Multiple sequence alignment - TraesCS5A01G191500

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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 TraesCS5A01G191500 chr5A 100.000 4317 0 0 1 4317 395836669 395832353 0.000000e+00 7973
1 TraesCS5A01G191500 chr5D 92.446 2396 117 15 20 2403 302018028 302020371 0.000000e+00 3363
2 TraesCS5A01G191500 chr5D 93.450 1084 57 10 2426 3497 302020364 302021445 0.000000e+00 1596
3 TraesCS5A01G191500 chr5D 94.545 330 17 1 1534 1862 328392812 328392483 3.850000e-140 508
4 TraesCS5A01G191500 chr5D 85.246 427 38 19 3668 4082 302021749 302022162 2.400000e-112 416
5 TraesCS5A01G191500 chr5D 95.455 88 4 0 3574 3661 302021625 302021712 1.620000e-29 141
6 TraesCS5A01G191500 chr5B 90.675 2327 130 27 28 2337 345050902 345053158 0.000000e+00 3014
7 TraesCS5A01G191500 chr5B 92.814 1002 53 13 2425 3410 345053181 345054179 0.000000e+00 1434
8 TraesCS5A01G191500 chr5B 85.145 276 21 1 3406 3661 345054300 345054575 9.210000e-67 265
9 TraesCS5A01G191500 chr5B 84.186 215 25 4 4068 4279 345055068 345055276 2.630000e-47 200
10 TraesCS5A01G191500 chr6A 89.970 329 31 2 1534 1861 536911679 536912006 1.440000e-114 424
11 TraesCS5A01G191500 chr7D 94.545 165 9 0 1542 1706 55445958 55446122 5.540000e-64 255
12 TraesCS5A01G191500 chr3B 97.810 137 3 0 1570 1706 612294627 612294763 2.010000e-58 237


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 TraesCS5A01G191500 chr5A 395832353 395836669 4316 True 7973.00 7973 100.00000 1 4317 1 chr5A.!!$R1 4316
1 TraesCS5A01G191500 chr5D 302018028 302022162 4134 False 1379.00 3363 91.64925 20 4082 4 chr5D.!!$F1 4062
2 TraesCS5A01G191500 chr5B 345050902 345055276 4374 False 1228.25 3014 88.20500 28 4279 4 chr5B.!!$F1 4251

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
799 829 0.179150 AGAGAGATGTTCGCTGCGTC 60.179 55.0 22.48 16.05 34.39 5.19 F
932 969 0.323629 TGTTAACTCTTCCCCGCTGG 59.676 55.0 7.22 0.00 0.00 4.85 F
970 1007 0.388134 CCGGTCACGACTCACGAATT 60.388 55.0 0.00 0.00 45.77 2.17 F
973 1010 0.438830 GTCACGACTCACGAATTGGC 59.561 55.0 0.00 0.00 45.77 4.52 F
2419 2471 0.107654 GGGACTGAAGGGAATGGTCG 60.108 60.0 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 2355 0.105039 GCGACCAAGGGTATGAGGAG 59.895 60.0 0.0 0.0 35.25 3.69 R
2404 2456 0.107654 GTCCCGACCATTCCCTTCAG 60.108 60.0 0.0 0.0 0.00 3.02 R
2411 2463 0.107654 CTCCCAAGTCCCGACCATTC 60.108 60.0 0.0 0.0 0.00 2.67 R
2665 2729 0.112995 TGACTGCCCTGCCTGAAAAT 59.887 50.0 0.0 0.0 0.00 1.82 R
3375 3442 0.310854 GTGTTTCAAACCTCAGCCGG 59.689 55.0 0.0 0.0 0.00 6.13 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
46 47 1.238439 CCGTGTGCAGAATTCAGGTT 58.762 50.000 8.44 0.00 0.00 3.50
58 59 7.066284 TGCAGAATTCAGGTTCTCTATAAAAGC 59.934 37.037 8.44 0.00 36.33 3.51
88 89 2.825205 CCAAGCAGGTGGAAACAAAAG 58.175 47.619 0.00 0.00 46.06 2.27
179 180 5.551760 AATTCCAGCACTAGAAAATCACG 57.448 39.130 0.00 0.00 0.00 4.35
195 196 5.695851 AATCACGGATGATAATTTCCAGC 57.304 39.130 0.00 0.00 45.26 4.85
213 214 3.612860 CCAGCACTAGACAAACACGATAC 59.387 47.826 0.00 0.00 0.00 2.24
275 276 7.142306 TCTACACCTATAGCACTTATAAGCG 57.858 40.000 12.54 4.18 35.48 4.68
287 288 6.071334 AGCACTTATAAGCGCCATATCTCTTA 60.071 38.462 19.36 0.00 34.73 2.10
289 290 6.531948 CACTTATAAGCGCCATATCTCTTACC 59.468 42.308 12.54 0.00 0.00 2.85
386 387 2.862541 ACAAACAATGCTGAGCTACCA 58.137 42.857 5.83 0.00 0.00 3.25
397 398 4.202295 TGCTGAGCTACCATGGATAAGAAG 60.202 45.833 21.47 10.05 0.00 2.85
406 407 7.547370 GCTACCATGGATAAGAAGACATCATAC 59.453 40.741 21.47 0.00 0.00 2.39
409 410 6.370994 CCATGGATAAGAAGACATCATACTGC 59.629 42.308 5.56 0.00 0.00 4.40
417 418 7.317842 AGAAGACATCATACTGCAATTTCAG 57.682 36.000 3.36 3.36 39.86 3.02
421 422 8.114331 AGACATCATACTGCAATTTCAGAAAA 57.886 30.769 12.25 0.00 37.51 2.29
422 423 8.242053 AGACATCATACTGCAATTTCAGAAAAG 58.758 33.333 12.25 0.00 37.51 2.27
423 424 8.114331 ACATCATACTGCAATTTCAGAAAAGA 57.886 30.769 12.25 4.78 37.51 2.52
424 425 8.242053 ACATCATACTGCAATTTCAGAAAAGAG 58.758 33.333 12.25 0.91 37.51 2.85
425 426 6.615088 TCATACTGCAATTTCAGAAAAGAGC 58.385 36.000 12.25 5.30 37.51 4.09
428 429 5.663456 ACTGCAATTTCAGAAAAGAGCAAA 58.337 33.333 12.25 1.79 37.53 3.68
429 430 5.751990 ACTGCAATTTCAGAAAAGAGCAAAG 59.248 36.000 12.25 10.91 37.53 2.77
430 431 4.508861 TGCAATTTCAGAAAAGAGCAAAGC 59.491 37.500 14.39 5.53 36.06 3.51
431 432 4.508861 GCAATTTCAGAAAAGAGCAAAGCA 59.491 37.500 0.00 0.00 31.81 3.91
432 433 5.006941 GCAATTTCAGAAAAGAGCAAAGCAA 59.993 36.000 0.00 0.00 31.81 3.91
433 434 6.293244 GCAATTTCAGAAAAGAGCAAAGCAAT 60.293 34.615 0.00 0.00 31.81 3.56
434 435 7.288672 CAATTTCAGAAAAGAGCAAAGCAATC 58.711 34.615 0.00 0.00 0.00 2.67
435 436 5.518848 TTCAGAAAAGAGCAAAGCAATCA 57.481 34.783 0.00 0.00 0.00 2.57
436 437 5.117355 TCAGAAAAGAGCAAAGCAATCAG 57.883 39.130 0.00 0.00 0.00 2.90
437 438 4.823442 TCAGAAAAGAGCAAAGCAATCAGA 59.177 37.500 0.00 0.00 0.00 3.27
438 439 4.916249 CAGAAAAGAGCAAAGCAATCAGAC 59.084 41.667 0.00 0.00 0.00 3.51
439 440 4.581824 AGAAAAGAGCAAAGCAATCAGACA 59.418 37.500 0.00 0.00 0.00 3.41
440 441 3.911661 AAGAGCAAAGCAATCAGACAC 57.088 42.857 0.00 0.00 0.00 3.67
441 442 2.157738 AGAGCAAAGCAATCAGACACC 58.842 47.619 0.00 0.00 0.00 4.16
442 443 1.881973 GAGCAAAGCAATCAGACACCA 59.118 47.619 0.00 0.00 0.00 4.17
