Multiple sequence alignment - TraesCS1D01G250200

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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 TraesCS1D01G250200 chr1D 100.000 3413 0 0 1 3413 342493258 342489846 0.000000e+00 6303
1 TraesCS1D01G250200 chr1D 91.677 793 34 10 1 788 445548683 445547918 0.000000e+00 1070
2 TraesCS1D01G250200 chr1B 92.667 1691 91 20 791 2467 458729435 458727764 0.000000e+00 2405
3 TraesCS1D01G250200 chr1B 89.556 900 64 15 2535 3413 458727755 458726865 0.000000e+00 1114
4 TraesCS1D01G250200 chr1A 92.007 1639 93 19 851 2468 442157829 442156208 0.000000e+00 2266
5 TraesCS1D01G250200 chr1A 91.834 845 45 14 2582 3413 442156096 442155263 0.000000e+00 1157
6 TraesCS1D01G250200 chr5D 93.805 791 43 4 1 789 545351371 545352157 0.000000e+00 1184
7 TraesCS1D01G250200 chr5D 97.094 413 12 0 373 785 545338864 545339276 0.000000e+00 697
8 TraesCS1D01G250200 chr3A 92.677 792 42 8 1 788 738402110 738401331 0.000000e+00 1127
9 TraesCS1D01G250200 chr3A 90.368 789 43 15 1 788 390991338 390992094 0.000000e+00 1005
10 TraesCS1D01G250200 chr7A 92.424 792 51 8 1 788 580344110 580344896 0.000000e+00 1122
11 TraesCS1D01G250200 chr7A 71.719 442 100 21 1878 2311 622372569 622372145 2.170000e-17 100
12 TraesCS1D01G250200 chr6A 91.740 799 43 12 1 786 566161267 566162055 0.000000e+00 1088
13 TraesCS1D01G250200 chr6A 90.875 800 46 15 1 786 565969557 565970343 0.000000e+00 1048
14 TraesCS1D01G250200 chr6A 90.595 723 48 8 76 786 566163354 566164068 0.000000e+00 941
15 TraesCS1D01G250200 chr7B 86.842 646 62 14 1 635 735744226 735744859 0.000000e+00 701


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 TraesCS1D01G250200 chr1D 342489846 342493258 3412 True 6303.0 6303 100.0000 1 3413 1 chr1D.!!$R1 3412
1 TraesCS1D01G250200 chr1D 445547918 445548683 765 True 1070.0 1070 91.6770 1 788 1 chr1D.!!$R2 787
2 TraesCS1D01G250200 chr1B 458726865 458729435 2570 True 1759.5 2405 91.1115 791 3413 2 chr1B.!!$R1 2622
3 TraesCS1D01G250200 chr1A 442155263 442157829 2566 True 1711.5 2266 91.9205 851 3413 2 chr1A.!!$R1 2562
4 TraesCS1D01G250200 chr5D 545351371 545352157 786 False 1184.0 1184 93.8050 1 789 1 chr5D.!!$F2 788
5 TraesCS1D01G250200 chr3A 738401331 738402110 779 True 1127.0 1127 92.6770 1 788 1 chr3A.!!$R1 787
6 TraesCS1D01G250200 chr3A 390991338 390992094 756 False 1005.0 1005 90.3680 1 788 1 chr3A.!!$F1 787
7 TraesCS1D01G250200 chr7A 580344110 580344896 786 False 1122.0 1122 92.4240 1 788 1 chr7A.!!$F1 787
8 TraesCS1D01G250200 chr6A 565969557 565970343 786 False 1048.0 1048 90.8750 1 786 1 chr6A.!!$F1 785
