Multiple sequence alignment - TraesCS3A01G167100

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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 TraesCS3A01G167100 chr3A 100.000 3715 0 0 1 3715 172628785 172632499 0.000000e+00 6861.0
1 TraesCS3A01G167100 chr3B 93.979 2425 85 28 597 2988 227419345 227416949 0.000000e+00 3613.0
2 TraesCS3A01G167100 chr3B 94.079 608 22 6 3 603 227425187 227424587 0.000000e+00 911.0
3 TraesCS3A01G167100 chr3D 93.918 2236 92 19 2 2218 153847275 153849485 0.000000e+00 3336.0
4 TraesCS3A01G167100 chr3D 94.595 740 22 4 2249 2988 153849587 153850308 0.000000e+00 1129.0
5 TraesCS3A01G167100 chr3D 86.731 731 83 9 2985 3713 4906183 4905465 0.000000e+00 800.0
6 TraesCS3A01G167100 chr3D 85.948 733 89 7 2984 3713 113577675 113576954 0.000000e+00 771.0
7 TraesCS3A01G167100 chr5B 88.649 740 72 6 2985 3713 423214029 423213291 0.000000e+00 891.0
8 TraesCS3A01G167100 chr6D 87.449 733 76 9 2985 3713 39514302 39515022 0.000000e+00 830.0
9 TraesCS3A01G167100 chr6A 83.151 730 116 7 2992 3714 181011763 181011034 0.000000e+00 660.0
10 TraesCS3A01G167100 chr6A 90.566 53 5 0 1958 2010 569692348 569692400 1.850000e-08 71.3
11 TraesCS3A01G167100 chr1D 82.609 736 117 10 2984 3713 189886960 189887690 1.130000e-179 640.0
12 TraesCS3A01G167100 chr5D 82.778 720 117 7 3000 3713 405165826 405165108 1.460000e-178 636.0
13 TraesCS3A01G167100 chr7A 82.177 735 123 7 2985 3713 207284498 207285230 3.150000e-175 625.0
14 TraesCS3A01G167100 chr1A 82.041 735 124 7 2985 3713 267987510 267988242 1.470000e-173 619.0
15 TraesCS3A01G167100 chrUn 87.705 244 29 1 2984 3227 37984174 37984416 2.180000e-72 283.0
16 TraesCS3A01G167100 chrUn 91.803 183 15 0 2984 3166 37362264 37362082 4.760000e-64 255.0


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 TraesCS3A01G167100 chr3A 172628785 172632499 3714 False 6861.0 6861 100.0000 1 3715 1 chr3A.!!$F1 3714
1 TraesCS3A01G167100 chr3B 227416949 227419345 2396 True 3613.0 3613 93.9790 597 2988 1 chr3B.!!$R1 2391
2 TraesCS3A01G167100 chr3B 227424587 227425187 600 True 911.0 911 94.0790 3 603 1 chr3B.!!$R2 600
3 TraesCS3A01G167100 chr3D 153847275 153850308 3033 False 2232.5 3336 94.2565 2 2988 2 chr3D.!!$F1 2986
4 TraesCS3A01G167100 chr3D 4905465 4906183 718 True 800.0 800 86.7310 2985 3713 1 chr3D.!!$R1 728
5 TraesCS3A01G167100 chr3D 113576954 113577675 721 True 771.0 771 85.9480 2984 3713 1 chr3D.!!$R2 729
6 TraesCS3A01G167100 chr5B 423213291 423214029 738 True 891.0 891 88.6490 2985 3713 1 chr5B.!!$R1 728
