Multiple sequence alignment - TraesCS4D01G189500

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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 TraesCS4D01G189500 chr4D 100.000 3356 0 0 1 3356 329132553 329135908 0.000000e+00 6198.0
1 TraesCS4D01G189500 chr4A 93.518 3363 95 45 81 3356 140984433 140981107 0.000000e+00 4889.0
2 TraesCS4D01G189500 chr4B 90.764 3205 157 58 236 3356 408974960 408978109 0.000000e+00 4150.0
3 TraesCS4D01G189500 chr4B 88.950 181 15 3 75 254 408974103 408974279 5.640000e-53 219.0
4 TraesCS4D01G189500 chr4B 91.379 58 2 2 1 55 180671201 180671144 3.590000e-10 76.8
5 TraesCS4D01G189500 chr1B 95.661 2028 58 16 335 2352 135827746 135825739 0.000000e+00 3230.0
6 TraesCS4D01G189500 chr1B 88.166 769 54 17 2611 3356 135819487 135818733 0.000000e+00 881.0
7 TraesCS4D01G189500 chr1B 92.941 255 16 2 81 334 135828060 135827807 1.470000e-98 370.0
8 TraesCS4D01G189500 chr1B 96.396 222 6 1 2350 2569 135825578 135825357 6.840000e-97 364.0
9 TraesCS4D01G189500 chr1B 100.000 45 0 0 1 45 314566594 314566638 2.150000e-12 84.2
10 TraesCS4D01G189500 chr1A 93.284 670 24 2 2687 3356 586341737 586342385 0.000000e+00 968.0
11 TraesCS4D01G189500 chr1A 86.257 684 43 13 2677 3356 587486338 587486974 0.000000e+00 695.0
12 TraesCS4D01G189500 chr5A 86.676 683 40 13 2677 3356 637292723 637292089 0.000000e+00 710.0
13 TraesCS4D01G189500 chr3A 86.423 685 42 17 2677 3356 55174354 55173716 0.000000e+00 702.0
14 TraesCS4D01G189500 chr7A 86.257 684 40 15 2677 3356 168660419 168659786 0.000000e+00 693.0
15 TraesCS4D01G189500 chr7A 97.872 47 1 0 1 47 20400164 20400118 7.720000e-12 82.4
16 TraesCS4D01G189500 chr6A 85.044 682 47 18 2677 3356 265618508 265617880 0.000000e+00 643.0
17 TraesCS4D01G189500 chr2D 93.917 411 7 3 1 393 407120141 407119731 3.700000e-169 604.0
18 TraesCS4D01G189500 chr2D 91.071 56 3 2 1 55 430723750 430723696 1.290000e-09 75.0
19 TraesCS4D01G189500 chr2D 92.453 53 2 2 1 52 439417418 439417469 1.290000e-09 75.0
20 TraesCS4D01G189500 chr5D 82.297 209 17 10 2475 2664 69952041 69952248 2.680000e-36 163.0
21 TraesCS4D01G189500 chr5D 100.000 31 0 0 1095 1125 218261284 218261254 1.300000e-04 58.4
22 TraesCS4D01G189500 chr7B 92.857 56 2 1 1 54 600579096 600579151 2.780000e-11 80.5
23 TraesCS4D01G189500 chr2B 95.745 47 2 0 1 47 652619007 652619053 3.590000e-10 76.8
24 TraesCS4D01G189500 chr5B 89.831 59 4 2 1 59 221844447 221844503 1.290000e-09 75.0


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 TraesCS4D01G189500 chr4D 329132553 329135908 3355 False 6198.000000 6198 100.000000 1 3356 1 chr4D.!!$F1 3355
1 TraesCS4D01G189500 chr4A 140981107 140984433 3326 True 4889.000000 4889 93.518000 81 3356 1 chr4A.!!$R1 3275
