Multiple sequence alignment - TraesCS2B01G025300

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 TraesCS2B01G025300 chr2B 100.000 3458 0 0 1 3458 11540658 11537201 0 6386
1 TraesCS2B01G025300 chr2B 89.383 2656 224 34 751 3370 12942190 12944823 0 3290
2 TraesCS2B01G025300 chr2B 81.055 1668 277 24 927 2586 11226499 11224863 0 1293
3 TraesCS2B01G025300 chr2B 79.010 1758 288 41 926 2629 12966365 12968095 0 1127
4 TraesCS2B01G025300 chr2B 79.539 1520 276 20 1000 2504 11400641 11402140 0 1051
5 TraesCS2B01G025300 chr2B 86.963 698 44 20 1 689 12941416 12942075 0 741
6 TraesCS2B01G025300 chr2D 88.094 2503 236 32 751 3237 9588065 9590521 0 2915
7 TraesCS2B01G025300 chr2D 79.564 1698 281 33 922 2573 9642906 9644583 0 1153
8 TraesCS2B01G025300 chr2D 83.224 1216 189 11 936 2142 9251968 9253177 0 1101
9 TraesCS2B01G025300 chr2D 87.552 723 49 13 1 693 9587220 9587931 0 798
10 TraesCS2B01G025300 chr2A 86.880 2279 223 41 1216 3458 8683201 8685439 0 2483
11 TraesCS2B01G025300 chr2A 81.145 1607 284 14 921 2516 8630881 8632479 0 1271
12 TraesCS2B01G025300 chr2A 80.235 1705 300 26 925 2615 9094556 9092875 0 1247
13 TraesCS2B01G025300 chr2A 89.695 524 32 8 184 693 8681844 8682359 0 649
14 TraesCS2B01G025300 chr4D 81.887 1579 276 7 925 2499 464204536 464206108 0 1323


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 TraesCS2B01G025300 chr2B 11537201 11540658 3457 True 6386.0 6386 100.0000 1 3458 1 chr2B.!!$R2 3457
1 TraesCS2B01G025300 chr2B 12941416 12944823 3407 False 2015.5 3290 88.1730 1 3370 2 chr2B.!!$F3 3369
2 TraesCS2B01G025300 chr2B 11224863 11226499 1636 True 1293.0 1293 81.0550 927 2586 1 chr2B.!!$R1 1659
3 TraesCS2B01G025300 chr2B 12966365 12968095 1730 False 1127.0 1127 79.0100 926 2629 1 chr2B.!!$F2 1703
4 TraesCS2B01G025300 chr2B 11400641 11402140 1499 False 1051.0 1051 79.5390 1000 2504 1 chr2B.!!$F1 1504
5 TraesCS2B01G025300 chr2D 9587220 9590521 3301 False 1856.5 2915 87.8230 1 3237 2 chr2D.!!$F3 3236
6 TraesCS2B01G025300 chr2D 9642906 9644583 1677 False 1153.0 1153 79.5640 922 2573 1 chr2D.!!$F2 1651
7 TraesCS2B01G025300 chr2D 9251968 9253177 1209 False 1101.0 1101 83.2240 936 2142 1 chr2D.!!$F1 1206
8 TraesCS2B01G025300 chr2A 8681844 8685439 3595 False 1566.0 2483 88.2875 184 3458 2 chr2A.!!$F2 3274
9 TraesCS2B01G025300 chr2A 8630881 8632479 1598 False 1271.0 1271 81.1450 921 2516 1 chr2A.!!$F1 1595
10 TraesCS2B01G025300 chr2A 9092875 9094556 1681 True 1247.0 1247 80.2350 925 2615 1 chr2A.!!$R1 1690
11 TraesCS2B01G025300 chr4D 464204536 464206108 1572 False 1323.0 1323 81.8870 925 2499 1 chr4D.!!$F1 1574

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
165 170 0.037882 CTCACTCTCGCTTGGCTTGA 60.038 55.000 0.0 0.0 0.00 3.02 F
900 1018 1.079543 CAGTCTCAGCAACCCTCGG 60.080 63.158 0.0 0.0 0.00 4.63 F