7 TraesCS3A01G167100 chr6D 39514302 39515022 720 False 830.0 830 87.4490 2985 3713 1 chr6D.!!$F1 728
8 TraesCS3A01G167100 chr6A 181011034 181011763 729 True 660.0 660 83.1510 2992 3714 1 chr6A.!!$R1 722
9 TraesCS3A01G167100 chr1D 189886960 189887690 730 False 640.0 640 82.6090 2984 3713 1 chr1D.!!$F1 729
10 TraesCS3A01G167100 chr5D 405165108 405165826 718 True 636.0 636 82.7780 3000 3713 1 chr5D.!!$R1 713
11 TraesCS3A01G167100 chr7A 207284498 207285230 732 False 625.0 625 82.1770 2985 3713 1 chr7A.!!$F1 728
12 TraesCS3A01G167100 chr1A 267987510 267988242 732 False 619.0 619 82.0410 2985 3713 1 chr1A.!!$F1 728

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
755 766 0.244994 ATCGAGACACCTGTGCTGTC 59.755 55.0 0.0 0.0 38.7 3.51 F
1128 1143 0.316841 GGATCATCGAGACCAGCCTC 59.683 60.0 0.0 0.0 0.0 4.70 F
2094 2132 0.037232 GCCTCCTGTACTCACACCAC 60.037 60.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2113 0.037232 GTGGTGTGAGTACAGGAGGC 60.037 60.0 0.0 0.0 37.52 4.70 R
2699 2840 0.179084 TGTACTATGCCAGCTTCGCC 60.179 55.0 0.0 0.0 0.00 5.54 R
3476 3633 0.110823 GTGCCGTCGTCAATGTTGTC 60.111 55.0 0.0 0.0 0.00 3.18 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
93 94 2.112815 GGACCCATTTTCGCGGAGG 61.113 63.158 6.13 0.00 0.00 4.30
95 96 2.438434 CCCATTTTCGCGGAGGCT 60.438 61.111 6.13 0.00 36.88 4.58
172 173 2.556622 GGCAAAAAGGACGAAATGGAGA 59.443 45.455 0.00 0.00 0.00 3.71
270 273 1.500512 TACACTTTTCGGGTGCGTGC 61.501 55.000 0.00 0.00 38.14 5.34
271 274 3.645975 ACTTTTCGGGTGCGTGCG 61.646 61.111 0.00 0.00 0.00 5.34
272 275 3.645975 CTTTTCGGGTGCGTGCGT 61.646 61.111 0.00 0.00 0.00 5.24
273 276 3.855209 CTTTTCGGGTGCGTGCGTG 62.855 63.158 0.00 0.00 0.00 5.34
402 405 4.148871 CGCATGTAAATCGAGATACTGGTG 59.851 45.833 10.61 8.35 0.00 4.17
441 444 5.810095 AGAAGGCAGCAAAGTAGTAATTCT 58.190 37.500 0.00 0.00 0.00 2.40
461 464 5.087923 TCTATACTGGGGCCAAGAGATAA 57.912 43.478 16.85 0.00 0.00 1.75
465 468 4.337264 ACTGGGGCCAAGAGATAATTTT 57.663 40.909 16.85 0.00 0.00 1.82
466 469 4.687976 ACTGGGGCCAAGAGATAATTTTT 58.312 39.130 16.85 0.00 0.00 1.94
561 564 5.458779 GGGAAAACTGAAAACGAATTGACAG 59.541 40.000 0.00 0.00 34.51 3.51
563 566 7.190871 GGAAAACTGAAAACGAATTGACAGTA 58.809 34.615 0.00 0.00 38.00 2.74
564 567 7.165318 GGAAAACTGAAAACGAATTGACAGTAC 59.835 37.037 0.00 0.00 38.00 2.73
565 568 5.668558 ACTGAAAACGAATTGACAGTACC 57.331 39.130 0.00 0.00 37.55 3.34
566 569 5.120399 ACTGAAAACGAATTGACAGTACCA 58.880 37.500 0.00 0.00 37.55 3.25
567 570 5.236478 ACTGAAAACGAATTGACAGTACCAG 59.764 40.000 0.00 0.00 37.55 4.00
585 596 3.825328 CCAGAGAATGGGATAAACTGGG 58.175 50.000 0.00 0.00 46.36 4.45
