Multiple sequence alignment - TraesCS7B01G014500

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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 TraesCS7B01G014500 chr7B 100.000 3319 0 0 1 3319 11528855 11532173 0.000000e+00 6130
1 TraesCS7B01G014500 chr7D 93.209 2518 109 29 655 3152 69264943 69267418 0.000000e+00 3646
2 TraesCS7B01G014500 chr7D 88.782 312 22 9 355 662 69264531 69264833 1.450000e-98 370
3 TraesCS7B01G014500 chr7D 97.059 170 5 0 3150 3319 69267734 69267903 1.510000e-73 287
4 TraesCS7B01G014500 chr7A 93.271 2363 94 27 653 2998 75034997 75037311 0.000000e+00 3422
5 TraesCS7B01G014500 chr7A 86.842 342 42 3 1 340 75034238 75034578 2.420000e-101 379
6 TraesCS7B01G014500 chr7A 95.402 174 4 1 3150 3319 75039113 75039286 1.170000e-69 274
7 TraesCS7B01G014500 chr7A 86.325 234 22 6 430 662 75034605 75034829 2.560000e-61 246
8 TraesCS7B01G014500 chrUn 74.922 319 74 5 13 327 328103884 328104200 1.240000e-29 141
9 TraesCS7B01G014500 chr1A 74.922 319 74 5 13 327 539710558 539710874 1.240000e-29 141


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 TraesCS7B01G014500 chr7B 11528855 11532173 3318 False 6130.000000 6130 100.000000 1 3319 1 chr7B.!!$F1 3318
1 TraesCS7B01G014500 chr7D 69264531 69267903 3372 False 1434.333333 3646 93.016667 355 3319 3 chr7D.!!$F1 2964
2 TraesCS7B01G014500 chr7A 75034238 75039286 5048 False 1080.250000 3422 90.460000 1 3319 4 chr7A.!!$F1 3318

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
264 266 0.180171 TGATGTTATGGCCCCACTCG 59.820 55.0 0.00 0.0 0.0 4.18 F
1267 1454 0.396139 CTACTACGGCCAGTACCCCA 60.396 60.0 2.24 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 1504 0.250727 CAACACCGAACACCAGGGAT 60.251 55.0 0.0 0.0 0.00 3.85 R
3043 3252 1.187567 AAACATTCCCAGTGCCCTGC 61.188 55.0 0.0 0.0 37.38 4.85 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
21 22 4.181309 GCCGTTCCCACAAAAATTATCA 57.819 40.909 0.00 0.00 0.00 2.15
52 53 4.694339 ACGTATTGTAGAATTGAGAGGCC 58.306 43.478 0.00 0.00 0.00 5.19
58 59 3.904339 TGTAGAATTGAGAGGCCCCTATC 59.096 47.826 0.00 2.04 35.10 2.08
61 62 1.439543 ATTGAGAGGCCCCTATCCAC 58.560 55.000 0.00 0.00 33.72 4.02
64 65 0.761802 GAGAGGCCCCTATCCACAAG 59.238 60.000 0.00 0.00 0.00 3.16
79 81 4.737578 TCCACAAGGTGTAGACTACTCTT 58.262 43.478 13.67 13.13 35.89 2.85
82 84 5.455056 ACAAGGTGTAGACTACTCTTGTG 57.545 43.478 30.98 20.90 44.08 3.33
91 93 5.808366 AGACTACTCTTGTGATTTGACCA 57.192 39.130 0.00 0.00 0.00 4.02
93 95 6.402222 AGACTACTCTTGTGATTTGACCATC 58.598 40.000 0.00 0.00 0.00 3.51
105 107 0.888736 TGACCATCCTGTTTGGCACG 60.889 55.000 0.00 0.00 37.81 5.34
