Multiple sequence alignment - TraesCS1D01G237800

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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 TraesCS1D01G237800 chr1D 100.000 7758 0 0 1 7758 326976550 326968793 0.000000e+00 14327.0
1 TraesCS1D01G237800 chr1D 97.368 38 1 0 7416 7453 361353625 361353662 1.810000e-06 65.8
2 TraesCS1D01G237800 chr1D 89.362 47 4 1 7368 7413 160501777 160501731 3.020000e-04 58.4
3 TraesCS1D01G237800 chr1A 92.580 3423 139 50 3 3359 409826824 409830197 0.000000e+00 4807.0
4 TraesCS1D01G237800 chr1A 93.215 2255 97 19 3345 5550 409830249 409832496 0.000000e+00 3265.0
5 TraesCS1D01G237800 chr1A 94.241 1528 57 18 5521 7040 409832526 409834030 0.000000e+00 2305.0
6 TraesCS1D01G237800 chr1A 88.372 301 17 7 7455 7755 409834770 409835052 5.760000e-91 346.0
7 TraesCS1D01G237800 chr1A 87.574 169 14 3 7025 7187 409834050 409834217 1.030000e-43 189.0
8 TraesCS1D01G237800 chr1A 93.103 87 6 0 4801 4887 409831654 409831740 2.270000e-25 128.0
9 TraesCS1D01G237800 chr1A 97.297 37 1 0 7416 7452 532230638 532230674 6.500000e-06 63.9
10 TraesCS1D01G237800 chr1B 93.697 2253 86 13 3345 5550 441657751 441655508 0.000000e+00 3323.0
11 TraesCS1D01G237800 chr1B 92.883 2248 87 33 1 2216 441661092 441658886 0.000000e+00 3197.0
12 TraesCS1D01G237800 chr1B 94.510 1876 59 20 5521 7371 441655508 441653652 0.000000e+00 2854.0
13 TraesCS1D01G237800 chr1B 95.330 1092 42 5 2274 3359 441658894 441657806 0.000000e+00 1725.0
14 TraesCS1D01G237800 chr1B 95.000 60 3 0 7620 7679 441653158 441653099 2.300000e-15 95.3
15 TraesCS1D01G237800 chr1B 90.909 44 4 0 7678 7721 441638279 441638236 8.410000e-05 60.2
16 TraesCS1D01G237800 chr2B 76.046 263 51 6 2098 2350 117609863 117610123 8.170000e-25 126.0
17 TraesCS1D01G237800 chr2B 93.333 45 2 1 7368 7411 31426010 31426054 1.810000e-06 65.8
18 TraesCS1D01G237800 chr5D 77.838 185 30 8 2101 2277 106983911 106983730 3.830000e-18 104.0
19 TraesCS1D01G237800 chr5D 93.333 45 3 0 4048 4092 556009375 556009331 5.020000e-07 67.6
20 TraesCS1D01G237800 chr5D 93.182 44 2 1 7416 7458 78311725 78311768 6.500000e-06 63.9
21 TraesCS1D01G237800 chr5D 97.368 38 0 1 7416 7453 565094096 565094132 6.500000e-06 63.9
22 TraesCS1D01G237800 chr3D 77.222 180 35 4 2100 2275 76398457 76398280 4.950000e-17 100.0
23 TraesCS1D01G237800 chr3D 90.196 51 4 1 4045 4094 305448613 305448563 1.810000e-06 65.8
24 TraesCS1D01G237800 chr3D 91.111 45 3 1 7370 7413 61553877 61553921 8.410000e-05 60.2
25 TraesCS1D01G237800 chr3B 77.222 180 35 4 2100 2275 123396888 123396711 4.950000e-17 100.0
26 TraesCS1D01G237800 chr3B 80.374 107 19 2 2101 2206 95164527 95164422 6.450000e-11 80.5
27 TraesCS1D01G237800 chr7B 97.500 40 1 0 2100 2139 594683768 594683729 1.400000e-07 69.4
28 TraesCS1D01G237800 chr7B 93.333 45 2 1 7368 7411 296348674 296348718 1.810000e-06 65.8
29 TraesCS1D01G237800 chrUn 93.333 45 3 0 7416 7460 394985370 394985326 5.020000e-07 67.6
30 TraesCS1D01G237800 chrUn 97.368 38 1 0 7416 7453 15373520 15373483 1.810000e-06 65.8
31 TraesCS1D01G237800 chr7D 81.928 83 12 2 2159 2239 78182173 78182254 5.020000e-07 67.6
32 TraesCS1D01G237800 chr5B 91.837 49 3 1 4045 4092 34252135 34252183 5.020000e-07 67.6
33 TraesCS1D01G237800 chr5B 91.111 45 3 1 7368 7411 128465973 128465929 8.410000e-05 60.2
34 TraesCS1D01G237800 chr7A 93.182 44 3 0 7368 7411 482484228 482484271 1.810000e-06 65.8
35 TraesCS1D01G237800 chr7A 85.484 62 8 1 2185 2246 81588358 81588418 6.500000e-06 63.9
36 TraesCS1D01G237800 chr5A 97.368 38 1 0 7416 7453 673214855 673214892 1.810000e-06 65.8
37 TraesCS1D01G237800 chr3A 93.333 45 2 1 7368 7411 531452020 531451976 1.810000e-06 65.8
38 TraesCS1D01G237800 chr3A 93.333 45 2 1 7368 7411 531452098 531452054 1.810000e-06 65.8
39 TraesCS1D01G237800 chr3A 89.362 47 3 2 2327 2372 387443469 387443424 3.020000e-04 58.4
40 TraesCS1D01G237800 chr6B 91.489 47 3 1 4048 4093 560191903 560191949 6.500000e-06 63.9
41 TraesCS1D01G237800 chr6A 88.679 53 5 1 4048 4099 500508933 500508881 6.500000e-06 63.9
42 TraesCS1D01G237800 chr2D 91.489 47 3 1 7368 7413 637030206 637030252 6.500000e-06 63.9
43 TraesCS1D01G237800 chr2D 88.462 52 4 2 7416 7466 20649010 20649060 2.340000e-05 62.1
44 TraesCS1D01G237800 chr2D 97.143 35 1 0 4049 4083 145890457 145890491 8.410000e-05 60.2
45 TraesCS1D01G237800 chr2D 100.000 29 0 0 2216 2244 98726372 98726344 4.000000e-03 54.7
46 TraesCS1D01G237800 chr2A 93.023 43 3 0 7416 7458 747308154 747308112 6.500000e-06 63.9
47 TraesCS1D01G237800 chr6D 93.023 43 2 1 2099 2141 211690485 211690526 2.340000e-05 62.1
48 TraesCS1D01G237800 chr4D 89.362 47 5 0 2200 2246 18467150 18467196 8.410000e-05 60.2
49 TraesCS1D01G237800 chr4A 91.111 45 3 1 4049 4092 66145672 66145628 8.410000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G237800 chr1D 326968793 326976550 7757 True 14327.00 14327 100.000000 1 7758 1 chr1D.!!$R2 7757
1 TraesCS1D01G237800 chr1A 409826824 409835052 8228 False 1840.00 4807 91.514167 3 7755 6 chr1A.!!$F2 7752
