Multiple sequence alignment - TraesCS1A01G343400

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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 TraesCS1A01G343400 chr1A 100.000 2642 0 0 1 2642 531987741 531985100 0.000000e+00 4879.0
1 TraesCS1A01G343400 chr1D 87.988 1998 132 45 21 1986 433465201 433463280 0.000000e+00 2261.0
2 TraesCS1A01G343400 chr1D 94.444 486 22 5 2159 2642 433462735 433462253 0.000000e+00 743.0
3 TraesCS1A01G343400 chr1B 87.275 2004 146 52 21 1986 585681408 585679476 0.000000e+00 2187.0
4 TraesCS1A01G343400 chr1B 94.467 488 20 5 2159 2642 585678895 585678411 0.000000e+00 745.0
5 TraesCS1A01G343400 chr3D 96.825 126 4 0 994 1119 384567792 384567667 7.410000e-51 211.0
6 TraesCS1A01G343400 chr3D 89.928 139 14 0 1504 1642 384567321 384567183 2.090000e-41 180.0
7 TraesCS1A01G343400 chr3D 82.911 158 27 0 1235 1392 384567571 384567414 2.740000e-30 143.0
8 TraesCS1A01G343400 chr3B 96.825 126 4 0 994 1119 499806135 499806010 7.410000e-51 211.0
9 TraesCS1A01G343400 chr3B 89.928 139 14 0 1504 1642 499805671 499805533 2.090000e-41 180.0
10 TraesCS1A01G343400 chr3B 82.468 154 27 0 1235 1388 499805913 499805760 4.590000e-28 135.0
11 TraesCS1A01G343400 chr3B 86.667 75 10 0 1562 1636 105367668 105367594 1.690000e-12 84.2
12 TraesCS1A01G343400 chr3A 96.032 126 5 0 994 1119 507120910 507120785 3.450000e-49 206.0
13 TraesCS1A01G343400 chr3A 89.928 139 14 0 1504 1642 507120447 507120309 2.090000e-41 180.0
14 TraesCS1A01G343400 chr3A 82.911 158 27 0 1235 1392 507120697 507120540 2.740000e-30 143.0


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 TraesCS1A01G343400 chr1A 531985100 531987741 2641 True 4879 4879 100.000 1 2642 1 chr1A.!!$R1 2641
1 TraesCS1A01G343400 chr1D 433462253 433465201 2948 True 1502 2261 91.216 21 2642 2 chr1D.!!$R1 2621
2 TraesCS1A01G343400 chr1B 585678411 585681408 2997 True 1466 2187 90.871 21 2642 2 chr1B.!!$R1 2621

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
582 598 0.179067 GGTTGAGTGTTCGTGGGTGA 60.179 55.0 0.0 0.0 0.0 4.02 F
590 606 0.309612 GTTCGTGGGTGAATGCGTTT 59.690 50.0 0.0 0.0 0.0 3.60 F
1415 1460 0.324614 TGCATCTCTCGGCTTTCCAA 59.675 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
1483 1528 0.392998 AGGTCGGATGAAGCGCAAAT 60.393 50.000 11.47 0.00 0.0 2.32 R
1490 1535 1.153289 CCCTGCAGGTCGGATGAAG 60.153 63.158 30.63 8.72 0.0 3.02 R
2278 2750 9.577110 CAAGATATTTTTGTTCAGTGCATACAT 57.423 29.630 0.00 0.00 0.0 2.29 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
40 41 2.952310 GACTCCACAAGTTTGCTTCCTT 59.048 45.455 0.00 0.00 38.74 3.36
65 66 8.648698 TCACAATTTGGATCTCAGGAATTAAA 57.351 30.769 0.78 0.00 0.00 1.52
87 88 9.796120 TTAAACCTTATTTTGAACTGTGTTCAG 57.204 29.630 12.04 3.53 46.18 3.02
