Multiple sequence alignment - TraesCS6D01G380700

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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 TraesCS6D01G380700 chr6D 100.000 3062 0 0 1 3062 461502905 461499844 0.000000e+00 5655.0
1 TraesCS6D01G380700 chr6D 95.580 1018 29 3 2057 3062 84654741 84655754 0.000000e+00 1616.0
2 TraesCS6D01G380700 chr6B 92.398 1618 79 14 476 2065 703390516 703388915 0.000000e+00 2266.0
3 TraesCS6D01G380700 chr6B 93.668 837 48 5 2056 2891 298817991 298817159 0.000000e+00 1247.0
4 TraesCS6D01G380700 chr6B 87.978 732 63 12 2338 3049 85211981 85212707 0.000000e+00 841.0
5 TraesCS6D01G380700 chr6B 94.377 409 19 1 8 416 703391753 703391349 2.590000e-175 625.0
6 TraesCS6D01G380700 chr6B 100.000 44 0 0 434 477 703391364 703391321 7.040000e-12 82.4
7 TraesCS6D01G380700 chr6A 92.397 1210 64 12 864 2065 608285980 608284791 0.000000e+00 1700.0
8 TraesCS6D01G380700 chr6A 91.420 1014 58 17 2057 3048 616209401 616210407 0.000000e+00 1363.0
9 TraesCS6D01G380700 chr6A 97.965 344 7 0 1722 2065 608156818 608156475 5.650000e-167 597.0
10 TraesCS6D01G380700 chr6A 90.000 90 8 1 1547 1635 608296575 608296486 6.940000e-22 115.0
11 TraesCS6D01G380700 chr6A 88.462 78 9 0 1325 1402 608296720 608296643 9.040000e-16 95.3
12 TraesCS6D01G380700 chr6A 94.915 59 2 1 764 821 234020750 234020692 1.170000e-14 91.6
13 TraesCS6D01G380700 chr4D 94.269 1012 34 9 2057 3048 419319223 419320230 0.000000e+00 1526.0
14 TraesCS6D01G380700 chr4D 89.474 57 6 0 765 821 398672190 398672246 4.240000e-09 73.1
15 TraesCS6D01G380700 chr3A 92.991 1013 47 12 2057 3048 550527425 550526416 0.000000e+00 1456.0
16 TraesCS6D01G380700 chr3A 93.548 62 3 1 761 821 24052304 24052365 1.170000e-14 91.6
17 TraesCS6D01G380700 chr3D 92.984 1012 46 10 2057 3048 123562956 123563962 0.000000e+00 1452.0
18 TraesCS6D01G380700 chr5B 92.278 1023 53 11 2056 3058 551767405 551766389 0.000000e+00 1428.0
19 TraesCS6D01G380700 chr5B 74.579 653 123 30 1411 2040 700418004 700417372 2.360000e-61 246.0
20 TraesCS6D01G380700 chr7B 91.793 987 57 11 2057 3026 150192988 150193967 0.000000e+00 1352.0
21 TraesCS6D01G380700 chr7B 87.252 706 70 18 2371 3062 706167876 706168575 0.000000e+00 787.0
22 TraesCS6D01G380700 chr7B 84.375 64 10 0 759 822 571894150 571894213 2.550000e-06 63.9
23 TraesCS6D01G380700 chr2B 90.936 1015 62 16 2057 3048 752860906 752859899 0.000000e+00 1338.0
24 TraesCS6D01G380700 chr2B 89.806 1030 65 11 2055 3048 673004158 673005183 0.000000e+00 1284.0
