Multiple sequence alignment - TraesCS2D01G382500

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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 TraesCS2D01G382500 chr2D 100.000 4493 0 0 1 4493 486396230 486391738 0.000000e+00 8298
1 TraesCS2D01G382500 chr2D 85.200 1277 116 32 3248 4493 487932173 487933407 0.000000e+00 1243
2 TraesCS2D01G382500 chr2D 85.894 1191 115 33 3312 4493 487722800 487723946 0.000000e+00 1219
3 TraesCS2D01G382500 chr2B 94.100 3661 165 25 856 4493 571350610 571346978 0.000000e+00 5517
4 TraesCS2D01G382500 chr2B 86.137 1284 109 30 3248 4493 572311733 572312985 0.000000e+00 1321
5 TraesCS2D01G382500 chr2B 84.462 1255 150 26 3248 4493 572177521 572178739 0.000000e+00 1195
6 TraesCS2D01G382500 chr2B 86.836 904 67 21 1 864 571353206 571352315 0.000000e+00 963
7 TraesCS2D01G382500 chr2B 82.432 148 25 1 1 148 646219425 646219571 1.310000e-25 128
8 TraesCS2D01G382500 chr2A 94.064 2544 101 29 1975 4493 631859106 631856588 0.000000e+00 3816
9 TraesCS2D01G382500 chr2A 93.501 1231 62 8 756 1977 631860420 631859199 0.000000e+00 1814
10 TraesCS2D01G382500 chr2A 84.640 1263 126 39 3248 4484 632586787 632588007 0.000000e+00 1195
11 TraesCS2D01G382500 chr2A 84.952 1050 119 19 3469 4493 46337766 46336731 0.000000e+00 1027
12 TraesCS2D01G382500 chr7D 85.333 1050 117 18 3469 4493 446550101 446551138 0.000000e+00 1051
13 TraesCS2D01G382500 chr3D 85.080 878 94 18 3469 4321 16450136 16449271 0.000000e+00 861
14 TraesCS2D01G382500 chr7A 84.766 768 88 14 3742 4493 321635865 321636619 0.000000e+00 743
15 TraesCS2D01G382500 chr6A 84.156 385 37 13 3248 3618 226334531 226334905 7.150000e-93 351
16 TraesCS2D01G382500 chr6A 83.436 163 25 2 46 207 404749618 404749779 2.800000e-32 150
17 TraesCS2D01G382500 chr3B 82.390 159 26 2 51 207 267235789 267235631 2.180000e-28 137


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 TraesCS2D01G382500 chr2D 486391738 486396230 4492 True 8298 8298 100.0000 1 4493 1 chr2D.!!$R1 4492
1 TraesCS2D01G382500 chr2D 487932173 487933407 1234 False 1243 1243 85.2000 3248 4493 1 chr2D.!!$F2 1245
2 TraesCS2D01G382500 chr2D 487722800 487723946 1146 False 1219 1219 85.8940 3312 4493 1 chr2D.!!$F1 1181
3 TraesCS2D01G382500 chr2B 571346978 571353206 6228 True 3240 5517 90.4680 1 4493 2 chr2B.!!$R1 4492
4 TraesCS2D01G382500 chr2B 572311733 572312985 1252 False 1321 1321 86.1370 3248 4493 1 chr2B.!!$F2 1245
5 TraesCS2D01G382500 chr2B 572177521 572178739 1218 False 1195 1195 84.4620 3248 4493 1 chr2B.!!$F1 1245
6 TraesCS2D01G382500 chr2A 631856588 631860420 3832 True 2815 3816 93.7825 756 4493 2 chr2A.!!$R2 3737
7 TraesCS2D01G382500 chr2A 632586787 632588007 1220 False 1195 1195 84.6400 3248 4484 1 chr2A.!!$F1 1236
8 TraesCS2D01G382500 chr2A 46336731 46337766 1035 True 1027 1027 84.9520 3469 4493 1 chr2A.!!$R1 1024
9 TraesCS2D01G382500 chr7D 446550101 446551138 1037 False 1051 1051 85.3330 3469 4493 1 chr7D.!!$F1 1024
10 TraesCS2D01G382500 chr3D 16449271 16450136 865 True 861 861 85.0800 3469 4321 1 chr3D.!!$R1 852
11 TraesCS2D01G382500 chr7A 321635865 321636619 754 False 743 743 84.7660 3742 4493 1 chr7A.!!$F1 751

