Multiple sequence alignment - TraesCS7B01G166400

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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 TraesCS7B01G166400 chr7B 100.000 3329 0 0 1 3329 229824889 229828217 0.000000e+00 6148
1 TraesCS7B01G166400 chr7D 93.608 2472 107 31 1 2447 252543441 252545886 0.000000e+00 3642
2 TraesCS7B01G166400 chr7D 86.815 766 55 24 2579 3329 252545952 252546686 0.000000e+00 813
3 TraesCS7B01G166400 chr7A 87.987 2539 173 55 854 3329 267570777 267568308 0.000000e+00 2878
4 TraesCS7B01G166400 chr7A 86.241 407 27 9 432 813 267571183 267570781 6.640000e-112 414
5 TraesCS7B01G166400 chr7A 89.954 219 14 5 161 375 267571834 267571620 3.270000e-70 276
6 TraesCS7B01G166400 chr7A 86.503 163 14 3 3 163 267572020 267571864 4.420000e-39 172
7 TraesCS7B01G166400 chr1D 89.673 978 89 11 968 1940 168798731 168799701 0.000000e+00 1236
8 TraesCS7B01G166400 chr3A 86.599 694 77 13 1249 1935 327916402 327917086 0.000000e+00 752
9 TraesCS7B01G166400 chr3A 85.920 696 81 14 1252 1940 162275705 162275020 0.000000e+00 726
10 TraesCS7B01G166400 chr3A 85.694 699 83 14 1249 1940 367859246 367859934 0.000000e+00 721
11 TraesCS7B01G166400 chr6D 84.646 508 46 10 1438 1940 934129 933649 8.360000e-131 477
12 TraesCS7B01G166400 chr3B 77.447 235 27 13 163 377 814705898 814706126 2.100000e-22 117


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 TraesCS7B01G166400 chr7B 229824889 229828217 3328 False 6148.0 6148 100.00000 1 3329 1 chr7B.!!$F1 3328
1 TraesCS7B01G166400 chr7D 252543441 252546686 3245 False 2227.5 3642 90.21150 1 3329 2 chr7D.!!$F1 3328
2 TraesCS7B01G166400 chr7A 267568308 267572020 3712 True 935.0 2878 87.67125 3 3329 4 chr7A.!!$R1 3326
3 TraesCS7B01G166400 chr1D 168798731 168799701 970 False 1236.0 1236 89.67300 968 1940 1 chr1D.!!$F1 972
4 TraesCS7B01G166400 chr3A 327916402 327917086 684 False 752.0 752 86.59900 1249 1935 1 chr3A.!!$F1 686
5 TraesCS7B01G166400 chr3A 162275020 162275705 685 True 726.0 726 85.92000 1252 1940 1 chr3A.!!$R1 688
6 TraesCS7B01G166400 chr3A 367859246 367859934 688 False 721.0 721 85.69400 1249 1940 1 chr3A.!!$F2 691

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
814 1270 2.097110 TTGTATATGGTCGGCCCTCT 57.903 50.0 2.12 0.0 0.00 3.69 F
1301 1758 0.716591 ATCCCAGGGTCAGTCACCTA 59.283 55.0 5.01 0.0 45.95 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 2705 0.032316 TCATCTGCAGCCTCCTCTCT 60.032 55.0 9.47 0.0 0.0 3.10 R
