Multiple sequence alignment - TraesCS5B01G545500

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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 TraesCS5B01G545500 chr5B 100.000 4163 0 0 1 4163 697852900 697848738 0.000000e+00 7688.0
1 TraesCS5B01G545500 chr5B 82.163 1267 204 11 1913 3165 698453902 698452644 0.000000e+00 1068.0
2 TraesCS5B01G545500 chr5B 82.527 372 54 5 3653 4013 697835205 697834834 2.420000e-82 316.0
3 TraesCS5B01G545500 chr5B 88.034 117 11 3 601 715 165290601 165290716 7.260000e-28 135.0
4 TraesCS5B01G545500 chr5D 91.247 3416 186 49 1 3358 552708309 552711669 0.000000e+00 4547.0
5 TraesCS5B01G545500 chr5D 90.045 221 9 5 3395 3613 552711670 552711879 1.470000e-69 274.0
6 TraesCS5B01G545500 chr5D 88.710 124 10 4 601 722 262765979 262765858 9.320000e-32 148.0
7 TraesCS5B01G545500 chr5D 90.265 113 10 1 601 713 142126853 142126742 3.350000e-31 147.0
8 TraesCS5B01G545500 chr4A 94.027 1942 64 17 1 1921 615440268 615438358 0.000000e+00 2896.0
9 TraesCS5B01G545500 chr4A 94.875 1444 65 2 1909 3343 615438324 615436881 0.000000e+00 2248.0
10 TraesCS5B01G545500 chr4A 78.751 1313 241 23 1932 3229 615942382 615941093 0.000000e+00 845.0
11 TraesCS5B01G545500 chr4A 84.368 838 77 31 3342 4147 615436798 615435983 0.000000e+00 773.0
12 TraesCS5B01G545500 chr3A 75.107 1169 213 44 1986 3109 9731531 9730396 3.770000e-130 475.0
13 TraesCS5B01G545500 chr3A 73.868 1148 257 32 1986 3101 9522534 9523670 6.440000e-113 418.0
14 TraesCS5B01G545500 chr3B 74.468 987 234 15 1986 2963 6243873 6244850 1.080000e-110 411.0
15 TraesCS5B01G545500 chr3B 91.111 90 8 0 601 690 381366295 381366384 5.650000e-24 122.0
16 TraesCS5B01G545500 chr5A 89.381 113 11 1 601 713 174460179 174460068 1.560000e-29 141.0
17 TraesCS5B01G545500 chr5A 93.103 58 4 0 716 773 515504031 515504088 7.420000e-13 86.1
18 TraesCS5B01G545500 chr6B 87.611 113 9 3 601 713 274873835 274873728 4.370000e-25 126.0
19 TraesCS5B01G545500 chr6B 84.375 96 11 4 716 809 34000525 34000432 1.590000e-14 91.6
20 TraesCS5B01G545500 chr4D 86.726 113 14 1 601 713 220168520 220168631 1.570000e-24 124.0
21 TraesCS5B01G545500 chr4D 79.412 102 17 2 714 811 113415665 113415766 7.470000e-08 69.4
22 TraesCS5B01G545500 chr6A 85.714 98 11 3 714 809 452332409 452332313 2.650000e-17 100.0
23 TraesCS5B01G545500 chr6A 91.667 60 5 0 716 775 603931326 603931267 2.670000e-12 84.2
24 TraesCS5B01G545500 chr7B 92.857 56 4 0 714 769 570184033 570184088 9.590000e-12 82.4
25 TraesCS5B01G545500 chr2B 86.667 60 6 2 716 773 482704482 482704541 9.660000e-07 65.8


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 TraesCS5B01G545500 chr5B 697848738 697852900 4162 True 7688.000000 7688 100.000 1 4163 1 chr5B.!!$R2 4162
1 TraesCS5B01G545500 chr5B 698452644 698453902 1258 True 1068.000000 1068 82.163 1913 3165 1 chr5B.!!$R3 1252
2 TraesCS5B01G545500 chr5D 552708309 552711879 3570 False 2410.500000 4547 90.646 1 3613 2 chr5D.!!$F1 3612
