Multiple sequence alignment - TraesCS7A01G355500

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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 TraesCS7A01G355500 chr7A 100.000 3043 0 0 1 3043 520562404 520565446 0.000000e+00 5620.0
1 TraesCS7A01G355500 chr7A 93.023 43 3 0 2777 2819 16368526 16368568 2.530000e-06 63.9
2 TraesCS7A01G355500 chr7B 90.188 2283 141 33 81 2295 499258174 499255907 0.000000e+00 2898.0
3 TraesCS7A01G355500 chr7B 92.053 151 10 1 2895 3043 499255757 499255607 8.550000e-51 211.0
4 TraesCS7A01G355500 chr7B 95.556 45 1 1 2819 2862 499255858 499255814 1.510000e-08 71.3
5 TraesCS7A01G355500 chr7D 94.598 1629 77 4 482 2106 475376396 475374775 0.000000e+00 2510.0
6 TraesCS7A01G355500 chr7D 92.689 424 28 3 2297 2718 449561808 449561386 2.590000e-170 608.0
7 TraesCS7A01G355500 chr7D 93.062 418 22 6 2301 2716 152093858 152094270 3.360000e-169 604.0
8 TraesCS7A01G355500 chr7D 81.141 403 53 9 81 462 475377154 475376754 4.930000e-78 302.0
9 TraesCS7A01G355500 chr7D 93.122 189 11 1 2109 2295 475374400 475374212 2.990000e-70 276.0
10 TraesCS7A01G355500 chr7D 93.519 108 7 0 2936 3043 475373986 475373879 8.730000e-36 161.0
11 TraesCS7A01G355500 chr3D 92.272 427 29 4 2297 2721 334019299 334019723 1.210000e-168 603.0
12 TraesCS7A01G355500 chr3D 93.023 43 3 0 2777 2819 461603873 461603831 2.530000e-06 63.9
13 TraesCS7A01G355500 chr3D 89.796 49 3 2 2777 2823 142494368 142494320 9.110000e-06 62.1
14 TraesCS7A01G355500 chr3D 92.857 42 3 0 2777 2818 548818051 548818010 9.110000e-06 62.1
15 TraesCS7A01G355500 chr2B 92.272 427 30 3 2297 2721 406089724 406090149 1.210000e-168 603.0
16 TraesCS7A01G355500 chr2B 80.000 240 42 6 1176 1412 624355475 624355239 4.030000e-39 172.0
17 TraesCS7A01G355500 chr3A 92.771 415 29 1 2297 2710 36665682 36665268 1.560000e-167 599.0
18 TraesCS7A01G355500 chr3A 91.529 425 32 3 2296 2718 730597615 730598037 1.570000e-162 582.0
19 TraesCS7A01G355500 chr4D 92.217 424 25 5 2297 2720 25387596 25387181 7.260000e-166 593.0
20 TraesCS7A01G355500 chr6B 91.943 422 30 2 2299 2718 704415383 704415802 3.380000e-164 588.0
21 TraesCS7A01G355500 chr6B 78.491 265 47 10 1166 1425 495806712 495806453 6.750000e-37 165.0
22 TraesCS7A01G355500 chr2D 91.943 422 27 7 2297 2717 135401042 135401457 4.370000e-163 584.0
23 TraesCS7A01G355500 chr2D 80.000 240 42 6 1176 1412 527293774 527293538 4.030000e-39 172.0
24 TraesCS7A01G355500 chr1B 84.800 250 27 9 1167 1409 418821471 418821716 1.090000e-59 241.0
25 TraesCS7A01G355500 chr1B 95.122 41 2 0 2777 2817 664973255 664973215 7.040000e-07 65.8
26 TraesCS7A01G355500 chr6A 78.767 292 53 9 1154 1439 465231904 465232192 1.440000e-43 187.0
27 TraesCS7A01G355500 chr2A 80.913 241 38 8 1176 1412 672292448 672292212 1.860000e-42 183.0
28 TraesCS7A01G355500 chr2A 95.455 44 2 0 2776 2819 719476535 719476578 1.510000e-08 71.3
29 TraesCS7A01G355500 chr6D 77.816 293 54 11 1154 1439 326540347 326540635 1.450000e-38 171.0
30 TraesCS7A01G355500 chr5A 76.142 197 34 7 170 360 275114999 275114810 1.160000e-14 91.6
31 TraesCS7A01G355500 chr5A 93.333 45 3 0 2777 2821 69085778 69085822 1.960000e-07 67.6
32 TraesCS7A01G355500 chr5B 84.000 75 12 0 298 372 679560418 679560492 4.210000e-09 73.1
33 TraesCS7A01G355500 chr4A 93.023 43 3 0 2777 2819 732285602 732285644 2.530000e-06 63.9
34 TraesCS7A01G355500 chr5D 94.872 39 2 0 2776 2814 524487918 524487956 9.110000e-06 62.1


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 TraesCS7A01G355500 chr7A 520562404 520565446 3042 False 5620.00 5620 100.000 1 3043 1 chr7A.!!$F2 3042
1 TraesCS7A01G355500 chr7B 499255607 499258174 2567 True 1060.10 2898 92.599 81 3043 3 chr7B.!!$R1 2962
2 TraesCS7A01G355500 chr7D 475373879 475377154 3275 True 812.25 2510 90.595 81 3043 4 chr7D.!!$R2 2962

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
52 53 0.033796 TACCACCAGTAGGGACGAGG 60.034 60.0 0.0 0.0 41.15 4.63 F
1130 1507 0.174617 GCGGAGTTCTGGAGAAGAGG 59.825 60.0 0.0 0.0 35.91 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 2331 0.314302 ACAGACGTGTACTGAGGCAC 59.686 55.0 9.51 0.37 38.55 5.01 R
2702 3456 0.109365 TGATCGCAAAATGCCAACGG 60.109 50.0 0.00 0.00 41.12 4.44 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
19 20 2.953640 GTAGTCTATGAGCGAGACCG 57.046 55.000 7.28 0.00 43.72 4.79
38 39 4.530325 CGCCGCCGCAAATACCAC 62.530 66.667 0.00 0.00 34.03 4.16
39 40 4.187810 GCCGCCGCAAATACCACC 62.188 66.667 0.00 0.00 34.03 4.61
40 41 2.748251 CCGCCGCAAATACCACCA 60.748 61.111 0.00 0.00 0.00 4.17
41 42 2.760159 CCGCCGCAAATACCACCAG 61.760 63.158 0.00 0.00 0.00 4.00
42 43 2.038269 CGCCGCAAATACCACCAGT 61.038 57.895 0.00 0.00 0.00 4.00
43 44 0.741574 CGCCGCAAATACCACCAGTA 60.742 55.000 0.00 0.00 34.76 2.74
44 45 1.014352 GCCGCAAATACCACCAGTAG 58.986 55.000 0.00 0.00 33.42 2.57
45 46 1.663695 CCGCAAATACCACCAGTAGG 58.336 55.000 0.00 0.00 42.21 3.18
46 47 1.663695 CGCAAATACCACCAGTAGGG 58.336 55.000 0.00 0.00 44.81 3.53
47 48 1.208535 CGCAAATACCACCAGTAGGGA 59.791 52.381 0.00 0.00 41.15 4.20
48 49 2.640184 GCAAATACCACCAGTAGGGAC 58.360 52.381 0.00 0.00 41.15 4.46
49 50 2.901249 CAAATACCACCAGTAGGGACG 58.099 52.381 0.00 0.00 41.15 4.79
50 51 2.498481 CAAATACCACCAGTAGGGACGA 59.502 50.000 0.00 0.00 41.15 4.20
