Multiple sequence alignment - TraesCS1D01G054000

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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 TraesCS1D01G054000 chr1D 100.000 3735 0 0 1 3735 35062092 35058358 0.000000e+00 6898.0
1 TraesCS1D01G054000 chr1B 90.688 2631 102 66 18 2594 53366847 53364306 0.000000e+00 3369.0
2 TraesCS1D01G054000 chr1B 88.170 541 25 14 2614 3136 53364243 53363724 3.190000e-170 608.0
3 TraesCS1D01G054000 chr1B 90.625 416 38 1 3317 3731 53363434 53363019 5.450000e-153 551.0
4 TraesCS1D01G054000 chr1B 92.833 293 21 0 3175 3467 53363727 53363435 3.450000e-115 425.0
5 TraesCS1D01G054000 chr1B 81.188 101 16 3 5 103 301365576 301365477 1.110000e-10 78.7
6 TraesCS1D01G054000 chr1A 89.028 1677 70 44 797 2426 33399108 33397499 0.000000e+00 1973.0
7 TraesCS1D01G054000 chr1A 90.327 765 41 20 18 760 33400226 33399473 0.000000e+00 972.0
8 TraesCS1D01G054000 chr1A 85.490 765 71 11 2834 3589 33396206 33395473 0.000000e+00 761.0
9 TraesCS1D01G054000 chr1A 85.248 766 71 13 2834 3589 33391415 33390682 0.000000e+00 750.0
10 TraesCS1D01G054000 chr1A 85.246 244 17 6 2609 2849 33391682 33391455 2.240000e-57 233.0
11 TraesCS1D01G054000 chr1A 85.246 244 17 6 2609 2849 33396473 33396246 2.240000e-57 233.0
12 TraesCS1D01G054000 chr1A 87.374 198 5 9 2241 2426 33392896 33392707 3.780000e-50 209.0
13 TraesCS1D01G054000 chr1A 91.753 97 7 1 2498 2594 33391844 33391749 2.340000e-27 134.0
14 TraesCS1D01G054000 chr1A 91.753 97 7 1 2498 2594 33396636 33396541 2.340000e-27 134.0
15 TraesCS1D01G054000 chr1A 88.119 101 12 0 3630 3730 33395470 33395370 1.820000e-23 121.0
16 TraesCS1D01G054000 chr1A 87.129 101 13 0 3630 3730 33390679 33390579 8.480000e-22 115.0
17 TraesCS1D01G054000 chr1A 94.737 57 1 2 2446 2501 33392541 33392486 1.850000e-13 87.9
18 TraesCS1D01G054000 chr1A 94.737 57 1 2 2446 2501 33397333 33397278 1.850000e-13 87.9
19 TraesCS1D01G054000 chr5D 89.163 203 22 0 1204 1406 254023397 254023599 1.720000e-63 254.0
20 TraesCS1D01G054000 chr5A 89.163 203 22 0 1204 1406 336950088 336950290 1.720000e-63 254.0
21 TraesCS1D01G054000 chr5A 83.125 160 25 2 1227 1385 111588881 111589039 1.080000e-30 145.0
22 TraesCS1D01G054000 chr5B 88.670 203 23 0 1204 1406 288892889 288892687 8.010000e-62 248.0
23 TraesCS1D01G054000 chr2B 83.770 191 29 2 1200 1389 740321098 740320909 2.960000e-41 180.0
24 TraesCS1D01G054000 chr2B 85.714 91 12 1 2 91 693066111 693066201 1.100000e-15 95.3
25 TraesCS1D01G054000 chr2D 83.246 191 30 2 1200 1389 606709655 606709844 1.380000e-39 174.0
26 TraesCS1D01G054000 chr2D 87.755 49 6 0 3668 3716 8401577 8401625 1.450000e-04 58.4
27 TraesCS1D01G054000 chr2A 82.723 191 31 2 1200 1389 738372126 738372315 6.420000e-38 169.0
28 TraesCS1D01G054000 chr4D 84.091 88 13 1 5 91 29018140 29018053 2.390000e-12 84.2
29 TraesCS1D01G054000 chr3B 86.301 73 10 0 2 74 652479824 652479896 3.090000e-11 80.5
30 TraesCS1D01G054000 chr7A 86.765 68 9 0 5 72 696327894 696327961 4.000000e-10 76.8
31 TraesCS1D01G054000 chr3A 80.645 93 13 4 2 91 12925893 12925983 2.410000e-07 67.6
32 TraesCS1D01G054000 chr7B 80.282 71 12 2 5 74 749158335 749158266 7.000000e-03 52.8


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 TraesCS1D01G054000 chr1D 35058358 35062092 3734 True 6898.000000 6898 100.000000 1 3735 1 chr1D.!!$R1 3734
1 TraesCS1D01G054000 chr1B 53363019 53366847 3828 True 1238.250000 3369 90.579000 18 3731 4 chr1B.!!$R2 3713
