Multiple sequence alignment - TraesCS6B01G132200

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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 TraesCS6B01G132200 chr6B 100.000 3926 0 0 1 3926 129267693 129271618 0.000000e+00 7251.0
1 TraesCS6B01G132200 chr6B 90.687 902 67 11 1 897 80959794 80958905 0.000000e+00 1184.0
2 TraesCS6B01G132200 chr6B 89.579 950 72 10 1 934 384967000 384967938 0.000000e+00 1181.0
3 TraesCS6B01G132200 chr6B 89.206 945 72 15 7 934 478886512 478885581 0.000000e+00 1153.0
4 TraesCS6B01G132200 chr6B 80.885 1491 248 30 990 2458 129447017 129448492 0.000000e+00 1140.0
5 TraesCS6B01G132200 chr6B 78.336 1454 269 34 990 2423 128016529 128017956 0.000000e+00 898.0
6 TraesCS6B01G132200 chr6B 78.101 1443 264 38 992 2411 129237149 129238562 0.000000e+00 867.0
7 TraesCS6B01G132200 chr6B 81.085 645 100 17 998 1628 129512959 129513595 2.720000e-136 496.0
8 TraesCS6B01G132200 chr6B 80.280 644 106 15 998 1626 129679492 129680129 2.140000e-127 466.0
9 TraesCS6B01G132200 chr6B 79.225 645 109 17 998 1628 125645140 125644507 3.630000e-115 425.0
10 TraesCS6B01G132200 chr6B 76.816 716 109 37 959 1627 130324344 130325049 2.240000e-92 350.0
11 TraesCS6B01G132200 chr6A 93.762 2036 106 1 935 2949 72429367 72431402 0.000000e+00 3037.0
12 TraesCS6B01G132200 chr6A 90.309 970 42 19 2988 3926 72431401 72432349 0.000000e+00 1223.0
13 TraesCS6B01G132200 chr6A 77.839 1462 277 37 989 2423 71948652 71950093 0.000000e+00 861.0
14 TraesCS6B01G132200 chr6A 77.941 1428 258 40 990 2398 72480305 72481694 0.000000e+00 839.0
15 TraesCS6B01G132200 chr6A 78.280 1349 244 37 1020 2344 73063636 73064959 0.000000e+00 822.0
16 TraesCS6B01G132200 chr6A 79.212 914 173 13 1366 2267 72506188 72507096 1.550000e-173 619.0
17 TraesCS6B01G132200 chr6A 87.500 56 4 2 897 949 96810375 96810320 1.180000e-05 62.1
18 TraesCS6B01G132200 chr3B 92.202 949 54 6 1 934 737517558 737516615 0.000000e+00 1325.0
19 TraesCS6B01G132200 chr3A 93.552 884 47 6 1 878 663280573 663281452 0.000000e+00 1308.0
20 TraesCS6B01G132200 chr2A 92.333 900 60 4 1 895 726094025 726093130 0.000000e+00 1271.0
21 TraesCS6B01G132200 chr2A 90.333 900 79 6 1 895 182411093 182411989 0.000000e+00 1173.0
22 TraesCS6B01G132200 chr4A 90.646 898 75 9 1 895 82730262 82731153 0.000000e+00 1184.0
23 TraesCS6B01G132200 chr4A 90.586 563 25 9 384 934 664235809 664235263 0.000000e+00 721.0
24 TraesCS6B01G132200 chr2B 89.590 951 71 13 1 934 796285713 796284774 0.000000e+00 1182.0
25 TraesCS6B01G132200 chr6D 95.978 721 21 3 935 1648 57215838 57216557 0.000000e+00 1164.0
26 TraesCS6B01G132200 chr6D 88.090 974 59 25 2988 3926 57217342 57218293 0.000000e+00 1103.0
27 TraesCS6B01G132200 chr6D 80.638 1317 215 25 990 2297 57514184 57515469 0.000000e+00 983.0
28 TraesCS6B01G132200 chr6D 77.930 1459 269 39 990 2423 57171264 57172694 0.000000e+00 861.0