3 TraesCS5B01G545500 chr4A 615435983 615440268 4285 True 1972.333333 2896 91.090 1 4147 3 chr4A.!!$R2 4146
4 TraesCS5B01G545500 chr4A 615941093 615942382 1289 True 845.000000 845 78.751 1932 3229 1 chr4A.!!$R1 1297
5 TraesCS5B01G545500 chr3A 9730396 9731531 1135 True 475.000000 475 75.107 1986 3109 1 chr3A.!!$R1 1123
6 TraesCS5B01G545500 chr3A 9522534 9523670 1136 False 418.000000 418 73.868 1986 3101 1 chr3A.!!$F1 1115
7 TraesCS5B01G545500 chr3B 6243873 6244850 977 False 411.000000 411 74.468 1986 2963 1 chr3B.!!$F1 977

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
379 384 0.107456 CTGTGTTGCACCAGAGGTCT 59.893 55.0 0.00 0.0 31.02 3.85 F
1565 1591 0.486879 ATCCAAGGCCTTCAACCCAA 59.513 50.0 17.29 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1662 0.391263 GGACAACGACATGGAGGTCC 60.391 60.000 0.0 3.21 38.15 4.46 R
3275 3429 1.069022 ACATGCAAACTGACGCACATC 60.069 47.619 0.0 0.00 41.79 3.06 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
25 26 8.411318 CAGGTTCAATAGGTGATTTTAATTGC 57.589 34.615 0.00 0.00 35.70 3.56
365 370 9.903682 CAGAAAATATTGAGTTTTCATCTGTGT 57.096 29.630 12.23 0.00 44.19 3.72
379 384 0.107456 CTGTGTTGCACCAGAGGTCT 59.893 55.000 0.00 0.00 31.02 3.85
466 472 9.305925 GTGATTTTATTGTCTCAAAATGGATCC 57.694 33.333 4.20 4.20 35.14 3.36
699 705 4.142093 CCATTTCTTGCATGGGGACTAAAG 60.142 45.833 0.00 0.00 38.05 1.85
705 711 2.091720 TGCATGGGGACTAAAGATGCAT 60.092 45.455 0.00 0.00 43.34 3.96
851 862 5.245531 TGTAGGAATCTTTTGCTTGATCGT 58.754 37.500 0.00 0.00 34.97 3.73
893 914 4.644103 ATGATGAGTTTGCTACCATTGC 57.356 40.909 0.00 0.00 0.00 3.56
894 915 3.419943 TGATGAGTTTGCTACCATTGCA 58.580 40.909 0.00 0.00 38.80 4.08
895 916 4.018490 TGATGAGTTTGCTACCATTGCAT 58.982 39.130 0.00 0.00 40.34 3.96
896 917 4.463539 TGATGAGTTTGCTACCATTGCATT 59.536 37.500 0.00 0.00 40.34 3.56
897 918 4.177165 TGAGTTTGCTACCATTGCATTG 57.823 40.909 1.49 1.49 40.34 2.82
926 947 3.808726 CAGGTTAGATCGACTACGTAGCT 59.191 47.826 22.40 12.89 40.69 3.32
955 976 2.042639 GCCCATCCATTGGCCAGT 60.043 61.111 5.11 0.00 44.97 4.00
1110 1131 5.570234 ACGTCCAAATTGTTAACACTTGT 57.430 34.783 20.37 9.52 0.00 3.16
1346 1368 4.860907 CCTTGCTGTTATGCTTTCATTCAC 59.139 41.667 0.00 0.00 34.22 3.18
1414 1440 2.746904 CGAAGCAAATATGGTGGTGTGA 59.253 45.455 0.00 0.00 37.35 3.58
1492 1518 0.974383 TCCTTCGGGTTCAGGACTTC 59.026 55.000 0.00 0.00 33.99 3.01
1504 1530 4.392921 TCAGGACTTCATCGAGGATTTC 57.607 45.455 0.00 0.00 0.00 2.17
1522 1548 5.726413 GGATTTCCACAAAAAGTTGCAAACG 60.726 40.000 0.00 0.00 43.83 3.60
1540 1566 5.179555 GCAAACGAGTCTTTTCCTCATAGTT 59.820 40.000 0.00 0.00 0.00 2.24
1559 1585 3.266772 AGTTGACATATCCAAGGCCTTCA 59.733 43.478 17.29 5.03 0.00 3.02
1565 1591 0.486879 ATCCAAGGCCTTCAACCCAA 59.513 50.000 17.29 0.00 0.00 4.12
1621 1647 3.309556 CCCTAGGGTTTGGCCAGAAATTA 60.310 47.826 20.88 0.00 39.65 1.40
1632 1658 2.678336 GCCAGAAATTACGAGGTTGGAG 59.322 50.000 0.00 0.00 0.00 3.86
