Multiple sequence alignment - TraesCS5B01G519800

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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 TraesCS5B01G519800 chr5B 100.000 2549 0 0 1 2549 682396564 682394016 0.000000e+00 4708
1 TraesCS5B01G519800 chr5B 96.774 1705 49 5 569 2270 81902666 81904367 0.000000e+00 2839
2 TraesCS5B01G519800 chr1B 97.181 1703 46 2 569 2270 307939705 307941406 0.000000e+00 2878
3 TraesCS5B01G519800 chr1B 97.011 1706 49 2 566 2270 616703969 616702265 0.000000e+00 2867
4 TraesCS5B01G519800 chr1B 95.753 1719 67 5 554 2270 561526116 561527830 0.000000e+00 2765
5 TraesCS5B01G519800 chr1B 95.736 1712 65 6 563 2270 581717566 581715859 0.000000e+00 2750
6 TraesCS5B01G519800 chr1B 95.785 1708 63 7 564 2267 671392205 671393907 0.000000e+00 2747
7 TraesCS5B01G519800 chr1B 98.282 291 3 2 2257 2547 645696050 645695762 2.260000e-140 508
8 TraesCS5B01G519800 chr1B 97.952 293 4 2 2255 2547 288522958 288522668 8.140000e-140 507
9 TraesCS5B01G519800 chr2B 96.838 1708 50 4 566 2270 776161410 776163116 0.000000e+00 2852
10 TraesCS5B01G519800 chr2B 95.733 1711 65 6 564 2270 692955891 692957597 0.000000e+00 2748
11 TraesCS5B01G519800 chr3B 95.833 1704 68 2 568 2270 46395681 46393980 0.000000e+00 2750
12 TraesCS5B01G519800 chr3B 97.324 299 5 2 2251 2549 562524430 562524135 2.930000e-139 505
13 TraesCS5B01G519800 chr5D 97.163 423 5 2 8 429 540061610 540061194 0.000000e+00 708
14 TraesCS5B01G519800 chr5D 96.690 423 7 2 8 429 540050633 540050217 0.000000e+00 697
15 TraesCS5B01G519800 chr5D 97.297 148 3 1 421 568 540043290 540043144 1.510000e-62 250
16 TraesCS5B01G519800 chr5D 97.297 148 3 1 421 568 540055977 540055831 1.510000e-62 250
17 TraesCS5B01G519800 chr5D 97.297 148 3 1 421 568 540069921 540069775 1.510000e-62 250
18 TraesCS5B01G519800 chr5D 97.297 148 3 1 421 568 540074430 540074284 1.510000e-62 250
19 TraesCS5B01G519800 chr4A 83.392 572 76 11 4 568 628002918 628002359 1.750000e-141 512
20 TraesCS5B01G519800 chr3A 98.955 287 2 1 2263 2549 260312455 260312740 1.750000e-141 512
21 TraesCS5B01G519800 chr3A 97.635 296 6 1 2253 2547 12298975 12299270 8.140000e-140 507
22 TraesCS5B01G519800 chr4B 98.288 292 3 1 2258 2549 182270040 182269751 6.290000e-141 510
23 TraesCS5B01G519800 chr7B 98.282 291 3 2 2257 2547 635723069 635723357 2.260000e-140 508
24 TraesCS5B01G519800 chr1A 98.282 291 4 1 2258 2548 94234652 94234363 2.260000e-140 508
25 TraesCS5B01G519800 chrUn 99.283 279 2 0 2269 2547 180731224 180731502 2.930000e-139 505
26 TraesCS5B01G519800 chrUn 97.297 148 3 1 421 568 311747638 311747492 1.510000e-62 250
27 TraesCS5B01G519800 chr5A 90.625 320 16 12 2230 2546 503116744 503116436 1.820000e-111 412


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 TraesCS5B01G519800 chr5B 682394016 682396564 2548 True 4708 4708 100.000 1 2549 1 chr5B.!!$R1 2548
1 TraesCS5B01G519800 chr5B 81902666 81904367 1701 False 2839 2839 96.774 569 2270 1 chr5B.!!$F1 1701
2 TraesCS5B01G519800 chr1B 307939705 307941406 1701 False 2878 2878 97.181 569 2270 1 chr1B.!!$F1 1701
3 TraesCS5B01G519800 chr1B 616702265 616703969 1704 True 2867 2867 97.011 566 2270 1 chr1B.!!$R3 1704
4 TraesCS5B01G519800 chr1B 561526116 561527830 1714 False 2765 2765 95.753 554 2270 1 chr1B.!!$F2 1716
5 TraesCS5B01G519800 chr1B 581715859 581717566 1707 True 2750 2750 95.736 563 2270 1 chr1B.!!$R2 1707
6 TraesCS5B01G519800 chr1B 671392205 671393907 1702 False 2747 2747 95.785 564 2267 1 chr1B.!!$F3 1703
7 TraesCS5B01G519800 chr2B 776161410 776163116 1706 False 2852 2852 96.838 566 2270 1 chr2B.!!$F2 1704
8 TraesCS5B01G519800 chr2B 692955891 692957597 1706 False 2748 2748 95.733 564 2270 1 chr2B.!!$F1 1706
9 TraesCS5B01G519800 chr3B 46393980 46395681 1701 True 2750 2750 95.833 568 2270 1 chr3B.!!$R1 1702
10 TraesCS5B01G519800 chr4A 628002359 628002918 559 True 512 512 83.392 4 568 1 chr4A.!!$R1 564

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
265 271 0.034089 GGGCCAAGGTGCTAGTTCAT 60.034 55.0 4.39 0.0 0.00 2.57 F
692 698 0.179234 TGTGAACTTTGGCGTCTCCA 59.821 50.0 0.00 0.0 44.85 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1363 1371 1.573108 TCGCCCTCCATCTCTTCTTT 58.427 50.0 0.0 0.0 0.0 2.52 R
2459 2484 1.367346 TGTCCATAGCCAGGAAACCA 58.633 50.0 0.0 0.0 36.8 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.903764 TTTGCATCATGTAAAGCAACAAC 57.096 34.783 13.40 0.00 45.53 3.32
35 36 6.314648 TGCATCATGTAAAGCAACAACAAAAA 59.685 30.769 0.00 0.00 33.48 1.94
36 37 6.847289 GCATCATGTAAAGCAACAACAAAAAG 59.153 34.615 0.00 0.00 32.02 2.27
37 38 7.254387 GCATCATGTAAAGCAACAACAAAAAGA 60.254 33.333 0.00 0.00 32.02 2.52
71 74 1.613437 ACAAACCTTGAGGGCATTTCG 59.387 47.619 1.54 0.00 40.27 3.46
