Multiple sequence alignment - TraesCS5A01G078700

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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 TraesCS5A01G078700 chr5A 100.000 2486 0 0 1 2486 97335649 97338134 0.000000e+00 4591.0
1 TraesCS5A01G078700 chr5A 91.568 1352 92 6 1 1332 97361111 97362460 0.000000e+00 1845.0
2 TraesCS5A01G078700 chr5A 89.440 1108 91 6 1363 2451 97362459 97363559 0.000000e+00 1375.0
3 TraesCS5A01G078700 chr5A 80.000 470 70 19 1938 2391 137165138 137165599 2.380000e-85 326.0
4 TraesCS5A01G078700 chr1D 86.745 1275 116 31 1 1245 144769516 144770767 0.000000e+00 1369.0
5 TraesCS5A01G078700 chr1D 86.761 1269 111 34 1 1237 144777238 144778481 0.000000e+00 1360.0
6 TraesCS5A01G078700 chr1D 89.069 924 69 25 1 904 215866567 215867478 0.000000e+00 1118.0
7 TraesCS5A01G078700 chr1D 86.279 481 44 6 1325 1790 275330407 275329934 1.030000e-138 503.0
8 TraesCS5A01G078700 chr1D 92.593 54 3 1 1854 1907 134363066 134363118 2.650000e-10 76.8
9 TraesCS5A01G078700 chr7D 85.658 1276 128 35 1 1245 470545122 470543871 0.000000e+00 1291.0
10 TraesCS5A01G078700 chr3D 89.921 883 74 15 1 875 131464063 131463188 0.000000e+00 1123.0
11 TraesCS5A01G078700 chr3D 85.979 1027 105 35 1 1000 307463974 307462960 0.000000e+00 1062.0
12 TraesCS5A01G078700 chr3D 81.048 496 72 19 1999 2484 251175055 251175538 2.330000e-100 375.0
13 TraesCS5A01G078700 chr3D 80.374 428 68 12 2067 2484 211800063 211800484 6.680000e-81 311.0
14 TraesCS5A01G078700 chr3D 91.753 97 8 0 1326 1422 436615541 436615637 4.310000e-28 135.0
15 TraesCS5A01G078700 chr2D 88.335 943 79 23 1 924 392928438 392927508 0.000000e+00 1103.0
16 TraesCS5A01G078700 chr2D 88.191 940 81 24 1 923 249716438 249715512 0.000000e+00 1094.0
17 TraesCS5A01G078700 chr2D 87.991 941 93 20 1 931 323469239 323468309 0.000000e+00 1094.0
18 TraesCS5A01G078700 chr2D 88.123 943 82 22 1 924 392936705 392935774 0.000000e+00 1094.0
19 TraesCS5A01G078700 chr2D 86.820 478 41 4 1325 1787 443805476 443805946 4.740000e-142 514.0
20 TraesCS5A01G078700 chr2D 85.804 479 45 5 1325 1787 532719012 532719483 1.030000e-133 486.0
21 TraesCS5A01G078700 chr2D 85.146 478 49 6 1325 1787 413561786 413562256 1.040000e-128 470.0
22 TraesCS5A01G078700 chr2D 89.197 361 32 3 1427 1787 310809303 310809656 6.310000e-121 444.0
23 TraesCS5A01G078700 chr6D 85.252 1051 110 34 1 1028 255740792 255741820 0.000000e+00 1040.0
24 TraesCS5A01G078700 chr6D 84.281 598 70 22 1866 2448 238948022 238948610 1.670000e-156 562.0
25 TraesCS5A01G078700 chr6D 85.714 462 44 4 1341 1787 36302996 36303450 3.740000e-128 468.0
26 TraesCS5A01G078700 chr6D 85.067 375 46 10 1852 2222 240114302 240113934 8.400000e-100 374.0
27 TraesCS5A01G078700 chr6D 85.286 367 37 13 1851 2212 240129039 240128685 1.820000e-96 363.0
