Multiple sequence alignment - TraesCS7A01G163800

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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 TraesCS7A01G163800 chr7A 100.000 4338 0 0 1 4338 120462808 120467145 0.000000e+00 8011.0
1 TraesCS7A01G163800 chr7A 84.189 721 74 19 806 1510 120217636 120218332 0.000000e+00 664.0
2 TraesCS7A01G163800 chr7A 85.843 664 41 26 3712 4338 446325928 446326575 0.000000e+00 656.0
3 TraesCS7A01G163800 chr7A 80.672 595 84 18 2824 3404 120218618 120219195 2.400000e-117 433.0
4 TraesCS7A01G163800 chr7D 91.258 2082 130 21 1340 3403 115823505 115825552 0.000000e+00 2789.0
5 TraesCS7A01G163800 chr7D 90.562 1335 103 14 2079 3404 116090776 116092096 0.000000e+00 1746.0
6 TraesCS7A01G163800 chr7D 89.841 1132 70 28 667 1764 116432822 116433942 0.000000e+00 1411.0
7 TraesCS7A01G163800 chr7D 92.065 857 57 6 1 852 115821235 115822085 0.000000e+00 1195.0
8 TraesCS7A01G163800 chr7D 88.354 893 65 15 2826 3703 116435706 116436574 0.000000e+00 1037.0
9 TraesCS7A01G163800 chr7D 94.537 659 24 4 3688 4338 116436588 116437242 0.000000e+00 1007.0
10 TraesCS7A01G163800 chr7D 95.104 531 25 1 844 1374 115822976 115823505 0.000000e+00 835.0
11 TraesCS7A01G163800 chr7D 91.327 565 47 2 1 564 116050851 116051414 0.000000e+00 771.0
12 TraesCS7A01G163800 chr7D 83.990 787 94 16 1836 2611 116434100 116434865 0.000000e+00 726.0
13 TraesCS7A01G163800 chr7D 92.444 450 33 1 754 1203 116052092 116052540 3.660000e-180 641.0
14 TraesCS7A01G163800 chr7D 86.946 406 27 13 3712 4092 393579472 393579876 2.400000e-117 433.0
15 TraesCS7A01G163800 chr7D 88.922 334 34 2 234 564 116432272 116432605 4.040000e-110 409.0
16 TraesCS7A01G163800 chr7D 90.295 237 20 2 1 237 116429481 116429714 1.520000e-79 307.0
17 TraesCS7A01G163800 chr7D 84.642 293 23 5 1534 1804 116063345 116063637 5.530000e-69 272.0
18 TraesCS7A01G163800 chr7D 87.831 189 16 4 4126 4308 393579874 393580061 9.450000e-52 215.0
19 TraesCS7A01G163800 chr7D 98.230 113 2 0 1836 1948 116063841 116063953 9.520000e-47 198.0
20 TraesCS7A01G163800 chr7D 91.935 62 4 1 668 728 116052026 116052087 7.730000e-13 86.1
21 TraesCS7A01G163800 chr7D 100.000 35 0 0 1802 1836 116063786 116063820 1.010000e-06 65.8
22 TraesCS7A01G163800 chr7B 90.548 1534 107 19 2826 4338 75026576 75028092 0.000000e+00 1995.0
23 TraesCS7A01G163800 chr7B 92.147 815 45 8 3541 4338 75034788 75035600 0.000000e+00 1133.0
24 TraesCS7A01G163800 chr7B 93.537 557 21 6 684 1240 75023943 75024484 0.000000e+00 815.0
25 TraesCS7A01G163800 chr7B 84.032 739 91 14 1902 2632 75024820 75025539 0.000000e+00 686.0
26 TraesCS7A01G163800 chr7B 88.163 566 37 5 1 564 75023084 75023621 0.000000e+00 647.0
27 TraesCS7A01G163800 chr7B 85.829 621 42 21 3741 4338 393318560 393319157 6.160000e-173 617.0
