Multiple sequence alignment - TraesCS3D01G289500

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 TraesCS3D01G289500 chr3D 100.000 3088 0 0 1 3088 399382022 399378935 0.000000e+00 5703.0
1 TraesCS3D01G289500 chr3D 85.470 117 13 4 1536 1650 390042179 390042293 5.410000e-23 119.0
2 TraesCS3D01G289500 chr3B 89.286 2940 138 71 13 2885 525243975 525241146 0.000000e+00 3520.0
3 TraesCS3D01G289500 chr3B 94.839 155 8 0 2934 3088 525241136 525240982 3.080000e-60 243.0
4 TraesCS3D01G289500 chr3B 86.325 117 12 4 1536 1650 507286943 507287057 1.160000e-24 124.0
5 TraesCS3D01G289500 chr3A 89.211 2549 132 61 18 2472 518644276 518641777 0.000000e+00 3051.0
6 TraesCS3D01G289500 chr3A 88.280 529 31 15 2572 3088 518641778 518641269 3.410000e-169 604.0
7 TraesCS3D01G289500 chr3A 83.810 420 47 14 939 1350 589913979 589914385 2.250000e-101 379.0
8 TraesCS3D01G289500 chr3A 87.179 117 11 4 1536 1650 510664230 510664344 2.500000e-26 130.0
9 TraesCS3D01G289500 chr1D 89.778 225 22 1 939 1163 405003486 405003709 1.400000e-73 287.0
10 TraesCS3D01G289500 chr1D 91.870 123 10 0 1537 1659 283617842 283617964 4.090000e-39 172.0
11 TraesCS3D01G289500 chr1D 94.737 57 3 0 1360 1416 481603266 481603322 4.240000e-14 89.8
12 TraesCS3D01G289500 chr4B 88.362 232 23 4 939 1169 616747014 616747242 3.030000e-70 276.0
13 TraesCS3D01G289500 chr7A 92.754 138 8 2 967 1104 68202953 68202818 6.750000e-47 198.0
14 TraesCS3D01G289500 chr2A 92.481 133 5 2 967 1099 505417413 505417286 5.260000e-43 185.0
15 TraesCS3D01G289500 chr2A 86.957 69 9 0 1348 1416 686214686 686214618 9.180000e-11 78.7
16 TraesCS3D01G289500 chr1B 91.870 123 10 0 1537 1659 385296794 385296916 4.090000e-39 172.0
17 TraesCS3D01G289500 chr1B 96.552 58 2 0 1359 1416 670202744 670202801 2.530000e-16 97.1
18 TraesCS3D01G289500 chr1A 91.870 123 10 0 1537 1659 355343726 355343848 4.090000e-39 172.0
19 TraesCS3D01G289500 chr2B 86.957 69 9 0 1348 1416 648653144 648653076 9.180000e-11 78.7


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 TraesCS3D01G289500 chr3D 399378935 399382022 3087 True 5703.0 5703 100.0000 1 3088 1 chr3D.!!$R1 3087
1 TraesCS3D01G289500 chr3B 525240982 525243975 2993 True 1881.5 3520 92.0625 13 3088 2 chr3B.!!$R1 3075
2 TraesCS3D01G289500 chr3A 518641269 518644276 3007 True 1827.5 3051 88.7455 18 3088 2 chr3A.!!$R1 3070

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
681 751 0.113776 GCACCCATCCATCCATCCAT 59.886 55.0 0.0 0.0 0.0 3.41 F
875 963 0.329931 TGAGCTTTTTATCCGGGGCA 59.670 50.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 1955 0.689055 TGACAGGCTTCTGCTCATGT 59.311 50.0 0.0 0.0 42.06 3.21 R
