Multiple sequence alignment - TraesCS5B01G060700

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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 TraesCS5B01G060700 chr5B 100.000 2618 0 0 1 2618 68048281 68050898 0.000000e+00 4835.0
1 TraesCS5B01G060700 chr5B 87.076 1679 128 31 1 1656 68194178 68195790 0.000000e+00 1816.0
2 TraesCS5B01G060700 chr5B 90.120 334 31 1 64 395 68052756 68052423 1.440000e-117 433.0
3 TraesCS5B01G060700 chr5B 89.855 69 6 1 1 68 68167565 68167497 1.290000e-13 87.9
4 TraesCS5B01G060700 chr5D 89.162 978 53 16 1683 2618 62478066 62477100 0.000000e+00 1170.0
5 TraesCS5B01G060700 chr5D 94.118 748 35 4 935 1682 62478875 62478137 0.000000e+00 1129.0
6 TraesCS5B01G060700 chr5D 88.652 890 44 16 766 1652 62510778 62509943 0.000000e+00 1031.0
7 TraesCS5B01G060700 chr5D 90.496 705 53 6 1 704 62479733 62479042 0.000000e+00 918.0
8 TraesCS5B01G060700 chr5D 89.466 693 56 6 12 702 62511481 62510804 0.000000e+00 859.0
9 TraesCS5B01G060700 chr5D 89.970 329 33 0 64 392 62475227 62475555 2.410000e-115 425.0
10 TraesCS5B01G060700 chr5D 87.963 108 12 1 1864 1970 439211538 439211645 2.740000e-25 126.0
11 TraesCS5B01G060700 chr5D 86.957 69 8 1 1 68 62326793 62326861 2.790000e-10 76.8
12 TraesCS5B01G060700 chr5A 94.072 641 32 1 964 1604 52357285 52356651 0.000000e+00 968.0
13 TraesCS5B01G060700 chr5A 85.585 881 76 25 1 851 52358189 52357330 0.000000e+00 876.0
14 TraesCS5B01G060700 chr2A 88.272 324 23 4 1861 2183 761485837 761485528 8.850000e-100 374.0
15 TraesCS5B01G060700 chr2A 88.672 256 27 2 1862 2116 41149825 41150079 7.040000e-81 311.0
16 TraesCS5B01G060700 chr2A 89.474 152 13 3 2261 2411 41153822 41153971 3.440000e-44 189.0
17 TraesCS5B01G060700 chr4A 85.933 327 29 9 1861 2184 13745923 13745611 1.500000e-87 333.0
18 TraesCS5B01G060700 chr4A 88.718 195 21 1 1862 2055 618191528 618191334 1.210000e-58 237.0
19 TraesCS5B01G060700 chr4A 86.923 130 16 1 1685 1813 56439668 56439797 7.550000e-31 145.0
20 TraesCS5B01G060700 chr4A 81.053 95 12 1 2470 2558 97526372 97526466 1.300000e-08 71.3
21 TraesCS5B01G060700 chr1A 85.985 264 34 3 2168 2430 71442570 71442831 1.980000e-71 279.0
22 TraesCS5B01G060700 chr7D 89.175 194 21 0 1862 2055 85030769 85030576 2.600000e-60 243.0
23 TraesCS5B01G060700 chr7D 85.385 130 13 1 2434 2557 636769320 636769191 2.110000e-26 130.0
24 TraesCS5B01G060700 chr7D 81.633 147 16 5 1917 2053 622178084 622178229 7.660000e-21 111.0
