Multiple sequence alignment - TraesCS7B01G041600

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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 TraesCS7B01G041600 chr7B 100.000 3125 0 0 1 3125 41198558 41195434 0.000000e+00 5771.0
1 TraesCS7B01G041600 chr7B 90.155 193 18 1 1 193 737273312 737273121 1.860000e-62 250.0
2 TraesCS7B01G041600 chr7D 96.000 1300 27 13 843 2127 90044624 90043335 0.000000e+00 2089.0
3 TraesCS7B01G041600 chr7D 90.456 461 30 9 2226 2681 90042974 90042523 2.070000e-166 595.0
4 TraesCS7B01G041600 chr7D 89.197 361 27 11 2679 3037 90042286 90041936 1.030000e-119 440.0
5 TraesCS7B01G041600 chr7D 97.753 89 2 0 2125 2213 90043046 90042958 1.500000e-33 154.0
6 TraesCS7B01G041600 chr7A 95.833 1296 29 10 841 2127 91545163 91543884 0.000000e+00 2071.0
7 TraesCS7B01G041600 chr7A 91.558 841 46 4 1 841 473950102 473950917 0.000000e+00 1136.0
8 TraesCS7B01G041600 chr7A 91.262 824 44 21 2226 3037 91543712 91542905 0.000000e+00 1098.0
9 TraesCS7B01G041600 chr7A 83.951 243 17 1 70 312 665439309 665439089 2.440000e-51 213.0
10 TraesCS7B01G041600 chr7A 94.444 90 5 0 2126 2215 91543783 91543694 4.200000e-29 139.0
11 TraesCS7B01G041600 chr3B 96.912 842 3 2 1 842 28078973 28078155 0.000000e+00 1389.0
12 TraesCS7B01G041600 chr3B 88.692 451 49 2 392 841 564028049 564027600 1.640000e-152 549.0
13 TraesCS7B01G041600 chr5A 91.439 841 47 4 1 841 22994140 22994955 0.000000e+00 1131.0
14 TraesCS7B01G041600 chr5A 96.472 652 21 1 192 841 457799178 457798527 0.000000e+00 1075.0
15 TraesCS7B01G041600 chr5A 95.000 80 2 2 274 353 457799137 457799060 1.180000e-24 124.0
16 TraesCS7B01G041600 chr5A 93.902 82 3 2 231 310 457799098 457799017 4.230000e-24 122.0
17 TraesCS7B01G041600 chr5A 89.362 94 5 4 272 362 22994347 22994438 2.550000e-21 113.0
18 TraesCS7B01G041600 chr3A 90.606 841 55 4 1 841 715693769 715694585 0.000000e+00 1094.0
19 TraesCS7B01G041600 chr3A 84.735 321 23 6 1 320 530198918 530198623 6.550000e-77 298.0
20 TraesCS7B01G041600 chr1A 90.193 571 49 5 274 843 466348846 466348282 0.000000e+00 737.0
21 TraesCS7B01G041600 chr2B 87.719 456 56 0 392 847 155817266 155816811 1.650000e-147 532.0
22 TraesCS7B01G041600 chr2B 85.758 330 21 7 1 327 94928991 94928685 3.010000e-85 326.0
23 TraesCS7B01G041600 chr4B 87.556 450 56 0 392 841 5822240 5821791 3.570000e-144 521.0
24 TraesCS7B01G041600 chr6B 85.670 321 20 6 1 320 144852092 144851797 6.510000e-82 315.0
25 TraesCS7B01G041600 chr5B 90.155 193 18 1 1 193 564596360 564596169 1.860000e-62 250.0
26 TraesCS7B01G041600 chr4D 87.288 118 14 1 2919 3036 466382761 466382645 1.960000e-27 134.0
27 TraesCS7B01G041600 chrUn 98.649 74 1 0 3052 3125 8614694 8614767 7.030000e-27 132.0
28 TraesCS7B01G041600 chrUn 98.649 74 1 0 3052 3125 47476186 47476113 7.030000e-27 132.0
29 TraesCS7B01G041600 chrUn 98.649 74 1 0 3052 3125 168683520 168683447 7.030000e-27 132.0
30 TraesCS7B01G041600 chrUn 98.649 74 1 0 3052 3125 202828769 202828696 7.030000e-27 132.0
