Multiple sequence alignment - TraesCS3B01G451100

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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 TraesCS3B01G451100 chr3B 100.000 3329 0 0 1 3329 691460353 691457025 0.000000e+00 6148.0
1 TraesCS3B01G451100 chr3B 91.039 279 13 6 167 434 691511756 691511479 1.890000e-97 366.0
2 TraesCS3B01G451100 chr3D 90.227 2957 136 52 487 3329 524201015 524203932 0.000000e+00 3718.0
3 TraesCS3B01G451100 chr3D 91.018 334 10 7 157 479 524197775 524198099 1.830000e-117 433.0
4 TraesCS3B01G451100 chr3A 90.521 2226 104 40 1183 3329 658843560 658841363 0.000000e+00 2843.0
5 TraesCS3B01G451100 chr3A 89.091 275 12 10 54 311 658845063 658844790 3.200000e-85 326.0
6 TraesCS3B01G451100 chr3A 79.276 497 32 34 486 954 658844623 658844170 7.030000e-72 281.0
7 TraesCS3B01G451100 chr3A 91.736 121 7 2 1026 1143 658843754 658843634 7.390000e-37 165.0
8 TraesCS3B01G451100 chr3A 94.595 37 2 0 946 982 658844161 658844125 1.290000e-04 58.4


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 TraesCS3B01G451100 chr3B 691457025 691460353 3328 True 6148.00 6148 100.0000 1 3329 1 chr3B.!!$R1 3328
1 TraesCS3B01G451100 chr3D 524197775 524203932 6157 False 2075.50 3718 90.6225 157 3329 2 chr3D.!!$F1 3172
2 TraesCS3B01G451100 chr3A 658841363 658845063 3700 True 734.68 2843 89.0438 54 3329 5 chr3A.!!$R1 3275

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
671 3647 0.110678 CATCAGCCATGGCCTCTCAT 59.889 55.0 33.14 14.63 43.17 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2529 6003 0.833949 CTCTTAGCTGGAGTTCCCCC 59.166 60.0 0.0 0.0 34.29 5.4 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
32 33 2.351777 GGGGGTCTTGTCCAAAAGC 58.648 57.895 0.00 0.00 0.00 3.51
33 34 1.185618 GGGGGTCTTGTCCAAAAGCC 61.186 60.000 0.00 0.00 0.00 4.35
34 35 1.185618 GGGGTCTTGTCCAAAAGCCC 61.186 60.000 4.95 4.95 40.21 5.19
35 36 0.469144 GGGTCTTGTCCAAAAGCCCA 60.469 55.000 9.94 0.00 40.44 5.36
36 37 0.961753 GGTCTTGTCCAAAAGCCCAG 59.038 55.000 0.00 0.00 0.00 4.45
37 38 1.692411 GTCTTGTCCAAAAGCCCAGT 58.308 50.000 0.00 0.00 0.00 4.00
38 39 2.031870 GTCTTGTCCAAAAGCCCAGTT 58.968 47.619 0.00 0.00 0.00 3.16
39 40 2.031120 TCTTGTCCAAAAGCCCAGTTG 58.969 47.619 0.00 0.00 0.00 3.16
40 41 1.756538 CTTGTCCAAAAGCCCAGTTGT 59.243 47.619 0.00 0.00 0.00 3.32
41 42 1.110442 TGTCCAAAAGCCCAGTTGTG 58.890 50.000 0.00 0.00 0.00 3.33
42 43 0.249447 GTCCAAAAGCCCAGTTGTGC 60.249 55.000 0.00 0.00 0.00 4.57
43 44 1.069596 CCAAAAGCCCAGTTGTGCC 59.930 57.895 0.00 0.00 0.00 5.01
44 45 1.069596 CAAAAGCCCAGTTGTGCCC 59.930 57.895 0.00 0.00 0.00 5.36
45 46 2.140138 AAAAGCCCAGTTGTGCCCC 61.140 57.895 0.00 0.00 0.00 5.80
46 47 2.887738 AAAAGCCCAGTTGTGCCCCA 62.888 55.000 0.00 0.00 0.00 4.96
