Multiple sequence alignment - TraesCS7B01G057700

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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 TraesCS7B01G057700 chr7B 100.000 3911 0 0 1 3911 60032207 60028297 0.000000e+00 7223
1 TraesCS7B01G057700 chr7B 80.343 1343 238 19 1520 2852 60496240 60494914 0.000000e+00 994
2 TraesCS7B01G057700 chr7B 79.066 1414 251 30 1522 2912 60091830 60090439 0.000000e+00 929
3 TraesCS7B01G057700 chr7B 81.207 1160 194 19 1520 2664 60565741 60564591 0.000000e+00 913
4 TraesCS7B01G057700 chr7B 78.438 1396 262 30 1519 2895 59822832 59821457 0.000000e+00 874
5 TraesCS7B01G057700 chr7B 76.483 1416 276 38 1520 2912 59667713 59666332 0.000000e+00 717
6 TraesCS7B01G057700 chr7B 75.666 826 173 17 1520 2339 61055019 61054216 1.700000e-103 387
7 TraesCS7B01G057700 chrUn 94.288 1593 69 11 1576 3148 91513105 91514695 0.000000e+00 2418
8 TraesCS7B01G057700 chrUn 90.345 580 45 9 883 1458 91510931 91511503 0.000000e+00 750
9 TraesCS7B01G057700 chrUn 90.402 448 29 10 459 904 91510490 91510925 9.420000e-161 577
10 TraesCS7B01G057700 chrUn 97.541 122 3 0 1459 1580 91511654 91511775 3.960000e-50 209
11 TraesCS7B01G057700 chr7A 95.521 1362 61 0 1465 2826 106294673 106293312 0.000000e+00 2178
12 TraesCS7B01G057700 chr7A 93.154 818 49 4 475 1285 106295871 106295054 0.000000e+00 1194
13 TraesCS7B01G057700 chr7A 82.609 1150 193 5 1519 2667 107602858 107601715 0.000000e+00 1009
14 TraesCS7B01G057700 chr7A 80.014 1381 253 16 1520 2895 106994477 106993115 0.000000e+00 1000
15 TraesCS7B01G057700 chr7A 79.439 1391 256 23 1520 2895 107152796 107151421 0.000000e+00 957
16 TraesCS7B01G057700 chr7A 78.951 1392 257 31 1520 2895 106744679 106743308 0.000000e+00 915
17 TraesCS7B01G057700 chr7A 80.908 1168 200 18 1520 2670 107322214 107321053 0.000000e+00 900
18 TraesCS7B01G057700 chr7A 93.626 455 26 3 25 477 106296683 106296230 0.000000e+00 676
19 TraesCS7B01G057700 chr7A 89.337 347 16 7 2822 3148 106291554 106291209 2.170000e-112 416
20 TraesCS7B01G057700 chr7A 88.764 178 15 4 1282 1458 106295012 106294839 3.060000e-51 213
21 TraesCS7B01G057700 chr2D 91.361 764 65 1 3149 3911 121259336 121260099 0.000000e+00 1044
22 TraesCS7B01G057700 chr2D 89.677 775 76 3 3138 3911 76387393 76386622 0.000000e+00 985
23 TraesCS7B01G057700 chr7D 82.971 1151 187 6 1519 2667 102755430 102754287 0.000000e+00 1031
24 TraesCS7B01G057700 chr7D 90.933 750 67 1 3163 3911 414244254 414245003 0.000000e+00 1007
25 TraesCS7B01G057700 chr7D 90.183 764 73 2 3149 3911 182502910 182502148 0.000000e+00 994
26 TraesCS7B01G057700 chr7D 85.616 146 18 3 366 510 94060533 94060676 2.430000e-32 150
27 TraesCS7B01G057700 chr3D 91.333 750 62 2 3164 3911 197864297 197863549 0.000000e+00 1022
