Multiple sequence alignment - TraesCS2D01G060300

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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 TraesCS2D01G060300 chr2D 100.000 3152 0 0 1 3152 25028325 25025174 0.000000e+00 5821.0
1 TraesCS2D01G060300 chr2D 78.848 851 143 21 1335 2152 18748488 18749334 9.950000e-150 540.0
2 TraesCS2D01G060300 chr2D 77.984 377 37 28 738 1092 25033261 25032909 8.920000e-46 195.0
3 TraesCS2D01G060300 chr2D 82.353 85 11 3 278 361 32394408 32394489 1.570000e-08 71.3
4 TraesCS2D01G060300 chr2A 90.276 2170 103 36 15 2161 27504293 27502209 0.000000e+00 2739.0
5 TraesCS2D01G060300 chr2A 93.478 782 13 9 2377 3152 27501040 27500291 0.000000e+00 1127.0
6 TraesCS2D01G060300 chr2A 78.960 846 148 19 1335 2152 20165093 20165936 1.650000e-152 549.0
7 TraesCS2D01G060300 chr2A 96.133 181 3 1 2174 2354 27502015 27501839 3.070000e-75 292.0
8 TraesCS2D01G060300 chr2B 93.110 1669 69 20 525 2161 40492250 40490596 0.000000e+00 2403.0
9 TraesCS2D01G060300 chr2B 75.362 828 154 32 1335 2152 30562063 30562850 1.390000e-93 353.0
10 TraesCS2D01G060300 chr2B 98.137 161 3 0 2001 2161 40488620 40488460 6.660000e-72 281.0
11 TraesCS2D01G060300 chr2B 97.516 161 4 0 2001 2161 40484351 40484191 3.100000e-70 276.0
12 TraesCS2D01G060300 chr2B 97.516 161 4 0 2001 2161 40489688 40489528 3.100000e-70 276.0
13 TraesCS2D01G060300 chr2B 96.273 161 6 0 2001 2161 40482216 40482056 6.700000e-67 265.0
14 TraesCS2D01G060300 chr2B 96.273 161 6 0 2001 2161 40486485 40486325 6.700000e-67 265.0
15 TraesCS2D01G060300 chr2B 95.652 161 7 0 2001 2161 40481148 40480988 3.120000e-65 259.0
16 TraesCS2D01G060300 chr2B 95.652 161 7 0 2001 2161 40483283 40483123 3.120000e-65 259.0
17 TraesCS2D01G060300 chr2B 87.302 126 12 1 2170 2295 40479696 40479575 1.180000e-29 141.0
18 TraesCS2D01G060300 chr2B 93.750 64 4 0 447 510 40492300 40492237 2.590000e-16 97.1
19 TraesCS2D01G060300 chr1B 87.321 560 68 1 2593 3152 654030295 654030851 3.430000e-179 638.0
20 TraesCS2D01G060300 chr1B 89.474 57 2 3 1077 1132 626229511 626229564 5.640000e-08 69.4
21 TraesCS2D01G060300 chr1A 87.161 553 60 8 2604 3152 564395885 564396430 4.470000e-173 617.0
22 TraesCS2D01G060300 chr1A 97.059 34 1 0 1079 1112 311683546 311683579 1.220000e-04 58.4
23 TraesCS2D01G060300 chr5B 77.465 284 50 9 1684 1966 470200561 470200291 1.170000e-34 158.0
24 TraesCS2D01G060300 chr5B 85.321 109 15 1 8 115 697256061 697256169 9.240000e-21 111.0
25 TraesCS2D01G060300 chr6B 87.059 85 10 1 7 91 710013120 710013203 9.310000e-16 95.3
26 TraesCS2D01G060300 chr6B 92.308 39 2 1 1076 1114 345417259 345417296 2.000000e-03 54.7
27 TraesCS2D01G060300 chr1D 83.178 107 14 4 16 119 461040333 461040228 9.310000e-16 95.3
