Multiple sequence alignment - TraesCS5D01G274400

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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 TraesCS5D01G274400 chr5D 100.000 4758 0 0 1 4758 377487034 377482277 0.000000e+00 8787.0
1 TraesCS5D01G274400 chr5D 93.711 159 8 1 4601 4757 6096459 6096301 2.210000e-58 237.0
2 TraesCS5D01G274400 chr5D 93.671 158 8 1 4601 4756 6083530 6083373 7.960000e-58 235.0
3 TraesCS5D01G274400 chr5A 90.365 3944 179 97 73 3932 478017863 478014037 0.000000e+00 4992.0
4 TraesCS5D01G274400 chr5A 90.250 400 26 4 4211 4601 478013633 478013238 1.180000e-140 510.0
5 TraesCS5D01G274400 chr5A 92.053 151 9 3 3930 4080 478014004 478013857 4.820000e-50 209.0
6 TraesCS5D01G274400 chr5A 100.000 38 0 0 13 50 478017907 478017870 2.380000e-08 71.3
7 TraesCS5D01G274400 chr5B 90.804 2153 82 52 192 2270 450772951 450770841 0.000000e+00 2772.0
8 TraesCS5D01G274400 chr5B 93.051 1511 66 20 2454 3932 450770760 450769257 0.000000e+00 2172.0
9 TraesCS5D01G274400 chr5B 91.129 372 24 3 4241 4607 450767534 450767167 3.310000e-136 496.0
10 TraesCS5D01G274400 chr5B 90.270 185 11 7 1 184 450773250 450773072 7.960000e-58 235.0
11 TraesCS5D01G274400 chr5B 88.889 117 10 2 3988 4104 450769157 450769044 1.790000e-29 141.0
12 TraesCS5D01G274400 chr5B 92.958 71 4 1 2350 2420 450770830 450770761 8.420000e-18 102.0
13 TraesCS5D01G274400 chr2D 92.973 185 12 1 4359 4542 119299346 119299530 7.850000e-68 268.0
14 TraesCS5D01G274400 chr2A 92.432 185 13 1 4359 4542 121225120 121225304 3.650000e-66 263.0
15 TraesCS5D01G274400 chr1D 97.315 149 4 0 4605 4753 63355586 63355734 2.200000e-63 254.0
16 TraesCS5D01G274400 chr1D 93.711 159 8 1 4601 4757 210082640 210082798 2.210000e-58 237.0
17 TraesCS5D01G274400 chr1D 94.156 154 7 1 4602 4753 130310060 130310213 2.860000e-57 233.0
18 TraesCS5D01G274400 chr7D 95.425 153 7 0 4601 4753 74601904 74602056 1.320000e-60 244.0
19 TraesCS5D01G274400 chr7D 91.124 169 11 3 4590 4756 93090292 93090126 4.790000e-55 226.0
20 TraesCS5D01G274400 chr6D 94.194 155 6 2 4601 4753 84029723 84029876 2.860000e-57 233.0
21 TraesCS5D01G274400 chr4A 94.156 154 7 1 4602 4753 101750114 101750267 2.860000e-57 233.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G274400 chr5D 377482277 377487034 4757 True 8787.000000 8787 100.0000 1 4758 1 chr5D.!!$R3 4757
1 TraesCS5D01G274400 chr5A 478013238 478017907 4669 True 1445.575000 4992 93.1670 13 4601 4 chr5A.!!$R1 4588
2 TraesCS5D01G274400 chr5B 450767167 450773250 6083 True 986.333333 2772 91.1835 1 4607 6 chr5B.!!$R1 4606

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
453 575 0.465460 AAAGAGACACCGCTTGCCAA 60.465 50.0 0.0 0.0 32.69 4.52 F
787 944 0.526211 GTGGAACGGAGAAATTGCCC 59.474 55.0 0.0 0.0 0.00 5.36 F
1970 2147 1.198759 TGTCCCTTCCCTTCCCTTCG 61.199 60.0 0.0 0.0 0.00 3.79 F
2311 2557 0.249398 GCTGTGGTAGTGGTAGGTGG 59.751 60.0 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2525 0.033781 CCACAGCAACAAACATGGGG 59.966 55.000 0.0 0.0 0.00 4.96 R
2312 2558 1.003355 CTGCTACACACCCACCTGG 60.003 63.158 0.0 0.0 41.37 4.45 R
3088 3367 0.172803 GCTTGGCAGCTTTCTGGATG 59.827 55.000 0.0 0.0 43.51 3.51 R
4290 6059 0.096454 GACGTGCCCTTTGTATTCGC 59.904 55.000 0.0 0.0 0.00 4.70 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
50 51 2.421073 TGTGTGCTGCTATGCTTTGATC 59.579 45.455 0.00 0.00 0.00 2.92
52 53 3.083293 TGTGCTGCTATGCTTTGATCAA 58.917 40.909 3.38 3.38 0.00 2.57
53 54 3.506844 TGTGCTGCTATGCTTTGATCAAA 59.493 39.130 19.45 19.45 0.00 2.69
60 61 7.019774 TGCTATGCTTTGATCAAATACTCAC 57.980 36.000 20.76 10.47 0.00 3.51
63 64 8.494347 GCTATGCTTTGATCAAATACTCACTAG 58.506 37.037 20.76 14.25 0.00 2.57
68 69 8.983724 GCTTTGATCAAATACTCACTAGATACC 58.016 37.037 20.76 0.00 0.00 2.73
170 172 5.749462 CATCCAAAGAGTTCCTCCAGTAAT 58.251 41.667 0.00 0.00 0.00 1.89
227 342 2.821366 GTCTGACATGGGCGGCTG 60.821 66.667 9.56 2.20 0.00 4.85
237 352 0.468400 TGGGCGGCTGGTTTAAAACT 60.468 50.000 9.56 0.00 0.00 2.66
241 356 2.542178 GGCGGCTGGTTTAAAACTTTTG 59.458 45.455 4.60 0.00 0.00 2.44
268 384 9.811995 ATTTTAGGAACAGTTGGTTTAAAACTC 57.188 29.630 4.60 0.00 40.63 3.01
288 405 5.202004 ACTCGGTGTACTAGAATCCTGAAT 58.798 41.667 0.00 0.00 0.00 2.57
300 417 8.407064 ACTAGAATCCTGAATTCACTACTTACG 58.593 37.037 3.38 0.00 45.34 3.18
332 449 4.511826 ACAATTTCGTCTTCACTCCTTCAC 59.488 41.667 0.00 0.00 0.00 3.18
