Multiple sequence alignment - TraesCS3B01G066300

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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 TraesCS3B01G066300 chr3B 100.000 3017 0 0 1 3017 39544184 39547200 0.000000e+00 5572
1 TraesCS3B01G066300 chr3B 90.498 663 31 9 2206 2838 780286892 780286232 0.000000e+00 846
2 TraesCS3B01G066300 chr4D 90.119 1680 123 18 544 2209 25364441 25362791 0.000000e+00 2143
3 TraesCS3B01G066300 chr4D 89.043 1296 113 11 921 2209 25321332 25320059 0.000000e+00 1580
4 TraesCS3B01G066300 chr4D 89.275 1035 101 7 983 2016 25194510 25193485 0.000000e+00 1288
5 TraesCS3B01G066300 chr4D 88.710 496 42 7 1 490 25365436 25364949 7.200000e-166 593
6 TraesCS3B01G066300 chr4D 95.370 108 4 1 2901 3007 25360951 25360844 1.440000e-38 171
7 TraesCS3B01G066300 chr4B 89.661 1683 128 24 544 2209 37297868 37296215 0.000000e+00 2102
8 TraesCS3B01G066300 chr4B 89.469 1035 99 7 983 2016 37174481 37173456 0.000000e+00 1299
9 TraesCS3B01G066300 chr4B 96.355 439 16 0 2206 2644 472070648 472071086 0.000000e+00 723
10 TraesCS3B01G066300 chr4B 87.927 439 47 4 68 504 37298818 37298384 2.070000e-141 512
11 TraesCS3B01G066300 chr4B 94.444 198 9 2 2642 2838 472071114 472071310 1.360000e-78 303
12 TraesCS3B01G066300 chr4B 93.909 197 12 0 2642 2838 17049641 17049445 6.320000e-77 298
13 TraesCS3B01G066300 chr4A 89.969 1595 112 19 546 2136 578176611 578175061 0.000000e+00 2015
14 TraesCS3B01G066300 chr4A 87.992 1574 133 25 562 2131 578006618 578008139 0.000000e+00 1808
15 TraesCS3B01G066300 chr4A 89.179 1035 102 8 983 2016 578233566 578234591 0.000000e+00 1282
16 TraesCS3B01G066300 chr4A 96.591 440 14 1 2206 2644 708541975 708541536 0.000000e+00 728
17 TraesCS3B01G066300 chr4A 88.306 496 42 9 1 490 578177633 578177148 5.610000e-162 580
18 TraesCS3B01G066300 chr4A 88.235 493 43 8 1 487 578005583 578006066 2.610000e-160 575
19 TraesCS3B01G066300 chr7A 96.583 439 15 0 2206 2644 460311742 460311304 0.000000e+00 728
20 TraesCS3B01G066300 chr5B 96.560 436 15 0 2206 2641 700196873 700196438 0.000000e+00 723
21 TraesCS3B01G066300 chr5B 95.909 440 17 1 2206 2644 671201617 671201178 0.000000e+00 712
22 TraesCS3B01G066300 chr5B 86.452 620 71 10 2207 2815 220840942 220840325 0.000000e+00 667
23 TraesCS3B01G066300 chr5B 95.431 197 9 0 2642 2838 700196407 700196211 6.280000e-82 315
24 TraesCS3B01G066300 chr3A 96.364 440 15 1 2206 2644 24994886 24995325 0.000000e+00 723
25 TraesCS3B01G066300 chr2B 96.364 440 15 1 2206 2644 747861436 747860997 0.000000e+00 723