28 TraesCS7A01G163800 chr7B 87.640 89 11 0 2590 2678 75025851 75025939 2.130000e-18 104.0


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 TraesCS7A01G163800 chr7A 120462808 120467145 4337 False 8011.000000 8011 100.000000 1 4338 1 chr7A.!!$F1 4337
1 TraesCS7A01G163800 chr7A 446325928 446326575 647 False 656.000000 656 85.843000 3712 4338 1 chr7A.!!$F2 626
2 TraesCS7A01G163800 chr7A 120217636 120219195 1559 False 548.500000 664 82.430500 806 3404 2 chr7A.!!$F3 2598
3 TraesCS7A01G163800 chr7D 116090776 116092096 1320 False 1746.000000 1746 90.562000 2079 3404 1 chr7D.!!$F1 1325
4 TraesCS7A01G163800 chr7D 115821235 115825552 4317 False 1606.333333 2789 92.809000 1 3403 3 chr7D.!!$F2 3402
5 TraesCS7A01G163800 chr7D 116429481 116437242 7761 False 816.166667 1411 89.323167 1 4338 6 chr7D.!!$F5 4337
6 TraesCS7A01G163800 chr7D 116050851 116052540 1689 False 499.366667 771 91.902000 1 1203 3 chr7D.!!$F3 1202
7 TraesCS7A01G163800 chr7D 393579472 393580061 589 False 324.000000 433 87.388500 3712 4308 2 chr7D.!!$F6 596
8 TraesCS7A01G163800 chr7B 75034788 75035600 812 False 1133.000000 1133 92.147000 3541 4338 1 chr7B.!!$F1 797
9 TraesCS7A01G163800 chr7B 75023084 75028092 5008 False 849.400000 1995 88.784000 1 4338 5 chr7B.!!$F3 4337
10 TraesCS7A01G163800 chr7B 393318560 393319157 597 False 617.000000 617 85.829000 3741 4338 1 chr7B.!!$F2 597

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 2911 0.854218 TGGTTTTTAGTGGAGGGCCA 59.146 50.0 6.18 0.0 43.47 5.36 F
1465 5699 0.179056 CTGTGTCAGGGTGGTCGTTT 60.179 55.0 0.00 0.0 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 5914 0.107456 AGGCGATGGATGATCACACC 59.893 55.0 12.27 12.27 0.00 4.16 R
3337 8604 0.035739 AATACCGACACGCCCTGTTT 59.964 50.0 0.00 0.00 31.03 2.83 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
106 107 7.031372 GTGCATCAAGACATAAACACATTCAT 58.969 34.615 0.00 0.00 0.00 2.57
108 109 8.400186 TGCATCAAGACATAAACACATTCATAG 58.600 33.333 0.00 0.00 0.00 2.23
211 212 8.667076 TGTCTCTCAAACATATTACCATCATG 57.333 34.615 0.00 0.00 0.00 3.07
212 213 7.716560 TGTCTCTCAAACATATTACCATCATGG 59.283 37.037 0.54 0.54 45.02 3.66
326 2888 2.096069 GCACTCACACGACGTCTACTTA 60.096 50.000 14.70 0.00 0.00 2.24
345 2907 6.954487 ACTTAGTTTGGTTTTTAGTGGAGG 57.046 37.500 0.00 0.00 0.00 4.30
348 2910 2.003937 TTGGTTTTTAGTGGAGGGCC 57.996 50.000 0.00 0.00 0.00 5.80
349 2911 0.854218 TGGTTTTTAGTGGAGGGCCA 59.146 50.000 6.18 0.00 43.47 5.36
356 2918 0.984230 TAGTGGAGGGCCAGTTCAAG 59.016 55.000 6.18 0.00 45.73 3.02
403 2965 5.006746 ACAATTGACTCTCAAACACGTTCTC 59.993 40.000 13.59 0.00 40.12 2.87
404 2966 2.727777 TGACTCTCAAACACGTTCTCG 58.272 47.619 0.00 0.00 43.34 4.04
405 2967 1.452399 GACTCTCAAACACGTTCTCGC 59.548 52.381 0.00 0.00 41.18 5.03
