Multiple sequence alignment - TraesCS2D01G253100

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 TraesCS2D01G253100 chr2D 100.000 4625 0 0 1 4625 304998484 304993860 0.000000e+00 8541
1 TraesCS2D01G253100 chr2A 96.075 3924 105 22 734 4625 383614114 383610208 0.000000e+00 6348
2 TraesCS2D01G253100 chr2A 91.000 600 33 6 146 735 383614728 383614140 0.000000e+00 789
3 TraesCS2D01G253100 chr2B 93.670 2433 104 13 63 2454 373501639 373499216 0.000000e+00 3594
4 TraesCS2D01G253100 chr2B 96.382 1520 39 4 2454 3957 373495830 373494311 0.000000e+00 2488
5 TraesCS2D01G253100 chr5A 79.985 1369 235 25 904 2242 670826646 670828005 0.000000e+00 974
6 TraesCS2D01G253100 chr5A 85.593 236 32 2 3374 3608 670834331 670834565 3.570000e-61 246
7 TraesCS2D01G253100 chr4B 84.322 236 35 2 3374 3608 627541788 627542022 3.600000e-56 230


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 TraesCS2D01G253100 chr2D 304993860 304998484 4624 True 8541.0 8541 100.0000 1 4625 1 chr2D.!!$R1 4624
1 TraesCS2D01G253100 chr2A 383610208 383614728 4520 True 3568.5 6348 93.5375 146 4625 2 chr2A.!!$R1 4479
2 TraesCS2D01G253100 chr2B 373494311 373501639 7328 True 3041.0 3594 95.0260 63 3957 2 chr2B.!!$R1 3894
3 TraesCS2D01G253100 chr5A 670826646 670828005 1359 False 974.0 974 79.9850 904 2242 1 chr5A.!!$F1 1338

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
44 45 0.032515 TTCTGGATGAGGTAGGCCGA 60.033 55.000 0.00 0.0 40.50 5.54 F
442 446 0.655733 GGTGCGTGGTAATCCATTCG 59.344 55.000 0.00 0.0 46.20 3.34 F
604 625 0.733909 GTTGCCGATCCTTTTGCAGC 60.734 55.000 0.00 0.0 34.81 5.25 F
1510 1575 1.537776 GCCAGACTGATCACTCCATCG 60.538 57.143 3.32 0.0 0.00 3.84 F
1873 1941 4.202441 CAAGGATCGAATGGTTGAGGAAT 58.798 43.478 0.00 0.0 0.00 3.01 F
2409 2494 5.185249 AGCTTCTCAAGAAACACGAGGTATA 59.815 40.000 0.00 0.0 33.07 1.47 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1502 2.000447 GGTCTGAACCGTGATAACTGC 59.000 52.381 0.0 0.0 35.36 4.40 R
1510 1575 3.002759 GTCCAGTCTTCAGCAAACTTGAC 59.997 47.826 0.0 0.0 31.26 3.18 R
1901 1969 3.523606 AATGCAGCAAAAACACACAGA 57.476 38.095 0.0 0.0 0.00 3.41 R
3220 6691 2.026729 TCTGACCATTGCCCGTCAAATA 60.027 45.455 0.0 0.0 38.48 1.40 R
3305 6791 2.067365 ACTGGAACAAGGACCCAAAC 57.933 50.000 0.0 0.0 38.70 2.93 R
3934 7421 0.403655 TAGATTTGCCCACACCTGCA 59.596 50.000 0.0 0.0 35.27 4.41 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 5.162000 GCTCCCGTGAATCTTATTTCTTG 57.838 43.478 0.00 0.00 0.00 3.02
