Multiple sequence alignment - TraesCS2B01G058700

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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 TraesCS2B01G058700 chr2B 100.000 2420 0 0 1 2420 28460211 28462630 0.000000e+00 4470
1 TraesCS2B01G058700 chr2B 83.055 779 104 10 1284 2059 764252785 764252032 0.000000e+00 682
2 TraesCS2B01G058700 chr2B 78.235 850 147 18 872 1690 711103170 711102328 5.970000e-141 510
3 TraesCS2B01G058700 chr2B 81.915 470 81 4 1192 1659 302061557 302061090 6.270000e-106 394
4 TraesCS2B01G058700 chr2B 82.650 317 43 9 142 458 187183468 187183772 1.100000e-68 270
5 TraesCS2B01G058700 chr2B 82.334 317 44 9 142 458 187170796 187171100 5.130000e-67 265
6 TraesCS2B01G058700 chr2B 82.019 317 45 9 142 458 187196177 187196481 2.390000e-65 259
7 TraesCS2B01G058700 chr6B 93.867 1875 100 4 548 2420 271843994 271842133 0.000000e+00 2811
8 TraesCS2B01G058700 chr6B 90.300 433 40 2 1990 2420 310874842 310875274 1.260000e-157 566
9 TraesCS2B01G058700 chr6B 89.838 433 42 2 1990 2420 310772758 310773190 2.720000e-154 555
10 TraesCS2B01G058700 chr6B 89.607 433 43 2 1990 2420 310865500 310865932 1.260000e-152 549
11 TraesCS2B01G058700 chr6B 89.607 433 43 2 1990 2420 310960252 310960684 1.260000e-152 549
12 TraesCS2B01G058700 chr4B 92.751 1876 112 10 547 2420 19011064 19012917 0.000000e+00 2689
13 TraesCS2B01G058700 chr4B 85.404 322 41 5 142 463 91954261 91953946 1.790000e-86 329
14 TraesCS2B01G058700 chr4B 91.753 97 7 1 1 96 270778843 270778939 1.510000e-27 134
15 TraesCS2B01G058700 chr4B 92.857 84 6 0 1 84 270576964 270577047 3.270000e-24 122
16 TraesCS2B01G058700 chr4B 97.143 70 2 0 15 84 270536897 270536966 4.230000e-23 119
17 TraesCS2B01G058700 chr2A 84.201 1076 146 11 1351 2420 241008201 241007144 0.000000e+00 1024
18 TraesCS2B01G058700 chr2A 93.007 143 8 2 1 141 214400429 214400571 8.770000e-50 207
19 TraesCS2B01G058700 chr2D 88.242 825 73 9 1258 2075 481607554 481606747 0.000000e+00 965
20 TraesCS2B01G058700 chr2D 83.711 706 101 5 1284 1988 303387475 303386783 0.000000e+00 654
21 TraesCS2B01G058700 chr2D 79.009 848 141 18 872 1690 535884517 535885356 1.640000e-151 545
22 TraesCS2B01G058700 chr2D 78.867 847 145 15 872 1690 535875161 535876001 2.120000e-150 542
23 TraesCS2B01G058700 chr4D 88.452 814 72 8 1267 2075 340809790 340808994 0.000000e+00 963
24 TraesCS2B01G058700 chr4D 88.452 814 72 8 1267 2075 340823217 340822421 0.000000e+00 963
25 TraesCS2B01G058700 chr4D 82.564 195 20 5 882 1062 11283140 11282946 2.490000e-35 159
26 TraesCS2B01G058700 chr3D 88.121 825 74 9 1258 2075 500416133 500415326 0.000000e+00 959
