Multiple sequence alignment - TraesCS7B01G051300

Loading Multiple Alignment...

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 TraesCS7B01G051300 chr7B 100.000 3575 0 0 1 3575 53637219 53633645 0.000000e+00 6602
1 TraesCS7B01G051300 chr7B 85.284 299 30 8 2 293 53642811 53642520 2.700000e-76 296
2 TraesCS7B01G051300 chr7B 91.803 122 8 1 400 521 53642358 53642239 6.140000e-38 169
3 TraesCS7B01G051300 chr7D 90.491 3155 169 60 2 3091 98627330 98624242 0.000000e+00 4043
4 TraesCS7B01G051300 chr7D 83.721 602 49 22 2923 3511 98624270 98623705 1.140000e-144 523
5 TraesCS7B01G051300 chr7D 79.531 469 30 22 97 511 98634368 98633912 1.260000e-69 274
6 TraesCS7B01G051300 chr7A 88.798 3178 184 66 2 3091 100725173 100722080 0.000000e+00 3738
7 TraesCS7B01G051300 chr7A 87.437 398 21 14 2930 3315 100722173 100721793 7.090000e-117 431
8 TraesCS7B01G051300 chr7A 81.425 393 43 19 132 511 100756808 100756433 9.710000e-76 294


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 TraesCS7B01G051300 chr7B 53633645 53637219 3574 True 6602.0 6602 100.0000 1 3575 1 chr7B.!!$R1 3574
1 TraesCS7B01G051300 chr7B 53642239 53642811 572 True 232.5 296 88.5435 2 521 2 chr7B.!!$R2 519
2 TraesCS7B01G051300 chr7D 98623705 98627330 3625 True 2283.0 4043 87.1060 2 3511 2 chr7D.!!$R2 3509
3 TraesCS7B01G051300 chr7A 100721793 100725173 3380 True 2084.5 3738 88.1175 2 3315 2 chr7A.!!$R2 3313

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
544 637 0.108615 GTGCATGCTCTCGTACCTGT 60.109 55.0 20.33 0.0 0.0 4.00 F
959 1072 0.179073 CGCACCCACCTTCCATCTAG 60.179 60.0 0.00 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2232 2379 1.077644 TTCCTCCTCGTCCTCCTCG 60.078 63.158 0.00 0.00 0.0 4.63 R
2596 2755 0.665670 CACACGTGAGCTGAGGTCTG 60.666 60.000 25.01 7.93 0.0 3.51 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
82 88 4.836125 CACAAAGCTTCCATGTGTTACT 57.164 40.909 17.82 0.00 39.60 2.24
83 89 4.539870 CACAAAGCTTCCATGTGTTACTG 58.460 43.478 17.82 3.71 39.60 2.74
84 90 3.004734 ACAAAGCTTCCATGTGTTACTGC 59.995 43.478 0.00 0.00 0.00 4.40
101 107 1.474077 CTGCAAGTTGATAACCTGCCC 59.526 52.381 7.16 0.00 45.88 5.36
103 109 1.474077 GCAAGTTGATAACCTGCCCTG 59.526 52.381 7.16 0.00 41.79 4.45
124 130 2.335092 CTGATCGGAGCCCCTGCAAT 62.335 60.000 0.00 0.00 41.13 3.56
140 146 4.202398 CCTGCAATGCCTTCCTCTAATCTA 60.202 45.833 1.53 0.00 0.00 1.98
212 220 0.680921 GTGCCAGGCCAGAAATGCTA 60.681 55.000 9.64 0.00 0.00 3.49
457 544 1.080366 ACGGCGCGTCAGTAATTCA 60.080 52.632 12.89 0.00 33.69 2.57
535 622 2.435586 GGCGTCAGTGCATGCTCT 60.436 61.111 20.33 18.23 36.28 4.09
544 637 0.108615 GTGCATGCTCTCGTACCTGT 60.109 55.000 20.33 0.00 0.00 4.00
765 864 1.724582 GCCGGGCTGCATTTAATCGT 61.725 55.000 12.87 0.00 0.00 3.73
793 892 7.063780 GCTATTTTTGAATGTGTTCTGGGATTG 59.936 37.037 0.00 0.00 35.33 2.67
794 893 6.477053 TTTTTGAATGTGTTCTGGGATTGA 57.523 33.333 0.00 0.00 35.33 2.57
796 895 6.477053 TTTGAATGTGTTCTGGGATTGAAA 57.523 33.333 0.00 0.00 35.33 2.69