2 TraesCS1D01G054000 chr1A 33390579 33400226 9647 True 446.984615 1973 88.937462 18 3730 13 chr1A.!!$R1 3712

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
232 257 0.681564 AAAGGCGTGGTGGTCACAAA 60.682 50.000 3.40 0.00 46.36 2.83 F
835 1194 1.079197 TCTACACACCCATGCGCTG 60.079 57.895 9.73 4.25 0.00 5.18 F
1849 2247 0.038166 GTGATTTCAGGGTGGAGGCA 59.962 55.000 0.00 0.00 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 2247 0.035881 TACTCCGGCGATCCTACGAT 59.964 55.0 9.3 0.0 35.09 3.73 R
2445 3021 0.108424 AGTACGACCTCGCTACGACT 60.108 55.0 0.0 0.0 44.43 4.18 R
3598 9790 0.036732 CTAGAAACCCTGTGGCAGCA 59.963 55.0 0.0 0.0 33.59 4.41 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
35 36 4.547532 ACTTCAGTGATTGTAGTCGTCAC 58.452 43.478 0.00 0.00 41.88 3.67
55 56 6.238759 CGTCACTAGATGGTCTATGAACATGA 60.239 42.308 0.00 0.00 40.37 3.07
61 62 6.873997 AGATGGTCTATGAACATGAACGTAA 58.126 36.000 0.00 0.00 40.37 3.18
99 114 8.689251 TTGTCTTCTTTGTACTGAATAGATCG 57.311 34.615 0.00 0.00 0.00 3.69
100 115 8.051901 TGTCTTCTTTGTACTGAATAGATCGA 57.948 34.615 0.00 0.00 0.00 3.59
110 126 6.301169 ACTGAATAGATCGAAGTTTTCCCT 57.699 37.500 0.00 0.00 0.00 4.20
112 128 6.819146 ACTGAATAGATCGAAGTTTTCCCTTC 59.181 38.462 0.00 0.00 37.96 3.46
122 138 5.462068 CGAAGTTTTCCCTTCATTTGTTTCC 59.538 40.000 0.00 0.00 40.72 3.13
123 139 4.944048 AGTTTTCCCTTCATTTGTTTCCG 58.056 39.130 0.00 0.00 0.00 4.30
124 140 4.647399 AGTTTTCCCTTCATTTGTTTCCGA 59.353 37.500 0.00 0.00 0.00 4.55
125 141 4.846779 TTTCCCTTCATTTGTTTCCGAG 57.153 40.909 0.00 0.00 0.00 4.63
126 142 2.790433 TCCCTTCATTTGTTTCCGAGG 58.210 47.619 0.00 0.00 0.00 4.63
127 143 1.818674 CCCTTCATTTGTTTCCGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
198 216 5.393027 GCTCTACTCTCAGTTCCTTCTCTTG 60.393 48.000 0.00 0.00 0.00 3.02
202 220 4.651503 ACTCTCAGTTCCTTCTCTTGAACA 59.348 41.667 5.32 0.00 42.57 3.18
210 228 5.186996 TCCTTCTCTTGAACATGCAAAAC 57.813 39.130 0.00 0.00 0.00 2.43
216 234 7.293402 TCTCTTGAACATGCAAAACAAAAAG 57.707 32.000 0.00 0.00 0.00 2.27
232 257 0.681564 AAAGGCGTGGTGGTCACAAA 60.682 50.000 3.40 0.00 46.36 2.83
243 268 2.808543 GTGGTCACAAACTCCTCACATC 59.191 50.000 0.00 0.00 0.00 3.06
244 269 2.437651 TGGTCACAAACTCCTCACATCA 59.562 45.455 0.00 0.00 0.00 3.07
325 350 2.353011 CGTGCATGCCTCTCCAATTTTT 60.353 45.455 16.68 0.00 0.00 1.94
456 481 3.599046 ACACGTAGTAGTAGCGTATGC 57.401 47.619 0.00 0.00 41.61 3.14
488 513 5.523552 CACTGACATGTATATTCCGCTTCAA 59.476 40.000 0.00 0.00 0.00 2.69
634 664 3.753797 GAGGAGACAGAACCAAAATGTCC 59.246 47.826 1.18 0.00 43.47 4.02
766 832 5.804473 CACACACACACACACACATTAATTT 59.196 36.000 0.00 0.00 0.00 1.82
834 1193 1.219124 CTCTACACACCCATGCGCT 59.781 57.895 9.73 0.00 0.00 5.92
835 1194 1.079197 TCTACACACCCATGCGCTG 60.079 57.895 9.73 4.25 0.00 5.18
873 1235 3.306088 CGTTCCCTCTCTAACACACACAT 60.306 47.826 0.00 0.00 0.00 3.21
874 1236 4.082408 CGTTCCCTCTCTAACACACACATA 60.082 45.833 0.00 0.00 0.00 2.29
875 1237 5.169295 GTTCCCTCTCTAACACACACATAC 58.831 45.833 0.00 0.00 0.00 2.39
876 1238 4.412843 TCCCTCTCTAACACACACATACA 58.587 43.478 0.00 0.00 0.00 2.29
877 1239 4.219944 TCCCTCTCTAACACACACATACAC 59.780 45.833 0.00 0.00 0.00 2.90
878 1240 4.220821 CCCTCTCTAACACACACATACACT 59.779 45.833 0.00 0.00 0.00 3.55
1058 1422 2.039613 CAGCAAACTCCCCTTCTCTTCT 59.960 50.000 0.00 0.00 0.00 2.85
1059 1423 2.304470 AGCAAACTCCCCTTCTCTTCTC 59.696 50.000 0.00 0.00 0.00 2.87
1060 1424 2.304470 GCAAACTCCCCTTCTCTTCTCT 59.696 50.000 0.00 0.00 0.00 3.10