27 TraesCS2B01G058700 chr3D 88.121 825 74 9 1258 2075 500445327 500444520 0.000000e+00 959
28 TraesCS2B01G058700 chr3D 79.385 650 105 14 872 1494 406432492 406433139 4.780000e-117 431
29 TraesCS2B01G058700 chr3D 87.651 332 41 0 972 1303 249280339 249280008 1.050000e-103 387
30 TraesCS2B01G058700 chr3D 86.970 330 43 0 967 1296 249668020 249667691 2.940000e-99 372
31 TraesCS2B01G058700 chr3D 86.350 337 46 0 967 1303 249652663 249652327 3.800000e-98 368
32 TraesCS2B01G058700 chr3D 92.000 150 12 0 279 428 2901835 2901984 6.780000e-51 211
33 TraesCS2B01G058700 chr5B 87.802 828 74 10 1258 2075 41101611 41102421 0.000000e+00 944
34 TraesCS2B01G058700 chr3B 96.263 562 19 2 1 561 650837051 650836491 0.000000e+00 920
35 TraesCS2B01G058700 chr7B 87.152 825 82 9 1258 2075 25385778 25384971 0.000000e+00 915
36 TraesCS2B01G058700 chr7B 90.698 430 38 2 1993 2420 25367619 25367190 2.700000e-159 571
37 TraesCS2B01G058700 chr7B 89.953 428 41 2 1995 2420 25384954 25384527 3.520000e-153 551
38 TraesCS2B01G058700 chr1B 83.243 740 108 6 1323 2060 355686664 355687389 0.000000e+00 665
39 TraesCS2B01G058700 chr1B 80.798 526 67 17 871 1366 173329988 173330509 4.880000e-102 381
40 TraesCS2B01G058700 chr1D 79.731 819 123 19 889 1680 386532093 386532895 9.780000e-154 553
41 TraesCS2B01G058700 chr3A 83.747 443 51 7 879 1303 666048255 666048694 1.350000e-107 399
42 TraesCS2B01G058700 chr4A 83.295 437 57 2 882 1303 258975585 258975150 2.920000e-104 388
43 TraesCS2B01G058700 chr4A 76.760 753 127 30 866 1581 312692714 312693455 6.320000e-101 377
44 TraesCS2B01G058700 chr1A 80.366 382 66 5 605 979 120848440 120848061 5.090000e-72 281
45 TraesCS2B01G058700 chrUn 96.947 131 3 1 1 130 295593418 295593548 4.050000e-53 219
46 TraesCS2B01G058700 chr5D 93.671 79 5 0 481 559 473073232 473073310 4.230000e-23 119


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 TraesCS2B01G058700 chr2B 28460211 28462630 2419 False 4470 4470 100.0000 1 2420 1 chr2B.!!$F1 2419
1 TraesCS2B01G058700 chr2B 764252032 764252785 753 True 682 682 83.0550 1284 2059 1 chr2B.!!$R3 775
2 TraesCS2B01G058700 chr2B 711102328 711103170 842 True 510 510 78.2350 872 1690 1 chr2B.!!$R2 818
3 TraesCS2B01G058700 chr6B 271842133 271843994 1861 True 2811 2811 93.8670 548 2420 1 chr6B.!!$R1 1872
4 TraesCS2B01G058700 chr4B 19011064 19012917 1853 False 2689 2689 92.7510 547 2420 1 chr4B.!!$F1 1873
5 TraesCS2B01G058700 chr2A 241007144 241008201 1057 True 1024 1024 84.2010 1351 2420 1 chr2A.!!$R1 1069
6 TraesCS2B01G058700 chr2D 481606747 481607554 807 True 965 965 88.2420 1258 2075 1 chr2D.!!$R2 817
7 TraesCS2B01G058700 chr2D 303386783 303387475 692 True 654 654 83.7110 1284 1988 1 chr2D.!!$R1 704
