.00 0.00 5.69
247 248 7.375053 ACAATAACAAACAATCTTTACCGCAT 58.625 30.769 0.00 0.00 0.00 4.73
249 250 4.173036 ACAAACAATCTTTACCGCATGG 57.827 40.909 0.00 0.00 42.84 3.66
259 260 2.358125 CCGCATGGTCACGTTGGA 60.358 61.111 0.00 0.00 0.00 3.53
260 261 1.745115 CCGCATGGTCACGTTGGAT 60.745 57.895 0.00 0.00 0.00 3.41
261 262 0.461163 CCGCATGGTCACGTTGGATA 60.461 55.000 0.00 0.00 0.00 2.59
263 264 1.062002 CGCATGGTCACGTTGGATAAC 59.938 52.381 0.00 0.00 0.00 1.89
264 265 2.080693 GCATGGTCACGTTGGATAACA 58.919 47.619 0.00 0.00 36.58 2.41
292 343 7.503902 GGAATAAAGCTTTGATAGAGGGACAAT 59.496 37.037 22.02 0.00 0.00 2.71
305 356 4.720773 AGAGGGACAATTCATCAGACATCT 59.279 41.667 0.00 0.00 0.00 2.90
306 357 4.778579 AGGGACAATTCATCAGACATCTG 58.221 43.478 2.24 2.24 45.08 2.90
325 376 9.539825 GACATCTGACTGATCTGTTATACAAAT 57.460 33.333 6.70 0.00 32.05 2.32
326 377 9.896645 ACATCTGACTGATCTGTTATACAAATT 57.103 29.630 6.70 0.00 32.05 1.82
346 397 5.557891 ATTGATGTCTTTCTTGCAGCTAC 57.442 39.130 0.00 0.00 0.00 3.58
347 398 4.006780 TGATGTCTTTCTTGCAGCTACA 57.993 40.909 0.00 0.00 0.00 2.74
365 416 5.476752 CTACAGAAGCTACTGGCAAAATC 57.523 43.478 0.00 0.00 44.79 2.17
366 417 3.754965 ACAGAAGCTACTGGCAAAATCA 58.245 40.909 0.00 0.00 44.79 2.57
367 418 3.503748 ACAGAAGCTACTGGCAAAATCAC 59.496 43.478 0.00 0.00 44.79 3.06
368 419 3.503363 CAGAAGCTACTGGCAAAATCACA 59.497 43.478 0.00 0.00 44.79 3.58
369 420 3.755378 AGAAGCTACTGGCAAAATCACAG 59.245 43.478 0.00 0.00 44.79 3.66
370 421 2.440409 AGCTACTGGCAAAATCACAGG 58.560 47.619 0.00 0.00 44.79 4.00
371 422 2.040278 AGCTACTGGCAAAATCACAGGA 59.960 45.455 0.00 0.00 44.79 3.86
372 423 2.162408 GCTACTGGCAAAATCACAGGAC 59.838 50.000 0.00 0.00 41.35 3.85
373 424 2.363306 ACTGGCAAAATCACAGGACA 57.637 45.000 0.00 0.00 36.57 4.02
374 425 2.665165 ACTGGCAAAATCACAGGACAA 58.335 42.857 0.00 0.00 36.57 3.18
375 426 3.030291 ACTGGCAAAATCACAGGACAAA 58.970 40.909 0.00 0.00 36.57 2.83
376 427 3.450457 ACTGGCAAAATCACAGGACAAAA 59.550 39.130 0.00 0.00 36.57 2.44
377 428 4.053295 CTGGCAAAATCACAGGACAAAAG 58.947 43.478 0.00 0.00 0.00 2.27
378 429 3.703556 TGGCAAAATCACAGGACAAAAGA 59.296 39.130 0.00 0.00 0.00 2.52
382 433 5.754890 GCAAAATCACAGGACAAAAGAACAT 59.245 36.000 0.00 0.00 0.00 2.71
385 436 7.581213 AAATCACAGGACAAAAGAACATGTA 57.419 32.000 0.00 0.00 0.00 2.29
387 438 5.924356 TCACAGGACAAAAGAACATGTAGA 58.076 37.500 0.00 0.00 0.00 2.59
402 453 3.006112 TGTAGAGGAGCTCGTCTCAAT 57.994 47.619 35.35 18.88 43.70 2.57
415 466 0.674581 TCTCAATGGTGCGAGCAAGG 60.675 55.000 0.00 0.00 0.00 3.61
450 501 2.419324 GACGTTCGACATAGGAGACACT 59.581 50.000 0.00 0.00 0.00 3.55
453 504 3.242673 CGTTCGACATAGGAGACACTACC 60.243 52.174 0.00 0.00 0.00 3.18
454 505 2.558378 TCGACATAGGAGACACTACCG 58.442 52.381 0.00 0.00 0.00 4.02
462 513 2.167398 GAGACACTACCGGCAAGCCA 62.167 60.000 12.19 0.00 35.37 4.75
465 516 3.246112 ACTACCGGCAAGCCACCA 61.246 61.111 12.19 0.00 35.37 4.17
466 517 2.272146 CTACCGGCAAGCCACCAT 59.728 61.111 12.19 0.00 35.37 3.55
471 522 2.037847 GGCAAGCCACCATCCCTT 59.962 61.111 6.14 0.00 35.81 3.95
476 527 0.034089 AAGCCACCATCCCTTGCTAC 60.034 55.000 0.00 0.00 0.00 3.58
479 530 1.227383 CACCATCCCTTGCTACCCC 59.773 63.158 0.00 0.00 0.00 4.95
492 543 1.969208 GCTACCCCGATAGCCTTTAGT 59.031 52.381 2.84 0.00 41.55 2.24
493 544 2.288886 GCTACCCCGATAGCCTTTAGTG 60.289 54.545 2.84 0.00 41.55 2.74
494 545 1.875488 ACCCCGATAGCCTTTAGTGT 58.125 50.000 0.00 0.00 0.00 3.55
498 2304 3.626217 CCCCGATAGCCTTTAGTGTTTTC 59.374 47.826 0.00 0.00 0.00 2.29
520 2326 4.514066 TCTTCATCGTCTATGCTAGCGTTA 59.486 41.667 16.03 5.89 35.38 3.18
544 2350 2.095364 CCGCTATATTAGTCGCCTTCGT 60.095 50.000 0.00 0.00 36.96 3.85
565 2371 5.641636 TCGTGCATGTATCTCTTTTGCTTTA 59.358 36.000 5.68 0.00 34.47 1.85
576 2382 6.630071 TCTCTTTTGCTTTACTTTGTTGCTT 58.370 32.000 0.00 0.00 0.00 3.91
578 2384 4.856115 TTTGCTTTACTTTGTTGCTTGC 57.144 36.364 0.00 0.00 0.00 4.01
583 2389 5.518487 TGCTTTACTTTGTTGCTTGCTAAAC 59.482 36.000 0.00 0.00 0.00 2.01
