Multiple sequence alignment - TraesCS5A01G105500

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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 TraesCS5A01G105500 chr5A 100.000 2533 0 0 1 2533 169818555 169816023 0.000000e+00 4678.0
1 TraesCS5A01G105500 chr5A 91.228 57 4 1 58 113 645133586 645133642 2.700000e-10 76.8
2 TraesCS5A01G105500 chr5D 92.789 2316 103 28 269 2533 135238788 135241090 0.000000e+00 3293.0
3 TraesCS5A01G105500 chr5D 93.182 88 6 0 103 190 135238668 135238755 2.050000e-26 130.0
4 TraesCS5A01G105500 chr5D 91.228 57 5 0 1 57 135238329 135238385 7.510000e-11 78.7
5 TraesCS5A01G105500 chr5D 89.286 56 5 1 49 104 221389938 221389992 4.520000e-08 69.4
6 TraesCS5A01G105500 chr5B 91.817 2322 98 45 267 2533 146913954 146916238 0.000000e+00 3151.0
7 TraesCS5A01G105500 chr1B 91.071 56 4 1 57 111 4339065 4339120 9.720000e-10 75.0
8 TraesCS5A01G105500 chr1B 95.745 47 1 1 60 105 594170370 594170416 9.720000e-10 75.0
9 TraesCS5A01G105500 chr4D 91.071 56 1 3 61 115 79147186 79147238 3.500000e-09 73.1
10 TraesCS5A01G105500 chr2A 92.157 51 2 2 62 110 764010683 764010733 1.260000e-08 71.3
11 TraesCS5A01G105500 chr1D 92.157 51 3 1 62 111 9875425 9875475 1.260000e-08 71.3
12 TraesCS5A01G105500 chr1D 90.385 52 4 1 63 113 104250976 104250925 1.630000e-07 67.6
13 TraesCS5A01G105500 chr3D 90.385 52 4 1 63 113 76672328 76672277 1.630000e-07 67.6


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 TraesCS5A01G105500 chr5A 169816023 169818555 2532 True 4678.000000 4678 100.000000 1 2533 1 chr5A.!!$R1 2532
1 TraesCS5A01G105500 chr5D 135238329 135241090 2761 False 1167.233333 3293 92.399667 1 2533 3 chr5D.!!$F2 2532
2 TraesCS5A01G105500 chr5B 146913954 146916238 2284 False 3151.000000 3151 91.817000 267 2533 1 chr5B.!!$F1 2266

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
437 680 0.170561 GTCTGACCGACGTGCATAGT 59.829 55.0 0.00 0.0 32.04 2.12 F
831 1091 0.741221 GAGGGTGTCGCCATCTCAAC 60.741 60.0 9.84 0.0 44.20 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 1537 0.171679 TCGATAAAAGGAGCGCGTGA 59.828 50.0 8.43 0.0 0.00 4.35 R
2421 2719 1.243902 TTCCGACCATCAAAAGTGGC 58.756 50.0 0.00 0.0 40.49 5.01 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
28 29 2.039084 AGTTGTTTCTCTCGGGAAGCAT 59.961 45.455 0.00 0.00 36.59 3.79
69 93 3.201045 AGAGCAAGGATTTTCTACTCCCC 59.799 47.826 0.00 0.00 31.49 4.81
89 113 5.710409 CCCCCGTCCCATAATATAAGAAT 57.290 43.478 0.00 0.00 0.00 2.40
90 114 5.437060 CCCCCGTCCCATAATATAAGAATG 58.563 45.833 0.00 0.00 0.00 2.67
91 115 5.045140 CCCCCGTCCCATAATATAAGAATGT 60.045 44.000 0.00 0.00 0.00 2.71
92 116 6.481643 CCCCGTCCCATAATATAAGAATGTT 58.518 40.000 0.00 0.00 0.00 2.71
93 117 6.946009 CCCCGTCCCATAATATAAGAATGTTT 59.054 38.462 0.00 0.00 0.00 2.83
94 118 7.450323 CCCCGTCCCATAATATAAGAATGTTTT 59.550 37.037 0.00 0.00 0.00 2.43
