Multiple sequence alignment - TraesCS3A01G350800

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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 TraesCS3A01G350800 chr3A 100.000 3900 0 0 1 3900 599387367 599383468 0.000000e+00 7203
1 TraesCS3A01G350800 chr3A 98.663 972 13 0 2929 3900 108303 109274 0.000000e+00 1724
2 TraesCS3A01G350800 chr3A 98.369 981 16 0 2920 3900 713783465 713782485 0.000000e+00 1724
3 TraesCS3A01G350800 chr3A 96.741 982 31 1 2919 3900 574916784 574915804 0.000000e+00 1635
4 TraesCS3A01G350800 chr3A 76.941 425 93 3 2369 2789 631776738 631777161 1.810000e-58 237
5 TraesCS3A01G350800 chr3D 91.577 2968 148 38 1 2925 456599639 456596731 0.000000e+00 4002
6 TraesCS3A01G350800 chr3B 91.524 2513 120 33 462 2906 603454301 603451814 0.000000e+00 3374
7 TraesCS3A01G350800 chr3B 98.663 972 13 0 2929 3900 751196739 751197710 0.000000e+00 1724
8 TraesCS3A01G350800 chr3B 85.437 206 18 3 1 206 603454786 603454593 1.840000e-48 204
9 TraesCS3A01G350800 chr5A 98.148 972 18 0 2929 3900 616085830 616086801 0.000000e+00 1696
10 TraesCS3A01G350800 chr7A 98.045 972 19 0 2929 3900 705669086 705668115 0.000000e+00 1690
11 TraesCS3A01G350800 chr7A 97.146 981 28 0 2920 3900 17017634 17018614 0.000000e+00 1657
12 TraesCS3A01G350800 chr7A 97.146 981 28 0 2920 3900 612108856 612109836 0.000000e+00 1657
13 TraesCS3A01G350800 chr2A 97.737 972 22 0 2929 3900 676162693 676161722 0.000000e+00 1674
14 TraesCS3A01G350800 chr2A 97.634 972 23 0 2929 3900 64352900 64353871 0.000000e+00 1668
15 TraesCS3A01G350800 chr4A 97.446 979 24 1 2923 3900 25498159 25499137 0.000000e+00 1668
16 TraesCS3A01G350800 chr4A 81.169 616 104 12 1254 1863 628090307 628089698 5.860000e-133 484
17 TraesCS3A01G350800 chr1B 97.047 982 29 0 2919 3900 635919248 635918267 0.000000e+00 1653
18 TraesCS3A01G350800 chr1B 86.364 616 66 12 1252 1867 526747864 526748461 0.000000e+00 656
19 TraesCS3A01G350800 chr1B 83.929 448 70 2 2353 2799 526749871 526750317 1.000000e-115 427
20 TraesCS3A01G350800 chr1B 90.847 295 27 0 1944 2238 526749329 526749623 2.820000e-106 396
21 TraesCS3A01G350800 chr6A 96.840 981 31 0 2920 3900 23929980 23930960 0.000000e+00 1640
22 TraesCS3A01G350800 chr7D 86.945 766 87 7 2918 3672 589518562 589517799 0.000000e+00 848
23 TraesCS3A01G350800 chr1D 87.480 623 59 12 1246 1867 394673064 394672460 0.000000e+00 701
24 TraesCS3A01G350800 chr1D 83.929 448 70 2 2353 2799 394671104 394670658 1.000000e-115 427
25 TraesCS3A01G350800 chr1D 90.365 301 29 0 1944 2244 394671714 394671414 2.820000e-106 396
