Multiple sequence alignment - TraesCS5D01G513300

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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 TraesCS5D01G513300 chr5D 100.000 7731 0 0 1 7731 537392493 537400223 0.000000e+00 14277.0
1 TraesCS5D01G513300 chr5D 99.401 167 1 0 7069 7235 435791435 435791601 3.510000e-78 303.0
2 TraesCS5D01G513300 chr5D 100.000 47 0 0 1380 1426 537393825 537393871 3.840000e-13 87.9
3 TraesCS5D01G513300 chr5D 100.000 47 0 0 1333 1379 537393872 537393918 3.840000e-13 87.9
4 TraesCS5D01G513300 chr4A 97.116 5651 105 13 1380 7016 632858724 632864330 0.000000e+00 9479.0
5 TraesCS5D01G513300 chr4A 92.878 1362 79 11 27 1381 632857422 632858772 0.000000e+00 1962.0
6 TraesCS5D01G513300 chr4A 96.610 177 4 2 7072 7248 560316465 560316291 7.590000e-75 292.0
7 TraesCS5D01G513300 chr5B 95.111 4929 142 35 1380 6234 677880965 677876062 0.000000e+00 7675.0
8 TraesCS5D01G513300 chr5B 91.210 1388 86 9 3 1375 677882289 677880923 0.000000e+00 1855.0
9 TraesCS5D01G513300 chr5B 94.313 844 40 6 6233 7071 677875980 677875140 0.000000e+00 1286.0
10 TraesCS5D01G513300 chr5B 94.103 390 8 1 7342 7731 677874888 677874514 5.200000e-161 579.0
11 TraesCS5D01G513300 chr5B 93.750 208 10 3 7254 7460 677875131 677874926 7.530000e-80 309.0
12 TraesCS5D01G513300 chrUn 99.408 169 1 0 7067 7235 61009612 61009444 2.710000e-79 307.0
13 TraesCS5D01G513300 chr1D 99.408 169 1 0 7071 7239 366677272 366677440 2.710000e-79 307.0
14 TraesCS5D01G513300 chr2D 97.222 180 4 1 7061 7239 628554913 628554734 3.510000e-78 303.0
15 TraesCS5D01G513300 chr2D 98.256 172 2 1 7064 7235 5377823 5377993 4.530000e-77 300.0
16 TraesCS5D01G513300 chr2D 98.214 168 3 0 7072 7239 18207139 18206972 2.110000e-75 294.0
17 TraesCS5D01G513300 chr2D 86.792 212 18 6 7324 7528 31947697 31947489 2.170000e-55 228.0
18 TraesCS5D01G513300 chr7D 98.802 167 2 0 7072 7238 579632797 579632631 1.630000e-76 298.0
19 TraesCS5D01G513300 chr4D 98.225 169 3 0 7068 7236 281177084 281177252 5.870000e-76 296.0
20 TraesCS5D01G513300 chr4D 93.333 90 6 0 7564 7653 56703206 56703117 4.870000e-27 134.0
21 TraesCS5D01G513300 chr2A 90.659 182 15 2 7068 7247 94112382 94112563 2.790000e-59 241.0
22 TraesCS5D01G513300 chr2A 91.011 178 9 6 7069 7244 2035840 2036012 4.660000e-57 233.0
23 TraesCS5D01G513300 chr2A 90.055 181 17 1 7068 7248 478761525 478761346 4.660000e-57 233.0
24 TraesCS5D01G513300 chr2A 90.395 177 12 4 7069 7244 2090841 2091013 2.170000e-55 228.0
25 TraesCS5D01G513300 chr2A 90.395 177 12 4 7069 7244 2127660 2127832 2.170000e-55 228.0
26 TraesCS5D01G513300 chr2A 89.503 181 17 2 7072 7250 525274857 525274677 2.170000e-55 228.0
27 TraesCS5D01G513300 chr2A 89.503 181 17 2 7072 7250 525348738 525348558 2.170000e-55 228.0
28 TraesCS5D01G513300 chr2A 89.831 177 13 4 7069 7244 1960896 1961068 1.010000e-53 222.0
29 TraesCS5D01G513300 chr3B 93.750 96 6 0 7558 7653 820706315 820706220 2.250000e-30 145.0
30 TraesCS5D01G513300 chr3B 93.617 94 6 0 7560 7653 820577335 820577242 2.910000e-29 141.0
31 TraesCS5D01G513300 chr3B 85.455 110 11 4 7319 7426 820577740 820577634 8.200000e-20 110.0
32 TraesCS5D01G513300 chr6A 91.919 99 8 0 7555 7653 2873398 2873496 1.050000e-28 139.0
33 TraesCS5D01G513300 chr3D 94.595 37 2 0 7237 7273 1934697 1934661 3.010000e-04 58.4


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 TraesCS5D01G513300 chr5D 537392493 537400223 7730 False 14277.0 14277 100.0000 1 7731 1 chr5D.!!$F2 7730
1 TraesCS5D01G513300 chr4A 632857422 632864330 6908 False 5720.5 9479 94.9970 27 7016 2 chr4A.!!$F1 6989
2 TraesCS5D01G513300 chr5B 677874514 677882289 7775 True 2340.8 7675 93.6974 3 7731 5 chr5B.!!$R1 7728

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
960 980 0.108019 GTTTCAGGAGGGTTGGTCGT 59.892 55.000 0.00 0.00 0.00 4.34 F
1392 1415 0.250038 GAGTGGTGTGCTCAGCTTGA 60.250 55.000 17.78 0.00 41.91 3.02 F
1393 1416 0.250209 AGTGGTGTGCTCAGCTTGAG 60.250 55.000 17.78 8.34 46.90 3.02 F
1404 1427 1.202915 TCAGCTTGAGAATTGGTGGCA 60.203 47.619 0.00 0.00 0.00 4.92 F
1405 1428 1.614903 CAGCTTGAGAATTGGTGGCAA 59.385 47.619 0.00 0.00 0.00 4.52 F
1406 1429 1.615392 AGCTTGAGAATTGGTGGCAAC 59.385 47.619 0.00 0.00 0.00 4.17 F
3170 3279 1.686587 TGACTCCGAGCTTTGACTGAA 59.313 47.619 0.00 0.00 0.00 3.02 F
3385 3502 2.435805 CTGGATTGCTTACAGGAGGCTA 59.564 50.000 0.00 0.00 0.00 3.93 F
3737 3861 2.893489 GAGAAACTTGGGGAATGTTGCT 59.107 45.455 0.00 0.00 35.07 3.91 F
5621 5747 0.330604 AGTGGAGTCGCCTGTACCTA 59.669 55.000 0.00 0.00 37.63 3.08 F
6295 6513 0.108585 TCTTGCAGGTGGGACTCAAC 59.891 55.000 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 1965 0.908910 TGGCTAAGGATTTCGCCTCA 59.091 50.000 0.00 0.00 41.98 3.86 R
2490 2563 2.040278 TGGGCTAAGTTGCTGAGAACAT 59.960 45.455 0.00 0.00 0.00 2.71 R
3358 3475 4.191544 TCCTGTAAGCAATCCAGAAATCG 58.808 43.478 0.00 0.00 0.00 3.34 R
3502 3626 4.041075 TCATAGACAACAAACAGTAGCCCA 59.959 41.667 0.00 0.00 0.00 5.36 R
3680 3804 3.821033 GCAACTCCTGACCTTGTAAATGT 59.179 43.478 0.00 0.00 0.00 2.71 R
3737 3861 9.709495 CAAAGTTCTTTTGGATCCAATGATTTA 57.291 29.630 27.53 9.13 41.99 1.40 R
4961 5087 0.107654 GGAGCAGCAACCGGACTAAT 60.108 55.000 9.46 0.00 0.00 1.73 R
5609 5735 2.497273 GGTTAAAGGTAGGTACAGGCGA 59.503 50.000 0.00 0.00 0.00 5.54 R
