Multiple sequence alignment - TraesCS1B01G201300

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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 TraesCS1B01G201300 chr1B 100.000 2300 0 0 1 2300 360513226 360510927 0.000000e+00 4248
1 TraesCS1B01G201300 chr1B 87.906 893 92 10 1423 2300 178281781 178280890 0.000000e+00 1037
2 TraesCS1B01G201300 chr1B 84.245 914 111 26 1412 2300 272955103 272956008 0.000000e+00 859
3 TraesCS1B01G201300 chr1D 92.111 1331 57 28 1 1317 252566177 252567473 0.000000e+00 1832
4 TraesCS1B01G201300 chr1D 82.561 367 56 7 964 1326 252596072 252596434 1.330000e-82 316
5 TraesCS1B01G201300 chr1A 87.313 938 49 28 18 946 323894275 323895151 0.000000e+00 1009
6 TraesCS1B01G201300 chr1A 90.395 354 12 2 1000 1331 323895148 323895501 1.620000e-121 446
7 TraesCS1B01G201300 chr1A 83.106 367 54 7 964 1326 323961200 323961562 6.130000e-86 327
8 TraesCS1B01G201300 chr5B 86.576 879 114 4 1424 2300 9944437 9943561 0.000000e+00 966
9 TraesCS1B01G201300 chr5B 84.222 900 113 22 1424 2298 400117405 400116510 0.000000e+00 848
10 TraesCS1B01G201300 chr5B 83.889 900 115 24 1424 2299 268806479 268805586 0.000000e+00 832
11 TraesCS1B01G201300 chr5B 82.883 888 127 20 1423 2293 248054988 248055867 0.000000e+00 774
12 TraesCS1B01G201300 chr4B 86.000 900 101 17 1421 2300 290569830 290568936 0.000000e+00 941
13 TraesCS1B01G201300 chr3B 82.720 897 128 23 1424 2300 226518260 226519149 0.000000e+00 773
14 TraesCS1B01G201300 chr3B 85.579 423 55 5 1421 1838 414902661 414902240 2.710000e-119 438
15 TraesCS1B01G201300 chr2B 87.793 639 73 5 1666 2300 174301826 174302463 0.000000e+00 743
16 TraesCS1B01G201300 chr3D 88.947 380 33 7 1421 1793 255400297 255399920 5.790000e-126 460
17 TraesCS1B01G201300 chr6D 88.220 382 36 7 1421 1798 240912715 240912339 4.510000e-122 448


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 TraesCS1B01G201300 chr1B 360510927 360513226 2299 True 4248.0 4248 100.000 1 2300 1 chr1B.!!$R2 2299
1 TraesCS1B01G201300 chr1B 178280890 178281781 891 True 1037.0 1037 87.906 1423 2300 1 chr1B.!!$R1 877
2 TraesCS1B01G201300 chr1B 272955103 272956008 905 False 859.0 859 84.245 1412 2300 1 chr1B.!!$F1 888
3 TraesCS1B01G201300 chr1D 252566177 252567473 1296 False 1832.0 1832 92.111 1 1317 1 chr1D.!!$F1 1316
4 TraesCS1B01G201300 chr1A 323894275 323895501 1226 False 727.5 1009 88.854 18 1331 2 chr1A.!!$F2 1313
5 TraesCS1B01G201300 chr5B 9943561 9944437 876 True 966.0 966 86.576 1424 2300 1 chr5B.!!$R1 876
6 TraesCS1B01G201300 chr5B 400116510 400117405 895 True 848.0 848 84.222 1424 2298 1 chr5B.!!$R3 874
7 TraesCS1B01G201300 chr5B 268805586 268806479 893 True 832.0 832 83.889 1424 2299 1 chr5B.!!$R2 875
8 TraesCS1B01G201300 chr5B 248054988 248055867 879 False 774.0 774 82.883 1423 2293 1 chr5B.!!$F1 870