588 2394 5.418676 ACTTTGTTGCTTGCTAAACATTGT 58.581 33.333 0.53 0.00 36.26 2.71
597 2403 5.051508 GCTTGCTAAACATTGTGTCACTTTG 60.052 40.000 4.27 4.54 0.00 2.77
620 2426 3.756434 ACGGACATGTTGGATTTGTAAGG 59.244 43.478 0.00 0.00 0.00 2.69
628 2440 5.636123 TGTTGGATTTGTAAGGGCTTAAGA 58.364 37.500 6.67 0.00 0.00 2.10
638 2450 0.681243 GGGCTTAAGACCAGGCAAGG 60.681 60.000 23.34 0.00 44.76 3.61
658 2474 3.056035 AGGGCCTCTAGAAAAACACGTAG 60.056 47.826 0.00 0.00 0.00 3.51
661 2477 3.995048 GCCTCTAGAAAAACACGTAGCTT 59.005 43.478 0.00 0.00 0.00 3.74
663 2479 5.389620 GCCTCTAGAAAAACACGTAGCTTTC 60.390 44.000 0.00 0.00 0.00 2.62
664 2480 5.927115 CCTCTAGAAAAACACGTAGCTTTCT 59.073 40.000 17.11 17.11 40.36 2.52
665 2481 6.424207 CCTCTAGAAAAACACGTAGCTTTCTT 59.576 38.462 17.79 7.44 38.65 2.52
667 2483 8.876275 TCTAGAAAAACACGTAGCTTTCTTAA 57.124 30.769 17.79 8.32 38.65 1.85
676 2492 7.764331 ACACGTAGCTTTCTTAAAAGGAAAAA 58.236 30.769 0.00 0.00 41.87 1.94
699 2522 0.107848 ACAGCCGAATAGAAACCCCG 60.108 55.000 0.00 0.00 0.00 5.73
704 2554 1.296727 CGAATAGAAACCCCGAAGCC 58.703 55.000 0.00 0.00 0.00 4.35
771 2621 1.068921 CAAAAACCAACCGCCCCAG 59.931 57.895 0.00 0.00 0.00 4.45
848 2698 4.498520 CACCGATCCGCGCACTCT 62.499 66.667 8.75 0.00 39.11 3.24
990 2840 4.918201 CGCGGATCCCCTCCAAGC 62.918 72.222 6.06 0.36 45.24 4.01
1068 2918 1.994507 CTCCAGGAGCTCCAAGGCT 60.995 63.158 33.90 10.85 46.11 4.58
1207 3057 2.415512 GAGGTGCGTGGAATTCTGTTAC 59.584 50.000 5.23 0.00 0.00 2.50
1216 3066 1.947456 GAATTCTGTTACCCGATGCCC 59.053 52.381 0.00 0.00 0.00 5.36
1226 3076 1.666209 CCCGATGCCCGATTTTGCTT 61.666 55.000 0.00 0.00 41.76 3.91
1227 3077 0.248621 CCGATGCCCGATTTTGCTTC 60.249 55.000 0.00 0.00 41.76 3.86
1231 3081 2.437200 TGCCCGATTTTGCTTCTTTG 57.563 45.000 0.00 0.00 0.00 2.77
1232 3082 1.000731 TGCCCGATTTTGCTTCTTTGG 59.999 47.619 0.00 0.00 0.00 3.28
1260 3111 1.461091 TTCGAGCGGTTGGTGTCTCT 61.461 55.000 1.22 0.00 0.00 3.10
1262 3113 0.600255 CGAGCGGTTGGTGTCTCTTT 60.600 55.000 0.00 0.00 0.00 2.52
1263 3114 1.149148 GAGCGGTTGGTGTCTCTTTC 58.851 55.000 0.00 0.00 0.00 2.62
1265 3116 1.566018 GCGGTTGGTGTCTCTTTCGG 61.566 60.000 0.00 0.00 0.00 4.30
1266 3117 0.249741 CGGTTGGTGTCTCTTTCGGT 60.250 55.000 0.00 0.00 0.00 4.69
1267 3118 1.509703 GGTTGGTGTCTCTTTCGGTC 58.490 55.000 0.00 0.00 0.00 4.79
1268 3119 1.070289 GGTTGGTGTCTCTTTCGGTCT 59.930 52.381 0.00 0.00 0.00 3.85
1269 3120 2.405172 GTTGGTGTCTCTTTCGGTCTC 58.595 52.381 0.00 0.00 0.00 3.36
1270 3121 0.596577 TGGTGTCTCTTTCGGTCTCG 59.403 55.000 0.00 0.00 37.82 4.04
1271 3122 0.597072 GGTGTCTCTTTCGGTCTCGT 59.403 55.000 0.00 0.00 37.69 4.18
1272 3123 1.401278 GGTGTCTCTTTCGGTCTCGTC 60.401 57.143 0.00 0.00 37.69 4.20
1273 3124 1.266175 GTGTCTCTTTCGGTCTCGTCA 59.734 52.381 0.00 0.00 37.69 4.35
1274 3125 1.951602 TGTCTCTTTCGGTCTCGTCAA 59.048 47.619 0.00 0.00 37.69 3.18
1330 3181 3.840124 AGGGTTTCGGATGAGGATAAC 57.160 47.619 0.00 0.00 0.00 1.89
1365 3216 1.065564 GCTCTCAGATTTGTCTGGGCT 60.066 52.381 5.68 0.00 38.09 5.19
1382 3233 0.955919 GCTTAGGCGGTTCTGCTTGT 60.956 55.000 3.62 0.00 34.52 3.16
1396 3247 3.433274 TCTGCTTGTTAATTGCACTCGAG 59.567 43.478 11.84 11.84 32.91 4.04
1423 3274 3.004944 TGTGGAATTTTGGAAGTAACCGC 59.995 43.478 0.00 0.00 0.00 5.68
1432 3283 1.641577 GAAGTAACCGCTGCGATTCT 58.358 50.000 25.45 11.93 0.00 2.40
1840 3697 3.440173 GTGTGGACAATGGTTACATCCTG 59.560 47.826 0.00 0.00 35.94 3.86
1863 3720 3.976942 TGTAAGTCGTTGCTAGTTCGTTC 59.023 43.478 0.00 0.00 0.00 3.95
1897 3754 3.002656 CACCTATGGATTGCTTACTTGCG 59.997 47.826 0.00 0.00 35.36 4.85
1922 3779 5.367945 TTTCTACCACTCTGTTCTTGGTT 57.632 39.130 0.00 0.00 40.98 3.67
1948 3805 7.178983 TGAAAATTTCCATGGTCTATTCTTGCT 59.821 33.333 12.58 0.00 0.00 3.91
1984 3841 7.108841 TGGTTAGAAAACTCGATATAGCTGT 57.891 36.000 0.00 0.00 35.81 4.40
2024 3881 9.643693 AAATTAATCTGTGAAGCTGTATTTTGG 57.356 29.630 0.00 0.00 0.00 3.28
2025 3882 4.708726 ATCTGTGAAGCTGTATTTTGGC 57.291 40.909 0.00 0.00 0.00 4.52