613 624 4.671687 AGTGGGAGAATTGATTGGGGATAT 59.328 41.667 0.00 0.00 0.00 1.63
615 626 4.202706 TGGGAGAATTGATTGGGGATATGG 60.203 45.833 0.00 0.00 0.00 2.74
629 640 1.888512 GATATGGATTTGGCACGGCAT 59.111 47.619 0.00 0.00 0.00 4.40
675 686 2.617308 GTCTGCCATTCACATGATCCAG 59.383 50.000 0.00 0.00 31.07 3.86
693 704 3.097921 GCCAGGCCCATTGATTGGC 62.098 63.158 13.54 13.54 46.39 4.52
755 766 0.244994 ATCGAGACACCTGTGCTGTC 59.755 55.000 0.00 0.00 38.70 3.51
760 771 2.670934 CACCTGTGCTGTCCCTGC 60.671 66.667 0.00 0.00 0.00 4.85
811 823 2.094675 ACAAATCCAAAGCATCCTCCG 58.905 47.619 0.00 0.00 0.00 4.63
835 847 4.035208 ACTCGCCGATTCCAAAACATATTC 59.965 41.667 0.00 0.00 0.00 1.75
873 885 4.534647 TCTTCCTAAGCTCAGAGATCCT 57.465 45.455 0.00 0.00 0.00 3.24
902 917 2.498167 TGCTTCTGTTGCCTTCTTCTC 58.502 47.619 0.00 0.00 0.00 2.87
907 922 2.631062 TCTGTTGCCTTCTTCTCGGTAA 59.369 45.455 0.00 0.00 0.00 2.85
908 923 2.996621 CTGTTGCCTTCTTCTCGGTAAG 59.003 50.000 0.00 0.00 0.00 2.34
909 924 2.367567 TGTTGCCTTCTTCTCGGTAAGT 59.632 45.455 0.00 0.00 0.00 2.24
947 962 3.307269 CCTCCTTTCTTGACTGATGCTGA 60.307 47.826 0.00 0.00 0.00 4.26
976 991 5.306678 AGGATCTTACAGGGATTCATCTGTC 59.693 44.000 12.98 2.53 42.51 3.51
1080 1095 3.468770 CAAGATGCTCATCTCCTTCCTG 58.531 50.000 12.29 3.34 46.75 3.86
1128 1143 0.316841 GGATCATCGAGACCAGCCTC 59.683 60.000 0.00 0.00 0.00 4.70
1139 1154 1.279271 GACCAGCCTCACAGGTAACAT 59.721 52.381 0.00 0.00 38.50 2.71
1165 1180 2.986019 TCTTCCCTCCCAAATGAGTTCA 59.014 45.455 0.00 0.00 0.00 3.18
1172 1187 4.823989 CCTCCCAAATGAGTTCATGGATAC 59.176 45.833 3.82 0.00 36.56 2.24
1178 1193 6.604795 CCAAATGAGTTCATGGATACCTTCTT 59.395 38.462 0.00 0.00 36.56 2.52
1179 1194 7.201767 CCAAATGAGTTCATGGATACCTTCTTC 60.202 40.741 0.00 0.00 36.56 2.87
1331 1353 2.029666 GACATCATCGGCTCCGGG 59.970 66.667 0.00 1.77 40.25 5.73
1481 1503 0.898320 ACAGGAACATCGTCCCTCTG 59.102 55.000 0.00 0.00 38.59 3.35
1851 1873 2.009774 CTGCCCGTCGAAATCTCAATT 58.990 47.619 0.00 0.00 0.00 2.32
1853 1875 2.161410 TGCCCGTCGAAATCTCAATTTG 59.839 45.455 0.00 0.00 35.21 2.32
2022 2060 1.586564 GAGGCCGACAGACGAATCG 60.587 63.158 0.00 0.00 45.77 3.34
2075 2113 2.486191 GGGTAAGCATCCACCTCTCATG 60.486 54.545 0.00 0.00 35.04 3.07
2094 2132 0.037232 GCCTCCTGTACTCACACCAC 60.037 60.000 0.00 0.00 0.00 4.16
2101 2139 1.607148 TGTACTCACACCACTGACTCG 59.393 52.381 0.00 0.00 0.00 4.18
2102 2140 1.068472 GTACTCACACCACTGACTCGG 60.068 57.143 0.00 0.00 0.00 4.63
2108 2146 3.070446 TCACACCACTGACTCGGTTAAAT 59.930 43.478 0.00 0.00 31.41 1.40
