Multiple sequence alignment - TraesCS2D01G221600

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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 TraesCS2D01G221600 chr2D 100.000 3017 0 0 1 3017 188880855 188883871 0.000000e+00 5572.0
1 TraesCS2D01G221600 chr2D 73.077 806 166 45 1033 1813 22785795 22786574 3.890000e-59 239.0
2 TraesCS2D01G221600 chr2A 95.681 1204 39 5 848 2047 203001877 203003071 0.000000e+00 1923.0
3 TraesCS2D01G221600 chr2A 93.233 532 25 6 2497 3017 203003586 203004117 0.000000e+00 773.0
4 TraesCS2D01G221600 chr2A 88.835 412 34 10 3 411 202986197 202986599 2.090000e-136 496.0
5 TraesCS2D01G221600 chr2A 91.611 298 23 1 2059 2356 195825303 195825008 7.780000e-111 411.0
6 TraesCS2D01G221600 chr2A 78.618 608 86 24 248 830 758367068 758366480 2.210000e-96 363.0
7 TraesCS2D01G221600 chr2A 78.775 457 70 22 248 697 760343843 760343407 6.370000e-72 281.0
8 TraesCS2D01G221600 chr2A 84.028 288 32 8 399 677 202986616 202986898 6.410000e-67 265.0
9 TraesCS2D01G221600 chr2A 76.961 408 75 18 1504 1900 24181442 24181043 6.550000e-52 215.0
10 TraesCS2D01G221600 chr2A 76.596 423 75 23 1495 1902 24407753 24408166 8.470000e-51 211.0
11 TraesCS2D01G221600 chr2A 76.984 378 70 16 1533 1900 24277122 24276752 1.830000e-47 200.0
12 TraesCS2D01G221600 chr2A 82.927 82 12 2 25 105 11214827 11214747 4.170000e-09 73.1
13 TraesCS2D01G221600 chr2B 95.152 1217 41 6 851 2058 245005857 245007064 0.000000e+00 1905.0
14 TraesCS2D01G221600 chr2B 91.840 674 40 7 2355 3017 245007716 245008385 0.000000e+00 926.0
15 TraesCS2D01G221600 chr2B 95.687 371 9 5 494 857 245001106 245001476 9.320000e-165 590.0
16 TraesCS2D01G221600 chr2B 91.914 371 13 1 2 355 245000731 245001101 1.250000e-138 503.0
17 TraesCS2D01G221600 chr2B 72.598 843 165 56 1091 1897 39333375 39334187 1.820000e-52 217.0
18 TraesCS2D01G221600 chr2B 76.123 423 77 21 1495 1902 38421162 38420749 1.830000e-47 200.0
19 TraesCS2D01G221600 chr3A 91.586 309 20 4 2059 2367 324869350 324869048 3.600000e-114 422.0
20 TraesCS2D01G221600 chr4A 91.946 298 21 2 2059 2356 585694192 585693898 6.020000e-112 414.0
21 TraesCS2D01G221600 chr4A 91.639 299 21 3 2059 2355 5351716 5352012 7.780000e-111 411.0
22 TraesCS2D01G221600 chr4A 89.899 297 27 2 2059 2355 320722901 320723194 2.200000e-101 379.0
23 TraesCS2D01G221600 chr5A 91.304 299 22 3 2059 2357 349875270 349874976 3.620000e-109 405.0
24 TraesCS2D01G221600 chr1D 79.206 428 67 12 300 711 383724977 383724556 8.240000e-71 278.0
25 TraesCS2D01G221600 chr7A 78.708 418 85 4 1508 1924 136283623 136284037 2.960000e-70 276.0
26 TraesCS2D01G221600 chr7D 78.772 391 79 4 1508 1897 136536129 136536516 2.980000e-65 259.0
27 TraesCS2D01G221600 chr7D 77.982 218 44 4 1049 1264 136535644 136535859 1.890000e-27 134.0
28 TraesCS2D01G221600 chr7D 87.209 86 10 1 485 569 451039061 451039146 2.480000e-16 97.1
29 TraesCS2D01G221600 chr7B 78.961 385 77 4 1515 1897 99593282 99592900 2.980000e-65 259.0
30 TraesCS2D01G221600 chr7B 76.404 267 57 6 1049 1312 99593772 99593509 4.060000e-29 139.0
31 TraesCS2D01G221600 chr7B 86.076 79 8 2 485 562 468824142 468824218 6.930000e-12 82.4
32 TraesCS2D01G221600 chr7B 77.193 114 23 3 248 359 458618248 458618136 2.510000e-06 63.9
33 TraesCS2D01G221600 chr6B 94.286 35 2 0 2321 2355 79643217 79643251 2.000000e-03 54.7


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 TraesCS2D01G221600 chr2D 188880855 188883871 3016 False 5572.0 5572 100.0000 1 3017 1 chr2D.!!$F2 3016
1 TraesCS2D01G221600 chr2D 22785795 22786574 779 False 239.0 239 73.0770 1033 1813 1 chr2D.!!$F1 780
2 TraesCS2D01G221600 chr2A 203001877 203004117 2240 False 1348.0 1923 94.4570 848 3017 2 chr2A.!!$F3 2169
3 TraesCS2D01G221600 chr2A 202986197 202986898 701 False 380.5 496 86.4315 3 677 2 chr2A.!!$F2 674
4 TraesCS2D01G221600 chr2A 758366480 758367068 588 True 363.0 363 78.6180 248 830 1 chr2A.!!$R5 582
5 TraesCS2D01G221600 chr2B 245005857 245008385 2528 False 1415.5 1905 93.4960 851 3017 2 chr2B.!!$F3 2166
6 TraesCS2D01G221600 chr2B 245000731 245001476 745 False 546.5 590 93.8005 2 857 2 chr2B.!!$F2 855
7 TraesCS2D01G221600 chr2B 39333375 39334187 812 False 217.0 217 72.5980 1091 1897 1 chr2B.!!$F1 806

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
677 747 1.457009 TTGGTTGCCCAGTTAACGGC 61.457 55.0 15.39 15.39 43.15 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 2909 0.100325 CCTGTGCGTTGCAACAGAAA 59.9 50.0 28.01 8.77 41.47 2.52 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
91 92 5.325239 ACCCCTTATGAAGAAAGAAACTGG 58.675 41.667 0.00 0.00 0.00 4.00