124 125 2.737679 GCCCCTAGTGTAACGCTAGTTG 60.738 54.545 11.58 4.96 45.86 3.16
134 135 6.093082 AGTGTAACGCTAGTTGTTTCTTGTTT 59.907 34.615 7.63 0.00 45.86 2.83
135 136 6.744082 GTGTAACGCTAGTTGTTTCTTGTTTT 59.256 34.615 7.63 0.00 41.35 2.43
181 182 9.840427 GTTTGAGTTTGTATATAGCAATTGTGT 57.160 29.630 7.40 0.00 0.00 3.72
187 188 6.117911 TGTATATAGCAATTGTGTGTGTGC 57.882 37.500 7.40 0.00 37.26 4.57
212 213 2.096268 CGTGCGTGAATTGAAGACATGT 60.096 45.455 0.00 0.00 0.00 3.21
299 301 7.010552 GGATTACATTATATGCCAAGCTAGTCG 59.989 40.741 0.00 0.00 0.00 4.18
302 304 5.011125 ACATTATATGCCAAGCTAGTCGTCT 59.989 40.000 0.00 0.00 0.00 4.18
308 310 2.610727 GCCAAGCTAGTCGTCTGTCTTT 60.611 50.000 0.00 0.00 0.00 2.52
309 311 3.654414 CCAAGCTAGTCGTCTGTCTTTT 58.346 45.455 0.00 0.00 0.00 2.27
379 390 7.560368 ACATAAGTTGTTTGGAACCATGAAAA 58.440 30.769 0.00 0.00 33.74 2.29
385 396 6.232581 TGTTTGGAACCATGAAAAATCACT 57.767 33.333 0.00 0.00 0.00 3.41
386 397 6.047870 TGTTTGGAACCATGAAAAATCACTG 58.952 36.000 0.00 0.00 0.00 3.66
397 408 2.793278 AAATCACTGAAACAACGGCC 57.207 45.000 0.00 0.00 0.00 6.13
402 413 0.953960 ACTGAAACAACGGCCGATCC 60.954 55.000 35.90 14.36 0.00 3.36
407 418 0.899720 AACAACGGCCGATCCTAGAA 59.100 50.000 35.90 0.00 0.00 2.10
414 425 2.289072 CGGCCGATCCTAGAATTGACAT 60.289 50.000 24.07 0.00 0.00 3.06
416 427 3.007398 GGCCGATCCTAGAATTGACATCT 59.993 47.826 0.00 0.00 0.00 2.90
417 428 4.220821 GGCCGATCCTAGAATTGACATCTA 59.779 45.833 0.00 0.00 0.00 1.98
424 435 7.348080 TCCTAGAATTGACATCTATGTTCGT 57.652 36.000 0.00 0.00 41.95 3.85
471 483 0.391661 CTGGATGTCCGTTCAGTGGG 60.392 60.000 0.00 0.00 39.43 4.61
481 493 1.666311 CGTTCAGTGGGAGAGACGTTC 60.666 57.143 0.00 0.00 0.00 3.95
483 495 1.996798 TCAGTGGGAGAGACGTTCTT 58.003 50.000 0.00 0.00 35.87 2.52
486 498 2.040178 AGTGGGAGAGACGTTCTTGTT 58.960 47.619 0.00 0.00 35.87 2.83
489 501 2.632996 TGGGAGAGACGTTCTTGTTGAT 59.367 45.455 0.00 0.00 35.87 2.57
495 507 5.526115 AGAGACGTTCTTGTTGATTACGAA 58.474 37.500 0.00 0.00 34.22 3.85
498 510 3.121126 ACGTTCTTGTTGATTACGAAGCG 60.121 43.478 0.00 0.00 34.22 4.68
499 511 3.153735 GTTCTTGTTGATTACGAAGCGC 58.846 45.455 0.00 0.00 0.00 5.92
501 513 0.800012 TTGTTGATTACGAAGCGCCC 59.200 50.000 2.29 0.00 0.00 6.13
502 514 1.347221 GTTGATTACGAAGCGCCCG 59.653 57.895 16.67 16.67 0.00 6.13
503 515 2.457778 TTGATTACGAAGCGCCCGC 61.458 57.895 17.92 4.20 42.33 6.13
527 539 6.699204 GCGAAGACTTCATCAATCTCAAGATA 59.301 38.462 15.36 0.00 33.73 1.98
549 561 1.476891 TGTACGGGCTCAAGATCTCAC 59.523 52.381 0.00 0.00 0.00 3.51
573 589 5.473504 CAGGTGCTAATAAAGGTTGAGTGTT 59.526 40.000 0.00 0.00 0.00 3.32
582 598 0.179067 GGTTGAGTGTTCGTGGGTGA 60.179 55.000 0.00 0.00 0.00 4.02
