Multiple sequence alignment - TraesCS1A01G222800

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 TraesCS1A01G222800 chr1A 100.000 4706 0 0 1 4706 392530821 392526116 0.000000e+00 8691
1 TraesCS1A01G222800 chr1A 86.442 2434 325 4 995 3424 47826769 47824337 0.000000e+00 2662
2 TraesCS1A01G222800 chr1A 81.548 1111 196 8 1803 2909 47211649 47210544 0.000000e+00 907
3 TraesCS1A01G222800 chr1A 82.213 461 75 3 2956 3416 47210539 47210086 1.590000e-104 390
4 TraesCS1A01G222800 chr1D 96.337 3986 108 18 10 3985 312974464 312970507 0.000000e+00 6517
5 TraesCS1A01G222800 chr1D 85.815 2707 358 18 995 3693 48024252 48021564 0.000000e+00 2848
6 TraesCS1A01G222800 chr1D 91.691 686 21 17 4054 4706 312970482 312969800 0.000000e+00 918
7 TraesCS1A01G222800 chr1D 81.515 1109 196 6 1802 2909 47329715 47328615 0.000000e+00 904
8 TraesCS1A01G222800 chr1D 78.812 741 115 20 2956 3686 47328610 47327902 1.190000e-125 460
9 TraesCS1A01G222800 chr1B 96.247 3997 115 16 10 4004 423210904 423206941 0.000000e+00 6517
10 TraesCS1A01G222800 chr1B 85.730 2705 364 16 995 3693 67683215 67680527 0.000000e+00 2837
11 TraesCS1A01G222800 chr1B 95.992 499 20 0 4208 4706 423206642 423206144 0.000000e+00 811
12 TraesCS1A01G222800 chr1B 80.162 1109 186 9 1803 2909 67053752 67052676 0.000000e+00 798
13 TraesCS1A01G222800 chr5D 72.862 1485 330 54 1005 2460 42555298 42556738 4.320000e-120 442
14 TraesCS1A01G222800 chr5D 71.976 1488 344 49 1005 2460 52617302 52615856 2.070000e-98 370
15 TraesCS1A01G222800 chr5B 72.353 1483 337 53 1005 2458 37059787 37058349 2.640000e-107 399
16 TraesCS1A01G222800 chr5B 71.553 1487 352 48 1005 2460 55625208 55623762 2.100000e-88 337
17 TraesCS1A01G222800 chr3B 71.713 1407 312 57 1957 3332 564319098 564320449 9.830000e-82 315
18 TraesCS1A01G222800 chr3D 71.793 1372 296 50 1990 3332 432135136 432136445 5.920000e-79 305
19 TraesCS1A01G222800 chr4D 82.734 139 24 0 4229 4367 336841717 336841579 1.780000e-24 124
20 TraesCS1A01G222800 chr4B 82.014 139 25 0 4229 4367 415122466 415122328 8.270000e-23 119


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 TraesCS1A01G222800 chr1A 392526116 392530821 4705 True 8691.0 8691 100.0000 1 4706 1 chr1A.!!$R2 4705
1 TraesCS1A01G222800 chr1A 47824337 47826769 2432 True 2662.0 2662 86.4420 995 3424 1 chr1A.!!$R1 2429
2 TraesCS1A01G222800 chr1A 47210086 47211649 1563 True 648.5 907 81.8805 1803 3416 2 chr1A.!!$R3 1613