28 TraesCS5A01G078700 chr6D 92.593 54 3 1 1854 1907 310841250 310841302 2.650000e-10 76.8
29 TraesCS5A01G078700 chr6D 92.593 54 3 1 1854 1907 310848816 310848868 2.650000e-10 76.8
30 TraesCS5A01G078700 chr4B 81.724 1067 130 40 7 1052 315366358 315365336 0.000000e+00 830.0
31 TraesCS5A01G078700 chr4B 73.581 458 86 28 1778 2214 96066839 96067282 2.580000e-30 143.0
32 TraesCS5A01G078700 chr4B 94.231 52 2 1 1854 1905 281142212 281142262 7.370000e-11 78.7
33 TraesCS5A01G078700 chr4D 82.886 596 80 21 1866 2448 268429080 268428494 1.320000e-142 516.0
34 TraesCS5A01G078700 chr4D 85.565 478 47 4 1325 1787 246446518 246446988 4.810000e-132 481.0
35 TraesCS5A01G078700 chr4D 92.553 94 7 0 1329 1422 473614114 473614021 4.310000e-28 135.0
36 TraesCS5A01G078700 chr6B 86.071 481 44 8 1325 1790 122892333 122891861 1.720000e-136 496.0
37 TraesCS5A01G078700 chr6B 93.056 72 4 1 1791 1862 109390420 109390350 1.220000e-18 104.0
38 TraesCS5A01G078700 chr6B 87.059 85 10 1 1778 1862 599174371 599174288 7.320000e-16 95.3
39 TraesCS5A01G078700 chr5D 85.239 481 49 4 1325 1790 249234889 249234416 2.240000e-130 475.0
40 TraesCS5A01G078700 chr5D 85.591 465 45 4 1341 1790 86339126 86338669 3.740000e-128 468.0
41 TraesCS5A01G078700 chr5D 84.731 465 49 4 1341 1790 86346897 86346440 1.750000e-121 446.0
42 TraesCS5A01G078700 chr2B 82.316 475 45 16 1325 1787 480207652 480207205 2.330000e-100 375.0
43 TraesCS5A01G078700 chr2B 82.119 453 65 13 2039 2484 625818671 625819114 8.400000e-100 374.0
44 TraesCS5A01G078700 chr2B 81.319 455 66 14 2039 2484 625811191 625811635 3.930000e-93 351.0
45 TraesCS5A01G078700 chr2B 78.882 322 44 19 1876 2179 134449021 134449336 1.950000e-46 196.0
46 TraesCS5A01G078700 chr2B 81.959 194 29 6 2296 2484 368155185 368154993 2.560000e-35 159.0
47 TraesCS5A01G078700 chr7B 81.847 314 43 12 1875 2182 191430426 191430121 4.100000e-63 252.0
48 TraesCS5A01G078700 chr3B 80.573 314 44 16 1875 2179 405340818 405340513 2.490000e-55 226.0
49 TraesCS5A01G078700 chr3B 80.317 315 38 18 1875 2182 292376028 292375731 1.500000e-52 217.0
50 TraesCS5A01G078700 chr3B 91.765 85 6 1 1778 1862 556449384 556449301 1.560000e-22 117.0
51 TraesCS5A01G078700 chr3B 90.588 85 7 1 1778 1862 433866230 433866313 7.270000e-21 111.0
52 TraesCS5A01G078700 chr3B 89.412 85 8 1 1778 1862 433858682 433858765 3.380000e-19 106.0
53 TraesCS5A01G078700 chr3B 89.412 85 8 1 1778 1862 556441496 556441413 3.380000e-19 106.0
54 TraesCS5A01G078700 chr3B 88.235 85 9 1 1778 1862 364612885 364612968 1.570000e-17 100.0
55 TraesCS5A01G078700 chr5B 73.581 458 75 35 1783 2214 96708548 96708111 1.550000e-27 134.0
56 TraesCS5A01G078700 chr5B 72.429 457 93 27 1778 2214 96715689 96715246 5.620000e-22 115.0
57 TraesCS5A01G078700 chr2A 74.238 361 64 22 1864 2213 643505720 643506062 9.340000e-25 124.0