26 TraesCS3B01G066300 chr2B 94.416 197 11 0 2642 2838 747860969 747860773 1.360000e-78 303
27 TraesCS3B01G066300 chr1B 95.672 439 19 0 2206 2644 99693034 99692596 0.000000e+00 706
28 TraesCS3B01G066300 chr1B 94.416 197 10 1 2642 2838 417094225 417094030 4.890000e-78 302
29 TraesCS3B01G066300 chr6B 95.431 197 9 0 2642 2838 137414222 137414026 6.280000e-82 315
30 TraesCS3B01G066300 chr2A 94.388 196 11 0 2642 2837 726299791 726299986 4.890000e-78 302


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 TraesCS3B01G066300 chr3B 39544184 39547200 3016 False 5572.0 5572 100.000000 1 3017 1 chr3B.!!$F1 3016
1 TraesCS3B01G066300 chr3B 780286232 780286892 660 True 846.0 846 90.498000 2206 2838 1 chr3B.!!$R1 632
2 TraesCS3B01G066300 chr4D 25320059 25321332 1273 True 1580.0 1580 89.043000 921 2209 1 chr4D.!!$R2 1288
3 TraesCS3B01G066300 chr4D 25193485 25194510 1025 True 1288.0 1288 89.275000 983 2016 1 chr4D.!!$R1 1033
4 TraesCS3B01G066300 chr4D 25360844 25365436 4592 True 969.0 2143 91.399667 1 3007 3 chr4D.!!$R3 3006
5 TraesCS3B01G066300 chr4B 37296215 37298818 2603 True 1307.0 2102 88.794000 68 2209 2 chr4B.!!$R3 2141
6 TraesCS3B01G066300 chr4B 37173456 37174481 1025 True 1299.0 1299 89.469000 983 2016 1 chr4B.!!$R2 1033
7 TraesCS3B01G066300 chr4B 472070648 472071310 662 False 513.0 723 95.399500 2206 2838 2 chr4B.!!$F1 632
8 TraesCS3B01G066300 chr4A 578175061 578177633 2572 True 1297.5 2015 89.137500 1 2136 2 chr4A.!!$R2 2135
9 TraesCS3B01G066300 chr4A 578233566 578234591 1025 False 1282.0 1282 89.179000 983 2016 1 chr4A.!!$F1 1033
10 TraesCS3B01G066300 chr4A 578005583 578008139 2556 False 1191.5 1808 88.113500 1 2131 2 chr4A.!!$F2 2130
11 TraesCS3B01G066300 chr5B 220840325 220840942 617 True 667.0 667 86.452000 2207 2815 1 chr5B.!!$R1 608
12 TraesCS3B01G066300 chr5B 700196211 700196873 662 True 519.0 723 95.995500 2206 2838 2 chr5B.!!$R3 632
13 TraesCS3B01G066300 chr2B 747860773 747861436 663 True 513.0 723 95.390000 2206 2838 2 chr2B.!!$R1 632

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
979 1513 0.294304 CTTGCAAAACACAACGCACG 59.706 50.0 0.0 0.0 33.29 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2498 3063 0.304401 TCGTCGTTCGTCTTCGTTCA 59.696 50.0 0.0 0.0 40.8 3.18 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
31 32 2.031163 ACGCTCAACCAGTCTGCC 59.969 61.111 0.00 0.00 0.00 4.85
52 53 7.670559 TCTGCCTCTTAGGACTAGTAAATATCC 59.329 40.741 0.00 0.00 37.67 2.59
60 61 2.824341 ACTAGTAAATATCCCCTCCGCG 59.176 50.000 0.00 0.00 0.00 6.46
87 89 7.040132 CCAGAAAAATATCTCCTGAATTAGGCC 60.040 40.741 0.00 0.00 46.87 5.19