350 467 3.486383 TCACCCAGAACAAAGATTGACC 58.514 45.455 0.00 0.00 0.00 4.02
361 478 5.670485 ACAAAGATTGACCGTAGATATGCA 58.330 37.500 0.00 0.00 0.00 3.96
362 479 5.523916 ACAAAGATTGACCGTAGATATGCAC 59.476 40.000 0.00 0.00 0.00 4.57
364 481 5.474578 AGATTGACCGTAGATATGCACAT 57.525 39.130 0.00 0.00 0.00 3.21
378 495 8.026341 AGATATGCACATTCGTAGATTCATTG 57.974 34.615 0.00 0.00 35.04 2.82
381 498 3.548818 GCACATTCGTAGATTCATTGGCC 60.549 47.826 0.00 0.00 35.04 5.36
382 499 3.627123 CACATTCGTAGATTCATTGGCCA 59.373 43.478 0.00 0.00 35.04 5.36
429 547 2.219875 CCCCACCTGTCAGTCAGCT 61.220 63.158 0.00 0.00 42.38 4.24
437 555 3.070018 CCTGTCAGTCAGCTAACCAAAG 58.930 50.000 0.00 0.00 42.38 2.77
453 575 0.465460 AAAGAGACACCGCTTGCCAA 60.465 50.000 0.00 0.00 32.69 4.52
463 585 3.613737 CACCGCTTGCCAAATTCAAATAG 59.386 43.478 0.00 0.00 0.00 1.73
480 624 6.349300 TCAAATAGTTTCCATACTCTGAGCC 58.651 40.000 4.19 0.00 0.00 4.70
535 682 2.483714 GGATCTAGCCATGACGCTGAAA 60.484 50.000 6.71 0.00 40.08 2.69
540 687 3.665745 AGCCATGACGCTGAAATTTTT 57.334 38.095 0.00 0.00 37.82 1.94
541 688 4.782019 AGCCATGACGCTGAAATTTTTA 57.218 36.364 0.00 0.00 37.82 1.52
543 690 4.458989 AGCCATGACGCTGAAATTTTTAGA 59.541 37.500 5.19 0.00 37.82 2.10
627 774 0.801067 CGTCAGGCTAACGGTAGTGC 60.801 60.000 9.69 0.00 36.51 4.40
684 833 4.344865 ACGCAGGAATTGGCCCGT 62.345 61.111 0.00 0.00 0.00 5.28
771 928 4.038080 GCGAAAACGCCCCTGTGG 62.038 66.667 3.16 0.00 37.09 4.17
787 944 0.526211 GTGGAACGGAGAAATTGCCC 59.474 55.000 0.00 0.00 0.00 5.36
1254 1425 1.235696 GGAGGAGGAGCAGGAGGAT 59.764 63.158 0.00 0.00 0.00 3.24
1377 1554 3.740141 GCGATCTCTCCATCGGGTAAAAA 60.740 47.826 5.10 0.00 44.89 1.94
1389 1566 8.084073 TCCATCGGGTAAAAACGATTATAGTAG 58.916 37.037 0.00 0.00 46.57 2.57
1390 1567 7.869429 CCATCGGGTAAAAACGATTATAGTAGT 59.131 37.037 0.00 0.00 46.57 2.73
1391 1568 9.897744 CATCGGGTAAAAACGATTATAGTAGTA 57.102 33.333 0.00 0.00 46.57 1.82
1392 1569 9.899226 ATCGGGTAAAAACGATTATAGTAGTAC 57.101 33.333 0.00 0.00 46.57 2.73
1393 1570 9.120538 TCGGGTAAAAACGATTATAGTAGTACT 57.879 33.333 8.14 8.14 33.69 2.73
1439 1616 4.404394 ACCGTTTGAATTGAAGGAAAACCT 59.596 37.500 0.00 0.00 0.00 3.50
1494 1671 2.810458 CTGCGGCCGCCATTTTTG 60.810 61.111 44.42 21.93 41.09 2.44
1543 1720 7.999213 ACTTGTTCGTTTTGTTTTTACTTGTC 58.001 30.769 0.00 0.00 0.00 3.18
1544 1721 6.599637 TGTTCGTTTTGTTTTTACTTGTCG 57.400 33.333 0.00 0.00 0.00 4.35
1776 1953 2.185608 GAGTCCAAGGAGAGCGCC 59.814 66.667 2.29 0.00 0.00 6.53
1890 2067 3.114616 CCCGTGTTCGAGCAGCTG 61.115 66.667 10.11 10.11 39.71 4.24
1965 2142 1.900545 CGTCCTGTCCCTTCCCTTCC 61.901 65.000 0.00 0.00 0.00 3.46
1970 2147 1.198759 TGTCCCTTCCCTTCCCTTCG 61.199 60.000 0.00 0.00 0.00 3.79
2004 2186 1.613437 CCCGCCATGTCAAAACTTTCT 59.387 47.619 0.00 0.00 0.00 2.52
2034 2216 4.837860 TGTTACTAGGGGTAAAAACGAGGA 59.162 41.667 0.00 0.00 41.41 3.71
2057 2239 4.751539 CGTAGACGTACACGGTGG 57.248 61.111 13.48 0.00 44.95 4.61
2278 2524 4.077184 GCACCCATGACGGACGGA 62.077 66.667 0.00 0.00 36.56 4.69
2279 2525 2.125673 CACCCATGACGGACGGAC 60.126 66.667 0.00 0.00 36.56 4.79
2302 2548 2.622942 CCATGTTTGTTGCTGTGGTAGT 59.377 45.455 0.00 0.00 0.00 2.73
2303 2549 3.550639 CCATGTTTGTTGCTGTGGTAGTG 60.551 47.826 0.00 0.00 0.00 2.74
2305 2551 2.021457 GTTTGTTGCTGTGGTAGTGGT 58.979 47.619 0.00 0.00 0.00 4.16
2306 2552 3.207778 GTTTGTTGCTGTGGTAGTGGTA 58.792 45.455 0.00 0.00 0.00 3.25
2307 2553 2.831685 TGTTGCTGTGGTAGTGGTAG 57.168 50.000 0.00 0.00 0.00 3.18
2309 2555 1.346722 GTTGCTGTGGTAGTGGTAGGT 59.653 52.381 0.00 0.00 0.00 3.08
2311 2557 0.249398 GCTGTGGTAGTGGTAGGTGG 59.751 60.000 0.00 0.00 0.00 4.61
2312 2558 0.249398 CTGTGGTAGTGGTAGGTGGC 59.751 60.000 0.00 0.00 0.00 5.01
2313 2559 1.196104 TGTGGTAGTGGTAGGTGGCC 61.196 60.000 0.00 0.00 0.00 5.36
2314 2560 1.158944 TGGTAGTGGTAGGTGGCCA 59.841 57.895 0.00 0.00 0.00 5.36
2315 2561 0.907704 TGGTAGTGGTAGGTGGCCAG 60.908 60.000 5.11 0.00 36.57 4.85
2316 2562 1.623542 GGTAGTGGTAGGTGGCCAGG 61.624 65.000 5.11 0.00 36.57 4.45
2317 2563 0.908180 GTAGTGGTAGGTGGCCAGGT 60.908 60.000 5.11 0.00 36.57 4.00
2318 2564 0.907704 TAGTGGTAGGTGGCCAGGTG 60.908 60.000 5.11 0.00 36.57 4.00
2319 2565 2.933287 TGGTAGGTGGCCAGGTGG 60.933 66.667 5.11 0.00 38.53 4.61
2320 2566 3.728373 GGTAGGTGGCCAGGTGGG 61.728 72.222 5.11 0.00 40.85 4.61
