Multiple sequence alignment - TraesCS2B01G080600

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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 TraesCS2B01G080600 chr2B 100.000 4409 0 0 1 4409 45033250 45028842 0.000000e+00 8142
1 TraesCS2B01G080600 chr2B 92.751 2828 122 22 1016 3775 45135922 45133110 0.000000e+00 4010
2 TraesCS2B01G080600 chr2B 87.814 3463 355 27 113 3514 44754747 44751291 0.000000e+00 3995
3 TraesCS2B01G080600 chr2B 87.450 2773 318 11 81 2827 45542327 45545095 0.000000e+00 3166
4 TraesCS2B01G080600 chr2B 90.539 2040 123 15 1339 3312 45667347 45669382 0.000000e+00 2634
5 TraesCS2B01G080600 chr2B 89.208 1844 182 11 1 1836 45041461 45039627 0.000000e+00 2287
6 TraesCS2B01G080600 chr2B 79.869 1371 211 27 2101 3429 44926462 44927809 0.000000e+00 942
7 TraesCS2B01G080600 chr2B 94.162 531 25 4 3775 4303 345473743 345474269 0.000000e+00 804
8 TraesCS2B01G080600 chr2B 86.792 318 39 3 3115 3430 45537400 45537716 7.020000e-93 351
9 TraesCS2B01G080600 chr2B 86.601 306 38 3 3127 3430 45038182 45037878 7.070000e-88 335
10 TraesCS2B01G080600 chr2B 83.333 246 27 7 3538 3775 45670006 45670245 9.600000e-52 215
11 TraesCS2B01G080600 chr2B 84.091 220 23 5 3566 3775 45546429 45546646 7.480000e-48 202
12 TraesCS2B01G080600 chr2D 94.855 3518 137 13 1 3475 27956678 27960194 0.000000e+00 5454
13 TraesCS2B01G080600 chr2D 88.879 3453 322 23 121 3514 28001767 27998318 0.000000e+00 4193
14 TraesCS2B01G080600 chr2D 89.919 1845 166 12 1 1836 28009349 28007516 0.000000e+00 2359
15 TraesCS2B01G080600 chr2D 82.027 2131 309 37 1347 3429 28417361 28415257 0.000000e+00 1746
16 TraesCS2B01G080600 chr2D 90.265 565 26 13 3240 3775 27976408 27975844 0.000000e+00 712
17 TraesCS2B01G080600 chr2D 87.736 318 36 3 3115 3430 28006083 28005767 6.970000e-98 368
18 TraesCS2B01G080600 chr2D 92.946 241 9 1 3543 3775 27960483 27960723 1.170000e-90 344
19 TraesCS2B01G080600 chr2D 85.020 247 27 5 3538 3775 27998251 27998006 4.410000e-60 243
20 TraesCS2B01G080600 chr2A 90.851 3574 257 25 1 3514 30165039 30161476 0.000000e+00 4724
21 TraesCS2B01G080600 chr2A 83.188 3331 480 34 155 3430 30300997 30304302 0.000000e+00 2976
22 TraesCS2B01G080600 chr2A 82.792 3324 491 35 158 3429 30272079 30268785 0.000000e+00 2894
23 TraesCS2B01G080600 chr2A 82.503 3332 492 49 155 3429 30246832 30243535 0.000000e+00 2839
24 TraesCS2B01G080600 chr2A 82.443 3332 495 49 155 3429 30256435 30253137 0.000000e+00 2830
25 TraesCS2B01G080600 chr2A 87.421 318 37 3 3115 3430 30184925 30184609 3.240000e-96 363
