Multiple sequence alignment - TraesCS7D01G460200

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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 TraesCS7D01G460200 chr7D 100.000 4066 0 0 1 4066 576893669 576897734 0.000000e+00 7509.0
1 TraesCS7D01G460200 chr7D 80.205 879 148 22 888 1752 15000424 14999558 1.590000e-178 636.0
2 TraesCS7D01G460200 chr7D 84.571 175 21 6 930 1101 594986854 594987025 6.990000e-38 169.0
3 TraesCS7D01G460200 chr7D 82.514 183 32 0 932 1114 191841194 191841012 1.170000e-35 161.0
4 TraesCS7D01G460200 chr7D 92.000 50 3 1 5 53 128123946 128123897 7.290000e-08 69.4
5 TraesCS7D01G460200 chr7B 91.142 4177 242 57 3 4066 639851455 639847294 0.000000e+00 5546.0
6 TraesCS7D01G460200 chr7B 75.641 546 123 8 1212 1752 337370265 337369725 3.120000e-66 263.0
7 TraesCS7D01G460200 chr7B 83.908 174 28 0 932 1105 337158795 337158622 2.510000e-37 167.0
8 TraesCS7D01G460200 chr7B 84.000 175 22 6 930 1101 666685332 666685161 3.250000e-36 163.0
9 TraesCS7D01G460200 chr7A 90.704 3539 187 59 1 3474 669032217 669028756 0.000000e+00 4582.0
10 TraesCS7D01G460200 chr7A 79.954 878 151 22 888 1752 14446959 14446094 1.240000e-174 623.0
11 TraesCS7D01G460200 chr7A 83.085 201 31 2 918 1115 200634377 200634177 3.230000e-41 180.0
12 TraesCS7D01G460200 chr7A 83.708 178 25 4 926 1101 682892223 682892048 9.040000e-37 165.0
13 TraesCS7D01G460200 chr7A 84.615 169 20 6 930 1095 687953189 687953354 3.250000e-36 163.0
14 TraesCS7D01G460200 chr5B 81.429 210 36 3 3456 3663 345517105 345517313 6.990000e-38 169.0
15 TraesCS7D01G460200 chr5B 79.024 205 42 1 3456 3659 502925742 502925538 5.480000e-29 139.0
16 TraesCS7D01G460200 chr5A 80.383 209 39 2 3456 3663 448120526 448120319 1.510000e-34 158.0
17 TraesCS7D01G460200 chr2D 79.904 209 41 1 3456 3663 103358764 103358556 7.040000e-33 152.0
18 TraesCS7D01G460200 chr2D 80.189 212 35 4 3456 3663 104409790 104409998 7.040000e-33 152.0
19 TraesCS7D01G460200 chr2D 92.233 103 8 0 3465 3567 152857777 152857675 3.270000e-31 147.0
20 TraesCS7D01G460200 chr3D 79.310 203 41 1 3456 3657 587195711 587195913 1.520000e-29 141.0
21 TraesCS7D01G460200 chr4B 78.302 212 37 9 3456 3663 51868167 51868373 1.190000e-25 128.0
22 TraesCS7D01G460200 chr3A 80.800 125 19 4 3543 3663 737872531 737872408 4.330000e-15 93.5


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 TraesCS7D01G460200 chr7D 576893669 576897734 4065 False 7509 7509 100.000 1 4066 1 chr7D.!!$F1 4065
1 TraesCS7D01G460200 chr7D 14999558 15000424 866 True 636 636 80.205 888 1752 1 chr7D.!!$R1 864
2 TraesCS7D01G460200 chr7B 639847294 639851455 4161 True 5546 5546 91.142 3 4066 1 chr7B.!!$R3 4063
3 TraesCS7D01G460200 chr7B 337369725 337370265 540 True 263 263 75.641 1212 1752 1 chr7B.!!$R2 540
4 TraesCS7D01G460200 chr7A 669028756 669032217 3461 True 4582 4582 90.704 1 3474 1 chr7A.!!$R3 3473
5 TraesCS7D01G460200 chr7A 14446094 14446959 865 True 623 623 79.954 888 1752 1 chr7A.!!$R1 864

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
