Multiple sequence alignment - TraesCS3A01G072300

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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 TraesCS3A01G072300 chr3A 100.000 4317 0 0 1 4317 44605605 44609921 0.000000e+00 7973
1 TraesCS3A01G072300 chr3D 95.166 3165 138 6 247 3407 32206638 32209791 0.000000e+00 4983
2 TraesCS3A01G072300 chr3D 88.201 517 40 11 3443 3950 32210544 32211048 7.990000e-167 597
3 TraesCS3A01G072300 chr3D 93.822 259 16 0 1 259 32193646 32193904 1.460000e-104 390
4 TraesCS3A01G072300 chr3D 91.739 230 17 1 3945 4174 32211074 32211301 6.970000e-83 318
5 TraesCS3A01G072300 chr3D 88.889 171 17 2 3641 3809 87925997 87926167 4.370000e-50 209
6 TraesCS3A01G072300 chr3D 88.387 155 9 2 4166 4314 32212351 32212502 1.230000e-40 178
7 TraesCS3A01G072300 chr5D 79.410 3356 634 45 1 3321 555635964 555639297 0.000000e+00 2316
8 TraesCS3A01G072300 chr5D 79.274 3334 633 47 3 3303 555906877 555910185 0.000000e+00 2276
9 TraesCS3A01G072300 chr5D 79.021 3351 660 33 3 3328 464701070 464697738 0.000000e+00 2254
10 TraesCS3A01G072300 chr5D 78.160 3315 668 46 1 3282 555555640 555558931 0.000000e+00 2060
11 TraesCS3A01G072300 chr5D 77.708 3342 694 46 5 3317 495551704 495548385 0.000000e+00 1997
12 TraesCS3A01G072300 chr5D 77.848 2379 478 36 971 3325 555488301 555490654 0.000000e+00 1428
13 TraesCS3A01G072300 chr5D 76.354 2068 458 28 1 2051 555046185 555048238 0.000000e+00 1081
14 TraesCS3A01G072300 chr5B 79.018 3360 640 52 1 3321 695814276 695810943 0.000000e+00 2239
15 TraesCS3A01G072300 chr5B 78.866 3350 657 40 3 3324 571606225 571609551 0.000000e+00 2217
16 TraesCS3A01G072300 chr5B 78.539 3355 641 62 3 3317 695493753 695490438 0.000000e+00 2134
17 TraesCS3A01G072300 chr5B 79.075 2681 505 46 675 3321 695695979 695693321 0.000000e+00 1792
18 TraesCS3A01G072300 chr5B 78.454 1954 383 32 1357 3292 695875784 695873851 0.000000e+00 1242
19 TraesCS3A01G072300 chr5B 75.037 1362 313 21 1 1348 695894109 695892761 1.330000e-169 606
20 TraesCS3A01G072300 chr5A 78.571 3360 663 46 3 3328 585201769 585198433 0.000000e+00 2163
21 TraesCS3A01G072300 chr1B 77.456 3105 644 43 233 3304 433644457 433641376 0.000000e+00 1805
22 TraesCS3A01G072300 chr6A 78.138 1665 341 18 1633 3292 584948982 584947336 0.000000e+00 1037
23 TraesCS3A01G072300 chr6A 79.798 1386 253 19 1946 3317 11233972 11232600 0.000000e+00 983
24 TraesCS3A01G072300 chr6D 80.020 996 181 15 1817 2805 436739065 436738081 0.000000e+00 721
25 TraesCS3A01G072300 chr6D 90.741 162 12 3 3644 3803 431160668 431160828 3.380000e-51 213
26 TraesCS3A01G072300 chr1A 77.752 863 182 8 3 858 402209015 402209874 4.950000e-144 521
27 TraesCS3A01G072300 chr1A 75.884 792 172 13 953 1737 402216066 402216845 1.880000e-103 387
28 TraesCS3A01G072300 chr1A 93.377 151 9 1 3655 3804 39438987 39438837 5.620000e-54 222
29 TraesCS3A01G072300 chr1A 90.303 165 14 2 3644 3806 566481008 566481172 9.400000e-52 215