72 75 0.603065 AAACCTTGAGGGCATTTCGC 59.397 50.000 1.54 0.00 40.27 4.70
104 107 1.799994 TGTGAGTCATGCATGTTGACG 59.200 47.619 25.43 0.00 46.39 4.35
106 109 2.224079 GTGAGTCATGCATGTTGACGTT 59.776 45.455 25.43 3.61 46.39 3.99
109 112 2.224079 AGTCATGCATGTTGACGTTGAC 59.776 45.455 25.43 14.08 46.39 3.18
110 113 1.194322 TCATGCATGTTGACGTTGACG 59.806 47.619 25.43 1.41 46.33 4.35
136 139 5.558463 CGACGTCGATGTCATAGTCAATAGT 60.558 44.000 33.35 0.00 43.02 2.12
140 143 6.273825 GTCGATGTCATAGTCAATAGTGGTT 58.726 40.000 0.00 0.00 0.00 3.67
141 144 6.199154 GTCGATGTCATAGTCAATAGTGGTTG 59.801 42.308 0.00 0.00 0.00 3.77
152 155 0.816018 TAGTGGTTGCCGTTGTGGTG 60.816 55.000 0.00 0.00 41.21 4.17
154 157 2.831284 GGTTGCCGTTGTGGTGGT 60.831 61.111 0.00 0.00 41.21 4.16
161 164 1.591504 CCGTTGTGGTGGTAATGGGC 61.592 60.000 0.00 0.00 30.89 5.36
162 165 1.591504 CGTTGTGGTGGTAATGGGCC 61.592 60.000 0.00 0.00 0.00 5.80
179 182 2.423538 GGGCCGTGGCATAATATGAATC 59.576 50.000 13.76 0.00 44.11 2.52
183 186 5.414454 GGCCGTGGCATAATATGAATCTTTA 59.586 40.000 13.76 0.00 44.11 1.85
249 255 6.534634 AGTATGACCTCATAATTACAAGGGC 58.465 40.000 15.86 14.11 40.18 5.19
252 258 4.017958 TGACCTCATAATTACAAGGGCCAA 60.018 41.667 15.21 0.00 35.95 4.52
253 259 4.536765 ACCTCATAATTACAAGGGCCAAG 58.463 43.478 6.18 0.00 32.97 3.61
256 262 4.277476 TCATAATTACAAGGGCCAAGGTG 58.723 43.478 6.18 0.03 0.00 4.00
264 270 1.133809 AGGGCCAAGGTGCTAGTTCA 61.134 55.000 6.18 0.00 0.00 3.18
265 271 0.034089 GGGCCAAGGTGCTAGTTCAT 60.034 55.000 4.39 0.00 0.00 2.57
266 272 1.616994 GGGCCAAGGTGCTAGTTCATT 60.617 52.381 4.39 0.00 0.00 2.57
267 273 2.356741 GGGCCAAGGTGCTAGTTCATTA 60.357 50.000 4.39 0.00 0.00 1.90
268 274 3.555966 GGCCAAGGTGCTAGTTCATTAT 58.444 45.455 0.00 0.00 0.00 1.28
269 275 3.954258 GGCCAAGGTGCTAGTTCATTATT 59.046 43.478 0.00 0.00 0.00 1.40
298 304 4.520492 TCAAATGTCTTTTCTCCTGGAAGC 59.480 41.667 0.00 0.00 35.16 3.86
308 314 8.055181 TCTTTTCTCCTGGAAGCACATTTATAT 58.945 33.333 0.00 0.00 35.16 0.86
314 320 8.262601 TCCTGGAAGCACATTTATATAGAGAA 57.737 34.615 0.00 0.00 0.00 2.87
316 322 7.933577 CCTGGAAGCACATTTATATAGAGAACA 59.066 37.037 0.00 0.00 0.00 3.18
401 407 1.549203 ATCAAATGGTGTGGAGGCAC 58.451 50.000 0.00 0.00 38.56 5.01
423 429 4.705991 ACGTTAGGCCCTAAGAGATATAGC 59.294 45.833 2.67 0.00 0.00 2.97
454 460 5.240403 TGCACATGTTACATTTGCAGAGTAA 59.760 36.000 28.29 10.53 38.25 2.24
455 461 5.569059 GCACATGTTACATTTGCAGAGTAAC 59.431 40.000 25.64 21.46 44.72 2.50
456 462 6.568462 GCACATGTTACATTTGCAGAGTAACT 60.568 38.462 25.64 15.26 44.75 2.24
466 472 7.435488 ACATTTGCAGAGTAACTATTACTAGCG 59.565 37.037 15.27 7.98 46.01 4.26
468 474 6.301687 TGCAGAGTAACTATTACTAGCGAG 57.698 41.667 15.27 0.00 46.01 5.03
472 478 7.171337 GCAGAGTAACTATTACTAGCGAGTACT 59.829 40.741 6.15 4.19 46.01 2.73
473 479 8.702438 CAGAGTAACTATTACTAGCGAGTACTC 58.298 40.741 13.18 13.18 46.01 2.59
481 487 9.828852 CTATTACTAGCGAGTACTCTTAAATGG 57.171 37.037 20.34 9.34 37.91 3.16
488 494 4.508124 CGAGTACTCTTAAATGGTGGCATC 59.492 45.833 20.34 0.00 0.00 3.91
490 496 5.675538 AGTACTCTTAAATGGTGGCATCTC 58.324 41.667 0.00 0.00 0.00 2.75
493 499 6.506538 ACTCTTAAATGGTGGCATCTCTAT 57.493 37.500 0.00 0.00 0.00 1.98
503 509 6.763355 TGGTGGCATCTCTATTCTCTTTATC 58.237 40.000 0.00 0.00 0.00 1.75
518 524 9.956640 ATTCTCTTTATCTTTTCTCAGATGTGT 57.043 29.630 0.00 0.00 35.08 3.72
528 534 1.925185 CTCAGATGTGTCACATGCTCG 59.075 52.381 23.08 12.95 39.27 5.03
533 539 2.743538 TGTCACATGCTCGCTGGC 60.744 61.111 0.00 0.00 0.00 4.85
547 553 2.060567 GCTGGCTGCCCCATCTATGA 62.061 60.000 17.53 0.00 44.33 2.15
553 559 1.071471 GCCCCATCTATGACCACGG 59.929 63.158 0.00 0.00 0.00 4.94
560 566 3.889538 CCATCTATGACCACGGTAGAGAA 59.110 47.826 0.00 0.00 0.00 2.87
562 568 5.011125 CCATCTATGACCACGGTAGAGAAAT 59.989 44.000 0.00 0.00 0.00 2.17
590 596 4.962362 AGGGTTAATTATCCTTTTGCCCTG 59.038 41.667 11.51 0.00 41.90 4.45
692 698 0.179234 TGTGAACTTTGGCGTCTCCA 59.821 50.000 0.00 0.00 44.85 3.86
721 727 1.002773 ACGTTTTGACTCGGCCCTTAT 59.997 47.619 0.00 0.00 0.00 1.73
764 770 2.481276 GCGGCCAATTTTATTCAGACCC 60.481 50.000 2.24 0.00 0.00 4.46
1267 1275 4.280436 TGCTTCTTTCTTTGGGTCGATA 57.720 40.909 0.00 0.00 0.00 2.92
1313 1321 1.989966 CTGCAAGAAGAGCATGGCGG 61.990 60.000 0.00 0.00 41.82 6.13
1321 1329 1.750399 GAGCATGGCGGATGGTTGT 60.750 57.895 0.00 0.00 43.03 3.32
1435 1443 6.120507 AGCTTAGGATGTTGAAGAAGAAGT 57.879 37.500 0.00 0.00 0.00 3.01
1897 1911 7.427214 TGTTTACACCTAGTGCCAAAATAAAC 58.573 34.615 0.00 2.88 36.98 2.01
1921 1937 7.033185 ACGAACATTTTTAAGGGCATTACATC 58.967 34.615 0.00 0.00 0.00 3.06
2032 2055 2.028876 GTTTGTGGTGTTTAGGGCTGT 58.971 47.619 0.00 0.00 0.00 4.40
2042 2065 1.358152 TTAGGGCTGTGCTGGTAACT 58.642 50.000 0.00 0.00 37.61 2.24