1633 1659 3.270877 CCAGAAATTACGAGGTTGGAGG 58.729 50.000 0.00 0.00 0.00 4.30
1634 1660 3.307480 CCAGAAATTACGAGGTTGGAGGT 60.307 47.826 0.00 0.00 0.00 3.85
1635 1661 4.324267 CAGAAATTACGAGGTTGGAGGTT 58.676 43.478 0.00 0.00 0.00 3.50
1636 1662 4.154195 CAGAAATTACGAGGTTGGAGGTTG 59.846 45.833 0.00 0.00 0.00 3.77
1637 1663 2.781681 ATTACGAGGTTGGAGGTTGG 57.218 50.000 0.00 0.00 0.00 3.77
1638 1664 1.719529 TTACGAGGTTGGAGGTTGGA 58.280 50.000 0.00 0.00 0.00 3.53
1739 1773 2.532715 AAGCAAGGGGCCTCCAGA 60.533 61.111 0.00 0.00 46.50 3.86
1796 1830 7.814264 ATTTTCTAATCCAGCGAGAATTCAT 57.186 32.000 8.44 0.00 0.00 2.57
1824 1859 2.036256 AGGGTGGCATGCCTGAAC 59.964 61.111 35.53 25.23 36.94 3.18
1832 1867 3.018856 TGGCATGCCTGAACTTTCTATG 58.981 45.455 35.53 0.00 36.94 2.23
2017 2105 1.601759 GTGACATGCACACTGGCCT 60.602 57.895 3.32 0.00 46.91 5.19
2218 2333 5.521735 CCTAATGTCTGGATTTTCAGAGACG 59.478 44.000 0.00 0.00 43.54 4.18
2371 2486 0.796927 GGGCAGCAGTCGTAAAGTTC 59.203 55.000 0.00 0.00 0.00 3.01
2390 2508 5.112686 AGTTCATCAAGGATCTTCTAACGC 58.887 41.667 0.00 0.00 0.00 4.84
2393 2511 1.136305 TCAAGGATCTTCTAACGCCGG 59.864 52.381 0.00 0.00 0.00 6.13
2493 2617 2.677524 GACCATGCAGCTGCCCAA 60.678 61.111 34.64 18.12 41.18 4.12
2502 2626 0.899720 CAGCTGCCCAATTCACCATT 59.100 50.000 0.00 0.00 0.00 3.16
2622 2749 0.339859 AGATGCTCCACAGGACCCTA 59.660 55.000 0.00 0.00 0.00 3.53
2643 2770 3.385384 CTCCTCCTGCTGGCGACA 61.385 66.667 4.42 0.00 39.59 4.35
2688 2815 0.036388 TGGGCGAGGATGTTGTTCTC 60.036 55.000 0.00 0.00 0.00 2.87
2922 3049 1.184970 TGTCATGTGGCGTCTCAGGA 61.185 55.000 1.89 1.89 0.00 3.86
3007 3152 1.856873 AAGGATGGTGGGGCTTCCA 60.857 57.895 0.00 0.00 44.79 3.53
3045 3190 5.070001 TGGGCATACATTTTACTCATAGCC 58.930 41.667 0.00 0.00 37.69 3.93
3239 3385 0.512518 CGGTGCTGTATGTGTGTGTG 59.487 55.000 0.00 0.00 0.00 3.82
3275 3429 1.933181 CATACATATACGGCGGCATGG 59.067 52.381 13.24 0.00 0.00 3.66
3306 3460 5.414454 GTCAGTTTGCATGTTAATACTGGGA 59.586 40.000 16.70 0.00 35.06 4.37
3366 3604 7.054491 AGTTGTGAAGGAACAAGCAATTTAT 57.946 32.000 0.00 0.00 40.60 1.40
3376 3614 9.740710 AGGAACAAGCAATTTATCTAACTAACT 57.259 29.630 0.00 0.00 0.00 2.24
3392 3637 9.650539 TCTAACTAACTAGTGTAGTCTGTACAG 57.349 37.037 17.17 17.17 38.26 2.74
3456 3701 1.866059 CATGTTGCATGTGCGCGAG 60.866 57.895 12.10 0.00 45.83 5.03
3462 3707 0.800683 TGCATGTGCGCGAGTAGTAC 60.801 55.000 12.10 0.00 45.83 2.73
3469 3714 0.109412 GCGCGAGTAGTACAGTTGGT 60.109 55.000 12.10 0.00 0.00 3.67
3483 3728 4.232091 ACAGTTGGTAAGAGGGAGAGAAA 58.768 43.478 0.00 0.00 0.00 2.52
3484 3729 4.284746 ACAGTTGGTAAGAGGGAGAGAAAG 59.715 45.833 0.00 0.00 0.00 2.62
3485 3730 4.528596 CAGTTGGTAAGAGGGAGAGAAAGA 59.471 45.833 0.00 0.00 0.00 2.52
3486 3731 4.775253 AGTTGGTAAGAGGGAGAGAAAGAG 59.225 45.833 0.00 0.00 0.00 2.85
3487 3732 4.676799 TGGTAAGAGGGAGAGAAAGAGA 57.323 45.455 0.00 0.00 0.00 3.10
