Multiple sequence alignment - TraesCS2B01G176800

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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 TraesCS2B01G176800 chr2B 100.000 2837 0 0 1 2837 151903467 151900631 0.000000e+00 5240.0
1 TraesCS2B01G176800 chr2B 92.375 341 26 0 2348 2688 37643208 37643548 1.180000e-133 486.0
2 TraesCS2B01G176800 chr2B 95.238 42 2 0 2283 2324 37643408 37643449 1.820000e-07 67.6
3 TraesCS2B01G176800 chr7D 92.991 1013 66 4 1250 2257 409605394 409606406 0.000000e+00 1472.0
4 TraesCS2B01G176800 chr7D 94.824 541 28 0 2267 2807 409606378 409606918 0.000000e+00 845.0
5 TraesCS2B01G176800 chr7D 91.203 557 36 5 689 1233 409604851 409605406 0.000000e+00 745.0
6 TraesCS2B01G176800 chr7D 97.436 39 1 0 2796 2834 409606933 409606971 1.820000e-07 67.6
7 TraesCS2B01G176800 chr2A 90.089 787 64 8 2055 2834 24415205 24414426 0.000000e+00 1009.0
8 TraesCS2B01G176800 chr2A 90.922 694 37 15 1 686 99787794 99787119 0.000000e+00 909.0
9 TraesCS2B01G176800 chr2A 92.500 240 18 0 1230 1469 24415441 24415202 7.520000e-91 344.0
10 TraesCS2B01G176800 chr2D 90.791 695 36 16 1 686 100184892 100184217 0.000000e+00 904.0
11 TraesCS2B01G176800 chr2D 94.043 235 14 0 1235 1469 22823207 22822973 9.670000e-95 357.0
12 TraesCS2B01G176800 chr5B 85.332 859 96 18 826 1657 462257284 462258139 0.000000e+00 861.0
13 TraesCS2B01G176800 chr6D 92.683 164 10 2 687 848 101720513 101720350 4.730000e-58 235.0
14 TraesCS2B01G176800 chr1D 92.638 163 10 2 688 848 24217333 24217171 1.700000e-57 233.0
15 TraesCS2B01G176800 chr4B 92.405 158 11 1 687 843 534954541 534954384 1.020000e-54 224.0
16 TraesCS2B01G176800 chr7A 96.269 134 5 0 705 838 732393007 732393140 1.320000e-53 220.0
17 TraesCS2B01G176800 chr3A 92.053 151 11 1 2378 2528 693553148 693552999 7.960000e-51 211.0
18 TraesCS2B01G176800 chr3A 92.661 109 8 0 2287 2395 693554905 693554797 1.050000e-34 158.0


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 TraesCS2B01G176800 chr2B 151900631 151903467 2836 True 5240.0 5240 100.0000 1 2837 1 chr2B.!!$R1 2836
1 TraesCS2B01G176800 chr7D 409604851 409606971 2120 False 782.4 1472 94.1135 689 2834 4 chr7D.!!$F1 2145
2 TraesCS2B01G176800 chr2A 99787119 99787794 675 True 909.0 909 90.9220 1 686 1 chr2A.!!$R1 685
3 TraesCS2B01G176800 chr2A 24414426 24415441 1015 True 676.5 1009 91.2945 1230 2834 2 chr2A.!!$R2 1604
4 TraesCS2B01G176800 chr2D 100184217 100184892 675 True 904.0 904 90.7910 1 686 1 chr2D.!!$R2 685
5 TraesCS2B01G176800 chr5B 462257284 462258139 855 False 861.0 861 85.3320 826 1657 1 chr5B.!!$F1 831

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
914 924 0.179145 CCACCCACGACGATACTGAC 60.179 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2082 0.896923 CCATAAAGCTGCCTTTGCCA 59.103 50.0 0.0 0.0 41.24 4.92 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