51 52 2.068834 ATACCACCAGTAGGGACGAG 57.931 55.000 0.00 0.00 41.15 4.18
52 53 0.033796 TACCACCAGTAGGGACGAGG 60.034 60.000 0.00 0.00 41.15 4.63
53 54 2.058595 CCACCAGTAGGGACGAGGG 61.059 68.421 0.00 0.00 41.15 4.30
54 55 2.363925 ACCAGTAGGGACGAGGGC 60.364 66.667 0.00 0.00 41.15 5.19
55 56 2.363795 CCAGTAGGGACGAGGGCA 60.364 66.667 0.00 0.00 40.01 5.36
56 57 1.987855 CCAGTAGGGACGAGGGCAA 60.988 63.158 0.00 0.00 40.01 4.52
57 58 1.218316 CAGTAGGGACGAGGGCAAC 59.782 63.158 0.00 0.00 0.00 4.17
105 107 3.626924 GGCCGACCTCCACACTGT 61.627 66.667 0.00 0.00 0.00 3.55
112 114 2.180276 GACCTCCACACTGTGTAGGAT 58.820 52.381 28.04 16.50 41.33 3.24
121 123 3.840666 ACACTGTGTAGGATGAAGTGGAT 59.159 43.478 12.53 0.00 42.00 3.41
126 128 1.412710 GTAGGATGAAGTGGATCGGCA 59.587 52.381 0.00 0.00 0.00 5.69
128 130 0.179000 GGATGAAGTGGATCGGCACT 59.821 55.000 0.00 0.00 0.00 4.40
130 132 1.667724 GATGAAGTGGATCGGCACTTG 59.332 52.381 18.50 0.00 41.19 3.16
131 133 0.396435 TGAAGTGGATCGGCACTTGT 59.604 50.000 18.50 0.17 41.19 3.16
134 136 1.965930 GTGGATCGGCACTTGTGCA 60.966 57.895 24.34 8.00 36.33 4.57
142 144 2.412525 CACTTGTGCAAGCGCCAA 59.587 55.556 2.29 0.00 41.99 4.52
168 170 4.124910 CAGGCACGACTGTTGTGT 57.875 55.556 24.88 7.60 39.53 3.72
174 176 3.041940 CGACTGTTGTGTCCCCGC 61.042 66.667 0.00 0.00 33.70 6.13
214 219 1.232621 ACTCCGATGACGACGACACA 61.233 55.000 0.00 0.00 42.66 3.72
218 223 1.125270 CGATGACGACGACACAAACA 58.875 50.000 0.00 0.00 42.66 2.83
222 227 0.503117 GACGACGACACAAACAGCTC 59.497 55.000 0.00 0.00 0.00 4.09
225 230 1.295792 GACGACACAAACAGCTCCAA 58.704 50.000 0.00 0.00 0.00 3.53
227 232 1.013596 CGACACAAACAGCTCCAACA 58.986 50.000 0.00 0.00 0.00 3.33
228 233 1.003545 CGACACAAACAGCTCCAACAG 60.004 52.381 0.00 0.00 0.00 3.16
256 261 3.238497 TAGGCCGGCCATGCGTAT 61.238 61.111 45.13 26.36 38.92 3.06
262 267 2.246739 CGGCCATGCGTATGAGGTG 61.247 63.158 15.64 0.00 36.36 4.00
263 268 1.893808 GGCCATGCGTATGAGGTGG 60.894 63.158 15.64 0.00 36.36 4.61
264 269 1.153168 GCCATGCGTATGAGGTGGT 60.153 57.895 15.64 0.00 36.36 4.16
286 291 2.162208 CGTCCGCTACAAGGTAGTGTAA 59.838 50.000 13.92 2.02 33.66 2.41
300 306 9.287373 CAAGGTAGTGTAATGTTTTAGGGTTTA 57.713 33.333 0.00 0.00 0.00 2.01
372 378 7.491048 AGCTTTAATGAATTTTGTCGTGTTTGT 59.509 29.630 0.00 0.00 0.00 2.83
373 379 7.578736 GCTTTAATGAATTTTGTCGTGTTTGTG 59.421 33.333 0.00 0.00 0.00 3.33
424 445 3.301222 ATGGTTGGATGGCCGGCTT 62.301 57.895 28.56 14.87 36.79 4.35
428 449 2.905996 TTGGATGGCCGGCTTCTGT 61.906 57.895 28.56 7.88 36.79 3.41
431 452 0.603975 GGATGGCCGGCTTCTGTATC 60.604 60.000 28.56 18.35 0.00 2.24
440 461 1.221414 GCTTCTGTATCCATGTCCGC 58.779 55.000 0.00 0.00 0.00 5.54
441 462 1.473257 GCTTCTGTATCCATGTCCGCA 60.473 52.381 0.00 0.00 0.00 5.69
456 477 3.179830 GTCCGCAGACAAGTATAGTGTG 58.820 50.000 0.00 0.00 42.99 3.82
462 483 5.388475 CGCAGACAAGTATAGTGTGTGTTTC 60.388 44.000 12.59 0.45 41.15 2.78
464 485 6.346919 GCAGACAAGTATAGTGTGTGTTTCAG 60.347 42.308 12.59 0.00 41.15 3.02
465 486 5.696724 AGACAAGTATAGTGTGTGTTTCAGC 59.303 40.000 0.00 0.00 0.00 4.26
466 487 5.611374 ACAAGTATAGTGTGTGTTTCAGCT 58.389 37.500 0.00 0.00 0.00 4.24
468 489 5.468540 AGTATAGTGTGTGTTTCAGCTGA 57.531 39.130 13.74 13.74 0.00 4.26
469 490 5.230942 AGTATAGTGTGTGTTTCAGCTGAC 58.769 41.667 18.03 7.32 0.00 3.51
470 491 1.290203 AGTGTGTGTTTCAGCTGACG 58.710 50.000 18.03 0.00 0.00 4.35
471 492 0.304705 GTGTGTGTTTCAGCTGACGG 59.695 55.000 18.03 0.00 0.00 4.79
472 493 1.279840 GTGTGTTTCAGCTGACGGC 59.720 57.895 18.03 10.05 42.19 5.68
487 846 0.604243 ACGGCGTTGGCAGTCATTTA 60.604 50.000 6.77 0.00 44.50 1.40
493 852 4.380023 GGCGTTGGCAGTCATTTATACAAA 60.380 41.667 0.00 0.00 42.47 2.83
500 859 6.434028 TGGCAGTCATTTATACAAAAGCTTCT 59.566 34.615 0.00 0.00 0.00 2.85
538 897 2.146342 CCATCGACCTACATGGATTGC 58.854 52.381 0.00 0.00 42.11 3.56
564 923 4.891168 TGTCAAAAAGGAGAAAAGGTACCC 59.109 41.667 8.74 0.00 0.00 3.69
571 930 2.237893 GGAGAAAAGGTACCCGGATTGA 59.762 50.000 8.74 0.00 0.00 2.57
644 1003 4.338118 TGAAAACCCTCATCACTGTGAAAC 59.662 41.667 15.31 0.00 37.35 2.78
652 1011 6.330278 CCTCATCACTGTGAAACTAATACGA 58.670 40.000 15.31 0.50 38.04 3.43
695 1066 5.587844 GCACTCATCTCTCCACAAACAATAT 59.412 40.000 0.00 0.00 0.00 1.28
722 1093 2.096664 TGTAAATTGCACAGCACGTACG 60.097 45.455 15.01 15.01 38.71 3.67
728 1099 1.695893 GCACAGCACGTACGCATCAT 61.696 55.000 16.72 0.00 0.00 2.45
775 1147 0.947244 CTGCTTTGCAACGGTCTCTT 59.053 50.000 0.00 0.00 38.41 2.85
776 1148 0.662619 TGCTTTGCAACGGTCTCTTG 59.337 50.000 0.00 0.00 34.76 3.02
777 1149 0.944386 GCTTTGCAACGGTCTCTTGA 59.056 50.000 0.00 0.00 0.00 3.02
778 1150 1.334149 GCTTTGCAACGGTCTCTTGAC 60.334 52.381 0.00 0.00 42.22 3.18
779 1151 2.213499 CTTTGCAACGGTCTCTTGACT 58.787 47.619 0.00 0.00 42.54 3.41
780 1152 1.865865 TTGCAACGGTCTCTTGACTC 58.134 50.000 0.00 0.00 42.54 3.36
781 1153 1.040646 TGCAACGGTCTCTTGACTCT 58.959 50.000 0.00 0.00 42.54 3.24
816 1188 2.427506 GTTAAGAGGGCACAACTCAGG 58.572 52.381 0.00 0.00 37.43 3.86
819 1191 1.673665 GAGGGCACAACTCAGGCAG 60.674 63.158 0.00 0.00 35.09 4.85
844 1216 2.055838 CGAGACTCGAGAGGTAGATCG 58.944 57.143 21.68 12.70 43.74 3.69
861 1233 8.696374 AGGTAGATCGATCTAGAAAAATGAACA 58.304 33.333 30.78 8.32 39.87 3.18
862 1234 8.973378 GGTAGATCGATCTAGAAAAATGAACAG 58.027 37.037 30.78 0.00 39.87 3.16