9 TraesCS1D01G250200 chr6A 566161267 566164068 2801 False 1014.5 1088 91.1675 1 786 2 chr6A.!!$F2 785
10 TraesCS1D01G250200 chr7B 735744226 735744859 633 False 701.0 701 86.8420 1 635 1 chr7B.!!$F1 634

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
920 2964 0.107945 GTGAGGACAGAGGGACATGC 60.108 60.0 0.0 0.0 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2531 4595 0.471617 AGGAACACAAGCAGCTCTGT 59.528 50.0 0.0 0.0 0.0 3.41 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
366 2390 6.415280 CGTAATTTGGAAAATGTTCACGTTGA 59.585 34.615 0.00 0.00 35.25 3.18
509 2553 0.108138 GGCTAGCGACATGTGGTCTT 60.108 55.000 1.15 0.00 44.68 3.01
517 2561 2.872245 CGACATGTGGTCTTGTCTTTGT 59.128 45.455 1.15 0.00 44.68 2.83
573 2617 2.969238 GCATCCGGCACATCGAGG 60.969 66.667 0.00 0.00 43.97 4.63
602 2646 5.841810 TGGCTTGTTCAAAATAAAGGACAG 58.158 37.500 0.00 0.00 0.00 3.51
635 2679 5.798125 TGACTTCCATGTGCCAATAAAAA 57.202 34.783 0.00 0.00 0.00 1.94
806 2850 7.594758 TGCTAGTAACAACAAAAATTCATCAGC 59.405 33.333 0.00 0.00 0.00 4.26
807 2851 6.991485 AGTAACAACAAAAATTCATCAGCG 57.009 33.333 0.00 0.00 0.00 5.18
840 2884 1.270571 TGGTGTGAGCGACTTATTGCA 60.271 47.619 0.00 0.00 37.75 4.08
875 2919 2.423185 CTGCCGTTCCAAATGCTCATAA 59.577 45.455 0.00 0.00 0.00 1.90
920 2964 0.107945 GTGAGGACAGAGGGACATGC 60.108 60.000 0.00 0.00 0.00 4.06
921 2965 0.545071 TGAGGACAGAGGGACATGCA 60.545 55.000 0.00 0.00 0.00 3.96
973 3020 2.145397 TGTAGGGATCAGCTCGTTCT 57.855 50.000 0.00 0.00 0.00 3.01
974 3021 2.457598 TGTAGGGATCAGCTCGTTCTT 58.542 47.619 0.00 0.00 0.00 2.52
995 3042 3.443052 TGGGGTACGAAGAGGACAAATA 58.557 45.455 0.00 0.00 0.00 1.40
1295 3348 4.380843 TCCTTGGTACATGTCCATTTGT 57.619 40.909 15.05 0.00 39.30 2.83
1296 3349 4.735369 TCCTTGGTACATGTCCATTTGTT 58.265 39.130 15.05 0.00 39.30 2.83
1297 3350 4.764823 TCCTTGGTACATGTCCATTTGTTC 59.235 41.667 15.05 0.00 39.30 3.18
1298 3351 4.766891 CCTTGGTACATGTCCATTTGTTCT 59.233 41.667 15.05 0.00 39.30 3.01
1299 3352 5.243730 CCTTGGTACATGTCCATTTGTTCTT 59.756 40.000 15.05 0.00 39.30 2.52
1300 3353 5.957842 TGGTACATGTCCATTTGTTCTTC 57.042 39.130 0.00 0.00 0.00 2.87
1302 3355 5.830457 TGGTACATGTCCATTTGTTCTTCAA 59.170 36.000 0.00 0.00 0.00 2.69
1303 3356 6.016360 TGGTACATGTCCATTTGTTCTTCAAG 60.016 38.462 0.00 0.00 37.35 3.02
1305 3358 6.713762 ACATGTCCATTTGTTCTTCAAGAA 57.286 33.333 0.00 0.00 37.35 2.52
1306 3359 7.111247 ACATGTCCATTTGTTCTTCAAGAAA 57.889 32.000 0.00 0.00 35.75 2.52
1307 3360 7.729116 ACATGTCCATTTGTTCTTCAAGAAAT 58.271 30.769 0.00 0.00 35.75 2.17
1308 3361 7.654520 ACATGTCCATTTGTTCTTCAAGAAATG 59.345 33.333 0.00 2.47 46.05 2.32
