Multiple sequence alignment - TraesCS2B01G414500

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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 TraesCS2B01G414500 chr2B 100.000 3486 0 0 1 3486 592531650 592528165 0.000000e+00 6438.0
1 TraesCS2B01G414500 chr2B 98.876 89 0 1 1 88 288948778 288948690 1.300000e-34 158.0
2 TraesCS2B01G414500 chr2B 95.745 94 4 0 1 94 687514287 687514194 6.030000e-33 152.0
3 TraesCS2B01G414500 chr2A 91.778 3442 162 54 152 3486 649622179 649618752 0.000000e+00 4676.0
4 TraesCS2B01G414500 chr2D 93.843 2160 72 18 875 2981 503584800 503582649 0.000000e+00 3195.0
5 TraesCS2B01G414500 chr2D 91.269 733 45 10 85 802 503585552 503584824 0.000000e+00 981.0
6 TraesCS2B01G414500 chr2D 86.517 89 6 4 3085 3173 503582623 503582541 3.700000e-15 93.5
7 TraesCS2B01G414500 chr2D 93.878 49 3 0 2995 3043 503582670 503582622 1.340000e-09 75.0
8 TraesCS2B01G414500 chr5A 80.837 454 71 12 1648 2095 662752327 662752770 3.330000e-90 342.0
9 TraesCS2B01G414500 chr4D 88.382 241 23 4 1640 1878 480815045 480814808 5.690000e-73 285.0
10 TraesCS2B01G414500 chr4D 83.832 167 24 3 1228 1391 480815494 480815328 4.660000e-34 156.0
11 TraesCS2B01G414500 chr4B 88.841 233 22 3 1648 1878 608624696 608624466 2.050000e-72 283.0
12 TraesCS2B01G414500 chr4B 91.549 142 9 2 502 643 335599576 335599438 3.550000e-45 193.0
13 TraesCS2B01G414500 chr4B 87.681 138 17 0 1961 2098 608624249 608624112 1.000000e-35 161.0
14 TraesCS2B01G414500 chrUn 100.000 89 0 0 1 89 87800182 87800270 7.740000e-37 165.0
15 TraesCS2B01G414500 chr6B 98.851 87 1 0 1 87 206463021 206462935 4.660000e-34 156.0
16 TraesCS2B01G414500 chr6B 98.851 87 1 0 1 87 707340220 707340134 4.660000e-34 156.0
17 TraesCS2B01G414500 chr1B 97.802 91 1 1 3 93 604971388 604971477 4.660000e-34 156.0
18 TraesCS2B01G414500 chr1B 100.000 81 0 0 1 81 180822543 180822623 2.170000e-32 150.0
19 TraesCS2B01G414500 chr1B 95.745 94 3 1 1 94 667848278 667848370 2.170000e-32 150.0
20 TraesCS2B01G414500 chr7B 100.000 80 0 0 1 80 721122652 721122731 7.800000e-32 148.0


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 TraesCS2B01G414500 chr2B 592528165 592531650 3485 True 6438.000 6438 100.00000 1 3486 1 chr2B.!!$R2 3485
1 TraesCS2B01G414500 chr2A 649618752 649622179 3427 True 4676.000 4676 91.77800 152 3486 1 chr2A.!!$R1 3334
2 TraesCS2B01G414500 chr2D 503582541 503585552 3011 True 1086.125 3195 91.37675 85 3173 4 chr2D.!!$R1 3088
3 TraesCS2B01G414500 chr4D 480814808 480815494 686 True 220.500 285 86.10700 1228 1878 2 chr4D.!!$R1 650