2337 2813 0.103026 CGGATCCATCGCTTGTCTGA 59.897 55.0 13.41 0.0 0.0 3.27 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
313 351 5.980698 ATGAGCAGAACGAACATCATAAG 57.019 39.130 0.00 0.00 0.00 1.73
478 904 5.121768 CAGCACCAACATAAACTACAGTACC 59.878 44.000 0.00 0.00 0.00 3.34
730 1186 4.452733 GGGGAGGACGGACAAGCG 62.453 72.222 0.00 0.00 0.00 4.68
813 1269 3.514309 AGTATTGTATATGGTCGGCCCTC 59.486 47.826 2.12 0.00 0.00 4.30
814 1270 2.097110 TTGTATATGGTCGGCCCTCT 57.903 50.000 2.12 0.00 0.00 3.69
818 1274 4.164981 TGTATATGGTCGGCCCTCTTAAT 58.835 43.478 2.12 0.00 0.00 1.40
820 1276 5.781306 TGTATATGGTCGGCCCTCTTAATAA 59.219 40.000 2.12 0.00 0.00 1.40
821 1277 3.771577 ATGGTCGGCCCTCTTAATAAG 57.228 47.619 2.12 0.00 0.00 1.73
822 1278 2.754465 TGGTCGGCCCTCTTAATAAGA 58.246 47.619 2.12 2.44 35.87 2.10
823 1279 2.433239 TGGTCGGCCCTCTTAATAAGAC 59.567 50.000 2.12 0.00 33.12 3.01
824 1280 2.699321 GGTCGGCCCTCTTAATAAGACT 59.301 50.000 0.00 0.00 33.12 3.24
825 1281 3.893813 GGTCGGCCCTCTTAATAAGACTA 59.106 47.826 0.00 0.00 33.12 2.59
826 1282 4.261952 GGTCGGCCCTCTTAATAAGACTAC 60.262 50.000 0.00 0.00 33.12 2.73
827 1283 4.583907 GTCGGCCCTCTTAATAAGACTACT 59.416 45.833 0.00 0.00 33.12 2.57
828 1284 5.767168 GTCGGCCCTCTTAATAAGACTACTA 59.233 44.000 0.00 0.00 33.12 1.82
829 1285 6.264067 GTCGGCCCTCTTAATAAGACTACTAA 59.736 42.308 0.00 0.00 33.12 2.24
830 1286 7.008941 TCGGCCCTCTTAATAAGACTACTAAT 58.991 38.462 0.00 0.00 33.12 1.73
831 1287 8.166061 TCGGCCCTCTTAATAAGACTACTAATA 58.834 37.037 0.00 0.00 33.12 0.98
1296 1753 2.187946 CGCATCCCAGGGTCAGTC 59.812 66.667 5.01 0.00 0.00 3.51
1297 1754 2.659063 CGCATCCCAGGGTCAGTCA 61.659 63.158 5.01 0.00 0.00 3.41
1299 1756 1.604378 CATCCCAGGGTCAGTCACC 59.396 63.158 5.01 0.00 45.97 4.02
1300 1757 0.911525 CATCCCAGGGTCAGTCACCT 60.912 60.000 5.01 0.00 45.95 4.00
1301 1758 0.716591 ATCCCAGGGTCAGTCACCTA 59.283 55.000 5.01 0.00 45.95 3.08
1302 1759 0.716591 TCCCAGGGTCAGTCACCTAT 59.283 55.000 5.01 0.00 45.95 2.57
1303 1760 1.934480 TCCCAGGGTCAGTCACCTATA 59.066 52.381 5.01 0.00 45.95 1.31
1319 1778 5.773680 TCACCTATATACCTACCTGAAGCAC 59.226 44.000 0.00 0.00 0.00 4.40
1362 1827 4.362279 TGGTACCTCGCGATTATTAACAC 58.638 43.478 10.36 0.00 0.00 3.32
1363 1828 3.423206 GGTACCTCGCGATTATTAACACG 59.577 47.826 10.36 0.00 0.00 4.49
1476 1944 1.535444 TTCCTCAAGGCCACCGAGA 60.535 57.895 15.53 0.00 34.44 4.04
1569 2043 1.066908 CCATTGTGTGGCTTGTTTCGT 59.933 47.619 0.00 0.00 42.12 3.85
1576 2050 1.002792 GTGGCTTGTTTCGTCAGTTCC 60.003 52.381 0.00 0.00 0.00 3.62
1577 2051 1.134220 TGGCTTGTTTCGTCAGTTCCT 60.134 47.619 0.00 0.00 0.00 3.36
