Multiple sequence alignment - TraesCS4D01G125400

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 TraesCS4D01G125400 chr4D 100.000 2432 0 0 1 2432 109907021 109909452 0.000000e+00 4492
1 TraesCS4D01G125400 chr4D 100.000 468 0 0 2775 3242 109909795 109910262 0.000000e+00 865
2 TraesCS4D01G125400 chr2D 93.571 871 52 4 9 876 570989411 570988542 0.000000e+00 1295
3 TraesCS4D01G125400 chr2D 92.659 899 63 3 1 896 57098816 57099714 0.000000e+00 1291
4 TraesCS4D01G125400 chr2D 92.449 874 64 2 1 872 531332540 531331667 0.000000e+00 1247
5 TraesCS4D01G125400 chr2A 93.249 874 57 2 1 872 748702804 748703677 0.000000e+00 1286
6 TraesCS4D01G125400 chr6D 92.593 891 58 8 1 886 413060967 413061854 0.000000e+00 1273
7 TraesCS4D01G125400 chr3D 92.914 875 59 3 1 873 413999081 413999954 0.000000e+00 1269
8 TraesCS4D01G125400 chr3D 91.554 888 71 3 1 886 449120190 449119305 0.000000e+00 1221
9 TraesCS4D01G125400 chr5A 92.423 871 63 3 8 876 35025662 35024793 0.000000e+00 1240
10 TraesCS4D01G125400 chr5A 92.237 876 66 2 8 883 565622867 565621994 0.000000e+00 1240
11 TraesCS4D01G125400 chr4A 94.109 713 29 8 1718 2429 466928937 466928237 0.000000e+00 1072
12 TraesCS4D01G125400 chr4A 94.322 317 13 1 1138 1449 466929658 466929342 6.290000e-132 481
13 TraesCS4D01G125400 chr4A 96.538 260 7 2 2775 3032 466928150 466927891 2.310000e-116 429
14 TraesCS4D01G125400 chr4A 92.336 274 12 5 1456 1721 466929291 466929019 6.560000e-102 381
15 TraesCS4D01G125400 chr4A 90.000 190 13 4 3055 3242 466927895 466927710 1.160000e-59 241
16 TraesCS4D01G125400 chr4A 84.362 243 18 12 915 1142 466934577 466934340 1.510000e-53 220
17 TraesCS4D01G125400 chr4B 91.794 719 37 7 1718 2432 171025632 171026332 0.000000e+00 981
18 TraesCS4D01G125400 chr4B 96.050 481 19 0 969 1449 171024759 171025239 0.000000e+00 784
19 TraesCS4D01G125400 chr4B 88.136 472 20 14 2775 3242 171026408 171026847 2.220000e-146 529
20 TraesCS4D01G125400 chr4B 94.074 270 11 2 1456 1721 171025288 171025556 3.890000e-109 405


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 TraesCS4D01G125400 chr4D 109907021 109910262 3241 False 2678.50 4492 100.0000 1 3242 2 chr4D.!!$F1 3241
1 TraesCS4D01G125400 chr2D 570988542 570989411 869 True 1295.00 1295 93.5710 9 876 1 chr2D.!!$R2 867
2 TraesCS4D01G125400 chr2D 57098816 57099714 898 False 1291.00 1291 92.6590 1 896 1 chr2D.!!$F1 895
3 TraesCS4D01G125400 chr2D 531331667 531332540 873 True 1247.00 1247 92.4490 1 872 1 chr2D.!!$R1 871
4 TraesCS4D01G125400 chr2A 748702804 748703677 873 False 1286.00 1286 93.2490 1 872 1 chr2A.!!$F1 871
5 TraesCS4D01G125400 chr6D 413060967 413061854 887 False 1273.00 1273 92.5930 1 886 1 chr6D.!!$F1 885
