Multiple sequence alignment - TraesCS5B01G098900

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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 TraesCS5B01G098900 chr5B 100.000 5299 0 0 1 5299 131313740 131319038 0.000000e+00 9786.0
1 TraesCS5B01G098900 chr5D 95.363 4507 129 33 851 5299 119000625 119005109 0.000000e+00 7092.0
2 TraesCS5B01G098900 chr5D 87.808 730 56 15 1 717 118998211 118998920 0.000000e+00 824.0
3 TraesCS5B01G098900 chr5D 87.654 81 9 1 4429 4509 119004299 119004378 5.650000e-15 93.5
4 TraesCS5B01G098900 chr5A 94.657 4230 142 37 1141 5299 129107342 129111558 0.000000e+00 6482.0
5 TraesCS5B01G098900 chr5A 90.884 735 50 8 1 724 129106263 129106991 0.000000e+00 970.0
6 TraesCS5B01G098900 chr5A 93.617 376 10 5 738 1109 129106976 129107341 2.790000e-152 549.0
7 TraesCS5B01G098900 chr5A 77.670 309 49 13 17 318 109939247 109938952 2.540000e-38 171.0
8 TraesCS5B01G098900 chr5A 87.805 82 7 3 4429 4509 129110748 129110827 5.650000e-15 93.5
9 TraesCS5B01G098900 chr6B 82.178 303 35 13 17 318 633552495 633552211 5.300000e-60 243.0
10 TraesCS5B01G098900 chr2B 79.448 326 47 14 1 318 233164154 233164467 4.160000e-51 213.0
11 TraesCS5B01G098900 chr2B 80.795 151 25 3 1518 1666 573826722 573826870 1.210000e-21 115.0
12 TraesCS5B01G098900 chr2B 86.792 53 5 2 267 318 227679337 227679286 2.060000e-04 58.4
13 TraesCS5B01G098900 chr7B 76.271 295 44 20 27 316 579443932 579443659 3.330000e-27 134.0
14 TraesCS5B01G098900 chr3B 81.203 133 21 3 187 316 204377656 204377525 2.610000e-18 104.0
15 TraesCS5B01G098900 chr3B 100.000 43 0 0 279 321 150990964 150990922 4.400000e-11 80.5
16 TraesCS5B01G098900 chrUn 75.962 208 27 13 1 204 10320212 10320400 9.460000e-13 86.1
17 TraesCS5B01G098900 chr3A 83.146 89 6 4 16 104 613435288 613435367 7.360000e-09 73.1
18 TraesCS5B01G098900 chr1D 85.965 57 5 2 1 54 469789465 469789521 2.060000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G098900 chr5B 131313740 131319038 5298 False 9786.000000 9786 100.00000 1 5299 1 chr5B.!!$F1 5298
1 TraesCS5B01G098900 chr5D 118998211 119005109 6898 False 2669.833333 7092 90.27500 1 5299 3 chr5D.!!$F1 5298
2 TraesCS5B01G098900 chr5A 129106263 129111558 5295 False 2023.625000 6482 91.74075 1 5299 4 chr5A.!!$F1 5298

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
541 546 0.034896 GAACGGCAGAGGAAGTTCCA 59.965 55.0 23.87 0.00 39.61 3.53 F
613 618 0.108138 GCTGCCTGTTATCGTCACCT 60.108 55.0 0.00 0.00 0.00 4.00 F
662 676 0.644843 CAAACGCACTGCCACAAAAC 59.355 50.0 0.00 0.00 0.00 2.43 F
2378 4058 0.799393 GCCTTCTTCGTTTGGAGCTC 59.201 55.0 4.71 4.71 0.00 4.09 F
2710 4396 0.251297 CCCCAAGATGTCACCAGCAA 60.251 55.0 0.00 0.00 0.00 3.91 F