1578 2052 2.103432 TGGCTTGTTTCGTCAGTTCCTA 59.897 45.455 0.00 0.00 0.00 2.94
1579 2053 2.737252 GGCTTGTTTCGTCAGTTCCTAG 59.263 50.000 0.00 0.00 0.00 3.02
1580 2054 3.391049 GCTTGTTTCGTCAGTTCCTAGT 58.609 45.455 0.00 0.00 0.00 2.57
1582 2056 4.272748 GCTTGTTTCGTCAGTTCCTAGTTT 59.727 41.667 0.00 0.00 0.00 2.66
1583 2057 5.464389 GCTTGTTTCGTCAGTTCCTAGTTTA 59.536 40.000 0.00 0.00 0.00 2.01
1584 2058 6.018507 GCTTGTTTCGTCAGTTCCTAGTTTAA 60.019 38.462 0.00 0.00 0.00 1.52
1585 2059 7.473027 TTGTTTCGTCAGTTCCTAGTTTAAG 57.527 36.000 0.00 0.00 0.00 1.85
1588 2062 5.130292 TCGTCAGTTCCTAGTTTAAGGTG 57.870 43.478 0.00 0.00 37.91 4.00
1589 2063 4.828939 TCGTCAGTTCCTAGTTTAAGGTGA 59.171 41.667 0.00 0.00 37.91 4.02
1591 2065 6.014840 TCGTCAGTTCCTAGTTTAAGGTGAAT 60.015 38.462 0.00 0.00 37.91 2.57
1592 2066 6.649557 CGTCAGTTCCTAGTTTAAGGTGAATT 59.350 38.462 0.00 0.00 37.91 2.17
1594 2068 7.660208 GTCAGTTCCTAGTTTAAGGTGAATTGA 59.340 37.037 0.00 0.00 37.91 2.57
1655 2130 6.151648 CCAATTTGAAGAATGTGAAGGAGCTA 59.848 38.462 0.00 0.00 0.00 3.32
1758 2233 7.587037 TTTTTGTGACATCTTCTGGAGATTT 57.413 32.000 0.00 0.00 42.55 2.17
1842 2317 1.699634 AGGAAGTACTCAGCAAGGCAA 59.300 47.619 0.00 0.00 0.00 4.52
1947 2423 8.163408 TCTGGACCAATAATAATGTATTCCAGG 58.837 37.037 12.63 0.00 35.57 4.45
1954 2430 2.622064 AATGTATTCCAGGCTCGGAC 57.378 50.000 5.34 0.00 33.75 4.79
1955 2431 1.794714 ATGTATTCCAGGCTCGGACT 58.205 50.000 5.34 3.79 33.75 3.85
1971 2447 1.880027 GGACTCGCCAAATTTGACACT 59.120 47.619 19.86 0.00 36.34 3.55
1972 2448 2.350772 GGACTCGCCAAATTTGACACTG 60.351 50.000 19.86 3.48 36.34 3.66
1978 2454 5.651530 TCGCCAAATTTGACACTGTAAAAA 58.348 33.333 19.86 0.00 0.00 1.94
2077 2553 9.214957 TCTTTCGTGATGATTTTGTAATGTACT 57.785 29.630 0.00 0.00 0.00 2.73
2157 2633 0.951558 GTTTGGAAGACGTGGTGCAT 59.048 50.000 0.00 0.00 0.00 3.96
2169 2645 2.440409 GTGGTGCATGAAATCTCCACT 58.560 47.619 10.67 0.00 41.14 4.00
2229 2705 1.202806 CCCTTCAAGCTCAAGTGTCCA 60.203 52.381 0.00 0.00 0.00 4.02
2336 2812 0.036022 AAGCTGAACTGAGGCAGTCC 59.964 55.000 0.00 0.00 44.62 3.85
2337 2813 0.835543 AGCTGAACTGAGGCAGTCCT 60.836 55.000 0.00 0.00 44.62 3.85
2406 2895 6.030228 GCATAGCTGAATGTACCTTTGTTTC 58.970 40.000 0.00 0.00 0.00 2.78
2463 2952 5.992217 ACGAAATAGCAGAAACTGTTCTTCT 59.008 36.000 0.00 0.00 41.55 2.85
2469 2958 3.406764 CAGAAACTGTTCTTCTCCCCTG 58.593 50.000 0.00 0.00 41.55 4.45
2470 2959 2.155279 GAAACTGTTCTTCTCCCCTGC 58.845 52.381 0.00 0.00 0.00 4.85