28 TraesCS7B01G057700 chr3D 90.788 749 68 1 3164 3911 295756510 295757258 0.000000e+00 1000
29 TraesCS7B01G057700 chr3D 81.818 187 30 4 110 293 33382467 33382652 1.880000e-33 154
30 TraesCS7B01G057700 chr3D 85.915 142 19 1 157 297 295261612 295261753 2.430000e-32 150
31 TraesCS7B01G057700 chr5D 90.872 745 67 1 3163 3907 132912671 132911928 0.000000e+00 998
32 TraesCS7B01G057700 chr1D 90.222 767 71 3 3148 3911 425699285 425700050 0.000000e+00 998
33 TraesCS7B01G057700 chr4D 90.289 762 68 3 3150 3911 305657641 305656886 0.000000e+00 992
34 TraesCS7B01G057700 chr5B 83.077 195 26 7 322 514 596698056 596697867 1.870000e-38 171
35 TraesCS7B01G057700 chr5A 82.178 202 29 7 315 514 606175587 606175783 2.420000e-37 167
36 TraesCS7B01G057700 chr3B 82.653 196 26 6 127 314 56343223 56343418 2.420000e-37 167
37 TraesCS7B01G057700 chr3A 82.759 174 28 2 127 298 405990600 405990773 1.880000e-33 154
38 TraesCS7B01G057700 chr4B 80.097 206 39 1 90 293 530237430 530237635 6.770000e-33 152
39 TraesCS7B01G057700 chr6B 79.897 194 36 2 81 271 469288131 469288324 5.270000e-29 139
40 TraesCS7B01G057700 chr6B 79.310 203 37 4 99 298 28114998 28115198 1.900000e-28 137
41 TraesCS7B01G057700 chr6A 77.727 220 43 3 101 314 481744651 481744870 3.170000e-26 130
42 TraesCS7B01G057700 chr1A 75.926 216 47 5 316 527 351865487 351865701 5.340000e-19 106


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 TraesCS7B01G057700 chr7B 60028297 60032207 3910 True 7223.0 7223 100.0000 1 3911 1 chr7B.!!$R3 3910
1 TraesCS7B01G057700 chr7B 60494914 60496240 1326 True 994.0 994 80.3430 1520 2852 1 chr7B.!!$R5 1332
2 TraesCS7B01G057700 chr7B 60090439 60091830 1391 True 929.0 929 79.0660 1522 2912 1 chr7B.!!$R4 1390
3 TraesCS7B01G057700 chr7B 60564591 60565741 1150 True 913.0 913 81.2070 1520 2664 1 chr7B.!!$R6 1144
4 TraesCS7B01G057700 chr7B 59821457 59822832 1375 True 874.0 874 78.4380 1519 2895 1 chr7B.!!$R2 1376
5 TraesCS7B01G057700 chr7B 59666332 59667713 1381 True 717.0 717 76.4830 1520 2912 1 chr7B.!!$R1 1392
6 TraesCS7B01G057700 chr7B 61054216 61055019 803 True 387.0 387 75.6660 1520 2339 1 chr7B.!!$R7 819
7 TraesCS7B01G057700 chrUn 91510490 91514695 4205 False 988.5 2418 93.1440 459 3148 4 chrUn.!!$F1 2689
8 TraesCS7B01G057700 chr7A 107601715 107602858 1143 True 1009.0 1009 82.6090 1519 2667 1 chr7A.!!$R5 1148
9 TraesCS7B01G057700 chr7A 106993115 106994477 1362 True 1000.0 1000 80.0140 1520 2895 1 chr7A.!!$R2 1375
10 TraesCS7B01G057700 chr7A 107151421 107152796 1375 True 957.0 957 79.4390 1520 2895 1 chr7A.!!$R3 1375
11 TraesCS7B01G057700 chr7A 106291209 106296683 5474 True 935.4 2178 92.0804 25 3148 5 chr7A.!!$R6 3123
12 TraesCS7B01G057700 chr7A 106743308 106744679 1371 True 915.0 915 78.9510 1520 2895 1 chr7A.!!$R1 1375
13 TraesCS7B01G057700 chr7A 107321053 107322214 1161 True 900.0 900 80.9080 1520 2670 1 chr7A.!!$R4 1150
