Multiple sequence alignment - TraesCS2D01G126800

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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 TraesCS2D01G126800 chr2D 100.000 3641 0 0 1 3641 73591422 73587782 0.000000e+00 6724.0
1 TraesCS2D01G126800 chr2A 95.456 2861 74 25 781 3632 73177711 73174898 0.000000e+00 4512.0
2 TraesCS2D01G126800 chr2A 90.096 313 27 3 1 312 73179093 73178784 1.570000e-108 403.0
3 TraesCS2D01G126800 chr2B 94.300 2035 81 10 878 2897 111665276 111663262 0.000000e+00 3083.0
4 TraesCS2D01G126800 chr2B 89.662 474 32 8 3161 3632 111663257 111662799 4.050000e-164 588.0
5 TraesCS2D01G126800 chr2B 81.618 272 47 3 196 466 568472312 568472581 4.730000e-54 222.0
6 TraesCS2D01G126800 chr2B 100.000 30 0 0 3112 3141 111663272 111663243 5.080000e-04 56.5
7 TraesCS2D01G126800 chr7D 81.766 351 56 8 199 544 199355989 199355642 1.650000e-73 287.0
8 TraesCS2D01G126800 chr7A 81.303 353 61 5 199 548 209155890 209155540 7.700000e-72 281.0
9 TraesCS2D01G126800 chr7A 77.541 423 88 7 195 612 439524592 439525012 7.810000e-62 248.0
10 TraesCS2D01G126800 chr7A 78.274 336 61 10 280 605 432693530 432693197 4.770000e-49 206.0
11 TraesCS2D01G126800 chr7B 80.563 355 61 7 199 548 163488713 163488362 2.160000e-67 267.0
12 TraesCS2D01G126800 chr5D 77.830 424 77 15 195 605 460939956 460939537 2.810000e-61 246.0
13 TraesCS2D01G126800 chr1D 78.348 351 66 8 195 541 377201104 377200760 6.120000e-53 219.0
14 TraesCS2D01G126800 chr6B 76.359 423 78 20 195 609 688745828 688745420 1.330000e-49 207.0


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 TraesCS2D01G126800 chr2D 73587782 73591422 3640 True 6724.0 6724 100.000 1 3641 1 chr2D.!!$R1 3640
1 TraesCS2D01G126800 chr2A 73174898 73179093 4195 True 2457.5 4512 92.776 1 3632 2 chr2A.!!$R1 3631
2 TraesCS2D01G126800 chr2B 111662799 111665276 2477 True 1242.5 3083 94.654 878 3632 3 chr2B.!!$R1 2754

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
197 198 0.390472 TGCATGTGTCGCGGTTCATA 60.390 50.0 6.13 2.42 0.00 2.15 F
1050 1677 0.415429 TCCTCTCCCTCCTCAAAGCT 59.585 55.0 0.00 0.00 0.00 3.74 F
1170 1806 0.032813 CCAATGGCTTCATCCAGGGT 60.033 55.0 0.00 0.00 39.89 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1068 1704 1.077068 AGAGGAGACGGAGGCAGAG 60.077 63.158 0.00 0.0 0.00 3.35 R
2157 2793 2.289320 CCATCTCCCTACTGCAGCATAC 60.289 54.545 15.27 0.0 0.00 2.39 R
2866 3502 2.538861 CACATGCGTGCAAATGAACAAA 59.461 40.909 5.64 0.0 36.06 2.83 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
