Multiple sequence alignment - TraesCS5A01G410000

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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 TraesCS5A01G410000 chr5A 100.000 3856 0 0 1 3856 599391487 599387632 0.000000e+00 7121.0
1 TraesCS5A01G410000 chr5A 89.255 1973 135 36 997 2899 599449047 599447082 0.000000e+00 2398.0
2 TraesCS5A01G410000 chr5A 87.275 723 56 16 1 695 599451931 599451217 0.000000e+00 793.0
3 TraesCS5A01G410000 chr5A 97.297 37 1 0 742 778 599451223 599451187 3.220000e-06 63.9
4 TraesCS5A01G410000 chr5B 93.271 2987 146 20 233 3179 588779051 588776080 0.000000e+00 4351.0
5 TraesCS5A01G410000 chr5B 87.291 1975 166 37 985 2899 588832600 588830651 0.000000e+00 2178.0
6 TraesCS5A01G410000 chr5B 86.037 709 57 22 1 674 588833500 588832799 0.000000e+00 723.0
7 TraesCS5A01G410000 chr5B 93.111 479 26 3 3379 3853 588775361 588774886 0.000000e+00 695.0
8 TraesCS5A01G410000 chr5B 95.154 227 11 0 1 227 588779332 588779106 3.660000e-95 359.0
9 TraesCS5A01G410000 chr5B 90.816 196 13 2 3192 3382 588776010 588775815 1.370000e-64 257.0
10 TraesCS5A01G410000 chr5B 89.333 75 3 2 704 778 588832795 588832726 5.310000e-14 89.8
11 TraesCS5A01G410000 chrUn 79.232 963 137 35 1000 1913 177132905 177131957 2.550000e-171 612.0
12 TraesCS5A01G410000 chrUn 79.232 963 137 35 1000 1913 306187850 306186902 2.550000e-171 612.0
13 TraesCS5A01G410000 chrUn 86.580 462 59 1 2399 2860 364582545 364583003 1.240000e-139 507.0
14 TraesCS5A01G410000 chrUn 85.302 381 45 6 1968 2338 177131867 177131488 2.170000e-102 383.0
15 TraesCS5A01G410000 chrUn 85.302 381 45 6 1968 2338 306186812 306186433 2.170000e-102 383.0
16 TraesCS5A01G410000 chr2B 79.310 957 135 35 1000 1907 3787559 3788501 2.550000e-171 612.0
17 TraesCS5A01G410000 chr2B 84.046 608 75 17 999 1589 3906186 3906788 2.010000e-157 566.0
18 TraesCS5A01G410000 chr2B 83.882 608 76 17 999 1589 4185191 4185793 9.360000e-156 560.0
19 TraesCS5A01G410000 chr2B 86.797 462 58 1 2399 2860 3789577 3790035 2.660000e-141 512.0
20 TraesCS5A01G410000 chr2B 86.580 462 59 1 2399 2860 1315357 1314899 1.240000e-139 507.0
21 TraesCS5A01G410000 chr2B 85.302 381 45 6 1968 2338 1316973 1316594 2.170000e-102 383.0
22 TraesCS5A01G410000 chr2B 85.302 381 45 6 1968 2338 3788597 3788976 2.170000e-102 383.0
23 TraesCS5A01G410000 chr2B 81.462 383 63 5 1964 2338 3907325 3907707 1.350000e-79 307.0
24 TraesCS5A01G410000 chr2B 100.000 28 0 0 3164 3191 484107486 484107513 7.000000e-03 52.8
25 TraesCS5A01G410000 chr2A 86.177 463 61 2 2399 2861 5783799 5783340 7.440000e-137 497.0
26 TraesCS5A01G410000 chr2A 86.990 392 45 6 1952 2342 5784449 5784063 1.640000e-118 436.0