2044 2067 1.073199 GGGCTGTGCTGGTAACTGT 59.927 57.895 0.00 0.00 37.92 3.55
2220 2245 2.493030 GCGCTGGTAACCGCTAGA 59.507 61.111 0.00 0.00 46.14 2.43
2258 2283 2.983192 TGACATGGGTAGGGAAGAAACA 59.017 45.455 0.00 0.00 0.00 2.83
2270 2295 8.648693 GGTAGGGAAGAAACATATACATAGTGT 58.351 37.037 0.00 0.00 0.00 3.55
2271 2296 9.477484 GTAGGGAAGAAACATATACATAGTGTG 57.523 37.037 0.00 0.00 0.00 3.82
2272 2297 8.090788 AGGGAAGAAACATATACATAGTGTGT 57.909 34.615 0.00 0.00 44.95 3.72
2273 2298 8.548877 AGGGAAGAAACATATACATAGTGTGTT 58.451 33.333 0.00 0.00 42.29 3.32
2274 2299 8.612619 GGGAAGAAACATATACATAGTGTGTTG 58.387 37.037 0.00 0.00 42.29 3.33
2275 2300 8.612619 GGAAGAAACATATACATAGTGTGTTGG 58.387 37.037 0.00 0.00 42.29 3.77
2276 2301 9.378551 GAAGAAACATATACATAGTGTGTTGGA 57.621 33.333 0.00 0.00 42.29 3.53
2277 2302 9.733556 AAGAAACATATACATAGTGTGTTGGAA 57.266 29.630 0.00 0.00 42.29 3.53
2278 2303 9.733556 AGAAACATATACATAGTGTGTTGGAAA 57.266 29.630 0.00 0.00 42.29 3.13
2284 2309 5.835113 ACATAGTGTGTTGGAAATATGCC 57.165 39.130 0.00 0.00 38.01 4.40
2285 2310 4.644685 ACATAGTGTGTTGGAAATATGCCC 59.355 41.667 0.00 0.00 38.01 5.36
2286 2311 3.456380 AGTGTGTTGGAAATATGCCCT 57.544 42.857 0.00 0.00 0.00 5.19
2287 2312 4.584638 AGTGTGTTGGAAATATGCCCTA 57.415 40.909 0.00 0.00 0.00 3.53
2288 2313 4.526970 AGTGTGTTGGAAATATGCCCTAG 58.473 43.478 0.00 0.00 0.00 3.02
2289 2314 4.227300 AGTGTGTTGGAAATATGCCCTAGA 59.773 41.667 0.00 0.00 0.00 2.43
2290 2315 4.576463 GTGTGTTGGAAATATGCCCTAGAG 59.424 45.833 0.00 0.00 0.00 2.43
2291 2316 4.137543 GTGTTGGAAATATGCCCTAGAGG 58.862 47.826 0.00 0.00 39.47 3.69
2307 2332 7.881775 CCCTAGAGGCAATAATAAAAGTGTT 57.118 36.000 0.00 0.00 0.00 3.32
2308 2333 8.974060 CCCTAGAGGCAATAATAAAAGTGTTA 57.026 34.615 0.00 0.00 0.00 2.41
2309 2334 9.574516 CCCTAGAGGCAATAATAAAAGTGTTAT 57.425 33.333 0.00 0.00 0.00 1.89
2369 2394 8.948631 ATTCATGCTATAACTGTATTATCCGG 57.051 34.615 0.00 0.00 0.00 5.14
2370 2395 7.712204 TCATGCTATAACTGTATTATCCGGA 57.288 36.000 6.61 6.61 0.00 5.14
2371 2396 8.129496 TCATGCTATAACTGTATTATCCGGAA 57.871 34.615 9.01 0.00 0.00 4.30
2372 2397 8.590204 TCATGCTATAACTGTATTATCCGGAAA 58.410 33.333 9.01 4.74 0.00 3.13
2373 2398 9.383519 CATGCTATAACTGTATTATCCGGAAAT 57.616 33.333 9.01 12.31 0.00 2.17
2374 2399 8.997621 TGCTATAACTGTATTATCCGGAAATC 57.002 34.615 9.01 5.33 0.00 2.17
2375 2400 7.758076 TGCTATAACTGTATTATCCGGAAATCG 59.242 37.037 9.01 5.25 38.88 3.34
2376 2401 7.758528 GCTATAACTGTATTATCCGGAAATCGT 59.241 37.037 9.01 5.81 37.11 3.73
2381 2406 8.976986 ACTGTATTATCCGGAAATCGTAATAC 57.023 34.615 25.06 25.06 40.20 1.89
2382 2407 8.579006 ACTGTATTATCCGGAAATCGTAATACA 58.421 33.333 28.89 28.89 43.27 2.29
2383 2408 8.746922 TGTATTATCCGGAAATCGTAATACAC 57.253 34.615 28.04 16.29 42.13 2.90
2399 2424 7.979037 CGTAATACACGTGTGAATACATAGAC 58.021 38.462 30.83 14.41 45.82 2.59
2400 2425 7.112565 CGTAATACACGTGTGAATACATAGACC 59.887 40.741 30.83 6.57 45.82 3.85
2401 2426 4.794278 ACACGTGTGAATACATAGACCA 57.206 40.909 22.71 0.00 39.39 4.02
2402 2427 4.491676 ACACGTGTGAATACATAGACCAC 58.508 43.478 22.71 0.00 39.39 4.16
2403 2428 4.021807 ACACGTGTGAATACATAGACCACA 60.022 41.667 22.71 0.00 39.39 4.17
2404 2429 4.926832 CACGTGTGAATACATAGACCACAA 59.073 41.667 7.58 0.00 39.13 3.33
2405 2430 5.580691 CACGTGTGAATACATAGACCACAAT 59.419 40.000 7.58 0.00 39.13 2.71
2406 2431 6.754675 CACGTGTGAATACATAGACCACAATA 59.245 38.462 7.58 0.00 39.13 1.90
2407 2432 7.438160 CACGTGTGAATACATAGACCACAATAT 59.562 37.037 7.58 0.00 39.13 1.28
2408 2433 7.438160 ACGTGTGAATACATAGACCACAATATG 59.562 37.037 0.00 0.00 39.13 1.78
2409 2434 7.438160 CGTGTGAATACATAGACCACAATATGT 59.562 37.037 0.00 3.60 43.31 2.29
2410 2435 8.765219 GTGTGAATACATAGACCACAATATGTC 58.235 37.037 0.00 0.00 40.78 3.06
2411 2436 7.931407 TGTGAATACATAGACCACAATATGTCC 59.069 37.037 1.37 0.00 40.78 4.02
2412 2437 7.387948 GTGAATACATAGACCACAATATGTCCC 59.612 40.741 1.37 0.00 40.78 4.46
2413 2438 7.292356 TGAATACATAGACCACAATATGTCCCT 59.708 37.037 1.37 0.00 40.78 4.20
2414 2439 8.736097 AATACATAGACCACAATATGTCCCTA 57.264 34.615 1.37 0.00 40.78 3.53
2415 2440 6.672266 ACATAGACCACAATATGTCCCTAG 57.328 41.667 0.00 0.00 37.98 3.02
2416 2441 6.143915 ACATAGACCACAATATGTCCCTAGT 58.856 40.000 0.00 0.00 37.98 2.57
2417 2442 6.042093 ACATAGACCACAATATGTCCCTAGTG 59.958 42.308 0.00 0.00 37.98 2.74
2418 2443 4.620723 AGACCACAATATGTCCCTAGTGA 58.379 43.478 0.00 0.00 31.76 3.41
2419 2444 4.651503 AGACCACAATATGTCCCTAGTGAG 59.348 45.833 0.00 0.00 31.76 3.51
2420 2445 3.134804 ACCACAATATGTCCCTAGTGAGC 59.865 47.826 0.00 0.00 0.00 4.26
2421 2446 3.495100 CCACAATATGTCCCTAGTGAGCC 60.495 52.174 0.00 0.00 0.00 4.70
2422 2447 3.389329 CACAATATGTCCCTAGTGAGCCT 59.611 47.826 0.00 0.00 0.00 4.58