184 186 1.957186 CGACGGCGGTCCTTTCAAA 60.957 57.895 17.71 0.00 40.17 2.69
195 197 2.361119 GTCCTTTCAAACCCCAAGTGTC 59.639 50.000 0.00 0.00 0.00 3.67
199 201 1.217916 TCAAACCCCAAGTGTCTGGA 58.782 50.000 0.00 0.00 38.96 3.86
227 229 9.836864 TTAATATCAAGATCAAGCTTAGCAGAA 57.163 29.630 7.07 0.00 0.00 3.02
362 369 6.263168 AGAACAAACACAGATAACAAAGGGAG 59.737 38.462 0.00 0.00 0.00 4.30
397 407 6.105333 ACATACAAAGCAAAATGTGTGTGTT 58.895 32.000 7.36 0.00 45.99 3.32
404 417 3.725740 GCAAAATGTGTGTGTTCTTCGAG 59.274 43.478 0.00 0.00 0.00 4.04
428 441 8.732746 AGTGAATAACATCATACAAACCCTAC 57.267 34.615 0.00 0.00 0.00 3.18
431 444 9.173021 TGAATAACATCATACAAACCCTACAAG 57.827 33.333 0.00 0.00 0.00 3.16
458 471 4.337555 ACATAATACAAGACTCGCGGTAGT 59.662 41.667 6.13 2.33 0.00 2.73
487 500 3.062234 GCTACGGACACACTAGCAAATTC 59.938 47.826 0.00 0.00 34.24 2.17
493 506 4.143094 GGACACACTAGCAAATTCGACTTC 60.143 45.833 0.00 0.00 0.00 3.01
495 508 3.997021 CACACTAGCAAATTCGACTTCCT 59.003 43.478 0.00 0.00 0.00 3.36
504 517 5.456822 GCAAATTCGACTTCCTTGATATTGC 59.543 40.000 0.00 0.00 31.82 3.56
505 518 5.757850 AATTCGACTTCCTTGATATTGCC 57.242 39.130 0.00 0.00 0.00 4.52
507 520 3.797039 TCGACTTCCTTGATATTGCCAG 58.203 45.455 0.00 0.00 0.00 4.85
508 521 3.450817 TCGACTTCCTTGATATTGCCAGA 59.549 43.478 0.00 0.00 0.00 3.86
519 1013 6.484364 TGATATTGCCAGAGAAGTGTATCA 57.516 37.500 0.00 0.00 0.00 2.15
523 1017 5.939764 TTGCCAGAGAAGTGTATCATACT 57.060 39.130 0.00 0.00 0.00 2.12
525 1019 7.603180 TTGCCAGAGAAGTGTATCATACTAT 57.397 36.000 0.00 0.00 0.00 2.12
526 1020 8.706322 TTGCCAGAGAAGTGTATCATACTATA 57.294 34.615 0.00 0.00 0.00 1.31
528 1022 7.094762 TGCCAGAGAAGTGTATCATACTATACG 60.095 40.741 0.00 0.00 35.48 3.06
529 1023 7.626664 GCCAGAGAAGTGTATCATACTATACGG 60.627 44.444 0.00 0.00 35.48 4.02
530 1024 7.606839 CCAGAGAAGTGTATCATACTATACGGA 59.393 40.741 0.00 0.00 35.48 4.69
531 1025 9.168451 CAGAGAAGTGTATCATACTATACGGAT 57.832 37.037 0.00 0.00 35.48 4.18
532 1026 9.386010 AGAGAAGTGTATCATACTATACGGATC 57.614 37.037 0.00 0.00 35.48 3.36
548 1050 2.359848 CGGATCCGTCACCAGTGTAATA 59.640 50.000 26.35 0.00 34.35 0.98
554 1056 3.066900 CCGTCACCAGTGTAATAGAGGAG 59.933 52.174 0.00 0.00 0.00 3.69
558 1060 5.185249 GTCACCAGTGTAATAGAGGAGAACA 59.815 44.000 0.00 0.00 0.00 3.18
559 1061 5.958380 TCACCAGTGTAATAGAGGAGAACAT 59.042 40.000 0.00 0.00 0.00 2.71
567 1069 9.601217 GTGTAATAGAGGAGAACATGTGTAAAT 57.399 33.333 0.00 0.00 0.00 1.40
588 1090 7.925703 AAATATTACATGTCTAAGACGACGG 57.074 36.000 0.00 0.00 36.71 4.79
