Multiple sequence alignment - TraesCS1D01G222200

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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 TraesCS1D01G222200 chr1D 100.000 4157 0 0 1 4157 309974216 309970060 0.000000e+00 7677.0
1 TraesCS1D01G222200 chr1B 91.629 4193 185 51 1 4157 419984178 419988240 0.000000e+00 5646.0
2 TraesCS1D01G222200 chr1B 92.157 102 4 1 2195 2296 640477641 640477544 1.560000e-29 141.0
3 TraesCS1D01G222200 chr3A 94.747 1523 64 8 638 2146 128564227 128565747 0.000000e+00 2355.0
4 TraesCS1D01G222200 chr3A 91.123 1656 98 20 2165 3810 128565827 128567443 0.000000e+00 2198.0
5 TraesCS1D01G222200 chr3A 87.041 517 22 13 68 569 128563729 128564215 3.660000e-150 542.0
6 TraesCS1D01G222200 chr3A 84.127 126 17 3 4028 4151 434446941 434447065 7.300000e-23 119.0
7 TraesCS1D01G222200 chr3A 83.465 127 19 2 4027 4151 343153722 343153596 2.630000e-22 117.0
8 TraesCS1D01G222200 chr1A 94.609 1521 64 10 638 2146 389821841 389820327 0.000000e+00 2338.0
9 TraesCS1D01G222200 chr1A 91.555 1646 99 22 2178 3810 389820332 389818714 0.000000e+00 2233.0
10 TraesCS1D01G222200 chr1A 83.554 529 22 20 68 569 389822343 389821853 6.380000e-118 435.0
11 TraesCS1D01G222200 chr1A 87.158 366 26 13 1 354 56982780 56983136 3.010000e-106 396.0
12 TraesCS1D01G222200 chr1A 85.559 367 31 12 1 354 212577498 212577855 8.490000e-97 364.0
13 TraesCS1D01G222200 chr2A 87.088 364 26 11 3 354 165942619 165942265 3.900000e-105 392.0
14 TraesCS1D01G222200 chr2A 91.892 111 9 0 1661 1771 745527300 745527410 5.560000e-34 156.0
15 TraesCS1D01G222200 chr2A 86.400 125 15 2 4027 4149 14478646 14478770 7.250000e-28 135.0
16 TraesCS1D01G222200 chr6A 86.885 366 27 11 1 354 214068949 214069305 1.400000e-104 390.0
17 TraesCS1D01G222200 chr3B 86.612 366 28 13 1 354 727664811 727664455 6.520000e-103 385.0
18 TraesCS1D01G222200 chr3B 85.714 315 22 13 50 354 511678842 511679143 1.120000e-80 311.0
19 TraesCS1D01G222200 chr3B 88.889 126 13 1 4027 4151 497085972 497085847 2.000000e-33 154.0
20 TraesCS1D01G222200 chr3B 87.302 63 6 2 3865 3925 521841174 521841112 2.070000e-08 71.3
21 TraesCS1D01G222200 chr3B 87.302 63 6 2 3865 3925 521846434 521846372 2.070000e-08 71.3
22 TraesCS1D01G222200 chr4A 87.302 315 21 8 50 354 362910384 362910689 3.980000e-90 342.0
23 TraesCS1D01G222200 chr4A 86.154 65 7 2 3862 3924 660806632 660806696 7.460000e-08 69.4