63 64 9.828852 TTTGTTTATTTAGCAATTACTACACCG 57.171 29.630 0.00 0.00 0.00 4.94
65 66 9.650539 TGTTTATTTAGCAATTACTACACCGTA 57.349 29.630 0.00 0.00 0.00 4.02
66 67 9.906111 GTTTATTTAGCAATTACTACACCGTAC 57.094 33.333 0.00 0.00 0.00 3.67
67 68 9.874205 TTTATTTAGCAATTACTACACCGTACT 57.126 29.630 0.00 0.00 0.00 2.73
68 69 7.766219 ATTTAGCAATTACTACACCGTACTG 57.234 36.000 0.00 0.00 0.00 2.74
70 71 2.606272 GCAATTACTACACCGTACTGGC 59.394 50.000 4.00 0.00 43.94 4.85
71 72 3.677976 GCAATTACTACACCGTACTGGCT 60.678 47.826 4.00 0.00 43.94 4.75
72 73 3.795623 ATTACTACACCGTACTGGCTG 57.204 47.619 4.00 0.00 43.94 4.85
76 77 2.103601 ACTACACCGTACTGGCTGTTTT 59.896 45.455 1.31 0.00 43.94 2.43
77 78 2.047002 ACACCGTACTGGCTGTTTTT 57.953 45.000 1.31 0.00 43.94 1.94
129 130 0.765510 GGGTGAGTTCTGGTTCCTGT 59.234 55.000 0.00 0.00 0.00 4.00
133 134 2.872858 GTGAGTTCTGGTTCCTGTTGTC 59.127 50.000 0.00 0.00 0.00 3.18
141 142 1.156736 GTTCCTGTTGTCGATGGTGG 58.843 55.000 0.00 0.00 0.00 4.61
182 183 6.317088 CAACATTGTCGAAGAAATAGTGCAT 58.683 36.000 0.00 0.00 39.69 3.96
188 189 3.612423 TCGAAGAAATAGTGCATGTGTCG 59.388 43.478 0.00 0.00 0.00 4.35
197 198 0.390472 TGCATGTGTCGCGGTTCATA 60.390 50.000 6.13 2.42 0.00 2.15
212 213 5.295787 GCGGTTCATATTGGTCAATTCACTA 59.704 40.000 1.28 0.00 32.50 2.74
216 217 9.736023 GGTTCATATTGGTCAATTCACTAATTC 57.264 33.333 0.00 0.00 32.87 2.17
270 271 3.803840 TATAGTCCGGACGAGCTGCCA 62.804 57.143 28.26 8.10 36.20 4.92
275 276 3.200593 GGACGAGCTGCCATGCTG 61.201 66.667 0.00 0.00 44.17 4.41
278 279 1.150567 GACGAGCTGCCATGCTGTAG 61.151 60.000 0.00 0.00 44.17 2.74
307 308 2.736670 AAGGGAGGCCATGTACATTC 57.263 50.000 5.37 0.88 0.00 2.67
312 313 3.181445 GGGAGGCCATGTACATTCATACA 60.181 47.826 5.37 0.00 39.35 2.29
314 315 5.072741 GGAGGCCATGTACATTCATACATT 58.927 41.667 5.37 0.00 41.98 2.71
315 316 5.048504 GGAGGCCATGTACATTCATACATTG 60.049 44.000 5.37 0.00 41.98 2.82
317 318 5.893255 AGGCCATGTACATTCATACATTGTT 59.107 36.000 5.37 0.00 41.98 2.83
318 319 5.978919 GGCCATGTACATTCATACATTGTTG 59.021 40.000 5.37 0.00 41.98 3.33
337 501 1.101331 GGATGAAGCTCAAGGGCAAG 58.899 55.000 0.00 0.00 34.17 4.01
338 502 0.455005 GATGAAGCTCAAGGGCAAGC 59.545 55.000 0.00 0.00 38.84 4.01
343 507 1.671054 GCTCAAGGGCAAGCGTGTA 60.671 57.895 0.59 0.00 0.00 2.90
357 521 2.094494 AGCGTGTATGAGAGGACTTGTG 60.094 50.000 0.00 0.00 0.00 3.33
358 522 2.352814 GCGTGTATGAGAGGACTTGTGT 60.353 50.000 0.00 0.00 0.00 3.72
361 525 3.190744 GTGTATGAGAGGACTTGTGTCGA 59.809 47.826 0.00 0.00 43.79 4.20