26 TraesCS2B01G080600 chr7D 83.034 2835 422 31 155 2955 302743603 302746412 0.000000e+00 2516
27 TraesCS2B01G080600 chr6B 93.023 559 36 3 3775 4332 400542033 400541477 0.000000e+00 813
28 TraesCS2B01G080600 chr5B 95.174 518 19 3 3775 4289 429556189 429555675 0.000000e+00 813
29 TraesCS2B01G080600 chr5B 93.233 532 31 4 3775 4304 266835537 266835009 0.000000e+00 778
30 TraesCS2B01G080600 chr5B 92.871 533 30 6 3772 4302 266857999 266857473 0.000000e+00 767
31 TraesCS2B01G080600 chr6D 93.645 535 25 7 3775 4301 295090971 295090438 0.000000e+00 791
32 TraesCS2B01G080600 chr6D 93.494 538 26 5 3781 4311 295098923 295098388 0.000000e+00 791
33 TraesCS2B01G080600 chr1B 93.762 529 30 3 3775 4302 231152672 231152146 0.000000e+00 791
34 TraesCS2B01G080600 chr4D 90.206 582 40 12 3775 4347 434948333 434947760 0.000000e+00 743


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 TraesCS2B01G080600 chr2B 45028842 45033250 4408 True 8142.0 8142 100.0000 1 4409 1 chr2B.!!$R2 4408
1 TraesCS2B01G080600 chr2B 45133110 45135922 2812 True 4010.0 4010 92.7510 1016 3775 1 chr2B.!!$R3 2759
2 TraesCS2B01G080600 chr2B 44751291 44754747 3456 True 3995.0 3995 87.8140 113 3514 1 chr2B.!!$R1 3401
3 TraesCS2B01G080600 chr2B 45542327 45546646 4319 False 1684.0 3166 85.7705 81 3775 2 chr2B.!!$F4 3694
4 TraesCS2B01G080600 chr2B 45667347 45670245 2898 False 1424.5 2634 86.9360 1339 3775 2 chr2B.!!$F5 2436
5 TraesCS2B01G080600 chr2B 45037878 45041461 3583 True 1311.0 2287 87.9045 1 3430 2 chr2B.!!$R4 3429
6 TraesCS2B01G080600 chr2B 44926462 44927809 1347 False 942.0 942 79.8690 2101 3429 1 chr2B.!!$F1 1328
7 TraesCS2B01G080600 chr2B 345473743 345474269 526 False 804.0 804 94.1620 3775 4303 1 chr2B.!!$F3 528
8 TraesCS2B01G080600 chr2D 27956678 27960723 4045 False 2899.0 5454 93.9005 1 3775 2 chr2D.!!$F1 3774
9 TraesCS2B01G080600 chr2D 27998006 28001767 3761 True 2218.0 4193 86.9495 121 3775 2 chr2D.!!$R3 3654
10 TraesCS2B01G080600 chr2D 28415257 28417361 2104 True 1746.0 1746 82.0270 1347 3429 1 chr2D.!!$R2 2082
11 TraesCS2B01G080600 chr2D 28005767 28009349 3582 True 1363.5 2359 88.8275 1 3430 2 chr2D.!!$R4 3429
12 TraesCS2B01G080600 chr2D 27975844 27976408 564 True 712.0 712 90.2650 3240 3775 1 chr2D.!!$R1 535
13 TraesCS2B01G080600 chr2A 30161476 30165039 3563 True 4724.0 4724 90.8510 1 3514 1 chr2A.!!$R1 3513
14 TraesCS2B01G080600 chr2A 30300997 30304302 3305 False 2976.0 2976 83.1880 155 3430 1 chr2A.!!$F1 3275