28 TraesCS2D01G060300 chr6D 93.023 43 3 0 7 49 465178094 465178136 2.620000e-06 63.9
29 TraesCS2D01G060300 chr6A 97.059 34 1 0 1079 1112 53429531 53429564 1.220000e-04 58.4
30 TraesCS2D01G060300 chr4A 97.059 34 1 0 1079 1112 597450886 597450853 1.220000e-04 58.4
31 TraesCS2D01G060300 chr4A 92.500 40 3 0 1079 1118 597583742 597583703 1.220000e-04 58.4
32 TraesCS2D01G060300 chr4A 97.059 34 1 0 1079 1112 597583736 597583703 1.220000e-04 58.4
33 TraesCS2D01G060300 chr5A 100.000 29 0 0 1079 1107 645692726 645692754 2.000000e-03 54.7


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 TraesCS2D01G060300 chr2D 25025174 25028325 3151 True 5821.00 5821 100.000000 1 3152 1 chr2D.!!$R1 3151
1 TraesCS2D01G060300 chr2D 18748488 18749334 846 False 540.00 540 78.848000 1335 2152 1 chr2D.!!$F1 817
2 TraesCS2D01G060300 chr2A 27500291 27504293 4002 True 1386.00 2739 93.295667 15 3152 3 chr2A.!!$R1 3137
3 TraesCS2D01G060300 chr2A 20165093 20165936 843 False 549.00 549 78.960000 1335 2152 1 chr2A.!!$F1 817
4 TraesCS2D01G060300 chr2B 40479575 40492300 12725 True 452.21 2403 95.118100 447 2295 10 chr2B.!!$R1 1848
5 TraesCS2D01G060300 chr2B 30562063 30562850 787 False 353.00 353 75.362000 1335 2152 1 chr2B.!!$F1 817
6 TraesCS2D01G060300 chr1B 654030295 654030851 556 False 638.00 638 87.321000 2593 3152 1 chr1B.!!$F2 559
7 TraesCS2D01G060300 chr1A 564395885 564396430 545 False 617.00 617 87.161000 2604 3152 1 chr1A.!!$F2 548

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
870 890 0.034283 TGGCACATGCATGGCTTCTA 60.034 50.0 29.41 10.94 45.16 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 5450 0.179097 GAGGCCGGAGACAATGAGAC 60.179 60.0 5.05 0.0 0.0 3.36 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
50 51 0.249447 CCAGGATAATGCGAGCACGA 60.249 55.000 8.01 0.00 42.66 4.35
62 63 1.336517 CGAGCACGAGGACTTAAACCA 60.337 52.381 0.00 0.00 42.66 3.67
69 70 3.206150 CGAGGACTTAAACCATGATGGG 58.794 50.000 17.04 0.00 43.37 4.00
72 73 2.689983 GGACTTAAACCATGATGGGCTG 59.310 50.000 17.04 3.79 43.37 4.85
105 106 2.661176 TCTCCTACCCATCCAACCTT 57.339 50.000 0.00 0.00 0.00 3.50
108 109 3.273886 TCTCCTACCCATCCAACCTTAGA 59.726 47.826 0.00 0.00 0.00 2.10
115 116 4.202781 ACCCATCCAACCTTAGATTGGTTT 60.203 41.667 5.11 0.00 44.54 3.27
120 121 2.817258 CAACCTTAGATTGGTTTGCGGA 59.183 45.455 0.00 0.00 44.54 5.54
123 124 4.196971 ACCTTAGATTGGTTTGCGGATAC 58.803 43.478 0.00 0.00 33.34 2.24
135 136 5.392595 GGTTTGCGGATACTTTGCTATTTGA 60.393 40.000 0.00 0.00 0.00 2.69
136 137 5.888691 TTGCGGATACTTTGCTATTTGAA 57.111 34.783 0.00 0.00 0.00 2.69
140 141 5.163754 GCGGATACTTTGCTATTTGAACTGT 60.164 40.000 0.00 0.00 0.00 3.55
