Multiple sequence alignment - TraesCS3A01G407500

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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 TraesCS3A01G407500 chr3A 100.000 5116 0 0 1 5116 652773851 652778966 0.000000e+00 9448
1 TraesCS3A01G407500 chr3A 100.000 370 0 0 5509 5878 652779359 652779728 0.000000e+00 684
2 TraesCS3A01G407500 chr3A 78.992 357 46 9 15 368 34843509 34843839 3.570000e-52 217
3 TraesCS3A01G407500 chr3B 93.438 4145 196 37 762 4887 680335790 680331703 0.000000e+00 6078
4 TraesCS3A01G407500 chr3B 88.038 744 61 15 15 750 680336495 680335772 0.000000e+00 856
5 TraesCS3A01G407500 chr3B 85.470 234 25 7 5509 5737 680331431 680331202 9.850000e-58 235
6 TraesCS3A01G407500 chr3B 79.213 356 58 10 15 368 42863020 42863361 3.540000e-57 233
7 TraesCS3A01G407500 chr3B 93.478 138 9 0 5741 5878 680318182 680318045 7.720000e-49 206
8 TraesCS3A01G407500 chr3D 90.457 1991 119 30 15 1974 516960050 516962000 0.000000e+00 2558
9 TraesCS3A01G407500 chr3D 91.218 1856 105 34 3282 5114 516963417 516965237 0.000000e+00 2471
10 TraesCS3A01G407500 chr3D 93.014 1274 66 11 2016 3280 516962002 516963261 0.000000e+00 1838
11 TraesCS3A01G407500 chr3D 88.947 380 31 8 5509 5878 516965311 516965689 5.370000e-125 459
12 TraesCS3A01G407500 chr3D 78.851 383 52 10 15 394 25755708 25756064 1.270000e-56 231
13 TraesCS3A01G407500 chr5A 81.308 321 43 9 15 328 602265651 602265341 1.640000e-60 244
14 TraesCS3A01G407500 chr6D 85.326 184 26 1 38 221 81675980 81675798 7.780000e-44 189
15 TraesCS3A01G407500 chr5D 83.516 182 26 4 15 196 368251683 368251860 3.640000e-37 167
16 TraesCS3A01G407500 chr5B 91.667 72 4 1 124 195 588574193 588574124 1.350000e-16 99


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 TraesCS3A01G407500 chr3A 652773851 652779728 5877 False 5066.000000 9448 100.000 1 5878 2 chr3A.!!$F2 5877
1 TraesCS3A01G407500 chr3B 680331202 680336495 5293 True 2389.666667 6078 88.982 15 5737 3 chr3B.!!$R2 5722
2 TraesCS3A01G407500 chr3D 516960050 516965689 5639 False 1831.500000 2558 90.909 15 5878 4 chr3D.!!$F2 5863

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
956 1009 0.673644 GTGCCCGCCATATATTCGCT 60.674 55.000 1.2 0.00 0.00 4.93 F
1529 1588 1.137872 CTTAGCCATTCTGCTCGACCT 59.862 52.381 0.0 0.00 41.68 3.85 F
2178 2254 0.603569 TCCGAGTCAGAACTTCCAGC 59.396 55.000 0.0 0.00 35.28 4.85 F
2197 2273 0.803117 CAATGCAGTGCTCTGTCCAG 59.197 55.000 17.6 2.54 43.05 3.86 F
2244 2321 1.107114 AGTGAGTGGTGGCTATCTCG 58.893 55.000 0.0 0.00 0.00 4.04 F
3649 3893 1.354368 GAGAATTTGGTGGGTGAGGGA 59.646 52.381 0.0 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2254 0.803117 CTGGACAGAGCACTGCATTG 59.197 55.0 11.37 0.00 46.95 2.82 R
3490 3734 0.930310 CGTACTGGCCGATCATGTTG 59.070 55.0 0.00 0.00 0.00 3.33 R
3675 3919 0.107459 GACCTGGCCATCCTTGAGTC 60.107 60.0 5.51 1.21 0.00 3.36 R
3975 4220 0.321919 TAAGCCTGCTGCCTTGTCTG 60.322 55.0 0.00 0.00 42.71 3.51 R
3988 4233 1.127567 TGTGCCACTCCAGTAAGCCT 61.128 55.0 0.00 0.00 0.00 4.58 R
4974 5240 0.407139 ATCCTTGCTGACCTGGCTTT 59.593 50.0 0.00 0.00 0.00 3.51 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
53 54 2.500509 TCCGAACCATTTGTTGTTGC 57.499 45.000 0.00 0.00 37.29 4.17
65 66 8.655092 ACCATTTGTTGTTGCATTAATTATTCG 58.345 29.630 0.00 0.00 0.00 3.34
115 116 5.068987 ACAGTTGTTGTATTGTGATTTGCCT 59.931 36.000 0.00 0.00 38.56 4.75
116 117 5.984926 CAGTTGTTGTATTGTGATTTGCCTT 59.015 36.000 0.00 0.00 0.00 4.35
137 140 6.593770 GCCTTTTGGACCATTTATAAGTTTGG 59.406 38.462 0.00 8.75 44.07 3.28
195 198 7.804843 TGAAAATCATGAATTTGCAAACCTT 57.195 28.000 15.41 5.81 39.52 3.50
196 199 8.223177 TGAAAATCATGAATTTGCAAACCTTT 57.777 26.923 15.41 4.98 39.52 3.11
215 218 4.983538 CCTTTTAAAAATTTGCGGTACCGT 59.016 37.500 33.34 12.88 42.09 4.83
216 219 5.107798 CCTTTTAAAAATTTGCGGTACCGTG 60.108 40.000 33.34 9.37 42.09 4.94
217 220 4.825546 TTAAAAATTTGCGGTACCGTGA 57.174 36.364 33.34 20.23 42.09 4.35
218 221 2.981400 AAAATTTGCGGTACCGTGAG 57.019 45.000 33.34 8.20 42.09 3.51
262 265 6.660521 GGATCATATCCTGTAAAATCATGCCA 59.339 38.462 0.00 0.00 46.19 4.92
275 278 5.769484 AATCATGCCACAAAAATTTTGCA 57.231 30.435 17.39 13.93 0.00 4.08
293 296 5.627499 TTGCAGGACAAGTTTACATGATC 57.373 39.130 0.00 0.00 33.24 2.92
313 317 2.525629 TTCCACCGAGGCCTCACA 60.526 61.111 31.67 7.75 37.29 3.58
328 332 2.159627 CCTCACAGTACCGCATTTGTTC 59.840 50.000 0.00 0.00 0.00 3.18
338 349 8.018520 CAGTACCGCATTTGTTCTTTTTACATA 58.981 33.333 0.00 0.00 0.00 2.29
343 354 5.861787 GCATTTGTTCTTTTTACATACGGCT 59.138 36.000 0.00 0.00 0.00 5.52
350 361 9.656040 TGTTCTTTTTACATACGGCTCTTATAA 57.344 29.630 0.00 0.00 0.00 0.98
364 375 5.034797 GCTCTTATAACAAATTTGCGGGAC 58.965 41.667 18.12 0.00 0.00 4.46
