Multiple sequence alignment - TraesCS3B01G544500

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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 TraesCS3B01G544500 chr3B 100.000 2813 0 0 1 2813 781860147 781862959 0.000000e+00 5195.0
1 TraesCS3B01G544500 chr3A 86.428 2063 265 12 759 2813 485516261 485518316 0.000000e+00 2244.0
2 TraesCS3B01G544500 chr3A 88.028 1445 168 5 905 2346 724010362 724011804 0.000000e+00 1705.0
3 TraesCS3B01G544500 chr2A 82.655 1868 300 19 756 2610 28667056 28668912 0.000000e+00 1633.0
4 TraesCS3B01G544500 chr2A 82.046 1916 301 32 761 2659 695344327 695342438 0.000000e+00 1592.0
5 TraesCS3B01G544500 chr6A 85.195 1101 152 8 1718 2813 720447 719353 0.000000e+00 1120.0
6 TraesCS3B01G544500 chr6A 88.541 925 102 3 761 1682 721372 720449 0.000000e+00 1118.0
7 TraesCS3B01G544500 chr6A 92.698 315 21 2 1 314 289021022 289021335 1.190000e-123 453.0
8 TraesCS3B01G544500 chr1B 91.910 754 54 3 1 749 44503514 44502763 0.000000e+00 1048.0
9 TraesCS3B01G544500 chr1B 89.021 756 72 7 1 749 62420636 62421387 0.000000e+00 926.0
10 TraesCS3B01G544500 chr1B 100.000 33 0 0 566 598 576746662 576746694 8.410000e-06 62.1
11 TraesCS3B01G544500 chr4B 89.228 492 51 2 761 1251 65618100 65617610 5.150000e-172 614.0
12 TraesCS3B01G544500 chr4B 82.863 461 69 9 1 457 129547943 129547489 3.370000e-109 405.0
13 TraesCS3B01G544500 chr2B 86.111 468 51 6 1 467 745765550 745766004 2.520000e-135 492.0
14 TraesCS3B01G544500 chr5B 85.961 463 49 8 6 467 43353613 43354060 5.450000e-132 481.0
15 TraesCS3B01G544500 chr5B 91.515 330 24 4 1 329 408962347 408962673 4.270000e-123 451.0
16 TraesCS3B01G544500 chr4D 85.563 471 51 13 1 468 64623418 64623874 7.050000e-131 477.0
17 TraesCS3B01G544500 chr6B 91.642 335 26 2 1 335 715857912 715857580 1.970000e-126 462.0
18 TraesCS3B01G544500 chr6B 100.000 33 0 0 566 598 18155671 18155639 8.410000e-06 62.1
19 TraesCS3B01G544500 chr5D 78.807 637 126 9 2088 2719 438584926 438584294 1.200000e-113 420.0
20 TraesCS3B01G544500 chr5D 75.731 787 177 13 998 1777 379017589 379016810 1.580000e-102 383.0
21 TraesCS3B01G544500 chr5D 72.887 284 70 7 1037 1317 424969308 424969587 1.070000e-14 91.6
22 TraesCS3B01G544500 chr2D 100.000 30 0 0 2102 2131 549512147 549512176 3.910000e-04 56.5
23 TraesCS3B01G544500 chr2D 100.000 30 0 0 2102 2131 549986173 549986202 3.910000e-04 56.5


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 TraesCS3B01G544500 chr3B 781860147 781862959 2812 False 5195 5195 100.000 1 2813 1 chr3B.!!$F1 2812
1 TraesCS3B01G544500 chr3A 485516261 485518316 2055 False 2244 2244 86.428 759 2813 1 chr3A.!!$F1 2054
2 TraesCS3B01G544500 chr3A 724010362 724011804 1442 False 1705 1705 88.028 905 2346 1 chr3A.!!$F2 1441
3 TraesCS3B01G544500 chr2A 28667056 28668912 1856 False 1633 1633 82.655 756 2610 1 chr2A.!!$F1 1854
4 TraesCS3B01G544500 chr2A 695342438 695344327 1889 True 1592 1592 82.046 761 2659 1 chr2A.!!$R1 1898
