Multiple sequence alignment - TraesCS4B01G361600

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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 TraesCS4B01G361600 chr4B 100.000 3271 0 0 1 3271 650885448 650888718 0.000000e+00 6041.0
1 TraesCS4B01G361600 chr4B 100.000 45 0 0 349 393 650885675 650885719 2.090000e-12 84.2
2 TraesCS4B01G361600 chr4B 100.000 45 0 0 228 272 650885796 650885840 2.090000e-12 84.2
3 TraesCS4B01G361600 chr4D 91.140 2009 129 12 1289 3271 504272029 504274014 0.000000e+00 2678.0
4 TraesCS4B01G361600 chr4D 86.933 1630 169 29 614 2227 504266192 504267793 0.000000e+00 1790.0
5 TraesCS4B01G361600 chr4D 98.352 364 5 1 63 426 504265585 504265947 3.560000e-179 638.0
6 TraesCS4B01G361600 chr4D 87.766 188 16 5 427 614 504265980 504266160 2.560000e-51 213.0
7 TraesCS4B01G361600 chr4D 98.276 58 1 0 1 58 14938852 14938795 5.770000e-18 102.0
8 TraesCS4B01G361600 chr4D 98.276 58 1 0 1 58 207559543 207559486 5.770000e-18 102.0
9 TraesCS4B01G361600 chr4D 98.276 58 1 0 1 58 426582324 426582267 5.770000e-18 102.0
10 TraesCS4B01G361600 chr4D 100.000 45 0 0 349 393 504265749 504265793 2.090000e-12 84.2
11 TraesCS4B01G361600 chr4D 97.778 45 1 0 228 272 504265870 504265914 9.730000e-11 78.7
12 TraesCS4B01G361600 chr5A 94.019 1371 46 8 1926 3271 688944090 688945449 0.000000e+00 2045.0
13 TraesCS4B01G361600 chr5A 84.686 986 78 20 841 1787 688943162 688944113 0.000000e+00 917.0
14 TraesCS4B01G361600 chr5A 83.718 823 111 15 1032 1847 688940090 688940896 0.000000e+00 756.0
15 TraesCS4B01G361600 chr5A 78.351 291 40 6 152 423 688939249 688939535 2.020000e-37 167.0
16 TraesCS4B01G361600 chr5A 96.000 50 2 0 350 399 688939326 688939375 7.520000e-12 82.4
17 TraesCS4B01G361600 chrUn 98.276 58 1 0 1 58 82710048 82709991 5.770000e-18 102.0
18 TraesCS4B01G361600 chrUn 98.276 58 1 0 1 58 122302170 122302113 5.770000e-18 102.0
19 TraesCS4B01G361600 chrUn 98.276 58 1 0 1 58 303192049 303191992 5.770000e-18 102.0
20 TraesCS4B01G361600 chrUn 86.667 90 4 6 1 84 35713272 35713359 3.480000e-15 93.5
21 TraesCS4B01G361600 chr1D 98.276 58 1 0 1 58 464771305 464771362 5.770000e-18 102.0
22 TraesCS4B01G361600 chr1B 96.721 61 2 0 2221 2281 156057193 156057133 5.770000e-18 102.0
23 TraesCS4B01G361600 chr5B 95.312 64 2 1 1 63 377021814 377021877 2.080000e-17 100.0
24 TraesCS4B01G361600 chr7B 92.593 54 3 1 631 683 245675062 245675115 3.500000e-10 76.8
25 TraesCS4B01G361600 chr7D 95.455 44 2 0 638 681 265262164 265262207 1.630000e-08 71.3
26 TraesCS4B01G361600 chr2B 93.333 45 3 0 622 666 139796550 139796594 2.110000e-07 67.6
27 TraesCS4B01G361600 chr2B 92.683 41 2 1 631 670 186464834 186464874 1.270000e-04 58.4


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 TraesCS4B01G361600 chr4B 650885448 650888718 3270 False 2069.80 6041 100.0000 1 3271 3 chr4B.!!$F1 3270