143 144 7.467623 GGATACTTTGCTATTTGAACTGTCTG 58.532 38.462 0.00 0.00 0.00 3.51
145 146 6.699575 ACTTTGCTATTTGAACTGTCTGTT 57.300 33.333 0.00 0.00 42.38 3.16
156 157 5.737860 TGAACTGTCTGTTAGATGCATGAT 58.262 37.500 2.46 0.00 39.30 2.45
184 185 8.199449 CCCAATTAATGAAGTGAATACTTGCAT 58.801 33.333 0.00 0.00 46.79 3.96
225 226 7.967854 CGAAAATGCTAATATCTGACACCAAAA 59.032 33.333 0.00 0.00 0.00 2.44
237 238 4.314121 TGACACCAAAATTTTAGGCATGC 58.686 39.130 9.90 9.90 0.00 4.06
252 253 7.779754 TTAGGCATGCCATATCAAATGTTAT 57.220 32.000 37.18 14.60 38.92 1.89
253 254 6.675413 AGGCATGCCATATCAAATGTTATT 57.325 33.333 37.18 8.89 38.92 1.40
254 255 6.694447 AGGCATGCCATATCAAATGTTATTC 58.306 36.000 37.18 4.63 38.92 1.75
255 256 6.268158 AGGCATGCCATATCAAATGTTATTCA 59.732 34.615 37.18 0.00 38.92 2.57
256 257 7.038587 AGGCATGCCATATCAAATGTTATTCAT 60.039 33.333 37.18 7.74 38.92 2.57
257 258 7.064134 GGCATGCCATATCAAATGTTATTCATG 59.936 37.037 32.08 13.04 34.90 3.07
258 259 7.064134 GCATGCCATATCAAATGTTATTCATGG 59.936 37.037 6.36 0.00 36.81 3.66
259 260 7.600231 TGCCATATCAAATGTTATTCATGGT 57.400 32.000 0.00 0.00 36.81 3.55
260 261 8.703378 TGCCATATCAAATGTTATTCATGGTA 57.297 30.769 0.00 0.00 36.81 3.25
301 302 2.715737 TGCAAGCACGGTAATTTTCC 57.284 45.000 0.00 0.00 0.00 3.13
358 361 5.229423 TGCTTGCCAATTAAACTTGTCATC 58.771 37.500 0.00 0.00 0.00 2.92
376 379 5.894807 GTCATCCTTGACCACCATAATTTG 58.105 41.667 0.00 0.00 45.45 2.32
384 387 8.310382 CCTTGACCACCATAATTTGTAATGAAA 58.690 33.333 0.00 0.00 0.00 2.69
420 423 6.370593 TGTCATGCTTAAAAATCTGACGTTC 58.629 36.000 0.00 0.00 36.63 3.95
421 424 5.795441 GTCATGCTTAAAAATCTGACGTTCC 59.205 40.000 0.00 0.00 0.00 3.62
423 426 4.394729 TGCTTAAAAATCTGACGTTCCCT 58.605 39.130 0.00 0.00 0.00 4.20
424 427 4.215399 TGCTTAAAAATCTGACGTTCCCTG 59.785 41.667 0.00 0.00 0.00 4.45
437 440 2.223525 CGTTCCCTGAATACTCGAGTCC 60.224 54.545 23.89 13.05 0.00 3.85
508 511 9.970553 AATATCTATGTCATAGCATGATTTGGT 57.029 29.630 14.14 0.00 42.04 3.67
509 512 9.970553 ATATCTATGTCATAGCATGATTTGGTT 57.029 29.630 14.14 0.00 42.04 3.67
510 513 7.734924 TCTATGTCATAGCATGATTTGGTTC 57.265 36.000 14.14 0.00 42.04 3.62
511 514 5.779529 ATGTCATAGCATGATTTGGTTCC 57.220 39.130 0.00 0.00 42.04 3.62
512 515 3.953612 TGTCATAGCATGATTTGGTTCCC 59.046 43.478 0.00 0.00 42.04 3.97
513 516 3.319122 GTCATAGCATGATTTGGTTCCCC 59.681 47.826 0.00 0.00 42.04 4.81
514 517 2.051334 TAGCATGATTTGGTTCCCCG 57.949 50.000 0.00 0.00 37.26 5.73
515 518 1.141665 GCATGATTTGGTTCCCCGC 59.858 57.895 0.00 0.00 0.00 6.13
516 519 1.603236 GCATGATTTGGTTCCCCGCA 61.603 55.000 0.00 0.00 0.00 5.69
517 520 0.894141 CATGATTTGGTTCCCCGCAA 59.106 50.000 0.00 0.00 0.00 4.85
