Multiple sequence alignment - TraesCS2A01G190900

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 TraesCS2A01G190900 chr2A 100.000 3326 0 0 1 3326 157545290 157548615 0.000000e+00 6143.0
1 TraesCS2A01G190900 chr2D 93.567 3218 101 42 35 3211 143759910 143756758 0.000000e+00 4698.0
2 TraesCS2A01G190900 chr2B 91.111 2610 95 53 35 2582 201771483 201768949 0.000000e+00 3408.0
3 TraesCS2A01G190900 chr2B 91.193 704 31 14 2606 3296 201768966 201768281 0.000000e+00 928.0
4 TraesCS2A01G190900 chr4D 87.654 81 10 0 2086 2166 435650744 435650824 9.820000e-16 95.3
5 TraesCS2A01G190900 chr4B 87.654 81 10 0 2086 2166 536919107 536919187 9.820000e-16 95.3
6 TraesCS2A01G190900 chr4A 87.654 81 10 0 2086 2166 37032308 37032388 9.820000e-16 95.3


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 TraesCS2A01G190900 chr2A 157545290 157548615 3325 False 6143 6143 100.000 1 3326 1 chr2A.!!$F1 3325
1 TraesCS2A01G190900 chr2D 143756758 143759910 3152 True 4698 4698 93.567 35 3211 1 chr2D.!!$R1 3176
2 TraesCS2A01G190900 chr2B 201768281 201771483 3202 True 2168 3408 91.152 35 3296 2 chr2B.!!$R1 3261

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
845 914 0.030369 CCGACGGTTCCTTATCTCCG 59.97 60.0 5.48 0.0 46.98 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2333 2417 0.041386 ACTACTCCGGCTTCCTTCCT 59.959 55.0 0.0 0.0 0.0 3.36 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
18 19 1.008079 AAGAGCAGCGCAACAAAGC 60.008 52.632 11.47 3.34 0.00 3.51
26 27 4.404654 GCAACAAAGCGCTCCCCG 62.405 66.667 12.06 1.52 40.75 5.73
70 71 1.301423 TTTTCCACCCGTATATGCGC 58.699 50.000 7.78 0.00 0.00 6.09
151 153 3.488090 GACGGCTAAGTGTGCGGC 61.488 66.667 0.00 0.00 34.72 6.53
174 188 2.050442 CACCGCCCGCTTTTGAAC 60.050 61.111 0.00 0.00 0.00 3.18
175 189 2.517402 ACCGCCCGCTTTTGAACA 60.517 55.556 0.00 0.00 0.00 3.18
176 190 2.050442 CCGCCCGCTTTTGAACAC 60.050 61.111 0.00 0.00 0.00 3.32
188 206 1.577468 TTGAACACTACCACTGCGTG 58.423 50.000 2.27 2.27 34.92 5.34
203 221 5.403766 CCACTGCGTGATCTGAATAATCTAC 59.596 44.000 9.75 0.00 35.23 2.59
227 245 4.712763 GCTAAGCGTGCCAATAATATCAC 58.287 43.478 0.00 0.00 0.00 3.06
339 370 2.250188 CCGAACAAGGCAATAAAAGCG 58.750 47.619 0.00 0.00 0.00 4.68
449 489 2.828877 TGGACTTTGGCGTTATATCCG 58.171 47.619 0.00 0.00 0.00 4.18
