Multiple sequence alignment - TraesCS1D01G132800

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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 TraesCS1D01G132800 chr1D 100.000 5080 0 0 1 5080 159902164 159907243 0.000000e+00 9382.0
1 TraesCS1D01G132800 chr1A 94.949 2554 77 17 83 2593 234795490 234798034 0.000000e+00 3954.0
2 TraesCS1D01G132800 chr1A 97.085 1475 34 4 2704 4174 234798038 234799507 0.000000e+00 2477.0
3 TraesCS1D01G132800 chr1A 97.606 543 11 2 4170 4711 234805992 234806533 0.000000e+00 929.0
4 TraesCS1D01G132800 chr1A 97.033 337 10 0 4744 5080 234806531 234806867 7.380000e-158 568.0
5 TraesCS1D01G132800 chr1B 97.242 1414 22 5 3022 4422 223146677 223145268 0.000000e+00 2379.0
6 TraesCS1D01G132800 chr1B 94.247 1460 38 12 750 2184 223151054 223149616 0.000000e+00 2189.0
7 TraesCS1D01G132800 chr1B 93.592 671 21 10 4419 5080 223144696 223144039 0.000000e+00 981.0
8 TraesCS1D01G132800 chr1B 87.857 700 64 15 65 753 223166031 223165342 0.000000e+00 802.0
9 TraesCS1D01G132800 chr1B 93.478 322 15 2 2712 3032 223148529 223148213 1.660000e-129 473.0
10 TraesCS1D01G132800 chr1B 97.129 209 5 1 2243 2450 223149018 223148810 8.090000e-93 351.0
11 TraesCS1D01G132800 chr1B 90.533 169 5 6 2429 2596 223148784 223148626 3.980000e-51 213.0
12 TraesCS1D01G132800 chr1B 91.228 114 8 2 2593 2705 624606870 624606758 2.450000e-33 154.0
13 TraesCS1D01G132800 chr1B 97.297 37 1 0 1 37 223166072 223166036 4.250000e-06 63.9
14 TraesCS1D01G132800 chr4A 84.582 467 63 6 3581 4044 559068227 559067767 6.000000e-124 455.0
15 TraesCS1D01G132800 chr4D 82.803 471 69 9 3581 4047 40568140 40567678 1.320000e-110 411.0
16 TraesCS1D01G132800 chr4D 96.939 98 3 0 2608 2705 103233845 103233942 1.130000e-36 165.0
17 TraesCS1D01G132800 chr4B 82.692 468 70 8 3581 4044 59236739 59236279 6.120000e-109 405.0
18 TraesCS1D01G132800 chr4B 83.430 344 51 5 3703 4044 59227173 59226834 1.060000e-81 315.0
19 TraesCS1D01G132800 chr4B 92.593 108 8 0 2608 2715 499586491 499586384 6.810000e-34 156.0
20 TraesCS1D01G132800 chr2A 81.156 467 79 8 3577 4040 6510824 6511284 2.890000e-97 366.0
21 TraesCS1D01G132800 chr2B 81.075 465 76 9 3577 4037 454825142 454825598 1.340000e-95 361.0
22 TraesCS1D01G132800 chr2B 90.517 116 10 1 2599 2714 418953559 418953673 8.810000e-33 152.0
23 TraesCS1D01G132800 chr3B 93.519 108 7 0 2608 2715 629921474 629921367 1.460000e-35 161.0
24 TraesCS1D01G132800 chr3B 77.982 218 40 6 500 709 545060208 545059991 4.130000e-26 130.0