879 1253 4.888823 TGAACAGAGAGATCTGGAGAGATG 59.111 45.833 0.00 0.00 39.19 2.90
1003 1378 1.092345 GCTTCCCCGCTAGCTTCAAG 61.092 60.000 13.93 10.16 34.57 3.02
1004 1379 0.537188 CTTCCCCGCTAGCTTCAAGA 59.463 55.000 13.93 0.00 0.00 3.02
1070 1447 4.379243 CTGAACAGCCCGGCGTCT 62.379 66.667 6.01 0.00 0.00 4.18
1130 1507 0.174617 GCGGAGTTCTGGAGAAGAGG 59.825 60.000 0.00 0.00 35.91 3.69
1132 1509 1.617263 CGGAGTTCTGGAGAAGAGGGA 60.617 57.143 0.00 0.00 35.91 4.20
1140 1517 1.653918 TGGAGAAGAGGGAGAGGGATT 59.346 52.381 0.00 0.00 0.00 3.01
1613 1990 4.323477 TTCGGGGGCACGTTCTGG 62.323 66.667 0.00 0.00 34.94 3.86
1790 2167 3.865745 CGCTCTTGTGGAACCTGTAATAG 59.134 47.826 0.00 0.00 34.36 1.73
1813 2190 3.448686 AGCAAATAATCCGTCACTCTCG 58.551 45.455 0.00 0.00 0.00 4.04
1870 2248 8.682936 TTCTCTCTTGTCAGCTTCTAATTTTT 57.317 30.769 0.00 0.00 0.00 1.94
1906 2284 3.142174 GACTATTTCTGGCTACCCATGC 58.858 50.000 0.00 0.00 41.21 4.06
1953 2331 7.137490 ACTGATGCACATTAATAATGATCGG 57.863 36.000 18.78 16.53 41.46 4.18
1968 2348 1.248785 ATCGGTGCCTCAGTACACGT 61.249 55.000 0.00 0.00 37.68 4.49
1976 2356 2.864968 CCTCAGTACACGTCTGTAAGC 58.135 52.381 0.00 0.00 34.53 3.09
1981 2361 4.049186 CAGTACACGTCTGTAAGCAAGTT 58.951 43.478 0.00 0.00 34.53 2.66
2043 2423 6.218019 TGCCAATATATGTACGTACCTGAAC 58.782 40.000 22.43 0.00 0.00 3.18
2067 2447 8.463456 ACTGTACGTAAAAATCTCTTTCTAGC 57.537 34.615 0.00 0.00 0.00 3.42
2100 2480 4.500837 CGTATTCAGACACATACAGCTGTC 59.499 45.833 25.56 8.14 37.63 3.51
2151 2903 3.565764 TTGATGCCTCGGATTCTGATT 57.434 42.857 0.00 0.00 0.00 2.57
2153 2905 1.534595 GATGCCTCGGATTCTGATTGC 59.465 52.381 9.21 9.21 0.00 3.56
2173 2925 2.213499 CTCTTGGCACTCGTTCTTGTT 58.787 47.619 0.00 0.00 0.00 2.83
2176 2928 0.380378 TGGCACTCGTTCTTGTTTGC 59.620 50.000 0.00 0.00 0.00 3.68
2188 2940 3.465871 TCTTGTTTGCCAAATGCCTTTC 58.534 40.909 0.00 0.00 40.16 2.62
2273 3027 2.233676 AGGAGTGTTCGCATGTGTGATA 59.766 45.455 6.09 0.00 34.19 2.15
2299 3053 1.822506 TAGTGCAGCACTACTCGAGT 58.177 50.000 28.29 23.66 43.46 4.18
2311 3065 2.846371 CTCGAGTGAGGGCTTTTGG 58.154 57.895 3.62 0.00 38.65 3.28
2312 3066 1.301677 CTCGAGTGAGGGCTTTTGGC 61.302 60.000 3.62 0.00 45.19 4.52
2344 3098 7.896383 CTCCATGGAGGTGGATATTTTAAAA 57.104 36.000 31.14 2.51 46.67 1.52
2345 3099 8.305046 CTCCATGGAGGTGGATATTTTAAAAA 57.695 34.615 31.14 0.00 46.67 1.94
2410 3164 8.657074 AAAAATTCTGCACATTCATATGGATG 57.343 30.769 20.61 20.61 36.01 3.51
2411 3165 6.971726 AATTCTGCACATTCATATGGATGT 57.028 33.333 21.93 21.93 36.01 3.06
2412 3166 8.467963 AAATTCTGCACATTCATATGGATGTA 57.532 30.769 25.97 13.06 36.01 2.29
2413 3167 8.645814 AATTCTGCACATTCATATGGATGTAT 57.354 30.769 25.97 14.60 36.01 2.29
2414 3168 8.645814 ATTCTGCACATTCATATGGATGTATT 57.354 30.769 25.97 4.67 36.01 1.89
2415 3169 7.677454 TCTGCACATTCATATGGATGTATTC 57.323 36.000 25.97 18.35 36.01 1.75
2416 3170 7.455891 TCTGCACATTCATATGGATGTATTCT 58.544 34.615 25.97 3.95 36.01 2.40
2417 3171 8.596293 TCTGCACATTCATATGGATGTATTCTA 58.404 33.333 25.97 10.67 36.01 2.10
2418 3172 8.552083 TGCACATTCATATGGATGTATTCTAC 57.448 34.615 25.97 13.36 36.01 2.59
2419 3173 8.156165 TGCACATTCATATGGATGTATTCTACA 58.844 33.333 25.97 15.30 38.37 2.74
2420 3174 9.170734 GCACATTCATATGGATGTATTCTACAT 57.829 33.333 25.97 1.16 42.11 2.29
2440 3194 9.083080 TCTACATGTGTATAAAATCTCACAACG 57.917 33.333 9.11 0.00 42.61 4.10
2441 3195 7.899178 ACATGTGTATAAAATCTCACAACGA 57.101 32.000 0.00 0.00 42.61 3.85
2442 3196 8.317891 ACATGTGTATAAAATCTCACAACGAA 57.682 30.769 0.00 0.00 42.61 3.85
2443 3197 8.779303 ACATGTGTATAAAATCTCACAACGAAA 58.221 29.630 0.00 0.00 42.61 3.46
2444 3198 9.773328 CATGTGTATAAAATCTCACAACGAAAT 57.227 29.630 0.00 0.00 42.61 2.17
2453 3207 7.539712 AATCTCACAACGAAATACAGTATGG 57.460 36.000 0.00 0.00 43.62 2.74
2454 3208 4.868171 TCTCACAACGAAATACAGTATGGC 59.132 41.667 0.00 0.00 43.62 4.40
2455 3209 3.615056 TCACAACGAAATACAGTATGGCG 59.385 43.478 11.72 11.72 43.62 5.69
2456 3210 3.615056 CACAACGAAATACAGTATGGCGA 59.385 43.478 17.55 0.00 43.62 5.54
2457 3211 3.863424 ACAACGAAATACAGTATGGCGAG 59.137 43.478 17.55 12.84 43.62 5.03
2458 3212 4.109766 CAACGAAATACAGTATGGCGAGA 58.890 43.478 17.55 0.00 43.62 4.04
2459 3213 3.966154 ACGAAATACAGTATGGCGAGAG 58.034 45.455 17.55 0.70 43.62 3.20
2475 3229 3.822996 CGAGAGCTACACGAAAAAGAGA 58.177 45.455 0.00 0.00 34.75 3.10
2476 3230 4.227538 CGAGAGCTACACGAAAAAGAGAA 58.772 43.478 0.00 0.00 34.75 2.87
2477 3231 4.680110 CGAGAGCTACACGAAAAAGAGAAA 59.320 41.667 0.00 0.00 34.75 2.52
2478 3232 5.175126 CGAGAGCTACACGAAAAAGAGAAAA 59.825 40.000 0.00 0.00 34.75 2.29
2479 3233 6.128795 CGAGAGCTACACGAAAAAGAGAAAAT 60.129 38.462 0.00 0.00 34.75 1.82
2480 3234 7.123160 AGAGCTACACGAAAAAGAGAAAATC 57.877 36.000 0.00 0.00 0.00 2.17
2481 3235 5.916969 AGCTACACGAAAAAGAGAAAATCG 58.083 37.500 0.00 0.00 39.30 3.34
2482 3236 5.465724 AGCTACACGAAAAAGAGAAAATCGT 59.534 36.000 0.00 0.00 46.54 3.73
2485 3239 4.545823 ACGAAAAAGAGAAAATCGTGCA 57.454 36.364 0.00 0.00 44.20 4.57
2486 3240 5.108385 ACGAAAAAGAGAAAATCGTGCAT 57.892 34.783 0.00 0.00 44.20 3.96
2487 3241 5.519722 ACGAAAAAGAGAAAATCGTGCATT 58.480 33.333 0.00 0.00 44.20 3.56
2488 3242 5.977129 ACGAAAAAGAGAAAATCGTGCATTT 59.023 32.000 0.00 0.00 44.20 2.32
2489 3243 6.142320 ACGAAAAAGAGAAAATCGTGCATTTC 59.858 34.615 2.86 2.86 44.20 2.17
