Multiple sequence alignment - TraesCS3D01G486900

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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 TraesCS3D01G486900 chr3D 100.000 3587 0 0 1 3587 582621227 582624813 0.000000e+00 6625.0
1 TraesCS3D01G486900 chr3D 85.327 2433 266 39 1110 3520 582733661 582736024 0.000000e+00 2431.0
2 TraesCS3D01G486900 chr3D 86.031 2162 243 30 1101 3232 582792604 582794736 0.000000e+00 2265.0
3 TraesCS3D01G486900 chr3D 76.826 1588 288 43 1265 2804 582108056 582106501 0.000000e+00 821.0
4 TraesCS3D01G486900 chr3D 89.501 381 40 0 112 492 96639073 96639453 1.940000e-132 483.0
5 TraesCS3D01G486900 chr3D 100.000 62 0 0 3526 3587 582737010 582737071 8.140000e-22 115.0
6 TraesCS3D01G486900 chr3B 96.017 2109 74 5 1484 3587 778552375 778550272 0.000000e+00 3421.0
7 TraesCS3D01G486900 chr3B 82.709 2510 314 54 1110 3586 778491126 778488704 0.000000e+00 2121.0
8 TraesCS3D01G486900 chr3B 91.970 1320 80 10 173 1488 778555667 778554370 0.000000e+00 1827.0
9 TraesCS3D01G486900 chr3B 77.360 1515 267 44 1254 2718 779510330 779511818 0.000000e+00 828.0
10 TraesCS3D01G486900 chr3B 78.091 1205 201 40 1611 2794 779072214 779071052 0.000000e+00 704.0
11 TraesCS3D01G486900 chr3B 77.015 918 151 38 1554 2435 725118343 725117450 4.190000e-129 472.0
12 TraesCS3D01G486900 chr3B 88.189 381 45 0 114 494 533445418 533445038 4.220000e-124 455.0
13 TraesCS3D01G486900 chr3B 76.202 853 134 38 1617 2435 779568432 779569249 1.560000e-103 387.0
14 TraesCS3D01G486900 chr3B 73.987 938 175 44 1565 2472 786043520 786042622 2.080000e-82 316.0
15 TraesCS3D01G486900 chrUn 95.514 2051 87 4 1540 3587 41505943 41507991 0.000000e+00 3273.0
16 TraesCS3D01G486900 chrUn 96.170 1906 63 4 1484 3383 336938502 336940403 0.000000e+00 3107.0
17 TraesCS3D01G486900 chrUn 96.403 1557 49 3 1833 3383 240406487 240404932 0.000000e+00 2558.0
18 TraesCS3D01G486900 chrUn 82.245 2281 290 55 1154 3402 41525095 41527292 0.000000e+00 1862.0
19 TraesCS3D01G486900 chrUn 92.043 842 63 4 173 1010 240411151 240410310 0.000000e+00 1181.0
20 TraesCS3D01G486900 chrUn 93.651 441 24 2 1110 1550 41505042 41505478 0.000000e+00 656.0
21 TraesCS3D01G486900 chrUn 96.094 384 15 0 1514 1897 480952537 480952920 8.450000e-176 627.0
22 TraesCS3D01G486900 chrUn 95.261 211 10 0 3377 3587 323159996 323160206 5.740000e-88 335.0
23 TraesCS3D01G486900 chrUn 95.238 84 4 0 1162 1245 41502861 41502944 2.250000e-27 134.0
24 TraesCS3D01G486900 chrUn 98.039 51 1 0 1438 1488 240409830 240409780 4.930000e-14 89.8