2749 2923 0.457035 GACAGGGCACGAATACGGTA 59.543 55.0 0.0 0.0 44.46 4.02 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
38 41 3.320826 TGTAGCAAGCAGTACTCAGAACA 59.679 43.478 0.00 0.00 0.00 3.18
42 45 3.321497 CAAGCAGTACTCAGAACACTCC 58.679 50.000 0.00 0.00 0.00 3.85
68 71 1.868498 CGCTACGGGTCAAAAACTGAA 59.132 47.619 0.00 0.00 35.22 3.02
70 73 3.242804 CGCTACGGGTCAAAAACTGAAAA 60.243 43.478 0.00 0.00 35.22 2.29
83 86 3.360249 ACTGAAAAACATGCACAGAGC 57.640 42.857 5.35 0.00 45.96 4.09
114 117 2.416260 GACGTATCCTGGCCGTCC 59.584 66.667 17.11 5.27 43.77 4.79
117 120 1.227263 CGTATCCTGGCCGTCCAAG 60.227 63.158 0.00 0.00 42.91 3.61
176 179 1.445582 GAACCCGACACCTGCTACG 60.446 63.158 0.00 0.00 0.00 3.51
210 216 2.124983 GCTCGCTGGATCAGGCAA 60.125 61.111 9.27 0.00 31.21 4.52
270 285 1.258458 CCGCACATGCACAAAACAAAG 59.742 47.619 4.49 0.00 42.21 2.77
271 286 1.258458 CGCACATGCACAAAACAAAGG 59.742 47.619 4.49 0.00 42.21 3.11
272 287 1.598601 GCACATGCACAAAACAAAGGG 59.401 47.619 0.00 0.00 41.59 3.95
273 288 2.741228 GCACATGCACAAAACAAAGGGA 60.741 45.455 0.00 0.00 41.59 4.20
274 289 3.529533 CACATGCACAAAACAAAGGGAA 58.470 40.909 0.00 0.00 0.00 3.97
275 290 3.937706 CACATGCACAAAACAAAGGGAAA 59.062 39.130 0.00 0.00 0.00 3.13
341 356 2.325583 TGATTGGCCAGATCGGTTAC 57.674 50.000 5.11 0.00 36.97 2.50
342 357 1.217882 GATTGGCCAGATCGGTTACG 58.782 55.000 5.11 0.00 42.74 3.18
404 441 3.999297 GACGTCGCCCTCCTCCTCT 62.999 68.421 0.00 0.00 0.00 3.69
405 442 3.213402 CGTCGCCCTCCTCCTCTC 61.213 72.222 0.00 0.00 0.00 3.20
406 443 3.213402 GTCGCCCTCCTCCTCTCG 61.213 72.222 0.00 0.00 0.00 4.04
409 446 3.223589 GCCCTCCTCCTCTCGCTC 61.224 72.222 0.00 0.00 0.00 5.03
410 447 2.520741 CCCTCCTCCTCTCGCTCC 60.521 72.222 0.00 0.00 0.00 4.70
411 448 2.600731 CCTCCTCCTCTCGCTCCT 59.399 66.667 0.00 0.00 0.00 3.69
412 449 1.827789 CCTCCTCCTCTCGCTCCTG 60.828 68.421 0.00 0.00 0.00 3.86
413 450 2.441164 TCCTCCTCTCGCTCCTGC 60.441 66.667 0.00 0.00 0.00 4.85
414 451 3.535962 CCTCCTCTCGCTCCTGCC 61.536 72.222 0.00 0.00 35.36 4.85
415 452 3.535962 CTCCTCTCGCTCCTGCCC 61.536 72.222 0.00 0.00 35.36 5.36
416 453 4.067512 TCCTCTCGCTCCTGCCCT 62.068 66.667 0.00 0.00 35.36 5.19
417 454 3.535962 CCTCTCGCTCCTGCCCTC 61.536 72.222 0.00 0.00 35.36 4.30
418 455 3.535962 CTCTCGCTCCTGCCCTCC 61.536 72.222 0.00 0.00 35.36 4.30
533 579 2.647481 GCGCACACACACAACACG 60.647 61.111 0.30 0.00 0.00 4.49
537 583 1.640210 GCACACACACAACACGTCCA 61.640 55.000 0.00 0.00 0.00 4.02
538 584 1.013596 CACACACACAACACGTCCAT 58.986 50.000 0.00 0.00 0.00 3.41
544 595 1.673920 ACACAACACGTCCATTTCCAC 59.326 47.619 0.00 0.00 0.00 4.02