443 444 1.884579 AGCAAAGCAATCAGACACCAG 59.115 47.619 0.00 0.00 0.00 4.00
444 445 1.881973 GCAAAGCAATCAGACACCAGA 59.118 47.619 0.00 0.00 0.00 3.86
445 446 2.351157 GCAAAGCAATCAGACACCAGAC 60.351 50.000 0.00 0.00 0.00 3.51
446 447 2.880268 CAAAGCAATCAGACACCAGACA 59.120 45.455 0.00 0.00 0.00 3.41
447 448 2.469274 AGCAATCAGACACCAGACAG 57.531 50.000 0.00 0.00 0.00 3.51
448 449 1.696336 AGCAATCAGACACCAGACAGT 59.304 47.619 0.00 0.00 0.00 3.55
459 477 3.056250 ACACCAGACAGTGCTAAGATCTG 60.056 47.826 0.00 0.00 41.67 2.90
485 503 1.414158 TGATTCCGATCCCTCCAGTC 58.586 55.000 0.00 0.00 0.00 3.51
517 536 4.492791 TGACTCAACGACAATCGACTAA 57.507 40.909 5.04 0.00 43.74 2.24
522 541 5.798934 ACTCAACGACAATCGACTAATACAC 59.201 40.000 5.04 0.00 43.74 2.90
679 698 3.077907 CCCACCACCGTCAGGATT 58.922 61.111 0.00 0.00 41.02 3.01
685 704 3.055675 CCACCACCGTCAGGATTAAGTTA 60.056 47.826 0.00 0.00 41.02 2.24
719 749 2.688515 GCCTCTCTGTAGAACCCTAGCT 60.689 54.545 0.00 0.00 0.00 3.32
799 829 0.179150 AGAGAGATGTTCGCTGCGTC 60.179 55.000 22.48 16.05 34.39 5.19
833 863 0.769873 AGATATGGGCTTCCCTGCTG 59.230 55.000 3.27 0.00 45.70 4.41
861 895 0.916086 AAGGTCCTGTGTGGTGTTGA 59.084 50.000 0.00 0.00 37.07 3.18
886 920 0.893727 CGTTAAAGGCCCAGGTGCTT 60.894 55.000 0.00 0.00 0.00 3.91
893 927 2.328099 GCCCAGGTGCTTCTTCACG 61.328 63.158 0.00 0.00 37.83 4.35
898 932 2.035442 GGTGCTTCTTCACGAGGCC 61.035 63.158 0.00 0.00 43.56 5.19
920 957 2.959465 AAGCCCAGCTTCTGTTAACT 57.041 45.000 7.22 0.00 46.77 2.24
921 958 2.481289 AGCCCAGCTTCTGTTAACTC 57.519 50.000 7.22 0.00 33.89 3.01
922 959 1.981495 AGCCCAGCTTCTGTTAACTCT 59.019 47.619 7.22 0.00 33.89 3.24
932 969 0.323629 TGTTAACTCTTCCCCGCTGG 59.676 55.000 7.22 0.00 0.00 4.85
967 1004 4.034258 GCCGGTCACGACTCACGA 62.034 66.667 1.90 0.00 45.77 4.35
968 1005 2.640989 CCGGTCACGACTCACGAA 59.359 61.111 0.00 0.00 45.77 3.85
969 1006 1.211969 CCGGTCACGACTCACGAAT 59.788 57.895 0.00 0.00 45.77 3.34
970 1007 0.388134 CCGGTCACGACTCACGAATT 60.388 55.000 0.00 0.00 45.77 2.17
971 1008 0.708370 CGGTCACGACTCACGAATTG 59.292 55.000 0.00 0.00 45.77 2.32
972 1009 1.068474 GGTCACGACTCACGAATTGG 58.932 55.000 0.00 0.00 45.77 3.16
973 1010 0.438830 GTCACGACTCACGAATTGGC 59.561 55.000 0.00 0.00 45.77 4.52
1055 1092 2.435586 CTGCCTCCTCCGTGCAAG 60.436 66.667 0.00 0.00 34.06 4.01
1185 1234 3.003763 GTGTCTTCCCCTCCGGCT 61.004 66.667 0.00 0.00 0.00 5.52
1209 1258 0.471780 TGTCTTCTGACCTCCCAGCA 60.472 55.000 0.00 0.00 42.28 4.41
1213 1262 0.471780 TTCTGACCTCCCAGCAGTCA 60.472 55.000 0.00 0.00 38.17 3.41
1376 1425 1.079819 CGGCCTCTCTGAAAAGCGA 60.080 57.895 0.00 0.00 0.00 4.93
1398 1447 1.925455 CCTCCAGGAGGGCCAAGAA 60.925 63.158 26.87 0.00 45.43 2.52
1477 1526 0.877743 GAAGAAGAGCAAGGTGGTGC 59.122 55.000 0.00 0.00 45.28 5.01
2163 2212 0.522180 AGCTGACGTCCAGACTTACG 59.478 55.000 14.12 5.73 45.78 3.18
2174 2223 2.362632 ACTTACGCCCGAGGAGCT 60.363 61.111 0.00 0.00 0.00 4.09
2178 2227 1.537814 TTACGCCCGAGGAGCTGAAA 61.538 55.000 0.00 0.00 0.00 2.69
2236 2285 8.425577 AACATACAGAATAAAGGTCTCATTCG 57.574 34.615 0.00 0.00 34.55 3.34
2237 2286 7.556844 ACATACAGAATAAAGGTCTCATTCGT 58.443 34.615 0.00 0.00 34.55 3.85
2263 2312 6.209192 TCCATCTTATGCACATTTTGTCAGTT 59.791 34.615 0.00 0.00 0.00 3.16
2298 2347 7.864108 TTAGGTGATATGTGGACAGATTTTG 57.136 36.000 0.00 0.00 0.00 2.44
2327 2376 1.338136 CCTCATACCCTTGGTCGCCT 61.338 60.000 0.00 0.00 37.09 5.52
2380 2429 7.636150 ACATAGCTACATCTGCTTTTCATTT 57.364 32.000 0.00 0.00 41.46 2.32
2403 2455 4.858850 AGCAATTGTGATTATGTGAGGGA 58.141 39.130 7.40 0.00 0.00 4.20
2404 2456 4.641989 AGCAATTGTGATTATGTGAGGGAC 59.358 41.667 7.40 0.00 0.00 4.46
2406 2458 5.449588 GCAATTGTGATTATGTGAGGGACTG 60.450 44.000 7.40 0.00 41.55 3.51
2407 2459 5.698741 ATTGTGATTATGTGAGGGACTGA 57.301 39.130 0.00 0.00 41.55 3.41
2408 2460 5.497464 TTGTGATTATGTGAGGGACTGAA 57.503 39.130 0.00 0.00 41.55 3.02
2409 2461 5.089970 TGTGATTATGTGAGGGACTGAAG 57.910 43.478 0.00 0.00 41.55 3.02
2410 2462 4.080919 TGTGATTATGTGAGGGACTGAAGG 60.081 45.833 0.00 0.00 41.55 3.46
2411 2463 3.455910 TGATTATGTGAGGGACTGAAGGG 59.544 47.826 0.00 0.00 41.55 3.95
2412 2464 2.940514 TATGTGAGGGACTGAAGGGA 57.059 50.000 0.00 0.00 41.55 4.20
2413 2465 2.044793 ATGTGAGGGACTGAAGGGAA 57.955 50.000 0.00 0.00 41.55 3.97
2414 2466 2.044793 TGTGAGGGACTGAAGGGAAT 57.955 50.000 0.00 0.00 41.55 3.01
2415 2467 1.630369 TGTGAGGGACTGAAGGGAATG 59.370 52.381 0.00 0.00 41.55 2.67
2416 2468 1.065126 GTGAGGGACTGAAGGGAATGG 60.065 57.143 0.00 0.00 41.55 3.16
2417 2469 1.290134 GAGGGACTGAAGGGAATGGT 58.710 55.000 0.00 0.00 41.55 3.55
2418 2470 1.210722 GAGGGACTGAAGGGAATGGTC 59.789 57.143 0.00 0.00 41.55 4.02
2419 2471 0.107654 GGGACTGAAGGGAATGGTCG 60.108 60.000 0.00 0.00 0.00 4.79
2420 2472 0.107654 GGACTGAAGGGAATGGTCGG 60.108 60.000 0.00 0.00 0.00 4.79
2421 2473 0.107654 GACTGAAGGGAATGGTCGGG 60.108 60.000 0.00 0.00 0.00 5.14
2422 2474 0.546747 ACTGAAGGGAATGGTCGGGA 60.547 55.000 0.00 0.00 0.00 5.14
2423 2475 0.107654 CTGAAGGGAATGGTCGGGAC 60.108 60.000 0.00 0.00 0.00 4.46
2424 2476 0.546747 TGAAGGGAATGGTCGGGACT 60.547 55.000 0.00 0.00 0.00 3.85
2425 2477 0.618981 GAAGGGAATGGTCGGGACTT 59.381 55.000 0.00 0.00 0.00 3.01
2426 2478 0.328258 AAGGGAATGGTCGGGACTTG 59.672 55.000 0.00 0.00 0.00 3.16
2427 2479 1.077716 GGGAATGGTCGGGACTTGG 60.078 63.158 0.00 0.00 0.00 3.61
