Multiple sequence alignment - TraesCS3D01G083000

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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 TraesCS3D01G083000 chr3D 100.000 3933 0 0 1 3933 42096780 42092848 0.000000e+00 7263.0
1 TraesCS3D01G083000 chr3D 91.144 271 20 4 383 653 295392192 295392458 8.030000e-97 364.0
2 TraesCS3D01G083000 chr3D 90.909 275 17 6 384 657 522508835 522508568 2.890000e-96 363.0
3 TraesCS3D01G083000 chr3B 95.986 1669 56 6 740 2400 65552129 65553794 0.000000e+00 2700.0
4 TraesCS3D01G083000 chr3B 88.809 1671 100 40 2334 3933 65553759 65555413 0.000000e+00 1969.0
5 TraesCS3D01G083000 chr3B 97.619 42 1 0 2415 2456 65553690 65553731 5.450000e-09 73.1
6 TraesCS3D01G083000 chr3A 95.825 1581 50 7 823 2400 53559248 53560815 0.000000e+00 2540.0
7 TraesCS3D01G083000 chr3A 89.419 860 49 17 2334 3158 53560780 53561632 0.000000e+00 1046.0
8 TraesCS3D01G083000 chr3A 91.027 769 55 10 1 761 53558209 53558971 0.000000e+00 1026.0
9 TraesCS3D01G083000 chr3A 89.223 798 61 11 3151 3933 53561661 53562448 0.000000e+00 974.0
10 TraesCS3D01G083000 chr3A 91.209 273 18 4 383 653 600926557 600926825 2.230000e-97 366.0
11 TraesCS3D01G083000 chr3A 94.915 59 2 1 747 804 53559192 53559250 1.510000e-14 91.6
12 TraesCS3D01G083000 chr2A 91.544 272 18 3 383 653 16367710 16367443 1.730000e-98 370.0
13 TraesCS3D01G083000 chr6B 90.975 277 19 6 378 653 262375818 262375547 6.210000e-98 368.0
14 TraesCS3D01G083000 chr7D 91.450 269 19 3 389 657 326788566 326788302 2.230000e-97 366.0
15 TraesCS3D01G083000 chr6D 91.450 269 18 4 389 657 388990882 388990619 8.030000e-97 364.0
16 TraesCS3D01G083000 chr6D 90.876 274 20 4 381 653 26353970 26354239 2.890000e-96 363.0
17 TraesCS3D01G083000 chr4B 76.410 390 84 5 1814 2202 11568053 11568435 1.850000e-48 204.0
18 TraesCS3D01G083000 chr4D 85.714 63 9 0 1097 1159 6379660 6379598 2.540000e-07 67.6


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 TraesCS3D01G083000 chr3D 42092848 42096780 3932 True 7263.00 7263 100.0000 1 3933 1 chr3D.!!$R1 3932
1 TraesCS3D01G083000 chr3B 65552129 65555413 3284 False 1580.70 2700 94.1380 740 3933 3 chr3B.!!$F1 3193
2 TraesCS3D01G083000 chr3A 53558209 53562448 4239 False 1135.52 2540 92.0818 1 3933 5 chr3A.!!$F2 3932

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
215 220 0.108138 CCGTTTCTCCCTCGCTTGAT 60.108 55.0 0.00 0.0 0.00 2.57 F
322 327 0.387929 CTATTAAGGTGGGCGAGCGA 59.612 55.0 0.00 0.0 0.00 4.93 F
817 1062 0.598158 GTCGTACGCCACAACTTCCA 60.598 55.0 11.24 0.0 0.00 3.53 F
2752 3069 0.315886 ACGGCGACTACATGTTGACA 59.684 50.0 16.62 0.0 37.99 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1751 1.737008 GGAGAACCAGCGGTCGAAC 60.737 63.158 0.0 0.00 33.12 3.95 R
2223 2480 1.522580 GCCTGCCCATTCGTCTCTC 60.523 63.158 0.0 0.00 0.00 3.20 R
2801 3118 0.249073 ATGGCTCGTCTCACGTATGC 60.249 55.000 0.0 0.41 43.14 3.14 R