1 TraesCS4B01G361600 chr4D 504272029 504274014 1985 False 2678.00 2678 91.1400 1289 3271 1 chr4D.!!$F1 1982
2 TraesCS4B01G361600 chr4D 504265585 504267793 2208 False 560.78 1790 94.1658 63 2227 5 chr4D.!!$F2 2164
3 TraesCS4B01G361600 chr5A 688939249 688945449 6200 False 793.48 2045 87.3548 152 3271 5 chr5A.!!$F1 3119

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
872 977 0.179189 GCAAAGCAAAGGATCCGTCG 60.179 55.0 5.98 0.00 0.00 5.12 F
1264 1391 0.107557 AAGTATTACCCCAACGGCCG 60.108 55.0 26.86 26.86 33.26 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 5196 0.037882 CACTGTGCTCGTGGAGACAT 60.038 55.0 0.00 0.0 46.14 3.06 R
2563 5839 0.179059 TCAAGTGAAGGTTGCGCTGA 60.179 50.0 9.73 0.0 0.00 4.26 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
28 29 7.657023 AGATGACCCGACTTTATACTAAAGT 57.343 36.000 11.09 11.09 42.62 2.66
29 30 8.075761 AGATGACCCGACTTTATACTAAAGTT 57.924 34.615 12.22 0.00 40.27 2.66
30 31 9.193806 AGATGACCCGACTTTATACTAAAGTTA 57.806 33.333 12.22 0.00 40.27 2.24
31 32 9.460906 GATGACCCGACTTTATACTAAAGTTAG 57.539 37.037 12.22 9.92 40.27 2.34
32 33 8.353423 TGACCCGACTTTATACTAAAGTTAGT 57.647 34.615 12.22 8.67 45.39 2.24
33 34 9.461312 TGACCCGACTTTATACTAAAGTTAGTA 57.539 33.333 12.18 12.18 46.74 1.82
34 35 9.723447 GACCCGACTTTATACTAAAGTTAGTAC 57.277 37.037 12.07 0.00 45.86 2.73
35 36 9.243105 ACCCGACTTTATACTAAAGTTAGTACA 57.757 33.333 12.07 0.00 45.86 2.90
56 57 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
57 58 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
58 59 8.103948 ACAAAGTTGAGTCATCTATTTTGGAG 57.896 34.615 14.35 1.25 40.00 3.86
59 60 7.175641 ACAAAGTTGAGTCATCTATTTTGGAGG 59.824 37.037 14.35 0.00 40.00 4.30
60 61 5.749462 AGTTGAGTCATCTATTTTGGAGGG 58.251 41.667 1.70 0.00 0.00 4.30
61 62 5.488919 AGTTGAGTCATCTATTTTGGAGGGA 59.511 40.000 1.70 0.00 0.00 4.20
78 79 5.071788 TGGAGGGAGTATTGGACAATGTATC 59.928 44.000 7.76 3.39 32.50 2.24
193 194 4.535526 AAATGGCCCTACATTGTGAAAC 57.464 40.909 0.00 0.00 40.71 2.78
409 429 5.332743 TCAAAGGAACAAGATAAAGCCCAT 58.667 37.500 0.00 0.00 0.00 4.00
427 447 7.961326 AGCCCATAAACTTTGATATTGTTCT 57.039 32.000 0.00 0.00 0.00 3.01
428 448 8.366359 AGCCCATAAACTTTGATATTGTTCTT 57.634 30.769 0.00 0.00 0.00 2.52
430 450 8.872845 GCCCATAAACTTTGATATTGTTCTTTG 58.127 33.333 0.00 0.00 0.00 2.77
473 525 6.458232 TGAACAAGCTAAAGCCAAAAACTA 57.542 33.333 0.00 0.00 43.38 2.24
474 526 7.049799 TGAACAAGCTAAAGCCAAAAACTAT 57.950 32.000 0.00 0.00 43.38 2.12
475 527 8.172352 TGAACAAGCTAAAGCCAAAAACTATA 57.828 30.769 0.00 0.00 43.38 1.31
476 528 8.802267 TGAACAAGCTAAAGCCAAAAACTATAT 58.198 29.630 0.00 0.00 43.38 0.86
487 539 8.567285 AGCCAAAAACTATATATGATACTGCC 57.433 34.615 0.00 0.00 0.00 4.85