3704 5390 0.038599 TCCTGTGCAAGCATGGTGAT 59.961 50.0 0.00 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2378 4058 0.179127 AGACGCACATGATCGGTCTG 60.179 55.000 0.00 0.00 0.00 3.51 R
2490 4170 1.673665 CTGTCTGACAAGGCCTGGC 60.674 63.158 5.69 11.05 0.00 4.85 R
2652 4338 4.283722 AGGAGATACCGAAAGAACTTGTGT 59.716 41.667 0.00 0.00 44.74 3.72 R
3684 5370 0.038599 TCACCATGCTTGCACAGGAT 59.961 50.000 18.61 0.00 32.66 3.24 R
3973 5659 0.818445 CCCTGCAGATGTCATCCAGC 60.818 60.000 17.39 16.87 0.00 4.85 R
5219 6926 0.314935 CAACATGCAAGTCACCACCC 59.685 55.000 0.00 0.00 0.00 4.61 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
25 29 1.409427 CGCGAAGATAAAGGAGGAGGT 59.591 52.381 0.00 0.00 0.00 3.85
150 154 4.454161 AGCTAGATCTCTACATAGTGCGTG 59.546 45.833 0.00 0.00 0.00 5.34
161 165 4.076394 ACATAGTGCGTGGGTTTTGTTAT 58.924 39.130 0.00 0.00 0.00 1.89
170 174 4.610231 CGTGGGTTTTGTTATTTTGCATGC 60.610 41.667 11.82 11.82 0.00 4.06
182 186 9.881649 TGTTATTTTGCATGCTTTTATATGGAA 57.118 25.926 20.33 0.00 33.65 3.53
210 214 7.446931 TGAGAATCTAGTATGAGATGTCCAGAC 59.553 40.741 0.00 0.00 36.28 3.51
215 219 2.687700 ATGAGATGTCCAGACACAGC 57.312 50.000 1.88 0.00 45.05 4.40
238 242 5.181245 GCTGTGCTAATTTAAAGAGTGTCCA 59.819 40.000 0.00 0.00 0.00 4.02
245 249 7.817962 GCTAATTTAAAGAGTGTCCAGTCACTA 59.182 37.037 5.02 0.00 46.81 2.74
305 310 4.275936 GGGGTCATATTTATCATATGCGGC 59.724 45.833 0.00 0.00 33.29 6.53
408 413 1.938577 CCATGAACTGATCCGCTCAAG 59.061 52.381 0.00 0.00 32.14 3.02
503 508 2.642254 TAACAGGGGTCCAGCGTCG 61.642 63.158 0.00 0.00 0.00 5.12
526 531 8.106348 GTCGGTGTAATAATCTTGTTAAGAACG 58.894 37.037 0.00 0.00 41.63 3.95
541 546 0.034896 GAACGGCAGAGGAAGTTCCA 59.965 55.000 23.87 0.00 39.61 3.53
545 550 1.004440 GCAGAGGAAGTTCCAGCGT 60.004 57.895 23.87 2.61 39.61 5.07
559 564 7.948278 AGTTCCAGCGTTATATAACTTCATC 57.052 36.000 20.54 7.13 34.12 2.92
611 616 1.999051 CGCTGCCTGTTATCGTCAC 59.001 57.895 0.00 0.00 0.00 3.67
613 618 0.108138 GCTGCCTGTTATCGTCACCT 60.108 55.000 0.00 0.00 0.00 4.00
614 619 1.136305 GCTGCCTGTTATCGTCACCTA 59.864 52.381 0.00 0.00 0.00 3.08
632 637 7.063544 CGTCACCTATACAAAGGAAAGAAGAAG 59.936 40.741 0.00 0.00 39.15 2.85
639 644 5.880341 ACAAAGGAAAGAAGAAGAACAACG 58.120 37.500 0.00 0.00 0.00 4.10
640 645 5.414765 ACAAAGGAAAGAAGAAGAACAACGT 59.585 36.000 0.00 0.00 0.00 3.99
662 676 0.644843 CAAACGCACTGCCACAAAAC 59.355 50.000 0.00 0.00 0.00 2.43
690 704 3.188667 GGCGGAAGTACCAAAGAAGAAAG 59.811 47.826 0.00 0.00 38.90 2.62
717 731 1.601903 GCCGTTGACAATCACAAGTCA 59.398 47.619 0.00 0.00 42.55 3.41
723 737 5.895636 TTGACAATCACAAGTCAAGTGTT 57.104 34.783 4.07 0.00 46.46 3.32
724 738 5.895636 TGACAATCACAAGTCAAGTGTTT 57.104 34.783 0.00 0.00 41.42 2.83
725 739 6.266168 TGACAATCACAAGTCAAGTGTTTT 57.734 33.333 0.00 0.00 41.42 2.43
