Multiple sequence alignment - TraesCS6D01G356400

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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 TraesCS6D01G356400 chr6D 100.000 4488 0 0 1 4488 450640889 450645376 0.000000e+00 8288.0
1 TraesCS6D01G356400 chr6D 94.715 246 11 2 1036 1280 76080446 76080202 9.110000e-102 381.0
2 TraesCS6D01G356400 chr6D 89.434 265 27 1 1360 1623 76080090 76079826 2.590000e-87 333.0
3 TraesCS6D01G356400 chr6A 93.209 1664 86 9 1360 3019 596163594 596165234 0.000000e+00 2422.0
4 TraesCS6D01G356400 chr6A 93.407 1259 61 8 3068 4325 596165239 596166476 0.000000e+00 1845.0
5 TraesCS6D01G356400 chr6A 86.893 1297 99 37 13 1277 596162222 596163479 0.000000e+00 1387.0
6 TraesCS6D01G356400 chr6B 95.477 1017 39 3 2001 3017 684387355 684388364 0.000000e+00 1616.0
7 TraesCS6D01G356400 chr6B 87.687 1267 100 24 3242 4487 684388575 684389806 0.000000e+00 1424.0
8 TraesCS6D01G356400 chr6B 89.062 640 52 9 1358 1989 684386657 684387286 0.000000e+00 778.0
9 TraesCS6D01G356400 chr6B 84.499 729 57 25 5 708 684384953 684385650 0.000000e+00 669.0
10 TraesCS6D01G356400 chr6B 83.599 439 38 20 663 1080 684385647 684386072 9.110000e-102 381.0
11 TraesCS6D01G356400 chr6B 89.103 156 15 2 3084 3238 684388380 684388534 4.580000e-45 193.0
12 TraesCS6D01G356400 chr6B 96.226 106 4 0 1175 1280 684386438 684386543 1.660000e-39 174.0
13 TraesCS6D01G356400 chr7D 80.279 573 89 13 3917 4488 98659355 98658806 1.160000e-110 411.0
14 TraesCS6D01G356400 chr7D 95.213 188 9 0 370 557 84178441 84178254 9.440000e-77 298.0
15 TraesCS6D01G356400 chr3D 93.208 265 14 4 1015 1277 382819987 382820249 1.960000e-103 387.0
16 TraesCS6D01G356400 chr3D 93.208 265 14 4 1015 1277 554658672 554658934 1.960000e-103 387.0
17 TraesCS6D01G356400 chr3D 89.434 265 27 1 1360 1623 382820364 382820628 2.590000e-87 333.0
18 TraesCS6D01G356400 chr3D 89.434 265 27 1 1360 1623 554659049 554659313 2.590000e-87 333.0
19 TraesCS6D01G356400 chr3D 88.679 212 20 4 1531 1738 599649120 599649331 5.760000e-64 255.0
20 TraesCS6D01G356400 chr1D 95.122 246 10 2 1036 1280 207148746 207148502 1.960000e-103 387.0
21 TraesCS6D01G356400 chr1D 89.057 265 28 1 1360 1623 207148390 207148126 1.200000e-85 327.0
22 TraesCS6D01G356400 chr7B 87.781 311 30 5 1512 1814 745807124 745806814 1.540000e-94 357.0
23 TraesCS6D01G356400 chr7B 87.781 311 31 4 1511 1814 745889030 745888720 1.540000e-94 357.0
24 TraesCS6D01G356400 chr7B 87.460 311 32 4 1511 1814 745863125 745862815 7.140000e-93 351.0
25 TraesCS6D01G356400 chr7B 86.817 311 34 5 1511 1814 745923934 745923624 1.550000e-89 340.0
26 TraesCS6D01G356400 chr7B 85.209 311 35 5 1511 1814 745841133 745840827 4.360000e-80 309.0
27 TraesCS6D01G356400 chr7B 94.681 188 10 0 370 557 33805613 33805426 4.390000e-75 292.0
28 TraesCS6D01G356400 chr7A 82.555 407 64 6 4083 4488 100771459 100771059 7.140000e-93 351.0
29 TraesCS6D01G356400 chr7A 93.085 188 13 0 370 557 85588906 85588719 4.420000e-70 276.0
30 TraesCS6D01G356400 chr5B 89.623 212 18 1 1531 1738 508086576 508086365 2.660000e-67 267.0
31 TraesCS6D01G356400 chr4D 100.000 38 0 0 4197 4234 449463087 449463124 2.240000e-08 71.3


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 TraesCS6D01G356400 chr6D 450640889 450645376 4487 False 8288.000000 8288 100.000000 1 4488 1 chr6D.!!$F1 4487
1 TraesCS6D01G356400 chr6D 76079826 76080446 620 True 357.000000 381 92.074500 1036 1623 2 chr6D.!!$R1 587
2 TraesCS6D01G356400 chr6A 596162222 596166476 4254 False 1884.666667 2422 91.169667 13 4325 3 chr6A.!!$F1 4312
3 TraesCS6D01G356400 chr6B 684384953 684389806 4853 False 747.857143 1616 89.379000 5 4487 7 chr6B.!!$F1 4482
4 TraesCS6D01G356400 chr7D 98658806 98659355 549 True 411.000000 411 80.279000 3917 4488 1 chr7D.!!$R2 571
5 TraesCS6D01G356400 chr3D 382819987 382820628 641 False 360.000000 387 91.321000 1015 1623 2 chr3D.!!$F2 608
6 TraesCS6D01G356400 chr3D 554658672 554659313 641 False 360.000000 387 91.321000 1015 1623 2 chr3D.!!$F3 608
7 TraesCS6D01G356400 chr1D 207148126 207148746 620 True 357.000000 387 92.089500 1036 1623 2 chr1D.!!$R1 587

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
748 829 0.029681 ATGGGAGGTGTGCCCTAGAT 60.030 55.0 0.00 0.0 46.51 1.98 F
1289 1692 0.467804 GGTCAGCCTCTCCCTCAATC 59.532 60.0 0.00 0.0 0.00 2.67 F
1292 1695 0.469070 CAGCCTCTCCCTCAATCCTG 59.531 60.0 0.00 0.0 0.00 3.86 F
1963 2404 0.734309 TATTGCGCATGCTGAACCTG 59.266 50.0 12.75 0.0 43.34 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2589 0.396278 GCAAGCCTAAGCCCTGGAAT 60.396 55.000 0.00 0.0 41.25 3.01 R
2705 3203 0.604511 CACTGCTGCACATCTCACCA 60.605 55.000 0.00 0.0 0.00 4.17 R