495 547 3.784511 ATATGATACTGCCAGCTTGCT 57.215 42.857 11.53 0.00 0.00 3.91
503 555 3.019564 ACTGCCAGCTTGCTAATTAAGG 58.980 45.455 11.53 0.00 0.00 2.69
614 670 1.326245 TCGTGTCGTGAGCAAAACTTG 59.674 47.619 0.00 0.00 0.00 3.16
615 671 1.594518 CGTGTCGTGAGCAAAACTTGG 60.595 52.381 0.00 0.00 0.00 3.61
617 673 2.290641 GTGTCGTGAGCAAAACTTGGAT 59.709 45.455 0.00 0.00 0.00 3.41
636 732 7.516209 ACTTGGATCCCTGGCTATTATAGTTTA 59.484 37.037 9.90 0.00 0.00 2.01
690 790 5.297029 ACAAGTAAAACCTTGACTGAAGCTC 59.703 40.000 7.84 0.00 43.65 4.09
759 859 1.151908 AAACGCACCCTAAAGCCCA 59.848 52.632 0.00 0.00 0.00 5.36
872 977 0.179189 GCAAAGCAAAGGATCCGTCG 60.179 55.000 5.98 0.00 0.00 5.12
934 1039 2.294233 CCACCTGCGGATCCATAAAATG 59.706 50.000 13.41 2.34 0.00 2.32
936 1041 4.133820 CACCTGCGGATCCATAAAATGTA 58.866 43.478 13.41 0.00 0.00 2.29
937 1042 4.024048 CACCTGCGGATCCATAAAATGTAC 60.024 45.833 13.41 0.00 0.00 2.90
938 1043 4.141482 ACCTGCGGATCCATAAAATGTACT 60.141 41.667 13.41 0.00 0.00 2.73
939 1044 4.452455 CCTGCGGATCCATAAAATGTACTC 59.548 45.833 13.41 0.00 0.00 2.59
991 1096 0.534427 CACCATGGATCATCGCTGCT 60.534 55.000 21.47 0.00 0.00 4.24
1019 1124 3.119673 CGCAGTTTGCATACCCATTGTAA 60.120 43.478 3.47 0.00 45.36 2.41
1020 1125 4.439974 CGCAGTTTGCATACCCATTGTAAT 60.440 41.667 3.47 0.00 45.36 1.89
1021 1126 5.043248 GCAGTTTGCATACCCATTGTAATC 58.957 41.667 3.47 0.00 44.26 1.75
1067 1194 0.322098 TAGCCATCAAACCGTGTGGG 60.322 55.000 0.00 0.00 40.75 4.61
1100 1227 7.811713 GGGTTTAGTATATACAAGATGTCGTCC 59.188 40.741 15.18 3.83 0.00 4.79
1112 1239 1.451747 GTCGTCCCGCTCTACCTCT 60.452 63.158 0.00 0.00 0.00 3.69
1118 1245 1.690219 CCCGCTCTACCTCTGCCATT 61.690 60.000 0.00 0.00 0.00 3.16
1127 1254 2.046023 TCTGCCATTGTCGCCAGG 60.046 61.111 0.00 0.00 0.00 4.45
1129 1256 3.925630 CTGCCATTGTCGCCAGGGT 62.926 63.158 0.00 0.00 0.00 4.34
1197 1324 2.868253 GTGGTCACCAATGGTAGGC 58.132 57.895 3.85 0.92 34.18 3.93
1203 1330 1.016627 CACCAATGGTAGGCACATCG 58.983 55.000 3.85 0.00 32.11 3.84
1205 1332 1.134401 ACCAATGGTAGGCACATCGAG 60.134 52.381 1.52 0.00 32.11 4.04
1208 1335 1.781786 ATGGTAGGCACATCGAGTCT 58.218 50.000 0.00 0.00 0.00 3.24
1213 1340 0.251354 AGGCACATCGAGTCTTGCAT 59.749 50.000 11.13 2.95 36.66 3.96
1214 1341 0.654683 GGCACATCGAGTCTTGCATC 59.345 55.000 11.13 0.00 36.66 3.91
1217 1344 2.030213 GCACATCGAGTCTTGCATCTTC 59.970 50.000 0.00 0.00 34.97 2.87
1218 1345 2.606725 CACATCGAGTCTTGCATCTTCC 59.393 50.000 0.00 0.00 0.00 3.46
1233 1360 3.770040 TCCATGTCGGAGGCCACG 61.770 66.667 5.01 9.92 39.64 4.94
1263 1390 1.065272 TCAAGTATTACCCCAACGGCC 60.065 52.381 0.00 0.00 33.26 6.13
1264 1391 0.107557 AAGTATTACCCCAACGGCCG 60.108 55.000 26.86 26.86 33.26 6.13
1265 1392 0.977108 AGTATTACCCCAACGGCCGA 60.977 55.000 35.90 6.79 33.26 5.54
1266 1393 0.107752 GTATTACCCCAACGGCCGAA 60.108 55.000 35.90 14.64 33.26 4.30