2321 2567 2.933834 GTAGGTGGCCAGGTGGGT 60.934 66.667 5.11 0.00 39.65 4.51
2322 2568 2.933287 TAGGTGGCCAGGTGGGTG 60.933 66.667 5.11 0.00 39.65 4.61
2323 2569 3.803311 TAGGTGGCCAGGTGGGTGT 62.803 63.158 5.11 0.00 39.65 4.16
2324 2570 4.974721 GGTGGCCAGGTGGGTGTG 62.975 72.222 5.11 0.00 39.65 3.82
2325 2571 4.204028 GTGGCCAGGTGGGTGTGT 62.204 66.667 5.11 0.00 39.65 3.72
2326 2572 2.448736 TGGCCAGGTGGGTGTGTA 60.449 61.111 0.00 0.00 39.65 2.90
2327 2573 2.351276 GGCCAGGTGGGTGTGTAG 59.649 66.667 0.00 0.00 39.65 2.74
2328 2574 2.359975 GCCAGGTGGGTGTGTAGC 60.360 66.667 0.00 0.00 39.65 3.58
2329 2575 3.156714 CCAGGTGGGTGTGTAGCA 58.843 61.111 0.00 0.00 0.00 3.49
2443 2690 1.371145 GTCATCTCTAGCCGAGCGC 60.371 63.158 0.00 0.00 39.70 5.92
2641 2913 1.064946 CAGCACTCGATCGAGGACC 59.935 63.158 39.70 28.43 45.88 4.46
2651 2923 0.757188 ATCGAGGACCCGAGATGCTT 60.757 55.000 10.24 0.00 42.21 3.91
2652 2924 1.227089 CGAGGACCCGAGATGCTTG 60.227 63.158 0.00 0.00 0.00 4.01
2654 2926 2.514824 GGACCCGAGATGCTTGGC 60.515 66.667 0.00 0.00 33.78 4.52
2738 3017 3.365265 CTGGTGGGTCCGCTTTGC 61.365 66.667 0.31 0.00 39.52 3.68
3097 3376 2.272146 GGGCCGCTCATCCAGAAA 59.728 61.111 0.00 0.00 0.00 2.52
3214 3493 1.985116 GGACGTTGAGGAGGAGGCT 60.985 63.158 0.00 0.00 0.00 4.58
3359 3644 2.743928 CTGCGGAAGAAGCGGCTT 60.744 61.111 16.36 16.36 37.44 4.35
3548 3833 2.520741 CGGAGGAGGAGGAGGAGC 60.521 72.222 0.00 0.00 0.00 4.70
3640 3925 1.068748 TCTAGCGCGACGAAGAAAAGT 60.069 47.619 12.10 0.00 0.00 2.66
3761 4046 0.396001 AGGAGGGAGGAAGTAGTCGC 60.396 60.000 0.00 0.00 0.00 5.19
3799 4084 5.386924 AGTAGATGTAGCCGGTAGAGATTT 58.613 41.667 1.90 0.00 0.00 2.17
3800 4085 6.540995 AGTAGATGTAGCCGGTAGAGATTTA 58.459 40.000 1.90 0.00 0.00 1.40
3801 4086 5.708877 AGATGTAGCCGGTAGAGATTTAC 57.291 43.478 1.90 0.00 0.00 2.01
3802 4087 3.976793 TGTAGCCGGTAGAGATTTACG 57.023 47.619 1.90 0.00 0.00 3.18
3803 4088 3.282021 TGTAGCCGGTAGAGATTTACGT 58.718 45.455 1.90 0.00 0.00 3.57
3811 4096 5.438972 CGGTAGAGATTTACGTGTACTAGC 58.561 45.833 0.00 2.74 0.00 3.42
3819 4104 7.649973 AGATTTACGTGTACTAGCATTAGGAG 58.350 38.462 0.00 0.00 0.00 3.69
3821 4106 3.894759 ACGTGTACTAGCATTAGGAGGA 58.105 45.455 0.00 0.00 0.00 3.71
3822 4107 4.275810 ACGTGTACTAGCATTAGGAGGAA 58.724 43.478 0.00 0.00 0.00 3.36
3823 4108 4.338682 ACGTGTACTAGCATTAGGAGGAAG 59.661 45.833 0.00 0.00 0.00 3.46
3824 4109 4.338682 CGTGTACTAGCATTAGGAGGAAGT 59.661 45.833 0.00 0.00 0.00 3.01
3825 4110 5.593010 GTGTACTAGCATTAGGAGGAAGTG 58.407 45.833 0.00 0.00 0.00 3.16
3826 4111 5.360144 GTGTACTAGCATTAGGAGGAAGTGA 59.640 44.000 0.00 0.00 0.00 3.41
3827 4112 6.041069 GTGTACTAGCATTAGGAGGAAGTGAT 59.959 42.308 0.00 0.00 0.00 3.06
3928 4223 4.920640 ATCGGACTAACAGATCGAATGT 57.079 40.909 1.05 1.05 33.53 2.71
3932 4227 3.791887 GGACTAACAGATCGAATGTCGTG 59.208 47.826 7.06 4.11 41.35 4.35
3934 4229 2.078849 AACAGATCGAATGTCGTGCA 57.921 45.000 7.06 0.00 41.35 4.57
4017 4367 2.484594 GGTCAGGAGCAAAGGATAGAGC 60.485 54.545 0.00 0.00 0.00 4.09
4021 4371 1.346068 GGAGCAAAGGATAGAGCGGAT 59.654 52.381 0.00 0.00 0.00 4.18
4053 4403 4.434330 CGACGACCTCTGAAATAAGCAAAC 60.434 45.833 0.00 0.00 0.00 2.93
4060 4410 4.783242 TCTGAAATAAGCAAACGCAACTC 58.217 39.130 0.00 0.00 0.00 3.01
4061 4411 4.515191 TCTGAAATAAGCAAACGCAACTCT 59.485 37.500 0.00 0.00 0.00 3.24
4062 4412 5.008613 TCTGAAATAAGCAAACGCAACTCTT 59.991 36.000 0.00 0.00 0.00 2.85
4106 4456 4.231753 CGTAGTTTGGCGACGTCA 57.768 55.556 17.16 0.00 40.50 4.35
4134 5792 4.806225 CGACACGCAAAGAGCAAG 57.194 55.556 0.00 0.00 46.13 4.01
4135 5793 1.205064 CGACACGCAAAGAGCAAGG 59.795 57.895 0.00 0.00 46.13 3.61
4136 5794 1.081840 GACACGCAAAGAGCAAGGC 60.082 57.895 0.00 0.00 46.13 4.35
4137 5795 2.256461 CACGCAAAGAGCAAGGCC 59.744 61.111 0.00 0.00 46.13 5.19
4139 5797 4.107051 CGCAAAGAGCAAGGCCGG 62.107 66.667 0.00 0.00 46.13 6.13
4140 5798 2.985847 GCAAAGAGCAAGGCCGGT 60.986 61.111 1.90 0.00 44.79 5.28
4141 5799 2.982744 GCAAAGAGCAAGGCCGGTC 61.983 63.158 0.00 0.00 44.79 4.79
4142 5800 1.600636 CAAAGAGCAAGGCCGGTCA 60.601 57.895 9.71 0.00 35.83 4.02
4143 5801 0.962356 CAAAGAGCAAGGCCGGTCAT 60.962 55.000 9.71 0.00 35.83 3.06
4144 5802 0.678048 AAAGAGCAAGGCCGGTCATC 60.678 55.000 9.71 0.00 35.83 2.92
4159 5826 3.624777 GGTCATCCAGTGGATCAAACAT 58.375 45.455 22.36 0.00 40.98 2.71
4226 5919 2.261671 CTCGTTCGTCCCCACTGG 59.738 66.667 0.00 0.00 0.00 4.00