383 396 3.573598 GACGAGTGATCTGGATATGCTG 58.426 50.000 0.00 0.00 0.00 4.41
394 407 2.158856 TGGATATGCTGGAGTTGCTCTG 60.159 50.000 0.00 0.00 0.00 3.35
406 419 3.932089 GAGTTGCTCTGAGAGTTTCATCC 59.068 47.826 11.64 0.00 34.68 3.51
426 439 2.050077 GGTCCTGCGTGCAAAAGC 60.050 61.111 0.00 0.00 0.00 3.51
428 441 2.518112 TCCTGCGTGCAAAAGCCA 60.518 55.556 7.47 0.00 0.00 4.75
433 446 2.597713 GCGTGCAAAAGCCAAAGCC 61.598 57.895 0.00 0.00 41.25 4.35
443 456 5.985530 GCAAAAGCCAAAGCCCTTATATTAG 59.014 40.000 0.00 0.00 41.25 1.73
446 459 7.530426 AAAGCCAAAGCCCTTATATTAGATG 57.470 36.000 0.00 0.00 41.25 2.90
497 510 2.173964 GCGATGTAACCGAAATTGCAC 58.826 47.619 0.00 0.00 32.03 4.57
583 596 1.604755 GCTCGATGACTAGGACGACAT 59.395 52.381 0.00 0.00 0.00 3.06
584 597 2.033550 GCTCGATGACTAGGACGACATT 59.966 50.000 0.00 0.00 0.00 2.71
611 624 9.562408 TTTTTCCCCCAAAATAAAATGAAGTAC 57.438 29.630 0.00 0.00 33.82 2.73
651 664 7.713942 AGAGTGATTCGTAACCATAATTTACCC 59.286 37.037 0.00 0.00 0.00 3.69
744 789 2.626743 ACCAGCGGCTTATATAACGAGT 59.373 45.455 0.00 1.81 0.00 4.18
745 790 3.069158 ACCAGCGGCTTATATAACGAGTT 59.931 43.478 0.00 0.00 0.00 3.01
746 791 3.673809 CCAGCGGCTTATATAACGAGTTC 59.326 47.826 0.00 0.00 0.00 3.01
747 792 3.673809 CAGCGGCTTATATAACGAGTTCC 59.326 47.826 0.00 0.00 0.00 3.62
748 793 3.573110 AGCGGCTTATATAACGAGTTCCT 59.427 43.478 9.07 0.00 0.00 3.36
749 794 4.038883 AGCGGCTTATATAACGAGTTCCTT 59.961 41.667 9.07 0.00 0.00 3.36
750 795 4.385146 GCGGCTTATATAACGAGTTCCTTC 59.615 45.833 9.07 0.00 0.00 3.46
751 796 4.615961 CGGCTTATATAACGAGTTCCTTCG 59.384 45.833 0.00 0.00 45.70 3.79
752 797 5.561532 CGGCTTATATAACGAGTTCCTTCGA 60.562 44.000 2.12 0.00 43.03 3.71
753 798 6.211515 GGCTTATATAACGAGTTCCTTCGAA 58.788 40.000 0.00 0.00 43.03 3.71
754 799 6.362820 GGCTTATATAACGAGTTCCTTCGAAG 59.637 42.308 18.51 18.51 43.03 3.79
755 800 7.137426 GCTTATATAACGAGTTCCTTCGAAGA 58.863 38.462 26.61 9.79 43.03 2.87
756 801 7.646922 GCTTATATAACGAGTTCCTTCGAAGAA 59.353 37.037 26.61 15.03 45.90 2.52
757 802 9.512435 CTTATATAACGAGTTCCTTCGAAGAAA 57.488 33.333 26.61 10.24 45.90 2.52
758 803 9.859427 TTATATAACGAGTTCCTTCGAAGAAAA 57.141 29.630 26.61 16.40 45.90 2.29
759 804 8.767478 ATATAACGAGTTCCTTCGAAGAAAAA 57.233 30.769 26.61 14.00 45.90 1.94
814 863 3.554342 CCCATCCCTGCTCCCTCG 61.554 72.222 0.00 0.00 0.00 4.63
815 864 4.247380 CCATCCCTGCTCCCTCGC 62.247 72.222 0.00 0.00 0.00 5.03
816 865 3.160047 CATCCCTGCTCCCTCGCT 61.160 66.667 0.00 0.00 0.00 4.93
881 930 4.389576 CGACAACAGCAAGGCGCC 62.390 66.667 21.89 21.89 44.04 6.53
924 977 2.388890 GATCATCCTCCGGCCACCTG 62.389 65.000 2.24 0.00 0.00 4.00
956 1009 0.673644 GTGCCCGCCATATATTCGCT 60.674 55.000 1.20 0.00 0.00 4.93
1246 1299 2.892425 CCAAGCTCGCGATGGACC 60.892 66.667 20.14 2.47 36.27 4.46
1410 1469 3.627218 GACATACTTCGCGGCGGC 61.627 66.667 23.46 6.12 0.00 6.53
1447 1506 2.504244 GCGTTCTCCACTCCGTCG 60.504 66.667 0.00 0.00 0.00 5.12
1529 1588 1.137872 CTTAGCCATTCTGCTCGACCT 59.862 52.381 0.00 0.00 41.68 3.85
1530 1589 2.067365 TAGCCATTCTGCTCGACCTA 57.933 50.000 0.00 0.00 41.68 3.08
1531 1590 1.195115 AGCCATTCTGCTCGACCTAA 58.805 50.000 0.00 0.00 36.75 2.69
1532 1591 1.765314 AGCCATTCTGCTCGACCTAAT 59.235 47.619 0.00 0.00 36.75 1.73
1565 1628 7.095439 ACTCTTGTTTAAATTGCTCTTCTCGAG 60.095 37.037 5.93 5.93 42.88 4.04
1589 1652 6.482641 AGTCTACATTCATCATTCATGTGCTC 59.517 38.462 0.00 0.00 33.19 4.26
1641 1704 2.159421 GCGATCGACCTCTGTAGTTGAA 60.159 50.000 21.57 0.00 31.48 2.69
1650 1713 6.253727 CGACCTCTGTAGTTGAATATTGTGTC 59.746 42.308 0.00 0.00 0.00 3.67
1702 1770 7.894708 TGATACATTTGGAATGTCAATGTGTT 58.105 30.769 9.37 0.00 32.28 3.32
1776 1848 6.228258 TCATTGTAGTGGTCAGGTAGAAAAC 58.772 40.000 0.00 0.00 0.00 2.43
1781 1853 7.439381 TGTAGTGGTCAGGTAGAAAACTTTAG 58.561 38.462 0.00 0.00 0.00 1.85
1794 1866 6.169800 AGAAAACTTTAGATGCTGTCCTCTC 58.830 40.000 0.00 0.00 0.00 3.20
1856 1928 5.221783 TGACAGATGCTTCCATATATGTGCT 60.222 40.000 11.73 3.99 0.00 4.40
1875 1947 1.471684 CTGATTGGCTTTCAGTCCTGC 59.528 52.381 8.52 0.00 36.64 4.85
1892 1964 2.224281 CCTGCTGGTCACTGTTTCACTA 60.224 50.000 0.51 0.00 0.00 2.74
1937 2009 4.118093 TGAAGAAGCATCATGGCATTTG 57.882 40.909 0.00 0.00 35.83 2.32
1945 2017 3.181469 GCATCATGGCATTTGGAATCACT 60.181 43.478 0.00 0.00 0.00 3.41
1946 2018 4.368315 CATCATGGCATTTGGAATCACTG 58.632 43.478 0.00 0.00 0.00 3.66
1952 2024 4.283978 TGGCATTTGGAATCACTGACATTT 59.716 37.500 0.00 0.00 0.00 2.32
1957 2029 7.274250 GCATTTGGAATCACTGACATTTTAGAC 59.726 37.037 0.00 0.00 0.00 2.59
1961 2033 6.430925 TGGAATCACTGACATTTTAGACAAGG 59.569 38.462 0.00 0.00 0.00 3.61
1965 2037 4.821805 CACTGACATTTTAGACAAGGGTGT 59.178 41.667 0.00 0.00 42.10 4.16
