Multiple sequence alignment - TraesCS3A01G160800

Loading Multiple Alignment...

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 TraesCS3A01G160800 chr3A 100.000 3189 0 0 1 3189 161452045 161448857 0.000000e+00 5890
1 TraesCS3A01G160800 chr3A 94.792 96 4 1 2498 2592 686127544 686127449 7.130000e-32 148
2 TraesCS3A01G160800 chr3A 91.743 109 5 4 2486 2591 750297118 750297225 7.130000e-32 148
3 TraesCS3A01G160800 chr3B 92.775 2533 116 39 1 2510 204287621 204285133 0.000000e+00 3602
4 TraesCS3A01G160800 chr3B 97.070 512 15 0 2589 3100 204285136 204284625 0.000000e+00 863
5 TraesCS3A01G160800 chr3B 91.489 94 7 1 3097 3189 204284543 204284450 9.290000e-26 128
6 TraesCS3A01G160800 chr3D 92.443 2329 108 28 204 2510 142481955 142479673 0.000000e+00 3264
7 TraesCS3A01G160800 chr3D 97.190 605 15 2 2587 3189 142479678 142479074 0.000000e+00 1022
8 TraesCS3A01G160800 chr3D 91.346 208 10 7 1 204 142482493 142482290 8.710000e-71 278
9 TraesCS3A01G160800 chr6D 85.000 160 23 1 1007 1166 466238555 466238713 9.150000e-36 161
10 TraesCS3A01G160800 chr6D 80.342 234 22 10 1447 1673 466249402 466249618 4.260000e-34 156
11 TraesCS3A01G160800 chr7D 97.753 89 1 1 2506 2593 45835327 45835415 5.510000e-33 152
12 TraesCS3A01G160800 chr2A 97.727 88 2 0 2506 2593 694958635 694958722 5.510000e-33 152
13 TraesCS3A01G160800 chr1A 94.000 100 4 2 2500 2597 584082905 584082806 1.980000e-32 150
14 TraesCS3A01G160800 chr7A 94.792 96 2 3 2507 2600 3014093 3013999 2.560000e-31 147
15 TraesCS3A01G160800 chr7B 89.076 119 10 3 2485 2600 414314561 414314443 9.220000e-31 145
16 TraesCS3A01G160800 chr2D 96.552 87 2 1 2506 2591 404795919 404795833 3.320000e-30 143
17 TraesCS3A01G160800 chr2D 86.777 121 11 5 2475 2593 233382101 233382218 2.580000e-26 130


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 TraesCS3A01G160800 chr3A 161448857 161452045 3188 True 5890.000000 5890 100.000000 1 3189 1 chr3A.!!$R1 3188
1 TraesCS3A01G160800 chr3B 204284450 204287621 3171 True 1531.000000 3602 93.778000 1 3189 3 chr3B.!!$R1 3188
2 TraesCS3A01G160800 chr3D 142479074 142482493 3419 True 1521.333333 3264 93.659667 1 3189 3 chr3D.!!$R1 3188

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
284 624 0.171455 CGACCCCTCAAGAGAACTCG 59.829 60.0 0.00 0.0 34.09 4.18 F
475 826 0.232303 CAGAACAACGAGTCGCAACC 59.768 55.0 13.59 0.0 0.00 3.77 F
962 1323 0.466124 GCTAGCCGGAAACCATCTCT 59.534 55.0 5.05 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 1973 1.472082 TGTTATGCGCATTTGGACCAG 59.528 47.619 30.42 0.0 0.00 4.00 R
2133 2504 2.171870 CCGGTGGAATTAGGAGCCTTAA 59.828 50.000 0.00 0.0 0.00 1.85 R