424 2987 3.429543 TCGCGTTACAACCATAACTTCAC 59.570 43.478 5.77 0.00 33.61 3.18
508 3074 4.119862 GCATAACGACACATACCTCACAT 58.880 43.478 0.00 0.00 0.00 3.21
553 3119 4.640771 AGTGGAGTACATGTTTGACCAT 57.359 40.909 2.30 0.00 0.00 3.55
566 3132 8.234546 ACATGTTTGACCATCTTCGTTAAATAC 58.765 33.333 0.00 0.00 0.00 1.89
567 3133 7.731882 TGTTTGACCATCTTCGTTAAATACA 57.268 32.000 0.00 0.00 0.00 2.29
593 3211 4.095610 GCAATACCCGACTTTCAAATTCG 58.904 43.478 2.99 2.99 0.00 3.34
675 3803 4.405116 TTTATGGGCAATGGATTTGAGC 57.595 40.909 0.00 0.00 37.53 4.26
962 5108 1.304952 CCTCTCCTCTCCTGACCGT 59.695 63.158 0.00 0.00 0.00 4.83
1079 5240 3.393970 CTCCTCTTCGGCTGGGCA 61.394 66.667 0.00 0.00 0.00 5.36
1338 5499 5.229260 GGATCGTTTGGAAATTATTGCGTTC 59.771 40.000 0.00 0.00 0.00 3.95
1435 5630 5.691754 CAGTAATGCAGGTGGTTTCTTTTTC 59.308 40.000 0.00 0.00 0.00 2.29
1465 5699 0.179056 CTGTGTCAGGGTGGTCGTTT 60.179 55.000 0.00 0.00 0.00 3.60
1524 5758 4.590553 TGAGGCTGTGGGGTGGGA 62.591 66.667 0.00 0.00 0.00 4.37
1525 5759 3.017581 GAGGCTGTGGGGTGGGAT 61.018 66.667 0.00 0.00 0.00 3.85
1526 5760 1.692749 GAGGCTGTGGGGTGGGATA 60.693 63.158 0.00 0.00 0.00 2.59
1527 5761 1.006092 AGGCTGTGGGGTGGGATAT 59.994 57.895 0.00 0.00 0.00 1.63
1528 5762 1.151450 GGCTGTGGGGTGGGATATG 59.849 63.158 0.00 0.00 0.00 1.78
1529 5763 1.151450 GCTGTGGGGTGGGATATGG 59.849 63.158 0.00 0.00 0.00 2.74
1530 5764 1.151450 CTGTGGGGTGGGATATGGC 59.849 63.158 0.00 0.00 0.00 4.40
1531 5765 2.357593 CTGTGGGGTGGGATATGGCC 62.358 65.000 0.00 0.00 0.00 5.36
1549 5797 5.654901 TGGCCATATGGGTAAAATACTCA 57.345 39.130 23.30 2.21 44.51 3.41
1561 5809 6.460123 GGGTAAAATACTCAGCATGTGGATTG 60.460 42.308 0.00 0.00 41.92 2.67
1562 5810 6.318648 GGTAAAATACTCAGCATGTGGATTGA 59.681 38.462 0.00 0.00 41.92 2.57
1563 5811 5.824904 AAATACTCAGCATGTGGATTGAC 57.175 39.130 0.00 0.00 41.92 3.18
1565 5813 0.376152 CTCAGCATGTGGATTGACGC 59.624 55.000 0.00 0.00 37.40 5.19
1655 5927 2.511373 GCGCGGTGTGATCATCCA 60.511 61.111 8.83 1.92 0.00 3.41
1660 5932 1.224069 CGGTGTGATCATCCATCGCC 61.224 60.000 16.44 10.54 40.84 5.54
1724 6013 9.392021 GTTCTATTATTGGTAGTTAGTACTCGC 57.608 37.037 0.00 0.00 35.78 5.03
1744 6033 2.159198 GCATAATGGTGCCAAACAGAGG 60.159 50.000 0.00 0.00 39.18 3.69
1749 6038 1.503542 GTGCCAAACAGAGGATGCG 59.496 57.895 0.00 0.00 0.00 4.73
1842 6196 1.269936 GCCAGCTGTTTCACATGCTTT 60.270 47.619 13.81 0.00 32.84 3.51
1847 6201 4.913924 CAGCTGTTTCACATGCTTTTAGTC 59.086 41.667 5.25 0.00 32.84 2.59
1848 6202 4.580167 AGCTGTTTCACATGCTTTTAGTCA 59.420 37.500 0.00 0.00 31.73 3.41
1874 6249 2.490991 AGTGCTCCGGTTGTTAGTTTC 58.509 47.619 0.00 0.00 0.00 2.78
2025 6405 4.825085 TGGTTGTGGTTTCCTAAATCTGAC 59.175 41.667 0.00 0.00 0.00 3.51
2208 6594 8.831715 ACATAAACATGAAATCTTTCCAAACC 57.168 30.769 0.00 0.00 36.36 3.27
