Multiple sequence alignment - TraesCS6D01G381000

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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 TraesCS6D01G381000 chr6D 100.000 4271 0 0 1 4271 461631479 461627209 0.000000e+00 7888
1 TraesCS6D01G381000 chr6D 86.885 305 22 11 2 290 420194261 420193959 4.120000e-85 326
2 TraesCS6D01G381000 chr6A 92.765 3483 147 42 821 4258 608359762 608356340 0.000000e+00 4939
3 TraesCS6D01G381000 chr6A 81.484 2533 325 71 955 3393 69348726 69351208 0.000000e+00 1947
4 TraesCS6D01G381000 chr6A 95.035 564 25 3 2 564 608361102 608360541 0.000000e+00 883
5 TraesCS6D01G381000 chr6A 87.900 281 15 7 553 824 608360323 608360053 3.210000e-81 313
6 TraesCS6D01G381000 chr6A 82.116 397 40 11 3876 4245 529572249 529571857 1.150000e-80 311
7 TraesCS6D01G381000 chr6A 80.285 421 57 17 3853 4248 202114480 202114061 1.160000e-75 294
8 TraesCS6D01G381000 chr6A 84.247 292 35 6 8 290 234088311 234088022 1.510000e-69 274
9 TraesCS6D01G381000 chr6B 83.126 2495 288 70 1077 3481 703562566 703560115 0.000000e+00 2152
10 TraesCS6D01G381000 chr6B 90.981 1519 101 19 2250 3761 703400837 703399348 0.000000e+00 2013
11 TraesCS6D01G381000 chr6B 80.516 2751 385 64 827 3481 703437686 703434991 0.000000e+00 1971
12 TraesCS6D01G381000 chr6B 91.323 1406 90 18 2249 3637 703448926 703447536 0.000000e+00 1892
13 TraesCS6D01G381000 chr6B 85.441 1202 130 22 2250 3410 703474530 703473333 0.000000e+00 1208
14 TraesCS6D01G381000 chr6B 84.087 1150 156 9 2247 3373 125611586 125612731 0.000000e+00 1085
15 TraesCS6D01G381000 chr6B 84.042 1153 150 17 2248 3373 125533264 125534409 0.000000e+00 1079
16 TraesCS6D01G381000 chr6B 84.615 1066 137 12 2249 3289 703502173 703501110 0.000000e+00 1035
17 TraesCS6D01G381000 chr6B 83.974 1067 144 12 2249 3289 703429567 703428502 0.000000e+00 998
18 TraesCS6D01G381000 chr6B 81.357 1282 161 47 918 2142 703450359 703449099 0.000000e+00 972
19 TraesCS6D01G381000 chr6B 81.900 1116 142 17 1097 2155 703402086 703400974 0.000000e+00 887
20 TraesCS6D01G381000 chr6B 81.574 1118 142 19 1097 2155 703475779 703474667 0.000000e+00 865
21 TraesCS6D01G381000 chr6B 79.984 1234 165 26 950 2142 125531921 125533113 0.000000e+00 835
22 TraesCS6D01G381000 chr6B 85.333 825 99 14 2249 3058 703509763 703508946 0.000000e+00 833
23 TraesCS6D01G381000 chr6B 80.563 1137 129 43 1077 2152 703503426 703502321 0.000000e+00 791
24 TraesCS6D01G381000 chr6B 87.163 631 51 17 1542 2142 703510512 703509882 0.000000e+00 689
25 TraesCS6D01G381000 chr6B 82.412 597 79 16 1077 1654 703430805 703430216 8.250000e-137 497
