Multiple sequence alignment - TraesCS2B01G072400

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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 TraesCS2B01G072400 chr2B 100.000 3044 0 0 1 3044 38422662 38419619 0.000000e+00 5622.0
1 TraesCS2B01G072400 chr2B 93.933 1368 64 7 682 2045 39091367 39090015 0.000000e+00 2049.0
2 TraesCS2B01G072400 chr2B 92.663 1322 62 17 795 2102 38050323 38049023 0.000000e+00 1871.0
3 TraesCS2B01G072400 chr2B 85.673 1033 127 14 999 2022 39333283 39334303 0.000000e+00 1068.0
4 TraesCS2B01G072400 chr2B 85.842 1010 123 14 999 1996 39158985 39157984 0.000000e+00 1055.0
5 TraesCS2B01G072400 chr2B 88.116 934 48 31 2142 3044 39089899 39088998 0.000000e+00 1051.0
6 TraesCS2B01G072400 chr2B 95.013 381 16 1 2130 2507 38090591 38090211 2.020000e-166 595.0
7 TraesCS2B01G072400 chr2B 92.718 206 13 2 433 638 483682942 483683145 2.290000e-76 296.0
8 TraesCS2B01G072400 chr2B 89.706 204 19 2 433 636 398698996 398698795 3.010000e-65 259.0
9 TraesCS2B01G072400 chr2B 89.583 144 8 3 1992 2128 38090851 38090708 3.120000e-40 176.0
10 TraesCS2B01G072400 chr2B 98.020 101 2 0 1 101 465136194 465136294 3.120000e-40 176.0
11 TraesCS2B01G072400 chr2B 78.838 241 32 8 1789 2022 39336049 39336277 8.800000e-31 145.0
12 TraesCS2B01G072400 chr2B 100.000 43 0 0 2130 2172 38090970 38090928 2.520000e-11 80.5
13 TraesCS2B01G072400 chr2A 91.417 1468 81 27 686 2128 24406933 24408380 0.000000e+00 1971.0
14 TraesCS2B01G072400 chr2A 86.155 1004 124 10 999 1999 24181947 24180956 0.000000e+00 1070.0
15 TraesCS2B01G072400 chr2A 85.902 915 107 12 1101 2002 24277567 24276662 0.000000e+00 955.0
16 TraesCS2B01G072400 chr2A 82.622 961 87 18 2125 3044 24408497 24409418 0.000000e+00 776.0
17 TraesCS2B01G072400 chr2A 88.116 345 40 1 94 437 684196310 684196654 2.830000e-110 409.0
18 TraesCS2B01G072400 chr2D 91.606 1370 80 23 682 2030 22795402 22796757 0.000000e+00 1860.0
19 TraesCS2B01G072400 chr2D 85.686 1006 126 13 999 1996 22785757 22786752 0.000000e+00 1044.0
20 TraesCS2B01G072400 chr2D 84.362 729 75 18 2333 3042 22817144 22817852 0.000000e+00 678.0
21 TraesCS2B01G072400 chr2D 80.967 331 35 9 999 1328 22446384 22446081 1.410000e-58 237.0
22 TraesCS2B01G072400 chr2D 96.094 128 3 2 2125 2250 22797013 22797140 1.110000e-49 207.0
23 TraesCS2B01G072400 chr2D 91.892 111 8 1 2234 2343 22814324 22814434 1.460000e-33 154.0
24 TraesCS2B01G072400 chr2D 85.714 140 14 3 1846 1979 22445149 22445010 3.160000e-30 143.0
25 TraesCS2B01G072400 chr1B 94.721 341 18 0 97 437 62459694 62460034 5.780000e-147 531.0
26 TraesCS2B01G072400 chr1B 90.594 202 18 1 435 636 677514560 677514360 1.800000e-67 267.0
27 TraesCS2B01G072400 chr4B 93.913 345 20 1 94 437 28066863 28066519 1.250000e-143 520.0
28 TraesCS2B01G072400 chr4B 87.826 345 36 3 94 437 417570477 417570138 1.700000e-107 399.0
29 TraesCS2B01G072400 chr4B 92.118 203 14 2 433 635 28066468 28066268 4.970000e-73 285.0
30 TraesCS2B01G072400 chr3B 91.304 345 29 1 94 437 386065893 386065549 1.280000e-128 470.0