30 TraesCS3A01G072300 chr2D 90.909 165 13 2 3641 3803 250630890 250630726 2.020000e-53 220
31 TraesCS3A01G072300 chr2A 90.909 165 13 2 3641 3803 249754623 249754459 2.020000e-53 220
32 TraesCS3A01G072300 chr7B 89.759 166 15 2 3640 3803 490208155 490207990 1.220000e-50 211
33 TraesCS3A01G072300 chr3B 89.017 173 15 4 3643 3812 529407789 529407960 1.220000e-50 211
34 TraesCS3A01G072300 chrUn 73.684 399 93 11 2939 3330 287475029 287475422 1.250000e-30 145
35 TraesCS3A01G072300 chrUn 73.684 399 93 11 2939 3330 296158690 296158297 1.250000e-30 145


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 TraesCS3A01G072300 chr3A 44605605 44609921 4316 False 7973 7973 100.00000 1 4317 1 chr3A.!!$F1 4316
1 TraesCS3A01G072300 chr3D 32206638 32212502 5864 False 1519 4983 90.87325 247 4314 4 chr3D.!!$F3 4067
2 TraesCS3A01G072300 chr5D 555635964 555639297 3333 False 2316 2316 79.41000 1 3321 1 chr5D.!!$F4 3320
3 TraesCS3A01G072300 chr5D 555906877 555910185 3308 False 2276 2276 79.27400 3 3303 1 chr5D.!!$F5 3300
4 TraesCS3A01G072300 chr5D 464697738 464701070 3332 True 2254 2254 79.02100 3 3328 1 chr5D.!!$R1 3325
5 TraesCS3A01G072300 chr5D 555555640 555558931 3291 False 2060 2060 78.16000 1 3282 1 chr5D.!!$F3 3281
6 TraesCS3A01G072300 chr5D 495548385 495551704 3319 True 1997 1997 77.70800 5 3317 1 chr5D.!!$R2 3312
7 TraesCS3A01G072300 chr5D 555488301 555490654 2353 False 1428 1428 77.84800 971 3325 1 chr5D.!!$F2 2354
8 TraesCS3A01G072300 chr5D 555046185 555048238 2053 False 1081 1081 76.35400 1 2051 1 chr5D.!!$F1 2050
9 TraesCS3A01G072300 chr5B 695810943 695814276 3333 True 2239 2239 79.01800 1 3321 1 chr5B.!!$R3 3320
10 TraesCS3A01G072300 chr5B 571606225 571609551 3326 False 2217 2217 78.86600 3 3324 1 chr5B.!!$F1 3321
11 TraesCS3A01G072300 chr5B 695490438 695493753 3315 True 2134 2134 78.53900 3 3317 1 chr5B.!!$R1 3314
12 TraesCS3A01G072300 chr5B 695693321 695695979 2658 True 1792 1792 79.07500 675 3321 1 chr5B.!!$R2 2646
13 TraesCS3A01G072300 chr5B 695873851 695875784 1933 True 1242 1242 78.45400 1357 3292 1 chr5B.!!$R4 1935
14 TraesCS3A01G072300 chr5B 695892761 695894109 1348 True 606 606 75.03700 1 1348 1 chr5B.!!$R5 1347
15 TraesCS3A01G072300 chr5A 585198433 585201769 3336 True 2163 2163 78.57100 3 3328 1 chr5A.!!$R1 3325
16 TraesCS3A01G072300 chr1B 433641376 433644457 3081 True 1805 1805 77.45600 233 3304 1 chr1B.!!$R1 3071
17 TraesCS3A01G072300 chr6A 584947336 584948982 1646 True 1037 1037 78.13800 1633 3292 1 chr6A.!!$R2 1659
18 TraesCS3A01G072300 chr6A 11232600 11233972 1372 True 983 983 79.79800 1946 3317 1 chr6A.!!$R1 1371
19 TraesCS3A01G072300 chr6D 436738081 436739065 984 True 721 721 80.02000 1817 2805 1 chr6D.!!$R1 988
20 TraesCS3A01G072300 chr1A 402209015 402209874 859 False 521 521 77.75200 3 858 1 chr1A.!!$F1 855
21 TraesCS3A01G072300 chr1A 402216066 402216845 779 False 387 387 75.88400 953 1737 1 chr1A.!!$F2 784

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