24 TraesCS1D01G222200 chr5B 81.043 211 32 8 3795 4000 229687884 229688091 1.200000e-35 161.0
25 TraesCS1D01G222200 chr5A 85.039 127 14 5 4027 4150 429240369 429240245 1.570000e-24 124.0
26 TraesCS1D01G222200 chr7B 87.736 106 11 2 4052 4155 718774198 718774093 5.640000e-24 122.0
27 TraesCS1D01G222200 chr2D 83.333 126 19 2 4027 4150 433222577 433222452 9.440000e-22 115.0
28 TraesCS1D01G222200 chr2D 91.525 59 4 1 1711 1769 615502489 615502546 3.440000e-11 80.5
29 TraesCS1D01G222200 chr4D 86.538 104 12 2 4050 4151 117639029 117638926 3.400000e-21 113.0
30 TraesCS1D01G222200 chr4D 97.143 35 1 0 1115 1149 469571276 469571310 4.490000e-05 60.2
31 TraesCS1D01G222200 chr6B 86.154 65 7 2 3862 3924 141889699 141889763 7.460000e-08 69.4
32 TraesCS1D01G222200 chr6B 86.154 65 7 2 3862 3924 260286665 260286729 7.460000e-08 69.4


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 TraesCS1D01G222200 chr1D 309970060 309974216 4156 True 7677.000000 7677 100.000000 1 4157 1 chr1D.!!$R1 4156
1 TraesCS1D01G222200 chr1B 419984178 419988240 4062 False 5646.000000 5646 91.629000 1 4157 1 chr1B.!!$F1 4156
2 TraesCS1D01G222200 chr3A 128563729 128567443 3714 False 1698.333333 2355 90.970333 68 3810 3 chr3A.!!$F2 3742
3 TraesCS1D01G222200 chr1A 389818714 389822343 3629 True 1668.666667 2338 89.906000 68 3810 3 chr1A.!!$R1 3742

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
324 355 0.038166 ACATGCAACCCAAGACCGAT 59.962 50.000 0.0 0.0 0.0 4.18 F
327 358 0.109532 TGCAACCCAAGACCGATCAA 59.890 50.000 0.0 0.0 0.0 2.57 F
379 410 1.079750 GGGTCTCCTGTCGTCAAGC 60.080 63.158 0.0 0.0 0.0 4.01 F
382 413 1.133407 GGTCTCCTGTCGTCAAGCTAG 59.867 57.143 0.0 0.0 0.0 3.42 F
397 435 1.439644 CTAGCTCCTCCTTGACCGC 59.560 63.158 0.0 0.0 0.0 5.68 F
2064 2139 1.065410 TCTGGTGCAAGGAAGGGGAA 61.065 55.000 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 1495 0.169009 GTCTGCTCGAAAATGGCCAC 59.831 55.000 8.16 0.00 0.00 5.01 R
1818 1893 1.067582 CATCGAGCCCTTACCGGTC 59.932 63.158 12.40 0.00 0.00 4.79 R
1908 1983 1.134521 TCCACACGAACTCAGCTTTGT 60.135 47.619 0.00 0.00 0.00 2.83 R
2058 2133 1.600916 GCGTTTCAGCAGTTCCCCT 60.601 57.895 0.00 0.00 37.05 4.79 R
2332 2477 1.873591 GGCTATGCCGTCAGTAATTGG 59.126 52.381 0.00 0.00 39.62 3.16 R
3642 3794 0.476611 ACTTTCCTTGGGAGGCTCCT 60.477 55.000 31.39 6.92 43.21 3.69 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