27 TraesCS5A01G410000 chr2A 90.614 277 26 0 999 1275 5785648 5785372 6.090000e-98 368.0
28 TraesCS5A01G410000 chr2A 100.000 29 0 0 3163 3191 694842534 694842506 2.000000e-03 54.7
29 TraesCS5A01G410000 chr3B 76.462 701 128 25 1662 2337 177493744 177493056 2.850000e-91 346.0
30 TraesCS5A01G410000 chr3B 100.000 31 0 0 3161 3191 62964300 62964270 1.500000e-04 58.4
31 TraesCS5A01G410000 chr6D 88.991 109 12 0 525 633 456251758 456251650 6.720000e-28 135.0
32 TraesCS5A01G410000 chr2D 100.000 31 0 0 3161 3191 540546303 540546333 1.500000e-04 58.4
33 TraesCS5A01G410000 chr2D 96.774 31 1 0 3161 3191 291953373 291953403 7.000000e-03 52.8
34 TraesCS5A01G410000 chr6A 94.444 36 2 0 3160 3195 337123216 337123181 5.380000e-04 56.5
35 TraesCS5A01G410000 chr4A 100.000 29 0 0 3165 3193 613368018 613367990 2.000000e-03 54.7
36 TraesCS5A01G410000 chr4A 96.875 32 1 0 3127 3158 633448586 633448617 2.000000e-03 54.7
37 TraesCS5A01G410000 chr4A 96.875 32 1 0 3127 3158 633489581 633489612 2.000000e-03 54.7
38 TraesCS5A01G410000 chr4A 96.875 32 1 0 3127 3158 633539328 633539359 2.000000e-03 54.7
39 TraesCS5A01G410000 chr4A 96.875 32 1 0 3127 3158 633721037 633721068 2.000000e-03 54.7
40 TraesCS5A01G410000 chr5D 96.774 31 1 0 3164 3194 494463689 494463659 7.000000e-03 52.8
41 TraesCS5A01G410000 chr1D 100.000 28 0 0 3167 3194 391258885 391258912 7.000000e-03 52.8


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 TraesCS5A01G410000 chr5A 599387632 599391487 3855 True 7121.000000 7121 100.000000 1 3856 1 chr5A.!!$R1 3855
1 TraesCS5A01G410000 chr5A 599447082 599451931 4849 True 1084.966667 2398 91.275667 1 2899 3 chr5A.!!$R2 2898
2 TraesCS5A01G410000 chr5B 588774886 588779332 4446 True 1415.500000 4351 93.088000 1 3853 4 chr5B.!!$R1 3852
3 TraesCS5A01G410000 chr5B 588830651 588833500 2849 True 996.933333 2178 87.553667 1 2899 3 chr5B.!!$R2 2898
4 TraesCS5A01G410000 chrUn 177131488 177132905 1417 True 497.500000 612 82.267000 1000 2338 2 chrUn.!!$R1 1338
5 TraesCS5A01G410000 chrUn 306186433 306187850 1417 True 497.500000 612 82.267000 1000 2338 2 chrUn.!!$R2 1338
6 TraesCS5A01G410000 chr2B 4185191 4185793 602 False 560.000000 560 83.882000 999 1589 1 chr2B.!!$F1 590
7 TraesCS5A01G410000 chr2B 3787559 3790035 2476 False 502.333333 612 83.803000 1000 2860 3 chr2B.!!$F3 1860
8 TraesCS5A01G410000 chr2B 1314899 1316973 2074 True 445.000000 507 85.941000 1968 2860 2 chr2B.!!$R1 892
9 TraesCS5A01G410000 chr2B 3906186 3907707 1521 False 436.500000 566 82.754000 999 2338 2 chr2B.!!$F4 1339
10 TraesCS5A01G410000 chr2A 5783340 5785648 2308 True 433.666667 497 87.927000 999 2861 3 chr2A.!!$R2 1862