25 TraesCS6D01G380700 chr2B 86.776 1036 97 16 2057 3062 67945351 67946376 0.000000e+00 1118.0
26 TraesCS6D01G380700 chr2B 88.498 426 32 4 2654 3062 523268056 523268481 1.640000e-137 499.0
27 TraesCS6D01G380700 chr1D 89.270 671 52 6 2395 3048 418311837 418311170 0.000000e+00 822.0
28 TraesCS6D01G380700 chr3B 88.321 685 54 12 2386 3048 419800301 419799621 0.000000e+00 798.0
29 TraesCS6D01G380700 chr3B 82.114 246 17 11 489 724 825536689 825536917 5.210000e-43 185.0
30 TraesCS6D01G380700 chr1B 87.151 716 67 12 2368 3062 461269129 461269840 0.000000e+00 789.0
31 TraesCS6D01G380700 chr1B 91.228 57 5 0 761 817 496511867 496511923 9.100000e-11 78.7
32 TraesCS6D01G380700 chr1B 97.561 41 1 0 781 821 645407630 645407670 1.520000e-08 71.3
33 TraesCS6D01G380700 chr5D 74.006 654 126 26 1411 2040 548954131 548953498 3.070000e-55 226.0
34 TraesCS6D01G380700 chr5D 89.062 64 7 0 759 822 497855829 497855766 2.530000e-11 80.5
35 TraesCS6D01G380700 chr5D 86.667 60 7 1 759 818 488866753 488866695 7.090000e-07 65.8
36 TraesCS6D01G380700 chr1A 94.828 58 2 1 764 820 385353329 385353272 4.210000e-14 89.8
37 TraesCS6D01G380700 chr1A 93.182 44 1 2 778 821 575797414 575797373 2.550000e-06 63.9
38 TraesCS6D01G380700 chr1A 96.774 31 1 0 761 791 42514684 42514714 6.000000e-03 52.8
39 TraesCS6D01G380700 chr1A 100.000 28 0 0 793 820 369280298 369280325 6.000000e-03 52.8
40 TraesCS6D01G380700 chr2D 90.323 62 5 1 761 821 601035316 601035377 2.530000e-11 80.5
41 TraesCS6D01G380700 chr2A 89.062 64 7 0 759 822 1475916 1475979 2.530000e-11 80.5
42 TraesCS6D01G380700 chr2A 87.879 66 6 2 764 829 100821174 100821111 3.270000e-10 76.8
43 TraesCS6D01G380700 chr7D 88.889 63 7 0 759 821 110048977 110049039 9.100000e-11 78.7
44 TraesCS6D01G380700 chr4A 90.385 52 4 1 1411 1462 620290586 620290636 1.970000e-07 67.6


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 TraesCS6D01G380700 chr6D 461499844 461502905 3061 True 5655.000000 5655 100.000000 1 3062 1 chr6D.!!$R1 3061
1 TraesCS6D01G380700 chr6D 84654741 84655754 1013 False 1616.000000 1616 95.580000 2057 3062 1 chr6D.!!$F1 1005
2 TraesCS6D01G380700 chr6B 298817159 298817991 832 True 1247.000000 1247 93.668000 2056 2891 1 chr6B.!!$R1 835
3 TraesCS6D01G380700 chr6B 703388915 703391753 2838 True 991.133333 2266 95.591667 8 2065 3 chr6B.!!$R2 2057
4 TraesCS6D01G380700 chr6B 85211981 85212707 726 False 841.000000 841 87.978000 2338 3049 1 chr6B.!!$F1 711
5 TraesCS6D01G380700 chr6A 608284791 608285980 1189 True 1700.000000 1700 92.397000 864 2065 1 chr6A.!!$R3 1201