15 TraesCS2B01G080600 chr2A 30268785 30272079 3294 True 2894.0 2894 82.7920 158 3429 1 chr2A.!!$R5 3271
16 TraesCS2B01G080600 chr2A 30243535 30246832 3297 True 2839.0 2839 82.5030 155 3429 1 chr2A.!!$R3 3274
17 TraesCS2B01G080600 chr2A 30253137 30256435 3298 True 2830.0 2830 82.4430 155 3429 1 chr2A.!!$R4 3274
18 TraesCS2B01G080600 chr7D 302743603 302746412 2809 False 2516.0 2516 83.0340 155 2955 1 chr7D.!!$F1 2800
19 TraesCS2B01G080600 chr6B 400541477 400542033 556 True 813.0 813 93.0230 3775 4332 1 chr6B.!!$R1 557
20 TraesCS2B01G080600 chr5B 429555675 429556189 514 True 813.0 813 95.1740 3775 4289 1 chr5B.!!$R3 514
21 TraesCS2B01G080600 chr5B 266835009 266835537 528 True 778.0 778 93.2330 3775 4304 1 chr5B.!!$R1 529
22 TraesCS2B01G080600 chr5B 266857473 266857999 526 True 767.0 767 92.8710 3772 4302 1 chr5B.!!$R2 530
23 TraesCS2B01G080600 chr6D 295090438 295090971 533 True 791.0 791 93.6450 3775 4301 1 chr6D.!!$R1 526
24 TraesCS2B01G080600 chr6D 295098388 295098923 535 True 791.0 791 93.4940 3781 4311 1 chr6D.!!$R2 530
25 TraesCS2B01G080600 chr1B 231152146 231152672 526 True 791.0 791 93.7620 3775 4302 1 chr1B.!!$R1 527
26 TraesCS2B01G080600 chr4D 434947760 434948333 573 True 743.0 743 90.2060 3775 4347 1 chr4D.!!$R1 572

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
60 65 1.533625 TCCGGCAGACAAATCCTTTG 58.466 50.000 0.00 0.0 45.95 2.77 F
370 395 1.537152 AAAGGGGCCATTTGCAGCT 60.537 52.632 16.43 0.0 43.89 4.24 F
643 668 2.552743 GGAAACAACACTCTTACAGGCC 59.447 50.000 0.00 0.0 0.00 5.19 F
1975 2100 0.881118 TGCCGTGCCTGAATTCTTTC 59.119 50.000 7.05 0.0 0.00 2.62 F
2858 3516 1.143373 GACGATAACATCACCGCGCA 61.143 55.000 8.75 0.0 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1095 1124 1.003233 GACTGGAGGTTTGGTAGTGGG 59.997 57.143 0.00 0.0 0.00 4.61 R
1802 1832 1.434513 TTCCAGTGGCAGTTCCCCAT 61.435 55.000 3.51 0.0 34.34 4.00 R
2481 2647 1.480954 GCCAATCTCCTGTCGGACTTA 59.519 52.381 9.88 0.0 34.92 2.24 R
3285 4020 0.320771 GCTTGTCCTTCGGAGCTTCA 60.321 55.000 0.00 0.0 29.39 3.02 R
4312 5772 0.340908 GGGTGGGGAGTTAGTAGGGA 59.659 60.000 0.00 0.0 0.00 4.20 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
60 65 1.533625 TCCGGCAGACAAATCCTTTG 58.466 50.000 0.00 0.00 45.95 2.77
195 213 5.353678 GTCTCTGCTCTGTATTTTGCTCATT 59.646 40.000 0.00 0.00 0.00 2.57
223 241 4.404394 TCTCCTTCAACACTACAACACTCA 59.596 41.667 0.00 0.00 0.00 3.41
291 316 2.799017 TGCTTCAAGTCTGGCATCAAT 58.201 42.857 0.00 0.00 0.00 2.57
359 384 1.546029 CTTTTGTAGCTGGAAAGGGGC 59.454 52.381 0.00 0.00 0.00 5.80