362 526 4.017126 TGTATGAGAGGACTTGTGTCGAT 58.983 43.478 0.00 0.00 43.79 3.59
371 535 5.103000 AGGACTTGTGTCGATTCTAATTCG 58.897 41.667 0.00 0.00 43.79 3.34
379 543 6.910972 TGTGTCGATTCTAATTCGAGTATCAC 59.089 38.462 0.00 2.56 36.53 3.06
403 567 7.009815 CACTGAATTTGGAATTGATGAATTCGG 59.990 37.037 10.90 12.08 45.92 4.30
437 601 9.376075 ACTAAACATTCAGTTATCTCAGATGTG 57.624 33.333 0.00 0.00 40.26 3.21
446 610 9.899226 TCAGTTATCTCAGATGTGATATTTACG 57.101 33.333 0.00 0.00 32.60 3.18
471 636 7.308348 CGTTTGAACTATTGTTGTACTGGGATT 60.308 37.037 0.00 0.00 36.39 3.01
476 641 9.614792 GAACTATTGTTGTACTGGGATTTCTAT 57.385 33.333 0.00 0.00 36.39 1.98
530 695 9.781834 TTTCTATAATTATTTTGAGTGTTGCGG 57.218 29.630 2.68 0.00 0.00 5.69
560 726 1.136110 ACAAAGGCAAACGTTCAAGGG 59.864 47.619 0.00 0.00 0.00 3.95
575 741 5.106157 CGTTCAAGGGATATAATTGGATGGC 60.106 44.000 0.00 0.00 0.00 4.40
577 743 3.652057 AGGGATATAATTGGATGGCCG 57.348 47.619 0.00 0.00 36.79 6.13
578 744 3.189606 AGGGATATAATTGGATGGCCGA 58.810 45.455 0.00 0.00 36.79 5.54
583 749 2.910688 TAATTGGATGGCCGACTCTC 57.089 50.000 0.00 0.00 36.79 3.20
586 752 2.105128 GGATGGCCGACTCTCGTG 59.895 66.667 0.00 0.00 38.40 4.35
588 754 1.226717 GATGGCCGACTCTCGTGTC 60.227 63.158 0.00 0.00 38.40 3.67
595 761 2.281517 CCGACTCTCGTGTCTGTATCT 58.718 52.381 0.00 0.00 38.40 1.98
597 763 2.537931 CGACTCTCGTGTCTGTATCTGC 60.538 54.545 0.00 0.00 34.72 4.26
605 771 0.528684 GTCTGTATCTGCGGACCAGC 60.529 60.000 15.95 9.60 41.50 4.85
608 774 2.364973 TATCTGCGGACCAGCCCA 60.365 61.111 0.00 0.00 41.50 5.36
617 783 4.681978 ACCAGCCCACGAGCGAAC 62.682 66.667 0.00 0.00 38.01 3.95
621 787 0.739462 CAGCCCACGAGCGAACAATA 60.739 55.000 0.00 0.00 38.01 1.90
625 791 1.593006 CCCACGAGCGAACAATATGTC 59.407 52.381 0.00 0.00 0.00 3.06
626 792 1.593006 CCACGAGCGAACAATATGTCC 59.407 52.381 0.00 0.00 0.00 4.02
627 793 2.540515 CACGAGCGAACAATATGTCCT 58.459 47.619 0.00 0.00 0.00 3.85
638 804 6.591834 CGAACAATATGTCCTTTCTGAGAGTT 59.408 38.462 0.00 0.00 0.00 3.01
661 827 6.928348 TGGTGTTGTTATTAGAGAGAGGAA 57.072 37.500 0.00 0.00 0.00 3.36
676 842 2.044353 AGAGGAAGAAGGGAGAGAAGCT 59.956 50.000 0.00 0.00 0.00 3.74
679 845 2.698274 GGAAGAAGGGAGAGAAGCTAGG 59.302 54.545 0.00 0.00 0.00 3.02
699 865 1.408266 GCCACCACTATTTGACCGGAT 60.408 52.381 9.46 0.00 0.00 4.18
706 872 4.142469 CCACTATTTGACCGGATTTGGTTC 60.142 45.833 9.46 0.00 44.01 3.62
709 875 6.373216 CACTATTTGACCGGATTTGGTTCTTA 59.627 38.462 9.46 0.00 44.01 2.10
719 885 5.163794 CGGATTTGGTTCTTAAACGTATGCT 60.164 40.000 0.00 0.00 36.16 3.79