1176 1303 0.179111 AGGCGGACACACGATACATG 60.179 55.000 0.0 0.0 35.47 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 1258 0.656259 CGATGGTGCAAGCTCTCATG 59.344 55.0 0.00 0.0 33.76 3.07 R
2261 2693 0.790207 CGTGACACTTGGTGATTCCG 59.210 55.0 3.68 0.0 39.52 4.30 R
3123 3646 0.109723 GTGGGACCTAGCCAACAACA 59.890 55.0 0.00 0.0 31.79 3.33 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
31 35 3.386543 GCATATCTGCCGTCAGGTT 57.613 52.632 0.00 0.00 42.88 3.50
88 92 9.703892 CTATATATCCTGCTAACCTGCATATTC 57.296 37.037 0.00 0.00 42.48 1.75
140 145 5.570234 TGGCGACCCTTATTTTACATTTC 57.430 39.130 0.00 0.00 0.00 2.17
165 170 0.037882 CTCACTCTCGCTTGGCTTGA 60.038 55.000 0.00 0.00 0.00 3.02
287 301 2.437359 GCGGGAGTCATTGCTGCT 60.437 61.111 0.00 0.00 45.30 4.24
330 344 4.194497 TCCACCCCACACCCAGGA 62.194 66.667 0.00 0.00 0.00 3.86
331 345 3.650950 CCACCCCACACCCAGGAG 61.651 72.222 0.00 0.00 0.00 3.69
332 346 4.351054 CACCCCACACCCAGGAGC 62.351 72.222 0.00 0.00 0.00 4.70
335 349 4.039092 CCCACACCCAGGAGCCAG 62.039 72.222 0.00 0.00 0.00 4.85
336 350 4.039092 CCACACCCAGGAGCCAGG 62.039 72.222 0.00 0.00 0.00 4.45
357 371 7.490402 GCCAGGAGATGAGTTTTATTGAAATTG 59.510 37.037 0.00 0.00 0.00 2.32
380 407 5.179929 TGCATAATGTCCGATGCTTTGATAG 59.820 40.000 8.20 0.00 46.98 2.08
390 417 5.468072 CCGATGCTTTGATAGTTGCTCTAAT 59.532 40.000 0.00 0.00 31.94 1.73
399 426 9.547753 TTTGATAGTTGCTCTAATCCTAATCAC 57.452 33.333 0.00 0.00 31.94 3.06
460 488 5.124138 TCCTAGTTTCGAACAGCAAACAAAA 59.876 36.000 0.00 0.00 35.33 2.44
469 497 5.052172 CGAACAGCAAACAAAATCAAGTCTG 60.052 40.000 0.00 0.00 0.00 3.51
560 595 5.066634 TGTGCAACGGATTTCAGTTAAAGAA 59.933 36.000 0.00 0.00 42.39 2.52
626 661 6.777580 TCTGAAGGACTAAAGGAGCAAAAATT 59.222 34.615 0.00 0.00 0.00 1.82
663 698 5.823045 GGTCAAATGTCCTCCGAAAGATTAT 59.177 40.000 0.00 0.00 0.00 1.28
675 710 5.296780 TCCGAAAGATTATTGAAGCATGGAC 59.703 40.000 0.00 0.00 0.00 4.02
680 715 5.128919 AGATTATTGAAGCATGGACTGGTC 58.871 41.667 0.00 0.00 33.48 4.02
693 730 2.103941 GGACTGGTCATCCTCATCTTCC 59.896 54.545 3.10 0.00 33.03 3.46
697 734 1.202746 GGTCATCCTCATCTTCCCTGC 60.203 57.143 0.00 0.00 0.00 4.85
724 815 1.112113 GACGTTCATCTAGCCCAGGA 58.888 55.000 0.00 0.00 0.00 3.86
748 839 7.201723 GGAAATTTCCACAATCAAACTTTGCTT 60.202 33.333 28.76 0.00 46.76 3.91
752 865 4.402155 TCCACAATCAAACTTTGCTTCAGT 59.598 37.500 0.00 0.00 0.00 3.41
769 882 5.813157 GCTTCAGTAGGAGTCAATAGAAACC 59.187 44.000 0.00 0.00 0.00 3.27
775 888 7.928706 CAGTAGGAGTCAATAGAAACCCAATAG 59.071 40.741 0.00 0.00 0.00 1.73
848 961 7.886405 AAAAATACTAGACAACCTCTTCGAC 57.114 36.000 0.00 0.00 0.00 4.20
849 962 6.585695 AAATACTAGACAACCTCTTCGACA 57.414 37.500 0.00 0.00 0.00 4.35
900 1018 1.079543 CAGTCTCAGCAACCCTCGG 60.080 63.158 0.00 0.00 0.00 4.63
954 1072 1.467920 GCAGAAGCCAGCCAAGTTAT 58.532 50.000 0.00 0.00 33.58 1.89