2 TraesCS4D01G189500 chr4B 408974103 408978109 4006 False 2184.500000 4150 89.857000 75 3356 2 chr4B.!!$F1 3281
3 TraesCS4D01G189500 chr1B 135825357 135828060 2703 True 1321.333333 3230 94.999333 81 2569 3 chr1B.!!$R2 2488
4 TraesCS4D01G189500 chr1B 135818733 135819487 754 True 881.000000 881 88.166000 2611 3356 1 chr1B.!!$R1 745
5 TraesCS4D01G189500 chr1A 586341737 586342385 648 False 968.000000 968 93.284000 2687 3356 1 chr1A.!!$F1 669
6 TraesCS4D01G189500 chr1A 587486338 587486974 636 False 695.000000 695 86.257000 2677 3356 1 chr1A.!!$F2 679
7 TraesCS4D01G189500 chr5A 637292089 637292723 634 True 710.000000 710 86.676000 2677 3356 1 chr5A.!!$R1 679
8 TraesCS4D01G189500 chr3A 55173716 55174354 638 True 702.000000 702 86.423000 2677 3356 1 chr3A.!!$R1 679
9 TraesCS4D01G189500 chr7A 168659786 168660419 633 True 693.000000 693 86.257000 2677 3356 1 chr7A.!!$R2 679
10 TraesCS4D01G189500 chr6A 265617880 265618508 628 True 643.000000 643 85.044000 2677 3356 1 chr6A.!!$R1 679

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
410 1179 0.099259 CGCACCCATACGAGTACGAA 59.901 55.0 0.0 0.0 42.66 3.85 F
433 1202 0.252789 TTAACCCCTGACCCATCCGA 60.253 55.0 0.0 0.0 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2818 1.221566 CACCATGGCCGACTGATCA 59.778 57.895 13.04 0.0 0.00 2.92 R
2641 3712 4.436523 GTGAAATGTACACTTGCGACAAAC 59.563 41.667 0.00 0.0 35.66 2.93 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
26 27 9.546428 AGACAAATTTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.39 4.12
27 28 9.541143 GACAAATTTAAGACAAGAATTTTGGGA 57.459 29.630 0.00 0.00 33.39 4.37
28 29 9.325198 ACAAATTTAAGACAAGAATTTTGGGAC 57.675 29.630 0.00 0.00 33.39 4.46
29 30 8.487176 CAAATTTAAGACAAGAATTTTGGGACG 58.513 33.333 0.00 0.00 32.35 4.79
30 31 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
31 32 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
32 33 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
33 34 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
34 35 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
35 36 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
36 37 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
37 38 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
38 39 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
39 40 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
40 41 0.178926 TTTGGGACGGAGGGAGTACA 60.179 55.000 0.00 0.00 0.00 2.90
41 42 0.178926 TTGGGACGGAGGGAGTACAA 60.179 55.000 0.00 0.00 0.00 2.41
42 43 0.901580 TGGGACGGAGGGAGTACAAC 60.902 60.000 0.00 0.00 0.00 3.32