6 TraesCS6D01G380700 chr6A 616209401 616210407 1006 False 1363.000000 1363 91.420000 2057 3048 1 chr6A.!!$F1 991
7 TraesCS6D01G380700 chr4D 419319223 419320230 1007 False 1526.000000 1526 94.269000 2057 3048 1 chr4D.!!$F2 991
8 TraesCS6D01G380700 chr3A 550526416 550527425 1009 True 1456.000000 1456 92.991000 2057 3048 1 chr3A.!!$R1 991
9 TraesCS6D01G380700 chr3D 123562956 123563962 1006 False 1452.000000 1452 92.984000 2057 3048 1 chr3D.!!$F1 991
10 TraesCS6D01G380700 chr5B 551766389 551767405 1016 True 1428.000000 1428 92.278000 2056 3058 1 chr5B.!!$R1 1002
11 TraesCS6D01G380700 chr5B 700417372 700418004 632 True 246.000000 246 74.579000 1411 2040 1 chr5B.!!$R2 629
12 TraesCS6D01G380700 chr7B 150192988 150193967 979 False 1352.000000 1352 91.793000 2057 3026 1 chr7B.!!$F1 969
13 TraesCS6D01G380700 chr7B 706167876 706168575 699 False 787.000000 787 87.252000 2371 3062 1 chr7B.!!$F3 691
14 TraesCS6D01G380700 chr2B 752859899 752860906 1007 True 1338.000000 1338 90.936000 2057 3048 1 chr2B.!!$R1 991
15 TraesCS6D01G380700 chr2B 673004158 673005183 1025 False 1284.000000 1284 89.806000 2055 3048 1 chr2B.!!$F3 993
16 TraesCS6D01G380700 chr2B 67945351 67946376 1025 False 1118.000000 1118 86.776000 2057 3062 1 chr2B.!!$F1 1005
17 TraesCS6D01G380700 chr1D 418311170 418311837 667 True 822.000000 822 89.270000 2395 3048 1 chr1D.!!$R1 653
18 TraesCS6D01G380700 chr3B 419799621 419800301 680 True 798.000000 798 88.321000 2386 3048 1 chr3B.!!$R1 662
19 TraesCS6D01G380700 chr1B 461269129 461269840 711 False 789.000000 789 87.151000 2368 3062 1 chr1B.!!$F1 694
20 TraesCS6D01G380700 chr5D 548953498 548954131 633 True 226.000000 226 74.006000 1411 2040 1 chr5D.!!$R3 629

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
205 206 0.093875 TGTATTTGTAACTGCGCGCG 59.906 50.0 28.44 28.44 0.00 6.86 F
697 1504 0.179048 CTGCCAGGTGTCACTCAACA 60.179 55.0 2.35 0.00 35.97 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1083 1906 0.254178 ATGGGGTCACTGATGCTGAC 59.746 55.0 0.0 0.0 37.84 3.51 R
2595 3473 0.329261 CACCATTCTCCTTCCTGGCA 59.671 55.0 0.0 0.0 35.26 4.92 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
24 25 1.530891 CGCTTCGGGGATCCTCCTA 60.531 63.158 12.58 0.36 36.57 2.94
26 27 0.393448 GCTTCGGGGATCCTCCTAAC 59.607 60.000 12.58 0.00 36.57 2.34
51 52 1.135199 CGCTTAAGAGGTCCGCTTACA 60.135 52.381 14.05 6.00 0.00 2.41
100 101 6.968250 AGAAGATTTGCAGAAGAAACAAGAG 58.032 36.000 0.00 0.00 0.00 2.85
132 133 3.764885 AACAGTCTGTGTGCAAACTTC 57.235 42.857 8.83 0.00 40.26 3.01
157 158 1.288188 TGGCCTCATGGAGTCAATGA 58.712 50.000 9.90 9.90 34.57 2.57