1276 1403 0.535335 AACGGCCGAAGCTCAGATAA 59.465 50.000 35.90 0.00 39.73 1.75
1278 1405 1.139058 ACGGCCGAAGCTCAGATAATT 59.861 47.619 35.90 0.00 39.73 1.40
1285 1412 5.755813 CCGAAGCTCAGATAATTCCAATTG 58.244 41.667 0.00 0.00 0.00 2.32
1309 1439 5.749620 CATATCTGTCTTCATTCAGCTTGC 58.250 41.667 0.00 0.00 0.00 4.01
1321 1451 1.171308 CAGCTTGCCAGTGTTAGCAT 58.829 50.000 9.98 0.00 39.11 3.79
1331 1461 0.811281 GTGTTAGCATGGACTTGCCC 59.189 55.000 6.57 0.00 43.83 5.36
1332 1462 0.698238 TGTTAGCATGGACTTGCCCT 59.302 50.000 6.57 0.00 43.83 5.19
1362 1495 1.284198 ACAAGGGCATCTCAGCTCAAT 59.716 47.619 0.00 0.00 37.50 2.57
1365 1498 1.022735 GGGCATCTCAGCTCAATGTG 58.977 55.000 0.00 0.00 34.32 3.21
1366 1499 1.681166 GGGCATCTCAGCTCAATGTGT 60.681 52.381 0.00 0.00 34.32 3.72
1414 1547 2.713167 AGCCTGTGCCATCATATACCTT 59.287 45.455 0.00 0.00 38.69 3.50
1422 1555 3.997021 GCCATCATATACCTTCACCTTCG 59.003 47.826 0.00 0.00 0.00 3.79
1429 1562 6.323996 TCATATACCTTCACCTTCGACAGAAT 59.676 38.462 0.00 0.00 35.56 2.40
1437 1570 2.806244 ACCTTCGACAGAATTTTCACGG 59.194 45.455 0.00 0.00 35.56 4.94
1440 1573 0.168128 CGACAGAATTTTCACGGCCC 59.832 55.000 0.00 0.00 0.00 5.80
1459 1592 3.185203 TGAAGGGCAGTGGGGCTT 61.185 61.111 0.00 0.00 42.84 4.35
1461 1594 3.185203 AAGGGCAGTGGGGCTTGA 61.185 61.111 0.00 0.00 42.84 3.02
1465 1598 1.607467 GGCAGTGGGGCTTGAACAT 60.607 57.895 0.00 0.00 39.42 2.71
1470 1603 2.689983 CAGTGGGGCTTGAACATATTCC 59.310 50.000 0.00 0.00 33.49 3.01
1481 1614 5.497464 TGAACATATTCCTCACAAGGTCA 57.503 39.130 0.00 0.00 43.82 4.02
1483 1616 5.248248 TGAACATATTCCTCACAAGGTCAGA 59.752 40.000 0.00 0.00 43.82 3.27
1484 1617 5.762179 ACATATTCCTCACAAGGTCAGAA 57.238 39.130 0.00 0.00 43.82 3.02
1485 1618 6.319048 ACATATTCCTCACAAGGTCAGAAT 57.681 37.500 0.00 0.00 43.82 2.40
1501 1634 4.453819 GTCAGAATTGGAGAACTCAGGTTG 59.546 45.833 4.23 0.00 35.58 3.77
1555 1688 2.158914 ACATCACTGTCACAGAGTTGCA 60.159 45.455 13.14 0.00 35.18 4.08
1575 1708 0.744874 CGCCGAGGAAACAGAGGATA 59.255 55.000 0.00 0.00 0.00 2.59
1584 1717 6.627087 AGGAAACAGAGGATAGTGATTTCA 57.373 37.500 0.00 0.00 0.00 2.69
1631 1767 3.070576 GTGGCCTTCCATGTGGGC 61.071 66.667 3.32 13.70 45.62 5.36
1716 1852 1.002868 GAAGCAGAGCTCCTTGGCA 60.003 57.895 10.93 0.00 38.25 4.92
1719 1855 1.378250 GCAGAGCTCCTTGGCATGT 60.378 57.895 10.93 0.00 34.17 3.21
1815 1951 5.670485 CTTTGCTCCACTACATATACACCA 58.330 41.667 0.00 0.00 0.00 4.17
1844 1980 1.842562 CCTGATGAGATGGACAAGGGT 59.157 52.381 0.00 0.00 0.00 4.34
1935 5178 4.142093 TGAAGATGATCTGCGAAGACATGA 60.142 41.667 11.72 0.00 0.00 3.07
1944 5195 2.488937 TGCGAAGACATGATGTGCAAAT 59.511 40.909 1.23 0.00 0.00 2.32
1945 5196 3.688673 TGCGAAGACATGATGTGCAAATA 59.311 39.130 1.23 0.00 0.00 1.40