724 890 5.408356 TGGTTCTTAAACGTATGCTCTCTC 58.592 41.667 0.00 0.00 36.16 3.20
725 891 5.185249 TGGTTCTTAAACGTATGCTCTCTCT 59.815 40.000 0.00 0.00 36.16 3.10
727 893 4.673441 TCTTAAACGTATGCTCTCTCTGC 58.327 43.478 0.00 0.00 0.00 4.26
737 903 2.881513 TGCTCTCTCTGCTCTTATACCG 59.118 50.000 0.00 0.00 0.00 4.02
742 908 6.561737 TCTCTCTGCTCTTATACCGTATTG 57.438 41.667 0.00 0.00 0.00 1.90
743 909 5.048643 TCTCTCTGCTCTTATACCGTATTGC 60.049 44.000 0.00 0.00 0.00 3.56
766 944 3.498018 GGTGCCACCATTTGTCAAAAATC 59.502 43.478 9.55 0.00 38.42 2.17
822 1432 3.847671 TGGGTGTTCACAAGACATGTA 57.152 42.857 0.00 0.00 41.46 2.29
824 1434 4.323417 TGGGTGTTCACAAGACATGTATC 58.677 43.478 0.00 0.00 41.46 2.24
831 1441 6.319911 TGTTCACAAGACATGTATCCACAAAA 59.680 34.615 0.00 0.00 41.46 2.44
870 1480 9.725019 AATATTGAATCGATAACTGAGGCAATA 57.275 29.630 0.00 0.00 33.62 1.90
871 1481 9.896645 ATATTGAATCGATAACTGAGGCAATAT 57.103 29.630 0.00 0.00 34.57 1.28
873 1483 9.896645 ATTGAATCGATAACTGAGGCAATATAT 57.103 29.630 0.00 0.00 0.00 0.86
874 1484 9.725019 TTGAATCGATAACTGAGGCAATATATT 57.275 29.630 0.00 0.00 0.00 1.28
914 1525 4.143556 CGGTTTCATGTTCTTGCATTTTCG 60.144 41.667 0.00 0.00 0.00 3.46
917 1528 6.146021 GGTTTCATGTTCTTGCATTTTCGAAT 59.854 34.615 0.00 0.00 0.00 3.34
984 1611 2.884639 ACCATGAACTACACAAGCCAAC 59.115 45.455 0.00 0.00 0.00 3.77
1050 1677 0.415429 TCCTCTCCCTCCTCAAAGCT 59.585 55.000 0.00 0.00 0.00 3.74
1055 1691 3.130160 CCTCCTCAAAGCTGCCGC 61.130 66.667 0.00 0.00 0.00 6.53
1056 1692 3.130160 CTCCTCAAAGCTGCCGCC 61.130 66.667 0.00 0.00 36.60 6.13
1128 1764 0.738975 CCGTCTACATCAAGCTCGGA 59.261 55.000 0.00 0.00 36.51 4.55
1134 1770 3.706594 TCTACATCAAGCTCGGATTCCTT 59.293 43.478 0.30 0.00 0.00 3.36
1170 1806 0.032813 CCAATGGCTTCATCCAGGGT 60.033 55.000 0.00 0.00 39.89 4.34
1516 2152 1.846439 GGATGATGGAGGAAGGGTTCA 59.154 52.381 0.00 0.00 0.00 3.18
1629 2265 2.610859 AACAGGCTCCGGTGGGAT 60.611 61.111 0.00 0.00 42.83 3.85
1815 2451 0.462789 GCCAAATGGAGCTTGATGGG 59.537 55.000 2.98 0.00 37.39 4.00
1917 2553 5.068723 GGAGCATTTCAACATGATCTCCAAT 59.931 40.000 0.00 0.00 39.19 3.16
2157 2793 2.014857 CATGTGCTCCTGTCCAATCTG 58.985 52.381 0.00 0.00 0.00 2.90
2514 3150 8.673626 TCAGAATTGTCAAAAATATTCGCTTC 57.326 30.769 0.00 0.00 33.38 3.86
2683 3319 2.874052 GCACAGTGGCAGTGGTATACAA 60.874 50.000 25.12 0.00 37.46 2.41
2713 3349 4.142609 TCTCAGTGTGAGTTTCTGCTTT 57.857 40.909 3.92 0.00 44.58 3.51
2859 3495 6.954944 TGAACTCCAAACGAACTAATGAAAG 58.045 36.000 0.00 0.00 0.00 2.62