2471 2960 0.402121 AACTGTTCTTCTCCCCTGCC 59.598 55.000 0.00 0.00 0.00 4.85
2472 2961 1.301293 CTGTTCTTCTCCCCTGCCC 59.699 63.158 0.00 0.00 0.00 5.36
2473 2962 1.151810 TGTTCTTCTCCCCTGCCCT 60.152 57.895 0.00 0.00 0.00 5.19
2474 2963 0.772124 TGTTCTTCTCCCCTGCCCTT 60.772 55.000 0.00 0.00 0.00 3.95
2475 2964 0.322906 GTTCTTCTCCCCTGCCCTTG 60.323 60.000 0.00 0.00 0.00 3.61
2478 2967 1.778383 TTCTCCCCTGCCCTTGGTT 60.778 57.895 0.00 0.00 0.00 3.67
2485 2974 2.043551 TGCCCTTGGTTGTGTGCA 60.044 55.556 0.00 0.00 0.00 4.57
2509 2998 0.867329 CTGCGCTTCGTGATCGATCA 60.867 55.000 23.99 23.99 45.65 2.92
2536 3025 3.003689 TGCTTTGCTGAAACTAGCTGTTC 59.996 43.478 0.00 0.00 44.01 3.18
2540 3029 3.133691 TGCTGAAACTAGCTGTTCACAG 58.866 45.455 19.12 19.12 44.01 3.66
2551 3040 4.261801 AGCTGTTCACAGTGTTTACTTGT 58.738 39.130 8.72 0.00 45.45 3.16
2554 3043 5.503520 GCTGTTCACAGTGTTTACTTGTACC 60.504 44.000 8.72 0.00 45.45 3.34
2555 3044 5.489249 TGTTCACAGTGTTTACTTGTACCA 58.511 37.500 0.00 0.00 34.07 3.25
2560 3049 4.879545 ACAGTGTTTACTTGTACCAACAGG 59.120 41.667 0.00 0.00 38.60 4.00
2563 3052 4.337274 GTGTTTACTTGTACCAACAGGCTT 59.663 41.667 0.00 0.00 36.19 4.35
2569 3058 1.074775 TACCAACAGGCTTGCCTGG 59.925 57.895 35.58 25.30 41.67 4.45
2576 3065 0.962356 CAGGCTTGCCTGGGTAGTTG 60.962 60.000 28.58 6.34 34.47 3.16
2579 3068 1.616994 GGCTTGCCTGGGTAGTTGATT 60.617 52.381 4.11 0.00 0.00 2.57
2630 3122 1.000486 AGGTTCTCTGGGCGCTCTA 60.000 57.895 9.62 0.00 0.00 2.43
2664 3156 4.572985 TTTGCCAGATTTGAGAACACTG 57.427 40.909 0.00 0.00 0.00 3.66
2672 3165 6.183360 CCAGATTTGAGAACACTGTCTGTTTT 60.183 38.462 0.00 0.00 43.60 2.43
2695 3188 1.066605 AGCAATTCTTCATGCCGCATC 59.933 47.619 1.86 0.00 43.57 3.91
2711 3204 1.471501 GCATCACTGACTGCATCGGTA 60.472 52.381 9.39 2.14 45.83 4.02
2722 3215 5.069119 TGACTGCATCGGTATCATAGAAAGT 59.931 40.000 0.00 0.00 0.00 2.66
2723 3216 6.264518 TGACTGCATCGGTATCATAGAAAGTA 59.735 38.462 0.00 0.00 0.00 2.24
2724 3217 7.039714 TGACTGCATCGGTATCATAGAAAGTAT 60.040 37.037 0.00 0.00 0.00 2.12
2739 3232 9.113838 CATAGAAAGTATAGAATGTGGCAAACT 57.886 33.333 0.00 0.00 0.00 2.66
2806 3309 1.064208 CGAGATAGCGGCGTATATGCT 59.936 52.381 16.31 6.89 42.58 3.79
2807 3310 2.722071 GAGATAGCGGCGTATATGCTC 58.278 52.381 16.31 11.68 40.06 4.26
2808 3311 1.064208 AGATAGCGGCGTATATGCTCG 59.936 52.381 16.31 17.29 40.06 5.03
2815 3318 2.615116 CGTATATGCTCGCTCGTCG 58.385 57.895 0.00 0.00 40.15 5.12
2819 3322 2.739523 ATATGCTCGCTCGTCGGCTG 62.740 60.000 0.00 0.00 39.05 4.85
2822 3325 3.506096 CTCGCTCGTCGGCTGGTA 61.506 66.667 0.00 0.00 39.05 3.25