25 TraesCS5B01G060700 chr6D 90.164 183 18 0 1862 2044 427725567 427725385 3.370000e-59 239.0
26 TraesCS5B01G060700 chr6D 90.184 163 16 0 1861 2023 446869191 446869029 2.040000e-51 213.0
27 TraesCS5B01G060700 chr6D 87.027 185 18 5 1862 2045 427748480 427748301 1.230000e-48 204.0
28 TraesCS5B01G060700 chr6D 82.171 129 17 1 2435 2557 258350334 258350206 3.560000e-19 106.0
29 TraesCS5B01G060700 chr7B 87.634 186 17 1 2439 2618 13863292 13863107 7.340000e-51 211.0
30 TraesCS5B01G060700 chr3B 85.204 196 18 8 2433 2618 820456294 820456100 9.560000e-45 191.0
31 TraesCS5B01G060700 chr1B 80.645 124 13 9 1684 1799 589928770 589928890 4.640000e-13 86.1
32 TraesCS5B01G060700 chr4D 78.195 133 25 3 1683 1811 165887641 165887509 6.010000e-12 82.4


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 TraesCS5B01G060700 chr5B 68048281 68050898 2617 False 4835.000000 4835 100.000000 1 2618 1 chr5B.!!$F1 2617
1 TraesCS5B01G060700 chr5B 68194178 68195790 1612 False 1816.000000 1816 87.076000 1 1656 1 chr5B.!!$F2 1655
2 TraesCS5B01G060700 chr5D 62477100 62479733 2633 True 1072.333333 1170 91.258667 1 2618 3 chr5D.!!$R1 2617
3 TraesCS5B01G060700 chr5D 62509943 62511481 1538 True 945.000000 1031 89.059000 12 1652 2 chr5D.!!$R2 1640
4 TraesCS5B01G060700 chr5A 52356651 52358189 1538 True 922.000000 968 89.828500 1 1604 2 chr5A.!!$R1 1603
5 TraesCS5B01G060700 chr2A 41149825 41153971 4146 False 250.000000 311 89.073000 1862 2411 2 chr2A.!!$F1 549

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
713 725 0.249868 TCGATCGCCTATTTGCCTGG 60.25 55.0 11.09 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2498 6284 0.321122 AGGAACTTCTGGCAGCTTCG 60.321 55.0 10.34 0.11 27.25 3.79 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
191 194 2.579249 GCGAGCAGCTCTGAGTCG 60.579 66.667 20.39 7.94 44.04 4.18
310 313 4.066139 GGCCCATCCCAGCACCTT 62.066 66.667 0.00 0.00 0.00 3.50
322 325 0.464735 AGCACCTTGTTGCCGTACAA 60.465 50.000 0.00 0.00 44.14 2.41
332 335 0.249953 TGCCGTACAACACCGTGATT 60.250 50.000 5.28 0.00 0.00 2.57
335 338 1.458064 CCGTACAACACCGTGATTGTC 59.542 52.381 17.29 11.23 39.67 3.18
483 486 4.736896 AGAAACTCGGGCCGTCGC 62.737 66.667 27.32 11.94 0.00 5.19
502 505 2.544267 CGCTCGGAGAAAATGAATACCC 59.456 50.000 9.69 0.00 34.09 3.69
504 507 3.433740 GCTCGGAGAAAATGAATACCCCT 60.434 47.826 9.69 0.00 34.09 4.79
507 510 3.431766 CGGAGAAAATGAATACCCCTCGT 60.432 47.826 0.00 0.00 0.00 4.18
514 517 5.687166 AATGAATACCCCTCGTAGACAAA 57.313 39.130 0.00 0.00 0.00 2.83