9 TraesCS1B01G201300 chr4B 290568936 290569830 894 True 941.0 941 86.000 1421 2300 1 chr4B.!!$R1 879
10 TraesCS1B01G201300 chr3B 226518260 226519149 889 False 773.0 773 82.720 1424 2300 1 chr3B.!!$F1 876
11 TraesCS1B01G201300 chr2B 174301826 174302463 637 False 743.0 743 87.793 1666 2300 1 chr2B.!!$F1 634

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
56 57 0.25589 CCATTGGTGTGTCCCTAGGG 59.744 60.0 23.22 23.22 34.77 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1414 0.034896 CACTCAGTAACAAGGCCCGT 59.965 55.0 0.0 0.0 0.0 5.28 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
51 52 3.056891 CACATTAACCATTGGTGTGTCCC 60.057 47.826 9.62 0.00 35.34 4.46
53 54 4.043561 ACATTAACCATTGGTGTGTCCCTA 59.956 41.667 9.62 0.00 35.34 3.53
54 55 2.879103 AACCATTGGTGTGTCCCTAG 57.121 50.000 9.62 0.00 35.34 3.02
55 56 0.991920 ACCATTGGTGTGTCCCTAGG 59.008 55.000 7.76 0.06 32.98 3.02
56 57 0.255890 CCATTGGTGTGTCCCTAGGG 59.744 60.000 23.22 23.22 34.77 3.53
57 58 0.991920 CATTGGTGTGTCCCTAGGGT 59.008 55.000 27.58 1.33 36.47 4.34
58 59 0.991920 ATTGGTGTGTCCCTAGGGTG 59.008 55.000 27.58 2.85 36.47 4.61
59 60 1.131303 TTGGTGTGTCCCTAGGGTGG 61.131 60.000 27.58 2.02 36.47 4.61
60 61 1.229400 GGTGTGTCCCTAGGGTGGA 60.229 63.158 27.58 5.53 36.47 4.02
61 62 0.620700 GGTGTGTCCCTAGGGTGGAT 60.621 60.000 27.58 0.00 33.65 3.41
62 63 1.343681 GGTGTGTCCCTAGGGTGGATA 60.344 57.143 27.58 4.67 33.65 2.59
105 106 1.271762 ACAGGCACAGCATTCATCACT 60.272 47.619 0.00 0.00 0.00 3.41
122 123 3.485394 TCACTGGCATTTAGTTTGCTGA 58.515 40.909 0.00 0.00 40.03 4.26
199 200 4.367386 CCAACAATGGCAAGATTCTCTC 57.633 45.455 0.00 0.00 40.58 3.20
200 201 3.760151 CCAACAATGGCAAGATTCTCTCA 59.240 43.478 0.00 0.00 40.58 3.27
201 202 4.401519 CCAACAATGGCAAGATTCTCTCAT 59.598 41.667 0.00 0.00 40.58 2.90
202 203 5.340803 CAACAATGGCAAGATTCTCTCATG 58.659 41.667 0.00 0.00 0.00 3.07
203 204 3.380637 ACAATGGCAAGATTCTCTCATGC 59.619 43.478 0.00 0.32 45.63 4.06
204 205 3.579534 ATGGCAAGATTCTCTCATGCT 57.420 42.857 7.74 0.00 45.64 3.79
256 257 1.931172 CAACGTTGGTCACTTCGAAGT 59.069 47.619 24.93 24.93 40.60 3.01
333 334 0.817634 CTTCTGGCCAACGTGACCAA 60.818 55.000 7.01 0.00 31.81 3.67
344 345 1.152756 GTGACCAAACCCCAGCAGT 60.153 57.895 0.00 0.00 0.00 4.40
349 350 1.427368 ACCAAACCCCAGCAGTATCAA 59.573 47.619 0.00 0.00 0.00 2.57
485 495 4.593864 GCCTCCGCCTCCGTCATC 62.594 72.222 0.00 0.00 0.00 2.92
486 496 4.271816 CCTCCGCCTCCGTCATCG 62.272 72.222 0.00 0.00 0.00 3.84
487 497 4.933064 CTCCGCCTCCGTCATCGC 62.933 72.222 0.00 0.00 35.54 4.58
491 501 4.148825 GCCTCCGTCATCGCCACT 62.149 66.667 0.00 0.00 35.54 4.00
492 502 2.105128 CCTCCGTCATCGCCACTC 59.895 66.667 0.00 0.00 35.54 3.51
493 503 2.418910 CCTCCGTCATCGCCACTCT 61.419 63.158 0.00 0.00 35.54 3.24
494 504 1.064946 CTCCGTCATCGCCACTCTC 59.935 63.158 0.00 0.00 35.54 3.20
