Multiple sequence alignment - TraesCS1D01G357300

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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 TraesCS1D01G357300 chr1D 100.000 5235 0 0 1 5235 441298509 441303743 0.000000e+00 9668.0
1 TraesCS1D01G357300 chr1A 92.233 2768 142 33 2521 5235 536662720 536659973 0.000000e+00 3853.0
2 TraesCS1D01G357300 chr1A 87.948 1311 83 34 834 2115 536664666 536663402 0.000000e+00 1476.0
3 TraesCS1D01G357300 chr1A 88.875 782 29 17 1 745 536665475 536664715 0.000000e+00 909.0
4 TraesCS1D01G357300 chr1A 94.000 400 19 3 2113 2512 536663206 536662812 7.500000e-168 601.0
5 TraesCS1D01G357300 chr1A 98.077 52 1 0 2113 2164 536663335 536663284 2.010000e-14 91.6
6 TraesCS1D01G357300 chr1B 92.214 1811 107 12 2527 4313 599338276 599340076 0.000000e+00 2532.0
7 TraesCS1D01G357300 chr1B 86.498 1459 87 40 696 2106 599336306 599337702 0.000000e+00 1502.0
8 TraesCS1D01G357300 chr1B 91.757 922 68 5 4316 5235 599340109 599341024 0.000000e+00 1275.0
9 TraesCS1D01G357300 chr1B 88.158 608 17 11 1 602 599334389 599334947 0.000000e+00 673.0
10 TraesCS1D01G357300 chr1B 92.424 396 22 2 2130 2517 599337791 599338186 4.580000e-155 558.0
11 TraesCS1D01G357300 chr7B 85.417 96 6 4 1763 1858 547961921 547961834 5.580000e-15 93.5
12 TraesCS1D01G357300 chr6A 82.692 104 9 5 1755 1858 264877026 264876932 3.360000e-12 84.2


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 TraesCS1D01G357300 chr1D 441298509 441303743 5234 False 9668.00 9668 100.0000 1 5235 1 chr1D.!!$F1 5234
1 TraesCS1D01G357300 chr1A 536659973 536665475 5502 True 1386.12 3853 92.2266 1 5235 5 chr1A.!!$R1 5234
2 TraesCS1D01G357300 chr1B 599334389 599341024 6635 False 1308.00 2532 90.2102 1 5235 5 chr1B.!!$F1 5234

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
783 2097 0.106967 GGTGATTTCTCTCCCAGGCC 60.107 60.0 0.0 0.0 0.0 5.19 F
1327 2686 0.035439 GAACGGATTCAGCAGGGGAA 60.035 55.0 0.0 0.0 34.7 3.97 F
2519 4112 0.246360 CCAGACTCACATGCACCGTA 59.754 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 2977 0.450184 AAAACGCATACGCATCCACC 59.550 50.000 0.0 0.0 45.53 4.61 R
2804 4509 1.065401 CAACTGCCTGCGACAAAAAGA 59.935 47.619 0.0 0.0 0.00 2.52 R
4260 5979 0.308993 GCATAATGCAAGAGTCGGCC 59.691 55.000 0.0 0.0 44.26 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
89 90 1.972198 CTCTACGGGTGGTTCTGCA 59.028 57.895 0.00 0.00 0.00 4.41
163 164 2.158885 GCCTTCCTTCCATGAGTACCTC 60.159 54.545 0.00 0.00 0.00 3.85
174 175 2.025727 GTACCTCCACGCGATCGG 59.974 66.667 15.93 10.69 40.69 4.18
343 352 1.136690 TTGTCGCACGCTTAGTTGAG 58.863 50.000 0.00 0.00 0.00 3.02
366 375 2.775911 TTGAAGCCTGGACAGATGAG 57.224 50.000 0.00 0.00 0.00 2.90
369 378 3.646534 TGAAGCCTGGACAGATGAGATA 58.353 45.455 0.00 0.00 0.00 1.98
404 413 0.531090 TTTGCCTTGCTTGCTTGCTG 60.531 50.000 3.47 0.00 0.00 4.41
407 416 0.249573 GCCTTGCTTGCTTGCTGAAA 60.250 50.000 3.47 0.00 0.00 2.69
417 443 1.001181 GCTTGCTGAAATCAGGGCAAA 59.999 47.619 12.09 0.00 42.76 3.68
418 444 2.354403 GCTTGCTGAAATCAGGGCAAAT 60.354 45.455 12.09 0.00 42.76 2.32
419 445 3.867216 GCTTGCTGAAATCAGGGCAAATT 60.867 43.478 12.09 0.00 42.76 1.82
420 446 4.621274 GCTTGCTGAAATCAGGGCAAATTA 60.621 41.667 12.09 0.00 42.76 1.40
421 447 4.454728 TGCTGAAATCAGGGCAAATTAC 57.545 40.909 12.09 0.00 43.94 1.89
422 448 3.119531 TGCTGAAATCAGGGCAAATTACG 60.120 43.478 12.09 0.00 43.94 3.18
423 449 3.438360 CTGAAATCAGGGCAAATTACGC 58.562 45.455 2.38 0.00 40.20 4.42
424 450 3.088532 TGAAATCAGGGCAAATTACGCT 58.911 40.909 0.34 0.00 0.00 5.07
425 451 3.128589 TGAAATCAGGGCAAATTACGCTC 59.871 43.478 0.34 0.00 0.00 5.03
426 452 2.717639 ATCAGGGCAAATTACGCTCT 57.282 45.000 0.00 0.00 42.32 4.09
427 453 2.489938 TCAGGGCAAATTACGCTCTT 57.510 45.000 0.00 0.00 38.45 2.85
428 454 2.356135 TCAGGGCAAATTACGCTCTTC 58.644 47.619 0.00 0.00 38.45 2.87
429 455 1.401905 CAGGGCAAATTACGCTCTTCC 59.598 52.381 0.00 0.00 38.45 3.46
430 456 1.004277 AGGGCAAATTACGCTCTTCCA 59.996 47.619 0.00 0.00 36.59 3.53