120 122 1.812571 GGCACGTTCAATCAAGATGGT 59.187 47.619 0.00 0.00 0.00 3.55
130 132 4.392754 TCAATCAAGATGGTCAACATGTCG 59.607 41.667 0.00 0.00 40.72 4.35
137 139 2.633488 TGGTCAACATGTCGACAACAA 58.367 42.857 24.13 6.30 42.37 2.83
141 143 3.968096 GTCAACATGTCGACAACAATGTG 59.032 43.478 24.13 17.12 42.37 3.21
165 167 8.260114 GTGGAATAACATTGGAGAAAATGGATT 58.740 33.333 2.34 1.77 41.06 3.01
173 175 4.609301 TGGAGAAAATGGATTACCTTGGG 58.391 43.478 0.00 0.00 37.04 4.12
174 176 4.045334 TGGAGAAAATGGATTACCTTGGGT 59.955 41.667 0.00 0.00 40.16 4.51
175 177 5.254267 TGGAGAAAATGGATTACCTTGGGTA 59.746 40.000 0.00 0.00 37.09 3.69
176 178 5.828328 GGAGAAAATGGATTACCTTGGGTAG 59.172 44.000 0.00 0.00 39.52 3.18
177 179 6.402981 AGAAAATGGATTACCTTGGGTAGT 57.597 37.500 0.00 0.00 39.52 2.73
178 180 6.424032 AGAAAATGGATTACCTTGGGTAGTC 58.576 40.000 9.73 9.73 41.99 2.59
197 199 6.717997 GGTAGTCCCTTTTCCATTTTGAAGTA 59.282 38.462 0.00 0.00 0.00 2.24
200 202 6.609616 AGTCCCTTTTCCATTTTGAAGTAACA 59.390 34.615 0.00 0.00 0.00 2.41
227 229 8.130307 CCAATGTTGGCATTAACTTTTATAGC 57.870 34.615 0.00 0.00 42.91 2.97
236 238 6.554419 CATTAACTTTTATAGCTGCACTGCA 58.446 36.000 3.11 3.11 36.92 4.41
264 266 0.180171 TGATGTTATGGCCCCACTCG 59.820 55.000 0.00 0.00 0.00 4.18
265 267 1.152963 ATGTTATGGCCCCACTCGC 60.153 57.895 0.00 0.00 0.00 5.03
266 268 1.920734 ATGTTATGGCCCCACTCGCA 61.921 55.000 0.00 0.00 0.00 5.10
273 275 1.728490 GGCCCCACTCGCATCATTTC 61.728 60.000 0.00 0.00 0.00 2.17
293 295 2.644299 TCTTGGAGAAGCCCTTCATTCA 59.356 45.455 10.37 3.18 41.84 2.57
294 296 3.074390 TCTTGGAGAAGCCCTTCATTCAA 59.926 43.478 10.37 9.51 41.84 2.69
297 299 3.010472 TGGAGAAGCCCTTCATTCAATGA 59.990 43.478 10.37 0.00 41.84 2.57
301 303 4.018597 AGAAGCCCTTCATTCAATGAGTCT 60.019 41.667 10.37 0.00 41.84 3.24
335 337 7.839680 AGGACCATTTGACTTTTTCATAAGT 57.160 32.000 0.00 0.00 40.92 2.24
336 338 8.250143 AGGACCATTTGACTTTTTCATAAGTT 57.750 30.769 0.00 0.00 38.43 2.66
337 339 8.704668 AGGACCATTTGACTTTTTCATAAGTTT 58.295 29.630 0.00 0.00 38.43 2.66
338 340 9.325198 GGACCATTTGACTTTTTCATAAGTTTT 57.675 29.630 0.00 0.00 38.43 2.43
455 458 2.803956 ACGACAACTACTCCATCCAGA 58.196 47.619 0.00 0.00 0.00 3.86
461 464 6.986817 CGACAACTACTCCATCCAGAATATTT 59.013 38.462 0.00 0.00 0.00 1.40
462 465 7.169982 CGACAACTACTCCATCCAGAATATTTC 59.830 40.741 0.00 0.00 0.00 2.17
463 466 8.095452 ACAACTACTCCATCCAGAATATTTCT 57.905 34.615 0.00 0.00 41.70 2.52
464 467 9.213777 ACAACTACTCCATCCAGAATATTTCTA 57.786 33.333 0.00 0.00 38.11 2.10
465 468 9.703892 CAACTACTCCATCCAGAATATTTCTAG 57.296 37.037 0.00 0.00 38.11 2.43