155 156 7.073342 AGTAAGAATGAATTAGTGGAAACGC 57.927 36.000 0.00 0.00 42.66 4.84
176 177 4.811557 CGCTATTAACCCTTGAGAAGAAGG 59.188 45.833 0.00 0.00 42.11 3.46
282 285 8.680001 TGTTACCTTTAAAGAACAAGGAAACTC 58.320 33.333 16.98 0.00 42.11 3.01
283 286 8.900781 GTTACCTTTAAAGAACAAGGAAACTCT 58.099 33.333 16.98 0.00 42.11 3.24
402 428 7.865707 ACACACAAATAAAAGTTGCACAAAAA 58.134 26.923 0.00 0.00 0.00 1.94
418 444 7.239972 TGCACAAAAATTTGCACTAAAACTTC 58.760 30.769 5.82 0.00 43.79 3.01
419 445 7.095060 TGCACAAAAATTTGCACTAAAACTTCA 60.095 29.630 5.82 0.00 43.79 3.02
420 446 7.216130 GCACAAAAATTTGCACTAAAACTTCAC 59.784 33.333 5.82 0.00 41.79 3.18
421 447 7.691877 CACAAAAATTTGCACTAAAACTTCACC 59.308 33.333 5.82 0.00 41.79 4.02
422 448 7.606073 ACAAAAATTTGCACTAAAACTTCACCT 59.394 29.630 5.82 0.00 41.79 4.00
423 449 8.450180 CAAAAATTTGCACTAAAACTTCACCTT 58.550 29.630 0.00 0.00 0.00 3.50
424 450 8.560355 AAAATTTGCACTAAAACTTCACCTTT 57.440 26.923 0.00 0.00 0.00 3.11
425 451 8.560355 AAATTTGCACTAAAACTTCACCTTTT 57.440 26.923 0.00 0.00 0.00 2.27
426 452 6.959671 TTTGCACTAAAACTTCACCTTTTG 57.040 33.333 0.00 0.00 0.00 2.44
427 453 5.652994 TGCACTAAAACTTCACCTTTTGT 57.347 34.783 0.00 0.00 0.00 2.83
677 747 1.457009 TTGGTTGCCCAGTTAACGGC 61.457 55.000 15.39 15.39 43.15 5.68
836 922 4.706842 TTTCTGGCAACTTACCTCTCTT 57.293 40.909 0.00 0.00 37.61 2.85
838 924 2.079925 CTGGCAACTTACCTCTCTTGC 58.920 52.381 0.00 0.00 38.64 4.01
839 925 1.699634 TGGCAACTTACCTCTCTTGCT 59.300 47.619 0.00 0.00 39.21 3.91
845 931 5.406649 CAACTTACCTCTCTTGCTAGACTG 58.593 45.833 0.00 0.00 0.00 3.51
857 943 7.502561 TCTCTTGCTAGACTGTACATAAGCATA 59.497 37.037 17.12 10.72 39.50 3.14
858 944 8.183104 TCTTGCTAGACTGTACATAAGCATAT 57.817 34.615 17.12 0.00 39.50 1.78
859 945 8.300286 TCTTGCTAGACTGTACATAAGCATATC 58.700 37.037 17.12 0.00 39.50 1.63
860 946 6.612306 TGCTAGACTGTACATAAGCATATCG 58.388 40.000 14.11 0.00 35.20 2.92
906 992 7.786030 TCTTTAATCCTTCTTCAGATCATCGT 58.214 34.615 0.00 0.00 0.00 3.73
909 995 6.674694 AATCCTTCTTCAGATCATCGTTTG 57.325 37.500 0.00 0.00 0.00 2.93
911 997 3.064545 CCTTCTTCAGATCATCGTTTGGC 59.935 47.826 0.00 0.00 0.00 4.52
912 998 3.333029 TCTTCAGATCATCGTTTGGCA 57.667 42.857 0.00 0.00 0.00 4.92
913 999 3.002791 TCTTCAGATCATCGTTTGGCAC 58.997 45.455 0.00 0.00 0.00 5.01
954 1041 2.096417 CGTTTTGACGTTGGAGTCCATC 60.096 50.000 14.00 11.63 40.26 3.51
1141 1242 3.284251 TGCTCCTCCTCCTCCCCA 61.284 66.667 0.00 0.00 0.00 4.96
1317 1420 1.447838 CGTCAATGTCCGGGACAGG 60.448 63.158 31.36 25.21 46.04 4.00
1905 2027 2.881352 CTCTTCTTCGCGCCCGTC 60.881 66.667 0.00 0.00 35.54 4.79
1953 2075 2.125106 GCCGAGTGCGAGGGAATT 60.125 61.111 0.00 0.00 40.82 2.17
2006 2128 2.124109 TGCACGCCTGGTTTGGAA 60.124 55.556 0.00 0.00 0.00 3.53
2007 2129 1.526575 CTGCACGCCTGGTTTGGAAT 61.527 55.000 0.00 0.00 0.00 3.01
2008 2130 1.112315 TGCACGCCTGGTTTGGAATT 61.112 50.000 0.00 0.00 0.00 2.17
2009 2131 0.667184 GCACGCCTGGTTTGGAATTG 60.667 55.000 0.00 0.00 0.00 2.32
2010 2132 0.038343 CACGCCTGGTTTGGAATTGG 60.038 55.000 0.00 0.00 0.00 3.16
2011 2133 0.178975 ACGCCTGGTTTGGAATTGGA 60.179 50.000 0.00 0.00 0.00 3.53
2012 2134 0.527565 CGCCTGGTTTGGAATTGGAG 59.472 55.000 0.00 0.00 0.00 3.86
2023 2145 1.747355 GGAATTGGAGCTGATGGTGTG 59.253 52.381 0.00 0.00 0.00 3.82
2050 2179 3.064324 GAACATGGCGGCAGGCTT 61.064 61.111 24.30 16.28 44.18 4.35
2058 2187 1.444383 GCGGCAGGCTTTACTTTGC 60.444 57.895 0.00 0.00 39.11 3.68
2059 2188 1.956043 CGGCAGGCTTTACTTTGCA 59.044 52.632 0.00 0.00 38.27 4.08
2060 2189 0.313672 CGGCAGGCTTTACTTTGCAA 59.686 50.000 0.00 0.00 38.27 4.08
2061 2190 1.666888 CGGCAGGCTTTACTTTGCAAG 60.667 52.381 0.00 0.00 38.27 4.01
2062 2191 1.337167 GGCAGGCTTTACTTTGCAAGG 60.337 52.381 7.07 7.07 38.27 3.61
2063 2192 1.613437 GCAGGCTTTACTTTGCAAGGA 59.387 47.619 16.36 0.00 36.59 3.36
2064 2193 2.035832 GCAGGCTTTACTTTGCAAGGAA 59.964 45.455 16.36 2.50 36.59 3.36
2065 2194 3.858503 GCAGGCTTTACTTTGCAAGGAAG 60.859 47.826 16.36 10.27 36.59 3.46
2066 2195 2.893489 AGGCTTTACTTTGCAAGGAAGG 59.107 45.455 16.36 7.04 31.74 3.46
2069 2656 4.202212 GGCTTTACTTTGCAAGGAAGGAAA 60.202 41.667 16.36 10.86 35.21 3.13
2071 2658 4.561735 TTACTTTGCAAGGAAGGAAACG 57.438 40.909 16.36 0.00 0.00 3.60
2074 2661 2.861462 TTGCAAGGAAGGAAACGTTG 57.139 45.000 0.00 0.00 36.58 4.10
2075 2662 3.179433 GCAAGGAAGGAAACGTTGC 57.821 52.632 0.00 0.00 46.22 4.17
2082 2669 3.252458 AGGAAGGAAACGTTGCATTACAC 59.748 43.478 17.86 6.53 0.00 2.90
2083 2670 3.252458 GGAAGGAAACGTTGCATTACACT 59.748 43.478 11.07 0.00 0.00 3.55
2086 2673 5.545658 AGGAAACGTTGCATTACACTATG 57.454 39.130 8.91 0.00 0.00 2.23
2088 2675 5.351465 AGGAAACGTTGCATTACACTATGAG 59.649 40.000 8.91 0.00 0.00 2.90
