Multiple sequence alignment - TraesCS2A01G419300

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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 TraesCS2A01G419300 chr2A 100.000 3443 0 0 1 3443 674531623 674535065 0.000000e+00 6359.0
1 TraesCS2A01G419300 chr2A 82.258 310 53 2 1300 1608 679977365 679977057 2.040000e-67 267.0
2 TraesCS2A01G419300 chr2A 100.000 51 0 0 917 967 674532461 674532511 1.020000e-15 95.3
3 TraesCS2A01G419300 chr2A 100.000 51 0 0 839 889 674532539 674532589 1.020000e-15 95.3
4 TraesCS2A01G419300 chr2D 95.229 1551 57 10 888 2437 529683740 529685274 0.000000e+00 2438.0
5 TraesCS2A01G419300 chr2D 84.511 736 79 18 2429 3152 91803836 91804548 0.000000e+00 695.0
6 TraesCS2A01G419300 chr2D 91.264 435 31 7 398 828 529683286 529683717 1.380000e-163 586.0
7 TraesCS2A01G419300 chr2D 92.334 287 15 3 1 280 529682999 529683285 5.350000e-108 401.0
8 TraesCS2A01G419300 chr2D 87.347 245 31 0 1374 1618 537438568 537438324 7.270000e-72 281.0
9 TraesCS2A01G419300 chr2D 92.715 151 10 1 3252 3402 636094241 636094092 2.080000e-52 217.0
10 TraesCS2A01G419300 chr2D 92.053 151 11 1 3252 3402 91804643 91804792 9.680000e-51 211.0
11 TraesCS2A01G419300 chr2D 100.000 41 0 0 3403 3443 529685257 529685297 3.680000e-10 76.8
12 TraesCS2A01G419300 chr2B 95.168 1552 62 7 888 2438 629814760 629816299 0.000000e+00 2438.0
13 TraesCS2A01G419300 chr2B 94.988 838 27 11 1 828 629813905 629814737 0.000000e+00 1301.0
14 TraesCS2A01G419300 chr2B 92.373 118 9 0 1318 1435 150891052 150891169 5.910000e-38 169.0
15 TraesCS2A01G419300 chr7A 96.973 991 22 3 2423 3412 19145628 19144645 0.000000e+00 1657.0
16 TraesCS2A01G419300 chr7A 93.333 645 37 5 2432 3072 5198202 5198844 0.000000e+00 948.0
17 TraesCS2A01G419300 chr6A 93.476 797 39 8 2429 3217 45376162 45375371 0.000000e+00 1171.0
18 TraesCS2A01G419300 chr6A 85.583 652 73 11 2428 3064 454659956 454660601 0.000000e+00 664.0
19 TraesCS2A01G419300 chr6A 85.429 652 74 13 2428 3064 166508937 166509582 0.000000e+00 658.0
20 TraesCS2A01G419300 chr6A 92.357 157 12 0 3246 3402 45375061 45374905 1.240000e-54 224.0
21 TraesCS2A01G419300 chr6A 90.385 156 10 3 3058 3212 166509609 166509760 2.100000e-47 200.0
22 TraesCS2A01G419300 chr6A 89.744 156 11 3 3058 3212 454660628 454660779 9.750000e-46 195.0
23 TraesCS2A01G419300 chr4B 86.370 719 78 10 2428 3131 237045076 237045789 0.000000e+00 767.0
24 TraesCS2A01G419300 chr4B 91.954 87 6 1 3126 3212 237055091 237055176 1.680000e-23 121.0
25 TraesCS2A01G419300 chr4B 88.506 87 9 1 3126 3212 237386474 237386559 1.690000e-18 104.0
26 TraesCS2A01G419300 chr1D 84.647 736 78 19 2429 3152 431807413 431806701 0.000000e+00 701.0
27 TraesCS2A01G419300 chr3D 84.396 737 78 18 2426 3148 433801171 433801884 0.000000e+00 689.0