2490 3244 6.360681 CGAAAAAGAGAAAATCGTGCATTTCT 59.639 34.615 11.81 11.81 45.85 2.52
2491 3245 7.533900 CGAAAAAGAGAAAATCGTGCATTTCTA 59.466 33.333 11.93 0.00 43.86 2.10
2492 3246 9.180678 GAAAAAGAGAAAATCGTGCATTTCTAA 57.819 29.630 11.93 0.00 43.86 2.10
2493 3247 9.696917 AAAAAGAGAAAATCGTGCATTTCTAAT 57.303 25.926 11.93 3.36 43.86 1.73
2495 3249 9.994432 AAAGAGAAAATCGTGCATTTCTAATAG 57.006 29.630 11.93 0.00 43.86 1.73
2496 3250 8.723942 AGAGAAAATCGTGCATTTCTAATAGT 57.276 30.769 11.93 0.00 43.86 2.12
2497 3251 8.607459 AGAGAAAATCGTGCATTTCTAATAGTG 58.393 33.333 11.93 0.00 43.86 2.74
2498 3252 8.492673 AGAAAATCGTGCATTTCTAATAGTGA 57.507 30.769 10.56 0.00 42.47 3.41
2499 3253 8.946085 AGAAAATCGTGCATTTCTAATAGTGAA 58.054 29.630 10.56 0.00 42.47 3.18
2500 3254 8.895932 AAAATCGTGCATTTCTAATAGTGAAC 57.104 30.769 0.00 0.00 33.16 3.18
2501 3255 7.609760 AATCGTGCATTTCTAATAGTGAACA 57.390 32.000 0.00 0.00 0.00 3.18
2502 3256 6.647212 TCGTGCATTTCTAATAGTGAACAG 57.353 37.500 0.00 0.00 0.00 3.16
2503 3257 6.163476 TCGTGCATTTCTAATAGTGAACAGT 58.837 36.000 0.00 0.00 0.00 3.55
2504 3258 6.090763 TCGTGCATTTCTAATAGTGAACAGTG 59.909 38.462 0.00 0.00 0.00 3.66
2505 3259 6.546395 GTGCATTTCTAATAGTGAACAGTGG 58.454 40.000 0.00 0.00 0.00 4.00
2506 3260 6.149474 GTGCATTTCTAATAGTGAACAGTGGT 59.851 38.462 0.00 0.00 0.00 4.16
2507 3261 6.371548 TGCATTTCTAATAGTGAACAGTGGTC 59.628 38.462 0.00 0.00 0.00 4.02
2508 3262 6.455646 GCATTTCTAATAGTGAACAGTGGTCG 60.456 42.308 3.19 0.00 0.00 4.79
2509 3263 4.106029 TCTAATAGTGAACAGTGGTCGC 57.894 45.455 14.03 14.03 0.00 5.19
2510 3264 2.831685 AATAGTGAACAGTGGTCGCA 57.168 45.000 23.11 9.98 0.00 5.10
2511 3265 2.080286 ATAGTGAACAGTGGTCGCAC 57.920 50.000 23.11 8.16 34.35 5.34
2512 3266 1.037493 TAGTGAACAGTGGTCGCACT 58.963 50.000 23.11 15.05 42.02 4.40
2517 3271 4.436515 CAGTGGTCGCACTGTTCA 57.563 55.556 13.25 0.00 45.40 3.18
2518 3272 2.918571 CAGTGGTCGCACTGTTCAT 58.081 52.632 13.25 0.00 45.40 2.57
2519 3273 0.792640 CAGTGGTCGCACTGTTCATC 59.207 55.000 13.25 0.00 45.40 2.92
2520 3274 0.392706 AGTGGTCGCACTGTTCATCA 59.607 50.000 0.00 0.00 33.58 3.07
2521 3275 3.746233 CAGTGGTCGCACTGTTCATCAG 61.746 54.545 13.25 0.00 45.40 2.90
2534 3288 6.664978 CTGTTCATCAGTTTGAAAATCACG 57.335 37.500 0.00 0.00 37.36 4.35
2535 3289 6.370433 TGTTCATCAGTTTGAAAATCACGA 57.630 33.333 0.00 0.00 37.36 4.35
2536 3290 6.969366 TGTTCATCAGTTTGAAAATCACGAT 58.031 32.000 0.00 0.00 37.36 3.73
2537 3291 7.424803 TGTTCATCAGTTTGAAAATCACGATT 58.575 30.769 0.00 0.00 37.36 3.34
2538 3292 7.920151 TGTTCATCAGTTTGAAAATCACGATTT 59.080 29.630 0.00 0.00 42.35 2.17
2539 3293 7.856492 TCATCAGTTTGAAAATCACGATTTG 57.144 32.000 5.80 0.00 40.57 2.32
2540 3294 7.424803 TCATCAGTTTGAAAATCACGATTTGT 58.575 30.769 5.80 0.00 40.57 2.83
2541 3295 7.591057 TCATCAGTTTGAAAATCACGATTTGTC 59.409 33.333 5.80 6.72 40.57 3.18
2542 3296 7.026631 TCAGTTTGAAAATCACGATTTGTCT 57.973 32.000 5.80 0.00 40.57 3.41
2543 3297 7.479980 TCAGTTTGAAAATCACGATTTGTCTT 58.520 30.769 5.80 0.00 40.57 3.01
2544 3298 7.973388 TCAGTTTGAAAATCACGATTTGTCTTT 59.027 29.630 5.80 0.00 40.57 2.52
2545 3299 8.594687 CAGTTTGAAAATCACGATTTGTCTTTT 58.405 29.630 5.80 0.00 40.57 2.27
2546 3300 9.150348 AGTTTGAAAATCACGATTTGTCTTTTT 57.850 25.926 5.80 0.00 40.57 1.94
2568 3322 8.565896 TTTTTGTGTAGCTCTCATCATAATGT 57.434 30.769 0.00 0.00 34.32 2.71
2569 3323 9.665719 TTTTTGTGTAGCTCTCATCATAATGTA 57.334 29.630 0.00 0.00 34.32 2.29
2570 3324 9.836864 TTTTGTGTAGCTCTCATCATAATGTAT 57.163 29.630 0.00 0.00 34.32 2.29
2571 3325 9.836864 TTTGTGTAGCTCTCATCATAATGTATT 57.163 29.630 0.00 0.00 34.32 1.89
2572 3326 9.836864 TTGTGTAGCTCTCATCATAATGTATTT 57.163 29.630 0.00 0.00 34.32 1.40
2573 3327 9.481340 TGTGTAGCTCTCATCATAATGTATTTC 57.519 33.333 0.00 0.00 34.32 2.17
2574 3328 9.481340 GTGTAGCTCTCATCATAATGTATTTCA 57.519 33.333 0.00 0.00 34.32 2.69
2596 3350 9.814899 TTTCATCTTCAAAATTTACACACATGT 57.185 25.926 0.00 0.00 43.30 3.21
2688 3442 3.905493 TTTTCCAAATACCCACCTCCA 57.095 42.857 0.00 0.00 0.00 3.86
2689 3443 4.412060 TTTTCCAAATACCCACCTCCAT 57.588 40.909 0.00 0.00 0.00 3.41
2690 3444 5.538082 TTTTCCAAATACCCACCTCCATA 57.462 39.130 0.00 0.00 0.00 2.74
2691 3445 4.788925 TTCCAAATACCCACCTCCATAG 57.211 45.455 0.00 0.00 0.00 2.23
2692 3446 4.015617 TCCAAATACCCACCTCCATAGA 57.984 45.455 0.00 0.00 0.00 1.98
2693 3447 3.973973 TCCAAATACCCACCTCCATAGAG 59.026 47.826 0.00 0.00 40.09 2.43
2702 3456 1.655329 CTCCATAGAGGTCGACCGC 59.345 63.158 28.69 28.69 42.08 5.68
2703 3457 1.797211 CTCCATAGAGGTCGACCGCC 61.797 65.000 31.43 24.51 42.08 6.13
2704 3458 2.331805 CATAGAGGTCGACCGCCG 59.668 66.667 31.43 18.20 42.08 6.46
2705 3459 2.124403 ATAGAGGTCGACCGCCGT 60.124 61.111 31.43 19.14 42.08 5.68
2706 3460 1.751927 ATAGAGGTCGACCGCCGTT 60.752 57.895 31.43 17.80 42.08 4.44
2707 3461 2.001361 ATAGAGGTCGACCGCCGTTG 62.001 60.000 31.43 0.00 42.08 4.10
2719 3473 4.887290 CCGTTGGCATTTTGCGAT 57.113 50.000 0.00 0.00 46.21 4.58
2720 3474 2.652548 CCGTTGGCATTTTGCGATC 58.347 52.632 0.00 0.00 46.21 3.69
2721 3475 0.109365 CCGTTGGCATTTTGCGATCA 60.109 50.000 0.00 0.00 46.21 2.92
2722 3476 0.984109 CGTTGGCATTTTGCGATCAC 59.016 50.000 0.00 0.00 46.21 3.06
2723 3477 1.401409 CGTTGGCATTTTGCGATCACT 60.401 47.619 0.00 0.00 46.21 3.41
2724 3478 2.159585 CGTTGGCATTTTGCGATCACTA 60.160 45.455 0.00 0.00 46.21 2.74