2014 2086 7.553881 AATGGTATACTGACAAGGAAAATCG 57.446 36.000 2.25 0.00 0.00 3.34
2038 2110 6.129717 CGACTTTAAAACAGCAGAATGAAACG 60.130 38.462 0.00 0.00 39.69 3.60
2043 2115 4.764679 AACAGCAGAATGAAACGCATTA 57.235 36.364 0.00 0.00 46.90 1.90
2053 2125 8.577939 CAGAATGAAACGCATTATGTGTAAAAG 58.422 33.333 12.00 0.00 46.18 2.27
2054 2126 8.296713 AGAATGAAACGCATTATGTGTAAAAGT 58.703 29.630 12.00 0.11 46.90 2.66
2056 2128 9.900710 AATGAAACGCATTATGTGTAAAAGTTA 57.099 25.926 12.00 0.00 45.16 2.24
2057 2129 8.716619 TGAAACGCATTATGTGTAAAAGTTAC 57.283 30.769 12.00 0.00 40.68 2.50
2063 2138 7.213706 CGCATTATGTGTAAAAGTTACAAGTCG 59.786 37.037 2.53 0.00 0.00 4.18
2095 2170 7.763528 GCATAAACACATGATTTTTGTATGGGA 59.236 33.333 0.00 0.00 0.00 4.37
2108 2183 7.391148 TTTTGTATGGGAGCAATTAGACTTC 57.609 36.000 0.00 0.00 0.00 3.01
2117 2192 5.654209 GGAGCAATTAGACTTCCCATTCTTT 59.346 40.000 0.00 0.00 0.00 2.52
2121 2196 7.015584 AGCAATTAGACTTCCCATTCTTTTTGT 59.984 33.333 0.00 0.00 0.00 2.83
2148 2223 9.965902 ATAAGATAGACTGTCCATTCTTGTTTT 57.034 29.630 19.46 4.36 0.00 2.43
2149 2224 7.678947 AGATAGACTGTCCATTCTTGTTTTG 57.321 36.000 3.76 0.00 0.00 2.44
2171 2247 4.220572 GAGCGTATAATCCGAGTCAGAAC 58.779 47.826 0.00 0.00 0.00 3.01
2178 2254 0.603569 TCCGAGTCAGAACTTCCAGC 59.396 55.000 0.00 0.00 35.28 4.85
2197 2273 0.803117 CAATGCAGTGCTCTGTCCAG 59.197 55.000 17.60 2.54 43.05 3.86
2236 2313 4.379813 GCATTGAATTGTAGTGAGTGGTGG 60.380 45.833 0.00 0.00 0.00 4.61
2244 2321 1.107114 AGTGAGTGGTGGCTATCTCG 58.893 55.000 0.00 0.00 0.00 4.04
2272 2349 4.497300 CTGATTATTGCTGTTGTTTGGGG 58.503 43.478 0.00 0.00 0.00 4.96
2294 2371 4.214332 GGATTTGGAGTCACTGTTCACTTC 59.786 45.833 0.00 0.00 0.00 3.01
2525 2602 2.432563 CGCCAAGTGGGGGTAACA 59.567 61.111 6.50 0.00 44.34 2.41
2535 2617 3.856206 AGTGGGGGTAACATTTCCTACAT 59.144 43.478 0.00 0.00 33.89 2.29
2569 2651 6.579865 TGTTAGGATAAGTAGCTGCTTTACC 58.420 40.000 22.51 22.35 0.00 2.85
2573 2655 5.897824 AGGATAAGTAGCTGCTTTACCAGTA 59.102 40.000 27.25 11.29 35.28 2.74
2584 2666 4.010349 GCTTTACCAGTAGGACTTGCAAT 58.990 43.478 0.00 0.00 38.69 3.56
2598 2680 7.725251 AGGACTTGCAATATTCTTGAAAACAA 58.275 30.769 0.00 0.00 0.00 2.83
2605 2687 9.941325 TGCAATATTCTTGAAAACAATGGTTAT 57.059 25.926 0.00 0.00 35.82 1.89
2725 2808 4.034285 AGTAAAGCTGCTTGGGTTGTAT 57.966 40.909 16.73 0.00 0.00 2.29
2810 2896 9.296400 GAGCATTTGTTTGTTCAGTAGTTAAAA 57.704 29.630 0.00 0.00 0.00 1.52
2811 2897 9.083080 AGCATTTGTTTGTTCAGTAGTTAAAAC 57.917 29.630 0.00 0.00 0.00 2.43
2812 2898 9.083080 GCATTTGTTTGTTCAGTAGTTAAAACT 57.917 29.630 0.39 0.39 42.91 2.66
3174 3260 2.994995 AGCGTCACGTCCATCCCA 60.995 61.111 0.00 0.00 0.00 4.37
3250 3336 7.061441 CACAATCATAAAGTTGCAACTAGCTTG 59.939 37.037 31.31 25.54 45.94 4.01
3252 3338 6.633500 TCATAAAGTTGCAACTAGCTTGTT 57.367 33.333 31.31 21.86 45.94 2.83
3287 3527 7.466860 CGAAATGTTAAAATGGGACCTAGTAGC 60.467 40.741 0.00 0.00 0.00 3.58
3307 3547 3.190744 AGCGCTTAAAAGGTAGAAAAGGC 59.809 43.478 2.64 0.00 0.00 4.35
3352 3596 6.432607 TTCATGCAGAATTCAAGAGCTTAG 57.567 37.500 8.44 1.75 0.00 2.18
3402 3646 6.465084 AGTAGCTGTAGTTTTACCTTCCAAG 58.535 40.000 0.00 0.00 0.00 3.61
3419 3663 6.540189 CCTTCCAAGAGATAATGTTACACAGG 59.460 42.308 0.00 0.00 0.00 4.00
3420 3664 5.428253 TCCAAGAGATAATGTTACACAGGC 58.572 41.667 0.00 0.00 0.00 4.85
3432 3676 4.941263 TGTTACACAGGCCATCTACAATTC 59.059 41.667 5.01 0.00 0.00 2.17
3434 3678 1.942657 CACAGGCCATCTACAATTCCG 59.057 52.381 5.01 0.00 0.00 4.30
3456 3700 5.060569 CCGTATTTACTCATACTACGCATGC 59.939 44.000 7.91 7.91 35.17 4.06
3505 3749 1.667724 GAAGACAACATGATCGGCCAG 59.332 52.381 2.24 0.00 0.00 4.85
3614 3858 3.870274 TCAGAGATCCAATCTGCAACAG 58.130 45.455 5.74 0.00 43.20 3.16
3643 3887 3.490348 CTCAAGTGAGAATTTGGTGGGT 58.510 45.455 1.88 0.00 44.74 4.51
3649 3893 1.354368 GAGAATTTGGTGGGTGAGGGA 59.646 52.381 0.00 0.00 0.00 4.20
3667 3911 2.424812 GGGAGGATTTGGGCATGTGTAT 60.425 50.000 0.00 0.00 0.00 2.29
3675 3919 3.576078 TGGGCATGTGTATAAAGGGAG 57.424 47.619 0.00 0.00 0.00 4.30
3676 3920 3.119319 TGGGCATGTGTATAAAGGGAGA 58.881 45.455 0.00 0.00 0.00 3.71
3884 4128 5.183713 TCTCTTGAGTGGCATTTATTTGGTG 59.816 40.000 0.00 0.00 0.00 4.17
3975 4220 6.534793 TCTTTTCTTTTGCCACTTGATGAAAC 59.465 34.615 0.00 0.00 0.00 2.78
3988 4233 1.881973 GATGAAACAGACAAGGCAGCA 59.118 47.619 0.00 0.00 0.00 4.41
4176 4421 6.934645 TCACTTCTTACTGGTACATTTGAAGG 59.065 38.462 0.00 0.00 38.20 3.46
4187 4432 4.961438 ACATTTGAAGGTGCAAATCCTT 57.039 36.364 6.79 6.79 44.30 3.36
4190 4435 6.633856 ACATTTGAAGGTGCAAATCCTTATC 58.366 36.000 7.05 0.00 44.30 1.75
4191 4436 6.438425 ACATTTGAAGGTGCAAATCCTTATCT 59.562 34.615 7.05 0.00 44.30 1.98
4202 4447 6.939730 TGCAAATCCTTATCTGTTCTGTTGTA 59.060 34.615 0.00 0.00 0.00 2.41