25 TraesCS3D01G486900 chr2D 89.119 386 41 1 109 494 58736941 58736557 2.510000e-131 479.0
26 TraesCS3D01G486900 chr7D 88.976 381 42 0 114 494 59576896 59576516 4.190000e-129 472.0
27 TraesCS3D01G486900 chr2B 88.714 381 43 0 114 494 43723353 43723733 1.950000e-127 466.0
28 TraesCS3D01G486900 chr2B 88.391 379 44 0 114 492 90303062 90303440 1.170000e-124 457.0
29 TraesCS3D01G486900 chr4B 88.482 382 43 1 114 494 603184594 603184213 9.070000e-126 460.0
30 TraesCS3D01G486900 chr7B 91.503 153 12 1 496 647 639187363 639187515 3.630000e-50 209.0
31 TraesCS3D01G486900 chr7B 84.884 86 12 1 658 743 723148737 723148821 6.380000e-13 86.1
32 TraesCS3D01G486900 chr1B 82.329 249 21 9 494 741 72482946 72482720 1.020000e-45 195.0
33 TraesCS3D01G486900 chr1A 79.503 161 31 2 756 915 341874685 341874526 2.930000e-21 113.0


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 TraesCS3D01G486900 chr3D 582621227 582624813 3586 False 6625.000000 6625 100.0000 1 3587 1 chr3D.!!$F2 3586
1 TraesCS3D01G486900 chr3D 582792604 582794736 2132 False 2265.000000 2265 86.0310 1101 3232 1 chr3D.!!$F3 2131
2 TraesCS3D01G486900 chr3D 582733661 582737071 3410 False 1273.000000 2431 92.6635 1110 3587 2 chr3D.!!$F4 2477
3 TraesCS3D01G486900 chr3D 582106501 582108056 1555 True 821.000000 821 76.8260 1265 2804 1 chr3D.!!$R1 1539
4 TraesCS3D01G486900 chr3B 778550272 778555667 5395 True 2624.000000 3421 93.9935 173 3587 2 chr3B.!!$R6 3414
5 TraesCS3D01G486900 chr3B 778488704 778491126 2422 True 2121.000000 2121 82.7090 1110 3586 1 chr3B.!!$R3 2476
6 TraesCS3D01G486900 chr3B 779510330 779511818 1488 False 828.000000 828 77.3600 1254 2718 1 chr3B.!!$F1 1464
7 TraesCS3D01G486900 chr3B 779071052 779072214 1162 True 704.000000 704 78.0910 1611 2794 1 chr3B.!!$R4 1183
8 TraesCS3D01G486900 chr3B 725117450 725118343 893 True 472.000000 472 77.0150 1554 2435 1 chr3B.!!$R2 881
9 TraesCS3D01G486900 chr3B 779568432 779569249 817 False 387.000000 387 76.2020 1617 2435 1 chr3B.!!$F2 818
10 TraesCS3D01G486900 chr3B 786042622 786043520 898 True 316.000000 316 73.9870 1565 2472 1 chr3B.!!$R5 907
11 TraesCS3D01G486900 chrUn 336938502 336940403 1901 False 3107.000000 3107 96.1700 1484 3383 1 chrUn.!!$F3 1899
12 TraesCS3D01G486900 chrUn 41525095 41527292 2197 False 1862.000000 1862 82.2450 1154 3402 1 chrUn.!!$F1 2248
13 TraesCS3D01G486900 chrUn 41502861 41507991 5130 False 1354.333333 3273 94.8010 1110 3587 3 chrUn.!!$F5 2477
14 TraesCS3D01G486900 chrUn 240404932 240411151 6219 True 1276.266667 2558 95.4950 173 3383 3 chrUn.!!$R1 3210