47 48 2.677968 AAAGCCCAGTTGTGCCCCAT 62.678 55.000 0.00 0.00 0.00 4.00
48 49 2.604382 GCCCAGTTGTGCCCCATT 60.604 61.111 0.00 0.00 0.00 3.16
49 50 2.946346 GCCCAGTTGTGCCCCATTG 61.946 63.158 0.00 0.00 0.00 2.82
50 51 1.228831 CCCAGTTGTGCCCCATTGA 60.229 57.895 0.00 0.00 0.00 2.57
51 52 1.535204 CCCAGTTGTGCCCCATTGAC 61.535 60.000 0.00 0.00 0.00 3.18
52 53 0.540365 CCAGTTGTGCCCCATTGACT 60.540 55.000 0.00 0.00 0.00 3.41
82 83 1.760613 TCTCACGACCAAGTGTTCCTT 59.239 47.619 0.00 0.00 42.40 3.36
94 95 5.229423 CAAGTGTTCCTTTCTCTCTCTCTG 58.771 45.833 0.00 0.00 0.00 3.35
95 96 4.735369 AGTGTTCCTTTCTCTCTCTCTGA 58.265 43.478 0.00 0.00 0.00 3.27
98 102 3.094484 TCCTTTCTCTCTCTCTGACCC 57.906 52.381 0.00 0.00 0.00 4.46
127 131 1.630369 TGGCCAGATTCTGCAGTTAGT 59.370 47.619 14.67 0.00 0.00 2.24
131 135 2.421424 CCAGATTCTGCAGTTAGTTGCC 59.579 50.000 14.67 0.00 43.43 4.52
132 136 3.341823 CAGATTCTGCAGTTAGTTGCCT 58.658 45.455 14.67 0.00 43.43 4.75
133 137 3.126514 CAGATTCTGCAGTTAGTTGCCTG 59.873 47.826 14.67 7.28 43.43 4.85
139 143 0.239347 CAGTTAGTTGCCTGCAGTGC 59.761 55.000 13.81 15.86 0.00 4.40
150 159 1.135199 CCTGCAGTGCACATTTCATCC 60.135 52.381 21.04 0.00 33.79 3.51
151 160 1.542472 CTGCAGTGCACATTTCATCCA 59.458 47.619 21.04 2.96 33.79 3.41
152 161 2.165641 CTGCAGTGCACATTTCATCCAT 59.834 45.455 21.04 0.00 33.79 3.41
153 162 3.354467 TGCAGTGCACATTTCATCCATA 58.646 40.909 21.04 0.00 31.71 2.74
154 163 3.955551 TGCAGTGCACATTTCATCCATAT 59.044 39.130 21.04 0.00 31.71 1.78
155 164 5.131784 TGCAGTGCACATTTCATCCATATA 58.868 37.500 21.04 0.00 31.71 0.86
223 241 1.002544 AGTCCAGTGAGTTTAGCCTGC 59.997 52.381 0.00 0.00 0.00 4.85
266 284 8.199449 TCCGATACAGTTAATTAACTAACCAGG 58.801 37.037 26.38 23.95 44.19 4.45
385 432 6.672266 TTTAGGAGGAGCATATTCGATCTT 57.328 37.500 0.00 0.00 0.00 2.40
386 433 4.533919 AGGAGGAGCATATTCGATCTTG 57.466 45.455 0.00 0.00 0.00 3.02
388 435 4.346418 AGGAGGAGCATATTCGATCTTGTT 59.654 41.667 0.00 0.00 0.00 2.83
389 436 4.450419 GGAGGAGCATATTCGATCTTGTTG 59.550 45.833 0.00 0.00 0.00 3.33
390 437 3.812053 AGGAGCATATTCGATCTTGTTGC 59.188 43.478 0.00 0.00 0.00 4.17
391 438 3.812053 GGAGCATATTCGATCTTGTTGCT 59.188 43.478 6.71 6.71 41.32 3.91
392 439 4.319333 GGAGCATATTCGATCTTGTTGCTG 60.319 45.833 10.48 0.00 38.93 4.41
393 440 3.562973 AGCATATTCGATCTTGTTGCTGG 59.437 43.478 6.32 0.00 37.55 4.85
394 441 3.851105 GCATATTCGATCTTGTTGCTGGC 60.851 47.826 0.00 0.00 0.00 4.85
395 442 2.119801 ATTCGATCTTGTTGCTGGCT 57.880 45.000 0.00 0.00 0.00 4.75
431 478 1.081892 CTCGATCAAGTGGGCAACAG 58.918 55.000 0.00 0.00 39.74 3.16
473 525 2.237066 GCAAGGTGTTTGGCGCAAC 61.237 57.895 10.83 6.71 37.26 4.17
479 531 0.865639 GTGTTTGGCGCAACACTCAC 60.866 55.000 27.31 16.46 0.00 3.51
481 533 0.941542 GTTTGGCGCAACACTCACTA 59.058 50.000 10.83 0.00 0.00 2.74