4236 5929 2.452064 CCCCACTGGTGTGAGGTGT 61.452 63.158 0.00 0.00 46.55 4.16
4237 5930 1.125093 CCCCACTGGTGTGAGGTGTA 61.125 60.000 0.00 0.00 46.55 2.90
4268 6035 4.065110 GGCATAGCCGGGATTCAC 57.935 61.111 2.18 0.00 39.62 3.18
4290 6059 4.168760 CCAAGCTCCTTATTTTTCAAGCG 58.831 43.478 0.00 0.00 34.99 4.68
4313 6082 0.035439 ATACAAAGGGCACGTCTGGG 60.035 55.000 0.00 0.00 0.00 4.45
4329 6106 1.078637 GGGAGGTAACAACTCGCCC 60.079 63.158 0.00 0.00 40.74 6.13
4335 6112 0.887387 GTAACAACTCGCCCTTGCCA 60.887 55.000 0.00 0.00 0.00 4.92
4336 6113 0.887387 TAACAACTCGCCCTTGCCAC 60.887 55.000 0.00 0.00 0.00 5.01
4337 6114 2.594303 CAACTCGCCCTTGCCACA 60.594 61.111 0.00 0.00 0.00 4.17
4338 6115 1.973281 CAACTCGCCCTTGCCACAT 60.973 57.895 0.00 0.00 0.00 3.21
4342 6119 2.045438 CGCCCTTGCCACATACCA 60.045 61.111 0.00 0.00 0.00 3.25
4373 6150 2.813042 GCTCACAGCAGCGACCTC 60.813 66.667 0.00 0.00 41.89 3.85
4420 6197 4.570663 CCGGGTGATCTCGGCGAC 62.571 72.222 4.99 0.00 39.78 5.19
4487 6264 0.299895 GCATCTCGATCACGTGCTTG 59.700 55.000 11.67 5.33 40.69 4.01
4572 6352 4.325741 CGCACACAACACTTGAATTCAAAA 59.674 37.500 20.82 0.94 35.15 2.44
4594 6374 0.040514 TTTTCGGTTCTGCATGCACG 60.041 50.000 18.46 18.85 0.00 5.34
4609 6389 1.129326 GCACGATGCGTATGTACTCC 58.871 55.000 0.00 0.00 38.32 3.85
4610 6390 1.767289 CACGATGCGTATGTACTCCC 58.233 55.000 0.00 0.00 38.32 4.30
4611 6391 1.337071 CACGATGCGTATGTACTCCCT 59.663 52.381 0.00 0.00 38.32 4.20
4612 6392 1.607628 ACGATGCGTATGTACTCCCTC 59.392 52.381 0.00 0.00 38.73 4.30
4613 6393 1.068472 CGATGCGTATGTACTCCCTCC 60.068 57.143 0.00 0.00 0.00 4.30
4614 6394 0.959553 ATGCGTATGTACTCCCTCCG 59.040 55.000 0.00 0.00 0.00 4.63
4615 6395 0.394762 TGCGTATGTACTCCCTCCGT 60.395 55.000 0.00 0.00 0.00 4.69
4616 6396 0.743097 GCGTATGTACTCCCTCCGTT 59.257 55.000 0.00 0.00 0.00 4.44
4617 6397 1.268948 GCGTATGTACTCCCTCCGTTC 60.269 57.143 0.00 0.00 0.00 3.95
4618 6398 1.336125 CGTATGTACTCCCTCCGTTCC 59.664 57.143 0.00 0.00 0.00 3.62
4619 6399 2.664015 GTATGTACTCCCTCCGTTCCT 58.336 52.381 0.00 0.00 0.00 3.36
4620 6400 3.745480 CGTATGTACTCCCTCCGTTCCTA 60.745 52.174 0.00 0.00 0.00 2.94
4621 6401 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
4622 6402 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
4623 6403 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
4624 6404 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
4625 6405 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
4626 6406 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
4627 6407 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4628 6408 7.564660 TGTACTCCCTCCGTTCCTAAATATTTA 59.435 37.037 7.66 7.66 0.00 1.40
4629 6409 7.628501 ACTCCCTCCGTTCCTAAATATTTAT 57.371 36.000 8.34 0.00 0.00 1.40
4630 6410 7.677892 ACTCCCTCCGTTCCTAAATATTTATC 58.322 38.462 8.34 0.61 0.00 1.75
4631 6411 7.513091 ACTCCCTCCGTTCCTAAATATTTATCT 59.487 37.037 8.34 0.00 0.00 1.98
4632 6412 8.271398 TCCCTCCGTTCCTAAATATTTATCTT 57.729 34.615 8.34 0.00 0.00 2.40
4633 6413 8.720537 TCCCTCCGTTCCTAAATATTTATCTTT 58.279 33.333 8.34 0.00 0.00 2.52
4634 6414 9.350951 CCCTCCGTTCCTAAATATTTATCTTTT 57.649 33.333 8.34 0.00 0.00 2.27
4662 6442 9.302345 AGATATTTCAACAAGTGACTACATACG 57.698 33.333 0.00 0.00 35.39 3.06
4663 6443 9.297586 GATATTTCAACAAGTGACTACATACGA 57.702 33.333 0.00 0.00 35.39 3.43
4664 6444 7.956420 ATTTCAACAAGTGACTACATACGAA 57.044 32.000 0.00 0.00 35.39 3.85
4665 6445 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
4666 6446 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
4667 6447 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
4668 6448 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
4669 6449 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
4670 6450 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
4671 6451 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
4672 6452 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
4673 6453 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
4674 6454 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
4675 6455 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
4676 6456 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
4677 6457 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
4678 6458 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
