Multiple sequence alignment - TraesCS5A01G467400

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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 TraesCS5A01G467400 chr5A 100.000 3474 0 0 815 4288 645260804 645264277 0.000000e+00 6416.0
1 TraesCS5A01G467400 chr5A 100.000 377 0 0 1 377 645259990 645260366 0.000000e+00 697.0
2 TraesCS5A01G467400 chr5A 95.000 160 8 0 2247 2406 645262156 645262315 7.120000e-63 252.0
3 TraesCS5A01G467400 chr5A 95.000 160 8 0 2167 2326 645262236 645262395 7.120000e-63 252.0
4 TraesCS5A01G467400 chr5A 89.062 128 14 0 2481 2608 315495850 315495977 4.440000e-35 159.0
5 TraesCS5A01G467400 chr5A 95.000 80 4 0 2327 2406 645262156 645262235 4.500000e-25 126.0
6 TraesCS5A01G467400 chr5A 95.000 80 4 0 2167 2246 645262316 645262395 4.500000e-25 126.0
7 TraesCS5A01G467400 chr5B 91.924 1585 71 31 2167 3714 650547385 650548949 0.000000e+00 2165.0
8 TraesCS5A01G467400 chr5B 93.079 838 45 4 1580 2406 650546718 650547553 0.000000e+00 1214.0
9 TraesCS5A01G467400 chr5B 93.248 785 47 5 815 1597 650545926 650546706 0.000000e+00 1151.0
10 TraesCS5A01G467400 chr5B 95.491 377 9 5 1 377 650545560 650545928 2.850000e-166 595.0
11 TraesCS5A01G467400 chr5B 87.865 445 32 12 3774 4206 650548948 650549382 1.780000e-138 503.0
12 TraesCS5A01G467400 chr5B 92.547 161 11 1 2167 2326 650547474 650547634 3.340000e-56 230.0
13 TraesCS5A01G467400 chr5B 91.124 169 6 1 2247 2406 650547305 650547473 2.010000e-53 220.0
14 TraesCS5A01G467400 chr5B 88.976 127 14 0 2482 2608 266005268 266005394 1.600000e-34 158.0
15 TraesCS5A01G467400 chr5B 100.000 79 0 0 2327 2405 650547305 650547383 3.460000e-31 147.0
16 TraesCS5A01G467400 chr5B 93.827 81 4 1 2167 2246 650547554 650547634 2.090000e-23 121.0
17 TraesCS5A01G467400 chr5B 100.000 34 0 0 3004 3037 162772805 162772772 3.580000e-06 63.9
18 TraesCS5A01G467400 chr5D 95.401 1196 44 7 815 2005 517840198 517841387 0.000000e+00 1893.0
19 TraesCS5A01G467400 chr5D 96.012 677 22 3 2327 3002 517841618 517842290 0.000000e+00 1096.0
20 TraesCS5A01G467400 chr5D 87.709 838 42 23 3172 3963 517842742 517843564 0.000000e+00 920.0
21 TraesCS5A01G467400 chr5D 95.225 377 10 3 1 377 517839832 517840200 1.330000e-164 590.0
22 TraesCS5A01G467400 chr5D 92.542 295 15 1 1959 2246 517841403 517841697 2.390000e-112 416.0
23 TraesCS5A01G467400 chr5D 94.340 159 6 1 3038 3196 517842567 517842722 1.540000e-59 241.0
24 TraesCS5A01G467400 chr5D 90.789 152 12 2 1090 1240 238712734 238712584 7.270000e-48 202.0
25 TraesCS5A01G467400 chr5D 91.837 147 5 1 3997 4136 517843567 517843713 9.410000e-47 198.0
26 TraesCS5A01G467400 chr5D 88.550 131 15 0 2481 2611 238711624 238711494 4.440000e-35 159.0
27 TraesCS5A01G467400 chr5D 92.500 80 6 0 2247 2326 517841618 517841697 9.740000e-22 115.0
28 TraesCS5A01G467400 chr5D 100.000 42 0 0 4247 4288 517843708 517843749 1.280000e-10 78.7
29 TraesCS5A01G467400 chr5D 100.000 34 0 0 3004 3037 127258334 127258301 3.580000e-06 63.9
30 TraesCS5A01G467400 chr3A 92.683 164 12 0 1081 1244 584276534 584276697 1.990000e-58 237.0
31 TraesCS5A01G467400 chr3D 92.073 164 13 0 1081 1244 443258969 443259132 9.270000e-57 231.0
32 TraesCS5A01G467400 chr3D 86.364 66 7 2 2988 3052 552290460 552290396 2.140000e-08 71.3
