Multiple sequence alignment - TraesCS3A01G153400

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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 TraesCS3A01G153400 chr3A 100.000 3133 0 0 1 3133 144154344 144151212 0 5786
1 TraesCS3A01G153400 chr3B 89.032 3173 178 90 44 3133 187805455 187802370 0 3775
2 TraesCS3A01G153400 chr3D 86.535 2384 133 79 4 2273 131354047 131351738 0 2451
3 TraesCS3A01G153400 chr3D 92.188 832 32 12 2317 3133 131351735 131350922 0 1146


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 TraesCS3A01G153400 chr3A 144151212 144154344 3132 True 5786.0 5786 100.0000 1 3133 1 chr3A.!!$R1 3132
1 TraesCS3A01G153400 chr3B 187802370 187805455 3085 True 3775.0 3775 89.0320 44 3133 1 chr3B.!!$R1 3089
2 TraesCS3A01G153400 chr3D 131350922 131354047 3125 True 1798.5 2451 89.3615 4 3133 2 chr3D.!!$R1 3129

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
495 569 0.163146 CCCGCGTCTCGTTTTCTTTC 59.837 55.0 4.92 0.0 36.19 2.62 F
1647 1785 0.456824 TCACGATGAACTGCTCGCTC 60.457 55.0 0.00 0.0 38.42 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1830 0.179936 GCTGGATGGAGGTGGAAGAG 59.820 60.0 0.0 0.0 0.0 2.85 R
2637 2802 1.372087 GGGCTGGAGACTTTGCATCG 61.372 60.0 0.0 0.0 0.0 3.84 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
101 116 2.764547 CGTTCCCTCCCTCCCTCC 60.765 72.222 0.00 0.00 0.00 4.30
102 117 2.367107 GTTCCCTCCCTCCCTCCC 60.367 72.222 0.00 0.00 0.00 4.30
103 118 2.543637 TTCCCTCCCTCCCTCCCT 60.544 66.667 0.00 0.00 0.00 4.20
104 119 2.647949 TTCCCTCCCTCCCTCCCTC 61.648 68.421 0.00 0.00 0.00 4.30
105 120 4.548513 CCCTCCCTCCCTCCCTCG 62.549 77.778 0.00 0.00 0.00 4.63
106 121 3.430497 CCTCCCTCCCTCCCTCGA 61.430 72.222 0.00 0.00 0.00 4.04
132 151 1.750399 CATGCGTCAAAGGGGGAGG 60.750 63.158 0.00 0.00 0.00 4.30
133 152 2.983879 ATGCGTCAAAGGGGGAGGG 61.984 63.158 0.00 0.00 0.00 4.30
134 153 3.327404 GCGTCAAAGGGGGAGGGA 61.327 66.667 0.00 0.00 0.00 4.20
135 154 2.990479 CGTCAAAGGGGGAGGGAG 59.010 66.667 0.00 0.00 0.00 4.30
178 197 3.179939 GACGAGCCGTTTCGAGCC 61.180 66.667 12.01 0.00 41.37 4.70
179 198 4.736896 ACGAGCCGTTTCGAGCCC 62.737 66.667 12.01 0.00 43.03 5.19
181 200 4.388499 GAGCCGTTTCGAGCCCCA 62.388 66.667 0.00 0.00 0.00 4.96
182 201 4.394712 AGCCGTTTCGAGCCCCAG 62.395 66.667 0.00 0.00 0.00 4.45
183 202 4.388499 GCCGTTTCGAGCCCCAGA 62.388 66.667 0.00 0.00 0.00 3.86
280 301 4.379243 AACAGGCGAGTGCTCCCG 62.379 66.667 0.00 0.00 42.25 5.14
297 318 1.484240 CCCGCCAATCTCTTTCTCTCT 59.516 52.381 0.00 0.00 0.00 3.10
304 325 2.838637 TCTCTTTCTCTCTCCCCTCC 57.161 55.000 0.00 0.00 0.00 4.30
306 327 2.243736 TCTCTTTCTCTCTCCCCTCCTC 59.756 54.545 0.00 0.00 0.00 3.71
309 330 2.541233 TTCTCTCTCCCCTCCTCTTG 57.459 55.000 0.00 0.00 0.00 3.02
310 331 1.388174 TCTCTCTCCCCTCCTCTTGT 58.612 55.000 0.00 0.00 0.00 3.16
370 415 2.315925 TCATTCCTCATCCAAGCGAC 57.684 50.000 0.00 0.00 0.00 5.19
371 416 1.134401 TCATTCCTCATCCAAGCGACC 60.134 52.381 0.00 0.00 0.00 4.79
396 441 0.391263 ACCGGCCGTTTCATCTTCTC 60.391 55.000 26.12 0.00 0.00 2.87