2090 2677 6.311935 GGAAACGTTGCATTACACTATGAGTA 59.688 38.462 8.91 0.00 0.00 2.59
2092 2679 7.843490 AACGTTGCATTACACTATGAGTATT 57.157 32.000 0.00 0.00 0.00 1.89
2123 2710 8.651589 AGTTAAAGGAAGGAAGATTTTTAGGG 57.348 34.615 0.00 0.00 0.00 3.53
2124 2711 7.178628 AGTTAAAGGAAGGAAGATTTTTAGGGC 59.821 37.037 0.00 0.00 0.00 5.19
2125 2712 4.955693 AGGAAGGAAGATTTTTAGGGCT 57.044 40.909 0.00 0.00 0.00 5.19
2126 2713 4.604156 AGGAAGGAAGATTTTTAGGGCTG 58.396 43.478 0.00 0.00 0.00 4.85
2127 2714 3.131223 GGAAGGAAGATTTTTAGGGCTGC 59.869 47.826 0.00 0.00 0.00 5.25
2128 2715 3.456380 AGGAAGATTTTTAGGGCTGCA 57.544 42.857 0.50 0.00 0.00 4.41
2129 2716 3.778265 AGGAAGATTTTTAGGGCTGCAA 58.222 40.909 0.50 0.00 0.00 4.08
2130 2717 4.159557 AGGAAGATTTTTAGGGCTGCAAA 58.840 39.130 0.50 0.00 0.00 3.68
2131 2718 4.592778 AGGAAGATTTTTAGGGCTGCAAAA 59.407 37.500 0.50 0.00 0.00 2.44
2133 2720 5.409520 GGAAGATTTTTAGGGCTGCAAAAAG 59.590 40.000 12.57 0.00 37.13 2.27
2134 2721 5.806654 AGATTTTTAGGGCTGCAAAAAGA 57.193 34.783 12.57 2.23 37.13 2.52
2135 2722 5.787380 AGATTTTTAGGGCTGCAAAAAGAG 58.213 37.500 12.57 0.00 37.13 2.85
2138 2725 5.705609 TTTTAGGGCTGCAAAAAGAGTAG 57.294 39.130 0.50 0.00 0.00 2.57
2139 2726 1.539157 AGGGCTGCAAAAAGAGTAGC 58.461 50.000 0.50 0.00 42.90 3.58
2142 2729 2.352127 GGGCTGCAAAAAGAGTAGCAAG 60.352 50.000 0.50 0.00 45.00 4.01
2143 2730 2.352127 GGCTGCAAAAAGAGTAGCAAGG 60.352 50.000 0.50 0.00 45.00 3.61
2145 2732 3.192212 GCTGCAAAAAGAGTAGCAAGGAT 59.808 43.478 0.00 0.00 43.09 3.24
2156 2743 4.395519 CAAGGATTGGGTGTGCGA 57.604 55.556 0.00 0.00 43.94 5.10
2158 2745 0.452987 CAAGGATTGGGTGTGCGATG 59.547 55.000 0.00 0.00 43.94 3.84
2159 2746 1.315257 AAGGATTGGGTGTGCGATGC 61.315 55.000 0.00 0.00 0.00 3.91
2162 2749 3.918253 ATTGGGTGTGCGATGCGGT 62.918 57.895 0.00 0.00 0.00 5.68
2180 2767 1.263217 GGTGCGCCGATTATTAACTGG 59.737 52.381 4.18 0.00 0.00 4.00
2184 2771 1.798813 CGCCGATTATTAACTGGAGGC 59.201 52.381 3.75 3.75 39.89 4.70
2185 2772 2.152016 GCCGATTATTAACTGGAGGCC 58.848 52.381 0.00 0.00 37.54 5.19
2186 2773 2.224548 GCCGATTATTAACTGGAGGCCT 60.225 50.000 3.86 3.86 37.54 5.19
2187 2774 3.007614 GCCGATTATTAACTGGAGGCCTA 59.992 47.826 4.42 0.00 37.54 3.93
2189 2776 5.617252 CCGATTATTAACTGGAGGCCTAAA 58.383 41.667 4.42 0.00 0.00 1.85
2190 2777 6.238648 CCGATTATTAACTGGAGGCCTAAAT 58.761 40.000 4.42 1.74 0.00 1.40
2192 2779 7.308589 CCGATTATTAACTGGAGGCCTAAATTG 60.309 40.741 4.42 0.00 0.00 2.32
2193 2780 7.228706 CGATTATTAACTGGAGGCCTAAATTGT 59.771 37.037 4.42 0.00 0.00 2.71
2194 2781 8.838649 ATTATTAACTGGAGGCCTAAATTGTT 57.161 30.769 4.42 9.63 0.00 2.83
2195 2782 6.775594 ATTAACTGGAGGCCTAAATTGTTC 57.224 37.500 4.42 0.00 0.00 3.18
2196 2783 2.711542 ACTGGAGGCCTAAATTGTTCG 58.288 47.619 4.42 0.00 0.00 3.95
2197 2784 2.017049 CTGGAGGCCTAAATTGTTCGG 58.983 52.381 4.42 0.00 0.00 4.30
2198 2785 1.631388 TGGAGGCCTAAATTGTTCGGA 59.369 47.619 4.42 0.00 0.00 4.55
2199 2786 2.289565 GGAGGCCTAAATTGTTCGGAG 58.710 52.381 4.42 0.00 0.00 4.63
2200 2787 2.093128 GGAGGCCTAAATTGTTCGGAGA 60.093 50.000 4.42 0.00 0.00 3.71
2201 2788 3.606687 GAGGCCTAAATTGTTCGGAGAA 58.393 45.455 4.42 0.00 45.90 2.87
2202 2789 4.200092 GAGGCCTAAATTGTTCGGAGAAT 58.800 43.478 4.42 0.00 45.90 2.40
2203 2790 3.947834 AGGCCTAAATTGTTCGGAGAATG 59.052 43.478 1.29 0.00 45.90 2.67
2204 2791 3.694566 GGCCTAAATTGTTCGGAGAATGT 59.305 43.478 0.00 0.00 45.90 2.71
2205 2792 4.879545 GGCCTAAATTGTTCGGAGAATGTA 59.120 41.667 0.00 0.00 45.90 2.29
2206 2793 5.531287 GGCCTAAATTGTTCGGAGAATGTAT 59.469 40.000 0.00 0.00 45.90 2.29
2209 2796 7.973944 GCCTAAATTGTTCGGAGAATGTATTTT 59.026 33.333 0.00 0.00 45.90 1.82
2210 2797 9.855021 CCTAAATTGTTCGGAGAATGTATTTTT 57.145 29.630 0.00 0.00 45.90 1.94
2231 2818 5.767816 TTTTCTCTAAACCTTGGCAACTC 57.232 39.130 0.00 0.00 37.61 3.01
2232 2819 3.418684 TCTCTAAACCTTGGCAACTCC 57.581 47.619 0.00 0.00 37.61 3.85
2233 2820 2.039879 TCTCTAAACCTTGGCAACTCCC 59.960 50.000 0.00 0.00 37.61 4.30
2234 2821 2.040412 CTCTAAACCTTGGCAACTCCCT 59.960 50.000 0.00 0.00 37.61 4.20
2236 2823 0.261696 AAACCTTGGCAACTCCCTGT 59.738 50.000 0.00 0.00 37.61 4.00
2237 2824 0.178990 AACCTTGGCAACTCCCTGTC 60.179 55.000 0.00 0.00 37.61 3.51
2238 2825 1.352622 ACCTTGGCAACTCCCTGTCA 61.353 55.000 0.00 0.00 37.61 3.58
2239 2826 0.038744 CCTTGGCAACTCCCTGTCAT 59.961 55.000 0.00 0.00 29.34 3.06
2240 2827 1.548582 CCTTGGCAACTCCCTGTCATT 60.549 52.381 0.00 0.00 29.34 2.57
2244 2831 1.541588 GGCAACTCCCTGTCATTGTTC 59.458 52.381 0.00 0.00 0.00 3.18
2245 2832 1.197721 GCAACTCCCTGTCATTGTTCG 59.802 52.381 0.00 0.00 0.00 3.95