3 TraesCS1A01G222800 chr1D 312969800 312974464 4664 True 3717.5 6517 94.0140 10 4706 2 chr1D.!!$R3 4696
4 TraesCS1A01G222800 chr1D 48021564 48024252 2688 True 2848.0 2848 85.8150 995 3693 1 chr1D.!!$R1 2698
5 TraesCS1A01G222800 chr1D 47327902 47329715 1813 True 682.0 904 80.1635 1802 3686 2 chr1D.!!$R2 1884
6 TraesCS1A01G222800 chr1B 423206144 423210904 4760 True 3664.0 6517 96.1195 10 4706 2 chr1B.!!$R3 4696
7 TraesCS1A01G222800 chr1B 67680527 67683215 2688 True 2837.0 2837 85.7300 995 3693 1 chr1B.!!$R2 2698
8 TraesCS1A01G222800 chr1B 67052676 67053752 1076 True 798.0 798 80.1620 1803 2909 1 chr1B.!!$R1 1106
9 TraesCS1A01G222800 chr5D 42555298 42556738 1440 False 442.0 442 72.8620 1005 2460 1 chr5D.!!$F1 1455
10 TraesCS1A01G222800 chr5D 52615856 52617302 1446 True 370.0 370 71.9760 1005 2460 1 chr5D.!!$R1 1455
11 TraesCS1A01G222800 chr5B 37058349 37059787 1438 True 399.0 399 72.3530 1005 2458 1 chr5B.!!$R1 1453
12 TraesCS1A01G222800 chr5B 55623762 55625208 1446 True 337.0 337 71.5530 1005 2460 1 chr5B.!!$R2 1455
13 TraesCS1A01G222800 chr3B 564319098 564320449 1351 False 315.0 315 71.7130 1957 3332 1 chr3B.!!$F1 1375
14 TraesCS1A01G222800 chr3D 432135136 432136445 1309 False 305.0 305 71.7930 1990 3332 1 chr3D.!!$F1 1342

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
196 197 0.107017 CCAGTTGGCCATCCTACAGG 60.107 60.0 6.09 3.94 40.00 4.00 F
203 211 0.181114 GCCATCCTACAGGTGCATCA 59.819 55.0 0.00 0.00 36.34 3.07 F
421 429 1.033746 AGCATTGTTCAGGGGCATCG 61.034 55.0 0.00 0.00 0.00 3.84 F
1229 1239 0.520847 GCAAAGAAGGAGCTGCTGAC 59.479 55.0 9.14 6.54 0.00 3.51 F
2380 2415 0.104855 TCCTCGTATCATGGCTGTGC 59.895 55.0 0.00 0.00 0.00 4.57 F
2529 2567 0.606401 TTGCTGCACTCCTTACTGCC 60.606 55.0 0.00 0.00 31.97 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1039 0.393537 GGTTGCCATCTGGAGACTGG 60.394 60.000 0.00 0.0 37.39 4.00 R
1229 1239 1.542915 CCAAGCTGACCCATTGTTGAG 59.457 52.381 0.00 0.0 0.00 3.02 R
1433 1446 1.608590 GAGTTGCTTGCTTTAGTGGCA 59.391 47.619 0.00 0.0 37.97 4.92 R
2616 2654 4.335315 TGGCCTATAATGCTTGAAGTTTCG 59.665 41.667 3.32 0.0 0.00 3.46 R
3609 3679 0.969894 ACTCCCTCAGGAACTCAACG 59.030 55.000 0.00 0.0 43.40 4.10 R
4126 4298 1.003003 TGCAAGTGGTGTAGCATAGCA 59.997 47.619 0.00 0.0 31.05 3.49 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