58 TraesCS5A01G078700 chr2A 86.170 94 6 5 1862 1953 643590493 643590581 7.320000e-16 95.3


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 TraesCS5A01G078700 chr5A 97335649 97338134 2485 False 4591 4591 100.000 1 2486 1 chr5A.!!$F1 2485
1 TraesCS5A01G078700 chr5A 97361111 97363559 2448 False 1610 1845 90.504 1 2451 2 chr5A.!!$F3 2450
2 TraesCS5A01G078700 chr1D 144769516 144770767 1251 False 1369 1369 86.745 1 1245 1 chr1D.!!$F2 1244
3 TraesCS5A01G078700 chr1D 144777238 144778481 1243 False 1360 1360 86.761 1 1237 1 chr1D.!!$F3 1236
4 TraesCS5A01G078700 chr1D 215866567 215867478 911 False 1118 1118 89.069 1 904 1 chr1D.!!$F4 903
5 TraesCS5A01G078700 chr7D 470543871 470545122 1251 True 1291 1291 85.658 1 1245 1 chr7D.!!$R1 1244
6 TraesCS5A01G078700 chr3D 131463188 131464063 875 True 1123 1123 89.921 1 875 1 chr3D.!!$R1 874
7 TraesCS5A01G078700 chr3D 307462960 307463974 1014 True 1062 1062 85.979 1 1000 1 chr3D.!!$R2 999
8 TraesCS5A01G078700 chr2D 392927508 392928438 930 True 1103 1103 88.335 1 924 1 chr2D.!!$R3 923
9 TraesCS5A01G078700 chr2D 249715512 249716438 926 True 1094 1094 88.191 1 923 1 chr2D.!!$R1 922
10 TraesCS5A01G078700 chr2D 323468309 323469239 930 True 1094 1094 87.991 1 931 1 chr2D.!!$R2 930
11 TraesCS5A01G078700 chr2D 392935774 392936705 931 True 1094 1094 88.123 1 924 1 chr2D.!!$R4 923
12 TraesCS5A01G078700 chr6D 255740792 255741820 1028 False 1040 1040 85.252 1 1028 1 chr6D.!!$F3 1027
13 TraesCS5A01G078700 chr6D 238948022 238948610 588 False 562 562 84.281 1866 2448 1 chr6D.!!$F2 582
14 TraesCS5A01G078700 chr4B 315365336 315366358 1022 True 830 830 81.724 7 1052 1 chr4B.!!$R1 1045
15 TraesCS5A01G078700 chr4D 268428494 268429080 586 True 516 516 82.886 1866 2448 1 chr4D.!!$R1 582

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
931 966 0.610232 GGCTGAATCTGGCAGGTTGT 60.61 55.0 19.5 0.0 34.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 1933 0.266152 ATTCCCCACCAAACCAACCA 59.734 50.0 0.0 0.0 0.0 3.67 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
95 99 2.972713 GAGGGTATGGTCATCTTGCCTA 59.027 50.000 0.00 0.00 0.00 3.93
172 176 1.736032 CGAATCCTCACAACTCCGGAC 60.736 57.143 0.00 0.00 0.00 4.79
211 215 2.040412 AGAGAAGCAACCCGGAAAGAAT 59.960 45.455 0.73 0.00 0.00 2.40
247 251 8.177119 AGTAAACAACCATCACATAAACATGT 57.823 30.769 0.00 0.00 34.64 3.21
326 331 7.608755 CAAAGTGCAACAAACAATACTACAAC 58.391 34.615 0.00 0.00 41.43 3.32
387 395 9.400638 GACGAAACACCACATTCAATTATTTAA 57.599 29.630 0.00 0.00 0.00 1.52
489 501 1.519408 GCAAGTTTAAGTGAGGCCGA 58.481 50.000 0.00 0.00 0.00 5.54
627 643 6.530019 AAACTATGCATTTTTCTACCCCAG 57.470 37.500 3.54 0.00 0.00 4.45
666 682 6.839820 ATTAAATTCGGAGCTACGGTTAAG 57.160 37.500 20.39 0.00 0.00 1.85
718 734 7.583230 TGGCATTTAAGCAAATTAAAGCAAAG 58.417 30.769 12.31 0.00 44.47 2.77