726 740 6.686630 TGACAATCACAAGTCAAGTGTTTTT 58.313 32.000 0.00 0.00 41.42 1.94
754 768 3.270877 GAGGTCACAAGTCAAGTGTTGT 58.729 45.455 0.00 0.00 37.37 3.32
764 778 6.373216 ACAAGTCAAGTGTTGTACTAAAAGCA 59.627 34.615 0.00 0.00 39.18 3.91
820 2425 1.494960 GGGGCTTGGATTATTTGCCA 58.505 50.000 0.00 0.00 44.85 4.92
941 2554 2.614013 TTGCCCCCTTCCTCCTCC 60.614 66.667 0.00 0.00 0.00 4.30
942 2555 3.208342 TTGCCCCCTTCCTCCTCCT 62.208 63.158 0.00 0.00 0.00 3.69
943 2556 2.770475 GCCCCCTTCCTCCTCCTC 60.770 72.222 0.00 0.00 0.00 3.71
944 2557 2.040359 CCCCCTTCCTCCTCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
945 2558 2.652113 CCCCCTTCCTCCTCCTCCT 61.652 68.421 0.00 0.00 0.00 3.69
946 2559 1.074850 CCCCTTCCTCCTCCTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
947 2560 1.074850 CCCTTCCTCCTCCTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
983 2596 0.911769 CCCTGCCAATGTACTCCTCA 59.088 55.000 0.00 0.00 0.00 3.86
1104 2717 2.288186 GAGATCGCTCGTCATGTGAGTA 59.712 50.000 15.69 7.89 35.85 2.59
1120 2733 2.365617 TGAGTATCCGCCTCTGGATTTC 59.634 50.000 0.00 1.21 46.74 2.17
1156 2769 2.163818 TCAACGCCTGGTCAACTTAG 57.836 50.000 0.00 0.00 0.00 2.18
1180 2793 1.732259 GTTTATATGCGATCCTGGGCG 59.268 52.381 5.67 5.67 0.00 6.13
1270 2883 2.309755 TGTTTGGCTTCAGAGGGATCAT 59.690 45.455 0.00 0.00 0.00 2.45
1277 2890 3.591789 CTTCAGAGGGATCATAGGGGAA 58.408 50.000 0.00 0.00 0.00 3.97
1283 2896 3.321950 AGGGATCATAGGGGAAGAGTTG 58.678 50.000 0.00 0.00 0.00 3.16
1285 2898 3.071747 GGGATCATAGGGGAAGAGTTGAC 59.928 52.174 0.00 0.00 0.00 3.18
1352 2965 3.493767 AACAAACCTCTTCCTGTCTCC 57.506 47.619 0.00 0.00 0.00 3.71
1353 2966 2.408565 ACAAACCTCTTCCTGTCTCCA 58.591 47.619 0.00 0.00 0.00 3.86
1371 2984 7.944061 TGTCTCCATATGCCTTTTGATTTATG 58.056 34.615 0.00 0.00 0.00 1.90
1372 2985 7.779326 TGTCTCCATATGCCTTTTGATTTATGA 59.221 33.333 0.00 0.00 0.00 2.15
1373 2986 8.295288 GTCTCCATATGCCTTTTGATTTATGAG 58.705 37.037 0.00 0.00 0.00 2.90
1374 2987 8.219868 TCTCCATATGCCTTTTGATTTATGAGA 58.780 33.333 0.00 0.00 0.00 3.27
1375 2988 8.765488 TCCATATGCCTTTTGATTTATGAGAA 57.235 30.769 0.00 0.00 0.00 2.87
1376 2989 8.632679 TCCATATGCCTTTTGATTTATGAGAAC 58.367 33.333 0.00 0.00 0.00 3.01
1377 2990 8.636213 CCATATGCCTTTTGATTTATGAGAACT 58.364 33.333 0.00 0.00 0.00 3.01
1382 2995 9.912634 TGCCTTTTGATTTATGAGAACTTTTAG 57.087 29.630 0.00 0.00 0.00 1.85
1383 2996 9.914131 GCCTTTTGATTTATGAGAACTTTTAGT 57.086 29.630 0.00 0.00 0.00 2.24
1393 3006 9.765295 TTATGAGAACTTTTAGTACTCCTACCT 57.235 33.333 0.00 0.00 0.00 3.08
1394 3007 7.463961 TGAGAACTTTTAGTACTCCTACCTG 57.536 40.000 0.00 0.00 0.00 4.00
1395 3008 7.008941 TGAGAACTTTTAGTACTCCTACCTGT 58.991 38.462 0.00 0.00 0.00 4.00
1396 3009 7.039923 TGAGAACTTTTAGTACTCCTACCTGTG 60.040 40.741 0.00 0.00 0.00 3.66