482 534 1.535462 GTTTGGCGCAACACTCACTAT 59.465 47.619 10.83 0.00 0.00 2.12
483 535 1.438651 TTGGCGCAACACTCACTATC 58.561 50.000 10.83 0.00 0.00 2.08
527 3491 2.442643 CACATCCCCACATGCCCC 60.443 66.667 0.00 0.00 0.00 5.80
537 3501 2.836360 CATGCCCCTCCATGTGCC 60.836 66.667 0.00 0.00 38.19 5.01
538 3502 3.349304 ATGCCCCTCCATGTGCCA 61.349 61.111 0.00 0.00 0.00 4.92
539 3503 2.933617 ATGCCCCTCCATGTGCCAA 61.934 57.895 0.00 0.00 0.00 4.52
637 3601 1.586541 CCGAGCTCACTGCACACTA 59.413 57.895 15.40 0.00 45.94 2.74
639 3603 0.242286 CGAGCTCACTGCACACTACT 59.758 55.000 15.40 0.00 45.94 2.57
641 3605 2.095212 CGAGCTCACTGCACACTACTTA 60.095 50.000 15.40 0.00 45.94 2.24
642 3606 3.246619 GAGCTCACTGCACACTACTTAC 58.753 50.000 9.40 0.00 45.94 2.34
643 3607 2.028930 AGCTCACTGCACACTACTTACC 60.029 50.000 0.00 0.00 45.94 2.85
644 3608 2.028930 GCTCACTGCACACTACTTACCT 60.029 50.000 0.00 0.00 42.31 3.08
646 3610 3.227614 TCACTGCACACTACTTACCTGA 58.772 45.455 0.00 0.00 0.00 3.86
647 3611 3.255888 TCACTGCACACTACTTACCTGAG 59.744 47.826 0.00 0.00 0.00 3.35
651 3615 2.417515 GCACACTACTTACCTGAGGAGC 60.418 54.545 4.99 0.00 30.20 4.70
670 3646 1.530283 CATCAGCCATGGCCTCTCA 59.470 57.895 33.14 12.89 43.17 3.27
671 3647 0.110678 CATCAGCCATGGCCTCTCAT 59.889 55.000 33.14 14.63 43.17 2.90
672 3648 0.400975 ATCAGCCATGGCCTCTCATC 59.599 55.000 33.14 3.07 43.17 2.92
678 3654 0.749049 CATGGCCTCTCATCTCGTCA 59.251 55.000 3.32 0.00 0.00 4.35
681 3657 1.137675 TGGCCTCTCATCTCGTCAATG 59.862 52.381 3.32 0.00 0.00 2.82
703 3705 0.675083 CATGGTGAAAGTTGGCAGCA 59.325 50.000 3.63 11.70 45.20 4.41
711 3713 4.331168 GTGAAAGTTGGCAGCATAGTAGAG 59.669 45.833 3.63 0.00 0.00 2.43
712 3714 2.611225 AGTTGGCAGCATAGTAGAGC 57.389 50.000 3.63 0.00 0.00 4.09
714 3716 1.936547 GTTGGCAGCATAGTAGAGCAC 59.063 52.381 0.00 0.00 0.00 4.40
716 3718 1.410517 TGGCAGCATAGTAGAGCACTC 59.589 52.381 0.00 0.00 38.80 3.51
717 3719 1.270041 GGCAGCATAGTAGAGCACTCC 60.270 57.143 0.00 0.00 38.80 3.85
718 3720 1.601663 GCAGCATAGTAGAGCACTCCG 60.602 57.143 0.00 0.00 38.80 4.63
719 3721 1.678627 CAGCATAGTAGAGCACTCCGT 59.321 52.381 0.00 0.00 38.80 4.69
720 3722 2.879026 CAGCATAGTAGAGCACTCCGTA 59.121 50.000 0.00 0.00 38.80 4.02
721 3723 3.058570 CAGCATAGTAGAGCACTCCGTAG 60.059 52.174 0.00 0.00 38.80 3.51
722 3724 2.879646 GCATAGTAGAGCACTCCGTAGT 59.120 50.000 0.00 0.00 38.80 2.73
723 3725 4.063689 GCATAGTAGAGCACTCCGTAGTA 58.936 47.826 0.00 0.00 38.80 1.82
724 3726 4.152759 GCATAGTAGAGCACTCCGTAGTAG 59.847 50.000 0.00 0.00 38.80 2.57
725 3727 5.539979 CATAGTAGAGCACTCCGTAGTAGA 58.460 45.833 0.00 0.00 38.80 2.59
726 3728 4.484537 AGTAGAGCACTCCGTAGTAGAA 57.515 45.455 0.00 0.00 33.48 2.10
727 3729 4.841422 AGTAGAGCACTCCGTAGTAGAAA 58.159 43.478 0.00 0.00 33.48 2.52
