Multiple sequence alignment - TraesCS3A01G007600

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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 TraesCS3A01G007600 chr3A 100.000 2561 0 0 1 2561 7654706 7657266 0.000000e+00 4730.0
1 TraesCS3A01G007600 chr3B 84.316 2206 139 78 438 2463 3308705 3306527 0.000000e+00 1965.0
2 TraesCS3A01G007600 chr3B 84.426 1708 113 68 758 2333 5408084 5409770 0.000000e+00 1539.0
3 TraesCS3A01G007600 chr3B 92.788 208 8 3 439 645 5407768 5407969 6.930000e-76 294.0
4 TraesCS3A01G007600 chr3B 78.873 284 30 14 10 283 5407394 5407657 5.670000e-37 165.0
5 TraesCS3A01G007600 chr3B 87.407 135 9 1 2331 2457 5409795 5409929 5.710000e-32 148.0
6 TraesCS3A01G007600 chr3B 86.364 88 9 1 155 239 3308939 3308852 2.710000e-15 93.5
7 TraesCS3A01G007600 chr3B 85.714 91 7 5 2465 2552 3306494 3306407 9.760000e-15 91.6
8 TraesCS3A01G007600 chr3B 85.714 91 7 5 2465 2553 5409968 5410054 9.760000e-15 91.6
9 TraesCS3A01G007600 chr3D 81.460 2384 156 135 266 2460 1316527 1314241 0.000000e+00 1690.0


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 TraesCS3A01G007600 chr3A 7654706 7657266 2560 False 4730.00 4730 100.000000 1 2561 1 chr3A.!!$F1 2560
1 TraesCS3A01G007600 chr3B 3306407 3308939 2532 True 716.70 1965 85.464667 155 2552 3 chr3B.!!$R1 2397
2 TraesCS3A01G007600 chr3B 5407394 5410054 2660 False 447.52 1539 85.841600 10 2553 5 chr3B.!!$F1 2543
3 TraesCS3A01G007600 chr3D 1314241 1316527 2286 True 1690.00 1690 81.460000 266 2460 1 chr3D.!!$R1 2194

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
646 691 0.034896 GTCACCTTTTCTGCGAGGGA 59.965 55.0 0.0 0.0 37.36 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1853 0.323629 CGGTTACCATGGTCACCACT 59.676 55.0 36.11 11.01 41.17 4.0 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
43 44 5.820947 ACAAAATGAAAACTCGACCTACAGT 59.179 36.000 0.00 0.00 0.00 3.55
48 49 6.152932 TGAAAACTCGACCTACAGTTACTT 57.847 37.500 0.00 0.00 32.36 2.24
49 50 5.981315 TGAAAACTCGACCTACAGTTACTTG 59.019 40.000 0.00 0.00 32.36 3.16
50 51 5.526506 AAACTCGACCTACAGTTACTTGT 57.473 39.130 0.00 0.00 32.36 3.16
51 52 6.639632 AAACTCGACCTACAGTTACTTGTA 57.360 37.500 0.00 0.00 32.36 2.41
52 53 5.619625 ACTCGACCTACAGTTACTTGTAC 57.380 43.478 0.00 0.00 32.56 2.90
53 54 5.065914 ACTCGACCTACAGTTACTTGTACA 58.934 41.667 0.00 0.00 32.56 2.90
54 55 5.532406 ACTCGACCTACAGTTACTTGTACAA 59.468 40.000 8.28 8.28 32.56 2.41
55 56 6.039717 ACTCGACCTACAGTTACTTGTACAAA 59.960 38.462 10.03 0.00 32.56 2.83
56 57 6.441274 TCGACCTACAGTTACTTGTACAAAG 58.559 40.000 10.03 6.63 32.56 2.77
57 58 6.039717 TCGACCTACAGTTACTTGTACAAAGT 59.960 38.462 10.03 11.86 32.56 2.66
58 59 6.698766 CGACCTACAGTTACTTGTACAAAGTT 59.301 38.462 10.03 0.00 32.56 2.66
59 60 7.862372 CGACCTACAGTTACTTGTACAAAGTTA 59.138 37.037 10.03 1.84 32.56 2.24
60 61 9.533253 GACCTACAGTTACTTGTACAAAGTTAA 57.467 33.333 10.03 5.03 32.56 2.01
93 94 7.980099 ACGTACTCATCAAAGTAAATTAGGAGG 59.020 37.037 0.00 0.00 33.68 4.30