146 147 0.599991 TAGGCAACGTGTCACTGCTG 60.600 55.0 14.72 5.76 46.39 4.41 F
774 779 1.648467 GCCGGTCAGTTTCCATCAGC 61.648 60.0 1.90 0.00 0.00 4.26 F
1425 1432 0.391597 TATTCACCGAGCCGATTCCC 59.608 55.0 0.00 0.00 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1144 1150 1.370900 GCACGGTCAAAGCTGCAAG 60.371 57.895 1.02 0.00 0.00 4.01 R
2665 2689 0.590195 GGCTTCAAGTCACAGTGCAG 59.410 55.000 0.00 0.00 0.00 4.41 R
3414 4218 0.395311 TCGTGCCCACTCTAGTAGGG 60.395 60.000 11.12 11.12 45.68 3.53 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
88 89 3.168528 AACTGGACCACCGGCACT 61.169 61.111 0.00 0.00 45.88 4.40
89 90 3.178540 AACTGGACCACCGGCACTC 62.179 63.158 0.00 0.00 45.88 3.51
126 127 2.125952 CATCTCGTGCAGCCGACA 60.126 61.111 2.24 0.00 32.57 4.35
146 147 0.599991 TAGGCAACGTGTCACTGCTG 60.600 55.000 14.72 5.76 46.39 4.41
158 159 2.100631 ACTGCTGTATCGTTGCCGC 61.101 57.895 0.00 0.00 0.00 6.53
161 162 2.695055 CTGTATCGTTGCCGCACG 59.305 61.111 0.00 0.46 41.78 5.34
217 218 5.622180 GGTAACCTCTCTTTCCTTTCTGTT 58.378 41.667 0.00 0.00 0.00 3.16
229 230 3.711704 TCCTTTCTGTTCTCAACCTCACT 59.288 43.478 0.00 0.00 0.00 3.41
238 239 2.365617 TCTCAACCTCACTCTCACCAAC 59.634 50.000 0.00 0.00 0.00 3.77
433 434 3.868661 TGCTACGTATGCACAACCTTATG 59.131 43.478 13.42 0.00 35.31 1.90
435 436 7.592645 TGCTACGTATGCACAACCTTATGGT 62.593 44.000 13.42 0.00 41.16 3.55
719 724 4.988540 GCAATCAAAGTTTTAACCTCCCAC 59.011 41.667 0.00 0.00 0.00 4.61
774 779 1.648467 GCCGGTCAGTTTCCATCAGC 61.648 60.000 1.90 0.00 0.00 4.26
869 875 5.220605 GGTTAGCCAAATTATCACGACTCAC 60.221 44.000 0.00 0.00 34.09 3.51
883 889 3.251571 CGACTCACCTGGCTTAACTTAC 58.748 50.000 0.00 0.00 0.00 2.34
884 890 3.305813 CGACTCACCTGGCTTAACTTACA 60.306 47.826 0.00 0.00 0.00 2.41
898 904 9.556030 GGCTTAACTTACAATCTAACAACATTC 57.444 33.333 0.00 0.00 0.00 2.67
948 954 3.336468 TCTCACCAGTCTTACTCGTCTC 58.664 50.000 0.00 0.00 0.00 3.36
1004 1010 3.809832 CCACCAGAATTAGGTCTTATGCG 59.190 47.826 0.00 0.00 37.23 4.73
1144 1150 4.332828 AGTACCAGCAACATTAGGGAAAC 58.667 43.478 0.00 0.00 0.00 2.78
1145 1151 3.525800 ACCAGCAACATTAGGGAAACT 57.474 42.857 0.00 0.00 0.00 2.66
1204 1211 7.147461 ACAATTTAGAGGGGAATCTAGACTTCC 60.147 40.741 18.43 18.43 41.26 3.46
1308 1315 1.602377 GGAAACCTCACTTCACGGTTG 59.398 52.381 0.00 0.00 40.67 3.77
1425 1432 0.391597 TATTCACCGAGCCGATTCCC 59.608 55.000 0.00 0.00 0.00 3.97
1536 1543 3.871485 TCGGAGTCTAGGACAGTTACTC 58.129 50.000 0.52 0.00 36.64 2.59
1580 1587 2.877097 TCCATACCAAGCAGCTTTGA 57.123 45.000 13.09 0.00 0.00 2.69
1700 1707 5.774184 TGGATGTTTCTCACAATTCCATTGA 59.226 36.000 3.47 0.00 38.96 2.57
1737 1753 6.534436 CAGATGATGTTTCTGGTCTAAGACAG 59.466 42.308 0.00 0.00 37.53 3.51
1740 1756 7.009179 TGATGTTTCTGGTCTAAGACAGATT 57.991 36.000 1.61 0.00 35.17 2.40
1741 1757 6.875726 TGATGTTTCTGGTCTAAGACAGATTG 59.124 38.462 1.61 0.00 35.17 2.67
1819 1837 5.051907 GGACAACTTGATATGCTAACGTACG 60.052 44.000 15.01 15.01 0.00 3.67
