Multiple sequence alignment - TraesCS3D01G152200

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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 TraesCS3D01G152200 chr3D 100.000 8229 0 0 1 8229 116398380 116390152 0.000000e+00 15197.0
1 TraesCS3D01G152200 chr3D 97.723 966 22 0 7264 8229 116351782 116350817 0.000000e+00 1663.0
2 TraesCS3D01G152200 chr3D 96.794 967 31 0 7263 8229 390069970 390070936 0.000000e+00 1615.0
3 TraesCS3D01G152200 chr6D 92.669 7270 388 64 61 7263 72353586 72360777 0.000000e+00 10338.0
4 TraesCS3D01G152200 chr6D 92.019 5438 341 62 315 5715 426967819 426962438 0.000000e+00 7552.0
5 TraesCS3D01G152200 chr6D 91.971 1644 104 18 312 1951 29939884 29941503 0.000000e+00 2279.0
6 TraesCS3D01G152200 chr6D 96.998 966 29 0 7264 8229 141941208 141942173 0.000000e+00 1624.0
7 TraesCS3D01G152200 chr6D 96.687 966 31 1 7264 8229 97871517 97870553 0.000000e+00 1605.0
8 TraesCS3D01G152200 chr6D 93.015 272 14 4 56 322 426968111 426967840 7.740000e-105 392.0
9 TraesCS3D01G152200 chr2D 91.701 7266 458 83 56 7265 543503636 543496460 0.000000e+00 9943.0
10 TraesCS3D01G152200 chr2D 93.181 6673 383 46 599 7250 428599395 428606016 0.000000e+00 9736.0
11 TraesCS3D01G152200 chr2D 93.959 6274 318 40 1018 7263 554143479 554137239 0.000000e+00 9430.0
12 TraesCS3D01G152200 chr2D 92.131 6748 415 58 313 7040 324886387 324879736 0.000000e+00 9413.0
13 TraesCS3D01G152200 chr2D 90.218 7033 547 87 312 7263 38172434 38165462 0.000000e+00 9046.0
14 TraesCS3D01G152200 chr2D 96.691 967 30 2 7264 8229 119798036 119797071 0.000000e+00 1607.0
15 TraesCS3D01G152200 chr2D 95.167 269 3 8 1 262 554303143 554302878 4.590000e-112 416.0
16 TraesCS3D01G152200 chr2D 100.000 51 0 0 1 51 428582573 428582623 2.450000e-15 95.3
17 TraesCS3D01G152200 chr5D 91.703 7256 464 75 56 7263 438205903 438198738 0.000000e+00 9937.0
18 TraesCS3D01G152200 chr5D 92.057 7000 442 65 314 7264 383615990 383609056 0.000000e+00 9742.0
19 TraesCS3D01G152200 chr5D 88.842 3083 266 52 692 3734 45277339 45274295 0.000000e+00 3716.0
20 TraesCS3D01G152200 chr5D 93.595 1608 90 13 408 2011 464294779 464296377 0.000000e+00 2386.0
21 TraesCS3D01G152200 chr5D 94.815 270 10 3 56 322 16438321 16438589 1.280000e-112 418.0
22 TraesCS3D01G152200 chr5D 92.754 276 13 6 52 322 464294067 464294340 7.740000e-105 392.0
23 TraesCS3D01G152200 chr5D 96.226 53 2 0 1 53 464293965 464294017 4.090000e-13 87.9
24 TraesCS3D01G152200 chr2B 91.507 7006 473 78 312 7263 366596881 366589944 0.000000e+00 9529.0
25 TraesCS3D01G152200 chr2B 93.431 274 11 6 56 322 366597171 366596898 4.630000e-107 399.0
26 TraesCS3D01G152200 chr4D 94.070 6020 292 34 1267 7263 179912092 179918069 0.000000e+00 9079.0