33 TraesCS5A01G467400 chr3B 91.463 164 14 0 1081 1244 581026438 581026601 4.310000e-55 226.0
34 TraesCS5A01G467400 chr3B 91.473 129 11 0 2482 2610 581029962 581030090 1.230000e-40 178.0
35 TraesCS5A01G467400 chr1D 91.463 164 14 0 1081 1244 403238768 403238605 4.310000e-55 226.0
36 TraesCS5A01G467400 chr1B 91.463 164 14 0 1081 1244 541469864 541469701 4.310000e-55 226.0
37 TraesCS5A01G467400 chr1B 87.500 48 4 2 3005 3052 170568816 170568771 2.000000e-03 54.7
38 TraesCS5A01G467400 chr1A 91.463 164 14 0 1081 1244 498454134 498453971 4.310000e-55 226.0
39 TraesCS5A01G467400 chr1A 100.000 35 0 0 3004 3038 576371108 576371074 9.950000e-07 65.8
40 TraesCS5A01G467400 chr2D 92.254 142 11 0 2473 2614 277680323 277680464 7.270000e-48 202.0
41 TraesCS5A01G467400 chr2D 95.000 40 1 1 3004 3043 380408313 380408275 1.290000e-05 62.1
42 TraesCS5A01G467400 chr2A 92.806 139 10 0 2476 2614 293936397 293936259 7.270000e-48 202.0
43 TraesCS5A01G467400 chr4B 97.297 37 1 0 3006 3042 807998 808034 3.580000e-06 63.9
44 TraesCS5A01G467400 chr4B 92.683 41 1 1 3004 3044 659147130 659147168 1.670000e-04 58.4
45 TraesCS5A01G467400 chr7D 87.500 48 4 2 3005 3051 474349089 474349043 2.000000e-03 54.7


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 TraesCS5A01G467400 chr5A 645259990 645264277 4287 False 1311.500000 6416 96.666667 1 4288 6 chr5A.!!$F2 4287
1 TraesCS5A01G467400 chr5B 650545560 650549382 3822 False 705.111111 2165 93.233889 1 4206 9 chr5B.!!$F2 4205
2 TraesCS5A01G467400 chr5D 517839832 517843749 3917 False 616.411111 1893 93.951778 1 4288 9 chr5D.!!$F1 4287
3 TraesCS5A01G467400 chr3B 581026438 581030090 3652 False 202.000000 226 91.468000 1081 2610 2 chr3B.!!$F1 1529

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
160 161 0.251634 CAAAGGCCACTCTCTCCCTC 59.748 60.0 5.01 0.0 0.0 4.30 F
1877 4738 0.025513 CGACTGCTTGCTTCGTATGC 59.974 55.0 8.36 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 4790 1.00243 TGGTCTAGCCTTTCAGCACAG 59.998 52.381 5.06 0.00 38.35 3.66 R
3720 7094 0.02811 GCAGGCGCTGTATAGTTTGC 59.972 55.000 7.64 0.26 33.43 3.68 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
159 160 1.846712 GCAAAGGCCACTCTCTCCCT 61.847 60.000 5.01 0.00 0.00 4.20
160 161 0.251634 CAAAGGCCACTCTCTCCCTC 59.748 60.000 5.01 0.00 0.00 4.30
161 162 0.912006 AAAGGCCACTCTCTCCCTCC 60.912 60.000 5.01 0.00 0.00 4.30
162 163 2.766229 GGCCACTCTCTCCCTCCC 60.766 72.222 0.00 0.00 0.00 4.30
163 164 2.766229 GCCACTCTCTCCCTCCCC 60.766 72.222 0.00 0.00 0.00 4.81
245 246 2.735100 GCGGATCGAGCGATTCCC 60.735 66.667 6.84 3.94 34.60 3.97
283 284 2.774351 CCTCCCTGGATCCACCCC 60.774 72.222 11.44 0.00 38.35 4.95
292 293 4.124126 ATCCACCCCCTCCCCCTC 62.124 72.222 0.00 0.00 0.00 4.30
342 343 1.360551 CATTCGCGAGATCCGTCCT 59.639 57.895 9.59 0.00 41.60 3.85
831 832 4.610844 CGGTTCGGTAGATCTCGC 57.389 61.111 0.00 0.00 0.00 5.03
1035 1036 1.887707 GCGTGGGGATCGTGATTCC 60.888 63.158 0.00 0.00 35.63 3.01
1478 3439 9.660180 AGTAGTTTTTGTTCATTAGGATCTCTC 57.340 33.333 0.00 0.00 0.00 3.20
1492 3453 3.655810 CTCTCTGCAGGTCACGGGC 62.656 68.421 15.13 0.00 0.00 6.13
1503 3464 4.301505 CACGGGCAGTGCACTTAT 57.698 55.556 18.94 0.00 44.72 1.73