6 TraesCS4D01G125400 chr3D 413999081 413999954 873 False 1269.00 1269 92.9140 1 873 1 chr3D.!!$F1 872
7 TraesCS4D01G125400 chr3D 449119305 449120190 885 True 1221.00 1221 91.5540 1 886 1 chr3D.!!$R1 885
8 TraesCS4D01G125400 chr5A 35024793 35025662 869 True 1240.00 1240 92.4230 8 876 1 chr5A.!!$R1 868
9 TraesCS4D01G125400 chr5A 565621994 565622867 873 True 1240.00 1240 92.2370 8 883 1 chr5A.!!$R2 875
10 TraesCS4D01G125400 chr4A 466927710 466929658 1948 True 520.80 1072 93.4610 1138 3242 5 chr4A.!!$R2 2104
11 TraesCS4D01G125400 chr4B 171024759 171026847 2088 False 674.75 981 92.5135 969 3242 4 chr4B.!!$F1 2273

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
491 492 0.034767 CTGTCTGGCATCATGGTGGT 60.035 55.0 8.33 0.0 0.00 4.16 F
563 564 0.104986 TGGACCGAGGGATGATGGAT 60.105 55.0 0.00 0.0 0.00 3.41 F
1452 1461 0.251297 TTTGGACTGGATGTGCCTGG 60.251 55.0 0.00 0.0 39.75 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 1578 1.005450 TGTTGGGAAGTAAGGATGGGC 59.995 52.381 0.00 0.0 0.00 5.36 R
1780 1927 1.213013 GAGCGCTTCTCACCTCGAA 59.787 57.895 13.26 0.0 41.51 3.71 R
3126 3288 2.351738 GCACAGAAGTTACATTGCACCC 60.352 50.000 0.00 0.0 0.00 4.61 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
22 23 3.366739 GATCGGCGGGTCTCGGTTT 62.367 63.158 7.21 0.00 39.69 3.27
47 48 3.957497 GGACTTCTCCTTGCTGAGATCTA 59.043 47.826 0.00 0.00 40.89 1.98
69 70 3.933722 CGGCGGCCTGGATCATCT 61.934 66.667 18.34 0.00 0.00 2.90
246 247 0.394488 CCACTCTCTGCTACCTCCGA 60.394 60.000 0.00 0.00 0.00 4.55
463 464 3.069980 GAGATGGACTCGCGCAGGT 62.070 63.158 8.75 4.83 35.84 4.00
491 492 0.034767 CTGTCTGGCATCATGGTGGT 60.035 55.000 8.33 0.00 0.00 4.16
519 520 2.045536 GAGAGGCCTGGCAAGGTG 60.046 66.667 22.05 0.00 46.43 4.00
563 564 0.104986 TGGACCGAGGGATGATGGAT 60.105 55.000 0.00 0.00 0.00 3.41
690 691 1.960417 TTGGTGCGATGTCTGTTTGA 58.040 45.000 0.00 0.00 0.00 2.69
835 836 2.409055 GGCTGCATGCATCGTCCAA 61.409 57.895 22.97 0.00 45.15 3.53
860 862 2.446036 GGCCGGGGTACATCCTCT 60.446 66.667 2.18 0.00 33.68 3.69
921 925 8.628630 AGAGGGAGTATTTCTTTTTCTTTCTG 57.371 34.615 0.00 0.00 0.00 3.02
922 926 8.221251 AGAGGGAGTATTTCTTTTTCTTTCTGT 58.779 33.333 0.00 0.00 0.00 3.41
923 927 8.397575 AGGGAGTATTTCTTTTTCTTTCTGTC 57.602 34.615 0.00 0.00 0.00 3.51
924 928 7.173390 AGGGAGTATTTCTTTTTCTTTCTGTCG 59.827 37.037 0.00 0.00 0.00 4.35
925 929 7.172703 GGGAGTATTTCTTTTTCTTTCTGTCGA 59.827 37.037 0.00 0.00 0.00 4.20
926 930 8.224437 GGAGTATTTCTTTTTCTTTCTGTCGAG 58.776 37.037 0.00 0.00 0.00 4.04
927 931 8.888579 AGTATTTCTTTTTCTTTCTGTCGAGA 57.111 30.769 0.00 0.00 0.00 4.04
928 932 8.983724 AGTATTTCTTTTTCTTTCTGTCGAGAG 58.016 33.333 2.50 2.50 0.00 3.20
929 933 8.979574 GTATTTCTTTTTCTTTCTGTCGAGAGA 58.020 33.333 8.43 8.43 38.16 3.10