11 TraesCS5A01G410000 chr3B 177493056 177493744 688 True 346.000000 346 76.462000 1662 2337 1 chr3B.!!$R2 675

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
85 86 0.106268 TTGGGGTTCATGTGCACTGT 60.106 50.0 19.41 3.75 0.00 3.55 F
102 103 0.386476 TGTGCCGTACGAAGAAGTGT 59.614 50.0 18.76 0.00 0.00 3.55 F
635 712 0.393077 ACACAAACTAGCTCCTGCGT 59.607 50.0 0.00 0.00 45.42 5.24 F
1693 3980 1.097547 GCAATAGCGTGGGAGTGCAT 61.098 55.0 0.00 0.00 32.29 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 4057 0.107361 TGGCTATCTCGTCGGAGTCA 60.107 55.000 0.00 0.0 41.26 3.41 R
1795 4089 1.228094 TTGCCCAACATCACTCGCA 60.228 52.632 0.00 0.0 0.00 5.10 R
2102 4541 0.393402 TTCTACATGCCTGCAGCTGG 60.393 55.000 17.12 14.0 44.23 4.85 R
3065 6717 0.036388 TCAGAACATGGAACCTCCGC 60.036 55.000 0.00 0.0 40.17 5.54 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
46 47 0.247460 CTCCAGCATGTCTCGTCCAA 59.753 55.000 0.00 0.00 0.00 3.53
85 86 0.106268 TTGGGGTTCATGTGCACTGT 60.106 50.000 19.41 3.75 0.00 3.55
102 103 0.386476 TGTGCCGTACGAAGAAGTGT 59.614 50.000 18.76 0.00 0.00 3.55
118 119 1.003112 TGTAAACAAGGCGGCGGAT 60.003 52.632 9.78 0.00 0.00 4.18
155 156 1.011333 CGTTCACCACGTTTCTGGTT 58.989 50.000 0.00 0.00 42.29 3.67
170 171 3.692406 GTTCCCTCCACGGCGACT 61.692 66.667 16.62 0.00 0.00 4.18
300 357 1.754745 GTTGGACACTGGAGAGGCA 59.245 57.895 0.00 0.00 0.00 4.75
312 369 1.003580 GGAGAGGCAACATGGAAGACA 59.996 52.381 0.00 0.00 41.41 3.41
317 374 1.895131 GGCAACATGGAAGACACCATT 59.105 47.619 0.00 0.00 47.00 3.16
416 473 2.092212 CCTCCAAGGTATGCAAGTGGAT 60.092 50.000 0.00 0.00 37.72 3.41
470 531 1.237285 ACGCCAAGCAAGTGATGGAC 61.237 55.000 7.52 0.28 36.27 4.02
474 535 2.012673 CCAAGCAAGTGATGGACTAGC 58.987 52.381 0.00 0.00 36.27 3.42
483 544 4.833390 AGTGATGGACTAGCAAAGGTAAC 58.167 43.478 0.00 0.00 30.86 2.50
484 545 4.532521 AGTGATGGACTAGCAAAGGTAACT 59.467 41.667 0.00 0.00 41.37 2.24
485 546 5.720041 AGTGATGGACTAGCAAAGGTAACTA 59.280 40.000 0.00 0.00 38.98 2.24
486 547 6.127310 AGTGATGGACTAGCAAAGGTAACTAG 60.127 42.308 0.00 0.00 38.98 2.57
522 599 3.335786 GCAAGATGCATGTGCTTAGAG 57.664 47.619 19.92 2.56 44.26 2.43
635 712 0.393077 ACACAAACTAGCTCCTGCGT 59.607 50.000 0.00 0.00 45.42 5.24
731 808 7.401246 AGACTAAATTGATTCTCTTTCCTGCT 58.599 34.615 0.00 0.00 0.00 4.24
732 809 8.543774 AGACTAAATTGATTCTCTTTCCTGCTA 58.456 33.333 0.00 0.00 0.00 3.49
733 810 8.499403 ACTAAATTGATTCTCTTTCCTGCTAC 57.501 34.615 0.00 0.00 0.00 3.58
734 811 6.428385 AAATTGATTCTCTTTCCTGCTACG 57.572 37.500 0.00 0.00 0.00 3.51
812 889 3.515562 CTGGCCTGGGTCTCTATCTAAT 58.484 50.000 3.32 0.00 0.00 1.73
821 898 9.589461 CCTGGGTCTCTATCTAATAACTTCTTA 57.411 37.037 0.00 0.00 0.00 2.10