808 907 0.662970 GATTGAAACTTGCCGCGCAA 60.663 50.000 8.75 13.76 46.80 4.85
862 969 1.810030 GTTCCTTGTCCTAGCGCCG 60.810 63.158 2.29 0.00 0.00 6.46
936 1043 1.067846 TCGAATTATCCATCTCCCGCG 60.068 52.381 0.00 0.00 0.00 6.46
959 1072 0.179073 CGCACCCACCTTCCATCTAG 60.179 60.000 0.00 0.00 0.00 2.43
989 1102 2.012051 GCTGGTTATTGGGGTGACGAG 61.012 57.143 0.00 0.00 0.00 4.18
1113 1229 2.976350 TCGGCGGCGATATCGTCT 60.976 61.111 31.46 0.00 42.59 4.18
1143 1259 0.525668 CGTCTATCCGAGCGTTGCTT 60.526 55.000 0.00 0.00 39.88 3.91
1144 1260 0.924090 GTCTATCCGAGCGTTGCTTG 59.076 55.000 0.00 0.00 39.88 4.01
1156 1272 4.680237 TGCTTGCGAGGACCGGTG 62.680 66.667 14.63 0.00 39.04 4.94
1216 1332 4.377708 TGCTGTCGCGCATCCTGT 62.378 61.111 8.75 0.00 39.65 4.00
1305 1421 1.269998 CGGTATGGTAGTAGCAGCTCC 59.730 57.143 8.22 8.69 0.00 4.70
1528 1650 4.541085 TGATGATGTTGATGTTGATCGC 57.459 40.909 0.00 0.00 0.00 4.58
1531 1653 4.968812 TGATGTTGATGTTGATCGCAAT 57.031 36.364 0.00 0.00 36.22 3.56
1537 1659 3.835779 TGATGTTGATCGCAATTTGTGG 58.164 40.909 9.91 0.00 36.22 4.17
1543 1665 5.356470 TGTTGATCGCAATTTGTGGATGATA 59.644 36.000 9.91 0.00 36.22 2.15
1545 1667 5.367302 TGATCGCAATTTGTGGATGATAGA 58.633 37.500 9.91 0.00 0.00 1.98
1608 1732 2.009774 GTCATGTCGATGAACCTTGGG 58.990 52.381 0.00 0.00 40.39 4.12
1715 1839 2.105128 GTCGGAGATCAGGCACGG 59.895 66.667 0.00 0.00 40.67 4.94
2025 2158 1.394572 CACGTACGATCGAGTGTACCA 59.605 52.381 24.34 0.00 38.12 3.25
2120 2267 1.002366 GATGATGCACGCGTCTTCTT 58.998 50.000 9.86 10.20 34.95 2.52
2182 2329 4.967730 TGCACGTGTCCGTCGACG 62.968 66.667 30.33 30.33 46.28 5.12
2209 2356 4.400109 GGAGCTGCGTCGTCGACA 62.400 66.667 24.13 5.81 39.71 4.35
2238 2385 2.473664 AAGTGAACGCCGACGAGGAG 62.474 60.000 0.00 5.04 45.00 3.69
2239 2386 3.744719 TGAACGCCGACGAGGAGG 61.745 66.667 0.00 0.00 44.78 4.30
2240 2387 3.437795 GAACGCCGACGAGGAGGA 61.438 66.667 0.00 0.00 44.78 3.71
2261 2408 1.047801 GAGGAGGAAGAGGATCAGCC 58.952 60.000 0.00 0.00 37.82 4.85
2298 2451 1.454295 GGACGAGGAGGAGGAGGAC 60.454 68.421 0.00 0.00 0.00 3.85
2301 2454 1.149627 CGAGGAGGAGGAGGACGAT 59.850 63.158 0.00 0.00 0.00 3.73
2583 2742 1.585521 AGTCCGATAAAGACGCGCG 60.586 57.895 30.96 30.96 39.31 6.86
2701 2869 1.000041 GGGGGAGAGGAGAGGAGGTA 61.000 65.000 0.00 0.00 0.00 3.08
2771 2940 4.101790 CTCGGTTTGGCGCGCAAT 62.102 61.111 34.42 0.00 0.00 3.56
2772 2941 4.096558 TCGGTTTGGCGCGCAATC 62.097 61.111 34.42 18.86 0.00 2.67
2774 2943 4.398598 GGTTTGGCGCGCAATCGT 62.399 61.111 34.42 0.00 38.14 3.73
2806 2975 1.521681 CTCGGAGATGGCGGGAAAC 60.522 63.158 0.00 0.00 33.89 2.78
2867 3042 2.739913 TGTGGTCTGCGCTGTAATAAAC 59.260 45.455 9.73 0.57 0.00 2.01
2868 3043 2.095372 GTGGTCTGCGCTGTAATAAACC 59.905 50.000 9.73 11.15 0.00 3.27
2871 3046 3.377172 GGTCTGCGCTGTAATAAACCATT 59.623 43.478 9.73 0.00 0.00 3.16
2872 3047 4.495844 GGTCTGCGCTGTAATAAACCATTC 60.496 45.833 9.73 0.00 0.00 2.67