2428 2480 1.077716 GGAATGGTCGGGACTTGGG 60.078 63.158 0.00 0.00 0.00 4.12
2429 2481 1.559065 GGAATGGTCGGGACTTGGGA 61.559 60.000 0.00 0.00 0.00 4.37
2430 2482 0.107654 GAATGGTCGGGACTTGGGAG 60.108 60.000 0.00 0.00 0.00 4.30
2431 2483 1.562672 AATGGTCGGGACTTGGGAGG 61.563 60.000 0.00 0.00 0.00 4.30
2432 2484 3.400054 GGTCGGGACTTGGGAGGG 61.400 72.222 0.00 0.00 0.00 4.30
2435 2487 3.400054 CGGGACTTGGGAGGGGTC 61.400 72.222 0.00 0.00 0.00 4.46
2440 2492 1.201424 GACTTGGGAGGGGTCGTTAT 58.799 55.000 0.00 0.00 0.00 1.89
2453 2505 4.439968 GGGTCGTTATTTCACCCTCTAAG 58.560 47.826 0.00 0.00 45.81 2.18
2465 2517 4.649674 TCACCCTCTAAGCAGTAACCATAG 59.350 45.833 0.00 0.00 0.00 2.23
2472 2525 8.204836 CCTCTAAGCAGTAACCATAGTATGTTT 58.795 37.037 9.28 3.86 0.00 2.83
2473 2526 9.601217 CTCTAAGCAGTAACCATAGTATGTTTT 57.399 33.333 9.28 4.76 0.00 2.43
2497 2550 5.581605 TCTGAAACTGAAGTTGACAAATGC 58.418 37.500 0.00 0.00 38.44 3.56
2501 2554 2.682856 ACTGAAGTTGACAAATGCGTGT 59.317 40.909 0.00 0.00 0.00 4.49
2502 2555 3.874543 ACTGAAGTTGACAAATGCGTGTA 59.125 39.130 0.00 0.00 0.00 2.90
2503 2556 4.515191 ACTGAAGTTGACAAATGCGTGTAT 59.485 37.500 0.00 0.00 0.00 2.29
2504 2557 5.008613 ACTGAAGTTGACAAATGCGTGTATT 59.991 36.000 0.00 0.00 0.00 1.89
2505 2558 5.211454 TGAAGTTGACAAATGCGTGTATTG 58.789 37.500 0.00 0.00 0.00 1.90
2561 2624 6.763610 AGTTTCAGTTCTTAGACCTTTGACTG 59.236 38.462 3.79 3.79 0.00 3.51
2665 2729 8.918961 ATTTCTAATTCGTTTTGTTCACAACA 57.081 26.923 0.00 0.00 40.21 3.33
2684 2748 0.112995 ATTTTCAGGCAGGGCAGTCA 59.887 50.000 0.00 0.00 0.00 3.41
2801 2865 0.958382 TGGGGAAGACCGAAAATGCG 60.958 55.000 0.00 0.00 41.60 4.73
3052 3119 3.624777 CATTTCAGGTCTTGGCTGGTAT 58.375 45.455 0.00 0.00 0.00 2.73
3161 3228 1.130561 GGGCGTCGATTTTTGAGGAAG 59.869 52.381 0.00 0.00 0.00 3.46
3190 3257 4.042398 TCTCAGTTTCAAAAGTCGTCTCG 58.958 43.478 0.00 0.00 0.00 4.04
3229 3296 7.665690 TGACAAATAAGCTGAAAGGCAATAAA 58.334 30.769 0.00 0.00 34.17 1.40
3255 3322 6.396829 AACAAACAAGAAGGAGATGAAAGG 57.603 37.500 0.00 0.00 0.00 3.11
3258 3325 4.313020 ACAAGAAGGAGATGAAAGGCAT 57.687 40.909 0.00 0.00 40.77 4.40
3261 3328 5.541484 ACAAGAAGGAGATGAAAGGCATTTT 59.459 36.000 0.00 0.00 37.34 1.82
3262 3329 5.656213 AGAAGGAGATGAAAGGCATTTTG 57.344 39.130 0.00 0.00 37.34 2.44
3322 3389 3.553511 CGGTCATAGATGCTTGAGTGTTC 59.446 47.826 0.00 0.00 0.00 3.18
3349 3416 5.977635 TCCATTCTGTGATACGAGTTTCAT 58.022 37.500 0.00 0.00 0.00 2.57
3353 3420 8.331022 CCATTCTGTGATACGAGTTTCATTTAG 58.669 37.037 0.00 1.30 0.00 1.85
3432 3625 1.910580 TTAAGCTTGCTCGGAGGGGG 61.911 60.000 9.86 0.00 0.00 5.40
3435 3628 3.049080 GCTTGCTCGGAGGGGGATT 62.049 63.158 7.20 0.00 0.00 3.01
3444 3637 1.545841 GGAGGGGGATTGTTGTTCAC 58.454 55.000 0.00 0.00 0.00 3.18
3445 3638 1.075536 GGAGGGGGATTGTTGTTCACT 59.924 52.381 0.00 0.00 0.00 3.41
3479 3672 0.819582 GAGCATGGGTGTCATTTGGG 59.180 55.000 0.00 0.00 32.92 4.12
3503 3779 6.238484 GGCTTGCTGTTGACTGGTAATAATAG 60.238 42.308 0.00 0.00 0.00 1.73
3505 3781 5.739959 TGCTGTTGACTGGTAATAATAGCA 58.260 37.500 0.00 0.00 42.36 3.49
3530 3806 9.749490 CAAAATATCAGTCAAATGAATGTTTGC 57.251 29.630 10.26 0.00 40.61 3.68
3532 3808 8.697846 AATATCAGTCAAATGAATGTTTGCTG 57.302 30.769 10.26 12.95 40.61 4.41
3542 3818 3.056678 TGAATGTTTGCTGGTATGCTTGG 60.057 43.478 0.00 0.00 0.00 3.61
3550 3826 2.551459 GCTGGTATGCTTGGCTCATAAG 59.449 50.000 0.00 0.00 0.00 1.73
3556 3832 3.423539 TGCTTGGCTCATAAGAACAGT 57.576 42.857 0.00 0.00 0.00 3.55
3591 3887 4.877823 TCTCATGTTTCAGCATCCATGTAC 59.122 41.667 0.00 0.00 36.81 2.90
3611 3907 8.928733 CATGTACCTAACGTTTTGTGTTACTAT 58.071 33.333 5.91 0.00 0.00 2.12
3630 3926 6.579666 ACTATGTCAAACATGCAGAATTGT 57.420 33.333 2.88 0.00 39.53 2.71
3631 3927 6.985117 ACTATGTCAAACATGCAGAATTGTT 58.015 32.000 2.88 0.00 39.53 2.83
3661 3957 8.292448 GTCAGTTTTTACATCTGAATCATGTGT 58.708 33.333 0.14 3.40 39.42 3.72
3662 3958 8.849168 TCAGTTTTTACATCTGAATCATGTGTT 58.151 29.630 6.08 0.00 35.95 3.32
3663 3959 9.467258 CAGTTTTTACATCTGAATCATGTGTTT 57.533 29.630 6.08 0.00 35.95 2.83
3664 3960 9.467258 AGTTTTTACATCTGAATCATGTGTTTG 57.533 29.630 6.08 0.00 35.95 2.93
3665 3961 7.872163 TTTTACATCTGAATCATGTGTTTGC 57.128 32.000 6.08 0.00 35.95 3.68
3666 3962 6.572167 TTACATCTGAATCATGTGTTTGCA 57.428 33.333 6.08 0.00 35.95 4.08
3681 4007 6.289834 TGTGTTTGCATTGGAATTTTGAGAT 58.710 32.000 0.00 0.00 0.00 2.75
3686 4012 9.374838 GTTTGCATTGGAATTTTGAGATAGAAT 57.625 29.630 0.00 0.00 0.00 2.40
3687 4013 9.590451 TTTGCATTGGAATTTTGAGATAGAATC 57.410 29.630 0.00 0.00 0.00 2.52
3688 4014 8.529424 TGCATTGGAATTTTGAGATAGAATCT 57.471 30.769 0.00 0.00 43.70 2.40
3689 4015 9.631257 TGCATTGGAATTTTGAGATAGAATCTA 57.369 29.630 0.00 0.00 40.38 1.98
3721 4050 5.859114 CCACAGATCGTTTATCTATCGAAGG 59.141 44.000 0.00 0.00 43.42 3.46
3746 4075 3.522553 CCAGAGACTTGTAAATCCCGTC 58.477 50.000 0.00 0.00 0.00 4.79
3747 4076 3.195825 CCAGAGACTTGTAAATCCCGTCT 59.804 47.826 0.00 0.00 37.63 4.18
3748 4077 4.401519 CCAGAGACTTGTAAATCCCGTCTA 59.598 45.833 0.00 0.00 35.29 2.59
3749 4078 5.341617 CAGAGACTTGTAAATCCCGTCTAC 58.658 45.833 0.00 0.00 35.29 2.59
3750 4079 5.014858 AGAGACTTGTAAATCCCGTCTACA 58.985 41.667 0.00 0.00 35.29 2.74
3753 4082 3.055602 ACTTGTAAATCCCGTCTACACCC 60.056 47.826 0.00 0.00 0.00 4.61
3754 4083 2.823959 TGTAAATCCCGTCTACACCCT 58.176 47.619 0.00 0.00 0.00 4.34