26 TraesCS6D01G381000 chr6B 78.481 711 119 18 957 1651 125604122 125604814 6.560000e-118 435
27 TraesCS6D01G381000 chr6B 81.190 420 65 7 2963 3373 125480751 125481165 4.120000e-85 326
28 TraesCS6D01G381000 chr6B 85.034 294 36 6 2 290 40438460 40438750 4.180000e-75 292
29 TraesCS6D01G381000 chr6B 80.055 361 37 20 3410 3762 703473159 703472826 7.140000e-58 235
30 TraesCS6D01G381000 chr7A 89.970 329 26 5 3932 4256 247210779 247210454 6.610000e-113 418
31 TraesCS6D01G381000 chr7A 87.387 111 12 2 1548 1657 666683233 666683124 4.480000e-25 126
32 TraesCS6D01G381000 chr5A 90.566 318 22 7 3932 4245 696281573 696281886 8.540000e-112 414
33 TraesCS6D01G381000 chr5A 88.571 105 10 2 3939 4042 695435122 695435019 4.480000e-25 126
34 TraesCS6D01G381000 chr7D 89.877 326 25 5 3932 4253 408463247 408462926 3.070000e-111 412
35 TraesCS6D01G381000 chr7D 88.991 327 30 5 3932 4253 492853820 492854145 2.390000e-107 399
36 TraesCS6D01G381000 chr3A 88.596 342 34 2 3932 4269 387303235 387303575 1.110000e-110 411
37 TraesCS6D01G381000 chr2B 88.563 341 34 4 3932 4269 637857409 637857747 3.980000e-110 409
38 TraesCS6D01G381000 chr3D 89.264 326 30 2 3932 4253 329293225 329293549 1.850000e-108 403
39 TraesCS6D01G381000 chr1A 87.427 342 38 2 3932 4269 226907178 226906838 5.180000e-104 388
40 TraesCS6D01G381000 chr1A 78.909 275 34 5 3853 4105 251225138 251225410 9.500000e-37 165
41 TraesCS6D01G381000 chr2A 84.953 319 42 5 3939 4253 430461301 430461617 6.890000e-83 318
42 TraesCS6D01G381000 chr2A 80.882 408 47 16 3853 4234 442457602 442457200 4.180000e-75 292
43 TraesCS6D01G381000 chr2A 78.205 312 42 12 3853 4140 25675111 25674802 4.390000e-40 176
44 TraesCS6D01G381000 chr3B 85.374 294 32 10 1 290 829092949 829093235 1.160000e-75 294
45 TraesCS6D01G381000 chr1D 86.667 270 23 10 29 290 489759007 489759271 1.940000e-73 287
46 TraesCS6D01G381000 chrUn 85.556 270 28 10 32 294 31678893 31678628 5.440000e-69 272
47 TraesCS6D01G381000 chr4D 84.014 294 31 9 1 292 486797712 486797991 7.040000e-68 268
48 TraesCS6D01G381000 chr5B 79.562 411 53 14 3865 4253 243904684 243904283 9.110000e-67 265
49 TraesCS6D01G381000 chr7B 85.171 263 28 10 2 260 161632634 161632889 4.240000e-65 259


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 TraesCS6D01G381000 chr6D 461627209 461631479 4270 True 7888.000000 7888 100.000000 1 4271 1 chr6D.!!$R2 4270
1 TraesCS6D01G381000 chr6A 608356340 608361102 4762 True 2045.000000 4939 91.900000 2 4258 3 chr6A.!!$R4 4256