26 TraesCS3A01G350800 chr1A 87.013 616 62 11 1252 1867 490411643 490412240 0.000000e+00 678
27 TraesCS3A01G350800 chr1A 91.186 295 26 0 1944 2238 490413096 490413390 6.070000e-108 401
28 TraesCS3A01G350800 chr4B 84.071 678 92 12 2929 3594 661659045 661658372 1.180000e-179 640
29 TraesCS3A01G350800 chr5D 81.818 616 100 12 1254 1863 540240501 540239892 1.250000e-139 507
30 TraesCS3A01G350800 chr5B 80.519 616 108 12 1254 1863 682538803 682538194 2.750000e-126 462
31 TraesCS3A01G350800 chr7B 90.066 302 29 1 1324 1624 6361103 6361404 1.310000e-104 390
32 TraesCS3A01G350800 chr2B 84.672 137 13 2 2449 2585 627652307 627652435 3.160000e-26 130


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 TraesCS3A01G350800 chr3A 599383468 599387367 3899 True 7203.0 7203 100.000000 1 3900 1 chr3A.!!$R2 3899
1 TraesCS3A01G350800 chr3A 108303 109274 971 False 1724.0 1724 98.663000 2929 3900 1 chr3A.!!$F1 971
2 TraesCS3A01G350800 chr3A 713782485 713783465 980 True 1724.0 1724 98.369000 2920 3900 1 chr3A.!!$R3 980
3 TraesCS3A01G350800 chr3A 574915804 574916784 980 True 1635.0 1635 96.741000 2919 3900 1 chr3A.!!$R1 981
4 TraesCS3A01G350800 chr3D 456596731 456599639 2908 True 4002.0 4002 91.577000 1 2925 1 chr3D.!!$R1 2924
5 TraesCS3A01G350800 chr3B 603451814 603454786 2972 True 1789.0 3374 88.480500 1 2906 2 chr3B.!!$R1 2905
6 TraesCS3A01G350800 chr3B 751196739 751197710 971 False 1724.0 1724 98.663000 2929 3900 1 chr3B.!!$F1 971
7 TraesCS3A01G350800 chr5A 616085830 616086801 971 False 1696.0 1696 98.148000 2929 3900 1 chr5A.!!$F1 971
8 TraesCS3A01G350800 chr7A 705668115 705669086 971 True 1690.0 1690 98.045000 2929 3900 1 chr7A.!!$R1 971
9 TraesCS3A01G350800 chr7A 17017634 17018614 980 False 1657.0 1657 97.146000 2920 3900 1 chr7A.!!$F1 980
10 TraesCS3A01G350800 chr7A 612108856 612109836 980 False 1657.0 1657 97.146000 2920 3900 1 chr7A.!!$F2 980
11 TraesCS3A01G350800 chr2A 676161722 676162693 971 True 1674.0 1674 97.737000 2929 3900 1 chr2A.!!$R1 971
12 TraesCS3A01G350800 chr2A 64352900 64353871 971 False 1668.0 1668 97.634000 2929 3900 1 chr2A.!!$F1 971
13 TraesCS3A01G350800 chr4A 25498159 25499137 978 False 1668.0 1668 97.446000 2923 3900 1 chr4A.!!$F1 977
14 TraesCS3A01G350800 chr4A 628089698 628090307 609 True 484.0 484 81.169000 1254 1863 1 chr4A.!!$R1 609
15 TraesCS3A01G350800 chr1B 635918267 635919248 981 True 1653.0 1653 97.047000 2919 3900 1 chr1B.!!$R1 981
16 TraesCS3A01G350800 chr1B 526747864 526750317 2453 False 493.0 656 87.046667 1252 2799 3 chr1B.!!$F1 1547
17 TraesCS3A01G350800 chr6A 23929980 23930960 980 False 1640.0 1640 96.840000 2920 3900 1 chr6A.!!$F1 980