3066 3564 1.065854 AGCAGCTGACACAGGGAATAC 60.066 52.381 20.43 0.0 31.21 1.89 R
3961 4520 1.076024 ACATGAAGGTCCATGCCAAGT 59.924 47.619 0.00 0.0 45.79 3.16 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
43 44 2.013400 TCGAGACAAAGCAACAGCAAA 58.987 42.857 0.00 0.00 0.00 3.68
48 49 4.427312 AGACAAAGCAACAGCAAAAAGAG 58.573 39.130 0.00 0.00 0.00 2.85
53 54 4.234530 AGCAACAGCAAAAAGAGCTAAG 57.765 40.909 0.00 0.00 41.14 2.18
54 55 2.728318 GCAACAGCAAAAAGAGCTAAGC 59.272 45.455 0.00 0.00 41.14 3.09
57 58 3.969899 ACAGCAAAAAGAGCTAAGCAAC 58.030 40.909 0.00 0.00 41.14 4.17
58 59 3.633986 ACAGCAAAAAGAGCTAAGCAACT 59.366 39.130 0.00 0.00 41.14 3.16
59 60 3.979495 CAGCAAAAAGAGCTAAGCAACTG 59.021 43.478 0.00 0.00 41.14 3.16
61 62 3.311966 CAAAAAGAGCTAAGCAACTGGC 58.688 45.455 0.00 0.00 45.30 4.85
70 71 3.279116 GCAACTGGCAGTCACGCA 61.279 61.111 22.31 0.00 43.97 5.24
72 73 1.951510 CAACTGGCAGTCACGCATT 59.048 52.632 22.31 0.00 0.00 3.56
73 74 0.386352 CAACTGGCAGTCACGCATTG 60.386 55.000 22.31 9.77 0.00 2.82
74 75 0.534877 AACTGGCAGTCACGCATTGA 60.535 50.000 22.31 0.00 0.00 2.57
75 76 0.321919 ACTGGCAGTCACGCATTGAT 60.322 50.000 15.88 0.00 36.32 2.57
76 77 0.806868 CTGGCAGTCACGCATTGATT 59.193 50.000 6.28 0.00 36.32 2.57
77 78 0.804364 TGGCAGTCACGCATTGATTC 59.196 50.000 0.00 0.00 36.32 2.52
80 83 2.159338 GGCAGTCACGCATTGATTCATT 60.159 45.455 0.00 0.00 36.32 2.57
91 94 5.228635 CGCATTGATTCATTGTTCAGCTAAC 59.771 40.000 9.58 0.00 38.67 2.34
92 95 6.327934 GCATTGATTCATTGTTCAGCTAACT 58.672 36.000 9.58 0.00 38.99 2.24
104 107 8.997621 TTGTTCAGCTAACTATTCGTTCTAAT 57.002 30.769 0.00 0.00 38.99 1.73
107 110 8.747666 GTTCAGCTAACTATTCGTTCTAATCAG 58.252 37.037 0.00 0.00 37.05 2.90
108 111 6.918569 TCAGCTAACTATTCGTTCTAATCAGC 59.081 38.462 0.00 0.00 37.05 4.26
110 113 6.697892 AGCTAACTATTCGTTCTAATCAGCAC 59.302 38.462 0.00 0.00 37.05 4.40
112 115 6.893958 AACTATTCGTTCTAATCAGCACTG 57.106 37.500 0.00 0.00 0.00 3.66
113 116 5.967088 ACTATTCGTTCTAATCAGCACTGT 58.033 37.500 0.00 0.00 0.00 3.55
114 117 7.096884 ACTATTCGTTCTAATCAGCACTGTA 57.903 36.000 0.00 0.00 0.00 2.74
115 118 7.197017 ACTATTCGTTCTAATCAGCACTGTAG 58.803 38.462 0.00 0.00 0.00 2.74
116 119 5.386958 TTCGTTCTAATCAGCACTGTAGT 57.613 39.130 0.00 0.00 0.00 2.73
117 120 6.505044 TTCGTTCTAATCAGCACTGTAGTA 57.495 37.500 0.00 0.00 0.00 1.82
119 122 7.797038 TCGTTCTAATCAGCACTGTAGTATA 57.203 36.000 0.00 0.00 0.00 1.47
120 123 7.637229 TCGTTCTAATCAGCACTGTAGTATAC 58.363 38.462 0.00 0.00 43.42 1.47
150 156 8.988064 ATAGGTATTGCAACTTATAGTCGATG 57.012 34.615 0.00 0.00 0.00 3.84
157 163 8.942338 TTGCAACTTATAGTCGATGAAATAGT 57.058 30.769 0.00 0.00 0.00 2.12
167 173 6.500041 AGTCGATGAAATAGTAGAAGCAGAC 58.500 40.000 0.00 0.00 0.00 3.51
168 174 5.688176 GTCGATGAAATAGTAGAAGCAGACC 59.312 44.000 0.00 0.00 0.00 3.85
179 185 3.058160 GCAGACCGCCACAAGCAT 61.058 61.111 0.00 0.00 44.04 3.79
189 195 4.937620 ACCGCCACAAGCATGATAATATAG 59.062 41.667 0.00 0.00 44.04 1.31
257 266 5.957842 TTTCCATTACCAACATCACAGTC 57.042 39.130 0.00 0.00 0.00 3.51
271 280 9.586435 CAACATCACAGTCAATTACAGATACTA 57.414 33.333 0.00 0.00 0.00 1.82
279 288 8.855110 CAGTCAATTACAGATACTAGATCAGGT 58.145 37.037 0.00 0.00 0.00 4.00
280 289 9.073475 AGTCAATTACAGATACTAGATCAGGTC 57.927 37.037 0.00 0.00 0.00 3.85
281 290 9.073475 GTCAATTACAGATACTAGATCAGGTCT 57.927 37.037 0.00 0.00 41.11 3.85
302 318 6.045318 GTCTTCTTCTTAGCATGCATACTGA 58.955 40.000 21.98 7.78 0.00 3.41
303 319 6.536582 GTCTTCTTCTTAGCATGCATACTGAA 59.463 38.462 21.98 14.56 0.00 3.02
304 320 7.226325 GTCTTCTTCTTAGCATGCATACTGAAT 59.774 37.037 21.98 0.00 0.00 2.57
305 321 8.424133 TCTTCTTCTTAGCATGCATACTGAATA 58.576 33.333 21.98 6.86 0.00 1.75
324 340 2.386661 AAACGGATCACAGCTACTGG 57.613 50.000 0.00 0.00 35.51 4.00
325 341 0.537188 AACGGATCACAGCTACTGGG 59.463 55.000 0.00 0.00 36.00 4.45
331 347 2.543777 TCACAGCTACTGGGAAACAC 57.456 50.000 0.00 0.00 41.30 3.32
332 348 1.148310 CACAGCTACTGGGAAACACG 58.852 55.000 0.00 0.00 36.97 4.49
522 541 4.660938 GTCTGGCCCCGCACCTTT 62.661 66.667 0.00 0.00 0.00 3.11
602 622 0.808453 ACCGACAACCACGACAACAG 60.808 55.000 0.00 0.00 0.00 3.16
606 626 2.542205 CGACAACCACGACAACAGTAGA 60.542 50.000 0.00 0.00 0.00 2.59
608 628 1.792949 CAACCACGACAACAGTAGAGC 59.207 52.381 0.00 0.00 0.00 4.09
617 637 3.034635 ACAACAGTAGAGCAGATAGGGG 58.965 50.000 0.00 0.00 0.00 4.79
620 640 1.883275 CAGTAGAGCAGATAGGGGTCG 59.117 57.143 0.00 0.00 37.81 4.79
623 643 0.178975 AGAGCAGATAGGGGTCGAGG 60.179 60.000 0.00 0.00 37.81 4.63
690 770 2.674033 TTCGGCGAGGAGAACGGA 60.674 61.111 10.46 0.00 0.00 4.69