96 120 9.677567 CCGTCCCATAATATAAGAATGTTTTTG 57.322 33.333 0.00 0.00 0.00 2.44
143 381 8.462143 TCTCAAAGAATCAAACGATACTACAC 57.538 34.615 0.00 0.00 0.00 2.90
146 384 9.917129 TCAAAGAATCAAACGATACTACACTTA 57.083 29.630 0.00 0.00 0.00 2.24
162 400 5.366829 ACACTTAAAGGGTGTAAATTCGC 57.633 39.130 0.00 0.00 44.72 4.70
183 421 2.397044 AGGTTTCAATTTGGGCAGGA 57.603 45.000 0.00 0.00 0.00 3.86
190 428 2.043664 TCAATTTGGGCAGGAATGGGTA 59.956 45.455 0.00 0.00 0.00 3.69
191 429 2.836981 CAATTTGGGCAGGAATGGGTAA 59.163 45.455 0.00 0.00 0.00 2.85
194 432 0.918983 TGGGCAGGAATGGGTAAGAG 59.081 55.000 0.00 0.00 0.00 2.85
196 434 1.564348 GGGCAGGAATGGGTAAGAGAA 59.436 52.381 0.00 0.00 0.00 2.87
197 435 2.175715 GGGCAGGAATGGGTAAGAGAAT 59.824 50.000 0.00 0.00 0.00 2.40
198 436 3.373110 GGGCAGGAATGGGTAAGAGAATT 60.373 47.826 0.00 0.00 0.00 2.17
199 437 4.281657 GGCAGGAATGGGTAAGAGAATTT 58.718 43.478 0.00 0.00 0.00 1.82
200 438 4.339530 GGCAGGAATGGGTAAGAGAATTTC 59.660 45.833 0.00 0.00 0.00 2.17
201 439 5.196695 GCAGGAATGGGTAAGAGAATTTCT 58.803 41.667 0.00 0.00 37.93 2.52
202 440 5.067023 GCAGGAATGGGTAAGAGAATTTCTG 59.933 44.000 3.03 0.00 38.26 3.02
203 441 6.183347 CAGGAATGGGTAAGAGAATTTCTGT 58.817 40.000 3.03 0.00 35.91 3.41
204 442 6.660949 CAGGAATGGGTAAGAGAATTTCTGTT 59.339 38.462 12.78 12.78 35.91 3.16
205 443 6.660949 AGGAATGGGTAAGAGAATTTCTGTTG 59.339 38.462 16.70 0.00 35.91 3.33
206 444 6.659242 GGAATGGGTAAGAGAATTTCTGTTGA 59.341 38.462 16.70 1.62 35.91 3.18
207 445 7.340487 GGAATGGGTAAGAGAATTTCTGTTGAT 59.660 37.037 16.70 3.63 35.91 2.57
208 446 7.636150 ATGGGTAAGAGAATTTCTGTTGATG 57.364 36.000 16.70 0.00 35.91 3.07
209 447 6.542821 TGGGTAAGAGAATTTCTGTTGATGT 58.457 36.000 16.70 0.00 35.91 3.06
210 448 7.004086 TGGGTAAGAGAATTTCTGTTGATGTT 58.996 34.615 16.70 0.00 35.91 2.71
211 449 7.174946 TGGGTAAGAGAATTTCTGTTGATGTTC 59.825 37.037 16.70 4.06 35.91 3.18
212 450 7.174946 GGGTAAGAGAATTTCTGTTGATGTTCA 59.825 37.037 16.70 0.00 35.91 3.18
213 451 8.567948 GGTAAGAGAATTTCTGTTGATGTTCAA 58.432 33.333 16.70 0.00 35.91 2.69
216 454 7.524912 AGAGAATTTCTGTTGATGTTCAATCG 58.475 34.615 3.03 0.00 38.79 3.34
217 455 6.088824 AGAATTTCTGTTGATGTTCAATCGC 58.911 36.000 0.00 0.00 38.79 4.58
218 456 5.633830 ATTTCTGTTGATGTTCAATCGCT 57.366 34.783 0.00 0.00 38.79 4.93
219 457 4.668576 TTCTGTTGATGTTCAATCGCTC 57.331 40.909 0.00 0.00 38.79 5.03
220 458 3.930336 TCTGTTGATGTTCAATCGCTCT 58.070 40.909 0.00 0.00 38.79 4.09
221 459 3.681417 TCTGTTGATGTTCAATCGCTCTG 59.319 43.478 0.00 0.00 38.79 3.35
222 460 3.402110 TGTTGATGTTCAATCGCTCTGT 58.598 40.909 0.00 0.00 38.79 3.41
223 461 3.814842 TGTTGATGTTCAATCGCTCTGTT 59.185 39.130 0.00 0.00 38.79 3.16
224 462 4.994217 TGTTGATGTTCAATCGCTCTGTTA 59.006 37.500 0.00 0.00 38.79 2.41
225 463 5.107104 TGTTGATGTTCAATCGCTCTGTTAC 60.107 40.000 0.00 0.00 38.79 2.50