2 TraesCS6D01G381000 chr6A 69348726 69351208 2482 False 1947.000000 1947 81.484000 955 3393 1 chr6A.!!$F1 2438
3 TraesCS6D01G381000 chr6B 703560115 703562566 2451 True 2152.000000 2152 83.126000 1077 3481 1 chr6B.!!$R2 2404
4 TraesCS6D01G381000 chr6B 703434991 703437686 2695 True 1971.000000 1971 80.516000 827 3481 1 chr6B.!!$R1 2654
5 TraesCS6D01G381000 chr6B 703399348 703402086 2738 True 1450.000000 2013 86.440500 1097 3761 2 chr6B.!!$R3 2664
6 TraesCS6D01G381000 chr6B 703447536 703450359 2823 True 1432.000000 1892 86.340000 918 3637 2 chr6B.!!$R5 2719
7 TraesCS6D01G381000 chr6B 125611586 125612731 1145 False 1085.000000 1085 84.087000 2247 3373 1 chr6B.!!$F4 1126
8 TraesCS6D01G381000 chr6B 125531921 125534409 2488 False 957.000000 1079 82.013000 950 3373 2 chr6B.!!$F5 2423
9 TraesCS6D01G381000 chr6B 703501110 703503426 2316 True 913.000000 1035 82.589000 1077 3289 2 chr6B.!!$R7 2212
10 TraesCS6D01G381000 chr6B 703472826 703475779 2953 True 769.333333 1208 82.356667 1097 3762 3 chr6B.!!$R6 2665
11 TraesCS6D01G381000 chr6B 703508946 703510512 1566 True 761.000000 833 86.248000 1542 3058 2 chr6B.!!$R8 1516
12 TraesCS6D01G381000 chr6B 703428502 703430805 2303 True 747.500000 998 83.193000 1077 3289 2 chr6B.!!$R4 2212
13 TraesCS6D01G381000 chr6B 125604122 125604814 692 False 435.000000 435 78.481000 957 1651 1 chr6B.!!$F3 694

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
646 877 0.252197 GTCCTGTACCATCCGGCTTT 59.748 55.0 0.0 0.0 34.57 3.51 F
648 879 0.463833 CCTGTACCATCCGGCTTTCC 60.464 60.0 0.0 0.0 34.57 3.13 F
2409 3128 0.394352 ATGGTTCCTGGCGACAATCC 60.394 55.0 0.0 0.0 42.06 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2801 0.033208 TTCCCCAGGGCAGCAATAAG 60.033 55.000 0.00 0.0 34.68 1.73 R
2622 3345 3.973206 TTGATTTGCCCTCTCTCGTAA 57.027 42.857 0.00 0.0 0.00 3.18 R
3651 4629 1.808945 CCACTTGTAGTACGTCGACCT 59.191 52.381 10.58 3.9 0.00 3.85 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
41 42 1.862827 CCCGATTCGGTTTTATCGTCC 59.137 52.381 22.83 0.00 46.80 4.79
48 50 3.919216 TCGGTTTTATCGTCCGGTTTTA 58.081 40.909 0.00 0.00 43.75 1.52
51 53 4.329528 CGGTTTTATCGTCCGGTTTTATCA 59.670 41.667 0.00 0.00 40.49 2.15
84 86 5.063438 AGTTCATCAAAACGTATCGACATGG 59.937 40.000 0.00 0.00 34.27 3.66
85 87 3.868661 TCATCAAAACGTATCGACATGGG 59.131 43.478 0.00 0.00 0.00 4.00
110 112 4.413087 TCTAGTTTTGAAGATCTCGACGC 58.587 43.478 0.00 0.00 0.00 5.19
148 150 0.454452 GCGGTTTGAGATTTGGACGC 60.454 55.000 0.00 0.00 38.94 5.19
196 198 7.298507 TGAATAAACGGATCTACGGAAAAAG 57.701 36.000 0.00 0.00 38.39 2.27
197 199 7.098477 TGAATAAACGGATCTACGGAAAAAGA 58.902 34.615 0.00 0.00 38.39 2.52