4 TraesCS2B01G414500 chr4B 608624112 608624696 584 True 222.000 283 88.26100 1648 2098 2 chr4B.!!$R2 450

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
898 926 0.105194 TTCCAGAGTCCAGTCACCCA 60.105 55.0 0.0 0.0 0.0 4.51 F
2228 2492 0.321653 ACATGGACAAGTTCGAGGGC 60.322 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2336 2611 0.321653 GGGTGCTTGTCCTGTACTGG 60.322 60.000 12.42 12.42 0.0 4.00 R
3274 3590 1.271871 ACGATGGATGGGCAGAAACAA 60.272 47.619 0.00 0.00 0.0 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
23 24 6.451064 TCGTTGCTTAGATGAACTCATAGA 57.549 37.500 0.00 0.00 36.57 1.98
24 25 7.043961 TCGTTGCTTAGATGAACTCATAGAT 57.956 36.000 0.00 0.00 36.57 1.98
25 26 6.920210 TCGTTGCTTAGATGAACTCATAGATG 59.080 38.462 0.00 0.00 36.57 2.90
26 27 6.145209 CGTTGCTTAGATGAACTCATAGATGG 59.855 42.308 0.00 0.00 36.57 3.51
27 28 6.983906 TGCTTAGATGAACTCATAGATGGA 57.016 37.500 0.00 0.00 36.57 3.41
28 29 7.550597 TGCTTAGATGAACTCATAGATGGAT 57.449 36.000 0.00 0.00 36.57 3.41
29 30 7.609960 TGCTTAGATGAACTCATAGATGGATC 58.390 38.462 0.00 0.00 36.57 3.36
30 31 7.454066 TGCTTAGATGAACTCATAGATGGATCT 59.546 37.037 0.00 0.00 40.86 2.75
31 32 8.313292 GCTTAGATGAACTCATAGATGGATCTT 58.687 37.037 0.00 0.00 38.32 2.40
32 33 9.642327 CTTAGATGAACTCATAGATGGATCTTG 57.358 37.037 0.00 0.00 38.32 3.02
33 34 7.006865 AGATGAACTCATAGATGGATCTTGG 57.993 40.000 0.00 0.00 38.32 3.61
34 35 6.558014 AGATGAACTCATAGATGGATCTTGGT 59.442 38.462 0.00 0.00 38.32 3.67
35 36 5.922053 TGAACTCATAGATGGATCTTGGTG 58.078 41.667 0.00 0.00 38.32 4.17
36 37 5.662657 TGAACTCATAGATGGATCTTGGTGA 59.337 40.000 0.00 0.00 38.32 4.02
37 38 6.156775 TGAACTCATAGATGGATCTTGGTGAA 59.843 38.462 0.00 0.00 38.32 3.18
38 39 6.566079 ACTCATAGATGGATCTTGGTGAAA 57.434 37.500 0.00 0.00 38.32 2.69
39 40 6.352516 ACTCATAGATGGATCTTGGTGAAAC 58.647 40.000 0.00 0.00 38.32 2.78
69 70 8.888716 AGGAAAAATTTTAATTTTCTGCAACGT 58.111 25.926 12.19 0.00 45.16 3.99
70 71 9.497030 GGAAAAATTTTAATTTTCTGCAACGTT 57.503 25.926 12.19 0.00 45.16 3.99
72 73 9.497030 AAAAATTTTAATTTTCTGCAACGTTCC 57.503 25.926 12.19 0.00 45.16 3.62
73 74 6.779115 ATTTTAATTTTCTGCAACGTTCCC 57.221 33.333 0.00 0.00 0.00 3.97
74 75 2.812358 AATTTTCTGCAACGTTCCCC 57.188 45.000 0.00 0.00 0.00 4.81
75 76 1.698506 ATTTTCTGCAACGTTCCCCA 58.301 45.000 0.00 0.00 0.00 4.96
76 77 1.475403 TTTTCTGCAACGTTCCCCAA 58.525 45.000 0.00 0.00 0.00 4.12
77 78 0.741915 TTTCTGCAACGTTCCCCAAC 59.258 50.000 0.00 0.00 0.00 3.77
78 79 0.394488 TTCTGCAACGTTCCCCAACA 60.394 50.000 0.00 0.00 32.14 3.33
