Multiple sequence alignment - TraesCS2A01G437100

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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 TraesCS2A01G437100 chr2A 100.000 6945 0 0 1 6945 688963338 688970282 0.000000e+00 12826.0
1 TraesCS2A01G437100 chr2D 92.963 5670 253 65 480 6065 544790342 544784735 0.000000e+00 8126.0
2 TraesCS2A01G437100 chr2D 84.750 400 41 15 6092 6477 544784746 544784353 3.930000e-102 383.0
3 TraesCS2A01G437100 chr2B 95.909 2151 67 13 4305 6443 650795233 650793092 0.000000e+00 3465.0
4 TraesCS2A01G437100 chr2B 93.098 2072 116 14 2216 4269 650797294 650795232 0.000000e+00 3009.0
5 TraesCS2A01G437100 chr2B 91.984 1522 71 15 674 2180 650798864 650797379 0.000000e+00 2087.0
6 TraesCS2A01G437100 chr2B 84.741 675 64 18 6 674 650800105 650799464 2.110000e-179 640.0
7 TraesCS2A01G437100 chr2B 91.935 434 14 3 6494 6908 650793083 650792652 7.760000e-164 588.0
8 TraesCS2A01G437100 chr2B 89.247 93 10 0 5546 5638 724693099 724693007 4.400000e-22 117.0
9 TraesCS2A01G437100 chr2B 87.342 79 8 1 102 180 651043366 651043290 9.590000e-14 89.8
10 TraesCS2A01G437100 chr7B 96.970 33 1 0 812 844 317170979 317170947 1.000000e-03 56.5


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 TraesCS2A01G437100 chr2A 688963338 688970282 6944 False 12826.0 12826 100.0000 1 6945 1 chr2A.!!$F1 6944
1 TraesCS2A01G437100 chr2D 544784353 544790342 5989 True 4254.5 8126 88.8565 480 6477 2 chr2D.!!$R1 5997
2 TraesCS2A01G437100 chr2B 650792652 650800105 7453 True 1957.8 3465 91.5334 6 6908 5 chr2B.!!$R3 6902

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
41 42 0.263172 TAGAGAGAGGGGCCCAAGAG 59.737 60.000 27.72 0.0 0.00 2.85 F
1754 2398 0.815734 CGAAAGCGAGAGGGGACTAA 59.184 55.000 0.00 0.0 40.09 2.24 F
2793 3507 0.397941 AAGCAGCAAGGTACAGAGCA 59.602 50.000 0.00 0.0 0.00 4.26 F
4169 4885 1.800586 TGCGAAACTCTGCTGCTTTAG 59.199 47.619 0.00 0.0 0.00 1.85 F
4928 5707 0.102300 TGATCGGCACATGGTCTACG 59.898 55.000 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2468 0.183492 AAGGGCCATGACACGCATAT 59.817 50.000 6.18 0.0 34.82 1.78 R
3580 4295 2.094545 ACCGGAATTCAAATCTGCAAGC 60.095 45.455 9.46 0.0 0.00 4.01 R
4267 4984 0.778083 GGAAGAACCTGAACCCCCTT 59.222 55.000 0.00 0.0 35.41 3.95 R
4974 5753 2.030457 GTGGATTGAATAGTCAACGCCG 59.970 50.000 7.92 0.0 46.40 6.46 R
6591 7390 0.105504 AAGTTTTGGGGCTTCTGGCT 60.106 50.000 0.00 0.0 41.46 4.75 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
31 32 4.501229 GGCACACATGATTCTAGAGAGAGG 60.501 50.000 0.00 0.00 31.77 3.69
34 35 3.006752 CACATGATTCTAGAGAGAGGGGC 59.993 52.174 0.00 0.00 31.77 5.80
41 42 0.263172 TAGAGAGAGGGGCCCAAGAG 59.737 60.000 27.72 0.00 0.00 2.85
49 50 1.213296 GGGGCCCAAGAGACTGAATA 58.787 55.000 26.86 0.00 0.00 1.75
86 87 4.213482 GTCAAGTTTTAGAGCAATGGTCGT 59.787 41.667 6.81 0.00 35.00 4.34
92 93 2.550830 AGAGCAATGGTCGTGTTCTT 57.449 45.000 6.81 0.00 33.29 2.52
94 95 1.126846 GAGCAATGGTCGTGTTCTTCG 59.873 52.381 0.00 0.00 0.00 3.79
187 188 3.157881 AGTGTTTCTCTCCACTCATCGA 58.842 45.455 0.00 0.00 37.34 3.59
198 199 5.006649 TCTCCACTCATCGAAATAATTTGCG 59.993 40.000 0.00 0.00 0.00 4.85
219 220 3.153919 GGTGATTTAGTGTGGGCTTTGA 58.846 45.455 0.00 0.00 0.00 2.69
228 229 1.463214 TGGGCTTTGAGGGAGTCCA 60.463 57.895 12.30 0.00 46.14 4.02
277 278 4.263949 ACTTGCCAAGGCCTTTACTCTAAT 60.264 41.667 17.61 0.00 41.09 1.73
278 279 3.886123 TGCCAAGGCCTTTACTCTAATC 58.114 45.455 17.61 0.00 41.09 1.75
279 280 3.265737 TGCCAAGGCCTTTACTCTAATCA 59.734 43.478 17.61 0.52 41.09 2.57
283 284 5.819901 CCAAGGCCTTTACTCTAATCAGAAG 59.180 44.000 17.61 0.00 0.00 2.85
301 302 8.743085 ATCAGAAGATGTATAATGCAAAGTGT 57.257 30.769 0.00 0.00 31.91 3.55
317 318 8.948853 TGCAAAGTGTTTAGAAAAATAGATCG 57.051 30.769 0.00 0.00 0.00 3.69
318 319 8.779303 TGCAAAGTGTTTAGAAAAATAGATCGA 58.221 29.630 0.00 0.00 0.00 3.59
319 320 9.607285 GCAAAGTGTTTAGAAAAATAGATCGAA 57.393 29.630 0.00 0.00 0.00 3.71
351 354 7.766219 TTAAGCAACGATAGAGATAAACACC 57.234 36.000 0.00 0.00 41.38 4.16
357 360 2.572191 TAGAGATAAACACCGGTGCG 57.428 50.000 34.26 12.93 0.00 5.34
362 365 2.997986 AGATAAACACCGGTGCGTAAAG 59.002 45.455 34.26 9.59 0.00 1.85
365 368 1.886886 AACACCGGTGCGTAAAGAAT 58.113 45.000 34.26 8.75 0.00 2.40
368 371 1.533731 CACCGGTGCGTAAAGAATTGT 59.466 47.619 24.02 0.00 0.00 2.71
371 374 3.814283 ACCGGTGCGTAAAGAATTGTTTA 59.186 39.130 6.12 3.78 0.00 2.01
405 408 2.286106 CTCATGCGAGAACTGAGCG 58.714 57.895 0.00 0.00 42.34 5.03
414 417 2.847133 CGAGAACTGAGCGTAACTTAGC 59.153 50.000 0.00 0.00 35.41 3.09
417 420 2.656560 ACTGAGCGTAACTTAGCTGG 57.343 50.000 0.00 0.00 44.69 4.85
420 423 3.244112 ACTGAGCGTAACTTAGCTGGTTT 60.244 43.478 11.18 0.00 44.69 3.27
426 429 4.779987 CGTAACTTAGCTGGTTTGGTTTC 58.220 43.478 11.18 0.00 0.00 2.78
431 434 4.097892 ACTTAGCTGGTTTGGTTTCTTGTG 59.902 41.667 0.00 0.00 0.00 3.33
441 444 4.986054 TGGTTTCTTGTGGTGGTACTAT 57.014 40.909 0.00 0.00 0.00 2.12
442 445 6.436738 TTGGTTTCTTGTGGTGGTACTATA 57.563 37.500 0.00 0.00 0.00 1.31