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
272 273 0.453793 CACGACAACAGCCACCAAAA 59.546 50.0 0.0 0.0 0.0 2.44 F
1388 2467 0.390472 CTCCCGCTGTCTTCCTCAAC 60.390 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 5972 1.135112 TCTGGTACTGTATGTGCGCTG 60.135 52.381 9.73 0.0 31.78 5.18 R
3187 7323 1.349688 AGAACCACGGCAACAATCCTA 59.650 47.619 0.00 0.0 0.00 2.94 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
19 20 1.419381 TGTCTACAACAGAGGTGGCA 58.581 50.000 0.00 0.00 32.51 4.92
24 25 1.303888 CAACAGAGGTGGCATGCCT 60.304 57.895 35.53 17.85 39.42 4.75
25 26 0.896940 CAACAGAGGTGGCATGCCTT 60.897 55.000 35.53 21.68 36.29 4.35
26 27 0.698238 AACAGAGGTGGCATGCCTTA 59.302 50.000 35.53 15.87 36.29 2.69
27 28 0.921896 ACAGAGGTGGCATGCCTTAT 59.078 50.000 35.53 21.43 36.29 1.73
28 29 2.126882 ACAGAGGTGGCATGCCTTATA 58.873 47.619 35.53 14.65 36.29 0.98
29 30 2.713167 ACAGAGGTGGCATGCCTTATAT 59.287 45.455 35.53 17.85 36.29 0.86
30 31 3.079578 CAGAGGTGGCATGCCTTATATG 58.920 50.000 35.53 23.10 36.29 1.78
31 32 2.713167 AGAGGTGGCATGCCTTATATGT 59.287 45.455 35.53 14.25 36.29 2.29
32 33 2.816087 GAGGTGGCATGCCTTATATGTG 59.184 50.000 35.53 0.00 36.29 3.21
33 34 2.175499 AGGTGGCATGCCTTATATGTGT 59.825 45.455 35.53 8.68 36.94 3.72
34 35 2.554032 GGTGGCATGCCTTATATGTGTC 59.446 50.000 35.53 13.03 36.94 3.67
35 36 2.554032 GTGGCATGCCTTATATGTGTCC 59.446 50.000 35.53 6.54 36.94 4.02
36 37 2.442878 TGGCATGCCTTATATGTGTCCT 59.557 45.455 35.53 0.00 36.94 3.85
37 38 3.650461 TGGCATGCCTTATATGTGTCCTA 59.350 43.478 35.53 8.95 36.94 2.94
39 40 4.637534 GGCATGCCTTATATGTGTCCTATG 59.362 45.833 29.98 0.00 0.00 2.23
40 41 5.248640 GCATGCCTTATATGTGTCCTATGT 58.751 41.667 6.36 0.00 0.00 2.29
41 42 6.406370 GCATGCCTTATATGTGTCCTATGTA 58.594 40.000 6.36 0.00 0.00 2.29
44 45 7.612065 TGCCTTATATGTGTCCTATGTACTT 57.388 36.000 0.00 0.00 0.00 2.24
45 46 8.029782 TGCCTTATATGTGTCCTATGTACTTT 57.970 34.615 0.00 0.00 0.00 2.66
46 47 7.931407 TGCCTTATATGTGTCCTATGTACTTTG 59.069 37.037 0.00 0.00 0.00 2.77
47 48 7.931948 GCCTTATATGTGTCCTATGTACTTTGT 59.068 37.037 0.00 0.00 0.00 2.83
51 52 6.614694 ATGTGTCCTATGTACTTTGTACCA 57.385 37.500 5.55 0.00 0.00 3.25
52 53 6.614694 TGTGTCCTATGTACTTTGTACCAT 57.385 37.500 5.55 2.98 0.00 3.55
53 54 7.721409 TGTGTCCTATGTACTTTGTACCATA 57.279 36.000 5.55 3.79 0.00 2.74
54 55 8.313944 TGTGTCCTATGTACTTTGTACCATAT 57.686 34.615 5.55 0.00 0.00 1.78
57 58 9.423964 TGTCCTATGTACTTTGTACCATATACA 57.576 33.333 5.55 0.00 0.00 2.29
61 62 7.652300 ATGTACTTTGTACCATATACATGCG 57.348 36.000 8.38 0.00 33.21 4.73