1585 1958 2.184579 GGCTACGACCAGCACCTC 59.815 66.667 9.84 0.00 43.67 3.85
1619 1992 1.141019 CCAGCTTCCGCTTACGCTA 59.859 57.895 0.00 0.00 46.47 4.26
1797 2184 3.157932 AGCTACGTTCATCTTGAGCTC 57.842 47.619 6.82 6.82 35.38 4.09
1834 2231 6.438741 CCTGACCTCATATATACCACTGTGAT 59.561 42.308 9.86 0.00 0.00 3.06
1849 2247 0.038166 GTGATTTCAGGGTGGAGGCA 59.962 55.000 0.00 0.00 0.00 4.75
1851 2249 1.064463 TGATTTCAGGGTGGAGGCATC 60.064 52.381 0.00 0.00 0.00 3.91
2064 2462 1.068753 CGCGATCAAGGAGGAGCAT 59.931 57.895 0.00 0.00 0.00 3.79
2108 2513 3.056465 CCAACCTATAGCTAGCTACCAGC 60.056 52.174 26.41 0.00 42.84 4.85
2120 2525 2.799814 CTACCAGCAGCAGCAGCAGT 62.800 60.000 12.92 11.16 45.49 4.40
2121 2526 3.738246 CCAGCAGCAGCAGCAGTG 61.738 66.667 12.92 2.28 45.49 3.66
2192 2603 0.729116 GTACGTACGCAGGTAGAGCA 59.271 55.000 16.72 0.00 0.00 4.26
2193 2604 1.012086 TACGTACGCAGGTAGAGCAG 58.988 55.000 16.72 0.00 0.00 4.24
2194 2605 1.586564 CGTACGCAGGTAGAGCAGC 60.587 63.158 0.52 0.00 0.00 5.25
2195 2606 1.511305 GTACGCAGGTAGAGCAGCA 59.489 57.895 0.00 0.00 0.00 4.41
2196 2607 0.526524 GTACGCAGGTAGAGCAGCAG 60.527 60.000 0.00 0.00 0.00 4.24
2197 2608 2.284798 TACGCAGGTAGAGCAGCAGC 62.285 60.000 0.00 0.00 42.56 5.25
2198 2609 2.267006 GCAGGTAGAGCAGCAGCA 59.733 61.111 3.17 0.00 45.49 4.41
2199 2610 1.814586 GCAGGTAGAGCAGCAGCAG 60.815 63.158 3.17 0.00 45.49 4.24
2200 2611 1.814586 CAGGTAGAGCAGCAGCAGC 60.815 63.158 3.17 0.46 45.49 5.25
2227 2638 8.406172 GTACGTAGGAGTACTATCATACTAGC 57.594 42.308 0.00 0.00 42.58 3.42
2231 2642 8.249638 CGTAGGAGTACTATCATACTAGCAGTA 58.750 40.741 0.00 0.00 35.48 2.74
2279 2690 8.609478 TTTTTCGTTGATTATTAATCCGCTTC 57.391 30.769 12.71 0.78 37.09 3.86
2282 2693 6.046593 TCGTTGATTATTAATCCGCTTCAGT 58.953 36.000 12.71 0.00 37.09 3.41
2444 3020 3.621682 AGCCAAGGACTAGCTAGGTAT 57.378 47.619 24.35 3.74 34.38 2.73
2445 3021 4.743705 AGCCAAGGACTAGCTAGGTATA 57.256 45.455 24.35 0.00 34.38 1.47
2446 3022 4.668636 AGCCAAGGACTAGCTAGGTATAG 58.331 47.826 24.35 10.99 34.38 1.31
2447 3023 4.106663 AGCCAAGGACTAGCTAGGTATAGT 59.893 45.833 24.35 4.87 34.38 2.12
2448 3024 4.460034 GCCAAGGACTAGCTAGGTATAGTC 59.540 50.000 24.35 13.91 44.69 2.59
2532 3753 3.525268 TCGACATGCATCTTAGCTTCA 57.475 42.857 0.00 0.00 34.99 3.02
2571 3793 1.001974 GAAATGTTCCTTGTTGCCCCC 59.998 52.381 0.00 0.00 0.00 5.40
2591 3813 2.050144 CCACTAGTGCATGGGTATCCT 58.950 52.381 17.86 0.00 31.83 3.24
2594 3816 4.102524 CCACTAGTGCATGGGTATCCTAAA 59.897 45.833 17.86 0.00 31.83 1.85
2595 3817 5.397447 CCACTAGTGCATGGGTATCCTAAAA 60.397 44.000 17.86 0.00 31.83 1.52
2596 3818 6.119536 CACTAGTGCATGGGTATCCTAAAAA 58.880 40.000 10.54 0.00 0.00 1.94
2599 3821 4.949856 AGTGCATGGGTATCCTAAAAACAG 59.050 41.667 0.00 0.00 0.00 3.16
2600 3822 4.947388 GTGCATGGGTATCCTAAAAACAGA 59.053 41.667 0.00 0.00 0.00 3.41
2601 3823 4.947388 TGCATGGGTATCCTAAAAACAGAC 59.053 41.667 0.00 0.00 0.00 3.51
2602 3824 4.947388 GCATGGGTATCCTAAAAACAGACA 59.053 41.667 0.00 0.00 0.00 3.41
2603 3825 5.417580 GCATGGGTATCCTAAAAACAGACAA 59.582 40.000 0.00 0.00 0.00 3.18
2604 3826 6.404734 GCATGGGTATCCTAAAAACAGACAAG 60.405 42.308 0.00 0.00 0.00 3.16
2606 3828 5.222048 TGGGTATCCTAAAAACAGACAAGCT 60.222 40.000 0.00 0.00 0.00 3.74
2607 3829 5.354513 GGGTATCCTAAAAACAGACAAGCTC 59.645 44.000 0.00 0.00 0.00 4.09
2612 3895 7.346751 TCCTAAAAACAGACAAGCTCAAAAT 57.653 32.000 0.00 0.00 0.00 1.82
2626 3909 3.942115 GCTCAAAATTGGGGACTAGAGTC 59.058 47.826 0.00 0.75 44.04 3.36
2628 3911 3.835978 TCAAAATTGGGGACTAGAGTCGA 59.164 43.478 0.00 0.00 45.65 4.20