443 446 6.436738 TGGTTTCTTGTGGTGGTACTATAA 57.563 37.500 0.00 0.00 0.00 0.98
444 447 6.469410 TGGTTTCTTGTGGTGGTACTATAAG 58.531 40.000 0.00 0.00 30.99 1.73
446 449 7.163441 GGTTTCTTGTGGTGGTACTATAAGAA 58.837 38.462 11.25 11.25 42.02 2.52
447 450 7.662669 GGTTTCTTGTGGTGGTACTATAAGAAA 59.337 37.037 18.64 18.64 46.25 2.52
448 451 8.611654 TTTCTTGTGGTGGTACTATAAGAAAC 57.388 34.615 18.64 0.00 44.87 2.78
449 452 6.704310 TCTTGTGGTGGTACTATAAGAAACC 58.296 40.000 2.88 0.00 34.82 3.27
450 453 5.425196 TGTGGTGGTACTATAAGAAACCC 57.575 43.478 0.00 0.00 0.00 4.11
451 454 4.845225 TGTGGTGGTACTATAAGAAACCCA 59.155 41.667 0.00 0.00 0.00 4.51
452 455 5.181009 GTGGTGGTACTATAAGAAACCCAC 58.819 45.833 0.00 0.00 40.05 4.61
453 456 5.046087 GTGGTGGTACTATAAGAAACCCACT 60.046 44.000 0.00 0.00 40.49 4.00
456 459 6.104665 GTGGTACTATAAGAAACCCACTGTC 58.895 44.000 0.00 0.00 38.24 3.51
457 460 5.188359 TGGTACTATAAGAAACCCACTGTCC 59.812 44.000 0.00 0.00 0.00 4.02
458 461 5.424573 GGTACTATAAGAAACCCACTGTCCT 59.575 44.000 0.00 0.00 0.00 3.85
459 462 6.070366 GGTACTATAAGAAACCCACTGTCCTT 60.070 42.308 0.00 0.00 0.00 3.36
460 463 7.124750 GGTACTATAAGAAACCCACTGTCCTTA 59.875 40.741 0.00 0.00 0.00 2.69
461 464 7.563724 ACTATAAGAAACCCACTGTCCTTAA 57.436 36.000 0.00 0.00 0.00 1.85
462 465 7.981142 ACTATAAGAAACCCACTGTCCTTAAA 58.019 34.615 0.00 0.00 0.00 1.52
463 466 8.442374 ACTATAAGAAACCCACTGTCCTTAAAA 58.558 33.333 0.00 0.00 0.00 1.52
464 467 9.462606 CTATAAGAAACCCACTGTCCTTAAAAT 57.537 33.333 0.00 0.00 0.00 1.82
465 468 8.721133 ATAAGAAACCCACTGTCCTTAAAATT 57.279 30.769 0.00 0.00 0.00 1.82
466 469 7.432148 AAGAAACCCACTGTCCTTAAAATTT 57.568 32.000 0.00 0.00 0.00 1.82
467 470 8.541899 AAGAAACCCACTGTCCTTAAAATTTA 57.458 30.769 0.00 0.00 0.00 1.40
468 471 7.948357 AGAAACCCACTGTCCTTAAAATTTAC 58.052 34.615 0.00 0.00 0.00 2.01
469 472 7.783119 AGAAACCCACTGTCCTTAAAATTTACT 59.217 33.333 0.00 0.00 0.00 2.24
470 473 8.999905 AAACCCACTGTCCTTAAAATTTACTA 57.000 30.769 0.00 0.00 0.00 1.82
471 474 8.631480 AACCCACTGTCCTTAAAATTTACTAG 57.369 34.615 0.00 0.00 0.00 2.57
472 475 7.752638 ACCCACTGTCCTTAAAATTTACTAGT 58.247 34.615 0.00 0.00 0.00 2.57
473 476 7.881751 ACCCACTGTCCTTAAAATTTACTAGTC 59.118 37.037 0.00 0.00 0.00 2.59
474 477 7.881232 CCCACTGTCCTTAAAATTTACTAGTCA 59.119 37.037 0.00 0.00 0.00 3.41
475 478 9.280174 CCACTGTCCTTAAAATTTACTAGTCAA 57.720 33.333 0.00 0.00 0.00 3.18
478 481 9.280174 CTGTCCTTAAAATTTACTAGTCAACCA 57.720 33.333 0.00 0.00 0.00 3.67
512 517 4.546829 AGTGCTCGGAATTTACCAGTAA 57.453 40.909 0.00 0.00 0.00 2.24
537 542 1.057566 CATGCGTTTTCATTTTCCGCG 59.942 47.619 0.00 0.00 46.77 6.46
543 548 1.083489 TTTCATTTTCCGCGCGATCT 58.917 45.000 34.63 8.01 0.00 2.75
544 549 1.083489 TTCATTTTCCGCGCGATCTT 58.917 45.000 34.63 9.02 0.00 2.40
577 582 7.655490 AGAGTGTCAATTTCTGAGGATTTTTG 58.345 34.615 0.00 0.00 33.60 2.44
585 590 8.866956 CAATTTCTGAGGATTTTTGTATGCTTC 58.133 33.333 0.00 0.00 0.00 3.86
586 591 7.765695 TTTCTGAGGATTTTTGTATGCTTCT 57.234 32.000 0.00 0.00 0.00 2.85
587 592 8.862325 TTTCTGAGGATTTTTGTATGCTTCTA 57.138 30.769 0.00 0.00 0.00 2.10
743 1351 1.222113 GCACTCCTGTAGGCCCTTC 59.778 63.158 0.00 0.00 34.44 3.46
744 1352 1.908483 CACTCCTGTAGGCCCTTCC 59.092 63.158 0.00 0.00 34.44 3.46
803 1418 2.483876 CACACCACACCACTAGAACAG 58.516 52.381 0.00 0.00 0.00 3.16
819 1434 3.576550 AGAACAGACCCACTCTCTTCTTC 59.423 47.826 0.00 0.00 0.00 2.87
820 1435 2.252714 ACAGACCCACTCTCTTCTTCC 58.747 52.381 0.00 0.00 0.00 3.46
821 1436 2.158234 ACAGACCCACTCTCTTCTTCCT 60.158 50.000 0.00 0.00 0.00 3.36
862 1480 3.551454 GGCTATAAATACTCGCCGTCACA 60.551 47.826 0.00 0.00 0.00 3.58
926 1544 1.671901 CCCTTCCACTCGCTCTCTCC 61.672 65.000 0.00 0.00 0.00 3.71
927 1545 1.671901 CCTTCCACTCGCTCTCTCCC 61.672 65.000 0.00 0.00 0.00 4.30
943 1561 1.150536 CCCTCCCTCTCTCTCTCCG 59.849 68.421 0.00 0.00 0.00 4.63
962 1580 1.610379 CCAGGGGGAAAGGCAAAGG 60.610 63.158 0.00 0.00 35.59 3.11
963 1581 1.464722 CAGGGGGAAAGGCAAAGGA 59.535 57.895 0.00 0.00 0.00 3.36
1324 1951 3.202706 GGCGGATTTCGTGGCTCC 61.203 66.667 0.00 0.00 41.72 4.70
1338 1965 4.569180 CTCCGCCGGCCCATCAAT 62.569 66.667 23.46 0.00 0.00 2.57
1339 1966 4.562425 TCCGCCGGCCCATCAATC 62.562 66.667 23.46 0.00 0.00 2.67
1393 2023 4.259356 AGGGTTTAATTGTTAGCGTCTCC 58.741 43.478 0.00 0.00 0.00 3.71
1396 2026 5.163784 GGGTTTAATTGTTAGCGTCTCCTTC 60.164 44.000 0.00 0.00 0.00 3.46
1399 2029 7.201504 GGTTTAATTGTTAGCGTCTCCTTCTAC 60.202 40.741 0.00 0.00 0.00 2.59
1472 2103 2.481185 TCAGTCAAACGCGGTTTAATCC 59.519 45.455 6.68 0.00 33.70 3.01
1473 2104 2.482721 CAGTCAAACGCGGTTTAATCCT 59.517 45.455 6.68 0.00 33.70 3.24
1476 2107 1.807742 CAAACGCGGTTTAATCCTCCA 59.192 47.619 6.68 0.00 33.70 3.86
1509 2140 2.159653 GCAATCAGATTTCGCGAGTTGT 60.160 45.455 9.59 0.00 0.00 3.32
1528 2159 7.376072 CGAGTTGTCTCAAACCAAAATACTTTC 59.624 37.037 0.00 0.00 40.44 2.62
1692 2333 9.722056 ACAATCATCTTTAATTCTTTATCACGC 57.278 29.630 0.00 0.00 0.00 5.34
1754 2398 0.815734 CGAAAGCGAGAGGGGACTAA 59.184 55.000 0.00 0.00 40.09 2.24
1823 2467 2.676471 GCTGGCGTTTGGTCCCAT 60.676 61.111 0.00 0.00 0.00 4.00
