Multiple sequence alignment - TraesCS6A01G143500

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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 TraesCS6A01G143500 chr6A 100.000 1477 0 0 1 1477 119789732 119788256 0.000000e+00 2728
1 TraesCS6A01G143500 chr6A 100.000 440 0 0 1895 2334 119787838 119787399 0.000000e+00 813
2 TraesCS6A01G143500 chr6B 90.200 1500 59 43 12 1477 184362213 184360768 0.000000e+00 1875
3 TraesCS6A01G143500 chr6B 88.102 353 34 3 1983 2334 184359196 184358851 1.670000e-111 412
4 TraesCS6A01G143500 chr6B 84.163 221 16 8 1137 1357 184324091 184324292 1.830000e-46 196
5 TraesCS6A01G143500 chr7D 85.915 71 9 1 2203 2273 520395874 520395805 8.940000e-10 75


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 TraesCS6A01G143500 chr6A 119787399 119789732 2333 True 1770.5 2728 100.000 1 2334 2 chr6A.!!$R1 2333
1 TraesCS6A01G143500 chr6B 184358851 184362213 3362 True 1143.5 1875 89.151 12 2334 2 chr6B.!!$R1 2322

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
763 794 0.1792 CGTAAATTGCGGCAGTGGAC 60.179 55.0 1.67 1.5 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 3298 0.252239 GGGAGGGGGCATGAAGTTTT 60.252 55.0 0.0 0.0 0.0 2.43 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
32 33 1.294780 CAGTCACCAGGTCAGGCTC 59.705 63.158 0.00 0.00 0.00 4.70
137 139 8.211629 GGCTTAAGGAGTCAGAAATCCTATTAA 58.788 37.037 4.29 2.74 45.39 1.40
138 140 9.267084 GCTTAAGGAGTCAGAAATCCTATTAAG 57.733 37.037 4.29 14.07 45.39 1.85
143 145 9.138596 AGGAGTCAGAAATCCTATTAAGTACTC 57.861 37.037 0.00 0.00 44.28 2.59
144 146 9.138596 GGAGTCAGAAATCCTATTAAGTACTCT 57.861 37.037 0.00 0.00 32.51 3.24
231 233 3.664107 TCCTACTAGTTGCTTGTGCTTG 58.336 45.455 0.00 0.00 40.48 4.01
275 278 4.201822 GCTTGTGCTTATTAGTTCCTTCGG 60.202 45.833 0.00 0.00 36.03 4.30
279 282 6.646267 TGTGCTTATTAGTTCCTTCGGTTAT 58.354 36.000 0.00 0.00 0.00 1.89
296 299 6.403049 TCGGTTATCTTTTGTGCTCTTCATA 58.597 36.000 0.00 0.00 0.00 2.15
297 300 6.876789 TCGGTTATCTTTTGTGCTCTTCATAA 59.123 34.615 0.00 0.00 0.00 1.90
300 303 9.294030 GGTTATCTTTTGTGCTCTTCATAATTG 57.706 33.333 0.00 0.00 0.00 2.32
306 311 9.252962 CTTTTGTGCTCTTCATAATTGTTCTTT 57.747 29.630 0.00 0.00 0.00 2.52
321 326 8.437360 AATTGTTCTTTCTTTTCCATTGAACC 57.563 30.769 0.00 0.00 33.57 3.62
