Multiple sequence alignment - TraesCS4D01G329300

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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 TraesCS4D01G329300 chr4D 100.000 3095 0 0 1 3095 487630864 487633958 0.000000e+00 5716
1 TraesCS4D01G329300 chr4B 91.893 2615 100 48 536 3095 623163161 623165718 0.000000e+00 3552
2 TraesCS4D01G329300 chr4B 85.430 151 18 3 256 406 623162896 623163042 1.490000e-33 154
3 TraesCS4D01G329300 chr5A 94.848 1650 43 24 647 2270 669564312 669565945 0.000000e+00 2538
4 TraesCS4D01G329300 chr5A 83.452 840 34 36 2272 3090 669566014 669566769 0.000000e+00 684
5 TraesCS4D01G329300 chr5A 86.286 525 45 15 1 517 669563308 669563813 2.100000e-151 545
6 TraesCS4D01G329300 chr5A 96.875 128 3 1 535 662 669564087 669564213 2.420000e-51 213
7 TraesCS4D01G329300 chr1A 88.758 1103 107 15 1001 2096 366543259 366544351 0.000000e+00 1334
8 TraesCS4D01G329300 chr1D 88.647 1101 112 13 1001 2096 294131591 294132683 0.000000e+00 1328
9 TraesCS4D01G329300 chr1B 88.364 1100 117 11 1001 2096 395752355 395753447 0.000000e+00 1312


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 TraesCS4D01G329300 chr4D 487630864 487633958 3094 False 5716 5716 100.00000 1 3095 1 chr4D.!!$F1 3094
1 TraesCS4D01G329300 chr4B 623162896 623165718 2822 False 1853 3552 88.66150 256 3095 2 chr4B.!!$F1 2839
2 TraesCS4D01G329300 chr5A 669563308 669566769 3461 False 995 2538 90.36525 1 3090 4 chr5A.!!$F1 3089
3 TraesCS4D01G329300 chr1A 366543259 366544351 1092 False 1334 1334 88.75800 1001 2096 1 chr1A.!!$F1 1095
4 TraesCS4D01G329300 chr1D 294131591 294132683 1092 False 1328 1328 88.64700 1001 2096 1 chr1D.!!$F1 1095
5 TraesCS4D01G329300 chr1B 395752355 395753447 1092 False 1312 1312 88.36400 1001 2096 1 chr1B.!!$F1 1095

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
67 68 0.179045 GAGATGCCCTTACCATGCGT 60.179 55.0 0.0 0.0 0.0 5.24 F
421 463 0.187606 GTTCCCACACCCTTTCCCTT 59.812 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 2482 1.033746 GGAGGACCACCATGTGCATG 61.034 60.0 2.58 5.26 38.94 4.06 R
2215 2654 2.005960 CTCTCCTCCCGGCTACAACG 62.006 65.0 0.00 0.00 0.00 4.10 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 2.099831 CGTACGGACAGCTCGGTC 59.900 66.667 7.57 0.00 37.06 4.79
54 55 2.480555 CGTTGGCGTTGGAGATGC 59.519 61.111 0.00 0.00 39.65 3.91
65 66 0.183492 TGGAGATGCCCTTACCATGC 59.817 55.000 0.00 0.00 34.97 4.06
66 67 0.886490 GGAGATGCCCTTACCATGCG 60.886 60.000 0.00 0.00 0.00 4.73
67 68 0.179045 GAGATGCCCTTACCATGCGT 60.179 55.000 0.00 0.00 0.00 5.24
