Multiple sequence alignment - TraesCS2B01G171700

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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 TraesCS2B01G171700 chr2B 100.000 2897 0 0 1 2897 146005936 146008832 0.000000e+00 5350
1 TraesCS2B01G171700 chr2B 94.650 785 42 0 2113 2897 341223747 341222963 0.000000e+00 1218
2 TraesCS2B01G171700 chr2A 90.643 2116 185 12 1 2112 91462399 91464505 0.000000e+00 2798
3 TraesCS2B01G171700 chr2D 90.553 2117 177 14 1 2112 94137245 94139343 0.000000e+00 2780
4 TraesCS2B01G171700 chr3B 95.165 786 38 0 2112 2897 561137317 561138102 0.000000e+00 1242
5 TraesCS2B01G171700 chr3B 94.784 786 40 1 2112 2897 665347855 665348639 0.000000e+00 1223
6 TraesCS2B01G171700 chr3B 73.498 283 69 5 1040 1319 154451568 154451289 5.110000e-18 102
7 TraesCS2B01G171700 chr5B 95.159 785 36 1 2113 2897 655089447 655090229 0.000000e+00 1238
8 TraesCS2B01G171700 chr4B 94.777 785 41 0 2113 2897 28610938 28610154 0.000000e+00 1223
9 TraesCS2B01G171700 chr1B 94.777 785 41 0 2113 2897 94859530 94858746 0.000000e+00 1223
10 TraesCS2B01G171700 chr7B 94.670 788 41 1 2110 2897 58999303 59000089 0.000000e+00 1221
11 TraesCS2B01G171700 chr7B 94.361 798 39 6 2102 2897 325642487 325643280 0.000000e+00 1219
12 TraesCS2B01G171700 chr4A 94.250 800 45 1 2098 2897 671828529 671827731 0.000000e+00 1221
13 TraesCS2B01G171700 chr4D 77.854 438 79 15 2 431 322805489 322805916 3.700000e-64 255
14 TraesCS2B01G171700 chr5D 81.481 216 31 7 223 433 356339207 356339418 4.960000e-38 169
15 TraesCS2B01G171700 chr3D 74.013 304 73 6 1040 1340 103820985 103820685 5.070000e-23 119


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 TraesCS2B01G171700 chr2B 146005936 146008832 2896 False 5350 5350 100.000 1 2897 1 chr2B.!!$F1 2896
1 TraesCS2B01G171700 chr2B 341222963 341223747 784 True 1218 1218 94.650 2113 2897 1 chr2B.!!$R1 784
2 TraesCS2B01G171700 chr2A 91462399 91464505 2106 False 2798 2798 90.643 1 2112 1 chr2A.!!$F1 2111
3 TraesCS2B01G171700 chr2D 94137245 94139343 2098 False 2780 2780 90.553 1 2112 1 chr2D.!!$F1 2111
4 TraesCS2B01G171700 chr3B 561137317 561138102 785 False 1242 1242 95.165 2112 2897 1 chr3B.!!$F1 785
5 TraesCS2B01G171700 chr3B 665347855 665348639 784 False 1223 1223 94.784 2112 2897 1 chr3B.!!$F2 785
6 TraesCS2B01G171700 chr5B 655089447 655090229 782 False 1238 1238 95.159 2113 2897 1 chr5B.!!$F1 784