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
550 577 0.179111 TAGCTGCCCGTGAAGAATCG 60.179 55.000 0.00 0.00 0.00 3.34 F
1397 3149 0.245266 TCGAACAACTGGCGAGCATA 59.755 50.000 0.00 0.00 0.00 3.14 F
2651 4509 0.395311 CCATCTTCACTGCCTGGCAT 60.395 55.000 23.64 9.78 38.13 4.40 F
3291 5152 4.039730 AGGATCAGTATCAAATCAGACGGG 59.960 45.833 0.00 0.00 33.41 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 3357 0.319297 AGGAAACACCGACTACGTGC 60.319 55.000 0.00 0.0 44.74 5.34 R
3291 5152 3.608316 TTAGTGGGCCAAAATTGATGC 57.392 42.857 8.40 0.0 0.00 3.91 R
3458 5337 0.163788 CGTGCTCGTGCCTTTGTAAG 59.836 55.000 7.05 0.0 38.71 2.34 R
4330 6343 1.068055 CCTGCAAAGTCAAGCATCACC 60.068 52.381 0.00 0.0 40.42 4.02 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
43 44 9.565090 TGGAATTATTATTTCACCAGATCTCTG 57.435 33.333 0.00 0.00 43.40 3.35
68 69 4.725556 TGCGTTGTGAATCACTCTAAAC 57.274 40.909 14.97 9.23 35.11 2.01
73 74 5.119279 CGTTGTGAATCACTCTAAACCTCTG 59.881 44.000 14.97 0.00 35.11 3.35
173 174 2.290960 ACCCTAAACATCTCCACAAGCC 60.291 50.000 0.00 0.00 0.00 4.35
177 178 0.773644 AACATCTCCACAAGCCTGGT 59.226 50.000 0.00 0.00 32.50 4.00
178 179 0.773644 ACATCTCCACAAGCCTGGTT 59.226 50.000 0.00 0.00 32.50 3.67
194 195 3.073946 CCTGGTTAAAGGGGTTCTTCTCA 59.926 47.826 0.00 0.00 33.94 3.27
197 198 5.076873 TGGTTAAAGGGGTTCTTCTCATTG 58.923 41.667 0.00 0.00 33.94 2.82
198 199 5.077564 GGTTAAAGGGGTTCTTCTCATTGT 58.922 41.667 0.00 0.00 33.94 2.71
199 200 6.183361 TGGTTAAAGGGGTTCTTCTCATTGTA 60.183 38.462 0.00 0.00 33.94 2.41
200 201 6.374613 GGTTAAAGGGGTTCTTCTCATTGTAG 59.625 42.308 0.00 0.00 33.94 2.74
201 202 3.636153 AGGGGTTCTTCTCATTGTAGC 57.364 47.619 0.00 0.00 0.00 3.58
202 203 2.912956 AGGGGTTCTTCTCATTGTAGCA 59.087 45.455 0.00 0.00 0.00 3.49
203 204 3.525199 AGGGGTTCTTCTCATTGTAGCAT 59.475 43.478 0.00 0.00 0.00 3.79
204 205 3.629398 GGGGTTCTTCTCATTGTAGCATG 59.371 47.826 0.00 0.00 0.00 4.06
205 206 4.265073 GGGTTCTTCTCATTGTAGCATGT 58.735 43.478 0.00 0.00 0.00 3.21
206 207 4.702131 GGGTTCTTCTCATTGTAGCATGTT 59.298 41.667 0.00 0.00 0.00 2.71
207 208 5.163713 GGGTTCTTCTCATTGTAGCATGTTC 60.164 44.000 0.00 0.00 0.00 3.18
219 236 8.623903 CATTGTAGCATGTTCTTATGGTTGTAT 58.376 33.333 0.00 0.00 39.33 2.29
245 263 7.406031 TGTAGTTCAGATCGTAATCCTCTTT 57.594 36.000 0.00 0.00 31.78 2.52
250 268 8.919145 AGTTCAGATCGTAATCCTCTTTCTATT 58.081 33.333 0.00 0.00 31.78 1.73
254 272 7.327275 CAGATCGTAATCCTCTTTCTATTTCGG 59.673 40.741 0.00 0.00 31.78 4.30
258 276 3.543680 TCCTCTTTCTATTTCGGGCTG 57.456 47.619 0.00 0.00 0.00 4.85
259 277 1.943340 CCTCTTTCTATTTCGGGCTGC 59.057 52.381 0.00 0.00 0.00 5.25
261 279 1.280710 TCTTTCTATTTCGGGCTGCCA 59.719 47.619 22.05 0.00 0.00 4.92
262 280 2.092429 TCTTTCTATTTCGGGCTGCCAT 60.092 45.455 22.05 7.76 0.00 4.40
276 294 2.689471 GCTGCCATTGAACCATATGTGA 59.311 45.455 1.24 0.00 0.00 3.58
374 392 6.825213 TCAGTTATGATCATCCAGGAACAAAG 59.175 38.462 12.53 5.50 0.00 2.77
381 399 2.260844 TCCAGGAACAAAGCTGACTG 57.739 50.000 0.00 0.00 0.00 3.51
432 450 3.571401 ACCTTTAACTCGTCGGAGAGAAA 59.429 43.478 13.53 5.36 43.27 2.52
439 458 4.745649 ACTCGTCGGAGAGAAATTTAAGG 58.254 43.478 13.53 0.00 43.27 2.69
