Multiple sequence alignment - TraesCS3D01G321000

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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 TraesCS3D01G321000 chr3D 100.000 2195 0 0 1 2195 433822245 433824439 0.000000e+00 4054.0
1 TraesCS3D01G321000 chr3D 75.922 515 91 19 1621 2122 280012653 280012159 1.310000e-57 233.0
2 TraesCS3D01G321000 chr3D 100.000 28 0 0 1430 1457 433823701 433823674 4.000000e-03 52.8
3 TraesCS3D01G321000 chr3B 90.486 988 58 20 363 1323 567135798 567136776 0.000000e+00 1271.0
4 TraesCS3D01G321000 chr3A 85.924 1229 123 17 991 2180 572527956 572529173 0.000000e+00 1266.0
5 TraesCS3D01G321000 chr3A 87.822 698 62 13 169 850 572527065 572527755 0.000000e+00 797.0
6 TraesCS3D01G321000 chr3A 75.351 499 92 17 1635 2119 502744940 502745421 6.140000e-51 211.0
7 TraesCS3D01G321000 chr3A 75.399 439 82 15 1692 2122 200736742 200736322 2.880000e-44 189.0
8 TraesCS3D01G321000 chr3A 92.000 125 9 1 10 133 56968021 56967897 8.060000e-40 174.0
9 TraesCS3D01G321000 chr3A 79.681 251 44 6 1876 2122 497618894 497618647 8.060000e-40 174.0
10 TraesCS3D01G321000 chr3A 94.595 37 2 0 926 962 572527907 572527943 8.460000e-05 58.4
11 TraesCS3D01G321000 chr7D 75.581 516 93 22 1621 2122 104488516 104488020 7.890000e-55 224.0
12 TraesCS3D01G321000 chr6A 75.586 512 92 19 1621 2119 573382453 573382944 2.840000e-54 222.0
13 TraesCS3D01G321000 chr6D 75.435 517 92 22 1621 2122 257141486 257140990 3.670000e-53 219.0
14 TraesCS3D01G321000 chr6D 97.917 96 2 0 34 129 78768765 78768670 1.350000e-37 167.0
15 TraesCS3D01G321000 chr5A 95.556 135 5 1 1 135 355856647 355856514 4.750000e-52 215.0
16 TraesCS3D01G321000 chr5A 78.199 211 36 7 1621 1824 459265691 459265484 2.290000e-25 126.0
17 TraesCS3D01G321000 chr7A 75.194 516 93 19 1621 2122 373150376 373149882 6.140000e-51 211.0
18 TraesCS3D01G321000 chr7A 74.806 516 95 23 1621 2122 658707454 658706960 1.330000e-47 200.0
19 TraesCS3D01G321000 chr7A 74.517 518 93 16 1621 2119 410761259 410761756 2.880000e-44 189.0
20 TraesCS3D01G321000 chr4A 75.000 512 94 22 1621 2119 408934861 408935351 2.860000e-49 206.0
21 TraesCS3D01G321000 chr4A 74.648 497 96 19 1639 2122 334720414 334719935 2.220000e-45 193.0
22 TraesCS3D01G321000 chr7B 95.868 121 5 0 1 121 103614536 103614656 1.720000e-46 196.0
23 TraesCS3D01G321000 chr7B 79.621 211 34 4 1621 1824 345537598 345537806 2.270000e-30 143.0
24 TraesCS3D01G321000 chr4B 95.868 121 5 0 9 129 450852611 450852731 1.720000e-46 196.0
25 TraesCS3D01G321000 chr4B 91.852 135 6 3 1 130 639473349 639473483 1.340000e-42 183.0
26 TraesCS3D01G321000 chr2A 74.560 511 99 22 1621 2119 77483138 77483629 6.180000e-46 195.0
27 TraesCS3D01G321000 chr2A 87.500 56 7 0 2130 2185 523864488 523864543 5.060000e-07 65.8
28 TraesCS3D01G321000 chr1D 93.798 129 6 2 2 128 476403230 476403358 2.220000e-45 193.0
29 TraesCS3D01G321000 chr1A 93.651 126 3 3 1 125 578778254 578778133 1.340000e-42 183.0
30 TraesCS3D01G321000 chr6B 93.458 107 7 0 23 129 2806617 2806723 2.260000e-35 159.0
31 TraesCS3D01G321000 chr5D 80.189 212 31 7 1621 1824 260383383 260383175 4.880000e-32 148.0
32 TraesCS3D01G321000 chr2B 97.143 35 1 0 2130 2164 458243814 458243848 2.350000e-05 60.2


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 TraesCS3D01G321000 chr3D 433822245 433824439 2194 False 4054.000000 4054 100.000 1 2195 1 chr3D.!!$F1 2194
1 TraesCS3D01G321000 chr3B 567135798 567136776 978 False 1271.000000 1271 90.486 363 1323 1 chr3B.!!$F1 960
2 TraesCS3D01G321000 chr3A 572527065 572529173 2108 False 707.133333 1266 89.447 169 2180 3 chr3A.!!$F2 2011

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
63 64 0.17691 GGAGAGGGAAGGCGAGAAAG 59.823 60.0 0.0 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 2095 0.036483 TGTCATGATGGACCACACGG 60.036 55.0 0.0 0.0 36.97 4.94 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
54 55 3.532155 CGGCGAGGGAGAGGGAAG 61.532 72.222 0.00 0.00 0.00 3.46
55 56 3.157949 GGCGAGGGAGAGGGAAGG 61.158 72.222 0.00 0.00 0.00 3.46