25 TraesCS1D01G132800 chr7B 93.396 106 7 0 2609 2714 40404559 40404454 1.890000e-34 158.0
26 TraesCS1D01G132800 chr5B 93.458 107 5 2 2609 2714 502503909 502504014 1.890000e-34 158.0
27 TraesCS1D01G132800 chr5B 91.818 110 9 0 2608 2717 91884531 91884422 2.450000e-33 154.0
28 TraesCS1D01G132800 chr6B 91.892 111 6 3 2605 2714 424080602 424080494 8.810000e-33 152.0
29 TraesCS1D01G132800 chr5A 74.396 414 73 14 326 714 567254872 567255277 4.100000e-31 147.0
30 TraesCS1D01G132800 chr5A 76.027 146 25 6 576 712 17226638 17226782 3.280000e-07 67.6


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 TraesCS1D01G132800 chr1D 159902164 159907243 5079 False 9382.000000 9382 100.000000 1 5080 1 chr1D.!!$F1 5079
1 TraesCS1D01G132800 chr1A 234795490 234799507 4017 False 3215.500000 3954 96.017000 83 4174 2 chr1A.!!$F1 4091
2 TraesCS1D01G132800 chr1A 234805992 234806867 875 False 748.500000 929 97.319500 4170 5080 2 chr1A.!!$F2 910
3 TraesCS1D01G132800 chr1B 223144039 223151054 7015 True 1097.666667 2379 94.370167 750 5080 6 chr1B.!!$R2 4330
4 TraesCS1D01G132800 chr1B 223165342 223166072 730 True 432.950000 802 92.577000 1 753 2 chr1B.!!$R3 752

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
63 64 0.460987 CGATGCTGACAGAAGGACCC 60.461 60.0 6.65 0.0 0.00 4.46 F
189 191 0.468029 GGGGCAAATCGGATGGTCAT 60.468 55.0 0.00 0.0 0.00 3.06 F
696 716 0.539051 CCTTCATGGAGACCGAGCTT 59.461 55.0 1.24 0.0 38.35 3.74 F
1996 2047 0.954452 GGTAGGGGTATACGGTGTCG 59.046 60.0 0.00 0.0 43.02 4.35 F
2624 3275 0.635009 AGATACTCCCTCCGTCCCAA 59.365 55.0 0.00 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1296 1316 4.329697 GCCGCGGACTCGATCGAT 62.330 66.667 33.48 8.99 39.00 3.59 R
2123 2174 1.066143 ACGGTGATTGGAAGGCACTAG 60.066 52.381 0.00 0.00 38.49 2.57 R
2605 3256 0.635009 TTGGGACGGAGGGAGTATCT 59.365 55.000 0.00 0.00 33.73 1.98 R
3867 6075 0.313043 AGGAACGTGACGGTGTACAG 59.687 55.000 10.66 0.00 0.00 2.74 R
4511 7302 0.875059 GTTCTGGCGGGACAAGAAAG 59.125 55.000 0.00 0.00 0.00 2.62 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
57 58 3.860717 CACGCGATGCTGACAGAA 58.139 55.556 15.93 0.00 0.00 3.02
58 59 1.706301 CACGCGATGCTGACAGAAG 59.294 57.895 15.93 0.00 0.00 2.85
59 60 1.446792 ACGCGATGCTGACAGAAGG 60.447 57.895 15.93 0.00 0.00 3.46
60 61 1.153765 CGCGATGCTGACAGAAGGA 60.154 57.895 6.65 0.00 0.00 3.36
61 62 1.416813 CGCGATGCTGACAGAAGGAC 61.417 60.000 6.65 0.00 0.00 3.85
62 63 1.086634 GCGATGCTGACAGAAGGACC 61.087 60.000 6.65 0.00 0.00 4.46