431 457 1.401905 GGGCAAATTACGCTCTTCCAG 59.598 52.381 0.34 0.00 0.00 3.86
432 458 2.356135 GGCAAATTACGCTCTTCCAGA 58.644 47.619 0.34 0.00 0.00 3.86
433 459 2.096013 GGCAAATTACGCTCTTCCAGAC 59.904 50.000 0.34 0.00 0.00 3.51
538 568 8.747471 TGGATGAATTTATCTGTAATGTTTGCA 58.253 29.630 9.80 0.00 0.00 4.08
579 609 1.680338 GGCAAATTACGCCTCCAGAT 58.320 50.000 10.81 0.00 46.56 2.90
608 638 1.406539 CTTCCCCATTTCATTGCTCCG 59.593 52.381 0.00 0.00 0.00 4.63
645 676 9.365906 TGAGTTGATATATGGTTATTTTGCCAT 57.634 29.630 0.00 0.00 46.24 4.40
654 699 6.543430 TGGTTATTTTGCCATGCTTAATCT 57.457 33.333 0.00 0.00 0.00 2.40
677 1964 3.603532 AGCGATTGCATACCCATATCAG 58.396 45.455 7.90 0.00 46.23 2.90
704 2018 4.827692 TCATACCAGTGATTTGTAACGCT 58.172 39.130 0.00 0.00 0.00 5.07
744 2058 3.589654 TAGCTGCTCGCCCACACAC 62.590 63.158 4.91 0.00 40.39 3.82
773 2087 2.584608 CCTCCGCCGGTGATTTCT 59.415 61.111 18.79 0.00 0.00 2.52
776 2090 0.528684 CTCCGCCGGTGATTTCTCTC 60.529 60.000 18.79 0.00 0.00 3.20
778 2092 1.521681 CGCCGGTGATTTCTCTCCC 60.522 63.158 10.20 0.00 32.42 4.30
779 2093 1.602237 GCCGGTGATTTCTCTCCCA 59.398 57.895 1.90 0.00 32.42 4.37
780 2094 0.462759 GCCGGTGATTTCTCTCCCAG 60.463 60.000 1.90 0.00 32.42 4.45
781 2095 0.179000 CCGGTGATTTCTCTCCCAGG 59.821 60.000 0.00 0.00 32.42 4.45
783 2097 0.106967 GGTGATTTCTCTCCCAGGCC 60.107 60.000 0.00 0.00 0.00 5.19
784 2098 0.462759 GTGATTTCTCTCCCAGGCCG 60.463 60.000 0.00 0.00 0.00 6.13
785 2099 1.147153 GATTTCTCTCCCAGGCCGG 59.853 63.158 0.00 0.00 0.00 6.13
830 2151 1.027792 TGATCACCGGTCGATGACGA 61.028 55.000 19.88 7.51 46.56 4.20
843 2164 1.466950 GATGACGAATTGACGGGCAAA 59.533 47.619 0.00 0.00 40.48 3.68
905 2227 3.749284 AAAGCCCCAAAGCCACCGT 62.749 57.895 0.00 0.00 0.00 4.83
1217 2564 4.292081 AGGTTAACCTCCGAGCTTGTCG 62.292 54.545 21.96 0.00 44.77 4.35
1225 2572 2.734673 CGAGCTTGTCGCCTTCAGC 61.735 63.158 0.00 0.00 43.03 4.26
1246 2605 2.017049 GCGGAATTAGCAGGATTGTGT 58.983 47.619 0.99 0.00 34.19 3.72
1248 2607 3.119495 GCGGAATTAGCAGGATTGTGTTT 60.119 43.478 0.99 0.00 34.19 2.83
1249 2608 4.095782 GCGGAATTAGCAGGATTGTGTTTA 59.904 41.667 0.99 0.00 34.19 2.01
1250 2609 5.730568 GCGGAATTAGCAGGATTGTGTTTAG 60.731 44.000 0.99 0.00 34.19 1.85
1253 2612 7.251281 GGAATTAGCAGGATTGTGTTTAGTTC 58.749 38.462 0.00 0.00 0.00 3.01
1254 2613 6.759497 ATTAGCAGGATTGTGTTTAGTTCC 57.241 37.500 0.00 0.00 0.00 3.62
1255 2614 3.074412 AGCAGGATTGTGTTTAGTTCCG 58.926 45.455 0.00 0.00 0.00 4.30
1256 2615 2.812011 GCAGGATTGTGTTTAGTTCCGT 59.188 45.455 0.00 0.00 0.00 4.69
1257 2616 3.364964 GCAGGATTGTGTTTAGTTCCGTG 60.365 47.826 0.00 0.00 0.00 4.94
1258 2617 2.812011 AGGATTGTGTTTAGTTCCGTGC 59.188 45.455 0.00 0.00 0.00 5.34
1259 2618 2.550606 GGATTGTGTTTAGTTCCGTGCA 59.449 45.455 0.00 0.00 0.00 4.57
1260 2619 3.364964 GGATTGTGTTTAGTTCCGTGCAG 60.365 47.826 0.00 0.00 0.00 4.41
1261 2620 2.605837 TGTGTTTAGTTCCGTGCAGA 57.394 45.000 0.00 0.00 0.00 4.26
1262 2621 2.907634 TGTGTTTAGTTCCGTGCAGAA 58.092 42.857 0.00 0.00 0.00 3.02
1263 2622 3.472652 TGTGTTTAGTTCCGTGCAGAAT 58.527 40.909 0.00 0.00 0.00 2.40
1264 2623 3.880490 TGTGTTTAGTTCCGTGCAGAATT 59.120 39.130 0.00 0.00 0.00 2.17
1265 2624 4.336993 TGTGTTTAGTTCCGTGCAGAATTT 59.663 37.500 0.00 0.00 0.00 1.82
1266 2625 4.909880 GTGTTTAGTTCCGTGCAGAATTTC 59.090 41.667 0.00 0.00 0.00 2.17
1269 2628 5.607119 TTAGTTCCGTGCAGAATTTCTTC 57.393 39.130 0.00 0.00 0.00 2.87
1276 2635 3.624861 CGTGCAGAATTTCTTCCTGCTAT 59.375 43.478 14.86 0.00 36.90 2.97
1283 2642 7.066284 GCAGAATTTCTTCCTGCTATAACAGAA 59.934 37.037 4.66 0.00 40.25 3.02
1294 2653 8.198109 TCCTGCTATAACAGAACAGAATTCTAC 58.802 37.037 7.86 3.20 40.25 2.59
1327 2686 0.035439 GAACGGATTCAGCAGGGGAA 60.035 55.000 0.00 0.00 34.70 3.97
1438 2800 0.729140 CGGCGACTGAATTTGTTGGC 60.729 55.000 0.00 13.01 39.92 4.52
1444 2806 2.028130 ACTGAATTTGTTGGCGGTTCA 58.972 42.857 0.00 0.00 0.00 3.18
1447 2809 1.726248 GAATTTGTTGGCGGTTCATGC 59.274 47.619 0.00 0.00 0.00 4.06
1450 2812 2.081425 TTGTTGGCGGTTCATGCACC 62.081 55.000 4.19 4.19 0.00 5.01
1486 2848 6.306837 CGATAAGTTCTGACTGAGAGTTTCAC 59.693 42.308 0.00 0.00 35.91 3.18