18 TraesCS3A01G350800 chr7D 589517799 589518562 763 True 848.0 848 86.945000 2918 3672 1 chr7D.!!$R1 754
19 TraesCS3A01G350800 chr1D 394670658 394673064 2406 True 508.0 701 87.258000 1246 2799 3 chr1D.!!$R1 1553
20 TraesCS3A01G350800 chr1A 490411643 490413390 1747 False 539.5 678 89.099500 1252 2238 2 chr1A.!!$F1 986
21 TraesCS3A01G350800 chr4B 661658372 661659045 673 True 640.0 640 84.071000 2929 3594 1 chr4B.!!$R1 665
22 TraesCS3A01G350800 chr5D 540239892 540240501 609 True 507.0 507 81.818000 1254 1863 1 chr5D.!!$R1 609
23 TraesCS3A01G350800 chr5B 682538194 682538803 609 True 462.0 462 80.519000 1254 1863 1 chr5B.!!$R1 609

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
735 869 0.924090 CGAGCCTAAACTGCGATGAC 59.076 55.0 0.00 0.00 0.0 3.06 F
1092 1227 0.526954 CATGGGGCTCACGTACGTAC 60.527 60.0 22.34 15.90 0.0 3.67 F
1093 1228 0.682209 ATGGGGCTCACGTACGTACT 60.682 55.0 22.34 7.87 0.0 2.73 F
1095 1230 1.028868 GGGGCTCACGTACGTACTCT 61.029 60.0 22.34 5.60 0.0 3.24 F
2324 3698 0.880278 TTGCTCAGTGTGCTTCGTCC 60.880 55.0 17.38 0.00 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 3677 0.601311 AAGGACGAAGCACACTGAGC 60.601 55.000 0.00 0.00 0.00 4.26 R
2309 3679 1.134521 ACAAAGGACGAAGCACACTGA 60.135 47.619 0.00 0.00 0.00 3.41 R
2320 3694 1.522258 GCAAATGCAACACAAAGGACG 59.478 47.619 0.00 0.00 41.59 4.79 R
2603 4046 2.674380 CTTGCCCACCTGCTGGAC 60.674 66.667 17.64 3.44 43.95 4.02 R
3674 5129 6.492007 AGCAAATATGTTGACTGAAGAGTG 57.508 37.500 0.00 0.00 30.16 3.51 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
34 35 1.472878 GAGACCATGTGCGTGACTAGA 59.527 52.381 0.00 0.00 0.00 2.43
43 44 3.193479 TGTGCGTGACTAGATGACTTGAT 59.807 43.478 0.00 0.00 0.00 2.57
47 48 5.979517 TGCGTGACTAGATGACTTGATAATG 59.020 40.000 0.00 0.00 0.00 1.90
105 106 4.381505 GCTGAAAAACCAGAGTCAAACCAA 60.382 41.667 0.00 0.00 36.29 3.67
111 112 4.021102 ACCAGAGTCAAACCAAATCGAT 57.979 40.909 0.00 0.00 0.00 3.59
117 118 4.389374 AGTCAAACCAAATCGATCTGTGT 58.611 39.130 0.00 0.00 0.00 3.72
119 120 3.501828 TCAAACCAAATCGATCTGTGTGG 59.498 43.478 0.00 4.54 0.00 4.17
208 209 3.747708 GCAAAGTGAACCCTAAGACAGGT 60.748 47.826 0.00 0.00 43.80 4.00
210 211 4.790718 AAGTGAACCCTAAGACAGGTTT 57.209 40.909 0.00 0.00 46.38 3.27
211 212 4.790718 AGTGAACCCTAAGACAGGTTTT 57.209 40.909 0.00 0.00 46.38 2.43
212 213 5.125367 AGTGAACCCTAAGACAGGTTTTT 57.875 39.130 0.00 0.00 46.38 1.94
233 234 3.650754 TAGGAGAGGGGGAGGGGGT 62.651 68.421 0.00 0.00 0.00 4.95
253 360 5.841783 GGGGTAATATGGACTTCTCTTCTCT 59.158 44.000 0.00 0.00 0.00 3.10