554 605 3.924686 CGTCCATTTCCACACAGTAGTAC 59.075 47.826 0.00 0.00 0.00 2.73
680 750 1.287773 TGCACCCATCCATCCATCCA 61.288 55.000 0.00 0.00 0.00 3.41
681 751 0.113776 GCACCCATCCATCCATCCAT 59.886 55.000 0.00 0.00 0.00 3.41
682 752 1.889699 GCACCCATCCATCCATCCATC 60.890 57.143 0.00 0.00 0.00 3.51
683 753 1.078955 ACCCATCCATCCATCCATCC 58.921 55.000 0.00 0.00 0.00 3.51
740 821 1.785647 CCCTGTACTACTACACCCCC 58.214 60.000 0.00 0.00 0.00 5.40
741 822 1.290130 CCCTGTACTACTACACCCCCT 59.710 57.143 0.00 0.00 0.00 4.79
752 837 3.612607 ACCCCCTCCTCCTCCGTT 61.613 66.667 0.00 0.00 0.00 4.44
753 838 2.764547 CCCCCTCCTCCTCCGTTC 60.765 72.222 0.00 0.00 0.00 3.95
754 839 2.764547 CCCCTCCTCCTCCGTTCC 60.765 72.222 0.00 0.00 0.00 3.62
755 840 2.764547 CCCTCCTCCTCCGTTCCC 60.765 72.222 0.00 0.00 0.00 3.97
756 841 2.764547 CCTCCTCCTCCGTTCCCC 60.765 72.222 0.00 0.00 0.00 4.81
757 842 2.364961 CTCCTCCTCCGTTCCCCT 59.635 66.667 0.00 0.00 0.00 4.79
758 843 1.758906 CTCCTCCTCCGTTCCCCTC 60.759 68.421 0.00 0.00 0.00 4.30
759 844 3.148279 CCTCCTCCGTTCCCCTCG 61.148 72.222 0.00 0.00 0.00 4.63
760 845 3.839432 CTCCTCCGTTCCCCTCGC 61.839 72.222 0.00 0.00 0.00 5.03
874 962 1.470051 TTGAGCTTTTTATCCGGGGC 58.530 50.000 0.00 0.00 0.00 5.80
875 963 0.329931 TGAGCTTTTTATCCGGGGCA 59.670 50.000 0.00 0.00 0.00 5.36
876 964 1.025041 GAGCTTTTTATCCGGGGCAG 58.975 55.000 0.00 0.00 0.00 4.85
877 965 1.037579 AGCTTTTTATCCGGGGCAGC 61.038 55.000 0.00 1.01 0.00 5.25
878 966 2.016393 GCTTTTTATCCGGGGCAGCC 62.016 60.000 1.26 1.26 0.00 4.85
879 967 0.682855 CTTTTTATCCGGGGCAGCCA 60.683 55.000 15.19 0.00 0.00 4.75
880 968 0.682855 TTTTTATCCGGGGCAGCCAG 60.683 55.000 15.19 6.46 0.00 4.85
881 969 3.714487 TTTATCCGGGGCAGCCAGC 62.714 63.158 15.19 0.00 44.65 4.85
918 1023 1.588082 GCCGGGACTTCTGTTACGA 59.412 57.895 2.18 0.00 0.00 3.43
946 1051 0.959372 GCTAGATAGCTCCGCCCGTA 60.959 60.000 4.58 0.00 45.62 4.02
1107 1226 3.043713 CAGAGCAAGCGCGACCAA 61.044 61.111 12.10 0.00 45.49 3.67
1155 1274 1.472728 CCCAAGCGGAGGTACATACAC 60.473 57.143 0.00 0.00 37.06 2.90
1159 1278 2.108168 AGCGGAGGTACATACACACAT 58.892 47.619 0.00 0.00 35.08 3.21
1160 1279 2.159099 AGCGGAGGTACATACACACATG 60.159 50.000 0.00 0.00 35.08 3.21
1162 1281 2.418060 CGGAGGTACATACACACATGCA 60.418 50.000 0.00 0.00 0.00 3.96
1169 1298 2.931969 ACATACACACATGCACATCTCG 59.068 45.455 0.00 0.00 0.00 4.04
1183 1312 2.158900 ACATCTCGATCCATGGAACCAC 60.159 50.000 20.67 9.75 0.00 4.16
1209 1338 8.792831 TCGAATCTCGATTAGTATTGGTTTAC 57.207 34.615 0.00 0.00 44.82 2.01
1210 1339 8.627403 TCGAATCTCGATTAGTATTGGTTTACT 58.373 33.333 0.00 0.00 44.82 2.24
1211 1340 8.903723 CGAATCTCGATTAGTATTGGTTTACTC 58.096 37.037 0.00 0.00 43.74 2.59