8 TraesCS2B01G058700 chr2D 535884517 535885356 839 False 545 545 79.0090 872 1690 1 chr2D.!!$F2 818
9 TraesCS2B01G058700 chr2D 535875161 535876001 840 False 542 542 78.8670 872 1690 1 chr2D.!!$F1 818
10 TraesCS2B01G058700 chr4D 340808994 340809790 796 True 963 963 88.4520 1267 2075 1 chr4D.!!$R2 808
11 TraesCS2B01G058700 chr4D 340822421 340823217 796 True 963 963 88.4520 1267 2075 1 chr4D.!!$R3 808
12 TraesCS2B01G058700 chr3D 500415326 500416133 807 True 959 959 88.1210 1258 2075 1 chr3D.!!$R4 817
13 TraesCS2B01G058700 chr3D 500444520 500445327 807 True 959 959 88.1210 1258 2075 1 chr3D.!!$R5 817
14 TraesCS2B01G058700 chr3D 406432492 406433139 647 False 431 431 79.3850 872 1494 1 chr3D.!!$F2 622
15 TraesCS2B01G058700 chr5B 41101611 41102421 810 False 944 944 87.8020 1258 2075 1 chr5B.!!$F1 817
16 TraesCS2B01G058700 chr3B 650836491 650837051 560 True 920 920 96.2630 1 561 1 chr3B.!!$R1 560
17 TraesCS2B01G058700 chr7B 25384527 25385778 1251 True 733 915 88.5525 1258 2420 2 chr7B.!!$R2 1162
18 TraesCS2B01G058700 chr1B 355686664 355687389 725 False 665 665 83.2430 1323 2060 1 chr1B.!!$F2 737
19 TraesCS2B01G058700 chr1B 173329988 173330509 521 False 381 381 80.7980 871 1366 1 chr1B.!!$F1 495
20 TraesCS2B01G058700 chr1D 386532093 386532895 802 False 553 553 79.7310 889 1680 1 chr1D.!!$F1 791
21 TraesCS2B01G058700 chr4A 312692714 312693455 741 False 377 377 76.7600 866 1581 1 chr4A.!!$F1 715

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
140 142 0.402121 AAAGACCAGAGGCCAGGAAC 59.598 55.0 14.97 8.69 0.0 3.62 F
1174 1203 0.098200 TGTCGCCGATGTCTACTTCG 59.902 55.0 10.47 10.47 41.4 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1241 1270 0.040514 CGTCATCCTAGCGAGCTCTG 60.041 60.0 12.85 6.68 0.0 3.35 R
2088 2775 0.756294 TGAAGACAAAGACTCCGCCA 59.244 50.0 0.00 0.00 0.0 5.69 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
41 42 3.866582 GATGGGGACGGCCAGAGG 61.867 72.222 11.00 0.00 35.15 3.69
56 57 1.402259 CAGAGGCTACGTGAGTACCTG 59.598 57.143 0.00 0.00 46.88 4.00
140 142 0.402121 AAAGACCAGAGGCCAGGAAC 59.598 55.000 14.97 8.69 0.00 3.62
150 152 1.004440 GCCAGGAACGAGAAGCACT 60.004 57.895 0.00 0.00 0.00 4.40
169 171 2.639286 GTGGTGCAGCGTCAAAGG 59.361 61.111 11.91 0.00 0.00 3.11
222 224 1.526917 GGCGCTGGCTATGTTCCAT 60.527 57.895 7.64 0.00 39.81 3.41
262 264 3.047877 GCTACGGTGGGTGTGTGC 61.048 66.667 0.00 0.00 0.00 4.57
343 345 1.795889 CGCGGCACTAGAGAAGAAGAC 60.796 57.143 0.00 0.00 0.00 3.01
486 488 1.681264 GGTCAAACAGGTTTCACAGGG 59.319 52.381 1.50 0.00 0.00 4.45
505 507 2.394563 GGAGGCAGAAGAACGCAGC 61.395 63.158 0.00 0.00 0.00 5.25