323 328 5.358442 TGTTCTTTCTTTTCCATTGAACCGA 59.642 36.000 0.00 0.00 33.57 4.69
355 360 2.665519 GCGACATGTGTTGACCATTGTC 60.666 50.000 1.15 0.00 42.12 3.18
359 364 5.122239 CGACATGTGTTGACCATTGTCTATT 59.878 40.000 1.15 0.00 42.28 1.73
363 368 4.518590 TGTGTTGACCATTGTCTATTGGTG 59.481 41.667 0.00 0.00 46.14 4.17
365 370 5.415701 GTGTTGACCATTGTCTATTGGTGAT 59.584 40.000 0.00 0.00 46.14 3.06
381 386 1.559682 GTGATTTGGTGAGCCCCTAGA 59.440 52.381 0.00 0.00 0.00 2.43
382 387 1.839994 TGATTTGGTGAGCCCCTAGAG 59.160 52.381 0.00 0.00 0.00 2.43
383 388 1.141858 GATTTGGTGAGCCCCTAGAGG 59.858 57.143 0.00 0.00 0.00 3.69
393 398 4.798682 CCTAGAGGGCCCGGGTGT 62.799 72.222 24.63 6.74 0.00 4.16
394 399 2.281091 CTAGAGGGCCCGGGTGTA 59.719 66.667 24.63 4.12 0.00 2.90
395 400 1.382146 CTAGAGGGCCCGGGTGTAA 60.382 63.158 24.63 2.09 0.00 2.41
396 401 1.382146 TAGAGGGCCCGGGTGTAAG 60.382 63.158 24.63 0.00 0.00 2.34
397 402 4.484872 GAGGGCCCGGGTGTAAGC 62.485 72.222 24.63 5.87 0.00 3.09
410 415 3.744660 GGTGTAAGCCATAATGCTAGCT 58.255 45.455 17.23 0.00 41.80 3.32
411 416 4.894784 GGTGTAAGCCATAATGCTAGCTA 58.105 43.478 17.23 0.60 41.80 3.32
417 422 5.398603 AGCCATAATGCTAGCTAGTGTAG 57.601 43.478 21.62 7.65 40.56 2.74
433 438 2.749621 GTGTAGGCCAAACTGAATCCTG 59.250 50.000 5.01 0.00 0.00 3.86
489 500 4.601019 AGTTCAAGTTTTCGAGCATTGTG 58.399 39.130 0.00 0.00 0.00 3.33
517 528 8.808529 CAAGAACGATCGAACTTGATAATTAGT 58.191 33.333 32.64 11.11 41.16 2.24
554 565 3.963428 ATGGTTGTAGAAGAGCTCGTT 57.037 42.857 8.37 2.98 0.00 3.85
670 693 2.403252 AAAACGATGGTAGCCCTCAG 57.597 50.000 0.00 0.00 0.00 3.35
677 700 1.861982 TGGTAGCCCTCAGGTTAGAC 58.138 55.000 0.00 0.00 34.57 2.59
723 754 4.125703 ACTCACAGCAACAAAGAAGAGAG 58.874 43.478 0.00 0.00 0.00 3.20
732 763 2.224646 ACAAAGAAGAGAGGAACCAGGC 60.225 50.000 0.00 0.00 0.00 4.85
763 794 0.179200 CGTAAATTGCGGCAGTGGAC 60.179 55.000 1.67 1.50 0.00 4.02
789 820 6.069994 TGCATATCCTGATTTGAGGCATTAA 58.930 36.000 2.32 0.00 32.51 1.40
809 840 9.132521 GCATTAAGTAATGGCATTTATGATGTC 57.867 33.333 19.21 9.39 42.46 3.06
814 845 7.810658 AGTAATGGCATTTATGATGTCGATTC 58.189 34.615 19.21 0.00 0.00 2.52
816 847 7.984422 AATGGCATTTATGATGTCGATTCTA 57.016 32.000 6.96 0.00 0.00 2.10