28 TraesCS2A01G419300 chr3D 92.715 151 10 1 3252 3402 590456038 590455889 2.080000e-52 217.0
29 TraesCS2A01G419300 chr3D 91.447 152 12 1 3252 3403 433801979 433802129 1.250000e-49 207.0
30 TraesCS2A01G419300 chr4D 84.354 735 80 18 2429 3150 380462028 380461316 0.000000e+00 688.0
31 TraesCS2A01G419300 chr4D 92.763 152 10 1 3252 3403 380461218 380461068 5.790000e-53 219.0
32 TraesCS2A01G419300 chr4A 85.846 650 72 10 2429 3064 564747262 564746619 0.000000e+00 673.0
33 TraesCS2A01G419300 chr4A 90.385 156 10 3 3058 3212 564746592 564746441 2.100000e-47 200.0
34 TraesCS2A01G419300 chr4A 89.333 150 12 2 3257 3405 564746436 564746290 5.870000e-43 185.0
35 TraesCS2A01G419300 chrUn 92.715 151 9 2 3252 3402 104483794 104483942 2.080000e-52 217.0


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 TraesCS2A01G419300 chr2A 674531623 674535065 3442 False 2183.200000 6359 100.000000 1 3443 3 chr2A.!!$F1 3442
1 TraesCS2A01G419300 chr2D 529682999 529685297 2298 False 875.450000 2438 94.706750 1 3443 4 chr2D.!!$F2 3442
2 TraesCS2A01G419300 chr2D 91803836 91804792 956 False 453.000000 695 88.282000 2429 3402 2 chr2D.!!$F1 973
3 TraesCS2A01G419300 chr2B 629813905 629816299 2394 False 1869.500000 2438 95.078000 1 2438 2 chr2B.!!$F2 2437
4 TraesCS2A01G419300 chr7A 19144645 19145628 983 True 1657.000000 1657 96.973000 2423 3412 1 chr7A.!!$R1 989
5 TraesCS2A01G419300 chr7A 5198202 5198844 642 False 948.000000 948 93.333000 2432 3072 1 chr7A.!!$F1 640
6 TraesCS2A01G419300 chr6A 45374905 45376162 1257 True 697.500000 1171 92.916500 2429 3402 2 chr6A.!!$R1 973
7 TraesCS2A01G419300 chr6A 454659956 454660779 823 False 429.500000 664 87.663500 2428 3212 2 chr6A.!!$F2 784
8 TraesCS2A01G419300 chr6A 166508937 166509760 823 False 429.000000 658 87.907000 2428 3212 2 chr6A.!!$F1 784
9 TraesCS2A01G419300 chr4B 237045076 237045789 713 False 767.000000 767 86.370000 2428 3131 1 chr4B.!!$F1 703
10 TraesCS2A01G419300 chr1D 431806701 431807413 712 True 701.000000 701 84.647000 2429 3152 1 chr1D.!!$R1 723
11 TraesCS2A01G419300 chr3D 433801171 433802129 958 False 448.000000 689 87.921500 2426 3403 2 chr3D.!!$F1 977
12 TraesCS2A01G419300 chr4D 380461068 380462028 960 True 453.500000 688 88.558500 2429 3403 2 chr4D.!!$R1 974
13 TraesCS2A01G419300 chr4A 564746290 564747262 972 True 352.666667 673 88.521333 2429 3405 3 chr4A.!!$R1 976

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
874 895 1.207089 CATTCTCTGGTAGTTCGGCCA 59.793 52.381 2.24 0.00 0.00 5.36 F
1050 1071 0.179056 CCGTGGCCGATTACTGGAAT 60.179 55.000 0.00 0.00 35.63 3.01 F
1226 1247 0.677731 ACTGACAATCACCATGGCCG 60.678 55.000 13.04 3.06 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 1939 0.524816 CCGGTTCCGACGATGTAGTG 60.525 60.0 13.08 0.0 0.0 2.74 R
2148 2169 0.676782 CCATGTTGACGAGGAACCCC 60.677 60.0 0.00 0.0 0.0 4.95 R