2881 3517 3.658852 GCGTTCATTTGTTCATTTGCACG 60.659 43.478 0.00 0.00 33.05 5.34
3041 3677 4.418392 ACTTAGGTTATACAACTCACGCG 58.582 43.478 3.53 3.53 34.88 6.01
3067 3703 6.525629 AGCATTATGTAAAGTAGCAGTAGGG 58.474 40.000 0.00 0.00 0.00 3.53
3072 3708 1.880941 AAAGTAGCAGTAGGGGAGGG 58.119 55.000 0.00 0.00 0.00 4.30
3228 3864 7.280428 GGTTAAGAAAGGCTAGAAATACCAGAC 59.720 40.741 0.00 0.00 0.00 3.51
3231 3867 7.922699 AGAAAGGCTAGAAATACCAGACTAT 57.077 36.000 0.00 0.00 0.00 2.12
3326 3963 8.836268 AACTTTGCACATCATAATTGTCAATT 57.164 26.923 14.98 14.98 34.90 2.32
3336 3973 9.740239 CATCATAATTGTCAATTTAGTCCTTGG 57.260 33.333 15.77 0.00 32.38 3.61
3429 4066 6.432581 GGTTAATTTTCCTCCTGGGACTATT 58.567 40.000 0.00 0.00 45.03 1.73
3626 4264 8.329502 AGTTCCTATTCATAAAAGGTTACTGCT 58.670 33.333 0.00 0.00 30.59 4.24
3632 4270 8.723942 ATTCATAAAAGGTTACTGCTGTAGAG 57.276 34.615 0.00 0.00 0.00 2.43
3633 4271 7.476540 TCATAAAAGGTTACTGCTGTAGAGA 57.523 36.000 0.00 0.00 0.00 3.10
3634 4272 8.079211 TCATAAAAGGTTACTGCTGTAGAGAT 57.921 34.615 0.00 0.00 0.00 2.75
3635 4273 7.981789 TCATAAAAGGTTACTGCTGTAGAGATG 59.018 37.037 0.00 3.58 0.00 2.90
3636 4274 6.360370 AAAAGGTTACTGCTGTAGAGATGA 57.640 37.500 0.00 0.00 0.00 2.92
3637 4275 6.552445 AAAGGTTACTGCTGTAGAGATGAT 57.448 37.500 0.00 0.00 0.00 2.45
3638 4276 7.661536 AAAGGTTACTGCTGTAGAGATGATA 57.338 36.000 0.00 0.00 0.00 2.15
3639 4277 6.892658 AGGTTACTGCTGTAGAGATGATAG 57.107 41.667 0.00 0.00 0.00 2.08
3640 4278 5.242838 AGGTTACTGCTGTAGAGATGATAGC 59.757 44.000 0.00 0.00 35.06 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 6.925165 CACCCATGTGCATTATTATTCTTTCC 59.075 38.462 0.00 0.00 35.31 3.13
120 121 0.762418 ACCATCGACAACAGGAACCA 59.238 50.000 0.00 0.00 0.00 3.67
129 130 2.741985 CGCTGCCACCATCGACAA 60.742 61.111 0.00 0.00 32.67 3.18
141 142 4.487412 GCCATGAACCAGCGCTGC 62.487 66.667 31.96 18.66 0.00 5.25
164 165 4.314961 ACACATGCACTATTTCTTCGACA 58.685 39.130 0.00 0.00 0.00 4.35
176 177 2.280797 AACCGCGACACATGCACT 60.281 55.556 8.23 0.00 0.00 4.40
182 183 1.338294 ACCAATATGAACCGCGACACA 60.338 47.619 8.23 4.41 0.00 3.72
188 189 4.096382 AGTGAATTGACCAATATGAACCGC 59.904 41.667 0.00 0.00 0.00 5.68
240 241 6.190954 TCGTCCGGACTATATAACATGATG 57.809 41.667 30.92 11.14 0.00 3.07
241 242 5.163642 GCTCGTCCGGACTATATAACATGAT 60.164 44.000 30.92 0.00 0.00 2.45
275 276 0.745468 CTCCCTTAGTCCGGTGCTAC 59.255 60.000 0.00 0.00 0.00 3.58
278 279 2.901042 CCTCCCTTAGTCCGGTGC 59.099 66.667 0.00 0.00 0.00 5.01
282 283 1.338136 ACATGGCCTCCCTTAGTCCG 61.338 60.000 3.32 0.00 0.00 4.79