728 3730 5.251764 AGTAGAGCACTCCGTAGTAGAAAA 58.748 41.667 0.00 0.00 33.48 2.29
729 3731 5.709164 AGTAGAGCACTCCGTAGTAGAAAAA 59.291 40.000 0.00 0.00 33.48 1.94
730 3732 5.662674 AGAGCACTCCGTAGTAGAAAAAT 57.337 39.130 0.00 0.00 33.48 1.82
731 3733 5.411781 AGAGCACTCCGTAGTAGAAAAATG 58.588 41.667 0.00 0.00 33.48 2.32
732 3734 5.185249 AGAGCACTCCGTAGTAGAAAAATGA 59.815 40.000 0.00 0.00 33.48 2.57
733 3735 5.790593 AGCACTCCGTAGTAGAAAAATGAA 58.209 37.500 0.00 0.00 33.48 2.57
739 3741 9.333724 ACTCCGTAGTAGAAAAATGAAGAAAAA 57.666 29.630 0.00 0.00 32.84 1.94
798 3803 1.441729 CGCGGAGGAATCAAGGCTA 59.558 57.895 0.00 0.00 0.00 3.93
861 3871 2.476854 GCATTTACTCGCTCCAAGCAAG 60.477 50.000 0.00 0.00 42.58 4.01
862 3872 1.156736 TTTACTCGCTCCAAGCAAGC 58.843 50.000 0.00 0.00 42.58 4.01
905 3941 1.320507 TCCTGGTTTAAAACGCCACC 58.679 50.000 0.00 0.00 0.00 4.61
1137 4517 0.394192 TCCTTGCTAGCCCATCATCG 59.606 55.000 13.29 0.00 0.00 3.84
1143 4523 1.674221 GCTAGCCCATCATCGATCCAC 60.674 57.143 2.29 0.00 0.00 4.02
1179 4559 2.735663 GTGTCTCTCAGTTCGTCGTAGA 59.264 50.000 0.00 0.00 0.00 2.59
1377 4799 0.389948 CGTGGTGTAGGAACCTGCTC 60.390 60.000 10.01 6.50 41.16 4.26
1527 4958 1.001764 CAAGGTGGAGATGCAGCCA 60.002 57.895 0.00 0.00 0.00 4.75
1662 5093 1.226211 CTACTACGTGGCGGTCGTG 60.226 63.158 0.00 5.49 41.62 4.35
1683 5114 4.767255 GGCGAGGAGGTGGTGCTG 62.767 72.222 0.00 0.00 0.00 4.41
1854 5285 0.389687 TGCACGACATCAGCATCGAA 60.390 50.000 0.00 0.00 40.86 3.71
2093 5539 4.047059 GCCGTCACCCGACTTCGA 62.047 66.667 0.00 0.00 43.02 3.71
2189 5639 1.810151 GCTCGCTAGCTAGCTAGATGT 59.190 52.381 42.59 15.68 46.56 3.06
2214 5664 9.410556 GTTCTTACCTACATTCGTTTGTTACTA 57.589 33.333 0.00 0.00 0.00 1.82
2259 5709 4.787260 TGATGGACATTTCACCATGTTG 57.213 40.909 0.00 0.00 45.41 3.33
2291 5741 9.740239 AACATACTACTACCATGTAATGTAACG 57.260 33.333 0.00 0.00 44.81 3.18
2297 5747 4.875544 ACCATGTAATGTAACGATGTGC 57.124 40.909 0.00 0.00 44.81 4.57
2395 5863 1.108776 GTGCATGCACATGGAGGATT 58.891 50.000 39.12 0.00 45.53 3.01
2398 5866 2.025344 GCATGCACATGGAGGATTGGA 61.025 52.381 14.21 0.00 39.16 3.53
2400 5868 0.394762 TGCACATGGAGGATTGGAGC 60.395 55.000 0.00 0.00 0.00 4.70
2529 6003 5.217393 CAATCAATCATGCTGGTTTATCCG 58.783 41.667 0.00 0.00 39.52 4.18
2569 6051 0.790993 ACTGGTCCCTCCTAACTCCA 59.209 55.000 0.00 0.00 37.07 3.86
2724 6227 5.401531 TGGACAAGGACACAAGATACTAC 57.598 43.478 0.00 0.00 0.00 2.73
2725 6228 5.084519 TGGACAAGGACACAAGATACTACT 58.915 41.667 0.00 0.00 0.00 2.57
2726 6229 6.250711 TGGACAAGGACACAAGATACTACTA 58.749 40.000 0.00 0.00 0.00 1.82
2729 6232 7.159322 ACAAGGACACAAGATACTACTAGTG 57.841 40.000 5.39 0.00 0.00 2.74
2741 6247 8.693120 AGATACTACTAGTGCAATAGCTGTAA 57.307 34.615 20.52 3.97 42.74 2.41