29 TraesCS6B01G132200 chr6D 77.400 1500 279 46 959 2423 57158792 57160266 0.000000e+00 837.0
30 TraesCS6B01G132200 chr6D 77.638 1431 249 50 992 2390 57482402 57483793 0.000000e+00 804.0
31 TraesCS6B01G132200 chr6D 92.659 504 16 1 2467 2949 57216840 57217343 0.000000e+00 706.0
32 TraesCS6B01G132200 chr6D 77.105 1223 209 47 1021 2209 58047118 58048303 3.310000e-180 641.0
33 TraesCS6B01G132200 chr6D 81.562 640 102 11 998 1626 57782680 57783314 7.520000e-142 514.0
34 TraesCS6B01G132200 chr7B 88.285 956 82 17 1 940 275463640 275462699 0.000000e+00 1118.0
35 TraesCS6B01G132200 chr1B 88.192 813 69 12 135 934 10370126 10369328 0.000000e+00 944.0
36 TraesCS6B01G132200 chr1B 85.461 564 55 11 384 933 592179246 592178696 2.650000e-156 562.0
37 TraesCS6B01G132200 chr2D 86.372 565 50 9 384 934 613315429 613315980 3.380000e-165 592.0
38 TraesCS6B01G132200 chr4B 85.211 568 49 19 382 934 392629414 392628867 5.730000e-153 551.0
39 TraesCS6B01G132200 chr5A 81.053 570 76 20 384 934 452705734 452706290 3.630000e-115 425.0


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 TraesCS6B01G132200 chr6B 129267693 129271618 3925 False 7251 7251 100.000000 1 3926 1 chr6B.!!$F3 3925
1 TraesCS6B01G132200 chr6B 80958905 80959794 889 True 1184 1184 90.687000 1 897 1 chr6B.!!$R1 896
2 TraesCS6B01G132200 chr6B 384967000 384967938 938 False 1181 1181 89.579000 1 934 1 chr6B.!!$F8 933
3 TraesCS6B01G132200 chr6B 478885581 478886512 931 True 1153 1153 89.206000 7 934 1 chr6B.!!$R3 927
4 TraesCS6B01G132200 chr6B 129447017 129448492 1475 False 1140 1140 80.885000 990 2458 1 chr6B.!!$F4 1468
5 TraesCS6B01G132200 chr6B 128016529 128017956 1427 False 898 898 78.336000 990 2423 1 chr6B.!!$F1 1433
6 TraesCS6B01G132200 chr6B 129237149 129238562 1413 False 867 867 78.101000 992 2411 1 chr6B.!!$F2 1419
7 TraesCS6B01G132200 chr6B 129512959 129513595 636 False 496 496 81.085000 998 1628 1 chr6B.!!$F5 630
8 TraesCS6B01G132200 chr6B 129679492 129680129 637 False 466 466 80.280000 998 1626 1 chr6B.!!$F6 628
9 TraesCS6B01G132200 chr6B 125644507 125645140 633 True 425 425 79.225000 998 1628 1 chr6B.!!$R2 630
10 TraesCS6B01G132200 chr6B 130324344 130325049 705 False 350 350 76.816000 959 1627 1 chr6B.!!$F7 668
11 TraesCS6B01G132200 chr6A 72429367 72432349 2982 False 2130 3037 92.035500 935 3926 2 chr6A.!!$F5 2991
12 TraesCS6B01G132200 chr6A 71948652 71950093 1441 False 861 861 77.839000 989 2423 1 chr6A.!!$F1 1434
13 TraesCS6B01G132200 chr6A 72480305 72481694 1389 False 839 839 77.941000 990 2398 1 chr6A.!!$F2 1408
14 TraesCS6B01G132200 chr6A 73063636 73064959 1323 False 822 822 78.280000 1020 2344 1 chr6A.!!$F4 1324
15 TraesCS6B01G132200 chr6A 72506188 72507096 908 False 619 619 79.212000 1366 2267 1 chr6A.!!$F3 901
