Multiple sequence alignment - TraesCS5D01G142900

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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 TraesCS5D01G142900 chr5D 100.000 7476 0 0 1 7476 228783711 228776236 0.000000e+00 13806
1 TraesCS5D01G142900 chr5A 94.762 5059 127 32 2491 7475 307353855 307348861 0.000000e+00 7747
2 TraesCS5D01G142900 chr5A 85.147 1535 96 45 504 1974 307356125 307354659 0.000000e+00 1450
3 TraesCS5D01G142900 chr5A 90.237 379 35 2 1 379 307356689 307356313 1.870000e-135 494
4 TraesCS5D01G142900 chr5A 81.818 374 27 16 2136 2480 307354200 307353839 7.390000e-70 276
5 TraesCS5D01G142900 chr5A 84.722 144 18 3 7334 7475 456056181 456056040 2.810000e-29 141
6 TraesCS5D01G142900 chr5A 90.526 95 9 0 4234 4328 703427126 703427032 7.870000e-25 126
7 TraesCS5D01G142900 chr5A 96.000 75 3 0 429 503 307356227 307356153 1.020000e-23 122
8 TraesCS5D01G142900 chr5B 96.173 4390 123 15 2491 6840 254577557 254573173 0.000000e+00 7134
9 TraesCS5D01G142900 chr5B 87.334 2179 133 59 1 2109 254579926 254577821 0.000000e+00 2362
10 TraesCS5D01G142900 chr5B 91.582 594 32 8 6900 7475 254573173 254572580 0.000000e+00 804
11 TraesCS5D01G142900 chr5B 90.222 225 17 3 2256 2480 254577760 254577541 9.490000e-74 289
12 TraesCS5D01G142900 chr5B 84.722 144 18 3 7334 7475 608332974 608332833 2.810000e-29 141
13 TraesCS5D01G142900 chr3B 80.882 204 22 7 7225 7418 455069488 455069292 2.170000e-30 145
14 TraesCS5D01G142900 chr1B 85.211 142 19 2 7334 7475 74127471 74127332 2.170000e-30 145
15 TraesCS5D01G142900 chr1B 84.459 148 17 5 7331 7475 629690536 629690680 2.810000e-29 141
16 TraesCS5D01G142900 chr4A 84.459 148 17 5 7331 7475 374493496 374493640 2.810000e-29 141
17 TraesCS5D01G142900 chr4A 83.673 147 20 3 7331 7475 27185172 27185316 1.310000e-27 135
18 TraesCS5D01G142900 chr2A 84.722 144 18 3 7334 7475 713201816 713201675 2.810000e-29 141


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 TraesCS5D01G142900 chr5D 228776236 228783711 7475 True 13806.00 13806 100.00000 1 7476 1 chr5D.!!$R1 7475
1 TraesCS5D01G142900 chr5A 307348861 307356689 7828 True 2017.80 7747 89.59280 1 7475 5 chr5A.!!$R3 7474
2 TraesCS5D01G142900 chr5B 254572580 254579926 7346 True 2647.25 7134 91.32775 1 7475 4 chr5B.!!$R2 7474

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
68 69 0.100503 GTTGCTGCAAAGAACGGTGT 59.899 50.000 17.80 0.0 0.00 4.16 F
789 908 0.469892 AAACAGCACCCCCTTCCTTG 60.470 55.000 0.00 0.0 0.00 3.61 F
2047 2252 0.179000 CGGACAGAGGGCTTAGCATT 59.821 55.000 6.53 0.0 0.00 3.56 F
2585 3184 0.109132 CACAGAATCTTTTGGCGGGC 60.109 55.000 0.00 0.0 0.00 6.13 F
2586 3185 0.251341 ACAGAATCTTTTGGCGGGCT 60.251 50.000 2.38 0.0 0.00 5.19 F
2587 3186 1.004277 ACAGAATCTTTTGGCGGGCTA 59.996 47.619 2.38 0.0 0.00 3.93 F
2588 3187 1.401905 CAGAATCTTTTGGCGGGCTAC 59.598 52.381 2.38 0.0 0.00 3.58 F
3666 4275 1.968540 GGACCAAGTGCCTGCTGAC 60.969 63.158 0.00 0.0 0.00 3.51 F
4848 5457 0.390472 GACCTGGAGTGAAGGAAGCG 60.390 60.000 0.00 0.0 38.27 4.68 F
5267 5876 1.278985 CATTGCAGGGACAGAGGTACA 59.721 52.381 0.00 0.0 0.00 2.90 F
6026 6675 0.747255 ACATCGAGGGTCCAGATTCG 59.253 55.000 0.69 0.0 34.56 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1247 1414 0.037877 GGGGAGAGATGATGCATGGG 59.962 60.000 2.46 0.00 0.00 4.00 R
2566 3164 0.109132 GCCCGCCAAAAGATTCTGTG 60.109 55.000 0.00 0.00 0.00 3.66 R
2915 3524 3.117131 AGGGAACATGAACAAGGGAAACT 60.117 43.478 0.00 0.00 0.00 2.66 R
4403 5012 6.095860 AGGAGTACCCAAAACAGTTTGTTTAC 59.904 38.462 7.53 2.85 42.31 2.01 R
4431 5040 7.989826 AGCCATATTCAAATATCGCTATTTCC 58.010 34.615 11.59 0.00 41.79 3.13 R
4794 5403 7.395206 TCCTTGATGCCAAATATGATTATCAGG 59.605 37.037 0.29 0.00 0.00 3.86 R
4815 5424 2.358737 GGTCGCACAGGGTCCTTG 60.359 66.667 0.00 0.00 0.00 3.61 R
5849 6498 1.074405 TCATTTGGAGGCTCAGTTGCT 59.926 47.619 17.69 0.00 0.00 3.91 R
6026 6675 0.507358 GCGTGTTGAGAACGGTCTTC 59.493 55.000 3.47 0.00 41.31 2.87 R
6128 6780 0.732571 ACATTGCCATTAGTTCGCCG 59.267 50.000 0.00 0.00 0.00 6.46 R
6843 7500 1.457303 CTCCTTCGCTGAAAGTTGTCG 59.543 52.381 0.00 0.00 35.30 4.35 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