583 599 1.658994 GTTGAGTGTTCGTGGGTGAA 58.341 50.000 0.00 0.00 0.00 3.18
587 603 1.206578 GTGTTCGTGGGTGAATGCG 59.793 57.895 0.00 0.00 0.00 4.73
590 606 0.309612 GTTCGTGGGTGAATGCGTTT 59.690 50.000 0.00 0.00 0.00 3.60
658 682 4.787598 CGTCAAATTTGCAACTAAGCTCT 58.212 39.130 13.54 0.00 34.99 4.09
660 684 6.546395 CGTCAAATTTGCAACTAAGCTCTAT 58.454 36.000 13.54 0.00 34.99 1.98
661 685 6.467047 CGTCAAATTTGCAACTAAGCTCTATG 59.533 38.462 13.54 0.00 34.99 2.23
679 703 0.604073 TGCCGGTTTACATCGTCTCA 59.396 50.000 1.90 0.00 0.00 3.27
688 712 5.411669 GGTTTACATCGTCTCAAAATGGAGT 59.588 40.000 0.00 0.00 36.30 3.85
885 919 1.339151 CGCCCTCCTCTATTTATGGCC 60.339 57.143 0.00 0.00 33.90 5.36
949 987 1.488393 CACTCCCCCAGAGAAATCCTC 59.512 57.143 0.00 0.00 46.50 3.71
950 988 1.135960 CTCCCCCAGAGAAATCCTCC 58.864 60.000 0.00 0.00 46.50 4.30
951 989 0.327576 TCCCCCAGAGAAATCCTCCC 60.328 60.000 0.00 0.00 42.97 4.30
952 990 0.327964 CCCCCAGAGAAATCCTCCCT 60.328 60.000 0.00 0.00 42.97 4.20
967 1005 2.182030 CCTCCTCACCTCGAACGC 59.818 66.667 0.00 0.00 0.00 4.84
1183 1224 4.397730 CCTGTATGATCTCTCCCGTAGATG 59.602 50.000 0.00 0.00 33.82 2.90
1223 1264 1.472552 GGTGCTGGTTGGTTTTGGTTC 60.473 52.381 0.00 0.00 0.00 3.62
1379 1420 1.066430 GTCATCCGTGGCAAGAAGGTA 60.066 52.381 0.76 0.00 0.00 3.08
1380 1421 1.837439 TCATCCGTGGCAAGAAGGTAT 59.163 47.619 0.76 0.00 0.00 2.73
1381 1422 3.035363 TCATCCGTGGCAAGAAGGTATA 58.965 45.455 0.76 0.00 0.00 1.47
1382 1423 2.973694 TCCGTGGCAAGAAGGTATAC 57.026 50.000 0.76 0.00 0.00 1.47
1383 1424 2.181125 TCCGTGGCAAGAAGGTATACA 58.819 47.619 5.01 0.00 0.00 2.29
1384 1425 2.769663 TCCGTGGCAAGAAGGTATACAT 59.230 45.455 5.01 0.00 0.00 2.29
1385 1426 2.872245 CCGTGGCAAGAAGGTATACATG 59.128 50.000 5.01 0.00 0.00 3.21
1386 1427 2.287915 CGTGGCAAGAAGGTATACATGC 59.712 50.000 5.01 6.73 0.00 4.06
1408 1449 1.574925 CATGCATGCATCTCTCGGC 59.425 57.895 30.07 0.00 33.90 5.54
1413 1458 0.942962 CATGCATCTCTCGGCTTTCC 59.057 55.000 0.00 0.00 0.00 3.13
1415 1460 0.324614 TGCATCTCTCGGCTTTCCAA 59.675 50.000 0.00 0.00 0.00 3.53
1423 1468 6.920569 TCTCTCGGCTTTCCAAAATTATAC 57.079 37.500 0.00 0.00 0.00 1.47
1424 1469 6.650120 TCTCTCGGCTTTCCAAAATTATACT 58.350 36.000 0.00 0.00 0.00 2.12
1425 1470 7.788026 TCTCTCGGCTTTCCAAAATTATACTA 58.212 34.615 0.00 0.00 0.00 1.82
1426 1471 7.709613 TCTCTCGGCTTTCCAAAATTATACTAC 59.290 37.037 0.00 0.00 0.00 2.73
1427 1472 6.764560 TCTCGGCTTTCCAAAATTATACTACC 59.235 38.462 0.00 0.00 0.00 3.18
1428 1473 6.416415 TCGGCTTTCCAAAATTATACTACCA 58.584 36.000 0.00 0.00 0.00 3.25
1429 1474 6.316890 TCGGCTTTCCAAAATTATACTACCAC 59.683 38.462 0.00 0.00 0.00 4.16
1430 1475 6.317893 CGGCTTTCCAAAATTATACTACCACT 59.682 38.462 0.00 0.00 0.00 4.00