176 177 2.419713 GCTTTACCCTGGTAGTGGTAGC 60.420 54.545 0.00 0.00 38.31 3.58
196 197 0.107017 CCAGTTGGCCATCCTACAGG 60.107 60.000 6.09 3.94 40.00 4.00
203 211 0.181114 GCCATCCTACAGGTGCATCA 59.819 55.000 0.00 0.00 36.34 3.07
205 213 1.202734 CCATCCTACAGGTGCATCAGG 60.203 57.143 0.00 0.00 36.34 3.86
206 214 1.135094 ATCCTACAGGTGCATCAGGG 58.865 55.000 0.00 0.00 36.34 4.45
255 263 6.812160 AGCGTATTTGTATGTATAGCTTAGCC 59.188 38.462 0.00 0.00 0.00 3.93
311 319 9.624697 GCTGTTGATTAGTACAATTTGATTTGA 57.375 29.630 2.79 0.00 0.00 2.69
329 337 1.168714 GACATGTTCAAGGTCCTGGC 58.831 55.000 0.00 0.00 33.37 4.85
336 344 1.656587 TCAAGGTCCTGGCAGTGTAT 58.343 50.000 14.43 0.00 0.00 2.29
337 345 1.555075 TCAAGGTCCTGGCAGTGTATC 59.445 52.381 14.43 0.00 0.00 2.24
346 354 6.476378 GTCCTGGCAGTGTATCCATATATTT 58.524 40.000 14.43 0.00 0.00 1.40
353 361 5.882557 CAGTGTATCCATATATTTCCCTGCC 59.117 44.000 0.00 0.00 0.00 4.85
371 379 5.221087 CCCTGCCGTAACTTTGTTTTCTTAA 60.221 40.000 0.00 0.00 0.00 1.85
373 381 7.308710 CCCTGCCGTAACTTTGTTTTCTTAATA 60.309 37.037 0.00 0.00 0.00 0.98
374 382 7.749126 CCTGCCGTAACTTTGTTTTCTTAATAG 59.251 37.037 0.00 0.00 0.00 1.73
375 383 8.156994 TGCCGTAACTTTGTTTTCTTAATAGT 57.843 30.769 0.00 0.00 0.00 2.12
376 384 9.270640 TGCCGTAACTTTGTTTTCTTAATAGTA 57.729 29.630 0.00 0.00 0.00 1.82
398 406 5.954296 ATACTCTTATTGTCCATGCATGC 57.046 39.130 21.69 11.82 0.00 4.06
399 407 3.623703 ACTCTTATTGTCCATGCATGCA 58.376 40.909 25.04 25.04 0.00 3.96
416 424 1.098050 GCAGTAGCATTGTTCAGGGG 58.902 55.000 0.00 0.00 41.58 4.79
421 429 1.033746 AGCATTGTTCAGGGGCATCG 61.034 55.000 0.00 0.00 0.00 3.84
434 442 3.394606 AGGGGCATCGTAATTTATCTGGT 59.605 43.478 0.00 0.00 0.00 4.00
444 452 9.661563 ATCGTAATTTATCTGGTTGTAGAACAA 57.338 29.630 5.00 0.00 35.42 2.83
459 467 7.447374 TGTAGAACAACTTCATATGGTTTGG 57.553 36.000 2.13 0.00 0.00 3.28
464 472 7.710475 AGAACAACTTCATATGGTTTGGTTTTG 59.290 33.333 2.13 0.00 0.00 2.44
465 473 6.883744 ACAACTTCATATGGTTTGGTTTTGT 58.116 32.000 2.13 0.00 0.00 2.83
466 474 6.983890 ACAACTTCATATGGTTTGGTTTTGTC 59.016 34.615 2.13 0.00 0.00 3.18
467 475 6.723298 ACTTCATATGGTTTGGTTTTGTCA 57.277 33.333 2.13 0.00 0.00 3.58
468 476 7.118496 ACTTCATATGGTTTGGTTTTGTCAA 57.882 32.000 2.13 0.00 0.00 3.18
517 525 5.882557 CAGTTGCCTCATGAATACCTAGTTT 59.117 40.000 0.00 0.00 0.00 2.66
518 526 7.047891 CAGTTGCCTCATGAATACCTAGTTTA 58.952 38.462 0.00 0.00 0.00 2.01