1524 2894 2.760634 TCAACCTAGCTCATCGCAAA 57.239 45.000 0.00 0.00 42.61 3.68
1646 3024 8.084073 CCACTTGAATGTTCTAATGTGATGTTT 58.916 33.333 0.00 0.00 0.00 2.83
1703 3081 3.609103 ACACTTCTAGCAAAAACGCTG 57.391 42.857 0.00 0.00 43.68 5.18
1773 3151 8.863049 CAATTACACAGGTAAAATCTTGCATTC 58.137 33.333 0.00 0.00 42.43 2.67
1805 3183 4.800914 GCCACTAGAAAGCTCTCTTTGACA 60.801 45.833 0.00 0.00 42.24 3.58
1806 3184 4.928615 CCACTAGAAAGCTCTCTTTGACAG 59.071 45.833 0.00 0.00 42.24 3.51
1807 3185 5.510520 CCACTAGAAAGCTCTCTTTGACAGT 60.511 44.000 0.00 0.00 42.24 3.55
1808 3186 5.988561 CACTAGAAAGCTCTCTTTGACAGTT 59.011 40.000 0.00 0.00 42.24 3.16
1809 3187 6.481644 CACTAGAAAGCTCTCTTTGACAGTTT 59.518 38.462 0.00 0.00 42.24 2.66
1810 3188 5.747951 AGAAAGCTCTCTTTGACAGTTTG 57.252 39.130 0.00 0.00 42.24 2.93
1811 3189 5.431765 AGAAAGCTCTCTTTGACAGTTTGA 58.568 37.500 0.00 0.00 42.24 2.69
1812 3190 5.295540 AGAAAGCTCTCTTTGACAGTTTGAC 59.704 40.000 0.00 0.00 42.24 3.18
1813 3191 4.414337 AGCTCTCTTTGACAGTTTGACT 57.586 40.909 0.00 0.00 0.00 3.41
1814 3192 5.065731 AAAGCTCTCTTTGACAGTTTGACTG 59.934 40.000 6.54 6.54 44.58 3.51
1815 3193 8.327513 AAAGCTCTCTTTGACAGTTTGACTGC 62.328 42.308 7.93 2.56 43.79 4.40
1834 3212 2.483877 TGCTCTCTTTAACGCATTGGTG 59.516 45.455 0.00 0.00 0.00 4.17
1933 3313 2.183679 CTCTTTCAGGCTGGGTACTCT 58.816 52.381 15.73 0.00 0.00 3.24
1978 3358 6.488006 TCGTCTACAAACTTCTAGTGGTACTT 59.512 38.462 0.00 0.00 0.00 2.24
1979 3359 7.661437 TCGTCTACAAACTTCTAGTGGTACTTA 59.339 37.037 0.00 0.00 0.00 2.24
2055 3435 5.814188 GTGGTGCCACTAGTTTTATACTACC 59.186 44.000 13.68 0.00 43.12 3.18
2078 3458 2.979813 CCATTGTGTTAAAACAGAGCGC 59.020 45.455 0.00 0.00 40.05 5.92
2080 3460 1.669604 TGTGTTAAAACAGAGCGCCA 58.330 45.000 2.29 0.00 40.05 5.69
2161 3746 1.470632 CCTCTTAGGCTGCTGACTTCG 60.471 57.143 3.50 0.00 31.35 3.79
2230 3815 1.604278 AGCTCGCAAAGAAGGTTGTTC 59.396 47.619 0.00 0.00 0.00 3.18
2249 3834 7.148689 GGTTGTTCAAAAGCATTTCTGATCATC 60.149 37.037 0.00 0.00 37.28 2.92
2301 3893 5.447279 GCCCATTACATGTACGCTAATATGC 60.447 44.000 4.68 0.96 0.00 3.14
2302 3894 5.064707 CCCATTACATGTACGCTAATATGCC 59.935 44.000 4.68 0.00 0.00 4.40
2319 3911 1.818060 TGCCACATTGGTACATTCAGC 59.182 47.619 0.00 0.00 40.46 4.26
2390 3982 5.855395 GCAAGCACTCTTAAAGATGTTTGAG 59.145 40.000 13.62 1.06 35.89 3.02
2414 4006 5.221501 GGGAACGGTAAGTGGCTATGTTATA 60.222 44.000 0.00 0.00 0.00 0.98
2426 4018 9.109393 AGTGGCTATGTTATATTTGTAGTTGTG 57.891 33.333 0.00 0.00 0.00 3.33
2484 4077 7.992180 ACAAAAAGATTTCTAGCACTGTTTG 57.008 32.000 0.00 0.00 40.93 2.93
2517 4110 0.738762 CTCCAGACTCACATGCACCG 60.739 60.000 0.00 0.00 0.00 4.94
2518 4111 1.004560 CCAGACTCACATGCACCGT 60.005 57.895 0.00 0.00 0.00 4.83
2519 4112 0.246360 CCAGACTCACATGCACCGTA 59.754 55.000 0.00 0.00 0.00 4.02
2521 4114 2.621338 CAGACTCACATGCACCGTATT 58.379 47.619 0.00 0.00 0.00 1.89
2522 4115 2.604914 CAGACTCACATGCACCGTATTC 59.395 50.000 0.00 0.00 0.00 1.75
2523 4116 1.588404 GACTCACATGCACCGTATTCG 59.412 52.381 0.00 0.00 0.00 3.34
2524 4117 1.203758 ACTCACATGCACCGTATTCGA 59.796 47.619 0.00 0.00 39.71 3.71
2540 4214 7.980099 ACCGTATTCGATTCTCTAAACAAGAAT 59.020 33.333 0.00 0.00 44.21 2.40
2566 4240 4.787551 TCCATGTTTGTGTTCTTAGGTGT 58.212 39.130 0.00 0.00 0.00 4.16
2583 4257 1.334869 GTGTTCAGTGTGCCAAGGAAG 59.665 52.381 0.00 0.00 0.00 3.46
2599 4273 4.104383 AGGAAGAGAAGTCAAAATGGCA 57.896 40.909 0.00 0.00 0.00 4.92
2616 4290 1.200716 GGCATGTCTCATGGTTGTGTG 59.799 52.381 10.96 0.00 0.00 3.82
2629 4303 3.634448 TGGTTGTGTGGAGGTAATTGTTG 59.366 43.478 0.00 0.00 0.00 3.33
2630 4304 3.886505 GGTTGTGTGGAGGTAATTGTTGA 59.113 43.478 0.00 0.00 0.00 3.18
2631 4305 4.023193 GGTTGTGTGGAGGTAATTGTTGAG 60.023 45.833 0.00 0.00 0.00 3.02
2632 4306 4.698201 TGTGTGGAGGTAATTGTTGAGA 57.302 40.909 0.00 0.00 0.00 3.27
2634 4310 5.630121 TGTGTGGAGGTAATTGTTGAGAAT 58.370 37.500 0.00 0.00 0.00 2.40
2707 4403 5.623673 CGTATTTCAACAGTTTAGCACCAAC 59.376 40.000 0.00 0.00 0.00 3.77