287 288 3.119319 TGAATGTACATGGCCTCCCTTA 58.881 45.455 9.63 0.00 0.00 2.69
288 289 1.922447 TGAATGTACATGGCCTCCCTT 59.078 47.619 9.63 0.00 0.00 3.95
300 301 7.645340 GCTTCATCCAACAATGTATGAATGTAC 59.355 37.037 9.63 0.00 37.62 2.90
307 308 5.823209 TGAGCTTCATCCAACAATGTATG 57.177 39.130 0.00 0.00 0.00 2.39
312 313 3.094572 CCCTTGAGCTTCATCCAACAAT 58.905 45.455 0.00 0.00 0.00 2.71
314 315 1.887956 GCCCTTGAGCTTCATCCAACA 60.888 52.381 0.00 0.00 0.00 3.33
315 316 0.813821 GCCCTTGAGCTTCATCCAAC 59.186 55.000 0.00 0.00 0.00 3.77
317 318 0.405198 TTGCCCTTGAGCTTCATCCA 59.595 50.000 0.00 0.00 0.00 3.41
318 319 1.101331 CTTGCCCTTGAGCTTCATCC 58.899 55.000 0.00 0.00 0.00 3.51
337 501 2.263077 CACAAGTCCTCTCATACACGC 58.737 52.381 0.00 0.00 0.00 5.34
338 502 3.502920 GACACAAGTCCTCTCATACACG 58.497 50.000 0.00 0.00 38.89 4.49
343 507 3.766591 AGAATCGACACAAGTCCTCTCAT 59.233 43.478 0.00 0.00 41.87 2.90
357 521 7.353497 TCAGTGATACTCGAATTAGAATCGAC 58.647 38.462 0.00 0.00 43.76 4.20
358 522 7.492352 TCAGTGATACTCGAATTAGAATCGA 57.508 36.000 0.00 0.00 46.18 3.59
362 526 9.098355 CCAAATTCAGTGATACTCGAATTAGAA 57.902 33.333 14.06 0.00 36.20 2.10
371 535 8.896744 TCATCAATTCCAAATTCAGTGATACTC 58.103 33.333 0.00 0.00 0.00 2.59
379 543 7.259882 TCCGAATTCATCAATTCCAAATTCAG 58.740 34.615 6.22 0.00 43.59 3.02
446 610 6.870971 TCCCAGTACAACAATAGTTCAAAC 57.129 37.500 0.00 0.00 35.28 2.93
449 613 7.458397 AGAAATCCCAGTACAACAATAGTTCA 58.542 34.615 0.00 0.00 35.28 3.18
507 672 8.612619 AGTCCGCAACACTCAAAATAATTATAG 58.387 33.333 0.00 0.00 0.00 1.31
543 709 1.995376 ATCCCTTGAACGTTTGCCTT 58.005 45.000 0.46 0.00 0.00 4.35
548 714 7.014230 CCATCCAATTATATCCCTTGAACGTTT 59.986 37.037 0.46 0.00 0.00 3.60
550 716 6.003950 CCATCCAATTATATCCCTTGAACGT 58.996 40.000 0.00 0.00 0.00 3.99
560 726 5.091261 AGAGTCGGCCATCCAATTATATC 57.909 43.478 2.24 0.00 0.00 1.63
583 749 0.525668 GGTCCGCAGATACAGACACG 60.526 60.000 0.00 0.00 0.00 4.49
586 752 0.528684 GCTGGTCCGCAGATACAGAC 60.529 60.000 8.32 0.00 33.86 3.51
588 754 1.227380 GGCTGGTCCGCAGATACAG 60.227 63.158 7.78 1.44 34.65 2.74
605 771 1.593006 GACATATTGTTCGCTCGTGGG 59.407 52.381 0.00 0.00 0.00 4.61
608 774 2.961526 AGGACATATTGTTCGCTCGT 57.038 45.000 0.00 0.00 29.06 4.18
612 778 4.870426 TCTCAGAAAGGACATATTGTTCGC 59.130 41.667 0.00 0.00 29.06 4.70
613 779 6.102663 ACTCTCAGAAAGGACATATTGTTCG 58.897 40.000 0.00 0.00 29.06 3.95
614 780 7.148340 CCAACTCTCAGAAAGGACATATTGTTC 60.148 40.741 0.00 0.00 0.00 3.18
