Multiple sequence alignment - TraesCS4D01G258800

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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 TraesCS4D01G258800 chr4D 100.000 6788 0 0 1 6788 428570900 428577687 0.000000e+00 12536.0
1 TraesCS4D01G258800 chr4A 92.289 4072 185 59 2465 6470 37822181 37818173 0.000000e+00 5661.0
2 TraesCS4D01G258800 chr4A 90.756 2196 138 26 2 2145 37824881 37822699 0.000000e+00 2870.0
3 TraesCS4D01G258800 chr4A 94.895 333 11 3 2145 2471 37822670 37822338 3.630000e-142 516.0
4 TraesCS4D01G258800 chr4B 91.743 2398 114 35 4420 6755 526947418 526945043 0.000000e+00 3254.0
5 TraesCS4D01G258800 chr4B 88.854 2207 139 44 2 2145 526952134 526949972 0.000000e+00 2614.0
6 TraesCS4D01G258800 chr4B 92.717 1373 57 19 3073 4419 526948846 526947491 0.000000e+00 1941.0
7 TraesCS4D01G258800 chr4B 93.624 941 49 6 2145 3077 526949941 526949004 0.000000e+00 1395.0
8 TraesCS4D01G258800 chr3D 96.875 32 1 0 6444 6475 299598529 299598560 3.000000e-03 54.7
9 TraesCS4D01G258800 chr3D 100.000 28 0 0 6448 6475 537914045 537914072 1.200000e-02 52.8
10 TraesCS4D01G258800 chr6B 100.000 28 0 0 6450 6477 605798778 605798805 1.200000e-02 52.8
11 TraesCS4D01G258800 chr5D 100.000 28 0 0 6448 6475 485358237 485358210 1.200000e-02 52.8
12 TraesCS4D01G258800 chr2B 100.000 28 0 0 6448 6475 88176788 88176761 1.200000e-02 52.8


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 TraesCS4D01G258800 chr4D 428570900 428577687 6787 False 12536.000000 12536 100.000000 1 6788 1 chr4D.!!$F1 6787
1 TraesCS4D01G258800 chr4A 37818173 37824881 6708 True 3015.666667 5661 92.646667 2 6470 3 chr4A.!!$R1 6468
2 TraesCS4D01G258800 chr4B 526945043 526952134 7091 True 2301.000000 3254 91.734500 2 6755 4 chr4B.!!$R1 6753

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
602 611 0.036388 TGTTGGGCTTCTCATCGTCC 60.036 55.000 0.00 0.00 0.00 4.79 F
703 737 0.116541 AGGAAGGGGAACTCGAAGGA 59.883 55.000 0.00 0.00 0.00 3.36 F
1601 1657 0.107752 TATGCAAGCATCCAGTCGCA 60.108 50.000 11.32 0.00 37.82 5.10 F
2519 2796 0.659957 GATGCGCCAAGGCTCTTTAG 59.340 55.000 4.18 0.00 39.32 1.85 F
2984 3263 0.737219 GCTTGCATGTGGATCACCTC 59.263 55.000 1.14 0.00 37.04 3.85 F
3401 3842 1.242076 AGCTTGCGACTCATTTTGCT 58.758 45.000 0.00 0.00 0.00 3.91 F
4409 4876 1.066908 ACCACACTGGAAAATTGCGTG 59.933 47.619 0.00 7.61 40.96 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 1654 1.085091 ATTCTTGCTCAAGCTCTGCG 58.915 50.000 3.32 0.00 42.66 5.18 R
2318 2428 1.135141 GCAGGCGGCATATCTAGAGAG 60.135 57.143 13.08 0.00 43.97 3.20 R
2904 3181 1.001974 TGGTACTGAGTGGCATGACAC 59.998 52.381 24.86 24.86 41.63 3.67 R
3813 4273 0.112218 AACCCATACAGCAGCCAACA 59.888 50.000 0.00 0.00 0.00 3.33 R
3845 4305 0.618680 ACAGTGATCCTGCCTAGCCA 60.619 55.000 0.00 0.00 45.68 4.75 R
4914 5478 1.003118 TCCCAACCTGCAGTACATCAC 59.997 52.381 13.81 0.00 0.00 3.06 R
6278 6853 0.387622 CACCAATTGCCAGCTCAACG 60.388 55.000 0.00 0.00 0.00 4.10 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.844257 CTCTTAATTCATCTAGGGTGAGATTTT 57.156 33.333 0.00 0.00 33.75 1.82
51 52 3.445008 TCTCTCAAGTTCCCACTGCTAT 58.555 45.455 0.00 0.00 31.60 2.97
55 56 4.041567 TCTCAAGTTCCCACTGCTATTTCA 59.958 41.667 0.00 0.00 31.60 2.69
60 61 2.422597 TCCCACTGCTATTTCACAACG 58.577 47.619 0.00 0.00 0.00 4.10
61 62 2.037902 TCCCACTGCTATTTCACAACGA 59.962 45.455 0.00 0.00 0.00 3.85
62 63 2.159627 CCCACTGCTATTTCACAACGAC 59.840 50.000 0.00 0.00 0.00 4.34
63 64 2.805671 CCACTGCTATTTCACAACGACA 59.194 45.455 0.00 0.00 0.00 4.35
64 65 3.436704 CCACTGCTATTTCACAACGACAT 59.563 43.478 0.00 0.00 0.00 3.06
65 66 4.629634 CCACTGCTATTTCACAACGACATA 59.370 41.667 0.00 0.00 0.00 2.29
66 67 5.445939 CCACTGCTATTTCACAACGACATAC 60.446 44.000 0.00 0.00 0.00 2.39
68 69 3.061563 TGCTATTTCACAACGACATACGC 59.938 43.478 0.00 0.00 46.94 4.42
76 77 5.555552 TCACAACGACATACGCAAAATATG 58.444 37.500 0.00 0.00 46.94 1.78
127 128 2.557452 CCTAATGCCCCAACAAACTCCT 60.557 50.000 0.00 0.00 0.00 3.69
130 131 0.821711 TGCCCCAACAAACTCCTTCG 60.822 55.000 0.00 0.00 0.00 3.79
153 154 4.223032 GTGTACTCTCATTCCCTTTCTCCA 59.777 45.833 0.00 0.00 0.00 3.86
160 161 6.848069 TCTCATTCCCTTTCTCCAAAGTAAA 58.152 36.000 0.00 0.00 37.87 2.01
225 232 3.118519 CCACCTTTGTACTTACCGGCTAT 60.119 47.826 0.00 0.00 0.00 2.97
252 259 6.537301 CCGTGCTATGTTACTTCTAATTCCAA 59.463 38.462 0.00 0.00 0.00 3.53
258 265 5.302360 TGTTACTTCTAATTCCAACACGCT 58.698 37.500 0.00 0.00 0.00 5.07
266 273 0.388134 TTCCAACACGCTACGAGCTC 60.388 55.000 2.73 2.73 39.60 4.09
279 286 4.316823 AGCTCGTGACCTCCCCCA 62.317 66.667 0.00 0.00 0.00 4.96
302 310 2.663188 GCGATGGGACGGAGATGC 60.663 66.667 0.00 0.00 0.00 3.91
354 362 5.554822 TTCGCTACTTTTAAATTCGCCAT 57.445 34.783 0.00 0.00 0.00 4.40
388 396 4.142881 GGATAACGAAACAGGTGCTCTTTC 60.143 45.833 0.00 0.00 0.00 2.62
402 411 0.952010 TCTTTCGGTTGGCGTTAGGC 60.952 55.000 0.00 0.00 44.11 3.93
426 435 2.672996 CCTCCGCCTTGGTTGTGG 60.673 66.667 0.00 0.00 39.52 4.17
427 436 2.113139 CTCCGCCTTGGTTGTGGT 59.887 61.111 0.00 0.00 39.52 4.16