1212 1341 9.968870 GAATCTCGATTAGTATTGGTTTACTCT 57.031 33.333 0.00 0.00 34.35 3.24
1214 1343 9.968870 ATCTCGATTAGTATTGGTTTACTCTTC 57.031 33.333 0.00 0.00 34.35 2.87
1215 1344 9.186837 TCTCGATTAGTATTGGTTTACTCTTCT 57.813 33.333 0.00 0.00 34.35 2.85
1216 1345 9.804758 CTCGATTAGTATTGGTTTACTCTTCTT 57.195 33.333 0.00 0.00 34.35 2.52
1217 1346 9.582431 TCGATTAGTATTGGTTTACTCTTCTTG 57.418 33.333 0.00 0.00 34.35 3.02
1218 1347 9.582431 CGATTAGTATTGGTTTACTCTTCTTGA 57.418 33.333 0.00 0.00 34.35 3.02
1222 1351 8.974060 AGTATTGGTTTACTCTTCTTGAAACA 57.026 30.769 0.00 0.00 34.22 2.83
1223 1352 9.403583 AGTATTGGTTTACTCTTCTTGAAACAA 57.596 29.630 0.00 0.00 34.22 2.83
1224 1353 9.447040 GTATTGGTTTACTCTTCTTGAAACAAC 57.553 33.333 0.00 0.00 34.22 3.32
1225 1354 6.114221 TGGTTTACTCTTCTTGAAACAACG 57.886 37.500 0.00 0.00 34.22 4.10
1226 1355 5.065474 TGGTTTACTCTTCTTGAAACAACGG 59.935 40.000 0.00 0.00 34.22 4.44
1227 1356 5.295045 GGTTTACTCTTCTTGAAACAACGGA 59.705 40.000 0.00 0.00 34.22 4.69
1228 1357 6.419771 GTTTACTCTTCTTGAAACAACGGAG 58.580 40.000 0.00 0.00 33.07 4.63
1231 1360 4.202367 ACTCTTCTTGAAACAACGGAGGAT 60.202 41.667 0.00 0.00 0.00 3.24
1248 1377 5.402398 GGAGGATTGAGTATGTTTGTTTGC 58.598 41.667 0.00 0.00 0.00 3.68
1254 1383 5.446143 TGAGTATGTTTGTTTGCCGATTT 57.554 34.783 0.00 0.00 0.00 2.17
1460 1603 2.795329 CAGGACAGGCTGGTAATTTGT 58.205 47.619 20.34 0.00 0.00 2.83
1472 1616 6.374053 GGCTGGTAATTTGTGGCAATTAAATT 59.626 34.615 17.03 17.03 37.64 1.82
1754 1898 4.704833 GAGTGCCAGCCCGAGCAA 62.705 66.667 0.00 0.00 41.48 3.91
1790 1955 0.546267 AGCAAGAGCAGGAGGAGGAA 60.546 55.000 0.00 0.00 45.49 3.36
2154 2323 1.595357 CTTTCCTCCGGCCGTAGTT 59.405 57.895 26.12 0.00 0.00 2.24
2381 2552 2.299867 AGCGAAAGGTTGGCATTTTCAT 59.700 40.909 15.35 5.23 40.01 2.57
2682 2856 1.905894 CACCAATCCCCGGGAAATTTT 59.094 47.619 26.32 7.76 34.34 1.82
2689 2863 1.288752 CCGGGAAATTTTGCGTGCT 59.711 52.632 0.00 0.00 0.00 4.40
2692 2866 0.316841 GGGAAATTTTGCGTGCTGGA 59.683 50.000 0.00 0.00 0.00 3.86
2701 2875 4.308458 CGTGCTGGACCGGGTCAA 62.308 66.667 27.32 16.83 33.68 3.18
2729 2903 2.476619 CGTCTTTGAGTGCGATGTCTTT 59.523 45.455 0.00 0.00 0.00 2.52
2749 2923 5.897824 TCTTTAATTCGGTCTCTATCCCTGT 59.102 40.000 0.00 0.00 0.00 4.00
2815 2990 6.017605 CGTGATATTTTTGGGAGAGGAATCTG 60.018 42.308 0.00 0.00 0.00 2.90
2839 3014 6.266558 TGCCTACAACCAGACAAACAAATTAT 59.733 34.615 0.00 0.00 0.00 1.28
2840 3015 7.151976 GCCTACAACCAGACAAACAAATTATT 58.848 34.615 0.00 0.00 0.00 1.40
2841 3016 7.116233 GCCTACAACCAGACAAACAAATTATTG 59.884 37.037 0.00 0.00 42.46 1.90
2842 3017 7.598493 CCTACAACCAGACAAACAAATTATTGG 59.402 37.037 4.27 0.00 41.01 3.16
