Multiple sequence alignment - TraesCS4A01G129400

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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 TraesCS4A01G129400 chr4A 100.000 3956 0 0 1 3956 168791099 168795054 0.000000e+00 7306
1 TraesCS4A01G129400 chr4D 94.316 3413 98 41 1 3367 308372680 308369318 0.000000e+00 5140
2 TraesCS4A01G129400 chr4D 90.120 334 23 8 3368 3699 308369353 308369028 3.650000e-115 425
3 TraesCS4A01G129400 chr4D 85.069 288 15 6 3685 3956 308361732 308361457 6.520000e-68 268
4 TraesCS4A01G129400 chr4B 95.219 2510 66 20 885 3367 384293097 384290615 0.000000e+00 3921
5 TraesCS4A01G129400 chr4B 88.305 932 37 30 2 880 384294042 384293130 0.000000e+00 1051
6 TraesCS4A01G129400 chr4B 90.285 597 31 13 3368 3951 384290655 384290073 0.000000e+00 756
7 TraesCS4A01G129400 chr2D 83.495 824 118 17 1202 2010 51192946 51192126 0.000000e+00 752
8 TraesCS4A01G129400 chr2A 83.538 814 112 18 1214 2010 52665867 52665059 0.000000e+00 741
9 TraesCS4A01G129400 chr2B 83.172 826 114 23 1202 2010 80122435 80121618 0.000000e+00 732


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 TraesCS4A01G129400 chr4A 168791099 168795054 3955 False 7306.000000 7306 100.000000 1 3956 1 chr4A.!!$F1 3955
1 TraesCS4A01G129400 chr4D 308369028 308372680 3652 True 2782.500000 5140 92.218000 1 3699 2 chr4D.!!$R2 3698
2 TraesCS4A01G129400 chr4B 384290073 384294042 3969 True 1909.333333 3921 91.269667 2 3951 3 chr4B.!!$R1 3949
3 TraesCS4A01G129400 chr2D 51192126 51192946 820 True 752.000000 752 83.495000 1202 2010 1 chr2D.!!$R1 808
4 TraesCS4A01G129400 chr2A 52665059 52665867 808 True 741.000000 741 83.538000 1214 2010 1 chr2A.!!$R1 796
5 TraesCS4A01G129400 chr2B 80121618 80122435 817 True 732.000000 732 83.172000 1202 2010 1 chr2B.!!$R1 808

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
272 314 0.517316 GGCGGACAGATGTGTTCAAC 59.483 55.0 1.69 0.0 36.88 3.18 F
575 635 1.010419 CCGGTGCTTGCTTCAATTGC 61.010 55.0 0.00 0.0 0.00 3.56 F
1845 1967 0.038744 ACAAGAAGCCCCATGACCTG 59.961 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 1967 0.693049 TGACCTTCCAGGCCTTCTTC 59.307 55.0 0.0 0.0 39.63 2.87 R
2162 2284 0.953960 GTTGAAGGCGGTTGGATCGT 60.954 55.0 0.0 0.0 0.00 3.73 R
3433 3610 0.030101 TGGCAAACAAACGTAGCTGC 59.970 50.0 0.0 0.0 0.00 5.25 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
146 174 1.003476 CATTTTGGCCAACCCCTGC 60.003 57.895 20.35 0.00 33.59 4.85