3488 3733 4.605183 TGGTAAGAGGGAGAGAAAGAGAG 58.395 47.826 0.00 0.00 0.00 3.20
3525 3770 3.828875 ACCTGGATTGCTAAGCTAGTC 57.171 47.619 0.00 0.00 0.00 2.59
3529 3774 3.470709 TGGATTGCTAAGCTAGTCATGC 58.529 45.455 0.00 0.00 0.00 4.06
3530 3775 3.118298 TGGATTGCTAAGCTAGTCATGCA 60.118 43.478 0.00 0.00 0.00 3.96
3531 3776 4.070716 GGATTGCTAAGCTAGTCATGCAT 58.929 43.478 0.00 0.00 0.00 3.96
3532 3777 4.083431 GGATTGCTAAGCTAGTCATGCATG 60.083 45.833 21.07 21.07 0.00 4.06
3636 3915 6.686484 ATCCTTGCCTCCTTTAATTGTTTT 57.314 33.333 0.00 0.00 0.00 2.43
3714 3993 9.914834 AACTGGATAATATTTACAAAGGTAGCA 57.085 29.630 0.00 0.00 0.00 3.49
3715 3994 9.914834 ACTGGATAATATTTACAAAGGTAGCAA 57.085 29.630 0.00 0.00 0.00 3.91
3749 4028 4.546674 ACAGGTTTGACCAATTCCTTTCT 58.453 39.130 0.00 0.00 41.95 2.52
3769 4048 6.660887 TTCTTTGGAAACATCAAAAACTGC 57.339 33.333 0.00 0.00 42.32 4.40
3770 4049 5.115480 TCTTTGGAAACATCAAAAACTGCC 58.885 37.500 0.00 0.00 42.32 4.85
3777 4056 2.034558 ACATCAAAAACTGCCGGAACTG 59.965 45.455 5.05 0.00 0.00 3.16
3779 4058 0.744281 CAAAAACTGCCGGAACTGGT 59.256 50.000 5.05 0.00 0.00 4.00
3791 4070 3.194116 CCGGAACTGGTAGTGCTAAACTA 59.806 47.826 0.00 0.00 40.56 2.24
3798 4077 8.591114 AACTGGTAGTGCTAAACTAGAAGATA 57.409 34.615 0.00 0.00 42.15 1.98
3801 4080 8.818622 TGGTAGTGCTAAACTAGAAGATAGAA 57.181 34.615 0.00 0.00 42.15 2.10
3806 4085 8.682710 AGTGCTAAACTAGAAGATAGAACTCAG 58.317 37.037 0.00 0.00 37.36 3.35
3814 4093 6.524101 AGAAGATAGAACTCAGTCCAACTC 57.476 41.667 0.00 0.00 0.00 3.01
3815 4094 5.420739 AGAAGATAGAACTCAGTCCAACTCC 59.579 44.000 0.00 0.00 0.00 3.85
3825 4104 4.517285 TCAGTCCAACTCCAGATAATTGC 58.483 43.478 0.00 0.00 0.00 3.56
3829 4108 6.543465 CAGTCCAACTCCAGATAATTGCAATA 59.457 38.462 13.39 1.72 0.00 1.90
3860 4139 5.480073 GTCTTACTCTATGGCTCATGATCCT 59.520 44.000 16.28 5.20 0.00 3.24
3889 4168 4.508861 CCTGTTTCAACAAAAGCTTCCATG 59.491 41.667 0.00 2.17 38.66 3.66
3906 4185 2.224867 CCATGTGAGAAGGTTGGGTCTT 60.225 50.000 0.00 0.00 0.00 3.01
3913 4192 8.331931 TGTGAGAAGGTTGGGTCTTATATTAT 57.668 34.615 0.00 0.00 0.00 1.28
3943 4222 3.760151 CAGATTGTTCCTCTGCATCCAAA 59.240 43.478 0.00 0.00 34.24 3.28
3951 4230 4.464008 TCCTCTGCATCCAAATATTCCAC 58.536 43.478 0.00 0.00 0.00 4.02
3955 4234 2.694628 TGCATCCAAATATTCCACCAGC 59.305 45.455 0.00 0.00 0.00 4.85
3956 4235 2.036346 GCATCCAAATATTCCACCAGCC 59.964 50.000 0.00 0.00 0.00 4.85
3960 4239 3.040477 CCAAATATTCCACCAGCCCATT 58.960 45.455 0.00 0.00 0.00 3.16
3961 4240 3.455543 CCAAATATTCCACCAGCCCATTT 59.544 43.478 0.00 0.00 0.00 2.32
3994 4282 0.110295 TGGAGGCAAAGCAGTAGCAA 59.890 50.000 0.00 0.00 45.49 3.91
4004 4292 5.284079 CAAAGCAGTAGCAACAAGTTGAAT 58.716 37.500 16.54 6.71 45.49 2.57
4019 4307 9.725019 AACAAGTTGAATATCAGTGATAACAGA 57.275 29.630 16.61 8.43 0.00 3.41
4030 4318 6.609533 TCAGTGATAACAGAAGTACTTCGTC 58.390 40.000 25.92 19.53 43.97 4.20
4046 4334 5.978814 ACTTCGTCTTCTGTTGGCTATAAT 58.021 37.500 0.00 0.00 0.00 1.28