14 TraesCS7B01G057700 chr2D 121259336 121260099 763 False 1044.0 1044 91.3610 3149 3911 1 chr2D.!!$F1 762
15 TraesCS7B01G057700 chr2D 76386622 76387393 771 True 985.0 985 89.6770 3138 3911 1 chr2D.!!$R1 773
16 TraesCS7B01G057700 chr7D 102754287 102755430 1143 True 1031.0 1031 82.9710 1519 2667 1 chr7D.!!$R1 1148
17 TraesCS7B01G057700 chr7D 414244254 414245003 749 False 1007.0 1007 90.9330 3163 3911 1 chr7D.!!$F2 748
18 TraesCS7B01G057700 chr7D 182502148 182502910 762 True 994.0 994 90.1830 3149 3911 1 chr7D.!!$R2 762
19 TraesCS7B01G057700 chr3D 197863549 197864297 748 True 1022.0 1022 91.3330 3164 3911 1 chr3D.!!$R1 747
20 TraesCS7B01G057700 chr3D 295756510 295757258 748 False 1000.0 1000 90.7880 3164 3911 1 chr3D.!!$F3 747
21 TraesCS7B01G057700 chr5D 132911928 132912671 743 True 998.0 998 90.8720 3163 3907 1 chr5D.!!$R1 744
22 TraesCS7B01G057700 chr1D 425699285 425700050 765 False 998.0 998 90.2220 3148 3911 1 chr1D.!!$F1 763
23 TraesCS7B01G057700 chr4D 305656886 305657641 755 True 992.0 992 90.2890 3150 3911 1 chr4D.!!$R1 761

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
776 1146 0.173708 GCGTTGGGTAGAGTCTCAGG 59.826 60.0 0.0 0.0 0.0 3.86 F
1322 1775 0.106918 ACACGCCAAACCTCTTCCAA 60.107 50.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2703 4693 0.033920 TCTGCATCGAATGGGGATCG 59.966 55.0 0.00 0.0 41.53 3.69 R
3300 7081 0.248012 TCGGGCACGAGCTCATTTTA 59.752 50.0 7.15 0.0 45.59 1.52 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
29 30 2.899303 ACCCAAATTACCTGACCCAG 57.101 50.000 0.00 0.00 0.00 4.45
34 35 4.402474 CCCAAATTACCTGACCCAGATTTC 59.598 45.833 0.00 0.00 32.44 2.17
129 132 9.574458 TCGAAATTTTAGACATGACAAAACAAA 57.426 25.926 0.00 0.00 0.00 2.83
176 179 3.525800 AGGATGGCAAGTTTAGTTGGT 57.474 42.857 0.00 0.00 0.00 3.67
198 201 1.341531 AGTATGAGAAATCCGCCTCCG 59.658 52.381 0.00 0.00 0.00 4.63
203 206 0.175073 AGAAATCCGCCTCCGTACAC 59.825 55.000 0.00 0.00 0.00 2.90
222 225 1.000843 ACTTTTCGCCAGGAAATTGCC 59.999 47.619 0.00 0.00 43.82 4.52
253 256 5.698832 CAAACTAAATTTGTCATCCTCGCA 58.301 37.500 0.00 0.00 42.46 5.10
290 293 9.716531 TTGTCATAAAATATGTTCAATTTGCCA 57.283 25.926 0.00 0.00 0.00 4.92
306 309 6.604735 ATTTGCCATGTCTAATCTAACGTC 57.395 37.500 0.00 0.00 0.00 4.34
307 310 4.729227 TGCCATGTCTAATCTAACGTCA 57.271 40.909 0.00 0.00 0.00 4.35
314 317 8.169268 CCATGTCTAATCTAACGTCAGTTTTTC 58.831 37.037 0.00 0.00 41.49 2.29
315 318 8.926710 CATGTCTAATCTAACGTCAGTTTTTCT 58.073 33.333 0.00 0.00 41.49 2.52
316 319 8.882415 TGTCTAATCTAACGTCAGTTTTTCTT 57.118 30.769 0.00 0.00 41.49 2.52
335 338 5.630896 TCTTCTTCTGAAAAACACGTACG 57.369 39.130 15.01 15.01 0.00 3.67
416 419 0.942962 GCTCCTCAAGCCAATCATCG 59.057 55.000 0.00 0.00 45.92 3.84
