Multiple sequence alignment - TraesCS2A01G518000

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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 TraesCS2A01G518000 chr2A 100.000 2396 0 0 1 2396 741372075 741374470 0.000000e+00 4425.0
1 TraesCS2A01G518000 chr2D 86.960 1365 72 30 112 1458 609424249 609425525 0.000000e+00 1437.0
2 TraesCS2A01G518000 chr2D 90.345 290 20 4 2065 2353 609427790 609428072 8.090000e-100 374.0
3 TraesCS2A01G518000 chr2D 83.774 265 21 5 1825 2071 609427298 609427558 5.150000e-57 231.0
4 TraesCS2A01G518000 chr2D 91.743 109 7 2 1720 1828 609427149 609427255 1.480000e-32 150.0
5 TraesCS2A01G518000 chr2B 90.143 629 50 7 987 1609 743695111 743695733 0.000000e+00 808.0
6 TraesCS2A01G518000 chr2B 87.092 736 47 16 1 707 743694192 743694908 0.000000e+00 789.0
7 TraesCS2A01G518000 chr2B 84.249 546 40 15 1825 2337 743697085 743697617 7.700000e-135 490.0
8 TraesCS2A01G518000 chr2B 80.755 265 35 11 1825 2082 743700018 743700273 2.430000e-45 193.0
9 TraesCS2A01G518000 chr7D 90.625 64 6 0 1201 1264 422106760 422106697 4.240000e-13 86.1
10 TraesCS2A01G518000 chr4A 91.228 57 5 0 1201 1257 685738558 685738502 7.100000e-11 78.7
11 TraesCS2A01G518000 chr6B 97.674 43 1 0 1215 1257 21012797 21012839 9.190000e-10 75.0


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 TraesCS2A01G518000 chr2A 741372075 741374470 2395 False 4425 4425 100.00000 1 2396 1 chr2A.!!$F1 2395
1 TraesCS2A01G518000 chr2D 609424249 609428072 3823 False 548 1437 88.20550 112 2353 4 chr2D.!!$F1 2241
2 TraesCS2A01G518000 chr2B 743694192 743700273 6081 False 570 808 85.55975 1 2337 4 chr2B.!!$F1 2336

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
896 940 0.096628 CTTGATCTGCTGCAGCGAAC 59.903 55.0 32.11 27.0 45.83 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 3773 0.468585 ACTACATCCGTCCCGCCATA 60.469 55.0 0.0 0.0 0.0 2.74 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
28 29 2.103537 ATTTACTTGGTTCGACCCCG 57.896 50.000 0.00 0.00 37.50 5.73
31 32 1.120795 TACTTGGTTCGACCCCGGTT 61.121 55.000 0.00 0.00 37.50 4.44
86 87 2.125350 GGTCTCCGCTGGCAGAAG 60.125 66.667 20.86 11.92 0.00 2.85
96 97 2.134630 CTGGCAGAAGGAAGGGCACT 62.135 60.000 9.42 0.00 33.26 4.40
99 100 2.069776 CAGAAGGAAGGGCACTCCA 58.930 57.895 7.14 0.00 38.24 3.86
101 102 0.474660 AGAAGGAAGGGCACTCCAGT 60.475 55.000 7.14 0.00 38.24 4.00
261 274 3.291101 GACCTTGGTCGTAGCGCCA 62.291 63.158 2.29 0.00 33.08 5.69
365 383 2.119495 GATCCCAACTCTTCTGCCCTA 58.881 52.381 0.00 0.00 0.00 3.53
371 394 1.859302 ACTCTTCTGCCCTACTCCAG 58.141 55.000 0.00 0.00 0.00 3.86
373 396 2.031120 CTCTTCTGCCCTACTCCAGAG 58.969 57.143 0.00 0.00 39.09 3.35
389 412 9.179909 CTACTCCAGAGAAAAACTACAGATCTA 57.820 37.037 0.70 0.00 0.00 1.98
391 414 7.451877 ACTCCAGAGAAAAACTACAGATCTACA 59.548 37.037 0.70 0.00 0.00 2.74