466 485 8.698854 CGATTTTGTAAGTAATGTTGCACAAAT 58.301 29.630 0.00 0.00 36.21 2.32
469 488 8.932945 TTTGTAAGTAATGTTGCACAAATTGA 57.067 26.923 0.00 0.00 32.58 2.57
470 489 9.539825 TTTGTAAGTAATGTTGCACAAATTGAT 57.460 25.926 0.00 0.00 32.58 2.57
471 490 9.539825 TTGTAAGTAATGTTGCACAAATTGATT 57.460 25.926 0.00 0.00 0.00 2.57
472 491 8.976471 TGTAAGTAATGTTGCACAAATTGATTG 58.024 29.630 0.00 0.00 44.95 2.67
473 492 7.424227 AAGTAATGTTGCACAAATTGATTGG 57.576 32.000 0.00 0.00 43.66 3.16
474 493 6.757237 AGTAATGTTGCACAAATTGATTGGA 58.243 32.000 0.00 0.00 43.66 3.53
475 494 5.927954 AATGTTGCACAAATTGATTGGAC 57.072 34.783 0.00 0.00 43.66 4.02
476 495 4.397481 TGTTGCACAAATTGATTGGACA 57.603 36.364 0.00 0.00 43.66 4.02
477 496 4.763073 TGTTGCACAAATTGATTGGACAA 58.237 34.783 0.00 0.00 43.66 3.18
478 497 5.181009 TGTTGCACAAATTGATTGGACAAA 58.819 33.333 0.00 0.00 43.66 2.83
479 498 5.645067 TGTTGCACAAATTGATTGGACAAAA 59.355 32.000 0.00 0.00 43.66 2.44
498 517 0.550914 ACTGGCACAACTCCTTTGGA 59.449 50.000 0.00 0.00 39.84 3.53
518 537 3.149196 GACTGGCCACTTTGAGAATGAA 58.851 45.455 0.00 0.00 0.00 2.57
522 541 2.887152 GGCCACTTTGAGAATGAACACT 59.113 45.455 0.00 0.00 0.00 3.55
524 543 4.083271 GGCCACTTTGAGAATGAACACTAC 60.083 45.833 0.00 0.00 0.00 2.73
539 566 3.991367 ACACTACGATTAATAGCTGCCC 58.009 45.455 0.00 0.00 0.00 5.36
540 567 2.987149 CACTACGATTAATAGCTGCCCG 59.013 50.000 0.00 0.00 0.00 6.13
541 568 2.626743 ACTACGATTAATAGCTGCCCGT 59.373 45.455 0.00 0.03 0.00 5.28
542 569 1.865865 ACGATTAATAGCTGCCCGTG 58.134 50.000 0.00 0.00 0.00 4.94
550 577 0.179111 TAGCTGCCCGTGAAGAATCG 60.179 55.000 0.00 0.00 0.00 3.34
551 578 1.741770 GCTGCCCGTGAAGAATCGT 60.742 57.895 0.00 0.00 0.00 3.73
585 613 4.401202 TCGCTCCACAATATTCTAGTGACA 59.599 41.667 6.09 0.00 35.33 3.58
597 625 9.520515 AATATTCTAGTGACACTGGAAAAATGT 57.479 29.630 30.56 19.49 46.33 2.71
599 627 5.924356 TCTAGTGACACTGGAAAAATGTGA 58.076 37.500 18.34 0.00 32.56 3.58
609 637 4.033709 TGGAAAAATGTGAAGGAAACCCA 58.966 39.130 0.00 0.00 0.00 4.51
611 639 4.996758 GGAAAAATGTGAAGGAAACCCATG 59.003 41.667 0.00 0.00 0.00 3.66
614 642 2.746279 TGTGAAGGAAACCCATGTGT 57.254 45.000 0.00 0.00 0.00 3.72
644 672 2.094906 TCTGGTGGTGAATTAGTCGTCG 60.095 50.000 0.00 0.00 0.00 5.12
674 710 6.206243 GCTGGTGTATGATTAATTGAGAGCAT 59.794 38.462 0.00 0.00 0.00 3.79
700 736 9.541143 TGGGCTCTTTAAAATAAAAACAGAAAG 57.459 29.630 0.00 0.00 0.00 2.62
701 737 9.758651 GGGCTCTTTAAAATAAAAACAGAAAGA 57.241 29.630 0.00 0.00 32.25 2.52
952 2704 3.861263 GGTCAATTCCGCGTCGCC 61.861 66.667 12.44 0.00 0.00 5.54
953 2705 3.861263 GTCAATTCCGCGTCGCCC 61.861 66.667 12.44 0.00 0.00 6.13
979 2731 2.041301 TCCCACCTACCCATCCCG 60.041 66.667 0.00 0.00 0.00 5.14
1014 2766 0.804989 GGGCCATGAAGAAGTCGTTG 59.195 55.000 4.39 0.00 0.00 4.10
1088 2840 2.508891 GCGTCTTCTGCGACATCGG 61.509 63.158 3.08 0.00 40.23 4.18
1171 2923 1.066303 CTTCTCCGATCTGAACTCCGG 59.934 57.143 0.00 0.00 43.02 5.14
1211 2963 1.222115 AAACGTGCGACCTTCTGCTC 61.222 55.000 0.00 0.00 0.00 4.26
1236 2988 1.354337 CGCAGGATGACAAGGTCGTG 61.354 60.000 0.00 0.00 39.69 4.35