370 395 1.537152 AAAGGGGCCATTTGCAGCT 60.537 52.632 16.43 0.00 43.89 4.24
436 461 3.197766 TCGTCTCAGTGGGCAAATATCTT 59.802 43.478 0.00 0.00 0.00 2.40
643 668 2.552743 GGAAACAACACTCTTACAGGCC 59.447 50.000 0.00 0.00 0.00 5.19
736 761 6.044404 TGGAGAGATCCCTTCTACTTTGTTTT 59.956 38.462 0.00 0.00 33.74 2.43
738 763 7.549842 GGAGAGATCCCTTCTACTTTGTTTTAC 59.450 40.741 0.00 0.00 33.74 2.01
745 770 9.112725 TCCCTTCTACTTTGTTTTACAACTTAC 57.887 33.333 0.00 0.00 37.90 2.34
897 926 7.703755 AGGAAATATTTCTTCCCTCACTTCTT 58.296 34.615 23.85 0.00 42.98 2.52
1095 1124 5.354234 CAGTTACCATCTTACATTGGTCACC 59.646 44.000 0.00 0.00 42.61 4.02
1096 1125 3.366052 ACCATCTTACATTGGTCACCC 57.634 47.619 0.00 0.00 42.61 4.61
1154 1183 3.092511 GCTGGAGGGCCTGATCCA 61.093 66.667 12.95 19.50 43.34 3.41
1399 1429 5.940470 CCTGTAGCAGTTGTTAATCTTTCCT 59.060 40.000 0.00 0.00 0.00 3.36
1802 1832 4.816385 GGACTTCTCACACAACAATCTCAA 59.184 41.667 0.00 0.00 0.00 3.02
1929 2054 5.588240 CAGTTAGTATCAACCGTGCAGATA 58.412 41.667 0.00 0.00 0.00 1.98
1975 2100 0.881118 TGCCGTGCCTGAATTCTTTC 59.119 50.000 7.05 0.00 0.00 2.62
2275 2400 3.513912 TCTTTGGAAGAGAGCGGTATTCA 59.486 43.478 8.41 0.00 32.71 2.57
2356 2498 7.882271 AGAAGAGAAGAGAAATGCATACAGTTT 59.118 33.333 0.00 0.00 33.46 2.66
2481 2647 7.728532 ACTGGATCAGTTTATTTTGGTAGGTTT 59.271 33.333 0.00 0.00 42.59 3.27
2669 2850 1.824230 GTTCATGGTTAATGGCAGCCA 59.176 47.619 18.99 18.99 36.86 4.75
2741 2922 6.658849 TGCTAAACTTTGGCAAGAGGATATA 58.341 36.000 9.91 0.00 44.47 0.86
2858 3516 1.143373 GACGATAACATCACCGCGCA 61.143 55.000 8.75 0.00 0.00 6.09
2936 3594 2.423947 GCCTGGATGATGTTGGAGGAAT 60.424 50.000 0.00 0.00 0.00 3.01
2968 3626 1.457009 GGCACCCGGTAAGTTTTGCA 61.457 55.000 0.00 0.00 0.00 4.08
3019 3678 6.807789 TGTCTGGTACGTATGTGCATTATTA 58.192 36.000 0.00 0.00 31.53 0.98
3054 3763 2.822399 GCAGAGTACGGGATGGGG 59.178 66.667 0.00 0.00 0.00 4.96
3125 3858 4.549458 CTGGAGTTGCTTATGTTTGTTGG 58.451 43.478 0.00 0.00 0.00 3.77
3147 3880 4.157246 GTGGACTTACCCTTCCCATTTTT 58.843 43.478 0.00 0.00 38.00 1.94
3285 4020 0.746063 TTGGACTGTCGTGTACCGTT 59.254 50.000 1.07 0.00 37.94 4.44
3349 4427 5.639506 GCAAAACTTACTGCTATCAGAGACA 59.360 40.000 0.00 0.00 42.95 3.41
3381 4460 0.647410 GCCGTGATGACATTGACGAG 59.353 55.000 17.82 11.24 0.00 4.18
3461 4557 5.219343 TCATTGTGCCCTGTCTATATGAG 57.781 43.478 0.00 0.00 0.00 2.90
3470 4566 5.740513 GCCCTGTCTATATGAGGAACTGAAC 60.741 48.000 0.00 0.00 41.55 3.18
3482 4578 5.820423 TGAGGAACTGAACGAAAATTTGAGA 59.180 36.000 0.00 0.00 41.55 3.27