2725 3479 3.171277 GTTGGCATTTTGCGATCACTAC 58.829 45.455 0.00 0.00 46.21 2.73
2738 3492 4.025647 GCGATCACTACTTGGCATACTTTC 60.026 45.833 0.00 0.00 0.00 2.62
2754 3508 1.608590 CTTTCCAGCCATGAACGTGTT 59.391 47.619 0.00 0.00 0.00 3.32
2755 3509 0.950836 TTCCAGCCATGAACGTGTTG 59.049 50.000 0.00 0.00 0.00 3.33
2765 3519 4.558470 CCATGAACGTGTTGTATTTGCATC 59.442 41.667 0.00 0.00 0.00 3.91
2785 3539 9.638239 TTGCATCATTAAAAATTTACTCACTCC 57.362 29.630 0.00 0.00 0.00 3.85
2786 3540 7.967854 TGCATCATTAAAAATTTACTCACTCCG 59.032 33.333 0.00 0.00 0.00 4.63
2787 3541 7.968405 GCATCATTAAAAATTTACTCACTCCGT 59.032 33.333 0.00 0.00 0.00 4.69
2788 3542 9.490663 CATCATTAAAAATTTACTCACTCCGTC 57.509 33.333 0.00 0.00 0.00 4.79
2789 3543 8.842358 TCATTAAAAATTTACTCACTCCGTCT 57.158 30.769 0.00 0.00 0.00 4.18
2790 3544 8.932791 TCATTAAAAATTTACTCACTCCGTCTC 58.067 33.333 0.00 0.00 0.00 3.36
2791 3545 8.717821 CATTAAAAATTTACTCACTCCGTCTCA 58.282 33.333 0.00 0.00 0.00 3.27
2792 3546 8.842358 TTAAAAATTTACTCACTCCGTCTCAT 57.158 30.769 0.00 0.00 0.00 2.90
2793 3547 9.932207 TTAAAAATTTACTCACTCCGTCTCATA 57.068 29.630 0.00 0.00 0.00 2.15
2794 3548 8.842358 AAAAATTTACTCACTCCGTCTCATAA 57.158 30.769 0.00 0.00 0.00 1.90
2795 3549 9.449719 AAAAATTTACTCACTCCGTCTCATAAT 57.550 29.630 0.00 0.00 0.00 1.28
2803 3557 9.530633 ACTCACTCCGTCTCATAATATAAAAAC 57.469 33.333 0.00 0.00 0.00 2.43
2804 3558 8.570096 TCACTCCGTCTCATAATATAAAAACG 57.430 34.615 0.00 0.00 0.00 3.60
2805 3559 8.192774 TCACTCCGTCTCATAATATAAAAACGT 58.807 33.333 0.00 0.00 0.00 3.99
2806 3560 8.814235 CACTCCGTCTCATAATATAAAAACGTT 58.186 33.333 0.00 0.00 0.00 3.99
2807 3561 9.374838 ACTCCGTCTCATAATATAAAAACGTTT 57.625 29.630 7.96 7.96 0.00 3.60
2921 3705 1.047002 CTAGCTATCTGCAGGGTGCT 58.953 55.000 23.67 23.67 45.31 4.40
2933 3717 0.469705 AGGGTGCTTGCAATCAACCA 60.470 50.000 32.75 9.40 42.42 3.67
2934 3718 0.609662 GGGTGCTTGCAATCAACCAT 59.390 50.000 28.21 0.00 39.79 3.55
2976 3790 4.496360 CGATCAGCTCAATATCATCTGCT 58.504 43.478 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.953640 CGGTCTCGCTCATAGACTAC 57.046 55.000 0.00 0.00 42.48 2.73
21 22 4.530325 GTGGTATTTGCGGCGGCG 62.530 66.667 28.70 28.70 44.10 6.46
22 23 4.187810 GGTGGTATTTGCGGCGGC 62.188 66.667 9.78 9.68 40.52 6.53
23 24 2.748251 TGGTGGTATTTGCGGCGG 60.748 61.111 9.78 0.00 0.00 6.13
24 25 0.741574 TACTGGTGGTATTTGCGGCG 60.742 55.000 0.51 0.51 0.00 6.46
25 26 1.014352 CTACTGGTGGTATTTGCGGC 58.986 55.000 0.00 0.00 0.00 6.53
26 27 1.663695 CCTACTGGTGGTATTTGCGG 58.336 55.000 0.00 0.00 0.00 5.69
27 28 1.208535 TCCCTACTGGTGGTATTTGCG 59.791 52.381 0.00 0.00 34.77 4.85
28 29 2.640184 GTCCCTACTGGTGGTATTTGC 58.360 52.381 0.00 0.00 34.77 3.68
29 30 2.498481 TCGTCCCTACTGGTGGTATTTG 59.502 50.000 0.00 0.00 34.77 2.32
30 31 2.764572 CTCGTCCCTACTGGTGGTATTT 59.235 50.000 0.00 0.00 34.77 1.40
31 32 2.385803 CTCGTCCCTACTGGTGGTATT 58.614 52.381 0.00 0.00 34.77 1.89
32 33 1.411216 CCTCGTCCCTACTGGTGGTAT 60.411 57.143 0.00 0.00 34.77 2.73
33 34 0.033796 CCTCGTCCCTACTGGTGGTA 60.034 60.000 0.00 0.00 34.77 3.25
34 35 1.305046 CCTCGTCCCTACTGGTGGT 60.305 63.158 0.00 0.00 34.77 4.16
35 36 2.058595 CCCTCGTCCCTACTGGTGG 61.059 68.421 0.00 0.00 34.77 4.61
36 37 2.722201 GCCCTCGTCCCTACTGGTG 61.722 68.421 0.00 0.00 34.77 4.17
37 38 2.363925 GCCCTCGTCCCTACTGGT 60.364 66.667 0.00 0.00 34.77 4.00
38 39 1.987855 TTGCCCTCGTCCCTACTGG 60.988 63.158 0.00 0.00 0.00 4.00
39 40 1.218316 GTTGCCCTCGTCCCTACTG 59.782 63.158 0.00 0.00 0.00 2.74
40 41 1.988406 GGTTGCCCTCGTCCCTACT 60.988 63.158 0.00 0.00 0.00 2.57
41 42 2.582978 GGTTGCCCTCGTCCCTAC 59.417 66.667 0.00 0.00 0.00 3.18
42 43 2.686106 GGGTTGCCCTCGTCCCTA 60.686 66.667 0.00 0.00 41.34 3.53
64 65 2.824041 AACACCGATCATGGCCGC 60.824 61.111 0.00 0.00 0.00 6.53
65 66 2.472059 CCAACACCGATCATGGCCG 61.472 63.158 0.00 0.00 0.00 6.13
66 67 3.513225 CCAACACCGATCATGGCC 58.487 61.111 0.00 0.00 0.00 5.36
68 69 1.378382 TGGCCAACACCGATCATGG 60.378 57.895 0.61 0.00 36.00 3.66
69 70 1.802636 GTGGCCAACACCGATCATG 59.197 57.895 7.24 0.00 44.49 3.07
70 71 4.319133 GTGGCCAACACCGATCAT 57.681 55.556 7.24 0.00 44.49 2.45
99 101 3.239449 TCCACTTCATCCTACACAGTGT 58.761 45.455 11.87 11.87 34.25 3.55
105 107 1.412710 GCCGATCCACTTCATCCTACA 59.587 52.381 0.00 0.00 0.00 2.74
126 128 2.723746 CTTGGCGCTTGCACAAGT 59.276 55.556 7.64 0.00 39.74 3.16
152 154 1.227556 GGACACAACAGTCGTGCCT 60.228 57.895 0.00 0.00 39.42 4.75
214 219 2.555547 GGCGCTGTTGGAGCTGTTT 61.556 57.895 7.64 0.00 46.64 2.83
256 261 2.034532 TAGCGGACGACCACCTCA 59.965 61.111 4.48 0.00 35.59 3.86
262 267 0.100146 CTACCTTGTAGCGGACGACC 59.900 60.000 0.00 0.00 0.00 4.79
263 268 0.807496 ACTACCTTGTAGCGGACGAC 59.193 55.000 0.00 0.00 0.00 4.34
264 269 0.806868 CACTACCTTGTAGCGGACGA 59.193 55.000 0.00 0.00 0.00 4.20
286 291 9.373603 GTTTGTTCAACTTAAACCCTAAAACAT 57.626 29.630 0.00 0.00 31.92 2.71
323 329 6.237996 GCTCGGACATAATTTACATGAAACGA 60.238 38.462 0.00 0.00 0.00 3.85
329 335 9.385902 CATTAAAGCTCGGACATAATTTACATG 57.614 33.333 0.00 0.00 0.00 3.21
401 422 1.809207 GGCCATCCAACCATGTTCG 59.191 57.895 0.00 0.00 0.00 3.95
424 445 1.409064 GTCTGCGGACATGGATACAGA 59.591 52.381 21.02 2.12 40.94 3.41
440 461 6.346919 GCTGAAACACACACTATACTTGTCTG 60.347 42.308 0.00 0.00 0.00 3.51