31 TraesCS2B01G072400 chr3B 90.547 201 17 2 433 633 181465670 181465472 6.470000e-67 265.0
32 TraesCS2B01G072400 chr3B 98.020 101 2 0 1 101 723463381 723463481 3.120000e-40 176.0
33 TraesCS2B01G072400 chr3B 95.283 106 5 0 1 106 241708467 241708362 5.220000e-38 169.0
34 TraesCS2B01G072400 chr1A 90.435 345 32 1 94 437 483010166 483010510 1.290000e-123 453.0
35 TraesCS2B01G072400 chr7B 87.536 345 39 3 94 437 508815216 508815557 2.200000e-106 396.0
36 TraesCS2B01G072400 chr7B 91.045 201 17 1 435 635 508815609 508815808 1.390000e-68 270.0
37 TraesCS2B01G072400 chr7B 98.980 98 1 0 1 98 70071838 70071741 3.120000e-40 176.0
38 TraesCS2B01G072400 chr7B 97.959 98 2 0 1 98 537509236 537509333 1.450000e-38 171.0
39 TraesCS2B01G072400 chr5A 89.145 304 31 1 134 437 36828006 36827705 7.970000e-101 377.0
40 TraesCS2B01G072400 chr5A 90.244 205 18 2 435 639 330176122 330175920 1.800000e-67 267.0
41 TraesCS2B01G072400 chr3D 84.814 349 46 5 94 437 108959629 108959975 8.080000e-91 344.0
42 TraesCS2B01G072400 chr6B 91.346 208 16 2 433 640 643537398 643537603 1.790000e-72 283.0
43 TraesCS2B01G072400 chr6B 98.000 100 2 0 1 100 703686059 703685960 1.120000e-39 174.0
44 TraesCS2B01G072400 chr6B 97.059 102 3 0 1 102 703801995 703802096 4.030000e-39 172.0
45 TraesCS2B01G072400 chr6B 74.519 208 43 8 2809 3013 224901064 224901264 6.990000e-12 82.4
46 TraesCS2B01G072400 chr1D 90.148 203 19 1 435 637 436975417 436975618 2.330000e-66 263.0
47 TraesCS2B01G072400 chrUn 93.966 116 5 2 1 115 132725606 132725492 1.120000e-39 174.0
48 TraesCS2B01G072400 chrUn 93.750 112 6 1 1 111 36800964 36800853 1.880000e-37 167.0


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 TraesCS2B01G072400 chr2B 38419619 38422662 3043 True 5622.000000 5622 100.000000 1 3044 1 chr2B.!!$R2 3043
1 TraesCS2B01G072400 chr2B 38049023 38050323 1300 True 1871.000000 1871 92.663000 795 2102 1 chr2B.!!$R1 1307
2 TraesCS2B01G072400 chr2B 39088998 39091367 2369 True 1550.000000 2049 91.024500 682 3044 2 chr2B.!!$R6 2362
3 TraesCS2B01G072400 chr2B 39157984 39158985 1001 True 1055.000000 1055 85.842000 999 1996 1 chr2B.!!$R3 997
4 TraesCS2B01G072400 chr2B 39333283 39336277 2994 False 606.500000 1068 82.255500 999 2022 2 chr2B.!!$F3 1023
5 TraesCS2B01G072400 chr2B 38090211 38090970 759 True 283.833333 595 94.865333 1992 2507 3 chr2B.!!$R5 515
6 TraesCS2B01G072400 chr2A 24406933 24409418 2485 False 1373.500000 1971 87.019500 686 3044 2 chr2A.!!$F2 2358
7 TraesCS2B01G072400 chr2A 24180956 24181947 991 True 1070.000000 1070 86.155000 999 1999 1 chr2A.!!$R1 1000
8 TraesCS2B01G072400 chr2A 24276662 24277567 905 True 955.000000 955 85.902000 1101 2002 1 chr2A.!!$R2 901
9 TraesCS2B01G072400 chr2D 22785757 22786752 995 False 1044.000000 1044 85.686000 999 1996 1 chr2D.!!$F1 997
10 TraesCS2B01G072400 chr2D 22795402 22797140 1738 False 1033.500000 1860 93.850000 682 2250 2 chr2D.!!$F2 1568
11 TraesCS2B01G072400 chr2D 22814324 22817852 3528 False 416.000000 678 88.127000 2234 3042 2 chr2D.!!$F3 808