930 934 8.614469 ATTTCTTTTTCTTTCTGTCGAGAGAT 57.386 30.769 13.68 0.00 45.19 2.75
931 935 9.712305 ATTTCTTTTTCTTTCTGTCGAGAGATA 57.288 29.630 13.68 7.83 45.19 1.98
932 936 9.712305 TTTCTTTTTCTTTCTGTCGAGAGATAT 57.288 29.630 13.68 0.00 45.19 1.63
933 937 9.712305 TTCTTTTTCTTTCTGTCGAGAGATATT 57.288 29.630 13.68 0.00 45.19 1.28
938 942 9.958234 TTTCTTTCTGTCGAGAGATATTATCAG 57.042 33.333 13.68 0.00 45.19 2.90
939 943 8.910351 TCTTTCTGTCGAGAGATATTATCAGA 57.090 34.615 13.68 2.00 45.19 3.27
940 944 8.779303 TCTTTCTGTCGAGAGATATTATCAGAC 58.221 37.037 13.68 9.48 45.19 3.51
941 945 8.684386 TTTCTGTCGAGAGATATTATCAGACT 57.316 34.615 13.68 2.89 45.19 3.24
942 946 7.665561 TCTGTCGAGAGATATTATCAGACTG 57.334 40.000 8.43 11.74 45.19 3.51
943 947 6.652900 TCTGTCGAGAGATATTATCAGACTGG 59.347 42.308 8.43 4.53 45.19 4.00
944 948 6.299922 TGTCGAGAGATATTATCAGACTGGT 58.700 40.000 1.81 0.00 45.19 4.00
945 949 6.205658 TGTCGAGAGATATTATCAGACTGGTG 59.794 42.308 1.81 0.00 45.19 4.17
946 950 6.428465 GTCGAGAGATATTATCAGACTGGTGA 59.572 42.308 1.81 0.00 45.19 4.02
947 951 6.428465 TCGAGAGATATTATCAGACTGGTGAC 59.572 42.308 1.81 0.00 33.31 3.67
948 952 6.429692 CGAGAGATATTATCAGACTGGTGACT 59.570 42.308 1.81 0.00 0.00 3.41
949 953 7.523293 AGAGATATTATCAGACTGGTGACTG 57.477 40.000 1.81 0.00 37.33 3.51
950 954 6.493115 AGAGATATTATCAGACTGGTGACTGG 59.507 42.308 1.81 0.00 36.79 4.00
951 955 6.139671 AGATATTATCAGACTGGTGACTGGT 58.860 40.000 1.81 0.00 36.79 4.00
952 956 4.744795 ATTATCAGACTGGTGACTGGTC 57.255 45.455 1.81 0.00 36.79 4.02
953 957 2.015456 ATCAGACTGGTGACTGGTCA 57.985 50.000 1.81 0.00 36.79 4.02
954 958 1.788229 TCAGACTGGTGACTGGTCAA 58.212 50.000 4.92 0.00 41.85 3.18
955 959 2.329267 TCAGACTGGTGACTGGTCAAT 58.671 47.619 4.92 0.00 41.85 2.57
956 960 2.037641 TCAGACTGGTGACTGGTCAATG 59.962 50.000 4.92 2.03 41.85 2.82
957 961 2.037641 CAGACTGGTGACTGGTCAATGA 59.962 50.000 4.92 0.00 41.85 2.57
958 962 2.909006 AGACTGGTGACTGGTCAATGAT 59.091 45.455 4.92 0.00 41.85 2.45
959 963 3.055530 AGACTGGTGACTGGTCAATGATC 60.056 47.826 4.92 2.46 41.85 2.92
960 964 2.909006 ACTGGTGACTGGTCAATGATCT 59.091 45.455 4.92 0.00 41.85 2.75
961 965 3.268330 CTGGTGACTGGTCAATGATCTG 58.732 50.000 4.92 0.00 41.85 2.90
962 966 2.905736 TGGTGACTGGTCAATGATCTGA 59.094 45.455 7.40 0.00 41.85 3.27
963 967 3.520721 TGGTGACTGGTCAATGATCTGAT 59.479 43.478 7.40 0.00 41.85 2.90
964 968 3.875727 GGTGACTGGTCAATGATCTGATG 59.124 47.826 7.40 0.00 41.85 3.07
965 969 3.875727 GTGACTGGTCAATGATCTGATGG 59.124 47.826 7.40 0.00 41.85 3.51
966 970 3.520721 TGACTGGTCAATGATCTGATGGT 59.479 43.478 7.40 0.00 36.53 3.55
967 971 4.019051 TGACTGGTCAATGATCTGATGGTT 60.019 41.667 7.40 0.00 36.53 3.67
1022 1026 1.380515 TAAGCGCTGCCTCCTCTCT 60.381 57.895 12.58 0.00 0.00 3.10