226 464 4.565022 TGATGTTCAATCGCTCTGTTACA 58.435 39.130 0.00 0.00 0.00 2.41
227 465 4.388773 TGATGTTCAATCGCTCTGTTACAC 59.611 41.667 0.00 0.00 0.00 2.90
228 466 3.990092 TGTTCAATCGCTCTGTTACACT 58.010 40.909 0.00 0.00 0.00 3.55
229 467 3.740832 TGTTCAATCGCTCTGTTACACTG 59.259 43.478 0.00 0.00 0.00 3.66
230 468 3.934457 TCAATCGCTCTGTTACACTGA 57.066 42.857 0.00 0.00 0.00 3.41
231 469 4.251543 TCAATCGCTCTGTTACACTGAA 57.748 40.909 0.00 0.00 0.00 3.02
232 470 4.627058 TCAATCGCTCTGTTACACTGAAA 58.373 39.130 0.00 0.00 0.00 2.69
245 483 6.939730 TGTTACACTGAAATGAAAGGCTGATA 59.060 34.615 0.00 0.00 0.00 2.15
251 489 6.597280 ACTGAAATGAAAGGCTGATAGAGTTC 59.403 38.462 0.00 0.00 0.00 3.01
252 490 6.475504 TGAAATGAAAGGCTGATAGAGTTCA 58.524 36.000 0.00 0.00 0.00 3.18
256 494 4.287067 TGAAAGGCTGATAGAGTTCAGGTT 59.713 41.667 3.85 0.00 42.78 3.50
257 495 5.483937 TGAAAGGCTGATAGAGTTCAGGTTA 59.516 40.000 3.85 0.00 42.78 2.85
258 496 5.346181 AAGGCTGATAGAGTTCAGGTTAC 57.654 43.478 3.85 0.00 42.78 2.50
259 497 4.615513 AGGCTGATAGAGTTCAGGTTACT 58.384 43.478 3.85 0.00 42.78 2.24
260 498 5.026790 AGGCTGATAGAGTTCAGGTTACTT 58.973 41.667 3.85 0.00 42.78 2.24
261 499 5.485708 AGGCTGATAGAGTTCAGGTTACTTT 59.514 40.000 3.85 0.00 42.78 2.66
262 500 5.582665 GGCTGATAGAGTTCAGGTTACTTTG 59.417 44.000 3.85 0.00 42.78 2.77
263 501 5.064071 GCTGATAGAGTTCAGGTTACTTTGC 59.936 44.000 3.85 0.00 42.78 3.68
264 502 6.109156 TGATAGAGTTCAGGTTACTTTGCA 57.891 37.500 0.00 0.00 0.00 4.08
265 503 6.530120 TGATAGAGTTCAGGTTACTTTGCAA 58.470 36.000 0.00 0.00 0.00 4.08
286 524 6.013206 TGCAAGGTACAGATAGGAAAACCTAA 60.013 38.462 0.00 0.00 36.34 2.69
348 591 1.890876 TGTGCAGGCATACGAACTTT 58.109 45.000 0.00 0.00 0.00 2.66
351 594 3.435327 TGTGCAGGCATACGAACTTTAAG 59.565 43.478 0.00 0.00 0.00 1.85
352 595 3.682858 GTGCAGGCATACGAACTTTAAGA 59.317 43.478 0.00 0.00 0.00 2.10
353 596 4.332819 GTGCAGGCATACGAACTTTAAGAT 59.667 41.667 0.00 0.00 0.00 2.40
354 597 4.570772 TGCAGGCATACGAACTTTAAGATC 59.429 41.667 0.00 0.00 0.00 2.75
377 620 5.702670 TCATCAGACCTAAAAGTGCTTCTTG 59.297 40.000 0.00 0.00 36.40 3.02
398 641 0.798776 CATTGCCTCCACGAACTCAC 59.201 55.000 0.00 0.00 0.00 3.51
408 651 2.159366 CCACGAACTCACGATCTTAGCT 60.159 50.000 0.00 0.00 37.03 3.32
437 680 0.170561 GTCTGACCGACGTGCATAGT 59.829 55.000 0.00 0.00 32.04 2.12
439 682 1.271379 TCTGACCGACGTGCATAGTTT 59.729 47.619 0.00 0.00 0.00 2.66
440 683 1.654105 CTGACCGACGTGCATAGTTTC 59.346 52.381 0.00 0.00 0.00 2.78
441 684 1.271379 TGACCGACGTGCATAGTTTCT 59.729 47.619 0.00 0.00 0.00 2.52
442 685 1.654105 GACCGACGTGCATAGTTTCTG 59.346 52.381 0.00 0.00 0.00 3.02
443 686 1.000506 ACCGACGTGCATAGTTTCTGT 59.999 47.619 0.00 0.00 0.00 3.41
444 687 2.066262 CCGACGTGCATAGTTTCTGTT 58.934 47.619 0.00 0.00 0.00 3.16
445 688 3.247442 CCGACGTGCATAGTTTCTGTTA 58.753 45.455 0.00 0.00 0.00 2.41
455 699 9.542462 GTGCATAGTTTCTGTTACCTTCATATA 57.458 33.333 0.00 0.00 0.00 0.86