516 518 0.880278 GAACGCAGCAGAACCTCACA 60.880 55.000 0.00 0.00 0.00 3.58
621 629 0.900647 AGGAGGTCCTGTGGAAGACG 60.901 60.000 0.00 0.00 46.55 4.18
624 632 3.112709 GTCCTGTGGAAGACGCGC 61.113 66.667 5.73 0.00 31.38 6.86
629 637 4.681978 GTGGAAGACGCGCCCACT 62.682 66.667 24.05 7.54 45.08 4.00
1074 1101 1.021390 GGTGCCACAAGGATCGTGAG 61.021 60.000 0.00 0.00 36.43 3.51
1100 1127 4.697756 CGCAAGGAGAACGCCCCA 62.698 66.667 0.00 0.00 0.00 4.96
1160 1189 3.195698 GCCCGTTGGAGATGTCGC 61.196 66.667 0.00 0.00 0.00 5.19
1161 1190 2.511600 CCCGTTGGAGATGTCGCC 60.512 66.667 0.00 0.00 36.28 5.54
1162 1191 2.885644 CCGTTGGAGATGTCGCCG 60.886 66.667 0.00 0.00 38.78 6.46
1163 1192 2.180769 CGTTGGAGATGTCGCCGA 59.819 61.111 0.00 0.00 38.78 5.54
1164 1193 1.226974 CGTTGGAGATGTCGCCGAT 60.227 57.895 0.00 0.00 38.78 4.18
1165 1194 1.482621 CGTTGGAGATGTCGCCGATG 61.483 60.000 0.00 0.00 38.78 3.84
1166 1195 0.460284 GTTGGAGATGTCGCCGATGT 60.460 55.000 0.00 0.00 38.78 3.06
1167 1196 0.179111 TTGGAGATGTCGCCGATGTC 60.179 55.000 0.00 0.00 38.78 3.06
1168 1197 1.037579 TGGAGATGTCGCCGATGTCT 61.038 55.000 4.23 4.23 38.78 3.41
1169 1198 0.952280 GGAGATGTCGCCGATGTCTA 59.048 55.000 4.52 0.00 0.00 2.59
1170 1199 1.335142 GGAGATGTCGCCGATGTCTAC 60.335 57.143 4.52 1.90 0.00 2.59
1171 1200 1.604755 GAGATGTCGCCGATGTCTACT 59.395 52.381 4.52 0.00 0.00 2.57
1172 1201 2.025155 AGATGTCGCCGATGTCTACTT 58.975 47.619 2.88 0.00 0.00 2.24
1173 1202 2.033550 AGATGTCGCCGATGTCTACTTC 59.966 50.000 2.88 0.00 0.00 3.01
1174 1203 0.098200 TGTCGCCGATGTCTACTTCG 59.902 55.000 10.47 10.47 41.40 3.79
1175 1204 0.098376 GTCGCCGATGTCTACTTCGT 59.902 55.000 14.75 0.00 40.52 3.85
1176 1205 0.376152 TCGCCGATGTCTACTTCGTC 59.624 55.000 14.75 4.07 40.52 4.20
1177 1206 0.098200 CGCCGATGTCTACTTCGTCA 59.902 55.000 14.75 0.00 40.52 4.35
1178 1207 1.466866 CGCCGATGTCTACTTCGTCAA 60.467 52.381 14.75 0.00 40.52 3.18
1179 1208 2.186076 GCCGATGTCTACTTCGTCAAG 58.814 52.381 14.75 3.82 40.52 3.02
1180 1209 2.186076 CCGATGTCTACTTCGTCAAGC 58.814 52.381 14.75 0.00 40.52 4.01
1181 1210 2.159366 CCGATGTCTACTTCGTCAAGCT 60.159 50.000 14.75 0.00 40.52 3.74
1182 1211 2.848887 CGATGTCTACTTCGTCAAGCTG 59.151 50.000 9.51 0.00 38.30 4.24
1183 1212 2.724977 TGTCTACTTCGTCAAGCTGG 57.275 50.000 0.00 0.00 32.09 4.85
1184 1213 2.235891 TGTCTACTTCGTCAAGCTGGA 58.764 47.619 0.00 0.00 32.09 3.86
1185 1214 2.826128 TGTCTACTTCGTCAAGCTGGAT 59.174 45.455 0.00 0.00 32.09 3.41
1186 1215 3.119459 TGTCTACTTCGTCAAGCTGGATC 60.119 47.826 0.00 0.00 32.09 3.36
1187 1216 2.427453 TCTACTTCGTCAAGCTGGATCC 59.573 50.000 4.20 4.20 32.09 3.36
1188 1217 0.250513 ACTTCGTCAAGCTGGATCCC 59.749 55.000 9.90 0.00 32.09 3.85