5 TraesCS3B01G544500 chr6A 719353 721372 2019 True 1119 1120 86.868 761 2813 2 chr6A.!!$R1 2052
6 TraesCS3B01G544500 chr1B 44502763 44503514 751 True 1048 1048 91.910 1 749 1 chr1B.!!$R1 748
7 TraesCS3B01G544500 chr1B 62420636 62421387 751 False 926 926 89.021 1 749 1 chr1B.!!$F1 748
8 TraesCS3B01G544500 chr5D 438584294 438584926 632 True 420 420 78.807 2088 2719 1 chr5D.!!$R2 631
9 TraesCS3B01G544500 chr5D 379016810 379017589 779 True 383 383 75.731 998 1777 1 chr5D.!!$R1 779

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
349 351 0.041576 CGTCGGATCGTGCGAAGATA 60.042 55.0 8.44 0.0 42.99 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2228 0.39606 CCCTCTTGCCCTCTATCTGC 59.604 60.0 0.0 0.0 0.0 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.231964 GGGGTAGACACACGATGTAACA 59.768 50.000 0.00 0.00 43.56 2.41
103 105 1.296392 CTTGTGCCGATGTCCAGGA 59.704 57.895 0.00 0.00 0.00 3.86
123 125 1.680735 ACGACCGGGTGCGTTATTATA 59.319 47.619 3.30 0.00 37.48 0.98
124 126 2.287788 ACGACCGGGTGCGTTATTATAG 60.288 50.000 3.30 0.00 37.48 1.31
133 135 4.687483 GGTGCGTTATTATAGCGGTGTTAT 59.313 41.667 10.22 0.00 32.80 1.89
137 139 5.472148 CGTTATTATAGCGGTGTTATGGGA 58.528 41.667 0.00 0.00 0.00 4.37
163 165 2.445845 CCATAGTCAGGCCCCGGA 60.446 66.667 0.73 0.00 0.00 5.14
198 200 4.128643 TCGGTGAACCTCGTTAACAAATT 58.871 39.130 6.39 0.00 28.88 1.82
200 202 5.066246 TCGGTGAACCTCGTTAACAAATTTT 59.934 36.000 6.39 0.00 28.88 1.82
206 208 5.968254 ACCTCGTTAACAAATTTTGGTGTT 58.032 33.333 9.95 0.47 40.88 3.32
246 248 1.008424 CCTCGGATGATCGACGGTG 60.008 63.158 0.00 0.00 35.18 4.94
251 253 1.153647 GATGATCGACGGTGTGCCA 60.154 57.895 0.00 0.00 34.09 4.92
340 342 1.725706 GATAGATCGTCGTCGGATCGT 59.274 52.381 1.55 0.00 37.69 3.73
349 351 0.041576 CGTCGGATCGTGCGAAGATA 60.042 55.000 8.44 0.00 42.99 1.98
375 377 9.060347 AGTATGCGAAGAAATCAATATTGATGT 57.940 29.630 27.46 23.46 46.60 3.06
426 428 3.670377 GCCGTCAGGTGGTTTGCC 61.670 66.667 0.00 0.00 40.50 4.52
440 442 3.519107 TGGTTTGCCATCAGACTAGATCA 59.481 43.478 0.00 0.00 40.46 2.92
457 459 2.024176 TCAAGAAGGAGCAATACGGC 57.976 50.000 0.00 0.00 0.00 5.68
469 471 1.132262 CAATACGGCGGCATGAAAAGT 59.868 47.619 13.24 0.00 0.00 2.66
475 477 0.874390 GCGGCATGAAAAGTGTCTCA 59.126 50.000 0.00 0.00 0.00 3.27
486 488 4.689612 AAAGTGTCTCAGCAGTTAAGGA 57.310 40.909 0.00 0.00 32.30 3.36
522 524 0.598680 AGTGAGTTGCAGCAGACGTC 60.599 55.000 7.70 7.70 0.00 4.34
523 525 1.300931 TGAGTTGCAGCAGACGTCC 60.301 57.895 13.01 0.00 0.00 4.79
526 528 2.049156 TTGCAGCAGACGTCCGAG 60.049 61.111 13.01 3.77 0.00 4.63
536 538 0.109226 GACGTCCGAGAAGTGGAAGG 60.109 60.000 3.51 0.00 39.03 3.46
656 663 2.509916 GCAGGAGGCCCATCTGAG 59.490 66.667 18.28 0.00 36.11 3.35
657 664 2.068821 GCAGGAGGCCCATCTGAGA 61.069 63.158 18.28 0.00 36.11 3.27
658 665 2.042404 GCAGGAGGCCCATCTGAGAG 62.042 65.000 18.28 0.00 36.11 3.20
659 666 0.398239 CAGGAGGCCCATCTGAGAGA 60.398 60.000 10.96 0.00 33.88 3.10