16 TraesCS6B01G132200 chr3B 737516615 737517558 943 True 1325 1325 92.202000 1 934 1 chr3B.!!$R1 933
17 TraesCS6B01G132200 chr3A 663280573 663281452 879 False 1308 1308 93.552000 1 878 1 chr3A.!!$F1 877
18 TraesCS6B01G132200 chr2A 726093130 726094025 895 True 1271 1271 92.333000 1 895 1 chr2A.!!$R1 894
19 TraesCS6B01G132200 chr2A 182411093 182411989 896 False 1173 1173 90.333000 1 895 1 chr2A.!!$F1 894
20 TraesCS6B01G132200 chr4A 82730262 82731153 891 False 1184 1184 90.646000 1 895 1 chr4A.!!$F1 894
21 TraesCS6B01G132200 chr4A 664235263 664235809 546 True 721 721 90.586000 384 934 1 chr4A.!!$R1 550
22 TraesCS6B01G132200 chr2B 796284774 796285713 939 True 1182 1182 89.590000 1 934 1 chr2B.!!$R1 933
23 TraesCS6B01G132200 chr6D 57215838 57218293 2455 False 991 1164 92.242333 935 3926 3 chr6D.!!$F7 2991
24 TraesCS6B01G132200 chr6D 57514184 57515469 1285 False 983 983 80.638000 990 2297 1 chr6D.!!$F4 1307
25 TraesCS6B01G132200 chr6D 57171264 57172694 1430 False 861 861 77.930000 990 2423 1 chr6D.!!$F2 1433
26 TraesCS6B01G132200 chr6D 57158792 57160266 1474 False 837 837 77.400000 959 2423 1 chr6D.!!$F1 1464
27 TraesCS6B01G132200 chr6D 57482402 57483793 1391 False 804 804 77.638000 992 2390 1 chr6D.!!$F3 1398
28 TraesCS6B01G132200 chr6D 58047118 58048303 1185 False 641 641 77.105000 1021 2209 1 chr6D.!!$F6 1188
29 TraesCS6B01G132200 chr6D 57782680 57783314 634 False 514 514 81.562000 998 1626 1 chr6D.!!$F5 628
30 TraesCS6B01G132200 chr7B 275462699 275463640 941 True 1118 1118 88.285000 1 940 1 chr7B.!!$R1 939
31 TraesCS6B01G132200 chr1B 10369328 10370126 798 True 944 944 88.192000 135 934 1 chr1B.!!$R1 799
32 TraesCS6B01G132200 chr1B 592178696 592179246 550 True 562 562 85.461000 384 933 1 chr1B.!!$R2 549
33 TraesCS6B01G132200 chr2D 613315429 613315980 551 False 592 592 86.372000 384 934 1 chr2D.!!$F1 550
34 TraesCS6B01G132200 chr4B 392628867 392629414 547 True 551 551 85.211000 382 934 1 chr4B.!!$R1 552
35 TraesCS6B01G132200 chr5A 452705734 452706290 556 False 425 425 81.053000 384 934 1 chr5A.!!$F1 550

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
35 36 2.048503 ACCGTGCCAGCGAAGTAC 60.049 61.111 0.00 0.0 0.00 2.73 F
549 627 2.413765 GAGGTCGATGACGGGAGC 59.586 66.667 0.00 0.0 40.21 4.70 F
1953 2175 0.099613 CTCTCGTCGGTGATCACAGG 59.900 60.000 26.47 17.4 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 1624 0.332972 GACCTGAATTCCCAAGGGCT 59.667 55.0 13.35 0.00 34.68 5.19 R
2040 2262 1.204146 AGTCATACTGTCCGGGCAAT 58.796 50.0 11.40 1.04 0.00 3.56 R
3081 3338 0.473755 TCCAGGCATGTGAACACACT 59.526 50.0 9.83 0.71 45.05 3.55 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
35 36 2.048503 ACCGTGCCAGCGAAGTAC 60.049 61.111 0.00 0.00 0.00 2.73
285 291 4.065281 AGTACCTCCGGCACACGC 62.065 66.667 0.00 0.00 42.52 5.34
547 625 3.515286 GCGAGGTCGATGACGGGA 61.515 66.667 2.94 0.00 43.02 5.14