400 445 2.437413 GGCCGTTTCATCTTCTCCTTT 58.563 47.619 0.00 0.00 0.00 3.11
418 484 6.014669 TCTCCTTTCCTCTTTCTTCTTCTCTG 60.015 42.308 0.00 0.00 0.00 3.35
419 485 5.012561 TCCTTTCCTCTTTCTTCTTCTCTGG 59.987 44.000 0.00 0.00 0.00 3.86
421 487 3.177228 TCCTCTTTCTTCTTCTCTGGGG 58.823 50.000 0.00 0.00 0.00 4.96
473 547 6.466885 TCATGCATGAGATCATCGATATCT 57.533 37.500 25.42 13.72 36.40 1.98
476 550 5.392480 GCATGAGATCATCGATATCTTGC 57.608 43.478 17.89 17.89 46.08 4.01
483 557 0.388649 ATCGATATCTTGCCCGCGTC 60.389 55.000 4.92 0.00 0.00 5.19
490 564 2.589442 TTGCCCGCGTCTCGTTTT 60.589 55.556 4.92 0.00 36.19 2.43
491 565 2.494504 CTTGCCCGCGTCTCGTTTTC 62.495 60.000 4.92 0.00 36.19 2.29
493 567 2.315386 GCCCGCGTCTCGTTTTCTT 61.315 57.895 4.92 0.00 36.19 2.52
495 569 0.163146 CCCGCGTCTCGTTTTCTTTC 59.837 55.000 4.92 0.00 36.19 2.62
497 571 1.525619 CCGCGTCTCGTTTTCTTTCTT 59.474 47.619 4.92 0.00 36.19 2.52
498 572 2.409879 CCGCGTCTCGTTTTCTTTCTTC 60.410 50.000 4.92 0.00 36.19 2.87
499 573 2.217847 CGCGTCTCGTTTTCTTTCTTCA 59.782 45.455 0.00 0.00 0.00 3.02
519 596 2.351726 CAGAAAAATACTTCTCCGGCGG 59.648 50.000 22.51 22.51 33.25 6.13
521 598 2.019948 AAAATACTTCTCCGGCGGTC 57.980 50.000 27.32 0.00 0.00 4.79
561 639 2.662527 TCGCGGTCGAAACCAACC 60.663 61.111 6.13 0.00 46.86 3.77
568 646 1.391144 GGTCGAAACCAACCGATTACG 59.609 52.381 0.00 0.00 45.68 3.18
569 647 2.061028 GTCGAAACCAACCGATTACGT 58.939 47.619 0.00 0.00 37.14 3.57
570 648 3.241701 GTCGAAACCAACCGATTACGTA 58.758 45.455 0.00 0.00 37.14 3.57
571 649 3.672867 GTCGAAACCAACCGATTACGTAA 59.327 43.478 11.02 11.02 37.14 3.18
572 650 3.672867 TCGAAACCAACCGATTACGTAAC 59.327 43.478 10.81 4.14 37.88 2.50
573 651 3.674753 CGAAACCAACCGATTACGTAACT 59.325 43.478 10.81 0.00 37.88 2.24
574 652 4.201523 CGAAACCAACCGATTACGTAACTC 60.202 45.833 10.81 8.62 37.88 3.01
577 655 4.427312 ACCAACCGATTACGTAACTCATC 58.573 43.478 10.81 3.34 37.88 2.92
598 682 2.595188 CGATTTGATTCGTGCGCTACAG 60.595 50.000 9.73 2.62 34.46 2.74
599 683 2.073117 TTTGATTCGTGCGCTACAGA 57.927 45.000 9.73 4.90 0.00 3.41
614 698 3.686726 GCTACAGAGAAGTTGGTCCATTG 59.313 47.826 0.00 0.00 0.00 2.82
616 700 3.744660 ACAGAGAAGTTGGTCCATTGAC 58.255 45.455 0.00 0.00 40.98 3.18
617 701 3.136443 ACAGAGAAGTTGGTCCATTGACA 59.864 43.478 0.00 0.00 43.65 3.58
619 703 4.023707 CAGAGAAGTTGGTCCATTGACAAC 60.024 45.833 0.00 0.00 43.65 3.32
624 708 3.822735 AGTTGGTCCATTGACAACTGATG 59.177 43.478 15.63 0.00 43.65 3.07
625 709 3.786368 TGGTCCATTGACAACTGATGA 57.214 42.857 0.00 0.00 43.65 2.92
626 710 4.305539 TGGTCCATTGACAACTGATGAT 57.694 40.909 0.00 0.00 43.65 2.45
627 711 4.264253 TGGTCCATTGACAACTGATGATC 58.736 43.478 0.00 0.00 43.65 2.92
628 712 4.263418 TGGTCCATTGACAACTGATGATCA 60.263 41.667 0.00 0.00 43.65 2.92
691 783 3.181530 CGCGGGATTATGATTTCATCGAC 60.182 47.826 0.00 0.00 37.76 4.20
697 789 5.633601 GGATTATGATTTCATCGACGTGCTA 59.366 40.000 0.00 0.00 37.76 3.49
698 790 5.883328 TTATGATTTCATCGACGTGCTAC 57.117 39.130 0.00 0.00 37.76 3.58
719 814 8.185505 TGCTACGTTAATAATTCCCAAACAATC 58.814 33.333 0.00 0.00 0.00 2.67