23 24 4.876107 GCTCCCGTGAATCTTATTTCTTGA 59.124 41.667 0.00 0.00 0.00 3.02
24 25 5.529060 GCTCCCGTGAATCTTATTTCTTGAT 59.471 40.000 0.00 0.00 0.00 2.57
25 26 6.038714 GCTCCCGTGAATCTTATTTCTTGATT 59.961 38.462 0.00 0.00 33.69 2.57
26 27 7.415653 GCTCCCGTGAATCTTATTTCTTGATTT 60.416 37.037 0.00 0.00 31.49 2.17
27 28 7.985476 TCCCGTGAATCTTATTTCTTGATTTC 58.015 34.615 0.00 0.00 31.49 2.17
28 29 7.829211 TCCCGTGAATCTTATTTCTTGATTTCT 59.171 33.333 0.00 0.00 31.49 2.52
29 30 7.912250 CCCGTGAATCTTATTTCTTGATTTCTG 59.088 37.037 0.00 0.00 31.49 3.02
30 31 7.912250 CCGTGAATCTTATTTCTTGATTTCTGG 59.088 37.037 0.00 0.00 31.49 3.86
31 32 8.668353 CGTGAATCTTATTTCTTGATTTCTGGA 58.332 33.333 0.00 0.00 31.49 3.86
36 37 8.743085 TCTTATTTCTTGATTTCTGGATGAGG 57.257 34.615 0.00 0.00 0.00 3.86
37 38 8.331740 TCTTATTTCTTGATTTCTGGATGAGGT 58.668 33.333 0.00 0.00 0.00 3.85
38 39 9.618890 CTTATTTCTTGATTTCTGGATGAGGTA 57.381 33.333 0.00 0.00 0.00 3.08
39 40 9.618890 TTATTTCTTGATTTCTGGATGAGGTAG 57.381 33.333 0.00 0.00 0.00 3.18
40 41 5.620738 TCTTGATTTCTGGATGAGGTAGG 57.379 43.478 0.00 0.00 0.00 3.18
41 42 3.845781 TGATTTCTGGATGAGGTAGGC 57.154 47.619 0.00 0.00 0.00 3.93
42 43 2.439507 TGATTTCTGGATGAGGTAGGCC 59.560 50.000 0.00 0.00 0.00 5.19
43 44 0.830648 TTTCTGGATGAGGTAGGCCG 59.169 55.000 0.00 0.00 40.50 6.13
44 45 0.032515 TTCTGGATGAGGTAGGCCGA 60.033 55.000 0.00 0.00 40.50 5.54
45 46 0.755698 TCTGGATGAGGTAGGCCGAC 60.756 60.000 7.59 7.59 40.50 4.79
46 47 2.076622 CTGGATGAGGTAGGCCGACG 62.077 65.000 10.10 0.00 40.50 5.12
47 48 2.027751 GATGAGGTAGGCCGACGC 59.972 66.667 10.10 5.29 40.50 5.19
48 49 3.825833 GATGAGGTAGGCCGACGCG 62.826 68.421 10.10 3.53 40.50 6.01
105 106 6.257423 TCGCATAAATAAAGACAAGCACATG 58.743 36.000 0.00 0.00 0.00 3.21
139 140 2.099098 GGCCAGAATTGTGAATAACGGG 59.901 50.000 3.74 0.00 0.00 5.28
140 141 2.752903 GCCAGAATTGTGAATAACGGGT 59.247 45.455 3.74 0.00 0.00 5.28
166 167 8.493787 AGGTGAAGGGGTTAAGTAAGATATAG 57.506 38.462 0.00 0.00 0.00 1.31
170 173 8.711170 TGAAGGGGTTAAGTAAGATATAGGTTG 58.289 37.037 0.00 0.00 0.00 3.77
260 264 3.521126 CCTTCTTCTCTGATTTCTCCCCA 59.479 47.826 0.00 0.00 0.00 4.96
262 266 4.833478 TCTTCTCTGATTTCTCCCCAAG 57.167 45.455 0.00 0.00 0.00 3.61
268 272 2.511218 CTGATTTCTCCCCAAGATCCCA 59.489 50.000 0.00 0.00 32.82 4.37
416 420 1.286354 TTTCGCGGTTCGTTGCCTAG 61.286 55.000 6.13 0.00 39.67 3.02