236 238 1.556591 GCGTGTGCATCAGTTGTCGA 61.557 55.000 0.00 0.00 42.15 4.20
243 245 1.197721 GCATCAGTTGTCGAAACCTGG 59.802 52.381 0.00 0.00 0.00 4.45
244 246 1.806542 CATCAGTTGTCGAAACCTGGG 59.193 52.381 0.00 0.00 0.00 4.45
250 252 1.961793 TGTCGAAACCTGGGAAGTTG 58.038 50.000 0.00 0.00 0.00 3.16
265 267 3.760684 GGAAGTTGGAGTGATCTTTGCAT 59.239 43.478 0.00 0.00 0.00 3.96
275 277 4.867047 AGTGATCTTTGCATCGAGTACTTG 59.133 41.667 3.44 3.44 0.00 3.16
283 285 4.733850 TGCATCGAGTACTTGTCAACTAG 58.266 43.478 10.00 0.00 0.00 2.57
330 332 4.785341 GCACGAAAATAAGGCCGTATCTTG 60.785 45.833 11.87 8.63 33.62 3.02
332 334 4.809426 ACGAAAATAAGGCCGTATCTTGAG 59.191 41.667 11.87 3.89 33.13 3.02
341 343 1.605712 CCGTATCTTGAGAATCGGGGC 60.606 57.143 14.85 0.00 39.14 5.80
346 348 0.820891 CTTGAGAATCGGGGCCCATG 60.821 60.000 26.86 16.26 38.61 3.66
576 807 1.220750 CTTCCTAGCCTCCCCCTCTTA 59.779 57.143 0.00 0.00 0.00 2.10
629 860 0.729816 GAGACTGACGCGTCAAGGTC 60.730 60.000 35.80 35.80 39.39 3.85
630 861 1.733399 GACTGACGCGTCAAGGTCC 60.733 63.158 38.11 22.86 39.39 4.46
631 862 2.143594 GACTGACGCGTCAAGGTCCT 62.144 60.000 38.11 18.53 39.39 3.85
634 865 1.174078 TGACGCGTCAAGGTCCTGTA 61.174 55.000 37.68 12.06 36.53 2.74
635 866 0.731855 GACGCGTCAAGGTCCTGTAC 60.732 60.000 33.09 1.78 0.00 2.90
644 875 3.630289 GTCCTGTACCATCCGGCT 58.370 61.111 0.00 0.00 34.57 5.52
645 876 1.905512 GTCCTGTACCATCCGGCTT 59.094 57.895 0.00 0.00 34.57 4.35
646 877 0.252197 GTCCTGTACCATCCGGCTTT 59.748 55.000 0.00 0.00 34.57 3.51
648 879 0.463833 CCTGTACCATCCGGCTTTCC 60.464 60.000 0.00 0.00 34.57 3.13
649 880 0.463833 CTGTACCATCCGGCTTTCCC 60.464 60.000 0.00 0.00 34.57 3.97
650 881 1.153025 GTACCATCCGGCTTTCCCC 60.153 63.158 0.00 0.00 34.57 4.81
651 882 2.380285 TACCATCCGGCTTTCCCCC 61.380 63.158 0.00 0.00 34.57 5.40
652 883 3.738481 CCATCCGGCTTTCCCCCA 61.738 66.667 0.00 0.00 0.00 4.96
653 884 2.603008 CATCCGGCTTTCCCCCAT 59.397 61.111 0.00 0.00 0.00 4.00
654 885 1.829533 CATCCGGCTTTCCCCCATG 60.830 63.158 0.00 0.00 0.00 3.66
655 886 2.316586 ATCCGGCTTTCCCCCATGT 61.317 57.895 0.00 0.00 0.00 3.21
656 887 2.284515 ATCCGGCTTTCCCCCATGTC 62.285 60.000 0.00 0.00 0.00 3.06
657 888 2.440247 CGGCTTTCCCCCATGTCC 60.440 66.667 0.00 0.00 0.00 4.02
658 889 2.770130 GGCTTTCCCCCATGTCCA 59.230 61.111 0.00 0.00 0.00 4.02
693 932 6.817140 GTGTTTAGACTCCCGATAACATTCTT 59.183 38.462 0.00 0.00 0.00 2.52
696 935 4.192317 AGACTCCCGATAACATTCTTTGC 58.808 43.478 0.00 0.00 0.00 3.68
707 946 1.913403 CATTCTTTGCGATCGTTTGGC 59.087 47.619 17.81 0.00 0.00 4.52