3491 4587 5.100751 ACGAAAATTTGAGACTTGAGCAG 57.899 39.130 0.00 0.00 0.00 4.24
3528 4861 5.413833 CAGTGAGCAACTATCCTTTGTTGAT 59.586 40.000 9.62 3.36 44.01 2.57
3531 4864 7.014615 AGTGAGCAACTATCCTTTGTTGATTTT 59.985 33.333 9.62 0.00 41.87 1.82
3533 4866 7.867403 TGAGCAACTATCCTTTGTTGATTTTTC 59.133 33.333 9.62 1.04 41.87 2.29
3564 4991 7.831690 TGAGGTGTATGTATGGCAAAATTCTTA 59.168 33.333 0.00 0.00 0.00 2.10
3636 5063 4.381292 CCCATGAAATCTTTTGTCCAGCTC 60.381 45.833 0.00 0.00 0.00 4.09
3880 5317 6.373359 GTTAGAAACCTAGTTCGAACTTCG 57.627 41.667 33.82 24.78 38.99 3.79
3970 5409 9.781633 ACAAATAATGCGTAGGTAATTATGGTA 57.218 29.630 0.00 0.00 0.00 3.25
4098 5543 4.892433 TGTTTAGGGTGCCAAATCAATTG 58.108 39.130 0.00 0.00 38.84 2.32
4312 5772 4.585216 TCCACCCCGGTCCACCTT 62.585 66.667 0.00 0.00 35.57 3.50
4328 5788 1.726352 ACCTTCCCTACTAACTCCCCA 59.274 52.381 0.00 0.00 0.00 4.96
4335 5795 1.814292 TACTAACTCCCCACCCCCGT 61.814 60.000 0.00 0.00 0.00 5.28
4336 5796 1.002017 CTAACTCCCCACCCCCGTA 59.998 63.158 0.00 0.00 0.00 4.02
4338 5798 0.178879 TAACTCCCCACCCCCGTAAA 60.179 55.000 0.00 0.00 0.00 2.01
4341 5801 2.937136 CCCCACCCCCGTAAACCT 60.937 66.667 0.00 0.00 0.00 3.50
4342 5802 1.616025 CCCCACCCCCGTAAACCTA 60.616 63.158 0.00 0.00 0.00 3.08
4343 5803 1.206811 CCCCACCCCCGTAAACCTAA 61.207 60.000 0.00 0.00 0.00 2.69
4344 5804 0.035152 CCCACCCCCGTAAACCTAAC 60.035 60.000 0.00 0.00 0.00 2.34
4345 5805 0.035152 CCACCCCCGTAAACCTAACC 60.035 60.000 0.00 0.00 0.00 2.85
4362 5822 4.798682 CCCCCTACTCGCCCCACT 62.799 72.222 0.00 0.00 0.00 4.00
4363 5823 3.155167 CCCCTACTCGCCCCACTC 61.155 72.222 0.00 0.00 0.00 3.51
4364 5824 3.155167 CCCTACTCGCCCCACTCC 61.155 72.222 0.00 0.00 0.00 3.85
4365 5825 3.155167 CCTACTCGCCCCACTCCC 61.155 72.222 0.00 0.00 0.00 4.30
4366 5826 2.042843 CTACTCGCCCCACTCCCT 60.043 66.667 0.00 0.00 0.00 4.20
4367 5827 2.043248 TACTCGCCCCACTCCCTC 60.043 66.667 0.00 0.00 0.00 4.30
4368 5828 2.575455 CTACTCGCCCCACTCCCTCT 62.575 65.000 0.00 0.00 0.00 3.69
4369 5829 2.569218 TACTCGCCCCACTCCCTCTC 62.569 65.000 0.00 0.00 0.00 3.20
4370 5830 4.779733 TCGCCCCACTCCCTCTCC 62.780 72.222 0.00 0.00 0.00 3.71
4374 5834 4.400251 CCCACTCCCTCTCCCCGT 62.400 72.222 0.00 0.00 0.00 5.28
4375 5835 2.760385 CCACTCCCTCTCCCCGTC 60.760 72.222 0.00 0.00 0.00 4.79
4376 5836 2.760385 CACTCCCTCTCCCCGTCC 60.760 72.222 0.00 0.00 0.00 4.79
4377 5837 4.077180 ACTCCCTCTCCCCGTCCC 62.077 72.222 0.00 0.00 0.00 4.46
