Multiple sequence alignment - TraesCS5A01G296500

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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 TraesCS5A01G296500 chr5A 100.000 3959 0 0 1 3959 504784558 504780600 0.000000e+00 7312
1 TraesCS5A01G296500 chr5A 91.087 2558 151 41 421 2919 504855726 504853187 0.000000e+00 3389
2 TraesCS5A01G296500 chr5B 90.817 2853 166 34 163 2944 479394327 479391500 0.000000e+00 3729
3 TraesCS5A01G296500 chr5B 92.499 1693 115 9 1229 2919 479503191 479501509 0.000000e+00 2412
4 TraesCS5A01G296500 chr5B 89.952 826 60 6 2941 3753 479391441 479390626 0.000000e+00 1044
5 TraesCS5A01G296500 chr5B 82.334 917 83 42 361 1226 479504117 479503229 0.000000e+00 723
6 TraesCS5A01G296500 chr5B 73.936 1151 254 30 1490 2611 711392741 711393874 4.730000e-114 422
7 TraesCS5A01G296500 chr5D 94.358 1737 82 8 1213 2945 399162074 399160350 0.000000e+00 2651
8 TraesCS5A01G296500 chr5D 90.920 826 54 4 2940 3753 399160293 399159477 0.000000e+00 1090
9 TraesCS5A01G296500 chr5D 86.458 192 18 6 361 550 399210122 399209937 1.870000e-48 204
10 TraesCS5A01G296500 chr5D 86.082 194 13 5 3771 3959 399159493 399159309 3.120000e-46 196
11 TraesCS5A01G296500 chr5D 88.462 156 16 2 840 994 399162229 399162075 1.880000e-43 187
12 TraesCS5A01G296500 chr5D 94.737 95 3 2 62 154 509426465 509426559 3.190000e-31 147
13 TraesCS5A01G296500 chr2A 77.905 1661 280 58 1321 2919 753694100 753695735 0.000000e+00 953
14 TraesCS5A01G296500 chr2A 90.291 103 9 1 67 169 617178890 617178789 2.480000e-27 134
15 TraesCS5A01G296500 chr7B 71.393 1206 268 55 1349 2503 697430207 697429028 1.100000e-60 244
16 TraesCS5A01G296500 chr7B 71.215 1202 271 53 1352 2503 695373711 695372535 2.380000e-57 233
17 TraesCS5A01G296500 chr7B 71.429 882 202 32 1356 2200 685079121 685078253 1.880000e-43 187
18 TraesCS5A01G296500 chr7B 92.784 97 6 1 63 158 386449670 386449766 5.330000e-29 139
19 TraesCS5A01G296500 chr4A 71.144 1005 220 54 1639 2611 729293077 729292111 6.760000e-43 185
20 TraesCS5A01G296500 chr4A 91.919 99 6 2 54 151 472397865 472397962 1.920000e-28 137
21 TraesCS5A01G296500 chr4A 70.886 790 168 49 1850 2611 729278647 729277892 1.150000e-25 128
22 TraesCS5A01G296500 chr2D 93.814 97 6 0 57 153 534925455 534925551 3.190000e-31 147
23 TraesCS5A01G296500 chr2B 95.506 89 3 1 63 151 790112939 790113026 1.480000e-29 141
24 TraesCS5A01G296500 chr2B 92.784 97 5 2 56 152 354879116 354879210 5.330000e-29 139
25 TraesCS5A01G296500 chr6B 89.623 106 8 2 55 160 713833458 713833560 8.930000e-27 132
26 TraesCS5A01G296500 chr6B 89.623 106 8 2 55 160 713960516 713960618 8.930000e-27 132


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 TraesCS5A01G296500 chr5A 504780600 504784558 3958 True 7312.0 7312 100.0000 1 3959 1 chr5A.!!$R1 3958
1 TraesCS5A01G296500 chr5A 504853187 504855726 2539 True 3389.0 3389 91.0870 421 2919 1 chr5A.!!$R2 2498
2 TraesCS5A01G296500 chr5B 479390626 479394327 3701 True 2386.5 3729 90.3845 163 3753 2 chr5B.!!$R1 3590
3 TraesCS5A01G296500 chr5B 479501509 479504117 2608 True 1567.5 2412 87.4165 361 2919 2 chr5B.!!$R2 2558
4 TraesCS5A01G296500 chr5B 711392741 711393874 1133 False 422.0 422 73.9360 1490 2611 1 chr5B.!!$F1 1121
5 TraesCS5A01G296500 chr5D 399159309 399162229 2920 True 1031.0 2651 89.9555 840 3959 4 chr5D.!!$R2 3119
6 TraesCS5A01G296500 chr2A 753694100 753695735 1635 False 953.0 953 77.9050 1321 2919 1 chr2A.!!$F1 1598
7 TraesCS5A01G296500 chr7B 697429028 697430207 1179 True 244.0 244 71.3930 1349 2503 1 chr7B.!!$R3 1154
8 TraesCS5A01G296500 chr7B 695372535 695373711 1176 True 233.0 233 71.2150 1352 2503 1 chr7B.!!$R2 1151

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
242 243 0.305922 CCAATCGAGCGAGGAAATGC 59.694 55.000 0.00 0.00 0.0 3.56 F
478 541 0.548682 AGCACCTTCCACCATCTCCT 60.549 55.000 0.00 0.00 0.0 3.69 F
952 1058 1.557269 ATCTCAGGTCACAGGTGCCC 61.557 60.000 8.58 0.78 0.0 5.36 F
1227 1345 2.356135 TCCTAGCAAAAGCGATGAACC 58.644 47.619 0.00 0.00 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2403 1.021390 CGTAGCTGCCCTCCAACAAG 61.021 60.0 0.00 0.0 0.00 3.16 R
2576 2776 1.620822 ACAATCACTTCCAGCAACCC 58.379 50.0 0.00 0.0 0.00 4.11 R
2730 2954 0.031857 TGCGCAGGTTGTCCAATTTG 59.968 50.0 5.66 0.0 35.89 2.32 R
3239 3531 0.034756 TCATGACCCCACGACAGTTG 59.965 55.0 0.00 0.0 0.00 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
23 24 5.876612 AAAGCAAAATTTGTTGAACAGCA 57.123 30.435 7.60 0.00 0.00 4.41
24 25 5.876612 AAGCAAAATTTGTTGAACAGCAA 57.123 30.435 7.60 0.32 0.00 3.91