43 44 0.614134 GGGACGGAGGGAGTACAACT 60.614 60.000 0.00 0.00 0.00 3.16
44 45 1.264295 GGACGGAGGGAGTACAACTT 58.736 55.000 0.00 0.00 0.00 2.66
45 46 2.450476 GGACGGAGGGAGTACAACTTA 58.550 52.381 0.00 0.00 0.00 2.24
46 47 3.029570 GGACGGAGGGAGTACAACTTAT 58.970 50.000 0.00 0.00 0.00 1.73
47 48 4.210331 GGACGGAGGGAGTACAACTTATA 58.790 47.826 0.00 0.00 0.00 0.98
48 49 4.831710 GGACGGAGGGAGTACAACTTATAT 59.168 45.833 0.00 0.00 0.00 0.86
49 50 5.303845 GGACGGAGGGAGTACAACTTATATT 59.696 44.000 0.00 0.00 0.00 1.28
50 51 6.183360 GGACGGAGGGAGTACAACTTATATTT 60.183 42.308 0.00 0.00 0.00 1.40
51 52 7.191593 ACGGAGGGAGTACAACTTATATTTT 57.808 36.000 0.00 0.00 0.00 1.82
52 53 7.046033 ACGGAGGGAGTACAACTTATATTTTG 58.954 38.462 0.00 0.00 0.00 2.44
53 54 7.046033 CGGAGGGAGTACAACTTATATTTTGT 58.954 38.462 0.00 5.17 39.31 2.83
54 55 7.551617 CGGAGGGAGTACAACTTATATTTTGTT 59.448 37.037 0.00 0.00 37.19 2.83
55 56 9.895138 GGAGGGAGTACAACTTATATTTTGTTA 57.105 33.333 0.00 0.00 37.19 2.41
78 79 5.917541 GTGAAATACACGGTTGAAGAAGA 57.082 39.130 0.00 0.00 39.78 2.87
79 80 6.295039 GTGAAATACACGGTTGAAGAAGAA 57.705 37.500 0.00 0.00 39.78 2.52
112 113 3.321111 CCAGGACGGTAGTAGCATGTTAT 59.679 47.826 0.00 0.00 0.00 1.89
247 249 3.494626 ACATCAAGTCTAACGTTGCAGTG 59.505 43.478 11.99 2.90 0.00 3.66
267 967 7.229306 TGCAGTGGATATGGAATTTTTAGCTAG 59.771 37.037 0.00 0.00 0.00 3.42
268 968 7.308830 GCAGTGGATATGGAATTTTTAGCTAGG 60.309 40.741 0.00 0.00 0.00 3.02
372 1135 2.656069 GGTTACCCGCAGAGCCAGA 61.656 63.158 0.00 0.00 0.00 3.86
403 1172 3.829044 CCGGTCGCACCCATACGA 61.829 66.667 0.00 0.00 33.75 3.43
404 1173 2.278596 CGGTCGCACCCATACGAG 60.279 66.667 0.00 0.00 39.30 4.18
405 1174 2.890371 GGTCGCACCCATACGAGT 59.110 61.111 0.00 0.00 39.30 4.18
407 1176 0.248784 GGTCGCACCCATACGAGTAC 60.249 60.000 0.00 0.00 39.30 2.73
409 1178 0.744057 TCGCACCCATACGAGTACGA 60.744 55.000 0.00 0.00 42.66 3.43
410 1179 0.099259 CGCACCCATACGAGTACGAA 59.901 55.000 0.00 0.00 42.66 3.85
412 1181 1.818850 CACCCATACGAGTACGAACG 58.181 55.000 0.00 8.16 42.66 3.95
414 1183 2.032550 CACCCATACGAGTACGAACGAT 59.967 50.000 14.59 4.26 42.66 3.73
415 1184 2.684881 ACCCATACGAGTACGAACGATT 59.315 45.455 14.59 2.16 42.66 3.34
417 1186 4.335315 ACCCATACGAGTACGAACGATTAA 59.665 41.667 14.59 0.00 42.66 1.40
418 1187 4.672413 CCCATACGAGTACGAACGATTAAC 59.328 45.833 14.59 0.00 42.66 2.01
419 1188 4.672413 CCATACGAGTACGAACGATTAACC 59.328 45.833 14.59 0.00 42.66 2.85
420 1189 3.136808 ACGAGTACGAACGATTAACCC 57.863 47.619 14.59 0.00 42.66 4.11
421 1190 2.159379 ACGAGTACGAACGATTAACCCC 60.159 50.000 14.59 0.00 42.66 4.95
422 1191 2.098117 CGAGTACGAACGATTAACCCCT 59.902 50.000 0.14 0.00 42.66 4.79