63 64 0.460987 CGATGCTGACAGAAGGACCC 60.461 60.000 6.65 0.00 0.00 4.46
70 71 4.148825 CAGAAGGACCCGGCCTCG 62.149 72.222 0.00 0.00 37.26 4.63
105 106 2.677971 GGCACACACTACTATGGCG 58.322 57.895 0.00 0.00 0.00 5.69
156 158 2.043652 CCCCGGGAAGTCGTCCTA 60.044 66.667 26.32 0.00 46.92 2.94
165 167 1.968050 AAGTCGTCCTAATGCGGGGG 61.968 60.000 0.00 0.00 0.00 5.40
186 188 2.124320 CGGGGCAAATCGGATGGT 60.124 61.111 0.00 0.00 0.00 3.55
188 190 1.077068 GGGGCAAATCGGATGGTCA 60.077 57.895 0.00 0.00 0.00 4.02
189 191 0.468029 GGGGCAAATCGGATGGTCAT 60.468 55.000 0.00 0.00 0.00 3.06
192 194 1.679139 GCAAATCGGATGGTCATGGA 58.321 50.000 0.00 0.00 0.00 3.41
196 198 2.462456 ATCGGATGGTCATGGAATCG 57.538 50.000 0.00 0.00 0.00 3.34
231 233 4.329545 GGAGGCCCTCGTGCAACA 62.330 66.667 4.29 0.00 35.74 3.33
289 291 1.990614 GAGGGGGCTCTCGGAAAGT 60.991 63.158 0.00 0.00 0.00 2.66
345 347 5.416952 AGATCGAAAATGTTGAATGGAGCTT 59.583 36.000 0.00 0.00 0.00 3.74
571 591 6.634436 CAGCTCGCATTTTAAGGTATTTCATC 59.366 38.462 0.00 0.00 0.00 2.92
574 594 7.259290 TCGCATTTTAAGGTATTTCATCCTC 57.741 36.000 0.00 0.00 33.09 3.71
618 638 4.935205 TCACATCCTTGTATGCTTGTACAC 59.065 41.667 0.00 0.00 34.50 2.90
696 716 0.539051 CCTTCATGGAGACCGAGCTT 59.461 55.000 1.24 0.00 38.35 3.74
863 883 2.095372 GGCACTATATAAATTCCGGCGC 59.905 50.000 0.00 0.00 0.00 6.53
1014 1034 2.996631 ACCAAGATGGAGTCATTGCTC 58.003 47.619 2.85 1.01 40.96 4.26
1577 1597 1.875514 GGCGCTGCATGAGATATTTGA 59.124 47.619 7.64 0.00 0.00 2.69
1674 1694 2.165319 GCCCCTAGCTGGTAATTACG 57.835 55.000 9.46 0.00 38.99 3.18
1745 1773 6.014156 GCATCCCCACTACTAGTATCAGAATT 60.014 42.308 2.33 0.00 0.00 2.17
1852 1899 4.305989 TGAGAAAAACTCCACAATGCAC 57.694 40.909 0.00 0.00 44.34 4.57
1909 1960 1.134220 AGGCGTGGTACATACATTGGG 60.134 52.381 0.00 0.00 44.52 4.12
1946 1997 3.056107 TCTGCCATACTAAAGTGCGAAGT 60.056 43.478 0.00 0.00 0.00 3.01
1952 2003 5.403246 CATACTAAAGTGCGAAGTGAGTCT 58.597 41.667 0.00 0.00 0.00 3.24
1996 2047 0.954452 GGTAGGGGTATACGGTGTCG 59.046 60.000 0.00 0.00 43.02 4.35
2123 2174 2.805671 GCATAACAAAGTGGCCCAAAAC 59.194 45.455 0.00 0.00 0.00 2.43
2598 3249 9.216117 AGAAAATTAAAGATTGTACGTGCTACT 57.784 29.630 4.97 0.00 0.00 2.57
2601 3252 9.649167 AAATTAAAGATTGTACGTGCTACTACT 57.351 29.630 4.97 0.00 0.00 2.57
2603 3254 4.030134 AGATTGTACGTGCTACTACTGC 57.970 45.455 4.97 0.00 0.00 4.40
2605 3256 4.880120 AGATTGTACGTGCTACTACTGCTA 59.120 41.667 4.97 0.00 0.00 3.49
2606 3257 4.611310 TTGTACGTGCTACTACTGCTAG 57.389 45.455 4.97 0.00 0.00 3.42