31 TraesCS7B01G041600 chrUn 98.649 74 1 0 3052 3125 268572116 268572189 7.030000e-27 132.0
32 TraesCS7B01G041600 chrUn 98.649 74 1 0 3052 3125 374420185 374420258 7.030000e-27 132.0
33 TraesCS7B01G041600 chr1B 98.649 74 1 0 3052 3125 12439379 12439306 7.030000e-27 132.0
34 TraesCS7B01G041600 chr1B 98.649 74 1 0 3052 3125 107513048 107512975 7.030000e-27 132.0
35 TraesCS7B01G041600 chr1B 98.649 74 1 0 3052 3125 310754649 310754722 7.030000e-27 132.0
36 TraesCS7B01G041600 chr6D 88.182 110 10 3 2922 3030 441667324 441667217 9.100000e-26 128.0
37 TraesCS7B01G041600 chr5D 87.273 110 13 1 2921 3030 377374242 377374350 1.180000e-24 124.0
38 TraesCS7B01G041600 chr5D 87.273 110 13 1 2921 3030 377374703 377374811 1.180000e-24 124.0
39 TraesCS7B01G041600 chr5D 88.889 90 9 1 2941 3030 377374086 377374174 3.300000e-20 110.0
40 TraesCS7B01G041600 chr5D 88.889 90 9 1 2941 3030 377374547 377374635 3.300000e-20 110.0
41 TraesCS7B01G041600 chr5D 85.185 81 10 2 2956 3036 506158294 506158216 7.180000e-12 82.4


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 TraesCS7B01G041600 chr7B 41195434 41198558 3124 True 5771.000000 5771 100.000000 1 3125 1 chr7B.!!$R1 3124
1 TraesCS7B01G041600 chr7D 90041936 90044624 2688 True 819.500000 2089 93.351500 843 3037 4 chr7D.!!$R1 2194
2 TraesCS7B01G041600 chr7A 473950102 473950917 815 False 1136.000000 1136 91.558000 1 841 1 chr7A.!!$F1 840
3 TraesCS7B01G041600 chr7A 91542905 91545163 2258 True 1102.666667 2071 93.846333 841 3037 3 chr7A.!!$R2 2196
4 TraesCS7B01G041600 chr3B 28078155 28078973 818 True 1389.000000 1389 96.912000 1 842 1 chr3B.!!$R1 841
5 TraesCS7B01G041600 chr5A 22994140 22994955 815 False 622.000000 1131 90.400500 1 841 2 chr5A.!!$F1 840
6 TraesCS7B01G041600 chr5A 457798527 457799178 651 True 440.333333 1075 95.124667 192 841 3 chr5A.!!$R1 649
7 TraesCS7B01G041600 chr3A 715693769 715694585 816 False 1094.000000 1094 90.606000 1 841 1 chr3A.!!$F1 840
8 TraesCS7B01G041600 chr1A 466348282 466348846 564 True 737.000000 737 90.193000 274 843 1 chr1A.!!$R1 569

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
592 596 1.144936 GGGACATGCGAGAGGAAGG 59.855 63.158 0.0 0.0 32.68 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2443 3.491964 GGGAACGATCGATACATGGACAA 60.492 47.826 24.34 0.0 0.0 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
592 596 1.144936 GGGACATGCGAGAGGAAGG 59.855 63.158 0.00 0.00 32.68 3.46
658 662 2.926242 AGAGGAACCGCGGGGAAA 60.926 61.111 31.76 0.00 36.97 3.13
885 889 1.381191 TACAGCGAGCTCATCCCCA 60.381 57.895 15.40 0.00 0.00 4.96
886 890 1.395045 TACAGCGAGCTCATCCCCAG 61.395 60.000 15.40 0.00 0.00 4.45
887 891 3.160047 AGCGAGCTCATCCCCAGG 61.160 66.667 15.40 0.00 0.00 4.45
888 892 4.925861 GCGAGCTCATCCCCAGGC 62.926 72.222 15.40 2.12 0.00 4.85
889 893 4.598894 CGAGCTCATCCCCAGGCG 62.599 72.222 15.40 0.00 0.00 5.52