2835 3338 1.035932 GCTGGTAGCCTGGTACTCGA 61.036 60.000 6.48 0.00 34.48 4.04
2845 3348 2.280552 GGTACTCGACCCAGCCACA 61.281 63.158 0.00 0.00 43.25 4.17
2906 3426 0.820871 GAGCTCCATCGTCTCCACTT 59.179 55.000 0.87 0.00 0.00 3.16
2936 3469 2.185350 CTCCACCTACCGCAGCAG 59.815 66.667 0.00 0.00 0.00 4.24
2941 3474 2.821366 CCTACCGCAGCAGCAAGG 60.821 66.667 0.82 0.73 42.27 3.61
2980 3516 2.029666 CGGGGAGGATGTCATCGC 59.970 66.667 6.74 3.50 38.61 4.58
3058 3594 2.754664 CTTCAAGGCAAGCTCCCCGT 62.755 60.000 0.00 0.00 0.00 5.28
3076 3618 3.782443 GCCCCCACCCTACTCACG 61.782 72.222 0.00 0.00 0.00 4.35
3100 3642 1.078759 ATCGCCTCTCGTTTTGCTCG 61.079 55.000 0.00 0.00 39.67 5.03
3102 3644 1.782181 GCCTCTCGTTTTGCTCGTC 59.218 57.895 0.00 0.00 0.00 4.20
3103 3645 0.667792 GCCTCTCGTTTTGCTCGTCT 60.668 55.000 0.00 0.00 0.00 4.18
3104 3646 1.784525 CCTCTCGTTTTGCTCGTCTT 58.215 50.000 0.00 0.00 0.00 3.01
3105 3647 1.721926 CCTCTCGTTTTGCTCGTCTTC 59.278 52.381 0.00 0.00 0.00 2.87
3106 3648 1.721926 CTCTCGTTTTGCTCGTCTTCC 59.278 52.381 0.00 0.00 0.00 3.46
3107 3649 1.067974 TCTCGTTTTGCTCGTCTTCCA 59.932 47.619 0.00 0.00 0.00 3.53
3108 3650 1.864711 CTCGTTTTGCTCGTCTTCCAA 59.135 47.619 0.00 0.00 0.00 3.53
3109 3651 1.864711 TCGTTTTGCTCGTCTTCCAAG 59.135 47.619 0.00 0.00 0.00 3.61
3110 3652 1.597663 CGTTTTGCTCGTCTTCCAAGT 59.402 47.619 0.00 0.00 0.00 3.16
3118 3660 3.861131 GCTCGTCTTCCAAGTAGCAGAAA 60.861 47.826 0.00 0.00 32.05 2.52
3119 3661 3.650139 TCGTCTTCCAAGTAGCAGAAAC 58.350 45.455 0.00 0.00 0.00 2.78
3127 3669 3.182967 CAAGTAGCAGAAACGCTAGGAG 58.817 50.000 0.00 0.00 44.92 3.69
3163 3714 2.556257 TGCGCTGCTAATTCGGATAAA 58.444 42.857 9.73 0.00 0.00 1.40
3168 3719 5.198274 CGCTGCTAATTCGGATAAAGAAAC 58.802 41.667 0.00 0.00 0.00 2.78
3170 3721 5.728351 TGCTAATTCGGATAAAGAAACCG 57.272 39.130 0.00 0.00 46.71 4.44
3254 3805 1.942657 CCCATAGCATCTGGTCGTTTG 59.057 52.381 0.00 0.00 31.44 2.93
3265 3816 1.135527 TGGTCGTTTGTATCGCTAGGG 59.864 52.381 0.00 0.00 0.00 3.53
3297 3848 3.243101 CCATTTGCTTCTGCTGCTATGAG 60.243 47.826 0.00 0.00 40.48 2.90
3308 3859 3.070018 GCTGCTATGAGTTGTTCACAGT 58.930 45.455 0.00 0.00 38.99 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
247 281 9.514093 TTAGGAATATATACAATATGGCTGGGA 57.486 33.333 0.00 0.00 0.00 4.37
313 351 1.130561 GACGGATTGGTGCTTAACTGC 59.869 52.381 0.00 0.00 0.00 4.40
341 383 5.758570 AAGTTTGCTCTCGTACGTAATTC 57.241 39.130 16.05 3.05 0.00 2.17
478 904 2.336945 GGACCCCCATAAAAGGTACG 57.663 55.000 0.00 0.00 32.81 3.67