871 948 4.101856 AGGGTATTCCTCTCTTTTCGGAA 58.898 43.478 0.00 0.00 44.06 4.30
872 949 4.534897 AGGGTATTCCTCTCTTTTCGGAAA 59.465 41.667 0.00 0.00 44.06 3.13
873 950 5.013808 AGGGTATTCCTCTCTTTTCGGAAAA 59.986 40.000 14.64 14.64 44.06 2.29
874 951 5.123502 GGGTATTCCTCTCTTTTCGGAAAAC 59.876 44.000 11.68 0.00 39.97 2.43
878 1003 6.709018 TTCCTCTCTTTTCGGAAAACAAAT 57.291 33.333 11.68 0.00 34.10 2.32
933 2949 7.513091 GGGGCCTAGTGCTATATAAATACCTAT 59.487 40.741 0.84 0.00 40.92 2.57
1312 3520 3.383505 TCTGTACCCAGATCGTTATGGTG 59.616 47.826 6.41 1.20 42.80 4.17
1317 3525 3.132289 ACCCAGATCGTTATGGTGTGTAG 59.868 47.826 6.41 0.00 34.58 2.74
1693 3980 1.097547 GCAATAGCGTGGGAGTGCAT 61.098 55.000 0.00 0.00 32.29 3.96
1763 4057 1.274728 GCCGAGATAGACATGAGGCAT 59.725 52.381 0.00 0.00 42.37 4.40
1795 4089 2.511218 AGATAGCCATGGGTGTCATTGT 59.489 45.455 33.56 16.50 36.44 2.71
2180 4631 1.135139 GAGTGCAGGACTCTATTCGCA 59.865 52.381 14.63 0.00 46.85 5.10
2189 4640 2.297597 GACTCTATTCGCAGCAGGGTAT 59.702 50.000 0.00 0.00 0.00 2.73
2390 6034 3.526385 GCACCGTGCATACATCTAATG 57.474 47.619 18.79 0.00 44.26 1.90
2706 6355 0.955428 GCAGAACTTCGCCATGGTCA 60.955 55.000 14.67 0.00 0.00 4.02
2823 6472 2.279408 GGTACGGGCTCCCTCTCT 59.721 66.667 3.11 0.00 0.00 3.10
2879 6531 0.388659 CTGGAGCTCCCTCGATCTTG 59.611 60.000 29.95 5.07 39.06 3.02
2909 6561 0.179148 CGTCATGTGCTACGCCTACA 60.179 55.000 0.00 0.00 31.66 2.74
2927 6579 8.423349 ACGCCTACACCATAATATTTACAGTAA 58.577 33.333 0.00 0.00 0.00 2.24
2981 6633 5.039984 TGACAATTGTGAACGTTTTGATGG 58.960 37.500 17.58 3.09 0.00 3.51
2985 6637 3.724508 TGTGAACGTTTTGATGGCAAT 57.275 38.095 0.46 0.00 33.25 3.56
2987 6639 3.801050 TGTGAACGTTTTGATGGCAATTG 59.199 39.130 0.46 0.00 33.25 2.32
2996 6648 4.418013 TTGATGGCAATTGTAGTTGTCG 57.582 40.909 7.40 0.00 36.51 4.35
2998 6650 4.570930 TGATGGCAATTGTAGTTGTCGTA 58.429 39.130 7.40 0.00 36.51 3.43
3003 6655 4.634443 GGCAATTGTAGTTGTCGTAAGGAT 59.366 41.667 7.40 0.00 38.47 3.24
3004 6656 5.447279 GGCAATTGTAGTTGTCGTAAGGATG 60.447 44.000 7.40 0.00 38.47 3.51
3005 6657 5.447279 GCAATTGTAGTTGTCGTAAGGATGG 60.447 44.000 7.40 0.00 38.47 3.51
3065 6717 3.378112 TCTGGTGAAAAACAGAACTGCAG 59.622 43.478 13.48 13.48 40.51 4.41
3079 6731 2.045926 GCAGCGGAGGTTCCATGT 60.046 61.111 0.00 0.00 35.91 3.21
3088 6740 2.616510 GGAGGTTCCATGTTCTGACCAG 60.617 54.545 0.00 0.00 36.28 4.00
3118 6771 3.606615 GCCACCAAAATTGTTCGCAAATG 60.607 43.478 0.00 0.00 40.90 2.32
3119 6772 3.543670 CACCAAAATTGTTCGCAAATGC 58.456 40.909 0.00 0.00 40.90 3.56
3140 6793 2.493278 CCATCTTTCCCAGCGAATGTTT 59.507 45.455 0.00 0.00 0.00 2.83
3176 6829 5.045797 GGGTCCAATATTATGTACTCCCTCC 60.046 48.000 0.00 0.00 0.00 4.30