2423 2448 3.643792 ACAATATGTCCCTAGTGAGCCTC 59.356 47.826 0.00 0.00 0.00 4.70
2424 2449 3.900601 CAATATGTCCCTAGTGAGCCTCT 59.099 47.826 0.00 0.00 0.00 3.69
2425 2450 5.080337 CAATATGTCCCTAGTGAGCCTCTA 58.920 45.833 0.00 0.00 0.00 2.43
2426 2451 2.738587 TGTCCCTAGTGAGCCTCTAG 57.261 55.000 0.00 0.00 35.86 2.43
2427 2452 1.923850 TGTCCCTAGTGAGCCTCTAGT 59.076 52.381 0.00 0.00 34.72 2.57
2428 2453 2.312140 TGTCCCTAGTGAGCCTCTAGTT 59.688 50.000 0.00 0.00 34.72 2.24
2429 2454 2.691011 GTCCCTAGTGAGCCTCTAGTTG 59.309 54.545 0.00 3.20 34.72 3.16
2430 2455 2.581246 TCCCTAGTGAGCCTCTAGTTGA 59.419 50.000 0.00 4.76 34.72 3.18
2431 2456 2.691011 CCCTAGTGAGCCTCTAGTTGAC 59.309 54.545 0.00 0.00 34.72 3.18
2432 2457 3.626222 CCCTAGTGAGCCTCTAGTTGACT 60.626 52.174 0.00 0.00 34.72 3.41
2433 2458 4.385421 CCCTAGTGAGCCTCTAGTTGACTA 60.385 50.000 0.00 0.00 34.72 2.59
2434 2459 4.819630 CCTAGTGAGCCTCTAGTTGACTAG 59.180 50.000 11.14 11.14 45.57 2.57
2435 2460 3.020984 AGTGAGCCTCTAGTTGACTAGC 58.979 50.000 12.30 3.61 44.24 3.42
2436 2461 3.020984 GTGAGCCTCTAGTTGACTAGCT 58.979 50.000 12.30 7.92 44.24 3.32
2437 2462 3.066203 GTGAGCCTCTAGTTGACTAGCTC 59.934 52.174 17.34 17.34 44.24 4.09
2438 2463 2.289547 GAGCCTCTAGTTGACTAGCTCG 59.710 54.545 12.30 0.00 44.24 5.03
2439 2464 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
2440 2465 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
2441 2466 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
2442 2467 3.440872 CCTCTAGTTGACTAGCTCGTTGT 59.559 47.826 12.30 0.00 44.24 3.32
2443 2468 4.407818 CTCTAGTTGACTAGCTCGTTGTG 58.592 47.826 12.30 0.00 44.24 3.33
2444 2469 4.070009 TCTAGTTGACTAGCTCGTTGTGA 58.930 43.478 12.30 0.00 44.24 3.58
2445 2470 3.944055 AGTTGACTAGCTCGTTGTGAT 57.056 42.857 0.00 0.00 0.00 3.06
2446 2471 3.839293 AGTTGACTAGCTCGTTGTGATC 58.161 45.455 0.00 0.00 0.00 2.92
2447 2472 3.255888 AGTTGACTAGCTCGTTGTGATCA 59.744 43.478 0.00 0.00 0.00 2.92
2448 2473 3.934457 TGACTAGCTCGTTGTGATCAA 57.066 42.857 0.00 0.00 0.00 2.57
2449 2474 8.771523 CTAGTTGACTAGCTCGTTGTGATCAAC 61.772 44.444 0.00 9.17 42.66 3.18
2462 2487 5.682234 TGTGATCAACAGATAGTCATGGT 57.318 39.130 0.00 0.00 33.78 3.55
2463 2488 6.053632 TGTGATCAACAGATAGTCATGGTT 57.946 37.500 0.00 0.00 33.78 3.67
2464 2489 6.475504 TGTGATCAACAGATAGTCATGGTTT 58.524 36.000 0.00 0.00 33.78 3.27
2465 2490 6.595326 TGTGATCAACAGATAGTCATGGTTTC 59.405 38.462 0.00 0.00 33.78 2.78
2466 2491 6.037610 GTGATCAACAGATAGTCATGGTTTCC 59.962 42.308 0.00 0.00 0.00 3.13
2467 2492 5.762179 TCAACAGATAGTCATGGTTTCCT 57.238 39.130 0.00 0.00 0.00 3.36
2468 2493 5.491070 TCAACAGATAGTCATGGTTTCCTG 58.509 41.667 0.00 0.00 0.00 3.86
2469 2494 4.494091 ACAGATAGTCATGGTTTCCTGG 57.506 45.455 0.00 0.00 0.00 4.45
2470 2495 3.209410 CAGATAGTCATGGTTTCCTGGC 58.791 50.000 0.00 0.00 0.00 4.85
2471 2496 3.118112 CAGATAGTCATGGTTTCCTGGCT 60.118 47.826 0.00 0.00 0.00 4.75
2472 2497 4.101585 CAGATAGTCATGGTTTCCTGGCTA 59.898 45.833 0.00 0.00 34.35 3.93
2473 2498 4.910304 AGATAGTCATGGTTTCCTGGCTAT 59.090 41.667 10.00 10.00 41.67 2.97
2474 2499 3.287867 AGTCATGGTTTCCTGGCTATG 57.712 47.619 0.00 0.00 0.00 2.23
2475 2500 2.092212 AGTCATGGTTTCCTGGCTATGG 60.092 50.000 0.00 0.00 0.00 2.74
2476 2501 2.092429 GTCATGGTTTCCTGGCTATGGA 60.092 50.000 0.00 0.00 0.00 3.41
2477 2502 2.092429 TCATGGTTTCCTGGCTATGGAC 60.092 50.000 0.00 0.00 32.65 4.02
2478 2503 1.367346 TGGTTTCCTGGCTATGGACA 58.633 50.000 0.00 0.00 32.65 4.02
2479 2504 1.922447 TGGTTTCCTGGCTATGGACAT 59.078 47.619 0.00 0.00 32.65 3.06
2480 2505 2.311542 TGGTTTCCTGGCTATGGACATT 59.688 45.455 0.00 0.00 32.65 2.71
2481 2506 2.689983 GGTTTCCTGGCTATGGACATTG 59.310 50.000 0.00 0.00 32.65 2.82
2482 2507 2.689983 GTTTCCTGGCTATGGACATTGG 59.310 50.000 0.00 0.00 32.65 3.16
2483 2508 1.891933 TCCTGGCTATGGACATTGGA 58.108 50.000 0.00 0.00 0.00 3.53
2484 2509 2.421725 TCCTGGCTATGGACATTGGAT 58.578 47.619 0.00 0.00 0.00 3.41
2485 2510 2.107031 TCCTGGCTATGGACATTGGATG 59.893 50.000 0.00 0.00 0.00 3.51
2498 2523 5.756195 ACATTGGATGTCGTTGATAATGG 57.244 39.130 0.00 0.00 39.92 3.16
2499 2524 4.580167 ACATTGGATGTCGTTGATAATGGG 59.420 41.667 0.00 0.00 39.92 4.00
2500 2525 4.495690 TTGGATGTCGTTGATAATGGGA 57.504 40.909 0.00 0.00 0.00 4.37
2501 2526 4.705110 TGGATGTCGTTGATAATGGGAT 57.295 40.909 0.00 0.00 0.00 3.85
2502 2527 4.641396 TGGATGTCGTTGATAATGGGATC 58.359 43.478 0.00 0.00 0.00 3.36
2503 2528 4.102367 TGGATGTCGTTGATAATGGGATCA 59.898 41.667 0.00 0.00 33.96 2.92
2504 2529 4.452455 GGATGTCGTTGATAATGGGATCAC 59.548 45.833 0.00 0.00 35.56 3.06
2505 2530 4.479786 TGTCGTTGATAATGGGATCACA 57.520 40.909 0.00 0.00 35.56 3.58
2506 2531 5.034852 TGTCGTTGATAATGGGATCACAT 57.965 39.130 4.06 4.06 35.56 3.21
2507 2532 5.056480 TGTCGTTGATAATGGGATCACATC 58.944 41.667 11.76 0.00 35.56 3.06
