Multiple sequence alignment - TraesCS2B01G377900

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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 TraesCS2B01G377900 chr2B 100.000 4053 0 0 1 4053 540809698 540805646 0.000000e+00 7485
1 TraesCS2B01G377900 chr2D 91.764 3424 189 46 678 4053 459335708 459332330 0.000000e+00 4674
2 TraesCS2B01G377900 chr2D 88.554 664 61 7 3 659 459336423 459335768 0.000000e+00 791
3 TraesCS2B01G377900 chr2A 91.213 3437 215 33 678 4053 602653585 602650175 0.000000e+00 4593
4 TraesCS2B01G377900 chr2A 85.940 633 54 15 11 636 602655313 602654709 0.000000e+00 643
5 TraesCS2B01G377900 chr4B 82.402 1449 221 22 1378 2803 637724199 637722762 0.000000e+00 1232
6 TraesCS2B01G377900 chr4B 77.576 1378 273 28 1441 2803 637731676 637730320 0.000000e+00 800
7 TraesCS2B01G377900 chr4B 77.387 796 143 22 1441 2234 637729908 637729148 4.810000e-119 438
8 TraesCS2B01G377900 chr4B 91.111 180 16 0 1133 1312 637724594 637724415 1.130000e-60 244
9 TraesCS2B01G377900 chr4D 81.568 1492 246 22 1331 2803 497152587 497151106 0.000000e+00 1205
10 TraesCS2B01G377900 chr4D 79.363 1381 243 32 1441 2803 497160179 497158823 0.000000e+00 933
11 TraesCS2B01G377900 chr4D 78.067 1345 241 34 1441 2773 497158427 497157125 0.000000e+00 800
12 TraesCS2B01G377900 chr4D 91.111 180 16 0 1133 1312 497152980 497152801 1.130000e-60 244
13 TraesCS2B01G377900 chr5A 81.989 1438 229 22 1387 2803 676951099 676949671 0.000000e+00 1194
14 TraesCS2B01G377900 chr5A 80.886 926 132 36 1393 2302 676943998 676943102 0.000000e+00 688
15 TraesCS2B01G377900 chr5A 76.511 1307 261 33 1441 2739 676960335 676959067 0.000000e+00 671
16 TraesCS2B01G377900 chr5A 83.789 475 74 1 2332 2803 676943107 676942633 7.990000e-122 448
17 TraesCS2B01G377900 chr5A 90.751 173 16 0 1126 1298 676951561 676951389 8.760000e-57 231
18 TraesCS2B01G377900 chr3D 86.170 188 23 2 1123 1307 554717218 554717031 2.470000e-47 200
19 TraesCS2B01G377900 chr3D 77.561 205 35 8 2602 2803 237823237 237823041 3.310000e-21 113
20 TraesCS2B01G377900 chr1A 75.522 335 78 4 2047 2379 577705877 577705545 1.170000e-35 161
21 TraesCS2B01G377900 chr3B 77.209 215 38 8 2592 2803 345704080 345703874 9.210000e-22 115


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 TraesCS2B01G377900 chr2B 540805646 540809698 4052 True 7485.0 7485 100.0000 1 4053 1 chr2B.!!$R1 4052
1 TraesCS2B01G377900 chr2D 459332330 459336423 4093 True 2732.5 4674 90.1590 3 4053 2 chr2D.!!$R1 4050
2 TraesCS2B01G377900 chr2A 602650175 602655313 5138 True 2618.0 4593 88.5765 11 4053 2 chr2A.!!$R1 4042
3 TraesCS2B01G377900 chr4B 637722762 637724594 1832 True 738.0 1232 86.7565 1133 2803 2 chr4B.!!$R1 1670
4 TraesCS2B01G377900 chr4B 637729148 637731676 2528 True 619.0 800 77.4815 1441 2803 2 chr4B.!!$R2 1362
5 TraesCS2B01G377900 chr4D 497157125 497160179 3054 True 866.5 933 78.7150 1441 2803 2 chr4D.!!$R2 1362