2843 3018 6.287525 ACAACCAGACAAACAAATTATTGGG 58.712 36.000 4.27 0.00 41.01 4.12
2886 3066 3.401033 TGAAAAGATCGAGCCAACTCA 57.599 42.857 0.00 0.00 43.66 3.41
2892 3072 1.996191 GATCGAGCCAACTCAACTGAC 59.004 52.381 0.00 0.00 43.66 3.51
2949 3129 5.127194 AGCGAAATGAATGAGTACTACTCCA 59.873 40.000 12.79 5.23 44.44 3.86
2966 3146 8.768501 ACTACTCCATCTGTCTCATAATACAA 57.231 34.615 0.00 0.00 0.00 2.41
2973 3153 7.202038 CCATCTGTCTCATAATACAAGAGGGAA 60.202 40.741 0.00 0.00 31.90 3.97
2985 3165 2.225068 AGAGGGAATACGTGCGAATG 57.775 50.000 0.00 0.00 0.00 2.67
3054 3240 5.068636 GGATGGTGAGTAGGTAGATTCGTA 58.931 45.833 0.00 0.00 0.00 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.223225 TGCTACATCGATCGATCATACTC 57.777 43.478 27.20 14.27 31.62 2.59
1 2 5.629079 TTGCTACATCGATCGATCATACT 57.371 39.130 27.20 4.02 31.62 2.12
2 3 4.264145 GCTTGCTACATCGATCGATCATAC 59.736 45.833 27.20 17.04 31.62 2.39
3 4 4.082787 TGCTTGCTACATCGATCGATCATA 60.083 41.667 27.20 19.90 31.62 2.15
4 5 3.249091 GCTTGCTACATCGATCGATCAT 58.751 45.455 27.20 19.85 31.62 2.45
5 6 2.034558 TGCTTGCTACATCGATCGATCA 59.965 45.455 27.20 18.77 31.62 2.92
6 7 2.660715 CTGCTTGCTACATCGATCGATC 59.339 50.000 27.20 16.42 31.62 3.69
7 8 2.035193 ACTGCTTGCTACATCGATCGAT 59.965 45.455 24.60 24.60 34.81 3.59
8 9 1.405463 ACTGCTTGCTACATCGATCGA 59.595 47.619 21.86 21.86 0.00 3.59
9 10 1.845266 ACTGCTTGCTACATCGATCG 58.155 50.000 9.36 9.36 0.00 3.69
10 11 3.971150 AGTACTGCTTGCTACATCGATC 58.029 45.455 0.00 0.00 0.00 3.69
11 12 3.381590 TGAGTACTGCTTGCTACATCGAT 59.618 43.478 0.00 0.00 0.00 3.59
68 71 1.806542 CTACCGCTCTGTGCATGTTTT 59.193 47.619 2.42 0.00 43.06 2.43
70 73 0.321671 ACTACCGCTCTGTGCATGTT 59.678 50.000 2.42 0.00 43.06 2.71
83 86 0.097499 TACGTCGATGCACACTACCG 59.903 55.000 4.06 0.00 0.00 4.02
114 117 5.021033 ACTGGAGCATCAGATTCTACTTG 57.979 43.478 12.34 0.00 38.11 3.16
117 120 4.125703 CCAACTGGAGCATCAGATTCTAC 58.874 47.826 12.34 0.00 38.11 2.59
176 179 2.244651 GCCGCCCGTGATCATGTAC 61.245 63.158 13.81 4.49 0.00 2.90
210 216 1.002134 ATGTACTTTGCCGCCTGCT 60.002 52.632 0.00 0.00 42.00 4.24
270 285 0.179129 CACATGGCGCATCTTTTCCC 60.179 55.000 10.83 0.00 0.00 3.97
271 286 0.527565 ACACATGGCGCATCTTTTCC 59.472 50.000 10.83 0.00 0.00 3.13
272 287 1.068333 ACACACATGGCGCATCTTTTC 60.068 47.619 10.83 0.00 0.00 2.29
273 288 0.961019 ACACACATGGCGCATCTTTT 59.039 45.000 10.83 0.00 0.00 2.27
274 289 1.468520 GTACACACATGGCGCATCTTT 59.531 47.619 10.83 0.00 0.00 2.52
275 290 1.086696 GTACACACATGGCGCATCTT 58.913 50.000 10.83 0.00 0.00 2.40
404 441 3.389139 TATGGGAGGGCAGGAGCGA 62.389 63.158 0.00 0.00 43.41 4.93