2640 3923 6.157211 GGACTAGAGTCGAATTCAAGTTTGA 58.843 40.000 6.22 0.00 45.65 2.69
2679 3965 8.507249 AGGTAAAAATGAGATTTGTTCGAGAAG 58.493 33.333 0.00 0.00 31.77 2.85
2727 4013 9.461312 TTCTGCCTCTGTGTGTAATTTAAATAT 57.539 29.630 0.01 0.00 0.00 1.28
2778 4064 4.532834 ACACCGCCTTAATTATTGATGGT 58.467 39.130 0.00 0.00 0.00 3.55
2786 4072 6.856426 GCCTTAATTATTGATGGTTTCGTAGC 59.144 38.462 0.00 0.00 0.00 3.58
2862 4210 2.142356 TTAACTGACATGGCATGGGG 57.858 50.000 29.49 20.10 33.60 4.96
2878 4227 4.680440 GCATGGGGCCAACATAAAACTAAG 60.680 45.833 4.39 0.00 36.11 2.18
2904 4255 3.609853 AGTTCAAACTGAGTGTGCAAGA 58.390 40.909 0.00 0.00 37.98 3.02
2954 4305 3.574074 CTGGTCCCCAGCCCAACAG 62.574 68.421 0.00 0.00 45.13 3.16
2987 4338 5.340403 CACACACACACAATCAAATCGAATC 59.660 40.000 0.00 0.00 0.00 2.52
3038 4390 8.773645 CGCAGATGGATTTACTCATGTAATTAA 58.226 33.333 0.00 0.00 38.31 1.40
3048 4400 4.947388 ACTCATGTAATTAACCAACGGCAT 59.053 37.500 0.00 0.00 0.00 4.40
3095 4447 4.666412 TTCCAAATGGACCCACATCTAA 57.334 40.909 0.54 0.00 45.39 2.10
3098 4450 4.955450 TCCAAATGGACCCACATCTAAATG 59.045 41.667 0.00 0.00 39.78 2.32
3143 4496 9.768215 AATCTACATATTTTCCCCTTTTTGAGA 57.232 29.630 0.00 0.00 0.00 3.27
3144 4497 9.768215 ATCTACATATTTTCCCCTTTTTGAGAA 57.232 29.630 0.00 0.00 0.00 2.87
3145 4498 9.594936 TCTACATATTTTCCCCTTTTTGAGAAA 57.405 29.630 0.00 0.00 0.00 2.52
3263 4662 2.150719 ATGTCGGTCAACCCCACCA 61.151 57.895 0.00 0.00 32.89 4.17
3300 4699 2.541466 CCCTTCTCAGTCCCACTAGTT 58.459 52.381 0.00 0.00 0.00 2.24
3345 4744 2.354103 CCCGCTCTTGATCTTCACTCAA 60.354 50.000 0.00 0.00 0.00 3.02
3361 4760 2.028567 ACTCAAGAGTTGCTCCAGCTAC 60.029 50.000 5.14 5.14 44.91 3.58
3396 9587 0.107410 ACAAGTTGTCCTTCGTGCCA 60.107 50.000 1.64 0.00 0.00 4.92
3428 9619 2.579201 CGATGGACCAAGACCGCT 59.421 61.111 0.00 0.00 0.00 5.52
3429 9620 1.813859 CGATGGACCAAGACCGCTA 59.186 57.895 0.00 0.00 0.00 4.26
3436 9627 0.324943 ACCAAGACCGCTACATGCTT 59.675 50.000 0.00 0.00 40.11 3.91
3449 9640 0.453282 CATGCTTGCCTTCAACGACG 60.453 55.000 0.00 0.00 0.00 5.12
3450 9641 0.602638 ATGCTTGCCTTCAACGACGA 60.603 50.000 0.00 0.00 0.00 4.20
3498 9689 0.325933 CCCAGTGCTCTCCAACATCA 59.674 55.000 0.00 0.00 0.00 3.07
3508 9699 2.644299 TCTCCAACATCACCCACTTCAT 59.356 45.455 0.00 0.00 0.00 2.57
3514 9705 2.108075 ACATCACCCACTTCATCACCAA 59.892 45.455 0.00 0.00 0.00 3.67
3535 9726 0.895530 TTTTTGTTTGGTGGTGCCGA 59.104 45.000 0.00 0.00 41.21 5.54
3572 9764 1.871080 CTTAGGTTCCTGCTATGCCG 58.129 55.000 1.12 0.00 0.00 5.69
3606 9798 1.339055 TGGTGTCTCTAATGCTGCCAC 60.339 52.381 0.00 0.00 0.00 5.01
3626 9818 1.455773 GGGTTTCTAGGGCATGGGC 60.456 63.158 0.00 0.00 40.13 5.36
3628 9820 0.466372 GGTTTCTAGGGCATGGGCTC 60.466 60.000 0.00 0.00 42.47 4.70
3671 9863 0.030908 GATAGAACTCCCCACTCGCG 59.969 60.000 0.00 0.00 0.00 5.87
3683 9875 0.734253 CACTCGCGAGGGCTATATGC 60.734 60.000 36.93 0.00 41.94 3.14
3684 9876 0.896019 ACTCGCGAGGGCTATATGCT 60.896 55.000 36.93 11.80 42.39 3.79
3731 9923 0.535335 CCTAAGGGCAACGTCTAGCA 59.465 55.000 9.36 0.00 37.60 3.49
3732 9924 1.066430 CCTAAGGGCAACGTCTAGCAA 60.066 52.381 9.36 0.00 37.60 3.91
3733 9925 2.271800 CTAAGGGCAACGTCTAGCAAG 58.728 52.381 9.36 0.00 37.60 4.01
3734 9926 0.955919 AAGGGCAACGTCTAGCAAGC 60.956 55.000 9.36 0.00 37.60 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.039074 CTGAAGTGAGCCGAAGACGT 60.039 55.000 0.00 0.00 37.88 4.34
1 2 0.039074 ACTGAAGTGAGCCGAAGACG 60.039 55.000 0.00 0.00 39.43 4.18