1036 1040 5.584251 GCCTCCTCTCTCTCATTTACTTTTG 59.416 44.000 0.00 0.00 0.00 2.44
1053 1057 1.379527 TTGTCGCATCGAGAGCTCTA 58.620 50.000 18.25 1.54 36.23 2.43
1251 1260 1.380524 CGCTCCTTCTTCTCCGACTA 58.619 55.000 0.00 0.00 0.00 2.59
1283 1292 1.508632 CCTGTGATCGTCGTTGGTTT 58.491 50.000 0.00 0.00 0.00 3.27
1408 1417 0.681175 AGCTGTTTGTGGAAATGCCC 59.319 50.000 0.00 0.00 34.97 5.36
1412 1421 1.910772 TTTGTGGAAATGCCCGGGG 60.911 57.895 25.28 9.31 34.97 5.73
1449 1458 1.000274 GTTGTTTGGACTGGATGTGCC 60.000 52.381 0.00 0.00 36.06 5.01
1450 1459 0.478072 TGTTTGGACTGGATGTGCCT 59.522 50.000 0.00 0.00 36.06 4.75
1451 1460 0.883833 GTTTGGACTGGATGTGCCTG 59.116 55.000 0.00 0.00 41.12 4.85
1452 1461 0.251297 TTTGGACTGGATGTGCCTGG 60.251 55.000 0.00 0.00 39.75 4.45
1475 1528 1.003233 GCCTCTTCCTGCCGTTCTT 60.003 57.895 0.00 0.00 0.00 2.52
1520 1578 3.812262 TCTGCACATGTTCCATGATAGG 58.188 45.455 10.96 0.00 0.00 2.57
1530 1588 3.290039 TCCATGATAGGCCCATCCTTA 57.710 47.619 8.81 0.00 44.75 2.69
1552 1610 3.642848 ACTTCCCAACAACTTGCAATGAT 59.357 39.130 7.04 0.00 0.00 2.45
1694 1756 7.672983 TGGTTCTCTAGAAACTGCAAAATAG 57.327 36.000 9.08 0.00 42.08 1.73
1764 1911 7.177744 TCAACTACACTACACTGATATTCCACA 59.822 37.037 0.00 0.00 0.00 4.17
1852 1999 3.967326 TGGGAGATTCCGTTGATGTATCT 59.033 43.478 0.00 0.00 37.43 1.98
1898 2045 3.138304 CGACCTCACTTTCCATTGACAA 58.862 45.455 0.00 0.00 0.00 3.18
1980 2131 4.638421 GGATTGTTCATTTACGTGGGATGA 59.362 41.667 0.00 2.12 0.00 2.92
2105 2256 1.071471 CCAAGGAACACCAGACGCT 59.929 57.895 0.00 0.00 0.00 5.07
2115 2266 3.067106 ACACCAGACGCTGTGAAATAAG 58.933 45.455 0.00 0.00 0.00 1.73
2308 2459 9.941325 ACCAATCATATCTTCATTCATCTAGTC 57.059 33.333 0.00 0.00 0.00 2.59
2816 2975 4.253685 AGATTGTACAAATCTGTCCACGG 58.746 43.478 13.23 0.00 35.79 4.94
2820 2980 4.200874 TGTACAAATCTGTCCACGGTTTT 58.799 39.130 0.00 0.00 36.96 2.43
2827 2987 2.103432 TCTGTCCACGGTTTTAGCTCAA 59.897 45.455 0.00 0.00 0.00 3.02
2892 3053 2.042831 GTGGTGCTGCACATCTCCC 61.043 63.158 31.35 15.50 35.86 4.30
2909 3070 4.985538 TCTCCCTGTTTGAGCTAAAATGT 58.014 39.130 0.00 0.00 0.00 2.71
2910 3071 6.121776 TCTCCCTGTTTGAGCTAAAATGTA 57.878 37.500 0.00 0.00 0.00 2.29
2993 3154 2.027285 TCCTTTCTTCATCATCGCCACA 60.027 45.455 0.00 0.00 0.00 4.17
3032 3193 3.980022 TCCTCCCATCCTATATGTGCAAA 59.020 43.478 0.00 0.00 0.00 3.68
3033 3194 4.415179 TCCTCCCATCCTATATGTGCAAAA 59.585 41.667 0.00 0.00 0.00 2.44
3034 3195 4.763793 CCTCCCATCCTATATGTGCAAAAG 59.236 45.833 0.00 0.00 0.00 2.27
3035 3196 5.380043 CTCCCATCCTATATGTGCAAAAGT 58.620 41.667 0.00 0.00 0.00 2.66
3036 3197 6.465751 CCTCCCATCCTATATGTGCAAAAGTA 60.466 42.308 0.00 0.00 0.00 2.24
3037 3198 7.090319 TCCCATCCTATATGTGCAAAAGTAT 57.910 36.000 0.00 0.00 0.00 2.12