2246 2833 1.806542 CAACTCCCTGTCATTGTTCGG 59.193 52.381 0.00 0.00 0.00 4.30
2247 2834 1.348064 ACTCCCTGTCATTGTTCGGA 58.652 50.000 0.00 0.00 0.00 4.55
2248 2835 1.909302 ACTCCCTGTCATTGTTCGGAT 59.091 47.619 0.00 0.00 0.00 4.18
2249 2836 2.283298 CTCCCTGTCATTGTTCGGATG 58.717 52.381 0.00 0.00 0.00 3.51
2250 2837 1.628340 TCCCTGTCATTGTTCGGATGT 59.372 47.619 0.00 0.00 0.00 3.06
2251 2838 2.009774 CCCTGTCATTGTTCGGATGTC 58.990 52.381 0.00 0.00 0.00 3.06
2255 2842 2.066262 GTCATTGTTCGGATGTCGTGT 58.934 47.619 0.00 0.00 40.32 4.49
2256 2843 2.478894 GTCATTGTTCGGATGTCGTGTT 59.521 45.455 0.00 0.00 40.32 3.32
2257 2844 2.478514 TCATTGTTCGGATGTCGTGTTG 59.521 45.455 0.00 0.00 40.32 3.33
2258 2845 0.584396 TTGTTCGGATGTCGTGTTGC 59.416 50.000 0.00 0.00 40.32 4.17
2260 2847 0.163788 GTTCGGATGTCGTGTTGCTG 59.836 55.000 0.00 0.00 40.32 4.41
2262 2849 1.667830 CGGATGTCGTGTTGCTGGT 60.668 57.895 0.00 0.00 0.00 4.00
2263 2850 0.389296 CGGATGTCGTGTTGCTGGTA 60.389 55.000 0.00 0.00 0.00 3.25
2266 2853 1.289109 ATGTCGTGTTGCTGGTACGC 61.289 55.000 0.00 0.00 37.70 4.42
2269 2856 0.601576 TCGTGTTGCTGGTACGCATT 60.602 50.000 0.00 0.00 37.64 3.56
2270 2857 0.237235 CGTGTTGCTGGTACGCATTT 59.763 50.000 0.00 0.00 37.64 2.32
2272 2859 2.050691 GTGTTGCTGGTACGCATTTTG 58.949 47.619 0.00 0.00 37.64 2.44
2273 2860 1.000827 TGTTGCTGGTACGCATTTTGG 60.001 47.619 0.00 0.00 37.64 3.28
2274 2861 0.038709 TTGCTGGTACGCATTTTGGC 60.039 50.000 0.00 0.00 37.64 4.52
2275 2862 1.153842 GCTGGTACGCATTTTGGCC 60.154 57.895 0.00 0.00 0.00 5.36
2276 2863 1.595093 GCTGGTACGCATTTTGGCCT 61.595 55.000 3.32 0.00 0.00 5.19
2277 2864 1.745232 CTGGTACGCATTTTGGCCTA 58.255 50.000 3.32 0.00 0.00 3.93
2278 2865 1.670811 CTGGTACGCATTTTGGCCTAG 59.329 52.381 3.32 0.00 0.00 3.02
2279 2866 0.380733 GGTACGCATTTTGGCCTAGC 59.619 55.000 3.32 0.00 0.00 3.42
2283 2870 3.629858 GCATTTTGGCCTAGCGAAG 57.370 52.632 3.32 0.00 0.00 3.79
2298 2885 0.109597 CGAAGCAAGGGTTGTCATGC 60.110 55.000 0.00 0.00 39.06 4.06
2301 2888 2.119801 AGCAAGGGTTGTCATGCTAG 57.880 50.000 0.00 0.00 46.61 3.42
2302 2889 0.453390 GCAAGGGTTGTCATGCTAGC 59.547 55.000 8.10 8.10 35.93 3.42
2303 2890 1.825090 CAAGGGTTGTCATGCTAGCA 58.175 50.000 21.85 21.85 0.00 3.49
2304 2891 1.470098 CAAGGGTTGTCATGCTAGCAC 59.530 52.381 22.07 8.34 0.00 4.40
2305 2892 0.692476 AGGGTTGTCATGCTAGCACA 59.308 50.000 22.07 11.28 0.00 4.57
2306 2893 1.283029 AGGGTTGTCATGCTAGCACAT 59.717 47.619 22.07 1.24 0.00 3.21
2308 2895 1.202222 GGTTGTCATGCTAGCACATGC 60.202 52.381 22.07 11.87 45.75 4.06
2309 2896 1.469703 GTTGTCATGCTAGCACATGCA 59.530 47.619 22.07 14.20 45.75 3.96
2310 2897 1.089112 TGTCATGCTAGCACATGCAC 58.911 50.000 22.07 14.78 45.75 4.57
2311 2898 0.027194 GTCATGCTAGCACATGCACG 59.973 55.000 22.07 2.87 45.75 5.34
2312 2899 1.298116 CATGCTAGCACATGCACGC 60.298 57.895 22.07 8.38 45.16 5.34
2313 2900 2.475466 ATGCTAGCACATGCACGCC 61.475 57.895 22.07 0.00 45.16 5.68
2314 2901 3.126879 GCTAGCACATGCACGCCA 61.127 61.111 10.63 0.00 45.16 5.69
2315 2902 2.689785 GCTAGCACATGCACGCCAA 61.690 57.895 10.63 0.00 45.16 4.52
2316 2903 1.996786 GCTAGCACATGCACGCCAAT 61.997 55.000 10.63 0.00 45.16 3.16
2317 2904 0.452987 CTAGCACATGCACGCCAATT 59.547 50.000 6.64 0.00 45.16 2.32
2318 2905 0.887247 TAGCACATGCACGCCAATTT 59.113 45.000 6.64 0.00 45.16 1.82
2319 2906 0.887247 AGCACATGCACGCCAATTTA 59.113 45.000 6.64 0.00 45.16 1.40
2320 2907 1.477700 AGCACATGCACGCCAATTTAT 59.522 42.857 6.64 0.00 45.16 1.40
2321 2908 2.094078 AGCACATGCACGCCAATTTATT 60.094 40.909 6.64 0.00 45.16 1.40
2322 2909 2.672381 GCACATGCACGCCAATTTATTT 59.328 40.909 0.00 0.00 41.59 1.40
2323 2910 3.124976 GCACATGCACGCCAATTTATTTT 59.875 39.130 0.00 0.00 41.59 1.82
2324 2911 4.378253 GCACATGCACGCCAATTTATTTTT 60.378 37.500 0.00 0.00 41.59 1.94
2325 2912 5.315195 CACATGCACGCCAATTTATTTTTC 58.685 37.500 0.00 0.00 0.00 2.29
2326 2913 5.120519 CACATGCACGCCAATTTATTTTTCT 59.879 36.000 0.00 0.00 0.00 2.52
2327 2914 5.120519 ACATGCACGCCAATTTATTTTTCTG 59.879 36.000 0.00 0.00 0.00 3.02
2328 2915 4.626042 TGCACGCCAATTTATTTTTCTGT 58.374 34.783 0.00 0.00 0.00 3.41
2329 2916 5.053145 TGCACGCCAATTTATTTTTCTGTT 58.947 33.333 0.00 0.00 0.00 3.16
2330 2917 5.050499 TGCACGCCAATTTATTTTTCTGTTG 60.050 36.000 0.00 0.00 0.00 3.33
2331 2918 5.373262 CACGCCAATTTATTTTTCTGTTGC 58.627 37.500 0.00 0.00 0.00 4.17
2332 2919 5.050499 CACGCCAATTTATTTTTCTGTTGCA 60.050 36.000 0.00 0.00 0.00 4.08
2333 2920 5.525378 ACGCCAATTTATTTTTCTGTTGCAA 59.475 32.000 0.00 0.00 0.00 4.08
2334 2921 5.845433 CGCCAATTTATTTTTCTGTTGCAAC 59.155 36.000 22.83 22.83 0.00 4.17
2335 2922 5.845433 GCCAATTTATTTTTCTGTTGCAACG 59.155 36.000 23.79 17.92 0.00 4.10