31 32 2.129555 AACTTCCTGAGCCGCCACAT 62.130 55.000 0.00 0.00 0.00 3.21
234 236 5.884792 AGAATTCTTGCTACAATTCTGAGGG 59.115 40.000 9.79 0.00 44.25 4.30
247 249 7.690256 ACAATTCTGAGGGTAGATGTTTAGTT 58.310 34.615 0.00 0.00 0.00 2.24
280 282 6.964908 TCAACATTTTCTCGTGCATAAAAGA 58.035 32.000 0.00 0.00 0.00 2.52
281 283 6.855914 TCAACATTTTCTCGTGCATAAAAGAC 59.144 34.615 0.00 0.00 0.00 3.01
282 284 6.560253 ACATTTTCTCGTGCATAAAAGACT 57.440 33.333 0.00 0.00 0.00 3.24
289 291 8.766000 TTCTCGTGCATAAAAGACTATTGTTA 57.234 30.769 0.00 0.00 0.00 2.41
292 294 8.312896 TCGTGCATAAAAGACTATTGTTAACA 57.687 30.769 3.59 3.59 0.00 2.41
354 356 4.195416 TGTTCATGTGATATTTAGCCGCA 58.805 39.130 0.00 0.00 0.00 5.69
357 359 3.247411 TCATGTGATATTTAGCCGCAACG 59.753 43.478 0.00 0.00 0.00 4.10
368 370 3.734776 AGCCGCAACGTATTTCTTTAC 57.265 42.857 0.00 0.00 0.00 2.01
400 402 4.155826 TGTTGTCCTCTGTTTTGAAGTGTG 59.844 41.667 0.00 0.00 0.00 3.82
410 412 5.342433 TGTTTTGAAGTGTGATGCTTTGAG 58.658 37.500 0.00 0.00 0.00 3.02
416 418 0.955428 TGTGATGCTTTGAGCGGACC 60.955 55.000 0.00 0.00 46.26 4.46
420 422 2.358247 GCTTTGAGCGGACCGGAA 60.358 61.111 17.22 0.00 0.00 4.30
449 451 2.816087 TGATGGAAAGCTTGAGCACTTC 59.184 45.455 0.00 7.39 45.16 3.01
451 453 0.519077 GGAAAGCTTGAGCACTTCCG 59.481 55.000 16.31 0.00 41.87 4.30
491 496 6.115450 CACAGATTGTGGTCATTCAGTATG 57.885 41.667 1.31 0.00 44.27 2.39
492 497 5.645067 CACAGATTGTGGTCATTCAGTATGT 59.355 40.000 1.31 0.00 44.27 2.29
500 505 8.212317 TGTGGTCATTCAGTATGTTATCATTG 57.788 34.615 0.00 0.00 37.40 2.82
543 548 7.589958 AGAGGTTAGATATGTTCAGTACTGG 57.410 40.000 22.48 4.59 0.00 4.00
550 555 7.004555 AGATATGTTCAGTACTGGTTGTCAA 57.995 36.000 22.48 5.71 0.00 3.18
551 556 7.624549 AGATATGTTCAGTACTGGTTGTCAAT 58.375 34.615 22.48 8.12 0.00 2.57
553 558 9.547753 GATATGTTCAGTACTGGTTGTCAATAT 57.452 33.333 22.48 13.42 0.00 1.28
555 560 8.948631 ATGTTCAGTACTGGTTGTCAATATAG 57.051 34.615 22.48 0.00 0.00 1.31
556 561 7.903145 TGTTCAGTACTGGTTGTCAATATAGT 58.097 34.615 22.48 0.00 0.00 2.12
558 563 7.712204 TCAGTACTGGTTGTCAATATAGTCA 57.288 36.000 22.48 0.00 0.00 3.41
577 582 4.646492 AGTCAAAGGTCATGGAATTATGGC 59.354 41.667 0.00 0.00 31.98 4.40
582 587 4.927049 AGGTCATGGAATTATGGCATAGG 58.073 43.478 7.35 0.00 34.40 2.57
603 608 3.506067 GGAAACCAGTGGTTAATCTGTGG 59.494 47.826 27.62 5.62 46.20 4.17
604 609 4.394729 GAAACCAGTGGTTAATCTGTGGA 58.605 43.478 27.62 0.00 46.20 4.02
605 610 3.703001 ACCAGTGGTTAATCTGTGGAG 57.297 47.619 9.70 0.00 27.29 3.86
606 611 2.290323 ACCAGTGGTTAATCTGTGGAGC 60.290 50.000 9.70 0.00 27.29 4.70
607 612 2.290260 CCAGTGGTTAATCTGTGGAGCA 60.290 50.000 0.00 0.00 0.00 4.26
608 613 3.005554 CAGTGGTTAATCTGTGGAGCAG 58.994 50.000 0.00 0.00 46.34 4.24