4047 4335 5.812642 ACTTCGTCTTCTGTTGGCTATAATG 59.187 40.000 0.00 0.00 0.00 1.90
4049 4337 4.404394 TCGTCTTCTGTTGGCTATAATGGA 59.596 41.667 0.00 0.00 0.00 3.41
4051 4339 5.760253 CGTCTTCTGTTGGCTATAATGGAAT 59.240 40.000 0.00 0.00 0.00 3.01
4052 4340 6.073548 CGTCTTCTGTTGGCTATAATGGAATC 60.074 42.308 0.00 0.00 0.00 2.52
4055 4343 3.750371 TGTTGGCTATAATGGAATCCCG 58.250 45.455 0.00 0.00 34.29 5.14
4056 4344 3.081804 GTTGGCTATAATGGAATCCCGG 58.918 50.000 0.00 0.00 34.29 5.73
4057 4345 2.344592 TGGCTATAATGGAATCCCGGT 58.655 47.619 0.00 0.00 34.29 5.28
4088 4379 1.901833 AGGTGCAATCCCAAAATGGAC 59.098 47.619 0.00 0.00 40.96 4.02
4097 4388 3.013921 TCCCAAAATGGACGCATAGTTC 58.986 45.455 0.00 0.00 40.96 3.01
4107 4398 4.887655 TGGACGCATAGTTCTCTCTTCATA 59.112 41.667 0.00 0.00 0.00 2.15
4120 4411 5.186603 TCTCTCTTCATAGTGAGTGTTGCAT 59.813 40.000 0.00 0.00 40.95 3.96
4147 4438 3.711704 CACAGGATTAGGAAGGGAGCTAA 59.288 47.826 0.00 0.00 0.00 3.09
4148 4439 4.164221 CACAGGATTAGGAAGGGAGCTAAA 59.836 45.833 0.00 0.00 0.00 1.85
4149 4440 4.788617 ACAGGATTAGGAAGGGAGCTAAAA 59.211 41.667 0.00 0.00 0.00 1.52
4150 4441 5.104318 ACAGGATTAGGAAGGGAGCTAAAAG 60.104 44.000 0.00 0.00 0.00 2.27
4151 4442 4.413851 AGGATTAGGAAGGGAGCTAAAAGG 59.586 45.833 0.00 0.00 0.00 3.11
4152 4443 4.412528 GGATTAGGAAGGGAGCTAAAAGGA 59.587 45.833 0.00 0.00 0.00 3.36
4153 4444 5.073827 GGATTAGGAAGGGAGCTAAAAGGAT 59.926 44.000 0.00 0.00 0.00 3.24
4154 4445 6.410970 GGATTAGGAAGGGAGCTAAAAGGATT 60.411 42.308 0.00 0.00 0.00 3.01
4155 4446 4.955693 AGGAAGGGAGCTAAAAGGATTT 57.044 40.909 0.00 0.00 42.41 2.17
4156 4447 4.861196 AGGAAGGGAGCTAAAAGGATTTC 58.139 43.478 0.00 0.00 37.28 2.17
4157 4448 3.954904 GGAAGGGAGCTAAAAGGATTTCC 59.045 47.826 0.00 0.00 37.28 3.13
4158 4449 3.671740 AGGGAGCTAAAAGGATTTCCC 57.328 47.619 0.00 0.00 37.28 3.97
4159 4450 2.245028 AGGGAGCTAAAAGGATTTCCCC 59.755 50.000 3.82 0.00 37.28 4.81
4160 4451 2.245028 GGGAGCTAAAAGGATTTCCCCT 59.755 50.000 0.00 0.00 37.28 4.79
4161 4452 3.291584 GGAGCTAAAAGGATTTCCCCTG 58.708 50.000 0.00 0.00 37.28 4.45
4162 4453 3.053619 GGAGCTAAAAGGATTTCCCCTGA 60.054 47.826 0.00 0.00 37.28 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.560253 ATTGCTTTGTAGTAACACCTGAAG 57.440 37.500 0.00 0.00 34.61 3.02
86 87 6.591448 AGTTTTCAGAACTTTTTCAAGCTTGG 59.409 34.615 25.73 11.97 33.72 3.61
365 370 2.906389 ACAGATAAGACCTCTGGTGCAA 59.094 45.455 5.41 0.00 43.58 4.08
452 458 5.636903 CCTCCTAAGGATCCATTTTGAGA 57.363 43.478 15.82 0.23 46.67 3.27
466 472 7.414540 GCTCATTGTGTTTTGTATCCTCCTAAG 60.415 40.741 0.00 0.00 0.00 2.18
468 474 5.880332 GCTCATTGTGTTTTGTATCCTCCTA 59.120 40.000 0.00 0.00 0.00 2.94
699 705 2.976903 GCTGCCTCGGGATGCATC 60.977 66.667 18.81 18.81 36.79 3.91
705 711 1.153168 GCTATTTGCTGCCTCGGGA 60.153 57.895 0.00 0.00 38.95 5.14
851 862 4.350368 TTGATAGCCCTGCATTAATCGA 57.650 40.909 0.00 0.00 0.00 3.59
893 914 1.825090 TCTAACCTGGCACTGCAATG 58.175 50.000 2.82 0.00 0.00 2.82