771 830 0.033503 ACCTCCCCATAAAAAGGCCG 60.034 55.0 0.00 0.0 31.79 6.13 F
1159 1232 0.036306 AAAGAATTCCGTGCCCTCGT 59.964 50.0 0.65 0.0 0.00 4.18 F
2113 2222 0.111639 TGGTACCACTTGGCCTTTCC 59.888 55.0 11.60 0.0 39.32 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1735 0.820891 AGGTGTTCTTGCAGGTGCTG 60.821 55.0 3.18 0.0 42.66 4.41 R
3038 3175 0.532573 CTGGAAGTAGGCGAGCTGAA 59.467 55.0 0.00 0.0 0.00 3.02 R
3992 4178 0.608640 AACAGTGTAGCTTCTCCCCG 59.391 55.0 0.00 0.0 0.00 5.73 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
233 245 1.062294 ACGACAGCGCGTTTTTAACAA 59.938 42.857 8.43 0.00 42.71 2.83
275 287 2.279186 AAAAGCCGCAACGCAACC 60.279 55.556 0.00 0.00 0.00 3.77
310 322 2.589720 CAGCTATGGATCCAATTGCCA 58.410 47.619 20.67 5.83 35.91 4.92
352 364 6.588719 TCACATCAAACCTTCCCATAAAAG 57.411 37.500 0.00 0.00 0.00 2.27
370 382 3.322191 AAGGGCTTTCCACCTTTAACA 57.678 42.857 0.00 0.00 44.41 2.41
380 392 5.238006 TCCACCTTTAACAACAAGTTTCG 57.762 39.130 0.00 0.00 41.64 3.46
382 394 4.416620 CACCTTTAACAACAAGTTTCGCA 58.583 39.130 0.00 0.00 41.64 5.10
384 396 4.082679 ACCTTTAACAACAAGTTTCGCACA 60.083 37.500 0.00 0.00 41.64 4.57
392 404 3.326747 ACAAGTTTCGCACAGGAGATAC 58.673 45.455 0.00 0.00 0.00 2.24
399 411 2.565391 TCGCACAGGAGATACTTTTGGA 59.435 45.455 0.00 0.00 0.00 3.53
400 412 3.197766 TCGCACAGGAGATACTTTTGGAT 59.802 43.478 0.00 0.00 0.00 3.41
452 464 0.736053 GTTTCAGACGCCCACAAACA 59.264 50.000 0.00 0.00 0.00 2.83
454 466 1.686355 TTCAGACGCCCACAAACATT 58.314 45.000 0.00 0.00 0.00 2.71
455 467 1.686355 TCAGACGCCCACAAACATTT 58.314 45.000 0.00 0.00 0.00 2.32
456 468 1.606668 TCAGACGCCCACAAACATTTC 59.393 47.619 0.00 0.00 0.00 2.17
492 505 5.389098 CCGGTTTACGAAAACACAGATACAG 60.389 44.000 0.00 0.00 45.68 2.74
494 507 5.697633 GGTTTACGAAAACACAGATACAGGA 59.302 40.000 0.00 0.00 45.68 3.86
517 535 6.267496 AGGAAAAATAAGGAATCGTGTTGG 57.733 37.500 0.00 0.00 0.00 3.77
527 549 6.937436 AGGAATCGTGTTGGATAATAAACC 57.063 37.500 0.00 0.00 0.00 3.27
530 555 8.269317 AGGAATCGTGTTGGATAATAAACCTTA 58.731 33.333 0.00 0.00 0.00 2.69
542 567 8.456471 GGATAATAAACCTTAACACACCTTGAC 58.544 37.037 0.00 0.00 0.00 3.18
550 575 1.342672 ACACACCTTGACCCGGAGTT 61.343 55.000 0.73 0.00 0.00 3.01
564 589 3.303526 CCCGGAGTTTTACAGACGTTTTG 60.304 47.826 0.73 0.00 0.00 2.44
606 634 2.616256 GCACATCTCATCACACCTTCCA 60.616 50.000 0.00 0.00 0.00 3.53
674 703 3.414700 GTGACGCGGTGGCAGAAG 61.415 66.667 12.47 0.00 39.92 2.85
685 714 4.326766 GCAGAAGCCGCAACGCAA 62.327 61.111 0.00 0.00 33.58 4.85
686 715 2.427410 CAGAAGCCGCAACGCAAC 60.427 61.111 0.00 0.00 0.00 4.17
687 716 2.899838 AGAAGCCGCAACGCAACA 60.900 55.556 0.00 0.00 0.00 3.33
688 717 2.025441 GAAGCCGCAACGCAACAA 59.975 55.556 0.00 0.00 0.00 2.83
689 718 1.587613 GAAGCCGCAACGCAACAAA 60.588 52.632 0.00 0.00 0.00 2.83
690 719 1.142778 GAAGCCGCAACGCAACAAAA 61.143 50.000 0.00 0.00 0.00 2.44
691 720 1.417577 AAGCCGCAACGCAACAAAAC 61.418 50.000 0.00 0.00 0.00 2.43