729 824 2.027561 TCCCAAACAATCCTGGTCTACG 60.028 50.000 0.00 0.00 0.00 3.51
732 827 3.056107 CCAAACAATCCTGGTCTACGAGA 60.056 47.826 0.00 0.00 0.00 4.04
733 828 4.383118 CCAAACAATCCTGGTCTACGAGAT 60.383 45.833 0.00 0.00 0.00 2.75
734 829 5.178797 CAAACAATCCTGGTCTACGAGATT 58.821 41.667 0.00 0.00 0.00 2.40
735 830 6.338146 CAAACAATCCTGGTCTACGAGATTA 58.662 40.000 0.00 0.00 0.00 1.75
736 831 6.732896 AACAATCCTGGTCTACGAGATTAT 57.267 37.500 0.00 0.00 0.00 1.28
742 843 9.930693 AATCCTGGTCTACGAGATTATAATTTC 57.069 33.333 6.02 6.02 0.00 2.17
763 864 2.359900 GTCCCGCTCTCAATCAATGTT 58.640 47.619 0.00 0.00 0.00 2.71
869 970 4.410883 TCCCTTTTCTTCCCATATAAGCGA 59.589 41.667 0.00 0.00 0.00 4.93
870 971 4.757149 CCCTTTTCTTCCCATATAAGCGAG 59.243 45.833 0.00 0.00 0.00 5.03
968 1072 6.015282 AGCTTCTCCAAGAAATCAAATCCTT 58.985 36.000 0.00 0.00 33.19 3.36
969 1073 6.152492 AGCTTCTCCAAGAAATCAAATCCTTC 59.848 38.462 0.00 0.00 33.19 3.46
971 1075 6.144845 TCTCCAAGAAATCAAATCCTTCCT 57.855 37.500 0.00 0.00 0.00 3.36
1086 1216 4.261781 CGGGCGGCCTACTACGTC 62.262 72.222 27.04 0.00 0.00 4.34
1398 1528 2.263540 GTCGCCGCCTTCTGGTTA 59.736 61.111 0.00 0.00 35.27 2.85
1407 1537 2.552031 GCCTTCTGGTTATCGGTTCTC 58.448 52.381 0.00 0.00 35.27 2.87
1413 1543 1.747355 TGGTTATCGGTTCTCGTCCTC 59.253 52.381 0.00 0.00 40.32 3.71
1485 1615 1.734477 CAGCGTCCTCGTCAAGGTG 60.734 63.158 0.00 0.00 46.32 4.00
1486 1616 3.112709 GCGTCCTCGTCAAGGTGC 61.113 66.667 0.00 0.00 46.32 5.01
1487 1617 2.338620 CGTCCTCGTCAAGGTGCA 59.661 61.111 0.00 0.00 46.32 4.57
1488 1618 1.079819 CGTCCTCGTCAAGGTGCAT 60.080 57.895 0.00 0.00 46.32 3.96
1489 1619 0.670546 CGTCCTCGTCAAGGTGCATT 60.671 55.000 0.00 0.00 46.32 3.56
1490 1620 1.523758 GTCCTCGTCAAGGTGCATTT 58.476 50.000 0.00 0.00 46.32 2.32
1491 1621 1.464997 GTCCTCGTCAAGGTGCATTTC 59.535 52.381 0.00 0.00 46.32 2.17
1492 1622 1.071542 TCCTCGTCAAGGTGCATTTCA 59.928 47.619 0.00 0.00 46.32 2.69
1497 1632 3.005554 CGTCAAGGTGCATTTCATCTCT 58.994 45.455 0.00 0.00 34.35 3.10
1499 1634 2.751259 TCAAGGTGCATTTCATCTCTGC 59.249 45.455 0.00 0.00 34.35 4.26
1518 1653 6.156949 TCTCTGCCACCTTAAATTCAGTATCT 59.843 38.462 0.00 0.00 0.00 1.98
1520 1655 5.437060 TGCCACCTTAAATTCAGTATCTCC 58.563 41.667 0.00 0.00 0.00 3.71
1525 1660 7.290248 CCACCTTAAATTCAGTATCTCCCTCTA 59.710 40.741 0.00 0.00 0.00 2.43
1526 1661 8.875168 CACCTTAAATTCAGTATCTCCCTCTAT 58.125 37.037 0.00 0.00 0.00 1.98
1532 1667 8.783660 AATTCAGTATCTCCCTCTATTACACA 57.216 34.615 0.00 0.00 0.00 3.72
1546 1684 9.449719 CCTCTATTACACAACCTTAGAATTTGT 57.550 33.333 0.00 0.00 33.69 2.83
1647 1785 0.456824 TCACGATGAACTGCTCGCTC 60.457 55.000 0.00 0.00 38.42 5.03
1653 1791 0.528017 TGAACTGCTCGCTCGAGATT 59.472 50.000 18.75 12.23 44.53 2.40
1692 1830 0.664761 CCATGTTCGGCATCCATGTC 59.335 55.000 0.00 0.00 35.19 3.06
1722 1860 3.513515 CCTCCATCCAGCTCTACTATTCC 59.486 52.174 0.00 0.00 0.00 3.01
1758 1902 0.928229 GCGGTCAGGTAATTAGCACG 59.072 55.000 16.53 14.54 0.00 5.34
1762 1906 2.352388 GTCAGGTAATTAGCACGCCAA 58.648 47.619 16.53 0.00 0.00 4.52