858 885 5.270979 AGCTAGGGGGTTTTCTGTAAAAT 57.729 39.130 0.00 0.00 36.96 1.82
931 966 0.610232 GGCTGAATCTGGCAGGTTGT 60.610 55.000 19.50 0.00 34.00 3.32
1008 1047 4.545706 GCCCGGTCGATGGATGCA 62.546 66.667 0.00 0.00 0.00 3.96
1105 1149 3.822192 CGGTCGTCCAGGCGATCA 61.822 66.667 14.45 0.00 41.63 2.92
1132 1176 2.029964 GCGGGTCGTCCTTGTTCA 59.970 61.111 0.00 0.00 0.00 3.18
1134 1178 0.953960 GCGGGTCGTCCTTGTTCATT 60.954 55.000 0.00 0.00 0.00 2.57
1142 1186 3.323691 TCGTCCTTGTTCATTCCTGAGAA 59.676 43.478 0.00 0.00 36.15 2.87
1151 1195 4.710423 TCATTCCTGAGAAAGAGAGACG 57.290 45.455 0.00 0.00 35.09 4.18
1179 1234 3.012274 TGAGAGAGAGGAAACCAGAGGAT 59.988 47.826 0.00 0.00 0.00 3.24
1199 1254 2.756283 AGAGAAGGGGTCGGCGAG 60.756 66.667 11.20 0.00 0.00 5.03
1202 1257 3.145551 GAAGGGGTCGGCGAGCTA 61.146 66.667 34.02 0.00 0.00 3.32
1303 1358 2.045926 AGGTGGTTCCAGCGATGC 60.046 61.111 14.09 0.00 39.18 3.91
1308 1363 1.675641 GGTTCCAGCGATGCCTTGT 60.676 57.895 0.00 0.00 0.00 3.16
1379 1434 1.003442 TAGAGGAGGCAGGCATGGT 59.997 57.895 0.00 0.00 0.00 3.55
1381 1436 2.937689 AGGAGGCAGGCATGGTGT 60.938 61.111 0.00 0.00 0.00 4.16
1383 1438 2.821366 GAGGCAGGCATGGTGTCG 60.821 66.667 0.00 0.00 0.00 4.35
1401 1456 2.684843 GCGCTCTGTTGAAGCAGGG 61.685 63.158 0.00 0.00 39.86 4.45
1441 1511 1.144057 CTCGGGTGCCATGGTCTAC 59.856 63.158 14.67 10.24 0.00 2.59
1466 1536 1.198637 GCTCCTGCATGAAGAACACAC 59.801 52.381 0.74 0.00 39.41 3.82
1478 1548 1.344763 AGAACACACGGAAAGGGAGAG 59.655 52.381 0.00 0.00 0.00 3.20
1489 1559 4.624125 CGGAAAGGGAGAGAGTTTAGCAAT 60.624 45.833 0.00 0.00 0.00 3.56
1496 1566 4.442753 GGAGAGAGTTTAGCAATGGGAGAG 60.443 50.000 0.00 0.00 0.00 3.20
1507 1578 0.473501 ATGGGAGAGAGAGGGATGGC 60.474 60.000 0.00 0.00 0.00 4.40
1555 1626 3.991051 CCTGCTCGTGGTCGTGGT 61.991 66.667 0.00 0.00 38.33 4.16
1557 1628 3.916392 CTGCTCGTGGTCGTGGTCC 62.916 68.421 0.00 0.00 38.33 4.46
1559 1630 2.989824 CTCGTGGTCGTGGTCCCT 60.990 66.667 0.00 0.00 38.33 4.20
1585 1656 1.599240 GCATTGGATCGGGAGGAGC 60.599 63.158 0.00 0.00 0.00 4.70
1588 1659 3.976490 TTGGATCGGGAGGAGCGGT 62.976 63.158 0.00 0.00 0.00 5.68
1624 1695 3.231736 GGATTCGCGGGGCCTCTA 61.232 66.667 6.13 0.00 0.00 2.43
1625 1696 2.584391 GGATTCGCGGGGCCTCTAT 61.584 63.158 6.13 0.00 0.00 1.98
1630 1701 2.124320 GCGGGGCCTCTATTTGCA 60.124 61.111 0.00 0.00 0.00 4.08
1640 1711 1.211457 CTCTATTTGCAGGAGGCTGGT 59.789 52.381 0.00 0.00 45.15 4.00
1644 1715 1.778017 TTTGCAGGAGGCTGGTAGCA 61.778 55.000 0.00 0.00 44.75 3.49
1652 1723 2.109126 GGCTGGTAGCAAGGCTTCG 61.109 63.158 0.00 0.00 44.75 3.79
1653 1724 2.109126 GCTGGTAGCAAGGCTTCGG 61.109 63.158 0.00 0.00 41.89 4.30
1656 1727 2.046314 GTAGCAAGGCTTCGGGCA 60.046 61.111 10.23 0.00 44.01 5.36
1665 1736 3.081133 CTTCGGGCATGAACGACG 58.919 61.111 11.03 6.62 39.04 5.12