21 22 2.092524 ACGTTCACAACAACACGTGTAC 59.907 45.455 23.69 12.60 43.94 2.90
46 47 1.160329 GCCGCTCCTCGCAACAATAT 61.160 55.000 0.00 0.00 39.08 1.28
63 64 5.464168 ACAATATGAGTTGCTGCAAAGAAC 58.536 37.500 17.80 5.28 32.32 3.01
68 69 0.100503 GTTGCTGCAAAGAACGGTGT 59.899 50.000 17.80 0.00 0.00 4.16
88 89 3.018149 GTGGGTTGAGTGGTTGTTGTTA 58.982 45.455 0.00 0.00 0.00 2.41
110 111 3.070159 ACAAGTATGGACTCATCGGATGG 59.930 47.826 17.42 10.75 33.58 3.51
133 135 2.500098 GGTGCTGTGAGAGTGGGTTATA 59.500 50.000 0.00 0.00 0.00 0.98
135 137 3.056107 GTGCTGTGAGAGTGGGTTATACA 60.056 47.826 0.00 0.00 0.00 2.29
136 138 3.774766 TGCTGTGAGAGTGGGTTATACAT 59.225 43.478 0.00 0.00 0.00 2.29
277 279 2.632377 GAGCGGAGACCAAAATGATGA 58.368 47.619 0.00 0.00 0.00 2.92
287 289 5.018539 ACCAAAATGATGATGCAATGAGG 57.981 39.130 0.00 0.00 0.00 3.86
332 334 1.461127 GAATGTTGTGAGCTGGACGAC 59.539 52.381 0.00 0.00 0.00 4.34
347 349 2.187946 GACCAGGTGATGCGAGGG 59.812 66.667 0.00 0.00 0.00 4.30
383 385 4.093998 GCGAGATGAGACAAACATCATTGT 59.906 41.667 0.00 0.00 45.82 2.71
460 518 4.323477 CCGACGGTTTGGGAGGCA 62.323 66.667 5.48 0.00 0.00 4.75
507 593 5.010012 GGGAGCCAACCATATATTTGTGAAG 59.990 44.000 0.00 0.00 0.00 3.02
572 658 3.183130 CACACAAGTGGGACCAACA 57.817 52.632 0.72 0.00 42.13 3.33
773 892 6.781138 GGTTTTTCAAATCTTCAACCCAAAC 58.219 36.000 0.00 0.00 0.00 2.93
789 908 0.469892 AAACAGCACCCCCTTCCTTG 60.470 55.000 0.00 0.00 0.00 3.61
1107 1250 1.443872 CCTCGTCGTCAAGAACCGG 60.444 63.158 0.00 0.00 0.00 5.28
1186 1329 2.799371 GCTCCGTCCAGGTACGAG 59.201 66.667 11.67 4.55 45.68 4.18
1187 1330 2.799371 CTCCGTCCAGGTACGAGC 59.201 66.667 11.67 0.00 45.68 5.03
1205 1351 2.412421 GCACTTGCTTCACTTTCCTG 57.588 50.000 0.00 0.00 38.21 3.86
1216 1362 3.873910 TCACTTTCCTGCATAACCTAGC 58.126 45.455 0.00 0.00 0.00 3.42
1217 1363 3.263170 TCACTTTCCTGCATAACCTAGCA 59.737 43.478 0.00 0.00 39.25 3.49
1247 1414 2.429739 GCTTGCTTGCGGCTTCAC 60.430 61.111 0.00 0.00 42.39 3.18
1251 1418 3.064324 GCTTGCGGCTTCACCCAT 61.064 61.111 0.00 0.00 38.06 4.00
1270 1437 1.301558 GCATCATCTCTCCCCTGCG 60.302 63.158 0.00 0.00 0.00 5.18
1274 1441 1.039785 TCATCTCTCCCCTGCGTCTG 61.040 60.000 0.00 0.00 0.00 3.51
1287 1457 3.182967 CTGCGTCTGAACATCTCTTACC 58.817 50.000 0.00 0.00 0.00 2.85
1291 1461 4.169508 CGTCTGAACATCTCTTACCACTG 58.830 47.826 0.00 0.00 0.00 3.66
1300 1470 7.661536 ACATCTCTTACCACTGCTATTTCTA 57.338 36.000 0.00 0.00 0.00 2.10
1301 1471 7.493367 ACATCTCTTACCACTGCTATTTCTAC 58.507 38.462 0.00 0.00 0.00 2.59
1303 1473 5.955959 TCTCTTACCACTGCTATTTCTACCA 59.044 40.000 0.00 0.00 0.00 3.25
1395 1569 2.380064 AATGGCCCAAGAACAGTTGA 57.620 45.000 0.00 0.00 0.00 3.18
1396 1570 2.610438 ATGGCCCAAGAACAGTTGAT 57.390 45.000 0.00 0.00 0.00 2.57
1397 1571 1.619654 TGGCCCAAGAACAGTTGATG 58.380 50.000 0.00 0.00 0.00 3.07
1398 1572 1.144708 TGGCCCAAGAACAGTTGATGA 59.855 47.619 0.00 0.00 0.00 2.92
1399 1573 2.225091 TGGCCCAAGAACAGTTGATGAT 60.225 45.455 0.00 0.00 0.00 2.45
1400 1574 2.827921 GGCCCAAGAACAGTTGATGATT 59.172 45.455 0.00 0.00 0.00 2.57
1401 1575 4.016444 GGCCCAAGAACAGTTGATGATTA 58.984 43.478 0.00 0.00 0.00 1.75
1458 1639 5.560966 TCAGATCGCTTTCCAAAATTACC 57.439 39.130 0.00 0.00 0.00 2.85
1483 1665 5.813080 AGTTTAATCTGCATTTCCGTACC 57.187 39.130 0.00 0.00 0.00 3.34
1535 1717 5.980116 CGAAGACTTAGAGAGAGAGAGAGAG 59.020 48.000 0.00 0.00 0.00 3.20
1539 1721 6.549364 AGACTTAGAGAGAGAGAGAGAGAGAG 59.451 46.154 0.00 0.00 0.00 3.20
1540 1722 6.436027 ACTTAGAGAGAGAGAGAGAGAGAGA 58.564 44.000 0.00 0.00 0.00 3.10
1541 1723 6.549364 ACTTAGAGAGAGAGAGAGAGAGAGAG 59.451 46.154 0.00 0.00 0.00 3.20
1542 1724 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
1543 1725 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
1544 1726 4.222336 AGAGAGAGAGAGAGAGAGAGGAG 58.778 52.174 0.00 0.00 0.00 3.69
1545 1727 4.078922 AGAGAGAGAGAGAGAGAGAGGAGA 60.079 50.000 0.00 0.00 0.00 3.71
1546 1728 4.222336 AGAGAGAGAGAGAGAGAGGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
1547 1729 4.078922 AGAGAGAGAGAGAGAGAGGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
1548 1730 4.222336 AGAGAGAGAGAGAGAGGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