890 894 3.157252 GAGCTCATCCCCAGGCGA 61.157 66.667 9.40 0.00 0.00 5.54
934 940 3.004951 CCTCAAGCTCCAGGCCAT 58.995 61.111 5.01 0.00 43.05 4.40
945 951 1.333636 CCAGGCCATCCTCGAGTTCT 61.334 60.000 12.31 0.00 41.93 3.01
946 952 1.403814 CAGGCCATCCTCGAGTTCTA 58.596 55.000 12.31 0.00 41.93 2.10
947 953 1.967066 CAGGCCATCCTCGAGTTCTAT 59.033 52.381 12.31 0.00 41.93 1.98
948 954 2.029470 CAGGCCATCCTCGAGTTCTATC 60.029 54.545 12.31 0.00 41.93 2.08
949 955 2.158385 AGGCCATCCTCGAGTTCTATCT 60.158 50.000 12.31 0.00 38.72 1.98
984 990 2.157668 GTGGTGAATTACGAGTGTGCTG 59.842 50.000 0.00 0.00 0.00 4.41
993 999 1.291877 CGAGTGTGCTGCCTAACACC 61.292 60.000 15.50 8.39 46.32 4.16
1200 1219 4.070552 GACAAGCTCCGGTCGGCT 62.071 66.667 0.00 7.46 40.85 5.52
1611 1630 2.737376 GTGGACAAGGTCGGCGAC 60.737 66.667 30.72 30.72 32.65 5.19
1728 1747 2.486042 GTGCTCCTCCTCGACGAC 59.514 66.667 0.00 0.00 0.00 4.34
2127 2146 1.209127 CGTTTCCGGCGCTTGATTT 59.791 52.632 7.64 0.00 0.00 2.17
2128 2147 0.444651 CGTTTCCGGCGCTTGATTTA 59.555 50.000 7.64 0.00 0.00 1.40
2133 2443 1.024579 CCGGCGCTTGATTTACCTGT 61.025 55.000 7.64 0.00 0.00 4.00
2216 2526 8.897872 AAATCAATCAATGAGAGTTGCTTTTT 57.102 26.923 0.00 0.00 42.53 1.94
2315 2630 6.653989 ACATAAGAATAGGACACCCTTCTTG 58.346 40.000 18.03 10.67 40.78 3.02
2332 2647 6.154021 CCCTTCTTGGATTCAAATGAATGACT 59.846 38.462 13.08 0.00 44.14 3.41
2384 2699 9.889128 TGGATTGAGTTTCAAAGAAAAAGAAAT 57.111 25.926 0.00 0.00 40.12 2.17
2641 2960 6.756221 TCCTATTTTTCTCCTATTCCTACGC 58.244 40.000 0.00 0.00 0.00 4.42
2644 2963 7.385478 CCTATTTTTCTCCTATTCCTACGCTTC 59.615 40.741 0.00 0.00 0.00 3.86
2660 2979 2.285977 GCTTCCGTAATCCCGTGAAAT 58.714 47.619 0.00 0.00 0.00 2.17
2880 3443 3.261580 GCAGAGGCAGTTGTTTTTGTTT 58.738 40.909 0.00 0.00 40.72 2.83
2893 3456 5.235516 TGTTTTTGTTTGGCCTTCGTTTTA 58.764 33.333 3.32 0.00 0.00 1.52
2902 3465 6.895607 TTGGCCTTCGTTTTAAAAGAAAAG 57.104 33.333 3.32 5.57 0.00 2.27
2947 3510 1.117150 ACGCACGGACCTATGGTTAT 58.883 50.000 0.00 0.00 35.25 1.89
2962 3525 4.295141 TGGTTATGGAATCAACGGACTT 57.705 40.909 0.00 0.00 0.00 3.01
2970 3533 6.349243 TGGAATCAACGGACTTTACTTAGA 57.651 37.500 0.00 0.00 0.00 2.10
2975 3538 3.160777 ACGGACTTTACTTAGATGGCG 57.839 47.619 0.00 0.00 0.00 5.69
2976 3539 2.494870 ACGGACTTTACTTAGATGGCGT 59.505 45.455 0.00 0.00 0.00 5.68
2978 3541 4.158394 ACGGACTTTACTTAGATGGCGTTA 59.842 41.667 0.00 0.00 0.00 3.18
3031 3595 2.559478 CCACCCCCATGAAAATCAGGAA 60.559 50.000 0.00 0.00 27.97 3.36
3035 3599 1.758862 CCCATGAAAATCAGGAAGGGC 59.241 52.381 0.00 0.00 27.97 5.19
3036 3600 1.406539 CCATGAAAATCAGGAAGGGCG 59.593 52.381 0.00 0.00 27.97 6.13
3037 3601 1.106285 ATGAAAATCAGGAAGGGCGC 58.894 50.000 0.00 0.00 0.00 6.53
3038 3602 1.305219 TGAAAATCAGGAAGGGCGCG 61.305 55.000 0.00 0.00 0.00 6.86
3039 3603 2.598619 GAAAATCAGGAAGGGCGCGC 62.599 60.000 25.94 25.94 0.00 6.86
3040 3604 3.628646 AAATCAGGAAGGGCGCGCT 62.629 57.895 32.29 22.73 0.00 5.92