2 TraesCS1D01G237800 chr1B 441653099 441661092 7993 True 2238.86 3323 94.284000 1 7679 5 chr1B.!!$R2 7678

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
578 610 1.053424 TCCCGTGTACCTTTGCTTCT 58.947 50.000 0.00 0.00 0.00 2.85 F
1375 1433 0.322546 ACGGTCTGCCCTTGATTTCC 60.323 55.000 0.00 0.00 0.00 3.13 F
1751 1812 0.243907 ACAGTTCGACAGATGACGGG 59.756 55.000 4.98 0.00 34.25 5.28 F
1752 1813 0.243907 CAGTTCGACAGATGACGGGT 59.756 55.000 4.98 0.00 34.25 5.28 F
3398 3553 1.014044 CCCACACGTGTTCGATCAGG 61.014 60.000 20.79 15.02 40.62 3.86 F
4273 4431 1.064060 GCCCGCACTAGCTTACATTTG 59.936 52.381 0.00 0.00 39.10 2.32 F
4737 4938 1.381076 GGGGTTGAATTGGTCCGGA 59.619 57.895 0.00 0.00 0.00 5.14 F
6450 6746 0.108329 CCAGTCGAGGCGGTTACATT 60.108 55.000 0.00 0.00 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 1799 0.172578 TAAGCACCCGTCATCTGTCG 59.827 55.000 0.00 0.0 0.00 4.35 R
3213 3299 1.177401 GAATGGCCAGGAAAGGTGTC 58.823 55.000 13.05 0.0 0.00 3.67 R
3686 3843 1.622811 GTGCAAATCCAATTCCACCCA 59.377 47.619 0.00 0.0 0.00 4.51 R
3703 3860 6.973229 AAATAAAGGAAATTGAGCATGTGC 57.027 33.333 0.00 0.0 42.49 4.57 R
4804 5005 0.099791 ACCAGTTCAACCGCAAAACG 59.900 50.000 0.00 0.0 43.15 3.60 R
5077 5278 2.227865 GGTCGCTTTGGACATAGCAAAA 59.772 45.455 13.66 0.0 38.70 2.44 R
6583 6879 1.026718 AAGCCTATGCCGCTTCACAC 61.027 55.000 0.00 0.0 42.94 3.82 R
7563 8621 0.839946 CCGGGTTCTCCAATCTCCAT 59.160 55.000 0.00 0.0 34.36 3.41 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
35 36 1.402613 TGTGGATGATGATGCTTTGCG 59.597 47.619 0.00 0.00 0.00 4.85
36 37 1.672363 GTGGATGATGATGCTTTGCGA 59.328 47.619 0.00 0.00 0.00 5.10
94 98 6.366340 TGGTACAATAGACCCACAAAAAGAA 58.634 36.000 0.00 0.00 35.99 2.52
176 180 2.359354 GGTGCACACCGCCACATA 60.359 61.111 20.43 0.00 43.83 2.29
222 232 2.886523 TGACAAAGACCCAAATCTGCTG 59.113 45.455 0.00 0.00 0.00 4.41
306 316 1.136305 CCGCCGTAATCTCCTTCTTCA 59.864 52.381 0.00 0.00 0.00 3.02
311 328 3.447586 CCGTAATCTCCTTCTTCACCTCA 59.552 47.826 0.00 0.00 0.00 3.86
397 425 2.830370 CGCCAGGGAATTCAGCCC 60.830 66.667 7.93 0.00 46.40 5.19
403 431 4.686695 GGAATTCAGCCCCTTCCC 57.313 61.111 7.93 0.00 33.74 3.97
426 454 2.221981 GGAGCAATTCGAGATTTAGGCG 59.778 50.000 0.00 0.00 0.00 5.52
468 496 2.671070 GCGCCGTCAGATTTGGAATTTT 60.671 45.455 0.00 0.00 0.00 1.82
469 497 2.916716 CGCCGTCAGATTTGGAATTTTG 59.083 45.455 0.00 0.00 0.00 2.44
470 498 3.253230 GCCGTCAGATTTGGAATTTTGG 58.747 45.455 0.00 0.00 0.00 3.28
471 499 3.056891 GCCGTCAGATTTGGAATTTTGGA 60.057 43.478 0.00 0.00 0.00 3.53
472 500 4.381932 GCCGTCAGATTTGGAATTTTGGAT 60.382 41.667 0.00 0.00 0.00 3.41
473 501 5.723295 CCGTCAGATTTGGAATTTTGGATT 58.277 37.500 0.00 0.00 0.00 3.01
474 502 6.165577 CCGTCAGATTTGGAATTTTGGATTT 58.834 36.000 0.00 0.00 0.00 2.17
475 503 6.650390 CCGTCAGATTTGGAATTTTGGATTTT 59.350 34.615 0.00 0.00 0.00 1.82
476 504 7.173047 CCGTCAGATTTGGAATTTTGGATTTTT 59.827 33.333 0.00 0.00 0.00 1.94
511 539 3.944422 AATTGCGACGCGATTTTATCT 57.056 38.095 26.07 6.67 39.34 1.98
517 545 4.201773 TGCGACGCGATTTTATCTTGATTT 60.202 37.500 15.93 0.00 0.00 2.17
521 549 6.897663 CGACGCGATTTTATCTTGATTTGTTA 59.102 34.615 15.93 0.00 0.00 2.41
537 569 9.460019 TTGATTTGTTATTCTACATCATGTCCA 57.540 29.630 0.00 0.00 0.00 4.02
578 610 1.053424 TCCCGTGTACCTTTGCTTCT 58.947 50.000 0.00 0.00 0.00 2.85
1223 1281 2.226200 TGTGACAATTCAACATCCGCAG 59.774 45.455 0.00 0.00 31.90 5.18
1230 1288 3.829886 TTCAACATCCGCAGTCAATTC 57.170 42.857 0.00 0.00 0.00 2.17
1357 1415 6.926272 ACTGAACTGTCTCTTGTCTAATTGAC 59.074 38.462 0.00 0.00 45.54 3.18
1368 1426 1.906574 TCTAATTGACGGTCTGCCCTT 59.093 47.619 9.88 0.00 0.00 3.95
1372 1430 0.400213 TTGACGGTCTGCCCTTGATT 59.600 50.000 9.88 0.00 0.00 2.57
1375 1433 0.322546 ACGGTCTGCCCTTGATTTCC 60.323 55.000 0.00 0.00 0.00 3.13
1395 1454 3.461458 TCCCAAGGCACACATGGATATTA 59.539 43.478 0.00 0.00 36.27 0.98
1493 1553 6.017440 TGGACGACTGAATTTTGTTTTCCTAG 60.017 38.462 0.00 0.00 0.00 3.02
1637 1698 4.260702 GGTTTTGGATACGTGACGTTTTCA 60.261 41.667 18.28 11.18 41.54 2.69
1663 1724 7.500992 TCAGTAGAGGATGCAAAGGTAATAAG 58.499 38.462 0.00 0.00 0.00 1.73
1692 1753 7.499563 GGAATCCCTTCAGTTTATTAGGACTTC 59.500 40.741 0.00 0.00 32.70 3.01
1733 1794 4.434713 CCAGTGGCAAAAGGTAATGTAC 57.565 45.455 0.00 0.00 0.00 2.90
1734 1795 3.823873 CCAGTGGCAAAAGGTAATGTACA 59.176 43.478 0.00 0.00 0.00 2.90
1735 1796 4.082787 CCAGTGGCAAAAGGTAATGTACAG 60.083 45.833 0.33 0.00 0.00 2.74
1736 1797 4.518970 CAGTGGCAAAAGGTAATGTACAGT 59.481 41.667 0.33 0.07 0.00 3.55
1737 1798 5.009610 CAGTGGCAAAAGGTAATGTACAGTT 59.990 40.000 0.00 0.00 0.00 3.16
1738 1799 5.240844 AGTGGCAAAAGGTAATGTACAGTTC 59.759 40.000 0.00 0.00 0.00 3.01
1739 1800 4.214545 TGGCAAAAGGTAATGTACAGTTCG 59.785 41.667 0.00 0.00 0.00 3.95
1740 1801 4.453136 GGCAAAAGGTAATGTACAGTTCGA 59.547 41.667 0.00 0.00 0.00 3.71
1741 1802 5.379827 GCAAAAGGTAATGTACAGTTCGAC 58.620 41.667 0.00 0.00 0.00 4.20
1742 1803 5.049954 GCAAAAGGTAATGTACAGTTCGACA 60.050 40.000 0.00 0.00 0.00 4.35
1743 1804 6.590357 CAAAAGGTAATGTACAGTTCGACAG 58.410 40.000 0.00 0.00 0.00 3.51
1744 1805 5.717078 AAGGTAATGTACAGTTCGACAGA 57.283 39.130 0.00 0.00 0.00 3.41