25 26 5.876612 AGCAAAATTTGTTGAACAGCAAA 57.123 30.435 16.27 16.27 43.68 3.68
26 27 6.251655 AGCAAAATTTGTTGAACAGCAAAA 57.748 29.167 17.44 5.30 43.00 2.44
27 28 6.085573 AGCAAAATTTGTTGAACAGCAAAAC 58.914 32.000 17.44 7.96 43.00 2.43
28 29 5.855395 GCAAAATTTGTTGAACAGCAAAACA 59.145 32.000 17.44 0.14 43.00 2.83
29 30 6.361748 GCAAAATTTGTTGAACAGCAAAACAA 59.638 30.769 17.44 3.58 43.00 2.83
30 31 7.616919 GCAAAATTTGTTGAACAGCAAAACAAC 60.617 33.333 17.44 0.00 43.00 3.32
31 32 6.799926 AATTTGTTGAACAGCAAAACAACT 57.200 29.167 17.44 2.31 43.00 3.16
32 33 6.799926 ATTTGTTGAACAGCAAAACAACTT 57.200 29.167 17.44 1.72 43.00 2.66
33 34 5.588568 TTGTTGAACAGCAAAACAACTTG 57.411 34.783 0.00 0.00 41.76 3.16
34 35 4.876125 TGTTGAACAGCAAAACAACTTGA 58.124 34.783 0.00 0.00 41.76 3.02
35 36 4.683781 TGTTGAACAGCAAAACAACTTGAC 59.316 37.500 0.00 0.00 41.76 3.18
36 37 4.511617 TGAACAGCAAAACAACTTGACA 57.488 36.364 0.00 0.00 0.00 3.58
37 38 5.070770 TGAACAGCAAAACAACTTGACAT 57.929 34.783 0.00 0.00 0.00 3.06
38 39 4.863689 TGAACAGCAAAACAACTTGACATG 59.136 37.500 0.00 0.00 0.00 3.21
39 40 4.717233 ACAGCAAAACAACTTGACATGA 57.283 36.364 0.00 0.00 0.00 3.07
40 41 5.266733 ACAGCAAAACAACTTGACATGAT 57.733 34.783 0.00 0.00 0.00 2.45
41 42 5.045215 ACAGCAAAACAACTTGACATGATG 58.955 37.500 0.00 0.00 0.00 3.07
42 43 4.053295 AGCAAAACAACTTGACATGATGC 58.947 39.130 0.00 0.00 0.00 3.91
43 44 3.121261 GCAAAACAACTTGACATGATGCG 60.121 43.478 0.00 0.00 0.00 4.73
44 45 3.988379 AAACAACTTGACATGATGCGT 57.012 38.095 0.00 0.00 0.00 5.24
45 46 5.211454 CAAAACAACTTGACATGATGCGTA 58.789 37.500 0.00 0.00 0.00 4.42
46 47 4.404507 AACAACTTGACATGATGCGTAC 57.595 40.909 0.00 0.00 0.00 3.67
47 48 3.398406 ACAACTTGACATGATGCGTACA 58.602 40.909 0.00 0.00 0.00 2.90
48 49 3.812609 ACAACTTGACATGATGCGTACAA 59.187 39.130 0.00 0.00 0.00 2.41
49 50 4.455533 ACAACTTGACATGATGCGTACAAT 59.544 37.500 0.00 0.00 0.00 2.71
50 51 5.048782 ACAACTTGACATGATGCGTACAATT 60.049 36.000 0.00 0.00 0.00 2.32
51 52 4.973396 ACTTGACATGATGCGTACAATTG 58.027 39.130 3.24 3.24 0.00 2.32
52 53 4.694982 ACTTGACATGATGCGTACAATTGA 59.305 37.500 13.59 0.00 0.00 2.57
53 54 5.355071 ACTTGACATGATGCGTACAATTGAT 59.645 36.000 13.59 0.00 0.00 2.57
54 55 5.408204 TGACATGATGCGTACAATTGATC 57.592 39.130 13.59 4.81 0.00 2.92
55 56 4.874966 TGACATGATGCGTACAATTGATCA 59.125 37.500 13.59 10.62 0.00 2.92
56 57 5.528320 TGACATGATGCGTACAATTGATCAT 59.472 36.000 13.59 12.45 34.75 2.45
57 58 6.705381 TGACATGATGCGTACAATTGATCATA 59.295 34.615 13.59 0.00 33.08 2.15
58 59 6.891624 ACATGATGCGTACAATTGATCATAC 58.108 36.000 13.59 3.18 33.08 2.39
59 60 6.482973 ACATGATGCGTACAATTGATCATACA 59.517 34.615 13.59 2.97 33.08 2.29
60 61 6.917217 TGATGCGTACAATTGATCATACAA 57.083 33.333 13.59 0.00 0.00 2.41
61 62 6.947258 TGATGCGTACAATTGATCATACAAG 58.053 36.000 13.59 0.00 33.22 3.16
62 63 6.760770 TGATGCGTACAATTGATCATACAAGA 59.239 34.615 13.59 0.00 33.22 3.02
63 64 7.442062 TGATGCGTACAATTGATCATACAAGAT 59.558 33.333 13.59 0.00 33.22 2.40
64 65 7.177498 TGCGTACAATTGATCATACAAGATC 57.823 36.000 13.59 0.00 43.69 2.75
76 77 9.012161 TGATCATACAAGATCATACTCTCTCTG 57.988 37.037 2.73 0.00 46.92 3.35
77 78 8.938801 ATCATACAAGATCATACTCTCTCTGT 57.061 34.615 0.00 0.00 0.00 3.41
79 80 9.853177 TCATACAAGATCATACTCTCTCTGTAA 57.147 33.333 0.00 0.00 0.00 2.41
112 113 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
113 114 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
114 115 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
115 116 8.954350 AGAGCGTTTAGATCACTACTTTAGTAA 58.046 33.333 0.00 0.00 37.82 2.24
116 117 9.733219 GAGCGTTTAGATCACTACTTTAGTAAT 57.267 33.333 0.00 0.00 37.23 1.89
117 118 9.733219 AGCGTTTAGATCACTACTTTAGTAATC 57.267 33.333 0.00 0.00 37.23 1.75
118 119 9.733219 GCGTTTAGATCACTACTTTAGTAATCT 57.267 33.333 4.72 4.72 37.23 2.40
124 125 9.733219 AGATCACTACTTTAGTAATCTAAACGC 57.267 33.333 0.00 0.00 40.05 4.84
125 126 9.733219 GATCACTACTTTAGTAATCTAAACGCT 57.267 33.333 0.00 0.00 40.05 5.07
126 127 9.733219 ATCACTACTTTAGTAATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
127 128 8.954350 TCACTACTTTAGTAATCTAAACGCTCT 58.046 33.333 0.00 0.00 40.05 4.09
128 129 9.570488 CACTACTTTAGTAATCTAAACGCTCTT 57.430 33.333 0.00 0.00 40.05 2.85
137 138 9.654663 AGTAATCTAAACGCTCTTACATTTCTT 57.345 29.630 0.00 0.00 0.00 2.52
141 142 7.946043 TCTAAACGCTCTTACATTTCTTTACG 58.054 34.615 0.00 0.00 0.00 3.18
142 143 5.526010 AACGCTCTTACATTTCTTTACGG 57.474 39.130 0.00 0.00 0.00 4.02
143 144 4.813027 ACGCTCTTACATTTCTTTACGGA 58.187 39.130 0.00 0.00 0.00 4.69
144 145 4.863131 ACGCTCTTACATTTCTTTACGGAG 59.137 41.667 0.00 0.00 0.00 4.63