2026 3883 3.485394 TCTGTGAAGCTGTATTTTGGCA 58.515 40.909 0.00 0.00 0.00 4.92
2027 3884 4.081406 TCTGTGAAGCTGTATTTTGGCAT 58.919 39.130 0.00 0.00 0.00 4.40
2028 3885 4.523943 TCTGTGAAGCTGTATTTTGGCATT 59.476 37.500 0.00 0.00 0.00 3.56
2029 3886 5.709631 TCTGTGAAGCTGTATTTTGGCATTA 59.290 36.000 0.00 0.00 0.00 1.90
2030 3887 5.953183 TGTGAAGCTGTATTTTGGCATTAG 58.047 37.500 0.00 0.00 0.00 1.73
2031 3888 5.476599 TGTGAAGCTGTATTTTGGCATTAGT 59.523 36.000 0.00 0.00 0.00 2.24
2032 3889 6.030228 GTGAAGCTGTATTTTGGCATTAGTC 58.970 40.000 0.00 0.00 0.00 2.59
2033 3890 5.945784 TGAAGCTGTATTTTGGCATTAGTCT 59.054 36.000 0.00 0.00 0.00 3.24
2034 3891 6.434028 TGAAGCTGTATTTTGGCATTAGTCTT 59.566 34.615 0.00 0.00 0.00 3.01
2035 3892 6.199937 AGCTGTATTTTGGCATTAGTCTTG 57.800 37.500 0.00 0.00 0.00 3.02
2036 3893 5.126061 AGCTGTATTTTGGCATTAGTCTTGG 59.874 40.000 0.00 0.00 0.00 3.61
2037 3894 5.105756 GCTGTATTTTGGCATTAGTCTTGGT 60.106 40.000 0.00 0.00 0.00 3.67
2038 3895 6.094881 GCTGTATTTTGGCATTAGTCTTGGTA 59.905 38.462 0.00 0.00 0.00 3.25
2039 3896 7.362574 GCTGTATTTTGGCATTAGTCTTGGTAA 60.363 37.037 0.00 0.00 0.00 2.85
2040 3897 7.822658 TGTATTTTGGCATTAGTCTTGGTAAC 58.177 34.615 0.00 0.00 0.00 2.50
2041 3898 7.668052 TGTATTTTGGCATTAGTCTTGGTAACT 59.332 33.333 0.00 0.00 37.61 2.24
2042 3899 6.969993 TTTTGGCATTAGTCTTGGTAACTT 57.030 33.333 0.00 0.00 37.61 2.66
2043 3900 6.969993 TTTGGCATTAGTCTTGGTAACTTT 57.030 33.333 0.00 0.00 37.61 2.66
2044 3901 6.969993 TTGGCATTAGTCTTGGTAACTTTT 57.030 33.333 0.00 0.00 37.61 2.27
2045 3902 6.569179 TGGCATTAGTCTTGGTAACTTTTC 57.431 37.500 0.00 0.00 37.61 2.29
2061 3921 2.736144 TTTCGACTACGGATGTGCTT 57.264 45.000 0.00 0.00 40.21 3.91
2063 3923 2.273370 TCGACTACGGATGTGCTTTC 57.727 50.000 0.00 0.00 40.21 2.62
2075 3935 4.462483 GGATGTGCTTTCCTTTACAATCCA 59.538 41.667 0.00 0.00 0.00 3.41
2087 3947 6.101150 TCCTTTACAATCCATAGGTGTGCTAT 59.899 38.462 0.00 0.00 0.00 2.97
2125 3985 0.178947 TGGAATTTTGGCGGGGAGTT 60.179 50.000 0.00 0.00 0.00 3.01
2131 3991 2.075355 TTTGGCGGGGAGTTGTGGAT 62.075 55.000 0.00 0.00 0.00 3.41
2133 3993 1.304134 GGCGGGGAGTTGTGGATTT 60.304 57.895 0.00 0.00 0.00 2.17
2142 4002 3.119137 GGAGTTGTGGATTTTGTATGGCC 60.119 47.826 0.00 0.00 0.00 5.36
2151 4011 5.762218 TGGATTTTGTATGGCCAAGTTTTTG 59.238 36.000 10.96 0.00 0.00 2.44
2153 4013 6.654582 GGATTTTGTATGGCCAAGTTTTTGAT 59.345 34.615 10.96 0.00 36.36 2.57
2158 4018 1.344114 TGGCCAAGTTTTTGATGAGCC 59.656 47.619 0.61 0.00 37.99 4.70
2160 4020 2.224257 GGCCAAGTTTTTGATGAGCCAA 60.224 45.455 0.00 0.00 37.65 4.52
2161 4021 3.062042 GCCAAGTTTTTGATGAGCCAAG 58.938 45.455 0.00 0.00 36.36 3.61
2162 4022 3.243839 GCCAAGTTTTTGATGAGCCAAGA 60.244 43.478 0.00 0.00 36.36 3.02
2163 4023 4.301628 CCAAGTTTTTGATGAGCCAAGAC 58.698 43.478 0.00 0.00 36.36 3.01
2164 4024 4.202141 CCAAGTTTTTGATGAGCCAAGACA 60.202 41.667 0.00 0.00 36.36 3.41
2165 4025 5.510179 CCAAGTTTTTGATGAGCCAAGACAT 60.510 40.000 0.00 0.00 36.36 3.06
2166 4026 5.796424 AGTTTTTGATGAGCCAAGACATT 57.204 34.783 0.00 0.00 0.00 2.71
2167 4027 6.165700 AGTTTTTGATGAGCCAAGACATTT 57.834 33.333 0.00 0.00 0.00 2.32
2168 4028 5.987347 AGTTTTTGATGAGCCAAGACATTTG 59.013 36.000 0.00 0.00 0.00 2.32
2169 4029 4.524316 TTTGATGAGCCAAGACATTTGG 57.476 40.909 1.59 1.59 42.37 3.28
2170 4030 3.438216 TGATGAGCCAAGACATTTGGA 57.562 42.857 9.99 0.00 42.06 3.53
2171 4031 3.765381 TGATGAGCCAAGACATTTGGAA 58.235 40.909 9.99 0.00 42.06 3.53
2172 4032 4.151121 TGATGAGCCAAGACATTTGGAAA 58.849 39.130 9.99 0.00 42.06 3.13
2173 4033 4.022068 TGATGAGCCAAGACATTTGGAAAC 60.022 41.667 9.99 1.46 42.06 2.78
2174 4034 3.295093 TGAGCCAAGACATTTGGAAACA 58.705 40.909 9.99 3.75 42.06 2.83
2175 4035 3.318839 TGAGCCAAGACATTTGGAAACAG 59.681 43.478 9.99 0.00 44.54 3.16
2176 4036 3.299503 AGCCAAGACATTTGGAAACAGT 58.700 40.909 9.99 0.00 44.54 3.55
2177 4037 3.068590 AGCCAAGACATTTGGAAACAGTG 59.931 43.478 9.99 0.00 44.54 3.66
2178 4038 3.383761 CCAAGACATTTGGAAACAGTGC 58.616 45.455 0.00 0.00 44.54 4.40