68 69 0.464373 AGATGCCCTTACCATGCGTG 60.464 55.000 0.00 0.00 0.00 5.34
69 70 0.748005 GATGCCCTTACCATGCGTGT 60.748 55.000 4.96 0.00 0.00 4.49
70 71 0.323360 ATGCCCTTACCATGCGTGTT 60.323 50.000 4.96 0.00 0.00 3.32
89 90 5.552178 GTGTTCTTGTATCTTGGAAGTCCT 58.448 41.667 0.00 0.00 36.82 3.85
100 101 5.445069 TCTTGGAAGTCCTGTGAATCAAAA 58.555 37.500 0.00 0.00 36.82 2.44
121 122 4.590850 AAAGGTCCAAAAATGAGCTCAC 57.409 40.909 20.97 3.07 39.51 3.51
147 149 8.706035 CAAAGCTCAAAATAAACTTTCATCCAG 58.294 33.333 0.00 0.00 0.00 3.86
169 171 6.462207 CCAGTTTATGAATGAAACACCAACCA 60.462 38.462 1.54 0.00 38.91 3.67
192 194 0.938713 CCGTACAAACACCTCGCAAA 59.061 50.000 0.00 0.00 0.00 3.68
198 200 0.875059 AAACACCTCGCAAAGCTAGC 59.125 50.000 6.62 6.62 0.00 3.42
282 284 5.064579 CGTGTGCTAACATGAATGACCATAA 59.935 40.000 0.00 0.00 44.75 1.90
386 428 2.895680 GTCGCATCAGGCTGGAGA 59.104 61.111 15.73 3.77 41.67 3.71
387 429 1.219124 GTCGCATCAGGCTGGAGAA 59.781 57.895 15.73 0.00 41.67 2.87
388 430 0.391661 GTCGCATCAGGCTGGAGAAA 60.392 55.000 15.73 0.00 41.67 2.52
389 431 0.324614 TCGCATCAGGCTGGAGAAAA 59.675 50.000 15.73 0.00 41.67 2.29
393 435 2.517959 CATCAGGCTGGAGAAAAACCA 58.482 47.619 15.73 0.00 35.96 3.67
399 441 2.732289 TGGAGAAAAACCAGGCTGC 58.268 52.632 9.56 0.00 33.22 5.25
400 442 0.827507 TGGAGAAAAACCAGGCTGCC 60.828 55.000 11.65 11.65 33.22 4.85
401 443 0.540597 GGAGAAAAACCAGGCTGCCT 60.541 55.000 17.22 17.22 0.00 4.75
410 452 3.177884 AGGCTGCCTGTTCCCACA 61.178 61.111 22.71 0.00 29.57 4.17
411 453 2.985847 GGCTGCCTGTTCCCACAC 60.986 66.667 12.43 0.00 0.00 3.82
413 455 2.282462 CTGCCTGTTCCCACACCC 60.282 66.667 0.00 0.00 0.00 4.61
414 456 2.776526 TGCCTGTTCCCACACCCT 60.777 61.111 0.00 0.00 0.00 4.34
416 458 1.152546 GCCTGTTCCCACACCCTTT 60.153 57.895 0.00 0.00 0.00 3.11
417 459 1.179174 GCCTGTTCCCACACCCTTTC 61.179 60.000 0.00 0.00 0.00 2.62
419 461 0.539669 CTGTTCCCACACCCTTTCCC 60.540 60.000 0.00 0.00 0.00 3.97
421 463 0.187606 GTTCCCACACCCTTTCCCTT 59.812 55.000 0.00 0.00 0.00 3.95
436 478 1.074727 TCCCTTCCCAGCGAAAAATGA 59.925 47.619 0.00 0.00 0.00 2.57
459 504 2.673893 GCCACCGAACCAAATCAAATCC 60.674 50.000 0.00 0.00 0.00 3.01
483 531 1.696336 TGCTGGCTCTCTGTTTCTTCT 59.304 47.619 0.00 0.00 0.00 2.85
485 533 2.741517 GCTGGCTCTCTGTTTCTTCTTC 59.258 50.000 0.00 0.00 0.00 2.87
491 539 7.054124 TGGCTCTCTGTTTCTTCTTCTTTTTA 58.946 34.615 0.00 0.00 0.00 1.52
500 548 9.377312 TGTTTCTTCTTCTTTTTAAATGTTGGG 57.623 29.630 0.00 0.00 0.00 4.12
510 558 1.915141 AAATGTTGGGTGGCTCTCTG 58.085 50.000 0.00 0.00 0.00 3.35