62 63 6.575267 TGTACTTTGTACCATATACATGCGT 58.425 36.000 5.55 0.00 0.00 5.24
64 65 4.272504 ACTTTGTACCATATACATGCGTGC 59.727 41.667 5.64 0.00 0.00 5.34
66 67 2.367241 TGTACCATATACATGCGTGCCT 59.633 45.455 5.64 0.00 0.00 4.75
68 69 2.930950 ACCATATACATGCGTGCCTTT 58.069 42.857 5.64 0.00 0.00 3.11
69 70 3.287222 ACCATATACATGCGTGCCTTTT 58.713 40.909 5.64 0.00 0.00 2.27
108 109 5.010516 TGCAGTTTATTTGCATGGTAGTTGT 59.989 36.000 0.00 0.00 45.89 3.32
109 110 6.207614 TGCAGTTTATTTGCATGGTAGTTGTA 59.792 34.615 0.00 0.00 45.89 2.41
111 112 7.574967 GCAGTTTATTTGCATGGTAGTTGTAGT 60.575 37.037 0.00 0.00 41.17 2.73
112 113 8.941977 CAGTTTATTTGCATGGTAGTTGTAGTA 58.058 33.333 0.00 0.00 0.00 1.82
113 114 9.681062 AGTTTATTTGCATGGTAGTTGTAGTAT 57.319 29.630 0.00 0.00 0.00 2.12
121 122 8.402472 TGCATGGTAGTTGTAGTATTTTATTGC 58.598 33.333 0.00 0.00 0.00 3.56
122 123 8.402472 GCATGGTAGTTGTAGTATTTTATTGCA 58.598 33.333 0.00 0.00 0.00 4.08
125 126 9.674068 TGGTAGTTGTAGTATTTTATTGCATGA 57.326 29.630 0.00 0.00 0.00 3.07
143 144 7.412137 TGCATGATAATACTTGTCTCATTCG 57.588 36.000 0.00 0.00 0.00 3.34
144 145 6.986231 TGCATGATAATACTTGTCTCATTCGT 59.014 34.615 0.00 0.00 0.00 3.85
145 146 8.141268 TGCATGATAATACTTGTCTCATTCGTA 58.859 33.333 0.00 0.00 0.00 3.43
146 147 9.144747 GCATGATAATACTTGTCTCATTCGTAT 57.855 33.333 0.00 0.00 0.00 3.06
156 157 9.436957 ACTTGTCTCATTCGTATCATAAAGTTT 57.563 29.630 0.00 0.00 0.00 2.66
232 233 2.369860 TCTCTGAGCTTGACACCAATGT 59.630 45.455 0.00 0.00 43.71 2.71
250 251 2.046507 CTGTCACCTGCCTCCAGC 60.047 66.667 0.00 0.00 44.14 4.85
262 263 1.595109 CTCCAGCAGCACGACAACA 60.595 57.895 0.00 0.00 0.00 3.33
267 268 2.633657 CAGCACGACAACAGCCAC 59.366 61.111 0.00 0.00 0.00 5.01
269 270 2.899838 GCACGACAACAGCCACCA 60.900 61.111 0.00 0.00 0.00 4.17
272 273 0.453793 CACGACAACAGCCACCAAAA 59.546 50.000 0.00 0.00 0.00 2.44
300 301 2.837947 TGATGAATCACCTCCTCACCT 58.162 47.619 0.00 0.00 0.00 4.00
307 308 0.902048 CACCTCCTCACCTGAGCTCA 60.902 60.000 17.19 17.19 40.75 4.26
311 312 0.827925 TCCTCACCTGAGCTCAACGT 60.828 55.000 18.85 13.74 40.75 3.99
383 384 1.152860 TGAAGCCCTTGCCGTTGAA 60.153 52.632 0.00 0.00 38.69 2.69
391 392 1.135972 CCTTGCCGTTGAACGAATCAG 60.136 52.381 20.47 8.95 46.05 2.90
415 416 2.109593 GAAACACCCCGGACACGT 59.890 61.111 0.73 0.00 38.78 4.49
455 456 2.346803 CACCCAACCATGACTAAGACG 58.653 52.381 0.00 0.00 0.00 4.18
462 463 1.134367 CCATGACTAAGACGCCGAAGA 59.866 52.381 0.00 0.00 0.00 2.87
497 498 3.540617 CATCATCCATGAACCACGGTAA 58.459 45.455 0.00 0.00 40.69 2.85
524 525 4.060900 ACTATATGCATGTCTTCTTGCCG 58.939 43.478 10.16 0.00 41.89 5.69