6 TraesCS2B01G377900 chr4D 497151106 497152980 1874 True 724.5 1205 86.3395 1133 2803 2 chr4D.!!$R1 1670
7 TraesCS2B01G377900 chr5A 676949671 676951561 1890 True 712.5 1194 86.3700 1126 2803 2 chr5A.!!$R3 1677
8 TraesCS2B01G377900 chr5A 676959067 676960335 1268 True 671.0 671 76.5110 1441 2739 1 chr5A.!!$R1 1298
9 TraesCS2B01G377900 chr5A 676942633 676943998 1365 True 568.0 688 82.3375 1393 2803 2 chr5A.!!$R2 1410

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
859 1964 0.033504 TTTCCGAGCAGCTTCTTCGT 59.966 50.0 0.00 0.00 0.00 3.85 F
1561 2907 0.399376 TTAAGGCTCCCGGGATAGCA 60.399 55.0 29.88 12.11 40.61 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 5357 1.303309 CCAATGCGAACTCCTGGATC 58.697 55.0 0.0 0.0 0.00 3.36 R
3533 6686 0.535335 ACGCCTATTCTTTCTCGGCA 59.465 50.0 0.0 0.0 40.72 5.69 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 4.032960 TCCAACAGAGGCACATTACATT 57.967 40.909 0.00 0.00 0.00 2.71
49 50 1.661463 AGAAGGCCCACTCATGAAGA 58.339 50.000 0.00 0.00 0.00 2.87
89 90 3.181514 GCCGCTACAACATAACAACGATT 60.182 43.478 0.00 0.00 0.00 3.34
114 115 2.611292 CAGGCGATTCAAAGAGGTCATC 59.389 50.000 0.00 0.00 0.00 2.92
120 121 4.675408 CGATTCAAAGAGGTCATCGAGTGA 60.675 45.833 0.00 0.00 39.26 3.41
121 122 3.857549 TCAAAGAGGTCATCGAGTGAG 57.142 47.619 0.00 0.00 37.56 3.51
135 142 1.444553 GTGAGGACGAGGAAGCGTG 60.445 63.158 0.00 0.00 45.72 5.34
163 170 2.810650 CCGTCGATCTTTTGGTAGAGG 58.189 52.381 0.00 0.00 0.00 3.69
230 237 6.249035 TGACTTATGGATTTTTGAACCGAC 57.751 37.500 0.00 0.00 0.00 4.79
241 248 3.980646 TTGAACCGACAGTCCAATTTG 57.019 42.857 0.00 0.00 0.00 2.32
274 281 5.611374 ACATATTCCTGTTCCTTATGACGG 58.389 41.667 0.00 0.00 0.00 4.79
285 292 2.017049 CTTATGACGGGGGCTTTGAAG 58.983 52.381 0.00 0.00 0.00 3.02
402 410 2.105649 GCAATCCCTAAGCTCTAAGCCT 59.894 50.000 0.00 0.00 43.77 4.58
522 530 4.509970 TGTATTCAAGTGTGGTCTTGTTCG 59.490 41.667 6.38 0.00 43.44 3.95
532 540 3.852536 GTGGTCTTGTTCGATAGTTCTCG 59.147 47.826 0.00 0.00 39.99 4.04
613 621 7.465353 TGCAATGGATTCAAATTTAGAGACA 57.535 32.000 0.00 0.00 0.00 3.41
614 622 7.894708 TGCAATGGATTCAAATTTAGAGACAA 58.105 30.769 0.00 0.00 0.00 3.18
615 623 8.030692 TGCAATGGATTCAAATTTAGAGACAAG 58.969 33.333 0.00 0.00 0.00 3.16
616 624 8.246180 GCAATGGATTCAAATTTAGAGACAAGA 58.754 33.333 0.00 0.00 0.00 3.02
617 625 9.565213 CAATGGATTCAAATTTAGAGACAAGAC 57.435 33.333 0.00 0.00 0.00 3.01
618 626 8.868522 ATGGATTCAAATTTAGAGACAAGACA 57.131 30.769 0.00 0.00 0.00 3.41
659 1707 6.183810 AGATGAGATGGATGAAGCATACAA 57.816 37.500 0.00 0.00 38.28 2.41
660 1708 5.996513 AGATGAGATGGATGAAGCATACAAC 59.003 40.000 0.00 0.00 38.28 3.32
661 1709 5.363562 TGAGATGGATGAAGCATACAACT 57.636 39.130 2.50 2.50 39.88 3.16
662 1710 5.921004 GAGATGGATGAAGCATACAACTC 57.079 43.478 12.27 12.27 43.65 3.01
664 1712 5.366460 AGATGGATGAAGCATACAACTCTG 58.634 41.667 0.00 0.00 38.28 3.35
666 1714 4.507710 TGGATGAAGCATACAACTCTGTC 58.492 43.478 0.00 0.00 30.95 3.51
667 1715 4.020307 TGGATGAAGCATACAACTCTGTCA 60.020 41.667 0.00 0.00 30.95 3.58