2811 6317 3.194861 GTTTTTCACCCAGGTTTTCAGC 58.805 45.455 0.00 0.00 0.00 4.26
2869 6382 3.204526 CAAGTTGAGATCTCAGGGATGC 58.795 50.000 23.92 11.88 41.13 3.91
2893 6407 3.089284 ACTGGGCCAGTTTTAATAGTGC 58.911 45.455 33.18 0.00 42.59 4.40
2923 6450 4.128925 TGCAGATGAAAGGCTACTACTG 57.871 45.455 0.00 0.00 0.00 2.74
2940 6467 7.911205 GCTACTACTGTGTTTCATACAGACTAG 59.089 40.741 11.65 6.67 46.52 2.57
2943 6470 8.298140 ACTACTGTGTTTCATACAGACTAGAAC 58.702 37.037 11.65 0.00 46.52 3.01
2946 6473 8.150945 ACTGTGTTTCATACAGACTAGAACAAT 58.849 33.333 11.65 0.00 46.52 2.71
2947 6474 8.310406 TGTGTTTCATACAGACTAGAACAATG 57.690 34.615 0.00 0.00 37.45 2.82
2949 6476 9.155975 GTGTTTCATACAGACTAGAACAATGAT 57.844 33.333 0.00 0.00 37.45 2.45
2964 6491 8.483307 AGAACAATGATAATTCAAAATGGTGC 57.517 30.769 0.00 0.00 34.96 5.01
2965 6492 7.550196 AGAACAATGATAATTCAAAATGGTGCC 59.450 33.333 0.00 0.00 34.96 5.01
2966 6493 6.114767 ACAATGATAATTCAAAATGGTGCCC 58.885 36.000 0.00 0.00 34.96 5.36
2967 6494 5.954153 ATGATAATTCAAAATGGTGCCCA 57.046 34.783 0.00 0.00 34.74 5.36
2968 6495 5.341872 TGATAATTCAAAATGGTGCCCAG 57.658 39.130 0.41 0.00 36.75 4.45
2970 6497 2.028561 ATTCAAAATGGTGCCCAGGT 57.971 45.000 0.41 0.00 36.75 4.00
3095 6624 0.396139 GCTCATGCCTTCCCCATTGA 60.396 55.000 0.00 0.00 0.00 2.57
3096 6625 1.756690 GCTCATGCCTTCCCCATTGAT 60.757 52.381 0.00 0.00 0.00 2.57
3103 6632 2.101917 GCCTTCCCCATTGATTGACATG 59.898 50.000 0.00 0.00 0.00 3.21
3125 6654 4.040217 TGCATTGTTTAAACCAGGAATGCT 59.960 37.500 32.23 5.17 41.40 3.79
3216 6745 0.965439 GCATCCTACGCTCTCCTCAT 59.035 55.000 0.00 0.00 0.00 2.90
3225 6754 2.295909 ACGCTCTCCTCATGATTCTAGC 59.704 50.000 0.00 3.12 0.00 3.42
3298 6834 4.148174 GCGAACATGGAAAAGTAAACTTGC 59.852 41.667 0.00 0.00 36.12 4.01
3319 6855 2.609459 CTGACCAAACAGCCGATATGAC 59.391 50.000 0.00 0.00 0.00 3.06
3324 6860 3.303329 CCAAACAGCCGATATGACGAATG 60.303 47.826 0.00 0.00 35.09 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.185618 GGCTTTTGGACAAGACCCCC 61.186 60.000 0.00 0.00 0.00 5.40
15 16 1.185618 GGGCTTTTGGACAAGACCCC 61.186 60.000 0.00 0.45 45.48 4.95
16 17 2.351777 GGGCTTTTGGACAAGACCC 58.648 57.895 0.00 4.15 45.48 4.46
18 19 1.692411 ACTGGGCTTTTGGACAAGAC 58.308 50.000 0.00 0.00 0.00 3.01
19 20 2.031120 CAACTGGGCTTTTGGACAAGA 58.969 47.619 0.00 0.00 0.00 3.02
20 21 1.756538 ACAACTGGGCTTTTGGACAAG 59.243 47.619 0.00 0.00 0.00 3.16
21 22 1.480137 CACAACTGGGCTTTTGGACAA 59.520 47.619 0.00 0.00 0.00 3.18
22 23 1.110442 CACAACTGGGCTTTTGGACA 58.890 50.000 0.00 0.00 0.00 4.02
23 24 0.249447 GCACAACTGGGCTTTTGGAC 60.249 55.000 0.00 0.00 42.27 4.02
24 25 1.398958 GGCACAACTGGGCTTTTGGA 61.399 55.000 3.57 0.00 45.56 3.53
25 26 1.069596 GGCACAACTGGGCTTTTGG 59.930 57.895 3.57 0.00 45.56 3.28