1824 2468 1.377987 GCTGGCGTTTGGTCCCATA 60.378 57.895 0.00 0.00 0.00 2.74
1832 2476 2.223144 CGTTTGGTCCCATATATGCGTG 59.777 50.000 7.24 0.00 0.00 5.34
1834 2478 2.831685 TGGTCCCATATATGCGTGTC 57.168 50.000 7.24 0.00 0.00 3.67
1929 2577 0.539438 TGTGGGTTCCTGATTGTGGC 60.539 55.000 0.00 0.00 0.00 5.01
1953 2601 1.944676 CGTGTTAGGCCGATCGAGC 60.945 63.158 18.66 17.69 0.00 5.03
1954 2602 1.944676 GTGTTAGGCCGATCGAGCG 60.945 63.158 17.57 17.57 0.00 5.03
1956 2604 1.370657 GTTAGGCCGATCGAGCGAG 60.371 63.158 26.68 15.65 0.00 5.03
2078 2726 2.496899 AGCTATGGGAGGTGTGTTTG 57.503 50.000 0.00 0.00 33.53 2.93
2088 2736 3.065371 GGAGGTGTGTTTGAACTTGTGAG 59.935 47.826 0.00 0.00 0.00 3.51
2157 2805 1.896660 TGTTGCTCTGTTTCCCGGC 60.897 57.895 0.00 0.00 0.00 6.13
2180 2828 2.318908 TGCATTATTGGAATGGAGGGC 58.681 47.619 0.00 0.00 0.00 5.19
2182 2830 2.757606 GCATTATTGGAATGGAGGGCCT 60.758 50.000 5.25 5.25 34.31 5.19
2185 2833 2.594365 ATTGGAATGGAGGGCCTGGC 62.594 60.000 12.95 11.05 34.31 4.85
2187 2835 2.123982 GAATGGAGGGCCTGGCAG 60.124 66.667 22.05 7.75 34.31 4.85
2188 2836 2.614969 AATGGAGGGCCTGGCAGA 60.615 61.111 22.05 0.00 34.31 4.26
2189 2837 2.900671 GAATGGAGGGCCTGGCAGAC 62.901 65.000 22.05 3.44 34.31 3.51
2190 2838 4.980592 TGGAGGGCCTGGCAGACA 62.981 66.667 22.05 10.57 34.31 3.41
2440 3153 9.880064 GTTAATCCTTCTTTTTACTCTTGTCAC 57.120 33.333 0.00 0.00 0.00 3.67
2444 3157 4.067972 TCTTTTTACTCTTGTCACGGCT 57.932 40.909 0.00 0.00 0.00 5.52
2445 3158 5.204409 TCTTTTTACTCTTGTCACGGCTA 57.796 39.130 0.00 0.00 0.00 3.93
2454 3167 6.875076 ACTCTTGTCACGGCTATACTTAAAT 58.125 36.000 0.00 0.00 0.00 1.40
2467 3180 7.702348 GGCTATACTTAAATTTTGTCAGGCAAG 59.298 37.037 17.08 8.37 38.47 4.01
2493 3207 5.357032 AGGTTCTAAACTTCTGTTTGGTGTG 59.643 40.000 4.64 0.00 45.01 3.82
2498 3212 2.936202 ACTTCTGTTTGGTGTGATGCT 58.064 42.857 0.00 0.00 0.00 3.79
2514 3228 2.579207 TGCTTGCATACGAGTAGGAC 57.421 50.000 0.00 0.00 0.00 3.85
2550 3264 7.982919 CCATTTTGAATTCTCCTGCATTATTGA 59.017 33.333 7.05 0.00 0.00 2.57
2599 3313 6.353323 TGCCAAATCTCAAGAATTATCCGTA 58.647 36.000 0.00 0.00 0.00 4.02
2679 3393 2.450609 TTTTAGACGCAGACCAGTCC 57.549 50.000 0.00 0.00 38.08 3.85
2793 3507 0.397941 AAGCAGCAAGGTACAGAGCA 59.602 50.000 0.00 0.00 0.00 4.26
2954 3668 3.746492 GCCTAACACGTTCTGATCAAGTT 59.254 43.478 0.00 0.00 0.00 2.66
3185 3900 5.185635 TCAAAATACAATCCCTTTCAGGCAG 59.814 40.000 0.00 0.00 32.73 4.85
3309 4024 2.087646 GCCTTCTCTGGTCATCCAAAC 58.912 52.381 0.00 0.00 43.81 2.93
3527 4242 4.880696 CCAGAGATCATGTTTCCTTCCTTC 59.119 45.833 0.00 0.00 0.00 3.46
3564 4279 3.815856 TCTGATTCTGCTCCTCATGTC 57.184 47.619 0.00 0.00 0.00 3.06
3584 4299 4.798574 GTCTTTGGACAAACTATGGCTTG 58.201 43.478 0.00 0.00 41.75 4.01
3591 4306 4.082026 GGACAAACTATGGCTTGCAGATTT 60.082 41.667 0.00 0.00 37.17 2.17
3639 4354 4.588951 GGACCCAAAGGAGATTTGTTTCTT 59.411 41.667 0.23 0.00 45.78 2.52
3645 4360 7.371159 CCAAAGGAGATTTGTTTCTTACTTCC 58.629 38.462 0.23 0.00 45.78 3.46
3675 4390 4.709397 AGAAACACCAACACTGATGGAAAA 59.291 37.500 12.12 0.00 40.56 2.29
3765 4480 5.628797 TGCAATTTCTTTTCCTCCCTTTT 57.371 34.783 0.00 0.00 0.00 2.27
3965 4681 5.417580 ACATGGTATTTGTGTCATTGGTACC 59.582 40.000 4.43 4.43 0.00 3.34
3999 4715 5.477637 ACCAAGAGTCTAAGACCAGTAGTTC 59.522 44.000 0.00 0.00 32.18 3.01
4001 4717 5.258216 AGAGTCTAAGACCAGTAGTTCCA 57.742 43.478 0.00 0.00 32.18 3.53
4038 4754 5.449177 GCAGATGTACAAATAGGCTGGTTTC 60.449 44.000 0.00 0.00 0.00 2.78
4169 4885 1.800586 TGCGAAACTCTGCTGCTTTAG 59.199 47.619 0.00 0.00 0.00 1.85
4203 4920 2.700722 TTGTTAGTGCCGGCATATGA 57.299 45.000 35.23 18.58 0.00 2.15
4267 4984 4.382040 GCCAGCAGTATGACAGTAGAGAAA 60.382 45.833 0.00 0.00 39.69 2.52
4268 4985 5.724328 CCAGCAGTATGACAGTAGAGAAAA 58.276 41.667 0.00 0.00 39.69 2.29
4269 4986 5.809562 CCAGCAGTATGACAGTAGAGAAAAG 59.190 44.000 0.00 0.00 39.69 2.27
4270 4987 5.809562 CAGCAGTATGACAGTAGAGAAAAGG 59.190 44.000 0.00 0.00 39.69 3.11
4271 4988 5.105146 AGCAGTATGACAGTAGAGAAAAGGG 60.105 44.000 0.00 0.00 39.69 3.95
4272 4989 5.665459 CAGTATGACAGTAGAGAAAAGGGG 58.335 45.833 0.00 0.00 39.69 4.79
4273 4990 4.717280 AGTATGACAGTAGAGAAAAGGGGG 59.283 45.833 0.00 0.00 0.00 5.40
4274 4991 2.986050 TGACAGTAGAGAAAAGGGGGT 58.014 47.619 0.00 0.00 0.00 4.95
4275 4992 3.323775 TGACAGTAGAGAAAAGGGGGTT 58.676 45.455 0.00 0.00 0.00 4.11
4276 4993 3.326880 TGACAGTAGAGAAAAGGGGGTTC 59.673 47.826 0.00 0.00 0.00 3.62
4277 4994 3.323775 ACAGTAGAGAAAAGGGGGTTCA 58.676 45.455 0.00 0.00 0.00 3.18
4278 4995 3.328050 ACAGTAGAGAAAAGGGGGTTCAG 59.672 47.826 0.00 0.00 0.00 3.02
4279 4996 2.913617 AGTAGAGAAAAGGGGGTTCAGG 59.086 50.000 0.00 0.00 0.00 3.86
4280 4997 1.834540 AGAGAAAAGGGGGTTCAGGT 58.165 50.000 0.00 0.00 0.00 4.00
4281 4998 2.144450 AGAGAAAAGGGGGTTCAGGTT 58.856 47.619 0.00 0.00 0.00 3.50
4282 4999 2.108425 AGAGAAAAGGGGGTTCAGGTTC 59.892 50.000 0.00 0.00 0.00 3.62
4283 5000 2.108425 GAGAAAAGGGGGTTCAGGTTCT 59.892 50.000 0.00 0.00 0.00 3.01
4284 5001 2.518407 AGAAAAGGGGGTTCAGGTTCTT 59.482 45.455 0.00 0.00 0.00 2.52