2705 3082 0.181114 TGGCAGGTCAGCATCATACC 59.819 55.000 0.00 0.0 35.83 2.73 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
28 29 4.510038 AGAGATTGTCATTTGTTGGCAC 57.490 40.909 0.00 0.00 40.39 5.01
67 72 3.699804 GCCTAAGCAAGTGACCACACAG 61.700 54.545 2.78 0.00 43.29 3.66
81 86 1.140852 CACACAGACTTGAACCTGGGA 59.859 52.381 0.00 0.00 37.27 4.37
82 87 1.843851 ACACAGACTTGAACCTGGGAA 59.156 47.619 0.00 0.00 37.27 3.97
83 88 2.443255 ACACAGACTTGAACCTGGGAAT 59.557 45.455 0.00 0.00 37.27 3.01
86 91 5.487488 ACACAGACTTGAACCTGGGAATATA 59.513 40.000 0.00 0.00 37.27 0.86
96 101 4.978099 ACCTGGGAATATAGCATCAACAG 58.022 43.478 0.00 0.00 0.00 3.16
117 122 9.577110 CAACAGCTATATTGTGAATGTTTCAAT 57.423 29.630 0.00 0.00 42.15 2.57
149 154 0.391927 TACCATGCTAACACACCGCC 60.392 55.000 0.00 0.00 0.00 6.13
163 168 4.188462 CACACCGCCAGAAGTATTATTCA 58.812 43.478 0.00 0.00 0.00 2.57
195 200 8.606754 ACATGACTTAGATATCTGATGGCTAT 57.393 34.615 15.79 0.00 0.00 2.97
235 575 1.389682 AACCTGGGGGAAGGGGAAA 60.390 57.895 0.00 0.00 42.11 3.13
254 594 4.101741 GGAAAATAGCTCTAGCAGAAGGGA 59.898 45.833 4.54 0.00 45.16 4.20
266 606 3.441572 AGCAGAAGGGAATCAATTTGACG 59.558 43.478 0.15 0.00 0.00 4.35
267 607 3.440173 GCAGAAGGGAATCAATTTGACGA 59.560 43.478 0.15 0.00 0.00 4.20
268 608 4.672801 GCAGAAGGGAATCAATTTGACGAC 60.673 45.833 0.15 0.00 0.00 4.34
284 624 0.171455 CGACCCCTCAAGAGAACTCG 59.829 60.000 0.00 0.00 34.09 4.18
285 625 0.533032 GACCCCTCAAGAGAACTCGG 59.467 60.000 0.00 0.00 34.09 4.63
400 745 2.421424 CACTCCATGCTTAGGAAACAGC 59.579 50.000 0.00 0.00 34.08 4.40
444 795 9.114952 CCATATCTACAGTACGAGTATGATGAT 57.885 37.037 15.27 11.18 0.00 2.45
458 809 6.577103 AGTATGATGATTATACCGGATGCAG 58.423 40.000 9.46 0.00 32.66 4.41
475 826 0.232303 CAGAACAACGAGTCGCAACC 59.768 55.000 13.59 0.00 0.00 3.77
505 856 4.278678 CGGGAGCACAATCAATAGAAAC 57.721 45.455 0.00 0.00 0.00 2.78
772 1130 5.701750 GGGAAACAAAAGAGAGGAGTAGAAC 59.298 44.000 0.00 0.00 0.00 3.01
776 1134 4.765856 ACAAAAGAGAGGAGTAGAACGCTA 59.234 41.667 0.00 0.00 0.00 4.26
839 1200 2.353323 GGCTACCCTCAACGTTTAAGG 58.647 52.381 16.38 16.38 0.00 2.69
859 1220 1.310715 CCCATTGGGCCCATCTCAA 59.689 57.895 29.23 11.27 35.35 3.02
869 1230 0.890683 CCCATCTCAAACAGCCCAAC 59.109 55.000 0.00 0.00 0.00 3.77
918 1279 1.976474 CCCACCCACATTGGTTCCG 60.976 63.158 0.00 0.00 36.12 4.30
941 1302 1.067416 TTTGTGTGACTCGAGCGCT 59.933 52.632 11.27 11.27 0.00 5.92
962 1323 0.466124 GCTAGCCGGAAACCATCTCT 59.534 55.000 5.05 0.00 0.00 3.10
965 1326 1.153147 GCCGGAAACCATCTCTCCC 60.153 63.158 5.05 0.00 0.00 4.30
991 1360 0.900647 CTCCTCCCGTCTCACCAAGT 60.901 60.000 0.00 0.00 0.00 3.16
1186 1555 1.134280 CCTCAACTAGCCAGATGTGGG 60.134 57.143 11.47 0.00 45.17 4.61