518 521 1.274728 CATGATTTGGTTCCCCGCAAA 59.725 47.619 0.00 0.00 0.00 3.68
519 522 1.414158 TGATTTGGTTCCCCGCAAAA 58.586 45.000 0.00 0.00 0.00 2.44
520 523 1.762957 TGATTTGGTTCCCCGCAAAAA 59.237 42.857 0.00 0.00 0.00 1.94
644 647 9.349713 TGAGTTAATGATTCCTGTTTGTACTTT 57.650 29.630 0.00 0.00 0.00 2.66
686 689 5.106197 TGCTGTTTAATCGATCAGTTGCATT 60.106 36.000 12.01 0.00 0.00 3.56
794 803 1.417592 CACAGCGTGCGTCTTGATC 59.582 57.895 0.00 0.00 0.00 2.92
870 890 0.034283 TGGCACATGCATGGCTTCTA 60.034 50.000 29.41 10.94 45.16 2.10
1101 1127 4.352893 CTTCTCCTTCTCCTTCTCCTTCT 58.647 47.826 0.00 0.00 0.00 2.85
1102 1128 3.976015 TCTCCTTCTCCTTCTCCTTCTC 58.024 50.000 0.00 0.00 0.00 2.87
1103 1129 3.031013 CTCCTTCTCCTTCTCCTTCTCC 58.969 54.545 0.00 0.00 0.00 3.71
1104 1130 2.657459 TCCTTCTCCTTCTCCTTCTCCT 59.343 50.000 0.00 0.00 0.00 3.69
1105 1131 3.078305 TCCTTCTCCTTCTCCTTCTCCTT 59.922 47.826 0.00 0.00 0.00 3.36
1106 1132 3.450817 CCTTCTCCTTCTCCTTCTCCTTC 59.549 52.174 0.00 0.00 0.00 3.46
1155 1181 0.671472 CAGATCACAAGCTGGCGTCA 60.671 55.000 0.00 0.00 35.22 4.35
1157 1183 1.089920 GATCACAAGCTGGCGTCATT 58.910 50.000 0.00 0.00 0.00 2.57
1172 1198 0.322816 TCATTGGACCAAGCTGCTCC 60.323 55.000 13.43 0.00 0.00 4.70
1194 1224 3.002042 CGAAGAAGCTCGATACGGTAAGA 59.998 47.826 0.00 0.00 41.44 2.10
1225 1255 8.352942 GTTCCTTTTGCTTCTTCTTTCTCATTA 58.647 33.333 0.00 0.00 0.00 1.90
1226 1256 8.463930 TCCTTTTGCTTCTTCTTTCTCATTAA 57.536 30.769 0.00 0.00 0.00 1.40
1229 1259 9.136952 CTTTTGCTTCTTCTTTCTCATTAATGG 57.863 33.333 15.36 6.60 0.00 3.16
1262 1293 3.000523 CCAAAATTAATCTGCATGCACGC 59.999 43.478 18.46 0.00 0.00 5.34
1277 1308 2.125350 CGCCTGAGCTCTGAACCC 60.125 66.667 21.10 6.37 36.60 4.11
1280 1311 2.659016 CTGAGCTCTGAACCCGCA 59.341 61.111 16.19 0.00 0.00 5.69
1282 1313 2.811317 GAGCTCTGAACCCGCACG 60.811 66.667 6.43 0.00 0.00 5.34
1312 1347 1.514678 GGTGAACAATGCTGCACGGA 61.515 55.000 3.57 0.00 32.24 4.69
1316 1351 0.031994 AACAATGCTGCACGGAAACC 59.968 50.000 3.57 0.00 0.00 3.27
1341 1388 1.226073 GGACGACGACGAGAAGCTC 60.226 63.158 15.32 0.00 42.66 4.09
1530 1577 3.239253 AAGGCGTTCGAGGGGTGT 61.239 61.111 0.00 0.00 0.00 4.16
2161 5444 4.429108 GCTCACTTACTGACATTCTCTCC 58.571 47.826 0.00 0.00 0.00 3.71
2163 5446 3.769844 TCACTTACTGACATTCTCTCCCC 59.230 47.826 0.00 0.00 0.00 4.81
2167 5450 1.912043 ACTGACATTCTCTCCCCCTTG 59.088 52.381 0.00 0.00 0.00 3.61
2168 5451 1.912043 CTGACATTCTCTCCCCCTTGT 59.088 52.381 0.00 0.00 0.00 3.16
2169 5452 1.909302 TGACATTCTCTCCCCCTTGTC 59.091 52.381 0.00 0.00 35.27 3.18
2170 5453 2.192263 GACATTCTCTCCCCCTTGTCT 58.808 52.381 0.00 0.00 32.69 3.41
2204 5708 2.158943 CCTCACCTCCCTTTTATCGTCC 60.159 54.545 0.00 0.00 0.00 4.79