4285 5002 2.677542 AAAGGGGGTTCAGGTTCTTC 57.322 50.000 0.00 0.00 0.00 2.87
4286 5003 0.778083 AAGGGGGTTCAGGTTCTTCC 59.222 55.000 0.00 0.00 0.00 3.46
4288 5005 0.778083 GGGGGTTCAGGTTCTTCCTT 59.222 55.000 0.00 0.00 45.67 3.36
4289 5006 1.147191 GGGGGTTCAGGTTCTTCCTTT 59.853 52.381 0.00 0.00 45.67 3.11
4290 5007 2.425829 GGGGGTTCAGGTTCTTCCTTTT 60.426 50.000 0.00 0.00 45.67 2.27
4291 5008 3.305720 GGGGTTCAGGTTCTTCCTTTTT 58.694 45.455 0.00 0.00 45.67 1.94
4292 5009 3.321111 GGGGTTCAGGTTCTTCCTTTTTC 59.679 47.826 0.00 0.00 45.67 2.29
4293 5010 3.321111 GGGTTCAGGTTCTTCCTTTTTCC 59.679 47.826 0.00 0.00 45.67 3.13
4294 5011 4.215908 GGTTCAGGTTCTTCCTTTTTCCT 58.784 43.478 0.00 0.00 45.67 3.36
4295 5012 4.278669 GGTTCAGGTTCTTCCTTTTTCCTC 59.721 45.833 0.00 0.00 45.67 3.71
4296 5013 5.133941 GTTCAGGTTCTTCCTTTTTCCTCT 58.866 41.667 0.00 0.00 45.67 3.69
4297 5014 4.718961 TCAGGTTCTTCCTTTTTCCTCTG 58.281 43.478 0.00 0.00 45.67 3.35
4298 5015 3.254411 CAGGTTCTTCCTTTTTCCTCTGC 59.746 47.826 0.00 0.00 45.67 4.26
4299 5016 3.139211 AGGTTCTTCCTTTTTCCTCTGCT 59.861 43.478 0.00 0.00 45.67 4.24
4300 5017 3.254411 GGTTCTTCCTTTTTCCTCTGCTG 59.746 47.826 0.00 0.00 0.00 4.41
4301 5018 3.146104 TCTTCCTTTTTCCTCTGCTGG 57.854 47.619 0.00 0.00 0.00 4.85
4302 5019 2.443255 TCTTCCTTTTTCCTCTGCTGGT 59.557 45.455 0.00 0.00 0.00 4.00
4303 5020 2.276732 TCCTTTTTCCTCTGCTGGTG 57.723 50.000 0.00 0.00 0.00 4.17
4373 5127 4.142026 GCTTGGGTGTTAAGTTGTTTCCTT 60.142 41.667 0.00 0.00 0.00 3.36
4631 5387 1.081094 CCGGTACCGTTTTAGCCTTG 58.919 55.000 31.24 9.39 37.81 3.61
4678 5434 3.976015 ACTGAAAACCAAAGTTCCAGGA 58.024 40.909 10.80 0.00 34.19 3.86
4710 5466 0.602905 CTCGCTTCCGTTTTCCACCT 60.603 55.000 0.00 0.00 35.54 4.00
4825 5592 0.440371 GCTGTAGCGACTCAACTTGC 59.560 55.000 0.00 0.00 0.00 4.01
4881 5655 1.883926 GCCTCTAGTCTAGCCTGTAGC 59.116 57.143 1.60 0.00 44.25 3.58
4928 5707 0.102300 TGATCGGCACATGGTCTACG 59.898 55.000 0.00 0.00 0.00 3.51
4938 5717 1.019278 ATGGTCTACGCTTTGCCACG 61.019 55.000 0.00 0.00 31.47 4.94
4940 5719 1.491563 GTCTACGCTTTGCCACGTG 59.508 57.895 9.08 9.08 43.44 4.49
4962 5741 5.006844 GTGATCACTTGAGAATGCTGATCAG 59.993 44.000 18.84 18.84 44.88 2.90
4974 5753 2.961741 TGCTGATCAGTCTGAGTATCCC 59.038 50.000 23.38 3.35 0.00 3.85
4994 5773 2.276201 CGGCGTTGACTATTCAATCCA 58.724 47.619 0.00 0.00 43.72 3.41
5019 5798 3.244156 TGCGCATAACAAGCTTGAAATG 58.756 40.909 32.50 29.12 0.00 2.32
5023 5802 4.029418 CGCATAACAAGCTTGAAATGTTCG 59.971 41.667 32.50 24.17 38.22 3.95
5177 5958 4.579869 ACTGACTGAATTAACCGAATGCT 58.420 39.130 0.00 0.00 0.00 3.79
5314 6097 5.069383 TCCCTGTTCCAATGCATCATAATTG 59.931 40.000 0.00 0.00 34.26 2.32
5426 6209 2.859165 AGGGAAAAGAGCGATTCACA 57.141 45.000 0.00 0.00 31.25 3.58
5518 6301 2.370281 GCTACAGCTGCTGACTTGTA 57.630 50.000 34.28 16.23 38.21 2.41
6226 7015 3.130633 GTTTTGATTTCAACACTGGGGC 58.869 45.455 3.02 0.00 34.63 5.80
6251 7040 4.536765 TGTCTTTGAGCCCTCTTTTCTTT 58.463 39.130 0.00 0.00 0.00 2.52
6263 7052 2.834549 TCTTTTCTTTGCCAAACCCACA 59.165 40.909 0.00 0.00 0.00 4.17
6287 7076 5.163723 ACTCTAACGAAATGCATGGTGATTG 60.164 40.000 0.00 0.00 0.00 2.67
6443 7240 4.211920 TGGGTTACAAAGTCTGGGAAAAG 58.788 43.478 0.00 0.00 0.00 2.27
6444 7241 4.079672 TGGGTTACAAAGTCTGGGAAAAGA 60.080 41.667 0.00 0.00 0.00 2.52
6446 7243 6.183361 TGGGTTACAAAGTCTGGGAAAAGATA 60.183 38.462 0.00 0.00 0.00 1.98
6447 7244 6.717997 GGGTTACAAAGTCTGGGAAAAGATAA 59.282 38.462 0.00 0.00 0.00 1.75
6469 7268 1.315690 CCACTGCATGGTGATCATCC 58.684 55.000 2.86 5.49 44.46 3.51
6477 7276 0.548031 TGGTGATCATCCCCAAGAGC 59.452 55.000 2.86 0.00 0.00 4.09
6478 7277 0.548031 GGTGATCATCCCCAAGAGCA 59.452 55.000 0.00 0.00 0.00 4.26
6479 7278 1.476471 GGTGATCATCCCCAAGAGCAG 60.476 57.143 0.00 0.00 29.89 4.24
6480 7279 1.487976 GTGATCATCCCCAAGAGCAGA 59.512 52.381 0.00 0.00 29.89 4.26
6481 7280 2.092753 GTGATCATCCCCAAGAGCAGAA 60.093 50.000 0.00 0.00 29.89 3.02
6482 7281 2.092753 TGATCATCCCCAAGAGCAGAAC 60.093 50.000 0.00 0.00 0.00 3.01
6483 7282 0.620556 TCATCCCCAAGAGCAGAACC 59.379 55.000 0.00 0.00 0.00 3.62
6484 7283 0.622665 CATCCCCAAGAGCAGAACCT 59.377 55.000 0.00 0.00 0.00 3.50
6485 7284 1.005215 CATCCCCAAGAGCAGAACCTT 59.995 52.381 0.00 0.00 0.00 3.50
6486 7285 1.149101 TCCCCAAGAGCAGAACCTTT 58.851 50.000 0.00 0.00 0.00 3.11
6487 7286 1.073923 TCCCCAAGAGCAGAACCTTTC 59.926 52.381 0.00 0.00 0.00 2.62
6488 7287 1.074566 CCCCAAGAGCAGAACCTTTCT 59.925 52.381 0.00 0.00 41.70 2.52
6489 7288 2.489802 CCCCAAGAGCAGAACCTTTCTT 60.490 50.000 0.00 0.00 38.11 2.52
6490 7289 3.225940 CCCAAGAGCAGAACCTTTCTTT 58.774 45.455 0.00 0.00 38.11 2.52
6491 7290 3.005155 CCCAAGAGCAGAACCTTTCTTTG 59.995 47.826 0.00 0.00 38.11 2.77
6492 7291 3.633986 CCAAGAGCAGAACCTTTCTTTGT 59.366 43.478 0.00 0.00 38.11 2.83
6560 7359 5.928976 ACAGGTAGCTAATTGCATATGACA 58.071 37.500 6.97 1.06 45.94 3.58
6561 7360 5.760253 ACAGGTAGCTAATTGCATATGACAC 59.240 40.000 6.97 0.00 45.94 3.67
6572 7371 8.553459 AATTGCATATGACACTAGGTATAAGC 57.447 34.615 6.97 0.00 0.00 3.09
6579 7378 4.588951 TGACACTAGGTATAAGCCTCATGG 59.411 45.833 0.00 0.00 39.94 3.66