609 614 1.740025 GTGGTTAATCTGTGGAGCAGC 59.260 52.381 0.00 0.00 44.66 5.25
610 615 1.340017 TGGTTAATCTGTGGAGCAGCC 60.340 52.381 0.00 0.00 44.66 4.85
638 643 5.005586 CAGCATGGTTGTTTAACTTGTGTTG 59.994 40.000 0.00 0.00 37.59 3.33
639 644 5.105554 AGCATGGTTGTTTAACTTGTGTTGA 60.106 36.000 0.00 0.00 37.59 3.18
640 645 5.752955 GCATGGTTGTTTAACTTGTGTTGAT 59.247 36.000 0.00 0.00 37.59 2.57
641 646 6.074356 GCATGGTTGTTTAACTTGTGTTGATC 60.074 38.462 0.00 0.00 37.59 2.92
642 647 5.574082 TGGTTGTTTAACTTGTGTTGATCG 58.426 37.500 0.00 0.00 37.59 3.69
643 648 5.124138 TGGTTGTTTAACTTGTGTTGATCGT 59.876 36.000 0.00 0.00 37.59 3.73
644 649 5.454232 GGTTGTTTAACTTGTGTTGATCGTG 59.546 40.000 0.00 0.00 37.59 4.35
645 650 6.252281 GTTGTTTAACTTGTGTTGATCGTGA 58.748 36.000 0.00 0.00 37.59 4.35
668 675 6.723515 TGATTCATGACCCTGTTTATTTTCCA 59.276 34.615 0.00 0.00 0.00 3.53
674 681 6.310941 TGACCCTGTTTATTTTCCATGAAGA 58.689 36.000 0.00 0.00 0.00 2.87
679 686 7.362401 CCCTGTTTATTTTCCATGAAGACTGAG 60.362 40.741 0.00 0.00 0.00 3.35
686 693 6.968131 TTTCCATGAAGACTGAGAATTACG 57.032 37.500 0.00 0.00 0.00 3.18
687 694 5.914898 TCCATGAAGACTGAGAATTACGA 57.085 39.130 0.00 0.00 0.00 3.43
692 699 3.512033 AGACTGAGAATTACGAGTGCC 57.488 47.619 0.00 0.00 0.00 5.01
701 708 4.330074 AGAATTACGAGTGCCGATTTTCAG 59.670 41.667 0.00 0.00 41.76 3.02
729 736 1.046472 CCACAGGTAGGCCGGTATCA 61.046 60.000 1.90 0.00 41.23 2.15
755 762 2.350458 CCGTTTGGGCCTTGGGATG 61.350 63.158 4.53 0.00 0.00 3.51
785 792 2.124151 GTGGGTGGCAGGCCTATG 60.124 66.667 3.98 0.00 36.94 2.23
799 806 2.880890 GGCCTATGCAGTGAAATACAGG 59.119 50.000 0.00 0.00 40.13 4.00
802 809 1.382522 ATGCAGTGAAATACAGGCCG 58.617 50.000 0.00 0.00 32.75 6.13
856 864 1.014352 GCGGCCATGACTTATCGTTT 58.986 50.000 2.24 0.00 0.00 3.60
913 923 1.317431 CCCACCCACGACGATACTGA 61.317 60.000 0.00 0.00 0.00 3.41
914 924 0.179145 CCACCCACGACGATACTGAC 60.179 60.000 0.00 0.00 0.00 3.51
916 926 0.674581 ACCCACGACGATACTGACGA 60.675 55.000 0.00 0.00 34.70 4.20
928 953 0.314302 ACTGACGACGAAACCAGAGG 59.686 55.000 0.00 0.00 0.00 3.69
976 1002 4.096003 CCCCATCTGGCGAACGGT 62.096 66.667 0.00 0.00 0.00 4.83
1047 1073 0.919710 GGTATGTTTGCTCCCCCTCT 59.080 55.000 0.00 0.00 0.00 3.69
1070 1096 2.224548 GCCAACCCTCACTTGAACTAGT 60.225 50.000 0.00 0.00 0.00 2.57
1109 1135 4.020543 CGGATTTTGGGGATTTCTTACCA 58.979 43.478 0.00 0.00 0.00 3.25
1119 1145 4.079253 GGATTTCTTACCAAGTTGGCTCA 58.921 43.478 22.25 4.55 42.67 4.26
1208 1234 0.747255 AGGATTCGATGAGTGTCCCG 59.253 55.000 0.00 0.00 0.00 5.14
1329 1356 1.376812 TGCTGATGCTCTGCCACAG 60.377 57.895 10.77 0.00 40.10 3.66
1416 1444 2.408271 TGATTCGGATTTCTGCAGCT 57.592 45.000 9.47 0.00 0.00 4.24
1435 1464 7.389232 TGCAGCTATTCATAGTATGTTATGCT 58.611 34.615 9.94 12.07 32.31 3.79
1436 1465 7.879677 TGCAGCTATTCATAGTATGTTATGCTT 59.120 33.333 9.94 0.00 32.31 3.91