4679 6459 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
4680 6460 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
4681 6461 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
4682 6462 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
4683 6463 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
4684 6464 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
4685 6465 6.372659 ACGAAGCAAAATGAGTGAATCTACAT 59.627 34.615 0.00 0.00 0.00 2.29
4686 6466 7.094634 ACGAAGCAAAATGAGTGAATCTACATT 60.095 33.333 0.00 0.00 34.99 2.71
4687 6467 7.427606 CGAAGCAAAATGAGTGAATCTACATTC 59.572 37.037 0.00 0.00 39.24 2.67
4688 6468 7.934855 AGCAAAATGAGTGAATCTACATTCT 57.065 32.000 0.00 0.00 39.49 2.40
4689 6469 9.453572 AAGCAAAATGAGTGAATCTACATTCTA 57.546 29.630 0.00 0.00 39.49 2.10
4690 6470 9.453572 AGCAAAATGAGTGAATCTACATTCTAA 57.546 29.630 0.00 0.00 39.49 2.10
4709 6489 9.261180 CATTCTAAAATGTCTACATACATCCGT 57.739 33.333 0.00 0.00 39.16 4.69
4722 6502 5.838529 CATACATCCGTATGTGGTAGTTCA 58.161 41.667 3.56 0.00 46.70 3.18
4723 6503 6.455647 CATACATCCGTATGTGGTAGTTCAT 58.544 40.000 3.56 0.00 46.70 2.57
4724 6504 5.353394 ACATCCGTATGTGGTAGTTCATT 57.647 39.130 0.00 0.00 44.79 2.57
4725 6505 5.741011 ACATCCGTATGTGGTAGTTCATTT 58.259 37.500 0.00 0.00 44.79 2.32
4726 6506 5.584649 ACATCCGTATGTGGTAGTTCATTTG 59.415 40.000 0.00 0.00 44.79 2.32
4727 6507 5.408880 TCCGTATGTGGTAGTTCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
4728 6508 5.795972 TCCGTATGTGGTAGTTCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
4729 6509 6.231951 TCCGTATGTGGTAGTTCATTTGAAA 58.768 36.000 0.00 0.00 35.58 2.69
4730 6510 6.882140 TCCGTATGTGGTAGTTCATTTGAAAT 59.118 34.615 0.00 0.00 35.58 2.17
4731 6511 6.966632 CCGTATGTGGTAGTTCATTTGAAATG 59.033 38.462 11.54 11.54 35.58 2.32
4732 6512 7.148323 CCGTATGTGGTAGTTCATTTGAAATGA 60.148 37.037 16.04 16.04 35.58 2.57
4733 6513 7.692291 CGTATGTGGTAGTTCATTTGAAATGAC 59.308 37.037 19.30 14.13 35.58 3.06
4734 6514 7.765695 ATGTGGTAGTTCATTTGAAATGACT 57.234 32.000 19.30 19.29 35.58 3.41
4735 6515 8.862325 ATGTGGTAGTTCATTTGAAATGACTA 57.138 30.769 19.30 18.45 35.58 2.59
4736 6516 8.322906 TGTGGTAGTTCATTTGAAATGACTAG 57.677 34.615 19.30 0.00 35.58 2.57
4737 6517 8.154203 TGTGGTAGTTCATTTGAAATGACTAGA 58.846 33.333 19.30 3.16 35.58 2.43
4738 6518 8.999431 GTGGTAGTTCATTTGAAATGACTAGAA 58.001 33.333 19.30 11.63 35.58 2.10
4739 6519 9.567776 TGGTAGTTCATTTGAAATGACTAGAAA 57.432 29.630 19.30 2.08 35.58 2.52
4743 6523 9.342308 AGTTCATTTGAAATGACTAGAAAGACA 57.658 29.630 19.30 0.00 35.58 3.41
4744 6524 9.950680 GTTCATTTGAAATGACTAGAAAGACAA 57.049 29.630 19.30 0.00 35.58 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.506437 CAAAGAAGCATCTTACTGTGTTGATTA 58.494 33.333 4.34 0.00 45.19 1.75
50 51 6.810911 ACTGCAGGTATCTAGTGAGTATTTG 58.189 40.000 19.93 0.00 0.00 2.32
52 53 8.713708 AATACTGCAGGTATCTAGTGAGTATT 57.286 34.615 19.93 6.04 39.94 1.89
53 54 8.713708 AAATACTGCAGGTATCTAGTGAGTAT 57.286 34.615 19.93 0.00 39.94 2.12
60 61 8.184304 ACTCCTTAAATACTGCAGGTATCTAG 57.816 38.462 19.93 8.25 39.94 2.43
63 64 5.921408 CGACTCCTTAAATACTGCAGGTATC 59.079 44.000 19.93 0.31 39.94 2.24
68 69 4.210120 GCATCGACTCCTTAAATACTGCAG 59.790 45.833 13.48 13.48 0.00 4.41
190 305 9.585099 GTCAGACCAATATTTGCATCAATTTTA 57.415 29.630 0.00 0.00 0.00 1.52
241 356 9.811995 AGTTTTAAACCAACTGTTCCTAAAATC 57.188 29.630 4.01 0.00 34.29 2.17
268 384 5.749109 GTGAATTCAGGATTCTAGTACACCG 59.251 44.000 8.80 0.00 43.74 4.94
308 425 5.694910 GTGAAGGAGTGAAGACGAAATTGTA 59.305 40.000 0.00 0.00 0.00 2.41
309 426 4.511826 GTGAAGGAGTGAAGACGAAATTGT 59.488 41.667 0.00 0.00 0.00 2.71
310 427 4.083802 GGTGAAGGAGTGAAGACGAAATTG 60.084 45.833 0.00 0.00 0.00 2.32
311 428 4.065789 GGTGAAGGAGTGAAGACGAAATT 58.934 43.478 0.00 0.00 0.00 1.82
312 429 3.557264 GGGTGAAGGAGTGAAGACGAAAT 60.557 47.826 0.00 0.00 0.00 2.17
314 431 1.343465 GGGTGAAGGAGTGAAGACGAA 59.657 52.381 0.00 0.00 0.00 3.85
315 432 0.966920 GGGTGAAGGAGTGAAGACGA 59.033 55.000 0.00 0.00 0.00 4.20
316 433 0.679505 TGGGTGAAGGAGTGAAGACG 59.320 55.000 0.00 0.00 0.00 4.18
317 434 1.971357 TCTGGGTGAAGGAGTGAAGAC 59.029 52.381 0.00 0.00 0.00 3.01
327 444 4.022849 GGTCAATCTTTGTTCTGGGTGAAG 60.023 45.833 0.00 0.00 35.01 3.02
332 449 2.504367 ACGGTCAATCTTTGTTCTGGG 58.496 47.619 0.00 0.00 0.00 4.45