45 48 0.737219 GCCGAGCTTTACTAGTCGGA 59.263 55.000 19.37 0.00 43.87 4.55
136 139 2.202743 TCCGGCGATCGAAGCAAG 60.203 61.111 21.57 10.13 42.43 4.01
175 178 1.814527 CCCTCACGTACCCTACAGC 59.185 63.158 0.00 0.00 0.00 4.40
199 203 1.019278 CGTGGAAACGGAGACATGGG 61.019 60.000 0.00 0.00 0.00 4.00
243 249 7.172757 CACACCTGAAAAATGAAAAAGAAACG 58.827 34.615 0.00 0.00 0.00 3.60
257 263 3.014604 AGAAACGGAAACAGAGAGTCG 57.985 47.619 0.00 0.00 0.00 4.18
287 293 6.086765 CGAACAAGCATGTGTAGAATTCAAAC 59.913 38.462 8.44 6.14 40.46 2.93
288 294 6.389830 ACAAGCATGTGTAGAATTCAAACA 57.610 33.333 8.44 8.77 38.69 2.83
289 295 6.804677 ACAAGCATGTGTAGAATTCAAACAA 58.195 32.000 13.38 6.71 38.69 2.83
290 296 6.919662 ACAAGCATGTGTAGAATTCAAACAAG 59.080 34.615 13.38 9.56 38.69 3.16
324 355 0.038166 ACATGCAACCCAAGACCGAT 59.962 50.000 0.00 0.00 0.00 4.18
325 356 0.734889 CATGCAACCCAAGACCGATC 59.265 55.000 0.00 0.00 0.00 3.69
326 357 0.327924 ATGCAACCCAAGACCGATCA 59.672 50.000 0.00 0.00 0.00 2.92
327 358 0.109532 TGCAACCCAAGACCGATCAA 59.890 50.000 0.00 0.00 0.00 2.57
379 410 1.079750 GGGTCTCCTGTCGTCAAGC 60.080 63.158 0.00 0.00 0.00 4.01
380 411 1.536943 GGGTCTCCTGTCGTCAAGCT 61.537 60.000 0.00 0.00 0.00 3.74
381 412 1.174783 GGTCTCCTGTCGTCAAGCTA 58.825 55.000 0.00 0.00 0.00 3.32
382 413 1.133407 GGTCTCCTGTCGTCAAGCTAG 59.867 57.143 0.00 0.00 0.00 3.42
397 435 1.439644 CTAGCTCCTCCTTGACCGC 59.560 63.158 0.00 0.00 0.00 5.68
402 440 4.148825 CCTCCTTGACCGCCCTCG 62.149 72.222 0.00 0.00 0.00 4.63
518 566 2.183478 TTCTCTTGGAAGCATCGCAA 57.817 45.000 0.00 0.00 0.00 4.85
550 598 4.083003 TGCAAGTTCAAACAAGTCTTCGTT 60.083 37.500 0.00 0.00 0.00 3.85
576 624 9.767684 TCAATTGACTAAACGTTGCTATATTTG 57.232 29.630 3.38 2.66 0.00 2.32
620 680 7.537991 CGTAGGTACAAGTTCAAACAAAACAAA 59.462 33.333 0.00 0.00 0.00 2.83
1043 1112 2.820787 GTGGTAGACTAGTGCTGAGTGT 59.179 50.000 0.00 0.00 0.00 3.55
1242 1311 2.359981 TATCCAAGATCCTCGTCGGT 57.640 50.000 0.00 0.00 0.00 4.69
1378 1451 2.044650 CCACTGCCCACTCCCATG 60.045 66.667 0.00 0.00 0.00 3.66
1381 1454 2.439701 CTGCCCACTCCCATGCTG 60.440 66.667 0.00 0.00 0.00 4.41
1420 1495 3.559655 TCTGAATGTTTCCGTCTGTTGTG 59.440 43.478 0.00 0.00 0.00 3.33
1908 1983 4.982295 CCGTATGATATCTCGTGCAAGAAA 59.018 41.667 3.39 0.00 0.00 2.52
2058 2133 1.271543 CCTGATGTCTGGTGCAAGGAA 60.272 52.381 0.00 0.00 0.00 3.36