1504 3465 1.796151 CACGGGCAGTGCACTTATG 59.204 57.895 18.94 8.58 44.72 1.90
1546 3507 3.909430 TGACATAACGACAGACAAGTCC 58.091 45.455 0.00 0.00 35.07 3.85
1578 3539 4.679654 CCGGTTGTTGCATTTCTTTCTTAC 59.320 41.667 0.00 0.00 0.00 2.34
1613 3603 2.393271 AGAAAATCGGTCCTGAGCTG 57.607 50.000 0.00 0.00 0.00 4.24
1788 4649 6.442513 AGCATCCAGTGAGTAATTAAAAGC 57.557 37.500 0.00 0.00 0.00 3.51
1801 4662 6.778559 AGTAATTAAAAGCCCACTACAACCAA 59.221 34.615 0.00 0.00 0.00 3.67
1877 4738 0.025513 CGACTGCTTGCTTCGTATGC 59.974 55.000 8.36 0.00 0.00 3.14
1936 4797 3.504863 GTGCATTTTATGGACTGTGCTG 58.495 45.455 0.00 0.00 46.53 4.41
1943 4804 0.403271 ATGGACTGTGCTGAAAGGCT 59.597 50.000 0.00 0.00 0.00 4.58
1956 4817 4.187694 CTGAAAGGCTAGACCATCTTGTC 58.812 47.826 0.00 0.00 43.14 3.18
2014 4937 9.139734 AGATATGGACATTTGTTAATCTGCAAT 57.860 29.630 0.00 0.00 0.00 3.56
2026 4949 7.977904 TGTTAATCTGCAATACATGTTCTCTG 58.022 34.615 2.30 0.00 0.00 3.35
2027 4950 7.607607 TGTTAATCTGCAATACATGTTCTCTGT 59.392 33.333 2.30 0.00 0.00 3.41
2202 5133 6.699575 AGTACCTGCAATGTATGATTTTCC 57.300 37.500 0.00 0.00 0.00 3.13
2215 5146 7.619965 TGTATGATTTTCCAGTATCTCACACA 58.380 34.615 0.00 0.00 0.00 3.72
2282 5302 5.611374 AGTACCTGCAATGTATGATGTACC 58.389 41.667 0.00 0.00 33.15 3.34
2286 5306 4.274214 CCTGCAATGTATGATGTACCAGTG 59.726 45.833 0.00 0.00 0.00 3.66
2291 5311 4.632538 TGTATGATGTACCAGTGTCTCG 57.367 45.455 0.00 0.00 0.00 4.04
2311 5331 7.979537 TGTCTCGCACATAATTTCTAATACACT 59.020 33.333 0.00 0.00 0.00 3.55
2440 5461 2.084610 TCTCTGGATTTGTCACGCAG 57.915 50.000 0.00 0.00 0.00 5.18
2628 5668 6.366877 TGAGGTAAATTCTTACACTACGCAAC 59.633 38.462 0.00 0.00 39.43 4.17
2652 5693 3.758554 GTCCCATCTGCATTACTTGTTGT 59.241 43.478 0.00 0.00 0.00 3.32
2686 5727 2.159920 CGATTTCGAGTGCTCACAGTTG 60.160 50.000 2.63 0.00 43.02 3.16
2699 5740 4.122046 CTCACAGTTGACATGTTCACTGA 58.878 43.478 30.65 16.90 37.08 3.41
2864 5905 4.787551 TCCCTTGCTTGTCTTTTCTGTAA 58.212 39.130 0.00 0.00 0.00 2.41
2895 5936 8.563732 AGATATATATGATCGTCATCCTTGTCG 58.436 37.037 0.00 0.00 38.26 4.35
2912 5953 5.354234 CCTTGTCGTTATAACTGGCTCATTT 59.646 40.000 13.56 0.00 0.00 2.32
2913 5954 5.794687 TGTCGTTATAACTGGCTCATTTG 57.205 39.130 13.56 0.00 0.00 2.32
2929 5970 2.088104 TTTGCCCCAACCAACACATA 57.912 45.000 0.00 0.00 0.00 2.29
2930 5971 2.317371 TTGCCCCAACCAACACATAT 57.683 45.000 0.00 0.00 0.00 1.78
2931 5972 3.458044 TTGCCCCAACCAACACATATA 57.542 42.857 0.00 0.00 0.00 0.86
2998 6039 3.264104 CCCTTTGGCTTTGTAATGCATG 58.736 45.455 0.00 0.00 0.00 4.06
3002 6043 3.316071 TGGCTTTGTAATGCATGTTGG 57.684 42.857 0.00 0.00 0.00 3.77
3004 6045 2.995258 GGCTTTGTAATGCATGTTGGTG 59.005 45.455 0.00 0.00 0.00 4.17
3005 6046 2.412770 GCTTTGTAATGCATGTTGGTGC 59.587 45.455 0.00 0.00 45.25 5.01
3006 6047 3.861886 GCTTTGTAATGCATGTTGGTGCT 60.862 43.478 0.00 0.00 45.27 4.40
3007 6048 3.574284 TTGTAATGCATGTTGGTGCTC 57.426 42.857 0.00 0.00 45.27 4.26
3009 6050 3.156293 TGTAATGCATGTTGGTGCTCTT 58.844 40.909 0.00 0.00 45.27 2.85
3012 6053 6.118852 TGTAATGCATGTTGGTGCTCTTATA 58.881 36.000 0.00 0.00 45.27 0.98
3013 6054 6.772233 TGTAATGCATGTTGGTGCTCTTATAT 59.228 34.615 0.00 0.00 45.27 0.86
3014 6055 6.720112 AATGCATGTTGGTGCTCTTATATT 57.280 33.333 0.00 0.00 45.27 1.28