466 469 9.440761 AACTACTCCATCCAGAATATTTCTAGT 57.559 33.333 0.00 0.00 38.11 2.57
470 473 9.836179 ACTCCATCCAGAATATTTCTAGTATCT 57.164 33.333 0.00 0.00 38.11 1.98
523 527 9.554395 TTTTTGGGAAAACAAATCTTATCCTTC 57.446 29.630 0.00 0.00 39.80 3.46
555 560 8.231692 TCAAAGTATCATTCGATCTCTTCTCT 57.768 34.615 0.00 0.00 32.73 3.10
578 583 9.462174 CTCTGTCTCTCATATACAAAGCTTAAG 57.538 37.037 0.00 0.00 0.00 1.85
579 584 9.190317 TCTGTCTCTCATATACAAAGCTTAAGA 57.810 33.333 6.67 0.00 0.00 2.10
580 585 9.979578 CTGTCTCTCATATACAAAGCTTAAGAT 57.020 33.333 6.67 0.00 0.00 2.40
624 629 4.785453 GCAGGCAGCCGGTTAGCT 62.785 66.667 13.66 0.00 46.45 3.32
628 633 2.589159 GCAGCCGGTTAGCTAGCC 60.589 66.667 16.26 16.26 42.61 3.93
638 643 3.005897 CGGTTAGCTAGCCTGTGTATCAT 59.994 47.826 22.55 0.00 0.00 2.45
645 650 5.070981 AGCTAGCCTGTGTATCATTGTATGT 59.929 40.000 12.13 0.00 0.00 2.29
694 878 7.112779 CCTTTCAGAAATCTTATGTACCCACT 58.887 38.462 0.00 0.00 0.00 4.00
733 917 0.611714 TGAAGAGGAGGTTAACGGGC 59.388 55.000 0.00 0.00 0.00 6.13
741 925 2.357446 GTTAACGGGCCCCACCAT 59.643 61.111 18.66 0.00 42.05 3.55
777 961 7.065803 TCAGTAACAAACCACTCTTCTGAAAAG 59.934 37.037 0.00 0.00 0.00 2.27
784 968 2.057922 ACTCTTCTGAAAAGGAGGCCA 58.942 47.619 5.01 0.00 0.00 5.36
924 1108 1.075600 CCTCACTCTCCTCCCCTCC 60.076 68.421 0.00 0.00 0.00 4.30
944 1128 1.680735 CCCTCTCCTCTCATCAGTTCG 59.319 57.143 0.00 0.00 0.00 3.95
953 1137 2.094700 TCTCATCAGTTCGGCTGTGTAC 60.095 50.000 7.56 0.00 45.23 2.90
968 1152 3.021695 TGTGTACCTTCATCTCTACGGG 58.978 50.000 0.00 0.00 0.00 5.28
976 1160 1.214673 TCATCTCTACGGGGTAGCAGT 59.785 52.381 0.00 0.00 36.22 4.40
1134 1318 2.617276 CCTCCTGTCCTACGTAGACACA 60.617 54.545 24.15 21.64 39.29 3.72
1212 1396 3.418068 GCGCAGTTCGAGCAGCTT 61.418 61.111 14.25 0.00 40.67 3.74
1267 1454 0.396139 CTACTACGGCCAGTACCCCA 60.396 60.000 2.24 0.00 0.00 4.96
1273 1460 3.253838 GCCAGTACCCCACCACCA 61.254 66.667 0.00 0.00 0.00 4.17
1278 1465 2.123180 TACCCCACCACCACCGAT 59.877 61.111 0.00 0.00 0.00 4.18
1284 1471 2.098233 CACCACCACCGATGCGTAC 61.098 63.158 0.00 0.00 0.00 3.67
1287 1474 1.079405 CACCACCGATGCGTACCTT 60.079 57.895 0.00 0.00 0.00 3.50
1294 1481 4.171103 ATGCGTACCTTCCCGGCC 62.171 66.667 0.00 0.00 35.61 6.13
1298 1488 2.686106 GTACCTTCCCGGCCCTCA 60.686 66.667 0.00 0.00 35.61 3.86
1314 1504 1.228337 TCAGAGGACCGGTTCGTCA 60.228 57.895 9.42 0.00 40.95 4.35
1331 1521 1.125093 TCATCCCTGGTGTTCGGTGT 61.125 55.000 0.00 0.00 0.00 4.16
1359 1549 0.617820 AGGAGTCGGCCTACATGGTT 60.618 55.000 10.45 0.00 36.22 3.67
1575 1765 3.306973 TCGATGCGTTCATTCATCTTGTC 59.693 43.478 0.00 0.00 37.52 3.18