496 536 4.507916 CCTCGCCCTCTCTCCCGA 62.508 72.222 0.00 0.00 0.00 5.14
498 538 4.816984 TCGCCCTCTCTCCCGACC 62.817 72.222 0.00 0.00 0.00 4.79
516 556 2.825836 CCGCCTGATTCCAGTGGC 60.826 66.667 3.51 0.00 38.74 5.01
550 591 4.477975 CGCCGGGACAGACGAGAC 62.478 72.222 2.18 0.00 0.00 3.36
557 598 1.283181 GACAGACGAGACACACGCT 59.717 57.895 0.00 0.00 0.00 5.07
575 616 0.459237 CTGGGTAAGCACGCTCTGAG 60.459 60.000 0.00 0.00 38.40 3.35
576 617 1.185618 TGGGTAAGCACGCTCTGAGT 61.186 55.000 6.53 0.00 38.40 3.41
577 618 0.458716 GGGTAAGCACGCTCTGAGTC 60.459 60.000 6.53 0.00 34.86 3.36
578 619 0.528470 GGTAAGCACGCTCTGAGTCT 59.472 55.000 6.53 0.00 0.00 3.24
579 620 1.623359 GTAAGCACGCTCTGAGTCTG 58.377 55.000 6.53 3.24 0.00 3.51
580 621 1.200252 GTAAGCACGCTCTGAGTCTGA 59.800 52.381 6.53 0.00 0.00 3.27
581 622 0.243365 AAGCACGCTCTGAGTCTGAG 59.757 55.000 19.73 19.73 33.52 3.35
582 623 0.893270 AGCACGCTCTGAGTCTGAGT 60.893 55.000 23.31 7.34 33.06 3.41
583 624 0.455972 GCACGCTCTGAGTCTGAGTC 60.456 60.000 23.31 16.07 33.06 3.36
584 625 1.164411 CACGCTCTGAGTCTGAGTCT 58.836 55.000 23.31 9.83 33.06 3.24
585 626 1.135717 CACGCTCTGAGTCTGAGTCTG 60.136 57.143 23.31 16.96 33.06 3.51
586 627 1.271108 ACGCTCTGAGTCTGAGTCTGA 60.271 52.381 23.31 17.64 33.06 3.27
587 628 1.398041 CGCTCTGAGTCTGAGTCTGAG 59.602 57.143 30.07 30.07 42.81 3.35
588 629 1.745087 GCTCTGAGTCTGAGTCTGAGG 59.255 57.143 32.54 21.78 41.28 3.86
589 630 2.368439 CTCTGAGTCTGAGTCTGAGGG 58.632 57.143 28.23 11.69 38.91 4.30
590 631 1.988846 TCTGAGTCTGAGTCTGAGGGA 59.011 52.381 15.52 4.19 0.00 4.20
591 632 2.091541 CTGAGTCTGAGTCTGAGGGAC 58.908 57.143 13.30 0.00 44.80 4.46
624 666 3.157932 TGTTTGCTTCCTTGTTTTCCG 57.842 42.857 0.00 0.00 0.00 4.30
716 780 2.302445 TCCCTGGCATGGAAATTTGTTG 59.698 45.455 9.23 0.00 0.00 3.33
739 803 4.467198 GGAGTTCTTTATCTCCGGTTGA 57.533 45.455 0.00 1.23 40.36 3.18
749 813 4.819105 ATCTCCGGTTGATGTTTGAGTA 57.181 40.909 0.00 0.00 0.00 2.59
750 814 4.188247 TCTCCGGTTGATGTTTGAGTAG 57.812 45.455 0.00 0.00 0.00 2.57
751 815 3.576982 TCTCCGGTTGATGTTTGAGTAGT 59.423 43.478 0.00 0.00 0.00 2.73
752 816 4.039973 TCTCCGGTTGATGTTTGAGTAGTT 59.960 41.667 0.00 0.00 0.00 2.24
753 817 4.062293 TCCGGTTGATGTTTGAGTAGTTG 58.938 43.478 0.00 0.00 0.00 3.16
814 878 1.263217 GGTTTGGTTCGCTGTACAGTG 59.737 52.381 27.05 27.05 40.15 3.66