3755 4084 3.175594 TGTAAATCCCGTCTACACCCTT 58.824 45.455 0.00 0.00 0.00 3.95
3756 4085 3.196254 TGTAAATCCCGTCTACACCCTTC 59.804 47.826 0.00 0.00 0.00 3.46
3757 4086 1.946984 AATCCCGTCTACACCCTTCA 58.053 50.000 0.00 0.00 0.00 3.02
3765 4094 3.554129 CGTCTACACCCTTCATCACACAA 60.554 47.826 0.00 0.00 0.00 3.33
3771 4100 5.136828 ACACCCTTCATCACACAATAACAA 58.863 37.500 0.00 0.00 0.00 2.83
3794 4125 5.733676 ACTTGTTTTGCCAAAGAACATCTT 58.266 33.333 0.00 0.00 38.59 2.40
3845 4176 4.949856 CCTTTTGCTGGACTGGTTATGTAT 59.050 41.667 0.00 0.00 0.00 2.29
3850 4181 4.471747 TGCTGGACTGGTTATGTATGGTTA 59.528 41.667 0.00 0.00 0.00 2.85
3877 4208 6.765512 TGTCTACATTTTCATTCAGTGTGACA 59.234 34.615 0.00 0.00 33.16 3.58
3894 4226 6.256321 AGTGTGACATTGTTTCTTGAAATTGC 59.744 34.615 0.00 0.00 0.00 3.56
3905 4237 7.550551 TGTTTCTTGAAATTGCACCATTGTTAA 59.449 29.630 0.00 0.00 0.00 2.01
3906 4238 8.558700 GTTTCTTGAAATTGCACCATTGTTAAT 58.441 29.630 0.00 0.00 0.00 1.40
3907 4239 7.655236 TCTTGAAATTGCACCATTGTTAATG 57.345 32.000 0.00 0.00 38.63 1.90
3908 4240 7.215789 TCTTGAAATTGCACCATTGTTAATGT 58.784 30.769 0.00 0.00 37.18 2.71
3909 4241 8.363390 TCTTGAAATTGCACCATTGTTAATGTA 58.637 29.630 0.00 0.00 37.18 2.29
3910 4242 7.881643 TGAAATTGCACCATTGTTAATGTAC 57.118 32.000 0.00 0.00 37.18 2.90
3911 4243 6.870965 TGAAATTGCACCATTGTTAATGTACC 59.129 34.615 0.00 0.00 37.18 3.34
3912 4244 6.603940 AATTGCACCATTGTTAATGTACCT 57.396 33.333 0.00 0.00 37.18 3.08
3913 4245 5.637006 TTGCACCATTGTTAATGTACCTC 57.363 39.130 0.00 0.00 37.18 3.85
3934 4268 5.240623 CCTCTGCTACCAAAAACACAACATA 59.759 40.000 0.00 0.00 0.00 2.29
3941 4275 7.651704 GCTACCAAAAACACAACATAATGTTCT 59.348 33.333 0.00 0.00 38.77 3.01
3942 4276 9.180678 CTACCAAAAACACAACATAATGTTCTC 57.819 33.333 0.00 0.00 38.77 2.87
3946 4280 9.520204 CAAAAACACAACATAATGTTCTCTCTT 57.480 29.630 0.00 0.00 38.77 2.85
3986 4320 7.485277 CAGAGATGTTTCAAGAAATCTTCATGC 59.515 37.037 0.00 0.00 33.11 4.06
4001 4336 2.345876 TCATGCGTGTACAATGGTCTG 58.654 47.619 5.68 0.00 0.00 3.51
4003 4338 2.760634 TGCGTGTACAATGGTCTGAT 57.239 45.000 0.00 0.00 0.00 2.90
4019 4354 3.701664 TCTGATAGAAGCAGACACAGGA 58.298 45.455 0.00 0.00 37.46 3.86
4051 4386 7.064609 GTCAATCGACAAGTTTTCTGGATGATA 59.935 37.037 0.00 0.00 42.13 2.15
4057 4392 7.959651 CGACAAGTTTTCTGGATGATAAAAGAG 59.040 37.037 0.00 0.00 0.00 2.85
4068 4403 5.277876 GGATGATAAAAGAGCAGCATGTGAG 60.278 44.000 0.00 0.00 39.31 3.51
4073 4408 0.810426 AGAGCAGCATGTGAGCATCG 60.810 55.000 0.00 0.00 39.31 3.84
4083 4474 1.449070 TGAGCATCGCTGAAGCCTG 60.449 57.895 0.00 0.00 39.88 4.85
4087 4478 0.742281 GCATCGCTGAAGCCTGAAGA 60.742 55.000 0.00 0.00 37.91 2.87
4088 4479 1.950828 CATCGCTGAAGCCTGAAGAT 58.049 50.000 0.00 0.00 37.91 2.40
4092 4483 2.233676 TCGCTGAAGCCTGAAGATGTTA 59.766 45.455 0.00 0.00 37.91 2.41
4094 4485 3.247173 CGCTGAAGCCTGAAGATGTTATC 59.753 47.826 0.00 0.00 37.91 1.75
4116 4507 7.736447 ATCTTCACATTCTTTTCTCGTTCTT 57.264 32.000 0.00 0.00 0.00 2.52
4132 4523 5.478407 TCGTTCTTGTTGAGAAGATGCATA 58.522 37.500 0.00 0.00 44.78 3.14
4135 4526 6.685828 CGTTCTTGTTGAGAAGATGCATATTG 59.314 38.462 12.07 0.00 44.78 1.90
4140 4533 7.080353 TGTTGAGAAGATGCATATTGTCAAG 57.920 36.000 33.94 0.00 40.40 3.02
4155 4548 9.334947 CATATTGTCAAGAGTCTGGAATTGTAT 57.665 33.333 0.00 0.00 0.00 2.29
4166 4559 5.874810 GTCTGGAATTGTATGCTGTGACTTA 59.125 40.000 0.00 0.00 0.00 2.24
4177 4570 5.801350 TGCTGTGACTTATAAATCTGCAC 57.199 39.130 0.00 0.00 0.00 4.57
4181 4574 5.185454 TGTGACTTATAAATCTGCACCAGG 58.815 41.667 0.00 0.00 31.51 4.45
4199 4592 6.567050 CACCAGGAAATCACATTAATTGGAG 58.433 40.000 0.00 0.00 0.00 3.86
4200 4593 6.377996 CACCAGGAAATCACATTAATTGGAGA 59.622 38.462 0.00 0.00 0.00 3.71
4201 4594 7.069085 CACCAGGAAATCACATTAATTGGAGAT 59.931 37.037 0.00 0.00 0.00 2.75
4202 4595 8.281531 ACCAGGAAATCACATTAATTGGAGATA 58.718 33.333 0.00 0.00 0.00 1.98
4242 4636 4.594920 AGCAGGTACTCCAGTTATATGCAT 59.405 41.667 3.79 3.79 34.60 3.96
4243 4637 4.692625 GCAGGTACTCCAGTTATATGCATG 59.307 45.833 10.16 0.00 34.60 4.06
4244 4638 5.743130 GCAGGTACTCCAGTTATATGCATGT 60.743 44.000 10.16 5.06 34.60 3.21
4245 4639 5.698089 CAGGTACTCCAGTTATATGCATGTG 59.302 44.000 10.16 0.00 34.60 3.21
4246 4640 4.452455 GGTACTCCAGTTATATGCATGTGC 59.548 45.833 10.16 0.00 42.50 4.57
4247 4641 8.099393 AGGTACTCCAGTTATATGCATGTGCA 62.099 42.308 10.16 10.44 45.55 4.57
4268 4662 0.311790 AATATTGGCGCATGCTTCCG 59.688 50.000 17.13 0.39 42.25 4.30
4271 4665 3.776680 TATTGGCGCATGCTTCCGTCT 62.777 52.381 17.13 7.75 42.25 4.18
4283 4677 2.869897 CTTCCGTCTCTGAAGCTGTAC 58.130 52.381 0.00 0.00 33.46 2.90
4284 4678 1.174783 TCCGTCTCTGAAGCTGTACC 58.825 55.000 0.00 0.00 0.00 3.34
4285 4679 1.178276 CCGTCTCTGAAGCTGTACCT 58.822 55.000 0.00 0.00 0.00 3.08
4286 4680 1.135257 CCGTCTCTGAAGCTGTACCTG 60.135 57.143 0.00 0.00 0.00 4.00
4287 4681 1.813178 CGTCTCTGAAGCTGTACCTGA 59.187 52.381 0.00 0.00 0.00 3.86
4288 4682 2.425312 CGTCTCTGAAGCTGTACCTGAT 59.575 50.000 0.00 0.00 0.00 2.90
4289 4683 3.733380 CGTCTCTGAAGCTGTACCTGATG 60.733 52.174 0.00 0.00 0.00 3.07
4290 4684 2.167281 TCTCTGAAGCTGTACCTGATGC 59.833 50.000 0.00 0.00 0.00 3.91
4291 4685 2.168106 CTCTGAAGCTGTACCTGATGCT 59.832 50.000 0.00 0.00 37.37 3.79
4292 4686 2.568956 TCTGAAGCTGTACCTGATGCTT 59.431 45.455 0.00 0.00 46.69 3.91
4293 4687 2.676839 CTGAAGCTGTACCTGATGCTTG 59.323 50.000 3.74 0.00 44.47 4.01