692 721 2.161486 GCCGCAACGCAACAAAACA 61.161 52.632 0.00 0.00 0.00 2.83
722 775 3.173540 CAGCGGTGGATCCAATTGA 57.826 52.632 18.20 0.00 35.57 2.57
771 830 0.033503 ACCTCCCCATAAAAAGGCCG 60.034 55.000 0.00 0.00 31.79 6.13
1159 1232 0.036306 AAAGAATTCCGTGCCCTCGT 59.964 50.000 0.65 0.00 0.00 4.18
1192 1272 4.479619 GCCGATTGCTGATTGATTAATCC 58.520 43.478 12.90 0.00 41.62 3.01
1193 1273 4.616835 GCCGATTGCTGATTGATTAATCCC 60.617 45.833 12.90 3.28 41.62 3.85
1228 1312 3.928779 ATGGCGACGGCGATGGAT 61.929 61.111 18.90 0.00 41.24 3.41
1438 1522 3.786918 GATCCCGTCGCTCGTCGTC 62.787 68.421 7.93 0.00 39.67 4.20
1651 1735 0.171455 CTCTGTACGTCAGGCTGTCC 59.829 60.000 15.27 5.65 43.76 4.02
1757 1841 2.880890 GCCATGATGATCTGGTTGGTAC 59.119 50.000 10.97 0.00 34.86 3.34
1851 1949 5.323371 TGCAAGTTGGAATAATTACTGCC 57.677 39.130 4.75 0.00 0.00 4.85
1968 2066 7.148255 TGTCAATATGGTAAGCACAATGTTCTC 60.148 37.037 0.00 0.00 0.00 2.87
2003 2101 9.447040 CATATCATTGTGTGATTTAAGCTTCAG 57.553 33.333 0.00 0.00 45.25 3.02
2007 2105 7.862372 TCATTGTGTGATTTAAGCTTCAGAAAC 59.138 33.333 0.00 0.00 0.00 2.78
2012 2110 9.899226 GTGTGATTTAAGCTTCAGAAACTAAAT 57.101 29.630 0.00 0.18 0.00 1.40
2060 2169 3.192001 TGTACTGTACTTAGTTGCTCCCG 59.808 47.826 17.98 0.00 32.19 5.14
2083 2192 1.074775 CAGCCTTAACACAGGGGCA 59.925 57.895 5.62 0.00 46.23 5.36
2113 2222 0.111639 TGGTACCACTTGGCCTTTCC 59.888 55.000 11.60 0.00 39.32 3.13
2175 2284 7.052873 AGACCAATTCTGAATCCAATGAGTAG 58.947 38.462 2.92 0.00 31.12 2.57
2184 2293 8.380867 TCTGAATCCAATGAGTAGCATTATGAT 58.619 33.333 0.00 0.00 45.23 2.45
2228 2341 9.612620 GTACAGTTTGAATTTTGATAAGTCCAG 57.387 33.333 0.00 0.00 0.00 3.86
2308 2423 1.082104 CTCAAACGAACTTGGCGCC 60.082 57.895 22.73 22.73 0.00 6.53
2623 2748 7.123547 ACACCAAATTTTCTCAACTGTAAAGGA 59.876 33.333 0.00 0.00 0.00 3.36
2632 2757 4.304110 TCAACTGTAAAGGAGTGCTTACG 58.696 43.478 0.00 0.00 31.84 3.18
2745 2870 4.210724 TCCACCTAAACGGAATGGTAAG 57.789 45.455 0.00 0.00 32.16 2.34
2805 2940 5.634118 TGGATGTCCTGAAATCTGAAACTT 58.366 37.500 0.09 0.00 36.82 2.66
2908 3043 4.273318 GTGCATAGATTGGGAAAAGGAGT 58.727 43.478 0.00 0.00 0.00 3.85
2961 3096 7.041098 AGGAGCAGTTTCATTGTTACAGTTTAG 60.041 37.037 0.00 0.00 0.00 1.85
2989 3124 6.998074 TGAAGACAGGACAATCTAATGTGTTT 59.002 34.615 0.00 0.00 32.57 2.83
3038 3175 1.073706 ACAGGACAGGGTCTTGGGT 60.074 57.895 12.23 0.00 42.66 4.51
3046 3183 1.376037 GGGTCTTGGGTTCAGCTCG 60.376 63.158 0.00 0.00 0.00 5.03
3278 3430 3.976169 GCTCTTGCTATAGGAGACAGTG 58.024 50.000 1.04 0.00 34.59 3.66
3297 3449 1.602041 TGTGGGTAAGCAATGCGCA 60.602 52.632 14.96 14.96 46.13 6.09
3325 3477 4.280819 ACCATTGTAATCTCCACCCAATG 58.719 43.478 0.00 0.00 41.12 2.82
3326 3478 3.068590 CCATTGTAATCTCCACCCAATGC 59.931 47.826 0.00 0.00 40.47 3.56
3327 3479 3.737559 TTGTAATCTCCACCCAATGCT 57.262 42.857 0.00 0.00 0.00 3.79
3330 3482 6.508030 TTGTAATCTCCACCCAATGCTATA 57.492 37.500 0.00 0.00 0.00 1.31
3418 3570 4.275936 GGAACACATAGCAACTGAAACTGT 59.724 41.667 0.00 0.00 0.00 3.55