589 1091 4.978083 ATTACATGTCTAAGACGACGGT 57.022 40.909 0.00 0.00 36.71 4.83
597 1101 3.091545 TCTAAGACGACGGTAACCCAAT 58.908 45.455 0.00 0.00 0.00 3.16
603 1107 1.134640 CGACGGTAACCCAATCATCCA 60.135 52.381 0.00 0.00 0.00 3.41
615 1119 3.056607 CCAATCATCCAGAACAAACCCAC 60.057 47.826 0.00 0.00 0.00 4.61
666 1171 4.360951 ACAGGGTATTTCGAAGGAAACA 57.639 40.909 0.00 0.00 44.43 2.83
679 1184 5.941058 TCGAAGGAAACATTTGGCATAACTA 59.059 36.000 0.00 0.00 0.00 2.24
681 1186 7.122055 TCGAAGGAAACATTTGGCATAACTATT 59.878 33.333 0.00 0.00 0.00 1.73
766 1289 3.947910 ATCCATTCTTGCACACTTTGG 57.052 42.857 0.00 0.00 0.00 3.28
777 1300 2.043411 CACACTTTGGCATCGTTTTCG 58.957 47.619 0.00 0.00 45.64 3.46
814 1338 6.496338 AAAAGAATCGGAAGTTACACATCC 57.504 37.500 0.00 0.00 32.91 3.51
821 1345 5.556915 TCGGAAGTTACACATCCAAATCTT 58.443 37.500 0.00 0.00 35.82 2.40
892 1421 6.261826 TCGTAGTATAAAGCTAACCTCACCTC 59.738 42.308 0.00 0.00 0.00 3.85
893 1422 5.873146 AGTATAAAGCTAACCTCACCTCC 57.127 43.478 0.00 0.00 0.00 4.30
894 1423 5.278061 AGTATAAAGCTAACCTCACCTCCA 58.722 41.667 0.00 0.00 0.00 3.86
895 1424 5.905913 AGTATAAAGCTAACCTCACCTCCAT 59.094 40.000 0.00 0.00 0.00 3.41
903 1432 1.073923 ACCTCACCTCCATCCACAAAC 59.926 52.381 0.00 0.00 0.00 2.93
918 1447 5.539979 TCCACAAACAAACATCATCCATTG 58.460 37.500 0.00 0.00 0.00 2.82
936 1465 6.334989 TCCATTGCTCAATCATCAATTTCAC 58.665 36.000 0.00 0.00 0.00 3.18
937 1466 6.071278 TCCATTGCTCAATCATCAATTTCACA 60.071 34.615 0.00 0.00 0.00 3.58
950 1479 9.122779 TCATCAATTTCACATCATACTATTGCA 57.877 29.630 0.00 0.00 0.00 4.08
953 1482 9.571810 TCAATTTCACATCATACTATTGCAAAC 57.428 29.630 1.71 0.00 0.00 2.93
975 1509 3.059306 CACAGTTCTTGCAAAACACAACG 59.941 43.478 19.59 9.36 0.00 4.10
979 1513 0.294304 CTTGCAAAACACAACGCACG 59.706 50.000 0.00 0.00 33.29 5.34
1207 1751 2.110213 GCACCGTCCACAAGGTCA 59.890 61.111 0.00 0.00 39.00 4.02
1337 1881 1.606889 GGTGTCACTCGGTCCTCCT 60.607 63.158 2.35 0.00 0.00 3.69
1343 1887 3.141488 CTCGGTCCTCCTGACGGG 61.141 72.222 0.00 0.00 45.46 5.28
1368 1912 0.798771 GCGACTCAGCGTTACTCCTG 60.799 60.000 0.00 0.00 0.00 3.86
1551 2095 4.954970 AACAGTGCCGGGCAGGTG 62.955 66.667 24.58 23.89 40.08 4.00
1641 2185 4.530857 GCCGCGTACATGAGCCCT 62.531 66.667 4.92 0.00 0.00 5.19
1965 2510 3.745803 GTCGCCGGGAGAGACGTT 61.746 66.667 2.18 0.00 0.00 3.99
2035 2590 4.319358 CACGCGCGTGTAAATGAC 57.681 55.556 45.19 0.00 40.91 3.06
2072 2627 7.758076 ACTGTCACATTCTCGAATCGTAAATAA 59.242 33.333 1.52 0.00 0.00 1.40
2083 2638 7.934457 TCGAATCGTAAATAACTAAGCTAGGT 58.066 34.615 1.52 0.00 0.00 3.08