517 520 4.773674 TGAATACCCCTCGTAGACAAAGAA 59.226 41.667 0.00 0.00 0.00 2.52
523 526 4.760204 CCCCTCGTAGACAAAGAAAACAAT 59.240 41.667 0.00 0.00 0.00 2.71
529 532 6.018262 TCGTAGACAAAGAAAACAATGGTGAG 60.018 38.462 0.00 0.00 0.00 3.51
550 553 3.127099 CCATGAGGCCAAGCATGAT 57.873 52.632 25.71 0.00 43.43 2.45
570 573 1.416813 GCACGCATCTCTTGTCCTCG 61.417 60.000 0.00 0.00 0.00 4.63
584 587 4.462417 CTCGTCGTCGGCGCTTCT 62.462 66.667 15.63 0.00 38.14 2.85
602 605 4.436998 GCACCGTCGCTAGCACCT 62.437 66.667 16.45 0.00 0.00 4.00
603 606 3.060020 GCACCGTCGCTAGCACCTA 62.060 63.158 16.45 0.00 0.00 3.08
604 607 1.064296 CACCGTCGCTAGCACCTAG 59.936 63.158 16.45 1.28 37.16 3.02
629 632 2.574222 GATGTACGTACGCTGCGCC 61.574 63.158 23.51 12.10 0.00 6.53
668 676 1.785430 TCGATCTCGAGATGTACGACG 59.215 52.381 31.88 25.02 44.22 5.12
669 677 1.521840 CGATCTCGAGATGTACGACGT 59.478 52.381 31.88 5.52 43.02 4.34
670 678 2.723143 CGATCTCGAGATGTACGACGTA 59.277 50.000 31.88 2.97 43.02 3.57
671 679 3.181178 CGATCTCGAGATGTACGACGTAA 59.819 47.826 31.88 0.00 43.02 3.18
672 680 4.317628 CGATCTCGAGATGTACGACGTAAA 60.318 45.833 31.88 4.51 43.02 2.01
704 716 3.120105 CCACAGCTCGATCGCCTA 58.880 61.111 11.09 0.00 0.00 3.93
705 717 1.662608 CCACAGCTCGATCGCCTAT 59.337 57.895 11.09 0.00 0.00 2.57
707 719 1.539065 CCACAGCTCGATCGCCTATTT 60.539 52.381 11.09 0.00 0.00 1.40
708 720 1.524355 CACAGCTCGATCGCCTATTTG 59.476 52.381 11.09 5.40 0.00 2.32
712 724 1.143305 CTCGATCGCCTATTTGCCTG 58.857 55.000 11.09 0.00 0.00 4.85
713 725 0.249868 TCGATCGCCTATTTGCCTGG 60.250 55.000 11.09 0.00 0.00 4.45
715 727 1.680338 GATCGCCTATTTGCCTGGTT 58.320 50.000 0.00 0.00 0.00 3.67
716 728 2.805295 CGATCGCCTATTTGCCTGGTTA 60.805 50.000 0.26 0.00 0.00 2.85
717 729 3.412386 GATCGCCTATTTGCCTGGTTAT 58.588 45.455 0.00 0.00 0.00 1.89
718 730 4.575885 GATCGCCTATTTGCCTGGTTATA 58.424 43.478 0.00 0.00 0.00 0.98
719 731 4.634012 TCGCCTATTTGCCTGGTTATAT 57.366 40.909 0.00 0.00 0.00 0.86
720 732 5.748670 TCGCCTATTTGCCTGGTTATATA 57.251 39.130 0.00 0.00 0.00 0.86
721 733 5.730550 TCGCCTATTTGCCTGGTTATATAG 58.269 41.667 0.00 0.48 0.00 1.31
722 734 4.332819 CGCCTATTTGCCTGGTTATATAGC 59.667 45.833 0.00 0.00 0.00 2.97
723 735 5.501156 GCCTATTTGCCTGGTTATATAGCT 58.499 41.667 0.00 0.00 0.00 3.32
724 736 5.946377 GCCTATTTGCCTGGTTATATAGCTT 59.054 40.000 0.00 0.00 0.00 3.74
725 737 6.434340 GCCTATTTGCCTGGTTATATAGCTTT 59.566 38.462 0.00 0.00 0.00 3.51