489 737 7.636150 AGTATCATGATATATGCCTTTTGCC 57.364 36.000 18.18 1.43 40.16 4.52
504 752 3.508845 TTTGCCCTAAAACTCTCAGCT 57.491 42.857 0.00 0.00 0.00 4.24
577 829 4.828296 CCTGGTCTGCCCCCATGC 62.828 72.222 0.00 0.00 0.00 4.06
586 838 1.232792 GCCCCCATGCTATTTCCCA 59.767 57.895 0.00 0.00 0.00 4.37
589 841 1.062962 CCCCCATGCTATTTCCCAGTT 60.063 52.381 0.00 0.00 0.00 3.16
600 852 5.335661 GCTATTTCCCAGTTACAAACCAGTG 60.336 44.000 0.00 0.00 0.00 3.66
611 863 0.956633 AAACCAGTGCACATGCTCAG 59.043 50.000 21.04 4.50 42.66 3.35
615 867 1.407025 CCAGTGCACATGCTCAGAGAT 60.407 52.381 21.04 0.00 42.66 2.75
623 875 4.033817 GCACATGCTCAGAGATAAACTGAC 59.966 45.833 0.00 0.00 39.10 3.51
739 999 1.466856 TGGCAAAGCAAGCTGGATAG 58.533 50.000 0.00 0.00 0.00 2.08
788 1048 4.320608 ACAGAGCTATAGAGAAGCAAGC 57.679 45.455 3.21 0.00 42.62 4.01
806 1066 4.166523 CAAGCACAATCATTCAGAAGCTG 58.833 43.478 0.00 0.00 0.00 4.24
815 1075 1.817357 TTCAGAAGCTGCACATGAGG 58.183 50.000 0.00 0.00 0.00 3.86
821 1081 2.393768 GCTGCACATGAGGGTGTCG 61.394 63.158 0.00 0.00 40.89 4.35
831 1091 0.741221 GAGGGTGTCGCCATCTCAAC 60.741 60.000 9.84 0.00 44.20 3.18
889 1149 5.105797 CCAGCACATAAACAAAGCTCCAATA 60.106 40.000 0.00 0.00 32.35 1.90
939 1201 6.800072 ATTGTTGGGAGAAAACTTTTGGTA 57.200 33.333 0.00 0.00 0.00 3.25
945 1207 6.133356 TGGGAGAAAACTTTTGGTACTCATT 58.867 36.000 0.00 0.00 0.00 2.57
949 1211 8.626526 GGAGAAAACTTTTGGTACTCATTTGTA 58.373 33.333 0.00 0.00 0.00 2.41
952 1214 8.642908 AAAACTTTTGGTACTCATTTGTAAGC 57.357 30.769 0.00 0.00 0.00 3.09
989 1251 1.476891 GAGGCTGATACTTCGTGTGGA 59.523 52.381 0.00 0.00 0.00 4.02
991 1253 2.101582 AGGCTGATACTTCGTGTGGATC 59.898 50.000 0.00 0.00 0.00 3.36
1088 1350 5.794894 CCAATGTCTGGTTAGAAGTAGTGT 58.205 41.667 0.00 0.00 40.78 3.55
1095 1357 7.030768 GTCTGGTTAGAAGTAGTGTCATCTTC 58.969 42.308 0.00 0.00 38.15 2.87
1114 1376 9.040259 TCATCTTCCTATCTATATTGGTGGAAG 57.960 37.037 17.92 17.92 46.01 3.46
1145 1407 4.970003 CGAGGAATGTGTCTTTTGTTGAAC 59.030 41.667 0.00 0.00 0.00 3.18
1216 1478 2.170187 AGGAGATGCAGGCTGTTAAGAG 59.830 50.000 17.16 0.00 0.00 2.85
1245 1507 2.224018 GCTCAGGCAAGAGAGGATACTG 60.224 54.545 10.65 0.00 43.23 2.74
1291 1580 2.384203 GCTCACGCGCTCCTTTTAT 58.616 52.632 5.73 0.00 0.00 1.40
1338 1627 2.112815 GCAACTGGGGGTGATACGC 61.113 63.158 0.00 0.00 0.00 4.42
1374 1663 2.564947 ACATCCAACTCTGAGTCTGGAC 59.435 50.000 28.15 0.00 37.83 4.02
1505 1794 1.112315 CGCAGTCTCCCTGGCTCTAT 61.112 60.000 0.00 0.00 41.81 1.98
1610 1899 5.957842 AAACTAATTCGTTGCAATCAGGA 57.042 34.783 0.59 0.00 0.00 3.86
1683 1973 4.712122 ACATTTCAAAGAACACCAACGT 57.288 36.364 0.00 0.00 0.00 3.99
1712 2002 6.671614 AAAAGTGAACGAACTGTGTAATCA 57.328 33.333 0.00 0.00 0.00 2.57
1713 2003 5.652744 AAGTGAACGAACTGTGTAATCAC 57.347 39.130 0.00 8.24 44.08 3.06