2254 5758 0.321653 TTGCCCTTCGAAGAGCTTCC 60.322 55.000 28.54 10.39 38.43 3.46
2255 5759 1.296715 GCCCTTCGAAGAGCTTCCA 59.703 57.895 26.61 0.00 38.43 3.53
2256 5760 1.021920 GCCCTTCGAAGAGCTTCCAC 61.022 60.000 26.61 2.80 38.43 4.02
2257 5761 0.321671 CCCTTCGAAGAGCTTCCACA 59.678 55.000 26.61 0.00 38.43 4.17
2260 5764 0.387929 TTCGAAGAGCTTCCACACGT 59.612 50.000 0.00 0.00 38.43 4.49
2269 5773 1.739371 GCTTCCACACGTACATCCCTC 60.739 57.143 0.00 0.00 0.00 4.30
2335 5855 4.298332 AGCATTTAACGCTTCAACTTTGG 58.702 39.130 0.00 0.00 35.82 3.28
2354 6967 4.142609 TGGAGTCATTGATGAAGCCTAC 57.857 45.455 12.02 1.86 38.75 3.18
2355 6968 3.118261 TGGAGTCATTGATGAAGCCTACC 60.118 47.826 12.02 0.00 38.75 3.18
2356 6969 3.118261 GGAGTCATTGATGAAGCCTACCA 60.118 47.826 0.00 0.00 38.75 3.25
2358 6971 4.521146 AGTCATTGATGAAGCCTACCAAG 58.479 43.478 0.00 0.00 38.75 3.61
2359 6972 4.225942 AGTCATTGATGAAGCCTACCAAGA 59.774 41.667 0.00 0.00 38.75 3.02
2360 6973 4.943705 GTCATTGATGAAGCCTACCAAGAA 59.056 41.667 0.00 0.00 38.75 2.52
2362 6975 6.096001 GTCATTGATGAAGCCTACCAAGAATT 59.904 38.462 0.00 0.00 38.75 2.17
2363 6976 6.664816 TCATTGATGAAGCCTACCAAGAATTT 59.335 34.615 0.00 0.00 33.08 1.82
2364 6977 6.916360 TTGATGAAGCCTACCAAGAATTTT 57.084 33.333 0.00 0.00 0.00 1.82
2365 6978 8.469200 CATTGATGAAGCCTACCAAGAATTTTA 58.531 33.333 0.00 0.00 0.00 1.52
2367 6980 7.175104 TGATGAAGCCTACCAAGAATTTTACT 58.825 34.615 0.00 0.00 0.00 2.24
2368 6981 7.669722 TGATGAAGCCTACCAAGAATTTTACTT 59.330 33.333 0.00 0.00 0.00 2.24
2372 6985 8.700439 AAGCCTACCAAGAATTTTACTTACAA 57.300 30.769 0.00 0.00 0.00 2.41
2373 6986 8.700439 AGCCTACCAAGAATTTTACTTACAAA 57.300 30.769 0.00 0.00 0.00 2.83
2374 6987 9.309224 AGCCTACCAAGAATTTTACTTACAAAT 57.691 29.630 0.00 0.00 0.00 2.32
2375 6988 9.569167 GCCTACCAAGAATTTTACTTACAAATC 57.431 33.333 0.00 0.00 0.00 2.17
2379 6992 9.280174 ACCAAGAATTTTACTTACAAATCGAGA 57.720 29.630 0.00 0.00 0.00 4.04
2449 13241 3.244353 ACCACCACAGAGAACTGAATCAG 60.244 47.826 8.98 8.98 46.03 2.90
2454 13246 4.689812 CCACAGAGAACTGAATCAGAGTTG 59.310 45.833 18.20 9.71 46.03 3.16
2505 13297 5.220586 GCGAAAATGACATAAATCGGAGTGA 60.221 40.000 15.10 0.00 0.00 3.41
2528 13320 2.613026 CATGCATGGATTGTTGGCAT 57.387 45.000 19.40 0.00 45.33 4.40
2529 13321 2.912771 CATGCATGGATTGTTGGCATT 58.087 42.857 19.40 0.00 42.81 3.56
2565 13357 3.806521 CAGATCGAATACAGCCCAGAAAG 59.193 47.826 0.00 0.00 0.00 2.62
2591 13383 0.437295 GTATGTCCGTGTGTCGTTGC 59.563 55.000 0.00 0.00 37.94 4.17
2952 13771 4.821589 CGCGAAGGCCAGGGACTC 62.822 72.222 5.01 0.00 34.60 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.363341 AAAATTTTCGGTGATGTGCGT 57.637 38.095 0.00 0.00 0.00 5.24