514 562 1.064017 TGTTGGGTGGCTCTCTGTTTT 60.064 47.619 0.00 0.00 0.00 2.43
515 563 1.609072 GTTGGGTGGCTCTCTGTTTTC 59.391 52.381 0.00 0.00 0.00 2.29
516 564 1.140312 TGGGTGGCTCTCTGTTTTCT 58.860 50.000 0.00 0.00 0.00 2.52
517 565 2.334977 TGGGTGGCTCTCTGTTTTCTA 58.665 47.619 0.00 0.00 0.00 2.10
518 566 2.303022 TGGGTGGCTCTCTGTTTTCTAG 59.697 50.000 0.00 0.00 0.00 2.43
520 568 2.289694 GGTGGCTCTCTGTTTTCTAGCA 60.290 50.000 0.00 0.00 34.85 3.49
521 569 3.604582 GTGGCTCTCTGTTTTCTAGCAT 58.395 45.455 0.00 0.00 34.85 3.79
522 570 3.620821 GTGGCTCTCTGTTTTCTAGCATC 59.379 47.826 0.00 0.00 34.85 3.91
523 571 2.863137 GGCTCTCTGTTTTCTAGCATCG 59.137 50.000 0.00 0.00 34.85 3.84
524 572 3.429547 GGCTCTCTGTTTTCTAGCATCGA 60.430 47.826 0.00 0.00 34.85 3.59
525 573 4.177026 GCTCTCTGTTTTCTAGCATCGAA 58.823 43.478 0.00 0.00 33.38 3.71
526 574 4.267452 GCTCTCTGTTTTCTAGCATCGAAG 59.733 45.833 0.00 0.00 33.38 3.79
530 578 6.366332 TCTCTGTTTTCTAGCATCGAAGAAAC 59.634 38.462 9.06 3.02 43.58 2.78
531 579 6.223852 TCTGTTTTCTAGCATCGAAGAAACT 58.776 36.000 9.06 0.00 43.58 2.66
532 580 7.375834 TCTGTTTTCTAGCATCGAAGAAACTA 58.624 34.615 9.06 2.43 43.58 2.24
533 581 7.328737 TCTGTTTTCTAGCATCGAAGAAACTAC 59.671 37.037 9.06 7.16 43.58 2.73
768 1184 4.200283 GAGGAGCGAGCGGTGGAG 62.200 72.222 0.00 0.00 0.00 3.86
797 1213 4.802051 CACCCCGCCTCCACCATG 62.802 72.222 0.00 0.00 0.00 3.66
808 1224 0.327924 TCCACCATGTCGCCAGAAAT 59.672 50.000 0.00 0.00 0.00 2.17
993 1411 4.239991 AGCTGAGCTCAAGGGGAA 57.760 55.556 18.85 0.00 30.62 3.97
994 1412 2.468015 AGCTGAGCTCAAGGGGAAA 58.532 52.632 18.85 0.00 30.62 3.13
2049 2482 1.668151 GACCGGCATATTCTCGCCC 60.668 63.158 0.00 0.00 46.04 6.13
2106 2542 0.791238 CCGAATAGAGCGAGCGATCG 60.791 60.000 20.40 20.40 35.44 3.69
2196 2632 8.317679 AGAGGCTTATTATTAGCTAATGGAGTG 58.682 37.037 25.99 14.90 38.67 3.51
2215 2654 3.629398 AGTGCTAGTGCTATTGATTTGGC 59.371 43.478 0.00 0.00 40.48 4.52
2283 2792 3.202829 TGGTGGTAGCTTTCGTTTTCT 57.797 42.857 0.00 0.00 0.00 2.52
2284 2793 3.547746 TGGTGGTAGCTTTCGTTTTCTT 58.452 40.909 0.00 0.00 0.00 2.52
2344 2853 6.017400 TGGATTCAGATTTGTTTCTGCTTC 57.983 37.500 0.00 0.00 42.37 3.86
2356 2865 1.687563 TCTGCTTCGATCCGTGGATA 58.312 50.000 0.33 0.00 34.60 2.59
2360 2869 2.229062 TGCTTCGATCCGTGGATAGATC 59.771 50.000 11.74 8.14 36.45 2.75
2361 2870 2.490115 GCTTCGATCCGTGGATAGATCT 59.510 50.000 11.74 0.00 36.45 2.75
2362 2871 3.057174 GCTTCGATCCGTGGATAGATCTT 60.057 47.826 11.74 0.00 36.45 2.40
2363 2872 4.728534 CTTCGATCCGTGGATAGATCTTC 58.271 47.826 11.74 0.00 36.45 2.87