1316 3369 6.005583 TGTTCTTCAAGAAATGAGATGCAC 57.994 37.500 0.00 0.00 39.77 4.57
1320 3373 3.076621 TCAAGAAATGAGATGCACGCTT 58.923 40.909 0.00 0.00 33.04 4.68
1334 3387 3.535860 GCACGCTTGCTCTTTAATATCG 58.464 45.455 8.12 0.00 46.17 2.92
1335 3388 3.245284 GCACGCTTGCTCTTTAATATCGA 59.755 43.478 8.12 0.00 46.17 3.59
1341 3398 6.789403 CGCTTGCTCTTTAATATCGATCTTTG 59.211 38.462 0.00 0.00 0.00 2.77
1348 3405 9.239002 CTCTTTAATATCGATCTTTGAACGAGT 57.761 33.333 0.00 0.00 39.88 4.18
1371 3430 1.000385 GCATTTGTGGTTGTGCAGCTA 60.000 47.619 0.00 0.00 37.52 3.32
1413 3472 1.272816 TGAACCCATACCTCGACAGGA 60.273 52.381 0.00 0.00 43.65 3.86
1415 3474 0.629596 ACCCATACCTCGACAGGAGA 59.370 55.000 0.00 0.00 46.23 3.71
1548 3607 2.027745 GTCCAGCTCAGATGGTTCAAGA 60.028 50.000 9.29 0.00 39.01 3.02
1569 3628 0.326264 GTTCATGAGCTCCACCACCT 59.674 55.000 12.15 0.00 0.00 4.00
1584 3643 0.549950 CACCTACTCCCCTCGAGGTA 59.450 60.000 29.25 16.26 43.57 3.08
1585 3644 0.845337 ACCTACTCCCCTCGAGGTAG 59.155 60.000 29.25 25.72 43.57 3.18
1586 3645 0.537828 CCTACTCCCCTCGAGGTAGC 60.538 65.000 29.25 0.00 43.57 3.58
1587 3646 0.885596 CTACTCCCCTCGAGGTAGCG 60.886 65.000 29.25 17.40 43.57 4.26
1588 3647 2.955022 TACTCCCCTCGAGGTAGCGC 62.955 65.000 29.25 0.00 43.57 5.92
1612 3671 1.280421 ACTGCCCTTCACCTTCTCATC 59.720 52.381 0.00 0.00 0.00 2.92
1614 3673 1.918262 TGCCCTTCACCTTCTCATCAT 59.082 47.619 0.00 0.00 0.00 2.45
1660 3724 6.073440 AGCACAAATTAAGCTGATGCAAAAAG 60.073 34.615 0.00 0.00 42.74 2.27
1800 3864 2.537560 CGACCCGATCAGCAATGCC 61.538 63.158 0.00 0.00 0.00 4.40
1869 3933 2.487934 GTCGTGCAATCCATAGCAGAT 58.512 47.619 0.00 0.00 42.14 2.90
1985 4049 1.953138 CATCGAGCTCCACATCGCC 60.953 63.158 8.47 0.00 38.79 5.54
2093 4157 4.101790 GTCGTACCCGGACGCGAA 62.102 66.667 15.93 0.00 42.62 4.70
2223 4287 3.195661 CGGCAGGGAGTATAACTTTGAC 58.804 50.000 0.00 0.00 0.00 3.18
2285 4349 4.659172 CCCAAGCAGGCGTCCCAA 62.659 66.667 0.00 0.00 35.39 4.12
2454 4518 1.072505 GTTTTGGGCCTCCGTCTGA 59.927 57.895 4.53 0.00 35.24 3.27
2468 4532 4.000325 TCCGTCTGATGTAACCACATTTG 59.000 43.478 0.00 0.00 45.58 2.32
2477 4541 2.745884 CCACATTTGGGCGAGCGA 60.746 61.111 0.00 0.00 39.57 4.93
2478 4542 2.331893 CCACATTTGGGCGAGCGAA 61.332 57.895 0.00 0.00 39.57 4.70
2480 4544 1.302511 ACATTTGGGCGAGCGAACT 60.303 52.632 0.00 0.00 0.00 3.01
2489 4553 2.254651 GAGCGAACTCGTGGTCGT 59.745 61.111 23.95 12.25 42.22 4.34
2490 4554 2.050351 AGCGAACTCGTGGTCGTG 60.050 61.111 23.95 0.13 42.22 4.35
2491 4555 3.103911 GCGAACTCGTGGTCGTGG 61.104 66.667 23.95 0.00 42.22 4.94
2492 4556 2.430244 CGAACTCGTGGTCGTGGG 60.430 66.667 16.33 0.00 38.33 4.61