2111 2149 3.435671 CACCACTGACTCGGTTAAATTCC 59.564 47.826 0.00 0.00 31.41 3.01
2133 2171 3.555547 CGAATGATCGGTTGTGCAAGATA 59.444 43.478 0.00 0.00 45.32 1.98
2134 2172 4.550831 CGAATGATCGGTTGTGCAAGATAC 60.551 45.833 0.00 0.00 45.32 2.24
2140 2178 1.064060 GGTTGTGCAAGATACGATGCC 59.936 52.381 0.00 0.00 41.87 4.40
2141 2179 1.064060 GTTGTGCAAGATACGATGCCC 59.936 52.381 0.00 0.00 41.87 5.36
2162 2200 5.221126 GCCCTGAGTAGAATAATTTGGCTTG 60.221 44.000 0.00 0.00 0.00 4.01
2176 2214 6.956202 ATTTGGCTTGAATCTCTAGAATGG 57.044 37.500 0.00 0.00 0.00 3.16
2182 2220 6.273825 GCTTGAATCTCTAGAATGGTCGTTA 58.726 40.000 0.00 0.00 0.00 3.18
2189 2227 7.284919 TCTCTAGAATGGTCGTTATATGCAA 57.715 36.000 0.00 0.00 0.00 4.08
2218 2256 7.123997 ACCAATGGATATGTTGCTGAAATAACA 59.876 33.333 6.16 0.00 40.65 2.41
2240 2278 5.944007 ACAAATAACCAACCAACCTAGCTAG 59.056 40.000 14.20 14.20 0.00 3.42
2242 2280 1.657804 ACCAACCAACCTAGCTAGCT 58.342 50.000 23.12 23.12 0.00 3.32
2244 2282 3.385115 ACCAACCAACCTAGCTAGCTAT 58.615 45.455 24.36 8.50 0.00 2.97
2245 2283 3.388350 ACCAACCAACCTAGCTAGCTATC 59.612 47.826 24.36 0.00 0.00 2.08
2247 2285 4.141711 CCAACCAACCTAGCTAGCTATCAA 60.142 45.833 24.36 4.75 0.00 2.57
2281 2399 4.763793 TCTGTACTCTGTAGTTGTACCCAC 59.236 45.833 0.00 0.00 37.15 4.61
2298 2416 1.548582 CCACCAGAAAACTGATGGGCT 60.549 52.381 2.90 0.00 38.48 5.19
2348 2474 2.485479 CCCAATGTACTCCCATCTTCCG 60.485 54.545 0.00 0.00 0.00 4.30
2354 2482 1.348064 ACTCCCATCTTCCGTGTCAA 58.652 50.000 0.00 0.00 0.00 3.18
2368 2496 1.986378 GTGTCAAGATCAACGAGGACG 59.014 52.381 0.00 0.00 45.75 4.79
2369 2497 1.067846 TGTCAAGATCAACGAGGACGG 60.068 52.381 0.00 0.00 44.46 4.79
2399 2540 7.658982 ACATTACTAGCGCAGTACAGTAGTATA 59.341 37.037 11.47 3.22 39.52 1.47
2400 2541 5.921004 ACTAGCGCAGTACAGTAGTATAC 57.079 43.478 11.47 0.00 37.54 1.47
2401 2542 4.447054 ACTAGCGCAGTACAGTAGTATACG 59.553 45.833 11.47 0.00 40.73 3.06
2402 2543 5.966555 ACTAGCGCAGTACAGTAGTATACGT 60.967 44.000 11.47 0.00 40.73 3.57
2403 2544 6.735968 ACTAGCGCAGTACAGTAGTATACGTA 60.736 42.308 11.47 0.00 40.73 3.57
2404 2545 8.160010 ACTAGCGCAGTACAGTAGTATACGTAA 61.160 40.741 11.47 0.00 40.73 3.18
2440 2581 6.483640 GTCTGATAATGGACATGTACCCTTTC 59.516 42.308 5.38 0.00 33.19 2.62
2457 2598 7.074653 ACCCTTTCTGTAGATGTGAAGTAAA 57.925 36.000 0.00 0.00 0.00 2.01
2624 2765 2.034001 GGAAGTCAAGTTCGTGTTCACG 60.034 50.000 17.57 17.57 0.00 4.35
3030 3172 5.046591 ACTCAATTGTATTCCTCGGAGTTGA 60.047 40.000 5.13 4.11 30.77 3.18
3033 3175 3.710326 TGTATTCCTCGGAGTTGATCG 57.290 47.619 4.02 0.00 0.00 3.69