1994 2290 2.572290 ACGCAAACTAGAAAAGCCTGT 58.428 42.857 0.00 0.00 0.00 4.00
1995 2291 2.548480 ACGCAAACTAGAAAAGCCTGTC 59.452 45.455 0.00 0.00 0.00 3.51
2061 2357 4.196193 TGTCTCTGTTTTGGTCGTTGAAT 58.804 39.130 0.00 0.00 0.00 2.57
2065 2361 7.015877 GTCTCTGTTTTGGTCGTTGAATATTC 58.984 38.462 8.60 8.60 0.00 1.75
2307 2605 2.105006 TCCTCAGTTCAGATTGCTGC 57.895 50.000 0.00 0.00 42.01 5.25
2313 2611 2.034939 CAGTTCAGATTGCTGCCAAACA 59.965 45.455 0.00 0.00 42.01 2.83
2333 2631 7.706179 CCAAACAAAGTTTGAAGCTCAAATAGA 59.294 33.333 22.23 0.00 46.55 1.98
2421 2719 4.706476 TCACAAAGAGGCCAATAAATGAGG 59.294 41.667 5.01 0.00 0.00 3.86
2494 2792 2.024941 GGGATTGTCTCACCTGGGAATT 60.025 50.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.416401 TGCTTCCCGAGAGAAACAACT 59.584 47.619 0.00 0.00 0.00 3.16
8 9 1.878953 TGCTTCCCGAGAGAAACAAC 58.121 50.000 0.00 0.00 0.00 3.32
10 11 3.973206 TTATGCTTCCCGAGAGAAACA 57.027 42.857 0.00 0.00 0.00 2.83
28 29 4.397103 GCTCTATATGCTTGCATGCCATTA 59.603 41.667 20.65 10.81 0.00 1.90
69 93 7.996098 AAACATTCTTATATTATGGGACGGG 57.004 36.000 0.00 0.00 0.00 5.28
81 105 9.667107 CTCCCTACTGTCAAAAACATTCTTATA 57.333 33.333 0.00 0.00 37.23 0.98
83 107 7.514721 ACTCCCTACTGTCAAAAACATTCTTA 58.485 34.615 0.00 0.00 37.23 2.10
84 108 6.365520 ACTCCCTACTGTCAAAAACATTCTT 58.634 36.000 0.00 0.00 37.23 2.52
85 109 5.941788 ACTCCCTACTGTCAAAAACATTCT 58.058 37.500 0.00 0.00 37.23 2.40
87 111 9.975218 ATTATACTCCCTACTGTCAAAAACATT 57.025 29.630 0.00 0.00 37.23 2.71
88 112 9.975218 AATTATACTCCCTACTGTCAAAAACAT 57.025 29.630 0.00 0.00 37.23 2.71
89 113 9.444600 GAATTATACTCCCTACTGTCAAAAACA 57.555 33.333 0.00 0.00 36.18 2.83
90 114 9.668497 AGAATTATACTCCCTACTGTCAAAAAC 57.332 33.333 0.00 0.00 0.00 2.43
96 120 9.742144 TGAGATAGAATTATACTCCCTACTGTC 57.258 37.037 0.00 0.00 0.00 3.51
143 381 5.878669 ACCTAGCGAATTTACACCCTTTAAG 59.121 40.000 0.00 0.00 0.00 1.85
146 384 4.296621 ACCTAGCGAATTTACACCCTTT 57.703 40.909 0.00 0.00 0.00 3.11
147 385 3.994931 ACCTAGCGAATTTACACCCTT 57.005 42.857 0.00 0.00 0.00 3.95
162 400 3.430453 TCCTGCCCAAATTGAAACCTAG 58.570 45.455 0.00 0.00 0.00 3.02
183 421 7.671398 ACATCAACAGAAATTCTCTTACCCATT 59.329 33.333 0.00 0.00 29.07 3.16
190 428 8.019669 CGATTGAACATCAACAGAAATTCTCTT 58.980 33.333 0.00 0.00 39.45 2.85
191 429 7.524912 CGATTGAACATCAACAGAAATTCTCT 58.475 34.615 0.00 0.00 39.45 3.10
194 432 6.088824 AGCGATTGAACATCAACAGAAATTC 58.911 36.000 0.00 0.00 39.45 2.17
196 434 5.413833 AGAGCGATTGAACATCAACAGAAAT 59.586 36.000 0.00 0.00 39.45 2.17
197 435 4.756642 AGAGCGATTGAACATCAACAGAAA 59.243 37.500 0.00 0.00 39.45 2.52
198 436 4.152938 CAGAGCGATTGAACATCAACAGAA 59.847 41.667 0.00 0.00 39.45 3.02
199 437 3.681417 CAGAGCGATTGAACATCAACAGA 59.319 43.478 0.00 0.00 39.45 3.41
200 438 3.434641 ACAGAGCGATTGAACATCAACAG 59.565 43.478 0.00 0.00 39.45 3.16
201 439 3.402110 ACAGAGCGATTGAACATCAACA 58.598 40.909 0.00 0.00 39.45 3.33
