Multiple sequence alignment - TraesCS4B01G173400

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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 TraesCS4B01G173400 chr4B 100.000 4662 0 0 406 5067 379415755 379420416 0.000000e+00 8610.0
1 TraesCS4B01G173400 chr4B 100.000 45 0 0 1 45 379415350 379415394 3.250000e-12 84.2
2 TraesCS4B01G173400 chr4A 95.001 4221 143 39 875 5067 175003057 174998877 0.000000e+00 6564.0
3 TraesCS4B01G173400 chr4A 82.707 399 56 5 408 805 175005143 175004757 4.860000e-90 342.0
4 TraesCS4B01G173400 chr4A 87.081 209 22 4 3473 3679 647922481 647922276 1.100000e-56 231.0
5 TraesCS4B01G173400 chr4D 95.550 3798 119 14 882 4670 304263346 304267102 0.000000e+00 6032.0
6 TraesCS4B01G173400 chr4D 94.763 401 15 4 4670 5067 304296041 304296438 2.000000e-173 619.0
7 TraesCS4B01G173400 chr4D 85.625 480 55 9 418 887 304262821 304263296 4.560000e-135 492.0
8 TraesCS4B01G173400 chrUn 86.842 228 29 1 3453 3679 46078885 46078658 2.340000e-63 254.0
9 TraesCS4B01G173400 chr6A 84.746 236 30 5 3448 3679 39065839 39066072 1.100000e-56 231.0
10 TraesCS4B01G173400 chr5B 87.681 138 16 1 3487 3624 181476399 181476263 5.250000e-35 159.0
11 TraesCS4B01G173400 chr3A 79.787 188 38 0 3157 3344 60631013 60630826 2.460000e-28 137.0
12 TraesCS4B01G173400 chr3A 87.324 71 9 0 2513 2583 60631660 60631590 1.170000e-11 82.4
13 TraesCS4B01G173400 chr3D 79.255 188 39 0 3157 3344 48424615 48424428 1.140000e-26 132.0
14 TraesCS4B01G173400 chr3D 84.722 72 10 1 2513 2583 48425262 48425191 2.530000e-08 71.3
15 TraesCS4B01G173400 chr3B 87.324 71 9 0 2513 2583 76483869 76483799 1.170000e-11 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 TraesCS4B01G173400 chr4B 379415350 379420416 5066 False 4347.1 8610 100.0000 1 5067 2 chr4B.!!$F1 5066
1 TraesCS4B01G173400 chr4A 174998877 175005143 6266 True 3453.0 6564 88.8540 408 5067 2 chr4A.!!$R2 4659
2 TraesCS4B01G173400 chr4D 304262821 304267102 4281 False 3262.0 6032 90.5875 418 4670 2 chr4D.!!$F2 4252

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
992 2637 0.034380 TAGTGACCAGAGGAGTCGGG 60.034 60.0 0.00 0.0 43.36 5.14 F
1923 3570 0.102300 GGCAACGTGGCAGTTTTTCT 59.898 50.0 18.47 0.0 43.14 2.52 F
2834 4481 0.391661 GGACAGATTCTCGCCTTGCA 60.392 55.0 0.00 0.0 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 3898 0.318441 CAAGACCAGGAGAGTTCGCA 59.682 55.0 0.0 0.0 0.00 5.10 R
3905 5555 0.036952 TGTAGCTCCTTGACAGCAGC 60.037 55.0 0.0 0.0 39.56 5.25 R
4767 6419 0.102120 TGGTTTTGCCTTTGTGCTCG 59.898 50.0 0.0 0.0 38.35 5.03 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
29 30 2.396590 CCTCTTGGCTACGGCTTTAA 57.603 50.000 0.00 0.00 38.73 1.52
30 31 2.706890 CCTCTTGGCTACGGCTTTAAA 58.293 47.619 0.00 0.00 38.73 1.52
31 32 2.418976 CCTCTTGGCTACGGCTTTAAAC 59.581 50.000 0.00 0.00 38.73 2.01