726 738 7.610305 GCCTATTTGCCTGGTTATATAGCTTTA 59.390 37.037 0.00 0.00 0.00 1.85
731 748 5.710099 TGCCTGGTTATATAGCTTTATTGGC 59.290 40.000 1.83 9.00 35.22 4.52
755 775 1.337728 TGCCAGACAGATACACAACGG 60.338 52.381 0.00 0.00 0.00 4.44
772 809 2.840974 GGGTTGGACACGATGACTG 58.159 57.895 0.00 0.00 0.00 3.51
856 902 5.421056 TCTTTCCTCGTTGTATACACAGGAT 59.579 40.000 20.65 0.00 36.07 3.24
858 904 5.670792 TCCTCGTTGTATACACAGGATTT 57.329 39.130 17.85 0.00 35.67 2.17
902 948 5.952526 TGACACGATATATACATCACCGT 57.047 39.130 0.00 0.00 0.00 4.83
918 964 2.152699 CGTCTCCAAGCTACACGCG 61.153 63.158 3.53 3.53 45.59 6.01
923 969 2.032550 TCTCCAAGCTACACGCGTATAC 59.967 50.000 13.44 1.39 45.59 1.47
924 970 2.019249 TCCAAGCTACACGCGTATACT 58.981 47.619 13.44 4.18 45.59 2.12
927 973 4.096231 TCCAAGCTACACGCGTATACTTTA 59.904 41.667 13.44 1.69 45.59 1.85
932 978 4.977963 GCTACACGCGTATACTTTATCCAA 59.022 41.667 13.44 0.00 0.00 3.53
934 980 6.019640 GCTACACGCGTATACTTTATCCAAAA 60.020 38.462 13.44 0.00 0.00 2.44
935 981 6.724694 ACACGCGTATACTTTATCCAAAAA 57.275 33.333 13.44 0.00 0.00 1.94
936 982 6.768078 ACACGCGTATACTTTATCCAAAAAG 58.232 36.000 13.44 0.00 41.35 2.27
937 983 5.675444 CACGCGTATACTTTATCCAAAAAGC 59.325 40.000 13.44 0.00 39.59 3.51
938 984 5.583457 ACGCGTATACTTTATCCAAAAAGCT 59.417 36.000 11.67 0.00 39.59 3.74
939 985 6.757947 ACGCGTATACTTTATCCAAAAAGCTA 59.242 34.615 11.67 0.00 39.59 3.32
940 986 7.061634 CGCGTATACTTTATCCAAAAAGCTAC 58.938 38.462 0.00 0.00 39.59 3.58
941 987 7.254185 CGCGTATACTTTATCCAAAAAGCTACA 60.254 37.037 0.00 0.00 39.59 2.74
942 988 7.849515 GCGTATACTTTATCCAAAAAGCTACAC 59.150 37.037 0.56 0.00 39.59 2.90
943 989 8.054236 CGTATACTTTATCCAAAAAGCTACACG 58.946 37.037 0.56 0.00 39.59 4.49
944 990 5.043189 ACTTTATCCAAAAAGCTACACGC 57.957 39.130 0.00 0.00 39.59 5.34
945 991 3.733024 TTATCCAAAAAGCTACACGCG 57.267 42.857 3.53 3.53 45.59 6.01
946 992 1.519408 ATCCAAAAAGCTACACGCGT 58.481 45.000 5.58 5.58 45.59 6.01
947 993 2.151881 TCCAAAAAGCTACACGCGTA 57.848 45.000 13.44 0.00 45.59 4.42
948 994 1.794116 TCCAAAAAGCTACACGCGTAC 59.206 47.619 13.44 1.40 45.59 3.67
949 995 1.527736 CCAAAAAGCTACACGCGTACA 59.472 47.619 13.44 0.65 45.59 2.90
950 996 2.158841 CCAAAAAGCTACACGCGTACAT 59.841 45.455 13.44 2.74 45.59 2.29
951 997 3.404564 CAAAAAGCTACACGCGTACATC 58.595 45.455 13.44 1.55 45.59 3.06
1037 1090 0.108567 GGTCTCCTCGCCTCTTTGAC 60.109 60.000 0.00 0.00 0.00 3.18
1038 1091 0.892063 GTCTCCTCGCCTCTTTGACT 59.108 55.000 0.00 0.00 0.00 3.41