519 527 7.011482 CAGTTGCCTCATGAATACCTAGTTTAC 59.989 40.741 0.00 0.00 0.00 2.01
520 528 5.925509 TGCCTCATGAATACCTAGTTTACC 58.074 41.667 0.00 0.00 0.00 2.85
521 529 4.989168 GCCTCATGAATACCTAGTTTACCG 59.011 45.833 0.00 0.00 0.00 4.02
539 547 1.283905 CCGGTGGGGTTCTTTATCCTT 59.716 52.381 0.00 0.00 0.00 3.36
547 555 6.888088 GTGGGGTTCTTTATCCTTTTTAGCTA 59.112 38.462 0.00 0.00 0.00 3.32
550 558 7.426410 GGGTTCTTTATCCTTTTTAGCTATGC 58.574 38.462 0.00 0.00 0.00 3.14
569 577 5.859205 ATGCCTCCTCAATCAAATAAACC 57.141 39.130 0.00 0.00 0.00 3.27
582 590 5.004448 TCAAATAAACCTAACGCATGGTCA 58.996 37.500 0.00 0.00 35.17 4.02
606 614 9.706691 TCAGATCCTTTGTAACTGTTTAACTAG 57.293 33.333 0.00 0.00 0.00 2.57
619 627 8.928270 ACTGTTTAACTAGGAAATATGTCTCG 57.072 34.615 0.00 0.00 0.00 4.04
639 647 7.073265 GTCTCGCTGATAGAGATAAACAGTAC 58.927 42.308 0.00 0.00 45.23 2.73
699 707 5.757886 CGTTGTTTCATTTGTGGTAGATGT 58.242 37.500 0.00 0.00 0.00 3.06
770 778 4.402583 CGTGTAACTGCATTATGTGGTTG 58.597 43.478 12.33 0.00 31.75 3.77
838 846 2.901338 ACTGGTCAGTAGCCTGTAGA 57.099 50.000 1.24 0.00 40.43 2.59
847 855 3.749088 CAGTAGCCTGTAGATCTAGGACG 59.251 52.174 14.74 0.00 36.11 4.79
849 857 1.495574 AGCCTGTAGATCTAGGACGGT 59.504 52.381 14.74 1.18 36.11 4.83
918 926 3.490439 TCCTTGAATGTTGCTGACTGA 57.510 42.857 0.00 0.00 0.00 3.41
919 927 3.141398 TCCTTGAATGTTGCTGACTGAC 58.859 45.455 0.00 0.00 0.00 3.51
1029 1039 1.138661 ACTCAGATTCTGCTAGCTGCC 59.861 52.381 17.23 8.11 42.00 4.85
1229 1239 0.520847 GCAAAGAAGGAGCTGCTGAC 59.479 55.000 9.14 6.54 0.00 3.51
2380 2415 0.104855 TCCTCGTATCATGGCTGTGC 59.895 55.000 0.00 0.00 0.00 4.57
2529 2567 0.606401 TTGCTGCACTCCTTACTGCC 60.606 55.000 0.00 0.00 31.97 4.85
2616 2654 7.783042 AGATTGTAAGAGTCAGTAACATACCC 58.217 38.462 0.00 0.00 0.00 3.69
3303 3363 1.202651 AGACGGGGAATATTTGAGGCG 60.203 52.381 0.00 0.00 0.00 5.52
3333 3393 3.412386 CATACTACAGGGCATAAAGGGC 58.588 50.000 0.00 0.00 0.00 5.19
3366 3426 6.456003 TCAGCTGATGATACCTTATGCAGGA 61.456 44.000 13.74 0.00 37.74 3.86
3428 3488 2.941720 GCAGGTCCATGTCATTTCTCTC 59.058 50.000 0.00 0.00 0.00 3.20
3513 3575 2.414161 GCATGCGTTTACTTTCAGGGAC 60.414 50.000 0.00 0.00 0.00 4.46
3619 3689 1.070289 ACCTCTTCCACGTTGAGTTCC 59.930 52.381 0.00 0.00 0.00 3.62
3699 3769 4.691216 GGGATGATAAACCAAGCGATAGTC 59.309 45.833 0.00 0.00 39.35 2.59
3764 3834 1.520342 GGTTTTGTTGCTGCGCCAA 60.520 52.632 4.18 0.00 0.00 4.52