2493 4557 2.732658 GAACTCGTGGTCGTGGGT 59.267 61.111 0.00 0.00 38.33 4.51
2494 4558 1.663702 GAACTCGTGGTCGTGGGTG 60.664 63.158 0.00 0.00 38.33 4.61
2495 4559 2.359570 GAACTCGTGGTCGTGGGTGT 62.360 60.000 0.00 0.00 38.33 4.16
2496 4560 2.049433 CTCGTGGTCGTGGGTGTC 60.049 66.667 0.00 0.00 38.33 3.67
2497 4561 3.569049 CTCGTGGTCGTGGGTGTCC 62.569 68.421 0.00 0.00 38.33 4.02
2498 4562 3.918977 CGTGGTCGTGGGTGTCCA 61.919 66.667 0.00 0.00 41.58 4.02
2499 4563 2.506962 GTGGTCGTGGGTGTCCAA 59.493 61.111 0.00 0.00 46.04 3.53
2500 4564 1.890510 GTGGTCGTGGGTGTCCAAC 60.891 63.158 0.00 0.00 46.04 3.77
2501 4565 2.663852 GGTCGTGGGTGTCCAACG 60.664 66.667 9.17 9.17 46.04 4.10
2502 4566 3.343421 GTCGTGGGTGTCCAACGC 61.343 66.667 10.44 3.29 46.04 4.84
2507 4571 2.904866 GGGTGTCCAACGCAAGCA 60.905 61.111 0.00 0.00 41.30 3.91
2508 4572 2.639286 GGTGTCCAACGCAAGCAG 59.361 61.111 0.00 0.00 45.62 4.24
2509 4573 1.891919 GGTGTCCAACGCAAGCAGA 60.892 57.895 0.00 0.00 45.62 4.26
2510 4574 1.571460 GTGTCCAACGCAAGCAGAG 59.429 57.895 0.00 0.00 45.62 3.35
2511 4575 2.253758 TGTCCAACGCAAGCAGAGC 61.254 57.895 0.00 0.00 45.62 4.09
2512 4576 1.963338 GTCCAACGCAAGCAGAGCT 60.963 57.895 0.00 0.00 42.56 4.09
2513 4577 1.962822 TCCAACGCAAGCAGAGCTG 60.963 57.895 0.00 0.00 39.62 4.24
2548 4612 3.427161 AAAACAGAGCTGCTTGTGTTC 57.573 42.857 23.40 4.39 31.94 3.18
2552 4616 0.761187 AGAGCTGCTTGTGTTCCTCA 59.239 50.000 2.53 0.00 0.00 3.86
2553 4617 1.141657 AGAGCTGCTTGTGTTCCTCAA 59.858 47.619 2.53 0.00 0.00 3.02
2615 4723 4.691175 TGCTTCATCTGTCTCTATTCAGC 58.309 43.478 0.00 0.00 0.00 4.26
2619 4727 3.316588 TCATCTGTCTCTATTCAGCGACC 59.683 47.826 0.00 0.00 35.96 4.79
2623 4731 1.751924 GTCTCTATTCAGCGACCCAGT 59.248 52.381 0.00 0.00 31.52 4.00
2637 4750 1.202627 ACCCAGTTGCGTACCGTTTAA 60.203 47.619 0.00 0.00 0.00 1.52
2670 4783 3.287222 GCTGTTGTATAAATGGAGCCCA 58.713 45.455 0.00 0.00 38.19 5.36
2674 4787 5.765510 TGTTGTATAAATGGAGCCCAGAAT 58.234 37.500 0.41 0.00 36.75 2.40
2682 4795 6.966534 AAATGGAGCCCAGAATTAGTAATG 57.033 37.500 0.00 0.00 36.75 1.90
2702 4815 4.069300 TGTTTGCCAGATTTTGCATGAA 57.931 36.364 0.00 0.00 37.33 2.57
2793 4910 6.701841 ACTCGACATATTATGTGATTGTCACC 59.298 38.462 13.93 0.00 46.40 4.02
2800 4917 1.674322 GTGATTGTCACCCCCACCG 60.674 63.158 0.00 0.00 41.37 4.94
2845 4962 1.498865 GCACACACACCCTGAGAACG 61.499 60.000 0.00 0.00 0.00 3.95
2910 5045 2.287909 ACGCACACGCAAACCAATAATT 60.288 40.909 0.00 0.00 45.53 1.40
2913 5048 3.608073 GCACACGCAAACCAATAATTCTC 59.392 43.478 0.00 0.00 38.36 2.87
2914 5049 4.165779 CACACGCAAACCAATAATTCTCC 58.834 43.478 0.00 0.00 0.00 3.71