548 549 3.898482 AGTCAGGTTGTAGTTTGCCTTT 58.102 40.909 0.00 0.00 0.00 3.11
555 556 5.419471 AGGTTGTAGTTTGCCTTTGTAAACA 59.581 36.000 8.56 0.00 45.95 2.83
625 626 1.892468 CGTGGTCTGTTCTAGCGTAC 58.108 55.000 0.00 0.00 0.00 3.67
776 778 0.882484 TGAAAGTCGCGGCATCAACA 60.882 50.000 15.58 2.49 0.00 3.33
835 837 2.044650 CCAGGGTGCCATGTCTGG 60.045 66.667 2.13 0.00 46.17 3.86
838 840 2.044946 GGGTGCCATGTCTGGTCC 60.045 66.667 0.00 0.00 45.10 4.46
844 846 0.811616 GCCATGTCTGGTCCGCTAAG 60.812 60.000 0.00 0.00 45.10 2.18
860 862 3.421844 GCTAAGCCCCATAATCCGATTT 58.578 45.455 0.00 0.00 0.00 2.17
915 918 5.690997 AGCTTAGCTTTGTCCTACAAAAC 57.309 39.130 0.00 2.80 46.15 2.43
924 927 6.037830 GCTTTGTCCTACAAAACTCACAGTTA 59.962 38.462 6.67 0.00 46.15 2.24
941 944 9.743057 CTCACAGTTAGACCTAAATATTCTCTG 57.257 37.037 0.00 0.00 0.00 3.35
942 945 9.475620 TCACAGTTAGACCTAAATATTCTCTGA 57.524 33.333 0.00 0.00 0.00 3.27
961 964 6.032956 TCTGATGTGTTATTCAGTTACGGT 57.967 37.500 0.00 0.00 40.22 4.83
969 972 1.769733 TTCAGTTACGGTGTACACGC 58.230 50.000 19.41 11.47 34.00 5.34
1010 1015 2.463752 AGCGAACACCCTATAAGTGGA 58.536 47.619 7.32 0.00 39.63 4.02
1178 2251 3.423154 GAAGCGCCGGACAAGGTG 61.423 66.667 5.05 0.00 44.25 4.00
1185 2258 2.281761 CGGACAAGGTGCTTGCCT 60.282 61.111 0.00 0.00 44.43 4.75
1388 2467 0.390472 CTCCCGCTGTCTTCCTCAAC 60.390 60.000 0.00 0.00 0.00 3.18
1422 2501 1.451567 TCCGCTACTCCTCGTCCAG 60.452 63.158 0.00 0.00 0.00 3.86
1508 4613 2.833913 CCCGCCTAGCCCATGGAAT 61.834 63.158 15.22 3.27 0.00 3.01
1509 4614 1.488705 CCCGCCTAGCCCATGGAATA 61.489 60.000 15.22 4.43 0.00 1.75
1835 5872 4.051237 CACAGTCTGATGTTCGTGAAAGA 58.949 43.478 6.91 0.00 0.00 2.52
1929 5972 2.742589 GTCGTTTCTTGGGGATGAACTC 59.257 50.000 0.00 0.00 0.00 3.01
1964 6010 2.051334 CCAGATGGTAATTTGGCGGA 57.949 50.000 0.00 0.00 31.75 5.54
2232 6298 5.221880 TCTTTGAATGAAATTGTTGCCGAG 58.778 37.500 0.00 0.00 36.07 4.63
2299 6365 3.552890 GGTCCTTCCAAGCATTTGTTGAC 60.553 47.826 0.00 0.00 35.97 3.18
2357 6430 3.806949 AAGGTACATTTGCTCCCTTGA 57.193 42.857 0.00 0.00 34.32 3.02
2462 6550 5.940192 TGAACTTGTGTATGAATGGACAC 57.060 39.130 0.00 0.00 45.06 3.67
2567 6670 6.128282 CGTTAATTGAGGACAGCAACAACTAT 60.128 38.462 0.00 0.00 0.00 2.12
2701 6820 0.466543 TGGGTAGTGTGTGTCGCTTT 59.533 50.000 0.00 0.00 38.01 3.51
2860 6989 0.832626 ACATCATGGATCTGACGCCA 59.167 50.000 3.86 3.86 38.78 5.69
3051 7184 6.067217 AGATACCCATTGTTTAGCTGAGTT 57.933 37.500 0.00 0.00 0.00 3.01
3094 7228 6.103997 TGGTCGTTGTATTTGGATAAGAGAC 58.896 40.000 0.00 0.00 0.00 3.36