495 505 2.278206 CCGTCATCGCCACTCTCG 60.278 66.667 0.00 0.00 35.54 4.04
649 683 5.767665 ACCACATTGTATCTGCAGTTTACAA 59.232 36.000 29.56 29.56 39.41 2.41
696 735 8.863049 GCAATGTAACACTGGATTTTTATCTTG 58.137 33.333 0.00 0.00 0.00 3.02
763 804 7.440523 AGTATTCTCTCGATTTTTGTTTGCT 57.559 32.000 0.00 0.00 0.00 3.91
877 922 6.054941 TCATCTTTCACAGCTGTAAACTCAA 58.945 36.000 21.20 5.32 0.00 3.02
952 997 0.610232 AGTTGGGTTGATGAGCAGGC 60.610 55.000 0.00 0.00 0.00 4.85
954 999 2.079088 TTGGGTTGATGAGCAGGCCA 62.079 55.000 5.01 0.00 0.00 5.36
984 1029 2.158842 AGAGCAGCAGTGTTCAGTTTCT 60.159 45.455 0.00 0.00 36.40 2.52
1003 1048 5.350504 TTCTTTTTGTTTGGCCAAGATGA 57.649 34.783 19.48 0.00 0.00 2.92
1074 1119 3.722295 ACAAATGTGCCGTCGCCG 61.722 61.111 0.00 0.00 0.00 6.46
1333 1403 8.589335 TCGACTTAATCTTGTATCCATTTAGC 57.411 34.615 0.00 0.00 0.00 3.09
1334 1404 7.656137 TCGACTTAATCTTGTATCCATTTAGCC 59.344 37.037 0.00 0.00 0.00 3.93
1335 1405 7.095187 CGACTTAATCTTGTATCCATTTAGCCC 60.095 40.741 0.00 0.00 0.00 5.19
1336 1406 7.816411 ACTTAATCTTGTATCCATTTAGCCCT 58.184 34.615 0.00 0.00 0.00 5.19
1337 1407 8.282256 ACTTAATCTTGTATCCATTTAGCCCTT 58.718 33.333 0.00 0.00 0.00 3.95
1338 1408 6.966534 AATCTTGTATCCATTTAGCCCTTG 57.033 37.500 0.00 0.00 0.00 3.61
1339 1409 5.708736 TCTTGTATCCATTTAGCCCTTGA 57.291 39.130 0.00 0.00 0.00 3.02
1340 1410 6.073447 TCTTGTATCCATTTAGCCCTTGAA 57.927 37.500 0.00 0.00 0.00 2.69
1341 1411 6.489603 TCTTGTATCCATTTAGCCCTTGAAA 58.510 36.000 0.00 0.00 0.00 2.69
1342 1412 6.951198 TCTTGTATCCATTTAGCCCTTGAAAA 59.049 34.615 0.00 0.00 0.00 2.29
1343 1413 7.453126 TCTTGTATCCATTTAGCCCTTGAAAAA 59.547 33.333 0.00 0.00 0.00 1.94
1360 1430 2.351706 AAAACGGGCCTTGTTACTGA 57.648 45.000 13.17 0.00 0.00 3.41
1361 1431 1.892209 AAACGGGCCTTGTTACTGAG 58.108 50.000 13.17 0.00 0.00 3.35
1362 1432 0.763035 AACGGGCCTTGTTACTGAGT 59.237 50.000 11.49 0.00 0.00 3.41
1363 1433 0.034896 ACGGGCCTTGTTACTGAGTG 59.965 55.000 0.84 0.00 0.00 3.51
1364 1434 1.298859 CGGGCCTTGTTACTGAGTGC 61.299 60.000 0.84 0.00 0.00 4.40
1365 1435 0.250727 GGGCCTTGTTACTGAGTGCA 60.251 55.000 0.84 0.00 0.00 4.57
1377 1447 3.637998 CTGAGTGCAGTGCTTTTGATT 57.362 42.857 17.60 0.00 37.37 2.57
1378 1448 3.973657 CTGAGTGCAGTGCTTTTGATTT 58.026 40.909 17.60 0.00 37.37 2.17
1379 1449 3.968649 TGAGTGCAGTGCTTTTGATTTC 58.031 40.909 17.60 3.24 0.00 2.17
1380 1450 3.633525 TGAGTGCAGTGCTTTTGATTTCT 59.366 39.130 17.60 1.06 0.00 2.52
1381 1451 4.225208 GAGTGCAGTGCTTTTGATTTCTC 58.775 43.478 17.60 6.43 0.00 2.87
1382 1452 3.633525 AGTGCAGTGCTTTTGATTTCTCA 59.366 39.130 17.60 0.00 0.00 3.27
1383 1453 4.098349 AGTGCAGTGCTTTTGATTTCTCAA 59.902 37.500 17.60 0.00 39.62 3.02
1384 1454 4.805192 GTGCAGTGCTTTTGATTTCTCAAA 59.195 37.500 17.60 0.00 46.92 2.69
1395 1465 7.510549 TTTGATTTCTCAAACGATCCTCTTT 57.489 32.000 0.00 0.00 44.46 2.52