3041 3605 4.845580 ATCAGGAAGGGCGCGCTG 62.846 66.667 32.29 20.13 0.00 5.18
3045 3609 4.537433 GGAAGGGCGCGCTGAGAT 62.537 66.667 32.29 12.37 0.00 2.75
3046 3610 3.267860 GAAGGGCGCGCTGAGATG 61.268 66.667 32.29 0.00 0.00 2.90
3053 3617 3.127533 GCGCTGAGATGCCCGTTT 61.128 61.111 0.00 0.00 0.00 3.60
3054 3618 1.813753 GCGCTGAGATGCCCGTTTA 60.814 57.895 0.00 0.00 0.00 2.01
3055 3619 1.766143 GCGCTGAGATGCCCGTTTAG 61.766 60.000 0.00 0.00 0.00 1.85
3056 3620 1.766143 CGCTGAGATGCCCGTTTAGC 61.766 60.000 0.00 0.00 0.00 3.09
3057 3621 1.440145 GCTGAGATGCCCGTTTAGCC 61.440 60.000 0.00 0.00 0.00 3.93
3058 3622 0.179000 CTGAGATGCCCGTTTAGCCT 59.821 55.000 0.00 0.00 0.00 4.58
3059 3623 0.178068 TGAGATGCCCGTTTAGCCTC 59.822 55.000 0.00 0.00 0.00 4.70
3060 3624 0.178068 GAGATGCCCGTTTAGCCTCA 59.822 55.000 0.00 0.00 0.00 3.86
3061 3625 0.618458 AGATGCCCGTTTAGCCTCAA 59.382 50.000 0.00 0.00 0.00 3.02
3062 3626 1.017387 GATGCCCGTTTAGCCTCAAG 58.983 55.000 0.00 0.00 0.00 3.02
3063 3627 0.618458 ATGCCCGTTTAGCCTCAAGA 59.382 50.000 0.00 0.00 0.00 3.02
3064 3628 0.321298 TGCCCGTTTAGCCTCAAGAC 60.321 55.000 0.00 0.00 0.00 3.01
3065 3629 0.036294 GCCCGTTTAGCCTCAAGACT 60.036 55.000 0.00 0.00 0.00 3.24
3066 3630 1.206371 GCCCGTTTAGCCTCAAGACTA 59.794 52.381 0.00 0.00 0.00 2.59
3067 3631 2.738964 GCCCGTTTAGCCTCAAGACTAG 60.739 54.545 0.00 0.00 0.00 2.57
3068 3632 2.496470 CCCGTTTAGCCTCAAGACTAGT 59.504 50.000 0.00 0.00 0.00 2.57
3069 3633 3.429135 CCCGTTTAGCCTCAAGACTAGTC 60.429 52.174 15.41 15.41 0.00 2.59
3070 3634 3.429135 CCGTTTAGCCTCAAGACTAGTCC 60.429 52.174 19.38 2.89 0.00 3.85
3071 3635 3.444388 CGTTTAGCCTCAAGACTAGTCCT 59.556 47.826 19.38 10.36 0.00 3.85
3072 3636 4.639310 CGTTTAGCCTCAAGACTAGTCCTA 59.361 45.833 19.38 9.39 0.00 2.94
3073 3637 5.220892 CGTTTAGCCTCAAGACTAGTCCTAG 60.221 48.000 19.38 13.33 39.04 3.02
3074 3638 2.661718 AGCCTCAAGACTAGTCCTAGC 58.338 52.381 19.38 14.54 36.66 3.42
3075 3639 1.684450 GCCTCAAGACTAGTCCTAGCC 59.316 57.143 19.38 0.89 36.66 3.93
3076 3640 2.688515 GCCTCAAGACTAGTCCTAGCCT 60.689 54.545 19.38 0.00 36.66 4.58
3077 3641 3.219281 CCTCAAGACTAGTCCTAGCCTC 58.781 54.545 19.38 0.00 36.66 4.70
3078 3642 3.117663 CCTCAAGACTAGTCCTAGCCTCT 60.118 52.174 19.38 0.00 36.66 3.69
3079 3643 4.134563 CTCAAGACTAGTCCTAGCCTCTC 58.865 52.174 19.38 0.00 36.66 3.20
3080 3644 3.783642 TCAAGACTAGTCCTAGCCTCTCT 59.216 47.826 19.38 0.00 36.66 3.10
3081 3645 4.228666 TCAAGACTAGTCCTAGCCTCTCTT 59.771 45.833 19.38 0.17 36.66 2.85
3082 3646 4.873724 AGACTAGTCCTAGCCTCTCTTT 57.126 45.455 19.38 0.00 36.66 2.52
3083 3647 5.979656 AGACTAGTCCTAGCCTCTCTTTA 57.020 43.478 19.38 0.00 36.66 1.85
3084 3648 5.937111 AGACTAGTCCTAGCCTCTCTTTAG 58.063 45.833 19.38 0.00 36.66 1.85
3085 3649 5.430745 AGACTAGTCCTAGCCTCTCTTTAGT 59.569 44.000 19.38 0.00 36.66 2.24
3086 3650 5.687780 ACTAGTCCTAGCCTCTCTTTAGTC 58.312 45.833 1.22 0.00 36.66 2.59
3087 3651 4.594675 AGTCCTAGCCTCTCTTTAGTCA 57.405 45.455 0.00 0.00 0.00 3.41