1437 1466 8.173775 GCAGCTATTCATAGTATGTTATGCTTG 58.826 37.037 9.94 10.71 32.31 4.01
1462 1491 5.838531 TTTGTTCTATTTTCGGTGGTGTT 57.161 34.783 0.00 0.00 0.00 3.32
1467 1496 4.501071 TCTATTTTCGGTGGTGTTCTAGC 58.499 43.478 0.00 0.00 0.00 3.42
1470 1499 0.320421 TTCGGTGGTGTTCTAGCTGC 60.320 55.000 0.00 0.00 0.00 5.25
1496 1527 2.731027 GCCGTGGATCATTTTCGGAAAC 60.731 50.000 1.96 0.00 43.22 2.78
1525 1556 6.615726 TGCTTCTGGGTAGGAAAATATAGAGT 59.384 38.462 0.00 0.00 0.00 3.24
1583 1620 8.784994 GTGATGTTAGCACTAATCTAGTAGCTA 58.215 37.037 10.96 10.96 40.75 3.32
1618 1656 6.988622 ATGTGGTAATTGGATTTTTGCATG 57.011 33.333 0.00 0.00 0.00 4.06
1662 1700 6.042437 ACAGAGATGTATGTAGATTGCATGGA 59.958 38.462 0.00 0.00 0.00 3.41
1675 1713 1.302366 GCATGGATGTCGAATCAGCA 58.698 50.000 0.00 0.00 0.00 4.41
1678 1716 3.400255 CATGGATGTCGAATCAGCATCT 58.600 45.455 11.40 0.00 39.04 2.90
1687 1725 5.215160 GTCGAATCAGCATCTTTGTTTTGT 58.785 37.500 0.00 0.00 0.00 2.83
1691 1729 7.918033 TCGAATCAGCATCTTTGTTTTGTAAAA 59.082 29.630 0.00 0.00 0.00 1.52
1706 1744 7.489757 TGTTTTGTAAAATTTGTACTCACAGGC 59.510 33.333 0.00 0.00 35.67 4.85
1721 1759 1.000827 ACAGGCTAGATCTGATTCGCG 60.001 52.381 16.97 0.00 36.22 5.87
1726 1764 0.315251 TAGATCTGATTCGCGCAGGG 59.685 55.000 8.75 0.00 44.04 4.45
1804 1842 1.077501 ATGAGTGCCCCCATTGTCG 60.078 57.895 0.00 0.00 0.00 4.35
1807 1845 1.899437 GAGTGCCCCCATTGTCGAGA 61.899 60.000 0.00 0.00 0.00 4.04
1923 1961 7.730364 TTTAGAAAGGTTGAGCTTTGTCTAG 57.270 36.000 12.39 0.00 0.00 2.43
1927 1965 6.931840 AGAAAGGTTGAGCTTTGTCTAGTTAG 59.068 38.462 12.39 0.00 0.00 2.34
1929 1967 4.040461 AGGTTGAGCTTTGTCTAGTTAGCA 59.960 41.667 0.00 0.00 36.11 3.49
1931 1969 5.412904 GGTTGAGCTTTGTCTAGTTAGCATT 59.587 40.000 0.00 0.00 36.11 3.56
1951 1989 3.063510 TGAAGTTGATCTGAAGCTGGG 57.936 47.619 0.00 0.00 0.00 4.45
2037 2075 8.739972 GGATGAGTAGTATGTTTGTTGGATTTT 58.260 33.333 0.00 0.00 0.00 1.82
2042 2080 5.402630 AGTATGTTTGTTGGATTTTCCCCT 58.597 37.500 0.00 0.00 35.03 4.79
2043 2081 4.622260 ATGTTTGTTGGATTTTCCCCTG 57.378 40.909 0.00 0.00 35.03 4.45
2044 2082 3.379452 TGTTTGTTGGATTTTCCCCTGT 58.621 40.909 0.00 0.00 35.03 4.00
2045 2083 3.133721 TGTTTGTTGGATTTTCCCCTGTG 59.866 43.478 0.00 0.00 35.03 3.66
2048 2086 0.189574 TTGGATTTTCCCCTGTGGCA 59.810 50.000 0.00 0.00 35.03 4.92
2070 2109 5.537188 CAAAGGCAGCTTTATGGTGTAAAA 58.463 37.500 0.00 0.00 45.23 1.52
2080 2119 6.376018 GCTTTATGGTGTAAAATGGGTAGTCA 59.624 38.462 0.00 0.00 0.00 3.41
2090 2129 9.132923 TGTAAAATGGGTAGTCAGAGTAGATAG 57.867 37.037 0.00 0.00 0.00 2.08
2172 2211 6.439675 TGGGTTTAGAATTGCCGTATTTAC 57.560 37.500 0.00 0.00 0.00 2.01
2184 2223 6.811253 TGCCGTATTTACTTGATGAGTTTT 57.189 33.333 0.00 0.00 39.86 2.43
2195 2234 3.411446 TGATGAGTTTTGCTACAGTGGG 58.589 45.455 0.00 0.00 0.00 4.61