173 174 5.527582 AGTCAATGATAATTGTAGCGAACCC 59.472 40.000 2.59 0.00 33.49 4.11
182 183 0.669625 GTAGCGAACCCTGGTGTGTC 60.670 60.000 0.00 0.00 0.00 3.67
202 203 5.957796 GTGTCTATTGTATTTGTAACTGCGC 59.042 40.000 0.00 0.00 0.00 6.09
203 204 5.188194 GTCTATTGTATTTGTAACTGCGCG 58.812 41.667 0.00 0.00 0.00 6.86
204 205 2.235238 TTGTATTTGTAACTGCGCGC 57.765 45.000 27.26 27.26 0.00 6.86
205 206 0.093875 TGTATTTGTAACTGCGCGCG 59.906 50.000 28.44 28.44 0.00 6.86
224 225 1.004560 TGAGAACCCAGCTTCTGCG 60.005 57.895 0.00 0.00 45.42 5.18
315 316 2.388232 GGGTTGCGCTTACGACCAG 61.388 63.158 9.73 0.00 43.93 4.00
404 405 1.374252 CGAAGCGTGTGCCCTAACT 60.374 57.895 0.00 0.00 44.31 2.24
405 406 0.949105 CGAAGCGTGTGCCCTAACTT 60.949 55.000 0.00 0.00 44.31 2.66
406 407 0.796927 GAAGCGTGTGCCCTAACTTC 59.203 55.000 0.00 0.00 44.31 3.01
407 408 0.396811 AAGCGTGTGCCCTAACTTCT 59.603 50.000 0.00 0.00 44.31 2.85
408 409 1.263356 AGCGTGTGCCCTAACTTCTA 58.737 50.000 0.00 0.00 44.31 2.10
409 410 1.204941 AGCGTGTGCCCTAACTTCTAG 59.795 52.381 0.00 0.00 44.31 2.43
410 411 1.641577 CGTGTGCCCTAACTTCTAGC 58.358 55.000 0.00 0.00 0.00 3.42
411 412 1.067142 CGTGTGCCCTAACTTCTAGCA 60.067 52.381 0.00 0.00 0.00 3.49
413 414 1.641577 GTGCCCTAACTTCTAGCACG 58.358 55.000 0.00 0.00 43.70 5.34
414 415 1.203994 GTGCCCTAACTTCTAGCACGA 59.796 52.381 0.00 0.00 43.70 4.35
415 416 2.108168 TGCCCTAACTTCTAGCACGAT 58.892 47.619 0.00 0.00 0.00 3.73
416 417 3.067742 GTGCCCTAACTTCTAGCACGATA 59.932 47.826 0.00 0.00 43.70 2.92
417 418 3.895656 TGCCCTAACTTCTAGCACGATAT 59.104 43.478 0.00 0.00 0.00 1.63
418 419 5.048224 GTGCCCTAACTTCTAGCACGATATA 60.048 44.000 0.00 0.00 43.70 0.86
419 420 5.715279 TGCCCTAACTTCTAGCACGATATAT 59.285 40.000 0.00 0.00 0.00 0.86
420 421 6.210784 TGCCCTAACTTCTAGCACGATATATT 59.789 38.462 0.00 0.00 0.00 1.28
421 422 7.097834 GCCCTAACTTCTAGCACGATATATTT 58.902 38.462 0.00 0.00 0.00 1.40
422 423 7.603024 GCCCTAACTTCTAGCACGATATATTTT 59.397 37.037 0.00 0.00 0.00 1.82
423 424 9.490379 CCCTAACTTCTAGCACGATATATTTTT 57.510 33.333 0.00 0.00 0.00 1.94
504 1311 2.478890 CGTCGAGGAGTATGGCCGT 61.479 63.158 1.35 1.35 0.00 5.68
506 1313 1.077285 TCGAGGAGTATGGCCGTGA 60.077 57.895 8.05 0.00 0.00 4.35
523 1330 0.456824 TGACGACGAGAGCAAGCATC 60.457 55.000 0.00 0.00 0.00 3.91
580 1387 1.003718 GAGGTGTGTGGCTGTACCC 60.004 63.158 0.00 0.00 37.83 3.69
581 1388 2.358247 GGTGTGTGGCTGTACCCG 60.358 66.667 0.00 0.00 37.83 5.28
603 1410 1.377202 CCGGCATGGTGCTAACACT 60.377 57.895 1.64 0.00 46.57 3.55