26 27 1.069596 GGGCACAACTGGGCTTTTG 59.930 57.895 3.57 0.00 45.56 2.44
27 28 2.140138 GGGGCACAACTGGGCTTTT 61.140 57.895 3.57 0.00 45.56 2.27
28 29 2.524148 GGGGCACAACTGGGCTTT 60.524 61.111 3.57 0.00 45.56 3.51
29 30 2.677968 AATGGGGCACAACTGGGCTT 62.678 55.000 3.57 0.00 45.56 4.35
30 31 3.164610 AATGGGGCACAACTGGGCT 62.165 57.895 3.57 0.00 45.56 5.19
31 32 2.604382 AATGGGGCACAACTGGGC 60.604 61.111 0.00 0.00 45.53 5.36
32 33 1.228831 TCAATGGGGCACAACTGGG 60.229 57.895 0.00 0.00 0.00 4.45
33 34 0.540365 AGTCAATGGGGCACAACTGG 60.540 55.000 0.00 0.00 0.00 4.00
34 35 0.599558 CAGTCAATGGGGCACAACTG 59.400 55.000 5.72 5.72 0.00 3.16
35 36 1.181098 GCAGTCAATGGGGCACAACT 61.181 55.000 0.00 0.00 0.00 3.16
36 37 1.181098 AGCAGTCAATGGGGCACAAC 61.181 55.000 0.00 0.00 0.00 3.32
37 38 0.895100 GAGCAGTCAATGGGGCACAA 60.895 55.000 0.00 0.00 0.00 3.33
38 39 1.303561 GAGCAGTCAATGGGGCACA 60.304 57.895 0.00 0.00 0.00 4.57
39 40 0.610232 AAGAGCAGTCAATGGGGCAC 60.610 55.000 0.00 0.00 0.00 5.01
40 41 0.112995 AAAGAGCAGTCAATGGGGCA 59.887 50.000 0.00 0.00 0.00 5.36
41 42 1.067354 CAAAAGAGCAGTCAATGGGGC 60.067 52.381 0.00 0.00 0.00 5.80
42 43 2.229784 GACAAAAGAGCAGTCAATGGGG 59.770 50.000 0.00 0.00 32.68 4.96
43 44 3.152341 AGACAAAAGAGCAGTCAATGGG 58.848 45.455 0.00 0.00 34.80 4.00
44 45 3.817084 TGAGACAAAAGAGCAGTCAATGG 59.183 43.478 0.00 0.00 34.80 3.16
45 46 4.610007 CGTGAGACAAAAGAGCAGTCAATG 60.610 45.833 0.00 0.00 34.80 2.82
46 47 3.496130 CGTGAGACAAAAGAGCAGTCAAT 59.504 43.478 0.00 0.00 34.80 2.57
47 48 2.866156 CGTGAGACAAAAGAGCAGTCAA 59.134 45.455 0.00 0.00 34.80 3.18
48 49 2.100749 TCGTGAGACAAAAGAGCAGTCA 59.899 45.455 0.00 0.00 34.80 3.41
49 50 2.743938 TCGTGAGACAAAAGAGCAGTC 58.256 47.619 0.00 0.00 33.31 3.51
50 51 2.890808 TCGTGAGACAAAAGAGCAGT 57.109 45.000 0.00 0.00 33.31 4.40
82 83 1.996291 TCTGGGGTCAGAGAGAGAGAA 59.004 52.381 0.00 0.00 44.39 2.87
94 95 0.897621 CTGGCCATTTTTCTGGGGTC 59.102 55.000 5.51 0.00 36.75 4.46
95 96 0.486879 TCTGGCCATTTTTCTGGGGT 59.513 50.000 5.51 0.00 36.75 4.95
98 102 3.677976 GCAGAATCTGGCCATTTTTCTGG 60.678 47.826 32.27 22.30 42.13 3.86
127 131 0.032403 GAAATGTGCACTGCAGGCAA 59.968 50.000 25.17 17.50 43.91 4.52
131 135 1.542472 TGGATGAAATGTGCACTGCAG 59.458 47.619 19.41 13.48 40.08 4.41
132 136 1.618487 TGGATGAAATGTGCACTGCA 58.382 45.000 19.41 10.80 35.60 4.41
133 137 2.953466 ATGGATGAAATGTGCACTGC 57.047 45.000 19.41 1.93 0.00 4.40
134 138 6.016527 AGCTTATATGGATGAAATGTGCACTG 60.017 38.462 19.41 0.00 0.00 3.66
135 139 6.016527 CAGCTTATATGGATGAAATGTGCACT 60.017 38.462 19.41 0.00 0.00 4.40
136 140 6.147581 CAGCTTATATGGATGAAATGTGCAC 58.852 40.000 10.75 10.75 0.00 4.57
137 141 5.278610 GCAGCTTATATGGATGAAATGTGCA 60.279 40.000 0.00 0.00 0.00 4.57
138 142 5.159209 GCAGCTTATATGGATGAAATGTGC 58.841 41.667 0.00 0.00 0.00 4.57
