Multiple sequence alignment - TraesCS5A01G184100

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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 TraesCS5A01G184100 chr5A 100.000 4077 0 0 1 4077 383884157 383880081 0.000000e+00 7529.0
1 TraesCS5A01G184100 chr5A 84.136 353 23 13 1578 1909 383882093 383881753 1.100000e-80 311.0
2 TraesCS5A01G184100 chr5A 84.136 353 23 13 2065 2405 383882580 383882249 1.100000e-80 311.0
3 TraesCS5A01G184100 chr5D 89.869 3889 212 71 1 3794 291502085 291498284 0.000000e+00 4831.0
4 TraesCS5A01G184100 chr5D 81.716 536 52 24 1578 2074 291499997 291499469 4.910000e-109 405.0
5 TraesCS5A01G184100 chr5D 93.194 191 10 2 3887 4077 291498266 291498079 1.120000e-70 278.0
6 TraesCS5A01G184100 chr5D 86.420 162 10 7 2256 2405 291500312 291500151 2.520000e-37 167.0
7 TraesCS5A01G184100 chr5B 86.899 2038 121 45 485 2423 332203511 332201521 0.000000e+00 2150.0
8 TraesCS5A01G184100 chr5B 94.234 1162 52 8 2463 3611 332201512 332200353 0.000000e+00 1760.0
9 TraesCS5A01G184100 chr5B 86.420 486 53 8 2 478 332204269 332203788 1.680000e-143 520.0
10 TraesCS5A01G184100 chr5B 91.389 360 24 5 3693 4050 332200353 332199999 1.700000e-133 486.0
11 TraesCS5A01G184100 chr5B 82.987 529 51 20 1578 2074 332201888 332201367 3.740000e-120 442.0
12 TraesCS5A01G184100 chr5B 85.675 363 30 14 2065 2405 332202406 332202044 3.000000e-96 363.0
13 TraesCS5A01G184100 chr1B 93.213 221 15 0 1001 1221 652458942 652458722 3.930000e-85 326.0
14 TraesCS5A01G184100 chr1B 100.000 28 0 0 2437 2464 482549845 482549818 7.000000e-03 52.8
15 TraesCS5A01G184100 chr1A 92.793 222 16 0 1001 1222 563685866 563685645 5.080000e-84 322.0
16 TraesCS5A01G184100 chr1D 92.760 221 16 0 1001 1221 470076701 470076481 1.830000e-83 320.0
17 TraesCS5A01G184100 chr7D 92.593 216 16 0 1007 1222 477072302 477072517 1.100000e-80 311.0
18 TraesCS5A01G184100 chr7B 92.593 216 16 0 1007 1222 501508511 501508726 1.100000e-80 311.0
19 TraesCS5A01G184100 chr7A 92.593 216 16 0 1007 1222 518809679 518809464 1.100000e-80 311.0
20 TraesCS5A01G184100 chr7A 96.429 84 2 1 3609 3691 398924432 398924515 1.980000e-28 137.0
21 TraesCS5A01G184100 chr7A 100.000 28 0 0 2434 2461 5101268 5101241 7.000000e-03 52.8
22 TraesCS5A01G184100 chr3B 90.498 221 20 1 1004 1223 525228211 525228431 1.430000e-74 291.0
23 TraesCS5A01G184100 chr3B 95.294 85 2 2 3604 3687 126580153 126580070 2.560000e-27 134.0
24 TraesCS5A01G184100 chr3B 95.238 84 3 1 3609 3691 680423298 680423381 9.200000e-27 132.0
25 TraesCS5A01G184100 chr3B 100.000 28 0 0 2434 2461 232569304 232569331 7.000000e-03 52.8
26 TraesCS5A01G184100 chr3B 100.000 28 0 0 2440 2467 330694720 330694693 7.000000e-03 52.8
27 TraesCS5A01G184100 chr3A 95.455 88 3 1 3605 3691 700747622 700747709 5.500000e-29 139.0
28 TraesCS5A01G184100 chr2A 95.349 86 2 1 3608 3691 593655995 593655910 7.110000e-28 135.0
29 TraesCS5A01G184100 chr2D 95.238 84 3 1 3609 3691 557267182 557267265 9.200000e-27 132.0
30 TraesCS5A01G184100 chr4A 91.667 96 5 3 3611 3705 590111549 590111642 3.310000e-26 130.0
31 TraesCS5A01G184100 chr2B 94.186 86 4 1 3608 3692 371164351 371164266 3.310000e-26 130.0
32 TraesCS5A01G184100 chr4D 100.000 29 0 0 2433 2461 115204112 115204084 2.000000e-03 54.7
33 TraesCS5A01G184100 chr4B 100.000 29 0 0 2436 2464 69613248 69613220 2.000000e-03 54.7
34 TraesCS5A01G184100 chr4B 100.000 28 0 0 2434 2461 23323110 23323083 7.000000e-03 52.8
35 TraesCS5A01G184100 chr4B 100.000 28 0 0 2437 2464 383894922 383894895 7.000000e-03 52.8
36 TraesCS5A01G184100 chr6B 100.000 28 0 0 2437 2464 347421860 347421833 7.000000e-03 52.8


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 TraesCS5A01G184100 chr5A 383880081 383884157 4076 True 2717.00 7529 89.42400 1 4077 3 chr5A.!!$R1 4076
1 TraesCS5A01G184100 chr5D 291498079 291502085 4006 True 1420.25 4831 87.79975 1 4077 4 chr5D.!!$R1 4076
2 TraesCS5A01G184100 chr5B 332199999 332204269 4270 True 953.50 2150 87.93400 2 4050 6 chr5B.!!$R1 4048

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
92 93 0.032017 ACCGCTCCTCCTCCTACAAT 60.032 55.0 0.0 0.0 0.0 2.71 F
93 94 0.390860 CCGCTCCTCCTCCTACAATG 59.609 60.0 0.0 0.0 0.0 2.82 F
99 100 0.537188 CTCCTCCTACAATGCACGGT 59.463 55.0 0.0 0.0 0.0 4.83 F
735 1024 0.594796 CAGCGAGCCAAACAACCAAC 60.595 55.0 0.0 0.0 0.0 3.77 F
1416 1756 0.252375 ATTGGGCAGAAACAGGGCAT 60.252 50.0 0.0 0.0 0.0 4.40 F
2818 3215 0.254178 ACAAAGCTGATCTCCGCCAT 59.746 50.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1588 0.548031 CCTGGCAGCCTAGAATGGAA 59.452 55.000 14.15 0.0 0.00 3.53 R
1393 1726 0.604578 CCTGTTTCTGCCCAATGTGG 59.395 55.000 0.00 0.0 37.25 4.17 R
1416 1756 1.430992 AAGGAAAGGAAGGTCACCGA 58.569 50.000 0.00 0.0 0.00 4.69 R
2731 3128 0.320771 CCTTCAACCACCTCTCCACG 60.321 60.000 0.00 0.0 0.00 4.94 R
2916 3313 0.034059 CAGAACCTCAGTGAAGGCGT 59.966 55.000 8.13 0.0 40.34 5.68 R
3633 4125 3.064820 GTCCATGACTGTGTCAAAAACGT 59.935 43.478 4.46 0.0 45.96 3.99 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