4294 4688 1.399791 GAAGCTGTACCTGATGCTTGC 59.600 52.381 3.74 0.00 44.47 4.01
4295 4689 0.617413 AGCTGTACCTGATGCTTGCT 59.383 50.000 0.00 0.00 30.96 3.91
4296 4690 1.004044 AGCTGTACCTGATGCTTGCTT 59.996 47.619 0.00 0.00 30.96 3.91
4297 4691 1.815003 GCTGTACCTGATGCTTGCTTT 59.185 47.619 0.00 0.00 0.00 3.51
4298 4692 2.159462 GCTGTACCTGATGCTTGCTTTC 60.159 50.000 0.00 0.00 0.00 2.62
4299 4693 2.076100 TGTACCTGATGCTTGCTTTCG 58.924 47.619 0.00 0.00 0.00 3.46
4300 4694 2.076863 GTACCTGATGCTTGCTTTCGT 58.923 47.619 0.00 0.00 0.00 3.85
4301 4695 1.609208 ACCTGATGCTTGCTTTCGTT 58.391 45.000 0.00 0.00 0.00 3.85
4302 4696 2.778299 ACCTGATGCTTGCTTTCGTTA 58.222 42.857 0.00 0.00 0.00 3.18
4303 4697 2.744202 ACCTGATGCTTGCTTTCGTTAG 59.256 45.455 0.00 0.00 0.00 2.34
4304 4698 2.744202 CCTGATGCTTGCTTTCGTTAGT 59.256 45.455 0.00 0.00 0.00 2.24
4305 4699 3.932710 CCTGATGCTTGCTTTCGTTAGTA 59.067 43.478 0.00 0.00 0.00 1.82
4306 4700 4.391830 CCTGATGCTTGCTTTCGTTAGTAA 59.608 41.667 0.00 0.00 0.00 2.24
4307 4701 5.277601 TGATGCTTGCTTTCGTTAGTAAC 57.722 39.130 2.72 2.72 0.00 2.50
4308 4702 4.752604 TGATGCTTGCTTTCGTTAGTAACA 59.247 37.500 13.33 0.00 0.00 2.41
4309 4703 5.237561 TGATGCTTGCTTTCGTTAGTAACAA 59.762 36.000 13.33 4.24 0.00 2.83
4310 4704 4.839796 TGCTTGCTTTCGTTAGTAACAAC 58.160 39.130 13.33 0.00 0.00 3.32
4311 4705 4.333095 TGCTTGCTTTCGTTAGTAACAACA 59.667 37.500 13.33 0.99 0.00 3.33
4312 4706 4.669283 GCTTGCTTTCGTTAGTAACAACAC 59.331 41.667 13.33 0.00 0.00 3.32
4313 4707 4.799419 TGCTTTCGTTAGTAACAACACC 57.201 40.909 13.33 0.00 0.00 4.16
4314 4708 3.245754 TGCTTTCGTTAGTAACAACACCG 59.754 43.478 13.33 0.00 0.00 4.94
4315 4709 3.363280 GCTTTCGTTAGTAACAACACCGG 60.363 47.826 13.33 0.00 0.00 5.28
4316 4710 3.724508 TTCGTTAGTAACAACACCGGA 57.275 42.857 9.46 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.614078 CGTGCCGAGTCTATATTCTTCTCC 60.614 50.000 0.00 0.00 0.00 3.71
1 2 4.468643 CGTGCCGAGTCTATATTCTTCTC 58.531 47.826 0.00 0.00 0.00 2.87
2 3 3.304794 GCGTGCCGAGTCTATATTCTTCT 60.305 47.826 0.00 0.00 0.00 2.85
3 4 2.981140 GCGTGCCGAGTCTATATTCTTC 59.019 50.000 0.00 0.00 0.00 2.87
4 5 2.361119 TGCGTGCCGAGTCTATATTCTT 59.639 45.455 0.00 0.00 0.00 2.52
5 6 1.954382 TGCGTGCCGAGTCTATATTCT 59.046 47.619 0.00 0.00 0.00 2.40
6 7 2.320367 CTGCGTGCCGAGTCTATATTC 58.680 52.381 0.00 0.00 0.00 1.75
7 8 1.603172 GCTGCGTGCCGAGTCTATATT 60.603 52.381 0.00 0.00 35.15 1.28
8 9 0.039074 GCTGCGTGCCGAGTCTATAT 60.039 55.000 0.00 0.00 35.15 0.86
9 10 1.359117 GCTGCGTGCCGAGTCTATA 59.641 57.895 0.00 0.00 35.15 1.31
10 11 2.105128 GCTGCGTGCCGAGTCTAT 59.895 61.111 0.00 0.00 35.15 1.98
26 27 1.237285 ACCTGAATTCTGCACACGGC 61.237 55.000 7.05 0.00 45.13 5.68
46 47 4.100189 GGCCAGTCTCAGCTTTTATAGAGA 59.900 45.833 0.00 0.00 34.95 3.10
58 59 1.376942 CCTGCTTGGCCAGTCTCAG 60.377 63.158 5.11 11.62 0.00 3.35
110 111 3.108376 GACAAGTAGTTCCCTGATCCCT 58.892 50.000 0.00 0.00 0.00 4.20
111 112 2.159085 CGACAAGTAGTTCCCTGATCCC 60.159 54.545 0.00 0.00 0.00 3.85
112 113 2.738964 GCGACAAGTAGTTCCCTGATCC 60.739 54.545 0.00 0.00 0.00 3.36
113 114 2.541556 GCGACAAGTAGTTCCCTGATC 58.458 52.381 0.00 0.00 0.00 2.92
114 115 1.207329 GGCGACAAGTAGTTCCCTGAT 59.793 52.381 0.00 0.00 0.00 2.90
115 116 0.606604 GGCGACAAGTAGTTCCCTGA 59.393 55.000 0.00 0.00 0.00 3.86
116 117 0.320374 TGGCGACAAGTAGTTCCCTG 59.680 55.000 0.00 0.00 37.44 4.45
179 180 6.291377 TGTCTAGTGCTGGAAATTATCATCC 58.709 40.000 0.00 0.00 36.21 3.51
195 196 7.582435 AATTCTGTATCGTGTTTGTCTAGTG 57.418 36.000 0.00 0.00 0.00 2.74
275 276 2.263077 CATCGCGGTAAGAGATATGGC 58.737 52.381 6.13 0.00 37.27 4.40
287 288 0.814010 GGTTATTCCTGCATCGCGGT 60.814 55.000 6.13 0.00 32.22 5.68
289 290 2.992089 AGGTTATTCCTGCATCGCG 58.008 52.632 0.00 0.00 46.19 5.87
386 387 7.071069 TGCAGTATGATGTCTTCTTATCCAT 57.929 36.000 0.00 0.00 39.69 3.41
397 398 8.239314 TCTTTTCTGAAATTGCAGTATGATGTC 58.761 33.333 13.35 0.00 39.69 3.06
406 407 5.333111 GCTTTGCTCTTTTCTGAAATTGCAG 60.333 40.000 7.16 7.16 35.69 4.41
409 410 6.592798 TTGCTTTGCTCTTTTCTGAAATTG 57.407 33.333 3.31 0.99 0.00 2.32
417 418 4.678742 GTGTCTGATTGCTTTGCTCTTTTC 59.321 41.667 0.00 0.00 0.00 2.29
421 422 2.157738 GGTGTCTGATTGCTTTGCTCT 58.842 47.619 0.00 0.00 0.00 4.09
422 423 1.881973 TGGTGTCTGATTGCTTTGCTC 59.118 47.619 0.00 0.00 0.00 4.26
423 424 1.884579 CTGGTGTCTGATTGCTTTGCT 59.115 47.619 0.00 0.00 0.00 3.91
424 425 1.881973 TCTGGTGTCTGATTGCTTTGC 59.118 47.619 0.00 0.00 0.00 3.68
425 426 2.880268 TGTCTGGTGTCTGATTGCTTTG 59.120 45.455 0.00 0.00 0.00 2.77
428 429 1.696336 ACTGTCTGGTGTCTGATTGCT 59.304 47.619 0.00 0.00 0.00 3.91
429 430 1.802960 CACTGTCTGGTGTCTGATTGC 59.197 52.381 0.00 0.00 33.04 3.56
430 431 1.802960 GCACTGTCTGGTGTCTGATTG 59.197 52.381 0.00 0.00 39.21 2.67
431 432 1.696336 AGCACTGTCTGGTGTCTGATT 59.304 47.619 0.00 0.00 39.21 2.57
432 433 1.346062 AGCACTGTCTGGTGTCTGAT 58.654 50.000 0.00 0.00 39.21 2.90
433 434 1.995376 TAGCACTGTCTGGTGTCTGA 58.005 50.000 0.00 0.00 39.21 3.27
434 435 2.297315 TCTTAGCACTGTCTGGTGTCTG 59.703 50.000 0.00 0.00 39.21 3.51
435 436 2.598565 TCTTAGCACTGTCTGGTGTCT 58.401 47.619 0.00 0.00 39.21 3.41
436 437 3.194542 AGATCTTAGCACTGTCTGGTGTC 59.805 47.826 0.00 0.00 39.21 3.67
437 438 3.056250 CAGATCTTAGCACTGTCTGGTGT 60.056 47.826 0.00 0.00 39.21 4.16