12 TraesCS2B01G072400 chr4B 28066268 28066863 595 True 402.500000 520 93.015500 94 635 2 chr4B.!!$R2 541
13 TraesCS2B01G072400 chr7B 508815216 508815808 592 False 333.000000 396 89.290500 94 635 2 chr7B.!!$F2 541

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
354 355 0.108804 TGCGAGATGGAGTTCGGTTC 60.109 55.0 0.00 0.0 37.3 3.62 F
359 360 0.179156 GATGGAGTTCGGTTCGCGTA 60.179 55.0 5.77 0.0 0.0 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1524 1.736126 CGAGCGTTGTACTGGTAGAGA 59.264 52.381 0.0 0.0 0.0 3.1 R
2128 2298 2.938451 TCAGAGCTGGCGATGTTTATTG 59.062 45.455 0.0 0.0 0.0 1.9 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
36 37 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
38 39 7.458409 AAGTGTAGATTCACTCATTTTGCAT 57.542 32.000 0.00 0.00 46.25 3.96
39 40 7.081526 AGTGTAGATTCACTCATTTTGCATC 57.918 36.000 0.00 0.00 44.07 3.91
40 41 5.961843 GTGTAGATTCACTCATTTTGCATCG 59.038 40.000 0.00 0.00 35.68 3.84
41 42 5.643348 TGTAGATTCACTCATTTTGCATCGT 59.357 36.000 0.00 0.00 0.00 3.73
42 43 6.816140 TGTAGATTCACTCATTTTGCATCGTA 59.184 34.615 0.00 0.00 0.00 3.43
43 44 6.932356 AGATTCACTCATTTTGCATCGTAT 57.068 33.333 0.00 0.00 0.00 3.06
44 45 6.722301 AGATTCACTCATTTTGCATCGTATG 58.278 36.000 0.00 0.00 0.00 2.39
45 46 5.878332 TTCACTCATTTTGCATCGTATGT 57.122 34.783 0.00 0.00 0.00 2.29
46 47 6.976636 TTCACTCATTTTGCATCGTATGTA 57.023 33.333 0.00 0.00 0.00 2.29
47 48 6.588348 TCACTCATTTTGCATCGTATGTAG 57.412 37.500 0.00 0.00 0.00 2.74
48 49 6.106003 TCACTCATTTTGCATCGTATGTAGT 58.894 36.000 0.00 0.00 0.00 2.73
50 51 6.035975 CACTCATTTTGCATCGTATGTAGTCA 59.964 38.462 0.00 0.00 0.00 3.41
51 52 6.036083 ACTCATTTTGCATCGTATGTAGTCAC 59.964 38.462 0.00 0.00 0.00 3.67
52 53 6.106003 TCATTTTGCATCGTATGTAGTCACT 58.894 36.000 0.00 0.00 0.00 3.41
55 56 4.450082 TGCATCGTATGTAGTCACTTGT 57.550 40.909 0.00 0.00 0.00 3.16
57 58 4.625311 TGCATCGTATGTAGTCACTTGTTG 59.375 41.667 0.00 0.00 0.00 3.33
59 60 5.347635 GCATCGTATGTAGTCACTTGTTGAA 59.652 40.000 0.00 0.00 35.39 2.69
60 61 6.128661 GCATCGTATGTAGTCACTTGTTGAAA 60.129 38.462 0.00 0.00 35.39 2.69
63 64 8.373048 TCGTATGTAGTCACTTGTTGAAATTT 57.627 30.769 0.00 0.00 35.39 1.82
64 65 8.492748 TCGTATGTAGTCACTTGTTGAAATTTC 58.507 33.333 11.41 11.41 35.39 2.17
65 66 8.495949 CGTATGTAGTCACTTGTTGAAATTTCT 58.504 33.333 18.64 0.00 35.39 2.52
68 69 9.778741 ATGTAGTCACTTGTTGAAATTTCTAGA 57.221 29.630 18.64 7.52 35.39 2.43
73 74 9.439537 GTCACTTGTTGAAATTTCTAGAAAGAC 57.560 33.333 21.75 19.93 35.39 3.01
74 75 9.173021 TCACTTGTTGAAATTTCTAGAAAGACA 57.827 29.630 21.75 17.21 33.32 3.41
75 76 9.787532 CACTTGTTGAAATTTCTAGAAAGACAA 57.212 29.630 21.75 20.91 33.32 3.18
88 89 9.635520 TTCTAGAAAGACAAGTATTTAGGAACG 57.364 33.333 1.68 0.00 0.00 3.95
89 90 8.248945 TCTAGAAAGACAAGTATTTAGGAACGG 58.751 37.037 0.00 0.00 0.00 4.44
90 91 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
93 94 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
96 97 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
115 116 2.700897 AGTACTAAGGAAGCCATCGCAT 59.299 45.455 0.00 0.00 37.52 4.73