47 48 0.323908 AGAGCTAGTTCTCCGCCAGT 60.324 55.000 2.81 0.00 33.66 4.00
56 57 1.078918 CTCCGCCAGTTGATGCTCA 60.079 57.895 0.00 0.00 0.00 4.26
62 63 1.472201 GCCAGTTGATGCTCATCGAGA 60.472 52.381 5.51 0.00 40.63 4.04
79 80 2.031857 CGAGAGATAGGTTGTACCGCTC 60.032 54.545 0.00 0.00 44.90 5.03
92 93 0.032017 ACCGCTCCTCCTCCTACAAT 60.032 55.000 0.00 0.00 0.00 2.71
93 94 0.390860 CCGCTCCTCCTCCTACAATG 59.609 60.000 0.00 0.00 0.00 2.82
99 100 0.537188 CTCCTCCTACAATGCACGGT 59.463 55.000 0.00 0.00 0.00 4.83
140 142 3.077556 GCTCCTCCTTCGCCTCCA 61.078 66.667 0.00 0.00 0.00 3.86
263 273 1.946768 CTGCTCTAGAGAGTTCGGAGG 59.053 57.143 24.24 0.00 43.85 4.30
319 329 4.760047 CGCCCTGGACCTTGGTCG 62.760 72.222 12.97 1.36 0.00 4.79
333 343 3.053291 GTCGCCATTCCGGTGCAA 61.053 61.111 0.00 0.00 45.70 4.08
337 347 3.004326 GCCATTCCGGTGCAATGCA 62.004 57.895 2.72 2.72 36.97 3.96
404 414 3.224324 GACGGGCGAGCTGGGATA 61.224 66.667 0.00 0.00 0.00 2.59
451 461 1.676968 CTTGGGGTGATGTCGGTCA 59.323 57.895 0.00 0.00 0.00 4.02
507 787 2.094026 TGATCCACACTCACTCATTCCG 60.094 50.000 0.00 0.00 0.00 4.30
706 995 2.898343 AAAACAAGCGCCCGTCGT 60.898 55.556 2.29 0.00 41.07 4.34
707 996 2.474612 AAAACAAGCGCCCGTCGTT 61.475 52.632 2.29 0.00 41.07 3.85
732 1021 2.050077 GCAGCGAGCCAAACAACC 60.050 61.111 0.00 0.00 37.23 3.77
734 1023 1.732917 CAGCGAGCCAAACAACCAA 59.267 52.632 0.00 0.00 0.00 3.67
735 1024 0.594796 CAGCGAGCCAAACAACCAAC 60.595 55.000 0.00 0.00 0.00 3.77
739 1028 1.801025 CGAGCCAAACAACCAACAACC 60.801 52.381 0.00 0.00 0.00 3.77
742 1031 1.650825 CCAAACAACCAACAACCTGC 58.349 50.000 0.00 0.00 0.00 4.85
819 1111 4.785453 GCGCTCCCTCCCCACAAG 62.785 72.222 0.00 0.00 0.00 3.16
820 1112 4.101448 CGCTCCCTCCCCACAAGG 62.101 72.222 0.00 0.00 0.00 3.61
851 1143 3.083997 CCCACCTCTCTTCCCCCG 61.084 72.222 0.00 0.00 0.00 5.73
920 1212 1.627297 CCTTCCCTTCCCTTCCTCGG 61.627 65.000 0.00 0.00 0.00 4.63
1209 1510 4.101448 ATCTGGGACACGGCAGGC 62.101 66.667 0.00 0.00 0.00 4.85
1221 1522 2.736826 GGCAGGCCAGGAGAGGTAC 61.737 68.421 5.01 0.00 35.81 3.34
1223 1524 1.268283 GCAGGCCAGGAGAGGTACTT 61.268 60.000 5.01 0.00 41.55 2.24
1224 1525 1.965318 GCAGGCCAGGAGAGGTACTTA 60.965 57.143 5.01 0.00 41.55 2.24
1227 1528 4.421131 CAGGCCAGGAGAGGTACTTATAT 58.579 47.826 5.01 0.00 41.55 0.86
1239 1541 9.413048 GAGAGGTACTTATATATCTGTTGTTGC 57.587 37.037 0.00 0.00 41.55 4.17
1249 1551 3.149436 TCTGTTGTTGCTTGAGTTTGC 57.851 42.857 0.00 0.00 0.00 3.68
1284 1588 5.529581 AAAAACACGACCAAATGATCCTT 57.470 34.783 0.00 0.00 0.00 3.36
1299 1603 2.717639 TCCTTTCCATTCTAGGCTGC 57.282 50.000 0.00 0.00 0.00 5.25
1313 1617 0.610232 GGCTGCCAGGTTCATCTTGT 60.610 55.000 15.17 0.00 0.00 3.16
1342 1646 9.621629 AACCATAGTCACGATTAATGGAAAATA 57.378 29.630 4.29 0.00 0.00 1.40
1344 1648 9.273016 CCATAGTCACGATTAATGGAAAATAGT 57.727 33.333 4.29 0.00 0.00 2.12
1346 1650 7.016361 AGTCACGATTAATGGAAAATAGTGC 57.984 36.000 4.29 1.88 38.83 4.40
1351 1655 7.376866 CACGATTAATGGAAAATAGTGCATCAC 59.623 37.037 4.29 0.00 34.62 3.06
1361 1665 9.807649 GGAAAATAGTGCATCACATTAAGAATT 57.192 29.630 0.00 0.00 36.74 2.17
1375 1708 9.985730 CACATTAAGAATTATATGTGCCCATTT 57.014 29.630 3.67 0.00 40.04 2.32
1393 1726 4.034510 CCATTTTCCTAGTTCTCATCGCAC 59.965 45.833 0.00 0.00 0.00 5.34
1416 1756 0.252375 ATTGGGCAGAAACAGGGCAT 60.252 50.000 0.00 0.00 0.00 4.40
1429 1769 2.990479 GGCATCGGTGACCTTCCT 59.010 61.111 0.00 0.00 0.00 3.36
1471 1811 7.230849 TCTGTACAATCCTGCATTTTCATTT 57.769 32.000 0.00 0.00 0.00 2.32
1516 1859 3.927854 GGTACCTTGTTCTCTCTGGAAC 58.072 50.000 4.06 0.00 43.97 3.62
1524 1867 3.471680 GTTCTCTCTGGAACAACAAGCT 58.528 45.455 0.00 0.00 43.40 3.74
1525 1868 4.632153 GTTCTCTCTGGAACAACAAGCTA 58.368 43.478 0.00 0.00 43.40 3.32
1526 1869 4.527509 TCTCTCTGGAACAACAAGCTAG 57.472 45.455 0.00 0.00 38.70 3.42
1527 1870 3.898123 TCTCTCTGGAACAACAAGCTAGT 59.102 43.478 0.00 0.00 38.70 2.57
1551 1894 7.888546 AGTATTTTATATTGCCCAGACCCATAC 59.111 37.037 0.00 0.00 0.00 2.39
1553 1896 7.395525 TTTTATATTGCCCAGACCCATACTA 57.604 36.000 0.00 0.00 0.00 1.82
1554 1897 7.395525 TTTATATTGCCCAGACCCATACTAA 57.604 36.000 0.00 0.00 0.00 2.24
1562 1905 6.378848 TGCCCAGACCCATACTAAAATTTAAC 59.621 38.462 0.00 0.00 0.00 2.01
1563 1906 6.605995 GCCCAGACCCATACTAAAATTTAACT 59.394 38.462 0.00 0.00 0.00 2.24
1564 1907 7.201794 GCCCAGACCCATACTAAAATTTAACTC 60.202 40.741 0.00 0.00 0.00 3.01
1565 1908 8.053355 CCCAGACCCATACTAAAATTTAACTCT 58.947 37.037 0.00 0.00 0.00 3.24
1622 1969 2.031560 TCGTTATTGGAATGCGTGATGC 59.968 45.455 0.00 0.00 46.70 3.91
1665 2021 5.813513 ATGATGTATAGATGTGTGAGCCA 57.186 39.130 0.00 0.00 0.00 4.75
1676 2040 5.591877 AGATGTGTGAGCCAAAAATCCTATC 59.408 40.000 0.00 0.00 0.00 2.08
1677 2041 4.661222 TGTGTGAGCCAAAAATCCTATCA 58.339 39.130 0.00 0.00 0.00 2.15
1678 2042 5.076182 TGTGTGAGCCAAAAATCCTATCAA 58.924 37.500 0.00 0.00 0.00 2.57
1704 2068 5.539955 GTCCACCTGGCATTGGATATAAAAT 59.460 40.000 18.16 0.00 43.85 1.82
1706 2070 6.719370 TCCACCTGGCATTGGATATAAAATAC 59.281 38.462 12.73 0.00 36.96 1.89