405 442 2.844362 TATGGGAGGGCAGGAGCG 60.844 66.667 0.00 0.00 43.41 5.03
406 443 2.832498 GTATGGGAGGGCAGGAGC 59.168 66.667 0.00 0.00 41.10 4.70
407 444 3.142393 CGTATGGGAGGGCAGGAG 58.858 66.667 0.00 0.00 0.00 3.69
408 445 3.161450 GCGTATGGGAGGGCAGGA 61.161 66.667 0.00 0.00 0.00 3.86
409 446 3.042733 TTGCGTATGGGAGGGCAGG 62.043 63.158 0.00 0.00 36.66 4.85
410 447 1.819632 GTTGCGTATGGGAGGGCAG 60.820 63.158 0.00 0.00 36.66 4.85
411 448 2.270850 GTTGCGTATGGGAGGGCA 59.729 61.111 0.00 0.00 0.00 5.36
412 449 1.819632 CTGTTGCGTATGGGAGGGC 60.820 63.158 0.00 0.00 0.00 5.19
413 450 1.819632 GCTGTTGCGTATGGGAGGG 60.820 63.158 0.00 0.00 0.00 4.30
414 451 3.813596 GCTGTTGCGTATGGGAGG 58.186 61.111 0.00 0.00 0.00 4.30
433 470 0.033109 TTGGATCGCTCTCCCTCTCA 60.033 55.000 0.00 0.00 34.12 3.27
435 472 1.337118 GATTGGATCGCTCTCCCTCT 58.663 55.000 0.00 0.00 34.12 3.69
486 531 1.262151 TCGCCTGTTTGTTTAGCGTTC 59.738 47.619 2.45 0.00 46.49 3.95
533 579 3.924686 CGTACTACTGTGTGGAAATGGAC 59.075 47.826 0.00 0.00 0.00 4.02
537 583 2.602878 CGCGTACTACTGTGTGGAAAT 58.397 47.619 0.00 0.00 0.00 2.17
538 584 1.931709 GCGCGTACTACTGTGTGGAAA 60.932 52.381 8.43 0.00 0.00 3.13
544 595 1.443702 TGCAGCGCGTACTACTGTG 60.444 57.895 8.43 0.00 33.87 3.66
680 750 1.379843 GGTGGAAATGGTGGCGGAT 60.380 57.895 0.00 0.00 0.00 4.18
681 751 2.034999 GGTGGAAATGGTGGCGGA 59.965 61.111 0.00 0.00 0.00 5.54
682 752 1.666209 GATGGTGGAAATGGTGGCGG 61.666 60.000 0.00 0.00 0.00 6.13
683 753 1.666209 GGATGGTGGAAATGGTGGCG 61.666 60.000 0.00 0.00 0.00 5.69
740 821 1.758906 GAGGGGAACGGAGGAGGAG 60.759 68.421 0.00 0.00 0.00 3.69
741 822 2.363361 GAGGGGAACGGAGGAGGA 59.637 66.667 0.00 0.00 0.00 3.71
752 837 0.178970 GTACTATCAGGGCGAGGGGA 60.179 60.000 0.00 0.00 0.00 4.81
753 838 0.469331 TGTACTATCAGGGCGAGGGG 60.469 60.000 0.00 0.00 0.00 4.79
754 839 0.674534 GTGTACTATCAGGGCGAGGG 59.325 60.000 0.00 0.00 0.00 4.30
755 840 1.609555 GAGTGTACTATCAGGGCGAGG 59.390 57.143 0.00 0.00 0.00 4.63
756 841 2.292016 CAGAGTGTACTATCAGGGCGAG 59.708 54.545 0.00 0.00 0.00 5.03
757 842 2.298610 CAGAGTGTACTATCAGGGCGA 58.701 52.381 0.00 0.00 0.00 5.54
758 843 2.025155 ACAGAGTGTACTATCAGGGCG 58.975 52.381 0.00 0.00 0.00 6.13
759 844 3.786635 CAACAGAGTGTACTATCAGGGC 58.213 50.000 0.00 0.00 0.00 5.19
760 845 3.735208 CGCAACAGAGTGTACTATCAGGG 60.735 52.174 0.00 0.00 0.00 4.45
804 892 2.050754 ATATATCTGTGGGCTGGGCT 57.949 50.000 0.00 0.00 0.00 5.19
1143 1262 3.595173 TGTGCATGTGTGTATGTACCTC 58.405 45.455 0.00 0.00 41.24 3.85
1155 1274 1.944032 TGGATCGAGATGTGCATGTG 58.056 50.000 0.00 0.00 0.00 3.21
1159 1278 1.122227 TCCATGGATCGAGATGTGCA 58.878 50.000 11.44 0.00 0.00 4.57