660 667 0.567182 AGGAGGCCCATCTGAGAGAT 59.433 55.000 0.00 0.00 34.74 2.75
661 668 0.975887 GGAGGCCCATCTGAGAGATC 59.024 60.000 0.00 0.00 31.32 2.75
675 682 1.670949 GAGATCCTGAGCTGCACGGA 61.671 60.000 7.51 9.77 0.00 4.69
749 756 2.491298 GCTGGAGATGCAGATCGAGATA 59.509 50.000 14.60 0.00 33.34 1.98
750 757 3.673052 GCTGGAGATGCAGATCGAGATAC 60.673 52.174 14.60 0.00 33.34 2.24
751 758 3.490348 TGGAGATGCAGATCGAGATACA 58.510 45.455 0.00 0.00 33.34 2.29
752 759 3.254411 TGGAGATGCAGATCGAGATACAC 59.746 47.826 0.00 0.00 33.34 2.90
753 760 3.254411 GGAGATGCAGATCGAGATACACA 59.746 47.826 0.00 0.00 33.34 3.72
754 761 4.082300 GGAGATGCAGATCGAGATACACAT 60.082 45.833 0.00 0.00 33.34 3.21
773 780 5.424252 ACACATAAATCTCCCCTCTCGTTAA 59.576 40.000 0.00 0.00 0.00 2.01
788 797 3.245441 TCGTTAAGGTTTCTCTCCCCTT 58.755 45.455 0.00 0.00 41.38 3.95
801 810 4.514577 CCCTTGAGCGACGGCGAT 62.515 66.667 18.90 8.95 46.35 4.58
841 851 4.394712 CTCCCCGGCTGTTTCGCT 62.395 66.667 0.00 0.00 0.00 4.93
844 854 4.697756 CCCGGCTGTTTCGCTCCA 62.698 66.667 0.00 0.00 0.00 3.86
846 856 2.753966 CCGGCTGTTTCGCTCCATG 61.754 63.158 0.00 0.00 0.00 3.66
901 911 2.434774 GGGGAAGGTGGCGACTTT 59.565 61.111 0.00 0.00 0.00 2.66
903 913 1.241990 GGGGAAGGTGGCGACTTTTC 61.242 60.000 0.00 0.00 0.00 2.29
956 968 1.586422 CAAGCGATGATGGGTTCGAT 58.414 50.000 0.00 0.00 37.55 3.59
964 976 3.836365 TGATGGGTTCGATTGCATCTA 57.164 42.857 0.00 0.00 0.00 1.98
1013 1025 3.087031 CTGCAATGATGGAGGAACTTGT 58.913 45.455 0.00 0.00 41.55 3.16
1224 1236 4.820897 TGTACTCGATGCAATTCTCTTGT 58.179 39.130 0.00 0.00 0.00 3.16
1230 1242 4.402474 TCGATGCAATTCTCTTGTCTAGGA 59.598 41.667 0.00 0.00 0.00 2.94
1292 1304 2.711547 AGGGGAAAGCAGTAGTTCTGTT 59.288 45.455 0.00 0.00 45.23 3.16
1301 1313 3.619038 GCAGTAGTTCTGTTGGAGTATGC 59.381 47.826 0.00 0.00 45.23 3.14
1329 1341 3.441222 TCACAAAGCCGTCGACTATAGAA 59.559 43.478 14.70 0.00 0.00 2.10
1345 1357 8.808529 CGACTATAGAACTTAACAAACTGGATG 58.191 37.037 6.78 0.00 0.00 3.51
1407 1419 1.322442 AGGTCAAAGCTTTGTCTGCC 58.678 50.000 32.46 27.32 39.18 4.85
1430 1442 6.942576 GCCACTGTGGGAGAATTTATATATGT 59.057 38.462 27.02 0.00 38.19 2.29
1518 1530 2.864343 ACCTCTGAAGAACGTTGTTTCG 59.136 45.455 12.37 6.71 0.00 3.46
1529 1541 5.236911 AGAACGTTGTTTCGCTGGTAATAAA 59.763 36.000 5.00 0.00 0.00 1.40
1539 1551 5.416947 TCGCTGGTAATAAAGAAGAAGGAC 58.583 41.667 0.00 0.00 0.00 3.85
1546 1558 2.171341 AAAGAAGAAGGACTCGGTGC 57.829 50.000 0.00 0.00 0.00 5.01
1569 1581 4.797868 CAGCGAGTCATCTTTAGAGTCAAG 59.202 45.833 0.00 0.00 35.63 3.02
1594 1606 0.610232 AAGATTGCCAGACTGGTGCC 60.610 55.000 22.58 6.99 40.46 5.01
1692 1704 1.798813 GACATCAAGGACACGTGGTTC 59.201 52.381 21.57 9.15 0.00 3.62
1729 1741 1.078918 CCGGATGAGAGCAGCAACA 60.079 57.895 0.00 0.00 30.33 3.33
1730 1742 0.463295 CCGGATGAGAGCAGCAACAT 60.463 55.000 0.00 0.00 30.33 2.71
1806 1818 2.156504 CAGTGCTGACTCATTTGACGAC 59.843 50.000 0.00 0.00 0.00 4.34