1549 1731 4.078922 AGAGAGAGAGAGAGAGGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
1588 1770 1.458486 CCTGTTTGGTGGTGGCCTA 59.542 57.895 3.32 0.00 0.00 3.93
1589 1771 0.609131 CCTGTTTGGTGGTGGCCTAG 60.609 60.000 3.32 0.00 0.00 3.02
1590 1772 1.228429 TGTTTGGTGGTGGCCTAGC 60.228 57.895 3.32 0.24 0.00 3.42
1634 1821 3.685139 ATCATGTTGACTTGACCGTCT 57.315 42.857 0.00 0.00 33.67 4.18
1772 1968 2.476185 CCAAAAGACAAGCTTATCGCCG 60.476 50.000 0.00 0.00 40.39 6.46
1961 2166 1.702957 ACCCTAGCTGGTTTGCAGTTA 59.297 47.619 0.00 0.00 33.91 2.24
1968 2173 5.782893 AGCTGGTTTGCAGTTATTAAACA 57.217 34.783 0.00 0.00 38.12 2.83
2006 2211 6.493115 ACTTCCTCCTCACATCTAGATACATG 59.507 42.308 4.54 4.82 0.00 3.21
2008 2213 4.525874 CCTCCTCACATCTAGATACATGCA 59.474 45.833 4.54 0.00 0.00 3.96
2017 2222 4.948847 TCTAGATACATGCATTTGAGCGT 58.051 39.130 0.00 0.00 37.31 5.07
2020 2225 3.940852 AGATACATGCATTTGAGCGTCAA 59.059 39.130 0.00 0.00 37.31 3.18
2021 2226 2.336554 ACATGCATTTGAGCGTCAAC 57.663 45.000 0.00 0.00 35.89 3.18
2026 2231 4.340894 TGCATTTGAGCGTCAACTAATC 57.659 40.909 0.76 0.00 35.89 1.75
2028 2233 4.093408 TGCATTTGAGCGTCAACTAATCTC 59.907 41.667 0.76 0.00 35.89 2.75
2033 2238 1.816835 AGCGTCAACTAATCTCGGACA 59.183 47.619 0.00 0.00 0.00 4.02
2039 2244 1.404843 ACTAATCTCGGACAGAGGGC 58.595 55.000 2.63 0.00 46.82 5.19
2040 2245 1.063567 ACTAATCTCGGACAGAGGGCT 60.064 52.381 2.63 0.00 46.82 5.19
2047 2252 0.179000 CGGACAGAGGGCTTAGCATT 59.821 55.000 6.53 0.00 0.00 3.56
2109 2341 5.220815 GCATGACAAGAGAAATGACTCCATC 60.221 44.000 0.00 0.00 37.60 3.51
2110 2342 5.488262 TGACAAGAGAAATGACTCCATCA 57.512 39.130 0.00 0.00 43.13 3.07
2113 2345 6.429078 TGACAAGAGAAATGACTCCATCAAAG 59.571 38.462 0.00 0.00 41.93 2.77
2114 2346 6.302269 ACAAGAGAAATGACTCCATCAAAGT 58.698 36.000 0.00 0.00 41.93 2.66
2117 2349 8.954350 CAAGAGAAATGACTCCATCAAAGTATT 58.046 33.333 0.00 0.00 41.93 1.89
2118 2350 8.729805 AGAGAAATGACTCCATCAAAGTATTC 57.270 34.615 0.00 0.00 41.93 1.75
2119 2351 8.547173 AGAGAAATGACTCCATCAAAGTATTCT 58.453 33.333 0.00 0.00 41.93 2.40
2125 2357 8.239038 TGACTCCATCAAAGTATTCTACTAGG 57.761 38.462 0.00 0.00 33.55 3.02
2127 2359 6.042208 ACTCCATCAAAGTATTCTACTAGGCC 59.958 42.308 0.00 0.00 38.26 5.19
2129 2361 6.385759 TCCATCAAAGTATTCTACTAGGCCAA 59.614 38.462 5.01 0.00 38.26 4.52
2130 2362 7.054124 CCATCAAAGTATTCTACTAGGCCAAA 58.946 38.462 5.01 0.00 38.26 3.28
2131 2363 7.556275 CCATCAAAGTATTCTACTAGGCCAAAA 59.444 37.037 5.01 0.00 38.26 2.44
2133 2365 9.700831 ATCAAAGTATTCTACTAGGCCAAAATT 57.299 29.630 5.01 0.00 38.26 1.82
2165 2735 4.635223 GGTAAACACCGGAGAGTAAAAGT 58.365 43.478 9.46 0.00 0.00 2.66
2166 2736 5.783111 GGTAAACACCGGAGAGTAAAAGTA 58.217 41.667 9.46 0.00 0.00 2.24
2167 2737 6.223120 GGTAAACACCGGAGAGTAAAAGTAA 58.777 40.000 9.46 0.00 0.00 2.24
2170 2740 7.628769 AAACACCGGAGAGTAAAAGTAAAAA 57.371 32.000 9.46 0.00 0.00 1.94
2203 2773 3.364023 CGACAGAAGAACACCAACGTATC 59.636 47.826 0.00 0.00 0.00 2.24
2224 2794 7.477422 CGTATCAAACAAAGACCATCTAAAACG 59.523 37.037 0.00 0.00 0.00 3.60
2229 2799 6.165659 ACAAAGACCATCTAAAACGATTCG 57.834 37.500 4.14 4.14 0.00 3.34
2237 2807 6.018751 ACCATCTAAAACGATTCGTCATCATG 60.019 38.462 12.80 10.65 39.99 3.07
2269 2845 5.473846 TGGCGTTCTTATGTTTTGACCATAA 59.526 36.000 0.00 0.00 34.51 1.90
2299 2897 7.197071 TGCACTATTTGAAATTAGTTGACGT 57.803 32.000 0.00 0.00 0.00 4.34
2300 2898 8.312896 TGCACTATTTGAAATTAGTTGACGTA 57.687 30.769 0.00 0.00 0.00 3.57
2346 2944 5.779529 ATGCAAGGATGGTTGATTGATAC 57.220 39.130 0.00 0.00 0.00 2.24
2347 2945 4.858850 TGCAAGGATGGTTGATTGATACT 58.141 39.130 0.00 0.00 0.00 2.12
2348 2946 5.263599 TGCAAGGATGGTTGATTGATACTT 58.736 37.500 0.00 0.00 0.00 2.24
2349 2947 6.422333 TGCAAGGATGGTTGATTGATACTTA 58.578 36.000 0.00 0.00 0.00 2.24
2350 2948 6.318648 TGCAAGGATGGTTGATTGATACTTAC 59.681 38.462 0.00 0.00 0.00 2.34
2397 2995 1.679311 GAGGGCCTGTGTGTCATGA 59.321 57.895 12.95 0.00 0.00 3.07
2478 3076 8.576442 CATGTAACTACAAAGTTGGGAATCTTT 58.424 33.333 1.11 0.00 45.63 2.52
2479 3077 8.161699 TGTAACTACAAAGTTGGGAATCTTTC 57.838 34.615 1.11 0.00 45.63 2.62
2480 3078 6.650427 AACTACAAAGTTGGGAATCTTTCC 57.350 37.500 0.00 0.00 44.40 3.13