3677 4051 0.539438 TTGCCAACGAGAATTGCCCT 60.539 50.000 0.0 0.00 0.00 5.19 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
26 27 2.223340 GGACCACATCGAATTGACATGC 60.223 50.000 0.00 0.00 0.00 4.06
27 28 2.419673 GACCACATCGAATTGACATGCA 59.580 45.455 0.00 0.00 0.00 3.96
38 39 2.097680 TGACATGCATCTTCGCAAGA 57.902 45.000 0.00 1.85 46.87 3.02
69 70 0.602638 GACCTTGTGCACCACGATCA 60.603 55.000 15.69 0.00 37.14 2.92
74 75 1.229975 TGTGCACCACGATCAGCAAG 61.230 55.000 15.69 0.00 38.91 4.01
127 131 2.259204 CATTGGCAGGTTGGTGCG 59.741 61.111 0.00 0.00 45.00 5.34
128 132 3.683937 ATTGGCAGGTTGGTGCGC 61.684 61.111 0.00 0.00 45.00 6.09
146 150 1.334960 CGCGAACAAGCCAAAGAACAT 60.335 47.619 0.00 0.00 0.00 2.71
157 161 2.159352 CCAAAGAACATGCGCATCATCA 60.159 45.455 22.51 0.00 31.79 3.07
215 220 0.108138 CCGTTTCTCCCTCGCTTGAT 60.108 55.000 0.00 0.00 0.00 2.57
223 228 1.817099 CCTCGCTTGATGGGCTCAC 60.817 63.158 0.00 0.00 32.17 3.51
234 239 2.550277 TGGGCTCACTGAGAGGATAA 57.450 50.000 10.45 0.00 44.86 1.75
248 253 3.395941 AGAGGATAATGGCGGAAAGGAAT 59.604 43.478 0.00 0.00 0.00 3.01
262 267 0.615331 AGGAATGACTGGCATCGTGT 59.385 50.000 0.00 0.00 35.78 4.49
284 289 3.181329 TGGATTGCTTAAGGGAGACTGA 58.819 45.455 4.29 0.00 0.00 3.41
322 327 0.387929 CTATTAAGGTGGGCGAGCGA 59.612 55.000 0.00 0.00 0.00 4.93
345 350 6.542574 ACGAGTAGTCCTAGATTATGTTCG 57.457 41.667 0.00 0.00 0.00 3.95
361 366 3.865446 TGTTCGTCTCCGAGTAGACATA 58.135 45.455 11.42 0.00 45.13 2.29
363 368 3.109044 TCGTCTCCGAGTAGACATAGG 57.891 52.381 11.42 0.00 45.13 2.57
403 408 6.814043 AGTTTATATGTACTCCCTCCGTTTC 58.186 40.000 0.00 0.00 0.00 2.78
404 409 6.610425 AGTTTATATGTACTCCCTCCGTTTCT 59.390 38.462 0.00 0.00 0.00 2.52
405 410 7.125356 AGTTTATATGTACTCCCTCCGTTTCTT 59.875 37.037 0.00 0.00 0.00 2.52
416 421 2.803956 CTCCGTTTCTTTTTACTCCGCA 59.196 45.455 0.00 0.00 0.00 5.69
543 549 9.192642 CATTCAATGGGGCATCTGATAATATTA 57.807 33.333 0.00 0.00 0.00 0.98
626 634 8.299570 AGCTTGACTTTGACCAAACTTTATATG 58.700 33.333 0.00 0.00 0.00 1.78
644 652 9.490663 CTTTATATGCAGACTAAAAAGAAACGG 57.509 33.333 0.00 0.00 0.00 4.44
667 675 3.967987 AGGGAGTAACATCTATGGTGGAC 59.032 47.826 0.00 0.00 0.00 4.02
680 688 2.915869 TGGTGGACTTGGGTTCTCTAT 58.084 47.619 0.00 0.00 0.00 1.98
684 692 2.838202 TGGACTTGGGTTCTCTATCCAC 59.162 50.000 0.00 0.00 29.85 4.02
707 715 8.289618 CCACCCATTTCTATAAAATATGACACG 58.710 37.037 0.00 0.00 0.00 4.49
712 720 8.895845 CATTTCTATAAAATATGACACGCAAGC 58.104 33.333 0.00 0.00 45.62 4.01
714 722 7.408132 TCTATAAAATATGACACGCAAGCTC 57.592 36.000 0.00 0.00 45.62 4.09
725 733 1.013323 GCAAGCTCGTGCGTATTCG 60.013 57.895 3.48 0.00 45.42 3.34
794 1039 1.760192 ACGGCCGACTACTTACTGAT 58.240 50.000 35.90 0.00 0.00 2.90
815 1060 1.611592 CGGTCGTACGCCACAACTTC 61.612 60.000 22.55 1.35 0.00 3.01
816 1061 1.287041 GGTCGTACGCCACAACTTCC 61.287 60.000 19.50 4.83 0.00 3.46
817 1062 0.598158 GTCGTACGCCACAACTTCCA 60.598 55.000 11.24 0.00 0.00 3.53