2 3 3.896317 ACTGAAGTGAGCCGAAGAC 57.104 52.632 0.00 0.00 0.00 3.01
12 13 4.383052 GTGACGACTACAATCACTGAAGTG 59.617 45.833 3.98 3.98 46.91 3.16
13 14 4.547532 GTGACGACTACAATCACTGAAGT 58.452 43.478 0.00 0.00 39.72 3.01
22 23 5.194432 AGACCATCTAGTGACGACTACAAT 58.806 41.667 0.00 0.00 33.21 2.71
28 29 5.066117 TGTTCATAGACCATCTAGTGACGAC 59.934 44.000 0.00 0.00 31.67 4.34
31 32 7.043961 TCATGTTCATAGACCATCTAGTGAC 57.956 40.000 0.00 0.00 31.67 3.67
35 36 6.507900 ACGTTCATGTTCATAGACCATCTAG 58.492 40.000 0.00 0.00 31.67 2.43
99 114 5.462068 CGGAAACAAATGAAGGGAAAACTTC 59.538 40.000 0.00 0.00 45.49 3.01
100 115 5.128008 TCGGAAACAAATGAAGGGAAAACTT 59.872 36.000 0.00 0.00 0.00 2.66
110 126 3.068873 CCAAACCCTCGGAAACAAATGAA 59.931 43.478 0.00 0.00 0.00 2.57
112 128 2.866065 GCCAAACCCTCGGAAACAAATG 60.866 50.000 0.00 0.00 0.00 2.32
122 138 2.368875 AGATACTATGGCCAAACCCTCG 59.631 50.000 10.96 0.00 37.83 4.63
123 139 3.648545 AGAGATACTATGGCCAAACCCTC 59.351 47.826 10.96 11.98 37.83 4.30
124 140 3.392616 CAGAGATACTATGGCCAAACCCT 59.607 47.826 10.96 2.04 37.83 4.34
125 141 3.391296 TCAGAGATACTATGGCCAAACCC 59.609 47.826 10.96 0.00 37.83 4.11
126 142 4.689612 TCAGAGATACTATGGCCAAACC 57.310 45.455 10.96 0.00 39.84 3.27
127 143 8.677148 TTTTATCAGAGATACTATGGCCAAAC 57.323 34.615 10.96 0.00 0.00 2.93
198 216 3.063316 ACGCCTTTTTGTTTTGCATGTTC 59.937 39.130 0.00 0.00 0.00 3.18
202 220 1.939255 CCACGCCTTTTTGTTTTGCAT 59.061 42.857 0.00 0.00 0.00 3.96
210 228 0.248866 GTGACCACCACGCCTTTTTG 60.249 55.000 0.00 0.00 35.86 2.44
232 257 0.107312 GGCTGCATGATGTGAGGAGT 60.107 55.000 0.50 0.00 0.00 3.85
243 268 1.735198 CGTGGCTTTTGGCTGCATG 60.735 57.895 0.50 0.00 46.20 4.06
244 269 1.252904 ATCGTGGCTTTTGGCTGCAT 61.253 50.000 0.50 0.00 46.20 3.96
325 350 5.983118 CGTATATGCTGTATGTGGAAGTTGA 59.017 40.000 0.00 0.00 0.00 3.18
456 481 3.520290 ATACATGTCAGTGGGTACGTG 57.480 47.619 0.00 2.04 38.35 4.49
506 531 4.860072 TCGCATGTGCTCTATAACACTAG 58.140 43.478 0.00 0.00 37.68 2.57
661 691 3.199891 GCCGGCCCGTTGTATGAC 61.200 66.667 18.11 0.00 0.00 3.06
834 1193 3.369681 GGAACGGTCTAGAGAGAGAGACA 60.370 52.174 0.00 0.00 43.28 3.41
835 1194 3.200483 GGAACGGTCTAGAGAGAGAGAC 58.800 54.545 0.00 0.00 41.19 3.36
873 1235 4.041075 AGAGAGAGTGAGTGAGTGAGTGTA 59.959 45.833 0.00 0.00 0.00 2.90
874 1236 3.146066 GAGAGAGTGAGTGAGTGAGTGT 58.854 50.000 0.00 0.00 0.00 3.55
875 1237 3.411446 AGAGAGAGTGAGTGAGTGAGTG 58.589 50.000 0.00 0.00 0.00 3.51
876 1238 3.327757 AGAGAGAGAGTGAGTGAGTGAGT 59.672 47.826 0.00 0.00 0.00 3.41
877 1239 3.935203 GAGAGAGAGAGTGAGTGAGTGAG 59.065 52.174 0.00 0.00 0.00 3.51
878 1240 3.582647 AGAGAGAGAGAGTGAGTGAGTGA 59.417 47.826 0.00 0.00 0.00 3.41
1058 1422 6.494952 AGGTGTACTAGGATGAAGAAGAAGA 58.505 40.000 0.00 0.00 0.00 2.87
1059 1423 6.783708 AGGTGTACTAGGATGAAGAAGAAG 57.216 41.667 0.00 0.00 0.00 2.85
1060 1424 7.554959 AAAGGTGTACTAGGATGAAGAAGAA 57.445 36.000 0.00 0.00 0.00 2.52
1225 1598 0.600518 CCAGGATCATCAGCTGCTCG 60.601 60.000 9.47 0.00 0.00 5.03
1538 1911 1.025812 CAGGAGGCGGAGTAGTACTG 58.974 60.000 7.76 0.00 0.00 2.74
1539 1912 0.752376 GCAGGAGGCGGAGTAGTACT 60.752 60.000 1.37 1.37 0.00 2.73
1540 1913 1.734748 GCAGGAGGCGGAGTAGTAC 59.265 63.158 0.00 0.00 0.00 2.73
1619 1992 4.394712 GGCGTACCCAGCAGCAGT 62.395 66.667 0.00 0.00 36.08 4.40
1690 2066 0.953960 GATGGAAGGACAACGGCGTT 60.954 55.000 21.19 21.19 0.00 4.84
1697 2073 1.444933 ACCTGGTGATGGAAGGACAA 58.555 50.000 0.00 0.00 34.97 3.18
1797 2184 2.219458 GAGGTCAGGTCATGCATGATG 58.781 52.381 30.89 24.82 40.21 3.07