1189 1218 0.807667 CTTCGTCAAGCTGGATCCCG 60.808 60.000 9.90 3.53 0.00 5.14
1190 1219 2.202932 CGTCAAGCTGGATCCCGG 60.203 66.667 9.90 3.20 0.00 5.73
1191 1220 2.721167 CGTCAAGCTGGATCCCGGA 61.721 63.158 9.90 0.00 29.82 5.14
1192 1221 1.144936 GTCAAGCTGGATCCCGGAG 59.855 63.158 9.90 0.60 29.82 4.63
1211 1240 3.842923 CGTGGAGCTCGCAGGGAT 61.843 66.667 7.83 0.00 0.00 3.85
1212 1241 2.202987 GTGGAGCTCGCAGGGATG 60.203 66.667 7.83 0.00 0.00 3.51
1213 1242 4.166888 TGGAGCTCGCAGGGATGC 62.167 66.667 7.83 0.00 0.00 3.91
1214 1243 4.925861 GGAGCTCGCAGGGATGCC 62.926 72.222 7.83 0.00 0.00 4.40
1240 1269 3.147595 CCACGGAGGATGGCGAGA 61.148 66.667 0.00 0.00 41.22 4.04
1241 1270 2.105128 CACGGAGGATGGCGAGAC 59.895 66.667 0.00 0.00 0.00 3.36
1242 1271 2.362503 ACGGAGGATGGCGAGACA 60.363 61.111 0.00 0.00 0.00 3.41
1243 1272 2.415010 CGGAGGATGGCGAGACAG 59.585 66.667 0.00 0.00 0.00 3.51
1244 1273 2.121538 CGGAGGATGGCGAGACAGA 61.122 63.158 0.00 0.00 0.00 3.41
1245 1274 1.739049 GGAGGATGGCGAGACAGAG 59.261 63.158 0.00 0.00 0.00 3.35
1246 1275 1.067250 GAGGATGGCGAGACAGAGC 59.933 63.158 0.00 0.00 0.00 4.09
1247 1276 1.381056 AGGATGGCGAGACAGAGCT 60.381 57.895 0.00 0.00 0.00 4.09
1248 1277 1.067250 GGATGGCGAGACAGAGCTC 59.933 63.158 5.27 5.27 0.00 4.09
1255 1284 3.088259 GAGACAGAGCTCGCTAGGA 57.912 57.895 8.37 0.00 0.00 2.94
1256 1285 1.604604 GAGACAGAGCTCGCTAGGAT 58.395 55.000 8.37 0.00 0.00 3.24
1257 1286 1.266718 GAGACAGAGCTCGCTAGGATG 59.733 57.143 8.37 1.41 0.00 3.51
1258 1287 1.133945 AGACAGAGCTCGCTAGGATGA 60.134 52.381 8.37 0.00 0.00 2.92
1259 1288 1.001815 GACAGAGCTCGCTAGGATGAC 60.002 57.143 8.37 0.00 0.00 3.06
1260 1289 0.040514 CAGAGCTCGCTAGGATGACG 60.041 60.000 8.37 0.00 0.00 4.35
1261 1290 1.371145 GAGCTCGCTAGGATGACGC 60.371 63.158 0.00 0.00 0.00 5.19
1265 1294 3.900892 CGCTAGGATGACGCCCGT 61.901 66.667 0.00 0.00 0.00 5.28
1408 1878 2.969238 CATGGAGGACGGATGCGC 60.969 66.667 6.51 0.00 0.00 6.09
1449 2031 2.125832 CGTACCGCGTTGGATGGT 60.126 61.111 4.92 0.00 42.00 3.55
1535 2119 4.803426 GTGGAGCTCGCAGGACGG 62.803 72.222 7.83 0.00 43.89 4.79
1714 2302 1.673920 GTGTTTCCTTTGTCTTGGCGA 59.326 47.619 0.00 0.00 0.00 5.54
1767 2355 1.270571 TGCACTCTTCATGGCGTACAA 60.271 47.619 0.00 0.00 0.00 2.41
1805 2393 0.605319 CGTGCCCCTTGTCTTAGCAA 60.605 55.000 0.00 0.00 34.79 3.91
1808 2396 1.133637 TGCCCCTTGTCTTAGCAAACA 60.134 47.619 0.00 0.00 0.00 2.83
1841 2429 3.900388 GTCTAGCTAGGACGTGGTATG 57.100 52.381 20.58 0.00 0.00 2.39
1871 2459 1.726791 CTTCCATGACGTCACCTTTCG 59.273 52.381 22.71 4.31 0.00 3.46
1901 2489 1.519408 GACGCTTTGCCCTTGTCTTA 58.481 50.000 0.00 0.00 0.00 2.10