3170 3310 0.544357 ACACCCTCGTTCATCTCCCA 60.544 55.0 0.00 0.0 0.0 4.37 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
290 298 1.739067 AGCTGGTTTAGTTCATCGGC 58.261 50.000 0.00 0.00 0.00 5.54
301 309 1.936547 GTTCATCGGCATGTCTCTTCC 59.063 52.381 0.00 0.00 0.00 3.46
350 358 4.044191 GGGGTAATAATTCCTATGCCAGGT 59.956 45.833 1.67 0.00 45.71 4.00
359 367 3.653164 TCCTATGCCAGGTCATCTGTTA 58.347 45.455 1.67 0.00 45.71 2.41
390 398 2.159612 CGTGTATCGTTGGAGTTCTCGA 60.160 50.000 0.00 0.00 36.77 4.04
700 708 9.331282 GCCTAATACTATGTTAATCATGGATCC 57.669 37.037 4.20 4.20 38.21 3.36
766 782 5.500645 AAAAAGTCGAAAGGTTTCCTCTG 57.499 39.130 0.00 0.00 33.68 3.35
807 825 9.302345 CGCATATTATTACGATGAATAGACCTT 57.698 33.333 0.00 0.00 0.00 3.50
828 849 5.045869 CCTTGTGGTTGGTCTATAAAGAGGA 60.046 44.000 0.00 0.00 30.45 3.71
829 850 5.416271 TGTGGTTGGTCTATAAAGAGGAC 57.584 43.478 0.00 0.00 30.45 3.85
830 851 4.081862 TGTGGTTGGTCTATAAAGAGGACG 60.082 45.833 0.00 0.00 30.45 4.79
831 852 4.159135 GTGGTTGGTCTATAAAGAGGACGA 59.841 45.833 0.00 0.00 30.45 4.20
835 856 7.146648 GGTTGGTCTATAAAGAGGACGAATAG 58.853 42.308 0.00 0.00 32.34 1.73
836 857 7.014038 GGTTGGTCTATAAAGAGGACGAATAGA 59.986 40.741 0.00 0.00 32.34 1.98
837 858 7.507733 TGGTCTATAAAGAGGACGAATAGAC 57.492 40.000 10.80 10.80 44.15 2.59
842 863 6.793505 ATAAAGAGGACGAATAGACCTTGT 57.206 37.500 0.00 0.00 44.84 3.16
845 866 4.345854 AGAGGACGAATAGACCTTGTTCT 58.654 43.478 0.00 0.00 44.84 3.01
846 867 4.773149 AGAGGACGAATAGACCTTGTTCTT 59.227 41.667 0.00 0.00 44.84 2.52
847 868 5.074584 AGGACGAATAGACCTTGTTCTTC 57.925 43.478 0.00 0.00 42.25 2.87
848 869 4.773149 AGGACGAATAGACCTTGTTCTTCT 59.227 41.667 0.00 0.00 42.25 2.85
849 870 5.103687 GGACGAATAGACCTTGTTCTTCTC 58.896 45.833 0.00 0.00 0.00 2.87
850 871 5.105675 GGACGAATAGACCTTGTTCTTCTCT 60.106 44.000 0.00 0.00 0.00 3.10
851 872 5.956642 ACGAATAGACCTTGTTCTTCTCTC 58.043 41.667 0.00 0.00 0.00 3.20
852 873 5.712917 ACGAATAGACCTTGTTCTTCTCTCT 59.287 40.000 0.00 0.00 0.00 3.10
853 874 6.209788 ACGAATAGACCTTGTTCTTCTCTCTT 59.790 38.462 0.00 0.00 0.00 2.85
854 875 6.750039 CGAATAGACCTTGTTCTTCTCTCTTC 59.250 42.308 0.00 0.00 0.00 2.87
855 876 7.546250 AATAGACCTTGTTCTTCTCTCTTCA 57.454 36.000 0.00 0.00 0.00 3.02
856 877 7.732222 ATAGACCTTGTTCTTCTCTCTTCAT 57.268 36.000 0.00 0.00 0.00 2.57
857 878 6.432403 AGACCTTGTTCTTCTCTCTTCATT 57.568 37.500 0.00 0.00 0.00 2.57
858 879 6.463360 AGACCTTGTTCTTCTCTCTTCATTC 58.537 40.000 0.00 0.00 0.00 2.67
859 880 6.269769 AGACCTTGTTCTTCTCTCTTCATTCT 59.730 38.462 0.00 0.00 0.00 2.40
860 881 6.463360 ACCTTGTTCTTCTCTCTTCATTCTC 58.537 40.000 0.00 0.00 0.00 2.87
861 882 6.269769 ACCTTGTTCTTCTCTCTTCATTCTCT 59.730 38.462 0.00 0.00 0.00 3.10
862 883 6.591062 CCTTGTTCTTCTCTCTTCATTCTCTG 59.409 42.308 0.00 0.00 0.00 3.35