617 783 6.093219 CACCAACTCTCAGAAAGGACATATTG 59.907 42.308 0.00 0.00 0.00 1.90
621 787 3.392616 ACACCAACTCTCAGAAAGGACAT 59.607 43.478 0.00 0.00 0.00 3.06
625 791 3.545703 ACAACACCAACTCTCAGAAAGG 58.454 45.455 0.00 0.00 0.00 3.11
626 792 6.867662 ATAACAACACCAACTCTCAGAAAG 57.132 37.500 0.00 0.00 0.00 2.62
627 793 8.208224 TCTAATAACAACACCAACTCTCAGAAA 58.792 33.333 0.00 0.00 0.00 2.52
638 804 6.724441 TCTTCCTCTCTCTAATAACAACACCA 59.276 38.462 0.00 0.00 0.00 4.17
661 827 1.691163 GGCCTAGCTTCTCTCCCTTCT 60.691 57.143 0.00 0.00 0.00 2.85
676 842 1.208535 CGGTCAAATAGTGGTGGCCTA 59.791 52.381 3.32 0.00 37.37 3.93
679 845 0.035820 TCCGGTCAAATAGTGGTGGC 60.036 55.000 0.00 0.00 0.00 5.01
699 865 6.228258 AGAGAGCATACGTTTAAGAACCAAA 58.772 36.000 0.00 0.00 31.93 3.28
706 872 4.677584 AGCAGAGAGAGCATACGTTTAAG 58.322 43.478 0.00 0.00 0.00 1.85
709 875 2.757868 AGAGCAGAGAGAGCATACGTTT 59.242 45.455 0.00 0.00 0.00 3.60
719 885 5.048643 GCAATACGGTATAAGAGCAGAGAGA 60.049 44.000 0.22 0.00 0.00 3.10
737 903 0.530288 AAATGGTGGCACCGCAATAC 59.470 50.000 30.14 6.52 42.58 1.89
742 908 2.258286 GACAAATGGTGGCACCGC 59.742 61.111 30.14 9.57 42.58 5.68
743 909 3.756802 TGACAAATGGTGGCACCG 58.243 55.556 30.14 18.71 41.83 4.94
798 1408 2.761559 TGTCTTGTGAACACCCATACG 58.238 47.619 2.46 0.00 0.00 3.06
799 1409 4.072131 ACATGTCTTGTGAACACCCATAC 58.928 43.478 0.00 0.00 37.11 2.39
800 1410 4.365514 ACATGTCTTGTGAACACCCATA 57.634 40.909 0.00 0.00 37.11 2.74
804 1414 4.323417 TGGATACATGTCTTGTGAACACC 58.677 43.478 0.00 0.00 46.17 4.16
843 1453 7.425577 TGCCTCAGTTATCGATTCAATATTG 57.574 36.000 9.29 9.29 0.00 1.90
870 1480 8.519799 AACCGAGTGGATTATGTTTGAAATAT 57.480 30.769 0.00 0.00 39.21 1.28
871 1481 7.931578 AACCGAGTGGATTATGTTTGAAATA 57.068 32.000 0.00 0.00 39.21 1.40
872 1482 6.834168 AACCGAGTGGATTATGTTTGAAAT 57.166 33.333 0.00 0.00 39.21 2.17
873 1483 6.263392 TGAAACCGAGTGGATTATGTTTGAAA 59.737 34.615 0.00 0.00 39.21 2.69
874 1484 5.765677 TGAAACCGAGTGGATTATGTTTGAA 59.234 36.000 0.00 0.00 39.21 2.69
891 1502 4.143556 CGAAAATGCAAGAACATGAAACCG 60.144 41.667 0.00 0.00 0.00 4.44
914 1525 5.588246 TGGCTTGTTTGGAAAAGGAAAATTC 59.412 36.000 0.00 0.00 0.00 2.17
917 1528 4.512484 CTGGCTTGTTTGGAAAAGGAAAA 58.488 39.130 0.00 0.00 0.00 2.29
984 1611 2.051076 ATGCGTGCGTGTTTGCTG 60.051 55.556 0.00 0.00 35.36 4.41
1025 1652 1.306568 AGGAGGGAGAGGAAGGTGC 60.307 63.158 0.00 0.00 0.00 5.01
1065 1701 4.200283 GAGACGGAGGCAGAGGCG 62.200 72.222 0.00 0.00 42.47 5.52
1066 1702 3.844090 GGAGACGGAGGCAGAGGC 61.844 72.222 0.00 0.00 40.13 4.70