748 829 0.029681 ATGGGAGGTGTGCCCTAGAT 60.030 55.000 0.00 0.00 46.51 1.98
822 907 3.264845 AGGCCCGTGGGAAATGGT 61.265 61.111 9.72 0.00 37.50 3.55
832 917 2.263153 GGAAATGGTCCGGTGTTGG 58.737 57.895 0.00 0.00 36.40 3.77
833 918 1.248101 GGAAATGGTCCGGTGTTGGG 61.248 60.000 0.00 0.00 36.40 4.12
834 919 1.873270 GAAATGGTCCGGTGTTGGGC 61.873 60.000 0.00 0.00 0.00 5.36
835 920 2.366153 AAATGGTCCGGTGTTGGGCT 62.366 55.000 0.00 0.00 32.87 5.19
836 921 2.366153 AATGGTCCGGTGTTGGGCTT 62.366 55.000 0.00 0.00 32.87 4.35
837 922 2.983592 GGTCCGGTGTTGGGCTTG 60.984 66.667 0.00 0.00 32.87 4.01
838 923 2.983592 GTCCGGTGTTGGGCTTGG 60.984 66.667 0.00 0.00 0.00 3.61
839 924 3.172106 TCCGGTGTTGGGCTTGGA 61.172 61.111 0.00 0.00 0.00 3.53
881 968 1.004394 GTAAAAGAGGTGGGGAGTGGG 59.996 57.143 0.00 0.00 0.00 4.61
905 992 2.328589 CCTCCCTCCTCCTCCTCCA 61.329 68.421 0.00 0.00 0.00 3.86
909 996 2.780693 CTCCTCCTCCTCCACCCA 59.219 66.667 0.00 0.00 0.00 4.51
1103 1205 1.065102 CATCGAAATCCAGGCAAGCAG 59.935 52.381 0.00 0.00 0.00 4.24
1177 1535 0.620700 AGGCTGACCCGGGTTATCTT 60.621 55.000 30.89 13.55 39.21 2.40
1185 1543 2.504585 ACCCGGGTTATCTTCTTCTTCC 59.495 50.000 24.16 0.00 0.00 3.46
1280 1653 1.378646 TCGACATCGGTCAGCCTCT 60.379 57.895 0.73 0.00 44.54 3.69
1281 1654 1.064946 CGACATCGGTCAGCCTCTC 59.935 63.158 0.00 0.00 44.54 3.20
1286 1689 2.230189 ATCGGTCAGCCTCTCCCTCA 62.230 60.000 0.00 0.00 0.00 3.86
1289 1692 0.467804 GGTCAGCCTCTCCCTCAATC 59.532 60.000 0.00 0.00 0.00 2.67
1292 1695 0.469070 CAGCCTCTCCCTCAATCCTG 59.531 60.000 0.00 0.00 0.00 3.86
1303 1706 2.624838 CCTCAATCCTGTGTTGCTTTGT 59.375 45.455 0.00 0.00 0.00 2.83
1304 1707 3.068590 CCTCAATCCTGTGTTGCTTTGTT 59.931 43.478 0.00 0.00 0.00 2.83
1305 1708 4.293415 CTCAATCCTGTGTTGCTTTGTTC 58.707 43.478 0.00 0.00 0.00 3.18
1306 1709 3.698539 TCAATCCTGTGTTGCTTTGTTCA 59.301 39.130 0.00 0.00 0.00 3.18
1307 1710 3.996150 ATCCTGTGTTGCTTTGTTCAG 57.004 42.857 0.00 0.00 0.00 3.02
1308 1711 2.997980 TCCTGTGTTGCTTTGTTCAGA 58.002 42.857 0.00 0.00 0.00 3.27
1309 1712 3.351740 TCCTGTGTTGCTTTGTTCAGAA 58.648 40.909 0.00 0.00 0.00 3.02
1310 1713 3.953612 TCCTGTGTTGCTTTGTTCAGAAT 59.046 39.130 0.00 0.00 0.00 2.40
1311 1714 4.402155 TCCTGTGTTGCTTTGTTCAGAATT 59.598 37.500 0.00 0.00 0.00 2.17
1312 1715 5.592282 TCCTGTGTTGCTTTGTTCAGAATTA 59.408 36.000 0.00 0.00 0.00 1.40
1313 1716 6.265196 TCCTGTGTTGCTTTGTTCAGAATTAT 59.735 34.615 0.00 0.00 0.00 1.28
1314 1717 6.925165 CCTGTGTTGCTTTGTTCAGAATTATT 59.075 34.615 0.00 0.00 0.00 1.40
1315 1718 8.081633 CCTGTGTTGCTTTGTTCAGAATTATTA 58.918 33.333 0.00 0.00 0.00 0.98
1316 1719 9.630098 CTGTGTTGCTTTGTTCAGAATTATTAT 57.370 29.630 0.00 0.00 0.00 1.28
1317 1720 9.409312 TGTGTTGCTTTGTTCAGAATTATTATG 57.591 29.630 0.00 0.00 0.00 1.90
1318 1721 8.375465 GTGTTGCTTTGTTCAGAATTATTATGC 58.625 33.333 0.00 0.00 0.00 3.14
1319 1722 7.545265 TGTTGCTTTGTTCAGAATTATTATGCC 59.455 33.333 0.00 0.00 0.00 4.40
1320 1723 6.572519 TGCTTTGTTCAGAATTATTATGCCC 58.427 36.000 0.00 0.00 0.00 5.36
1321 1724 5.985530 GCTTTGTTCAGAATTATTATGCCCC 59.014 40.000 0.00 0.00 0.00 5.80
1322 1725 6.478512 TTTGTTCAGAATTATTATGCCCCC 57.521 37.500 0.00 0.00 0.00 5.40
1323 1726 5.402054 TGTTCAGAATTATTATGCCCCCT 57.598 39.130 0.00 0.00 0.00 4.79
1324 1727 5.776358 TGTTCAGAATTATTATGCCCCCTT 58.224 37.500 0.00 0.00 0.00 3.95
1325 1728 6.201591 TGTTCAGAATTATTATGCCCCCTTT 58.798 36.000 0.00 0.00 0.00 3.11
1326 1729 6.098124 TGTTCAGAATTATTATGCCCCCTTTG 59.902 38.462 0.00 0.00 0.00 2.77
1332 1735 3.999764 ATTATGCCCCCTTTGGAGAAT 57.000 42.857 0.00 0.00 35.39 2.40
1353 1762 3.023119 TCCTTGTGCTGTGTTGAATTGT 58.977 40.909 0.00 0.00 0.00 2.71
1354 1763 3.117794 CCTTGTGCTGTGTTGAATTGTG 58.882 45.455 0.00 0.00 0.00 3.33
1356 1765 2.098614 TGTGCTGTGTTGAATTGTGGT 58.901 42.857 0.00 0.00 0.00 4.16
1387 1819 4.754667 GGGTGCGGTTCCGGACTC 62.755 72.222 28.38 24.00 46.99 3.36
1453 1885 4.332428 TGATATCTCACAGTCCATGCTG 57.668 45.455 3.98 0.00 41.92 4.41
1505 1941 1.282570 GGCATGTTGGTGTGTCACG 59.717 57.895 0.00 0.00 34.83 4.35
1506 1942 1.163420 GGCATGTTGGTGTGTCACGA 61.163 55.000 0.00 0.00 34.83 4.35
1509 1945 0.944386 ATGTTGGTGTGTCACGAAGC 59.056 50.000 0.00 0.00 33.17 3.86
1513 1949 1.013596 TGGTGTGTCACGAAGCTTTG 58.986 50.000 12.41 12.41 34.83 2.77
1524 1960 3.063997 CACGAAGCTTTGTGTTTGAGAGT 59.936 43.478 30.99 0.00 37.70 3.24
1580 2017 2.196229 CGGGAGACGGAGGGAGAT 59.804 66.667 0.00 0.00 39.42 2.75
1645 2082 5.009610 GGCATTGGATTAGCCGAGAATTTTA 59.990 40.000 0.00 0.00 38.86 1.52
1752 2190 5.091261 ACTGTTAGAAGGTATCCTTGCTG 57.909 43.478 5.73 1.65 44.82 4.41
1761 2199 7.166851 AGAAGGTATCCTTGCTGATGATAATG 58.833 38.462 5.73 0.00 44.82 1.90