2 3 5.814314 TTTAAAATTTTCGGTGATGTGCG 57.186 34.783 6.72 0.00 0.00 5.34
50 51 2.582636 AGCCCATCATGGTTTAAGTCCT 59.417 45.455 2.07 0.00 35.17 3.85
62 63 0.403304 TGGTATCCCCAGCCCATCAT 60.403 55.000 0.00 0.00 38.72 2.45
69 70 2.303311 GGAGAATAGTGGTATCCCCAGC 59.697 54.545 0.00 0.00 46.45 4.85
72 73 4.095211 GGTAGGAGAATAGTGGTATCCCC 58.905 52.174 0.00 0.00 0.00 4.81
84 85 3.151542 AGGTTGGATGGGTAGGAGAAT 57.848 47.619 0.00 0.00 0.00 2.40
86 87 2.661176 AAGGTTGGATGGGTAGGAGA 57.339 50.000 0.00 0.00 0.00 3.71
105 106 4.095782 GCAAAGTATCCGCAAACCAATCTA 59.904 41.667 0.00 0.00 0.00 1.98
108 109 2.825532 AGCAAAGTATCCGCAAACCAAT 59.174 40.909 0.00 0.00 0.00 3.16
115 116 4.941263 AGTTCAAATAGCAAAGTATCCGCA 59.059 37.500 0.00 0.00 0.00 5.69
120 121 7.986085 ACAGACAGTTCAAATAGCAAAGTAT 57.014 32.000 0.00 0.00 0.00 2.12
123 124 8.087982 TCTAACAGACAGTTCAAATAGCAAAG 57.912 34.615 0.00 0.00 41.64 2.77
135 136 5.121811 GGATCATGCATCTAACAGACAGTT 58.878 41.667 0.00 0.00 44.27 3.16
136 137 4.444022 GGGATCATGCATCTAACAGACAGT 60.444 45.833 0.00 0.00 0.00 3.55
140 141 3.047857 TGGGGATCATGCATCTAACAGA 58.952 45.455 0.00 0.00 0.00 3.41
143 144 6.899393 TTAATTGGGGATCATGCATCTAAC 57.101 37.500 0.00 0.00 0.00 2.34
145 146 6.792424 TCATTAATTGGGGATCATGCATCTA 58.208 36.000 0.00 0.00 0.00 1.98
156 157 7.147915 GCAAGTATTCACTTCATTAATTGGGGA 60.148 37.037 0.00 0.00 43.30 4.81
184 185 6.908825 AGCATTTTCGTACAATTTCTAGCAA 58.091 32.000 0.00 0.00 0.00 3.91
214 215 4.389687 GCATGCCTAAAATTTTGGTGTCAG 59.610 41.667 13.76 1.69 0.00 3.51
225 226 7.069877 ACATTTGATATGGCATGCCTAAAAT 57.930 32.000 35.53 26.20 36.94 1.82
252 253 7.809546 TCGCACCAATATAAATTACCATGAA 57.190 32.000 0.00 0.00 0.00 2.57
253 254 7.994425 ATCGCACCAATATAAATTACCATGA 57.006 32.000 0.00 0.00 0.00 3.07
254 255 8.946085 ACTATCGCACCAATATAAATTACCATG 58.054 33.333 0.00 0.00 0.00 3.66
255 256 9.515226 AACTATCGCACCAATATAAATTACCAT 57.485 29.630 0.00 0.00 0.00 3.55
256 257 8.911918 AACTATCGCACCAATATAAATTACCA 57.088 30.769 0.00 0.00 0.00 3.25
257 258 9.607285 CAAACTATCGCACCAATATAAATTACC 57.393 33.333 0.00 0.00 0.00 2.85
258 259 9.113876 GCAAACTATCGCACCAATATAAATTAC 57.886 33.333 0.00 0.00 0.00 1.89
259 260 8.841300 TGCAAACTATCGCACCAATATAAATTA 58.159 29.630 0.00 0.00 31.95 1.40
260 261 7.711846 TGCAAACTATCGCACCAATATAAATT 58.288 30.769 0.00 0.00 31.95 1.82
275 276 4.616181 ATTACCGTGCTTGCAAACTATC 57.384 40.909 0.00 0.00 0.00 2.08
358 361 7.403312 TCATTACAAATTATGGTGGTCAAGG 57.597 36.000 0.00 0.00 0.00 3.61
392 395 7.867403 ACGTCAGATTTTTAAGCATGACAAATT 59.133 29.630 0.00 0.00 37.50 1.82
398 401 5.106317 GGGAACGTCAGATTTTTAAGCATGA 60.106 40.000 0.00 0.00 0.00 3.07
413 416 2.422479 CTCGAGTATTCAGGGAACGTCA 59.578 50.000 3.62 0.00 0.00 4.35