1039 1092 1.273886 GTCTCCTCGCCTCTTTGACTT 59.726 52.381 0.00 0.00 0.00 3.01
1040 1093 1.546476 TCTCCTCGCCTCTTTGACTTC 59.454 52.381 0.00 0.00 0.00 3.01
1041 1094 0.243907 TCCTCGCCTCTTTGACTTCG 59.756 55.000 0.00 0.00 0.00 3.79
1042 1095 0.243907 CCTCGCCTCTTTGACTTCGA 59.756 55.000 0.00 0.00 0.00 3.71
1083 1136 4.560128 TCTTCGACAACTGGAAGATTCTG 58.440 43.478 0.00 0.00 42.62 3.02
1146 1199 1.593750 CATGCTAGCTCACGGCCTC 60.594 63.158 17.23 0.00 43.05 4.70
1187 1240 1.189524 TTCTCCATGGAACCCGTCGT 61.190 55.000 17.00 0.00 0.00 4.34
1655 1710 4.948621 TGAGTTAGCCTAGGAGTACACTTC 59.051 45.833 14.75 1.31 0.00 3.01
1661 1716 2.159226 CCTAGGAGTACACTTCCGCTTG 60.159 54.545 1.05 0.00 0.00 4.01
1763 1889 7.559533 TGTAAATTAATCCACATGTATGCAGGT 59.440 33.333 0.00 0.00 40.58 4.00
1764 1890 7.422465 AAATTAATCCACATGTATGCAGGTT 57.578 32.000 0.00 0.00 37.55 3.50
1765 1891 7.422465 AATTAATCCACATGTATGCAGGTTT 57.578 32.000 0.00 0.00 37.55 3.27
1823 1950 4.220602 TGCTATAGTGTCAGTGTGTCACAT 59.779 41.667 9.31 0.00 38.55 3.21
1855 1982 1.112315 TCAAAACTGGCGCCCACAAT 61.112 50.000 26.77 4.38 0.00 2.71
1859 1986 3.202001 CTGGCGCCCACAATACCG 61.202 66.667 26.77 0.00 0.00 4.02
1883 2010 6.454186 CGGGAGTATTTAACGAAAAACTACCG 60.454 42.308 22.37 22.37 45.46 4.02
1893 2020 3.363182 CGAAAAACTACCGCATTTCGTCA 60.363 43.478 10.37 0.00 45.32 4.35
1909 2036 1.070175 CGTCAAACCGTGCCTACAAAG 60.070 52.381 0.00 0.00 0.00 2.77
1912 2039 3.749609 GTCAAACCGTGCCTACAAAGTAT 59.250 43.478 0.00 0.00 0.00 2.12
1937 2065 6.758886 TCACTTTACAAATTTGTGCCGAAAAT 59.241 30.769 29.72 12.18 42.31 1.82
2183 2312 7.172019 CCCAAGAAACACGTACTAAATACAACT 59.828 37.037 0.00 0.00 32.79 3.16
2259 2389 0.038744 CCAGAGGTCAGTGGCCAATT 59.961 55.000 17.90 0.00 0.00 2.32
2325 6080 4.292306 ACCCATCACCTAACCAAATCTCTT 59.708 41.667 0.00 0.00 0.00 2.85
2326 6081 4.641989 CCCATCACCTAACCAAATCTCTTG 59.358 45.833 0.00 0.00 0.00 3.02
2491 6277 2.286523 CGGAAGGAGCTGTGGGAGT 61.287 63.158 0.00 0.00 0.00 3.85
2495 6281 4.416738 GGAGCTGTGGGAGTGGCC 62.417 72.222 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 104 1.065418 ACCTCTATTTTGGGAGTGCCG 60.065 52.381 0.00 0.00 33.83 5.69
206 209 2.733542 CGACGTGCTTCTCACAGATGAT 60.734 50.000 0.00 0.00 45.92 2.45
212 215 2.355837 GCCGACGTGCTTCTCACA 60.356 61.111 0.00 0.00 45.92 3.58
332 335 1.367471 CTGCAGGGAGAACGTGACA 59.633 57.895 5.57 0.00 37.13 3.58
335 338 1.374758 GACCTGCAGGGAGAACGTG 60.375 63.158 35.42 8.48 40.27 4.49