1745 1806 5.916661 AGGTAATGTACAGTTCGACAGAT 57.083 39.130 0.00 0.00 0.00 2.90
1746 1807 5.651530 AGGTAATGTACAGTTCGACAGATG 58.348 41.667 0.00 0.00 0.00 2.90
1747 1808 5.417894 AGGTAATGTACAGTTCGACAGATGA 59.582 40.000 0.00 0.00 0.00 2.92
1748 1809 5.515626 GGTAATGTACAGTTCGACAGATGAC 59.484 44.000 0.00 0.00 0.00 3.06
1749 1810 3.197434 TGTACAGTTCGACAGATGACG 57.803 47.619 0.00 0.00 34.74 4.35
1750 1811 2.095415 TGTACAGTTCGACAGATGACGG 60.095 50.000 4.98 0.00 34.25 4.79
1751 1812 0.243907 ACAGTTCGACAGATGACGGG 59.756 55.000 4.98 0.00 34.25 5.28
1752 1813 0.243907 CAGTTCGACAGATGACGGGT 59.756 55.000 4.98 0.00 34.25 5.28
1753 1814 0.243907 AGTTCGACAGATGACGGGTG 59.756 55.000 4.98 0.00 34.25 4.61
1769 1834 3.635836 ACGGGTGCTTACTCTCTATTACC 59.364 47.826 0.00 0.00 0.00 2.85
1881 1946 6.605471 ACTGTACATCTAGTTGATCACCAA 57.395 37.500 7.81 0.00 32.05 3.67
1918 1985 7.177216 TCTCCTCAGTTTTAACGTCCTGTAATA 59.823 37.037 0.00 0.00 0.00 0.98
1944 2011 7.035004 GCATCTTGCTTGTTTATCAACCATTA 58.965 34.615 0.00 0.00 40.96 1.90
1967 2037 6.670695 AAAAGAAAATGGGCAACTAGTCAT 57.329 33.333 0.00 0.00 0.00 3.06
2169 2240 6.866248 TCGAATTTCTTTATTTTTGACCAGGC 59.134 34.615 0.00 0.00 0.00 4.85
2179 2251 8.732746 TTATTTTTGACCAGGCTTATAGAGAC 57.267 34.615 0.00 0.00 0.00 3.36
2355 2428 2.847234 AACGGAGGGAGTGTGCCA 60.847 61.111 0.00 0.00 0.00 4.92
2403 2476 5.774690 AGCAATACATTTTCCTTTGTCCTGA 59.225 36.000 0.00 0.00 0.00 3.86
2430 2503 6.791887 TGCTTTAGTCAACTGAATGAAGAG 57.208 37.500 13.77 0.00 37.76 2.85
2472 2545 7.463961 AGGATATGATTTGATGGCATCTTTC 57.536 36.000 26.49 19.37 0.00 2.62
2520 2593 3.886505 CTCCTGTCGCCTCTATTAACTCT 59.113 47.826 0.00 0.00 0.00 3.24
2531 2604 7.041030 CGCCTCTATTAACTCTGATTCTCTGTA 60.041 40.741 0.00 0.00 0.00 2.74
2619 2694 5.112129 AGCGACTCCCAAGGTAAATATTT 57.888 39.130 5.89 5.89 0.00 1.40
2629 2704 8.871125 TCCCAAGGTAAATATTTGCAAAAAGTA 58.129 29.630 17.19 4.62 0.00 2.24
2696 2771 3.126073 CAGACCTTTGCTTGCCTTTTTC 58.874 45.455 0.00 0.00 0.00 2.29
2832 2908 1.472376 GCAGGTGAGCTCCAGTACATC 60.472 57.143 12.15 0.00 0.00 3.06
2841 2917 2.162408 GCTCCAGTACATCTTTTGCCAC 59.838 50.000 0.00 0.00 0.00 5.01
2883 2959 8.491152 CCTTCAATATATGAACTTGTCTAAGCG 58.509 37.037 0.00 0.00 43.08 4.68
2956 3032 4.437682 TTATATGCCCAAGGTGAGGAAG 57.562 45.455 0.00 0.00 0.00 3.46
2965 3041 3.496870 CCAAGGTGAGGAAGTTAAGCTGT 60.497 47.826 0.00 0.00 0.00 4.40
2968 3044 5.763876 AGGTGAGGAAGTTAAGCTGTTAT 57.236 39.130 0.00 0.00 0.00 1.89
3014 3090 3.326747 AGTGCCGTCATCTAGTTTTGTC 58.673 45.455 0.00 0.00 0.00 3.18
3033 3112 9.821662 GTTTTGTCCATGTTAGTGTATTTACTC 57.178 33.333 0.00 0.00 32.19 2.59
3108 3192 8.635765 TTTTCTGTAATATCTGCAACCTTCTT 57.364 30.769 0.00 0.00 0.00 2.52
3144 3230 6.769822 AGTACATTGAAGATATTTCCAGCCAG 59.230 38.462 0.00 0.00 0.00 4.85
3200 3286 8.385898 TCACGTTAAAGATCACCAAATTACTT 57.614 30.769 0.00 0.00 0.00 2.24
3234 3320 1.077663 ACACCTTTCCTGGCCATTCAT 59.922 47.619 5.51 0.00 0.00 2.57
3313 3399 9.384682 CAATTAAAAATTGATGTTGTTCAAGCC 57.615 29.630 6.53 0.00 38.90 4.35
3395 3550 1.740296 CCCCCACACGTGTTCGATC 60.740 63.158 20.79 0.00 40.62 3.69
3398 3553 1.014044 CCCACACGTGTTCGATCAGG 61.014 60.000 20.79 15.02 40.62 3.86
3428 3583 2.292267 CTGACAAGACACAGTGCCTTT 58.708 47.619 0.00 0.00 0.00 3.11
3467 3622 4.221703 ACTGTTGAAGAGAGATTCGTCCAT 59.778 41.667 0.00 0.00 33.90 3.41
3469 3624 5.551233 TGTTGAAGAGAGATTCGTCCATTT 58.449 37.500 0.00 0.00 33.90 2.32
3537 3694 8.181904 TGATTTTTCATAGTCTTTGGAGCTTT 57.818 30.769 0.00 0.00 0.00 3.51
3654 3811 1.346068 GTTGAGGAGTCTGGTCAGCTT 59.654 52.381 0.00 0.00 0.00 3.74
3703 3860 4.223477 ACAAGATGGGTGGAATTGGATTTG 59.777 41.667 0.00 0.00 0.00 2.32
3711 3868 2.568062 TGGAATTGGATTTGCACATGCT 59.432 40.909 5.92 0.00 42.66 3.79
3873 4030 4.389374 GTTTTGTTCTCCCACTGATCTCA 58.611 43.478 0.00 0.00 0.00 3.27
3963 4120 7.794810 CGTGTATAGAATCTTCTAAGAGACGTG 59.205 40.741 17.53 0.00 42.55 4.49
4027 4184 4.601857 AGAGGAAAAATGTTACTCCCTCCA 59.398 41.667 0.00 0.00 39.48 3.86
4033 4190 4.510167 AATGTTACTCCCTCCAATCCTG 57.490 45.455 0.00 0.00 0.00 3.86
4034 4191 2.915869 TGTTACTCCCTCCAATCCTGT 58.084 47.619 0.00 0.00 0.00 4.00
4233 4391 3.375922 ACCCATAACCTTAAATTCACGCG 59.624 43.478 3.53 3.53 0.00 6.01
4243 4401 1.303091 AATTCACGCGGTAGGGTTGC 61.303 55.000 12.47 0.00 41.93 4.17
4273 4431 1.064060 GCCCGCACTAGCTTACATTTG 59.936 52.381 0.00 0.00 39.10 2.32
4276 4441 3.181510 CCCGCACTAGCTTACATTTGTTC 60.182 47.826 0.00 0.00 39.10 3.18
4279 4444 5.334879 CCGCACTAGCTTACATTTGTTCTTT 60.335 40.000 0.00 0.00 39.10 2.52
4341 4506 3.710209 ACATTCTTCTGCCTAAGTGCT 57.290 42.857 0.00 0.00 0.00 4.40
4449 4621 5.304101 ACTTCCATTTGCTTCACCATTTACA 59.696 36.000 0.00 0.00 0.00 2.41
4451 4623 6.357579 TCCATTTGCTTCACCATTTACAAT 57.642 33.333 0.00 0.00 0.00 2.71
4457 4629 7.517614 TTGCTTCACCATTTACAATGAGTAA 57.482 32.000 0.00 0.00 40.83 2.24
4458 4630 7.701539 TGCTTCACCATTTACAATGAGTAAT 57.298 32.000 0.00 0.00 42.03 1.89
4502 4676 9.233232 CCTGTTTAGCTTTAGTTTGTAACTTTG 57.767 33.333 0.00 0.00 42.81 2.77