105 106 9.975218 AAGTAAATTAGGAGGCTCATTAAGAAA 57.025 29.630 17.69 0.00 0.00 2.52
108 109 6.582929 ATTAGGAGGCTCATTAAGAAACCT 57.417 37.500 17.69 2.99 35.99 3.50
146 157 1.928653 CGTGCGTTTTCAGAACGGA 59.071 52.632 12.45 7.36 43.25 4.69
150 161 1.529438 TGCGTTTTCAGAACGGACATC 59.471 47.619 12.45 0.00 43.25 3.06
151 162 1.529438 GCGTTTTCAGAACGGACATCA 59.471 47.619 12.45 0.00 43.25 3.07
152 163 2.661979 GCGTTTTCAGAACGGACATCAC 60.662 50.000 12.45 0.00 43.25 3.06
153 164 2.800544 CGTTTTCAGAACGGACATCACT 59.199 45.455 3.56 0.00 39.73 3.41
162 173 1.591703 GGACATCACTGAGGCGTCA 59.408 57.895 9.07 9.07 0.00 4.35
198 209 0.537188 GGCCTCGACCAAATCTCTCA 59.463 55.000 0.00 0.00 0.00 3.27
201 212 2.427453 GCCTCGACCAAATCTCTCACTA 59.573 50.000 0.00 0.00 0.00 2.74
211 225 5.410924 CAAATCTCTCACTATCACCAACGA 58.589 41.667 0.00 0.00 0.00 3.85
306 324 9.918630 ATGGCAATAGAATAATGAATTTGTAGC 57.081 29.630 0.00 0.00 0.00 3.58
313 333 6.264067 AGAATAATGAATTTGTAGCCTCTGCC 59.736 38.462 0.00 0.00 38.69 4.85
316 336 2.019984 GAATTTGTAGCCTCTGCCCAG 58.980 52.381 0.00 0.00 38.69 4.45
328 348 4.280819 CCTCTGCCCAGGAATAAATTCAA 58.719 43.478 5.15 0.00 38.53 2.69
339 359 8.087750 CCAGGAATAAATTCAAAAAGTAGCACA 58.912 33.333 5.15 0.00 38.53 4.57
340 360 9.132521 CAGGAATAAATTCAAAAAGTAGCACAG 57.867 33.333 5.15 0.00 38.53 3.66
342 362 7.598493 GGAATAAATTCAAAAAGTAGCACAGCA 59.402 33.333 5.15 0.00 38.53 4.41
344 364 6.774354 AAATTCAAAAAGTAGCACAGCATG 57.226 33.333 0.00 0.00 46.00 4.06
363 391 2.463752 TGCAGTTTCTATCTACCCGGT 58.536 47.619 0.00 0.00 0.00 5.28
365 393 3.382546 TGCAGTTTCTATCTACCCGGTAC 59.617 47.826 0.00 0.00 0.00 3.34
368 396 5.589192 CAGTTTCTATCTACCCGGTACTTG 58.411 45.833 0.00 0.00 0.00 3.16
371 399 4.736611 TCTATCTACCCGGTACTTGGAT 57.263 45.455 0.00 0.00 0.00 3.41
383 411 7.042335 CCCGGTACTTGGATATTCAGATTATC 58.958 42.308 0.00 4.34 0.00 1.75
400 428 6.002704 AGATTATCCCAAGCACAGATTGATC 58.997 40.000 0.00 0.00 29.71 2.92
419 447 7.459795 TTGATCTGTGCCTACTGATAGATAG 57.540 40.000 0.00 0.00 43.07 2.08
424 452 8.152023 TCTGTGCCTACTGATAGATAGATAGA 57.848 38.462 0.00 0.00 30.90 1.98
477 506 4.927422 TGAAAAACATTCCGGTCACTTTC 58.073 39.130 0.00 5.56 0.00 2.62
478 507 4.399618 TGAAAAACATTCCGGTCACTTTCA 59.600 37.500 0.00 8.05 31.13 2.69
479 508 4.568152 AAAACATTCCGGTCACTTTCAG 57.432 40.909 0.00 0.00 0.00 3.02
480 509 2.185004 ACATTCCGGTCACTTTCAGG 57.815 50.000 0.00 0.00 0.00 3.86
503 532 4.259850 GCAGCGGTCGACTAGAAAATAAAG 60.260 45.833 16.46 0.00 0.00 1.85
527 556 1.796796 GGAGAAAGATGTGCGTGCC 59.203 57.895 0.00 0.00 0.00 5.01
532 561 1.810151 GAAAGATGTGCGTGCCCTTTA 59.190 47.619 0.00 0.00 0.00 1.85
547 582 4.245660 GCCCTTTAATTTCTTTCTGGTGC 58.754 43.478 0.00 0.00 0.00 5.01
549 584 5.511373 GCCCTTTAATTTCTTTCTGGTGCTT 60.511 40.000 0.00 0.00 0.00 3.91
550 585 6.159293 CCCTTTAATTTCTTTCTGGTGCTTC 58.841 40.000 0.00 0.00 0.00 3.86
552 593 7.087007 CCTTTAATTTCTTTCTGGTGCTTCTC 58.913 38.462 0.00 0.00 0.00 2.87