548 978 2.762043 GCGCTCTCCTCTCCCCTT 60.762 66.667 0.00 0.00 0.00 3.95
730 1186 3.119495 ACAGAAATATTTTCGGCAGGTGC 60.119 43.478 1.43 0.00 41.14 5.01
731 1187 4.701956 ACAGAAATATTTTCGGCAGGTG 57.298 40.909 1.43 0.00 0.00 4.00
818 1274 9.719433 AACCCACCAGTTATATTAGTAGTCTTA 57.281 33.333 0.00 0.00 0.00 2.10
820 1276 7.014038 CGAACCCACCAGTTATATTAGTAGTCT 59.986 40.741 0.00 0.00 0.00 3.24
821 1277 7.144000 CGAACCCACCAGTTATATTAGTAGTC 58.856 42.308 0.00 0.00 0.00 2.59
822 1278 6.041296 CCGAACCCACCAGTTATATTAGTAGT 59.959 42.308 0.00 0.00 0.00 2.73
823 1279 6.453092 CCGAACCCACCAGTTATATTAGTAG 58.547 44.000 0.00 0.00 0.00 2.57
824 1280 5.221501 GCCGAACCCACCAGTTATATTAGTA 60.222 44.000 0.00 0.00 0.00 1.82
825 1281 4.443881 GCCGAACCCACCAGTTATATTAGT 60.444 45.833 0.00 0.00 0.00 2.24
826 1282 4.062991 GCCGAACCCACCAGTTATATTAG 58.937 47.826 0.00 0.00 0.00 1.73
827 1283 3.712733 AGCCGAACCCACCAGTTATATTA 59.287 43.478 0.00 0.00 0.00 0.98
828 1284 2.508300 AGCCGAACCCACCAGTTATATT 59.492 45.455 0.00 0.00 0.00 1.28
829 1285 2.124411 AGCCGAACCCACCAGTTATAT 58.876 47.619 0.00 0.00 0.00 0.86
830 1286 1.575419 AGCCGAACCCACCAGTTATA 58.425 50.000 0.00 0.00 0.00 0.98
831 1287 0.696501 AAGCCGAACCCACCAGTTAT 59.303 50.000 0.00 0.00 0.00 1.89
1172 1629 0.955919 CTCCTTGTTGCGGAACTCCC 60.956 60.000 20.82 0.00 32.79 4.30
1296 1753 5.335740 CGTGCTTCAGGTAGGTATATAGGTG 60.336 48.000 0.00 0.00 0.00 4.00
1297 1754 4.765856 CGTGCTTCAGGTAGGTATATAGGT 59.234 45.833 0.00 0.00 0.00 3.08
1299 1756 4.217767 TGCGTGCTTCAGGTAGGTATATAG 59.782 45.833 0.00 0.00 0.00 1.31
1300 1757 4.022589 GTGCGTGCTTCAGGTAGGTATATA 60.023 45.833 0.00 0.00 0.00 0.86
1301 1758 2.963101 TGCGTGCTTCAGGTAGGTATAT 59.037 45.455 0.00 0.00 0.00 0.86
1302 1759 2.100252 GTGCGTGCTTCAGGTAGGTATA 59.900 50.000 0.00 0.00 0.00 1.47
1303 1760 1.134788 GTGCGTGCTTCAGGTAGGTAT 60.135 52.381 0.00 0.00 0.00 2.73
1319 1778 0.234106 CAGCAAGTCAGACAAGTGCG 59.766 55.000 14.71 8.70 40.17 5.34
1362 1827 1.523501 CAATCACACGCGAAAATCCG 58.476 50.000 15.93 0.00 0.00 4.18
1363 1828 1.259316 GCAATCACACGCGAAAATCC 58.741 50.000 15.93 0.00 0.00 3.01
1569 2043 7.741785 TCAATTCACCTTAAACTAGGAACTGA 58.258 34.615 0.00 0.00 41.52 3.41
1580 2054 9.829507 ACAACATTCAATTCAATTCACCTTAAA 57.170 25.926 0.00 0.00 0.00 1.52
1583 2057 9.829507 TTAACAACATTCAATTCAATTCACCTT 57.170 25.926 0.00 0.00 0.00 3.50
1591 2065 8.954950 ACACCAATTAACAACATTCAATTCAA 57.045 26.923 0.00 0.00 0.00 2.69
1592 2066 8.200120 TGACACCAATTAACAACATTCAATTCA 58.800 29.630 0.00 0.00 0.00 2.57