439 448 2.708861 TGGTTGTGGTGAGTAGATTGGT 59.291 45.455 0.00 0.00 0.00 3.67
489 498 8.355169 AGACGACACATTACACTACTTCTAAAA 58.645 33.333 0.00 0.00 0.00 1.52
494 503 8.208903 ACACATTACACTACTTCTAAAACCACT 58.791 33.333 0.00 0.00 0.00 4.00
501 510 2.063266 CTTCTAAAACCACTACGCGCA 58.937 47.619 5.73 0.00 0.00 6.09
502 511 2.151881 TCTAAAACCACTACGCGCAA 57.848 45.000 5.73 0.00 0.00 4.85
509 518 0.527600 CCACTACGCGCAAGAGCATA 60.528 55.000 15.24 0.00 42.78 3.14
515 524 2.550978 ACGCGCAAGAGCATAATAACT 58.449 42.857 5.73 0.00 42.78 2.24
534 543 3.505808 GAAGACGCTCTTCTGTGCT 57.494 52.632 15.92 0.00 46.98 4.40
535 544 2.638556 GAAGACGCTCTTCTGTGCTA 57.361 50.000 15.92 0.00 46.98 3.49
549 558 2.043248 GCTACGTCAGGGGAGGGA 60.043 66.667 0.00 0.00 33.26 4.20
553 562 1.807771 TACGTCAGGGGAGGGACCTT 61.808 60.000 0.00 0.00 35.78 3.50
554 563 1.918800 CGTCAGGGGAGGGACCTTT 60.919 63.158 0.00 0.00 35.78 3.11
601 610 1.936547 GATGTTGGGCTTCTCATCGTC 59.063 52.381 0.00 0.00 0.00 4.20
602 611 0.036388 TGTTGGGCTTCTCATCGTCC 60.036 55.000 0.00 0.00 0.00 4.79
604 613 0.250234 TTGGGCTTCTCATCGTCCAG 59.750 55.000 0.00 0.00 0.00 3.86
607 616 1.139853 GGGCTTCTCATCGTCCAGAAT 59.860 52.381 0.00 0.00 0.00 2.40
684 693 2.131709 CCCTTCCACGGGCTATCGA 61.132 63.158 0.00 0.00 37.41 3.59
687 696 1.076559 TTCCACGGGCTATCGAGGA 60.077 57.895 8.89 8.89 45.37 3.71
688 697 1.076559 TCCACGGGCTATCGAGGAA 60.077 57.895 10.05 0.00 44.42 3.36
689 698 1.107538 TCCACGGGCTATCGAGGAAG 61.108 60.000 10.05 0.00 44.42 3.46
703 737 0.116541 AGGAAGGGGAACTCGAAGGA 59.883 55.000 0.00 0.00 0.00 3.36
725 759 4.209307 AGAGCAAAAGTAAGCTACTCCC 57.791 45.455 0.00 0.00 42.04 4.30
738 772 0.469331 TACTCCCTCCGATCCGCAAT 60.469 55.000 0.00 0.00 0.00 3.56
800 839 6.323203 TCTTAAACTTGACGCTACTACTGT 57.677 37.500 0.00 0.00 0.00 3.55
804 843 9.435802 CTTAAACTTGACGCTACTACTGTATAG 57.564 37.037 0.00 0.00 0.00 1.31
962 1015 4.038804 CCCCTCCCCTTCTCCCCA 62.039 72.222 0.00 0.00 0.00 4.96
1149 1202 2.420568 CCCTAGAACCCTACGCGCA 61.421 63.158 5.73 0.00 0.00 6.09
1191 1245 2.033194 CCCCTTGTTTCGAGCGGTC 61.033 63.158 4.06 4.06 0.00 4.79
1367 1421 3.767630 GACCGCACCACCACCAAGT 62.768 63.158 0.00 0.00 0.00 3.16
1451 1505 2.042404 TAGGGTGCGACGGTTTGGTT 62.042 55.000 0.00 0.00 0.00 3.67
1483 1539 8.272173 AGCCTTTTTAGGTCTTGTATATAAGCA 58.728 33.333 4.43 0.00 0.00 3.91
1496 1552 8.918202 TTGTATATAAGCATTTTAGGACCTGG 57.082 34.615 3.53 0.00 0.00 4.45
1505 1561 5.279456 GCATTTTAGGACCTGGTGATTGTTT 60.279 40.000 2.82 0.00 0.00 2.83
1598 1654 5.818136 TTTTACTATGCAAGCATCCAGTC 57.182 39.130 11.32 0.00 37.82 3.51
1601 1657 0.107752 TATGCAAGCATCCAGTCGCA 60.108 50.000 11.32 0.00 37.82 5.10
1662 1719 0.914902 AGGGAGTTGAGGGGGCTAAC 60.915 60.000 0.00 0.00 0.00 2.34
1702 1759 4.391155 TGGACAAGCGTTTATAAGTTGGT 58.609 39.130 0.00 0.00 0.00 3.67
1738 1795 5.455872 TCCCTTGTTATCCTAGTCCTAGTG 58.544 45.833 0.96 0.00 0.00 2.74
1768 1825 3.854666 TGAGAGATTGACTTAGTGCTGC 58.145 45.455 0.00 0.00 0.00 5.25
1776 1833 6.486657 AGATTGACTTAGTGCTGCTTTTGTTA 59.513 34.615 0.00 0.00 0.00 2.41
1777 1834 5.418310 TGACTTAGTGCTGCTTTTGTTAC 57.582 39.130 0.00 0.00 0.00 2.50
1912 1990 7.042335 AGATTGTCCCTTTTGATTCTACTACG 58.958 38.462 0.00 0.00 0.00 3.51
1916 1994 5.350640 GTCCCTTTTGATTCTACTACGGTTG 59.649 44.000 0.00 0.00 0.00 3.77
1982 2060 4.105486 GGCCGCTTGAGAAACATTTTATC 58.895 43.478 0.00 0.00 0.00 1.75
2001 2079 1.554617 TCGATCAAGCCTCACCATGAA 59.445 47.619 0.00 0.00 0.00 2.57
2027 2105 6.299805 TCTCCAGTGAACTATGCATAAGTT 57.700 37.500 16.49 16.49 39.84 2.66
2139 2217 1.892474 ACATGTGTGGTGTTTATGGGC 59.108 47.619 0.00 0.00 0.00 5.36
2158 2267 7.672983 ATGGGCTACTAATCAAAATGTATCG 57.327 36.000 0.00 0.00 0.00 2.92
2186 2295 8.641498 ACTTGTCTATGAACTTCATTCCAATT 57.359 30.769 9.57 3.25 38.26 2.32
2188 2297 8.868522 TTGTCTATGAACTTCATTCCAATTCT 57.131 30.769 9.57 0.00 38.26 2.40
2199 2308 7.234166 ACTTCATTCCAATTCTGGTCAAAGAAT 59.766 33.333 0.00 0.00 46.52 2.40
2318 2428 6.532657 AGCAATATGTTAGCATGTTTTCTTGC 59.467 34.615 1.80 2.49 46.82 4.01
2418 2533 4.238514 GGCAGAGTAGTATGGCTAATTCG 58.761 47.826 11.24 0.00 37.48 3.34
2471 2586 7.055314 AGAGGATGAAGTAGATGGGAGATAT 57.945 40.000 0.00 0.00 0.00 1.63
2472 2587 6.896860 AGAGGATGAAGTAGATGGGAGATATG 59.103 42.308 0.00 0.00 0.00 1.78
2505 2782 8.909708 TTTCTTACTTGATAAAAATGGATGCG 57.090 30.769 0.00 0.00 0.00 4.73
2519 2796 0.659957 GATGCGCCAAGGCTCTTTAG 59.340 55.000 4.18 0.00 39.32 1.85
2555 2832 8.708742 GCCCTAACAAATTGATTCTAAACAAAC 58.291 33.333 0.00 0.00 0.00 2.93
2559 2836 8.574196 AACAAATTGATTCTAAACAAACCTCG 57.426 30.769 0.00 0.00 0.00 4.63
2599 2876 9.866655 ATCTTATCTGTAATTGATTTAAGGCCA 57.133 29.630 5.01 0.00 0.00 5.36
2612 2889 2.134789 AAGGCCAAGGCTAAGATGTG 57.865 50.000 5.01 0.00 37.50 3.21
2620 2897 4.130118 CAAGGCTAAGATGTGTCATACCC 58.870 47.826 0.00 0.00 0.00 3.69
2627 2904 6.998673 GCTAAGATGTGTCATACCCCTTATTT 59.001 38.462 0.00 0.00 0.00 1.40
2646 2923 2.128771 TGCTTAAGGCCCAAGCTAAG 57.871 50.000 29.80 16.97 46.85 2.18