440 444 3.541632 CTTAGGTGCGTGGTAATCCATT 58.458 45.455 0.00 0.00 46.20 3.16
442 446 0.655733 GGTGCGTGGTAATCCATTCG 59.344 55.000 0.00 0.00 46.20 3.34
456 460 4.374843 TCCATTCGCCATTCTTTGATTG 57.625 40.909 0.00 0.00 0.00 2.67
461 465 6.073112 CCATTCGCCATTCTTTGATTGTTTTT 60.073 34.615 0.00 0.00 0.00 1.94
487 499 4.572389 CGGACAAGAGGAATCCAATTACTG 59.428 45.833 0.61 0.00 32.31 2.74
529 541 2.035449 CCTTGGGGTTTTTCCGTTCTTC 59.965 50.000 0.00 0.00 37.00 2.87
552 572 1.228398 TGGCAGCGATCAACCCAAA 60.228 52.632 0.00 0.00 0.00 3.28
569 589 3.068590 CCCAAATCCAAATCATTCTCCCG 59.931 47.826 0.00 0.00 0.00 5.14
576 597 0.753262 AATCATTCTCCCGTCCCTCG 59.247 55.000 0.00 0.00 39.52 4.63
596 617 2.936498 CGTTGATTTAGTTGCCGATCCT 59.064 45.455 0.00 0.00 0.00 3.24
604 625 0.733909 GTTGCCGATCCTTTTGCAGC 60.734 55.000 0.00 0.00 34.81 5.25
1154 1219 1.740025 CTGCCTAGGGAAAAAGAAGCG 59.260 52.381 11.72 0.00 0.00 4.68
1378 1443 4.469657 GTGGATGGGCATTCTGGTTAATA 58.530 43.478 0.00 0.00 0.00 0.98
1437 1502 6.073548 GGGAGAGTGAGCATATGTTAAAATCG 60.074 42.308 4.29 0.00 0.00 3.34
1510 1575 1.537776 GCCAGACTGATCACTCCATCG 60.538 57.143 3.32 0.00 0.00 3.84
1873 1941 4.202441 CAAGGATCGAATGGTTGAGGAAT 58.798 43.478 0.00 0.00 0.00 3.01
2409 2494 5.185249 AGCTTCTCAAGAAACACGAGGTATA 59.815 40.000 0.00 0.00 33.07 1.47
3290 6776 8.352942 ACTGAAGTATTTGAATTTCAACTGGAC 58.647 33.333 11.30 7.36 35.89 4.02
3305 6791 2.092753 ACTGGACACATTGCTATCCTGG 60.093 50.000 10.86 0.00 35.19 4.45
3310 6796 3.091545 ACACATTGCTATCCTGGTTTGG 58.908 45.455 0.00 0.00 0.00 3.28
3372 6858 3.067461 AGCCTGTGATTCTGATAGACGTC 59.933 47.826 7.70 7.70 0.00 4.34
3612 7098 1.136502 GCGAGCAAGAACAAGAGAACG 60.137 52.381 0.00 0.00 0.00 3.95
3671 7158 0.400213 TGTAGTTTCTGGCCTGTGGG 59.600 55.000 3.32 0.00 0.00 4.61
3723 7210 6.314784 ACTTGATGCTTAGTAAATTGCGAAC 58.685 36.000 0.00 0.00 0.00 3.95
3725 7212 4.627900 TGATGCTTAGTAAATTGCGAACGA 59.372 37.500 0.00 0.00 0.00 3.85
3800 7287 2.093447 ACTAAGCTCCCACGAAATGAGG 60.093 50.000 0.00 0.00 0.00 3.86
3808 7295 1.611673 CCACGAAATGAGGCCTCTTGT 60.612 52.381 32.28 22.18 0.00 3.16
3843 7330 0.519519 TTGTTGCGTTTATGGCCTCG 59.480 50.000 3.32 2.39 0.00 4.63
3868 7355 1.068588 TCAAAGAGTGGACAGGTCGTG 59.931 52.381 0.00 0.00 0.00 4.35
3934 7421 4.708177 CGTGATCCATGGATTACCTCTTT 58.292 43.478 32.71 10.77 37.70 2.52
3953 7440 0.403655 TGCAGGTGTGGGCAAATCTA 59.596 50.000 0.00 0.00 37.03 1.98