145 146 4.267928 CGCTCTTACATTTCTTTACGGAGG 59.732 45.833 0.00 0.00 0.00 4.30
146 147 4.571176 GCTCTTACATTTCTTTACGGAGGG 59.429 45.833 0.00 0.00 0.00 4.30
147 148 5.626116 GCTCTTACATTTCTTTACGGAGGGA 60.626 44.000 0.00 0.00 0.00 4.20
148 149 5.974108 TCTTACATTTCTTTACGGAGGGAG 58.026 41.667 0.00 0.00 0.00 4.30
149 150 5.482878 TCTTACATTTCTTTACGGAGGGAGT 59.517 40.000 0.00 0.00 0.00 3.85
150 151 6.664816 TCTTACATTTCTTTACGGAGGGAGTA 59.335 38.462 0.00 0.00 0.00 2.59
151 152 5.082251 ACATTTCTTTACGGAGGGAGTAC 57.918 43.478 0.00 0.00 0.00 2.73
152 153 4.529377 ACATTTCTTTACGGAGGGAGTACA 59.471 41.667 0.00 0.00 0.00 2.90
153 154 5.012354 ACATTTCTTTACGGAGGGAGTACAA 59.988 40.000 0.00 0.00 0.00 2.41
154 155 4.796038 TTCTTTACGGAGGGAGTACAAG 57.204 45.455 0.00 0.00 0.00 3.16
155 156 3.094572 TCTTTACGGAGGGAGTACAAGG 58.905 50.000 0.00 0.00 0.00 3.61
156 157 2.610438 TTACGGAGGGAGTACAAGGT 57.390 50.000 0.00 0.00 0.00 3.50
157 158 3.737559 TTACGGAGGGAGTACAAGGTA 57.262 47.619 0.00 0.00 0.00 3.08
158 159 2.842645 ACGGAGGGAGTACAAGGTAT 57.157 50.000 0.00 0.00 0.00 2.73
159 160 2.385803 ACGGAGGGAGTACAAGGTATG 58.614 52.381 0.00 0.00 0.00 2.39
160 161 2.024655 ACGGAGGGAGTACAAGGTATGA 60.025 50.000 0.00 0.00 0.00 2.15
161 162 2.623889 CGGAGGGAGTACAAGGTATGAG 59.376 54.545 0.00 0.00 0.00 2.90
171 172 2.758979 ACAAGGTATGAGGTAGACCACG 59.241 50.000 0.66 0.00 43.30 4.94
202 203 1.890041 CACGCGTTTGAGGGGACAA 60.890 57.895 10.22 0.00 0.00 3.18
228 229 6.805713 TGTGAGGTTTTTCTTTCTTCCAATC 58.194 36.000 0.00 0.00 0.00 2.67
230 231 5.825679 TGAGGTTTTTCTTTCTTCCAATCGA 59.174 36.000 0.00 0.00 0.00 3.59
239 240 1.548719 TCTTCCAATCGAGCGAGGAAA 59.451 47.619 12.64 4.45 39.47 3.13
242 243 0.305922 CCAATCGAGCGAGGAAATGC 59.694 55.000 0.00 0.00 0.00 3.56
269 274 4.796606 CACCAGATCAATAATTGAGGGGT 58.203 43.478 0.00 0.00 43.98 4.95
283 288 0.752658 AGGGGTGCAGTTTGAAAAGC 59.247 50.000 0.00 0.00 0.00 3.51
303 308 2.458620 CTAAACGAGGGAGGGAGACTT 58.541 52.381 0.00 0.00 0.00 3.01
311 323 1.552792 GGGAGGGAGACTTGAGACTTG 59.447 57.143 0.00 0.00 0.00 3.16
331 343 3.057547 CTCTCGCCACACCTCTCGG 62.058 68.421 0.00 0.00 0.00 4.63
407 420 4.864334 CCGCCTCCAGCCACCATC 62.864 72.222 0.00 0.00 38.78 3.51
409 422 4.864334 GCCTCCAGCCACCATCGG 62.864 72.222 0.00 0.00 34.35 4.18
418 431 4.838152 CACCATCGGCCGTCCCTG 62.838 72.222 27.15 17.46 0.00 4.45
469 532 2.293318 ATCAGCCGAGCACCTTCCA 61.293 57.895 0.00 0.00 0.00 3.53
470 533 2.527951 ATCAGCCGAGCACCTTCCAC 62.528 60.000 0.00 0.00 0.00 4.02
478 541 0.548682 AGCACCTTCCACCATCTCCT 60.549 55.000 0.00 0.00 0.00 3.69
606 702 2.092968 TCGGCATACTCTCCAGCAAATT 60.093 45.455 0.00 0.00 0.00 1.82
616 712 1.656818 CCAGCAAATTGCCGGACGAT 61.657 55.000 14.74 0.00 43.51 3.73
733 838 1.978361 AAGCCTCTTCCCTCCTCAAT 58.022 50.000 0.00 0.00 0.00 2.57
869 974 5.652518 ACGATCTTAAGTCTGCTTTCTACC 58.347 41.667 1.63 0.00 36.22 3.18
910 1015 6.127168 TGGATGATGTTGAGTATTACCGTCTT 60.127 38.462 0.00 0.00 0.00 3.01
939 1044 9.462174 GAAACAGATACAAGATGACTATCTCAG 57.538 37.037 0.00 0.00 42.80 3.35
944 1049 5.590530 ACAAGATGACTATCTCAGGTCAC 57.409 43.478 0.00 0.00 42.80 3.67
952 1058 1.557269 ATCTCAGGTCACAGGTGCCC 61.557 60.000 8.58 0.78 0.00 5.36
1211 1329 6.824958 ACTTAGCAACCATATCCTTTCCTA 57.175 37.500 0.00 0.00 0.00 2.94
1222 1340 3.350219 TCCTTTCCTAGCAAAAGCGAT 57.650 42.857 9.29 0.00 33.33 4.58
1226 1344 4.406943 CTTTCCTAGCAAAAGCGATGAAC 58.593 43.478 0.00 0.00 0.00 3.18
1227 1345 2.356135 TCCTAGCAAAAGCGATGAACC 58.644 47.619 0.00 0.00 0.00 3.62
1323 1477 8.415553 TGTTTCTCGGATCCGTAGAAATATTTA 58.584 33.333 36.43 25.97 38.98 1.40
1367 1522 5.195001 TGGTATTTTGTTTTGCAGGACTC 57.805 39.130 3.63 0.00 0.00 3.36
1369 1524 6.065374 TGGTATTTTGTTTTGCAGGACTCTA 58.935 36.000 3.63 0.00 0.00 2.43
1619 1780 6.252599 AGATGCTCAACCAGATACCAATAA 57.747 37.500 0.00 0.00 0.00 1.40
1749 1949 3.542648 TGTTATGTGGGTTCACGTTTCA 58.457 40.909 0.00 0.00 46.42 2.69
1852 2052 6.426937 TCTTGACACCTTACAGACTAATTTGC 59.573 38.462 0.00 0.00 0.00 3.68
2059 2259 4.641989 AGCAAAGATGTATTCCCATGTCAC 59.358 41.667 0.00 0.00 0.00 3.67
2061 2261 5.449588 GCAAAGATGTATTCCCATGTCACTG 60.450 44.000 0.00 0.00 0.00 3.66
2136 2336 2.743752 CGTTGCTGCTGATGACCGG 61.744 63.158 0.00 0.00 0.00 5.28
2203 2403 3.365265 CACCTCTGGCGGCCAAAC 61.365 66.667 23.94 0.00 30.80 2.93
2238 2438 2.544267 GCTACGTATGAGGCCAAACATC 59.456 50.000 5.01 0.00 0.00 3.06
2529 2729 8.030106 CCTGAAGTAAAGAAGTACTCCAGTAAG 58.970 40.741 0.00 0.00 35.34 2.34
2637 2858 4.968719 TGGAAACAGATAGGAGATGGCTTA 59.031 41.667 0.00 0.00 35.01 3.09