147 148 2.048597 CGCAAGGACACGCTGGTA 60.049 61.111 0.00 0.00 0.00 3.25
180 181 3.473647 TGGCGGCCTCCTGATGAG 61.474 66.667 21.46 0.00 41.07 2.90
198 199 5.411361 TGATGAGGGTTTTGTAAAGATCACG 59.589 40.000 0.00 0.00 0.00 4.35
259 260 0.678048 GGGAGGCATTGCTCGTTCTT 60.678 55.000 8.82 0.00 0.00 2.52
354 355 0.108804 TGCGAGATGGAGTTCGGTTC 60.109 55.000 0.00 0.00 37.30 3.62
359 360 0.179156 GATGGAGTTCGGTTCGCGTA 60.179 55.000 5.77 0.00 0.00 4.42
378 379 1.927895 ATCTTCGTGGATTCTCGCAC 58.072 50.000 0.00 0.00 0.00 5.34
388 389 3.181480 TGGATTCTCGCACGTGATAATGA 60.181 43.478 22.23 7.19 0.00 2.57
396 397 3.539592 CGCACGTGATAATGAAAGTCGAC 60.540 47.826 22.23 7.70 0.00 4.20
415 416 1.233019 CTGCTTGGAGTTGGTGACAG 58.767 55.000 0.00 0.00 44.54 3.51
448 503 6.640499 CACTCGCCACAATTTTTCATCTTTTA 59.360 34.615 0.00 0.00 0.00 1.52
490 545 1.137872 CAGCTAATCTTCCGGCTCACT 59.862 52.381 0.00 0.00 32.30 3.41
552 607 0.543410 TGGCTTGACGAGACCCCTAA 60.543 55.000 0.00 0.00 29.50 2.69
557 612 1.171308 TGACGAGACCCCTAACTTCG 58.829 55.000 0.00 0.00 0.00 3.79
571 626 1.374758 CTTCGTGGTGTCCAGCCTC 60.375 63.158 0.00 0.00 32.34 4.70
572 627 2.788191 CTTCGTGGTGTCCAGCCTCC 62.788 65.000 0.00 0.00 32.34 4.30
655 710 5.565592 AAAAAGATAACATGAGCATGCGA 57.434 34.783 13.01 3.11 42.39 5.10
656 711 4.808077 AAAGATAACATGAGCATGCGAG 57.192 40.909 13.01 6.12 42.39 5.03
657 712 2.763933 AGATAACATGAGCATGCGAGG 58.236 47.619 13.01 7.47 42.39 4.63
658 713 2.366590 AGATAACATGAGCATGCGAGGA 59.633 45.455 13.01 0.00 42.39 3.71
659 714 1.939974 TAACATGAGCATGCGAGGAC 58.060 50.000 13.01 3.67 42.39 3.85
660 715 1.086067 AACATGAGCATGCGAGGACG 61.086 55.000 13.01 2.71 42.39 4.79
661 716 1.227060 CATGAGCATGCGAGGACGA 60.227 57.895 13.01 0.00 42.66 4.20
662 717 1.067084 ATGAGCATGCGAGGACGAG 59.933 57.895 13.01 0.00 42.66 4.18
663 718 2.959071 GAGCATGCGAGGACGAGC 60.959 66.667 13.01 0.00 42.66 5.03
665 720 3.558411 GCATGCGAGGACGAGCAC 61.558 66.667 0.00 0.00 46.83 4.40
666 721 3.250323 CATGCGAGGACGAGCACG 61.250 66.667 0.76 0.76 46.83 5.34
678 733 2.953806 CGAGCACGTCTACGAATTTC 57.046 50.000 9.86 1.10 43.02 2.17
679 734 2.516923 CGAGCACGTCTACGAATTTCT 58.483 47.619 9.86 0.00 43.02 2.52
680 735 2.276540 CGAGCACGTCTACGAATTTCTG 59.723 50.000 9.86 0.00 43.02 3.02
716 772 7.006509 CCCATTCTCTATGTTTCCCATGTATT 58.993 38.462 0.00 0.00 34.86 1.89
805 864 2.887152 GGCCATCTTGTCAAGTTGTCTT 59.113 45.455 18.15 0.00 0.00 3.01
811 870 6.093219 CCATCTTGTCAAGTTGTCTTATCCAG 59.907 42.308 18.15 1.48 32.07 3.86
818 877 9.219603 TGTCAAGTTGTCTTATCCAGAATTTAG 57.780 33.333 2.11 0.00 31.28 1.85
837 903 8.494016 AATTTAGTAGCTTATCACAACCTCAC 57.506 34.615 0.00 0.00 0.00 3.51
838 904 4.473477 AGTAGCTTATCACAACCTCACC 57.527 45.455 0.00 0.00 0.00 4.02
840 906 3.618690 AGCTTATCACAACCTCACCTC 57.381 47.619 0.00 0.00 0.00 3.85
841 907 2.906389 AGCTTATCACAACCTCACCTCA 59.094 45.455 0.00 0.00 0.00 3.86
842 908 3.521126 AGCTTATCACAACCTCACCTCAT 59.479 43.478 0.00 0.00 0.00 2.90
843 909 3.624861 GCTTATCACAACCTCACCTCATG 59.375 47.826 0.00 0.00 0.00 3.07
844 910 4.836825 CTTATCACAACCTCACCTCATGT 58.163 43.478 0.00 0.00 0.00 3.21