2138 2701 1.825474 CTTGGAAGGGTCTCGCTCTAA 59.175 52.381 0.00 0.00 0.00 2.10
2158 2721 4.686191 AACATCTCTAGCAGATCCCTTG 57.314 45.455 0.00 0.00 40.20 3.61
2258 2823 8.899771 TCATCTTCAATCATAGTAGTACAACGA 58.100 33.333 2.52 0.00 0.00 3.85
2413 2978 1.598962 AGTCGGGAAGTCGTCGTGA 60.599 57.895 0.00 0.00 0.00 4.35
2433 2998 0.787084 TAAGGCCCCATGGAACCAAA 59.213 50.000 15.22 3.36 0.00 3.28
2434 2999 0.118952 AAGGCCCCATGGAACCAAAT 59.881 50.000 15.22 1.95 0.00 2.32
2498 3063 2.915604 AGGATCCAACCTGAAGACACAT 59.084 45.455 15.82 0.00 39.01 3.21
2546 3111 3.499338 TGAGCAAATCCACCAAAGACAT 58.501 40.909 0.00 0.00 0.00 3.06
2864 3459 7.664318 CCTTAAACCTGTTTTACAGTACCATCT 59.336 37.037 0.00 0.00 44.50 2.90
2871 3466 5.071250 TGTTTTACAGTACCATCTGGACAGT 59.929 40.000 2.55 3.27 39.48 3.55
2891 3486 2.674796 AGCGGAACAGATCCTGTAAC 57.325 50.000 0.00 0.00 44.62 2.50
2926 5314 2.224209 ACGAATATTCCCCGTGGTCATC 60.224 50.000 9.87 0.00 35.02 2.92
2936 5324 2.488153 CCCGTGGTCATCTTTTTCTTCC 59.512 50.000 0.00 0.00 0.00 3.46
2972 5360 2.342650 GCGAAATCCAGGCAGGCAA 61.343 57.895 0.00 0.00 37.29 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.300931 GCAGACTGGTTGAGCGTGA 60.301 57.895 4.26 0.00 0.00 4.35
14 15 2.031163 GGCAGACTGGTTGAGCGT 59.969 61.111 4.26 0.00 0.00 5.07
31 32 7.616542 GGAGGGGATATTTACTAGTCCTAAGAG 59.383 44.444 0.00 0.00 0.00 2.85
52 53 0.746563 TATTTTTCTGGCGCGGAGGG 60.747 55.000 8.83 0.00 46.11 4.30
87 89 7.667043 TGGTAAGCTTAGTGTGAAAACATAG 57.333 36.000 6.38 0.00 0.00 2.23
151 153 2.871133 CCGTCGCTAATGAACACTGTA 58.129 47.619 0.00 0.00 0.00 2.74
155 157 1.343821 CGCCGTCGCTAATGAACAC 59.656 57.895 0.00 0.00 0.00 3.32
161 163 2.234913 AAAGGACCGCCGTCGCTAAT 62.235 55.000 0.00 0.00 40.17 1.73
184 186 4.675063 ATTAATTCCAGACACTTGGGGT 57.325 40.909 0.00 0.00 38.81 4.95
227 229 9.975218 GTCAAGTGGGGTTATATAATTATCCAT 57.025 33.333 0.00 0.00 0.00 3.41
343 349 5.304686 TGTCTCCCTTTGTTATCTGTGTT 57.695 39.130 0.00 0.00 0.00 3.32
349 355 8.573035 TGTTTATGTTTGTCTCCCTTTGTTATC 58.427 33.333 0.00 0.00 0.00 1.75
354 360 7.881142 TGTATGTTTATGTTTGTCTCCCTTTG 58.119 34.615 0.00 0.00 0.00 2.77
397 407 8.869897 GTTTGTATGATGTTATTCACTCGAAGA 58.130 33.333 0.00 0.00 33.74 2.87
404 417 8.500753 TGTAGGGTTTGTATGATGTTATTCAC 57.499 34.615 0.00 0.00 0.00 3.18
428 441 7.358435 CCGCGAGTCTTGTATTATGTTATCTTG 60.358 40.741 8.23 0.00 0.00 3.02
431 444 5.919141 ACCGCGAGTCTTGTATTATGTTATC 59.081 40.000 8.23 0.00 0.00 1.75
470 483 3.326747 AGTCGAATTTGCTAGTGTGTCC 58.673 45.455 0.00 0.00 0.00 4.02
471 484 4.143094 GGAAGTCGAATTTGCTAGTGTGTC 60.143 45.833 0.00 0.00 0.00 3.67