548 626 2.716244 CGAGGTCGATGACGGGAG 59.284 66.667 0.00 0.00 43.02 4.30
549 627 2.413765 GAGGTCGATGACGGGAGC 59.586 66.667 0.00 0.00 40.21 4.70
550 628 3.471244 GAGGTCGATGACGGGAGCG 62.471 68.421 0.00 0.00 40.21 5.03
551 629 4.570663 GGTCGATGACGGGAGCGG 62.571 72.222 0.00 0.00 40.21 5.52
552 630 3.515286 GTCGATGACGGGAGCGGA 61.515 66.667 0.00 0.00 40.21 5.54
553 631 3.209812 TCGATGACGGGAGCGGAG 61.210 66.667 0.00 0.00 40.21 4.63
556 634 4.779733 ATGACGGGAGCGGAGGGT 62.780 66.667 0.00 0.00 0.00 4.34
1796 2018 0.530650 AATGATCGCACTGGCTACCG 60.531 55.000 0.00 0.00 38.10 4.02
1849 2071 2.777832 AGATGTTTCTGCCAGAGACC 57.222 50.000 12.36 0.00 29.05 3.85
1953 2175 0.099613 CTCTCGTCGGTGATCACAGG 59.900 60.000 26.47 17.40 0.00 4.00
1955 2177 1.938657 CTCGTCGGTGATCACAGGCT 61.939 60.000 26.47 0.00 0.00 4.58
1956 2178 1.079819 CGTCGGTGATCACAGGCTT 60.080 57.895 26.47 0.00 0.00 4.35
2028 2250 1.318158 CCAAGGAATGGCAGCTGGAC 61.318 60.000 17.12 0.00 43.80 4.02
2040 2262 3.278574 GCAGCTGGACAATATTGTACCA 58.721 45.455 24.91 25.15 41.42 3.25
2070 2292 4.430007 GACAGTATGACTATTTCACCGCA 58.570 43.478 0.00 0.00 39.69 5.69
2267 2489 8.830580 CCATTATGAAGATGTTTACTGGTACTG 58.169 37.037 0.00 0.00 0.00 2.74
2305 2530 7.591006 TCTTTGTCAAAACCGAGTATATGAC 57.409 36.000 0.00 0.00 38.08 3.06
2476 2712 2.927429 TGTGACCGCAATTTCATTTCG 58.073 42.857 0.00 0.00 0.00 3.46
2613 2849 5.560722 TGGACTCTTTGAAATAGTGACCA 57.439 39.130 0.40 0.98 31.78 4.02
2644 2880 9.787532 GCTTATGTGCTTTGATTCTTTAATACA 57.212 29.630 0.00 0.00 0.00 2.29
2724 2960 8.830580 TGCATATTGTGAGTTTCTTATTAGAGC 58.169 33.333 0.00 0.00 0.00 4.09
2847 3104 4.073293 ACTCGAGCCCTGGTATTATTTG 57.927 45.455 13.61 0.00 0.00 2.32
2904 3161 2.953648 TCCATGTGCAGCATATTTCAGG 59.046 45.455 1.05 1.02 35.74 3.86
2974 3231 6.804534 TGCAATTATTAAGCATGTTTACGC 57.195 33.333 0.96 0.13 32.55 4.42
2975 3232 6.325596 TGCAATTATTAAGCATGTTTACGCA 58.674 32.000 0.96 2.47 32.55 5.24
2976 3233 6.808704 TGCAATTATTAAGCATGTTTACGCAA 59.191 30.769 0.96 0.00 32.55 4.85
2977 3234 7.009083 TGCAATTATTAAGCATGTTTACGCAAG 59.991 33.333 0.96 0.00 36.94 4.01
2978 3235 7.219917 GCAATTATTAAGCATGTTTACGCAAGA 59.780 33.333 0.96 0.00 43.62 3.02
2979 3236 8.523464 CAATTATTAAGCATGTTTACGCAAGAC 58.477 33.333 0.96 0.00 43.62 3.01
2980 3237 5.621197 ATTAAGCATGTTTACGCAAGACA 57.379 34.783 0.96 0.00 43.62 3.41
2981 3238 5.621197 TTAAGCATGTTTACGCAAGACAT 57.379 34.783 0.96 0.00 43.62 3.06
2985 3242 5.900934 AAGCATGTTTACGCAAGACATGATG 60.901 40.000 19.89 0.00 46.15 3.07
2986 3243 8.224965 AAGCATGTTTACGCAAGACATGATGT 62.225 38.462 19.89 0.00 46.15 3.06
2987 3244 5.627499 ATGTTTACGCAAGACATGATGTT 57.373 34.783 0.00 0.00 43.62 2.71
3004 3261 7.546667 ACATGATGTTAGGCAAGCTTAATTTTG 59.453 33.333 0.00 0.00 0.00 2.44
3072 3329 4.003648 GAGAATGACACACCCTAAACCTG 58.996 47.826 0.00 0.00 0.00 4.00