27 TraesCS3D01G152200 chr4D 89.374 7049 536 118 312 7263 276871824 276864892 0.000000e+00 8671.0
28 TraesCS3D01G152200 chr4D 96.998 966 28 1 7264 8229 100194644 100195608 0.000000e+00 1622.0
29 TraesCS3D01G152200 chr4D 96.894 966 30 0 7264 8229 371784894 371783929 0.000000e+00 1618.0
30 TraesCS3D01G152200 chr4D 96.791 966 31 0 7264 8229 100187755 100188720 0.000000e+00 1613.0
31 TraesCS3D01G152200 chr4D 93.407 273 12 4 56 322 179896963 179897235 4.630000e-107 399.0
32 TraesCS3D01G152200 chr4A 88.848 6851 639 83 468 7263 348497531 348504311 0.000000e+00 8303.0
33 TraesCS3D01G152200 chr4A 85.774 3135 318 59 692 3767 279447509 279450574 0.000000e+00 3201.0
34 TraesCS3D01G152200 chr4A 89.091 275 15 8 313 583 163306621 163306358 2.210000e-85 327.0
35 TraesCS3D01G152200 chr4B 89.092 5409 490 69 1895 7263 115055819 115050471 0.000000e+00 6628.0
36 TraesCS3D01G152200 chr7A 89.748 4994 426 57 312 5272 206773160 206768220 0.000000e+00 6307.0
37 TraesCS3D01G152200 chr1A 89.132 4987 445 65 312 5262 278228694 278223769 0.000000e+00 6117.0
38 TraesCS3D01G152200 chr1A 89.464 4869 416 69 56 4881 124221345 124216531 0.000000e+00 6059.0
39 TraesCS3D01G152200 chr1A 88.841 4884 425 65 312 5152 252738828 252743634 0.000000e+00 5890.0
40 TraesCS3D01G152200 chr2A 90.101 4657 373 49 312 4951 771244898 771249483 0.000000e+00 5965.0
41 TraesCS3D01G152200 chr7D 91.795 2803 155 31 312 3105 195581675 195578939 0.000000e+00 3832.0
42 TraesCS3D01G152200 chr7D 90.594 2020 130 39 56 2034 122819916 122817916 0.000000e+00 2623.0
43 TraesCS3D01G152200 chr7D 96.907 970 30 0 7260 8229 122963919 122964888 0.000000e+00 1626.0
44 TraesCS3D01G152200 chr1D 91.607 2228 106 23 56 2249 56174375 56176555 0.000000e+00 3003.0
45 TraesCS3D01G152200 chrUn 91.882 271 18 4 56 322 89954139 89954409 7.800000e-100 375.0


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 TraesCS3D01G152200 chr3D 116390152 116398380 8228 True 15197.0 15197 100.000000 1 8229 1 chr3D.!!$R2 8228
1 TraesCS3D01G152200 chr3D 116350817 116351782 965 True 1663.0 1663 97.723000 7264 8229 1 chr3D.!!$R1 965
2 TraesCS3D01G152200 chr3D 390069970 390070936 966 False 1615.0 1615 96.794000 7263 8229 1 chr3D.!!$F1 966
3 TraesCS3D01G152200 chr6D 72353586 72360777 7191 False 10338.0 10338 92.669000 61 7263 1 chr6D.!!$F2 7202
4 TraesCS3D01G152200 chr6D 426962438 426968111 5673 True 3972.0 7552 92.517000 56 5715 2 chr6D.!!$R2 5659
5 TraesCS3D01G152200 chr6D 29939884 29941503 1619 False 2279.0 2279 91.971000 312 1951 1 chr6D.!!$F1 1639
6 TraesCS3D01G152200 chr6D 141941208 141942173 965 False 1624.0 1624 96.998000 7264 8229 1 chr6D.!!$F3 965