350 467 6.801862 TGAATCTACGAATGTGCATATCTACG 59.198 38.462 12.92 12.92 0.00 3.51
361 478 3.884895 TGGCCAATGAATCTACGAATGT 58.115 40.909 0.61 0.00 0.00 2.71
362 479 6.558771 TTATGGCCAATGAATCTACGAATG 57.441 37.500 10.96 0.00 0.00 2.67
364 481 6.375736 TGTTTTATGGCCAATGAATCTACGAA 59.624 34.615 10.96 0.00 0.00 3.85
378 495 1.204704 GCAACCTCCTGTTTTATGGCC 59.795 52.381 0.00 0.00 34.00 5.36
381 498 3.913089 GGTTGCAACCTCCTGTTTTATG 58.087 45.455 36.26 0.00 45.75 1.90
429 547 2.489971 CAAGCGGTGTCTCTTTGGTTA 58.510 47.619 0.00 0.00 0.00 2.85
437 555 0.598065 AATTTGGCAAGCGGTGTCTC 59.402 50.000 0.00 0.00 30.97 3.36
453 575 8.897752 GCTCAGAGTATGGAAACTATTTGAATT 58.102 33.333 0.00 0.00 0.00 2.17
463 585 3.895232 TGAGGCTCAGAGTATGGAAAC 57.105 47.619 14.43 0.00 0.00 2.78
535 682 7.095607 CGTCACTGAGCTAAACTGTCTAAAAAT 60.096 37.037 0.00 0.00 0.00 1.82
540 687 3.366070 GCGTCACTGAGCTAAACTGTCTA 60.366 47.826 0.00 0.00 0.00 2.59
541 688 2.608261 GCGTCACTGAGCTAAACTGTCT 60.608 50.000 0.00 0.00 0.00 3.41
543 690 1.784525 GCGTCACTGAGCTAAACTGT 58.215 50.000 0.00 0.00 0.00 3.55
627 774 0.039074 GATCACTGATCGGCCTACGG 60.039 60.000 0.00 0.00 44.45 4.02
631 778 1.406065 CCCTGATCACTGATCGGCCT 61.406 60.000 19.07 0.00 42.32 5.19
769 926 0.958382 CGGGCAATTTCTCCGTTCCA 60.958 55.000 0.00 0.00 39.04 3.53
771 928 1.136774 GCGGGCAATTTCTCCGTTC 59.863 57.895 11.09 0.00 44.97 3.95
1389 1566 7.327032 GGTTTTATCGGTTCGGATATACAGTAC 59.673 40.741 1.97 0.00 0.00 2.73
1390 1567 7.014134 TGGTTTTATCGGTTCGGATATACAGTA 59.986 37.037 1.97 0.00 0.00 2.74
1391 1568 6.183360 TGGTTTTATCGGTTCGGATATACAGT 60.183 38.462 1.97 0.00 0.00 3.55
1392 1569 6.145048 GTGGTTTTATCGGTTCGGATATACAG 59.855 42.308 1.97 0.00 0.00 2.74
1393 1570 5.984926 GTGGTTTTATCGGTTCGGATATACA 59.015 40.000 1.97 0.00 0.00 2.29
1494 1671 8.122952 AGTAAATAAATAAACATCGTGCTCTGC 58.877 33.333 0.00 0.00 0.00 4.26
1525 1702 4.028026 CCTGCGACAAGTAAAAACAAAACG 60.028 41.667 0.00 0.00 0.00 3.60
1543 1720 3.782244 GCTCTGCAACGTCCTGCG 61.782 66.667 7.66 3.35 45.74 5.18
1544 1721 2.180131 CTTGCTCTGCAACGTCCTGC 62.180 60.000 5.26 5.26 43.99 4.85
1890 2067 2.200373 TTTTTACCTGGCTCTCCTGC 57.800 50.000 0.00 0.00 0.00 4.85
1986 2168 3.354089 ACAGAAAGTTTTGACATGGCG 57.646 42.857 0.00 0.00 0.00 5.69
2004 2186 7.440856 CGTTTTTACCCCTAGTAACAGTAAACA 59.559 37.037 0.00 0.00 40.70 2.83
2012 2194 5.185828 TCTCCTCGTTTTTACCCCTAGTAAC 59.814 44.000 0.00 0.00 40.70 2.50
2057 2239 1.333619 TGCTTCGTGCTCTTTGGTTTC 59.666 47.619 5.00 0.00 43.37 2.78
2196 2434 3.896133 TCACGTAGATCGGGCGGC 61.896 66.667 0.00 0.00 43.41 6.53
2197 2435 2.025727 GTCACGTAGATCGGGCGG 59.974 66.667 10.34 0.00 43.41 6.13
2198 2436 2.025727 GGTCACGTAGATCGGGCG 59.974 66.667 0.00 5.36 43.41 6.13
2264 2510 4.157120 GGGTCCGTCCGTCATGGG 62.157 72.222 0.00 0.00 38.76 4.00
2265 2511 4.157120 GGGGTCCGTCCGTCATGG 62.157 72.222 0.00 0.00 37.00 3.66
2266 2512 2.731571 ATGGGGTCCGTCCGTCATG 61.732 63.158 0.00 0.00 37.00 3.07
2267 2513 2.365105 ATGGGGTCCGTCCGTCAT 60.365 61.111 0.00 0.00 37.00 3.06
2268 2514 3.387091 CATGGGGTCCGTCCGTCA 61.387 66.667 0.00 0.00 37.00 4.35
2269 2515 2.459202 AAACATGGGGTCCGTCCGTC 62.459 60.000 0.00 0.00 37.00 4.79
2270 2516 2.522367 AAACATGGGGTCCGTCCGT 61.522 57.895 0.00 0.00 37.00 4.69
2271 2517 2.038269 CAAACATGGGGTCCGTCCG 61.038 63.158 0.00 0.00 37.00 4.79
2272 2518 0.538746 AACAAACATGGGGTCCGTCC 60.539 55.000 0.00 0.00 0.00 4.79
2273 2519 0.596082 CAACAAACATGGGGTCCGTC 59.404 55.000 0.00 0.00 0.00 4.79
2274 2520 1.460273 GCAACAAACATGGGGTCCGT 61.460 55.000 0.00 0.00 0.00 4.69
2275 2521 1.178534 AGCAACAAACATGGGGTCCG 61.179 55.000 0.00 0.00 0.00 4.79
2276 2522 0.318120 CAGCAACAAACATGGGGTCC 59.682 55.000 0.00 0.00 0.00 4.46
2277 2523 1.039856 ACAGCAACAAACATGGGGTC 58.960 50.000 0.00 0.00 0.00 4.46
2278 2524 0.752054 CACAGCAACAAACATGGGGT 59.248 50.000 0.00 0.00 0.00 4.95
2279 2525 0.033781 CCACAGCAACAAACATGGGG 59.966 55.000 0.00 0.00 0.00 4.96
2302 2548 2.933287 CCACCTGGCCACCTACCA 60.933 66.667 0.00 0.00 35.40 3.25
2303 2549 3.728373 CCCACCTGGCCACCTACC 61.728 72.222 0.00 0.00 0.00 3.18
2305 2551 2.933287 CACCCACCTGGCCACCTA 60.933 66.667 0.00 0.00 37.83 3.08
2307 2553 4.974721 CACACCCACCTGGCCACC 62.975 72.222 0.00 0.00 37.83 4.61
2309 2555 2.448736 TACACACCCACCTGGCCA 60.449 61.111 4.71 4.71 37.83 5.36
2311 2557 2.359975 GCTACACACCCACCTGGC 60.360 66.667 0.00 0.00 37.83 4.85