441 462 5.696724 GCTGAAACACACACTATACTTGTCT 59.303 40.000 0.00 0.00 0.00 3.41
447 468 4.090066 CGTCAGCTGAAACACACACTATAC 59.910 45.833 20.19 0.00 0.00 1.47
456 477 1.772063 AACGCCGTCAGCTGAAACAC 61.772 55.000 20.19 5.50 40.39 3.32
465 486 3.414700 GACTGCCAACGCCGTCAG 61.415 66.667 3.20 3.20 45.59 3.51
468 489 0.604243 TAAATGACTGCCAACGCCGT 60.604 50.000 0.00 0.00 34.82 5.68
469 490 0.732571 ATAAATGACTGCCAACGCCG 59.267 50.000 0.00 0.00 0.00 6.46
470 491 2.680841 TGTATAAATGACTGCCAACGCC 59.319 45.455 0.00 0.00 0.00 5.68
471 492 4.349663 TTGTATAAATGACTGCCAACGC 57.650 40.909 0.00 0.00 0.00 4.84
472 493 5.286082 GCTTTTGTATAAATGACTGCCAACG 59.714 40.000 2.55 0.00 0.00 4.10
473 494 6.389906 AGCTTTTGTATAAATGACTGCCAAC 58.610 36.000 2.55 0.00 0.00 3.77
474 495 6.588719 AGCTTTTGTATAAATGACTGCCAA 57.411 33.333 2.55 0.00 0.00 4.52
475 496 6.434028 AGAAGCTTTTGTATAAATGACTGCCA 59.566 34.615 0.00 0.00 0.00 4.92
476 497 6.856895 AGAAGCTTTTGTATAAATGACTGCC 58.143 36.000 0.00 0.00 0.00 4.85
477 498 7.636359 CGTAGAAGCTTTTGTATAAATGACTGC 59.364 37.037 0.00 0.00 0.00 4.40
538 897 5.535753 ACCTTTTCTCCTTTTTGACATGG 57.464 39.130 0.00 0.00 0.00 3.66
564 923 1.672881 GGATGGCTTTCTGTCAATCCG 59.327 52.381 0.00 0.00 32.16 4.18
571 930 2.827921 GTGGAATTGGATGGCTTTCTGT 59.172 45.455 0.00 0.00 0.00 3.41
644 1003 7.534085 TCTTAACTTGTTGCCATCGTATTAG 57.466 36.000 0.00 0.00 0.00 1.73
652 1011 2.621055 TGCGTTCTTAACTTGTTGCCAT 59.379 40.909 0.00 0.00 0.00 4.40
667 1026 1.067565 TGTGGAGAGATGAGTGCGTTC 60.068 52.381 0.00 0.00 0.00 3.95
695 1066 4.914504 CGTGCTGTGCAATTTACATTTACA 59.085 37.500 0.00 0.00 41.47 2.41
778 1150 9.774742 CCTCTTAACGGATAAATTTTTGAAGAG 57.225 33.333 0.00 6.00 37.17 2.85
779 1151 8.736244 CCCTCTTAACGGATAAATTTTTGAAGA 58.264 33.333 0.00 0.00 0.00 2.87
780 1152 7.488150 GCCCTCTTAACGGATAAATTTTTGAAG 59.512 37.037 0.00 0.00 0.00 3.02
781 1153 7.039644 TGCCCTCTTAACGGATAAATTTTTGAA 60.040 33.333 0.00 0.00 0.00 2.69
816 1188 0.741574 TCTCGAGTCTCGACCTCTGC 60.742 60.000 20.85 0.00 44.82 4.26
819 1191 0.108041 ACCTCTCGAGTCTCGACCTC 60.108 60.000 20.85 0.00 44.82 3.85
861 1233 3.982730 TCTCCATCTCTCCAGATCTCTCT 59.017 47.826 0.00 0.00 37.25 3.10
862 1234 4.042062 TCTCTCCATCTCTCCAGATCTCTC 59.958 50.000 0.00 0.00 37.25 3.20
879 1253 1.813192 CAACGCTCCTCCTCTCTCC 59.187 63.158 0.00 0.00 0.00 3.71
1024 1401 3.193267 GTCAGGCATTTCCAATGCAAGTA 59.807 43.478 20.19 3.23 46.21 2.24
1107 1484 1.258445 TTCTCCAGAACTCCGCCTCC 61.258 60.000 0.00 0.00 0.00 4.30
1130 1507 2.512355 GCCTCCGGAATCCCTCTCC 61.512 68.421 5.23 0.00 0.00 3.71
1132 1509 0.695803 ATTGCCTCCGGAATCCCTCT 60.696 55.000 5.23 0.00 0.00 3.69
1626 2003 2.985282 TTCGTACCACGGCTCGGT 60.985 61.111 0.00 0.18 42.81 4.69
1790 2167 4.441415 CGAGAGTGACGGATTATTTGCTAC 59.559 45.833 0.00 0.00 0.00 3.58
1813 2190 6.372659 TCCATATTCACAAGTCAAGAAAGAGC 59.627 38.462 0.00 0.00 0.00 4.09
1870 2248 7.386848 CCAGAAATAGTCAAACTAAAGGACGAA 59.613 37.037 0.00 0.00 33.89 3.85
1871 2249 6.872020 CCAGAAATAGTCAAACTAAAGGACGA 59.128 38.462 0.00 0.00 33.89 4.20
1881 2259 4.585879 TGGGTAGCCAGAAATAGTCAAAC 58.414 43.478 10.27 0.00 0.00 2.93
1906 2284 5.815233 ATCAACCACCTATAGATCACAGG 57.185 43.478 0.00 0.33 35.45 4.00
1953 2331 0.314302 ACAGACGTGTACTGAGGCAC 59.686 55.000 9.51 0.37 38.55 5.01
1968 2348 6.263516 ACGTATCTACAACTTGCTTACAGA 57.736 37.500 0.00 0.00 0.00 3.41
1976 2356 8.743099 CATGTACATGTACGTATCTACAACTTG 58.257 37.037 26.31 9.24 38.85 3.16
1981 2361 6.380095 TGCATGTACATGTACGTATCTACA 57.620 37.500 31.10 16.66 40.80 2.74
2043 2423 8.690680 AGCTAGAAAGAGATTTTTACGTACAG 57.309 34.615 0.00 0.00 0.00 2.74
2067 2447 5.880341 TGTGTCTGAATACGACATGTAGAG 58.120 41.667 13.30 3.50 42.68 2.43
2100 2480 5.977635 TCAGCCTCCAATCGTTATATATGG 58.022 41.667 0.00 0.00 0.00 2.74
2153 2905 1.871080 ACAAGAACGAGTGCCAAGAG 58.129 50.000 0.00 0.00 0.00 2.85
2162 2914 2.472488 GCATTTGGCAAACAAGAACGAG 59.528 45.455 16.00 0.00 43.97 4.18
2176 2928 5.745294 CGAGATATTTGTGAAAGGCATTTGG 59.255 40.000 0.00 0.00 0.00 3.28
2188 2940 2.794910 CTGCCGTACCGAGATATTTGTG 59.205 50.000 0.00 0.00 0.00 3.33
2226 2978 3.119602 TGCGTAGTTATTCTCTCGCAAGT 60.120 43.478 7.54 0.00 46.83 3.16
2251 3005 1.616374 TCACACATGCGAACACTCCTA 59.384 47.619 0.00 0.00 0.00 2.94
2273 3027 4.023622 CGAGTAGTGCTGCACTATAGACAT 60.024 45.833 36.50 21.62 46.56 3.06
2294 3048 1.302511 GCCAAAAGCCCTCACTCGA 60.303 57.895 0.00 0.00 34.35 4.04
2295 3049 2.680913 CGCCAAAAGCCCTCACTCG 61.681 63.158 0.00 0.00 38.78 4.18
2296 3050 2.335712 CCGCCAAAAGCCCTCACTC 61.336 63.158 0.00 0.00 38.78 3.51
2297 3051 2.282462 CCGCCAAAAGCCCTCACT 60.282 61.111 0.00 0.00 38.78 3.41
2298 3052 3.373565 CCCGCCAAAAGCCCTCAC 61.374 66.667 0.00 0.00 38.78 3.51
2305 3059 3.431725 GAGGTCGCCCGCCAAAAG 61.432 66.667 4.50 0.00 35.12 2.27
2312 3066 4.227134 CTCCATGGAGGTCGCCCG 62.227 72.222 31.14 6.42 38.51 6.13
2385 3139 8.262227 ACATCCATATGAATGTGCAGAATTTTT 58.738 29.630 6.79 0.00 36.54 1.94
2386 3140 7.788026 ACATCCATATGAATGTGCAGAATTTT 58.212 30.769 6.79 0.00 36.54 1.82
2387 3141 7.356089 ACATCCATATGAATGTGCAGAATTT 57.644 32.000 6.79 0.00 36.54 1.82
2388 3142 6.971726 ACATCCATATGAATGTGCAGAATT 57.028 33.333 6.79 0.00 36.54 2.17
2389 3143 8.645814 AATACATCCATATGAATGTGCAGAAT 57.354 30.769 17.05 0.00 36.54 2.40
2390 3144 7.940688 AGAATACATCCATATGAATGTGCAGAA 59.059 33.333 17.05 0.00 36.54 3.02