310 418 2.375146 GTTGTTGGCCCTACCTAATGG 58.625 52.381 0.00 0.00 40.22 3.16
321 429 1.739067 ACCTAATGGCGAACTCTTGC 58.261 50.000 0.00 0.00 36.63 4.01
363 471 6.515272 AAAATACTCTTGTTCATGCGGATT 57.485 33.333 0.00 0.00 0.00 3.01
365 473 1.470098 ACTCTTGTTCATGCGGATTGC 59.530 47.619 0.00 0.00 46.70 3.56
428 536 4.809815 GAGGTTATACTCGTAAGCTCGT 57.190 45.455 9.28 0.00 44.40 4.18
456 564 4.677182 AGTGGCAAGTGATTTTCCCTTAT 58.323 39.130 0.00 0.00 0.00 1.73
459 567 6.723977 AGTGGCAAGTGATTTTCCCTTATAAA 59.276 34.615 0.00 0.00 0.00 1.40
564 677 1.378531 TCGGGCTGGATTCAAATTCG 58.621 50.000 0.00 0.00 0.00 3.34
567 680 2.031682 CGGGCTGGATTCAAATTCGATC 60.032 50.000 0.00 0.00 0.00 3.69
613 727 9.815936 CTAAATTCAATGAATTTTGCAAGGAAC 57.184 29.630 30.98 0.00 46.07 3.62
682 816 7.903995 AATATCGTTGGTACCGAAAACTTAA 57.096 32.000 2.45 0.00 37.93 1.85
704 838 4.598036 ACCATTGTTCAGATCCTTGGAT 57.402 40.909 1.18 1.18 0.00 3.41
735 869 0.924090 CGAGCCTAAACTGCGATGAC 59.076 55.000 0.00 0.00 0.00 3.06
750 884 2.361119 CGATGACCGAGATCCAAACCTA 59.639 50.000 0.00 0.00 41.76 3.08
774 908 7.435068 ACAAGCTGTAGAAAATAACGAACAT 57.565 32.000 0.00 0.00 0.00 2.71
775 909 7.298122 ACAAGCTGTAGAAAATAACGAACATG 58.702 34.615 0.00 0.00 0.00 3.21
776 910 5.869350 AGCTGTAGAAAATAACGAACATGC 58.131 37.500 0.00 0.00 0.00 4.06
777 911 5.643777 AGCTGTAGAAAATAACGAACATGCT 59.356 36.000 0.00 0.00 0.00 3.79
778 912 5.734498 GCTGTAGAAAATAACGAACATGCTG 59.266 40.000 0.00 0.00 0.00 4.41
779 913 5.627172 TGTAGAAAATAACGAACATGCTGC 58.373 37.500 0.00 0.00 0.00 5.25
856 990 2.821366 CCGCGAATGGCTGCTCTT 60.821 61.111 8.23 0.00 40.44 2.85
874 1009 1.359475 TGTACGTGCGCAGTACACA 59.641 52.632 31.18 21.96 46.38 3.72
883 1018 2.073816 GCGCAGTACACACTTTGGTAT 58.926 47.619 0.30 0.00 30.46 2.73
884 1019 2.159707 GCGCAGTACACACTTTGGTATG 60.160 50.000 0.30 0.00 30.46 2.39
886 1021 4.239304 CGCAGTACACACTTTGGTATGTA 58.761 43.478 0.00 0.00 34.65 2.29
891 1026 6.034161 GTACACACTTTGGTATGTACTCCT 57.966 41.667 9.54 0.00 46.68 3.69
892 1027 7.161773 GTACACACTTTGGTATGTACTCCTA 57.838 40.000 9.54 0.00 46.68 2.94
893 1028 6.034161 ACACACTTTGGTATGTACTCCTAC 57.966 41.667 0.00 0.00 30.59 3.18
894 1029 5.541101 ACACACTTTGGTATGTACTCCTACA 59.459 40.000 0.00 0.00 37.28 2.74
895 1030 6.212791 ACACACTTTGGTATGTACTCCTACAT 59.787 38.462 0.00 0.00 44.42 2.29
896 1031 7.103641 CACACTTTGGTATGTACTCCTACATT 58.896 38.462 0.00 0.00 40.16 2.71
897 1032 8.255206 CACACTTTGGTATGTACTCCTACATTA 58.745 37.037 0.00 0.00 40.16 1.90
908 1043 8.612486 TGTACTCCTACATTATAAACAAGGGA 57.388 34.615 9.33 4.76 0.00 4.20