2684 2961 7.742767 TCTAATTGATTACCCCTAGCCTAAAC 58.257 38.462 0.00 0.00 0.00 2.01
2689 2966 1.117994 ACCCCTAGCCTAAACGCTAC 58.882 55.000 0.00 0.00 40.39 3.58
2703 2980 7.922811 GCCTAAACGCTACTATTCCTAACTTTA 59.077 37.037 0.00 0.00 0.00 1.85
2744 3021 4.651503 TCTCTTAATTGGAGTCAGCTAGGG 59.348 45.833 9.16 0.00 33.06 3.53
2794 3071 5.827267 CCCATCCACATGACAATAATACACA 59.173 40.000 0.00 0.00 30.57 3.72
2801 3078 7.229106 CCACATGACAATAATACACATGATCCA 59.771 37.037 0.00 0.00 40.13 3.41
2830 3107 2.362077 GGTGCTTCAAGTTGTGTTGGAT 59.638 45.455 2.11 0.00 0.00 3.41
2839 3116 6.969366 TCAAGTTGTGTTGGATTTATGACAG 58.031 36.000 2.11 0.00 0.00 3.51
2890 3167 9.959749 TTCCTAACAATCTGAATTTTACACAAC 57.040 29.630 0.00 0.00 0.00 3.32
2904 3181 5.749596 TTACACAACCACATCTTGAACTG 57.250 39.130 0.00 0.00 0.00 3.16
2908 3185 3.627577 ACAACCACATCTTGAACTGTGTC 59.372 43.478 2.43 0.00 40.89 3.67
2976 3255 2.070783 GATTTGGTTGCTTGCATGTGG 58.929 47.619 1.14 0.00 0.00 4.17
2984 3263 0.737219 GCTTGCATGTGGATCACCTC 59.263 55.000 1.14 0.00 37.04 3.85
3105 3546 9.975218 AAAGGTATTGGACTAATCACACTTAAT 57.025 29.630 0.00 0.00 0.00 1.40
3106 3547 9.975218 AAGGTATTGGACTAATCACACTTAATT 57.025 29.630 0.00 0.00 0.00 1.40
3107 3548 9.975218 AGGTATTGGACTAATCACACTTAATTT 57.025 29.630 0.00 0.00 0.00 1.82
3150 3591 4.384647 GGGGAATCTGTAGAAGCAGTGATT 60.385 45.833 0.00 0.00 37.70 2.57
3288 3729 6.228995 ACCAGTGCTTTAGTAAGACCTAAAC 58.771 40.000 0.00 0.00 34.20 2.01
3297 3738 9.931210 CTTTAGTAAGACCTAAACACTTGTTTG 57.069 33.333 16.04 4.50 39.77 2.93
3324 3765 8.741603 AATGGCGTAAATTGTTTAGGTAGTAT 57.258 30.769 4.67 0.00 34.44 2.12
3389 3830 6.052840 ACTATGATCATTGTTAAGCTTGCG 57.947 37.500 14.65 0.00 0.00 4.85
3393 3834 4.093408 TGATCATTGTTAAGCTTGCGACTC 59.907 41.667 9.86 0.00 0.00 3.36
3394 3835 3.398406 TCATTGTTAAGCTTGCGACTCA 58.602 40.909 9.86 0.00 0.00 3.41
3395 3836 4.002982 TCATTGTTAAGCTTGCGACTCAT 58.997 39.130 9.86 0.11 0.00 2.90
3397 3838 4.829064 TTGTTAAGCTTGCGACTCATTT 57.171 36.364 9.86 0.00 0.00 2.32
3398 3839 4.829064 TGTTAAGCTTGCGACTCATTTT 57.171 36.364 9.86 0.00 0.00 1.82
3399 3840 4.536065 TGTTAAGCTTGCGACTCATTTTG 58.464 39.130 9.86 0.00 0.00 2.44
3400 3841 2.056094 AAGCTTGCGACTCATTTTGC 57.944 45.000 0.00 0.00 0.00 3.68
3401 3842 1.242076 AGCTTGCGACTCATTTTGCT 58.758 45.000 0.00 0.00 0.00 3.91
3522 3980 3.443045 CTGGTCCATGCAACCCGC 61.443 66.667 11.70 0.00 42.89 6.13
3620 4078 4.584874 TCGAAAGAAAATCATGCCCACTA 58.415 39.130 0.00 0.00 37.03 2.74
3621 4079 5.192927 TCGAAAGAAAATCATGCCCACTAT 58.807 37.500 0.00 0.00 37.03 2.12
3623 4081 6.826231 TCGAAAGAAAATCATGCCCACTATAA 59.174 34.615 0.00 0.00 37.03 0.98
3700 4158 4.727507 TTTTGTGTGTACTTTGCATGGT 57.272 36.364 0.00 0.00 0.00 3.55
3701 4159 5.836821 TTTTGTGTGTACTTTGCATGGTA 57.163 34.783 0.00 0.00 0.00 3.25
3707 4165 8.116651 TGTGTGTACTTTGCATGGTAATTTAT 57.883 30.769 0.00 0.00 0.00 1.40
3741 4199 3.323751 AAGCCATGGTGCATCTTTTTC 57.676 42.857 14.67 0.00 0.00 2.29
3758 4216 5.527951 TCTTTTTCAGTGTTGCCGTTGTATA 59.472 36.000 0.00 0.00 0.00 1.47
3783 4242 5.045668 TGTTGTTGTTTCATGATCGATGG 57.954 39.130 0.54 0.00 32.26 3.51
3792 4251 7.825681 TGTTTCATGATCGATGGTTGTAAATT 58.174 30.769 0.54 0.00 32.26 1.82
3845 4305 5.183140 GCTGTATGGGTTTGTTCTTGTATGT 59.817 40.000 0.00 0.00 0.00 2.29
3955 4419 3.257375 TGTACTTGTATCGGTGAGTGCTT 59.743 43.478 0.00 0.00 0.00 3.91
3957 4421 2.271800 CTTGTATCGGTGAGTGCTTCC 58.728 52.381 0.00 0.00 0.00 3.46
3958 4422 1.262417 TGTATCGGTGAGTGCTTCCA 58.738 50.000 0.00 0.00 0.00 3.53
3959 4423 1.067142 TGTATCGGTGAGTGCTTCCAC 60.067 52.381 0.00 0.00 42.39 4.02
3975 4440 6.477033 GTGCTTCCACTATCTTATGTGTACAG 59.523 42.308 0.00 0.00 38.93 2.74
4101 4566 9.868277 AAACAGTATTCTCTAGATGACTTTCAG 57.132 33.333 0.00 0.00 0.00 3.02
4121 4586 4.020218 TCAGTTTATGTACTTGCTCTGCCT 60.020 41.667 0.00 0.00 0.00 4.75
4306 4771 8.625786 TTCTTGAGATGATTTTCTGATGACAA 57.374 30.769 0.00 0.00 0.00 3.18
4309 4774 7.242914 TGAGATGATTTTCTGATGACAATCG 57.757 36.000 0.00 0.00 40.42 3.34
4310 4775 6.820152 TGAGATGATTTTCTGATGACAATCGT 59.180 34.615 0.00 0.00 40.42 3.73
4311 4776 7.981225 TGAGATGATTTTCTGATGACAATCGTA 59.019 33.333 0.00 0.00 40.42 3.43
4312 4777 8.899427 AGATGATTTTCTGATGACAATCGTAT 57.101 30.769 0.00 0.00 40.42 3.06
4313 4778 8.771766 AGATGATTTTCTGATGACAATCGTATG 58.228 33.333 0.00 0.00 40.42 2.39
4314 4779 7.848223 TGATTTTCTGATGACAATCGTATGT 57.152 32.000 0.00 0.00 40.42 2.29
4315 4780 8.267620 TGATTTTCTGATGACAATCGTATGTT 57.732 30.769 0.00 0.00 40.42 2.71
4316 4781 9.377312 TGATTTTCTGATGACAATCGTATGTTA 57.623 29.630 0.00 0.00 40.42 2.41
4317 4782 9.855361 GATTTTCTGATGACAATCGTATGTTAG 57.145 33.333 0.00 0.00 35.37 2.34
4318 4783 8.771920 TTTTCTGATGACAATCGTATGTTAGT 57.228 30.769 0.00 0.00 35.37 2.24
4319 4784 9.863845 TTTTCTGATGACAATCGTATGTTAGTA 57.136 29.630 0.00 0.00 35.37 1.82
4320 4785 9.516314 TTTCTGATGACAATCGTATGTTAGTAG 57.484 33.333 0.00 0.00 35.37 2.57
4321 4786 7.139392 TCTGATGACAATCGTATGTTAGTAGC 58.861 38.462 0.00 0.00 35.37 3.58