2002 2020 2.923629 AGGTTAGAAGGCCAAATACCCA 59.076 45.455 5.01 0.00 0.00 4.51
2184 2202 4.221262 AGTGCCATTGTCATTTGCTTGTAT 59.779 37.500 0.00 0.00 0.00 2.29
2240 2259 6.906659 AGAACAATGCTTCTGTTGATACAAG 58.093 36.000 3.81 0.00 37.14 3.16
2485 2506 5.455849 CGTAACCTGATCAAGATACTCAACG 59.544 44.000 9.33 0.00 0.00 4.10
2629 2653 1.781555 CTCGACGTGTCAATGGCAC 59.218 57.895 8.09 8.09 0.00 5.01
2665 2689 4.020396 ACCATGATCACTATGAGCTGATCC 60.020 45.833 0.00 0.00 41.45 3.36
2754 2778 0.108945 GCATTGCAAGGTGGCTTCTC 60.109 55.000 13.30 0.00 34.04 2.87
2765 2789 0.037326 TGGCTTCTCGGTGATGACAC 60.037 55.000 0.00 0.00 45.27 3.67
2832 2856 4.684703 GCACCAGGTACATAATTAGCTACG 59.315 45.833 0.00 0.00 0.00 3.51
2856 2911 9.940166 ACGTCTTATTACAAACTGGTTTTTAAG 57.060 29.630 9.58 8.55 31.03 1.85
3013 3074 5.355350 CGGGATTATGCTTCTTGAAGTCTTT 59.645 40.000 11.41 0.00 0.00 2.52
3104 3165 0.473755 TCCTGCAGAGCTTGTCCAAA 59.526 50.000 17.39 0.00 0.00 3.28
3226 3287 0.468226 ACTCGCCTGACCAAAGAACA 59.532 50.000 0.00 0.00 0.00 3.18
3379 3446 1.083489 CAACGATGCGTGGGTGTATT 58.917 50.000 0.00 0.00 39.99 1.89
3384 3451 2.095466 CGATGCGTGGGTGTATTTGTTT 60.095 45.455 0.00 0.00 0.00 2.83
3385 3452 3.498082 GATGCGTGGGTGTATTTGTTTC 58.502 45.455 0.00 0.00 0.00 2.78
3414 4218 1.082690 GCACTAAGAGCAGCCACTTC 58.917 55.000 5.82 0.00 0.00 3.01
3415 4219 1.731720 CACTAAGAGCAGCCACTTCC 58.268 55.000 5.82 0.00 0.00 3.46
3422 4226 1.410882 GAGCAGCCACTTCCCTACTAG 59.589 57.143 0.00 0.00 0.00 2.57
3423 4227 1.007238 AGCAGCCACTTCCCTACTAGA 59.993 52.381 0.00 0.00 0.00 2.43
3424 4228 1.410882 GCAGCCACTTCCCTACTAGAG 59.589 57.143 0.00 0.00 0.00 2.43
3425 4229 2.741145 CAGCCACTTCCCTACTAGAGT 58.259 52.381 0.00 0.00 0.00 3.24
3426 4230 2.428890 CAGCCACTTCCCTACTAGAGTG 59.571 54.545 0.00 0.00 39.29 3.51
3429 4233 1.757699 CACTTCCCTACTAGAGTGGGC 59.242 57.143 6.56 0.00 44.32 5.36
3430 4234 1.361543 ACTTCCCTACTAGAGTGGGCA 59.638 52.381 6.56 0.00 44.32 5.36
3431 4235 1.757699 CTTCCCTACTAGAGTGGGCAC 59.242 57.143 6.56 0.00 44.32 5.01
3432 4236 0.395311 TCCCTACTAGAGTGGGCACG 60.395 60.000 6.56 0.00 44.32 5.34
3433 4237 0.395311 CCCTACTAGAGTGGGCACGA 60.395 60.000 6.56 0.00 44.32 4.35
3434 4238 1.471119 CCTACTAGAGTGGGCACGAA 58.529 55.000 0.00 0.00 39.82 3.85
3435 4239 2.032620 CCTACTAGAGTGGGCACGAAT 58.967 52.381 0.00 0.00 39.82 3.34
3436 4240 2.223829 CCTACTAGAGTGGGCACGAATG 60.224 54.545 0.00 0.00 39.82 2.67
3437 4241 1.557099 ACTAGAGTGGGCACGAATGA 58.443 50.000 0.00 0.00 36.20 2.57
3438 4242 1.899814 ACTAGAGTGGGCACGAATGAA 59.100 47.619 0.00 0.00 36.20 2.57
3439 4243 2.501723 ACTAGAGTGGGCACGAATGAAT 59.498 45.455 0.00 0.00 36.20 2.57
3440 4244 1.742761 AGAGTGGGCACGAATGAATG 58.257 50.000 0.00 0.00 36.20 2.67
3441 4245 1.003580 AGAGTGGGCACGAATGAATGT 59.996 47.619 0.00 0.00 36.20 2.71
3457 4261 7.467131 CGAATGAATGTGAGTATTTGGCATGTA 60.467 37.037 0.00 0.00 0.00 2.29
3462 4266 4.457603 TGTGAGTATTTGGCATGTACAACC 59.542 41.667 0.00 5.41 0.00 3.77