3156 7290 3.433343 AGAATCCATTGGTCACATTGCA 58.567 40.909 1.86 0.00 0.00 4.08
3180 7316 0.877071 CAGTTTGCTGTGCCTAGGTG 59.123 55.000 11.31 0.00 37.92 4.00
3187 7323 1.967319 CTGTGCCTAGGTGTGTTTGT 58.033 50.000 11.31 0.00 0.00 2.83
3446 7582 0.534873 GTGGCCAAGTTGTTGTTGGT 59.465 50.000 7.24 0.00 45.51 3.67
3489 7625 1.600058 AGTGATGATGGATGTGGGGT 58.400 50.000 0.00 0.00 0.00 4.95
3508 7644 2.615912 GGTGCCTGATTCAGTATGCTTC 59.384 50.000 12.54 6.73 34.76 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.419381 TGCCACCTCTGTTGTAGACA 58.581 50.000 0.00 0.00 36.65 3.41
1 2 2.350522 CATGCCACCTCTGTTGTAGAC 58.649 52.381 0.00 0.00 0.00 2.59
2 3 1.339055 GCATGCCACCTCTGTTGTAGA 60.339 52.381 6.36 0.00 0.00 2.59
3 4 1.089920 GCATGCCACCTCTGTTGTAG 58.910 55.000 6.36 0.00 0.00 2.74
4 5 0.322456 GGCATGCCACCTCTGTTGTA 60.322 55.000 32.08 0.00 35.81 2.41
5 6 1.604593 GGCATGCCACCTCTGTTGT 60.605 57.895 32.08 0.00 35.81 3.32
7 8 0.698238 TAAGGCATGCCACCTCTGTT 59.302 50.000 37.18 22.68 36.14 3.16
8 9 0.921896 ATAAGGCATGCCACCTCTGT 59.078 50.000 37.18 13.31 36.14 3.41
9 10 2.936919 TATAAGGCATGCCACCTCTG 57.063 50.000 37.18 0.00 36.14 3.35
11 12 2.816087 CACATATAAGGCATGCCACCTC 59.184 50.000 37.18 11.30 36.14 3.85
13 14 2.554032 GACACATATAAGGCATGCCACC 59.446 50.000 37.18 12.11 38.92 4.61
15 16 2.442878 AGGACACATATAAGGCATGCCA 59.557 45.455 37.18 19.62 38.92 4.92
16 17 3.146104 AGGACACATATAAGGCATGCC 57.854 47.619 30.12 30.12 0.00 4.40
17 18 5.248640 ACATAGGACACATATAAGGCATGC 58.751 41.667 9.90 9.90 0.00 4.06
19 20 7.798710 AGTACATAGGACACATATAAGGCAT 57.201 36.000 0.00 0.00 0.00 4.40
25 26 9.423964 TGGTACAAAGTACATAGGACACATATA 57.576 33.333 9.27 0.00 31.92 0.86
26 27 8.313944 TGGTACAAAGTACATAGGACACATAT 57.686 34.615 9.27 0.00 31.92 1.78
27 28 7.721409 TGGTACAAAGTACATAGGACACATA 57.279 36.000 9.27 0.00 31.92 2.29
28 29 6.614694 TGGTACAAAGTACATAGGACACAT 57.385 37.500 9.27 0.00 31.92 3.21
46 47 3.040147 AGGCACGCATGTATATGGTAC 57.960 47.619 1.33 0.00 34.79 3.34
47 48 3.762407 AAGGCACGCATGTATATGGTA 57.238 42.857 1.33 0.00 34.79 3.25
48 49 2.638480 AAGGCACGCATGTATATGGT 57.362 45.000 1.33 0.00 34.79 3.55
49 50 3.988379 AAAAGGCACGCATGTATATGG 57.012 42.857 1.33 0.00 34.79 2.74
85 86 5.469479 ACAACTACCATGCAAATAAACTGC 58.531 37.500 0.00 0.00 40.35 4.40
86 87 7.816640 ACTACAACTACCATGCAAATAAACTG 58.183 34.615 0.00 0.00 0.00 3.16
87 88 7.996098 ACTACAACTACCATGCAAATAAACT 57.004 32.000 0.00 0.00 0.00 2.66
95 96 8.402472 GCAATAAAATACTACAACTACCATGCA 58.598 33.333 0.00 0.00 0.00 3.96
96 97 8.402472 TGCAATAAAATACTACAACTACCATGC 58.598 33.333 0.00 0.00 0.00 4.06