7 TraesCS2B01G171700 chr4B 28610154 28610938 784 True 1223 1223 94.777 2113 2897 1 chr4B.!!$R1 784
8 TraesCS2B01G171700 chr1B 94858746 94859530 784 True 1223 1223 94.777 2113 2897 1 chr1B.!!$R1 784
9 TraesCS2B01G171700 chr7B 58999303 59000089 786 False 1221 1221 94.670 2110 2897 1 chr7B.!!$F1 787
10 TraesCS2B01G171700 chr7B 325642487 325643280 793 False 1219 1219 94.361 2102 2897 1 chr7B.!!$F2 795
11 TraesCS2B01G171700 chr4A 671827731 671828529 798 True 1221 1221 94.250 2098 2897 1 chr4A.!!$R1 799

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
187 190 0.106769 TGCATGTGCCCGTATGGAAT 60.107 50.0 1.27 0.0 41.18 3.01 F
1388 1393 0.171455 GCGTGAGAACCGTGAGATCT 59.829 55.0 0.00 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1616 0.105760 TTGGTGTCAAGCCAACCCAT 60.106 50.0 0.0 0.0 40.69 4.00 R
2554 2560 0.689745 CTGGATTAGGGGGTGTCCGA 60.690 60.0 0.0 0.0 36.01 4.55 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
27 28 3.176924 AGTTAGAAGGCTCTCTGGTGA 57.823 47.619 8.77 0.00 32.70 4.02
38 39 4.183101 GCTCTCTGGTGATTCTTCTTCTG 58.817 47.826 0.00 0.00 0.00 3.02
59 60 7.156876 TCTGTGAATCTCTTCTCTCTCTTTC 57.843 40.000 0.00 0.00 32.29 2.62
78 81 0.883833 CTTCTGGATGTGGTTGTGGC 59.116 55.000 0.00 0.00 0.00 5.01
80 83 1.302431 CTGGATGTGGTTGTGGCGA 60.302 57.895 0.00 0.00 0.00 5.54
81 84 1.300971 CTGGATGTGGTTGTGGCGAG 61.301 60.000 0.00 0.00 0.00 5.03
115 118 4.589908 GATGTGTCTACCCCTTCACAAAT 58.410 43.478 0.00 0.00 42.61 2.32
138 141 4.830046 TGTGTCTTCTATAGATGAGAGGGC 59.170 45.833 16.47 7.22 34.79 5.19
142 145 2.796557 TCTATAGATGAGAGGGCACGG 58.203 52.381 0.00 0.00 0.00 4.94
164 167 1.699634 ACTTCATACAGCCGGCCATAT 59.300 47.619 26.15 18.50 0.00 1.78
187 190 0.106769 TGCATGTGCCCGTATGGAAT 60.107 50.000 1.27 0.00 41.18 3.01
201 204 1.462616 TGGAATCCCATGTTTCGCTG 58.537 50.000 0.00 0.00 37.58 5.18
228 231 1.338020 GCCAGGTGACAAAACTTCCAG 59.662 52.381 0.00 0.00 0.00 3.86
267 270 9.474920 TCCATTTTGACTTGATTTGTTGTAATC 57.525 29.630 0.00 0.00 35.54 1.75
322 325 6.257630 CCTACAAAACAATGGAAAACAGGTTG 59.742 38.462 0.00 0.00 32.76 3.77
334 337 5.359194 AAAACAGGTTGTCTTCTCTCTCA 57.641 39.130 0.00 0.00 0.00 3.27
392 395 2.965147 ACCCCAGTGAAAACCAAATGAG 59.035 45.455 0.00 0.00 0.00 2.90
401 404 6.039829 AGTGAAAACCAAATGAGAACTCCTTC 59.960 38.462 0.00 0.00 0.00 3.46