2916 5051 4.522789 ACACGCAAACCAATAATTCTCCTT 59.477 37.500 0.00 0.00 0.00 3.36
2917 5052 4.858692 CACGCAAACCAATAATTCTCCTTG 59.141 41.667 0.00 0.00 0.00 3.61
2918 5053 3.859386 CGCAAACCAATAATTCTCCTTGC 59.141 43.478 0.00 0.00 35.67 4.01
2919 5054 4.183865 GCAAACCAATAATTCTCCTTGCC 58.816 43.478 0.00 0.00 33.50 4.52
2920 5055 4.322650 GCAAACCAATAATTCTCCTTGCCA 60.323 41.667 0.00 0.00 33.50 4.92
2921 5056 5.792741 CAAACCAATAATTCTCCTTGCCAA 58.207 37.500 0.00 0.00 0.00 4.52
2922 5057 5.665916 AACCAATAATTCTCCTTGCCAAG 57.334 39.130 0.00 0.00 0.00 3.61
2923 5058 4.934356 ACCAATAATTCTCCTTGCCAAGA 58.066 39.130 5.89 0.00 0.00 3.02
2924 5059 5.522641 ACCAATAATTCTCCTTGCCAAGAT 58.477 37.500 5.89 0.00 0.00 2.40
2925 5060 5.361857 ACCAATAATTCTCCTTGCCAAGATG 59.638 40.000 5.89 0.00 0.00 2.90
2926 5061 5.595542 CCAATAATTCTCCTTGCCAAGATGA 59.404 40.000 5.89 0.63 0.00 2.92
2927 5062 6.267014 CCAATAATTCTCCTTGCCAAGATGAT 59.733 38.462 5.89 0.00 0.00 2.45
2935 5070 4.141344 TCCTTGCCAAGATGATGATGATGA 60.141 41.667 5.89 0.00 0.00 2.92
2959 5094 3.189287 GCACCTTCAAATAGACCACACTG 59.811 47.826 0.00 0.00 0.00 3.66
3005 5143 1.552337 GATCAGACCCTTGCTCTGACA 59.448 52.381 4.87 0.00 45.43 3.58
3021 5159 4.415150 CACCCATGGGCGTCTGCT 62.415 66.667 31.73 6.30 42.25 4.24
3142 5282 1.299240 GAGCCGCGTTAGCTAGGTC 60.299 63.158 8.36 0.61 41.75 3.85
3150 5290 1.993370 CGTTAGCTAGGTCACACAAGC 59.007 52.381 0.00 0.00 35.16 4.01
3154 5294 1.151668 GCTAGGTCACACAAGCACAG 58.848 55.000 0.00 0.00 35.05 3.66
3158 5298 0.886490 GGTCACACAAGCACAGGAGG 60.886 60.000 0.00 0.00 0.00 4.30
3159 5299 0.886490 GTCACACAAGCACAGGAGGG 60.886 60.000 0.00 0.00 0.00 4.30
3160 5300 1.053835 TCACACAAGCACAGGAGGGA 61.054 55.000 0.00 0.00 0.00 4.20
3161 5301 0.037303 CACACAAGCACAGGAGGGAT 59.963 55.000 0.00 0.00 0.00 3.85
3274 5416 2.450243 GAGGGTGAGGGTCCAGGA 59.550 66.667 0.00 0.00 0.00 3.86
3365 5507 2.418910 CGAGGTGGAGATGCCGACT 61.419 63.158 0.00 0.00 40.66 4.18
3370 5512 4.521062 GGAGATGCCGACTGCGCT 62.521 66.667 9.73 0.00 45.60 5.92
3391 5533 1.068753 CCAGGAGCGCGAAGATGAT 59.931 57.895 12.10 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
332 2356 8.406172 ACATTTTCCAAATTACGAACATATGC 57.594 30.769 1.58 0.00 0.00 3.14
335 2359 9.400638 GTGAACATTTTCCAAATTACGAACATA 57.599 29.630 0.00 0.00 0.00 2.29
336 2360 7.114247 CGTGAACATTTTCCAAATTACGAACAT 59.886 33.333 0.00 0.00 29.58 2.71
418 2462 9.567848 AAAGAATATAATGCAACGTCGAAATTT 57.432 25.926 0.00 0.00 0.00 1.82
509 2553 2.546778 GAACTCACGACCACAAAGACA 58.453 47.619 0.00 0.00 0.00 3.41
517 2561 3.786809 GTGATCGAACTCACGACCA 57.213 52.632 3.54 0.00 44.84 4.02
573 2617 7.923878 TCCTTTATTTTGAACAAGCCAACTTAC 59.076 33.333 0.00 0.00 33.74 2.34