3038 3182 0.933097 CCTCGGAGTTGATCGCAATG 59.067 55.000 4.02 0.00 36.22 2.82
3061 3205 4.578913 ACGAGATGTCTTGCGTGG 57.421 55.556 0.00 0.00 35.44 4.94
3088 3232 6.084738 AGCCAACTAATCCTACCATATCTCA 58.915 40.000 0.00 0.00 0.00 3.27
3090 3234 7.072454 AGCCAACTAATCCTACCATATCTCAAA 59.928 37.037 0.00 0.00 0.00 2.69
3091 3235 7.719633 GCCAACTAATCCTACCATATCTCAAAA 59.280 37.037 0.00 0.00 0.00 2.44
3166 3320 2.912690 TATGTCACGTTCAACACCCA 57.087 45.000 0.00 0.00 0.00 4.51
3168 3322 0.250793 TGTCACGTTCAACACCCACT 59.749 50.000 0.00 0.00 0.00 4.00
3175 3331 2.294074 GTTCAACACCCACTGCAGTTA 58.706 47.619 18.94 0.00 0.00 2.24
3237 3393 0.960364 GGAATGCAGCGGTTGGAAGA 60.960 55.000 0.00 0.00 0.00 2.87
3430 3587 3.719214 CCGTAGCTTCGGGATTGC 58.281 61.111 22.88 0.00 45.88 3.56
3461 3618 3.469008 TCACCAAGTAGTTGACACAGG 57.531 47.619 12.04 0.00 35.46 4.00
3476 3633 0.882042 ACAGGCAACAAGTCTCAGCG 60.882 55.000 0.00 0.00 41.41 5.18
3486 3643 2.802247 CAAGTCTCAGCGACAACATTGA 59.198 45.455 0.00 0.00 45.32 2.57
3555 3712 1.115467 CCGCTTAGAGGACCATGAGT 58.885 55.000 0.00 0.00 0.00 3.41
3566 3723 3.143807 GACCATGAGTCAAGAGAGTCG 57.856 52.381 0.00 0.00 45.39 4.18
3588 3745 2.761208 CCGAAGAAGACACAGTATCCCT 59.239 50.000 0.00 0.00 0.00 4.20
3623 3780 3.324930 TCAGGACAGCCAGCCCAG 61.325 66.667 0.00 0.00 36.29 4.45
3626 3783 3.325753 GGACAGCCAGCCCAGTCT 61.326 66.667 7.22 0.00 0.00 3.24
3633 3790 1.748122 CCAGCCCAGTCTGCATCAC 60.748 63.158 0.00 0.00 32.87 3.06
3661 3818 2.125350 GAGCTCAGTGGAAGCGGG 60.125 66.667 9.40 0.00 0.00 6.13
3672 3829 3.682292 GAAGCGGGGGCACGAAGAT 62.682 63.158 4.98 0.00 35.47 2.40
3681 3838 3.093278 CACGAAGATGAAGGCCGC 58.907 61.111 0.00 0.00 0.00 6.53
3714 3872 2.031420 CGCGAAGATACCGGAGAATGTA 60.031 50.000 9.46 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.568612 GCCGCCTCCAGCTTTTTC 59.431 61.111 0.00 0.00 40.39 2.29
93 94 2.846918 GACGTTGTCGCTGTCAGC 59.153 61.111 15.22 15.22 41.18 4.26
145 146 1.533625 TCGTCCTTTTTGCCATGGAG 58.466 50.000 18.40 2.70 0.00 3.86
172 173 6.041069 GTCGCCCTATCTATCTATAATTGGCT 59.959 42.308 0.00 0.00 33.08 4.75
270 273 2.246761 TAAAGGGCGGTGGGATCACG 62.247 60.000 0.00 0.00 44.50 4.35
271 274 0.463833 CTAAAGGGCGGTGGGATCAC 60.464 60.000 0.00 0.00 42.91 3.06
272 275 0.912487 ACTAAAGGGCGGTGGGATCA 60.912 55.000 0.00 0.00 0.00 2.92
273 276 0.463833 CACTAAAGGGCGGTGGGATC 60.464 60.000 0.00 0.00 0.00 3.36
352 355 7.672983 ATGTACAATCTACAGGTCAAACTTG 57.327 36.000 0.00 0.00 0.00 3.16
441 444 6.780198 AAATTATCTCTTGGCCCCAGTATA 57.220 37.500 0.00 0.00 0.00 1.47
465 468 9.720769 AGTGCTTAATTACTCTTTAGCTACAAA 57.279 29.630 0.00 0.00 0.00 2.83