3179 6832 5.479375 TCCAATATTATGTACTCCCTCCGTC 59.521 44.000 0.00 0.00 0.00 4.79
3180 6833 5.480772 CCAATATTATGTACTCCCTCCGTCT 59.519 44.000 0.00 0.00 0.00 4.18
3182 6835 3.657398 TTATGTACTCCCTCCGTCTCA 57.343 47.619 0.00 0.00 0.00 3.27
3183 6836 2.757894 ATGTACTCCCTCCGTCTCAT 57.242 50.000 0.00 0.00 0.00 2.90
3188 6841 5.888901 TGTACTCCCTCCGTCTCATAATAT 58.111 41.667 0.00 0.00 0.00 1.28
3189 6842 7.024345 TGTACTCCCTCCGTCTCATAATATA 57.976 40.000 0.00 0.00 0.00 0.86
3190 6843 7.464273 TGTACTCCCTCCGTCTCATAATATAA 58.536 38.462 0.00 0.00 0.00 0.98
3229 6939 4.794169 CCACTTTGGCATACACTTGTAAC 58.206 43.478 0.00 0.00 33.76 2.50
3235 6945 4.185394 TGGCATACACTTGTAACGTATGG 58.815 43.478 9.96 0.00 41.71 2.74
3244 6954 6.019152 CACTTGTAACGTATGGTTATGTTGC 58.981 40.000 0.00 1.32 42.74 4.17
3347 7062 3.400439 TTTTTAAGCACCGGACCGT 57.600 47.368 9.46 0.00 0.00 4.83
3349 7064 1.794512 TTTTAAGCACCGGACCGTAC 58.205 50.000 9.46 1.26 0.00 3.67
3393 7565 2.149578 CAGAAAGAACCACTCCTGCAG 58.850 52.381 6.78 6.78 0.00 4.41
3401 7573 1.064758 ACCACTCCTGCAGACAAACAA 60.065 47.619 17.39 0.00 0.00 2.83
3492 7665 7.822334 TGAATGGAACGACTTGATTATACTTGT 59.178 33.333 0.00 0.00 0.00 3.16
3493 7666 6.961359 TGGAACGACTTGATTATACTTGTG 57.039 37.500 0.00 0.00 0.00 3.33
3512 7685 8.715191 ACTTGTGAATGCAATTTGAAACTTTA 57.285 26.923 0.00 0.00 36.07 1.85
3515 7688 8.085720 TGTGAATGCAATTTGAAACTTTATGG 57.914 30.769 0.00 0.00 36.07 2.74
3519 7692 6.483385 TGCAATTTGAAACTTTATGGCATG 57.517 33.333 10.98 0.00 0.00 4.06
3552 7725 2.448926 TGCATGGTTATATAGCGCGT 57.551 45.000 8.43 0.00 0.00 6.01
3648 7821 7.432350 TTTAAACGAATACCCAAACATACGT 57.568 32.000 0.00 0.00 0.00 3.57
3692 7865 6.127925 ACACATTAGCACCAATGTTGTCATAG 60.128 38.462 8.20 0.80 44.75 2.23
3713 7886 3.515901 AGAGTAACACCAGAAGATGACCC 59.484 47.826 0.00 0.00 0.00 4.46
3715 7888 4.684724 AGTAACACCAGAAGATGACCCTA 58.315 43.478 0.00 0.00 0.00 3.53
3717 7890 4.494091 AACACCAGAAGATGACCCTATG 57.506 45.455 0.00 0.00 0.00 2.23
3770 7943 3.137176 CCATATCAGTTCCACAGTCCCAT 59.863 47.826 0.00 0.00 0.00 4.00
3772 7945 0.692476 TCAGTTCCACAGTCCCATGG 59.308 55.000 4.14 4.14 37.32 3.66
3778 7951 2.927856 ACAGTCCCATGGTGCCGA 60.928 61.111 11.73 0.00 0.00 5.54
3782 7955 1.224592 GTCCCATGGTGCCGATTCT 59.775 57.895 11.73 0.00 0.00 2.40
3798 7971 3.118992 CGATTCTCAGTCCACATCCAAGA 60.119 47.826 0.00 0.00 0.00 3.02
3799 7972 4.621510 CGATTCTCAGTCCACATCCAAGAA 60.622 45.833 0.00 0.00 0.00 2.52
3832 8008 3.201708 AGGGTGAGGGAAGATGAAAGATG 59.798 47.826 0.00 0.00 0.00 2.90
3836 8012 5.586643 GGTGAGGGAAGATGAAAGATGTAAC 59.413 44.000 0.00 0.00 0.00 2.50
3849 8025 3.711086 AGATGTAACGCATGAGTAGCTG 58.289 45.455 1.37 0.00 38.06 4.24