2336 2923 5.845433 CCAATTTATTTTTCTGTTGCAACGC 59.155 36.000 23.79 2.38 0.00 4.84
2337 2924 6.417327 CAATTTATTTTTCTGTTGCAACGCA 58.583 32.000 23.79 10.48 36.47 5.24
2338 2925 5.382573 TTTATTTTTCTGTTGCAACGCAC 57.617 34.783 23.79 1.83 38.71 5.34
2339 2926 2.354109 TTTTTCTGTTGCAACGCACA 57.646 40.000 23.79 6.94 38.71 4.57
2340 2927 1.906757 TTTTCTGTTGCAACGCACAG 58.093 45.000 23.79 16.51 38.71 3.66
2341 2928 0.100325 TTTCTGTTGCAACGCACAGG 59.900 50.000 23.79 9.89 38.71 4.00
2342 2929 2.335052 TTCTGTTGCAACGCACAGGC 62.335 55.000 23.79 0.00 38.71 4.85
2343 2930 3.123523 CTGTTGCAACGCACAGGCA 62.124 57.895 23.79 3.60 38.71 4.75
2344 2931 2.336088 GTTGCAACGCACAGGCAT 59.664 55.556 14.90 0.00 38.71 4.40
2345 2932 1.169034 TGTTGCAACGCACAGGCATA 61.169 50.000 23.79 0.00 38.71 3.14
2346 2933 0.171007 GTTGCAACGCACAGGCATAT 59.829 50.000 14.90 0.00 38.71 1.78
2347 2934 0.170784 TTGCAACGCACAGGCATATG 59.829 50.000 0.00 0.00 38.71 1.78
2348 2935 1.587088 GCAACGCACAGGCATATGC 60.587 57.895 19.79 19.79 41.24 3.14
2378 3009 9.099454 AGTAGAACTCATTAAAATTGATCGTCC 57.901 33.333 0.00 0.00 0.00 4.79
2396 3027 4.081642 TCGTCCTTTCAGTGGAGGAAATAG 60.082 45.833 15.12 9.14 43.35 1.73
2411 3043 6.144078 AGGAAATAGTTTCGTTTTTGTGCT 57.856 33.333 0.00 0.00 40.57 4.40
2467 3099 3.070159 TGCCATAGTCTGACTATTGAGCC 59.930 47.826 24.98 12.71 39.26 4.70
2490 3124 3.059982 CTCCAGTGGAGTCCGCAA 58.940 61.111 28.38 8.67 44.25 4.85
2554 3191 3.368843 GCAATGCTAAAGAAACATGCACC 59.631 43.478 0.00 0.00 36.44 5.01
2589 3226 4.299586 TCACTTCATACATGCCTGGAAA 57.700 40.909 0.00 0.00 0.00 3.13
2601 3238 3.437642 CTGGAAACCCAGGCTTGAA 57.562 52.632 0.00 0.00 45.86 2.69
2727 3367 2.172293 AGATGAAGGATCACTTGCTCCC 59.828 50.000 0.00 0.00 40.21 4.30
2746 3389 1.457346 CTCCCATGTTTGAGGAGCAC 58.543 55.000 2.49 0.00 40.75 4.40
2748 3391 1.308069 CCCATGTTTGAGGAGCACCG 61.308 60.000 0.00 0.00 41.83 4.94
2756 3399 1.125093 TGAGGAGCACCGGGAAAGAA 61.125 55.000 6.32 0.00 41.83 2.52
2765 3408 1.072806 ACCGGGAAAGAAGGGTTGTAC 59.927 52.381 6.32 0.00 0.00 2.90
2844 3488 5.298777 ACGGTACACCATGTCTAAGATACTC 59.701 44.000 0.00 0.00 35.14 2.59
3011 3659 4.220413 CCACTGCTGGCTGATCTG 57.780 61.111 6.47 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.403866 AGCCAAAATTTCGCCATTATATGA 57.596 33.333 6.59 0.00 0.00 2.15
130 131 7.064728 AGCGTTTCCACTAATTCATTCTTACTC 59.935 37.037 0.00 0.00 0.00 2.59
155 156 8.863872 TTTTCCTTCTTCTCAAGGGTTAATAG 57.136 34.615 0.00 0.00 43.07 1.73
230 231 9.019656 ACCAATTCCATATTATAAAAGCGCATA 57.980 29.630 11.47 0.00 0.00 3.14
378 404 8.892887 ATTTTTGTGCAACTTTTATTTGTGTG 57.107 26.923 0.00 0.00 38.04 3.82
402 428 7.102993 ACAAAAGGTGAAGTTTTAGTGCAAAT 58.897 30.769 0.00 0.00 0.00 2.32
677 747 1.064825 ATACCTTAATGGGCCGAGGG 58.935 55.000 16.29 9.14 41.11 4.30
836 922 6.612306 CGATATGCTTATGTACAGTCTAGCA 58.388 40.000 19.56 19.56 42.14 3.49
838 924 6.524933 GTGCGATATGCTTATGTACAGTCTAG 59.475 42.308 0.33 0.00 46.63 2.43
839 925 6.016610 TGTGCGATATGCTTATGTACAGTCTA 60.017 38.462 0.33 0.00 46.63 2.59
845 931 4.055360 TGGTGTGCGATATGCTTATGTAC 58.945 43.478 0.00 1.37 46.63 2.90
860 946 2.725815 GCGAACGCTTTGGTGTGC 60.726 61.111 11.97 0.00 36.20 4.57
904 990 1.588674 TGAAGGTGTAGTGCCAAACG 58.411 50.000 0.00 0.00 0.00 3.60
906 992 2.890311 CCAATGAAGGTGTAGTGCCAAA 59.110 45.455 0.00 0.00 0.00 3.28
909 995 2.489938 TCCAATGAAGGTGTAGTGCC 57.510 50.000 0.00 0.00 0.00 5.01
911 997 4.509230 CGATGATCCAATGAAGGTGTAGTG 59.491 45.833 0.00 0.00 0.00 2.74
912 998 4.162320 ACGATGATCCAATGAAGGTGTAGT 59.838 41.667 0.00 0.00 0.00 2.73
913 999 4.697514 ACGATGATCCAATGAAGGTGTAG 58.302 43.478 0.00 0.00 0.00 2.74
954 1041 1.202627 GCTGACCTGCTAAGATCTGGG 60.203 57.143 0.00 0.00 0.00 4.45
963 1050 4.457496 GCCGCTGCTGACCTGCTA 62.457 66.667 0.00 0.00 36.37 3.49
1012 1107 2.042831 CCAGTGCAAGGCTGGCTAC 61.043 63.158 16.23 11.46 45.72 3.58
1141 1242 1.626631 GGAGAAGGTGAAGGGGAGGAT 60.627 57.143 0.00 0.00 0.00 3.24
1905 2027 3.536917 TCCAGCCCGCTCCGTATG 61.537 66.667 0.00 0.00 0.00 2.39
1950 2072 0.324091 CCTCCAGCAAGGCCAGAATT 60.324 55.000 5.01 0.00 37.29 2.17
1989 2111 1.112315 AATTCCAAACCAGGCGTGCA 61.112 50.000 0.00 0.00 0.00 4.57
2006 2128 0.682209 GGCACACCATCAGCTCCAAT 60.682 55.000 0.00 0.00 35.26 3.16
2007 2129 1.303561 GGCACACCATCAGCTCCAA 60.304 57.895 0.00 0.00 35.26 3.53
2008 2130 2.189191 GAGGCACACCATCAGCTCCA 62.189 60.000 0.00 0.00 39.06 3.86
2009 2131 1.451028 GAGGCACACCATCAGCTCC 60.451 63.158 0.00 0.00 39.06 4.70
2010 2132 1.023513 GTGAGGCACACCATCAGCTC 61.024 60.000 3.47 0.00 43.05 4.09
2011 2133 1.002868 GTGAGGCACACCATCAGCT 60.003 57.895 3.47 0.00 43.05 4.24