450 454 2.036256 CCCTTGCACTTGGGGGAG 59.964 66.667 10.03 0.00 41.25 4.30
484 488 1.202582 TCGTAGTTGAGAGGAAGCAGC 59.797 52.381 0.00 0.00 0.00 5.25
524 528 3.906846 CCTCCATTAGTAAGCTCCCATCT 59.093 47.826 0.00 0.00 0.00 2.90
540 544 5.015515 TCCCATCTGTAATTGATTGTGCAA 58.984 37.500 0.00 0.00 0.00 4.08
600 605 7.118060 TGATATTTTCTCAACATGTGATGGGA 58.882 34.615 0.00 0.00 35.07 4.37
685 690 8.991243 TGTAAACGTAGCTAAAACACATATCT 57.009 30.769 0.00 0.00 0.00 1.98
727 732 5.119694 GTTCTTTGAGAGACACTTTCCAGT 58.880 41.667 0.00 0.00 33.02 4.00
786 791 5.175856 CACCATTATTCTCTCGAACGATTCC 59.824 44.000 0.00 0.00 30.67 3.01
787 792 5.163447 ACCATTATTCTCTCGAACGATTCCA 60.163 40.000 0.00 0.00 30.67 3.53
790 795 6.887376 TTATTCTCTCGAACGATTCCAAAG 57.113 37.500 0.00 0.00 30.67 2.77
810 815 6.692681 CCAAAGGATTTTGCGTAATGATACAG 59.307 38.462 0.00 0.00 41.87 2.74
914 919 7.730364 ATTTACGCCAAAGTTAGAGATATGG 57.270 36.000 0.00 0.00 0.00 2.74
972 977 2.356135 CCGATCCGCCCCTATAAATTG 58.644 52.381 0.00 0.00 0.00 2.32
975 980 3.556213 CGATCCGCCCCTATAAATTGACA 60.556 47.826 0.00 0.00 0.00 3.58
978 983 1.871039 CGCCCCTATAAATTGACACCG 59.129 52.381 0.00 0.00 0.00 4.94
988 993 2.254546 ATTGACACCGCTTGACTTGA 57.745 45.000 0.00 0.00 0.00 3.02
1009 1014 6.279513 TGATTTCAACTCACAAAACCAGTT 57.720 33.333 0.00 0.00 0.00 3.16
1011 1016 7.479980 TGATTTCAACTCACAAAACCAGTTAG 58.520 34.615 0.00 0.00 0.00 2.34
1021 1026 5.068460 CACAAAACCAGTTAGTTCCATTCCA 59.932 40.000 0.00 0.00 0.00 3.53
1022 1027 5.068591 ACAAAACCAGTTAGTTCCATTCCAC 59.931 40.000 0.00 0.00 0.00 4.02
1072 1077 4.693532 CGCAAGAAGGTGGCACTA 57.306 55.556 18.45 0.00 43.02 2.74
1074 1079 0.602638 CGCAAGAAGGTGGCACTACA 60.603 55.000 18.45 0.00 43.02 2.74
1095 1100 4.761739 ACAATACATCCACAACAGGTCAAG 59.238 41.667 0.00 0.00 0.00 3.02
1096 1101 4.908601 ATACATCCACAACAGGTCAAGA 57.091 40.909 0.00 0.00 0.00 3.02
1099 1104 0.828022 TCCACAACAGGTCAAGACGT 59.172 50.000 0.00 0.00 0.00 4.34
1112 1117 3.060740 GTCAAGACGTTGTGTTACCTTCG 60.061 47.826 0.00 0.00 34.98 3.79
1117 1122 3.784338 ACGTTGTGTTACCTTCGAGAAA 58.216 40.909 0.00 0.00 0.00 2.52
1118 1123 4.374399 ACGTTGTGTTACCTTCGAGAAAT 58.626 39.130 0.00 0.00 0.00 2.17
1140 1145 3.181462 TGTCGCAATAGCCTGATGAAGAT 60.181 43.478 0.00 0.00 37.52 2.40
1234 1239 2.124695 GTCTTCCCATCCCACGCC 60.125 66.667 0.00 0.00 0.00 5.68