203 232 8.012241 GGACGCTTAGACATGATTCAATTATTC 58.988 37.037 0.00 0.00 0.00 1.75
252 292 6.938030 TCTAGTATTTGGTAAAACCCTGTGTG 59.062 38.462 0.00 0.00 37.50 3.82
253 293 4.830600 AGTATTTGGTAAAACCCTGTGTGG 59.169 41.667 0.00 0.00 37.50 4.17
272 314 0.517316 GGCGGACAGATGTGTTCAAC 59.483 55.000 1.69 0.00 36.88 3.18
396 446 7.496529 TGTCACAGAGAAAAACAAGATAAGG 57.503 36.000 0.00 0.00 0.00 2.69
409 459 8.499403 AAACAAGATAAGGCTTCTGTTAGATC 57.501 34.615 1.30 0.00 0.00 2.75
444 494 4.748679 GCGTGCGCTGCCTTCTTG 62.749 66.667 9.73 0.00 38.26 3.02
445 495 3.043713 CGTGCGCTGCCTTCTTGA 61.044 61.111 9.73 0.00 0.00 3.02
446 496 2.558313 GTGCGCTGCCTTCTTGAC 59.442 61.111 9.73 0.00 0.00 3.18
487 547 3.173953 AGGAGAGGATCATAGCAGAGG 57.826 52.381 0.00 0.00 37.82 3.69
488 548 2.450500 AGGAGAGGATCATAGCAGAGGT 59.549 50.000 0.00 0.00 37.82 3.85
489 549 2.562298 GGAGAGGATCATAGCAGAGGTG 59.438 54.545 0.00 0.00 37.82 4.00
490 550 3.230134 GAGAGGATCATAGCAGAGGTGT 58.770 50.000 0.00 0.00 37.82 4.16
491 551 2.964464 AGAGGATCATAGCAGAGGTGTG 59.036 50.000 0.00 0.00 37.82 3.82
492 552 2.697751 GAGGATCATAGCAGAGGTGTGT 59.302 50.000 0.00 0.00 33.17 3.72
493 553 2.433604 AGGATCATAGCAGAGGTGTGTG 59.566 50.000 0.00 0.00 0.00 3.82
494 554 2.169352 GGATCATAGCAGAGGTGTGTGT 59.831 50.000 0.00 0.00 0.00 3.72
495 555 2.749280 TCATAGCAGAGGTGTGTGTG 57.251 50.000 0.00 0.00 0.00 3.82
517 577 4.098960 TGGTGTGGGTTAGATAAGATCGAC 59.901 45.833 0.00 0.00 0.00 4.20
535 595 2.474526 CGACTGCGTTTTGATTAGCCAG 60.475 50.000 0.00 0.00 0.00 4.85
575 635 1.010419 CCGGTGCTTGCTTCAATTGC 61.010 55.000 0.00 0.00 0.00 3.56
619 679 1.186917 TTGTCTCGGCTCCGGGTTAA 61.187 55.000 8.17 2.34 41.31 2.01
657 727 8.894731 TGTTTTGTGAACTAATACAGCTGTTTA 58.105 29.630 27.06 19.83 0.00 2.01
672 742 7.454225 ACAGCTGTTTACTTTAAGGAGAAGAT 58.546 34.615 15.25 0.00 0.00 2.40
739 809 7.231519 CCTGATTAAGTTCCCTCAAAGAAAACT 59.768 37.037 0.00 0.00 0.00 2.66
740 810 9.284968 CTGATTAAGTTCCCTCAAAGAAAACTA 57.715 33.333 0.00 0.00 30.37 2.24
741 811 9.284968 TGATTAAGTTCCCTCAAAGAAAACTAG 57.715 33.333 0.00 0.00 30.37 2.57
747 817 6.356186 TCCCTCAAAGAAAACTAGTACCTC 57.644 41.667 0.00 0.00 0.00 3.85
880 953 5.327891 GTTTAGACTCAGCAAGCAATAAGC 58.672 41.667 0.00 0.00 46.19 3.09
946 1047 2.037251 CACCACCACAGCTACAAGTAGT 59.963 50.000 8.85 0.00 35.65 2.73
947 1048 3.257375 CACCACCACAGCTACAAGTAGTA 59.743 47.826 8.85 0.00 35.65 1.82
970 1071 4.829492 AGTGGAAGGAAGTGGAATTTCTTG 59.171 41.667 0.00 0.00 32.53 3.02