527 893 5.177511 ACCACAAGCAATATGATAACGATCG 59.822 40.000 14.88 14.88 34.49 3.69
607 973 5.759059 TCCATAGAGAAACGGAGGTTAGTA 58.241 41.667 0.00 0.00 34.62 1.82
745 1111 5.647658 ACTGAATTTGAGCATTTATCCGTGA 59.352 36.000 0.00 0.00 0.00 4.35
776 1146 0.173708 GCGTTGGGTAGAGTCTCAGG 59.826 60.000 0.00 0.00 0.00 3.86
824 1194 3.762288 TGTAGCACCTGTACCTCACTTAG 59.238 47.826 0.00 0.00 0.00 2.18
844 1218 1.610522 GAACAATGCAACACTCTGGCT 59.389 47.619 0.00 0.00 0.00 4.75
854 1228 4.293415 CAACACTCTGGCTGATTTTGTTC 58.707 43.478 10.97 0.00 0.00 3.18
856 1230 2.549754 CACTCTGGCTGATTTTGTTCGT 59.450 45.455 0.00 0.00 0.00 3.85
899 1273 2.414138 GTCATGCAATTTGCTTGGCTTC 59.586 45.455 25.87 15.42 45.84 3.86
938 1342 2.050836 TTTGCAGCCGAGGACCTGAA 62.051 55.000 0.00 0.00 0.00 3.02
971 1375 0.394762 GTGCAAGCCATCATCTGGGA 60.395 55.000 0.00 0.00 46.06 4.37
976 1380 2.173356 CAAGCCATCATCTGGGACCTTA 59.827 50.000 0.00 0.00 46.06 2.69
983 1388 1.207089 CATCTGGGACCTTAAGACGCA 59.793 52.381 3.36 10.86 0.00 5.24
1002 1407 3.435566 GCAGAACAATGCAGATCACATG 58.564 45.455 0.00 0.00 45.77 3.21
1044 1449 0.539051 ACATTCCGGCTCTCTCCTTG 59.461 55.000 0.00 0.00 0.00 3.61
1092 1497 2.167693 AGATCCAGTAAACGATTCCGCA 59.832 45.455 0.00 0.00 39.95 5.69
1132 1537 7.053316 TCAAATGACACCATGATGTTTCTTT 57.947 32.000 0.00 0.00 32.36 2.52
1210 1615 8.118976 ACAAAATCATGAACTTCAGATGATGT 57.881 30.769 0.00 10.11 29.44 3.06
1215 1620 7.933215 TCATGAACTTCAGATGATGTTGAAT 57.067 32.000 16.18 8.76 40.88 2.57
1262 1667 6.356190 CCTATTTTCGAGAAACAAAACGTCAC 59.644 38.462 0.00 0.00 0.00 3.67
1265 1670 3.199677 TCGAGAAACAAAACGTCACCAT 58.800 40.909 0.00 0.00 0.00 3.55
1274 1682 5.302360 ACAAAACGTCACCATGTACAGTAT 58.698 37.500 0.33 0.00 0.00 2.12
1276 1684 6.930164 ACAAAACGTCACCATGTACAGTATTA 59.070 34.615 0.33 0.00 0.00 0.98
1291 1744 9.201989 TGTACAGTATTATTGAAGATCCTCACT 57.798 33.333 0.00 0.00 0.00 3.41
1294 1747 8.762645 ACAGTATTATTGAAGATCCTCACTCAA 58.237 33.333 0.00 0.00 0.00 3.02
1295 1748 9.775854 CAGTATTATTGAAGATCCTCACTCAAT 57.224 33.333 0.00 2.42 0.00 2.57
1297 1750 9.213799 GTATTATTGAAGATCCTCACTCAATCC 57.786 37.037 0.00 0.00 0.00 3.01
1304 1757 1.757118 TCCTCACTCAATCCATCGGAC 59.243 52.381 0.00 0.00 32.98 4.79
1310 1763 1.449423 CAATCCATCGGACACGCCA 60.449 57.895 0.00 0.00 40.69 5.69
1312 1765 0.322098 AATCCATCGGACACGCCAAA 60.322 50.000 0.00 0.00 40.69 3.28
1322 1775 0.106918 ACACGCCAAACCTCTTCCAA 60.107 50.000 0.00 0.00 0.00 3.53
1334 1787 4.775236 ACCTCTTCCAAGATGATGCTTAC 58.225 43.478 0.00 0.00 33.93 2.34
1355 1808 1.139654 TGGTGAGCACTATGATGAGCC 59.860 52.381 0.16 0.00 0.00 4.70
1404 1857 2.737252 GCTTACTCCTACACACTTGCAC 59.263 50.000 0.00 0.00 0.00 4.57
1424 1877 4.202121 GCACCTCATCCTCACGAAGTATTA 60.202 45.833 0.00 0.00 41.61 0.98
1486 2098 9.912634 CATTCTAACCTTTGCTAAATTTCTTGA 57.087 29.630 0.00 0.00 0.00 3.02