2199 2238 1.421646 AGTTTTGCTACAGTGGGAGCT 59.578 47.619 17.27 0.00 39.54 4.09
2203 2242 1.866015 TGCTACAGTGGGAGCTACAT 58.134 50.000 17.27 0.00 39.54 2.29
2246 2286 8.505625 ACGCGATAAATTTGGAGTAAAACTTTA 58.494 29.630 15.93 0.00 0.00 1.85
2249 2289 8.995906 CGATAAATTTGGAGTAAAACTTTAGCG 58.004 33.333 0.00 0.00 32.57 4.26
2250 2290 9.285770 GATAAATTTGGAGTAAAACTTTAGCGG 57.714 33.333 0.00 0.00 0.00 5.52
2251 2291 6.887626 AATTTGGAGTAAAACTTTAGCGGA 57.112 33.333 0.00 0.00 0.00 5.54
2265 2305 1.745489 GCGGATGGTTGAGTGGGAC 60.745 63.158 0.00 0.00 0.00 4.46
2268 2308 1.340017 CGGATGGTTGAGTGGGACAAT 60.340 52.381 0.00 0.00 44.16 2.71
2376 2416 3.100671 AGTTTGCAGTTTGGGGTGTTAA 58.899 40.909 0.00 0.00 0.00 2.01
2402 2443 7.679783 TGATGTTGGATCCAGTATAACCATAG 58.320 38.462 15.53 0.00 0.00 2.23
2517 2560 5.128499 TGGGACAAAAGTGTTCATCAATGTT 59.872 36.000 0.00 0.00 38.41 2.71
2574 2617 1.826385 TTTTCTAGAGGCAAGCTGGC 58.174 50.000 3.79 3.79 44.10 4.85
2624 2667 3.199727 TGAAAGCATGCCCACTGTCTATA 59.800 43.478 15.66 0.00 0.00 1.31
2646 2689 5.897377 ACAAATTCACCAATGTAGCTACC 57.103 39.130 21.01 4.03 0.00 3.18
2692 2739 3.627123 TCACACAACAACCTGATGTTCTG 59.373 43.478 0.00 0.00 41.44 3.02
2693 2740 2.358898 ACACAACAACCTGATGTTCTGC 59.641 45.455 0.00 0.00 41.44 4.26
2705 2752 0.108851 TGTTCTGCGAGCTAATGCGA 60.109 50.000 0.00 0.00 45.42 5.10
2736 2783 2.672996 ATTCAGCGGCGGCAAGTT 60.673 55.556 19.21 0.00 43.41 2.66
2834 2907 7.148590 GGAAATGCCATGTAACTGTTTTTCATC 60.149 37.037 0.00 0.00 36.34 2.92
2835 2908 5.132897 TGCCATGTAACTGTTTTTCATCC 57.867 39.130 0.00 0.00 0.00 3.51
2836 2909 4.586421 TGCCATGTAACTGTTTTTCATCCA 59.414 37.500 0.00 0.25 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.037687 CCTTCCATGGGCAAGCCA 59.962 61.111 13.02 0.00 37.98 4.75
40 41 2.511218 TCTCCATTTCTCCCCTTCCATG 59.489 50.000 0.00 0.00 0.00 3.66
253 255 6.552859 TTATGCACGAGAAAATGTTGAGAA 57.447 33.333 0.00 0.00 0.00 2.87
258 260 6.970484 AGTCTTTTATGCACGAGAAAATGTT 58.030 32.000 0.00 0.00 0.00 2.71
280 282 4.352893 AGTCCCAACCCTGTTAACAATAGT 59.647 41.667 10.03 4.51 0.00 2.12
281 283 4.918588 AGTCCCAACCCTGTTAACAATAG 58.081 43.478 10.03 3.87 0.00 1.73
282 284 5.074115 CAAGTCCCAACCCTGTTAACAATA 58.926 41.667 10.03 0.00 0.00 1.90
289 291 0.930726 TTCCAAGTCCCAACCCTGTT 59.069 50.000 0.00 0.00 0.00 3.16
292 294 1.231963 AGTTTCCAAGTCCCAACCCT 58.768 50.000 0.00 0.00 0.00 4.34
351 353 6.681178 CCTACATTGTAAAGAAATACGTTGCG 59.319 38.462 0.00 0.00 0.00 4.85
354 356 8.611654 ACACCTACATTGTAAAGAAATACGTT 57.388 30.769 0.00 0.00 0.00 3.99
357 359 9.821662 GACAACACCTACATTGTAAAGAAATAC 57.178 33.333 0.00 0.00 39.13 1.89
368 370 4.008074 ACAGAGGACAACACCTACATTG 57.992 45.455 0.00 0.00 40.73 2.82
400 402 2.464459 CCGGTCCGCTCAAAGCATC 61.464 63.158 5.50 0.00 42.58 3.91