1396 1466 8.615878 TTTGATTTCTCAAACGATCCTCTTTA 57.384 30.769 0.00 0.00 44.46 1.85
1397 1467 7.596749 TGATTTCTCAAACGATCCTCTTTAC 57.403 36.000 0.00 0.00 0.00 2.01
1398 1468 7.386851 TGATTTCTCAAACGATCCTCTTTACT 58.613 34.615 0.00 0.00 0.00 2.24
1399 1469 8.528643 TGATTTCTCAAACGATCCTCTTTACTA 58.471 33.333 0.00 0.00 0.00 1.82
1400 1470 9.535878 GATTTCTCAAACGATCCTCTTTACTAT 57.464 33.333 0.00 0.00 0.00 2.12
1401 1471 9.892130 ATTTCTCAAACGATCCTCTTTACTATT 57.108 29.630 0.00 0.00 0.00 1.73
1402 1472 8.928270 TTCTCAAACGATCCTCTTTACTATTC 57.072 34.615 0.00 0.00 0.00 1.75
1403 1473 7.490000 TCTCAAACGATCCTCTTTACTATTCC 58.510 38.462 0.00 0.00 0.00 3.01
1404 1474 6.579865 TCAAACGATCCTCTTTACTATTCCC 58.420 40.000 0.00 0.00 0.00 3.97
1405 1475 6.383147 TCAAACGATCCTCTTTACTATTCCCT 59.617 38.462 0.00 0.00 0.00 4.20
1406 1476 6.408107 AACGATCCTCTTTACTATTCCCTC 57.592 41.667 0.00 0.00 0.00 4.30
1407 1477 5.707495 ACGATCCTCTTTACTATTCCCTCT 58.293 41.667 0.00 0.00 0.00 3.69
1408 1478 6.850234 ACGATCCTCTTTACTATTCCCTCTA 58.150 40.000 0.00 0.00 0.00 2.43
1409 1479 7.471890 ACGATCCTCTTTACTATTCCCTCTAT 58.528 38.462 0.00 0.00 0.00 1.98
1410 1480 7.951245 ACGATCCTCTTTACTATTCCCTCTATT 59.049 37.037 0.00 0.00 0.00 1.73
1411 1481 8.463607 CGATCCTCTTTACTATTCCCTCTATTC 58.536 40.741 0.00 0.00 0.00 1.75
1412 1482 8.673456 ATCCTCTTTACTATTCCCTCTATTCC 57.327 38.462 0.00 0.00 0.00 3.01
1413 1483 7.601942 TCCTCTTTACTATTCCCTCTATTCCA 58.398 38.462 0.00 0.00 0.00 3.53
1414 1484 8.242325 TCCTCTTTACTATTCCCTCTATTCCAT 58.758 37.037 0.00 0.00 0.00 3.41
1415 1485 9.548631 CCTCTTTACTATTCCCTCTATTCCATA 57.451 37.037 0.00 0.00 0.00 2.74
1433 1503 4.629634 TCCATAATGTAGTTGTTCGCACAG 59.370 41.667 0.00 0.00 33.22 3.66
1457 1528 1.436600 ACGTCACGTGTACTCTCGAT 58.563 50.000 16.51 1.79 39.18 3.59
1463 1534 0.589229 CGTGTACTCTCGATGTCGGC 60.589 60.000 2.25 0.00 40.29 5.54
1499 1572 0.452950 CACGTCGAAGGAGTCTCACG 60.453 60.000 0.00 5.22 36.65 4.35
1506 1579 0.832135 AAGGAGTCTCACGGGAAGCA 60.832 55.000 1.47 0.00 0.00 3.91
1560 1634 0.178912 ACCCGAAACCCTACACTCCT 60.179 55.000 0.00 0.00 0.00 3.69
1562 1636 1.263356 CCGAAACCCTACACTCCTGA 58.737 55.000 0.00 0.00 0.00 3.86
1664 1760 1.406180 TCTCCAACACGAAGAACGACA 59.594 47.619 0.00 0.00 45.77 4.35
1673 1789 3.000476 CACGAAGAACGACAAAGAACGAA 60.000 43.478 0.00 0.00 45.77 3.85
1740 1862 5.635417 TTGTGTGTTGTTGTTCAATCAGA 57.365 34.783 0.00 0.00 38.38 3.27
1756 1878 4.909696 ATCAGACGTCACCTCTTATCTG 57.090 45.455 19.50 2.96 35.87 2.90
1842 1964 4.950205 TCTAACCAAACTCGGACTTCTT 57.050 40.909 0.00 0.00 0.00 2.52
1874 1996 2.190578 GGATGTCCGGCTCTTGGG 59.809 66.667 0.00 0.00 0.00 4.12
1981 2103 9.498307 GACGAATTTTATATCAAAATCAACCGT 57.502 29.630 0.00 0.00 31.29 4.83
1994 2116 1.406180 TCAACCGTTCTCGACAAGACA 59.594 47.619 0.00 0.00 39.71 3.41
2003 2125 3.444916 TCTCGACAAGACACACAACTTC 58.555 45.455 0.00 0.00 0.00 3.01