5785 5911 1.425428 GGCAGATTTTCCTCGCACG 59.575 57.895 0.00 0.00 0.00 5.34 R
6430 6648 0.677731 GGCACATGCTGCTAGGAACA 60.678 55.000 16.34 0.00 46.25 3.18 R
7220 7446 1.192428 ACATGTACTCCCTCCGTTCC 58.808 55.000 0.00 0.00 0.00 3.62 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
18 19 4.452733 CGACCTCCTCAACCGCCC 62.453 72.222 0.00 0.00 0.00 6.13
19 20 4.097361 GACCTCCTCAACCGCCCC 62.097 72.222 0.00 0.00 0.00 5.80
20 21 4.658786 ACCTCCTCAACCGCCCCT 62.659 66.667 0.00 0.00 0.00 4.79
21 22 3.330720 CCTCCTCAACCGCCCCTT 61.331 66.667 0.00 0.00 0.00 3.95
23 24 2.528127 TCCTCAACCGCCCCTTGA 60.528 61.111 0.00 0.00 0.00 3.02
24 25 2.124507 CTCCTCAACCGCCCCTTGAA 62.125 60.000 0.00 0.00 0.00 2.69
25 26 1.000896 CCTCAACCGCCCCTTGAAT 60.001 57.895 0.00 0.00 0.00 2.57
58 59 4.518217 GTTTCAAGATGATATCCGCAACG 58.482 43.478 0.00 0.00 0.00 4.10
59 60 3.726291 TCAAGATGATATCCGCAACGA 57.274 42.857 0.00 0.00 0.00 3.85
89 90 6.145209 CGTCATCTGCTAGATATCAACCAAAG 59.855 42.308 5.32 0.00 32.12 2.77
148 149 2.548295 GCCGCACCGAAAGTTTCCA 61.548 57.895 10.01 0.00 0.00 3.53
165 166 3.159213 TCCACCTCTCTTACGTTACCA 57.841 47.619 0.00 0.00 0.00 3.25
175 178 4.942852 TCTTACGTTACCACCTTTTCGAA 58.057 39.130 0.00 0.00 0.00 3.71
176 179 5.355596 TCTTACGTTACCACCTTTTCGAAA 58.644 37.500 6.47 6.47 0.00 3.46
183 186 1.332375 CCACCTTTTCGAAAAGCGTCA 59.668 47.619 34.89 10.76 43.07 4.35
228 236 2.292267 GATGCGAGTTTGACCATCCAT 58.708 47.619 0.00 0.00 0.00 3.41
401 410 8.482852 AAATAAACAATGAATATCTCCCCCTG 57.517 34.615 0.00 0.00 0.00 4.45
402 411 3.515602 ACAATGAATATCTCCCCCTGC 57.484 47.619 0.00 0.00 0.00 4.85
403 412 2.108952 ACAATGAATATCTCCCCCTGCC 59.891 50.000 0.00 0.00 0.00 4.85
404 413 2.108776 CAATGAATATCTCCCCCTGCCA 59.891 50.000 0.00 0.00 0.00 4.92
405 414 1.438469 TGAATATCTCCCCCTGCCAG 58.562 55.000 0.00 0.00 0.00 4.85
406 415 0.695347 GAATATCTCCCCCTGCCAGG 59.305 60.000 2.91 2.91 34.30 4.45
475 484 1.902508 CAGGCCAGTTCCTTCTACTCA 59.097 52.381 5.01 0.00 33.25 3.41
476 485 1.903183 AGGCCAGTTCCTTCTACTCAC 59.097 52.381 5.01 0.00 30.82 3.51
482 491 4.321601 CCAGTTCCTTCTACTCACACTCAG 60.322 50.000 0.00 0.00 0.00 3.35
496 511 3.057547 CTCAGACTCAGCCGTCCCG 62.058 68.421 0.00 0.00 34.46 5.14
586 602 1.454847 CCCTCCAGTCCTCCTCTCG 60.455 68.421 0.00 0.00 0.00 4.04
592 608 0.750182 CAGTCCTCCTCTCGTCTCCC 60.750 65.000 0.00 0.00 0.00 4.30
627 643 3.622826 AGTCCACCGTTCCCACCG 61.623 66.667 0.00 0.00 0.00 4.94
700 716 3.905678 CCGGAGCTCGATTCGCCT 61.906 66.667 7.83 0.00 42.43 5.52
853 873 4.593864 GGTCTGGATCCGCGGCTC 62.594 72.222 23.51 21.88 0.00 4.70
958 978 0.605589 CGGTTTCAGGAGGGTTGGTC 60.606 60.000 0.00 0.00 0.00 4.02
960 980 0.108019 GTTTCAGGAGGGTTGGTCGT 59.892 55.000 0.00 0.00 0.00 4.34
974 994 0.586802 GGTCGTTTGGTGAGTGCTTC 59.413 55.000 0.00 0.00 0.00 3.86
996 1016 1.838077 CTCTAGGGTTTCGTGGGGATT 59.162 52.381 0.00 0.00 0.00 3.01
1173 1193 2.676471 GCGGCTGTGGGAAATGGT 60.676 61.111 0.00 0.00 0.00 3.55
1174 1194 2.275380 GCGGCTGTGGGAAATGGTT 61.275 57.895 0.00 0.00 0.00 3.67
1287 1307 2.679837 GCGAGTGGTTGTCATTCATGAT 59.320 45.455 0.00 0.00 39.30 2.45
1377 1400 2.111043 ACCGTTGCTGGTGGAGTG 59.889 61.111 0.00 0.00 41.85 3.51
1378 1401 2.669569 CCGTTGCTGGTGGAGTGG 60.670 66.667 0.00 0.00 0.00 4.00
1379 1402 2.111043 CGTTGCTGGTGGAGTGGT 59.889 61.111 0.00 0.00 0.00 4.16
1380 1403 2.253758 CGTTGCTGGTGGAGTGGTG 61.254 63.158 0.00 0.00 0.00 4.17
1381 1404 1.152963 GTTGCTGGTGGAGTGGTGT 60.153 57.895 0.00 0.00 0.00 4.16
1382 1405 1.152984 TTGCTGGTGGAGTGGTGTG 60.153 57.895 0.00 0.00 0.00 3.82
1383 1406 2.980233 GCTGGTGGAGTGGTGTGC 60.980 66.667 0.00 0.00 0.00 4.57
1384 1407 2.831770 CTGGTGGAGTGGTGTGCT 59.168 61.111 0.00 0.00 0.00 4.40
1385 1408 1.302033 CTGGTGGAGTGGTGTGCTC 60.302 63.158 0.00 0.00 0.00 4.26
1386 1409 2.043604 CTGGTGGAGTGGTGTGCTCA 62.044 60.000 0.00 0.00 34.83 4.26
1387 1410 1.302033 GGTGGAGTGGTGTGCTCAG 60.302 63.158 0.00 0.00 34.83 3.35
1388 1411 1.963338 GTGGAGTGGTGTGCTCAGC 60.963 63.158 10.89 10.89 41.77 4.26
1389 1412 2.142761 TGGAGTGGTGTGCTCAGCT 61.143 57.895 17.78 3.71 41.91 4.24
1390 1413 1.072159 GGAGTGGTGTGCTCAGCTT 59.928 57.895 17.78 7.28 41.91 3.74
1391 1414 1.233285 GGAGTGGTGTGCTCAGCTTG 61.233 60.000 17.78 0.00 41.91 4.01
1392 1415 0.250038 GAGTGGTGTGCTCAGCTTGA 60.250 55.000 17.78 0.00 41.91 3.02
1393 1416 0.250209 AGTGGTGTGCTCAGCTTGAG 60.250 55.000 17.78 8.34 46.90 3.02
1403 1426 1.538047 TCAGCTTGAGAATTGGTGGC 58.462 50.000 0.00 0.00 0.00 5.01
1404 1427 1.202915 TCAGCTTGAGAATTGGTGGCA 60.203 47.619 0.00 0.00 0.00 4.92
1405 1428 1.614903 CAGCTTGAGAATTGGTGGCAA 59.385 47.619 0.00 0.00 0.00 4.52
1406 1429 1.615392 AGCTTGAGAATTGGTGGCAAC 59.385 47.619 0.00 0.00 0.00 4.17
1417 1440 3.215568 TGGCAACACCGTTGCTGG 61.216 61.111 25.85 0.00 46.17 4.85
1418 1441 3.216292 GGCAACACCGTTGCTGGT 61.216 61.111 25.85 0.00 45.21 4.00
1436 1459 3.083997 GGAGTGGCGGAGGATGGT 61.084 66.667 0.00 0.00 0.00 3.55
1663 1686 3.746492 AGCAGGTCAGTTTTACGATTGAC 59.254 43.478 0.00 0.00 39.29 3.18
1668 1691 3.071479 TCAGTTTTACGATTGACCTGCC 58.929 45.455 0.00 0.00 0.00 4.85
1724 1747 5.315645 TCATATGGGAATGTATGGGTGGAAT 59.684 40.000 2.13 0.00 0.00 3.01
1741 1764 7.068839 TGGGTGGAATATATTATGCACGTTTTT 59.931 33.333 0.00 0.00 38.60 1.94