6583 7382 6.041751 ACACTAGGTATAAGCCTCATGGTTAC 59.958 42.308 0.00 0.00 39.58 2.50
6591 7390 2.371841 AGCCTCATGGTTACAAGTCACA 59.628 45.455 0.00 0.00 35.27 3.58
6600 7399 2.169832 TACAAGTCACAGCCAGAAGC 57.830 50.000 0.00 0.00 44.25 3.86
6601 7400 0.536006 ACAAGTCACAGCCAGAAGCC 60.536 55.000 0.00 0.00 45.47 4.35
6619 7418 3.026694 AGCCCCAAAACTTATCATCAGC 58.973 45.455 0.00 0.00 0.00 4.26
6781 7596 4.887071 ACACACACACACAAATAATGAGGT 59.113 37.500 0.00 0.00 0.00 3.85
6798 7613 6.628644 ATGAGGTATAAAGAATAGGAGGGC 57.371 41.667 0.00 0.00 0.00 5.19
6929 7747 2.822215 TCCGACTAGGAGGCCATTC 58.178 57.895 5.01 0.00 45.98 2.67
6930 7748 1.107538 TCCGACTAGGAGGCCATTCG 61.108 60.000 5.01 0.00 45.98 3.34
6931 7749 1.364171 CGACTAGGAGGCCATTCGG 59.636 63.158 5.01 0.00 0.00 4.30
6932 7750 1.392710 CGACTAGGAGGCCATTCGGT 61.393 60.000 5.01 0.00 33.28 4.69
6933 7751 1.700955 GACTAGGAGGCCATTCGGTA 58.299 55.000 5.01 0.00 33.28 4.02
6934 7752 1.340568 GACTAGGAGGCCATTCGGTAC 59.659 57.143 5.01 0.00 33.28 3.34
6935 7753 0.680061 CTAGGAGGCCATTCGGTACC 59.320 60.000 5.01 0.16 33.28 3.34
6936 7754 0.263765 TAGGAGGCCATTCGGTACCT 59.736 55.000 10.90 2.92 36.06 3.08
6937 7755 1.049289 AGGAGGCCATTCGGTACCTC 61.049 60.000 10.90 0.00 46.61 3.85
6938 7756 1.049289 GGAGGCCATTCGGTACCTCT 61.049 60.000 10.90 0.00 46.54 3.69
6939 7757 0.389757 GAGGCCATTCGGTACCTCTC 59.610 60.000 10.90 2.17 44.41 3.20
6940 7758 1.049289 AGGCCATTCGGTACCTCTCC 61.049 60.000 10.90 2.63 33.28 3.71
6942 7760 1.067582 CCATTCGGTACCTCTCCGC 59.932 63.158 10.90 0.00 46.49 5.54
6943 7761 1.392710 CCATTCGGTACCTCTCCGCT 61.393 60.000 10.90 0.00 46.49 5.52
6944 7762 0.030908 CATTCGGTACCTCTCCGCTC 59.969 60.000 10.90 0.00 46.49 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.574006 ATCATGTGTGCCAAGAGTGT 57.426 45.000 0.00 0.00 0.00 3.55
1 2 3.079578 AGAATCATGTGTGCCAAGAGTG 58.920 45.455 0.00 0.00 0.00 3.51
2 3 3.430042 AGAATCATGTGTGCCAAGAGT 57.570 42.857 0.00 0.00 0.00 3.24
3 4 4.763073 TCTAGAATCATGTGTGCCAAGAG 58.237 43.478 0.00 0.00 0.00 2.85
4 5 4.467438 TCTCTAGAATCATGTGTGCCAAGA 59.533 41.667 0.00 0.00 0.00 3.02
17 18 1.133009 TGGGCCCCTCTCTCTAGAATC 60.133 57.143 22.27 0.00 0.00 2.52
31 32 3.366052 TTTATTCAGTCTCTTGGGCCC 57.634 47.619 17.59 17.59 0.00 5.80
55 56 5.437060 TGCTCTAAAACTTGACTTCCAACT 58.563 37.500 0.00 0.00 0.00 3.16
66 67 4.134563 ACACGACCATTGCTCTAAAACTT 58.865 39.130 0.00 0.00 0.00 2.66
68 69 4.213482 AGAACACGACCATTGCTCTAAAAC 59.787 41.667 0.00 0.00 0.00 2.43
69 70 4.385825 AGAACACGACCATTGCTCTAAAA 58.614 39.130 0.00 0.00 0.00 1.52
70 71 4.002906 AGAACACGACCATTGCTCTAAA 57.997 40.909 0.00 0.00 0.00 1.85
71 72 3.678056 AGAACACGACCATTGCTCTAA 57.322 42.857 0.00 0.00 0.00 2.10
72 73 3.585862 GAAGAACACGACCATTGCTCTA 58.414 45.455 0.00 0.00 0.00 2.43
73 74 2.417719 GAAGAACACGACCATTGCTCT 58.582 47.619 0.00 0.00 0.00 4.09
74 75 1.126846 CGAAGAACACGACCATTGCTC 59.873 52.381 0.00 0.00 0.00 4.26
75 76 1.148310 CGAAGAACACGACCATTGCT 58.852 50.000 0.00 0.00 0.00 3.91
76 77 0.865769 ACGAAGAACACGACCATTGC 59.134 50.000 0.00 0.00 34.70 3.56
86 87 0.321564 CCTCCCATGCACGAAGAACA 60.322 55.000 0.00 0.00 0.00 3.18
92 93 0.616395 TAGGAACCTCCCATGCACGA 60.616 55.000 0.00 0.00 37.19 4.35
94 95 2.092323 GTTTAGGAACCTCCCATGCAC 58.908 52.381 0.00 0.00 37.19 4.57
156 157 3.312697 GGAGAGAAACACTTGTGTTGTCC 59.687 47.826 18.21 16.53 31.64 4.02
187 188 6.811170 CCACACTAAATCACCGCAAATTATTT 59.189 34.615 0.00 0.00 0.00 1.40
198 199 3.153919 TCAAAGCCCACACTAAATCACC 58.846 45.455 0.00 0.00 0.00 4.02
219 220 0.413832 TCTAAGGCAGTGGACTCCCT 59.586 55.000 0.00 0.00 35.07 4.20
228 229 5.812642 CGATACAATGTTCTTCTAAGGCAGT 59.187 40.000 0.00 0.00 0.00 4.40
277 278 8.565896 AACACTTTGCATTATACATCTTCTGA 57.434 30.769 0.00 0.00 0.00 3.27
311 312 9.142515 TCGTTGCTTAAATAAAAGTTCGATCTA 57.857 29.630 0.00 0.00 0.00 1.98
313 314 8.822105 ATCGTTGCTTAAATAAAAGTTCGATC 57.178 30.769 0.00 0.00 34.33 3.69
315 316 9.142515 TCTATCGTTGCTTAAATAAAAGTTCGA 57.857 29.630 0.00 0.00 33.51 3.71
316 317 9.409949 CTCTATCGTTGCTTAAATAAAAGTTCG 57.590 33.333 0.00 0.00 0.00 3.95
326 329 7.009815 CGGTGTTTATCTCTATCGTTGCTTAAA 59.990 37.037 0.00 0.00 0.00 1.52
343 346 3.042871 TCTTTACGCACCGGTGTTTAT 57.957 42.857 33.92 19.44 38.92 1.40
348 351 1.533731 ACAATTCTTTACGCACCGGTG 59.466 47.619 30.66 30.66 0.00 4.94
351 354 6.921332 AAATAAACAATTCTTTACGCACCG 57.079 33.333 0.00 0.00 0.00 4.94
368 371 9.071221 CGCATGAGCAATGTTTAGTAAAATAAA 57.929 29.630 0.00 0.00 42.27 1.40
371 374 6.851609 TCGCATGAGCAATGTTTAGTAAAAT 58.148 32.000 0.00 0.00 42.27 1.82
379 382 2.816087 AGTTCTCGCATGAGCAATGTTT 59.184 40.909 0.00 0.00 42.26 2.83
387 390 0.457509 ACGCTCAGTTCTCGCATGAG 60.458 55.000 0.00 0.00 42.70 2.90
392 395 1.699343 AAGTTACGCTCAGTTCTCGC 58.301 50.000 0.00 0.00 0.00 5.03
393 396 2.847133 GCTAAGTTACGCTCAGTTCTCG 59.153 50.000 0.00 0.00 0.00 4.04
405 408 6.183360 ACAAGAAACCAAACCAGCTAAGTTAC 60.183 38.462 1.98 0.00 0.00 2.50
414 417 2.159114 CCACCACAAGAAACCAAACCAG 60.159 50.000 0.00 0.00 0.00 4.00