1273 1278 2.154854 ATCGATACAAGGACATGCCG 57.845 50.000 0.00 0.00 43.43 5.69
1276 1281 1.270305 CGATACAAGGACATGCCGGAT 60.270 52.381 5.05 0.00 43.43 4.18
1315 1320 1.707427 ACTGTGAGCCAGGAGGAATTT 59.293 47.619 0.00 0.00 46.06 1.82
1356 1361 1.956477 GCTCAAAGAAGAGGCCAACAA 59.044 47.619 5.01 0.00 36.15 2.83
1362 1367 3.297134 AGAAGAGGCCAACAAGTTTCA 57.703 42.857 5.01 0.00 0.00 2.69
1381 1386 2.050351 CGTGAGCGTGAGAACCGT 60.050 61.111 0.00 0.00 0.00 4.83
1388 1393 0.171455 GCGTGAGAACCGTGAGATCT 59.829 55.000 0.00 0.00 0.00 2.75
1389 1394 1.402984 GCGTGAGAACCGTGAGATCTT 60.403 52.381 0.00 0.00 0.00 2.40
1422 1427 0.336048 AAGGCCATGCTTGGTGGTAT 59.664 50.000 19.05 0.52 45.57 2.73
1462 1467 2.067386 ACCCTTGTTGGCCCTAAGTTA 58.933 47.619 0.00 0.00 0.00 2.24
1524 1529 2.711009 TCAGTCAGAACTTGGAACCCAT 59.289 45.455 0.00 0.00 31.71 4.00
1543 1548 0.834612 TCGGTCTTCCAACCACAAGT 59.165 50.000 0.00 0.00 39.43 3.16
1582 1587 3.781307 CGACATGGGGCCTCCGAA 61.781 66.667 0.00 0.00 38.76 4.30
1601 1606 4.269603 CCGAAGATGTATCAAGTGCTTCAG 59.730 45.833 0.00 0.00 33.27 3.02
1602 1607 4.867047 CGAAGATGTATCAAGTGCTTCAGT 59.133 41.667 0.00 0.00 33.27 3.41
1627 1632 2.890945 AGTAAATGGGTTGGCTTGACAC 59.109 45.455 0.00 0.00 0.00 3.67
1660 1665 2.171448 GGACATCAGCACCTTGGTCTAT 59.829 50.000 0.00 0.00 0.00 1.98
1663 1668 5.455326 GGACATCAGCACCTTGGTCTATAAT 60.455 44.000 0.00 0.00 0.00 1.28
1734 1739 6.316640 CCTGCTTCTCCAATGATGATATGATC 59.683 42.308 0.00 0.00 0.00 2.92
1772 1777 1.525175 AGGTTTGGGTTGTAGTGGGA 58.475 50.000 0.00 0.00 0.00 4.37
1774 1779 1.133730 GGTTTGGGTTGTAGTGGGACA 60.134 52.381 0.00 0.00 0.00 4.02
1974 1979 7.693951 GTCGTTGAAATTGTTATTCTGGATCTG 59.306 37.037 0.00 0.00 0.00 2.90
1975 1980 7.606073 TCGTTGAAATTGTTATTCTGGATCTGA 59.394 33.333 0.00 0.00 0.00 3.27
1976 1981 8.236586 CGTTGAAATTGTTATTCTGGATCTGAA 58.763 33.333 0.00 0.00 0.00 3.02
2049 2055 9.140286 CGATAAGTTTCAACATCTCTTTGAGTA 57.860 33.333 0.00 0.00 34.50 2.59
2054 2060 8.956426 AGTTTCAACATCTCTTTGAGTAAACAA 58.044 29.630 0.00 0.00 34.50 2.83
2150 2156 1.542679 GATCTCGGGTAGGGGGTCT 59.457 63.158 0.00 0.00 0.00 3.85
2161 2167 2.741092 GGGGTCTCGAACTGTGCA 59.259 61.111 0.00 0.00 0.00 4.57
2169 2175 1.135915 CTCGAACTGTGCATCTAGGCT 59.864 52.381 0.00 0.00 34.04 4.58
2224 2230 3.003173 CAGGTTCGGGCCCTCTCA 61.003 66.667 22.43 0.00 0.00 3.27