1812 1824 4.556233 CTGACTCATTTGACGACCAGTAA 58.444 43.478 0.00 0.00 0.00 2.24
1830 1842 2.879103 AACATGAGGAACGGGAACAT 57.121 45.000 0.00 0.00 0.00 2.71
1853 1865 3.244009 CGAGATGGAGATGTAGCAATGGT 60.244 47.826 0.00 0.00 0.00 3.55
1859 1871 2.551459 GAGATGTAGCAATGGTGGATGC 59.449 50.000 0.00 0.00 42.87 3.91
1896 1908 3.393941 AGAGAGGGGCTAATGATCCAAAG 59.606 47.826 0.00 0.00 0.00 2.77
1898 1910 1.570501 AGGGGCTAATGATCCAAAGCA 59.429 47.619 11.10 0.00 36.68 3.91
1900 1912 1.334869 GGGCTAATGATCCAAAGCACG 59.665 52.381 11.10 0.00 36.68 5.34
1953 1965 2.126467 CAACTGTTTTTGCCATCACCG 58.874 47.619 0.00 0.00 0.00 4.94
1954 1966 1.686355 ACTGTTTTTGCCATCACCGA 58.314 45.000 0.00 0.00 0.00 4.69
1988 2000 2.761465 CCCCTCCCAAGCAGGATCC 61.761 68.421 2.48 2.48 41.22 3.36
2003 2015 4.578105 GCAGGATCCGAAGAGATCAAAATT 59.422 41.667 5.98 0.00 43.79 1.82
2006 2018 7.040823 GCAGGATCCGAAGAGATCAAAATTAAT 60.041 37.037 5.98 0.00 43.79 1.40
2008 2020 8.435982 AGGATCCGAAGAGATCAAAATTAATCT 58.564 33.333 5.98 0.00 43.79 2.40
2010 2022 9.875675 GATCCGAAGAGATCAAAATTAATCTTG 57.124 33.333 0.00 0.00 41.96 3.02
2013 2025 8.887717 CCGAAGAGATCAAAATTAATCTTGTCT 58.112 33.333 1.57 4.41 32.43 3.41
2055 2067 6.174049 GGAGAAGAGTACAGCTTTTACCAAT 58.826 40.000 0.00 0.00 0.00 3.16
2066 2078 5.418840 CAGCTTTTACCAATAACCCTGATGT 59.581 40.000 0.00 0.00 0.00 3.06
2075 2087 2.307496 AACCCTGATGTGCATTTGGA 57.693 45.000 0.00 0.00 0.00 3.53
2118 2131 3.316588 CCTAGCGCAATGAGTCTTCTCTA 59.683 47.826 11.47 0.00 40.98 2.43
2203 2216 1.555967 TTGCCCCCTCTATTGTTTGC 58.444 50.000 0.00 0.00 0.00 3.68
2215 2228 6.306356 CCTCTATTGTTTGCATTCTTGAAACG 59.694 38.462 0.00 0.00 33.18 3.60
2270 2283 9.046846 TGGCTGATAGTATAGGCTACAATAAAT 57.953 33.333 0.00 0.00 39.90 1.40
2315 2328 3.490348 AGAAGTGGTGGTCTTGGAATTG 58.510 45.455 0.00 0.00 0.00 2.32
2501 2515 1.412710 GACGCAGAATAGACCATGGGA 59.587 52.381 18.09 0.54 0.00 4.37
2505 2519 2.173569 GCAGAATAGACCATGGGAGGTT 59.826 50.000 18.09 5.54 43.38 3.50
2535 2549 8.743714 GGAGATTTTAATGAGGTTCTTCACATT 58.256 33.333 0.00 0.00 36.94 2.71
2548 2562 7.830697 AGGTTCTTCACATTCATGAACATGATA 59.169 33.333 19.17 11.09 46.12 2.15
2582 2596 2.834638 AGCCAAGCCCAAATAGATGT 57.165 45.000 0.00 0.00 0.00 3.06
2596 2610 2.957402 AGATGTGTTCAGGGAAGCAA 57.043 45.000 0.00 0.00 0.00 3.91
2610 2624 3.701040 GGGAAGCAATTGATACATGTGGT 59.299 43.478 10.34 0.00 0.00 4.16
2613 2627 5.126061 GGAAGCAATTGATACATGTGGTCTT 59.874 40.000 10.34 0.00 0.00 3.01
2636 2650 3.511540 TCAGATATTGGATACTCCGGCTG 59.488 47.826 0.00 0.00 40.17 4.85
2653 2667 2.608752 GGCTGCAGTTGGACATTTGAAG 60.609 50.000 16.64 0.00 0.00 3.02
2667 2681 6.840780 ACATTTGAAGAAAAGGTCATAGGG 57.159 37.500 0.00 0.00 38.34 3.53
2672 2686 1.566231 AGAAAAGGTCATAGGGGGCAG 59.434 52.381 0.00 0.00 0.00 4.85
2679 2693 1.204941 GTCATAGGGGGCAGCTATACG 59.795 57.143 0.00 0.00 0.00 3.06
2689 2703 0.672342 CAGCTATACGCGGGTTAGGT 59.328 55.000 11.50 14.15 45.59 3.08