420 422 1.963985 AGCTTTCCATCAGGAGACCT 58.036 50.000 0.00 0.00 46.74 3.85
519 524 7.126733 ACCAGTACTGAACATATCTAACCTCT 58.873 38.462 24.68 0.00 0.00 3.69
523 528 8.033038 TGACAACCAGTACTGAACATATCTAAC 58.967 37.037 24.68 4.38 0.00 2.34
543 548 7.552687 TCCATGACCTTTGACTATATTGACAAC 59.447 37.037 0.00 0.00 0.00 3.32
550 555 9.745018 CCATAATTCCATGACCTTTGACTATAT 57.255 33.333 0.00 0.00 0.00 0.86
551 556 7.665559 GCCATAATTCCATGACCTTTGACTATA 59.334 37.037 0.00 0.00 0.00 1.31
553 558 5.827797 GCCATAATTCCATGACCTTTGACTA 59.172 40.000 0.00 0.00 0.00 2.59
554 559 4.646492 GCCATAATTCCATGACCTTTGACT 59.354 41.667 0.00 0.00 0.00 3.41
555 560 4.402155 TGCCATAATTCCATGACCTTTGAC 59.598 41.667 0.00 0.00 0.00 3.18
556 561 4.608269 TGCCATAATTCCATGACCTTTGA 58.392 39.130 0.00 0.00 0.00 2.69
558 563 5.776716 CCTATGCCATAATTCCATGACCTTT 59.223 40.000 0.00 0.00 0.00 3.11
577 582 6.094048 CACAGATTAACCACTGGTTTCCTATG 59.906 42.308 18.75 12.67 44.33 2.23
582 587 4.394729 TCCACAGATTAACCACTGGTTTC 58.605 43.478 18.75 11.14 44.33 2.78
606 611 2.749044 AACCATGCTGCTCGGCTG 60.749 61.111 0.00 0.00 0.00 4.85
607 612 2.749044 CAACCATGCTGCTCGGCT 60.749 61.111 0.00 0.00 0.00 5.52
608 613 2.146073 AAACAACCATGCTGCTCGGC 62.146 55.000 0.00 0.00 0.00 5.54
609 614 1.164411 TAAACAACCATGCTGCTCGG 58.836 50.000 0.00 3.66 0.00 4.63
610 615 2.226437 AGTTAAACAACCATGCTGCTCG 59.774 45.455 0.00 0.00 0.00 5.03
623 628 6.612247 ATCACGATCAACACAAGTTAAACA 57.388 33.333 0.00 0.00 35.85 2.83
638 643 3.185246 ACAGGGTCATGAATCACGATC 57.815 47.619 0.00 0.00 0.00 3.69
639 644 3.634397 AACAGGGTCATGAATCACGAT 57.366 42.857 0.00 0.00 0.00 3.73
640 645 3.417069 AAACAGGGTCATGAATCACGA 57.583 42.857 0.00 0.00 0.00 4.35
641 646 5.818136 AATAAACAGGGTCATGAATCACG 57.182 39.130 0.00 0.00 0.00 4.35
642 647 7.035612 GGAAAATAAACAGGGTCATGAATCAC 58.964 38.462 0.00 0.00 0.00 3.06
643 648 6.723515 TGGAAAATAAACAGGGTCATGAATCA 59.276 34.615 0.00 0.00 0.00 2.57
644 649 7.169158 TGGAAAATAAACAGGGTCATGAATC 57.831 36.000 0.00 0.00 0.00 2.52
645 650 7.399765 TCATGGAAAATAAACAGGGTCATGAAT 59.600 33.333 0.00 0.00 36.55 2.57
668 675 5.105752 GCACTCGTAATTCTCAGTCTTCAT 58.894 41.667 0.00 0.00 0.00 2.57
674 681 1.816835 TCGGCACTCGTAATTCTCAGT 59.183 47.619 0.00 0.00 40.32 3.41
679 686 4.328983 TCTGAAAATCGGCACTCGTAATTC 59.671 41.667 0.00 0.00 40.32 2.17
686 693 0.729690 GCCTCTGAAAATCGGCACTC 59.270 55.000 0.44 0.00 42.06 3.51
687 694 0.678048 GGCCTCTGAAAATCGGCACT 60.678 55.000 0.00 0.00 44.23 4.40
692 699 1.432270 GGCTCGGCCTCTGAAAATCG 61.432 60.000 0.00 0.00 46.69 3.34
714 721 0.836400 CCCATGATACCGGCCTACCT 60.836 60.000 0.00 0.00 0.00 3.08
724 731 0.655733 CAAACGGACGCCCATGATAC 59.344 55.000 0.00 0.00 0.00 2.24
767 774 2.613696 ATAGGCCTGCCACCCACA 60.614 61.111 17.99 0.00 38.92 4.17