1431 1476 7.496591 CGGCTTTCCAAAATTATACTACCACTA 59.503 37.037 0.00 0.00 0.00 2.74
1432 1477 9.350951 GGCTTTCCAAAATTATACTACCACTAT 57.649 33.333 0.00 0.00 0.00 2.12
1445 1490 6.790285 ACTACCACTATTACGTGTTTTTGG 57.210 37.500 0.00 1.77 33.07 3.28
1461 1506 7.306515 CGTGTTTTTGGAAAATTGATTGATCGT 60.307 33.333 0.00 0.00 0.00 3.73
1483 1528 2.037902 TCCCTGTGCTTCGTCATGTTAA 59.962 45.455 0.00 0.00 0.00 2.01
1490 1535 2.276282 GCTTCGTCATGTTAATTTGCGC 59.724 45.455 0.00 0.00 0.00 6.09
1499 1544 2.744741 TGTTAATTTGCGCTTCATCCGA 59.255 40.909 9.73 0.00 0.00 4.55
1623 1668 2.362632 AGGCTCGGCGACTACCTT 60.363 61.111 4.99 0.00 0.00 3.50
1626 1671 1.516603 GCTCGGCGACTACCTTGTC 60.517 63.158 4.99 0.00 0.00 3.18
1659 1705 5.858876 TGTAGGCCACCCATCAATATAAT 57.141 39.130 5.01 0.00 0.00 1.28
1684 1734 1.123655 CCACGATGATCGATCACACG 58.876 55.000 34.19 34.19 43.74 4.49
1895 1946 5.046529 TGTTGACAACAAATTTTGCGCTAT 58.953 33.333 18.56 0.00 38.72 2.97
1896 1947 5.051173 TGTTGACAACAAATTTTGCGCTATG 60.051 36.000 18.56 0.00 38.72 2.23
1911 1962 3.780801 GCGCTATGTTTCTTTCGATTGTG 59.219 43.478 0.00 0.00 0.00 3.33
1966 2017 8.831715 TTTATTTTGAAAAGGCCTCTTTGATC 57.168 30.769 5.23 0.00 41.92 2.92
1978 2029 3.181494 CCTCTTTGATCGCAATGCAATCA 60.181 43.478 4.53 4.53 33.25 2.57
1986 2037 7.148355 TGATCGCAATGCAATCACATATATT 57.852 32.000 4.53 0.00 0.00 1.28
1987 2038 8.266392 TGATCGCAATGCAATCACATATATTA 57.734 30.769 4.53 0.00 0.00 0.98
1988 2039 8.728833 TGATCGCAATGCAATCACATATATTAA 58.271 29.630 4.53 0.00 0.00 1.40
2005 2387 8.725148 CATATATTAATCCTCTTCTGTTGTGGC 58.275 37.037 0.00 0.00 0.00 5.01
2028 2452 5.448162 GCTGCGTTTATAATCGTCAAGAAAC 59.552 40.000 15.35 0.00 0.00 2.78
2046 2470 6.952935 AGAAACGACATAGTTGCTTAGAAG 57.047 37.500 0.00 0.00 36.64 2.85
2047 2471 6.688578 AGAAACGACATAGTTGCTTAGAAGA 58.311 36.000 0.00 0.00 36.64 2.87
2048 2472 7.152645 AGAAACGACATAGTTGCTTAGAAGAA 58.847 34.615 0.00 0.00 36.64 2.52
2049 2473 7.819900 AGAAACGACATAGTTGCTTAGAAGAAT 59.180 33.333 0.00 0.00 36.64 2.40
2050 2474 7.907214 AACGACATAGTTGCTTAGAAGAATT 57.093 32.000 0.00 0.00 32.39 2.17
2051 2475 7.295952 ACGACATAGTTGCTTAGAAGAATTG 57.704 36.000 0.00 0.00 0.00 2.32
2052 2476 6.313905 ACGACATAGTTGCTTAGAAGAATTGG 59.686 38.462 0.00 0.00 0.00 3.16
2053 2477 6.313905 CGACATAGTTGCTTAGAAGAATTGGT 59.686 38.462 0.00 0.00 0.00 3.67
2072 2496 4.942852 TGGTTGTTTCGCAAAAATGAGAT 58.057 34.783 0.00 0.00 39.03 2.75
2078 2502 6.902466 TTGTTTCGCAAAAATGAGATGGAACA 60.902 34.615 0.00 0.00 37.04 3.18
2101 2525 6.538381 ACATTCCACTTTTGCCTTAAAAACAG 59.462 34.615 0.00 0.00 37.78 3.16
2109 2533 4.503741 TGCCTTAAAAACAGCTTGCTAG 57.496 40.909 0.00 0.00 0.00 3.42
2129 2553 3.296628 AGCACTAAATTTTTCACGCACG 58.703 40.909 0.00 0.00 0.00 5.34