2523 3121 3.068307 TCTTTCTAGTCAATAGGCGGCTC 59.932 47.826 17.67 0.00 31.83 4.70
2562 3160 6.149142 CAGAGATGGAGAATAATTTAGGCAGC 59.851 42.308 0.00 0.00 0.00 5.25
2563 3161 6.044171 AGAGATGGAGAATAATTTAGGCAGCT 59.956 38.462 0.00 0.00 0.00 4.24
2566 3164 8.046107 AGATGGAGAATAATTTAGGCAGCTATC 58.954 37.037 0.00 0.00 0.00 2.08
2584 3183 1.533625 TCACAGAATCTTTTGGCGGG 58.466 50.000 0.00 0.00 0.00 6.13
2585 3184 0.109132 CACAGAATCTTTTGGCGGGC 60.109 55.000 0.00 0.00 0.00 6.13
2586 3185 0.251341 ACAGAATCTTTTGGCGGGCT 60.251 50.000 2.38 0.00 0.00 5.19
2587 3186 1.004277 ACAGAATCTTTTGGCGGGCTA 59.996 47.619 2.38 0.00 0.00 3.93
2588 3187 1.401905 CAGAATCTTTTGGCGGGCTAC 59.598 52.381 2.38 0.00 0.00 3.58
2647 3255 3.609853 CAATCAGCCTGCCAACTACTTA 58.390 45.455 0.00 0.00 0.00 2.24
2721 3329 4.949856 ACCCAGATGCTTCACGATTATTTT 59.050 37.500 2.07 0.00 0.00 1.82
2756 3364 4.161189 ACTCCAGTCTTGATGTGGATGTAG 59.839 45.833 5.50 0.00 39.66 2.74
2830 3439 4.309099 GAAAATTGCAGGCTCACATTCAA 58.691 39.130 0.00 0.00 0.00 2.69
2935 3544 4.937201 AAGTTTCCCTTGTTCATGTTCC 57.063 40.909 0.00 0.00 30.18 3.62
3003 3612 4.022416 TGCAATCACTTTCATTGGTGGTAC 60.022 41.667 0.00 0.00 32.66 3.34
3666 4275 1.968540 GGACCAAGTGCCTGCTGAC 60.969 63.158 0.00 0.00 0.00 3.51
3786 4395 2.226674 GGCAGGAACTAAAGTGCAAGAC 59.773 50.000 0.00 0.00 36.02 3.01
4397 5006 2.291741 GTGCAGAGGTTGTCAAAGGAAG 59.708 50.000 0.00 0.00 0.00 3.46
4403 5012 3.490348 AGGTTGTCAAAGGAAGTGATGG 58.510 45.455 0.00 0.00 0.00 3.51
4428 5037 4.245251 ACAAACTGTTTTGGGTACTCCT 57.755 40.909 2.41 0.00 45.65 3.69
4431 5040 3.672767 ACTGTTTTGGGTACTCCTACG 57.327 47.619 0.00 0.00 36.20 3.51
4794 5403 3.664551 AGCCCTCCTAATGGTTTTACC 57.335 47.619 0.00 0.00 39.22 2.85
4815 5424 8.579850 TTACCCTGATAATCATATTTGGCATC 57.420 34.615 0.00 0.00 0.00 3.91
4830 5439 1.296392 CATCAAGGACCCTGTGCGA 59.704 57.895 0.00 0.00 0.00 5.10
4848 5457 0.390472 GACCTGGAGTGAAGGAAGCG 60.390 60.000 0.00 0.00 38.27 4.68
5011 5620 1.683319 GCCCAGAAGAAATGAGGGACC 60.683 57.143 0.00 0.00 42.25 4.46
5054 5663 9.756461 GGTTTGTTTCGTCTTTCTTATTCTATC 57.244 33.333 0.00 0.00 0.00 2.08
5064 5673 8.386606 GTCTTTCTTATTCTATCAAGTGCACTG 58.613 37.037 22.49 14.60 0.00 3.66
5069 5678 9.283768 TCTTATTCTATCAAGTGCACTGAAAAA 57.716 29.630 22.49 14.40 0.00 1.94
5070 5679 9.552114 CTTATTCTATCAAGTGCACTGAAAAAG 57.448 33.333 22.49 14.23 0.00 2.27
5256 5865 3.451665 GCTATGGGCATTGCAGGG 58.548 61.111 11.39 0.00 38.95 4.45
5267 5876 1.278985 CATTGCAGGGACAGAGGTACA 59.721 52.381 0.00 0.00 0.00 2.90
5317 5928 6.674694 AGTAGCATCAGTAGAAAATTGCAG 57.325 37.500 0.00 0.00 30.35 4.41
5335 5946 5.598416 TGCAGAGTTAGATGCTTAAGCTA 57.402 39.130 26.90 14.45 42.98 3.32
5410 6025 8.911918 TTGGCAATGATAACCTATTTACGTAT 57.088 30.769 0.00 0.00 0.00 3.06
5428 6046 8.961294 TTACGTATCCTATAATTCTCTTTCGC 57.039 34.615 0.00 0.00 0.00 4.70
5456 6091 6.708949 GTGGTTGGAGTAGACAGAAATAAACA 59.291 38.462 0.00 0.00 0.00 2.83
5487 6122 9.953565 ACAAATCCATCATCATTTTCATTTTCT 57.046 25.926 0.00 0.00 0.00 2.52
5500 6148 9.282247 CATTTTCATTTTCTTCACTATCTTCGG 57.718 33.333 0.00 0.00 0.00 4.30
5524 6172 4.379174 GCAGGTTGCGAAGGAGAA 57.621 55.556 0.00 0.00 31.71 2.87
5729 6377 9.476202 GTATTCATTTAACAGCTTGGTTTTTCT 57.524 29.630 0.00 0.00 32.29 2.52
5734 6383 4.326504 AACAGCTTGGTTTTTCTCCATG 57.673 40.909 0.00 0.00 34.75 3.66
5837 6486 7.498900 GTGAACATGATTATGGACACATTAGGA 59.501 37.037 17.52 0.00 40.58 2.94
5993 6642 2.785258 GTTCTCATGTTCGCCGGC 59.215 61.111 19.07 19.07 0.00 6.13
6012 6661 3.674423 GGCGAAAATCTTCTGAACATCG 58.326 45.455 0.00 0.00 0.00 3.84
6026 6675 0.747255 ACATCGAGGGTCCAGATTCG 59.253 55.000 0.69 0.00 34.56 3.34
6089 6738 1.281577 TGCCAGGTGAGTGATGCATTA 59.718 47.619 0.00 0.00 0.00 1.90
6097 6746 4.510711 GGTGAGTGATGCATTATGAGACAG 59.489 45.833 0.00 0.00 0.00 3.51
6098 6747 5.354767 GTGAGTGATGCATTATGAGACAGA 58.645 41.667 0.00 0.00 0.00 3.41
6100 6752 6.482641 GTGAGTGATGCATTATGAGACAGATT 59.517 38.462 0.00 0.00 0.00 2.40
6116 6768 8.131731 TGAGACAGATTCTAGTCATTTACATCG 58.868 37.037 14.52 0.00 37.23 3.84
6128 6780 5.627780 GTCATTTACATCGTTGTTCCAAACC 59.372 40.000 4.14 0.00 37.28 3.27