3088 3652 4.532834 AGTCCTAGCCTCTCTTTAGTCAG 58.467 47.826 0.00 0.00 0.00 3.51
3089 3653 3.634910 GTCCTAGCCTCTCTTTAGTCAGG 59.365 52.174 0.00 0.00 0.00 3.86
3090 3654 2.962421 CCTAGCCTCTCTTTAGTCAGGG 59.038 54.545 0.00 0.00 0.00 4.45
3091 3655 1.872773 AGCCTCTCTTTAGTCAGGGG 58.127 55.000 0.00 0.00 0.00 4.79
3092 3656 1.079658 AGCCTCTCTTTAGTCAGGGGT 59.920 52.381 0.00 0.00 0.00 4.95
3093 3657 1.208293 GCCTCTCTTTAGTCAGGGGTG 59.792 57.143 0.00 0.00 0.00 4.61
3094 3658 1.208293 CCTCTCTTTAGTCAGGGGTGC 59.792 57.143 0.00 0.00 0.00 5.01
3095 3659 2.183679 CTCTCTTTAGTCAGGGGTGCT 58.816 52.381 0.00 0.00 0.00 4.40
3096 3660 2.569404 CTCTCTTTAGTCAGGGGTGCTT 59.431 50.000 0.00 0.00 0.00 3.91
3097 3661 2.303022 TCTCTTTAGTCAGGGGTGCTTG 59.697 50.000 0.00 0.00 0.00 4.01
3098 3662 1.351017 TCTTTAGTCAGGGGTGCTTGG 59.649 52.381 0.00 0.00 0.00 3.61
3099 3663 1.351017 CTTTAGTCAGGGGTGCTTGGA 59.649 52.381 0.00 0.00 0.00 3.53
3100 3664 1.440618 TTAGTCAGGGGTGCTTGGAA 58.559 50.000 0.00 0.00 0.00 3.53
3101 3665 0.690762 TAGTCAGGGGTGCTTGGAAC 59.309 55.000 0.00 0.00 0.00 3.62
3102 3666 1.062488 AGTCAGGGGTGCTTGGAACT 61.062 55.000 0.00 0.00 0.00 3.01
3103 3667 0.178990 GTCAGGGGTGCTTGGAACTT 60.179 55.000 0.00 0.00 0.00 2.66
3104 3668 0.555769 TCAGGGGTGCTTGGAACTTT 59.444 50.000 0.00 0.00 0.00 2.66
3105 3669 1.777878 TCAGGGGTGCTTGGAACTTTA 59.222 47.619 0.00 0.00 0.00 1.85
3106 3670 2.162681 CAGGGGTGCTTGGAACTTTAG 58.837 52.381 0.00 0.00 0.00 1.85
3107 3671 0.888619 GGGGTGCTTGGAACTTTAGC 59.111 55.000 0.00 0.00 35.50 3.09
3108 3672 0.888619 GGGTGCTTGGAACTTTAGCC 59.111 55.000 0.00 0.00 34.03 3.93
3109 3673 1.547901 GGGTGCTTGGAACTTTAGCCT 60.548 52.381 0.00 0.00 34.03 4.58
3110 3674 1.813178 GGTGCTTGGAACTTTAGCCTC 59.187 52.381 0.00 0.00 34.03 4.70
3111 3675 2.553247 GGTGCTTGGAACTTTAGCCTCT 60.553 50.000 0.00 0.00 34.03 3.69
3112 3676 3.307480 GGTGCTTGGAACTTTAGCCTCTA 60.307 47.826 0.00 0.00 34.03 2.43
3113 3677 4.324267 GTGCTTGGAACTTTAGCCTCTAA 58.676 43.478 0.00 0.00 34.03 2.10
3114 3678 4.760204 GTGCTTGGAACTTTAGCCTCTAAA 59.240 41.667 0.00 0.00 34.03 1.85
3115 3679 5.240844 GTGCTTGGAACTTTAGCCTCTAAAA 59.759 40.000 0.00 0.00 34.03 1.52
3116 3680 5.473504 TGCTTGGAACTTTAGCCTCTAAAAG 59.526 40.000 0.00 0.00 38.41 2.27
3117 3681 5.705905 GCTTGGAACTTTAGCCTCTAAAAGA 59.294 40.000 2.08 0.00 36.43 2.52
3118 3682 6.128145 GCTTGGAACTTTAGCCTCTAAAAGAG 60.128 42.308 2.08 0.00 41.96 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.684788 GTCAACTGAACGTATTGGCAGAT 59.315 43.478 0.00 0.00 32.86 2.90
658 662 2.654079 CGCCTGTGCCTTCTCTCCT 61.654 63.158 0.00 0.00 0.00 3.69
886 890 2.417719 CTCCATTTATACAGGCTCGCC 58.582 52.381 0.00 0.00 0.00 5.54
887 891 2.224305 ACCTCCATTTATACAGGCTCGC 60.224 50.000 0.00 0.00 0.00 5.03
888 892 3.393800 CACCTCCATTTATACAGGCTCG 58.606 50.000 0.00 0.00 0.00 5.03
889 893 3.142174 GCACCTCCATTTATACAGGCTC 58.858 50.000 0.00 0.00 0.00 4.70
890 894 2.158608 GGCACCTCCATTTATACAGGCT 60.159 50.000 0.00 0.00 34.01 4.58