825 1070 2.292016 CGCCACAACTTCCAACATGTAA 59.708 45.455 0.00 0.00 0.00 2.41
879 1124 6.987386 TGGGCCCAACATATTAAAATATTCG 58.013 36.000 26.33 0.00 29.35 3.34
881 1126 7.040062 TGGGCCCAACATATTAAAATATTCGAG 60.040 37.037 26.33 0.00 29.35 4.04
882 1127 7.039993 GGGCCCAACATATTAAAATATTCGAGT 60.040 37.037 19.95 0.00 29.35 4.18
883 1128 9.005777 GGCCCAACATATTAAAATATTCGAGTA 57.994 33.333 0.00 0.00 29.35 2.59
950 1198 1.684049 CCTTCCTCTCCGTGCTCCT 60.684 63.158 0.00 0.00 0.00 3.69
951 1199 1.671901 CCTTCCTCTCCGTGCTCCTC 61.672 65.000 0.00 0.00 0.00 3.71
952 1200 1.671901 CTTCCTCTCCGTGCTCCTCC 61.672 65.000 0.00 0.00 0.00 4.30
959 1207 3.506096 CGTGCTCCTCCGCTCGTA 61.506 66.667 0.00 0.00 40.70 3.43
1044 1301 2.107903 GCTTCTGCTGCTCCTGCTC 61.108 63.158 0.00 0.00 40.48 4.26
1047 1304 1.486997 TTCTGCTGCTCCTGCTCCTT 61.487 55.000 0.00 0.00 40.48 3.36
1707 1964 0.613777 CCCTCTTCTACCGCAACCTT 59.386 55.000 0.00 0.00 0.00 3.50
2223 2480 5.095145 TCAGATCTGATTTCCTCACCAAG 57.905 43.478 21.67 0.00 34.14 3.61
2301 2558 1.838077 ACAGATTGCCCAGGTACTACC 59.162 52.381 0.00 0.00 36.02 3.18
2320 2577 4.256983 ACCACTGAGGATCTCTCACATA 57.743 45.455 9.14 0.00 46.71 2.29
2416 2710 9.535878 CACTTAATTTGGATCCTCTCTACTTAC 57.464 37.037 14.23 0.00 0.00 2.34
2450 2744 4.622260 TCTCTCACATGAACACAATGGA 57.378 40.909 0.00 0.00 0.00 3.41
2558 2856 5.185828 AGAATGGGAAATTTGGCAGAACTAC 59.814 40.000 0.00 0.00 0.00 2.73
2600 2898 3.949754 TGGATGCTCTCTGCTTAATTTGG 59.050 43.478 0.00 0.00 43.37 3.28
2660 2977 3.008330 CCAGAAGTGCCATTTGAGAGAG 58.992 50.000 0.00 0.00 0.00 3.20
2677 2994 0.514691 GAGCAACACCAGCGAAAGAG 59.485 55.000 0.00 0.00 37.01 2.85
2752 3069 0.315886 ACGGCGACTACATGTTGACA 59.684 50.000 16.62 0.00 37.99 3.58
2806 3123 2.511600 AAGCAGGCCGACGCATAC 60.512 61.111 15.81 0.00 36.38 2.39
2854 3171 4.065281 GCAAGCAAGCAGGCCAGG 62.065 66.667 5.01 0.00 0.00 4.45
2933 3250 4.527427 AGAGTACCACCTCAAGTCCTTAAC 59.473 45.833 0.00 0.00 33.75 2.01
2943 3260 7.976734 CACCTCAAGTCCTTAACTAGATAAGTG 59.023 40.741 16.09 9.39 38.88 3.16
2944 3261 7.674772 ACCTCAAGTCCTTAACTAGATAAGTGT 59.325 37.037 16.09 1.02 38.88 3.55
2947 3264 9.750783 TCAAGTCCTTAACTAGATAAGTGTACT 57.249 33.333 16.09 13.25 38.88 2.73
2951 3268 9.085250 GTCCTTAACTAGATAAGTGTACTTTGC 57.915 37.037 16.09 0.00 38.88 3.68
2969 3290 4.687901 TTGCAGGCTAGCATCTACAATA 57.312 40.909 18.24 0.00 45.19 1.90
3012 3335 6.718522 ATGAAATGCCATGTAACATGATCA 57.281 33.333 0.00 0.00 31.51 2.92
3013 3336 6.718522 TGAAATGCCATGTAACATGATCAT 57.281 33.333 1.18 1.18 0.00 2.45
3014 3337 7.820578 TGAAATGCCATGTAACATGATCATA 57.179 32.000 8.15 0.00 0.00 2.15
3015 3338 8.411991 TGAAATGCCATGTAACATGATCATAT 57.588 30.769 8.15 3.13 0.00 1.78
3016 3339 8.862085 TGAAATGCCATGTAACATGATCATATT 58.138 29.630 8.15 6.11 0.00 1.28
3017 3340 9.350357 GAAATGCCATGTAACATGATCATATTC 57.650 33.333 8.15 0.00 0.00 1.75
3036 3359 4.706842 TTCATAACTGAATAGGGGGCTC 57.293 45.455 0.00 0.00 36.46 4.70