1955 5206 3.622612 TGATGTGCAAATATGTCTCCACG 59.377 43.478 0.00 0.00 0.00 4.94
2368 5644 2.670148 CCGGGTGGAAAGCCTAGCT 61.670 63.158 0.00 0.00 37.89 3.32
2369 5645 1.335132 CCGGGTGGAAAGCCTAGCTA 61.335 60.000 0.00 0.00 35.69 3.32
2370 5646 0.105039 CGGGTGGAAAGCCTAGCTAG 59.895 60.000 14.20 14.20 38.25 3.42
2371 5647 0.179043 GGGTGGAAAGCCTAGCTAGC 60.179 60.000 15.74 6.62 38.25 3.42
2563 5839 5.278808 GGGCCTCGATTTCTAAAACTTTGTT 60.279 40.000 0.84 0.00 0.00 2.83
2689 5965 2.558313 GCTGCGCTGGTGAAGTTC 59.442 61.111 16.47 0.00 0.00 3.01
2748 6024 3.708403 ACACCAGCTCAATCATGAAGA 57.292 42.857 0.00 0.00 34.49 2.87
2779 6055 3.507162 TGCTTGTCTTGGATCCTTCAA 57.493 42.857 14.23 11.31 0.00 2.69
2885 6161 8.646900 TCCCACAAAAGCAATAAGTAATTTTCT 58.353 29.630 0.00 0.00 0.00 2.52
2886 6162 9.921637 CCCACAAAAGCAATAAGTAATTTTCTA 57.078 29.630 0.00 0.00 0.00 2.10
2939 6215 8.462016 AGCAGTTGAATCCTTCATATTTTACAC 58.538 33.333 0.00 0.00 39.84 2.90
3043 6319 9.825972 CGAAGAACAACATTTATCAACAGTTAT 57.174 29.630 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.364653 ACTTTAGTATAAAGTCGGGTCATCTAT 57.635 33.333 8.72 0.00 35.76 1.98
3 4 8.757982 ACTTTAGTATAAAGTCGGGTCATCTA 57.242 34.615 8.72 0.00 35.76 1.98
4 5 7.657023 ACTTTAGTATAAAGTCGGGTCATCT 57.343 36.000 8.72 0.00 35.76 2.90
5 6 9.460906 CTAACTTTAGTATAAAGTCGGGTCATC 57.539 37.037 13.67 0.00 39.36 2.92
6 7 8.975295 ACTAACTTTAGTATAAAGTCGGGTCAT 58.025 33.333 13.67 1.94 41.92 3.06
7 8 8.353423 ACTAACTTTAGTATAAAGTCGGGTCA 57.647 34.615 13.67 0.00 41.92 4.02
8 9 9.723447 GTACTAACTTTAGTATAAAGTCGGGTC 57.277 37.037 13.67 4.27 45.11 4.46
9 10 9.243105 TGTACTAACTTTAGTATAAAGTCGGGT 57.757 33.333 13.67 13.72 45.11 5.28
30 31 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
31 32 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
32 33 9.219603 CTCCAAAATAGATGACTCAACTTTGTA 57.780 33.333 0.00 0.00 0.00 2.41
33 34 7.175641 CCTCCAAAATAGATGACTCAACTTTGT 59.824 37.037 0.00 0.00 0.00 2.83
34 35 7.362401 CCCTCCAAAATAGATGACTCAACTTTG 60.362 40.741 0.00 0.00 0.00 2.77
35 36 6.660949 CCCTCCAAAATAGATGACTCAACTTT 59.339 38.462 0.00 0.00 0.00 2.66
36 37 6.012508 TCCCTCCAAAATAGATGACTCAACTT 60.013 38.462 0.00 0.00 0.00 2.66
37 38 5.488919 TCCCTCCAAAATAGATGACTCAACT 59.511 40.000 0.00 0.00 0.00 3.16
38 39 5.745227 TCCCTCCAAAATAGATGACTCAAC 58.255 41.667 0.00 0.00 0.00 3.18
39 40 5.488919 ACTCCCTCCAAAATAGATGACTCAA 59.511 40.000 0.00 0.00 0.00 3.02
40 41 5.032846 ACTCCCTCCAAAATAGATGACTCA 58.967 41.667 0.00 0.00 0.00 3.41
41 42 5.622346 ACTCCCTCCAAAATAGATGACTC 57.378 43.478 0.00 0.00 0.00 3.36
42 43 7.420680 CCAATACTCCCTCCAAAATAGATGACT 60.421 40.741 0.00 0.00 0.00 3.41
43 44 6.712547 CCAATACTCCCTCCAAAATAGATGAC 59.287 42.308 0.00 0.00 0.00 3.06
44 45 6.619437 TCCAATACTCCCTCCAAAATAGATGA 59.381 38.462 0.00 0.00 0.00 2.92