863 884 6.035368 TGTTCTTCTCTCTTCATTCTCTGG 57.965 41.667 0.00 0.00 0.00 3.86
864 885 5.541868 TGTTCTTCTCTCTTCATTCTCTGGT 59.458 40.000 0.00 0.00 0.00 4.00
865 886 6.721668 TGTTCTTCTCTCTTCATTCTCTGGTA 59.278 38.462 0.00 0.00 0.00 3.25
866 887 7.093988 TGTTCTTCTCTCTTCATTCTCTGGTAG 60.094 40.741 0.00 0.00 0.00 3.18
867 888 6.489603 TCTTCTCTCTTCATTCTCTGGTAGT 58.510 40.000 0.00 0.00 0.00 2.73
868 889 6.951198 TCTTCTCTCTTCATTCTCTGGTAGTT 59.049 38.462 0.00 0.00 0.00 2.24
869 890 6.767524 TCTCTCTTCATTCTCTGGTAGTTC 57.232 41.667 0.00 0.00 0.00 3.01
870 891 5.355630 TCTCTCTTCATTCTCTGGTAGTTCG 59.644 44.000 0.00 0.00 0.00 3.95
871 892 4.399618 TCTCTTCATTCTCTGGTAGTTCGG 59.600 45.833 0.00 0.00 0.00 4.30
872 893 2.961526 TCATTCTCTGGTAGTTCGGC 57.038 50.000 0.00 0.00 0.00 5.54
873 894 1.480954 TCATTCTCTGGTAGTTCGGCC 59.519 52.381 0.00 0.00 0.00 6.13
874 895 1.207089 CATTCTCTGGTAGTTCGGCCA 59.793 52.381 2.24 0.00 0.00 5.36
875 896 1.568504 TTCTCTGGTAGTTCGGCCAT 58.431 50.000 2.24 0.00 33.84 4.40
876 897 1.568504 TCTCTGGTAGTTCGGCCATT 58.431 50.000 2.24 0.00 33.84 3.16
877 898 1.906574 TCTCTGGTAGTTCGGCCATTT 59.093 47.619 2.24 0.00 33.84 2.32
878 899 2.304761 TCTCTGGTAGTTCGGCCATTTT 59.695 45.455 2.24 0.00 33.84 1.82
879 900 2.420022 CTCTGGTAGTTCGGCCATTTTG 59.580 50.000 2.24 0.00 33.84 2.44
880 901 2.159382 CTGGTAGTTCGGCCATTTTGT 58.841 47.619 2.24 0.00 33.84 2.83
881 902 3.008157 TCTGGTAGTTCGGCCATTTTGTA 59.992 43.478 2.24 0.00 33.84 2.41
882 903 3.945285 CTGGTAGTTCGGCCATTTTGTAT 59.055 43.478 2.24 0.00 33.84 2.29
883 904 4.337145 TGGTAGTTCGGCCATTTTGTATT 58.663 39.130 2.24 0.00 0.00 1.89
884 905 4.767928 TGGTAGTTCGGCCATTTTGTATTT 59.232 37.500 2.24 0.00 0.00 1.40
885 906 5.099575 GGTAGTTCGGCCATTTTGTATTTG 58.900 41.667 2.24 0.00 0.00 2.32
886 907 4.864704 AGTTCGGCCATTTTGTATTTGT 57.135 36.364 2.24 0.00 0.00 2.83
893 914 6.016192 TCGGCCATTTTGTATTTGTTAACTGA 60.016 34.615 2.24 0.00 0.00 3.41
902 923 7.744087 TGTATTTGTTAACTGATGCAGTCTT 57.256 32.000 7.22 0.00 44.62 3.01
917 938 3.563390 GCAGTCTTTTGCTTCTCAACTCT 59.437 43.478 0.00 0.00 40.89 3.24
943 964 6.721668 TGTTCTTCTCTCTTCATTCTCTGGTA 59.278 38.462 0.00 0.00 0.00 3.25
947 968 6.767524 TCTCTCTTCATTCTCTGGTAGTTC 57.232 41.667 0.00 0.00 0.00 3.01
956 977 2.304761 TCTCTGGTAGTTCGGCCATTTT 59.695 45.455 2.24 0.00 33.84 1.82
957 978 2.420022 CTCTGGTAGTTCGGCCATTTTG 59.580 50.000 2.24 0.00 33.84 2.44
958 979 2.159382 CTGGTAGTTCGGCCATTTTGT 58.841 47.619 2.24 0.00 33.84 2.83
959 980 3.008157 TCTGGTAGTTCGGCCATTTTGTA 59.992 43.478 2.24 0.00 33.84 2.41
962 983 4.767928 TGGTAGTTCGGCCATTTTGTATTT 59.232 37.500 2.24 0.00 0.00 1.40
963 984 5.099575 GGTAGTTCGGCCATTTTGTATTTG 58.900 41.667 2.24 0.00 0.00 2.32
964 985 4.864704 AGTTCGGCCATTTTGTATTTGT 57.135 36.364 2.24 0.00 0.00 2.83