1289 3041 0.672401 TACTTGCTGGCCGTTGTAGC 60.672 55.000 5.08 5.08 37.93 3.58
1327 3079 0.456312 GTCGCTGTCGTTGGTCTAGG 60.456 60.000 0.00 0.00 36.96 3.02
1338 3090 3.681593 GTTGGTCTAGGTGTGGCATTAA 58.318 45.455 0.00 0.00 0.00 1.40
1397 3149 0.245266 TCGAACAACTGGCGAGCATA 59.755 50.000 0.00 0.00 0.00 3.14
1402 3154 1.290203 CAACTGGCGAGCATAACGAT 58.710 50.000 0.00 0.00 0.00 3.73
1568 3321 5.398711 GTGTTAAGAGACTGTCGTGTAGTTG 59.601 44.000 1.52 0.00 0.00 3.16
1604 3357 4.216042 TCACACAGTTGCTGTTTATCATGG 59.784 41.667 0.00 0.00 42.59 3.66
1631 3384 2.293399 AGTCGGTGTTTCCTTTCAATGC 59.707 45.455 0.00 0.00 0.00 3.56
1644 3397 4.937620 CCTTTCAATGCTTGCTACTCACTA 59.062 41.667 0.00 0.00 0.00 2.74
1652 3405 2.516227 TGCTACTCACTACCAGAGCT 57.484 50.000 0.00 0.00 36.58 4.09
1700 3453 2.036475 CTGAGAACCTAGTGTGTGCTGT 59.964 50.000 0.00 0.00 0.00 4.40
1701 3454 3.227614 TGAGAACCTAGTGTGTGCTGTA 58.772 45.455 0.00 0.00 0.00 2.74
1702 3455 3.832490 TGAGAACCTAGTGTGTGCTGTAT 59.168 43.478 0.00 0.00 0.00 2.29
1719 3481 5.513849 TGCTGTATTCACACGTAATAGTTCG 59.486 40.000 0.00 0.00 0.00 3.95
1744 3506 7.362056 CGTTGAGACCAATATTTTTCTGGACAT 60.362 37.037 0.00 0.00 34.39 3.06
1803 3565 2.924290 CACTTCTTGAGTAGCGTTAGCC 59.076 50.000 0.00 0.00 39.67 3.93
1812 3574 2.806244 AGTAGCGTTAGCCTTGTGTTTG 59.194 45.455 0.00 0.00 46.67 2.93
1823 3585 6.715347 AGCCTTGTGTTTGTTTTAATCTCT 57.285 33.333 0.00 0.00 0.00 3.10
1827 3589 6.074888 CCTTGTGTTTGTTTTAATCTCTTGCG 60.075 38.462 0.00 0.00 0.00 4.85
1859 3621 9.794685 GTGACATAGATGACATATGGTATACAG 57.205 37.037 7.80 0.00 35.19 2.74
2178 4035 2.785540 TGATCAGCTTGTGCATACCA 57.214 45.000 0.00 0.00 42.74 3.25
2180 4037 3.208594 TGATCAGCTTGTGCATACCATC 58.791 45.455 0.00 0.00 42.74 3.51
2252 4110 2.365617 AGGCACTATCTTGTCATACCCG 59.634 50.000 0.00 0.00 36.02 5.28
2254 4112 3.431766 GGCACTATCTTGTCATACCCGTT 60.432 47.826 0.00 0.00 0.00 4.44
2354 4212 4.220693 TCATGTAACACTGGCTTGCTAT 57.779 40.909 0.00 0.00 0.00 2.97
2404 4262 8.682710 GGATGCTTGGTGAACTATAACATTTTA 58.317 33.333 0.00 0.00 0.00 1.52
2495 4353 7.769044 TCTGAGGAACATAGGTATTGCTAAAAC 59.231 37.037 0.00 0.00 0.00 2.43
2651 4509 0.395311 CCATCTTCACTGCCTGGCAT 60.395 55.000 23.64 9.78 38.13 4.40
2967 4826 6.656314 TTGTACGATCATTTGTATGTGGTC 57.344 37.500 0.00 0.00 33.34 4.02
2997 4856 6.071334 TCCCTATTACTATTCTTGGATCGCTG 60.071 42.308 0.00 0.00 0.00 5.18
3014 4873 5.511088 TCGCTGTAAATTCGAAAGACTTC 57.489 39.130 0.00 0.00 41.84 3.01
3036 4895 7.223582 ACTTCGTCAGAAATGCTATACTTCATG 59.776 37.037 0.00 0.00 35.71 3.07
3050 4909 7.170658 GCTATACTTCATGTCTTCATCCTGAAC 59.829 40.741 0.00 0.00 32.21 3.18
3288 5147 6.418057 AGGAGGATCAGTATCAAATCAGAC 57.582 41.667 0.00 0.00 36.25 3.51
3291 5152 4.039730 AGGATCAGTATCAAATCAGACGGG 59.960 45.833 0.00 0.00 33.41 5.28
3458 5337 7.410800 TCAATTGATTGCAGTCAAATTTGAC 57.589 32.000 34.21 34.21 45.36 3.18
3588 5506 7.476540 TGTATGTACACCATATATGAGGTCC 57.523 40.000 14.54 3.75 38.29 4.46
3613 5533 1.988107 AGGAACCTCTGGAGCATTTGA 59.012 47.619 0.00 0.00 0.00 2.69
4073 6042 0.247460 TGTCGAGATGCTTCCTGTGG 59.753 55.000 0.00 0.00 0.00 4.17
4093 6062 3.071023 TGGAACACGGTTTCTCTGATCTT 59.929 43.478 0.00 0.00 0.00 2.40