2298 2304 3.827302 ACAAGAGTTGATCTACCACGAGT 59.173 43.478 3.54 1.59 37.23 4.18
2346 2352 6.263168 GCTAGCCTATGGTATGATTGTTGTTT 59.737 38.462 2.29 0.00 0.00 2.83
2369 2375 4.620086 TCCTATGGACTAAACCTCTCCA 57.380 45.455 0.00 0.00 38.47 3.86
2396 2402 0.627451 TAGACACCGGAGAGGGCTAA 59.373 55.000 9.46 0.00 46.96 3.09
2444 2450 5.888724 GGGAGGAGATCTTCATATCGTATCA 59.111 44.000 3.21 0.00 0.00 2.15
2518 2524 9.823647 GAGGTCTTCAATCTTGTATCTTCATAA 57.176 33.333 0.00 0.00 0.00 1.90
2546 2552 1.483415 GTCCGGCCAAAGGTCATAGTA 59.517 52.381 2.24 0.00 0.00 1.82
2547 2553 2.104281 GTCCGGCCAAAGGTCATAGTAT 59.896 50.000 2.24 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.357325 AGAATCACCAGAGAGCCTTCTAA 58.643 43.478 0.00 0.00 32.53 2.10
17 18 5.047448 TCACAGAAGAAGAATCACCAGAGAG 60.047 44.000 0.00 0.00 0.00 3.20
27 28 8.137745 AGAGAAGAGATTCACAGAAGAAGAAT 57.862 34.615 0.00 0.00 34.88 2.40
38 39 7.756722 CAGAAGAAAGAGAGAGAAGAGATTCAC 59.243 40.741 0.00 0.00 0.00 3.18
59 60 0.883833 GCCACAACCACATCCAGAAG 59.116 55.000 0.00 0.00 0.00 2.85
78 81 2.159366 ACACATCGGAGAAAGCTACTCG 60.159 50.000 12.56 9.24 43.58 4.18
80 83 3.093057 AGACACATCGGAGAAAGCTACT 58.907 45.455 0.00 0.00 43.58 2.57
81 84 3.512033 AGACACATCGGAGAAAGCTAC 57.488 47.619 0.00 0.00 43.58 3.58
85 88 2.159085 GGGGTAGACACATCGGAGAAAG 60.159 54.545 0.00 0.00 43.58 2.62
115 118 4.830046 GCCCTCTCATCTATAGAAGACACA 59.170 45.833 6.52 0.00 36.93 3.72
138 141 2.089854 GGCTGTATGAAGTGCCGTG 58.910 57.895 0.00 0.00 35.79 4.94
142 145 2.472909 GGCCGGCTGTATGAAGTGC 61.473 63.158 28.56 0.00 0.00 4.40
164 167 0.744057 CATACGGGCACATGCACTCA 60.744 55.000 4.31 0.00 43.67 3.41
187 190 0.888736 CACCACAGCGAAACATGGGA 60.889 55.000 0.00 0.00 36.47 4.37
201 204 4.927782 TGTCACCTGGCGCACCAC 62.928 66.667 10.83 0.00 42.67 4.16
250 253 5.705609 AAGCGGATTACAACAAATCAAGT 57.294 34.783 0.00 0.00 37.56 3.16
267 270 1.256812 ATGGAAGGAAACCAAAGCGG 58.743 50.000 0.00 0.00 40.93 5.52
322 325 8.785329 AATGTTAATCCTTTGAGAGAGAAGAC 57.215 34.615 0.00 0.00 0.00 3.01
356 359 3.270877 CTGGGGTTCCGTTATTTCTCAG 58.729 50.000 0.00 0.00 35.24 3.35
458 462 4.082679 GCTTCCTCTCAACTACGAAGAAGA 60.083 45.833 0.00 0.00 33.33 2.87
461 465 3.154710 TGCTTCCTCTCAACTACGAAGA 58.845 45.455 0.00 0.00 33.33 2.87
484 488 1.376609 GGGCCTAATGTTGCACCTCG 61.377 60.000 0.84 0.00 0.00 4.63
494 498 4.042187 AGCTTACTAATGGAGGGCCTAATG 59.958 45.833 5.73 0.00 34.31 1.90