602 2646 5.973565 GCACATGGAAGTCAATAAGTTATGC 59.026 40.000 0.00 0.00 0.00 3.14
789 2833 3.652274 ACCCGCTGATGAATTTTTGTTG 58.348 40.909 0.00 0.00 0.00 3.33
806 2850 3.966543 ACCAAGCCCCTTGACCCG 61.967 66.667 6.54 0.00 43.42 5.28
807 2851 2.283173 CACCAAGCCCCTTGACCC 60.283 66.667 6.54 0.00 43.42 4.46
875 2919 8.035394 CAGAAATACACAGATACAGTTGGTAGT 58.965 37.037 0.00 0.00 34.92 2.73
973 3020 1.719529 TTGTCCTCTTCGTACCCCAA 58.280 50.000 0.00 0.00 0.00 4.12
974 3021 1.719529 TTTGTCCTCTTCGTACCCCA 58.280 50.000 0.00 0.00 0.00 4.96
995 3042 2.486907 GCTAGAGCAAGAGCCATGGATT 60.487 50.000 18.40 1.53 43.56 3.01
1295 3348 4.378770 GCGTGCATCTCATTTCTTGAAGAA 60.379 41.667 3.02 3.02 32.78 2.52
1296 3349 3.125829 GCGTGCATCTCATTTCTTGAAGA 59.874 43.478 0.00 0.00 32.78 2.87
1297 3350 3.126514 AGCGTGCATCTCATTTCTTGAAG 59.873 43.478 0.00 0.00 32.78 3.02
1298 3351 3.076621 AGCGTGCATCTCATTTCTTGAA 58.923 40.909 0.00 0.00 32.78 2.69
1299 3352 2.703416 AGCGTGCATCTCATTTCTTGA 58.297 42.857 0.00 0.00 0.00 3.02
1300 3353 3.168963 CAAGCGTGCATCTCATTTCTTG 58.831 45.455 0.00 0.00 0.00 3.02
1316 3369 6.459257 AAGATCGATATTAAAGAGCAAGCG 57.541 37.500 2.85 0.00 0.00 4.68
1320 3373 7.704899 TCGTTCAAAGATCGATATTAAAGAGCA 59.295 33.333 5.58 0.00 30.40 4.26
1326 3379 7.167635 GCTCACTCGTTCAAAGATCGATATTAA 59.832 37.037 5.58 0.00 34.12 1.40
1329 3382 4.979197 GCTCACTCGTTCAAAGATCGATAT 59.021 41.667 0.00 0.00 34.12 1.63
1330 3383 4.142469 TGCTCACTCGTTCAAAGATCGATA 60.142 41.667 0.00 0.00 34.12 2.92
1331 3384 3.182967 GCTCACTCGTTCAAAGATCGAT 58.817 45.455 0.00 0.00 34.12 3.59
1332 3385 2.030274 TGCTCACTCGTTCAAAGATCGA 60.030 45.455 0.00 0.00 33.63 3.59
1333 3386 2.328473 TGCTCACTCGTTCAAAGATCG 58.672 47.619 0.00 0.00 0.00 3.69
1334 3387 4.935885 AATGCTCACTCGTTCAAAGATC 57.064 40.909 0.00 0.00 0.00 2.75
1335 3388 4.516698 ACAAATGCTCACTCGTTCAAAGAT 59.483 37.500 0.00 0.00 0.00 2.40
1341 3398 1.873591 ACCACAAATGCTCACTCGTTC 59.126 47.619 0.00 0.00 0.00 3.95
1348 3405 1.067364 CTGCACAACCACAAATGCTCA 59.933 47.619 0.00 0.00 38.90 4.26
1371 3430 3.095347 GCGGGAGGCCGAGATCTTT 62.095 63.158 0.00 0.00 34.80 2.52
1394 3453 1.409427 CTCCTGTCGAGGTATGGGTTC 59.591 57.143 0.00 0.00 40.76 3.62
1494 3553 3.327404 GGTGTGGGGGACGGTGAT 61.327 66.667 0.00 0.00 0.00 3.06
1548 3607 1.271597 GGTGGTGGAGCTCATGAACTT 60.272 52.381 17.19 0.00 0.00 2.66
1585 3644 2.740826 TGAAGGGCAGTAACGCGC 60.741 61.111 5.73 0.00 44.66 6.86
1586 3645 2.388232 GGTGAAGGGCAGTAACGCG 61.388 63.158 3.53 3.53 0.00 6.01
1587 3646 0.605589 AAGGTGAAGGGCAGTAACGC 60.606 55.000 0.00 0.00 0.00 4.84