1742 1765 7.381139 GGGTGGAATATATTATGCACGTTTTTG 59.619 37.037 0.00 0.00 38.60 2.44
1744 1767 8.742188 GTGGAATATATTATGCACGTTTTTGTG 58.258 33.333 0.00 0.00 42.81 3.33
1912 1965 4.498520 CACGCTGGCGAGACGGAT 62.499 66.667 21.77 0.00 42.83 4.18
2470 2542 9.252962 CCATGCCACTCAGATATTTTAATTTTC 57.747 33.333 0.00 0.00 0.00 2.29
2825 2920 9.869757 GTGTACCTTCTAAAATATTGGCAAATT 57.130 29.630 3.01 3.00 0.00 1.82
3027 3122 4.734398 TCTTGGAATATGCGCCAATTTT 57.266 36.364 4.18 0.00 42.79 1.82
3170 3279 1.686587 TGACTCCGAGCTTTGACTGAA 59.313 47.619 0.00 0.00 0.00 3.02
3263 3372 5.695851 AAGTCGATGTTCTTGCTGATTTT 57.304 34.783 0.00 0.00 0.00 1.82
3358 3475 5.125417 TGAAGTTTACTATTGCTTGATGCCC 59.875 40.000 0.00 0.00 42.00 5.36
3385 3502 2.435805 CTGGATTGCTTACAGGAGGCTA 59.564 50.000 0.00 0.00 0.00 3.93
3737 3861 2.893489 GAGAAACTTGGGGAATGTTGCT 59.107 45.455 0.00 0.00 35.07 3.91
4000 4124 9.185680 GACATATAACCATTTTTAACTCCCAGT 57.814 33.333 0.00 0.00 0.00 4.00
4016 4140 3.193267 TCCCAGTAAATGTTTGCTCATGC 59.807 43.478 0.00 0.00 40.20 4.06
4261 4385 8.742777 TCAGGTTTATCATTTTGATCCTTTCAG 58.257 33.333 0.00 0.00 38.26 3.02
4866 4992 6.827641 TCATTAAGCTGTACGTCAATGTTTC 58.172 36.000 0.00 0.00 0.00 2.78
4961 5087 6.070481 TCACCATTACTGCAAGGTCTTATGTA 60.070 38.462 0.00 0.00 39.30 2.29
5609 5735 8.814038 AATTTCTAAGCATGATAAAGTGGAGT 57.186 30.769 0.00 0.00 0.00 3.85
5621 5747 0.330604 AGTGGAGTCGCCTGTACCTA 59.669 55.000 0.00 0.00 37.63 3.08
5756 5882 0.398318 GCAGTCTCCCAAAGAGGTGT 59.602 55.000 0.00 0.00 43.44 4.16
5785 5911 4.518970 TCAGAAAATTTGGTACACTCTGCC 59.481 41.667 8.34 0.00 39.29 4.85
5836 5962 2.857186 TTCTGCTGACATACAAGCCA 57.143 45.000 0.00 0.00 0.00 4.75
6049 6175 5.412904 GTGTTCTATGTTGCCTAGCTTTCTT 59.587 40.000 0.00 0.00 0.00 2.52
6059 6185 5.003804 TGCCTAGCTTTCTTCACCTTTAAG 58.996 41.667 0.00 0.00 0.00 1.85
6071 6197 7.781056 TCTTCACCTTTAAGTTTCATTGCTTT 58.219 30.769 0.00 0.00 0.00 3.51
6104 6230 5.945784 AGCTTCAATAAGTACATGAAAGGCA 59.054 36.000 0.00 0.00 34.99 4.75
6105 6231 6.434028 AGCTTCAATAAGTACATGAAAGGCAA 59.566 34.615 0.00 0.00 34.99 4.52
6106 6232 6.528072 GCTTCAATAAGTACATGAAAGGCAAC 59.472 38.462 0.00 0.00 34.99 4.17
6107 6233 7.575720 GCTTCAATAAGTACATGAAAGGCAACT 60.576 37.037 0.00 0.00 41.78 3.16
6295 6513 0.108585 TCTTGCAGGTGGGACTCAAC 59.891 55.000 0.00 0.00 0.00 3.18
6430 6648 2.958355 CAAAGGTCATGTTGTCCTTGGT 59.042 45.455 6.77 0.00 43.34 3.67
6467 6685 0.110486 CCCTGGAATAACCGATGGGG 59.890 60.000 0.00 0.00 40.25 4.96
6530 6748 1.541147 CAATGACAACAACATCCGCCT 59.459 47.619 0.00 0.00 0.00 5.52
6628 6846 0.682292 TGTTCACTGTGATGGGCGTA 59.318 50.000 11.86 0.00 0.00 4.42
6926 7147 5.288472 CGGCTGTTTATTTCTATTTGGTTGC 59.712 40.000 0.00 0.00 0.00 4.17
6946 7167 3.119531 TGCAATTTAGGCTGTGGAAATCG 60.120 43.478 0.00 0.00 0.00 3.34
7022 7243 9.268282 AGAAGAGAACCAGAATATAACAGGTTA 57.732 33.333 8.74 0.00 42.26 2.85
7076 7302 9.717942 ATAGATTTGCTATTTCACATCTACTCC 57.282 33.333 2.83 0.00 38.08 3.85
7077 7303 6.995091 AGATTTGCTATTTCACATCTACTCCC 59.005 38.462 0.00 0.00 33.22 4.30
7078 7304 5.957771 TTGCTATTTCACATCTACTCCCT 57.042 39.130 0.00 0.00 0.00 4.20
7079 7305 5.537300 TGCTATTTCACATCTACTCCCTC 57.463 43.478 0.00 0.00 0.00 4.30
7080 7306 4.345257 TGCTATTTCACATCTACTCCCTCC 59.655 45.833 0.00 0.00 0.00 4.30
7081 7307 4.559704 GCTATTTCACATCTACTCCCTCCG 60.560 50.000 0.00 0.00 0.00 4.63
7082 7308 2.526888 TTCACATCTACTCCCTCCGT 57.473 50.000 0.00 0.00 0.00 4.69
7083 7309 2.526888 TCACATCTACTCCCTCCGTT 57.473 50.000 0.00 0.00 0.00 4.44
7084 7310 2.376109 TCACATCTACTCCCTCCGTTC 58.624 52.381 0.00 0.00 0.00 3.95
7085 7311 1.409427 CACATCTACTCCCTCCGTTCC 59.591 57.143 0.00 0.00 0.00 3.62
7086 7312 1.288335 ACATCTACTCCCTCCGTTCCT 59.712 52.381 0.00 0.00 0.00 3.36
7087 7313 2.512896 ACATCTACTCCCTCCGTTCCTA 59.487 50.000 0.00 0.00 0.00 2.94
7088 7314 3.053095 ACATCTACTCCCTCCGTTCCTAA 60.053 47.826 0.00 0.00 0.00 2.69
7089 7315 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
7090 7316 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
7091 7317 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
7092 7318 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
7093 7319 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
7094 7320 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
7095 7321 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
7096 7322 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
7097 7323 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
7098 7324 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
7099 7325 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
7100 7326 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
7101 7327 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
7102 7328 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
7103 7329 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
7104 7330 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
7105 7331 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
7118 7344 8.924511 TTGTCTTTCTAGAGATTTCAAATGGT 57.075 30.769 0.00 0.00 0.00 3.55
7119 7345 8.553459 TGTCTTTCTAGAGATTTCAAATGGTC 57.447 34.615 0.00 0.00 0.00 4.02
7120 7346 8.156820 TGTCTTTCTAGAGATTTCAAATGGTCA 58.843 33.333 0.00 0.00 0.00 4.02