2702 2716 0.109723 GTTAGGTTGGACAGGTGCCA 59.890 55.000 0.00 0.00 0.00 4.92
2706 2720 1.898574 GTTGGACAGGTGCCAGGTG 60.899 63.158 0.00 0.00 36.64 4.00
2721 2735 1.002069 AGGTGAATCCTGAATGGGCA 58.998 50.000 0.00 0.00 46.19 5.36
2724 2738 1.747355 GTGAATCCTGAATGGGCACTG 59.253 52.381 0.00 0.00 36.20 3.66
2739 2753 0.545171 CACTGGCCCTCACATCATCT 59.455 55.000 0.00 0.00 0.00 2.90
2740 2754 0.545171 ACTGGCCCTCACATCATCTG 59.455 55.000 0.00 0.00 0.00 2.90
2744 2758 0.534652 GCCCTCACATCATCTGAGCC 60.535 60.000 0.00 0.00 34.84 4.70
2745 2759 0.249784 CCCTCACATCATCTGAGCCG 60.250 60.000 0.00 0.00 34.84 5.52
2747 2761 1.568606 CTCACATCATCTGAGCCGTG 58.431 55.000 0.00 0.00 0.00 4.94
2751 2765 0.534427 CATCATCTGAGCCGTGGCAT 60.534 55.000 14.29 0.00 44.88 4.40
2754 2768 1.202568 TCATCTGAGCCGTGGCATAAG 60.203 52.381 14.29 7.35 44.88 1.73
2758 2772 1.153369 GAGCCGTGGCATAAGAGCA 60.153 57.895 14.29 0.00 44.88 4.26
2759 2773 0.533755 GAGCCGTGGCATAAGAGCAT 60.534 55.000 14.29 0.00 44.88 3.79
2760 2774 0.816825 AGCCGTGGCATAAGAGCATG 60.817 55.000 14.29 0.00 44.88 4.06
2775 2789 3.647113 AGAGCATGGCTAGTTCAGATCAT 59.353 43.478 0.00 0.00 39.88 2.45
2776 2790 3.995705 GAGCATGGCTAGTTCAGATCATC 59.004 47.826 0.00 0.00 39.88 2.92
2778 2792 3.995705 GCATGGCTAGTTCAGATCATCTC 59.004 47.826 0.00 0.00 0.00 2.75
2781 2795 2.301583 GGCTAGTTCAGATCATCTCCCC 59.698 54.545 0.00 0.00 0.00 4.81
2784 2798 4.322650 GCTAGTTCAGATCATCTCCCCATC 60.323 50.000 0.00 0.00 0.00 3.51
2787 2801 4.140591 AGTTCAGATCATCTCCCCATCCTA 60.141 45.833 0.00 0.00 0.00 2.94
2790 2804 4.608028 TCAGATCATCTCCCCATCCTACTA 59.392 45.833 0.00 0.00 0.00 1.82
2798 2812 2.516702 TCCCCATCCTACTACAGCTACA 59.483 50.000 0.00 0.00 0.00 2.74
2803 2817 5.073428 CCATCCTACTACAGCTACATGAGA 58.927 45.833 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 5.879763 TCCTGTGCTATTATGTTGGCATAT 58.120 37.500 0.00 0.00 37.42 1.78
86 88 1.003839 GTCCTGGACATCGGCACAA 60.004 57.895 21.70 0.00 32.09 3.33
94 96 3.075005 CCCGGTCGTCCTGGACAT 61.075 66.667 25.42 0.00 39.99 3.06
103 105 0.461135 ATAATAACGCACCCGGTCGT 59.539 50.000 0.00 4.05 41.06 4.34
116 118 6.270463 TCCTTCCCATAACACCGCTATAATAA 59.730 38.462 0.00 0.00 0.00 1.40
123 125 0.541863 CTCCTTCCCATAACACCGCT 59.458 55.000 0.00 0.00 0.00 5.52
124 126 1.095807 GCTCCTTCCCATAACACCGC 61.096 60.000 0.00 0.00 0.00 5.68
137 139 1.690219 CCTGACTATGGGCGCTCCTT 61.690 60.000 3.94 6.68 36.20 3.36
148 150 0.833834 CATCTCCGGGGCCTGACTAT 60.834 60.000 15.75 0.31 0.00 2.12
163 165 3.006967 GGTTCACCGATATGGCTACATCT 59.993 47.826 0.00 0.00 43.94 2.90
198 200 0.449786 CACACGAGCACAACACCAAA 59.550 50.000 0.00 0.00 0.00 3.28
200 202 0.179059 ATCACACGAGCACAACACCA 60.179 50.000 0.00 0.00 0.00 4.17
206 208 0.587768 CAAGCAATCACACGAGCACA 59.412 50.000 0.00 0.00 0.00 4.57
246 248 5.123344 ACTTGTTAGAATAAATCCGTGGCAC 59.877 40.000 7.79 7.79 0.00 5.01
251 253 8.262227 TGATACCACTTGTTAGAATAAATCCGT 58.738 33.333 0.00 0.00 0.00 4.69