4367 4832 5.275067 AGTGACTTTCTGGATGAGCTATC 57.725 43.478 0.00 0.00 34.93 2.08
4409 4876 1.066908 ACCACACTGGAAAATTGCGTG 59.933 47.619 0.00 7.61 40.96 5.34
4410 4877 1.602668 CCACACTGGAAAATTGCGTGG 60.603 52.381 11.67 0.00 40.96 4.94
4413 4880 2.034558 ACACTGGAAAATTGCGTGGAAG 59.965 45.455 11.67 0.00 31.48 3.46
4439 4978 8.962884 ATATAGTTGACAACTGTGCAATGATA 57.037 30.769 27.44 15.74 42.84 2.15
4502 5044 3.056536 GGATGTACTTGTCTGCTGAGTGA 60.057 47.826 0.00 0.00 0.00 3.41
4516 5058 7.495279 GTCTGCTGAGTGATCATCTTCTATTTT 59.505 37.037 0.00 0.00 0.00 1.82
4524 5066 8.887717 AGTGATCATCTTCTATTTTAGTGTTGC 58.112 33.333 0.00 0.00 0.00 4.17
4544 5086 6.867816 TGTTGCTAATTATTTTGCTGTCCAAG 59.132 34.615 5.60 0.00 35.07 3.61
4577 5119 5.741011 TGTTGGTTACCTGGATCATAAGAC 58.259 41.667 0.00 0.00 0.00 3.01
4579 5121 5.614324 TGGTTACCTGGATCATAAGACAG 57.386 43.478 0.00 0.00 0.00 3.51
4583 5125 3.784511 CCTGGATCATAAGACAGGCAT 57.215 47.619 0.00 0.00 43.41 4.40
4589 5131 4.446889 GGATCATAAGACAGGCATTTCCCT 60.447 45.833 0.00 0.00 34.93 4.20
4618 5160 4.080356 ACTCCACCTATTATTGAAGCTGCA 60.080 41.667 1.02 0.00 0.00 4.41
4620 5162 6.183361 ACTCCACCTATTATTGAAGCTGCATA 60.183 38.462 0.00 0.00 0.00 3.14
4635 5177 3.320541 GCTGCATACAGTCTAGACTCCAT 59.679 47.826 22.76 14.96 46.30 3.41
4638 5180 6.641169 TGCATACAGTCTAGACTCCATAAG 57.359 41.667 22.76 12.68 40.20 1.73
4639 5181 5.010112 TGCATACAGTCTAGACTCCATAAGC 59.990 44.000 22.76 20.55 40.20 3.09
4660 5202 3.377172 GCGGATAAACCTGTATTGCAGTT 59.623 43.478 0.98 0.00 43.55 3.16
4688 5230 1.609072 GTTCCTGTCCTTTTGTCTGGC 59.391 52.381 0.00 0.00 0.00 4.85
4740 5282 9.390795 GATATTAATTTGTGCTCTTGTGCTATG 57.609 33.333 0.00 0.00 0.00 2.23
4747 5311 3.624861 GTGCTCTTGTGCTATGCATACTT 59.375 43.478 1.16 0.00 41.91 2.24
4764 5328 5.449999 GCATACTTTTATGGCTTGTGTACCC 60.450 44.000 0.00 0.00 36.35 3.69
4813 5377 6.318648 TGCCCTGCTAATATTTAGTTGAACTG 59.681 38.462 8.33 0.00 0.00 3.16
4900 5464 8.084590 AGCAACTGTTGTAAATCTTAGTGTAC 57.915 34.615 20.57 0.00 0.00 2.90
5020 5584 1.476891 GCTCCTGACCAAGACATACGA 59.523 52.381 0.00 0.00 0.00 3.43
5092 5656 9.970395 ATGAATGCATTACAATCGTATCAAAAT 57.030 25.926 12.97 0.00 30.11 1.82
5445 6012 4.539726 ACATAATGCCATGACCTGTTGAT 58.460 39.130 0.00 0.00 0.00 2.57
5453 6020 4.022589 GCCATGACCTGTTGATCATAATGG 60.023 45.833 0.00 0.44 33.73 3.16
5459 6026 7.999679 TGACCTGTTGATCATAATGGATTTTC 58.000 34.615 0.00 0.00 0.00 2.29
5460 6027 7.031226 ACCTGTTGATCATAATGGATTTTCG 57.969 36.000 0.00 0.00 0.00 3.46
5466 6033 6.057533 TGATCATAATGGATTTTCGAGTGCT 58.942 36.000 0.00 0.00 0.00 4.40
5471 6038 1.952990 TGGATTTTCGAGTGCTTTGCA 59.047 42.857 0.00 0.00 35.60 4.08
5514 6081 2.503331 TGATGGTCGCATGTTGAAACT 58.497 42.857 0.00 0.00 0.00 2.66
5583 6152 1.097232 TCAATCCAATTGGCTCAGCG 58.903 50.000 20.33 4.89 40.61 5.18
5661 6230 1.863454 GGCATCTACAGCATCAGAACG 59.137 52.381 0.00 0.00 0.00 3.95
5700 6269 1.090052 GTCAAGACATAGCCGGTGCC 61.090 60.000 1.90 0.00 38.69 5.01
5769 6338 2.972713 GGCCACCCTTCTGTCAGATATA 59.027 50.000 2.68 0.00 0.00 0.86
5886 6456 1.274447 ACTAGCACCGTAGTTCCCAAC 59.726 52.381 0.00 0.00 28.15 3.77
5894 6464 1.804748 CGTAGTTCCCAACCAAGCTTC 59.195 52.381 0.00 0.00 0.00 3.86
5917 6487 7.026631 TCAAAATATAGACCTGATTTTGGCG 57.973 36.000 20.00 0.00 44.82 5.69
5945 6515 2.357952 GTGTGTGTTTCCCTTCCAACTC 59.642 50.000 0.00 0.00 0.00 3.01
5948 6519 0.109723 TGTTTCCCTTCCAACTCGGG 59.890 55.000 0.00 0.00 39.41 5.14
6017 6588 0.681175 GGGCAGCAACTGGAAAATGT 59.319 50.000 0.00 0.00 31.21 2.71
6210 6785 4.626604 TCTTCTTTGCTGCTTGTTTGTTTG 59.373 37.500 0.00 0.00 0.00 2.93
6211 6786 3.924144 TCTTTGCTGCTTGTTTGTTTGT 58.076 36.364 0.00 0.00 0.00 2.83
6278 6853 0.806868 CATGTGTGAGGTGATGGTGC 59.193 55.000 0.00 0.00 0.00 5.01
6281 6856 0.884704 GTGTGAGGTGATGGTGCGTT 60.885 55.000 0.00 0.00 0.00 4.84
6339 6915 0.110056 GCAAGACATGGTGAAGCACG 60.110 55.000 0.00 0.00 34.83 5.34
6344 6920 1.230635 ACATGGTGAAGCACGTGAGC 61.231 55.000 22.23 8.58 34.83 4.26
6452 7031 2.105729 GCCGGGCTTACGAGTACC 59.894 66.667 12.87 0.00 35.47 3.34
6475 7054 3.418047 CCTCCGTCCCAAAATAAGTGTT 58.582 45.455 0.00 0.00 0.00 3.32
6489 7069 1.209127 GTGTTGCCGATTTGGGACG 59.791 57.895 0.00 0.00 38.10 4.79
6501 7081 2.077687 TTGGGACGGAGGGAGTATAC 57.922 55.000 0.00 0.00 0.00 1.47
6510 7090 3.655384 GGAGGGAGTATACTGGAAGGTT 58.345 50.000 10.90 0.00 39.30 3.50
6511 7091 3.642377 GGAGGGAGTATACTGGAAGGTTC 59.358 52.174 10.90 0.00 39.30 3.62
6525 7105 8.250143 ACTGGAAGGTTCTAATTTTTCATGTT 57.750 30.769 0.00 0.00 39.30 2.71
6545 7125 5.136828 TGTTCCTATTTTCAAGTTGCCTGA 58.863 37.500 0.00 0.00 0.00 3.86
6551 7131 6.760770 CCTATTTTCAAGTTGCCTGAAAAACA 59.239 34.615 13.04 5.59 42.39 2.83
6560 7140 3.539604 TGCCTGAAAAACAATTTGGTGG 58.460 40.909 0.78 0.00 0.00 4.61
6564 7144 5.220835 GCCTGAAAAACAATTTGGTGGAAAG 60.221 40.000 0.78 0.00 0.00 2.62
6574 7154 7.108847 ACAATTTGGTGGAAAGTTGATTTTCA 58.891 30.769 0.78 0.00 38.51 2.69
6579 7159 5.221422 TGGTGGAAAGTTGATTTTCATGGAC 60.221 40.000 0.00 0.00 38.67 4.02
6589 7169 6.975196 TGATTTTCATGGACAAGAAAAGGA 57.025 33.333 17.00 6.88 44.18 3.36