1707 2071 6.721208 CCACCTGGCATTGGATATAAAATACT 59.279 38.462 9.21 0.00 34.46 2.12
1740 2118 1.898330 TAAGAGGCATGCGAGCACCA 61.898 55.000 12.44 0.00 35.83 4.17
1832 2214 5.538849 TTCCCCTAATTGTTGTCCAAAAC 57.461 39.130 0.00 0.00 36.44 2.43
1834 2216 3.319689 CCCCTAATTGTTGTCCAAAACGT 59.680 43.478 0.00 0.00 36.44 3.99
1856 2240 6.015010 ACGTATCTTGCTGCTAAGGATATTCT 60.015 38.462 0.00 0.00 0.00 2.40
1944 2328 0.520404 GCCACACATTCAGTCTGCTG 59.480 55.000 0.00 0.00 43.87 4.41
1956 2340 5.086104 TCAGTCTGCTGTAGGGATTTTAC 57.914 43.478 0.00 0.00 43.05 2.01
1958 2342 4.923733 CAGTCTGCTGTAGGGATTTTACCC 60.924 50.000 0.00 0.00 42.49 3.69
2032 2417 1.891919 TCGCCAGTTTCACCAGCAC 60.892 57.895 0.00 0.00 0.00 4.40
2050 2435 5.450965 CCAGCACAATTCCTACATCAATTCC 60.451 44.000 0.00 0.00 0.00 3.01
2061 2446 9.486123 TTCCTACATCAATTCCCAATATTTTGA 57.514 29.630 2.79 2.79 34.60 2.69
2090 2475 5.686841 TGTCAGCAAATTCTGTTTGAAATCG 59.313 36.000 4.81 0.00 38.29 3.34
2101 2486 9.927668 ATTCTGTTTGAAATCGTTATTGGAATT 57.072 25.926 0.00 0.00 38.29 2.17
2172 2557 8.154203 TGAGCCGATGTTATTTAAATCCTATCA 58.846 33.333 3.39 0.00 0.00 2.15
2173 2558 8.324163 AGCCGATGTTATTTAAATCCTATCAC 57.676 34.615 3.39 3.19 0.00 3.06
2177 2562 9.231297 CGATGTTATTTAAATCCTATCACCCAT 57.769 33.333 3.39 0.00 0.00 4.00
2186 2571 2.107031 TCCTATCACCCATCTGGCATTG 59.893 50.000 0.00 0.00 37.83 2.82
2187 2572 2.511659 CTATCACCCATCTGGCATTGG 58.488 52.381 9.13 9.13 37.83 3.16
2188 2573 0.928505 ATCACCCATCTGGCATTGGA 59.071 50.000 15.99 0.00 37.83 3.53
2189 2574 0.928505 TCACCCATCTGGCATTGGAT 59.071 50.000 15.99 0.33 37.83 3.41
2270 2657 5.480073 TGTATTTGCAAACCTGGCTCTAAAT 59.520 36.000 15.41 0.00 0.00 1.40
2273 2660 3.084039 TGCAAACCTGGCTCTAAATGAG 58.916 45.455 0.00 0.00 45.33 2.90
2346 2742 6.072508 TCCAAAAAGTATGTTGCTGCTAAGAG 60.073 38.462 0.00 0.00 0.00 2.85
2347 2743 4.954092 AAAGTATGTTGCTGCTAAGAGC 57.046 40.909 0.00 0.00 42.82 4.09
2402 2798 7.503521 TGATGTTTACAGACAAATAGTTGCA 57.496 32.000 2.17 0.00 38.39 4.08
2405 2801 8.615878 ATGTTTACAGACAAATAGTTGCACTA 57.384 30.769 2.17 0.00 38.39 2.74
2407 2803 7.172532 TGTTTACAGACAAATAGTTGCACTAGG 59.827 37.037 2.17 0.00 38.39 3.02
2409 2805 4.256920 CAGACAAATAGTTGCACTAGGCT 58.743 43.478 2.17 0.00 45.15 4.58
2410 2806 4.697352 CAGACAAATAGTTGCACTAGGCTT 59.303 41.667 2.17 0.00 45.15 4.35
2424 2820 1.601759 GGCTTTGCACAGAGGCTCA 60.602 57.895 18.26 0.00 35.60 4.26
2439 2835 1.131504 GGCTCACGTGTGTTTGACAAA 59.868 47.619 16.51 0.00 35.91 2.83
2440 2836 2.223479 GGCTCACGTGTGTTTGACAAAT 60.223 45.455 16.51 0.00 35.91 2.32
2441 2837 3.002862 GGCTCACGTGTGTTTGACAAATA 59.997 43.478 16.51 0.00 35.91 1.40
2442 2838 3.966218 GCTCACGTGTGTTTGACAAATAC 59.034 43.478 16.51 18.00 35.91 1.89
2443 2839 4.260620 GCTCACGTGTGTTTGACAAATACT 60.261 41.667 23.11 5.95 35.91 2.12
2444 2840 5.398176 TCACGTGTGTTTGACAAATACTC 57.602 39.130 23.11 19.34 35.91 2.59
2445 2841 4.271533 TCACGTGTGTTTGACAAATACTCC 59.728 41.667 23.11 14.86 35.91 3.85
2446 2842 3.562557 ACGTGTGTTTGACAAATACTCCC 59.437 43.478 23.11 12.99 35.91 4.30
2447 2843 3.813166 CGTGTGTTTGACAAATACTCCCT 59.187 43.478 23.11 0.00 35.91 4.20
2448 2844 4.084013 CGTGTGTTTGACAAATACTCCCTC 60.084 45.833 23.11 11.00 35.91 4.30
2449 2845 4.215613 GTGTGTTTGACAAATACTCCCTCC 59.784 45.833 23.11 1.86 35.91 4.30
2450 2846 3.435671 GTGTTTGACAAATACTCCCTCCG 59.564 47.826 17.66 0.00 30.81 4.63
2451 2847 3.071892 TGTTTGACAAATACTCCCTCCGT 59.928 43.478 3.49 0.00 0.00 4.69
2452 2848 4.070009 GTTTGACAAATACTCCCTCCGTT 58.930 43.478 3.49 0.00 0.00 4.44
2453 2849 3.604875 TGACAAATACTCCCTCCGTTC 57.395 47.619 0.00 0.00 0.00 3.95
2454 2850 2.235402 TGACAAATACTCCCTCCGTTCC 59.765 50.000 0.00 0.00 0.00 3.62
2455 2851 2.235402 GACAAATACTCCCTCCGTTCCA 59.765 50.000 0.00 0.00 0.00 3.53
2456 2852 2.640826 ACAAATACTCCCTCCGTTCCAA 59.359 45.455 0.00 0.00 0.00 3.53
2457 2853 3.073356 ACAAATACTCCCTCCGTTCCAAA 59.927 43.478 0.00 0.00 0.00 3.28
2458 2854 4.076394 CAAATACTCCCTCCGTTCCAAAA 58.924 43.478 0.00 0.00 0.00 2.44
2459 2855 4.586306 AATACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
2460 2856 5.703730 AATACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
2461 2857 3.345508 ACTCCCTCCGTTCCAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
2470 2866 5.004448 TCCGTTCCAAAATACTATGTGCAA 58.996 37.500 0.00 0.00 0.00 4.08
2493 2889 2.681848 CTGCTGTAGGGATTTTGCTGAG 59.318 50.000 0.00 0.00 0.00 3.35
2494 2890 2.305635 TGCTGTAGGGATTTTGCTGAGA 59.694 45.455 0.00 0.00 0.00 3.27
2495 2891 2.941720 GCTGTAGGGATTTTGCTGAGAG 59.058 50.000 0.00 0.00 0.00 3.20
2514 2910 7.577046 GCTGAGAGTGTTCTGTATAACCTGTTA 60.577 40.741 0.00 0.00 32.53 2.41
2515 2911 8.185506 TGAGAGTGTTCTGTATAACCTGTTAA 57.814 34.615 0.00 0.00 32.53 2.01
2523 2919 7.385778 TCTGTATAACCTGTTAAAACATGGC 57.614 36.000 0.00 0.00 38.41 4.40
2526 2922 8.184304 TGTATAACCTGTTAAAACATGGCTTT 57.816 30.769 0.00 0.00 38.41 3.51
2527 2923 8.643324 TGTATAACCTGTTAAAACATGGCTTTT 58.357 29.630 0.00 0.00 38.41 2.27
2545 2941 5.356470 GGCTTTTACTCAATCAGCTCTCAAT 59.644 40.000 0.00 0.00 0.00 2.57