4212 4457 6.092955 TCTGTTCTGTTGTAATTACGTCCT 57.907 37.500 10.92 0.00 0.00 3.85
4348 4593 6.540189 CCGATAATCTCAACTCTGTTCCATTT 59.460 38.462 0.00 0.00 0.00 2.32
4411 4656 5.649395 GGATTTTCTTGTCATGTCCATCAGA 59.351 40.000 0.00 0.00 0.00 3.27
4477 4722 2.094675 ACAGATGTGTATGCCTTTGGC 58.905 47.619 0.00 1.01 41.91 4.52
4540 4785 1.518056 AACATGAAGGGCAGTGCACG 61.518 55.000 18.61 7.77 36.86 5.34
4567 4812 9.814899 CACATATTGCAATGGGTATTCTTTTTA 57.185 29.630 22.27 0.00 0.00 1.52
4575 4820 9.952188 GCAATGGGTATTCTTTTTAGTAGATTC 57.048 33.333 0.00 0.00 0.00 2.52
4592 4837 8.049655 AGTAGATTCTTCTCCTTTTCATTTGC 57.950 34.615 0.00 0.00 33.17 3.68
4593 4838 6.278172 AGATTCTTCTCCTTTTCATTTGCC 57.722 37.500 0.00 0.00 0.00 4.52
4594 4839 5.776716 AGATTCTTCTCCTTTTCATTTGCCA 59.223 36.000 0.00 0.00 0.00 4.92
4595 4840 5.867903 TTCTTCTCCTTTTCATTTGCCAA 57.132 34.783 0.00 0.00 0.00 4.52
4596 4841 5.200368 TCTTCTCCTTTTCATTTGCCAAC 57.800 39.130 0.00 0.00 0.00 3.77
4597 4842 3.641437 TCTCCTTTTCATTTGCCAACG 57.359 42.857 0.00 0.00 0.00 4.10
4598 4843 2.955660 TCTCCTTTTCATTTGCCAACGT 59.044 40.909 0.00 0.00 0.00 3.99
4603 4848 5.242838 TCCTTTTCATTTGCCAACGTCTTAT 59.757 36.000 0.00 0.00 0.00 1.73
4606 4851 4.875544 TCATTTGCCAACGTCTTATAGC 57.124 40.909 0.00 0.00 0.00 2.97
4607 4852 3.625764 TCATTTGCCAACGTCTTATAGCC 59.374 43.478 0.00 0.00 0.00 3.93
4608 4853 1.647346 TTGCCAACGTCTTATAGCCG 58.353 50.000 0.00 0.00 0.00 5.52
4610 4855 1.411246 TGCCAACGTCTTATAGCCGAT 59.589 47.619 0.00 0.00 0.00 4.18
4628 4873 4.178540 CCGATTTGCAGCATTCATTTTCT 58.821 39.130 0.00 0.00 0.00 2.52
4629 4874 4.628333 CCGATTTGCAGCATTCATTTTCTT 59.372 37.500 0.00 0.00 0.00 2.52
4631 4876 4.735662 TTTGCAGCATTCATTTTCTTGC 57.264 36.364 0.00 0.00 35.34 4.01
4638 4883 6.679638 GCAGCATTCATTTTCTTGCATCTCTA 60.680 38.462 0.00 0.00 37.56 2.43
4641 4886 8.566260 AGCATTCATTTTCTTGCATCTCTATAC 58.434 33.333 0.00 0.00 37.56 1.47
4688 4933 0.441533 GTCTTGCACTGCACGATCTG 59.558 55.000 12.88 0.00 38.93 2.90
4881 5126 9.757227 TCATCCCACATTTTACAAAGTAAAAAG 57.243 29.630 16.20 14.55 31.26 2.27
4883 5128 9.981114 ATCCCACATTTTACAAAGTAAAAAGAG 57.019 29.630 18.63 12.99 31.26 2.85
4885 5130 9.463443 CCCACATTTTACAAAGTAAAAAGAGAG 57.537 33.333 18.63 11.06 31.26 3.20
4894 5139 8.472007 ACAAAGTAAAAAGAGAGAGAGAGAGA 57.528 34.615 0.00 0.00 0.00 3.10
4895 5140 8.576442 ACAAAGTAAAAAGAGAGAGAGAGAGAG 58.424 37.037 0.00 0.00 0.00 3.20
4896 5141 8.792633 CAAAGTAAAAAGAGAGAGAGAGAGAGA 58.207 37.037 0.00 0.00 0.00 3.10
4898 5143 7.918076 AGTAAAAAGAGAGAGAGAGAGAGAGA 58.082 38.462 0.00 0.00 0.00 3.10
4899 5144 8.043710 AGTAAAAAGAGAGAGAGAGAGAGAGAG 58.956 40.741 0.00 0.00 0.00 3.20
4900 5145 6.627087 AAAAGAGAGAGAGAGAGAGAGAGA 57.373 41.667 0.00 0.00 0.00 3.10
4901 5146 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
4902 5147 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
4903 5148 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4904 5149 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4905 5150 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4906 5151 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4907 5152 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4908 5153 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4909 5154 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4910 5155 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4911 5156 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
4912 5157 5.774690 AGAGAGAGAGAGAGAGAGAGAGATC 59.225 48.000 0.00 0.00 0.00 2.75
4913 5158 4.837860 AGAGAGAGAGAGAGAGAGAGATCC 59.162 50.000 0.00 0.00 0.00 3.36
4914 5159 4.825445 AGAGAGAGAGAGAGAGAGATCCT 58.175 47.826 0.00 0.00 0.00 3.24
4915 5160 5.970289 AGAGAGAGAGAGAGAGAGATCCTA 58.030 45.833 0.00 0.00 0.00 2.94
4916 5161 5.777732 AGAGAGAGAGAGAGAGAGATCCTAC 59.222 48.000 0.00 0.00 0.00 3.18
4919 5164 3.576982 GAGAGAGAGAGAGATCCTACGGA 59.423 52.174 0.00 0.00 35.55 4.69
4921 5166 3.576982 GAGAGAGAGAGATCCTACGGAGA 59.423 52.174 0.00 0.00 34.05 3.71
4934 5179 3.319198 GGAGAAGCCCCGTGGACA 61.319 66.667 0.00 0.00 0.00 4.02
4938 5183 1.141053 GAGAAGCCCCGTGGACAATAT 59.859 52.381 0.00 0.00 0.00 1.28
4944 5189 5.313280 AGCCCCGTGGACAATATATTAAA 57.687 39.130 0.00 0.00 0.00 1.52
4945 5190 5.313712 AGCCCCGTGGACAATATATTAAAG 58.686 41.667 0.00 0.00 0.00 1.85
4960 5205 0.041535 TAAAGGTAGAGCCCACCCGA 59.958 55.000 0.00 0.00 36.67 5.14
4974 5240 0.697079 ACCCGAGTGAGGTAGAGTCA 59.303 55.000 0.00 0.00 35.24 3.41
4977 5243 2.164624 CCCGAGTGAGGTAGAGTCAAAG 59.835 54.545 0.00 0.00 0.00 2.77
5038 5304 8.070171 CACTCACATTTTACGAAGTGAAGAAAT 58.930 33.333 0.00 0.00 45.73 2.17
5044 5310 8.717821 CATTTTACGAAGTGAAGAAATAGTCCA 58.282 33.333 0.00 0.00 45.73 4.02