670 1718 6.072508 GGATGAAGCATACAACTCTGTCAAAA 60.073 38.462 0.00 0.00 36.96 2.44
672 1720 6.728200 TGAAGCATACAACTCTGTCAAAAAG 58.272 36.000 0.00 0.00 36.96 2.27
673 1721 5.113502 AGCATACAACTCTGTCAAAAAGC 57.886 39.130 0.00 0.00 36.96 3.51
674 1722 3.908382 GCATACAACTCTGTCAAAAAGCG 59.092 43.478 0.00 0.00 36.96 4.68
676 1724 3.951979 ACAACTCTGTCAAAAAGCGAG 57.048 42.857 0.00 0.00 0.00 5.03
731 1821 3.328931 TGAGCTGTCTTCCTCTTCCAAAT 59.671 43.478 0.00 0.00 0.00 2.32
738 1828 5.163405 TGTCTTCCTCTTCCAAATATCTCCG 60.163 44.000 0.00 0.00 0.00 4.63
754 1844 3.575630 TCTCCGCGCTGCTTATATAAAG 58.424 45.455 5.56 0.00 0.00 1.85
767 1859 8.980481 TGCTTATATAAAGAAAGAAGGGGAAG 57.020 34.615 0.00 0.00 0.00 3.46
769 1861 9.800572 GCTTATATAAAGAAAGAAGGGGAAGAT 57.199 33.333 0.00 0.00 0.00 2.40
831 1936 4.273969 CACTACGAGATAGTCCTCCTTGTC 59.726 50.000 0.00 0.00 42.62 3.18
834 1939 2.657143 GAGATAGTCCTCCTTGTCCGT 58.343 52.381 0.00 0.00 0.00 4.69
837 1942 4.805744 AGATAGTCCTCCTTGTCCGTATT 58.194 43.478 0.00 0.00 0.00 1.89
859 1964 0.033504 TTTCCGAGCAGCTTCTTCGT 59.966 50.000 0.00 0.00 0.00 3.85
900 2011 3.895232 TCACTATCCTGCTTCCTTGTC 57.105 47.619 0.00 0.00 0.00 3.18
902 2013 1.840635 ACTATCCTGCTTCCTTGTCCC 59.159 52.381 0.00 0.00 0.00 4.46
908 2019 2.239654 CCTGCTTCCTTGTCCCTATCAA 59.760 50.000 0.00 0.00 0.00 2.57
919 2030 2.872858 GTCCCTATCAATTTCCGAGCAC 59.127 50.000 0.00 0.00 0.00 4.40
926 2037 3.486383 TCAATTTCCGAGCACCTTCTTT 58.514 40.909 0.00 0.00 0.00 2.52
1055 2167 5.328691 CGTCTTGTTTTGTTTTGTAGCTCA 58.671 37.500 0.00 0.00 0.00 4.26
1056 2168 5.227184 CGTCTTGTTTTGTTTTGTAGCTCAC 59.773 40.000 0.00 0.00 0.00 3.51
1058 2170 5.184096 TCTTGTTTTGTTTTGTAGCTCACCA 59.816 36.000 0.00 0.00 0.00 4.17
1078 2196 4.100529 CCAATGTCGATGAAGCATTTCAC 58.899 43.478 0.00 0.00 45.54 3.18
1079 2197 4.379708 CCAATGTCGATGAAGCATTTCACA 60.380 41.667 0.00 0.00 45.54 3.58
1109 2227 7.978982 TCTTCTGAAATACTAATGCTTTCTGC 58.021 34.615 0.00 0.00 43.25 4.26
1351 2643 3.829044 CCGTCCGTGGATGCCGTA 61.829 66.667 2.41 0.00 0.00 4.02
1561 2907 0.399376 TTAAGGCTCCCGGGATAGCA 60.399 55.000 29.88 12.11 40.61 3.49
1621 2967 4.719369 GCGCCTGTCGACCTCGTT 62.719 66.667 14.12 0.00 41.67 3.85
1894 5011 3.950254 CTCGACGAGCGCCGGTAT 61.950 66.667 12.67 2.05 43.93 2.73
1906 5023 1.299620 CCGGTATAGGAACGGCGTG 60.300 63.158 15.70 0.00 41.23 5.34
2282 5405 1.980232 TCCGGGCTTTACGAGAGCA 60.980 57.895 0.00 0.00 41.89 4.26
2389 5512 1.174712 TGCCAAGAGCTGAAGCAACC 61.175 55.000 4.90 0.00 45.16 3.77
2631 5757 1.791103 GCGGTGGAGATCCTCGAGAG 61.791 65.000 15.71 4.11 36.20 3.20
3072 6198 7.763172 ATTAGTAGCTTTCTGAGATTGTTCG 57.237 36.000 0.00 0.00 0.00 3.95
3080 6206 2.234661 TCTGAGATTGTTCGCCACAGAT 59.765 45.455 0.00 0.00 36.48 2.90
3086 6212 6.150976 TGAGATTGTTCGCCACAGATTTAATT 59.849 34.615 0.00 0.00 36.48 1.40
3124 6250 9.529325 CAGTAGCTAATATACACTTACAAAGCA 57.471 33.333 0.00 0.00 0.00 3.91