7 TraesCS3D01G152200 chr6D 97870553 97871517 964 True 1605.0 1605 96.687000 7264 8229 1 chr6D.!!$R1 965
8 TraesCS3D01G152200 chr2D 543496460 543503636 7176 True 9943.0 9943 91.701000 56 7265 1 chr2D.!!$R4 7209
9 TraesCS3D01G152200 chr2D 428599395 428606016 6621 False 9736.0 9736 93.181000 599 7250 1 chr2D.!!$F2 6651
10 TraesCS3D01G152200 chr2D 554137239 554143479 6240 True 9430.0 9430 93.959000 1018 7263 1 chr2D.!!$R5 6245
11 TraesCS3D01G152200 chr2D 324879736 324886387 6651 True 9413.0 9413 92.131000 313 7040 1 chr2D.!!$R3 6727
12 TraesCS3D01G152200 chr2D 38165462 38172434 6972 True 9046.0 9046 90.218000 312 7263 1 chr2D.!!$R1 6951
13 TraesCS3D01G152200 chr2D 119797071 119798036 965 True 1607.0 1607 96.691000 7264 8229 1 chr2D.!!$R2 965
14 TraesCS3D01G152200 chr5D 438198738 438205903 7165 True 9937.0 9937 91.703000 56 7263 1 chr5D.!!$R3 7207
15 TraesCS3D01G152200 chr5D 383609056 383615990 6934 True 9742.0 9742 92.057000 314 7264 1 chr5D.!!$R2 6950
16 TraesCS3D01G152200 chr5D 45274295 45277339 3044 True 3716.0 3716 88.842000 692 3734 1 chr5D.!!$R1 3042
17 TraesCS3D01G152200 chr5D 464293965 464296377 2412 False 955.3 2386 94.191667 1 2011 3 chr5D.!!$F2 2010
18 TraesCS3D01G152200 chr2B 366589944 366597171 7227 True 4964.0 9529 92.469000 56 7263 2 chr2B.!!$R1 7207
19 TraesCS3D01G152200 chr4D 179912092 179918069 5977 False 9079.0 9079 94.070000 1267 7263 1 chr4D.!!$F4 5996
20 TraesCS3D01G152200 chr4D 276864892 276871824 6932 True 8671.0 8671 89.374000 312 7263 1 chr4D.!!$R1 6951
21 TraesCS3D01G152200 chr4D 100194644 100195608 964 False 1622.0 1622 96.998000 7264 8229 1 chr4D.!!$F2 965
22 TraesCS3D01G152200 chr4D 371783929 371784894 965 True 1618.0 1618 96.894000 7264 8229 1 chr4D.!!$R2 965
23 TraesCS3D01G152200 chr4D 100187755 100188720 965 False 1613.0 1613 96.791000 7264 8229 1 chr4D.!!$F1 965
24 TraesCS3D01G152200 chr4A 348497531 348504311 6780 False 8303.0 8303 88.848000 468 7263 1 chr4A.!!$F2 6795
25 TraesCS3D01G152200 chr4A 279447509 279450574 3065 False 3201.0 3201 85.774000 692 3767 1 chr4A.!!$F1 3075
26 TraesCS3D01G152200 chr4B 115050471 115055819 5348 True 6628.0 6628 89.092000 1895 7263 1 chr4B.!!$R1 5368
27 TraesCS3D01G152200 chr7A 206768220 206773160 4940 True 6307.0 6307 89.748000 312 5272 1 chr7A.!!$R1 4960
28 TraesCS3D01G152200 chr1A 278223769 278228694 4925 True 6117.0 6117 89.132000 312 5262 1 chr1A.!!$R2 4950
29 TraesCS3D01G152200 chr1A 124216531 124221345 4814 True 6059.0 6059 89.464000 56 4881 1 chr1A.!!$R1 4825
30 TraesCS3D01G152200 chr1A 252738828 252743634 4806 False 5890.0 5890 88.841000 312 5152 1 chr1A.!!$F1 4840