3017 6058 5.887598 TGCATGTTGGTGCTCTTATATTTCT 59.112 36.000 0.00 0.00 45.27 2.52
3018 6059 6.377996 TGCATGTTGGTGCTCTTATATTTCTT 59.622 34.615 0.00 0.00 45.27 2.52
3020 6061 8.405531 GCATGTTGGTGCTCTTATATTTCTTTA 58.594 33.333 0.00 0.00 41.82 1.85
3021 6062 9.722056 CATGTTGGTGCTCTTATATTTCTTTAC 57.278 33.333 0.00 0.00 0.00 2.01
3023 6064 7.065324 TGTTGGTGCTCTTATATTTCTTTACGG 59.935 37.037 0.00 0.00 0.00 4.02
3025 6066 6.984474 TGGTGCTCTTATATTTCTTTACGGAG 59.016 38.462 0.00 0.00 0.00 4.63
3027 6068 6.424207 GTGCTCTTATATTTCTTTACGGAGGG 59.576 42.308 0.00 0.00 0.00 4.30
3028 6069 6.325545 TGCTCTTATATTTCTTTACGGAGGGA 59.674 38.462 0.00 0.00 0.00 4.20
3029 6070 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
3030 6071 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
3032 6073 9.425248 TCTTATATTTCTTTACGGAGGGAGTAA 57.575 33.333 0.00 0.00 32.84 2.24
3163 6445 2.315925 TGCATAGGCTTTCCTTCTCG 57.684 50.000 0.00 0.00 40.66 4.04
3164 6446 1.134401 TGCATAGGCTTTCCTTCTCGG 60.134 52.381 0.00 0.00 40.66 4.63
3165 6447 1.134371 GCATAGGCTTTCCTTCTCGGT 60.134 52.381 0.00 0.00 40.66 4.69
3217 6546 4.120244 ACGCAGTCTCCCATCTGT 57.880 55.556 0.00 0.00 29.74 3.41
3268 6597 6.477688 GTCAGTTCATTAATGCCATCCATTTG 59.522 38.462 10.76 0.15 41.29 2.32
3269 6598 6.380560 TCAGTTCATTAATGCCATCCATTTGA 59.619 34.615 10.76 2.23 41.29 2.69
3271 6600 7.237920 GTTCATTAATGCCATCCATTTGAAC 57.762 36.000 10.76 13.39 45.15 3.18
3272 6601 5.590145 TCATTAATGCCATCCATTTGAACG 58.410 37.500 10.76 0.00 41.29 3.95
3273 6602 2.298411 AATGCCATCCATTTGAACGC 57.702 45.000 0.00 0.00 41.29 4.84
3274 6603 1.184431 ATGCCATCCATTTGAACGCA 58.816 45.000 0.00 0.00 36.05 5.24
3282 6614 0.780002 CATTTGAACGCACTTGCAGC 59.220 50.000 1.48 0.00 42.21 5.25
3496 6829 5.116180 TGTATTCGAGCCCTAAGATGTTTG 58.884 41.667 0.00 0.00 0.00 2.93
3615 6959 6.216569 TCCACTTTTATTTGCGCATTTGTTA 58.783 32.000 12.75 0.00 0.00 2.41
3623 6967 1.466950 TGCGCATTTGTTAGTAGCACC 59.533 47.619 5.66 0.00 0.00 5.01
3720 7094 0.390472 GAGAAGGTCCCTTGTGCGAG 60.390 60.000 2.65 0.00 36.26 5.03
3762 7144 1.303236 CATTGCGACACCCAAGGGA 60.303 57.895 13.15 0.00 38.96 4.20
3766 7148 2.700773 GCGACACCCAAGGGATTGC 61.701 63.158 13.15 10.95 38.96 3.56
3781 7163 3.119101 GGGATTGCTCTCTGTTAAGTCGA 60.119 47.826 0.00 0.00 0.00 4.20
3796 7178 9.355215 CTGTTAAGTCGACATACAAAGTTATCT 57.645 33.333 19.50 0.00 0.00 1.98
3801 7183 6.973474 AGTCGACATACAAAGTTATCTACAGC 59.027 38.462 19.50 0.00 0.00 4.40
3859 7241 1.149101 AAAAGAACTGCCCAGGGAGA 58.851 50.000 10.89 0.00 37.03 3.71
3865 7247 0.105246 ACTGCCCAGGGAGAGATAGG 60.105 60.000 10.89 0.00 37.03 2.57
3899 7281 0.462047 GGCGAAACATCATCCCTCGT 60.462 55.000 0.00 0.00 32.23 4.18
3903 7285 2.858344 CGAAACATCATCCCTCGTGTAC 59.142 50.000 0.00 0.00 0.00 2.90
3934 7316 4.308458 CGGCGGTGTGGAAGTGGA 62.308 66.667 0.00 0.00 0.00 4.02
3936 7318 2.258726 GGCGGTGTGGAAGTGGAAC 61.259 63.158 0.00 0.00 0.00 3.62
4010 7395 1.906574 ACCTGAATAACTTGCCGGAGA 59.093 47.619 5.05 0.00 0.00 3.71
4049 7434 0.737219 CTGCCTGTTAATGGAGCTGC 59.263 55.000 0.00 0.00 0.00 5.25
4066 7451 1.739562 GCTGGACTGAGCGGAACAG 60.740 63.158 0.00 0.00 40.68 3.16
4149 7549 5.209818 TGGTCGGAATTATACTCATCACC 57.790 43.478 0.00 0.00 0.00 4.02