1205 1574 1.335324 GGCTGATGATTGTAATGGCGC 60.335 52.381 0.00 0.00 0.00 6.53
1262 1631 4.687215 GTGGAGTCGCTGCTGCCA 62.687 66.667 10.24 0.00 35.36 4.92
1304 1673 1.066136 CGCGGATGACATCTATGCTG 58.934 55.000 14.95 9.28 0.00 4.41
1360 1729 5.612351 GGAAGGTGAAACTGAAACTACTCT 58.388 41.667 0.00 0.00 36.74 3.24
1373 1742 6.238648 TGAAACTACTCTTCCCCTTCAAATC 58.761 40.000 0.00 0.00 0.00 2.17
1437 1808 9.781834 ATAAATTCATGTGTTACGGTGTAATTG 57.218 29.630 0.00 0.00 0.00 2.32
1444 1815 5.992829 TGTGTTACGGTGTAATTGAGACAAT 59.007 36.000 0.00 0.00 0.00 2.71
1445 1816 7.153315 TGTGTTACGGTGTAATTGAGACAATA 58.847 34.615 0.00 0.00 0.00 1.90
1446 1817 7.116662 TGTGTTACGGTGTAATTGAGACAATAC 59.883 37.037 0.00 0.00 0.00 1.89
1447 1818 7.116662 GTGTTACGGTGTAATTGAGACAATACA 59.883 37.037 0.00 0.00 0.00 2.29
1448 1819 7.329962 TGTTACGGTGTAATTGAGACAATACAG 59.670 37.037 0.00 0.00 0.00 2.74
1449 1820 5.790593 ACGGTGTAATTGAGACAATACAGT 58.209 37.500 0.00 0.00 0.00 3.55
1450 1821 6.927416 ACGGTGTAATTGAGACAATACAGTA 58.073 36.000 0.00 0.00 0.00 2.74
1451 1822 7.033791 ACGGTGTAATTGAGACAATACAGTAG 58.966 38.462 0.00 0.00 0.00 2.57
1452 1823 7.094075 ACGGTGTAATTGAGACAATACAGTAGA 60.094 37.037 0.00 0.00 0.00 2.59
1453 1824 7.921214 CGGTGTAATTGAGACAATACAGTAGAT 59.079 37.037 0.00 0.00 0.00 1.98
1454 1825 9.601217 GGTGTAATTGAGACAATACAGTAGATT 57.399 33.333 0.00 0.00 0.00 2.40
1462 1833 9.554395 TGAGACAATACAGTAGATTTGTTTTGA 57.446 29.630 13.00 0.00 38.76 2.69
1486 1857 9.918630 TGATATGAATCATATGTCAGTAGTGTG 57.081 33.333 19.38 0.00 37.20 3.82
1496 1867 3.576550 TGTCAGTAGTGTGCCTATTGTCA 59.423 43.478 0.00 0.00 35.47 3.58
1568 1939 3.548745 TGATCCCAGTGTGCATAAGAG 57.451 47.619 0.00 0.00 0.00 2.85
1602 1973 5.407691 GCACTACCTTAGTCTTGGTTAACAC 59.592 44.000 8.10 0.00 36.76 3.32
1612 1983 4.583073 GTCTTGGTTAACACTGGTCCAAAT 59.417 41.667 8.10 0.00 37.65 2.32
1614 1985 2.625790 TGGTTAACACTGGTCCAAATGC 59.374 45.455 8.10 0.00 0.00 3.56
1622 1993 1.472082 CTGGTCCAAATGCGCATAACA 59.528 47.619 25.61 15.94 0.00 2.41
1624 1995 2.495270 TGGTCCAAATGCGCATAACAAT 59.505 40.909 25.61 4.11 0.00 2.71
1634 2005 6.624352 ATGCGCATAACAATTTCTCTGTAT 57.376 33.333 24.02 0.00 0.00 2.29
1640 2011 7.528516 CGCATAACAATTTCTCTGTATCATTCG 59.471 37.037 0.00 0.00 0.00 3.34
1657 2028 2.214376 TCGCCCAATTCCTTCAACAT 57.786 45.000 0.00 0.00 0.00 2.71
1661 2032 2.417787 GCCCAATTCCTTCAACATCTGC 60.418 50.000 0.00 0.00 0.00 4.26
1675 2046 9.649167 CTTCAACATCTGCATCATACTATATGA 57.351 33.333 1.18 1.18 0.00 2.15
1677 2048 9.428097 TCAACATCTGCATCATACTATATGAAC 57.572 33.333 2.79 0.27 0.00 3.18
1773 2144 3.703001 TCATTCTCCAGTCCTGTTTCC 57.297 47.619 0.00 0.00 0.00 3.13