3992 7479 6.866010 TTTCTACCGGTTTTAGGAAGTTTC 57.134 37.500 15.04 0.00 0.00 2.78
4004 7491 9.468532 GTTTTAGGAAGTTTCTAGAACGTTCTA 57.531 33.333 30.65 30.65 38.70 2.10
4009 7496 7.124448 AGGAAGTTTCTAGAACGTTCTATGGAT 59.876 37.037 32.25 18.90 38.95 3.41
4011 7498 7.406031 AGTTTCTAGAACGTTCTATGGATCA 57.594 36.000 32.25 15.04 38.95 2.92
4030 7517 1.133482 CAGGTTTCCCCCTGTGTTTCT 60.133 52.381 0.00 0.00 45.81 2.52
4050 7537 7.174253 TGTTTCTATTTGCTGATTTTACGAGGT 59.826 33.333 0.00 0.00 0.00 3.85
4053 7540 7.526608 TCTATTTGCTGATTTTACGAGGTTTG 58.473 34.615 0.00 0.00 0.00 2.93
4063 7550 8.460428 TGATTTTACGAGGTTTGTTTTAGTGTT 58.540 29.630 0.00 0.00 0.00 3.32
4064 7551 9.292846 GATTTTACGAGGTTTGTTTTAGTGTTT 57.707 29.630 0.00 0.00 0.00 2.83
4065 7552 8.672214 TTTTACGAGGTTTGTTTTAGTGTTTC 57.328 30.769 0.00 0.00 0.00 2.78
4121 7608 6.954944 TGTGAACACTTTCTTAAAATCGGAG 58.045 36.000 6.51 0.00 32.36 4.63
4124 7611 7.586664 GTGAACACTTTCTTAAAATCGGAGAAC 59.413 37.037 0.00 0.00 34.07 3.01
4128 7615 8.630037 ACACTTTCTTAAAATCGGAGAACATTT 58.370 29.630 0.00 0.00 43.58 2.32
4179 7668 6.481643 TGGGGAACTAGTTTTCAAATCCTAG 58.518 40.000 10.02 3.80 34.44 3.02
4181 7670 7.173032 GGGGAACTAGTTTTCAAATCCTAGAA 58.827 38.462 10.02 0.00 32.93 2.10
4182 7671 7.120873 GGGGAACTAGTTTTCAAATCCTAGAAC 59.879 40.741 10.02 0.00 32.93 3.01
4183 7672 7.664318 GGGAACTAGTTTTCAAATCCTAGAACA 59.336 37.037 10.02 0.00 32.93 3.18
4184 7673 9.232473 GGAACTAGTTTTCAAATCCTAGAACAT 57.768 33.333 10.02 0.00 32.93 2.71
4261 7750 7.710676 TTTGGAGATTCGGGAAATATTTTGA 57.289 32.000 1.43 0.00 0.00 2.69
4343 7851 8.355806 CAATTTCGTAAACATTTTCTAGTTCGC 58.644 33.333 0.00 0.00 0.00 4.70
4349 7857 7.375017 CGTAAACATTTTCTAGTTCGCAAACTT 59.625 33.333 0.00 0.00 43.28 2.66
4415 7924 4.339530 AGCTTTCCTTCCTGTCTGTTTTTC 59.660 41.667 0.00 0.00 0.00 2.29
4417 7926 4.519906 TTCCTTCCTGTCTGTTTTTCCT 57.480 40.909 0.00 0.00 0.00 3.36
4427 7936 5.650543 TGTCTGTTTTTCCTTTGCTTCTTC 58.349 37.500 0.00 0.00 0.00 2.87
4474 7983 1.630878 ACTAGCTAGCCAACCAAAGCT 59.369 47.619 20.91 0.95 46.58 3.74
4487 7996 4.625607 ACCAAAGCTAGTATATCCTGGC 57.374 45.455 0.00 0.00 39.06 4.85
4500 8009 1.525995 CCTGGCCGTGTGTGTTTCT 60.526 57.895 0.00 0.00 0.00 2.52
4511 8020 3.493503 GTGTGTGTTTCTTAGTCCTTCGG 59.506 47.826 0.00 0.00 0.00 4.30
4605 8114 2.071540 TCTGCTTCATGCGTTTGAGAG 58.928 47.619 0.00 0.00 46.63 3.20