1036 1154 4.119862 GTCTGTAGTTGCAAGTGAACTGA 58.880 43.478 17.21 13.49 35.30 3.41
1108 1235 2.524306 CAGAGTCAGAGGAGAAGGTGT 58.476 52.381 0.00 0.00 0.00 4.16
1131 1258 2.278854 GAGAGGTTGCAGCATCTTCTC 58.721 52.381 22.84 22.84 32.26 2.87
1176 1303 0.179111 AGGCGGACACACGATACATG 60.179 55.000 0.00 0.00 35.47 3.21
1186 1313 2.565391 ACACGATACATGACCAACTCCA 59.435 45.455 0.00 0.00 0.00 3.86
1187 1314 3.197766 ACACGATACATGACCAACTCCAT 59.802 43.478 0.00 0.00 0.00 3.41
1206 1333 3.317993 CCATGATGATGATGCAGCTCAAA 59.682 43.478 2.53 0.00 0.00 2.69
1230 1615 0.324368 TCTCAGAGGCCATGTACCGT 60.324 55.000 5.01 0.00 0.00 4.83
1298 1683 0.885196 GGGCGCATTGACAAGGTTAA 59.115 50.000 10.83 0.00 0.00 2.01
1342 1736 2.163613 AGTTTGTATTTAGCCAAGCGCC 59.836 45.455 2.29 0.00 38.78 6.53
1351 1745 3.055719 CCAAGCGCCCACGAACAT 61.056 61.111 2.29 0.00 43.93 2.71
1455 1867 0.770499 TGCTTCTGGGTGGATGTGAA 59.230 50.000 0.00 0.00 0.00 3.18
1513 1929 3.313249 CACTGACAACTTCATGTTCAGCA 59.687 43.478 0.00 0.00 36.63 4.41
1539 1955 4.916983 TGCTGAAAAGCAAAAGCTCTTA 57.083 36.364 0.00 0.00 42.40 2.10
1779 2198 2.163818 TCGAGTTTGCTTCCGATGTT 57.836 45.000 0.00 0.00 0.00 2.71
1781 2200 1.725931 CGAGTTTGCTTCCGATGTTGC 60.726 52.381 0.00 0.00 0.00 4.17
1816 2235 4.209080 GGCAAAGGTTTCAGTCATTTTTCG 59.791 41.667 0.00 0.00 0.00 3.46
1849 2268 6.786959 AGGTAGAGGAAGCAAGATAATCATCT 59.213 38.462 0.00 0.00 43.67 2.90
2001 2420 4.092968 CCACGGTTAGTTCAAATAGCAGAC 59.907 45.833 0.00 0.00 0.00 3.51
2208 2634 2.094906 TCGAGTGGACATAACGGACTTG 60.095 50.000 0.00 0.00 0.00 3.16
2232 2658 1.655484 TGCATCCACTTAGCATGACG 58.345 50.000 0.00 0.00 32.55 4.35
2277 2709 0.321653 AGGCGGAATCACCAAGTGTC 60.322 55.000 0.00 0.00 38.90 3.67
2286 2718 0.462937 CACCAAGTGTCACGTTGGGA 60.463 55.000 25.27 0.00 46.53 4.37
2308 2740 5.775701 GGAGGACTTATAGCAGATCCAAGTA 59.224 44.000 0.00 0.00 29.89 2.24
2317 2749 5.283457 AGCAGATCCAAGTATTAGACCAC 57.717 43.478 0.00 0.00 0.00 4.16
2352 2784 9.973661 TTTATTCTAACTTCATGGGAATCAAGA 57.026 29.630 0.00 0.00 31.34 3.02
2431 2878 0.253327 AGGTAGTGCTTTGCTAGGGC 59.747 55.000 0.00 0.00 39.26 5.19
2518 2975 9.701098 TGTATTTCTGATATATGGTAAACGGTC 57.299 33.333 0.00 0.00 0.00 4.79
2616 3083 4.598036 ATCAGATCCAACAATCCACCTT 57.402 40.909 0.00 0.00 0.00 3.50
2617 3084 4.387026 TCAGATCCAACAATCCACCTTT 57.613 40.909 0.00 0.00 0.00 3.11
2624 3091 3.189287 CCAACAATCCACCTTTCTCTTCG 59.811 47.826 0.00 0.00 0.00 3.79
2643 3110 7.968956 TCTCTTCGTAGACATCATGAACTAAAC 59.031 37.037 0.00 0.00 34.32 2.01
2645 3112 4.796830 TCGTAGACATCATGAACTAAACGC 59.203 41.667 14.66 2.74 0.00 4.84
2650 3117 5.577164 AGACATCATGAACTAAACGCACTAC 59.423 40.000 0.00 0.00 0.00 2.73
2676 3143 7.651304 CAGATCTCAGTAAGTTGGCTTATACTG 59.349 40.741 0.00 11.46 40.25 2.74
2766 3234 8.832521 TGTGACTAAAATTTACTACAGTTGGTG 58.167 33.333 0.00 0.00 0.00 4.17