1786 2157 4.695928 GTCCTGTTTCCAGTCTTATTGACC 59.304 45.833 0.00 0.00 46.46 4.02
2279 2650 6.803807 GGCAGTATTGAAGAGAACAAATTGAC 59.196 38.462 0.00 0.00 0.00 3.18
2390 2763 2.531522 AAATTGCAGGGCACTGTTTC 57.468 45.000 19.18 0.79 46.62 2.78
2509 2886 7.675962 TTTTAACATTTGGCTATGACGTACT 57.324 32.000 7.09 0.00 0.00 2.73
2510 2887 6.897259 TTAACATTTGGCTATGACGTACTC 57.103 37.500 7.09 0.00 0.00 2.59
2511 2888 3.793559 ACATTTGGCTATGACGTACTCC 58.206 45.455 7.09 0.00 0.00 3.85
2512 2889 2.973694 TTTGGCTATGACGTACTCCC 57.026 50.000 0.00 0.00 0.00 4.30
2513 2890 2.154567 TTGGCTATGACGTACTCCCT 57.845 50.000 0.00 0.00 0.00 4.20
2514 2891 1.688772 TGGCTATGACGTACTCCCTC 58.311 55.000 0.00 0.00 0.00 4.30
2515 2892 1.214673 TGGCTATGACGTACTCCCTCT 59.785 52.381 0.00 0.00 0.00 3.69
2516 2893 1.609555 GGCTATGACGTACTCCCTCTG 59.390 57.143 0.00 0.00 0.00 3.35
2517 2894 2.299521 GCTATGACGTACTCCCTCTGT 58.700 52.381 0.00 0.00 0.00 3.41
2518 2895 3.474600 GCTATGACGTACTCCCTCTGTA 58.525 50.000 0.00 0.00 0.00 2.74
2519 2896 3.881688 GCTATGACGTACTCCCTCTGTAA 59.118 47.826 0.00 0.00 0.00 2.41
2520 2897 4.337555 GCTATGACGTACTCCCTCTGTAAA 59.662 45.833 0.00 0.00 0.00 2.01
2521 2898 4.715527 ATGACGTACTCCCTCTGTAAAC 57.284 45.455 0.00 0.00 0.00 2.01
2522 2899 3.759581 TGACGTACTCCCTCTGTAAACT 58.240 45.455 0.00 0.00 0.00 2.66
2523 2900 4.910195 TGACGTACTCCCTCTGTAAACTA 58.090 43.478 0.00 0.00 0.00 2.24
2524 2901 4.697352 TGACGTACTCCCTCTGTAAACTAC 59.303 45.833 0.00 0.00 0.00 2.73
2525 2902 4.916183 ACGTACTCCCTCTGTAAACTACT 58.084 43.478 0.00 0.00 0.00 2.57
2526 2903 6.054860 ACGTACTCCCTCTGTAAACTACTA 57.945 41.667 0.00 0.00 0.00 1.82
2527 2904 6.657875 ACGTACTCCCTCTGTAAACTACTAT 58.342 40.000 0.00 0.00 0.00 2.12
2528 2905 7.796054 ACGTACTCCCTCTGTAAACTACTATA 58.204 38.462 0.00 0.00 0.00 1.31
2529 2906 8.267894 ACGTACTCCCTCTGTAAACTACTATAA 58.732 37.037 0.00 0.00 0.00 0.98
2530 2907 8.772705 CGTACTCCCTCTGTAAACTACTATAAG 58.227 40.741 0.00 0.00 0.00 1.73
2531 2908 9.844257 GTACTCCCTCTGTAAACTACTATAAGA 57.156 37.037 0.00 0.00 0.00 2.10
2532 2909 8.983702 ACTCCCTCTGTAAACTACTATAAGAG 57.016 38.462 0.00 0.00 0.00 2.85
2533 2910 8.559175 ACTCCCTCTGTAAACTACTATAAGAGT 58.441 37.037 0.00 0.00 42.69 3.24
2534 2911 8.749026 TCCCTCTGTAAACTACTATAAGAGTG 57.251 38.462 0.00 0.00 39.39 3.51
2535 2912 8.334734 TCCCTCTGTAAACTACTATAAGAGTGT 58.665 37.037 0.00 0.00 39.39 3.55
2536 2913 8.968969 CCCTCTGTAAACTACTATAAGAGTGTT 58.031 37.037 0.00 0.00 39.39 3.32
2584 2961 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
2585 2962 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
2586 2963 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
2587 2964 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