3481 4286 3.436700 CCGTTTGGTCAGCTTTTCTTT 57.563 42.857 0.00 0.00 0.00 2.52
3490 4295 3.315470 GTCAGCTTTTCTTTTCTCCGGTT 59.685 43.478 0.00 0.00 0.00 4.44
3492 4297 2.034685 AGCTTTTCTTTTCTCCGGTTGC 59.965 45.455 0.00 0.00 0.00 4.17
3525 4330 8.718734 ACGTAACATTCTTGTTTCCTTTCTATC 58.281 33.333 0.00 0.00 43.57 2.08
3579 4388 0.107831 AACAAGACCAGTGCGCCTAA 59.892 50.000 4.18 0.00 0.00 2.69
3592 4401 1.225376 CGCCTAACGCTTTGACCACA 61.225 55.000 0.00 0.00 34.21 4.17
3641 4450 3.641436 TGATATACCGAGTCAAGTGCCAT 59.359 43.478 0.00 0.00 0.00 4.40
3647 4456 3.181475 ACCGAGTCAAGTGCCATATACTG 60.181 47.826 0.00 0.00 0.00 2.74
3651 4460 3.134458 GTCAAGTGCCATATACTGCCTC 58.866 50.000 0.00 0.00 0.00 4.70
3655 4464 2.304180 AGTGCCATATACTGCCTCCATC 59.696 50.000 0.00 0.00 0.00 3.51
3656 4465 1.630369 TGCCATATACTGCCTCCATCC 59.370 52.381 0.00 0.00 0.00 3.51
3658 4467 3.107601 GCCATATACTGCCTCCATCCTA 58.892 50.000 0.00 0.00 0.00 2.94
3661 4470 5.339530 GCCATATACTGCCTCCATCCTAAAT 60.340 44.000 0.00 0.00 0.00 1.40
3662 4471 6.126768 GCCATATACTGCCTCCATCCTAAATA 60.127 42.308 0.00 0.00 0.00 1.40
3663 4472 7.420680 GCCATATACTGCCTCCATCCTAAATAT 60.421 40.741 0.00 0.00 0.00 1.28
3704 4515 9.549078 TTCCAATATGTATTACATACGAAGCAA 57.451 29.630 16.75 5.19 43.13 3.91
3705 4516 9.549078 TCCAATATGTATTACATACGAAGCAAA 57.451 29.630 16.75 0.00 43.13 3.68
3798 4609 8.959705 AAAGACTTATATTTAGGAACGGAAGG 57.040 34.615 0.00 0.00 0.00 3.46
3841 4652 4.554723 CGAGAACACATTCAAGTTTCACCC 60.555 45.833 0.00 0.00 37.29 4.61
3909 4722 5.423015 CATAGAGGCACAATACTTGACTGT 58.577 41.667 0.00 0.00 0.00 3.55
3930 4743 7.773149 ACTGTCTTCCAACATAGATGTACTAC 58.227 38.462 0.00 0.00 40.80 2.73
3954 4767 3.820777 TTTTGCAACAACCAAACTTGC 57.179 38.095 0.00 0.00 40.63 4.01
3965 4809 3.030291 ACCAAACTTGCCATCTTTGACA 58.970 40.909 0.00 0.00 0.00 3.58
4024 4868 8.987890 CGATGGATTGAACATTTTAACCTTTTT 58.012 29.630 0.00 0.00 0.00 1.94
4056 4900 4.689612 TTAAAGACAGGCAGACTTCACT 57.310 40.909 0.00 0.00 31.00 3.41
4095 4939 7.898309 CGTATGAAGTCCTCATTTAAGAAAACG 59.102 37.037 0.00 0.00 42.46 3.60
4097 4941 5.529430 TGAAGTCCTCATTTAAGAAAACGCA 59.471 36.000 0.00 0.00 0.00 5.24
4102 4946 4.618489 CCTCATTTAAGAAAACGCAAGCAG 59.382 41.667 0.00 0.00 45.62 4.24
4113 4957 1.447314 GCAAGCAGAAGCATTGCCC 60.447 57.895 4.70 0.00 43.14 5.36
4114 4958 1.217244 CAAGCAGAAGCATTGCCCC 59.783 57.895 4.70 0.00 45.49 5.80
4115 4959 2.345760 AAGCAGAAGCATTGCCCCG 61.346 57.895 4.70 0.00 45.49 5.73
4148 4992 1.203038 AGCATGTCCAATCACAACCCA 60.203 47.619 0.00 0.00 0.00 4.51
4178 6080 3.545703 AGCTCCGAAATAGTCAAATGGG 58.454 45.455 0.00 0.00 0.00 4.00
4204 6106 2.093500 GGCCCAATTTTTGAAGCCCTAG 60.093 50.000 0.00 0.00 41.33 3.02
4222 6130 5.139727 CCCTAGAAATGGCACCAATAATGA 58.860 41.667 0.00 0.00 0.00 2.57
4267 6175 6.360370 TTCTTATGACATATAGGACCAGCC 57.640 41.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 1.476110 CCAACCCAACGACAGAAAGGA 60.476 52.381 0.00 0.00 0.00 3.36
89 90 0.951558 CCAACCCAACGACAGAAAGG 59.048 55.000 0.00 0.00 0.00 3.11