438 439 3.194329 TCAGATCTTAGCACTGTCTGGTG 59.806 47.826 0.00 0.00 37.49 4.17
439 440 3.435275 TCAGATCTTAGCACTGTCTGGT 58.565 45.455 0.00 0.00 37.49 4.00
440 441 3.737663 GCTCAGATCTTAGCACTGTCTGG 60.738 52.174 21.45 0.00 38.63 3.86
441 442 3.446799 GCTCAGATCTTAGCACTGTCTG 58.553 50.000 21.45 0.00 38.63 3.51
442 443 2.430332 GGCTCAGATCTTAGCACTGTCT 59.570 50.000 26.06 0.00 40.61 3.41
443 444 2.797792 CGGCTCAGATCTTAGCACTGTC 60.798 54.545 26.06 10.63 40.61 3.51
444 445 1.135915 CGGCTCAGATCTTAGCACTGT 59.864 52.381 26.06 0.00 40.61 3.55
445 446 1.406898 TCGGCTCAGATCTTAGCACTG 59.593 52.381 26.06 16.61 40.61 3.66
446 447 1.769026 TCGGCTCAGATCTTAGCACT 58.231 50.000 26.06 0.00 40.61 4.40
447 448 2.035193 TCATCGGCTCAGATCTTAGCAC 59.965 50.000 26.06 16.05 40.61 4.40
448 449 2.310538 TCATCGGCTCAGATCTTAGCA 58.689 47.619 26.06 10.64 40.61 3.49
459 477 0.390472 GGGATCGGAATCATCGGCTC 60.390 60.000 0.00 0.00 33.21 4.70
485 503 0.240945 GTTGAGTCAATTGCGGTGGG 59.759 55.000 9.18 0.00 0.00 4.61
517 536 2.375345 CCCCCTCCCTTGCGTGTAT 61.375 63.158 0.00 0.00 0.00 2.29
679 698 2.264813 GCGATGGCGTTGACTAACTTA 58.735 47.619 0.00 0.00 40.36 2.24
685 704 2.125512 GAGGCGATGGCGTTGACT 60.126 61.111 0.61 0.61 41.24 3.41
719 749 2.564458 CGACGATCCACACCACGA 59.436 61.111 0.00 0.00 0.00 4.35
799 829 0.179137 TATCTCAACGCCTCAGCACG 60.179 55.000 0.00 0.00 39.83 5.34
853 887 0.110678 TTAACGGGCCATCAACACCA 59.889 50.000 4.39 0.00 0.00 4.17
880 914 2.035442 GGCCTCGTGAAGAAGCACC 61.035 63.158 0.00 0.00 38.04 5.01
886 920 1.374252 GCTTTCGGCCTCGTGAAGA 60.374 57.895 0.00 0.00 34.87 2.87
932 969 2.281276 GGTGGGTGTTGGACGTCC 60.281 66.667 28.17 28.17 0.00 4.79
961 998 3.864686 CCGCCGCCAATTCGTGAG 61.865 66.667 0.00 0.00 0.00 3.51
1062 1099 4.083862 GGGTGAGGGGACGAGTGC 62.084 72.222 0.00 0.00 0.00 4.40
1071 1108 2.760385 GTCGGAGGAGGGTGAGGG 60.760 72.222 0.00 0.00 0.00 4.30
1185 1234 1.048601 GGAGGTCAGAAGACACCACA 58.951 55.000 0.00 0.00 46.80 4.17
1209 1258 2.783135 CACTTGCCATTGGTACTGACT 58.217 47.619 4.26 0.00 0.00 3.41
1398 1447 4.016706 CCGCCCTCCCGTGAGTTT 62.017 66.667 0.00 0.00 36.86 2.66
1626 1675 3.046087 TCGAAGTCCGACGCGTCT 61.046 61.111 33.94 17.46 43.23 4.18
1719 1768 4.867599 GGGAGGTTAGACGGCGCG 62.868 72.222 6.90 0.00 0.00 6.86
2163 2212 1.003233 AAGTTTCAGCTCCTCGGGC 60.003 57.895 0.00 0.00 0.00 6.13
2236 2285 6.389091 TGACAAAATGTGCATAAGATGGAAC 58.611 36.000 0.00 0.00 30.45 3.62
2237 2286 6.209192 ACTGACAAAATGTGCATAAGATGGAA 59.791 34.615 0.00 0.00 30.45 3.53
2263 2312 9.913310 TCCACATATCACCTAATCACAAAATTA 57.087 29.630 0.00 0.00 0.00 1.40
2286 2335 3.554934 AGACAAGCACAAAATCTGTCCA 58.445 40.909 0.00 0.00 35.47 4.02
2298 2347 1.834263 AGGGTATGAGGAGACAAGCAC 59.166 52.381 0.00 0.00 0.00 4.40
2306 2355 0.105039 GCGACCAAGGGTATGAGGAG 59.895 60.000 0.00 0.00 35.25 3.69
2380 2429 5.822519 GTCCCTCACATAATCACAATTGCTA 59.177 40.000 5.05 0.00 0.00 3.49
2403 2455 0.546747 TCCCGACCATTCCCTTCAGT 60.547 55.000 0.00 0.00 0.00 3.41
2404 2456 0.107654 GTCCCGACCATTCCCTTCAG 60.108 60.000 0.00 0.00 0.00 3.02
2405 2457 0.546747 AGTCCCGACCATTCCCTTCA 60.547 55.000 0.00 0.00 0.00 3.02
2406 2458 0.618981 AAGTCCCGACCATTCCCTTC 59.381 55.000 0.00 0.00 0.00 3.46
2407 2459 0.328258 CAAGTCCCGACCATTCCCTT 59.672 55.000 0.00 0.00 0.00 3.95
2408 2460 1.562672 CCAAGTCCCGACCATTCCCT 61.563 60.000 0.00 0.00 0.00 4.20
2409 2461 1.077716 CCAAGTCCCGACCATTCCC 60.078 63.158 0.00 0.00 0.00 3.97
2410 2462 1.077716 CCCAAGTCCCGACCATTCC 60.078 63.158 0.00 0.00 0.00 3.01
2411 2463 0.107654 CTCCCAAGTCCCGACCATTC 60.108 60.000 0.00 0.00 0.00 2.67
2412 2464 1.562672 CCTCCCAAGTCCCGACCATT 61.563 60.000 0.00 0.00 0.00 3.16
2413 2465 1.995626 CCTCCCAAGTCCCGACCAT 60.996 63.158 0.00 0.00 0.00 3.55
2414 2466 2.606519 CCTCCCAAGTCCCGACCA 60.607 66.667 0.00 0.00 0.00 4.02
2415 2467 3.400054 CCCTCCCAAGTCCCGACC 61.400 72.222 0.00 0.00 0.00 4.79
2416 2468 3.400054 CCCCTCCCAAGTCCCGAC 61.400 72.222 0.00 0.00 0.00 4.79
2417 2469 3.918328 GACCCCTCCCAAGTCCCGA 62.918 68.421 0.00 0.00 0.00 5.14
2418 2470 3.400054 GACCCCTCCCAAGTCCCG 61.400 72.222 0.00 0.00 0.00 5.14
2419 2471 3.400054 CGACCCCTCCCAAGTCCC 61.400 72.222 0.00 0.00 0.00 4.46
2420 2472 0.906282 TAACGACCCCTCCCAAGTCC 60.906 60.000 0.00 0.00 0.00 3.85
2421 2473 1.201424 ATAACGACCCCTCCCAAGTC 58.799 55.000 0.00 0.00 0.00 3.01
2422 2474 1.665137 AATAACGACCCCTCCCAAGT 58.335 50.000 0.00 0.00 0.00 3.16
2423 2475 2.026636 TGAAATAACGACCCCTCCCAAG 60.027 50.000 0.00 0.00 0.00 3.61
2424 2476 1.986631 TGAAATAACGACCCCTCCCAA 59.013 47.619 0.00 0.00 0.00 4.12
2425 2477 1.279846 GTGAAATAACGACCCCTCCCA 59.720 52.381 0.00 0.00 0.00 4.37
2426 2478 1.407851 GGTGAAATAACGACCCCTCCC 60.408 57.143 0.00 0.00 0.00 4.30
2427 2479 1.407851 GGGTGAAATAACGACCCCTCC 60.408 57.143 0.00 0.00 43.30 4.30
2428 2480 2.034104 GGGTGAAATAACGACCCCTC 57.966 55.000 0.00 0.00 43.30 4.30
2432 2484 3.869832 GCTTAGAGGGTGAAATAACGACC 59.130 47.826 0.00 0.00 0.00 4.79
2435 2487 4.504858 ACTGCTTAGAGGGTGAAATAACG 58.495 43.478 0.00 0.00 0.00 3.18
2440 2492 3.649023 TGGTTACTGCTTAGAGGGTGAAA 59.351 43.478 0.00 0.00 0.00 2.69
2453 2505 8.263940 TCAGAAAAACATACTATGGTTACTGC 57.736 34.615 19.00 0.96 39.78 4.40
2465 2517 9.010366 GTCAACTTCAGTTTCAGAAAAACATAC 57.990 33.333 0.00 0.00 35.83 2.39
2472 2525 6.531240 GCATTTGTCAACTTCAGTTTCAGAAA 59.469 34.615 0.00 0.00 35.83 2.52