202 440 4.410492 AACAGAGCGATTGAACATCAAC 57.590 40.909 0.00 0.00 39.45 3.18
203 441 4.994217 TGTAACAGAGCGATTGAACATCAA 59.006 37.500 0.00 0.00 41.09 2.57
204 442 4.388773 GTGTAACAGAGCGATTGAACATCA 59.611 41.667 0.00 0.00 36.32 3.07
205 443 4.627467 AGTGTAACAGAGCGATTGAACATC 59.373 41.667 0.00 0.00 41.43 3.06
206 444 4.389992 CAGTGTAACAGAGCGATTGAACAT 59.610 41.667 0.00 0.00 41.43 2.71
207 445 3.740832 CAGTGTAACAGAGCGATTGAACA 59.259 43.478 0.00 0.00 41.43 3.18
208 446 3.987868 TCAGTGTAACAGAGCGATTGAAC 59.012 43.478 0.00 0.00 41.43 3.18
209 447 4.251543 TCAGTGTAACAGAGCGATTGAA 57.748 40.909 0.00 0.00 41.43 2.69
210 448 3.934457 TCAGTGTAACAGAGCGATTGA 57.066 42.857 0.00 0.00 41.43 2.57
211 449 4.990543 TTTCAGTGTAACAGAGCGATTG 57.009 40.909 0.00 0.00 41.43 2.67
212 450 5.237815 TCATTTCAGTGTAACAGAGCGATT 58.762 37.500 0.00 0.00 41.43 3.34
213 451 4.820897 TCATTTCAGTGTAACAGAGCGAT 58.179 39.130 0.00 0.00 41.43 4.58
214 452 4.251543 TCATTTCAGTGTAACAGAGCGA 57.748 40.909 0.00 0.00 41.43 4.93
215 453 4.990543 TTCATTTCAGTGTAACAGAGCG 57.009 40.909 0.00 0.00 41.43 5.03
216 454 5.693814 CCTTTCATTTCAGTGTAACAGAGC 58.306 41.667 0.00 0.00 41.43 4.09
217 455 5.471456 AGCCTTTCATTTCAGTGTAACAGAG 59.529 40.000 0.00 0.00 41.43 3.35
218 456 5.239306 CAGCCTTTCATTTCAGTGTAACAGA 59.761 40.000 0.00 0.00 41.43 3.41
219 457 5.239306 TCAGCCTTTCATTTCAGTGTAACAG 59.761 40.000 0.00 0.00 41.43 3.16
220 458 5.129634 TCAGCCTTTCATTTCAGTGTAACA 58.870 37.500 0.00 0.00 41.43 2.41
221 459 5.689383 TCAGCCTTTCATTTCAGTGTAAC 57.311 39.130 0.00 0.00 0.00 2.50
222 460 7.394016 TCTATCAGCCTTTCATTTCAGTGTAA 58.606 34.615 0.00 0.00 0.00 2.41
223 461 6.946340 TCTATCAGCCTTTCATTTCAGTGTA 58.054 36.000 0.00 0.00 0.00 2.90
224 462 5.809001 TCTATCAGCCTTTCATTTCAGTGT 58.191 37.500 0.00 0.00 0.00 3.55
225 463 5.879223 ACTCTATCAGCCTTTCATTTCAGTG 59.121 40.000 0.00 0.00 0.00 3.66
226 464 6.059787 ACTCTATCAGCCTTTCATTTCAGT 57.940 37.500 0.00 0.00 0.00 3.41
227 465 6.596888 TGAACTCTATCAGCCTTTCATTTCAG 59.403 38.462 0.00 0.00 0.00 3.02
228 466 6.475504 TGAACTCTATCAGCCTTTCATTTCA 58.524 36.000 0.00 0.00 0.00 2.69
229 467 6.038050 CCTGAACTCTATCAGCCTTTCATTTC 59.962 42.308 0.00 0.00 44.43 2.17
230 468 5.884792 CCTGAACTCTATCAGCCTTTCATTT 59.115 40.000 0.00 0.00 44.43 2.32
231 469 5.045286 ACCTGAACTCTATCAGCCTTTCATT 60.045 40.000 0.00 0.00 44.43 2.57
232 470 4.472833 ACCTGAACTCTATCAGCCTTTCAT 59.527 41.667 0.00 0.00 44.43 2.57
245 483 4.137543 CCTTGCAAAGTAACCTGAACTCT 58.862 43.478 0.00 0.00 44.25 3.24
251 489 4.385825 TCTGTACCTTGCAAAGTAACCTG 58.614 43.478 9.46 3.58 44.25 4.00
252 490 4.699925 TCTGTACCTTGCAAAGTAACCT 57.300 40.909 9.46 0.00 44.25 3.50
256 494 6.614694 TTCCTATCTGTACCTTGCAAAGTA 57.385 37.500 3.72 3.72 44.25 2.24
257 495 5.499004 TTCCTATCTGTACCTTGCAAAGT 57.501 39.130 5.90 5.90 44.25 2.66