392 415 8.367660 TCCAGAGAAAAACTACAGATCTACAT 57.632 34.615 0.00 0.00 0.00 2.29
393 416 9.475620 TCCAGAGAAAAACTACAGATCTACATA 57.524 33.333 0.00 0.00 0.00 2.29
434 457 0.915364 GGAGATCCTGACCAAAGGCT 59.085 55.000 0.00 0.00 37.24 4.58
445 468 0.318107 CCAAAGGCTGAAGCAACACG 60.318 55.000 4.43 0.00 44.36 4.49
446 469 0.936297 CAAAGGCTGAAGCAACACGC 60.936 55.000 4.43 0.00 44.36 5.34
523 546 3.066190 CCGCCGTCTCCCTGTGTA 61.066 66.667 0.00 0.00 0.00 2.90
581 608 0.806868 TGAGCTCCCAACGTACGTAG 59.193 55.000 23.12 16.12 0.00 3.51
649 683 1.004918 GCTGGTTGGCTCACGTACT 60.005 57.895 0.00 0.00 0.00 2.73
726 764 0.821517 ATCGTGCCGTGTCATCCTTA 59.178 50.000 0.00 0.00 0.00 2.69
765 809 0.179020 TGTCCAACACAGCCTGGAAG 60.179 55.000 0.00 0.00 43.32 3.46
792 836 1.654220 GTGCAATGCCGAACACACT 59.346 52.632 1.53 0.00 33.23 3.55
814 858 5.098218 TCATGCACACCGTAAAAGTAAAC 57.902 39.130 0.00 0.00 0.00 2.01
841 885 2.004017 GGAATTGCGGAATCGTGTGTA 58.996 47.619 1.48 0.00 38.89 2.90
861 905 6.007677 GTGTACATCTCGCTTTACTTTTTCG 58.992 40.000 0.00 0.00 0.00 3.46
862 906 4.066710 ACATCTCGCTTTACTTTTTCGC 57.933 40.909 0.00 0.00 0.00 4.70
863 907 2.848562 TCTCGCTTTACTTTTTCGCG 57.151 45.000 0.00 0.00 44.63 5.87
879 923 2.047274 CGATCACGGCACACCCTT 60.047 61.111 0.00 0.00 35.72 3.95
891 935 0.322277 ACACCCTTGATCTGCTGCAG 60.322 55.000 23.31 23.31 0.00 4.41
892 936 1.378250 ACCCTTGATCTGCTGCAGC 60.378 57.895 31.89 31.89 42.50 5.25
893 937 2.470362 CCCTTGATCTGCTGCAGCG 61.470 63.158 32.11 25.46 45.83 5.18
896 940 0.096628 CTTGATCTGCTGCAGCGAAC 59.903 55.000 32.11 27.00 45.83 3.95
899 943 0.802222 GATCTGCTGCAGCGAACGTA 60.802 55.000 32.11 13.90 45.83 3.57
900 944 0.179100 ATCTGCTGCAGCGAACGTAT 60.179 50.000 32.11 16.03 45.83 3.06
901 945 0.454196 TCTGCTGCAGCGAACGTATA 59.546 50.000 32.11 12.38 45.83 1.47
902 946 0.572590 CTGCTGCAGCGAACGTATAC 59.427 55.000 32.11 3.94 45.83 1.47
903 947 0.804544 TGCTGCAGCGAACGTATACC 60.805 55.000 32.11 3.40 45.83 2.73
904 948 0.527817 GCTGCAGCGAACGTATACCT 60.528 55.000 25.23 0.00 0.00 3.08
905 949 1.200483 CTGCAGCGAACGTATACCTG 58.800 55.000 0.00 0.00 0.00 4.00
907 951 0.101759 GCAGCGAACGTATACCTGGA 59.898 55.000 0.00 0.00 0.00 3.86
910 954 1.820519 AGCGAACGTATACCTGGACAA 59.179 47.619 0.00 0.00 0.00 3.18
911 955 2.429610 AGCGAACGTATACCTGGACAAT 59.570 45.455 0.00 0.00 0.00 2.71
912 956 3.633525 AGCGAACGTATACCTGGACAATA 59.366 43.478 0.00 0.00 0.00 1.90
924 968 1.003696 TGGACAATACGGTGGCAATGA 59.996 47.619 0.00 0.00 0.00 2.57
927 971 2.682856 GACAATACGGTGGCAATGATGT 59.317 45.455 0.00 0.00 0.00 3.06
973 1017 1.665442 GTGGCAACGGCTCCAAATT 59.335 52.632 0.00 0.00 40.87 1.82
1047 1091 3.443925 CTCGCACTCCTCCTCGCA 61.444 66.667 0.00 0.00 0.00 5.10
1073 1117 4.821589 GTTCTCCTCAGCCGCCGG 62.822 72.222 0.00 0.00 0.00 6.13