3767 3837 0.108424 TTTTGTTGCTGCGCCAAACT 60.108 45.000 4.18 0.00 0.00 2.66
3781 3851 2.217429 CAAACTCCGTTTGGGTTTGG 57.783 50.000 9.30 0.00 46.10 3.28
3782 3852 1.478916 CAAACTCCGTTTGGGTTTGGT 59.521 47.619 9.30 0.00 46.10 3.67
3920 3990 1.752694 CGGCAGTGGGGTTTATGGG 60.753 63.158 0.00 0.00 0.00 4.00
3986 4056 2.397777 TTGTGTTGCGTACTTGCATG 57.602 45.000 0.00 0.00 45.78 4.06
4019 4181 2.907634 CTGCTGATGTCTCTTCTGCAT 58.092 47.619 13.86 0.00 43.92 3.96
4026 4188 3.213206 TGTCTCTTCTGCATGGTGTTT 57.787 42.857 0.00 0.00 0.00 2.83
4027 4189 3.141398 TGTCTCTTCTGCATGGTGTTTC 58.859 45.455 0.00 0.00 0.00 2.78
4034 4196 1.154150 GCATGGTGTTTCTGCGAGC 60.154 57.895 0.00 0.00 0.00 5.03
4114 4286 3.664025 GTGAAGCGAAAATACAAGCACAC 59.336 43.478 0.00 0.00 34.43 3.82
4118 4290 3.317993 AGCGAAAATACAAGCACACCTTT 59.682 39.130 0.00 0.00 0.00 3.11
4124 4296 2.128771 ACAAGCACACCTTTGTCACT 57.871 45.000 0.00 0.00 31.66 3.41
4125 4297 3.275617 ACAAGCACACCTTTGTCACTA 57.724 42.857 0.00 0.00 31.66 2.74
4126 4298 3.820557 ACAAGCACACCTTTGTCACTAT 58.179 40.909 0.00 0.00 31.66 2.12
4127 4299 3.565482 ACAAGCACACCTTTGTCACTATG 59.435 43.478 0.00 0.00 31.66 2.23
4168 4340 3.038017 CACACTGCGATTTCAACTGTTG 58.962 45.455 14.24 14.24 0.00 3.33
4171 4343 3.249799 CACTGCGATTTCAACTGTTGGTA 59.750 43.478 19.55 8.96 0.00 3.25
4181 4353 5.717078 TCAACTGTTGGTATACGAACTCT 57.283 39.130 25.15 11.76 35.89 3.24
4437 4635 2.593978 CTCAGGCCAGGGTCCATG 59.406 66.667 5.01 0.00 0.00 3.66
4560 4758 0.108377 CCATGCCGTAGCTGTACACA 60.108 55.000 0.00 0.00 40.80 3.72
4650 4854 0.241213 CGTCCGAGCAGAAGAAGACA 59.759 55.000 0.00 0.00 0.00 3.41
4656 4860 0.610174 AGCAGAAGAAGACATCCGCA 59.390 50.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.552273 CGGTGAGACGGATATAAACAGGG 60.552 52.174 0.00 0.00 0.00 4.45
1 2 3.639538 CGGTGAGACGGATATAAACAGG 58.360 50.000 0.00 0.00 0.00 4.00
2 3 3.050619 GCGGTGAGACGGATATAAACAG 58.949 50.000 0.00 0.00 0.00 3.16
3 4 2.223876 GGCGGTGAGACGGATATAAACA 60.224 50.000 0.00 0.00 0.00 2.83
4 5 2.401351 GGCGGTGAGACGGATATAAAC 58.599 52.381 0.00 0.00 0.00 2.01
5 6 2.806608 GGCGGTGAGACGGATATAAA 57.193 50.000 0.00 0.00 0.00 1.40
120 121 9.760077 GTATATAGGCGGCTTACAATAATACAT 57.240 33.333 19.76 1.84 0.00 2.29
121 122 7.916977 CGTATATAGGCGGCTTACAATAATACA 59.083 37.037 19.76 0.00 0.00 2.29
122 123 7.096312 GCGTATATAGGCGGCTTACAATAATAC 60.096 40.741 19.76 12.83 0.00 1.89