844 875 3.248602 GGAAAGATAAGGCGCATGTACTG 59.751 47.826 10.83 0.00 0.00 2.74
895 928 7.739995 TCCATAATATCTGAGGTATTGAGGG 57.260 40.000 8.20 6.83 0.00 4.30
896 929 7.487338 TCCATAATATCTGAGGTATTGAGGGA 58.513 38.462 8.20 8.80 0.00 4.20
897 930 7.621285 TCCATAATATCTGAGGTATTGAGGGAG 59.379 40.741 8.20 0.00 0.00 4.30
898 931 7.147585 CCATAATATCTGAGGTATTGAGGGAGG 60.148 44.444 8.20 0.00 0.00 4.30
943 976 3.576550 CTCCTAGCTAGACCCATTTCTCC 59.423 52.174 22.70 0.00 0.00 3.71
955 988 1.852157 ATTTCTCCTCGCCCCAGCAA 61.852 55.000 0.00 0.00 39.83 3.91
959 992 3.058160 CCTCGCCCCAGCAACAAG 61.058 66.667 0.00 0.00 39.83 3.16
961 994 2.032528 TCGCCCCAGCAACAAGAG 59.967 61.111 0.00 0.00 39.83 2.85
966 999 1.986882 CCCCAGCAACAAGAGTTTCT 58.013 50.000 0.00 0.00 35.28 2.52
979 1012 3.217626 AGAGTTTCTTTCACCTGCTTGG 58.782 45.455 0.00 0.00 42.93 3.61
1023 1056 4.043200 GCCAAGGTTGCAGCGACC 62.043 66.667 23.17 23.17 38.16 4.79
1066 1099 1.341383 CCTTTGCTTATGGTGAGCCCT 60.341 52.381 0.00 0.00 39.38 5.19
1069 1102 2.128771 TGCTTATGGTGAGCCCTTTC 57.871 50.000 0.00 0.00 39.38 2.62
1073 1106 1.213296 TATGGTGAGCCCTTTCTCCC 58.787 55.000 0.00 0.00 31.28 4.30
1080 1113 1.286257 GAGCCCTTTCTCCCCTGAAAT 59.714 52.381 0.00 0.00 35.68 2.17
1097 1130 6.703165 CCCTGAAATTTCTTATTAAGCATGGC 59.297 38.462 18.64 0.00 0.00 4.40
1131 1164 7.549488 TCTTAACTTCTTAAGCTGATAACTGGC 59.451 37.037 0.00 0.00 39.12 4.85
1132 1165 4.184629 ACTTCTTAAGCTGATAACTGGCG 58.815 43.478 0.00 0.00 0.00 5.69
1133 1166 3.179443 TCTTAAGCTGATAACTGGCGG 57.821 47.619 0.00 0.00 0.00 6.13
1134 1167 2.500098 TCTTAAGCTGATAACTGGCGGT 59.500 45.455 0.00 0.00 0.00 5.68
1135 1168 2.309528 TAAGCTGATAACTGGCGGTG 57.690 50.000 0.00 0.00 0.00 4.94
1136 1169 0.613260 AAGCTGATAACTGGCGGTGA 59.387 50.000 0.00 0.00 0.00 4.02
1137 1170 0.108138 AGCTGATAACTGGCGGTGAC 60.108 55.000 0.00 0.00 0.00 3.67
1264 1297 1.207488 AAGGTGGATACTGCAGCCCA 61.207 55.000 15.27 15.90 36.87 5.36
1316 1349 2.822764 AGTGTCACGACCAAACTCTTC 58.177 47.619 0.00 0.00 0.00 2.87
1353 1386 1.227380 GATGTACGGGAGCCAGCAG 60.227 63.158 0.00 0.00 0.00 4.24
1372 1406 5.574443 CAGCAGGCTTTAATTAGCAGAAAAC 59.426 40.000 2.76 0.00 43.02 2.43
1376 1410 4.864806 GGCTTTAATTAGCAGAAAACTGGC 59.135 41.667 2.76 0.00 43.02 4.85
1382 1416 2.806608 AGCAGAAAACTGGCAATGTG 57.193 45.000 0.00 0.00 0.00 3.21