1125 1229 1.522092 CTCCCTTATGCCGCAGACA 59.478 57.895 0.00 0.00 0.00 3.41
1845 1967 0.038744 ACAAGAAGCCCCATGACCTG 59.961 55.000 0.00 0.00 0.00 4.00
1926 2048 3.718210 GAAGATCCGGCGCCTCGTT 62.718 63.158 26.68 10.48 0.00 3.85
2243 2365 0.179000 CCCATGAAAGAGGAGACCGG 59.821 60.000 0.00 0.00 0.00 5.28
2247 2369 0.970937 TGAAAGAGGAGACCGGCGAT 60.971 55.000 9.30 0.00 0.00 4.58
2361 2483 3.512516 AGCGACTACGGGTACGGC 61.513 66.667 0.00 0.00 46.48 5.68
2446 2568 3.353836 GCGCGGAGAACAAGGCAA 61.354 61.111 8.83 0.00 0.00 4.52
2520 2642 1.546029 GGGCTCAACAACCTGGATTTC 59.454 52.381 0.00 0.00 0.00 2.17
2526 2648 0.322546 ACAACCTGGATTTCGGCCTC 60.323 55.000 0.00 0.00 0.00 4.70
2535 2657 2.284515 ATTTCGGCCTCCCCATGGAC 62.285 60.000 15.22 0.00 35.03 4.02
2578 2700 3.584834 CTGATGAACATGTACGACACCA 58.415 45.455 0.00 0.00 0.00 4.17
2652 2774 2.363760 CCCAATGCCATCACCCCA 59.636 61.111 0.00 0.00 0.00 4.96
2815 2967 0.096628 GCAGCAGCAGTTCTTCATCG 59.903 55.000 0.00 0.00 41.58 3.84
2943 3095 2.281276 AAGAACGACGGCCCCAAC 60.281 61.111 0.00 0.00 0.00 3.77
2971 3126 9.315525 GGTACTACTGAATGAAGAATAAACTCC 57.684 37.037 0.00 0.00 0.00 3.85
2981 3136 8.798975 ATGAAGAATAAACTCCTAGGGTCATA 57.201 34.615 9.46 4.06 0.00 2.15
2983 3138 8.705594 TGAAGAATAAACTCCTAGGGTCATAAG 58.294 37.037 9.46 0.00 0.00 1.73
2984 3139 7.068686 AGAATAAACTCCTAGGGTCATAAGC 57.931 40.000 9.46 0.00 0.00 3.09
2985 3140 6.847036 AGAATAAACTCCTAGGGTCATAAGCT 59.153 38.462 9.46 0.00 0.00 3.74
3166 3335 0.687354 TCCAGCTGGTGAACCTCTTC 59.313 55.000 31.58 0.00 36.82 2.87
3167 3336 0.689623 CCAGCTGGTGAACCTCTTCT 59.310 55.000 25.53 0.00 36.82 2.85
3168 3337 1.338579 CCAGCTGGTGAACCTCTTCTC 60.339 57.143 25.53 0.00 36.82 2.87
3169 3338 1.622811 CAGCTGGTGAACCTCTTCTCT 59.377 52.381 5.57 0.00 36.82 3.10
3170 3339 2.038295 CAGCTGGTGAACCTCTTCTCTT 59.962 50.000 5.57 0.00 36.82 2.85
3259 3429 5.107375 GGCTGTCAAATTGCTTGTGTATTTG 60.107 40.000 0.00 0.00 39.46 2.32
3330 3505 3.973425 TGTGATCTCTCTCTGGTGATGA 58.027 45.455 0.00 0.00 0.00 2.92
3331 3506 3.698539 TGTGATCTCTCTCTGGTGATGAC 59.301 47.826 0.00 0.00 0.00 3.06
3332 3507 3.953612 GTGATCTCTCTCTGGTGATGACT 59.046 47.826 0.00 0.00 0.00 3.41
3333 3508 4.402155 GTGATCTCTCTCTGGTGATGACTT 59.598 45.833 0.00 0.00 0.00 3.01
3334 3509 5.022122 TGATCTCTCTCTGGTGATGACTTT 58.978 41.667 0.00 0.00 0.00 2.66
3335 3510 5.126869 TGATCTCTCTCTGGTGATGACTTTC 59.873 44.000 0.00 0.00 0.00 2.62