1115 1159 1.079819 CACGTAGGGTGCTGTGGAG 60.080 63.158 0.00 0.00 40.33 3.86
1412 1456 4.204775 CGTGTGACATGTTGATGTTGTTTG 59.795 41.667 0.00 0.00 43.22 2.93
1415 1459 4.739716 GTGACATGTTGATGTTGTTTGGTC 59.260 41.667 0.00 0.00 43.22 4.02
1429 1473 1.407656 TTGGTCTGGTGGAAGCGAGT 61.408 55.000 0.00 0.00 36.92 4.18
1459 1507 0.465287 TTGAGCAGTGCTGTCTGTCA 59.535 50.000 25.35 10.60 39.88 3.58
1525 1610 1.199097 CACTTCCCGGTGTATGCAAAC 59.801 52.381 0.00 0.00 33.04 2.93
1527 1612 0.250381 TTCCCGGTGTATGCAAACGT 60.250 50.000 0.00 0.00 0.00 3.99
1561 1648 7.065683 TGTTTGCGTCAACTATACATGAATCAT 59.934 33.333 0.00 0.00 0.00 2.45
1567 1654 7.149063 CGTCAACTATACATGAATCATCGTCAG 60.149 40.741 0.00 0.66 0.00 3.51
1609 1697 1.559965 AAGGAGAGGCCGGGGTTTAC 61.560 60.000 2.18 0.00 43.43 2.01
1675 3579 9.703892 ATCTCACATATAGAATGCTTACAGAAC 57.296 33.333 0.00 0.00 0.00 3.01
1679 3583 8.920665 CACATATAGAATGCTTACAGAACTAGC 58.079 37.037 0.00 0.00 35.50 3.42
1685 3590 3.985008 TGCTTACAGAACTAGCGTGAAA 58.015 40.909 0.00 0.00 37.73 2.69
1734 3705 3.954258 GCTAGGCAGAACCATACCATTTT 59.046 43.478 0.00 0.00 43.14 1.82
1750 3721 9.853555 CATACCATTTTTACATGCTAAACTCAA 57.146 29.630 0.00 0.00 0.00 3.02
1795 3766 5.460419 TGGTCAAATTTGTAAACATTGACGC 59.540 36.000 17.47 16.20 42.73 5.19
1802 3773 1.325338 GTAAACATTGACGCGCGGTAT 59.675 47.619 35.22 20.27 0.00 2.73
1805 3776 1.136690 ACATTGACGCGCGGTATATG 58.863 50.000 35.22 28.65 0.00 1.78
1829 3846 2.444351 GGACGGATGTAGTACGAAACG 58.556 52.381 0.00 0.90 37.67 3.60
1836 3853 2.170166 TGTAGTACGAAACGGGATGGT 58.830 47.619 0.00 0.00 0.00 3.55
1863 3880 1.099689 TGCATCAGGTCGATCGTACA 58.900 50.000 15.94 0.00 29.21 2.90
1877 3895 3.469008 TCGTACATTGATCCCCATGAC 57.531 47.619 0.00 0.00 0.00 3.06
1908 3926 3.795638 GGTCGATCTTTCACCGGC 58.204 61.111 0.00 0.00 0.00 6.13
1926 3944 0.865769 GCTCGTTTTGATGTGACGGT 59.134 50.000 0.00 0.00 37.39 4.83
1939 3957 0.678366 TGACGGTGCACCAAACTTGT 60.678 50.000 34.16 22.57 35.14 3.16
1995 4019 2.532715 ACCATGACCACTGGCCCT 60.533 61.111 0.00 0.00 37.27 5.19
2017 4053 2.848678 TGGTACTGGAGAGCTATGGT 57.151 50.000 0.00 0.00 0.00 3.55
2074 4356 0.454600 GGAACCTGCGAGATACACGA 59.545 55.000 0.00 0.00 0.00 4.35
2082 4364 4.559251 CCTGCGAGATACACGATAATTAGC 59.441 45.833 0.00 0.00 0.00 3.09
2095 4377 2.225068 AATTAGCGTGGATCGGAGTG 57.775 50.000 0.00 0.00 40.26 3.51
2096 4378 1.399714 ATTAGCGTGGATCGGAGTGA 58.600 50.000 0.00 0.00 40.26 3.41
2097 4379 0.738975 TTAGCGTGGATCGGAGTGAG 59.261 55.000 0.00 0.00 40.26 3.51
2098 4380 0.393944 TAGCGTGGATCGGAGTGAGT 60.394 55.000 0.00 0.00 40.26 3.41
2099 4381 1.517257 GCGTGGATCGGAGTGAGTG 60.517 63.158 0.00 0.00 40.26 3.51
2102 4384 0.108615 GTGGATCGGAGTGAGTGGTG 60.109 60.000 0.00 0.00 0.00 4.17
2186 4478 4.499399 CACACCTCGTGTTATCTCGTTATG 59.501 45.833 0.00 0.00 45.08 1.90