1910 2498 2.311542 TGCCCTTGTCTTATTGGACCAT 59.688 45.455 0.00 0.00 35.54 3.55
1911 2499 2.952310 GCCCTTGTCTTATTGGACCATC 59.048 50.000 0.00 0.00 35.54 3.51
1912 2500 3.206150 CCCTTGTCTTATTGGACCATCG 58.794 50.000 0.00 0.00 35.54 3.84
1913 2501 3.370527 CCCTTGTCTTATTGGACCATCGT 60.371 47.826 0.00 0.00 35.54 3.73
1914 2502 4.141801 CCCTTGTCTTATTGGACCATCGTA 60.142 45.833 0.00 0.00 35.54 3.43
1915 2503 5.454755 CCCTTGTCTTATTGGACCATCGTAT 60.455 44.000 0.00 0.00 35.54 3.06
1916 2504 6.055588 CCTTGTCTTATTGGACCATCGTATT 58.944 40.000 0.00 0.00 35.54 1.89
1917 2505 6.017934 CCTTGTCTTATTGGACCATCGTATTG 60.018 42.308 0.00 0.00 35.54 1.90
1918 2506 5.364778 TGTCTTATTGGACCATCGTATTGG 58.635 41.667 0.00 1.17 42.82 3.16
1919 2507 5.129650 TGTCTTATTGGACCATCGTATTGGA 59.870 40.000 0.00 0.00 39.25 3.53
1920 2508 5.465724 GTCTTATTGGACCATCGTATTGGAC 59.534 44.000 0.00 3.12 39.25 4.02
1923 2511 2.930826 GGACCATCGTATTGGACCAT 57.069 50.000 14.45 0.00 46.78 3.55
2078 2765 4.660771 CCCCTCTAAGATGTTACCTTCCAT 59.339 45.833 0.00 0.00 0.00 3.41
2088 2775 1.344065 TACCTTCCATGGTGTCGTGT 58.656 50.000 12.58 4.68 41.05 4.49
2238 2928 4.697756 CGAGGCGAACCCCTTGCA 62.698 66.667 0.00 0.00 34.69 4.08
2261 2951 0.738412 CCCGACGAAACCGCTACATT 60.738 55.000 0.00 0.00 0.00 2.71
2306 2996 1.357420 ACCCATGCTATTCCAACACCA 59.643 47.619 0.00 0.00 0.00 4.17
2317 3007 6.095440 GCTATTCCAACACCAACTACATCAAT 59.905 38.462 0.00 0.00 0.00 2.57
2416 3106 2.032681 GAGGACACGGGCTTTGCT 59.967 61.111 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.141234 GGCCAGGTACTCACGTAGC 59.859 63.158 0.00 0.00 42.86 3.58
150 152 2.202946 TTTGACGCTGCACCACGA 60.203 55.556 0.00 0.00 0.00 4.35
169 171 4.619140 CGTACGTCCGCCCGATCC 62.619 72.222 7.22 0.00 0.00 3.36
222 224 1.148273 GCCGGCCCATCACATAGAA 59.852 57.895 18.11 0.00 0.00 2.10
383 385 4.389576 CAAACGCCTGCTCGCCAC 62.390 66.667 0.00 0.00 0.00 5.01
461 463 4.561105 TGTGAAACCTGTTTGACCAAAAC 58.439 39.130 9.35 0.00 42.13 2.43
486 488 1.743252 CTGCGTTCTTCTGCCTCCC 60.743 63.158 0.00 0.00 0.00 4.30
505 507 0.677288 TGTACGGGTGTGAGGTTCTG 59.323 55.000 0.00 0.00 0.00 3.02
529 531 2.507324 GCTTCGTGCCTCGTCTCC 60.507 66.667 0.00 0.00 40.80 3.71
536 538 1.220206 CTCCTGATGCTTCGTGCCT 59.780 57.895 0.00 0.00 42.00 4.75
635 643 4.104417 AGAGCCGACGTGCGTCTC 62.104 66.667 20.19 12.28 44.79 3.36
636 644 4.406173 CAGAGCCGACGTGCGTCT 62.406 66.667 20.19 4.16 42.54 4.18
840 848 2.048023 CATGGCATCGGCTTGGTGT 61.048 57.895 0.00 0.00 40.87 4.16
1074 1101 4.168291 CTCCTTGCGAGCTCCCCC 62.168 72.222 8.47 0.00 0.00 5.40
1100 1127 6.756157 GCTCCAGCATGACGAAGTAGATGT 62.756 50.000 0.00 0.00 41.07 3.06