7121 7347 8.447053 GTCTTTCTAGAGATTTCAAATGGTCAC 58.553 37.037 0.00 0.00 0.00 3.67
7122 7348 7.607991 TCTTTCTAGAGATTTCAAATGGTCACC 59.392 37.037 0.00 0.00 0.00 4.02
7123 7349 6.373005 TCTAGAGATTTCAAATGGTCACCA 57.627 37.500 0.00 0.00 38.19 4.17
7124 7350 6.173339 TCTAGAGATTTCAAATGGTCACCAC 58.827 40.000 0.00 0.00 35.80 4.16
7125 7351 4.728772 AGAGATTTCAAATGGTCACCACA 58.271 39.130 0.00 0.00 35.80 4.17
7126 7352 5.327732 AGAGATTTCAAATGGTCACCACAT 58.672 37.500 0.00 0.00 35.80 3.21
7127 7353 6.484288 AGAGATTTCAAATGGTCACCACATA 58.516 36.000 0.00 0.00 35.80 2.29
7128 7354 6.375455 AGAGATTTCAAATGGTCACCACATAC 59.625 38.462 0.00 0.00 35.80 2.39
7129 7355 4.757799 TTTCAAATGGTCACCACATACG 57.242 40.909 0.00 0.00 35.80 3.06
7130 7356 2.705730 TCAAATGGTCACCACATACGG 58.294 47.619 0.00 0.00 35.80 4.02
7131 7357 2.303311 TCAAATGGTCACCACATACGGA 59.697 45.455 0.00 0.00 35.80 4.69
7132 7358 3.054728 TCAAATGGTCACCACATACGGAT 60.055 43.478 0.00 0.00 35.80 4.18
7133 7359 2.620251 ATGGTCACCACATACGGATG 57.380 50.000 5.94 5.94 35.80 3.51
7135 7361 2.458620 TGGTCACCACATACGGATGTA 58.541 47.619 14.23 0.00 44.82 2.29
7136 7362 3.035363 TGGTCACCACATACGGATGTAT 58.965 45.455 14.23 1.38 44.82 2.29
7137 7363 4.216708 TGGTCACCACATACGGATGTATA 58.783 43.478 14.23 0.00 44.82 1.47
7138 7364 4.836175 TGGTCACCACATACGGATGTATAT 59.164 41.667 14.23 0.00 44.82 0.86
7139 7365 6.011481 TGGTCACCACATACGGATGTATATA 58.989 40.000 14.23 0.00 44.82 0.86
7140 7366 6.152154 TGGTCACCACATACGGATGTATATAG 59.848 42.308 14.23 0.00 44.82 1.31
7141 7367 6.376299 GGTCACCACATACGGATGTATATAGA 59.624 42.308 14.23 4.80 44.82 1.98
7142 7368 7.249147 GTCACCACATACGGATGTATATAGAC 58.751 42.308 14.23 12.97 44.82 2.59
7143 7369 6.943718 TCACCACATACGGATGTATATAGACA 59.056 38.462 14.23 2.07 44.82 3.41
7144 7370 7.614192 TCACCACATACGGATGTATATAGACAT 59.386 37.037 14.23 12.70 44.82 3.06
7145 7371 8.899771 CACCACATACGGATGTATATAGACATA 58.100 37.037 14.23 0.00 44.82 2.29
7146 7372 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
7175 7401 8.885494 AGAGTATAGATTCACTCATTTTGCTC 57.115 34.615 4.70 0.00 42.99 4.26
7176 7402 7.930865 AGAGTATAGATTCACTCATTTTGCTCC 59.069 37.037 4.70 0.00 42.99 4.70
7177 7403 5.998454 ATAGATTCACTCATTTTGCTCCG 57.002 39.130 0.00 0.00 0.00 4.63
7178 7404 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
7179 7405 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
7180 7406 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
7181 7407 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
7182 7408 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
7183 7409 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
7184 7410 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
7185 7411 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
7186 7412 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
7187 7413 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
7188 7414 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
7189 7415 2.953466 TTGCTCCGTATGTAGTCACC 57.047 50.000 0.00 0.00 0.00 4.02
7190 7416 1.842052 TGCTCCGTATGTAGTCACCA 58.158 50.000 0.00 0.00 0.00 4.17
7191 7417 2.384828 TGCTCCGTATGTAGTCACCAT 58.615 47.619 0.00 0.00 0.00 3.55
7192 7418 2.764010 TGCTCCGTATGTAGTCACCATT 59.236 45.455 0.00 0.00 0.00 3.16
7193 7419 3.196901 TGCTCCGTATGTAGTCACCATTT 59.803 43.478 0.00 0.00 0.00 2.32
7194 7420 3.555956 GCTCCGTATGTAGTCACCATTTG 59.444 47.826 0.00 0.00 0.00 2.32
7195 7421 4.679639 GCTCCGTATGTAGTCACCATTTGA 60.680 45.833 0.00 0.00 0.00 2.69
7196 7422 5.408880 TCCGTATGTAGTCACCATTTGAA 57.591 39.130 0.00 0.00 35.39 2.69
7197 7423 5.795972 TCCGTATGTAGTCACCATTTGAAA 58.204 37.500 0.00 0.00 35.39 2.69
7198 7424 5.640357 TCCGTATGTAGTCACCATTTGAAAC 59.360 40.000 0.00 0.00 35.39 2.78
7199 7425 5.163794 CCGTATGTAGTCACCATTTGAAACC 60.164 44.000 0.00 0.00 35.39 3.27
7200 7426 5.642063 CGTATGTAGTCACCATTTGAAACCT 59.358 40.000 0.00 0.00 35.39 3.50
7201 7427 6.183360 CGTATGTAGTCACCATTTGAAACCTC 60.183 42.308 0.00 0.00 35.39 3.85
7202 7428 5.304686 TGTAGTCACCATTTGAAACCTCT 57.695 39.130 0.00 0.00 35.39 3.69
7203 7429 6.428083 TGTAGTCACCATTTGAAACCTCTA 57.572 37.500 0.00 0.00 35.39 2.43
7204 7430 6.464222 TGTAGTCACCATTTGAAACCTCTAG 58.536 40.000 0.00 0.00 35.39 2.43
7205 7431 5.825593 AGTCACCATTTGAAACCTCTAGA 57.174 39.130 0.00 0.00 35.39 2.43
7206 7432 6.187727 AGTCACCATTTGAAACCTCTAGAA 57.812 37.500 0.00 0.00 35.39 2.10
7207 7433 6.601332 AGTCACCATTTGAAACCTCTAGAAA 58.399 36.000 0.00 0.00 35.39 2.52
7208 7434 6.712547 AGTCACCATTTGAAACCTCTAGAAAG 59.287 38.462 0.00 0.00 35.39 2.62
7209 7435 6.710744 GTCACCATTTGAAACCTCTAGAAAGA 59.289 38.462 0.00 0.00 35.39 2.52
7210 7436 6.710744 TCACCATTTGAAACCTCTAGAAAGAC 59.289 38.462 0.00 0.00 0.00 3.01
7211 7437 6.486657 CACCATTTGAAACCTCTAGAAAGACA 59.513 38.462 0.00 0.00 0.00 3.41
7212 7438 7.013274 CACCATTTGAAACCTCTAGAAAGACAA 59.987 37.037 0.00 0.00 0.00 3.18
7213 7439 7.013369 ACCATTTGAAACCTCTAGAAAGACAAC 59.987 37.037 0.00 0.00 0.00 3.32
7214 7440 7.229506 CCATTTGAAACCTCTAGAAAGACAACT 59.770 37.037 0.00 0.00 0.00 3.16
7215 7441 9.273016 CATTTGAAACCTCTAGAAAGACAACTA 57.727 33.333 0.00 0.00 0.00 2.24
7217 7443 9.847224 TTTGAAACCTCTAGAAAGACAACTATT 57.153 29.630 0.00 0.00 0.00 1.73
7218 7444 9.847224 TTGAAACCTCTAGAAAGACAACTATTT 57.153 29.630 0.00 0.00 0.00 1.40