894 915 2.648059 GATCTAACCTGGCACTGCAAT 58.352 47.619 2.82 0.00 0.00 3.56
895 916 1.675714 CGATCTAACCTGGCACTGCAA 60.676 52.381 2.82 0.00 0.00 4.08
896 917 0.108186 CGATCTAACCTGGCACTGCA 60.108 55.000 2.82 0.00 0.00 4.41
897 918 0.175760 TCGATCTAACCTGGCACTGC 59.824 55.000 0.00 0.00 0.00 4.40
926 947 1.907807 GATGGGCCAACTTGGTGCA 60.908 57.895 11.89 0.00 40.46 4.57
955 976 0.889186 GAAGAGGTTTTCGCAGCCCA 60.889 55.000 0.00 0.00 0.00 5.36
1015 1036 0.032130 ACATCGCGTGACTTGACTGT 59.968 50.000 5.77 0.00 0.00 3.55
1087 1108 5.802956 CACAAGTGTTAACAATTTGGACGTT 59.197 36.000 25.68 11.12 31.17 3.99
1346 1368 3.902881 AGGCTGATAGGTCAAACTCAG 57.097 47.619 0.00 0.00 38.49 3.35
1394 1420 4.782019 TTCACACCACCATATTTGCTTC 57.218 40.909 0.00 0.00 0.00 3.86
1414 1440 1.816835 TGACTCGCGGAGACAACTATT 59.183 47.619 6.13 0.00 32.27 1.73
1492 1518 5.376854 ACTTTTTGTGGAAATCCTCGATG 57.623 39.130 0.44 0.00 36.82 3.84
1504 1530 3.249917 ACTCGTTTGCAACTTTTTGTGG 58.750 40.909 0.00 0.00 34.90 4.17
1522 1548 9.255304 GATATGTCAACTATGAGGAAAAGACTC 57.745 37.037 0.00 0.00 35.88 3.36
1540 1566 3.620488 GTTGAAGGCCTTGGATATGTCA 58.380 45.455 26.25 9.36 0.00 3.58
1559 1585 3.010584 AGGTAGCATCAGTTCATTGGGTT 59.989 43.478 0.00 0.00 0.00 4.11
1565 1591 6.780031 ACATAGAGTAGGTAGCATCAGTTCAT 59.220 38.462 0.00 0.00 0.00 2.57
1621 1647 1.752833 GTCCAACCTCCAACCTCGT 59.247 57.895 0.00 0.00 0.00 4.18
1636 1662 0.391263 GGACAACGACATGGAGGTCC 60.391 60.000 0.00 3.21 38.15 4.46
1637 1663 0.391263 GGGACAACGACATGGAGGTC 60.391 60.000 0.00 0.00 34.42 3.85
1638 1664 0.836400 AGGGACAACGACATGGAGGT 60.836 55.000 0.00 0.00 0.00 3.85
1721 1755 2.362120 CTGGAGGCCCCTTGCTTG 60.362 66.667 0.00 0.00 40.92 4.01
1776 1810 5.282055 ACATGAATTCTCGCTGGATTAGA 57.718 39.130 7.05 0.00 0.00 2.10
1796 1830 3.636300 GCATGCCACCCTGAATATTTACA 59.364 43.478 6.36 0.00 0.00 2.41
1824 1859 9.411801 ACGATAATGCAGTACATACATAGAAAG 57.588 33.333 0.00 0.00 38.34 2.62
1832 1867 7.148474 CCCCATTTACGATAATGCAGTACATAC 60.148 40.741 0.00 0.00 38.34 2.39
1951 2033 8.345565 CGATACCCCAAGATTTTCTGAAATAAG 58.654 37.037 3.31 0.00 35.65 1.73
2017 2105 4.756642 CACTTGGAAATTGACTAGACAGCA 59.243 41.667 0.00 0.00 0.00 4.41
2101 2195 4.645809 GGAGATGGCAACCTCCAC 57.354 61.111 25.31 7.33 46.28 4.02
2218 2333 3.242673 GCTATGAGCACAAGAATGACTGC 60.243 47.826 0.00 0.00 41.89 4.40
2371 2486 2.797156 CGGCGTTAGAAGATCCTTGATG 59.203 50.000 0.00 0.00 0.00 3.07
2390 2508 5.238650 ACAGTTTTCATTTTAGTCTCACCGG 59.761 40.000 0.00 0.00 0.00 5.28
2393 2511 7.259290 TCCACAGTTTTCATTTTAGTCTCAC 57.741 36.000 0.00 0.00 0.00 3.51
2493 2617 4.082125 GGAGGAACTGTGAAATGGTGAAT 58.918 43.478 0.00 0.00 41.55 2.57
2592 2719 4.521062 AGCATCTCCGACGCCAGC 62.521 66.667 0.00 0.00 0.00 4.85
2615 2742 1.783071 CAGGAGGAGAAGTAGGGTCC 58.217 60.000 0.00 0.00 0.00 4.46
2622 2749 2.654079 CGCCAGCAGGAGGAGAAGT 61.654 63.158 0.00 0.00 36.89 3.01