3038 3199 7.168219 TCCCATCCTATATGTGCAAAAGTATC 58.832 38.462 0.00 0.00 0.00 2.24
3039 3200 7.017551 TCCCATCCTATATGTGCAAAAGTATCT 59.982 37.037 0.00 0.00 0.00 1.98
3040 3201 7.667219 CCCATCCTATATGTGCAAAAGTATCTT 59.333 37.037 0.00 0.00 0.00 2.40
3041 3202 9.071276 CCATCCTATATGTGCAAAAGTATCTTT 57.929 33.333 0.00 0.00 0.00 2.52
3051 3212 9.515020 TGTGCAAAAGTATCTTTAGTTTCTTTG 57.485 29.630 0.00 0.00 31.20 2.77
3052 3213 8.968242 GTGCAAAAGTATCTTTAGTTTCTTTGG 58.032 33.333 0.00 0.00 31.20 3.28
3053 3214 8.908903 TGCAAAAGTATCTTTAGTTTCTTTGGA 58.091 29.630 0.00 0.00 31.20 3.53
3054 3215 9.914131 GCAAAAGTATCTTTAGTTTCTTTGGAT 57.086 29.630 0.00 0.00 31.20 3.41
3056 3217 9.914131 AAAAGTATCTTTAGTTTCTTTGGATGC 57.086 29.630 0.00 0.00 31.20 3.91
3057 3218 8.635765 AAGTATCTTTAGTTTCTTTGGATGCA 57.364 30.769 0.00 0.00 0.00 3.96
3058 3219 8.635765 AGTATCTTTAGTTTCTTTGGATGCAA 57.364 30.769 0.00 0.00 0.00 4.08
3135 3298 3.515104 AGGTCCTATTTTTGGGTGCAATG 59.485 43.478 0.00 0.00 0.00 2.82
3143 3306 5.606348 TTTTTGGGTGCAATGTAACTTCT 57.394 34.783 0.00 0.00 0.00 2.85
3148 3311 2.574322 GTGCAATGTAACTTCTGTGCG 58.426 47.619 0.00 0.00 0.00 5.34
3170 3333 4.042398 GTCAGATCGCGTATGTGTAATGT 58.958 43.478 5.77 0.00 30.88 2.71
3171 3334 5.209977 GTCAGATCGCGTATGTGTAATGTA 58.790 41.667 5.77 0.00 30.88 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.387947 AAACCGAGACCCGCCGAT 61.388 61.111 0.00 0.00 36.84 4.18
6 7 4.367023 CAAACCGAGACCCGCCGA 62.367 66.667 0.00 0.00 36.84 5.54
22 23 0.473694 TCAGCAAGGAGAAGTCCCCA 60.474 55.000 0.00 0.00 45.26 4.96
69 70 1.140852 CGCCATCCTTGTTGGGATCTA 59.859 52.381 0.00 0.00 43.55 1.98
77 78 2.746277 GTCGCCGCCATCCTTGTT 60.746 61.111 0.00 0.00 0.00 2.83
78 79 4.778143 GGTCGCCGCCATCCTTGT 62.778 66.667 0.00 0.00 0.00 3.16
163 164 4.673298 ACAACGTCGCCATCGCCA 62.673 61.111 0.00 0.00 35.26 5.69
266 267 1.227380 GAGCCGCTGTCATCCGATT 60.227 57.895 0.00 0.00 0.00 3.34
357 358 3.365265 GCACCGCTCCACCAAAGG 61.365 66.667 0.00 0.00 0.00 3.11
463 464 1.203441 ATGCCAGACAGCTTCCTCCA 61.203 55.000 0.00 0.00 0.00 3.86
519 520 0.036022 AGAGCAGAACTGAAGCACCC 59.964 55.000 5.97 0.00 0.00 4.61
690 691 1.278127 CCGAATGTCCGGGCCTAATAT 59.722 52.381 2.12 0.00 45.43 1.28
725 726 1.342674 ACCGTTGCTACTCCTATCCCA 60.343 52.381 0.00 0.00 0.00 4.37
835 836 2.690881 TACCCCGGCCTCTGCATT 60.691 61.111 0.00 0.00 40.13 3.56
896 900 8.221251 ACAGAAAGAAAAAGAAATACTCCCTCT 58.779 33.333 0.00 0.00 0.00 3.69
897 901 8.397575 ACAGAAAGAAAAAGAAATACTCCCTC 57.602 34.615 0.00 0.00 0.00 4.30
898 902 7.173390 CGACAGAAAGAAAAAGAAATACTCCCT 59.827 37.037 0.00 0.00 0.00 4.20
899 903 7.172703 TCGACAGAAAGAAAAAGAAATACTCCC 59.827 37.037 0.00 0.00 0.00 4.30
900 904 8.084590 TCGACAGAAAGAAAAAGAAATACTCC 57.915 34.615 0.00 0.00 0.00 3.85