3042 3365 1.419387 CTGAATAGGGGGCTCCAAGAG 59.581 57.143 5.99 0.00 38.24 2.85
3058 3381 4.833380 TCCAAGAGCCTTCGTAATATAGCT 59.167 41.667 0.00 0.00 0.00 3.32
3084 3407 8.028354 TCTGTTTGCCAATGTAATACTCATTTG 58.972 33.333 0.00 0.00 33.92 2.32
3090 3413 7.613801 TGCCAATGTAATACTCATTTGTACCTT 59.386 33.333 0.00 0.00 33.92 3.50
3091 3414 7.915397 GCCAATGTAATACTCATTTGTACCTTG 59.085 37.037 0.00 0.00 33.92 3.61
3105 3429 4.242475 TGTACCTTGAAATGTAGAGTGCG 58.758 43.478 0.00 0.00 0.00 5.34
3110 3434 2.279741 TGAAATGTAGAGTGCGCATCC 58.720 47.619 15.91 8.83 0.00 3.51
3112 3436 0.175760 AATGTAGAGTGCGCATCCGT 59.824 50.000 15.91 0.94 36.67 4.69
3132 3456 5.480073 TCCGTGGATCATTTCCTTGAATTTT 59.520 36.000 0.00 0.00 45.68 1.82
3147 3471 9.753674 TCCTTGAATTTTGTTATAGAGGAACAT 57.246 29.630 0.00 0.00 36.71 2.71
3208 3569 0.108041 CAAATGATTGCCTGGGGTGC 60.108 55.000 0.00 0.00 0.00 5.01
3252 3617 1.209019 CACTGAGACTGATTGGAGGGG 59.791 57.143 0.00 0.00 0.00 4.79
3317 3682 4.810191 TTGTTTGGTTTATATGGGCCAC 57.190 40.909 9.28 0.00 0.00 5.01
3318 3683 3.779444 TGTTTGGTTTATATGGGCCACA 58.221 40.909 9.28 0.00 0.00 4.17
3319 3684 4.160329 TGTTTGGTTTATATGGGCCACAA 58.840 39.130 9.28 3.45 0.00 3.33
3320 3685 4.221703 TGTTTGGTTTATATGGGCCACAAG 59.778 41.667 9.28 0.00 0.00 3.16
3321 3686 3.748645 TGGTTTATATGGGCCACAAGT 57.251 42.857 9.28 0.00 0.00 3.16
3322 3687 3.626930 TGGTTTATATGGGCCACAAGTC 58.373 45.455 9.28 0.00 0.00 3.01
3323 3688 2.956333 GGTTTATATGGGCCACAAGTCC 59.044 50.000 9.28 3.89 0.00 3.85
3324 3689 3.626222 GGTTTATATGGGCCACAAGTCCA 60.626 47.826 9.28 0.00 34.79 4.02
3343 3708 2.954318 CCATAACCCATTGAGCTTCTGG 59.046 50.000 0.00 0.00 0.00 3.86
3381 3748 5.993106 GGCAAAGCCTATTAAGTAGTCAG 57.007 43.478 0.00 0.00 46.69 3.51
3386 3753 7.634522 CAAAGCCTATTAAGTAGTCAGCATTC 58.365 38.462 0.00 0.00 0.00 2.67
3388 3755 5.366768 AGCCTATTAAGTAGTCAGCATTCCA 59.633 40.000 0.00 0.00 0.00 3.53
3389 3756 5.698545 GCCTATTAAGTAGTCAGCATTCCAG 59.301 44.000 0.00 0.00 0.00 3.86
3449 3817 2.687700 AGCATAGCAGACACAGAAGG 57.312 50.000 0.00 0.00 0.00 3.46
3452 3820 1.833630 CATAGCAGACACAGAAGGGGA 59.166 52.381 0.00 0.00 0.00 4.81
3489 3860 2.124411 ACTAGTTGGTTGACCCAGTGT 58.876 47.619 0.00 0.00 46.31 3.55
3503 3874 1.843368 CAGTGTTGGATGCCTGGATT 58.157 50.000 0.00 0.00 0.00 3.01
3504 3875 1.747355 CAGTGTTGGATGCCTGGATTC 59.253 52.381 0.00 0.00 0.00 2.52
3506 3877 1.031571 TGTTGGATGCCTGGATTCGC 61.032 55.000 0.00 0.00 0.00 4.70
3581 3952 2.889170 TACAGCCCTGTTTGCCAATA 57.111 45.000 6.21 0.00 41.83 1.90
3589 3960 6.040842 CAGCCCTGTTTGCCAATATAACTAAT 59.959 38.462 0.00 0.00 0.00 1.73
3633 4007 3.005684 TGTGTGGACCATTTGCTTGAATC 59.994 43.478 0.00 0.00 0.00 2.52
3640 4014 5.447818 GGACCATTTGCTTGAATCTCGTTAG 60.448 44.000 0.00 0.00 0.00 2.34
3686 4060 5.066968 TGAAAAATTACGGAGGGCAATTC 57.933 39.130 0.00 0.00 0.00 2.17
3689 4063 2.240493 ATTACGGAGGGCAATTCTCG 57.760 50.000 0.00 0.00 32.34 4.04