2610 3261 5.464722 TGTACGTGCTACTACTGCTAGATAC 59.535 44.000 4.97 0.00 0.00 2.24
2612 3263 4.751098 ACGTGCTACTACTGCTAGATACTC 59.249 45.833 0.00 0.00 0.00 2.59
2613 3264 4.152759 CGTGCTACTACTGCTAGATACTCC 59.847 50.000 0.00 0.00 0.00 3.85
2614 3265 4.456566 GTGCTACTACTGCTAGATACTCCC 59.543 50.000 0.00 0.00 0.00 4.30
2615 3266 4.351407 TGCTACTACTGCTAGATACTCCCT 59.649 45.833 0.00 0.00 0.00 4.20
2616 3267 4.939439 GCTACTACTGCTAGATACTCCCTC 59.061 50.000 0.00 0.00 0.00 4.30
2617 3268 4.376225 ACTACTGCTAGATACTCCCTCC 57.624 50.000 0.00 0.00 0.00 4.30
2618 3269 2.279935 ACTGCTAGATACTCCCTCCG 57.720 55.000 0.00 0.00 0.00 4.63
2619 3270 1.495574 ACTGCTAGATACTCCCTCCGT 59.504 52.381 0.00 0.00 0.00 4.69
2620 3271 2.156098 CTGCTAGATACTCCCTCCGTC 58.844 57.143 0.00 0.00 0.00 4.79
2622 3273 1.887522 GCTAGATACTCCCTCCGTCCC 60.888 61.905 0.00 0.00 0.00 4.46
2623 3274 1.424302 CTAGATACTCCCTCCGTCCCA 59.576 57.143 0.00 0.00 0.00 4.37
2624 3275 0.635009 AGATACTCCCTCCGTCCCAA 59.365 55.000 0.00 0.00 0.00 4.12
2625 3276 1.007963 AGATACTCCCTCCGTCCCAAA 59.992 52.381 0.00 0.00 0.00 3.28
2626 3277 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
2627 3278 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2628 3279 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2630 3281 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2632 3283 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2633 3284 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2634 3285 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2635 3286 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2637 3288 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
2639 3290 4.517453 CCGTCCCAAAATAAGTGTCTTGAA 59.483 41.667 0.00 0.00 0.00 2.69
2640 3291 5.449304 CGTCCCAAAATAAGTGTCTTGAAC 58.551 41.667 0.00 0.00 0.00 3.18
2644 3295 8.290325 GTCCCAAAATAAGTGTCTTGAACTTAG 58.710 37.037 2.85 0.00 41.95 2.18
2645 3296 7.996644 TCCCAAAATAAGTGTCTTGAACTTAGT 59.003 33.333 2.85 0.00 41.95 2.24
2664 3315 9.892130 AACTTAGTATAAATTTGCACTAGAGCT 57.108 29.630 13.47 0.00 34.99 4.09
2669 3320 9.968870 AGTATAAATTTGCACTAGAGCTAGTAC 57.031 33.333 13.47 5.52 43.98 2.73
2676 3327 6.968131 TGCACTAGAGCTAGTACAAAATTG 57.032 37.500 13.47 0.00 43.98 2.32
2679 3330 7.036220 GCACTAGAGCTAGTACAAAATTGAGA 58.964 38.462 9.66 0.00 43.98 3.27
2680 3331 7.009723 GCACTAGAGCTAGTACAAAATTGAGAC 59.990 40.741 9.66 0.00 43.98 3.36
2681 3332 8.029522 CACTAGAGCTAGTACAAAATTGAGACA 58.970 37.037 9.66 0.00 43.98 3.41