1397 3010 6.781507 AGAACTTTTAGTACTCCTACCTGTGT 59.218 38.462 0.00 0.00 0.00 3.72
1398 3011 7.946776 AGAACTTTTAGTACTCCTACCTGTGTA 59.053 37.037 0.00 0.00 0.00 2.90
1399 3012 8.661752 AACTTTTAGTACTCCTACCTGTGTAT 57.338 34.615 0.00 0.00 0.00 2.29
1400 3013 9.759473 AACTTTTAGTACTCCTACCTGTGTATA 57.241 33.333 0.00 0.00 0.00 1.47
1401 3014 9.759473 ACTTTTAGTACTCCTACCTGTGTATAA 57.241 33.333 0.00 0.00 0.00 0.98
1404 3017 9.705103 TTTAGTACTCCTACCTGTGTATAATGT 57.295 33.333 0.00 0.00 0.00 2.71
1405 3018 7.584122 AGTACTCCTACCTGTGTATAATGTG 57.416 40.000 0.00 0.00 0.00 3.21
1406 3019 5.277857 ACTCCTACCTGTGTATAATGTGC 57.722 43.478 0.00 0.00 0.00 4.57
1470 3133 1.790755 TTCGTACTTTGCGACATGCT 58.209 45.000 0.00 0.00 46.63 3.79
1620 3284 3.577919 GGAGGAGGTAGAGAAAGCCATA 58.422 50.000 0.00 0.00 0.00 2.74
1643 3307 1.878088 CAGACAATTCAGTGCAGCAGT 59.122 47.619 0.00 0.00 0.00 4.40
1899 3578 7.065085 CCTGTTTACACCATGATGAAGTTAGAG 59.935 40.741 0.00 0.00 0.00 2.43
1933 3612 2.426406 GCCCTTAAGGTGGCCATGC 61.426 63.158 20.22 10.48 41.97 4.06
1945 3624 0.968405 GGCCATGCTTGAAAACCTCA 59.032 50.000 0.00 0.00 0.00 3.86
2096 3775 1.913419 AGTATGGGGCCGAGAGAAAAA 59.087 47.619 0.00 0.00 0.00 1.94
2303 3983 2.505982 CAGGGTGGAGGGTATGCG 59.494 66.667 0.00 0.00 0.00 4.73
2378 4058 0.799393 GCCTTCTTCGTTTGGAGCTC 59.201 55.000 4.71 4.71 0.00 4.09
2476 4156 3.254903 GGCGTTTGGAAAAGATTGGTAGT 59.745 43.478 0.00 0.00 0.00 2.73
2479 4159 6.349860 GGCGTTTGGAAAAGATTGGTAGTAAT 60.350 38.462 0.00 0.00 0.00 1.89
2490 4170 1.764134 TGGTAGTAATGGGGCTTACCG 59.236 52.381 0.00 0.00 41.60 4.02
2580 4260 6.628644 AGAGAAGCTATTGAAGGTAAAGGT 57.371 37.500 0.00 0.00 33.87 3.50
2642 4328 6.016024 TGCTTTCATAGAACAAAGTTGCTGAT 60.016 34.615 0.00 0.00 32.96 2.90
2647 4333 8.791327 TCATAGAACAAAGTTGCTGATATTGA 57.209 30.769 0.00 0.00 0.00 2.57
2652 4338 9.066892 AGAACAAAGTTGCTGATATTGAACTAA 57.933 29.630 0.00 0.00 0.00 2.24
2653 4339 9.118236 GAACAAAGTTGCTGATATTGAACTAAC 57.882 33.333 0.00 0.00 0.00 2.34
2680 4366 4.575645 AGTTCTTTCGGTATCTCCTCTACG 59.424 45.833 0.00 0.00 0.00 3.51
2710 4396 0.251297 CCCCAAGATGTCACCAGCAA 60.251 55.000 0.00 0.00 0.00 3.91
2901 4587 5.721960 AGAGAAGGTGCTTTATCCTCACTTA 59.278 40.000 0.00 0.00 33.09 2.24
2930 4616 8.481314 TCAGATAGCAGATTTTCTCACTAATGT 58.519 33.333 0.00 0.00 0.00 2.71
3379 5065 5.490139 AATCTAAGGCGTTGTCATCAATG 57.510 39.130 0.97 0.00 41.81 2.82
3461 5147 3.356290 AGCCATCAAATAGTCACCCAAC 58.644 45.455 0.00 0.00 0.00 3.77
3704 5390 0.038599 TCCTGTGCAAGCATGGTGAT 59.961 50.000 0.00 0.00 0.00 3.06
3847 5533 4.096984 CCCTGTCGGTAGTTTAACGTCTAT 59.903 45.833 0.00 0.00 40.40 1.98
3961 5647 6.433716 TGATATTTGATGGTGACTTGCTTTGA 59.566 34.615 0.00 0.00 0.00 2.69