1710 1781 2.902846 CGAGAGACGGCCGGATCT 60.903 66.667 31.76 29.66 38.46 2.75
1711 1782 1.597302 CGAGAGACGGCCGGATCTA 60.597 63.158 31.76 0.00 38.46 1.98
1712 1783 1.843734 CGAGAGACGGCCGGATCTAC 61.844 65.000 31.76 20.95 38.46 2.59
1722 1793 3.992317 GGATCTACGGGCGCCTCC 61.992 72.222 28.56 20.43 0.00 4.30
1743 1814 1.842381 GAGTTGGTGAGGGAGGTGGG 61.842 65.000 0.00 0.00 0.00 4.61
1760 1831 2.770130 GGGGATTGGGTTGGCTGA 59.230 61.111 0.00 0.00 0.00 4.26
1762 1833 2.046285 GGGATTGGGTTGGCTGACG 61.046 63.158 0.00 0.00 0.00 4.35
1764 1835 1.971167 GATTGGGTTGGCTGACGCA 60.971 57.895 7.11 7.11 40.21 5.24
1772 1843 2.200899 GTTGGCTGACGCAAAAATTGT 58.799 42.857 0.00 0.00 38.10 2.71
1823 1894 2.125350 CTTGCTCCAGTCGAGGCC 60.125 66.667 0.00 0.00 39.22 5.19
1833 1904 0.684805 AGTCGAGGCCGAGGAGAAAT 60.685 55.000 0.00 0.00 46.52 2.17
1844 1915 0.915364 AGGAGAAATGAGGAGGTGGC 59.085 55.000 0.00 0.00 0.00 5.01
1848 1919 1.372087 GAAATGAGGAGGTGGCTGCG 61.372 60.000 0.00 0.00 0.00 5.18
1862 1933 0.825010 GCTGCGGGATTGGATGGATT 60.825 55.000 0.00 0.00 0.00 3.01
1931 2005 3.083997 GCTGGTGATCCCGAGGGT 61.084 66.667 8.20 0.00 35.15 4.34
1988 2063 5.893824 CCTAGAAAATAGGGTTTGGCTTGAT 59.106 40.000 0.00 0.00 0.00 2.57
2053 2128 3.343941 TTCGACCCTCCGATCAAAATT 57.656 42.857 0.00 0.00 38.45 1.82
2096 2172 4.236147 GTTAGGAGAGTCCAACGAGAAAC 58.764 47.826 0.00 0.00 39.61 2.78
2153 2229 1.014044 CCATTGGTCACGACAGTCCG 61.014 60.000 0.00 0.00 0.00 4.79
2197 2273 2.442272 CGGGAGAGGGGTCGATGT 60.442 66.667 0.00 0.00 0.00 3.06
2225 2301 3.866582 GAGGGGTCAGGCGGATGG 61.867 72.222 0.00 0.00 0.00 3.51
2237 2315 1.144057 CGGATGGGGTCTAGTGTGC 59.856 63.158 0.00 0.00 0.00 4.57
2273 2351 4.695455 TGGTCATCGAAGAAAAATGGTCTC 59.305 41.667 0.00 0.00 43.58 3.36
2404 2491 2.330231 AAAACATGACAATGACGGCG 57.670 45.000 4.80 4.80 37.24 6.46
2425 2512 3.660865 GAATAACTGAACGACACCTGGT 58.339 45.455 0.00 0.00 0.00 4.00
2451 2538 1.005867 TCTCGGGGCGTTACAACAC 60.006 57.895 0.00 0.00 0.00 3.32
2452 2539 1.005394 CTCGGGGCGTTACAACACT 60.005 57.895 0.00 0.00 0.00 3.55
2453 2540 1.005867 TCGGGGCGTTACAACACTC 60.006 57.895 0.00 0.00 0.00 3.51
2454 2541 2.030958 CGGGGCGTTACAACACTCC 61.031 63.158 0.00 0.00 0.00 3.85
2455 2542 1.071814 GGGGCGTTACAACACTCCA 59.928 57.895 0.00 0.00 0.00 3.86
2456 2543 1.232621 GGGGCGTTACAACACTCCAC 61.233 60.000 0.00 0.00 0.00 4.02
2457 2544 1.232621 GGGCGTTACAACACTCCACC 61.233 60.000 0.00 0.00 0.00 4.61
2458 2545 0.533308 GGCGTTACAACACTCCACCA 60.533 55.000 0.00 0.00 0.00 4.17
2459 2546 0.584876 GCGTTACAACACTCCACCAC 59.415 55.000 0.00 0.00 0.00 4.16
2460 2547 1.808891 GCGTTACAACACTCCACCACT 60.809 52.381 0.00 0.00 0.00 4.00
2461 2548 2.546373 GCGTTACAACACTCCACCACTA 60.546 50.000 0.00 0.00 0.00 2.74
2462 2549 3.054878 CGTTACAACACTCCACCACTAC 58.945 50.000 0.00 0.00 0.00 2.73