821 890 0.109458 TCGCTGTACAGTGGTAAGCG 60.109 55.000 30.71 22.81 46.42 4.68
845 914 0.030369 CCGACGGTTCCTTATCTCCG 59.970 60.000 5.48 0.00 46.98 4.63
899 968 1.004080 CTGCTCTCCCACCTGTGTG 60.004 63.158 0.00 0.00 42.39 3.82
901 970 2.888447 GCTCTCCCACCTGTGTGCT 61.888 63.158 0.00 0.00 41.35 4.40
903 972 2.033141 CTCCCACCTGTGTGCTGG 59.967 66.667 0.00 0.00 41.35 4.85
904 973 3.557903 CTCCCACCTGTGTGCTGGG 62.558 68.421 0.00 0.00 45.58 4.45
905 974 4.666253 CCCACCTGTGTGCTGGGG 62.666 72.222 0.00 0.00 41.08 4.96
915 984 0.037590 TGTGCTGGGGAATTAACGCT 59.962 50.000 0.00 0.00 0.00 5.07
971 1043 2.133742 CTTGGTTGCAGTTGCGGAGG 62.134 60.000 0.00 0.00 45.83 4.30
1149 1224 1.339055 TGCATCTACCACAAGCAGGAC 60.339 52.381 0.00 0.00 0.00 3.85
1245 1320 1.599797 CCCGGTGTTTGACCAGTCC 60.600 63.158 0.00 0.00 46.55 3.85
1509 1584 2.202892 GTCATTCCCGTCTCGCCC 60.203 66.667 0.00 0.00 0.00 6.13
1973 2057 1.355916 CGGAGGTCGATTCGTCTCC 59.644 63.158 26.13 26.13 41.10 3.71
2326 2410 1.478916 GAAGCCGAGCCTTCTTCTAGT 59.521 52.381 0.00 0.00 38.50 2.57
2327 2411 1.562783 AGCCGAGCCTTCTTCTAGTT 58.437 50.000 0.00 0.00 0.00 2.24
2328 2412 1.478916 AGCCGAGCCTTCTTCTAGTTC 59.521 52.381 0.00 0.00 0.00 3.01
2329 2413 1.478916 GCCGAGCCTTCTTCTAGTTCT 59.521 52.381 0.00 0.00 0.00 3.01
2330 2414 2.688958 GCCGAGCCTTCTTCTAGTTCTA 59.311 50.000 0.00 0.00 0.00 2.10
2331 2415 3.243267 GCCGAGCCTTCTTCTAGTTCTAG 60.243 52.174 0.83 0.83 0.00 2.43
2332 2416 3.316868 CCGAGCCTTCTTCTAGTTCTAGG 59.683 52.174 6.96 0.00 0.00 3.02
2333 2417 4.200874 CGAGCCTTCTTCTAGTTCTAGGA 58.799 47.826 6.96 0.00 0.00 2.94
2338 2422 5.068591 GCCTTCTTCTAGTTCTAGGAGGAAG 59.931 48.000 13.33 16.30 40.48 3.46
2355 2439 1.900545 AAGGAAGCCGGAGTAGTGCC 61.901 60.000 5.05 0.00 0.00 5.01
2477 2566 1.757699 ACTTAGGCTTCGTCAGATCCC 59.242 52.381 0.00 0.00 0.00 3.85
2507 2596 1.745827 GCGGAAATTAGCTGCCCTGTA 60.746 52.381 0.00 0.00 0.00 2.74
2635 2727 5.816258 AGACATCTGAATGTGAGTTGCTATG 59.184 40.000 0.00 0.00 46.20 2.23
2670 2762 2.110213 TCCCGCTTGAAACGCACT 59.890 55.556 0.00 0.00 0.00 4.40
2678 2770 4.374906 CCGCTTGAAACGCACTAAAATTTG 60.375 41.667 0.00 0.00 0.00 2.32
2703 2796 7.715249 TGCAGGAATTTCATAGGTAGTATCAAC 59.285 37.037 0.00 0.00 0.00 3.18
2731 2824 1.335964 GCGTGAGACAGCAACAGAGTA 60.336 52.381 0.00 0.00 0.00 2.59
2736 2829 1.001406 AGACAGCAACAGAGTAGTGGC 59.999 52.381 0.00 0.00 38.77 5.01