417 420 3.697542 AGTACCACCACAAGAAACCAAAC 59.302 43.478 0.00 0.00 0.00 2.93
420 423 4.986054 ATAGTACCACCACAAGAAACCA 57.014 40.909 0.00 0.00 0.00 3.67
426 429 5.878669 GGGTTTCTTATAGTACCACCACAAG 59.121 44.000 0.00 0.00 32.20 3.16
431 434 5.046087 ACAGTGGGTTTCTTATAGTACCACC 60.046 44.000 0.00 0.00 45.99 4.61
441 444 8.541899 AAATTTTAAGGACAGTGGGTTTCTTA 57.458 30.769 0.00 0.00 0.00 2.10
442 445 7.432148 AAATTTTAAGGACAGTGGGTTTCTT 57.568 32.000 0.00 0.00 0.00 2.52
443 446 7.783119 AGTAAATTTTAAGGACAGTGGGTTTCT 59.217 33.333 0.00 0.00 0.00 2.52
444 447 7.948357 AGTAAATTTTAAGGACAGTGGGTTTC 58.052 34.615 0.00 0.00 0.00 2.78
446 449 8.222637 ACTAGTAAATTTTAAGGACAGTGGGTT 58.777 33.333 0.00 0.00 0.00 4.11
447 450 7.752638 ACTAGTAAATTTTAAGGACAGTGGGT 58.247 34.615 0.00 0.00 0.00 4.51
448 451 7.881232 TGACTAGTAAATTTTAAGGACAGTGGG 59.119 37.037 0.00 0.00 0.00 4.61
449 452 8.842358 TGACTAGTAAATTTTAAGGACAGTGG 57.158 34.615 0.00 0.00 0.00 4.00
451 454 9.281371 GGTTGACTAGTAAATTTTAAGGACAGT 57.719 33.333 0.00 0.00 0.00 3.55
452 455 9.280174 TGGTTGACTAGTAAATTTTAAGGACAG 57.720 33.333 0.00 0.00 0.00 3.51
453 456 9.629878 TTGGTTGACTAGTAAATTTTAAGGACA 57.370 29.630 0.00 0.00 0.00 4.02
460 463 8.630037 CCAAGTCTTGGTTGACTAGTAAATTTT 58.370 33.333 21.76 0.00 45.49 1.82
461 464 8.166422 CCAAGTCTTGGTTGACTAGTAAATTT 57.834 34.615 21.76 0.00 45.49 1.82
462 465 7.745620 CCAAGTCTTGGTTGACTAGTAAATT 57.254 36.000 21.76 0.00 45.49 1.82
492 495 5.616488 TTTTACTGGTAAATTCCGAGCAC 57.384 39.130 6.74 0.00 35.27 4.40
495 498 7.432252 GCATGAATTTTACTGGTAAATTCCGAG 59.568 37.037 18.45 12.70 35.27 4.63
499 502 8.460831 AACGCATGAATTTTACTGGTAAATTC 57.539 30.769 16.20 16.20 35.27 2.17
507 512 9.305110 GAAAATGAAAACGCATGAATTTTACTG 57.695 29.630 0.00 0.00 29.82 2.74
512 517 5.914746 CGGAAAATGAAAACGCATGAATTT 58.085 33.333 0.00 0.00 0.00 1.82
537 542 3.321497 ACACTCTTGTCTCAAAGATCGC 58.679 45.455 0.00 0.00 35.67 4.58
577 582 6.258947 GGAATCCAAAGACAGTAGAAGCATAC 59.741 42.308 0.00 0.00 0.00 2.39
585 590 2.932614 CGCAGGAATCCAAAGACAGTAG 59.067 50.000 0.61 0.00 0.00 2.57
586 591 2.301870 ACGCAGGAATCCAAAGACAGTA 59.698 45.455 0.61 0.00 0.00 2.74
587 592 1.072331 ACGCAGGAATCCAAAGACAGT 59.928 47.619 0.61 0.00 0.00 3.55
667 673 0.392863 CGGTGTCATCCATGGCAAGA 60.393 55.000 6.96 1.31 44.94 3.02
709 1315 4.210304 GCGTGCGTCATCGGCTTC 62.210 66.667 0.00 0.00 37.56 3.86
727 1333 1.686110 CGGAAGGGCCTACAGGAGT 60.686 63.158 6.41 0.00 37.39 3.85
777 1387 3.415983 TGGTGTGGTGTGGCCTGT 61.416 61.111 3.32 0.00 38.35 4.00
803 1418 2.815158 AGAGGAAGAAGAGAGTGGGTC 58.185 52.381 0.00 0.00 0.00 4.46
819 1434 2.107366 GGAGTGAGGAGGAAGAAGAGG 58.893 57.143 0.00 0.00 0.00 3.69
820 1435 1.748493 CGGAGTGAGGAGGAAGAAGAG 59.252 57.143 0.00 0.00 0.00 2.85
821 1436 1.617263 CCGGAGTGAGGAGGAAGAAGA 60.617 57.143 0.00 0.00 0.00 2.87
862 1480 5.341169 AGAAGAGAGAGAGGAATCCAAAGT 58.659 41.667 0.61 0.00 0.00 2.66
926 1544 1.528309 GCGGAGAGAGAGAGGGAGG 60.528 68.421 0.00 0.00 0.00 4.30
927 1545 1.528309 GGCGGAGAGAGAGAGGGAG 60.528 68.421 0.00 0.00 0.00 4.30
943 1561 2.203773 TTTGCCTTTCCCCCTGGC 60.204 61.111 0.00 0.00 46.26 4.85
957 1575 1.783284 GCGCCTTCCTTTTTCCTTTG 58.217 50.000 0.00 0.00 0.00 2.77
960 1578 1.971695 CCGCGCCTTCCTTTTTCCT 60.972 57.895 0.00 0.00 0.00 3.36
962 1580 1.923227 CTCCCGCGCCTTCCTTTTTC 61.923 60.000 0.00 0.00 0.00 2.29
963 1581 1.971695 CTCCCGCGCCTTCCTTTTT 60.972 57.895 0.00 0.00 0.00 1.94
984 1602 4.047125 ATTCCCCACCACCGGCTG 62.047 66.667 0.00 0.00 0.00 4.85
1263 1890 0.953471 TGTGATTCTGAAACCGGCGG 60.953 55.000 27.06 27.06 0.00 6.13
1321 1948 4.569180 ATTGATGGGCCGGCGGAG 62.569 66.667 33.44 3.96 0.00 4.63
1327 1954 2.281070 CCTCGGATTGATGGGCCG 60.281 66.667 0.00 0.00 46.08 6.13
1338 1965 1.299850 CGACATAATGCGCCTCGGA 60.300 57.895 4.18 0.00 0.00 4.55
1339 1966 0.318360 TACGACATAATGCGCCTCGG 60.318 55.000 4.18 0.00 0.00 4.63
1382 2012 4.422840 GAAAGGTAGAAGGAGACGCTAAC 58.577 47.826 0.00 0.00 32.24 2.34
1393 2023 5.570320 TGATCAAAAGGGGAAAGGTAGAAG 58.430 41.667 0.00 0.00 0.00 2.85
1396 2026 5.179452 TCTGATCAAAAGGGGAAAGGTAG 57.821 43.478 0.00 0.00 0.00 3.18
1399 2029 3.010584 TCCTCTGATCAAAAGGGGAAAGG 59.989 47.826 19.03 6.31 41.53 3.11
1482 2113 1.135689 GCGAAATCTGATTGCAACGGT 60.136 47.619 0.00 0.00 0.00 4.83
1484 2115 1.174352 CGCGAAATCTGATTGCAACG 58.826 50.000 0.00 7.61 0.00 4.10
1509 2140 4.273969 ACGCGAAAGTATTTTGGTTTGAGA 59.726 37.500 15.93 0.00 39.27 3.27
1588 2226 1.741706 CCAAGCTGTGAATGCTACAGG 59.258 52.381 7.19 0.00 44.36 4.00
1823 2467 1.055849 AGGGCCATGACACGCATATA 58.944 50.000 6.18 0.00 34.82 0.86
1824 2468 0.183492 AAGGGCCATGACACGCATAT 59.817 50.000 6.18 0.00 34.82 1.78
1910 2558 0.539438 GCCACAATCAGGAACCCACA 60.539 55.000 0.00 0.00 0.00 4.17
1953 2601 5.235305 AGTTAAATTTGGTATGCAGCTCG 57.765 39.130 0.00 0.00 0.00 5.03
1954 2602 7.090173 TCAAAGTTAAATTTGGTATGCAGCTC 58.910 34.615 23.72 0.00 39.99 4.09
1956 2604 7.832503 ATCAAAGTTAAATTTGGTATGCAGC 57.167 32.000 23.72 0.00 39.99 5.25
2078 2726 4.187694 AGCATAGCTAAGCTCACAAGTTC 58.812 43.478 17.46 0.00 40.44 3.01