2688 2815 1.227674 GACCTCCGGCAAGCATAGG 60.228 63.158 0.00 0.00 0.00 2.57
2922 3049 6.042781 TGAACACAAGGTAGTAGGTCAGAATT 59.957 38.462 0.00 0.00 0.00 2.17
3031 3176 1.226746 GCCGCGGCTATGAGTAAAAT 58.773 50.000 41.71 0.00 38.26 1.82
3052 3197 1.534235 ACTTGAGCAGGAGGGACGT 60.534 57.895 0.00 0.00 0.00 4.34
3060 3205 1.876156 GAAACCAGACACTTGAGCAGG 59.124 52.381 0.00 0.00 0.00 4.85
3239 3385 3.183754 TGTATGCACGTATGTACAGTGC 58.816 45.455 24.34 24.34 46.51 4.40
3275 3429 1.069022 ACATGCAAACTGACGCACATC 60.069 47.619 0.00 0.00 41.79 3.06
3281 3435 5.323900 CCAGTATTAACATGCAAACTGACG 58.676 41.667 12.99 0.00 37.18 4.35
3366 3604 9.650539 CTGTACAGACTACACTAGTTAGTTAGA 57.349 37.037 18.45 6.03 39.59 2.10
3374 3612 8.034215 CACTAGTACTGTACAGACTACACTAGT 58.966 40.741 28.45 28.45 42.86 2.57
3375 3613 8.034215 ACACTAGTACTGTACAGACTACACTAG 58.966 40.741 29.30 28.24 32.50 2.57
3376 3614 7.901029 ACACTAGTACTGTACAGACTACACTA 58.099 38.462 29.30 21.34 0.00 2.74
3377 3615 6.767456 ACACTAGTACTGTACAGACTACACT 58.233 40.000 29.30 21.36 0.00 3.55
3378 3616 7.296660 CAACACTAGTACTGTACAGACTACAC 58.703 42.308 29.30 16.36 0.00 2.90
3456 3701 5.259632 TCTCCCTCTTACCAACTGTACTAC 58.740 45.833 0.00 0.00 0.00 2.73
3462 3707 4.528596 TCTTTCTCTCCCTCTTACCAACTG 59.471 45.833 0.00 0.00 0.00 3.16
3469 3714 5.729229 TCTCTCTCTCTTTCTCTCCCTCTTA 59.271 44.000 0.00 0.00 0.00 2.10
3483 3728 5.070580 GGTAGCTAACTCTCTCTCTCTCTCT 59.929 48.000 0.09 0.00 0.00 3.10
3484 3729 5.070580 AGGTAGCTAACTCTCTCTCTCTCTC 59.929 48.000 5.15 0.00 0.00 3.20
3485 3730 4.969359 AGGTAGCTAACTCTCTCTCTCTCT 59.031 45.833 5.15 0.00 0.00 3.10
3486 3731 5.057149 CAGGTAGCTAACTCTCTCTCTCTC 58.943 50.000 8.79 0.00 0.00 3.20
3487 3732 4.141482 CCAGGTAGCTAACTCTCTCTCTCT 60.141 50.000 8.79 0.00 0.00 3.10
3488 3733 4.134563 CCAGGTAGCTAACTCTCTCTCTC 58.865 52.174 8.79 0.00 0.00 3.20
3529 3774 8.319143 TGAAATATCACAGAGATGCATACATG 57.681 34.615 0.00 0.65 37.57 3.21
3530 3775 8.913487 TTGAAATATCACAGAGATGCATACAT 57.087 30.769 0.00 0.00 37.57 2.29
3531 3776 8.206189 TCTTGAAATATCACAGAGATGCATACA 58.794 33.333 0.00 0.00 37.57 2.29
3532 3777 8.494347 GTCTTGAAATATCACAGAGATGCATAC 58.506 37.037 0.00 0.00 37.57 2.39
3636 3915 8.723311 CAATGGTTCTACGGTCAATACTTAAAA 58.277 33.333 0.00 0.00 0.00 1.52
3689 3968 9.914834 TTGCTACCTTTGTAAATATTATCCAGT 57.085 29.630 0.00 0.00 0.00 4.00
3715 3994 9.679661 ATTGGTCAAACCTGTAATTTTCTTTTT 57.320 25.926 0.00 0.00 39.58 1.94
3716 3995 9.679661 AATTGGTCAAACCTGTAATTTTCTTTT 57.320 25.926 0.00 0.00 39.58 2.27
3717 3996 9.325198 GAATTGGTCAAACCTGTAATTTTCTTT 57.675 29.630 0.00 0.00 39.58 2.52
3718 3997 7.931407 GGAATTGGTCAAACCTGTAATTTTCTT 59.069 33.333 0.00 0.00 39.58 2.52
3719 3998 7.290014 AGGAATTGGTCAAACCTGTAATTTTCT 59.710 33.333 10.35 0.00 39.58 2.52
3734 4013 5.423610 TGTTTCCAAAGAAAGGAATTGGTCA 59.576 36.000 3.92 1.01 44.14 4.02
3735 4014 5.912892 TGTTTCCAAAGAAAGGAATTGGTC 58.087 37.500 3.92 0.00 44.14 4.02