2771 3239 7.768807 AAAATTTACTACAGTTGGTGCCATA 57.231 32.000 0.00 0.00 0.00 2.74
2814 3283 2.865551 GACCAACCAAAAATGCAGTGTG 59.134 45.455 0.00 0.00 0.00 3.82
2834 3304 3.921021 GTGACTACATGTGAAAGAGGACG 59.079 47.826 9.11 0.00 0.00 4.79
2914 3389 6.049955 TGAACTCAAATTACCGAGGAATCT 57.950 37.500 0.00 0.00 33.36 2.40
2915 3390 6.472887 TGAACTCAAATTACCGAGGAATCTT 58.527 36.000 0.00 0.00 33.36 2.40
2926 3401 6.901081 ACCGAGGAATCTTTTTCAAAGAAT 57.099 33.333 3.13 0.00 0.00 2.40
2928 3403 7.726216 ACCGAGGAATCTTTTTCAAAGAATTT 58.274 30.769 3.13 0.00 40.26 1.82
2965 3440 4.052608 TGGTACACTACATTCACAACACG 58.947 43.478 0.00 0.00 0.00 4.49
2969 3444 1.525197 ACTACATTCACAACACGCACG 59.475 47.619 0.00 0.00 0.00 5.34
3016 3536 1.300963 GAGCCCTTGAGGTGATGCA 59.699 57.895 0.00 0.00 38.26 3.96
3042 3562 3.743017 ATCCCACCGCCATGGCTT 61.743 61.111 33.07 18.08 43.94 4.35
3049 3569 2.088423 CACCGCCATGGCTTAGTTTAA 58.912 47.619 33.07 0.00 43.94 1.52
3054 3574 3.632145 CGCCATGGCTTAGTTTAAGGAAT 59.368 43.478 33.07 0.00 39.32 3.01
3075 3598 6.784473 GGAATGAGAATGGGGGATAAATTTCT 59.216 38.462 0.00 0.00 0.00 2.52
3083 3606 3.821033 GGGGGATAAATTTCTGATGGACG 59.179 47.826 0.00 0.00 0.00 4.79
3096 3619 2.032860 ATGGACGCTCCCATCGGAAG 62.033 60.000 1.36 0.00 43.07 3.46
3112 3635 3.690628 TCGGAAGAGAAACGGTTTGTTTT 59.309 39.130 11.43 8.52 42.93 2.43
3115 3638 7.125293 TCGGAAGAGAAACGGTTTGTTTTCTA 61.125 38.462 23.74 14.74 42.93 2.10
3116 3639 8.379476 TCGGAAGAGAAACGGTTTGTTTTCTAT 61.379 37.037 23.74 7.22 42.93 1.98
3148 3671 1.144057 GGCTAGGTCCCACATGTCG 59.856 63.158 0.00 0.00 0.00 4.35
3155 3678 0.179073 GTCCCACATGTCGATGGAGG 60.179 60.000 4.30 0.00 38.34 4.30
3158 3681 1.473965 CCCACATGTCGATGGAGGAAG 60.474 57.143 4.30 0.00 38.34 3.46
3162 3685 2.834549 ACATGTCGATGGAGGAAGAAGT 59.165 45.455 0.00 0.00 33.39 3.01
3175 3698 1.886542 GAAGAAGTTGGGCCGATGTTT 59.113 47.619 0.00 0.00 0.00 2.83
3176 3699 2.871096 AGAAGTTGGGCCGATGTTTA 57.129 45.000 0.00 0.00 0.00 2.01
3177 3700 2.433436 AGAAGTTGGGCCGATGTTTAC 58.567 47.619 0.00 0.00 0.00 2.01
3181 3704 2.156098 GTTGGGCCGATGTTTACTCAA 58.844 47.619 0.00 0.00 0.00 3.02
3199 3722 6.065976 ACTCAACCAAGATGGATTGTGATA 57.934 37.500 2.85 0.00 40.96 2.15
3206 3729 3.759581 AGATGGATTGTGATATGCCACC 58.240 45.455 0.00 0.00 36.26 4.61
3227 3750 4.346418 ACCATGGCTCAAATTTTGTTGGTA 59.654 37.500 13.04 0.00 33.38 3.25
3237 3760 8.044060 TCAAATTTTGTTGGTAGAGCTAGATG 57.956 34.615 8.89 0.00 0.00 2.90
3241 3764 4.991153 TGTTGGTAGAGCTAGATGACTG 57.009 45.455 0.00 0.00 0.00 3.51
3273 3796 9.998106 TCCTCTTAAAAGATATATGGTGCTAAC 57.002 33.333 0.00 0.00 33.93 2.34
3297 3820 2.236146 TCGAAGCAACACCCTGTATCAT 59.764 45.455 0.00 0.00 0.00 2.45
3302 3825 2.939640 GCAACACCCTGTATCATCCGTT 60.940 50.000 0.00 0.00 0.00 4.44
3304 3827 2.184533 ACACCCTGTATCATCCGTTCA 58.815 47.619 0.00 0.00 0.00 3.18