2365 2874 3.085533 CGATCCGTGGATAGATCTTCCT 58.914 50.000 18.73 4.73 37.37 3.36
2407 2919 7.875316 ATCGTCATCTATATTTTGTCTTCCG 57.125 36.000 0.00 0.00 0.00 4.30
2408 2920 5.690409 TCGTCATCTATATTTTGTCTTCCGC 59.310 40.000 0.00 0.00 0.00 5.54
2416 2928 9.391006 TCTATATTTTGTCTTCCGCAACTAAAT 57.609 29.630 0.00 0.00 35.80 1.40
2422 2934 4.142116 TGTCTTCCGCAACTAAATATCGGA 60.142 41.667 0.00 0.00 46.13 4.55
2428 2940 5.186215 TCCGCAACTAAATATCGGATGGATA 59.814 40.000 0.00 0.00 43.42 2.59
2437 2949 7.639113 AAATATCGGATGGATAGAGTCTCTC 57.361 40.000 5.39 0.00 40.83 3.20
2472 2984 5.733620 AATTGTGCAGGAAATCAATCAGT 57.266 34.783 0.00 0.00 31.41 3.41
2478 2990 6.489700 TGTGCAGGAAATCAATCAGTCTTTTA 59.510 34.615 0.00 0.00 0.00 1.52
2479 2991 7.177216 TGTGCAGGAAATCAATCAGTCTTTTAT 59.823 33.333 0.00 0.00 0.00 1.40
2505 3018 7.430992 TGAATCAATCAGTCAGTTTTGAGAG 57.569 36.000 0.00 0.00 30.57 3.20
2506 3019 5.876612 ATCAATCAGTCAGTTTTGAGAGC 57.123 39.130 0.00 0.00 32.98 4.09
2507 3020 4.965814 TCAATCAGTCAGTTTTGAGAGCT 58.034 39.130 0.00 0.00 32.98 4.09
2508 3021 4.993584 TCAATCAGTCAGTTTTGAGAGCTC 59.006 41.667 5.27 5.27 32.98 4.09
2509 3022 4.613925 ATCAGTCAGTTTTGAGAGCTCA 57.386 40.909 17.77 0.00 37.91 4.26
2522 3035 5.078411 TGAGAGCTCATCAGTTTTCTACC 57.922 43.478 17.77 0.00 34.14 3.18
2524 3050 3.198853 AGAGCTCATCAGTTTTCTACCCC 59.801 47.826 17.77 0.00 0.00 4.95
2544 3070 2.663852 GGTTCCCGTCCGTGTGTG 60.664 66.667 0.00 0.00 0.00 3.82
2546 3072 2.107343 TTCCCGTCCGTGTGTGTG 59.893 61.111 0.00 0.00 0.00 3.82
2547 3073 2.723237 TTCCCGTCCGTGTGTGTGT 61.723 57.895 0.00 0.00 0.00 3.72
2548 3074 2.202960 CCCGTCCGTGTGTGTGTT 60.203 61.111 0.00 0.00 0.00 3.32
2549 3075 2.530497 CCCGTCCGTGTGTGTGTTG 61.530 63.158 0.00 0.00 0.00 3.33
2594 3121 3.047877 CGTTCCCCGTTCACTGCC 61.048 66.667 0.00 0.00 0.00 4.85
2595 3122 3.047877 GTTCCCCGTTCACTGCCG 61.048 66.667 0.00 0.00 0.00 5.69
2598 3125 4.077184 CCCCGTTCACTGCCGCTA 62.077 66.667 0.00 0.00 0.00 4.26
2599 3126 2.813908 CCCGTTCACTGCCGCTAC 60.814 66.667 0.00 0.00 0.00 3.58
2600 3127 2.048597 CCGTTCACTGCCGCTACA 60.049 61.111 0.00 0.00 0.00 2.74
2601 3128 2.094659 CCGTTCACTGCCGCTACAG 61.095 63.158 1.62 1.62 43.59 2.74
2641 3168 1.076850 TCACCGGCCTCCACGTATA 60.077 57.895 0.00 0.00 0.00 1.47
2652 3179 1.006281 TCCACGTATACTCCACCCAGT 59.994 52.381 0.56 0.00 0.00 4.00
2657 3184 2.323599 GTATACTCCACCCAGTACCCC 58.676 57.143 0.00 0.00 31.53 4.95
2772 3299 0.235144 ATCGGATCTCGTTCGTAGCG 59.765 55.000 0.00 0.00 40.32 4.26