2876 3051 4.697828 TGCGCTGTAATAAACCATTCTTCA 59.302 37.500 9.73 0.00 0.00 3.02
2979 3311 0.966179 GGCCAGGTTTCCGAATTTGT 59.034 50.000 0.00 0.00 0.00 2.83
3001 3333 2.141517 CTGAGCTCTGTTGTGTTCTGG 58.858 52.381 16.19 0.00 0.00 3.86
3029 3361 5.728637 AATTCTGCGAGGGAAAAAGAAAT 57.271 34.783 0.00 0.00 31.14 2.17
3043 3375 3.903530 AAGAAATGGGACCTGGTTTCT 57.096 42.857 0.00 2.61 41.30 2.52
3058 3390 3.813166 TGGTTTCTGAATTCGGTCTGAAC 59.187 43.478 13.95 13.17 40.00 3.18
3066 3398 4.202212 TGAATTCGGTCTGAACTCTGTTCA 60.202 41.667 11.83 11.83 40.00 3.18
3087 3428 1.786441 TGTTCCAAATTCTGGGAGGGT 59.214 47.619 6.77 0.00 46.44 4.34
3138 3481 3.377346 ACTACATTATCCTGAGCAGCG 57.623 47.619 0.00 0.00 0.00 5.18
3145 3488 0.969917 ATCCTGAGCAGCGACTGTCT 60.970 55.000 6.21 6.24 33.43 3.41
3153 3496 0.997932 CAGCGACTGTCTGATTCTGC 59.002 55.000 6.21 0.00 33.54 4.26
3173 3516 0.040499 TGGAATTTACTGGGGGTGCC 59.960 55.000 0.00 0.00 0.00 5.01
3277 3632 5.493809 GGGCAGTAACAGTGGTAAGAAATA 58.506 41.667 0.00 0.00 0.00 1.40
3278 3633 5.353400 GGGCAGTAACAGTGGTAAGAAATAC 59.647 44.000 0.00 0.00 0.00 1.89
3279 3634 5.063060 GGCAGTAACAGTGGTAAGAAATACG 59.937 44.000 0.00 0.00 35.19 3.06
3280 3635 5.636543 GCAGTAACAGTGGTAAGAAATACGT 59.363 40.000 0.00 0.00 35.19 3.57
3281 3636 6.808212 GCAGTAACAGTGGTAAGAAATACGTA 59.192 38.462 0.00 0.00 35.19 3.57
3282 3637 7.008992 GCAGTAACAGTGGTAAGAAATACGTAG 59.991 40.741 0.08 0.00 35.19 3.51
3283 3638 7.487189 CAGTAACAGTGGTAAGAAATACGTAGG 59.513 40.741 0.08 0.00 35.19 3.18
3388 3746 2.922283 ACCTCAACTCCTTCCCATGATT 59.078 45.455 0.00 0.00 0.00 2.57
3389 3747 3.054065 ACCTCAACTCCTTCCCATGATTC 60.054 47.826 0.00 0.00 0.00 2.52
3410 3768 2.224314 CGGGAGTTTTCTCTTTCAGTGC 59.776 50.000 0.00 0.00 45.52 4.40
3415 3773 2.554462 GTTTTCTCTTTCAGTGCCCCTC 59.446 50.000 0.00 0.00 0.00 4.30
3416 3774 0.693049 TTCTCTTTCAGTGCCCCTCC 59.307 55.000 0.00 0.00 0.00 4.30
3417 3775 0.178891 TCTCTTTCAGTGCCCCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
3418 3776 0.035630 CTCTTTCAGTGCCCCTCCTG 60.036 60.000 0.00 0.00 0.00 3.86
3419 3777 1.001641 CTTTCAGTGCCCCTCCTGG 60.002 63.158 0.00 0.00 0.00 4.45
3420 3778 1.774217 TTTCAGTGCCCCTCCTGGT 60.774 57.895 0.00 0.00 0.00 4.00
3421 3779 2.067932 TTTCAGTGCCCCTCCTGGTG 62.068 60.000 0.00 0.00 0.00 4.17
3422 3780 4.729918 CAGTGCCCCTCCTGGTGC 62.730 72.222 0.00 0.00 0.00 5.01
3424 3782 4.729918 GTGCCCCTCCTGGTGCAG 62.730 72.222 0.00 0.00 39.85 4.41
3443 3801 3.136123 CGCAGGTGCAGAATGGGG 61.136 66.667 2.33 0.00 42.21 4.96
3444 3802 2.757099 GCAGGTGCAGAATGGGGG 60.757 66.667 0.00 0.00 41.59 5.40
3445 3803 3.089838 CAGGTGCAGAATGGGGGA 58.910 61.111 0.00 0.00 35.86 4.81
3446 3804 1.616921 CAGGTGCAGAATGGGGGAT 59.383 57.895 0.00 0.00 35.86 3.85
3447 3805 0.754217 CAGGTGCAGAATGGGGGATG 60.754 60.000 0.00 0.00 35.86 3.51
3448 3806 1.217057 AGGTGCAGAATGGGGGATGT 61.217 55.000 0.00 0.00 35.86 3.06
3449 3807 0.753111 GGTGCAGAATGGGGGATGTC 60.753 60.000 0.00 0.00 35.86 3.06