2312 2558 1.003355 CTGCTACACACCCACCTGG 60.003 63.158 0.00 0.00 41.37 4.45
2313 2559 1.672356 GCTGCTACACACCCACCTG 60.672 63.158 0.00 0.00 0.00 4.00
2314 2560 1.843376 AGCTGCTACACACCCACCT 60.843 57.895 0.00 0.00 0.00 4.00
2315 2561 1.672356 CAGCTGCTACACACCCACC 60.672 63.158 0.00 0.00 0.00 4.61
2316 2562 2.328099 GCAGCTGCTACACACCCAC 61.328 63.158 31.33 0.00 38.21 4.61
2317 2563 2.032528 GCAGCTGCTACACACCCA 59.967 61.111 31.33 0.00 38.21 4.51
2449 2696 1.081376 ACGAGCTCGAACGAACAGG 60.081 57.895 40.58 9.75 43.02 4.00
2478 2725 5.560567 GCAGCAACTTTTCTCTCTTCTCTTG 60.561 44.000 0.00 0.00 0.00 3.02
2641 2913 1.386533 AAATCTGCCAAGCATCTCGG 58.613 50.000 0.00 0.00 38.13 4.63
2668 2943 7.623268 AAAAATCACAAATGAAAGCGTAGAC 57.377 32.000 0.00 0.00 38.69 2.59
3088 3367 0.172803 GCTTGGCAGCTTTCTGGATG 59.827 55.000 0.00 0.00 43.51 3.51
3169 3448 2.444140 GCGGCCTCCTCCTTCCTA 60.444 66.667 0.00 0.00 0.00 2.94
3214 3493 3.040414 CTTCTCGCCGTCGCTCTCA 62.040 63.158 0.00 0.00 35.26 3.27
3274 3553 0.967380 GGGTCTTCTTCGTCCCCGTA 60.967 60.000 0.00 0.00 34.32 4.02
3620 3905 1.068748 ACTTTTCTTCGTCGCGCTAGA 60.069 47.619 5.56 0.00 0.00 2.43
3761 4046 6.412362 ACATCTACTAAGCTACTCCAATGG 57.588 41.667 0.00 0.00 0.00 3.16
3799 4084 5.039920 TCCTCCTAATGCTAGTACACGTA 57.960 43.478 0.00 0.00 0.00 3.57
3800 4085 3.894759 TCCTCCTAATGCTAGTACACGT 58.105 45.455 0.00 0.00 0.00 4.49
3801 4086 4.338682 ACTTCCTCCTAATGCTAGTACACG 59.661 45.833 0.00 0.00 0.00 4.49
3802 4087 5.360144 TCACTTCCTCCTAATGCTAGTACAC 59.640 44.000 0.00 0.00 0.00 2.90
3803 4088 5.516044 TCACTTCCTCCTAATGCTAGTACA 58.484 41.667 0.00 0.00 0.00 2.90
3811 4096 5.163364 ACACAGCTATCACTTCCTCCTAATG 60.163 44.000 0.00 0.00 0.00 1.90
3819 4104 5.874810 TGATTTACACACAGCTATCACTTCC 59.125 40.000 0.00 0.00 0.00 3.46
3821 4106 6.881065 ACATGATTTACACACAGCTATCACTT 59.119 34.615 0.00 0.00 0.00 3.16
3822 4107 6.409704 ACATGATTTACACACAGCTATCACT 58.590 36.000 0.00 0.00 0.00 3.41
3823 4108 6.668541 ACATGATTTACACACAGCTATCAC 57.331 37.500 0.00 0.00 0.00 3.06
3824 4109 7.492344 CACTACATGATTTACACACAGCTATCA 59.508 37.037 0.00 0.00 0.00 2.15
3825 4110 7.492669 ACACTACATGATTTACACACAGCTATC 59.507 37.037 0.00 0.00 0.00 2.08
3826 4111 7.278646 CACACTACATGATTTACACACAGCTAT 59.721 37.037 0.00 0.00 0.00 2.97
3827 4112 6.589907 CACACTACATGATTTACACACAGCTA 59.410 38.462 0.00 0.00 0.00 3.32
3872 4167 3.570125 TCAGTTCAGTGGTGAGTGTCTAG 59.430 47.826 0.00 0.00 32.98 2.43
3999 4349 1.539929 CCGCTCTATCCTTTGCTCCTG 60.540 57.143 0.00 0.00 0.00 3.86
4017 4367 3.541831 CGTCGCGTGAACCATCCG 61.542 66.667 5.77 0.00 0.00 4.18
4021 4371 3.547249 GAGGTCGTCGCGTGAACCA 62.547 63.158 19.30 0.00 0.00 3.67
4069 4419 8.031848 ACTACGTTTCTTCACTAGACTAGAAG 57.968 38.462 16.55 10.25 39.98 2.85
4090 4440 1.771044 CGTGACGTCGCCAAACTAC 59.229 57.895 22.62 5.96 0.00 2.73
4132 5790 2.671070 CACTGGATGACCGGCCTT 59.329 61.111 0.00 0.00 45.88 4.35
4134 5792 2.666596 GATCCACTGGATGACCGGCC 62.667 65.000 15.78 0.00 43.27 6.13
4135 5793 1.227674 GATCCACTGGATGACCGGC 60.228 63.158 15.78 0.00 43.27 6.13
4136 5794 0.541392 TTGATCCACTGGATGACCGG 59.459 55.000 15.78 0.00 43.27 5.28
4137 5795 2.009774 GTTTGATCCACTGGATGACCG 58.990 52.381 15.78 0.00 43.27 4.79
4139 5797 6.757897 TTTATGTTTGATCCACTGGATGAC 57.242 37.500 15.78 11.08 43.27 3.06
4140 5798 9.473007 TTTATTTATGTTTGATCCACTGGATGA 57.527 29.630 15.78 3.94 43.27 2.92
4143 5801 9.473007 TGATTTATTTATGTTTGATCCACTGGA 57.527 29.630 0.00 0.00 35.55 3.86
4182 5856 8.571336 TGTGAGGTTTTGTAGTAGTAGTAGAAC 58.429 37.037 0.00 0.00 0.00 3.01
4183 5857 8.571336 GTGTGAGGTTTTGTAGTAGTAGTAGAA 58.429 37.037 0.00 0.00 0.00 2.10
4184 5858 7.941238 AGTGTGAGGTTTTGTAGTAGTAGTAGA 59.059 37.037 0.00 0.00 0.00 2.59
4185 5859 8.108551 AGTGTGAGGTTTTGTAGTAGTAGTAG 57.891 38.462 0.00 0.00 0.00 2.57
4186 5860 7.095060 CGAGTGTGAGGTTTTGTAGTAGTAGTA 60.095 40.741 0.00 0.00 0.00 1.82
4187 5861 6.293845 CGAGTGTGAGGTTTTGTAGTAGTAGT 60.294 42.308 0.00 0.00 0.00 2.73
4188 5862 6.084925 CGAGTGTGAGGTTTTGTAGTAGTAG 58.915 44.000 0.00 0.00 0.00 2.57
4190 5864 4.340381 ACGAGTGTGAGGTTTTGTAGTAGT 59.660 41.667 0.00 0.00 0.00 2.73
4268 6035 4.168760 CGCTTGAAAAATAAGGAGCTTGG 58.831 43.478 0.00 0.00 0.00 3.61
4290 6059 0.096454 GACGTGCCCTTTGTATTCGC 59.904 55.000 0.00 0.00 0.00 4.70
4313 6082 1.439679 CAAGGGCGAGTTGTTACCTC 58.560 55.000 0.00 0.00 0.00 3.85