79 80 0.817634 TCTGCAACGTTCCCCAACAG 60.818 55.000 0.00 0.00 32.14 3.16
80 81 1.795170 CTGCAACGTTCCCCAACAGG 61.795 60.000 0.00 0.00 32.14 4.00
81 82 1.527380 GCAACGTTCCCCAACAGGA 60.527 57.895 0.00 0.00 38.24 3.86
82 83 1.792118 GCAACGTTCCCCAACAGGAC 61.792 60.000 0.00 0.00 38.24 3.85
83 84 1.149854 AACGTTCCCCAACAGGACC 59.850 57.895 0.00 0.00 38.24 4.46
123 124 5.928976 AGGGGTCAATTTTCCAAAAGAAAG 58.071 37.500 0.00 0.00 45.11 2.62
128 129 8.154203 GGGTCAATTTTCCAAAAGAAAGGATTA 58.846 33.333 0.00 0.00 45.11 1.75
307 319 0.836606 TGGGGATACATCACATGCGT 59.163 50.000 0.00 0.00 39.74 5.24
328 348 3.806949 TCAATTACCCAAACTCCTGCT 57.193 42.857 0.00 0.00 0.00 4.24
361 381 1.085893 TGCCTGATGCGTACAACATG 58.914 50.000 3.24 0.00 45.60 3.21
428 448 1.029681 AAACAACAGCCCTTCGTTCC 58.970 50.000 0.00 0.00 0.00 3.62
482 502 3.244111 GCTATTCTCGGCTTCTTTCTTCG 59.756 47.826 0.00 0.00 0.00 3.79
491 511 4.653004 GGCTTCTTTCTTCGCATACTTTC 58.347 43.478 0.00 0.00 0.00 2.62
531 552 2.159170 CGCTTTTGAGTTTTTGACCCCA 60.159 45.455 0.00 0.00 0.00 4.96
532 553 3.492482 CGCTTTTGAGTTTTTGACCCCAT 60.492 43.478 0.00 0.00 0.00 4.00
546 567 1.075482 CCCATATTCCATGGCGGCT 59.925 57.895 11.43 0.00 37.85 5.52
632 653 1.134848 CAGAGAAGAGAAGGGAAGCCG 60.135 57.143 0.00 0.00 0.00 5.52
667 688 2.658422 GCCCTTGGCCACACAATG 59.342 61.111 3.88 0.00 44.06 2.82
751 772 4.847516 CGAATCGGACGGCTCGCA 62.848 66.667 0.00 0.00 0.00 5.10
816 840 5.645497 CAGATTTCCAGTTTCCCTACTTCTG 59.355 44.000 0.00 0.00 0.00 3.02
824 848 0.978146 TCCCTACTTCTGCCTCCAGC 60.978 60.000 0.00 0.00 39.00 4.85
897 925 0.610687 CTTCCAGAGTCCAGTCACCC 59.389 60.000 0.00 0.00 0.00 4.61
898 926 0.105194 TTCCAGAGTCCAGTCACCCA 60.105 55.000 0.00 0.00 0.00 4.51
903 931 1.360852 AGAGTCCAGTCACCCATCTCT 59.639 52.381 0.00 0.00 0.00 3.10
934 962 4.434354 AGCTCCCTCGCTCCGTCT 62.434 66.667 0.00 0.00 34.57 4.18
938 966 4.200283 CCCTCGCTCCGTCTCTGC 62.200 72.222 0.00 0.00 0.00 4.26
969 997 0.601046 CTCCGAGAAAGTGCAGTGCA 60.601 55.000 15.37 15.37 35.60 4.57
991 1019 1.616187 CCAAGGGAGTGTACCGAGAGA 60.616 57.143 0.00 0.00 0.00 3.10
1420 1482 4.436852 GCCATTCGTTTTCGCTATCTTTCA 60.437 41.667 0.00 0.00 43.73 2.69
1423 1485 5.464965 TTCGTTTTCGCTATCTTTCATCC 57.535 39.130 0.00 0.00 43.73 3.51
1426 1488 6.334989 TCGTTTTCGCTATCTTTCATCCTTA 58.665 36.000 0.00 0.00 43.73 2.69
1434 1496 6.514063 GCTATCTTTCATCCTTACCGTTAGT 58.486 40.000 0.00 0.00 0.00 2.24
1444 1506 1.246649 TACCGTTAGTGAGTGGCGAA 58.753 50.000 0.00 0.00 0.00 4.70