688 693 9.412460 TCTCAAAGAACCATGCATCTTTATTAT 57.588 29.630 18.11 0.84 42.41 1.28
786 791 7.471721 TCTGTATCATTACGCAAAATCCTTTG 58.528 34.615 0.00 0.00 44.11 2.77
787 792 7.624360 TCTGTATCATTACGCAAAATCCTTT 57.376 32.000 0.00 0.00 0.00 3.11
790 795 8.682128 TTTTTCTGTATCATTACGCAAAATCC 57.318 30.769 0.00 0.00 28.98 3.01
912 917 4.954875 CAACCTTTTGCCTTAATTGTCCA 58.045 39.130 0.00 0.00 0.00 4.02
937 942 1.943340 GATCGGCCAGGATGAGAAAAC 59.057 52.381 2.24 0.00 39.69 2.43
972 977 2.548057 TGAAATCAAGTCAAGCGGTGTC 59.452 45.455 0.00 0.00 0.00 3.67
975 980 3.214328 AGTTGAAATCAAGTCAAGCGGT 58.786 40.909 0.00 0.00 34.64 5.68
988 993 7.404671 ACTAACTGGTTTTGTGAGTTGAAAT 57.595 32.000 0.00 0.00 32.27 2.17
1009 1014 9.498176 GTAAAACTAGAAAGTGGAATGGAACTA 57.502 33.333 0.00 0.00 35.62 2.24
1011 1016 7.309012 GGGTAAAACTAGAAAGTGGAATGGAAC 60.309 40.741 0.00 0.00 35.62 3.62
1072 1077 4.365514 TGACCTGTTGTGGATGTATTGT 57.634 40.909 0.00 0.00 0.00 2.71
1074 1079 5.003804 GTCTTGACCTGTTGTGGATGTATT 58.996 41.667 0.00 0.00 0.00 1.89
1095 1100 3.004024 TCTCGAAGGTAACACAACGTC 57.996 47.619 0.00 0.00 41.41 4.34
1096 1101 3.441496 TTCTCGAAGGTAACACAACGT 57.559 42.857 0.00 0.00 41.41 3.99
1099 1104 4.446385 CGACATTTCTCGAAGGTAACACAA 59.554 41.667 0.00 0.00 35.58 3.33
1112 1117 3.198068 TCAGGCTATTGCGACATTTCTC 58.802 45.455 0.00 0.00 40.82 2.87
1117 1122 2.916702 TCATCAGGCTATTGCGACAT 57.083 45.000 0.00 0.00 40.82 3.06
1118 1123 2.168313 TCTTCATCAGGCTATTGCGACA 59.832 45.455 0.00 0.00 40.82 4.35
1140 1145 3.497115 TGCCCAACTCACCTGCCA 61.497 61.111 0.00 0.00 0.00 4.92
1234 1239 4.592192 AGGATCGGCACCGCATCG 62.592 66.667 3.66 0.00 39.59 3.84
1258 1263 2.050144 AGATCCGGCATGTCCTTGTAT 58.950 47.619 0.00 0.00 0.00 2.29
1315 1320 3.058155 GCTTAGTAATCCGCTCGATGAGA 60.058 47.826 0.00 0.00 0.00 3.27
1340 1345 4.023291 TGAAACTTGTTGGCCTCTTCTTT 58.977 39.130 3.32 0.00 0.00 2.52
1376 1381 4.290942 AGGAGGATTAAGATCTCACGGTT 58.709 43.478 0.00 0.00 32.66 4.44
1381 1386 7.353414 CTTGTGTAGGAGGATTAAGATCTCA 57.647 40.000 0.00 0.00 32.66 3.27
1422 1427 0.965866 AAGCTCATGGACGTCGAGGA 60.966 55.000 14.15 14.15 0.00 3.71
1524 1529 0.834612 ACTTGTGGTTGGAAGACCGA 59.165 50.000 0.00 0.00 42.83 4.69
1543 1548 1.143889 TGTTGTTGGTGACCTATGGCA 59.856 47.619 2.11 0.00 0.00 4.92
1601 1606 2.723273 AGCCAACCCATTTACTGCTAC 58.277 47.619 0.00 0.00 0.00 3.58