4567 4741 4.098960 AATCATGAGATTGATGGCACAACC 59.901 41.667 0.09 0.00 42.41 3.77
4698 4872 3.978672 ACTAGAACTAACACCCAGGGTTT 59.021 43.478 9.12 9.72 31.02 3.27
4711 4912 3.332783 CCCAGGGTTTAAAGTAGGAAGGT 59.667 47.826 0.00 0.00 0.00 3.50
4728 4929 4.384757 GGAAGGTTTGTTTTGGGGTTGAAT 60.385 41.667 0.00 0.00 0.00 2.57
4737 4938 1.381076 GGGGTTGAATTGGTCCGGA 59.619 57.895 0.00 0.00 0.00 5.14
4753 4954 6.627243 TGGTCCGGATTGTAATATCTAATCG 58.373 40.000 7.81 0.00 32.88 3.34
4776 4977 5.699458 CGTACCATGATCCTACCAATTTACC 59.301 44.000 0.00 0.00 0.00 2.85
4791 4992 5.253330 CAATTTACCCCTTCTAGTGCTTGA 58.747 41.667 0.00 0.00 0.00 3.02
4905 5106 5.742562 AAAGGGGTTATATTGGACATGGA 57.257 39.130 0.00 0.00 0.00 3.41
5041 5242 8.134895 GTCAAGTGTCCAATCTGAACATTTTTA 58.865 33.333 0.00 0.00 0.00 1.52
5077 5278 6.127647 TGCAGTCAGAGTTTTTGAAGTTTGAT 60.128 34.615 0.00 0.00 0.00 2.57
5093 5294 7.652909 TGAAGTTTGATTTTGCTATGTCCAAAG 59.347 33.333 0.00 0.00 34.10 2.77
5108 5309 4.173256 GTCCAAAGCGACCAATTTTATGG 58.827 43.478 0.00 0.00 46.38 2.74
5111 5312 4.625311 CCAAAGCGACCAATTTTATGGAAC 59.375 41.667 0.00 0.00 43.54 3.62
5255 5457 4.062293 TCTTGTTTGATGAACCTGTACGG 58.938 43.478 0.00 0.00 37.45 4.02
5272 5474 5.736813 TGTACGGGCAAATGTTTCTATACT 58.263 37.500 0.00 0.00 0.00 2.12
5274 5476 4.839121 ACGGGCAAATGTTTCTATACTGA 58.161 39.130 0.00 0.00 0.00 3.41
5391 5596 9.425893 CAGTATGAAAGCATATAAAGAACAACG 57.574 33.333 0.00 0.00 39.69 4.10
5495 5700 5.140454 ACAACCATGATTCTATAAAGGGCC 58.860 41.667 0.00 0.00 0.00 5.80
5503 5708 5.193728 TGATTCTATAAAGGGCCTCTTTGGT 59.806 40.000 22.34 15.48 44.68 3.67
5514 5719 3.756963 GGCCTCTTTGGTACGAAGAAATT 59.243 43.478 0.00 0.00 38.35 1.82
5528 5733 4.515191 CGAAGAAATTGAAACACTCAGGGA 59.485 41.667 0.00 0.00 34.81 4.20
5563 5857 7.255242 GCACATGATTATAGTGTTATGGCTTGT 60.255 37.037 0.00 0.00 35.75 3.16
5623 5918 5.368145 ACAGAGCTGTTTGAATACTGACAA 58.632 37.500 0.00 0.00 41.83 3.18
5649 5944 5.375417 TGCACACATTTTGAGATTAGGTG 57.625 39.130 0.00 0.00 0.00 4.00
5656 5951 8.567948 ACACATTTTGAGATTAGGTGTTACTTG 58.432 33.333 0.00 0.00 34.65 3.16
5729 6025 5.720041 ACTGGTGCTCTAGTTATCCACTTAA 59.280 40.000 0.00 0.00 36.88 1.85
6188 6484 4.710324 TGACAACTTACAAACCCTAGTGG 58.290 43.478 0.00 0.00 41.37 4.00
6450 6746 0.108329 CCAGTCGAGGCGGTTACATT 60.108 55.000 0.00 0.00 0.00 2.71
6465 6761 2.035626 ATTGAACCACCTGGGCCG 59.964 61.111 0.00 0.00 42.05 6.13
6615 6911 5.066505 CGGCATAGGCTTCAAATTAGTTTCT 59.933 40.000 0.00 0.00 40.87 2.52
6656 6952 6.025749 TCTCGATTATCACTTGTGAGTTGT 57.974 37.500 9.39 0.00 32.54 3.32
6665 6961 5.185454 TCACTTGTGAGTTGTGAGACATTT 58.815 37.500 0.00 0.00 36.03 2.32
6797 7093 2.419673 TCACAGCATTTAAGCGACATGG 59.580 45.455 0.00 0.00 40.15 3.66
6798 7094 2.162208 CACAGCATTTAAGCGACATGGT 59.838 45.455 0.00 0.00 40.15 3.55
6799 7095 3.373748 CACAGCATTTAAGCGACATGGTA 59.626 43.478 0.00 0.00 40.15 3.25
6800 7096 3.623060 ACAGCATTTAAGCGACATGGTAG 59.377 43.478 0.00 0.00 40.15 3.18
6912 7208 9.088987 ACTTATGTTTGTTTTTGTCCAGGATAT 57.911 29.630 0.00 0.00 0.00 1.63
6938 7234 4.498345 GCGTAACCCTTTTTGTTCATGACA 60.498 41.667 0.00 0.00 36.19 3.58
6970 7267 2.796557 TCATGTGCCACCGGAAATTTA 58.203 42.857 9.46 0.00 0.00 1.40
7002 7299 1.202794 TGGCAGACTCTGAACATTGCA 60.203 47.619 10.45 0.00 32.44 4.08
7042 7380 0.598065 GGGTTAGCTGTGCAGTTTGG 59.402 55.000 0.00 0.00 0.00 3.28
7063 7401 1.666054 TACGTTTTTCAGCGTTGGGT 58.334 45.000 0.00 0.00 41.77 4.51
7114 7456 1.774894 TAGCCAAGGTTCCGGTTGCT 61.775 55.000 0.00 0.00 0.00 3.91
7121 7463 0.521735 GGTTCCGGTTGCTCATGTTC 59.478 55.000 0.00 0.00 0.00 3.18
7127 7469 2.419990 CCGGTTGCTCATGTTCTATCCA 60.420 50.000 0.00 0.00 0.00 3.41
7128 7470 3.470709 CGGTTGCTCATGTTCTATCCAT 58.529 45.455 0.00 0.00 0.00 3.41
7154 7497 9.659503 TGGATTTCCTCTAAAATGCACATGTGC 62.660 40.741 38.00 38.00 46.03 4.57
7179 7522 2.556534 GCATCTGGCAATCACTGAAC 57.443 50.000 0.00 0.00 43.97 3.18
7192 7563 2.124109 TGAACCAAAGGCGCACCA 60.124 55.556 10.83 0.00 39.06 4.17
7202 7573 3.451894 GCGCACCATTCCCTTGGG 61.452 66.667 0.30 0.00 41.35 4.12
7205 7576 1.184970 CGCACCATTCCCTTGGGTTT 61.185 55.000 5.51 0.00 41.35 3.27
7249 7627 1.339727 CCTACTGGGCCTTGTTACCAC 60.340 57.143 4.53 0.00 0.00 4.16
7299 7677 3.825908 TGCCTCCCAAAAAGAAGGTAT 57.174 42.857 0.00 0.00 0.00 2.73
7301 7679 4.488770 TGCCTCCCAAAAAGAAGGTATTT 58.511 39.130 0.00 0.00 0.00 1.40
7309 7687 6.200097 CCCAAAAAGAAGGTATTTGAAACGTG 59.800 38.462 0.00 0.00 36.41 4.49
7338 7950 4.143494 GCCAAACGGTAAAATAAGCAAACG 60.143 41.667 0.00 0.00 0.00 3.60
7360 7972 3.466836 AGTCAGACAAGCACGATTTCAA 58.533 40.909 2.66 0.00 0.00 2.69
7363 7975 5.034152 GTCAGACAAGCACGATTTCAAAAA 58.966 37.500 0.00 0.00 0.00 1.94
7366 7978 3.453424 ACAAGCACGATTTCAAAAACCC 58.547 40.909 0.00 0.00 0.00 4.11
7367 7979 3.118956 ACAAGCACGATTTCAAAAACCCA 60.119 39.130 0.00 0.00 0.00 4.51
7369 7981 4.335400 AGCACGATTTCAAAAACCCATT 57.665 36.364 0.00 0.00 0.00 3.16
7370 7982 5.461032 AGCACGATTTCAAAAACCCATTA 57.539 34.783 0.00 0.00 0.00 1.90
7371 7983 5.848406 AGCACGATTTCAAAAACCCATTAA 58.152 33.333 0.00 0.00 0.00 1.40