616 1423 1.816835 CTAACACTAGTGGCAGTCGGA 59.183 52.381 26.12 2.16 34.19 4.55
635 1442 3.426159 CGGAATTTCACAACTGGGATTCG 60.426 47.826 0.00 0.00 0.00 3.34
644 1451 2.744202 CAACTGGGATTCGGACTTTCAG 59.256 50.000 0.00 0.00 0.00 3.02
652 1459 4.867608 GGATTCGGACTTTCAGAGAAGAAG 59.132 45.833 0.00 0.00 0.00 2.85
660 1467 2.469274 TCAGAGAAGAAGCTGCCTTG 57.531 50.000 6.38 0.00 32.27 3.61
663 1470 1.905215 AGAGAAGAAGCTGCCTTGCTA 59.095 47.619 6.38 0.00 43.24 3.49
667 1474 1.818642 AGAAGCTGCCTTGCTACTTG 58.181 50.000 0.00 0.00 43.24 3.16
697 1504 0.179048 CTGCCAGGTGTCACTCAACA 60.179 55.000 2.35 0.00 35.97 3.33
716 1523 3.370104 ACAGAGTGGGTCTCCAGATTAG 58.630 50.000 0.00 0.00 45.05 1.73
736 1548 9.179909 AGATTAGAAGTATATATGACCAGGTCG 57.820 37.037 15.24 0.00 34.95 4.79
738 1550 5.077564 AGAAGTATATATGACCAGGTCGCA 58.922 41.667 15.24 5.25 34.95 5.10
741 1553 6.701145 AGTATATATGACCAGGTCGCATAG 57.299 41.667 15.24 0.00 34.95 2.23
744 1556 1.496060 ATGACCAGGTCGCATAGGAA 58.504 50.000 15.24 0.00 34.95 3.36
786 1599 2.201830 CCTGGTGGGTTAGGAATACCA 58.798 52.381 0.00 0.00 38.98 3.25
799 1612 5.161943 AGGAATACCACTGTTCACCTAAC 57.838 43.478 0.00 0.00 38.94 2.34
839 1655 7.864108 TGATTCAACTACATGGATAACTTGG 57.136 36.000 0.00 0.00 0.00 3.61
841 1657 8.106462 TGATTCAACTACATGGATAACTTGGAA 58.894 33.333 0.00 0.00 0.00 3.53
845 1661 8.768397 TCAACTACATGGATAACTTGGAACTAT 58.232 33.333 0.00 0.00 0.00 2.12
894 1710 4.596585 CCCCAAGCACCCGGTGTT 62.597 66.667 18.95 10.47 35.75 3.32
914 1730 1.149401 TTGGTGTTCATGCCCGTCA 59.851 52.632 0.00 0.00 0.00 4.35
983 1799 0.818445 GCCTCGTGACCGATCTCCTA 60.818 60.000 0.00 0.00 43.27 2.94
1065 1888 3.319198 AGACATCACGGCCGGGTT 61.319 61.111 29.71 17.93 0.00 4.11
1076 1899 2.178521 CCGGGTTGAGACGAGACG 59.821 66.667 0.00 0.00 0.00 4.18
1079 1902 2.572284 GGTTGAGACGAGACGGGG 59.428 66.667 0.00 0.00 0.00 5.73
1083 1906 1.248785 TTGAGACGAGACGGGGAAGG 61.249 60.000 0.00 0.00 0.00 3.46
1093 1916 1.153289 CGGGGAAGGTCAGCATCAG 60.153 63.158 0.00 0.00 0.00 2.90
1130 1953 8.929260 TGAGATCAACAAATAATGCATATCCT 57.071 30.769 0.00 0.00 0.00 3.24
1321 2151 1.204146 TTCTAGGCACATCTCCACCC 58.796 55.000 0.00 0.00 0.00 4.61
1385 2219 9.982651 GTATTCAAAATATACAGAGCACCTAGA 57.017 33.333 0.00 0.00 0.00 2.43
1466 2303 6.266103 TGCATGATTCTCTTTCCTTTTCAACT 59.734 34.615 0.00 0.00 0.00 3.16
1513 2350 3.840831 GCATACTGCAGTGACAGGA 57.159 52.632 29.57 8.56 44.26 3.86
1542 2379 3.799366 TCCTCACACGAAGCTTTTTACA 58.201 40.909 0.00 0.00 0.00 2.41
1751 2606 3.192230 CATCGCCGCCGCTAAACA 61.192 61.111 0.00 0.00 0.00 2.83