3452 3810 1.358787 TGCAGAATGGGGGATGTCTTT 59.641 47.619 0.00 0.00 35.86 2.52
3453 3811 1.753073 GCAGAATGGGGGATGTCTTTG 59.247 52.381 0.00 0.00 35.86 2.77
3454 3812 2.885554 GCAGAATGGGGGATGTCTTTGT 60.886 50.000 0.00 0.00 35.86 2.83
3455 3813 3.624707 GCAGAATGGGGGATGTCTTTGTA 60.625 47.826 0.00 0.00 35.86 2.41
3459 3817 4.772886 ATGGGGGATGTCTTTGTAGTAC 57.227 45.455 0.00 0.00 0.00 2.73
3467 3825 8.265764 GGGGATGTCTTTGTAGTACTATCTTTT 58.734 37.037 5.75 0.00 0.00 2.27
3511 3869 9.559958 CCAATACAAATATGTCTTTCTCAACAC 57.440 33.333 0.00 0.00 41.05 3.32
3512 3870 9.559958 CAATACAAATATGTCTTTCTCAACACC 57.440 33.333 0.00 0.00 41.05 4.16
3513 3871 9.520515 AATACAAATATGTCTTTCTCAACACCT 57.479 29.630 0.00 0.00 41.05 4.00
3515 3873 8.324163 ACAAATATGTCTTTCTCAACACCTAC 57.676 34.615 0.00 0.00 33.41 3.18
3516 3874 7.117812 ACAAATATGTCTTTCTCAACACCTACG 59.882 37.037 0.00 0.00 33.41 3.51
3517 3875 4.602340 ATGTCTTTCTCAACACCTACGT 57.398 40.909 0.00 0.00 0.00 3.57
3518 3876 3.713288 TGTCTTTCTCAACACCTACGTG 58.287 45.455 0.00 0.00 46.11 4.49
3542 3900 7.404139 GTCAGTAGACGTAAAAGACACAATT 57.596 36.000 0.00 0.00 34.60 2.32
3543 3901 7.499868 GTCAGTAGACGTAAAAGACACAATTC 58.500 38.462 0.00 0.00 34.60 2.17
3544 3902 6.361481 TCAGTAGACGTAAAAGACACAATTCG 59.639 38.462 0.00 0.00 0.00 3.34
3545 3903 6.361481 CAGTAGACGTAAAAGACACAATTCGA 59.639 38.462 0.00 0.00 0.00 3.71
3546 3904 5.571778 AGACGTAAAAGACACAATTCGAC 57.428 39.130 0.00 0.00 0.00 4.20
3547 3905 5.045215 AGACGTAAAAGACACAATTCGACA 58.955 37.500 0.00 0.00 0.00 4.35
3548 3906 5.694910 AGACGTAAAAGACACAATTCGACAT 59.305 36.000 0.00 0.00 0.00 3.06
3549 3907 6.864685 AGACGTAAAAGACACAATTCGACATA 59.135 34.615 0.00 0.00 0.00 2.29
3550 3908 7.383029 AGACGTAAAAGACACAATTCGACATAA 59.617 33.333 0.00 0.00 0.00 1.90
3551 3909 7.853524 ACGTAAAAGACACAATTCGACATAAA 58.146 30.769 0.00 0.00 0.00 1.40
3552 3910 8.500773 ACGTAAAAGACACAATTCGACATAAAT 58.499 29.630 0.00 0.00 0.00 1.40
3553 3911 8.775884 CGTAAAAGACACAATTCGACATAAATG 58.224 33.333 0.00 0.00 0.00 2.32
3554 3912 9.820229 GTAAAAGACACAATTCGACATAAATGA 57.180 29.630 0.00 0.00 0.00 2.57
3555 3913 8.728088 AAAAGACACAATTCGACATAAATGAC 57.272 30.769 0.00 0.00 0.00 3.06
3556 3914 6.094739 AGACACAATTCGACATAAATGACG 57.905 37.500 8.23 8.23 44.83 4.35
3557 3915 4.647964 ACACAATTCGACATAAATGACGC 58.352 39.130 9.44 0.00 43.57 5.19
3558 3916 4.028383 CACAATTCGACATAAATGACGCC 58.972 43.478 9.44 0.00 43.57 5.68
3559 3917 3.687212 ACAATTCGACATAAATGACGCCA 59.313 39.130 9.44 0.85 43.57 5.69
3560 3918 4.155099 ACAATTCGACATAAATGACGCCAA 59.845 37.500 9.44 1.82 43.57 4.52
3561 3919 4.955925 ATTCGACATAAATGACGCCAAA 57.044 36.364 9.44 1.22 43.57 3.28
3562 3920 3.733024 TCGACATAAATGACGCCAAAC 57.267 42.857 9.44 0.00 43.57 2.93
3563 3921 3.331150 TCGACATAAATGACGCCAAACT 58.669 40.909 9.44 0.00 43.57 2.66
3564 3922 4.496360 TCGACATAAATGACGCCAAACTA 58.504 39.130 9.44 0.00 43.57 2.24
3565 3923 4.930405 TCGACATAAATGACGCCAAACTAA 59.070 37.500 9.44 0.00 43.57 2.24