3464 3616 1.277557 CAGTTGCAAGCTACTCCCTCT 59.722 52.381 0.00 0.00 30.18 3.69
3478 3630 5.216614 ACTCCCTCTGTTTCTTGTTAGTC 57.783 43.478 0.00 0.00 0.00 2.59
3486 3638 7.201591 CCTCTGTTTCTTGTTAGTCTGCATATG 60.202 40.741 0.00 0.00 0.00 1.78
3495 3647 9.282247 CTTGTTAGTCTGCATATGAAATTTGTC 57.718 33.333 6.97 0.00 0.00 3.18
3496 3648 7.761409 TGTTAGTCTGCATATGAAATTTGTCC 58.239 34.615 6.97 0.00 0.00 4.02
3497 3649 5.490139 AGTCTGCATATGAAATTTGTCCG 57.510 39.130 6.97 0.00 0.00 4.79
3500 3652 6.150976 AGTCTGCATATGAAATTTGTCCGAAA 59.849 34.615 6.97 0.00 0.00 3.46
3509 3661 7.692908 TGAAATTTGTCCGAAATCAAACTTC 57.307 32.000 0.00 0.00 38.99 3.01
3512 3664 5.987777 TTTGTCCGAAATCAAACTTCGTA 57.012 34.783 4.49 0.00 43.21 3.43
3513 3665 5.987777 TTGTCCGAAATCAAACTTCGTAA 57.012 34.783 4.49 0.00 43.21 3.18
3533 3685 7.302524 TCGTAAAGTTTGACCAAATTCATAGC 58.697 34.615 0.00 0.00 32.36 2.97
3580 3733 7.658179 ACGATATCAATGTCATTACATGGAC 57.342 36.000 0.00 0.00 46.54 4.02
3583 3736 7.360353 CGATATCAATGTCATTACATGGACCAC 60.360 40.741 0.00 0.00 46.54 4.16
3585 3738 2.394930 TGTCATTACATGGACCACCG 57.605 50.000 0.00 0.00 39.42 4.94
3590 3744 5.120399 GTCATTACATGGACCACCGATTAA 58.880 41.667 0.00 0.00 39.42 1.40
3600 3754 6.181190 TGGACCACCGATTAATTTTCATACA 58.819 36.000 0.00 0.00 39.42 2.29
3667 3821 9.651913 AAATTTGATCAAACTTTGTGTACAACT 57.348 25.926 22.71 0.00 32.41 3.16
3668 3822 8.856490 ATTTGATCAAACTTTGTGTACAACTC 57.144 30.769 22.71 0.00 32.41 3.01
3669 3823 6.993786 TGATCAAACTTTGTGTACAACTCA 57.006 33.333 0.00 0.00 35.28 3.41
3671 3825 7.995289 TGATCAAACTTTGTGTACAACTCAAT 58.005 30.769 0.00 0.00 35.28 2.57
3673 3827 8.633075 ATCAAACTTTGTGTACAACTCAATTG 57.367 30.769 0.00 0.00 44.60 2.32
3716 3890 9.750125 GAATGTATTACATCACTGTATGAGACA 57.250 33.333 9.68 0.00 41.91 3.41
3808 3982 0.994995 CGTGTTCTCGAATGCTGAGG 59.005 55.000 0.00 0.00 34.19 3.86
3809 3983 0.723981 GTGTTCTCGAATGCTGAGGC 59.276 55.000 0.00 0.00 39.26 4.70
3812 3986 2.079925 GTTCTCGAATGCTGAGGCTTT 58.920 47.619 0.00 0.00 38.31 3.51
3813 3987 3.262420 GTTCTCGAATGCTGAGGCTTTA 58.738 45.455 0.00 0.00 36.23 1.85
3814 3988 3.827008 TCTCGAATGCTGAGGCTTTAT 57.173 42.857 0.00 0.00 36.23 1.40
3817 3991 5.292765 TCTCGAATGCTGAGGCTTTATAAG 58.707 41.667 0.00 0.00 36.23 1.73
3837 4011 2.545526 AGACTGACTTGTTGCATTGTCG 59.454 45.455 0.00 0.00 32.64 4.35
3844 4018 3.565482 ACTTGTTGCATTGTCGTTCTCAT 59.435 39.130 0.00 0.00 0.00 2.90
3847 4021 3.435327 TGTTGCATTGTCGTTCTCATACC 59.565 43.478 0.00 0.00 0.00 2.73
3859 4033 2.248248 TCTCATACCGATGGCCCTTAG 58.752 52.381 0.00 0.00 33.49 2.18
3860 4034 1.971357 CTCATACCGATGGCCCTTAGT 59.029 52.381 0.00 0.00 33.49 2.24
3861 4035 3.162666 CTCATACCGATGGCCCTTAGTA 58.837 50.000 0.00 0.00 33.49 1.82
3862 4036 2.895404 TCATACCGATGGCCCTTAGTAC 59.105 50.000 0.00 0.00 33.49 2.73
3863 4037 1.321474 TACCGATGGCCCTTAGTACG 58.679 55.000 0.00 0.00 0.00 3.67
3864 4038 0.685458 ACCGATGGCCCTTAGTACGT 60.685 55.000 0.00 0.00 0.00 3.57
3865 4039 0.249322 CCGATGGCCCTTAGTACGTG 60.249 60.000 0.00 0.00 0.00 4.49