4329 6106 1.796151 CGTGCTGGTATGTGGCAAG 59.204 57.895 0.00 0.00 37.73 4.01
4335 6112 0.391130 ATTCGTGCGTGCTGGTATGT 60.391 50.000 0.00 0.00 0.00 2.29
4336 6113 0.026674 CATTCGTGCGTGCTGGTATG 59.973 55.000 0.00 0.00 0.00 2.39
4337 6114 1.089481 CCATTCGTGCGTGCTGGTAT 61.089 55.000 0.00 0.00 0.00 2.73
4338 6115 1.739929 CCATTCGTGCGTGCTGGTA 60.740 57.895 0.00 0.00 0.00 3.25
4342 6119 3.121030 GAGCCATTCGTGCGTGCT 61.121 61.111 0.00 0.00 34.40 4.40
4462 6239 1.203928 CGTGATCGAGATGCTGAACC 58.796 55.000 0.00 0.00 39.71 3.62
4594 6374 1.068472 CGGAGGGAGTACATACGCATC 60.068 57.143 0.00 0.00 0.00 3.91
4601 6381 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
4602 6382 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
4607 6387 7.867160 AGATAAATATTTAGGAACGGAGGGA 57.133 36.000 13.15 0.00 0.00 4.20
4608 6388 8.919777 AAAGATAAATATTTAGGAACGGAGGG 57.080 34.615 13.15 0.00 0.00 4.30
4636 6416 9.302345 CGTATGTAGTCACTTGTTGAAATATCT 57.698 33.333 0.00 0.00 35.39 1.98
4637 6417 9.297586 TCGTATGTAGTCACTTGTTGAAATATC 57.702 33.333 0.00 0.00 35.39 1.63
4638 6418 9.647797 TTCGTATGTAGTCACTTGTTGAAATAT 57.352 29.630 0.00 0.00 35.39 1.28
4639 6419 9.135843 CTTCGTATGTAGTCACTTGTTGAAATA 57.864 33.333 0.00 0.00 35.39 1.40
4640 6420 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
4641 6421 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
4642 6422 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
4643 6423 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
4644 6424 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
4645 6425 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
4646 6426 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
4647 6427 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
4648 6428 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
4649 6429 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
4650 6430 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
4651 6431 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
4652 6432 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
4653 6433 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
4654 6434 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
4655 6435 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
4656 6436 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
4657 6437 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
4658 6438 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
4659 6439 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
4660 6440 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
4661 6441 6.169419 TGTAGATTCACTCATTTTGCTTCG 57.831 37.500 0.00 0.00 0.00 3.79
4662 6442 8.457261 AGAATGTAGATTCACTCATTTTGCTTC 58.543 33.333 14.46 0.00 40.59 3.86
4663 6443 8.345724 AGAATGTAGATTCACTCATTTTGCTT 57.654 30.769 14.46 0.00 40.59 3.91
4664 6444 7.934855 AGAATGTAGATTCACTCATTTTGCT 57.065 32.000 14.46 0.00 40.59 3.91
4683 6463 9.261180 ACGGATGTATGTAGACATTTTAGAATG 57.739 33.333 4.50 4.50 46.47 2.67
4700 6480 6.665992 ATGAACTACCACATACGGATGTAT 57.334 37.500 14.23 7.46 44.82 2.29
4701 6481 6.474140 AATGAACTACCACATACGGATGTA 57.526 37.500 14.23 0.00 44.82 2.29
4703 6483 5.815222 TCAAATGAACTACCACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
4704 6484 5.984725 TCAAATGAACTACCACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
4705 6485 5.408880 TCAAATGAACTACCACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
4706 6486 6.489127 TTTCAAATGAACTACCACATACGG 57.511 37.500 0.00 0.00 33.13 4.02
4707 6487 7.692291 GTCATTTCAAATGAACTACCACATACG 59.308 37.037 14.56 0.00 33.13 3.06
4708 6488 8.730680 AGTCATTTCAAATGAACTACCACATAC 58.269 33.333 14.56 0.00 33.13 2.39
4709 6489 8.862325 AGTCATTTCAAATGAACTACCACATA 57.138 30.769 14.56 0.00 33.13 2.29
4710 6490 7.765695 AGTCATTTCAAATGAACTACCACAT 57.234 32.000 14.56 0.00 33.13 3.21
4711 6491 8.154203 TCTAGTCATTTCAAATGAACTACCACA 58.846 33.333 14.56 0.00 33.13 4.17
4712 6492 8.547967 TCTAGTCATTTCAAATGAACTACCAC 57.452 34.615 14.56 1.36 33.13 4.16
4713 6493 9.567776 TTTCTAGTCATTTCAAATGAACTACCA 57.432 29.630 14.56 4.29 33.13 3.25
4717 6497 9.342308 TGTCTTTCTAGTCATTTCAAATGAACT 57.658 29.630 14.56 15.00 33.13 3.01
4718 6498 9.950680 TTGTCTTTCTAGTCATTTCAAATGAAC 57.049 29.630 14.56 7.28 33.13 3.18


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

AutoCloner maintained by Alex Coulton.