2463 2550 3.491276 CGTTACAACACTCCACCACTACA 60.491 47.826 0.00 0.00 0.00 2.74
2464 2551 4.444536 GTTACAACACTCCACCACTACAA 58.555 43.478 0.00 0.00 0.00 2.41
2465 2552 3.194005 ACAACACTCCACCACTACAAG 57.806 47.619 0.00 0.00 0.00 3.16
2466 2553 2.769663 ACAACACTCCACCACTACAAGA 59.230 45.455 0.00 0.00 0.00 3.02
2467 2554 3.181465 ACAACACTCCACCACTACAAGAG 60.181 47.826 0.00 0.00 0.00 2.85
2468 2555 1.971357 ACACTCCACCACTACAAGAGG 59.029 52.381 0.00 0.00 31.82 3.69
2469 2556 2.248248 CACTCCACCACTACAAGAGGA 58.752 52.381 0.00 0.00 30.04 3.71
2470 2557 2.834549 CACTCCACCACTACAAGAGGAT 59.165 50.000 0.00 0.00 30.04 3.24
2471 2558 3.100671 ACTCCACCACTACAAGAGGATC 58.899 50.000 0.00 0.00 30.04 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 99 1.909302 TCTTCTTCCTTGCGGGATCTT 59.091 47.619 0.00 0.00 44.66 2.40
172 176 2.409975 TCTCGTTAGCTTCGGTTTTGG 58.590 47.619 10.26 0.00 0.00 3.28
211 215 6.488344 TGATGGTTGTTTACTATGTTGCTTGA 59.512 34.615 0.00 0.00 0.00 3.02
247 251 4.587891 TCATACTTGGTTGTGCATCATGA 58.412 39.130 0.00 0.00 0.00 3.07
326 331 4.025396 CGTTGCATATTGAGCTCCACTTAG 60.025 45.833 12.15 0.00 0.00 2.18
435 444 9.841295 TTAGTTTACTTATGTTTCACCTCTTGT 57.159 29.630 0.00 0.00 0.00 3.16
480 492 1.197036 GCTTGTAGTTTTCGGCCTCAC 59.803 52.381 0.00 0.00 0.00 3.51
489 501 6.463995 TCCAGAATTGTTGCTTGTAGTTTT 57.536 33.333 0.00 0.00 0.00 2.43
858 885 9.379791 GCTTTAGCTAATTTCCAGAGTTTACTA 57.620 33.333 7.08 0.00 38.21 1.82
902 936 2.868583 CCAGATTCAGCCTGTATCGTTG 59.131 50.000 5.78 0.80 30.71 4.10
960 999 3.252284 CTGAGGCCACACCCCAGT 61.252 66.667 5.01 0.00 40.58 4.00
1052 1096 4.636435 CCGTTGACCGTGGCCCTT 62.636 66.667 0.00 0.00 33.66 3.95
1078 1122 1.300697 GGACGACCGCAAGAACAGT 60.301 57.895 0.00 0.00 43.02 3.55
1082 1126 2.342279 CCTGGACGACCGCAAGAA 59.658 61.111 0.00 0.00 43.02 2.52
1083 1127 4.373116 GCCTGGACGACCGCAAGA 62.373 66.667 0.00 0.00 43.02 3.02
1105 1149 4.394712 CGACCCGCCCTCTGCTTT 62.395 66.667 0.00 0.00 38.05 3.51
1132 1176 2.167487 GGCGTCTCTCTTTCTCAGGAAT 59.833 50.000 0.00 0.00 0.00 3.01
1134 1178 1.178276 GGCGTCTCTCTTTCTCAGGA 58.822 55.000 0.00 0.00 0.00 3.86
1142 1186 1.403679 CTCTCAATCGGCGTCTCTCTT 59.596 52.381 6.85 0.00 0.00 2.85
1151 1195 2.545731 GTTTCCTCTCTCTCAATCGGC 58.454 52.381 0.00 0.00 0.00 5.54
1179 1234 2.683933 GCCGACCCCTTCTCTCCA 60.684 66.667 0.00 0.00 0.00 3.86
1273 1328 1.338136 ACCACCTCCATTAGCCTCCG 61.338 60.000 0.00 0.00 0.00 4.63
1281 1336 1.002134 CGCTGGAACCACCTCCATT 60.002 57.895 0.00 0.00 44.59 3.16
1284 1339 1.450312 CATCGCTGGAACCACCTCC 60.450 63.158 0.00 0.00 39.86 4.30
1346 1401 2.648102 CTACCTCGCGCTCGTTCG 60.648 66.667 5.56 0.00 36.96 3.95
1347 1402 1.297745 CTCTACCTCGCGCTCGTTC 60.298 63.158 5.56 0.00 36.96 3.95
1348 1403 2.762234 CCTCTACCTCGCGCTCGTT 61.762 63.158 5.56 0.00 36.96 3.85