1762 2200 5.813383 AGGTATCCTTGCTGATGATAATGG 58.187 41.667 0.00 0.00 0.00 3.16
1794 2232 4.449068 ACTTGTGTTCAACATGATCTCGAC 59.551 41.667 0.00 0.00 38.99 4.20
1823 2261 8.567948 CAAACCTGATTGACACTGTAAAAGTAT 58.432 33.333 0.00 0.00 32.64 2.12
1824 2262 8.691661 AACCTGATTGACACTGTAAAAGTATT 57.308 30.769 0.00 0.00 36.83 1.89
1888 2328 5.514274 TCCAAAGAACCTGAACATTTCAC 57.486 39.130 0.00 0.00 35.46 3.18
1889 2329 4.952957 TCCAAAGAACCTGAACATTTCACA 59.047 37.500 0.00 0.00 35.46 3.58
1890 2330 5.598005 TCCAAAGAACCTGAACATTTCACAT 59.402 36.000 0.00 0.00 35.46 3.21
1891 2331 6.098124 TCCAAAGAACCTGAACATTTCACATT 59.902 34.615 0.00 0.00 35.46 2.71
1892 2332 6.762661 CCAAAGAACCTGAACATTTCACATTT 59.237 34.615 0.00 0.00 35.46 2.32
1893 2333 7.042523 CCAAAGAACCTGAACATTTCACATTTC 60.043 37.037 0.00 0.00 35.46 2.17
1894 2334 6.713762 AGAACCTGAACATTTCACATTTCA 57.286 33.333 0.00 0.00 35.46 2.69
1895 2335 7.294017 AGAACCTGAACATTTCACATTTCAT 57.706 32.000 0.00 0.00 35.46 2.57
1906 2346 7.599998 ACATTTCACATTTCATTACTGCCTTTC 59.400 33.333 0.00 0.00 0.00 2.62
1963 2404 0.734309 TATTGCGCATGCTGAACCTG 59.266 50.000 12.75 0.00 43.34 4.00
1966 2407 2.758089 GCGCATGCTGAACCTGAGG 61.758 63.158 17.13 0.00 38.39 3.86
1972 2413 1.267121 TGCTGAACCTGAGGTCCTAC 58.733 55.000 3.76 0.00 33.12 3.18
1981 2422 4.805744 ACCTGAGGTCCTACGAAGATTAT 58.194 43.478 0.00 0.00 0.00 1.28
1991 2432 7.115947 GGTCCTACGAAGATTATGAAATTACCG 59.884 40.741 0.00 0.00 0.00 4.02
2024 2522 4.764679 TTTCGCTTCATACAACTGCATT 57.235 36.364 0.00 0.00 0.00 3.56
2067 2565 5.968528 ACCACAGTTTGTTGTTACTTGAA 57.031 34.783 0.00 0.00 0.00 2.69
2133 2631 1.477558 CCAGGAGTTATGGATGGTGCC 60.478 57.143 0.00 0.00 40.51 5.01
2308 2806 4.387862 AGATTGCGGTTAAAGTACGTGAAG 59.612 41.667 0.00 0.00 0.00 3.02
2548 3046 4.591321 AGGTAAGGATTTCATTGCCTCA 57.409 40.909 8.51 0.00 46.91 3.86
2594 3092 6.818644 GTCTTATGGATTTCTTGTCTGCTGTA 59.181 38.462 0.00 0.00 0.00 2.74
2610 3108 2.797156 GCTGTAGACTTATGTGGATGCG 59.203 50.000 0.00 0.00 0.00 4.73
2627 3125 1.138069 TGCGTTTCCTCTGACAGTTCA 59.862 47.619 1.59 0.00 0.00 3.18
2673 3171 5.185249 GTCCTCACTTGTGGTACATCTTCTA 59.815 44.000 0.00 0.00 44.52 2.10
2703 3201 2.675658 TCCAAAGGGGAAAGGTGAAG 57.324 50.000 0.00 0.00 44.80 3.02
2705 3203 2.721906 TCCAAAGGGGAAAGGTGAAGAT 59.278 45.455 0.00 0.00 44.80 2.40
2840 3338 9.772973 TTTACTGCTTTTAATCTCTGTGTCTTA 57.227 29.630 0.00 0.00 0.00 2.10
2867 3365 3.349927 TGCTTCATTCCACCTTGATCAG 58.650 45.455 0.00 0.00 0.00 2.90
2924 3422 7.274033 CACATACCAGTTGCATAAGAAATGTTG 59.726 37.037 0.00 0.00 0.00 3.33
2925 3423 5.789643 ACCAGTTGCATAAGAAATGTTGT 57.210 34.783 0.00 0.00 0.00 3.32
2926 3424 6.160576 ACCAGTTGCATAAGAAATGTTGTT 57.839 33.333 0.00 0.00 0.00 2.83
2927 3425 7.283625 ACCAGTTGCATAAGAAATGTTGTTA 57.716 32.000 0.00 0.00 0.00 2.41
2928 3426 7.721402 ACCAGTTGCATAAGAAATGTTGTTAA 58.279 30.769 0.00 0.00 0.00 2.01
2929 3427 8.200792 ACCAGTTGCATAAGAAATGTTGTTAAA 58.799 29.630 0.00 0.00 0.00 1.52
2930 3428 9.206870 CCAGTTGCATAAGAAATGTTGTTAAAT 57.793 29.630 0.00 0.00 0.00 1.40
2969 3467 7.721399 ACCAAATAGGCCATTACTCTCTTATTG 59.279 37.037 5.01 0.00 43.14 1.90
2973 3471 4.475016 AGGCCATTACTCTCTTATTGTGGT 59.525 41.667 5.01 0.00 0.00 4.16
3019 3517 5.185249 GTGGTGATCTTTCTACCTGTCTGTA 59.815 44.000 0.00 0.00 35.51 2.74
3021 3519 6.440647 TGGTGATCTTTCTACCTGTCTGTATT 59.559 38.462 0.00 0.00 35.51 1.89
3022 3520 7.038302 TGGTGATCTTTCTACCTGTCTGTATTT 60.038 37.037 0.00 0.00 35.51 1.40
3023 3521 7.824779 GGTGATCTTTCTACCTGTCTGTATTTT 59.175 37.037 0.00 0.00 0.00 1.82
3024 3522 9.220767 GTGATCTTTCTACCTGTCTGTATTTTT 57.779 33.333 0.00 0.00 0.00 1.94
3044 3542 4.387026 TTTTCCCACTGTCATGATTCCT 57.613 40.909 0.00 0.00 0.00 3.36
3045 3543 3.634397 TTCCCACTGTCATGATTCCTC 57.366 47.619 0.00 0.00 0.00 3.71
3046 3544 2.550175 TCCCACTGTCATGATTCCTCA 58.450 47.619 0.00 0.00 35.41 3.86
3047 3545 2.502947 TCCCACTGTCATGATTCCTCAG 59.497 50.000 0.00 3.55 34.12 3.35
3048 3546 2.502947 CCCACTGTCATGATTCCTCAGA 59.497 50.000 15.11 0.00 34.12 3.27
3049 3547 3.054875 CCCACTGTCATGATTCCTCAGAA 60.055 47.826 15.11 0.00 34.12 3.02
3050 3548 4.566278 CCCACTGTCATGATTCCTCAGAAA 60.566 45.833 15.11 0.00 35.09 2.52
3051 3549 4.634883 CCACTGTCATGATTCCTCAGAAAG 59.365 45.833 15.11 6.33 35.09 2.62
3052 3550 5.485620 CACTGTCATGATTCCTCAGAAAGA 58.514 41.667 15.11 0.00 35.09 2.52
3053 3551 5.936372 CACTGTCATGATTCCTCAGAAAGAA 59.064 40.000 15.11 0.00 35.09 2.52
3054 3552 6.429078 CACTGTCATGATTCCTCAGAAAGAAA 59.571 38.462 15.11 0.00 35.09 2.52
3055 3553 7.000472 ACTGTCATGATTCCTCAGAAAGAAAA 59.000 34.615 15.11 0.00 35.09 2.29
3056 3554 7.503566 ACTGTCATGATTCCTCAGAAAGAAAAA 59.496 33.333 15.11 0.00 35.09 1.94