176 177 0.107017 CTGTAGGATGGCCAACTGGG 60.107 60.000 20.24 8.62 40.85 4.45
196 197 1.098050 GGACACAATCCCTGATGCAC 58.902 55.000 0.00 0.00 42.46 4.57
206 214 2.875933 TCGAACCAACTTGGACACAATC 59.124 45.455 15.14 2.56 40.96 2.67
255 263 2.519377 TTCATACTAATCCACGGCGG 57.481 50.000 13.24 0.00 0.00 6.13
311 319 0.478072 TGCCAGGACCTTGAACATGT 59.522 50.000 0.00 0.00 0.00 3.21
336 344 4.595781 AGTTACGGCAGGGAAATATATGGA 59.404 41.667 0.00 0.00 0.00 3.41
337 345 4.906618 AGTTACGGCAGGGAAATATATGG 58.093 43.478 0.00 0.00 0.00 2.74
346 354 2.351706 AAACAAAGTTACGGCAGGGA 57.648 45.000 0.00 0.00 0.00 4.20
371 379 9.881649 CATGCATGGACAATAAGAGTATACTAT 57.118 33.333 19.40 0.00 0.00 2.12
373 381 6.652481 GCATGCATGGACAATAAGAGTATACT 59.348 38.462 27.34 4.68 0.00 2.12
374 382 6.427853 TGCATGCATGGACAATAAGAGTATAC 59.572 38.462 27.34 5.53 0.00 1.47
375 383 6.532826 TGCATGCATGGACAATAAGAGTATA 58.467 36.000 27.34 0.00 0.00 1.47
376 384 5.379187 TGCATGCATGGACAATAAGAGTAT 58.621 37.500 27.34 0.00 0.00 2.12
377 385 4.779696 TGCATGCATGGACAATAAGAGTA 58.220 39.130 27.34 0.00 0.00 2.59
378 386 3.623703 TGCATGCATGGACAATAAGAGT 58.376 40.909 27.34 0.00 0.00 3.24
379 387 3.630769 ACTGCATGCATGGACAATAAGAG 59.369 43.478 27.34 12.81 0.00 2.85
380 388 3.623703 ACTGCATGCATGGACAATAAGA 58.376 40.909 27.34 0.00 0.00 2.10
383 391 2.880268 GCTACTGCATGCATGGACAATA 59.120 45.455 27.34 13.80 39.41 1.90
398 406 1.098050 GCCCCTGAACAATGCTACTG 58.902 55.000 0.00 0.00 0.00 2.74
399 407 0.698238 TGCCCCTGAACAATGCTACT 59.302 50.000 0.00 0.00 0.00 2.57
408 416 5.049405 CAGATAAATTACGATGCCCCTGAAC 60.049 44.000 0.00 0.00 0.00 3.18
409 417 5.063204 CAGATAAATTACGATGCCCCTGAA 58.937 41.667 0.00 0.00 0.00 3.02
413 421 3.751518 ACCAGATAAATTACGATGCCCC 58.248 45.455 0.00 0.00 0.00 5.80
414 422 4.578928 ACAACCAGATAAATTACGATGCCC 59.421 41.667 0.00 0.00 0.00 5.36
416 424 7.709269 TCTACAACCAGATAAATTACGATGC 57.291 36.000 0.00 0.00 0.00 3.91
434 442 7.504238 ACCAAACCATATGAAGTTGTTCTACAA 59.496 33.333 3.65 0.00 35.42 2.41
444 452 6.723298 TGACAAAACCAAACCATATGAAGT 57.277 33.333 3.65 0.00 0.00 3.01
458 466 3.392882 CAGGGCTGATTTTGACAAAACC 58.607 45.455 15.36 11.60 32.37 3.27
459 467 3.181466 ACCAGGGCTGATTTTGACAAAAC 60.181 43.478 15.36 10.07 32.37 2.43
464 472 1.909700 TCACCAGGGCTGATTTTGAC 58.090 50.000 0.00 0.00 0.00 3.18
465 473 2.225091 ACATCACCAGGGCTGATTTTGA 60.225 45.455 0.00 0.00 0.00 2.69