1510 2122 4.142160 GGATAAACAGGTGAATTTGGGAGC 60.142 45.833 0.00 0.00 0.00 4.70
1789 3735 2.438021 AGCACTTCAACCTGTAACTCCA 59.562 45.455 0.00 0.00 0.00 3.86
1986 3949 4.816385 AGCTTGTCATCCATATTAACCACG 59.184 41.667 0.00 0.00 0.00 4.94
2267 4233 5.170021 TGATTTTATGATGCTTGGTTGCAC 58.830 37.500 0.00 0.00 46.33 4.57
2360 4336 0.734889 AGCGCCATACTGCATTGTTC 59.265 50.000 2.29 0.00 0.00 3.18
2381 4365 6.755141 TGTTCGGACTACTTGCTAACATTATC 59.245 38.462 0.00 0.00 0.00 1.75
2443 4427 6.209192 AGTGCAAAATCATTCAACTACCATCA 59.791 34.615 0.00 0.00 0.00 3.07
2774 4764 1.906824 AACTCCTCCACGAAGCCGA 60.907 57.895 0.00 0.00 39.50 5.54
2861 6616 1.081094 CAGCAGAATGTCATGCACGA 58.919 50.000 0.00 0.00 45.01 4.35
2865 6620 2.011947 CAGAATGTCATGCACGATGGT 58.988 47.619 0.00 0.00 32.26 3.55
2922 6677 6.949352 AACAATGTCTGAGTCAAGAAATGT 57.051 33.333 0.00 0.00 0.00 2.71
2935 6698 0.657840 GAAATGTCCGGGAAGCATCG 59.342 55.000 0.00 0.00 0.00 3.84
2992 6764 3.515630 TCTCTCGTCATTGAAGTGATGC 58.484 45.455 5.11 0.00 35.56 3.91
2997 6769 0.448990 TCATTGAAGTGATGCTGCGC 59.551 50.000 0.00 0.00 0.00 6.09
3079 6851 5.180117 AGAGAAATTGATGTTCAACGAGTGG 59.820 40.000 0.00 0.00 39.45 4.00
3098 6870 8.421784 ACGAGTGGATGTGTATATTGTCTATTT 58.578 33.333 0.00 0.00 0.00 1.40
3160 6935 7.476540 ACATACTAGAATCACTGGTACAACA 57.523 36.000 0.00 0.00 43.37 3.33
3196 6971 2.237643 GGTTTTTAACCCCTTACCGCA 58.762 47.619 0.00 0.00 46.12 5.69
3216 6991 2.178912 ACGACATTTGGAACCATCGT 57.821 45.000 12.44 12.44 34.47 3.73
3218 6993 2.289444 ACGACATTTGGAACCATCGTCT 60.289 45.455 12.44 0.00 34.26 4.18
3246 7027 2.076803 GGGCGATAGGGGGTCCTTT 61.077 63.158 0.00 0.00 41.56 3.11
3250 7031 1.435256 CGATAGGGGGTCCTTTCCAT 58.565 55.000 0.00 0.00 41.56 3.41
3287 7068 3.568578 GGATAGGCCCTCCTGGTG 58.431 66.667 13.60 0.00 44.08 4.17
3300 7081 2.772191 TGGTGCACAGACTGGGGT 60.772 61.111 20.43 0.00 0.00 4.95
3315 7096 0.733150 GGGGTAAAATGAGCTCGTGC 59.267 55.000 9.75 0.07 40.05 5.34
3316 7097 0.733150 GGGTAAAATGAGCTCGTGCC 59.267 55.000 9.75 9.51 40.80 5.01
3349 7130 2.352323 GGCATCGAAACCCAATCGTTTT 60.352 45.455 0.00 0.00 40.99 2.43
3383 7164 0.251916 TCCCACACGATGAATCCCAC 59.748 55.000 0.00 0.00 0.00 4.61
3424 7207 9.665719 TTGTATGTATATCACACACAGTCAATT 57.334 29.630 0.00 0.00 44.99 2.32
3489 7272 3.301274 TCCAGGGAAAACATTTCCGTTT 58.699 40.909 12.89 1.61 40.79 3.60
3553 7336 4.569162 CGTTCGTATGTAAATCCCACACAT 59.431 41.667 0.00 0.00 36.82 3.21
3554 7337 5.749588 CGTTCGTATGTAAATCCCACACATA 59.250 40.000 0.00 0.00 34.78 2.29
3568 7351 6.717289 TCCCACACATATTTATGTATAGGCC 58.283 40.000 0.00 0.00 44.57 5.19
3590 7373 4.418392 CCGTGTGTGATAGGTGTAACTAC 58.582 47.826 0.00 0.00 36.74 2.73
3699 7482 2.406130 CCGTCACAACCGCTTTTACTA 58.594 47.619 0.00 0.00 0.00 1.82
3709 7492 2.856557 CCGCTTTTACTACTAGAACCGC 59.143 50.000 0.00 0.00 0.00 5.68