3973 5659 7.965107 GGTGACTTGCTTTGAATCTAATTAGTG 59.035 37.037 12.19 0.00 0.00 2.74
4226 5912 4.741837 GCATTGAAGCTAGCATCTGTAGGA 60.742 45.833 19.79 0.00 0.00 2.94
4543 6230 3.062639 CGTGTGGAGCTTGTATTGTGATC 59.937 47.826 0.00 0.00 0.00 2.92
4639 6339 3.587797 AGCATGCAATTTCCTGAAGTG 57.412 42.857 21.98 0.00 36.45 3.16
4650 6350 2.416747 TCCTGAAGTGCATTTGAGACG 58.583 47.619 9.95 0.00 0.00 4.18
4992 6696 3.409026 TCCAAGGAGCTTCAAGAAGAC 57.591 47.619 13.70 6.48 40.79 3.01
5010 6714 6.790282 AGAAGACACTTCTTTTGAAAAGCTC 58.210 36.000 12.62 2.84 42.53 4.09
5049 6753 2.802792 CAGAATGCCATGCACGGG 59.197 61.111 0.00 0.53 43.04 5.28
5050 6754 2.048023 CAGAATGCCATGCACGGGT 61.048 57.895 0.00 0.00 43.04 5.28
5219 6926 5.147162 GTTTGTAGTCTTTTCTGCGATTGG 58.853 41.667 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.756283 CGCTCCGACCTCCTCCTT 60.756 66.667 0.00 0.00 0.00 3.36
121 125 6.821665 CACTATGTAGAGATCTAGCTACTCCC 59.178 46.154 17.79 0.16 38.21 4.30
150 154 5.687770 AAGCATGCAAAATAACAAAACCC 57.312 34.783 21.98 0.00 0.00 4.11
161 165 9.100554 CTCAATTCCATATAAAAGCATGCAAAA 57.899 29.630 21.98 2.19 0.00 2.44
182 186 8.718158 TGGACATCTCATACTAGATTCTCAAT 57.282 34.615 0.00 0.00 33.87 2.57
215 219 6.428159 ACTGGACACTCTTTAAATTAGCACAG 59.572 38.462 0.00 0.00 0.00 3.66
238 242 1.433879 GCGTCCGCAGATAGTGACT 59.566 57.895 6.82 0.00 41.49 3.41
327 332 2.817396 GCTCACTTCCTCCGCTGC 60.817 66.667 0.00 0.00 0.00 5.25
328 333 2.125350 GGCTCACTTCCTCCGCTG 60.125 66.667 0.00 0.00 0.00 5.18
333 338 2.156051 AACGGTCGGCTCACTTCCTC 62.156 60.000 0.00 0.00 0.00 3.71
408 413 1.848886 ATCGTGGTGGGGAAGGTTCC 61.849 60.000 0.00 0.00 46.82 3.62
503 508 7.148373 TGCCGTTCTTAACAAGATTATTACACC 60.148 37.037 0.00 0.00 37.38 4.16
526 531 1.743252 CGCTGGAACTTCCTCTGCC 60.743 63.158 9.31 0.00 37.46 4.85
584 589 0.606401 AACAGGCAGCGCAATGTACT 60.606 50.000 11.47 0.00 31.54 2.73
593 598 1.421410 GGTGACGATAACAGGCAGCG 61.421 60.000 0.00 0.00 0.00 5.18
611 616 8.848474 TGTTCTTCTTCTTTCCTTTGTATAGG 57.152 34.615 0.00 0.00 36.59 2.57
613 618 8.770828 CGTTGTTCTTCTTCTTTCCTTTGTATA 58.229 33.333 0.00 0.00 0.00 1.47
614 619 7.282450 ACGTTGTTCTTCTTCTTTCCTTTGTAT 59.718 33.333 0.00 0.00 0.00 2.29
639 644 1.299089 GTGGCAGTGCGTTTGGAAC 60.299 57.895 9.45 0.00 0.00 3.62
640 645 1.315981 TTGTGGCAGTGCGTTTGGAA 61.316 50.000 9.45 0.00 0.00 3.53
672 686 5.648526 GGATCCCTTTCTTCTTTGGTACTTC 59.351 44.000 0.00 0.00 0.00 3.01
690 704 1.436983 GATTGTCAACGGCGGATCCC 61.437 60.000 13.24 0.00 0.00 3.85
728 742 4.764823 ACACTTGACTTGTGACCTCAAAAA 59.235 37.500 0.00 0.00 38.65 1.94
729 743 4.331968 ACACTTGACTTGTGACCTCAAAA 58.668 39.130 0.00 0.00 38.65 2.44
730 744 3.950397 ACACTTGACTTGTGACCTCAAA 58.050 40.909 0.00 0.00 38.65 2.69
731 745 3.627395 ACACTTGACTTGTGACCTCAA 57.373 42.857 0.00 0.00 38.65 3.02