2012 2134 2.393768 CGTGAGGCACACCATCAGC 61.394 63.158 9.50 0.00 45.73 4.26
2050 2179 3.949113 ACGTTTCCTTCCTTGCAAAGTAA 59.051 39.130 0.00 0.00 44.25 2.24
2058 2187 3.369546 AATGCAACGTTTCCTTCCTTG 57.630 42.857 0.00 0.00 0.00 3.61
2059 2188 3.886505 TGTAATGCAACGTTTCCTTCCTT 59.113 39.130 0.00 0.00 0.00 3.36
2060 2189 3.252458 GTGTAATGCAACGTTTCCTTCCT 59.748 43.478 0.00 0.00 0.00 3.36
2061 2190 3.252458 AGTGTAATGCAACGTTTCCTTCC 59.748 43.478 0.00 0.00 0.00 3.46
2062 2191 4.483476 AGTGTAATGCAACGTTTCCTTC 57.517 40.909 0.00 0.00 0.00 3.46
2063 2192 5.703592 TCATAGTGTAATGCAACGTTTCCTT 59.296 36.000 0.00 0.00 0.00 3.36
2064 2193 5.242434 TCATAGTGTAATGCAACGTTTCCT 58.758 37.500 0.00 0.00 0.00 3.36
2065 2194 5.121768 ACTCATAGTGTAATGCAACGTTTCC 59.878 40.000 0.00 0.00 0.00 3.13
2066 2195 6.165659 ACTCATAGTGTAATGCAACGTTTC 57.834 37.500 0.00 0.00 0.00 2.78
2069 2656 7.843490 AAATACTCATAGTGTAATGCAACGT 57.157 32.000 0.00 0.00 0.00 3.99
2097 2684 9.090103 CCCTAAAAATCTTCCTTCCTTTAACTT 57.910 33.333 0.00 0.00 0.00 2.66
2099 2686 7.178628 AGCCCTAAAAATCTTCCTTCCTTTAAC 59.821 37.037 0.00 0.00 0.00 2.01
2100 2687 7.178451 CAGCCCTAAAAATCTTCCTTCCTTTAA 59.822 37.037 0.00 0.00 0.00 1.52
2104 2691 4.604156 CAGCCCTAAAAATCTTCCTTCCT 58.396 43.478 0.00 0.00 0.00 3.36
2105 2692 3.131223 GCAGCCCTAAAAATCTTCCTTCC 59.869 47.826 0.00 0.00 0.00 3.46
2106 2693 3.763897 TGCAGCCCTAAAAATCTTCCTTC 59.236 43.478 0.00 0.00 0.00 3.46
2107 2694 3.778265 TGCAGCCCTAAAAATCTTCCTT 58.222 40.909 0.00 0.00 0.00 3.36
2108 2695 3.456380 TGCAGCCCTAAAAATCTTCCT 57.544 42.857 0.00 0.00 0.00 3.36
2110 2697 6.223120 TCTTTTTGCAGCCCTAAAAATCTTC 58.777 36.000 3.12 0.00 35.82 2.87
2113 2700 5.541845 ACTCTTTTTGCAGCCCTAAAAATC 58.458 37.500 3.12 0.00 35.82 2.17
2114 2701 5.551305 ACTCTTTTTGCAGCCCTAAAAAT 57.449 34.783 3.12 0.00 35.82 1.82
2115 2702 5.508994 GCTACTCTTTTTGCAGCCCTAAAAA 60.509 40.000 0.00 0.00 35.29 1.94
2117 2704 3.506067 GCTACTCTTTTTGCAGCCCTAAA 59.494 43.478 0.00 0.00 0.00 1.85
2119 2706 2.039746 TGCTACTCTTTTTGCAGCCCTA 59.960 45.455 0.00 0.00 0.00 3.53
2120 2707 1.202927 TGCTACTCTTTTTGCAGCCCT 60.203 47.619 0.00 0.00 0.00 5.19
2121 2708 1.247567 TGCTACTCTTTTTGCAGCCC 58.752 50.000 0.00 0.00 0.00 5.19
2123 2710 2.554032 TCCTTGCTACTCTTTTTGCAGC 59.446 45.455 0.00 0.00 36.75 5.25
2124 2711 5.159209 CAATCCTTGCTACTCTTTTTGCAG 58.841 41.667 0.00 0.00 36.75 4.41
2125 2712 4.022068 CCAATCCTTGCTACTCTTTTTGCA 60.022 41.667 0.00 0.00 0.00 4.08
2126 2713 4.488879 CCAATCCTTGCTACTCTTTTTGC 58.511 43.478 0.00 0.00 0.00 3.68
2127 2714 4.524328 ACCCAATCCTTGCTACTCTTTTTG 59.476 41.667 0.00 0.00 0.00 2.44
2128 2715 4.524328 CACCCAATCCTTGCTACTCTTTTT 59.476 41.667 0.00 0.00 0.00 1.94
2129 2716 4.082125 CACCCAATCCTTGCTACTCTTTT 58.918 43.478 0.00 0.00 0.00 2.27
2130 2717 3.074538 ACACCCAATCCTTGCTACTCTTT 59.925 43.478 0.00 0.00 0.00 2.52
2131 2718 2.644798 ACACCCAATCCTTGCTACTCTT 59.355 45.455 0.00 0.00 0.00 2.85
2133 2720 2.359900 CACACCCAATCCTTGCTACTC 58.640 52.381 0.00 0.00 0.00 2.59
2134 2721 1.614317 GCACACCCAATCCTTGCTACT 60.614 52.381 0.00 0.00 0.00 2.57
2135 2722 0.811281 GCACACCCAATCCTTGCTAC 59.189 55.000 0.00 0.00 0.00 3.58
2138 2725 1.315257 ATCGCACACCCAATCCTTGC 61.315 55.000 0.00 0.00 0.00 4.01
2139 2726 0.452987 CATCGCACACCCAATCCTTG 59.547 55.000 0.00 0.00 0.00 3.61
2142 2729 2.800736 GCATCGCACACCCAATCC 59.199 61.111 0.00 0.00 0.00 3.01
2143 2730 2.404789 CGCATCGCACACCCAATC 59.595 61.111 0.00 0.00 0.00 2.67
2145 2732 4.634703 ACCGCATCGCACACCCAA 62.635 61.111 0.00 0.00 0.00 4.12
2162 2749 2.479837 CTCCAGTTAATAATCGGCGCA 58.520 47.619 10.83 0.00 0.00 6.09
2163 2750 1.798813 CCTCCAGTTAATAATCGGCGC 59.201 52.381 0.00 0.00 0.00 6.53
2164 2751 1.798813 GCCTCCAGTTAATAATCGGCG 59.201 52.381 0.00 0.00 0.00 6.46
2165 2752 2.152016 GGCCTCCAGTTAATAATCGGC 58.848 52.381 0.00 0.00 35.63 5.54
2166 2753 3.771577 AGGCCTCCAGTTAATAATCGG 57.228 47.619 0.00 0.00 0.00 4.18
2167 2754 7.228706 ACAATTTAGGCCTCCAGTTAATAATCG 59.771 37.037 9.68 0.00 0.00 3.34
2168 2755 8.465273 ACAATTTAGGCCTCCAGTTAATAATC 57.535 34.615 9.68 0.00 0.00 1.75
2171 2758 6.540914 CGAACAATTTAGGCCTCCAGTTAATA 59.459 38.462 9.68 0.00 0.00 0.98
2172 2759 5.357032 CGAACAATTTAGGCCTCCAGTTAAT 59.643 40.000 9.68 0.00 0.00 1.40
2173 2760 4.698304 CGAACAATTTAGGCCTCCAGTTAA 59.302 41.667 9.68 0.00 0.00 2.01
2174 2761 4.258543 CGAACAATTTAGGCCTCCAGTTA 58.741 43.478 9.68 0.00 0.00 2.24
2176 2763 2.618045 CCGAACAATTTAGGCCTCCAGT 60.618 50.000 9.68 0.00 0.00 4.00
2177 2764 2.017049 CCGAACAATTTAGGCCTCCAG 58.983 52.381 9.68 0.00 0.00 3.86
2180 2767 3.261981 TCTCCGAACAATTTAGGCCTC 57.738 47.619 9.68 0.00 0.00 4.70