7221 7447 9.945904 AAACCTCTAGAAAGACAACTATTTAGG 57.054 33.333 0.00 0.00 0.00 2.69
7222 7448 8.896722 ACCTCTAGAAAGACAACTATTTAGGA 57.103 34.615 0.00 0.00 0.00 2.94
7223 7449 9.322769 ACCTCTAGAAAGACAACTATTTAGGAA 57.677 33.333 0.00 0.00 0.00 3.36
7224 7450 9.589111 CCTCTAGAAAGACAACTATTTAGGAAC 57.411 37.037 0.00 0.00 0.00 3.62
7225 7451 9.291664 CTCTAGAAAGACAACTATTTAGGAACG 57.708 37.037 0.00 0.00 0.00 3.95
7226 7452 8.248945 TCTAGAAAGACAACTATTTAGGAACGG 58.751 37.037 0.00 0.00 0.00 4.44
7227 7453 7.001099 AGAAAGACAACTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
7228 7454 7.097834 AGAAAGACAACTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
7229 7455 5.340439 AGACAACTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
7230 7456 4.161754 AGACAACTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
7231 7457 4.098894 ACAACTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
7232 7458 4.161754 ACAACTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
7233 7459 3.991683 ACTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
7234 7460 5.134725 ACTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
7235 7461 4.892345 ACTATTTAGGAACGGAGGGAGTAC 59.108 45.833 0.00 0.00 0.00 2.73
7236 7462 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
7237 7463 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
7238 7464 1.486211 AGGAACGGAGGGAGTACATG 58.514 55.000 0.00 0.00 0.00 3.21
7239 7465 1.192428 GGAACGGAGGGAGTACATGT 58.808 55.000 2.69 2.69 0.00 3.21
7240 7466 2.024655 AGGAACGGAGGGAGTACATGTA 60.025 50.000 0.08 0.08 0.00 2.29
7241 7467 2.762327 GGAACGGAGGGAGTACATGTAA 59.238 50.000 7.25 0.00 0.00 2.41
7242 7468 3.387050 GGAACGGAGGGAGTACATGTAAT 59.613 47.826 7.25 6.28 0.00 1.89
7243 7469 4.586001 GGAACGGAGGGAGTACATGTAATA 59.414 45.833 7.25 0.00 0.00 0.98
7244 7470 5.245526 GGAACGGAGGGAGTACATGTAATAT 59.754 44.000 7.25 0.00 0.00 1.28
7245 7471 6.435277 GGAACGGAGGGAGTACATGTAATATA 59.565 42.308 7.25 0.00 0.00 0.86
7246 7472 7.123847 GGAACGGAGGGAGTACATGTAATATAT 59.876 40.741 7.25 0.00 0.00 0.86
7247 7473 8.431910 AACGGAGGGAGTACATGTAATATATT 57.568 34.615 7.25 2.97 0.00 1.28
7248 7474 9.537852 AACGGAGGGAGTACATGTAATATATTA 57.462 33.333 7.25 0.81 0.00 0.98
7249 7475 9.710818 ACGGAGGGAGTACATGTAATATATTAT 57.289 33.333 7.25 0.00 0.00 1.28
7282 7508 2.941720 GTCTAGTATCGTCTTCCCGTGT 59.058 50.000 0.00 0.00 0.00 4.49
7386 7767 4.613925 ATTCTTGACTCACTCTGCTTCA 57.386 40.909 0.00 0.00 0.00 3.02
7461 7842 6.203072 TGCTCTACCTATAAAAGAAGGGTCT 58.797 40.000 0.00 0.00 37.18 3.85
7495 7876 5.335191 CGCTTGCCTTCTTCACTCTATTTTT 60.335 40.000 0.00 0.00 0.00 1.94
7496 7877 6.128282 CGCTTGCCTTCTTCACTCTATTTTTA 60.128 38.462 0.00 0.00 0.00 1.52
7497 7878 7.414540 CGCTTGCCTTCTTCACTCTATTTTTAT 60.415 37.037 0.00 0.00 0.00 1.40
7498 7879 7.912773 GCTTGCCTTCTTCACTCTATTTTTATC 59.087 37.037 0.00 0.00 0.00 1.75
7499 7880 9.171877 CTTGCCTTCTTCACTCTATTTTTATCT 57.828 33.333 0.00 0.00 0.00 1.98
7500 7881 9.520515 TTGCCTTCTTCACTCTATTTTTATCTT 57.479 29.630 0.00 0.00 0.00 2.40
7501 7882 9.520515 TGCCTTCTTCACTCTATTTTTATCTTT 57.479 29.630 0.00 0.00 0.00 2.52
7653 8034 2.126467 CCTTTTGATGTTTGTGTGCGG 58.874 47.619 0.00 0.00 0.00 5.69
7679 8060 0.107459 TTTTTGTTTGTGCCTGGGCC 60.107 50.000 9.28 0.00 41.09 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.452733 GGCGGTTGAGGAGGTCGG 62.453 72.222 0.00 0.00 0.00 4.79
1 2 4.452733 GGGCGGTTGAGGAGGTCG 62.453 72.222 0.00 0.00 0.00 4.79
2 3 4.097361 GGGGCGGTTGAGGAGGTC 62.097 72.222 0.00 0.00 0.00 3.85
3 4 4.658786 AGGGGCGGTTGAGGAGGT 62.659 66.667 0.00 0.00 0.00 3.85
4 5 3.330720 AAGGGGCGGTTGAGGAGG 61.331 66.667 0.00 0.00 0.00 4.30
6 7 1.497309 ATTCAAGGGGCGGTTGAGGA 61.497 55.000 1.12 0.00 35.39 3.71
7 8 1.000896 ATTCAAGGGGCGGTTGAGG 60.001 57.895 1.12 0.00 35.39 3.86
9 10 1.304052 CCATTCAAGGGGCGGTTGA 60.304 57.895 0.00 0.00 31.98 3.18
10 11 2.350458 CCCATTCAAGGGGCGGTTG 61.350 63.158 0.00 0.00 45.60 3.77
11 12 2.037208 CCCATTCAAGGGGCGGTT 59.963 61.111 0.00 0.00 45.60 4.44
18 19 1.750193 ACGTATGTGCCCATTCAAGG 58.250 50.000 0.00 0.00 32.29 3.61
19 20 3.190327 TGAAACGTATGTGCCCATTCAAG 59.810 43.478 0.00 0.00 32.29 3.02
20 21 3.149981 TGAAACGTATGTGCCCATTCAA 58.850 40.909 0.00 0.00 32.29 2.69
21 22 2.784347 TGAAACGTATGTGCCCATTCA 58.216 42.857 0.00 0.00 32.29 2.57
23 24 3.417101 TCTTGAAACGTATGTGCCCATT 58.583 40.909 0.00 0.00 32.29 3.16
24 25 3.066291 TCTTGAAACGTATGTGCCCAT 57.934 42.857 0.00 0.00 34.97 4.00
25 26 2.552599 TCTTGAAACGTATGTGCCCA 57.447 45.000 0.00 0.00 0.00 5.36
58 59 2.515926 TCTAGCAGATGACGCCAATC 57.484 50.000 0.00 0.00 0.00 2.67
59 60 4.221482 TGATATCTAGCAGATGACGCCAAT 59.779 41.667 3.98 0.00 35.37 3.16
69 70 6.327365 TGATCCTTTGGTTGATATCTAGCAGA 59.673 38.462 16.49 12.56 31.59 4.26
89 90 5.459107 GCGGTCATTATGTCGTATATGATCC 59.541 44.000 0.00 0.00 0.00 3.36
128 129 0.952010 GGAAACTTTCGGTGCGGCTA 60.952 55.000 0.00 0.00 0.00 3.93
135 136 2.047830 AGAGAGGTGGAAACTTTCGGT 58.952 47.619 0.00 0.00 0.00 4.69
148 149 3.166560 AGGTGGTAACGTAAGAGAGGT 57.833 47.619 0.00 0.00 43.62 3.85
165 166 1.332686 GGTGACGCTTTTCGAAAAGGT 59.667 47.619 38.06 33.24 44.24 3.50
200 203 3.682292 AAACTCGCATCCCTCCGGC 62.682 63.158 0.00 0.00 0.00 6.13
201 204 1.815421 CAAACTCGCATCCCTCCGG 60.815 63.158 0.00 0.00 0.00 5.14