861 1396 1.880819 ATGCTTGGCTTTCCTTGGCG 61.881 55.000 0.00 0.00 0.00 5.69
885 1420 8.779561 GCGTCGCTGAATAATCAATAATTTATG 58.220 33.333 10.68 0.00 34.49 1.90
935 1471 0.466124 GGGTTGATCCTCCTTCTCGG 59.534 60.000 0.00 0.00 36.25 4.63
1033 1574 4.943705 TCTCAAATATGGACAAAGACTGCC 59.056 41.667 0.00 0.00 0.00 4.85
1042 1583 1.271597 ACAAAGACTGCCCCAGTGATC 60.272 52.381 2.12 0.00 45.44 2.92
1048 1589 2.435805 GACTGCCCCAGTGATCTATTGA 59.564 50.000 2.12 0.00 45.44 2.57
1059 1600 6.758886 CCAGTGATCTATTGAACTACTTCACC 59.241 42.308 0.00 0.00 36.06 4.02
1090 1631 2.169561 GGAGAAAGACTAAGAGGGCAGG 59.830 54.545 0.00 0.00 0.00 4.85
1224 1765 1.047596 TGGCTGCCACCACATTGTTT 61.048 50.000 19.30 0.00 33.75 2.83
1321 1904 4.032900 CCATAGTAGTGAAATGTCGTGCAC 59.967 45.833 6.82 6.82 0.00 4.57
1322 1905 3.106242 AGTAGTGAAATGTCGTGCACA 57.894 42.857 18.64 0.81 40.18 4.57
1772 2418 5.952347 ACAGAGTGAGAGGTGATATGTACAA 59.048 40.000 0.00 0.00 0.00 2.41
1775 2421 5.967088 AGTGAGAGGTGATATGTACAACAC 58.033 41.667 17.12 17.12 0.00 3.32
1923 2569 1.343821 GCTACGGTGTCGAATTGCG 59.656 57.895 0.00 0.00 40.11 4.85
1938 2584 6.476863 CGAATTGCGAAATACACAATTACC 57.523 37.500 0.00 0.00 42.45 2.85
2094 2740 8.636213 CCAATCATATATTCAAAGAGTTGGCTT 58.364 33.333 0.00 0.00 35.29 4.35
2155 2801 1.753073 ACTGCTTGCCAGCCATAATTC 59.247 47.619 7.41 0.00 46.74 2.17
2215 2909 2.064573 TGACTGTGATGTGTACTGCG 57.935 50.000 0.00 0.00 0.00 5.18
2236 2931 4.621886 GCGAGGGTATTTCTTATGACGATC 59.378 45.833 0.00 0.00 0.00 3.69
2241 2936 7.565680 AGGGTATTTCTTATGACGATCAAGTT 58.434 34.615 0.00 0.00 0.00 2.66
2409 3128 0.394352 ATGGTTCCTGGCGACAATCC 60.394 55.000 0.00 0.00 42.06 3.01
2622 3345 1.880027 GTCGGTGCATTGAGAAAAGGT 59.120 47.619 0.00 0.00 0.00 3.50
2724 3447 3.007635 GACATTTGGGGAAAGAGGTACG 58.992 50.000 0.00 0.00 0.00 3.67
2977 3741 5.707242 TTCGATGTCTGAAGTTGAGTACT 57.293 39.130 0.00 0.00 39.32 2.73
3090 3866 3.130160 GAGGCAGCTTGGAAGGCG 61.130 66.667 0.00 0.00 34.52 5.52
3111 3887 2.251371 GCTGCGTTTTGGTCGGAC 59.749 61.111 0.00 0.00 0.00 4.79
3504 4482 3.187842 GCCCGTTAGTTTGTTTCTACTGG 59.812 47.826 0.00 0.00 0.00 4.00
3505 4483 3.187842 CCCGTTAGTTTGTTTCTACTGGC 59.812 47.826 0.00 0.00 0.00 4.85
3506 4484 3.810941 CCGTTAGTTTGTTTCTACTGGCA 59.189 43.478 0.00 0.00 0.00 4.92
3507 4485 4.454504 CCGTTAGTTTGTTTCTACTGGCAT 59.545 41.667 0.00 0.00 0.00 4.40
3608 4586 2.295349 TCAGTTAGACGTGGAACAGACC 59.705 50.000 10.80 0.00 41.80 3.85
3651 4629 3.882888 CTGGTTCCAGTTGAAAAGTAGCA 59.117 43.478 10.40 0.00 33.94 3.49
3755 4736 2.000447 AGCCTTCGCTTAAGCTAAACG 59.000 47.619 24.33 13.35 45.55 3.60