1423 1457 4.859245 GGAATGAATTCGCAGTTTTTCCTC 59.141 41.667 0.04 0.00 37.67 3.71
1424 1458 5.335976 GGAATGAATTCGCAGTTTTTCCTCT 60.336 40.000 0.04 0.00 37.67 3.69
1425 1459 4.749245 TGAATTCGCAGTTTTTCCTCTC 57.251 40.909 0.04 0.00 0.00 3.20
1426 1460 4.389374 TGAATTCGCAGTTTTTCCTCTCT 58.611 39.130 0.04 0.00 0.00 3.10
1427 1461 4.452455 TGAATTCGCAGTTTTTCCTCTCTC 59.548 41.667 0.04 0.00 0.00 3.20
1428 1462 3.753294 TTCGCAGTTTTTCCTCTCTCT 57.247 42.857 0.00 0.00 0.00 3.10
1918 1952 3.339141 GTGGGCTCTTTCTTCTCGAATT 58.661 45.455 0.00 0.00 0.00 2.17
1938 1972 2.419457 AGATGATGCCCTCTCATCCT 57.581 50.000 9.12 0.00 46.67 3.24
1944 3298 3.523157 TGATGCCCTCTCATCCTGTTTTA 59.477 43.478 1.84 0.00 41.54 1.52
1953 3307 7.177392 CCCTCTCATCCTGTTTTAAAACTTCAT 59.823 37.037 26.76 14.94 39.59 2.57
1954 3308 8.025445 CCTCTCATCCTGTTTTAAAACTTCATG 58.975 37.037 26.76 22.74 39.59 3.07
1960 3314 3.970640 TGTTTTAAAACTTCATGCCCCCT 59.029 39.130 26.76 0.00 39.59 4.79
1992 3365 4.430765 CCGTCAACCGACTCCCCG 62.431 72.222 0.00 0.00 40.23 5.73
2016 3389 2.943345 CTGTGACGCACCTTGTCGC 61.943 63.158 7.38 0.02 44.90 5.19
2099 3472 2.435938 GCACCGGATTCGCTCCAA 60.436 61.111 9.46 0.00 45.24 3.53
2104 3477 2.582436 GGATTCGCTCCAACCCGA 59.418 61.111 0.00 0.00 44.26 5.14
2106 3479 1.218316 GATTCGCTCCAACCCGACT 59.782 57.895 0.00 0.00 32.60 4.18
2130 3503 3.939837 CTGCCGTCGGAGCACATGT 62.940 63.158 17.49 0.00 36.01 3.21
2167 3540 4.060667 CCCCCGGCCAAATCCTGT 62.061 66.667 2.24 0.00 0.00 4.00
2168 3541 2.755469 CCCCGGCCAAATCCTGTG 60.755 66.667 2.24 0.00 0.00 3.66
2169 3542 2.755469 CCCGGCCAAATCCTGTGG 60.755 66.667 2.24 0.00 39.33 4.17
2243 3616 5.232161 CGAAATGTCGCAAAGGTTAAAAC 57.768 39.130 0.00 0.00 41.08 2.43
2248 3621 8.649973 AAATGTCGCAAAGGTTAAAACAAATA 57.350 26.923 0.00 0.00 0.00 1.40
2249 3622 8.649973 AATGTCGCAAAGGTTAAAACAAATAA 57.350 26.923 0.00 0.00 0.00 1.40
2292 3665 6.323996 TCTTTTCTCATGTCCCATACGAGTAT 59.676 38.462 0.00 0.00 0.00 2.12
2293 3666 5.707242 TTCTCATGTCCCATACGAGTATC 57.293 43.478 0.00 0.00 0.00 2.24
2295 3668 4.762251 TCTCATGTCCCATACGAGTATCAG 59.238 45.833 0.00 0.00 33.17 2.90
2330 3704 4.864806 TGACGTGCATTTCTAGTCTTGATC 59.135 41.667 0.00 0.00 33.40 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.314440 TGACCTGGTGACTGCCGC 62.314 66.667 2.82 0.00 0.00 6.53