901 905 8.979574 TCTCGACAGAAAGAAAAAGAAATACTC 58.020 33.333 0.00 0.00 0.00 2.59
902 906 8.888579 TCTCGACAGAAAGAAAAAGAAATACT 57.111 30.769 0.00 0.00 0.00 2.12
903 907 8.979574 TCTCTCGACAGAAAGAAAAAGAAATAC 58.020 33.333 0.00 0.00 0.00 1.89
904 908 9.712305 ATCTCTCGACAGAAAGAAAAAGAAATA 57.288 29.630 0.00 0.00 0.00 1.40
905 909 8.614469 ATCTCTCGACAGAAAGAAAAAGAAAT 57.386 30.769 0.00 0.00 0.00 2.17
906 910 9.712305 ATATCTCTCGACAGAAAGAAAAAGAAA 57.288 29.630 0.00 0.00 0.00 2.52
907 911 9.712305 AATATCTCTCGACAGAAAGAAAAAGAA 57.288 29.630 0.00 0.00 0.00 2.52
912 916 9.958234 CTGATAATATCTCTCGACAGAAAGAAA 57.042 33.333 1.66 0.00 0.00 2.52
913 917 9.343539 TCTGATAATATCTCTCGACAGAAAGAA 57.656 33.333 1.66 0.00 31.69 2.52
914 918 8.779303 GTCTGATAATATCTCTCGACAGAAAGA 58.221 37.037 1.66 0.00 35.47 2.52
915 919 8.783093 AGTCTGATAATATCTCTCGACAGAAAG 58.217 37.037 1.66 0.00 35.47 2.62
916 920 8.563732 CAGTCTGATAATATCTCTCGACAGAAA 58.436 37.037 1.66 0.00 35.47 2.52
917 921 7.174080 CCAGTCTGATAATATCTCTCGACAGAA 59.826 40.741 0.00 0.00 35.47 3.02
918 922 6.652900 CCAGTCTGATAATATCTCTCGACAGA 59.347 42.308 0.00 0.00 0.00 3.41
919 923 6.429692 ACCAGTCTGATAATATCTCTCGACAG 59.570 42.308 0.00 0.00 0.00 3.51
920 924 6.205658 CACCAGTCTGATAATATCTCTCGACA 59.794 42.308 0.00 0.00 0.00 4.35
921 925 6.428465 TCACCAGTCTGATAATATCTCTCGAC 59.572 42.308 0.00 3.88 0.00 4.20
922 926 6.428465 GTCACCAGTCTGATAATATCTCTCGA 59.572 42.308 0.00 0.00 0.00 4.04
923 927 6.429692 AGTCACCAGTCTGATAATATCTCTCG 59.570 42.308 0.00 0.00 0.00 4.04
924 928 7.309133 CCAGTCACCAGTCTGATAATATCTCTC 60.309 44.444 0.00 0.00 33.49 3.20
925 929 6.493115 CCAGTCACCAGTCTGATAATATCTCT 59.507 42.308 0.00 0.00 33.49 3.10
926 930 6.266558 ACCAGTCACCAGTCTGATAATATCTC 59.733 42.308 0.00 0.00 33.49 2.75
927 931 6.139671 ACCAGTCACCAGTCTGATAATATCT 58.860 40.000 0.00 0.00 33.49 1.98
928 932 6.040955 TGACCAGTCACCAGTCTGATAATATC 59.959 42.308 0.00 0.00 33.49 1.63
929 933 5.899547 TGACCAGTCACCAGTCTGATAATAT 59.100 40.000 0.00 0.00 33.49 1.28
930 934 5.269189 TGACCAGTCACCAGTCTGATAATA 58.731 41.667 0.00 0.00 33.49 0.98
931 935 4.096681 TGACCAGTCACCAGTCTGATAAT 58.903 43.478 0.00 0.00 33.49 1.28
932 936 3.506398 TGACCAGTCACCAGTCTGATAA 58.494 45.455 0.00 0.00 33.49 1.75
933 937 3.169512 TGACCAGTCACCAGTCTGATA 57.830 47.619 0.00 0.00 33.49 2.15
934 938 2.015456 TGACCAGTCACCAGTCTGAT 57.985 50.000 0.00 0.00 33.49 2.90
935 939 1.788229 TTGACCAGTCACCAGTCTGA 58.212 50.000 0.00 0.00 39.66 3.27
936 940 2.037641 TCATTGACCAGTCACCAGTCTG 59.962 50.000 0.00 0.00 39.66 3.51
937 941 2.329267 TCATTGACCAGTCACCAGTCT 58.671 47.619 0.00 0.00 39.66 3.24
938 942 2.839486 TCATTGACCAGTCACCAGTC 57.161 50.000 0.00 0.00 39.66 3.51
939 943 2.909006 AGATCATTGACCAGTCACCAGT 59.091 45.455 0.00 0.00 39.66 4.00