258 496 6.349363 GGTTTTCCTATCTGTACCTTGCAAAG 60.349 42.308 0.00 0.00 39.45 2.77
259 497 5.475564 GGTTTTCCTATCTGTACCTTGCAAA 59.524 40.000 0.00 0.00 36.94 3.68
260 498 5.007682 GGTTTTCCTATCTGTACCTTGCAA 58.992 41.667 0.00 0.00 36.94 4.08
261 499 4.585879 GGTTTTCCTATCTGTACCTTGCA 58.414 43.478 0.00 0.00 36.94 4.08
313 556 4.866486 CCTGCACAATTCTAATTTTGGCTC 59.134 41.667 4.31 0.00 0.00 4.70
348 591 7.187824 AGCACTTTTAGGTCTGATGATCTTA 57.812 36.000 0.00 0.00 34.99 2.10
351 594 6.112058 AGAAGCACTTTTAGGTCTGATGATC 58.888 40.000 0.00 0.00 0.00 2.92
352 595 6.059787 AGAAGCACTTTTAGGTCTGATGAT 57.940 37.500 0.00 0.00 0.00 2.45
353 596 5.489792 AGAAGCACTTTTAGGTCTGATGA 57.510 39.130 0.00 0.00 0.00 2.92
354 597 5.618640 GCAAGAAGCACTTTTAGGTCTGATG 60.619 44.000 0.00 0.00 44.79 3.07
377 620 1.648467 GAGTTCGTGGAGGCAATGGC 61.648 60.000 0.00 0.00 40.13 4.40
398 641 5.689514 CAGACAATTAGGACAGCTAAGATCG 59.310 44.000 0.00 0.00 0.00 3.69
482 727 3.823304 AGCTGAGAGTTTTAGGGCAAAAG 59.177 43.478 0.00 0.00 36.79 2.27
489 737 7.148340 CCTTGTGAATTAGCTGAGAGTTTTAGG 60.148 40.741 0.00 0.00 0.00 2.69
562 814 1.288508 AATAGCATGGGGGCAGACCA 61.289 55.000 0.00 0.00 42.91 4.02
568 820 0.829182 CTGGGAAATAGCATGGGGGC 60.829 60.000 0.00 0.00 0.00 5.80
577 829 5.335661 GCACTGGTTTGTAACTGGGAAATAG 60.336 44.000 0.00 0.00 0.00 1.73
586 838 2.034558 GCATGTGCACTGGTTTGTAACT 59.965 45.455 19.41 0.00 41.59 2.24
589 841 1.879380 GAGCATGTGCACTGGTTTGTA 59.121 47.619 19.41 0.00 45.16 2.41
600 852 4.033817 GTCAGTTTATCTCTGAGCATGTGC 59.966 45.833 0.00 0.00 41.66 4.57
611 863 9.303537 GACCTAACACATTAGTCAGTTTATCTC 57.696 37.037 0.00 0.00 36.77 2.75
615 867 7.728148 TGTGACCTAACACATTAGTCAGTTTA 58.272 34.615 0.00 0.00 44.29 2.01
739 999 9.482627 CAAGTTCTATTATTCTCCACATAGGAC 57.517 37.037 0.00 0.00 43.07 3.85
788 1048 3.057806 TGTGCAGCTTCTGAATGATTGTG 60.058 43.478 0.00 0.00 32.44 3.33
806 1066 3.127533 GGCGACACCCTCATGTGC 61.128 66.667 0.00 0.00 39.93 4.57
821 1081 4.585955 TTATCTCCTACGTTGAGATGGC 57.414 45.455 27.47 0.00 46.38 4.40
831 1091 4.441415 GCTTGTCGTGAATTATCTCCTACG 59.559 45.833 0.00 0.00 0.00 3.51
907 1168 7.775120 AGTTTTCTCCCAACAATAGCAATATG 58.225 34.615 0.00 0.00 0.00 1.78
910 1171 6.670695 AAGTTTTCTCCCAACAATAGCAAT 57.329 33.333 0.00 0.00 0.00 3.56
939 1201 5.426689 TCATCAGAGGCTTACAAATGAGT 57.573 39.130 0.00 0.00 0.00 3.41
945 1207 4.202461 ACCTGTTTCATCAGAGGCTTACAA 60.202 41.667 0.00 0.00 37.61 2.41
949 1211 2.373169 TCACCTGTTTCATCAGAGGCTT 59.627 45.455 0.00 0.00 37.61 4.35
952 1214 2.938756 GCCTCACCTGTTTCATCAGAGG 60.939 54.545 0.00 0.00 37.61 3.69
989 1251 3.304911 TCTTCTCCATCTCTCACCGAT 57.695 47.619 0.00 0.00 0.00 4.18
991 1253 3.056536 TGTTTCTTCTCCATCTCTCACCG 60.057 47.826 0.00 0.00 0.00 4.94
1088 1350 8.972662 TTCCACCAATATAGATAGGAAGATGA 57.027 34.615 0.00 0.00 0.00 2.92
1114 1376 6.481954 AAAGACACATTCCTCGTTGAATAC 57.518 37.500 2.66 0.00 33.27 1.89