3081 3338 3.202595 ACACCCTAAACCTGTTTGTGGTA 59.797 43.478 14.00 0.00 36.37 3.25
3134 3396 2.164827 TGCAGCCACAAAGAATATGCTG 59.835 45.455 5.01 5.01 46.70 4.41
3138 3400 2.736400 GCCACAAAGAATATGCTGTGCC 60.736 50.000 0.07 0.00 38.26 5.01
3159 3421 0.107066 TGCTCGCCATGTTCATCCAT 60.107 50.000 0.00 0.00 0.00 3.41
3163 3425 2.882761 CTCGCCATGTTCATCCATCATT 59.117 45.455 0.00 0.00 0.00 2.57
3164 3426 2.880268 TCGCCATGTTCATCCATCATTC 59.120 45.455 0.00 0.00 0.00 2.67
3165 3427 2.030540 CGCCATGTTCATCCATCATTCC 60.031 50.000 0.00 0.00 0.00 3.01
3217 3497 9.476202 AGTTATTTTTGCTTCAGTGTTTATTCC 57.524 29.630 0.00 0.00 0.00 3.01
3219 3499 3.552604 TTGCTTCAGTGTTTATTCCGC 57.447 42.857 0.00 0.00 0.00 5.54
3220 3500 2.499197 TGCTTCAGTGTTTATTCCGCA 58.501 42.857 0.00 0.00 0.00 5.69
3221 3501 3.081061 TGCTTCAGTGTTTATTCCGCAT 58.919 40.909 0.00 0.00 0.00 4.73
3222 3502 3.126858 TGCTTCAGTGTTTATTCCGCATC 59.873 43.478 0.00 0.00 0.00 3.91
3223 3503 3.375299 GCTTCAGTGTTTATTCCGCATCT 59.625 43.478 0.00 0.00 0.00 2.90
3224 3504 4.728882 GCTTCAGTGTTTATTCCGCATCTG 60.729 45.833 0.00 0.00 0.00 2.90
3225 3505 4.200838 TCAGTGTTTATTCCGCATCTGA 57.799 40.909 0.00 0.00 0.00 3.27
3226 3506 4.769688 TCAGTGTTTATTCCGCATCTGAT 58.230 39.130 0.00 0.00 0.00 2.90
3227 3507 4.571984 TCAGTGTTTATTCCGCATCTGATG 59.428 41.667 13.26 13.26 0.00 3.07
3228 3508 3.879295 AGTGTTTATTCCGCATCTGATGG 59.121 43.478 18.60 9.02 0.00 3.51
3229 3509 3.627577 GTGTTTATTCCGCATCTGATGGT 59.372 43.478 18.60 0.00 0.00 3.55
3230 3510 4.096382 GTGTTTATTCCGCATCTGATGGTT 59.904 41.667 18.60 0.04 0.00 3.67
3231 3511 4.335315 TGTTTATTCCGCATCTGATGGTTC 59.665 41.667 18.60 2.12 0.00 3.62
3232 3512 2.715749 ATTCCGCATCTGATGGTTCA 57.284 45.000 18.60 0.00 0.00 3.18
3256 3536 8.188139 TCAGTACCTTTTCAAAGTCATTTTCAC 58.812 33.333 0.00 0.00 34.20 3.18
3325 3620 8.347004 TGAAGCAATCCACAAAATAGTCATTA 57.653 30.769 0.00 0.00 0.00 1.90
3348 3643 5.116084 TCACTCTAATTTTAGGCTGGCAT 57.884 39.130 3.38 0.00 0.00 4.40
3371 3666 2.233271 CACACTCCACTCTGCCAAAAT 58.767 47.619 0.00 0.00 0.00 1.82
3372 3667 3.181445 ACACACTCCACTCTGCCAAAATA 60.181 43.478 0.00 0.00 0.00 1.40
3373 3668 3.438087 CACACTCCACTCTGCCAAAATAG 59.562 47.826 0.00 0.00 0.00 1.73
3409 3718 3.655276 AGCAAATGCAGAAGTTCCAAG 57.345 42.857 8.28 0.00 45.16 3.61
3421 3730 6.813649 GCAGAAGTTCCAAGGATAAAAATTCC 59.186 38.462 0.00 0.00 0.00 3.01
3467 3776 3.139077 CTGAACCTGAAACGTTAAGCCT 58.861 45.455 0.00 0.00 0.00 4.58
3502 3814 5.043248 CACCTGATTGAACAAGTCCAAAAC 58.957 41.667 0.00 0.00 0.00 2.43
3504 3816 4.342092 CCTGATTGAACAAGTCCAAAACCT 59.658 41.667 0.00 0.00 0.00 3.50
3606 3919 3.942829 CCTGCAGAAGGTAGATGACAAA 58.057 45.455 17.39 0.00 41.74 2.83
3752 4065 1.963515 GCCAGTTCACCTTGGTGAATT 59.036 47.619 30.26 25.23 43.99 2.17
3784 4097 6.426328 CCAGTATGAAATGTATCAGCTCCTTC 59.574 42.308 0.00 0.00 39.69 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