1014 1149 3.927142 CACGGGACATGAGAAAAGACTAC 59.073 47.826 0.00 0.00 0.00 2.73
1091 1226 0.680601 TCATGGGGCTCACGTACGTA 60.681 55.000 22.34 3.59 0.00 3.57
1092 1227 0.526954 CATGGGGCTCACGTACGTAC 60.527 60.000 22.34 15.90 0.00 3.67
1093 1228 0.682209 ATGGGGCTCACGTACGTACT 60.682 55.000 22.34 7.87 0.00 2.73
1094 1229 1.308069 TGGGGCTCACGTACGTACTC 61.308 60.000 22.34 13.27 0.00 2.59
1095 1230 1.028868 GGGGCTCACGTACGTACTCT 61.029 60.000 22.34 5.60 0.00 3.24
1096 1231 1.656652 GGGCTCACGTACGTACTCTA 58.343 55.000 22.34 7.27 0.00 2.43
1097 1232 1.328986 GGGCTCACGTACGTACTCTAC 59.671 57.143 22.34 9.28 0.00 2.59
1104 1239 1.134401 CGTACGTACTCTACCTCCCCA 60.134 57.143 22.55 0.00 0.00 4.96
1165 1300 4.570663 GGAGCCGCGTCGCAGTAT 62.571 66.667 18.75 0.00 0.00 2.12
1168 1303 4.899687 GCCGCGTCGCAGTATCGA 62.900 66.667 18.75 0.00 35.95 3.59
1169 1304 2.051256 CCGCGTCGCAGTATCGAT 60.051 61.111 18.75 2.16 40.84 3.59
1172 1307 1.082951 GCGTCGCAGTATCGATCGA 60.083 57.895 21.86 21.86 40.84 3.59
1174 1309 1.515172 CGTCGCAGTATCGATCGATC 58.485 55.000 32.50 22.59 40.84 3.69
1175 1310 1.136336 CGTCGCAGTATCGATCGATCA 60.136 52.381 32.50 16.71 40.84 2.92
1176 1311 2.500888 GTCGCAGTATCGATCGATCAG 58.499 52.381 32.50 22.82 40.84 2.90
1182 1340 3.064931 AGTATCGATCGATCAGCACGTA 58.935 45.455 32.50 11.23 36.17 3.57
1186 1344 4.377124 TATCGATCGATCAGCACGTAAGTC 60.377 45.833 32.50 0.00 41.88 3.01
1365 1523 1.946650 GCTCTACGGCAGCATCGTC 60.947 63.158 0.00 0.00 41.38 4.20
1884 2135 1.071128 TTACCACGGGTCCGGTTTG 59.929 57.895 14.25 3.15 44.69 2.93
1922 3046 5.230182 GTGGTGGACATTTCTGAATTTTCC 58.770 41.667 9.47 9.47 0.00 3.13
2247 3422 2.435938 GCGCAGGTTCCGAATCCA 60.436 61.111 0.30 0.00 0.00 3.41
2249 3424 1.375396 CGCAGGTTCCGAATCCACA 60.375 57.895 0.00 0.00 0.00 4.17
2256 3431 4.030913 AGGTTCCGAATCCACATTCTCTA 58.969 43.478 0.00 0.00 36.93 2.43
2262 3437 4.034510 CCGAATCCACATTCTCTAAACTGC 59.965 45.833 0.00 0.00 36.93 4.40
2267 3637 5.724328 TCCACATTCTCTAAACTGCACTAG 58.276 41.667 0.00 0.00 0.00 2.57
2269 3639 6.014584 TCCACATTCTCTAAACTGCACTAGAA 60.015 38.462 0.00 0.00 0.00 2.10
2287 3657 8.083462 CACTAGAATTTTAGTGTTGTACTGCA 57.917 34.615 22.13 0.00 43.48 4.41
2288 3658 8.009974 CACTAGAATTTTAGTGTTGTACTGCAC 58.990 37.037 22.13 10.87 43.48 4.57
2289 3659 6.935741 AGAATTTTAGTGTTGTACTGCACA 57.064 33.333 17.88 6.19 40.65 4.57
2303 3673 4.040445 ACTGCACAAGTTTATTTTGCGT 57.960 36.364 0.00 0.00 34.57 5.24
2304 3674 4.429108 ACTGCACAAGTTTATTTTGCGTT 58.571 34.783 0.00 0.00 34.57 4.84
2307 3677 5.554636 TGCACAAGTTTATTTTGCGTTTTG 58.445 33.333 0.00 0.00 35.90 2.44