2181 4041 5.221224 CCAAGACATTTGGAAACAGTGCTTA 60.221 40.000 0.00 0.00 44.54 3.09
2209 4072 4.873827 GGAAATACTTGCGATCTAACACCA 59.126 41.667 0.00 0.00 0.00 4.17
2210 4073 5.006746 GGAAATACTTGCGATCTAACACCAG 59.993 44.000 0.00 0.00 0.00 4.00
2211 4074 1.726853 ACTTGCGATCTAACACCAGC 58.273 50.000 0.00 0.00 0.00 4.85
2299 4163 0.780002 CGCTGCACATTGTTTTGAGC 59.220 50.000 0.00 0.00 34.31 4.26
2322 4186 0.248661 CTGACTATCCAGACGGTGCG 60.249 60.000 0.00 0.00 36.29 5.34
2344 4208 5.435820 GGAAACGGTAGGTACAGATAGAG 57.564 47.826 0.00 0.00 0.00 2.43
2345 4209 4.277921 GGAAACGGTAGGTACAGATAGAGG 59.722 50.000 0.00 0.00 0.00 3.69
2346 4210 4.785346 AACGGTAGGTACAGATAGAGGA 57.215 45.455 0.00 0.00 0.00 3.71
2347 4211 4.785346 ACGGTAGGTACAGATAGAGGAA 57.215 45.455 0.00 0.00 0.00 3.36
2348 4212 5.121380 ACGGTAGGTACAGATAGAGGAAA 57.879 43.478 0.00 0.00 0.00 3.13
2349 4213 4.886489 ACGGTAGGTACAGATAGAGGAAAC 59.114 45.833 0.00 0.00 0.00 2.78
2350 4214 4.024218 CGGTAGGTACAGATAGAGGAAACG 60.024 50.000 0.00 0.00 0.00 3.60
2351 4215 5.128919 GGTAGGTACAGATAGAGGAAACGA 58.871 45.833 0.00 0.00 0.00 3.85
2352 4216 5.591877 GGTAGGTACAGATAGAGGAAACGAA 59.408 44.000 0.00 0.00 0.00 3.85
2353 4217 5.838531 AGGTACAGATAGAGGAAACGAAG 57.161 43.478 0.00 0.00 0.00 3.79
2358 4222 2.110226 GATAGAGGAAACGAAGCGACG 58.890 52.381 0.00 4.25 39.31 5.12
2385 4249 0.108138 AGCAGTGCGAATCTGGTACC 60.108 55.000 10.00 4.43 40.99 3.34
2395 4259 2.930109 ATCTGGTACCAGGTCTCACT 57.070 50.000 35.94 13.38 43.75 3.41
2429 4293 1.003355 CACACCAAGTCGCCCAGAT 60.003 57.895 0.00 0.00 0.00 2.90
2434 4298 3.131396 CACCAAGTCGCCCAGATTATAC 58.869 50.000 0.00 0.00 0.00 1.47
2477 4343 4.021719 AGGATGTTTCAGTTGAAAGCATGG 60.022 41.667 18.50 0.00 43.82 3.66
2489 4355 2.282701 AAGCATGGCAATTTACAGCG 57.717 45.000 0.00 0.00 0.00 5.18
2520 4387 2.658325 GCAAAAGTATTGTCAAGCGCAG 59.342 45.455 11.47 0.72 0.00 5.18
2538 4405 3.256558 GCAGGCAAAAGAATCCAATGTC 58.743 45.455 0.00 0.00 0.00 3.06
2573 4440 5.470098 TGTGGTGCATCTCTTTCTTTCTAAC 59.530 40.000 0.00 0.00 0.00 2.34
2574 4441 5.470098 GTGGTGCATCTCTTTCTTTCTAACA 59.530 40.000 0.00 0.00 0.00 2.41
2576 4443 5.470098 GGTGCATCTCTTTCTTTCTAACACA 59.530 40.000 0.00 0.00 0.00 3.72
2577 4444 6.366630 GTGCATCTCTTTCTTTCTAACACAC 58.633 40.000 0.00 0.00 0.00 3.82
2591 4462 9.292195 CTTTCTAACACACTATTCCCCTAAAAA 57.708 33.333 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.356330 CGGATAGGTTGCAAGGGGTTAA 60.356 50.000 0.00 0.00 0.00 2.01
11 12 3.496160 CCTTTCATACCCCGGATAGGTTG 60.496 52.174 0.73 3.80 38.89 3.77
12 13 2.709397 CCTTTCATACCCCGGATAGGTT 59.291 50.000 0.73 0.00 38.89 3.50
63 64 2.028778 GCGTGCCATTTGCCACAA 59.971 55.556 0.00 0.00 40.16 3.33
65 66 0.108898 TATTGCGTGCCATTTGCCAC 60.109 50.000 0.00 0.00 40.16 5.01
72 73 1.599071 CGTGATTCTATTGCGTGCCAT 59.401 47.619 0.00 0.00 0.00 4.40
102 103 2.546584 GGCCTTTTCTTTTCTGCACCTG 60.547 50.000 0.00 0.00 0.00 4.00
104 105 1.270305 GGGCCTTTTCTTTTCTGCACC 60.270 52.381 0.84 0.00 0.00 5.01
108 109 0.603065 CCCGGGCCTTTTCTTTTCTG 59.397 55.000 8.08 0.00 0.00 3.02
110 111 1.292223 GCCCGGGCCTTTTCTTTTC 59.708 57.895 36.64 1.62 34.56 2.29
122 123 3.903282 CATTTGCCATCGCCCGGG 61.903 66.667 19.09 19.09 0.00 5.73
124 125 3.141522 ATGCATTTGCCATCGCCCG 62.142 57.895 0.00 0.00 41.18 6.13
134 135 0.533491 CCCCACACCAGATGCATTTG 59.467 55.000 10.22 10.22 0.00 2.32
161 162 5.239525 TCGACATAAGATGTGATCACGATCT 59.760 40.000 23.71 23.71 45.03 2.75
166 167 4.746611 TGCATCGACATAAGATGTGATCAC 59.253 41.667 19.27 19.27 45.03 3.06
181 182 2.610694 CGGGCCATGATGCATCGAC 61.611 63.158 21.34 9.67 33.37 4.20
184 185 0.963962 AAATCGGGCCATGATGCATC 59.036 50.000 20.14 20.14 0.00 3.91
191 192 0.964860 TCCACACAAATCGGGCCATG 60.965 55.000 4.39 0.00 0.00 3.66
199 200 1.463444 GTACGGCACTCCACACAAATC 59.537 52.381 0.00 0.00 0.00 2.17
212 213 2.452295 TTGTTATTGTCCGTACGGCA 57.548 45.000 29.64 25.31 34.68 5.69
215 216 6.160664 AGATTGTTTGTTATTGTCCGTACG 57.839 37.500 8.69 8.69 0.00 3.67