493 496 4.968197 GGATAGCCATCGTCCGTC 57.032 61.111 0.00 0.00 31.33 4.79
561 564 5.368989 CCAGTTTATCCCATTCTCTGGTAC 58.631 45.833 0.00 0.00 44.30 3.34
563 566 3.203040 CCCAGTTTATCCCATTCTCTGGT 59.797 47.826 0.00 0.00 44.30 4.00
564 567 3.459598 TCCCAGTTTATCCCATTCTCTGG 59.540 47.826 0.00 0.00 45.51 3.86
565 568 4.778213 TCCCAGTTTATCCCATTCTCTG 57.222 45.455 0.00 0.00 0.00 3.35
566 569 5.015178 TGTTTCCCAGTTTATCCCATTCTCT 59.985 40.000 0.00 0.00 0.00 3.10
567 570 5.261216 TGTTTCCCAGTTTATCCCATTCTC 58.739 41.667 0.00 0.00 0.00 2.87
585 596 4.082026 CCCAATCAATTCTCCCACTGTTTC 60.082 45.833 0.00 0.00 0.00 2.78
613 624 0.897401 TTGATGCCGTGCCAAATCCA 60.897 50.000 0.00 0.00 0.00 3.41
615 626 1.134753 TGATTGATGCCGTGCCAAATC 59.865 47.619 0.00 0.00 0.00 2.17
629 640 6.272318 CCAAGCACAACTACTTTTTGATTGA 58.728 36.000 3.40 0.00 0.00 2.57
675 686 3.223226 CCAATCAATGGGCCTGGC 58.777 61.111 11.05 11.05 46.27 4.85
693 704 0.527565 CCGGAGAAAAGGTGCATTGG 59.472 55.000 0.00 0.00 0.00 3.16
699 710 0.107165 GGGGATCCGGAGAAAAGGTG 60.107 60.000 11.34 0.00 0.00 4.00
755 766 1.672030 TGACAATGTGAGCGCAGGG 60.672 57.895 11.47 0.00 0.00 4.45
811 823 1.153353 TGTTTTGGAATCGGCGAGTC 58.847 50.000 27.26 27.26 0.00 3.36
873 885 1.804151 GCAACAGAAGCAACCGTATGA 59.196 47.619 0.00 0.00 0.00 2.15
902 917 2.381911 TCCCCAGCTTACTACTTACCG 58.618 52.381 0.00 0.00 0.00 4.02
907 922 3.310193 GAGGAATCCCCAGCTTACTACT 58.690 50.000 0.00 0.00 37.41 2.57
908 923 2.369203 GGAGGAATCCCCAGCTTACTAC 59.631 54.545 0.00 0.00 37.41 2.73
909 924 2.250273 AGGAGGAATCCCCAGCTTACTA 59.750 50.000 9.05 0.00 37.41 1.82
947 962 5.032846 TGAATCCCTGTAAGATCCTCAGTT 58.967 41.667 8.05 0.00 34.07 3.16
976 991 6.003950 TCTTCCAATTTACCCTGAACAAGAG 58.996 40.000 0.00 0.00 0.00 2.85
1080 1095 1.443802 GAGCCCACTTCTTGTAGCAC 58.556 55.000 0.00 0.00 31.71 4.40
1128 1143 4.003648 GGGAAGAACTCATGTTACCTGTG 58.996 47.826 0.00 0.00 36.39 3.66
1139 1154 2.986019 TCATTTGGGAGGGAAGAACTCA 59.014 45.455 0.00 0.00 36.70 3.41
1165 1180 7.277405 AGAGAAAAAGGAAGAAGGTATCCAT 57.723 36.000 0.00 0.00 38.23 3.41
1172 1187 5.598417 TCCCAAAAGAGAAAAAGGAAGAAGG 59.402 40.000 0.00 0.00 0.00 3.46
1178 1193 7.675161 ATTTCTTCCCAAAAGAGAAAAAGGA 57.325 32.000 2.37 0.00 41.24 3.36
1179 1194 9.830975 TTTATTTCTTCCCAAAAGAGAAAAAGG 57.169 29.630 2.37 0.00 41.24 3.11
1331 1353 2.362375 TACACCGTCCCGTACCCC 60.362 66.667 0.00 0.00 0.00 4.95
1355 1377 2.687805 CGACTTCTCGTCCAGCCGA 61.688 63.158 0.00 0.00 39.56 5.54
2013 2051 4.727235 GTTTTCAAGGAACGATTCGTCT 57.273 40.909 12.80 3.29 39.99 4.18