1586 1776 9.055248 GTTCATTCATCTTGTCTTTAATTCGTG 57.945 33.333 0.00 0.00 0.00 4.35
1595 1785 3.185797 GTCTTTAATTCGTGGCACTTCGT 59.814 43.478 16.72 1.07 0.00 3.85
1646 1837 7.447238 TCTCGTGATTCTTTAATTTTTCTGGGT 59.553 33.333 0.00 0.00 0.00 4.51
1777 1968 1.686110 GAGAAGAAGAGGGGCCGGA 60.686 63.158 5.05 0.00 0.00 5.14
1797 1988 4.083862 GAGCACCAGGGGGACGTC 62.084 72.222 7.13 7.13 38.05 4.34
1844 2035 1.621672 GGAGAAGGGGAGTGCTCTGG 61.622 65.000 0.00 0.00 0.00 3.86
2052 2243 0.323542 ACCTCCACCTAGACCTCGTG 60.324 60.000 0.00 0.00 0.00 4.35
2143 2334 7.906160 CGTCACAACGGATCTCTTAATTAATT 58.094 34.615 5.89 5.89 45.21 1.40
2171 2363 6.420604 CACATATCATGCATGTACGTTCAGTA 59.579 38.462 25.43 3.20 34.88 2.74
2197 2389 9.803507 ATTCTCAAGAATCAAGATATATGCCAA 57.196 29.630 0.00 0.00 40.49 4.52
2222 2414 7.601705 AAAAGAAGGATGATGGTTTTCTTGA 57.398 32.000 0.00 0.00 37.93 3.02
2255 2449 6.369615 TGTTGATGTATATGCAGATTCATCCG 59.630 38.462 27.59 0.00 33.20 4.18
2258 2452 3.837731 TGTATATGCAGATTCATCCGGGA 59.162 43.478 0.00 0.00 0.00 5.14
2320 2514 3.101643 AGTGGTGGATGAGTACTAGCA 57.898 47.619 0.00 0.00 0.00 3.49
2321 2515 3.027412 AGTGGTGGATGAGTACTAGCAG 58.973 50.000 0.00 0.00 0.00 4.24
2322 2516 1.757118 TGGTGGATGAGTACTAGCAGC 59.243 52.381 0.00 0.00 0.00 5.25
2340 2534 3.193263 CAGCAGCTCGTTATCTTGTCAT 58.807 45.455 0.00 0.00 0.00 3.06
2341 2535 3.001026 CAGCAGCTCGTTATCTTGTCATG 59.999 47.826 0.00 0.00 0.00 3.07
2393 2598 2.918712 AGGGTTCTTGGATATCTGCG 57.081 50.000 2.05 0.00 0.00 5.18
2422 2627 5.304614 TCAGTACTTCAGTAGTTCTTTGGCT 59.695 40.000 0.00 0.00 38.33 4.75
2423 2628 5.992217 CAGTACTTCAGTAGTTCTTTGGCTT 59.008 40.000 0.00 0.00 38.33 4.35
2424 2629 6.483640 CAGTACTTCAGTAGTTCTTTGGCTTT 59.516 38.462 0.00 0.00 38.33 3.51
2425 2630 7.656137 CAGTACTTCAGTAGTTCTTTGGCTTTA 59.344 37.037 0.00 0.00 38.33 1.85
2426 2631 7.873505 AGTACTTCAGTAGTTCTTTGGCTTTAG 59.126 37.037 0.00 0.00 38.33 1.85
2427 2632 5.470437 ACTTCAGTAGTTCTTTGGCTTTAGC 59.530 40.000 0.00 0.00 35.05 3.09
2430 2635 6.062095 TCAGTAGTTCTTTGGCTTTAGCTTT 58.938 36.000 0.00 0.00 41.70 3.51
2432 2637 7.717875 TCAGTAGTTCTTTGGCTTTAGCTTTAA 59.282 33.333 0.00 0.00 41.70 1.52
2742 2948 9.098355 CTCCTTCAGATATTATTTTTGTGTCGA 57.902 33.333 0.00 0.00 0.00 4.20
2933 3139 1.549203 ATGATTGCTGTTTCGCCCTT 58.451 45.000 0.00 0.00 0.00 3.95
2954 3160 4.998671 TGTCTTTGCCTGAATTTGTTCA 57.001 36.364 0.00 0.00 0.00 3.18
3006 3213 3.181429 TGGATGCAAATATTCTCCTCCCC 60.181 47.826 0.00 0.00 0.00 4.81
3015 3222 2.284699 CTCCTCCCCCGGTGTCTT 60.285 66.667 0.00 0.00 0.00 3.01
3018 3225 2.663196 CTCCCCCGGTGTCTTGTC 59.337 66.667 0.00 0.00 0.00 3.18