32 33 2.070783 TCTTGGCTACGGCTTTAAACG 58.929 47.619 0.00 0.00 38.73 3.60
33 34 1.129811 CTTGGCTACGGCTTTAAACGG 59.870 52.381 3.64 0.19 38.73 4.44
34 35 0.035176 TGGCTACGGCTTTAAACGGT 59.965 50.000 3.64 5.19 38.73 4.83
35 36 1.159285 GGCTACGGCTTTAAACGGTT 58.841 50.000 0.00 0.00 38.73 4.44
36 37 1.135888 GGCTACGGCTTTAAACGGTTG 60.136 52.381 0.00 5.04 38.73 3.77
37 38 1.532437 GCTACGGCTTTAAACGGTTGT 59.468 47.619 0.00 0.00 35.22 3.32
38 39 2.031769 GCTACGGCTTTAAACGGTTGTT 60.032 45.455 0.00 0.00 36.16 2.83
39 40 2.478547 ACGGCTTTAAACGGTTGTTG 57.521 45.000 0.00 0.00 38.62 3.33
40 41 1.744522 ACGGCTTTAAACGGTTGTTGT 59.255 42.857 0.00 0.00 38.62 3.32
41 42 2.164017 ACGGCTTTAAACGGTTGTTGTT 59.836 40.909 0.00 0.00 38.62 2.83
42 43 3.376546 ACGGCTTTAAACGGTTGTTGTTA 59.623 39.130 0.00 0.00 38.62 2.41
43 44 4.036616 ACGGCTTTAAACGGTTGTTGTTAT 59.963 37.500 0.00 0.00 38.62 1.89
44 45 4.613866 CGGCTTTAAACGGTTGTTGTTATC 59.386 41.667 0.00 0.00 38.62 1.75
441 442 9.297037 AGTATTAATAATCCGAATCAAAAGGGG 57.703 33.333 0.00 0.00 0.00 4.79
444 445 8.776061 TTAATAATCCGAATCAAAAGGGGAAT 57.224 30.769 0.00 0.00 0.00 3.01
457 460 5.646692 AAAGGGGAATATGATTCGAGGAA 57.353 39.130 0.00 0.00 0.00 3.36
478 482 6.380846 AGGAAGCAAACATTGATTATTAGGCA 59.619 34.615 0.00 0.00 39.73 4.75
491 495 8.696043 TGATTATTAGGCAAATTGAGCATAGT 57.304 30.769 0.00 2.69 29.39 2.12
495 499 2.762327 AGGCAAATTGAGCATAGTTGGG 59.238 45.455 0.00 0.00 0.00 4.12
510 514 7.488187 CATAGTTGGGATGACTATGTTTCTG 57.512 40.000 13.44 0.00 46.02 3.02
552 557 6.759827 TCCGATTATAGTTTTAGACTTGGCAC 59.240 38.462 0.00 0.00 39.86 5.01
555 560 1.235724 AGTTTTAGACTTGGCACGGC 58.764 50.000 0.00 0.00 33.92 5.68
606 611 7.981789 TCAATATTTTCTGCGTTACTCTCTCAT 59.018 33.333 0.00 0.00 0.00 2.90
608 613 8.804688 ATATTTTCTGCGTTACTCTCTCATAC 57.195 34.615 0.00 0.00 0.00 2.39
615 620 8.095169 TCTGCGTTACTCTCTCATACTGATATA 58.905 37.037 0.00 0.00 0.00 0.86
622 627 7.001073 ACTCTCTCATACTGATATAGTGTGCA 58.999 38.462 0.00 0.00 45.18 4.57
626 631 8.635765 TCTCATACTGATATAGTGTGCATGTA 57.364 34.615 0.00 0.00 45.18 2.29
632 637 8.873215 ACTGATATAGTGTGCATGTAAACTAC 57.127 34.615 15.21 4.94 38.49 2.73
638 643 3.906008 GTGTGCATGTAAACTACAAAGCG 59.094 43.478 0.00 0.00 42.80 4.68
684 689 5.878406 AATATCTGTCGTCCCAATCTCTT 57.122 39.130 0.00 0.00 0.00 2.85
704 711 3.119009 TGGAGGTTTATAAGGGTCGGA 57.881 47.619 0.00 0.00 0.00 4.55
707 714 3.390311 GGAGGTTTATAAGGGTCGGATGT 59.610 47.826 0.00 0.00 0.00 3.06
811 2387 7.631717 ATTCAGCCTTTGGTCTAAAATAGTC 57.368 36.000 0.00 0.00 0.00 2.59
814 2390 4.019591 AGCCTTTGGTCTAAAATAGTCGGT 60.020 41.667 0.00 0.00 0.00 4.69
908 2548 0.553819 ACACCCACCCTGCAGTTAAA 59.446 50.000 13.81 0.00 0.00 1.52
992 2637 0.034380 TAGTGACCAGAGGAGTCGGG 60.034 60.000 0.00 0.00 43.36 5.14
1131 2776 1.627834 CTCCAGCTCTCCACCTTCTTT 59.372 52.381 0.00 0.00 0.00 2.52