2064 2139 1.065410 TCTGGTGCAAGGAAGGGGAA 61.065 55.000 0.00 0.00 0.00 3.97
2101 2184 6.018994 CACAAGAAAAGGTACAGACTACACAC 60.019 42.308 0.00 0.00 0.00 3.82
2102 2185 5.864418 AGAAAAGGTACAGACTACACACA 57.136 39.130 0.00 0.00 0.00 3.72
2104 2187 4.332428 AAAGGTACAGACTACACACACC 57.668 45.455 0.00 0.00 0.00 4.16
2105 2188 3.240310 AGGTACAGACTACACACACCT 57.760 47.619 0.00 0.00 0.00 4.00
2156 2239 8.506168 TGGATCAACATCTTTTATACTCCAAC 57.494 34.615 0.00 0.00 0.00 3.77
2182 2325 7.420800 CAAGGTGATTAAGGTGCATAATCTTC 58.579 38.462 15.90 10.59 39.44 2.87
2227 2370 6.127730 GGGGATTTACACAGGACAAAAGTATG 60.128 42.308 0.00 0.00 0.00 2.39
2284 2429 5.869753 AACTCTGACTGCACAATATCAAC 57.130 39.130 0.00 0.00 0.00 3.18
2305 2450 5.505181 ACTGATTGTCCATTTGTCCTACT 57.495 39.130 0.00 0.00 0.00 2.57
2307 2452 6.407202 ACTGATTGTCCATTTGTCCTACTAC 58.593 40.000 0.00 0.00 0.00 2.73
2439 2584 3.181461 ACAAGAGTAAGTTCAGCAGCACT 60.181 43.478 0.00 0.00 0.00 4.40
2449 2594 2.221169 TCAGCAGCACTCGAAACAAAT 58.779 42.857 0.00 0.00 0.00 2.32
2453 2598 3.062639 AGCAGCACTCGAAACAAATATCG 59.937 43.478 0.00 0.00 40.31 2.92
2456 2601 5.481472 CAGCACTCGAAACAAATATCGTAC 58.519 41.667 0.00 0.00 39.91 3.67
2457 2602 5.061684 CAGCACTCGAAACAAATATCGTACA 59.938 40.000 0.00 0.00 39.91 2.90
2475 2620 3.618690 ACACTACCATTTCTGCCTCTC 57.381 47.619 0.00 0.00 0.00 3.20
2478 2623 2.428890 ACTACCATTTCTGCCTCTCTCG 59.571 50.000 0.00 0.00 0.00 4.04
2489 2634 1.997669 CCTCTCTCGGTGTAGTTTGC 58.002 55.000 0.00 0.00 0.00 3.68
2500 2645 5.640357 TCGGTGTAGTTTGCGAGATTTTAAT 59.360 36.000 0.00 0.00 0.00 1.40
2557 2702 1.204231 TGGTTTACGGCGTATACAGCA 59.796 47.619 31.36 24.25 36.08 4.41
2616 2761 5.988310 TCATGGATGAGAAATGCTGTTTT 57.012 34.783 0.00 0.00 32.11 2.43
2761 2906 1.546476 AGCTGGAGTCGGTAGTGAAAG 59.454 52.381 0.00 0.00 0.00 2.62
3026 3172 4.864704 AAGAGTTGAGAGAAGACTCACC 57.135 45.455 0.00 0.00 44.94 4.02
3047 3193 2.413112 CAGTTGCTCCACACTTGTATCG 59.587 50.000 0.00 0.00 0.00 2.92
3061 3207 0.519961 GTATCGTGTGTGGGCAAACC 59.480 55.000 0.00 0.00 40.81 3.27
3110 3256 4.343231 TCCATGCCAACATTCTACATGTT 58.657 39.130 2.30 0.00 42.38 2.71
3241 3387 2.531522 AAGCAAAATCACAAGGTGGC 57.468 45.000 0.00 0.00 33.87 5.01
3242 3388 0.314935 AGCAAAATCACAAGGTGGCG 59.685 50.000 0.00 0.00 33.87 5.69
3265 3411 4.326504 AGGAGTCTTTTGTGGCAAAATG 57.673 40.909 7.38 0.00 0.00 2.32