32 33 2.356553 CACACCACCACGTACGGG 60.357 66.667 21.06 16.64 0.00 5.28
139 141 9.916360 TGTGACTGAGAAATATAAGGTAGAGTA 57.084 33.333 0.00 0.00 0.00 2.59
140 142 8.824756 TGTGACTGAGAAATATAAGGTAGAGT 57.175 34.615 0.00 0.00 0.00 3.24
143 145 7.923344 CCACTGTGACTGAGAAATATAAGGTAG 59.077 40.741 9.86 0.00 0.00 3.18
144 146 7.618117 TCCACTGTGACTGAGAAATATAAGGTA 59.382 37.037 9.86 0.00 0.00 3.08
145 147 6.440647 TCCACTGTGACTGAGAAATATAAGGT 59.559 38.462 9.86 0.00 0.00 3.50
146 148 6.758886 GTCCACTGTGACTGAGAAATATAAGG 59.241 42.308 9.86 0.00 32.39 2.69
147 149 7.551585 AGTCCACTGTGACTGAGAAATATAAG 58.448 38.462 9.86 0.00 43.80 1.73
148 150 7.482169 AGTCCACTGTGACTGAGAAATATAA 57.518 36.000 9.86 0.00 43.80 0.98
275 278 9.846248 ACAATTATGAAGAGCACAAAAGATAAC 57.154 29.630 0.00 0.00 0.00 1.89
279 282 8.169977 AGAACAATTATGAAGAGCACAAAAGA 57.830 30.769 0.00 0.00 0.00 2.52
296 299 7.224557 CGGTTCAATGGAAAAGAAAGAACAATT 59.775 33.333 0.00 0.00 36.52 2.32
297 300 6.701400 CGGTTCAATGGAAAAGAAAGAACAAT 59.299 34.615 0.00 0.00 36.52 2.71
300 303 5.827666 TCGGTTCAATGGAAAAGAAAGAAC 58.172 37.500 0.00 0.00 34.13 3.01
306 311 5.070001 ACTCAATCGGTTCAATGGAAAAGA 58.930 37.500 0.00 0.00 34.13 2.52
331 336 2.173382 GTCAACACATGTCGCGCC 59.827 61.111 0.00 0.00 0.00 6.53
355 360 2.689983 GGGCTCACCAAATCACCAATAG 59.310 50.000 0.00 0.00 39.85 1.73
359 364 1.076549 GGGGCTCACCAAATCACCA 59.923 57.895 0.00 0.00 42.91 4.17
363 368 1.141858 CCTCTAGGGGCTCACCAAATC 59.858 57.143 0.00 0.00 42.91 2.17
365 370 2.696864 CCTCTAGGGGCTCACCAAA 58.303 57.895 0.00 0.00 42.91 3.28
383 388 2.273588 TTATGGCTTACACCCGGGCC 62.274 60.000 24.08 15.94 44.31 5.80
384 389 0.179001 ATTATGGCTTACACCCGGGC 60.179 55.000 24.08 4.66 0.00 6.13
385 390 1.604604 CATTATGGCTTACACCCGGG 58.395 55.000 22.25 22.25 0.00 5.73
386 391 0.951558 GCATTATGGCTTACACCCGG 59.048 55.000 0.00 0.00 0.00 5.73
387 392 1.967319 AGCATTATGGCTTACACCCG 58.033 50.000 0.00 0.00 42.71 5.28
389 394 3.744660 AGCTAGCATTATGGCTTACACC 58.255 45.455 18.83 0.00 42.71 4.16
391 396 5.070446 ACACTAGCTAGCATTATGGCTTACA 59.930 40.000 20.91 0.00 42.71 2.41
392 397 5.542779 ACACTAGCTAGCATTATGGCTTAC 58.457 41.667 20.91 0.00 42.71 2.34