466 474 2.173519 ACATCACCAGGGCTGATTTTG 58.826 47.619 0.00 0.00 0.00 2.44
467 475 2.610438 ACATCACCAGGGCTGATTTT 57.390 45.000 0.00 0.00 0.00 1.82
468 476 2.578021 ACTACATCACCAGGGCTGATTT 59.422 45.455 0.00 0.00 0.00 2.17
519 527 0.916809 AGGATAAAGAACCCCACCGG 59.083 55.000 0.00 0.00 37.81 5.28
520 528 2.801077 AAGGATAAAGAACCCCACCG 57.199 50.000 0.00 0.00 0.00 4.94
521 529 5.105473 GCTAAAAAGGATAAAGAACCCCACC 60.105 44.000 0.00 0.00 0.00 4.61
528 536 7.502561 GGAGGCATAGCTAAAAAGGATAAAGAA 59.497 37.037 0.00 0.00 0.00 2.52
530 538 7.001073 AGGAGGCATAGCTAAAAAGGATAAAG 58.999 38.462 0.00 0.00 0.00 1.85
535 543 3.780294 TGAGGAGGCATAGCTAAAAAGGA 59.220 43.478 0.00 0.00 0.00 3.36
539 547 5.372343 TGATTGAGGAGGCATAGCTAAAA 57.628 39.130 0.00 0.00 0.00 1.52
547 555 5.522641 AGGTTTATTTGATTGAGGAGGCAT 58.477 37.500 0.00 0.00 0.00 4.40
550 558 6.458342 GCGTTAGGTTTATTTGATTGAGGAGG 60.458 42.308 0.00 0.00 0.00 4.30
569 577 2.898729 AGGATCTGACCATGCGTTAG 57.101 50.000 0.00 0.00 0.00 2.34
582 590 8.877195 TCCTAGTTAAACAGTTACAAAGGATCT 58.123 33.333 6.35 0.00 0.00 2.75
606 614 6.260870 TCTCTATCAGCGAGACATATTTCC 57.739 41.667 0.00 0.00 32.86 3.13
619 627 9.238368 AGATAGGTACTGTTTATCTCTATCAGC 57.762 37.037 0.00 0.00 41.52 4.26
639 647 7.565323 AGTTACCGTTACTTCAGTAGATAGG 57.435 40.000 0.00 0.00 0.00 2.57
749 757 5.049060 TGACAACCACATAATGCAGTTACAC 60.049 40.000 0.00 0.00 0.00 2.90
770 778 8.968242 CACAAGTAAAATTAAGAAAGGCTTGAC 58.032 33.333 0.00 0.00 37.42 3.18
838 846 2.353803 GCACTTGTGAACCGTCCTAGAT 60.354 50.000 4.79 0.00 0.00 1.98
847 855 6.902224 AAAACAAAATAGCACTTGTGAACC 57.098 33.333 4.79 0.00 35.95 3.62
903 911 2.874701 ACTGTGTCAGTCAGCAACATTC 59.125 45.455 0.00 0.00 41.21 2.67
918 926 1.734655 ATGGGAGGAACAGACTGTGT 58.265 50.000 9.33 0.00 43.24 3.72
919 927 4.494091 AATATGGGAGGAACAGACTGTG 57.506 45.455 9.33 0.00 0.00 3.66
1029 1039 0.393537 GGTTGCCATCTGGAGACTGG 60.394 60.000 0.00 0.00 37.39 4.00
1229 1239 1.542915 CCAAGCTGACCCATTGTTGAG 59.457 52.381 0.00 0.00 0.00 3.02
1326 1336 5.112220 TCTTTGCAATGACTTGTGATGAC 57.888 39.130 10.76 0.00 34.69 3.06
1433 1446 1.608590 GAGTTGCTTGCTTTAGTGGCA 59.391 47.619 0.00 0.00 37.97 4.92
2616 2654 4.335315 TGGCCTATAATGCTTGAAGTTTCG 59.665 41.667 3.32 0.00 0.00 3.46
3303 3363 2.036089 GCCCTGTAGTATGCCAGAGTAC 59.964 54.545 0.00 0.00 0.00 2.73
3366 3426 3.198409 TCAGTGAACTGCAACAGATGT 57.802 42.857 5.55 0.00 43.46 3.06