1834 2231 1.299648 CGATGCCTCCACCCTGAAA 59.700 57.895 0.00 0.00 0.00 2.69
1849 2247 0.035881 TACTCCGGCGATCCTACGAT 59.964 55.000 9.30 0.00 35.09 3.73
1851 2249 0.883814 AGTACTCCGGCGATCCTACG 60.884 60.000 9.30 0.00 0.00 3.51
1994 2392 4.052229 AGAACAGCCCCGTCGTCG 62.052 66.667 0.00 0.00 0.00 5.12
1995 2393 2.432628 CAGAACAGCCCCGTCGTC 60.433 66.667 0.00 0.00 0.00 4.20
1996 2394 4.681978 GCAGAACAGCCCCGTCGT 62.682 66.667 0.00 0.00 0.00 4.34
2108 2513 3.420606 CGACCACTGCTGCTGCTG 61.421 66.667 18.66 18.66 42.70 4.41
2120 2525 2.530177 CTCTACGTACTACGACGACCA 58.470 52.381 15.49 0.00 46.05 4.02
2121 2526 1.256635 GCTCTACGTACTACGACGACC 59.743 57.143 15.49 0.00 46.05 4.79
2170 2581 2.778659 CTCTACCTGCGTACGTACAAC 58.221 52.381 24.50 16.16 0.00 3.32
2171 2582 1.131126 GCTCTACCTGCGTACGTACAA 59.869 52.381 24.50 11.63 0.00 2.41
2192 2603 0.965866 TCCTACGTACTGCTGCTGCT 60.966 55.000 17.00 0.00 40.48 4.24
2193 2604 0.526524 CTCCTACGTACTGCTGCTGC 60.527 60.000 8.89 8.89 40.20 5.25
2194 2605 0.811915 ACTCCTACGTACTGCTGCTG 59.188 55.000 4.89 4.89 0.00 4.41
2195 2606 2.015587 GTACTCCTACGTACTGCTGCT 58.984 52.381 0.00 0.00 37.39 4.24
2196 2607 2.015587 AGTACTCCTACGTACTGCTGC 58.984 52.381 3.08 0.00 46.08 5.25
2197 2608 5.055144 TGATAGTACTCCTACGTACTGCTG 58.945 45.833 12.45 0.00 46.91 4.41
2198 2609 5.287674 TGATAGTACTCCTACGTACTGCT 57.712 43.478 12.45 2.04 46.91 4.24
2199 2610 6.873076 AGTATGATAGTACTCCTACGTACTGC 59.127 42.308 12.45 6.43 46.91 4.40
2200 2611 9.571810 CTAGTATGATAGTACTCCTACGTACTG 57.428 40.741 20.72 13.21 46.91 2.74
2227 2638 8.141909 TCGATGGGAATTACTACAAAGATACTG 58.858 37.037 0.00 0.00 0.00 2.74
2231 2642 8.980481 AAATCGATGGGAATTACTACAAAGAT 57.020 30.769 0.00 0.00 0.00 2.40
2237 2648 7.242914 ACGAAAAATCGATGGGAATTACTAC 57.757 36.000 0.00 0.00 36.85 2.73
2238 2649 7.549842 TCAACGAAAAATCGATGGGAATTACTA 59.450 33.333 0.00 0.00 36.71 1.82
2239 2650 6.373216 TCAACGAAAAATCGATGGGAATTACT 59.627 34.615 0.00 0.00 36.71 2.24
2279 2690 5.982516 GCTGAAGATCATCAGGTACTAACTG 59.017 44.000 25.01 0.00 45.60 3.16
2427 2852 5.307204 ACGACTATACCTAGCTAGTCCTTG 58.693 45.833 19.31 6.23 40.38 3.61
2444 3020 1.135139 AGTACGACCTCGCTACGACTA 59.865 52.381 0.00 0.00 44.43 2.59
2445 3021 0.108424 AGTACGACCTCGCTACGACT 60.108 55.000 0.00 0.00 44.43 4.18
2446 3022 0.723981 AAGTACGACCTCGCTACGAC 59.276 55.000 0.00 0.00 44.43 4.34
2447 3023 1.927174 GTAAGTACGACCTCGCTACGA 59.073 52.381 0.00 0.00 44.43 3.43
2448 3024 2.359523 GTAAGTACGACCTCGCTACG 57.640 55.000 0.00 0.00 44.43 3.51
2532 3753 5.981088 TTTCATCCATGCATACACACTTT 57.019 34.783 0.00 0.00 0.00 2.66
2571 3793 2.050144 AGGATACCCATGCACTAGTGG 58.950 52.381 23.95 9.72 35.22 4.00
2572 3794 4.955811 TTAGGATACCCATGCACTAGTG 57.044 45.455 18.93 18.93 33.88 2.74
2573 3795 5.968676 TTTTAGGATACCCATGCACTAGT 57.031 39.130 0.00 0.00 33.88 2.57
2587 3809 6.959639 TTTGAGCTTGTCTGTTTTTAGGAT 57.040 33.333 0.00 0.00 0.00 3.24
2591 3813 6.760770 CCCAATTTTGAGCTTGTCTGTTTTTA 59.239 34.615 0.00 0.00 0.00 1.52
2594 3816 4.443315 CCCCAATTTTGAGCTTGTCTGTTT 60.443 41.667 0.00 0.00 0.00 2.83
2595 3817 3.070015 CCCCAATTTTGAGCTTGTCTGTT 59.930 43.478 0.00 0.00 0.00 3.16
2596 3818 2.629617 CCCCAATTTTGAGCTTGTCTGT 59.370 45.455 0.00 0.00 0.00 3.41
2599 3821 2.893489 AGTCCCCAATTTTGAGCTTGTC 59.107 45.455 0.00 0.00 0.00 3.18
2600 3822 2.962859 AGTCCCCAATTTTGAGCTTGT 58.037 42.857 0.00 0.00 0.00 3.16
2601 3823 4.335416 TCTAGTCCCCAATTTTGAGCTTG 58.665 43.478 0.00 0.00 0.00 4.01