2071 2193 3.753272 GGCTGTTTTCTAACATCTGCAGA 59.247 43.478 20.79 20.79 43.02 4.26
2110 2233 4.007457 CGGACTTCTACCCGGACA 57.993 61.111 0.73 0.00 41.89 4.02
2157 2281 0.325671 ACTGGACCCTGATCATCCGT 60.326 55.000 8.88 7.22 35.06 4.69
2159 2283 1.364171 GGACCCTGATCATCCGTCG 59.636 63.158 0.00 0.00 0.00 5.12
2250 2375 3.190327 CCGTCCAAACATTATTGCAGTGA 59.810 43.478 0.00 0.00 0.00 3.41
2252 2377 5.401550 CGTCCAAACATTATTGCAGTGAAT 58.598 37.500 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 3.495100 GCCAACATCTGTATCCACCCTAG 60.495 52.174 0.00 0.00 0.00 3.02
53 54 1.212935 GCCAACATCTGTATCCACCCT 59.787 52.381 0.00 0.00 0.00 4.34
54 55 1.064758 TGCCAACATCTGTATCCACCC 60.065 52.381 0.00 0.00 0.00 4.61
55 56 2.017049 GTGCCAACATCTGTATCCACC 58.983 52.381 0.00 0.00 0.00 4.61
56 57 2.679837 CAGTGCCAACATCTGTATCCAC 59.320 50.000 0.00 0.00 0.00 4.02
57 58 2.940971 GCAGTGCCAACATCTGTATCCA 60.941 50.000 2.85 0.00 31.53 3.41
58 59 1.672881 GCAGTGCCAACATCTGTATCC 59.327 52.381 2.85 0.00 31.53 2.59
59 60 2.611292 GAGCAGTGCCAACATCTGTATC 59.389 50.000 12.58 0.00 31.53 2.24
60 61 2.026915 TGAGCAGTGCCAACATCTGTAT 60.027 45.455 12.58 0.00 31.53 2.29
61 62 1.347378 TGAGCAGTGCCAACATCTGTA 59.653 47.619 12.58 0.00 31.53 2.74
62 63 0.109153 TGAGCAGTGCCAACATCTGT 59.891 50.000 12.58 0.00 31.53 3.41
105 106 8.093307 TGAATTTATTCAGCAAACTAAATGCCA 58.907 29.630 1.12 0.00 41.51 4.92
122 123 6.350906 CATTCCATTGTGGGCTGAATTTATT 58.649 36.000 0.00 0.00 38.32 1.40
159 160 1.453155 GCGAAGGGAAATGCTCTCAA 58.547 50.000 0.00 0.00 0.00 3.02
197 198 0.452184 CTGAGCCAGCAAAGCATGAG 59.548 55.000 0.00 0.00 0.00 2.90
198 199 0.963856 CCTGAGCCAGCAAAGCATGA 60.964 55.000 0.00 0.00 0.00 3.07
199 200 1.511305 CCTGAGCCAGCAAAGCATG 59.489 57.895 0.00 0.00 0.00 4.06
200 201 2.348888 GCCTGAGCCAGCAAAGCAT 61.349 57.895 0.00 0.00 0.00 3.79
201 202 2.987547 GCCTGAGCCAGCAAAGCA 60.988 61.111 0.00 0.00 0.00 3.91
202 203 2.675772 AGCCTGAGCCAGCAAAGC 60.676 61.111 0.00 0.00 41.25 3.51
203 204 1.002379 AGAGCCTGAGCCAGCAAAG 60.002 57.895 0.00 0.00 41.25 2.77
204 205 1.002868 GAGAGCCTGAGCCAGCAAA 60.003 57.895 0.00 0.00 41.25 3.68
256 257 1.984570 CTCGGCCTTCCTCTGTGGA 60.985 63.158 0.00 0.00 44.51 4.02
285 286 4.992511 GGCACCGGTGGCGTGTAA 62.993 66.667 40.73 0.00 46.08 2.41
333 334 1.063717 CCCATTGATACTGCTGGGGTT 60.064 52.381 0.00 0.00 43.91 4.11
344 345 4.224147 TCGAACCAAGAAGTCCCATTGATA 59.776 41.667 0.00 0.00 0.00 2.15
349 350 2.257207 TCTCGAACCAAGAAGTCCCAT 58.743 47.619 0.00 0.00 0.00 4.00
447 457 4.394712 GGCGAGAGTGGTGGTGGG 62.395 72.222 0.00 0.00 0.00 4.61
474 484 4.148825 AGTGGCGATGACGGAGGC 62.149 66.667 0.00 0.00 40.15 4.70
475 485 2.105128 GAGTGGCGATGACGGAGG 59.895 66.667 0.00 0.00 40.15 4.30
476 486 1.064946 GAGAGTGGCGATGACGGAG 59.935 63.158 0.00 0.00 40.15 4.63
477 487 2.761195 CGAGAGTGGCGATGACGGA 61.761 63.158 0.00 0.00 40.15 4.69