2658 2882 7.040823 GGCTTAATAATGGAAGGATGTGAAGAG 60.041 40.741 0.00 0.00 0.00 2.85
2780 3004 4.406648 TTGATGGCGTAGATGTCAGAAT 57.593 40.909 0.00 0.00 0.00 2.40
2797 3021 7.279615 TGTCAGAATACAAGTTGAGGAGAAAA 58.720 34.615 10.54 0.00 0.00 2.29
2798 3022 7.226720 TGTCAGAATACAAGTTGAGGAGAAAAC 59.773 37.037 10.54 0.00 0.00 2.43
2962 3254 9.136323 AGACTAGATTTTTCTGGTGTTGAAAAT 57.864 29.630 0.00 0.00 41.25 1.82
2963 3255 9.399403 GACTAGATTTTTCTGGTGTTGAAAATC 57.601 33.333 0.00 10.72 41.25 2.17
3145 3437 4.021925 GGCCTCAACCAGCTCCGT 62.022 66.667 0.00 0.00 0.00 4.69
3239 3531 1.251251 AGAAGGGCTCACAACATTGC 58.749 50.000 0.00 0.00 0.00 3.56
3246 3538 2.388121 GCTCACAACATTGCAACTGTC 58.612 47.619 0.00 0.00 0.00 3.51
3260 3552 0.537188 ACTGTCGTGGGGTCATGATC 59.463 55.000 0.00 0.00 40.59 2.92
3261 3553 0.536724 CTGTCGTGGGGTCATGATCA 59.463 55.000 8.54 0.00 40.59 2.92
3262 3554 1.139654 CTGTCGTGGGGTCATGATCAT 59.860 52.381 8.54 1.18 40.59 2.45
3263 3555 1.134431 TGTCGTGGGGTCATGATCATG 60.134 52.381 26.79 26.79 40.59 3.07
3264 3556 1.138859 GTCGTGGGGTCATGATCATGA 59.861 52.381 30.27 30.27 44.83 3.07
3298 3590 2.550180 GTTGAAGAAACAGGAGGCTCAC 59.450 50.000 17.69 5.85 38.75 3.51
3349 3641 2.593346 AGCATCTCGAATCACTGACC 57.407 50.000 0.00 0.00 0.00 4.02
3379 3671 1.595311 ACCATGGCTTGAGATACCCA 58.405 50.000 13.04 0.00 0.00 4.51
3382 3674 2.092212 CCATGGCTTGAGATACCCAAGT 60.092 50.000 0.00 0.00 42.11 3.16
3395 3687 1.477553 CCCAAGTTGGATGATGGGTG 58.522 55.000 24.06 0.00 46.13 4.61
3402 3694 1.524621 GGATGATGGGTGAGCACGG 60.525 63.158 0.00 0.00 0.00 4.94
3419 3711 3.887868 GCGGCGGCCCAAAGTATG 61.888 66.667 14.55 0.00 0.00 2.39
3424 3716 0.451783 GCGGCCCAAAGTATGTGAAG 59.548 55.000 0.00 0.00 0.00 3.02
3549 3853 2.807045 GCACCTGACGTCGCTCAG 60.807 66.667 11.62 14.24 37.94 3.35
3613 3917 2.811317 CTGCCGCGGTCTCTTGAC 60.811 66.667 28.70 7.68 42.22 3.18
3635 3939 1.346068 ACTTGAGTCTCACCTTCTGCC 59.654 52.381 0.78 0.00 0.00 4.85
3717 4021 4.032900 GCACGTTCCTTATGTATGTGTCAG 59.967 45.833 0.00 0.00 0.00 3.51
3724 4028 4.268644 CCTTATGTATGTGTCAGCGACTTG 59.731 45.833 9.49 0.00 33.15 3.16
3735 4039 4.161565 TGTCAGCGACTTGGAGGTAATAAT 59.838 41.667 9.49 0.00 33.15 1.28
3736 4040 5.361571 TGTCAGCGACTTGGAGGTAATAATA 59.638 40.000 9.49 0.00 33.15 0.98
3737 4041 5.921408 GTCAGCGACTTGGAGGTAATAATAG 59.079 44.000 0.00 0.00 0.00 1.73
3756 4060 9.965902 AATAATAGATCACCATATCTTCCAACC 57.034 33.333 0.00 0.00 37.41 3.77
3757 4061 4.342862 AGATCACCATATCTTCCAACCG 57.657 45.455 0.00 0.00 32.09 4.44
3758 4062 2.325583 TCACCATATCTTCCAACCGC 57.674 50.000 0.00 0.00 0.00 5.68
3759 4063 1.557371 TCACCATATCTTCCAACCGCA 59.443 47.619 0.00 0.00 0.00 5.69
3760 4064 2.026729 TCACCATATCTTCCAACCGCAA 60.027 45.455 0.00 0.00 0.00 4.85
3761 4065 2.752354 CACCATATCTTCCAACCGCAAA 59.248 45.455 0.00 0.00 0.00 3.68
3762 4066 3.192422 CACCATATCTTCCAACCGCAAAA 59.808 43.478 0.00 0.00 0.00 2.44
3763 4067 3.829601 ACCATATCTTCCAACCGCAAAAA 59.170 39.130 0.00 0.00 0.00 1.94
3810 4114 3.253921 TGGCATTGTCAAGACTTGTCATG 59.746 43.478 14.53 14.53 29.54 3.07
3811 4115 3.503363 GGCATTGTCAAGACTTGTCATGA 59.497 43.478 14.53 4.81 0.00 3.07
3812 4116 4.157289 GGCATTGTCAAGACTTGTCATGAT 59.843 41.667 14.53 5.20 0.00 2.45
3813 4117 5.330295 GCATTGTCAAGACTTGTCATGATC 58.670 41.667 14.53 6.74 0.00 2.92
3814 4118 5.557388 CATTGTCAAGACTTGTCATGATCG 58.443 41.667 14.53 0.00 0.00 3.69
3815 4119 4.257267 TGTCAAGACTTGTCATGATCGT 57.743 40.909 14.75 0.00 0.00 3.73
3816 4120 4.631131 TGTCAAGACTTGTCATGATCGTT 58.369 39.130 14.75 0.00 0.00 3.85
3825 4129 7.278868 AGACTTGTCATGATCGTTTCTTAATCC 59.721 37.037 0.00 0.00 0.00 3.01
3831 4135 6.592220 TCATGATCGTTTCTTAATCCGTTTGA 59.408 34.615 0.00 0.00 0.00 2.69
3856 4160 2.613026 TGTCAAACACAGGACGACAT 57.387 45.000 0.00 0.00 36.83 3.06
3858 4162 3.649073 TGTCAAACACAGGACGACATAG 58.351 45.455 0.00 0.00 36.83 2.23
3859 4163 3.069016 TGTCAAACACAGGACGACATAGT 59.931 43.478 0.00 0.00 36.83 2.12
3861 4165 2.736721 CAAACACAGGACGACATAGTGG 59.263 50.000 0.00 0.00 34.65 4.00
3863 4167 1.819288 ACACAGGACGACATAGTGGAG 59.181 52.381 0.00 0.00 34.65 3.86
3864 4168 2.092323 CACAGGACGACATAGTGGAGA 58.908 52.381 0.00 0.00 0.00 3.71
3865 4169 2.093106 ACAGGACGACATAGTGGAGAC 58.907 52.381 0.00 0.00 0.00 3.36
3868 4177 1.331138 GGACGACATAGTGGAGACGAG 59.669 57.143 0.00 0.00 0.00 4.18
3874 4183 0.820074 ATAGTGGAGACGAGAGCCCG 60.820 60.000 0.00 0.00 0.00 6.13
3882 4191 0.029567 GACGAGAGCCCGTGTAGATG 59.970 60.000 1.07 0.00 43.49 2.90
3932 4241 2.282958 ACTCCCTCGAGCGTGGAA 60.283 61.111 6.99 0.00 40.03 3.53
3937 4246 4.421479 CTCGAGCGTGGAAGCCGT 62.421 66.667 0.00 0.00 38.01 5.68