940 944 3.055602 TCAGATCATTGACCAGTCACCAG 60.056 47.826 0.00 0.00 39.66 4.00
941 945 2.905736 TCAGATCATTGACCAGTCACCA 59.094 45.455 0.00 0.00 39.66 4.17
942 946 3.616956 TCAGATCATTGACCAGTCACC 57.383 47.619 0.00 0.00 39.66 4.02
943 947 3.875727 CCATCAGATCATTGACCAGTCAC 59.124 47.826 0.00 0.00 39.66 3.67
944 948 3.520721 ACCATCAGATCATTGACCAGTCA 59.479 43.478 0.00 0.00 37.91 3.41
945 949 4.148128 ACCATCAGATCATTGACCAGTC 57.852 45.455 0.00 0.00 0.00 3.51
946 950 4.581309 AACCATCAGATCATTGACCAGT 57.419 40.909 0.00 0.00 0.00 4.00
947 951 4.097437 CCAAACCATCAGATCATTGACCAG 59.903 45.833 0.00 0.00 0.00 4.00
948 952 4.018490 CCAAACCATCAGATCATTGACCA 58.982 43.478 0.00 0.00 0.00 4.02
949 953 4.019174 ACCAAACCATCAGATCATTGACC 58.981 43.478 0.00 0.00 0.00 4.02
950 954 5.649782 AACCAAACCATCAGATCATTGAC 57.350 39.130 0.00 0.00 0.00 3.18
951 955 5.047164 CCAAACCAAACCATCAGATCATTGA 60.047 40.000 0.00 0.00 0.00 2.57
952 956 5.172934 CCAAACCAAACCATCAGATCATTG 58.827 41.667 0.00 0.00 0.00 2.82
953 957 4.840115 ACCAAACCAAACCATCAGATCATT 59.160 37.500 0.00 0.00 0.00 2.57
954 958 4.419282 ACCAAACCAAACCATCAGATCAT 58.581 39.130 0.00 0.00 0.00 2.45
955 959 3.843422 ACCAAACCAAACCATCAGATCA 58.157 40.909 0.00 0.00 0.00 2.92
956 960 4.871933 AACCAAACCAAACCATCAGATC 57.128 40.909 0.00 0.00 0.00 2.75
957 961 4.202346 CCAAACCAAACCAAACCATCAGAT 60.202 41.667 0.00 0.00 0.00 2.90
958 962 3.133721 CCAAACCAAACCAAACCATCAGA 59.866 43.478 0.00 0.00 0.00 3.27
959 963 3.118445 ACCAAACCAAACCAAACCATCAG 60.118 43.478 0.00 0.00 0.00 2.90
960 964 2.840651 ACCAAACCAAACCAAACCATCA 59.159 40.909 0.00 0.00 0.00 3.07
961 965 3.552132 ACCAAACCAAACCAAACCATC 57.448 42.857 0.00 0.00 0.00 3.51
962 966 4.308526 AAACCAAACCAAACCAAACCAT 57.691 36.364 0.00 0.00 0.00 3.55
963 967 3.790089 AAACCAAACCAAACCAAACCA 57.210 38.095 0.00 0.00 0.00 3.67
964 968 4.817464 GGATAAACCAAACCAAACCAAACC 59.183 41.667 0.00 0.00 38.79 3.27
965 969 4.508492 CGGATAAACCAAACCAAACCAAAC 59.492 41.667 0.00 0.00 38.90 2.93
966 970 4.404715 TCGGATAAACCAAACCAAACCAAA 59.595 37.500 0.00 0.00 38.90 3.28
967 971 3.958798 TCGGATAAACCAAACCAAACCAA 59.041 39.130 0.00 0.00 38.90 3.67
1001 1005 1.520342 GAGGAGGCAGCGCTTACAG 60.520 63.158 7.50 0.00 0.00 2.74
1022 1026 4.926832 TCGATGCGACAAAAGTAAATGAGA 59.073 37.500 0.00 0.00 0.00 3.27
1036 1040 0.040781 GGTAGAGCTCTCGATGCGAC 60.041 60.000 22.17 10.86 35.28 5.19
1251 1260 2.346766 TCACAGGCATTTCCGCATAT 57.653 45.000 0.00 0.00 40.77 1.78
1283 1292 4.841813 TGAAGTTTCCAGTGGGTATGTCTA 59.158 41.667 9.92 0.00 34.93 2.59
1408 1417 1.843368 TATCTATCTAACCGCCCCCG 58.157 55.000 0.00 0.00 0.00 5.73
1412 1421 6.018180 CCAAACAACTTATCTATCTAACCGCC 60.018 42.308 0.00 0.00 0.00 6.13