2562 2958 5.305585 TCTCAATCTAACACCAGTTTCACC 58.694 41.667 0.00 0.00 39.15 4.02
2572 2968 2.362077 ACCAGTTTCACCAGCACAATTC 59.638 45.455 0.00 0.00 0.00 2.17
2573 2969 2.605338 CCAGTTTCACCAGCACAATTCG 60.605 50.000 0.00 0.00 0.00 3.34
2581 2977 3.002791 ACCAGCACAATTCGTACATCAG 58.997 45.455 0.00 0.00 0.00 2.90
2587 2983 4.388773 GCACAATTCGTACATCAGTTCTCA 59.611 41.667 0.00 0.00 0.00 3.27
2624 3021 3.322369 TGTAGCATGGACTTAACGTGTG 58.678 45.455 0.00 0.00 0.00 3.82
2631 3028 3.537580 TGGACTTAACGTGTGCTCTTTT 58.462 40.909 0.00 0.00 0.00 2.27
2639 3036 3.798202 ACGTGTGCTCTTTTCTTTCTCT 58.202 40.909 0.00 0.00 0.00 3.10
2680 3077 2.198287 TGCGTACTATCGAGGGGCC 61.198 63.158 0.00 0.00 0.00 5.80
2683 3080 1.849976 CGTACTATCGAGGGGCCGTC 61.850 65.000 16.17 16.17 0.00 4.79
2731 3128 1.197721 CGCCATGTGACCTTTGAGAAC 59.802 52.381 0.00 0.00 0.00 3.01
2812 3209 1.442769 TCGGCAACAAAGCTGATCTC 58.557 50.000 0.00 0.00 44.55 2.75
2818 3215 0.254178 ACAAAGCTGATCTCCGCCAT 59.746 50.000 0.00 0.00 0.00 4.40
2839 3236 3.300388 TCTTAGGGCTGTATCAGTGGAG 58.700 50.000 0.00 0.00 33.43 3.86
2908 3305 2.517875 GCGCTGGAGGCCATGAAT 60.518 61.111 5.01 0.00 37.74 2.57
2916 3313 2.041485 TGGAGGCCATGAATGTTGAGAA 59.959 45.455 5.01 0.00 0.00 2.87
3128 3525 5.745312 TGCTCACCTGATTATATGGGTAG 57.255 43.478 0.00 0.00 0.00 3.18
3183 3580 4.876107 CCTGGTTGTTTGCGAGATTATACT 59.124 41.667 0.00 0.00 0.00 2.12
3186 3583 4.873827 GGTTGTTTGCGAGATTATACTGGA 59.126 41.667 0.00 0.00 0.00 3.86
3208 3605 5.358298 AGCACCAAGAATTTCGTTTAGAC 57.642 39.130 0.00 0.00 0.00 2.59
3294 3691 5.598830 TGTGGTTGCCTTTTATGGTTTCTTA 59.401 36.000 0.00 0.00 0.00 2.10
3349 3746 5.874093 AGAATCCTCTCAACATTTCACTGT 58.126 37.500 0.00 0.00 0.00 3.55
3357 3754 1.696063 ACATTTCACTGTGCAGCCTT 58.304 45.000 2.12 0.00 0.00 4.35
3602 4011 7.696992 TGTTTCTTATCACCCTATGTTTTCC 57.303 36.000 0.00 0.00 0.00 3.13
3611 4103 5.665812 TCACCCTATGTTTTCCTATGCTACT 59.334 40.000 0.00 0.00 0.00 2.57
3612 4104 5.992217 CACCCTATGTTTTCCTATGCTACTC 59.008 44.000 0.00 0.00 0.00 2.59
3613 4105 5.071923 ACCCTATGTTTTCCTATGCTACTCC 59.928 44.000 0.00 0.00 0.00 3.85
3614 4106 5.513267 CCCTATGTTTTCCTATGCTACTCCC 60.513 48.000 0.00 0.00 0.00 4.30
3615 4107 5.308237 CCTATGTTTTCCTATGCTACTCCCT 59.692 44.000 0.00 0.00 0.00 4.20
3616 4108 4.755266 TGTTTTCCTATGCTACTCCCTC 57.245 45.455 0.00 0.00 0.00 4.30
3617 4109 4.362677 TGTTTTCCTATGCTACTCCCTCT 58.637 43.478 0.00 0.00 0.00 3.69
3618 4110 4.162320 TGTTTTCCTATGCTACTCCCTCTG 59.838 45.833 0.00 0.00 0.00 3.35
3619 4111 3.689872 TTCCTATGCTACTCCCTCTGT 57.310 47.619 0.00 0.00 0.00 3.41
3620 4112 4.808767 TTCCTATGCTACTCCCTCTGTA 57.191 45.455 0.00 0.00 0.00 2.74
3621 4113 4.808767 TCCTATGCTACTCCCTCTGTAA 57.191 45.455 0.00 0.00 0.00 2.41
3622 4114 4.471548 TCCTATGCTACTCCCTCTGTAAC 58.528 47.826 0.00 0.00 0.00 2.50
3623 4115 4.168283 TCCTATGCTACTCCCTCTGTAACT 59.832 45.833 0.00 0.00 0.00 2.24
3624 4116 4.896482 CCTATGCTACTCCCTCTGTAACTT 59.104 45.833 0.00 0.00 0.00 2.66
3625 4117 6.069331 CCTATGCTACTCCCTCTGTAACTTA 58.931 44.000 0.00 0.00 0.00 2.24
3626 4118 6.550108 CCTATGCTACTCCCTCTGTAACTTAA 59.450 42.308 0.00 0.00 0.00 1.85
3627 4119 7.233757 CCTATGCTACTCCCTCTGTAACTTAAT 59.766 40.741 0.00 0.00 0.00 1.40
3628 4120 9.298250 CTATGCTACTCCCTCTGTAACTTAATA 57.702 37.037 0.00 0.00 0.00 0.98
3629 4121 8.728596 ATGCTACTCCCTCTGTAACTTAATAT 57.271 34.615 0.00 0.00 0.00 1.28
3630 4122 9.824216 ATGCTACTCCCTCTGTAACTTAATATA 57.176 33.333 0.00 0.00 0.00 0.86
3631 4123 9.650714 TGCTACTCCCTCTGTAACTTAATATAA 57.349 33.333 0.00 0.00 0.00 0.98
3635 4127 8.848182 ACTCCCTCTGTAACTTAATATAAGACG 58.152 37.037 4.24 0.00 0.00 4.18
3636 4128 8.757982 TCCCTCTGTAACTTAATATAAGACGT 57.242 34.615 4.24 0.00 0.00 4.34
3637 4129 9.193806 TCCCTCTGTAACTTAATATAAGACGTT 57.806 33.333 4.24 0.00 0.00 3.99
3638 4130 9.813446 CCCTCTGTAACTTAATATAAGACGTTT 57.187 33.333 4.24 0.00 0.00 3.60
3650 4142 7.956420 ATATAAGACGTTTTTGACACAGTCA 57.044 32.000 0.00 0.00 41.09 3.41
3651 4143 6.861065 ATAAGACGTTTTTGACACAGTCAT 57.139 33.333 0.00 0.00 42.40 3.06
3652 4144 4.536364 AGACGTTTTTGACACAGTCATG 57.464 40.909 0.12 0.00 42.40 3.07
3653 4145 3.312421 AGACGTTTTTGACACAGTCATGG 59.688 43.478 0.12 0.00 42.40 3.66
3654 4146 3.275143 ACGTTTTTGACACAGTCATGGA 58.725 40.909 0.12 0.00 42.40 3.41
3655 4147 3.064820 ACGTTTTTGACACAGTCATGGAC 59.935 43.478 0.12 0.00 42.40 4.02
3656 4148 3.312421 CGTTTTTGACACAGTCATGGACT 59.688 43.478 0.12 0.00 44.44 3.85
3657 4149 4.552767 CGTTTTTGACACAGTCATGGACTC 60.553 45.833 0.12 0.00 41.37 3.36
3658 4150 4.422073 TTTTGACACAGTCATGGACTCT 57.578 40.909 0.12 0.00 41.37 3.24
3659 4151 5.545063 TTTTGACACAGTCATGGACTCTA 57.455 39.130 0.12 0.00 41.37 2.43
3660 4152 5.545063 TTTGACACAGTCATGGACTCTAA 57.455 39.130 0.12 0.00 41.37 2.10
3661 4153 5.545063 TTGACACAGTCATGGACTCTAAA 57.455 39.130 0.12 0.00 41.37 1.85
3662 4154 5.545063 TGACACAGTCATGGACTCTAAAA 57.455 39.130 0.00 0.00 41.37 1.52
3663 4155 5.924356 TGACACAGTCATGGACTCTAAAAA 58.076 37.500 0.00 0.00 41.37 1.94