4380 5840 4.541648 CCCTCTCCCCGTCCCGAT 62.542 72.222 0.00 0.00 0.00 4.18
4381 5841 2.913060 CCTCTCCCCGTCCCGATC 60.913 72.222 0.00 0.00 0.00 3.69
4382 5842 3.288290 CTCTCCCCGTCCCGATCG 61.288 72.222 8.51 8.51 0.00 3.69
4383 5843 4.889112 TCTCCCCGTCCCGATCGG 62.889 72.222 27.65 27.65 46.49 4.18
4387 5847 4.203076 CCCGTCCCGATCGGTGAC 62.203 72.222 30.38 30.38 45.63 3.67
4399 5859 4.373771 GGTGACGAAACCCCACTC 57.626 61.111 0.00 0.00 33.79 3.51
4400 5860 1.302271 GGTGACGAAACCCCACTCC 60.302 63.158 0.00 0.00 33.79 3.85
4401 5861 1.302271 GTGACGAAACCCCACTCCC 60.302 63.158 0.00 0.00 0.00 4.30
4402 5862 2.350134 GACGAAACCCCACTCCCC 59.650 66.667 0.00 0.00 0.00 4.81
4403 5863 2.448931 ACGAAACCCCACTCCCCA 60.449 61.111 0.00 0.00 0.00 4.96
4404 5864 2.033602 CGAAACCCCACTCCCCAC 59.966 66.667 0.00 0.00 0.00 4.61
4405 5865 2.526046 CGAAACCCCACTCCCCACT 61.526 63.158 0.00 0.00 0.00 4.00
4406 5866 1.379146 GAAACCCCACTCCCCACTC 59.621 63.158 0.00 0.00 0.00 3.51
4407 5867 1.072930 AAACCCCACTCCCCACTCT 60.073 57.895 0.00 0.00 0.00 3.24
4408 5868 1.134438 AAACCCCACTCCCCACTCTC 61.134 60.000 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 65 3.947196 TGTGTAGAATGTGGATGCCATTC 59.053 43.478 15.70 15.70 45.46 2.67
195 213 6.315393 GTGTTGTAGTGTTGAAGGAGAAAAGA 59.685 38.462 0.00 0.00 0.00 2.52
223 241 2.195922 CTTGTTTTCTTGCGCTGCTTT 58.804 42.857 9.73 0.00 0.00 3.51
291 316 2.502745 AGGATGCCAAGGGGATAAGAA 58.497 47.619 0.00 0.00 32.75 2.52
337 362 2.558359 CCCCTTTCCAGCTACAAAAGTG 59.442 50.000 11.51 3.33 0.00 3.16
359 384 2.611224 GGGAACTTTGAGCTGCAAATGG 60.611 50.000 1.02 4.84 44.90 3.16
370 395 2.840576 CCGGGGTGGGAACTTTGA 59.159 61.111 0.00 0.00 0.00 2.69
436 461 3.769739 AGTCAAGTTGCCTACACATCA 57.230 42.857 0.00 0.00 0.00 3.07
643 668 2.959030 TGGTCAATGAGAGAGGGATACG 59.041 50.000 0.00 0.00 37.60 3.06
745 770 4.651503 TCTGGAGATCAACCTTAGCTTAGG 59.348 45.833 17.22 17.22 41.31 2.69
897 926 3.699038 AGCTTATTTTGGCCGAGCAATAA 59.301 39.130 8.84 8.84 35.86 1.40
1095 1124 1.003233 GACTGGAGGTTTGGTAGTGGG 59.997 57.143 0.00 0.00 0.00 4.61
1096 1125 1.003233 GGACTGGAGGTTTGGTAGTGG 59.997 57.143 0.00 0.00 0.00 4.00
1154 1183 5.420725 TGACATGTTGGCTAGTGAAGTAT 57.579 39.130 0.00 0.00 0.00 2.12
1290 1319 5.655488 AGAGATGTAAGAAATGACCAGTCG 58.345 41.667 0.00 0.00 0.00 4.18
1529 1559 3.230134 AGGTTTTGCAGCTTACCAATGA 58.770 40.909 11.97 0.00 33.02 2.57
1802 1832 1.434513 TTCCAGTGGCAGTTCCCCAT 61.435 55.000 3.51 0.00 34.34 4.00
1929 2054 7.066284 CCGGATAAGTCATTGTGAGAAAGATTT 59.934 37.037 0.00 0.00 0.00 2.17