3336 3511 4.411013 TCTCTCTCTGGTGATGACTTTCA 58.589 43.478 0.00 0.00 0.00 2.69
3337 3512 4.462132 TCTCTCTCTGGTGATGACTTTCAG 59.538 45.833 0.00 0.00 0.00 3.02
3338 3513 4.155709 TCTCTCTGGTGATGACTTTCAGT 58.844 43.478 0.00 0.00 0.00 3.41
3339 3514 4.590647 TCTCTCTGGTGATGACTTTCAGTT 59.409 41.667 0.00 0.00 0.00 3.16
3340 3515 4.635223 TCTCTGGTGATGACTTTCAGTTG 58.365 43.478 0.00 0.00 0.00 3.16
3341 3516 3.743521 TCTGGTGATGACTTTCAGTTGG 58.256 45.455 0.00 0.00 0.00 3.77
3342 3517 3.390967 TCTGGTGATGACTTTCAGTTGGA 59.609 43.478 0.00 0.00 0.00 3.53
3343 3518 4.042062 TCTGGTGATGACTTTCAGTTGGAT 59.958 41.667 0.00 0.00 0.00 3.41
3344 3519 4.728772 TGGTGATGACTTTCAGTTGGATT 58.271 39.130 0.00 0.00 0.00 3.01
3345 3520 5.139727 TGGTGATGACTTTCAGTTGGATTT 58.860 37.500 0.00 0.00 0.00 2.17
3346 3521 5.598005 TGGTGATGACTTTCAGTTGGATTTT 59.402 36.000 0.00 0.00 0.00 1.82
3347 3522 6.098124 TGGTGATGACTTTCAGTTGGATTTTT 59.902 34.615 0.00 0.00 0.00 1.94
3433 3610 7.485810 CCGGGGAATTTTGTTAAATAGTTAGG 58.514 38.462 0.00 0.00 32.85 2.69
3542 3719 6.841229 AGATCTTTTTCTTCCCCTGAACTTTT 59.159 34.615 0.00 0.00 0.00 2.27
3544 3721 4.400529 TTTTCTTCCCCTGAACTTTTGC 57.599 40.909 0.00 0.00 0.00 3.68
3545 3722 1.995376 TCTTCCCCTGAACTTTTGCC 58.005 50.000 0.00 0.00 0.00 4.52
3661 3840 1.423541 TCCTCACTTTGCCTAAAGCCA 59.576 47.619 0.00 0.00 45.72 4.75
3707 3886 4.079665 CCTAAGAAAAGTTAGGCAACGC 57.920 45.455 0.00 0.00 42.06 4.84
3739 3918 1.327303 TTTGGTGCTCGCCAGAAAAT 58.673 45.000 2.18 0.00 40.01 1.82
3741 3920 1.737838 TGGTGCTCGCCAGAAAATAG 58.262 50.000 0.00 0.00 33.97 1.73
3749 3928 3.674997 TCGCCAGAAAATAGTCTTTGCT 58.325 40.909 0.00 0.00 0.00 3.91
3754 3933 5.464168 CCAGAAAATAGTCTTTGCTTGGTG 58.536 41.667 0.00 0.00 0.00 4.17
3781 3960 9.846248 ATCTTAAAAAGAAAGAAACATGGATCG 57.154 29.630 0.00 0.00 41.63 3.69
3783 3962 5.391312 AAAAGAAAGAAACATGGATCGGG 57.609 39.130 0.00 0.00 0.00 5.14
3791 3970 2.826674 ACATGGATCGGGTTGGATTT 57.173 45.000 0.00 0.00 0.00 2.17
3810 3989 3.904800 TTGATGGTCCTCGCTTTGATA 57.095 42.857 0.00 0.00 0.00 2.15
3815 4003 2.238646 TGGTCCTCGCTTTGATAACCAT 59.761 45.455 0.00 0.00 36.60 3.55
3838 4026 1.066929 CCTTTATTGCTTGGTGGCACC 60.067 52.381 29.75 29.75 42.27 5.01
3839 4027 1.895131 CTTTATTGCTTGGTGGCACCT 59.105 47.619 34.69 17.75 42.27 4.00
3840 4028 2.889170 TTATTGCTTGGTGGCACCTA 57.111 45.000 34.69 27.25 42.27 3.08
3842 4030 1.767759 ATTGCTTGGTGGCACCTATC 58.232 50.000 34.69 24.09 42.27 2.08