3866 4040 0.742505 CGATGGCCCTTAGTACGTGA 59.257 55.000 0.00 0.00 0.00 4.35
3870 4044 4.321750 CGATGGCCCTTAGTACGTGAATAT 60.322 45.833 0.00 0.00 0.00 1.28
3874 4048 4.056050 GCCCTTAGTACGTGAATATGGTG 58.944 47.826 0.00 0.00 0.00 4.17
3895 4079 7.551585 TGGTGAATGTAAGTTTGTGACAAATT 58.448 30.769 14.40 7.17 0.00 1.82
3896 4080 8.037758 TGGTGAATGTAAGTTTGTGACAAATTT 58.962 29.630 19.98 19.98 0.00 1.82
3902 4086 8.818141 TGTAAGTTTGTGACAAATTTTTGACA 57.182 26.923 21.01 16.62 40.55 3.58
3903 4087 9.429359 TGTAAGTTTGTGACAAATTTTTGACAT 57.571 25.926 21.01 1.30 42.70 3.06
3904 4088 9.900264 GTAAGTTTGTGACAAATTTTTGACATC 57.100 29.630 21.01 2.59 42.70 3.06
3905 4089 8.545229 AAGTTTGTGACAAATTTTTGACATCA 57.455 26.923 14.40 7.89 42.70 3.07
4003 4189 4.920828 TTTTTGCGGGGAGAAGCT 57.079 50.000 0.00 0.00 0.00 3.74
4012 4198 1.822990 CGGGGAGAAGCTACACTGTTA 59.177 52.381 0.00 0.00 0.00 2.41
4015 4201 3.451178 GGGGAGAAGCTACACTGTTATGA 59.549 47.826 0.00 0.00 0.00 2.15
4021 4207 7.650104 GGAGAAGCTACACTGTTATGAAGATAC 59.350 40.741 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 13 6.567687 TCGGAAATACAAAGCATCTCAAAA 57.432 33.333 0.00 0.00 0.00 2.44
122 134 4.000988 ACAATGCCTCGACGATTTTAACT 58.999 39.130 0.00 0.00 0.00 2.24
164 176 2.705127 ACCGTTGTTTGGTTAGGGTCTA 59.295 45.455 0.00 0.00 35.82 2.59
167 179 1.682740 CACCGTTGTTTGGTTAGGGT 58.317 50.000 0.00 0.00 37.72 4.34
195 207 3.867493 GTCGTTATCGTTTCCCTAAAGGG 59.133 47.826 8.93 8.93 46.19 3.95
205 217 1.005294 ACGCGCTGTCGTTATCGTTT 61.005 50.000 5.73 0.00 40.07 3.60
233 245 3.118298 AGCTTTTGGCAAACTTTGATGGT 60.118 39.130 13.10 0.00 44.79 3.55
275 287 5.123820 TCCATAGCTGGATTTTCTTGTTTCG 59.876 40.000 0.00 0.00 46.95 3.46
310 322 4.936823 GTGACCGTGTGACGCCGT 62.937 66.667 0.00 0.00 40.91 5.68
352 364 2.696187 TGTTGTTAAAGGTGGAAAGCCC 59.304 45.455 0.00 0.00 0.00 5.19
356 368 6.094061 CGAAACTTGTTGTTAAAGGTGGAAA 58.906 36.000 0.00 0.00 38.03 3.13
370 382 2.325583 TCTCCTGTGCGAAACTTGTT 57.674 45.000 0.00 0.00 0.00 2.83
380 392 5.904362 AAATCCAAAAGTATCTCCTGTGC 57.096 39.130 0.00 0.00 0.00 4.57
382 394 8.960591 CATGTAAAATCCAAAAGTATCTCCTGT 58.039 33.333 0.00 0.00 0.00 4.00
384 396 7.068716 GCCATGTAAAATCCAAAAGTATCTCCT 59.931 37.037 0.00 0.00 0.00 3.69
392 404 4.173256 GACCGCCATGTAAAATCCAAAAG 58.827 43.478 0.00 0.00 0.00 2.27
399 411 2.091541 CACCTGACCGCCATGTAAAAT 58.908 47.619 0.00 0.00 0.00 1.82
400 412 1.529226 CACCTGACCGCCATGTAAAA 58.471 50.000 0.00 0.00 0.00 1.52
452 464 2.604139 ACCGGACACAAATTGGGAAAT 58.396 42.857 9.46 0.00 0.00 2.17
454 466 2.074729 AACCGGACACAAATTGGGAA 57.925 45.000 9.46 0.00 0.00 3.97
455 467 2.074729 AAACCGGACACAAATTGGGA 57.925 45.000 9.46 0.00 0.00 4.37
456 468 2.350964 CGTAAACCGGACACAAATTGGG 60.351 50.000 9.46 0.00 0.00 4.12
482 495 7.338710 TCCTTATTTTTCCTCCTGTATCTGTG 58.661 38.462 0.00 0.00 0.00 3.66
492 505 6.322491 CAACACGATTCCTTATTTTTCCTCC 58.678 40.000 0.00 0.00 0.00 4.30
494 507 6.007703 TCCAACACGATTCCTTATTTTTCCT 58.992 36.000 0.00 0.00 0.00 3.36