1773 1917 0.039256 GCACGCCAAAAAGCATCAGA 60.039 50.000 0.00 0.00 0.00 3.27
1774 1918 1.973138 CACGCCAAAAAGCATCAGAG 58.027 50.000 0.00 0.00 0.00 3.35
1776 1920 1.808945 ACGCCAAAAAGCATCAGAGAG 59.191 47.619 0.00 0.00 0.00 3.20
1777 1921 1.131883 CGCCAAAAAGCATCAGAGAGG 59.868 52.381 0.00 0.00 0.00 3.69
1779 1923 2.821969 GCCAAAAAGCATCAGAGAGGAA 59.178 45.455 0.00 0.00 0.00 3.36
1797 1941 2.480802 GGAACTCCGCTTTCTGAAGTTC 59.519 50.000 8.46 8.46 35.25 3.01
1814 1958 0.535335 TTCCTCCGTCAGAATTCCGG 59.465 55.000 13.57 13.57 43.03 5.14
1830 1974 4.363034 GGTAGCTAATGCCGCCTC 57.637 61.111 0.00 0.00 40.80 4.70
1831 1975 1.301795 GGTAGCTAATGCCGCCTCC 60.302 63.158 0.00 0.00 40.80 4.30
1832 1976 1.749033 GTAGCTAATGCCGCCTCCT 59.251 57.895 0.00 0.00 40.80 3.69
1833 1977 0.966920 GTAGCTAATGCCGCCTCCTA 59.033 55.000 0.00 0.00 40.80 2.94
1836 1980 0.601311 GCTAATGCCGCCTCCTACTG 60.601 60.000 0.00 0.00 0.00 2.74
1839 1983 2.599645 AATGCCGCCTCCTACTGCTG 62.600 60.000 0.00 0.00 0.00 4.41
2084 2228 1.403514 CCGGTTCTTGTGAGCTCTCTC 60.404 57.143 16.19 6.25 39.78 3.20
2106 2250 1.475571 CCGACAAGCCCATCATGATCA 60.476 52.381 4.86 0.00 0.00 2.92
2139 2283 4.551702 TGCAGCTACTCTTGATTTGGTA 57.448 40.909 0.00 0.00 0.00 3.25
2143 2287 5.819901 GCAGCTACTCTTGATTTGGTAATCT 59.180 40.000 0.00 0.00 40.68 2.40
2170 2317 7.928908 TGCTTGAGATGTTGTTAATTTTGAC 57.071 32.000 0.00 0.00 0.00 3.18
2183 2330 9.820229 TTGTTAATTTTGACAAGTATAAGAGCG 57.180 29.630 0.00 0.00 32.62 5.03
2217 2364 5.810074 TGTGATCGTGTAGATATTGTTGTGG 59.190 40.000 0.00 0.00 40.26 4.17
2219 2366 6.019801 GTGATCGTGTAGATATTGTTGTGGTC 60.020 42.308 0.00 0.00 40.26 4.02
2227 2374 4.635765 AGATATTGTTGTGGTCGTTCATGG 59.364 41.667 0.00 0.00 0.00 3.66
2231 2378 1.269448 GTTGTGGTCGTTCATGGCATT 59.731 47.619 0.00 0.00 0.00 3.56
2243 2390 1.411246 CATGGCATTGGAACCATCTGG 59.589 52.381 0.00 0.00 44.97 3.86
2331 2478 0.687354 GCTGTTTGAGGGGAGTCTGA 59.313 55.000 0.00 0.00 0.00 3.27
2349 2496 3.450096 TCTGATCTGTGGAATGGTGAGAG 59.550 47.826 0.00 0.00 0.00 3.20
2350 2497 3.176411 TGATCTGTGGAATGGTGAGAGT 58.824 45.455 0.00 0.00 0.00 3.24
2351 2498 3.055602 TGATCTGTGGAATGGTGAGAGTG 60.056 47.826 0.00 0.00 0.00 3.51
2352 2499 2.608623 TCTGTGGAATGGTGAGAGTGA 58.391 47.619 0.00 0.00 0.00 3.41
2353 2500 2.564504 TCTGTGGAATGGTGAGAGTGAG 59.435 50.000 0.00 0.00 0.00 3.51
2354 2501 2.564504 CTGTGGAATGGTGAGAGTGAGA 59.435 50.000 0.00 0.00 0.00 3.27
2457 2621 7.170277 GGAAGAATTGGGTTTTACAGGTAGTA 58.830 38.462 0.00 0.00 0.00 1.82
2458 2622 7.336176 GGAAGAATTGGGTTTTACAGGTAGTAG 59.664 40.741 0.00 0.00 33.43 2.57
2459 2623 7.325725 AGAATTGGGTTTTACAGGTAGTAGT 57.674 36.000 0.00 0.00 33.43 2.73
2560 2725 1.676967 CCACCCTGCTTCTGCCTTC 60.677 63.158 0.00 0.00 38.71 3.46
2562 2727 3.130160 CCCTGCTTCTGCCTTCGC 61.130 66.667 0.00 0.00 38.71 4.70
2564 2729 2.105466 CCTGCTTCTGCCTTCGCTC 61.105 63.158 0.00 0.00 38.71 5.03
2580 2745 1.675641 CTCCCTGCAAAACCCCGAG 60.676 63.158 0.00 0.00 0.00 4.63
2698 2863 2.186826 ACCTGCACGAAACTGGCAC 61.187 57.895 0.00 0.00 33.34 5.01