2157 2805 3.259876 CCCTCCATTCCAATAATGCATGG 59.740 47.826 0.00 0.00 37.27 3.66
2180 2828 0.678048 GCCTTAGGTTGTCTGCCAGG 60.678 60.000 0.00 0.00 0.00 4.45
2182 2830 0.698238 ATGCCTTAGGTTGTCTGCCA 59.302 50.000 0.00 0.00 0.00 4.92
2185 2833 6.825721 AGAAATTAGATGCCTTAGGTTGTCTG 59.174 38.462 0.00 0.00 0.00 3.51
2187 2835 7.121315 ACAAGAAATTAGATGCCTTAGGTTGTC 59.879 37.037 0.00 0.00 0.00 3.18
2188 2836 6.948309 ACAAGAAATTAGATGCCTTAGGTTGT 59.052 34.615 0.00 0.00 0.00 3.32
2189 2837 7.253422 CACAAGAAATTAGATGCCTTAGGTTG 58.747 38.462 0.00 0.00 0.00 3.77
2190 2838 6.378280 CCACAAGAAATTAGATGCCTTAGGTT 59.622 38.462 0.00 0.00 0.00 3.50
2312 3017 3.127203 CCACAGACCACAAACACGTTTTA 59.873 43.478 0.00 0.00 0.00 1.52
2318 3023 0.663153 GCTCCACAGACCACAAACAC 59.337 55.000 0.00 0.00 0.00 3.32
2440 3153 6.183360 TGCCTGACAAAATTTAAGTATAGCCG 60.183 38.462 0.00 0.00 0.00 5.52
2445 3158 8.306761 CCTTCTTGCCTGACAAAATTTAAGTAT 58.693 33.333 0.00 0.00 37.96 2.12
2454 3167 3.631250 AGAACCTTCTTGCCTGACAAAA 58.369 40.909 0.00 0.00 37.96 2.44
2467 3180 6.095021 ACACCAAACAGAAGTTTAGAACCTTC 59.905 38.462 0.00 0.00 45.80 3.46
2493 3207 3.053455 GTCCTACTCGTATGCAAGCATC 58.947 50.000 11.32 2.99 37.82 3.91
2514 3228 4.337555 AGAATTCAAAATGGATGCTCCGAG 59.662 41.667 8.44 0.00 40.17 4.63
2517 3231 4.648307 AGGAGAATTCAAAATGGATGCTCC 59.352 41.667 15.48 15.48 39.65 4.70
2520 3234 4.117685 GCAGGAGAATTCAAAATGGATGC 58.882 43.478 8.44 2.92 0.00 3.91
2523 3237 7.664552 ATAATGCAGGAGAATTCAAAATGGA 57.335 32.000 8.44 2.67 0.00 3.41
2550 3264 1.382914 AGGGTGGAAAGGTTAGGCAT 58.617 50.000 0.00 0.00 0.00 4.40
2599 3313 7.933033 CCAGGCCATAAATATTTATTTTGCAGT 59.067 33.333 22.79 13.74 37.16 4.40
2679 3393 7.148853 GCAAAAGACAAGACAATTGATTAGCAG 60.149 37.037 13.59 0.00 0.00 4.24
2822 3536 6.370442 TCGATACAACAAAGTAATGACTTGGG 59.630 38.462 2.19 0.00 45.50 4.12
2954 3668 2.942804 TGTGGTCATGCTCAAAAGGAA 58.057 42.857 0.00 0.00 0.00 3.36
3185 3900 2.851195 TGCTCCTGGAGACTTGAAAAC 58.149 47.619 27.53 6.56 0.00 2.43
3309 4024 8.394877 TGTTCCAAACTGCATTTATATAGTTCG 58.605 33.333 0.00 0.00 32.61 3.95
3527 4242 3.264947 TCAGAATTGGCGACATGAAGAG 58.735 45.455 0.00 0.00 42.32 2.85
3564 4279 3.005684 TGCAAGCCATAGTTTGTCCAAAG 59.994 43.478 0.00 0.00 36.63 2.77
3575 4290 5.287226 GGAATTCAAATCTGCAAGCCATAG 58.713 41.667 7.93 0.00 0.00 2.23
3580 4295 2.094545 ACCGGAATTCAAATCTGCAAGC 60.095 45.455 9.46 0.00 0.00 4.01
3584 4299 5.123979 ACTCTTAACCGGAATTCAAATCTGC 59.876 40.000 9.46 0.00 0.00 4.26
3591 4306 4.000988 GAGCAACTCTTAACCGGAATTCA 58.999 43.478 9.46 0.00 0.00 2.57
3639 4354 5.486735 TGGTGTTTCTAATTCGGGAAGTA 57.513 39.130 0.00 0.00 0.00 2.24
3645 4360 4.513692 TCAGTGTTGGTGTTTCTAATTCGG 59.486 41.667 0.00 0.00 0.00 4.30
3675 4390 8.970020 TGATATGCAAATGTAAATGAGAAAGGT 58.030 29.630 0.00 0.00 0.00 3.50
3915 4631 2.273619 AGCCTCTTGAAAGGTGGATCT 58.726 47.619 0.00 0.00 38.79 2.75
3965 4681 1.546476 AGACTCTTGGTAGTTGGCTCG 59.454 52.381 0.00 0.00 0.00 5.03
4038 4754 9.063615 GTATTAACAATATGAAACCAGGGTAGG 57.936 37.037 0.00 0.00 0.00 3.18
4203 4920 8.611757 GCAAGACCAATATTTTGAAAAGTTGTT 58.388 29.630 13.74 4.05 34.60 2.83
4267 4984 0.778083 GGAAGAACCTGAACCCCCTT 59.222 55.000 0.00 0.00 35.41 3.95
4268 4985 2.476081 GGAAGAACCTGAACCCCCT 58.524 57.895 0.00 0.00 35.41 4.79
4278 4995 3.254411 CAGCAGAGGAAAAAGGAAGAACC 59.746 47.826 0.00 0.00 39.35 3.62
4279 4996 3.254411 CCAGCAGAGGAAAAAGGAAGAAC 59.746 47.826 0.00 0.00 0.00 3.01
4280 4997 3.117512 ACCAGCAGAGGAAAAAGGAAGAA 60.118 43.478 0.00 0.00 0.00 2.52
4281 4998 2.443255 ACCAGCAGAGGAAAAAGGAAGA 59.557 45.455 0.00 0.00 0.00 2.87
4282 4999 2.555757 CACCAGCAGAGGAAAAAGGAAG 59.444 50.000 0.00 0.00 0.00 3.46
4283 5000 2.174639 TCACCAGCAGAGGAAAAAGGAA 59.825 45.455 0.00 0.00 0.00 3.36
4284 5001 1.774254 TCACCAGCAGAGGAAAAAGGA 59.226 47.619 0.00 0.00 0.00 3.36
4285 5002 2.276732 TCACCAGCAGAGGAAAAAGG 57.723 50.000 0.00 0.00 0.00 3.11
4286 5003 2.951642 TGTTCACCAGCAGAGGAAAAAG 59.048 45.455 0.00 0.00 0.00 2.27
4287 5004 3.011566 TGTTCACCAGCAGAGGAAAAA 57.988 42.857 0.00 0.00 0.00 1.94
4288 5005 2.727123 TGTTCACCAGCAGAGGAAAA 57.273 45.000 0.00 0.00 0.00 2.29
4289 5006 2.957402 ATGTTCACCAGCAGAGGAAA 57.043 45.000 0.00 0.00 0.00 3.13
4290 5007 4.019411 TGAATATGTTCACCAGCAGAGGAA 60.019 41.667 0.03 0.00 39.36 3.36
4291 5008 3.519107 TGAATATGTTCACCAGCAGAGGA 59.481 43.478 0.03 0.00 39.36 3.71
4292 5009 3.877559 TGAATATGTTCACCAGCAGAGG 58.122 45.455 0.03 0.00 39.36 3.69
4293 5010 4.940046 ACTTGAATATGTTCACCAGCAGAG 59.060 41.667 4.14 0.79 43.72 3.35
4294 5011 4.910195 ACTTGAATATGTTCACCAGCAGA 58.090 39.130 4.14 0.00 43.72 4.26
4295 5012 6.741992 TTACTTGAATATGTTCACCAGCAG 57.258 37.500 4.14 2.17 43.72 4.24
4296 5013 7.701539 AATTACTTGAATATGTTCACCAGCA 57.298 32.000 4.14 0.00 43.72 4.41
4331 5085 5.845953 CCAAGCATACGTTTATTTATCTGCG 59.154 40.000 0.00 0.00 33.76 5.18
4373 5127 3.081061 CCATTGACTCAATCCCAACGAA 58.919 45.455 0.92 0.00 31.05 3.85
4631 5387 2.026542 ACCAATTCCTCCGAACTAACCC 60.027 50.000 0.00 0.00 0.00 4.11
4825 5592 2.603892 GCATCACACAAGCTGACAAGTG 60.604 50.000 0.00 0.00 37.95 3.16