1419 1428 7.496346 TCCAGTCCAAACAACTTATCTATCT 57.504 36.000 0.00 0.00 0.00 1.98
1475 1528 7.508977 AGATGTAGTTTCCCTGGAAAATTTTCA 59.491 33.333 27.53 15.18 44.40 2.69
1520 1578 1.005450 TGTTGGGAAGTAAGGATGGGC 59.995 52.381 0.00 0.00 0.00 5.36
1530 1588 3.030291 TCATTGCAAGTTGTTGGGAAGT 58.970 40.909 4.94 0.00 33.87 3.01
1592 1650 9.988350 GGACAAGAAATTACACATTACATACAG 57.012 33.333 0.00 0.00 0.00 2.74
1694 1756 8.083462 GGAAGCATGTATTTACCTAGTAGAGTC 58.917 40.741 0.00 0.00 0.00 3.36
1780 1927 1.213013 GAGCGCTTCTCACCTCGAA 59.787 57.895 13.26 0.00 41.51 3.71
1842 1989 8.650490 TGGACTATTTGCTATGAGATACATCAA 58.350 33.333 0.00 0.00 40.07 2.57
1852 1999 7.598869 CGCTACTTATTGGACTATTTGCTATGA 59.401 37.037 0.00 0.00 0.00 2.15
1898 2045 9.139174 CCTGCACGAATGAAAAGTAAAATATTT 57.861 29.630 0.00 0.00 0.00 1.40
1907 2054 4.393062 CAGATACCTGCACGAATGAAAAGT 59.607 41.667 0.00 0.00 33.07 2.66
1980 2131 5.273944 GTCGCAACTTCATCAAACTTTCTT 58.726 37.500 0.00 0.00 0.00 2.52
2058 2209 5.863935 TCATTACAGAGAATTGACTGACACG 59.136 40.000 13.24 0.00 37.54 4.49
2063 2214 7.041167 TGGTTTGTCATTACAGAGAATTGACTG 60.041 37.037 6.85 6.85 36.83 3.51
2308 2459 4.719273 AGGGAGAAGAAACATAGAGGGAAG 59.281 45.833 0.00 0.00 0.00 3.46
2309 2460 4.699994 AGGGAGAAGAAACATAGAGGGAA 58.300 43.478 0.00 0.00 0.00 3.97
2310 2461 4.264850 TGAGGGAGAAGAAACATAGAGGGA 60.265 45.833 0.00 0.00 0.00 4.20
2892 3053 8.905702 GTGAAACATACATTTTAGCTCAAACAG 58.094 33.333 0.00 0.00 36.32 3.16
2910 3071 9.120538 GAGAGATCTAGTTCTAGAGTGAAACAT 57.879 37.037 13.75 0.00 41.43 2.71
2993 3154 9.972106 GATGGGAGGATAGATTATTCAGAATTT 57.028 33.333 0.00 0.00 0.00 1.82
3032 3193 8.635765 TGCATCCAAAGAAACTAAAGATACTT 57.364 30.769 0.00 0.00 0.00 2.24
3033 3194 8.635765 TTGCATCCAAAGAAACTAAAGATACT 57.364 30.769 0.00 0.00 0.00 2.12
3037 3198 9.912634 CTTTATTGCATCCAAAGAAACTAAAGA 57.087 29.630 8.70 0.00 32.77 2.52
3038 3199 9.696917 ACTTTATTGCATCCAAAGAAACTAAAG 57.303 29.630 17.30 0.00 34.89 1.85
3068 3229 9.334947 CCAGTTTACTCAGTTGATGATGATTAT 57.665 33.333 0.00 0.00 37.28 1.28
3077 3238 6.299805 TGATAGCCAGTTTACTCAGTTGAT 57.700 37.500 0.00 0.00 0.00 2.57
3126 3288 2.351738 GCACAGAAGTTACATTGCACCC 60.352 50.000 0.00 0.00 0.00 4.61
3148 3311 4.042398 ACATTACACATACGCGATCTGAC 58.958 43.478 15.93 0.00 0.00 3.51
3155 3318 8.663771 TTGAGTATATACATTACACATACGCG 57.336 34.615 15.18 3.53 0.00 6.01
3182 3345 9.214957 TGACAATGTAAGGAACAACAAGTATAG 57.785 33.333 0.00 0.00 42.70 1.31
3191 3354 5.432645 TGACACTGACAATGTAAGGAACAA 58.567 37.500 2.36 0.00 42.70 2.83
3195 3358 3.557054 GGCTGACACTGACAATGTAAGGA 60.557 47.826 3.63 0.00 30.10 3.36
3196 3359 2.744202 GGCTGACACTGACAATGTAAGG 59.256 50.000 3.63 0.00 30.10 2.69


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

AutoCloner maintained by Alex Coulton.