5046 5312 8.665643 TTTACGAAGTGAAGAAATAGTCCAAA 57.334 30.769 0.00 0.00 45.73 3.28
5048 5314 5.701290 ACGAAGTGAAGAAATAGTCCAAAGG 59.299 40.000 0.00 0.00 42.51 3.11
5052 5318 7.929941 AGTGAAGAAATAGTCCAAAGGAATC 57.070 36.000 0.00 0.00 31.38 2.52
5054 5320 6.659242 GTGAAGAAATAGTCCAAAGGAATCCA 59.341 38.462 0.61 0.00 31.38 3.41
5055 5321 6.886459 TGAAGAAATAGTCCAAAGGAATCCAG 59.114 38.462 0.61 0.00 31.38 3.86
5056 5322 6.394345 AGAAATAGTCCAAAGGAATCCAGT 57.606 37.500 0.61 0.00 31.38 4.00
5058 5324 8.107196 AGAAATAGTCCAAAGGAATCCAGTAT 57.893 34.615 0.61 0.00 31.38 2.12
5059 5325 7.995488 AGAAATAGTCCAAAGGAATCCAGTATG 59.005 37.037 0.61 0.00 31.38 2.39
5061 5327 5.983333 AGTCCAAAGGAATCCAGTATGAT 57.017 39.130 0.61 0.00 32.09 2.45
5071 5339 9.736414 AAGGAATCCAGTATGATATTTCATCAG 57.264 33.333 0.61 0.00 41.73 2.90
5541 5809 7.014230 GCATAAAATGGTGTGTACATAGGGAAT 59.986 37.037 0.00 0.00 0.00 3.01
5542 5810 8.912988 CATAAAATGGTGTGTACATAGGGAATT 58.087 33.333 0.00 0.00 0.00 2.17
5544 5812 7.875327 AAATGGTGTGTACATAGGGAATTAC 57.125 36.000 0.00 0.00 0.00 1.89
5586 5859 7.250569 CCTGCGTATCTTTGTAAATGAAATGT 58.749 34.615 0.00 0.00 33.45 2.71
5595 5868 9.268268 TCTTTGTAAATGAAATGTCGTTCTACT 57.732 29.630 0.00 0.00 31.47 2.57
5596 5869 9.878599 CTTTGTAAATGAAATGTCGTTCTACTT 57.121 29.630 0.00 0.00 31.47 2.24
5636 5910 1.274703 TGTTCCCTGGCCCTCATCTC 61.275 60.000 0.00 0.00 0.00 2.75
5666 5940 0.855349 CGTCTGTTCTGCTGTGTGTC 59.145 55.000 0.00 0.00 0.00 3.67
5670 5944 1.596260 CTGTTCTGCTGTGTGTCTGTG 59.404 52.381 0.00 0.00 0.00 3.66
5743 6019 2.113910 TTTTTCCGTTGAAGCGCTTC 57.886 45.000 37.21 37.21 39.91 3.86
5744 6020 1.305201 TTTTCCGTTGAAGCGCTTCT 58.695 45.000 40.70 16.83 40.14 2.85
5745 6021 0.586319 TTTCCGTTGAAGCGCTTCTG 59.414 50.000 40.70 30.88 40.14 3.02
5746 6022 1.227999 TTCCGTTGAAGCGCTTCTGG 61.228 55.000 40.70 36.13 40.14 3.86
5759 6036 2.067932 CTTCTGGGCCTGGGTCACAA 62.068 60.000 10.79 0.00 0.00 3.33
5761 6038 1.604593 CTGGGCCTGGGTCACAAAG 60.605 63.158 4.53 0.00 0.00 2.77
5770 6047 1.699634 TGGGTCACAAAGAGAAGGAGG 59.300 52.381 0.00 0.00 0.00 4.30
5773 6050 3.558109 GGGTCACAAAGAGAAGGAGGAAG 60.558 52.174 0.00 0.00 0.00 3.46
5799 6078 3.435275 TCTGTTCCAGCATCTACTGACT 58.565 45.455 0.00 0.00 40.25 3.41
5803 6082 2.103373 TCCAGCATCTACTGACTCCAC 58.897 52.381 0.00 0.00 40.25 4.02
5813 6092 3.045601 ACTGACTCCACCGAATTGAAG 57.954 47.619 0.00 0.00 0.00 3.02
5833 6112 4.326255 GCCATGTGCAGCTTAGGT 57.674 55.556 0.00 0.00 40.77 3.08
5860 6139 4.035324 TGTTTTCGTTTACTTTCGCCATCA 59.965 37.500 0.00 0.00 0.00 3.07
5861 6140 4.398549 TTTCGTTTACTTTCGCCATCAG 57.601 40.909 0.00 0.00 0.00 2.90
5862 6141 1.730064 TCGTTTACTTTCGCCATCAGC 59.270 47.619 0.00 0.00 38.52 4.26
5863 6142 1.732259 CGTTTACTTTCGCCATCAGCT 59.268 47.619 0.00 0.00 40.39 4.24
5869 6148 1.876497 TTTCGCCATCAGCTTTGCCC 61.876 55.000 0.00 0.00 40.39 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.653526 TTATTCAAATATGTGATGCCCCTG 57.346 37.500 0.00 0.00 0.00 4.45
1 2 7.860649 AATTATTCAAATATGTGATGCCCCT 57.139 32.000 0.00 0.00 0.00 4.79
18 19 6.801575 TGGTTCGGAAGGCAAATAATTATTC 58.198 36.000 11.08 0.25 0.00 1.75
74 75 5.583061 ACAACTGTCTTCGTCACAACAAATA 59.417 36.000 0.00 0.00 0.00 1.40
84 85 5.233476 TCACAATACAACAACTGTCTTCGTC 59.767 40.000 0.00 0.00 39.64 4.20
86 87 5.651172 TCACAATACAACAACTGTCTTCG 57.349 39.130 0.00 0.00 39.64 3.79
93 94 5.789643 AGGCAAATCACAATACAACAACT 57.210 34.783 0.00 0.00 0.00 3.16
192 195 4.983538 ACGGTACCGCAAATTTTTAAAAGG 59.016 37.500 33.62 1.95 44.19 3.11
193 196 5.686397 TCACGGTACCGCAAATTTTTAAAAG 59.314 36.000 33.62 2.36 44.19 2.27
195 198 5.179045 TCACGGTACCGCAAATTTTTAAA 57.821 34.783 33.62 1.11 44.19 1.52
196 199 4.320348 CCTCACGGTACCGCAAATTTTTAA 60.320 41.667 33.62 6.37 44.19 1.52
198 201 2.030628 CCTCACGGTACCGCAAATTTTT 60.031 45.455 33.62 9.23 44.19 1.94
215 218 2.922503 TGGAAGCCTCACGCCTCA 60.923 61.111 0.00 0.00 38.78 3.86
216 219 2.125350 CTGGAAGCCTCACGCCTC 60.125 66.667 0.00 0.00 38.78 4.70
260 263 4.635324 ACTTGTCCTGCAAAATTTTTGTGG 59.365 37.500 19.98 20.11 36.53 4.17
262 265 6.816134 AAACTTGTCCTGCAAAATTTTTGT 57.184 29.167 19.98 0.00 36.53 2.83
275 278 5.940470 GGAACAGATCATGTAAACTTGTCCT 59.060 40.000 0.00 0.00 43.00 3.85
293 296 2.266055 GAGGCCTCGGTGGAACAG 59.734 66.667 19.06 0.00 41.80 3.16
313 317 6.380095 TGTAAAAAGAACAAATGCGGTACT 57.620 33.333 0.00 0.00 0.00 2.73
338 349 4.438200 CCGCAAATTTGTTATAAGAGCCGT 60.438 41.667 19.03 0.00 0.00 5.68
343 354 4.936411 TCGTCCCGCAAATTTGTTATAAGA 59.064 37.500 19.03 9.92 0.00 2.10
350 361 0.591170 CACTCGTCCCGCAAATTTGT 59.409 50.000 19.03 0.00 0.00 2.83
364 375 2.560105 TCCAGCATATCCAGATCACTCG 59.440 50.000 0.00 0.00 0.00 4.18