7372 7984 5.694458 AGCACGATTTCAAAAACCCATTAAC 59.306 36.000 0.00 0.00 0.00 2.01
7374 7986 6.201997 GCACGATTTCAAAAACCCATTAACTT 59.798 34.615 0.00 0.00 0.00 2.66
7375 7987 7.254624 GCACGATTTCAAAAACCCATTAACTTT 60.255 33.333 0.00 0.00 0.00 2.66
7376 7988 9.250624 CACGATTTCAAAAACCCATTAACTTTA 57.749 29.630 0.00 0.00 0.00 1.85
7378 7990 9.471084 CGATTTCAAAAACCCATTAACTTTAGT 57.529 29.630 0.00 0.00 0.00 2.24
7388 8000 8.756486 ACCCATTAACTTTAGTACAAAGTTGT 57.244 30.769 27.85 20.09 46.41 3.32
7389 8001 9.850198 ACCCATTAACTTTAGTACAAAGTTGTA 57.150 29.630 27.85 21.04 46.41 2.41
7543 8601 1.595794 TCTTCTTTCGCCGTTGTCAAC 59.404 47.619 5.58 5.58 0.00 3.18
7544 8602 0.658897 TTCTTTCGCCGTTGTCAACC 59.341 50.000 10.12 0.00 0.00 3.77
7546 8604 0.041312 CTTTCGCCGTTGTCAACCAG 60.041 55.000 10.12 3.33 0.00 4.00
7547 8605 0.745128 TTTCGCCGTTGTCAACCAGT 60.745 50.000 10.12 0.00 0.00 4.00
7548 8606 0.104487 TTCGCCGTTGTCAACCAGTA 59.896 50.000 10.12 0.00 0.00 2.74
7550 8608 0.719465 CGCCGTTGTCAACCAGTATC 59.281 55.000 10.12 0.00 0.00 2.24
7551 8609 1.803334 GCCGTTGTCAACCAGTATCA 58.197 50.000 10.12 0.00 0.00 2.15
7552 8610 2.147958 GCCGTTGTCAACCAGTATCAA 58.852 47.619 10.12 0.00 0.00 2.57
7554 8612 3.190535 GCCGTTGTCAACCAGTATCAAAT 59.809 43.478 10.12 0.00 0.00 2.32
7555 8613 4.393680 GCCGTTGTCAACCAGTATCAAATA 59.606 41.667 10.12 0.00 0.00 1.40
7556 8614 5.106475 GCCGTTGTCAACCAGTATCAAATAA 60.106 40.000 10.12 0.00 0.00 1.40
7557 8615 6.404293 GCCGTTGTCAACCAGTATCAAATAAT 60.404 38.462 10.12 0.00 0.00 1.28
7558 8616 7.186804 CCGTTGTCAACCAGTATCAAATAATC 58.813 38.462 10.12 0.00 0.00 1.75
7559 8617 7.065803 CCGTTGTCAACCAGTATCAAATAATCT 59.934 37.037 10.12 0.00 0.00 2.40
7560 8618 7.904977 CGTTGTCAACCAGTATCAAATAATCTG 59.095 37.037 10.12 0.00 0.00 2.90
7561 8619 8.730680 GTTGTCAACCAGTATCAAATAATCTGT 58.269 33.333 4.21 0.00 0.00 3.41
7562 8620 8.492673 TGTCAACCAGTATCAAATAATCTGTC 57.507 34.615 0.00 0.00 0.00 3.51
7563 8621 8.100164 TGTCAACCAGTATCAAATAATCTGTCA 58.900 33.333 0.00 0.00 0.00 3.58
7564 8622 9.113838 GTCAACCAGTATCAAATAATCTGTCAT 57.886 33.333 0.00 0.00 0.00 3.06
7565 8623 9.112725 TCAACCAGTATCAAATAATCTGTCATG 57.887 33.333 0.00 0.00 0.00 3.07
7566 8624 8.347771 CAACCAGTATCAAATAATCTGTCATGG 58.652 37.037 0.00 0.00 0.00 3.66
7567 8625 7.805163 ACCAGTATCAAATAATCTGTCATGGA 58.195 34.615 0.00 0.00 0.00 3.41
7568 8626 7.935755 ACCAGTATCAAATAATCTGTCATGGAG 59.064 37.037 0.00 0.00 0.00 3.86
7569 8627 8.152898 CCAGTATCAAATAATCTGTCATGGAGA 58.847 37.037 0.00 0.00 0.00 3.71
7570 8628 9.722184 CAGTATCAAATAATCTGTCATGGAGAT 57.278 33.333 0.00 0.00 0.00 2.75
7614 8672 4.436998 CTGGACGTCACTCGGGGC 62.437 72.222 18.91 0.00 44.69 5.80
7704 8762 1.188219 TGGAGCTCGTCTTGCTTCCT 61.188 55.000 7.83 0.00 41.30 3.36
7705 8763 0.459411 GGAGCTCGTCTTGCTTCCTC 60.459 60.000 7.83 0.00 41.30 3.71
7713 8771 0.473694 TCTTGCTTCCTCCCCAGTCA 60.474 55.000 0.00 0.00 0.00 3.41
7725 8783 2.037367 CAGTCAGAGGACCCCGGA 59.963 66.667 0.73 0.00 45.48 5.14
7738 8796 2.679342 CCCGGAAAGGCTCCATGGA 61.679 63.158 15.27 15.27 45.74 3.41
7748 8806 1.368950 CTCCATGGATCGGCGTCAT 59.631 57.895 16.63 7.04 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 81 9.952030 TTTTTCTTTTTCTTTTTGTGGGTCTAT 57.048 25.926 0.00 0.00 0.00 1.98
106 110 5.126545 GTCTACCCCAATTACCATTGTTTCC 59.873 44.000 0.00 0.00 38.58 3.13
107 111 5.949952 AGTCTACCCCAATTACCATTGTTTC 59.050 40.000 0.00 0.00 38.58 2.78
109 113 5.530176 AGTCTACCCCAATTACCATTGTT 57.470 39.130 0.00 0.00 38.58 2.83
110 114 6.841781 ATAGTCTACCCCAATTACCATTGT 57.158 37.500 0.00 0.00 38.58 2.71
111 115 9.807921 ATTTATAGTCTACCCCAATTACCATTG 57.192 33.333 0.00 0.00 39.79 2.82
115 119 9.856162 TCAAATTTATAGTCTACCCCAATTACC 57.144 33.333 0.00 0.00 0.00 2.85
311 328 0.107945 GGAAGAGAAGCGCACCTGAT 60.108 55.000 11.47 0.00 0.00 2.90
322 339 1.346722 GGAACGAAGGTGGGAAGAGAA 59.653 52.381 0.00 0.00 0.00 2.87
397 425 1.819632 CGAATTGCTCCGGGGAAGG 60.820 63.158 4.80 0.00 0.00 3.46
403 431 2.802816 CCTAAATCTCGAATTGCTCCGG 59.197 50.000 0.00 0.00 0.00 5.14
426 454 1.742268 GTCAAGCCATCTTCTTGGAGC 59.258 52.381 3.33 0.00 40.82 4.70
474 502 5.520288 TCGCAATTTTCAAACCATCGAAAAA 59.480 32.000 0.00 0.00 42.58 1.94
475 503 5.043903 TCGCAATTTTCAAACCATCGAAAA 58.956 33.333 0.00 0.00 43.23 2.29
476 504 4.442733 GTCGCAATTTTCAAACCATCGAAA 59.557 37.500 0.00 0.00 0.00 3.46
477 505 3.978217 GTCGCAATTTTCAAACCATCGAA 59.022 39.130 0.00 0.00 0.00 3.71
511 539 9.460019 TGGACATGATGTAGAATAACAAATCAA 57.540 29.630 0.00 0.00 32.02 2.57
517 545 7.572814 TGGATTGGACATGATGTAGAATAACA 58.427 34.615 0.00 0.90 0.00 2.41
521 549 6.505048 TCTGGATTGGACATGATGTAGAAT 57.495 37.500 0.00 0.00 0.00 2.40
537 569 0.831307 GTAGGGTTCGGCTCTGGATT 59.169 55.000 0.00 0.00 0.00 3.01
578 610 0.984230 ACAGGATTCAGGCGGAAGAA 59.016 50.000 6.20 0.00 39.30 2.52
731 788 3.138884 TGGCATGAAGAACAGTAGCAA 57.861 42.857 0.00 0.00 0.00 3.91
951 1008 0.112412 TCAGGCCAAGAAAACTCCCC 59.888 55.000 5.01 0.00 0.00 4.81
985 1043 1.143305 GCCATGCTATCACTACGCAG 58.857 55.000 0.00 0.00 37.06 5.18
986 1044 0.752658 AGCCATGCTATCACTACGCA 59.247 50.000 0.00 0.00 36.99 5.24