225 226 6.071616 ACCATGCGGTAAAGATTGTTTGTTAT 60.072 34.615 0.00 0.00 46.71 1.89
228 229 3.572255 ACCATGCGGTAAAGATTGTTTGT 59.428 39.130 0.00 0.00 46.71 2.83
242 243 0.461163 TATCCAACGTGACCATGCGG 60.461 55.000 0.00 0.00 38.77 5.69
243 244 1.062002 GTTATCCAACGTGACCATGCG 59.938 52.381 0.00 0.00 0.00 4.73
244 245 2.080693 TGTTATCCAACGTGACCATGC 58.919 47.619 0.00 0.00 37.48 4.06
245 246 3.126858 CCTTGTTATCCAACGTGACCATG 59.873 47.826 0.00 0.00 37.48 3.66
246 247 3.008594 TCCTTGTTATCCAACGTGACCAT 59.991 43.478 0.00 0.00 37.48 3.55
247 248 2.369203 TCCTTGTTATCCAACGTGACCA 59.631 45.455 0.00 0.00 37.48 4.02
249 250 6.730960 TTATTCCTTGTTATCCAACGTGAC 57.269 37.500 0.00 0.00 37.48 3.67
250 251 6.128117 GCTTTATTCCTTGTTATCCAACGTGA 60.128 38.462 0.00 0.00 37.48 4.35
251 252 6.027749 GCTTTATTCCTTGTTATCCAACGTG 58.972 40.000 0.00 0.00 37.48 4.49
252 253 5.944007 AGCTTTATTCCTTGTTATCCAACGT 59.056 36.000 0.00 0.00 37.48 3.99
253 254 6.436843 AGCTTTATTCCTTGTTATCCAACG 57.563 37.500 0.00 0.00 37.48 4.10
260 261 9.396022 CCTCTATCAAAGCTTTATTCCTTGTTA 57.604 33.333 12.25 0.00 0.00 2.41
261 262 7.340487 CCCTCTATCAAAGCTTTATTCCTTGTT 59.660 37.037 12.25 0.00 0.00 2.83
263 264 7.012799 GTCCCTCTATCAAAGCTTTATTCCTTG 59.987 40.741 12.25 0.00 0.00 3.61
264 265 7.057264 GTCCCTCTATCAAAGCTTTATTCCTT 58.943 38.462 12.25 0.00 0.00 3.36
305 356 9.671279 ACATCAATTTGTATAACAGATCAGTCA 57.329 29.630 0.00 0.00 0.00 3.41
307 358 9.896645 AGACATCAATTTGTATAACAGATCAGT 57.103 29.630 0.00 0.00 0.00 3.41
325 376 4.388485 TGTAGCTGCAAGAAAGACATCAA 58.612 39.130 0.43 0.00 34.07 2.57
326 377 3.999001 CTGTAGCTGCAAGAAAGACATCA 59.001 43.478 5.84 0.00 34.07 3.07
328 379 4.277515 TCTGTAGCTGCAAGAAAGACAT 57.722 40.909 5.84 0.00 34.07 3.06
346 397 3.503363 TGTGATTTTGCCAGTAGCTTCTG 59.497 43.478 13.08 13.08 44.23 3.02
347 398 3.754965 TGTGATTTTGCCAGTAGCTTCT 58.245 40.909 0.00 0.00 44.23 2.85
357 408 4.320608 TCTTTTGTCCTGTGATTTTGCC 57.679 40.909 0.00 0.00 0.00 4.52
359 410 6.757947 ACATGTTCTTTTGTCCTGTGATTTTG 59.242 34.615 0.00 0.00 0.00 2.44
360 411 6.877236 ACATGTTCTTTTGTCCTGTGATTTT 58.123 32.000 0.00 0.00 0.00 1.82
361 412 6.469782 ACATGTTCTTTTGTCCTGTGATTT 57.530 33.333 0.00 0.00 0.00 2.17
362 413 6.998074 TCTACATGTTCTTTTGTCCTGTGATT 59.002 34.615 2.30 0.00 0.00 2.57
363 414 6.533730 TCTACATGTTCTTTTGTCCTGTGAT 58.466 36.000 2.30 0.00 0.00 3.06
364 415 5.924356 TCTACATGTTCTTTTGTCCTGTGA 58.076 37.500 2.30 0.00 0.00 3.58
365 416 5.180117 CCTCTACATGTTCTTTTGTCCTGTG 59.820 44.000 2.30 0.00 0.00 3.66
366 417 5.071788 TCCTCTACATGTTCTTTTGTCCTGT 59.928 40.000 2.30 0.00 0.00 4.00
367 418 5.551233 TCCTCTACATGTTCTTTTGTCCTG 58.449 41.667 2.30 0.00 0.00 3.86
368 419 5.799213 CTCCTCTACATGTTCTTTTGTCCT 58.201 41.667 2.30 0.00 0.00 3.85
369 420 4.393371 GCTCCTCTACATGTTCTTTTGTCC 59.607 45.833 2.30 0.00 0.00 4.02
370 421 5.241662 AGCTCCTCTACATGTTCTTTTGTC 58.758 41.667 2.30 0.00 0.00 3.18
371 422 5.234466 AGCTCCTCTACATGTTCTTTTGT 57.766 39.130 2.30 0.00 0.00 2.83
372 423 4.328440 CGAGCTCCTCTACATGTTCTTTTG 59.672 45.833 8.47 0.00 0.00 2.44
373 424 4.021016 ACGAGCTCCTCTACATGTTCTTTT 60.021 41.667 8.47 0.00 0.00 2.27
374 425 3.511934 ACGAGCTCCTCTACATGTTCTTT 59.488 43.478 8.47 0.00 0.00 2.52
375 426 3.093057 ACGAGCTCCTCTACATGTTCTT 58.907 45.455 8.47 0.00 0.00 2.52
376 427 2.685897 GACGAGCTCCTCTACATGTTCT 59.314 50.000 8.47 0.00 0.00 3.01
377 428 2.685897 AGACGAGCTCCTCTACATGTTC 59.314 50.000 12.88 0.00 0.00 3.18
378 429 2.685897 GAGACGAGCTCCTCTACATGTT 59.314 50.000 14.27 0.00 37.69 2.71
382 433 2.491675 TTGAGACGAGCTCCTCTACA 57.508 50.000 14.27 11.33 43.26 2.74
385 436 1.110442 CCATTGAGACGAGCTCCTCT 58.890 55.000 14.20 14.20 43.26 3.69
387 438 0.534412 CACCATTGAGACGAGCTCCT 59.466 55.000 8.47 0.00 43.26 3.69
402 453 4.560743 TGCACCTTGCTCGCACCA 62.561 61.111 0.00 0.00 45.31 4.17
415 466 3.470567 CGTCGAAGCTCGGTGCAC 61.471 66.667 8.80 8.80 45.94 4.57
444 495 2.214216 TGGCTTGCCGGTAGTGTCT 61.214 57.895 1.90 0.00 0.00 3.41