6141 6793 0.450184 CCAAACCGGCGAACTAATGG 59.550 55.000 9.30 4.04 0.00 3.16
6265 6917 4.840168 GGGGTAATAAGCGCGACA 57.160 55.556 12.10 0.00 0.00 4.35
6277 6929 1.017177 GCGCGACAGTGGTATTCCAA 61.017 55.000 12.10 0.00 46.15 3.53
6403 7055 4.194640 GAGCTATCTTGAAGTGCATTCCA 58.805 43.478 0.00 0.00 37.08 3.53
6574 7226 7.621832 TTTTCTTGAATTCATTTGTAGTGCG 57.378 32.000 9.40 0.00 0.00 5.34
6618 7271 0.106335 TGGTGCTGCATTTGTTTGGG 59.894 50.000 5.27 0.00 0.00 4.12
6843 7500 5.901552 TCAAAACCCAATCTCACTGAAAAC 58.098 37.500 0.00 0.00 0.00 2.43
6865 7525 3.330267 GACAACTTTCAGCGAAGGAGAT 58.670 45.455 7.25 0.00 0.00 2.75
6911 7571 0.464916 GTTCCAAACCGTCCACAGGT 60.465 55.000 0.00 0.00 45.29 4.00
6912 7572 0.179040 TTCCAAACCGTCCACAGGTC 60.179 55.000 0.00 0.00 41.95 3.85
6979 7639 0.867746 GAACGCAGCAACATCACTCA 59.132 50.000 0.00 0.00 0.00 3.41
7027 7687 7.149192 CGTTGGAAAAACATTTCGACATAAGTC 60.149 37.037 0.00 0.00 41.46 3.01
7081 7741 0.038599 AACTGTGGAGCCATCATGCA 59.961 50.000 0.00 0.00 0.00 3.96
7232 7893 8.995220 GGTGAACTACAGAACATTAATGTGTTA 58.005 33.333 21.46 9.47 42.08 2.41
7297 7978 4.040445 ACACCTGCATACACAAACAAAC 57.960 40.909 0.00 0.00 0.00 2.93
7373 8064 3.439857 ACCAAGCAGAAAATAGAGCCA 57.560 42.857 0.00 0.00 0.00 4.75
7423 8115 2.092429 TGAAGCTTCAGAACAGTTGGGT 60.092 45.455 25.16 0.00 32.50 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 0.662619 CCGTTCTTTGCAGCAACTCA 59.337 50.000 7.54 0.00 0.00 3.41
63 64 1.153046 AACCACTCAACCCACACCG 60.153 57.895 0.00 0.00 0.00 4.94
68 69 2.223803 AACAACAACCACTCAACCCA 57.776 45.000 0.00 0.00 0.00 4.51
88 89 3.070159 CCATCCGATGAGTCCATACTTGT 59.930 47.826 10.12 0.00 35.56 3.16
110 111 2.740055 CCACTCTCACAGCACCGC 60.740 66.667 0.00 0.00 0.00 5.68
133 135 2.559668 CCTTGAAGCACCATTGTCATGT 59.440 45.455 0.00 0.00 0.00 3.21
135 137 3.159213 TCCTTGAAGCACCATTGTCAT 57.841 42.857 0.00 0.00 0.00 3.06
136 138 2.655090 TCCTTGAAGCACCATTGTCA 57.345 45.000 0.00 0.00 0.00 3.58
305 307 1.202639 AGCTCACAACATTCGTCACCA 60.203 47.619 0.00 0.00 0.00 4.17
308 310 1.069978 TCCAGCTCACAACATTCGTCA 59.930 47.619 0.00 0.00 0.00 4.35
332 334 1.227764 CATCCCTCGCATCACCTGG 60.228 63.158 0.00 0.00 0.00 4.45
347 349 3.918220 CTCGCCGCTCGCAACATC 61.918 66.667 0.00 0.00 37.30 3.06
383 385 0.463654 GCATCACCCCTCGCATAACA 60.464 55.000 0.00 0.00 0.00 2.41
460 518 3.160269 CTGCAGGGAGGAAAAATCAGTT 58.840 45.455 5.57 0.00 0.00 3.16
491 549 9.739276 TTCAAGTTCTCTTCACAAATATATGGT 57.261 29.630 0.00 0.00 0.00 3.55
507 593 2.222027 CCACTGGTGGTTCAAGTTCTC 58.778 52.381 11.29 0.00 45.53 2.87
529 615 1.003112 CCGAATCAAACCCGGGTGA 60.003 57.895 31.05 22.38 39.59 4.02
530 616 2.696759 GCCGAATCAAACCCGGGTG 61.697 63.158 31.05 16.91 43.17 4.61
568 654 3.500982 CCATTTGTACGGCAGATTGTTG 58.499 45.455 0.00 0.00 0.00 3.33
572 658 1.102978 GCCCATTTGTACGGCAGATT 58.897 50.000 4.07 0.00 42.52 2.40
773 892 2.677875 GCAAGGAAGGGGGTGCTG 60.678 66.667 0.00 0.00 34.13 4.41
789 908 0.465278 GCAGATTCAGGGAGGAAGGC 60.465 60.000 0.00 0.00 0.00 4.35
875 994 6.147492 CGAGGTGCAGGTACTACTAATACTAG 59.853 46.154 0.00 0.00 36.02 2.57
996 1139 3.324713 AGGTACTGCTCCATGGCC 58.675 61.111 6.96 0.00 37.18 5.36
1186 1329 1.601412 GCAGGAAAGTGAAGCAAGTGC 60.601 52.381 0.00 0.00 42.49 4.40
1187 1330 1.677576 TGCAGGAAAGTGAAGCAAGTG 59.322 47.619 0.00 0.00 31.42 3.16
1205 1351 2.481952 GCATACTGCTGCTAGGTTATGC 59.518 50.000 0.00 9.28 40.96 3.14
1218 1364 1.990563 CAAGCAAGCAAAGCATACTGC 59.009 47.619 0.00 0.00 45.46 4.40
1247 1414 0.037877 GGGGAGAGATGATGCATGGG 59.962 60.000 2.46 0.00 0.00 4.00
1251 1418 1.834996 GCAGGGGAGAGATGATGCA 59.165 57.895 0.00 0.00 33.92 3.96
1270 1437 3.929610 GCAGTGGTAAGAGATGTTCAGAC 59.070 47.826 0.00 0.00 0.00 3.51
1274 1441 7.044798 AGAAATAGCAGTGGTAAGAGATGTTC 58.955 38.462 6.07 2.72 0.00 3.18
1287 1457 8.680903 AGATTTGAAATGGTAGAAATAGCAGTG 58.319 33.333 0.00 0.00 0.00 3.66
1291 1461 7.012421 ACCGAGATTTGAAATGGTAGAAATAGC 59.988 37.037 0.00 0.00 0.00 2.97
1300 1470 3.081804 GGTCACCGAGATTTGAAATGGT 58.918 45.455 0.00 0.00 0.00 3.55
1301 1471 3.764885 GGTCACCGAGATTTGAAATGG 57.235 47.619 0.00 0.00 0.00 3.16
1395 1569 4.639334 AGCAGCAATCGATCAGTAATCAT 58.361 39.130 0.00 0.00 33.65 2.45