3019 3226 2.122769 TCCCCCGGTGTCTTGTCA 60.123 61.111 0.00 0.00 0.00 3.58
3064 3275 2.524306 CAGGGCACTGGGAATGTTTAA 58.476 47.619 8.54 0.00 41.13 1.52
3146 4730 7.277539 CCTTTAGCACATAAGTTTCTGAGAGAG 59.722 40.741 0.00 0.00 0.00 3.20
3233 5145 8.357290 TCATGGAAATTCAAATGTGAGATCTT 57.643 30.769 0.00 0.00 34.49 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.658609 CAATGACATGATAATTTTTGTGGGAAC 58.341 33.333 0.00 0.00 0.00 3.62
5 6 8.034215 GTCAATGACATGATAATTTTTGTGGGA 58.966 33.333 8.74 0.00 32.09 4.37
16 17 9.810545 TTCTACAATACGTCAATGACATGATAA 57.189 29.630 14.24 2.46 32.09 1.75
17 18 9.981114 ATTCTACAATACGTCAATGACATGATA 57.019 29.630 14.24 0.63 32.09 2.15
20 21 8.603181 TCAATTCTACAATACGTCAATGACATG 58.397 33.333 14.24 8.70 32.09 3.21
21 22 8.716646 TCAATTCTACAATACGTCAATGACAT 57.283 30.769 14.24 0.00 32.09 3.06
52 53 3.375699 AGTCTACACCTTGTGGATAGGG 58.624 50.000 0.00 0.00 39.99 3.53
58 59 4.281182 ACAAGAGTAGTCTACACCTTGTGG 59.719 45.833 29.84 16.82 44.85 4.17
61 62 5.707242 TCACAAGAGTAGTCTACACCTTG 57.293 43.478 26.67 26.67 42.24 3.61
64 65 6.586844 GTCAAATCACAAGAGTAGTCTACACC 59.413 42.308 12.54 3.89 30.45 4.16
79 81 3.573538 CCAAACAGGATGGTCAAATCACA 59.426 43.478 0.00 0.00 27.21 3.58
82 84 2.562298 TGCCAAACAGGATGGTCAAATC 59.438 45.455 0.00 0.00 27.21 2.17
91 93 1.686355 TTGAACGTGCCAAACAGGAT 58.314 45.000 0.00 0.00 41.22 3.24
93 95 1.336440 TGATTGAACGTGCCAAACAGG 59.664 47.619 7.57 0.00 40.08 4.00
105 107 6.017400 ACATGTTGACCATCTTGATTGAAC 57.983 37.500 0.00 0.00 0.00 3.18
120 122 3.003171 CCACATTGTTGTCGACATGTTGA 59.997 43.478 20.80 11.98 38.26 3.18
137 139 7.399765 TCCATTTTCTCCAATGTTATTCCACAT 59.600 33.333 0.00 0.00 39.17 3.21
141 143 9.750125 GTAATCCATTTTCTCCAATGTTATTCC 57.250 33.333 0.00 0.00 32.95 3.01
153 155 6.424032 ACTACCCAAGGTAATCCATTTTCTC 58.576 40.000 0.00 0.00 37.76 2.87
173 175 6.650427 ACTTCAAAATGGAAAAGGGACTAC 57.350 37.500 0.00 0.00 38.49 2.73
174 176 7.780745 TGTTACTTCAAAATGGAAAAGGGACTA 59.219 33.333 0.00 0.00 38.49 2.59
176 178 6.811954 TGTTACTTCAAAATGGAAAAGGGAC 58.188 36.000 0.00 0.00 0.00 4.46
177 179 7.269316 GTTGTTACTTCAAAATGGAAAAGGGA 58.731 34.615 0.00 0.00 0.00 4.20
178 180 6.481976 GGTTGTTACTTCAAAATGGAAAAGGG 59.518 38.462 0.00 0.00 0.00 3.95
185 187 7.629130 CAACATTGGTTGTTACTTCAAAATGG 58.371 34.615 0.00 0.00 46.90 3.16
220 222 2.212652 CGGATGCAGTGCAGCTATAAA 58.787 47.619 30.41 1.25 44.90 1.40
236 238 1.945819 GCCATAACATCATCGCCGGAT 60.946 52.381 5.05 0.00 0.00 4.18
264 266 2.100418 GGGCTTCTCCAAGAAATGATGC 59.900 50.000 0.00 0.00 33.19 3.91
265 267 3.629087 AGGGCTTCTCCAAGAAATGATG 58.371 45.455 0.00 0.00 33.19 3.07