366 377 3.585360 ACTCCAGCATATCCAGATCACT 58.415 45.455 0.00 0.00 0.00 3.41
368 379 3.495629 GCAACTCCAGCATATCCAGATCA 60.496 47.826 0.00 0.00 0.00 2.92
369 380 3.072944 GCAACTCCAGCATATCCAGATC 58.927 50.000 0.00 0.00 0.00 2.75
370 381 2.709934 AGCAACTCCAGCATATCCAGAT 59.290 45.455 0.00 0.00 0.00 2.90
372 383 2.104451 AGAGCAACTCCAGCATATCCAG 59.896 50.000 0.00 0.00 0.00 3.86
373 384 2.121948 AGAGCAACTCCAGCATATCCA 58.878 47.619 0.00 0.00 0.00 3.41
375 386 3.069300 TCTCAGAGCAACTCCAGCATATC 59.931 47.826 0.00 0.00 0.00 1.63
376 387 3.036819 TCTCAGAGCAACTCCAGCATAT 58.963 45.455 0.00 0.00 0.00 1.78
377 388 2.429971 CTCTCAGAGCAACTCCAGCATA 59.570 50.000 0.00 0.00 0.00 3.14
383 396 3.393089 TGAAACTCTCAGAGCAACTCC 57.607 47.619 0.00 0.00 32.04 3.85
394 407 2.104170 AGGACCTCGGATGAAACTCTC 58.896 52.381 0.00 0.00 0.00 3.20
406 419 2.175184 CTTTTGCACGCAGGACCTCG 62.175 60.000 10.59 10.59 0.00 4.63
426 439 9.574516 AAACTACATCTAATATAAGGGCTTTGG 57.425 33.333 0.00 0.00 0.00 3.28
443 456 3.699538 GGACCCCCAATGAAAACTACATC 59.300 47.826 0.00 0.00 0.00 3.06
446 459 3.451402 AGGACCCCCAATGAAAACTAC 57.549 47.619 0.00 0.00 33.88 2.73
474 487 3.119673 TGCAATTTCGGTTACATCGCATT 60.120 39.130 0.00 0.00 0.00 3.56
497 510 2.100584 GACCTAGGAGCTGACATGAGTG 59.899 54.545 17.98 0.00 0.00 3.51
539 552 3.925299 TGTTATGTTGCCATTGCGAAATG 59.075 39.130 9.35 9.35 41.78 2.32
590 603 7.475137 TGAGTACTTCATTTTATTTTGGGGG 57.525 36.000 0.00 0.00 0.00 5.40
611 624 6.644592 ACGAATCACTCTTTCTCTTCTTTGAG 59.355 38.462 0.00 0.00 35.52 3.02
651 664 0.250295 TGTGCTTTCCTCCGTCTTGG 60.250 55.000 0.00 0.00 40.09 3.61
714 727 4.388499 GCCGCTGGTCCCTTTCGA 62.388 66.667 0.00 0.00 0.00 3.71
770 815 2.373269 CTCGCCTGTATAACGAACTCG 58.627 52.381 0.00 0.00 46.33 4.18
771 816 2.117910 GCTCGCCTGTATAACGAACTC 58.882 52.381 0.00 0.00 35.07 3.01
772 817 1.533338 CGCTCGCCTGTATAACGAACT 60.533 52.381 0.00 0.00 35.07 3.01
773 818 0.844503 CGCTCGCCTGTATAACGAAC 59.155 55.000 0.00 0.00 35.07 3.95
1267 1326 2.388890 GACAGGGAGATGGGCATCGG 62.389 65.000 0.00 0.00 42.48 4.18
1302 1361 3.311110 ACCACGACCATCTGCGGT 61.311 61.111 0.00 0.00 43.91 5.68
1410 1469 2.752238 AGCACGAGGAGGGAGTCG 60.752 66.667 0.00 0.00 42.04 4.18
1447 1506 2.514824 GCCCTCACTCGGATTGGC 60.515 66.667 0.00 0.00 36.52 4.52
1529 1588 9.699703 GCAATTTAAACAAGAGTGGGTTAATTA 57.300 29.630 0.00 0.00 0.00 1.40
1530 1589 8.428852 AGCAATTTAAACAAGAGTGGGTTAATT 58.571 29.630 0.00 0.00 0.00 1.40
1531 1590 7.962441 AGCAATTTAAACAAGAGTGGGTTAAT 58.038 30.769 0.00 0.00 0.00 1.40
1532 1591 7.286775 AGAGCAATTTAAACAAGAGTGGGTTAA 59.713 33.333 0.00 0.00 0.00 2.01
1565 1628 6.259387 TGAGCACATGAATGATGAATGTAGAC 59.741 38.462 0.00 0.00 35.80 2.59
1589 1652 6.293571 GGAAGCATTTTTGGGAAGTTCAATTG 60.294 38.462 5.01 0.00 0.00 2.32
1650 1713 9.973450 GTCTATCACCTATGTATATAAGCATGG 57.027 37.037 0.00 1.13 0.00 3.66
1757 1825 7.664758 TCTAAAGTTTTCTACCTGACCACTAC 58.335 38.462 0.00 0.00 0.00 2.73
1776 1848 4.081198 ACAAGGAGAGGACAGCATCTAAAG 60.081 45.833 0.00 0.00 34.88 1.85
1781 1853 2.777832 AACAAGGAGAGGACAGCATC 57.222 50.000 0.00 0.00 0.00 3.91
1794 1866 4.750098 CACCTAACACACACTCTAACAAGG 59.250 45.833 0.00 0.00 0.00 3.61
1856 1928 1.074405 AGCAGGACTGAAAGCCAATCA 59.926 47.619 3.00 0.00 37.60 2.57
1875 1947 4.322080 TGACTAGTGAAACAGTGACCAG 57.678 45.455 0.00 0.00 41.43 4.00
1892 1964 6.831664 AGGGACATCTATTACCAAATGACT 57.168 37.500 0.00 0.00 0.00 3.41
1937 2009 6.127897 CCCTTGTCTAAAATGTCAGTGATTCC 60.128 42.308 0.00 0.00 0.00 3.01
1957 2029 6.406370 TCAATAGACAATAGTGACACCCTTG 58.594 40.000 13.44 13.44 0.00 3.61
1961 2033 5.665459 AGCTCAATAGACAATAGTGACACC 58.335 41.667 0.84 0.00 0.00 4.16
1969 2041 9.851686 ACCATTTATGAAGCTCAATAGACAATA 57.148 29.630 0.00 0.00 0.00 1.90
1970 2042 8.757982 ACCATTTATGAAGCTCAATAGACAAT 57.242 30.769 0.00 0.00 0.00 2.71
1971 2043 9.851686 ATACCATTTATGAAGCTCAATAGACAA 57.148 29.630 0.00 0.00 0.00 3.18
1999 2071 7.913297 TGTTTTAAAGTCGATTTTCCTTGTCAG 59.087 33.333 9.37 0.00 32.01 3.51
2014 2086 6.345015 GCGTTTCATTCTGCTGTTTTAAAGTC 60.345 38.462 0.00 0.00 0.00 3.01
2038 2110 8.225107 TCGACTTGTAACTTTTACACATAATGC 58.775 33.333 0.00 0.00 0.00 3.56
2043 2115 7.724305 ACATCGACTTGTAACTTTTACACAT 57.276 32.000 0.00 0.00 0.00 3.21
2051 2123 6.795098 TTATGCAACATCGACTTGTAACTT 57.205 33.333 0.00 0.00 0.00 2.66
2053 2125 6.367421 TGTTTATGCAACATCGACTTGTAAC 58.633 36.000 0.00 1.43 40.71 2.50
2054 2126 6.546972 TGTTTATGCAACATCGACTTGTAA 57.453 33.333 0.00 0.00 40.71 2.41
2065 2140 7.783090 ACAAAAATCATGTGTTTATGCAACA 57.217 28.000 0.00 0.00 43.55 3.33
2078 2153 8.415553 TCTAATTGCTCCCATACAAAAATCATG 58.584 33.333 0.00 0.00 0.00 3.07
2079 2154 8.416329 GTCTAATTGCTCCCATACAAAAATCAT 58.584 33.333 0.00 0.00 0.00 2.45