2788 3315 0.603569 AGCGTAGAGAACTGTGGGTG 59.396 55.000 0.00 0.00 0.00 4.61
2789 3316 0.389948 GCGTAGAGAACTGTGGGTGG 60.390 60.000 0.00 0.00 0.00 4.61
2790 3317 0.966920 CGTAGAGAACTGTGGGTGGT 59.033 55.000 0.00 0.00 0.00 4.16
2791 3318 2.165167 CGTAGAGAACTGTGGGTGGTA 58.835 52.381 0.00 0.00 0.00 3.25
2870 3420 3.773630 CGACGCGCCATGTTTCGT 61.774 61.111 5.73 3.56 37.92 3.85
2918 3474 1.460273 TTTTGTCCGGAAAGCTGGCC 61.460 55.000 5.23 0.00 40.61 5.36
2946 3502 0.040067 CGTGCCTGTCCTTTGCTTTC 60.040 55.000 0.00 0.00 0.00 2.62
3048 3618 2.198406 TCGAAAATATCCGTTGGAGCG 58.802 47.619 0.00 0.00 34.05 5.03
3053 3623 0.810031 ATATCCGTTGGAGCGTGTGC 60.810 55.000 0.00 0.00 43.24 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.039202 GGCATCTCCAACGCCAACG 62.039 63.158 0.00 0.00 45.52 4.10
38 39 2.877691 GGCATCTCCAACGCCAAC 59.122 61.111 0.00 0.00 45.52 3.77
54 55 1.468520 CAAGAACACGCATGGTAAGGG 59.531 52.381 0.00 0.00 0.00 3.95
55 56 2.151202 ACAAGAACACGCATGGTAAGG 58.849 47.619 0.00 0.00 0.00 2.69
58 59 4.465632 AGATACAAGAACACGCATGGTA 57.534 40.909 0.00 0.00 0.00 3.25
65 66 4.389077 GGACTTCCAAGATACAAGAACACG 59.611 45.833 0.00 0.00 35.64 4.49
66 67 5.409826 CAGGACTTCCAAGATACAAGAACAC 59.590 44.000 0.00 0.00 38.89 3.32
67 68 5.071788 ACAGGACTTCCAAGATACAAGAACA 59.928 40.000 0.00 0.00 38.89 3.18
68 69 5.409826 CACAGGACTTCCAAGATACAAGAAC 59.590 44.000 0.00 0.00 38.89 3.01
69 70 5.306937 TCACAGGACTTCCAAGATACAAGAA 59.693 40.000 0.00 0.00 38.89 2.52
70 71 4.838423 TCACAGGACTTCCAAGATACAAGA 59.162 41.667 0.00 0.00 38.89 3.02
100 101 3.960102 TGTGAGCTCATTTTTGGACCTTT 59.040 39.130 21.47 0.00 0.00 3.11
121 122 8.592105 TGGATGAAAGTTTATTTTGAGCTTTG 57.408 30.769 0.00 0.00 30.64 2.77
147 149 6.983890 ACTTGGTTGGTGTTTCATTCATAAAC 59.016 34.615 0.00 0.00 37.35 2.01
157 159 1.385528 ACGGACTTGGTTGGTGTTTC 58.614 50.000 0.00 0.00 0.00 2.78
169 171 1.870993 GCGAGGTGTTTGTACGGACTT 60.871 52.381 0.00 0.00 0.00 3.01
192 194 0.462047 CCGGGAAAATGTCGCTAGCT 60.462 55.000 13.93 0.00 37.05 3.32
243 245 0.381089 ACACGTGCGAGCTATACCTC 59.619 55.000 17.22 0.00 0.00 3.85
245 247 2.578369 CACACGTGCGAGCTATACC 58.422 57.895 17.22 0.00 0.00 2.73
282 284 2.485582 CTCACGATCCTCGCACGT 59.514 61.111 0.00 0.00 45.12 4.49
393 435 3.177884 TGTGGGAACAGGCAGCCT 61.178 61.111 8.70 8.70 44.46 4.58
394 436 2.985847 GTGTGGGAACAGGCAGCC 60.986 66.667 1.84 1.84 44.46 4.85
395 437 2.985847 GGTGTGGGAACAGGCAGC 60.986 66.667 0.00 0.00 44.46 5.25
397 439 1.943730 AAAGGGTGTGGGAACAGGCA 61.944 55.000 0.00 0.00 44.46 4.75
398 440 1.152546 AAAGGGTGTGGGAACAGGC 60.153 57.895 0.00 0.00 44.46 4.85