2140 2564 2.979401 TCACGCACGCATTTTGTATT 57.021 40.000 0.00 0.00 0.00 1.89
2159 2583 7.929941 TGTATTTGGTGTATTCATGTTGCTA 57.070 32.000 0.00 0.00 0.00 3.49
2171 2643 3.689161 TCATGTTGCTACACATTACCAGC 59.311 43.478 2.28 0.00 35.03 4.85
2172 2644 3.133141 TGTTGCTACACATTACCAGCA 57.867 42.857 0.00 0.00 42.03 4.41
2173 2645 3.684908 TGTTGCTACACATTACCAGCAT 58.315 40.909 0.00 0.00 43.13 3.79
2197 2669 7.776933 TGGAAATCTGACGAGAATAATTCAG 57.223 36.000 0.00 0.00 37.43 3.02
2278 2750 7.033791 GTCGATGGAAAACTAGAGTTGTATCA 58.966 38.462 0.00 0.00 38.44 2.15
2293 2765 6.172630 AGTTGTATCATGTATGCACTGAACA 58.827 36.000 0.00 0.00 28.95 3.18
2616 3096 9.009327 CATTATTGTATTTTACTCCGCAAACAG 57.991 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.192633 AGCAAACTTGTGGAGTCGTTTTT 59.807 39.130 0.00 0.00 37.72 1.94
14 15 2.752903 AGCAAACTTGTGGAGTCGTTTT 59.247 40.909 0.00 0.00 37.72 2.43
15 16 2.365582 AGCAAACTTGTGGAGTCGTTT 58.634 42.857 0.00 0.00 37.72 3.60
16 17 2.038387 AGCAAACTTGTGGAGTCGTT 57.962 45.000 0.00 0.00 37.72 3.85
17 18 1.940613 GAAGCAAACTTGTGGAGTCGT 59.059 47.619 0.00 0.00 37.72 4.34
18 19 1.264288 GGAAGCAAACTTGTGGAGTCG 59.736 52.381 0.00 0.00 37.72 4.18
19 20 2.576615 AGGAAGCAAACTTGTGGAGTC 58.423 47.619 0.00 0.00 37.72 3.36
40 41 8.522830 GTTTAATTCCTGAGATCCAAATTGTGA 58.477 33.333 0.00 0.00 0.00 3.58
65 66 6.039382 GGACTGAACACAGTTCAAAATAAGGT 59.961 38.462 12.94 6.29 43.70 3.50
78 79 7.036220 CACCTACTATTTAGGACTGAACACAG 58.964 42.308 4.30 0.00 38.09 3.66
124 125 9.710900 AAATCTCATCCCATTAAAACAAGAAAC 57.289 29.630 0.00 0.00 0.00 2.78
134 135 7.669304 TCAAACTCACAAATCTCATCCCATTAA 59.331 33.333 0.00 0.00 0.00 1.40
135 136 7.174413 TCAAACTCACAAATCTCATCCCATTA 58.826 34.615 0.00 0.00 0.00 1.90
269 271 7.661040 AGCTTGGCATATAATGTAATCCAAAC 58.339 34.615 0.00 0.00 32.50 2.93
279 281 5.347093 CAGACGACTAGCTTGGCATATAATG 59.653 44.000 0.96 0.00 0.00 1.90
280 282 5.011125 ACAGACGACTAGCTTGGCATATAAT 59.989 40.000 0.96 0.00 0.00 1.28
379 390 0.591170 CGGCCGTTGTTTCAGTGATT 59.409 50.000 19.50 0.00 0.00 2.57
385 396 0.609151 TAGGATCGGCCGTTGTTTCA 59.391 50.000 27.15 3.40 43.43 2.69
386 397 1.134907 TCTAGGATCGGCCGTTGTTTC 60.135 52.381 27.15 14.57 43.43 2.78
397 408 7.272299 CGAACATAGATGTCAATTCTAGGATCG 59.728 40.741 11.05 11.05 42.18 3.69
407 418 8.124823 CAGCAAAATACGAACATAGATGTCAAT 58.875 33.333 0.00 0.00 40.80 2.57
417 428 9.853555 TGAATAAATTCAGCAAAATACGAACAT 57.146 25.926 1.23 0.00 41.51 2.71
445 457 0.322546 AACGGACATCCAGGGAAAGC 60.323 55.000 0.00 0.00 35.14 3.51
450 462 0.391661 CACTGAACGGACATCCAGGG 60.392 60.000 0.00 0.00 35.14 4.45
453 465 0.834261 TCCCACTGAACGGACATCCA 60.834 55.000 0.00 0.00 35.14 3.41