4162 7563 4.666512 ACTCATCACCTAGCCAAACAAAT 58.333 39.130 0.00 0.00 0.00 2.32
4163 7564 5.079643 ACTCATCACCTAGCCAAACAAATT 58.920 37.500 0.00 0.00 0.00 1.82
4206 7607 0.962356 GCCACAACCAGAGGTGATGG 60.962 60.000 12.42 12.42 41.68 3.51
4207 7608 0.322816 CCACAACCAGAGGTGATGGG 60.323 60.000 9.91 0.00 42.48 4.00
4208 7609 0.322816 CACAACCAGAGGTGATGGGG 60.323 60.000 0.00 0.00 42.48 4.96
4209 7610 1.379044 CAACCAGAGGTGATGGGGC 60.379 63.158 0.00 0.00 42.48 5.80
4210 7611 2.616458 AACCAGAGGTGATGGGGCC 61.616 63.158 0.00 0.00 42.48 5.80
4211 7612 2.693864 CCAGAGGTGATGGGGCCT 60.694 66.667 0.84 0.00 37.91 5.19
4212 7613 2.593978 CAGAGGTGATGGGGCCTG 59.406 66.667 0.84 0.00 34.81 4.85
4213 7614 2.693864 AGAGGTGATGGGGCCTGG 60.694 66.667 0.84 0.00 34.81 4.45
4214 7615 3.813724 GAGGTGATGGGGCCTGGG 61.814 72.222 0.84 0.00 34.81 4.45
4217 7618 4.828296 GTGATGGGGCCTGGGCAG 62.828 72.222 22.68 0.00 44.11 4.85
4233 7634 2.362120 AGCATTGCTGGGGTCTGC 60.362 61.111 11.09 0.00 37.57 4.26
4234 7635 3.455469 GCATTGCTGGGGTCTGCC 61.455 66.667 0.16 0.00 37.08 4.85
4235 7636 2.357836 CATTGCTGGGGTCTGCCT 59.642 61.111 0.00 0.00 37.08 4.75
4236 7637 1.304713 CATTGCTGGGGTCTGCCTT 60.305 57.895 0.00 0.00 37.08 4.35
4237 7638 0.901580 CATTGCTGGGGTCTGCCTTT 60.902 55.000 0.00 0.00 37.08 3.11
4238 7639 0.178924 ATTGCTGGGGTCTGCCTTTT 60.179 50.000 0.00 0.00 37.08 2.27
4239 7640 0.398381 TTGCTGGGGTCTGCCTTTTT 60.398 50.000 0.00 0.00 37.08 1.94
4240 7641 1.114722 TGCTGGGGTCTGCCTTTTTG 61.115 55.000 0.00 0.00 37.08 2.44
4241 7642 1.667722 CTGGGGTCTGCCTTTTTGC 59.332 57.895 0.00 0.00 34.45 3.68
4242 7643 1.075674 TGGGGTCTGCCTTTTTGCA 60.076 52.632 0.00 0.00 39.37 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 0.912006 GGAGGGAGAGAGTGGCCTTT 60.912 60.000 3.32 0.00 0.00 3.11
143 144 1.306568 GGAGGGAGAGAGTGGCCTT 60.307 63.158 3.32 0.00 0.00 4.35
161 162 2.440430 TCGCGAGAGAGAAGGGGG 60.440 66.667 3.71 0.00 36.84 5.40
162 163 2.776913 GGTCGCGAGAGAGAAGGGG 61.777 68.421 10.24 0.00 42.92 4.79
163 164 1.720694 GAGGTCGCGAGAGAGAAGGG 61.721 65.000 10.24 0.00 42.92 3.95
292 293 3.023735 CAAAGGGGAGGGAGGGGG 61.024 72.222 0.00 0.00 0.00 5.40
293 294 3.744155 GCAAAGGGGAGGGAGGGG 61.744 72.222 0.00 0.00 0.00 4.79
342 343 1.080366 CGTGATCCACCGACGGAAA 60.080 57.895 23.38 5.43 38.95 3.13
831 832 0.541296 GGAATGGCCATGGATCCCTG 60.541 60.000 21.63 9.92 36.34 4.45
1035 1036 3.114616 CGCCTCTCCTGCAACACG 61.115 66.667 0.00 0.00 0.00 4.49
1264 1265 8.393259 TGGTATGAATAAATAGGCAGGAATCAT 58.607 33.333 0.00 0.00 0.00 2.45
1269 1270 7.149202 ACTTGGTATGAATAAATAGGCAGGA 57.851 36.000 0.00 0.00 0.00 3.86
1452 3413 9.660180 GAGAGATCCTAATGAACAAAAACTACT 57.340 33.333 0.00 0.00 0.00 2.57
1503 3464 7.345392 TGTCAATATATATCCCTATGAGCAGCA 59.655 37.037 0.00 0.00 0.00 4.41
1504 3465 7.730084 TGTCAATATATATCCCTATGAGCAGC 58.270 38.462 0.00 0.00 0.00 5.25
1578 3539 8.392612 ACCGATTTTCTTACGTTTATATGGTTG 58.607 33.333 0.00 0.00 0.00 3.77
1591 3581 3.619038 CAGCTCAGGACCGATTTTCTTAC 59.381 47.826 0.00 0.00 0.00 2.34
1613 3603 1.468914 GAACTTCGCCAAAGGACATCC 59.531 52.381 0.00 0.00 39.47 3.51
1788 4649 3.369157 GGTAGCTAGTTGGTTGTAGTGGG 60.369 52.174 0.00 0.00 0.00 4.61
1801 4662 6.546772 GTGTACTTTGAGATAGGGTAGCTAGT 59.453 42.308 0.00 0.00 0.00 2.57