1349 1404 3.203412 CCTCTACCTCGCGCTCGT 61.203 66.667 5.56 0.37 36.96 4.18
1350 1405 2.887889 CTCCTCTACCTCGCGCTCG 61.888 68.421 5.56 0.00 0.00 5.03
1351 1406 2.548295 CCTCCTCTACCTCGCGCTC 61.548 68.421 5.56 0.00 0.00 5.03
1352 1407 2.517402 CCTCCTCTACCTCGCGCT 60.517 66.667 5.56 0.00 0.00 5.92
1353 1408 4.273257 GCCTCCTCTACCTCGCGC 62.273 72.222 0.00 0.00 0.00 6.86
1354 1409 2.829003 TGCCTCCTCTACCTCGCG 60.829 66.667 0.00 0.00 0.00 5.87
1355 1410 2.494530 CCTGCCTCCTCTACCTCGC 61.495 68.421 0.00 0.00 0.00 5.03
1356 1411 2.494530 GCCTGCCTCCTCTACCTCG 61.495 68.421 0.00 0.00 0.00 4.63
1357 1412 0.762461 ATGCCTGCCTCCTCTACCTC 60.762 60.000 0.00 0.00 0.00 3.85
1358 1413 1.053264 CATGCCTGCCTCCTCTACCT 61.053 60.000 0.00 0.00 0.00 3.08
1359 1414 1.449353 CATGCCTGCCTCCTCTACC 59.551 63.158 0.00 0.00 0.00 3.18
1360 1415 1.341156 ACCATGCCTGCCTCCTCTAC 61.341 60.000 0.00 0.00 0.00 2.59
1361 1416 1.003442 ACCATGCCTGCCTCCTCTA 59.997 57.895 0.00 0.00 0.00 2.43
1379 1434 2.310233 GCTTCAACAGAGCGCGACA 61.310 57.895 12.10 0.00 0.00 4.35
1381 1436 2.023771 CTGCTTCAACAGAGCGCGA 61.024 57.895 12.10 0.00 43.02 5.87
1383 1438 2.684843 CCCTGCTTCAACAGAGCGC 61.685 63.158 0.00 0.00 43.02 5.92
1384 1439 2.037136 CCCCTGCTTCAACAGAGCG 61.037 63.158 0.00 0.00 43.02 5.03
1388 1443 0.250295 TCGTTCCCCTGCTTCAACAG 60.250 55.000 0.00 0.00 37.42 3.16
1429 1499 1.078214 GCAGCAGTAGACCATGGCA 60.078 57.895 13.04 0.00 0.00 4.92
1454 1524 2.105821 TCCCTTTCCGTGTGTTCTTCAT 59.894 45.455 0.00 0.00 0.00 2.57
1466 1536 2.233922 TGCTAAACTCTCTCCCTTTCCG 59.766 50.000 0.00 0.00 0.00 4.30
1478 1548 4.442753 CCTCTCTCTCCCATTGCTAAACTC 60.443 50.000 0.00 0.00 0.00 3.01
1489 1559 1.074926 GCCATCCCTCTCTCTCCCA 60.075 63.158 0.00 0.00 0.00 4.37
1496 1566 3.237741 CCCCTCGCCATCCCTCTC 61.238 72.222 0.00 0.00 0.00 3.20
1542 1613 2.989824 AGGGACCACGACCACGAG 60.990 66.667 0.00 0.00 42.66 4.18
1557 1628 0.466922 GATCCAATGCACCCTCCAGG 60.467 60.000 0.00 0.00 43.78 4.45
1559 1630 1.224315 CGATCCAATGCACCCTCCA 59.776 57.895 0.00 0.00 0.00 3.86
1566 1637 1.832219 CTCCTCCCGATCCAATGCA 59.168 57.895 0.00 0.00 0.00 3.96
1569 1640 2.511452 CCGCTCCTCCCGATCCAAT 61.511 63.158 0.00 0.00 0.00 3.16
1596 1667 2.333225 CGAATCCTCTCGCTCCCG 59.667 66.667 0.00 0.00 31.04 5.14
1624 1695 0.394899 GCTACCAGCCTCCTGCAAAT 60.395 55.000 0.00 0.00 44.83 2.32
1625 1696 1.002134 GCTACCAGCCTCCTGCAAA 60.002 57.895 0.00 0.00 44.83 3.68
1630 1701 2.674220 GCCTTGCTACCAGCCTCCT 61.674 63.158 0.00 0.00 41.51 3.69
1640 1711 1.451927 CATGCCCGAAGCCTTGCTA 60.452 57.895 0.00 0.00 42.71 3.49
1644 1715 2.040544 CGTTCATGCCCGAAGCCTT 61.041 57.895 0.00 0.00 42.71 4.35
1656 1727 3.467226 ATCCCCGGCGTCGTTCAT 61.467 61.111 9.28 0.00 33.95 2.57
1710 1781 4.753662 ACTCTGGAGGCGCCCGTA 62.754 66.667 26.15 8.55 34.97 4.02
1718 1789 0.545309 TCCCTCACCAACTCTGGAGG 60.545 60.000 0.00 0.00 46.92 4.30