471 483 5.152097 TCGTAATCAACAAGAACGTCTCTC 58.848 41.667 0.00 0.00 33.37 3.20
481 493 1.202031 GGGCGCTTCGTAATCAACAAG 60.202 52.381 7.64 0.00 0.00 3.16
483 495 1.355796 CGGGCGCTTCGTAATCAACA 61.356 55.000 7.64 0.00 0.00 3.33
486 498 2.888534 GCGGGCGCTTCGTAATCA 60.889 61.111 20.46 0.00 38.26 2.57
489 501 4.721111 TTCGCGGGCGCTTCGTAA 62.721 61.111 20.46 14.06 39.59 3.18
498 510 1.019278 TTGATGAAGTCTTCGCGGGC 61.019 55.000 6.13 0.00 0.00 6.13
499 511 1.594862 GATTGATGAAGTCTTCGCGGG 59.405 52.381 6.13 0.00 0.00 6.13
501 513 3.182182 TGAGATTGATGAAGTCTTCGCG 58.818 45.455 0.00 0.00 0.00 5.87
502 514 4.867047 TCTTGAGATTGATGAAGTCTTCGC 59.133 41.667 8.06 3.57 0.00 4.70
503 515 8.815141 ATATCTTGAGATTGATGAAGTCTTCG 57.185 34.615 8.06 0.00 36.05 3.79
513 525 5.934625 GCCCGTACAATATCTTGAGATTGAT 59.065 40.000 20.38 10.07 36.69 2.57
527 539 2.766263 TGAGATCTTGAGCCCGTACAAT 59.234 45.455 0.00 0.00 0.00 2.71
532 544 0.534412 CTGTGAGATCTTGAGCCCGT 59.466 55.000 0.00 0.00 0.00 5.28
549 561 5.003804 ACACTCAACCTTTATTAGCACCTG 58.996 41.667 0.00 0.00 0.00 4.00
573 589 1.735018 CATAAACGCATTCACCCACGA 59.265 47.619 0.00 0.00 0.00 4.35
582 598 2.643551 CCTCACCTCCATAAACGCATT 58.356 47.619 0.00 0.00 0.00 3.56
583 599 1.134098 CCCTCACCTCCATAAACGCAT 60.134 52.381 0.00 0.00 0.00 4.73
587 603 2.576615 GATGCCCTCACCTCCATAAAC 58.423 52.381 0.00 0.00 0.00 2.01
590 606 0.030195 TGGATGCCCTCACCTCCATA 60.030 55.000 0.00 0.00 32.92 2.74
658 682 2.427812 TGAGACGATGTAAACCGGCATA 59.572 45.455 0.00 0.00 36.01 3.14
660 684 0.604073 TGAGACGATGTAAACCGGCA 59.396 50.000 0.00 0.00 36.01 5.69
661 685 1.717194 TTGAGACGATGTAAACCGGC 58.283 50.000 0.00 0.00 0.00 6.13
679 703 0.322546 GGACCTCGCCACTCCATTTT 60.323 55.000 0.00 0.00 0.00 1.82
688 712 0.031585 CGAATATTCGGACCTCGCCA 59.968 55.000 26.61 0.00 46.30 5.69
707 731 0.179129 CATGGGCATCGGTTTTGCTC 60.179 55.000 0.00 0.00 41.11 4.26
718 742 2.427320 CCGTCGATCCATGGGCAT 59.573 61.111 13.02 0.00 0.00 4.40
885 919 2.438434 GTGGATTGGGCGGTGGAG 60.438 66.667 0.00 0.00 0.00 3.86
949 987 2.885861 CGTTCGAGGTGAGGAGGG 59.114 66.667 0.00 0.00 0.00 4.30
950 988 2.182030 GCGTTCGAGGTGAGGAGG 59.818 66.667 0.00 0.00 0.00 4.30
951 989 1.137825 GAGCGTTCGAGGTGAGGAG 59.862 63.158 0.00 0.00 0.00 3.69
952 990 2.341101 GGAGCGTTCGAGGTGAGGA 61.341 63.158 0.00 0.00 0.00 3.71
967 1005 2.680913 CGTTTGCTGCTTCCCGGAG 61.681 63.158 0.73 0.00 0.00 4.63
1150 1190 7.153985 GGAGAGATCATACAGGAAATCTGAAG 58.846 42.308 0.00 0.00 46.18 3.02
1151 1191 6.042552 GGGAGAGATCATACAGGAAATCTGAA 59.957 42.308 0.00 0.00 46.18 3.02
1152 1192 5.541868 GGGAGAGATCATACAGGAAATCTGA 59.458 44.000 0.00 0.00 46.18 3.27
1183 1224 1.597663 CGTGAGATATGGGGAAAACGC 59.402 52.381 0.00 0.00 0.00 4.84
1223 1264 1.831389 CGAACTGGACGCCACACAAG 61.831 60.000 0.00 0.00 0.00 3.16