4618 8127 3.827898 GAGAGGGGGCGACGACAG 61.828 72.222 1.63 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.876107 TCAAGAAATAAGATTCACGGGAGC 59.124 41.667 0.00 0.00 0.00 4.70
1 2 7.559590 AATCAAGAAATAAGATTCACGGGAG 57.440 36.000 0.00 0.00 0.00 4.30
2 3 7.829211 AGAAATCAAGAAATAAGATTCACGGGA 59.171 33.333 0.00 0.00 31.21 5.14
5 6 8.668353 TCCAGAAATCAAGAAATAAGATTCACG 58.332 33.333 0.00 0.00 31.21 4.35
10 11 9.352191 CCTCATCCAGAAATCAAGAAATAAGAT 57.648 33.333 0.00 0.00 0.00 2.40
11 12 8.331740 ACCTCATCCAGAAATCAAGAAATAAGA 58.668 33.333 0.00 0.00 0.00 2.10
12 13 8.517062 ACCTCATCCAGAAATCAAGAAATAAG 57.483 34.615 0.00 0.00 0.00 1.73
13 14 9.618890 CTACCTCATCCAGAAATCAAGAAATAA 57.381 33.333 0.00 0.00 0.00 1.40
14 15 8.213679 CCTACCTCATCCAGAAATCAAGAAATA 58.786 37.037 0.00 0.00 0.00 1.40
15 16 7.059156 CCTACCTCATCCAGAAATCAAGAAAT 58.941 38.462 0.00 0.00 0.00 2.17
16 17 6.418101 CCTACCTCATCCAGAAATCAAGAAA 58.582 40.000 0.00 0.00 0.00 2.52
17 18 5.630069 GCCTACCTCATCCAGAAATCAAGAA 60.630 44.000 0.00 0.00 0.00 2.52
18 19 4.141620 GCCTACCTCATCCAGAAATCAAGA 60.142 45.833 0.00 0.00 0.00 3.02
19 20 4.133078 GCCTACCTCATCCAGAAATCAAG 58.867 47.826 0.00 0.00 0.00 3.02
20 21 3.117888 GGCCTACCTCATCCAGAAATCAA 60.118 47.826 0.00 0.00 0.00 2.57
21 22 2.439507 GGCCTACCTCATCCAGAAATCA 59.560 50.000 0.00 0.00 0.00 2.57
22 23 2.548920 CGGCCTACCTCATCCAGAAATC 60.549 54.545 0.00 0.00 0.00 2.17
23 24 1.417890 CGGCCTACCTCATCCAGAAAT 59.582 52.381 0.00 0.00 0.00 2.17
24 25 0.830648 CGGCCTACCTCATCCAGAAA 59.169 55.000 0.00 0.00 0.00 2.52
25 26 0.032515 TCGGCCTACCTCATCCAGAA 60.033 55.000 0.00 0.00 0.00 3.02
26 27 0.755698 GTCGGCCTACCTCATCCAGA 60.756 60.000 0.00 0.00 0.00 3.86
27 28 1.742768 GTCGGCCTACCTCATCCAG 59.257 63.158 0.00 0.00 0.00 3.86
28 29 2.125326 CGTCGGCCTACCTCATCCA 61.125 63.158 0.00 0.00 0.00 3.41
29 30 2.728817 CGTCGGCCTACCTCATCC 59.271 66.667 0.00 0.00 0.00 3.51
30 31 2.027751 GCGTCGGCCTACCTCATC 59.972 66.667 0.00 0.00 0.00 2.92
31 32 3.900892 CGCGTCGGCCTACCTCAT 61.901 66.667 0.00 0.00 35.02 2.90
68 69 9.891828 CTTTATTTATGCGATTATTAAGTGGCA 57.108 29.630 0.00 0.00 34.60 4.92
77 78 8.620416 TGTGCTTGTCTTTATTTATGCGATTAT 58.380 29.630 0.00 0.00 0.00 1.28
96 97 1.610038 TCTGAGGCAAACATGTGCTTG 59.390 47.619 0.00 2.03 44.31 4.01
97 98 1.985473 TCTGAGGCAAACATGTGCTT 58.015 45.000 0.00 0.00 44.31 3.91
125 126 4.829872 TCACCTACCCGTTATTCACAAT 57.170 40.909 0.00 0.00 0.00 2.71
126 127 4.563993 CCTTCACCTACCCGTTATTCACAA 60.564 45.833 0.00 0.00 0.00 3.33