56 57 3.855853 GCGAGGGAGAGGGAAGGC 61.856 72.222 0.00 0.00 0.00 4.35
57 58 3.532155 CGAGGGAGAGGGAAGGCG 61.532 72.222 0.00 0.00 0.00 5.52
58 59 2.042843 GAGGGAGAGGGAAGGCGA 60.043 66.667 0.00 0.00 0.00 5.54
59 60 2.042435 AGGGAGAGGGAAGGCGAG 60.042 66.667 0.00 0.00 0.00 5.03
60 61 2.042843 GGGAGAGGGAAGGCGAGA 60.043 66.667 0.00 0.00 0.00 4.04
61 62 1.686110 GGGAGAGGGAAGGCGAGAA 60.686 63.158 0.00 0.00 0.00 2.87
62 63 1.265454 GGGAGAGGGAAGGCGAGAAA 61.265 60.000 0.00 0.00 0.00 2.52
63 64 0.176910 GGAGAGGGAAGGCGAGAAAG 59.823 60.000 0.00 0.00 0.00 2.62
64 65 0.176910 GAGAGGGAAGGCGAGAAAGG 59.823 60.000 0.00 0.00 0.00 3.11
65 66 1.222113 GAGGGAAGGCGAGAAAGGG 59.778 63.158 0.00 0.00 0.00 3.95
66 67 2.258748 GAGGGAAGGCGAGAAAGGGG 62.259 65.000 0.00 0.00 0.00 4.79
67 68 2.298661 GGGAAGGCGAGAAAGGGGA 61.299 63.158 0.00 0.00 0.00 4.81
68 69 1.222113 GGAAGGCGAGAAAGGGGAG 59.778 63.158 0.00 0.00 0.00 4.30
69 70 1.450491 GAAGGCGAGAAAGGGGAGC 60.450 63.158 0.00 0.00 0.00 4.70
70 71 3.316573 AAGGCGAGAAAGGGGAGCG 62.317 63.158 0.00 0.00 0.00 5.03
71 72 4.840005 GGCGAGAAAGGGGAGCGG 62.840 72.222 0.00 0.00 0.00 5.52
74 75 4.840005 GAGAAAGGGGAGCGGCGG 62.840 72.222 9.78 0.00 0.00 6.13
89 90 3.912907 CGGCGGCGATCTAGGGTT 61.913 66.667 29.19 0.00 0.00 4.11
90 91 2.029221 GGCGGCGATCTAGGGTTC 59.971 66.667 12.98 0.00 0.00 3.62
91 92 2.029221 GCGGCGATCTAGGGTTCC 59.971 66.667 12.98 0.00 0.00 3.62
92 93 2.335369 CGGCGATCTAGGGTTCCG 59.665 66.667 0.00 0.00 0.00 4.30
93 94 2.029221 GGCGATCTAGGGTTCCGC 59.971 66.667 0.00 0.00 44.45 5.54
94 95 2.029221 GCGATCTAGGGTTCCGCC 59.971 66.667 0.00 0.00 39.97 6.13
149 150 2.002505 CGGGGTCTCCTGTATCATCT 57.997 55.000 0.00 0.00 34.69 2.90
150 151 1.889829 CGGGGTCTCCTGTATCATCTC 59.110 57.143 0.00 0.00 34.69 2.75
151 152 2.489985 CGGGGTCTCCTGTATCATCTCT 60.490 54.545 0.00 0.00 34.69 3.10
152 153 3.244946 CGGGGTCTCCTGTATCATCTCTA 60.245 52.174 0.00 0.00 34.69 2.43
153 154 4.340617 GGGGTCTCCTGTATCATCTCTAG 58.659 52.174 0.00 0.00 0.00 2.43
154 155 4.340617 GGGTCTCCTGTATCATCTCTAGG 58.659 52.174 0.00 0.00 0.00 3.02
155 156 4.202631 GGGTCTCCTGTATCATCTCTAGGT 60.203 50.000 0.00 0.00 0.00 3.08
156 157 5.007682 GGTCTCCTGTATCATCTCTAGGTC 58.992 50.000 0.00 0.00 0.00 3.85
157 158 5.222048 GGTCTCCTGTATCATCTCTAGGTCT 60.222 48.000 0.00 0.00 0.00 3.85
158 159 6.303839 GTCTCCTGTATCATCTCTAGGTCTT 58.696 44.000 0.00 0.00 0.00 3.01
159 160 6.206634 GTCTCCTGTATCATCTCTAGGTCTTG 59.793 46.154 0.00 0.00 0.00 3.02
160 161 6.019656 TCCTGTATCATCTCTAGGTCTTGT 57.980 41.667 0.00 0.00 0.00 3.16
161 162 6.436027 TCCTGTATCATCTCTAGGTCTTGTT 58.564 40.000 0.00 0.00 0.00 2.83
162 163 7.583625 TCCTGTATCATCTCTAGGTCTTGTTA 58.416 38.462 0.00 0.00 0.00 2.41
163 164 7.502895 TCCTGTATCATCTCTAGGTCTTGTTAC 59.497 40.741 0.00 0.00 0.00 2.50
164 165 7.255660 CCTGTATCATCTCTAGGTCTTGTTACC 60.256 44.444 0.00 0.00 40.06 2.85
165 166 7.123383 TGTATCATCTCTAGGTCTTGTTACCA 58.877 38.462 0.00 0.00 42.40 3.25
166 167 7.618117 TGTATCATCTCTAGGTCTTGTTACCAA 59.382 37.037 0.00 0.00 42.40 3.67
167 168 6.928348 TCATCTCTAGGTCTTGTTACCAAA 57.072 37.500 0.00 0.00 42.40 3.28
188 189 4.766404 AAAAACCTTCCGTGATTAGCAG 57.234 40.909 0.00 0.00 0.00 4.24
194 196 1.460504 TCCGTGATTAGCAGACGTCT 58.539 50.000 13.58 13.58 0.00 4.18
196 198 1.457738 CGTGATTAGCAGACGTCTCG 58.542 55.000 16.96 12.53 0.00 4.04
199 201 1.472878 TGATTAGCAGACGTCTCGCTT 59.527 47.619 32.46 22.31 37.20 4.68
200 202 2.113289 GATTAGCAGACGTCTCGCTTC 58.887 52.381 32.46 24.80 37.20 3.86
202 204 2.019948 TAGCAGACGTCTCGCTTCTA 57.980 50.000 32.46 20.07 37.20 2.10
207 209 2.095668 CAGACGTCTCGCTTCTAACACT 60.096 50.000 16.96 0.00 0.00 3.55
236 241 2.413371 GCTGTTTTCATGGTCTCGCTTC 60.413 50.000 0.00 0.00 0.00 3.86
239 244 1.019278 TTTCATGGTCTCGCTTCGGC 61.019 55.000 0.00 0.00 37.65 5.54
269 274 2.783135 GAGCCCTGAGACATTTTGACA 58.217 47.619 0.00 0.00 0.00 3.58
272 277 2.485814 GCCCTGAGACATTTTGACAGTC 59.514 50.000 0.00 0.00 0.00 3.51
276 281 3.476552 TGAGACATTTTGACAGTCCCAC 58.523 45.455 0.00 0.00 32.82 4.61
282 290 4.706476 ACATTTTGACAGTCCCACCATATG 59.294 41.667 0.00 0.00 0.00 1.78