487 500 3.797039 TCTGGCAATATCAAGGAAGTCG 58.203 45.455 0.00 0.00 0.00 4.18
493 506 4.521146 ACACTTCTCTGGCAATATCAAGG 58.479 43.478 0.00 0.00 0.00 3.61
495 508 6.888105 TGATACACTTCTCTGGCAATATCAA 58.112 36.000 0.00 0.00 0.00 2.57
504 517 7.606839 TCCGTATAGTATGATACACTTCTCTGG 59.393 40.741 5.28 0.00 32.70 3.86
505 518 8.549338 TCCGTATAGTATGATACACTTCTCTG 57.451 38.462 5.28 0.00 32.70 3.35
507 520 8.614346 GGATCCGTATAGTATGATACACTTCTC 58.386 40.741 5.28 0.00 32.70 2.87
508 521 7.280428 CGGATCCGTATAGTATGATACACTTCT 59.720 40.741 26.35 0.00 32.70 2.85
528 1022 2.981859 ATTACACTGGTGACGGATCC 57.018 50.000 0.00 0.00 41.09 3.36
529 1023 4.261656 CCTCTATTACACTGGTGACGGATC 60.262 50.000 7.78 0.00 41.09 3.36
530 1024 3.637229 CCTCTATTACACTGGTGACGGAT 59.363 47.826 7.78 0.00 41.09 4.18
531 1025 3.021695 CCTCTATTACACTGGTGACGGA 58.978 50.000 7.78 0.00 41.09 4.69
532 1026 3.021695 TCCTCTATTACACTGGTGACGG 58.978 50.000 7.78 0.00 44.60 4.79
535 1029 5.330233 TGTTCTCCTCTATTACACTGGTGA 58.670 41.667 7.78 0.00 0.00 4.02
536 1030 5.661056 TGTTCTCCTCTATTACACTGGTG 57.339 43.478 0.00 0.00 0.00 4.17
537 1031 5.721960 ACATGTTCTCCTCTATTACACTGGT 59.278 40.000 0.00 0.00 0.00 4.00
539 1033 6.634805 ACACATGTTCTCCTCTATTACACTG 58.365 40.000 0.00 0.00 0.00 3.66
540 1034 6.859112 ACACATGTTCTCCTCTATTACACT 57.141 37.500 0.00 0.00 0.00 3.55
567 1069 7.409697 GTTACCGTCGTCTTAGACATGTAATA 58.590 38.462 13.14 0.00 40.98 0.98
576 1078 2.198827 TGGGTTACCGTCGTCTTAGA 57.801 50.000 0.00 0.00 40.75 2.10
578 1080 2.824936 TGATTGGGTTACCGTCGTCTTA 59.175 45.455 0.00 0.00 40.75 2.10
581 1083 2.199236 GATGATTGGGTTACCGTCGTC 58.801 52.381 0.00 1.31 40.75 4.20
585 1087 2.193127 TCTGGATGATTGGGTTACCGT 58.807 47.619 0.00 0.00 40.75 4.83
588 1090 5.336451 GGTTTGTTCTGGATGATTGGGTTAC 60.336 44.000 0.00 0.00 0.00 2.50
589 1091 4.770010 GGTTTGTTCTGGATGATTGGGTTA 59.230 41.667 0.00 0.00 0.00 2.85
597 1101 1.780309 AGGTGGGTTTGTTCTGGATGA 59.220 47.619 0.00 0.00 0.00 2.92
603 1107 4.724279 AATAGACAGGTGGGTTTGTTCT 57.276 40.909 0.00 0.00 0.00 3.01
641 1146 6.943718 TGTTTCCTTCGAAATACCCTGTATTT 59.056 34.615 11.00 11.00 40.08 1.40
642 1147 6.478129 TGTTTCCTTCGAAATACCCTGTATT 58.522 36.000 0.00 0.00 40.08 1.89
643 1148 6.057321 TGTTTCCTTCGAAATACCCTGTAT 57.943 37.500 0.00 0.00 40.08 2.29
644 1149 5.486735 TGTTTCCTTCGAAATACCCTGTA 57.513 39.130 0.00 0.00 40.08 2.74
646 1151 5.897377 AATGTTTCCTTCGAAATACCCTG 57.103 39.130 0.00 0.00 40.08 4.45
647 1152 5.185056 CCAAATGTTTCCTTCGAAATACCCT 59.815 40.000 0.00 0.00 40.08 4.34
723 1228 7.765360 GGATATTCATGATGTTCCTTGCAAAAA 59.235 33.333 0.00 0.00 0.00 1.94