3746 7529 7.069331 CCATGACCCATTTAGCAGGTTTATTAA 59.931 37.037 0.00 0.00 32.81 1.40
3825 7608 5.422666 TTGCTAATTTCATATCAGGCACG 57.577 39.130 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.045416 GTCAGGTAATTTGGGTTTTCAAAACT 58.955 34.615 12.74 0.00 39.64 2.66
1 2 6.259167 GGTCAGGTAATTTGGGTTTTCAAAAC 59.741 38.462 4.25 4.25 39.64 2.43
2 3 6.350103 GGTCAGGTAATTTGGGTTTTCAAAA 58.650 36.000 0.00 0.00 39.64 2.44
3 4 5.163290 GGGTCAGGTAATTTGGGTTTTCAAA 60.163 40.000 0.00 0.00 40.37 2.69
4 5 4.345547 GGGTCAGGTAATTTGGGTTTTCAA 59.654 41.667 0.00 0.00 0.00 2.69
5 6 3.898741 GGGTCAGGTAATTTGGGTTTTCA 59.101 43.478 0.00 0.00 0.00 2.69
6 7 3.898741 TGGGTCAGGTAATTTGGGTTTTC 59.101 43.478 0.00 0.00 0.00 2.29
7 8 3.901222 CTGGGTCAGGTAATTTGGGTTTT 59.099 43.478 0.00 0.00 0.00 2.43
8 9 3.141272 TCTGGGTCAGGTAATTTGGGTTT 59.859 43.478 0.00 0.00 31.51 3.27
9 10 2.719705 TCTGGGTCAGGTAATTTGGGTT 59.280 45.455 0.00 0.00 31.51 4.11
10 11 2.354328 TCTGGGTCAGGTAATTTGGGT 58.646 47.619 0.00 0.00 31.51 4.51
11 12 3.669939 ATCTGGGTCAGGTAATTTGGG 57.330 47.619 0.00 0.00 31.51 4.12
12 13 5.126061 CAGAAATCTGGGTCAGGTAATTTGG 59.874 44.000 2.38 0.00 40.20 3.28
13 14 6.199937 CAGAAATCTGGGTCAGGTAATTTG 57.800 41.667 2.38 0.00 40.20 2.32
148 151 2.270352 ACTTGCCATCCTTGACGAAA 57.730 45.000 0.00 0.00 0.00 3.46
152 155 4.321230 CCAACTAAACTTGCCATCCTTGAC 60.321 45.833 0.00 0.00 0.00 3.18
176 179 2.365617 GGAGGCGGATTTCTCATACTCA 59.634 50.000 0.00 0.00 0.00 3.41
198 201 4.226761 CAATTTCCTGGCGAAAAGTGTAC 58.773 43.478 0.00 0.00 43.61 2.90
203 206 1.000731 TGGCAATTTCCTGGCGAAAAG 59.999 47.619 0.00 0.00 43.61 2.27
275 278 8.523915 AGATTAGACATGGCAAATTGAACATA 57.476 30.769 0.00 0.00 0.00 2.29
276 279 7.414222 AGATTAGACATGGCAAATTGAACAT 57.586 32.000 0.00 0.00 0.00 2.71
285 288 5.079689 TGACGTTAGATTAGACATGGCAA 57.920 39.130 0.00 0.00 0.00 4.52
290 293 9.490379 AAGAAAAACTGACGTTAGATTAGACAT 57.510 29.630 15.04 0.00 31.86 3.06
314 317 4.025979 AGCGTACGTGTTTTTCAGAAGAAG 60.026 41.667 17.90 0.00 34.71 2.85
315 318 3.866910 AGCGTACGTGTTTTTCAGAAGAA 59.133 39.130 17.90 0.00 0.00 2.52
316 319 3.450578 AGCGTACGTGTTTTTCAGAAGA 58.549 40.909 17.90 0.00 0.00 2.87
414 417 1.007963 AGATAGAGTTTCCCCACCCGA 59.992 52.381 0.00 0.00 0.00 5.14
416 419 3.136077 GGTTAGATAGAGTTTCCCCACCC 59.864 52.174 0.00 0.00 0.00 4.61
527 893 3.181480 GGAATAGAGGACAGTCAGCAGAC 60.181 52.174 0.05 0.05 45.31 3.51
607 973 8.832521 TCACGTTGAGTTTTTCTATTTGTACAT 58.167 29.630 0.00 0.00 0.00 2.29
745 1111 1.079819 CCAACGCAGACTGTCGGAT 60.080 57.895 18.83 8.38 0.00 4.18
776 1146 1.231958 TGGTTCATTCGGTTGACGGC 61.232 55.000 0.00 0.00 44.45 5.68
824 1194 1.610522 AGCCAGAGTGTTGCATTGTTC 59.389 47.619 0.00 0.00 0.00 3.18
844 1218 9.632807 CAATTAGGGAATTAACGAACAAAATCA 57.367 29.630 0.00 0.00 33.33 2.57