517 535 8.456471 GGTCAAGGTGTGTTAAGGTTTATTATC 58.544 37.037 0.00 0.00 0.00 1.75
527 549 1.071071 TCCGGGTCAAGGTGTGTTAAG 59.929 52.381 0.00 0.00 0.00 1.85
530 555 1.342672 ACTCCGGGTCAAGGTGTGTT 61.343 55.000 0.00 0.00 34.58 3.32
542 567 2.159327 AACGTCTGTAAAACTCCGGG 57.841 50.000 0.00 0.00 0.00 5.73
550 575 2.158986 TCGTCCCCAAAACGTCTGTAAA 60.159 45.455 0.00 0.00 40.86 2.01
669 698 2.427410 GTTGCGTTGCGGCTTCTG 60.427 61.111 0.00 0.00 0.00 3.02
670 699 1.999071 TTTGTTGCGTTGCGGCTTCT 61.999 50.000 0.00 0.00 0.00 2.85
671 700 1.142778 TTTTGTTGCGTTGCGGCTTC 61.143 50.000 0.00 0.00 0.00 3.86
672 701 1.153745 TTTTGTTGCGTTGCGGCTT 60.154 47.368 0.00 0.00 0.00 4.35
673 702 1.876263 GTTTTGTTGCGTTGCGGCT 60.876 52.632 0.00 0.00 0.00 5.52
674 703 2.161486 TGTTTTGTTGCGTTGCGGC 61.161 52.632 0.00 0.00 0.00 6.53
675 704 1.073216 TGTGTTTTGTTGCGTTGCGG 61.073 50.000 0.00 0.00 0.00 5.69
676 705 0.710567 TTGTGTTTTGTTGCGTTGCG 59.289 45.000 0.00 0.00 0.00 4.85
677 706 2.410053 TCTTTGTGTTTTGTTGCGTTGC 59.590 40.909 0.00 0.00 0.00 4.17
678 707 4.637574 TTCTTTGTGTTTTGTTGCGTTG 57.362 36.364 0.00 0.00 0.00 4.10
679 708 5.659048 TTTTCTTTGTGTTTTGTTGCGTT 57.341 30.435 0.00 0.00 0.00 4.84
680 709 5.163903 GGATTTTCTTTGTGTTTTGTTGCGT 60.164 36.000 0.00 0.00 0.00 5.24
681 710 5.163913 TGGATTTTCTTTGTGTTTTGTTGCG 60.164 36.000 0.00 0.00 0.00 4.85
682 711 6.175712 TGGATTTTCTTTGTGTTTTGTTGC 57.824 33.333 0.00 0.00 0.00 4.17
683 712 6.250089 GCTGGATTTTCTTTGTGTTTTGTTG 58.750 36.000 0.00 0.00 0.00 3.33
684 713 5.063312 CGCTGGATTTTCTTTGTGTTTTGTT 59.937 36.000 0.00 0.00 0.00 2.83
685 714 4.566360 CGCTGGATTTTCTTTGTGTTTTGT 59.434 37.500 0.00 0.00 0.00 2.83
686 715 4.025813 CCGCTGGATTTTCTTTGTGTTTTG 60.026 41.667 0.00 0.00 0.00 2.44
687 716 4.119136 CCGCTGGATTTTCTTTGTGTTTT 58.881 39.130 0.00 0.00 0.00 2.43
688 717 3.132111 ACCGCTGGATTTTCTTTGTGTTT 59.868 39.130 1.50 0.00 0.00 2.83
689 718 2.693074 ACCGCTGGATTTTCTTTGTGTT 59.307 40.909 1.50 0.00 0.00 3.32
690 719 2.034558 CACCGCTGGATTTTCTTTGTGT 59.965 45.455 1.50 0.00 0.00 3.72
691 720 2.607771 CCACCGCTGGATTTTCTTTGTG 60.608 50.000 0.00 0.00 40.55 3.33
692 721 1.613437 CCACCGCTGGATTTTCTTTGT 59.387 47.619 0.00 0.00 40.55 2.83
722 775 4.295119 GACCGTGTGACGCTGGGT 62.295 66.667 10.69 0.00 40.91 4.51
742 801 1.863155 ATGGGGAGGTTTGATGCGGT 61.863 55.000 0.00 0.00 0.00 5.68
1159 1232 0.391661 GCAATCGGCTGTCTCCAAGA 60.392 55.000 0.00 0.00 40.25 3.02
1328 1412 0.257039 GTGTTGGCCCAGATGAGGAT 59.743 55.000 0.00 0.00 0.00 3.24
1447 1531 1.079197 CCGTATGTGGCACTGCAGA 60.079 57.895 23.35 0.00 0.00 4.26
1651 1735 0.820891 AGGTGTTCTTGCAGGTGCTG 60.821 55.000 3.18 0.00 42.66 4.41
1916 2014 3.870274 TGATGTCTCAAGCTGAGGATTG 58.130 45.455 11.63 0.00 44.39 2.67
1985 2083 6.942532 AGTTTCTGAAGCTTAAATCACACA 57.057 33.333 0.00 0.00 0.00 3.72
2012 2110 8.737633 AGAGATGGAGCCATATATATAGGTGTA 58.262 37.037 1.21 0.00 36.70 2.90
2027 2125 3.292460 AGTACAGTACAGAGATGGAGCC 58.708 50.000 13.37 0.00 0.00 4.70
2028 2126 4.993029 AAGTACAGTACAGAGATGGAGC 57.007 45.455 13.37 0.00 0.00 4.70