3949 4258 0.798776 GAAGCCGTGTGTGATCCTTG 59.201 55.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.251655 TGCTGTTCAACAAATTTTGCTTTT 57.748 29.167 9.04 0.00 0.00 2.27
2 3 5.876612 TTGCTGTTCAACAAATTTTGCTT 57.123 30.435 9.04 0.94 0.00 3.91
3 4 5.876612 TTTGCTGTTCAACAAATTTTGCT 57.123 30.435 9.04 0.00 33.73 3.91
4 5 5.855395 TGTTTTGCTGTTCAACAAATTTTGC 59.145 32.000 9.04 0.00 35.81 3.68
5 6 7.590689 AGTTGTTTTGCTGTTCAACAAATTTTG 59.409 29.630 7.59 7.59 41.00 2.44
6 7 7.647228 AGTTGTTTTGCTGTTCAACAAATTTT 58.353 26.923 14.05 0.00 41.00 1.82
7 8 7.200778 AGTTGTTTTGCTGTTCAACAAATTT 57.799 28.000 14.05 0.00 41.00 1.82
8 9 6.799926 AGTTGTTTTGCTGTTCAACAAATT 57.200 29.167 14.05 0.00 41.00 1.82
9 10 6.426328 TCAAGTTGTTTTGCTGTTCAACAAAT 59.574 30.769 2.11 0.00 41.00 2.32
10 11 5.755375 TCAAGTTGTTTTGCTGTTCAACAAA 59.245 32.000 2.11 0.00 41.00 2.83
11 12 5.176590 GTCAAGTTGTTTTGCTGTTCAACAA 59.823 36.000 2.11 0.00 41.43 2.83
12 13 4.683781 GTCAAGTTGTTTTGCTGTTCAACA 59.316 37.500 2.11 0.00 41.43 3.33
13 14 4.683781 TGTCAAGTTGTTTTGCTGTTCAAC 59.316 37.500 2.11 0.00 39.95 3.18
14 15 4.876125 TGTCAAGTTGTTTTGCTGTTCAA 58.124 34.783 2.11 0.00 0.00 2.69
15 16 4.511617 TGTCAAGTTGTTTTGCTGTTCA 57.488 36.364 2.11 0.00 0.00 3.18
16 17 5.101628 TCATGTCAAGTTGTTTTGCTGTTC 58.898 37.500 2.11 0.00 0.00 3.18
17 18 5.070770 TCATGTCAAGTTGTTTTGCTGTT 57.929 34.783 2.11 0.00 0.00 3.16
18 19 4.717233 TCATGTCAAGTTGTTTTGCTGT 57.283 36.364 2.11 0.00 0.00 4.40
19 20 4.084745 GCATCATGTCAAGTTGTTTTGCTG 60.085 41.667 2.11 2.73 0.00 4.41
20 21 4.053295 GCATCATGTCAAGTTGTTTTGCT 58.947 39.130 2.11 0.00 0.00 3.91
21 22 3.121261 CGCATCATGTCAAGTTGTTTTGC 60.121 43.478 2.11 4.73 0.00 3.68
22 23 4.043750 ACGCATCATGTCAAGTTGTTTTG 58.956 39.130 2.11 0.00 0.00 2.44
23 24 4.305989 ACGCATCATGTCAAGTTGTTTT 57.694 36.364 2.11 0.00 0.00 2.43
24 25 3.988379 ACGCATCATGTCAAGTTGTTT 57.012 38.095 2.11 0.00 0.00 2.83
25 26 3.812609 TGTACGCATCATGTCAAGTTGTT 59.187 39.130 2.11 0.00 0.00 2.83
26 27 3.398406 TGTACGCATCATGTCAAGTTGT 58.602 40.909 2.11 0.00 0.00 3.32
27 28 4.403015 TTGTACGCATCATGTCAAGTTG 57.597 40.909 0.00 0.00 0.00 3.16
28 29 5.181056 TCAATTGTACGCATCATGTCAAGTT 59.819 36.000 5.13 0.00 0.00 2.66
29 30 4.694982 TCAATTGTACGCATCATGTCAAGT 59.305 37.500 5.13 0.00 0.00 3.16
30 31 5.220557 TCAATTGTACGCATCATGTCAAG 57.779 39.130 5.13 0.00 0.00 3.02
31 32 5.353678 TGATCAATTGTACGCATCATGTCAA 59.646 36.000 5.13 0.00 0.00 3.18
32 33 4.874966 TGATCAATTGTACGCATCATGTCA 59.125 37.500 5.13 0.00 0.00 3.58
33 34 5.408204 TGATCAATTGTACGCATCATGTC 57.592 39.130 5.13 0.00 0.00 3.06
34 35 6.482973 TGTATGATCAATTGTACGCATCATGT 59.517 34.615 21.24 7.30 35.46 3.21
35 36 6.890558 TGTATGATCAATTGTACGCATCATG 58.109 36.000 21.24 0.00 35.46 3.07
36 37 7.442062 TCTTGTATGATCAATTGTACGCATCAT 59.558 33.333 18.30 18.30 37.79 2.45
37 38 6.760770 TCTTGTATGATCAATTGTACGCATCA 59.239 34.615 5.13 7.24 0.00 3.07
38 39 7.177498 TCTTGTATGATCAATTGTACGCATC 57.823 36.000 5.13 1.35 0.00 3.91
39 40 7.442062 TGATCTTGTATGATCAATTGTACGCAT 59.558 33.333 5.13 7.62 46.60 4.73
40 41 6.760770 TGATCTTGTATGATCAATTGTACGCA 59.239 34.615 5.13 0.47 46.60 5.24
41 42 7.177498 TGATCTTGTATGATCAATTGTACGC 57.823 36.000 5.13 0.00 46.60 4.42
51 52 9.013229 ACAGAGAGAGTATGATCTTGTATGATC 57.987 37.037 0.00 0.00 42.19 2.92
52 53 8.938801 ACAGAGAGAGTATGATCTTGTATGAT 57.061 34.615 0.00 0.00 0.00 2.45
53 54 9.853177 TTACAGAGAGAGTATGATCTTGTATGA 57.147 33.333 0.00 0.00 0.00 2.15
86 87 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
87 88 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
88 89 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
89 90 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
90 91 9.733219 ATTACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
91 92 9.733219 GATTACTAAAGTAGTGATCTAAACGCT 57.267 33.333 11.11 0.00 44.10 5.07
99 100 9.733219 AGCGTTTAGATTACTAAAGTAGTGATC 57.267 33.333 10.62 10.62 46.38 2.92
100 101 9.733219 GAGCGTTTAGATTACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
101 102 8.954350 AGAGCGTTTAGATTACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
102 103 9.570488 AAGAGCGTTTAGATTACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
111 112 9.654663 AAGAAATGTAAGAGCGTTTAGATTACT 57.345 29.630 6.22 0.00 29.47 2.24
115 116 8.592998 CGTAAAGAAATGTAAGAGCGTTTAGAT 58.407 33.333 0.00 0.00 0.00 1.98
116 117 7.062605 CCGTAAAGAAATGTAAGAGCGTTTAGA 59.937 37.037 0.00 0.00 0.00 2.10
117 118 7.062605 TCCGTAAAGAAATGTAAGAGCGTTTAG 59.937 37.037 0.00 0.00 0.00 1.85
118 119 6.867816 TCCGTAAAGAAATGTAAGAGCGTTTA 59.132 34.615 0.00 0.00 0.00 2.01