2080 2155 7.615365 AGTCTAATTGCTCCCATACAAAAATCA 59.385 33.333 0.00 0.00 0.00 2.57
2081 2156 8.000780 AGTCTAATTGCTCCCATACAAAAATC 57.999 34.615 0.00 0.00 0.00 2.17
2082 2157 7.961326 AGTCTAATTGCTCCCATACAAAAAT 57.039 32.000 0.00 0.00 0.00 1.82
2083 2158 7.093945 GGAAGTCTAATTGCTCCCATACAAAAA 60.094 37.037 0.00 0.00 0.00 1.94
2084 2159 6.377146 GGAAGTCTAATTGCTCCCATACAAAA 59.623 38.462 0.00 0.00 0.00 2.44
2095 2170 7.015584 ACAAAAAGAATGGGAAGTCTAATTGCT 59.984 33.333 0.00 0.00 0.00 3.91
2136 2211 6.912591 GGATTATACGCTCAAAACAAGAATGG 59.087 38.462 0.00 0.00 0.00 3.16
2148 2223 3.473625 TCTGACTCGGATTATACGCTCA 58.526 45.455 0.00 0.00 0.00 4.26
2149 2224 4.023878 AGTTCTGACTCGGATTATACGCTC 60.024 45.833 0.00 0.00 0.00 5.03
2171 2247 4.883026 GCACTGCATTGCTGGAAG 57.117 55.556 20.72 6.35 39.59 3.46
2178 2254 0.803117 CTGGACAGAGCACTGCATTG 59.197 55.000 11.37 0.00 46.95 2.82
2236 2313 2.810439 AATCAGGAGCACGAGATAGC 57.190 50.000 0.00 0.00 0.00 2.97
2244 2321 3.441572 ACAACAGCAATAATCAGGAGCAC 59.558 43.478 0.00 0.00 0.00 4.40
2272 2349 4.084328 CGAAGTGAACAGTGACTCCAAATC 60.084 45.833 0.00 0.00 0.00 2.17
2294 2371 6.334102 AGGAGCCAAAATCTATACTCTACG 57.666 41.667 0.00 0.00 0.00 3.51
2535 2617 9.959721 AGCTACTTATCCTAACAGAAAAATGAA 57.040 29.630 0.00 0.00 0.00 2.57
2548 2630 5.897824 ACTGGTAAAGCAGCTACTTATCCTA 59.102 40.000 16.18 0.00 0.00 2.94
2569 2651 7.615582 TTCAAGAATATTGCAAGTCCTACTG 57.384 36.000 4.94 0.00 0.00 2.74
2573 2655 7.288810 TGTTTTCAAGAATATTGCAAGTCCT 57.711 32.000 4.94 0.00 0.00 3.85
2598 2680 8.956426 ACAAAATGAACGTCAGAATATAACCAT 58.044 29.630 0.00 0.00 0.00 3.55
2756 2839 4.290459 AGGATAGCATGCCAGGAATGATTA 59.710 41.667 15.66 3.16 0.00 1.75
2757 2840 3.075582 AGGATAGCATGCCAGGAATGATT 59.924 43.478 15.66 0.76 0.00 2.57
2892 2978 3.179048 GTTATCTTGAAATGCCGCAACC 58.821 45.455 0.00 0.00 0.00 3.77
2898 2984 4.702131 ACTGACAGGTTATCTTGAAATGCC 59.298 41.667 7.51 0.00 0.00 4.40
3174 3260 5.588958 TGAATTCAGTCTCATCGATCACT 57.411 39.130 3.38 0.00 0.00 3.41
3250 3336 9.323963 CCATTTTAACATTTCGGCAAAATAAAC 57.676 29.630 0.00 0.00 35.77 2.01
3252 3338 7.878127 TCCCATTTTAACATTTCGGCAAAATAA 59.122 29.630 0.00 0.00 35.77 1.40
3287 3527 3.756963 AGGCCTTTTCTACCTTTTAAGCG 59.243 43.478 0.00 0.00 0.00 4.68
3324 3568 5.066117 GCTCTTGAATTCTGCATGAATGAGA 59.934 40.000 17.92 15.43 43.99 3.27
3419 3663 6.704493 TGAGTAAATACGGAATTGTAGATGGC 59.296 38.462 0.00 0.00 0.00 4.40
3420 3664 8.833231 ATGAGTAAATACGGAATTGTAGATGG 57.167 34.615 0.00 0.00 0.00 3.51
3456 3700 3.634397 TTGCTGTAAAGATCAGGGGAG 57.366 47.619 0.00 0.00 33.98 4.30
3490 3734 0.930310 CGTACTGGCCGATCATGTTG 59.070 55.000 0.00 0.00 0.00 3.33
3505 3749 5.411781 ACTGGTCTTTCTGATGAATCGTAC 58.588 41.667 0.00 0.00 31.56 3.67
3643 3887 0.259647 CATGCCCAAATCCTCCCTCA 59.740 55.000 0.00 0.00 0.00 3.86
3649 3893 4.895297 CCTTTATACACATGCCCAAATCCT 59.105 41.667 0.00 0.00 0.00 3.24
3667 3911 2.505819 GCCATCCTTGAGTCTCCCTTTA 59.494 50.000 0.00 0.00 0.00 1.85
3675 3919 0.107459 GACCTGGCCATCCTTGAGTC 60.107 60.000 5.51 1.21 0.00 3.36
3676 3920 0.842030 TGACCTGGCCATCCTTGAGT 60.842 55.000 5.51 0.00 0.00 3.41
3884 4128 2.097466 ACTTTATGCATACCAAGCACGC 59.903 45.455 15.18 0.00 45.95 5.34
3944 4188 2.541346 GTGGCAAAAGAAAAGAGCAAGC 59.459 45.455 0.00 0.00 0.00 4.01
3975 4220 0.321919 TAAGCCTGCTGCCTTGTCTG 60.322 55.000 0.00 0.00 42.71 3.51
3988 4233 1.127567 TGTGCCACTCCAGTAAGCCT 61.128 55.000 0.00 0.00 0.00 4.58
4176 4421 5.886960 ACAGAACAGATAAGGATTTGCAC 57.113 39.130 0.00 0.00 0.00 4.57
4187 4432 7.758076 CAGGACGTAATTACAACAGAACAGATA 59.242 37.037 15.67 0.00 0.00 1.98
4190 4435 5.694910 ACAGGACGTAATTACAACAGAACAG 59.305 40.000 15.67 0.00 0.00 3.16
4191 4436 5.603596 ACAGGACGTAATTACAACAGAACA 58.396 37.500 15.67 0.00 0.00 3.18
4348 4593 3.010138 ACAGGAGCAAAAGGGTAGCATAA 59.990 43.478 0.00 0.00 0.00 1.90
4411 4656 1.541233 GCATACTCAGGCGCCAAGTAT 60.541 52.381 32.61 32.61 36.82 2.12
4477 4722 5.332883 CGATATCAGCTGGAAAAGAACGATG 60.333 44.000 15.13 0.00 0.00 3.84
4570 4815 5.776716 TGGCAAATGAAAAGGAGAAGAATCT 59.223 36.000 0.00 0.00 39.10 2.40
4575 4820 3.983344 CGTTGGCAAATGAAAAGGAGAAG 59.017 43.478 0.00 0.00 0.00 2.85
4578 4823 3.004734 AGACGTTGGCAAATGAAAAGGAG 59.995 43.478 0.00 0.00 0.00 3.69
4582 4827 6.090129 GCTATAAGACGTTGGCAAATGAAAA 58.910 36.000 0.00 0.00 0.00 2.29
4583 4828 5.392595 GGCTATAAGACGTTGGCAAATGAAA 60.393 40.000 0.00 0.00 0.00 2.69
4584 4829 4.095782 GGCTATAAGACGTTGGCAAATGAA 59.904 41.667 0.00 0.00 0.00 2.57
4585 4830 3.625764 GGCTATAAGACGTTGGCAAATGA 59.374 43.478 0.00 0.00 0.00 2.57
4587 4832 2.612212 CGGCTATAAGACGTTGGCAAAT 59.388 45.455 0.00 0.00 42.99 2.32
4589 4834 1.647346 CGGCTATAAGACGTTGGCAA 58.353 50.000 0.00 0.00 42.99 4.52
4590 4835 3.355816 CGGCTATAAGACGTTGGCA 57.644 52.632 0.00 0.00 42.99 4.92