4107 6076 1.047801 GATCTTCCTGAGAGCCCTCC 58.952 60.000 0.00 0.00 37.93 4.30
4129 6098 1.346068 CTTCTCTTCCGATCCCCCATC 59.654 57.143 0.00 0.00 0.00 3.51
4152 6121 4.756084 AACTGCTCATACTGAAAGCAAC 57.244 40.909 0.00 0.00 44.79 4.17
4157 6126 4.214119 TGCTCATACTGAAAGCAACAAGAC 59.786 41.667 0.00 0.00 42.71 3.01
4158 6127 4.667668 GCTCATACTGAAAGCAACAAGACG 60.668 45.833 0.00 0.00 37.60 4.18
4160 6129 1.378531 ACTGAAAGCAACAAGACGCA 58.621 45.000 0.00 0.00 37.60 5.24
4161 6130 1.949525 ACTGAAAGCAACAAGACGCAT 59.050 42.857 0.00 0.00 37.60 4.73
4162 6131 2.358898 ACTGAAAGCAACAAGACGCATT 59.641 40.909 0.00 0.00 37.60 3.56
4168 6147 6.148645 TGAAAGCAACAAGACGCATTATTAGA 59.851 34.615 0.00 0.00 0.00 2.10
4205 6184 6.680758 GCAAAACAAAACACGTGAAAATTAGG 59.319 34.615 25.01 9.59 0.00 2.69
4233 6217 7.870445 ACAGAGAAGATGAACTAGACAAGAAAC 59.130 37.037 0.00 0.00 0.00 2.78
4242 6252 4.962155 ACTAGACAAGAAACAACTGGGAG 58.038 43.478 0.00 0.00 0.00 4.30
4255 6265 5.757988 ACAACTGGGAGTTTTGTTACCTTA 58.242 37.500 0.00 0.00 36.03 2.69
4322 6332 2.123982 GGCTGGGCATAAGCAGCT 60.124 61.111 11.54 0.00 44.61 4.24
4330 6343 1.636988 GCATAAGCAGCTGCCTTTTG 58.363 50.000 34.39 27.51 43.38 2.44
4417 6433 2.874701 GTCACCATACTCCATGACATGC 59.125 50.000 10.10 0.00 40.95 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.790344 AGAGATCTGGTGAAATAATAATTCCAG 57.210 33.333 0.00 0.00 36.56 3.86
34 35 2.350804 CACAACGCATTCCAGAGATCTG 59.649 50.000 0.00 2.72 43.40 2.90
43 44 2.744202 AGAGTGATTCACAACGCATTCC 59.256 45.455 18.57 0.00 36.74 3.01
49 50 5.119279 CAGAGGTTTAGAGTGATTCACAACG 59.881 44.000 18.57 0.00 36.74 4.10
68 69 6.356556 TCATGTTGTGGGTTATAATCAGAGG 58.643 40.000 0.00 0.00 0.00 3.69
73 74 7.122055 TGTTCCTTCATGTTGTGGGTTATAATC 59.878 37.037 0.00 0.00 0.00 1.75
173 174 4.367039 TGAGAAGAACCCCTTTAACCAG 57.633 45.455 0.00 0.00 34.68 4.00
177 178 5.944007 GCTACAATGAGAAGAACCCCTTTAA 59.056 40.000 0.00 0.00 34.68 1.52
178 179 5.013704 TGCTACAATGAGAAGAACCCCTTTA 59.986 40.000 0.00 0.00 34.68 1.85
194 195 8.752005 ATACAACCATAAGAACATGCTACAAT 57.248 30.769 0.00 0.00 0.00 2.71
197 198 9.273016 ACATATACAACCATAAGAACATGCTAC 57.727 33.333 0.00 0.00 0.00 3.58
199 200 9.494271 CTACATATACAACCATAAGAACATGCT 57.506 33.333 0.00 0.00 0.00 3.79
200 201 9.273016 ACTACATATACAACCATAAGAACATGC 57.727 33.333 0.00 0.00 0.00 4.06
219 236 8.693120 AAGAGGATTACGATCTGAACTACATA 57.307 34.615 0.00 0.00 32.66 2.29
233 250 4.448060 GCCCGAAATAGAAAGAGGATTACG 59.552 45.833 0.00 0.00 0.00 3.18
245 263 1.211703 TCAATGGCAGCCCGAAATAGA 59.788 47.619 9.64 0.00 0.00 1.98
250 268 1.976474 GGTTCAATGGCAGCCCGAA 60.976 57.895 9.64 6.46 0.00 4.30
254 272 2.034124 ACATATGGTTCAATGGCAGCC 58.966 47.619 3.66 3.66 0.00 4.85
258 276 4.082300 TGTGTTCACATATGGTTCAATGGC 60.082 41.667 7.80 0.00 0.00 4.40
259 277 5.641783 TGTGTTCACATATGGTTCAATGG 57.358 39.130 7.80 0.00 0.00 3.16
261 279 7.725251 AGTTTTGTGTTCACATATGGTTCAAT 58.275 30.769 7.80 0.00 0.00 2.57
262 280 7.106439 AGTTTTGTGTTCACATATGGTTCAA 57.894 32.000 7.80 1.57 0.00 2.69
276 294 3.801594 CCAAGCGCAATAAGTTTTGTGTT 59.198 39.130 11.47 4.89 38.92 3.32
358 376 3.009916 AGTCAGCTTTGTTCCTGGATGAT 59.990 43.478 0.00 0.00 0.00 2.45