3566 3924 5.062934 TCGACATAAATGACGCCAAACTAAG 59.937 40.000 9.44 0.00 43.57 2.18
3567 3925 5.062934 CGACATAAATGACGCCAAACTAAGA 59.937 40.000 2.19 0.00 38.84 2.10
3568 3926 6.238103 CGACATAAATGACGCCAAACTAAGAT 60.238 38.462 2.19 0.00 38.84 2.40
3569 3927 7.016361 ACATAAATGACGCCAAACTAAGATC 57.984 36.000 0.00 0.00 0.00 2.75
3570 3928 4.600012 AAATGACGCCAAACTAAGATCG 57.400 40.909 0.00 0.00 0.00 3.69
3571 3929 2.736144 TGACGCCAAACTAAGATCGT 57.264 45.000 0.00 0.00 0.00 3.73
3572 3930 2.602878 TGACGCCAAACTAAGATCGTC 58.397 47.619 5.74 5.74 44.31 4.20
3573 3931 2.230508 TGACGCCAAACTAAGATCGTCT 59.769 45.455 12.64 0.00 44.34 4.18
3574 3932 3.251571 GACGCCAAACTAAGATCGTCTT 58.748 45.455 5.48 5.74 41.84 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 90 2.749621 GACAGGGCAGGTTATCAACTTG 59.250 50.000 0.00 0.00 41.02 3.16
101 107 1.760086 AGGGGCTCCGATCAGACAG 60.760 63.158 0.00 0.00 38.33 3.51
103 109 2.818132 CAGGGGCTCCGATCAGAC 59.182 66.667 0.00 0.00 38.33 3.51
124 130 1.964223 CGGCTAGATTAGAGGAAGGCA 59.036 52.381 0.00 0.00 33.30 4.75
140 146 2.045926 GACCAGATTGGCACGGCT 60.046 61.111 0.00 0.00 42.67 5.52
182 188 1.522355 CCTGGCACTATGTCCGCAG 60.522 63.158 0.00 0.00 0.00 5.18
274 287 2.820922 CAGTGCGCTGCTGCCATA 60.821 61.111 15.44 0.00 35.77 2.74
337 390 0.034089 AGGGAATTTTCGGCCTGAGG 60.034 55.000 0.00 0.00 0.00 3.86
367 420 1.580845 GGCGTGACAGCTGCTGAATT 61.581 55.000 34.28 13.88 35.18 2.17
368 421 2.037136 GGCGTGACAGCTGCTGAAT 61.037 57.895 34.28 14.66 35.18 2.57
369 422 2.666190 GGCGTGACAGCTGCTGAA 60.666 61.111 34.28 19.41 35.18 3.02
457 544 4.401022 TGAAATGGAAGCTGTGATTCTGT 58.599 39.130 0.00 0.00 0.00 3.41
535 622 1.942657 GCGGTACAGATACAGGTACGA 59.057 52.381 0.00 0.00 40.53 3.43
544 637 3.440151 GCGGAGGCGGTACAGATA 58.560 61.111 0.00 0.00 0.00 1.98
765 864 5.279406 CCCAGAACACATTCAAAAATAGCCA 60.279 40.000 0.00 0.00 37.29 4.75
837 943 2.933056 GCTAGGACAAGGAACAGAGCAC 60.933 54.545 0.00 0.00 0.00 4.40
862 969 1.718396 GACGCCCGGTATTTATAGGC 58.282 55.000 0.00 0.00 40.33 3.93
951 1058 0.839946 GCTTGCTTCCCCTAGATGGA 59.160 55.000 0.00 0.00 38.35 3.41
955 1062 0.547712 ACCAGCTTGCTTCCCCTAGA 60.548 55.000 0.00 0.00 0.00 2.43
959 1072 1.478105 CAATAACCAGCTTGCTTCCCC 59.522 52.381 0.00 0.00 0.00 4.81
989 1102 2.022129 CGGGCCATCGATCGTTAGC 61.022 63.158 15.94 15.14 0.00 3.09
1062 1175 2.364842 GGAGGCAGAGGCAGAGGA 60.365 66.667 0.00 0.00 43.71 3.71
1128 1244 2.164663 CGCAAGCAACGCTCGGATA 61.165 57.895 0.00 0.00 38.25 2.59
1134 1250 3.044305 GTCCTCGCAAGCAACGCT 61.044 61.111 0.00 0.00 42.56 5.07
1138 1254 3.936203 ACCGGTCCTCGCAAGCAA 61.936 61.111 0.00 0.00 37.59 3.91
1281 1397 0.664761 TGCTACTACCATACCGTCGC 59.335 55.000 0.00 0.00 0.00 5.19
1284 1400 1.955080 GAGCTGCTACTACCATACCGT 59.045 52.381 0.15 0.00 0.00 4.83
1305 1421 0.099968 TGATACTTTCGCCGACGGAG 59.900 55.000 20.50 16.01 40.63 4.63
1413 1529 2.352422 GTGTCCATGGGCAGCTCA 59.648 61.111 22.11 0.00 0.00 4.26