2713 4409 2.158755 ACAGTTTAGCACCAACAGCTCT 60.159 45.455 0.00 0.00 42.32 4.09
2714 4410 3.071023 ACAGTTTAGCACCAACAGCTCTA 59.929 43.478 0.00 0.00 42.32 2.43
2735 4431 8.624776 GCTCTAAAACTATTGAATGGTGCTATT 58.375 33.333 0.00 0.00 0.00 1.73
2748 4444 8.486210 TGAATGGTGCTATTACTTTGATAGTCT 58.514 33.333 0.00 0.00 38.33 3.24
2750 4446 8.894768 ATGGTGCTATTACTTTGATAGTCTTC 57.105 34.615 0.00 0.00 38.33 2.87
2752 4448 8.318412 TGGTGCTATTACTTTGATAGTCTTCAA 58.682 33.333 0.00 0.00 38.33 2.69
2753 4449 9.331282 GGTGCTATTACTTTGATAGTCTTCAAT 57.669 33.333 0.00 0.00 38.33 2.57
2793 4498 3.807622 AGTGACATGTGGTTAACTGAACG 59.192 43.478 1.15 0.00 39.12 3.95
2795 4500 3.558006 TGACATGTGGTTAACTGAACGTG 59.442 43.478 1.15 18.77 39.12 4.49
2796 4501 2.875933 ACATGTGGTTAACTGAACGTGG 59.124 45.455 21.74 11.41 39.12 4.94
2797 4502 1.301423 TGTGGTTAACTGAACGTGGC 58.699 50.000 5.42 0.00 39.12 5.01
2798 4503 1.134340 TGTGGTTAACTGAACGTGGCT 60.134 47.619 5.42 0.00 39.12 4.75
2800 4505 1.134340 TGGTTAACTGAACGTGGCTGT 60.134 47.619 5.42 0.00 39.12 4.40
2803 4508 2.319136 TAACTGAACGTGGCTGTTGT 57.681 45.000 18.04 2.75 30.75 3.32
2804 4509 1.459450 AACTGAACGTGGCTGTTGTT 58.541 45.000 11.38 0.00 30.75 2.83
2805 4510 1.014352 ACTGAACGTGGCTGTTGTTC 58.986 50.000 0.00 3.25 41.75 3.18
2814 4527 2.851824 GTGGCTGTTGTTCTTTTTGTCG 59.148 45.455 0.00 0.00 0.00 4.35
2890 4603 2.483014 TTACAATGACGAGTTGGGGG 57.517 50.000 0.00 0.00 0.00 5.40
2972 4685 4.699257 CCTTCTCTGACTTGGGAAAGATTG 59.301 45.833 0.00 0.00 0.00 2.67
3026 4739 9.157104 CTTTTGGAACTATCCTACTCTTCTTTC 57.843 37.037 0.00 0.00 46.70 2.62
3057 4770 3.688185 CCTCCATGTCATGTCTGAAAGTG 59.312 47.826 11.84 0.00 31.85 3.16
3152 4865 1.536766 TGCTTTGACGAATGCTCTTGG 59.463 47.619 0.00 0.00 34.17 3.61
3153 4866 1.135575 GCTTTGACGAATGCTCTTGGG 60.136 52.381 0.00 0.00 31.14 4.12
3159 4872 0.383231 CGAATGCTCTTGGGCAATCC 59.617 55.000 0.00 0.00 45.68 3.01
3160 4873 0.383231 GAATGCTCTTGGGCAATCCG 59.617 55.000 0.00 0.00 45.68 4.18
3209 4922 3.190118 ACCGGTTTTGTGACACGTTTTAA 59.810 39.130 0.00 0.00 0.00 1.52
3212 4928 5.275974 CCGGTTTTGTGACACGTTTTAATTG 60.276 40.000 0.22 0.00 0.00 2.32
3237 4953 3.003394 TGCCCACATTGATACAAGAGG 57.997 47.619 0.00 0.00 0.00 3.69
3248 4964 9.477484 ACATTGATACAAGAGGTAATATTCGAC 57.523 33.333 0.00 0.00 35.14 4.20
3393 5109 5.116055 GCAAACTTTTTGCACATTTTTGC 57.884 34.783 16.79 13.20 44.34 3.68
3460 5176 2.371841 TGCTTCCAGAAGGTCTGCTTTA 59.628 45.455 9.36 0.00 42.98 1.85
3485 5201 4.158764 AGTCCAGTCTACTACATTCTGCAC 59.841 45.833 0.00 0.00 0.00 4.57
3486 5202 4.158764 GTCCAGTCTACTACATTCTGCACT 59.841 45.833 0.00 0.00 0.00 4.40
3560 5276 2.015456 TTCAGGTTCTCAGAGAGCCA 57.985 50.000 29.50 11.83 46.66 4.75
3590 5306 5.410067 GCAATAGGCAAGCAATACAAGAAA 58.590 37.500 0.00 0.00 43.97 2.52
3616 5332 7.615582 TGTTCAAGATGAATGATGTTAGTCC 57.384 36.000 0.00 0.00 38.79 3.85
3629 5345 2.477375 TGTTAGTCCGTGATTTGTTCGC 59.523 45.455 0.00 0.00 0.00 4.70
3641 5357 3.750639 TTTGTTCGCGTCAGAAGTTTT 57.249 38.095 5.77 0.00 0.00 2.43
3649 5365 6.586868 TCGCGTCAGAAGTTTTAACTAAAA 57.413 33.333 5.77 0.00 38.57 1.52
3797 5516 1.152943 AGCGAGAGGCCTACGATCA 60.153 57.895 28.21 0.00 45.17 2.92
3952 5671 5.843969 AGGAGAGGGGAAAGAGAAGATAATC 59.156 44.000 0.00 0.00 0.00 1.75
4114 5833 1.134250 TGCAGTATCATTTGCCGGCTA 60.134 47.619 29.70 19.10 39.54 3.93
4162 5881 4.211374 GCTAAGCTGTGGGTTTATCATACG 59.789 45.833 0.00 0.00 34.76 3.06
4248 5967 7.153217 TCACAGAATGAAGTACAGTTCGATA 57.847 36.000 0.00 0.00 39.69 2.92
4261 5980 9.168451 AGTACAGTTCGATATCAGATAGTATGG 57.832 37.037 3.12 0.00 0.00 2.74
4263 5985 6.127591 ACAGTTCGATATCAGATAGTATGGCC 60.128 42.308 3.12 0.00 0.00 5.36
4266 5988 4.575236 TCGATATCAGATAGTATGGCCGAC 59.425 45.833 3.12 0.00 0.00 4.79
4270 5992 3.833732 TCAGATAGTATGGCCGACTCTT 58.166 45.455 13.14 3.45 0.00 2.85
4271 5993 3.570125 TCAGATAGTATGGCCGACTCTTG 59.430 47.826 13.14 10.32 0.00 3.02
4276 5998 2.434336 AGTATGGCCGACTCTTGCATTA 59.566 45.455 4.29 0.00 0.00 1.90
4288 6010 4.880696 ACTCTTGCATTATGCTCTCTTTCC 59.119 41.667 18.44 0.00 45.31 3.13