2764 2935 2.729862 GCAGCTTGTCGTCGTCGT 60.730 61.111 1.33 0.00 38.33 4.34
2765 2936 2.708059 GCAGCTTGTCGTCGTCGTC 61.708 63.158 1.33 0.00 38.33 4.20
2766 2937 2.127345 AGCTTGTCGTCGTCGTCG 60.127 61.111 5.50 5.50 38.33 5.12
2767 2938 2.426425 GCTTGTCGTCGTCGTCGT 60.426 61.111 11.41 0.00 38.33 4.34
2768 2939 2.415997 GCTTGTCGTCGTCGTCGTC 61.416 63.158 11.41 6.94 38.33 4.20
2769 2940 2.128017 TTGTCGTCGTCGTCGTCG 60.128 61.111 14.18 14.18 46.06 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.492482 GGAAGACAGCTGCTTCTCCTATC 60.492 52.174 31.50 19.55 41.11 2.08
1 2 2.433970 GGAAGACAGCTGCTTCTCCTAT 59.566 50.000 31.50 11.50 41.11 2.57
2 3 1.827969 GGAAGACAGCTGCTTCTCCTA 59.172 52.381 31.50 0.00 41.11 2.94
101 116 2.789917 GCATGCAGCTGTTCGAGG 59.210 61.111 16.64 0.10 41.15 4.63
102 117 2.288926 GACGCATGCAGCTGTTCGAG 62.289 60.000 19.57 7.99 42.61 4.04
103 118 2.357396 ACGCATGCAGCTGTTCGA 60.357 55.556 19.57 0.00 42.61 3.71
104 119 2.097160 GACGCATGCAGCTGTTCG 59.903 61.111 19.57 15.12 42.61 3.95
105 120 0.040157 TTTGACGCATGCAGCTGTTC 60.040 50.000 19.57 0.00 42.61 3.18
106 121 0.039798 CTTTGACGCATGCAGCTGTT 60.040 50.000 19.57 0.00 42.61 3.16
247 266 2.357034 TTCTTCGCCCACGCAGAC 60.357 61.111 0.00 0.00 41.29 3.51
280 301 2.158827 GGGGAGAGAGAAAGAGATTGGC 60.159 54.545 0.00 0.00 0.00 4.52
297 318 1.985895 GGAAGAAACAAGAGGAGGGGA 59.014 52.381 0.00 0.00 0.00 4.81
383 428 4.826556 AGAGGAAAGGAGAAGATGAAACG 58.173 43.478 0.00 0.00 0.00 3.60
389 434 6.950860 AGAAGAAAGAGGAAAGGAGAAGAT 57.049 37.500 0.00 0.00 0.00 2.40
396 441 5.244755 CCAGAGAAGAAGAAAGAGGAAAGG 58.755 45.833 0.00 0.00 0.00 3.11
400 445 3.177228 CCCCAGAGAAGAAGAAAGAGGA 58.823 50.000 0.00 0.00 0.00 3.71
443 509 3.650139 TGATCTCATGCATGATCTGACG 58.350 45.455 28.81 16.31 39.63 4.35
473 547 2.589442 AAAACGAGACGCGGGCAA 60.589 55.556 12.47 0.00 46.49 4.52
476 550 0.163146 GAAAGAAAACGAGACGCGGG 59.837 55.000 12.47 0.00 46.49 6.13
490 564 7.387948 CCGGAGAAGTATTTTTCTGAAGAAAGA 59.612 37.037 0.00 2.44 43.90 2.52
491 565 7.522374 CCGGAGAAGTATTTTTCTGAAGAAAG 58.478 38.462 0.00 0.00 43.90 2.62
493 567 5.411669 GCCGGAGAAGTATTTTTCTGAAGAA 59.588 40.000 5.05 0.00 37.53 2.52
495 569 4.201724 CGCCGGAGAAGTATTTTTCTGAAG 60.202 45.833 5.05 0.00 37.53 3.02
497 571 3.259064 CGCCGGAGAAGTATTTTTCTGA 58.741 45.455 5.05 0.00 37.53 3.27
498 572 2.351726 CCGCCGGAGAAGTATTTTTCTG 59.648 50.000 5.05 0.00 37.53 3.02
499 573 2.027469 ACCGCCGGAGAAGTATTTTTCT 60.027 45.455 11.71 0.00 40.02 2.52
549 626 2.061028 ACGTAATCGGTTGGTTTCGAC 58.939 47.619 0.00 0.00 41.85 4.20
556 634 3.484649 CGATGAGTTACGTAATCGGTTGG 59.515 47.826 17.21 1.40 41.85 3.77
558 636 4.621068 TCGATGAGTTACGTAATCGGTT 57.379 40.909 22.04 5.22 41.64 4.44
560 638 5.684184 TCAAATCGATGAGTTACGTAATCGG 59.316 40.000 22.04 10.94 41.64 4.18
561 639 6.727569 TCAAATCGATGAGTTACGTAATCG 57.272 37.500 18.37 18.37 42.45 3.34
562 640 7.939910 CGAATCAAATCGATGAGTTACGTAATC 59.060 37.037 11.86 10.37 45.48 1.75
563 641 7.434307 ACGAATCAAATCGATGAGTTACGTAAT 59.566 33.333 11.86 0.64 45.48 1.89