2022 2060 1.835121 GTGTGCCGTTTTCAAGGAAC 58.165 50.000 0.00 0.00 36.58 3.62
2075 2113 0.037232 GTGGTGTGAGTACAGGAGGC 60.037 60.000 0.00 0.00 37.52 4.70
2111 2149 1.731709 TCTTGCACAACCGATCATTCG 59.268 47.619 0.00 0.00 45.08 3.34
2133 2171 5.552870 AATTATTCTACTCAGGGCATCGT 57.447 39.130 0.00 0.00 0.00 3.73
2134 2172 5.180117 CCAAATTATTCTACTCAGGGCATCG 59.820 44.000 0.00 0.00 0.00 3.84
2140 2178 7.630242 TTCAAGCCAAATTATTCTACTCAGG 57.370 36.000 0.00 0.00 0.00 3.86
2141 2179 9.118300 AGATTCAAGCCAAATTATTCTACTCAG 57.882 33.333 0.00 0.00 0.00 3.35
2162 2200 8.029522 TGCATATAACGACCATTCTAGAGATTC 58.970 37.037 0.00 0.00 0.00 2.52
2176 2214 5.238432 TCCATTGGTCATTGCATATAACGAC 59.762 40.000 1.86 0.00 0.00 4.34
2182 2220 7.608153 CAACATATCCATTGGTCATTGCATAT 58.392 34.615 1.86 0.00 0.00 1.78
2189 2227 4.795469 TCAGCAACATATCCATTGGTCAT 58.205 39.130 1.86 0.00 34.42 3.06
2218 2256 4.948004 GCTAGCTAGGTTGGTTGGTTATTT 59.052 41.667 22.10 0.00 0.00 1.40
2221 2259 3.178865 AGCTAGCTAGGTTGGTTGGTTA 58.821 45.455 17.69 0.00 0.00 2.85
2222 2260 1.985895 AGCTAGCTAGGTTGGTTGGTT 59.014 47.619 17.69 0.00 0.00 3.67
2224 2262 3.388024 TGATAGCTAGCTAGGTTGGTTGG 59.612 47.826 28.98 0.00 35.39 3.77
2226 2264 5.896073 ATTGATAGCTAGCTAGGTTGGTT 57.104 39.130 28.98 10.76 35.39 3.67
2227 2265 6.078664 AGTATTGATAGCTAGCTAGGTTGGT 58.921 40.000 28.98 16.09 35.39 3.67
2240 2278 9.134734 GAGTACAGATTGCTAAGTATTGATAGC 57.865 37.037 0.00 0.00 43.78 2.97
2244 2282 8.067751 ACAGAGTACAGATTGCTAAGTATTGA 57.932 34.615 0.00 0.00 0.00 2.57
2245 2283 9.457110 CTACAGAGTACAGATTGCTAAGTATTG 57.543 37.037 0.00 0.00 0.00 1.90
2247 2285 8.754991 ACTACAGAGTACAGATTGCTAAGTAT 57.245 34.615 0.00 0.00 32.65 2.12
2281 2399 1.542915 CACAGCCCATCAGTTTTCTGG 59.457 52.381 0.00 0.00 46.94 3.86
2348 2474 1.986378 CGTCCTCGTTGATCTTGACAC 59.014 52.381 0.00 0.00 0.00 3.67
2354 2482 2.015587 GTACTCCGTCCTCGTTGATCT 58.984 52.381 0.00 0.00 35.01 2.75
2368 2496 3.712091 ACTGCGCTAGTAATGTACTCC 57.288 47.619 9.73 0.00 40.14 3.85
2369 2497 5.165911 TGTACTGCGCTAGTAATGTACTC 57.834 43.478 17.41 7.52 43.24 2.59
2399 2540 7.870509 TTATCAGACCATACTACTGTTACGT 57.129 36.000 0.00 0.00 33.93 3.57
2400 2541 7.808381 CCATTATCAGACCATACTACTGTTACG 59.192 40.741 0.00 0.00 33.93 3.18
2401 2542 8.857098 TCCATTATCAGACCATACTACTGTTAC 58.143 37.037 0.00 0.00 33.93 2.50
2402 2543 8.857098 GTCCATTATCAGACCATACTACTGTTA 58.143 37.037 0.00 0.00 33.93 2.41
2403 2544 7.344612 TGTCCATTATCAGACCATACTACTGTT 59.655 37.037 0.00 0.00 33.93 3.16
2404 2545 6.839134 TGTCCATTATCAGACCATACTACTGT 59.161 38.462 0.00 0.00 33.93 3.55