845 911 2.549064 TCACAACCTCACCTCATGTG 57.451 50.000 0.00 0.00 46.88 3.21
846 912 1.072173 TCACAACCTCACCTCATGTGG 59.928 52.381 12.29 12.29 45.48 4.17
847 913 0.401738 ACAACCTCACCTCATGTGGG 59.598 55.000 17.76 11.57 44.91 4.61
848 914 0.962356 CAACCTCACCTCATGTGGGC 60.962 60.000 17.76 0.00 44.69 5.36
849 915 1.426251 AACCTCACCTCATGTGGGCA 61.426 55.000 17.76 3.12 44.69 5.36
850 916 1.377725 CCTCACCTCATGTGGGCAC 60.378 63.158 17.76 0.00 44.69 5.01
851 917 1.742880 CTCACCTCATGTGGGCACG 60.743 63.158 17.76 4.02 45.48 5.34
852 918 2.171209 CTCACCTCATGTGGGCACGA 62.171 60.000 17.76 7.77 45.48 4.35
853 919 1.078214 CACCTCATGTGGGCACGAT 60.078 57.895 17.76 0.00 41.52 3.73
860 927 2.813908 GTGGGCACGATCGACACC 60.814 66.667 24.34 19.21 0.00 4.16
1011 1097 1.101635 CGACGACCATGGAGCTCCTA 61.102 60.000 32.28 19.38 36.82 2.94
1404 1524 2.524394 ATAGCCGCCATCCTCCGT 60.524 61.111 0.00 0.00 0.00 4.69
1929 2052 4.988598 CCGCTGTGCAAGGACGGT 62.989 66.667 9.78 0.00 39.05 4.83
2083 2253 3.632145 ACTCTAACCAAGCAACCAAACAG 59.368 43.478 0.00 0.00 0.00 3.16
2128 2298 7.768120 ACCATGATAAAGTCTGAGAGATGAAAC 59.232 37.037 0.00 0.00 0.00 2.78
2405 6194 4.816385 CACTGACAGTTAGGATGTGTTTGT 59.184 41.667 5.04 0.00 0.00 2.83
2458 6428 4.488770 ACCCACTTTTGGTTGATTGGTAT 58.511 39.130 0.00 0.00 42.10 2.73
2478 6448 2.842462 TGCACAGGACCACCTCGT 60.842 61.111 0.00 0.00 45.94 4.18
2493 6463 2.172717 ACCTCGTGCTTAGCCCAAATAT 59.827 45.455 0.29 0.00 0.00 1.28
2494 6464 3.389983 ACCTCGTGCTTAGCCCAAATATA 59.610 43.478 0.29 0.00 0.00 0.86
2502 6472 5.537295 TGCTTAGCCCAAATATACTCGTAGA 59.463 40.000 0.29 0.00 0.00 2.59
2564 6538 0.786581 CATGACTGTGCACGAGTGAC 59.213 55.000 21.48 11.73 0.00 3.67
2960 7004 4.681074 GGGGGAATTCAAAAGTGTTCAA 57.319 40.909 7.93 0.00 0.00 2.69
2978 7022 8.067784 AGTGTTCAACATGTTTAAACAGATACG 58.932 33.333 25.66 12.54 43.04 3.06
2984 7028 6.354130 ACATGTTTAAACAGATACGGGCTAT 58.646 36.000 24.22 2.37 43.04 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.961843 CGATGCAAAATGAGTGAATCTACAC 59.038 40.000 0.00 0.00 40.60 2.90
17 18 5.643348 ACGATGCAAAATGAGTGAATCTACA 59.357 36.000 0.00 0.00 29.84 2.74
18 19 6.111768 ACGATGCAAAATGAGTGAATCTAC 57.888 37.500 0.00 0.00 29.84 2.59
19 20 7.495606 ACATACGATGCAAAATGAGTGAATCTA 59.504 33.333 0.00 0.00 29.84 1.98
21 22 6.489675 ACATACGATGCAAAATGAGTGAATC 58.510 36.000 0.00 0.00 0.00 2.52
22 23 6.441093 ACATACGATGCAAAATGAGTGAAT 57.559 33.333 0.00 0.00 0.00 2.57
23 24 5.878332 ACATACGATGCAAAATGAGTGAA 57.122 34.783 0.00 0.00 0.00 3.18
25 26 6.035975 TGACTACATACGATGCAAAATGAGTG 59.964 38.462 0.00 0.00 0.00 3.51
26 27 6.036083 GTGACTACATACGATGCAAAATGAGT 59.964 38.462 0.00 0.00 0.00 3.41
28 29 6.106003 AGTGACTACATACGATGCAAAATGA 58.894 36.000 0.00 0.00 0.00 2.57
29 30 6.349973 AGTGACTACATACGATGCAAAATG 57.650 37.500 0.00 0.00 0.00 2.32
30 31 6.371548 ACAAGTGACTACATACGATGCAAAAT 59.628 34.615 0.00 0.00 0.00 1.82
31 32 5.699001 ACAAGTGACTACATACGATGCAAAA 59.301 36.000 0.00 0.00 0.00 2.44
32 33 5.234752 ACAAGTGACTACATACGATGCAAA 58.765 37.500 0.00 0.00 0.00 3.68