3319 3465 0.950116 GAGTTGCTTGCTCAAGTGCT 59.050 50.000 10.86 6.88 40.45 4.40
3341 3487 2.957006 GCCTACGGGAGAATCTAGACAA 59.043 50.000 0.00 0.00 33.73 3.18
3352 3498 5.837437 AGAATCTAGACAATTGGAGCTACG 58.163 41.667 10.83 3.77 0.00 3.51
3378 3524 3.766051 GACAATCAGGAAATTTCTGGCCT 59.234 43.478 17.42 4.30 33.36 5.19
3449 3595 3.981071 ACTGGCTATGACAAAGCTGTA 57.019 42.857 0.00 0.00 39.97 2.74
3497 3644 3.399330 TGGTACTGCAACTAACAAGAGC 58.601 45.455 0.00 0.00 0.00 4.09
3528 3675 1.745653 GAAAACATGCACCTCCCTAGC 59.254 52.381 0.00 0.00 0.00 3.42
3542 3694 0.459899 CCTAGCTACATGACGGTGCA 59.540 55.000 0.00 0.00 0.00 4.57
3642 3794 1.605453 GGGCCTCCGACCAATGTAA 59.395 57.895 0.84 0.00 0.00 2.41
3644 3796 0.463833 GGCCTCCGACCAATGTAAGG 60.464 60.000 0.00 0.00 0.00 2.69
3656 3808 1.216990 ATGTAAGGAGCCTCCCAAGG 58.783 55.000 7.26 0.00 46.44 3.61
3704 3856 3.453059 AAGGACTCTTCTACCGAGGAA 57.547 47.619 0.00 0.00 32.83 3.36
3752 3904 1.457643 CCATAGGCCTCGTCCTCCA 60.458 63.158 9.68 0.00 37.66 3.86
3757 3909 1.051812 AGGCCTCGTCCTCCATTATG 58.948 55.000 0.00 0.00 0.00 1.90
3790 3942 1.666011 GATAGCTCGGGGCATCGAA 59.334 57.895 1.17 0.00 44.79 3.71
3873 4025 6.466308 GTGTTTTCCACCAGCAATTAAATC 57.534 37.500 0.00 0.00 38.18 2.17
3880 4032 4.628333 CCACCAGCAATTAAATCAAAGCAG 59.372 41.667 0.00 0.00 0.00 4.24
3962 4114 1.819632 CTGGTACTTCCGGCCATGC 60.820 63.158 2.24 0.00 39.52 4.06
3966 4118 0.530870 GTACTTCCGGCCATGCTCTC 60.531 60.000 2.24 0.00 0.00 3.20
3983 4135 1.063867 TCTCCACCCTACTGAGGCTAC 60.064 57.143 0.00 0.00 42.21 3.58
3988 4140 2.363680 CACCCTACTGAGGCTACTGATG 59.636 54.545 0.00 0.00 42.21 3.07
3994 4147 5.582665 CCTACTGAGGCTACTGATGTTTTTC 59.417 44.000 0.00 0.00 35.54 2.29
3998 4151 4.927425 TGAGGCTACTGATGTTTTTCGTAC 59.073 41.667 0.00 0.00 0.00 3.67
4000 4153 3.061697 GGCTACTGATGTTTTTCGTACCG 59.938 47.826 0.00 0.00 0.00 4.02
4007 4160 3.929417 TGTTTTTCGTACCGTCAGTTG 57.071 42.857 0.00 0.00 0.00 3.16
4044 4197 4.081752 GGGCATGATCATTGGTTGTGTTAA 60.082 41.667 5.16 0.00 0.00 2.01
4058 4211 7.429633 TGGTTGTGTTAATAAACTCATGTTGG 58.570 34.615 0.00 0.00 38.50 3.77
4061 4214 9.308318 GTTGTGTTAATAAACTCATGTTGGTTT 57.692 29.630 14.55 14.55 38.50 3.27
4097 4251 6.098266 AGGTCACTTAAGGAAAATTGTTGCTT 59.902 34.615 7.53 0.00 34.47 3.91
4112 4266 0.673437 TGCTTGCTACAAACCCTTGC 59.327 50.000 0.00 0.00 35.84 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 156 1.105759 GTAGGGTACGTGAGGGCGAT 61.106 60.000 0.00 0.00 35.59 4.58