3853 8029 2.455674 AACGCATGAGTAGCTGTGAA 57.544 45.000 1.37 0.00 0.00 3.18
3854 8030 2.680312 ACGCATGAGTAGCTGTGAAT 57.320 45.000 0.00 0.00 0.00 2.57
3855 8031 3.801114 ACGCATGAGTAGCTGTGAATA 57.199 42.857 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.613630 AGAAGCCCCGACACCATCT 60.614 57.895 0.00 0.00 0.00 2.90
85 86 3.052036 GTTTACACTTCTTCGTACGGCA 58.948 45.455 16.52 1.37 0.00 5.69
102 103 2.403378 GCATCCGCCGCCTTGTTTA 61.403 57.895 0.00 0.00 0.00 2.01
170 171 2.234661 CTCTGTGTAGGAACTCATGCCA 59.765 50.000 0.00 0.00 41.75 4.92
300 357 2.559668 CTGCAATGGTGTCTTCCATGTT 59.440 45.455 0.00 0.00 46.14 2.71
312 369 1.033746 CCTTCGATGGCTGCAATGGT 61.034 55.000 4.15 0.00 0.00 3.55
470 531 5.010213 CCTCCTAGCTAGTTACCTTTGCTAG 59.990 48.000 19.31 11.87 42.69 3.42
474 535 6.980416 ATACCTCCTAGCTAGTTACCTTTG 57.020 41.667 19.31 1.76 0.00 2.77
483 544 8.575589 CATCTTGCATATATACCTCCTAGCTAG 58.424 40.741 14.20 14.20 0.00 3.42
484 545 7.014711 GCATCTTGCATATATACCTCCTAGCTA 59.985 40.741 0.00 0.00 44.26 3.32
485 546 6.183360 GCATCTTGCATATATACCTCCTAGCT 60.183 42.308 0.00 0.00 44.26 3.32
486 547 5.988561 GCATCTTGCATATATACCTCCTAGC 59.011 44.000 0.00 0.00 44.26 3.42
522 599 1.108132 CCGCTAGAGACCCAGGTACC 61.108 65.000 2.73 2.73 0.00 3.34
731 808 5.721876 CACAAGGAAAGTTTGTGTACGTA 57.278 39.130 9.34 0.00 46.37 3.57
732 809 4.609691 CACAAGGAAAGTTTGTGTACGT 57.390 40.909 9.34 0.00 46.37 3.57
782 859 0.623324 ACCCAGGCCAGGTATAAGCA 60.623 55.000 15.53 0.00 35.24 3.91
824 901 3.129287 GCTATGCACACAGCCATAACTTT 59.871 43.478 5.66 0.00 44.83 2.66
826 903 2.292267 GCTATGCACACAGCCATAACT 58.708 47.619 5.66 0.00 44.83 2.24
859 936 8.899771 AGTTAGAATTTGTTTTCCGAAAAGAGA 58.100 29.630 6.54 1.73 0.00 3.10
893 2892 1.607612 GCCCCACTTGCCTAGCTTA 59.392 57.895 0.00 0.00 0.00 3.09
933 2949 3.449377 TGTTCTCCGGTTGCTGATGTATA 59.551 43.478 0.00 0.00 0.00 1.47
983 2999 5.112686 GCTCCATGACTCTACTTTTGGTAG 58.887 45.833 0.00 0.00 46.79 3.18
993 3009 3.643320 CCATGTTAGGCTCCATGACTCTA 59.357 47.826 21.99 0.00 40.70 2.43
1296 3493 2.691409 ACACACCATAACGATCTGGG 57.309 50.000 2.20 0.00 36.82 4.45
1622 3855 6.207213 ACGTATGTAATGTTCTCTTCCGATC 58.793 40.000 0.00 0.00 0.00 3.69
1644 3928 5.574830 TGGACTGAAAACAAACATTCAAACG 59.425 36.000 0.00 0.00 35.31 3.60
1693 3980 1.450134 CGTTCCATAGCCTGCTGCA 60.450 57.895 0.88 0.88 44.83 4.41
1703 3990 2.435234 GCGCACCACCGTTCCATA 60.435 61.111 0.30 0.00 0.00 2.74
1763 4057 0.107361 TGGCTATCTCGTCGGAGTCA 60.107 55.000 0.00 0.00 41.26 3.41
1795 4089 1.228094 TTGCCCAACATCACTCGCA 60.228 52.632 0.00 0.00 0.00 5.10
1920 4218 4.651778 TCATTCATTCTGGACGGTCTTTT 58.348 39.130 8.23 0.00 0.00 2.27
2102 4541 0.393402 TTCTACATGCCTGCAGCTGG 60.393 55.000 17.12 14.00 44.23 4.85