340 342 3.982576 TCTTCGCATACTATCTTCGCA 57.017 42.857 0.00 0.00 0.00 5.10
349 351 9.060347 ACATCAATATTGATTTCTTCGCATACT 57.940 29.630 25.16 0.86 45.13 2.12
370 372 3.878699 CCAATCGATCACCATTGACATCA 59.121 43.478 0.00 0.00 33.38 3.07
375 377 3.643199 TTCCCAATCGATCACCATTGA 57.357 42.857 0.00 0.00 32.56 2.57
379 381 3.931907 AGAATTCCCAATCGATCACCA 57.068 42.857 0.00 0.00 0.00 4.17
381 383 4.800471 GCAAAAGAATTCCCAATCGATCAC 59.200 41.667 0.00 0.00 0.00 3.06
426 428 5.068855 TGCTCCTTCTTGATCTAGTCTGATG 59.931 44.000 4.06 0.00 0.00 3.07
434 436 4.501571 GCCGTATTGCTCCTTCTTGATCTA 60.502 45.833 0.00 0.00 0.00 1.98
440 442 0.462047 CCGCCGTATTGCTCCTTCTT 60.462 55.000 0.00 0.00 0.00 2.52
457 459 1.135859 GCTGAGACACTTTTCATGCCG 60.136 52.381 0.00 0.00 0.00 5.69
469 471 4.245660 CGATTTCCTTAACTGCTGAGACA 58.754 43.478 0.00 0.00 0.00 3.41
475 477 2.359900 CTGCCGATTTCCTTAACTGCT 58.640 47.619 0.00 0.00 0.00 4.24
486 488 0.392998 ACTGATTCCGCTGCCGATTT 60.393 50.000 0.00 0.00 36.29 2.17
522 524 1.153745 CGAGCCTTCCACTTCTCGG 60.154 63.158 2.91 0.00 43.13 4.63
523 525 4.485554 CGAGCCTTCCACTTCTCG 57.514 61.111 0.00 0.00 41.66 4.04
526 528 2.048127 ACGCGAGCCTTCCACTTC 60.048 61.111 15.93 0.00 0.00 3.01
655 662 1.674764 CCGTGCAGCTCAGGATCTCT 61.675 60.000 0.00 0.00 32.56 3.10
656 663 1.227205 CCGTGCAGCTCAGGATCTC 60.227 63.158 0.00 0.00 32.56 2.75
657 664 1.260538 TTCCGTGCAGCTCAGGATCT 61.261 55.000 8.29 0.00 32.56 2.75
658 665 0.391661 TTTCCGTGCAGCTCAGGATC 60.392 55.000 8.29 0.00 32.56 3.36
659 666 0.254178 ATTTCCGTGCAGCTCAGGAT 59.746 50.000 8.29 0.00 32.56 3.24
660 667 0.036732 AATTTCCGTGCAGCTCAGGA 59.963 50.000 0.00 0.00 32.56 3.86
661 668 0.169672 CAATTTCCGTGCAGCTCAGG 59.830 55.000 0.00 0.00 0.00 3.86
675 682 1.595093 CCCTTCGCTTCGCCCAATTT 61.595 55.000 0.00 0.00 0.00 1.82
749 756 3.375699 ACGAGAGGGGAGATTTATGTGT 58.624 45.455 0.00 0.00 0.00 3.72
750 757 4.408182 AACGAGAGGGGAGATTTATGTG 57.592 45.455 0.00 0.00 0.00 3.21
751 758 5.070580 CCTTAACGAGAGGGGAGATTTATGT 59.929 44.000 0.00 0.00 0.00 2.29
752 759 5.070580 ACCTTAACGAGAGGGGAGATTTATG 59.929 44.000 0.00 0.00 38.65 1.90
753 760 5.217400 ACCTTAACGAGAGGGGAGATTTAT 58.783 41.667 0.00 0.00 38.65 1.40
754 761 4.617593 ACCTTAACGAGAGGGGAGATTTA 58.382 43.478 0.00 0.00 38.65 1.40
801 810 2.363276 ATCCCTACGGTGTCGGCA 60.363 61.111 0.00 0.00 41.39 5.69
844 854 4.957684 CTCAGCGATCGCCGGCAT 62.958 66.667 34.89 18.88 43.17 4.40
889 899 2.032071 CCCGAAAAGTCGCCACCT 59.968 61.111 0.00 0.00 46.28 4.00
918 929 1.602327 GCTCGAGGTTAGGGTTCCGT 61.602 60.000 15.58 0.00 0.00 4.69
956 968 2.031069 GCCGTACTCGATCTAGATGCAA 60.031 50.000 10.74 0.00 39.71 4.08
964 976 2.716244 CGCAGCCGTACTCGATCT 59.284 61.111 0.00 0.00 39.71 2.75
1013 1025 7.191593 TCAATCAGATCATCTTCTTTCAGGA 57.808 36.000 0.00 0.00 0.00 3.86
1060 1072 0.597637 CGCGTATCTTCCTTCGGCAT 60.598 55.000 0.00 0.00 0.00 4.40
1224 1236 1.227249 CCCTCTCCCAGTCTCCTAGA 58.773 60.000 0.00 0.00 0.00 2.43