483 486 4.381411 GAGGGGTATTCATTTTCTCCGAG 58.619 47.826 0.00 0.00 0.00 4.63
492 495 5.424252 TCTTTGTCTACGAGGGGTATTCATT 59.576 40.000 0.00 0.00 0.00 2.57
502 505 5.238650 ACCATTGTTTTCTTTGTCTACGAGG 59.761 40.000 0.00 0.00 0.00 4.63
504 507 5.818336 TCACCATTGTTTTCTTTGTCTACGA 59.182 36.000 0.00 0.00 0.00 3.43
507 510 5.534654 CCCTCACCATTGTTTTCTTTGTCTA 59.465 40.000 0.00 0.00 0.00 2.59
514 517 1.133199 TGGCCCTCACCATTGTTTTCT 60.133 47.619 0.00 0.00 33.75 2.52
538 541 2.103538 CGTGCATCATGCTTGGCC 59.896 61.111 11.84 0.00 45.31 5.36
550 553 0.390340 GAGGACAAGAGATGCGTGCA 60.390 55.000 0.00 0.00 0.00 4.57
560 563 2.974489 GCCGACGACGAGGACAAGA 61.974 63.158 9.28 0.00 42.66 3.02
584 587 4.735132 GGTGCTAGCGACGGTGCA 62.735 66.667 10.77 14.05 37.31 4.57
591 594 1.954382 CATGGTACTAGGTGCTAGCGA 59.046 52.381 10.77 0.00 37.57 4.93
602 605 4.024641 CAGCGTACGTACATCATGGTACTA 60.025 45.833 24.50 0.00 41.12 1.82
603 606 2.947652 AGCGTACGTACATCATGGTACT 59.052 45.455 24.50 5.25 41.12 2.73
604 607 3.040795 CAGCGTACGTACATCATGGTAC 58.959 50.000 24.50 0.00 40.14 3.34
659 667 6.460987 GTCGCTTAATTTTTACGTCGTACAT 58.539 36.000 4.17 0.00 0.00 2.29
661 669 4.938073 CGTCGCTTAATTTTTACGTCGTAC 59.062 41.667 4.17 0.00 32.31 3.67
662 670 4.615121 ACGTCGCTTAATTTTTACGTCGTA 59.385 37.500 0.00 0.00 44.03 3.43
663 671 3.425193 ACGTCGCTTAATTTTTACGTCGT 59.575 39.130 2.21 2.21 39.11 4.34
664 672 3.764889 CACGTCGCTTAATTTTTACGTCG 59.235 43.478 0.00 0.00 41.17 5.12
665 673 3.531827 GCACGTCGCTTAATTTTTACGTC 59.468 43.478 0.00 0.00 41.17 4.34
666 674 3.472431 GCACGTCGCTTAATTTTTACGT 58.528 40.909 0.00 0.00 43.62 3.57
667 675 2.836161 GGCACGTCGCTTAATTTTTACG 59.164 45.455 9.31 0.00 41.91 3.18
668 676 3.600786 GTGGCACGTCGCTTAATTTTTAC 59.399 43.478 0.00 0.00 41.91 2.01
669 677 3.250280 TGTGGCACGTCGCTTAATTTTTA 59.750 39.130 13.77 0.00 41.91 1.52
670 678 2.033550 TGTGGCACGTCGCTTAATTTTT 59.966 40.909 13.77 0.00 41.91 1.94
671 679 1.604755 TGTGGCACGTCGCTTAATTTT 59.395 42.857 13.77 0.00 41.91 1.82
672 680 1.196808 CTGTGGCACGTCGCTTAATTT 59.803 47.619 13.77 0.00 41.91 1.82
704 716 8.806146 CCAATAAAGCTATATAACCAGGCAAAT 58.194 33.333 0.00 0.00 0.00 2.32
705 717 7.255801 GCCAATAAAGCTATATAACCAGGCAAA 60.256 37.037 0.00 0.00 36.03 3.68
707 719 5.710099 GCCAATAAAGCTATATAACCAGGCA 59.290 40.000 0.00 0.00 36.03 4.75
708 720 5.163754 CGCCAATAAAGCTATATAACCAGGC 60.164 44.000 0.00 0.00 0.00 4.85
712 724 5.123344 CACCCGCCAATAAAGCTATATAACC 59.877 44.000 0.00 0.00 0.00 2.85