1152 1181 1.681538 AGTAGACATCGGCGACATCT 58.318 50.000 23.29 23.29 0.00 2.90
1170 1199 0.807667 CGGGATCCAGCTTGACGAAG 60.808 60.000 15.23 0.00 0.00 3.79
1171 1200 1.218047 CGGGATCCAGCTTGACGAA 59.782 57.895 15.23 0.00 0.00 3.85
1172 1201 2.721167 CCGGGATCCAGCTTGACGA 61.721 63.158 15.23 0.00 0.00 4.20
1173 1202 2.202932 CCGGGATCCAGCTTGACG 60.203 66.667 15.23 5.69 0.00 4.35
1174 1203 1.144936 CTCCGGGATCCAGCTTGAC 59.855 63.158 15.23 0.00 0.00 3.18
1175 1204 2.066393 CCTCCGGGATCCAGCTTGA 61.066 63.158 15.23 1.55 33.58 3.02
1176 1205 2.507944 CCTCCGGGATCCAGCTTG 59.492 66.667 15.23 2.28 33.58 4.01
1177 1206 3.483869 GCCTCCGGGATCCAGCTT 61.484 66.667 15.23 0.00 33.58 3.74
1180 1209 4.227134 CACGCCTCCGGGATCCAG 62.227 72.222 15.23 9.92 41.39 3.86
1183 1212 3.917760 CTCCACGCCTCCGGGATC 61.918 72.222 0.00 0.00 41.39 3.36
1194 1223 3.842923 ATCCCTGCGAGCTCCACG 61.843 66.667 8.47 0.00 0.00 4.94
1195 1224 2.202987 CATCCCTGCGAGCTCCAC 60.203 66.667 8.47 0.73 0.00 4.02
1196 1225 4.166888 GCATCCCTGCGAGCTCCA 62.167 66.667 8.47 6.43 38.92 3.86
1223 1252 3.147595 TCTCGCCATCCTCCGTGG 61.148 66.667 0.00 0.00 39.80 4.94
1224 1253 2.105128 GTCTCGCCATCCTCCGTG 59.895 66.667 0.00 0.00 0.00 4.94
1225 1254 2.362503 TGTCTCGCCATCCTCCGT 60.363 61.111 0.00 0.00 0.00 4.69
1226 1255 2.069465 CTCTGTCTCGCCATCCTCCG 62.069 65.000 0.00 0.00 0.00 4.63
1227 1256 1.739049 CTCTGTCTCGCCATCCTCC 59.261 63.158 0.00 0.00 0.00 4.30
1228 1257 1.067250 GCTCTGTCTCGCCATCCTC 59.933 63.158 0.00 0.00 0.00 3.71
1229 1258 1.381056 AGCTCTGTCTCGCCATCCT 60.381 57.895 0.00 0.00 0.00 3.24
1230 1259 1.067250 GAGCTCTGTCTCGCCATCC 59.933 63.158 6.43 0.00 0.00 3.51
1231 1260 4.728058 GAGCTCTGTCTCGCCATC 57.272 61.111 6.43 0.00 0.00 3.51
1237 1266 1.266718 CATCCTAGCGAGCTCTGTCTC 59.733 57.143 12.85 0.00 0.00 3.36
1238 1267 1.133945 TCATCCTAGCGAGCTCTGTCT 60.134 52.381 12.85 8.54 0.00 3.41
1239 1268 1.001815 GTCATCCTAGCGAGCTCTGTC 60.002 57.143 12.85 0.65 0.00 3.51
1240 1269 1.028905 GTCATCCTAGCGAGCTCTGT 58.971 55.000 12.85 0.66 0.00 3.41
1241 1270 0.040514 CGTCATCCTAGCGAGCTCTG 60.041 60.000 12.85 6.68 0.00 3.35
1242 1271 1.791103 GCGTCATCCTAGCGAGCTCT 61.791 60.000 12.85 0.00 0.00 4.09
1243 1272 1.371145 GCGTCATCCTAGCGAGCTC 60.371 63.158 2.73 2.73 0.00 4.09
1244 1273 2.725008 GCGTCATCCTAGCGAGCT 59.275 61.111 2.25 2.25 0.00 4.09
1245 1274 2.355244 GGCGTCATCCTAGCGAGC 60.355 66.667 0.00 0.00 0.00 5.03
1246 1275 2.336809 GGGCGTCATCCTAGCGAG 59.663 66.667 0.00 0.00 0.00 5.03
1247 1276 3.592814 CGGGCGTCATCCTAGCGA 61.593 66.667 0.00 0.00 0.00 4.93
1248 1277 3.825833 GACGGGCGTCATCCTAGCG 62.826 68.421 0.00 0.00 44.02 4.26
1249 1278 2.027751 GACGGGCGTCATCCTAGC 59.972 66.667 0.00 0.00 44.02 3.42