3700 4075 2.945278 GCAATTCTCGTTGGCAAATGA 58.055 42.857 0.00 2.03 0.00 2.57
3796 4173 8.579850 TTCAAGTTGGACATAATCAAGCTTAT 57.420 30.769 0.00 0.00 0.00 1.73
3798 4175 7.283127 TCAAGTTGGACATAATCAAGCTTATCC 59.717 37.037 0.00 0.00 0.00 2.59
3800 4177 6.769822 AGTTGGACATAATCAAGCTTATCCTG 59.230 38.462 0.00 0.00 0.00 3.86
3921 4298 1.483827 CAGTGGCAGCTATTGAGGAGA 59.516 52.381 0.00 0.00 0.00 3.71
3929 4306 5.163519 GGCAGCTATTGAGGAGAGATCTATC 60.164 48.000 8.93 8.93 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.073678 TGTCAATTCGATGTGGTCCAAG 58.926 45.455 0.00 0.00 0.00 3.61
9 10 4.547406 AGATGCATGTCAATTCGATGTG 57.453 40.909 2.46 0.00 0.00 3.21
26 27 2.285220 CCATACCGTTCTTGCGAAGATG 59.715 50.000 0.00 0.00 37.38 2.90
27 28 2.167693 TCCATACCGTTCTTGCGAAGAT 59.832 45.455 0.00 0.00 37.38 2.40
38 39 1.278127 CACAAGGTCCTCCATACCGTT 59.722 52.381 0.00 0.00 42.15 4.44
127 131 2.053627 CATGTTCTTTGGCTTGTTCGC 58.946 47.619 0.00 0.00 0.00 4.70
128 132 2.053627 GCATGTTCTTTGGCTTGTTCG 58.946 47.619 0.00 0.00 0.00 3.95
146 150 4.006780 ACTATGGTTATGATGATGCGCA 57.993 40.909 14.96 14.96 0.00 6.09
190 195 0.249489 CGAGGGAGAAACGGCCATAG 60.249 60.000 2.24 0.00 0.00 2.23
194 199 3.607370 AAGCGAGGGAGAAACGGCC 62.607 63.158 0.00 0.00 0.00 6.13
195 200 2.047179 AAGCGAGGGAGAAACGGC 60.047 61.111 0.00 0.00 0.00 5.68
196 201 0.108138 ATCAAGCGAGGGAGAAACGG 60.108 55.000 0.00 0.00 0.00 4.44
199 204 0.253044 CCCATCAAGCGAGGGAGAAA 59.747 55.000 0.00 0.00 46.44 2.52
215 220 2.550277 TTATCCTCTCAGTGAGCCCA 57.450 50.000 15.72 1.35 41.35 5.36
223 228 3.397482 CTTTCCGCCATTATCCTCTCAG 58.603 50.000 0.00 0.00 0.00 3.35
234 239 1.683011 CCAGTCATTCCTTTCCGCCAT 60.683 52.381 0.00 0.00 0.00 4.40
248 253 0.324614 ATCCAACACGATGCCAGTCA 59.675 50.000 0.00 0.00 0.00 3.41
262 267 3.587061 TCAGTCTCCCTTAAGCAATCCAA 59.413 43.478 0.00 0.00 0.00 3.53
284 289 4.367023 TCCGCTGCTACGCCGTTT 62.367 61.111 0.00 0.00 0.00 3.60
299 304 0.756903 TCGCCCACCTTAATAGCTCC 59.243 55.000 0.00 0.00 0.00 4.70
300 305 1.874320 GCTCGCCCACCTTAATAGCTC 60.874 57.143 0.00 0.00 0.00 4.09
322 327 6.054295 ACGAACATAATCTAGGACTACTCGT 58.946 40.000 0.00 0.00 0.00 4.18
345 350 2.809696 GCTCCTATGTCTACTCGGAGAC 59.190 54.545 12.86 2.26 43.02 3.36
403 408 9.581099 ACCAAATTTTATATGCGGAGTAAAAAG 57.419 29.630 11.91 7.15 32.84 2.27
404 409 9.575783 GACCAAATTTTATATGCGGAGTAAAAA 57.424 29.630 11.91 5.26 32.84 1.94
405 410 8.740906 TGACCAAATTTTATATGCGGAGTAAAA 58.259 29.630 10.79 10.79 33.41 1.52
502 508 9.354673 CCCCATTGAATGTATTTTCATACTACT 57.645 33.333 4.27 0.00 36.87 2.57
503 509 8.082242 GCCCCATTGAATGTATTTTCATACTAC 58.918 37.037 4.27 0.00 36.87 2.73
601 609 7.062255 GCATATAAAGTTTGGTCAAAGTCAAGC 59.938 37.037 0.00 0.00 33.15 4.01
606 614 7.448469 AGTCTGCATATAAAGTTTGGTCAAAGT 59.552 33.333 0.00 0.00 35.61 2.66
607 615 7.820648 AGTCTGCATATAAAGTTTGGTCAAAG 58.179 34.615 0.00 0.00 0.00 2.77
626 634 3.188667 CCCTCCGTTTCTTTTTAGTCTGC 59.811 47.826 0.00 0.00 0.00 4.26