31 TraesCS3D01G152200 chr2A 771244898 771249483 4585 False 5965.0 5965 90.101000 312 4951 1 chr2A.!!$F1 4639
32 TraesCS3D01G152200 chr7D 195578939 195581675 2736 True 3832.0 3832 91.795000 312 3105 1 chr7D.!!$R2 2793
33 TraesCS3D01G152200 chr7D 122817916 122819916 2000 True 2623.0 2623 90.594000 56 2034 1 chr7D.!!$R1 1978
34 TraesCS3D01G152200 chr7D 122963919 122964888 969 False 1626.0 1626 96.907000 7260 8229 1 chr7D.!!$F1 969
35 TraesCS3D01G152200 chr1D 56174375 56176555 2180 False 3003.0 3003 91.607000 56 2249 1 chr1D.!!$F1 2193

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
506 945 1.885871 GTCCAGTTGCCATGCTTCC 59.114 57.895 0.00 0.0 0.00 3.46 F
1408 1894 0.461961 GCCTACCACATCTCTTCGCT 59.538 55.000 0.00 0.0 0.00 4.93 F
2681 3258 0.532573 TGTTTGGTGCGCCTCAAAAA 59.467 45.000 21.27 15.9 35.08 1.94 F
3900 4566 0.038021 TTGCTGCATGGCAACTCCTA 59.962 50.000 9.14 0.0 45.64 2.94 F
4908 5591 0.037232 GCAGACTGCGTCTTTACCCT 60.037 55.000 12.53 0.0 41.37 4.34 F
4951 5634 0.108424 CTGCGCACTTCTAAGCTCCT 60.108 55.000 5.66 0.0 0.00 3.69 F
5731 6460 0.178967 TTTGATCCTTGCAGCCACCA 60.179 50.000 0.00 0.0 0.00 4.17 F
5975 6704 1.429463 GAGCAGAACCAGTTGTACGG 58.571 55.000 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 2285 0.773644 AGGGGTGCCATACATGATCC 59.226 55.000 0.00 0.0 0.00 3.36 R
3018 3648 0.392461 GCAACCAGTTGGCCGATCTA 60.392 55.000 12.20 0.0 40.74 1.98 R
4408 5091 0.033405 AGCAGCATCCTTCATTGCCT 60.033 50.000 0.00 0.0 39.72 4.75 R
5287 5971 0.322008 CTTCACAGCCTTCCTCCCAC 60.322 60.000 0.00 0.0 0.00 4.61 R
5986 6715 1.611491 GGACCTCGCATTTCCAAAACA 59.389 47.619 0.00 0.0 0.00 2.83 R
6851 7619 2.507484 CTCCTGCAACATGAGGAACAA 58.493 47.619 0.00 0.0 37.93 2.83 R
7139 7908 1.203001 GGTTTGGGATTGGTGTGGAGA 60.203 52.381 0.00 0.0 0.00 3.71 R
7448 8227 3.051581 ACTCATGTCCATGGCTAGGAAT 58.948 45.455 6.96 0.0 39.24 3.01 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
53 54 6.239402 GGCAGGATAATGGCAAATTCACTATT 60.239 38.462 0.00 0.00 44.71 1.73
54 55 6.643770 GCAGGATAATGGCAAATTCACTATTG 59.356 38.462 0.00 0.00 0.00 1.90
262 322 3.119352 TGCCACATTATATGTTTGCGCAA 60.119 39.130 21.02 21.02 42.70 4.85
361 471 2.037511 AGTTGCCACATTTCATGTTGGG 59.962 45.455 0.00 0.00 42.70 4.12
506 945 1.885871 GTCCAGTTGCCATGCTTCC 59.114 57.895 0.00 0.00 0.00 3.46
523 964 3.673338 GCTTCCGCAATTTACTTTTCCAC 59.327 43.478 0.00 0.00 35.78 4.02
739 1198 3.609853 TCTTACCTTAGCACAATGGCTG 58.390 45.455 6.50 0.00 45.44 4.85
942 1415 7.768120 ACAAATGTTCCTTTTTCTGTTATGCAA 59.232 29.630 0.00 0.00 0.00 4.08
1284 1770 0.703488 TGTTTCCTGGGATGGCATCA 59.297 50.000 27.39 9.15 0.00 3.07
1368 1854 8.897752 GTTTTTAAGATGAAGCTCCTCATGTAT 58.102 33.333 5.62 0.00 36.15 2.29