318 326 4.699735 TGCATCCGTGTCAAGTTAATGAAT 59.300 37.500 0.00 0.00 0.00 2.57
319 327 5.163764 TGCATCCGTGTCAAGTTAATGAATC 60.164 40.000 0.00 0.00 0.00 2.52
335 344 9.000018 GTTAATGAATCATCGTGCTTTTTACTC 58.000 33.333 0.00 0.00 0.00 2.59
340 349 6.604735 ATCATCGTGCTTTTTACTCCATAC 57.395 37.500 0.00 0.00 0.00 2.39
345 354 7.298507 TCGTGCTTTTTACTCCATACATTAC 57.701 36.000 0.00 0.00 0.00 1.89
346 355 6.874664 TCGTGCTTTTTACTCCATACATTACA 59.125 34.615 0.00 0.00 0.00 2.41
349 358 9.503427 GTGCTTTTTACTCCATACATTACAATC 57.497 33.333 0.00 0.00 0.00 2.67
394 404 2.027024 ACGCTCTCGACAAACGCA 59.973 55.556 0.00 0.00 42.26 5.24
416 433 1.011904 CGATGCGCGTCCAATCAAG 60.012 57.895 23.36 4.06 34.64 3.02
491 508 1.658686 CTACGCAAGCGAGGGAGACT 61.659 60.000 22.30 0.00 42.83 3.24
503 520 1.087501 GGGAGACTTTGCGTTCCATC 58.912 55.000 0.00 0.00 0.00 3.51
523 540 2.558313 GCGGCTTGTTCTGCTCAC 59.442 61.111 0.00 0.00 35.53 3.51
592 609 6.935741 TCCATAATGGAGATAAAAACCACG 57.064 37.500 0.00 0.00 42.67 4.94
609 626 2.412770 CCACGTACGTACCAAATCCAAC 59.587 50.000 22.34 0.00 0.00 3.77
685 702 3.006110 CACACCACTTACCCTCTAAACGA 59.994 47.826 0.00 0.00 0.00 3.85
741 758 7.395190 ACATCATTTCGAATCAATTTCCTCA 57.605 32.000 0.00 0.00 0.00 3.86
861 881 5.625921 GCTAGCTAGCTATAGTTAACGGT 57.374 43.478 33.71 0.00 45.62 4.83
909 991 6.272318 CGGACCATGCATAAATACACAATTT 58.728 36.000 0.00 0.00 40.87 1.82
915 997 7.254185 CCATGCATAAATACACAATTTCAGCAC 60.254 37.037 0.00 0.00 43.90 4.40
1041 1138 1.735376 GCGCATTCCTCCTCGTCCTA 61.735 60.000 0.30 0.00 0.00 2.94
1044 1141 1.757699 GCATTCCTCCTCGTCCTACTT 59.242 52.381 0.00 0.00 0.00 2.24
1197 1301 2.590007 GCCATGCTCCTGTAGGCG 60.590 66.667 0.00 0.00 35.42 5.52
1198 1302 2.903357 CCATGCTCCTGTAGGCGT 59.097 61.111 0.00 0.00 34.44 5.68
1218 1324 1.886313 CTGCGTGCCTCAGCTATGG 60.886 63.158 0.00 0.00 40.80 2.74
1219 1325 2.302199 CTGCGTGCCTCAGCTATGGA 62.302 60.000 8.21 0.00 40.80 3.41
1254 1363 2.271800 GCCTGGAGATCTTTGTACGTG 58.728 52.381 0.00 0.00 0.00 4.49
1255 1364 2.893637 CCTGGAGATCTTTGTACGTGG 58.106 52.381 0.00 0.00 0.00 4.94
1256 1365 2.233922 CCTGGAGATCTTTGTACGTGGT 59.766 50.000 0.00 0.00 0.00 4.16
1270 1379 6.542574 TGTACGTGGTACTTTGGTAATTTG 57.457 37.500 0.00 0.00 39.49 2.32
1271 1380 6.054295 TGTACGTGGTACTTTGGTAATTTGT 58.946 36.000 0.00 0.00 39.49 2.83
1288 1411 8.028938 GGTAATTTGTTGTGTGCTTGAGATATT 58.971 33.333 0.00 0.00 0.00 1.28
1298 1421 7.148356 TGTGTGCTTGAGATATTTCTGAATGAC 60.148 37.037 0.00 0.00 30.30 3.06
1310 1433 3.766151 TCTGAATGACGTCGTGGTAATC 58.234 45.455 11.82 5.25 0.00 1.75
1354 1477 7.311092 TCCCTTTGTCTAGATTGTTAAGTGA 57.689 36.000 0.00 0.00 0.00 3.41
1369 1492 5.886474 TGTTAAGTGACTCGATGGATAGACT 59.114 40.000 0.00 0.00 0.00 3.24
1413 1536 3.644805 ATATACGTGTTGGTTTTCGCG 57.355 42.857 0.00 0.00 42.16 5.87
1414 1537 0.513820 ATACGTGTTGGTTTTCGCGG 59.486 50.000 6.13 0.00 41.02 6.46
1417 1540 2.188161 GTGTTGGTTTTCGCGGGGA 61.188 57.895 6.13 0.00 0.00 4.81
1418 1541 1.894756 TGTTGGTTTTCGCGGGGAG 60.895 57.895 6.13 0.00 0.00 4.30
1420 1543 2.820400 TTGGTTTTCGCGGGGAGGA 61.820 57.895 6.13 0.00 0.00 3.71
1421 1544 2.032987 GGTTTTCGCGGGGAGGAA 59.967 61.111 6.13 0.00 0.00 3.36
1424 1547 2.333291 TTTTCGCGGGGAGGAAAAC 58.667 52.632 6.13 0.00 37.26 2.43
1425 1548 0.465824 TTTTCGCGGGGAGGAAAACA 60.466 50.000 6.13 0.00 37.26 2.83
1426 1549 0.465824 TTTCGCGGGGAGGAAAACAA 60.466 50.000 6.13 0.00 0.00 2.83
1428 1551 0.614294 TCGCGGGGAGGAAAACAATA 59.386 50.000 6.13 0.00 0.00 1.90
1429 1552 0.730840 CGCGGGGAGGAAAACAATAC 59.269 55.000 0.00 0.00 0.00 1.89
1432 1555 2.163613 GCGGGGAGGAAAACAATACAAG 59.836 50.000 0.00 0.00 0.00 3.16
1436 1571 4.556233 GGGAGGAAAACAATACAAGTTGC 58.444 43.478 1.81 0.00 32.32 4.17
1441 1576 7.042725 GGAGGAAAACAATACAAGTTGCTTTTC 60.043 37.037 1.81 8.31 37.75 2.29
1470 1605 2.935201 GCAACTTGGTTGTGCAAATGAA 59.065 40.909 11.27 0.00 44.40 2.57
1481 1616 4.684877 TGTGCAAATGAATGATGTATGCC 58.315 39.130 0.00 0.00 0.00 4.40
1484 1619 4.645588 TGCAAATGAATGATGTATGCCTGA 59.354 37.500 0.00 0.00 0.00 3.86