6590 7170 6.985117 TGATTTTCATGGACAAGAAAAGGAG 58.015 36.000 17.00 0.00 44.18 3.69
6640 7243 2.291153 CCAGACTTGGGGATGATGTTGT 60.291 50.000 0.00 0.00 41.05 3.32
6649 7252 2.631696 GATGATGTTGTTCGCCGCGG 62.632 60.000 24.05 24.05 0.00 6.46
6676 7280 1.141019 GCGTGTAGCGGGATGAAGA 59.859 57.895 0.00 0.00 41.69 2.87
6685 7289 1.530183 GGGATGAAGATGGCAGGGC 60.530 63.158 0.00 0.00 0.00 5.19
6724 7328 0.672401 TCCGACGGTTCAGCCAAATC 60.672 55.000 14.79 0.00 36.97 2.17
6733 7337 3.648339 TTCAGCCAAATCAACTGAAGC 57.352 42.857 0.75 0.00 43.55 3.86
6734 7338 1.888512 TCAGCCAAATCAACTGAAGCC 59.111 47.619 0.00 0.00 37.49 4.35
6747 7351 2.267324 AAGCCGAGCTTCTCAGGC 59.733 61.111 16.28 16.28 46.77 4.85
6755 7359 1.202582 GAGCTTCTCAGGCGACTTACA 59.797 52.381 0.00 0.00 40.21 2.41
6756 7360 1.203523 AGCTTCTCAGGCGACTTACAG 59.796 52.381 0.00 0.00 40.21 2.74
6757 7361 1.202582 GCTTCTCAGGCGACTTACAGA 59.797 52.381 0.00 0.00 40.21 3.41
6758 7362 2.159170 GCTTCTCAGGCGACTTACAGAT 60.159 50.000 0.00 0.00 40.21 2.90
6759 7363 3.066900 GCTTCTCAGGCGACTTACAGATA 59.933 47.826 0.00 0.00 40.21 1.98
6760 7364 4.791411 GCTTCTCAGGCGACTTACAGATAG 60.791 50.000 0.00 0.00 40.21 2.08
6761 7365 3.215151 TCTCAGGCGACTTACAGATAGG 58.785 50.000 0.00 0.00 40.21 2.57
6762 7366 1.681793 TCAGGCGACTTACAGATAGGC 59.318 52.381 0.00 0.00 40.21 3.93
6763 7367 1.409064 CAGGCGACTTACAGATAGGCA 59.591 52.381 0.00 0.00 40.21 4.75
6764 7368 1.683917 AGGCGACTTACAGATAGGCAG 59.316 52.381 0.00 0.00 37.44 4.85
6765 7369 1.409427 GGCGACTTACAGATAGGCAGT 59.591 52.381 0.00 0.00 0.00 4.40
6766 7370 2.544069 GGCGACTTACAGATAGGCAGTC 60.544 54.545 0.00 0.00 0.00 3.51
6767 7371 2.099263 GCGACTTACAGATAGGCAGTCA 59.901 50.000 0.00 0.00 34.67 3.41
6768 7372 3.793801 GCGACTTACAGATAGGCAGTCAG 60.794 52.174 0.00 0.00 34.67 3.51
6769 7373 3.378742 CGACTTACAGATAGGCAGTCAGT 59.621 47.826 0.00 0.00 34.67 3.41
6770 7374 4.575236 CGACTTACAGATAGGCAGTCAGTA 59.425 45.833 0.00 0.00 34.67 2.74
6771 7375 5.239744 CGACTTACAGATAGGCAGTCAGTAT 59.760 44.000 0.00 0.00 34.67 2.12
6772 7376 6.238786 CGACTTACAGATAGGCAGTCAGTATT 60.239 42.308 0.00 0.00 34.67 1.89
6773 7377 7.425224 ACTTACAGATAGGCAGTCAGTATTT 57.575 36.000 0.00 0.00 0.00 1.40
6774 7378 7.852263 ACTTACAGATAGGCAGTCAGTATTTT 58.148 34.615 0.00 0.00 0.00 1.82
6775 7379 8.978472 ACTTACAGATAGGCAGTCAGTATTTTA 58.022 33.333 0.00 0.00 0.00 1.52
6776 7380 9.817809 CTTACAGATAGGCAGTCAGTATTTTAA 57.182 33.333 0.00 0.00 0.00 1.52
6779 7383 9.686683 ACAGATAGGCAGTCAGTATTTTAATTT 57.313 29.630 0.00 0.00 0.00 1.82
6783 7387 7.631717 AGGCAGTCAGTATTTTAATTTCTCC 57.368 36.000 0.00 0.00 0.00 3.71
6784 7388 6.603599 AGGCAGTCAGTATTTTAATTTCTCCC 59.396 38.462 0.00 0.00 0.00 4.30
6785 7389 6.603599 GGCAGTCAGTATTTTAATTTCTCCCT 59.396 38.462 0.00 0.00 0.00 4.20
6786 7390 7.201741 GGCAGTCAGTATTTTAATTTCTCCCTC 60.202 40.741 0.00 0.00 0.00 4.30
6787 7391 7.336931 GCAGTCAGTATTTTAATTTCTCCCTCA 59.663 37.037 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.660771 CACCCTAGATGAATTAAGAGGGGT 59.339 45.833 9.50 6.85 46.79 4.95
30 31 1.722034 AGCAGTGGGAACTTGAGAGA 58.278 50.000 0.00 0.00 0.00 3.10
51 52 3.946308 TTTGCGTATGTCGTTGTGAAA 57.054 38.095 0.00 0.00 42.13 2.69
55 56 4.201871 CCCATATTTTGCGTATGTCGTTGT 60.202 41.667 0.00 0.00 42.13 3.32
60 61 6.204688 TCTCAATCCCATATTTTGCGTATGTC 59.795 38.462 0.00 0.00 0.00 3.06
61 62 6.017109 GTCTCAATCCCATATTTTGCGTATGT 60.017 38.462 0.00 0.00 0.00 2.29
62 63 6.205464 AGTCTCAATCCCATATTTTGCGTATG 59.795 38.462 0.00 0.00 0.00 2.39
63 64 6.299141 AGTCTCAATCCCATATTTTGCGTAT 58.701 36.000 0.00 0.00 0.00 3.06
64 65 5.680619 AGTCTCAATCCCATATTTTGCGTA 58.319 37.500 0.00 0.00 0.00 4.42
65 66 4.526970 AGTCTCAATCCCATATTTTGCGT 58.473 39.130 0.00 0.00 0.00 5.24
66 67 5.760253 ACTAGTCTCAATCCCATATTTTGCG 59.240 40.000 0.00 0.00 0.00 4.85
67 68 8.677148 TTACTAGTCTCAATCCCATATTTTGC 57.323 34.615 0.00 0.00 0.00 3.68
76 77 7.496263 GGAAAGTTGATTACTAGTCTCAATCCC 59.504 40.741 18.54 14.25 35.54 3.85
127 128 4.527038 AGAAAGGGAATGAGAGTACACGAA 59.473 41.667 0.00 0.00 0.00 3.85
130 131 4.223032 TGGAGAAAGGGAATGAGAGTACAC 59.777 45.833 0.00 0.00 0.00 2.90
153 154 6.146673 GGTGCGTATCACTTAGTGTTTACTTT 59.853 38.462 12.41 0.00 44.98 2.66
160 161 1.814394 TCGGTGCGTATCACTTAGTGT 59.186 47.619 12.41 2.78 44.98 3.55
225 232 6.759827 GGAATTAGAAGTAACATAGCACGGAA 59.240 38.462 0.00 0.00 0.00 4.30
229 236 8.175716 GTGTTGGAATTAGAAGTAACATAGCAC 58.824 37.037 0.00 0.00 31.68 4.40
235 242 5.302360 AGCGTGTTGGAATTAGAAGTAACA 58.698 37.500 0.00 0.00 0.00 2.41
266 273 0.464373 CAATCATGGGGGAGGTCACG 60.464 60.000 0.00 0.00 0.00 4.35
279 286 0.250038 CTCCGTCCCATCGCAATCAT 60.250 55.000 0.00 0.00 0.00 2.45
317 325 0.447801 GCGAAACATGGCATCTTCGT 59.552 50.000 28.20 11.41 41.98 3.85
354 362 2.715749 TCGTTATCCTACTCCCGACA 57.284 50.000 0.00 0.00 0.00 4.35
388 396 2.510691 ATCGCCTAACGCCAACCG 60.511 61.111 0.00 0.00 43.23 4.44
413 422 0.250124 TACTCACCACAACCAAGGCG 60.250 55.000 0.00 0.00 0.00 5.52