364 382 3.615849 GAACAGTCAGCTTTGTTCCTG 57.384 47.619 18.25 6.80 44.56 3.86
370 388 2.684881 ACCTGTTGAACAGTCAGCTTTG 59.315 45.455 22.40 8.24 44.50 2.77
374 392 3.664107 TCATACCTGTTGAACAGTCAGC 58.336 45.455 22.40 0.00 44.50 4.26
415 433 6.327934 CCTTAAATTTCTCTCCGACGAGTTA 58.672 40.000 0.00 0.00 37.40 2.24
417 435 4.745649 CCTTAAATTTCTCTCCGACGAGT 58.254 43.478 0.00 0.00 37.40 4.18
439 458 5.627367 TGTGCAACATTACTTACAAAATCGC 59.373 36.000 0.00 0.00 45.67 4.58
456 475 5.731599 TTTGTCCAATCAATTTGTGCAAC 57.268 34.783 0.00 0.00 33.15 4.17
466 485 2.762887 TGTGCCAGTTTTGTCCAATCAA 59.237 40.909 0.00 0.00 0.00 2.57
467 486 2.382882 TGTGCCAGTTTTGTCCAATCA 58.617 42.857 0.00 0.00 0.00 2.57
468 487 3.123050 GTTGTGCCAGTTTTGTCCAATC 58.877 45.455 0.00 0.00 0.00 2.67
469 488 2.765699 AGTTGTGCCAGTTTTGTCCAAT 59.234 40.909 0.00 0.00 0.00 3.16
470 489 2.165437 GAGTTGTGCCAGTTTTGTCCAA 59.835 45.455 0.00 0.00 0.00 3.53
471 490 1.748493 GAGTTGTGCCAGTTTTGTCCA 59.252 47.619 0.00 0.00 0.00 4.02
472 491 1.067060 GGAGTTGTGCCAGTTTTGTCC 59.933 52.381 0.00 0.00 0.00 4.02
473 492 2.024414 AGGAGTTGTGCCAGTTTTGTC 58.976 47.619 0.00 0.00 0.00 3.18
474 493 2.143876 AGGAGTTGTGCCAGTTTTGT 57.856 45.000 0.00 0.00 0.00 2.83
475 494 3.189285 CAAAGGAGTTGTGCCAGTTTTG 58.811 45.455 0.00 0.00 32.08 2.44
476 495 2.168313 CCAAAGGAGTTGTGCCAGTTTT 59.832 45.455 0.00 0.00 35.23 2.43
477 496 1.756538 CCAAAGGAGTTGTGCCAGTTT 59.243 47.619 0.00 0.00 35.23 2.66
478 497 1.064017 TCCAAAGGAGTTGTGCCAGTT 60.064 47.619 0.00 0.00 35.23 3.16
479 498 0.550914 TCCAAAGGAGTTGTGCCAGT 59.449 50.000 0.00 0.00 35.23 4.00
498 517 2.887152 GTTCATTCTCAAAGTGGCCAGT 59.113 45.455 5.11 6.41 0.00 4.00
518 537 3.552273 CGGGCAGCTATTAATCGTAGTGT 60.552 47.826 0.00 0.00 0.00 3.55
522 541 2.624364 TCACGGGCAGCTATTAATCGTA 59.376 45.455 0.00 0.00 0.00 3.43
524 543 2.148916 TCACGGGCAGCTATTAATCG 57.851 50.000 0.00 0.00 0.00 3.34
539 566 3.782893 GGTTACTACGACGATTCTTCACG 59.217 47.826 0.00 0.00 0.00 4.35
540 567 4.979388 AGGTTACTACGACGATTCTTCAC 58.021 43.478 0.00 0.00 0.00 3.18
541 568 4.201753 CGAGGTTACTACGACGATTCTTCA 60.202 45.833 0.00 0.00 0.00 3.02
542 569 4.270102 CGAGGTTACTACGACGATTCTTC 58.730 47.826 0.00 0.00 0.00 2.87
550 577 1.089920 TGGAGCGAGGTTACTACGAC 58.910 55.000 0.00 0.00 0.00 4.34
551 578 1.089920 GTGGAGCGAGGTTACTACGA 58.910 55.000 0.00 0.00 0.00 3.43
585 613 4.100963 GGGTTTCCTTCACATTTTTCCAGT 59.899 41.667 0.00 0.00 0.00 4.00
597 625 2.286365 GGACACATGGGTTTCCTTCA 57.714 50.000 0.00 0.00 40.14 3.02
609 637 2.304056 CCAGAGCCCCAGGACACAT 61.304 63.158 0.00 0.00 0.00 3.21
611 639 2.930562 ACCAGAGCCCCAGGACAC 60.931 66.667 0.00 0.00 0.00 3.67
614 642 4.270153 ACCACCAGAGCCCCAGGA 62.270 66.667 0.00 0.00 0.00 3.86
617 645 1.434513 AATTCACCACCAGAGCCCCA 61.435 55.000 0.00 0.00 0.00 4.96
644 672 9.056005 TCTCAATTAATCATACACCAGCATTAC 57.944 33.333 0.00 0.00 0.00 1.89
674 710 9.541143 CTTTCTGTTTTTATTTTAAAGAGCCCA 57.459 29.630 0.00 0.00 0.00 5.36
713 749 6.219473 TCAGCTTTCTTTTTGTTTTGTGTCA 58.781 32.000 0.00 0.00 0.00 3.58
722 758 7.010460 GCACTGTAATTTCAGCTTTCTTTTTGT 59.990 33.333 11.61 0.00 38.84 2.83