1320 2965 1.463528 CGTTCGGCGATTCTTTGTTCC 60.464 52.381 11.76 0.00 44.77 3.62
1448 3094 6.522510 CGTTAGATAGGATCGAATCGTTTACC 59.477 42.308 1.52 2.63 0.00 2.85
1455 3101 2.813061 TCGAATCGTTTACCGGGAATC 58.187 47.619 6.32 0.79 37.11 2.52
1509 3155 6.769134 TCTTGGTGTAGATCGTTAATCTGA 57.231 37.500 0.00 0.00 44.69 3.27
1542 3188 4.780275 TGTTCGGAAATTCATGATTGCA 57.220 36.364 0.00 0.00 0.00 4.08
1598 3244 6.374333 TCTTAATTAGTGCATGTCTTGGTTCC 59.626 38.462 0.00 0.00 0.00 3.62
1602 3248 3.299503 AGTGCATGTCTTGGTTCCTTTT 58.700 40.909 0.00 0.00 0.00 2.27
1614 3260 5.096443 TGGTTCCTTTTGTTTTCAATGCT 57.904 34.783 0.00 0.00 39.70 3.79
1765 3411 2.101415 CCTGTGATGCGAGTCCTTATGA 59.899 50.000 0.00 0.00 0.00 2.15
1885 3531 9.367160 ACATGGAGATAATTGGTATTTTAAGGG 57.633 33.333 0.00 0.00 0.00 3.95
1886 3532 8.806146 CATGGAGATAATTGGTATTTTAAGGGG 58.194 37.037 0.00 0.00 0.00 4.79
1888 3534 8.570470 TGGAGATAATTGGTATTTTAAGGGGAA 58.430 33.333 0.00 0.00 0.00 3.97
1923 3570 0.102300 GGCAACGTGGCAGTTTTTCT 59.898 50.000 18.47 0.00 43.14 2.52
1928 3575 1.940613 ACGTGGCAGTTTTTCTCTGTC 59.059 47.619 0.00 0.00 37.94 3.51
1956 3603 6.013725 ACAGTGAGGTTCTAATCACCATGTTA 60.014 38.462 0.00 0.00 45.61 2.41
2069 3716 8.230486 CCTACTGTGTAGTTTGATTTTGACATC 58.770 37.037 4.36 0.00 38.36 3.06
2101 3748 5.554437 TCAACTGGTAGTGGTGTTGATAA 57.446 39.130 0.00 0.00 42.25 1.75
2107 3754 5.424757 TGGTAGTGGTGTTGATAATAGCAC 58.575 41.667 11.12 11.12 46.92 4.40
2118 3765 8.504005 GTGTTGATAATAGCACAACTGTTTACT 58.496 33.333 0.00 0.00 42.60 2.24
2124 3771 1.069906 GCACAACTGTTTACTCTGGCG 60.070 52.381 0.00 0.00 0.00 5.69
2150 3797 4.501071 TGATAAGTTCAGGCGGAGTAAAC 58.499 43.478 0.00 0.00 0.00 2.01
2167 3814 5.309638 AGTAAACCTTTCTTTCTCTCCTGC 58.690 41.667 0.00 0.00 0.00 4.85
2178 3825 2.672098 TCTCTCCTGCAGGATCTTACC 58.328 52.381 35.11 0.00 44.46 2.85
2245 3892 3.689411 GCGAGCTGCGGTTAGTAC 58.311 61.111 0.00 0.00 41.29 2.73
2250 3897 2.670229 CGAGCTGCGGTTAGTACTGAAA 60.670 50.000 5.39 0.00 36.03 2.69
2251 3898 3.522553 GAGCTGCGGTTAGTACTGAAAT 58.477 45.455 5.39 0.00 31.98 2.17
2252 3899 3.262420 AGCTGCGGTTAGTACTGAAATG 58.738 45.455 5.39 0.00 31.98 2.32
2253 3900 2.223044 GCTGCGGTTAGTACTGAAATGC 60.223 50.000 5.39 2.99 31.98 3.56
2254 3901 1.996898 TGCGGTTAGTACTGAAATGCG 59.003 47.619 5.39 0.00 31.98 4.73
2256 3903 2.669434 GCGGTTAGTACTGAAATGCGAA 59.331 45.455 5.39 0.00 31.98 4.70
2257 3904 3.483085 GCGGTTAGTACTGAAATGCGAAC 60.483 47.826 5.39 0.00 31.98 3.95
2258 3905 3.924686 CGGTTAGTACTGAAATGCGAACT 59.075 43.478 5.39 0.00 31.98 3.01
2259 3906 4.031426 CGGTTAGTACTGAAATGCGAACTC 59.969 45.833 5.39 0.00 31.98 3.01
2260 3907 5.169295 GGTTAGTACTGAAATGCGAACTCT 58.831 41.667 5.39 0.00 0.00 3.24
2261 3908 5.288952 GGTTAGTACTGAAATGCGAACTCTC 59.711 44.000 5.39 0.00 0.00 3.20
2307 3954 7.148641 TGTTAGCTTTCATCTACAGCTATAGC 58.851 38.462 17.33 17.33 43.90 2.97