450 501 2.270850 GATGGTGGCTTGCCGGTA 59.729 61.111 1.90 0.00 0.00 4.02
453 504 3.944250 AAGGGATGGTGGCTTGCCG 62.944 63.158 7.18 0.00 0.00 5.69
454 505 2.037847 AAGGGATGGTGGCTTGCC 59.962 61.111 4.43 4.43 0.00 4.52
462 513 2.375345 CGGGGTAGCAAGGGATGGT 61.375 63.158 0.00 0.00 43.54 3.55
465 516 1.645710 CTATCGGGGTAGCAAGGGAT 58.354 55.000 0.00 0.00 0.00 3.85
466 517 1.119574 GCTATCGGGGTAGCAAGGGA 61.120 60.000 6.09 0.00 45.03 4.20
471 522 1.968493 CTAAAGGCTATCGGGGTAGCA 59.032 52.381 12.62 0.00 46.97 3.49
476 527 3.277142 AAACACTAAAGGCTATCGGGG 57.723 47.619 0.00 0.00 0.00 5.73
479 530 6.721571 TGAAGAAAACACTAAAGGCTATCG 57.278 37.500 0.00 0.00 0.00 2.92
492 543 5.520288 GCTAGCATAGACGATGAAGAAAACA 59.480 40.000 10.63 0.00 42.77 2.83
493 544 5.331905 CGCTAGCATAGACGATGAAGAAAAC 60.332 44.000 16.45 0.00 42.77 2.43
494 545 4.740205 CGCTAGCATAGACGATGAAGAAAA 59.260 41.667 16.45 0.00 42.77 2.29
498 2304 3.275400 ACGCTAGCATAGACGATGAAG 57.725 47.619 16.45 0.00 42.77 3.02
520 2326 0.109412 GGCGACTAATATAGCGGCGT 60.109 55.000 9.37 0.00 39.45 5.68
530 2336 1.290203 CATGCACGAAGGCGACTAAT 58.710 50.000 0.00 0.00 42.68 1.73
532 2338 0.812549 TACATGCACGAAGGCGACTA 59.187 50.000 0.00 0.00 42.68 2.59
534 2340 0.577269 GATACATGCACGAAGGCGAC 59.423 55.000 0.00 0.00 41.64 5.19
535 2341 0.459899 AGATACATGCACGAAGGCGA 59.540 50.000 0.00 0.00 41.64 5.54
544 2350 7.452880 AAGTAAAGCAAAAGAGATACATGCA 57.547 32.000 0.00 0.00 39.42 3.96
565 2371 5.291614 CACAATGTTTAGCAAGCAACAAAGT 59.708 36.000 2.68 2.53 36.50 2.66
576 2382 5.577835 GTCAAAGTGACACAATGTTTAGCA 58.422 37.500 8.59 0.00 46.22 3.49
597 2403 4.142687 CCTTACAAATCCAACATGTCCGTC 60.143 45.833 0.00 0.00 0.00 4.79
602 2408 3.778265 AGCCCTTACAAATCCAACATGT 58.222 40.909 0.00 0.00 0.00 3.21
620 2426 0.681243 CCCTTGCCTGGTCTTAAGCC 60.681 60.000 0.00 3.33 0.00 4.35
638 2450 2.671888 GCTACGTGTTTTTCTAGAGGCC 59.328 50.000 0.00 0.00 0.00 5.19
644 2456 9.925268 CTTTTAAGAAAGCTACGTGTTTTTCTA 57.075 29.630 17.54 6.30 38.54 2.10
646 2462 7.911727 TCCTTTTAAGAAAGCTACGTGTTTTTC 59.088 33.333 0.00 5.40 40.75 2.29
648 2464 7.324354 TCCTTTTAAGAAAGCTACGTGTTTT 57.676 32.000 0.00 0.00 40.75 2.43
676 2492 3.257375 GGGGTTTCTATTCGGCTGTTTTT 59.743 43.478 0.00 0.00 0.00 1.94
681 2497 0.177141 TCGGGGTTTCTATTCGGCTG 59.823 55.000 0.00 0.00 0.00 4.85
682 2498 0.906775 TTCGGGGTTTCTATTCGGCT 59.093 50.000 0.00 0.00 0.00 5.52
683 2499 1.296727 CTTCGGGGTTTCTATTCGGC 58.703 55.000 0.00 0.00 0.00 5.54
848 2698 1.384502 AGGGGATCCAATGCGAGGA 60.385 57.895 15.23 0.00 39.97 3.71
957 2807 1.269309 CCGCGGTTGTGAAATGGAAAA 60.269 47.619 19.50 0.00 0.00 2.29
987 2837 0.391661 CGGCCATGTCTACAGTGCTT 60.392 55.000 2.24 0.00 0.00 3.91
990 2840 0.249120 TTCCGGCCATGTCTACAGTG 59.751 55.000 2.24 0.00 0.00 3.66
1068 2918 4.974438 ACGGGGAACTGGAGCCCA 62.974 66.667 0.00 0.00 46.57 5.36
1197 3047 1.745827 CGGGCATCGGGTAACAGAATT 60.746 52.381 0.00 0.00 46.28 2.17
1207 3057 1.666209 AAGCAAAATCGGGCATCGGG 61.666 55.000 0.00 0.00 39.77 5.14
1216 3066 2.035832 ACCACCCAAAGAAGCAAAATCG 59.964 45.455 0.00 0.00 0.00 3.34
1226 3076 2.778299 CTCGAATTCACCACCCAAAGA 58.222 47.619 6.22 0.00 0.00 2.52
1227 3077 1.200020 GCTCGAATTCACCACCCAAAG 59.800 52.381 6.22 0.00 0.00 2.77
1231 3081 2.106683 CCGCTCGAATTCACCACCC 61.107 63.158 6.22 0.00 0.00 4.61
1232 3082 0.953960 AACCGCTCGAATTCACCACC 60.954 55.000 6.22 0.00 0.00 4.61
1260 3111 0.599558 ACCGATTGACGAGACCGAAA 59.400 50.000 0.00 0.00 45.77 3.46
1262 3113 1.504900 CACCGATTGACGAGACCGA 59.495 57.895 0.00 0.00 45.77 4.69
1263 3114 1.516386 CCACCGATTGACGAGACCG 60.516 63.158 0.00 0.00 45.77 4.79
1265 3116 1.068474 CAACCACCGATTGACGAGAC 58.932 55.000 0.00 0.00 45.77 3.36
1266 3117 0.037697 CCAACCACCGATTGACGAGA 60.038 55.000 0.00 0.00 45.77 4.04
1267 3118 0.320421 ACCAACCACCGATTGACGAG 60.320 55.000 0.00 0.00 45.77 4.18
1268 3119 0.107081 AACCAACCACCGATTGACGA 59.893 50.000 0.00 0.00 45.77 4.20
1269 3120 0.515564 GAACCAACCACCGATTGACG 59.484 55.000 0.00 0.00 42.18 4.35