1528 1650 7.423199 CAAGTCCATCTATCATCCACAAATTG 58.577 38.462 0.00 0.00 0.00 2.32
1531 1653 4.883585 GCAAGTCCATCTATCATCCACAAA 59.116 41.667 0.00 0.00 0.00 2.83
1537 1659 4.070009 TGCATGCAAGTCCATCTATCATC 58.930 43.478 20.30 0.00 0.00 2.92
1690 1814 1.983196 CTGATCTCCGACACGAGCGT 61.983 60.000 0.00 0.00 0.00 5.07
1715 1839 1.946475 CTTCTCCTTCCCGACGGTCC 61.946 65.000 13.94 0.00 0.00 4.46
1833 1957 1.374758 GGAGCAGTTGTCGGACAGG 60.375 63.158 11.14 6.56 0.00 4.00
2025 2158 4.437239 GTGCTACTCAAGATATGCAGTGT 58.563 43.478 0.00 0.00 0.00 3.55
2029 2162 3.801114 ACGTGCTACTCAAGATATGCA 57.199 42.857 0.00 0.00 0.00 3.96
2095 2242 1.581912 CGCGTGCATCATCAGCAAC 60.582 57.895 0.00 0.00 44.64 4.17
2209 2356 4.307908 GTTCACTTGCGCCGCGTT 62.308 61.111 15.34 0.00 0.00 4.84
2232 2379 1.077644 TTCCTCCTCGTCCTCCTCG 60.078 63.158 0.00 0.00 0.00 4.63
2238 2385 1.324383 GATCCTCTTCCTCCTCGTCC 58.676 60.000 0.00 0.00 0.00 4.79
2239 2386 1.953686 CTGATCCTCTTCCTCCTCGTC 59.046 57.143 0.00 0.00 0.00 4.20
2240 2387 2.026905 GCTGATCCTCTTCCTCCTCGT 61.027 57.143 0.00 0.00 0.00 4.18
2261 2408 1.301423 CTCTTCGTAGTCCTCCTCGG 58.699 60.000 0.00 0.00 0.00 4.63
2298 2451 2.576053 CCACCGTCGTCGTCATCG 60.576 66.667 0.71 0.00 38.55 3.84
2559 2712 1.536284 CGTCTTTATCGGACTGGCTCC 60.536 57.143 0.00 0.00 35.33 4.70
2592 2751 3.385384 TGAGCTGAGGTCTGGCGG 61.385 66.667 13.27 0.00 0.00 6.13
2593 2752 2.125753 GTGAGCTGAGGTCTGGCG 60.126 66.667 13.27 0.00 0.00 5.69
2594 2753 2.125753 CGTGAGCTGAGGTCTGGC 60.126 66.667 13.27 2.75 0.00 4.85
2596 2755 0.665670 CACACGTGAGCTGAGGTCTG 60.666 60.000 25.01 7.93 0.00 3.51
2597 2756 1.662608 CACACGTGAGCTGAGGTCT 59.337 57.895 25.01 0.00 0.00 3.85
2598 2757 2.024319 GCACACGTGAGCTGAGGTC 61.024 63.158 27.53 4.41 0.00 3.85
2599 2758 2.029666 GCACACGTGAGCTGAGGT 59.970 61.111 27.53 0.00 0.00 3.85
2693 2861 1.359475 GTGACCGCGATACCTCCTC 59.641 63.158 8.23 0.00 0.00 3.71
2694 2862 2.478890 CGTGACCGCGATACCTCCT 61.479 63.158 8.23 0.00 0.00 3.69
2695 2863 2.025727 CGTGACCGCGATACCTCC 59.974 66.667 8.23 0.00 0.00 4.30
2725 2893 2.629051 GGAGCTGTTATTAACACCGCT 58.371 47.619 18.14 18.14 43.14 5.52
2844 3013 1.014044 ATTACAGCGCAGACCACACG 61.014 55.000 11.47 0.00 0.00 4.49
2867 3042 5.689068 GCTGAAACAAAACTCTGAAGAATGG 59.311 40.000 0.00 0.00 0.00 3.16
2868 3043 6.417044 CAGCTGAAACAAAACTCTGAAGAATG 59.583 38.462 8.42 0.00 0.00 2.67
2871 3046 4.943705 ACAGCTGAAACAAAACTCTGAAGA 59.056 37.500 23.35 0.00 0.00 2.87
2872 3047 5.240713 ACAGCTGAAACAAAACTCTGAAG 57.759 39.130 23.35 0.00 0.00 3.02
2876 3051 3.629398 CAGGACAGCTGAAACAAAACTCT 59.371 43.478 23.35 0.00 0.00 3.24
2971 3303 4.024556 ACAACAGAGCTCAGAACAAATTCG 60.025 41.667 17.77 0.00 40.04 3.34
2979 3311 3.461061 CAGAACACAACAGAGCTCAGAA 58.539 45.455 17.77 0.00 0.00 3.02
3001 3333 1.821216 TCCCTCGCAGAATTTGGAAC 58.179 50.000 0.00 0.00 34.09 3.62
3029 3361 2.552155 CGAATTCAGAAACCAGGTCCCA 60.552 50.000 6.22 0.00 0.00 4.37