45 46 6.712547 GTCCAATACTCCCTCCAAAATAGATG 59.287 42.308 0.00 0.00 0.00 2.90
46 47 6.389869 TGTCCAATACTCCCTCCAAAATAGAT 59.610 38.462 0.00 0.00 0.00 1.98
47 48 5.729229 TGTCCAATACTCCCTCCAAAATAGA 59.271 40.000 0.00 0.00 0.00 1.98
48 49 6.001449 TGTCCAATACTCCCTCCAAAATAG 57.999 41.667 0.00 0.00 0.00 1.73
49 50 6.395780 TTGTCCAATACTCCCTCCAAAATA 57.604 37.500 0.00 0.00 0.00 1.40
50 51 4.946160 TGTCCAATACTCCCTCCAAAAT 57.054 40.909 0.00 0.00 0.00 1.82
51 52 4.733077 TTGTCCAATACTCCCTCCAAAA 57.267 40.909 0.00 0.00 0.00 2.44
52 53 4.044065 ACATTGTCCAATACTCCCTCCAAA 59.956 41.667 0.00 0.00 0.00 3.28
53 54 3.591527 ACATTGTCCAATACTCCCTCCAA 59.408 43.478 0.00 0.00 0.00 3.53
54 55 3.189606 ACATTGTCCAATACTCCCTCCA 58.810 45.455 0.00 0.00 0.00 3.86
55 56 3.933861 ACATTGTCCAATACTCCCTCC 57.066 47.619 0.00 0.00 0.00 4.30
56 57 6.426646 AGATACATTGTCCAATACTCCCTC 57.573 41.667 0.00 0.00 0.00 4.30
57 58 7.931015 TTAGATACATTGTCCAATACTCCCT 57.069 36.000 0.00 0.00 0.00 4.20
58 59 8.974060 TTTTAGATACATTGTCCAATACTCCC 57.026 34.615 0.00 0.00 0.00 4.30
96 97 5.245751 AGCATGTGTGTTGATATTTTGGGAA 59.754 36.000 0.00 0.00 0.00 3.97
142 143 3.135414 ACGGATTTTGTGCATCAATCG 57.865 42.857 0.00 2.22 35.84 3.34
193 194 9.128107 CACAAACTAATGCAATTACTACCTTTG 57.872 33.333 0.00 0.00 37.87 2.77
386 406 4.735369 TGGGCTTTATCTTGTTCCTTTGA 58.265 39.130 0.00 0.00 0.00 2.69
426 446 8.192774 TCAATTGGCAAGCTAAGAATATCAAAG 58.807 33.333 5.96 0.00 0.00 2.77
427 447 8.065473 TCAATTGGCAAGCTAAGAATATCAAA 57.935 30.769 5.96 0.00 0.00 2.69
428 448 7.643569 TCAATTGGCAAGCTAAGAATATCAA 57.356 32.000 5.96 0.00 0.00 2.57
430 450 7.483307 TGTTCAATTGGCAAGCTAAGAATATC 58.517 34.615 5.96 0.00 0.00 1.63
431 451 7.408756 TGTTCAATTGGCAAGCTAAGAATAT 57.591 32.000 5.96 0.00 0.00 1.28
432 452 6.832520 TGTTCAATTGGCAAGCTAAGAATA 57.167 33.333 5.96 1.31 0.00 1.75
473 525 5.432680 AGCAAGCTGGCAGTATCATATAT 57.567 39.130 17.28 0.00 35.83 0.86
474 526 4.897509 AGCAAGCTGGCAGTATCATATA 57.102 40.909 17.28 0.00 35.83 0.86
475 527 3.784511 AGCAAGCTGGCAGTATCATAT 57.215 42.857 17.28 0.00 35.83 1.78
476 528 4.687901 TTAGCAAGCTGGCAGTATCATA 57.312 40.909 17.28 1.76 35.83 2.15
477 529 3.565764 TTAGCAAGCTGGCAGTATCAT 57.434 42.857 17.28 2.74 35.83 2.45
478 530 3.565764 ATTAGCAAGCTGGCAGTATCA 57.434 42.857 17.28 0.00 35.83 2.15
483 535 2.223665 GCCTTAATTAGCAAGCTGGCAG 60.224 50.000 17.28 10.94 38.99 4.85
486 538 2.360165 CCAGCCTTAATTAGCAAGCTGG 59.640 50.000 22.16 22.16 39.09 4.85
487 539 3.282021 TCCAGCCTTAATTAGCAAGCTG 58.718 45.455 15.61 15.61 32.09 4.24
592 648 2.004017 AGTTTTGCTCACGACACGAAA 58.996 42.857 0.00 0.00 0.00 3.46
594 650 1.326245 CAAGTTTTGCTCACGACACGA 59.674 47.619 0.00 0.00 0.00 4.35
595 651 1.594518 CCAAGTTTTGCTCACGACACG 60.595 52.381 0.00 0.00 0.00 4.49
596 652 1.668751 TCCAAGTTTTGCTCACGACAC 59.331 47.619 0.00 0.00 0.00 3.67