2325 6715 5.531287 TGATCGTACTAGCTAGAGCAATTCA 59.469 40.000 27.45 17.26 45.16 2.57
2326 6716 5.425577 TCGTACTAGCTAGAGCAATTCAG 57.574 43.478 27.45 0.00 45.16 3.02
2375 6765 8.579850 TGAAGCTATTTGTTCATGAACCTTAT 57.420 30.769 30.66 22.62 40.46 1.73
2761 7729 7.231467 TCTTTTTCTTTAGCTGGTGGATAACT 58.769 34.615 0.00 0.00 0.00 2.24
2768 7736 2.509548 AGCTGGTGGATAACTATGGCAA 59.490 45.455 0.00 0.00 0.00 4.52
2813 7783 4.397420 TCCAGCCAATAATGCATTATCGT 58.603 39.130 27.77 13.85 32.08 3.73
2815 7785 4.456911 CCAGCCAATAATGCATTATCGTCT 59.543 41.667 27.77 20.81 32.08 4.18
2818 7788 5.764686 AGCCAATAATGCATTATCGTCTTCA 59.235 36.000 27.77 3.92 32.08 3.02
2819 7789 5.853282 GCCAATAATGCATTATCGTCTTCAC 59.147 40.000 27.77 11.20 32.08 3.18
2921 8173 1.000938 CCAGTTCTTTGGCAAGTGCTC 60.001 52.381 0.00 0.00 41.70 4.26
3004 8256 1.743252 GAAGCGCAAGGGTCCTCTG 60.743 63.158 11.47 0.00 38.28 3.35
3054 8312 3.027419 GCAAAGAGCTGAACCCTGT 57.973 52.632 0.00 0.00 41.15 4.00
3056 8314 1.000938 GCAAAGAGCTGAACCCTGTTG 60.001 52.381 0.00 0.00 41.15 3.33
3057 8315 1.000938 CAAAGAGCTGAACCCTGTTGC 60.001 52.381 0.00 0.00 0.00 4.17
3133 8391 2.977914 GCTACAAGCAGTTCTCCATCA 58.022 47.619 0.00 0.00 41.89 3.07
3247 8513 1.110442 CACCTGTTGGCCTTCAAACA 58.890 50.000 3.32 5.13 37.08 2.83
3249 8515 0.030638 CCTGTTGGCCTTCAAACACG 59.969 55.000 3.32 0.00 37.08 4.49
3251 8517 0.736053 TGTTGGCCTTCAAACACGAC 59.264 50.000 3.32 0.00 37.08 4.34
3253 8519 1.440938 TTGGCCTTCAAACACGACCG 61.441 55.000 3.32 0.00 31.46 4.79
3262 8529 1.721389 CAAACACGACCGATCTCAGTG 59.279 52.381 0.00 0.00 38.63 3.66
3268 8535 1.732732 CGACCGATCTCAGTGTCAACC 60.733 57.143 0.00 0.00 0.00 3.77
3270 8537 1.078759 CCGATCTCAGTGTCAACCGC 61.079 60.000 0.00 0.00 0.00 5.68
3337 8604 3.192633 GGGAAAAGCGCAGGAAGAATTAA 59.807 43.478 11.47 0.00 0.00 1.40
3393 8661 3.411446 CTGGTGTCCATTTTAGACTGCA 58.589 45.455 0.00 0.00 35.21 4.41
3411 8679 3.365472 TGCAGAATCTAGTGGCTAGTCA 58.635 45.455 0.00 0.00 35.72 3.41
3445 8716 7.803189 CCATATTCGGTACAATGCTTTGATTAC 59.197 37.037 18.35 10.89 36.64 1.89
3446 8717 6.751514 ATTCGGTACAATGCTTTGATTACA 57.248 33.333 18.35 0.00 36.64 2.41
3447 8718 6.561737 TTCGGTACAATGCTTTGATTACAA 57.438 33.333 18.35 3.69 36.64 2.41
3448 8719 6.751514 TCGGTACAATGCTTTGATTACAAT 57.248 33.333 18.35 0.00 36.64 2.71
3449 8720 6.550843 TCGGTACAATGCTTTGATTACAATG 58.449 36.000 18.35 6.25 36.64 2.82
3450 8721 6.150307 TCGGTACAATGCTTTGATTACAATGT 59.850 34.615 18.35 0.00 36.64 2.71
3451 8722 6.806249 CGGTACAATGCTTTGATTACAATGTT 59.194 34.615 18.35 0.00 36.64 2.71
3452 8723 7.008266 CGGTACAATGCTTTGATTACAATGTTC 59.992 37.037 18.35 0.00 36.64 3.18
3453 8724 7.812191 GGTACAATGCTTTGATTACAATGTTCA 59.188 33.333 18.35 0.00 36.64 3.18