785 792 1.429423 GCGGCCTGTATTTCACTGC 59.571 57.895 0.00 0.00 0.00 4.40
802 809 1.286260 CACTCCCTAGCCGTATCGC 59.714 63.158 0.00 0.00 0.00 4.58
856 864 1.153269 TGTCGCCTGTGCTGTTTCA 60.153 52.632 0.00 0.00 34.43 2.69
913 923 1.300697 GTGCCTCTGGTTTCGTCGT 60.301 57.895 0.00 0.00 0.00 4.34
914 924 2.372690 CGTGCCTCTGGTTTCGTCG 61.373 63.158 0.00 0.00 0.00 5.12
916 926 2.665185 GCGTGCCTCTGGTTTCGT 60.665 61.111 0.00 0.00 0.00 3.85
918 928 2.970974 GCTGCGTGCCTCTGGTTTC 61.971 63.158 0.00 0.00 35.15 2.78
982 1008 3.414700 CTCGCCGGAGCAACACAC 61.415 66.667 5.05 0.00 39.83 3.82
1018 1044 1.539827 GCAAACATACCCGTTGAGCTT 59.460 47.619 0.00 0.00 31.59 3.74
1047 1073 0.467290 GTTCAAGTGAGGGTTGGCCA 60.467 55.000 0.00 0.00 36.17 5.36
1070 1096 2.970324 GCGGCGGTGAACAGACAA 60.970 61.111 9.78 0.00 0.00 3.18
1109 1135 2.079925 GAATCGAAGCTGAGCCAACTT 58.920 47.619 0.00 0.00 0.00 2.66
1119 1145 2.219458 CATCCTGCATGAATCGAAGCT 58.781 47.619 0.00 0.00 33.80 3.74
1154 1180 2.027625 GACGAAACTGCTCCACGGG 61.028 63.158 0.00 0.00 0.00 5.28
1168 1194 0.250597 TGACTCGACTGGGAAGACGA 60.251 55.000 0.00 0.88 35.14 4.20
1208 1234 2.424640 GCGCCAAACACGACGTTC 60.425 61.111 0.00 0.00 36.59 3.95
1297 1323 2.029666 AGCACACTGACCTGCGTC 59.970 61.111 0.00 0.00 38.51 5.19
1329 1356 1.264288 CACGGCACTCCAAAGAAGAAC 59.736 52.381 0.00 0.00 0.00 3.01
1435 1464 7.013464 ACACCACCGAAAATAGAACAAATACAA 59.987 33.333 0.00 0.00 0.00 2.41
1436 1465 6.487331 ACACCACCGAAAATAGAACAAATACA 59.513 34.615 0.00 0.00 0.00 2.29
1437 1466 6.905578 ACACCACCGAAAATAGAACAAATAC 58.094 36.000 0.00 0.00 0.00 1.89
1462 1491 1.448365 CACGGCATGTGCAGCTAGA 60.448 57.895 7.36 0.00 42.70 2.43
1496 1527 9.388506 CTATATTTTCCTACCCAGAAGCATATG 57.611 37.037 0.00 0.00 0.00 1.78
1525 1556 5.659463 CACTTCCAACAATCTCCAAAACAA 58.341 37.500 0.00 0.00 0.00 2.83
1583 1620 8.780616 TCCAATTACCACATTATGAATCCAAT 57.219 30.769 0.00 0.00 0.00 3.16
1595 1632 6.594937 GTCATGCAAAAATCCAATTACCACAT 59.405 34.615 0.00 0.00 0.00 3.21
1618 1656 6.710744 TCTCTGTAAATTTCAAACCTCCAGTC 59.289 38.462 0.00 0.00 0.00 3.51
1662 1700 5.633830 AAACAAAGATGCTGATTCGACAT 57.366 34.783 0.00 0.00 0.00 3.06
1687 1725 8.540388 AGATCTAGCCTGTGAGTACAAATTTTA 58.460 33.333 0.00 0.00 36.14 1.52
1691 1729 5.658634 TCAGATCTAGCCTGTGAGTACAAAT 59.341 40.000 0.00 0.00 36.14 2.32
1700 1738 2.402305 GCGAATCAGATCTAGCCTGTG 58.598 52.381 0.00 0.00 33.57 3.66
1701 1739 1.000827 CGCGAATCAGATCTAGCCTGT 60.001 52.381 0.00 0.00 33.57 4.00
1706 1744 1.668337 CCCTGCGCGAATCAGATCTAG 60.668 57.143 12.10 0.00 33.54 2.43
1749 1787 3.000727 CACTGGTAGAACGGAACCAATC 58.999 50.000 0.00 0.00 44.92 2.67
1807 1845 4.690719 TTTGCCGACCGCGTCCAT 62.691 61.111 4.92 0.00 42.08 3.41
1923 1961 6.026513 GCTTCAGATCAACTTCAATGCTAAC 58.973 40.000 0.00 0.00 0.00 2.34
1927 1965 4.413087 CAGCTTCAGATCAACTTCAATGC 58.587 43.478 0.00 0.00 0.00 3.56