1594 2068 7.168972 CGTGACACCAATTAACAACATTCAATT 59.831 33.333 0.00 0.00 0.00 2.32
1655 2130 2.081462 CCGCGACCCTTCTTGTAAATT 58.919 47.619 8.23 0.00 0.00 1.82
1737 2212 6.013379 ACCTAAATCTCCAGAAGATGTCACAA 60.013 38.462 0.00 0.00 44.26 3.33
1758 2233 3.904800 TGAATCGAATGCCTGAACCTA 57.095 42.857 0.00 0.00 0.00 3.08
1947 2423 0.179189 CAAATTTGGCGAGTCCGAGC 60.179 55.000 10.49 0.00 38.22 5.03
1954 2430 4.481930 TTACAGTGTCAAATTTGGCGAG 57.518 40.909 17.44 11.83 35.00 5.03
1955 2431 4.902443 TTTACAGTGTCAAATTTGGCGA 57.098 36.364 17.44 4.75 35.00 5.54
2054 2530 8.771920 AGAGTACATTACAAAATCATCACGAA 57.228 30.769 0.00 0.00 0.00 3.85
2077 2553 7.490079 ACAAAGCACGTACGATGATTATAAAGA 59.510 33.333 24.41 0.00 0.00 2.52
2157 2633 0.036388 GCCCGACAGTGGAGATTTCA 60.036 55.000 0.00 0.00 0.00 2.69
2169 2645 4.680237 CTGAAGTGCGGCCCGACA 62.680 66.667 7.68 0.69 0.00 4.35
2229 2705 0.032316 TCATCTGCAGCCTCCTCTCT 60.032 55.000 9.47 0.00 0.00 3.10
2336 2812 1.863267 GGATCCATCGCTTGTCTGAG 58.137 55.000 6.95 0.00 0.00 3.35
2337 2813 0.103026 CGGATCCATCGCTTGTCTGA 59.897 55.000 13.41 0.00 0.00 3.27
2340 2816 2.218953 TAACGGATCCATCGCTTGTC 57.781 50.000 13.41 0.00 0.00 3.18
2406 2895 4.016706 ACTCGGGCAGGGTTTCCG 62.017 66.667 0.00 0.00 44.59 4.30
2435 2924 5.786401 ACAGTTTCTGCTATTTCGTGATC 57.214 39.130 0.00 0.00 34.37 2.92
2463 2952 2.780924 ACAACCAAGGGCAGGGGA 60.781 61.111 0.00 0.00 0.00 4.81
2469 2958 2.417097 GTGCACACAACCAAGGGC 59.583 61.111 13.17 0.00 0.00 5.19
2470 2959 2.721231 CGTGCACACAACCAAGGG 59.279 61.111 18.64 0.00 0.00 3.95
2471 2960 2.026014 GCGTGCACACAACCAAGG 59.974 61.111 18.64 0.00 0.00 3.61
2472 2961 1.009675 GAGCGTGCACACAACCAAG 60.010 57.895 18.64 0.00 0.00 3.61
2473 2962 1.451207 AGAGCGTGCACACAACCAA 60.451 52.632 18.64 0.00 0.00 3.67
2474 2963 2.179547 CAGAGCGTGCACACAACCA 61.180 57.895 18.64 0.00 0.00 3.67
2475 2964 2.633657 CAGAGCGTGCACACAACC 59.366 61.111 18.64 0.77 0.00 3.77
2509 2998 1.103398 AGTTTCAGCAAAGCACGGCT 61.103 50.000 0.00 0.00 42.56 5.52
2560 3049 1.745653 GAATCAACTACCCAGGCAAGC 59.254 52.381 0.00 0.00 0.00 4.01
2563 3052 0.981183 ACGAATCAACTACCCAGGCA 59.019 50.000 0.00 0.00 0.00 4.75
2569 3058 3.000727 CCAACCTCACGAATCAACTACC 58.999 50.000 0.00 0.00 0.00 3.18
2576 3065 5.334414 GCAATATCATCCAACCTCACGAATC 60.334 44.000 0.00 0.00 0.00 2.52
2579 3068 3.118445 TGCAATATCATCCAACCTCACGA 60.118 43.478 0.00 0.00 0.00 4.35
2630 3122 9.189156 TCAAATCTGGCAAAATAGCTAAAGTAT 57.811 29.630 0.00 0.00 34.17 2.12
2672 3165 1.401552 GCGGCATGAAGAATTGCTGTA 59.598 47.619 0.00 0.00 45.12 2.74