399 441 0.539669 GGAAAGGGTGTGGGAACAGG 60.540 60.000 0.00 0.00 44.46 4.00
400 442 0.539669 GGGAAAGGGTGTGGGAACAG 60.540 60.000 0.00 0.00 44.46 3.16
401 443 0.996762 AGGGAAAGGGTGTGGGAACA 60.997 55.000 0.00 0.00 38.70 3.18
402 444 0.187606 AAGGGAAAGGGTGTGGGAAC 59.812 55.000 0.00 0.00 0.00 3.62
404 446 1.432023 GGAAGGGAAAGGGTGTGGGA 61.432 60.000 0.00 0.00 0.00 4.37
405 447 1.076727 GGAAGGGAAAGGGTGTGGG 59.923 63.158 0.00 0.00 0.00 4.61
408 450 2.081585 GCTGGGAAGGGAAAGGGTGT 62.082 60.000 0.00 0.00 0.00 4.16
410 452 2.907179 CGCTGGGAAGGGAAAGGGT 61.907 63.158 0.00 0.00 0.00 4.34
411 453 2.044946 CGCTGGGAAGGGAAAGGG 60.045 66.667 0.00 0.00 0.00 3.95
413 455 1.616159 TTTTCGCTGGGAAGGGAAAG 58.384 50.000 14.88 0.00 46.33 2.62
414 456 2.074729 TTTTTCGCTGGGAAGGGAAA 57.925 45.000 12.32 12.32 44.95 3.13
416 458 1.074727 TCATTTTTCGCTGGGAAGGGA 59.925 47.619 7.24 2.24 35.70 4.20
417 459 1.202348 GTCATTTTTCGCTGGGAAGGG 59.798 52.381 7.24 0.09 35.70 3.95
419 461 2.247311 CGTCATTTTTCGCTGGGAAG 57.753 50.000 7.24 0.00 35.70 3.46
436 478 0.820074 TTGATTTGGTTCGGTGGCGT 60.820 50.000 0.00 0.00 0.00 5.68
459 504 0.320247 AAACAGAGAGCCAGCACTCG 60.320 55.000 10.75 8.72 41.77 4.18
483 531 5.365314 AGAGCCACCCAACATTTAAAAAGAA 59.635 36.000 0.00 0.00 0.00 2.52
485 533 5.011023 AGAGAGCCACCCAACATTTAAAAAG 59.989 40.000 0.00 0.00 0.00 2.27
491 539 1.145738 ACAGAGAGCCACCCAACATTT 59.854 47.619 0.00 0.00 0.00 2.32
496 544 1.494721 AGAAAACAGAGAGCCACCCAA 59.505 47.619 0.00 0.00 0.00 4.12
500 548 3.045601 TGCTAGAAAACAGAGAGCCAC 57.954 47.619 0.00 0.00 31.98 5.01
510 558 6.089150 ACGTAGTTTCTTCGATGCTAGAAAAC 59.911 38.462 10.73 7.68 37.78 2.43
514 562 4.959596 ACGTAGTTTCTTCGATGCTAGA 57.040 40.909 0.00 0.00 37.78 2.43
515 563 6.256686 AGTTACGTAGTTTCTTCGATGCTAG 58.743 40.000 0.00 0.00 37.78 3.42
516 564 6.187125 AGTTACGTAGTTTCTTCGATGCTA 57.813 37.500 0.00 0.00 37.78 3.49
517 565 5.056894 AGTTACGTAGTTTCTTCGATGCT 57.943 39.130 0.00 0.00 37.78 3.79
518 566 6.859715 TTAGTTACGTAGTTTCTTCGATGC 57.140 37.500 0.00 0.00 37.78 3.91
660 1076 0.480252 GATTGGGATGAAGGAGGGGG 59.520 60.000 0.00 0.00 0.00 5.40
664 1080 2.158696 GGGTGAGATTGGGATGAAGGAG 60.159 54.545 0.00 0.00 0.00 3.69
797 1213 2.246719 AGGCTGATATTTCTGGCGAC 57.753 50.000 9.98 0.00 46.71 5.19
808 1224 0.179468 GGTGCGGGTTTAGGCTGATA 59.821 55.000 0.00 0.00 0.00 2.15
959 1377 4.507916 TCGAGGAGGAGGAGGGCG 62.508 72.222 0.00 0.00 0.00 6.13
960 1378 2.520741 CTCGAGGAGGAGGAGGGC 60.521 72.222 3.91 0.00 0.00 5.19