2275 2400 6.112058 ACACAACAGCCAATTGTAAAAATGT 58.888 32.000 4.43 0.00 38.22 2.71
2323 2465 6.070021 TGCATTTCTCTTCTCTTCTTATGGGA 60.070 38.462 0.00 0.00 0.00 4.37
2329 2471 7.393216 ACTGTATGCATTTCTCTTCTCTTCTT 58.607 34.615 3.54 0.00 0.00 2.52
2481 2647 1.480954 GCCAATCTCCTGTCGGACTTA 59.519 52.381 9.88 0.00 34.92 2.24
2501 2667 6.072286 ACTCAAGTTGAATACTTTGATGGCAG 60.072 38.462 7.06 0.00 44.73 4.85
2530 2696 5.683859 CACTTCACACTCAATAAAGTCAGC 58.316 41.667 0.00 0.00 0.00 4.26
2669 2850 4.382470 GCTCAGAGTGTAACCATCTGTCAT 60.382 45.833 0.00 0.00 41.01 3.06
2741 2922 1.524621 GCCACATCTGCCGCTATGT 60.525 57.895 6.21 6.21 36.78 2.29
2762 2943 4.158394 GGTTGTGGACATAATCAAGCACAT 59.842 41.667 0.00 0.00 37.93 3.21
2765 2946 3.760738 TGGTTGTGGACATAATCAAGCA 58.239 40.909 0.00 0.00 42.91 3.91
2858 3516 2.434428 CTGAGCCAAAATCACTGAGCT 58.566 47.619 0.00 0.00 0.00 4.09
3000 3659 8.714179 TGCTTTATAATAATGCACATACGTACC 58.286 33.333 0.00 0.00 0.00 3.34
3035 3744 2.423898 CCCATCCCGTACTCTGCGT 61.424 63.158 0.00 0.00 0.00 5.24
3054 3763 2.548493 AGCTCCTACGGAGATCTCGTAC 60.548 54.545 16.46 9.71 46.28 3.67
3125 3858 3.451402 AAATGGGAAGGGTAAGTCCAC 57.549 47.619 0.00 0.00 38.11 4.02
3147 3880 7.092712 ACTCTATCAGGAAACATGGATTCAGAA 60.093 37.037 13.46 0.00 0.00 3.02
3162 3897 2.025155 GTCTCCGCAACTCTATCAGGA 58.975 52.381 0.00 0.00 0.00 3.86
3285 4020 0.320771 GCTTGTCCTTCGGAGCTTCA 60.321 55.000 0.00 0.00 29.39 3.02
3302 4037 4.021719 CACAAACATCTTTCATTCCAGGCT 60.022 41.667 0.00 0.00 0.00 4.58
3349 4427 2.270352 TCACGGCATTCCAGAAAAGT 57.730 45.000 0.00 0.00 0.00 2.66
3446 4542 3.898123 TCAGTTCCTCATATAGACAGGGC 59.102 47.826 0.00 0.00 0.00 5.19
3461 4557 6.061231 AGTCTCAAATTTTCGTTCAGTTCC 57.939 37.500 0.00 0.00 0.00 3.62
3470 4566 5.178252 TCTCTGCTCAAGTCTCAAATTTTCG 59.822 40.000 0.00 0.00 0.00 3.46
3482 4578 5.005740 TGCAAAACATATCTCTGCTCAAGT 58.994 37.500 0.00 0.00 34.10 3.16
3528 4861 7.870445 GCCATACATACACCTCAAAAAGAAAAA 59.130 33.333 0.00 0.00 0.00 1.94
3531 4864 6.007076 TGCCATACATACACCTCAAAAAGAA 58.993 36.000 0.00 0.00 0.00 2.52
3533 4866 5.895636 TGCCATACATACACCTCAAAAAG 57.104 39.130 0.00 0.00 0.00 2.27
3880 5317 7.489574 TGATGTTTGCCTTGGTTTTAAATTC 57.510 32.000 0.00 0.00 0.00 2.17
3890 5328 5.353678 TGAAAACTTTTGATGTTTGCCTTGG 59.646 36.000 0.00 0.00 37.64 3.61
3937 5375 3.560068 CCTACGCATTATTTGTCACCTCC 59.440 47.826 0.00 0.00 0.00 4.30
4191 5640 5.005394 GGTTTGCTCGTTTTCCTTTTCTTTC 59.995 40.000 0.00 0.00 0.00 2.62
4192 5641 4.868171 GGTTTGCTCGTTTTCCTTTTCTTT 59.132 37.500 0.00 0.00 0.00 2.52