965 986 5.208463 AGTTCGGCCATTTTGTATTTGTT 57.792 34.783 2.24 0.00 0.00 2.83
966 987 6.334102 AGTTCGGCCATTTTGTATTTGTTA 57.666 33.333 2.24 0.00 0.00 2.41
967 988 6.153756 AGTTCGGCCATTTTGTATTTGTTAC 58.846 36.000 2.24 0.00 0.00 2.50
968 989 4.724303 TCGGCCATTTTGTATTTGTTACG 58.276 39.130 2.24 0.00 33.15 3.18
972 993 6.402334 CGGCCATTTTGTATTTGTTACGTAGA 60.402 38.462 2.24 0.00 33.15 2.59
989 1010 6.837471 ACGTAGATTCCAGTAGTTCTCTTT 57.163 37.500 0.00 0.00 0.00 2.52
995 1016 5.367945 TTCCAGTAGTTCTCTTTGGTTGT 57.632 39.130 0.00 0.00 32.59 3.32
1050 1071 0.179056 CCGTGGCCGATTACTGGAAT 60.179 55.000 0.00 0.00 35.63 3.01
1056 1077 0.843984 CCGATTACTGGAATGGGGGT 59.156 55.000 5.79 0.00 39.22 4.95
1213 1234 4.293610 TGGAGAGCACCACTGACA 57.706 55.556 0.00 0.00 34.77 3.58
1222 1243 1.200716 GCACCACTGACAATCACCATG 59.799 52.381 0.00 0.00 0.00 3.66
1223 1244 1.814394 CACCACTGACAATCACCATGG 59.186 52.381 11.19 11.19 0.00 3.66
1224 1245 0.813184 CCACTGACAATCACCATGGC 59.187 55.000 13.04 0.00 0.00 4.40
1225 1246 0.813184 CACTGACAATCACCATGGCC 59.187 55.000 13.04 0.00 0.00 5.36
1226 1247 0.677731 ACTGACAATCACCATGGCCG 60.678 55.000 13.04 3.06 0.00 6.13
1295 1316 1.888436 TTCGAGGACAAGCTCGGCAT 61.888 55.000 0.00 0.00 42.61 4.40
1297 1318 1.817099 GAGGACAAGCTCGGCATGG 60.817 63.158 0.00 0.00 31.12 3.66
1325 1346 0.840722 AAGATCCACCTGTTCCCGGT 60.841 55.000 0.00 0.00 34.38 5.28
1489 1510 1.742880 TCCGTCGAGGAGGTGTACG 60.743 63.158 6.70 0.00 45.98 3.67
1956 1977 1.444553 CACCAAGCTCTCGTCCGAC 60.445 63.158 0.00 0.00 0.00 4.79
1957 1978 1.604023 ACCAAGCTCTCGTCCGACT 60.604 57.895 0.00 0.00 0.00 4.18
1958 1979 1.137825 CCAAGCTCTCGTCCGACTC 59.862 63.158 0.00 0.00 0.00 3.36
1959 1980 1.137825 CAAGCTCTCGTCCGACTCC 59.862 63.158 0.00 0.00 0.00 3.85
2095 2116 2.198304 GATGGGCGTCAAGAAGGGGT 62.198 60.000 0.00 0.00 0.00 4.95
2190 2211 2.341543 CTGGAGCTGTGCACGACT 59.658 61.111 13.13 11.91 0.00 4.18
2201 2222 0.607217 TGCACGACTCCGGACTTCTA 60.607 55.000 0.00 0.00 40.78 2.10
2340 2361 2.651361 CTGACCAACGAGGACGCT 59.349 61.111 5.70 0.00 43.96 5.07
2361 2382 1.523258 CCGCCTCTTCATCAGCCTG 60.523 63.158 0.00 0.00 0.00 4.85
2392 2413 4.301027 GGCCCGGGAGATGCTACG 62.301 72.222 29.31 0.00 0.00 3.51
2453 2474 1.333177 CGGCCCTAGCATCTTAGAGT 58.667 55.000 0.00 0.00 42.56 3.24
2724 2751 1.383523 TTCATGCAACGACACAACCA 58.616 45.000 0.00 0.00 0.00 3.67
2937 2977 1.609061 CCTGGACTTCACGTCTGCATT 60.609 52.381 0.00 0.00 42.44 3.56
3012 3062 3.330720 CGTTCTTCCCAGGGGCCT 61.331 66.667 5.33 0.00 34.68 5.19
3018 3068 2.553438 CTTCCCAGGGGCCTAGGACT 62.553 65.000 16.16 4.82 33.74 3.85
3170 3310 9.498039 AATTAATTGGGAAAGAAGATGGAGAAT 57.502 29.630 0.00 0.00 0.00 2.40
3221 3361 3.629398 AGCCAGCGAAGGATAAAGATTTG 59.371 43.478 0.00 0.00 0.00 2.32
3225 3527 5.269313 CAGCGAAGGATAAAGATTTGCTTC 58.731 41.667 0.00 0.00 40.82 3.86