3310 3833 3.627123 CCTGTATCATCCGTTCATTTGCA 59.373 43.478 0.00 0.00 0.00 4.08
3311 3834 4.260907 CCTGTATCATCCGTTCATTTGCAG 60.261 45.833 0.00 0.00 0.00 4.41
3332 3857 2.561209 TGTAATAGTGCCCTCCCAGA 57.439 50.000 0.00 0.00 0.00 3.86
3334 3859 2.705658 TGTAATAGTGCCCTCCCAGATG 59.294 50.000 0.00 0.00 0.00 2.90
3350 3875 4.384056 CCAGATGTGATGGGATCTTGTAC 58.616 47.826 0.00 0.00 33.94 2.90
3371 3897 2.726760 CGCTAATGATCGCCTTGTAGTC 59.273 50.000 0.00 0.00 0.00 2.59
3427 3953 4.497473 TCGTGGCCTTTGTAAATGAAAG 57.503 40.909 3.32 0.00 0.00 2.62
3432 3958 6.612306 GTGGCCTTTGTAAATGAAAGACTAG 58.388 40.000 3.32 0.00 33.01 2.57
3439 3965 4.847512 TGTAAATGAAAGACTAGGGGTGGA 59.152 41.667 0.00 0.00 0.00 4.02
3441 3967 6.674861 TGTAAATGAAAGACTAGGGGTGGATA 59.325 38.462 0.00 0.00 0.00 2.59
3451 3977 4.593634 ACTAGGGGTGGATAGCTAACAATC 59.406 45.833 0.00 0.00 0.00 2.67
3452 3978 3.393687 AGGGGTGGATAGCTAACAATCA 58.606 45.455 0.00 0.00 0.00 2.57
3453 3979 3.392616 AGGGGTGGATAGCTAACAATCAG 59.607 47.826 0.00 0.00 0.00 2.90
3454 3980 3.142174 GGGTGGATAGCTAACAATCAGC 58.858 50.000 0.00 0.00 39.41 4.26
3456 3982 4.199310 GGTGGATAGCTAACAATCAGCAA 58.801 43.478 0.00 0.00 41.66 3.91
3457 3983 4.035675 GGTGGATAGCTAACAATCAGCAAC 59.964 45.833 0.00 0.00 41.66 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 35 3.120792 GTGTGTGTCTCTTCGTGCTTTA 58.879 45.455 0.00 0.00 0.00 1.85
111 116 2.038387 ATAAGGGTCGCCATGTGTTC 57.962 50.000 0.00 0.00 0.00 3.18
140 145 2.072298 CCAAGCGAGAGTGAGAAAAGG 58.928 52.381 0.00 0.00 0.00 3.11
165 170 2.108952 ACCATGCTTCTTCCTGGAAAGT 59.891 45.455 10.86 0.00 32.92 2.66
267 281 3.329889 AGCAATGACTCCCGCCCA 61.330 61.111 0.00 0.00 0.00 5.36
330 344 5.441718 TCAATAAAACTCATCTCCTGGCT 57.558 39.130 0.00 0.00 0.00 4.75
331 345 6.515272 TTTCAATAAAACTCATCTCCTGGC 57.485 37.500 0.00 0.00 0.00 4.85
332 346 7.490402 GCAATTTCAATAAAACTCATCTCCTGG 59.510 37.037 0.00 0.00 0.00 4.45
333 347 8.030692 TGCAATTTCAATAAAACTCATCTCCTG 58.969 33.333 0.00 0.00 0.00 3.86
334 348 8.125978 TGCAATTTCAATAAAACTCATCTCCT 57.874 30.769 0.00 0.00 0.00 3.69
335 349 8.937634 ATGCAATTTCAATAAAACTCATCTCC 57.062 30.769 0.00 0.00 0.00 3.71
380 407 6.926272 CCTGTAGTGATTAGGATTAGAGCAAC 59.074 42.308 0.00 0.00 33.33 4.17
390 417 2.504175 GTTGCCCCTGTAGTGATTAGGA 59.496 50.000 0.00 0.00 33.33 2.94
399 426 3.320541 TGAAATTGTTGTTGCCCCTGTAG 59.679 43.478 0.00 0.00 0.00 2.74
460 488 5.906113 ACTTCAGACGATACAGACTTGAT 57.094 39.130 0.00 0.00 0.00 2.57
469 497 5.980116 AGTATGATGCAACTTCAGACGATAC 59.020 40.000 7.66 0.00 39.63 2.24
536 571 4.576873 TCTTTAACTGAAATCCGTTGCACA 59.423 37.500 0.00 0.00 0.00 4.57
626 661 7.560368 AGGACATTTGACCATTTTGTTTGTAA 58.440 30.769 2.08 0.00 32.26 2.41
663 698 2.618816 GGATGACCAGTCCATGCTTCAA 60.619 50.000 0.00 0.00 35.76 2.69