1129 1187 7.042335 ACTCTTTTAATCCTTCTGTATCCACG 58.958 38.462 0.00 0.00 0.00 4.94
1223 1281 6.595772 AAGACTATGCTTCATCGAATTGAC 57.404 37.500 0.00 0.00 0.00 3.18
1230 1288 5.349817 ACACAAGAAAGACTATGCTTCATCG 59.650 40.000 0.00 0.00 0.00 3.84
1311 1369 7.254852 TCAGTTTTCAACGTTGCTTAAAGAAT 58.745 30.769 23.47 4.41 36.23 2.40
1357 1415 1.032114 GGGAAATCAAGGGCAGACCG 61.032 60.000 0.00 0.00 46.96 4.79
1368 1426 1.894466 CATGTGTGCCTTGGGAAATCA 59.106 47.619 0.00 0.00 0.00 2.57
1372 1430 0.409092 ATCCATGTGTGCCTTGGGAA 59.591 50.000 0.00 0.00 38.59 3.97
1375 1433 5.771666 AGAATAATATCCATGTGTGCCTTGG 59.228 40.000 0.00 0.00 39.25 3.61
1465 1525 7.013846 AGGAAAACAAAATTCAGTCGTCCATTA 59.986 33.333 11.49 0.00 0.00 1.90
1468 1528 4.642885 AGGAAAACAAAATTCAGTCGTCCA 59.357 37.500 11.49 0.00 0.00 4.02
1493 1553 4.725790 AAAAGATGATGTAGCCCAAAGC 57.274 40.909 0.00 0.00 44.25 3.51
1637 1698 5.957771 TTACCTTTGCATCCTCTACTGAT 57.042 39.130 0.00 0.00 0.00 2.90
1692 1753 6.204301 CACTGGCCTCAGATAAGATACAATTG 59.796 42.308 3.32 3.24 43.49 2.32
1723 1784 5.417894 TCATCTGTCGAACTGTACATTACCT 59.582 40.000 0.00 0.00 0.00 3.08
1731 1792 1.471287 CCCGTCATCTGTCGAACTGTA 59.529 52.381 0.00 0.00 0.00 2.74
1732 1793 0.243907 CCCGTCATCTGTCGAACTGT 59.756 55.000 0.00 0.00 0.00 3.55
1733 1794 0.243907 ACCCGTCATCTGTCGAACTG 59.756 55.000 0.00 0.00 0.00 3.16
1734 1795 0.243907 CACCCGTCATCTGTCGAACT 59.756 55.000 0.00 0.00 0.00 3.01
1735 1796 1.352156 GCACCCGTCATCTGTCGAAC 61.352 60.000 0.00 0.00 0.00 3.95
1736 1797 1.080093 GCACCCGTCATCTGTCGAA 60.080 57.895 0.00 0.00 0.00 3.71
1737 1798 1.532604 AAGCACCCGTCATCTGTCGA 61.533 55.000 0.00 0.00 0.00 4.20
1738 1799 0.172578 TAAGCACCCGTCATCTGTCG 59.827 55.000 0.00 0.00 0.00 4.35
1739 1800 1.204941 AGTAAGCACCCGTCATCTGTC 59.795 52.381 0.00 0.00 0.00 3.51
1740 1801 1.204941 GAGTAAGCACCCGTCATCTGT 59.795 52.381 0.00 0.00 0.00 3.41
1741 1802 1.478510 AGAGTAAGCACCCGTCATCTG 59.521 52.381 0.00 0.00 0.00 2.90
1742 1803 1.751924 GAGAGTAAGCACCCGTCATCT 59.248 52.381 0.00 0.00 0.00 2.90
1743 1804 1.751924 AGAGAGTAAGCACCCGTCATC 59.248 52.381 0.00 0.00 0.00 2.92
1744 1805 1.853963 AGAGAGTAAGCACCCGTCAT 58.146 50.000 0.00 0.00 0.00 3.06
1745 1806 2.502142 TAGAGAGTAAGCACCCGTCA 57.498 50.000 0.00 0.00 0.00 4.35
1746 1807 4.261530 GGTAATAGAGAGTAAGCACCCGTC 60.262 50.000 0.00 0.00 0.00 4.79
1747 1808 3.635836 GGTAATAGAGAGTAAGCACCCGT 59.364 47.826 0.00 0.00 0.00 5.28
1748 1809 3.890147 AGGTAATAGAGAGTAAGCACCCG 59.110 47.826 0.00 0.00 0.00 5.28
1749 1810 5.873146 AAGGTAATAGAGAGTAAGCACCC 57.127 43.478 0.00 0.00 0.00 4.61
1750 1811 6.875076 TGAAAGGTAATAGAGAGTAAGCACC 58.125 40.000 0.00 0.00 0.00 5.01
1751 1812 8.950208 AATGAAAGGTAATAGAGAGTAAGCAC 57.050 34.615 0.00 0.00 0.00 4.40
1752 1813 8.204836 GGAATGAAAGGTAATAGAGAGTAAGCA 58.795 37.037 0.00 0.00 0.00 3.91
1753 1814 8.425703 AGGAATGAAAGGTAATAGAGAGTAAGC 58.574 37.037 0.00 0.00 0.00 3.09
1769 1834 9.559958 GTTATGTACATTGTCAAGGAATGAAAG 57.440 33.333 14.77 0.00 40.50 2.62
1805 1870 3.451141 TCTTTGTCGCAAAAGGCAATT 57.549 38.095 9.03 0.00 45.17 2.32
1843 1908 7.321153 AGATGTACAGTATACAACCACAAGAC 58.679 38.462 5.50 1.50 0.00 3.01
1877 1942 2.625639 AGGAGAACCTCACTCATTGGT 58.374 47.619 0.00 0.00 44.13 3.67
1944 2011 6.670695 ATGACTAGTTGCCCATTTTCTTTT 57.329 33.333 0.00 0.00 0.00 2.27
2063 2133 7.259088 AGAACACTGATAAAGTACCCATCTT 57.741 36.000 0.00 0.00 36.83 2.40
2142 2212 9.423061 CCTGGTCAAAAATAAAGAAATTCGATT 57.577 29.630 0.00 0.00 0.00 3.34
2158 2229 5.755409 TGTCTCTATAAGCCTGGTCAAAA 57.245 39.130 0.00 0.00 0.00 2.44
2320 2393 8.047310 CCCTCCGTTCCAAAATATAAGCTATAT 58.953 37.037 0.00 0.00 32.90 0.86
2325 2398 4.457466 TCCCTCCGTTCCAAAATATAAGC 58.543 43.478 0.00 0.00 0.00 3.09
2329 2402 3.265995 ACACTCCCTCCGTTCCAAAATAT 59.734 43.478 0.00 0.00 0.00 1.28
2380 2453 6.024552 TCAGGACAAAGGAAAATGTATTGC 57.975 37.500 0.00 0.00 0.00 3.56
2403 2476 7.609146 TCTTCATTCAGTTGACTAAAGCATGAT 59.391 33.333 0.00 0.00 0.00 2.45
2430 2503 9.823647 TCATATCCTAATCACTTCTCAAAACTC 57.176 33.333 0.00 0.00 0.00 3.01
2619 2694 8.730680 GGTAGATGAGATTTTCTACTTTTTGCA 58.269 33.333 9.28 0.00 42.50 4.08
2629 2704 6.654161 GCTGCATATGGTAGATGAGATTTTCT 59.346 38.462 4.56 0.00 0.00 2.52
2696 2771 4.174009 AGAACTCAATCACATCGTTACCG 58.826 43.478 0.00 0.00 0.00 4.02
2710 2785 7.468631 GCATTTCTTCCTGTGTTTAGAACTCAA 60.469 37.037 0.00 0.00 34.84 3.02
2832 2908 3.667960 GCGTAGATCAACAGTGGCAAAAG 60.668 47.826 0.00 0.00 0.00 2.27
2841 2917 3.325870 TGAAGGTTGCGTAGATCAACAG 58.674 45.455 7.95 0.00 44.02 3.16
2883 2959 4.305989 TGCCTGTTCAAACAATCTCAAC 57.694 40.909 0.00 0.00 38.66 3.18
2998 3074 5.862924 AACATGGACAAAACTAGATGACG 57.137 39.130 0.00 0.00 0.00 4.35
3014 3090 9.436957 AGAGTTTGAGTAAATACACTAACATGG 57.563 33.333 13.94 0.00 35.98 3.66
3050 3129 7.148507 CCAATCAGCAACTGTTTTTGTTGTTTA 60.149 33.333 8.15 0.00 44.54 2.01
3116 3200 9.944376 GGCTGGAAATATCTTCAATGTACTATA 57.056 33.333 0.00 0.00 0.00 1.31
3200 3286 6.934645 CAGGAAAGGTGTCAAGTCACTAAATA 59.065 38.462 0.00 0.00 38.28 1.40
3206 3292 2.222027 CCAGGAAAGGTGTCAAGTCAC 58.778 52.381 0.00 0.00 37.57 3.67