209 212 2.425143 ATGGATGGTCAAACTCGCAT 57.575 45.000 0.00 0.00 0.00 4.73
387 396 0.695347 CCTGGCAGGGGGAGATATTC 59.305 60.000 26.34 0.00 0.00 1.75
402 411 3.136123 CACGCCAATCTGCCCTGG 61.136 66.667 0.00 0.00 35.67 4.45
403 412 2.360350 ACACGCCAATCTGCCCTG 60.360 61.111 0.00 0.00 0.00 4.45
404 413 2.360350 CACACGCCAATCTGCCCT 60.360 61.111 0.00 0.00 0.00 5.19
405 414 2.672996 ACACACGCCAATCTGCCC 60.673 61.111 0.00 0.00 0.00 5.36
406 415 0.953471 TACACACACGCCAATCTGCC 60.953 55.000 0.00 0.00 0.00 4.85
475 484 1.528292 GGACGGCTGAGTCTGAGTGT 61.528 60.000 0.00 0.00 40.76 3.55
476 485 1.214062 GGACGGCTGAGTCTGAGTG 59.786 63.158 0.00 0.00 40.76 3.51
627 643 0.945099 GAATTCGGGAGCGGGATTTC 59.055 55.000 0.00 0.00 0.00 2.17
974 994 1.153628 CCCACGAAACCCTAGAGCG 60.154 63.158 0.00 0.00 0.00 5.03
996 1016 4.100084 CTGGCCGCCTCCATGTCA 62.100 66.667 11.61 0.00 35.22 3.58
1173 1193 0.303493 GCGAACTGTTGAGCGACAAA 59.697 50.000 0.00 0.00 40.36 2.83
1174 1194 1.495584 GGCGAACTGTTGAGCGACAA 61.496 55.000 0.00 0.00 36.02 3.18
1287 1307 3.118992 CCTCATCCTTCTCATTGTCGTCA 60.119 47.826 0.00 0.00 0.00 4.35
1292 1315 2.507471 GGGTCCTCATCCTTCTCATTGT 59.493 50.000 0.00 0.00 0.00 2.71
1293 1316 2.484417 CGGGTCCTCATCCTTCTCATTG 60.484 54.545 0.00 0.00 0.00 2.82
1294 1317 1.765314 CGGGTCCTCATCCTTCTCATT 59.235 52.381 0.00 0.00 0.00 2.57
1360 1383 2.111043 CACTCCACCAGCAACGGT 59.889 61.111 0.00 0.00 41.07 4.83
1362 1385 2.111043 ACCACTCCACCAGCAACG 59.889 61.111 0.00 0.00 0.00 4.10
1376 1399 0.469494 TTCTCAAGCTGAGCACACCA 59.531 50.000 7.39 0.00 43.95 4.17
1377 1400 1.818642 ATTCTCAAGCTGAGCACACC 58.181 50.000 7.39 0.00 43.95 4.16
1378 1401 2.095364 CCAATTCTCAAGCTGAGCACAC 60.095 50.000 7.39 0.00 43.95 3.82
1379 1402 2.156917 CCAATTCTCAAGCTGAGCACA 58.843 47.619 7.39 0.00 43.95 4.57
1380 1403 2.095364 CACCAATTCTCAAGCTGAGCAC 60.095 50.000 7.39 0.00 43.95 4.40
1381 1404 2.156917 CACCAATTCTCAAGCTGAGCA 58.843 47.619 7.39 0.00 43.95 4.26
1382 1405 1.471684 CCACCAATTCTCAAGCTGAGC 59.528 52.381 0.00 0.00 43.95 4.26
1383 1406 1.471684 GCCACCAATTCTCAAGCTGAG 59.528 52.381 6.79 6.79 45.59 3.35
1384 1407 1.202915 TGCCACCAATTCTCAAGCTGA 60.203 47.619 0.00 0.00 0.00 4.26
1385 1408 1.250328 TGCCACCAATTCTCAAGCTG 58.750 50.000 0.00 0.00 0.00 4.24
1386 1409 1.615392 GTTGCCACCAATTCTCAAGCT 59.385 47.619 0.00 0.00 32.75 3.74
1387 1410 1.340889 TGTTGCCACCAATTCTCAAGC 59.659 47.619 0.00 0.00 32.75 4.01
1388 1411 3.017265 GTGTTGCCACCAATTCTCAAG 57.983 47.619 0.00 0.00 35.44 3.02
1399 1422 2.026014 CAGCAACGGTGTTGCCAC 59.974 61.111 25.94 4.68 45.98 5.01
1400 1423 3.215568 CCAGCAACGGTGTTGCCA 61.216 61.111 25.94 0.00 45.98 4.92
1401 1424 3.216292 ACCAGCAACGGTGTTGCC 61.216 61.111 25.94 11.98 45.98 4.52
1407 1430 2.111043 CACTCCACCAGCAACGGT 59.889 61.111 0.00 0.00 41.07 4.83
1408 1431 2.669569 CCACTCCACCAGCAACGG 60.670 66.667 0.00 0.00 0.00 4.44
1409 1432 3.357079 GCCACTCCACCAGCAACG 61.357 66.667 0.00 0.00 0.00 4.10
1410 1433 3.357079 CGCCACTCCACCAGCAAC 61.357 66.667 0.00 0.00 0.00 4.17
1411 1434 4.641645 CCGCCACTCCACCAGCAA 62.642 66.667 0.00 0.00 0.00 3.91
1413 1436 4.767255 CTCCGCCACTCCACCAGC 62.767 72.222 0.00 0.00 0.00 4.85
1414 1437 4.087892 CCTCCGCCACTCCACCAG 62.088 72.222 0.00 0.00 0.00 4.00
1415 1438 3.924013 ATCCTCCGCCACTCCACCA 62.924 63.158 0.00 0.00 0.00 4.17
1416 1439 3.083997 ATCCTCCGCCACTCCACC 61.084 66.667 0.00 0.00 0.00 4.61
1417 1440 2.187946 CATCCTCCGCCACTCCAC 59.812 66.667 0.00 0.00 0.00 4.02
1418 1441 3.083349 CCATCCTCCGCCACTCCA 61.083 66.667 0.00 0.00 0.00 3.86
1419 1442 3.083997 ACCATCCTCCGCCACTCC 61.084 66.667 0.00 0.00 0.00 3.85
1420 1443 2.187946 CACCATCCTCCGCCACTC 59.812 66.667 0.00 0.00 0.00 3.51
1421 1444 3.402681 CCACCATCCTCCGCCACT 61.403 66.667 0.00 0.00 0.00 4.00
1422 1445 3.717294 ACCACCATCCTCCGCCAC 61.717 66.667 0.00 0.00 0.00 5.01
1423 1446 3.716195 CACCACCATCCTCCGCCA 61.716 66.667 0.00 0.00 0.00 5.69
1436 1459 0.757561 TGTCCTCCTCGTTCACACCA 60.758 55.000 0.00 0.00 0.00 4.17
1505 1528 2.667418 CAGCCCTCCACCTGACAG 59.333 66.667 0.00 0.00 0.00 3.51
1663 1686 7.706179 CACATGTAAATAAAAGGTAATGGCAGG 59.294 37.037 0.00 0.00 0.00 4.85
1724 1747 7.585867 ACACACACAAAAACGTGCATAATATA 58.414 30.769 0.00 0.00 40.73 0.86
1741 1764 4.133820 CAGACCCAAAATAGACACACACA 58.866 43.478 0.00 0.00 0.00 3.72
1742 1765 4.134563 ACAGACCCAAAATAGACACACAC 58.865 43.478 0.00 0.00 0.00 3.82
1744 1767 5.507315 CCAAACAGACCCAAAATAGACACAC 60.507 44.000 0.00 0.00 0.00 3.82
1836 1859 2.237392 GTGGACAGGAAACTCTGGCTAT 59.763 50.000 0.00 0.00 42.28 2.97
1880 1933 1.899521 GCGTGCCGGCGTTAAAGTTA 61.900 55.000 23.90 0.00 0.00 2.24
1912 1965 0.908910 TGGCTAAGGATTTCGCCTCA 59.091 50.000 0.00 0.00 41.98 3.86
2348 2419 5.377478 ACTGAAAAGGGGAAACTAAGAGTG 58.623 41.667 0.00 0.00 0.00 3.51
2490 2563 2.040278 TGGGCTAAGTTGCTGAGAACAT 59.960 45.455 0.00 0.00 0.00 2.71
2825 2920 7.093509 TGCACATAATGTAAGGTAGTCAAGAGA 60.094 37.037 0.00 0.00 0.00 3.10
3027 3122 6.823497 ACCTTCAAAGCAGTACTTACAGTTA 58.177 36.000 0.00 0.00 37.75 2.24
3114 3209 9.449719 CAGATGGTTAAGTGGAAAACTAACTAT 57.550 33.333 0.00 0.00 38.56 2.12
3170 3279 4.546829 TTAGGTCAACGCCAAGTAGAAT 57.453 40.909 0.00 0.00 0.00 2.40
3263 3372 8.690884 TCTAGTGTTTCAATCAAAATGTCCAAA 58.309 29.630 0.00 0.00 0.00 3.28