119 120 5.697633 TCCGTAAAGAAATGTAAGAGCGTTT 59.302 36.000 0.00 0.00 0.00 3.60
120 121 5.232463 TCCGTAAAGAAATGTAAGAGCGTT 58.768 37.500 0.00 0.00 0.00 4.84
121 122 4.813027 TCCGTAAAGAAATGTAAGAGCGT 58.187 39.130 0.00 0.00 0.00 5.07
122 123 4.267928 CCTCCGTAAAGAAATGTAAGAGCG 59.732 45.833 0.00 0.00 0.00 5.03
123 124 4.571176 CCCTCCGTAAAGAAATGTAAGAGC 59.429 45.833 0.00 0.00 0.00 4.09
124 125 5.974108 TCCCTCCGTAAAGAAATGTAAGAG 58.026 41.667 0.00 0.00 0.00 2.85
125 126 5.482878 ACTCCCTCCGTAAAGAAATGTAAGA 59.517 40.000 0.00 0.00 0.00 2.10
126 127 5.731591 ACTCCCTCCGTAAAGAAATGTAAG 58.268 41.667 0.00 0.00 0.00 2.34
127 128 5.750352 ACTCCCTCCGTAAAGAAATGTAA 57.250 39.130 0.00 0.00 0.00 2.41
128 129 5.716228 TGTACTCCCTCCGTAAAGAAATGTA 59.284 40.000 0.00 0.00 0.00 2.29
129 130 4.529377 TGTACTCCCTCCGTAAAGAAATGT 59.471 41.667 0.00 0.00 0.00 2.71
130 131 5.080969 TGTACTCCCTCCGTAAAGAAATG 57.919 43.478 0.00 0.00 0.00 2.32
131 132 5.338137 CCTTGTACTCCCTCCGTAAAGAAAT 60.338 44.000 0.00 0.00 0.00 2.17
132 133 4.020839 CCTTGTACTCCCTCCGTAAAGAAA 60.021 45.833 0.00 0.00 0.00 2.52
133 134 3.512724 CCTTGTACTCCCTCCGTAAAGAA 59.487 47.826 0.00 0.00 0.00 2.52
134 135 3.094572 CCTTGTACTCCCTCCGTAAAGA 58.905 50.000 0.00 0.00 0.00 2.52
135 136 2.830321 ACCTTGTACTCCCTCCGTAAAG 59.170 50.000 0.00 0.00 0.00 1.85
136 137 2.893424 ACCTTGTACTCCCTCCGTAAA 58.107 47.619 0.00 0.00 0.00 2.01
137 138 2.610438 ACCTTGTACTCCCTCCGTAA 57.390 50.000 0.00 0.00 0.00 3.18
138 139 3.202818 TCATACCTTGTACTCCCTCCGTA 59.797 47.826 0.00 0.00 0.00 4.02
139 140 2.024655 TCATACCTTGTACTCCCTCCGT 60.025 50.000 0.00 0.00 0.00 4.69
140 141 2.623889 CTCATACCTTGTACTCCCTCCG 59.376 54.545 0.00 0.00 0.00 4.63
141 142 2.966516 CCTCATACCTTGTACTCCCTCC 59.033 54.545 0.00 0.00 0.00 4.30
142 143 3.644335 ACCTCATACCTTGTACTCCCTC 58.356 50.000 0.00 0.00 0.00 4.30
143 144 3.778622 ACCTCATACCTTGTACTCCCT 57.221 47.619 0.00 0.00 0.00 4.20
144 145 4.583907 GTCTACCTCATACCTTGTACTCCC 59.416 50.000 0.00 0.00 0.00 4.30
145 146 4.583907 GGTCTACCTCATACCTTGTACTCC 59.416 50.000 0.00 0.00 0.00 3.85
146 147 5.067544 GTGGTCTACCTCATACCTTGTACTC 59.932 48.000 0.02 0.00 36.82 2.59
147 148 4.954826 GTGGTCTACCTCATACCTTGTACT 59.045 45.833 0.02 0.00 36.82 2.73
148 149 4.201990 CGTGGTCTACCTCATACCTTGTAC 60.202 50.000 0.02 0.00 36.82 2.90
149 150 3.949754 CGTGGTCTACCTCATACCTTGTA 59.050 47.826 0.02 0.00 36.82 2.41
150 151 2.758979 CGTGGTCTACCTCATACCTTGT 59.241 50.000 0.02 0.00 36.82 3.16
151 152 2.758979 ACGTGGTCTACCTCATACCTTG 59.241 50.000 0.02 0.00 36.82 3.61
152 153 3.097342 ACGTGGTCTACCTCATACCTT 57.903 47.619 0.02 0.00 36.82 3.50
153 154 2.822707 ACGTGGTCTACCTCATACCT 57.177 50.000 0.02 0.00 36.82 3.08
154 155 3.194116 TCAAACGTGGTCTACCTCATACC 59.806 47.826 0.02 0.00 36.82 2.73
155 156 4.082354 AGTCAAACGTGGTCTACCTCATAC 60.082 45.833 0.02 0.00 36.82 2.39
156 157 4.082408 CAGTCAAACGTGGTCTACCTCATA 60.082 45.833 0.02 0.00 36.82 2.15
157 158 2.897969 AGTCAAACGTGGTCTACCTCAT 59.102 45.455 0.02 0.00 36.82 2.90
158 159 2.035449 CAGTCAAACGTGGTCTACCTCA 59.965 50.000 0.02 0.00 36.82 3.86
159 160 2.035576 ACAGTCAAACGTGGTCTACCTC 59.964 50.000 0.02 0.00 36.82 3.85
160 161 2.037144 ACAGTCAAACGTGGTCTACCT 58.963 47.619 0.02 0.00 36.82 3.08
161 162 2.521105 ACAGTCAAACGTGGTCTACC 57.479 50.000 0.00 0.00 0.00 3.18
171 172 0.372334 ACGCGTGACAACAGTCAAAC 59.628 50.000 12.93 0.00 43.37 2.93
202 203 5.261216 TGGAAGAAAGAAAAACCTCACAGT 58.739 37.500 0.00 0.00 0.00 3.55
228 229 1.712081 CACTGCATTTCCTCGCTCG 59.288 57.895 0.00 0.00 0.00 5.03
230 231 1.302752 TGCACTGCATTTCCTCGCT 60.303 52.632 0.00 0.00 31.71 4.93
239 240 2.139323 ATTGATCTGGTGCACTGCAT 57.861 45.000 17.98 5.73 41.91 3.96
242 243 5.220989 CCTCAATTATTGATCTGGTGCACTG 60.221 44.000 17.98 10.30 39.30 3.66
269 274 4.497340 CCTCGTTTAGCTTTTCAAACTGCA 60.497 41.667 7.93 0.00 33.43 4.41
283 288 2.146920 AGTCTCCCTCCCTCGTTTAG 57.853 55.000 0.00 0.00 0.00 1.85
303 308 3.036431 TGGCGAGAGTCAAGTCTCA 57.964 52.632 13.76 0.00 46.60 3.27
311 323 1.509004 GAGAGGTGTGGCGAGAGTC 59.491 63.158 0.00 0.00 0.00 3.36
343 355 4.496927 CCGGAAATGCAAGGGCGC 62.497 66.667 0.00 0.00 45.35 6.53
373 386 2.315386 GGTCGGCGTGTCTTGGTTC 61.315 63.158 6.85 0.00 0.00 3.62
401 414 4.838152 CAGGGACGGCCGATGGTG 62.838 72.222 35.90 19.35 33.83 4.17
403 416 4.530857 GTCAGGGACGGCCGATGG 62.531 72.222 35.90 16.04 33.83 3.51
404 417 4.530857 GGTCAGGGACGGCCGATG 62.531 72.222 35.90 23.16 32.65 3.84
405 418 4.779733 AGGTCAGGGACGGCCGAT 62.780 66.667 35.90 16.95 32.65 4.18
409 422 3.775654 CTGGAGGTCAGGGACGGC 61.776 72.222 0.00 0.00 39.76 5.68