154 157 1.750399 GTAGGGTACGTGAGGGCGA 60.750 63.158 0.00 0.00 35.59 5.54
155 158 2.001361 CTGTAGGGTACGTGAGGGCG 62.001 65.000 0.00 0.00 37.94 6.13
156 159 1.814527 CTGTAGGGTACGTGAGGGC 59.185 63.158 0.00 0.00 0.00 5.19
175 178 1.001048 TGTCTCCGTTTCCACGTACAG 60.001 52.381 0.00 0.00 45.62 2.74
243 249 1.135632 CGTCTCCGACTCTCTGTTTCC 60.136 57.143 0.00 0.00 35.63 3.13
257 263 1.512926 ACACATGCTTGTTCGTCTCC 58.487 50.000 1.83 0.00 32.34 3.71
264 270 6.804677 TGTTTGAATTCTACACATGCTTGTT 58.195 32.000 7.05 0.00 32.34 2.83
274 280 6.489700 TCCATCTTGCTTGTTTGAATTCTACA 59.510 34.615 7.05 8.27 0.00 2.74
287 293 4.321008 GCATGTATCCATCCATCTTGCTTG 60.321 45.833 0.00 0.00 0.00 4.01
288 294 3.825014 GCATGTATCCATCCATCTTGCTT 59.175 43.478 0.00 0.00 0.00 3.91
289 295 3.181437 TGCATGTATCCATCCATCTTGCT 60.181 43.478 0.00 0.00 32.85 3.91
290 296 3.151554 TGCATGTATCCATCCATCTTGC 58.848 45.455 0.00 0.00 0.00 4.01
324 355 4.373116 GCCGGTCGGTCTGCTTGA 62.373 66.667 11.25 0.00 37.65 3.02
379 410 1.439644 GCGGTCAAGGAGGAGCTAG 59.560 63.158 0.00 0.00 33.24 3.42
380 411 2.058595 GGCGGTCAAGGAGGAGCTA 61.059 63.158 0.00 0.00 33.24 3.32
381 412 3.394836 GGCGGTCAAGGAGGAGCT 61.395 66.667 0.00 0.00 33.24 4.09
382 413 4.475135 GGGCGGTCAAGGAGGAGC 62.475 72.222 0.00 0.00 0.00 4.70
402 440 1.591594 TATGCTACGGCTGCGCTTC 60.592 57.895 9.73 0.00 39.59 3.86
518 566 2.645730 TTGAACTTGCAGCAACGTTT 57.354 40.000 18.28 7.67 0.00 3.60
550 598 9.767684 CAAATATAGCAACGTTTAGTCAATTGA 57.232 29.630 3.38 3.38 0.00 2.57
575 623 2.224426 ACGGTTGTTGGAGCTGTATTCA 60.224 45.455 0.00 0.00 0.00 2.57
576 624 2.423577 ACGGTTGTTGGAGCTGTATTC 58.576 47.619 0.00 0.00 0.00 1.75
629 689 2.519771 TCTGGACGTACCACCTACAT 57.480 50.000 0.00 0.00 44.64 2.29
892 957 0.040067 CGTGGCAGAAAGAACAAGGC 60.040 55.000 0.00 0.00 0.00 4.35
1043 1112 0.105709 TCCCACACAGTCACTCTCCA 60.106 55.000 0.00 0.00 0.00 3.86
1242 1311 2.938354 GAAGCAGCTCTTCTTGCCA 58.062 52.632 14.82 0.00 45.99 4.92
1378 1451 1.185315 AAGGAGAGAGCAGAGACAGC 58.815 55.000 0.00 0.00 0.00 4.40
1381 1454 3.088532 TCAGAAAGGAGAGAGCAGAGAC 58.911 50.000 0.00 0.00 0.00 3.36
1420 1495 0.169009 GTCTGCTCGAAAATGGCCAC 59.831 55.000 8.16 0.00 0.00 5.01
1818 1893 1.067582 CATCGAGCCCTTACCGGTC 59.932 63.158 12.40 0.00 0.00 4.79
1830 1905 3.554692 GCCGTTCACCGCATCGAG 61.555 66.667 0.00 0.00 34.38 4.04