732 746 3.270027 CAACACTTGACTTGTGACCTCA 58.730 45.455 0.00 0.00 38.65 3.86
733 747 3.270877 ACAACACTTGACTTGTGACCTC 58.729 45.455 0.00 0.00 38.65 3.85
734 748 3.350219 ACAACACTTGACTTGTGACCT 57.650 42.857 0.00 0.00 38.65 3.85
735 749 4.189231 AGTACAACACTTGACTTGTGACC 58.811 43.478 0.00 0.00 38.65 4.02
737 751 7.413657 GCTTTTAGTACAACACTTGACTTGTGA 60.414 37.037 0.00 0.00 38.80 3.58
739 753 6.373216 TGCTTTTAGTACAACACTTGACTTGT 59.627 34.615 0.00 0.00 38.80 3.16
741 755 6.995511 TGCTTTTAGTACAACACTTGACTT 57.004 33.333 0.00 0.00 38.80 3.01
742 756 7.387948 CCTATGCTTTTAGTACAACACTTGACT 59.612 37.037 0.00 0.00 38.80 3.41
745 759 6.072728 TGCCTATGCTTTTAGTACAACACTTG 60.073 38.462 0.00 0.00 37.23 3.16
754 768 6.128391 CGTTTGAGTTGCCTATGCTTTTAGTA 60.128 38.462 0.00 0.00 38.71 1.82
764 778 2.076863 GACAGCGTTTGAGTTGCCTAT 58.923 47.619 0.00 0.00 0.00 2.57
783 797 1.301401 CCGGCCAAAGACAAGACGA 60.301 57.895 2.24 0.00 0.00 4.20
786 800 2.434331 CCCCGGCCAAAGACAAGA 59.566 61.111 2.24 0.00 0.00 3.02
820 2425 2.943036 TCTCGGGCCAAAGTAAAACT 57.057 45.000 4.39 0.00 0.00 2.66
941 2554 3.627237 GGGCTGATATAGAGGAGGAGGAG 60.627 56.522 0.00 0.00 0.00 3.69
942 2555 2.313342 GGGCTGATATAGAGGAGGAGGA 59.687 54.545 0.00 0.00 0.00 3.71
943 2556 2.625617 GGGGCTGATATAGAGGAGGAGG 60.626 59.091 0.00 0.00 0.00 4.30
944 2557 2.625617 GGGGGCTGATATAGAGGAGGAG 60.626 59.091 0.00 0.00 0.00 3.69
945 2558 1.362932 GGGGGCTGATATAGAGGAGGA 59.637 57.143 0.00 0.00 0.00 3.71
946 2559 1.872773 GGGGGCTGATATAGAGGAGG 58.127 60.000 0.00 0.00 0.00 4.30
975 2588 3.780850 GGGAAGAAAGGGAATGAGGAGTA 59.219 47.826 0.00 0.00 0.00 2.59
983 2596 2.894007 GCCATTGGGGAAGAAAGGGAAT 60.894 50.000 4.53 0.00 40.01 3.01
1130 2743 4.522789 AGTTGACCAGGCGTTGATTTTATT 59.477 37.500 0.00 0.00 0.00 1.40
1156 2769 3.189287 CCCAGGATCGCATATAAACAAGC 59.811 47.826 0.00 0.00 0.00 4.01
1180 2793 0.175989 GACACGGGACCTTCAGATCC 59.824 60.000 0.00 0.00 0.00 3.36
1270 2883 1.203087 TGGTCGTCAACTCTTCCCCTA 60.203 52.381 0.00 0.00 0.00 3.53
1277 2890 2.868044 GCTGAACATGGTCGTCAACTCT 60.868 50.000 6.21 0.00 0.00 3.24
1283 2896 3.002656 CCATATTGCTGAACATGGTCGTC 59.997 47.826 6.21 0.47 34.46 4.20
1285 2898 2.945008 ACCATATTGCTGAACATGGTCG 59.055 45.455 6.21 2.21 46.42 4.79
1371 2984 7.039853 ACACAGGTAGGAGTACTAAAAGTTCTC 60.040 40.741 0.00 5.43 40.54 2.87
1372 2985 6.781507 ACACAGGTAGGAGTACTAAAAGTTCT 59.218 38.462 0.00 0.00 32.37 3.01
1373 2986 6.990798 ACACAGGTAGGAGTACTAAAAGTTC 58.009 40.000 0.00 0.00 32.37 3.01
1374 2987 6.990908 ACACAGGTAGGAGTACTAAAAGTT 57.009 37.500 0.00 0.00 32.37 2.66
1375 2988 9.759473 TTATACACAGGTAGGAGTACTAAAAGT 57.241 33.333 0.00 0.00 32.37 2.66
1378 2991 9.705103 ACATTATACACAGGTAGGAGTACTAAA 57.295 33.333 0.00 0.00 32.37 1.85