1408 1894 0.461961 GCCTACCACATCTCTTCGCT 59.538 55.000 0.00 0.00 0.00 4.93
1498 1989 2.591571 TCTGATGTCATCTGGAAGCG 57.408 50.000 16.95 0.00 0.00 4.68
1500 1991 2.159184 TCTGATGTCATCTGGAAGCGAC 60.159 50.000 16.95 0.00 36.84 5.19
1776 2280 5.527582 GTCAGTTGTTGATAAGTGTGAACCT 59.472 40.000 0.00 0.00 38.29 3.50
1781 2285 7.226720 AGTTGTTGATAAGTGTGAACCTTACAG 59.773 37.037 0.00 0.00 0.00 2.74
1789 2293 4.287067 AGTGTGAACCTTACAGGATCATGT 59.713 41.667 18.14 18.14 46.71 3.21
2012 2557 3.562973 CAGCATAACAGGATGGCAACTAG 59.437 47.826 0.00 0.00 43.62 2.57
2090 2639 3.519667 TGGCAAATCTTTTCCCTTCCAT 58.480 40.909 0.00 0.00 0.00 3.41
2091 2640 3.909364 TGGCAAATCTTTTCCCTTCCATT 59.091 39.130 0.00 0.00 0.00 3.16
2092 2641 4.350520 TGGCAAATCTTTTCCCTTCCATTT 59.649 37.500 0.00 0.00 0.00 2.32
2164 2716 1.746787 CATAGCATGCTGGCAACTGAA 59.253 47.619 30.42 7.00 37.83 3.02
2533 3102 0.874607 ACTCTGCCGTTCGTGTTGAC 60.875 55.000 0.00 0.00 0.00 3.18
2671 3248 1.937899 AGACTACAACGTGTTTGGTGC 59.062 47.619 0.00 0.00 39.84 5.01
2681 3258 0.532573 TGTTTGGTGCGCCTCAAAAA 59.467 45.000 21.27 15.90 35.08 1.94
2739 3320 3.173151 TGTCCTGCTGAGGTAATCAAGA 58.827 45.455 0.00 0.00 40.76 3.02
3071 3701 1.203187 ACTACAACAGCTCCCAGGAGA 60.203 52.381 18.08 0.00 44.53 3.71
3100 3730 2.868583 CACGCAAGATGAACTAGATGGG 59.131 50.000 0.00 0.00 43.62 4.00
3900 4566 0.038021 TTGCTGCATGGCAACTCCTA 59.962 50.000 9.14 0.00 45.64 2.94
3976 4644 2.584835 ATGGCAACTACCAGCTTTCA 57.415 45.000 0.00 0.00 44.71 2.69
4381 5064 3.131933 AGTGATGAGTCAGTATCTGCCAC 59.868 47.826 0.00 0.00 36.26 5.01
4400 5083 1.759445 ACGACTGCTGAGATATTGCCT 59.241 47.619 0.00 0.00 0.00 4.75
4408 5091 3.244009 GCTGAGATATTGCCTACTCTGCA 60.244 47.826 15.83 0.00 46.07 4.41
4443 5126 2.747460 CTGTGACCCATGCCACCG 60.747 66.667 8.11 0.40 32.61 4.94
4531 5214 1.671054 CGGATTCCAAGCGTGTGGT 60.671 57.895 3.09 0.00 39.88 4.16
4580 5263 2.764314 GGCTGCGGCGACAATTCAT 61.764 57.895 12.98 0.00 39.81 2.57
4610 5293 1.206610 CCATCCACAGGTGAGACTCTG 59.793 57.143 3.68 0.00 37.07 3.35
4826 5509 4.088648 GCAATGTTATGGAGAAAACGACG 58.911 43.478 0.00 0.00 0.00 5.12
4908 5591 0.037232 GCAGACTGCGTCTTTACCCT 60.037 55.000 12.53 0.00 41.37 4.34
4951 5634 0.108424 CTGCGCACTTCTAAGCTCCT 60.108 55.000 5.66 0.00 0.00 3.69
4984 5667 1.173913 GTCCCATACAGCCCAAACAC 58.826 55.000 0.00 0.00 0.00 3.32
5173 5857 3.961414 GGCCTTCACCCCACCGAA 61.961 66.667 0.00 0.00 0.00 4.30
5291 5975 2.428925 GCATCCAATGGCTGGTGGG 61.429 63.158 5.20 0.00 46.51 4.61
5495 6191 2.676632 TGCCATGTTGCAATTCCATC 57.323 45.000 0.59 0.00 38.56 3.51
5551 6247 2.158534 TGGCAACTACAGTTCAACCCAT 60.159 45.455 0.00 0.00 35.83 4.00