2184 2771 9.855021 AAAAATACATTCTCCGAACAATTTAGG 57.145 29.630 0.00 0.00 0.00 2.69
2209 2796 4.583073 GGAGTTGCCAAGGTTTAGAGAAAA 59.417 41.667 0.00 0.00 36.34 2.29
2210 2797 4.142038 GGAGTTGCCAAGGTTTAGAGAAA 58.858 43.478 0.00 0.00 36.34 2.52
2211 2798 3.497942 GGGAGTTGCCAAGGTTTAGAGAA 60.498 47.826 0.00 0.00 38.95 2.87
2213 2800 2.040412 AGGGAGTTGCCAAGGTTTAGAG 59.960 50.000 0.00 0.00 38.95 2.43
2214 2801 2.062636 AGGGAGTTGCCAAGGTTTAGA 58.937 47.619 0.00 0.00 38.95 2.10
2216 2803 1.497286 ACAGGGAGTTGCCAAGGTTTA 59.503 47.619 0.00 0.00 38.95 2.01
2217 2804 0.261696 ACAGGGAGTTGCCAAGGTTT 59.738 50.000 0.00 0.00 38.95 3.27
2218 2805 0.178990 GACAGGGAGTTGCCAAGGTT 60.179 55.000 0.00 0.00 38.95 3.50
2219 2806 1.352622 TGACAGGGAGTTGCCAAGGT 61.353 55.000 0.00 0.00 38.95 3.50
2221 2808 1.542915 CAATGACAGGGAGTTGCCAAG 59.457 52.381 0.00 0.00 38.95 3.61
2223 2810 0.478072 ACAATGACAGGGAGTTGCCA 59.522 50.000 0.00 0.00 38.95 4.92
2224 2811 1.541588 GAACAATGACAGGGAGTTGCC 59.458 52.381 0.00 0.00 0.00 4.52
2226 2813 1.806542 CCGAACAATGACAGGGAGTTG 59.193 52.381 0.00 0.00 0.00 3.16
2228 2815 1.348064 TCCGAACAATGACAGGGAGT 58.652 50.000 0.00 0.00 0.00 3.85
2229 2816 2.283298 CATCCGAACAATGACAGGGAG 58.717 52.381 0.00 0.00 0.00 4.30
2231 2818 2.009774 GACATCCGAACAATGACAGGG 58.990 52.381 0.00 0.00 0.00 4.45
2232 2819 1.660607 CGACATCCGAACAATGACAGG 59.339 52.381 0.00 0.00 41.76 4.00
2233 2820 2.092681 CACGACATCCGAACAATGACAG 59.907 50.000 0.00 0.00 41.76 3.51
2234 2821 2.065512 CACGACATCCGAACAATGACA 58.934 47.619 0.00 0.00 41.76 3.58
2236 2823 2.448926 ACACGACATCCGAACAATGA 57.551 45.000 0.00 0.00 41.76 2.57
2237 2824 2.838275 CAACACGACATCCGAACAATG 58.162 47.619 0.00 0.00 41.76 2.82
2238 2825 1.196808 GCAACACGACATCCGAACAAT 59.803 47.619 0.00 0.00 41.76 2.71
2239 2826 0.584396 GCAACACGACATCCGAACAA 59.416 50.000 0.00 0.00 41.76 2.83
2240 2827 0.249699 AGCAACACGACATCCGAACA 60.250 50.000 0.00 0.00 41.76 3.18
2244 2831 0.389296 TACCAGCAACACGACATCCG 60.389 55.000 0.00 0.00 45.44 4.18
2245 2832 1.076332 GTACCAGCAACACGACATCC 58.924 55.000 0.00 0.00 0.00 3.51
2246 2833 0.713883 CGTACCAGCAACACGACATC 59.286 55.000 0.00 0.00 37.89 3.06
2247 2834 1.289109 GCGTACCAGCAACACGACAT 61.289 55.000 0.00 0.00 37.89 3.06
2248 2835 1.952133 GCGTACCAGCAACACGACA 60.952 57.895 0.00 0.00 37.89 4.35
2249 2836 1.952133 TGCGTACCAGCAACACGAC 60.952 57.895 0.00 0.00 45.06 4.34
2250 2837 2.417936 TGCGTACCAGCAACACGA 59.582 55.556 0.00 0.00 45.06 4.35
2257 2844 1.153842 GGCCAAAATGCGTACCAGC 60.154 57.895 0.00 0.00 37.71 4.85
2258 2845 1.670811 CTAGGCCAAAATGCGTACCAG 59.329 52.381 5.01 0.00 0.00 4.00
2260 2847 0.380733 GCTAGGCCAAAATGCGTACC 59.619 55.000 5.01 0.00 0.00 3.34
2262 2849 0.108089 TCGCTAGGCCAAAATGCGTA 60.108 50.000 20.70 10.04 45.69 4.42
2263 2850 0.958382 TTCGCTAGGCCAAAATGCGT 60.958 50.000 20.70 0.00 45.69 5.24
2266 2853 0.810648 TGCTTCGCTAGGCCAAAATG 59.189 50.000 5.01 0.00 0.00 2.32
2269 2856 0.960364 CCTTGCTTCGCTAGGCCAAA 60.960 55.000 5.01 0.00 43.48 3.28
2270 2857 1.377202 CCTTGCTTCGCTAGGCCAA 60.377 57.895 5.01 0.00 43.48 4.52
2272 2859 2.514824 CCCTTGCTTCGCTAGGCC 60.515 66.667 10.23 0.00 46.98 5.19
2273 2860 1.377333 AACCCTTGCTTCGCTAGGC 60.377 57.895 10.23 0.00 46.98 3.93
2275 2862 1.079503 GACAACCCTTGCTTCGCTAG 58.920 55.000 0.00 0.00 0.00 3.42
2276 2863 0.394938 TGACAACCCTTGCTTCGCTA 59.605 50.000 0.00 0.00 0.00 4.26
2277 2864 0.250901 ATGACAACCCTTGCTTCGCT 60.251 50.000 0.00 0.00 0.00 4.93
2278 2865 0.109597 CATGACAACCCTTGCTTCGC 60.110 55.000 0.00 0.00 0.00 4.70
2279 2866 0.109597 GCATGACAACCCTTGCTTCG 60.110 55.000 0.00 0.00 35.23 3.79
2280 2867 1.251251 AGCATGACAACCCTTGCTTC 58.749 50.000 0.00 0.00 42.53 3.86
2281 2868 2.440409 CTAGCATGACAACCCTTGCTT 58.560 47.619 5.85 0.00 42.53 3.91
2282 2869 1.952367 GCTAGCATGACAACCCTTGCT 60.952 52.381 10.63 5.84 45.56 3.91
2283 2870 0.453390 GCTAGCATGACAACCCTTGC 59.547 55.000 10.63 0.00 37.44 4.01
2284 2871 1.470098 GTGCTAGCATGACAACCCTTG 59.530 52.381 22.51 0.00 0.00 3.61
2285 2872 1.073763 TGTGCTAGCATGACAACCCTT 59.926 47.619 22.51 0.00 0.00 3.95
2286 2873 0.692476 TGTGCTAGCATGACAACCCT 59.308 50.000 22.51 0.00 0.00 4.34
2287 2874 1.402968 CATGTGCTAGCATGACAACCC 59.597 52.381 22.51 5.68 46.65 4.11
2288 2875 1.202222 GCATGTGCTAGCATGACAACC 60.202 52.381 22.51 6.49 46.65 3.77
2289 2876 1.469703 TGCATGTGCTAGCATGACAAC 59.530 47.619 22.51 11.22 46.65 3.32
2290 2877 1.469703 GTGCATGTGCTAGCATGACAA 59.530 47.619 22.51 4.44 46.65 3.18
2291 2878 1.089112 GTGCATGTGCTAGCATGACA 58.911 50.000 22.51 14.89 46.65 3.58
2292 2879 3.911989 GTGCATGTGCTAGCATGAC 57.088 52.632 22.51 8.90 46.65 3.06
2294 2881 4.989588 CGTGCATGTGCTAGCATG 57.010 55.556 22.51 17.14 46.50 4.06