126 127 0.321671 AGCAGTGACACGTTGCCTAT 59.678 50.000 14.34 0.00 38.58 2.57
217 218 2.365617 GTTGGTGAGAGTGAGGTTGAGA 59.634 50.000 0.00 0.00 0.00 3.27
229 230 1.754745 GCCTGTGAGGTTGGTGAGA 59.245 57.895 0.00 0.00 37.80 3.27
238 239 0.967380 GTGGAATTGGGCCTGTGAGG 60.967 60.000 4.53 0.00 38.80 3.86
360 361 2.791655 GGTTGAAACCTAGGTCAAGGG 58.208 52.381 16.64 0.00 45.75 3.95
433 434 9.807649 AGATCATTGCTGAACAAATTAATTACC 57.192 29.630 0.01 0.00 42.86 2.85
719 724 8.978539 TCTATATAGTGAAATAAAGCGCAACAG 58.021 33.333 11.47 0.00 0.00 3.16
774 779 0.304705 GTACCGGCATGATTCAAGCG 59.695 55.000 0.00 3.87 0.00 4.68
869 875 7.174253 TGTTGTTAGATTGTAAGTTAAGCCAGG 59.826 37.037 0.00 0.00 0.00 4.45
883 889 4.220382 TGGGCCAAGAATGTTGTTAGATTG 59.780 41.667 2.13 0.00 0.00 2.67
884 890 4.415596 TGGGCCAAGAATGTTGTTAGATT 58.584 39.130 2.13 0.00 0.00 2.40
948 954 1.476085 AGACTGCAGTTGGAGAGATCG 59.524 52.381 22.65 0.00 36.93 3.69
1004 1010 8.177378 TGTAAGAGACAGAAACGAGAGTTCCC 62.177 46.154 0.00 0.00 43.16 3.97
1129 1135 3.578688 CTGCAAGTTTCCCTAATGTTGC 58.421 45.455 0.00 0.00 38.27 4.17
1144 1150 1.370900 GCACGGTCAAAGCTGCAAG 60.371 57.895 1.02 0.00 0.00 4.01
1145 1151 1.383456 AAGCACGGTCAAAGCTGCAA 61.383 50.000 1.02 0.00 38.86 4.08
1204 1211 1.801178 GCACTGGGAAAGACTCGAAAG 59.199 52.381 0.00 0.00 0.00 2.62
1234 1241 9.096823 AGAATTATTATGTATACCGAGGAACCA 57.903 33.333 0.00 0.00 0.00 3.67
1308 1315 4.965119 ATAACCTGCTCGAAAAATGGTC 57.035 40.909 0.00 0.00 0.00 4.02
1536 1543 4.986659 CCTGAGAATTTGTTTGCTTCAAGG 59.013 41.667 0.00 0.00 0.00 3.61
1737 1753 8.824781 TTCGAAGAGAGATCAATTTGATCAATC 58.175 33.333 31.06 26.78 46.90 2.67
1740 1756 7.326454 AGTTCGAAGAGAGATCAATTTGATCA 58.674 34.615 31.06 12.82 46.90 2.92
1741 1757 7.769272 AGTTCGAAGAGAGATCAATTTGATC 57.231 36.000 25.38 25.38 45.74 2.92
1761 1777 3.942115 GGATGCTTCCTACCAAGAAGTTC 59.058 47.826 11.34 0.00 42.27 3.01
2205 2223 6.016443 CAGAAGCATTGTTCTTCTCCTTCTTT 60.016 38.462 2.59 0.00 46.01 2.52
2240 2259 1.635663 CTCGTGACCCGGAACATTGC 61.636 60.000 0.73 0.00 37.11 3.56
2463 2483 5.348986 GCGTTGAGTATCTTGATCAGGTTA 58.651 41.667 4.57 0.00 34.92 2.85
2485 2506 1.797025 AAGTCAAGGTTAGAGCACGC 58.203 50.000 0.00 0.00 0.00 5.34
2629 2653 4.510711 GTGATCATGGTGCAGATACTCAAG 59.489 45.833 0.00 0.00 0.00 3.02
2665 2689 0.590195 GGCTTCAAGTCACAGTGCAG 59.410 55.000 0.00 0.00 0.00 4.41
2765 2789 5.039984 GCATGCTCGTACATATCATAGAGG 58.960 45.833 11.37 0.00 0.00 3.69
2832 2856 9.188588 GCCTTAAAAACCAGTTTGTAATAAGAC 57.811 33.333 6.40 0.21 33.29 3.01
2856 2911 8.677148 TCTTGGAGACACTATTTATAATTGCC 57.323 34.615 0.00 0.00 42.67 4.52
3013 3074 3.192844 CGTCAGTTGGCTTCCTTCTAGTA 59.807 47.826 0.00 0.00 0.00 1.82
3104 3165 2.288702 GCAGTAGCTGACCATCGATGAT 60.289 50.000 26.86 10.22 37.91 2.45
3226 3287 1.351430 CGACCACATCACGCATCGTT 61.351 55.000 0.00 0.00 38.32 3.85
3317 3384 0.462759 CAGGCTAAAAGGGAGCTCGG 60.463 60.000 7.83 0.00 39.98 4.63