1396 1570 4.063998 AGCAGCAATCGATCAGTAATCA 57.936 40.909 0.00 0.00 33.65 2.57
1397 1571 4.770287 CAAGCAGCAATCGATCAGTAATC 58.230 43.478 0.00 0.00 0.00 1.75
1398 1572 3.003068 GCAAGCAGCAATCGATCAGTAAT 59.997 43.478 0.00 0.00 44.79 1.89
1399 1573 2.352651 GCAAGCAGCAATCGATCAGTAA 59.647 45.455 0.00 0.00 44.79 2.24
1400 1574 1.935873 GCAAGCAGCAATCGATCAGTA 59.064 47.619 0.00 0.00 44.79 2.74
1401 1575 0.731417 GCAAGCAGCAATCGATCAGT 59.269 50.000 0.00 0.00 44.79 3.41
1458 1639 7.352739 GGTACGGAAATGCAGATTAAACTATG 58.647 38.462 0.00 0.00 0.00 2.23
1483 1665 1.154413 GAGTCAATGGTGCGTTGCG 60.154 57.895 0.00 0.00 31.18 4.85
1535 1717 3.545703 CAGGAACTCTCTCTCCTCTCTC 58.454 54.545 0.00 0.00 40.22 3.20
1539 1721 0.738389 CGCAGGAACTCTCTCTCCTC 59.262 60.000 0.00 0.00 40.22 3.71
1540 1722 2.880770 CGCAGGAACTCTCTCTCCT 58.119 57.895 0.00 0.00 43.12 3.69
1593 1775 3.434319 GACGCATGGTGCCCACTG 61.434 66.667 0.00 0.00 41.12 3.66
1594 1776 4.722700 GGACGCATGGTGCCCACT 62.723 66.667 0.00 0.00 41.12 4.00
1634 1821 3.083349 CTCCGTCCTCCATGGCCA 61.083 66.667 8.56 8.56 35.26 5.36
1668 1863 2.592993 CCGCCCAGGGAAGTGAGAA 61.593 63.158 10.89 0.00 35.97 2.87
1772 1968 1.439644 GCCCTCATCGACAGGAGAC 59.560 63.158 12.98 1.99 31.91 3.36
1888 2085 2.742053 TGCTAGATTCTCCAACGCAAAC 59.258 45.455 0.00 0.00 0.00 2.93
1894 2091 4.754114 GGACATGATGCTAGATTCTCCAAC 59.246 45.833 0.00 0.00 0.00 3.77
1981 2186 6.019656 TGTATCTAGATGTGAGGAGGAAGT 57.980 41.667 15.79 0.00 0.00 3.01
1982 2187 6.572119 GCATGTATCTAGATGTGAGGAGGAAG 60.572 46.154 15.79 0.00 30.38 3.46
1983 2188 5.244851 GCATGTATCTAGATGTGAGGAGGAA 59.755 44.000 15.79 0.00 30.38 3.36
1985 2190 4.525874 TGCATGTATCTAGATGTGAGGAGG 59.474 45.833 15.79 0.00 30.38 4.30
1986 2191 5.718724 TGCATGTATCTAGATGTGAGGAG 57.281 43.478 15.79 0.52 30.38 3.69
1987 2192 6.676990 AATGCATGTATCTAGATGTGAGGA 57.323 37.500 15.79 4.81 30.38 3.71
1988 2193 6.932960 TCAAATGCATGTATCTAGATGTGAGG 59.067 38.462 15.79 2.06 30.38 3.86
1989 2194 7.360185 GCTCAAATGCATGTATCTAGATGTGAG 60.360 40.741 15.79 8.29 33.43 3.51
1990 2195 6.426025 GCTCAAATGCATGTATCTAGATGTGA 59.574 38.462 15.79 0.00 30.38 3.58
1991 2196 6.600350 GCTCAAATGCATGTATCTAGATGTG 58.400 40.000 15.79 11.82 30.38 3.21
1992 2197 5.407691 CGCTCAAATGCATGTATCTAGATGT 59.592 40.000 15.79 0.00 30.38 3.06
1993 2198 5.407691 ACGCTCAAATGCATGTATCTAGATG 59.592 40.000 15.79 0.83 0.00 2.90
1994 2199 5.545588 ACGCTCAAATGCATGTATCTAGAT 58.454 37.500 10.73 10.73 0.00 1.98
1995 2200 4.948847 ACGCTCAAATGCATGTATCTAGA 58.051 39.130 0.00 0.00 0.00 2.43
1996 2201 4.746611 TGACGCTCAAATGCATGTATCTAG 59.253 41.667 0.00 0.00 0.00 2.43
2006 2211 4.582459 GAGATTAGTTGACGCTCAAATGC 58.418 43.478 9.77 0.00 38.22 3.56
2008 2213 3.865745 CCGAGATTAGTTGACGCTCAAAT 59.134 43.478 6.10 6.10 38.22 2.32
2017 2222 3.024547 CCCTCTGTCCGAGATTAGTTGA 58.975 50.000 0.00 0.00 42.62 3.18
2020 2225 1.063567 AGCCCTCTGTCCGAGATTAGT 60.064 52.381 0.00 0.00 42.62 2.24
2021 2226 1.698506 AGCCCTCTGTCCGAGATTAG 58.301 55.000 0.00 0.00 42.62 1.73
2026 2231 1.323271 TGCTAAGCCCTCTGTCCGAG 61.323 60.000 0.00 0.00 39.57 4.63
2028 2233 0.179000 AATGCTAAGCCCTCTGTCCG 59.821 55.000 0.00 0.00 0.00 4.79
2033 2238 2.200081 TCCAAGAATGCTAAGCCCTCT 58.800 47.619 0.00 0.00 0.00 3.69
2039 2244 2.658285 TGGCCATCCAAGAATGCTAAG 58.342 47.619 0.00 0.00 39.99 2.18
2040 2245 2.824689 TGGCCATCCAAGAATGCTAA 57.175 45.000 0.00 0.00 39.99 3.09
2084 2316 3.376546 GGAGTCATTTCTCTTGTCATGCC 59.623 47.826 0.00 0.00 35.11 4.40
2114 2346 9.403583 CCTGTAAAATTTTGGCCTAGTAGAATA 57.596 33.333 13.76 0.00 0.00 1.75
2117 2349 5.650703 GCCTGTAAAATTTTGGCCTAGTAGA 59.349 40.000 16.30 0.00 37.81 2.59
2118 2350 5.891451 GCCTGTAAAATTTTGGCCTAGTAG 58.109 41.667 16.30 0.00 37.81 2.57
2119 2351 5.907866 GCCTGTAAAATTTTGGCCTAGTA 57.092 39.130 16.30 0.00 37.81 1.82
2125 2357 1.001520 ACCGGCCTGTAAAATTTTGGC 59.998 47.619 18.09 18.09 42.56 4.52
2127 2359 5.176039 GTGTTTACCGGCCTGTAAAATTTTG 59.824 40.000 27.71 0.00 41.09 2.44
2129 2361 4.262121 GGTGTTTACCGGCCTGTAAAATTT 60.262 41.667 27.71 0.00 41.09 1.82
2130 2362 3.256383 GGTGTTTACCGGCCTGTAAAATT 59.744 43.478 27.71 0.00 41.09 1.82
2131 2363 2.821378 GGTGTTTACCGGCCTGTAAAAT 59.179 45.455 27.71 0.00 41.09 1.82