2695 3188 2.584492 TGATACCGATGCAGTCAGTG 57.416 50.000 0.00 0.00 0.00 3.66
2711 3204 9.851686 TTTGCCACATTCTATACTTTCTATGAT 57.148 29.630 0.00 0.00 0.00 2.45
2722 3215 3.947196 CCTGCAGTTTGCCACATTCTATA 59.053 43.478 13.81 0.00 44.23 1.31
2723 3216 2.756760 CCTGCAGTTTGCCACATTCTAT 59.243 45.455 13.81 0.00 44.23 1.98
2724 3217 2.161855 CCTGCAGTTTGCCACATTCTA 58.838 47.619 13.81 0.00 44.23 2.10
2742 3235 4.101448 GGACACGGATGCAGGCCT 62.101 66.667 0.00 0.00 0.00 5.19
2743 3236 4.408821 TGGACACGGATGCAGGCC 62.409 66.667 0.00 0.00 0.00 5.19
2806 3309 3.506096 CTACCAGCCGACGAGCGA 61.506 66.667 0.00 0.00 44.57 4.93
2906 3426 2.449518 TGGAGGTGGGCTGTGGAA 60.450 61.111 0.00 0.00 0.00 3.53
2966 3502 2.663188 GCGGCGATGACATCCTCC 60.663 66.667 12.98 9.97 0.00 4.30
2988 3524 1.392710 CCAGCCTCTCGAATACCGGT 61.393 60.000 13.98 13.98 39.14 5.28
2994 3530 3.854669 CCGGCCAGCCTCTCGAAT 61.855 66.667 2.24 0.00 0.00 3.34
3058 3594 2.609610 GTGAGTAGGGTGGGGGCA 60.610 66.667 0.00 0.00 0.00 5.36
3070 3612 1.153745 GAGGCGATTCTGCGTGAGT 60.154 57.895 0.00 0.00 35.06 3.41
3076 3618 1.079503 AAAACGAGAGGCGATTCTGC 58.920 50.000 0.00 0.00 44.57 4.26
3100 3642 2.157863 GCGTTTCTGCTACTTGGAAGAC 59.842 50.000 0.00 0.00 0.00 3.01
3102 3644 2.417719 AGCGTTTCTGCTACTTGGAAG 58.582 47.619 0.00 0.00 45.14 3.46
3103 3645 2.543777 AGCGTTTCTGCTACTTGGAA 57.456 45.000 0.00 0.00 45.14 3.53
3104 3646 2.094182 CCTAGCGTTTCTGCTACTTGGA 60.094 50.000 0.00 0.00 45.14 3.53
3105 3647 2.094182 TCCTAGCGTTTCTGCTACTTGG 60.094 50.000 0.00 0.00 45.14 3.61
3106 3648 3.182967 CTCCTAGCGTTTCTGCTACTTG 58.817 50.000 0.00 0.00 45.14 3.16
3107 3649 2.826725 ACTCCTAGCGTTTCTGCTACTT 59.173 45.455 0.00 0.00 45.14 2.24
3108 3650 2.448453 ACTCCTAGCGTTTCTGCTACT 58.552 47.619 0.00 0.00 45.14 2.57
3109 3651 2.943449 ACTCCTAGCGTTTCTGCTAC 57.057 50.000 0.00 0.00 45.14 3.58
3110 3652 3.349927 TGTACTCCTAGCGTTTCTGCTA 58.650 45.455 0.00 0.00 45.14 3.49
3118 3660 3.451178 ACCAATTCATGTACTCCTAGCGT 59.549 43.478 0.00 0.00 0.00 5.07
3119 3661 4.051922 GACCAATTCATGTACTCCTAGCG 58.948 47.826 0.00 0.00 0.00 4.26
3127 3669 2.420022 AGCGCAAGACCAATTCATGTAC 59.580 45.455 11.47 0.00 43.02 2.90
3163 3714 0.743345 GAACCCTATGCGCGGTTTCT 60.743 55.000 16.94 0.00 42.48 2.52
3168 3719 2.896801 GCATGAACCCTATGCGCGG 61.897 63.158 8.83 0.00 41.16 6.46
3297 3848 3.617263 AGACAAACTCGACTGTGAACAAC 59.383 43.478 0.00 0.00 0.00 3.32
3308 3859 1.301716 GCCTGCCAGACAAACTCGA 60.302 57.895 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.