2309 3679 5.726413 GCACAAGTTTATTTTGCGTTTTGCT 60.726 36.000 0.00 0.00 46.63 3.91
2320 3694 1.746760 CGTTTTGCTCAGTGTGCTTC 58.253 50.000 17.38 5.41 0.00 3.86
2324 3698 0.880278 TTGCTCAGTGTGCTTCGTCC 60.880 55.000 17.38 0.00 0.00 4.79
2350 3750 2.125431 GCATTTGCATGGCGGCTT 60.125 55.556 11.43 0.00 41.59 4.35
2925 4368 0.310854 CTGGTGCCCGTTGTTCTTTC 59.689 55.000 0.00 0.00 0.00 2.62
2938 4381 5.617187 CGTTGTTCTTTCTTGAGTGAATTCG 59.383 40.000 0.04 0.00 0.00 3.34
3333 4788 1.206132 CATGTTCACCATGCCTGCATT 59.794 47.619 0.97 0.00 44.21 3.56
3369 4824 3.647771 GGAGTTCCCGTTGGCCCT 61.648 66.667 0.00 0.00 0.00 5.19
3477 4932 3.637694 CTCTCAATCATCTCTGGCTCTGA 59.362 47.826 0.00 0.00 0.00 3.27
3674 5129 3.560068 ACAGCTAGCAAGTAACAACACAC 59.440 43.478 18.83 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.973450 ATGTACATTATCAAGTCATCTAGTCAC 57.027 33.333 1.41 0.00 0.00 3.67
47 48 8.945930 CGATTTTCTCGTCTCTTTACTATGTAC 58.054 37.037 0.00 0.00 42.56 2.90
75 76 6.480763 TGACTCTGGTTTTTCAGCCATATTA 58.519 36.000 0.00 0.00 34.91 0.98
105 106 1.141657 CATCCCCCACACAGATCGATT 59.858 52.381 0.00 0.00 0.00 3.34
111 112 0.323633 CAATGCATCCCCCACACAGA 60.324 55.000 0.00 0.00 0.00 3.41
117 118 1.265236 GTTTCACAATGCATCCCCCA 58.735 50.000 0.00 0.00 0.00 4.96
119 120 0.887933 ACGTTTCACAATGCATCCCC 59.112 50.000 0.00 0.00 0.00 4.81
176 177 6.418057 AGGGTTCACTTTGCAATCATTAAA 57.582 33.333 0.00 0.00 0.00 1.52
211 212 1.559584 CCCCTCCCCCTCTCCTAAAAA 60.560 57.143 0.00 0.00 0.00 1.94
212 213 0.045778 CCCCTCCCCCTCTCCTAAAA 59.954 60.000 0.00 0.00 0.00 1.52
216 217 3.650754 TACCCCCTCCCCCTCTCCT 62.651 68.421 0.00 0.00 0.00 3.69
219 220 1.154434 CATATTACCCCCTCCCCCTCT 59.846 57.143 0.00 0.00 0.00 3.69
221 222 0.198696 CCATATTACCCCCTCCCCCT 59.801 60.000 0.00 0.00 0.00 4.79
224 225 2.435203 AGTCCATATTACCCCCTCCC 57.565 55.000 0.00 0.00 0.00 4.30
233 234 9.261035 ACTTTGAGAGAAGAGAAGTCCATATTA 57.739 33.333 0.00 0.00 0.00 0.98
253 360 8.801882 TTTTTCACTTCTTCTCCTTACTTTGA 57.198 30.769 0.00 0.00 0.00 2.69
287 394 0.988832 TAGGTAGGGCCAACAACCAG 59.011 55.000 6.18 0.00 40.61 4.00
289 396 2.375146 CATTAGGTAGGGCCAACAACC 58.625 52.381 6.18 7.82 40.61 3.77
356 464 3.507924 GTGGCATCGCAATCCGCA 61.508 61.111 0.00 0.00 42.60 5.69
423 531 3.682858 TCACTTGCCACTTTATTACGAGC 59.317 43.478 0.00 0.00 0.00 5.03
427 535 6.811665 GGGAAAATCACTTGCCACTTTATTAC 59.188 38.462 0.00 0.00 36.82 1.89
428 536 6.723977 AGGGAAAATCACTTGCCACTTTATTA 59.276 34.615 0.00 0.00 39.18 0.98
462 570 9.918630 CTGATATGAAAACCTCAAATTTCAAGT 57.081 29.630 5.19 0.00 45.56 3.16
564 677 9.567848 TTAGACGAATTTAAGCAAATTTGGATC 57.432 29.630 19.47 3.39 44.71 3.36