266 268 4.264083 TGAAGGGCTTCTCCAAGAAATGAT 60.264 41.667 0.00 0.00 40.14 2.45
273 275 3.077484 TGAATGAAGGGCTTCTCCAAG 57.923 47.619 0.00 0.00 40.14 3.61
293 295 4.161377 GGTCCTTTCTCTAGCAGACTCATT 59.839 45.833 0.00 0.00 0.00 2.57
294 296 3.704061 GGTCCTTTCTCTAGCAGACTCAT 59.296 47.826 0.00 0.00 0.00 2.90
297 299 3.176924 TGGTCCTTTCTCTAGCAGACT 57.823 47.619 0.00 0.00 0.00 3.24
301 303 4.287067 AGTCAAATGGTCCTTTCTCTAGCA 59.713 41.667 0.00 0.00 0.00 3.49
341 343 5.393027 GCTTATCAAGAATCTCCCGCAAAAA 60.393 40.000 0.00 0.00 0.00 1.94
342 344 4.096382 GCTTATCAAGAATCTCCCGCAAAA 59.904 41.667 0.00 0.00 0.00 2.44
343 345 3.627577 GCTTATCAAGAATCTCCCGCAAA 59.372 43.478 0.00 0.00 0.00 3.68
344 346 3.118261 AGCTTATCAAGAATCTCCCGCAA 60.118 43.478 0.00 0.00 0.00 4.85
345 347 2.435805 AGCTTATCAAGAATCTCCCGCA 59.564 45.455 0.00 0.00 0.00 5.69
346 348 3.118905 AGCTTATCAAGAATCTCCCGC 57.881 47.619 0.00 0.00 0.00 6.13
347 349 5.586243 TGAAAAGCTTATCAAGAATCTCCCG 59.414 40.000 0.00 0.00 0.00 5.14
348 350 7.396540 TTGAAAAGCTTATCAAGAATCTCCC 57.603 36.000 0.00 0.00 32.14 4.30
349 351 8.908172 CTTTGAAAAGCTTATCAAGAATCTCC 57.092 34.615 0.00 0.00 36.93 3.71
406 409 1.723870 GTTCATGAGATGCACCGGC 59.276 57.895 0.00 0.00 41.68 6.13
407 410 1.431488 CCGTTCATGAGATGCACCGG 61.431 60.000 0.00 0.00 0.00 5.28
408 411 0.740868 ACCGTTCATGAGATGCACCG 60.741 55.000 0.00 0.00 0.00 4.94
419 422 1.855513 TCGTTCACGAAACCGTTCAT 58.144 45.000 0.00 0.00 46.30 2.57
436 439 3.868757 TTCTGGATGGAGTAGTTGTCG 57.131 47.619 0.00 0.00 0.00 4.35
439 442 9.703892 CTAGAAATATTCTGGATGGAGTAGTTG 57.296 37.037 2.94 0.00 40.34 3.16
523 527 9.861138 GAGATCGAATGATACTTTGATTTTCTG 57.139 33.333 0.00 0.00 34.09 3.02
531 535 7.920151 ACAGAGAAGAGATCGAATGATACTTTG 59.080 37.037 0.00 0.00 34.03 2.77
555 560 9.755804 CATCTTAAGCTTTGTATATGAGAGACA 57.244 33.333 3.20 0.00 0.00 3.41
621 626 5.070981 ACATACAATGATACACAGGCTAGCT 59.929 40.000 15.72 0.00 0.00 3.32
622 627 5.178252 CACATACAATGATACACAGGCTAGC 59.822 44.000 6.04 6.04 0.00 3.42
623 628 6.201615 CACACATACAATGATACACAGGCTAG 59.798 42.308 0.00 0.00 0.00 3.42
624 629 6.048509 CACACATACAATGATACACAGGCTA 58.951 40.000 0.00 0.00 0.00 3.93
628 633 5.065090 CCCACACACATACAATGATACACAG 59.935 44.000 0.00 0.00 0.00 3.66
638 643 3.898741 TGTCTCTACCCACACACATACAA 59.101 43.478 0.00 0.00 0.00 2.41
645 650 0.685097 GCCTTGTCTCTACCCACACA 59.315 55.000 0.00 0.00 0.00 3.72
694 878 2.294791 CACCGGACACTGGCAATTTTTA 59.705 45.455 9.46 0.00 0.00 1.52
733 917 2.636893 CTGAGATTCCTCTATGGTGGGG 59.363 54.545 0.00 0.00 40.10 4.96