330 336 2.445155 GGCCCCCTTCACCATTGT 59.555 61.111 0.00 0.00 0.00 2.71
547 625 1.896122 CGAAACCCTAACCCTCCGCT 61.896 60.000 0.00 0.00 0.00 5.52
548 626 1.449070 CGAAACCCTAACCCTCCGC 60.449 63.158 0.00 0.00 0.00 5.54
549 627 0.175073 CTCGAAACCCTAACCCTCCG 59.825 60.000 0.00 0.00 0.00 4.63
550 628 0.540454 CCTCGAAACCCTAACCCTCC 59.460 60.000 0.00 0.00 0.00 4.30
551 629 0.540454 CCCTCGAAACCCTAACCCTC 59.460 60.000 0.00 0.00 0.00 4.30
552 630 0.178882 ACCCTCGAAACCCTAACCCT 60.179 55.000 0.00 0.00 0.00 4.34
553 631 0.035725 CACCCTCGAAACCCTAACCC 60.036 60.000 0.00 0.00 0.00 4.11
556 634 0.604578 CGACACCCTCGAAACCCTAA 59.395 55.000 0.00 0.00 46.14 2.69
873 969 1.658686 AACGAACAAAACAGGCGGCA 61.659 50.000 13.08 0.00 0.00 5.69
904 1011 2.230940 CGCGCGACCCTATCTTGTG 61.231 63.158 28.94 0.00 0.00 3.33
1453 1624 0.332972 GACCTGAATTCCCAAGGGCT 59.667 55.000 13.35 0.00 34.68 5.19
1660 1878 2.190578 GAAGCCACGGGATCCCTG 59.809 66.667 28.42 22.68 35.68 4.45
1796 2018 1.510776 GAGCCATCTGAGCTGCATAC 58.489 55.000 1.02 0.00 41.75 2.39
1849 2071 1.328680 GCGTTGTCTGTCCAGCATATG 59.671 52.381 0.00 0.00 0.00 1.78
1953 2175 3.873952 AGAGATGAAACGAGCCATTAAGC 59.126 43.478 0.00 0.00 0.00 3.09
1955 2177 6.701841 GTGATAGAGATGAAACGAGCCATTAA 59.298 38.462 0.00 0.00 0.00 1.40
1956 2178 6.183360 TGTGATAGAGATGAAACGAGCCATTA 60.183 38.462 0.00 0.00 0.00 1.90
2040 2262 1.204146 AGTCATACTGTCCGGGCAAT 58.796 50.000 11.40 1.04 0.00 3.56
2070 2292 3.397613 GAATCCCTCAGCTGCGCCT 62.398 63.158 9.47 0.00 0.00 5.52
2267 2489 1.272147 ACAAAGATGGAGGGAAGCCAC 60.272 52.381 0.00 0.00 38.44 5.01
2305 2530 2.415697 ACAAAAATGGACTTTCCGCG 57.584 45.000 0.00 0.00 40.17 6.46
2310 2535 8.599774 CAACGAACATAAACAAAAATGGACTTT 58.400 29.630 0.00 0.00 0.00 2.66
2476 2712 2.094545 CCTACAATGCCTTTGCTGGAAC 60.095 50.000 0.00 0.00 39.03 3.62
2613 2849 6.336842 AGAATCAAAGCACATAAGCTGTTT 57.663 33.333 0.00 0.00 45.89 2.83
2644 2880 6.449698 CCTGATATGCAAAACTGAAAACAGT 58.550 36.000 0.00 0.00 36.92 3.55
2645 2881 5.346822 GCCTGATATGCAAAACTGAAAACAG 59.653 40.000 0.00 0.00 0.00 3.16
2647 2883 4.627035 GGCCTGATATGCAAAACTGAAAAC 59.373 41.667 0.00 0.00 0.00 2.43
2724 2960 5.122396 GTCCCTGCAGATGTGTTTTAGTTAG 59.878 44.000 17.39 0.00 0.00 2.34
2847 3104 5.615289 AGCACATAATGGATAGTTCCTGAC 58.385 41.667 0.00 0.00 43.07 3.51
2904 3161 4.537135 TCACCTCCTACAACATGTCTTC 57.463 45.455 0.00 0.00 0.00 2.87
2948 3205 9.128107 GCGTAAACATGCTTAATAATTGCATAT 57.872 29.630 0.00 0.00 44.39 1.78
2949 3206 8.131731 TGCGTAAACATGCTTAATAATTGCATA 58.868 29.630 0.00 0.00 44.39 3.14
2950 3207 6.977502 TGCGTAAACATGCTTAATAATTGCAT 59.022 30.769 0.00 0.00 46.74 3.96
2951 3208 6.325596 TGCGTAAACATGCTTAATAATTGCA 58.674 32.000 0.00 0.00 41.13 4.08
2952 3209 6.804534 TGCGTAAACATGCTTAATAATTGC 57.195 33.333 0.00 0.00 0.00 3.56