723 759 7.010367 TGCACTGTAATTTCAGCTTTCTTTTTG 59.990 33.333 11.61 1.55 38.84 2.44
724 760 7.041107 TGCACTGTAATTTCAGCTTTCTTTTT 58.959 30.769 11.61 0.00 38.84 1.94
751 790 3.252974 CTGGAAGCCCAACTACTAGTG 57.747 52.381 5.39 0.00 42.98 2.74
821 860 3.160585 CAACTGGTGGCTCTGGGA 58.839 61.111 0.00 0.00 0.00 4.37
952 2704 3.943137 TAGGTGGGAGGCAGTGGGG 62.943 68.421 0.00 0.00 0.00 4.96
953 2705 2.285368 TAGGTGGGAGGCAGTGGG 60.285 66.667 0.00 0.00 0.00 4.61
954 2706 2.670148 GGTAGGTGGGAGGCAGTGG 61.670 68.421 0.00 0.00 0.00 4.00
955 2707 2.670148 GGGTAGGTGGGAGGCAGTG 61.670 68.421 0.00 0.00 0.00 3.66
956 2708 2.285442 GGGTAGGTGGGAGGCAGT 60.285 66.667 0.00 0.00 0.00 4.40
957 2709 1.694169 ATGGGTAGGTGGGAGGCAG 60.694 63.158 0.00 0.00 0.00 4.85
958 2710 1.692749 GATGGGTAGGTGGGAGGCA 60.693 63.158 0.00 0.00 0.00 4.75
959 2711 2.452937 GGATGGGTAGGTGGGAGGC 61.453 68.421 0.00 0.00 0.00 4.70
1171 2923 0.730494 GCAAGCAAATCGACAGGTGC 60.730 55.000 0.00 0.00 37.26 5.01
1211 2963 0.167470 CTTGTCATCCTGCGCACAAG 59.833 55.000 18.07 18.07 39.74 3.16
1236 2988 1.017387 GATTGATGTCCTGGAACGCC 58.983 55.000 0.00 0.00 0.00 5.68
1289 3041 1.961277 ACGGCGCTGAAAGAACAGG 60.961 57.895 25.98 0.00 38.22 4.00
1338 3090 2.324332 CTACGTCGACGAGGCATGCT 62.324 60.000 41.52 20.54 43.02 3.79
1343 3095 0.026027 CACTACTACGTCGACGAGGC 59.974 60.000 41.52 1.77 43.02 4.70
1348 3100 2.159234 ACAAGAGCACTACTACGTCGAC 59.841 50.000 5.18 5.18 0.00 4.20
1386 3138 3.120546 CCAATTATCGTTATGCTCGCCAG 60.121 47.826 0.00 0.00 0.00 4.85
1482 3234 2.750948 AGCAAACAAATCAAGCAGCTG 58.249 42.857 10.11 10.11 0.00 4.24
1533 3286 8.764524 ACAGTCTCTTAACACAATCAGAATAC 57.235 34.615 0.00 0.00 0.00 1.89
1568 3321 3.740115 ACTGTGTGACCTGATAAACACC 58.260 45.455 2.64 0.00 41.75 4.16
1604 3357 0.319297 AGGAAACACCGACTACGTGC 60.319 55.000 0.00 0.00 44.74 5.34
1631 3384 2.757868 AGCTCTGGTAGTGAGTAGCAAG 59.242 50.000 0.54 3.32 38.67 4.01
1700 3453 7.482743 GTCTCAACGAACTATTACGTGTGAATA 59.517 37.037 0.00 0.00 42.43 1.75
1701 3454 6.307318 GTCTCAACGAACTATTACGTGTGAAT 59.693 38.462 0.00 0.00 42.43 2.57
1702 3455 5.626543 GTCTCAACGAACTATTACGTGTGAA 59.373 40.000 0.00 0.00 42.43 3.18
1708 3470 7.925703 ATATTGGTCTCAACGAACTATTACG 57.074 36.000 0.00 0.00 35.48 3.18
1714 3476 7.308589 CCAGAAAAATATTGGTCTCAACGAACT 60.309 37.037 0.00 0.00 35.48 3.01
1719 3481 7.214467 TGTCCAGAAAAATATTGGTCTCAAC 57.786 36.000 0.00 0.00 35.48 3.18
1735 3497 4.382685 GGTGTTTCGGATAGATGTCCAGAA 60.383 45.833 0.00 0.00 38.21 3.02
1744 3506 0.899720 AAGGCGGTGTTTCGGATAGA 59.100 50.000 0.00 0.00 0.00 1.98
1803 3565 6.690957 TCGCAAGAGATTAAAACAAACACAAG 59.309 34.615 0.00 0.00 45.01 3.16
1823 3585 3.951680 TCATCTATGTCACTACCTCGCAA 59.048 43.478 0.00 0.00 0.00 4.85
1827 3589 7.177568 ACCATATGTCATCTATGTCACTACCTC 59.822 40.741 1.24 0.00 0.00 3.85
2225 4083 3.689347 TGACAAGATAGTGCCTGCAAAT 58.311 40.909 0.00 0.00 0.00 2.32
2354 4212 6.927936 CCATGGTTGAACAAAATGACATGTAA 59.072 34.615 2.57 0.00 34.28 2.41
2404 4262 3.838244 TGTGACTAACTGCAAAGGAGT 57.162 42.857 0.00 0.00 0.00 3.85
2495 4353 9.643693 ATGCCAGAACAAATGTATTTCTTTTAG 57.356 29.630 0.00 0.00 0.00 1.85