934 940 5.534278 TCGTCTACTAGATAGAACTCGAGGA 59.466 44.000 18.41 0.00 41.75 3.71
945 951 3.129109 CCACTGCGTCGTCTACTAGATA 58.871 50.000 0.00 0.00 0.00 1.98
946 952 1.941294 CCACTGCGTCGTCTACTAGAT 59.059 52.381 0.00 0.00 0.00 1.98
947 953 1.338484 ACCACTGCGTCGTCTACTAGA 60.338 52.381 0.00 0.00 0.00 2.43
948 954 1.085091 ACCACTGCGTCGTCTACTAG 58.915 55.000 0.00 0.00 0.00 2.57
949 955 0.800631 CACCACTGCGTCGTCTACTA 59.199 55.000 0.00 0.00 0.00 1.82
971 977 1.341852 TGTTAGGCAGCACACTCGTAA 59.658 47.619 0.00 0.00 0.00 3.18
984 990 0.965363 CCATGGTGGTGGTGTTAGGC 60.965 60.000 2.57 0.00 34.46 3.93
1174 1193 4.443266 GAGCTTGTCGGCCTCGCT 62.443 66.667 0.00 0.48 36.13 4.93
1200 1219 3.663815 GAGGCCCCAGGAGTCGAGA 62.664 68.421 0.00 0.00 0.00 4.04
1205 1224 2.685380 CGAAGAGGCCCCAGGAGT 60.685 66.667 0.00 0.00 0.00 3.85
1233 1252 4.077184 GGGTCCGTCATGCCGTGA 62.077 66.667 0.00 0.00 0.00 4.35
1365 1384 4.790962 TCGACGCCGTAGCCCTCT 62.791 66.667 0.00 0.00 37.05 3.69
2133 2443 3.491964 GGGAACGATCGATACATGGACAA 60.492 47.826 24.34 0.00 0.00 3.18
2217 2527 5.629020 GCAACTCTCATTGTATTCGCAAAAA 59.371 36.000 0.00 0.00 31.83 1.94
2218 2528 5.048782 AGCAACTCTCATTGTATTCGCAAAA 60.049 36.000 0.00 0.00 31.83 2.44
2219 2529 4.455533 AGCAACTCTCATTGTATTCGCAAA 59.544 37.500 0.00 0.00 31.83 3.68
2220 2530 4.002982 AGCAACTCTCATTGTATTCGCAA 58.997 39.130 0.00 0.00 31.83 4.85
2221 2531 3.599343 AGCAACTCTCATTGTATTCGCA 58.401 40.909 0.00 0.00 31.83 5.10
2222 2532 4.606457 AAGCAACTCTCATTGTATTCGC 57.394 40.909 0.00 0.00 31.83 4.70
2223 2533 7.295952 AGTAAAGCAACTCTCATTGTATTCG 57.704 36.000 0.00 0.00 31.83 3.34
2224 2534 8.940952 AGAAGTAAAGCAACTCTCATTGTATTC 58.059 33.333 0.00 0.00 31.83 1.75
2225 2535 8.725148 CAGAAGTAAAGCAACTCTCATTGTATT 58.275 33.333 0.00 0.00 31.83 1.89
2226 2536 7.880195 ACAGAAGTAAAGCAACTCTCATTGTAT 59.120 33.333 0.00 0.00 31.83 2.29
2227 2537 7.217200 ACAGAAGTAAAGCAACTCTCATTGTA 58.783 34.615 0.00 0.00 31.83 2.41
2228 2538 6.058183 ACAGAAGTAAAGCAACTCTCATTGT 58.942 36.000 0.00 0.00 31.83 2.71
2229 2539 6.551385 ACAGAAGTAAAGCAACTCTCATTG 57.449 37.500 0.00 0.00 0.00 2.82
2230 2540 7.389053 CCTTACAGAAGTAAAGCAACTCTCATT 59.611 37.037 0.00 0.00 39.58 2.57
2231 2541 6.876257 CCTTACAGAAGTAAAGCAACTCTCAT 59.124 38.462 0.00 0.00 39.58 2.90
2232 2542 6.223852 CCTTACAGAAGTAAAGCAACTCTCA 58.776 40.000 0.00 0.00 39.58 3.27
2233 2543 5.639931 CCCTTACAGAAGTAAAGCAACTCTC 59.360 44.000 0.00 0.00 39.58 3.20
2234 2544 5.071923 ACCCTTACAGAAGTAAAGCAACTCT 59.928 40.000 0.00 0.00 39.58 3.24
2235 2545 5.306394 ACCCTTACAGAAGTAAAGCAACTC 58.694 41.667 0.00 0.00 39.58 3.01
2236 2546 5.071923 AGACCCTTACAGAAGTAAAGCAACT 59.928 40.000 0.00 0.00 39.58 3.16
2237 2547 5.306394 AGACCCTTACAGAAGTAAAGCAAC 58.694 41.667 0.00 0.00 39.58 4.17
2238 2548 5.307196 AGAGACCCTTACAGAAGTAAAGCAA 59.693 40.000 0.00 0.00 39.58 3.91
2239 2549 4.838986 AGAGACCCTTACAGAAGTAAAGCA 59.161 41.667 0.00 0.00 39.58 3.91