3378 3799 3.338126 CTAGGCCGTCGCACTCGTT 62.338 63.158 0.00 0.00 36.38 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 129 7.278868 GGTGTCCTGTAGAAATTGATCAAGTAG 59.721 40.741 14.54 5.07 0.00 2.57
153 161 5.363580 TGTTCCAAAAATCTCCTCTGCTTTT 59.636 36.000 0.00 0.00 0.00 2.27
359 367 1.174783 ACGATACACGCTCTCTTGGT 58.825 50.000 0.00 0.00 46.94 3.67
408 416 4.164030 TGGCCTATGCACAGATTTCTAAGA 59.836 41.667 3.32 0.00 40.13 2.10
546 554 9.546428 CAATTACACAGACCAATATATCTGACA 57.454 33.333 15.10 1.77 44.32 3.58
700 708 4.202151 CCTGGAGGAACCTTTTCAACTTTG 60.202 45.833 0.00 0.00 39.86 2.77
807 825 4.081862 CGTCCTCTTTATAGACCAACCACA 60.082 45.833 0.00 0.00 0.00 4.17
810 830 4.996788 TCGTCCTCTTTATAGACCAACC 57.003 45.455 0.00 0.00 0.00 3.77
828 849 5.712917 AGAGAGAAGAACAAGGTCTATTCGT 59.287 40.000 0.00 0.00 0.00 3.85
829 850 6.202516 AGAGAGAAGAACAAGGTCTATTCG 57.797 41.667 0.00 0.00 0.00 3.34
830 851 7.607250 TGAAGAGAGAAGAACAAGGTCTATTC 58.393 38.462 0.00 0.00 36.47 1.75
831 852 7.546250 TGAAGAGAGAAGAACAAGGTCTATT 57.454 36.000 0.00 0.00 0.00 1.73
835 856 6.463360 AGAATGAAGAGAGAAGAACAAGGTC 58.537 40.000 0.00 0.00 0.00 3.85
836 857 6.269769 AGAGAATGAAGAGAGAAGAACAAGGT 59.730 38.462 0.00 0.00 0.00 3.50
837 858 6.591062 CAGAGAATGAAGAGAGAAGAACAAGG 59.409 42.308 0.00 0.00 0.00 3.61
838 859 6.591062 CCAGAGAATGAAGAGAGAAGAACAAG 59.409 42.308 0.00 0.00 0.00 3.16
839 860 6.042552 ACCAGAGAATGAAGAGAGAAGAACAA 59.957 38.462 0.00 0.00 0.00 2.83
842 863 6.951198 ACTACCAGAGAATGAAGAGAGAAGAA 59.049 38.462 0.00 0.00 0.00 2.52
845 866 6.127869 CGAACTACCAGAGAATGAAGAGAGAA 60.128 42.308 0.00 0.00 0.00 2.87
846 867 5.355630 CGAACTACCAGAGAATGAAGAGAGA 59.644 44.000 0.00 0.00 0.00 3.10
847 868 5.449862 CCGAACTACCAGAGAATGAAGAGAG 60.450 48.000 0.00 0.00 0.00 3.20
848 869 4.399618 CCGAACTACCAGAGAATGAAGAGA 59.600 45.833 0.00 0.00 0.00 3.10
849 870 4.677584 CCGAACTACCAGAGAATGAAGAG 58.322 47.826 0.00 0.00 0.00 2.85
850 871 3.119101 GCCGAACTACCAGAGAATGAAGA 60.119 47.826 0.00 0.00 0.00 2.87
851 872 3.190874 GCCGAACTACCAGAGAATGAAG 58.809 50.000 0.00 0.00 0.00 3.02
852 873 2.093658 GGCCGAACTACCAGAGAATGAA 60.094 50.000 0.00 0.00 0.00 2.57
853 874 1.480954 GGCCGAACTACCAGAGAATGA 59.519 52.381 0.00 0.00 0.00 2.57
854 875 1.207089 TGGCCGAACTACCAGAGAATG 59.793 52.381 0.00 0.00 0.00 2.67
855 876 1.568504 TGGCCGAACTACCAGAGAAT 58.431 50.000 0.00 0.00 0.00 2.40
856 877 1.568504 ATGGCCGAACTACCAGAGAA 58.431 50.000 0.00 0.00 39.88 2.87
857 878 1.568504 AATGGCCGAACTACCAGAGA 58.431 50.000 0.00 0.00 39.88 3.10
858 879 2.403252 AAATGGCCGAACTACCAGAG 57.597 50.000 0.00 0.00 39.88 3.35
859 880 2.224670 ACAAAATGGCCGAACTACCAGA 60.225 45.455 0.00 0.00 39.88 3.86
860 881 2.159382 ACAAAATGGCCGAACTACCAG 58.841 47.619 0.00 0.00 39.88 4.00