3043 3375 4.202212 TGAACAGAGTTCAGACCGAATTCA 60.202 41.667 8.39 0.00 41.57 2.57
3087 3428 2.672703 ACCTGGTCCCTACCCATTTA 57.327 50.000 0.00 0.00 46.16 1.40
3111 3454 6.060136 TGCTCAGGATAATGTAGTACTACGT 58.940 40.000 24.36 22.24 38.85 3.57
3120 3463 2.959030 AGTCGCTGCTCAGGATAATGTA 59.041 45.455 0.00 0.00 0.00 2.29
3121 3464 1.759445 AGTCGCTGCTCAGGATAATGT 59.241 47.619 0.00 0.00 0.00 2.71
3122 3465 2.133553 CAGTCGCTGCTCAGGATAATG 58.866 52.381 0.00 0.00 0.00 1.90
3129 3472 0.173029 ATCAGACAGTCGCTGCTCAG 59.827 55.000 6.74 0.00 34.37 3.35
3138 3481 3.325293 TTCCAGCAGAATCAGACAGTC 57.675 47.619 0.00 0.00 0.00 3.51
3145 3488 4.272489 CCCAGTAAATTCCAGCAGAATCA 58.728 43.478 2.81 0.00 44.75 2.57
3153 3496 1.474330 GCACCCCCAGTAAATTCCAG 58.526 55.000 0.00 0.00 0.00 3.86
3231 3586 1.534595 CAGCAGCTGTCAGTTTCTTCC 59.465 52.381 16.64 0.00 0.00 3.46
3235 3590 0.590195 CCACAGCAGCTGTCAGTTTC 59.410 55.000 25.89 0.00 43.43 2.78
3277 3632 0.626916 AGCTTCTCCTCCTCCTACGT 59.373 55.000 0.00 0.00 0.00 3.57
3278 3633 1.028905 CAGCTTCTCCTCCTCCTACG 58.971 60.000 0.00 0.00 0.00 3.51
3279 3634 0.750249 GCAGCTTCTCCTCCTCCTAC 59.250 60.000 0.00 0.00 0.00 3.18
3280 3635 0.633921 AGCAGCTTCTCCTCCTCCTA 59.366 55.000 0.00 0.00 0.00 2.94
3281 3636 0.687427 GAGCAGCTTCTCCTCCTCCT 60.687 60.000 1.38 0.00 0.00 3.69
3282 3637 0.687427 AGAGCAGCTTCTCCTCCTCC 60.687 60.000 9.94 0.00 33.66 4.30
3283 3638 1.194218 AAGAGCAGCTTCTCCTCCTC 58.806 55.000 9.94 0.00 33.66 3.71
3328 3686 4.129737 TCTGCTGCTACCGGCGTC 62.130 66.667 6.01 0.00 46.59 5.19
3388 3746 3.728845 CACTGAAAGAGAAAACTCCCGA 58.271 45.455 0.00 0.00 37.43 5.14
3389 3747 2.224314 GCACTGAAAGAGAAAACTCCCG 59.776 50.000 0.00 0.00 37.43 5.14
3400 3758 1.492133 CCAGGAGGGGCACTGAAAGA 61.492 60.000 0.00 0.00 36.86 2.52
3422 3780 2.749044 ATTCTGCACCTGCGCCTG 60.749 61.111 4.18 0.00 45.83 4.85
3423 3781 2.749044 CATTCTGCACCTGCGCCT 60.749 61.111 4.18 0.00 45.83 5.52
3424 3782 3.818787 CCATTCTGCACCTGCGCC 61.819 66.667 4.18 0.00 45.83 6.53
3426 3784 3.136123 CCCCATTCTGCACCTGCG 61.136 66.667 0.00 0.00 45.83 5.18
3431 3789 0.257039 AGACATCCCCCATTCTGCAC 59.743 55.000 0.00 0.00 0.00 4.57
3443 3801 9.654663 ACAAAAGATAGTACTACAAAGACATCC 57.345 33.333 4.31 0.00 0.00 3.51
3484 3842 9.295825 TGTTGAGAAAGACATATTTGTATTGGT 57.704 29.630 0.00 0.00 37.36 3.67
3485 3843 9.559958 GTGTTGAGAAAGACATATTTGTATTGG 57.440 33.333 0.00 0.00 37.36 3.16
3486 3844 9.559958 GGTGTTGAGAAAGACATATTTGTATTG 57.440 33.333 0.00 0.00 37.36 1.90
3496 3854 4.307432 CACGTAGGTGTTGAGAAAGACAT 58.693 43.478 7.41 0.00 39.38 3.06
3497 3855 3.713288 CACGTAGGTGTTGAGAAAGACA 58.287 45.455 7.41 0.00 39.38 3.41
3515 3873 4.378030 GTGTCTTTTACGTCTACTGACACG 59.622 45.833 18.60 0.00 41.73 4.49
3516 3874 5.802812 GTGTCTTTTACGTCTACTGACAC 57.197 43.478 18.60 18.60 43.40 3.67
3517 3875 5.503662 TGTGTCTTTTACGTCTACTGACA 57.496 39.130 0.00 0.00 43.06 3.58
3518 3876 7.404139 AATTGTGTCTTTTACGTCTACTGAC 57.596 36.000 0.00 0.00 39.70 3.51