741 925 6.497259 AGTGGTTTGTTACTGAGATTCCTCTA 59.503 38.462 0.00 0.00 40.10 2.43
812 996 3.942748 GTGAAAGGGACACTTGTACAACA 59.057 43.478 3.59 0.00 39.96 3.33
924 1108 1.680735 CGAACTGATGAGAGGAGAGGG 59.319 57.143 0.00 0.00 0.00 4.30
944 1128 3.489398 CGTAGAGATGAAGGTACACAGCC 60.489 52.174 0.00 0.00 0.00 4.85
953 1137 1.614413 GCTACCCCGTAGAGATGAAGG 59.386 57.143 3.00 0.00 38.29 3.46
968 1152 0.249489 CGGATGTGCCTACTGCTACC 60.249 60.000 0.00 0.00 42.00 3.18
976 1160 0.912487 AGGGGAAACGGATGTGCCTA 60.912 55.000 0.00 0.00 0.00 3.93
982 1166 2.292267 CATCTTCAGGGGAAACGGATG 58.708 52.381 0.00 0.00 31.23 3.51
983 1167 1.916181 ACATCTTCAGGGGAAACGGAT 59.084 47.619 0.00 0.00 31.35 4.18
984 1168 1.358152 ACATCTTCAGGGGAAACGGA 58.642 50.000 0.00 0.00 31.35 4.69
985 1169 3.118408 TGATACATCTTCAGGGGAAACGG 60.118 47.826 0.00 0.00 31.35 4.44
986 1170 3.871594 GTGATACATCTTCAGGGGAAACG 59.128 47.826 0.00 0.00 31.35 3.60
1159 1343 1.739371 GCCGCCGAAGAAGTACTCAAT 60.739 52.381 0.00 0.00 0.00 2.57
1267 1454 2.263540 GTACGCATCGGTGGTGGT 59.736 61.111 0.00 0.00 0.00 4.16
1273 1460 2.897972 GGGAAGGTACGCATCGGT 59.102 61.111 0.00 0.00 0.00 4.69
1284 1471 3.474570 CTCTGAGGGCCGGGAAGG 61.475 72.222 2.18 0.00 44.97 3.46
1287 1474 4.779733 GTCCTCTGAGGGCCGGGA 62.780 72.222 23.00 0.14 32.63 5.14
1294 1481 1.935327 GACGAACCGGTCCTCTGAGG 61.935 65.000 17.84 17.84 36.46 3.86
1295 1482 1.241990 TGACGAACCGGTCCTCTGAG 61.242 60.000 8.04 0.00 36.07 3.35
1298 1488 1.321074 GGATGACGAACCGGTCCTCT 61.321 60.000 8.04 0.00 36.07 3.69
1314 1504 0.250727 CAACACCGAACACCAGGGAT 60.251 55.000 0.00 0.00 0.00 3.85
1359 1549 4.704833 GAGCACTGGAAGCCGCCA 62.705 66.667 0.00 0.00 36.40 5.69
1575 1765 3.806316 ACGAAGTGCCACGAATTAAAG 57.194 42.857 0.00 0.00 42.51 1.85
2143 2334 6.758886 TGAACGTACATGCATGATATGTGTAA 59.241 34.615 32.75 16.05 39.03 2.41
2148 2339 5.912360 ACTGAACGTACATGCATGATATG 57.088 39.130 32.75 24.15 0.00 1.78
2171 2363 9.803507 TTGGCATATATCTTGATTCTTGAGAAT 57.196 29.630 5.95 5.95 46.54 2.40
2197 2389 8.021898 TCAAGAAAACCATCATCCTTCTTTTT 57.978 30.769 0.00 0.00 34.84 1.94
2212 2404 8.829612 ACATCAACAAATGAAATCAAGAAAACC 58.170 29.630 0.00 0.00 42.54 3.27
2255 2449 2.353109 GCTTGCAAAAACTGGAGATCCC 60.353 50.000 0.00 0.00 34.29 3.85
2258 2452 1.336240 GCGCTTGCAAAAACTGGAGAT 60.336 47.619 0.00 0.00 38.92 2.75
2320 2514 3.193263 CATGACAAGATAACGAGCTGCT 58.807 45.455 0.00 0.00 0.00 4.24
2321 2515 2.286294 CCATGACAAGATAACGAGCTGC 59.714 50.000 0.00 0.00 0.00 5.25
2322 2516 2.868583 CCCATGACAAGATAACGAGCTG 59.131 50.000 0.00 0.00 0.00 4.24
2327 2521 2.221749 CGCATCCCATGACAAGATAACG 59.778 50.000 0.00 0.00 0.00 3.18