854 1228 4.261031 CCGGAAGCAATTAGGGAATTAACG 60.261 45.833 0.00 0.00 33.33 3.18
856 1230 4.211920 CCCGGAAGCAATTAGGGAATTAA 58.788 43.478 0.73 0.00 44.70 1.40
899 1273 6.018588 TGCAAAGCTCAAATGAATCACAAAAG 60.019 34.615 0.00 0.00 0.00 2.27
938 1342 1.342174 CTTGCACTTGGGCATTCTTGT 59.658 47.619 0.00 0.00 44.48 3.16
971 1375 2.484264 GCATTGTTCTGCGTCTTAAGGT 59.516 45.455 1.85 0.00 31.49 3.50
976 1380 1.882912 TCTGCATTGTTCTGCGTCTT 58.117 45.000 0.00 0.00 45.30 3.01
983 1388 2.426024 GGCATGTGATCTGCATTGTTCT 59.574 45.455 7.62 0.00 41.47 3.01
1077 1482 0.743345 GGCCTGCGGAATCGTTTACT 60.743 55.000 0.00 0.00 38.89 2.24
1092 1497 3.806949 TTTGATCCAAGTGTAAGGCCT 57.193 42.857 0.00 0.00 0.00 5.19
1132 1537 6.314400 CCGTTTATTTTCTCGGTTCTTGGATA 59.686 38.462 0.00 0.00 38.45 2.59
1189 1594 7.933215 TCAACATCATCTGAAGTTCATGATT 57.067 32.000 16.06 4.91 34.22 2.57
1198 1603 7.253651 CGCAAAATCATTCAACATCATCTGAAG 60.254 37.037 0.00 0.00 35.14 3.02
1199 1604 6.528774 CGCAAAATCATTCAACATCATCTGAA 59.471 34.615 0.00 0.00 36.08 3.02
1262 1667 9.429359 GAGGATCTTCAATAATACTGTACATGG 57.571 37.037 0.00 0.00 0.00 3.66
1265 1670 9.201989 AGTGAGGATCTTCAATAATACTGTACA 57.798 33.333 9.39 0.00 34.92 2.90
1274 1682 7.199167 TGGATTGAGTGAGGATCTTCAATAA 57.801 36.000 9.39 0.00 44.25 1.40
1276 1684 5.705397 TGGATTGAGTGAGGATCTTCAAT 57.295 39.130 9.39 8.47 45.67 2.57
1291 1744 1.153449 GGCGTGTCCGATGGATTGA 60.153 57.895 0.00 0.00 32.73 2.57
1294 1747 1.024579 GTTTGGCGTGTCCGATGGAT 61.025 55.000 0.00 0.00 37.80 3.41
1295 1748 1.669760 GTTTGGCGTGTCCGATGGA 60.670 57.895 0.00 0.00 37.80 3.41
1297 1750 1.635663 GAGGTTTGGCGTGTCCGATG 61.636 60.000 0.00 0.00 37.80 3.84
1304 1757 0.593128 CTTGGAAGAGGTTTGGCGTG 59.407 55.000 0.00 0.00 0.00 5.34
1310 1763 4.313020 AGCATCATCTTGGAAGAGGTTT 57.687 40.909 1.32 0.00 38.66 3.27
1312 1765 4.472833 AGTAAGCATCATCTTGGAAGAGGT 59.527 41.667 1.32 0.00 38.66 3.85
1322 1775 2.502947 TGCTCACCAGTAAGCATCATCT 59.497 45.455 0.00 0.00 43.30 2.90
1334 1787 2.481854 GCTCATCATAGTGCTCACCAG 58.518 52.381 0.00 0.00 0.00 4.00
1404 1857 7.495934 ACAAAATAATACTTCGTGAGGATGAGG 59.504 37.037 0.00 0.00 0.00 3.86
1449 1902 9.067986 AGCAAAGGTTAGAATGTATATTTAGGC 57.932 33.333 0.00 0.00 0.00 3.93
1486 2098 5.264395 CTCCCAAATTCACCTGTTTATCCT 58.736 41.667 0.00 0.00 0.00 3.24
1532 2144 2.862536 CACAATCATAGACGCACCAGAG 59.137 50.000 0.00 0.00 0.00 3.35
2129 4095 2.947652 GCAGCAGCATATTCTTCCTTCA 59.052 45.455 0.00 0.00 41.58 3.02
2267 4233 3.198068 CCAAATCCAGGAGTCGTGTATG 58.802 50.000 11.65 5.14 0.00 2.39
2357 4333 6.979238 AGATAATGTTAGCAAGTAGTCCGAAC 59.021 38.462 0.00 0.00 0.00 3.95
2360 4336 7.772332 AAAGATAATGTTAGCAAGTAGTCCG 57.228 36.000 0.00 0.00 0.00 4.79
2381 4365 5.059404 ACGAAATGTCTGGCCATAAAAAG 57.941 39.130 5.51 0.00 0.00 2.27