2391 3145 7.455891 AGAATACATCCATATGAATGTGCAGA 58.544 34.615 17.05 0.00 36.54 4.26
2392 3146 7.683437 AGAATACATCCATATGAATGTGCAG 57.317 36.000 17.05 0.00 36.54 4.41
2393 3147 8.552083 GTAGAATACATCCATATGAATGTGCA 57.448 34.615 17.05 0.00 42.43 4.57
2414 3168 9.083080 CGTTGTGAGATTTTATACACATGTAGA 57.917 33.333 0.00 0.00 41.67 2.59
2415 3169 9.083080 TCGTTGTGAGATTTTATACACATGTAG 57.917 33.333 0.00 0.00 41.67 2.74
2416 3170 8.989653 TCGTTGTGAGATTTTATACACATGTA 57.010 30.769 0.00 0.00 41.67 2.29
2417 3171 7.899178 TCGTTGTGAGATTTTATACACATGT 57.101 32.000 0.00 0.00 41.67 3.21
2418 3172 9.773328 ATTTCGTTGTGAGATTTTATACACATG 57.227 29.630 0.00 0.00 41.67 3.21
2427 3181 8.450964 CCATACTGTATTTCGTTGTGAGATTTT 58.549 33.333 0.00 0.00 0.00 1.82
2428 3182 7.414098 GCCATACTGTATTTCGTTGTGAGATTT 60.414 37.037 0.00 0.00 0.00 2.17
2429 3183 6.037172 GCCATACTGTATTTCGTTGTGAGATT 59.963 38.462 0.00 0.00 0.00 2.40
2430 3184 5.523916 GCCATACTGTATTTCGTTGTGAGAT 59.476 40.000 0.00 0.00 0.00 2.75
2431 3185 4.868171 GCCATACTGTATTTCGTTGTGAGA 59.132 41.667 0.00 0.00 0.00 3.27
2432 3186 4.259810 CGCCATACTGTATTTCGTTGTGAG 60.260 45.833 0.00 0.00 0.00 3.51
2433 3187 3.615056 CGCCATACTGTATTTCGTTGTGA 59.385 43.478 0.00 0.00 0.00 3.58
2434 3188 3.615056 TCGCCATACTGTATTTCGTTGTG 59.385 43.478 14.22 0.00 0.00 3.33
2435 3189 3.852286 TCGCCATACTGTATTTCGTTGT 58.148 40.909 14.22 0.00 0.00 3.32
2436 3190 4.109766 TCTCGCCATACTGTATTTCGTTG 58.890 43.478 14.22 10.44 0.00 4.10
2437 3191 4.360563 CTCTCGCCATACTGTATTTCGTT 58.639 43.478 14.22 0.00 0.00 3.85
2438 3192 3.795826 GCTCTCGCCATACTGTATTTCGT 60.796 47.826 14.22 0.00 0.00 3.85
2439 3193 2.726760 GCTCTCGCCATACTGTATTTCG 59.273 50.000 0.00 5.05 0.00 3.46
2440 3194 3.983741 AGCTCTCGCCATACTGTATTTC 58.016 45.455 0.00 0.00 36.60 2.17
2441 3195 4.341235 TGTAGCTCTCGCCATACTGTATTT 59.659 41.667 0.00 0.00 36.60 1.40
2442 3196 3.889538 TGTAGCTCTCGCCATACTGTATT 59.110 43.478 0.00 0.00 36.60 1.89
2443 3197 3.253677 GTGTAGCTCTCGCCATACTGTAT 59.746 47.826 0.00 0.00 36.60 2.29
2444 3198 2.617308 GTGTAGCTCTCGCCATACTGTA 59.383 50.000 0.00 0.00 36.60 2.74
2445 3199 1.405821 GTGTAGCTCTCGCCATACTGT 59.594 52.381 0.00 0.00 36.60 3.55
2446 3200 1.598183 CGTGTAGCTCTCGCCATACTG 60.598 57.143 0.00 0.00 36.60 2.74
2447 3201 0.663688 CGTGTAGCTCTCGCCATACT 59.336 55.000 0.00 0.00 36.60 2.12
2448 3202 0.661552 TCGTGTAGCTCTCGCCATAC 59.338 55.000 0.00 0.00 36.60 2.39
2449 3203 1.385528 TTCGTGTAGCTCTCGCCATA 58.614 50.000 0.00 0.00 36.60 2.74
2450 3204 0.530744 TTTCGTGTAGCTCTCGCCAT 59.469 50.000 0.00 0.00 36.60 4.40
2451 3205 0.315886 TTTTCGTGTAGCTCTCGCCA 59.684 50.000 0.00 0.00 36.60 5.69
2452 3206 1.390463 CTTTTTCGTGTAGCTCTCGCC 59.610 52.381 0.00 0.00 36.60 5.54
2453 3207 2.325761 TCTTTTTCGTGTAGCTCTCGC 58.674 47.619 0.00 0.00 33.77 5.03
2454 3208 3.822996 TCTCTTTTTCGTGTAGCTCTCG 58.177 45.455 0.00 0.00 34.85 4.04
2455 3209 6.526566 TTTTCTCTTTTTCGTGTAGCTCTC 57.473 37.500 0.00 0.00 0.00 3.20
2456 3210 6.128795 CGATTTTCTCTTTTTCGTGTAGCTCT 60.129 38.462 0.00 0.00 0.00 4.09
2457 3211 6.010074 CGATTTTCTCTTTTTCGTGTAGCTC 58.990 40.000 0.00 0.00 0.00 4.09
2458 3212 5.465724 ACGATTTTCTCTTTTTCGTGTAGCT 59.534 36.000 0.00 0.00 41.09 3.32
2459 3213 5.676953 ACGATTTTCTCTTTTTCGTGTAGC 58.323 37.500 0.00 0.00 41.09 3.58
2464 3218 4.545823 TGCACGATTTTCTCTTTTTCGT 57.454 36.364 0.00 0.00 43.18 3.85
2465 3219 6.360681 AGAAATGCACGATTTTCTCTTTTTCG 59.639 34.615 7.12 0.00 37.58 3.46
2466 3220 7.629027 AGAAATGCACGATTTTCTCTTTTTC 57.371 32.000 7.12 0.78 37.58 2.29
2467 3221 9.696917 ATTAGAAATGCACGATTTTCTCTTTTT 57.303 25.926 14.63 0.00 40.42 1.94
2469 3223 9.994432 CTATTAGAAATGCACGATTTTCTCTTT 57.006 29.630 14.63 5.92 40.42 2.52
2470 3224 9.167311 ACTATTAGAAATGCACGATTTTCTCTT 57.833 29.630 14.63 7.86 40.42 2.85
2471 3225 8.607459 CACTATTAGAAATGCACGATTTTCTCT 58.393 33.333 14.63 8.00 40.42 3.10
2472 3226 8.604035 TCACTATTAGAAATGCACGATTTTCTC 58.396 33.333 14.63 0.00 40.42 2.87
2473 3227 8.492673 TCACTATTAGAAATGCACGATTTTCT 57.507 30.769 15.35 15.35 42.96 2.52
2474 3228 9.000018 GTTCACTATTAGAAATGCACGATTTTC 58.000 33.333 2.86 2.86 34.18 2.29
2475 3229 8.511321 TGTTCACTATTAGAAATGCACGATTTT 58.489 29.630 0.00 0.00 34.18 1.82
2476 3230 8.039603 TGTTCACTATTAGAAATGCACGATTT 57.960 30.769 0.00 0.00 36.94 2.17
2477 3231 7.334421 ACTGTTCACTATTAGAAATGCACGATT 59.666 33.333 0.00 0.00 0.00 3.34
2478 3232 6.818644 ACTGTTCACTATTAGAAATGCACGAT 59.181 34.615 0.00 0.00 0.00 3.73
2479 3233 6.090763 CACTGTTCACTATTAGAAATGCACGA 59.909 38.462 0.00 0.00 0.00 4.35
2480 3234 6.243551 CACTGTTCACTATTAGAAATGCACG 58.756 40.000 0.00 0.00 0.00 5.34
2481 3235 6.149474 ACCACTGTTCACTATTAGAAATGCAC 59.851 38.462 0.00 0.00 0.00 4.57
2482 3236 6.237901 ACCACTGTTCACTATTAGAAATGCA 58.762 36.000 0.00 0.00 0.00 3.96
2483 3237 6.455646 CGACCACTGTTCACTATTAGAAATGC 60.456 42.308 0.00 0.00 0.00 3.56
2484 3238 6.455646 GCGACCACTGTTCACTATTAGAAATG 60.456 42.308 0.00 0.00 0.00 2.32
2485 3239 5.581085 GCGACCACTGTTCACTATTAGAAAT 59.419 40.000 0.00 0.00 0.00 2.17
2486 3240 4.927425 GCGACCACTGTTCACTATTAGAAA 59.073 41.667 0.00 0.00 0.00 2.52
2487 3241 4.021807 TGCGACCACTGTTCACTATTAGAA 60.022 41.667 0.00 0.00 0.00 2.10
2488 3242 3.508402 TGCGACCACTGTTCACTATTAGA 59.492 43.478 0.00 0.00 0.00 2.10