3497 3557 3.243336 CTCTCGTCCCTGAAAGTAAACG 58.757 50.000 0.00 0.00 34.06 3.60
3513 3575 1.373497 AGCCTTTGTCACGCTCTCG 60.373 57.895 0.00 0.00 42.43 4.04
3609 3679 0.969894 ACTCCCTCAGGAACTCAACG 59.030 55.000 0.00 0.00 43.40 4.10
3699 3769 5.627367 CGCAAGATAATTTCTCGTCTAGGAG 59.373 44.000 0.00 0.00 43.02 3.69
3767 3837 1.064611 TCTGAACCAAACCCAAACGGA 60.065 47.619 0.00 0.00 34.64 4.69
3782 3852 3.907474 TGGTACCCTTCTGTTCATCTGAA 59.093 43.478 10.07 0.00 33.95 3.02
3920 3990 1.400242 GCTGTTCAAGACGTCCAATGC 60.400 52.381 13.01 8.01 0.00 3.56
3996 4066 2.272678 CAGAAGAGACATCAGCAGCAG 58.727 52.381 0.00 0.00 0.00 4.24
4004 4074 2.983229 ACACCATGCAGAAGAGACATC 58.017 47.619 0.00 0.00 0.00 3.06
4019 4181 2.253758 GCAGCTCGCAGAAACACCA 61.254 57.895 3.64 0.00 41.79 4.17
4048 4219 4.154918 CAGATTTTGTAACCAGACTGCCTC 59.845 45.833 0.00 0.00 0.00 4.70
4052 4223 5.063204 TGTCCAGATTTTGTAACCAGACTG 58.937 41.667 0.00 0.00 0.00 3.51
4114 4286 5.235186 GTGTAGCATAGCATAGTGACAAAGG 59.765 44.000 0.00 0.00 0.00 3.11
4118 4290 3.704061 TGGTGTAGCATAGCATAGTGACA 59.296 43.478 0.00 0.00 0.00 3.58
4124 4296 3.118445 TGCAAGTGGTGTAGCATAGCATA 60.118 43.478 0.00 0.00 31.05 3.14
4125 4297 2.292267 GCAAGTGGTGTAGCATAGCAT 58.708 47.619 0.00 0.00 0.00 3.79
4126 4298 1.003003 TGCAAGTGGTGTAGCATAGCA 59.997 47.619 0.00 0.00 31.05 3.49
4127 4299 1.398390 GTGCAAGTGGTGTAGCATAGC 59.602 52.381 0.00 0.00 39.43 2.97
4159 4331 5.717078 AGAGTTCGTATACCAACAGTTGA 57.283 39.130 15.36 0.00 0.00 3.18
4168 4340 5.290400 GGTTTGCTACAAGAGTTCGTATACC 59.710 44.000 0.00 0.00 0.00 2.73
4171 4343 4.929808 CAGGTTTGCTACAAGAGTTCGTAT 59.070 41.667 0.00 0.00 0.00 3.06
4181 4353 4.002982 CTGAGCATACAGGTTTGCTACAA 58.997 43.478 15.63 5.99 45.46 2.41
4201 4374 2.045536 GGCCACCTGAAGGAGCTG 60.046 66.667 2.62 0.00 37.85 4.24
4202 4375 2.204059 AGGCCACCTGAAGGAGCT 60.204 61.111 5.01 0.00 37.85 4.09
4368 4566 2.758327 AGGCTGGACGGCGTGATA 60.758 61.111 21.19 1.70 44.22 2.15
4437 4635 3.363844 GAGGCAGCTGAGGGACGTC 62.364 68.421 20.43 7.13 0.00 4.34
4560 4758 2.282958 TCCGACAGGGAGAGCGTT 60.283 61.111 0.00 0.00 40.94 4.84
4635 4839 1.554392 CGGATGTCTTCTTCTGCTCG 58.446 55.000 0.00 0.00 0.00 5.03
4650 4854 3.211963 GCGGCCAAGATTGCGGAT 61.212 61.111 2.24 0.00 0.00 4.18
4656 4860 2.100631 CGACTTCGCGGCCAAGATT 61.101 57.895 14.31 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.