2739 2832 0.322975 AGCAACAGAGTAGTGGCCAG 59.677 55.000 5.11 0.00 39.32 4.85
2792 2897 6.358991 TGGTATTTGATGATTCTGCAGATCA 58.641 36.000 19.04 21.33 0.00 2.92
3041 3146 1.443407 CTACCATGGACCTCGCCAG 59.557 63.158 21.47 0.00 42.15 4.85
3083 3188 1.135575 GCCGAGGCAAGAAAACATCAG 60.136 52.381 9.58 0.00 41.49 2.90
3100 3205 5.678583 ACATCAGATCTGTTTGATTCCGAT 58.321 37.500 25.15 7.62 35.14 4.18
3181 3288 6.749036 ATGAGTAAGTTACAATAGGAGGGG 57.251 41.667 15.28 0.00 0.00 4.79
3185 3292 7.093024 TGAGTAAGTTACAATAGGAGGGGAAAG 60.093 40.741 15.28 0.00 0.00 2.62
3214 3321 7.506938 AGAGAAGAAAGGAAAACAATCATTGGA 59.493 33.333 1.58 0.00 34.12 3.53
3225 3332 5.793030 ACAATCATTGGACCGGTTAAAAA 57.207 34.783 9.42 1.13 34.12 1.94
3268 3375 7.961326 AGGAATAAAACAGCCATAACAAGAT 57.039 32.000 0.00 0.00 0.00 2.40
3271 3378 9.516314 GGAATAAAACAGCCATAACAAGATTAC 57.484 33.333 0.00 0.00 0.00 1.89
3281 3388 7.443575 AGCCATAACAAGATTACATGTGATCTC 59.556 37.037 27.66 15.48 35.24 2.75
3296 3403 5.423015 TGTGATCTCTTATCCAAGCTTGAC 58.577 41.667 28.05 13.03 0.00 3.18
3297 3404 5.046376 TGTGATCTCTTATCCAAGCTTGACA 60.046 40.000 28.05 15.41 0.00 3.58
3298 3405 5.877012 GTGATCTCTTATCCAAGCTTGACAA 59.123 40.000 28.05 15.79 0.00 3.18
3299 3406 5.877012 TGATCTCTTATCCAAGCTTGACAAC 59.123 40.000 28.05 6.63 0.00 3.32
3300 3407 5.227569 TCTCTTATCCAAGCTTGACAACA 57.772 39.130 28.05 6.27 0.00 3.33
3301 3408 5.620206 TCTCTTATCCAAGCTTGACAACAA 58.380 37.500 28.05 12.21 34.65 2.83
3314 3421 6.545504 CTTGACAACAAGCAACATAGTACT 57.454 37.500 0.00 0.00 45.19 2.73
3315 3422 6.935741 TTGACAACAAGCAACATAGTACTT 57.064 33.333 0.00 0.00 0.00 2.24
3316 3423 6.299023 TGACAACAAGCAACATAGTACTTG 57.701 37.500 0.00 2.03 43.99 3.16
3324 3431 6.969828 AGCAACATAGTACTTGTCTTAAGC 57.030 37.500 0.00 6.19 0.00 3.09
3325 3432 6.464222 AGCAACATAGTACTTGTCTTAAGCA 58.536 36.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.008079 GCTTTGTTGCGCTGCTCTT 60.008 52.632 9.73 0.00 0.00 2.85
1 2 2.641559 GCTTTGTTGCGCTGCTCT 59.358 55.556 9.73 0.00 0.00 4.09
9 10 4.404654 CGGGGAGCGCTTTGTTGC 62.405 66.667 13.26 0.00 0.00 4.17
10 11 4.404654 GCGGGGAGCGCTTTGTTG 62.405 66.667 13.26 1.91 35.41 3.33
70 71 0.030908 CGTAGCTTTAGAGAGCCGGG 59.969 60.000 2.18 0.00 43.74 5.73
75 76 0.595310 GCCGCCGTAGCTTTAGAGAG 60.595 60.000 0.00 0.00 36.60 3.20