3882 4863 4.502016 TCTGTATATAGTCTAGGGTCGCG 58.498 47.826 0.00 0.00 0.00 5.87
3893 4874 1.299926 GGGTCGCGCTATTCGTCAT 60.300 57.895 5.56 0.00 41.07 3.06
3895 4876 1.276145 GGTCGCGCTATTCGTCATCC 61.276 60.000 5.56 0.00 41.07 3.51
3899 4880 0.032130 GCGCTATTCGTCATCCTGGA 59.968 55.000 0.00 0.00 41.07 3.86
3915 4896 7.500992 TCATCCTGGATGAGTAACAGTTATTC 58.499 38.462 30.63 8.55 43.11 1.75
3937 4940 8.846423 ATTCTTCACTCCCTCTCTATTTTAGA 57.154 34.615 0.00 0.00 0.00 2.10
4098 5103 8.472007 TCTGGTTTTATGACCTATTTTTGTGT 57.528 30.769 0.00 0.00 40.47 3.72
4155 5164 9.619316 TGAATGAAACTATTTGTATTCCAAACG 57.381 29.630 0.00 0.00 45.43 3.60
4159 5168 8.085296 TGAAACTATTTGTATTCCAAACGCAAT 58.915 29.630 0.00 0.00 45.43 3.56
4203 5212 9.315525 GTAAGATTACCTCAGGTGAAGAATAAC 57.684 37.037 6.61 0.00 36.19 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 86 5.980715 GTCGAGATCTTCAAAACTAGATCCC 59.019 44.000 0.00 0.00 38.24 3.85
85 87 5.683743 CGTCGAGATCTTCAAAACTAGATCC 59.316 44.000 0.00 1.33 38.24 3.36
110 112 1.128692 GCTTTCACCGTTGGATTCTCG 59.871 52.381 0.00 0.00 0.00 4.04
148 150 4.985044 ACGTTTTATCTCTCAAACCGTG 57.015 40.909 0.00 0.00 30.37 4.94
168 170 6.651755 TCCGTAGATCCGTTTATTCAAAAC 57.348 37.500 0.00 0.00 0.00 2.43
181 183 7.062906 GAGTTTTCTCTTTTTCCGTAGATCC 57.937 40.000 0.00 0.00 43.12 3.36
197 199 2.029844 GCGCGCCTGAGAGTTTTCT 61.030 57.895 23.24 0.00 36.01 2.52
219 221 2.602217 GGTTTCGACAACTGATGCACAC 60.602 50.000 0.00 0.00 0.00 3.82
226 228 1.124780 TCCCAGGTTTCGACAACTGA 58.875 50.000 18.11 0.00 32.86 3.41
236 238 1.850345 TCACTCCAACTTCCCAGGTTT 59.150 47.619 0.00 0.00 0.00 3.27
243 245 3.149196 TGCAAAGATCACTCCAACTTCC 58.851 45.455 0.00 0.00 0.00 3.46
244 246 4.436584 CGATGCAAAGATCACTCCAACTTC 60.437 45.833 0.00 0.00 0.00 3.01
250 252 2.898705 ACTCGATGCAAAGATCACTCC 58.101 47.619 0.00 0.00 0.00 3.85
265 267 6.570672 AATCACTAGTTGACAAGTACTCGA 57.429 37.500 0.00 0.00 36.92 4.04
275 277 7.606456 TCAGTTATCCCAAAATCACTAGTTGAC 59.394 37.037 0.00 0.00 36.92 3.18
283 285 4.702131 ACAGCTCAGTTATCCCAAAATCAC 59.298 41.667 0.00 0.00 0.00 3.06
330 332 2.595754 GCATGGGCCCCGATTCTC 60.596 66.667 22.27 0.00 0.00 2.87
576 807 5.009410 GCATTGGCATTGCTAGTAAGATTCT 59.991 40.000 23.17 0.00 40.72 2.40
617 848 1.288127 GTACAGGACCTTGACGCGT 59.712 57.895 13.85 13.85 0.00 6.01
629 860 3.794189 GGGAAAGCCGGATGGTACAGG 62.794 61.905 5.05 0.00 36.91 4.00
630 861 0.463833 GGGAAAGCCGGATGGTACAG 60.464 60.000 5.05 0.00 36.91 2.74
631 862 1.605453 GGGAAAGCCGGATGGTACA 59.395 57.895 5.05 0.00 37.81 2.90