3081 3579 5.127845 ACTGTCTATGTATTCCCTGTGTCAG 59.872 44.000 0.00 0.00 0.00 3.51
3220 3718 7.602644 TGCATCATACTTATCTTATTCCGTTCC 59.397 37.037 0.00 0.00 0.00 3.62
3346 3882 2.093711 CACATATGGACGGAACAGGTCA 60.094 50.000 7.80 0.00 36.12 4.02
3497 4033 1.463444 CCCGCTTCTAAGTCGGTTTTG 59.537 52.381 17.93 5.57 41.14 2.44
3499 4035 1.136057 CGCTTCTAAGTCGGTTTTGGC 60.136 52.381 0.00 0.00 0.00 4.52
3500 4036 1.136057 GCTTCTAAGTCGGTTTTGGCG 60.136 52.381 0.00 0.00 0.00 5.69
3540 4077 2.615447 TCAGAAGCAGCAAGAGTGTTTG 59.385 45.455 0.00 0.00 0.00 2.93
3545 4082 1.401552 GCAGCAAGAGTGTTTGTGTCA 59.598 47.619 0.00 0.00 0.00 3.58
3549 4086 4.036027 CAGCAAGAGTGTTTGTGTCAGAAT 59.964 41.667 0.00 0.00 0.00 2.40
3555 4092 6.582636 AGAGTGTTTGTGTCAGAATAGTTGA 58.417 36.000 0.00 0.00 0.00 3.18
3641 4178 5.551760 AATGCTAGTAGTGTCATGTTTGC 57.448 39.130 0.00 0.00 0.00 3.68
3757 4294 8.289618 CGATGATATACCCTTTGTGTTATTTGG 58.710 37.037 0.00 0.00 0.00 3.28
3792 4329 6.363357 GTGTAGATGCTGAAACAAAATGGTTC 59.637 38.462 1.22 1.22 44.06 3.62
3857 4395 9.271738 CAAACGCAACATAAAAATTTCTGTTTT 57.728 25.926 6.85 0.00 35.95 2.43
3961 4520 1.525197 CGTGTTGCGCTTGACTAAGAA 59.475 47.619 9.73 0.00 35.92 2.52
4121 4680 1.154016 CGTCAGTGTGCTACCTCGG 60.154 63.158 0.00 0.00 0.00 4.63
4149 4710 4.081642 GCCTCTTCTCTGTGGTATTGTGTA 60.082 45.833 0.00 0.00 0.00 2.90
4164 4725 5.818136 ATTGTGTATGGAGTATGTTGTGC 57.182 39.130 0.00 0.00 0.00 4.57
4240 4801 3.243839 GCAATTCTCTTCTTTTGCACCCA 60.244 43.478 1.89 0.00 43.00 4.51
4289 4850 3.173599 CACGCATGCAAATTCACCTAAG 58.826 45.455 19.57 0.00 0.00 2.18
4346 4907 3.035942 GTTCAACATGACGAAACTGCAC 58.964 45.455 0.00 0.00 0.00 4.57
4454 5016 2.472695 ACTTGTGCATACACCGACAT 57.527 45.000 0.00 0.00 46.86 3.06
4462 5024 3.687212 TGCATACACCGACATAAAACCAG 59.313 43.478 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.026607 TCGATTTGAGAACTTTTCAACTTTGTT 58.973 29.630 0.00 0.00 34.50 2.83
1 2 7.535139 TCGATTTGAGAACTTTTCAACTTTGT 58.465 30.769 0.00 0.00 34.50 2.83
2 3 7.969387 TCGATTTGAGAACTTTTCAACTTTG 57.031 32.000 0.00 0.00 34.50 2.77
17 18 4.461405 CTGTTGCTTTGTCTCGATTTGAG 58.539 43.478 0.00 0.00 46.72 3.02
36 37 3.633986 AGTTGCTTAGCTCTTTTTGCTGT 59.366 39.130 5.60 0.00 41.32 4.40
43 44 2.157738 CTGCCAGTTGCTTAGCTCTTT 58.842 47.619 5.60 0.00 42.00 2.52
48 49 0.519077 GTGACTGCCAGTTGCTTAGC 59.481 55.000 0.00 0.00 42.00 3.09
53 54 2.133742 AATGCGTGACTGCCAGTTGC 62.134 55.000 0.00 4.76 41.77 4.17
54 55 0.386352 CAATGCGTGACTGCCAGTTG 60.386 55.000 0.00 0.00 0.00 3.16
57 58 0.806868 AATCAATGCGTGACTGCCAG 59.193 50.000 0.00 0.00 39.72 4.85
58 59 0.804364 GAATCAATGCGTGACTGCCA 59.196 50.000 0.00 0.00 39.72 4.92
59 60 0.804364 TGAATCAATGCGTGACTGCC 59.196 50.000 0.00 0.00 39.72 4.85
61 62 4.087510 ACAATGAATCAATGCGTGACTG 57.912 40.909 0.00 0.00 39.72 3.51
62 63 4.216042 TGAACAATGAATCAATGCGTGACT 59.784 37.500 0.00 0.00 39.72 3.41
63 64 4.475028 TGAACAATGAATCAATGCGTGAC 58.525 39.130 0.00 0.00 39.72 3.67
64 65 4.725359 CTGAACAATGAATCAATGCGTGA 58.275 39.130 0.00 0.00 41.67 4.35
65 66 3.302434 GCTGAACAATGAATCAATGCGTG 59.698 43.478 0.00 0.00 0.00 5.34
66 67 3.192001 AGCTGAACAATGAATCAATGCGT 59.808 39.130 0.00 0.00 0.00 5.24
67 68 3.766151 AGCTGAACAATGAATCAATGCG 58.234 40.909 0.00 0.00 0.00 4.73
68 69 6.327934 AGTTAGCTGAACAATGAATCAATGC 58.672 36.000 0.00 0.00 40.86 3.56
72 73 7.549134 ACGAATAGTTAGCTGAACAATGAATCA 59.451 33.333 0.00 0.00 40.86 2.57
73 74 7.910304 ACGAATAGTTAGCTGAACAATGAATC 58.090 34.615 0.00 0.00 40.86 2.52
74 75 7.849804 ACGAATAGTTAGCTGAACAATGAAT 57.150 32.000 0.00 0.00 40.86 2.57
75 76 7.602644 AGAACGAATAGTTAGCTGAACAATGAA 59.397 33.333 0.00 0.00 44.35 2.57
76 77 7.097192 AGAACGAATAGTTAGCTGAACAATGA 58.903 34.615 0.00 0.00 44.35 2.57
77 78 7.295952 AGAACGAATAGTTAGCTGAACAATG 57.704 36.000 0.00 0.00 44.35 2.82
80 83 8.248253 TGATTAGAACGAATAGTTAGCTGAACA 58.752 33.333 0.00 0.00 44.35 3.18
91 94 7.197017 ACTACAGTGCTGATTAGAACGAATAG 58.803 38.462 6.17 0.00 37.56 1.73
92 95 7.096884 ACTACAGTGCTGATTAGAACGAATA 57.903 36.000 6.17 0.00 37.56 1.75
126 130 8.173542 TCATCGACTATAAGTTGCAATACCTA 57.826 34.615 0.59 0.00 29.55 3.08
142 146 7.255173 GGTCTGCTTCTACTATTTCATCGACTA 60.255 40.741 0.00 0.00 0.00 2.59
145 149 5.505819 CGGTCTGCTTCTACTATTTCATCGA 60.506 44.000 0.00 0.00 0.00 3.59
150 156 3.124560 GGCGGTCTGCTTCTACTATTTC 58.875 50.000 3.10 0.00 45.43 2.17
156 162 0.320421 TTGTGGCGGTCTGCTTCTAC 60.320 55.000 3.10 0.00 45.43 2.59
157 163 0.037326 CTTGTGGCGGTCTGCTTCTA 60.037 55.000 3.10 0.00 45.43 2.10
167 173 4.333649 CCTATATTATCATGCTTGTGGCGG 59.666 45.833 0.00 0.00 45.43 6.13