3206 6332 9.177608 TCTTGATAATGTTTTGGATGTAGGAAG 57.822 33.333 0.00 0.00 0.00 3.46
3241 6367 3.006323 TGCTCTGAAGAGTTCTCTGAACC 59.994 47.826 9.03 0.25 43.85 3.62
3362 6499 9.979578 ATTATTTGTGATGCTACTTGTCAAAAA 57.020 25.926 0.00 0.00 34.58 1.94
3392 6530 7.604657 TTTGGAGATAGAGTTCCTCTTATCC 57.395 40.000 0.00 5.80 41.50 2.59
3398 6537 8.257602 AGATAGAGTTCCTCTTATCCTTTTCC 57.742 38.462 0.00 0.00 41.50 3.13
3399 6538 8.071229 AGATAGAGTTCCTCTTATCCTTTTCCT 58.929 37.037 0.00 0.00 41.50 3.36
3407 6546 7.939781 TCCTCTTATCCTTTTCCTTGGTTTAT 58.060 34.615 0.00 0.00 0.00 1.40
3410 6549 4.983671 ATCCTTTTCCTTGGTTTATCGC 57.016 40.909 0.00 0.00 0.00 4.58
3415 6554 5.048013 CCTTTTCCTTGGTTTATCGCTTTCT 60.048 40.000 0.00 0.00 0.00 2.52
3420 6559 3.695830 TGGTTTATCGCTTTCTGTCCT 57.304 42.857 0.00 0.00 0.00 3.85
3449 6589 9.776158 TTTATATATAAAGCACACAACCAAACG 57.224 29.630 12.90 0.00 0.00 3.60
3450 6590 5.699097 ATATAAAGCACACAACCAAACGT 57.301 34.783 0.00 0.00 0.00 3.99
3455 6595 4.379339 AGCACACAACCAAACGTTAAAT 57.621 36.364 0.00 0.00 31.77 1.40
3484 6627 2.387757 AGCCCTCAAACAAAGCAGAAA 58.612 42.857 0.00 0.00 0.00 2.52
3489 6632 5.278957 GCCCTCAAACAAAGCAGAAAATAGA 60.279 40.000 0.00 0.00 0.00 1.98
3490 6633 6.738453 GCCCTCAAACAAAGCAGAAAATAGAA 60.738 38.462 0.00 0.00 0.00 2.10
3517 6660 1.660607 CAGACAACATTCATCGGACGG 59.339 52.381 0.00 0.00 0.00 4.79
3533 6686 2.890474 GGATGCCGCGACAACGAT 60.890 61.111 8.23 0.00 42.66 3.73
3534 6687 2.321060 GATGCCGCGACAACGATG 59.679 61.111 8.23 0.00 42.66 3.84
3535 6688 3.773649 GATGCCGCGACAACGATGC 62.774 63.158 8.23 0.00 42.66 3.91
3539 6692 3.902063 CGCGACAACGATGCCGAG 61.902 66.667 5.42 0.00 42.66 4.63
3540 6693 2.506217 GCGACAACGATGCCGAGA 60.506 61.111 5.42 0.00 42.66 4.04
3541 6694 2.092291 GCGACAACGATGCCGAGAA 61.092 57.895 5.42 0.00 42.66 2.87
3542 6695 1.623081 GCGACAACGATGCCGAGAAA 61.623 55.000 5.42 0.00 42.66 2.52
3543 6696 0.366871 CGACAACGATGCCGAGAAAG 59.633 55.000 0.00 0.00 42.66 2.62
3544 6697 1.710013 GACAACGATGCCGAGAAAGA 58.290 50.000 0.00 0.00 39.50 2.52
3545 6698 2.066262 GACAACGATGCCGAGAAAGAA 58.934 47.619 0.00 0.00 39.50 2.52
3546 6699 2.673368 GACAACGATGCCGAGAAAGAAT 59.327 45.455 0.00 0.00 39.50 2.40
3603 6759 3.058016 TCACCTTAGTTCTACGACAACGG 60.058 47.826 0.00 0.00 44.46 4.44
3610 6766 0.675083 TCTACGACAACGGCCTCAAA 59.325 50.000 0.00 0.00 44.46 2.69
3617 6773 0.598065 CAACGGCCTCAAAAGGGAAG 59.402 55.000 0.00 0.00 43.58 3.46
3619 6775 2.690778 CGGCCTCAAAAGGGAAGCG 61.691 63.158 0.00 0.00 43.58 4.68
3637 6793 2.699910 GCACAAAGCGTCACAATCG 58.300 52.632 0.00 0.00 0.00 3.34
3640 6796 0.506932 ACAAAGCGTCACAATCGTCG 59.493 50.000 0.00 0.00 0.00 5.12
3644 6800 2.681666 CGTCACAATCGTCGCGTC 59.318 61.111 5.77 0.00 0.00 5.19
3677 6833 1.273327 CAATGCTTTCACCTGGAACCC 59.727 52.381 0.00 0.00 34.56 4.11
3678 6834 0.779997 ATGCTTTCACCTGGAACCCT 59.220 50.000 0.00 0.00 34.56 4.34
3679 6835 0.178992 TGCTTTCACCTGGAACCCTG 60.179 55.000 0.00 0.00 34.56 4.45
3680 6836 0.110486 GCTTTCACCTGGAACCCTGA 59.890 55.000 0.00 0.00 34.56 3.86