553 594 7.040132 CCTTTAATTTCTTTCTGGTGCTTCTCT 60.040 37.037 0.00 0.00 0.00 3.10
555 596 3.845781 TTCTTTCTGGTGCTTCTCTGT 57.154 42.857 0.00 0.00 0.00 3.41
556 597 3.117491 TCTTTCTGGTGCTTCTCTGTG 57.883 47.619 0.00 0.00 0.00 3.66
641 686 1.148310 ATCACGTCACCTTTTCTGCG 58.852 50.000 0.00 0.00 0.00 5.18
645 690 1.291877 CGTCACCTTTTCTGCGAGGG 61.292 60.000 0.00 0.00 37.36 4.30
646 691 0.034896 GTCACCTTTTCTGCGAGGGA 59.965 55.000 0.00 0.00 37.36 4.20
657 714 3.227276 CGAGGGAGGGTCCATCCG 61.227 72.222 16.30 1.41 43.97 4.18
658 723 2.041819 GAGGGAGGGTCCATCCGT 60.042 66.667 17.38 17.38 41.21 4.69
713 809 2.262471 CTTAGCTTGGCTGCCGCTTG 62.262 60.000 23.03 14.02 40.10 4.01
741 837 1.480954 ACCTGCTAGAATACACCCACG 59.519 52.381 0.00 0.00 0.00 4.94
759 855 1.300156 GCACGCACACACTGAGAGA 60.300 57.895 0.00 0.00 0.00 3.10
760 856 1.280886 GCACGCACACACTGAGAGAG 61.281 60.000 0.00 0.00 0.00 3.20
761 857 1.006805 ACGCACACACTGAGAGAGC 60.007 57.895 0.00 0.00 0.00 4.09
765 861 1.669502 GCACACACTGAGAGAGCAGAG 60.670 57.143 0.00 0.00 39.20 3.35
867 990 6.350612 CCGACCATTATAACCCACACAAATTT 60.351 38.462 0.00 0.00 0.00 1.82
874 997 0.684535 CCCACACAAATTTCCCACCC 59.315 55.000 0.00 0.00 0.00 4.61
879 1002 1.895131 CACAAATTTCCCACCCAGAGG 59.105 52.381 0.00 0.00 40.04 3.69
894 1024 2.364448 AGGAGAGAACCCCGAGCC 60.364 66.667 0.00 0.00 0.00 4.70
895 1025 3.839432 GGAGAGAACCCCGAGCCG 61.839 72.222 0.00 0.00 0.00 5.52
896 1026 2.754658 GAGAGAACCCCGAGCCGA 60.755 66.667 0.00 0.00 0.00 5.54
898 1028 4.516195 GAGAACCCCGAGCCGAGC 62.516 72.222 0.00 0.00 0.00 5.03
925 1066 2.373502 ACACCAAAAAGGAGAGGAGGAG 59.626 50.000 0.00 0.00 41.22 3.69
966 1107 4.914420 CTAGAGAGCACGGCCGCG 62.914 72.222 28.58 19.05 36.85 6.46
1100 1254 4.717629 CGAGAAGTGCACGGGCGA 62.718 66.667 12.01 0.00 45.35 5.54
1607 1764 1.305219 CCATGGCAAGGTACACGTGG 61.305 60.000 21.57 1.25 34.08 4.94
1612 1769 4.692475 AAGGTACACGTGGGCGCC 62.692 66.667 21.18 21.18 42.83 6.53
1675 1846 4.100084 CCATGGAGCCGGTGAGCA 62.100 66.667 5.56 0.00 34.23 4.26
1726 1915 1.202087 GCATGCATGGCGTACGTTTTA 60.202 47.619 27.34 1.26 0.00 1.52
1829 2034 2.942376 TGAGTTTTCATTCGTGCTGTGT 59.058 40.909 0.00 0.00 0.00 3.72
1839 2044 1.866601 TCGTGCTGTGTTCATGTTCAG 59.133 47.619 0.00 0.00 0.00 3.02
1888 2094 4.393934 CGTTCTTGTCATGTACGTACGTA 58.606 43.478 23.60 23.60 0.00 3.57
1889 2095 4.845598 CGTTCTTGTCATGTACGTACGTAA 59.154 41.667 28.34 18.52 31.86 3.18
1929 2143 4.641989 CACTTTGGTCAATCATAGGAAGGG 59.358 45.833 0.00 0.00 0.00 3.95
1931 2145 5.015178 ACTTTGGTCAATCATAGGAAGGGAA 59.985 40.000 0.00 0.00 0.00 3.97
1932 2146 5.528600 TTGGTCAATCATAGGAAGGGAAA 57.471 39.130 0.00 0.00 0.00 3.13
1933 2147 5.116084 TGGTCAATCATAGGAAGGGAAAG 57.884 43.478 0.00 0.00 0.00 2.62
1934 2148 4.079787 TGGTCAATCATAGGAAGGGAAAGG 60.080 45.833 0.00 0.00 0.00 3.11
1936 2150 4.079730 GTCAATCATAGGAAGGGAAAGGGT 60.080 45.833 0.00 0.00 0.00 4.34
1937 2151 4.166144 TCAATCATAGGAAGGGAAAGGGTC 59.834 45.833 0.00 0.00 0.00 4.46