2602 3824 4.043435 ACTCTAGTCCCCAATTTTGAGCTT 59.957 41.667 0.00 0.00 0.00 3.74
2603 3825 3.589288 ACTCTAGTCCCCAATTTTGAGCT 59.411 43.478 0.00 0.00 0.00 4.09
2604 3826 3.942115 GACTCTAGTCCCCAATTTTGAGC 59.058 47.826 0.00 0.00 39.07 4.26
2606 3828 3.835978 TCGACTCTAGTCCCCAATTTTGA 59.164 43.478 4.58 0.00 41.86 2.69
2607 3829 4.202245 TCGACTCTAGTCCCCAATTTTG 57.798 45.455 4.58 0.00 41.86 2.44
2612 3895 3.437213 TGAATTCGACTCTAGTCCCCAA 58.563 45.455 4.58 0.00 41.86 4.12
2626 3909 4.083537 TGAATCCGGTCAAACTTGAATTCG 60.084 41.667 0.00 6.94 39.21 3.34
2628 3911 4.022329 GGTGAATCCGGTCAAACTTGAATT 60.022 41.667 0.00 0.00 39.21 2.17
2640 3923 3.512219 TTTTACCTTGGTGAATCCGGT 57.488 42.857 0.00 0.00 39.52 5.28
2679 3965 8.861101 CAGAAAATCTCAAAATTGCTCTGAATC 58.139 33.333 0.00 0.00 34.42 2.52
2732 4018 9.575783 TGTTAAAAGCTAAAGAAAACGACATTT 57.424 25.926 0.00 0.00 0.00 2.32
2733 4019 9.016623 GTGTTAAAAGCTAAAGAAAACGACATT 57.983 29.630 0.00 0.00 0.00 2.71
2734 4020 7.646526 GGTGTTAAAAGCTAAAGAAAACGACAT 59.353 33.333 0.00 0.00 0.00 3.06
2736 4022 6.139638 CGGTGTTAAAAGCTAAAGAAAACGAC 59.860 38.462 0.00 0.00 0.00 4.34
2737 4023 6.193761 CGGTGTTAAAAGCTAAAGAAAACGA 58.806 36.000 0.00 0.00 0.00 3.85
2738 4024 5.108518 GCGGTGTTAAAAGCTAAAGAAAACG 60.109 40.000 0.00 0.00 0.00 3.60
2739 4025 5.174398 GGCGGTGTTAAAAGCTAAAGAAAAC 59.826 40.000 0.00 0.00 0.00 2.43
2740 4026 5.068067 AGGCGGTGTTAAAAGCTAAAGAAAA 59.932 36.000 0.00 0.00 0.00 2.29
2741 4027 4.581409 AGGCGGTGTTAAAAGCTAAAGAAA 59.419 37.500 0.00 0.00 0.00 2.52
2742 4028 4.139038 AGGCGGTGTTAAAAGCTAAAGAA 58.861 39.130 0.00 0.00 0.00 2.52
2743 4029 3.746940 AGGCGGTGTTAAAAGCTAAAGA 58.253 40.909 0.00 0.00 0.00 2.52
2744 4030 4.499037 AAGGCGGTGTTAAAAGCTAAAG 57.501 40.909 0.00 0.00 0.00 1.85
2745 4031 6.578163 ATTAAGGCGGTGTTAAAAGCTAAA 57.422 33.333 0.00 0.00 0.00 1.85
2746 4032 6.578163 AATTAAGGCGGTGTTAAAAGCTAA 57.422 33.333 0.00 0.00 0.00 3.09
2747 4033 7.868906 ATAATTAAGGCGGTGTTAAAAGCTA 57.131 32.000 0.00 0.00 0.00 3.32
2748 4034 6.769134 ATAATTAAGGCGGTGTTAAAAGCT 57.231 33.333 0.00 0.00 0.00 3.74
2749 4035 7.030768 TCAATAATTAAGGCGGTGTTAAAAGC 58.969 34.615 0.00 0.00 0.00 3.51
2750 4036 9.019764 CATCAATAATTAAGGCGGTGTTAAAAG 57.980 33.333 0.00 0.00 0.00 2.27
2756 4042 4.532834 ACCATCAATAATTAAGGCGGTGT 58.467 39.130 0.00 0.00 0.00 4.16
2778 4064 0.108992 CGCCACCAGTAGCTACGAAA 60.109 55.000 17.99 0.00 0.00 3.46
2862 4210 7.918562 TGAACTTGAACTTAGTTTTATGTTGGC 59.081 33.333 14.33 6.58 36.04 4.52
2870 4219 8.793592 ACTCAGTTTGAACTTGAACTTAGTTTT 58.206 29.630 0.00 0.00 37.14 2.43
2878 4227 4.098416 GCACACTCAGTTTGAACTTGAAC 58.902 43.478 0.00 0.00 37.08 3.18
2904 4255 3.369892 CGACAGGGAAGAACATTCTCCAT 60.370 47.826 0.00 0.00 36.28 3.41
2954 4305 1.269569 TGTGTGTGTGTGGTCGATCTC 60.270 52.381 0.00 0.00 0.00 2.75
2987 4338 1.695893 CTGCGCAGTGGTGGTTATCG 61.696 60.000 29.24 0.00 0.00 2.92
2990 4341 2.668212 GCTGCGCAGTGGTGGTTA 60.668 61.111 35.80 0.00 0.00 2.85
3008 4359 1.258982 GAGTAAATCCATCTGCGTGCG 59.741 52.381 0.00 0.00 0.00 5.34
3009 4360 2.279741 TGAGTAAATCCATCTGCGTGC 58.720 47.619 0.00 0.00 0.00 5.34
3010 4361 3.873361 ACATGAGTAAATCCATCTGCGTG 59.127 43.478 0.00 0.00 0.00 5.34
3011 4362 4.142609 ACATGAGTAAATCCATCTGCGT 57.857 40.909 0.00 0.00 0.00 5.24
3048 4400 2.280524 CACTCGTCGTTGGGCCAA 60.281 61.111 16.66 16.66 0.00 4.52
3119 4472 9.594936 TTTCTCAAAAAGGGGAAAATATGTAGA 57.405 29.630 0.00 0.00 0.00 2.59
3149 4502 9.530633 GGTATGTTCTTCTCGTTGTATTTAGAT 57.469 33.333 0.00 0.00 0.00 1.98