3843 4031 0.403655 TTGCTTGGTGGCACCTATCA 59.596 50.000 34.69 26.32 42.27 2.15
3844 4032 0.625316 TGCTTGGTGGCACCTATCAT 59.375 50.000 34.69 0.00 39.58 2.45
3845 4033 1.312815 GCTTGGTGGCACCTATCATC 58.687 55.000 34.69 15.33 39.58 2.92
3846 4034 1.972872 CTTGGTGGCACCTATCATCC 58.027 55.000 34.69 8.91 39.58 3.51
3847 4035 0.180171 TTGGTGGCACCTATCATCCG 59.820 55.000 34.69 0.00 39.58 4.18
3848 4036 0.980754 TGGTGGCACCTATCATCCGT 60.981 55.000 34.69 0.00 39.58 4.69
3849 4037 0.532862 GGTGGCACCTATCATCCGTG 60.533 60.000 29.22 0.00 34.73 4.94
3850 4038 0.532862 GTGGCACCTATCATCCGTGG 60.533 60.000 6.29 0.00 0.00 4.94
3875 4063 1.820877 GCATCTTATCCCTTGGCCTGG 60.821 57.143 3.32 6.32 0.00 4.45
3876 4064 0.480252 ATCTTATCCCTTGGCCTGGC 59.520 55.000 11.05 11.05 0.00 4.85
3929 4117 0.464870 CCCTCCTCACATGCTCTCAG 59.535 60.000 0.00 0.00 0.00 3.35
3940 4128 1.832883 TGCTCTCAGTCTCACTCTCC 58.167 55.000 0.00 0.00 0.00 3.71
3945 4133 0.693622 TCAGTCTCACTCTCCGAGGT 59.306 55.000 0.00 0.00 33.35 3.85
3951 4139 3.999285 ACTCTCCGAGGTGCCCCT 61.999 66.667 0.00 0.00 46.66 4.79
3952 4140 3.465403 CTCTCCGAGGTGCCCCTG 61.465 72.222 0.00 0.00 42.86 4.45
3953 4141 4.316823 TCTCCGAGGTGCCCCTGT 62.317 66.667 0.00 0.00 42.86 4.00
3954 4142 3.775654 CTCCGAGGTGCCCCTGTC 61.776 72.222 0.00 0.00 42.86 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 113 4.562143 CCTTTTCAAGGGAAGAAAGCCATG 60.562 45.833 0.00 0.00 45.27 3.66
115 143 3.056322 GGCCAAAATGATGAGAAAGCAGT 60.056 43.478 0.00 0.00 0.00 4.40
146 174 4.497006 GGATTGCTTTGATCCAATCACTCG 60.497 45.833 18.32 0.00 45.63 4.18
186 215 8.818141 TCCTACGAGAATAATTGAATCATGTC 57.182 34.615 0.00 0.00 0.00 3.06
203 232 8.361139 AGAACTGTTTCCATATAATCCTACGAG 58.639 37.037 0.00 0.00 31.28 4.18
252 292 0.605319 TTGAACACATCTGTCCGCCC 60.605 55.000 0.00 0.00 0.00 6.13
253 293 0.517316 GTTGAACACATCTGTCCGCC 59.483 55.000 0.00 0.00 0.00 6.13
254 294 1.512926 AGTTGAACACATCTGTCCGC 58.487 50.000 0.00 0.00 0.00 5.54
255 295 3.809832 AGAAAGTTGAACACATCTGTCCG 59.190 43.478 0.00 0.00 0.00 4.79
272 314 7.337942 ACACTAATGGAAGAATAAGGCAGAAAG 59.662 37.037 0.00 0.00 0.00 2.62
313 359 6.442952 GTGTGTTATGCATGACCACTAAAAA 58.557 36.000 23.64 3.83 0.00 1.94
314 360 5.048364 GGTGTGTTATGCATGACCACTAAAA 60.048 40.000 26.74 7.13 34.42 1.52
315 361 4.457603 GGTGTGTTATGCATGACCACTAAA 59.542 41.667 26.74 7.68 34.42 1.85
316 362 4.006989 GGTGTGTTATGCATGACCACTAA 58.993 43.478 26.74 8.25 34.42 2.24
317 363 3.605634 GGTGTGTTATGCATGACCACTA 58.394 45.455 26.74 8.54 34.42 2.74