2248 4542 1.252904 ACATGCGCTCAGGCCAAAAT 61.253 50.000 9.73 0.00 34.44 1.82
2291 4585 2.358898 ACCTTGCATTGTGACACTGTTC 59.641 45.455 7.20 0.00 0.00 3.18
2339 4633 6.303839 AGGCTTGTATTTGGTGAGAGTTTTA 58.696 36.000 0.00 0.00 0.00 1.52
2340 4634 6.431234 AGGCTTGTATTTGGTGAGAGTTTTAG 59.569 38.462 0.00 0.00 0.00 1.85
2349 4643 5.882040 TGGTGAGAGTTTTAGAGAGAGAGA 58.118 41.667 0.00 0.00 0.00 3.10
2354 4648 7.278868 GTGAGAGTTTTAGAGAGAGAGAGAGAG 59.721 44.444 0.00 0.00 0.00 3.20
2355 4649 7.180229 TGAGAGTTTTAGAGAGAGAGAGAGAGA 59.820 40.741 0.00 0.00 0.00 3.10
2356 4650 7.560368 AGAGTTTTAGAGAGAGAGAGAGAGAG 58.440 42.308 0.00 0.00 0.00 3.20
2358 4652 7.560368 AGTTTTAGAGAGAGAGAGAGAGAGAG 58.440 42.308 0.00 0.00 0.00 3.20
2359 4653 7.400339 AGTTTTAGAGAGAGAGAGAGAGAGAGA 59.600 40.741 0.00 0.00 0.00 3.10
2360 4654 6.968263 TTAGAGAGAGAGAGAGAGAGAGAG 57.032 45.833 0.00 0.00 0.00 3.20
2361 4655 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2362 4656 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2363 4657 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2364 4658 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2366 4660 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2368 4662 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2370 4664 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2371 4665 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2373 4667 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2374 4668 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2375 4669 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2376 4670 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2378 4672 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2379 4673 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2380 4674 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2382 4676 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2383 4677 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2386 4680 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2389 4683 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2390 4684 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2391 4685 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2392 4686 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2393 4687 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2394 4688 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2395 4689 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.453136 GGTCGAACCAAGTAAATAACTGCA 59.547 41.667 0.00 0.00 38.88 4.41
75 76 2.437359 CCCTTCCTTCTGCCAGCG 60.437 66.667 0.00 0.00 0.00 5.18
80 81 1.377856 GGAGTGCCCTTCCTTCTGC 60.378 63.158 0.00 0.00 0.00 4.26
96 97 1.253100 TCACGATGCTACACACTGGA 58.747 50.000 0.00 0.00 0.00 3.86
99 100 2.080286 GGTTCACGATGCTACACACT 57.920 50.000 0.00 0.00 0.00 3.55