3150 4503 7.977853 GGGTATGTTCTTCTCGTTGTATTTAGA 59.022 37.037 0.00 0.00 0.00 2.10
3151 4504 7.980099 AGGGTATGTTCTTCTCGTTGTATTTAG 59.020 37.037 0.00 0.00 0.00 1.85
3152 4505 7.844009 AGGGTATGTTCTTCTCGTTGTATTTA 58.156 34.615 0.00 0.00 0.00 1.40
3153 4506 6.708285 AGGGTATGTTCTTCTCGTTGTATTT 58.292 36.000 0.00 0.00 0.00 1.40
3154 4507 6.295719 AGGGTATGTTCTTCTCGTTGTATT 57.704 37.500 0.00 0.00 0.00 1.89
3155 4508 5.163437 GGAGGGTATGTTCTTCTCGTTGTAT 60.163 44.000 0.00 0.00 0.00 2.29
3156 4509 4.159135 GGAGGGTATGTTCTTCTCGTTGTA 59.841 45.833 0.00 0.00 0.00 2.41
3157 4510 3.056035 GGAGGGTATGTTCTTCTCGTTGT 60.056 47.826 0.00 0.00 0.00 3.32
3158 4511 3.056107 TGGAGGGTATGTTCTTCTCGTTG 60.056 47.826 0.00 0.00 0.00 4.10
3159 4512 3.170717 TGGAGGGTATGTTCTTCTCGTT 58.829 45.455 0.00 0.00 0.00 3.85
3160 4513 2.816411 TGGAGGGTATGTTCTTCTCGT 58.184 47.619 0.00 0.00 0.00 4.18
3161 4514 3.133003 ACATGGAGGGTATGTTCTTCTCG 59.867 47.826 0.00 0.00 35.32 4.04
3162 4515 4.762289 ACATGGAGGGTATGTTCTTCTC 57.238 45.455 0.00 0.00 35.32 2.87
3163 4516 5.251700 AGAAACATGGAGGGTATGTTCTTCT 59.748 40.000 0.00 2.55 45.28 2.85
3164 4517 5.501156 AGAAACATGGAGGGTATGTTCTTC 58.499 41.667 0.00 0.54 45.28 2.87
3165 4518 5.520748 AGAAACATGGAGGGTATGTTCTT 57.479 39.130 0.00 0.00 45.28 2.52
3166 4519 5.520748 AAGAAACATGGAGGGTATGTTCT 57.479 39.130 0.00 1.92 45.28 3.01
3167 4520 6.590234 AAAAGAAACATGGAGGGTATGTTC 57.410 37.500 0.00 0.00 45.28 3.18
3169 4522 7.728532 AGTTAAAAAGAAACATGGAGGGTATGT 59.271 33.333 0.00 0.00 40.30 2.29
3170 4523 8.122472 AGTTAAAAAGAAACATGGAGGGTATG 57.878 34.615 0.00 0.00 0.00 2.39
3171 4524 8.721133 AAGTTAAAAAGAAACATGGAGGGTAT 57.279 30.769 0.00 0.00 0.00 2.73
3172 4525 8.417884 CAAAGTTAAAAAGAAACATGGAGGGTA 58.582 33.333 0.00 0.00 0.00 3.69
3173 4526 7.125053 TCAAAGTTAAAAAGAAACATGGAGGGT 59.875 33.333 0.00 0.00 0.00 4.34
3263 4662 2.555547 GGGACTTGCAGCAAACGCT 61.556 57.895 9.65 0.00 41.67 5.07
3300 4699 2.571757 GACATGGCGGAGTGACGA 59.428 61.111 0.00 0.00 35.47 4.20
3332 4731 4.562347 GGAGCAACTCTTGAGTGAAGATCA 60.562 45.833 3.87 0.00 40.06 2.92
3345 4744 1.893786 CGGTAGCTGGAGCAACTCT 59.106 57.895 0.00 0.00 45.16 3.24
3361 4760 2.997986 ACTTGTATTGTAACGGAAGCGG 59.002 45.455 0.00 0.00 0.00 5.52
3396 9587 3.329542 ATCGCCGACAGTGCCCATT 62.330 57.895 0.00 0.00 0.00 3.16
3428 9619 1.804151 GTCGTTGAAGGCAAGCATGTA 59.196 47.619 0.00 0.00 34.01 2.29
3429 9620 0.593128 GTCGTTGAAGGCAAGCATGT 59.407 50.000 0.00 0.00 34.01 3.21
3436 9627 0.103390 TGAAGTCGTCGTTGAAGGCA 59.897 50.000 0.00 0.00 0.00 4.75
3449 9640 4.429108 GGTATGAGCAGAGAGTTGAAGTC 58.571 47.826 0.00 0.00 0.00 3.01
3450 9641 3.119316 CGGTATGAGCAGAGAGTTGAAGT 60.119 47.826 0.00 0.00 0.00 3.01
3572 9764 3.933515 ACCACTGGTGTTGGTTGC 58.066 55.556 0.00 0.00 32.98 4.17
3593 9785 0.698238 AACCCTGTGGCAGCATTAGA 59.302 50.000 0.00 0.00 33.59 2.10
3598 9790 0.036732 CTAGAAACCCTGTGGCAGCA 59.963 55.000 0.00 0.00 33.59 4.41
3606 9798 0.106519 CCCATGCCCTAGAAACCCTG 60.107 60.000 0.00 0.00 0.00 4.45
3626 9818 0.737367 TGATTGACAAGCTCGGCGAG 60.737 55.000 31.40 31.40 0.00 5.03
3628 9820 2.161831 TTGATTGACAAGCTCGGCG 58.838 52.632 0.00 0.00 34.20 6.46
3636 9828 7.009179 AGTTCTATCAGTCCTTGATTGACAA 57.991 36.000 0.00 0.00 44.14 3.18
3683 9875 2.702592 TTAGGAATTGGTACGGGCAG 57.297 50.000 0.00 0.00 0.00 4.85
3684 9876 3.071892 CCTATTAGGAATTGGTACGGGCA 59.928 47.826 3.41 0.00 37.67 5.36


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

AutoCloner maintained by Alex Coulton.