3213 3299 1.177401 GAATGGCCAGGAAAGGTGTC 58.823 55.000 13.05 0.00 0.00 3.67
3234 3320 3.726557 ATTTGCCTCCTTGAGTGATCA 57.273 42.857 0.00 0.00 0.00 2.92
3294 3380 5.796424 AGAGGCTTGAACAACATCAATTT 57.204 34.783 0.00 0.00 38.55 1.82
3303 3389 4.431416 TGTCCTAAAGAGGCTTGAACAA 57.569 40.909 0.00 0.00 43.40 2.83
3359 3445 3.039011 GGGGAAGTAGCTTGACCATAGA 58.961 50.000 0.00 0.00 0.00 1.98
3398 3553 3.438781 TGTGTCTTGTCAGGTGTTCAAAC 59.561 43.478 0.00 0.00 0.00 2.93
3428 3583 7.766738 TCTTCAACAGTACACACTTGACAAATA 59.233 33.333 0.00 0.00 30.46 1.40
3654 3811 8.040727 TCTATTCTAACTAAAGTGATGCAAGCA 58.959 33.333 0.00 0.00 0.00 3.91
3686 3843 1.622811 GTGCAAATCCAATTCCACCCA 59.377 47.619 0.00 0.00 0.00 4.51
3703 3860 6.973229 AAATAAAGGAAATTGAGCATGTGC 57.027 33.333 0.00 0.00 42.49 4.57
3711 3868 9.243105 CAGGGACTAGAAAATAAAGGAAATTGA 57.757 33.333 0.00 0.00 36.02 2.57
3873 4030 2.380064 TTTGAACCCAGTTCCTGCAT 57.620 45.000 5.09 0.00 41.35 3.96
4011 4168 4.292306 ACAGGATTGGAGGGAGTAACATTT 59.708 41.667 0.00 0.00 0.00 2.32
4279 4444 9.444600 AGTCAAAACTCTAGTTACAAAACAGAA 57.555 29.630 0.00 0.00 37.25 3.02
4451 4623 8.038944 GGTTGTTGAGGAACACTATATTACTCA 58.961 37.037 0.00 0.00 43.81 3.41
4457 4629 6.374417 ACAGGTTGTTGAGGAACACTATAT 57.626 37.500 0.00 0.00 41.92 0.86
4458 4630 5.818678 ACAGGTTGTTGAGGAACACTATA 57.181 39.130 0.00 0.00 41.92 1.31
4502 4676 6.021596 CCACGCATTCTACAAATTACAGTTC 58.978 40.000 0.00 0.00 0.00 3.01
4567 4741 1.772966 GTTGCACGATCAACAACAACG 59.227 47.619 14.35 0.00 44.18 4.10
4601 4775 6.067217 ACACTGAGCTAAGTAAATTGGGAT 57.933 37.500 2.48 0.00 0.00 3.85
4604 4778 7.202016 TCAAACACTGAGCTAAGTAAATTGG 57.798 36.000 2.48 0.00 0.00 3.16
4610 4784 5.758296 CCAAGTTCAAACACTGAGCTAAGTA 59.242 40.000 2.48 0.00 44.17 2.24
4648 4822 6.109359 AGTATTAGAGATGGAGCACACAAAC 58.891 40.000 0.00 0.00 0.00 2.93
4698 4872 5.599242 CCCCAAAACAAACCTTCCTACTTTA 59.401 40.000 0.00 0.00 0.00 1.85
4711 4912 4.518249 GACCAATTCAACCCCAAAACAAA 58.482 39.130 0.00 0.00 0.00 2.83
4728 4929 7.094631 CGATTAGATATTACAATCCGGACCAA 58.905 38.462 6.12 0.00 0.00 3.67
4753 4954 6.002082 GGGTAAATTGGTAGGATCATGGTAC 58.998 44.000 0.00 0.00 0.00 3.34
4776 4977 3.503748 CCACTTTTCAAGCACTAGAAGGG 59.496 47.826 0.00 0.00 0.00 3.95
4791 4992 3.092334 GCAAAACGATCCACCACTTTT 57.908 42.857 0.00 0.00 0.00 2.27
4804 5005 0.099791 ACCAGTTCAACCGCAAAACG 59.900 50.000 0.00 0.00 43.15 3.60
4905 5106 3.175594 AGTTGCATTTTGGGGATCATGT 58.824 40.909 0.00 0.00 0.00 3.21
5015 5216 5.695851 AATGTTCAGATTGGACACTTGAC 57.304 39.130 0.00 0.00 0.00 3.18
5019 5220 8.912988 TCTTTAAAAATGTTCAGATTGGACACT 58.087 29.630 0.00 0.00 0.00 3.55
5041 5242 8.798859 AAAACTCTGACTGCATATGTATCTTT 57.201 30.769 4.29 0.00 0.00 2.52
5077 5278 2.227865 GGTCGCTTTGGACATAGCAAAA 59.772 45.455 13.66 0.00 38.70 2.44
5093 5294 5.054390 TCAAGTTCCATAAAATTGGTCGC 57.946 39.130 0.00 0.00 41.95 5.19
5183 5385 6.966021 TCCAACTTCTTAAGTAACACATTGC 58.034 36.000 1.63 0.00 41.91 3.56
5184 5386 8.076178 CCTTCCAACTTCTTAAGTAACACATTG 58.924 37.037 1.63 0.11 41.91 2.82
5185 5387 7.778382 ACCTTCCAACTTCTTAAGTAACACATT 59.222 33.333 1.63 0.00 41.91 2.71
5255 5457 9.638239 TTTTCAATCAGTATAGAAACATTTGCC 57.362 29.630 0.00 0.00 30.47 4.52
5340 5542 6.389906 CCTCCATTTTCCAGTACATTGAAAC 58.610 40.000 0.00 0.00 0.00 2.78
5391 5596 7.586714 AAGCAAAATTTAGCATTTAGTCTGC 57.413 32.000 0.00 0.00 39.97 4.26
5467 5672 8.163408 CCCTTTATAGAATCATGGTTGTATCCA 58.837 37.037 11.39 0.00 42.01 3.41
5474 5679 5.373854 AGAGGCCCTTTATAGAATCATGGTT 59.626 40.000 0.00 0.00 0.00 3.67
5483 5688 4.100498 CGTACCAAAGAGGCCCTTTATAGA 59.900 45.833 16.03 3.51 42.88 1.98
5495 5700 7.376072 GTGTTTCAATTTCTTCGTACCAAAGAG 59.624 37.037 5.72 0.00 34.42 2.85
5503 5708 5.468746 CCCTGAGTGTTTCAATTTCTTCGTA 59.531 40.000 0.00 0.00 34.81 3.43
5514 5719 3.855255 TTCACATCCCTGAGTGTTTCA 57.145 42.857 0.00 0.00 37.07 2.69
5563 5857 4.227073 TGGTTGTGTCTCATATGGGATCAA 59.773 41.667 8.92 13.97 0.00 2.57
5623 5918 6.015180 ACCTAATCTCAAAATGTGTGCATGTT 60.015 34.615 0.00 0.00 35.15 2.71
5661 5957 9.520204 CTTGTTCTTGATCTCTTTATCTCTCTC 57.480 37.037 0.00 0.00 0.00 3.20
5729 6025 6.296145 GCTATGTAGGAGGGAAAGCAATATCT 60.296 42.308 0.00 0.00 0.00 1.98
5979 6275 6.311735 TCAAGTAACCTCCTAGCCAATTTTT 58.688 36.000 0.00 0.00 0.00 1.94
6450 6746 1.921346 ATACGGCCCAGGTGGTTCA 60.921 57.895 0.00 0.00 36.04 3.18
6582 6878 2.813179 GCCTATGCCGCTTCACACG 61.813 63.158 0.00 0.00 0.00 4.49
6583 6879 1.026718 AAGCCTATGCCGCTTCACAC 61.027 55.000 0.00 0.00 42.94 3.82
6665 6961 6.037720 TGAAACGTGAGAAAGATTTGTTAGCA 59.962 34.615 0.00 0.00 0.00 3.49
6912 7208 5.473846 TCATGAACAAAAAGGGTTACGCATA 59.526 36.000 1.60 0.00 0.00 3.14
6913 7209 4.279671 TCATGAACAAAAAGGGTTACGCAT 59.720 37.500 1.60 0.00 0.00 4.73
6938 7234 5.622007 CGGTGGCACATGAATACAGAAAAAT 60.622 40.000 20.82 0.00 44.52 1.82
6970 7267 5.130975 TCAGAGTCTGCCACACCATATAATT 59.869 40.000 15.72 0.00 0.00 1.40
7002 7299 2.351253 CGTCTGCGAGCTAGCATAATCT 60.351 50.000 22.22 0.00 46.97 2.40
7016 7319 2.094659 CACAGCTAACCCGTCTGCG 61.095 63.158 0.00 0.00 37.95 5.18