1939 2153 2.844348 TCATAGGAAGGGAAAGGGTCAC 59.156 50.000 0.00 0.00 0.00 3.67
1940 2154 2.735259 TAGGAAGGGAAAGGGTCACT 57.265 50.000 0.00 0.00 44.21 3.41
1942 2156 2.267192 AGGAAGGGAAAGGGTCACTAC 58.733 52.381 0.00 0.00 39.99 2.73
1944 2158 2.576648 GGAAGGGAAAGGGTCACTACAT 59.423 50.000 0.00 0.00 39.99 2.29
1945 2159 3.610911 GAAGGGAAAGGGTCACTACATG 58.389 50.000 0.00 0.00 39.99 3.21
1946 2160 2.632537 AGGGAAAGGGTCACTACATGT 58.367 47.619 2.69 2.69 38.66 3.21
1947 2161 2.986728 AGGGAAAGGGTCACTACATGTT 59.013 45.455 2.30 0.00 38.66 2.71
1948 2162 3.009143 AGGGAAAGGGTCACTACATGTTC 59.991 47.826 2.30 0.00 38.66 3.18
1956 2182 3.859961 GGTCACTACATGTTCATCAGACG 59.140 47.826 2.30 0.00 0.00 4.18
1976 2202 9.014297 TCAGACGATGTGATACTGATACATATT 57.986 33.333 0.00 0.00 35.35 1.28
2032 2265 5.807909 TCCATGTTTCATGTCTCATCTTCA 58.192 37.500 8.57 0.00 0.00 3.02
2044 2290 5.812127 TGTCTCATCTTCATGGTATGTTTCG 59.188 40.000 0.00 0.00 0.00 3.46
2124 2400 3.072211 GTGTGCAACCTAACTAACCTCC 58.928 50.000 0.00 0.00 34.36 4.30
2206 2524 1.934589 CACACGCCATCCGATCTTTA 58.065 50.000 0.00 0.00 41.02 1.85
2207 2525 1.860950 CACACGCCATCCGATCTTTAG 59.139 52.381 0.00 0.00 41.02 1.85
2208 2526 0.861837 CACGCCATCCGATCTTTAGC 59.138 55.000 0.00 0.00 41.02 3.09
2209 2527 0.753262 ACGCCATCCGATCTTTAGCT 59.247 50.000 0.00 0.00 41.02 3.32
2211 2529 2.364324 ACGCCATCCGATCTTTAGCTAA 59.636 45.455 0.86 0.86 41.02 3.09
2212 2530 3.181469 ACGCCATCCGATCTTTAGCTAAA 60.181 43.478 17.71 17.71 41.02 1.85
2213 2531 3.430218 CGCCATCCGATCTTTAGCTAAAG 59.570 47.826 31.88 31.88 40.66 1.85
2214 2532 4.381411 GCCATCCGATCTTTAGCTAAAGT 58.619 43.478 34.28 25.13 42.43 2.66
2217 2538 6.049149 CCATCCGATCTTTAGCTAAAGTTGA 58.951 40.000 34.28 26.70 42.43 3.18
2219 2540 5.661458 TCCGATCTTTAGCTAAAGTTGAGG 58.339 41.667 34.28 30.16 42.43 3.86
2223 2544 7.259161 CGATCTTTAGCTAAAGTTGAGGTAGT 58.741 38.462 34.28 16.52 42.43 2.73
2241 2562 7.039011 TGAGGTAGTATATCCATCCATGAACAC 60.039 40.741 0.00 0.00 0.00 3.32
2278 2609 2.546795 GGTCGATCGATGGAGAGCAAAT 60.547 50.000 22.50 0.00 0.00 2.32
2338 2700 0.579630 GAAATGTGTGTGTGCGTCGA 59.420 50.000 0.00 0.00 0.00 4.20
2353 2715 1.007336 GTCGAGGCAAACGTGTCGAT 61.007 55.000 9.47 0.00 42.89 3.59
2358 2720 1.225376 GGCAAACGTGTCGATGTCCA 61.225 55.000 0.00 0.00 0.00 4.02
2367 2729 1.079503 GTCGATGTCCAAGACCAAGC 58.920 55.000 0.00 0.00 0.00 4.01
2381 2743 4.719369 AAGCGGTCGCACTCGGTC 62.719 66.667 17.71 0.00 44.88 4.79
2457 2827 1.007502 AGGCGTGCAAACGTACGTA 60.008 52.632 23.12 2.29 43.40 3.57
2504 2905 3.329231 GCGTGTGCAGTGCAAGTA 58.671 55.556 21.67 6.63 41.47 2.24
2505 2906 1.868997 GCGTGTGCAGTGCAAGTAT 59.131 52.632 21.67 0.00 41.47 2.12
2508 2909 2.065512 CGTGTGCAGTGCAAGTATGTA 58.934 47.619 21.67 0.00 41.47 2.29
2509 2910 2.092681 CGTGTGCAGTGCAAGTATGTAG 59.907 50.000 21.67 1.94 41.47 2.74
2510 2911 2.076100 TGTGCAGTGCAAGTATGTAGC 58.924 47.619 21.67 4.38 41.47 3.58
2511 2912 1.061131 GTGCAGTGCAAGTATGTAGCG 59.939 52.381 21.67 0.00 41.47 4.26