139 140 6.556974 ATCTTACTTAACCCCTTCACCTAC 57.443 41.667 0.00 0.00 0.00 3.18
140 141 9.597681 CTATATCTTACTTAACCCCTTCACCTA 57.402 37.037 0.00 0.00 0.00 3.08
186 190 2.332104 GGTTTACGAACGGAGGAACTC 58.668 52.381 0.00 0.00 42.84 3.01
188 192 1.432514 GGGTTTACGAACGGAGGAAC 58.567 55.000 0.00 0.00 36.61 3.62
260 264 0.537188 ACGAGAATGCGTGGGATCTT 59.463 50.000 0.00 0.00 43.79 2.40
262 266 4.835927 ACGAGAATGCGTGGGATC 57.164 55.556 0.00 0.00 43.79 3.36
295 299 0.037232 GTAGGCCTCGCTTCTTGTGT 60.037 55.000 9.68 0.00 0.00 3.72
416 420 2.547826 GATTACCACGCACCTAAGGAC 58.452 52.381 0.00 0.00 0.00 3.85
440 444 5.461737 GTGAAAAACAATCAAAGAATGGCGA 59.538 36.000 0.00 0.00 0.00 5.54
442 446 5.333263 CCGTGAAAAACAATCAAAGAATGGC 60.333 40.000 0.00 0.00 0.00 4.40
456 460 4.320275 GGATTCCTCTTGTCCGTGAAAAAC 60.320 45.833 0.00 0.00 0.00 2.43
461 465 1.639722 TGGATTCCTCTTGTCCGTGA 58.360 50.000 3.95 0.00 34.72 4.35
487 499 4.082026 AGGGCAAAATTAACACTGATCAGC 60.082 41.667 22.83 4.64 0.00 4.26
552 572 2.158608 GGGACGGGAGAATGATTTGGAT 60.159 50.000 0.00 0.00 0.00 3.41
569 589 2.418976 GGCAACTAAATCAACGAGGGAC 59.581 50.000 0.00 0.00 0.00 4.46
576 597 4.965119 AAGGATCGGCAACTAAATCAAC 57.035 40.909 0.00 0.00 0.00 3.18
596 617 5.294060 GGAAAAAGAAGTGATTGCTGCAAAA 59.706 36.000 20.06 8.09 0.00 2.44
604 625 5.669477 TGTTTGGGGAAAAAGAAGTGATTG 58.331 37.500 0.00 0.00 0.00 2.67
925 975 4.607293 TTCAGTCAGTGCTATCAACTGT 57.393 40.909 7.14 0.00 38.71 3.55
962 1016 4.474651 TGAGAGATAAAATGCCCTGAGGAA 59.525 41.667 0.00 0.00 33.47 3.36
1154 1219 6.254589 CAGAAGATCCTTGACGTTGTAATCTC 59.745 42.308 0.00 0.00 0.00 2.75
1378 1443 6.191657 TGTATCCATCAAATCAGCTGGTAT 57.808 37.500 15.13 0.00 0.00 2.73
1437 1502 2.000447 GGTCTGAACCGTGATAACTGC 59.000 52.381 0.00 0.00 35.36 4.40
1510 1575 3.002759 GTCCAGTCTTCAGCAAACTTGAC 59.997 47.826 0.00 0.00 31.26 3.18
1601 1666 5.468746 TCGTCCATTTTACAGTTTCTTCTGG 59.531 40.000 0.00 0.00 39.48 3.86
1901 1969 3.523606 AATGCAGCAAAAACACACAGA 57.476 38.095 0.00 0.00 0.00 3.41
2221 2305 7.753630 AGATAAAATAGCATTGGAGGAGACAT 58.246 34.615 0.00 0.00 0.00 3.06
3220 6691 2.026729 TCTGACCATTGCCCGTCAAATA 60.027 45.455 0.00 0.00 38.48 1.40
3290 6776 2.428171 CCCAAACCAGGATAGCAATGTG 59.572 50.000 0.00 0.00 0.00 3.21
3305 6791 2.067365 ACTGGAACAAGGACCCAAAC 57.933 50.000 0.00 0.00 38.70 2.93
3310 6796 5.300792 TGTTTTCATTACTGGAACAAGGACC 59.699 40.000 0.00 0.00 38.70 4.46