1446 1508 1.001633 ACCGTTAGTGAGTGGCGAATT 59.998 47.619 0.00 0.00 0.00 2.17
1456 1518 2.399611 GGCGAATTCGAAGCCGTG 59.600 61.111 31.01 0.00 41.53 4.94
1461 1523 2.029970 GCGAATTCGAAGCCGTGATTTA 59.970 45.455 31.01 0.00 43.02 1.40
1635 1717 2.292292 GCGAAGAACACCAGGCTAAAAA 59.708 45.455 0.00 0.00 0.00 1.94
1836 1958 3.976701 CTTCCACCGCGGCCTCATT 62.977 63.158 28.58 0.00 33.14 2.57
1902 2024 3.058160 CCTGCTCAGCCCAAACCG 61.058 66.667 0.00 0.00 0.00 4.44
1912 2037 1.227823 CCCAAACCGCAGTGTCTCA 60.228 57.895 0.00 0.00 0.00 3.27
1913 2038 0.606401 CCCAAACCGCAGTGTCTCAT 60.606 55.000 0.00 0.00 0.00 2.90
1914 2039 0.798776 CCAAACCGCAGTGTCTCATC 59.201 55.000 0.00 0.00 0.00 2.92
1915 2040 1.609061 CCAAACCGCAGTGTCTCATCT 60.609 52.381 0.00 0.00 0.00 2.90
2121 2377 2.636412 CGAGCCCAACGACCTCTCA 61.636 63.158 0.00 0.00 0.00 3.27
2186 2450 7.599998 AGAAATTTTTGTGCTGATTATGTGGTC 59.400 33.333 0.00 0.00 0.00 4.02
2228 2492 0.321653 ACATGGACAAGTTCGAGGGC 60.322 55.000 0.00 0.00 0.00 5.19
2300 2564 2.416972 GCCTATCGTTTTGTCCTCTCGT 60.417 50.000 0.00 0.00 0.00 4.18
2343 2618 1.057275 TGGCCAAGTGACCCAGTACA 61.057 55.000 0.61 0.00 0.00 2.90
2509 2784 2.105477 GACTCTGGACATGGTGGCATAT 59.895 50.000 0.00 0.00 0.00 1.78
2613 2889 6.942532 TGATTTAATTGATGGTACTGGAGC 57.057 37.500 0.00 0.00 0.00 4.70
3040 3338 4.414337 ACTCATAGCATCTCTTCCAACC 57.586 45.455 0.00 0.00 0.00 3.77
3051 3349 1.203313 TCTTCCAACCCTAGCCACTCT 60.203 52.381 0.00 0.00 0.00 3.24
3075 3374 7.759886 TCTTGATTTCTAAACACGGAGATGTAG 59.240 37.037 0.00 0.00 30.75 2.74
3143 3448 0.965363 AACTAACATTGGCCAGCCCG 60.965 55.000 5.11 0.00 35.87 6.13
3173 3478 8.995220 GCCATTGCAATCACAATTAATAATCAT 58.005 29.630 9.53 0.00 38.19 2.45
3188 3493 2.914734 ATCATCGCCCTTCCCCTCCA 62.915 60.000 0.00 0.00 0.00 3.86
3192 3497 1.228737 CGCCCTTCCCCTCCAAAAA 60.229 57.895 0.00 0.00 0.00 1.94
3226 3542 8.267894 CGAGATCCATACCCCTTCATAATTAAT 58.732 37.037 0.00 0.00 0.00 1.40
3290 3606 1.358787 AGGATTGTTTCTGCCCATCCA 59.641 47.619 0.00 0.00 0.00 3.41
3294 3610 0.327924 TGTTTCTGCCCATCCATCGT 59.672 50.000 0.00 0.00 0.00 3.73
3303 3619 1.402720 CCCATCCATCGTGTGTTTTGC 60.403 52.381 0.00 0.00 0.00 3.68
3339 3655 4.788521 GCCTTCTTTGATAATTAACCCGCG 60.789 45.833 0.00 0.00 0.00 6.46
3342 3658 3.872771 TCTTTGATAATTAACCCGCGGTC 59.127 43.478 26.12 12.88 33.12 4.79
3358 3674 3.791887 CGCGGTCTATCTTTAAGTGACAG 59.208 47.826 0.00 11.45 0.00 3.51
3376 3692 9.803315 AAGTGACAGAAATTAAAAAGAAACTCC 57.197 29.630 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.451064 TCTATGAGTTCATCTAAGCAACGA 57.549 37.500 0.00 0.00 37.76 3.85