4223 5676 3.491342 GGGTCCTGCTTTCTTTTCTCTT 58.509 45.455 0.00 0.00 0.00 2.85
4295 5755 4.585216 AAGGTGGACCGGGGTGGA 62.585 66.667 6.32 0.00 42.00 4.02
4312 5772 0.340908 GGGTGGGGAGTTAGTAGGGA 59.659 60.000 0.00 0.00 0.00 4.20
4328 5788 1.207488 GGGGTTAGGTTTACGGGGGT 61.207 60.000 0.00 0.00 0.00 4.95
4345 5805 4.798682 AGTGGGGCGAGTAGGGGG 62.799 72.222 0.00 0.00 0.00 5.40
4349 5809 2.042843 AGGGAGTGGGGCGAGTAG 60.043 66.667 0.00 0.00 0.00 2.57
4350 5810 2.043248 GAGGGAGTGGGGCGAGTA 60.043 66.667 0.00 0.00 0.00 2.59
4351 5811 3.966930 GAGAGGGAGTGGGGCGAGT 62.967 68.421 0.00 0.00 0.00 4.18
4352 5812 3.151022 GAGAGGGAGTGGGGCGAG 61.151 72.222 0.00 0.00 0.00 5.03
4353 5813 4.779733 GGAGAGGGAGTGGGGCGA 62.780 72.222 0.00 0.00 0.00 5.54
4357 5817 4.400251 ACGGGGAGAGGGAGTGGG 62.400 72.222 0.00 0.00 0.00 4.61
4358 5818 2.760385 GACGGGGAGAGGGAGTGG 60.760 72.222 0.00 0.00 0.00 4.00
4359 5819 2.760385 GGACGGGGAGAGGGAGTG 60.760 72.222 0.00 0.00 0.00 3.51
4360 5820 4.077180 GGGACGGGGAGAGGGAGT 62.077 72.222 0.00 0.00 0.00 3.85
4373 5833 1.074872 GTTTCGTCACCGATCGGGAC 61.075 60.000 35.87 32.59 43.80 4.46
4374 5834 1.213537 GTTTCGTCACCGATCGGGA 59.786 57.895 35.87 26.24 43.80 5.14
4375 5835 1.808390 GGTTTCGTCACCGATCGGG 60.808 63.158 35.87 24.50 43.80 5.14
4376 5836 1.808390 GGGTTTCGTCACCGATCGG 60.808 63.158 32.20 32.20 43.80 4.18
4377 5837 1.808390 GGGGTTTCGTCACCGATCG 60.808 63.158 8.51 8.51 43.80 3.69
4378 5838 1.017701 GTGGGGTTTCGTCACCGATC 61.018 60.000 0.00 0.00 43.80 3.69
4379 5839 1.004200 GTGGGGTTTCGTCACCGAT 60.004 57.895 0.00 0.00 43.80 4.18
4380 5840 2.091102 GAGTGGGGTTTCGTCACCGA 62.091 60.000 0.00 0.00 42.41 4.69
4381 5841 1.666872 GAGTGGGGTTTCGTCACCG 60.667 63.158 0.00 0.00 37.76 4.94
4382 5842 1.302271 GGAGTGGGGTTTCGTCACC 60.302 63.158 0.00 0.00 35.88 4.02
4383 5843 1.302271 GGGAGTGGGGTTTCGTCAC 60.302 63.158 0.00 0.00 0.00 3.67
4384 5844 2.522367 GGGGAGTGGGGTTTCGTCA 61.522 63.158 0.00 0.00 0.00 4.35
4385 5845 2.350134 GGGGAGTGGGGTTTCGTC 59.650 66.667 0.00 0.00 0.00 4.20
4386 5846 2.448931 TGGGGAGTGGGGTTTCGT 60.449 61.111 0.00 0.00 0.00 3.85
4387 5847 2.033602 GTGGGGAGTGGGGTTTCG 59.966 66.667 0.00 0.00 0.00 3.46
4388 5848 1.134438 AGAGTGGGGAGTGGGGTTTC 61.134 60.000 0.00 0.00 0.00 2.78
4389 5849 1.072930 AGAGTGGGGAGTGGGGTTT 60.073 57.895 0.00 0.00 0.00 3.27
4390 5850 1.539124 GAGAGTGGGGAGTGGGGTT 60.539 63.158 0.00 0.00 0.00 4.11
4391 5851 2.122954 GAGAGTGGGGAGTGGGGT 59.877 66.667 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.