2321 3968 2.288273 GCTATAGCGTCCAACTACCCTG 60.288 54.545 9.40 0.00 0.00 4.45
2402 4049 4.260907 CGCTATTTGAATCTGACCATGGTG 60.261 45.833 25.52 9.30 0.00 4.17
2473 4120 0.868406 CTCACACTTCCTTTCGGTGC 59.132 55.000 0.00 0.00 34.70 5.01
2512 4159 2.816087 ACTTGCAATTGCTGACTCGATT 59.184 40.909 29.37 4.06 42.66 3.34
2554 4201 9.903682 GTGATTTTGGAGATATATTTGATGTGG 57.096 33.333 0.00 0.00 0.00 4.17
2787 4434 4.323792 CCTTCCAGATCTTGCCTCTTGTAA 60.324 45.833 0.00 0.00 0.00 2.41
2834 4481 0.391661 GGACAGATTCTCGCCTTGCA 60.392 55.000 0.00 0.00 0.00 4.08
3387 5034 7.756395 AGCAGATCATAATTTAACATCCAGG 57.244 36.000 0.00 0.00 0.00 4.45
3471 5118 6.483974 AGATGCTTTTATCTGAAGATGAGCTG 59.516 38.462 17.99 3.80 37.28 4.24
3665 5312 7.040478 GCCACCATGTGTATGTGTTATTATGAT 60.040 37.037 0.00 0.00 32.21 2.45
3703 5353 5.134661 GGGAAGTCTAGTGTACAGCTATCT 58.865 45.833 0.00 0.00 0.00 1.98
3709 5359 3.895232 AGTGTACAGCTATCTTGTGGG 57.105 47.619 0.00 0.00 0.00 4.61
3751 5401 0.458260 TCGCGGCTATAGTGAGCAAA 59.542 50.000 6.13 2.44 44.76 3.68
3973 5623 0.881118 GAAAAGTCATCGCAGGGCAA 59.119 50.000 0.00 0.00 0.00 4.52
4116 5766 4.151867 CGGTACAGAAGGCTGAAGTTAAAC 59.848 45.833 0.00 0.00 45.17 2.01
4126 5776 4.214758 GGCTGAAGTTAAACACGGTAACAT 59.785 41.667 0.00 0.00 34.50 2.71
4422 6074 1.641577 CGGCCTTACTCAGCTGTAAC 58.358 55.000 14.67 0.00 0.00 2.50
4506 6158 4.213270 TGTTGTAGTGTTAGATTGCAGCAC 59.787 41.667 0.00 0.00 0.00 4.40
4623 6275 3.181503 GGCATTGAGCTTGTATGACACTG 60.182 47.826 7.57 0.00 44.79 3.66
4684 6336 4.572389 GCACACCATACTGATAACTTGAGG 59.428 45.833 0.00 0.00 0.00 3.86
4685 6337 5.118990 CACACCATACTGATAACTTGAGGG 58.881 45.833 0.00 0.00 0.00 4.30
4686 6338 5.030147 ACACCATACTGATAACTTGAGGGA 58.970 41.667 0.00 0.00 0.00 4.20
4687 6339 5.129485 ACACCATACTGATAACTTGAGGGAG 59.871 44.000 0.00 0.00 0.00 4.30
4696 6348 8.606830 ACTGATAACTTGAGGGAGATTTTTAGT 58.393 33.333 0.00 0.00 0.00 2.24
4704 6356 4.704965 AGGGAGATTTTTAGTGTATCGCC 58.295 43.478 0.00 0.00 37.48 5.54
4716 6368 1.454295 TATCGCCTGGTAGCCACGA 60.454 57.895 0.00 3.90 36.68 4.35
4744 6396 8.621532 TTAATATCTGATACCACAAGCATTCC 57.378 34.615 0.00 0.00 0.00 3.01
4764 6416 7.117667 GCATTCCACTTGTTTTGTAAATAAGGG 59.882 37.037 11.57 8.21 0.00 3.95
4767 6419 5.694458 CCACTTGTTTTGTAAATAAGGGCAC 59.306 40.000 11.57 0.00 0.00 5.01
4768 6420 5.401079 CACTTGTTTTGTAAATAAGGGCACG 59.599 40.000 11.57 0.00 0.00 5.34
4771 6423 4.163552 GTTTTGTAAATAAGGGCACGAGC 58.836 43.478 0.00 0.00 41.10 5.03
4772 6424 2.772077 TGTAAATAAGGGCACGAGCA 57.228 45.000 7.26 0.00 44.61 4.26
4782 6441 1.065600 GCACGAGCACAAAGGCAAA 59.934 52.632 0.00 0.00 41.58 3.68
4790 6449 2.435437 AGCACAAAGGCAAAACCATCTT 59.565 40.909 0.00 0.00 43.14 2.40
4793 6452 3.556775 CACAAAGGCAAAACCATCTTGTG 59.443 43.478 8.82 8.82 43.43 3.33