168 174 5.178061 TCCTATATTATCATGCTTGTGGCG 58.822 41.667 0.00 0.00 45.43 5.69
257 266 9.906660 GAAGACCTGATCTAGTATCTGTAATTG 57.093 37.037 0.00 0.00 36.27 2.32
271 280 5.684552 GCATGCTAAGAAGAAGACCTGATCT 60.685 44.000 11.37 0.00 40.46 2.75
275 284 3.603532 TGCATGCTAAGAAGAAGACCTG 58.396 45.455 20.33 0.00 0.00 4.00
279 288 6.225981 TCAGTATGCATGCTAAGAAGAAGA 57.774 37.500 17.42 5.12 34.76 2.87
280 289 6.915544 TTCAGTATGCATGCTAAGAAGAAG 57.084 37.500 17.42 2.71 34.76 2.85
281 290 8.962884 TTATTCAGTATGCATGCTAAGAAGAA 57.037 30.769 17.42 16.46 34.76 2.52
302 318 4.442706 CCAGTAGCTGTGATCCGTTTATT 58.557 43.478 0.00 0.00 0.00 1.40
303 319 3.181465 CCCAGTAGCTGTGATCCGTTTAT 60.181 47.826 0.00 0.00 0.00 1.40
304 320 2.167693 CCCAGTAGCTGTGATCCGTTTA 59.832 50.000 0.00 0.00 0.00 2.01
305 321 1.066143 CCCAGTAGCTGTGATCCGTTT 60.066 52.381 0.00 0.00 0.00 3.60
360 376 4.040706 TCCTCCGAGAAGTAGATCTAGGTC 59.959 50.000 1.64 3.67 41.45 3.85
602 622 2.156098 CTCGACCCCTATCTGCTCTAC 58.844 57.143 0.00 0.00 0.00 2.59
606 626 1.152440 CCCTCGACCCCTATCTGCT 60.152 63.158 0.00 0.00 0.00 4.24
608 628 1.534235 CCCCCTCGACCCCTATCTG 60.534 68.421 0.00 0.00 0.00 2.90
713 793 3.774528 ATCAGCAGAAGCCGCCGA 61.775 61.111 0.00 0.00 43.56 5.54
748 829 3.060611 CCTCTATAAAATCCCCCACCCA 58.939 50.000 0.00 0.00 0.00 4.51
756 837 2.303311 AGCCCTCGCCTCTATAAAATCC 59.697 50.000 0.00 0.00 34.57 3.01
803 888 3.451894 CATTTCCCACGGGCCTGC 61.452 66.667 12.89 0.00 34.68 4.85
804 889 2.755469 CCATTTCCCACGGGCCTG 60.755 66.667 11.02 11.02 34.68 4.85
805 890 3.264845 ACCATTTCCCACGGGCCT 61.265 61.111 0.84 0.00 34.68 5.19
818 903 2.840753 AAGCCCAACACCGGACCAT 61.841 57.895 9.46 0.00 0.00 3.55
822 907 3.172106 TCCAAGCCCAACACCGGA 61.172 61.111 9.46 0.00 0.00 5.14
826 911 0.883833 CACATCTCCAAGCCCAACAC 59.116 55.000 0.00 0.00 0.00 3.32
827 912 0.251297 CCACATCTCCAAGCCCAACA 60.251 55.000 0.00 0.00 0.00 3.33
828 913 1.598701 GCCACATCTCCAAGCCCAAC 61.599 60.000 0.00 0.00 0.00 3.77
829 914 1.304381 GCCACATCTCCAAGCCCAA 60.304 57.895 0.00 0.00 0.00 4.12
830 915 2.356278 GCCACATCTCCAAGCCCA 59.644 61.111 0.00 0.00 0.00 5.36
831 916 2.440980 GGCCACATCTCCAAGCCC 60.441 66.667 0.00 0.00 37.66 5.19
832 917 2.440980 GGGCCACATCTCCAAGCC 60.441 66.667 4.39 0.00 43.09 4.35
833 918 2.825836 CGGGCCACATCTCCAAGC 60.826 66.667 4.39 0.00 0.00 4.01
834 919 0.251916 TAACGGGCCACATCTCCAAG 59.748 55.000 4.39 0.00 0.00 3.61
835 920 0.251916 CTAACGGGCCACATCTCCAA 59.748 55.000 4.39 0.00 0.00 3.53
836 921 1.622607 CCTAACGGGCCACATCTCCA 61.623 60.000 4.39 0.00 0.00 3.86
837 922 1.146263 CCTAACGGGCCACATCTCC 59.854 63.158 4.39 0.00 0.00 3.71
838 923 1.146263 CCCTAACGGGCCACATCTC 59.854 63.158 4.39 0.00 45.33 2.75
839 924 3.320359 CCCTAACGGGCCACATCT 58.680 61.111 4.39 0.00 45.33 2.90
881 968 2.367107 GGAGGAGGGAGGGGGTTC 60.367 72.222 0.00 0.00 0.00 3.62
886 973 2.612251 GAGGAGGAGGAGGGAGGG 59.388 72.222 0.00 0.00 0.00 4.30
905 992 0.680061 GGTTCTGTTCTCTCGTGGGT 59.320 55.000 0.00 0.00 0.00 4.51
909 996 0.882474 CGAGGGTTCTGTTCTCTCGT 59.118 55.000 12.90 0.00 41.37 4.18
985 1081 1.531840 GCATCTCGCCCCCTCTCTA 60.532 63.158 0.00 0.00 32.94 2.43
1124 1226 1.148273 GAGCTCCCCACACAACACA 59.852 57.895 0.87 0.00 0.00 3.72
1177 1535 0.247736 GCCTGCGAAGAGGAAGAAGA 59.752 55.000 0.00 0.00 34.69 2.87
1280 1653 1.067295 AGCAACACAGGATTGAGGGA 58.933 50.000 0.00 0.00 0.00 4.20
1281 1654 1.915141 AAGCAACACAGGATTGAGGG 58.085 50.000 0.00 0.00 0.00 4.30
1286 1689 3.953612 TCTGAACAAAGCAACACAGGATT 59.046 39.130 0.00 0.00 0.00 3.01
1289 1692 3.781079 TTCTGAACAAAGCAACACAGG 57.219 42.857 0.00 0.00 0.00 4.00
1292 1695 8.375465 GCATAATAATTCTGAACAAAGCAACAC 58.625 33.333 0.00 0.00 0.00 3.32
1303 1706 5.602145 CCAAAGGGGGCATAATAATTCTGAA 59.398 40.000 0.00 0.00 0.00 3.02
1304 1707 5.103301 TCCAAAGGGGGCATAATAATTCTGA 60.103 40.000 0.00 0.00 37.22 3.27
1305 1708 5.147032 TCCAAAGGGGGCATAATAATTCTG 58.853 41.667 0.00 0.00 37.22 3.02
1306 1709 5.136048 TCTCCAAAGGGGGCATAATAATTCT 59.864 40.000 0.00 0.00 33.18 2.40
1307 1710 5.393866 TCTCCAAAGGGGGCATAATAATTC 58.606 41.667 0.00 0.00 33.18 2.17
1308 1711 5.417170 TCTCCAAAGGGGGCATAATAATT 57.583 39.130 0.00 0.00 33.18 1.40
1309 1712 5.417170 TTCTCCAAAGGGGGCATAATAAT 57.583 39.130 0.00 0.00 33.18 1.28
1310 1713 4.890499 TTCTCCAAAGGGGGCATAATAA 57.110 40.909 0.00 0.00 33.18 1.40
1311 1714 4.202673 GGATTCTCCAAAGGGGGCATAATA 60.203 45.833 0.00 0.00 36.28 0.98
1312 1715 3.438520 GGATTCTCCAAAGGGGGCATAAT 60.439 47.826 0.00 0.00 36.28 1.28
1313 1716 2.091333 GGATTCTCCAAAGGGGGCATAA 60.091 50.000 0.00 0.00 36.28 1.90
1314 1717 1.499007 GGATTCTCCAAAGGGGGCATA 59.501 52.381 0.00 0.00 36.28 3.14
1315 1718 0.262876 GGATTCTCCAAAGGGGGCAT 59.737 55.000 0.00 0.00 36.28 4.40