2508 2533 5.056480 GTCGTTGATAATGGGATCACATCA 58.944 41.667 11.76 2.91 35.56 3.07
2509 2534 5.702670 GTCGTTGATAATGGGATCACATCAT 59.297 40.000 11.76 0.88 35.56 2.45
2510 2535 6.205464 GTCGTTGATAATGGGATCACATCATT 59.795 38.462 11.76 9.08 35.56 2.57
2511 2536 7.387673 GTCGTTGATAATGGGATCACATCATTA 59.612 37.037 11.76 10.83 35.56 1.90
2512 2537 7.603784 TCGTTGATAATGGGATCACATCATTAG 59.396 37.037 11.76 1.42 36.97 1.73
2513 2538 7.148356 CGTTGATAATGGGATCACATCATTAGG 60.148 40.741 11.76 0.00 36.97 2.69
2514 2539 7.572546 TGATAATGGGATCACATCATTAGGA 57.427 36.000 11.76 0.55 36.97 2.94
2515 2540 7.627311 TGATAATGGGATCACATCATTAGGAG 58.373 38.462 11.76 0.00 36.97 3.69
2516 2541 7.458806 TGATAATGGGATCACATCATTAGGAGA 59.541 37.037 11.76 0.00 36.97 3.71
2517 2542 6.520021 AATGGGATCACATCATTAGGAGAA 57.480 37.500 11.76 0.00 30.35 2.87
2518 2543 6.715350 ATGGGATCACATCATTAGGAGAAT 57.285 37.500 4.06 0.00 0.00 2.40
2519 2544 5.872963 TGGGATCACATCATTAGGAGAATG 58.127 41.667 0.00 0.00 0.00 2.67
2520 2545 5.608015 TGGGATCACATCATTAGGAGAATGA 59.392 40.000 0.00 2.66 40.50 2.57
2521 2546 6.273965 TGGGATCACATCATTAGGAGAATGAT 59.726 38.462 0.00 6.90 45.40 2.45
2529 2554 6.752285 TCATTAGGAGAATGATGTGATGGA 57.248 37.500 0.00 0.00 32.21 3.41
2530 2555 6.528321 TCATTAGGAGAATGATGTGATGGAC 58.472 40.000 0.00 0.00 32.21 4.02
2531 2556 5.955961 TTAGGAGAATGATGTGATGGACA 57.044 39.130 0.00 0.00 39.53 4.02
2532 2557 4.849813 AGGAGAATGATGTGATGGACAA 57.150 40.909 0.00 0.00 38.36 3.18
2533 2558 4.778579 AGGAGAATGATGTGATGGACAAG 58.221 43.478 0.00 0.00 38.36 3.16
2534 2559 4.472470 AGGAGAATGATGTGATGGACAAGA 59.528 41.667 0.00 0.00 38.36 3.02
2535 2560 4.574013 GGAGAATGATGTGATGGACAAGAC 59.426 45.833 0.00 0.00 38.36 3.01
2536 2561 4.521146 AGAATGATGTGATGGACAAGACC 58.479 43.478 0.00 0.00 38.36 3.85
2537 2562 2.787473 TGATGTGATGGACAAGACCC 57.213 50.000 0.00 0.00 38.36 4.46
2538 2563 1.984424 TGATGTGATGGACAAGACCCA 59.016 47.619 0.00 0.00 38.36 4.51
2539 2564 2.374839 TGATGTGATGGACAAGACCCAA 59.625 45.455 0.00 0.00 38.36 4.12
2540 2565 3.010472 TGATGTGATGGACAAGACCCAAT 59.990 43.478 0.00 0.00 38.36 3.16
2541 2566 3.071874 TGTGATGGACAAGACCCAATC 57.928 47.619 0.00 0.00 37.22 2.67
2542 2567 2.290896 TGTGATGGACAAGACCCAATCC 60.291 50.000 0.00 0.00 37.22 3.01
2543 2568 2.025887 GTGATGGACAAGACCCAATCCT 60.026 50.000 0.00 0.00 37.22 3.24
2544 2569 3.199946 GTGATGGACAAGACCCAATCCTA 59.800 47.826 0.00 0.00 37.22 2.94
2545 2570 3.849574 TGATGGACAAGACCCAATCCTAA 59.150 43.478 0.00 0.00 37.22 2.69
2546 2571 4.080356 TGATGGACAAGACCCAATCCTAAG 60.080 45.833 0.00 0.00 37.22 2.18
2547 2572 2.026262 TGGACAAGACCCAATCCTAAGC 60.026 50.000 0.00 0.00 32.06 3.09
2548 2573 2.644676 GACAAGACCCAATCCTAAGCC 58.355 52.381 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.484649 GCTTTACATGATGCAAAGCGATG 59.515 43.478 22.83 0.00 43.97 3.84
15 16 7.754069 TCTCTTTTTGTTGTTGCTTTACATG 57.246 32.000 0.00 0.00 0.00 3.21
16 17 8.770438 TTTCTCTTTTTGTTGTTGCTTTACAT 57.230 26.923 0.00 0.00 0.00 2.29
48 51 4.261825 CGAAATGCCCTCAAGGTTTGTAAA 60.262 41.667 0.00 0.00 38.26 2.01
71 74 2.098934 TGACTCACACAATGTGTTTGGC 59.901 45.455 17.31 14.49 45.08 4.52
72 75 4.292599 CATGACTCACACAATGTGTTTGG 58.707 43.478 17.31 11.69 45.08 3.28
88 91 2.224079 GTCAACGTCAACATGCATGACT 59.776 45.455 32.75 16.19 43.93 3.41
112 115 2.732001 TGACTATGACATCGACGTCG 57.268 50.000 31.30 31.30 38.84 5.12
113 116 5.621634 CACTATTGACTATGACATCGACGTC 59.378 44.000 4.33 4.33 36.40 4.34
115 118 4.912187 CCACTATTGACTATGACATCGACG 59.088 45.833 0.00 0.00 0.00 5.12
116 119 5.833082 ACCACTATTGACTATGACATCGAC 58.167 41.667 0.00 0.00 0.00 4.20
117 120 6.273071 CAACCACTATTGACTATGACATCGA 58.727 40.000 0.00 0.00 0.00 3.59
118 121 5.050769 GCAACCACTATTGACTATGACATCG 60.051 44.000 0.00 0.00 0.00 3.84
119 122 5.237344 GGCAACCACTATTGACTATGACATC 59.763 44.000 0.00 0.00 34.49 3.06
126 129 3.244284 ACAACGGCAACCACTATTGACTA 60.244 43.478 0.00 0.00 35.24 2.59
136 139 2.266816 TACCACCACAACGGCAACCA 62.267 55.000 0.00 0.00 39.03 3.67
140 143 0.891449 CCATTACCACCACAACGGCA 60.891 55.000 0.00 0.00 39.03 5.69
141 144 1.591504 CCCATTACCACCACAACGGC 61.592 60.000 0.00 0.00 39.03 5.68
152 155 0.466555 TTATGCCACGGCCCATTACC 60.467 55.000 5.42 0.00 41.09 2.85
154 157 3.009584 TCATATTATGCCACGGCCCATTA 59.990 43.478 5.42 0.00 41.09 1.90
161 164 8.267620 TCATAAAGATTCATATTATGCCACGG 57.732 34.615 0.00 0.00 37.09 4.94
223 226 7.502561 GCCCTTGTAATTATGAGGTCATACTTT 59.497 37.037 13.15 4.53 38.44 2.66
227 230 5.371176 TGGCCCTTGTAATTATGAGGTCATA 59.629 40.000 0.00 0.00 37.76 2.15
237 243 2.042433 AGCACCTTGGCCCTTGTAATTA 59.958 45.455 0.00 0.00 0.00 1.40
239 245 0.409484 AGCACCTTGGCCCTTGTAAT 59.591 50.000 0.00 0.00 0.00 1.89
284 290 9.342308 CTATATAAATGTGCTTCCAGGAGAAAA 57.658 33.333 0.00 0.00 32.88 2.29