861 882 2.279935 ACAAAATGGCCGAACTACCA 57.720 45.000 0.00 0.00 41.06 3.25
862 883 4.976224 AATACAAAATGGCCGAACTACC 57.024 40.909 0.00 0.00 0.00 3.18
863 884 5.705902 ACAAATACAAAATGGCCGAACTAC 58.294 37.500 0.00 0.00 0.00 2.73
864 885 5.968528 ACAAATACAAAATGGCCGAACTA 57.031 34.783 0.00 0.00 0.00 2.24
865 886 4.864704 ACAAATACAAAATGGCCGAACT 57.135 36.364 0.00 0.00 0.00 3.01
866 887 6.643360 AGTTAACAAATACAAAATGGCCGAAC 59.357 34.615 8.61 0.00 0.00 3.95
867 888 6.642950 CAGTTAACAAATACAAAATGGCCGAA 59.357 34.615 8.61 0.00 0.00 4.30
868 889 6.016192 TCAGTTAACAAATACAAAATGGCCGA 60.016 34.615 8.61 0.00 0.00 5.54
869 890 6.153067 TCAGTTAACAAATACAAAATGGCCG 58.847 36.000 8.61 0.00 0.00 6.13
870 891 7.412891 GCATCAGTTAACAAATACAAAATGGCC 60.413 37.037 8.61 0.00 0.00 5.36
871 892 7.117523 TGCATCAGTTAACAAATACAAAATGGC 59.882 33.333 8.61 0.00 0.00 4.40
872 893 8.531622 TGCATCAGTTAACAAATACAAAATGG 57.468 30.769 8.61 0.00 0.00 3.16
873 894 9.195411 ACTGCATCAGTTAACAAATACAAAATG 57.805 29.630 8.61 0.00 42.59 2.32
874 895 9.410556 GACTGCATCAGTTAACAAATACAAAAT 57.589 29.630 8.61 0.00 45.44 1.82
875 896 8.629158 AGACTGCATCAGTTAACAAATACAAAA 58.371 29.630 8.61 0.00 45.44 2.44
876 897 8.165239 AGACTGCATCAGTTAACAAATACAAA 57.835 30.769 8.61 0.00 45.44 2.83
877 898 7.744087 AGACTGCATCAGTTAACAAATACAA 57.256 32.000 8.61 0.00 45.44 2.41
878 899 7.744087 AAGACTGCATCAGTTAACAAATACA 57.256 32.000 8.61 1.21 45.44 2.29
879 900 8.905702 CAAAAGACTGCATCAGTTAACAAATAC 58.094 33.333 8.61 0.00 45.44 1.89
880 901 7.594758 GCAAAAGACTGCATCAGTTAACAAATA 59.405 33.333 8.61 0.00 45.44 1.40
881 902 6.421801 GCAAAAGACTGCATCAGTTAACAAAT 59.578 34.615 8.61 0.00 45.44 2.32
882 903 5.748152 GCAAAAGACTGCATCAGTTAACAAA 59.252 36.000 8.61 0.00 45.44 2.83
883 904 5.067674 AGCAAAAGACTGCATCAGTTAACAA 59.932 36.000 8.61 0.00 45.44 2.83
884 905 4.580167 AGCAAAAGACTGCATCAGTTAACA 59.420 37.500 8.61 0.00 45.44 2.41
885 906 5.113502 AGCAAAAGACTGCATCAGTTAAC 57.886 39.130 0.00 0.00 45.44 2.01
886 907 5.532406 AGAAGCAAAAGACTGCATCAGTTAA 59.468 36.000 0.66 0.00 45.44 2.01
893 914 3.887716 AGTTGAGAAGCAAAAGACTGCAT 59.112 39.130 0.00 0.00 45.18 3.96
902 923 5.882557 AGAAGAACAAGAGTTGAGAAGCAAA 59.117 36.000 0.00 0.00 38.30 3.68
917 938 6.042552 ACCAGAGAATGAAGAGAGAAGAACAA 59.957 38.462 0.00 0.00 0.00 2.83
943 964 4.864704 ACAAATACAAAATGGCCGAACT 57.135 36.364 0.00 0.00 0.00 3.01
947 968 4.477780 ACGTAACAAATACAAAATGGCCG 58.522 39.130 0.00 0.00 33.89 6.13
956 977 8.742777 ACTACTGGAATCTACGTAACAAATACA 58.257 33.333 0.00 0.00 33.89 2.29
957 978 9.578439 AACTACTGGAATCTACGTAACAAATAC 57.422 33.333 0.00 0.00 0.00 1.89
958 979 9.793252 GAACTACTGGAATCTACGTAACAAATA 57.207 33.333 0.00 0.00 0.00 1.40
959 980 8.529476 AGAACTACTGGAATCTACGTAACAAAT 58.471 33.333 0.00 0.00 0.00 2.32
962 983 6.883217 AGAGAACTACTGGAATCTACGTAACA 59.117 38.462 0.00 0.00 0.00 2.41