3454 8725 7.878477 ACAATGCTTTGATTACAATGTTCAG 57.122 32.000 18.35 0.00 36.64 3.02
3455 8726 7.436118 ACAATGCTTTGATTACAATGTTCAGT 58.564 30.769 18.35 0.00 36.64 3.41
3456 8727 7.596248 ACAATGCTTTGATTACAATGTTCAGTC 59.404 33.333 18.35 0.00 36.64 3.51
3487 8758 4.941873 GTGGTTTTGTATAGTGCTAGCCTT 59.058 41.667 13.29 2.52 0.00 4.35
3560 8833 7.788026 TGAGAAAGGGACGCTTTATCTTATAA 58.212 34.615 28.76 13.78 34.34 0.98
3577 8850 5.939883 TCTTATAAGCCATATGCGCTTTGAT 59.060 36.000 26.14 19.54 44.03 2.57
3580 8853 2.689471 AAGCCATATGCGCTTTGATCAA 59.311 40.909 19.61 3.38 44.03 2.57
3581 8854 2.388121 GCCATATGCGCTTTGATCAAC 58.612 47.619 7.89 0.00 0.00 3.18
3592 8872 5.164061 GCGCTTTGATCAACGATTTTTCATT 60.164 36.000 19.27 0.00 0.00 2.57
3593 8873 6.452735 CGCTTTGATCAACGATTTTTCATTC 58.547 36.000 15.59 0.00 0.00 2.67
3613 8893 3.958704 TCGTTGTGCATTTACCTGTTTG 58.041 40.909 0.00 0.00 0.00 2.93
3630 8910 3.885901 TGTTTGGTTTCATTCATGGACGA 59.114 39.130 0.00 0.00 0.00 4.20
3672 8956 6.128553 TGTTTTGTTTTGCGCAGTTTGATTTA 60.129 30.769 11.31 0.00 0.00 1.40
3673 8957 6.595772 TTTGTTTTGCGCAGTTTGATTTAT 57.404 29.167 11.31 0.00 0.00 1.40
3674 8958 6.595772 TTGTTTTGCGCAGTTTGATTTATT 57.404 29.167 11.31 0.00 0.00 1.40
3675 8959 6.595772 TGTTTTGCGCAGTTTGATTTATTT 57.404 29.167 11.31 0.00 0.00 1.40
3676 8960 7.700322 TGTTTTGCGCAGTTTGATTTATTTA 57.300 28.000 11.31 0.00 0.00 1.40
3732 9046 3.507622 GGATGACCAAAGACCAAAGGAAG 59.492 47.826 0.00 0.00 35.97 3.46
3743 9062 2.509964 ACCAAAGGAAGTCAGGTTCACT 59.490 45.455 0.00 0.00 0.00 3.41
3891 9216 4.503296 GCAAGGTTAGGTTCTTGAGACAGA 60.503 45.833 7.18 0.00 41.94 3.41
3892 9217 5.799213 CAAGGTTAGGTTCTTGAGACAGAT 58.201 41.667 0.00 0.00 41.94 2.90
3893 9218 6.234177 CAAGGTTAGGTTCTTGAGACAGATT 58.766 40.000 0.00 0.00 41.94 2.40
4107 9458 6.677781 AAACTGAACTCGTGAAGAAATGAA 57.322 33.333 0.00 0.00 0.00 2.57
4129 9480 0.621571 TCTGGGGACATGGGAGAAGG 60.622 60.000 0.00 0.00 41.51 3.46
4149 9500 3.974642 AGGGTTCAGTTTCCTACAACTCT 59.025 43.478 0.00 0.00 34.60 3.24
4165 9516 5.611374 ACAACTCTTTACTTGCAGAGCTAA 58.389 37.500 0.00 0.00 40.35 3.09
4171 9528 7.547370 ACTCTTTACTTGCAGAGCTAACTAATG 59.453 37.037 0.00 0.00 40.35 1.90
4189 9552 7.592885 ACTAATGAAATCATATGCTTTGGCT 57.407 32.000 9.18 0.00 35.97 4.75
4263 9626 2.545532 CGAGTTCCTGCTCTGATCCATC 60.546 54.545 0.00 0.00 33.55 3.51
4266 9629 1.714541 TCCTGCTCTGATCCATCCTC 58.285 55.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 9.262358 ACTAAAAACTGAACTGAGTAGATGTTC 57.738 33.333 0.00 0.00 40.09 3.18
120 121 5.367060 ACTCCTCTCCACTAAAAACTGAACT 59.633 40.000 0.00 0.00 0.00 3.01
188 189 6.712095 GCCATGATGGTAATATGTTTGAGAGA 59.288 38.462 13.84 0.00 40.46 3.10
211 212 3.113745 CCGTGATGCCATGAAGCC 58.886 61.111 0.00 0.00 0.00 4.35
212 213 1.731433 ATGCCGTGATGCCATGAAGC 61.731 55.000 0.00 0.00 0.00 3.86