420 423 3.887621 TTTGGACTCGAGTATTCAGGG 57.112 47.619 20.09 0.00 0.00 4.45
421 424 6.743575 AAAATTTGGACTCGAGTATTCAGG 57.256 37.500 20.09 0.00 0.00 3.86
423 426 9.667107 AGAATAAAATTTGGACTCGAGTATTCA 57.333 29.630 20.09 14.27 31.08 2.57
482 485 9.970553 ACCAAATCATGCTATGACATAGATATT 57.029 29.630 23.87 13.69 43.01 1.28
489 492 5.779529 GGAACCAAATCATGCTATGACAT 57.220 39.130 0.00 0.00 43.01 3.06
520 523 5.033589 TGGTCAACCAAATCATGCTTTTT 57.966 34.783 0.00 0.00 44.35 1.94
521 524 4.686191 TGGTCAACCAAATCATGCTTTT 57.314 36.364 0.00 0.00 44.35 2.27
610 613 5.063944 CAGGAATCATTAACTCACCGTCAAG 59.936 44.000 0.00 0.00 0.00 3.02
611 614 4.935205 CAGGAATCATTAACTCACCGTCAA 59.065 41.667 0.00 0.00 0.00 3.18
644 647 8.764524 AAACAGCAATTTTTACTTACAACACA 57.235 26.923 0.00 0.00 0.00 3.72
686 689 3.764434 GTGTAGTCTCTTCCCTGTGATGA 59.236 47.826 0.00 0.00 0.00 2.92
746 752 6.231951 TCATTACCGTTGATAAGGTTTGACA 58.768 36.000 0.00 0.00 41.63 3.58
794 803 4.214332 CCGGGAGACAAGAAAGAAAAGAAG 59.786 45.833 0.00 0.00 0.00 2.85
891 914 0.538057 ACGACGGTGAACTGGACCTA 60.538 55.000 0.00 0.00 0.00 3.08
1172 1198 3.002042 TCTTACCGTATCGAGCTTCTTCG 59.998 47.826 0.00 0.00 41.79 3.79
1194 1224 8.864087 AGAAAGAAGAAGCAAAAGGAACATAAT 58.136 29.630 0.00 0.00 0.00 1.28
1262 1293 2.125350 GCGGGTTCAGAGCTCAGG 60.125 66.667 17.77 7.84 0.00 3.86
1282 1313 2.360475 GTTCACCCCCTGCAGCTC 60.360 66.667 8.66 0.00 0.00 4.09
1312 1347 1.174712 TCGTCGTCCTCTTCCGGTTT 61.175 55.000 0.00 0.00 0.00 3.27
1316 1351 2.097918 CGTCGTCGTCCTCTTCCG 59.902 66.667 0.00 0.00 0.00 4.30
1841 1919 2.997897 AGTCCGCGAAGAAGGCCT 60.998 61.111 8.23 0.00 0.00 5.19
2161 5444 1.406069 CGGAGACAATGAGACAAGGGG 60.406 57.143 0.00 0.00 0.00 4.79
2163 5446 2.009042 GCCGGAGACAATGAGACAAGG 61.009 57.143 5.05 0.00 0.00 3.61
2167 5450 0.179097 GAGGCCGGAGACAATGAGAC 60.179 60.000 5.05 0.00 0.00 3.36
2168 5451 0.614697 TGAGGCCGGAGACAATGAGA 60.615 55.000 5.05 0.00 0.00 3.27
2169 5452 0.460987 GTGAGGCCGGAGACAATGAG 60.461 60.000 5.05 0.00 0.00 2.90
2170 5453 1.596934 GTGAGGCCGGAGACAATGA 59.403 57.895 5.05 0.00 0.00 2.57
2204 5708 5.953183 TGAGAACATGAAAATTGAATCGGG 58.047 37.500 0.00 0.00 0.00 5.14
2254 5758 2.618053 GAAAGGAGGGATGTACGTGTG 58.382 52.381 0.00 0.00 0.00 3.82
2255 5759 1.203994 CGAAAGGAGGGATGTACGTGT 59.796 52.381 0.00 0.00 0.00 4.49
2256 5760 1.203994 ACGAAAGGAGGGATGTACGTG 59.796 52.381 0.00 0.00 0.00 4.49
2257 5761 1.203994 CACGAAAGGAGGGATGTACGT 59.796 52.381 0.00 0.00 0.00 3.57
2260 5764 1.568504 AGCACGAAAGGAGGGATGTA 58.431 50.000 0.00 0.00 0.00 2.29
2269 5773 3.621794 CTTCTTTGACAAGCACGAAAGG 58.378 45.455 0.00 0.00 0.00 3.11
2335 5855 4.142609 TGGTAGGCTTCATCAATGACTC 57.857 45.455 0.00 0.00 36.36 3.36