1 2 6.145209 CCATCTATGAGTTCATCTAAGCAACG 59.855 42.308 0.00 0.00 37.76 4.10
2 3 7.212976 TCCATCTATGAGTTCATCTAAGCAAC 58.787 38.462 0.00 0.00 37.76 4.17
3 4 7.365497 TCCATCTATGAGTTCATCTAAGCAA 57.635 36.000 0.00 0.00 37.76 3.91
4 5 6.983906 TCCATCTATGAGTTCATCTAAGCA 57.016 37.500 0.00 0.00 37.76 3.91
5 6 7.839907 AGATCCATCTATGAGTTCATCTAAGC 58.160 38.462 0.00 0.00 37.76 3.09
6 7 9.642327 CAAGATCCATCTATGAGTTCATCTAAG 57.358 37.037 0.00 0.00 35.76 2.18
7 8 8.591940 CCAAGATCCATCTATGAGTTCATCTAA 58.408 37.037 0.00 0.00 35.76 2.10
8 9 7.732140 ACCAAGATCCATCTATGAGTTCATCTA 59.268 37.037 0.00 0.00 35.76 1.98
9 10 6.558014 ACCAAGATCCATCTATGAGTTCATCT 59.442 38.462 0.00 0.00 35.76 2.90
10 11 6.649973 CACCAAGATCCATCTATGAGTTCATC 59.350 42.308 0.00 0.00 35.76 2.92
11 12 6.328410 TCACCAAGATCCATCTATGAGTTCAT 59.672 38.462 0.00 0.00 35.76 2.57
12 13 5.662657 TCACCAAGATCCATCTATGAGTTCA 59.337 40.000 0.00 0.00 35.76 3.18
13 14 6.166984 TCACCAAGATCCATCTATGAGTTC 57.833 41.667 0.00 0.00 35.76 3.01
14 15 6.566079 TTCACCAAGATCCATCTATGAGTT 57.434 37.500 0.00 0.00 35.76 3.01
15 16 6.352516 GTTTCACCAAGATCCATCTATGAGT 58.647 40.000 0.00 0.00 35.76 3.41
16 17 5.762218 GGTTTCACCAAGATCCATCTATGAG 59.238 44.000 0.00 0.00 38.42 2.90
17 18 5.684704 GGTTTCACCAAGATCCATCTATGA 58.315 41.667 0.00 0.00 38.42 2.15
18 19 4.512944 CGGTTTCACCAAGATCCATCTATG 59.487 45.833 0.00 0.00 38.47 2.23
19 20 4.164221 ACGGTTTCACCAAGATCCATCTAT 59.836 41.667 0.00 0.00 38.47 1.98
20 21 3.517901 ACGGTTTCACCAAGATCCATCTA 59.482 43.478 0.00 0.00 38.47 1.98
21 22 2.305927 ACGGTTTCACCAAGATCCATCT 59.694 45.455 0.00 0.00 38.47 2.90
22 23 2.711542 ACGGTTTCACCAAGATCCATC 58.288 47.619 0.00 0.00 38.47 3.51
23 24 2.879103 ACGGTTTCACCAAGATCCAT 57.121 45.000 0.00 0.00 38.47 3.41
24 25 2.027561 CCTACGGTTTCACCAAGATCCA 60.028 50.000 0.00 0.00 38.47 3.41
25 26 2.235402 TCCTACGGTTTCACCAAGATCC 59.765 50.000 0.00 0.00 38.47 3.36
26 27 3.604875 TCCTACGGTTTCACCAAGATC 57.395 47.619 0.00 0.00 38.47 2.75
27 28 4.360951 TTTCCTACGGTTTCACCAAGAT 57.639 40.909 0.00 0.00 38.47 2.40
28 29 3.842007 TTTCCTACGGTTTCACCAAGA 57.158 42.857 0.00 0.00 38.47 3.02
29 30 4.904253 TTTTTCCTACGGTTTCACCAAG 57.096 40.909 0.00 0.00 38.47 3.61
30 31 5.855740 AATTTTTCCTACGGTTTCACCAA 57.144 34.783 0.00 0.00 38.47 3.67
31 32 5.855740 AAATTTTTCCTACGGTTTCACCA 57.144 34.783 0.00 0.00 38.47 4.17
32 33 8.821147 ATTAAAATTTTTCCTACGGTTTCACC 57.179 30.769 9.06 0.00 34.05 4.02
38 39 8.984764 GCAGAAAATTAAAATTTTTCCTACGGT 58.015 29.630 9.06 0.00 45.70 4.83