215 227 1.128692 GTCCATGACAGTAAGCAACGC 59.871 52.381 0.00 0.00 32.09 4.84
216 228 2.412870 TGTCCATGACAGTAAGCAACG 58.587 47.619 0.00 0.00 37.67 4.10
349 367 1.208293 GGAGTAGGGCAGAAGAGTTGG 59.792 57.143 0.00 0.00 0.00 3.77
350 368 1.902508 TGGAGTAGGGCAGAAGAGTTG 59.097 52.381 0.00 0.00 0.00 3.16
365 383 6.926630 AGATCTGTAGTTTTTCTCTGGAGT 57.073 37.500 0.00 0.00 0.00 3.85
389 412 5.124457 CCACACAGCAGCTTAGAATTTATGT 59.876 40.000 0.00 0.00 0.00 2.29
391 414 5.500234 TCCACACAGCAGCTTAGAATTTAT 58.500 37.500 0.00 0.00 0.00 1.40
392 415 4.905429 TCCACACAGCAGCTTAGAATTTA 58.095 39.130 0.00 0.00 0.00 1.40
393 416 3.754965 TCCACACAGCAGCTTAGAATTT 58.245 40.909 0.00 0.00 0.00 1.82
394 417 3.341823 CTCCACACAGCAGCTTAGAATT 58.658 45.455 0.00 0.00 0.00 2.17
395 418 2.355513 CCTCCACACAGCAGCTTAGAAT 60.356 50.000 0.00 0.00 0.00 2.40
396 419 1.002430 CCTCCACACAGCAGCTTAGAA 59.998 52.381 0.00 0.00 0.00 2.10
397 420 0.610174 CCTCCACACAGCAGCTTAGA 59.390 55.000 0.00 0.00 0.00 2.10
398 421 0.610174 TCCTCCACACAGCAGCTTAG 59.390 55.000 0.00 0.00 0.00 2.18
399 422 0.610174 CTCCTCCACACAGCAGCTTA 59.390 55.000 0.00 0.00 0.00 3.09
400 423 1.123861 TCTCCTCCACACAGCAGCTT 61.124 55.000 0.00 0.00 0.00 3.74
401 424 0.908656 ATCTCCTCCACACAGCAGCT 60.909 55.000 0.00 0.00 0.00 4.24
523 546 0.673644 CGTCGAAGGGAACAAGGCAT 60.674 55.000 0.00 0.00 0.00 4.40
588 615 3.369385 CATTTTCTCCATGAATGCGCTC 58.631 45.455 9.73 0.00 34.24 5.03
726 764 2.275134 TTGCATGATGTGTGACTGGT 57.725 45.000 0.00 0.00 0.00 4.00
765 809 2.581409 GCATTGCACGATGCTGCC 60.581 61.111 14.76 0.00 46.85 4.85
781 825 1.207593 GTGCATGAGTGTGTTCGGC 59.792 57.895 0.00 0.00 0.00 5.54
782 826 0.235665 GTGTGCATGAGTGTGTTCGG 59.764 55.000 0.00 0.00 0.00 4.30
792 836 4.023878 GGTTTACTTTTACGGTGTGCATGA 60.024 41.667 0.00 0.00 0.00 3.07
814 858 1.001378 GATTCCGCAATTCCCGATTGG 60.001 52.381 0.00 0.00 44.34 3.16
841 885 4.066710 GCGAAAAAGTAAAGCGAGATGT 57.933 40.909 0.00 0.00 0.00 3.06
861 905 4.760047 AGGGTGTGCCGTGATCGC 62.760 66.667 0.00 0.00 34.97 4.58
862 906 2.047274 AAGGGTGTGCCGTGATCG 60.047 61.111 0.00 0.00 34.97 3.69
863 907 0.392998 ATCAAGGGTGTGCCGTGATC 60.393 55.000 0.00 0.00 36.19 2.92
864 908 0.392998 GATCAAGGGTGTGCCGTGAT 60.393 55.000 0.00 0.00 40.65 3.06
865 909 1.003839 GATCAAGGGTGTGCCGTGA 60.004 57.895 0.00 0.00 35.04 4.35
879 923 2.096442 CGTTCGCTGCAGCAGATCA 61.096 57.895 36.03 17.71 42.21 2.92
891 935 2.282701 TTGTCCAGGTATACGTTCGC 57.717 50.000 0.00 0.00 0.00 4.70
892 936 3.970610 CGTATTGTCCAGGTATACGTTCG 59.029 47.826 16.63 0.00 41.12 3.95
893 937 4.202050 ACCGTATTGTCCAGGTATACGTTC 60.202 45.833 20.19 0.00 43.24 3.95
896 940 3.551454 CCACCGTATTGTCCAGGTATACG 60.551 52.174 17.36 17.36 43.95 3.06
899 943 1.140252 GCCACCGTATTGTCCAGGTAT 59.860 52.381 0.00 0.00 34.83 2.73