1379 2992 9.128404 CACATTATACACAGGTAGGAGTACTAA 57.872 37.037 0.00 0.00 32.37 2.24
1381 2994 6.040616 GCACATTATACACAGGTAGGAGTACT 59.959 42.308 0.00 0.00 31.88 2.73
1382 2995 6.040616 AGCACATTATACACAGGTAGGAGTAC 59.959 42.308 0.00 0.00 31.88 2.73
1383 2996 6.134055 AGCACATTATACACAGGTAGGAGTA 58.866 40.000 0.00 0.00 31.88 2.59
1384 2997 4.962995 AGCACATTATACACAGGTAGGAGT 59.037 41.667 0.00 0.00 31.88 3.85
1385 2998 5.537300 AGCACATTATACACAGGTAGGAG 57.463 43.478 0.00 0.00 31.88 3.69
1386 2999 5.188948 ACAAGCACATTATACACAGGTAGGA 59.811 40.000 0.00 0.00 31.88 2.94
1387 3000 5.428253 ACAAGCACATTATACACAGGTAGG 58.572 41.667 0.00 0.00 31.88 3.18
1388 3001 6.106003 TGACAAGCACATTATACACAGGTAG 58.894 40.000 0.00 0.00 31.88 3.18
1389 3002 6.043854 TGACAAGCACATTATACACAGGTA 57.956 37.500 0.00 0.00 0.00 3.08
1390 3003 4.905429 TGACAAGCACATTATACACAGGT 58.095 39.130 0.00 0.00 0.00 4.00
1391 3004 5.163723 CCTTGACAAGCACATTATACACAGG 60.164 44.000 9.85 0.00 0.00 4.00
1392 3005 5.674569 GCCTTGACAAGCACATTATACACAG 60.675 44.000 9.85 0.00 0.00 3.66
1393 3006 4.155826 GCCTTGACAAGCACATTATACACA 59.844 41.667 9.85 0.00 0.00 3.72
1394 3007 4.396166 AGCCTTGACAAGCACATTATACAC 59.604 41.667 9.85 0.00 0.00 2.90
1395 3008 4.588899 AGCCTTGACAAGCACATTATACA 58.411 39.130 9.85 0.00 0.00 2.29
1396 3009 6.049149 TCTAGCCTTGACAAGCACATTATAC 58.951 40.000 9.85 0.00 0.00 1.47
1397 3010 6.233905 TCTAGCCTTGACAAGCACATTATA 57.766 37.500 9.85 0.00 0.00 0.98
1398 3011 5.102953 TCTAGCCTTGACAAGCACATTAT 57.897 39.130 9.85 0.00 0.00 1.28
1399 3012 4.551702 TCTAGCCTTGACAAGCACATTA 57.448 40.909 9.85 0.00 0.00 1.90
1400 3013 3.423539 TCTAGCCTTGACAAGCACATT 57.576 42.857 9.85 0.00 0.00 2.71
1401 3014 3.077359 GTTCTAGCCTTGACAAGCACAT 58.923 45.455 9.85 0.00 0.00 3.21
1402 3015 2.158827 TGTTCTAGCCTTGACAAGCACA 60.159 45.455 9.85 3.73 0.00 4.57
1403 3016 2.481952 CTGTTCTAGCCTTGACAAGCAC 59.518 50.000 9.85 4.16 0.00 4.40
1404 3017 2.771089 CTGTTCTAGCCTTGACAAGCA 58.229 47.619 9.85 0.00 0.00 3.91
1436 3099 9.783256 GCAAAGTACGAAAAATGAATAATAGGT 57.217 29.630 0.00 0.00 0.00 3.08
1451 3114 1.459209 CAGCATGTCGCAAAGTACGAA 59.541 47.619 0.00 0.00 46.13 3.85
1453 3116 0.519175 GCAGCATGTCGCAAAGTACG 60.519 55.000 0.00 0.00 46.13 3.67
1454 3117 0.519175 CGCAGCATGTCGCAAAGTAC 60.519 55.000 8.83 0.00 46.13 2.73
1455 3118 0.669012 TCGCAGCATGTCGCAAAGTA 60.669 50.000 8.83 0.00 46.13 2.24
1458 3121 0.652071 CTATCGCAGCATGTCGCAAA 59.348 50.000 8.83 0.00 46.13 3.68
1470 3133 7.479603 GTTGTAAACGTCGATATATCTATCGCA 59.520 37.037 13.96 3.92 45.36 5.10
1493 3156 0.961019 TGCTTGGCCTTTAGCTGTTG 59.039 50.000 20.55 0.00 43.05 3.33
1620 3284 3.151554 TGCTGCACTGAATTGTCTGAAT 58.848 40.909 0.00 0.00 0.00 2.57
1668 3341 4.898861 AGTTTTACCATGGCAAAGGAGAAA 59.101 37.500 13.04 11.45 0.00 2.52