478 488 2.278206 CGAGAGTGGCGATGACGG 60.278 66.667 0.00 0.00 40.15 4.79
479 489 2.951745 GCGAGAGTGGCGATGACG 60.952 66.667 0.00 0.00 42.93 4.35
480 490 2.583593 GGCGAGAGTGGCGATGAC 60.584 66.667 0.00 0.00 0.00 3.06
504 514 2.514824 GGAGGCGAGAATGGTGGC 60.515 66.667 0.00 0.00 0.00 5.01
531 541 2.761195 CGAGAGTGGCGATGACGGA 61.761 63.158 0.00 0.00 40.15 4.69
532 542 2.278206 CGAGAGTGGCGATGACGG 60.278 66.667 0.00 0.00 40.15 4.79
533 543 2.951745 GCGAGAGTGGCGATGACG 60.952 66.667 0.00 0.00 42.93 4.35
534 544 2.583593 GGCGAGAGTGGCGATGAC 60.584 66.667 0.00 0.00 0.00 3.06
566 597 2.223665 GCTACACCCACGTGATAGTACC 60.224 54.545 19.30 4.20 43.14 3.34
649 683 9.034544 CATTGCTTTGAAAACTAGCTTAAAACT 57.965 29.630 0.00 0.00 35.93 2.66
696 735 3.391506 AAATTTCTCACTGGGCAAAGC 57.608 42.857 0.00 0.00 0.00 3.51
778 819 4.262938 GGTTTTCTGCCCTGAAGTACTACT 60.263 45.833 0.00 0.00 0.00 2.57
779 820 4.001652 GGTTTTCTGCCCTGAAGTACTAC 58.998 47.826 0.00 0.00 0.00 2.73
780 821 3.908103 AGGTTTTCTGCCCTGAAGTACTA 59.092 43.478 0.00 0.00 0.00 1.82
877 922 0.331278 TTTGTCCCGGAATCATGGCT 59.669 50.000 0.73 0.00 0.00 4.75
952 997 1.227205 GCTGCTCTCGGTGAGATGG 60.227 63.158 11.04 1.71 45.39 3.51
954 999 0.969917 ACTGCTGCTCTCGGTGAGAT 60.970 55.000 11.04 0.00 45.39 2.75
984 1029 4.405358 AGTCTCATCTTGGCCAAACAAAAA 59.595 37.500 20.91 1.23 0.00 1.94
1003 1048 3.648009 CGAAGAGCTTGAAGAACAGTCT 58.352 45.455 0.00 0.00 34.72 3.24
1074 1119 1.227383 CCTCCCCCATACACCAAGC 59.773 63.158 0.00 0.00 0.00 4.01
1075 1120 0.546598 GTCCTCCCCCATACACCAAG 59.453 60.000 0.00 0.00 0.00 3.61
1340 1410 2.621526 CTCAGTAACAAGGCCCGTTTTT 59.378 45.455 13.01 0.00 0.00 1.94
1341 1411 2.227194 CTCAGTAACAAGGCCCGTTTT 58.773 47.619 13.01 0.00 0.00 2.43
1342 1412 1.142262 ACTCAGTAACAAGGCCCGTTT 59.858 47.619 13.01 0.00 0.00 3.60
1343 1413 0.763035 ACTCAGTAACAAGGCCCGTT 59.237 50.000 12.45 12.45 0.00 4.44
1344 1414 0.034896 CACTCAGTAACAAGGCCCGT 59.965 55.000 0.00 0.00 0.00 5.28
1345 1415 1.298859 GCACTCAGTAACAAGGCCCG 61.299 60.000 0.00 0.00 0.00 6.13
1346 1416 0.250727 TGCACTCAGTAACAAGGCCC 60.251 55.000 0.00 0.00 0.00 5.80
1347 1417 1.160137 CTGCACTCAGTAACAAGGCC 58.840 55.000 0.00 0.00 35.61 5.19
1357 1427 3.637998 AATCAAAAGCACTGCACTCAG 57.362 42.857 3.30 0.00 45.71 3.35
1358 1428 3.633525 AGAAATCAAAAGCACTGCACTCA 59.366 39.130 3.30 0.00 0.00 3.41
1359 1429 4.225208 GAGAAATCAAAAGCACTGCACTC 58.775 43.478 3.30 0.00 0.00 3.51
1360 1430 3.633525 TGAGAAATCAAAAGCACTGCACT 59.366 39.130 3.30 0.00 0.00 4.40
1361 1431 3.968649 TGAGAAATCAAAAGCACTGCAC 58.031 40.909 3.30 0.00 0.00 4.57
1362 1432 4.652421 TTGAGAAATCAAAAGCACTGCA 57.348 36.364 3.30 0.00 0.00 4.41
1363 1433 4.085415 CGTTTGAGAAATCAAAAGCACTGC 60.085 41.667 5.07 0.00 40.70 4.40
1364 1434 5.273170 TCGTTTGAGAAATCAAAAGCACTG 58.727 37.500 10.51 0.00 40.70 3.66