2029 2127 7.476667 CAACTAAGTACAGTACAGAGATGGAG 58.523 42.308 13.37 1.29 0.00 3.86
2031 2129 6.037098 GCAACTAAGTACAGTACAGAGATGG 58.963 44.000 13.37 5.92 0.00 3.51
2032 2130 6.857956 AGCAACTAAGTACAGTACAGAGATG 58.142 40.000 13.37 13.50 0.00 2.90
2033 2131 6.095720 GGAGCAACTAAGTACAGTACAGAGAT 59.904 42.308 13.37 1.76 0.00 2.75
2060 2169 1.000274 CCCTGTGTTAAGGCTGCAAAC 60.000 52.381 0.50 3.47 35.85 2.93
2083 2192 2.257207 AGTGGTACCATGTACAGCAGT 58.743 47.619 19.72 1.01 0.00 4.40
2113 2222 7.708752 GGAATTACAACTGACCTGATAGAAGAG 59.291 40.741 0.00 0.00 0.00 2.85
2184 2293 5.843969 ACTGTACCACATATATGATGGGACA 59.156 40.000 30.31 30.31 43.77 4.02
2564 2679 5.889853 TCTTGCTCTTATGGATTGCTGATTT 59.110 36.000 0.00 0.00 0.00 2.17
2601 2716 7.168135 GCACTCCTTTACAGTTGAGAAAATTTG 59.832 37.037 0.00 0.00 0.00 2.32
2603 2718 6.547510 AGCACTCCTTTACAGTTGAGAAAATT 59.452 34.615 0.00 0.00 0.00 1.82
2604 2719 6.064717 AGCACTCCTTTACAGTTGAGAAAAT 58.935 36.000 0.00 0.00 0.00 1.82
2623 2748 2.347490 CCACTGCCCGTAAGCACT 59.653 61.111 0.00 0.00 38.00 4.40
2632 2757 2.598394 TTCTGCTTGCCACTGCCC 60.598 61.111 0.00 0.00 36.33 5.36
2871 3006 1.160989 TGCACCACGCGATAAATGTT 58.839 45.000 15.93 0.00 46.97 2.71
2908 3043 8.934697 AGTGATTGGTAGGTCTGCTATATTTAA 58.065 33.333 0.00 0.00 0.00 1.52
2961 3096 6.312426 CACATTAGATTGTCCTGTCTTCAGAC 59.688 42.308 0.00 0.00 43.76 3.51
2979 3114 6.898041 TCGGATGAACAAGAAAACACATTAG 58.102 36.000 0.00 0.00 0.00 1.73
2989 3124 3.009723 GCCTGAATCGGATGAACAAGAA 58.990 45.455 0.00 0.00 0.00 2.52
3038 3175 0.532573 CTGGAAGTAGGCGAGCTGAA 59.467 55.000 0.00 0.00 0.00 3.02
3101 3242 2.954756 GAATGCCTCATCAACGCGCG 62.955 60.000 30.96 30.96 0.00 6.86
3129 3273 2.964209 ACATCCGAGGACCATATGTCT 58.036 47.619 1.24 0.00 43.89 3.41
3278 3430 1.154035 GCGCATTGCTTACCCACAC 60.154 57.895 0.30 0.00 41.73 3.82
3297 3449 3.689649 GTGGAGATTACAATGGTTTCGCT 59.310 43.478 0.00 0.00 0.00 4.93
3325 3477 6.527722 CCACACAACAAACATCATTGTATAGC 59.472 38.462 0.00 0.00 42.49 2.97
3326 3478 6.527722 GCCACACAACAAACATCATTGTATAG 59.472 38.462 0.00 0.00 42.49 1.31
3327 3479 6.015940 TGCCACACAACAAACATCATTGTATA 60.016 34.615 0.00 0.00 42.49 1.47
3330 3482 3.118847 TGCCACACAACAAACATCATTGT 60.119 39.130 0.00 0.00 45.12 2.71
3427 3579 4.986659 GCAACTGATCAAGTGCTTCAAATT 59.013 37.500 18.58 0.00 39.81 1.82
3436 3588 3.750130 AGTAGCTTGCAACTGATCAAGTG 59.250 43.478 0.00 0.00 39.81 3.16
3464 3616 7.977789 TTCATATGCAGACTAACAAGAAACA 57.022 32.000 0.00 0.00 0.00 2.83
3478 3630 6.974048 TGATTTCGGACAAATTTCATATGCAG 59.026 34.615 0.00 0.00 0.00 4.41
3486 3638 6.797215 CGAAGTTTGATTTCGGACAAATTTC 58.203 36.000 13.24 13.24 43.00 2.17
3509 3661 7.081349 TGCTATGAATTTGGTCAAACTTTACG 58.919 34.615 0.00 0.00 32.51 3.18
3512 3664 8.729805 TTTTGCTATGAATTTGGTCAAACTTT 57.270 26.923 0.00 0.00 32.51 2.66
3513 3665 8.729805 TTTTTGCTATGAATTTGGTCAAACTT 57.270 26.923 0.00 0.00 32.51 2.66
3542 3695 9.108284 ACATTGATATCGTATTGTGAATGTTGA 57.892 29.630 7.57 0.00 30.53 3.18