2240 2550 5.408880 AGAGACCCTTACAGAAGTAAAGC 57.591 43.478 0.00 0.00 39.58 3.51
2295 2605 4.175962 TCCAAGAAGGGTGTCCTATTCTT 58.824 43.478 11.02 11.02 44.07 2.52
2346 2661 7.461749 TGAAACTCAATCCAGGTTTCTCTATT 58.538 34.615 15.46 0.00 44.99 1.73
2347 2662 7.020827 TGAAACTCAATCCAGGTTTCTCTAT 57.979 36.000 15.46 0.00 44.99 1.98
2348 2663 6.433847 TGAAACTCAATCCAGGTTTCTCTA 57.566 37.500 15.46 0.00 44.99 2.43
2349 2664 5.310409 TGAAACTCAATCCAGGTTTCTCT 57.690 39.130 15.46 0.00 44.99 3.10
2356 2671 7.491682 TCTTTTTCTTTGAAACTCAATCCAGG 58.508 34.615 0.00 0.00 36.11 4.45
2391 2706 8.641498 ATGCAAAAGGGTTTATATGGATCTAG 57.359 34.615 0.00 0.00 0.00 2.43
2394 2709 7.015584 AGGAATGCAAAAGGGTTTATATGGATC 59.984 37.037 0.00 0.00 0.00 3.36
2445 2764 6.985188 AGATTGTCATTACGCAACTTATGT 57.015 33.333 0.00 0.00 0.00 2.29
2641 2960 6.425577 TTTTATTTCACGGGATTACGGAAG 57.574 37.500 0.00 0.00 38.39 3.46
2874 3436 6.164176 TCTTTTAAAACGAAGGCCAAACAAA 58.836 32.000 5.01 0.00 0.00 2.83
2880 3443 4.806775 GCTTTTCTTTTAAAACGAAGGCCA 59.193 37.500 5.01 0.00 0.00 5.36
2893 3456 8.903820 ACTGTTCTGTAACATAGCTTTTCTTTT 58.096 29.630 0.00 0.00 44.43 2.27
2902 3465 6.910536 AGCATTACTGTTCTGTAACATAGC 57.089 37.500 4.84 7.02 44.43 2.97
2947 3510 6.349243 TCTAAGTAAAGTCCGTTGATTCCA 57.651 37.500 0.00 0.00 0.00 3.53
2970 3533 8.576442 CCTAATCTCCAATAAAAATAACGCCAT 58.424 33.333 0.00 0.00 0.00 4.40
2978 3541 7.503902 GCCTCACTCCTAATCTCCAATAAAAAT 59.496 37.037 0.00 0.00 0.00 1.82
3010 3574 1.006998 TCCTGATTTTCATGGGGGTGG 59.993 52.381 0.00 0.00 0.00 4.61
3017 3581 1.202336 GCGCCCTTCCTGATTTTCATG 60.202 52.381 0.00 0.00 0.00 3.07
3036 3600 1.766143 CTAAACGGGCATCTCAGCGC 61.766 60.000 0.00 0.00 43.25 5.92
3037 3601 1.766143 GCTAAACGGGCATCTCAGCG 61.766 60.000 0.00 0.00 34.64 5.18
3038 3602 1.440145 GGCTAAACGGGCATCTCAGC 61.440 60.000 0.00 0.00 0.00 4.26
3039 3603 0.179000 AGGCTAAACGGGCATCTCAG 59.821 55.000 0.00 0.00 0.00 3.35
3040 3604 0.178068 GAGGCTAAACGGGCATCTCA 59.822 55.000 0.00 0.00 37.49 3.27
3041 3605 0.178068 TGAGGCTAAACGGGCATCTC 59.822 55.000 0.00 0.00 40.52 2.75
3042 3606 0.618458 TTGAGGCTAAACGGGCATCT 59.382 50.000 0.00 0.00 40.52 2.90
3043 3607 1.017387 CTTGAGGCTAAACGGGCATC 58.983 55.000 0.00 0.00 40.33 3.91
3044 3608 0.618458 TCTTGAGGCTAAACGGGCAT 59.382 50.000 0.00 0.00 0.00 4.40
3045 3609 0.321298 GTCTTGAGGCTAAACGGGCA 60.321 55.000 0.00 0.00 0.00 5.36
3046 3610 0.036294 AGTCTTGAGGCTAAACGGGC 60.036 55.000 0.00 0.00 0.00 6.13
3047 3611 2.496470 ACTAGTCTTGAGGCTAAACGGG 59.504 50.000 0.00 0.00 0.00 5.28
3048 3612 3.429135 GGACTAGTCTTGAGGCTAAACGG 60.429 52.174 21.88 0.00 0.00 4.44
3049 3613 3.444388 AGGACTAGTCTTGAGGCTAAACG 59.556 47.826 21.88 0.00 0.00 3.60
3050 3614 5.450826 GCTAGGACTAGTCTTGAGGCTAAAC 60.451 48.000 21.88 5.89 35.65 2.01
3051 3615 4.645588 GCTAGGACTAGTCTTGAGGCTAAA 59.354 45.833 21.88 0.00 35.65 1.85
3052 3616 4.208746 GCTAGGACTAGTCTTGAGGCTAA 58.791 47.826 21.88 0.00 35.65 3.09