2513 2914 1.061131 GCAGTGCAAGTATGTAGCGTG 59.939 52.381 11.09 0.00 0.00 5.34
2516 2918 1.075542 TGCAAGTATGTAGCGTGTGC 58.924 50.000 0.00 0.00 43.24 4.57
2547 2949 0.391597 TTCGGAGTGACGGAAGCTTT 59.608 50.000 0.00 0.00 33.91 3.51
2548 2950 0.319555 TCGGAGTGACGGAAGCTTTG 60.320 55.000 0.00 0.00 0.00 2.77
2549 2951 1.869690 GGAGTGACGGAAGCTTTGC 59.130 57.895 0.00 0.00 0.00 3.68
2550 2952 0.884704 GGAGTGACGGAAGCTTTGCA 60.885 55.000 0.00 0.00 0.00 4.08
2551 2953 1.160137 GAGTGACGGAAGCTTTGCAT 58.840 50.000 0.00 0.00 0.00 3.96
2552 2954 0.877071 AGTGACGGAAGCTTTGCATG 59.123 50.000 0.00 0.00 0.00 4.06
2553 2955 0.874390 GTGACGGAAGCTTTGCATGA 59.126 50.000 0.00 0.00 0.00 3.07
2554 2956 1.135859 GTGACGGAAGCTTTGCATGAG 60.136 52.381 0.00 0.00 0.00 2.90
2555 2957 1.160137 GACGGAAGCTTTGCATGAGT 58.840 50.000 0.00 0.00 0.00 3.41
2556 2958 1.129437 GACGGAAGCTTTGCATGAGTC 59.871 52.381 0.00 0.00 0.00 3.36
2557 2959 1.271054 ACGGAAGCTTTGCATGAGTCT 60.271 47.619 0.00 0.00 0.00 3.24
2558 2960 1.396301 CGGAAGCTTTGCATGAGTCTC 59.604 52.381 0.00 0.00 0.00 3.36
2559 2961 2.709213 GGAAGCTTTGCATGAGTCTCT 58.291 47.619 0.00 0.00 0.00 3.10
2560 2962 2.677337 GGAAGCTTTGCATGAGTCTCTC 59.323 50.000 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 7.090953 TGTAGGTCGAGTTTTCATTTTGTTT 57.909 32.000 0.00 0.00 0.00 2.83
20 21 6.300354 ACTGTAGGTCGAGTTTTCATTTTG 57.700 37.500 0.00 0.00 0.00 2.44
48 49 9.825972 GAGTACGTACTGTATTAACTTTGTACA 57.174 33.333 31.91 0.00 36.50 2.90
49 50 9.825972 TGAGTACGTACTGTATTAACTTTGTAC 57.174 33.333 31.91 12.15 36.50 2.90
51 52 9.565213 GATGAGTACGTACTGTATTAACTTTGT 57.435 33.333 31.91 3.41 36.50 2.83
52 53 9.563898 TGATGAGTACGTACTGTATTAACTTTG 57.436 33.333 31.91 0.00 36.50 2.77
55 56 9.784680 CTTTGATGAGTACGTACTGTATTAACT 57.215 33.333 31.91 7.30 36.50 2.24
56 57 9.565213 ACTTTGATGAGTACGTACTGTATTAAC 57.435 33.333 31.91 15.95 36.50 2.01
93 94 4.427312 CAATGGCAGGTTTCTTAATGAGC 58.573 43.478 0.00 0.00 0.00 4.26
146 157 1.293498 GGTGACGCCTCAGTGATGT 59.707 57.895 0.00 0.00 0.00 3.06
150 161 2.357517 GTGGGTGACGCCTCAGTG 60.358 66.667 4.75 0.00 37.43 3.66
151 162 2.524394 AGTGGGTGACGCCTCAGT 60.524 61.111 4.75 1.76 37.43 3.41
152 163 2.047844 CAGTGGGTGACGCCTCAG 60.048 66.667 4.75 0.00 37.43 3.35
153 164 2.523168 TCAGTGGGTGACGCCTCA 60.523 61.111 4.75 0.00 37.43 3.86
162 173 2.029073 CTTGACGCGTCAGTGGGT 59.971 61.111 37.06 0.77 41.13 4.51
220 234 6.571925 CGCCTCATCATCTTCATCTTCTGATA 60.572 42.308 0.00 0.00 32.72 2.15
221 235 5.553123 GCCTCATCATCTTCATCTTCTGAT 58.447 41.667 0.00 0.00 32.72 2.90
222 236 4.501058 CGCCTCATCATCTTCATCTTCTGA 60.501 45.833 0.00 0.00 0.00 3.27
224 238 3.803021 GCGCCTCATCATCTTCATCTTCT 60.803 47.826 0.00 0.00 0.00 2.85
286 304 9.007901 GCAGAGGCTACAAATTCATTATTCTAT 57.992 33.333 0.00 0.00 36.96 1.98
296 314 2.019984 CTGGGCAGAGGCTACAAATTC 58.980 52.381 0.00 0.00 40.87 2.17
305 323 2.371658 ATTTATTCCTGGGCAGAGGC 57.628 50.000 0.00 0.00 40.13 4.70
306 324 3.902218 TGAATTTATTCCTGGGCAGAGG 58.098 45.455 0.00 0.00 35.97 3.69