3664 4156 5.758296 TGACACAGTCATGGACTCTAAAAAC 59.242 40.000 0.00 0.00 41.37 2.43
3665 4157 4.750098 ACACAGTCATGGACTCTAAAAACG 59.250 41.667 0.00 0.00 41.37 3.60
3666 4158 4.750098 CACAGTCATGGACTCTAAAAACGT 59.250 41.667 0.00 0.00 41.37 3.99
3667 4159 4.989168 ACAGTCATGGACTCTAAAAACGTC 59.011 41.667 0.00 0.00 41.37 4.34
3668 4160 5.221461 ACAGTCATGGACTCTAAAAACGTCT 60.221 40.000 0.00 0.00 41.37 4.18
3669 4161 5.696724 CAGTCATGGACTCTAAAAACGTCTT 59.303 40.000 0.00 0.00 41.37 3.01
3670 4162 6.866770 CAGTCATGGACTCTAAAAACGTCTTA 59.133 38.462 0.00 0.00 41.37 2.10
3671 4163 7.545965 CAGTCATGGACTCTAAAAACGTCTTAT 59.454 37.037 0.00 0.00 41.37 1.73
3672 4164 8.746530 AGTCATGGACTCTAAAAACGTCTTATA 58.253 33.333 0.00 0.00 38.71 0.98
3673 4165 9.362539 GTCATGGACTCTAAAAACGTCTTATAA 57.637 33.333 0.00 0.00 0.00 0.98
3674 4166 9.932207 TCATGGACTCTAAAAACGTCTTATAAA 57.068 29.630 0.00 0.00 0.00 1.40
3687 4179 9.551734 AAACGTCTTATAAAAAGTTACAGAGGT 57.448 29.630 0.00 0.00 34.97 3.85
3689 4181 9.852091 ACGTCTTATAAAAAGTTACAGAGGTAG 57.148 33.333 0.00 0.00 33.39 3.18
3690 4182 9.852091 CGTCTTATAAAAAGTTACAGAGGTAGT 57.148 33.333 0.00 0.00 0.00 2.73
3692 4184 9.649167 TCTTATAAAAAGTTACAGAGGTAGTGC 57.351 33.333 0.00 0.00 0.00 4.40
3706 4198 4.461198 AGGTAGTGCCATTTTATGCCTAC 58.539 43.478 0.00 0.00 40.61 3.18
3736 4228 4.695455 TCACTATGCTGCTGTTTAAGGAAC 59.305 41.667 0.00 0.00 38.78 3.62
3744 4236 6.594159 TGCTGCTGTTTAAGGAACTACTTATC 59.406 38.462 0.00 0.00 38.49 1.75
3832 4324 6.889722 CCCCTTCCATGTATTTTACTTTCTCA 59.110 38.462 0.00 0.00 0.00 3.27
3834 4326 7.414098 CCCTTCCATGTATTTTACTTTCTCACG 60.414 40.741 0.00 0.00 0.00 4.35
3844 4336 8.672823 ATTTTACTTTCTCACGGGGTATTATC 57.327 34.615 0.00 0.00 0.00 1.75
3854 4346 5.657745 TCACGGGGTATTATCTGACTTTGTA 59.342 40.000 0.00 0.00 0.00 2.41
3859 4351 7.011109 CGGGGTATTATCTGACTTTGTAAACTG 59.989 40.741 0.00 0.00 0.00 3.16
3865 4357 4.973168 TCTGACTTTGTAAACTGGCATCT 58.027 39.130 0.00 0.00 0.00 2.90
3883 4377 5.220854 GGCATCTTTATTTGCTCGTGTGTAT 60.221 40.000 0.00 0.00 38.88 2.29
3908 4402 6.013206 TGCAAACTACCTTGATAGAGGGTTAA 60.013 38.462 0.00 0.00 41.31 2.01
3941 4435 3.119137 AGAGTTTGTTCTTGTTGGCAACC 60.119 43.478 26.31 11.76 0.00 3.77
3944 4438 4.404073 AGTTTGTTCTTGTTGGCAACCATA 59.596 37.500 26.31 11.59 31.53 2.74
3997 4491 0.687354 ACAGTCTGTTAGGTGGGCTG 59.313 55.000 0.00 0.00 0.00 4.85
4065 4559 8.691797 AGCAAATTTCAGAACTGTAAAGGTTTA 58.308 29.630 1.73 0.00 0.00 2.01
4071 4565 8.918202 TTCAGAACTGTAAAGGTTTATGTCAT 57.082 30.769 1.73 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 2.553172 GCGGTACAACCTATCTCTCGAT 59.447 50.000 0.00 0.00 35.66 3.59
62 63 2.308690 GAGGAGCGGTACAACCTATCT 58.691 52.381 0.00 0.00 35.66 1.98
79 80 0.179073 CCGTGCATTGTAGGAGGAGG 60.179 60.000 0.00 0.00 0.00 4.30
92 93 3.031457 GCGTTCGTGTACCGTGCA 61.031 61.111 4.11 0.00 37.94 4.57
93 94 3.770424 GGCGTTCGTGTACCGTGC 61.770 66.667 4.11 6.70 37.94 5.34
111 112 1.153549 GAGGAGCCTAAGTGCCACG 60.154 63.158 0.00 0.00 0.00 4.94
140 142 4.253685 CAACACTACAACCGGATTCTGAT 58.746 43.478 9.46 0.00 0.00 2.90
229 239 0.174617 GAGCAGAGCTTAGACGGCTT 59.825 55.000 0.00 0.00 39.88 4.35
232 242 2.548057 CTCTAGAGCAGAGCTTAGACGG 59.452 54.545 6.86 0.00 44.34 4.79
263 273 2.359478 ACATTCCGACGGGCCAAC 60.359 61.111 15.25 0.00 0.00 3.77
301 311 3.637273 GACCAAGGTCCAGGGCGT 61.637 66.667 8.06 0.00 39.08 5.68
304 314 4.410400 GGCGACCAAGGTCCAGGG 62.410 72.222 13.35 0.98 41.76 4.45
319 329 2.202783 GCATTGCACCGGAATGGC 60.203 61.111 9.46 6.85 43.94 4.40
333 343 2.359107 CGGCTGTCACCACTGCAT 60.359 61.111 6.37 0.00 46.61 3.96
337 347 4.008933 GAGGCGGCTGTCACCACT 62.009 66.667 19.63 0.00 0.00 4.00
404 414 2.516227 TCCGATCACCTTCTCTGACT 57.484 50.000 0.00 0.00 0.00 3.41
426 436 0.550147 ACATCACCCCAAGCCCTACT 60.550 55.000 0.00 0.00 0.00 2.57
433 443 0.391661 CTGACCGACATCACCCCAAG 60.392 60.000 0.00 0.00 0.00 3.61
507 787 0.749454 ATTCACGCCCTTCCTCATGC 60.749 55.000 0.00 0.00 0.00 4.06
587 867 3.492011 GCTTTTGTCTTTGTCAGGCAATG 59.508 43.478 0.00 0.00 46.74 2.82
732 1021 1.270826 TCTCTCTCTCGCAGGTTGTTG 59.729 52.381 0.00 0.00 0.00 3.33
734 1023 0.885196 GTCTCTCTCTCGCAGGTTGT 59.115 55.000 0.00 0.00 0.00 3.32
735 1024 0.179176 CGTCTCTCTCTCGCAGGTTG 60.179 60.000 0.00 0.00 0.00 3.77
739 1028 0.096281 GTGTCGTCTCTCTCTCGCAG 59.904 60.000 0.00 0.00 0.00 5.18
742 1031 0.093875 CGTGTGTCGTCTCTCTCTCG 59.906 60.000 0.00 0.00 34.52 4.04
813 1105 1.101049 AGAACGTTGTGGCCTTGTGG 61.101 55.000 5.00 0.00 0.00 4.17
814 1106 0.307760 GAGAACGTTGTGGCCTTGTG 59.692 55.000 5.00 0.00 0.00 3.33
815 1107 0.818040 GGAGAACGTTGTGGCCTTGT 60.818 55.000 5.00 0.00 0.00 3.16
816 1108 1.515521 GGGAGAACGTTGTGGCCTTG 61.516 60.000 5.00 0.00 0.00 3.61
817 1109 1.228154 GGGAGAACGTTGTGGCCTT 60.228 57.895 5.00 0.00 0.00 4.35
818 1110 2.430367 GGGAGAACGTTGTGGCCT 59.570 61.111 5.00 0.00 0.00 5.19
819 1111 2.671963 GGGGAGAACGTTGTGGCC 60.672 66.667 5.00 0.00 0.00 5.36
820 1112 2.112297 TGGGGAGAACGTTGTGGC 59.888 61.111 5.00 0.00 0.00 5.01
851 1143 1.192146 TGGCGTATATGAGAGGGCCC 61.192 60.000 16.46 16.46 39.78 5.80