673 807 8.360390 AGGATCTGAACAATGGTTTAAGTTTTC 58.640 33.333 0.00 0.00 37.36 2.29
682 816 4.387026 TCCAAGGATCTGAACAATGGTT 57.613 40.909 7.68 0.00 40.76 3.67
704 838 0.611618 TAGGCTCGGTTAACCACGGA 60.612 55.000 24.14 12.30 35.14 4.69
735 869 2.093447 AGCTTGTAGGTTTGGATCTCGG 60.093 50.000 0.00 0.00 0.00 4.63
750 884 6.854496 TGTTCGTTATTTTCTACAGCTTGT 57.146 33.333 0.00 0.00 0.00 3.16
774 908 0.321034 CTCCTTGTACAGCTGCAGCA 60.321 55.000 38.24 17.55 45.16 4.41
775 909 0.036952 TCTCCTTGTACAGCTGCAGC 60.037 55.000 31.53 31.53 42.49 5.25
776 910 1.719600 GTCTCCTTGTACAGCTGCAG 58.280 55.000 15.27 10.11 0.00 4.41
777 911 0.038251 CGTCTCCTTGTACAGCTGCA 60.038 55.000 15.27 0.00 0.00 4.41
778 912 1.355066 GCGTCTCCTTGTACAGCTGC 61.355 60.000 15.27 0.00 0.00 5.25
779 913 0.244994 AGCGTCTCCTTGTACAGCTG 59.755 55.000 13.48 13.48 31.76 4.24
855 989 0.248949 TGTGTACTGCGCACGTACAA 60.249 50.000 33.89 25.74 46.03 2.41
856 990 0.935831 GTGTGTACTGCGCACGTACA 60.936 55.000 31.18 31.18 46.77 2.90
883 1018 8.612486 TCCCTTGTTTATAATGTAGGAGTACA 57.388 34.615 0.00 0.00 43.43 2.90
884 1019 9.490379 CATCCCTTGTTTATAATGTAGGAGTAC 57.510 37.037 8.20 0.00 0.00 2.73
886 1021 7.421382 CCCATCCCTTGTTTATAATGTAGGAGT 60.421 40.741 8.20 0.00 0.00 3.85
887 1022 6.942576 CCCATCCCTTGTTTATAATGTAGGAG 59.057 42.308 8.20 1.68 0.00 3.69
888 1023 6.621931 TCCCATCCCTTGTTTATAATGTAGGA 59.378 38.462 8.20 2.81 0.00 2.94
889 1024 6.715264 GTCCCATCCCTTGTTTATAATGTAGG 59.285 42.308 0.00 0.00 0.00 3.18
890 1025 7.287061 TGTCCCATCCCTTGTTTATAATGTAG 58.713 38.462 0.00 0.00 0.00 2.74
891 1026 7.214460 TGTCCCATCCCTTGTTTATAATGTA 57.786 36.000 0.00 0.00 0.00 2.29
892 1027 6.086011 TGTCCCATCCCTTGTTTATAATGT 57.914 37.500 0.00 0.00 0.00 2.71
893 1028 6.459573 CGTTGTCCCATCCCTTGTTTATAATG 60.460 42.308 0.00 0.00 0.00 1.90
894 1029 5.592688 CGTTGTCCCATCCCTTGTTTATAAT 59.407 40.000 0.00 0.00 0.00 1.28
895 1030 4.944930 CGTTGTCCCATCCCTTGTTTATAA 59.055 41.667 0.00 0.00 0.00 0.98
896 1031 4.019141 ACGTTGTCCCATCCCTTGTTTATA 60.019 41.667 0.00 0.00 0.00 0.98
897 1032 3.245122 ACGTTGTCCCATCCCTTGTTTAT 60.245 43.478 0.00 0.00 0.00 1.40
908 1043 2.038426 TGAACATCTCACGTTGTCCCAT 59.962 45.455 0.00 0.00 0.00 4.00
955 1090 1.405933 GGCTTCATTGGCATTTCCACC 60.406 52.381 0.00 0.00 46.55 4.61
1091 1226 0.192566 TTGGTGTGGGGAGGTAGAGT 59.807 55.000 0.00 0.00 0.00 3.24
1092 1227 0.613777 GTTGGTGTGGGGAGGTAGAG 59.386 60.000 0.00 0.00 0.00 2.43
1093 1228 0.838987 GGTTGGTGTGGGGAGGTAGA 60.839 60.000 0.00 0.00 0.00 2.59
1094 1229 1.683441 GGTTGGTGTGGGGAGGTAG 59.317 63.158 0.00 0.00 0.00 3.18