313 333 8.087750 TGTGCTACTTTTTGAATTTATTCCTGG 58.912 33.333 0.32 0.00 35.97 4.45
316 336 7.598493 TGCTGTGCTACTTTTTGAATTTATTCC 59.402 33.333 0.32 0.00 35.97 3.01
339 359 3.493350 CGGGTAGATAGAAACTGCATGCT 60.493 47.826 20.33 0.00 0.00 3.79
340 360 2.802816 CGGGTAGATAGAAACTGCATGC 59.197 50.000 11.82 11.82 0.00 4.06
342 362 3.039011 ACCGGGTAGATAGAAACTGCAT 58.961 45.455 6.32 0.00 0.00 3.96
344 364 3.635836 AGTACCGGGTAGATAGAAACTGC 59.364 47.826 7.25 0.00 0.00 4.40
345 365 5.451520 CCAAGTACCGGGTAGATAGAAACTG 60.452 48.000 7.25 0.00 0.00 3.16
346 366 4.648307 CCAAGTACCGGGTAGATAGAAACT 59.352 45.833 7.25 0.00 0.00 2.66
347 367 4.646492 TCCAAGTACCGGGTAGATAGAAAC 59.354 45.833 7.25 0.00 0.00 2.78
348 368 4.870636 TCCAAGTACCGGGTAGATAGAAA 58.129 43.478 7.25 0.00 0.00 2.52
349 369 4.524802 TCCAAGTACCGGGTAGATAGAA 57.475 45.455 7.25 0.00 0.00 2.10
368 396 6.240894 TGTGCTTGGGATAATCTGAATATCC 58.759 40.000 19.30 19.30 45.39 2.59
371 399 6.499106 TCTGTGCTTGGGATAATCTGAATA 57.501 37.500 0.00 0.00 0.00 1.75
400 428 8.978874 ATCTATCTATCTATCAGTAGGCACAG 57.021 38.462 0.00 0.00 0.00 3.66
477 506 1.934220 TTCTAGTCGACCGCTGCCTG 61.934 60.000 13.01 0.00 0.00 4.85
478 507 1.248785 TTTCTAGTCGACCGCTGCCT 61.249 55.000 13.01 0.00 0.00 4.75
479 508 0.389426 TTTTCTAGTCGACCGCTGCC 60.389 55.000 13.01 0.00 0.00 4.85
480 509 1.641577 ATTTTCTAGTCGACCGCTGC 58.358 50.000 13.01 0.00 0.00 5.25
503 532 1.648467 GCACATCTTTCTCCGCACCC 61.648 60.000 0.00 0.00 0.00 4.61
527 556 6.986250 AGAAGCACCAGAAAGAAATTAAAGG 58.014 36.000 0.00 0.00 0.00 3.11
532 561 5.009410 CACAGAGAAGCACCAGAAAGAAATT 59.991 40.000 0.00 0.00 0.00 1.82
547 582 3.698289 TCCTACCCTACACACAGAGAAG 58.302 50.000 0.00 0.00 0.00 2.85
549 584 3.684697 CGATCCTACCCTACACACAGAGA 60.685 52.174 0.00 0.00 0.00 3.10
550 585 2.619177 CGATCCTACCCTACACACAGAG 59.381 54.545 0.00 0.00 0.00 3.35
552 593 2.358267 GTCGATCCTACCCTACACACAG 59.642 54.545 0.00 0.00 0.00 3.66
553 594 2.025605 AGTCGATCCTACCCTACACACA 60.026 50.000 0.00 0.00 0.00 3.72
555 596 2.744166 CGAGTCGATCCTACCCTACACA 60.744 54.545 6.73 0.00 0.00 3.72
556 597 1.872313 CGAGTCGATCCTACCCTACAC 59.128 57.143 6.73 0.00 0.00 2.90
641 686 2.041819 ACGGATGGACCCTCCCTC 60.042 66.667 10.00 0.00 35.03 4.30
645 690 2.248248 TCATATCACGGATGGACCCTC 58.752 52.381 0.00 0.00 34.64 4.30
646 691 2.398754 TCATATCACGGATGGACCCT 57.601 50.000 0.00 0.00 34.64 4.34
721 817 1.480954 CGTGGGTGTATTCTAGCAGGT 59.519 52.381 0.00 0.00 0.00 4.00
741 837 1.280886 CTCTCTCAGTGTGTGCGTGC 61.281 60.000 0.00 0.00 0.00 5.34
751 847 2.566724 CCTTTTCCTCTGCTCTCTCAGT 59.433 50.000 0.00 0.00 35.63 3.41
759 855 1.548269 CTCGTCTCCTTTTCCTCTGCT 59.452 52.381 0.00 0.00 0.00 4.24
760 856 1.546476 TCTCGTCTCCTTTTCCTCTGC 59.454 52.381 0.00 0.00 0.00 4.26
761 857 2.414824 CGTCTCGTCTCCTTTTCCTCTG 60.415 54.545 0.00 0.00 0.00 3.35
765 861 1.728502 CGTCGTCTCGTCTCCTTTTCC 60.729 57.143 0.00 0.00 0.00 3.13
795 896 2.048127 GAGTGGAGTGGTGCGGTC 60.048 66.667 0.00 0.00 0.00 4.79