1908 1983 1.134521 TCCACACGAACTCAGCTTTGT 60.135 47.619 0.00 0.00 0.00 2.83
2058 2133 1.600916 GCGTTTCAGCAGTTCCCCT 60.601 57.895 0.00 0.00 37.05 4.79
2101 2184 5.571784 ATGTTCTGAATATTGCACAGGTG 57.428 39.130 0.00 0.00 33.19 4.00
2102 2185 5.711506 TGAATGTTCTGAATATTGCACAGGT 59.288 36.000 15.74 0.00 33.19 4.00
2104 2187 6.849502 ACTGAATGTTCTGAATATTGCACAG 58.150 36.000 15.74 16.85 0.00 3.66
2105 2188 6.430616 TGACTGAATGTTCTGAATATTGCACA 59.569 34.615 15.74 7.94 0.00 4.57
2156 2239 5.829924 AGATTATGCACCTTAATCACCTTGG 59.170 40.000 16.88 0.00 38.14 3.61
2227 2370 3.511934 AGACCTCCTGTTGATGTAGACAC 59.488 47.826 0.00 0.00 0.00 3.67
2284 2429 6.406370 TGTAGTAGGACAAATGGACAATCAG 58.594 40.000 0.00 0.00 0.00 2.90
2319 2464 8.836413 CCGTCAGTAATTGGACATACATTTATT 58.164 33.333 7.29 0.00 33.66 1.40
2320 2465 7.041372 GCCGTCAGTAATTGGACATACATTTAT 60.041 37.037 7.29 0.00 33.66 1.40
2321 2466 6.259167 GCCGTCAGTAATTGGACATACATTTA 59.741 38.462 7.29 0.00 33.66 1.40
2328 2473 2.779755 TGCCGTCAGTAATTGGACAT 57.220 45.000 7.29 0.00 33.66 3.06
2332 2477 1.873591 GGCTATGCCGTCAGTAATTGG 59.126 52.381 0.00 0.00 39.62 3.16
2439 2584 6.619744 TGGTAGTGTACGATATTTGTTTCGA 58.380 36.000 0.00 0.00 38.67 3.71
2449 2594 4.647853 AGGCAGAAATGGTAGTGTACGATA 59.352 41.667 0.00 0.00 0.00 2.92
2453 2598 4.160626 AGAGAGGCAGAAATGGTAGTGTAC 59.839 45.833 0.00 0.00 0.00 2.90
2456 2601 3.736433 CGAGAGAGGCAGAAATGGTAGTG 60.736 52.174 0.00 0.00 0.00 2.74
2457 2602 2.428890 CGAGAGAGGCAGAAATGGTAGT 59.571 50.000 0.00 0.00 0.00 2.73
2475 2620 2.279582 ATCTCGCAAACTACACCGAG 57.720 50.000 2.78 2.78 46.11 4.63
2478 2623 7.903431 CAGTATTAAAATCTCGCAAACTACACC 59.097 37.037 0.00 0.00 0.00 4.16
2489 2634 6.114288 CGAAACGCTCAGTATTAAAATCTCG 58.886 40.000 0.00 0.00 0.00 4.04
2557 2702 1.827399 ATCACCCACGTCGGAAGCTT 61.827 55.000 6.09 0.00 36.56 3.74
2634 2779 4.036027 TGACACTCGAATTCTACGATACCC 59.964 45.833 3.52 0.00 39.02 3.69
2761 2906 1.577328 CGGCTCACACATCAACCCAC 61.577 60.000 0.00 0.00 0.00 4.61
2863 3008 7.656137 CAGAGCTGAACTAAACTACCTTACAAA 59.344 37.037 0.00 0.00 0.00 2.83
2868 3013 5.810080 ACAGAGCTGAACTAAACTACCTT 57.190 39.130 4.21 0.00 0.00 3.50
2882 3027 6.849588 TGTATGCATTACAATACAGAGCTG 57.150 37.500 3.54 0.00 37.87 4.24
3026 3172 2.413112 CGATACAAGTGTGGAGCAACTG 59.587 50.000 0.00 0.00 0.00 3.16
3047 3193 2.417097 GCAGGTTTGCCCACACAC 59.583 61.111 0.00 0.00 44.74 3.82