420 429 4.002906 TCACCAATCTACTCACCACAAC 57.997 45.455 0.00 0.00 0.00 3.32
426 435 3.941483 CCCAACATCACCAATCTACTCAC 59.059 47.826 0.00 0.00 0.00 3.51
427 436 3.622206 GCCCAACATCACCAATCTACTCA 60.622 47.826 0.00 0.00 0.00 3.41
439 448 2.905996 AAGGAGCGGCCCAACATCA 61.906 57.895 0.00 0.00 37.37 3.07
489 498 2.432628 GCTCTTGCGCGTAGTGGT 60.433 61.111 8.43 0.00 39.19 4.16
494 503 3.489416 CAGTTATTATGCTCTTGCGCGTA 59.511 43.478 8.43 0.00 43.34 4.42
501 510 5.665459 AGCGTCTTCAGTTATTATGCTCTT 58.335 37.500 0.00 0.00 0.00 2.85
502 511 5.269505 AGCGTCTTCAGTTATTATGCTCT 57.730 39.130 0.00 0.00 0.00 4.09
528 537 1.513158 CTCCCCTGACGTAGCACAG 59.487 63.158 0.00 0.00 35.63 3.66
529 538 1.982395 CCTCCCCTGACGTAGCACA 60.982 63.158 0.00 0.00 0.00 4.57
534 543 1.807771 AAGGTCCCTCCCCTGACGTA 61.808 60.000 0.00 0.00 36.75 3.57
535 544 2.691240 AAAGGTCCCTCCCCTGACGT 62.691 60.000 0.00 0.00 36.75 4.34
549 558 1.608590 CGACACAATCAAGGCAAAGGT 59.391 47.619 0.00 0.00 0.00 3.50
553 562 2.254546 ACTCGACACAATCAAGGCAA 57.745 45.000 0.00 0.00 0.00 4.52
554 563 2.353704 CCTACTCGACACAATCAAGGCA 60.354 50.000 0.00 0.00 0.00 4.75
599 608 4.708726 AGCAAAACATAGCATTCTGGAC 57.291 40.909 0.00 0.00 0.00 4.02
601 610 5.824904 AGTAGCAAAACATAGCATTCTGG 57.175 39.130 0.00 0.00 0.00 3.86
602 611 7.081526 AGAAGTAGCAAAACATAGCATTCTG 57.918 36.000 0.00 0.00 32.68 3.02
607 616 7.609918 TGGATTTAGAAGTAGCAAAACATAGCA 59.390 33.333 0.00 0.00 0.00 3.49
684 693 0.116541 TCCTTCGAGTTCCCCTTCCT 59.883 55.000 0.00 0.00 0.00 3.36
687 696 1.903183 CTCTTCCTTCGAGTTCCCCTT 59.097 52.381 0.00 0.00 0.00 3.95
688 697 1.562783 CTCTTCCTTCGAGTTCCCCT 58.437 55.000 0.00 0.00 0.00 4.79
689 698 0.108089 GCTCTTCCTTCGAGTTCCCC 60.108 60.000 0.00 0.00 0.00 4.81
703 737 4.287326 AGGGAGTAGCTTACTTTTGCTCTT 59.713 41.667 0.00 0.00 39.59 2.85
725 759 6.761242 TCCATATTAATTATTGCGGATCGGAG 59.239 38.462 4.16 0.00 0.00 4.63
942 990 2.040359 GGAGAAGGGGAGGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
948 1001 3.083997 CGGTGGGGAGAAGGGGAG 61.084 72.222 0.00 0.00 0.00 4.30
1191 1245 1.730902 CCGACACAGAGTGAGCACG 60.731 63.158 3.88 4.50 36.96 5.34
1367 1421 2.586245 CTGGAGGCGGATGAGCAA 59.414 61.111 0.00 0.00 39.27 3.91
1393 1447 0.660005 GATCTGACGCGAGCAGCTAG 60.660 60.000 15.93 0.00 45.59 3.42
1451 1505 8.700439 ATACAAGACCTAAAAAGGCTTACAAA 57.300 30.769 0.00 0.00 0.00 2.83
1483 1539 6.239572 CCAAAACAATCACCAGGTCCTAAAAT 60.240 38.462 0.00 0.00 0.00 1.82
1491 1547 2.765689 TCCCAAAACAATCACCAGGT 57.234 45.000 0.00 0.00 0.00 4.00
1496 1552 4.858692 CGATGTGAATCCCAAAACAATCAC 59.141 41.667 0.00 0.00 38.08 3.06
1505 1561 2.817258 GGTGAAACGATGTGAATCCCAA 59.183 45.455 0.00 0.00 38.12 4.12
1565 1621 9.177608 TGCTTGCATAGTAAAAACTAGAATGAT 57.822 29.630 0.00 0.00 0.00 2.45
1598 1654 1.085091 ATTCTTGCTCAAGCTCTGCG 58.915 50.000 3.32 0.00 42.66 5.18
1601 1657 5.184711 CCTCTTAATTCTTGCTCAAGCTCT 58.815 41.667 3.32 0.00 42.66 4.09
1738 1795 8.243426 CACTAAGTCAATCTCTCATATCTAGGC 58.757 40.741 0.00 0.00 0.00 3.93
1768 1825 3.751698 GGTAGGACTGCAGGTAACAAAAG 59.248 47.826 19.93 0.00 41.41 2.27
1776 1833 1.613630 CCAGGGTAGGACTGCAGGT 60.614 63.158 19.93 3.31 34.65 4.00
1777 1834 1.201429 AACCAGGGTAGGACTGCAGG 61.201 60.000 19.93 0.00 34.65 4.85
1864 1922 7.144000 TCTTTTGCAAAAGCAAAACACAAAAT 58.856 26.923 36.33 0.00 43.85 1.82
1888 1946 6.258068 CCGTAGTAGAATCAAAAGGGACAATC 59.742 42.308 0.00 0.00 0.00 2.67
1982 2060 1.667724 GTTCATGGTGAGGCTTGATCG 59.332 52.381 0.00 0.00 0.00 3.69
2001 2079 4.833478 ATGCATAGTTCACTGGAGAAGT 57.167 40.909 0.00 0.00 40.93 3.01
2027 2105 3.570125 CCTTCTACACGCTATGATCCAGA 59.430 47.826 0.00 0.00 0.00 3.86
2158 2267 7.103641 TGGAATGAAGTTCATAGACAAGTACC 58.896 38.462 18.56 10.77 35.76 3.34
2186 2295 6.489700 TCAAACAGCATAATTCTTTGACCAGA 59.510 34.615 0.00 0.00 0.00 3.86
2188 2297 6.647334 TCAAACAGCATAATTCTTTGACCA 57.353 33.333 0.00 0.00 0.00 4.02
2199 2308 5.450592 TGCACTTGAATCAAACAGCATAA 57.549 34.783 11.01 0.00 0.00 1.90
2318 2428 1.135141 GCAGGCGGCATATCTAGAGAG 60.135 57.143 13.08 0.00 43.97 3.20
2401 2516 3.833070 CCTCCCGAATTAGCCATACTACT 59.167 47.826 0.00 0.00 0.00 2.57
2403 2518 3.170717 CCCTCCCGAATTAGCCATACTA 58.829 50.000 0.00 0.00 0.00 1.82
2418 2533 6.452330 TCCCCAATATAATTATAACCCCTCCC 59.548 42.308 9.20 0.00 0.00 4.30
2452 2567 7.623999 ACAACATATCTCCCATCTACTTCAT 57.376 36.000 0.00 0.00 0.00 2.57
2480 2757 7.487829 GCGCATCCATTTTTATCAAGTAAGAAA 59.512 33.333 0.30 0.00 0.00 2.52
2519 2796 3.560636 TTTGTTAGGGCCAGCTCTATC 57.439 47.619 6.18 0.30 0.00 2.08
2582 2859 5.598416 AGCCTTGGCCTTAAATCAATTAC 57.402 39.130 3.32 0.00 0.00 1.89
2599 2876 3.136626 GGGGTATGACACATCTTAGCCTT 59.863 47.826 14.45 0.00 45.73 4.35
2612 2889 6.635030 CCTTAAGCAAATAAGGGGTATGAC 57.365 41.667 12.69 0.00 45.46 3.06
2646 2923 9.262358 GGTAATCAATTAGAGGTAAGACATCAC 57.738 37.037 0.00 0.00 30.12 3.06
2668 2945 1.870064 AGCGTTTAGGCTAGGGGTAA 58.130 50.000 0.00 0.00 42.62 2.85
2723 3000 3.134804 GCCCTAGCTGACTCCAATTAAGA 59.865 47.826 0.00 0.00 35.50 2.10
2729 3006 3.727387 GGCCCTAGCTGACTCCAA 58.273 61.111 0.00 0.00 39.73 3.53