1209 1510 8.744652 CAACAGATATATAAGTACCTCTCCTGG 58.255 40.741 0.00 0.00 0.00 4.45
1223 1524 8.397906 GCAAACTCAAGCAACAACAGATATATA 58.602 33.333 0.00 0.00 0.00 0.86
1224 1525 7.121759 AGCAAACTCAAGCAACAACAGATATAT 59.878 33.333 0.00 0.00 0.00 0.86
1227 1528 4.580167 AGCAAACTCAAGCAACAACAGATA 59.420 37.500 0.00 0.00 0.00 1.98
1239 1541 7.672983 TTTCTATCTACCAAGCAAACTCAAG 57.327 36.000 0.00 0.00 0.00 3.02
1280 1584 1.212935 GGCAGCCTAGAATGGAAAGGA 59.787 52.381 3.29 0.00 31.64 3.36
1281 1585 1.064463 TGGCAGCCTAGAATGGAAAGG 60.064 52.381 14.15 0.00 0.00 3.11
1282 1586 2.295885 CTGGCAGCCTAGAATGGAAAG 58.704 52.381 14.15 0.00 0.00 2.62
1283 1587 1.064463 CCTGGCAGCCTAGAATGGAAA 60.064 52.381 14.15 0.00 0.00 3.13
1284 1588 0.548031 CCTGGCAGCCTAGAATGGAA 59.452 55.000 14.15 0.00 0.00 3.53
1299 1603 3.221771 TGGTTGAACAAGATGAACCTGG 58.778 45.455 0.00 0.00 38.96 4.45
1313 1617 6.645306 TCCATTAATCGTGACTATGGTTGAA 58.355 36.000 0.00 0.00 37.58 2.69
1361 1665 7.147391 TGAGAACTAGGAAAATGGGCACATATA 60.147 37.037 0.00 0.00 35.94 0.86
1366 1699 3.686016 TGAGAACTAGGAAAATGGGCAC 58.314 45.455 0.00 0.00 0.00 5.01
1375 1708 2.094182 GTGGTGCGATGAGAACTAGGAA 60.094 50.000 0.00 0.00 0.00 3.36
1393 1726 0.604578 CCTGTTTCTGCCCAATGTGG 59.395 55.000 0.00 0.00 37.25 4.17
1416 1756 1.430992 AAGGAAAGGAAGGTCACCGA 58.569 50.000 0.00 0.00 0.00 4.69
1425 1765 5.774690 AGAACAACATGCATAAGGAAAGGAA 59.225 36.000 0.00 0.00 0.00 3.36
1426 1766 5.183713 CAGAACAACATGCATAAGGAAAGGA 59.816 40.000 0.00 0.00 0.00 3.36
1427 1767 5.047802 ACAGAACAACATGCATAAGGAAAGG 60.048 40.000 0.00 0.00 0.00 3.11
1428 1768 6.017400 ACAGAACAACATGCATAAGGAAAG 57.983 37.500 0.00 0.00 0.00 2.62
1429 1769 6.488344 TGTACAGAACAACATGCATAAGGAAA 59.512 34.615 0.00 0.00 34.29 3.13
1471 1811 5.896678 CCCCTGATTAACATTTATTGGGACA 59.103 40.000 0.00 0.00 34.34 4.02
1488 1828 2.197465 GAGAACAAGGTACCCCCTGAT 58.803 52.381 8.74 0.00 45.47 2.90
1490 1830 1.555533 GAGAGAACAAGGTACCCCCTG 59.444 57.143 8.74 6.49 45.47 4.45
1492 1832 1.555533 CAGAGAGAACAAGGTACCCCC 59.444 57.143 8.74 0.00 0.00 5.40
1516 1859 8.629158 TGGGCAATATAAAATACTAGCTTGTTG 58.371 33.333 6.03 0.00 0.00 3.33
1522 1865 6.374613 GGGTCTGGGCAATATAAAATACTAGC 59.625 42.308 0.00 0.00 0.00 3.42
1524 1867 7.395525 TGGGTCTGGGCAATATAAAATACTA 57.604 36.000 0.00 0.00 0.00 1.82
1525 1868 6.274322 TGGGTCTGGGCAATATAAAATACT 57.726 37.500 0.00 0.00 0.00 2.12
1526 1869 7.888546 AGTATGGGTCTGGGCAATATAAAATAC 59.111 37.037 0.00 0.00 0.00 1.89
1527 1870 7.995663 AGTATGGGTCTGGGCAATATAAAATA 58.004 34.615 0.00 0.00 0.00 1.40
1553 1896 7.824779 AGCGATGGTTAGAGAGAGTTAAATTTT 59.175 33.333 0.00 0.00 0.00 1.82
1554 1897 7.278868 CAGCGATGGTTAGAGAGAGTTAAATTT 59.721 37.037 0.00 0.00 0.00 1.82
1562 1905 2.685388 TGACAGCGATGGTTAGAGAGAG 59.315 50.000 5.32 0.00 0.00 3.20
1563 1906 2.723273 TGACAGCGATGGTTAGAGAGA 58.277 47.619 5.32 0.00 0.00 3.10
1564 1907 3.182967 GTTGACAGCGATGGTTAGAGAG 58.817 50.000 5.32 0.00 0.00 3.20
1565 1908 2.560981 TGTTGACAGCGATGGTTAGAGA 59.439 45.455 5.32 0.00 0.00 3.10
1614 1961 2.118228 TGACAAAACAAGCATCACGC 57.882 45.000 0.00 0.00 42.91 5.34
1650 2006 5.513233 AGGATTTTTGGCTCACACATCTAT 58.487 37.500 0.00 0.00 0.00 1.98
1656 2012 5.402398 GTTGATAGGATTTTTGGCTCACAC 58.598 41.667 0.00 0.00 0.00 3.82
1665 2021 4.700213 CAGGTGGACGTTGATAGGATTTTT 59.300 41.667 0.00 0.00 0.00 1.94
1676 2040 1.580942 CAATGCCAGGTGGACGTTG 59.419 57.895 0.00 5.72 37.39 4.10
1677 2041 1.603455 CCAATGCCAGGTGGACGTT 60.603 57.895 0.00 0.00 37.03 3.99
1678 2042 1.852157 ATCCAATGCCAGGTGGACGT 61.852 55.000 0.00 0.00 46.53 4.34
1704 2068 4.498241 CTCTTACAGATGTTGCAGCAGTA 58.502 43.478 9.71 3.28 0.00 2.74
1706 2070 2.676839 CCTCTTACAGATGTTGCAGCAG 59.323 50.000 9.71 0.00 0.00 4.24
1707 2071 2.703416 CCTCTTACAGATGTTGCAGCA 58.297 47.619 5.46 5.46 0.00 4.41
1733 2111 3.056607 AGGTTTGCAAATACATGGTGCTC 60.057 43.478 16.21 0.00 39.09 4.26
1740 2118 3.434309 AGAGCCAGGTTTGCAAATACAT 58.566 40.909 16.21 0.00 0.00 2.29
1786 2168 9.522804 GAATTAAATAGTCGATCTATAGCTGGG 57.477 37.037 0.00 0.00 38.29 4.45
1832 2214 6.393990 AGAATATCCTTAGCAGCAAGATACG 58.606 40.000 0.00 0.00 0.00 3.06
1834 2216 9.060347 CAAAAGAATATCCTTAGCAGCAAGATA 57.940 33.333 0.00 0.00 0.00 1.98
1870 2254 7.717436 TGTCTGTAAACATCAACTGAATAACCA 59.283 33.333 0.00 0.00 0.00 3.67
1872 2256 9.944663 TTTGTCTGTAAACATCAACTGAATAAC 57.055 29.630 2.01 0.00 0.00 1.89
1932 2316 9.698201 GGGTAAAATCCCTACAGCAGACTGAAT 62.698 44.444 6.65 0.00 44.17 2.57
1973 2357 4.729868 ACTAAGCCATGTTGAGAAAGGTT 58.270 39.130 0.00 0.00 0.00 3.50
1976 2360 5.947228 TTGACTAAGCCATGTTGAGAAAG 57.053 39.130 0.00 0.00 0.00 2.62
1982 2367 3.693085 AGCTGATTGACTAAGCCATGTTG 59.307 43.478 0.00 0.00 37.68 3.33
2050 2435 5.961395 GCTGACAGCAATCAAAATATTGG 57.039 39.130 22.62 0.00 41.89 3.16
2080 2465 9.834628 TCACTAATTCCAATAACGATTTCAAAC 57.165 29.630 0.00 0.00 0.00 2.93
2159 2544 5.103728 TGCCAGATGGGTGATAGGATTTAAA 60.104 40.000 0.12 0.00 39.65 1.52
2172 2557 5.337956 TTTATATCCAATGCCAGATGGGT 57.662 39.130 0.12 0.00 39.65 4.51