2019 2874 4.198530 AGAACAAAAATTTGGCCCACTTG 58.801 39.130 0.00 0.00 42.34 3.16
2273 3147 2.809174 CAACATGAGCGTCGCGGA 60.809 61.111 12.30 2.27 0.00 5.54
2595 3473 2.365617 AGTGGTGTCGAAGAAGTGATGT 59.634 45.455 0.00 0.00 39.69 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.067582 GATCCCCGAAGCGTACCAG 59.932 63.158 0.00 0.00 0.00 4.00
1 2 2.428925 GGATCCCCGAAGCGTACCA 61.429 63.158 0.00 0.00 0.00 3.25
3 4 1.363080 GAGGATCCCCGAAGCGTAC 59.637 63.158 8.55 0.00 37.58 3.67
4 5 3.851955 GAGGATCCCCGAAGCGTA 58.148 61.111 8.55 0.00 37.58 4.42
24 25 1.275573 GGACCTCTTAAGCGACTGGTT 59.724 52.381 0.00 0.00 39.56 3.67
26 27 0.179134 CGGACCTCTTAAGCGACTGG 60.179 60.000 0.00 0.00 0.00 4.00
51 52 6.158598 TCTTTGCCGTTACTTATTCGTAACT 58.841 36.000 10.84 0.00 44.32 2.24
87 88 7.904558 AAGGATTTTTCCTCTTGTTTCTTCT 57.095 32.000 0.00 0.00 39.65 2.85
100 101 6.438763 CACACAGACTGTTAAGGATTTTTCC 58.561 40.000 5.04 0.00 0.00 3.13
132 133 3.824133 TGACTCCATGAGGCCATAATTG 58.176 45.455 5.01 0.00 36.76 2.32
157 158 3.054655 ACACCAGGGTTCGCTACAATTAT 60.055 43.478 0.00 0.00 0.00 1.28
173 174 8.443160 CAGTTACAAATACAATAGACACACCAG 58.557 37.037 0.00 0.00 0.00 4.00
182 183 3.960002 GCGCGCAGTTACAAATACAATAG 59.040 43.478 29.10 0.00 0.00 1.73
202 203 2.357517 AAGCTGGGTTCTCACGCG 60.358 61.111 3.53 3.53 38.73 6.01
203 204 1.004440 AGAAGCTGGGTTCTCACGC 60.004 57.895 8.94 0.00 30.55 5.34
204 205 1.294659 GCAGAAGCTGGGTTCTCACG 61.295 60.000 11.44 3.70 34.38 4.35
205 206 1.294659 CGCAGAAGCTGGGTTCTCAC 61.295 60.000 11.44 6.95 39.17 3.51
224 225 9.431887 TGACAAAATAGGTGTTACTAATGAGTC 57.568 33.333 0.00 0.00 37.10 3.36
276 277 9.529823 CAACCCTAAGTATGACTGGTATATAGA 57.470 37.037 0.00 0.00 0.00 1.98
279 280 6.295123 CGCAACCCTAAGTATGACTGGTATAT 60.295 42.308 0.00 0.00 0.00 0.86
284 285 2.550978 CGCAACCCTAAGTATGACTGG 58.449 52.381 0.00 0.00 0.00 4.00
296 297 2.047560 GGTCGTAAGCGCAACCCT 60.048 61.111 11.47 0.00 38.14 4.34
315 316 7.227049 TGACCCAAAAAGAAAAGATGATACC 57.773 36.000 0.00 0.00 0.00 2.73
364 365 3.879295 GGTGATCTTGACACACCCATATG 59.121 47.826 13.81 0.00 45.53 1.78
386 387 0.949105 AAGTTAGGGCACACGCTTCG 60.949 55.000 0.00 0.00 40.12 3.79
422 423 4.465886 TGCTAGAAGTTACCCAGCAAAAA 58.534 39.130 0.00 0.00 39.18 1.94
423 424 4.093472 TGCTAGAAGTTACCCAGCAAAA 57.907 40.909 0.00 0.00 39.18 2.44
424 425 3.780804 TGCTAGAAGTTACCCAGCAAA 57.219 42.857 0.00 0.00 39.18 3.68
425 426 3.263170 TCATGCTAGAAGTTACCCAGCAA 59.737 43.478 0.00 0.00 44.68 3.91
426 427 2.837591 TCATGCTAGAAGTTACCCAGCA 59.162 45.455 0.00 0.00 45.51 4.41