3681 6837 1.884067 GCTTTCACCTGGAACCCTGAG 60.884 57.143 0.00 0.00 34.56 3.35
3682 6838 1.699634 CTTTCACCTGGAACCCTGAGA 59.300 52.381 0.00 0.00 34.56 3.27
3683 6839 1.352083 TTCACCTGGAACCCTGAGAG 58.648 55.000 0.00 0.00 0.00 3.20
3694 6850 3.450028 CCTGAGAGGGAAAAGCGAG 57.550 57.895 0.00 0.00 0.00 5.03
3696 6852 0.610687 CTGAGAGGGAAAAGCGAGGT 59.389 55.000 0.00 0.00 0.00 3.85
3707 6863 2.964438 AAGCGAGGTTGCGACAACGA 62.964 55.000 20.78 0.00 42.66 3.85
3797 6953 1.658114 CTTCCACGAGTCACCACGA 59.342 57.895 0.00 0.00 0.00 4.35
3801 6957 4.039357 ACGAGTCACCACGAGGCG 62.039 66.667 0.00 0.00 39.06 5.52
3823 6979 1.160137 GTCAGCCATTGCGAGAAAGT 58.840 50.000 0.00 0.00 44.33 2.66
3841 6997 1.202770 AGTTGAAACCTCCAGAACCCG 60.203 52.381 0.00 0.00 0.00 5.28
3844 7000 1.278127 TGAAACCTCCAGAACCCGATC 59.722 52.381 0.00 0.00 0.00 3.69
3878 7037 2.034376 ACAGAGAGGACGCGAGGT 59.966 61.111 15.93 0.00 0.00 3.85
3910 7069 3.005539 ACCTCTCGCCAGCCACAT 61.006 61.111 0.00 0.00 0.00 3.21
3915 7074 3.610619 CTCGCCAGCCACATGACCA 62.611 63.158 0.00 0.00 0.00 4.02
3933 7092 1.608055 CAAGAAGCACACCATCACCA 58.392 50.000 0.00 0.00 0.00 4.17
3935 7094 0.473755 AGAAGCACACCATCACCACA 59.526 50.000 0.00 0.00 0.00 4.17
3936 7095 1.133823 AGAAGCACACCATCACCACAA 60.134 47.619 0.00 0.00 0.00 3.33
4002 7161 3.710631 TCCCCAGCATCCCTCCCT 61.711 66.667 0.00 0.00 0.00 4.20
4018 7177 0.329261 CCCTGAACCTCTCAATGGCA 59.671 55.000 0.00 0.00 32.17 4.92
4027 7186 3.256631 ACCTCTCAATGGCATCAAAACAC 59.743 43.478 0.00 0.00 0.00 3.32
4033 7192 0.665835 TGGCATCAAAACACGTGGAC 59.334 50.000 21.57 2.18 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.733150 GCCTCTGTTGGATTTACCGC 59.267 55.000 0.00 0.00 42.61 5.68
1 2 1.737793 GTGCCTCTGTTGGATTTACCG 59.262 52.381 0.00 0.00 42.61 4.02
8 9 3.719268 ATGTAATGTGCCTCTGTTGGA 57.281 42.857 0.00 0.00 0.00 3.53
29 30 2.832838 TCTTCATGAGTGGGCCTTCTA 58.167 47.619 4.53 0.00 0.00 2.10
49 50 0.039888 GCGGTTGCACGTGGTTATTT 60.040 50.000 18.88 0.00 42.15 1.40
114 115 1.137825 GCTTCCTCGTCCTCACTCG 59.862 63.158 0.00 0.00 0.00 4.18
120 121 3.382832 CCCACGCTTCCTCGTCCT 61.383 66.667 0.00 0.00 41.21 3.85
121 122 4.452733 CCCCACGCTTCCTCGTCC 62.453 72.222 0.00 0.00 41.21 4.79
140 147 1.659098 CTACCAAAAGATCGACGGCAC 59.341 52.381 0.00 0.00 0.00 5.01
203 210 7.229707 TCGGTTCAAAAATCCATAAGTCAAAGA 59.770 33.333 0.00 0.00 0.00 2.52
213 220 3.506067 GGACTGTCGGTTCAAAAATCCAT 59.494 43.478 1.07 0.00 0.00 3.41
216 223 4.561735 TTGGACTGTCGGTTCAAAAATC 57.438 40.909 2.76 0.00 40.19 2.17
218 225 4.993029 AATTGGACTGTCGGTTCAAAAA 57.007 36.364 9.65 0.00 45.45 1.94
223 230 4.062991 AGTACAAATTGGACTGTCGGTTC 58.937 43.478 10.53 0.00 40.76 3.62
241 248 8.788325 AGGAACAGGAATATGTAACAAAGTAC 57.212 34.615 0.00 0.00 31.70 2.73
259 266 0.463833 GCCCCCGTCATAAGGAACAG 60.464 60.000 0.00 0.00 0.00 3.16
327 334 8.020819 TGAATTTATCGTTCATGAAACTTGGTC 58.979 33.333 10.35 2.51 35.59 4.02