318 364 2.436417 GGTGTGTTATGCATGACCACT 58.564 47.619 26.74 1.99 34.42 4.00
319 365 1.472480 GGGTGTGTTATGCATGACCAC 59.528 52.381 23.22 23.22 35.38 4.16
444 494 9.770097 TCCTTCACAATTATAGATCATCAAGTC 57.230 33.333 0.00 0.00 0.00 3.01
445 495 9.775854 CTCCTTCACAATTATAGATCATCAAGT 57.224 33.333 0.00 0.00 0.00 3.16
446 496 9.993454 TCTCCTTCACAATTATAGATCATCAAG 57.007 33.333 0.00 0.00 0.00 3.02
487 547 1.134340 TCTAACCCACACCACACACAC 60.134 52.381 0.00 0.00 0.00 3.82
488 548 1.205055 TCTAACCCACACCACACACA 58.795 50.000 0.00 0.00 0.00 3.72
489 549 2.561478 ATCTAACCCACACCACACAC 57.439 50.000 0.00 0.00 0.00 3.82
490 550 3.904965 TCTTATCTAACCCACACCACACA 59.095 43.478 0.00 0.00 0.00 3.72
491 551 4.546829 TCTTATCTAACCCACACCACAC 57.453 45.455 0.00 0.00 0.00 3.82
492 552 4.142026 CGATCTTATCTAACCCACACCACA 60.142 45.833 0.00 0.00 0.00 4.17
493 553 4.098960 TCGATCTTATCTAACCCACACCAC 59.901 45.833 0.00 0.00 0.00 4.16
494 554 4.098960 GTCGATCTTATCTAACCCACACCA 59.901 45.833 0.00 0.00 0.00 4.17
495 555 4.341520 AGTCGATCTTATCTAACCCACACC 59.658 45.833 0.00 0.00 0.00 4.16
517 577 2.483877 TGTCTGGCTAATCAAAACGCAG 59.516 45.455 0.00 0.00 0.00 5.18
575 635 3.726607 TGTGGCATAAAAGCAAGTTTGG 58.273 40.909 0.00 0.00 35.83 3.28
619 679 6.725364 AGTTCACAAAACATCCCAGATCTAT 58.275 36.000 0.00 0.00 0.00 1.98
657 727 6.960542 TCCAGTTCCTATCTTCTCCTTAAAGT 59.039 38.462 0.00 0.00 0.00 2.66
672 742 4.406648 CACATATGTGCTCCAGTTCCTA 57.593 45.455 22.27 0.00 39.39 2.94
880 953 4.236527 AGAGGCCAGGTTAATTACAAGG 57.763 45.455 5.01 0.00 0.00 3.61
881 954 5.622233 GCAAAGAGGCCAGGTTAATTACAAG 60.622 44.000 5.01 0.00 0.00 3.16
882 955 4.219725 GCAAAGAGGCCAGGTTAATTACAA 59.780 41.667 5.01 0.00 0.00 2.41
883 956 3.761752 GCAAAGAGGCCAGGTTAATTACA 59.238 43.478 5.01 0.00 0.00 2.41
946 1047 5.843019 AGAAATTCCACTTCCTTCCACTA 57.157 39.130 0.00 0.00 0.00 2.74
947 1048 4.731313 AGAAATTCCACTTCCTTCCACT 57.269 40.909 0.00 0.00 0.00 4.00
948 1049 4.584743 ACAAGAAATTCCACTTCCTTCCAC 59.415 41.667 0.00 0.00 0.00 4.02
949 1050 4.584325 CACAAGAAATTCCACTTCCTTCCA 59.416 41.667 0.00 0.00 0.00 3.53
950 1051 4.584743 ACACAAGAAATTCCACTTCCTTCC 59.415 41.667 0.00 0.00 0.00 3.46
951 1052 5.507985 CCACACAAGAAATTCCACTTCCTTC 60.508 44.000 0.00 0.00 0.00 3.46
952 1053 4.342092 CCACACAAGAAATTCCACTTCCTT 59.658 41.667 0.00 0.00 0.00 3.36
970 1071 2.225467 AGCAGCTCTTTTTCTCCACAC 58.775 47.619 0.00 0.00 0.00 3.82