2473 2526 6.035843 GCATTTGTCAACTTCAGTTTCAGAA 58.964 36.000 0.00 0.00 35.83 3.02
2497 2550 3.119637 GGTGTCAATTTCCCCAATACACG 60.120 47.826 0.00 0.00 36.05 4.49
2501 2554 3.335183 TCAGGGTGTCAATTTCCCCAATA 59.665 43.478 0.00 0.00 41.95 1.90
2502 2555 2.111613 TCAGGGTGTCAATTTCCCCAAT 59.888 45.455 0.00 0.00 41.95 3.16
2503 2556 1.501170 TCAGGGTGTCAATTTCCCCAA 59.499 47.619 0.00 0.00 41.95 4.12
2504 2557 1.075374 CTCAGGGTGTCAATTTCCCCA 59.925 52.381 0.00 0.00 41.95 4.96
2505 2558 1.075536 ACTCAGGGTGTCAATTTCCCC 59.924 52.381 0.00 0.00 41.95 4.81
2574 2637 4.071423 TGTCATTTCGGATTGAAGCAGAA 58.929 39.130 0.00 0.00 37.99 3.02
2665 2729 0.112995 TGACTGCCCTGCCTGAAAAT 59.887 50.000 0.00 0.00 0.00 1.82
2684 2748 4.220821 CGCACCAGTCCTCCTATATGTATT 59.779 45.833 0.00 0.00 0.00 1.89
2801 2865 7.226325 CCAAAGTGATCTTTCATCATAGACTCC 59.774 40.741 0.00 0.00 41.31 3.85
3052 3119 0.253044 CTCCTTTCAGCCCGATTCCA 59.747 55.000 0.00 0.00 0.00 3.53
3161 3228 5.444663 ACTTTTGAAACTGAGAATCCTGC 57.555 39.130 0.00 0.00 0.00 4.85
3190 3257 0.815213 TTGTCATGCTATCTGCCCGC 60.815 55.000 0.00 0.00 42.00 6.13
3229 3296 7.765819 CCTTTCATCTCCTTCTTGTTTGTTTTT 59.234 33.333 0.00 0.00 0.00 1.94
3255 3322 5.574443 GGTACTTCAGAAGATTGCAAAATGC 59.426 40.000 17.56 0.00 45.29 3.56
3258 3325 6.061441 TCTGGTACTTCAGAAGATTGCAAAA 58.939 36.000 17.56 0.00 40.43 2.44
3261 3328 4.890158 TCTGGTACTTCAGAAGATTGCA 57.110 40.909 17.56 0.00 40.43 4.08
3322 3389 4.697514 ACTCGTATCACAGAATGGAATGG 58.302 43.478 0.00 0.00 43.62 3.16
3353 3420 8.552034 GCCGGCAGTTTATAAGATATGATTATC 58.448 37.037 24.80 0.00 35.41 1.75
3375 3442 0.310854 GTGTTTCAAACCTCAGCCGG 59.689 55.000 0.00 0.00 0.00 6.13
3432 3625 8.323140 CACAAAAATCTTCAGTGAACAACAATC 58.677 33.333 0.08 0.00 32.14 2.67
3435 3628 6.098679 CCACAAAAATCTTCAGTGAACAACA 58.901 36.000 0.08 0.00 32.14 3.33
3444 3637 4.491676 CATGCTCCCACAAAAATCTTCAG 58.508 43.478 0.00 0.00 0.00 3.02
3445 3638 3.258872 CCATGCTCCCACAAAAATCTTCA 59.741 43.478 0.00 0.00 0.00 3.02
3479 3672 5.567138 ATTATTACCAGTCAACAGCAAGC 57.433 39.130 0.00 0.00 0.00 4.01
3503 3779 9.749490 CAAACATTCATTTGACTGATATTTTGC 57.251 29.630 5.08 0.00 41.28 3.68
3505 3781 9.715121 AGCAAACATTCATTTGACTGATATTTT 57.285 25.926 5.08 0.00 41.28 1.82
3519 3795 4.382254 CCAAGCATACCAGCAAACATTCAT 60.382 41.667 0.00 0.00 36.85 2.57
3525 3801 0.890683 AGCCAAGCATACCAGCAAAC 59.109 50.000 0.00 0.00 36.85 2.93
3530 3806 4.077300 TCTTATGAGCCAAGCATACCAG 57.923 45.455 0.00 0.00 0.00 4.00
3532 3808 4.199310 TGTTCTTATGAGCCAAGCATACC 58.801 43.478 0.00 0.00 0.00 2.73
3542 3818 6.018343 GGCATTCTCTTACTGTTCTTATGAGC 60.018 42.308 0.00 0.00 0.00 4.26
3591 3887 7.410800 TGACATAGTAACACAAAACGTTAGG 57.589 36.000 0.00 0.00 29.74 2.69
3611 3907 8.109705 ACTATAACAATTCTGCATGTTTGACA 57.890 30.769 8.59 0.00 40.14 3.58
3661 3957 9.590451 GATTCTATCTCAAAATTCCAATGCAAA 57.410 29.630 0.00 0.00 0.00 3.68
3662 3958 8.974238 AGATTCTATCTCAAAATTCCAATGCAA 58.026 29.630 0.00 0.00 33.42 4.08
3663 3959 8.529424 AGATTCTATCTCAAAATTCCAATGCA 57.471 30.769 0.00 0.00 33.42 3.96
3688 4014 7.735917 AGATAAACGATCTGTGGAAATCCATA 58.264 34.615 5.27 1.80 43.71 2.74
3689 4015 6.595682 AGATAAACGATCTGTGGAAATCCAT 58.404 36.000 5.27 0.00 43.71 3.41
3690 4016 5.989477 AGATAAACGATCTGTGGAAATCCA 58.011 37.500 0.00 0.00 43.71 3.41
3691 4017 7.062371 CGATAGATAAACGATCTGTGGAAATCC 59.938 40.741 0.00 0.00 45.05 3.01
3693 4019 7.658261 TCGATAGATAAACGATCTGTGGAAAT 58.342 34.615 0.00 0.00 45.05 2.17
3694 4020 7.034685 TCGATAGATAAACGATCTGTGGAAA 57.965 36.000 0.00 0.00 45.05 3.13
3721 4050 3.440522 GGGATTTACAAGTCTCTGGCAAC 59.559 47.826 0.00 0.00 0.00 4.17
3746 4075 5.937540 TGTTATTGTGTGATGAAGGGTGTAG 59.062 40.000 0.00 0.00 0.00 2.74
3747 4076 5.870706 TGTTATTGTGTGATGAAGGGTGTA 58.129 37.500 0.00 0.00 0.00 2.90
3748 4077 4.724399 TGTTATTGTGTGATGAAGGGTGT 58.276 39.130 0.00 0.00 0.00 4.16
3749 4078 5.241506 AGTTGTTATTGTGTGATGAAGGGTG 59.758 40.000 0.00 0.00 0.00 4.61
3750 4079 5.385198 AGTTGTTATTGTGTGATGAAGGGT 58.615 37.500 0.00 0.00 0.00 4.34
3753 4082 8.633075 AAACAAGTTGTTATTGTGTGATGAAG 57.367 30.769 21.14 0.00 40.14 3.02
3754 4083 8.867935 CAAAACAAGTTGTTATTGTGTGATGAA 58.132 29.630 21.14 0.00 40.14 2.57
3755 4084 7.009999 GCAAAACAAGTTGTTATTGTGTGATGA 59.990 33.333 26.40 0.00 40.14 2.92
3756 4085 7.118724 GCAAAACAAGTTGTTATTGTGTGATG 58.881 34.615 26.40 15.75 40.14 3.07
3757 4086 6.257630 GGCAAAACAAGTTGTTATTGTGTGAT 59.742 34.615 26.40 10.09 40.14 3.06
3765 4094 6.876257 TGTTCTTTGGCAAAACAAGTTGTTAT 59.124 30.769 21.14 9.22 40.14 1.89
3771 4100 5.343307 AGATGTTCTTTGGCAAAACAAGT 57.657 34.783 18.34 6.19 36.57 3.16
3794 4125 4.397420 TGAAGCAGCAAAAGGATTCAGTA 58.603 39.130 0.00 0.00 0.00 2.74
3845 4176 9.295825 ACTGAATGAAAATGTAGACAATAACCA 57.704 29.630 0.00 0.00 0.00 3.67
3850 4181 8.292448 GTCACACTGAATGAAAATGTAGACAAT 58.708 33.333 0.00 0.00 0.00 2.71
3863 4194 6.318396 TCAAGAAACAATGTCACACTGAATGA 59.682 34.615 0.00 0.00 0.00 2.57
3868 4199 7.614908 CAATTTCAAGAAACAATGTCACACTG 58.385 34.615 0.00 0.00 32.51 3.66
3870 4201 6.035866 TGCAATTTCAAGAAACAATGTCACAC 59.964 34.615 0.00 0.00 32.51 3.82
3877 4208 6.543100 ACAATGGTGCAATTTCAAGAAACAAT 59.457 30.769 0.00 0.00 32.51 2.71
3894 4226 4.943705 AGCAGAGGTACATTAACAATGGTG 59.056 41.667 0.00 0.00 43.21 4.17
3905 4237 4.760204 GTGTTTTTGGTAGCAGAGGTACAT 59.240 41.667 8.41 0.00 38.14 2.29