985 1403 2.450476 CTCCATGGTTCTTTCCCCTTG 58.550 52.381 12.58 0.00 0.00 3.61
987 1405 0.332972 GCTCCATGGTTCTTTCCCCT 59.667 55.000 12.58 0.00 0.00 4.79
988 1406 0.684479 GGCTCCATGGTTCTTTCCCC 60.684 60.000 12.58 0.00 0.00 4.81
989 1407 1.032114 CGGCTCCATGGTTCTTTCCC 61.032 60.000 12.58 2.25 0.00 3.97
990 1408 1.032114 CCGGCTCCATGGTTCTTTCC 61.032 60.000 12.58 4.37 0.00 3.13
992 1410 1.678970 GCCGGCTCCATGGTTCTTT 60.679 57.895 22.15 0.00 0.00 2.52
993 1411 2.044946 GCCGGCTCCATGGTTCTT 60.045 61.111 22.15 0.00 0.00 2.52
994 1412 4.473520 CGCCGGCTCCATGGTTCT 62.474 66.667 26.68 0.00 0.00 3.01
2040 2473 2.411535 CATGTGCATGGGCGAGAAT 58.588 52.632 4.35 0.00 45.35 2.40
2049 2482 1.033746 GGAGGACCACCATGTGCATG 61.034 60.000 2.58 5.26 38.94 4.06
2134 2570 4.765339 CCCGGTTTTTCTTACCTCTGATTT 59.235 41.667 0.00 0.00 33.35 2.17
2135 2571 4.042435 TCCCGGTTTTTCTTACCTCTGATT 59.958 41.667 0.00 0.00 33.35 2.57
2196 2632 2.614057 ACGCCAAATCAATAGCACTAGC 59.386 45.455 0.00 0.00 42.56 3.42
2215 2654 2.005960 CTCTCCTCCCGGCTACAACG 62.006 65.000 0.00 0.00 0.00 4.10
2283 2792 5.112686 CAACTCCACCCAAAAATCGAAAAA 58.887 37.500 0.00 0.00 0.00 1.94
2284 2793 4.442192 CCAACTCCACCCAAAAATCGAAAA 60.442 41.667 0.00 0.00 0.00 2.29
2344 2853 3.085533 AGGAAGATCTATCCACGGATCG 58.914 50.000 19.67 0.00 42.02 3.69
2381 2893 9.406828 CGGAAGACAAAATATAGATGACGATTA 57.593 33.333 0.00 0.00 0.00 1.75
2382 2894 7.095607 GCGGAAGACAAAATATAGATGACGATT 60.096 37.037 0.00 0.00 0.00 3.34
2390 2902 8.780846 TTTAGTTGCGGAAGACAAAATATAGA 57.219 30.769 0.00 0.00 0.00 1.98
2405 2917 3.659786 TCCATCCGATATTTAGTTGCGG 58.340 45.455 0.00 0.00 43.11 5.69
2406 2918 6.330278 TCTATCCATCCGATATTTAGTTGCG 58.670 40.000 0.00 0.00 32.88 4.85
2407 2919 7.324178 ACTCTATCCATCCGATATTTAGTTGC 58.676 38.462 0.00 0.00 32.88 4.17
2408 2920 8.744652 AGACTCTATCCATCCGATATTTAGTTG 58.255 37.037 0.00 0.00 32.88 3.16
2416 2928 4.223255 ACGAGAGACTCTATCCATCCGATA 59.777 45.833 4.57 0.00 31.92 2.92
2422 2934 3.067461 GTGCAACGAGAGACTCTATCCAT 59.933 47.826 4.57 0.00 0.00 3.41
2428 2940 1.000827 CAGTGTGCAACGAGAGACTCT 60.001 52.381 4.14 4.14 42.39 3.24
2492 3005 4.314121 ACTGATGAGCTCTCAAAACTGAC 58.686 43.478 16.19 0.00 43.58 3.51
2495 3008 6.060788 AGAAAACTGATGAGCTCTCAAAACT 58.939 36.000 16.19 8.16 43.58 2.66
2499 3012 5.482908 GGTAGAAAACTGATGAGCTCTCAA 58.517 41.667 16.19 0.00 43.58 3.02
2500 3013 4.081420 GGGTAGAAAACTGATGAGCTCTCA 60.081 45.833 16.19 14.32 44.59 3.27
2501 3014 4.438148 GGGTAGAAAACTGATGAGCTCTC 58.562 47.826 16.19 10.43 0.00 3.20
2502 3015 3.198853 GGGGTAGAAAACTGATGAGCTCT 59.801 47.826 16.19 0.00 0.00 4.09