1929 1967 4.015084 CCCAGCTTCAGATCAACTTCAAT 58.985 43.478 0.00 0.00 0.00 2.57
1931 1969 2.373169 ACCCAGCTTCAGATCAACTTCA 59.627 45.455 0.00 0.00 0.00 3.02
1985 2023 4.575645 ACAAATTTGTCCCAAATTGCACTG 59.424 37.500 18.13 11.11 36.50 3.66
2016 2054 6.436218 GGGGAAAATCCAACAAACATACTACT 59.564 38.462 0.00 0.00 38.64 2.57
2037 2075 3.506743 TGCCTTTGCCACAGGGGA 61.507 61.111 0.00 0.00 40.01 4.81
2042 2080 1.273048 CATAAAGCTGCCTTTGCCACA 59.727 47.619 0.00 0.00 41.24 4.17
2043 2081 1.404583 CCATAAAGCTGCCTTTGCCAC 60.405 52.381 0.00 0.00 41.24 5.01
2044 2082 0.896923 CCATAAAGCTGCCTTTGCCA 59.103 50.000 0.00 0.00 41.24 4.92
2045 2083 0.897621 ACCATAAAGCTGCCTTTGCC 59.102 50.000 0.00 0.00 41.24 4.52
2048 2086 5.799827 TTTTACACCATAAAGCTGCCTTT 57.200 34.783 0.00 0.00 43.43 3.11
2070 2109 5.592587 AGCTATCTACTCTGACTACCCAT 57.407 43.478 0.00 0.00 0.00 4.00
2128 2167 3.154827 ACATCACTAACCCCCAAAGTG 57.845 47.619 0.00 0.00 41.58 3.16
2172 2211 4.083110 CCCACTGTAGCAAAACTCATCAAG 60.083 45.833 0.00 0.00 0.00 3.02
2184 2223 1.482182 CATGTAGCTCCCACTGTAGCA 59.518 52.381 0.00 0.00 41.32 3.49
2223 2263 8.995906 CGCTAAAGTTTTACTCCAAATTTATCG 58.004 33.333 0.00 0.00 0.00 2.92
2246 2286 1.918293 TCCCACTCAACCATCCGCT 60.918 57.895 0.00 0.00 0.00 5.52
2249 2289 2.514458 ATTGTCCCACTCAACCATCC 57.486 50.000 0.00 0.00 0.00 3.51
2250 2290 3.056607 CCAAATTGTCCCACTCAACCATC 60.057 47.826 0.00 0.00 0.00 3.51
2251 2291 2.899256 CCAAATTGTCCCACTCAACCAT 59.101 45.455 0.00 0.00 0.00 3.55
2265 2305 9.546428 AATCCTCAAAAGTTTTACTCCAAATTG 57.454 29.630 0.00 0.00 0.00 2.32
2268 2308 8.073467 ACAATCCTCAAAAGTTTTACTCCAAA 57.927 30.769 0.00 0.00 0.00 3.28
2367 2407 3.636764 GGATCCAACATCATTAACACCCC 59.363 47.826 6.95 0.00 0.00 4.95
2376 2416 6.514012 TGGTTATACTGGATCCAACATCAT 57.486 37.500 17.00 7.11 0.00 2.45
2402 2443 6.418819 CACTGGATCAAAACTCATCAAACAAC 59.581 38.462 0.00 0.00 0.00 3.32
2503 2546 3.573967 ACCCCAAGAACATTGATGAACAC 59.426 43.478 0.00 0.00 0.00 3.32
2517 2560 2.488891 CCTGTGTGAAATCACCCCAAGA 60.489 50.000 10.83 0.00 45.88 3.02
2542 2585 5.675538 CCTCTAGAAAATCCTCAAACGGAT 58.324 41.667 0.00 0.00 45.59 4.18
2545 2588 4.253685 TGCCTCTAGAAAATCCTCAAACG 58.746 43.478 0.00 0.00 0.00 3.60
2574 2617 3.111853 TGACTGACAACCTAAGCACAG 57.888 47.619 0.00 0.00 0.00 3.66
2624 2667 4.394920 CGGTAGCTACATTGGTGAATTTGT 59.605 41.667 24.75 0.00 0.00 2.83
2646 2689 3.589988 ACAGAGTTTCCTGCAAGATACG 58.410 45.455 0.96 0.00 37.68 3.06
2692 2739 1.643292 TGCATTCGCATTAGCTCGC 59.357 52.632 0.00 0.00 45.36 5.03
2705 2752 1.551883 GCTGAATGGTTCCCTTGCATT 59.448 47.619 0.00 0.00 0.00 3.56
2757 2804 5.005586 TGTTTTACAGAACAACGAACTACCG 59.994 40.000 0.00 0.00 36.64 4.02


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

AutoCloner maintained by Alex Coulton.