724 1229 7.093421 TGGATATTCATGATGTTCCTTGCAAAA 60.093 33.333 15.42 0.00 0.00 2.44
725 1230 6.380560 TGGATATTCATGATGTTCCTTGCAAA 59.619 34.615 15.42 0.00 0.00 3.68
726 1231 5.892686 TGGATATTCATGATGTTCCTTGCAA 59.107 36.000 15.42 0.00 0.00 4.08
727 1232 5.447757 TGGATATTCATGATGTTCCTTGCA 58.552 37.500 15.42 0.00 0.00 4.08
728 1233 6.585695 ATGGATATTCATGATGTTCCTTGC 57.414 37.500 15.42 0.00 0.00 4.01
729 1234 8.405418 AGAATGGATATTCATGATGTTCCTTG 57.595 34.615 15.42 0.00 44.14 3.61
730 1235 8.857098 CAAGAATGGATATTCATGATGTTCCTT 58.143 33.333 15.42 9.18 41.95 3.36
731 1236 7.039923 GCAAGAATGGATATTCATGATGTTCCT 60.040 37.037 15.42 1.68 41.95 3.36
732 1237 7.088905 GCAAGAATGGATATTCATGATGTTCC 58.911 38.462 0.00 3.86 41.95 3.62
733 1238 7.594015 GTGCAAGAATGGATATTCATGATGTTC 59.406 37.037 0.00 0.00 41.95 3.18
814 1338 3.076621 TGGCTGACTGTGCTAAGATTTG 58.923 45.455 0.00 0.00 0.00 2.32
821 1345 4.458989 CCTTAAATTTGGCTGACTGTGCTA 59.541 41.667 0.00 0.00 0.00 3.49
892 1421 4.021280 TGGATGATGTTTGTTTGTGGATGG 60.021 41.667 0.00 0.00 0.00 3.51
893 1422 5.136816 TGGATGATGTTTGTTTGTGGATG 57.863 39.130 0.00 0.00 0.00 3.51
894 1423 6.167685 CAATGGATGATGTTTGTTTGTGGAT 58.832 36.000 0.00 0.00 0.00 3.41
895 1424 5.539979 CAATGGATGATGTTTGTTTGTGGA 58.460 37.500 0.00 0.00 0.00 4.02
903 1432 5.656480 TGATTGAGCAATGGATGATGTTTG 58.344 37.500 0.00 0.00 0.00 2.93
918 1447 8.350722 AGTATGATGTGAAATTGATGATTGAGC 58.649 33.333 0.00 0.00 0.00 4.26
936 1465 7.755591 AGAACTGTGTTTGCAATAGTATGATG 58.244 34.615 0.00 0.00 0.00 3.07
937 1466 7.928307 AGAACTGTGTTTGCAATAGTATGAT 57.072 32.000 0.00 0.00 0.00 2.45
950 1479 4.626042 TGTGTTTTGCAAGAACTGTGTTT 58.374 34.783 18.68 0.00 0.00 2.83
953 1482 3.059306 CGTTGTGTTTTGCAAGAACTGTG 59.941 43.478 18.68 6.98 0.00 3.66
979 1513 1.852895 GATCTTGATCGCCGTGTGTAC 59.147 52.381 0.00 0.00 0.00 2.90
1233 1777 1.372582 GGTGAATGATCTTGAGCGCA 58.627 50.000 11.47 0.00 0.00 6.09
1269 1813 2.872732 ACAACTTCTACCTCCTCGTCA 58.127 47.619 0.00 0.00 0.00 4.35
1343 1887 2.807631 TAACGCTGAGTCGCCGGAAC 62.808 60.000 5.05 1.52 0.00 3.62
1356 1900 0.612174 TCAGCTCCAGGAGTAACGCT 60.612 55.000 18.37 6.32 31.39 5.07
1368 1912 4.899239 CCGCCGTCCATCAGCTCC 62.899 72.222 0.00 0.00 0.00 4.70
1641 2185 3.610791 CTCCGTGTCGAAGCGCTCA 62.611 63.158 12.06 0.00 0.00 4.26
1734 2278 1.076923 GAGGAGCTCCAGGACGGTA 60.077 63.158 33.90 0.00 38.89 4.02
2028 2583 9.114952 TGTGACAGTTCAACATTTAGTCATTTA 57.885 29.630 0.00 0.00 36.96 1.40
2029 2584 7.995289 TGTGACAGTTCAACATTTAGTCATTT 58.005 30.769 0.00 0.00 36.96 2.32