2335 2529 3.558931 ATAGAAACGCATCCCATGACA 57.441 42.857 0.00 0.00 0.00 3.58
2340 2534 4.085357 AGCAATATAGAAACGCATCCCA 57.915 40.909 0.00 0.00 0.00 4.37
2341 2535 4.093556 GCTAGCAATATAGAAACGCATCCC 59.906 45.833 10.63 0.00 0.00 3.85
2381 2586 6.004574 AGTACTGATAGACGCAGATATCCAA 58.995 40.000 0.00 0.00 36.86 3.53
2393 2598 9.562583 CAAAGAACTACTGAAGTACTGATAGAC 57.437 37.037 0.00 0.00 37.50 2.59
2422 2627 9.187455 GATCAAAACGTCCAAATTAAAGCTAAA 57.813 29.630 0.00 0.00 0.00 1.85
2423 2628 7.810759 GGATCAAAACGTCCAAATTAAAGCTAA 59.189 33.333 0.00 0.00 34.57 3.09
2424 2629 7.040340 TGGATCAAAACGTCCAAATTAAAGCTA 60.040 33.333 0.00 0.00 41.36 3.32
2425 2630 6.156519 GGATCAAAACGTCCAAATTAAAGCT 58.843 36.000 0.00 0.00 34.57 3.74
2426 2631 5.923684 TGGATCAAAACGTCCAAATTAAAGC 59.076 36.000 0.00 0.00 41.36 3.51
2465 2670 9.988815 AGATACCAAAACACTCAGACATATATC 57.011 33.333 0.00 0.00 0.00 1.63
2740 2946 6.929049 TGTTGTAATTAAGCTCCTATCCATCG 59.071 38.462 0.00 0.00 0.00 3.84
2742 2948 6.998673 GGTGTTGTAATTAAGCTCCTATCCAT 59.001 38.462 0.00 0.00 0.00 3.41
2933 3139 4.998671 TGAACAAATTCAGGCAAAGACA 57.001 36.364 0.00 0.00 40.01 3.41
3006 3213 5.371115 AAATAATTGTGACAAGACACCGG 57.629 39.130 3.74 0.00 39.69 5.28
3041 3250 1.380785 CATTCCCAGTGCCCTGCAT 60.381 57.895 0.00 0.00 41.91 3.96
3043 3252 1.187567 AAACATTCCCAGTGCCCTGC 61.188 55.000 0.00 0.00 37.38 4.85
3045 3254 2.807676 CTTAAACATTCCCAGTGCCCT 58.192 47.619 0.00 0.00 0.00 5.19
3047 3258 1.892474 TGCTTAAACATTCCCAGTGCC 59.108 47.619 0.00 0.00 0.00 5.01
3064 3275 9.678260 GAGGAATATTAGGAAATGTATGATGCT 57.322 33.333 0.00 0.00 0.00 3.79
3104 3323 8.736244 TGTGCTAAAGGGAAATAAACTATTGTC 58.264 33.333 0.00 0.00 0.00 3.18
3110 3329 8.879427 ACTTATGTGCTAAAGGGAAATAAACT 57.121 30.769 0.00 0.00 27.54 2.66
3111 3330 9.923143 AAACTTATGTGCTAAAGGGAAATAAAC 57.077 29.630 0.00 0.00 27.54 2.01
3113 3332 9.528489 AGAAACTTATGTGCTAAAGGGAAATAA 57.472 29.630 0.00 0.00 0.00 1.40
3114 3333 8.956426 CAGAAACTTATGTGCTAAAGGGAAATA 58.044 33.333 0.00 0.00 0.00 1.40
3115 3334 7.669722 TCAGAAACTTATGTGCTAAAGGGAAAT 59.330 33.333 0.00 0.00 0.00 2.17
3116 3335 7.001674 TCAGAAACTTATGTGCTAAAGGGAAA 58.998 34.615 0.00 0.00 0.00 3.13
3119 4703 6.173339 TCTCAGAAACTTATGTGCTAAAGGG 58.827 40.000 0.00 0.00 0.00 3.95
3121 4705 7.816995 ACTCTCTCAGAAACTTATGTGCTAAAG 59.183 37.037 0.00 0.00 0.00 1.85
3146 4730 2.393271 ACATGGTTAGCTCAGCTCAC 57.607 50.000 0.00 1.08 40.44 3.51
3236 5148 9.709495 CATTAATCTTTCTTTGGGAAACATTGA 57.291 29.630 0.00 0.00 38.81 2.57


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

AutoCloner maintained by Alex Coulton.