634 865 3.739613 GGGGGAAAGCCGGATGGT 61.740 66.667 5.05 0.00 37.67 3.55
635 866 3.073599 ATGGGGGAAAGCCGGATGG 62.074 63.158 5.05 0.00 38.77 3.51
636 867 1.829533 CATGGGGGAAAGCCGGATG 60.830 63.158 5.05 0.00 33.83 3.51
637 868 2.284515 GACATGGGGGAAAGCCGGAT 62.285 60.000 5.05 0.00 33.83 4.18
638 869 2.938798 ACATGGGGGAAAGCCGGA 60.939 61.111 5.05 0.00 33.83 5.14
639 870 2.440247 GACATGGGGGAAAGCCGG 60.440 66.667 0.00 0.00 33.83 6.13
640 871 2.440247 GGACATGGGGGAAAGCCG 60.440 66.667 0.00 0.00 33.83 5.52
642 873 0.324645 ACATGGACATGGGGGAAAGC 60.325 55.000 15.94 0.00 42.91 3.51
644 875 3.687847 CACATGGACATGGGGGAAA 57.312 52.632 15.94 0.00 42.91 3.13
649 880 0.896923 CCAAACCACATGGACATGGG 59.103 55.000 15.94 12.01 42.91 4.00
650 881 1.273048 CACCAAACCACATGGACATGG 59.727 52.381 15.94 11.54 42.91 3.66
651 882 1.962807 ACACCAAACCACATGGACATG 59.037 47.619 10.57 10.57 40.56 3.21
652 883 2.380064 ACACCAAACCACATGGACAT 57.620 45.000 4.53 0.00 40.56 3.06
653 884 2.151502 AACACCAAACCACATGGACA 57.848 45.000 4.53 0.00 40.56 4.02
654 885 3.886505 TCTAAACACCAAACCACATGGAC 59.113 43.478 4.53 0.00 40.56 4.02
655 886 3.886505 GTCTAAACACCAAACCACATGGA 59.113 43.478 4.53 0.00 40.56 3.41
656 887 3.888930 AGTCTAAACACCAAACCACATGG 59.111 43.478 0.00 0.00 43.84 3.66
657 888 4.023193 GGAGTCTAAACACCAAACCACATG 60.023 45.833 0.00 0.00 36.27 3.21
658 889 4.142038 GGAGTCTAAACACCAAACCACAT 58.858 43.478 0.00 0.00 36.27 3.21
693 932 1.169661 ACCAAGCCAAACGATCGCAA 61.170 50.000 16.60 0.00 0.00 4.85
696 935 1.724654 CGAAACCAAGCCAAACGATCG 60.725 52.381 14.88 14.88 0.00 3.69
707 946 1.272212 CCCATTCCCAACGAAACCAAG 59.728 52.381 0.00 0.00 33.08 3.61
772 1011 1.019278 ATTGGCTTACACACGCTCCG 61.019 55.000 0.00 0.00 0.00 4.63
885 1420 3.365297 CATCGATTGATGCGCATAGAC 57.635 47.619 25.40 12.02 45.06 2.59
907 1442 2.513897 GATCAACCCCCGGCTTCG 60.514 66.667 0.00 0.00 0.00 3.79
910 1445 3.090532 GAGGATCAACCCCCGGCT 61.091 66.667 0.00 0.00 40.05 5.52
935 1471 5.695363 AGTACGAGGTTGCTAAGACTTTTTC 59.305 40.000 0.00 0.00 0.00 2.29
1033 1574 6.758886 GTGAAGTAGTTCAATAGATCACTGGG 59.241 42.308 14.56 0.00 44.44 4.45
1059 1600 7.363443 CCTCTTAGTCTTTCTCCTACCTTCTTG 60.363 44.444 0.00 0.00 0.00 3.02
1073 1614 4.455070 AAAACCTGCCCTCTTAGTCTTT 57.545 40.909 0.00 0.00 0.00 2.52
1090 1631 6.024049 CCATAAGAGCATTGACTCGAAAAAC 58.976 40.000 0.00 0.00 41.77 2.43
1224 1765 6.100279 AGACAATATAAGAGACAATGGGCAGA 59.900 38.462 0.00 0.00 0.00 4.26
1293 1846 5.163540 ACGACATTTCACTACTATGGTCTCC 60.164 44.000 0.00 0.00 0.00 3.71
1298 1881 4.032900 GTGCACGACATTTCACTACTATGG 59.967 45.833 0.00 0.00 0.00 2.74