326 2888 2.963101 GCCCTCCACTAAAAACCAAACT 59.037 45.455 0.00 0.00 0.00 2.66
345 2907 2.328099 CGAGGTGCTTGAACTGGCC 61.328 63.158 0.00 0.00 0.00 5.36
356 2918 4.912528 GCTTAGATATTAAGCGAGGTGC 57.087 45.455 11.38 0.00 46.98 5.01
403 2965 3.719763 CGTGAAGTTATGGTTGTAACGCG 60.720 47.826 3.53 3.53 39.09 6.01
404 2966 3.423907 CCGTGAAGTTATGGTTGTAACGC 60.424 47.826 0.00 0.00 39.09 4.84
405 2967 3.423907 GCCGTGAAGTTATGGTTGTAACG 60.424 47.826 0.00 0.00 39.09 3.18
424 2987 2.351418 ACATTAACATGTCGTGATGCCG 59.649 45.455 0.00 0.00 39.69 5.69
508 3074 4.530710 AAGCCAAACATAGTAGACGTCA 57.469 40.909 19.50 0.48 0.00 4.35
553 3119 9.048446 GGGTATTGCTTATGTATTTAACGAAGA 57.952 33.333 0.00 0.00 0.00 2.87
566 3132 5.811399 TTGAAAGTCGGGTATTGCTTATG 57.189 39.130 0.00 0.00 0.00 1.90
567 3133 7.404671 AATTTGAAAGTCGGGTATTGCTTAT 57.595 32.000 0.00 0.00 0.00 1.73
647 3267 8.203485 TCAAATCCATTGCCCATAAAAATACTC 58.797 33.333 0.00 0.00 38.98 2.59
651 3271 5.824097 GCTCAAATCCATTGCCCATAAAAAT 59.176 36.000 0.00 0.00 38.98 1.82
652 3272 5.184711 GCTCAAATCCATTGCCCATAAAAA 58.815 37.500 0.00 0.00 38.98 1.94
675 3803 7.827819 TGAACATATTACTTCCTTCTTGTCG 57.172 36.000 0.00 0.00 0.00 4.35
714 3952 2.587522 TCTGGTAGATCACGATCAGGG 58.412 52.381 9.60 0.00 40.22 4.45
1104 5265 2.179517 GACTCCTCGAGGTGCACG 59.820 66.667 30.17 16.35 33.35 5.34
1435 5630 2.600731 CCTGACACAGCTACTTTCTCG 58.399 52.381 0.00 0.00 0.00 4.04
1465 5699 6.057321 AGAAATCCCCATACTTCGTAACAA 57.943 37.500 0.00 0.00 0.00 2.83
1513 5747 2.391130 GGCCATATCCCACCCCACA 61.391 63.158 0.00 0.00 0.00 4.17
1517 5751 1.063717 CCATATGGCCATATCCCACCC 60.064 57.143 31.50 0.00 34.68 4.61
1524 5758 7.938686 TGAGTATTTTACCCATATGGCCATAT 58.061 34.615 29.24 29.24 37.83 1.78
1525 5759 7.336475 TGAGTATTTTACCCATATGGCCATA 57.664 36.000 27.36 27.36 37.83 2.74
1526 5760 6.212840 TGAGTATTTTACCCATATGGCCAT 57.787 37.500 24.45 24.45 37.83 4.40
1527 5761 5.630121 CTGAGTATTTTACCCATATGGCCA 58.370 41.667 16.97 8.56 37.83 5.36
1528 5762 4.459337 GCTGAGTATTTTACCCATATGGCC 59.541 45.833 16.97 0.00 37.83 5.36
1529 5763 5.070001 TGCTGAGTATTTTACCCATATGGC 58.930 41.667 16.97 0.00 37.83 4.40
1530 5764 6.716628 ACATGCTGAGTATTTTACCCATATGG 59.283 38.462 15.41 15.41 41.37 2.74
1531 5765 7.308770 CCACATGCTGAGTATTTTACCCATATG 60.309 40.741 0.00 0.00 0.00 1.78
1549 5797 1.482182 TCTAGCGTCAATCCACATGCT 59.518 47.619 0.00 0.00 38.46 3.79
1561 5809 1.064952 GCTCAGTTCCTCTCTAGCGTC 59.935 57.143 0.00 0.00 0.00 5.19
1562 5810 1.099689 GCTCAGTTCCTCTCTAGCGT 58.900 55.000 0.00 0.00 0.00 5.07
1563 5811 1.388547 AGCTCAGTTCCTCTCTAGCG 58.611 55.000 0.00 0.00 37.32 4.26
1565 5813 7.817418 ACTATTAAGCTCAGTTCCTCTCTAG 57.183 40.000 0.00 0.00 0.00 2.43
1642 5914 0.107456 AGGCGATGGATGATCACACC 59.893 55.000 12.27 12.27 0.00 4.16