3053 3617 3.435313 GGCTAGGACTAGTCTTGAGGCTA 60.435 52.174 24.87 16.06 35.06 3.93
3054 3618 2.661718 GCTAGGACTAGTCTTGAGGCT 58.338 52.381 21.88 11.79 35.65 4.58
3055 3619 1.684450 GGCTAGGACTAGTCTTGAGGC 59.316 57.143 21.88 21.38 35.06 4.70
3056 3620 3.306472 AGGCTAGGACTAGTCTTGAGG 57.694 52.381 21.88 10.56 45.03 3.86
3062 3626 5.687780 ACTAAAGAGAGGCTAGGACTAGTC 58.312 45.833 14.87 14.87 38.03 2.59
3063 3627 5.192121 TGACTAAAGAGAGGCTAGGACTAGT 59.808 44.000 0.00 0.00 35.65 2.57
3064 3628 5.686753 TGACTAAAGAGAGGCTAGGACTAG 58.313 45.833 1.98 1.98 36.29 2.57
3065 3629 5.398126 CCTGACTAAAGAGAGGCTAGGACTA 60.398 48.000 0.00 0.00 29.08 2.59
3066 3630 4.532834 CTGACTAAAGAGAGGCTAGGACT 58.467 47.826 0.00 0.00 0.00 3.85
3067 3631 3.634910 CCTGACTAAAGAGAGGCTAGGAC 59.365 52.174 0.00 0.00 29.08 3.85
3068 3632 3.373220 CCCTGACTAAAGAGAGGCTAGGA 60.373 52.174 0.00 0.00 29.08 2.94
3069 3633 2.962421 CCCTGACTAAAGAGAGGCTAGG 59.038 54.545 0.00 0.00 0.00 3.02
3070 3634 2.962421 CCCCTGACTAAAGAGAGGCTAG 59.038 54.545 0.00 0.00 0.00 3.42
3071 3635 2.315155 ACCCCTGACTAAAGAGAGGCTA 59.685 50.000 0.00 0.00 0.00 3.93
3072 3636 1.079658 ACCCCTGACTAAAGAGAGGCT 59.920 52.381 0.00 0.00 0.00 4.58
3073 3637 1.208293 CACCCCTGACTAAAGAGAGGC 59.792 57.143 0.00 0.00 0.00 4.70
3074 3638 1.208293 GCACCCCTGACTAAAGAGAGG 59.792 57.143 0.00 0.00 0.00 3.69
3075 3639 2.183679 AGCACCCCTGACTAAAGAGAG 58.816 52.381 0.00 0.00 0.00 3.20
3076 3640 2.303022 CAAGCACCCCTGACTAAAGAGA 59.697 50.000 0.00 0.00 0.00 3.10
3077 3641 2.616510 CCAAGCACCCCTGACTAAAGAG 60.617 54.545 0.00 0.00 0.00 2.85
3078 3642 1.351017 CCAAGCACCCCTGACTAAAGA 59.649 52.381 0.00 0.00 0.00 2.52
3079 3643 1.351017 TCCAAGCACCCCTGACTAAAG 59.649 52.381 0.00 0.00 0.00 1.85
3080 3644 1.440618 TCCAAGCACCCCTGACTAAA 58.559 50.000 0.00 0.00 0.00 1.85
3081 3645 1.073284 GTTCCAAGCACCCCTGACTAA 59.927 52.381 0.00 0.00 0.00 2.24
3082 3646 0.690762 GTTCCAAGCACCCCTGACTA 59.309 55.000 0.00 0.00 0.00 2.59
3083 3647 1.062488 AGTTCCAAGCACCCCTGACT 61.062 55.000 0.00 0.00 0.00 3.41
3084 3648 0.178990 AAGTTCCAAGCACCCCTGAC 60.179 55.000 0.00 0.00 0.00 3.51
3085 3649 0.555769 AAAGTTCCAAGCACCCCTGA 59.444 50.000 0.00 0.00 0.00 3.86
3086 3650 2.162681 CTAAAGTTCCAAGCACCCCTG 58.837 52.381 0.00 0.00 0.00 4.45
3087 3651 1.547901 GCTAAAGTTCCAAGCACCCCT 60.548 52.381 0.00 0.00 36.26 4.79
3088 3652 0.888619 GCTAAAGTTCCAAGCACCCC 59.111 55.000 0.00 0.00 36.26 4.95
3089 3653 0.888619 GGCTAAAGTTCCAAGCACCC 59.111 55.000 7.02 0.00 38.01 4.61
3090 3654 1.813178 GAGGCTAAAGTTCCAAGCACC 59.187 52.381 0.00 0.00 38.01 5.01
3091 3655 2.784347 AGAGGCTAAAGTTCCAAGCAC 58.216 47.619 0.00 2.09 38.01 4.40
3092 3656 4.634012 TTAGAGGCTAAAGTTCCAAGCA 57.366 40.909 0.00 0.00 38.01 3.91
3093 3657 5.705905 TCTTTTAGAGGCTAAAGTTCCAAGC 59.294 40.000 7.84 0.00 33.97 4.01
3094 3658 7.371126 CTCTTTTAGAGGCTAAAGTTCCAAG 57.629 40.000 7.84 0.00 38.67 3.61


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

AutoCloner maintained by Alex Coulton.