292 298 9.679661 TTTGTTCTCTATATAAATGTGCTTCCA 57.320 29.630 0.00 0.00 0.00 3.53
370 376 4.202243 ACACCATTTGATTTGTTGGAGGTG 60.202 41.667 0.00 0.00 46.95 4.00
371 377 3.966665 ACACCATTTGATTTGTTGGAGGT 59.033 39.130 0.00 0.00 0.00 3.85
376 382 4.309099 CCTCCACACCATTTGATTTGTTG 58.691 43.478 0.00 0.00 0.00 3.33
377 383 3.244181 GCCTCCACACCATTTGATTTGTT 60.244 43.478 0.00 0.00 0.00 2.83
401 407 4.951094 AGCTATATCTCTTAGGGCCTAACG 59.049 45.833 22.01 16.94 0.00 3.18
447 453 8.592105 AGTACTCGCTAGTAATAGTTACTCTG 57.408 38.462 5.70 3.03 44.90 3.35
455 461 9.828852 CCATTTAAGAGTACTCGCTAGTAATAG 57.171 37.037 17.07 0.00 39.90 1.73
456 462 9.347240 ACCATTTAAGAGTACTCGCTAGTAATA 57.653 33.333 17.07 0.15 39.90 0.98
460 466 5.163540 CCACCATTTAAGAGTACTCGCTAGT 60.164 44.000 17.07 7.08 39.91 2.57
464 470 2.608090 GCCACCATTTAAGAGTACTCGC 59.392 50.000 17.07 6.76 34.09 5.03
466 472 5.675538 AGATGCCACCATTTAAGAGTACTC 58.324 41.667 15.41 15.41 0.00 2.59
468 474 5.675538 AGAGATGCCACCATTTAAGAGTAC 58.324 41.667 0.00 0.00 0.00 2.73
472 478 7.071698 AGAGAATAGAGATGCCACCATTTAAGA 59.928 37.037 0.00 0.00 0.00 2.10
473 479 7.222872 AGAGAATAGAGATGCCACCATTTAAG 58.777 38.462 0.00 0.00 0.00 1.85
481 487 8.900983 AAAGATAAAGAGAATAGAGATGCCAC 57.099 34.615 0.00 0.00 0.00 5.01
493 499 9.429359 GACACATCTGAGAAAAGATAAAGAGAA 57.571 33.333 0.00 0.00 35.09 2.87
503 509 4.454847 AGCATGTGACACATCTGAGAAAAG 59.545 41.667 18.27 5.37 36.53 2.27
518 524 2.435410 CAGCCAGCGAGCATGTGA 60.435 61.111 3.80 0.00 34.23 3.58
528 534 1.602888 CATAGATGGGGCAGCCAGC 60.603 63.158 15.19 0.00 44.65 4.85
533 539 0.250038 CGTGGTCATAGATGGGGCAG 60.250 60.000 0.00 0.00 0.00 4.85
539 545 5.515797 TTTCTCTACCGTGGTCATAGATG 57.484 43.478 0.00 0.00 0.00 2.90
543 549 8.582437 CCTTATTATTTCTCTACCGTGGTCATA 58.418 37.037 0.00 0.00 0.00 2.15
547 553 5.664457 ACCCTTATTATTTCTCTACCGTGGT 59.336 40.000 0.00 0.00 0.00 4.16
562 568 9.150028 GGGCAAAAGGATAATTAACCCTTATTA 57.850 33.333 17.67 0.00 39.21 0.98
590 596 0.610174 TGAGCAGATGGACACCACTC 59.390 55.000 0.00 0.00 35.80 3.51
1267 1275 1.949799 ATCAGAGTCTTGGCCAGAGT 58.050 50.000 5.11 8.92 37.96 3.24
1363 1371 1.573108 TCGCCCTCCATCTCTTCTTT 58.427 50.000 0.00 0.00 0.00 2.52
1897 1911 6.196353 CGATGTAATGCCCTTAAAAATGTTCG 59.804 38.462 0.00 0.00 0.00 3.95
1972 1989 2.195683 CCCCAGCCGCACCAATAT 59.804 61.111 0.00 0.00 0.00 1.28
1973 1990 3.012119 TCCCCAGCCGCACCAATA 61.012 61.111 0.00 0.00 0.00 1.90
2032 2055 3.678056 CTGTCCTAACAGTTACCAGCA 57.322 47.619 0.00 0.00 46.52 4.41
2042 2065 2.906389 ACTCTTGCCATCTGTCCTAACA 59.094 45.455 0.00 0.00 0.00 2.41
2044 2067 4.041567 TCAAACTCTTGCCATCTGTCCTAA 59.958 41.667 0.00 0.00 32.14 2.69
2154 2179 3.319198 GGGTTCGAGTCCCCAGCA 61.319 66.667 14.49 0.00 40.88 4.41
2220 2245 3.554934 TGTCAAACTCTTGCCATCTGTT 58.445 40.909 0.00 0.00 32.14 3.16
2258 2283 9.231297 GGCATATTTCCAACACACTATGTATAT 57.769 33.333 0.00 0.00 42.31 0.86
2270 2295 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
2283 2308 7.881775 AACACTTTTATTATTGCCTCTAGGG 57.118 36.000 0.00 0.00 35.18 3.53
2344 2369 8.758829 TCCGGATAATACAGTTATAGCATGAAT 58.241 33.333 0.00 0.00 0.00 2.57
2345 2370 8.129496 TCCGGATAATACAGTTATAGCATGAA 57.871 34.615 0.00 0.00 0.00 2.57
2346 2371 7.712204 TCCGGATAATACAGTTATAGCATGA 57.288 36.000 0.00 0.00 0.00 3.07
2347 2372 8.771920 TTTCCGGATAATACAGTTATAGCATG 57.228 34.615 4.15 0.00 0.00 4.06
2348 2373 9.601217 GATTTCCGGATAATACAGTTATAGCAT 57.399 33.333 4.15 0.00 0.00 3.79
2349 2374 7.758076 CGATTTCCGGATAATACAGTTATAGCA 59.242 37.037 4.15 0.00 33.91 3.49
2350 2375 7.758528 ACGATTTCCGGATAATACAGTTATAGC 59.241 37.037 4.15 0.00 43.93 2.97
2355 2380 9.415544 GTATTACGATTTCCGGATAATACAGTT 57.584 33.333 26.02 11.20 39.68 3.16
2356 2381 8.579006 TGTATTACGATTTCCGGATAATACAGT 58.421 33.333 28.04 20.31 41.92 3.55
2357 2382 8.857216 GTGTATTACGATTTCCGGATAATACAG 58.143 37.037 30.32 18.57 44.29 2.74
2358 2383 8.746922 GTGTATTACGATTTCCGGATAATACA 57.253 34.615 28.04 28.04 43.07 2.29
2375 2400 7.916977 TGGTCTATGTATTCACACGTGTATTAC 59.083 37.037 22.90 20.91 37.54 1.89
2376 2401 7.916977 GTGGTCTATGTATTCACACGTGTATTA 59.083 37.037 22.90 9.93 37.54 0.98
2377 2402 6.755141 GTGGTCTATGTATTCACACGTGTATT 59.245 38.462 22.90 11.42 37.54 1.89
2378 2403 6.127563 TGTGGTCTATGTATTCACACGTGTAT 60.128 38.462 22.90 14.96 37.54 2.29
2379 2404 5.183522 TGTGGTCTATGTATTCACACGTGTA 59.816 40.000 22.90 7.35 37.54 2.90
2380 2405 4.021807 TGTGGTCTATGTATTCACACGTGT 60.022 41.667 17.22 17.22 37.54 4.49
2381 2406 4.490743 TGTGGTCTATGTATTCACACGTG 58.509 43.478 15.48 15.48 37.54 4.49
2382 2407 4.794278 TGTGGTCTATGTATTCACACGT 57.206 40.909 0.00 0.00 37.54 4.49
2383 2408 7.438160 ACATATTGTGGTCTATGTATTCACACG 59.562 37.037 0.00 0.00 36.93 4.49