2953 3210 8.523464 GTCTTGCGTAAACATGCTTAATAATTG 58.477 33.333 0.00 0.00 0.00 2.32
2954 3211 8.240682 TGTCTTGCGTAAACATGCTTAATAATT 58.759 29.630 0.00 0.00 0.00 1.40
2955 3212 7.757526 TGTCTTGCGTAAACATGCTTAATAAT 58.242 30.769 0.00 0.00 0.00 1.28
2956 3213 7.135089 TGTCTTGCGTAAACATGCTTAATAA 57.865 32.000 0.00 0.00 0.00 1.40
2957 3214 6.729391 TGTCTTGCGTAAACATGCTTAATA 57.271 33.333 0.00 0.00 0.00 0.98
2958 3215 5.621197 TGTCTTGCGTAAACATGCTTAAT 57.379 34.783 0.00 0.00 0.00 1.40
2959 3216 5.180304 TCATGTCTTGCGTAAACATGCTTAA 59.820 36.000 23.30 12.39 46.25 1.85
2960 3217 4.693095 TCATGTCTTGCGTAAACATGCTTA 59.307 37.500 23.30 12.61 46.25 3.09
2961 3218 3.501828 TCATGTCTTGCGTAAACATGCTT 59.498 39.130 23.30 0.00 46.25 3.91
2962 3219 3.073678 TCATGTCTTGCGTAAACATGCT 58.926 40.909 23.30 3.56 46.25 3.79
2963 3220 3.469899 TCATGTCTTGCGTAAACATGC 57.530 42.857 23.30 2.65 46.25 4.06
2965 3222 5.627499 AACATCATGTCTTGCGTAAACAT 57.373 34.783 0.00 7.74 34.03 2.71
2966 3223 5.121611 CCTAACATCATGTCTTGCGTAAACA 59.878 40.000 0.00 4.41 0.00 2.83
2967 3224 5.560148 CCTAACATCATGTCTTGCGTAAAC 58.440 41.667 0.00 0.00 0.00 2.01
2968 3225 4.094294 GCCTAACATCATGTCTTGCGTAAA 59.906 41.667 0.00 0.00 0.00 2.01
2969 3226 3.621268 GCCTAACATCATGTCTTGCGTAA 59.379 43.478 0.00 0.00 0.00 3.18
2970 3227 3.194861 GCCTAACATCATGTCTTGCGTA 58.805 45.455 0.00 0.00 0.00 4.42
2971 3228 2.009774 GCCTAACATCATGTCTTGCGT 58.990 47.619 0.00 0.00 0.00 5.24
2972 3229 2.009051 TGCCTAACATCATGTCTTGCG 58.991 47.619 0.00 0.00 0.00 4.85
2973 3230 3.733077 GCTTGCCTAACATCATGTCTTGC 60.733 47.826 0.00 0.00 0.00 4.01
2974 3231 3.693085 AGCTTGCCTAACATCATGTCTTG 59.307 43.478 0.00 0.00 0.00 3.02
2975 3232 3.960571 AGCTTGCCTAACATCATGTCTT 58.039 40.909 0.00 0.00 0.00 3.01
2976 3233 3.641434 AGCTTGCCTAACATCATGTCT 57.359 42.857 0.00 0.00 0.00 3.41
2977 3234 5.818136 TTAAGCTTGCCTAACATCATGTC 57.182 39.130 9.86 0.00 0.00 3.06
2978 3235 6.780457 AATTAAGCTTGCCTAACATCATGT 57.220 33.333 9.86 0.00 0.00 3.21
2979 3236 7.546667 ACAAAATTAAGCTTGCCTAACATCATG 59.453 33.333 9.86 0.00 0.00 3.07
2980 3237 7.614494 ACAAAATTAAGCTTGCCTAACATCAT 58.386 30.769 9.86 0.00 0.00 2.45
2981 3238 6.991938 ACAAAATTAAGCTTGCCTAACATCA 58.008 32.000 9.86 0.00 0.00 3.07
2982 3239 6.251376 CGACAAAATTAAGCTTGCCTAACATC 59.749 38.462 9.86 0.00 0.00 3.06
2983 3240 6.072175 TCGACAAAATTAAGCTTGCCTAACAT 60.072 34.615 9.86 0.00 0.00 2.71
2984 3241 5.239744 TCGACAAAATTAAGCTTGCCTAACA 59.760 36.000 9.86 0.00 0.00 2.41
2985 3242 5.695818 TCGACAAAATTAAGCTTGCCTAAC 58.304 37.500 9.86 0.00 0.00 2.34
2986 3243 5.950758 TCGACAAAATTAAGCTTGCCTAA 57.049 34.783 9.86 0.00 0.00 2.69
2987 3244 5.472137 AGTTCGACAAAATTAAGCTTGCCTA 59.528 36.000 9.86 0.00 0.00 3.93
3033 3290 5.765677 TCATTCTCCCAACACACGATAAAAA 59.234 36.000 0.00 0.00 0.00 1.94
3034 3291 5.180492 GTCATTCTCCCAACACACGATAAAA 59.820 40.000 0.00 0.00 0.00 1.52