3906 4238 4.131596 GTGTTTTTGGTAGCAGAGGTACA 58.868 43.478 8.41 0.00 38.14 2.90
3907 4239 4.131596 TGTGTTTTTGGTAGCAGAGGTAC 58.868 43.478 0.00 0.00 36.00 3.34
3908 4240 4.425180 TGTGTTTTTGGTAGCAGAGGTA 57.575 40.909 0.00 0.00 0.00 3.08
3909 4241 3.290948 TGTGTTTTTGGTAGCAGAGGT 57.709 42.857 0.00 0.00 0.00 3.85
3910 4242 3.380004 TGTTGTGTTTTTGGTAGCAGAGG 59.620 43.478 0.00 0.00 0.00 3.69
3911 4243 4.630894 TGTTGTGTTTTTGGTAGCAGAG 57.369 40.909 0.00 0.00 0.00 3.35
3912 4244 6.701145 TTATGTTGTGTTTTTGGTAGCAGA 57.299 33.333 0.00 0.00 0.00 4.26
3913 4245 6.922957 ACATTATGTTGTGTTTTTGGTAGCAG 59.077 34.615 0.00 0.00 0.00 4.24
3956 4290 9.741647 GAAGATTTCTTGAAACATCTCTGTTTT 57.258 29.630 5.31 0.00 44.23 2.43
3957 4291 8.906867 TGAAGATTTCTTGAAACATCTCTGTTT 58.093 29.630 3.53 3.53 45.46 2.83
3958 4292 8.455903 TGAAGATTTCTTGAAACATCTCTGTT 57.544 30.769 0.00 0.00 40.80 3.16
3959 4293 8.512956 CATGAAGATTTCTTGAAACATCTCTGT 58.487 33.333 0.00 0.00 37.08 3.41
3960 4294 7.485277 GCATGAAGATTTCTTGAAACATCTCTG 59.515 37.037 0.00 0.94 37.08 3.35
3961 4295 7.536855 GCATGAAGATTTCTTGAAACATCTCT 58.463 34.615 0.00 0.00 37.08 3.10
3966 4300 5.214417 CACGCATGAAGATTTCTTGAAACA 58.786 37.500 0.00 0.00 37.08 2.83
3981 4315 2.028567 TCAGACCATTGTACACGCATGA 60.029 45.455 7.46 0.26 0.00 3.07
3986 4320 4.504461 GCTTCTATCAGACCATTGTACACG 59.496 45.833 0.00 0.00 0.00 4.49
4001 4336 3.559242 GCAATCCTGTGTCTGCTTCTATC 59.441 47.826 0.00 0.00 0.00 2.08
4003 4338 2.568956 AGCAATCCTGTGTCTGCTTCTA 59.431 45.455 0.00 0.00 42.37 2.10
4031 4366 7.806690 TCTTTTATCATCCAGAAAACTTGTCG 58.193 34.615 0.00 0.00 0.00 4.35
4051 4386 1.612676 TGCTCACATGCTGCTCTTTT 58.387 45.000 0.00 0.00 0.00 2.27
4057 4392 2.024305 GCGATGCTCACATGCTGC 59.976 61.111 0.00 0.00 36.35 5.25
4068 4403 0.742281 TCTTCAGGCTTCAGCGATGC 60.742 55.000 0.00 7.54 43.26 3.91
4073 4408 4.450053 AGATAACATCTTCAGGCTTCAGC 58.550 43.478 0.00 0.00 35.76 4.26
4087 4478 8.553459 ACGAGAAAAGAATGTGAAGATAACAT 57.447 30.769 0.00 0.00 39.95 2.71
4088 4479 7.962964 ACGAGAAAAGAATGTGAAGATAACA 57.037 32.000 0.00 0.00 0.00 2.41
4092 4483 7.227512 ACAAGAACGAGAAAAGAATGTGAAGAT 59.772 33.333 0.00 0.00 0.00 2.40
4094 4485 6.719365 ACAAGAACGAGAAAAGAATGTGAAG 58.281 36.000 0.00 0.00 0.00 3.02
4097 4488 6.486248 TCAACAAGAACGAGAAAAGAATGTG 58.514 36.000 0.00 0.00 0.00 3.21
4103 4494 6.589830 TCTTCTCAACAAGAACGAGAAAAG 57.410 37.500 0.00 0.00 43.29 2.27
4107 4498 3.990469 GCATCTTCTCAACAAGAACGAGA 59.010 43.478 0.00 0.00 39.12 4.04
4108 4499 3.742882 TGCATCTTCTCAACAAGAACGAG 59.257 43.478 0.00 0.00 39.12 4.18
4116 4507 6.880529 TCTTGACAATATGCATCTTCTCAACA 59.119 34.615 0.19 0.00 0.00 3.33
4132 4523 6.094603 GCATACAATTCCAGACTCTTGACAAT 59.905 38.462 0.00 0.00 0.00 2.71
4135 4526 5.064452 CAGCATACAATTCCAGACTCTTGAC 59.936 44.000 0.00 0.00 0.00 3.18
4140 4533 4.331168 GTCACAGCATACAATTCCAGACTC 59.669 45.833 0.00 0.00 0.00 3.36
4155 4548 4.635765 GGTGCAGATTTATAAGTCACAGCA 59.364 41.667 19.26 16.91 0.00 4.41
4166 4559 5.263599 TGTGATTTCCTGGTGCAGATTTAT 58.736 37.500 0.00 0.00 32.44 1.40
4177 4570 7.592885 ATCTCCAATTAATGTGATTTCCTGG 57.407 36.000 0.00 0.00 0.00 4.45
4242 4636 2.269172 CATGCGCCAATATTTTGCACA 58.731 42.857 4.18 4.53 38.54 4.57
4243 4637 1.004715 GCATGCGCCAATATTTTGCAC 60.005 47.619 4.18 0.00 38.54 4.57
4244 4638 1.134759 AGCATGCGCCAATATTTTGCA 60.135 42.857 13.01 8.08 39.83 4.08
4245 4639 1.574134 AGCATGCGCCAATATTTTGC 58.426 45.000 13.01 1.28 39.83 3.68
4246 4640 2.540931 GGAAGCATGCGCCAATATTTTG 59.459 45.455 22.66 0.00 39.83 2.44
4247 4641 2.799207 CGGAAGCATGCGCCAATATTTT 60.799 45.455 25.53 7.90 39.83 1.82
4252 4646 2.751436 ACGGAAGCATGCGCCAAT 60.751 55.556 25.53 14.25 45.18 3.16
4268 4662 3.779759 CATCAGGTACAGCTTCAGAGAC 58.220 50.000 0.00 0.00 0.00 3.36
4271 4665 2.182827 AGCATCAGGTACAGCTTCAGA 58.817 47.619 0.00 0.00 32.52 3.27
4279 4673 2.076100 CGAAAGCAAGCATCAGGTACA 58.924 47.619 0.00 0.00 0.00 2.90
4280 4674 2.076863 ACGAAAGCAAGCATCAGGTAC 58.923 47.619 0.00 0.00 0.00 3.34
4281 4675 2.472695 ACGAAAGCAAGCATCAGGTA 57.527 45.000 0.00 0.00 0.00 3.08
4282 4676 1.609208 AACGAAAGCAAGCATCAGGT 58.391 45.000 0.00 0.00 0.00 4.00
4283 4677 2.744202 ACTAACGAAAGCAAGCATCAGG 59.256 45.455 0.00 0.00 0.00 3.86
4284 4678 5.107104 TGTTACTAACGAAAGCAAGCATCAG 60.107 40.000 0.00 0.00 0.00 2.90
4285 4679 4.752604 TGTTACTAACGAAAGCAAGCATCA 59.247 37.500 0.00 0.00 0.00 3.07
4286 4680 5.277601 TGTTACTAACGAAAGCAAGCATC 57.722 39.130 0.00 0.00 0.00 3.91
4287 4681 5.008217 TGTTGTTACTAACGAAAGCAAGCAT 59.992 36.000 0.00 0.00 33.28 3.79
4288 4682 4.333095 TGTTGTTACTAACGAAAGCAAGCA 59.667 37.500 0.00 0.00 33.28 3.91
4289 4683 4.669283 GTGTTGTTACTAACGAAAGCAAGC 59.331 41.667 0.00 0.00 33.28 4.01
4290 4684 5.202640 GGTGTTGTTACTAACGAAAGCAAG 58.797 41.667 4.29 0.00 31.99 4.01
4291 4685 4.260294 CGGTGTTGTTACTAACGAAAGCAA 60.260 41.667 8.62 0.00 31.28 3.91
4292 4686 3.245754 CGGTGTTGTTACTAACGAAAGCA 59.754 43.478 8.62 0.00 31.28 3.91
4293 4687 3.363280 CCGGTGTTGTTACTAACGAAAGC 60.363 47.826 0.00 0.00 33.28 3.51
4294 4688 4.050553 TCCGGTGTTGTTACTAACGAAAG 58.949 43.478 0.00 0.00 33.28 2.62
4295 4689 4.052159 TCCGGTGTTGTTACTAACGAAA 57.948 40.909 0.00 0.00 33.28 3.46
4296 4690 3.724508 TCCGGTGTTGTTACTAACGAA 57.275 42.857 0.00 0.00 33.28 3.85


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

AutoCloner maintained by Alex Coulton.