2189 4640 4.927782 ACGCTGGCGCTGGTTTCA 62.928 61.111 15.04 0.00 44.19 2.69
2370 4975 3.130633 TCATTAGATGTATGCACGGTGC 58.869 45.455 25.55 25.55 45.29 5.01
2374 4979 3.185188 GGCACTCATTAGATGTATGCACG 59.815 47.826 15.58 0.00 41.05 5.34
2390 6034 4.314440 TCACCACGGCAGGCACTC 62.314 66.667 0.00 0.00 34.60 3.51
2706 6355 2.025981 TGGCTATCACAATCTGCACCTT 60.026 45.455 0.00 0.00 0.00 3.50
2823 6472 1.301716 GCTGCAGGTTCCTGACGAA 60.302 57.895 21.32 3.97 36.24 3.85
2851 6503 1.494960 GGGAGCTCCAGAAGATCACT 58.505 55.000 33.29 0.00 40.81 3.41
2879 6531 2.224079 AGCACATGACGACACATCAAAC 59.776 45.455 0.00 0.00 0.00 2.93
2927 6579 4.807834 CAGCGAACACTCACTGATTATCAT 59.192 41.667 0.00 0.00 34.22 2.45
2929 6581 3.553511 CCAGCGAACACTCACTGATTATC 59.446 47.826 0.00 0.00 34.22 1.75
2938 6590 2.583441 CCCTCCCAGCGAACACTCA 61.583 63.158 0.00 0.00 0.00 3.41
2939 6591 1.617947 ATCCCTCCCAGCGAACACTC 61.618 60.000 0.00 0.00 0.00 3.51
2941 6593 1.450312 CATCCCTCCCAGCGAACAC 60.450 63.158 0.00 0.00 0.00 3.32
2981 6633 5.447279 CCATCCTTACGACAACTACAATTGC 60.447 44.000 5.05 0.00 32.47 3.56
2985 6637 3.007074 TGCCATCCTTACGACAACTACAA 59.993 43.478 0.00 0.00 0.00 2.41
2987 6639 3.241067 TGCCATCCTTACGACAACTAC 57.759 47.619 0.00 0.00 0.00 2.73
2996 6648 2.378038 TGCCATCTTTGCCATCCTTAC 58.622 47.619 0.00 0.00 0.00 2.34
2998 6650 1.941377 TTGCCATCTTTGCCATCCTT 58.059 45.000 0.00 0.00 0.00 3.36
3003 6655 2.428171 GCTAGAATTGCCATCTTTGCCA 59.572 45.455 0.00 0.00 0.00 4.92
3004 6656 2.692041 AGCTAGAATTGCCATCTTTGCC 59.308 45.455 0.00 0.00 0.00 4.52
3005 6657 4.110482 CAAGCTAGAATTGCCATCTTTGC 58.890 43.478 0.00 0.00 0.00 3.68
3024 6676 3.180980 CAGAAAATTGTCGTGCTTGCAAG 59.819 43.478 22.44 22.44 0.00 4.01
3065 6717 0.036388 TCAGAACATGGAACCTCCGC 60.036 55.000 0.00 0.00 40.17 5.54
3079 6731 0.961019 GGCATTTGTGCTGGTCAGAA 59.039 50.000 1.65 0.00 34.73 3.02
3088 6740 2.617774 ACAATTTTGGTGGCATTTGTGC 59.382 40.909 0.00 0.00 0.00 4.57
3100 6753 2.547211 TGGCATTTGCGAACAATTTTGG 59.453 40.909 0.00 0.00 43.26 3.28
3118 6771 0.383231 CATTCGCTGGGAAAGATGGC 59.617 55.000 11.31 0.00 38.36 4.40
3119 6772 1.755179 ACATTCGCTGGGAAAGATGG 58.245 50.000 15.19 4.83 38.36 3.51
3140 6793 1.505151 TTGGACCCCAATAGCCAGCA 61.505 55.000 0.00 0.00 38.75 4.41
3169 6822 8.754991 ACTATTATATTATGAGACGGAGGGAG 57.245 38.462 0.00 0.00 0.00 4.30
3188 6841 6.415206 AGTGGCCGAGCTTATTAACTATTA 57.585 37.500 0.00 0.00 0.00 0.98
3189 6842 5.291905 AGTGGCCGAGCTTATTAACTATT 57.708 39.130 0.00 0.00 0.00 1.73
3190 6843 4.957684 AGTGGCCGAGCTTATTAACTAT 57.042 40.909 0.00 0.00 0.00 2.12
3222 6932 6.417191 AGCAACATAACCATACGTTACAAG 57.583 37.500 0.00 0.00 39.75 3.16