963 984 7.319142 AGAGAACTACTGGAATCTACGTAAC 57.681 40.000 0.00 0.00 0.00 2.50
964 985 7.934855 AAGAGAACTACTGGAATCTACGTAA 57.065 36.000 0.00 0.00 0.00 3.18
965 986 7.148120 CCAAAGAGAACTACTGGAATCTACGTA 60.148 40.741 0.00 0.00 33.57 3.57
966 987 6.350277 CCAAAGAGAACTACTGGAATCTACGT 60.350 42.308 0.00 0.00 33.57 3.57
967 988 6.037098 CCAAAGAGAACTACTGGAATCTACG 58.963 44.000 0.00 0.00 33.57 3.51
968 989 6.937392 ACCAAAGAGAACTACTGGAATCTAC 58.063 40.000 0.00 0.00 34.93 2.59
972 993 5.941788 ACAACCAAAGAGAACTACTGGAAT 58.058 37.500 0.00 0.00 34.93 3.01
989 1010 1.067364 CTTGCTGCATGTCAACAACCA 59.933 47.619 1.84 0.00 28.75 3.67
995 1016 2.566833 AGGTACTTGCTGCATGTCAA 57.433 45.000 22.31 5.82 27.25 3.18
1209 1230 1.378382 CCGGCCATGGTGATTGTCA 60.378 57.895 14.67 0.00 0.00 3.58
1213 1234 1.153249 CGTACCGGCCATGGTGATT 60.153 57.895 14.67 0.00 43.68 2.57
1222 1243 2.588034 GCTCCATTCGTACCGGCC 60.588 66.667 0.00 0.00 0.00 6.13
1223 1244 2.960129 CGCTCCATTCGTACCGGC 60.960 66.667 0.00 0.00 0.00 6.13
1224 1245 2.279252 CCGCTCCATTCGTACCGG 60.279 66.667 0.00 0.00 0.00 5.28
1225 1246 1.588139 GACCGCTCCATTCGTACCG 60.588 63.158 0.00 0.00 0.00 4.02
1226 1247 1.227176 GGACCGCTCCATTCGTACC 60.227 63.158 0.00 0.00 36.42 3.34
1295 1316 1.680989 TGGATCTTCGTCTCCGCCA 60.681 57.895 0.00 0.00 34.05 5.69
1297 1318 1.227002 GGTGGATCTTCGTCTCCGC 60.227 63.158 0.00 0.00 40.58 5.54
1325 1346 2.981302 CGAGGTCCACCATGCTCA 59.019 61.111 0.00 0.00 38.89 4.26
1642 1663 3.507009 CCCCTCCTCGTCGTCGTC 61.507 72.222 1.33 0.00 38.33 4.20
1653 1674 1.411651 GGTCTACTGCCATCCCCTCC 61.412 65.000 0.00 0.00 0.00 4.30
1918 1939 0.524816 CCGGTTCCGACGATGTAGTG 60.525 60.000 13.08 0.00 0.00 2.74
1959 1980 3.686045 GATAGGCCGCGGGAGGAG 61.686 72.222 29.38 0.00 0.00 3.69
2148 2169 0.676782 CCATGTTGACGAGGAACCCC 60.677 60.000 0.00 0.00 0.00 4.95
2190 2211 1.751927 GGCCTCGTAGAAGTCCGGA 60.752 63.158 0.00 0.00 34.09 5.14
2340 2361 1.680522 GGCTGATGAAGAGGCGGAGA 61.681 60.000 0.00 0.00 0.00 3.71
2408 2429 1.409427 GGACCCTGTAGTTCTCGATGG 59.591 57.143 0.00 0.00 0.00 3.51
2453 2474 0.901827 TATGAAGCTCGCACAAGGGA 59.098 50.000 0.00 0.00 35.21 4.20
2937 2977 1.526686 CAGTGTGTGAGGGCAAGCA 60.527 57.895 0.00 0.00 0.00 3.91
2971 3011 2.626780 GCAGTTTGGCCGTCCTTCC 61.627 63.158 0.00 0.00 0.00 3.46
3012 3062 1.747709 GGCGACACACTCTAGTCCTA 58.252 55.000 0.00 0.00 0.00 2.94
3018 3068 2.675423 AGCCGGCGACACACTCTA 60.675 61.111 23.20 0.00 0.00 2.43
3170 3310 0.544357 ACACCCTCGTTCATCTCCCA 60.544 55.000 0.00 0.00 0.00 4.37
3403 3824 2.768344 ACCGGCCTATGGACCCTG 60.768 66.667 0.00 0.00 0.00 4.45
3404 3825 2.768344 CACCGGCCTATGGACCCT 60.768 66.667 0.00 0.00 0.00 4.34
3405 3826 4.564110 GCACCGGCCTATGGACCC 62.564 72.222 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.