867 990 0.252284 GTTCTCTCCTCTGGGTGGGA 60.252 60.000 0.00 0.00 34.19 4.37
874 997 1.671901 GCTCGGGGTTCTCTCCTCTG 61.672 65.000 0.00 0.00 0.00 3.35
879 1002 2.754658 TCGGCTCGGGGTTCTCTC 60.755 66.667 0.00 0.00 0.00 3.20
894 1024 1.781025 TTTTTGGTGTGCTCGGCTCG 61.781 55.000 0.00 0.00 0.00 5.03
895 1025 0.040067 CTTTTTGGTGTGCTCGGCTC 60.040 55.000 0.00 0.00 0.00 4.70
896 1026 1.455383 CCTTTTTGGTGTGCTCGGCT 61.455 55.000 0.00 0.00 0.00 5.52
898 1028 0.593128 CTCCTTTTTGGTGTGCTCGG 59.407 55.000 0.00 0.00 37.07 4.63
899 1029 1.532868 CTCTCCTTTTTGGTGTGCTCG 59.467 52.381 0.00 0.00 37.07 5.03
900 1030 1.882623 CCTCTCCTTTTTGGTGTGCTC 59.117 52.381 0.00 0.00 37.07 4.26
901 1031 1.494721 TCCTCTCCTTTTTGGTGTGCT 59.505 47.619 0.00 0.00 37.07 4.40
902 1032 1.882623 CTCCTCTCCTTTTTGGTGTGC 59.117 52.381 0.00 0.00 37.07 4.57
903 1033 2.106511 TCCTCCTCTCCTTTTTGGTGTG 59.893 50.000 0.00 0.00 37.07 3.82
904 1034 2.373502 CTCCTCCTCTCCTTTTTGGTGT 59.626 50.000 0.00 0.00 37.07 4.16
905 1035 2.290577 CCTCCTCCTCTCCTTTTTGGTG 60.291 54.545 0.00 0.00 37.07 4.17
906 1036 1.988846 CCTCCTCCTCTCCTTTTTGGT 59.011 52.381 0.00 0.00 37.07 3.67
907 1037 2.269940 TCCTCCTCCTCTCCTTTTTGG 58.730 52.381 0.00 0.00 37.10 3.28
908 1038 3.584848 TCTTCCTCCTCCTCTCCTTTTTG 59.415 47.826 0.00 0.00 0.00 2.44
925 1066 1.268335 CGCGACTCTCTAGCTTCTTCC 60.268 57.143 0.00 0.00 0.00 3.46
1420 1577 2.652530 GGTCAGGTACGACGGCAA 59.347 61.111 0.00 0.00 36.73 4.52
1593 1750 3.419759 CGCCCACGTGTACCTTGC 61.420 66.667 15.65 6.13 33.53 4.01
1612 1769 4.883354 GCCCCATGCCTTCCGGAG 62.883 72.222 3.34 0.00 0.00 4.63
1675 1846 1.064003 TTACCATGGTCACCACTGCT 58.936 50.000 23.76 0.00 35.80 4.24
1678 1853 0.323629 CGGTTACCATGGTCACCACT 59.676 55.000 36.11 11.01 41.17 4.00
1726 1915 4.217550 ACACGGAATCAACGGAATTCAATT 59.782 37.500 7.93 0.00 35.23 2.32
1829 2034 2.267426 CGATGTACGGCTGAACATGAA 58.733 47.619 0.00 0.00 36.48 2.57
1888 2094 4.618920 AGTGAAATACGAGACCCAACTT 57.381 40.909 0.00 0.00 0.00 2.66
1889 2095 4.618920 AAGTGAAATACGAGACCCAACT 57.381 40.909 0.00 0.00 0.00 3.16
1890 2096 4.083484 CCAAAGTGAAATACGAGACCCAAC 60.083 45.833 0.00 0.00 0.00 3.77
1891 2097 4.069304 CCAAAGTGAAATACGAGACCCAA 58.931 43.478 0.00 0.00 0.00 4.12
1902 2112 7.123247 CCTTCCTATGATTGACCAAAGTGAAAT 59.877 37.037 0.00 0.00 0.00 2.17
1929 2143 5.245531 TGATGAACATGTAGTGACCCTTTC 58.754 41.667 0.00 0.00 0.00 2.62
1931 2145 4.532126 TCTGATGAACATGTAGTGACCCTT 59.468 41.667 0.00 0.00 0.00 3.95
1932 2146 4.081420 GTCTGATGAACATGTAGTGACCCT 60.081 45.833 0.00 0.00 0.00 4.34
1933 2147 4.184629 GTCTGATGAACATGTAGTGACCC 58.815 47.826 0.00 0.00 0.00 4.46
1934 2148 3.859961 CGTCTGATGAACATGTAGTGACC 59.140 47.826 0.00 0.00 0.00 4.02
1936 2150 5.582689 ATCGTCTGATGAACATGTAGTGA 57.417 39.130 0.00 0.00 32.21 3.41
1976 2202 7.386059 TCAAGTGTGAGTAATCAGAAGCATAA 58.614 34.615 0.00 0.00 0.00 1.90
1980 2206 6.734104 ATTCAAGTGTGAGTAATCAGAAGC 57.266 37.500 0.00 0.00 34.49 3.86