1230 1242 1.344496 CCCATAACCCTCTCCCAGTCT 60.344 57.143 0.00 0.00 0.00 3.24
1292 1304 0.983467 TGTGAAGCCAGCATACTCCA 59.017 50.000 0.00 0.00 0.00 3.86
1345 1357 4.337555 CAGGTCATGAATCTGGATCCAAAC 59.662 45.833 17.00 7.91 0.00 2.93
1407 1419 9.559732 TCAACATATATAAATTCTCCCACAGTG 57.440 33.333 0.00 0.00 0.00 3.66
1422 1434 7.618117 TCCGGAAATCTAGGCTCAACATATATA 59.382 37.037 0.00 0.00 0.00 0.86
1430 1442 4.503714 AAATCCGGAAATCTAGGCTCAA 57.496 40.909 9.01 0.00 0.00 3.02
1442 1454 4.453136 CGAAGTTACCTTCAAAATCCGGAA 59.547 41.667 9.01 0.00 46.19 4.30
1477 1489 6.157645 AGAGGTTTAGTGACATCAATCCTGAT 59.842 38.462 6.41 0.00 43.40 2.90
1518 1530 5.520649 CGAGTCCTTCTTCTTTATTACCAGC 59.479 44.000 0.00 0.00 0.00 4.85
1529 1541 0.605589 CTGCACCGAGTCCTTCTTCT 59.394 55.000 0.00 0.00 0.00 2.85
1546 1558 4.362932 TGACTCTAAAGATGACTCGCTG 57.637 45.455 0.00 0.00 0.00 5.18
1569 1581 4.095483 CACCAGTCTGGCAATCTTTCATAC 59.905 45.833 19.40 0.00 42.67 2.39
1594 1606 1.066143 ACCTAGATGTCCGCAAACTGG 60.066 52.381 0.00 0.00 0.00 4.00
1682 1694 1.826487 GGGCCTTTGAACCACGTGT 60.826 57.895 15.65 0.00 0.00 4.49
1692 1704 2.993264 CCACTGCCAGGGCCTTTG 60.993 66.667 1.32 0.00 41.09 2.77
1715 1727 1.005097 TCCCAATGTTGCTGCTCTCAT 59.995 47.619 0.00 0.27 0.00 2.90
1729 1741 3.483869 GCCTCGGCCTCTCCCAAT 61.484 66.667 0.00 0.00 34.56 3.16
1806 1818 1.553248 TCCCGTTCCTCATGTTACTGG 59.447 52.381 0.00 0.00 0.00 4.00
1812 1824 1.405526 CGATGTTCCCGTTCCTCATGT 60.406 52.381 0.00 0.00 0.00 3.21
1830 1842 3.006217 CCATTGCTACATCTCCATCTCGA 59.994 47.826 0.00 0.00 0.00 4.04
1853 1865 4.832823 TCTTCCTATTACGATCAGCATCCA 59.167 41.667 0.00 0.00 0.00 3.41
1859 1871 4.461081 CCCCTCTCTTCCTATTACGATCAG 59.539 50.000 0.00 0.00 0.00 2.90
1896 1908 3.050275 GAGGTTGGGAGTGCGTGC 61.050 66.667 0.00 0.00 0.00 5.34
1898 1910 1.371558 GAAGAGGTTGGGAGTGCGT 59.628 57.895 0.00 0.00 0.00 5.24
1900 1912 0.398318 ACTGAAGAGGTTGGGAGTGC 59.602 55.000 0.00 0.00 0.00 4.40
1953 1965 2.187163 GGGCTAAGAGGCACCGTC 59.813 66.667 2.24 0.00 43.44 4.79
1954 1966 3.400054 GGGGCTAAGAGGCACCGT 61.400 66.667 2.24 0.00 46.38 4.83
2003 2015 6.546403 AGCCGACTCATTAGTAGACAAGATTA 59.454 38.462 0.00 0.00 35.56 1.75
2006 2018 4.270834 AGCCGACTCATTAGTAGACAAGA 58.729 43.478 0.00 0.00 35.56 3.02
2008 2020 3.380637 GGAGCCGACTCATTAGTAGACAA 59.619 47.826 0.00 0.00 45.42 3.18
2010 2022 2.031857 CGGAGCCGACTCATTAGTAGAC 60.032 54.545 2.00 0.00 45.42 2.59
2013 2025 1.134007 TCCGGAGCCGACTCATTAGTA 60.134 52.381 11.05 0.00 45.42 1.82
2025 2037 0.741915 CTGTACTCTTCTCCGGAGCC 59.258 60.000 27.39 8.22 34.46 4.70
2055 2067 3.355378 CTCCAAATGCACATCAGGGTTA 58.645 45.455 0.00 0.00 0.00 2.85
2118 2131 1.468520 CAATTCCGCGACAGTTCCAAT 59.531 47.619 8.23 0.00 0.00 3.16
2147 2160 0.459237 CGAAGCTCTCTGAATGCCGT 60.459 55.000 0.00 0.00 0.00 5.68
2203 2216 4.272018 CCCTCTATCTGCGTTTCAAGAATG 59.728 45.833 0.00 0.00 0.00 2.67
2215 2228 0.396060 CCCTCTTGCCCTCTATCTGC 59.604 60.000 0.00 0.00 0.00 4.26