2744 3021 2.033602 ACACTAAACCCAGCCGGC 59.966 61.111 21.89 21.89 33.26 6.13
2810 3087 3.715628 ATCCAACACAACTTGAAGCAC 57.284 42.857 0.00 0.00 0.00 4.40
2839 3116 7.230466 ACTATAAAACTAATACAGCACACGC 57.770 36.000 0.00 0.00 38.99 5.34
2904 3181 1.001974 TGGTACTGAGTGGCATGACAC 59.998 52.381 24.86 24.86 41.63 3.67
2908 3185 3.346315 TGAAATGGTACTGAGTGGCATG 58.654 45.455 0.00 0.00 0.00 4.06
2976 3255 7.040409 ACAACAATAACAAAAGGAGAGGTGATC 60.040 37.037 0.00 0.00 0.00 2.92
2984 3263 7.479980 TCTGACAACAACAATAACAAAAGGAG 58.520 34.615 0.00 0.00 0.00 3.69
3114 3555 2.057922 GATTCCCCATTCTAGAGCCCA 58.942 52.381 0.00 0.00 0.00 5.36
3115 3556 2.039613 CAGATTCCCCATTCTAGAGCCC 59.960 54.545 0.00 0.00 0.00 5.19
3129 3570 6.073331 GCATAATCACTGCTTCTACAGATTCC 60.073 42.308 0.00 0.00 40.25 3.01
3150 3591 3.552068 CCAGTCGTGAATCATACCGCATA 60.552 47.826 0.00 0.00 0.00 3.14
3288 3729 6.419413 ACAATTTACGCCATTACAAACAAGTG 59.581 34.615 0.00 0.00 0.00 3.16
3297 3738 7.977904 ACTACCTAAACAATTTACGCCATTAC 58.022 34.615 0.00 0.00 0.00 1.89
3324 3765 1.679139 CAACAGGTCCACAGAAGCAA 58.321 50.000 0.00 0.00 0.00 3.91
3397 3838 7.936847 CCCAACCTGTGTTATATTATAGAGCAA 59.063 37.037 0.00 0.00 32.09 3.91
3398 3839 7.071950 ACCCAACCTGTGTTATATTATAGAGCA 59.928 37.037 0.00 0.00 32.09 4.26
3399 3840 7.387948 CACCCAACCTGTGTTATATTATAGAGC 59.612 40.741 0.00 0.00 32.09 4.09
3400 3841 7.387948 GCACCCAACCTGTGTTATATTATAGAG 59.612 40.741 0.00 0.00 36.11 2.43
3401 3842 7.147461 TGCACCCAACCTGTGTTATATTATAGA 60.147 37.037 0.00 0.00 36.11 1.98
3570 4028 7.458397 AGAAATATCAGGGAACTTGTAACACA 58.542 34.615 0.00 0.00 40.21 3.72
3578 4036 7.996098 TTCGAAAAGAAATATCAGGGAACTT 57.004 32.000 0.00 0.00 35.13 2.66
3580 4038 8.040716 TCTTTCGAAAAGAAATATCAGGGAAC 57.959 34.615 12.41 0.00 46.60 3.62
3640 4098 5.128499 ACCAAACAACACAAATGAATCAGGA 59.872 36.000 0.00 0.00 0.00 3.86
3682 4140 6.398234 AAATTACCATGCAAAGTACACACA 57.602 33.333 0.00 0.00 0.00 3.72
3700 4158 7.450014 TGGCTTTGACTTTCTGACCATAAATTA 59.550 33.333 0.00 0.00 0.00 1.40
3701 4159 6.267471 TGGCTTTGACTTTCTGACCATAAATT 59.733 34.615 0.00 0.00 0.00 1.82
3707 4165 2.727123 TGGCTTTGACTTTCTGACCA 57.273 45.000 0.00 0.00 0.00 4.02
3741 4199 5.041951 ACAAATATACAACGGCAACACTG 57.958 39.130 0.00 0.00 0.00 3.66
3758 4216 6.587226 CCATCGATCATGAAACAACAACAAAT 59.413 34.615 0.00 0.00 33.80 2.32
3806 4266 0.464870 ACAGCAGCCAACATTTTGCA 59.535 45.000 0.00 0.00 38.97 4.08
3812 4272 0.332632 ACCCATACAGCAGCCAACAT 59.667 50.000 0.00 0.00 0.00 2.71
3813 4273 0.112218 AACCCATACAGCAGCCAACA 59.888 50.000 0.00 0.00 0.00 3.33
3845 4305 0.618680 ACAGTGATCCTGCCTAGCCA 60.619 55.000 0.00 0.00 45.68 4.75
3955 4419 6.436218 ACACACTGTACACATAAGATAGTGGA 59.564 38.462 9.88 0.00 39.99 4.02
3957 4421 7.539436 AGACACACTGTACACATAAGATAGTG 58.461 38.462 0.00 0.00 41.40 2.74
3958 4422 7.704578 AGACACACTGTACACATAAGATAGT 57.295 36.000 0.00 0.00 0.00 2.12
3959 4423 8.988064 AAAGACACACTGTACACATAAGATAG 57.012 34.615 0.00 0.00 0.00 2.08
4101 4566 6.927294 ATAAGGCAGAGCAAGTACATAAAC 57.073 37.500 0.00 0.00 0.00 2.01
4121 4586 2.649312 CTCCCCCATTCCCTGCATATAA 59.351 50.000 0.00 0.00 0.00 0.98
4306 4771 9.909644 CAATAAGGTTAGCTACTAACATACGAT 57.090 33.333 16.84 4.74 45.57 3.73
4311 4776 9.379791 GTGTTCAATAAGGTTAGCTACTAACAT 57.620 33.333 16.84 8.94 45.57 2.71
4312 4777 8.591072 AGTGTTCAATAAGGTTAGCTACTAACA 58.409 33.333 16.84 0.00 45.57 2.41
4313 4778 8.999220 AGTGTTCAATAAGGTTAGCTACTAAC 57.001 34.615 8.64 8.64 43.75 2.34
4367 4832 4.533919 TTATCACAAAACAGGGGCAATG 57.466 40.909 0.00 0.00 0.00 2.82
4409 4876 5.874810 TGCACAGTTGTCAACTATATCTTCC 59.125 40.000 17.76 2.58 40.46 3.46
4410 4877 6.968131 TGCACAGTTGTCAACTATATCTTC 57.032 37.500 17.76 4.61 40.46 2.87
4413 4880 7.307493 TCATTGCACAGTTGTCAACTATATC 57.693 36.000 17.76 8.31 40.46 1.63
4473 5015 6.436218 TCAGCAGACAAGTACATCCTTACTAA 59.564 38.462 0.00 0.00 31.73 2.24
4474 5016 5.949952 TCAGCAGACAAGTACATCCTTACTA 59.050 40.000 0.00 0.00 31.73 1.82
4475 5017 4.772624 TCAGCAGACAAGTACATCCTTACT 59.227 41.667 0.00 0.00 33.48 2.24
4516 5058 7.175816 TGGACAGCAAAATAATTAGCAACACTA 59.824 33.333 0.00 0.00 0.00 2.74
4544 5086 7.690952 TCCAGGTAACCAACAACATTATTAC 57.309 36.000 0.00 0.00 37.17 1.89
4552 5094 6.093633 GTCTTATGATCCAGGTAACCAACAAC 59.906 42.308 0.00 0.00 37.17 3.32
4618 5160 4.762765 CCGCTTATGGAGTCTAGACTGTAT 59.237 45.833 29.84 22.57 42.66 2.29
4620 5162 2.952978 CCGCTTATGGAGTCTAGACTGT 59.047 50.000 29.84 16.79 42.66 3.55
4635 5177 4.771903 TGCAATACAGGTTTATCCGCTTA 58.228 39.130 0.00 0.00 41.99 3.09
4638 5180 3.609103 CTGCAATACAGGTTTATCCGC 57.391 47.619 0.00 0.00 43.19 5.54
4660 5202 5.265989 ACAAAAGGACAGGAACAAAGGTAA 58.734 37.500 0.00 0.00 0.00 2.85
4688 5230 6.219473 AGTTATCAGCATCCATAAGTCTTCG 58.781 40.000 0.00 0.00 0.00 3.79
4740 5282 5.449999 GGGTACACAAGCCATAAAAGTATGC 60.450 44.000 0.00 0.00 45.71 3.14
4764 5328 7.095060 GCATACTTACACCATGATGAACCATAG 60.095 40.741 0.00 0.00 0.00 2.23
4813 5377 9.968743 CTACATTAATCCTAAACAAAACTCGAC 57.031 33.333 0.00 0.00 0.00 4.20