900 944 0.538118 GCCACCGTATTGTCCAGGTA 59.462 55.000 0.00 0.00 34.83 3.08
901 945 1.298667 GCCACCGTATTGTCCAGGT 59.701 57.895 0.00 0.00 37.49 4.00
902 946 0.322098 TTGCCACCGTATTGTCCAGG 60.322 55.000 0.00 0.00 0.00 4.45
903 947 1.401552 CATTGCCACCGTATTGTCCAG 59.598 52.381 0.00 0.00 0.00 3.86
904 948 1.003696 TCATTGCCACCGTATTGTCCA 59.996 47.619 0.00 0.00 0.00 4.02
905 949 1.745232 TCATTGCCACCGTATTGTCC 58.255 50.000 0.00 0.00 0.00 4.02
907 951 2.682856 GACATCATTGCCACCGTATTGT 59.317 45.455 0.00 0.00 0.00 2.71
910 954 2.092968 ACTGACATCATTGCCACCGTAT 60.093 45.455 0.00 0.00 0.00 3.06
911 955 1.277842 ACTGACATCATTGCCACCGTA 59.722 47.619 0.00 0.00 0.00 4.02
912 956 0.036732 ACTGACATCATTGCCACCGT 59.963 50.000 0.00 0.00 0.00 4.83
924 968 7.960738 GTGTTACGTGCATTTTTATACTGACAT 59.039 33.333 0.00 0.00 0.00 3.06
927 971 7.292292 GTGTGTTACGTGCATTTTTATACTGA 58.708 34.615 0.00 0.00 0.00 3.41
1016 1060 3.733960 CGAGGACTGACGCGGTGA 61.734 66.667 12.47 0.00 0.00 4.02
1047 1091 4.117661 GAGGAGAACGTCGCCGCT 62.118 66.667 0.00 0.00 41.52 5.52
1065 1109 4.710167 GTGGGTAAACCGGCGGCT 62.710 66.667 28.71 12.24 44.64 5.52
1412 1456 1.374758 CACTCGCTTCCACCAGACC 60.375 63.158 0.00 0.00 0.00 3.85
1415 1459 2.743928 GGCACTCGCTTCCACCAG 60.744 66.667 0.00 0.00 38.60 4.00
1441 1485 0.465287 TTGACAGACAGCACTGCTCA 59.535 50.000 0.00 0.00 41.06 4.26
1443 1487 1.134280 ACTTTGACAGACAGCACTGCT 60.134 47.619 0.00 0.00 41.06 4.24
1471 1519 5.117897 GTCTACAAGTCGAAGAAGAAAGCAG 59.882 44.000 0.00 0.00 39.69 4.24
1525 1610 2.579541 TGACGCAAACATGCAATTACG 58.420 42.857 0.00 0.00 34.41 3.18
1527 1612 4.235939 AGTTGACGCAAACATGCAATTA 57.764 36.364 0.00 0.00 32.21 1.40
1542 1629 7.649705 ACTGACGATGATTCATGTATAGTTGAC 59.350 37.037 3.32 0.00 0.00 3.18
1544 1631 7.936950 ACTGACGATGATTCATGTATAGTTG 57.063 36.000 3.32 0.00 0.00 3.16
1545 1632 8.948631 AAACTGACGATGATTCATGTATAGTT 57.051 30.769 3.32 12.16 0.00 2.24
1561 1648 8.353684 TGGAAAGCAAAATAAATAAACTGACGA 58.646 29.630 0.00 0.00 0.00 4.20
1567 1654 8.432359 CCTTCGTGGAAAGCAAAATAAATAAAC 58.568 33.333 0.00 0.00 38.35 2.01
1572 1659 5.533154 TCTCCTTCGTGGAAAGCAAAATAAA 59.467 36.000 2.05 0.00 45.63 1.40
1585 1673 4.148825 CCGGCCTCTCCTTCGTGG 62.149 72.222 0.00 0.00 37.10 4.94
1625 3012 7.739498 TTTGTAGTCAAAAGTATTCCTCACC 57.261 36.000 0.00 0.00 40.08 4.02
1698 3603 7.414208 GGTTCTGCCTAGCTTGTAAATACTTTC 60.414 40.741 0.00 0.00 0.00 2.62
1734 3705 9.278978 TGAAAGTGTATTGAGTTTAGCATGTAA 57.721 29.630 0.00 0.00 0.00 2.41
1750 3721 7.936847 TGACCACTAATCTTTGTGAAAGTGTAT 59.063 33.333 6.15 0.00 39.30 2.29
1802 3773 0.468585 ACTACATCCGTCCCGCCATA 60.469 55.000 0.00 0.00 0.00 2.74
1805 3776 1.361632 GTACTACATCCGTCCCGCC 59.638 63.158 0.00 0.00 0.00 6.13
1818 3789 2.445427 TGACCATCCCGTTTCGTACTA 58.555 47.619 0.00 0.00 0.00 1.82
1829 3846 1.884579 GATGCATGTGATGACCATCCC 59.115 52.381 2.46 0.00 37.02 3.85