393 398 5.808366 ACACTAGCTAGCATTATGGCTTA 57.192 39.130 20.91 0.00 42.71 3.09
394 399 4.696479 ACACTAGCTAGCATTATGGCTT 57.304 40.909 20.91 0.00 42.71 4.35
396 401 4.499183 CCTACACTAGCTAGCATTATGGC 58.501 47.826 20.91 0.00 0.00 4.40
397 402 4.499183 GCCTACACTAGCTAGCATTATGG 58.501 47.826 20.91 15.18 0.00 2.74
398 403 4.021104 TGGCCTACACTAGCTAGCATTATG 60.021 45.833 20.91 13.07 0.00 1.90
399 404 4.160329 TGGCCTACACTAGCTAGCATTAT 58.840 43.478 20.91 4.54 0.00 1.28
400 405 3.572642 TGGCCTACACTAGCTAGCATTA 58.427 45.455 20.91 8.31 0.00 1.90
401 406 2.398588 TGGCCTACACTAGCTAGCATT 58.601 47.619 20.91 7.56 0.00 3.56
402 407 2.088104 TGGCCTACACTAGCTAGCAT 57.912 50.000 20.91 11.33 0.00 3.79
403 408 1.860641 TTGGCCTACACTAGCTAGCA 58.139 50.000 20.91 5.80 0.00 3.49
404 409 2.168728 AGTTTGGCCTACACTAGCTAGC 59.831 50.000 20.91 6.62 0.00 3.42
405 410 3.447586 TCAGTTTGGCCTACACTAGCTAG 59.552 47.826 19.44 19.44 0.00 3.42
406 411 3.437213 TCAGTTTGGCCTACACTAGCTA 58.563 45.455 3.32 0.00 0.00 3.32
407 412 2.257207 TCAGTTTGGCCTACACTAGCT 58.743 47.619 3.32 0.00 0.00 3.32
408 413 2.762535 TCAGTTTGGCCTACACTAGC 57.237 50.000 3.32 0.00 0.00 3.42
409 414 4.080863 AGGATTCAGTTTGGCCTACACTAG 60.081 45.833 3.32 0.00 0.00 2.57
410 415 3.844211 AGGATTCAGTTTGGCCTACACTA 59.156 43.478 3.32 0.00 0.00 2.74
411 416 2.644798 AGGATTCAGTTTGGCCTACACT 59.355 45.455 3.32 0.00 0.00 3.55
417 422 0.244721 GTGCAGGATTCAGTTTGGCC 59.755 55.000 0.00 0.00 0.00 5.36
471 482 2.053627 GCCACAATGCTCGAAAACTTG 58.946 47.619 0.00 0.00 0.00 3.16
489 500 2.066262 TCAAGTTCGATCGTTCTTGCC 58.934 47.619 30.16 11.26 37.68 4.52
569 580 3.517612 ACACTTGAGTACTGGTACCCAT 58.482 45.455 10.07 0.00 36.75 4.00
575 586 4.100963 TCATGTCAACACTTGAGTACTGGT 59.899 41.667 0.00 0.00 41.01 4.00
576 587 4.449068 GTCATGTCAACACTTGAGTACTGG 59.551 45.833 0.00 0.00 41.01 4.00
577 588 5.049828 TGTCATGTCAACACTTGAGTACTG 58.950 41.667 0.00 0.00 41.01 2.74
578 589 5.276461 TGTCATGTCAACACTTGAGTACT 57.724 39.130 0.00 0.00 41.01 2.73
579 590 5.466728 ACATGTCATGTCAACACTTGAGTAC 59.533 40.000 12.87 0.00 39.92 2.73
580 591 5.466393 CACATGTCATGTCAACACTTGAGTA 59.534 40.000 15.73 0.00 42.70 2.59
581 592 4.274214 CACATGTCATGTCAACACTTGAGT 59.726 41.667 15.73 0.00 42.70 3.41
582 593 4.512571 TCACATGTCATGTCAACACTTGAG 59.487 41.667 15.73 1.28 42.70 3.02