4859 5423 3.258622 AGTTGCTCCAAGTCCAGTACTAC 59.741 47.826 0.00 0.00 37.50 2.73
4863 5427 2.047061 ACAGTTGCTCCAAGTCCAGTA 58.953 47.619 0.00 0.00 0.00 2.74
4865 5429 1.605710 CAACAGTTGCTCCAAGTCCAG 59.394 52.381 0.00 0.00 0.00 3.86
4900 5464 9.139174 TGCAGTACATCACATAATATTACGATG 57.861 33.333 19.90 19.90 37.01 3.84
4914 5478 1.003118 TCCCAACCTGCAGTACATCAC 59.997 52.381 13.81 0.00 0.00 3.06
5092 5656 5.730550 ACATTTGTAGAATCTTACCTCGCA 58.269 37.500 0.00 0.00 0.00 5.10
5327 5894 5.475220 TGGTTCACAACAGTTTTGAAGAAGA 59.525 36.000 14.02 0.00 29.97 2.87
5328 5895 5.708948 TGGTTCACAACAGTTTTGAAGAAG 58.291 37.500 14.02 0.00 29.97 2.85
5329 5896 5.713792 TGGTTCACAACAGTTTTGAAGAA 57.286 34.783 14.02 4.38 29.97 2.52
5330 5897 5.652014 AGATGGTTCACAACAGTTTTGAAGA 59.348 36.000 14.02 5.88 29.97 2.87
5331 5898 5.745294 CAGATGGTTCACAACAGTTTTGAAG 59.255 40.000 14.02 0.04 29.97 3.02
5422 5989 3.947196 TCAACAGGTCATGGCATTATGTC 59.053 43.478 0.00 0.00 0.00 3.06
5439 6006 7.679400 GCACTCGAAAATCCATTATGATCAACA 60.679 37.037 0.00 0.00 0.00 3.33
5445 6012 6.554419 CAAAGCACTCGAAAATCCATTATGA 58.446 36.000 0.00 0.00 0.00 2.15
5453 6020 5.580911 AAATTGCAAAGCACTCGAAAATC 57.419 34.783 1.71 0.00 38.71 2.17
5514 6081 8.637099 CAGTGATTAGGAGAAGAGTGATGATTA 58.363 37.037 0.00 0.00 0.00 1.75
5583 6152 0.937304 TGCTTGTCTTGAACGTGCTC 59.063 50.000 0.00 0.00 32.22 4.26
5661 6230 1.519455 CATCTCCTGGCGAACGGTC 60.519 63.158 0.00 0.00 0.00 4.79
5788 6357 1.823295 GCAACAGGCGGGATAGAGA 59.177 57.895 0.00 0.00 0.00 3.10
5886 6456 7.814264 ATCAGGTCTATATTTTGAAGCTTGG 57.186 36.000 2.10 0.00 0.00 3.61
5894 6464 7.026631 TCGCCAAAATCAGGTCTATATTTTG 57.973 36.000 16.03 16.03 44.49 2.44
5917 6487 0.872388 GGGAAACACACACCACGATC 59.128 55.000 0.00 0.00 0.00 3.69
5945 6515 1.139163 GCAGCAAAATTGTGTTCCCG 58.861 50.000 0.00 0.00 0.00 5.14
5948 6519 3.061006 CGAACAGCAGCAAAATTGTGTTC 60.061 43.478 13.27 13.27 40.13 3.18
6017 6588 6.154534 TCACAAGGCTTAGATAGAGTTGCTAA 59.845 38.462 0.00 0.00 31.66 3.09
6210 6785 1.209127 CAATCCCGCCGACACAAAC 59.791 57.895 0.00 0.00 0.00 2.93
6211 6786 0.820074 AACAATCCCGCCGACACAAA 60.820 50.000 0.00 0.00 0.00 2.83
6278 6853 0.387622 CACCAATTGCCAGCTCAACG 60.388 55.000 0.00 0.00 0.00 4.10
6281 6856 1.607178 CCCACCAATTGCCAGCTCA 60.607 57.895 0.00 0.00 0.00 4.26
6312 6888 3.760738 TCACCATGTCTTGCCATTACAA 58.239 40.909 0.00 0.00 0.00 2.41
6316 6892 1.547372 GCTTCACCATGTCTTGCCATT 59.453 47.619 0.00 0.00 0.00 3.16
6317 6893 1.180029 GCTTCACCATGTCTTGCCAT 58.820 50.000 0.00 0.00 0.00 4.40
6344 6920 4.496895 CAGAAAAGAAAACGAGCAACACAG 59.503 41.667 0.00 0.00 0.00 3.66
6397 6976 5.439721 CATCCACATTTCCTAGACAATCCA 58.560 41.667 0.00 0.00 0.00 3.41
6402 6981 4.264253 CAAGCATCCACATTTCCTAGACA 58.736 43.478 0.00 0.00 0.00 3.41
6442 7021 0.394352 GACGGAGGGGGTACTCGTAA 60.394 60.000 0.00 0.00 38.39 3.18
6452 7031 1.283905 ACTTATTTTGGGACGGAGGGG 59.716 52.381 0.00 0.00 0.00 4.79
6475 7054 2.267642 CTCCGTCCCAAATCGGCA 59.732 61.111 0.00 0.00 45.44 5.69
6489 7069 3.331718 ACCTTCCAGTATACTCCCTCC 57.668 52.381 1.26 0.00 0.00 4.30
6501 7081 7.814587 GGAACATGAAAAATTAGAACCTTCCAG 59.185 37.037 0.00 0.00 0.00 3.86
6545 7125 7.936496 ATCAACTTTCCACCAAATTGTTTTT 57.064 28.000 0.00 0.00 0.00 1.94
6551 7131 7.229106 CCATGAAAATCAACTTTCCACCAAATT 59.771 33.333 0.00 0.00 34.91 1.82
6560 7140 8.647143 TTTCTTGTCCATGAAAATCAACTTTC 57.353 30.769 0.00 0.00 33.38 2.62
6564 7144 7.209475 TCCTTTTCTTGTCCATGAAAATCAAC 58.791 34.615 16.60 0.00 40.92 3.18
6574 7154 1.351017 TCGCCTCCTTTTCTTGTCCAT 59.649 47.619 0.00 0.00 0.00 3.41
6579 7159 1.198637 CTGCTTCGCCTCCTTTTCTTG 59.801 52.381 0.00 0.00 0.00 3.02
6589 7169 2.359230 GCCAAGTCTGCTTCGCCT 60.359 61.111 0.00 0.00 33.60 5.52
6590 7170 2.359230 AGCCAAGTCTGCTTCGCC 60.359 61.111 0.00 0.00 39.21 5.54
6653 7256 3.426117 ATCCCGCTACACGCCTTCG 62.426 63.158 0.00 0.00 41.76 3.79
6654 7257 1.883084 CATCCCGCTACACGCCTTC 60.883 63.158 0.00 0.00 41.76 3.46
6660 7264 1.871080 CCATCTTCATCCCGCTACAC 58.129 55.000 0.00 0.00 0.00 2.90
6661 7265 0.106708 GCCATCTTCATCCCGCTACA 59.893 55.000 0.00 0.00 0.00 2.74
6667 7271 1.530183 GCCCTGCCATCTTCATCCC 60.530 63.158 0.00 0.00 0.00 3.85
6685 7289 2.361610 ATTCCAACGGCTGCCCTG 60.362 61.111 14.12 10.67 0.00 4.45
6733 7337 2.202676 GTCGCCTGAGAAGCTCGG 60.203 66.667 0.00 0.00 36.69 4.63
6734 7338 0.452184 TAAGTCGCCTGAGAAGCTCG 59.548 55.000 0.00 0.00 32.35 5.03
6747 7351 3.378742 ACTGACTGCCTATCTGTAAGTCG 59.621 47.826 0.00 0.00 40.10 4.18
6757 7361 9.343539 GGAGAAATTAAAATACTGACTGCCTAT 57.656 33.333 0.00 0.00 0.00 2.57
6758 7362 7.773690 GGGAGAAATTAAAATACTGACTGCCTA 59.226 37.037 0.00 0.00 32.24 3.93
6759 7363 6.603599 GGGAGAAATTAAAATACTGACTGCCT 59.396 38.462 0.00 0.00 32.24 4.75
6760 7364 6.603599 AGGGAGAAATTAAAATACTGACTGCC 59.396 38.462 0.00 0.00 34.46 4.85
6761 7365 7.336931 TGAGGGAGAAATTAAAATACTGACTGC 59.663 37.037 0.00 0.00 0.00 4.40
6762 7366 8.792830 TGAGGGAGAAATTAAAATACTGACTG 57.207 34.615 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.