4799 6458 3.317993 GGCAAAACCATCTTGTGTACTGT 59.682 43.478 0.00 0.00 38.86 3.55
4800 6459 4.517453 GGCAAAACCATCTTGTGTACTGTA 59.483 41.667 0.00 0.00 38.86 2.74
4801 6460 5.009210 GGCAAAACCATCTTGTGTACTGTAA 59.991 40.000 0.00 0.00 38.86 2.41
4802 6461 5.912955 GCAAAACCATCTTGTGTACTGTAAC 59.087 40.000 0.00 0.00 0.00 2.50
4803 6462 6.238648 GCAAAACCATCTTGTGTACTGTAACT 60.239 38.462 0.00 0.00 0.00 2.24
4804 6463 6.861065 AAACCATCTTGTGTACTGTAACTG 57.139 37.500 0.00 0.00 0.00 3.16
4808 6467 6.706270 ACCATCTTGTGTACTGTAACTGAAAG 59.294 38.462 0.00 0.00 42.29 2.62
4827 6486 7.819900 ACTGAAAGCGTACTTCTCTAAATGAAT 59.180 33.333 0.00 0.00 37.60 2.57
4876 6535 0.449388 CACTTTCATTCCAGCGGCTC 59.551 55.000 0.00 0.00 0.00 4.70
4885 6544 2.338015 CCAGCGGCTCATTTGCAGT 61.338 57.895 0.00 0.00 34.04 4.40
4886 6545 1.154093 CAGCGGCTCATTTGCAGTG 60.154 57.895 0.00 0.00 34.04 3.66
4918 6577 5.120519 TCACACCCGATAACGACAATAAAAC 59.879 40.000 0.00 0.00 42.66 2.43
4922 6581 7.333921 ACACCCGATAACGACAATAAAACAATA 59.666 33.333 0.00 0.00 42.66 1.90
5012 6690 3.181397 CTGTCAGCAAACCACAAACAAG 58.819 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.396590 TTAAAGCCGTAGCCAAGAGG 57.603 50.000 0.00 0.00 41.25 3.69
11 12 2.093783 CGTTTAAAGCCGTAGCCAAGAG 59.906 50.000 0.00 0.00 41.25 2.85
12 13 2.070783 CGTTTAAAGCCGTAGCCAAGA 58.929 47.619 0.00 0.00 41.25 3.02
13 14 1.129811 CCGTTTAAAGCCGTAGCCAAG 59.870 52.381 0.00 0.00 41.25 3.61
14 15 1.158434 CCGTTTAAAGCCGTAGCCAA 58.842 50.000 0.00 0.00 41.25 4.52
15 16 0.035176 ACCGTTTAAAGCCGTAGCCA 59.965 50.000 0.00 0.00 41.25 4.75
16 17 1.135888 CAACCGTTTAAAGCCGTAGCC 60.136 52.381 0.00 0.00 41.25 3.93
17 18 1.532437 ACAACCGTTTAAAGCCGTAGC 59.468 47.619 0.00 0.00 40.32 3.58
18 19 3.002553 ACAACAACCGTTTAAAGCCGTAG 59.997 43.478 0.00 0.00 31.13 3.51
19 20 2.941720 ACAACAACCGTTTAAAGCCGTA 59.058 40.909 0.00 0.00 31.13 4.02
20 21 1.744522 ACAACAACCGTTTAAAGCCGT 59.255 42.857 0.00 0.00 31.13 5.68
21 22 2.478547 ACAACAACCGTTTAAAGCCG 57.521 45.000 0.00 0.00 31.13 5.52
440 441 5.296780 TGTTTGCTTCCTCGAATCATATTCC 59.703 40.000 0.00 0.00 0.00 3.01
441 442 6.363577 TGTTTGCTTCCTCGAATCATATTC 57.636 37.500 0.00 0.00 0.00 1.75
444 445 5.879777 TCAATGTTTGCTTCCTCGAATCATA 59.120 36.000 0.00 0.00 0.00 2.15
457 460 8.885722 CAATTTGCCTAATAATCAATGTTTGCT 58.114 29.630 0.00 0.00 0.00 3.91
478 482 5.513233 AGTCATCCCAACTATGCTCAATTT 58.487 37.500 0.00 0.00 0.00 1.82
491 495 3.270027 CGCAGAAACATAGTCATCCCAA 58.730 45.455 0.00 0.00 0.00 4.12
495 499 2.609459 CCACCGCAGAAACATAGTCATC 59.391 50.000 0.00 0.00 0.00 2.92
531 536 5.296035 GCCGTGCCAAGTCTAAAACTATAAT 59.704 40.000 0.00 0.00 37.17 1.28
534 539 3.007635 GCCGTGCCAAGTCTAAAACTAT 58.992 45.455 0.00 0.00 37.17 2.12
535 540 2.038033 AGCCGTGCCAAGTCTAAAACTA 59.962 45.455 0.00 0.00 37.17 2.24
583 588 8.634444 AGTATGAGAGAGTAACGCAGAAAATAT 58.366 33.333 0.00 0.00 0.00 1.28