376 384 1.134371 AGAGCTTAGGGATTGCGGTTC 60.134 52.381 0.00 0.00 0.00 3.62
381 389 2.105649 AGGCTTAGAGCTTAGGGATTGC 59.894 50.000 0.00 0.00 41.99 3.56
402 410 7.713073 CCAAGTTCATTTGCTTTTAGGGTTTAA 59.287 33.333 0.00 0.00 0.00 1.52
522 530 7.576750 TGTATTTGTTGTGACGAGAACTATC 57.423 36.000 0.00 0.00 0.00 2.08
532 540 7.944120 CGTTTGCATATTTGTATTTGTTGTGAC 59.056 33.333 0.00 0.00 0.00 3.67
566 574 6.199719 GCATCTTTTGAACAGAAAGTCCAAAG 59.800 38.462 0.00 0.00 35.95 2.77
613 621 8.380742 TCTCCCATACTTCTTTATCTTGTCTT 57.619 34.615 0.00 0.00 0.00 3.01
614 622 7.979786 TCTCCCATACTTCTTTATCTTGTCT 57.020 36.000 0.00 0.00 0.00 3.41
615 623 8.424918 TCATCTCCCATACTTCTTTATCTTGTC 58.575 37.037 0.00 0.00 0.00 3.18
616 624 8.324191 TCATCTCCCATACTTCTTTATCTTGT 57.676 34.615 0.00 0.00 0.00 3.16
617 625 8.646004 TCTCATCTCCCATACTTCTTTATCTTG 58.354 37.037 0.00 0.00 0.00 3.02
618 626 8.789767 TCTCATCTCCCATACTTCTTTATCTT 57.210 34.615 0.00 0.00 0.00 2.40
623 631 5.907662 TCCATCTCATCTCCCATACTTCTTT 59.092 40.000 0.00 0.00 0.00 2.52
659 1707 4.662145 CAAAACTCGCTTTTTGACAGAGT 58.338 39.130 13.21 0.00 45.54 3.24
660 1708 3.483558 GCAAAACTCGCTTTTTGACAGAG 59.516 43.478 19.55 0.00 45.54 3.35
661 1709 3.128589 AGCAAAACTCGCTTTTTGACAGA 59.871 39.130 19.55 0.00 45.54 3.41
662 1710 3.438360 AGCAAAACTCGCTTTTTGACAG 58.562 40.909 19.55 0.00 45.54 3.51
731 1821 4.976224 TTATATAAGCAGCGCGGAGATA 57.024 40.909 13.03 5.37 0.00 1.98
738 1828 6.366630 CCTTCTTTCTTTATATAAGCAGCGC 58.633 40.000 0.00 0.00 0.00 5.92
754 1844 6.596309 AAACAATGATCTTCCCCTTCTTTC 57.404 37.500 0.00 0.00 0.00 2.62
767 1859 4.508124 CCTCGTAGTGCCTAAACAATGATC 59.492 45.833 0.00 0.00 0.00 2.92
769 1861 3.259876 ACCTCGTAGTGCCTAAACAATGA 59.740 43.478 0.00 0.00 0.00 2.57
831 1936 3.131396 AGCTGCTCGGAAATTAATACGG 58.869 45.455 0.00 2.08 0.00 4.02
834 1939 5.234329 CGAAGAAGCTGCTCGGAAATTAATA 59.766 40.000 1.00 0.00 0.00 0.98
837 1942 2.930040 CGAAGAAGCTGCTCGGAAATTA 59.070 45.455 1.00 0.00 0.00 1.40
900 2011 2.158755 AGGTGCTCGGAAATTGATAGGG 60.159 50.000 0.00 0.00 0.00 3.53
902 2013 4.446371 AGAAGGTGCTCGGAAATTGATAG 58.554 43.478 0.00 0.00 0.00 2.08
908 2019 1.541588 GCAAAGAAGGTGCTCGGAAAT 59.458 47.619 0.00 0.00 39.00 2.17
919 2030 1.438651 TGATTCGTCCGCAAAGAAGG 58.561 50.000 0.00 0.00 0.00 3.46
926 2037 1.521457 GCCAGATGATTCGTCCGCA 60.521 57.895 2.18 0.00 0.00 5.69
994 2105 4.357325 TGCTTAGTTCCTTCCATCTCTCT 58.643 43.478 0.00 0.00 0.00 3.10
1055 2167 3.758023 TGAAATGCTTCATCGACATTGGT 59.242 39.130 0.00 0.00 36.62 3.67
1056 2168 4.100529 GTGAAATGCTTCATCGACATTGG 58.899 43.478 0.00 0.00 43.39 3.16
1058 2170 5.375417 TTGTGAAATGCTTCATCGACATT 57.625 34.783 0.00 0.00 43.39 2.71
1115 2236 2.373524 TTCGTCTGCGTGCAAAGCAC 62.374 55.000 13.32 11.86 46.42 4.40
1131 2252 1.645455 CAGATGGCGCAAGGATTCG 59.355 57.895 10.83 0.00 38.28 3.34
1176 2297 2.270205 CCGTGAAGATGGCCTGCT 59.730 61.111 3.32 0.00 0.00 4.24
1351 2643 3.812019 CGTACTCGCCGAGGCTGT 61.812 66.667 19.61 12.62 39.32 4.40