3364 3431 3.498082 GAAACAAATACACCCACGCATC 58.502 45.455 0.00 0.00 0.00 3.91
3379 3446 3.502191 AGTGCAAAAGAAGCGAAACAA 57.498 38.095 0.00 0.00 33.85 2.83
3384 3451 2.480419 GCTCTTAGTGCAAAAGAAGCGA 59.520 45.455 12.44 0.00 32.77 4.93
3385 3452 2.224079 TGCTCTTAGTGCAAAAGAAGCG 59.776 45.455 6.50 4.55 37.51 4.68
3414 4218 0.395311 TCGTGCCCACTCTAGTAGGG 60.395 60.000 11.12 11.12 45.68 3.53
3415 4219 1.471119 TTCGTGCCCACTCTAGTAGG 58.529 55.000 0.00 0.00 0.00 3.18
3422 4226 1.131126 CACATTCATTCGTGCCCACTC 59.869 52.381 0.00 0.00 0.00 3.51
3423 4227 1.167851 CACATTCATTCGTGCCCACT 58.832 50.000 0.00 0.00 0.00 4.00
3424 4228 1.131126 CTCACATTCATTCGTGCCCAC 59.869 52.381 0.00 0.00 33.03 4.61
3425 4229 1.271325 ACTCACATTCATTCGTGCCCA 60.271 47.619 0.00 0.00 33.03 5.36
3426 4230 1.453155 ACTCACATTCATTCGTGCCC 58.547 50.000 0.00 0.00 33.03 5.36
3427 4231 4.882671 AATACTCACATTCATTCGTGCC 57.117 40.909 0.00 0.00 33.03 5.01
3428 4232 5.030295 CCAAATACTCACATTCATTCGTGC 58.970 41.667 0.00 0.00 33.03 5.34
3429 4233 5.030295 GCCAAATACTCACATTCATTCGTG 58.970 41.667 0.00 0.00 34.34 4.35
3430 4234 4.699735 TGCCAAATACTCACATTCATTCGT 59.300 37.500 0.00 0.00 0.00 3.85
3431 4235 5.233957 TGCCAAATACTCACATTCATTCG 57.766 39.130 0.00 0.00 0.00 3.34
3432 4236 6.567050 ACATGCCAAATACTCACATTCATTC 58.433 36.000 0.00 0.00 0.00 2.67
3433 4237 6.534475 ACATGCCAAATACTCACATTCATT 57.466 33.333 0.00 0.00 0.00 2.57
3434 4238 6.602803 TGTACATGCCAAATACTCACATTCAT 59.397 34.615 0.00 0.00 0.00 2.57
3435 4239 5.942826 TGTACATGCCAAATACTCACATTCA 59.057 36.000 0.00 0.00 0.00 2.57
3436 4240 6.435430 TGTACATGCCAAATACTCACATTC 57.565 37.500 0.00 0.00 0.00 2.67
3437 4241 6.350110 GGTTGTACATGCCAAATACTCACATT 60.350 38.462 10.94 0.00 0.00 2.71
3438 4242 5.125417 GGTTGTACATGCCAAATACTCACAT 59.875 40.000 10.94 0.00 0.00 3.21
3439 4243 4.457603 GGTTGTACATGCCAAATACTCACA 59.542 41.667 10.94 0.00 0.00 3.58
3440 4244 4.436852 CGGTTGTACATGCCAAATACTCAC 60.437 45.833 14.76 0.00 0.00 3.51
3441 4245 3.687212 CGGTTGTACATGCCAAATACTCA 59.313 43.478 14.76 0.00 0.00 3.41
3457 4261 1.470051 AAAGCTGACCAAACGGTTGT 58.530 45.000 13.07 0.00 36.70 3.32
3462 4266 4.672409 AGAAAAGAAAAGCTGACCAAACG 58.328 39.130 0.00 0.00 0.00 3.60
3481 4286 0.038892 GTACTCACGCAACCGGAGAA 60.039 55.000 9.46 0.00 39.22 2.87
3490 4295 4.793678 ACAAGAATGTTACGTACTCACGCA 60.794 41.667 0.00 0.00 44.37 5.24
3504 4309 9.918630 CAATTGATAGAAAGGAAACAAGAATGT 57.081 29.630 0.00 0.00 43.14 2.71
3512 4317 7.468141 AGGGTTCAATTGATAGAAAGGAAAC 57.532 36.000 9.40 0.00 0.00 2.78
3525 4330 5.092781 CGTATTTCGGAAAGGGTTCAATTG 58.907 41.667 9.30 0.00 35.25 2.32
3551 4360 5.107453 GCGCACTGGTCTTGTTCATATATAC 60.107 44.000 0.30 0.00 0.00 1.47
3579 4388 1.065401 CACACATTGTGGTCAAAGCGT 59.935 47.619 20.33 0.00 44.27 5.07
3612 4421 6.378564 CACTTGACTCGGTATATCATAGGGAT 59.621 42.308 0.00 0.00 40.14 3.85
3625 4434 3.031736 AGTATATGGCACTTGACTCGGT 58.968 45.455 0.00 0.00 0.00 4.69
3641 4450 9.422681 GACTATATTTAGGATGGAGGCAGTATA 57.577 37.037 0.00 0.00 0.00 1.47