423 1192 3.442100 GAGTACGAACGATTAACCCCTG 58.558 50.000 0.14 0.00 0.00 4.45
424 1193 3.091545 AGTACGAACGATTAACCCCTGA 58.908 45.455 0.14 0.00 0.00 3.86
425 1194 2.375173 ACGAACGATTAACCCCTGAC 57.625 50.000 0.14 0.00 0.00 3.51
426 1195 1.066645 ACGAACGATTAACCCCTGACC 60.067 52.381 0.14 0.00 0.00 4.02
427 1196 1.741394 CGAACGATTAACCCCTGACCC 60.741 57.143 0.00 0.00 0.00 4.46
429 1198 1.591768 ACGATTAACCCCTGACCCAT 58.408 50.000 0.00 0.00 0.00 4.00
430 1199 1.489230 ACGATTAACCCCTGACCCATC 59.511 52.381 0.00 0.00 0.00 3.51
431 1200 1.202770 CGATTAACCCCTGACCCATCC 60.203 57.143 0.00 0.00 0.00 3.51
432 1201 0.843984 ATTAACCCCTGACCCATCCG 59.156 55.000 0.00 0.00 0.00 4.18
433 1202 0.252789 TTAACCCCTGACCCATCCGA 60.253 55.000 0.00 0.00 0.00 4.55
434 1203 0.689745 TAACCCCTGACCCATCCGAG 60.690 60.000 0.00 0.00 0.00 4.63
435 1204 3.866582 CCCCTGACCCATCCGAGC 61.867 72.222 0.00 0.00 0.00 5.03
437 1206 3.866582 CCTGACCCATCCGAGCCC 61.867 72.222 0.00 0.00 0.00 5.19
438 1207 3.083349 CTGACCCATCCGAGCCCA 61.083 66.667 0.00 0.00 0.00 5.36
439 1208 3.391665 CTGACCCATCCGAGCCCAC 62.392 68.421 0.00 0.00 0.00 4.61
440 1209 3.083997 GACCCATCCGAGCCCACT 61.084 66.667 0.00 0.00 0.00 4.00
442 1211 3.083349 CCCATCCGAGCCCACTGA 61.083 66.667 0.00 0.00 0.00 3.41
451 1250 1.515521 GAGCCCACTGAAACAACGGG 61.516 60.000 0.00 0.00 40.11 5.28
524 1346 3.444703 TCAAATCAAACCAACCAACGG 57.555 42.857 0.00 0.00 0.00 4.44
978 1854 1.458064 TGTTTTCGTTCGATTCGGCTC 59.542 47.619 6.18 0.00 0.00 4.70
981 1857 3.617538 CGTTCGATTCGGCTCGGC 61.618 66.667 6.18 0.00 39.13 5.54
1515 2401 5.047566 TCCTCAAGTCCATCAAGAACAAA 57.952 39.130 0.00 0.00 0.00 2.83
1932 2818 1.745489 GCCGGTCTTTGAAGCCGAT 60.745 57.895 20.42 0.00 43.53 4.18
2641 3712 5.988092 TCGGTAAAACAGTTACCATTTTCG 58.012 37.500 14.04 1.48 43.48 3.46
2684 3755 9.927668 ATTTCACTTCCCTAAATGTTATTGTTG 57.072 29.630 0.00 0.00 0.00 3.33
2906 3999 6.942005 AGCACTTAATATGGCTGCAATACATA 59.058 34.615 0.00 6.99 34.83 2.29
2931 4025 8.965986 AAGTTTTTGTGTAGTTTGAAGTTCTC 57.034 30.769 4.17 0.00 0.00 2.87
2979 4074 4.098155 TGTTAGTGCTGGGTGGTCTATAA 58.902 43.478 0.00 0.00 0.00 0.98
2993 4088 7.389053 GGGTGGTCTATAAATCAGTGATGATTC 59.611 40.741 6.34 0.00 37.52 2.52
3308 4442 5.184864 CCATAACTTTTGGCTCCATGTGTTA 59.815 40.000 0.00 9.07 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.546428 CCCAAAATTCTTGTCTTAAATTTGTCT 57.454 29.630 0.00 0.00 33.95 3.41
1 2 9.541143 TCCCAAAATTCTTGTCTTAAATTTGTC 57.459 29.630 0.00 0.00 33.95 3.18
3 4 8.487176 CGTCCCAAAATTCTTGTCTTAAATTTG 58.513 33.333 0.00 0.00 33.95 2.32
4 5 7.655732 CCGTCCCAAAATTCTTGTCTTAAATTT 59.344 33.333 0.00 0.00 34.86 1.82
5 6 7.014808 TCCGTCCCAAAATTCTTGTCTTAAATT 59.985 33.333 0.00 0.00 0.00 1.82