1621 2967 1.138883 GCTGACATCGAGCACCGTA 59.861 57.895 0.00 0.00 39.75 4.02
1642 2988 2.747460 TTGCTCCCGTGCATGCTC 60.747 61.111 20.33 14.84 42.96 4.26
1894 5011 2.872557 CTCGACACGCCGTTCCTA 59.127 61.111 0.00 0.00 0.00 2.94
1925 5042 4.309950 GTTGTCCTGGCCGTCGGT 62.310 66.667 13.94 0.00 0.00 4.69
2234 5357 1.303309 CCAATGCGAACTCCTGGATC 58.697 55.000 0.00 0.00 0.00 3.36
2239 5362 1.448540 CGAGCCAATGCGAACTCCT 60.449 57.895 0.00 0.00 44.33 3.69
2310 5433 1.816835 AGAGTTCGCCGACTACAATCA 59.183 47.619 0.00 0.00 0.00 2.57
3049 6175 5.577164 GCGAACAATCTCAGAAAGCTACTAA 59.423 40.000 0.00 0.00 0.00 2.24
3072 6198 7.279981 GGTTTCCCAAATAATTAAATCTGTGGC 59.720 37.037 0.00 0.00 0.00 5.01
3080 6206 8.658840 AGCTACTGGTTTCCCAAATAATTAAA 57.341 30.769 0.00 0.00 41.27 1.52
3206 6332 3.698029 TCAGAGCAGAAACAAAGCAAC 57.302 42.857 0.00 0.00 0.00 4.17
3337 6474 9.979578 ATTTTTGACAAGTAGCATCACAAATAA 57.020 25.926 0.00 0.00 33.26 1.40
3389 6527 4.600062 AGCGATAAACCAAGGAAAAGGAT 58.400 39.130 0.00 0.00 0.00 3.24
3390 6528 4.028993 AGCGATAAACCAAGGAAAAGGA 57.971 40.909 0.00 0.00 0.00 3.36
3391 6529 4.783764 AAGCGATAAACCAAGGAAAAGG 57.216 40.909 0.00 0.00 0.00 3.11
3392 6530 5.858581 CAGAAAGCGATAAACCAAGGAAAAG 59.141 40.000 0.00 0.00 0.00 2.27
3398 6537 4.003648 AGGACAGAAAGCGATAAACCAAG 58.996 43.478 0.00 0.00 0.00 3.61
3399 6538 3.751175 CAGGACAGAAAGCGATAAACCAA 59.249 43.478 0.00 0.00 0.00 3.67
3407 6546 2.831685 TAAAGCAGGACAGAAAGCGA 57.168 45.000 0.00 0.00 0.00 4.93
3441 6581 6.643360 GCTTCAATACCATTTAACGTTTGGTT 59.357 34.615 24.11 12.03 40.87 3.67
3442 6582 6.153756 GCTTCAATACCATTTAACGTTTGGT 58.846 36.000 22.89 22.89 45.48 3.67
3449 6589 6.524101 TTGAGGGCTTCAATACCATTTAAC 57.476 37.500 8.09 0.00 40.82 2.01
3450 6590 6.495181 TGTTTGAGGGCTTCAATACCATTTAA 59.505 34.615 13.13 0.00 44.90 1.52
3455 6595 3.517296 TGTTTGAGGGCTTCAATACCA 57.483 42.857 13.13 7.67 44.90 3.25
3496 6639 2.337583 CGTCCGATGAATGTTGTCTGT 58.662 47.619 0.00 0.00 0.00 3.41
3497 6640 1.660607 CCGTCCGATGAATGTTGTCTG 59.339 52.381 0.00 0.00 0.00 3.51
3517 6660 2.321060 CATCGTTGTCGCGGCATC 59.679 61.111 16.97 13.90 36.96 3.91
3531 6684 1.795286 CGCCTATTCTTTCTCGGCATC 59.205 52.381 0.00 0.00 40.72 3.91
3533 6686 0.535335 ACGCCTATTCTTTCTCGGCA 59.465 50.000 0.00 0.00 40.72 5.69
3534 6687 1.593469 GAACGCCTATTCTTTCTCGGC 59.407 52.381 0.00 0.00 37.40 5.54
3535 6688 2.159085 AGGAACGCCTATTCTTTCTCGG 60.159 50.000 0.00 0.00 44.74 4.63
3536 6689 3.166489 AGGAACGCCTATTCTTTCTCG 57.834 47.619 0.00 0.00 44.74 4.04
3537 6690 6.256104 GTCTTTAGGAACGCCTATTCTTTCTC 59.744 42.308 0.00 0.00 45.96 2.87
3538 6691 6.070710 AGTCTTTAGGAACGCCTATTCTTTCT 60.071 38.462 0.00 0.00 45.96 2.52
3539 6692 6.107343 AGTCTTTAGGAACGCCTATTCTTTC 58.893 40.000 0.00 0.00 45.96 2.62
3540 6693 6.051179 AGTCTTTAGGAACGCCTATTCTTT 57.949 37.500 0.00 0.00 45.96 2.52
3541 6694 5.678955 AGTCTTTAGGAACGCCTATTCTT 57.321 39.130 0.00 0.00 45.96 2.52
3542 6695 5.655532 TGTAGTCTTTAGGAACGCCTATTCT 59.344 40.000 0.00 0.00 45.96 2.40