2705 3082 4.646040 TGGATAACAGCTGAAATTGATGGG 59.354 41.667 23.35 0.00 0.00 4.00
2801 3178 6.421801 GCATGCTTTTCTTTTTCTGTATGTGT 59.578 34.615 11.37 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 42 5.402398 GTCACTTGCTTAGGCCTTTTATTG 58.598 41.667 12.58 0.15 37.74 1.90
38 43 4.462834 GGTCACTTGCTTAGGCCTTTTATT 59.537 41.667 12.58 0.00 37.74 1.40
67 72 5.036117 TGCTATATTCCCAGGTTCAAGTC 57.964 43.478 0.00 0.00 0.00 3.01
86 91 6.544931 ACATTCACAATATAGCTGTTGATGCT 59.455 34.615 13.18 0.00 43.79 3.79
149 154 9.899226 TCATGTATCGACTGAATAATACTTCTG 57.101 33.333 0.00 0.00 0.00 3.02
163 168 9.679661 ATCAGATATCTAAGTCATGTATCGACT 57.320 33.333 4.54 0.00 45.62 4.18
195 200 6.211785 GGTTGGGGGAACATCTTAACATTTTA 59.788 38.462 0.00 0.00 36.12 1.52
224 564 3.497048 GCTAGAGCTATTTTCCCCTTCCC 60.497 52.174 0.00 0.00 38.21 3.97
226 566 4.101741 TCTGCTAGAGCTATTTTCCCCTTC 59.898 45.833 2.72 0.00 42.66 3.46
235 575 4.904251 TGATTCCCTTCTGCTAGAGCTATT 59.096 41.667 2.72 0.00 42.66 1.73
254 594 3.433306 TGAGGGGTCGTCAAATTGATT 57.567 42.857 0.00 0.00 0.00 2.57
266 606 0.533032 CCGAGTTCTCTTGAGGGGTC 59.467 60.000 0.00 0.00 0.00 4.46
267 607 1.545706 GCCGAGTTCTCTTGAGGGGT 61.546 60.000 0.00 0.00 0.00 4.95
268 608 1.219393 GCCGAGTTCTCTTGAGGGG 59.781 63.158 0.00 0.00 0.00 4.79
284 624 3.123116 TGAAAACGAAAACAAAAACGGCC 59.877 39.130 0.00 0.00 0.00 6.13
285 625 4.143284 ACTGAAAACGAAAACAAAAACGGC 60.143 37.500 0.00 0.00 0.00 5.68
363 708 3.300533 GAGTGCGTTTGCGTGCAGTTA 62.301 52.381 0.00 0.00 44.40 2.24
400 745 6.601613 AGATATGGTAGGATAAGAAGCGAGAG 59.398 42.308 0.00 0.00 0.00 3.20
444 795 3.119065 TCGTTGTTCTGCATCCGGTATAA 60.119 43.478 0.00 0.00 0.00 0.98
450 801 0.716108 GACTCGTTGTTCTGCATCCG 59.284 55.000 0.00 0.00 0.00 4.18
458 809 1.200839 CGGTTGCGACTCGTTGTTC 59.799 57.895 3.59 0.00 0.00 3.18
475 826 2.887568 GTGCTCCCGCTCATGTCG 60.888 66.667 0.00 0.00 36.97 4.35
479 830 0.035152 TTGATTGTGCTCCCGCTCAT 60.035 50.000 0.00 0.00 39.16 2.90
505 856 0.460284 AGCCCTCGTTGCATTCGTAG 60.460 55.000 10.66 7.56 0.00 3.51
618 969 4.115199 ATCCTTGCCGAGTGCCCC 62.115 66.667 0.00 0.00 40.16 5.80
640 991 1.884464 GATTCATCGCGCCTCTGCA 60.884 57.895 0.00 0.00 37.32 4.41
859 1220 2.365293 GTCCATTTCTTGTTGGGCTGTT 59.635 45.455 0.00 0.00 34.70 3.16
869 1230 1.734465 GTCTGCTCGGTCCATTTCTTG 59.266 52.381 0.00 0.00 0.00 3.02
918 1279 1.523095 GCTCGAGTCACACAAACAGAC 59.477 52.381 15.13 0.00 0.00 3.51
941 1302 1.687123 GAGATGGTTTCCGGCTAGCTA 59.313 52.381 15.72 0.00 0.00 3.32
962 1323 3.036959 GGGAGGAGGAGGAGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
965 1326 2.123640 GACGGGAGGAGGAGGAGG 60.124 72.222 0.00 0.00 0.00 4.30