1160 1279 1.869767 GTTCCATGGATCGAGATGTGC 59.130 52.381 17.06 0.00 0.00 4.57
1162 1281 2.118679 TGGTTCCATGGATCGAGATGT 58.881 47.619 17.06 0.00 0.00 3.06
1169 1298 2.691409 TTCGAGTGGTTCCATGGATC 57.309 50.000 17.06 15.10 0.00 3.36
1197 1326 8.974060 TGTTTCAAGAAGAGTAAACCAATACT 57.026 30.769 0.00 0.00 38.81 2.12
1198 1327 9.447040 GTTGTTTCAAGAAGAGTAAACCAATAC 57.553 33.333 0.00 0.00 32.18 1.89
1200 1329 7.193595 CGTTGTTTCAAGAAGAGTAAACCAAT 58.806 34.615 0.00 0.00 32.18 3.16
1201 1330 6.403855 CCGTTGTTTCAAGAAGAGTAAACCAA 60.404 38.462 0.00 0.00 32.18 3.67
1203 1332 5.295045 TCCGTTGTTTCAAGAAGAGTAAACC 59.705 40.000 0.00 0.00 32.18 3.27
1204 1333 6.354039 TCCGTTGTTTCAAGAAGAGTAAAC 57.646 37.500 0.00 0.00 33.46 2.01
1205 1334 5.526111 CCTCCGTTGTTTCAAGAAGAGTAAA 59.474 40.000 0.00 0.00 0.00 2.01
1206 1335 5.054477 CCTCCGTTGTTTCAAGAAGAGTAA 58.946 41.667 0.00 0.00 0.00 2.24
1207 1336 4.342951 TCCTCCGTTGTTTCAAGAAGAGTA 59.657 41.667 0.00 0.00 0.00 2.59
1208 1337 3.134081 TCCTCCGTTGTTTCAAGAAGAGT 59.866 43.478 0.00 0.00 0.00 3.24
1209 1338 3.728845 TCCTCCGTTGTTTCAAGAAGAG 58.271 45.455 0.00 0.00 0.00 2.85
1210 1339 3.830744 TCCTCCGTTGTTTCAAGAAGA 57.169 42.857 0.00 0.00 0.00 2.87
1211 1340 4.515191 TCAATCCTCCGTTGTTTCAAGAAG 59.485 41.667 0.00 0.00 0.00 2.85
1212 1341 4.456535 TCAATCCTCCGTTGTTTCAAGAA 58.543 39.130 0.00 0.00 0.00 2.52
1213 1342 4.065088 CTCAATCCTCCGTTGTTTCAAGA 58.935 43.478 0.00 0.00 0.00 3.02
1214 1343 3.815401 ACTCAATCCTCCGTTGTTTCAAG 59.185 43.478 0.00 0.00 0.00 3.02
1215 1344 3.815809 ACTCAATCCTCCGTTGTTTCAA 58.184 40.909 0.00 0.00 0.00 2.69
1216 1345 3.485463 ACTCAATCCTCCGTTGTTTCA 57.515 42.857 0.00 0.00 0.00 2.69
1217 1346 4.935808 ACATACTCAATCCTCCGTTGTTTC 59.064 41.667 0.00 0.00 0.00 2.78
1218 1347 4.906618 ACATACTCAATCCTCCGTTGTTT 58.093 39.130 0.00 0.00 0.00 2.83
1219 1348 4.553330 ACATACTCAATCCTCCGTTGTT 57.447 40.909 0.00 0.00 0.00 2.83
1220 1349 4.553330 AACATACTCAATCCTCCGTTGT 57.447 40.909 0.00 0.00 0.00 3.32
1221 1350 4.695455 ACAAACATACTCAATCCTCCGTTG 59.305 41.667 0.00 0.00 0.00 4.10
1222 1351 4.906618 ACAAACATACTCAATCCTCCGTT 58.093 39.130 0.00 0.00 0.00 4.44
1223 1352 4.553330 ACAAACATACTCAATCCTCCGT 57.447 40.909 0.00 0.00 0.00 4.69
1224 1353 5.631026 CAAACAAACATACTCAATCCTCCG 58.369 41.667 0.00 0.00 0.00 4.63
1225 1354 5.402398 GCAAACAAACATACTCAATCCTCC 58.598 41.667 0.00 0.00 0.00 4.30
1226 1355 5.402398 GGCAAACAAACATACTCAATCCTC 58.598 41.667 0.00 0.00 0.00 3.71
1227 1356 4.082787 CGGCAAACAAACATACTCAATCCT 60.083 41.667 0.00 0.00 0.00 3.24
1228 1357 4.083003 TCGGCAAACAAACATACTCAATCC 60.083 41.667 0.00 0.00 0.00 3.01
1231 1360 5.446143 AATCGGCAAACAAACATACTCAA 57.554 34.783 0.00 0.00 0.00 3.02