3543 6696 5.747675 GTGTAGTCTTTAGGAACGCCTATTC 59.252 44.000 0.00 0.00 45.96 1.75
3544 6697 5.186409 TGTGTAGTCTTTAGGAACGCCTATT 59.814 40.000 0.00 0.00 45.96 1.73
3545 6698 4.708421 TGTGTAGTCTTTAGGAACGCCTAT 59.292 41.667 0.00 0.00 45.96 2.57
3546 6699 4.081406 TGTGTAGTCTTTAGGAACGCCTA 58.919 43.478 0.00 0.00 44.74 3.93
3550 6703 4.092968 GGCATTGTGTAGTCTTTAGGAACG 59.907 45.833 0.00 0.00 0.00 3.95
3558 6711 2.884639 GTTGGTGGCATTGTGTAGTCTT 59.115 45.455 0.00 0.00 0.00 3.01
3603 6759 2.268076 TGCGCTTCCCTTTTGAGGC 61.268 57.895 9.73 0.00 34.29 4.70
3610 6766 3.042560 GCTTTGTGCGCTTCCCTT 58.957 55.556 9.73 0.00 0.00 3.95
3619 6775 0.041312 ACGATTGTGACGCTTTGTGC 60.041 50.000 0.00 0.00 38.57 4.57
3637 6793 2.582202 TACATTCCGTCGGACGCGAC 62.582 60.000 24.26 6.56 40.91 5.19
3640 6796 0.733566 TTGTACATTCCGTCGGACGC 60.734 55.000 24.26 9.75 40.91 5.19
3644 6800 1.651987 AGCATTGTACATTCCGTCGG 58.348 50.000 4.39 4.39 0.00 4.79
3648 6804 3.440173 AGGTGAAAGCATTGTACATTCCG 59.560 43.478 0.00 0.00 36.26 4.30
3653 6809 3.500448 TCCAGGTGAAAGCATTGTACA 57.500 42.857 0.00 0.00 36.26 2.90
3677 6833 0.610687 ACCTCGCTTTTCCCTCTCAG 59.389 55.000 0.00 0.00 0.00 3.35
3678 6834 1.056660 AACCTCGCTTTTCCCTCTCA 58.943 50.000 0.00 0.00 0.00 3.27
3679 6835 1.443802 CAACCTCGCTTTTCCCTCTC 58.556 55.000 0.00 0.00 0.00 3.20
3680 6836 0.606673 GCAACCTCGCTTTTCCCTCT 60.607 55.000 0.00 0.00 0.00 3.69
3681 6837 1.876664 GCAACCTCGCTTTTCCCTC 59.123 57.895 0.00 0.00 0.00 4.30
3682 6838 1.966451 CGCAACCTCGCTTTTCCCT 60.966 57.895 0.00 0.00 0.00 4.20
3683 6839 1.964373 TCGCAACCTCGCTTTTCCC 60.964 57.895 0.00 0.00 0.00 3.97
3686 6842 0.028902 GTTGTCGCAACCTCGCTTTT 59.971 50.000 10.43 0.00 0.00 2.27
3694 6850 1.155424 TTGAGGTCGTTGTCGCAACC 61.155 55.000 14.31 4.69 35.20 3.77
3696 6852 0.103390 TCTTGAGGTCGTTGTCGCAA 59.897 50.000 0.00 0.00 36.96 4.85
3707 6863 0.331954 TACCGCTCTCCTCTTGAGGT 59.668 55.000 15.44 0.00 41.76 3.85
3766 6922 3.680490 TCGTGGAAGCAACCATATGAAA 58.320 40.909 3.65 0.00 42.17 2.69
3801 6957 1.442769 TTCTCGCAATGGCTGACTTC 58.557 50.000 0.00 0.00 38.10 3.01
3813 6969 2.218603 GGAGGTTTCAACTTTCTCGCA 58.781 47.619 0.00 0.00 0.00 5.10
3815 6971 3.728845 TCTGGAGGTTTCAACTTTCTCG 58.271 45.455 0.00 0.00 0.00 4.04
3823 6979 1.133363 TCGGGTTCTGGAGGTTTCAA 58.867 50.000 0.00 0.00 0.00 2.69
3878 7037 1.385347 AGGTGTTGAGGTGGGTGGA 60.385 57.895 0.00 0.00 0.00 4.02
3910 7069 1.142667 TGATGGTGTGCTTCTTGGTCA 59.857 47.619 0.00 0.00 0.00 4.02
3915 7074 1.133823 TGTGGTGATGGTGTGCTTCTT 60.134 47.619 0.00 0.00 0.00 2.52
3991 7150 0.985490 AGAGGTTCAGGGAGGGATGC 60.985 60.000 0.00 0.00 0.00 3.91
4002 7161 3.438216 TTGATGCCATTGAGAGGTTCA 57.562 42.857 0.00 0.00 0.00 3.18
4018 7177 0.816018 TGGCGTCCACGTGTTTTGAT 60.816 50.000 15.65 0.00 42.22 2.57
4033 7192 1.379977 TCCCCTCTAGTCAGTGGCG 60.380 63.158 0.00 0.00 34.62 5.69


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

AutoCloner maintained by Alex Coulton.