33 34 4.816392 ACAAGTGACTACATACGATGCAA 58.184 39.130 0.00 0.00 0.00 4.08
34 35 4.450082 ACAAGTGACTACATACGATGCA 57.550 40.909 0.00 0.00 0.00 3.96
35 36 4.862574 TCAACAAGTGACTACATACGATGC 59.137 41.667 0.00 0.00 0.00 3.91
36 37 6.944557 TTCAACAAGTGACTACATACGATG 57.055 37.500 0.00 0.00 35.39 3.84
38 39 7.956420 AATTTCAACAAGTGACTACATACGA 57.044 32.000 0.00 0.00 35.39 3.43
39 40 8.495949 AGAAATTTCAACAAGTGACTACATACG 58.504 33.333 19.99 0.00 35.39 3.06
42 43 9.778741 TCTAGAAATTTCAACAAGTGACTACAT 57.221 29.630 19.99 0.00 35.39 2.29
43 44 9.607988 TTCTAGAAATTTCAACAAGTGACTACA 57.392 29.630 19.99 0.00 35.39 2.74
46 47 9.396022 TCTTTCTAGAAATTTCAACAAGTGACT 57.604 29.630 18.02 0.00 35.39 3.41
47 48 9.439537 GTCTTTCTAGAAATTTCAACAAGTGAC 57.560 33.333 18.02 12.64 31.18 3.67
48 49 9.173021 TGTCTTTCTAGAAATTTCAACAAGTGA 57.827 29.630 18.02 5.04 30.65 3.41
63 64 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
64 65 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
65 66 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
66 67 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
68 69 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
70 71 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
71 72 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
73 74 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
74 75 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
75 76 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
76 77 4.892345 AGTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
77 78 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
78 79 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
80 81 4.530875 CTTAGTACTCCCTCCGTTCCTAA 58.469 47.826 0.00 0.00 0.00 2.69
81 82 3.117738 CCTTAGTACTCCCTCCGTTCCTA 60.118 52.174 0.00 0.00 0.00 2.94
82 83 2.357986 CCTTAGTACTCCCTCCGTTCCT 60.358 54.545 0.00 0.00 0.00 3.36
83 84 2.030371 CCTTAGTACTCCCTCCGTTCC 58.970 57.143 0.00 0.00 0.00 3.62
84 85 3.010200 TCCTTAGTACTCCCTCCGTTC 57.990 52.381 0.00 0.00 0.00 3.95
85 86 3.363627 CTTCCTTAGTACTCCCTCCGTT 58.636 50.000 0.00 0.00 0.00 4.44
87 88 1.682323 GCTTCCTTAGTACTCCCTCCG 59.318 57.143 0.00 0.00 0.00 4.63
88 89 2.040939 GGCTTCCTTAGTACTCCCTCC 58.959 57.143 0.00 0.00 0.00 4.30
89 90 2.748388 TGGCTTCCTTAGTACTCCCTC 58.252 52.381 0.00 0.00 0.00 4.30
90 91 2.942604 TGGCTTCCTTAGTACTCCCT 57.057 50.000 0.00 0.00 0.00 4.20
93 94 2.100916 TGCGATGGCTTCCTTAGTACTC 59.899 50.000 0.00 0.00 40.82 2.59
96 97 3.838244 AATGCGATGGCTTCCTTAGTA 57.162 42.857 0.15 0.00 40.82 1.82
115 116 1.160946 TTGCGCGGCAAGTGAAGTAA 61.161 50.000 8.83 0.00 43.99 2.24
180 181 3.120442 CGGTCGTGATCTTTACAAAACCC 60.120 47.826 0.00 0.00 0.00 4.11
198 199 1.686052 AGATTGAGAGCTCCATCGGTC 59.314 52.381 10.93 0.21 36.99 4.79
233 234 3.106986 GCAATGCCTCCCGCTCCTA 62.107 63.158 0.00 0.00 38.78 2.94
259 260 1.654954 GCACCGAGTAGAGCCGAAGA 61.655 60.000 0.00 0.00 0.00 2.87
293 294 1.749033 GGATCCGAGATCCCCACAC 59.251 63.158 17.50 0.00 32.09 3.82