2270 2283 3.064207 CGGAACTACTAACTGCAAAGCA 58.936 45.455 0.00 0.00 36.92 3.91
2315 2328 9.143631 CTTCCACTTTTATTCATCATTCCAAAC 57.856 33.333 0.00 0.00 0.00 2.93
2416 2430 2.202851 CTGAGCTTCGCCGCAGAT 60.203 61.111 0.00 0.00 34.76 2.90
2420 2434 2.886124 GTACCTGAGCTTCGCCGC 60.886 66.667 0.00 0.00 0.00 6.53
2421 2435 2.202756 GGTACCTGAGCTTCGCCG 60.203 66.667 4.06 0.00 0.00 6.46
2501 2515 7.226059 ACCTCATTAAAATCTCCCATAACCT 57.774 36.000 0.00 0.00 0.00 3.50
2505 2519 8.556589 TGAAGAACCTCATTAAAATCTCCCATA 58.443 33.333 0.00 0.00 0.00 2.74
2535 2549 4.224818 TGTCCCACACTATCATGTTCATGA 59.775 41.667 16.19 16.19 34.73 3.07
2548 2562 0.550914 TGGCTTCTTTGTCCCACACT 59.449 50.000 0.00 0.00 0.00 3.55
2582 2596 4.661222 TGTATCAATTGCTTCCCTGAACA 58.339 39.130 0.00 0.00 0.00 3.18
2636 2650 4.746611 CCTTTTCTTCAAATGTCCAACTGC 59.253 41.667 0.00 0.00 0.00 4.40
2653 2667 2.024306 GCTGCCCCCTATGACCTTTTC 61.024 57.143 0.00 0.00 0.00 2.29
2663 2677 2.273179 CGCGTATAGCTGCCCCCTA 61.273 63.158 0.00 0.00 45.59 3.53
2667 2681 2.091102 TAACCCGCGTATAGCTGCCC 62.091 60.000 4.92 0.00 45.59 5.36
2672 2686 1.494824 CAACCTAACCCGCGTATAGC 58.505 55.000 4.92 0.00 43.95 2.97
2679 2693 1.376812 CCTGTCCAACCTAACCCGC 60.377 63.158 0.00 0.00 0.00 6.13
2689 2703 1.640593 TTCACCTGGCACCTGTCCAA 61.641 55.000 0.00 0.00 32.41 3.53
2706 2720 1.396653 CCAGTGCCCATTCAGGATTC 58.603 55.000 0.00 0.00 41.22 2.52
2721 2735 0.545171 CAGATGATGTGAGGGCCAGT 59.455 55.000 6.18 0.00 0.00 4.00
2724 2738 0.534652 GCTCAGATGATGTGAGGGCC 60.535 60.000 19.50 0.00 41.60 5.80
2731 2745 1.153289 GCCACGGCTCAGATGATGT 60.153 57.895 0.00 0.00 38.26 3.06
2739 2753 1.153369 GCTCTTATGCCACGGCTCA 60.153 57.895 9.92 0.00 42.51 4.26
2740 2754 0.533755 ATGCTCTTATGCCACGGCTC 60.534 55.000 9.92 0.00 42.51 4.70
2744 2758 0.816825 AGCCATGCTCTTATGCCACG 60.817 55.000 0.00 0.00 30.62 4.94
2745 2759 2.149578 CTAGCCATGCTCTTATGCCAC 58.850 52.381 0.00 0.00 40.44 5.01
2747 2761 2.557920 ACTAGCCATGCTCTTATGCC 57.442 50.000 0.00 0.00 40.44 4.40
2751 2765 4.651045 TGATCTGAACTAGCCATGCTCTTA 59.349 41.667 0.00 0.00 40.44 2.10
2754 2768 3.465742 TGATCTGAACTAGCCATGCTC 57.534 47.619 0.00 0.00 40.44 4.26
2758 2772 3.582208 GGGAGATGATCTGAACTAGCCAT 59.418 47.826 0.00 0.00 0.00 4.40
2759 2773 2.968574 GGGAGATGATCTGAACTAGCCA 59.031 50.000 0.00 0.00 0.00 4.75
2760 2774 2.301583 GGGGAGATGATCTGAACTAGCC 59.698 54.545 0.00 0.00 0.00 3.93
2775 2789 1.860240 AGCTGTAGTAGGATGGGGAGA 59.140 52.381 0.00 0.00 0.00 3.71
2776 2790 2.390225 AGCTGTAGTAGGATGGGGAG 57.610 55.000 0.00 0.00 0.00 4.30
2778 2792 2.958818 TGTAGCTGTAGTAGGATGGGG 58.041 52.381 0.00 0.00 0.00 4.96
2781 2795 6.619744 CATCTCATGTAGCTGTAGTAGGATG 58.380 44.000 0.00 0.00 0.00 3.51
2784 2798 4.279420 TGCATCTCATGTAGCTGTAGTAGG 59.721 45.833 0.00 0.00 0.00 3.18
2787 2801 4.629092 CATGCATCTCATGTAGCTGTAGT 58.371 43.478 0.00 0.00 45.79 2.73


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

AutoCloner maintained by Alex Coulton.