2030 2585 7.566760 TGTGACAGTTCAACATTTAGTCATT 57.433 32.000 0.00 0.00 36.96 2.57
2031 2586 7.750229 ATGTGACAGTTCAACATTTAGTCAT 57.250 32.000 0.00 0.00 36.96 3.06
2032 2587 7.498900 AGAATGTGACAGTTCAACATTTAGTCA 59.501 33.333 10.08 0.00 35.44 3.41
2033 2588 7.865707 AGAATGTGACAGTTCAACATTTAGTC 58.134 34.615 10.08 0.00 35.44 2.59
2034 2589 7.307396 CGAGAATGTGACAGTTCAACATTTAGT 60.307 37.037 10.08 2.13 35.44 2.24
2035 2590 7.011773 CGAGAATGTGACAGTTCAACATTTAG 58.988 38.462 10.08 4.14 35.44 1.85
2072 2627 6.884832 TGTATGTGCAAATACCTAGCTTAGT 58.115 36.000 21.78 0.00 32.93 2.24
2083 2638 6.126911 TGGTCCACTATCTGTATGTGCAAATA 60.127 38.462 0.00 0.00 0.00 1.40
2138 2701 3.652055 ACAAGGGATCTGCTAGAGATGT 58.348 45.455 8.78 1.43 41.91 3.06
2284 2849 3.031736 GCTAGGTGGTCTATGGTTCTGA 58.968 50.000 0.00 0.00 0.00 3.27
2292 2857 1.134159 AGTCGTCGCTAGGTGGTCTAT 60.134 52.381 0.00 0.00 0.00 1.98
2413 2978 1.014804 TTGGTTCCATGGGGCCTTAT 58.985 50.000 20.89 0.00 0.00 1.73
2433 2998 1.237285 GCGGTTGCTGTTCTGGTGAT 61.237 55.000 0.00 0.00 38.39 3.06
2434 2999 1.891919 GCGGTTGCTGTTCTGGTGA 60.892 57.895 0.00 0.00 38.39 4.02
2498 3063 0.304401 TCGTCGTTCGTCTTCGTTCA 59.696 50.000 0.00 0.00 40.80 3.18
2546 3111 2.420568 GGTGTGTCTCCGGCGGATA 61.421 63.158 31.23 20.74 0.00 2.59
2810 3405 4.452733 GCCGCCTCCAACGTAGCT 62.453 66.667 0.00 0.00 0.00 3.32
2841 3436 7.202112 TCCAGATGGTACTGTAAAACAGGTTTA 60.202 37.037 11.47 0.00 42.42 2.01
2842 3437 6.409925 TCCAGATGGTACTGTAAAACAGGTTT 60.410 38.462 11.47 0.00 42.42 3.27
2843 3438 5.072600 TCCAGATGGTACTGTAAAACAGGTT 59.927 40.000 11.47 0.00 42.42 3.50
2844 3439 4.595781 TCCAGATGGTACTGTAAAACAGGT 59.404 41.667 11.47 0.84 42.42 4.00
2845 3440 4.935808 GTCCAGATGGTACTGTAAAACAGG 59.064 45.833 11.47 0.00 42.42 4.00
2846 3441 5.547465 TGTCCAGATGGTACTGTAAAACAG 58.453 41.667 5.53 5.53 43.12 3.16
2847 3442 5.071250 ACTGTCCAGATGGTACTGTAAAACA 59.929 40.000 0.40 0.00 36.30 2.83
2853 3448 2.761208 GCTACTGTCCAGATGGTACTGT 59.239 50.000 0.40 13.90 36.30 3.55
2855 3450 2.025155 CGCTACTGTCCAGATGGTACT 58.975 52.381 0.40 0.00 36.34 2.73
2864 3459 1.476891 GATCTGTTCCGCTACTGTCCA 59.523 52.381 0.00 0.00 0.00 4.02
2891 3486 8.179615 GGGGAATATTCGTTTTACAGTAAACAG 58.820 37.037 9.32 3.36 37.77 3.16
2926 5314 3.002348 AGACGCGTGAAAGGAAGAAAAAG 59.998 43.478 20.70 0.00 0.00 2.27
2936 5324 3.777925 CGGCCAGACGCGTGAAAG 61.778 66.667 20.70 3.21 38.94 2.62
2956 5344 1.325476 CCCTTGCCTGCCTGGATTTC 61.325 60.000 0.00 0.00 38.35 2.17


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

AutoCloner maintained by Alex Coulton.