3573 3726 5.013547 TGAAAATTAATCGGTGGTCCATGT 58.986 37.500 0.00 0.00 0.00 3.21
3648 3802 8.633075 CAATTGAGTTGTACACAAAGTTTGAT 57.367 30.769 22.23 11.71 37.63 2.57
3706 3880 6.764379 TCCATGTTACTGTTTGTCTCATACA 58.236 36.000 0.00 0.00 35.88 2.29
3710 3884 5.883115 TGTTTCCATGTTACTGTTTGTCTCA 59.117 36.000 0.00 0.00 0.00 3.27
3711 3885 6.371809 TGTTTCCATGTTACTGTTTGTCTC 57.628 37.500 0.00 0.00 0.00 3.36
3716 3890 9.569122 AGTAGTTATGTTTCCATGTTACTGTTT 57.431 29.630 0.00 0.00 32.29 2.83
3752 3926 6.768381 TGTGACACACTGTATATTTTGTTCCA 59.232 34.615 3.56 0.00 35.11 3.53
3753 3927 7.197071 TGTGACACACTGTATATTTTGTTCC 57.803 36.000 3.56 0.00 35.11 3.62
3789 3963 0.994995 CCTCAGCATTCGAGAACACG 59.005 55.000 0.00 0.00 31.84 4.49
3792 3966 1.731720 AAGCCTCAGCATTCGAGAAC 58.268 50.000 0.00 0.00 43.56 3.01
3808 3982 6.241207 TGCAACAAGTCAGTCTTATAAAGC 57.759 37.500 0.00 0.00 34.66 3.51
3809 3983 8.292448 ACAATGCAACAAGTCAGTCTTATAAAG 58.708 33.333 0.00 0.00 34.66 1.85
3812 3986 6.090763 CGACAATGCAACAAGTCAGTCTTATA 59.909 38.462 0.00 0.00 34.66 0.98
3813 3987 5.106948 CGACAATGCAACAAGTCAGTCTTAT 60.107 40.000 0.00 0.00 34.66 1.73
3814 3988 4.211164 CGACAATGCAACAAGTCAGTCTTA 59.789 41.667 0.00 0.00 34.66 2.10
3817 3991 2.287915 ACGACAATGCAACAAGTCAGTC 59.712 45.455 0.00 0.00 0.00 3.51
3821 3995 3.002246 TGAGAACGACAATGCAACAAGTC 59.998 43.478 0.00 0.00 0.00 3.01
3823 3997 3.607422 TGAGAACGACAATGCAACAAG 57.393 42.857 0.00 0.00 0.00 3.16
3837 4011 0.759346 AGGGCCATCGGTATGAGAAC 59.241 55.000 6.18 0.00 34.84 3.01
3844 4018 1.321474 CGTACTAAGGGCCATCGGTA 58.679 55.000 6.18 1.27 0.00 4.02
3847 4021 0.742505 TCACGTACTAAGGGCCATCG 59.257 55.000 6.18 0.00 0.00 3.84
3859 4033 7.766219 ACTTACATTCACCATATTCACGTAC 57.234 36.000 0.00 0.00 0.00 3.67
3860 4034 8.661257 CAAACTTACATTCACCATATTCACGTA 58.339 33.333 0.00 0.00 0.00 3.57
3861 4035 7.174253 ACAAACTTACATTCACCATATTCACGT 59.826 33.333 0.00 0.00 0.00 4.49
3862 4036 7.481483 CACAAACTTACATTCACCATATTCACG 59.519 37.037 0.00 0.00 0.00 4.35
3863 4037 8.511321 TCACAAACTTACATTCACCATATTCAC 58.489 33.333 0.00 0.00 0.00 3.18
3864 4038 8.511321 GTCACAAACTTACATTCACCATATTCA 58.489 33.333 0.00 0.00 0.00 2.57
3865 4039 8.511321 TGTCACAAACTTACATTCACCATATTC 58.489 33.333 0.00 0.00 0.00 1.75
3866 4040 8.402798 TGTCACAAACTTACATTCACCATATT 57.597 30.769 0.00 0.00 0.00 1.28
3870 4044 6.516739 TTTGTCACAAACTTACATTCACCA 57.483 33.333 0.00 0.00 0.00 4.17
3921 4105 6.271566 GCATCCAAGGAAGATGAAAAGAATC 58.728 40.000 4.98 0.00 43.15 2.52
3925 4109 3.765511 TGGCATCCAAGGAAGATGAAAAG 59.234 43.478 4.98 0.00 43.15 2.27
3992 4178 0.608640 AACAGTGTAGCTTCTCCCCG 59.391 55.000 0.00 0.00 0.00 5.73
3994 4180 4.737855 TCATAACAGTGTAGCTTCTCCC 57.262 45.455 0.00 0.00 0.00 4.30
4015 4201 9.143155 AGGAGGTTTTACAACATTTTGTATCTT 57.857 29.630 5.33 0.00 45.60 2.40
4021 4207 9.541143 AAACATAGGAGGTTTTACAACATTTTG 57.459 29.630 0.00 0.00 35.01 2.44


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

AutoCloner maintained by Alex Coulton.