3265 3374 7.502226 ACTCTAGTGTTTCAATCAAAATGTCCA 59.498 33.333 0.00 0.00 0.00 4.02
3358 3475 4.191544 TCCTGTAAGCAATCCAGAAATCG 58.808 43.478 0.00 0.00 0.00 3.34
3502 3626 4.041075 TCATAGACAACAAACAGTAGCCCA 59.959 41.667 0.00 0.00 0.00 5.36
3680 3804 3.821033 GCAACTCCTGACCTTGTAAATGT 59.179 43.478 0.00 0.00 0.00 2.71
3737 3861 9.709495 CAAAGTTCTTTTGGATCCAATGATTTA 57.291 29.630 27.53 9.13 41.99 1.40
4961 5087 0.107654 GGAGCAGCAACCGGACTAAT 60.108 55.000 9.46 0.00 0.00 1.73
5609 5735 2.497273 GGTTAAAGGTAGGTACAGGCGA 59.503 50.000 0.00 0.00 0.00 5.54
5621 5747 4.566488 CCTGAATCTCAGCAGGTTAAAGGT 60.566 45.833 0.00 0.00 45.21 3.50
5756 5882 9.349713 AGAGTGTACCAAATTTTCTGACAATAA 57.650 29.630 0.00 0.00 0.00 1.40
5785 5911 1.425428 GGCAGATTTTCCTCGCACG 59.575 57.895 0.00 0.00 0.00 5.34
5836 5962 6.883744 TGCAGTTTCCTTCAGGTTTTTATTT 58.116 32.000 0.00 0.00 36.34 1.40
5934 6060 4.987963 TCCAATACATCCTCTGCATCAT 57.012 40.909 0.00 0.00 0.00 2.45
6049 6175 7.106439 TCAAAGCAATGAAACTTAAAGGTGA 57.894 32.000 0.00 0.00 0.00 4.02
6430 6648 0.677731 GGCACATGCTGCTAGGAACA 60.678 55.000 16.34 0.00 46.25 3.18
6467 6685 2.216898 GCTGATATCACCTGCCTTCAC 58.783 52.381 0.00 0.00 0.00 3.18
6628 6846 2.680913 GCAAACGCAGATCACGGCT 61.681 57.895 12.08 0.00 35.22 5.52
6926 7147 4.701956 ACGATTTCCACAGCCTAAATTG 57.298 40.909 0.00 0.00 32.53 2.32
7071 7297 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
7073 7299 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
7074 7300 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
7075 7301 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
7076 7302 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
7077 7303 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
7078 7304 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
7079 7305 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
7092 7318 9.354673 ACCATTTGAAATCTCTAGAAAGACAAA 57.645 29.630 0.00 4.41 0.00 2.83
7093 7319 8.924511 ACCATTTGAAATCTCTAGAAAGACAA 57.075 30.769 0.00 0.00 0.00 3.18
7094 7320 8.156820 TGACCATTTGAAATCTCTAGAAAGACA 58.843 33.333 0.00 0.00 0.00 3.41
7095 7321 8.447053 GTGACCATTTGAAATCTCTAGAAAGAC 58.553 37.037 0.00 0.00 0.00 3.01
7096 7322 7.607991 GGTGACCATTTGAAATCTCTAGAAAGA 59.392 37.037 0.00 0.00 0.00 2.52
7097 7323 7.391554 TGGTGACCATTTGAAATCTCTAGAAAG 59.608 37.037 0.00 0.00 0.00 2.62
7098 7324 7.174946 GTGGTGACCATTTGAAATCTCTAGAAA 59.825 37.037 7.94 0.00 35.28 2.52
7099 7325 6.655003 GTGGTGACCATTTGAAATCTCTAGAA 59.345 38.462 7.94 0.00 35.28 2.10
7100 7326 6.173339 GTGGTGACCATTTGAAATCTCTAGA 58.827 40.000 7.94 0.00 35.28 2.43
7101 7327 5.939883 TGTGGTGACCATTTGAAATCTCTAG 59.060 40.000 7.94 0.00 35.28 2.43
7102 7328 5.875224 TGTGGTGACCATTTGAAATCTCTA 58.125 37.500 7.94 0.00 35.28 2.43
7103 7329 4.728772 TGTGGTGACCATTTGAAATCTCT 58.271 39.130 7.94 0.00 35.28 3.10
7104 7330 5.649782 ATGTGGTGACCATTTGAAATCTC 57.350 39.130 7.94 0.00 35.28 2.75
7105 7331 5.123820 CGTATGTGGTGACCATTTGAAATCT 59.876 40.000 7.94 0.00 35.28 2.40
7106 7332 5.331902 CGTATGTGGTGACCATTTGAAATC 58.668 41.667 7.94 0.00 35.28 2.17
7107 7333 4.157656 CCGTATGTGGTGACCATTTGAAAT 59.842 41.667 7.94 0.00 35.28 2.17
7108 7334 3.504134 CCGTATGTGGTGACCATTTGAAA 59.496 43.478 7.94 0.00 35.28 2.69
7109 7335 3.078097 CCGTATGTGGTGACCATTTGAA 58.922 45.455 7.94 0.00 35.28 2.69
7110 7336 2.303311 TCCGTATGTGGTGACCATTTGA 59.697 45.455 7.94 0.00 35.28 2.69
7111 7337 2.705730 TCCGTATGTGGTGACCATTTG 58.294 47.619 7.94 0.00 35.28 2.32
7112 7338 3.278574 CATCCGTATGTGGTGACCATTT 58.721 45.455 7.94 0.45 35.28 2.32
7113 7339 2.238646 ACATCCGTATGTGGTGACCATT 59.761 45.455 7.94 0.86 44.79 3.16
7114 7340 1.837439 ACATCCGTATGTGGTGACCAT 59.163 47.619 7.94 0.00 44.79 3.55
7115 7341 1.271856 ACATCCGTATGTGGTGACCA 58.728 50.000 0.00 0.00 44.79 4.02
7116 7342 3.746045 ATACATCCGTATGTGGTGACC 57.254 47.619 3.56 0.00 45.99 4.02
7117 7343 7.094506 TGTCTATATACATCCGTATGTGGTGAC 60.095 40.741 3.56 5.93 45.99 3.67
7118 7344 6.943718 TGTCTATATACATCCGTATGTGGTGA 59.056 38.462 3.56 0.00 45.99 4.02
7119 7345 7.153217 TGTCTATATACATCCGTATGTGGTG 57.847 40.000 3.56 0.00 45.99 4.17
7120 7346 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
7149 7375 9.973450 GAGCAAAATGAGTGAATCTATACTCTA 57.027 33.333 0.00 0.00 42.86 2.43
7150 7376 7.930865 GGAGCAAAATGAGTGAATCTATACTCT 59.069 37.037 0.00 0.00 42.86 3.24
7151 7377 7.095857 CGGAGCAAAATGAGTGAATCTATACTC 60.096 40.741 0.00 0.00 42.77 2.59
7152 7378 6.703607 CGGAGCAAAATGAGTGAATCTATACT 59.296 38.462 0.00 0.00 0.00 2.12
7153 7379 6.480320 ACGGAGCAAAATGAGTGAATCTATAC 59.520 38.462 0.00 0.00 0.00 1.47
7154 7380 6.582636 ACGGAGCAAAATGAGTGAATCTATA 58.417 36.000 0.00 0.00 0.00 1.31
7155 7381 5.431765 ACGGAGCAAAATGAGTGAATCTAT 58.568 37.500 0.00 0.00 0.00 1.98
7156 7382 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
7157 7383 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
7158 7384 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
7159 7385 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
7160 7386 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
7161 7387 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
7162 7388 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
7163 7389 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