1176 1280 1.554042 CGTCCGGGAAGTTGTTCGTG 61.554 60.000 0.00 0.00 32.92 4.35
1180 1284 2.281276 GGCGTCCGGGAAGTTGTT 60.281 61.111 11.61 0.00 0.00 2.83
1200 1304 2.667199 TCGTCGCTGTCGTCCTCA 60.667 61.111 0.00 0.00 36.96 3.86
1845 1967 0.693049 TGACCTTCCAGGCCTTCTTC 59.307 55.000 0.00 0.00 39.63 2.87
1854 1976 1.739562 GAGCACGCTGACCTTCCAG 60.740 63.158 0.00 0.00 37.23 3.86
1926 2048 1.377202 GAGGCATTTGGACTGGCGA 60.377 57.895 0.00 0.00 43.43 5.54
2162 2284 0.953960 GTTGAAGGCGGTTGGATCGT 60.954 55.000 0.00 0.00 0.00 3.73
2384 2506 2.525877 AGGTGTACCGGTGGCTGT 60.526 61.111 19.93 0.00 42.08 4.40
2393 2515 3.670625 TCATTGTACTTGCAGGTGTACC 58.329 45.455 12.40 0.00 38.48 3.34
2526 2648 4.181010 CTCTGGCCGTCCATGGGG 62.181 72.222 13.02 7.35 42.51 4.96
2535 2657 4.899239 GCGATGGACCTCTGGCCG 62.899 72.222 0.00 0.00 0.00 6.13
2538 2660 3.144120 CTCGGCGATGGACCTCTGG 62.144 68.421 11.27 0.00 0.00 3.86
2578 2700 4.280019 GTTGGTGGCCGGGAAGGT 62.280 66.667 2.18 0.00 43.70 3.50
2652 2774 4.324267 CAAAGAAACCCTCGTCCATTACT 58.676 43.478 0.00 0.00 0.00 2.24
2724 2852 2.011947 TGCTGCTGCATCATGTTACTC 58.988 47.619 14.93 0.00 45.31 2.59
2943 3095 9.877178 AGTTTATTCTTCATTCAGTAGTACCAG 57.123 33.333 0.00 0.00 0.00 4.00
2971 3126 4.806247 CACGAAGAAAGCTTATGACCCTAG 59.194 45.833 0.00 0.00 33.61 3.02
2981 3136 2.481276 GGTTTTGCCACGAAGAAAGCTT 60.481 45.455 0.00 0.00 37.17 3.74
2983 3138 1.202359 TGGTTTTGCCACGAAGAAAGC 60.202 47.619 0.00 0.00 43.61 3.51
2984 3139 2.861462 TGGTTTTGCCACGAAGAAAG 57.139 45.000 0.00 0.00 43.61 2.62
3026 3193 0.320683 TTAGGAGGACGACGACGACA 60.321 55.000 15.32 0.00 42.66 4.35
3027 3194 0.373024 CTTAGGAGGACGACGACGAC 59.627 60.000 15.32 7.84 42.66 4.34
3028 3195 0.247460 TCTTAGGAGGACGACGACGA 59.753 55.000 15.32 0.00 42.66 4.20
3211 3381 4.708421 AGCCAGTCATATGAACAGCATTTT 59.292 37.500 18.86 2.01 38.44 1.82
3259 3429 4.475944 CAATCACAAGGAACGGAATCAAC 58.524 43.478 0.00 0.00 0.00 3.18
3348 3523 6.205464 TGAAAATTGGAAGTTTTGCACACAAA 59.795 30.769 0.00 0.00 43.97 2.83
3349 3524 5.702670 TGAAAATTGGAAGTTTTGCACACAA 59.297 32.000 0.00 0.00 0.00 3.33
3350 3525 5.240891 TGAAAATTGGAAGTTTTGCACACA 58.759 33.333 0.00 0.00 0.00 3.72
3351 3526 5.793026 TGAAAATTGGAAGTTTTGCACAC 57.207 34.783 0.00 0.00 0.00 3.82
3352 3527 6.998968 ATTGAAAATTGGAAGTTTTGCACA 57.001 29.167 0.00 0.00 0.00 4.57
3353 3528 7.667984 CAATTGAAAATTGGAAGTTTTGCAC 57.332 32.000 0.00 0.00 0.00 4.57
3390 3565 1.526464 CGGCATGGAAGTTTTGCAAAC 59.474 47.619 12.39 7.48 38.12 2.93