2384 2409 8.662781 ACATATTGTGGTCTATGTATTCACAC 57.337 34.615 0.00 0.00 36.93 3.82
2385 2410 7.931407 GGACATATTGTGGTCTATGTATTCACA 59.069 37.037 0.00 0.00 38.38 3.58
2386 2411 7.387948 GGGACATATTGTGGTCTATGTATTCAC 59.612 40.741 0.00 0.00 38.38 3.18
2387 2412 7.292356 AGGGACATATTGTGGTCTATGTATTCA 59.708 37.037 0.00 0.00 38.38 2.57
2388 2413 7.680730 AGGGACATATTGTGGTCTATGTATTC 58.319 38.462 0.00 0.00 38.38 1.75
2389 2414 7.633018 AGGGACATATTGTGGTCTATGTATT 57.367 36.000 0.00 0.00 38.38 1.89
2390 2415 7.956315 ACTAGGGACATATTGTGGTCTATGTAT 59.044 37.037 0.00 0.00 38.38 2.29
2391 2416 7.232737 CACTAGGGACATATTGTGGTCTATGTA 59.767 40.741 0.00 0.00 38.38 2.29
2392 2417 6.042093 CACTAGGGACATATTGTGGTCTATGT 59.958 42.308 0.00 0.00 40.38 2.29
2393 2418 6.267699 TCACTAGGGACATATTGTGGTCTATG 59.732 42.308 0.00 0.00 34.49 2.23
2394 2419 6.382087 TCACTAGGGACATATTGTGGTCTAT 58.618 40.000 0.00 0.00 34.49 1.98
2395 2420 5.773091 TCACTAGGGACATATTGTGGTCTA 58.227 41.667 0.00 0.00 34.49 2.59
2396 2421 4.620723 TCACTAGGGACATATTGTGGTCT 58.379 43.478 0.00 0.00 34.49 3.85
2397 2422 4.740934 GCTCACTAGGGACATATTGTGGTC 60.741 50.000 0.00 0.00 0.00 4.02
2398 2423 3.134804 GCTCACTAGGGACATATTGTGGT 59.865 47.826 0.00 0.00 0.00 4.16
2399 2424 3.495100 GGCTCACTAGGGACATATTGTGG 60.495 52.174 0.00 0.00 0.00 4.17
2400 2425 3.389329 AGGCTCACTAGGGACATATTGTG 59.611 47.826 0.00 0.00 0.00 3.33
2401 2426 3.643792 GAGGCTCACTAGGGACATATTGT 59.356 47.826 10.25 0.00 0.00 2.71
2402 2427 3.900601 AGAGGCTCACTAGGGACATATTG 59.099 47.826 18.26 0.00 0.00 1.90
2403 2428 4.206244 AGAGGCTCACTAGGGACATATT 57.794 45.455 18.26 0.00 0.00 1.28
2404 2429 3.913370 AGAGGCTCACTAGGGACATAT 57.087 47.619 18.26 0.00 0.00 1.78
2405 2430 3.722627 ACTAGAGGCTCACTAGGGACATA 59.277 47.826 18.26 0.00 40.86 2.29
2406 2431 2.516277 ACTAGAGGCTCACTAGGGACAT 59.484 50.000 18.26 0.00 40.86 3.06
2407 2432 1.923850 ACTAGAGGCTCACTAGGGACA 59.076 52.381 18.26 0.00 40.86 4.02
2408 2433 2.691011 CAACTAGAGGCTCACTAGGGAC 59.309 54.545 18.26 0.00 40.86 4.46
2409 2434 2.581246 TCAACTAGAGGCTCACTAGGGA 59.419 50.000 18.26 9.66 40.86 4.20
2410 2435 2.691011 GTCAACTAGAGGCTCACTAGGG 59.309 54.545 18.26 7.64 40.86 3.53
2411 2436 3.626930 AGTCAACTAGAGGCTCACTAGG 58.373 50.000 18.26 3.24 40.86 3.02
2412 2437 4.274950 GCTAGTCAACTAGAGGCTCACTAG 59.725 50.000 23.14 23.14 46.80 2.57
2413 2438 4.080243 AGCTAGTCAACTAGAGGCTCACTA 60.080 45.833 18.26 12.80 46.80 2.74
2414 2439 3.020984 GCTAGTCAACTAGAGGCTCACT 58.979 50.000 18.26 12.32 46.80 3.41
2415 2440 3.020984 AGCTAGTCAACTAGAGGCTCAC 58.979 50.000 18.26 4.72 46.80 3.51
2416 2441 3.283751 GAGCTAGTCAACTAGAGGCTCA 58.716 50.000 18.26 1.80 46.80 4.26
2417 2442 2.289547 CGAGCTAGTCAACTAGAGGCTC 59.710 54.545 19.03 16.73 46.80 4.70
2418 2443 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
2419 2444 2.018515 ACGAGCTAGTCAACTAGAGGC 58.981 52.381 19.03 6.58 46.80 4.70
2420 2445 3.440872 ACAACGAGCTAGTCAACTAGAGG 59.559 47.826 19.03 10.05 46.80 3.69
2421 2446 4.154375 TCACAACGAGCTAGTCAACTAGAG 59.846 45.833 19.03 11.89 46.80 2.43
2422 2447 4.070009 TCACAACGAGCTAGTCAACTAGA 58.930 43.478 19.03 0.00 46.80 2.43
2423 2448 4.421033 TCACAACGAGCTAGTCAACTAG 57.579 45.455 11.99 11.99 46.63 2.57
2424 2449 4.457949 TGATCACAACGAGCTAGTCAACTA 59.542 41.667 0.00 0.00 0.00 2.24
2425 2450 3.255888 TGATCACAACGAGCTAGTCAACT 59.744 43.478 0.00 0.00 0.00 3.16
2426 2451 3.575630 TGATCACAACGAGCTAGTCAAC 58.424 45.455 0.00 0.00 0.00 3.18
2427 2452 3.934457 TGATCACAACGAGCTAGTCAA 57.066 42.857 0.00 0.00 0.00 3.18
2428 2453 3.575630 GTTGATCACAACGAGCTAGTCA 58.424 45.455 0.00 0.00 45.06 3.41
2439 2464 6.053632 ACCATGACTATCTGTTGATCACAA 57.946 37.500 0.00 0.00 33.87 3.33
2440 2465 5.682234 ACCATGACTATCTGTTGATCACA 57.318 39.130 0.00 0.00 34.32 3.58
2441 2466 6.037610 GGAAACCATGACTATCTGTTGATCAC 59.962 42.308 0.00 0.00 34.32 3.06
2442 2467 6.070021 AGGAAACCATGACTATCTGTTGATCA 60.070 38.462 0.00 0.00 34.32 2.92
2443 2468 6.259608 CAGGAAACCATGACTATCTGTTGATC 59.740 42.308 0.00 0.00 34.32 2.92
2444 2469 6.118170 CAGGAAACCATGACTATCTGTTGAT 58.882 40.000 0.00 0.00 36.74 2.57
2445 2470 5.491070 CAGGAAACCATGACTATCTGTTGA 58.509 41.667 0.00 0.00 0.00 3.18
2446 2471 4.637534 CCAGGAAACCATGACTATCTGTTG 59.362 45.833 0.00 0.00 0.00 3.33
2447 2472 4.848357 CCAGGAAACCATGACTATCTGTT 58.152 43.478 0.00 0.00 0.00 3.16
2448 2473 3.370953 GCCAGGAAACCATGACTATCTGT 60.371 47.826 0.00 0.00 0.00 3.41
2449 2474 3.118112 AGCCAGGAAACCATGACTATCTG 60.118 47.826 0.00 0.00 0.00 2.90
2450 2475 3.118531 AGCCAGGAAACCATGACTATCT 58.881 45.455 0.00 0.00 0.00 1.98
2451 2476 3.567478 AGCCAGGAAACCATGACTATC 57.433 47.619 0.00 0.00 0.00 2.08
2452 2477 4.202503 CCATAGCCAGGAAACCATGACTAT 60.203 45.833 0.00 0.00 0.00 2.12
2453 2478 3.136443 CCATAGCCAGGAAACCATGACTA 59.864 47.826 0.00 0.00 0.00 2.59