1660 5932 0.672401 ATGCCAAACACGGTCCGTAG 60.672 55.000 18.38 13.88 38.32 3.51
1724 6013 3.355378 TCCTCTGTTTGGCACCATTATG 58.645 45.455 0.00 0.00 0.00 1.90
1842 6196 2.753452 CCGGAGCACTAGTCTTGACTAA 59.247 50.000 11.09 0.00 0.00 2.24
1847 6201 1.000955 ACAACCGGAGCACTAGTCTTG 59.999 52.381 9.46 0.00 0.00 3.02
1848 6202 1.339097 ACAACCGGAGCACTAGTCTT 58.661 50.000 9.46 0.00 0.00 3.01
1874 6249 2.094417 GCTTACAAAAGAGCAGGCTACG 59.906 50.000 0.00 0.00 38.73 3.51
1956 6333 8.258007 GGGCGGCATATATAGAAATATAGCATA 58.742 37.037 12.47 0.00 34.71 3.14
1964 6341 5.045578 AGTCTTGGGCGGCATATATAGAAAT 60.046 40.000 12.47 0.00 0.00 2.17
1967 6344 3.441101 AGTCTTGGGCGGCATATATAGA 58.559 45.455 12.47 0.62 0.00 1.98
1975 6352 2.632602 TTTTGGAGTCTTGGGCGGCA 62.633 55.000 12.47 0.00 0.00 5.69
1976 6353 1.901464 TTTTGGAGTCTTGGGCGGC 60.901 57.895 0.00 0.00 0.00 6.53
1977 6354 0.537371 AGTTTTGGAGTCTTGGGCGG 60.537 55.000 0.00 0.00 0.00 6.13
2025 6405 6.698766 GGAACTAACGGTTATACATACCAGTG 59.301 42.308 0.29 0.00 38.41 3.66
2197 6583 8.884124 AATTTCTGATAGATGGTTTGGAAAGA 57.116 30.769 0.00 0.00 0.00 2.52
2300 6690 5.621197 ATTGCTCTAGCTAGTACGATCAG 57.379 43.478 20.10 9.50 42.66 2.90
2325 6715 5.068591 GGGAAAACAAACATAGGACAACACT 59.931 40.000 0.00 0.00 0.00 3.55
2326 6716 5.068591 AGGGAAAACAAACATAGGACAACAC 59.931 40.000 0.00 0.00 0.00 3.32
2391 6781 5.796350 AGAACTGCCGATTTACACATTAC 57.204 39.130 0.00 0.00 0.00 1.89
2706 7674 8.489489 TCTTCTCATCTAGCTGATTGGTTAAAT 58.511 33.333 0.00 0.00 32.05 1.40
2788 7758 5.048504 CGATAATGCATTATTGGCTGGAACT 60.049 40.000 28.60 9.06 33.37 3.01
2815 7785 9.678941 CACTCTTAATATGTAAGATAGCGTGAA 57.321 33.333 12.87 0.00 32.45 3.18
2818 7788 9.069082 AGTCACTCTTAATATGTAAGATAGCGT 57.931 33.333 7.42 2.24 33.61 5.07
2819 7789 9.900710 AAGTCACTCTTAATATGTAAGATAGCG 57.099 33.333 7.42 0.00 33.61 4.26
2921 8173 1.021390 GGTGAGAGCACAACATCCCG 61.021 60.000 0.00 0.00 46.96 5.14
3004 8256 0.462581 TCTGGTCGATGCTGAATGGC 60.463 55.000 0.00 0.00 0.00 4.40
3048 8300 1.729267 ATCCCCAACAGCAACAGGGT 61.729 55.000 0.00 0.00 39.76 4.34
3054 8312 3.448093 TGTTGATATCCCCAACAGCAA 57.552 42.857 0.00 0.00 46.03 3.91
3099 8357 2.052782 TGTAGCAGCTGGAGACGATA 57.947 50.000 17.12 0.00 0.00 2.92
3170 8436 1.135527 CAGGTTATGGCAAGGCATGTG 59.864 52.381 18.10 7.34 0.00 3.21
3247 8513 1.068472 GTTGACACTGAGATCGGTCGT 60.068 52.381 0.00 0.00 32.07 4.34
3249 8515 1.732732 CGGTTGACACTGAGATCGGTC 60.733 57.143 0.00 0.00 32.07 4.79
3251 8517 1.078759 GCGGTTGACACTGAGATCGG 61.079 60.000 0.00 0.00 0.00 4.18
3253 8519 1.354040 CAGCGGTTGACACTGAGATC 58.646 55.000 0.00 0.00 33.10 2.75
3270 8537 0.679002 CCCCACATCTTGCTGACCAG 60.679 60.000 0.00 0.00 0.00 4.00
3283 8550 1.995066 ATCAGTCGATGCCCCCACA 60.995 57.895 0.00 0.00 0.00 4.17