2133 2365 1.894881 GGTGTTTACCGGCCTGTAAA 58.105 50.000 23.85 23.85 38.13 2.01
2174 2744 4.196193 TGGTGTTCTTCTGTCGTGATTTT 58.804 39.130 0.00 0.00 0.00 1.82
2175 2745 3.804036 TGGTGTTCTTCTGTCGTGATTT 58.196 40.909 0.00 0.00 0.00 2.17
2176 2746 3.469008 TGGTGTTCTTCTGTCGTGATT 57.531 42.857 0.00 0.00 0.00 2.57
2177 2747 3.131396 GTTGGTGTTCTTCTGTCGTGAT 58.869 45.455 0.00 0.00 0.00 3.06
2178 2748 2.546778 GTTGGTGTTCTTCTGTCGTGA 58.453 47.619 0.00 0.00 0.00 4.35
2179 2749 1.257936 CGTTGGTGTTCTTCTGTCGTG 59.742 52.381 0.00 0.00 0.00 4.35
2180 2750 1.134907 ACGTTGGTGTTCTTCTGTCGT 60.135 47.619 0.00 0.00 0.00 4.34
2181 2751 1.567504 ACGTTGGTGTTCTTCTGTCG 58.432 50.000 0.00 0.00 0.00 4.35
2189 2759 5.679792 GTCTTTGTTTGATACGTTGGTGTTC 59.320 40.000 0.00 0.00 0.00 3.18
2203 2773 7.059488 CGAATCGTTTTAGATGGTCTTTGTTTG 59.941 37.037 0.00 0.00 0.00 2.93
2224 2794 5.755813 CCATTCCTTTCATGATGACGAATC 58.244 41.667 0.00 0.00 35.67 2.52
2229 2799 2.684881 ACGCCATTCCTTTCATGATGAC 59.315 45.455 0.00 0.00 0.00 3.06
2237 2807 4.965119 ACATAAGAACGCCATTCCTTTC 57.035 40.909 0.00 0.00 38.16 2.62
2293 2891 6.183360 CGTCTTAGTCAAGTATCCTACGTCAA 60.183 42.308 0.00 0.00 33.20 3.18
2300 2898 9.367444 CATTTAAACGTCTTAGTCAAGTATCCT 57.633 33.333 0.00 0.00 33.20 3.24
2311 2909 6.128007 ACCATCCTTGCATTTAAACGTCTTAG 60.128 38.462 0.00 0.00 0.00 2.18
2318 2916 6.873076 TCAATCAACCATCCTTGCATTTAAAC 59.127 34.615 0.00 0.00 0.00 2.01
2322 2920 5.687166 ATCAATCAACCATCCTTGCATTT 57.313 34.783 0.00 0.00 0.00 2.32
2359 2957 5.823045 CCCTCCACTTTTATGATTGTACTCC 59.177 44.000 0.00 0.00 0.00 3.85
2360 2958 5.297029 GCCCTCCACTTTTATGATTGTACTC 59.703 44.000 0.00 0.00 0.00 2.59
2375 2973 2.448542 ACACACAGGCCCTCCACT 60.449 61.111 0.00 0.00 33.74 4.00
2397 2995 5.144100 CAGTCCAGATCCAGTATAGGAGTT 58.856 45.833 0.00 0.00 41.90 3.01
2488 3086 8.533569 TTGACTAGAAAGATTCCCAACTTTTT 57.466 30.769 0.00 0.00 36.63 1.94
2489 3087 8.712228 ATTGACTAGAAAGATTCCCAACTTTT 57.288 30.769 0.00 0.00 36.63 2.27
2490 3088 9.454859 CTATTGACTAGAAAGATTCCCAACTTT 57.545 33.333 0.00 0.00 38.74 2.66
2491 3089 8.049721 CCTATTGACTAGAAAGATTCCCAACTT 58.950 37.037 0.00 0.00 0.00 2.66
2492 3090 7.569240 CCTATTGACTAGAAAGATTCCCAACT 58.431 38.462 0.00 0.00 0.00 3.16
2493 3091 6.261158 GCCTATTGACTAGAAAGATTCCCAAC 59.739 42.308 0.00 0.00 0.00 3.77
2494 3092 6.357367 GCCTATTGACTAGAAAGATTCCCAA 58.643 40.000 0.00 0.00 0.00 4.12
2495 3093 5.453339 CGCCTATTGACTAGAAAGATTCCCA 60.453 44.000 0.00 0.00 0.00 4.37
2496 3094 4.991687 CGCCTATTGACTAGAAAGATTCCC 59.008 45.833 0.00 0.00 0.00 3.97
2497 3095 4.991687 CCGCCTATTGACTAGAAAGATTCC 59.008 45.833 0.00 0.00 0.00 3.01
2498 3096 4.449405 GCCGCCTATTGACTAGAAAGATTC 59.551 45.833 0.00 0.00 0.00 2.52
2499 3097 4.101741 AGCCGCCTATTGACTAGAAAGATT 59.898 41.667 0.00 0.00 0.00 2.40
2500 3098 3.643792 AGCCGCCTATTGACTAGAAAGAT 59.356 43.478 0.00 0.00 0.00 2.40
2501 3099 3.031736 AGCCGCCTATTGACTAGAAAGA 58.968 45.455 0.00 0.00 0.00 2.52
2502 3100 3.181475 TGAGCCGCCTATTGACTAGAAAG 60.181 47.826 0.00 0.00 0.00 2.62
2503 3101 2.764010 TGAGCCGCCTATTGACTAGAAA 59.236 45.455 0.00 0.00 0.00 2.52
2504 3102 2.362397 CTGAGCCGCCTATTGACTAGAA 59.638 50.000 0.00 0.00 0.00 2.10
2523 3121 3.341823 CATCTCTGGGAAGTGGAAACTG 58.658 50.000 0.00 0.00 0.00 3.16
2562 3160 3.313526 CCCGCCAAAAGATTCTGTGATAG 59.686 47.826 0.00 0.00 0.00 2.08
2563 3161 3.278574 CCCGCCAAAAGATTCTGTGATA 58.721 45.455 0.00 0.00 0.00 2.15
2566 3164 0.109132 GCCCGCCAAAAGATTCTGTG 60.109 55.000 0.00 0.00 0.00 3.66
2584 3183 4.193826 TCAAGACTTGATGGTCAGTAGC 57.806 45.455 13.99 0.00 38.57 3.58
2585 3184 6.459066 TCTTTCAAGACTTGATGGTCAGTAG 58.541 40.000 18.38 6.71 39.84 2.57
2586 3185 6.419484 TCTTTCAAGACTTGATGGTCAGTA 57.581 37.500 18.38 0.00 39.84 2.74
2587 3186 5.296151 TCTTTCAAGACTTGATGGTCAGT 57.704 39.130 18.38 0.00 39.84 3.41
2588 3187 5.704515 ACATCTTTCAAGACTTGATGGTCAG 59.295 40.000 18.38 9.74 39.84 3.51
2721 3329 4.640771 AGACTGGAGTATTTGCCAAGAA 57.359 40.909 0.00 0.00 32.95 2.52
2756 3364 6.206829 AGTTCACCTGTTAAACATAAAGGAGC 59.793 38.462 0.00 0.00 0.00 4.70
2804 3413 0.604578 TGAGCCTGCAATTTTCCTGC 59.395 50.000 0.00 0.00 40.35 4.85