1270 3121 0.515564 CGAACCAACCACCGATTGAC 59.484 55.000 0.00 0.00 0.00 3.18
1271 3122 0.604243 CCGAACCAACCACCGATTGA 60.604 55.000 0.00 0.00 0.00 2.57
1272 3123 1.873165 CCGAACCAACCACCGATTG 59.127 57.895 0.00 0.00 0.00 2.67
1273 3124 1.969589 GCCGAACCAACCACCGATT 60.970 57.895 0.00 0.00 0.00 3.34
1274 3125 2.359478 GCCGAACCAACCACCGAT 60.359 61.111 0.00 0.00 0.00 4.18
1330 3181 2.033757 AGCAGGCAGAGGCAAGTG 59.966 61.111 0.00 0.00 43.71 3.16
1365 3216 2.843401 TAACAAGCAGAACCGCCTAA 57.157 45.000 0.00 0.00 0.00 2.69
1382 3233 4.213270 CCACAAAGTCTCGAGTGCAATTAA 59.787 41.667 13.13 0.00 0.00 1.40
1396 3247 6.700081 GGTTACTTCCAAAATTCCACAAAGTC 59.300 38.462 0.00 0.00 0.00 3.01
1423 3274 2.031769 TGCACAAACAAGAGAATCGCAG 60.032 45.455 0.00 0.00 42.67 5.18
1432 3283 2.023673 CCAGAACCTGCACAAACAAGA 58.976 47.619 0.00 0.00 0.00 3.02
1840 3697 3.303406 ACGAACTAGCAACGACTTACAC 58.697 45.455 9.99 0.00 0.00 2.90
1846 3703 6.859715 TTTATAGAACGAACTAGCAACGAC 57.140 37.500 9.99 4.96 0.00 4.34
1863 3720 7.013655 AGCAATCCATAGGTGCAACTTTTATAG 59.986 37.037 10.94 0.00 40.83 1.31
1897 3754 5.998363 ACCAAGAACAGAGTGGTAGAAATTC 59.002 40.000 0.00 0.00 43.90 2.17
1922 3779 7.178983 AGCAAGAATAGACCATGGAAATTTTCA 59.821 33.333 21.47 0.54 0.00 2.69
2009 3866 5.945784 AGACTAATGCCAAAATACAGCTTCA 59.054 36.000 0.00 0.00 0.00 3.02
2018 3875 7.539034 AAGTTACCAAGACTAATGCCAAAAT 57.461 32.000 0.00 0.00 0.00 1.82
2019 3876 6.969993 AAGTTACCAAGACTAATGCCAAAA 57.030 33.333 0.00 0.00 0.00 2.44
2020 3877 6.969993 AAAGTTACCAAGACTAATGCCAAA 57.030 33.333 0.00 0.00 0.00 3.28
2021 3878 6.293735 CGAAAAGTTACCAAGACTAATGCCAA 60.294 38.462 0.00 0.00 0.00 4.52
2022 3879 5.180492 CGAAAAGTTACCAAGACTAATGCCA 59.820 40.000 0.00 0.00 0.00 4.92
2023 3880 5.410439 TCGAAAAGTTACCAAGACTAATGCC 59.590 40.000 0.00 0.00 0.00 4.40
2024 3881 6.147328 AGTCGAAAAGTTACCAAGACTAATGC 59.853 38.462 0.00 0.00 35.95 3.56
2025 3882 7.653767 AGTCGAAAAGTTACCAAGACTAATG 57.346 36.000 0.00 0.00 35.95 1.90
2026 3883 7.540055 CGTAGTCGAAAAGTTACCAAGACTAAT 59.460 37.037 4.30 0.00 40.13 1.73
2027 3884 6.857964 CGTAGTCGAAAAGTTACCAAGACTAA 59.142 38.462 4.30 0.00 40.13 2.24
2028 3885 6.373779 CGTAGTCGAAAAGTTACCAAGACTA 58.626 40.000 0.00 0.00 38.30 2.59
2029 3886 5.218139 CGTAGTCGAAAAGTTACCAAGACT 58.782 41.667 0.00 0.91 40.16 3.24
2030 3887 4.383948 CCGTAGTCGAAAAGTTACCAAGAC 59.616 45.833 0.00 0.00 39.71 3.01
2031 3888 4.278170 TCCGTAGTCGAAAAGTTACCAAGA 59.722 41.667 0.00 0.00 39.71 3.02
2032 3889 4.549458 TCCGTAGTCGAAAAGTTACCAAG 58.451 43.478 0.00 0.00 39.71 3.61
2033 3890 4.582701 TCCGTAGTCGAAAAGTTACCAA 57.417 40.909 0.00 0.00 39.71 3.67
2034 3891 4.022068 ACATCCGTAGTCGAAAAGTTACCA 60.022 41.667 0.00 0.00 39.71 3.25
2035 3892 4.325472 CACATCCGTAGTCGAAAAGTTACC 59.675 45.833 0.00 0.00 39.71 2.85
2036 3893 4.201561 GCACATCCGTAGTCGAAAAGTTAC 60.202 45.833 0.00 0.00 39.71 2.50
2037 3894 3.922240 GCACATCCGTAGTCGAAAAGTTA 59.078 43.478 0.00 0.00 39.71 2.24
2038 3895 2.735134 GCACATCCGTAGTCGAAAAGTT 59.265 45.455 0.00 0.00 39.71 2.66
2039 3896 2.029290 AGCACATCCGTAGTCGAAAAGT 60.029 45.455 0.00 0.00 39.71 2.66
2040 3897 2.607187 AGCACATCCGTAGTCGAAAAG 58.393 47.619 0.00 0.00 39.71 2.27
2041 3898 2.736144 AGCACATCCGTAGTCGAAAA 57.264 45.000 0.00 0.00 39.71 2.29
2042 3899 2.736144 AAGCACATCCGTAGTCGAAA 57.264 45.000 0.00 0.00 39.71 3.46
2043 3900 2.602878 GAAAGCACATCCGTAGTCGAA 58.397 47.619 0.00 0.00 39.71 3.71
2044 3901 1.135199 GGAAAGCACATCCGTAGTCGA 60.135 52.381 0.00 0.00 39.71 4.20
2045 3902 1.135083 AGGAAAGCACATCCGTAGTCG 60.135 52.381 0.00 0.00 42.03 4.18
2061 3921 4.947388 GCACACCTATGGATTGTAAAGGAA 59.053 41.667 0.00 0.00 0.00 3.36
2063 3923 4.526970 AGCACACCTATGGATTGTAAAGG 58.473 43.478 0.00 0.00 0.00 3.11
2075 3935 3.501349 ACTCGATCCATAGCACACCTAT 58.499 45.455 0.00 0.00 37.22 2.57
2087 3947 4.747583 TCCATTATCCCTAACTCGATCCA 58.252 43.478 0.00 0.00 0.00 3.41
2090 3950 7.448469 CCAAAATTCCATTATCCCTAACTCGAT 59.552 37.037 0.00 0.00 0.00 3.59