585 590 6.754209 CAGTATGAGAGAGTAACGCAGAAAAT 59.246 38.462 0.00 0.00 39.69 1.82
606 611 9.961265 GTAGTTTACATGCACACTATATCAGTA 57.039 33.333 0.00 0.00 34.98 2.74
608 613 8.871686 TGTAGTTTACATGCACACTATATCAG 57.128 34.615 0.00 0.00 32.89 2.90
615 620 4.319477 CGCTTTGTAGTTTACATGCACACT 60.319 41.667 0.00 0.00 38.68 3.55
660 665 6.978674 AGAGATTGGGACGACAGATATTTA 57.021 37.500 0.00 0.00 0.00 1.40
661 666 5.878406 AGAGATTGGGACGACAGATATTT 57.122 39.130 0.00 0.00 0.00 1.40
684 689 3.119009 TCCGACCCTTATAAACCTCCA 57.881 47.619 0.00 0.00 0.00 3.86
696 703 1.292223 CACACGAACATCCGACCCT 59.708 57.895 0.00 0.00 0.00 4.34
704 711 2.631428 GCACGCACACACGAACAT 59.369 55.556 0.00 0.00 36.70 2.71
811 2387 4.841443 AGGCCTACTTAAAACAAAACCG 57.159 40.909 1.29 0.00 0.00 4.44
908 2548 1.344953 TGTTCTGCCACAGACTGGGT 61.345 55.000 7.51 0.00 40.46 4.51
954 2594 5.725110 ACTAACTAGTGGTCGTGTATACG 57.275 43.478 5.56 5.56 42.42 3.06
978 2618 2.363147 GCTCCCGACTCCTCTGGT 60.363 66.667 0.00 0.00 0.00 4.00
1010 2655 2.820037 CCGGAAGCGAGGCCTTTC 60.820 66.667 6.77 6.96 0.00 2.62
1053 2698 3.910490 GCCCAGCGCAACAAACCA 61.910 61.111 11.47 0.00 37.47 3.67
1131 2776 2.683933 GGCGAGAGGGGAAGACCA 60.684 66.667 0.00 0.00 42.91 4.02
1164 2809 1.523938 GTTCCCTATGCAGGACGGC 60.524 63.158 0.00 0.00 45.91 5.68
1189 2834 4.021925 GGAGGCGGTTGCAGAGGT 62.022 66.667 0.00 0.00 45.35 3.85
1320 2965 1.173913 GATTCCAAGAACCCAACCCG 58.826 55.000 0.00 0.00 0.00 5.28
1448 3094 1.740043 GCTCGTTCGTTCGATTCCCG 61.740 60.000 5.38 0.00 39.12 5.14
1455 3101 3.479269 GCTGGGCTCGTTCGTTCG 61.479 66.667 0.00 0.00 0.00 3.95
1509 3155 0.258484 TCCGAACATCCCAATGGCAT 59.742 50.000 0.00 0.00 37.19 4.40
1542 3188 5.368145 TGCAACTATGAACTCACAACTTCT 58.632 37.500 0.00 0.00 0.00 2.85
1598 3244 6.908284 CACCAAATCAGCATTGAAAACAAAAG 59.092 34.615 0.00 0.00 36.78 2.27
1602 3248 4.378774 CCACCAAATCAGCATTGAAAACA 58.621 39.130 0.00 0.00 36.78 2.83
1614 3260 2.461300 TTGACCAACCCACCAAATCA 57.539 45.000 0.00 0.00 0.00 2.57
1667 3313 7.922811 CCAAAACAATCAATTATTCTCTAGCCC 59.077 37.037 0.00 0.00 0.00 5.19
1765 3411 4.741928 AATTAAGACCCCCACTTTCTGT 57.258 40.909 0.00 0.00 0.00 3.41
1768 3414 4.587262 ACACAAATTAAGACCCCCACTTTC 59.413 41.667 0.00 0.00 0.00 2.62
1774 3420 4.637276 CCAAAACACAAATTAAGACCCCC 58.363 43.478 0.00 0.00 0.00 5.40
1897 3544 2.051345 GCCACGTTGCCGAAACAG 60.051 61.111 0.00 0.00 38.84 3.16
1928 3575 3.997021 GGTGATTAGAACCTCACTGTGTG 59.003 47.826 7.79 5.24 41.21 3.82
1956 3603 5.869579 ACAGTTTCTGTTGGATGTATCACT 58.130 37.500 0.00 0.00 42.59 3.41
2069 3716 3.558829 CACTACCAGTTGATGCTGCATAG 59.441 47.826 16.23 9.04 35.28 2.23
2101 3748 4.003648 GCCAGAGTAAACAGTTGTGCTAT 58.996 43.478 0.00 0.00 0.00 2.97
2107 3754 1.225855 TGCGCCAGAGTAAACAGTTG 58.774 50.000 4.18 0.00 0.00 3.16