1186 1555 1.605710 AGCGCCATTACAATCATCAGC 59.394 47.619 2.29 0.00 0.00 4.26
1205 1574 1.564622 CGACCTGCACAACGAACAG 59.435 57.895 0.00 0.00 0.00 3.16
1360 1729 8.682710 CGAATTAATAACAGATTTGAAGGGGAA 58.317 33.333 0.00 0.00 0.00 3.97
1460 1831 9.918630 CACACTACTGACATATGATTCATATCA 57.081 33.333 14.88 11.52 44.52 2.15
1461 1832 8.867935 GCACACTACTGACATATGATTCATATC 58.132 37.037 14.88 7.95 35.18 1.63
1462 1833 7.821359 GGCACACTACTGACATATGATTCATAT 59.179 37.037 10.38 12.48 37.51 1.78
1463 1834 7.015584 AGGCACACTACTGACATATGATTCATA 59.984 37.037 10.38 8.76 0.00 2.15
1464 1835 5.994054 GGCACACTACTGACATATGATTCAT 59.006 40.000 10.38 4.28 0.00 2.57
1465 1836 5.129320 AGGCACACTACTGACATATGATTCA 59.871 40.000 10.38 2.67 0.00 2.57
1466 1837 5.605534 AGGCACACTACTGACATATGATTC 58.394 41.667 10.38 0.00 0.00 2.52
1467 1838 5.620738 AGGCACACTACTGACATATGATT 57.379 39.130 10.38 0.00 0.00 2.57
1468 1839 6.924913 ATAGGCACACTACTGACATATGAT 57.075 37.500 10.38 0.00 33.70 2.45
1469 1840 6.098266 ACAATAGGCACACTACTGACATATGA 59.902 38.462 10.38 0.00 32.78 2.15
1496 1867 2.949447 AGCTTGAGTTGGATTGTTGGT 58.051 42.857 0.00 0.00 0.00 3.67
1511 1882 4.684703 ACTGCTACTACAACGTTTAGCTTG 59.315 41.667 23.20 18.81 38.23 4.01
1568 1939 4.003648 ACTAAGGTAGTGCAAGTCAATGC 58.996 43.478 0.00 0.00 46.58 3.56
1602 1973 1.472082 TGTTATGCGCATTTGGACCAG 59.528 47.619 30.42 0.00 0.00 4.00
1612 1983 5.584251 TGATACAGAGAAATTGTTATGCGCA 59.416 36.000 14.96 14.96 0.00 6.09
1614 1985 7.528516 CGAATGATACAGAGAAATTGTTATGCG 59.471 37.037 0.00 0.00 0.00 4.73
1622 1993 4.780815 TGGGCGAATGATACAGAGAAATT 58.219 39.130 0.00 0.00 0.00 1.82
1624 1995 3.904800 TGGGCGAATGATACAGAGAAA 57.095 42.857 0.00 0.00 0.00 2.52
1634 2005 2.491693 GTTGAAGGAATTGGGCGAATGA 59.508 45.455 0.00 0.00 0.00 2.57
1640 2011 2.417787 GCAGATGTTGAAGGAATTGGGC 60.418 50.000 0.00 0.00 0.00 5.36
1675 2046 7.254863 GCATCCATTGATTTGTGTTTGAAAGTT 60.255 33.333 0.00 0.00 0.00 2.66
1677 2048 6.203145 TGCATCCATTGATTTGTGTTTGAAAG 59.797 34.615 0.00 0.00 0.00 2.62
1773 2144 4.938226 GGGTCTCTTTGGTCAATAAGACTG 59.062 45.833 17.56 0.00 46.72 3.51
1786 2157 5.582689 AAACAGAAAAGTGGGTCTCTTTG 57.417 39.130 0.00 0.00 35.65 2.77
1928 2299 5.704053 AGGTTTGGTAGTCGTTTAAGATTGG 59.296 40.000 0.00 0.00 0.00 3.16
2133 2504 2.171870 CCGGTGGAATTAGGAGCCTTAA 59.828 50.000 0.00 0.00 0.00 1.85
2279 2650 8.879759 TGTCCGCTTAGAACTTTTAGATATTTG 58.120 33.333 0.00 0.00 0.00 2.32
2459 2833 7.916128 AATCAGTTTCTCTACGATATGAACG 57.084 36.000 0.00 0.00 0.00 3.95
2489 2866 4.189231 GGAGTACGTCATAGCCAAATGTT 58.811 43.478 0.00 0.00 0.00 2.71
2504 2881 8.668510 TTATAGTAGTTTACAGAGGGAGTACG 57.331 38.462 0.00 0.00 0.00 3.67