1067 1703 2.043450 AGGAGACGGAGGCAGAGG 60.043 66.667 0.00 0.00 0.00 3.69
1068 1704 1.077068 AGAGGAGACGGAGGCAGAG 60.077 63.158 0.00 0.00 0.00 3.35
1069 1705 1.077357 GAGAGGAGACGGAGGCAGA 60.077 63.158 0.00 0.00 0.00 4.26
1070 1706 2.477176 CGAGAGGAGACGGAGGCAG 61.477 68.421 0.00 0.00 0.00 4.85
1071 1707 2.438614 CGAGAGGAGACGGAGGCA 60.439 66.667 0.00 0.00 0.00 4.75
1072 1708 3.894947 GCGAGAGGAGACGGAGGC 61.895 72.222 0.00 0.00 0.00 4.70
1128 1764 3.055719 CGCGTGTGGGCAAGGAAT 61.056 61.111 0.00 0.00 0.00 3.01
1629 2265 3.319198 GCCGTCCCCAGGAACTCA 61.319 66.667 0.00 0.00 34.60 3.41
1716 2352 1.416243 TCCAGGTACACGTGTTCCTT 58.584 50.000 35.85 22.14 42.18 3.36
1815 2451 2.100989 ACTTCATCCGGTACCACTCTC 58.899 52.381 13.54 0.00 0.00 3.20
1917 2553 7.293771 TCAAGGATTAACCCTATGCCATACTTA 59.706 37.037 0.00 0.00 40.05 2.24
2157 2793 2.289320 CCATCTCCCTACTGCAGCATAC 60.289 54.545 15.27 0.00 0.00 2.39
2506 3142 2.880890 GGCAATCCATACAGAAGCGAAT 59.119 45.455 0.00 0.00 0.00 3.34
2514 3150 4.487948 CAAACTTGTGGCAATCCATACAG 58.512 43.478 0.00 0.00 45.62 2.74
2713 3349 9.871238 CTACTAAAGAGTAAACAGGAATTAGCA 57.129 33.333 0.00 0.00 37.72 3.49
2859 3495 3.658852 CGTGCAAATGAACAAATGAACGC 60.659 43.478 9.52 0.00 37.94 4.84
2866 3502 2.538861 CACATGCGTGCAAATGAACAAA 59.461 40.909 5.64 0.00 36.06 2.83
2894 3530 8.738645 AAATAGTTCCTTGTCCTCATCAATAC 57.261 34.615 0.00 0.00 0.00 1.89
2932 3568 6.377146 ACCCGCAACAATAGTAAATTCAAGAT 59.623 34.615 0.00 0.00 0.00 2.40
3041 3677 7.599245 CCCTACTGCTACTTTACATAATGCTAC 59.401 40.741 0.00 0.00 0.00 3.58
3067 3703 9.172060 AGTATATATTTATCAATAGGGCCCTCC 57.828 37.037 32.80 0.00 0.00 4.30
3173 3809 4.217118 GGCAGTTTCATCAAGACATTCAGT 59.783 41.667 0.00 0.00 0.00 3.41
3174 3810 4.670992 CGGCAGTTTCATCAAGACATTCAG 60.671 45.833 0.00 0.00 0.00 3.02
3180 3816 2.160417 CCTTCGGCAGTTTCATCAAGAC 59.840 50.000 0.00 0.00 0.00 3.01
3228 3864 9.838339 AGGTATTAACACATCCAAAGAGAATAG 57.162 33.333 0.00 0.00 0.00 1.73
3231 3867 7.918076 AGAGGTATTAACACATCCAAAGAGAA 58.082 34.615 0.00 0.00 29.53 2.87
3296 3933 4.782019 TTATGATGTGCAAAGTTCCACC 57.218 40.909 0.00 0.00 0.00 4.61
3326 3963 5.815581 ACATAATGCAGTTCCAAGGACTAA 58.184 37.500 0.00 0.00 0.00 2.24
3336 3973 5.863935 GGTTTTCAAGGACATAATGCAGTTC 59.136 40.000 0.00 0.00 0.00 3.01
3429 4066 3.251484 CTTGGAAGCTCCTATATCCCCA 58.749 50.000 0.00 0.00 37.46 4.96
3601 4239 8.398665 CAGCAGTAACCTTTTATGAATAGGAAC 58.601 37.037 3.12 1.89 33.21 3.62


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

AutoCloner maintained by Alex Coulton.