3035 3292 4.693566 GTCATTCTCCCAACACACGATAAA 59.306 41.667 0.00 0.00 0.00 1.40
3036 3293 4.250464 GTCATTCTCCCAACACACGATAA 58.750 43.478 0.00 0.00 0.00 1.75
3037 3294 3.259625 TGTCATTCTCCCAACACACGATA 59.740 43.478 0.00 0.00 0.00 2.92
3038 3295 2.038426 TGTCATTCTCCCAACACACGAT 59.962 45.455 0.00 0.00 0.00 3.73
3039 3296 1.414550 TGTCATTCTCCCAACACACGA 59.585 47.619 0.00 0.00 0.00 4.35
3072 3329 4.597079 CATGTGAACACACTACCACAAAC 58.403 43.478 9.83 0.00 45.05 2.93
3081 3338 0.473755 TCCAGGCATGTGAACACACT 59.526 50.000 9.83 0.71 45.05 3.55
3125 3382 0.950116 GAGCAGGGCACAGCATATTC 59.050 55.000 5.99 0.00 33.33 1.75
3138 3400 1.442526 GGATGAACATGGCGAGCAGG 61.443 60.000 0.00 0.00 0.00 4.85
3159 3421 2.093021 TGAACCATCAGATGCGGAATGA 60.093 45.455 4.68 0.00 0.00 2.57
3163 3425 1.485895 TCATGAACCATCAGATGCGGA 59.514 47.619 4.68 0.00 39.39 5.54
3164 3426 1.600957 GTCATGAACCATCAGATGCGG 59.399 52.381 4.68 0.00 39.39 5.69
3165 3427 2.287103 CAGTCATGAACCATCAGATGCG 59.713 50.000 4.68 1.39 39.39 4.73
3228 3508 8.926715 AAAATGACTTTGAAAAGGTACTGAAC 57.073 30.769 7.65 0.00 35.70 3.18
3229 3509 8.744652 TGAAAATGACTTTGAAAAGGTACTGAA 58.255 29.630 7.65 0.00 35.70 3.02
3230 3510 8.188139 GTGAAAATGACTTTGAAAAGGTACTGA 58.812 33.333 7.65 0.00 35.70 3.41
3231 3511 7.973388 TGTGAAAATGACTTTGAAAAGGTACTG 59.027 33.333 7.65 0.00 35.70 2.74
3232 3512 8.062065 TGTGAAAATGACTTTGAAAAGGTACT 57.938 30.769 7.65 0.00 35.70 2.73
3242 3522 5.756195 TCCTGACTGTGAAAATGACTTTG 57.244 39.130 0.00 0.00 0.00 2.77
3243 3523 6.736794 GCATTCCTGACTGTGAAAATGACTTT 60.737 38.462 6.32 0.00 0.00 2.66
3256 3536 7.762615 ACATTATCAAATTTGCATTCCTGACTG 59.237 33.333 13.54 2.99 0.00 3.51
3319 3614 8.778358 CCAGCCTAAAATTAGAGTGATAATGAC 58.222 37.037 1.75 0.00 32.47 3.06
3325 3620 5.116084 TGCCAGCCTAAAATTAGAGTGAT 57.884 39.130 1.75 0.00 32.47 3.06
3333 3628 4.772100 AGTGTGTTATGCCAGCCTAAAATT 59.228 37.500 0.00 0.00 0.00 1.82
3348 3643 1.419381 TGGCAGAGTGGAGTGTGTTA 58.581 50.000 0.00 0.00 0.00 2.41
3409 3718 6.496338 AGACTGTTCACGGAATTTTTATCC 57.504 37.500 0.00 0.00 0.00 2.59
3421 3730 6.991485 ATGCAAAATTTTAGACTGTTCACG 57.009 33.333 2.44 0.00 0.00 4.35
3467 3776 6.775142 TGTTCAATCAGGTGGTTGATTTCTAA 59.225 34.615 6.50 0.00 43.41 2.10
3502 3814 3.428534 GCAATTGTCGGTGCTTAAAAAGG 59.571 43.478 7.40 0.00 37.78 3.11
3504 3816 3.068873 AGGCAATTGTCGGTGCTTAAAAA 59.931 39.130 7.40 0.00 40.70 1.94
3586 3899 5.471456 ACTTTTTGTCATCTACCTTCTGCAG 59.529 40.000 7.63 7.63 0.00 4.41
3606 3919 5.828299 TTCTTTGGAACGTTCATGACTTT 57.172 34.783 28.24 0.00 0.00 2.66
3618 3931 8.730680 TGTAGATAGCTCAAAATTCTTTGGAAC 58.269 33.333 0.00 0.00 41.98 3.62
3752 4065 5.610557 TGATACATTTCATACTGGGGATGGA 59.389 40.000 0.00 0.00 0.00 3.41
3784 4097 3.444034 TCGACTCCATTACAGTGAGGAAG 59.556 47.826 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.