1119 1381 4.552166 ACAAAAGACACATTCCTCGTTG 57.448 40.909 0.00 0.00 0.00 4.10
1124 1386 4.709397 TGGTTCAACAAAAGACACATTCCT 59.291 37.500 0.00 0.00 0.00 3.36
1125 1387 5.004922 TGGTTCAACAAAAGACACATTCC 57.995 39.130 0.00 0.00 0.00 3.01
1126 1388 5.043248 CCTGGTTCAACAAAAGACACATTC 58.957 41.667 0.00 0.00 0.00 2.67
1127 1389 4.466015 ACCTGGTTCAACAAAAGACACATT 59.534 37.500 0.00 0.00 0.00 2.71
1128 1390 4.023291 ACCTGGTTCAACAAAAGACACAT 58.977 39.130 0.00 0.00 0.00 3.21
1130 1392 4.421058 GAACCTGGTTCAACAAAAGACAC 58.579 43.478 29.80 2.80 41.62 3.67
1131 1393 4.712122 GAACCTGGTTCAACAAAAGACA 57.288 40.909 29.80 0.00 41.62 3.41
1145 1407 1.399440 CGATGCAACTCATGAACCTGG 59.601 52.381 0.00 0.00 35.05 4.45
1154 1416 1.064357 TCGTATACGCGATGCAACTCA 59.936 47.619 20.42 0.00 39.60 3.41
1158 1420 0.382873 ACCTCGTATACGCGATGCAA 59.617 50.000 20.42 0.35 40.29 4.08
1256 1518 2.366590 TGAGCGATCTGTATCCAGCATT 59.633 45.455 0.90 0.00 38.66 3.56
1274 1536 0.572590 CGATAAAAGGAGCGCGTGAG 59.427 55.000 8.43 0.00 0.00 3.51
1275 1537 0.171679 TCGATAAAAGGAGCGCGTGA 59.828 50.000 8.43 0.00 0.00 4.35
1279 1541 1.202428 AGTCCTCGATAAAAGGAGCGC 60.202 52.381 0.00 0.00 43.54 5.92
1285 1574 4.631813 CCAGGTTGAAGTCCTCGATAAAAG 59.368 45.833 0.00 0.00 32.37 2.27
1289 1578 3.024547 CTCCAGGTTGAAGTCCTCGATA 58.975 50.000 0.00 0.00 32.37 2.92
1291 1580 1.257743 CTCCAGGTTGAAGTCCTCGA 58.742 55.000 0.00 0.00 32.37 4.04
1338 1627 2.208431 GGATGTCATCTCTTGCTTCCG 58.792 52.381 12.54 0.00 0.00 4.30
1364 1653 0.757561 TCACCGTTGGTCCAGACTCA 60.758 55.000 0.00 0.00 31.02 3.41
1374 1663 1.081041 TCGACGATGTCACCGTTGG 60.081 57.895 7.15 0.00 40.67 3.77
1427 1716 3.099905 CCTCAGGTCTACATTGGACTCA 58.900 50.000 0.00 0.00 34.47 3.41
1505 1794 6.240894 AGCCATCTTGAGACTTAAACATTGA 58.759 36.000 0.00 0.00 0.00 2.57
1531 1820 0.249911 CCACCCGTAGCTAAGCCATC 60.250 60.000 0.00 0.00 0.00 3.51
1609 1898 5.292765 TGACTTCCTATTGATCGCATTCTC 58.707 41.667 0.00 0.00 0.00 2.87
1610 1899 5.282055 TGACTTCCTATTGATCGCATTCT 57.718 39.130 0.00 0.00 0.00 2.40
1662 1952 4.156922 TGACGTTGGTGTTCTTTGAAATGT 59.843 37.500 0.00 0.00 0.00 2.71
1683 1973 5.180492 ACACAGTTCGTTCACTTTTTCTTGA 59.820 36.000 0.00 0.00 0.00 3.02
1712 2002 2.550208 CCCTTGTACGCAGAAAGAAGGT 60.550 50.000 0.00 0.00 36.39 3.50
1713 2003 2.076863 CCCTTGTACGCAGAAAGAAGG 58.923 52.381 0.00 0.00 37.28 3.46
1994 2290 6.108687 TCGTTTTCAGTAGAGTAGTATCCGA 58.891 40.000 0.00 0.00 0.00 4.55
1995 2291 6.355397 TCGTTTTCAGTAGAGTAGTATCCG 57.645 41.667 0.00 0.00 0.00 4.18
2073 2369 5.065218 GTCATTACCACCAACTAGCTCATTG 59.935 44.000 0.00 0.00 0.00 2.82
2085 2381 2.672295 GGGCCGTCATTACCACCA 59.328 61.111 0.00 0.00 0.00 4.17
2421 2719 1.243902 TTCCGACCATCAAAAGTGGC 58.756 50.000 0.00 0.00 40.49 5.01
2494 2792 8.354711 AGTCCTCTAATTGCTTGATCGATATA 57.645 34.615 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.