139 143 6.147581 GTGCAGCTTATATGGATGAAATGTG 58.852 40.000 0.00 0.00 0.00 3.21
223 241 0.249489 GGATTCCGTCAGGTGGATCG 60.249 60.000 0.00 0.00 39.05 3.69
252 270 5.297799 AGGATCCTCCCTGGTTAGTTAATT 58.702 41.667 9.02 0.00 37.19 1.40
473 525 1.418334 CCTCTGGGGGATAGTGAGTG 58.582 60.000 0.00 0.00 0.00 3.51
479 531 0.400525 TTCTGGCCTCTGGGGGATAG 60.401 60.000 3.32 0.00 35.12 2.08
481 533 0.628668 ATTTCTGGCCTCTGGGGGAT 60.629 55.000 3.32 0.00 35.12 3.85
482 534 1.230281 ATTTCTGGCCTCTGGGGGA 60.230 57.895 3.32 0.00 35.12 4.81
483 535 1.228510 GATTTCTGGCCTCTGGGGG 59.771 63.158 3.32 0.00 35.12 5.40
527 3491 0.104120 CATGGCATTGGCACATGGAG 59.896 55.000 15.84 0.00 41.84 3.86
537 3501 1.687563 TGCTGGAGATCATGGCATTG 58.312 50.000 0.00 0.00 0.00 2.82
538 3502 2.239400 CATGCTGGAGATCATGGCATT 58.761 47.619 0.00 0.00 40.93 3.56
539 3503 1.145119 ACATGCTGGAGATCATGGCAT 59.855 47.619 0.00 0.00 43.11 4.40
595 3559 2.447765 TATCTTGGGGGCTCGGGG 60.448 66.667 0.00 0.00 0.00 5.73
596 3560 0.471211 TACTATCTTGGGGGCTCGGG 60.471 60.000 0.00 0.00 0.00 5.14
611 3575 1.471119 CAGTGAGCTCGGGGTTACTA 58.529 55.000 11.94 0.00 37.62 1.82
637 3601 2.114616 CTGATGGCTCCTCAGGTAAGT 58.885 52.381 0.00 0.00 37.15 2.24
639 3603 0.833287 GCTGATGGCTCCTCAGGTAA 59.167 55.000 12.12 0.00 40.40 2.85
641 3605 2.373707 GGCTGATGGCTCCTCAGGT 61.374 63.158 12.12 0.00 40.40 4.00
642 3606 1.706995 ATGGCTGATGGCTCCTCAGG 61.707 60.000 12.12 0.00 40.40 3.86
643 3607 0.535328 CATGGCTGATGGCTCCTCAG 60.535 60.000 7.61 7.61 42.47 3.35
644 3608 1.530283 CATGGCTGATGGCTCCTCA 59.470 57.895 0.00 0.00 41.46 3.86
646 3610 2.924640 CCATGGCTGATGGCTCCT 59.075 61.111 0.00 0.00 45.58 3.69
670 3646 2.169144 TCACCATGAGCATTGACGAGAT 59.831 45.455 0.00 0.00 0.00 2.75
671 3647 1.550072 TCACCATGAGCATTGACGAGA 59.450 47.619 0.00 0.00 0.00 4.04
672 3648 2.014335 TCACCATGAGCATTGACGAG 57.986 50.000 0.00 0.00 0.00 4.18
678 3654 2.028748 GCCAACTTTCACCATGAGCATT 60.029 45.455 0.00 0.00 0.00 3.56
681 3657 0.961019 TGCCAACTTTCACCATGAGC 59.039 50.000 0.00 0.00 0.00 4.26
703 3705 5.804944 TCTACTACGGAGTGCTCTACTAT 57.195 43.478 11.61 0.00 45.73 2.12
711 3713 5.867716 TCTTCATTTTTCTACTACGGAGTGC 59.132 40.000 11.61 0.00 45.73 4.40
712 3714 7.884816 TTCTTCATTTTTCTACTACGGAGTG 57.115 36.000 11.61 0.19 45.73 3.51
861 3871 4.838152 TCCTCCGCTTGCCATCGC 62.838 66.667 0.00 0.00 0.00 4.58
862 3872 2.125147 TTCCTCCGCTTGCCATCG 60.125 61.111 0.00 0.00 0.00 3.84
864 3874 0.393537 CTTCTTCCTCCGCTTGCCAT 60.394 55.000 0.00 0.00 0.00 4.40
865 3875 1.003355 CTTCTTCCTCCGCTTGCCA 60.003 57.895 0.00 0.00 0.00 4.92
866 3876 1.746991 CCTTCTTCCTCCGCTTGCC 60.747 63.158 0.00 0.00 0.00 4.52
1137 4517 2.230992 CGAGAGGATGGATGAGTGGATC 59.769 54.545 0.00 0.00 0.00 3.36