3647 4456 8.926092 AAAAAGACTATATTTAGGATGGAGGC 57.074 34.615 0.00 0.00 0.00 4.70
3691 4502 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
3698 4509 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
3776 4587 7.724287 ACTCCTTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
3789 4600 5.579904 GGACTATTTGTTACTCCTTCCGTTC 59.420 44.000 0.00 0.00 0.00 3.95
3792 4603 5.080969 TGGACTATTTGTTACTCCTTCCG 57.919 43.478 0.00 0.00 0.00 4.30
3793 4604 6.051179 ACTGGACTATTTGTTACTCCTTCC 57.949 41.667 0.00 0.00 0.00 3.46
3794 4605 6.107343 GGACTGGACTATTTGTTACTCCTTC 58.893 44.000 0.00 0.00 0.00 3.46
3795 4606 5.337330 CGGACTGGACTATTTGTTACTCCTT 60.337 44.000 0.00 0.00 0.00 3.36
3796 4607 4.159879 CGGACTGGACTATTTGTTACTCCT 59.840 45.833 0.00 0.00 0.00 3.69
3797 4608 4.159135 TCGGACTGGACTATTTGTTACTCC 59.841 45.833 0.00 0.00 0.00 3.85
3798 4609 5.125097 TCTCGGACTGGACTATTTGTTACTC 59.875 44.000 0.00 0.00 0.00 2.59
3814 4625 3.753294 ACTTGAATGTGTTCTCGGACT 57.247 42.857 0.00 0.00 35.33 3.85
3847 4660 3.939740 AGGCATGCCTGAGAAAATAGA 57.060 42.857 38.23 0.00 46.22 1.98
3946 4759 4.046462 CACTGTCAAAGATGGCAAGTTTG 58.954 43.478 15.30 15.30 41.46 2.93
3950 4763 3.316029 TCAACACTGTCAAAGATGGCAAG 59.684 43.478 0.00 0.00 41.46 4.01
3951 4764 3.066621 GTCAACACTGTCAAAGATGGCAA 59.933 43.478 0.00 0.00 41.46 4.52
3952 4765 2.618241 GTCAACACTGTCAAAGATGGCA 59.382 45.455 0.00 0.00 39.29 4.92
3954 4767 4.129380 TGAGTCAACACTGTCAAAGATGG 58.871 43.478 0.00 0.00 30.63 3.51
3965 4809 9.778741 TTAGTATTTGAGAAATGAGTCAACACT 57.221 29.630 0.00 0.00 34.70 3.55
3995 4839 6.432783 AGGTTAAAATGTTCAATCCATCGACA 59.567 34.615 0.00 0.00 0.00 4.35
4030 4874 7.389053 AGTGAAGTCTGCCTGTCTTTAATAAAG 59.611 37.037 6.42 6.42 39.88 1.85
4040 4884 2.805099 CAAGAAGTGAAGTCTGCCTGTC 59.195 50.000 0.00 0.00 0.00 3.51
4042 4886 3.117491 TCAAGAAGTGAAGTCTGCCTG 57.883 47.619 0.00 0.00 31.51 4.85
4056 4900 5.351465 GGACTTCATACGAAAGCATCAAGAA 59.649 40.000 0.00 0.00 0.00 2.52
4095 4939 1.447314 GGGCAATGCTTCTGCTTGC 60.447 57.895 4.82 12.92 44.57 4.01
4097 4941 2.345760 CGGGGCAATGCTTCTGCTT 61.346 57.895 4.82 0.00 39.82 3.91
4102 4946 1.372087 CTGAGACGGGGCAATGCTTC 61.372 60.000 4.82 0.00 0.00 3.86
4113 4957 2.360483 ACATGCTCTATCACTGAGACGG 59.640 50.000 0.00 0.00 33.68 4.79
4114 4958 3.549827 GGACATGCTCTATCACTGAGACG 60.550 52.174 0.00 0.00 33.68 4.18
4115 4959 3.382865 TGGACATGCTCTATCACTGAGAC 59.617 47.826 0.00 0.00 33.68 3.36
4160 5004 5.368145 CATCTCCCATTTGACTATTTCGGA 58.632 41.667 0.00 0.00 0.00 4.55
4163 5007 4.279420 GGCCATCTCCCATTTGACTATTTC 59.721 45.833 0.00 0.00 0.00 2.17
4167 5011 1.494721 GGGCCATCTCCCATTTGACTA 59.505 52.381 4.39 0.00 45.82 2.59
4178 6080 3.264947 GCTTCAAAAATTGGGCCATCTC 58.735 45.455 7.26 0.00 0.00 2.75
4204 6106 4.646492 AGGAGTCATTATTGGTGCCATTTC 59.354 41.667 0.00 0.00 0.00 2.17
4222 6130 0.988832 TGGGGTTGCGAATTAGGAGT 59.011 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.