427 428 3.543680 TCATGCTAGAAGTTACCCAGC 57.456 47.619 0.00 0.00 0.00 4.85
428 429 5.698545 GCTAATCATGCTAGAAGTTACCCAG 59.301 44.000 0.00 0.00 0.00 4.45
429 430 5.366768 AGCTAATCATGCTAGAAGTTACCCA 59.633 40.000 0.00 0.00 39.21 4.51
430 431 5.859495 AGCTAATCATGCTAGAAGTTACCC 58.141 41.667 0.00 0.00 39.21 3.69
431 432 7.382759 GTGTAGCTAATCATGCTAGAAGTTACC 59.617 40.741 0.00 0.00 42.74 2.85
432 433 7.921214 TGTGTAGCTAATCATGCTAGAAGTTAC 59.079 37.037 0.00 4.14 42.74 2.50
433 434 8.007405 TGTGTAGCTAATCATGCTAGAAGTTA 57.993 34.615 0.00 0.00 42.74 2.24
434 435 6.878317 TGTGTAGCTAATCATGCTAGAAGTT 58.122 36.000 0.00 0.00 42.74 2.66
435 436 6.471233 TGTGTAGCTAATCATGCTAGAAGT 57.529 37.500 0.00 0.00 42.74 3.01
436 437 7.776933 TTTGTGTAGCTAATCATGCTAGAAG 57.223 36.000 0.00 0.00 42.74 2.85
504 1311 0.456824 GATGCTTGCTCTCGTCGTCA 60.457 55.000 0.00 0.00 0.00 4.35
506 1313 0.457509 CAGATGCTTGCTCTCGTCGT 60.458 55.000 0.00 0.00 0.00 4.34
523 1330 1.949525 CCCCTGTTCACAACACTTCAG 59.050 52.381 0.00 0.00 36.25 3.02
581 1388 4.794648 TAGCACCATGCCGGCCAC 62.795 66.667 26.77 6.66 46.52 5.01
603 1410 2.037902 TGTGAAATTCCGACTGCCACTA 59.962 45.455 0.00 0.00 0.00 2.74
616 1423 3.506067 GTCCGAATCCCAGTTGTGAAATT 59.494 43.478 0.00 0.00 0.00 1.82
635 1442 2.741517 GCAGCTTCTTCTCTGAAAGTCC 59.258 50.000 0.00 0.00 33.76 3.85
644 1451 2.006169 GTAGCAAGGCAGCTTCTTCTC 58.994 52.381 9.73 0.00 43.70 2.87
652 1459 0.036010 TCTCCAAGTAGCAAGGCAGC 60.036 55.000 0.00 0.00 0.00 5.25
660 1467 2.544069 GCAGTACGGATCTCCAAGTAGC 60.544 54.545 0.00 0.00 35.14 3.58
663 1470 0.824759 GGCAGTACGGATCTCCAAGT 59.175 55.000 0.00 0.00 35.14 3.16
667 1474 1.043673 ACCTGGCAGTACGGATCTCC 61.044 60.000 14.43 0.00 0.00 3.71
697 1504 4.264623 ACTTCTAATCTGGAGACCCACTCT 60.265 45.833 0.00 0.00 44.37 3.24
716 1523 5.386958 TGCGACCTGGTCATATATACTTC 57.613 43.478 25.42 0.00 32.09 3.01
753 1565 2.446435 CCACCAGGGTTGAAGTTATGG 58.554 52.381 0.00 0.00 0.00 2.74
786 1599 3.497942 GGTTGGATGGTTAGGTGAACAGT 60.498 47.826 0.00 0.00 40.09 3.55
787 1600 3.081804 GGTTGGATGGTTAGGTGAACAG 58.918 50.000 0.00 0.00 40.09 3.16
791 1604 2.039746 CTGTGGTTGGATGGTTAGGTGA 59.960 50.000 0.00 0.00 0.00 4.02
817 1633 8.109634 AGTTCCAAGTTATCCATGTAGTTGAAT 58.890 33.333 0.00 0.00 0.00 2.57
839 1655 9.988350 AACGTGAATTGATCAATGTTATAGTTC 57.012 29.630 21.39 13.22 40.50 3.01
845 1661 9.767684 GAACATAACGTGAATTGATCAATGTTA 57.232 29.630 21.39 21.62 42.01 2.41
867 1683 3.372730 GCTTGGGGCGCATGAACA 61.373 61.111 19.51 0.00 0.00 3.18
887 1703 1.028905 ATGAACACCAACAACACCGG 58.971 50.000 0.00 0.00 0.00 5.28