2415 4399 6.714810 TGGTAGTTGAATGATTTTGCACTAGT 59.285 34.615 0.00 0.00 0.00 2.57
2443 4427 2.361085 ACCCCTTCTGGTAGGTTCAT 57.639 50.000 0.00 0.00 36.67 2.57
2703 4693 0.033920 TCTGCATCGAATGGGGATCG 59.966 55.000 0.00 0.00 41.53 3.69
2774 4764 4.796606 CACACCCTGGGAATTATCATCTT 58.203 43.478 22.23 0.00 0.00 2.40
2861 6616 0.327480 TCCTGCAGGGGTGATACCAT 60.327 55.000 32.23 0.00 41.02 3.55
2865 6620 0.252696 AGTGTCCTGCAGGGGTGATA 60.253 55.000 32.23 9.40 35.41 2.15
2935 6698 4.829064 TTGGCGTATTTCTATTGCATCC 57.171 40.909 0.00 0.00 0.00 3.51
2941 6704 5.576447 CCAAGGTTTGGCGTATTTCTATT 57.424 39.130 0.00 0.00 45.17 1.73
2992 6764 1.079503 GTCCAAGGTTTAGAGCGCAG 58.920 55.000 11.47 0.00 0.00 5.18
2997 6769 8.581253 AATTCTAATTGGTCCAAGGTTTAGAG 57.419 34.615 18.86 6.90 29.88 2.43
3098 6870 4.023107 GCGTGAGGTAGCAATATCAGTCTA 60.023 45.833 0.00 0.00 0.00 2.59
3160 6935 9.120232 GGTTAAAAACCGTGTGTATAGCACCTT 62.120 40.741 0.00 0.00 43.68 3.50
3191 6966 0.309612 GTTCCAAATGTCGTTGCGGT 59.690 50.000 0.00 0.00 0.00 5.68
3196 6971 2.482721 GACGATGGTTCCAAATGTCGTT 59.517 45.455 15.89 4.44 41.69 3.85
3216 6991 3.561528 CCCTATCGCCCATACTCACTAGA 60.562 52.174 0.00 0.00 0.00 2.43
3218 6993 2.556782 CCCCTATCGCCCATACTCACTA 60.557 54.545 0.00 0.00 0.00 2.74
3246 7027 3.243737 CGACGATTTCTGGGTCATATGGA 60.244 47.826 2.13 0.00 0.00 3.41
3250 7031 1.411246 CCCGACGATTTCTGGGTCATA 59.589 52.381 0.00 0.00 34.86 2.15
3286 7067 2.107378 TCATTTTACCCCAGTCTGTGCA 59.893 45.455 0.00 0.00 0.00 4.57
3287 7068 2.749621 CTCATTTTACCCCAGTCTGTGC 59.250 50.000 0.00 0.00 0.00 4.57
3293 7074 1.628846 ACGAGCTCATTTTACCCCAGT 59.371 47.619 15.40 0.00 0.00 4.00
3300 7081 0.248012 TCGGGCACGAGCTCATTTTA 59.752 50.000 7.15 0.00 45.59 1.52
3316 7097 2.837883 CGATGCCTTGCCCAATCGG 61.838 63.158 0.00 0.00 0.00 4.18
3349 7130 4.689071 GTGTGGGATGTACATATGAACGA 58.311 43.478 8.71 0.00 0.00 3.85
3456 7239 1.728323 TCCCTGGATTGACTGTGTGA 58.272 50.000 0.00 0.00 0.00 3.58
3489 7272 6.800072 TTGACTGTGTGGGATGTACATATA 57.200 37.500 8.71 0.00 0.00 0.86
3553 7336 5.304871 TCACACACGGGCCTATACATAAATA 59.695 40.000 0.84 0.00 0.00 1.40
3554 7337 4.101898 TCACACACGGGCCTATACATAAAT 59.898 41.667 0.84 0.00 0.00 1.40
3568 7351 3.587797 AGTTACACCTATCACACACGG 57.412 47.619 0.00 0.00 0.00 4.94
3590 7373 1.592400 CCAAGGCAGAGCATGTGTGG 61.592 60.000 0.00 0.00 0.00 4.17
3678 7461 0.236449 GTAAAAGCGGTTGTGACGGG 59.764 55.000 0.00 0.00 0.00 5.28
3681 7464 5.464168 TCTAGTAGTAAAAGCGGTTGTGAC 58.536 41.667 0.00 0.00 0.00 3.67
3688 7471 2.856557 GCGGTTCTAGTAGTAAAAGCGG 59.143 50.000 15.00 0.59 41.44 5.52
3699 7482 2.256117 ACTTTGCAAGCGGTTCTAGT 57.744 45.000 0.00 0.00 0.00 2.57
3709 7492 1.962807 TGGGTCATGGAACTTTGCAAG 59.037 47.619 0.00 0.00 30.51 4.01


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

AutoCloner maintained by Alex Coulton.