4597 4842 3.528009 GCTGCAAATCGGCTATAAGAC 57.472 47.619 0.00 0.00 43.74 3.01
4606 4851 4.178540 AGAAAATGAATGCTGCAAATCGG 58.821 39.130 6.36 0.00 0.00 4.18
4607 4852 5.547341 CAAGAAAATGAATGCTGCAAATCG 58.453 37.500 6.36 0.00 0.00 3.34
4608 4853 5.106869 TGCAAGAAAATGAATGCTGCAAATC 60.107 36.000 6.36 9.13 39.49 2.17
4610 4855 4.127907 TGCAAGAAAATGAATGCTGCAAA 58.872 34.783 6.36 0.00 39.49 3.68
4628 4873 6.121590 TGCCTGAAAATGTATAGAGATGCAA 58.878 36.000 0.00 0.00 30.89 4.08
4629 4874 5.683681 TGCCTGAAAATGTATAGAGATGCA 58.316 37.500 0.00 0.00 31.73 3.96
4631 4876 6.147492 GCTCTGCCTGAAAATGTATAGAGATG 59.853 42.308 0.00 0.00 33.95 2.90
4664 4909 1.287730 CGTGCAGTGCAAGACTCTCC 61.288 60.000 24.50 6.61 41.47 3.71
4688 4933 2.243810 GCAATGCGCTCGTCGATC 59.756 61.111 9.73 0.00 41.67 3.69
4880 5125 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4881 5126 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4883 5128 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4885 5130 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4886 5131 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4891 5136 4.837860 AGGATCTCTCTCTCTCTCTCTCTC 59.162 50.000 0.00 0.00 0.00 3.20
4893 5138 5.336055 CGTAGGATCTCTCTCTCTCTCTCTC 60.336 52.000 0.00 0.00 0.00 3.20
4894 5139 4.524714 CGTAGGATCTCTCTCTCTCTCTCT 59.475 50.000 0.00 0.00 0.00 3.10
4895 5140 4.810790 CGTAGGATCTCTCTCTCTCTCTC 58.189 52.174 0.00 0.00 0.00 3.20
4896 5141 4.873746 CGTAGGATCTCTCTCTCTCTCT 57.126 50.000 0.00 0.00 0.00 3.10
4919 5164 1.213296 ATATTGTCCACGGGGCTTCT 58.787 50.000 0.00 0.00 0.00 2.85
4921 5166 3.876309 AATATATTGTCCACGGGGCTT 57.124 42.857 0.00 0.00 0.00 4.35
4934 5179 6.296259 CGGGTGGGCTCTACCTTTAATATATT 60.296 42.308 2.97 2.97 38.30 1.28
4938 5183 2.701951 CGGGTGGGCTCTACCTTTAATA 59.298 50.000 7.47 0.00 38.30 0.98
4944 5189 2.042843 CTCGGGTGGGCTCTACCT 60.043 66.667 7.47 0.00 38.30 3.08
4945 5190 2.363925 ACTCGGGTGGGCTCTACC 60.364 66.667 0.00 0.00 37.48 3.18
4960 5205 2.564947 CTGGCTTTGACTCTACCTCACT 59.435 50.000 0.00 0.00 0.00 3.41
4966 5211 2.933056 GCTGACCTGGCTTTGACTCTAC 60.933 54.545 0.00 0.00 0.00 2.59
4971 5231 0.595095 CTTGCTGACCTGGCTTTGAC 59.405 55.000 0.00 0.00 0.00 3.18
4974 5240 0.407139 ATCCTTGCTGACCTGGCTTT 59.593 50.000 0.00 0.00 0.00 3.51
4977 5243 2.413142 GCATCCTTGCTGACCTGGC 61.413 63.158 0.00 0.00 45.77 4.85
4997 5263 1.004918 AGTGGTAAGGTCGCAGTGC 60.005 57.895 4.58 4.58 0.00 4.40
5038 5304 8.742125 ATATCATACTGGATTCCTTTGGACTA 57.258 34.615 3.95 0.00 0.00 2.59
5046 5312 8.888419 ACTGATGAAATATCATACTGGATTCCT 58.112 33.333 3.95 0.00 46.30 3.36
5048 5314 9.716531 TCACTGATGAAATATCATACTGGATTC 57.283 33.333 0.00 0.00 46.30 2.52
5052 5318 8.899427 ACTTCACTGATGAAATATCATACTGG 57.101 34.615 0.00 0.00 46.30 4.00
5070 5338 3.868077 GCGAGCATCATAGAAACTTCACT 59.132 43.478 0.00 0.00 33.17 3.41
5071 5339 3.618594 TGCGAGCATCATAGAAACTTCAC 59.381 43.478 0.00 0.00 33.17 3.18
5560 5829 5.811399 TTCATTTACAAAGATACGCAGGG 57.189 39.130 0.00 0.00 0.00 4.45
5561 5830 7.250569 ACATTTCATTTACAAAGATACGCAGG 58.749 34.615 0.00 0.00 0.00 4.85
5562 5831 7.162546 CGACATTTCATTTACAAAGATACGCAG 59.837 37.037 0.00 0.00 0.00 5.18
5563 5832 6.958752 CGACATTTCATTTACAAAGATACGCA 59.041 34.615 0.00 0.00 0.00 5.24
5564 5833 6.959311 ACGACATTTCATTTACAAAGATACGC 59.041 34.615 0.00 0.00 0.00 4.42
5565 5834 8.874745 AACGACATTTCATTTACAAAGATACG 57.125 30.769 0.00 0.00 0.00 3.06
5586 5859 5.987347 CAGAAAAGTAACCCAAGTAGAACGA 59.013 40.000 0.00 0.00 0.00 3.85
5595 5868 7.234661 ACAAAAACTCAGAAAAGTAACCCAA 57.765 32.000 0.00 0.00 0.00 4.12
5596 5869 6.844097 ACAAAAACTCAGAAAAGTAACCCA 57.156 33.333 0.00 0.00 0.00 4.51
5636 5910 2.983136 CAGAACAGACGAACAGTAGCAG 59.017 50.000 0.00 0.00 0.00 4.24
5666 5940 2.141517 CAGACTCTTCAACAGCCACAG 58.858 52.381 0.00 0.00 0.00 3.66
5670 5944 3.559242 GCATATCAGACTCTTCAACAGCC 59.441 47.826 0.00 0.00 0.00 4.85
5743 6019 1.604593 CTTTGTGACCCAGGCCCAG 60.605 63.158 0.00 0.00 0.00 4.45
5744 6020 2.067932 CTCTTTGTGACCCAGGCCCA 62.068 60.000 0.00 0.00 0.00 5.36
5745 6021 1.303643 CTCTTTGTGACCCAGGCCC 60.304 63.158 0.00 0.00 0.00 5.80
5746 6022 0.110486 TTCTCTTTGTGACCCAGGCC 59.890 55.000 0.00 0.00 0.00 5.19
5759 6036 6.446909 ACAGATTTTCTTCCTCCTTCTCTT 57.553 37.500 0.00 0.00 0.00 2.85
5761 6038 5.645929 GGAACAGATTTTCTTCCTCCTTCTC 59.354 44.000 0.00 0.00 0.00 2.87
5799 6078 0.960364 GGCAGCTTCAATTCGGTGGA 60.960 55.000 0.00 0.00 0.00 4.02
5803 6082 0.813184 ACATGGCAGCTTCAATTCGG 59.187 50.000 0.00 0.00 0.00 4.30
5833 6112 3.726730 GCGAAAGTAAACGAAAACATGCA 59.273 39.130 0.00 0.00 0.00 3.96
5836 6115 4.555348 TGGCGAAAGTAAACGAAAACAT 57.445 36.364 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.