1346 1387 2.434884 ATGACAGCGCCAGGTTCG 60.435 61.111 2.29 0.00 0.00 3.95
1423 1468 7.424227 TTCCAAAAACACGTAATAGTGGTAG 57.576 36.000 0.00 0.00 41.90 3.18
1424 1469 7.798596 TTTCCAAAAACACGTAATAGTGGTA 57.201 32.000 0.00 0.00 41.90 3.25
1425 1470 6.696441 TTTCCAAAAACACGTAATAGTGGT 57.304 33.333 0.00 0.00 45.14 4.16
1426 1471 8.484008 CAATTTTCCAAAAACACGTAATAGTGG 58.516 33.333 0.00 0.00 45.80 4.00
1427 1472 9.239002 TCAATTTTCCAAAAACACGTAATAGTG 57.761 29.630 0.00 0.00 46.83 2.74
1428 1473 9.974980 ATCAATTTTCCAAAAACACGTAATAGT 57.025 25.926 0.00 0.00 0.00 2.12
1431 1476 9.319143 TCAATCAATTTTCCAAAAACACGTAAT 57.681 25.926 0.00 0.00 0.00 1.89
1432 1477 8.703604 TCAATCAATTTTCCAAAAACACGTAA 57.296 26.923 0.00 0.00 0.00 3.18
1433 1478 8.879342 ATCAATCAATTTTCCAAAAACACGTA 57.121 26.923 0.00 0.00 0.00 3.57
1434 1479 7.306515 CGATCAATCAATTTTCCAAAAACACGT 60.307 33.333 0.00 0.00 0.00 4.49
1435 1480 7.003072 CGATCAATCAATTTTCCAAAAACACG 58.997 34.615 0.00 0.00 0.00 4.49
1436 1481 7.850501 ACGATCAATCAATTTTCCAAAAACAC 58.149 30.769 0.00 0.00 0.00 3.32
1441 1486 6.014669 AGGGAACGATCAATCAATTTTCCAAA 60.015 34.615 0.00 0.00 0.00 3.28
1445 1490 5.801947 CACAGGGAACGATCAATCAATTTTC 59.198 40.000 0.00 0.00 0.00 2.29
1461 1506 0.396435 ACATGACGAAGCACAGGGAA 59.604 50.000 0.00 0.00 0.00 3.97
1483 1528 0.392998 AGGTCGGATGAAGCGCAAAT 60.393 50.000 11.47 0.00 0.00 2.32
1490 1535 1.153289 CCCTGCAGGTCGGATGAAG 60.153 63.158 30.63 8.72 0.00 3.02
1623 1668 1.943968 GCCTACATGCCTTGTTCGACA 60.944 52.381 0.00 0.00 39.87 4.35
1659 1705 1.734388 ATCGATCATCGTGGACGCCA 61.734 55.000 7.00 0.00 41.35 5.69
1822 1873 4.967036 ACCCACTGAAGAAGAAGAAGAAG 58.033 43.478 0.00 0.00 0.00 2.85
1823 1874 4.202367 GGACCCACTGAAGAAGAAGAAGAA 60.202 45.833 0.00 0.00 0.00 2.52
1824 1875 3.325135 GGACCCACTGAAGAAGAAGAAGA 59.675 47.826 0.00 0.00 0.00 2.87
1825 1876 3.071602 TGGACCCACTGAAGAAGAAGAAG 59.928 47.826 0.00 0.00 0.00 2.85
1826 1877 3.045634 TGGACCCACTGAAGAAGAAGAA 58.954 45.455 0.00 0.00 0.00 2.52
1827 1878 2.689658 TGGACCCACTGAAGAAGAAGA 58.310 47.619 0.00 0.00 0.00 2.87
1939 1990 9.797642 ATCAAAGAGGCCTTTTCAAAATAAAAT 57.202 25.926 6.77 0.00 40.42 1.82
1940 1991 9.271828 GATCAAAGAGGCCTTTTCAAAATAAAA 57.728 29.630 6.77 0.00 40.42 1.52
1941 1992 7.598493 CGATCAAAGAGGCCTTTTCAAAATAAA 59.402 33.333 6.77 0.00 40.42 1.40
1942 1993 7.090173 CGATCAAAGAGGCCTTTTCAAAATAA 58.910 34.615 6.77 0.00 40.42 1.40
1943 1994 6.620678 CGATCAAAGAGGCCTTTTCAAAATA 58.379 36.000 6.77 0.00 40.42 1.40
1944 1995 5.473039 CGATCAAAGAGGCCTTTTCAAAAT 58.527 37.500 6.77 0.00 40.42 1.82
1945 1996 4.795962 GCGATCAAAGAGGCCTTTTCAAAA 60.796 41.667 6.77 0.00 40.42 2.44