713 725 5.391629 GCACCCGCCAATAAAGCTATATAAC 60.392 44.000 0.00 0.00 0.00 1.89
715 727 4.258543 GCACCCGCCAATAAAGCTATATA 58.741 43.478 0.00 0.00 0.00 0.86
716 728 3.081804 GCACCCGCCAATAAAGCTATAT 58.918 45.455 0.00 0.00 0.00 0.86
717 729 2.500229 GCACCCGCCAATAAAGCTATA 58.500 47.619 0.00 0.00 0.00 1.31
718 730 1.318576 GCACCCGCCAATAAAGCTAT 58.681 50.000 0.00 0.00 0.00 2.97
719 731 2.788515 GCACCCGCCAATAAAGCTA 58.211 52.632 0.00 0.00 0.00 3.32
720 732 3.603365 GCACCCGCCAATAAAGCT 58.397 55.556 0.00 0.00 0.00 3.74
731 748 0.460284 GTGTATCTGTCTGGCACCCG 60.460 60.000 0.00 0.00 0.00 5.28
741 758 1.695242 TCCAACCCGTTGTGTATCTGT 59.305 47.619 6.81 0.00 38.85 3.41
755 775 1.000955 AGACAGTCATCGTGTCCAACC 59.999 52.381 2.66 0.00 44.65 3.77
856 902 4.019681 ACGAGGTAATTGGTCTCCATGAAA 60.020 41.667 0.00 0.00 31.53 2.69
858 904 3.104512 ACGAGGTAATTGGTCTCCATGA 58.895 45.455 0.00 0.00 31.53 3.07
902 948 1.100510 ATACGCGTGTAGCTTGGAGA 58.899 50.000 24.59 0.00 45.59 3.71
918 964 7.849515 GCGTGTAGCTTTTTGGATAAAGTATAC 59.150 37.037 0.00 0.00 44.04 1.47
923 969 4.088648 CGCGTGTAGCTTTTTGGATAAAG 58.911 43.478 0.00 0.00 45.59 1.85
924 970 3.499157 ACGCGTGTAGCTTTTTGGATAAA 59.501 39.130 12.93 0.00 45.59 1.40
927 973 1.519408 ACGCGTGTAGCTTTTTGGAT 58.481 45.000 12.93 0.00 45.59 3.41
932 978 2.955614 AGATGTACGCGTGTAGCTTTT 58.044 42.857 24.59 0.00 45.59 2.27
934 980 2.649331 AAGATGTACGCGTGTAGCTT 57.351 45.000 24.59 20.68 45.59 3.74
935 981 2.649331 AAAGATGTACGCGTGTAGCT 57.351 45.000 24.59 15.71 45.59 3.32
936 982 3.717350 AAAAAGATGTACGCGTGTAGC 57.283 42.857 24.59 13.46 43.95 3.58
1039 1092 4.501285 ATCGGAGTCGCCCCTCGA 62.501 66.667 0.00 0.00 46.29 4.04
1040 1093 4.271816 CATCGGAGTCGCCCCTCG 62.272 72.222 0.00 0.00 40.15 4.63
1041 1094 3.917760 CCATCGGAGTCGCCCCTC 61.918 72.222 0.00 0.00 36.13 4.30
1083 1136 0.955919 CGAGGAAGGTGAACAAGGCC 60.956 60.000 0.00 0.00 0.00 5.19
1146 1199 2.584835 TGATCCTCCCAACAAACTGG 57.415 50.000 0.00 0.00 36.10 4.00
1317 1371 0.531200 CGGAGTAGACCACTTCCACC 59.469 60.000 0.00 0.00 37.72 4.61
1655 1710 0.895530 TCCTTCTACTCCACAAGCGG 59.104 55.000 0.00 0.00 0.00 5.52
1661 1716 2.158885 GCCCAGAATCCTTCTACTCCAC 60.159 54.545 0.00 0.00 38.11 4.02
1802 1929 5.714047 ACATGTGACACACTGACACTATAG 58.286 41.667 11.22 0.00 42.09 1.31
1807 1934 2.032054 CCAACATGTGACACACTGACAC 59.968 50.000 11.22 0.00 41.97 3.67
1808 1935 2.287769 CCAACATGTGACACACTGACA 58.712 47.619 11.22 0.00 35.11 3.58