564 642 6.748658 ACGAATCAAATCGATGAGTTACGTAA 59.251 34.615 3.29 3.29 45.48 3.18
565 643 6.195798 CACGAATCAAATCGATGAGTTACGTA 59.804 38.462 0.00 0.00 45.48 3.57
566 644 5.004440 CACGAATCAAATCGATGAGTTACGT 59.996 40.000 0.00 5.43 45.48 3.57
567 645 5.415366 CACGAATCAAATCGATGAGTTACG 58.585 41.667 0.00 4.78 45.48 3.18
568 646 5.191059 GCACGAATCAAATCGATGAGTTAC 58.809 41.667 0.00 0.00 45.48 2.50
569 647 4.026886 CGCACGAATCAAATCGATGAGTTA 60.027 41.667 0.00 0.00 45.48 2.24
570 648 3.242091 CGCACGAATCAAATCGATGAGTT 60.242 43.478 0.00 0.00 45.48 3.01
571 649 2.282555 CGCACGAATCAAATCGATGAGT 59.717 45.455 0.00 0.00 45.48 3.41
572 650 2.884088 CGCACGAATCAAATCGATGAG 58.116 47.619 0.00 0.00 45.48 2.90
573 651 1.005032 GCGCACGAATCAAATCGATGA 60.005 47.619 0.30 0.00 45.48 2.92
574 652 1.004610 AGCGCACGAATCAAATCGATG 60.005 47.619 11.47 0.00 45.48 3.84
598 682 4.023707 CAGTTGTCAATGGACCAACTTCTC 60.024 45.833 12.63 0.00 43.65 2.87
599 683 3.885297 CAGTTGTCAATGGACCAACTTCT 59.115 43.478 12.63 0.00 43.65 2.85
614 698 7.846644 AGAAGAGAATTGATCATCAGTTGTC 57.153 36.000 11.01 11.01 36.89 3.18
616 700 8.948145 AGAAAGAAGAGAATTGATCATCAGTTG 58.052 33.333 0.00 0.00 0.00 3.16
617 701 9.517868 AAGAAAGAAGAGAATTGATCATCAGTT 57.482 29.630 0.00 0.00 0.00 3.16
619 703 9.386010 AGAAGAAAGAAGAGAATTGATCATCAG 57.614 33.333 0.00 0.00 0.00 2.90
624 708 8.791675 ACCAAAGAAGAAAGAAGAGAATTGATC 58.208 33.333 0.00 0.00 0.00 2.92
625 709 8.574737 CACCAAAGAAGAAAGAAGAGAATTGAT 58.425 33.333 0.00 0.00 0.00 2.57
626 710 7.775093 TCACCAAAGAAGAAAGAAGAGAATTGA 59.225 33.333 0.00 0.00 0.00 2.57
627 711 7.859875 GTCACCAAAGAAGAAAGAAGAGAATTG 59.140 37.037 0.00 0.00 0.00 2.32
628 712 7.557719 TGTCACCAAAGAAGAAAGAAGAGAATT 59.442 33.333 0.00 0.00 0.00 2.17
675 767 5.117135 CGTAGCACGTCGATGAAATCATAAT 59.883 40.000 12.58 0.00 39.13 1.28
697 789 7.363443 CCAGGATTGTTTGGGAATTATTAACGT 60.363 37.037 0.00 0.00 0.00 3.99
698 790 6.978080 CCAGGATTGTTTGGGAATTATTAACG 59.022 38.462 0.00 0.00 0.00 3.18
708 803 2.027561 CGTAGACCAGGATTGTTTGGGA 60.028 50.000 0.00 0.00 38.82 4.37
719 814 7.368833 ACGAAATTATAATCTCGTAGACCAGG 58.631 38.462 22.05 0.00 42.36 4.45
744 845 2.027285 TGAACATTGATTGAGAGCGGGA 60.027 45.455 0.00 0.00 0.00 5.14
745 846 2.096496 GTGAACATTGATTGAGAGCGGG 59.904 50.000 0.00 0.00 0.00 6.13
776 877 4.301637 TGACGCGCTATAATTGAAGAGA 57.698 40.909 5.73 0.00 0.00 3.10
869 970 2.618241 TGAAGATTGCAAGTTTGACGCT 59.382 40.909 4.94 0.00 0.00 5.07
870 971 2.975851 CTGAAGATTGCAAGTTTGACGC 59.024 45.455 4.94 0.00 0.00 5.19
1146 1276 2.359478 GGGCTGTTGTACACGGGG 60.359 66.667 0.00 0.00 31.45 5.73
1398 1528 2.772691 GGCGAGGACGAGAACCGAT 61.773 63.158 0.00 0.00 42.66 4.18
1407 1537 3.358076 GAGGGTGAAGGCGAGGACG 62.358 68.421 0.00 0.00 42.93 4.79
1413 1543 2.125912 CAGACGAGGGTGAAGGCG 60.126 66.667 0.00 0.00 0.00 5.52
1461 1591 1.180456 TGACGAGGACGCTGGGTTTA 61.180 55.000 0.00 0.00 43.96 2.01
1485 1615 1.760192 AGGTGGCAGAGATGAAATGC 58.240 50.000 0.00 0.00 39.25 3.56
1486 1616 5.902613 TTTAAGGTGGCAGAGATGAAATG 57.097 39.130 0.00 0.00 0.00 2.32
