Multiple sequence alignment - TraesCS4B01G319700

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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 TraesCS4B01G319700 chr4B 100.000 3170 0 0 1 3170 610436485 610433316 0.000000e+00 5854.0
1 TraesCS4B01G319700 chr4B 75.598 209 40 11 1617 1820 531094081 531094283 3.370000e-15 93.5
2 TraesCS4B01G319700 chr4D 89.449 2360 119 53 559 2891 481448896 481446640 0.000000e+00 2859.0
3 TraesCS4B01G319700 chr4D 89.236 576 23 13 1 551 481449498 481448937 0.000000e+00 684.0
4 TraesCS4B01G319700 chr4D 91.071 280 25 0 2891 3170 481440496 481440217 2.310000e-101 379.0
5 TraesCS4B01G319700 chr5A 87.466 1827 127 56 259 2033 661220799 661222575 0.000000e+00 2012.0
6 TraesCS4B01G319700 chr5A 90.395 531 40 3 2647 3169 661223280 661223807 0.000000e+00 688.0
7 TraesCS4B01G319700 chr5A 89.474 456 25 14 2192 2642 661222805 661223242 3.570000e-154 555.0
8 TraesCS4B01G319700 chr5A 91.000 100 6 1 2101 2197 661222603 661222702 7.130000e-27 132.0
9 TraesCS4B01G319700 chr5A 98.246 57 1 0 1 57 661220613 661220669 2.010000e-17 100.0
10 TraesCS4B01G319700 chr4A 75.641 234 43 14 1617 1843 34294923 34295149 1.560000e-18 104.0


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 TraesCS4B01G319700 chr4B 610433316 610436485 3169 True 5854.0 5854 100.0000 1 3170 1 chr4B.!!$R1 3169
1 TraesCS4B01G319700 chr4D 481446640 481449498 2858 True 1771.5 2859 89.3425 1 2891 2 chr4D.!!$R2 2890
2 TraesCS4B01G319700 chr5A 661220613 661223807 3194 False 697.4 2012 91.3162 1 3169 5 chr5A.!!$F1 3168

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
620 695 0.320421 TTGCTTGCGTGGACTAGGAC 60.32 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2293 2520 0.977627 ACTCGGCCTCATGATGGTCA 60.978 55.0 13.82 3.55 0.0 4.02 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
66 73 4.819761 TCAGCTCATCACGGCCGC 62.820 66.667 28.58 6.76 0.00 6.53
92 99 3.261981 ACCTAACCAACCGATGCTTAG 57.738 47.619 0.00 0.00 30.19 2.18
100 107 5.797051 ACCAACCGATGCTTAGTTAACTAA 58.203 37.500 23.31 23.31 36.99 2.24
101 108 6.412214 ACCAACCGATGCTTAGTTAACTAAT 58.588 36.000 24.61 12.93 37.75 1.73
102 109 7.558604 ACCAACCGATGCTTAGTTAACTAATA 58.441 34.615 24.61 17.85 37.75 0.98
217 232 5.294306 GTCGAGCAAATGAGGTATGATGAAA 59.706 40.000 0.00 0.00 0.00 2.69
330 352 1.034838 AGCAAACAAAGTGGCGTCCA 61.035 50.000 0.00 0.00 0.00 4.02
333 355 1.021968 AAACAAAGTGGCGTCCAGTC 58.978 50.000 6.67 0.00 35.94 3.51
342 364 2.425592 CGTCCAGTCCCAGCACAA 59.574 61.111 0.00 0.00 0.00 3.33
343 365 1.669115 CGTCCAGTCCCAGCACAAG 60.669 63.158 0.00 0.00 0.00 3.16
347 369 1.526686 CAGTCCCAGCACAAGCACA 60.527 57.895 0.00 0.00 45.49 4.57
370 392 2.417933 CGTTTCTTCCAAGGCATCTCAG 59.582 50.000 0.00 0.00 0.00 3.35
377 399 2.367894 TCCAAGGCATCTCAGCTCATAG 59.632 50.000 0.00 0.00 34.17 2.23
378 400 2.104451 CCAAGGCATCTCAGCTCATAGT 59.896 50.000 0.00 0.00 34.17 2.12
379 401 3.323115 CCAAGGCATCTCAGCTCATAGTA 59.677 47.826 0.00 0.00 34.17 1.82
380 402 4.558178 CAAGGCATCTCAGCTCATAGTAG 58.442 47.826 0.00 0.00 34.17 2.57