4289 6011 4.847198 TCTTGCATTATGCTCTCTTTCCA 58.153 39.130 18.44 0.00 45.31 3.53
4296 6018 6.484643 GCATTATGCTCTCTTTCCATAGTTCA 59.515 38.462 10.27 0.00 40.96 3.18
4298 6020 8.719648 CATTATGCTCTCTTTCCATAGTTCATC 58.280 37.037 0.00 0.00 0.00 2.92
4313 6035 0.401356 TCATCTTGCAGTTCCAGCCA 59.599 50.000 0.00 0.00 0.00 4.75
4322 6074 3.019564 GCAGTTCCAGCCAGAAATACAT 58.980 45.455 0.00 0.00 0.00 2.29
4393 6145 5.756833 TCCATGACAATTCATCAAGATCTCG 59.243 40.000 0.00 0.00 40.79 4.04
4441 6194 5.297547 TCAATCACAGTTACACAAGGTCTC 58.702 41.667 0.00 0.00 0.00 3.36
4487 6241 5.362717 TCGAAACCTTTATAGCCATCAGAGA 59.637 40.000 0.00 0.00 0.00 3.10
4519 6273 6.435591 AGATTGATGCTCCTAGAATCGATACA 59.564 38.462 0.00 0.00 35.02 2.29
4528 6282 7.308229 GCTCCTAGAATCGATACAAAAATGCAT 60.308 37.037 0.00 0.00 0.00 3.96
4543 6310 2.955477 TGCATGACTAGTGCTCAGAG 57.045 50.000 0.00 0.00 42.92 3.35
4795 6562 4.143333 GCCGCAGCCTCGTCCTTA 62.143 66.667 0.00 0.00 0.00 2.69
4854 6621 2.925170 AAGTGCCTCTGCCCTCGT 60.925 61.111 0.00 0.00 36.33 4.18
4921 6688 2.076863 ACGTCTTCATACAGCTTTGCC 58.923 47.619 0.00 0.00 0.00 4.52
4976 6743 1.836166 CTTCCAGAAGCTCCCTCATCA 59.164 52.381 0.00 0.00 0.00 3.07
5010 6777 4.082125 ACCACATTCTCATCCAAAAGGAC 58.918 43.478 0.00 0.00 0.00 3.85
5128 6895 3.695357 TCCTTCTCCCTCATCTGATCA 57.305 47.619 0.00 0.00 0.00 2.92
5149 6916 2.310779 AGTACTCCTGAGCCTTGTCA 57.689 50.000 0.00 0.00 0.00 3.58
5164 6931 3.300009 CTTGTCAAGCAAGCTTAAACCG 58.700 45.455 7.03 0.00 46.68 4.44
5173 6940 0.109723 AGCTTAAACCGACCAAGCCA 59.890 50.000 2.13 0.00 44.57 4.75
5179 6946 2.107041 AACCGACCAAGCCATCGACA 62.107 55.000 0.00 0.00 40.86 4.35
5191 6958 5.946942 AGCCATCGACAATCCTATGATAT 57.053 39.130 0.00 0.00 0.00 1.63
5192 6959 5.668471 AGCCATCGACAATCCTATGATATG 58.332 41.667 0.00 0.00 0.00 1.78
5193 6960 4.272018 GCCATCGACAATCCTATGATATGC 59.728 45.833 0.00 0.00 0.00 3.14
5194 6961 5.422145 CCATCGACAATCCTATGATATGCA 58.578 41.667 0.00 0.00 0.00 3.96
5197 6964 5.714047 TCGACAATCCTATGATATGCAGAC 58.286 41.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 2.532317 GTCTTCAGCTCTTAATCGACGC 59.468 50.000 0.00 0.00 0.00 5.19
343 352 2.479566 TCTGTCCAGGCTTCAATCAC 57.520 50.000 0.00 0.00 0.00 3.06
366 375 5.220739 GGCAAACATCACAGTCACAGATATC 60.221 44.000 0.00 0.00 0.00 1.63
369 378 2.816087 GGCAAACATCACAGTCACAGAT 59.184 45.455 0.00 0.00 0.00 2.90
404 413 3.378427 AGAGCGTAATTTGCCCTGATTTC 59.622 43.478 0.00 0.00 0.00 2.17
407 416 2.717639 AGAGCGTAATTTGCCCTGAT 57.282 45.000 0.00 0.00 0.00 2.90
424 450 6.172630 TCATTTCATCATTTCGTCTGGAAGA 58.827 36.000 0.00 0.00 43.69 2.87
425 451 6.426980 TCATTTCATCATTTCGTCTGGAAG 57.573 37.500 0.00 0.00 35.70 3.46
426 452 6.816134 TTCATTTCATCATTTCGTCTGGAA 57.184 33.333 0.00 0.00 0.00 3.53
427 453 7.395190 AATTCATTTCATCATTTCGTCTGGA 57.605 32.000 0.00 0.00 0.00 3.86
428 454 7.756272 TCAAATTCATTTCATCATTTCGTCTGG 59.244 33.333 0.00 0.00 0.00 3.86
429 455 8.581263 GTCAAATTCATTTCATCATTTCGTCTG 58.419 33.333 0.00 0.00 0.00 3.51
430 456 8.517878 AGTCAAATTCATTTCATCATTTCGTCT 58.482 29.630 0.00 0.00 0.00 4.18
431 457 8.679288 AGTCAAATTCATTTCATCATTTCGTC 57.321 30.769 0.00 0.00 0.00 4.20
432 458 8.918658 CAAGTCAAATTCATTTCATCATTTCGT 58.081 29.630 0.00 0.00 0.00 3.85
433 459 8.377681 CCAAGTCAAATTCATTTCATCATTTCG 58.622 33.333 0.00 0.00 0.00 3.46
538 568 3.367292 CCTGATTTTGGTACGCAAGCAAT 60.367 43.478 4.11 0.00 44.64 3.56
572 602 4.141321 TGGGGAAGATCATTTCATCTGGAG 60.141 45.833 0.00 0.00 33.13 3.86
608 638 9.236006 ACCATATATCAACTCAATTTAGATGCC 57.764 33.333 0.00 0.00 0.00 4.40
654 699 5.159273 TGATATGGGTATGCAATCGCTTA 57.841 39.130 0.00 0.00 39.64 3.09
677 1964 6.314784 GTTACAAATCACTGGTATGAACTGC 58.685 40.000 0.00 0.00 30.82 4.40
704 2018 3.608662 GGCAGCAGCTTTGCACCA 61.609 61.111 18.73 0.00 43.28 4.17
766 2080 1.626356 CCGGCCTGGGAGAGAAATCA 61.626 60.000 0.00 0.00 0.00 2.57
830 2151 3.436359 GCAATTTGATTTGCCCGTCAATT 59.564 39.130 0.00 0.00 44.94 2.32
831 2152 3.002102 GCAATTTGATTTGCCCGTCAAT 58.998 40.909 0.00 0.00 44.94 2.57