1487 1617 6.664816 TGAATTTAAGGTGGCAGAGATGAAAT 59.335 34.615 0.00 0.00 0.00 2.17
1488 1618 6.009589 TGAATTTAAGGTGGCAGAGATGAAA 58.990 36.000 0.00 0.00 0.00 2.69
1489 1619 5.569355 TGAATTTAAGGTGGCAGAGATGAA 58.431 37.500 0.00 0.00 0.00 2.57
1490 1620 5.178096 TGAATTTAAGGTGGCAGAGATGA 57.822 39.130 0.00 0.00 0.00 2.92
1491 1621 4.946157 ACTGAATTTAAGGTGGCAGAGATG 59.054 41.667 0.00 0.00 0.00 2.90
1492 1622 5.184892 ACTGAATTTAAGGTGGCAGAGAT 57.815 39.130 0.00 0.00 0.00 2.75
1497 1632 5.437060 GGAGATACTGAATTTAAGGTGGCA 58.563 41.667 0.00 0.00 0.00 4.92
1499 1634 6.100424 AGAGGGAGATACTGAATTTAAGGTGG 59.900 42.308 0.00 0.00 0.00 4.61
1518 1653 7.989947 ATTCTAAGGTTGTGTAATAGAGGGA 57.010 36.000 0.00 0.00 0.00 4.20
1520 1655 9.449719 ACAAATTCTAAGGTTGTGTAATAGAGG 57.550 33.333 0.00 0.00 34.28 3.69
1525 1660 8.700973 ACCAAACAAATTCTAAGGTTGTGTAAT 58.299 29.630 0.00 0.00 35.70 1.89
1526 1661 8.068892 ACCAAACAAATTCTAAGGTTGTGTAA 57.931 30.769 0.00 0.00 35.70 2.41
1531 1666 7.222611 CACAGAACCAAACAAATTCTAAGGTTG 59.777 37.037 0.00 0.00 37.95 3.77
1532 1667 7.264947 CACAGAACCAAACAAATTCTAAGGTT 58.735 34.615 0.00 0.00 40.31 3.50
1546 1684 1.677576 CAAGCTCTGCACAGAACCAAA 59.322 47.619 1.42 0.00 36.94 3.28
1647 1785 1.068474 GGTTGTGGACGTCAATCTCG 58.932 55.000 18.91 0.00 0.00 4.04
1653 1791 2.513259 GGAGGGGTTGTGGACGTCA 61.513 63.158 18.91 0.27 0.00 4.35
1692 1830 0.179936 GCTGGATGGAGGTGGAAGAG 59.820 60.000 0.00 0.00 0.00 2.85
1722 1860 1.302033 GCTGGCGATGGGTATCTGG 60.302 63.158 0.00 0.00 0.00 3.86
1758 1902 2.440409 TCCTCTCTGATGCTTTTTGGC 58.560 47.619 0.00 0.00 0.00 4.52
1762 1906 3.949132 GGAGTTCCTCTCTGATGCTTTT 58.051 45.455 0.00 0.00 42.40 2.27
1773 1917 1.633774 TCAGAAAGCGGAGTTCCTCT 58.366 50.000 0.00 0.00 31.21 3.69
1774 1918 2.289133 ACTTCAGAAAGCGGAGTTCCTC 60.289 50.000 0.00 0.00 35.81 3.71
1776 1920 2.171341 ACTTCAGAAAGCGGAGTTCC 57.829 50.000 0.00 0.00 35.81 3.62
1777 1921 2.480802 GGAACTTCAGAAAGCGGAGTTC 59.519 50.000 3.21 3.21 35.81 3.01
1779 1923 1.694696 AGGAACTTCAGAAAGCGGAGT 59.305 47.619 0.00 0.00 35.81 3.85
1781 1925 1.002087 GGAGGAACTTCAGAAAGCGGA 59.998 52.381 0.00 0.00 41.55 5.54
1782 1926 1.443802 GGAGGAACTTCAGAAAGCGG 58.556 55.000 0.00 0.00 41.55 5.52
1783 1927 1.071605 CGGAGGAACTTCAGAAAGCG 58.928 55.000 0.00 0.00 41.55 4.68
1784 1928 2.070028 GACGGAGGAACTTCAGAAAGC 58.930 52.381 0.00 0.00 41.55 3.51
1785 1929 3.005897 TCTGACGGAGGAACTTCAGAAAG 59.994 47.826 0.00 0.00 41.16 2.62
1786 1930 2.963101 TCTGACGGAGGAACTTCAGAAA 59.037 45.455 0.00 0.00 41.16 2.52
1787 1931 2.594131 TCTGACGGAGGAACTTCAGAA 58.406 47.619 0.00 0.00 41.16 3.02
1814 1958 0.966920 TAGGAGGCGGCATTAGCTAC 59.033 55.000 13.08 0.00 41.70 3.58
1828 1972 1.814586 GCAGCAGCAGCAGTAGGAG 60.815 63.158 4.63 0.00 45.49 3.69
1829 1973 2.267006 GCAGCAGCAGCAGTAGGA 59.733 61.111 4.63 0.00 45.49 2.94
1830 1974 2.107292 CAGCAGCAGCAGCAGTAGG 61.107 63.158 12.92 0.00 45.49 3.18
1831 1975 3.487417 CAGCAGCAGCAGCAGTAG 58.513 61.111 12.92 0.00 45.49 2.57