2125 3985 3.505386 ACTTGGCCATACAAAATCCACA 58.495 40.909 6.09 0.00 0.00 4.17
2131 3991 6.586344 TCATCAAAAACTTGGCCATACAAAA 58.414 32.000 6.09 0.00 0.00 2.44
2133 3993 5.782047 CTCATCAAAAACTTGGCCATACAA 58.218 37.500 6.09 0.00 0.00 2.41
2142 4002 4.935702 TGTCTTGGCTCATCAAAAACTTG 58.064 39.130 0.00 0.00 0.00 3.16
2151 4011 4.022068 TGTTTCCAAATGTCTTGGCTCATC 60.022 41.667 0.00 0.00 39.38 2.92
2153 4013 3.295093 TGTTTCCAAATGTCTTGGCTCA 58.705 40.909 0.00 0.00 39.38 4.26
2158 4018 4.311816 AGCACTGTTTCCAAATGTCTTG 57.688 40.909 0.00 0.00 0.00 3.02
2160 4020 4.520492 CCTAAGCACTGTTTCCAAATGTCT 59.480 41.667 0.00 0.00 0.00 3.41
2161 4021 4.798574 CCTAAGCACTGTTTCCAAATGTC 58.201 43.478 0.00 0.00 0.00 3.06
2162 4022 3.005791 GCCTAAGCACTGTTTCCAAATGT 59.994 43.478 0.00 0.00 39.53 2.71
2163 4023 3.578688 GCCTAAGCACTGTTTCCAAATG 58.421 45.455 0.00 0.00 39.53 2.32
2164 4024 2.228822 CGCCTAAGCACTGTTTCCAAAT 59.771 45.455 0.00 0.00 39.83 2.32
2165 4025 1.606668 CGCCTAAGCACTGTTTCCAAA 59.393 47.619 0.00 0.00 39.83 3.28
2166 4026 1.234821 CGCCTAAGCACTGTTTCCAA 58.765 50.000 0.00 0.00 39.83 3.53
2167 4027 0.605319 CCGCCTAAGCACTGTTTCCA 60.605 55.000 0.00 0.00 39.83 3.53
2168 4028 1.305930 CCCGCCTAAGCACTGTTTCC 61.306 60.000 0.00 0.00 39.83 3.13
2169 4029 0.321298 TCCCGCCTAAGCACTGTTTC 60.321 55.000 0.00 0.00 39.83 2.78
2170 4030 0.109723 TTCCCGCCTAAGCACTGTTT 59.890 50.000 0.00 0.00 39.83 2.83
2171 4031 0.109723 TTTCCCGCCTAAGCACTGTT 59.890 50.000 0.00 0.00 39.83 3.16
2172 4032 0.328258 ATTTCCCGCCTAAGCACTGT 59.672 50.000 0.00 0.00 39.83 3.55
2173 4033 1.940613 GTATTTCCCGCCTAAGCACTG 59.059 52.381 0.00 0.00 39.83 3.66
2174 4034 1.838077 AGTATTTCCCGCCTAAGCACT 59.162 47.619 0.00 0.00 39.83 4.40
2175 4035 2.327200 AGTATTTCCCGCCTAAGCAC 57.673 50.000 0.00 0.00 39.83 4.40
2176 4036 2.639065 CAAGTATTTCCCGCCTAAGCA 58.361 47.619 0.00 0.00 39.83 3.91
2177 4037 1.333931 GCAAGTATTTCCCGCCTAAGC 59.666 52.381 0.00 0.00 0.00 3.09
2178 4038 1.597663 CGCAAGTATTTCCCGCCTAAG 59.402 52.381 0.00 0.00 0.00 2.18
2181 4041 0.180406 ATCGCAAGTATTTCCCGCCT 59.820 50.000 0.00 0.00 39.48 5.52
2231 4094 3.068732 TCATCTCCGTGCCATTTCTCTAG 59.931 47.826 0.00 0.00 0.00 2.43
2234 4097 2.315925 TCATCTCCGTGCCATTTCTC 57.684 50.000 0.00 0.00 0.00 2.87
2299 4163 1.360551 CGTCTGGATAGTCAGGGCG 59.639 63.158 0.00 0.00 35.58 6.13
2322 4186 4.277921 CCTCTATCTGTACCTACCGTTTCC 59.722 50.000 0.00 0.00 0.00 3.13
2341 4205 0.386985 GTCGTCGCTTCGTTTCCTCT 60.387 55.000 0.00 0.00 0.00 3.69
2342 4206 0.662374 TGTCGTCGCTTCGTTTCCTC 60.662 55.000 0.00 0.00 0.00 3.71
2343 4207 0.663568 CTGTCGTCGCTTCGTTTCCT 60.664 55.000 0.00 0.00 0.00 3.36
2344 4208 1.773496 CTGTCGTCGCTTCGTTTCC 59.227 57.895 0.00 0.00 0.00 3.13
2345 4209 1.128015 GCTGTCGTCGCTTCGTTTC 59.872 57.895 0.00 0.00 0.00 2.78
2346 4210 1.590525 TGCTGTCGTCGCTTCGTTT 60.591 52.632 0.00 0.00 0.00 3.60
2347 4211 2.027024 TGCTGTCGTCGCTTCGTT 59.973 55.556 0.00 0.00 0.00 3.85
2348 4212 2.729862 GTGCTGTCGTCGCTTCGT 60.730 61.111 0.00 0.00 0.00 3.85
2349 4213 2.710971 CTGTGCTGTCGTCGCTTCG 61.711 63.158 0.00 0.00 0.00 3.79
2350 4214 3.004734 GCTGTGCTGTCGTCGCTTC 62.005 63.158 0.00 0.00 0.00 3.86
2351 4215 3.038417 GCTGTGCTGTCGTCGCTT 61.038 61.111 0.00 0.00 0.00 4.68
2352 4216 4.284860 TGCTGTGCTGTCGTCGCT 62.285 61.111 0.00 0.00 0.00 4.93
2353 4217 3.771491 CTGCTGTGCTGTCGTCGC 61.771 66.667 0.00 0.00 0.00 5.19
2385 4249 1.271001 TGCAATGTGGAGTGAGACCTG 60.271 52.381 0.00 0.00 0.00 4.00
2429 4293 3.855379 GTGTTCGCGTCATGTGAGTATAA 59.145 43.478 5.77 0.00 38.57 0.98
2434 4298 0.161658 GTGTGTTCGCGTCATGTGAG 59.838 55.000 5.77 0.00 38.57 3.51
2473 4339 1.655099 GCAACGCTGTAAATTGCCATG 59.345 47.619 0.00 0.00 42.32 3.66
2520 4387 6.455360 TCATAGACATTGGATTCTTTTGCC 57.545 37.500 0.00 0.00 0.00 4.52
2538 4405 0.036105 TGCACCACACAGGCTCATAG 60.036 55.000 0.00 0.00 43.14 2.23


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

AutoCloner maintained by Alex Coulton.