2354 6967 9.760660 CTCTCGATTTGTAAGTAAAATTCTTGG 57.239 33.333 0.00 0.00 0.00 3.61
2365 6978 9.831737 CAAATCATTTTCTCTCGATTTGTAAGT 57.168 29.630 13.09 0.00 44.84 2.24
2367 6980 9.008965 TCCAAATCATTTTCTCTCGATTTGTAA 57.991 29.630 17.61 7.18 46.86 2.41
2368 6981 8.560355 TCCAAATCATTTTCTCTCGATTTGTA 57.440 30.769 17.61 4.53 46.86 2.41
2372 6985 7.977853 CCAAATCCAAATCATTTTCTCTCGATT 59.022 33.333 0.00 0.00 0.00 3.34
2373 6986 7.340232 TCCAAATCCAAATCATTTTCTCTCGAT 59.660 33.333 0.00 0.00 0.00 3.59
2374 6987 6.658816 TCCAAATCCAAATCATTTTCTCTCGA 59.341 34.615 0.00 0.00 0.00 4.04
2375 6988 6.855836 TCCAAATCCAAATCATTTTCTCTCG 58.144 36.000 0.00 0.00 0.00 4.04
2378 6991 7.046033 AGCATCCAAATCCAAATCATTTTCTC 58.954 34.615 0.00 0.00 0.00 2.87
2379 6992 6.954232 AGCATCCAAATCCAAATCATTTTCT 58.046 32.000 0.00 0.00 0.00 2.52
2449 13241 4.573607 TGATGCTTGCTGATGTATCAACTC 59.426 41.667 0.00 0.00 36.18 3.01
2454 13246 4.213694 CCTCTTGATGCTTGCTGATGTATC 59.786 45.833 0.00 0.00 0.00 2.24
2526 13318 0.386352 CTGCCACTGTCGCAACAATG 60.386 55.000 1.04 0.00 35.40 2.82
2527 13319 0.534877 TCTGCCACTGTCGCAACAAT 60.535 50.000 1.04 0.00 35.40 2.71
2528 13320 0.534877 ATCTGCCACTGTCGCAACAA 60.535 50.000 1.04 0.00 35.40 2.83
2529 13321 0.950555 GATCTGCCACTGTCGCAACA 60.951 55.000 1.04 0.00 35.40 3.33
2565 13357 1.404391 ACACACGGACATACGGAGATC 59.596 52.381 0.00 0.00 38.39 2.75
2591 13383 0.858583 TGCAAGACATGTGTTCGTCG 59.141 50.000 1.15 0.00 37.23 5.12
2634 13429 2.223829 GGATTGATCACCGTCATCGAGT 60.224 50.000 0.00 0.00 39.71 4.18
2743 13538 1.983035 ATGGCCAGGAGGAGGAGGAT 61.983 60.000 13.05 0.00 36.89 3.24
2935 13754 4.821589 GAGTCCCTGGCCTTCGCG 62.822 72.222 3.32 0.00 35.02 5.87
2936 13755 4.821589 CGAGTCCCTGGCCTTCGC 62.822 72.222 3.32 0.00 0.00 4.70
2937 13756 4.821589 GCGAGTCCCTGGCCTTCG 62.822 72.222 3.32 5.21 0.00 3.79
2938 13757 3.394836 AGCGAGTCCCTGGCCTTC 61.395 66.667 3.32 0.00 35.84 3.46
2939 13758 3.710722 CAGCGAGTCCCTGGCCTT 61.711 66.667 3.32 0.00 35.84 4.35
2940 13759 4.704103 TCAGCGAGTCCCTGGCCT 62.704 66.667 3.32 0.00 35.84 5.19
2941 13760 4.154347 CTCAGCGAGTCCCTGGCC 62.154 72.222 4.98 0.00 35.84 5.36
2942 13761 4.154347 CCTCAGCGAGTCCCTGGC 62.154 72.222 4.98 0.00 35.46 4.85
2943 13762 4.154347 GCCTCAGCGAGTCCCTGG 62.154 72.222 4.98 0.00 0.00 4.45
2944 13763 4.154347 GGCCTCAGCGAGTCCCTG 62.154 72.222 0.00 0.00 41.24 4.45
2947 13766 4.459089 GTGGGCCTCAGCGAGTCC 62.459 72.222 4.53 1.78 41.24 3.85
2948 13767 4.459089 GGTGGGCCTCAGCGAGTC 62.459 72.222 4.53 0.00 41.24 3.36
2950 13769 4.767255 GTGGTGGGCCTCAGCGAG 62.767 72.222 4.53 0.00 46.16 5.03
2983 13802 0.379669 GCAAGATCGCCAACCAGATG 59.620 55.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.