2109 3756 1.806542 CATTGCGCCAGAGTAAACAGT 59.193 47.619 4.18 0.00 0.00 3.55
2118 3765 2.938451 CTGAACTTATCATTGCGCCAGA 59.062 45.455 4.18 0.00 37.44 3.86
2124 3771 2.288666 TCCGCCTGAACTTATCATTGC 58.711 47.619 0.00 0.00 37.44 3.56
2142 3789 5.935206 CAGGAGAGAAAGAAAGGTTTACTCC 59.065 44.000 0.00 0.00 40.11 3.85
2150 3797 2.304180 TCCTGCAGGAGAGAAAGAAAGG 59.696 50.000 32.00 1.41 39.78 3.11
2167 3814 3.703420 CCGTTACTTCGGTAAGATCCTG 58.297 50.000 0.00 0.00 44.77 3.86
2178 3825 9.079833 TGAAATAAGAAGATAACCGTTACTTCG 57.920 33.333 18.06 0.00 42.09 3.79
2245 3892 2.005451 CCAGGAGAGTTCGCATTTCAG 58.995 52.381 0.00 0.00 0.00 3.02
2250 3897 1.066573 CAAGACCAGGAGAGTTCGCAT 60.067 52.381 0.00 0.00 0.00 4.73
2251 3898 0.318441 CAAGACCAGGAGAGTTCGCA 59.682 55.000 0.00 0.00 0.00 5.10
2252 3899 0.318762 ACAAGACCAGGAGAGTTCGC 59.681 55.000 0.00 0.00 0.00 4.70
2253 3900 1.341531 ACACAAGACCAGGAGAGTTCG 59.658 52.381 0.00 0.00 0.00 3.95
2254 3901 3.477210 AACACAAGACCAGGAGAGTTC 57.523 47.619 0.00 0.00 0.00 3.01
2256 3903 3.322254 CAGTAACACAAGACCAGGAGAGT 59.678 47.826 0.00 0.00 0.00 3.24
2257 3904 3.574396 TCAGTAACACAAGACCAGGAGAG 59.426 47.826 0.00 0.00 0.00 3.20
2258 3905 3.572642 TCAGTAACACAAGACCAGGAGA 58.427 45.455 0.00 0.00 0.00 3.71
2259 3906 4.336889 TTCAGTAACACAAGACCAGGAG 57.663 45.455 0.00 0.00 0.00 3.69
2260 3907 4.764050 TTTCAGTAACACAAGACCAGGA 57.236 40.909 0.00 0.00 0.00 3.86
2261 3908 4.821805 ACATTTCAGTAACACAAGACCAGG 59.178 41.667 0.00 0.00 0.00 4.45
2307 3954 0.892755 TAGCACAGGGTAGTTGGACG 59.107 55.000 0.00 0.00 0.00 4.79
2317 3964 1.134007 TCATGGAGCATTAGCACAGGG 60.134 52.381 0.00 0.00 45.49 4.45
2318 3965 2.336945 TCATGGAGCATTAGCACAGG 57.663 50.000 0.00 0.00 45.49 4.00
2321 3968 2.686915 AGCTTTCATGGAGCATTAGCAC 59.313 45.455 19.54 0.00 45.49 4.40
2402 4049 5.297029 GGATTGCTTATCAAGTTCAGGTACC 59.703 44.000 2.73 2.73 38.22 3.34
2473 4120 6.845302 TGCAAGTTCTAACTGCATAATCAAG 58.155 36.000 12.73 0.00 39.66 3.02
2512 4159 8.417106 TCCAAAATCACTGCAAAGTACAAATAA 58.583 29.630 0.00 0.00 0.00 1.40
2726 4373 6.609212 ACAGTAAGAATCAAGCAGAGGATAGA 59.391 38.462 0.00 0.00 0.00 1.98
2787 4434 6.628919 AAAACGTATAACCTTGTGCTTTCT 57.371 33.333 0.00 0.00 0.00 2.52
2834 4481 2.978156 TCAGAGGAAGGCCATTGTTT 57.022 45.000 5.01 0.00 36.29 2.83
3020 4667 4.136796 CTGTTTCTTGACCAGAACATCCA 58.863 43.478 0.00 0.00 41.56 3.41
3432 5079 2.320781 AGCATCTCCTTACGCACCTAT 58.679 47.619 0.00 0.00 0.00 2.57
3471 5118 2.287009 CGAGTGTTTTTGGAAGAGGTGC 60.287 50.000 0.00 0.00 0.00 5.01
3665 5312 3.391296 GACTTCCCACCCAGCTAATCATA 59.609 47.826 0.00 0.00 0.00 2.15
3703 5353 3.222173 AGCAAACATCTACACCCACAA 57.778 42.857 0.00 0.00 0.00 3.33
3709 5359 6.521133 CGATTCTTCAAAGCAAACATCTACAC 59.479 38.462 0.00 0.00 0.00 2.90
3751 5401 5.594199 ACCTAGGGGTGTTCATTTTACTT 57.406 39.130 14.81 0.00 45.43 2.24
3905 5555 0.036952 TGTAGCTCCTTGACAGCAGC 60.037 55.000 0.00 0.00 39.56 5.25