2915 3524 3.117131 AGGGAACATGAACAAGGGAAACT 60.117 43.478 0.00 0.00 0.00 2.66
3786 4395 6.504398 TGTTACTATCATCTTAGCAGAACCG 58.496 40.000 0.00 0.00 30.76 4.44
4403 5012 6.095860 AGGAGTACCCAAAACAGTTTGTTTAC 59.904 38.462 7.53 2.85 42.31 2.01
4428 5037 9.093970 CCATATTCAAATATCGCTATTTCCGTA 57.906 33.333 1.34 0.00 35.77 4.02
4431 5040 7.989826 AGCCATATTCAAATATCGCTATTTCC 58.010 34.615 11.59 0.00 41.79 3.13
4794 5403 7.395206 TCCTTGATGCCAAATATGATTATCAGG 59.605 37.037 0.29 0.00 0.00 3.86
4815 5424 2.358737 GGTCGCACAGGGTCCTTG 60.359 66.667 0.00 0.00 0.00 3.61
4830 5439 1.674057 CGCTTCCTTCACTCCAGGT 59.326 57.895 0.00 0.00 32.59 4.00
4932 5541 4.023450 CCATCATCAGTCAATATGCCACAC 60.023 45.833 0.00 0.00 0.00 3.82
5054 5663 5.863397 TCTTTCAACTTTTTCAGTGCACTTG 59.137 36.000 18.94 13.06 35.12 3.16
5214 5823 3.002348 GCCCAATATCTGCTTCGTGTAAC 59.998 47.826 0.00 0.00 0.00 2.50
5256 5865 7.119846 ACTGCATAAGAAAATTGTACCTCTGTC 59.880 37.037 0.00 0.00 0.00 3.51
5361 5972 3.879892 GGCCATTCTGTCATCTTACTTCC 59.120 47.826 0.00 0.00 0.00 3.46
5384 5995 7.633193 ACGTAAATAGGTTATCATTGCCAAA 57.367 32.000 0.00 0.00 0.00 3.28
5410 6025 5.453339 CCACAGGCGAAAGAGAATTATAGGA 60.453 44.000 0.00 0.00 0.00 2.94
5428 6046 2.248248 TCTGTCTACTCCAACCACAGG 58.752 52.381 0.00 0.00 36.04 4.00
5479 6114 7.979444 AAACCGAAGATAGTGAAGAAAATGA 57.021 32.000 0.00 0.00 0.00 2.57
5480 6115 8.076178 ACAAAACCGAAGATAGTGAAGAAAATG 58.924 33.333 0.00 0.00 0.00 2.32
5481 6116 8.076178 CACAAAACCGAAGATAGTGAAGAAAAT 58.924 33.333 0.00 0.00 0.00 1.82
5487 6122 4.130857 TGCACAAAACCGAAGATAGTGAA 58.869 39.130 0.00 0.00 0.00 3.18
5488 6123 3.734463 TGCACAAAACCGAAGATAGTGA 58.266 40.909 0.00 0.00 0.00 3.41
5500 6148 1.199624 CTTCGCAACCTGCACAAAAC 58.800 50.000 0.00 0.00 45.36 2.43
5524 6172 5.067805 TCGTCAAGTACTATGACATCAGCAT 59.932 40.000 24.81 0.00 45.90 3.79
5713 6361 3.070015 CCATGGAGAAAAACCAAGCTGTT 59.930 43.478 5.56 0.00 40.93 3.16
5849 6498 1.074405 TCATTTGGAGGCTCAGTTGCT 59.926 47.619 17.69 0.00 0.00 3.91
5993 6642 4.033358 CCCTCGATGTTCAGAAGATTTTCG 59.967 45.833 0.00 0.00 38.38 3.46
6012 6661 1.137282 GGTCTTCGAATCTGGACCCTC 59.863 57.143 18.84 0.34 41.48 4.30
6026 6675 0.507358 GCGTGTTGAGAACGGTCTTC 59.493 55.000 3.47 0.00 41.31 2.87
6089 6738 9.979578 GATGTAAATGACTAGAATCTGTCTCAT 57.020 33.333 0.00 4.61 37.84 2.90
6097 6746 8.328864 GGAACAACGATGTAAATGACTAGAATC 58.671 37.037 0.00 0.00 39.40 2.52
6098 6747 7.822334 TGGAACAACGATGTAAATGACTAGAAT 59.178 33.333 0.00 0.00 39.40 2.40
6100 6752 6.693466 TGGAACAACGATGTAAATGACTAGA 58.307 36.000 0.00 0.00 39.40 2.43
6128 6780 0.732571 ACATTGCCATTAGTTCGCCG 59.267 50.000 0.00 0.00 0.00 6.46
6141 6793 3.991605 ACATCGTCGAAAGTACATTGC 57.008 42.857 0.00 0.00 0.00 3.56
6265 6917 3.587061 TGATCACCACTTGGAATACCACT 59.413 43.478 1.14 0.00 46.80 4.00
6277 6929 4.116747 GAGAAACTCGATGATCACCACT 57.883 45.455 0.00 0.00 0.00 4.00
6403 7055 7.020827 TCCAGAGATTTCACCTGATTTAACT 57.979 36.000 0.00 0.00 0.00 2.24
6574 7226 2.037136 AATCCTGCAGCGCACACTC 61.037 57.895 11.47 0.00 33.79 3.51
6618 7271 1.000955 TCTCAAGCCGGAGTTGACTTC 59.999 52.381 5.05 0.00 36.30 3.01
6843 7500 1.457303 CTCCTTCGCTGAAAGTTGTCG 59.543 52.381 0.00 0.00 35.30 4.35
6865 7525 3.457099 TGCTGTCGCATATGCTTGA 57.543 47.368 24.56 13.12 42.25 3.02
6878 7538 4.202151 GGTTTGGAACTCTGAAAATGCTGT 60.202 41.667 0.00 0.00 0.00 4.40
6911 7571 4.163458 GGAAACTGGTGTATGATGGTAGGA 59.837 45.833 0.00 0.00 0.00 2.94
6912 7572 4.080582 TGGAAACTGGTGTATGATGGTAGG 60.081 45.833 0.00 0.00 0.00 3.18
6979 7639 5.358725 ACGGAGGTGTAGTTTGTTTGAATTT 59.641 36.000 0.00 0.00 0.00 1.82
7027 7687 1.670811 AGCTTTGAGTGTGTTGTTCCG 59.329 47.619 0.00 0.00 0.00 4.30
7081 7741 3.245016 TGACTGTGCTCCCTTTCATCATT 60.245 43.478 0.00 0.00 0.00 2.57
7232 7893 9.920946 ATTTCCCATCATTATACTACACAAACT 57.079 29.630 0.00 0.00 0.00 2.66
7287 7955 6.747280 CAGTCCTAACTCTTTGTTTGTTTGTG 59.253 38.462 0.00 0.00 39.89 3.33
7297 7978 8.842358 TGGTTTATAACAGTCCTAACTCTTTG 57.158 34.615 0.00 0.00 31.71 2.77
7423 8115 8.735315 TCTTCCGTTTTATGAATTAAAGATGCA 58.265 29.630 0.00 0.00 31.57 3.96


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

AutoCloner maintained by Alex Coulton.