614 670 9.755122 AAAATAAACTATAATAGCCAGGGATCC 57.245 33.333 1.92 1.92 0.00 3.36
771 871 2.203139 TGTCGTGGGTGGCTTGTG 60.203 61.111 0.00 0.00 0.00 3.33
772 872 2.203153 GTGTCGTGGGTGGCTTGT 60.203 61.111 0.00 0.00 0.00 3.16
773 873 2.702751 TACGTGTCGTGGGTGGCTTG 62.703 60.000 0.00 0.00 41.39 4.01
774 874 2.030490 TTACGTGTCGTGGGTGGCTT 62.030 55.000 0.00 0.00 41.39 4.35
776 876 2.029369 TTACGTGTCGTGGGTGGC 59.971 61.111 0.00 0.00 41.39 5.01
777 877 1.665599 GGTTACGTGTCGTGGGTGG 60.666 63.158 0.00 0.00 41.39 4.61
778 878 0.942410 CAGGTTACGTGTCGTGGGTG 60.942 60.000 0.00 0.00 41.39 4.61
786 886 1.623811 AGAAGATGCCAGGTTACGTGT 59.376 47.619 0.00 0.00 0.00 4.49
847 947 2.159462 GGATCCTTTGCTTTGCTTCGAG 60.159 50.000 3.84 0.00 0.00 4.04
872 977 5.180117 TCTGATAAGACTTGCAAGTTTCTGC 59.820 40.000 31.58 18.78 39.88 4.26
936 1041 8.850156 ACAAGCAAAGTTAGTTAATGAATGAGT 58.150 29.630 0.00 0.00 0.00 3.41
1067 1194 2.159327 ATATACTAAACCCCGTGCGC 57.841 50.000 0.00 0.00 0.00 6.09
1100 1227 0.531532 CAATGGCAGAGGTAGAGCGG 60.532 60.000 0.00 0.00 0.00 5.52
1112 1239 3.965258 ACCCTGGCGACAATGGCA 61.965 61.111 6.40 0.00 42.06 4.92
1118 1245 3.625897 CTCACCACCCTGGCGACA 61.626 66.667 0.00 0.00 42.67 4.35
1146 1273 0.738975 TACCCGTCGATCTTGAGCAG 59.261 55.000 0.00 0.00 0.00 4.24
1188 1315 2.111384 AGACTCGATGTGCCTACCATT 58.889 47.619 0.00 0.00 0.00 3.16
1196 1323 1.649664 AGATGCAAGACTCGATGTGC 58.350 50.000 0.00 0.00 37.51 4.57
1197 1324 2.606725 GGAAGATGCAAGACTCGATGTG 59.393 50.000 0.00 0.00 0.00 3.21
1203 1330 2.606725 CGACATGGAAGATGCAAGACTC 59.393 50.000 0.00 0.00 0.00 3.36
1205 1332 1.667724 CCGACATGGAAGATGCAAGAC 59.332 52.381 0.00 0.00 42.00 3.01
1233 1360 1.264288 GTAATACTTGATGCGCCAGGC 59.736 52.381 4.18 0.00 43.96 4.85
1234 1361 1.873591 GGTAATACTTGATGCGCCAGG 59.126 52.381 4.18 0.00 0.00 4.45
1241 1368 2.616842 GCCGTTGGGGTAATACTTGATG 59.383 50.000 0.00 0.00 38.44 3.07
1263 1390 5.210715 GCAATTGGAATTATCTGAGCTTCG 58.789 41.667 7.72 0.00 0.00 3.79
1264 1391 6.140303 TGCAATTGGAATTATCTGAGCTTC 57.860 37.500 7.72 0.00 0.00 3.86
1265 1392 6.726490 ATGCAATTGGAATTATCTGAGCTT 57.274 33.333 2.94 0.00 0.00 3.74
1266 1393 7.889073 AGATATGCAATTGGAATTATCTGAGCT 59.111 33.333 17.43 0.00 0.00 4.09
1276 1403 7.834881 ATGAAGACAGATATGCAATTGGAAT 57.165 32.000 2.94 0.00 0.00 3.01
1278 1405 6.829811 TGAATGAAGACAGATATGCAATTGGA 59.170 34.615 7.72 4.46 0.00 3.53
1285 1412 5.749620 CAAGCTGAATGAAGACAGATATGC 58.250 41.667 0.00 0.00 36.38 3.14
1309 1439 1.470098 GCAAGTCCATGCTAACACTGG 59.530 52.381 0.00 0.00 43.06 4.00
1362 1495 0.753867 TCCAGTAAACCGAGCACACA 59.246 50.000 0.00 0.00 0.00 3.72
1365 1498 2.836944 GGTCCAGTAAACCGAGCAC 58.163 57.895 0.00 0.00 0.00 4.40
1414 1547 3.493129 CGTGAAAATTCTGTCGAAGGTGA 59.507 43.478 0.00 0.00 31.60 4.02