894 1710 1.152860 ACGGGCATGAACACCAACA 60.153 52.632 0.00 0.00 0.00 3.33
914 1730 0.311790 CCAAAGTGCGTGCTGAACAT 59.688 50.000 0.00 0.00 0.00 2.71
983 1799 0.109458 CATCGCACAACAGCAATGCT 60.109 50.000 0.00 0.00 40.77 3.79
1065 1888 1.677966 CCTTCCCCGTCTCGTCTCA 60.678 63.158 0.00 0.00 0.00 3.27
1076 1899 0.393537 CACTGATGCTGACCTTCCCC 60.394 60.000 0.00 0.00 0.00 4.81
1083 1906 0.254178 ATGGGGTCACTGATGCTGAC 59.746 55.000 0.00 0.00 37.84 3.51
1130 1953 2.116983 GAGCAGCAAGACAGGACCCA 62.117 60.000 0.00 0.00 0.00 4.51
1219 2048 7.892778 TGCGTTTAAGAATACAGATTGTACA 57.107 32.000 0.00 0.00 35.42 2.90
1279 2109 9.832445 AGAAAGAGTACAGATTGTGTTTAAGAA 57.168 29.630 0.00 0.00 40.94 2.52
1282 2112 9.706691 CCTAGAAAGAGTACAGATTGTGTTTAA 57.293 33.333 0.00 0.00 40.94 1.52
1283 2113 7.817962 GCCTAGAAAGAGTACAGATTGTGTTTA 59.182 37.037 0.00 0.00 40.94 2.01
1284 2114 6.651225 GCCTAGAAAGAGTACAGATTGTGTTT 59.349 38.462 0.00 0.00 40.94 2.83
1285 2115 6.166982 GCCTAGAAAGAGTACAGATTGTGTT 58.833 40.000 0.00 0.00 40.94 3.32
1286 2116 5.246203 TGCCTAGAAAGAGTACAGATTGTGT 59.754 40.000 0.00 0.00 43.86 3.72
1287 2117 5.578727 GTGCCTAGAAAGAGTACAGATTGTG 59.421 44.000 0.00 0.00 0.00 3.33
1288 2118 5.246203 TGTGCCTAGAAAGAGTACAGATTGT 59.754 40.000 0.00 0.00 0.00 2.71
1289 2119 5.724328 TGTGCCTAGAAAGAGTACAGATTG 58.276 41.667 0.00 0.00 0.00 2.67
1290 2120 6.382570 AGATGTGCCTAGAAAGAGTACAGATT 59.617 38.462 0.00 0.00 0.00 2.40
1291 2121 5.896678 AGATGTGCCTAGAAAGAGTACAGAT 59.103 40.000 0.00 0.00 0.00 2.90
1292 2122 5.265191 AGATGTGCCTAGAAAGAGTACAGA 58.735 41.667 0.00 0.00 0.00 3.41
1293 2123 5.451242 GGAGATGTGCCTAGAAAGAGTACAG 60.451 48.000 0.00 0.00 0.00 2.74
1385 2219 8.962679 TCGGTATTAAAATTAATGGTCTTGCTT 58.037 29.630 8.34 0.00 35.20 3.91
1510 2347 1.681793 CGTGTGAGGATCCGTATTCCT 59.318 52.381 5.98 0.00 46.41 3.36
1511 2348 1.679680 TCGTGTGAGGATCCGTATTCC 59.320 52.381 5.98 0.00 0.00 3.01
1512 2349 3.372954 CTTCGTGTGAGGATCCGTATTC 58.627 50.000 5.98 0.00 0.00 1.75
1513 2350 2.481449 GCTTCGTGTGAGGATCCGTATT 60.481 50.000 5.98 0.00 0.00 1.89
1542 2379 0.407139 AGGGCTGCATTTGAAGGAGT 59.593 50.000 0.50 0.00 0.00 3.85
2019 2874 2.357009 CAGAAATGTGATGCTACTGGCC 59.643 50.000 0.00 0.00 40.92 5.36
2123 2981 7.875041 CCCTCCAAGTCTTGTACTCAATATATG 59.125 40.741 11.61 0.00 37.50 1.78
2273 3147 1.996798 TTCTCTCCAGTCTGACCGTT 58.003 50.000 3.76 0.00 0.00 4.44
2595 3473 0.329261 CACCATTCTCCTTCCTGGCA 59.671 55.000 0.00 0.00 35.26 4.92
3026 3927 1.358759 CGCCGCACTTTTCTTTGGT 59.641 52.632 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.