2405 2546 7.290110 TGTCCATTATCAGACCATACTACTG 57.710 40.000 0.00 0.00 31.76 2.74
2406 2547 7.510685 ACATGTCCATTATCAGACCATACTACT 59.489 37.037 0.00 0.00 31.76 2.57
2407 2548 7.671302 ACATGTCCATTATCAGACCATACTAC 58.329 38.462 0.00 0.00 31.76 2.73
2408 2549 7.855784 ACATGTCCATTATCAGACCATACTA 57.144 36.000 0.00 0.00 31.76 1.82
2409 2550 6.753913 ACATGTCCATTATCAGACCATACT 57.246 37.500 0.00 0.00 31.76 2.12
2410 2551 6.874134 GGTACATGTCCATTATCAGACCATAC 59.126 42.308 0.00 0.00 31.76 2.39
2411 2552 6.013725 GGGTACATGTCCATTATCAGACCATA 60.014 42.308 0.00 0.00 31.76 2.74
2412 2553 5.221925 GGGTACATGTCCATTATCAGACCAT 60.222 44.000 0.00 0.00 31.76 3.55
2413 2554 4.102524 GGGTACATGTCCATTATCAGACCA 59.897 45.833 0.00 0.00 31.76 4.02
2440 2581 7.251281 TCGTCATCTTTACTTCACATCTACAG 58.749 38.462 0.00 0.00 0.00 2.74
2457 2598 4.261741 GCATGCCCAATTAATTCGTCATCT 60.262 41.667 6.36 0.00 0.00 2.90
2699 2840 0.179084 TGTACTATGCCAGCTTCGCC 60.179 55.000 0.00 0.00 0.00 5.54
2702 2843 1.139853 AGCCTGTACTATGCCAGCTTC 59.860 52.381 0.00 0.00 0.00 3.86
3030 3172 4.871513 ACATCTCGTGTATACATTGCGAT 58.128 39.130 14.98 11.01 39.91 4.58
3033 3175 5.557136 GCAAGACATCTCGTGTATACATTGC 60.557 44.000 9.18 13.04 42.36 3.56
3038 3182 3.482472 CACGCAAGACATCTCGTGTATAC 59.518 47.826 12.55 0.00 44.84 1.47
3061 3205 2.999331 TGGTAGGATTAGTTGGCTTGC 58.001 47.619 0.00 0.00 0.00 4.01
3166 3320 1.566018 GCCGACGCTTTAACTGCAGT 61.566 55.000 15.25 15.25 0.00 4.40
3168 3322 2.663478 CGCCGACGCTTTAACTGCA 61.663 57.895 0.00 0.00 0.00 4.41
3237 3393 7.497909 CAGTTTACCGATATTATGACCAAAGGT 59.502 37.037 0.00 0.00 39.44 3.50
3384 3540 1.735018 TGTGATAATGTTTCGGCCACG 59.265 47.619 2.24 0.00 42.74 4.94
3430 3587 0.249741 ACTTGGTGAACTTCGGGTCG 60.250 55.000 0.00 0.00 33.61 4.79
3476 3633 0.110823 GTGCCGTCGTCAATGTTGTC 60.111 55.000 0.00 0.00 0.00 3.18
3486 3643 2.127118 CGAGTAACGTGCCGTCGT 60.127 61.111 0.00 0.00 46.19 4.34
3497 3654 1.890894 GAGTGCTGAGGCCGAGTAA 59.109 57.895 0.00 0.00 37.74 2.24
3530 3687 2.683572 TCCTCTAAGCGGCAGCCA 60.684 61.111 13.30 0.00 46.67 4.75
3555 3712 1.200252 CTTCTTCGGCGACTCTCTTGA 59.800 52.381 10.16 0.00 0.00 3.02
3566 3723 2.541556 GGATACTGTGTCTTCTTCGGC 58.458 52.381 4.53 0.00 0.00 5.54
3623 3780 2.099141 TTGCCTACAGTGATGCAGAC 57.901 50.000 0.00 0.00 34.81 3.51
3626 3783 2.703416 CTCTTTGCCTACAGTGATGCA 58.297 47.619 0.00 0.00 0.00 3.96
3633 3790 2.344950 CACTGAGCTCTTTGCCTACAG 58.655 52.381 16.19 3.44 44.23 2.74
3661 3818 2.115291 GGCCTTCATCTTCGTGCCC 61.115 63.158 0.00 0.00 32.74 5.36


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

AutoCloner maintained by Alex Coulton.