2651 4509 4.475381 TCAGTACCTGGGTATAAATGGCAA 59.525 41.667 2.63 0.00 32.82 4.52
2761 4619 8.206867 CCTCCAACTGTCAAGATGAAGAATATA 58.793 37.037 0.00 0.00 0.00 0.86
2765 4623 4.645535 CCTCCAACTGTCAAGATGAAGAA 58.354 43.478 0.00 0.00 0.00 2.52
2776 4634 6.759497 ATATTTTACTTGCCTCCAACTGTC 57.241 37.500 0.00 0.00 0.00 3.51
2949 4808 6.146184 GGATACAGACCACATACAAATGATCG 59.854 42.308 0.00 0.00 36.54 3.69
2950 4809 6.428159 GGGATACAGACCACATACAAATGATC 59.572 42.308 0.00 0.00 35.90 2.92
3014 4873 6.699204 AGACATGAAGTATAGCATTTCTGACG 59.301 38.462 0.00 0.00 32.14 4.35
3018 4877 9.270640 GATGAAGACATGAAGTATAGCATTTCT 57.729 33.333 0.00 0.00 36.82 2.52
3050 4909 3.689347 TGGAGTTGAACTTCCATGGATG 58.311 45.455 22.73 22.73 0.00 3.51
3288 5147 4.519182 GGCCAAAATTGATGCCCG 57.481 55.556 0.00 0.00 37.94 6.13
3291 5152 3.608316 TTAGTGGGCCAAAATTGATGC 57.392 42.857 8.40 0.00 0.00 3.91
3458 5337 0.163788 CGTGCTCGTGCCTTTGTAAG 59.836 55.000 7.05 0.00 38.71 2.34
3564 5482 7.013834 TGGACCTCATATATGGTGTACATACA 58.986 38.462 12.78 1.85 44.41 2.29
3565 5483 7.476540 TGGACCTCATATATGGTGTACATAC 57.523 40.000 12.78 0.00 44.41 2.39
3566 5484 6.154534 GCTGGACCTCATATATGGTGTACATA 59.845 42.308 16.17 0.00 45.60 2.29
3567 5485 5.046304 GCTGGACCTCATATATGGTGTACAT 60.046 44.000 16.17 0.00 43.68 2.29
3568 5486 4.283467 GCTGGACCTCATATATGGTGTACA 59.717 45.833 12.78 14.37 36.59 2.90
3569 5487 4.528596 AGCTGGACCTCATATATGGTGTAC 59.471 45.833 12.78 10.91 36.59 2.90
3570 5488 4.752063 AGCTGGACCTCATATATGGTGTA 58.248 43.478 12.78 0.00 36.59 2.90
3571 5489 3.591789 AGCTGGACCTCATATATGGTGT 58.408 45.455 12.78 9.83 36.59 4.16
3588 5506 0.463620 GCTCCAGAGGTTCCTAGCTG 59.536 60.000 0.00 3.26 30.79 4.24
3613 5533 2.103771 CTGCAGTACATGGGAGCAGTAT 59.896 50.000 17.92 0.00 45.57 2.12
3844 5802 5.921408 GGTTGAACTTACTCTGTAGTCTGTG 59.079 44.000 0.00 0.00 37.15 3.66
4073 6042 3.680458 GGAAGATCAGAGAAACCGTGTTC 59.320 47.826 0.00 0.00 0.00 3.18
4086 6055 1.688197 GAGGGCTCTCAGGAAGATCAG 59.312 57.143 9.30 0.00 39.74 2.90
4152 6121 9.559958 AAATTTGTCTTCTAATAATGCGTCTTG 57.440 29.630 0.00 0.00 0.00 3.02
4157 6126 6.751425 TGCCAAATTTGTCTTCTAATAATGCG 59.249 34.615 16.73 0.00 0.00 4.73
4158 6127 8.477984 TTGCCAAATTTGTCTTCTAATAATGC 57.522 30.769 16.73 8.49 0.00 3.56
4161 6130 9.823647 TGTTTTGCCAAATTTGTCTTCTAATAA 57.176 25.926 16.73 0.00 0.00 1.40
4162 6131 9.823647 TTGTTTTGCCAAATTTGTCTTCTAATA 57.176 25.926 16.73 0.29 0.00 0.98
4168 6147 6.860539 GTGTTTTGTTTTGCCAAATTTGTCTT 59.139 30.769 16.73 0.00 34.50 3.01
4205 6184 7.598278 TCTTGTCTAGTTCATCTTCTCTGTTC 58.402 38.462 0.00 0.00 0.00 3.18
4233 6217 6.894339 ATAAGGTAACAAAACTCCCAGTTG 57.106 37.500 0.00 0.00 37.56 3.16
4242 6252 9.535878 TTTTCATGTGGAATAAGGTAACAAAAC 57.464 29.630 0.00 0.00 35.03 2.43
4255 6265 5.277974 CGCCGATATTCTTTTCATGTGGAAT 60.278 40.000 0.00 2.16 34.91 3.01
4322 6332 1.340889 GTCAAGCATCACCAAAAGGCA 59.659 47.619 0.00 0.00 0.00 4.75
4327 6340 2.429971 TGCAAAGTCAAGCATCACCAAA 59.570 40.909 0.00 0.00 35.51 3.28
4330 6343 1.068055 CCTGCAAAGTCAAGCATCACC 60.068 52.381 0.00 0.00 40.42 4.02
4417 6433 4.976731 CGAAATGAGTCCAGTATAGGTTCG 59.023 45.833 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.