1485 1620 4.980434 GCAAATGAATGATGTATGCCTGAC 59.020 41.667 0.00 0.00 0.00 3.51
1500 1635 8.892723 TGTATGCCTGACTATTCTATTTGTTTG 58.107 33.333 0.00 0.00 0.00 2.93
1505 1640 9.476202 GCCTGACTATTCTATTTGTTTGTTTTT 57.524 29.630 0.00 0.00 0.00 1.94
1570 1705 7.121974 CGAAGCCATGAATAATAACTACTGG 57.878 40.000 0.00 0.00 0.00 4.00
1573 1708 8.451908 AAGCCATGAATAATAACTACTGGTTC 57.548 34.615 0.00 0.00 39.17 3.62
1577 1712 7.096189 CCATGAATAATAACTACTGGTTCGTCG 60.096 40.741 0.00 0.00 39.17 5.12
1603 1738 9.539825 GACAGTCTATGATGAAATGTTATCACT 57.460 33.333 0.00 0.00 36.26 3.41
1675 1817 0.106918 ACGGTGCACCTTCTTTTCCA 60.107 50.000 32.28 0.00 0.00 3.53
1684 1826 3.005155 CACCTTCTTTTCCAGGCTGAAAG 59.995 47.826 17.94 17.96 35.77 2.62
1701 1843 6.239317 GGCTGAAAGGAACCTCAAAATTAAGT 60.239 38.462 0.00 0.00 0.00 2.24
1705 1847 5.453567 AGGAACCTCAAAATTAAGTGTGC 57.546 39.130 0.00 0.00 0.00 4.57
1709 1851 7.040409 AGGAACCTCAAAATTAAGTGTGCTTAG 60.040 37.037 0.00 0.00 38.31 2.18
1714 1856 6.446318 TCAAAATTAAGTGTGCTTAGCTTGG 58.554 36.000 5.60 0.00 38.31 3.61
1725 1867 2.554032 GCTTAGCTTGGAGCAACTTGAA 59.446 45.455 10.47 0.00 45.56 2.69
1731 1873 3.613432 GCTTGGAGCAACTTGAAGATTGG 60.613 47.826 0.00 0.00 41.89 3.16
1737 1879 2.159517 GCAACTTGAAGATTGGTAGCCG 60.160 50.000 0.00 0.00 0.00 5.52
1743 1885 2.693591 TGAAGATTGGTAGCCGACTAGG 59.306 50.000 0.00 0.00 44.97 3.02
1762 1904 2.997485 GAAGTTGATTCCAGGTGCAC 57.003 50.000 8.80 8.80 31.14 4.57
1768 1910 0.807496 GATTCCAGGTGCACAAGAGC 59.193 55.000 20.43 0.00 0.00 4.09
1792 1934 2.911102 GCATAAAGTGCGCAGAAAAGAC 59.089 45.455 12.22 0.00 45.23 3.01
1801 1943 4.625742 GTGCGCAGAAAAGACTAGTATTGA 59.374 41.667 12.22 0.00 0.00 2.57
1808 1950 7.900352 GCAGAAAAGACTAGTATTGATTTGTCG 59.100 37.037 2.98 0.00 0.00 4.35
1814 1956 3.080300 AGTATTGATTTGTCGGGCCAA 57.920 42.857 4.39 0.00 0.00 4.52
1835 1977 6.183360 GCCAATCTAGATCCTAGGTATTAGCC 60.183 46.154 9.08 0.00 0.00 3.93
1841 1983 0.037232 CCTAGGTATTAGCCAGCCGC 60.037 60.000 0.00 0.00 37.98 6.53
1845 1987 1.641677 GTATTAGCCAGCCGCAACG 59.358 57.895 0.00 0.00 41.38 4.10
1847 1989 0.808453 TATTAGCCAGCCGCAACGAC 60.808 55.000 0.00 0.00 41.38 4.34
1866 2008 3.404899 GACCAAGAACCGGTGTATTTGA 58.595 45.455 8.52 0.00 36.69 2.69
1884 2026 2.455557 TGACTGGGGCATTACAATTGG 58.544 47.619 10.83 0.00 0.00 3.16
1888 2030 4.619679 ACTGGGGCATTACAATTGGTATT 58.380 39.130 10.83 0.00 0.00 1.89
1903 2045 0.039346 GTATTAGAGCCGACCCTCGC 60.039 60.000 0.00 0.00 38.82 5.03
1913 2055 4.060038 ACCCTCGCGGTTACACGG 62.060 66.667 6.13 0.00 45.36 4.94
1914 2056 4.807039 CCCTCGCGGTTACACGGG 62.807 72.222 6.13 1.25 46.53 5.28
1946 2088 3.496131 GTACACGGGCATGTGGCG 61.496 66.667 12.79 0.00 46.16 5.69
1964 2106 2.986290 CATAGCCCGTGTGGTCCA 59.014 61.111 0.00 0.00 36.04 4.02
1965 2107 1.526887 CATAGCCCGTGTGGTCCAT 59.473 57.895 0.00 0.00 36.04 3.41
1966 2108 0.532862 CATAGCCCGTGTGGTCCATC 60.533 60.000 0.00 0.00 36.04 3.51
1967 2109 0.980754 ATAGCCCGTGTGGTCCATCA 60.981 55.000 0.00 0.00 36.04 3.07
1982 2124 1.869132 CCATCATGACACACGGCATAG 59.131 52.381 0.00 0.00 0.00 2.23
1988 2130 1.086696 GACACACGGCATAGCACATT 58.913 50.000 0.00 0.00 0.00 2.71
1990 2132 2.675844 GACACACGGCATAGCACATTTA 59.324 45.455 0.00 0.00 0.00 1.40
1998 2140 3.493699 GGCATAGCACATTTACCGGACTA 60.494 47.826 9.46 0.00 0.00 2.59
2005 2147 2.190981 CATTTACCGGACTAGACGCAC 58.809 52.381 9.46 0.00 0.00 5.34
2006 2148 1.538047 TTTACCGGACTAGACGCACT 58.462 50.000 9.46 0.00 0.00 4.40
2010 2152 1.226046 CGGACTAGACGCACTGACG 60.226 63.158 0.00 0.00 39.50 4.35
2052 2194 2.083774 TGTTGGATTGGCGAAGATGTC 58.916 47.619 0.00 0.00 0.00 3.06
2064 2206 3.064207 CGAAGATGTCGGTTCCTTTGAA 58.936 45.455 0.00 0.00 46.45 2.69
2069 2211 1.173913 GTCGGTTCCTTTGAATGGGG 58.826 55.000 0.00 0.00 31.98 4.96
2107 2249 5.014858 CCGGCTTAATAGGATGGTAGACTA 58.985 45.833 0.00 0.00 0.00 2.59
2108 2250 5.105837 CCGGCTTAATAGGATGGTAGACTAC 60.106 48.000 3.86 3.86 0.00 2.73
2109 2251 5.711036 CGGCTTAATAGGATGGTAGACTACT 59.289 44.000 12.31 0.00 0.00 2.57
2110 2252 6.208994 CGGCTTAATAGGATGGTAGACTACTT 59.791 42.308 12.31 0.87 0.00 2.24