39 40 8.983724 TGCAGAAAATTAAAATTTTTCCTACGG 58.016 29.630 9.06 4.45 45.70 4.02
43 44 8.888716 ACGTTGCAGAAAATTAAAATTTTTCCT 58.111 25.926 9.06 5.83 45.70 3.36
44 45 9.497030 AACGTTGCAGAAAATTAAAATTTTTCC 57.503 25.926 9.06 3.98 45.70 3.13
46 47 9.497030 GGAACGTTGCAGAAAATTAAAATTTTT 57.503 25.926 15.52 0.00 45.70 1.94
48 49 7.254966 GGGGAACGTTGCAGAAAATTAAAATTT 60.255 33.333 21.74 0.00 40.15 1.82
49 50 6.203915 GGGGAACGTTGCAGAAAATTAAAATT 59.796 34.615 21.74 0.00 0.00 1.82
50 51 5.699001 GGGGAACGTTGCAGAAAATTAAAAT 59.301 36.000 21.74 0.00 0.00 1.82
51 52 5.051153 GGGGAACGTTGCAGAAAATTAAAA 58.949 37.500 21.74 0.00 0.00 1.52
52 53 4.099573 TGGGGAACGTTGCAGAAAATTAAA 59.900 37.500 21.74 0.00 0.00 1.52
53 54 3.637229 TGGGGAACGTTGCAGAAAATTAA 59.363 39.130 21.74 0.00 0.00 1.40
54 55 3.223435 TGGGGAACGTTGCAGAAAATTA 58.777 40.909 21.74 0.00 0.00 1.40
55 56 2.035632 TGGGGAACGTTGCAGAAAATT 58.964 42.857 21.74 0.00 0.00 1.82
56 57 1.698506 TGGGGAACGTTGCAGAAAAT 58.301 45.000 21.74 0.00 0.00 1.82
57 58 1.135333 GTTGGGGAACGTTGCAGAAAA 59.865 47.619 21.74 6.84 0.00 2.29
58 59 0.741915 GTTGGGGAACGTTGCAGAAA 59.258 50.000 21.74 9.26 0.00 2.52
59 60 0.394488 TGTTGGGGAACGTTGCAGAA 60.394 50.000 21.74 10.10 0.00 3.02
60 61 0.817634 CTGTTGGGGAACGTTGCAGA 60.818 55.000 21.74 3.97 0.00 4.26
61 62 1.654220 CTGTTGGGGAACGTTGCAG 59.346 57.895 21.74 5.93 0.00 4.41
62 63 1.826054 CCTGTTGGGGAACGTTGCA 60.826 57.895 21.74 0.00 0.00 4.08
63 64 1.527380 TCCTGTTGGGGAACGTTGC 60.527 57.895 11.85 11.85 35.33 4.17
64 65 1.170290 GGTCCTGTTGGGGAACGTTG 61.170 60.000 5.00 0.00 37.10 4.10
65 66 1.149854 GGTCCTGTTGGGGAACGTT 59.850 57.895 0.00 0.00 37.10 3.99
66 67 2.826003 GGGTCCTGTTGGGGAACGT 61.826 63.158 0.00 0.00 43.62 3.99
67 68 2.033602 GGGTCCTGTTGGGGAACG 59.966 66.667 0.00 0.00 43.62 3.95
68 69 1.228459 GTGGGTCCTGTTGGGGAAC 60.228 63.158 0.00 0.00 42.07 3.62
69 70 1.386772 AGTGGGTCCTGTTGGGGAA 60.387 57.895 0.00 0.00 37.10 3.97
70 71 2.153401 CAGTGGGTCCTGTTGGGGA 61.153 63.158 0.00 0.00 35.33 4.81
71 72 2.129555 CTCAGTGGGTCCTGTTGGGG 62.130 65.000 0.00 0.00 34.02 4.96
72 73 1.376466 CTCAGTGGGTCCTGTTGGG 59.624 63.158 0.00 0.00 34.02 4.12
73 74 1.376466 CCTCAGTGGGTCCTGTTGG 59.624 63.158 0.00 0.00 34.02 3.77
83 84 4.715130 TCCCGACCCCCTCAGTGG 62.715 72.222 0.00 0.00 0.00 4.00
98 99 3.901222 TCTTTTGGAAAATTGACCCCTCC 59.099 43.478 0.00 0.00 0.00 4.30
140 141 2.118403 TGACACTCCTCTTTTCCCCT 57.882 50.000 0.00 0.00 0.00 4.79
141 142 2.951229 TTGACACTCCTCTTTTCCCC 57.049 50.000 0.00 0.00 0.00 4.81