4098 5748 3.058914 CCGTGTTTAACTTCAGCCTTCTG 60.059 47.826 0.00 0.00 41.67 3.02
4116 5766 2.350388 GCTGTCAAACCATGTTACCGTG 60.350 50.000 0.00 0.00 0.00 4.94
4126 5776 5.664457 CATCTAGATGTAGCTGTCAAACCA 58.336 41.667 22.42 0.00 34.23 3.67
4422 6074 2.615447 ACAGTTCACTCACATGTTGCAG 59.385 45.455 0.00 0.00 0.00 4.41
4461 6113 1.296392 CATCTGGTGCGACCCAAGA 59.704 57.895 3.33 1.62 37.50 3.02
4506 6158 7.867403 ACAAGGTTTATGTACATCAAAAGCAAG 59.133 33.333 24.54 19.87 32.58 4.01
4564 6216 4.911610 CCAGTCATTCGCACTTACAAAAAG 59.088 41.667 0.00 0.00 0.00 2.27
4612 6264 0.394216 GCATGCCCCAGTGTCATACA 60.394 55.000 6.36 0.00 0.00 2.29
4623 6275 1.824230 TCTACAAAACATGCATGCCCC 59.176 47.619 26.53 0.00 0.00 5.80
4684 6336 4.511826 CCAGGCGATACACTAAAAATCTCC 59.488 45.833 0.00 0.00 0.00 3.71
4685 6337 5.116882 ACCAGGCGATACACTAAAAATCTC 58.883 41.667 0.00 0.00 0.00 2.75
4686 6338 5.099042 ACCAGGCGATACACTAAAAATCT 57.901 39.130 0.00 0.00 0.00 2.40
4687 6339 5.050295 GCTACCAGGCGATACACTAAAAATC 60.050 44.000 0.00 0.00 0.00 2.17
4695 6347 0.529992 GTGGCTACCAGGCGATACAC 60.530 60.000 0.00 0.00 44.78 2.90
4696 6348 1.820581 GTGGCTACCAGGCGATACA 59.179 57.895 0.00 0.00 44.78 2.29
4704 6356 6.071896 TCAGATATTAAGATCGTGGCTACCAG 60.072 42.308 4.50 0.00 32.34 4.00
4744 6396 5.401079 CGTGCCCTTATTTACAAAACAAGTG 59.599 40.000 0.00 0.00 0.00 3.16
4753 6405 2.289756 TGTGCTCGTGCCCTTATTTACA 60.290 45.455 7.05 0.00 38.71 2.41
4764 6416 0.527385 TTTTGCCTTTGTGCTCGTGC 60.527 50.000 1.71 1.71 40.20 5.34
4767 6419 0.102120 TGGTTTTGCCTTTGTGCTCG 59.898 50.000 0.00 0.00 38.35 5.03
4768 6420 2.036346 AGATGGTTTTGCCTTTGTGCTC 59.964 45.455 0.00 0.00 38.35 4.26
4771 6423 3.556775 CACAAGATGGTTTTGCCTTTGTG 59.443 43.478 11.29 11.29 42.31 3.33
4772 6424 3.197549 ACACAAGATGGTTTTGCCTTTGT 59.802 39.130 0.00 0.00 37.42 2.83
4782 6441 6.169557 TCAGTTACAGTACACAAGATGGTT 57.830 37.500 0.00 0.00 0.00 3.67
4790 6449 4.049546 ACGCTTTCAGTTACAGTACACA 57.950 40.909 0.00 0.00 0.00 3.72
4793 6452 6.148264 AGAAGTACGCTTTCAGTTACAGTAC 58.852 40.000 0.00 0.00 34.61 2.73
4799 6458 8.301720 TCATTTAGAGAAGTACGCTTTCAGTTA 58.698 33.333 0.00 0.00 34.61 2.24
4800 6459 7.152645 TCATTTAGAGAAGTACGCTTTCAGTT 58.847 34.615 0.00 0.00 34.61 3.16
4801 6460 6.688578 TCATTTAGAGAAGTACGCTTTCAGT 58.311 36.000 0.00 0.00 34.61 3.41
4802 6461 7.582435 TTCATTTAGAGAAGTACGCTTTCAG 57.418 36.000 0.00 0.00 34.61 3.02
4803 6462 9.647797 TTATTCATTTAGAGAAGTACGCTTTCA 57.352 29.630 0.00 0.00 34.61 2.69
4876 6535 3.302555 GTGATGACACACACTGCAAATG 58.697 45.455 7.18 0.00 45.32 2.32
4950 6627 0.447801 CTGTTGGAGCCACGCATTAC 59.552 55.000 0.00 0.00 0.00 1.89
5012 6690 2.224042 TGATGTACCTGGATCATCGTGC 60.224 50.000 20.86 7.69 40.25 5.34


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

AutoCloner maintained by Alex Coulton.