1316 1719 0.850883 AGGATTCTCCAAAGGGGGCA 60.851 55.000 0.00 0.00 39.61 5.36
1317 1720 0.336392 AAGGATTCTCCAAAGGGGGC 59.664 55.000 0.00 0.00 39.61 5.80
1318 1721 1.359130 ACAAGGATTCTCCAAAGGGGG 59.641 52.381 0.00 0.00 39.61 5.40
1319 1722 2.450476 CACAAGGATTCTCCAAAGGGG 58.550 52.381 0.00 0.00 39.61 4.79
1320 1723 1.821136 GCACAAGGATTCTCCAAAGGG 59.179 52.381 0.00 0.00 39.61 3.95
1321 1724 2.490903 CAGCACAAGGATTCTCCAAAGG 59.509 50.000 0.00 0.00 39.61 3.11
1322 1725 3.057736 CACAGCACAAGGATTCTCCAAAG 60.058 47.826 0.00 0.00 39.61 2.77
1323 1726 2.886523 CACAGCACAAGGATTCTCCAAA 59.113 45.455 0.00 0.00 39.61 3.28
1324 1727 2.158623 ACACAGCACAAGGATTCTCCAA 60.159 45.455 0.00 0.00 39.61 3.53
1325 1728 1.421268 ACACAGCACAAGGATTCTCCA 59.579 47.619 0.00 0.00 39.61 3.86
1326 1729 2.191128 ACACAGCACAAGGATTCTCC 57.809 50.000 0.00 0.00 36.58 3.71
1332 1735 3.023119 ACAATTCAACACAGCACAAGGA 58.977 40.909 0.00 0.00 0.00 3.36
1335 1738 2.495270 ACCACAATTCAACACAGCACAA 59.505 40.909 0.00 0.00 0.00 3.33
1340 1749 3.858812 CACACAACCACAATTCAACACAG 59.141 43.478 0.00 0.00 0.00 3.66
1341 1750 3.507622 TCACACAACCACAATTCAACACA 59.492 39.130 0.00 0.00 0.00 3.72
1342 1751 4.103365 TCACACAACCACAATTCAACAC 57.897 40.909 0.00 0.00 0.00 3.32
1345 1754 4.605968 CGATTCACACAACCACAATTCAA 58.394 39.130 0.00 0.00 0.00 2.69
1353 1762 0.888736 CCCTGCGATTCACACAACCA 60.889 55.000 0.00 0.00 0.00 3.67
1354 1763 0.889186 ACCCTGCGATTCACACAACC 60.889 55.000 0.00 0.00 0.00 3.77
1356 1765 1.514678 GCACCCTGCGATTCACACAA 61.515 55.000 0.00 0.00 31.71 3.33
1414 1846 2.124983 CAGCCGATCCAGTGGTGG 60.125 66.667 9.54 10.97 46.63 4.61
1505 1941 5.640732 TGAAACTCTCAAACACAAAGCTTC 58.359 37.500 0.00 0.00 0.00 3.86
1506 1942 5.183904 ACTGAAACTCTCAAACACAAAGCTT 59.816 36.000 0.00 0.00 32.17 3.74
1509 1945 7.382218 ACAAAACTGAAACTCTCAAACACAAAG 59.618 33.333 0.00 0.00 32.17 2.77
1513 1949 7.637709 AAACAAAACTGAAACTCTCAAACAC 57.362 32.000 0.00 0.00 32.17 3.32
1524 1960 3.429684 GCGAGGGGAAAACAAAACTGAAA 60.430 43.478 0.00 0.00 0.00 2.69
1580 2017 1.514553 CATGTCTGCGAGCAGGAGA 59.485 57.895 22.93 10.21 45.39 3.71
1645 2082 3.010584 ACCCAAACATAGCATCTGGAACT 59.989 43.478 0.00 0.00 0.00 3.01
1689 2126 6.494842 TCAACTGTAACAAGAAGAATTGCAC 58.505 36.000 0.00 0.00 33.28 4.57
1729 2167 5.955959 TCAGCAAGGATACCTTCTAACAGTA 59.044 40.000 0.00 0.00 42.67 2.74
1752 2190 5.066893 ACAAGTCATGCACACCATTATCATC 59.933 40.000 0.00 0.00 29.71 2.92
1761 2199 1.675483 TGAACACAAGTCATGCACACC 59.325 47.619 0.00 0.00 0.00 4.16
1762 2200 3.108144 GTTGAACACAAGTCATGCACAC 58.892 45.455 0.00 0.00 0.00 3.82
1823 2261 1.906574 AGACATAGGTTCGAAGGCCAA 59.093 47.619 5.01 0.00 0.00 4.52
1824 2262 1.207089 CAGACATAGGTTCGAAGGCCA 59.793 52.381 5.01 0.00 0.00 5.36
1888 2328 7.814264 ATAGAGGAAAGGCAGTAATGAAATG 57.186 36.000 0.00 0.00 0.00 2.32
1906 2346 7.822334 TCGGCAACCATACAATTATTATAGAGG 59.178 37.037 0.00 0.00 0.00 3.69
1963 2404 9.194271 GTAATTTCATAATCTTCGTAGGACCTC 57.806 37.037 0.00 0.00 0.00 3.85
1966 2407 7.650903 ACGGTAATTTCATAATCTTCGTAGGAC 59.349 37.037 0.00 0.00 0.00 3.85
1972 2413 9.370126 GAAATCACGGTAATTTCATAATCTTCG 57.630 33.333 11.10 0.00 40.97 3.79
1981 2422 7.327275 CGAAAATTGGAAATCACGGTAATTTCA 59.673 33.333 16.48 0.21 42.37 2.69
1991 2432 6.806249 TGTATGAAGCGAAAATTGGAAATCAC 59.194 34.615 0.00 0.00 0.00 3.06
2003 2501 4.215185 TCAATGCAGTTGTATGAAGCGAAA 59.785 37.500 0.00 0.00 38.95 3.46
2091 2589 0.396278 GCAAGCCTAAGCCCTGGAAT 60.396 55.000 0.00 0.00 41.25 3.01
2133 2631 5.295292 CACCTGGACTGCTGAAATACTAATG 59.705 44.000 0.00 0.00 0.00 1.90
2308 2806 5.008316 CCCAAGGGATACGTTACAAAATAGC 59.992 44.000 0.00 0.00 44.23 2.97
2347 2845 8.416329 GGAAATTATGCACATCAAGGTTAAGAT 58.584 33.333 0.00 0.00 0.00 2.40
2548 3046 3.009473 ACTGTTCATACAACCATGGCTCT 59.991 43.478 13.04 0.00 32.92 4.09
2594 3092 3.055094 AGGAAACGCATCCACATAAGTCT 60.055 43.478 9.51 0.00 42.27 3.24
2610 3108 4.096382 TGCTTTTGAACTGTCAGAGGAAAC 59.904 41.667 6.91 0.00 34.49 2.78
2627 3125 5.201243 ACAAGGTAGGACTTCTTTGCTTTT 58.799 37.500 1.71 0.00 0.00 2.27
2673 3171 1.133976 CCCCTTTGGAAGAGATGCGAT 60.134 52.381 0.00 0.00 35.39 4.58
2703 3201 1.015109 CTGCTGCACATCTCACCATC 58.985 55.000 0.00 0.00 0.00 3.51
2705 3203 0.604511 CACTGCTGCACATCTCACCA 60.605 55.000 0.00 0.00 0.00 4.17
2840 3338 4.225942 TCAAGGTGGAATGAAGCAGTAGAT 59.774 41.667 0.00 0.00 0.00 1.98
2867 3365 4.755266 ACTGGGTCACATATAGTTCCAC 57.245 45.455 0.00 0.00 0.00 4.02
2902 3400 6.892658 ACAACATTTCTTATGCAACTGGTA 57.107 33.333 0.00 0.00 0.00 3.25
2927 3425 7.981225 GCCTATTTGGTCATGTCATTAACATTT 59.019 33.333 0.00 0.00 41.57 2.32