7042 7380 2.223317 ACCCAACGCTGAAAAACGTAAC 60.223 45.455 0.00 0.00 42.68 2.50
7063 7401 3.181423 ACCCAAGGAGCAAACCAAATAGA 60.181 43.478 0.00 0.00 0.00 1.98
7114 7456 6.331042 AGAGGAAATCCATGGATAGAACATGA 59.669 38.462 27.54 0.00 46.60 3.07
7121 7463 7.449395 TGCATTTTAGAGGAAATCCATGGATAG 59.551 37.037 27.54 0.00 38.89 2.08
7127 7469 6.381994 ACATGTGCATTTTAGAGGAAATCCAT 59.618 34.615 0.00 0.00 38.89 3.41
7128 7470 5.716228 ACATGTGCATTTTAGAGGAAATCCA 59.284 36.000 0.00 0.00 38.89 3.41
7154 7497 1.400846 GTGATTGCCAGATGCTGACAG 59.599 52.381 0.00 0.00 42.00 3.51
7157 7500 1.279846 TCAGTGATTGCCAGATGCTGA 59.720 47.619 0.00 0.00 42.00 4.26
7179 7522 2.573340 GGAATGGTGCGCCTTTGG 59.427 61.111 21.05 0.00 32.96 3.28
7192 7563 5.375773 CAACATTCAAAAACCCAAGGGAAT 58.624 37.500 13.15 0.00 38.96 3.01
7202 7573 7.538303 AATCACTTGACCAACATTCAAAAAC 57.462 32.000 0.00 0.00 32.61 2.43
7205 7576 7.069331 AGGTTAATCACTTGACCAACATTCAAA 59.931 33.333 2.66 0.00 42.15 2.69
7249 7627 3.049912 GCAACCGCAAACTAAGAAAAGG 58.950 45.455 0.00 0.00 38.36 3.11
7299 7677 5.765072 GTTTGGCTAAAACACGTTTCAAA 57.235 34.783 0.00 0.29 46.30 2.69
7309 7687 6.641723 TGCTTATTTTACCGTTTGGCTAAAAC 59.358 34.615 0.00 1.19 44.04 2.43
7338 7950 3.059884 TGAAATCGTGCTTGTCTGACTC 58.940 45.455 9.51 0.00 0.00 3.36
7363 7975 8.756486 ACAACTTTGTACTAAAGTTAATGGGT 57.244 30.769 23.56 17.73 45.57 4.51
7415 8027 9.511144 CCGTCTCAAAATAAGTGTTTTAACTTT 57.489 29.630 0.00 0.00 40.77 2.66
7416 8028 8.895737 TCCGTCTCAAAATAAGTGTTTTAACTT 58.104 29.630 0.00 0.00 42.89 2.66
7417 8029 8.441312 TCCGTCTCAAAATAAGTGTTTTAACT 57.559 30.769 0.00 0.00 30.56 2.24
7418 8030 7.801783 CCTCCGTCTCAAAATAAGTGTTTTAAC 59.198 37.037 0.00 0.00 30.56 2.01
7420 8032 6.428771 CCCTCCGTCTCAAAATAAGTGTTTTA 59.571 38.462 0.00 0.00 30.56 1.52
7421 8033 5.240844 CCCTCCGTCTCAAAATAAGTGTTTT 59.759 40.000 0.00 0.00 0.00 2.43
7422 8034 4.760204 CCCTCCGTCTCAAAATAAGTGTTT 59.240 41.667 0.00 0.00 0.00 2.83
7423 8035 4.041198 TCCCTCCGTCTCAAAATAAGTGTT 59.959 41.667 0.00 0.00 0.00 3.32
7424 8036 3.581332 TCCCTCCGTCTCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
7426 8038 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
7427 8039 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
7428 8040 5.021458 ACTACTCCCTCCGTCTCAAAATAA 58.979 41.667 0.00 0.00 0.00 1.40
7429 8041 4.607239 ACTACTCCCTCCGTCTCAAAATA 58.393 43.478 0.00 0.00 0.00 1.40
7430 8042 3.442076 ACTACTCCCTCCGTCTCAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
7432 8044 2.599408 ACTACTCCCTCCGTCTCAAA 57.401 50.000 0.00 0.00 0.00 2.69
7434 8046 3.009916 AGTTTACTACTCCCTCCGTCTCA 59.990 47.826 0.00 0.00 28.23 3.27
7435 8047 3.619419 AGTTTACTACTCCCTCCGTCTC 58.381 50.000 0.00 0.00 28.23 3.36
7437 8049 4.891627 GTAGTTTACTACTCCCTCCGTC 57.108 50.000 11.80 0.00 44.06 4.79
7461 8519 1.282738 ACTGGGTCATGCACATCATCA 59.717 47.619 0.00 0.00 31.79 3.07
7543 8601 8.152898 TCTCCATGACAGATTATTTGATACTGG 58.847 37.037 0.00 0.00 33.57 4.00
7544 8602 9.722184 ATCTCCATGACAGATTATTTGATACTG 57.278 33.333 0.00 0.00 35.14 2.74
7547 8605 9.511272 CCAATCTCCATGACAGATTATTTGATA 57.489 33.333 15.63 0.00 38.33 2.15
7548 8606 8.222637 TCCAATCTCCATGACAGATTATTTGAT 58.777 33.333 15.63 0.00 38.33 2.57
7550 8608 7.718314 TCTCCAATCTCCATGACAGATTATTTG 59.282 37.037 15.63 8.30 38.33 2.32
7551 8609 7.809238 TCTCCAATCTCCATGACAGATTATTT 58.191 34.615 15.63 0.00 38.33 1.40
7552 8610 7.384524 TCTCCAATCTCCATGACAGATTATT 57.615 36.000 15.63 0.00 38.33 1.40
7554 8612 6.408548 GGTTCTCCAATCTCCATGACAGATTA 60.409 42.308 15.63 5.22 38.33 1.75
7555 8613 5.435291 GTTCTCCAATCTCCATGACAGATT 58.565 41.667 11.98 11.98 40.58 2.40
7556 8614 4.141528 GGTTCTCCAATCTCCATGACAGAT 60.142 45.833 0.00 0.00 31.51 2.90
7557 8615 3.198635 GGTTCTCCAATCTCCATGACAGA 59.801 47.826 0.00 0.00 0.00 3.41
7558 8616 3.539604 GGTTCTCCAATCTCCATGACAG 58.460 50.000 0.00 0.00 0.00 3.51
7559 8617 2.239654 GGGTTCTCCAATCTCCATGACA 59.760 50.000 0.00 0.00 35.00 3.58
7560 8618 2.743183 CGGGTTCTCCAATCTCCATGAC 60.743 54.545 0.00 0.00 34.36 3.06
7561 8619 1.486310 CGGGTTCTCCAATCTCCATGA 59.514 52.381 0.00 0.00 34.36 3.07
7562 8620 1.475751 CCGGGTTCTCCAATCTCCATG 60.476 57.143 0.00 0.00 34.36 3.66
7563 8621 0.839946 CCGGGTTCTCCAATCTCCAT 59.160 55.000 0.00 0.00 34.36 3.41
7564 8622 1.910580 GCCGGGTTCTCCAATCTCCA 61.911 60.000 2.18 0.00 34.36 3.86
7565 8623 1.153147 GCCGGGTTCTCCAATCTCC 60.153 63.158 2.18 0.00 34.36 3.71
7566 8624 1.521681 CGCCGGGTTCTCCAATCTC 60.522 63.158 2.18 0.00 34.36 2.75
7567 8625 1.838073 AACGCCGGGTTCTCCAATCT 61.838 55.000 2.18 0.00 31.79 2.40
7568 8626 1.376812 AACGCCGGGTTCTCCAATC 60.377 57.895 2.18 0.00 31.79 2.67
7569 8627 2.754375 AACGCCGGGTTCTCCAAT 59.246 55.556 2.18 0.00 31.79 3.16
7704 8762 2.450243 GGGTCCTCTGACTGGGGA 59.550 66.667 0.00 0.00 41.47 4.81
7705 8763 2.689034 GGGGTCCTCTGACTGGGG 60.689 72.222 0.00 0.00 41.47 4.96
7713 8771 3.009714 GCCTTTCCGGGGTCCTCT 61.010 66.667 0.00 0.00 0.00 3.69
7725 8783 1.152881 GCCGATCCATGGAGCCTTT 60.153 57.895 23.90 4.22 0.00 3.11


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

AutoCloner maintained by Alex Coulton.