5689 6414 6.315144 ACCCTTTCACAATAAACTTGTTTTGC 59.685 34.615 4.00 0.00 0.00 3.68
5731 6460 0.178967 TTTGATCCTTGCAGCCACCA 60.179 50.000 0.00 0.00 0.00 4.17
5755 6484 4.256110 TGAGGAGATTACGTCGTCACTTA 58.744 43.478 0.00 0.00 34.68 2.24
5790 6519 2.130193 AGGATTGAGGAGGCAGCATTA 58.870 47.619 0.00 0.00 0.00 1.90
5975 6704 1.429463 GAGCAGAACCAGTTGTACGG 58.571 55.000 0.00 0.00 0.00 4.02
5986 6715 4.202284 ACCAGTTGTACGGTATTGTCAAGT 60.202 41.667 0.00 0.00 32.31 3.16
6181 6922 9.750882 CATGTTATATCATTTTCATACAGCTCG 57.249 33.333 0.00 0.00 0.00 5.03
6468 7213 7.913674 AGAAATGTGTGAGTATTCCTTCTTC 57.086 36.000 0.00 0.00 0.00 2.87
6473 7218 8.697507 ATGTGTGAGTATTCCTTCTTCTTTTT 57.302 30.769 0.00 0.00 0.00 1.94
6699 7457 6.237901 ACACATGGCAACTAAACATTCTCTA 58.762 36.000 0.00 0.00 37.61 2.43
6851 7619 9.528489 TTTTCCTTTATCTTACTTTGCAGGTAT 57.472 29.630 3.12 0.00 0.00 2.73
6865 7633 3.758023 TGCAGGTATTGTTCCTCATGTTG 59.242 43.478 0.00 0.00 32.37 3.33
6887 7655 1.887242 GAGCTTGCACCACACGACA 60.887 57.895 0.00 0.00 0.00 4.35
7001 7769 2.223735 GCAGACCTTACTACGCATGCTA 60.224 50.000 17.13 6.42 0.00 3.49
7359 8138 8.677148 ATTCATGCTAGAATTGTATTAACCGT 57.323 30.769 0.00 0.00 34.70 4.83
7448 8227 5.351465 GCTCGTTAATTGAAGATGGTTGAGA 59.649 40.000 0.00 0.00 0.00 3.27
7846 8625 2.945668 GAGTTAGTTGTGGGATGATGCC 59.054 50.000 0.00 0.00 0.00 4.40
8031 8810 0.530870 GAGCATCCAGGTTCCGCTAC 60.531 60.000 0.00 0.00 31.86 3.58
8077 8856 5.944599 TCTCGGTCTTGTCTACATAGTTCTT 59.055 40.000 0.00 0.00 0.00 2.52
8125 8905 4.427312 AGTTTGGTGACGATCGGTATTAC 58.573 43.478 20.98 10.05 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.244402 TGAATTTGCCATTATCCTGCCTATG 59.756 40.000 0.00 0.00 0.00 2.23
53 54 5.312895 AGTTGCCATGTAATACAGTCAACA 58.687 37.500 23.61 8.29 37.66 3.33
54 55 5.411361 TGAGTTGCCATGTAATACAGTCAAC 59.589 40.000 18.63 18.63 36.58 3.18
92 144 0.539438 GTGGCAATTCACACCCTGGA 60.539 55.000 0.00 0.00 37.57 3.86
376 502 3.030611 AACACCCAACCACCCCCA 61.031 61.111 0.00 0.00 0.00 4.96
377 503 2.203582 GAACACCCAACCACCCCC 60.204 66.667 0.00 0.00 0.00 5.40
378 504 1.428718 TAGGAACACCCAACCACCCC 61.429 60.000 0.00 0.00 37.41 4.95
379 505 0.702316 ATAGGAACACCCAACCACCC 59.298 55.000 0.00 0.00 37.41 4.61
380 506 1.353022 TCATAGGAACACCCAACCACC 59.647 52.381 0.00 0.00 37.41 4.61
381 507 2.871096 TCATAGGAACACCCAACCAC 57.129 50.000 0.00 0.00 37.41 4.16
382 508 3.054434 CAGATCATAGGAACACCCAACCA 60.054 47.826 0.00 0.00 37.41 3.67
383 509 3.545703 CAGATCATAGGAACACCCAACC 58.454 50.000 0.00 0.00 37.41 3.77
384 510 2.945668 GCAGATCATAGGAACACCCAAC 59.054 50.000 0.00 0.00 37.41 3.77
385 511 2.092429 GGCAGATCATAGGAACACCCAA 60.092 50.000 0.00 0.00 37.41 4.12