2111 2253 7.255871 CGGCTTAATAGGATGGTAGACTACTTT 60.256 40.741 12.31 0.52 0.00 2.66
2112 2254 9.086758 GGCTTAATAGGATGGTAGACTACTTTA 57.913 37.037 12.31 0.65 0.00 1.85
2129 2271 9.869844 GACTACTTTATATCAACAACATGCATC 57.130 33.333 0.00 0.00 0.00 3.91
2130 2272 8.551205 ACTACTTTATATCAACAACATGCATCG 58.449 33.333 0.00 0.00 0.00 3.84
2145 2287 0.109597 CATCGTGTTTGGCTTGGAGC 60.110 55.000 0.00 0.00 41.46 4.70
2153 2295 4.448732 GTGTTTGGCTTGGAGCAATTTAAG 59.551 41.667 2.04 0.00 44.75 1.85
2156 2298 3.711863 TGGCTTGGAGCAATTTAAGGAT 58.288 40.909 2.04 0.00 44.75 3.24
2169 2311 0.548926 TAAGGATGGGTGACTGGCCA 60.549 55.000 4.71 4.71 0.00 5.36
2180 2322 3.552890 GGTGACTGGCCAAAAAGTTGATC 60.553 47.826 7.01 0.00 36.83 2.92
2181 2323 2.627699 TGACTGGCCAAAAAGTTGATCC 59.372 45.455 7.01 0.00 36.83 3.36
2182 2324 1.970640 ACTGGCCAAAAAGTTGATCCC 59.029 47.619 7.01 0.00 36.83 3.85
2183 2325 2.250924 CTGGCCAAAAAGTTGATCCCT 58.749 47.619 7.01 0.00 36.83 4.20
2184 2326 1.969923 TGGCCAAAAAGTTGATCCCTG 59.030 47.619 0.61 0.00 36.83 4.45
2185 2327 1.338105 GGCCAAAAAGTTGATCCCTGC 60.338 52.381 0.00 0.00 36.83 4.85
2186 2328 1.344114 GCCAAAAAGTTGATCCCTGCA 59.656 47.619 0.00 0.00 36.83 4.41
2187 2329 2.611224 GCCAAAAAGTTGATCCCTGCAG 60.611 50.000 6.78 6.78 36.83 4.41
2188 2330 2.892852 CCAAAAAGTTGATCCCTGCAGA 59.107 45.455 17.39 0.00 36.83 4.26
2189 2331 3.512724 CCAAAAAGTTGATCCCTGCAGAT 59.487 43.478 17.39 0.65 36.83 2.90
2190 2332 4.491676 CAAAAAGTTGATCCCTGCAGATG 58.508 43.478 17.39 6.04 36.83 2.90
2191 2333 1.760192 AAGTTGATCCCTGCAGATGC 58.240 50.000 17.39 1.94 42.50 3.91
2192 2334 0.463295 AGTTGATCCCTGCAGATGCG 60.463 55.000 17.39 0.00 45.83 4.73
2193 2335 1.820906 TTGATCCCTGCAGATGCGC 60.821 57.895 17.39 0.00 45.83 6.09
2194 2336 2.203112 GATCCCTGCAGATGCGCA 60.203 61.111 14.96 14.96 45.83 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.532155 CTTCCCTCTCCCTCGCCG 61.532 72.222 0.00 0.00 0.00 6.46
38 39 3.157949 CCTTCCCTCTCCCTCGCC 61.158 72.222 0.00 0.00 0.00 5.54
39 40 3.855853 GCCTTCCCTCTCCCTCGC 61.856 72.222 0.00 0.00 0.00 5.03
40 41 3.532155 CGCCTTCCCTCTCCCTCG 61.532 72.222 0.00 0.00 0.00 4.63
41 42 2.042843 TCGCCTTCCCTCTCCCTC 60.043 66.667 0.00 0.00 0.00 4.30
42 43 2.042435 CTCGCCTTCCCTCTCCCT 60.042 66.667 0.00 0.00 0.00 4.20
43 44 1.265454 TTTCTCGCCTTCCCTCTCCC 61.265 60.000 0.00 0.00 0.00 4.30
44 45 0.176910 CTTTCTCGCCTTCCCTCTCC 59.823 60.000 0.00 0.00 0.00 3.71
45 46 0.176910 CCTTTCTCGCCTTCCCTCTC 59.823 60.000 0.00 0.00 0.00 3.20
46 47 1.268283 CCCTTTCTCGCCTTCCCTCT 61.268 60.000 0.00 0.00 0.00 3.69
47 48 1.222113 CCCTTTCTCGCCTTCCCTC 59.778 63.158 0.00 0.00 0.00 4.30
48 49 2.301738 CCCCTTTCTCGCCTTCCCT 61.302 63.158 0.00 0.00 0.00 4.20
49 50 2.258748 CTCCCCTTTCTCGCCTTCCC 62.259 65.000 0.00 0.00 0.00 3.97
50 51 1.222113 CTCCCCTTTCTCGCCTTCC 59.778 63.158 0.00 0.00 0.00 3.46
51 52 1.450491 GCTCCCCTTTCTCGCCTTC 60.450 63.158 0.00 0.00 0.00 3.46
52 53 2.671682 GCTCCCCTTTCTCGCCTT 59.328 61.111 0.00 0.00 0.00 4.35
53 54 3.775654 CGCTCCCCTTTCTCGCCT 61.776 66.667 0.00 0.00 0.00 5.52
54 55 4.840005 CCGCTCCCCTTTCTCGCC 62.840 72.222 0.00 0.00 0.00 5.54
57 58 4.840005 CCGCCGCTCCCCTTTCTC 62.840 72.222 0.00 0.00 0.00 2.87
72 73 3.843117 GAACCCTAGATCGCCGCCG 62.843 68.421 0.00 0.00 0.00 6.46
73 74 2.029221 GAACCCTAGATCGCCGCC 59.971 66.667 0.00 0.00 0.00 6.13
74 75 2.029221 GGAACCCTAGATCGCCGC 59.971 66.667 0.00 0.00 0.00 6.53
75 76 2.335369 CGGAACCCTAGATCGCCG 59.665 66.667 0.00 0.00 0.00 6.46
76 77 2.029221 GCGGAACCCTAGATCGCC 59.971 66.667 0.00 0.00 40.44 5.54
77 78 2.029221 GGCGGAACCCTAGATCGC 59.971 66.667 0.00 0.00 44.80 4.58
121 122 4.125695 GAGACCCCGTTCCCGTCG 62.126 72.222 0.00 0.00 0.00 5.12
122 123 3.767806 GGAGACCCCGTTCCCGTC 61.768 72.222 0.00 0.00 0.00 4.79
123 124 4.312152 AGGAGACCCCGTTCCCGT 62.312 66.667 0.00 0.00 40.87 5.28
124 125 3.771160 CAGGAGACCCCGTTCCCG 61.771 72.222 0.00 0.00 40.87 5.14
125 126 0.690077 ATACAGGAGACCCCGTTCCC 60.690 60.000 0.00 0.00 40.87 3.97
126 127 0.751452 GATACAGGAGACCCCGTTCC 59.249 60.000 0.00 0.00 40.87 3.62