832 2153 2.411904 GCAATTTGATTTGCCCGTCAA 58.588 42.857 0.00 0.00 44.94 3.18
833 2154 2.077413 GCAATTTGATTTGCCCGTCA 57.923 45.000 0.00 0.00 44.94 4.35
843 2164 7.629222 GCAAGGAGTTACACTATGCAATTTGAT 60.629 37.037 0.00 0.00 34.50 2.57
883 2204 1.338107 GTGGCTTTGGGGCTTTTACT 58.662 50.000 0.00 0.00 41.48 2.24
905 2227 3.695825 GGGAGGGGGAGGAGGTCA 61.696 72.222 0.00 0.00 0.00 4.02
928 2252 1.019805 CCGGCTCTTCCTCGGTTTTC 61.020 60.000 0.00 0.00 39.04 2.29
947 2271 0.810016 GTCGATCGGCTACCTATCCC 59.190 60.000 13.54 0.00 0.00 3.85
1080 2421 3.151022 GAGTAGCAGGAGGGCGCT 61.151 66.667 7.64 1.38 42.34 5.92
1217 2564 1.643832 CTAATTCCGCGCTGAAGGC 59.356 57.895 19.06 0.00 37.64 4.35
1219 2566 0.302890 CTGCTAATTCCGCGCTGAAG 59.697 55.000 19.06 7.45 0.00 3.02
1222 2569 0.882042 ATCCTGCTAATTCCGCGCTG 60.882 55.000 5.56 0.00 0.00 5.18
1225 2572 1.003545 CACAATCCTGCTAATTCCGCG 60.004 52.381 0.00 0.00 0.00 6.46
1246 2605 5.048991 GGAAGAAATTCTGCACGGAACTAAA 60.049 40.000 3.03 0.00 0.00 1.85
1248 2607 4.000988 GGAAGAAATTCTGCACGGAACTA 58.999 43.478 3.03 0.00 0.00 2.24
1249 2608 2.814336 GGAAGAAATTCTGCACGGAACT 59.186 45.455 3.03 0.00 0.00 3.01
1250 2609 2.814336 AGGAAGAAATTCTGCACGGAAC 59.186 45.455 3.03 0.00 0.00 3.62
1253 2612 2.907910 CAGGAAGAAATTCTGCACGG 57.092 50.000 3.03 0.00 0.00 4.94
1258 2617 8.394121 GTTCTGTTATAGCAGGAAGAAATTCTG 58.606 37.037 15.63 0.00 37.12 3.02
1259 2618 8.103305 TGTTCTGTTATAGCAGGAAGAAATTCT 58.897 33.333 15.63 0.00 37.12 2.40
1260 2619 8.268850 TGTTCTGTTATAGCAGGAAGAAATTC 57.731 34.615 15.63 0.00 37.12 2.17
1261 2620 8.103305 TCTGTTCTGTTATAGCAGGAAGAAATT 58.897 33.333 15.63 0.00 37.12 1.82
1262 2621 7.624549 TCTGTTCTGTTATAGCAGGAAGAAAT 58.375 34.615 15.63 0.00 37.12 2.17
1263 2622 7.004555 TCTGTTCTGTTATAGCAGGAAGAAA 57.995 36.000 15.63 0.83 37.12 2.52
1264 2623 6.605471 TCTGTTCTGTTATAGCAGGAAGAA 57.395 37.500 15.63 1.44 37.12 2.52
1265 2624 6.605471 TTCTGTTCTGTTATAGCAGGAAGA 57.395 37.500 15.63 12.65 37.12 2.87
1266 2625 7.768120 AGAATTCTGTTCTGTTATAGCAGGAAG 59.232 37.037 15.63 10.88 37.12 3.46
1269 2628 8.200792 AGTAGAATTCTGTTCTGTTATAGCAGG 58.799 37.037 18.47 1.16 37.12 4.85
1283 2642 6.852420 TGGCTTGTACTAGTAGAATTCTGT 57.148 37.500 18.47 9.58 0.00 3.41
1294 2653 3.520290 TCCGTTCATGGCTTGTACTAG 57.480 47.619 8.18 0.00 0.00 2.57
1299 2658 2.086869 CTGAATCCGTTCATGGCTTGT 58.913 47.619 0.00 0.00 43.08 3.16
1327 2686 1.975407 GAGCACCTGCACAGCCAAT 60.975 57.895 0.00 0.00 45.16 3.16
1450 2812 2.049985 CTTATCGGAGGGCTCGCG 60.050 66.667 0.00 0.00 0.00 5.87
1452 2814 1.033574 AGAACTTATCGGAGGGCTCG 58.966 55.000 0.00 0.00 0.00 5.03
1486 2848 1.608590 GATCACCACCACAACCACAAG 59.391 52.381 0.00 0.00 0.00 3.16
1599 2977 0.450184 AAAACGCATACGCATCCACC 59.550 50.000 0.00 0.00 45.53 4.61
1646 3024 2.096335 CGCATCACATTAGCAAGCAAGA 59.904 45.455 0.00 0.00 0.00 3.02
1773 3151 2.417933 GCTTTCTAGTGGCATGTGACAG 59.582 50.000 0.00 0.00 30.83 3.51
1805 3183 3.495001 GCGTTAAAGAGAGCAGTCAAACT 59.505 43.478 0.00 0.00 0.00 2.66
1806 3184 3.247648 TGCGTTAAAGAGAGCAGTCAAAC 59.752 43.478 0.00 0.00 34.39 2.93
1807 3185 3.462982 TGCGTTAAAGAGAGCAGTCAAA 58.537 40.909 0.00 0.00 34.39 2.69
1808 3186 3.106242 TGCGTTAAAGAGAGCAGTCAA 57.894 42.857 0.00 0.00 34.39 3.18
1809 3187 2.812358 TGCGTTAAAGAGAGCAGTCA 57.188 45.000 0.00 0.00 34.39 3.41
1810 3188 3.181516 CCAATGCGTTAAAGAGAGCAGTC 60.182 47.826 0.00 0.00 43.20 3.51
1811 3189 2.744202 CCAATGCGTTAAAGAGAGCAGT 59.256 45.455 0.00 0.00 43.20 4.40
1812 3190 2.744202 ACCAATGCGTTAAAGAGAGCAG 59.256 45.455 0.00 0.00 43.20 4.24
1813 3191 2.483877 CACCAATGCGTTAAAGAGAGCA 59.516 45.455 0.00 0.00 44.13 4.26
1814 3192 2.159517 CCACCAATGCGTTAAAGAGAGC 60.160 50.000 0.00 0.00 0.00 4.09
1815 3193 3.074412 ACCACCAATGCGTTAAAGAGAG 58.926 45.455 0.00 0.00 0.00 3.20
1816 3194 3.134574 ACCACCAATGCGTTAAAGAGA 57.865 42.857 0.00 0.00 0.00 3.10
1817 3195 3.252215 TGAACCACCAATGCGTTAAAGAG 59.748 43.478 0.00 0.00 0.00 2.85
1818 3196 3.215151 TGAACCACCAATGCGTTAAAGA 58.785 40.909 0.00 0.00 0.00 2.52