1365 1435 5.499139 TCGTTTGAGAAATCAAAAGCACT 57.501 34.783 10.51 0.00 40.70 4.40
1366 1436 5.343325 GGATCGTTTGAGAAATCAAAAGCAC 59.657 40.000 10.51 7.57 40.70 4.40
1367 1437 5.241506 AGGATCGTTTGAGAAATCAAAAGCA 59.758 36.000 10.51 3.03 40.70 3.91
1368 1438 5.703876 AGGATCGTTTGAGAAATCAAAAGC 58.296 37.500 10.51 0.00 40.70 3.51
1369 1439 7.138692 AGAGGATCGTTTGAGAAATCAAAAG 57.861 36.000 5.07 7.49 42.67 2.27
1370 1440 7.510549 AAGAGGATCGTTTGAGAAATCAAAA 57.489 32.000 5.07 0.00 42.67 2.44
1371 1441 7.510549 AAAGAGGATCGTTTGAGAAATCAAA 57.489 32.000 0.00 0.00 42.67 2.69
1372 1442 7.878127 AGTAAAGAGGATCGTTTGAGAAATCAA 59.122 33.333 0.00 0.00 42.67 2.57
1373 1443 7.386851 AGTAAAGAGGATCGTTTGAGAAATCA 58.613 34.615 0.00 0.00 42.67 2.57
1374 1444 7.835634 AGTAAAGAGGATCGTTTGAGAAATC 57.164 36.000 0.00 0.00 42.67 2.17
1375 1445 9.892130 AATAGTAAAGAGGATCGTTTGAGAAAT 57.108 29.630 0.00 0.00 42.67 2.17
1376 1446 9.367444 GAATAGTAAAGAGGATCGTTTGAGAAA 57.633 33.333 0.00 0.00 42.67 2.52
1377 1447 7.980099 GGAATAGTAAAGAGGATCGTTTGAGAA 59.020 37.037 0.00 0.00 42.67 2.87
1378 1448 7.417570 GGGAATAGTAAAGAGGATCGTTTGAGA 60.418 40.741 0.00 0.00 42.67 3.27
1379 1449 6.702282 GGGAATAGTAAAGAGGATCGTTTGAG 59.298 42.308 0.00 0.00 42.67 3.02
1380 1450 6.383147 AGGGAATAGTAAAGAGGATCGTTTGA 59.617 38.462 0.00 0.00 42.67 2.69
1381 1451 6.583562 AGGGAATAGTAAAGAGGATCGTTTG 58.416 40.000 0.00 0.00 42.67 2.93
1382 1452 6.612049 AGAGGGAATAGTAAAGAGGATCGTTT 59.388 38.462 0.00 0.00 42.67 3.60
1383 1453 6.137559 AGAGGGAATAGTAAAGAGGATCGTT 58.862 40.000 0.00 0.00 42.67 3.85
1384 1454 5.707495 AGAGGGAATAGTAAAGAGGATCGT 58.293 41.667 0.00 0.00 42.67 3.73
1385 1455 7.948034 ATAGAGGGAATAGTAAAGAGGATCG 57.052 40.000 0.00 0.00 42.67 3.69
1386 1456 8.755028 GGAATAGAGGGAATAGTAAAGAGGATC 58.245 40.741 0.00 0.00 0.00 3.36
1387 1457 8.242325 TGGAATAGAGGGAATAGTAAAGAGGAT 58.758 37.037 0.00 0.00 0.00 3.24
1388 1458 7.601942 TGGAATAGAGGGAATAGTAAAGAGGA 58.398 38.462 0.00 0.00 0.00 3.71
1389 1459 7.857404 TGGAATAGAGGGAATAGTAAAGAGG 57.143 40.000 0.00 0.00 0.00 3.69
1396 1466 9.845214 ACTACATTATGGAATAGAGGGAATAGT 57.155 33.333 0.00 0.00 0.00 2.12
1399 1469 8.949421 ACAACTACATTATGGAATAGAGGGAAT 58.051 33.333 0.00 0.00 0.00 3.01
1400 1470 8.331931 ACAACTACATTATGGAATAGAGGGAA 57.668 34.615 0.00 0.00 0.00 3.97
1401 1471 7.931015 ACAACTACATTATGGAATAGAGGGA 57.069 36.000 0.00 0.00 0.00 4.20
1402 1472 7.385205 CGAACAACTACATTATGGAATAGAGGG 59.615 40.741 0.00 0.00 0.00 4.30
1403 1473 7.095607 GCGAACAACTACATTATGGAATAGAGG 60.096 40.741 0.00 0.00 0.00 3.69
1404 1474 7.438160 TGCGAACAACTACATTATGGAATAGAG 59.562 37.037 0.00 0.00 0.00 2.43
1405 1475 7.223971 GTGCGAACAACTACATTATGGAATAGA 59.776 37.037 0.00 0.00 0.00 1.98
1406 1476 7.011016 TGTGCGAACAACTACATTATGGAATAG 59.989 37.037 0.00 0.00 0.00 1.73
1407 1477 6.819146 TGTGCGAACAACTACATTATGGAATA 59.181 34.615 0.00 0.00 0.00 1.75