354 355 2.044860 GAGAATCCACGAAGATACGCG 58.955 52.381 3.53 3.53 36.70 6.01
359 360 1.927895 GTGCGAGAATCCACGAAGAT 58.072 50.000 0.00 0.00 0.00 2.40
378 379 3.859961 AGCAGTCGACTTTCATTATCACG 59.140 43.478 17.26 0.68 0.00 4.35
388 389 2.213499 CAACTCCAAGCAGTCGACTTT 58.787 47.619 17.26 5.94 0.00 2.66
396 397 1.233019 CTGTCACCAACTCCAAGCAG 58.767 55.000 0.00 0.00 0.00 4.24
415 416 2.048127 GTGGCGAGTGGTCCAGAC 60.048 66.667 0.00 0.00 32.15 3.51
448 503 7.394359 AGCTGACCTGTTTACATGTTGAATAAT 59.606 33.333 2.30 0.00 0.00 1.28
557 612 2.348998 CAGGAGGCTGGACACCAC 59.651 66.667 0.00 0.00 0.00 4.16
584 639 4.701956 ATTGAGTAAACGCATTCTTGGG 57.298 40.909 0.00 0.00 41.36 4.12
635 690 3.562973 CCTCGCATGCTCATGTTATCTTT 59.437 43.478 17.13 0.00 40.80 2.52
636 691 3.136763 CCTCGCATGCTCATGTTATCTT 58.863 45.455 17.13 0.00 40.80 2.40
637 692 2.366590 TCCTCGCATGCTCATGTTATCT 59.633 45.455 17.13 0.00 40.80 1.98
638 693 2.478134 GTCCTCGCATGCTCATGTTATC 59.522 50.000 17.13 0.00 40.80 1.75
639 694 2.487934 GTCCTCGCATGCTCATGTTAT 58.512 47.619 17.13 0.00 40.80 1.89
640 695 1.802508 CGTCCTCGCATGCTCATGTTA 60.803 52.381 17.13 0.23 40.80 2.41
641 696 1.086067 CGTCCTCGCATGCTCATGTT 61.086 55.000 17.13 0.00 40.80 2.71
642 697 1.520120 CGTCCTCGCATGCTCATGT 60.520 57.895 17.13 0.00 40.80 3.21
643 698 1.213733 CTCGTCCTCGCATGCTCATG 61.214 60.000 17.13 5.53 41.60 3.07
644 699 1.067084 CTCGTCCTCGCATGCTCAT 59.933 57.895 17.13 0.00 36.96 2.90
645 700 2.491621 CTCGTCCTCGCATGCTCA 59.508 61.111 17.13 0.58 36.96 4.26
646 701 2.959071 GCTCGTCCTCGCATGCTC 60.959 66.667 17.13 0.23 36.96 4.26
647 702 3.763356 TGCTCGTCCTCGCATGCT 61.763 61.111 17.13 0.00 36.96 3.79
648 703 3.558411 GTGCTCGTCCTCGCATGC 61.558 66.667 7.91 7.91 38.56 4.06
649 704 3.250323 CGTGCTCGTCCTCGCATG 61.250 66.667 0.00 0.00 38.56 4.06
659 714 2.276540 CAGAAATTCGTAGACGTGCTCG 59.723 50.000 6.63 6.63 40.80 5.03
660 715 3.243336 ACAGAAATTCGTAGACGTGCTC 58.757 45.455 0.00 0.00 40.80 4.26
661 716 3.299340 ACAGAAATTCGTAGACGTGCT 57.701 42.857 0.00 0.00 40.80 4.40
662 717 5.697848 ATTACAGAAATTCGTAGACGTGC 57.302 39.130 0.00 0.00 40.80 5.34
663 718 8.433126 AGAAAATTACAGAAATTCGTAGACGTG 58.567 33.333 0.00 0.00 36.76 4.49
664 719 8.433126 CAGAAAATTACAGAAATTCGTAGACGT 58.567 33.333 1.46 0.00 36.76 4.34
665 720 7.422746 GCAGAAAATTACAGAAATTCGTAGACG 59.577 37.037 0.00 0.00 36.76 4.18
666 721 7.692705 GGCAGAAAATTACAGAAATTCGTAGAC 59.307 37.037 0.00 0.00 36.76 2.59
667 722 7.148306 GGGCAGAAAATTACAGAAATTCGTAGA 60.148 37.037 0.00 0.00 36.76 2.59
668 723 6.967199 GGGCAGAAAATTACAGAAATTCGTAG 59.033 38.462 0.00 0.00 36.76 3.51
669 724 6.431543 TGGGCAGAAAATTACAGAAATTCGTA 59.568 34.615 0.00 0.00 36.76 3.43
670 725 5.242838 TGGGCAGAAAATTACAGAAATTCGT 59.757 36.000 0.00 0.00 36.76 3.85
671 726 5.708948 TGGGCAGAAAATTACAGAAATTCG 58.291 37.500 0.00 0.00 36.76 3.34
672 727 8.037166 AGAATGGGCAGAAAATTACAGAAATTC 58.963 33.333 0.00 0.00 36.76 2.17
673 728 7.910584 AGAATGGGCAGAAAATTACAGAAATT 58.089 30.769 0.00 0.00 39.56 1.82
674 729 7.398332 AGAGAATGGGCAGAAAATTACAGAAAT 59.602 33.333 0.00 0.00 0.00 2.17