2454 2479 2.092212 CCATAGCCAGGAAACCATGACT 60.092 50.000 0.00 0.00 0.00 3.41
2455 2480 2.092429 TCCATAGCCAGGAAACCATGAC 60.092 50.000 0.00 0.00 30.71 3.06
2456 2481 2.092429 GTCCATAGCCAGGAAACCATGA 60.092 50.000 0.00 0.00 36.80 3.07
2457 2482 2.301346 GTCCATAGCCAGGAAACCATG 58.699 52.381 0.00 0.00 36.80 3.66
2458 2483 1.922447 TGTCCATAGCCAGGAAACCAT 59.078 47.619 0.00 0.00 36.80 3.55
2459 2484 1.367346 TGTCCATAGCCAGGAAACCA 58.633 50.000 0.00 0.00 36.80 3.67
2460 2485 2.689983 CAATGTCCATAGCCAGGAAACC 59.310 50.000 0.00 0.00 36.80 3.27
2461 2486 2.689983 CCAATGTCCATAGCCAGGAAAC 59.310 50.000 0.00 0.00 36.80 2.78
2462 2487 2.580322 TCCAATGTCCATAGCCAGGAAA 59.420 45.455 0.00 0.00 36.80 3.13
2463 2488 2.204463 TCCAATGTCCATAGCCAGGAA 58.796 47.619 0.00 0.00 36.80 3.36
2464 2489 1.891933 TCCAATGTCCATAGCCAGGA 58.108 50.000 0.00 0.00 0.00 3.86
2465 2490 2.158564 ACATCCAATGTCCATAGCCAGG 60.159 50.000 0.00 0.00 39.92 4.45
2466 2491 3.219176 ACATCCAATGTCCATAGCCAG 57.781 47.619 0.00 0.00 39.92 4.85
2477 2502 4.821260 TCCCATTATCAACGACATCCAATG 59.179 41.667 0.00 0.00 0.00 2.82
2478 2503 5.047566 TCCCATTATCAACGACATCCAAT 57.952 39.130 0.00 0.00 0.00 3.16
2479 2504 4.495690 TCCCATTATCAACGACATCCAA 57.504 40.909 0.00 0.00 0.00 3.53
2480 2505 4.102367 TGATCCCATTATCAACGACATCCA 59.898 41.667 0.00 0.00 32.97 3.41
2481 2506 4.452455 GTGATCCCATTATCAACGACATCC 59.548 45.833 0.00 0.00 37.61 3.51
2482 2507 5.056480 TGTGATCCCATTATCAACGACATC 58.944 41.667 0.00 0.00 37.61 3.06
2483 2508 5.034852 TGTGATCCCATTATCAACGACAT 57.965 39.130 0.00 0.00 37.61 3.06
2484 2509 4.479786 TGTGATCCCATTATCAACGACA 57.520 40.909 0.00 0.00 37.61 4.35
2485 2510 5.056480 TGATGTGATCCCATTATCAACGAC 58.944 41.667 0.00 0.00 37.61 4.34
2486 2511 5.289083 TGATGTGATCCCATTATCAACGA 57.711 39.130 0.00 0.00 37.61 3.85
2487 2512 6.564709 AATGATGTGATCCCATTATCAACG 57.435 37.500 0.00 0.00 37.61 4.10
2488 2513 7.884877 TCCTAATGATGTGATCCCATTATCAAC 59.115 37.037 0.00 0.00 37.61 3.18
2489 2514 7.987820 TCCTAATGATGTGATCCCATTATCAA 58.012 34.615 0.00 0.00 37.61 2.57
2490 2515 7.458806 TCTCCTAATGATGTGATCCCATTATCA 59.541 37.037 0.00 0.00 33.79 2.15
2491 2516 7.855375 TCTCCTAATGATGTGATCCCATTATC 58.145 38.462 0.00 0.00 33.79 1.75
2492 2517 7.819521 TCTCCTAATGATGTGATCCCATTAT 57.180 36.000 0.00 0.00 33.79 1.28
2493 2518 7.631510 TTCTCCTAATGATGTGATCCCATTA 57.368 36.000 0.00 0.00 33.21 1.90
2494 2519 6.520021 TTCTCCTAATGATGTGATCCCATT 57.480 37.500 0.00 0.00 35.09 3.16
2495 2520 6.273965 TCATTCTCCTAATGATGTGATCCCAT 59.726 38.462 0.00 0.00 32.21 4.00
2496 2521 5.608015 TCATTCTCCTAATGATGTGATCCCA 59.392 40.000 0.00 0.00 32.21 4.37
2497 2522 6.119240 TCATTCTCCTAATGATGTGATCCC 57.881 41.667 0.00 0.00 32.21 3.85
2505 2530 7.166851 GTCCATCACATCATTCTCCTAATGAT 58.833 38.462 7.28 7.28 45.40 2.45
2506 2531 6.100134 TGTCCATCACATCATTCTCCTAATGA 59.900 38.462 3.13 3.13 40.50 2.57
2507 2532 6.293698 TGTCCATCACATCATTCTCCTAATG 58.706 40.000 0.00 0.00 0.00 1.90
2508 2533 6.505048 TGTCCATCACATCATTCTCCTAAT 57.495 37.500 0.00 0.00 0.00 1.73
2509 2534 5.955961 TGTCCATCACATCATTCTCCTAA 57.044 39.130 0.00 0.00 0.00 2.69
2510 2535 5.662657 TCTTGTCCATCACATCATTCTCCTA 59.337 40.000 0.00 0.00 33.90 2.94
2511 2536 4.472470 TCTTGTCCATCACATCATTCTCCT 59.528 41.667 0.00 0.00 33.90 3.69
2512 2537 4.574013 GTCTTGTCCATCACATCATTCTCC 59.426 45.833 0.00 0.00 33.90 3.71
2513 2538 4.574013 GGTCTTGTCCATCACATCATTCTC 59.426 45.833 0.00 0.00 33.90 2.87
2514 2539 4.521146 GGTCTTGTCCATCACATCATTCT 58.479 43.478 0.00 0.00 33.90 2.40
2515 2540 3.629398 GGGTCTTGTCCATCACATCATTC 59.371 47.826 0.00 0.00 33.90 2.67
2516 2541 3.010472 TGGGTCTTGTCCATCACATCATT 59.990 43.478 0.00 0.00 33.90 2.57
2517 2542 2.577563 TGGGTCTTGTCCATCACATCAT 59.422 45.455 0.00 0.00 33.90 2.45
2518 2543 1.984424 TGGGTCTTGTCCATCACATCA 59.016 47.619 0.00 0.00 33.90 3.07
2519 2544 2.787473 TGGGTCTTGTCCATCACATC 57.213 50.000 0.00 0.00 33.90 3.06
2520 2545 3.624777 GATTGGGTCTTGTCCATCACAT 58.375 45.455 0.00 0.00 33.90 3.21
2521 2546 2.290896 GGATTGGGTCTTGTCCATCACA 60.291 50.000 0.00 0.00 33.82 3.58
2522 2547 2.025887 AGGATTGGGTCTTGTCCATCAC 60.026 50.000 0.00 0.00 33.82 3.06
2523 2548 2.278245 AGGATTGGGTCTTGTCCATCA 58.722 47.619 0.00 0.00 33.82 3.07
2524 2549 4.455606 CTTAGGATTGGGTCTTGTCCATC 58.544 47.826 0.00 0.00 33.82 3.51
2525 2550 3.372025 GCTTAGGATTGGGTCTTGTCCAT 60.372 47.826 0.00 0.00 33.82 3.41
2526 2551 2.026262 GCTTAGGATTGGGTCTTGTCCA 60.026 50.000 0.00 0.00 33.12 4.02
2527 2552 2.644676 GCTTAGGATTGGGTCTTGTCC 58.355 52.381 0.00 0.00 0.00 4.02
2528 2553 2.644676 GGCTTAGGATTGGGTCTTGTC 58.355 52.381 0.00 0.00 0.00 3.18
2529 2554 2.808906 GGCTTAGGATTGGGTCTTGT 57.191 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.