3749 4028 3.868077 CGGCAGTTTTTGATGTTTCCAAA 59.132 39.130 0.00 0.00 0.00 3.28
3769 4048 2.028385 AGTTTAGCACTACCAGTTCCGG 60.028 50.000 0.00 0.00 31.97 5.14
3770 4049 3.314541 AGTTTAGCACTACCAGTTCCG 57.685 47.619 0.00 0.00 31.97 4.30
3777 4056 8.905850 AGTTCTATCTTCTAGTTTAGCACTACC 58.094 37.037 0.00 0.00 36.88 3.18
3779 4058 9.682465 TGAGTTCTATCTTCTAGTTTAGCACTA 57.318 33.333 0.00 0.00 36.88 2.74
3791 4070 5.420739 GGAGTTGGACTGAGTTCTATCTTCT 59.579 44.000 0.00 0.00 0.00 2.85
3798 4077 2.964209 TCTGGAGTTGGACTGAGTTCT 58.036 47.619 0.00 0.00 0.00 3.01
3801 4080 5.738909 CAATTATCTGGAGTTGGACTGAGT 58.261 41.667 0.00 0.00 0.00 3.41
3806 4085 5.841957 ATTGCAATTATCTGGAGTTGGAC 57.158 39.130 5.99 0.00 0.00 4.02
3825 4104 9.988815 AGCCATAGAGTAAGACAAGTTATATTG 57.011 33.333 0.00 0.00 36.22 1.90
3829 4108 7.661536 TGAGCCATAGAGTAAGACAAGTTAT 57.338 36.000 0.00 0.00 0.00 1.89
3860 4139 4.889409 AGCTTTTGTTGAAACAGGATCTCA 59.111 37.500 0.00 0.00 40.50 3.27
3869 4148 5.108517 TCACATGGAAGCTTTTGTTGAAAC 58.891 37.500 0.00 0.00 0.00 2.78
3889 4168 8.429641 TCATAATATAAGACCCAACCTTCTCAC 58.570 37.037 0.00 0.00 0.00 3.51
3913 4192 4.037923 GCAGAGGAACAATCTGGTTTTTCA 59.962 41.667 5.22 0.00 43.61 2.69
3920 4199 2.295885 GGATGCAGAGGAACAATCTGG 58.704 52.381 5.22 0.00 43.61 3.86
3943 4222 3.686227 TGAAATGGGCTGGTGGAATAT 57.314 42.857 0.00 0.00 0.00 1.28
3951 4230 5.537674 AGAAATAGCTATTGAAATGGGCTGG 59.462 40.000 19.53 0.00 33.35 4.85
3955 4234 6.208204 CCTCCAGAAATAGCTATTGAAATGGG 59.792 42.308 24.71 18.32 0.00 4.00
3956 4235 6.294397 GCCTCCAGAAATAGCTATTGAAATGG 60.294 42.308 19.53 21.05 0.00 3.16
3960 4239 5.372343 TGCCTCCAGAAATAGCTATTGAA 57.628 39.130 19.53 0.00 0.00 2.69
3961 4240 5.372343 TTGCCTCCAGAAATAGCTATTGA 57.628 39.130 19.53 11.16 0.00 2.57
3994 4282 9.725019 TTCTGTTATCACTGATATTCAACTTGT 57.275 29.630 0.00 0.00 31.47 3.16
4004 4292 8.277490 ACGAAGTACTTCTGTTATCACTGATA 57.723 34.615 28.30 0.00 41.94 2.15
4030 4318 5.474876 GGGATTCCATTATAGCCAACAGAAG 59.525 44.000 4.80 0.00 0.00 2.85
4046 4334 1.074775 CCCTCCTACCGGGATTCCA 60.075 63.158 6.32 0.00 44.90 3.53
4047 4335 2.517798 GCCCTCCTACCGGGATTCC 61.518 68.421 6.32 0.00 44.90 3.01
4049 4337 0.917333 TTTGCCCTCCTACCGGGATT 60.917 55.000 6.32 0.00 44.90 3.01
4051 4339 1.993391 CTTTGCCCTCCTACCGGGA 60.993 63.158 6.32 0.00 44.90 5.14
4052 4340 2.590092 CTTTGCCCTCCTACCGGG 59.410 66.667 6.32 0.00 44.89 5.73
4055 4343 1.378646 GCACCTTTGCCCTCCTACC 60.379 63.158 0.00 0.00 43.66 3.18
4056 4344 4.320910 GCACCTTTGCCCTCCTAC 57.679 61.111 0.00 0.00 43.66 3.18
4085 4376 3.784701 TGAAGAGAGAACTATGCGTCC 57.215 47.619 0.00 0.00 0.00 4.79
4088 4379 6.066054 TCACTATGAAGAGAGAACTATGCG 57.934 41.667 0.00 0.00 0.00 4.73
4097 4388 4.814147 TGCAACACTCACTATGAAGAGAG 58.186 43.478 0.00 0.00 43.71 3.20
4120 4411 4.955335 TCCCTTCCTAATCCTGTGTTCTA 58.045 43.478 0.00 0.00 0.00 2.10
4129 4420 4.412528 TCCTTTTAGCTCCCTTCCTAATCC 59.587 45.833 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.