1857 2001 1.673033 CGGCTGGTAGAACTTGTCCAG 60.673 57.143 5.79 5.79 46.96 3.86
1979 2123 2.358737 GCCAAGTCCACGGTGAGG 60.359 66.667 10.28 4.64 0.00 3.86
2084 2228 0.392863 TCATGATGGGCTTGTCGGTG 60.393 55.000 0.00 0.00 0.00 4.94
2168 2312 8.700644 CAACCATTATACGCTCTTATACTTGTC 58.299 37.037 0.00 0.00 0.00 3.18
2170 2317 8.487970 CACAACCATTATACGCTCTTATACTTG 58.512 37.037 0.00 0.00 0.00 3.16
2176 2323 5.918576 CGATCACAACCATTATACGCTCTTA 59.081 40.000 0.00 0.00 0.00 2.10
2177 2324 4.745125 CGATCACAACCATTATACGCTCTT 59.255 41.667 0.00 0.00 0.00 2.85
2178 2325 4.202121 ACGATCACAACCATTATACGCTCT 60.202 41.667 0.00 0.00 0.00 4.09
2179 2326 4.049186 ACGATCACAACCATTATACGCTC 58.951 43.478 0.00 0.00 0.00 5.03
2180 2327 3.802139 CACGATCACAACCATTATACGCT 59.198 43.478 0.00 0.00 0.00 5.07
2181 2328 3.554324 ACACGATCACAACCATTATACGC 59.446 43.478 0.00 0.00 0.00 4.42
2182 2329 6.203647 TCTACACGATCACAACCATTATACG 58.796 40.000 0.00 0.00 0.00 3.06
2183 2330 9.856488 ATATCTACACGATCACAACCATTATAC 57.144 33.333 0.00 0.00 33.48 1.47
2217 2364 1.135402 GGTTCCAATGCCATGAACGAC 60.135 52.381 0.00 0.00 39.36 4.34
2219 2366 0.887247 TGGTTCCAATGCCATGAACG 59.113 50.000 0.00 0.00 39.36 3.95
2243 2390 7.559590 ACACTGATGCTGGAGAATTATTAAC 57.440 36.000 0.00 0.00 0.00 2.01
2255 2402 3.754850 TCTCAATCAAACACTGATGCTGG 59.245 43.478 0.00 0.00 44.43 4.85
2331 2478 3.176411 TCACTCTCACCATTCCACAGAT 58.824 45.455 0.00 0.00 0.00 2.90
2349 2496 4.109050 GGTCTTCGATTCAGATGTCTCAC 58.891 47.826 0.00 0.00 0.00 3.51
2350 2497 3.763897 TGGTCTTCGATTCAGATGTCTCA 59.236 43.478 0.00 0.00 0.00 3.27
2351 2498 4.377839 TGGTCTTCGATTCAGATGTCTC 57.622 45.455 0.00 0.00 0.00 3.36
2352 2499 4.808414 TTGGTCTTCGATTCAGATGTCT 57.192 40.909 0.00 0.00 0.00 3.41
2353 2500 4.872691 ACATTGGTCTTCGATTCAGATGTC 59.127 41.667 0.00 0.00 0.00 3.06
2354 2501 4.633126 CACATTGGTCTTCGATTCAGATGT 59.367 41.667 0.00 0.00 0.00 3.06
2422 2586 6.771934 AACCCAATTCTTCCCCAAAATTTA 57.228 33.333 0.00 0.00 0.00 1.40
2423 2587 5.661503 AACCCAATTCTTCCCCAAAATTT 57.338 34.783 0.00 0.00 0.00 1.82
2424 2588 5.661503 AAACCCAATTCTTCCCCAAAATT 57.338 34.783 0.00 0.00 0.00 1.82
2425 2589 5.661503 AAAACCCAATTCTTCCCCAAAAT 57.338 34.783 0.00 0.00 0.00 1.82
2426 2590 5.428783 TGTAAAACCCAATTCTTCCCCAAAA 59.571 36.000 0.00 0.00 0.00 2.44
2427 2591 4.969359 TGTAAAACCCAATTCTTCCCCAAA 59.031 37.500 0.00 0.00 0.00 3.28
2457 2621 2.146342 GCTGTTCAGCACATGTACACT 58.854 47.619 18.26 0.00 34.62 3.55
2458 2622 1.872952 TGCTGTTCAGCACATGTACAC 59.127 47.619 21.30 0.00 40.23 2.90
2459 2623 2.252976 TGCTGTTCAGCACATGTACA 57.747 45.000 21.30 0.00 40.23 2.90
2562 2727 1.675641 CTCGGGGTTTTGCAGGGAG 60.676 63.158 0.00 0.00 0.00 4.30
2564 2729 2.499303 ATCCTCGGGGTTTTGCAGGG 62.499 60.000 0.00 0.00 0.00 4.45
2580 2745 2.279120 CAGCTCCGACTGCGATCC 60.279 66.667 0.00 0.00 40.82 3.36
2637 2802 1.372087 GGGCTGGAGACTTTGCATCG 61.372 60.000 0.00 0.00 0.00 3.84
3046 3217 4.690719 CGCCGCCAGGGTGTACAA 62.691 66.667 0.00 0.00 41.61 2.41


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

AutoCloner maintained by Alex Coulton.