638 646 3.889520 AGATGTTACTCCCTCCGTTTC 57.110 47.619 0.00 0.00 0.00 2.78
639 647 4.101119 CCATAGATGTTACTCCCTCCGTTT 59.899 45.833 0.00 0.00 0.00 3.60
640 648 3.641906 CCATAGATGTTACTCCCTCCGTT 59.358 47.826 0.00 0.00 0.00 4.44
641 649 3.231818 CCATAGATGTTACTCCCTCCGT 58.768 50.000 0.00 0.00 0.00 4.69
642 650 3.005897 CACCATAGATGTTACTCCCTCCG 59.994 52.174 0.00 0.00 0.00 4.63
643 651 3.325135 CCACCATAGATGTTACTCCCTCC 59.675 52.174 0.00 0.00 0.00 4.30
644 652 4.039366 GTCCACCATAGATGTTACTCCCTC 59.961 50.000 0.00 0.00 0.00 4.30
680 688 9.349713 GTGTCATATTTTATAGAAATGGGTGGA 57.650 33.333 0.00 0.00 0.00 4.02
684 692 7.870826 TGCGTGTCATATTTTATAGAAATGGG 58.129 34.615 0.00 0.00 0.00 4.00
686 694 8.895845 GCTTGCGTGTCATATTTTATAGAAATG 58.104 33.333 0.00 0.00 0.00 2.32
687 695 8.840321 AGCTTGCGTGTCATATTTTATAGAAAT 58.160 29.630 0.00 0.00 0.00 2.17
707 715 1.013323 CGAATACGCACGAGCTTGC 60.013 57.895 0.00 0.00 39.10 4.01
794 1039 1.081509 GTTGTGGCGTACGACCGTA 60.082 57.895 20.48 9.28 37.67 4.02
815 1060 3.062909 CGTATTCCCGTGTTACATGTTGG 59.937 47.826 2.30 0.00 0.00 3.77
816 1061 3.484557 GCGTATTCCCGTGTTACATGTTG 60.485 47.826 2.30 0.00 0.00 3.33
817 1062 2.674357 GCGTATTCCCGTGTTACATGTT 59.326 45.455 2.30 0.00 0.00 2.71
825 1070 2.582436 CCCTGCGTATTCCCGTGT 59.418 61.111 0.00 0.00 0.00 4.49
879 1124 3.889520 ATTCGGTCCAAACCTCTACTC 57.110 47.619 0.00 0.00 44.04 2.59
881 1126 3.736126 CGGTATTCGGTCCAAACCTCTAC 60.736 52.174 0.00 0.00 44.04 2.59
882 1127 2.428171 CGGTATTCGGTCCAAACCTCTA 59.572 50.000 0.00 0.00 44.04 2.43
883 1128 1.206371 CGGTATTCGGTCCAAACCTCT 59.794 52.381 0.00 0.00 44.04 3.69
884 1129 1.648504 CGGTATTCGGTCCAAACCTC 58.351 55.000 0.00 0.00 44.04 3.85
885 1130 0.392060 GCGGTATTCGGTCCAAACCT 60.392 55.000 0.00 0.00 44.04 3.50
886 1131 1.371337 GGCGGTATTCGGTCCAAACC 61.371 60.000 0.00 0.00 42.66 3.27
887 1132 0.674269 TGGCGGTATTCGGTCCAAAC 60.674 55.000 0.00 0.00 39.69 2.93
888 1133 0.036448 TTGGCGGTATTCGGTCCAAA 59.964 50.000 0.00 0.00 39.69 3.28
889 1134 0.036448 TTTGGCGGTATTCGGTCCAA 59.964 50.000 0.00 0.00 39.69 3.53
950 1198 1.748122 GAGGGAGTGTACGAGCGGA 60.748 63.158 0.00 0.00 0.00 5.54
951 1199 2.044555 TGAGGGAGTGTACGAGCGG 61.045 63.158 0.00 0.00 0.00 5.52
952 1200 1.136984 GTGAGGGAGTGTACGAGCG 59.863 63.158 0.00 0.00 0.00 5.03
959 1207 1.122019 GGTGAGTGGTGAGGGAGTGT 61.122 60.000 0.00 0.00 0.00 3.55
1211 1468 2.928396 AGGAGTTGGTGGGGTCGG 60.928 66.667 0.00 0.00 0.00 4.79
1494 1751 1.737008 GGAGAACCAGCGGTCGAAC 60.737 63.158 0.00 0.00 33.12 3.95
1896 2153 2.729862 GCCCGCAGCGTATCGTAG 60.730 66.667 15.05 0.00 0.00 3.51
2034 2291 3.120165 GGTCGAACTTGAAGAAGAATGGC 60.120 47.826 0.00 0.00 32.98 4.40
2037 2294 3.326747 CCGGTCGAACTTGAAGAAGAAT 58.673 45.455 0.00 0.00 32.98 2.40
2223 2480 1.522580 GCCTGCCCATTCGTCTCTC 60.523 63.158 0.00 0.00 0.00 3.20
2320 2577 2.441001 TGCCAAATTCCCCATTGTGTTT 59.559 40.909 0.00 0.00 0.00 2.83