3061 3207 7.600752 AGAGAAAACTAACTTAACTAGCTGCAG 59.399 37.037 10.11 10.11 0.00 4.41
3110 3256 0.913924 TCAATGGCATCTGCTGGAGA 59.086 50.000 0.00 0.07 41.70 3.71
3241 3387 2.163818 TGCCACAAAAGACTCCTACG 57.836 50.000 0.00 0.00 0.00 3.51
3242 3388 4.911514 TTTTGCCACAAAAGACTCCTAC 57.088 40.909 1.50 0.00 0.00 3.18
3341 3487 3.195610 TGATTGTCAGACGTAGCTCCAAT 59.804 43.478 0.00 0.00 0.00 3.16
3378 3524 6.095300 CACCATGACTTGCCTGTAATTTCATA 59.905 38.462 0.00 0.00 0.00 2.15
3497 3644 4.690280 GGTGCATGTTTTCCCTTTGTAATG 59.310 41.667 0.00 0.00 0.00 1.90
3528 3675 3.639538 GGTATAGTGCACCGTCATGTAG 58.360 50.000 14.63 0.00 0.00 2.74
3542 3694 1.456331 CCACCCCGACCGGTATAGT 60.456 63.158 7.34 0.00 33.67 2.12
3642 3794 0.476611 ACTTTCCTTGGGAGGCTCCT 60.477 55.000 31.39 6.92 43.21 3.69
3644 3796 0.988063 AGACTTTCCTTGGGAGGCTC 59.012 55.000 5.78 5.78 43.21 4.70
3656 3808 0.802607 CGCCTAGACGCCAGACTTTC 60.803 60.000 0.00 0.00 0.00 2.62
3704 3856 5.074790 AGAGTACTAAATCGACCTAGGGGAT 59.925 44.000 14.81 12.49 36.25 3.85
3717 3869 7.347485 AGGCCTATGGTTACAAGAGTACTAAAT 59.653 37.037 1.29 0.00 0.00 1.40
3762 3914 2.143419 CGAGCTATCCCCTGGCCTT 61.143 63.158 3.32 0.00 30.08 4.35
3790 3942 5.046529 GCTACTGAGACGATGACAATGATT 58.953 41.667 0.00 0.00 0.00 2.57
3851 4003 6.166984 TGATTTAATTGCTGGTGGAAAACA 57.833 33.333 0.00 0.00 0.00 2.83
3852 4004 7.489574 TTTGATTTAATTGCTGGTGGAAAAC 57.510 32.000 0.00 0.00 0.00 2.43
3873 4025 3.756963 GGTAAAACCCTACTCCTGCTTTG 59.243 47.826 0.00 0.00 30.04 2.77
3880 4032 3.328637 TGGTTGAGGTAAAACCCTACTCC 59.671 47.826 3.04 0.00 45.49 3.85
3932 4084 1.867363 AGTACCAGAGGGGATCACAC 58.133 55.000 0.00 0.00 41.15 3.82
3934 4086 1.763545 GGAAGTACCAGAGGGGATCAC 59.236 57.143 0.00 0.00 41.15 3.06
3962 4114 2.510664 GCCTCAGTAGGGTGGAGAG 58.489 63.158 0.00 0.00 43.87 3.20
4000 4153 2.591715 ACTGGCGTGCCAACTGAC 60.592 61.111 15.46 0.00 46.63 3.51
4023 4176 8.594687 GTTTATTAACACAACCAATGATCATGC 58.405 33.333 9.46 0.00 34.31 4.06
4058 4211 8.669243 CCTTAAGTGACCTCAAGATTATCAAAC 58.331 37.037 0.97 0.00 0.00 2.93
4061 4214 7.733773 TCCTTAAGTGACCTCAAGATTATCA 57.266 36.000 0.97 0.00 0.00 2.15
4097 4251 1.680735 CAACTGCAAGGGTTTGTAGCA 59.319 47.619 5.47 0.00 46.98 3.49
4119 4273 2.038557 TCAACTAGAAGGTGTTGGGCTC 59.961 50.000 0.00 0.00 42.48 4.70


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

AutoCloner maintained by Alex Coulton.