99 100 9.674068 TCATGCAATAAAATACTACAACTACCA 57.326 29.630 0.00 0.00 0.00 3.25
117 118 8.501580 CGAATGAGACAAGTATTATCATGCAAT 58.498 33.333 0.00 0.00 31.24 3.56
130 131 9.436957 AAACTTTATGATACGAATGAGACAAGT 57.563 29.630 0.00 0.00 0.00 3.16
159 160 9.477484 CATGTTAGTCTTTACTTGACTTGTACT 57.523 33.333 1.67 0.00 41.45 2.73
160 161 9.472361 TCATGTTAGTCTTTACTTGACTTGTAC 57.528 33.333 1.67 0.00 41.45 2.90
161 162 9.692749 CTCATGTTAGTCTTTACTTGACTTGTA 57.307 33.333 1.67 0.00 41.45 2.41
162 163 8.421784 TCTCATGTTAGTCTTTACTTGACTTGT 58.578 33.333 1.67 0.00 41.45 3.16
163 164 8.818141 TCTCATGTTAGTCTTTACTTGACTTG 57.182 34.615 1.67 0.00 41.45 3.16
164 165 9.832445 TTTCTCATGTTAGTCTTTACTTGACTT 57.168 29.630 1.67 0.00 41.45 3.01
166 167 9.865484 GTTTTCTCATGTTAGTCTTTACTTGAC 57.135 33.333 0.00 0.00 37.15 3.18
167 168 9.832445 AGTTTTCTCATGTTAGTCTTTACTTGA 57.168 29.630 0.00 0.00 37.15 3.02
168 169 9.869844 CAGTTTTCTCATGTTAGTCTTTACTTG 57.130 33.333 0.00 0.00 37.15 3.16
169 170 9.832445 TCAGTTTTCTCATGTTAGTCTTTACTT 57.168 29.630 0.00 0.00 37.15 2.24
204 205 4.081972 GGTGTCAAGCTCAGAGATGTTCTA 60.082 45.833 0.00 0.00 33.83 2.10
232 233 2.587247 GCTGGAGGCAGGTGACAGA 61.587 63.158 0.00 0.00 41.35 3.41
250 251 2.633657 GTGGCTGTTGTCGTGCTG 59.366 61.111 0.00 0.00 0.00 4.41
251 252 2.591715 GGTGGCTGTTGTCGTGCT 60.592 61.111 0.00 0.00 0.00 4.40
272 273 6.950041 TGAGGAGGTGATTCATCATTCTTTTT 59.050 34.615 0.00 0.00 39.30 1.94
283 284 2.182827 CTCAGGTGAGGAGGTGATTCA 58.817 52.381 0.00 0.00 38.48 2.57
300 301 0.608130 ATGTAGCCACGTTGAGCTCA 59.392 50.000 13.74 13.74 40.56 4.26
383 384 1.069513 TGTTTCACCGGTCTGATTCGT 59.930 47.619 2.59 0.00 0.00 3.85
410 411 1.244816 TCTGGAGTTCGATGACGTGT 58.755 50.000 0.00 0.00 40.69 4.49
437 438 1.369625 GCGTCTTAGTCATGGTTGGG 58.630 55.000 0.00 0.00 0.00 4.12
440 441 0.892755 TCGGCGTCTTAGTCATGGTT 59.107 50.000 6.85 0.00 0.00 3.67
455 456 2.014857 GGTATGGTTTCCTTCTTCGGC 58.985 52.381 0.00 0.00 0.00 5.54
462 463 3.531397 TGGATGATGGGTATGGTTTCCTT 59.469 43.478 0.00 0.00 0.00 3.36
497 498 7.173907 GGCAAGAAGACATGCATATAGTACAAT 59.826 37.037 0.00 0.00 41.66 2.71
524 525 2.552743 GGCAAACTACAACCTGACTTCC 59.447 50.000 0.00 0.00 0.00 3.46
582 583 6.261118 GCACAAGAATTAACCAAGCTAGATG 58.739 40.000 0.00 0.00 0.00 2.90
625 626 6.767456 AGCTATCTGGACATCCTAAATTCTG 58.233 40.000 0.00 0.00 36.82 3.02
700 701 4.326548 GGATAGAAAACGAACGGTGAAGAG 59.673 45.833 0.00 0.00 0.00 2.85
702 703 4.243270 AGGATAGAAAACGAACGGTGAAG 58.757 43.478 0.00 0.00 0.00 3.02
744 745 6.128929 GCCGCGACTTTCAAAAATAAATCTTT 60.129 34.615 8.23 0.00 0.00 2.52