1877 4738 7.235935 ACTGGCAAATAATATCATCCAATGG 57.764 36.000 0.00 0.00 0.00 3.16
1913 4774 3.765511 AGCACAGTCCATAAAATGCACAT 59.234 39.130 0.00 0.00 35.51 3.21
1929 4790 1.002430 TGGTCTAGCCTTTCAGCACAG 59.998 52.381 5.06 0.00 38.35 3.66
1936 4797 3.198853 AGGACAAGATGGTCTAGCCTTTC 59.801 47.826 5.06 2.99 37.91 2.62
1943 4804 4.019411 TGCATGAAAGGACAAGATGGTCTA 60.019 41.667 0.00 0.00 37.91 2.59
1981 4842 8.958119 TTAACAAATGTCCATATCTGACCTAC 57.042 34.615 0.63 0.00 31.60 3.18
1992 4853 8.065473 TGTATTGCAGATTAACAAATGTCCAT 57.935 30.769 0.00 0.00 0.00 3.41
2014 4937 7.857734 TTGAGAAAAACACAGAGAACATGTA 57.142 32.000 0.00 0.00 0.00 2.29
2026 4949 8.479313 AGGAAAGACAATTTTGAGAAAAACAC 57.521 30.769 0.00 0.00 33.47 3.32
2027 4950 7.763985 GGAGGAAAGACAATTTTGAGAAAAACA 59.236 33.333 0.00 0.00 33.47 2.83
2149 5073 1.603456 TTCAGTTTCAAGGCGCATCA 58.397 45.000 10.83 0.00 0.00 3.07
2150 5074 2.919229 CAATTCAGTTTCAAGGCGCATC 59.081 45.455 10.83 0.00 0.00 3.91
2245 5176 9.301153 CATTGCAGGTACTATAAAAACAATTCC 57.699 33.333 0.00 0.00 36.02 3.01
2286 5306 8.354011 AGTGTATTAGAAATTATGTGCGAGAC 57.646 34.615 0.00 0.00 0.00 3.36
2628 5668 1.942657 CAAGTAATGCAGATGGGACCG 59.057 52.381 0.00 0.00 0.00 4.79
2652 5693 6.436261 CACTCGAAATCGCTAGGATAAAGTA 58.564 40.000 0.00 0.00 39.60 2.24
2686 5727 3.076621 TCCTGCAATCAGTGAACATGTC 58.923 45.455 0.00 0.00 38.66 3.06
2699 5740 3.610040 TCACGTAACTCATCCTGCAAT 57.390 42.857 0.00 0.00 0.00 3.56
2912 5953 3.458044 TTATATGTGTTGGTTGGGGCA 57.542 42.857 0.00 0.00 0.00 5.36
2913 5954 6.664428 ATTATTATATGTGTTGGTTGGGGC 57.336 37.500 0.00 0.00 0.00 5.80
2946 5987 9.472361 AGATCAATTTCATTTTCTTCACACAAG 57.528 29.630 0.00 0.00 0.00 3.16
2998 6039 7.279313 TCCGTAAAGAAATATAAGAGCACCAAC 59.721 37.037 0.00 0.00 0.00 3.77
3002 6043 6.424207 CCCTCCGTAAAGAAATATAAGAGCAC 59.576 42.308 0.00 0.00 0.00 4.40
3004 6045 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
3005 6046 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3006 6047 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3012 6053 9.916360 AATTTATTACTCCCTCCGTAAAGAAAT 57.084 29.630 0.00 0.00 33.06 2.17
3013 6054 9.169592 CAATTTATTACTCCCTCCGTAAAGAAA 57.830 33.333 0.00 0.00 31.36 2.52
3014 6055 8.323567 ACAATTTATTACTCCCTCCGTAAAGAA 58.676 33.333 0.00 0.00 31.36 2.52
3017 6058 7.884354 ACAACAATTTATTACTCCCTCCGTAAA 59.116 33.333 0.00 0.00 31.36 2.01
3018 6059 7.396418 ACAACAATTTATTACTCCCTCCGTAA 58.604 34.615 0.00 0.00 0.00 3.18
3020 6061 5.812286 ACAACAATTTATTACTCCCTCCGT 58.188 37.500 0.00 0.00 0.00 4.69
3021 6062 6.150474 ACAACAACAATTTATTACTCCCTCCG 59.850 38.462 0.00 0.00 0.00 4.63
3023 6064 8.357402 ACAACAACAACAATTTATTACTCCCTC 58.643 33.333 0.00 0.00 0.00 4.30
3025 6066 8.760569 CAACAACAACAACAATTTATTACTCCC 58.239 33.333 0.00 0.00 0.00 4.30
3027 6068 9.030301 AGCAACAACAACAACAATTTATTACTC 57.970 29.630 0.00 0.00 0.00 2.59
3028 6069 8.940768 AGCAACAACAACAACAATTTATTACT 57.059 26.923 0.00 0.00 0.00 2.24
3029 6070 9.419737 CAAGCAACAACAACAACAATTTATTAC 57.580 29.630 0.00 0.00 0.00 1.89
3030 6071 8.119226 GCAAGCAACAACAACAACAATTTATTA 58.881 29.630 0.00 0.00 0.00 0.98
3032 6073 6.093219 TGCAAGCAACAACAACAACAATTTAT 59.907 30.769 0.00 0.00 0.00 1.40