675 710 2.104451 CAGGGAAGATGAGGATGACCAG 59.896 54.545 0.00 0.00 38.94 4.00
680 715 1.138568 AGGCAGGGAAGATGAGGATG 58.861 55.000 0.00 0.00 0.00 3.51
693 730 0.249868 TGAACGTCAGTCAAGGCAGG 60.250 55.000 0.00 0.00 0.00 4.85
697 734 3.182967 GCTAGATGAACGTCAGTCAAGG 58.817 50.000 0.00 0.00 0.00 3.61
724 815 7.336427 TGAAGCAAAGTTTGATTGTGGAAATTT 59.664 29.630 22.87 0.00 39.73 1.82
734 825 6.064717 ACTCCTACTGAAGCAAAGTTTGATT 58.935 36.000 18.47 18.47 42.77 2.57
735 826 5.625150 ACTCCTACTGAAGCAAAGTTTGAT 58.375 37.500 19.82 10.52 0.00 2.57
748 839 5.338632 TGGGTTTCTATTGACTCCTACTGA 58.661 41.667 0.00 0.00 0.00 3.41
752 865 6.615726 AGCTATTGGGTTTCTATTGACTCCTA 59.384 38.462 0.00 0.00 0.00 2.94
769 882 8.974060 TTAAGTAGGTCCAAATTAGCTATTGG 57.026 34.615 16.90 16.90 46.03 3.16
775 888 7.859325 TCACATTAAGTAGGTCCAAATTAGC 57.141 36.000 0.00 0.00 0.00 3.09
824 937 7.439381 TGTCGAAGAGGTTGTCTAGTATTTTT 58.561 34.615 0.00 0.00 36.95 1.94
825 938 6.989659 TGTCGAAGAGGTTGTCTAGTATTTT 58.010 36.000 0.00 0.00 36.95 1.82
826 939 6.585695 TGTCGAAGAGGTTGTCTAGTATTT 57.414 37.500 0.00 0.00 36.95 1.40
828 941 5.652891 ACATGTCGAAGAGGTTGTCTAGTAT 59.347 40.000 0.00 0.00 36.95 2.12
829 942 5.008331 ACATGTCGAAGAGGTTGTCTAGTA 58.992 41.667 0.00 0.00 36.95 1.82
830 943 3.827302 ACATGTCGAAGAGGTTGTCTAGT 59.173 43.478 0.00 0.00 36.95 2.57
831 944 4.442375 ACATGTCGAAGAGGTTGTCTAG 57.558 45.455 0.00 0.00 36.95 2.43
832 945 4.763279 TGTACATGTCGAAGAGGTTGTCTA 59.237 41.667 0.00 0.00 36.95 2.59
833 946 3.572682 TGTACATGTCGAAGAGGTTGTCT 59.427 43.478 0.00 0.00 36.95 3.41
834 947 3.673809 GTGTACATGTCGAAGAGGTTGTC 59.326 47.826 0.00 0.00 36.95 3.18
835 948 3.069016 TGTGTACATGTCGAAGAGGTTGT 59.931 43.478 0.00 0.00 36.95 3.32
836 949 3.649073 TGTGTACATGTCGAAGAGGTTG 58.351 45.455 0.00 0.00 36.95 3.77
837 950 4.537135 ATGTGTACATGTCGAAGAGGTT 57.463 40.909 0.00 0.00 36.95 3.50
838 951 5.854010 ATATGTGTACATGTCGAAGAGGT 57.146 39.130 0.00 0.00 35.75 3.85
839 952 7.379797 CACTTATATGTGTACATGTCGAAGAGG 59.620 40.741 0.00 0.00 35.75 3.69
840 953 8.274851 CACTTATATGTGTACATGTCGAAGAG 57.725 38.462 0.00 0.00 35.75 2.85
867 980 0.390472 GACTGTCCAGCTTCCCTTCG 60.390 60.000 0.00 0.00 0.00 3.79
900 1018 2.672195 GCAAGGATGGTTTTAGCTGCAC 60.672 50.000 1.02 0.00 0.00 4.57
954 1072 5.626142 TGCCTTTTGGTGTCTAGACAAATA 58.374 37.500 26.74 13.18 43.77 1.40
1036 1154 1.207791 AAGGAGATGAACCGGCTCAT 58.792 50.000 20.13 20.13 38.79 2.90
1108 1235 0.694771 AGATGCTGCAACCTCTCCAA 59.305 50.000 6.36 0.00 0.00 3.53
1131 1258 0.656259 CGATGGTGCAAGCTCTCATG 59.344 55.000 0.00 0.00 33.76 3.07
1176 1303 3.252701 GCATCATCATCATGGAGTTGGTC 59.747 47.826 0.00 0.00 0.00 4.02
1186 1313 4.497507 CGTTTTGAGCTGCATCATCATCAT 60.498 41.667 1.02 0.00 0.00 2.45
1187 1314 3.181504 CGTTTTGAGCTGCATCATCATCA 60.182 43.478 1.02 0.00 0.00 3.07
1206 1333 1.220206 CATGGCCTCTGAGAGCGTT 59.780 57.895 3.32 0.00 0.00 4.84