506 945 7.406799 AATCAAAGTGGAAAAGTAAATTGCG 57.593 32.000 0.00 0.00 0.00 4.85
661 1117 4.451096 GCCGACAGATACAGAAAAGAAACA 59.549 41.667 0.00 0.00 0.00 2.83
662 1118 4.691216 AGCCGACAGATACAGAAAAGAAAC 59.309 41.667 0.00 0.00 0.00 2.78
666 1122 3.369147 CACAGCCGACAGATACAGAAAAG 59.631 47.826 0.00 0.00 0.00 2.27
739 1198 3.195698 GTCTTGATGGTCGCCGCC 61.196 66.667 0.00 0.00 0.00 6.13
763 1222 3.270877 GCGGTAACTCCATGAAGTCATT 58.729 45.455 0.00 0.00 33.61 2.57
874 1345 6.849305 CGTGAAAGTTTAGTTTCTAACGCAAT 59.151 34.615 10.46 0.00 37.34 3.56
877 1348 5.837703 GTCGTGAAAGTTTAGTTTCTAACGC 59.162 40.000 13.65 8.47 36.51 4.84
892 1363 3.670055 GCCATGTTTCAATGTCGTGAAAG 59.330 43.478 0.76 0.00 45.65 2.62
923 1395 8.474025 TCTTCTTTTGCATAACAGAAAAAGGAA 58.526 29.630 7.18 0.00 42.13 3.36
942 1415 7.682021 GCCCTATTGCGATAATGTTTCTTCTTT 60.682 37.037 0.00 0.00 0.00 2.52
1204 1690 5.395768 CCTCATACGGGACTTTGATTTCTCT 60.396 44.000 0.00 0.00 0.00 3.10
1284 1770 0.040425 GCAAAGTCGTGTTCGGCATT 60.040 50.000 0.00 0.00 44.74 3.56
1368 1854 3.120199 GCGCAAAAACAGCTAAGATCAGA 60.120 43.478 0.30 0.00 0.00 3.27
1713 2215 5.217978 ACATTCAACCGTGGTAAGAGTAA 57.782 39.130 0.00 0.00 0.00 2.24
1776 2280 3.181445 GGGTGCCATACATGATCCTGTAA 60.181 47.826 13.84 0.00 35.37 2.41
1781 2285 0.773644 AGGGGTGCCATACATGATCC 59.226 55.000 0.00 0.00 0.00 3.36
1789 2293 2.964209 TGAAAACAAAGGGGTGCCATA 58.036 42.857 0.00 0.00 0.00 2.74
1914 2453 7.335422 AGAGAGTGGATGTATGAAAATGAACAC 59.665 37.037 0.00 0.00 0.00 3.32
1915 2454 7.335171 CAGAGAGTGGATGTATGAAAATGAACA 59.665 37.037 0.00 0.00 0.00 3.18
1917 2456 7.397221 ACAGAGAGTGGATGTATGAAAATGAA 58.603 34.615 0.00 0.00 0.00 2.57
1919 2458 7.621428 AACAGAGAGTGGATGTATGAAAATG 57.379 36.000 0.00 0.00 0.00 2.32
2012 2557 2.165030 AGTTGCCATCTTGTTATGCTGC 59.835 45.455 0.00 0.00 0.00 5.25
2091 2640 5.068987 CAGTCATCAAGTTGAAGGGGAAAAA 59.931 40.000 10.14 0.00 0.00 1.94
2092 2641 4.584325 CAGTCATCAAGTTGAAGGGGAAAA 59.416 41.667 10.14 0.00 0.00 2.29
2447 3015 9.778741 CATGGCTAACAAGGTATTTATCTCTTA 57.221 33.333 0.00 0.00 0.00 2.10
2671 3248 2.221517 CACTTGCCAAATTTTTGAGGCG 59.778 45.455 11.43 2.81 40.55 5.52
2681 3258 2.498481 CACATCCATCCACTTGCCAAAT 59.502 45.455 0.00 0.00 0.00 2.32
3018 3648 0.392461 GCAACCAGTTGGCCGATCTA 60.392 55.000 12.20 0.00 40.74 1.98
3020 3650 2.877691 GCAACCAGTTGGCCGATC 59.122 61.111 12.20 0.00 40.74 3.69
3071 3701 0.904649 TCATCTTGCGTGTCAGGGAT 59.095 50.000 0.00 0.00 0.00 3.85
3100 3730 1.003580 TCCTTGTCAAGACCAGCATCC 59.996 52.381 14.42 0.00 0.00 3.51
3478 4124 1.196808 ACTGCACGTAGAAAAATGGCG 59.803 47.619 0.00 0.00 0.00 5.69
3645 4297 3.322254 AGTCTTCCAACACGACAGAATCT 59.678 43.478 0.00 0.00 0.00 2.40