410 423 3.775654 GCTGGAGGTCAGGGACGG 61.776 72.222 0.00 0.00 43.54 4.79
411 424 3.775654 GGCTGGAGGTCAGGGACG 61.776 72.222 0.00 0.00 43.54 4.79
412 425 3.775654 CGGCTGGAGGTCAGGGAC 61.776 72.222 0.00 0.00 43.54 4.46
415 428 4.463879 CAGCGGCTGGAGGTCAGG 62.464 72.222 22.11 0.00 43.54 3.86
416 429 2.947532 TTCAGCGGCTGGAGGTCAG 61.948 63.158 28.18 1.61 46.03 3.51
417 430 2.922503 TTCAGCGGCTGGAGGTCA 60.923 61.111 28.18 6.43 31.51 4.02
418 431 2.435059 GTTCAGCGGCTGGAGGTC 60.435 66.667 28.18 5.88 31.51 3.85
419 432 4.379243 CGTTCAGCGGCTGGAGGT 62.379 66.667 28.18 0.00 36.85 3.85
469 532 0.908198 GCTGAAGGTCAGGAGATGGT 59.092 55.000 7.34 0.00 44.43 3.55
470 533 0.179936 GGCTGAAGGTCAGGAGATGG 59.820 60.000 7.34 0.00 44.43 3.51
606 702 1.433053 CGCCATTAAATCGTCCGGCA 61.433 55.000 0.00 0.00 39.56 5.69
616 712 0.253610 ACACCGGATCCGCCATTAAA 59.746 50.000 29.12 0.00 38.24 1.52
721 826 3.777087 TGCATCAAAATTGAGGAGGGAA 58.223 40.909 11.61 0.00 41.15 3.97
733 838 0.179166 GCTTCCGCGATGCATCAAAA 60.179 50.000 25.70 12.40 33.71 2.44
828 933 2.493675 TCGTTGAACAGCTGCTCTAGAT 59.506 45.455 15.27 0.00 0.00 1.98
832 937 1.274728 AGATCGTTGAACAGCTGCTCT 59.725 47.619 15.27 0.00 0.00 4.09
869 974 2.775911 TCCAAGATGTCCTCTGCTTG 57.224 50.000 0.00 0.00 37.93 4.01
910 1015 9.194972 AGATAGTCATCTTGTATCTGTTTCTCA 57.805 33.333 0.00 0.00 38.41 3.27
965 1071 4.395542 AGAGCTTCTTCACATGATTCTTGC 59.604 41.667 0.00 0.00 0.00 4.01
1026 1132 0.326264 AGAGGCAGTAAAGCACCTGG 59.674 55.000 0.00 0.00 35.83 4.45
1182 1300 7.865706 AAGGATATGGTTGCTAAGTTGTAAG 57.134 36.000 0.00 0.00 0.00 2.34
1211 1329 4.989279 AATATGGTTCATCGCTTTTGCT 57.011 36.364 0.00 0.00 44.80 3.91
1289 1442 5.287226 ACGGATCCGAGAAACATACATTAC 58.713 41.667 39.55 0.00 42.83 1.89
1323 1477 3.119316 AAGCGAGAAGTCGATGAATGAGT 60.119 43.478 0.00 0.00 46.16 3.41
1336 1490 5.107875 GCAAAACAAAATACCAAGCGAGAAG 60.108 40.000 0.00 0.00 0.00 2.85
1367 1522 6.169419 TCAACTCGATTTTTGACATGCTAG 57.831 37.500 0.00 0.00 0.00 3.42
1369 1524 5.437289 TTCAACTCGATTTTTGACATGCT 57.563 34.783 0.00 0.00 31.42 3.79
1619 1780 5.093285 CGATTACGGAATAGCATTGAGCCT 61.093 45.833 0.00 0.00 38.96 4.58
1749 1949 5.772393 TGGTATCCACACTAAAATCCTGT 57.228 39.130 0.00 0.00 0.00 4.00
1852 2052 3.976942 CGTTTTCCATGCAGTTTCTTCTG 59.023 43.478 0.00 0.00 38.35 3.02
2040 2240 4.080129 AGCAGTGACATGGGAATACATCTT 60.080 41.667 0.00 0.00 0.00 2.40
2136 2336 5.578727 AGTTGCAATGTCTTCGAGTCTTATC 59.421 40.000 0.59 0.00 0.00 1.75
2203 2403 1.021390 CGTAGCTGCCCTCCAACAAG 61.021 60.000 0.00 0.00 0.00 3.16
2576 2776 1.620822 ACAATCACTTCCAGCAACCC 58.379 50.000 0.00 0.00 0.00 4.11
2637 2858 6.581388 TCCTCTTCACATCCTTCCATTATT 57.419 37.500 0.00 0.00 0.00 1.40
2658 2882 1.295746 GACGTCTGGGGGAACTTCC 59.704 63.158 8.70 0.00 35.23 3.46
2730 2954 0.031857 TGCGCAGGTTGTCCAATTTG 59.968 50.000 5.66 0.00 35.89 2.32
2780 3004 4.141892 TGACGGTTTTCTCCTCAACTTGTA 60.142 41.667 0.00 0.00 0.00 2.41
2797 3021 2.167693 TCACAAACAGACTCTTGACGGT 59.832 45.455 1.62 0.00 0.00 4.83
2798 3022 2.797156 CTCACAAACAGACTCTTGACGG 59.203 50.000 1.62 0.00 0.00 4.79
2962 3254 2.028876 TCACGAGAGTTGAACACCAGA 58.971 47.619 0.00 0.00 46.40 3.86
2963 3255 2.509052 TCACGAGAGTTGAACACCAG 57.491 50.000 0.00 0.00 46.40 4.00
3085 3377 2.365293 CCCTTGTTCCTTTCCCACTTTG 59.635 50.000 0.00 0.00 0.00 2.77
3133 3425 2.192861 TTTGCCACGGAGCTGGTTG 61.193 57.895 0.00 0.00 32.63 3.77
3142 3434 0.999406 CGATACTCAGTTTGCCACGG 59.001 55.000 0.00 0.00 0.00 4.94
3145 3437 0.739462 CCGCGATACTCAGTTTGCCA 60.739 55.000 8.23 0.00 0.00 4.92
3239 3531 0.034756 TCATGACCCCACGACAGTTG 59.965 55.000 0.00 0.00 0.00 3.16
3260 3552 4.732672 TCAACTCTCCTCTCACATCATG 57.267 45.455 0.00 0.00 0.00 3.07
3261 3553 5.022122 TCTTCAACTCTCCTCTCACATCAT 58.978 41.667 0.00 0.00 0.00 2.45
3262 3554 4.411013 TCTTCAACTCTCCTCTCACATCA 58.589 43.478 0.00 0.00 0.00 3.07
3263 3555 5.398603 TTCTTCAACTCTCCTCTCACATC 57.601 43.478 0.00 0.00 0.00 3.06
3264 3556 5.070981 TGTTTCTTCAACTCTCCTCTCACAT 59.929 40.000 0.00 0.00 36.21 3.21
3265 3557 4.405680 TGTTTCTTCAACTCTCCTCTCACA 59.594 41.667 0.00 0.00 36.21 3.58
3266 3558 4.950050 TGTTTCTTCAACTCTCCTCTCAC 58.050 43.478 0.00 0.00 36.21 3.51
3267 3559 4.039730 CCTGTTTCTTCAACTCTCCTCTCA 59.960 45.833 0.00 0.00 36.21 3.27
3298 3590 2.177594 GACCCTCCAGCACCTCTGTG 62.178 65.000 0.00 0.00 45.65 3.66
3325 3617 0.659957 GTGATTCGAGATGCTTGGGC 59.340 55.000 0.00 0.00 39.26 5.36
3349 3641 5.069648 TCTCAAGCCATGGTAAGAGTAGATG 59.930 44.000 14.67 0.00 0.00 2.90
3379 3671 1.355381 TGCTCACCCATCATCCAACTT 59.645 47.619 0.00 0.00 0.00 2.66