1588 3647 1.002087 AGAAGGTGAAGGGCAGTAACG 59.998 52.381 0.00 0.00 0.00 3.18
1589 3648 2.038557 TGAGAAGGTGAAGGGCAGTAAC 59.961 50.000 0.00 0.00 0.00 2.50
1590 3649 2.334977 TGAGAAGGTGAAGGGCAGTAA 58.665 47.619 0.00 0.00 0.00 2.24
1612 3671 4.717233 TGGTGGCAAGTTAATTAGCATG 57.283 40.909 1.97 1.31 0.00 4.06
1614 3673 4.560513 GCTTTGGTGGCAAGTTAATTAGCA 60.561 41.667 1.97 0.00 0.00 3.49
1824 3888 0.797542 GTACGAGTGAGAGAGCGTGT 59.202 55.000 0.00 0.00 37.56 4.49
1869 3933 3.573229 AGCACCTCCTTGGCTGCA 61.573 61.111 0.50 0.00 41.81 4.41
1968 4032 2.419198 GGCGATGTGGAGCTCGAT 59.581 61.111 7.83 0.00 37.05 3.59
2007 4071 0.679505 CCAGGACGTTGAAGGAGACA 59.320 55.000 0.00 0.00 0.00 3.41
2109 4173 1.811860 GAGGTAGGCGGCGAAGTAA 59.188 57.895 12.98 0.00 0.00 2.24
2206 4270 6.597562 TGTTGTTGTCAAAGTTATACTCCCT 58.402 36.000 0.00 0.00 35.20 4.20
2223 4287 2.332514 CCGCACAGCCTGTTGTTG 59.667 61.111 0.00 0.00 0.00 3.33
2271 4335 2.281761 CAGTTGGGACGCCTGCTT 60.282 61.111 0.00 0.00 0.00 3.91
2474 4538 3.103911 CCACGACCACGAGTTCGC 61.104 66.667 0.00 0.00 44.43 4.70
2475 4539 2.430244 CCCACGACCACGAGTTCG 60.430 66.667 0.00 0.00 46.33 3.95
2476 4540 1.663702 CACCCACGACCACGAGTTC 60.664 63.158 0.00 0.00 42.66 3.01
2477 4541 2.359570 GACACCCACGACCACGAGTT 62.360 60.000 0.00 0.00 42.66 3.01
2478 4542 2.836360 ACACCCACGACCACGAGT 60.836 61.111 0.00 0.00 42.66 4.18
2480 4544 3.608662 GGACACCCACGACCACGA 61.609 66.667 0.00 0.00 42.66 4.35
2482 4546 1.890510 GTTGGACACCCACGACCAC 60.891 63.158 0.00 0.00 43.41 4.16
2483 4547 2.506962 GTTGGACACCCACGACCA 59.493 61.111 0.00 0.00 43.41 4.02
2484 4548 2.663852 CGTTGGACACCCACGACC 60.664 66.667 8.38 0.00 43.41 4.79
2485 4549 3.343421 GCGTTGGACACCCACGAC 61.343 66.667 16.38 6.02 43.41 4.34
2486 4550 3.387225 TTGCGTTGGACACCCACGA 62.387 57.895 16.38 1.83 43.41 4.35
2487 4551 2.892334 CTTGCGTTGGACACCCACG 61.892 63.158 9.49 9.49 43.41 4.94
2488 4552 3.030652 CTTGCGTTGGACACCCAC 58.969 61.111 0.00 0.00 43.41 4.61
2489 4553 2.904866 GCTTGCGTTGGACACCCA 60.905 61.111 0.00 0.00 41.64 4.51
2490 4554 2.904866 TGCTTGCGTTGGACACCC 60.905 61.111 0.00 0.00 0.00 4.61
2491 4555 1.845809 CTCTGCTTGCGTTGGACACC 61.846 60.000 0.00 0.00 0.00 4.16
2492 4556 1.571460 CTCTGCTTGCGTTGGACAC 59.429 57.895 0.00 0.00 0.00 3.67
2493 4557 2.253758 GCTCTGCTTGCGTTGGACA 61.254 57.895 0.00 0.00 0.00 4.02
2494 4558 1.963338 AGCTCTGCTTGCGTTGGAC 60.963 57.895 0.00 0.00 33.89 4.02
2495 4559 1.962822 CAGCTCTGCTTGCGTTGGA 60.963 57.895 0.00 0.00 36.40 3.53
2496 4560 2.559840 CAGCTCTGCTTGCGTTGG 59.440 61.111 0.00 0.00 36.40 3.77
2506 4570 5.679734 TTTTAGACAAAGAAGCAGCTCTG 57.320 39.130 0.00 0.00 0.00 3.35