7164 7390 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
7165 7391 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
7166 7392 4.034048 GGTGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
7167 7393 4.189231 GGTGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
7168 7394 3.007074 TGGTGACTACATACGGAGCAAAA 59.993 43.478 0.00 0.00 0.00 2.44
7169 7395 2.563620 TGGTGACTACATACGGAGCAAA 59.436 45.455 0.00 0.00 0.00 3.68
7170 7396 2.172679 TGGTGACTACATACGGAGCAA 58.827 47.619 0.00 0.00 0.00 3.91
7171 7397 1.842052 TGGTGACTACATACGGAGCA 58.158 50.000 0.00 0.00 0.00 4.26
7172 7398 3.454371 AATGGTGACTACATACGGAGC 57.546 47.619 0.00 0.00 0.00 4.70
7173 7399 5.006153 TCAAATGGTGACTACATACGGAG 57.994 43.478 0.00 0.00 0.00 4.63
7174 7400 5.408880 TTCAAATGGTGACTACATACGGA 57.591 39.130 0.00 0.00 35.39 4.69
7175 7401 5.163794 GGTTTCAAATGGTGACTACATACGG 60.164 44.000 0.00 0.00 35.39 4.02
7176 7402 5.642063 AGGTTTCAAATGGTGACTACATACG 59.358 40.000 0.00 0.00 35.39 3.06
7177 7403 6.879458 AGAGGTTTCAAATGGTGACTACATAC 59.121 38.462 0.00 0.00 35.39 2.39
7178 7404 7.016153 AGAGGTTTCAAATGGTGACTACATA 57.984 36.000 0.00 0.00 35.39 2.29
7179 7405 5.880901 AGAGGTTTCAAATGGTGACTACAT 58.119 37.500 0.00 0.00 35.39 2.29
7180 7406 5.304686 AGAGGTTTCAAATGGTGACTACA 57.695 39.130 0.00 0.00 35.39 2.74
7181 7407 6.698380 TCTAGAGGTTTCAAATGGTGACTAC 58.302 40.000 0.00 0.00 35.39 2.73
7182 7408 6.928348 TCTAGAGGTTTCAAATGGTGACTA 57.072 37.500 0.00 0.00 35.39 2.59
7183 7409 5.825593 TCTAGAGGTTTCAAATGGTGACT 57.174 39.130 0.00 0.00 35.39 3.41
7184 7410 6.710744 TCTTTCTAGAGGTTTCAAATGGTGAC 59.289 38.462 0.00 0.00 35.39 3.67
7185 7411 6.710744 GTCTTTCTAGAGGTTTCAAATGGTGA 59.289 38.462 0.00 0.00 0.00 4.02
7186 7412 6.486657 TGTCTTTCTAGAGGTTTCAAATGGTG 59.513 38.462 0.00 0.00 0.00 4.17
7187 7413 6.601332 TGTCTTTCTAGAGGTTTCAAATGGT 58.399 36.000 0.00 0.00 0.00 3.55
7188 7414 7.229506 AGTTGTCTTTCTAGAGGTTTCAAATGG 59.770 37.037 0.00 0.00 0.00 3.16
7189 7415 8.159344 AGTTGTCTTTCTAGAGGTTTCAAATG 57.841 34.615 0.00 0.00 0.00 2.32
7191 7417 9.847224 AATAGTTGTCTTTCTAGAGGTTTCAAA 57.153 29.630 0.00 0.00 0.00 2.69
7192 7418 9.847224 AAATAGTTGTCTTTCTAGAGGTTTCAA 57.153 29.630 0.00 0.00 0.00 2.69
7195 7421 9.945904 CCTAAATAGTTGTCTTTCTAGAGGTTT 57.054 33.333 0.00 0.00 0.00 3.27
7196 7422 9.322769 TCCTAAATAGTTGTCTTTCTAGAGGTT 57.677 33.333 0.00 0.00 0.00 3.50
7197 7423 8.896722 TCCTAAATAGTTGTCTTTCTAGAGGT 57.103 34.615 0.00 0.00 0.00 3.85
7198 7424 9.589111 GTTCCTAAATAGTTGTCTTTCTAGAGG 57.411 37.037 0.00 0.00 0.00 3.69
7199 7425 9.291664 CGTTCCTAAATAGTTGTCTTTCTAGAG 57.708 37.037 0.00 0.00 0.00 2.43
7200 7426 8.248945 CCGTTCCTAAATAGTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
7201 7427 8.248945 TCCGTTCCTAAATAGTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
7202 7428 8.125978 TCCGTTCCTAAATAGTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
7203 7429 7.001099 TCCGTTCCTAAATAGTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
7204 7430 6.313164 CCTCCGTTCCTAAATAGTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
7205 7431 6.171213 CCTCCGTTCCTAAATAGTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
7206 7432 5.338137 CCCTCCGTTCCTAAATAGTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
7207 7433 4.161754 CCCTCCGTTCCTAAATAGTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
7208 7434 4.161001 TCCCTCCGTTCCTAAATAGTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
7209 7435 4.098894 TCCCTCCGTTCCTAAATAGTTGT 58.901 43.478 0.00 0.00 0.00 3.32
7210 7436 4.161754 ACTCCCTCCGTTCCTAAATAGTTG 59.838 45.833 0.00 0.00 0.00 3.16
7211 7437 4.359996 ACTCCCTCCGTTCCTAAATAGTT 58.640 43.478 0.00 0.00 0.00 2.24
7212 7438 3.991683 ACTCCCTCCGTTCCTAAATAGT 58.008 45.455 0.00 0.00 0.00 2.12
7213 7439 4.891756 TGTACTCCCTCCGTTCCTAAATAG 59.108 45.833 0.00 0.00 0.00 1.73
7214 7440 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
7215 7441 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
7216 7442 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
7217 7443 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
7218 7444 2.024655 ACATGTACTCCCTCCGTTCCTA 60.025 50.000 0.00 0.00 0.00 2.94
7219 7445 1.273098 ACATGTACTCCCTCCGTTCCT 60.273 52.381 0.00 0.00 0.00 3.36
7220 7446 1.192428 ACATGTACTCCCTCCGTTCC 58.808 55.000 0.00 0.00 0.00 3.62
7221 7447 4.667519 ATTACATGTACTCCCTCCGTTC 57.332 45.455 4.68 0.00 0.00 3.95
7222 7448 8.431910 AATATATTACATGTACTCCCTCCGTT 57.568 34.615 4.68 0.00 0.00 4.44
7223 7449 9.710818 ATAATATATTACATGTACTCCCTCCGT 57.289 33.333 4.68 0.00 0.00 4.69
7251 7477 9.656040 GGAAGACGATACTAGACTTAGATATGA 57.344 37.037 0.00 0.00 0.00 2.15
7252 7478 8.885722 GGGAAGACGATACTAGACTTAGATATG 58.114 40.741 0.00 0.00 0.00 1.78
7312 7538 8.744011 CATTAGTAGAGAACGGAAAAAGATACG 58.256 37.037 0.00 0.00 0.00 3.06
7373 7754 6.263842 AGAAGATAGAGATGAAGCAGAGTGAG 59.736 42.308 0.00 0.00 0.00 3.51
7461 7842 4.966787 GGCAAGCGACCAACCCCA 62.967 66.667 0.00 0.00 0.00 4.96
7626 8007 5.516339 CACACAAACATCAAAAGGAAGTCAC 59.484 40.000 0.00 0.00 0.00 3.67
7653 8034 3.492011 CAGGCACAAACAAAAAGATCAGC 59.508 43.478 0.00 0.00 0.00 4.26
7689 8070 4.692625 CAGACACAGACATAAAAGGACCAG 59.307 45.833 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.