2682 3333 8.030106 ACTAGAGCTAGTACAAAATTGAGACAC 58.970 37.037 8.35 0.00 43.98 3.67
2683 3334 6.998802 AGAGCTAGTACAAAATTGAGACACT 58.001 36.000 0.00 1.09 0.00 3.55
2684 3335 7.445945 AGAGCTAGTACAAAATTGAGACACTT 58.554 34.615 0.00 0.00 0.00 3.16
2686 3337 9.372369 GAGCTAGTACAAAATTGAGACACTTAT 57.628 33.333 0.00 0.00 0.00 1.73
2687 3338 9.726438 AGCTAGTACAAAATTGAGACACTTATT 57.274 29.630 0.00 0.00 0.00 1.40
2696 3347 9.893305 AAAATTGAGACACTTATTTTAAGACGG 57.107 29.630 1.47 0.00 30.69 4.79
2697 3348 8.842358 AATTGAGACACTTATTTTAAGACGGA 57.158 30.769 1.47 0.00 0.00 4.69
2698 3349 7.884816 TTGAGACACTTATTTTAAGACGGAG 57.115 36.000 1.47 0.00 0.00 4.63
2699 3350 6.395629 TGAGACACTTATTTTAAGACGGAGG 58.604 40.000 1.47 0.00 0.00 4.30
2700 3351 5.731591 AGACACTTATTTTAAGACGGAGGG 58.268 41.667 1.47 0.00 0.00 4.30
2701 3352 5.482878 AGACACTTATTTTAAGACGGAGGGA 59.517 40.000 1.47 0.00 0.00 4.20
2702 3353 5.731591 ACACTTATTTTAAGACGGAGGGAG 58.268 41.667 1.47 0.00 0.00 4.30
2878 3529 5.693555 CGAAATACCTTTCCTACGGGATAAC 59.306 44.000 0.00 0.00 41.87 1.89
2922 3573 3.465871 AGCTAGGTACTACTCACTACGC 58.534 50.000 0.00 0.00 41.75 4.42
2958 3609 5.096849 GTCGCACTTTTGAACTGGTTTTAA 58.903 37.500 0.00 0.00 0.00 1.52
2965 3616 9.753669 CACTTTTGAACTGGTTTTAATTCAAAC 57.246 29.630 10.45 6.69 45.74 2.93
3090 5287 5.038683 CGTCCTAGTTGCACGTGATTAATA 58.961 41.667 22.23 5.90 0.00 0.98
3167 5371 8.236586 TCTCTTTAATTGTGGAATTGATGAACG 58.763 33.333 0.00 0.00 33.63 3.95
3867 6075 3.936772 TTCATGAACCCCAGCCCGC 62.937 63.158 3.38 0.00 0.00 6.13
4028 6236 2.267961 GACAAGTACCGGGCCCTG 59.732 66.667 22.43 17.38 0.00 4.45
4061 6269 2.100631 CATCGTGGACGTCAAGCCC 61.101 63.158 18.91 0.00 40.80 5.19
4321 6533 7.473593 AGGAATAATAGATGAGAAAATGGGGG 58.526 38.462 0.00 0.00 0.00 5.40
4458 7245 4.569162 TCAACAAGTAAAGACCACGTCAAG 59.431 41.667 0.00 0.00 34.60 3.02
4459 7246 4.395959 ACAAGTAAAGACCACGTCAAGA 57.604 40.909 0.00 0.00 34.60 3.02
4460 7247 4.761975 ACAAGTAAAGACCACGTCAAGAA 58.238 39.130 0.00 0.00 34.60 2.52
4511 7302 1.730064 CATTTTGTGCTGCCATCTTGC 59.270 47.619 0.00 0.00 0.00 4.01
4717 7508 3.141398 CTCCAGCTGCAGTTTCTTGTAA 58.859 45.455 16.64 0.00 0.00 2.41
4721 7512 4.531332 CAGCTGCAGTTTCTTGTAAGAAC 58.469 43.478 16.64 3.50 44.18 3.01
4798 7589 1.227943 CAGTCACACACACCCTGGG 60.228 63.158 12.28 12.28 0.00 4.45
4839 7630 0.666374 TATCGATGCCGTGTGACGAT 59.334 50.000 8.54 0.00 46.05 3.73
5001 7792 1.982395 ATTCTCGTCCTCGCACCCA 60.982 57.895 0.00 0.00 36.96 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.690283 CCTTCTGTCAGCATCGCGTG 61.690 60.000 5.77 5.06 0.00 5.34