6 7 6.492087 TCCGTCCCAAAATTCTTGTCTTAAAT 59.508 34.615 0.00 0.00 0.00 1.40
7 8 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
8 9 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
9 10 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
10 11 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
11 12 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
12 13 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
13 14 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
14 15 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
15 16 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
16 17 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
17 18 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
18 19 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
19 20 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
20 21 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
21 22 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
22 23 0.178926 TTGTACTCCCTCCGTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
23 24 0.901580 GTTGTACTCCCTCCGTCCCA 60.902 60.000 0.00 0.00 0.00 4.37
24 25 0.614134 AGTTGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
25 26 1.264295 AAGTTGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
26 27 6.402456 AATATAAGTTGTACTCCCTCCGTC 57.598 41.667 0.00 0.00 0.00 4.79
27 28 6.803366 AAATATAAGTTGTACTCCCTCCGT 57.197 37.500 0.00 0.00 0.00 4.69
28 29 7.046033 ACAAAATATAAGTTGTACTCCCTCCG 58.954 38.462 3.27 0.00 36.22 4.63
29 30 8.803397 AACAAAATATAAGTTGTACTCCCTCC 57.197 34.615 5.17 0.00 36.97 4.30
45 46 9.834628 CAACCGTGTATTTCACTAACAAAATAT 57.165 29.630 0.00 0.00 44.16 1.28
46 47 9.053840 TCAACCGTGTATTTCACTAACAAAATA 57.946 29.630 0.00 0.00 44.16 1.40
47 48 7.932335 TCAACCGTGTATTTCACTAACAAAAT 58.068 30.769 0.00 0.00 44.16 1.82
48 49 7.317842 TCAACCGTGTATTTCACTAACAAAA 57.682 32.000 0.00 0.00 44.16 2.44
49 50 6.922247 TCAACCGTGTATTTCACTAACAAA 57.078 33.333 0.00 0.00 44.16 2.83
50 51 6.762187 TCTTCAACCGTGTATTTCACTAACAA 59.238 34.615 0.00 0.00 44.16 2.83
51 52 6.282167 TCTTCAACCGTGTATTTCACTAACA 58.718 36.000 0.00 0.00 44.16 2.41
52 53 6.774354 TCTTCAACCGTGTATTTCACTAAC 57.226 37.500 0.00 0.00 44.16 2.34
53 54 7.211573 TCTTCTTCAACCGTGTATTTCACTAA 58.788 34.615 0.00 0.00 44.16 2.24
54 55 6.751157 TCTTCTTCAACCGTGTATTTCACTA 58.249 36.000 0.00 0.00 44.16 2.74
55 56 5.607477 TCTTCTTCAACCGTGTATTTCACT 58.393 37.500 0.00 0.00 44.16 3.41
56 57 5.917541 TCTTCTTCAACCGTGTATTTCAC 57.082 39.130 0.00 0.00 43.03 3.18
57 58 6.202188 GTCTTCTTCTTCAACCGTGTATTTCA 59.798 38.462 0.00 0.00 0.00 2.69
58 59 6.424207 AGTCTTCTTCTTCAACCGTGTATTTC 59.576 38.462 0.00 0.00 0.00 2.17