1981 2207 8.545229 AGAATTCAAGTGTGAGTAATCAGAAG 57.455 34.615 8.44 0.00 34.49 2.85
1982 2208 9.424319 GTAGAATTCAAGTGTGAGTAATCAGAA 57.576 33.333 8.44 0.00 34.49 3.02
2032 2265 5.034852 TGGTGATCATCGAAACATACCAT 57.965 39.130 0.00 0.00 32.47 3.55
2044 2290 2.357009 GGTGCATGAGTTGGTGATCATC 59.643 50.000 0.00 0.00 33.91 2.92
2076 2352 2.227865 TCGGGATAGCAAAAGCAACAAC 59.772 45.455 0.00 0.00 0.00 3.32
2148 2446 2.249535 GCATGTGCGGATGCTCGAT 61.250 57.895 11.50 0.00 44.57 3.59
2206 2524 8.728596 ATGGATATACTACCTCAACTTTAGCT 57.271 34.615 0.00 0.00 0.00 3.32
2207 2525 8.035984 GGATGGATATACTACCTCAACTTTAGC 58.964 40.741 0.00 0.00 0.00 3.09
2208 2526 9.090103 TGGATGGATATACTACCTCAACTTTAG 57.910 37.037 3.42 0.00 0.00 1.85
2209 2527 9.615660 ATGGATGGATATACTACCTCAACTTTA 57.384 33.333 3.42 0.00 0.00 1.85
2211 2529 7.734865 TCATGGATGGATATACTACCTCAACTT 59.265 37.037 0.00 0.00 0.00 2.66
2212 2530 7.248976 TCATGGATGGATATACTACCTCAACT 58.751 38.462 0.00 0.00 0.00 3.16
2213 2531 7.482169 TCATGGATGGATATACTACCTCAAC 57.518 40.000 0.00 0.00 0.00 3.18
2214 2532 7.512402 TGTTCATGGATGGATATACTACCTCAA 59.488 37.037 0.00 0.00 0.00 3.02
2217 2538 6.071334 CGTGTTCATGGATGGATATACTACCT 60.071 42.308 0.00 0.00 0.00 3.08
2219 2540 5.577164 GCGTGTTCATGGATGGATATACTAC 59.423 44.000 0.00 0.00 0.00 2.73
2223 2544 4.890158 AGCGTGTTCATGGATGGATATA 57.110 40.909 0.00 0.00 0.00 0.86
2241 2562 4.554363 CCTCGTCGGCCACTAGCG 62.554 72.222 2.24 0.00 45.17 4.26
2338 2700 0.949105 GGACATCGACACGTTTGCCT 60.949 55.000 0.00 0.00 0.00 4.75
2353 2715 3.236391 ACCGCTTGGTCTTGGACA 58.764 55.556 0.14 0.00 45.05 4.02
2367 2729 2.114331 ATATCGACCGAGTGCGACCG 62.114 60.000 0.00 0.00 39.56 4.79
2460 2830 1.526575 ATTTGCCTTGGGTGCGACTG 61.527 55.000 0.00 0.00 0.00 3.51
2463 2833 0.611618 ATGATTTGCCTTGGGTGCGA 60.612 50.000 0.00 0.00 0.00 5.10
2497 2898 1.075542 GCACACGCTACATACTTGCA 58.924 50.000 0.00 0.00 34.30 4.08
2498 2899 1.075542 TGCACACGCTACATACTTGC 58.924 50.000 0.00 0.00 39.64 4.01
2499 2900 2.929398 TGATGCACACGCTACATACTTG 59.071 45.455 0.00 0.00 39.64 3.16
2500 2901 3.245518 TGATGCACACGCTACATACTT 57.754 42.857 0.00 0.00 39.64 2.24
2502 2903 3.303329 CCAATGATGCACACGCTACATAC 60.303 47.826 0.00 0.00 39.64 2.39
2503 2904 2.871633 CCAATGATGCACACGCTACATA 59.128 45.455 0.00 0.00 39.64 2.29
2504 2905 1.672363 CCAATGATGCACACGCTACAT 59.328 47.619 0.00 0.00 39.64 2.29
2505 2906 1.085893 CCAATGATGCACACGCTACA 58.914 50.000 0.00 0.00 39.64 2.74
2508 2909 0.523072 GTTCCAATGATGCACACGCT 59.477 50.000 0.00 0.00 39.64 5.07
2509 2910 0.523072 AGTTCCAATGATGCACACGC 59.477 50.000 0.00 0.00 39.24 5.34
2510 2911 2.725759 CGAAGTTCCAATGATGCACACG 60.726 50.000 0.00 0.00 0.00 4.49
2511 2912 2.414559 CCGAAGTTCCAATGATGCACAC 60.415 50.000 0.00 0.00 0.00 3.82
2513 2914 2.083774 TCCGAAGTTCCAATGATGCAC 58.916 47.619 0.00 0.00 0.00 4.57
2516 2918 3.372206 GTCACTCCGAAGTTCCAATGATG 59.628 47.826 0.00 0.00 31.71 3.07


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

AutoCloner maintained by Alex Coulton.