127 128 1.481871 TGATACAGGAGACCCCGTTC 58.518 55.000 0.00 0.00 40.87 3.95
128 129 2.040178 GATGATACAGGAGACCCCGTT 58.960 52.381 0.00 0.00 40.87 4.44
129 130 1.218196 AGATGATACAGGAGACCCCGT 59.782 52.381 0.00 0.00 40.87 5.28
130 131 1.889829 GAGATGATACAGGAGACCCCG 59.110 57.143 0.00 0.00 40.87 5.73
131 132 3.252554 AGAGATGATACAGGAGACCCC 57.747 52.381 0.00 0.00 0.00 4.95
132 133 4.202631 ACCTAGAGATGATACAGGAGACCC 60.203 50.000 0.00 0.00 0.00 4.46
133 134 4.993028 ACCTAGAGATGATACAGGAGACC 58.007 47.826 0.00 0.00 0.00 3.85
134 135 5.876357 AGACCTAGAGATGATACAGGAGAC 58.124 45.833 0.00 0.00 0.00 3.36
135 136 6.126332 ACAAGACCTAGAGATGATACAGGAGA 60.126 42.308 0.00 0.00 0.00 3.71
136 137 6.068010 ACAAGACCTAGAGATGATACAGGAG 58.932 44.000 0.00 0.00 0.00 3.69
137 138 6.019656 ACAAGACCTAGAGATGATACAGGA 57.980 41.667 0.00 0.00 0.00 3.86
138 139 6.723298 AACAAGACCTAGAGATGATACAGG 57.277 41.667 0.00 0.00 0.00 4.00
139 140 7.653647 GGTAACAAGACCTAGAGATGATACAG 58.346 42.308 0.00 0.00 36.47 2.74
140 141 7.584122 GGTAACAAGACCTAGAGATGATACA 57.416 40.000 0.00 0.00 36.47 2.29
167 168 4.215613 GTCTGCTAATCACGGAAGGTTTTT 59.784 41.667 0.00 0.00 0.00 1.94
178 179 1.192793 GCGAGACGTCTGCTAATCAC 58.807 55.000 25.58 4.56 0.00 3.06
179 180 1.095600 AGCGAGACGTCTGCTAATCA 58.904 50.000 29.06 0.00 37.15 2.57
184 185 1.135632 GTTAGAAGCGAGACGTCTGCT 60.136 52.381 25.58 26.16 37.69 4.24
185 186 1.261097 GTTAGAAGCGAGACGTCTGC 58.739 55.000 25.58 24.44 37.69 4.26
188 189 2.615489 AGTGTTAGAAGCGAGACGTC 57.385 50.000 7.70 7.70 0.00 4.34
194 196 3.250040 GCCTTTTCAAGTGTTAGAAGCGA 59.750 43.478 0.00 0.00 0.00 4.93
196 198 4.036852 ACAGCCTTTTCAAGTGTTAGAAGC 59.963 41.667 0.00 0.00 0.00 3.86
199 201 6.151985 TGAAAACAGCCTTTTCAAGTGTTAGA 59.848 34.615 14.54 0.00 43.10 2.10
200 202 6.329496 TGAAAACAGCCTTTTCAAGTGTTAG 58.671 36.000 14.54 0.00 43.10 2.34
202 204 5.146010 TGAAAACAGCCTTTTCAAGTGTT 57.854 34.783 14.54 0.00 43.10 3.32
214 216 0.169009 GCGAGACCATGAAAACAGCC 59.831 55.000 0.00 0.00 0.00 4.85
215 217 1.160137 AGCGAGACCATGAAAACAGC 58.840 50.000 0.00 0.00 0.00 4.40
219 221 1.438651 CCGAAGCGAGACCATGAAAA 58.561 50.000 0.00 0.00 0.00 2.29
248 253 1.734465 GTCAAAATGTCTCAGGGCTCG 59.266 52.381 0.00 0.00 0.00 5.03
249 254 2.746362 CTGTCAAAATGTCTCAGGGCTC 59.254 50.000 0.00 0.00 0.00 4.70
254 259 3.499918 GTGGGACTGTCAAAATGTCTCAG 59.500 47.826 10.38 0.00 41.20 3.35
269 274 5.428457 TCATCTTGTAACATATGGTGGGACT 59.572 40.000 2.68 0.00 0.00 3.85
272 277 6.515531 GCATTCATCTTGTAACATATGGTGGG 60.516 42.308 2.68 0.00 0.00 4.61
276 281 7.310664 GGATGCATTCATCTTGTAACATATGG 58.689 38.462 7.80 0.00 46.41 2.74
282 290 4.094887 ACACGGATGCATTCATCTTGTAAC 59.905 41.667 5.66 0.00 46.41 2.50
305 313 6.741992 AAGCACGATGATTCATTAACTTGA 57.258 33.333 0.00 0.00 0.00 3.02
318 326 5.483811 TGTATGGAGTAAAAAGCACGATGA 58.516 37.500 0.00 0.00 0.00 2.92
319 327 5.794687 TGTATGGAGTAAAAAGCACGATG 57.205 39.130 0.00 0.00 0.00 3.84
375 384 2.014554 GCGTTTGTCGAGAGCGTGA 61.015 57.895 9.54 0.00 42.86 4.35
383 392 0.781787 CATCGTCTTGCGTTTGTCGA 59.218 50.000 0.00 0.00 42.86 4.20
385 395 2.987535 GCATCGTCTTGCGTTTGTC 58.012 52.632 0.00 0.00 42.13 3.18
416 433 1.079503 CCTTTCTTGGAGTACGCTGC 58.920 55.000 0.00 0.00 0.00 5.25
523 540 2.236395 ACTAGGATTTCCAGGTCAACCG 59.764 50.000 0.00 0.00 42.08 4.44
591 608 2.093152 GCAGTTGGATTTGGTACGTACG 59.907 50.000 18.98 15.01 0.00 3.67
592 609 2.417586 GGCAGTTGGATTTGGTACGTAC 59.582 50.000 17.56 17.56 0.00 3.67
609 626 1.180029 CTTCCATTCCAGGTTGGCAG 58.820 55.000 6.37 2.34 37.47 4.85
685 702 4.021016 GTCTGTACCTCATGACTGGACTTT 60.021 45.833 7.95 0.00 0.00 2.66
692 709 3.940221 GACTACGTCTGTACCTCATGACT 59.060 47.826 0.00 0.00 0.00 3.41
741 758 7.554476 GGTGCTCTTATCTTCTTCAATTAGGTT 59.446 37.037 0.00 0.00 0.00 3.50
850 870 4.737054 CCAGACGTGTTACCGTTAACTAT 58.263 43.478 4.42 0.00 41.98 2.12
851 871 3.611530 GCCAGACGTGTTACCGTTAACTA 60.612 47.826 4.42 0.00 41.98 2.24
861 881 0.753867 TGACCTTGCCAGACGTGTTA 59.246 50.000 0.00 0.00 0.00 2.41