1819 3197 3.634568 TGAACCACCAATGCGTTAAAG 57.365 42.857 0.00 0.00 0.00 1.85
1820 3198 4.519350 TGTATGAACCACCAATGCGTTAAA 59.481 37.500 0.00 0.00 0.00 1.52
1821 3199 4.072839 TGTATGAACCACCAATGCGTTAA 58.927 39.130 0.00 0.00 0.00 2.01
1822 3200 3.676093 TGTATGAACCACCAATGCGTTA 58.324 40.909 0.00 0.00 0.00 3.18
1823 3201 2.509569 TGTATGAACCACCAATGCGTT 58.490 42.857 0.00 0.00 0.00 4.84
1824 3202 2.192664 TGTATGAACCACCAATGCGT 57.807 45.000 0.00 0.00 0.00 5.24
1825 3203 2.423185 ACATGTATGAACCACCAATGCG 59.577 45.455 0.00 0.00 0.00 4.73
1834 3212 2.092968 TCTGCCAGGACATGTATGAACC 60.093 50.000 11.23 2.55 0.00 3.62
1933 3313 3.685265 CGATTGATTCCACATCTTCCCCA 60.685 47.826 0.00 0.00 0.00 4.96
1978 3358 8.526978 GTCAGAACAGATTCATAGGCTGATATA 58.473 37.037 0.00 0.00 37.29 0.86
1979 3359 7.235193 AGTCAGAACAGATTCATAGGCTGATAT 59.765 37.037 0.00 0.00 37.29 1.63
2078 3458 6.148150 ACAACTAAATTGCTGAAATGCATTGG 59.852 34.615 13.82 7.74 42.62 3.16
2080 3460 8.711457 GTTACAACTAAATTGCTGAAATGCATT 58.289 29.630 5.99 5.99 42.62 3.56
2161 3746 1.750572 CGCTCTGCAGCTTCGACATC 61.751 60.000 9.47 0.00 44.40 3.06
2230 3815 7.977293 TGGTAATGATGATCAGAAATGCTTTTG 59.023 33.333 0.09 0.00 0.00 2.44
2301 3893 2.352651 CGAGCTGAATGTACCAATGTGG 59.647 50.000 0.00 0.00 45.02 4.17
2302 3894 2.352651 CCGAGCTGAATGTACCAATGTG 59.647 50.000 0.00 0.00 0.00 3.21
2319 3911 2.266055 GTCCTCCTGGCAACCGAG 59.734 66.667 0.00 0.00 0.00 4.63
2390 3982 1.208776 ACATAGCCACTTACCGTTCCC 59.791 52.381 0.00 0.00 0.00 3.97
2414 4006 7.715249 TCTTCTAAAGAGCACACAACTACAAAT 59.285 33.333 0.00 0.00 32.71 2.32
2478 4071 6.744112 TGGAGTTTATTTACTTGGCAAACAG 58.256 36.000 0.00 0.00 32.75 3.16
2479 4072 6.547880 TCTGGAGTTTATTTACTTGGCAAACA 59.452 34.615 0.00 0.00 32.75 2.83
2484 4077 5.938125 TGAGTCTGGAGTTTATTTACTTGGC 59.062 40.000 0.00 0.00 0.00 4.52
2492 4085 4.697352 GTGCATGTGAGTCTGGAGTTTATT 59.303 41.667 0.00 0.00 0.00 1.40
2521 4114 8.040727 TGGAATCATTCTTGTTTAGAGAATCGA 58.959 33.333 0.00 0.00 40.82 3.59
2522 4115 8.201554 TGGAATCATTCTTGTTTAGAGAATCG 57.798 34.615 0.00 0.00 40.82 3.34
2523 4116 9.947669 CATGGAATCATTCTTGTTTAGAGAATC 57.052 33.333 0.00 0.00 40.82 2.52
2524 4117 9.471702 ACATGGAATCATTCTTGTTTAGAGAAT 57.528 29.630 0.00 0.00 42.89 2.40
2540 4214 6.016360 CACCTAAGAACACAAACATGGAATCA 60.016 38.462 0.00 0.00 0.00 2.57
2566 4240 1.768275 TCTCTTCCTTGGCACACTGAA 59.232 47.619 0.00 0.00 39.29 3.02
2583 4257 4.456911 TGAGACATGCCATTTTGACTTCTC 59.543 41.667 0.00 0.00 0.00 2.87
2599 4273 2.290514 CCTCCACACAACCATGAGACAT 60.291 50.000 0.00 0.00 0.00 3.06
2691 4387 2.618709 GAGCTGTTGGTGCTAAACTGTT 59.381 45.455 0.00 0.00 41.30 3.16
2707 4403 6.094603 AGCACCATTCAATAGTTTTAGAGCTG 59.905 38.462 0.00 0.00 0.00 4.24
2748 4444 4.280425 TCAGGCAAGCAACAACATATTGAA 59.720 37.500 0.00 0.00 39.30 2.69
2750 4446 4.171005 CTCAGGCAAGCAACAACATATTG 58.829 43.478 0.00 0.00 41.98 1.90
2752 4448 3.192001 CACTCAGGCAAGCAACAACATAT 59.808 43.478 0.00 0.00 0.00 1.78
2753 4449 2.553602 CACTCAGGCAAGCAACAACATA 59.446 45.455 0.00 0.00 0.00 2.29
2754 4450 1.338973 CACTCAGGCAAGCAACAACAT 59.661 47.619 0.00 0.00 0.00 2.71
2793 4498 2.851824 CGACAAAAAGAACAACAGCCAC 59.148 45.455 0.00 0.00 0.00 5.01
2795 4500 1.852280 GCGACAAAAAGAACAACAGCC 59.148 47.619 0.00 0.00 0.00 4.85
2796 4501 2.525055 TGCGACAAAAAGAACAACAGC 58.475 42.857 0.00 0.00 0.00 4.40
2797 4502 3.108144 CCTGCGACAAAAAGAACAACAG 58.892 45.455 0.00 0.00 0.00 3.16
2798 4503 2.733858 GCCTGCGACAAAAAGAACAACA 60.734 45.455 0.00 0.00 0.00 3.33
2800 4505 1.474478 TGCCTGCGACAAAAAGAACAA 59.526 42.857 0.00 0.00 0.00 2.83
2803 4508 1.388547 ACTGCCTGCGACAAAAAGAA 58.611 45.000 0.00 0.00 0.00 2.52
2804 4509 1.065401 CAACTGCCTGCGACAAAAAGA 59.935 47.619 0.00 0.00 0.00 2.52
2805 4510 1.480205 CAACTGCCTGCGACAAAAAG 58.520 50.000 0.00 0.00 0.00 2.27
2814 4527 2.680913 CGTACTGCCAACTGCCTGC 61.681 63.158 0.00 0.00 40.16 4.85
2868 4581 3.605634 CCCCAACTCGTCATTGTAATGA 58.394 45.455 3.28 3.28 42.78 2.57
2890 4603 8.821894 TCAACCTGCAAAACAAATTAAACATAC 58.178 29.630 0.00 0.00 0.00 2.39