3649 4301 2.429250 TCAAGTCTTCCAACACGACAGA 59.571 45.455 0.00 0.00 0.00 3.41
3900 4566 2.035066 GCAGTTTCCATGCAGAACAAGT 59.965 45.455 0.00 0.00 43.31 3.16
4381 5064 2.522836 AGGCAATATCTCAGCAGTCG 57.477 50.000 0.00 0.00 0.00 4.18
4400 5083 1.908619 TCCTTCATTGCCTGCAGAGTA 59.091 47.619 17.39 1.64 0.00 2.59
4408 5091 0.033405 AGCAGCATCCTTCATTGCCT 60.033 50.000 0.00 0.00 39.72 4.75
4443 5126 2.227388 CCACTTCAACACTTGCTGATCC 59.773 50.000 0.00 0.00 0.00 3.36
4580 5263 2.779430 ACCTGTGGATGGCATCTCATTA 59.221 45.455 25.48 13.75 0.00 1.90
4610 5293 3.368571 GCTGGAGCTGTTGTGCCC 61.369 66.667 0.00 0.00 38.21 5.36
4826 5509 3.665675 ATCAGTTGCGCTCCGGACC 62.666 63.158 9.73 0.00 0.00 4.46
4908 5591 1.415672 AAGCTGGGGTTCTCCACGAA 61.416 55.000 0.00 0.00 40.71 3.85
4984 5667 2.982470 GCAACTTTCTTGCCAATCTTCG 59.018 45.455 0.00 0.00 39.38 3.79
5173 5857 2.498167 GATCGATGCCAAGGCTACAAT 58.502 47.619 12.96 0.00 42.51 2.71
5287 5971 0.322008 CTTCACAGCCTTCCTCCCAC 60.322 60.000 0.00 0.00 0.00 4.61
5291 5975 1.268079 GCAAACTTCACAGCCTTCCTC 59.732 52.381 0.00 0.00 0.00 3.71
5515 6211 0.534877 TGCCATGTTGCAACGACTCT 60.535 50.000 23.79 4.07 38.56 3.24
5689 6414 5.209659 ACAGTGGGTTAGGATACCTAGAAG 58.790 45.833 0.00 0.00 37.42 2.85
5731 6460 2.419324 GTGACGACGTAATCTCCTCAGT 59.581 50.000 0.00 0.00 0.00 3.41
5975 6704 6.345723 CGCATTTCCAAAACACTTGACAATAC 60.346 38.462 0.00 0.00 0.00 1.89
5986 6715 1.611491 GGACCTCGCATTTCCAAAACA 59.389 47.619 0.00 0.00 0.00 2.83
6085 6818 8.517062 ACAAAGCATCTCTAGAATAGCAAAAT 57.483 30.769 11.19 0.00 38.99 1.82
6181 6922 3.882888 TGATCTTGGTTCTGTCCAAACAC 59.117 43.478 0.00 4.34 45.26 3.32
6258 7000 5.699458 ACATTCTTCGACATTTTACCGAGTT 59.301 36.000 0.00 0.00 33.66 3.01
6339 7081 4.222810 AGGTCACACTGTACTGCATGATTA 59.777 41.667 0.00 0.00 0.00 1.75
6473 7218 3.237746 TCATGGGAGGAAAATGTGCAAA 58.762 40.909 0.00 0.00 0.00 3.68
6474 7219 2.886913 TCATGGGAGGAAAATGTGCAA 58.113 42.857 0.00 0.00 0.00 4.08
6475 7220 2.601240 TCATGGGAGGAAAATGTGCA 57.399 45.000 0.00 0.00 0.00 4.57
6699 7457 3.876309 AGTGTCCAAAAGTACACCCAT 57.124 42.857 0.00 0.00 45.70 4.00
6851 7619 2.507484 CTCCTGCAACATGAGGAACAA 58.493 47.619 0.00 0.00 37.93 2.83
6865 7633 2.595463 TGTGGTGCAAGCTCCTGC 60.595 61.111 13.58 3.32 42.95 4.85
7001 7769 8.010733 TCTTTGAGGTTGTTGATGAAGAATTT 57.989 30.769 0.00 0.00 0.00 1.82
7139 7908 1.203001 GGTTTGGGATTGGTGTGGAGA 60.203 52.381 0.00 0.00 0.00 3.71
7448 8227 3.051581 ACTCATGTCCATGGCTAGGAAT 58.948 45.455 6.96 0.00 39.24 3.01
7717 8496 8.926710 CAAATCCTAATCTCGAAATACGCTAAT 58.073 33.333 0.00 0.00 42.26 1.73
8125 8905 5.170625 CGGTACATCAAAACACAAAAACTCG 59.829 40.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.