1809 1936 1.002468 GCCAACATGTGACACACTGAC 60.002 52.381 11.22 0.00 35.11 3.51
1810 1937 1.308047 GCCAACATGTGACACACTGA 58.692 50.000 11.22 0.00 35.11 3.41
1811 1938 1.002142 CTGCCAACATGTGACACACTG 60.002 52.381 11.22 12.52 35.11 3.66
1812 1939 1.311859 CTGCCAACATGTGACACACT 58.688 50.000 11.22 0.00 35.11 3.55
1813 1940 1.024271 ACTGCCAACATGTGACACAC 58.976 50.000 11.22 1.42 34.56 3.82
1814 1941 2.493035 CTACTGCCAACATGTGACACA 58.507 47.619 11.41 11.41 0.00 3.72
1823 1950 2.948979 CAGTTTTGACCTACTGCCAACA 59.051 45.455 0.00 0.00 35.79 3.33
1855 1982 6.463360 AGTTTTTCGTTAAATACTCCCGGTA 58.537 36.000 0.00 0.00 33.28 4.02
1859 1986 6.673076 GCGGTAGTTTTTCGTTAAATACTCCC 60.673 42.308 0.00 0.00 37.79 4.30
1883 2010 1.001745 GGCACGGTTTGACGAAATGC 61.002 55.000 0.00 0.00 37.61 3.56
1893 2020 3.749609 GTGATACTTTGTAGGCACGGTTT 59.250 43.478 0.00 0.00 0.00 3.27
1909 2036 6.375377 TCGGCACAAATTTGTAAAGTGATAC 58.625 36.000 22.87 5.64 39.91 2.24
1912 2039 4.902443 TCGGCACAAATTTGTAAAGTGA 57.098 36.364 22.87 13.45 39.91 3.41
1961 2089 4.150897 AGCAGTCACTAGTGTTTTTGGA 57.849 40.909 21.99 0.00 0.00 3.53
2032 2160 4.397420 AGTTGACTATTGTGCCATGTCAA 58.603 39.130 0.00 0.00 42.81 3.18
2067 2195 9.730420 CACATATCATAACGGTCGATATAATGA 57.270 33.333 5.29 0.00 32.41 2.57
2069 2197 8.141909 CCCACATATCATAACGGTCGATATAAT 58.858 37.037 5.29 0.00 32.41 1.28
2074 2202 3.056107 CCCCACATATCATAACGGTCGAT 60.056 47.826 0.00 0.00 0.00 3.59
2151 2280 5.494632 AGTACGTGTTTCTTGGGAAAAAG 57.505 39.130 0.00 0.00 42.22 2.27
2158 2287 8.080083 AGTTGTATTTAGTACGTGTTTCTTGG 57.920 34.615 0.00 0.00 36.01 3.61
2190 2319 8.886719 ACTAGTTGTATTTAGGCCGTATTTTTC 58.113 33.333 0.00 0.00 0.00 2.29
2191 2320 8.797350 ACTAGTTGTATTTAGGCCGTATTTTT 57.203 30.769 0.00 0.00 0.00 1.94
2244 2374 3.011708 AGGATTAAATTGGCCACTGACCT 59.988 43.478 3.88 5.51 0.00 3.85
2259 2389 9.895138 GATAGGTTAGTGGTTTGTTAGGATTAA 57.105 33.333 0.00 0.00 0.00 1.40
2430 6186 2.912025 CCAAACCAACGCCAGGCT 60.912 61.111 10.54 0.00 0.00 4.58
2436 6192 1.104577 TTCCAGTCCCAAACCAACGC 61.105 55.000 0.00 0.00 0.00 4.84
2437 6193 0.666374 GTTCCAGTCCCAAACCAACG 59.334 55.000 0.00 0.00 0.00 4.10
2477 6263 3.325753 GCCACTCCCACAGCTCCT 61.326 66.667 0.00 0.00 0.00 3.69
2498 6284 0.321122 AGGAACTTCTGGCAGCTTCG 60.321 55.000 10.34 0.11 27.25 3.79
2509 6295 2.269241 CGGCCTGGGAGGAACTTC 59.731 66.667 0.00 0.00 41.55 3.01


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

AutoCloner maintained by Alex Coulton.