2972 4685 7.781056 AGAGATCTGAATAACCTTTCTGAGAC 58.219 38.462 0.00 0.00 37.12 3.36
3026 4739 8.534496 TCAGACATGACATGGAGGTTATATATG 58.466 37.037 19.39 3.26 33.60 1.78
3057 4770 3.904136 AGTCTTGCATAGCACACAAAC 57.096 42.857 0.00 0.00 38.71 2.93
3159 4872 1.734465 CTTACCTCTTCAAGCAAGCCG 59.266 52.381 0.00 0.00 31.26 5.52
3160 4873 1.470494 GCTTACCTCTTCAAGCAAGCC 59.530 52.381 1.62 0.00 45.20 4.35
3209 4922 6.788598 TGTATCAATGTGGGCATTAACAAT 57.211 33.333 0.00 0.00 42.91 2.71
3212 4928 6.449635 TCTTGTATCAATGTGGGCATTAAC 57.550 37.500 0.00 0.00 42.91 2.01
3251 4967 7.937649 TCGTCATTCTCGATCTAAATAAGGAA 58.062 34.615 0.00 0.00 32.30 3.36
3384 5100 4.218312 AGTCAGGAAGGAAGCAAAAATGT 58.782 39.130 0.00 0.00 0.00 2.71
3393 5109 7.834181 TCCCAAATAAAATAGTCAGGAAGGAAG 59.166 37.037 0.00 0.00 0.00 3.46
3460 5176 6.039941 GTGCAGAATGTAGTAGACTGGACTAT 59.960 42.308 0.00 0.00 43.11 2.12
3485 5201 5.524646 ACAAAATGGAATGAAAACACTGCAG 59.475 36.000 13.48 13.48 0.00 4.41
3486 5202 5.426504 ACAAAATGGAATGAAAACACTGCA 58.573 33.333 0.00 0.00 0.00 4.41
3500 5216 6.370166 GGTTTTCAAGTTGTTGACAAAATGGA 59.630 34.615 2.11 0.00 42.60 3.41
3560 5276 1.885887 TGCTTGCCTATTGCGTTCTTT 59.114 42.857 0.00 0.00 45.60 2.52
3590 5306 8.680903 GGACTAACATCATTCATCTTGAACAAT 58.319 33.333 0.00 0.00 39.45 2.71
3616 5332 0.781787 TCTGACGCGAACAAATCACG 59.218 50.000 15.93 0.00 39.45 4.35
3776 5495 3.955101 CGTAGGCCTCTCGCTCCG 61.955 72.222 9.68 0.00 37.74 4.63
3779 5498 0.752009 TTGATCGTAGGCCTCTCGCT 60.752 55.000 9.68 7.52 37.74 4.93
3797 5516 5.271598 TCTGTCAAAATGCCCTCCATTATT 58.728 37.500 0.00 0.00 43.22 1.40
3952 5671 5.853282 GGATTCTTCATCAACAAGAACAACG 59.147 40.000 0.00 0.00 41.55 4.10
4114 5833 2.041620 TGAAAAGGCTACCAGAAGGCAT 59.958 45.455 0.00 0.00 44.19 4.40
4147 5866 6.848451 ACAATCAAACGTATGATAAACCCAC 58.152 36.000 0.00 0.00 39.08 4.61
4151 5870 9.274065 GGAGAAACAATCAAACGTATGATAAAC 57.726 33.333 0.00 0.00 39.08 2.01
4162 5881 7.640240 GCGTATATTGAGGAGAAACAATCAAAC 59.360 37.037 0.00 0.00 37.75 2.93
4243 5962 4.575236 GTCGGCCATACTATCTGATATCGA 59.425 45.833 2.24 0.00 0.00 3.59
4248 5967 4.040936 AGAGTCGGCCATACTATCTGAT 57.959 45.455 2.24 0.00 0.00 2.90
4259 5978 1.667236 CATAATGCAAGAGTCGGCCA 58.333 50.000 2.24 0.00 0.00 5.36
4260 5979 0.308993 GCATAATGCAAGAGTCGGCC 59.691 55.000 0.00 0.00 44.26 6.13
4261 5980 3.833706 GCATAATGCAAGAGTCGGC 57.166 52.632 0.00 3.22 44.26 5.54
4271 5993 6.484643 TGAACTATGGAAAGAGAGCATAATGC 59.515 38.462 0.00 0.00 45.46 3.56
4276 5998 6.497624 AGATGAACTATGGAAAGAGAGCAT 57.502 37.500 0.00 0.00 0.00 3.79
4288 6010 5.481200 CTGGAACTGCAAGATGAACTATG 57.519 43.478 0.00 0.00 37.43 2.23
4393 6145 4.092091 GCATAGCAATAGAGCGATAACCAC 59.908 45.833 0.00 0.00 40.15 4.16
4453 6206 7.309920 GCTATAAAGGTTTCGAATTTCAACCA 58.690 34.615 16.26 0.00 42.25 3.67
4457 6210 7.338196 TGATGGCTATAAAGGTTTCGAATTTCA 59.662 33.333 0.00 0.00 0.00 2.69
4487 6241 7.550597 TTCTAGGAGCATCAATCTGTATGAT 57.449 36.000 0.00 0.00 38.02 2.45
4519 6273 5.005740 TCTGAGCACTAGTCATGCATTTTT 58.994 37.500 0.00 0.00 45.92 1.94
4543 6310 1.738030 GCCATCTTGTCCTGCATTTGC 60.738 52.381 0.00 0.00 42.50 3.68
4641 6408 1.003233 GGCCTCAGTTCACCTGGAC 60.003 63.158 0.00 0.00 41.83 4.02
4780 6547 2.583593 GCTAAGGACGAGGCTGCG 60.584 66.667 0.00 0.00 37.29 5.18
4825 6592 4.500265 GCACTTGCCAGGGAAGAA 57.500 55.556 26.63 0.00 34.31 2.52
4854 6621 1.890894 CGGGCGGAAGAAGAGAAGA 59.109 57.895 0.00 0.00 0.00 2.87
4921 6688 0.549950 AGGGCAGGGAAGATGACATG 59.450 55.000 0.00 0.00 0.00 3.21
4976 6743 5.132502 TGAGAATGTGGTTTTCAGTGATGT 58.867 37.500 0.00 0.00 0.00 3.06
5010 6777 1.267806 CAGCCAAGGTAGCAAAGTGTG 59.732 52.381 0.00 0.00 0.00 3.82
5128 6895 2.972713 TGACAAGGCTCAGGAGTACTTT 59.027 45.455 0.00 0.00 0.00 2.66
5149 6916 1.975660 TGGTCGGTTTAAGCTTGCTT 58.024 45.000 9.86 12.65 0.00 3.91
5164 6931 1.017387 GGATTGTCGATGGCTTGGTC 58.983 55.000 0.00 0.00 0.00 4.02
5173 6940 6.336566 GTCTGCATATCATAGGATTGTCGAT 58.663 40.000 0.00 0.00 34.89 3.59


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

AutoCloner maintained by Alex Coulton.