3433 3610 0.030101 TGGCAAACAAACGTAGCTGC 59.970 50.000 0.00 0.00 0.00 5.25
3488 3665 3.067180 GTCCGTTTCTATACCGACATCCA 59.933 47.826 0.00 0.00 0.00 3.41
3516 3693 5.565509 AGTTCAGGGGAAGAAAAAGATCTC 58.434 41.667 0.00 0.00 32.62 2.75
3542 3719 6.767524 ACAGGATGAATTTATTTTACGGCA 57.232 33.333 0.00 0.00 39.69 5.69
3544 3721 8.458843 ACTCAACAGGATGAATTTATTTTACGG 58.541 33.333 0.00 0.00 39.69 4.02
3545 3722 9.840427 AACTCAACAGGATGAATTTATTTTACG 57.160 29.630 0.00 0.00 39.69 3.18
3661 3840 2.597455 CCACTTTGAATTGACCCACCT 58.403 47.619 0.00 0.00 0.00 4.00
3739 3918 8.458573 TTTTTAAGATCACCAAGCAAAGACTA 57.541 30.769 0.00 0.00 0.00 2.59
3741 3920 7.425606 TCTTTTTAAGATCACCAAGCAAAGAC 58.574 34.615 0.00 0.00 31.20 3.01
3781 3960 2.379005 GAGGACCATCAAATCCAACCC 58.621 52.381 0.00 0.00 37.47 4.11
3783 3962 1.401905 GCGAGGACCATCAAATCCAAC 59.598 52.381 0.00 0.00 37.47 3.77
3791 3970 3.531538 GTTATCAAAGCGAGGACCATCA 58.468 45.455 0.00 0.00 0.00 3.07
3810 3989 3.106827 CCAAGCAATAAAGGGGATGGTT 58.893 45.455 0.00 0.00 34.13 3.67
3815 4003 1.894978 GCCACCAAGCAATAAAGGGGA 60.895 52.381 0.00 0.00 0.00 4.81
3838 4026 1.956170 GCACGGCCACGGATGATAG 60.956 63.158 2.24 0.00 46.48 2.08
3839 4027 2.038814 ATGCACGGCCACGGATGATA 62.039 55.000 2.24 0.00 46.48 2.15
3840 4028 3.405093 ATGCACGGCCACGGATGAT 62.405 57.895 2.24 0.00 46.48 2.45
3842 4030 3.576356 GATGCACGGCCACGGATG 61.576 66.667 2.24 0.00 46.48 3.51
3843 4031 1.966901 TAAGATGCACGGCCACGGAT 61.967 55.000 2.24 0.00 46.48 4.18
3844 4032 1.966901 ATAAGATGCACGGCCACGGA 61.967 55.000 2.24 0.00 46.48 4.69
3845 4033 1.498865 GATAAGATGCACGGCCACGG 61.499 60.000 2.24 0.00 46.48 4.94
3847 4035 1.166531 GGGATAAGATGCACGGCCAC 61.167 60.000 2.24 0.00 0.00 5.01
3848 4036 1.148273 GGGATAAGATGCACGGCCA 59.852 57.895 2.24 0.00 0.00 5.36
3849 4037 0.179018 AAGGGATAAGATGCACGGCC 60.179 55.000 0.00 0.00 0.00 6.13
3850 4038 0.947244 CAAGGGATAAGATGCACGGC 59.053 55.000 0.00 0.00 0.00 5.68
3875 4063 0.036875 ACTACCTTGGCTTGACAGGC 59.963 55.000 0.00 0.00 46.16 4.85
3876 4064 1.611673 CCACTACCTTGGCTTGACAGG 60.612 57.143 0.00 0.00 0.00 4.00
3877 4065 1.072331 ACCACTACCTTGGCTTGACAG 59.928 52.381 0.00 0.00 40.77 3.51
3878 4066 1.136828 ACCACTACCTTGGCTTGACA 58.863 50.000 0.00 0.00 40.77 3.58
3879 4067 1.523758 CACCACTACCTTGGCTTGAC 58.476 55.000 0.00 0.00 40.77 3.18


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

AutoCloner maintained by Alex Coulton.