142 143 3.507622 CCATTTGACACTCCTCTTTTCCC 59.492 47.826 0.00 0.00 0.00 3.97
307 319 4.112634 AGCAGGAGTTTGGGTAATTGAA 57.887 40.909 0.00 0.00 0.00 2.69
328 348 4.527816 GCATCAGGCATTTAATGGGGAATA 59.472 41.667 7.08 0.00 43.97 1.75
361 381 1.448540 CCTGACACGGCATGGACTC 60.449 63.158 0.00 0.00 0.00 3.36
531 552 0.035056 GCCTAGCCGCCATGGAATAT 60.035 55.000 18.40 0.00 42.00 1.28
532 553 1.374947 GCCTAGCCGCCATGGAATA 59.625 57.895 18.40 0.56 42.00 1.75
601 622 2.299297 TCTCTTCTCTGGACCGAAAACC 59.701 50.000 0.00 0.00 0.00 3.27
632 653 1.739562 CAGAACACGCTCCTGCCTC 60.740 63.158 0.00 0.00 35.36 4.70
688 709 3.312973 CAGATCGTTCGAACTACTAGGCT 59.687 47.826 24.80 10.00 0.00 4.58
816 840 2.647297 GTGTGCAAAGCTGGAGGC 59.353 61.111 0.00 0.00 42.19 4.70
824 848 0.042880 TTTCGTACGCGTGTGCAAAG 60.043 50.000 24.59 3.44 42.97 2.77
897 925 3.791245 CTCGAAAGGGGAAGAAGAGATG 58.209 50.000 0.00 0.00 0.00 2.90
898 926 2.169561 GCTCGAAAGGGGAAGAAGAGAT 59.830 50.000 0.00 0.00 0.00 2.75
903 931 0.613777 GGAGCTCGAAAGGGGAAGAA 59.386 55.000 7.83 0.00 0.00 2.52
934 962 1.347707 CGGAGGCTATAAATGGGCAGA 59.652 52.381 2.83 0.00 36.27 4.26
938 966 4.202367 ACTTTCTCGGAGGCTATAAATGGG 60.202 45.833 4.96 0.00 0.00 4.00
969 997 0.903454 CTCGGTACACTCCCTTGGGT 60.903 60.000 5.51 0.00 0.00 4.51
1110 1138 2.047560 GTGAACGGGGAGAACGGG 60.048 66.667 0.00 0.00 35.23 5.28
1420 1482 2.167900 GCCACTCACTAACGGTAAGGAT 59.832 50.000 0.00 0.00 0.00 3.24
1423 1485 1.200716 TCGCCACTCACTAACGGTAAG 59.799 52.381 0.00 0.00 0.00 2.34
1426 1488 0.606604 ATTCGCCACTCACTAACGGT 59.393 50.000 0.00 0.00 0.00 4.83
1434 1496 1.019278 GGCTTCGAATTCGCCACTCA 61.019 55.000 22.90 1.46 43.25 3.41
1444 1506 3.181510 GCACTTAAATCACGGCTTCGAAT 60.182 43.478 0.00 0.00 37.63 3.34
1446 1508 1.730064 GCACTTAAATCACGGCTTCGA 59.270 47.619 0.00 0.00 37.63 3.71
1456 1518 1.347221 CCGTCCGCGCACTTAAATC 59.653 57.895 8.75 0.00 36.67 2.17
1579 1661 0.527565 GTTCTACCAACGGACCGCTA 59.472 55.000 15.39 0.00 0.00 4.26
1580 1662 1.183676 AGTTCTACCAACGGACCGCT 61.184 55.000 15.39 0.00 0.00 5.52
1581 1663 0.735287 GAGTTCTACCAACGGACCGC 60.735 60.000 15.39 0.00 0.00 5.68
1582 1664 0.886563 AGAGTTCTACCAACGGACCG 59.113 55.000 13.61 13.61 0.00 4.79
1583 1665 2.685100 CAAGAGTTCTACCAACGGACC 58.315 52.381 0.00 0.00 0.00 4.46
1584 1666 2.067013 GCAAGAGTTCTACCAACGGAC 58.933 52.381 0.00 0.00 0.00 4.79
1585 1667 1.968493 AGCAAGAGTTCTACCAACGGA 59.032 47.619 0.00 0.00 0.00 4.69
1587 1669 1.986378 CGAGCAAGAGTTCTACCAACG 59.014 52.381 0.00 0.00 0.00 4.10
1588 1670 1.727335 GCGAGCAAGAGTTCTACCAAC 59.273 52.381 0.00 0.00 0.00 3.77