59 60 6.289064 AGTCTTCTTCTTCAACCGTGTATTT 58.711 36.000 0.00 0.00 0.00 1.40
60 61 5.855045 AGTCTTCTTCTTCAACCGTGTATT 58.145 37.500 0.00 0.00 0.00 1.89
61 62 5.470047 AGTCTTCTTCTTCAACCGTGTAT 57.530 39.130 0.00 0.00 0.00 2.29
62 63 4.931661 AGTCTTCTTCTTCAACCGTGTA 57.068 40.909 0.00 0.00 0.00 2.90
63 64 3.821421 AGTCTTCTTCTTCAACCGTGT 57.179 42.857 0.00 0.00 0.00 4.49
64 65 7.884816 TTATTAGTCTTCTTCTTCAACCGTG 57.115 36.000 0.00 0.00 0.00 4.94
65 66 7.387122 GGTTTATTAGTCTTCTTCTTCAACCGT 59.613 37.037 0.00 0.00 0.00 4.83
66 67 7.386848 TGGTTTATTAGTCTTCTTCTTCAACCG 59.613 37.037 0.00 0.00 32.98 4.44
67 68 8.617290 TGGTTTATTAGTCTTCTTCTTCAACC 57.383 34.615 0.00 0.00 0.00 3.77
68 69 8.722394 CCTGGTTTATTAGTCTTCTTCTTCAAC 58.278 37.037 0.00 0.00 0.00 3.18
69 70 8.656806 TCCTGGTTTATTAGTCTTCTTCTTCAA 58.343 33.333 0.00 0.00 0.00 2.69
70 71 8.095169 GTCCTGGTTTATTAGTCTTCTTCTTCA 58.905 37.037 0.00 0.00 0.00 3.02
71 72 7.275999 CGTCCTGGTTTATTAGTCTTCTTCTTC 59.724 40.741 0.00 0.00 0.00 2.87
72 73 7.097834 CGTCCTGGTTTATTAGTCTTCTTCTT 58.902 38.462 0.00 0.00 0.00 2.52
73 74 6.351117 CCGTCCTGGTTTATTAGTCTTCTTCT 60.351 42.308 0.00 0.00 0.00 2.85
74 75 5.811100 CCGTCCTGGTTTATTAGTCTTCTTC 59.189 44.000 0.00 0.00 0.00 2.87
75 76 5.731591 CCGTCCTGGTTTATTAGTCTTCTT 58.268 41.667 0.00 0.00 0.00 2.52
76 77 5.340439 CCGTCCTGGTTTATTAGTCTTCT 57.660 43.478 0.00 0.00 0.00 2.85
247 249 8.300286 GCTTTCCTAGCTAAAAATTCCATATCC 58.700 37.037 0.00 0.00 46.77 2.59
268 968 4.622701 AAGCGATGGAAATGTAGCTTTC 57.377 40.909 0.00 0.00 41.45 2.62
274 974 5.120399 ACGGATAAAAGCGATGGAAATGTA 58.880 37.500 0.00 0.00 0.00 2.29
331 1094 0.035598 TTTGCCCGTTGCTGCTAGTA 59.964 50.000 0.00 0.00 42.00 1.82
332 1095 1.228124 TTTGCCCGTTGCTGCTAGT 60.228 52.632 0.00 0.00 42.00 2.57
333 1096 1.210155 GTTTGCCCGTTGCTGCTAG 59.790 57.895 0.00 0.00 42.00 3.42
372 1135 3.953775 CCGGGTCTGGGTTGCTGT 61.954 66.667 0.00 0.00 0.00 4.40
399 1168 3.064820 GGGGTTAATCGTTCGTACTCGTA 59.935 47.826 0.00 0.00 38.33 3.43
403 1172 3.091545 TCAGGGGTTAATCGTTCGTACT 58.908 45.455 0.00 0.00 0.00 2.73
404 1173 3.182182 GTCAGGGGTTAATCGTTCGTAC 58.818 50.000 0.00 0.00 0.00 3.67
405 1174 2.166254 GGTCAGGGGTTAATCGTTCGTA 59.834 50.000 0.00 0.00 0.00 3.43
407 1176 1.648504 GGTCAGGGGTTAATCGTTCG 58.351 55.000 0.00 0.00 0.00 3.95
409 1178 1.364269 TGGGTCAGGGGTTAATCGTT 58.636 50.000 0.00 0.00 0.00 3.85
410 1179 1.489230 GATGGGTCAGGGGTTAATCGT 59.511 52.381 0.00 0.00 0.00 3.73
412 1181 1.202770 CGGATGGGTCAGGGGTTAATC 60.203 57.143 0.00 0.00 0.00 1.75
414 1183 0.252789 TCGGATGGGTCAGGGGTTAA 60.253 55.000 0.00 0.00 0.00 2.01
415 1184 0.689745 CTCGGATGGGTCAGGGGTTA 60.690 60.000 0.00 0.00 0.00 2.85