1946 1997 3.305335 GCGATCAAAGAGGCCTTTTCAAA 60.305 43.478 6.77 0.00 40.42 2.69
1966 2017 8.186163 AGGATTAATATATGTGATTGCATTGCG 58.814 33.333 3.84 0.00 0.00 4.85
1978 2029 9.784531 CCACAACAGAAGAGGATTAATATATGT 57.215 33.333 0.00 0.00 0.00 2.29
1986 2037 3.869912 GCAGCCACAACAGAAGAGGATTA 60.870 47.826 0.00 0.00 0.00 1.75
1987 2038 2.787994 CAGCCACAACAGAAGAGGATT 58.212 47.619 0.00 0.00 0.00 3.01
1988 2039 1.612726 GCAGCCACAACAGAAGAGGAT 60.613 52.381 0.00 0.00 0.00 3.24
1998 2380 3.181514 ACGATTATAAACGCAGCCACAAC 60.182 43.478 14.26 0.00 0.00 3.32
2000 2382 2.605818 GACGATTATAAACGCAGCCACA 59.394 45.455 14.26 0.00 0.00 4.17
2001 2383 2.605818 TGACGATTATAAACGCAGCCAC 59.394 45.455 14.26 1.96 0.00 5.01
2005 2387 5.666878 CGTTTCTTGACGATTATAAACGCAG 59.333 40.000 14.26 8.62 45.47 5.18
2028 2452 6.313905 ACCAATTCTTCTAAGCAACTATGTCG 59.686 38.462 0.00 0.00 0.00 4.35
2046 2470 6.019156 TCTCATTTTTGCGAAACAACCAATTC 60.019 34.615 0.00 0.00 38.23 2.17
2047 2471 5.814705 TCTCATTTTTGCGAAACAACCAATT 59.185 32.000 0.00 0.00 38.23 2.32
2048 2472 5.355596 TCTCATTTTTGCGAAACAACCAAT 58.644 33.333 0.00 0.00 38.23 3.16
2049 2473 4.748892 TCTCATTTTTGCGAAACAACCAA 58.251 34.783 0.00 0.00 38.23 3.67
2050 2474 4.377839 TCTCATTTTTGCGAAACAACCA 57.622 36.364 0.00 0.00 38.23 3.67
2051 2475 4.150451 CCATCTCATTTTTGCGAAACAACC 59.850 41.667 0.00 0.00 38.23 3.77
2052 2476 4.981674 TCCATCTCATTTTTGCGAAACAAC 59.018 37.500 0.00 0.00 38.23 3.32
2053 2477 5.193663 TCCATCTCATTTTTGCGAAACAA 57.806 34.783 0.00 0.00 36.13 2.83
2072 2496 6.352222 TTTTAAGGCAAAAGTGGAATGTTCCA 60.352 34.615 10.34 10.34 41.60 3.53
2078 2502 5.527214 GCTGTTTTTAAGGCAAAAGTGGAAT 59.473 36.000 0.00 0.00 37.42 3.01
2081 2505 4.441792 AGCTGTTTTTAAGGCAAAAGTGG 58.558 39.130 0.00 0.00 37.42 4.00
2109 2533 2.160156 GCGTGCGTGAAAAATTTAGTGC 60.160 45.455 0.00 0.00 0.00 4.40
2115 2539 3.308323 ACAAAATGCGTGCGTGAAAAATT 59.692 34.783 0.00 0.00 0.00 1.82
2129 2553 8.477984 ACATGAATACACCAAATACAAAATGC 57.522 30.769 0.00 0.00 0.00 3.56
2140 2564 5.066593 TGTGTAGCAACATGAATACACCAA 58.933 37.500 20.73 9.35 44.67 3.67
2159 2583 4.400251 CAGATTTCCATGCTGGTAATGTGT 59.600 41.667 16.14 2.09 40.89 3.72
2171 2643 8.146479 TGAATTATTCTCGTCAGATTTCCATG 57.854 34.615 6.50 0.00 0.00 3.66
2172 2644 7.989741 ACTGAATTATTCTCGTCAGATTTCCAT 59.010 33.333 6.50 0.00 39.94 3.41
2173 2645 7.331026 ACTGAATTATTCTCGTCAGATTTCCA 58.669 34.615 6.50 0.00 39.94 3.53
2197 2669 5.181690 TGCTTCAATACTTGGTGAACAAC 57.818 39.130 0.00 0.00 34.76 3.32
2278 2750 9.577110 CAAGATATTTTTGTTCAGTGCATACAT 57.423 29.630 0.00 0.00 0.00 2.29
2322 2795 9.866655 ACATAAAGATGAGGGCATAATTTAGAA 57.133 29.630 0.00 0.00 36.48 2.10


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

AutoCloner maintained by Alex Coulton.