2928 3426 7.417797 GGCCTATTTGGTCATGTCATTAACATT 60.418 37.037 0.00 0.00 41.57 2.71
2929 3427 6.040842 GGCCTATTTGGTCATGTCATTAACAT 59.959 38.462 0.00 0.00 43.07 2.71
2930 3428 5.359576 GGCCTATTTGGTCATGTCATTAACA 59.640 40.000 0.00 0.00 40.97 2.41
2973 3471 9.838339 ACCACAAAAATAACAAACATTTCCATA 57.162 25.926 0.00 0.00 0.00 2.74
3022 3520 4.739793 AGGAATCATGACAGTGGGAAAAA 58.260 39.130 0.00 0.00 0.00 1.94
3023 3521 4.202556 TGAGGAATCATGACAGTGGGAAAA 60.203 41.667 0.00 0.00 0.00 2.29
3024 3522 3.330405 TGAGGAATCATGACAGTGGGAAA 59.670 43.478 0.00 0.00 0.00 3.13
3025 3523 2.912295 TGAGGAATCATGACAGTGGGAA 59.088 45.455 0.00 0.00 0.00 3.97
3026 3524 2.502947 CTGAGGAATCATGACAGTGGGA 59.497 50.000 0.00 0.00 0.00 4.37
3027 3525 2.502947 TCTGAGGAATCATGACAGTGGG 59.497 50.000 0.00 0.00 0.00 4.61
3028 3526 3.900966 TCTGAGGAATCATGACAGTGG 57.099 47.619 0.00 0.00 0.00 4.00
3029 3527 5.485620 TCTTTCTGAGGAATCATGACAGTG 58.514 41.667 0.00 0.00 0.00 3.66
3030 3528 5.752036 TCTTTCTGAGGAATCATGACAGT 57.248 39.130 0.00 0.00 0.00 3.55
3031 3529 7.444629 TTTTCTTTCTGAGGAATCATGACAG 57.555 36.000 0.00 0.10 0.00 3.51
3032 3530 7.822161 TTTTTCTTTCTGAGGAATCATGACA 57.178 32.000 0.00 0.00 0.00 3.58
3053 3551 7.231467 ACACAGGGAATACATAGACAGTTTTT 58.769 34.615 0.00 0.00 0.00 1.94
3054 3552 6.779860 ACACAGGGAATACATAGACAGTTTT 58.220 36.000 0.00 0.00 0.00 2.43
3055 3553 6.013725 TGACACAGGGAATACATAGACAGTTT 60.014 38.462 0.00 0.00 0.00 2.66
3056 3554 5.483937 TGACACAGGGAATACATAGACAGTT 59.516 40.000 0.00 0.00 0.00 3.16
3057 3555 5.023452 TGACACAGGGAATACATAGACAGT 58.977 41.667 0.00 0.00 0.00 3.55
3058 3556 5.595885 CTGACACAGGGAATACATAGACAG 58.404 45.833 0.00 0.00 0.00 3.51
3059 3557 4.141937 GCTGACACAGGGAATACATAGACA 60.142 45.833 0.00 0.00 31.21 3.41
3060 3558 4.100189 AGCTGACACAGGGAATACATAGAC 59.900 45.833 0.00 0.00 31.21 2.59
3061 3559 4.100035 CAGCTGACACAGGGAATACATAGA 59.900 45.833 8.42 0.00 31.21 1.98
3062 3560 4.375272 CAGCTGACACAGGGAATACATAG 58.625 47.826 8.42 0.00 31.21 2.23
3063 3561 3.432186 GCAGCTGACACAGGGAATACATA 60.432 47.826 20.43 0.00 31.21 2.29
3064 3562 2.681976 GCAGCTGACACAGGGAATACAT 60.682 50.000 20.43 0.00 31.21 2.29
3065 3563 1.339055 GCAGCTGACACAGGGAATACA 60.339 52.381 20.43 0.00 31.21 2.29
3066 3564 1.065854 AGCAGCTGACACAGGGAATAC 60.066 52.381 20.43 0.00 31.21 1.89
3081 3579 2.903798 AGAACTGAAGATGCTAGCAGC 58.096 47.619 25.19 25.19 42.82 5.25
3215 3713 4.730949 TGGACTATTAAGTGAGGGAACG 57.269 45.455 0.00 0.00 35.56 3.95
3220 3718 5.902681 TCAACGATGGACTATTAAGTGAGG 58.097 41.667 0.00 0.00 35.56 3.86
3346 3882 2.952310 GTTCACCTTCTGCCTCTTGTTT 59.048 45.455 0.00 0.00 0.00 2.83
3451 3987 1.173913 GCTTCCGCCCTGTGTATTTT 58.826 50.000 0.00 0.00 0.00 1.82
3497 4033 3.439129 ACAAGCTAAACTAAATGACCGCC 59.561 43.478 0.00 0.00 0.00 6.13
3499 4035 5.637810 TCTGACAAGCTAAACTAAATGACCG 59.362 40.000 0.00 0.00 0.00 4.79
3500 4036 7.435068 TTCTGACAAGCTAAACTAAATGACC 57.565 36.000 0.00 0.00 0.00 4.02
3540 4077 5.230306 GCGATACAGTCAACTATTCTGACAC 59.770 44.000 5.81 0.00 44.68 3.67
3545 4082 3.066900 AGCGCGATACAGTCAACTATTCT 59.933 43.478 12.10 0.00 0.00 2.40
3549 4086 2.479049 GGAAGCGCGATACAGTCAACTA 60.479 50.000 12.10 0.00 0.00 2.24
3555 4092 1.076533 CAACGGAAGCGCGATACAGT 61.077 55.000 12.10 0.49 0.00 3.55
3641 4178 9.591792 ACAATGTCATCATTACATATATCCTCG 57.408 33.333 0.00 0.00 41.66 4.63
3792 4329 5.435557 CGCAGCTTAAGAAAATAATCTCCG 58.564 41.667 6.67 0.00 0.00 4.63
3857 4395 6.456315 GCTCGTGCATACAATACAATACACAA 60.456 38.462 4.26 0.00 39.41 3.33
3961 4520 1.076024 ACATGAAGGTCCATGCCAAGT 59.924 47.619 0.00 0.00 45.79 3.16
4121 4680 0.248843 CCACAGAGAAGAGGCCTCAC 59.751 60.000 33.90 25.31 33.25 3.51
4149 4710 2.289382 TGACACGCACAACATACTCCAT 60.289 45.455 0.00 0.00 0.00 3.41
4164 4725 0.586319 ACAAACCGCAGAATGACACG 59.414 50.000 0.00 0.00 39.69 4.49
4240 4801 6.316390 ACACTGAGTCGTTTCTTTCTTGAAAT 59.684 34.615 0.00 0.00 38.09 2.17
4289 4850 3.299340 TCTCTCACAAACGAGGTTAGC 57.701 47.619 0.00 0.00 33.59 3.09
4346 4907 4.201950 CCTTATCCCATGAACTCGCAAAAG 60.202 45.833 0.00 0.00 0.00 2.27
4358 4920 3.504906 CAGCATGCTAACCTTATCCCATG 59.495 47.826 22.19 0.00 34.68 3.66
4397 4959 4.038402 GCCATTTTAGTGGAATCCATGAGG 59.962 45.833 4.81 2.62 42.02 3.86
4399 4961 4.608269 TGCCATTTTAGTGGAATCCATGA 58.392 39.130 4.81 0.00 42.02 3.07
4404 4966 3.696051 TGAGCTGCCATTTTAGTGGAATC 59.304 43.478 0.00 0.00 42.02 2.52
4448 5010 5.737290 CGCTTAATTTCTGGTTTTATGTCGG 59.263 40.000 0.00 0.00 0.00 4.79
4454 5016 6.887626 AACCTCGCTTAATTTCTGGTTTTA 57.112 33.333 0.00 0.00 33.16 1.52
4462 5024 6.126741 GCAAAAACAAACCTCGCTTAATTTC 58.873 36.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.