2173 2558 6.669125 TTTTTATATCCAATGCCAGATGGG 57.331 37.500 0.12 0.00 37.31 4.00
2211 2598 3.118629 CCCTCTTACAGATGTTGCAGCTA 60.119 47.826 1.17 0.00 0.00 3.32
2241 2628 3.194542 GCCAGGTTTGCAAATACATGGTA 59.805 43.478 26.95 0.00 45.42 3.25
2270 2657 0.820226 AGCAGATAAGCAGCGTCTCA 59.180 50.000 0.00 0.00 36.85 3.27
2273 2660 0.926846 GACAGCAGATAAGCAGCGTC 59.073 55.000 0.00 0.00 36.85 5.19
2312 2699 7.011295 AGCAACATACTTTTTGGACAACAATTG 59.989 33.333 3.24 3.24 39.21 2.32
2346 2742 5.252969 TCTATGCATGAACAAAGGAATGC 57.747 39.130 10.16 0.00 44.49 3.56
2347 2743 9.976511 AATAATCTATGCATGAACAAAGGAATG 57.023 29.630 10.16 0.00 0.00 2.67
2402 2798 0.322008 GCCTCTGTGCAAAGCCTAGT 60.322 55.000 0.00 0.00 0.00 2.57
2405 2801 1.303155 GAGCCTCTGTGCAAAGCCT 60.303 57.895 0.00 0.00 0.00 4.58
2407 2803 1.578423 GTGAGCCTCTGTGCAAAGC 59.422 57.895 0.00 0.00 0.00 3.51
2409 2805 1.146041 ACGTGAGCCTCTGTGCAAA 59.854 52.632 0.00 0.00 0.00 3.68
2410 2806 1.595109 CACGTGAGCCTCTGTGCAA 60.595 57.895 10.90 0.00 0.00 4.08
2424 2820 3.562557 GGGAGTATTTGTCAAACACACGT 59.437 43.478 9.30 0.00 33.41 4.49
2439 2835 4.720273 AGTATTTTGGAACGGAGGGAGTAT 59.280 41.667 0.00 0.00 0.00 2.12
2440 2836 4.098894 AGTATTTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
2441 2837 2.910977 AGTATTTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2442 2838 3.629142 AGTATTTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
2443 2839 4.472108 ACATAGTATTTTGGAACGGAGGGA 59.528 41.667 0.00 0.00 0.00 4.20
2444 2840 4.574828 CACATAGTATTTTGGAACGGAGGG 59.425 45.833 0.00 0.00 0.00 4.30
2445 2841 4.035208 GCACATAGTATTTTGGAACGGAGG 59.965 45.833 0.00 0.00 0.00 4.30
2446 2842 4.634004 TGCACATAGTATTTTGGAACGGAG 59.366 41.667 0.00 0.00 0.00 4.63
2447 2843 4.580868 TGCACATAGTATTTTGGAACGGA 58.419 39.130 0.00 0.00 0.00 4.69
2448 2844 4.955925 TGCACATAGTATTTTGGAACGG 57.044 40.909 0.00 0.00 0.00 4.44
2449 2845 6.688385 CAGATTGCACATAGTATTTTGGAACG 59.312 38.462 0.00 0.00 0.00 3.95
2450 2846 6.473455 GCAGATTGCACATAGTATTTTGGAAC 59.527 38.462 0.00 0.00 44.26 3.62
2451 2847 6.563422 GCAGATTGCACATAGTATTTTGGAA 58.437 36.000 0.00 0.00 44.26 3.53
2452 2848 6.135290 GCAGATTGCACATAGTATTTTGGA 57.865 37.500 0.00 0.00 44.26 3.53
2470 2866 3.054139 TCAGCAAAATCCCTACAGCAGAT 60.054 43.478 0.00 0.00 0.00 2.90
2493 2889 9.048446 TGTTTTAACAGGTTATACAGAACACTC 57.952 33.333 0.00 0.00 34.30 3.51
2494 2890 8.967664 TGTTTTAACAGGTTATACAGAACACT 57.032 30.769 0.00 0.00 34.30 3.55
2495 2891 9.607285 CATGTTTTAACAGGTTATACAGAACAC 57.393 33.333 1.50 0.00 43.04 3.32
2514 2910 5.928264 GCTGATTGAGTAAAAGCCATGTTTT 59.072 36.000 0.00 0.00 34.07 2.43
2515 2911 5.244626 AGCTGATTGAGTAAAAGCCATGTTT 59.755 36.000 0.00 0.00 32.74 2.83
2523 2919 7.846644 AGATTGAGAGCTGATTGAGTAAAAG 57.153 36.000 0.00 0.00 0.00 2.27
2526 2922 7.761704 GTGTTAGATTGAGAGCTGATTGAGTAA 59.238 37.037 0.00 0.00 0.00 2.24
2527 2923 7.261325 GTGTTAGATTGAGAGCTGATTGAGTA 58.739 38.462 0.00 0.00 0.00 2.59
2545 2941 2.171659 TGCTGGTGAAACTGGTGTTAGA 59.828 45.455 0.00 0.00 34.96 2.10
2562 2958 4.389992 AGAACTGATGTACGAATTGTGCTG 59.610 41.667 0.00 0.00 33.83 4.41
2572 2968 7.974675 ACCAAAATATTGAGAACTGATGTACG 58.025 34.615 0.00 0.00 38.94 3.67
2573 2969 9.774742 GAACCAAAATATTGAGAACTGATGTAC 57.225 33.333 0.00 0.00 38.94 2.90
2581 2977 6.681777 ACAGCAGAACCAAAATATTGAGAAC 58.318 36.000 0.00 0.00 38.94 3.01
2614 3010 6.018669 AGAGAAAGAAAAGAGCACACGTTAAG 60.019 38.462 0.00 0.00 0.00 1.85
2624 3021 6.474102 CGATACCTACAGAGAAAGAAAAGAGC 59.526 42.308 0.00 0.00 0.00 4.09
2631 3028 2.957006 GCCCGATACCTACAGAGAAAGA 59.043 50.000 0.00 0.00 0.00 2.52
2639 3036 4.162698 ACTTGTAATTGCCCGATACCTACA 59.837 41.667 0.00 0.00 0.00 2.74
2665 3062 1.849976 CGACGGCCCCTCGATAGTAC 61.850 65.000 11.31 0.00 32.65 2.73
2683 3080 2.731721 TACACGACAAGCGCACCG 60.732 61.111 11.47 9.73 46.04 4.94
2731 3128 0.320771 CCTTCAACCACCTCTCCACG 60.321 60.000 0.00 0.00 0.00 4.94
2818 3215 3.300388 CTCCACTGATACAGCCCTAAGA 58.700 50.000 0.00 0.00 34.37 2.10
2839 3236 3.521796 GCGAAGGCCTTGGCATCC 61.522 66.667 38.34 17.15 42.66 3.51
2893 3290 0.458669 CAACATTCATGGCCTCCAGC 59.541 55.000 3.32 0.00 36.75 4.85
2908 3305 1.138069 TCAGTGAAGGCGTTCTCAACA 59.862 47.619 19.07 0.00 33.38 3.33
2916 3313 0.034059 CAGAACCTCAGTGAAGGCGT 59.966 55.000 8.13 0.00 40.34 5.68
2947 3344 1.230635 CCTTCTTGCTGACCACACGG 61.231 60.000 0.00 0.00 38.77 4.94
3019 3416 1.203038 ACATCATCCTTGCCACCAACA 60.203 47.619 0.00 0.00 0.00 3.33
3128 3525 5.220529 GCAAAAAGGATGTCATATTTGCAGC 60.221 40.000 21.17 11.92 41.96 5.25
3183 3580 2.270352 ACGAAATTCTTGGTGCTCCA 57.730 45.000 2.64 2.64 42.66 3.86
3186 3583 4.819630 TGTCTAAACGAAATTCTTGGTGCT 59.180 37.500 0.00 0.00 0.00 4.40
3208 3605 5.016173 TCAACCTGGGGTTAAATCTTGATG 58.984 41.667 0.00 0.00 45.01 3.07
3241 3638 6.265196 TCACTGACATTCCAAAGTTAGCATTT 59.735 34.615 0.00 0.00 0.00 2.32
3242 3639 5.769662 TCACTGACATTCCAAAGTTAGCATT 59.230 36.000 0.00 0.00 0.00 3.56
3294 3691 0.035056 GGTGGGACAATACAGCAGCT 60.035 55.000 0.00 0.00 44.16 4.24