3382 3674 0.392863 CGTGCTCACCCATCATCCAA 60.393 55.000 0.00 0.00 0.00 3.53
3402 3694 3.887868 CATACTTTGGGCCGCCGC 61.888 66.667 2.55 0.00 0.00 6.53
3419 3711 2.614229 GGAAGAGGCTGAGTTCCTTCAC 60.614 54.545 11.89 0.98 37.38 3.18
3424 3716 2.363683 CAATGGAAGAGGCTGAGTTCC 58.636 52.381 11.34 11.34 40.29 3.62
3613 3917 3.367910 GGCAGAAGGTGAGACTCAAGTAG 60.368 52.174 6.76 0.00 0.00 2.57
3627 3931 1.134189 TCAGCATCTCATGGCAGAAGG 60.134 52.381 0.00 0.00 0.00 3.46
3635 3939 1.527311 CGCACTCATCAGCATCTCATG 59.473 52.381 0.00 0.00 0.00 3.07
3689 3993 5.121611 CACATACATAAGGAACGTGCTGAAA 59.878 40.000 0.00 0.00 0.00 2.69
3717 4021 6.586844 GTGATCTATTATTACCTCCAAGTCGC 59.413 42.308 0.00 0.00 0.00 5.19
3735 4039 4.262463 GCGGTTGGAAGATATGGTGATCTA 60.262 45.833 0.00 0.00 35.01 1.98
3736 4040 3.495100 GCGGTTGGAAGATATGGTGATCT 60.495 47.826 0.00 0.00 37.81 2.75
3737 4041 2.808543 GCGGTTGGAAGATATGGTGATC 59.191 50.000 0.00 0.00 0.00 2.92
3769 4073 4.837860 TGCCAAGGAAGATATGGTGTTTTT 59.162 37.500 0.00 0.00 36.57 1.94
3770 4074 4.415596 TGCCAAGGAAGATATGGTGTTTT 58.584 39.130 0.00 0.00 36.57 2.43
3771 4075 4.046286 TGCCAAGGAAGATATGGTGTTT 57.954 40.909 0.00 0.00 36.57 2.83
3772 4076 3.737559 TGCCAAGGAAGATATGGTGTT 57.262 42.857 0.00 0.00 36.57 3.32
3773 4077 3.956199 CAATGCCAAGGAAGATATGGTGT 59.044 43.478 0.00 0.00 36.57 4.16
3774 4078 3.956199 ACAATGCCAAGGAAGATATGGTG 59.044 43.478 0.00 0.00 36.57 4.17
3775 4079 4.210331 GACAATGCCAAGGAAGATATGGT 58.790 43.478 0.00 0.00 36.57 3.55
3776 4080 4.209538 TGACAATGCCAAGGAAGATATGG 58.790 43.478 0.00 0.00 37.29 2.74
3777 4081 5.591472 TCTTGACAATGCCAAGGAAGATATG 59.409 40.000 9.34 0.00 40.88 1.78
3778 4082 5.591877 GTCTTGACAATGCCAAGGAAGATAT 59.408 40.000 9.34 0.00 40.88 1.63
3779 4083 4.943705 GTCTTGACAATGCCAAGGAAGATA 59.056 41.667 9.34 0.00 40.88 1.98
3780 4084 3.760684 GTCTTGACAATGCCAAGGAAGAT 59.239 43.478 9.34 0.00 40.88 2.40
3781 4085 3.149196 GTCTTGACAATGCCAAGGAAGA 58.851 45.455 9.34 0.00 40.88 2.87
3782 4086 3.152341 AGTCTTGACAATGCCAAGGAAG 58.848 45.455 9.34 0.00 40.88 3.46
3783 4087 3.228188 AGTCTTGACAATGCCAAGGAA 57.772 42.857 9.34 0.00 40.88 3.36
3784 4088 2.886523 CAAGTCTTGACAATGCCAAGGA 59.113 45.455 9.34 0.00 40.88 3.36
3785 4089 2.624838 ACAAGTCTTGACAATGCCAAGG 59.375 45.455 19.53 0.00 40.88 3.61
3786 4090 3.316029 TGACAAGTCTTGACAATGCCAAG 59.684 43.478 19.53 2.76 41.63 3.61
3810 4114 9.207042 GTTTATCAAACGGATTAAGAAACGATC 57.793 33.333 0.00 0.00 37.44 3.69
3811 4115 8.943002 AGTTTATCAAACGGATTAAGAAACGAT 58.057 29.630 0.00 0.00 45.88 3.73
3812 4116 8.225107 CAGTTTATCAAACGGATTAAGAAACGA 58.775 33.333 0.00 0.00 45.88 3.85
3813 4117 8.013378 ACAGTTTATCAAACGGATTAAGAAACG 58.987 33.333 8.56 0.00 45.88 3.60
3814 4118 9.326339 GACAGTTTATCAAACGGATTAAGAAAC 57.674 33.333 8.56 0.00 45.88 2.78
3815 4119 9.058174 TGACAGTTTATCAAACGGATTAAGAAA 57.942 29.630 8.56 0.00 45.88 2.52
3816 4120 8.610248 TGACAGTTTATCAAACGGATTAAGAA 57.390 30.769 8.56 0.00 45.88 2.52
3847 4151 1.065636 TCGTCTCCACTATGTCGTCCT 60.066 52.381 0.00 0.00 0.00 3.85
3848 4152 1.331138 CTCGTCTCCACTATGTCGTCC 59.669 57.143 0.00 0.00 0.00 4.79
3849 4153 2.277969 TCTCGTCTCCACTATGTCGTC 58.722 52.381 0.00 0.00 0.00 4.20
3850 4154 2.281517 CTCTCGTCTCCACTATGTCGT 58.718 52.381 0.00 0.00 0.00 4.34
3852 4156 1.335496 GGCTCTCGTCTCCACTATGTC 59.665 57.143 0.00 0.00 0.00 3.06
3853 4157 1.394618 GGCTCTCGTCTCCACTATGT 58.605 55.000 0.00 0.00 0.00 2.29
3854 4158 0.671251 GGGCTCTCGTCTCCACTATG 59.329 60.000 0.00 0.00 0.00 2.23
3855 4159 0.820074 CGGGCTCTCGTCTCCACTAT 60.820 60.000 0.00 0.00 0.00 2.12
3856 4160 1.451567 CGGGCTCTCGTCTCCACTA 60.452 63.158 0.00 0.00 0.00 2.74
3858 4162 3.063084 ACGGGCTCTCGTCTCCAC 61.063 66.667 0.00 0.00 39.34 4.02
3859 4163 2.473891 TACACGGGCTCTCGTCTCCA 62.474 60.000 0.00 0.00 41.86 3.86
3861 4165 0.743701 TCTACACGGGCTCTCGTCTC 60.744 60.000 0.00 0.00 41.86 3.36
3863 4167 0.029567 CATCTACACGGGCTCTCGTC 59.970 60.000 0.00 0.00 41.86 4.20
3864 4168 1.384989 CCATCTACACGGGCTCTCGT 61.385 60.000 0.00 0.00 44.91 4.18
3865 4169 1.360551 CCATCTACACGGGCTCTCG 59.639 63.158 0.00 0.00 0.00 4.04
3868 4177 2.279517 CGCCATCTACACGGGCTC 60.280 66.667 0.00 0.00 45.53 4.70
3874 4183 4.530857 AGCCGCCGCCATCTACAC 62.531 66.667 0.00 0.00 34.57 2.90
3882 4191 4.838152 TGATGAAGAGCCGCCGCC 62.838 66.667 0.00 0.00 34.57 6.13
3932 4241 0.396435 TTCAAGGATCACACACGGCT 59.604 50.000 0.00 0.00 0.00 5.52
3936 4245 1.537202 GCAGGTTCAAGGATCACACAC 59.463 52.381 0.00 0.00 0.00 3.82
3937 4246 1.545428 GGCAGGTTCAAGGATCACACA 60.545 52.381 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.