1635 1717 1.750399 GACCTGCATCACGCCCAAT 60.750 57.895 0.00 0.00 41.33 3.16
1912 2037 1.135094 ATCGGATGGTTCTGGCAGAT 58.865 50.000 19.50 2.42 0.00 2.90
1913 2038 0.911769 AATCGGATGGTTCTGGCAGA 59.088 50.000 14.43 14.43 0.00 4.26
1914 2039 2.487934 CTAATCGGATGGTTCTGGCAG 58.512 52.381 8.58 8.58 0.00 4.85
1915 2040 1.140852 CCTAATCGGATGGTTCTGGCA 59.859 52.381 0.00 0.00 33.16 4.92
2121 2377 1.535687 ACGTACTGCCCCAAGGAGT 60.536 57.895 0.00 0.00 33.47 3.85
2186 2450 3.076258 TATCTGCCACGGAGCCACG 62.076 63.158 0.00 0.00 40.31 4.94
2300 2564 2.124612 ACAGCACAGCACAGCACA 60.125 55.556 0.00 0.00 0.00 4.57
2336 2611 0.321653 GGGTGCTTGTCCTGTACTGG 60.322 60.000 12.42 12.42 0.00 4.00
2343 2618 1.280421 GAAGATCAGGGTGCTTGTCCT 59.720 52.381 0.00 0.00 0.00 3.85
2676 2967 3.717294 GGACACATCCACGCCCCT 61.717 66.667 0.00 0.00 45.47 4.79
2988 3286 5.601662 ACAATAGTGTGACATTCTATCCCG 58.398 41.667 0.00 0.00 36.31 5.14
2990 3288 7.849804 ACAACAATAGTGTGACATTCTATCC 57.150 36.000 0.00 0.00 38.27 2.59
3000 3298 5.606505 TGAGTAGCAACAACAATAGTGTGA 58.393 37.500 0.00 0.00 38.27 3.58
3040 3338 6.092807 GTGTTTAGAAATCAAGAGTGGCTAGG 59.907 42.308 0.00 0.00 0.00 3.02
3051 3349 7.608153 TCTACATCTCCGTGTTTAGAAATCAA 58.392 34.615 0.00 0.00 33.62 2.57
3075 3374 8.131100 TCTCTTCAAAATCAACAGTGATGTTTC 58.869 33.333 0.00 0.00 44.02 2.78
3143 3448 2.063156 TTGTGATTGCAATGGCGAAC 57.937 45.000 18.59 7.64 45.35 3.95
3173 3478 1.721093 TTTTTGGAGGGGAAGGGCGA 61.721 55.000 0.00 0.00 0.00 5.54
3192 3497 2.434702 GGGTATGGATCTCGACCTTGTT 59.565 50.000 9.38 0.00 32.24 2.83
3194 3499 1.344763 GGGGTATGGATCTCGACCTTG 59.655 57.143 9.38 0.00 32.24 3.61
3200 3516 5.683876 ATTATGAAGGGGTATGGATCTCG 57.316 43.478 0.00 0.00 0.00 4.04
3204 3520 8.243403 TCCATTAATTATGAAGGGGTATGGAT 57.757 34.615 5.88 0.00 35.39 3.41
3274 3590 1.271871 ACGATGGATGGGCAGAAACAA 60.272 47.619 0.00 0.00 0.00 2.83
3286 3602 2.503331 TCTGCAAAACACACGATGGAT 58.497 42.857 0.00 0.00 0.00 3.41
3303 3619 2.575805 AGAAGGCAGGGAGTTTTCTG 57.424 50.000 0.00 0.00 0.00 3.02
3312 3628 5.069119 GGGTTAATTATCAAAGAAGGCAGGG 59.931 44.000 0.00 0.00 0.00 4.45
3315 3631 4.097286 GCGGGTTAATTATCAAAGAAGGCA 59.903 41.667 0.00 0.00 0.00 4.75
3443 3759 9.765295 ATGTTAGAACTAGAGTTAGGGTTTAGA 57.235 33.333 0.00 0.00 38.56 2.10
3444 3760 9.804758 CATGTTAGAACTAGAGTTAGGGTTTAG 57.195 37.037 0.00 0.00 38.56 1.85
3445 3761 9.317827 ACATGTTAGAACTAGAGTTAGGGTTTA 57.682 33.333 0.00 0.00 38.56 2.01


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

AutoCloner maintained by Alex Coulton.