2507 2884 8.559175 ACTCTTATAGTAGTTTACAGAGGGAGT 58.441 37.037 0.00 0.00 36.36 3.85
2508 2885 8.842280 CACTCTTATAGTAGTTTACAGAGGGAG 58.158 40.741 0.00 0.00 35.76 4.30
2509 2886 8.334734 ACACTCTTATAGTAGTTTACAGAGGGA 58.665 37.037 2.59 0.00 35.76 4.20
2510 2887 8.522542 ACACTCTTATAGTAGTTTACAGAGGG 57.477 38.462 0.00 0.00 35.76 4.30
2558 2935 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
2559 2936 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
2560 2937 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
2561 2938 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
2562 2939 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
2563 2940 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2564 2941 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2565 2942 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
2568 2945 9.240734 CATAGTACTCCCTCCGTAAACTAATAT 57.759 37.037 0.00 0.00 0.00 1.28
2569 2946 8.439971 TCATAGTACTCCCTCCGTAAACTAATA 58.560 37.037 0.00 0.00 0.00 0.98
2570 2947 7.293073 TCATAGTACTCCCTCCGTAAACTAAT 58.707 38.462 0.00 0.00 0.00 1.73
2571 2948 6.662755 TCATAGTACTCCCTCCGTAAACTAA 58.337 40.000 0.00 0.00 0.00 2.24
2572 2949 6.252599 TCATAGTACTCCCTCCGTAAACTA 57.747 41.667 0.00 0.00 0.00 2.24
2573 2950 5.121380 TCATAGTACTCCCTCCGTAAACT 57.879 43.478 0.00 0.00 0.00 2.66
2574 2951 5.841957 TTCATAGTACTCCCTCCGTAAAC 57.158 43.478 0.00 0.00 0.00 2.01
2575 2952 5.716228 TGTTTCATAGTACTCCCTCCGTAAA 59.284 40.000 0.00 0.00 0.00 2.01
2576 2953 5.126061 GTGTTTCATAGTACTCCCTCCGTAA 59.874 44.000 0.00 0.00 0.00 3.18
2577 2954 4.641989 GTGTTTCATAGTACTCCCTCCGTA 59.358 45.833 0.00 0.00 0.00 4.02
2578 2955 3.446516 GTGTTTCATAGTACTCCCTCCGT 59.553 47.826 0.00 0.00 0.00 4.69
2579 2956 3.181478 GGTGTTTCATAGTACTCCCTCCG 60.181 52.174 0.00 0.00 0.00 4.63
2580 2957 3.134262 GGGTGTTTCATAGTACTCCCTCC 59.866 52.174 0.00 0.00 42.25 4.30
2581 2958 4.403585 GGGTGTTTCATAGTACTCCCTC 57.596 50.000 0.00 0.00 42.25 4.30
2583 2960 3.118371 CCAGGGTGTTTCATAGTACTCCC 60.118 52.174 0.00 0.59 44.62 4.30
2584 2961 3.773119 TCCAGGGTGTTTCATAGTACTCC 59.227 47.826 0.00 0.00 0.00 3.85
2585 2962 5.416271 TTCCAGGGTGTTTCATAGTACTC 57.584 43.478 0.00 0.00 0.00 2.59
2586 2963 5.836024 TTTCCAGGGTGTTTCATAGTACT 57.164 39.130 0.00 0.00 0.00 2.73
2587 2964 6.002082 ACTTTTCCAGGGTGTTTCATAGTAC 58.998 40.000 0.00 0.00 0.00 2.73
2705 3082 0.181114 TGGCAGGTCAGCATCATACC 59.819 55.000 0.00 0.00 35.83 2.73
2853 3230 4.884164 GGTTAATGAAGATGAAGGTGGGAG 59.116 45.833 0.00 0.00 0.00 4.30
3142 3605 4.414337 TGCCTTTTTGCCTGTGTAATTT 57.586 36.364 0.00 0.00 0.00 1.82
3144 3607 3.387699 ACTTGCCTTTTTGCCTGTGTAAT 59.612 39.130 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.