675 730 6.721208 AGAGAATGGGCAGAAAATTACAGAAA 59.279 34.615 0.00 0.00 0.00 2.52
676 731 6.248433 AGAGAATGGGCAGAAAATTACAGAA 58.752 36.000 0.00 0.00 0.00 3.02
677 732 5.819991 AGAGAATGGGCAGAAAATTACAGA 58.180 37.500 0.00 0.00 0.00 3.41
678 733 7.284034 ACATAGAGAATGGGCAGAAAATTACAG 59.716 37.037 0.00 0.00 40.16 2.74
679 734 7.118723 ACATAGAGAATGGGCAGAAAATTACA 58.881 34.615 0.00 0.00 40.16 2.41
680 735 7.573968 ACATAGAGAATGGGCAGAAAATTAC 57.426 36.000 0.00 0.00 40.16 1.89
746 802 7.852971 AAAATGCTCCACATAATCATTTTGG 57.147 32.000 9.54 0.00 42.33 3.28
785 844 5.163713 GGATAAGACAACTTGACAAGATGGC 60.164 44.000 24.23 22.55 39.43 4.40
811 870 8.604890 GTGAGGTTGTGATAAGCTACTAAATTC 58.395 37.037 0.00 0.00 0.00 2.17
818 877 4.081642 TGAGGTGAGGTTGTGATAAGCTAC 60.082 45.833 0.00 0.00 0.00 3.58
837 903 1.884464 CGATCGTGCCCACATGAGG 60.884 63.158 7.03 0.00 44.85 3.86
838 904 1.141665 TCGATCGTGCCCACATGAG 59.858 57.895 15.94 0.00 44.85 2.90
840 906 1.447663 TGTCGATCGTGCCCACATG 60.448 57.895 15.94 0.00 0.00 3.21
841 907 1.447838 GTGTCGATCGTGCCCACAT 60.448 57.895 15.94 0.00 0.00 3.21
842 908 2.048597 GTGTCGATCGTGCCCACA 60.049 61.111 15.94 8.78 0.00 4.17
843 909 2.813908 GGTGTCGATCGTGCCCAC 60.814 66.667 15.94 16.02 0.00 4.61
844 910 4.429212 CGGTGTCGATCGTGCCCA 62.429 66.667 15.94 5.30 39.00 5.36
845 911 4.430765 ACGGTGTCGATCGTGCCC 62.431 66.667 15.94 11.70 37.60 5.36
846 912 2.879462 GACGGTGTCGATCGTGCC 60.879 66.667 15.94 14.00 39.69 5.01
860 927 6.206600 AGTTGTCAGTGTATTTTAACGACG 57.793 37.500 0.00 0.00 0.00 5.12
901 968 2.731968 GCAATAATGTTGAGTGGCACGG 60.732 50.000 12.71 0.00 0.00 4.94
990 1076 1.517257 GAGCTCCATGGTCGTCGTG 60.517 63.158 12.58 0.00 33.25 4.35
991 1077 2.711922 GGAGCTCCATGGTCGTCGT 61.712 63.158 28.43 0.00 43.60 4.34
1404 1524 1.736126 CGAGCGTTGTACTGGTAGAGA 59.264 52.381 0.00 0.00 0.00 3.10
1929 2052 2.999648 AGCAGCTTCTCCTCGCCA 61.000 61.111 0.00 0.00 0.00 5.69
2024 2150 9.994432 CTGAAATTTATTTTCCTACTGCTAGTG 57.006 33.333 0.00 0.00 42.63 2.74
2073 2243 3.731089 ACAATGCAATCCTGTTTGGTTG 58.269 40.909 0.00 0.00 37.07 3.77
2083 2253 5.132897 TGGTAAACAAGACAATGCAATCC 57.867 39.130 0.00 0.00 0.00 3.01
2128 2298 2.938451 TCAGAGCTGGCGATGTTTATTG 59.062 45.455 0.00 0.00 0.00 1.90
2405 6194 4.601406 AATTTACCCTCATGCACCCTAA 57.399 40.909 0.00 0.00 0.00 2.69
2478 6448 4.682778 ACGAGTATATTTGGGCTAAGCA 57.317 40.909 0.00 0.00 0.00 3.91
2502 6472 3.111853 TGTGTTCTCTCTTCGTGCATT 57.888 42.857 0.00 0.00 0.00 3.56
2549 6523 2.658593 GCGTCACTCGTGCACAGT 60.659 61.111 18.64 15.86 42.13 3.55
2550 6524 3.756677 CGCGTCACTCGTGCACAG 61.757 66.667 18.64 15.21 42.93 3.66
2575 6549 9.743057 AATTTCTGAACATATTTTGAAACACGA 57.257 25.926 0.00 0.00 0.00 4.35
2953 6997 7.322699 CCGTATCTGTTTAAACATGTTGAACAC 59.677 37.037 25.22 18.28 38.41 3.32
2960 7004 4.585879 AGCCCGTATCTGTTTAAACATGT 58.414 39.130 20.83 14.43 38.41 3.21
2978 7022 3.366374 GCTGACACTTTGTTTGATAGCCC 60.366 47.826 0.00 0.00 0.00 5.19
2984 7028 2.355756 GCTGAGCTGACACTTTGTTTGA 59.644 45.455 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.