1143 4523 2.293122 GAGACACGAGAGGATGGATGAG 59.707 54.545 0.00 0.00 0.00 2.90
1179 4559 0.339859 TCCTGTCTGCCCCTCACTAT 59.660 55.000 0.00 0.00 0.00 2.12
1302 4724 2.803670 CGGTACACCAGCGTCACG 60.804 66.667 0.00 0.00 43.13 4.35
1365 4787 2.284331 TGGGCGAGCAGGTTCCTA 60.284 61.111 0.00 0.00 0.00 2.94
2079 5519 2.804090 GCGTCGAAGTCGGGTGAC 60.804 66.667 0.00 0.00 45.86 3.67
2101 5547 4.849329 GAACTCGTCGGCGGCGAT 62.849 66.667 37.15 24.07 37.74 4.58
2189 5639 9.410556 GTAGTAACAAACGAATGTAGGTAAGAA 57.589 33.333 0.00 0.00 32.02 2.52
2214 5664 1.447838 CGCTCTGTAATGTGGCGGT 60.448 57.895 0.00 0.00 41.77 5.68
2259 5709 5.661458 ACATGGTAGTAGTATGTTGCTCAC 58.339 41.667 0.00 0.00 31.38 3.51
2291 5741 1.471676 CCCCTCTTACACTCGCACATC 60.472 57.143 0.00 0.00 0.00 3.06
2297 5747 1.835494 TCACTCCCCTCTTACACTCG 58.165 55.000 0.00 0.00 0.00 4.18
2398 5866 3.696518 TATCCTGTGCCCCTCCGCT 62.697 63.158 0.00 0.00 0.00 5.52
2400 5868 1.749334 GACTATCCTGTGCCCCTCCG 61.749 65.000 0.00 0.00 0.00 4.63
2529 6003 0.833949 CTCTTAGCTGGAGTTCCCCC 59.166 60.000 0.00 0.00 34.29 5.40
2569 6051 7.713507 CAGTGTAGAGTAGAGTACTGCTAGATT 59.286 40.741 0.00 0.00 39.07 2.40
2724 6227 8.648557 TGAGTTAATTACAGCTATTGCACTAG 57.351 34.615 6.72 6.72 42.74 2.57
2725 6228 8.648557 CTGAGTTAATTACAGCTATTGCACTA 57.351 34.615 1.12 0.00 42.74 2.74
2726 6229 7.545362 CTGAGTTAATTACAGCTATTGCACT 57.455 36.000 1.12 0.00 42.74 4.40
2741 6247 7.921786 TTAACAATAGTGCAGCTGAGTTAAT 57.078 32.000 20.43 1.80 31.03 1.40
2754 6260 3.938963 ACCAGTCGCCATTAACAATAGTG 59.061 43.478 0.00 0.00 0.00 2.74
2755 6261 4.189231 GACCAGTCGCCATTAACAATAGT 58.811 43.478 0.00 0.00 0.00 2.12
2869 6382 1.937191 ATTAAAACTGGCCCAGTGGG 58.063 50.000 25.22 25.22 44.62 4.61
2893 6407 3.314635 GCCTTTCATCTGCATCTGTTAGG 59.685 47.826 0.00 1.20 0.00 2.69
2923 6450 8.534333 TCATTGTTCTAGTCTGTATGAAACAC 57.466 34.615 0.00 0.00 33.45 3.32
2940 6467 7.687445 GGCACCATTTTGAATTATCATTGTTC 58.313 34.615 0.00 0.00 34.96 3.18
2999 6528 4.371624 ACATGATTGACCTGTTCTCCAA 57.628 40.909 0.00 0.00 0.00 3.53
3095 6624 5.933463 CCTGGTTTAAACAATGCATGTCAAT 59.067 36.000 19.57 0.00 42.99 2.57
3096 6625 5.069648 TCCTGGTTTAAACAATGCATGTCAA 59.930 36.000 19.57 0.00 42.99 3.18
3103 6632 4.568956 AGCATTCCTGGTTTAAACAATGC 58.431 39.130 29.05 29.05 41.27 3.56
3172 6701 9.692749 GCTGTTGATTGCAAGTATACTAGTATA 57.307 33.333 17.03 17.03 34.01 1.47
3173 6702 8.204160 TGCTGTTGATTGCAAGTATACTAGTAT 58.796 33.333 19.07 19.07 36.15 2.12
3174 6703 7.552459 TGCTGTTGATTGCAAGTATACTAGTA 58.448 34.615 5.65 4.77 36.15 1.82
3225 6754 9.696917 GCAGTCCCCATTTTATTCTATTTTATG 57.303 33.333 0.00 0.00 0.00 1.90
3298 6834 2.609459 GTCATATCGGCTGTTTGGTCAG 59.391 50.000 0.00 0.00 38.35 3.51


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

AutoCloner maintained by Alex Coulton.