933 1030 2.003301 GAGCGTGTGATTTCCTTCTCC 58.997 52.381 0.00 0.00 0.00 3.71
969 1066 3.833645 CCTACACGCGGGCTAGCA 61.834 66.667 18.24 0.00 36.85 3.49
1041 1138 3.316573 GAGGCTGGCCACGCTAAGT 62.317 63.158 21.48 8.57 38.92 2.24
1044 1141 3.083349 ATGAGGCTGGCCACGCTA 61.083 61.111 21.48 12.00 38.92 4.26
1207 1313 4.097135 CCGTATATCACTCCATAGCTGAGG 59.903 50.000 0.00 0.00 34.06 3.86
1218 1324 0.969894 AGGCCAGCCGTATATCACTC 59.030 55.000 5.01 0.00 41.95 3.51
1219 1325 0.681733 CAGGCCAGCCGTATATCACT 59.318 55.000 5.01 0.00 41.95 3.41
1254 1363 5.460748 GCACACAACAAATTACCAAAGTACC 59.539 40.000 0.00 0.00 0.00 3.34
1255 1364 6.270064 AGCACACAACAAATTACCAAAGTAC 58.730 36.000 0.00 0.00 0.00 2.73
1256 1365 6.458232 AGCACACAACAAATTACCAAAGTA 57.542 33.333 0.00 0.00 0.00 2.24
1270 1379 6.486253 TCAGAAATATCTCAAGCACACAAC 57.514 37.500 0.00 0.00 32.03 3.32
1271 1380 7.391275 TCATTCAGAAATATCTCAAGCACACAA 59.609 33.333 0.00 0.00 32.03 3.33
1288 1411 3.646611 TTACCACGACGTCATTCAGAA 57.353 42.857 17.16 0.00 0.00 3.02
1298 1421 2.514013 GCTGCCGATTACCACGACG 61.514 63.158 0.00 0.00 0.00 5.12
1310 1433 0.598158 ATGCAAAGTTGTTGCTGCCG 60.598 50.000 11.91 0.00 45.13 5.69
1331 1454 7.162082 AGTCACTTAACAATCTAGACAAAGGG 58.838 38.462 0.00 0.00 0.00 3.95
1354 1477 7.589958 ACAAAGAATAGTCTATCCATCGAGT 57.410 36.000 0.00 0.00 32.16 4.18
1398 1521 2.051703 CCCGCGAAAACCAACACG 60.052 61.111 8.23 0.00 0.00 4.49
1400 1523 1.894756 CTCCCCGCGAAAACCAACA 60.895 57.895 8.23 0.00 0.00 3.33
1401 1524 2.622962 CCTCCCCGCGAAAACCAAC 61.623 63.158 8.23 0.00 0.00 3.77
1402 1525 2.281900 CCTCCCCGCGAAAACCAA 60.282 61.111 8.23 0.00 0.00 3.67
1403 1526 2.340673 TTTCCTCCCCGCGAAAACCA 62.341 55.000 8.23 0.00 0.00 3.67
1404 1527 1.174078 TTTTCCTCCCCGCGAAAACC 61.174 55.000 8.23 0.00 34.03 3.27
1405 1528 0.039798 GTTTTCCTCCCCGCGAAAAC 60.040 55.000 8.23 11.76 46.07 2.43
1406 1529 0.465824 TGTTTTCCTCCCCGCGAAAA 60.466 50.000 8.23 1.74 36.02 2.29
1408 1531 0.250989 ATTGTTTTCCTCCCCGCGAA 60.251 50.000 8.23 0.00 0.00 4.70
1410 1533 0.730840 GTATTGTTTTCCTCCCCGCG 59.269 55.000 0.00 0.00 0.00 6.46
1411 1534 1.828979 TGTATTGTTTTCCTCCCCGC 58.171 50.000 0.00 0.00 0.00 6.13
1412 1535 3.418047 ACTTGTATTGTTTTCCTCCCCG 58.582 45.455 0.00 0.00 0.00 5.73
1413 1536 4.560716 GCAACTTGTATTGTTTTCCTCCCC 60.561 45.833 0.00 0.00 31.83 4.81
1414 1537 4.280929 AGCAACTTGTATTGTTTTCCTCCC 59.719 41.667 0.00 0.00 31.83 4.30
1417 1540 7.327214 TGAAAAGCAACTTGTATTGTTTTCCT 58.673 30.769 15.51 0.76 40.70 3.36
1418 1541 7.532682 TGAAAAGCAACTTGTATTGTTTTCC 57.467 32.000 15.51 2.42 40.70 3.13
1420 1543 8.715191 TCATGAAAAGCAACTTGTATTGTTTT 57.285 26.923 0.00 0.00 42.58 2.43
1421 1544 8.715191 TTCATGAAAAGCAACTTGTATTGTTT 57.285 26.923 5.45 0.00 34.85 2.83
1441 1576 3.001533 GCACAACCAAGTTGCTTTTCATG 59.998 43.478 7.36 0.00 46.20 3.07
1457 1592 5.005971 GGCATACATCATTCATTTGCACAAC 59.994 40.000 0.00 0.00 0.00 3.32
1470 1605 9.445878 CAAATAGAATAGTCAGGCATACATCAT 57.554 33.333 0.00 0.00 0.00 2.45
1500 1635 6.478673 ACCACGGAAATGAAAATGAGAAAAAC 59.521 34.615 0.00 0.00 0.00 2.43
1505 1640 4.824537 TCAACCACGGAAATGAAAATGAGA 59.175 37.500 0.00 0.00 0.00 3.27
1506 1641 5.119931 TCAACCACGGAAATGAAAATGAG 57.880 39.130 0.00 0.00 0.00 2.90
1510 1645 5.379732 GGTATCAACCACGGAAATGAAAA 57.620 39.130 0.00 0.00 45.98 2.29
1546 1681 6.706270 ACCAGTAGTTATTATTCATGGCTTCG 59.294 38.462 0.00 0.00 0.00 3.79
1560 1695 3.755378 ACTGTCGACGAACCAGTAGTTAT 59.245 43.478 16.83 0.00 39.40 1.89
1565 1700 1.888215 AGACTGTCGACGAACCAGTA 58.112 50.000 17.95 0.00 39.43 2.74
1567 1702 2.418976 TCATAGACTGTCGACGAACCAG 59.581 50.000 11.62 12.48 0.00 4.00
1569 1704 3.064958 TCATCATAGACTGTCGACGAACC 59.935 47.826 11.62 0.00 0.00 3.62
1570 1705 4.274421 TCATCATAGACTGTCGACGAAC 57.726 45.455 11.62 4.38 0.00 3.95
1573 1708 5.037385 ACATTTCATCATAGACTGTCGACG 58.963 41.667 11.62 8.41 0.00 5.12
1577 1712 9.539825 AGTGATAACATTTCATCATAGACTGTC 57.460 33.333 0.00 0.00 33.92 3.51
1657 1799 0.593128 CTGGAAAAGAAGGTGCACCG 59.407 55.000 29.68 7.96 42.08 4.94
1675 1817 3.312736 TTTTGAGGTTCCTTTCAGCCT 57.687 42.857 0.00 0.00 0.00 4.58