3033 6074 5.409520 TGCAAGCAACAACAACAACAATTTA 59.590 32.000 0.00 0.00 0.00 1.40
3034 6075 4.214971 TGCAAGCAACAACAACAACAATTT 59.785 33.333 0.00 0.00 0.00 1.82
3036 6077 3.332919 TGCAAGCAACAACAACAACAAT 58.667 36.364 0.00 0.00 0.00 2.71
3151 6433 0.875059 CAACCACCGAGAAGGAAAGC 59.125 55.000 0.00 0.00 45.00 3.51
3155 6437 1.343465 GAAGACAACCACCGAGAAGGA 59.657 52.381 0.00 0.00 45.00 3.36
3163 6445 3.699538 AGGAAGTTTTGAAGACAACCACC 59.300 43.478 0.00 0.00 35.63 4.61
3164 6446 4.983671 AGGAAGTTTTGAAGACAACCAC 57.016 40.909 0.00 0.00 35.63 4.16
3165 6447 5.261216 AGAAGGAAGTTTTGAAGACAACCA 58.739 37.500 0.00 0.00 35.63 3.67
3199 6481 0.459237 CACAGATGGGAGACTGCGTC 60.459 60.000 0.00 1.15 37.61 5.19
3201 6483 0.247460 TTCACAGATGGGAGACTGCG 59.753 55.000 0.00 0.00 37.61 5.18
3233 6562 6.917477 GCATTAATGAACTGACAAACAAGTCA 59.083 34.615 19.73 0.00 45.64 3.41
3246 6575 6.795144 TCAAATGGATGGCATTAATGAACT 57.205 33.333 19.73 1.86 0.00 3.01
3268 6597 1.234615 TTAGGGCTGCAAGTGCGTTC 61.235 55.000 0.50 0.00 45.83 3.95
3269 6598 0.821711 TTTAGGGCTGCAAGTGCGTT 60.822 50.000 0.50 0.00 45.83 4.84
3271 6600 0.527565 AATTTAGGGCTGCAAGTGCG 59.472 50.000 0.50 0.00 45.83 5.34
3272 6601 2.749280 AAATTTAGGGCTGCAAGTGC 57.251 45.000 0.50 0.00 42.50 4.40
3273 6602 3.244976 CGAAAATTTAGGGCTGCAAGTG 58.755 45.455 0.50 0.00 35.30 3.16
3274 6603 2.890945 ACGAAAATTTAGGGCTGCAAGT 59.109 40.909 0.50 0.00 35.30 3.16
3282 6614 8.810652 TTCAAAATCTTGACGAAAATTTAGGG 57.189 30.769 0.00 0.00 41.34 3.53
3479 6812 2.972625 TCACAAACATCTTAGGGCTCG 58.027 47.619 0.00 0.00 0.00 5.03
3496 6829 6.366604 GGACTCTCTTTAGCTGTTTACTTCAC 59.633 42.308 0.00 0.00 0.00 3.18
3568 6912 6.425210 AGCAGTGCTGAAATATATACAGGA 57.575 37.500 18.98 12.89 37.57 3.86
3579 6923 2.057137 AAAGTGGAGCAGTGCTGAAA 57.943 45.000 25.35 4.44 39.88 2.69
3615 6959 2.621070 TCTTCTTTCCCAGGTGCTACT 58.379 47.619 0.00 0.00 0.00 2.57
3623 6967 6.809196 GCATATCGTACTATCTTCTTTCCCAG 59.191 42.308 0.00 0.00 0.00 4.45
3667 7023 0.251474 TGCCTTTGAGCAGCTCCATT 60.251 50.000 20.16 0.00 38.00 3.16
3720 7094 0.028110 GCAGGCGCTGTATAGTTTGC 59.972 55.000 7.64 0.26 33.43 3.68
3743 7125 1.303236 CCCTTGGGTGTCGCAATGA 60.303 57.895 0.00 0.00 35.84 2.57
3762 7144 4.521130 TGTCGACTTAACAGAGAGCAAT 57.479 40.909 17.92 0.00 0.00 3.56
3766 7148 7.085116 ACTTTGTATGTCGACTTAACAGAGAG 58.915 38.462 26.83 20.77 0.00 3.20
3781 7163 5.520288 CGCAGCTGTAGATAACTTTGTATGT 59.480 40.000 16.64 0.00 0.00 2.29
3796 7178 1.003839 CTTCCAACCCGCAGCTGTA 60.004 57.895 16.64 0.00 0.00 2.74
3797 7179 2.281761 CTTCCAACCCGCAGCTGT 60.282 61.111 16.64 0.00 0.00 4.40
3801 7183 0.250727 TTTCTCCTTCCAACCCGCAG 60.251 55.000 0.00 0.00 0.00 5.18
3899 7281 2.609491 GCCGCCTCATGATATTCGTACA 60.609 50.000 0.00 0.00 0.00 2.90
3903 7285 1.354337 CCGCCGCCTCATGATATTCG 61.354 60.000 0.00 0.00 0.00 3.34
3930 7312 1.348594 GCGAGCGCATAAGTTCCAC 59.651 57.895 11.47 0.00 41.49 4.02
3932 7314 2.165301 ACGCGAGCGCATAAGTTCC 61.165 57.895 15.93 0.00 44.19 3.62
3933 7315 1.013323 CACGCGAGCGCATAAGTTC 60.013 57.895 15.93 0.00 44.19 3.01
3934 7316 3.081133 CACGCGAGCGCATAAGTT 58.919 55.556 15.93 0.00 44.19 2.66
3963 7348 3.857052 TCGGGCACTTATAAGTTCTGTG 58.143 45.455 15.60 6.43 37.08 3.66