41 42 1.446792 CCTTCTGTCAGCATCGCGT 60.447 57.895 5.77 0.00 0.00 6.01
42 43 1.153765 TCCTTCTGTCAGCATCGCG 60.154 57.895 0.00 0.00 0.00 5.87
43 44 1.086634 GGTCCTTCTGTCAGCATCGC 61.087 60.000 0.00 0.00 0.00 4.58
44 45 0.460987 GGGTCCTTCTGTCAGCATCG 60.461 60.000 0.00 0.00 0.00 3.84
45 46 0.460987 CGGGTCCTTCTGTCAGCATC 60.461 60.000 0.00 0.00 0.00 3.91
46 47 1.599047 CGGGTCCTTCTGTCAGCAT 59.401 57.895 0.00 0.00 0.00 3.79
47 48 2.583441 CCGGGTCCTTCTGTCAGCA 61.583 63.158 0.00 0.00 0.00 4.41
48 49 2.266055 CCGGGTCCTTCTGTCAGC 59.734 66.667 0.00 0.00 0.00 4.26
49 50 2.266055 GCCGGGTCCTTCTGTCAG 59.734 66.667 2.18 0.00 0.00 3.51
50 51 3.319198 GGCCGGGTCCTTCTGTCA 61.319 66.667 2.18 0.00 0.00 3.58
51 52 3.003763 AGGCCGGGTCCTTCTGTC 61.004 66.667 2.18 0.00 30.82 3.51
52 53 3.003763 GAGGCCGGGTCCTTCTGT 61.004 66.667 2.18 0.00 36.38 3.41
53 54 4.148825 CGAGGCCGGGTCCTTCTG 62.149 72.222 2.18 0.00 36.38 3.02
85 86 0.108329 GCCATAGTAGTGTGTGCCGT 60.108 55.000 0.00 0.00 0.00 5.68
170 172 0.468029 ATGACCATCCGATTTGCCCC 60.468 55.000 0.00 0.00 0.00 5.80
171 173 0.670162 CATGACCATCCGATTTGCCC 59.330 55.000 0.00 0.00 0.00 5.36
186 188 0.465705 GCTCCCTGACGATTCCATGA 59.534 55.000 0.00 0.00 0.00 3.07
188 190 1.967066 CTAGCTCCCTGACGATTCCAT 59.033 52.381 0.00 0.00 0.00 3.41
189 191 1.403814 CTAGCTCCCTGACGATTCCA 58.596 55.000 0.00 0.00 0.00 3.53
192 194 0.687757 TGGCTAGCTCCCTGACGATT 60.688 55.000 15.72 0.00 0.00 3.34
196 198 2.496817 CGTGGCTAGCTCCCTGAC 59.503 66.667 15.72 0.00 0.00 3.51
225 227 3.567478 ATCCGCGTCGTCTGTTGCA 62.567 57.895 4.92 0.00 0.00 4.08
275 277 1.262640 TACCCACTTTCCGAGAGCCC 61.263 60.000 0.00 0.00 0.00 5.19
316 318 7.252708 TCCATTCAACATTTTCGATCTCATTG 58.747 34.615 0.00 0.00 0.00 2.82
345 347 3.691342 CGGCCTTCGTGGAGGTCA 61.691 66.667 0.00 0.00 41.62 4.02
571 591 8.341903 TGATGTGTATATGCGTAAAATTTGAGG 58.658 33.333 0.00 0.00 0.00 3.86
574 594 8.833976 TGTGATGTGTATATGCGTAAAATTTG 57.166 30.769 0.00 0.00 0.00 2.32
663 683 4.778958 TCCATGAAGGCCAGAATTTTTGAT 59.221 37.500 5.01 0.00 37.29 2.57
696 716 8.072321 AGTCTCATTAGAGTAGAGCATTTTGA 57.928 34.615 0.00 0.00 42.66 2.69
878 898 1.407656 TTGGGTTGAGTCGAGCCTGT 61.408 55.000 25.57 0.00 36.45 4.00
1296 1316 4.329697 GCCGCGGACTCGATCGAT 62.330 66.667 33.48 8.99 39.00 3.59
1577 1597 4.796231 GCACGTCGCCATCCTCGT 62.796 66.667 0.00 0.00 36.99 4.18
1700 1720 6.924060 GGATGCTACGAAGAATTACACTATGT 59.076 38.462 0.00 0.00 0.00 2.29