157 159 2.050442 GTTCAAAAGCGGGCGGTG 60.050 61.111 0.00 0.00 0.00 4.94
160 162 0.110373 GTAGTGTTCAAAAGCGGGCG 60.110 55.000 0.00 0.00 0.00 6.13
188 206 5.513495 CGCTTAGCCGTAGATTATTCAGATC 59.487 44.000 0.00 0.00 0.00 2.75
227 245 5.352569 GCAGGATGATTGATAATCTAACCGG 59.647 44.000 0.00 0.00 39.69 5.28
321 352 2.917343 GCTCGCTTTTATTGCCTTGTTC 59.083 45.455 0.00 0.00 0.00 3.18
339 370 1.066358 ACCCTTTACCTAACTGCGCTC 60.066 52.381 9.73 0.00 0.00 5.03
479 519 4.507916 TCGGGAGAGAGGGCGAGG 62.508 72.222 0.00 0.00 0.00 4.63
480 520 3.213402 GTCGGGAGAGAGGGCGAG 61.213 72.222 0.00 0.00 41.26 5.03
495 535 2.190578 CTGGAATCAGGCGGGGTC 59.809 66.667 0.00 0.00 37.36 4.46
496 536 2.610859 ACTGGAATCAGGCGGGGT 60.611 61.111 0.00 0.00 44.99 4.95
498 538 2.124570 CCACTGGAATCAGGCGGG 60.125 66.667 0.00 0.00 44.99 6.13
557 598 1.185618 ACTCAGAGCGTGCTTACCCA 61.186 55.000 0.00 0.00 0.00 4.51
567 608 1.398041 CTCAGACTCAGACTCAGAGCG 59.602 57.143 0.00 0.00 36.58 5.03
575 616 0.806241 GACGTCCCTCAGACTCAGAC 59.194 60.000 3.51 0.00 43.91 3.51
576 617 0.322636 GGACGTCCCTCAGACTCAGA 60.323 60.000 24.75 0.00 43.91 3.27
577 618 2.185238 GGACGTCCCTCAGACTCAG 58.815 63.158 24.75 0.00 43.91 3.35
578 619 4.417641 GGACGTCCCTCAGACTCA 57.582 61.111 24.75 0.00 43.91 3.41
607 649 1.407258 CCACGGAAAACAAGGAAGCAA 59.593 47.619 0.00 0.00 0.00 3.91
666 708 0.608640 CGATGCATAGGTAGGTCCCC 59.391 60.000 0.00 0.00 36.75 4.81
672 714 4.155099 AGAAGTCGATCGATGCATAGGTAG 59.845 45.833 22.50 0.00 0.00 3.18
673 715 4.072839 AGAAGTCGATCGATGCATAGGTA 58.927 43.478 22.50 0.00 0.00 3.08
674 716 2.887783 AGAAGTCGATCGATGCATAGGT 59.112 45.455 22.50 0.00 0.00 3.08
734 798 6.260050 TCAACTCAACTACTCAAACATCAACC 59.740 38.462 0.00 0.00 0.00 3.77
739 803 7.047891 TCAACTCAACTCAACTACTCAAACAT 58.952 34.615 0.00 0.00 0.00 2.71
749 813 4.950050 ACTCGATTCAACTCAACTCAACT 58.050 39.130 0.00 0.00 0.00 3.16
750 814 5.435557 CAACTCGATTCAACTCAACTCAAC 58.564 41.667 0.00 0.00 0.00 3.18
751 815 4.511454 CCAACTCGATTCAACTCAACTCAA 59.489 41.667 0.00 0.00 0.00 3.02
752 816 4.058124 CCAACTCGATTCAACTCAACTCA 58.942 43.478 0.00 0.00 0.00 3.41
753 817 3.120511 GCCAACTCGATTCAACTCAACTC 60.121 47.826 0.00 0.00 0.00 3.01
788 852 1.895231 AGCGAACCAAACCGGAACC 60.895 57.895 9.46 0.00 38.63 3.62
899 968 3.477530 AGATTAGCGTTAATTCCCCAGC 58.522 45.455 5.96 0.00 29.67 4.85