1684 1826 5.453567 AGCACACTTAATTTTGAGGTTCC 57.546 39.130 0.00 0.00 0.00 3.62
1705 1847 4.067896 TCTTCAAGTTGCTCCAAGCTAAG 58.932 43.478 0.00 0.00 42.97 2.18
1709 1851 3.572584 CAATCTTCAAGTTGCTCCAAGC 58.427 45.455 0.00 0.00 42.82 4.01
1714 1856 3.127721 GGCTACCAATCTTCAAGTTGCTC 59.872 47.826 0.00 0.00 32.64 4.26
1720 1862 3.252974 AGTCGGCTACCAATCTTCAAG 57.747 47.619 0.00 0.00 0.00 3.02
1725 1867 2.750141 TCCTAGTCGGCTACCAATCT 57.250 50.000 0.00 0.00 0.00 2.40
1731 1873 4.361420 GAATCAACTTCCTAGTCGGCTAC 58.639 47.826 0.00 0.00 31.99 3.58
1743 1885 2.229792 TGTGCACCTGGAATCAACTTC 58.770 47.619 15.69 0.00 0.00 3.01
1781 1923 7.743104 ACAAATCAATACTAGTCTTTTCTGCG 58.257 34.615 0.00 0.00 0.00 5.18
1792 1934 3.804036 TGGCCCGACAAATCAATACTAG 58.196 45.455 0.00 0.00 0.00 2.57
1801 1943 3.496870 GGATCTAGATTGGCCCGACAAAT 60.497 47.826 6.70 0.00 33.48 2.32
1808 1950 2.909217 ACCTAGGATCTAGATTGGCCC 58.091 52.381 17.98 3.33 0.00 5.80
1814 1956 6.133356 GCTGGCTAATACCTAGGATCTAGAT 58.867 44.000 17.98 4.47 0.00 1.98
1835 1977 2.250939 TTCTTGGTCGTTGCGGCTG 61.251 57.895 0.00 0.00 0.00 4.85
1841 1983 0.812412 ACACCGGTTCTTGGTCGTTG 60.812 55.000 2.97 0.00 37.72 4.10
1845 1987 3.187842 GTCAAATACACCGGTTCTTGGTC 59.812 47.826 2.97 0.55 37.72 4.02
1847 1989 3.188460 CAGTCAAATACACCGGTTCTTGG 59.812 47.826 2.97 0.00 0.00 3.61
1866 2008 2.621556 ACCAATTGTAATGCCCCAGT 57.378 45.000 4.43 0.00 0.00 4.00
1884 2026 0.039346 GCGAGGGTCGGCTCTAATAC 60.039 60.000 0.00 0.00 40.84 1.89
1923 2065 2.098233 CATGCCCGTGTACGTGACC 61.098 63.158 0.00 0.00 37.74 4.02
1928 2070 3.496131 GCCACATGCCCGTGTACG 61.496 66.667 0.00 0.00 34.98 3.67
1946 2088 2.513897 GGACCACACGGGCTATGC 60.514 66.667 0.00 0.00 41.90 3.14
1953 2095 0.036483 TGTCATGATGGACCACACGG 60.036 55.000 0.00 0.00 36.97 4.94
1964 2106 1.134431 TGCTATGCCGTGTGTCATGAT 60.134 47.619 0.00 0.00 0.00 2.45
1965 2107 0.248843 TGCTATGCCGTGTGTCATGA 59.751 50.000 0.00 0.00 0.00 3.07
1966 2108 0.374758 GTGCTATGCCGTGTGTCATG 59.625 55.000 0.00 0.00 0.00 3.07
1967 2109 0.036483 TGTGCTATGCCGTGTGTCAT 60.036 50.000 0.00 0.00 0.00 3.06
1982 2124 2.190981 CGTCTAGTCCGGTAAATGTGC 58.809 52.381 0.00 0.00 0.00 4.57
1988 2130 0.806868 CAGTGCGTCTAGTCCGGTAA 59.193 55.000 0.00 0.00 0.00 2.85
1990 2132 1.303074 TCAGTGCGTCTAGTCCGGT 60.303 57.895 0.00 0.00 0.00 5.28
2005 2147 2.047844 CCTCCTGGCACACGTCAG 60.048 66.667 0.00 0.00 44.93 3.51
2006 2148 3.625897 CCCTCCTGGCACACGTCA 61.626 66.667 0.00 0.00 0.00 4.35
2010 2152 2.358737 CGTTCCCTCCTGGCACAC 60.359 66.667 0.00 0.00 0.00 3.82
2034 2176 1.368641 CGACATCTTCGCCAATCCAA 58.631 50.000 0.00 0.00 41.87 3.53
2042 2184 5.916529 ATTCAAAGGAACCGACATCTTCGC 61.917 45.833 0.00 0.00 39.60 4.70
2052 2194 0.251608 ACCCCCATTCAAAGGAACCG 60.252 55.000 0.00 0.00 35.46 4.44
2069 2211 1.623811 AGCCGGGATGTCATATACACC 59.376 52.381 2.18 0.00 42.09 4.16
2107 2249 7.148255 ACACGATGCATGTTGTTGATATAAAGT 60.148 33.333 2.46 0.00 0.00 2.66
2108 2250 7.188834 ACACGATGCATGTTGTTGATATAAAG 58.811 34.615 2.46 0.00 0.00 1.85
2109 2251 7.082700 ACACGATGCATGTTGTTGATATAAA 57.917 32.000 2.46 0.00 0.00 1.40
2110 2252 6.676237 ACACGATGCATGTTGTTGATATAA 57.324 33.333 2.46 0.00 0.00 0.98
2111 2253 6.676237 AACACGATGCATGTTGTTGATATA 57.324 33.333 17.71 0.00 38.84 0.86
2112 2254 5.565592 AACACGATGCATGTTGTTGATAT 57.434 34.783 17.71 0.00 38.84 1.63
2113 2255 5.152804 CAAACACGATGCATGTTGTTGATA 58.847 37.500 18.69 0.00 40.16 2.15
2114 2256 3.921119 AACACGATGCATGTTGTTGAT 57.079 38.095 17.71 0.00 38.84 2.57
2129 2271 0.314935 ATTGCTCCAAGCCAAACACG 59.685 50.000 0.00 0.00 41.51 4.49
2130 2272 2.531522 AATTGCTCCAAGCCAAACAC 57.468 45.000 0.00 0.00 41.51 3.32
2145 2287 3.131046 GCCAGTCACCCATCCTTAAATTG 59.869 47.826 0.00 0.00 0.00 2.32
2153 2295 0.541764 TTTTGGCCAGTCACCCATCC 60.542 55.000 5.11 0.00 0.00 3.51
2156 2298 0.032615 ACTTTTTGGCCAGTCACCCA 60.033 50.000 5.11 0.00 0.00 4.51
2169 2311 3.056322 GCATCTGCAGGGATCAACTTTTT 60.056 43.478 15.13 0.00 41.59 1.94


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

AutoCloner maintained by Alex Coulton.