3519 3877 6.361481 CGAATTGTGTCTTTTACGTCTACTGA 59.639 38.462 0.00 0.00 0.00 3.41
3520 3878 6.361481 TCGAATTGTGTCTTTTACGTCTACTG 59.639 38.462 0.00 0.00 0.00 2.74
3521 3879 6.361748 GTCGAATTGTGTCTTTTACGTCTACT 59.638 38.462 0.00 0.00 0.00 2.57
3522 3880 6.142798 TGTCGAATTGTGTCTTTTACGTCTAC 59.857 38.462 0.00 0.00 0.00 2.59
3523 3881 6.207928 TGTCGAATTGTGTCTTTTACGTCTA 58.792 36.000 0.00 0.00 0.00 2.59
3524 3882 5.045215 TGTCGAATTGTGTCTTTTACGTCT 58.955 37.500 0.00 0.00 0.00 4.18
3525 3883 5.319232 TGTCGAATTGTGTCTTTTACGTC 57.681 39.130 0.00 0.00 0.00 4.34
3526 3884 5.917541 ATGTCGAATTGTGTCTTTTACGT 57.082 34.783 0.00 0.00 0.00 3.57
3527 3885 8.775884 CATTTATGTCGAATTGTGTCTTTTACG 58.224 33.333 0.00 0.00 0.00 3.18
3528 3886 9.820229 TCATTTATGTCGAATTGTGTCTTTTAC 57.180 29.630 0.00 0.00 0.00 2.01
3529 3887 9.820229 GTCATTTATGTCGAATTGTGTCTTTTA 57.180 29.630 0.00 0.00 0.00 1.52
3530 3888 7.533900 CGTCATTTATGTCGAATTGTGTCTTTT 59.466 33.333 3.80 0.00 40.77 2.27
3531 3889 7.015289 CGTCATTTATGTCGAATTGTGTCTTT 58.985 34.615 3.80 0.00 40.77 2.52
3532 3890 6.534059 CGTCATTTATGTCGAATTGTGTCTT 58.466 36.000 3.80 0.00 40.77 3.01
3533 3891 5.445939 GCGTCATTTATGTCGAATTGTGTCT 60.446 40.000 12.31 0.00 40.77 3.41
3534 3892 4.723862 GCGTCATTTATGTCGAATTGTGTC 59.276 41.667 12.31 0.00 40.77 3.67
3535 3893 4.436852 GGCGTCATTTATGTCGAATTGTGT 60.437 41.667 12.31 0.00 40.77 3.72
3536 3894 4.028383 GGCGTCATTTATGTCGAATTGTG 58.972 43.478 12.31 0.00 40.77 3.33
3537 3895 3.687212 TGGCGTCATTTATGTCGAATTGT 59.313 39.130 12.31 0.00 40.77 2.71
3538 3896 4.271590 TGGCGTCATTTATGTCGAATTG 57.728 40.909 12.31 0.00 40.77 2.32
3539 3897 4.955925 TTGGCGTCATTTATGTCGAATT 57.044 36.364 12.31 0.00 40.77 2.17
3540 3898 4.394920 AGTTTGGCGTCATTTATGTCGAAT 59.605 37.500 12.31 0.00 40.77 3.34
3541 3899 3.749088 AGTTTGGCGTCATTTATGTCGAA 59.251 39.130 12.31 0.00 40.77 3.71
3542 3900 3.331150 AGTTTGGCGTCATTTATGTCGA 58.669 40.909 12.31 0.00 40.77 4.20
3543 3901 3.740044 AGTTTGGCGTCATTTATGTCG 57.260 42.857 0.00 5.25 41.13 4.35
3544 3902 6.417191 TCTTAGTTTGGCGTCATTTATGTC 57.583 37.500 0.00 0.00 0.00 3.06
3545 3903 6.238103 CGATCTTAGTTTGGCGTCATTTATGT 60.238 38.462 0.00 0.00 0.00 2.29
3546 3904 6.129393 CGATCTTAGTTTGGCGTCATTTATG 58.871 40.000 0.00 0.00 0.00 1.90
3547 3905 5.815740 ACGATCTTAGTTTGGCGTCATTTAT 59.184 36.000 0.00 0.00 0.00 1.40
3548 3906 5.172934 ACGATCTTAGTTTGGCGTCATTTA 58.827 37.500 0.00 0.00 0.00 1.40
3549 3907 4.000988 ACGATCTTAGTTTGGCGTCATTT 58.999 39.130 0.00 0.00 0.00 2.32
3550 3908 3.596214 ACGATCTTAGTTTGGCGTCATT 58.404 40.909 0.00 0.00 0.00 2.57
3551 3909 3.187700 GACGATCTTAGTTTGGCGTCAT 58.812 45.455 0.00 0.00 45.10 3.06
3552 3910 2.602878 GACGATCTTAGTTTGGCGTCA 58.397 47.619 0.00 0.00 45.10 4.35
3553 3911 2.877335 AGACGATCTTAGTTTGGCGTC 58.123 47.619 0.00 0.00 45.83 5.19
3554 3912 3.314541 AAGACGATCTTAGTTTGGCGT 57.685 42.857 0.00 0.00 34.42 5.68


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

AutoCloner maintained by Alex Coulton.