583 594 4.450053 TCACATGTCATGTCAACACTTGA 58.550 39.130 15.73 5.09 42.70 3.02
584 595 4.816786 TCACATGTCATGTCAACACTTG 57.183 40.909 15.73 2.75 42.70 3.16
670 693 2.723719 GCGTTGCCGTCGTCTAACC 61.724 63.158 0.00 0.00 36.15 2.85
677 700 3.185365 TGCTATGCGTTGCCGTCG 61.185 61.111 9.88 0.00 36.15 5.12
693 724 1.269569 TGTTGCTGTGAGTACGAGGTG 60.270 52.381 0.00 0.00 0.00 4.00
696 727 3.381045 TCTTTGTTGCTGTGAGTACGAG 58.619 45.455 0.00 0.00 0.00 4.18
723 754 2.911928 GCCTCCTAGCCTGGTTCC 59.088 66.667 0.00 0.00 0.00 3.62
732 763 2.561569 CAATTTACGTGGGCCTCCTAG 58.438 52.381 4.53 0.00 0.00 3.02
746 777 1.472082 CATGTCCACTGCCGCAATTTA 59.528 47.619 0.00 0.00 0.00 1.40
763 794 3.824443 TGCCTCAAATCAGGATATGCATG 59.176 43.478 10.16 0.00 35.20 4.06
789 820 7.663081 AGAATCGACATCATAAATGCCATTACT 59.337 33.333 0.00 0.00 0.00 2.24
809 840 5.641209 CCTTATCTTTCCAGGCATAGAATCG 59.359 44.000 0.00 0.00 0.00 3.34
869 900 9.439461 CCCTCAATACCTCAGATATTATGGATA 57.561 37.037 0.00 0.00 0.00 2.59
870 901 8.131627 TCCCTCAATACCTCAGATATTATGGAT 58.868 37.037 0.00 0.00 0.00 3.41
871 902 7.487338 TCCCTCAATACCTCAGATATTATGGA 58.513 38.462 0.00 0.00 0.00 3.41
873 904 7.634649 GCCTCCCTCAATACCTCAGATATTATG 60.635 44.444 0.00 0.00 0.00 1.90
877 910 4.100373 GCCTCCCTCAATACCTCAGATAT 58.900 47.826 0.00 0.00 0.00 1.63
895 928 3.334583 TTATAGGATGGATTGCGCCTC 57.665 47.619 4.18 0.89 32.04 4.70
896 929 3.788227 TTTATAGGATGGATTGCGCCT 57.212 42.857 4.18 0.00 34.56 5.52
897 930 5.294552 GTCTATTTATAGGATGGATTGCGCC 59.705 44.000 4.18 0.00 0.00 6.53
898 931 6.109359 AGTCTATTTATAGGATGGATTGCGC 58.891 40.000 0.00 0.00 0.00 6.09
943 976 2.032528 TCTTGTTGCTGGGGCGAG 59.967 61.111 0.00 0.00 42.25 5.03
955 988 3.891049 AGCAGGTGAAAGAAACTCTTGT 58.109 40.909 0.00 0.00 36.71 3.16
959 992 3.214328 TCCAAGCAGGTGAAAGAAACTC 58.786 45.455 0.00 0.00 39.02 3.01
961 994 3.365364 CGATCCAAGCAGGTGAAAGAAAC 60.365 47.826 0.00 0.00 39.02 2.78
966 999 2.749076 CAATCGATCCAAGCAGGTGAAA 59.251 45.455 0.00 0.00 39.02 2.69
979 1012 2.159184 TGGCAGACAGTCTCAATCGATC 60.159 50.000 0.00 0.00 0.00 3.69
1023 1056 1.681486 GGAGGAGGAAGAAGAGGGCG 61.681 65.000 0.00 0.00 0.00 6.13
1029 1062 2.246091 AGGTGAGGAGGAGGAAGAAG 57.754 55.000 0.00 0.00 0.00 2.85