1933 3612 4.739195 TGGTCGTTTTTGAGGTTTTCAAG 58.261 39.130 0.00 0.00 46.01 3.02
1945 3624 4.548494 ACAACGTTTTTCTGGTCGTTTTT 58.452 34.783 0.00 0.00 43.03 1.94
2096 3775 1.676006 CACCGTTGAGGAGTTTTGCTT 59.324 47.619 0.00 0.00 45.00 3.91
2097 3776 1.134220 TCACCGTTGAGGAGTTTTGCT 60.134 47.619 0.00 0.00 45.00 3.91
2303 3983 7.598493 TGAAAAGCTTAAATGTGAGGCAAATAC 59.402 33.333 0.00 0.00 0.00 1.89
2357 4037 1.168714 GCTCCAAACGAAGAAGGCAT 58.831 50.000 0.00 0.00 0.00 4.40
2378 4058 0.179127 AGACGCACATGATCGGTCTG 60.179 55.000 0.00 0.00 0.00 3.51
2490 4170 1.673665 CTGTCTGACAAGGCCTGGC 60.674 63.158 5.69 11.05 0.00 4.85
2624 4310 9.236006 AGTTCAATATCAGCAACTTTGTTCTAT 57.764 29.630 0.00 0.00 0.00 1.98
2647 4333 7.215085 AGATACCGAAAGAACTTGTGTTAGTT 58.785 34.615 0.00 0.00 40.92 2.24
2652 4338 4.283722 AGGAGATACCGAAAGAACTTGTGT 59.716 41.667 0.00 0.00 44.74 3.72
2653 4339 4.822026 AGGAGATACCGAAAGAACTTGTG 58.178 43.478 0.00 0.00 44.74 3.33
2669 4355 5.370679 GGAAAGTCTAGACGTAGAGGAGAT 58.629 45.833 17.07 0.00 35.87 2.75
2680 4366 4.223032 TGACATCTTGGGGAAAGTCTAGAC 59.777 45.833 15.41 15.41 37.18 2.59
2901 4587 6.945218 AGTGAGAAAATCTGCTATCTGAAGT 58.055 36.000 0.00 0.00 0.00 3.01
3200 4886 1.526686 CTGTGCTGACCTGCCAACA 60.527 57.895 0.00 0.00 0.00 3.33
3358 5044 4.517285 ACATTGATGACAACGCCTTAGAT 58.483 39.130 0.00 0.00 38.90 1.98
3379 5065 0.524862 CCACTGAAGCCTGCATGAAC 59.475 55.000 0.00 0.00 0.00 3.18
3461 5147 6.040729 TGGCTTGGATCATATGGTGTAATTTG 59.959 38.462 2.13 0.00 0.00 2.32
3684 5370 0.038599 TCACCATGCTTGCACAGGAT 59.961 50.000 18.61 0.00 32.66 3.24
3772 5458 9.793259 TGATTTTGTTCAGTTTAAGAGTATCCT 57.207 29.630 0.00 0.00 33.66 3.24
3847 5533 4.566278 GCATAGAATCCATGGCTGTATCCA 60.566 45.833 6.96 0.00 40.97 3.41
3961 5647 7.660617 CAGATGTCATCCAGCACTAATTAGATT 59.339 37.037 19.38 1.34 0.00 2.40
3973 5659 0.818445 CCCTGCAGATGTCATCCAGC 60.818 60.000 17.39 16.87 0.00 4.85
4279 5965 2.504367 GTCATGTTGTTGGTACCAGCT 58.496 47.619 26.61 6.37 0.00 4.24
4492 6179 7.718334 TCTGTCACAACTAAGATCCAGATAA 57.282 36.000 0.00 0.00 0.00 1.75
4521 6208 2.412870 TCACAATACAAGCTCCACACG 58.587 47.619 0.00 0.00 0.00 4.49
4639 6339 7.754924 TCATTTTAAAAGGATCGTCTCAAATGC 59.245 33.333 11.06 0.00 31.87 3.56
4650 6350 6.808704 GCACCTCACTTCATTTTAAAAGGATC 59.191 38.462 15.37 0.00 0.00 3.36
4742 6442 7.341769 AGACAGGCCATGTTTATAGCATTTTTA 59.658 33.333 5.01 0.00 44.17 1.52
4992 6696 7.450627 CAACAAAGAGCTTTTCAAAAGAAGTG 58.549 34.615 14.39 6.10 0.00 3.16
5010 6714 3.314553 CTGGCAAATCAGAGCAACAAAG 58.685 45.455 0.00 0.00 36.93 2.77
5219 6926 0.314935 CAACATGCAAGTCACCACCC 59.685 55.000 0.00 0.00 0.00 4.61
5265 6972 2.806244 TCGCTTTAACCTGTTCTTCTGC 59.194 45.455 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.