2295 2882 2.475466 GGCGTGCATGTGCTAGCAT 61.475 57.895 22.51 2.08 43.44 3.79
2296 2883 3.126879 GGCGTGCATGTGCTAGCA 61.127 61.111 14.93 14.93 42.53 3.49
2297 2884 1.996786 ATTGGCGTGCATGTGCTAGC 61.997 55.000 8.10 8.10 42.66 3.42
2298 2885 0.452987 AATTGGCGTGCATGTGCTAG 59.547 50.000 7.93 1.67 42.66 3.42
2299 2886 0.887247 AAATTGGCGTGCATGTGCTA 59.113 45.000 7.93 0.00 42.66 3.49
2300 2887 0.887247 TAAATTGGCGTGCATGTGCT 59.113 45.000 7.93 0.00 42.66 4.40
2301 2888 1.925229 ATAAATTGGCGTGCATGTGC 58.075 45.000 7.93 3.82 42.50 4.57
2302 2889 4.925061 AAAATAAATTGGCGTGCATGTG 57.075 36.364 7.93 0.00 0.00 3.21
2303 2890 5.120519 CAGAAAAATAAATTGGCGTGCATGT 59.879 36.000 7.93 0.00 0.00 3.21
2304 2891 5.120519 ACAGAAAAATAAATTGGCGTGCATG 59.879 36.000 0.09 0.09 0.00 4.06
2305 2892 5.237048 ACAGAAAAATAAATTGGCGTGCAT 58.763 33.333 0.00 0.00 0.00 3.96
2306 2893 4.626042 ACAGAAAAATAAATTGGCGTGCA 58.374 34.783 0.00 0.00 0.00 4.57
2307 2894 5.373262 CAACAGAAAAATAAATTGGCGTGC 58.627 37.500 0.00 0.00 0.00 5.34
2308 2895 5.050499 TGCAACAGAAAAATAAATTGGCGTG 60.050 36.000 0.00 0.00 0.00 5.34
2309 2896 5.053145 TGCAACAGAAAAATAAATTGGCGT 58.947 33.333 0.00 0.00 0.00 5.68
2310 2897 5.588568 TGCAACAGAAAAATAAATTGGCG 57.411 34.783 0.00 0.00 0.00 5.69
2311 2898 5.845433 CGTTGCAACAGAAAAATAAATTGGC 59.155 36.000 28.01 0.00 0.00 4.52
2312 2899 5.845433 GCGTTGCAACAGAAAAATAAATTGG 59.155 36.000 28.01 7.85 0.00 3.16
2313 2900 6.354102 GTGCGTTGCAACAGAAAAATAAATTG 59.646 34.615 28.01 8.47 41.47 2.32
2314 2901 6.036517 TGTGCGTTGCAACAGAAAAATAAATT 59.963 30.769 28.01 0.00 41.47 1.82
2315 2902 5.521735 TGTGCGTTGCAACAGAAAAATAAAT 59.478 32.000 28.01 0.00 41.47 1.40
2316 2903 4.864806 TGTGCGTTGCAACAGAAAAATAAA 59.135 33.333 28.01 0.65 41.47 1.40
2317 2904 4.424626 TGTGCGTTGCAACAGAAAAATAA 58.575 34.783 28.01 1.93 41.47 1.40
2318 2905 4.033990 TGTGCGTTGCAACAGAAAAATA 57.966 36.364 28.01 4.13 41.47 1.40
2319 2906 2.859538 CTGTGCGTTGCAACAGAAAAAT 59.140 40.909 28.01 0.00 41.47 1.82
2320 2907 2.257894 CTGTGCGTTGCAACAGAAAAA 58.742 42.857 28.01 8.21 41.47 1.94
2321 2908 1.468908 CCTGTGCGTTGCAACAGAAAA 60.469 47.619 28.01 10.65 41.47 2.29
2322 2909 0.100325 CCTGTGCGTTGCAACAGAAA 59.900 50.000 28.01 8.77 41.47 2.52
2323 2910 1.726865 CCTGTGCGTTGCAACAGAA 59.273 52.632 28.01 13.44 41.47 3.02
2324 2911 2.833533 GCCTGTGCGTTGCAACAGA 61.834 57.895 28.01 11.66 41.47 3.41
2325 2912 2.353839 GCCTGTGCGTTGCAACAG 60.354 61.111 28.01 20.60 41.47 3.16
2326 2913 1.169034 TATGCCTGTGCGTTGCAACA 61.169 50.000 28.01 9.56 41.47 3.33
2327 2914 0.171007 ATATGCCTGTGCGTTGCAAC 59.829 50.000 19.89 19.89 41.47 4.17
2328 2915 0.170784 CATATGCCTGTGCGTTGCAA 59.829 50.000 0.00 0.00 41.47 4.08
2329 2916 1.801983 CATATGCCTGTGCGTTGCA 59.198 52.632 0.00 0.00 41.78 4.08
2330 2917 1.587088 GCATATGCCTGTGCGTTGC 60.587 57.895 17.26 0.00 41.78 4.17
2331 2918 4.696078 GCATATGCCTGTGCGTTG 57.304 55.556 17.26 0.00 41.78 4.10
2341 2928 4.873746 TGAGTTCTACTAGGGCATATGC 57.126 45.455 19.79 19.79 41.14 3.14
2342 2929 9.778741 TTTTAATGAGTTCTACTAGGGCATATG 57.221 33.333 0.00 0.00 0.00 1.78
2345 2932 9.125026 CAATTTTAATGAGTTCTACTAGGGCAT 57.875 33.333 0.00 0.00 0.00 4.40
2346 2933 8.325787 TCAATTTTAATGAGTTCTACTAGGGCA 58.674 33.333 0.00 0.00 0.00 5.36
2347 2934 8.732746 TCAATTTTAATGAGTTCTACTAGGGC 57.267 34.615 0.00 0.00 0.00 5.19
2352 2939 9.099454 GGACGATCAATTTTAATGAGTTCTACT 57.901 33.333 0.00 0.00 0.00 2.57
2353 2940 9.099454 AGGACGATCAATTTTAATGAGTTCTAC 57.901 33.333 0.00 0.00 0.00 2.59
2378 3009 5.701290 ACGAAACTATTTCCTCCACTGAAAG 59.299 40.000 0.00 0.00 35.36 2.62
2396 3027 5.004061 GGAAACTACAGCACAAAAACGAAAC 59.996 40.000 0.00 0.00 0.00 2.78
2411 3043 2.068834 TTTTTGCGGGGGAAACTACA 57.931 45.000 0.00 0.00 0.00 2.74
2438 3070 8.144478 TCAATAGTCAGACTATGGCATAAGTTC 58.856 37.037 21.68 5.62 40.32 3.01
2449 3081 5.416326 GGATACGGCTCAATAGTCAGACTAT 59.584 44.000 16.34 16.34 42.86 2.12
2454 3086 3.057174 GGAGGATACGGCTCAATAGTCAG 60.057 52.174 0.00 0.00 46.39 3.51
2589 3226 1.053424 TACGACTTTCAAGCCTGGGT 58.947 50.000 0.00 0.00 0.00 4.51
2721 3361 0.329261 CTCAAACATGGGAGGGAGCA 59.671 55.000 0.00 0.00 0.00 4.26
2727 3367 1.457346 GTGCTCCTCAAACATGGGAG 58.543 55.000 9.85 9.85 46.65 4.30
2746 3389 1.072648 TGTACAACCCTTCTTTCCCGG 59.927 52.381 0.00 0.00 0.00 5.73
2748 3391 3.217681 TGTGTACAACCCTTCTTTCCC 57.782 47.619 0.00 0.00 0.00 3.97
2756 3399 0.771127 AGGCACATGTGTACAACCCT 59.229 50.000 26.01 19.01 0.00 4.34
2765 3408 4.409218 GGCGTGCAGGCACATGTG 62.409 66.667 30.35 21.83 46.47 3.21


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

AutoCloner maintained by Alex Coulton.