417 1186 2.365635 CTCGGATGGGTCAGGGGT 60.366 66.667 0.00 0.00 0.00 4.95
418 1187 3.866582 GCTCGGATGGGTCAGGGG 61.867 72.222 0.00 0.00 0.00 4.79
419 1188 3.866582 GGCTCGGATGGGTCAGGG 61.867 72.222 0.00 0.00 0.00 4.45
420 1189 3.866582 GGGCTCGGATGGGTCAGG 61.867 72.222 0.00 0.00 0.00 3.86
421 1190 3.083349 TGGGCTCGGATGGGTCAG 61.083 66.667 0.00 0.00 0.00 3.51
422 1191 3.399181 GTGGGCTCGGATGGGTCA 61.399 66.667 0.00 0.00 0.00 4.02
423 1192 3.083997 AGTGGGCTCGGATGGGTC 61.084 66.667 0.00 0.00 0.00 4.46
424 1193 3.402681 CAGTGGGCTCGGATGGGT 61.403 66.667 0.00 0.00 0.00 4.51
425 1194 2.196997 TTTCAGTGGGCTCGGATGGG 62.197 60.000 0.00 0.00 0.00 4.00
426 1195 1.026718 GTTTCAGTGGGCTCGGATGG 61.027 60.000 0.00 0.00 0.00 3.51
427 1196 0.321564 TGTTTCAGTGGGCTCGGATG 60.322 55.000 0.00 0.00 0.00 3.51
429 1198 0.534203 GTTGTTTCAGTGGGCTCGGA 60.534 55.000 0.00 0.00 0.00 4.55
430 1199 1.841663 CGTTGTTTCAGTGGGCTCGG 61.842 60.000 0.00 0.00 0.00 4.63
431 1200 1.569493 CGTTGTTTCAGTGGGCTCG 59.431 57.895 0.00 0.00 0.00 5.03
432 1201 1.515521 CCCGTTGTTTCAGTGGGCTC 61.516 60.000 0.00 0.00 32.09 4.70
433 1202 1.528309 CCCGTTGTTTCAGTGGGCT 60.528 57.895 0.00 0.00 32.09 5.19
434 1203 3.039134 CCCGTTGTTTCAGTGGGC 58.961 61.111 0.00 0.00 32.09 5.36
435 1204 1.826054 TGCCCGTTGTTTCAGTGGG 60.826 57.895 0.00 0.00 43.02 4.61
437 1206 1.358759 GGTGCCCGTTGTTTCAGTG 59.641 57.895 0.00 0.00 0.00 3.66
438 1207 2.184167 CGGTGCCCGTTGTTTCAGT 61.184 57.895 5.56 0.00 42.73 3.41
439 1208 2.637025 CGGTGCCCGTTGTTTCAG 59.363 61.111 5.56 0.00 42.73 3.02
451 1250 3.961414 TGGGGGAAGGAACGGTGC 61.961 66.667 0.00 0.00 0.00 5.01
456 1255 2.350134 GGACGTGGGGGAAGGAAC 59.650 66.667 0.00 0.00 0.00 3.62
792 1653 2.965716 GATGGGGGCGAGTGGGATTG 62.966 65.000 0.00 0.00 0.00 2.67
793 1654 2.696125 ATGGGGGCGAGTGGGATT 60.696 61.111 0.00 0.00 0.00 3.01
794 1655 3.171388 GATGGGGGCGAGTGGGAT 61.171 66.667 0.00 0.00 0.00 3.85
1689 2575 3.376935 CTCCCACGGCAGCTCGAAT 62.377 63.158 9.87 0.00 0.00 3.34
1932 2818 1.221566 CACCATGGCCGACTGATCA 59.778 57.895 13.04 0.00 0.00 2.92
2641 3712 4.436523 GTGAAATGTACACTTGCGACAAAC 59.563 41.667 0.00 0.00 35.66 2.93
2684 3755 4.518970 TGAAGAAGAACCAATAAGCACACC 59.481 41.667 0.00 0.00 0.00 4.16
2906 3999 8.573035 TGAGAACTTCAAACTACACAAAAACTT 58.427 29.630 0.00 0.00 31.34 2.66
2931 4025 8.048534 AGTTCATATCAACTCTCAATTTGGTG 57.951 34.615 0.00 0.00 30.25 4.17
2979 4074 9.774671 CTCATGACGAGGGAATCATCACTGATT 62.775 44.444 0.65 0.65 44.51 2.57
2993 4088 4.342862 AACCATAATCTCATGACGAGGG 57.657 45.455 0.00 0.00 42.55 4.30
3322 4456 0.898320 CTGAACACCGACCAGATCCT 59.102 55.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.