1230 1615 3.774766 AGTTATCCAGCACACTGTATCCA 59.225 43.478 0.00 0.00 42.81 3.41
1298 1683 3.193263 CTGCTAGATGAATCGTTGCTGT 58.807 45.455 0.00 0.00 0.00 4.40
1342 1736 3.063997 GCCTTATCAGTTGATGTTCGTGG 59.936 47.826 4.90 0.48 36.05 4.94
1351 1745 2.833794 GCGTATGGCCTTATCAGTTGA 58.166 47.619 3.32 0.00 34.80 3.18
1455 1867 1.676678 ATGGCCTACGAGACATGCGT 61.677 55.000 3.32 0.00 45.01 5.24
1779 2198 2.429250 CCTTTGCCAATCATCATCAGCA 59.571 45.455 0.00 0.00 0.00 4.41
1781 2200 4.730949 AACCTTTGCCAATCATCATCAG 57.269 40.909 0.00 0.00 0.00 2.90
1816 2235 7.349412 TCTTGCTTCCTCTACCTATTCTTAC 57.651 40.000 0.00 0.00 0.00 2.34
1849 2268 9.886132 CCTAGCTAATCCTTTCAGTTTACTTAA 57.114 33.333 0.00 0.00 0.00 1.85
1860 2279 5.467063 CGATCCAAACCTAGCTAATCCTTTC 59.533 44.000 0.00 0.00 0.00 2.62
1918 2337 6.884280 CTTGAAAAGGTACCTCAACTCATT 57.116 37.500 16.64 0.18 41.27 2.57
2001 2420 4.667262 TGTTCAACACCTTGACAAATTCG 58.333 39.130 0.00 0.00 36.06 3.34
2208 2634 3.691118 TCATGCTAAGTGGATGCAAAGTC 59.309 43.478 0.00 0.00 43.11 3.01
2261 2693 0.790207 CGTGACACTTGGTGATTCCG 59.210 55.000 3.68 0.00 39.52 4.30
2277 2709 2.167693 TGCTATAAGTCCTCCCAACGTG 59.832 50.000 0.00 0.00 0.00 4.49
2286 2718 7.863901 AATACTTGGATCTGCTATAAGTCCT 57.136 36.000 0.00 0.00 33.93 3.85
2308 2740 8.152023 AGAATAAAGTCTCCTTGTGGTCTAAT 57.848 34.615 0.00 0.00 34.23 1.73
2317 2749 8.887717 CCATGAAGTTAGAATAAAGTCTCCTTG 58.112 37.037 0.00 0.00 0.00 3.61
2431 2878 2.125912 CACTCCTGGTCGCTTCCG 60.126 66.667 0.00 0.00 0.00 4.30
2505 2962 5.904941 ACATGAATACGACCGTTTACCATA 58.095 37.500 0.00 0.00 0.00 2.74
2616 3083 6.516739 AGTTCATGATGTCTACGAAGAGAA 57.483 37.500 0.00 0.00 30.45 2.87
2617 3084 7.625828 TTAGTTCATGATGTCTACGAAGAGA 57.374 36.000 0.00 0.00 30.45 3.10
2624 3091 5.577164 AGTGCGTTTAGTTCATGATGTCTAC 59.423 40.000 0.00 0.00 0.00 2.59
2643 3110 4.624336 ACTTACTGAGATCTGTAGTGCG 57.376 45.455 15.96 10.49 33.02 5.34
2645 3112 5.105554 AGCCAACTTACTGAGATCTGTAGTG 60.106 44.000 15.96 6.17 33.02 2.74
2650 3117 7.651304 CAGTATAAGCCAACTTACTGAGATCTG 59.349 40.741 0.00 0.00 41.82 2.90
2714 3182 2.482721 TGCGATGATGATGATGATGCAC 59.517 45.455 0.00 0.00 0.00 4.57
2771 3239 0.887247 TTGCAAGCGTGTATGCCAAT 59.113 45.000 0.00 0.00 41.87 3.16
2809 3277 4.588951 TCCTCTTTCACATGTAGTCACACT 59.411 41.667 0.00 0.00 37.54 3.55
2814 3283 4.436242 TCGTCCTCTTTCACATGTAGTC 57.564 45.455 0.00 0.00 0.00 2.59
2834 3304 8.812329 CATTTACTAATCTACACACAGAGCTTC 58.188 37.037 0.00 0.00 0.00 3.86
2914 3389 4.335037 GTGCCCTGCAAATTCTTTGAAAAA 59.665 37.500 3.87 0.00 43.26 1.94
2915 3390 3.876320 GTGCCCTGCAAATTCTTTGAAAA 59.124 39.130 3.87 0.00 43.26 2.29
2926 3401 2.200930 ACCATGGTGCCCTGCAAA 59.799 55.556 18.99 0.00 41.47 3.68
2928 3403 4.682334 CCACCATGGTGCCCTGCA 62.682 66.667 35.34 0.00 44.16 4.41