1321 1904 5.391310 GGACAAAGATGATGTGTAGTGCTTG 60.391 44.000 0.00 0.00 0.00 4.01
1322 1905 4.697352 GGACAAAGATGATGTGTAGTGCTT 59.303 41.667 0.00 0.00 0.00 3.91
1327 1910 9.212641 CCATATAAGGACAAAGATGATGTGTAG 57.787 37.037 0.00 0.00 0.00 2.74
1513 2105 7.171678 CGGTCCAAGAAGAAATAATATCACCTC 59.828 40.741 0.00 0.00 0.00 3.85
1772 2418 5.016831 TGTACATATCACCTCTCACTGTGT 58.983 41.667 7.79 0.00 34.14 3.72
1775 2421 5.965922 TGTTGTACATATCACCTCTCACTG 58.034 41.667 0.00 0.00 0.00 3.66
1923 2569 5.413523 ACCAACCTCGGTAATTGTGTATTTC 59.586 40.000 0.00 0.00 37.57 2.17
1938 2584 1.812571 CCCTTGATGAAACCAACCTCG 59.187 52.381 0.00 0.00 0.00 4.63
2094 2740 0.534873 TGAATCCGCTCACGATTGGA 59.465 50.000 0.00 0.00 43.93 3.53
2155 2801 0.033208 TTCCCCAGGGCAGCAATAAG 60.033 55.000 0.00 0.00 34.68 1.73
2215 2909 7.210873 ACTTGATCGTCATAAGAAATACCCTC 58.789 38.462 0.00 0.00 0.00 4.30
2622 3345 3.973206 TTGATTTGCCCTCTCTCGTAA 57.027 42.857 0.00 0.00 0.00 3.18
2724 3447 2.029649 ACACACAAGCATGATTTCAGCC 60.030 45.455 0.00 0.00 0.00 4.85
2977 3741 2.553028 GCAACTGAATCAACCTCCTCCA 60.553 50.000 0.00 0.00 0.00 3.86
3090 3866 2.127232 GACCAAAACGCAGCGAGC 60.127 61.111 24.65 0.00 40.87 5.03
3111 3887 2.036346 TGGAGCGACATACAGGATCATG 59.964 50.000 5.68 5.68 0.00 3.07
3608 4586 2.692041 GGCAAAGATTGATCTGGGGAAG 59.308 50.000 0.00 0.00 37.19 3.46
3651 4629 1.808945 CCACTTGTAGTACGTCGACCT 59.191 52.381 10.58 3.90 0.00 3.85
3806 4787 9.349713 TCACTTATTTTGTTTTGGATGTAGTCT 57.650 29.630 0.00 0.00 0.00 3.24
3827 4808 8.108551 AGACGTACTTTAGTGTAGATTCACTT 57.891 34.615 4.72 0.00 44.92 3.16
3858 4839 6.279123 CGCGACCCTAGACTATATACAGATA 58.721 44.000 0.00 0.00 0.00 1.98
3868 4849 2.149578 GAATAGCGCGACCCTAGACTA 58.850 52.381 12.10 0.00 0.00 2.59
3882 4863 3.006323 ACTCATCCAGGATGACGAATAGC 59.994 47.826 26.17 0.00 43.11 2.97
3893 4874 7.180229 TGAAGAATAACTGTTACTCATCCAGGA 59.820 37.037 11.11 0.00 0.00 3.86
3895 4876 8.037758 AGTGAAGAATAACTGTTACTCATCCAG 58.962 37.037 11.11 0.00 0.00 3.86
3899 4880 7.181125 AGGGAGTGAAGAATAACTGTTACTCAT 59.819 37.037 11.11 0.00 36.38 2.90
3903 4884 6.937392 AGAGGGAGTGAAGAATAACTGTTAC 58.063 40.000 1.73 0.00 0.00 2.50
3904 4885 6.954684 AGAGAGGGAGTGAAGAATAACTGTTA 59.045 38.462 2.26 2.26 0.00 2.41
3907 4888 5.930837 AGAGAGGGAGTGAAGAATAACTG 57.069 43.478 0.00 0.00 0.00 3.16
3915 4896 9.541143 GAAATCTAAAATAGAGAGGGAGTGAAG 57.459 37.037 0.00 0.00 38.38 3.02
4176 5185 7.741554 ATTCTTCACCTGAGGTAATCTTACT 57.258 36.000 2.59 0.00 32.11 2.24


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

AutoCloner maintained by Alex Coulton.