2503 3016 3.198853 AGGGGTAGAAAACTGATGAGCTC 59.801 47.826 6.82 6.82 0.00 4.09
2504 3017 3.185455 AGGGGTAGAAAACTGATGAGCT 58.815 45.455 0.00 0.00 0.00 4.09
2505 3018 3.536570 GAGGGGTAGAAAACTGATGAGC 58.463 50.000 0.00 0.00 0.00 4.26
2506 3019 3.430929 CCGAGGGGTAGAAAACTGATGAG 60.431 52.174 0.00 0.00 0.00 2.90
2507 3020 2.500098 CCGAGGGGTAGAAAACTGATGA 59.500 50.000 0.00 0.00 0.00 2.92
2508 3021 2.906354 CCGAGGGGTAGAAAACTGATG 58.094 52.381 0.00 0.00 0.00 3.07
2544 3070 0.236449 CGTTTCTTACCGCCCAACAC 59.764 55.000 0.00 0.00 0.00 3.32
2546 3072 0.514255 GTCGTTTCTTACCGCCCAAC 59.486 55.000 0.00 0.00 0.00 3.77
2547 3073 0.106335 TGTCGTTTCTTACCGCCCAA 59.894 50.000 0.00 0.00 0.00 4.12
2548 3074 0.106335 TTGTCGTTTCTTACCGCCCA 59.894 50.000 0.00 0.00 0.00 5.36
2549 3075 1.069703 GTTTGTCGTTTCTTACCGCCC 60.070 52.381 0.00 0.00 0.00 6.13
2594 3121 2.290464 AGGTAGAGTAGCACTGTAGCG 58.710 52.381 13.10 0.00 44.21 4.26
2595 3122 5.766174 AGATAAGGTAGAGTAGCACTGTAGC 59.234 44.000 11.85 11.85 41.17 3.58
2596 3123 7.811117 AAGATAAGGTAGAGTAGCACTGTAG 57.189 40.000 0.00 0.00 0.00 2.74
2597 3124 8.053963 AGAAAGATAAGGTAGAGTAGCACTGTA 58.946 37.037 0.00 0.00 0.00 2.74
2598 3125 6.893005 AGAAAGATAAGGTAGAGTAGCACTGT 59.107 38.462 0.00 0.00 0.00 3.55
2599 3126 7.067615 TGAGAAAGATAAGGTAGAGTAGCACTG 59.932 40.741 0.00 0.00 0.00 3.66
2600 3127 7.067737 GTGAGAAAGATAAGGTAGAGTAGCACT 59.932 40.741 0.00 0.00 0.00 4.40
2601 3128 7.197703 GTGAGAAAGATAAGGTAGAGTAGCAC 58.802 42.308 0.00 0.00 0.00 4.40
2641 3168 1.229529 CAGGGGTACTGGGTGGAGT 60.230 63.158 0.00 0.00 43.70 3.85
2765 3292 1.736126 CCACAGTTCTCTACGCTACGA 59.264 52.381 0.00 0.00 0.00 3.43
2766 3293 1.202154 CCCACAGTTCTCTACGCTACG 60.202 57.143 0.00 0.00 0.00 3.51
2767 3294 1.817447 ACCCACAGTTCTCTACGCTAC 59.183 52.381 0.00 0.00 0.00 3.58
2768 3295 1.816835 CACCCACAGTTCTCTACGCTA 59.183 52.381 0.00 0.00 0.00 4.26
2772 3299 2.496470 CCTACCACCCACAGTTCTCTAC 59.504 54.545 0.00 0.00 0.00 2.59
2788 3315 0.533951 CCGACCACAACCTACCTACC 59.466 60.000 0.00 0.00 0.00 3.18
2789 3316 0.533951 CCCGACCACAACCTACCTAC 59.466 60.000 0.00 0.00 0.00 3.18
2790 3317 0.615544 CCCCGACCACAACCTACCTA 60.616 60.000 0.00 0.00 0.00 3.08
2791 3318 1.916777 CCCCGACCACAACCTACCT 60.917 63.158 0.00 0.00 0.00 3.08
2923 3479 2.980233 AAAGGACAGGCACGCAGC 60.980 61.111 0.00 0.00 44.65 5.25
3048 3618 3.376078 CCCACCTGCCATGCACAC 61.376 66.667 0.00 0.00 33.79 3.82
3053 3623 3.567579 AACGACCCCACCTGCCATG 62.568 63.158 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.