2945 3420 3.491639 TGCGTGTTGTGAATGTAGTGTAC 59.508 43.478 0.00 0.00 0.00 2.90
2946 3421 3.491639 GTGCGTGTTGTGAATGTAGTGTA 59.508 43.478 0.00 0.00 0.00 2.90
2969 3444 2.978010 CGACTGGTGGGTGGCAAC 60.978 66.667 0.00 0.00 0.00 4.17
2994 3494 0.326264 ATCACCTCAAGGGCTCACAC 59.674 55.000 0.29 0.00 40.27 3.82
3016 3536 2.591753 CGGTGGGATGCAGGTGAT 59.408 61.111 0.00 0.00 0.00 3.06
3040 3560 6.547510 CCCCCATTCTCATTCCTTAAACTAAG 59.452 42.308 0.00 0.00 35.56 2.18
3042 3562 5.734140 TCCCCCATTCTCATTCCTTAAACTA 59.266 40.000 0.00 0.00 0.00 2.24
3049 3569 5.955850 ATTTATCCCCCATTCTCATTCCT 57.044 39.130 0.00 0.00 0.00 3.36
3054 3574 6.339999 TCAGAAATTTATCCCCCATTCTCA 57.660 37.500 0.00 0.00 0.00 3.27
3083 3606 1.657822 GTTTCTCTTCCGATGGGAGC 58.342 55.000 0.00 0.00 44.98 4.70
3112 3635 7.228590 ACCTAGCCAACAACAAAGTTAATAGA 58.771 34.615 0.00 0.00 0.00 1.98
3115 3638 5.243060 GGACCTAGCCAACAACAAAGTTAAT 59.757 40.000 0.00 0.00 0.00 1.40
3116 3639 4.581409 GGACCTAGCCAACAACAAAGTTAA 59.419 41.667 0.00 0.00 0.00 2.01
3123 3646 0.109723 GTGGGACCTAGCCAACAACA 59.890 55.000 0.00 0.00 31.79 3.33
3148 3671 1.683319 GGCCCAACTTCTTCCTCCATC 60.683 57.143 0.00 0.00 0.00 3.51
3155 3678 1.534729 AACATCGGCCCAACTTCTTC 58.465 50.000 0.00 0.00 0.00 2.87
3158 3681 2.418976 GAGTAAACATCGGCCCAACTTC 59.581 50.000 0.00 0.00 0.00 3.01
3162 3685 2.156098 GTTGAGTAAACATCGGCCCAA 58.844 47.619 0.00 0.00 38.75 4.12
3175 3698 5.497464 TCACAATCCATCTTGGTTGAGTA 57.503 39.130 12.61 0.73 39.03 2.59
3176 3699 4.371624 TCACAATCCATCTTGGTTGAGT 57.628 40.909 12.61 0.00 39.03 3.41
3177 3700 6.514541 GCATATCACAATCCATCTTGGTTGAG 60.515 42.308 12.61 7.44 39.03 3.02
3181 3704 4.147321 GGCATATCACAATCCATCTTGGT 58.853 43.478 0.00 0.00 39.03 3.67
3206 3729 5.782047 TCTACCAACAAAATTTGAGCCATG 58.218 37.500 13.19 3.59 0.00 3.66
3227 3750 6.383726 AGAGGAATTTTCAGTCATCTAGCTCT 59.616 38.462 0.00 0.00 36.43 4.09
3273 3796 1.157870 ACAGGGTGTTGCTTCGAACG 61.158 55.000 0.00 0.00 0.00 3.95
3297 3820 6.037062 CACTATTACATCTGCAAATGAACGGA 59.963 38.462 7.10 0.00 0.00 4.69
3302 3825 4.580167 GGGCACTATTACATCTGCAAATGA 59.420 41.667 7.10 0.00 0.00 2.57
3304 3827 4.796606 AGGGCACTATTACATCTGCAAAT 58.203 39.130 0.00 0.00 0.00 2.32
3310 3833 2.975489 CTGGGAGGGCACTATTACATCT 59.025 50.000 0.00 0.00 0.00 2.90
3311 3834 2.972713 TCTGGGAGGGCACTATTACATC 59.027 50.000 0.00 0.00 0.00 3.06
3332 3857 2.435805 AGCGTACAAGATCCCATCACAT 59.564 45.455 0.00 0.00 0.00 3.21
3334 3859 2.604046 AGCGTACAAGATCCCATCAC 57.396 50.000 0.00 0.00 0.00 3.06
3350 3875 2.726760 GACTACAAGGCGATCATTAGCG 59.273 50.000 0.00 0.00 37.63 4.26
3408 3934 5.453567 AGTCTTTCATTTACAAAGGCCAC 57.546 39.130 5.01 0.00 36.31 5.01
3427 3953 3.573695 TGTTAGCTATCCACCCCTAGTC 58.426 50.000 0.00 0.00 0.00 2.59
3432 3958 3.744660 CTGATTGTTAGCTATCCACCCC 58.255 50.000 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.