3372 6858 3.629398 GGACTATTTCCTGCACCATTCAG 59.371 47.826 0.00 0.00 41.95 3.02
3570 7056 3.937706 CCTTCCACTGCTTGAGAATGTAG 59.062 47.826 0.00 0.00 0.00 2.74
3612 7098 4.034742 GTCGATCTCACTCAGGAGAAGTAC 59.965 50.000 2.79 0.00 46.28 2.73
3671 7158 6.692681 TGTTACTACGATACGATTTTACAGCC 59.307 38.462 0.00 0.00 0.00 4.85
3723 7210 4.145276 TCGTCGCAATTGTGTTTATTTCG 58.855 39.130 18.08 11.94 0.00 3.46
3725 7212 4.472286 CCTCGTCGCAATTGTGTTTATTT 58.528 39.130 18.08 0.00 0.00 1.40
3843 7330 4.246458 GACCTGTCCACTCTTTGACATAC 58.754 47.826 0.00 0.00 40.46 2.39
3934 7421 0.403655 TAGATTTGCCCACACCTGCA 59.596 50.000 0.00 0.00 35.27 4.41
3971 7458 5.813513 AGAAACTTCCTAAAACCGGTAGA 57.186 39.130 8.00 0.00 0.00 2.59
3992 7479 5.776173 ACCTGATCCATAGAACGTTCTAG 57.224 43.478 34.13 26.11 42.55 2.43
4030 7517 7.209471 ACAAACCTCGTAAAATCAGCAAATA 57.791 32.000 0.00 0.00 0.00 1.40
4095 7582 7.763356 TCCGATTTTAAGAAAGTGTTCACAAA 58.237 30.769 5.74 0.00 36.09 2.83
4117 7604 7.582319 GCACACAAATTTTAAAAATGTTCTCCG 59.418 33.333 15.98 9.76 0.00 4.63
4118 7605 8.394121 TGCACACAAATTTTAAAAATGTTCTCC 58.606 29.630 15.98 8.68 0.00 3.71
4153 7642 6.140377 AGGATTTGAAAACTAGTTCCCCAAA 58.860 36.000 21.53 21.53 0.00 3.28
4222 7711 8.987890 CGAATCTCCAAAAATGTTACCAAATTT 58.012 29.630 0.00 0.00 0.00 1.82
4231 7720 5.799827 TTTCCCGAATCTCCAAAAATGTT 57.200 34.783 0.00 0.00 0.00 2.71
4247 7736 7.812191 TGTTCACAAATCTCAAAATATTTCCCG 59.188 33.333 0.10 0.00 0.00 5.14
4261 7750 8.945481 TGATTTTGTCAAATGTTCACAAATCT 57.055 26.923 0.00 0.00 39.23 2.40
4317 7825 8.355806 GCGAACTAGAAAATGTTTACGAAATTG 58.644 33.333 0.00 0.00 0.00 2.32
4325 7833 9.575783 AAAAGTTTGCGAACTAGAAAATGTTTA 57.424 25.926 19.76 0.00 45.18 2.01
4405 7914 4.735338 CGAAGAAGCAAAGGAAAAACAGAC 59.265 41.667 0.00 0.00 0.00 3.51
4415 7924 0.453390 GCCATCCGAAGAAGCAAAGG 59.547 55.000 0.00 0.00 0.00 3.11
4417 7926 0.251121 TGGCCATCCGAAGAAGCAAA 60.251 50.000 0.00 0.00 34.14 3.68
4450 7959 0.613853 TGGTTGGCTAGCTAGTCGGT 60.614 55.000 20.02 0.00 0.00 4.69
4474 7983 2.626266 CACACACGGCCAGGATATACTA 59.374 50.000 2.24 0.00 0.00 1.82
4477 7986 1.491668 ACACACACGGCCAGGATATA 58.508 50.000 2.24 0.00 0.00 0.86
4478 7987 0.618458 AACACACACGGCCAGGATAT 59.382 50.000 2.24 0.00 0.00 1.63
4487 7996 3.107642 AGGACTAAGAAACACACACGG 57.892 47.619 0.00 0.00 0.00 4.94
4593 8102 2.044946 GCCCCCTCTCAAACGCAT 60.045 61.111 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.