1602 1607 3.088532 CAAGCCAACCCATTTACTGCTA 58.911 45.455 0.00 0.00 0.00 3.49
1611 1616 0.105760 TTGGTGTCAAGCCAACCCAT 60.106 50.000 0.00 0.00 40.69 4.00
1643 1648 5.367937 AGTCATTATAGACCAAGGTGCTGAT 59.632 40.000 0.00 0.00 39.34 2.90
1660 1665 5.427157 TGTGGCCTCCATTACTTAGTCATTA 59.573 40.000 3.32 0.00 35.28 1.90
1663 1668 3.178046 TGTGGCCTCCATTACTTAGTCA 58.822 45.455 3.32 0.00 35.28 3.41
1711 1716 7.017319 AGATCATATCATCATTGGAGAAGCA 57.983 36.000 0.00 0.00 0.00 3.91
1772 1777 1.356124 AGATGCTCCAGAGTTGGTGT 58.644 50.000 0.00 0.00 45.26 4.16
1774 1779 2.264455 AGAAGATGCTCCAGAGTTGGT 58.736 47.619 0.00 0.00 45.26 3.67
1860 1865 6.211587 CAATTCCTGCATCTTAACCATGAA 57.788 37.500 0.00 0.00 0.00 2.57
1887 1892 8.388656 AGACTAAATGTCCCTCCTTATTAACA 57.611 34.615 0.00 0.00 46.46 2.41
1974 1979 8.424274 AGAACAAAGAACAAACCATGAAATTC 57.576 30.769 0.00 0.00 0.00 2.17
1976 1981 9.480053 CATAGAACAAAGAACAAACCATGAAAT 57.520 29.630 0.00 0.00 0.00 2.17
2021 2027 8.777865 TCAAAGAGATGTTGAAACTTATCGAT 57.222 30.769 2.16 2.16 32.13 3.59
2022 2028 7.872993 ACTCAAAGAGATGTTGAAACTTATCGA 59.127 33.333 0.31 0.00 34.68 3.59
2023 2029 8.023050 ACTCAAAGAGATGTTGAAACTTATCG 57.977 34.615 0.31 0.00 34.68 2.92
2071 2077 9.489084 AGTGTCGTAATATACACAATTATGCAT 57.511 29.630 3.79 3.79 46.71 3.96
2150 2156 1.134995 CAGCCTAGATGCACAGTTCGA 60.135 52.381 0.00 0.00 0.00 3.71
2161 2167 5.955355 GTCTCCTATTACCATCAGCCTAGAT 59.045 44.000 0.00 0.00 0.00 1.98
2169 2175 4.654262 GTCCCTTGTCTCCTATTACCATCA 59.346 45.833 0.00 0.00 0.00 3.07
2224 2230 3.179685 GGAGTAGGGTTTTACCTCCACT 58.820 50.000 0.00 0.00 42.09 4.00
2298 2304 4.332683 TCTAGGGTTTAGCCTCTCTGAA 57.667 45.455 3.32 0.00 37.43 3.02
2369 2375 5.078256 CCCTCTCCGGTGTCTATATAAACT 58.922 45.833 0.00 0.00 0.00 2.66
2396 2402 3.225104 TGTAACCGACTCTGTGTAACCT 58.775 45.455 0.00 0.00 34.36 3.50
2444 2450 1.898574 CGTGGAAGGCAAGCTTGGT 60.899 57.895 27.10 0.00 0.00 3.67
2546 2552 2.275418 GGGTGTCCGAATGGCCAT 59.725 61.111 14.09 14.09 34.14 4.40
2547 2553 4.041762 GGGGTGTCCGAATGGCCA 62.042 66.667 8.56 8.56 34.14 5.36
2554 2560 0.689745 CTGGATTAGGGGGTGTCCGA 60.690 60.000 0.00 0.00 36.01 4.55
2811 2818 7.749126 GGTGGAACAGTAAAACGATTCAAATAG 59.251 37.037 0.00 0.00 41.80 1.73


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

AutoCloner maintained by Alex Coulton.