1250 1279 2.331805 CGACGGGCGTCATCCTAG 59.668 66.667 0.00 0.00 44.77 3.02
1259 1288 3.031964 ACGAAGTAGACGACGGGCG 62.032 63.158 0.00 0.00 41.94 6.13
1260 1289 2.873288 ACGAAGTAGACGACGGGC 59.127 61.111 0.00 0.00 41.94 6.13
1368 1727 1.528129 CCAGCTTGGTGAAGAAGACC 58.472 55.000 1.00 0.00 31.35 3.85
1408 1878 2.202987 GCACCCTCATGAGCTCCG 60.203 66.667 17.76 2.17 0.00 4.63
1435 2017 2.358247 GTCACCATCCAACGCGGT 60.358 61.111 12.47 0.00 35.57 5.68
1535 2119 0.179108 GAGGTAGACATCGGTGGTGC 60.179 60.000 0.00 0.00 0.00 5.01
1576 2160 2.905736 TGTGTCATCTTCATGGACTCCA 59.094 45.455 0.00 0.00 38.19 3.86
1767 2355 2.045242 TGCCTCTACGCCGAGACT 60.045 61.111 0.00 0.00 32.74 3.24
1841 2429 1.002624 TCATGGAAGGGCGTGGTTC 60.003 57.895 0.00 0.00 0.00 3.62
1884 2472 2.415893 CCAATAAGACAAGGGCAAAGCG 60.416 50.000 0.00 0.00 0.00 4.68
1901 2489 3.208747 GGTCCAATACGATGGTCCAAT 57.791 47.619 14.21 0.00 44.93 3.16
1912 2500 2.735134 GCCGTATTCGATGGTCCAATAC 59.265 50.000 0.00 0.00 39.71 1.89
1913 2501 2.608506 CGCCGTATTCGATGGTCCAATA 60.609 50.000 0.00 0.00 39.71 1.90
1914 2502 1.872237 CGCCGTATTCGATGGTCCAAT 60.872 52.381 0.00 0.00 39.71 3.16
1915 2503 0.528901 CGCCGTATTCGATGGTCCAA 60.529 55.000 0.00 0.00 39.71 3.53
1916 2504 1.066752 CGCCGTATTCGATGGTCCA 59.933 57.895 0.00 0.00 39.71 4.02
1917 2505 0.938168 GACGCCGTATTCGATGGTCC 60.938 60.000 0.00 0.00 39.71 4.46
1918 2506 0.938168 GGACGCCGTATTCGATGGTC 60.938 60.000 0.00 0.00 39.71 4.02
1919 2507 1.066918 GGACGCCGTATTCGATGGT 59.933 57.895 0.00 0.00 39.71 3.55
1920 2508 0.528901 TTGGACGCCGTATTCGATGG 60.529 55.000 0.00 0.00 39.71 3.51
1921 2509 1.005347 GTTTGGACGCCGTATTCGATG 60.005 52.381 0.00 0.00 39.71 3.84
1922 2510 1.283736 GTTTGGACGCCGTATTCGAT 58.716 50.000 0.00 0.00 39.71 3.59
1923 2511 1.072116 CGTTTGGACGCCGTATTCGA 61.072 55.000 0.00 0.00 43.03 3.71
2088 2775 0.756294 TGAAGACAAAGACTCCGCCA 59.244 50.000 0.00 0.00 0.00 5.69
2141 2828 2.518349 CGGTGTGGTTGGTGCCTT 60.518 61.111 0.00 0.00 0.00 4.35
2238 2928 1.037030 TAGCGGTTTCGTCGGGGTAT 61.037 55.000 0.00 0.00 38.89 2.73
2261 2951 1.270826 CTCTGCTCGGACTTCTTGACA 59.729 52.381 0.00 0.00 0.00 3.58
2296 2986 4.022416 GCATTGATGTAGTTGGTGTTGGAA 60.022 41.667 0.00 0.00 0.00 3.53
2306 2996 4.697352 GGTCTTGACAGCATTGATGTAGTT 59.303 41.667 7.67 0.00 30.17 2.24
2317 3007 1.285950 CTCGTCGGTCTTGACAGCA 59.714 57.895 3.08 0.00 38.84 4.41
2361 3051 3.864583 GCTCAAAACATGACTTTGTGCAA 59.135 39.130 27.55 11.89 45.66 4.08
2371 3061 1.163420 ACGTGCCGCTCAAAACATGA 61.163 50.000 0.00 0.00 36.38 3.07


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

AutoCloner maintained by Alex Coulton.