3349 3746 3.281727 CCTTTATCAGGTAAGGCTGCA 57.718 47.619 0.50 0.00 37.99 4.41
3542 3951 4.943705 GCAAATTCTGTACATCTGGGAAGA 59.056 41.667 0.00 0.00 0.00 2.87
3602 4011 7.584122 TTAAGTTACAGAGGGAGTAGCATAG 57.416 40.000 0.00 0.00 0.00 2.23
3611 4103 8.757982 ACGTCTTATATTAAGTTACAGAGGGA 57.242 34.615 0.00 0.00 0.00 4.20
3612 4104 9.813446 AAACGTCTTATATTAAGTTACAGAGGG 57.187 33.333 0.00 0.00 0.00 4.30
3624 4116 9.478768 TGACTGTGTCAAAAACGTCTTATATTA 57.521 29.630 0.00 0.00 39.78 0.98
3625 4117 8.373048 TGACTGTGTCAAAAACGTCTTATATT 57.627 30.769 0.00 0.00 39.78 1.28
3626 4118 7.956420 TGACTGTGTCAAAAACGTCTTATAT 57.044 32.000 0.00 0.00 39.78 0.86
3627 4119 7.095397 CCATGACTGTGTCAAAAACGTCTTATA 60.095 37.037 4.46 0.00 45.96 0.98
3628 4120 6.293407 CCATGACTGTGTCAAAAACGTCTTAT 60.293 38.462 4.46 0.00 45.96 1.73
3629 4121 5.007234 CCATGACTGTGTCAAAAACGTCTTA 59.993 40.000 4.46 0.00 45.96 2.10
3630 4122 4.201910 CCATGACTGTGTCAAAAACGTCTT 60.202 41.667 4.46 0.00 45.96 3.01
3631 4123 3.312421 CCATGACTGTGTCAAAAACGTCT 59.688 43.478 4.46 0.00 45.96 4.18
3632 4124 3.311322 TCCATGACTGTGTCAAAAACGTC 59.689 43.478 4.46 0.00 45.96 4.34
3633 4125 3.064820 GTCCATGACTGTGTCAAAAACGT 59.935 43.478 4.46 0.00 45.96 3.99
3634 4126 3.312421 AGTCCATGACTGTGTCAAAAACG 59.688 43.478 4.46 0.00 45.96 3.60
3635 4127 4.576463 AGAGTCCATGACTGTGTCAAAAAC 59.424 41.667 0.69 3.75 45.96 2.43
3636 4128 4.780815 AGAGTCCATGACTGTGTCAAAAA 58.219 39.130 0.69 0.00 45.96 1.94
3637 4129 4.422073 AGAGTCCATGACTGTGTCAAAA 57.578 40.909 0.69 0.00 45.96 2.44
3638 4130 5.545063 TTAGAGTCCATGACTGTGTCAAA 57.455 39.130 0.69 0.00 45.96 2.69
3639 4131 5.545063 TTTAGAGTCCATGACTGTGTCAA 57.455 39.130 0.69 0.00 45.96 3.18
3640 4132 5.545063 TTTTAGAGTCCATGACTGTGTCA 57.455 39.130 0.69 2.77 43.53 3.58
3641 4133 5.107453 CGTTTTTAGAGTCCATGACTGTGTC 60.107 44.000 0.69 0.00 43.53 3.67
3642 4134 4.750098 CGTTTTTAGAGTCCATGACTGTGT 59.250 41.667 0.69 0.00 43.53 3.72
3643 4135 4.750098 ACGTTTTTAGAGTCCATGACTGTG 59.250 41.667 0.69 0.00 43.53 3.66
3644 4136 4.957296 ACGTTTTTAGAGTCCATGACTGT 58.043 39.130 0.69 0.02 43.53 3.55
3645 4137 5.230942 AGACGTTTTTAGAGTCCATGACTG 58.769 41.667 0.69 0.00 43.53 3.51
3646 4138 5.470047 AGACGTTTTTAGAGTCCATGACT 57.530 39.130 0.00 0.00 46.42 3.41
3647 4139 7.829378 ATAAGACGTTTTTAGAGTCCATGAC 57.171 36.000 0.00 0.00 35.65 3.06
3648 4140 9.932207 TTTATAAGACGTTTTTAGAGTCCATGA 57.068 29.630 0.00 0.00 35.65 3.07
3661 4153 9.551734 ACCTCTGTAACTTTTTATAAGACGTTT 57.448 29.630 3.66 0.00 0.00 3.60
3663 4155 9.852091 CTACCTCTGTAACTTTTTATAAGACGT 57.148 33.333 0.00 0.00 0.00 4.34
3664 4156 9.852091 ACTACCTCTGTAACTTTTTATAAGACG 57.148 33.333 0.00 0.00 0.00 4.18
3666 4158 9.649167 GCACTACCTCTGTAACTTTTTATAAGA 57.351 33.333 0.00 0.00 0.00 2.10
3667 4159 8.880750 GGCACTACCTCTGTAACTTTTTATAAG 58.119 37.037 0.00 0.00 34.51 1.73
3668 4160 8.377034 TGGCACTACCTCTGTAACTTTTTATAA 58.623 33.333 0.00 0.00 40.22 0.98
3669 4161 7.909518 TGGCACTACCTCTGTAACTTTTTATA 58.090 34.615 0.00 0.00 40.22 0.98
3670 4162 6.775708 TGGCACTACCTCTGTAACTTTTTAT 58.224 36.000 0.00 0.00 40.22 1.40
3671 4163 6.177310 TGGCACTACCTCTGTAACTTTTTA 57.823 37.500 0.00 0.00 40.22 1.52
3672 4164 5.043737 TGGCACTACCTCTGTAACTTTTT 57.956 39.130 0.00 0.00 40.22 1.94
3673 4165 4.699925 TGGCACTACCTCTGTAACTTTT 57.300 40.909 0.00 0.00 40.22 2.27
3674 4166 4.910458 ATGGCACTACCTCTGTAACTTT 57.090 40.909 0.00 0.00 40.22 2.66
3675 4167 4.910458 AATGGCACTACCTCTGTAACTT 57.090 40.909 0.00 0.00 40.22 2.66
3676 4168 4.910458 AAATGGCACTACCTCTGTAACT 57.090 40.909 0.00 0.00 40.22 2.24
3677 4169 6.458342 GCATAAAATGGCACTACCTCTGTAAC 60.458 42.308 0.00 0.00 40.22 2.50
3678 4170 5.588648 GCATAAAATGGCACTACCTCTGTAA 59.411 40.000 0.00 0.00 40.22 2.41
3679 4171 5.123227 GCATAAAATGGCACTACCTCTGTA 58.877 41.667 0.00 0.00 40.22 2.74
3680 4172 3.947834 GCATAAAATGGCACTACCTCTGT 59.052 43.478 0.00 0.00 40.22 3.41
3681 4173 4.558538 GCATAAAATGGCACTACCTCTG 57.441 45.455 0.00 0.00 40.22 3.35
3691 4183 7.661847 AGTGAATACTAGTAGGCATAAAATGGC 59.338 37.037 8.85 5.38 44.92 4.40
3706 4198 8.648557 TTAAACAGCAGCATAGTGAATACTAG 57.351 34.615 0.00 0.00 42.36 2.57
3799 4291 6.590656 AAATACATGGAAGGGGATTGTCTA 57.409 37.500 0.00 0.00 0.00 2.59
3802 4294 6.741724 AGTAAAATACATGGAAGGGGATTGT 58.258 36.000 0.00 0.00 0.00 2.71
3806 4298 7.039722 AGAAAGTAAAATACATGGAAGGGGA 57.960 36.000 0.00 0.00 0.00 4.81
3832 4324 6.549433 TTACAAAGTCAGATAATACCCCGT 57.451 37.500 0.00 0.00 0.00 5.28
3834 4326 7.282450 CCAGTTTACAAAGTCAGATAATACCCC 59.718 40.741 0.00 0.00 0.00 4.95
3844 4336 5.695851 AAGATGCCAGTTTACAAAGTCAG 57.304 39.130 0.00 0.00 0.00 3.51
3854 4346 4.218417 ACGAGCAAATAAAGATGCCAGTTT 59.782 37.500 0.00 0.00 43.57 2.66
3859 4351 3.119849 ACACACGAGCAAATAAAGATGCC 60.120 43.478 0.00 0.00 43.57 4.40
3865 4357 5.363979 TTGCATACACACGAGCAAATAAA 57.636 34.783 0.00 0.00 43.24 1.40
3883 4377 3.844211 ACCCTCTATCAAGGTAGTTTGCA 59.156 43.478 0.00 0.00 34.34 4.08


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

AutoCloner maintained by Alex Coulton.