381 403 3.843422 AGGCATCTCAGCTCATAGTAGT 58.157 45.455 0.00 0.00 34.17 2.73
382 404 4.991776 AGGCATCTCAGCTCATAGTAGTA 58.008 43.478 0.00 0.00 34.17 1.82
383 405 5.009631 AGGCATCTCAGCTCATAGTAGTAG 58.990 45.833 0.00 0.00 34.17 2.57
384 406 4.764823 GGCATCTCAGCTCATAGTAGTAGT 59.235 45.833 0.00 0.00 34.17 2.73
385 407 5.941058 GGCATCTCAGCTCATAGTAGTAGTA 59.059 44.000 0.00 0.00 34.17 1.82
445 476 8.737168 TCTGATCCACAAATCAAATAGGTTAG 57.263 34.615 0.00 0.00 35.32 2.34
446 477 8.328758 TCTGATCCACAAATCAAATAGGTTAGT 58.671 33.333 0.00 0.00 35.32 2.24
447 478 9.613428 CTGATCCACAAATCAAATAGGTTAGTA 57.387 33.333 0.00 0.00 35.32 1.82
448 479 9.391006 TGATCCACAAATCAAATAGGTTAGTAC 57.609 33.333 0.00 0.00 32.80 2.73
449 480 9.391006 GATCCACAAATCAAATAGGTTAGTACA 57.609 33.333 0.00 0.00 0.00 2.90
450 481 9.920946 ATCCACAAATCAAATAGGTTAGTACAT 57.079 29.630 0.00 0.00 0.00 2.29
474 505 2.913603 ATAATCAGGCCCATCCCATG 57.086 50.000 0.00 0.00 34.51 3.66
476 507 1.164313 AATCAGGCCCATCCCATGAT 58.836 50.000 0.00 0.00 34.51 2.45
488 524 2.126882 TCCCATGATCAAATCTCCCGT 58.873 47.619 0.00 0.00 0.00 5.28
522 558 1.213537 CGCTTCCCTCGTCCGTTTA 59.786 57.895 0.00 0.00 0.00 2.01
532 568 1.541147 TCGTCCGTTTATCTGTTCCGT 59.459 47.619 0.00 0.00 0.00 4.69
541 577 2.449031 ATCTGTTCCGTCCGCTGCAA 62.449 55.000 0.00 0.00 0.00 4.08
566 641 2.703798 CGGACCGCTAGTTTCCCGA 61.704 63.158 0.00 0.00 39.31 5.14
615 690 2.980233 GCCTTGCTTGCGTGGACT 60.980 61.111 7.64 0.00 0.00 3.85
616 691 1.671054 GCCTTGCTTGCGTGGACTA 60.671 57.895 7.64 0.00 0.00 2.59
618 693 1.021390 CCTTGCTTGCGTGGACTAGG 61.021 60.000 0.00 0.00 0.00 3.02
620 695 0.320421 TTGCTTGCGTGGACTAGGAC 60.320 55.000 0.00 0.00 0.00 3.85
650 725 1.296727 GATGCAAACCTACGGCTACC 58.703 55.000 0.00 0.00 0.00 3.18
729 804 0.807275 GCCAATGCCCGCTGAATTTC 60.807 55.000 0.00 0.00 0.00 2.17
749 831 0.810823 AGAGACTCGATCGTCCGGAC 60.811 60.000 25.28 25.28 34.46 4.79
750 832 0.810823 GAGACTCGATCGTCCGGACT 60.811 60.000 30.92 14.84 34.46 3.85
751 833 0.810823 AGACTCGATCGTCCGGACTC 60.811 60.000 30.92 21.43 34.46 3.36
752 834 1.774046 GACTCGATCGTCCGGACTCC 61.774 65.000 30.92 18.17 0.00 3.85
831 913 1.133253 CTGTGCGCTGATGGAAACG 59.867 57.895 9.73 0.00 0.00 3.60
840 922 2.726241 GCTGATGGAAACGCTGTTTTTC 59.274 45.455 7.83 6.83 33.00 2.29
846 928 4.668289 TGGAAACGCTGTTTTTCTTTCTC 58.332 39.130 7.83 0.00 34.06 2.87
848 930 5.105917 TGGAAACGCTGTTTTTCTTTCTCTT 60.106 36.000 7.83 0.00 34.06 2.85
890 972 5.047847 TCGTGCTAATTATTACTGCTGGTC 58.952 41.667 0.00 0.00 0.00 4.02
891 973 4.808895 CGTGCTAATTATTACTGCTGGTCA 59.191 41.667 0.00 0.00 0.00 4.02
962 1044 3.810310 GCTGGTGCTCTGATACTACTT 57.190 47.619 0.00 0.00 36.03 2.24
978 1060 9.917129 TGATACTACTTGTTTTTAGTCGATTGA 57.083 29.630 0.00 0.00 30.97 2.57
1010 1093 4.876125 ACTTGGATCTATATGCGTGTCTG 58.124 43.478 0.00 0.00 0.00 3.51
1020 1105 2.378858 GCGTGTCTGTCTCTGCAGC 61.379 63.158 9.47 0.00 36.49 5.25
1072 1157 3.061928 CGCAACAAAAGAATTGTGTGACG 60.062 43.478 0.00 0.00 32.78 4.35
1075 1160 3.694734 ACAAAAGAATTGTGTGACGCTG 58.305 40.909 0.00 0.00 0.00 5.18