1248 1377 1.709147 CTCCGGCTGCAAGAAATCGG 61.709 60.000 0.50 3.27 36.60 4.18
1254 1383 1.260538 ACAGATCTCCGGCTGCAAGA 61.261 55.000 0.50 1.35 34.07 3.02
1490 1634 4.401202 TCACACAAATCAGACGAGCCTATA 59.599 41.667 0.00 0.00 0.00 1.31
1491 1635 3.195610 TCACACAAATCAGACGAGCCTAT 59.804 43.478 0.00 0.00 0.00 2.57
1790 1955 0.689055 TGACAGGCTTCTGCTCATGT 59.311 50.000 0.00 0.00 42.06 3.21
1859 2024 1.106944 CGAAGCTCTCCTCCTCCTCC 61.107 65.000 0.00 0.00 0.00 4.30
2154 2323 4.043184 ACCTCCAAATTACTCCGGGTAAAA 59.957 41.667 16.29 1.61 42.74 1.52
2345 2516 1.082104 CGCTGCTTTTCGGTGGAAC 60.082 57.895 0.00 0.00 0.00 3.62
2381 2552 2.649034 GGTGACGAGGAGAACGCA 59.351 61.111 0.00 0.00 0.00 5.24
2415 2586 1.336795 TGTGTGTGTGTCTATCTGCGG 60.337 52.381 0.00 0.00 0.00 5.69
2416 2587 1.721389 GTGTGTGTGTGTCTATCTGCG 59.279 52.381 0.00 0.00 0.00 5.18
2417 2588 2.989840 GAGTGTGTGTGTGTCTATCTGC 59.010 50.000 0.00 0.00 0.00 4.26
2418 2589 3.256879 AGGAGTGTGTGTGTGTCTATCTG 59.743 47.826 0.00 0.00 0.00 2.90
2422 2593 1.607148 CGAGGAGTGTGTGTGTGTCTA 59.393 52.381 0.00 0.00 0.00 2.59
2600 2771 1.510844 GCCAGGCACCAAATTACCG 59.489 57.895 6.55 0.00 0.00 4.02
2689 2863 2.934570 GCGTACTTGACCCGGTCCA 61.935 63.158 15.24 2.91 0.00 4.02
2692 2866 4.060038 CGGCGTACTTGACCCGGT 62.060 66.667 0.00 0.00 37.89 5.28
2700 2874 1.779569 CACTCAAAGACGGCGTACTT 58.220 50.000 14.74 15.31 0.00 2.24
2701 2875 0.666577 GCACTCAAAGACGGCGTACT 60.667 55.000 14.74 9.49 0.00 2.73
2729 2903 5.075493 GGTACAGGGATAGAGACCGAATTA 58.925 45.833 0.00 0.00 0.00 1.40
2749 2923 0.457035 GACAGGGCACGAATACGGTA 59.543 55.000 0.00 0.00 44.46 4.02
2815 2990 4.584327 ATTTGTTTGTCTGGTTGTAGGC 57.416 40.909 0.00 0.00 0.00 3.93
2839 3014 1.383248 CCAACCCAACCCAACCCAA 60.383 57.895 0.00 0.00 0.00 4.12
2840 3015 2.283809 CCAACCCAACCCAACCCA 59.716 61.111 0.00 0.00 0.00 4.51
2841 3016 2.525629 CCCAACCCAACCCAACCC 60.526 66.667 0.00 0.00 0.00 4.11
2842 3017 3.238497 GCCCAACCCAACCCAACC 61.238 66.667 0.00 0.00 0.00 3.77
2843 3018 3.238497 GGCCCAACCCAACCCAAC 61.238 66.667 0.00 0.00 0.00 3.77
2886 3066 1.771255 GGCTGGATAGATGGGTCAGTT 59.229 52.381 0.00 0.00 0.00 3.16
2892 3072 1.281287 CTGGATGGCTGGATAGATGGG 59.719 57.143 0.00 0.00 0.00 4.00
2920 3100 7.819900 AGTAGTACTCATTCATTTCGCTTTTCT 59.180 33.333 0.00 0.00 0.00 2.52
2949 3129 7.921041 TTCCCTCTTGTATTATGAGACAGAT 57.079 36.000 0.00 0.00 33.55 2.90
2966 3146 1.806623 GCATTCGCACGTATTCCCTCT 60.807 52.381 0.00 0.00 38.36 3.69
2973 3153 1.721487 GCCAAGCATTCGCACGTAT 59.279 52.632 0.00 0.00 42.27 3.06
2985 3165 0.247695 GCTCGAATACAACGCCAAGC 60.248 55.000 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.