3965 7350 4.950050 AGATCGGGCACTTATAAGTTCTG 58.050 43.478 15.60 14.72 37.08 3.02
3967 7352 4.202223 TGGAGATCGGGCACTTATAAGTTC 60.202 45.833 15.60 10.95 37.08 3.01
3968 7353 3.709653 TGGAGATCGGGCACTTATAAGTT 59.290 43.478 15.60 0.00 37.08 2.66
3969 7354 3.069729 GTGGAGATCGGGCACTTATAAGT 59.930 47.826 12.50 12.50 40.60 2.24
3970 7355 3.555168 GGTGGAGATCGGGCACTTATAAG 60.555 52.174 11.05 11.05 0.00 1.73
3971 7356 2.367567 GGTGGAGATCGGGCACTTATAA 59.632 50.000 0.00 0.00 0.00 0.98
3972 7357 1.968493 GGTGGAGATCGGGCACTTATA 59.032 52.381 0.00 0.00 0.00 0.98
3973 7358 0.759346 GGTGGAGATCGGGCACTTAT 59.241 55.000 0.00 0.00 0.00 1.73
3974 7359 0.325296 AGGTGGAGATCGGGCACTTA 60.325 55.000 0.00 0.00 0.00 2.24
3975 7360 1.613630 AGGTGGAGATCGGGCACTT 60.614 57.895 0.00 0.00 0.00 3.16
4010 7395 0.960364 ATGGTGCGCATCCTCGTTTT 60.960 50.000 19.88 0.00 0.00 2.43
4049 7434 1.079543 CCTGTTCCGCTCAGTCCAG 60.080 63.158 0.00 0.00 0.00 3.86
4149 7549 2.028748 AGGCAGCAATTTGTTTGGCTAG 60.029 45.455 21.64 0.00 43.55 3.42
4182 7583 1.672356 CCTCTGGTTGTGGCTTCCG 60.672 63.158 0.00 0.00 0.00 4.30
4192 7593 2.616458 GGCCCCATCACCTCTGGTT 61.616 63.158 0.00 0.00 31.02 3.67
4197 7598 3.813724 CCCAGGCCCCATCACCTC 61.814 72.222 0.00 0.00 32.56 3.85
4216 7617 2.362120 GCAGACCCCAGCAATGCT 60.362 61.111 0.00 0.00 40.77 3.79
4217 7618 3.455469 GGCAGACCCCAGCAATGC 61.455 66.667 0.00 0.00 36.16 3.56
4218 7619 0.901580 AAAGGCAGACCCCAGCAATG 60.902 55.000 0.00 0.00 36.11 2.82
4219 7620 0.178924 AAAAGGCAGACCCCAGCAAT 60.179 50.000 0.00 0.00 36.11 3.56
4220 7621 0.398381 AAAAAGGCAGACCCCAGCAA 60.398 50.000 0.00 0.00 36.11 3.91
4221 7622 1.114722 CAAAAAGGCAGACCCCAGCA 61.115 55.000 0.00 0.00 36.11 4.41
4222 7623 1.667722 CAAAAAGGCAGACCCCAGC 59.332 57.895 0.00 0.00 36.11 4.85
4223 7624 1.114722 TGCAAAAAGGCAGACCCCAG 61.115 55.000 0.00 0.00 39.25 4.45
4224 7625 1.075674 TGCAAAAAGGCAGACCCCA 60.076 52.632 0.00 0.00 39.25 4.96
4225 7626 3.869481 TGCAAAAAGGCAGACCCC 58.131 55.556 0.00 0.00 39.25 4.95
4231 7632 2.027897 CGCTGCTGCAAAAAGGCA 59.972 55.556 16.29 0.00 42.53 4.75
4232 7633 2.697992 TTCCGCTGCTGCAAAAAGGC 62.698 55.000 16.29 1.94 39.64 4.35
4233 7634 0.249405 TTTCCGCTGCTGCAAAAAGG 60.249 50.000 16.29 8.14 39.64 3.11
4234 7635 1.134226 CTTTCCGCTGCTGCAAAAAG 58.866 50.000 16.29 17.71 39.64 2.27
4235 7636 0.459489 ACTTTCCGCTGCTGCAAAAA 59.541 45.000 16.29 12.93 39.64 1.94
4236 7637 0.459489 AACTTTCCGCTGCTGCAAAA 59.541 45.000 16.29 13.25 39.64 2.44
4237 7638 1.001815 GTAACTTTCCGCTGCTGCAAA 60.002 47.619 16.29 8.43 39.64 3.68
4238 7639 0.591170 GTAACTTTCCGCTGCTGCAA 59.409 50.000 16.29 0.13 39.64 4.08
4239 7640 1.234615 GGTAACTTTCCGCTGCTGCA 61.235 55.000 16.29 0.88 39.64 4.41
4240 7641 1.502190 GGTAACTTTCCGCTGCTGC 59.498 57.895 5.34 5.34 0.00 5.25
4241 7642 1.305930 GGGGTAACTTTCCGCTGCTG 61.306 60.000 0.00 0.00 35.46 4.41
4242 7643 1.002502 GGGGTAACTTTCCGCTGCT 60.003 57.895 0.00 0.00 35.46 4.24
4243 7644 1.302993 TGGGGTAACTTTCCGCTGC 60.303 57.895 3.62 0.00 38.47 5.25
4244 7645 0.250553 TGTGGGGTAACTTTCCGCTG 60.251 55.000 3.62 0.00 38.47 5.18
4245 7646 0.250597 GTGTGGGGTAACTTTCCGCT 60.251 55.000 3.62 0.00 38.47 5.52


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

AutoCloner maintained by Alex Coulton.