1745 1773 4.769488 TGCATGCTAAACCATCCAAAGTTA 59.231 37.500 20.33 0.00 0.00 2.24
1996 2047 4.478206 TGCATATAATAGAGCTGAGCCC 57.522 45.455 0.00 0.00 0.00 5.19
2123 2174 1.066143 ACGGTGATTGGAAGGCACTAG 60.066 52.381 0.00 0.00 38.49 2.57
2256 2856 5.179452 AGTGCACAATAGGGATAGTTGTT 57.821 39.130 21.04 0.00 34.09 2.83
2324 2925 2.412605 GCATGGGAGCCAAGATGTC 58.587 57.895 0.00 0.00 36.95 3.06
2486 3133 3.507622 ACCACCACTTACGGACTTACTAC 59.492 47.826 0.00 0.00 0.00 2.73
2487 3134 3.766545 ACCACCACTTACGGACTTACTA 58.233 45.455 0.00 0.00 0.00 1.82
2488 3135 2.601905 ACCACCACTTACGGACTTACT 58.398 47.619 0.00 0.00 0.00 2.24
2596 3247 3.244630 CGGAGGGAGTATCTAGCAGTAGT 60.245 52.174 0.00 0.00 33.73 2.73
2598 3249 2.709934 ACGGAGGGAGTATCTAGCAGTA 59.290 50.000 0.00 0.00 33.73 2.74
2599 3250 1.495574 ACGGAGGGAGTATCTAGCAGT 59.504 52.381 0.00 0.00 33.73 4.40
2601 3252 1.202903 GGACGGAGGGAGTATCTAGCA 60.203 57.143 0.00 0.00 33.73 3.49
2603 3254 1.424302 TGGGACGGAGGGAGTATCTAG 59.576 57.143 0.00 0.00 33.73 2.43
2605 3256 0.635009 TTGGGACGGAGGGAGTATCT 59.365 55.000 0.00 0.00 33.73 1.98
2606 3257 1.492764 TTTGGGACGGAGGGAGTATC 58.507 55.000 0.00 0.00 0.00 2.24
2610 3261 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2612 3263 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2613 3264 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2614 3265 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
2615 3266 4.069304 CAAGACACTTATTTTGGGACGGA 58.931 43.478 0.00 0.00 0.00 4.69
2616 3267 4.069304 TCAAGACACTTATTTTGGGACGG 58.931 43.478 0.00 0.00 0.00 4.79
2617 3268 5.238650 AGTTCAAGACACTTATTTTGGGACG 59.761 40.000 0.00 0.00 0.00 4.79
2618 3269 6.635030 AGTTCAAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 0.00 4.46
2619 3270 7.996644 ACTAAGTTCAAGACACTTATTTTGGGA 59.003 33.333 0.00 0.00 36.39 4.37
2620 3271 8.166422 ACTAAGTTCAAGACACTTATTTTGGG 57.834 34.615 0.00 0.00 36.39 4.12
2654 3305 7.009723 GTCTCAATTTTGTACTAGCTCTAGTGC 59.990 40.741 17.32 16.27 45.25 4.40
2655 3306 8.029522 TGTCTCAATTTTGTACTAGCTCTAGTG 58.970 37.037 17.32 1.42 45.25 2.74
2657 3308 8.247562 AGTGTCTCAATTTTGTACTAGCTCTAG 58.752 37.037 0.00 2.55 39.04 2.43
2659 3310 6.998802 AGTGTCTCAATTTTGTACTAGCTCT 58.001 36.000 0.00 0.00 0.00 4.09
2660 3311 7.659652 AAGTGTCTCAATTTTGTACTAGCTC 57.340 36.000 0.00 0.00 0.00 4.09
2661 3312 9.726438 AATAAGTGTCTCAATTTTGTACTAGCT 57.274 29.630 0.00 0.00 0.00 3.32
2672 3323 8.842358 TCCGTCTTAAAATAAGTGTCTCAATT 57.158 30.769 0.00 0.00 0.00 2.32