3244 6954 9.862371 AGCTCGGAAGAACAACAATATATATAG 57.138 33.333 0.00 0.00 41.32 1.31
3331 7045 0.678395 TGTACGGTCCGGTGCTTAAA 59.322 50.000 17.28 0.00 0.00 1.52
3334 7048 1.301165 GTTGTACGGTCCGGTGCTT 60.301 57.895 17.28 0.00 0.00 3.91
3336 7050 1.594836 TTGTTGTACGGTCCGGTGC 60.595 57.895 17.28 5.65 0.00 5.01
3337 7051 0.249573 AGTTGTTGTACGGTCCGGTG 60.250 55.000 17.28 0.00 0.00 4.94
3338 7052 0.249573 CAGTTGTTGTACGGTCCGGT 60.250 55.000 17.28 3.88 0.00 5.28
3339 7053 0.249573 ACAGTTGTTGTACGGTCCGG 60.250 55.000 17.28 0.00 38.56 5.14
3340 7054 1.574134 AACAGTTGTTGTACGGTCCG 58.426 50.000 10.48 10.48 39.73 4.79
3347 7062 6.350103 TCCACTCATTGTAACAGTTGTTGTA 58.650 36.000 7.73 0.00 39.73 2.41
3349 7064 5.749596 TCCACTCATTGTAACAGTTGTTG 57.250 39.130 7.73 0.00 38.90 3.33
3375 7090 2.147150 GTCTGCAGGAGTGGTTCTTTC 58.853 52.381 15.13 0.00 0.00 2.62
3401 7573 6.294473 AGTTCAAGATCAGAGACAAACATGT 58.706 36.000 0.00 0.00 0.00 3.21
3492 7665 6.709397 TGCCATAAAGTTTCAAATTGCATTCA 59.291 30.769 0.00 0.00 0.00 2.57
3493 7666 7.131498 TGCCATAAAGTTTCAAATTGCATTC 57.869 32.000 0.00 0.00 0.00 2.67
3512 7685 4.276678 GCATACATCACAAGTACATGCCAT 59.723 41.667 0.00 0.00 0.00 4.40
3515 7688 4.880886 TGCATACATCACAAGTACATGC 57.119 40.909 0.00 0.25 31.45 4.06
3519 7692 5.818136 AACCATGCATACATCACAAGTAC 57.182 39.130 0.00 0.00 32.87 2.73
3552 7725 9.996554 CATACATGTAGTACCATTCAAGGATAA 57.003 33.333 11.91 0.00 35.05 1.75
3584 7757 5.258051 TGGTTGAGGTTTTTGTAGTGAGTT 58.742 37.500 0.00 0.00 0.00 3.01
3585 7758 4.850680 TGGTTGAGGTTTTTGTAGTGAGT 58.149 39.130 0.00 0.00 0.00 3.41
3586 7759 7.687941 ATATGGTTGAGGTTTTTGTAGTGAG 57.312 36.000 0.00 0.00 0.00 3.51
3630 7803 6.477688 AGTTATCACGTATGTTTGGGTATTCG 59.522 38.462 0.00 0.00 0.00 3.34
3692 7865 3.515901 AGGGTCATCTTCTGGTGTTACTC 59.484 47.826 0.00 0.00 0.00 2.59
3713 7886 6.608539 ATTGAGGATCTCCACATCTCATAG 57.391 41.667 0.00 0.00 36.51 2.23
3715 7888 7.006865 CTTATTGAGGATCTCCACATCTCAT 57.993 40.000 0.00 0.00 36.51 2.90
3743 7916 5.241403 ACTGTGGAACTGATATGGTTTCA 57.759 39.130 0.00 0.00 39.30 2.69
3745 7918 4.567747 GGGACTGTGGAACTGATATGGTTT 60.568 45.833 0.00 0.00 39.30 3.27
3762 7935 1.077501 AATCGGCACCATGGGACTG 60.078 57.895 18.09 12.60 0.00 3.51
3778 7951 4.916041 TTCTTGGATGTGGACTGAGAAT 57.084 40.909 0.00 0.00 0.00 2.40
3782 7955 3.743521 CACTTTCTTGGATGTGGACTGA 58.256 45.455 0.00 0.00 0.00 3.41
3798 7971 1.978580 CCTCACCCTACACTCCACTTT 59.021 52.381 0.00 0.00 0.00 2.66
3799 7972 1.645710 CCTCACCCTACACTCCACTT 58.354 55.000 0.00 0.00 0.00 3.16
3832 8008 2.876091 TCACAGCTACTCATGCGTTAC 58.124 47.619 0.00 0.00 35.28 2.50


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

AutoCloner maintained by Alex Coulton.