2381 2640 8.599624 AGGATCCAAATTAAGTGAAATGTGAT 57.400 30.769 15.82 0.00 0.00 3.06
2450 2744 8.749026 ACTATGATTCTGCTGAAATGAATTCT 57.251 30.769 10.27 0.00 38.92 2.40
2558 2856 7.062605 GCATCCAAATTAAGTGAATTGTGACTG 59.937 37.037 0.00 0.00 37.82 3.51
2600 2898 6.573434 AGGATGAAAACAGAACAAAGTTTCC 58.427 36.000 0.00 0.00 36.98 3.13
2660 2977 1.081840 GCTCTTTCGCTGGTGTTGC 60.082 57.895 0.00 0.00 0.00 4.17
2677 2994 1.941325 AATCCGAGAGAATTCCGTGC 58.059 50.000 0.65 0.00 0.00 5.34
2711 3028 5.446473 CGTTCAAGAAGCTTGCTAATTCGAT 60.446 40.000 2.10 0.00 0.00 3.59
2752 3069 1.587054 CGTCTCCTGAGCGGAACTT 59.413 57.895 3.96 0.00 42.53 2.66
2801 3118 0.249073 ATGGCTCGTCTCACGTATGC 60.249 55.000 0.00 0.41 43.14 3.14
2806 3123 0.994995 CTTTGATGGCTCGTCTCACG 59.005 55.000 0.00 0.00 44.19 4.35
2933 3250 5.665459 AGCCTGCAAAGTACACTTATCTAG 58.335 41.667 0.00 0.00 34.61 2.43
2943 3260 2.911484 AGATGCTAGCCTGCAAAGTAC 58.089 47.619 13.29 0.00 46.61 2.73
2944 3261 3.450817 TGTAGATGCTAGCCTGCAAAGTA 59.549 43.478 13.29 0.00 46.61 2.24
2946 3263 2.910199 TGTAGATGCTAGCCTGCAAAG 58.090 47.619 13.29 0.00 46.61 2.77
2947 3264 3.348647 TTGTAGATGCTAGCCTGCAAA 57.651 42.857 17.62 6.15 46.61 3.68
2948 3265 3.565764 ATTGTAGATGCTAGCCTGCAA 57.434 42.857 20.59 20.59 46.61 4.08
2949 3266 5.455183 ACAATATTGTAGATGCTAGCCTGCA 60.455 40.000 19.51 9.90 42.75 4.41
2950 3267 4.999950 ACAATATTGTAGATGCTAGCCTGC 59.000 41.667 19.51 7.19 40.16 4.85
2951 3268 6.226052 TCACAATATTGTAGATGCTAGCCTG 58.774 40.000 20.39 4.40 39.91 4.85
3015 3338 5.133425 TGGAGCCCCCTATTCAGTTATGAA 61.133 45.833 0.00 0.00 41.86 2.57
3016 3339 2.979678 GGAGCCCCCTATTCAGTTATGA 59.020 50.000 0.00 0.00 0.00 2.15
3017 3340 2.711009 TGGAGCCCCCTATTCAGTTATG 59.289 50.000 0.00 0.00 35.38 1.90
3023 3346 1.511613 CTCTTGGAGCCCCCTATTCA 58.488 55.000 0.00 0.00 35.38 2.57
3036 3359 5.140747 AGCTATATTACGAAGGCTCTTGG 57.859 43.478 0.00 0.00 0.00 3.61
3042 3365 5.333416 GCAAACAGAGCTATATTACGAAGGC 60.333 44.000 0.00 0.00 0.00 4.35
3047 3370 5.984233 TTGGCAAACAGAGCTATATTACG 57.016 39.130 0.00 0.00 0.00 3.18
3048 3371 7.264373 ACATTGGCAAACAGAGCTATATTAC 57.736 36.000 3.01 0.00 0.00 1.89
3049 3372 8.972458 TTACATTGGCAAACAGAGCTATATTA 57.028 30.769 3.01 0.00 0.00 0.98
3050 3373 7.880160 TTACATTGGCAAACAGAGCTATATT 57.120 32.000 3.01 0.00 0.00 1.28
3051 3374 9.003658 GTATTACATTGGCAAACAGAGCTATAT 57.996 33.333 3.01 0.00 0.00 0.86
3058 3381 7.701539 AATGAGTATTACATTGGCAAACAGA 57.298 32.000 3.01 0.00 36.74 3.41
3060 3383 7.665690 ACAAATGAGTATTACATTGGCAAACA 58.334 30.769 3.01 0.00 37.89 2.83
3061 3384 9.072294 GTACAAATGAGTATTACATTGGCAAAC 57.928 33.333 3.01 0.00 37.89 2.93
3084 3407 3.062234 GCGCACTCTACATTTCAAGGTAC 59.938 47.826 0.30 0.00 0.00 3.34
3090 3413 2.279741 GGATGCGCACTCTACATTTCA 58.720 47.619 14.90 0.00 0.00 2.69
3091 3414 1.258982 CGGATGCGCACTCTACATTTC 59.741 52.381 14.90 2.02 0.00 2.17
3164 3525 7.132863 GTCAAAGACAATTGTCCTCAGTAAAC 58.867 38.462 30.34 15.97 45.85 2.01