1719 1790 0.901124 CTCCCTCACCAACTCTGGAG 59.099 60.000 0.00 0.00 46.92 3.86
1722 1793 0.322975 CACCTCCCTCACCAACTCTG 59.677 60.000 0.00 0.00 0.00 3.35
1728 1799 4.675303 CCCCCACCTCCCTCACCA 62.675 72.222 0.00 0.00 0.00 4.17
1743 1814 1.682344 GTCAGCCAACCCAATCCCC 60.682 63.158 0.00 0.00 0.00 4.81
1758 1829 1.339610 CCTCCCACAATTTTTGCGTCA 59.660 47.619 0.00 0.00 0.00 4.35
1760 1831 1.068434 CACCTCCCACAATTTTTGCGT 59.932 47.619 0.00 0.00 0.00 5.24
1762 1833 1.416030 ACCACCTCCCACAATTTTTGC 59.584 47.619 0.00 0.00 0.00 3.68
1764 1835 1.960689 CGACCACCTCCCACAATTTTT 59.039 47.619 0.00 0.00 0.00 1.94
1814 1885 0.684805 ATTTCTCCTCGGCCTCGACT 60.685 55.000 0.00 0.00 40.88 4.18
1823 1894 1.137872 CCACCTCCTCATTTCTCCTCG 59.862 57.143 0.00 0.00 0.00 4.63
1844 1915 0.956633 CAATCCATCCAATCCCGCAG 59.043 55.000 0.00 0.00 0.00 5.18
1848 1919 2.041701 CCAACCAATCCATCCAATCCC 58.958 52.381 0.00 0.00 0.00 3.85
1862 1933 0.266152 ATTCCCCACCAAACCAACCA 59.734 50.000 0.00 0.00 0.00 3.67
1931 2005 1.267121 GCCACCACTCTCTCTGGTTA 58.733 55.000 0.00 0.00 40.25 2.85
1947 2021 4.880426 GGATCCTCCTCCCCGCCA 62.880 72.222 3.84 0.00 32.53 5.69
1988 2063 8.766492 ATATATAGATCAACCCCTACCCAAAA 57.234 34.615 0.00 0.00 0.00 2.44
2035 2110 1.670811 CCAATTTTGATCGGAGGGTCG 59.329 52.381 0.00 0.00 0.00 4.79
2053 2128 4.543689 ACCTATTTATCTGAGACCGTCCA 58.456 43.478 0.00 0.00 0.00 4.02
2096 2172 5.048504 CCAAACATCCCTAAATCATCATCGG 60.049 44.000 0.00 0.00 0.00 4.18
2153 2229 2.046604 CTTCCCCGAACCCGAACC 60.047 66.667 0.00 0.00 38.22 3.62
2197 2273 1.347707 CTGACCCCTCTTTGCACAGTA 59.652 52.381 0.00 0.00 0.00 2.74
2225 2301 2.027192 TCAATCCAAGCACACTAGACCC 60.027 50.000 0.00 0.00 0.00 4.46
2237 2315 4.445453 TCGATGACCATTCTCAATCCAAG 58.555 43.478 0.00 0.00 0.00 3.61
2273 2351 1.868997 GTCTCCGTGGCATGTTGTG 59.131 57.895 5.89 0.00 0.00 3.33
2299 2377 2.886124 GTTCGTAGCTGCCGCCTC 60.886 66.667 0.00 0.00 36.60 4.70
2308 2386 1.969103 AACTCGTAACCGTTCGTAGC 58.031 50.000 0.00 0.00 35.01 3.58
2402 2489 2.092211 CAGGTGTCGTTCAGTTATTCGC 59.908 50.000 0.00 0.00 0.00 4.70
2404 2491 3.432252 CACCAGGTGTCGTTCAGTTATTC 59.568 47.826 11.99 0.00 0.00 1.75
2425 2512 4.680237 CGCCCCGAGACTGTTGCA 62.680 66.667 0.00 0.00 0.00 4.08
2451 2538 3.370104 AGATCCTCTTGTAGTGGTGGAG 58.630 50.000 0.00 0.00 31.13 3.86
2452 2539 3.245622 TGAGATCCTCTTGTAGTGGTGGA 60.246 47.826 0.00 0.00 31.13 4.02
2453 2540 3.099905 TGAGATCCTCTTGTAGTGGTGG 58.900 50.000 0.00 0.00 31.13 4.61
2454 2541 4.202202 GGATGAGATCCTCTTGTAGTGGTG 60.202 50.000 0.00 0.00 46.19 4.17
2455 2542 3.964031 GGATGAGATCCTCTTGTAGTGGT 59.036 47.826 0.00 0.00 46.19 4.16
2456 2543 4.599047 GGATGAGATCCTCTTGTAGTGG 57.401 50.000 0.00 0.00 46.19 4.00


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

AutoCloner maintained by Alex Coulton.