1422 1555 0.526211 GGGGCCGTGAAAATTCTGTC 59.474 55.000 0.00 0.00 0.00 3.51
1429 1562 1.228429 CCTTCAGGGGCCGTGAAAA 60.228 57.895 33.64 18.91 33.56 2.29
1449 1582 2.689983 GGAATATGTTCAAGCCCCACTG 59.310 50.000 4.48 0.00 36.01 3.66
1450 1583 2.582636 AGGAATATGTTCAAGCCCCACT 59.417 45.455 4.48 0.00 36.01 4.00
1451 1584 2.952310 GAGGAATATGTTCAAGCCCCAC 59.048 50.000 4.48 0.00 36.01 4.61
1459 1592 5.248248 TCTGACCTTGTGAGGAATATGTTCA 59.752 40.000 4.48 0.00 46.74 3.18
1461 1594 5.762179 TCTGACCTTGTGAGGAATATGTT 57.238 39.130 0.00 0.00 46.74 2.71
1465 1598 5.250543 TCCAATTCTGACCTTGTGAGGAATA 59.749 40.000 0.00 0.00 46.74 1.75
1470 1603 4.277515 TCTCCAATTCTGACCTTGTGAG 57.722 45.455 9.19 9.19 0.00 3.51
1481 1614 3.416156 GCAACCTGAGTTCTCCAATTCT 58.584 45.455 0.00 0.00 32.45 2.40
1483 1616 2.108952 AGGCAACCTGAGTTCTCCAATT 59.891 45.455 0.00 0.00 32.45 2.32
1484 1617 1.707427 AGGCAACCTGAGTTCTCCAAT 59.293 47.619 0.00 0.00 32.45 3.16
1485 1618 1.072331 GAGGCAACCTGAGTTCTCCAA 59.928 52.381 0.00 0.00 31.76 3.53
1501 1634 1.004440 AAGCAGTCGTCCTTGAGGC 60.004 57.895 0.00 0.00 34.44 4.70
1551 1684 2.203084 TGTTTCCTCGGCGTGCAA 60.203 55.556 6.85 0.00 0.00 4.08
1555 1688 1.258445 ATCCTCTGTTTCCTCGGCGT 61.258 55.000 6.85 0.00 0.00 5.68
1575 1708 2.834549 ACAGGAGATCGGTGAAATCACT 59.165 45.455 12.87 0.00 45.73 3.41
1679 1815 1.174783 CTGCTGCTGCCTTCAAGATT 58.825 50.000 13.47 0.00 38.71 2.40
1716 1852 3.173965 TCTTCTTCTCCCTTTCCGACAT 58.826 45.455 0.00 0.00 0.00 3.06
1719 1855 3.258622 GTCTTCTTCTTCTCCCTTTCCGA 59.741 47.826 0.00 0.00 0.00 4.55
1755 1891 2.558795 CCTCCATGTCGTCGATCCTTAT 59.441 50.000 0.00 0.00 0.00 1.73
1815 1951 2.628178 CCATCTCATCAGGCAATGCATT 59.372 45.455 5.99 5.99 0.00 3.56
1844 1980 0.674269 TTGCTGTCGCTGCATCATCA 60.674 50.000 10.95 0.00 38.06 3.07
1886 5129 2.894126 CTCCATCTTGTACCTATCCGCT 59.106 50.000 0.00 0.00 0.00 5.52
1935 5178 3.872696 TCGTGGAGACATATTTGCACAT 58.127 40.909 0.00 0.00 46.14 3.21
1944 5195 1.202348 CACTGTGCTCGTGGAGACATA 59.798 52.381 0.00 0.00 46.14 2.29
1945 5196 0.037882 CACTGTGCTCGTGGAGACAT 60.038 55.000 0.00 0.00 46.14 3.06
1955 5206 0.721718 GCGTGGTTATCACTGTGCTC 59.278 55.000 2.12 0.00 43.94 4.26
2368 5644 4.581105 CCACGGAGGCTAGAGCTA 57.419 61.111 0.81 0.00 41.70 3.32
2483 5759 1.133668 GCTTGGCATGGAATAGGAGGT 60.134 52.381 2.33 0.00 0.00 3.85
2563 5839 0.179059 TCAAGTGAAGGTTGCGCTGA 60.179 50.000 9.73 0.00 0.00 4.26
2597 5873 2.165030 GCAGTGATTGTTTGGGATGAGG 59.835 50.000 0.00 0.00 0.00 3.86
2748 6024 3.079578 CAAGACAAGCATCAGGTGTCAT 58.920 45.455 5.88 0.00 32.46 3.06
2846 6122 5.605534 CTTTTGTGGGATATCATCGAGTCT 58.394 41.667 4.83 0.00 0.00 3.24
3043 6319 6.682423 CATGATTACATGCAAAGTCCACTA 57.318 37.500 0.00 0.00 45.51 2.74


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

AutoCloner maintained by Alex Coulton.