3165 3526 6.826231 TGTCAAAGACAATTGTCCTCAGTAAA 59.174 34.615 30.34 10.73 45.85 2.01
3198 3559 1.069596 CAAACAAAGCACCCCAGGC 59.930 57.895 0.00 0.00 0.00 4.85
3279 3644 8.650143 ACCAAACAATGTCCACTCTAAAATAT 57.350 30.769 0.00 0.00 0.00 1.28
3317 3682 3.624777 AGCTCAATGGGTTATGGACTTG 58.375 45.455 0.00 0.00 0.00 3.16
3318 3683 4.018050 AGAAGCTCAATGGGTTATGGACTT 60.018 41.667 0.00 0.00 0.00 3.01
3319 3684 3.525199 AGAAGCTCAATGGGTTATGGACT 59.475 43.478 0.00 0.00 0.00 3.85
3320 3685 3.629398 CAGAAGCTCAATGGGTTATGGAC 59.371 47.826 0.00 0.00 33.88 4.02
3321 3686 3.889815 CAGAAGCTCAATGGGTTATGGA 58.110 45.455 0.00 0.00 33.88 3.41
3322 3687 2.954318 CCAGAAGCTCAATGGGTTATGG 59.046 50.000 10.96 10.96 45.22 2.74
3323 3688 3.624777 ACCAGAAGCTCAATGGGTTATG 58.375 45.455 14.35 0.00 38.48 1.90
3324 3689 5.370880 AGATACCAGAAGCTCAATGGGTTAT 59.629 40.000 14.35 5.94 38.48 1.89
3343 3708 4.513318 GCTTTGCCATAGAGGTTGAGATAC 59.487 45.833 0.00 0.00 40.61 2.24
3381 3748 5.581085 AGAAGTACAAATACGACTGGAATGC 59.419 40.000 0.00 0.00 36.33 3.56
3386 3753 5.466819 TCACAGAAGTACAAATACGACTGG 58.533 41.667 0.00 7.10 40.38 4.00
3388 3755 5.162075 GCTCACAGAAGTACAAATACGACT 58.838 41.667 0.00 0.00 36.33 4.18
3389 3756 4.921515 TGCTCACAGAAGTACAAATACGAC 59.078 41.667 0.00 0.00 36.33 4.34
3449 3817 4.548669 AGTTACTACTCCTGATTCCTCCC 58.451 47.826 0.00 0.00 0.00 4.30
3452 3820 6.608002 CCAACTAGTTACTACTCCTGATTCCT 59.392 42.308 8.04 0.00 35.78 3.36
3489 3860 1.453745 GGCGAATCCAGGCATCCAA 60.454 57.895 0.00 0.00 34.01 3.53
3503 3874 1.301716 GTCACAAGGCTCTTGGCGA 60.302 57.895 16.21 10.70 44.18 5.54
3504 3875 0.957395 ATGTCACAAGGCTCTTGGCG 60.957 55.000 16.21 9.04 44.18 5.69
3506 3877 6.949352 ATAATTATGTCACAAGGCTCTTGG 57.051 37.500 16.21 7.90 0.00 3.61
3511 3882 9.632638 ATTCAGTTATAATTATGTCACAAGGCT 57.367 29.630 8.28 0.00 0.00 4.58
3546 3917 3.432749 GGCTGTATCATGAAGGCTCTTGA 60.433 47.826 11.21 0.00 39.36 3.02
3548 3919 2.158696 GGGCTGTATCATGAAGGCTCTT 60.159 50.000 16.39 0.00 36.76 2.85
3664 4038 4.770010 AGAATTGCCCTCCGTAATTTTTCA 59.230 37.500 0.00 0.00 36.96 2.69
3667 4041 3.377172 CGAGAATTGCCCTCCGTAATTTT 59.623 43.478 0.00 0.00 36.96 1.82
3677 4051 0.539438 TTGCCAACGAGAATTGCCCT 60.539 50.000 0.00 0.00 0.00 5.19
3680 4054 2.945278 TCATTTGCCAACGAGAATTGC 58.055 42.857 0.00 0.00 0.00 3.56
3686 4060 5.277974 CCATAGGTAATCATTTGCCAACGAG 60.278 44.000 0.00 0.00 39.87 4.18
3689 4063 5.591099 CACCATAGGTAATCATTTGCCAAC 58.409 41.667 0.00 0.00 39.87 3.77
3694 4068 5.750067 GCAAAGCACCATAGGTAATCATTTG 59.250 40.000 0.00 0.00 32.11 2.32
3700 4075 7.475137 TTTAAAGCAAAGCACCATAGGTAAT 57.525 32.000 0.00 0.00 32.11 1.89
3798 4175 9.305925 GGCCAATCTAAAATGAAAAGATAACAG 57.694 33.333 0.00 0.00 29.89 3.16
3800 4177 9.822185 ATGGCCAATCTAAAATGAAAAGATAAC 57.178 29.630 10.96 0.00 29.89 1.89


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

AutoCloner maintained by Alex Coulton.