901 970 4.850680 ACAAGATTAGCGTTAATTCCCCA 58.149 39.130 5.96 0.00 29.67 4.96
903 972 6.708949 TCCATACAAGATTAGCGTTAATTCCC 59.291 38.462 5.96 0.00 29.67 3.97
904 973 7.724305 TCCATACAAGATTAGCGTTAATTCC 57.276 36.000 5.96 0.00 29.67 3.01
971 1043 4.577246 CACCTCCGCCGCTAGCTC 62.577 72.222 13.93 3.42 40.39 4.09
1021 1096 1.372087 GAAACCGCCTCCATCTGCTG 61.372 60.000 0.00 0.00 0.00 4.41
1022 1097 1.078143 GAAACCGCCTCCATCTGCT 60.078 57.895 0.00 0.00 0.00 4.24
1023 1098 1.078143 AGAAACCGCCTCCATCTGC 60.078 57.895 0.00 0.00 0.00 4.26
1024 1099 1.372087 GCAGAAACCGCCTCCATCTG 61.372 60.000 0.00 0.00 40.30 2.90
1025 1100 1.078143 GCAGAAACCGCCTCCATCT 60.078 57.895 0.00 0.00 0.00 2.90
1026 1101 2.464459 CGCAGAAACCGCCTCCATC 61.464 63.158 0.00 0.00 0.00 3.51
1470 1545 2.202837 GGCACGACCCCGATGTAC 60.203 66.667 0.00 0.00 39.50 2.90
1584 1659 3.870633 AACTCCATGTTCTCGTAGTCC 57.129 47.619 0.00 0.00 32.63 3.85
1671 1746 3.056313 GCTCTGCGTTTCCATGGCC 62.056 63.158 6.96 0.00 0.00 5.36
1829 1904 4.624364 TGGTGGACACGCTGCTGG 62.624 66.667 0.00 0.00 0.00 4.85
1896 1971 3.479269 GCGTTTCCTGACGGCTCG 61.479 66.667 0.00 0.00 42.98 5.03
1973 2057 2.266055 GGCTCTCCTGAACGGTGG 59.734 66.667 0.00 0.00 0.00 4.61
2044 2128 1.021390 AAGTTGAAGCTCATCGCCGG 61.021 55.000 0.00 0.00 40.39 6.13
2045 2129 0.371645 GAAGTTGAAGCTCATCGCCG 59.628 55.000 0.00 0.00 40.39 6.46
2046 2130 0.371645 CGAAGTTGAAGCTCATCGCC 59.628 55.000 0.00 0.00 40.39 5.54
2251 2335 2.356673 GGCCGTCGGTTTCTTCGT 60.357 61.111 13.94 0.00 0.00 3.85
2326 2410 1.486211 CGGCTTCCTTCCTCCTAGAA 58.514 55.000 0.00 0.00 0.00 2.10
2327 2411 0.397254 CCGGCTTCCTTCCTCCTAGA 60.397 60.000 0.00 0.00 0.00 2.43
2328 2412 0.397254 TCCGGCTTCCTTCCTCCTAG 60.397 60.000 0.00 0.00 0.00 3.02
2329 2413 0.397254 CTCCGGCTTCCTTCCTCCTA 60.397 60.000 0.00 0.00 0.00 2.94
2330 2414 1.687493 CTCCGGCTTCCTTCCTCCT 60.687 63.158 0.00 0.00 0.00 3.69
2331 2415 0.686769 TACTCCGGCTTCCTTCCTCC 60.687 60.000 0.00 0.00 0.00 4.30
2332 2416 0.747852 CTACTCCGGCTTCCTTCCTC 59.252 60.000 0.00 0.00 0.00 3.71
2333 2417 0.041386 ACTACTCCGGCTTCCTTCCT 59.959 55.000 0.00 0.00 0.00 3.36
2338 2422 2.187163 GGCACTACTCCGGCTTCC 59.813 66.667 0.00 0.00 0.00 3.46
2358 2442 4.802051 TAGTCCGGGGTCCGTCCG 62.802 72.222 0.00 0.00 46.80 4.79
2359 2443 2.832201 CTAGTCCGGGGTCCGTCC 60.832 72.222 0.00 0.00 46.80 4.79