1066 1099 8.749354 GCTTAATAAGAAATTTCAGGGGAGAAA 58.251 33.333 19.99 3.70 41.31 2.52
1069 1102 7.645058 TGCTTAATAAGAAATTTCAGGGGAG 57.355 36.000 19.99 10.87 0.00 4.30
1073 1106 7.267128 TGCCATGCTTAATAAGAAATTTCAGG 58.733 34.615 19.99 0.99 0.00 3.86
1080 1113 5.595542 AGATGCTGCCATGCTTAATAAGAAA 59.404 36.000 3.88 0.00 0.00 2.52
1097 1130 7.332926 TCAGCTTAAGAAGTTAAGAAGATGCTG 59.667 37.037 6.67 0.00 45.67 4.41
1129 1162 2.433318 GCTCAGTCAGTCACCGCC 60.433 66.667 0.00 0.00 0.00 6.13
1131 1164 1.080230 CCTGCTCAGTCAGTCACCG 60.080 63.158 0.00 0.00 32.32 4.94
1132 1165 1.188219 TCCCTGCTCAGTCAGTCACC 61.188 60.000 0.00 0.00 32.32 4.02
1133 1166 0.681733 TTCCCTGCTCAGTCAGTCAC 59.318 55.000 0.00 0.00 32.32 3.67
1134 1167 0.972134 CTTCCCTGCTCAGTCAGTCA 59.028 55.000 0.00 0.00 32.32 3.41
1135 1168 1.261480 TCTTCCCTGCTCAGTCAGTC 58.739 55.000 0.00 0.00 32.32 3.51
1136 1169 1.622811 CTTCTTCCCTGCTCAGTCAGT 59.377 52.381 0.00 0.00 32.32 3.41
1137 1170 1.066286 CCTTCTTCCCTGCTCAGTCAG 60.066 57.143 0.00 0.00 0.00 3.51
1264 1297 0.610232 GGCATGTGTTGAGCCTTCCT 60.610 55.000 0.00 0.00 44.92 3.36
1353 1386 4.864806 GCCAGTTTTCTGCTAATTAAAGCC 59.135 41.667 0.00 0.00 45.76 4.35
1363 1396 2.034124 ACACATTGCCAGTTTTCTGCT 58.966 42.857 0.00 0.00 45.76 4.24
1364 1397 2.514205 ACACATTGCCAGTTTTCTGC 57.486 45.000 0.00 0.00 45.76 4.26
1376 1410 6.851837 CCATTGTTATTGTTTGCAACACATTG 59.148 34.615 0.00 3.01 41.97 2.82
1382 1416 7.418840 TCATTCCATTGTTATTGTTTGCAAC 57.581 32.000 0.00 0.00 37.44 4.17
1938 1972 3.970640 AGGGGGCATGAAGTTTTAAAACA 59.029 39.130 28.03 12.04 41.30 2.83
1944 3298 0.252239 GGGAGGGGGCATGAAGTTTT 60.252 55.000 0.00 0.00 0.00 2.43
2031 3404 0.745845 CGCATCTGGAAAGGTGGGAG 60.746 60.000 0.00 0.00 0.00 4.30
2032 3405 1.299648 CGCATCTGGAAAGGTGGGA 59.700 57.895 0.00 0.00 0.00 4.37
2033 3406 1.750399 CCGCATCTGGAAAGGTGGG 60.750 63.158 0.00 0.00 0.00 4.61
2205 3578 0.878523 TTCGTCAAGCACGTTGAGGG 60.879 55.000 8.18 0.00 46.18 4.30
2207 3580 2.032894 ACATTTCGTCAAGCACGTTGAG 60.033 45.455 0.00 0.00 46.18 3.02
2292 3665 1.686587 ACGTCACACAATCTCACCTGA 59.313 47.619 0.00 0.00 0.00 3.86
2293 3666 1.794701 CACGTCACACAATCTCACCTG 59.205 52.381 0.00 0.00 0.00 4.00
2295 3668 0.512952 GCACGTCACACAATCTCACC 59.487 55.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.