1408 1478 5.645929 TGTGCGAACAACTACATTATGGAAT 59.354 36.000 0.00 0.00 0.00 3.01
1409 1479 4.998033 TGTGCGAACAACTACATTATGGAA 59.002 37.500 0.00 0.00 0.00 3.53
1410 1480 4.570930 TGTGCGAACAACTACATTATGGA 58.429 39.130 0.00 0.00 0.00 3.41
1411 1481 4.201812 CCTGTGCGAACAACTACATTATGG 60.202 45.833 0.00 0.00 0.00 2.74
1412 1482 4.629634 TCCTGTGCGAACAACTACATTATG 59.370 41.667 0.00 0.00 0.00 1.90
1413 1483 4.827692 TCCTGTGCGAACAACTACATTAT 58.172 39.130 0.00 0.00 0.00 1.28
1414 1484 4.260139 TCCTGTGCGAACAACTACATTA 57.740 40.909 0.00 0.00 0.00 1.90
1415 1485 3.120321 TCCTGTGCGAACAACTACATT 57.880 42.857 0.00 0.00 0.00 2.71
1416 1486 2.806244 GTTCCTGTGCGAACAACTACAT 59.194 45.455 0.00 0.00 41.51 2.29
1417 1487 2.206750 GTTCCTGTGCGAACAACTACA 58.793 47.619 0.00 0.00 41.51 2.74
1418 1488 2.206750 TGTTCCTGTGCGAACAACTAC 58.793 47.619 0.00 0.00 46.92 2.73
1419 1489 2.605837 TGTTCCTGTGCGAACAACTA 57.394 45.000 0.00 0.00 46.92 2.24
1420 1490 3.469564 TGTTCCTGTGCGAACAACT 57.530 47.368 0.00 0.00 46.92 3.16
1451 1522 1.141665 CACCATGCCGACATCGAGA 59.858 57.895 2.09 0.00 43.02 4.04
1463 1534 3.807538 GAGCTGCGGTGCACCATG 61.808 66.667 34.16 22.95 33.79 3.66
1499 1572 1.298859 ACTTGCGAATCGTGCTTCCC 61.299 55.000 4.07 0.00 0.00 3.97
1537 1611 0.689055 GTGTAGGGTTTCGGGTCCTT 59.311 55.000 0.00 0.00 32.46 3.36
1560 1634 4.753662 CCGACGGGGTCCCTCTCA 62.754 72.222 8.15 0.00 0.00 3.27
1642 1717 1.679680 TCGTTCTTCGTGTTGGAGAGT 59.320 47.619 0.00 0.00 40.80 3.24
1664 1760 5.106436 ACGTTTTGTTCCTTCTTCGTTCTTT 60.106 36.000 0.00 0.00 0.00 2.52
1673 1789 7.562454 TTTTCATCTACGTTTTGTTCCTTCT 57.438 32.000 0.00 0.00 0.00 2.85
1709 1828 4.876125 ACAACAACACACAATCACAAACA 58.124 34.783 0.00 0.00 0.00 2.83
1756 1878 5.203060 AGAAGTCCATTCGCCTCTTATAC 57.797 43.478 0.00 0.00 43.16 1.47
1768 1890 5.701290 CCTTTTCTTGTACGAGAAGTCCATT 59.299 40.000 21.93 0.00 37.01 3.16
1981 2103 3.520290 AGTTGTGTGTCTTGTCGAGAA 57.480 42.857 0.00 0.00 35.79 2.87
1994 2116 4.016444 AGTGTTCAACATGGAAGTTGTGT 58.984 39.130 0.00 0.00 46.78 3.72
2003 2125 2.772568 TCGCAAAGTGTTCAACATGG 57.227 45.000 0.00 0.00 0.00 3.66
2019 2141 2.545532 CCTCAAGATGACCTCAGATCGC 60.546 54.545 0.00 0.00 0.00 4.58
2110 2233 2.765807 CCAGATGGAGGCCGGACT 60.766 66.667 11.50 11.50 37.39 3.85
2147 2271 0.317854 GCGATGACGACGGATGATCA 60.318 55.000 0.00 0.00 42.66 2.92
2157 2281 0.389817 CAGAAGGTTGGCGATGACGA 60.390 55.000 0.00 0.00 42.66 4.20
2159 2283 1.523758 AACAGAAGGTTGGCGATGAC 58.476 50.000 0.00 0.00 38.60 3.06
2231 2356 7.701539 ACTATTCACTGCAATAATGTTTGGA 57.298 32.000 0.00 0.00 0.00 3.53
2250 2375 6.578023 TGCAAAAGTTACAGGCAAAACTATT 58.422 32.000 0.00 0.00 34.91 1.73
2252 2377 5.584253 TGCAAAAGTTACAGGCAAAACTA 57.416 34.783 0.00 0.00 34.91 2.24


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

AutoCloner maintained by Alex Coulton.