2673 3324 7.549488 CCTCCGTCTTAAAATAAGTGTCTCAAT 59.451 37.037 0.00 0.00 0.00 2.57
2674 3325 6.872020 CCTCCGTCTTAAAATAAGTGTCTCAA 59.128 38.462 0.00 0.00 0.00 3.02
2675 3326 6.395629 CCTCCGTCTTAAAATAAGTGTCTCA 58.604 40.000 0.00 0.00 0.00 3.27
2676 3327 5.811100 CCCTCCGTCTTAAAATAAGTGTCTC 59.189 44.000 0.00 0.00 0.00 3.36
2679 3330 5.247792 ACTCCCTCCGTCTTAAAATAAGTGT 59.752 40.000 0.00 0.00 0.00 3.55
2680 3331 5.731591 ACTCCCTCCGTCTTAAAATAAGTG 58.268 41.667 0.00 0.00 0.00 3.16
2681 3332 7.486407 TTACTCCCTCCGTCTTAAAATAAGT 57.514 36.000 0.00 0.00 0.00 2.24
2684 3335 9.205513 ACTTATTACTCCCTCCGTCTTAAAATA 57.794 33.333 0.00 0.00 0.00 1.40
2686 3337 7.486407 ACTTATTACTCCCTCCGTCTTAAAA 57.514 36.000 0.00 0.00 0.00 1.52
2687 3338 8.593945 TTACTTATTACTCCCTCCGTCTTAAA 57.406 34.615 0.00 0.00 0.00 1.52
2689 3340 7.577303 TCTTACTTATTACTCCCTCCGTCTTA 58.423 38.462 0.00 0.00 0.00 2.10
2690 3341 6.430007 TCTTACTTATTACTCCCTCCGTCTT 58.570 40.000 0.00 0.00 0.00 3.01
2691 3342 6.011122 TCTTACTTATTACTCCCTCCGTCT 57.989 41.667 0.00 0.00 0.00 4.18
2692 3343 6.096001 TGTTCTTACTTATTACTCCCTCCGTC 59.904 42.308 0.00 0.00 0.00 4.79
2694 3345 6.461110 TGTTCTTACTTATTACTCCCTCCG 57.539 41.667 0.00 0.00 0.00 4.63
2695 3346 8.075761 TCTTGTTCTTACTTATTACTCCCTCC 57.924 38.462 0.00 0.00 0.00 4.30
2878 3529 9.469807 AGCTATCTCGTGACTAATATTTTCTTG 57.530 33.333 0.00 0.00 0.00 3.02
2987 3638 3.575256 ACACCAAACACGTATCACCTCTA 59.425 43.478 0.00 0.00 0.00 2.43
3090 5287 3.773117 GCAGTGCGCACTAAAATGT 57.227 47.368 40.17 16.72 40.20 2.71
3867 6075 0.313043 AGGAACGTGACGGTGTACAG 59.687 55.000 10.66 0.00 0.00 2.74
4061 6269 1.466167 AGCTAGCGTGCTTTGTTCATG 59.534 47.619 9.55 0.00 40.93 3.07
4194 6402 8.246430 TGGAGTACGTAATAATCAAAGAGGAT 57.754 34.615 0.00 0.00 28.99 3.24
4321 6533 2.286418 CGAGCACGAATAATTTCCTGCC 60.286 50.000 0.00 0.13 41.81 4.85
4322 6534 2.351726 ACGAGCACGAATAATTTCCTGC 59.648 45.455 11.40 2.71 41.43 4.85
4458 7245 9.474920 AAAACGATCTGATCTGATCTTATCTTC 57.525 33.333 29.14 11.46 40.32 2.87
4459 7246 9.474920 GAAAACGATCTGATCTGATCTTATCTT 57.525 33.333 29.14 18.49 40.32 2.40
4460 7247 8.859090 AGAAAACGATCTGATCTGATCTTATCT 58.141 33.333 29.14 23.94 40.32 1.98
4511 7302 0.875059 GTTCTGGCGGGACAAGAAAG 59.125 55.000 0.00 0.00 0.00 2.62
4717 7508 8.226819 TGTAAGATCTATCATCTTGTCGTTCT 57.773 34.615 0.00 0.00 38.66 3.01
4803 7594 6.403636 GCATCGATAAATTATTGGCCCAGTAG 60.404 42.308 0.00 0.00 0.00 2.57
4839 7630 2.567862 TCTTAATCCACCCATCCACCA 58.432 47.619 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.