2531 4595 0.471617 AGGAACACAAGCAGCTCTGT 59.528 50.000 0.00 0.00 0.00 3.41
2570 4634 3.893720 AGCTTTCACAAATTCAGAAGCG 58.106 40.909 0.00 0.00 0.00 4.68
2670 4783 9.643693 CAAAATCTGGCAAACATTACTAATTCT 57.356 29.630 0.00 0.00 0.00 2.40
2674 4787 6.753180 TGCAAAATCTGGCAAACATTACTAA 58.247 32.000 0.00 0.00 37.03 2.24
2682 4795 3.808726 TGTTCATGCAAAATCTGGCAAAC 59.191 39.130 0.00 0.00 44.20 2.93
2702 4815 9.515020 CAAAATCTGGCAAATATATAACGTTGT 57.485 29.630 11.99 6.97 0.00 3.32
2800 4917 1.313091 GGTGAAATTGTCTCCGGCCC 61.313 60.000 0.00 0.00 30.44 5.80
2910 5045 3.457012 TCATCATCATCTTGGCAAGGAGA 59.543 43.478 25.92 22.31 0.00 3.71
2913 5048 4.142038 TCATCATCATCATCTTGGCAAGG 58.858 43.478 25.92 11.90 0.00 3.61
2914 5049 5.703876 CATCATCATCATCATCTTGGCAAG 58.296 41.667 21.17 21.17 0.00 4.01
2916 5051 3.506067 GCATCATCATCATCATCTTGGCA 59.494 43.478 0.00 0.00 0.00 4.92
2917 5052 3.506067 TGCATCATCATCATCATCTTGGC 59.494 43.478 0.00 0.00 0.00 4.52
2918 5053 4.082733 GGTGCATCATCATCATCATCTTGG 60.083 45.833 0.00 0.00 0.00 3.61
2919 5054 4.762251 AGGTGCATCATCATCATCATCTTG 59.238 41.667 0.00 0.00 0.00 3.02
2920 5055 4.986783 AGGTGCATCATCATCATCATCTT 58.013 39.130 0.00 0.00 0.00 2.40
2921 5056 4.642466 AGGTGCATCATCATCATCATCT 57.358 40.909 0.00 0.00 0.00 2.90
2922 5057 4.760204 TGAAGGTGCATCATCATCATCATC 59.240 41.667 0.00 0.00 0.00 2.92
2923 5058 4.725490 TGAAGGTGCATCATCATCATCAT 58.275 39.130 0.00 0.00 0.00 2.45
2924 5059 4.159244 TGAAGGTGCATCATCATCATCA 57.841 40.909 0.00 0.00 0.00 3.07
2925 5060 5.509716 TTTGAAGGTGCATCATCATCATC 57.490 39.130 5.61 0.00 0.00 2.92
2926 5061 7.002276 TCTATTTGAAGGTGCATCATCATCAT 58.998 34.615 5.61 4.42 0.00 2.45
2927 5062 6.261603 GTCTATTTGAAGGTGCATCATCATCA 59.738 38.462 5.61 0.00 0.00 3.07
2935 5070 3.758554 GTGTGGTCTATTTGAAGGTGCAT 59.241 43.478 0.00 0.00 0.00 3.96
3005 5143 4.101448 GAGCAGACGCCCATGGGT 62.101 66.667 31.58 13.70 39.83 4.51
3142 5282 0.037303 ATCCCTCCTGTGCTTGTGTG 59.963 55.000 0.00 0.00 0.00 3.82
3150 5290 1.763968 TCTGTCGTATCCCTCCTGTG 58.236 55.000 0.00 0.00 0.00 3.66
3154 5294 2.559231 GGAGAATCTGTCGTATCCCTCC 59.441 54.545 0.00 0.00 33.73 4.30
3158 5298 5.201713 TCAATGGAGAATCTGTCGTATCC 57.798 43.478 0.00 0.00 33.73 2.59
3159 5299 7.721286 AAATCAATGGAGAATCTGTCGTATC 57.279 36.000 0.00 0.00 33.73 2.24
3160 5300 8.424918 AGTAAATCAATGGAGAATCTGTCGTAT 58.575 33.333 0.00 0.00 33.73 3.06
3161 5301 7.706607 CAGTAAATCAATGGAGAATCTGTCGTA 59.293 37.037 0.00 0.00 33.73 3.43
3296 5438 3.274586 CCCGCCAGCATGATGTCG 61.275 66.667 7.52 7.52 39.69 4.35
3391 5533 3.234630 CTGGCGACGGGGTTCTTCA 62.235 63.158 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.