1095 1230 2.218454 CGGTTGGTGTGGGGAGGTA 61.218 63.158 0.00 0.00 0.00 3.08
1096 1231 3.566210 CGGTTGGTGTGGGGAGGT 61.566 66.667 0.00 0.00 0.00 3.85
1161 1296 1.874231 ACGTGCTGATCGATCGATACT 59.126 47.619 29.45 10.24 34.60 2.12
1164 1299 2.290916 ACTTACGTGCTGATCGATCGAT 59.709 45.455 29.76 29.76 37.59 3.59
1165 1300 1.669265 ACTTACGTGCTGATCGATCGA 59.331 47.619 21.86 21.86 0.00 3.59
1168 1303 1.268589 CGGACTTACGTGCTGATCGAT 60.269 52.381 0.00 0.00 0.00 3.59
1169 1304 0.098200 CGGACTTACGTGCTGATCGA 59.902 55.000 0.00 0.00 0.00 3.59
1182 1340 2.284405 ATCACCCCCGACGGACTT 60.284 61.111 17.49 0.00 0.00 3.01
1186 1344 4.203076 GTCGATCACCCCCGACGG 62.203 72.222 6.99 6.99 44.23 4.79
1192 1350 1.472480 CATTGTTTGGTCGATCACCCC 59.528 52.381 0.00 0.00 46.18 4.95
1365 1523 0.250295 TGACGGCCCACTTCTTCTTG 60.250 55.000 0.00 0.00 0.00 3.02
1922 3046 3.956320 CGAACGCGGCGTATCACG 61.956 66.667 29.63 24.52 45.88 4.35
2132 3307 4.008933 AGGCAGGTCCACGTGAGC 62.009 66.667 19.30 12.72 41.93 4.26
2247 3422 8.854614 AAATTCTAGTGCAGTTTAGAGAATGT 57.145 30.769 14.99 9.05 34.66 2.71
2267 3637 7.193595 ACTTGTGCAGTACAACACTAAAATTC 58.806 34.615 16.35 0.00 44.07 2.17
2269 3639 6.693315 ACTTGTGCAGTACAACACTAAAAT 57.307 33.333 16.35 0.00 44.07 1.82
2284 3654 5.554636 CAAAACGCAAAATAAACTTGTGCA 58.445 33.333 1.48 0.00 37.72 4.57
2285 3655 4.432984 GCAAAACGCAAAATAAACTTGTGC 59.567 37.500 0.00 0.00 41.79 4.57
2286 3656 5.794720 AGCAAAACGCAAAATAAACTTGTG 58.205 33.333 0.00 0.00 46.13 3.33
2287 3657 5.578727 TGAGCAAAACGCAAAATAAACTTGT 59.421 32.000 0.00 0.00 46.13 3.16
2288 3658 6.030379 TGAGCAAAACGCAAAATAAACTTG 57.970 33.333 0.00 0.00 46.13 3.16
2289 3659 5.810074 ACTGAGCAAAACGCAAAATAAACTT 59.190 32.000 0.00 0.00 46.13 2.66
2303 3673 1.330521 GACGAAGCACACTGAGCAAAA 59.669 47.619 1.10 0.00 0.00 2.44
2304 3674 0.937304 GACGAAGCACACTGAGCAAA 59.063 50.000 1.10 0.00 0.00 3.68
2307 3677 0.601311 AAGGACGAAGCACACTGAGC 60.601 55.000 0.00 0.00 0.00 4.26
2309 3679 1.134521 ACAAAGGACGAAGCACACTGA 60.135 47.619 0.00 0.00 0.00 3.41
2320 3694 1.522258 GCAAATGCAACACAAAGGACG 59.478 47.619 0.00 0.00 41.59 4.79
2349 3749 4.519612 TGTGCACCAGCCCTGCAA 62.520 61.111 15.69 0.00 46.04 4.08
2603 4046 2.674380 CTTGCCCACCTGCTGGAC 60.674 66.667 17.64 3.44 43.95 4.02
2925 4368 5.458015 GGTAAAAACCCGAATTCACTCAAG 58.542 41.667 6.22 0.00 0.00 3.02
3369 4824 6.757010 GGACAGCGTTAATTATCAGAAGAAGA 59.243 38.462 0.00 0.00 0.00 2.87
3674 5129 6.492007 AGCAAATATGTTGACTGAAGAGTG 57.508 37.500 0.00 0.00 30.16 3.51


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

AutoCloner maintained by Alex Coulton.