765 767 3.869272 CCTCGCTGTTGATGCCGC 61.869 66.667 0.00 0.00 0.00 6.53
776 778 3.149005 AGCTAGACTATAAGCCTCGCT 57.851 47.619 0.00 0.00 42.56 4.93
779 781 5.968528 TGCTTAGCTAGACTATAAGCCTC 57.031 43.478 18.67 1.21 46.95 4.70
835 837 1.610886 GGATTATGGGGCTTAGCGGAC 60.611 57.143 0.00 0.00 0.00 4.79
838 840 0.320374 TCGGATTATGGGGCTTAGCG 59.680 55.000 0.00 0.00 0.00 4.26
844 846 4.200092 GGATAGAAATCGGATTATGGGGC 58.800 47.826 3.22 0.00 32.44 5.80
915 918 9.743057 CAGAGAATATTTAGGTCTAACTGTGAG 57.257 37.037 0.00 0.00 0.00 3.51
941 944 6.587226 TGTACACCGTAACTGAATAACACATC 59.413 38.462 0.00 0.00 0.00 3.06
942 945 6.366877 GTGTACACCGTAACTGAATAACACAT 59.633 38.462 15.42 0.00 34.96 3.21
961 964 4.123506 TCTGAGAAACAAATGCGTGTACA 58.876 39.130 0.00 0.00 0.00 2.90
969 972 5.225642 GCTTTTCCCTCTGAGAAACAAATG 58.774 41.667 6.17 3.50 33.11 2.32
1010 1015 2.351276 CAACGGCAGGCCTAGGTT 59.649 61.111 3.98 7.23 0.00 3.50
1302 2381 3.591254 GAGGGTCGTCAAGCGGCTT 62.591 63.158 9.94 9.94 45.81 4.35
1422 2501 4.077188 GCGGCAGACGTCTTGTGC 62.077 66.667 17.26 17.32 46.52 4.57
1508 4613 1.980052 CCGAAGCAGGTGGGTCTTA 59.020 57.895 0.00 0.00 0.00 2.10
1509 4614 2.750350 CCGAAGCAGGTGGGTCTT 59.250 61.111 0.00 0.00 0.00 3.01
1835 5872 3.350219 AAATCAACGCATAGAGGGTGT 57.650 42.857 0.00 0.00 43.40 4.16
1929 5972 1.135112 TCTGGTACTGTATGTGCGCTG 60.135 52.381 9.73 0.00 31.78 5.18
1964 6010 1.539560 ATGACACTCTGCGAGCCAGT 61.540 55.000 5.63 3.07 42.38 4.00
2215 6281 3.192633 GGGTACTCGGCAACAATTTCATT 59.807 43.478 0.00 0.00 0.00 2.57
2232 6298 2.548067 CGATACTGATTGCCCTGGGTAC 60.548 54.545 15.56 0.00 0.00 3.34
2701 6820 1.673923 CGCTCATTGCAGGAGTGAAGA 60.674 52.381 20.29 0.00 43.78 2.87
2795 6919 2.846532 CAAGGGGAAGGGCTGTGT 59.153 61.111 0.00 0.00 0.00 3.72
2860 6989 2.102757 TGTGCATGCCATTGTTTTCTGT 59.897 40.909 16.68 0.00 0.00 3.41
3010 7142 3.801114 TCTACATTGGACTCATGACCG 57.199 47.619 0.00 0.00 0.00 4.79
3051 7184 2.550855 CCAAAGTTCTGAGGCAGCTACA 60.551 50.000 0.00 0.00 0.00 2.74
3094 7228 6.276832 ACATTTCTCATCAACCTTCCAATG 57.723 37.500 0.00 0.00 0.00 2.82
3180 7316 2.292292 ACGGCAACAATCCTACAAACAC 59.708 45.455 0.00 0.00 0.00 3.32
3187 7323 1.349688 AGAACCACGGCAACAATCCTA 59.650 47.619 0.00 0.00 0.00 2.94
3428 7564 2.028130 CTACCAACAACAACTTGGCCA 58.972 47.619 0.00 0.00 41.85 5.36
3446 7582 3.953712 TCAAGATTTCTGTCGCCACTA 57.046 42.857 0.00 0.00 0.00 2.74
3489 7625 2.554142 CGAAGCATACTGAATCAGGCA 58.446 47.619 15.38 2.19 35.51 4.75


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

AutoCloner maintained by Alex Coulton.