3337 8604 0.035739 AATACCGACACGCCCTGTTT 59.964 50.000 0.00 0.00 31.03 2.83
3371 8639 2.162408 GCAGTCTAAAATGGACACCAGC 59.838 50.000 0.00 0.00 36.75 4.85
3393 8661 3.957497 CCACTGACTAGCCACTAGATTCT 59.043 47.826 8.57 0.00 37.49 2.40
3445 8716 3.251729 CCACCACTGAAGACTGAACATTG 59.748 47.826 0.00 0.00 0.00 2.82
3446 8717 3.117888 ACCACCACTGAAGACTGAACATT 60.118 43.478 0.00 0.00 0.00 2.71
3447 8718 2.439507 ACCACCACTGAAGACTGAACAT 59.560 45.455 0.00 0.00 0.00 2.71
3448 8719 1.837439 ACCACCACTGAAGACTGAACA 59.163 47.619 0.00 0.00 0.00 3.18
3449 8720 2.622064 ACCACCACTGAAGACTGAAC 57.378 50.000 0.00 0.00 0.00 3.18
3450 8721 3.644966 AAACCACCACTGAAGACTGAA 57.355 42.857 0.00 0.00 0.00 3.02
3451 8722 3.278574 CAAAACCACCACTGAAGACTGA 58.721 45.455 0.00 0.00 0.00 3.41
3452 8723 3.016736 ACAAAACCACCACTGAAGACTG 58.983 45.455 0.00 0.00 0.00 3.51
3453 8724 3.366052 ACAAAACCACCACTGAAGACT 57.634 42.857 0.00 0.00 0.00 3.24
3454 8725 5.995897 ACTATACAAAACCACCACTGAAGAC 59.004 40.000 0.00 0.00 0.00 3.01
3455 8726 5.995282 CACTATACAAAACCACCACTGAAGA 59.005 40.000 0.00 0.00 0.00 2.87
3456 8727 5.334879 GCACTATACAAAACCACCACTGAAG 60.335 44.000 0.00 0.00 0.00 3.02
3524 8797 5.278022 GCGTCCCTTTCTCAATTCCATATTC 60.278 44.000 0.00 0.00 0.00 1.75
3526 8799 4.137543 GCGTCCCTTTCTCAATTCCATAT 58.862 43.478 0.00 0.00 0.00 1.78
3560 8833 1.971481 TGATCAAAGCGCATATGGCT 58.029 45.000 11.47 11.55 44.02 4.75
3581 8854 5.499268 AATGCACAACGAATGAAAAATCG 57.501 34.783 0.00 0.00 44.33 3.34
3592 8872 3.243234 CCAAACAGGTAAATGCACAACGA 60.243 43.478 0.00 0.00 0.00 3.85
3593 8873 3.049206 CCAAACAGGTAAATGCACAACG 58.951 45.455 0.00 0.00 0.00 4.10
3613 8893 2.432444 TGGTCGTCCATGAATGAAACC 58.568 47.619 0.00 0.00 39.03 3.27
3732 9046 5.578727 CAGTTGAGCTATAAGTGAACCTGAC 59.421 44.000 10.93 0.00 31.63 3.51
3743 9062 5.982356 ACAGCATCTTCAGTTGAGCTATAA 58.018 37.500 0.00 0.00 0.00 0.98
3891 9216 4.474651 TGATAGTTGGATGGACACCTGAAT 59.525 41.667 0.00 0.00 0.00 2.57
3892 9217 3.843619 TGATAGTTGGATGGACACCTGAA 59.156 43.478 0.00 0.00 0.00 3.02
3893 9218 3.197766 GTGATAGTTGGATGGACACCTGA 59.802 47.826 0.00 0.00 0.00 3.86
4129 9480 6.990939 AGTAAAGAGTTGTAGGAAACTGAACC 59.009 38.462 0.00 0.00 40.48 3.62
4149 9500 8.615878 TTTCATTAGTTAGCTCTGCAAGTAAA 57.384 30.769 0.00 0.00 33.76 2.01
4165 9516 7.592885 AGCCAAAGCATATGATTTCATTAGT 57.407 32.000 15.79 0.00 43.56 2.24
4171 9528 6.101332 TGTTCAAGCCAAAGCATATGATTTC 58.899 36.000 15.79 6.51 43.56 2.17
4189 9552 2.548057 GCCGTGAGTCTCAAATGTTCAA 59.452 45.455 3.51 0.00 0.00 2.69
4263 9626 0.820226 TCGTGCTGGAGAATGAGAGG 59.180 55.000 0.00 0.00 0.00 3.69
4266 9629 2.675519 GCTCGTGCTGGAGAATGAG 58.324 57.895 1.41 0.00 39.30 2.90


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

AutoCloner maintained by Alex Coulton.