4881 5655 3.188460 ACACGCAATAACAAGCCTACAAG 59.812 43.478 0.00 0.00 0.00 3.16
4928 5707 0.593128 AAGTGATCACGTGGCAAAGC 59.407 50.000 19.85 0.00 36.20 3.51
4938 5717 4.874396 TGATCAGCATTCTCAAGTGATCAC 59.126 41.667 18.47 18.47 45.35 3.06
4940 5719 5.117584 ACTGATCAGCATTCTCAAGTGATC 58.882 41.667 22.83 4.09 42.54 2.92
4962 5741 0.527817 CAACGCCGGGATACTCAGAC 60.528 60.000 2.18 0.00 0.00 3.51
4974 5753 2.030457 GTGGATTGAATAGTCAACGCCG 59.970 50.000 7.92 0.00 46.40 6.46
4994 5773 2.228582 TCAAGCTTGTTATGCGCAATGT 59.771 40.909 25.19 0.00 35.28 2.71
5060 5839 6.894339 AACCGAAGTTGACCAGAATTTAAT 57.106 33.333 0.00 0.00 33.97 1.40
5140 5920 7.789273 TTCAGTCAGTTCGTTTGGTAAATAA 57.211 32.000 0.00 0.00 0.00 1.40
5177 5958 4.890158 TTTGCACTGAGATTAGTCCTGA 57.110 40.909 0.00 0.00 0.00 3.86
5518 6301 9.252962 CTTTATCAATCTTCACAGCAAAGTTTT 57.747 29.630 0.00 0.00 0.00 2.43
6085 6873 6.970484 TGCAGAATTCTCAAAGTTAACTTCC 58.030 36.000 20.78 4.22 34.61 3.46
6124 6912 7.649306 CCAACTATTCCAAGAACACAAAGAAAG 59.351 37.037 0.00 0.00 0.00 2.62
6128 6916 6.391227 ACCAACTATTCCAAGAACACAAAG 57.609 37.500 0.00 0.00 0.00 2.77
6226 7015 5.495640 AGAAAAGAGGGCTCAAAGACATAG 58.504 41.667 0.00 0.00 0.00 2.23
6251 7040 1.812324 CGTTAGAGTGTGGGTTTGGCA 60.812 52.381 0.00 0.00 0.00 4.92
6263 7052 3.937814 TCACCATGCATTTCGTTAGAGT 58.062 40.909 0.00 0.00 0.00 3.24
6287 7076 2.552373 CCCTCTCACCCCAAACACTAAC 60.552 54.545 0.00 0.00 0.00 2.34
6371 7168 7.880195 GGCTTATCAGTACAATGGAATAGTCAT 59.120 37.037 0.00 0.00 0.00 3.06
6385 7182 5.760743 GGAGATTTTCCTGGCTTATCAGTAC 59.239 44.000 0.00 0.00 43.16 2.73
6415 7212 4.586841 CCCAGACTTTGTAACCCATTTTGA 59.413 41.667 0.00 0.00 0.00 2.69
6469 7268 2.575805 AGAAAGGTTCTGCTCTTGGG 57.424 50.000 0.00 0.00 38.91 4.12
6477 7276 3.879295 TGAGCTGACAAAGAAAGGTTCTG 59.121 43.478 0.00 0.00 40.59 3.02
6478 7277 4.156455 TGAGCTGACAAAGAAAGGTTCT 57.844 40.909 0.00 0.00 43.15 3.01
6479 7278 4.791974 CATGAGCTGACAAAGAAAGGTTC 58.208 43.478 0.00 0.00 0.00 3.62
6480 7279 3.005155 GCATGAGCTGACAAAGAAAGGTT 59.995 43.478 0.00 0.00 37.91 3.50
6481 7280 2.555757 GCATGAGCTGACAAAGAAAGGT 59.444 45.455 0.00 0.00 37.91 3.50
6482 7281 2.094854 GGCATGAGCTGACAAAGAAAGG 60.095 50.000 0.00 0.00 41.70 3.11
6483 7282 2.094854 GGGCATGAGCTGACAAAGAAAG 60.095 50.000 0.00 0.00 41.70 2.62
6484 7283 1.888512 GGGCATGAGCTGACAAAGAAA 59.111 47.619 0.00 0.00 41.70 2.52
6485 7284 1.074405 AGGGCATGAGCTGACAAAGAA 59.926 47.619 0.00 0.00 41.70 2.52
6486 7285 0.694771 AGGGCATGAGCTGACAAAGA 59.305 50.000 0.00 0.00 41.70 2.52
6487 7286 2.286872 CTAGGGCATGAGCTGACAAAG 58.713 52.381 0.00 0.00 41.70 2.77
6488 7287 1.065199 CCTAGGGCATGAGCTGACAAA 60.065 52.381 0.00 0.00 41.70 2.83
6489 7288 0.543277 CCTAGGGCATGAGCTGACAA 59.457 55.000 0.00 0.00 41.70 3.18
6490 7289 2.215191 CCTAGGGCATGAGCTGACA 58.785 57.895 0.00 0.00 41.70 3.58
6560 7359 6.141083 TGTAACCATGAGGCTTATACCTAGT 58.859 40.000 0.00 0.00 41.32 2.57
6561 7360 6.665992 TGTAACCATGAGGCTTATACCTAG 57.334 41.667 0.00 0.00 41.32 3.02
6572 7371 2.744202 GCTGTGACTTGTAACCATGAGG 59.256 50.000 0.00 0.00 42.21 3.86
6579 7378 2.224314 GCTTCTGGCTGTGACTTGTAAC 59.776 50.000 0.00 0.00 38.06 2.50
6583 7382 1.239968 GGGCTTCTGGCTGTGACTTG 61.240 60.000 0.00 0.00 41.46 3.16
6591 7390 0.105504 AAGTTTTGGGGCTTCTGGCT 60.106 50.000 0.00 0.00 41.46 4.75
6600 7399 3.382546 CCAGCTGATGATAAGTTTTGGGG 59.617 47.826 17.39 0.00 0.00 4.96
6601 7400 4.019174 ACCAGCTGATGATAAGTTTTGGG 58.981 43.478 17.39 0.00 0.00 4.12
6781 7596 6.488769 TTTCACGCCCTCCTATTCTTTATA 57.511 37.500 0.00 0.00 0.00 0.98
6798 7613 3.619233 AATTTCCCACGACTTTTCACG 57.381 42.857 0.00 0.00 0.00 4.35
6841 7656 8.478877 CCATCTCTAATTCCAAACAGTAGTACT 58.521 37.037 0.00 0.00 0.00 2.73
6848 7666 9.442047 GGATATACCATCTCTAATTCCAAACAG 57.558 37.037 0.00 0.00 38.79 3.16
6908 7726 2.930109 ATGGCCTCCTAGTCGGATAT 57.070 50.000 3.32 0.00 42.12 1.63
6909 7727 2.526432 GAATGGCCTCCTAGTCGGATA 58.474 52.381 3.32 0.00 42.12 2.59
6910 7728 1.343069 GAATGGCCTCCTAGTCGGAT 58.657 55.000 3.32 0.00 42.12 4.18
6911 7729 1.107538 CGAATGGCCTCCTAGTCGGA 61.108 60.000 3.32 0.00 40.30 4.55
6912 7730 1.364171 CGAATGGCCTCCTAGTCGG 59.636 63.158 3.32 0.00 0.00 4.79
6913 7731 1.364171 CCGAATGGCCTCCTAGTCG 59.636 63.158 3.32 3.66 0.00 4.18
6914 7732 1.340568 GTACCGAATGGCCTCCTAGTC 59.659 57.143 3.32 0.00 39.70 2.59
6915 7733 1.411041 GTACCGAATGGCCTCCTAGT 58.589 55.000 3.32 0.00 39.70 2.57
6916 7734 0.680061 GGTACCGAATGGCCTCCTAG 59.320 60.000 3.32 0.00 39.70 3.02
6917 7735 0.263765 AGGTACCGAATGGCCTCCTA 59.736 55.000 6.18 0.00 39.70 2.94
6918 7736 1.003051 AGGTACCGAATGGCCTCCT 59.997 57.895 6.18 0.00 39.70 3.69
6919 7737 1.049289 AGAGGTACCGAATGGCCTCC 61.049 60.000 6.18 0.00 46.37 4.30
6920 7738 0.389757 GAGAGGTACCGAATGGCCTC 59.610 60.000 6.18 0.00 45.75 4.70
6921 7739 1.049289 GGAGAGGTACCGAATGGCCT 61.049 60.000 6.18 0.00 39.70 5.19
6922 7740 1.446366 GGAGAGGTACCGAATGGCC 59.554 63.158 6.18 0.00 39.70 5.36


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

AutoCloner maintained by Alex Coulton.