2489 3243 3.612860 GTGCGACCACTGTTCACTATTAG 59.387 47.826 0.00 0.00 38.93 1.73
2490 3244 3.581755 GTGCGACCACTGTTCACTATTA 58.418 45.455 0.00 0.00 38.93 0.98
2491 3245 2.413837 GTGCGACCACTGTTCACTATT 58.586 47.619 0.00 0.00 38.93 1.73
2492 3246 2.080286 GTGCGACCACTGTTCACTAT 57.920 50.000 0.00 0.00 38.93 2.12
2493 3247 3.580904 GTGCGACCACTGTTCACTA 57.419 52.632 0.00 0.00 38.93 2.74
2494 3248 4.438346 GTGCGACCACTGTTCACT 57.562 55.556 0.00 0.00 38.93 3.41
2502 3256 0.792640 CTGATGAACAGTGCGACCAC 59.207 55.000 0.00 0.00 41.30 4.16
2503 3257 3.215642 CTGATGAACAGTGCGACCA 57.784 52.632 0.00 0.00 41.30 4.02
2512 3266 6.370433 TCGTGATTTTCAAACTGATGAACA 57.630 33.333 1.28 0.00 38.95 3.18
2513 3267 7.858052 AATCGTGATTTTCAAACTGATGAAC 57.142 32.000 1.28 0.00 38.95 3.18
2514 3268 7.920151 ACAAATCGTGATTTTCAAACTGATGAA 59.080 29.630 5.12 0.00 38.84 2.57
2515 3269 7.424803 ACAAATCGTGATTTTCAAACTGATGA 58.575 30.769 5.12 0.00 38.84 2.92
2516 3270 7.592533 AGACAAATCGTGATTTTCAAACTGATG 59.407 33.333 5.12 0.00 38.84 3.07
2517 3271 7.651808 AGACAAATCGTGATTTTCAAACTGAT 58.348 30.769 5.12 0.00 38.84 2.90
2518 3272 7.026631 AGACAAATCGTGATTTTCAAACTGA 57.973 32.000 5.12 0.00 38.84 3.41
2519 3273 7.684062 AAGACAAATCGTGATTTTCAAACTG 57.316 32.000 5.12 0.00 38.84 3.16
2520 3274 8.702163 AAAAGACAAATCGTGATTTTCAAACT 57.298 26.923 5.12 0.00 38.84 2.66
2543 3297 8.565896 ACATTATGATGAGAGCTACACAAAAA 57.434 30.769 4.20 0.00 36.73 1.94
2544 3298 9.836864 ATACATTATGATGAGAGCTACACAAAA 57.163 29.630 4.20 0.00 36.73 2.44
2545 3299 9.836864 AATACATTATGATGAGAGCTACACAAA 57.163 29.630 4.20 0.00 36.73 2.83
2546 3300 9.836864 AAATACATTATGATGAGAGCTACACAA 57.163 29.630 4.20 0.00 36.73 3.33
2547 3301 9.481340 GAAATACATTATGATGAGAGCTACACA 57.519 33.333 4.20 0.00 36.73 3.72
2548 3302 9.481340 TGAAATACATTATGATGAGAGCTACAC 57.519 33.333 4.20 0.00 36.73 2.90
2570 3324 9.814899 ACATGTGTGTAAATTTTGAAGATGAAA 57.185 25.926 0.00 0.00 36.63 2.69
2667 3421 4.200447 TGGAGGTGGGTATTTGGAAAAA 57.800 40.909 0.00 0.00 0.00 1.94
2668 3422 3.905493 TGGAGGTGGGTATTTGGAAAA 57.095 42.857 0.00 0.00 0.00 2.29
2669 3423 4.791334 TCTATGGAGGTGGGTATTTGGAAA 59.209 41.667 0.00 0.00 0.00 3.13
2670 3424 4.376223 TCTATGGAGGTGGGTATTTGGAA 58.624 43.478 0.00 0.00 0.00 3.53
2671 3425 3.973973 CTCTATGGAGGTGGGTATTTGGA 59.026 47.826 0.00 0.00 36.03 3.53
2672 3426 4.357918 CTCTATGGAGGTGGGTATTTGG 57.642 50.000 0.00 0.00 36.03 3.28
2684 3438 1.655329 GCGGTCGACCTCTATGGAG 59.345 63.158 30.92 14.56 39.71 3.86
2685 3439 1.826921 GGCGGTCGACCTCTATGGA 60.827 63.158 30.92 0.00 39.71 3.41
2686 3440 2.728817 GGCGGTCGACCTCTATGG 59.271 66.667 30.92 16.01 42.93 2.74
2687 3441 2.001361 AACGGCGGTCGACCTCTATG 62.001 60.000 30.92 18.93 42.43 2.23
2688 3442 1.751927 AACGGCGGTCGACCTCTAT 60.752 57.895 30.92 13.50 42.43 1.98
2689 3443 2.360350 AACGGCGGTCGACCTCTA 60.360 61.111 30.92 0.00 42.43 2.43
2690 3444 4.052229 CAACGGCGGTCGACCTCT 62.052 66.667 30.92 6.78 42.43 3.69
2702 3456 0.109365 TGATCGCAAAATGCCAACGG 60.109 50.000 0.00 0.00 41.12 4.44
2703 3457 0.984109 GTGATCGCAAAATGCCAACG 59.016 50.000 0.16 0.00 41.12 4.10
2704 3458 2.352503 AGTGATCGCAAAATGCCAAC 57.647 45.000 9.33 0.00 41.12 3.77
2705 3459 3.081061 AGTAGTGATCGCAAAATGCCAA 58.919 40.909 9.33 0.00 41.12 4.52
2706 3460 2.710377 AGTAGTGATCGCAAAATGCCA 58.290 42.857 9.33 0.00 41.12 4.92
2707 3461 3.429085 CAAGTAGTGATCGCAAAATGCC 58.571 45.455 9.33 0.00 41.12 4.40
2708 3462 3.429085 CCAAGTAGTGATCGCAAAATGC 58.571 45.455 9.33 0.00 40.69 3.56
2709 3463 3.119884 TGCCAAGTAGTGATCGCAAAATG 60.120 43.478 9.33 2.44 0.00 2.32
2710 3464 3.081061 TGCCAAGTAGTGATCGCAAAAT 58.919 40.909 9.33 0.00 0.00 1.82
2711 3465 2.499197 TGCCAAGTAGTGATCGCAAAA 58.501 42.857 9.33 0.00 0.00 2.44
2712 3466 2.177394 TGCCAAGTAGTGATCGCAAA 57.823 45.000 9.33 0.00 0.00 3.68
2713 3467 2.401583 ATGCCAAGTAGTGATCGCAA 57.598 45.000 9.33 0.00 0.00 4.85
2714 3468 2.430694 AGTATGCCAAGTAGTGATCGCA 59.569 45.455 9.33 0.00 0.00 5.10
2715 3469 3.099267 AGTATGCCAAGTAGTGATCGC 57.901 47.619 0.00 0.00 0.00 4.58
2716 3470 4.508124 GGAAAGTATGCCAAGTAGTGATCG 59.492 45.833 0.00 0.00 0.00 3.69
2717 3471 5.428253 TGGAAAGTATGCCAAGTAGTGATC 58.572 41.667 0.00 0.00 0.00 2.92
2718 3472 5.431765 CTGGAAAGTATGCCAAGTAGTGAT 58.568 41.667 0.00 0.00 32.95 3.06
2719 3473 4.832248 CTGGAAAGTATGCCAAGTAGTGA 58.168 43.478 0.00 0.00 32.95 3.41
2720 3474 3.375299 GCTGGAAAGTATGCCAAGTAGTG 59.625 47.826 0.00 0.00 32.95 2.74
2721 3475 3.610911 GCTGGAAAGTATGCCAAGTAGT 58.389 45.455 0.00 0.00 32.95 2.73
2722 3476 2.945668 GGCTGGAAAGTATGCCAAGTAG 59.054 50.000 0.00 0.00 44.34 2.57
2723 3477 2.999331 GGCTGGAAAGTATGCCAAGTA 58.001 47.619 0.00 0.00 44.34 2.24
2724 3478 1.839424 GGCTGGAAAGTATGCCAAGT 58.161 50.000 0.00 0.00 44.34 3.16
2738 3492 1.518325 TACAACACGTTCATGGCTGG 58.482 50.000 0.00 0.00 0.00 4.85
2871 3635 1.051812 AGCCACTTGCACTGTCTAGT 58.948 50.000 0.00 0.00 44.83 2.57
2872 3636 1.436600 CAGCCACTTGCACTGTCTAG 58.563 55.000 0.00 0.00 44.83 2.43
2877 3641 1.302752 TAGCCAGCCACTTGCACTG 60.303 57.895 0.00 0.00 44.83 3.66
2948 3762 2.243602 TATTGAGCTGATCGCATGCA 57.756 45.000 19.57 5.34 42.61 3.96
2971 3785 1.067846 AGATTGCGTTCGTACAGCAGA 60.068 47.619 10.34 4.94 42.19 4.26
2976 3790 0.457166 CCGGAGATTGCGTTCGTACA 60.457 55.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.