2360 2444 1.379044 TTCTAGTCCGGGGTCCGTC 60.379 63.158 0.00 0.00 46.80 4.79
2361 2445 1.379576 CTTCTAGTCCGGGGTCCGT 60.380 63.158 0.00 0.00 46.80 4.69
2398 2482 2.213499 ACCAAGTTTTCAGCTGAGACG 58.787 47.619 17.43 9.63 0.00 4.18
2477 2566 3.127548 AGCTAATTTCCGCATGTGTCTTG 59.872 43.478 5.38 0.00 0.00 3.02
2598 2687 8.986991 ACATTCAGATGTCTATACTCTCCTTTT 58.013 33.333 0.00 0.00 42.83 2.27
2599 2688 8.420222 CACATTCAGATGTCTATACTCTCCTTT 58.580 37.037 0.00 0.00 44.55 3.11
2602 2691 7.230510 ACTCACATTCAGATGTCTATACTCTCC 59.769 40.741 0.00 0.00 44.55 3.71
2603 2692 8.165239 ACTCACATTCAGATGTCTATACTCTC 57.835 38.462 0.00 0.00 44.55 3.20
2635 2727 3.536570 GGGACCTAAGAAGATTGCAGAC 58.463 50.000 0.00 0.00 0.00 3.51
2678 2770 7.173390 GGTTGATACTACCTATGAAATTCCTGC 59.827 40.741 0.00 0.00 32.75 4.85
2703 2796 3.978723 CTGTCTCACGCCGCTCTGG 62.979 68.421 0.00 0.00 42.50 3.86
2731 2824 0.896940 CAAACATGGAGCTGGCCACT 60.897 55.000 0.00 4.06 41.56 4.00
2736 2829 3.367703 GGAAACATCAAACATGGAGCTGG 60.368 47.826 0.00 0.00 0.00 4.85
2739 2832 3.940209 TGGAAACATCAAACATGGAGC 57.060 42.857 0.00 0.00 33.40 4.70
2792 2897 1.568504 TCGTCCTAACCCTTGAGCAT 58.431 50.000 0.00 0.00 0.00 3.79
2869 2974 2.622942 GCTTCAACTTTCCACATCCACA 59.377 45.455 0.00 0.00 0.00 4.17
3083 3188 4.878397 AGGAACATCGGAATCAAACAGATC 59.122 41.667 0.00 0.00 35.39 2.75
3181 3288 9.809096 ATTGTTTTCCTTTCTTCTCTTTCTTTC 57.191 29.630 0.00 0.00 0.00 2.62
3185 3292 9.755804 AATGATTGTTTTCCTTTCTTCTCTTTC 57.244 29.630 0.00 0.00 0.00 2.62
3225 3332 5.975988 TCCTAGAGCTGGAATTGGTTAAT 57.024 39.130 0.00 0.00 0.00 1.40
3254 3361 6.682423 TCACATGTAATCTTGTTATGGCTG 57.318 37.500 0.00 0.00 31.09 4.85
3268 3375 7.129457 AGCTTGGATAAGAGATCACATGTAA 57.871 36.000 0.00 0.00 35.92 2.41
3271 3378 6.018098 GTCAAGCTTGGATAAGAGATCACATG 60.018 42.308 25.73 0.00 35.92 3.21
3273 3380 5.046376 TGTCAAGCTTGGATAAGAGATCACA 60.046 40.000 25.73 14.62 35.92 3.58
3299 3406 7.095229 TGCTTAAGACAAGTACTATGTTGCTTG 60.095 37.037 6.67 0.00 42.65 4.01
3300 3407 6.934645 TGCTTAAGACAAGTACTATGTTGCTT 59.065 34.615 6.67 6.60 0.00 3.91
3301 3408 6.464222 TGCTTAAGACAAGTACTATGTTGCT 58.536 36.000 6.67 0.00 0.00 3.91
3302 3409 6.721571 TGCTTAAGACAAGTACTATGTTGC 57.278 37.500 6.67 5.40 0.00 4.17


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

AutoCloner maintained by Alex Coulton.