1836 3853 1.481772 TCGACCTGATGCATGTGATGA 59.518 47.619 2.46 0.00 0.00 2.92
1863 3880 0.855598 CCAGGGTCATGGGGATCAAT 59.144 55.000 0.00 0.00 36.64 2.57
1908 3926 1.398451 GCACCGTCACATCAAAACGAG 60.398 52.381 0.00 0.00 38.65 4.18
1926 3944 1.666700 GTCGTACACAAGTTTGGTGCA 59.333 47.619 0.00 0.00 39.87 4.57
1939 3957 1.132453 CAATCTGCCTCGAGTCGTACA 59.868 52.381 13.12 8.40 0.00 2.90
1995 4019 3.234353 CCATAGCTCTCCAGTACCATCA 58.766 50.000 0.00 0.00 0.00 3.07
2017 4053 4.693283 ACTTTCTGATTAATCGATCGGCA 58.307 39.130 16.41 0.00 33.36 5.69
2074 4356 3.572682 TCACTCCGATCCACGCTAATTAT 59.427 43.478 0.00 0.00 41.07 1.28
2082 4364 1.139734 CCACTCACTCCGATCCACG 59.860 63.158 0.00 0.00 42.18 4.94
2095 4377 3.063997 CCAAATTCGATACTGCACCACTC 59.936 47.826 0.00 0.00 0.00 3.51
2096 4378 3.009723 CCAAATTCGATACTGCACCACT 58.990 45.455 0.00 0.00 0.00 4.00
2097 4379 2.747446 ACCAAATTCGATACTGCACCAC 59.253 45.455 0.00 0.00 0.00 4.16
2098 4380 3.066291 ACCAAATTCGATACTGCACCA 57.934 42.857 0.00 0.00 0.00 4.17
2099 4381 3.427503 CCAACCAAATTCGATACTGCACC 60.428 47.826 0.00 0.00 0.00 5.01
2102 4384 2.099098 CCCCAACCAAATTCGATACTGC 59.901 50.000 0.00 0.00 0.00 4.40
2138 4420 1.084370 CGTGAAGAATCCGGCACTCC 61.084 60.000 0.00 0.00 0.00 3.85
2236 4530 6.867662 ACGAAGATTATATTTTGGCCTGAG 57.132 37.500 3.32 0.00 0.00 3.35
2248 4542 7.107542 AGGTTTACAAGCCAACGAAGATTATA 58.892 34.615 0.00 0.00 0.00 0.98
2291 4585 2.435938 AGGCCATGCACGTAACCG 60.436 61.111 5.01 0.00 40.83 4.44
2310 4604 4.761739 TCTCACCAAATACAAGCCTTTCAG 59.238 41.667 0.00 0.00 0.00 3.02
2324 4618 6.778069 TCTCTCTCTCTAAAACTCTCACCAAA 59.222 38.462 0.00 0.00 0.00 3.28
2339 4633 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2340 4634 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2349 4643 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2354 4648 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2355 4649 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2356 4650 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2358 4652 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2359 4653 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2360 4654 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2361 4655 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2362 4656 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2363 4657 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2364 4658 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2366 4660 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2368 4662 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2370 4664 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2371 4665 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2373 4667 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.