1160 1250 6.958192 TCTAGTTCCTTTTCTTCCCTTAGCTA 59.042 38.462 0.00 0.00 0.00 3.32
1180 1272 1.676678 CCTCGCTAGCCAAGTAGCCA 61.677 60.000 9.66 0.00 42.21 4.75
1193 1285 1.841103 TAGCCAGGCCAGTCACACA 60.841 57.895 8.22 0.00 0.00 3.72
1194 1286 2.111999 TAGCCAGGCCAGTCACACAC 62.112 60.000 8.22 0.00 0.00 3.82
1199 1291 2.546494 GGCCAGTCACACACACTGC 61.546 63.158 0.00 0.00 40.10 4.40
1216 1308 2.864931 GCGCTCGAGAATCAAGGCG 61.865 63.158 18.75 12.01 45.02 5.52
1491 1586 4.399395 CTCCTGCGCCAGCTCCAA 62.399 66.667 4.18 0.00 45.42 3.53
2034 2133 1.746760 GATCCGATGAAAACATGCGC 58.253 50.000 0.00 0.00 0.00 6.09
2148 2253 6.872628 TCCTGTAAAGATATCATCGTACGT 57.127 37.500 16.05 0.00 31.41 3.57
2293 2520 0.322277 GCTGATCGCCATGGATCCAT 60.322 55.000 22.15 22.15 41.71 3.41
2336 2563 1.751927 CATGCTTGGTGGGAGAGGC 60.752 63.158 0.00 0.00 0.00 4.70
2343 2570 4.106925 GTGGGAGAGGCAGGCAGG 62.107 72.222 0.00 0.00 0.00 4.85
2462 2697 3.543680 ACGGGATCGAATTGATTGACT 57.456 42.857 0.00 0.00 37.47 3.41
2463 2698 3.198068 ACGGGATCGAATTGATTGACTG 58.802 45.455 0.00 0.00 37.47 3.51
2464 2699 3.118775 ACGGGATCGAATTGATTGACTGA 60.119 43.478 0.00 0.00 37.47 3.41
2465 2700 3.246226 CGGGATCGAATTGATTGACTGAC 59.754 47.826 0.00 0.00 37.47 3.51
2466 2701 4.446371 GGGATCGAATTGATTGACTGACT 58.554 43.478 0.00 0.00 37.47 3.41
2467 2702 4.272018 GGGATCGAATTGATTGACTGACTG 59.728 45.833 0.00 0.00 37.47 3.51
2468 2703 5.111989 GGATCGAATTGATTGACTGACTGA 58.888 41.667 0.00 0.00 37.47 3.41
2469 2704 5.006165 GGATCGAATTGATTGACTGACTGAC 59.994 44.000 0.00 0.00 37.47 3.51
2477 2712 4.525874 TGATTGACTGACTGACTGACTGAT 59.474 41.667 0.00 0.00 0.00 2.90
2490 2729 5.873164 TGACTGACTGATTGATTGATGTGAG 59.127 40.000 0.00 0.00 0.00 3.51
2644 2887 3.103911 CCGCTGACGTCCGTGTTC 61.104 66.667 14.12 0.00 37.70 3.18
2645 2888 2.050351 CGCTGACGTCCGTGTTCT 60.050 61.111 14.12 0.00 33.53 3.01
2649 2925 1.454653 GCTGACGTCCGTGTTCTTTAC 59.545 52.381 14.12 0.00 0.00 2.01
2655 2931 2.473984 CGTCCGTGTTCTTTACTTGTCC 59.526 50.000 0.00 0.00 0.00 4.02
2656 2932 2.473984 GTCCGTGTTCTTTACTTGTCCG 59.526 50.000 0.00 0.00 0.00 4.79
2664 2940 1.796459 CTTTACTTGTCCGGGTTCGTG 59.204 52.381 0.00 0.00 33.95 4.35
2676 2952 2.109126 GTTCGTGCCCATGCCTCTC 61.109 63.158 0.00 0.00 36.33 3.20
2730 3008 1.637724 TTTTCCCGGGTGTCACCTGT 61.638 55.000 26.02 0.00 43.22 4.00
2733 3011 2.592993 CCCGGGTGTCACCTGTCAT 61.593 63.158 26.02 0.00 43.22 3.06
2751 3029 1.750778 CATGGGTGCCTGACAAATACC 59.249 52.381 0.00 0.00 0.00 2.73
2753 3031 1.271871 TGGGTGCCTGACAAATACCAG 60.272 52.381 0.00 0.00 33.10 4.00
2825 3103 1.469126 CGTCCAACGATTACGCCGAG 61.469 60.000 0.00 0.00 46.05 4.63
2830 3108 2.542205 CCAACGATTACGCCGAGTGATA 60.542 50.000 0.00 0.00 43.96 2.15
2899 3177 2.668617 CATGCATGCATGTACCGTAC 57.331 50.000 40.30 9.65 46.20 3.67
2987 3268 1.409064 GTGCCACATGATCTCCGTCTA 59.591 52.381 0.00 0.00 0.00 2.59
2999 3280 3.250744 TCTCCGTCTAATGAAACGCTTG 58.749 45.455 0.00 0.00 37.56 4.01
3004 3285 4.152759 CCGTCTAATGAAACGCTTGGTTAA 59.847 41.667 0.00 0.00 38.08 2.01
3024 3305 0.331616 AAAATGGGGCGAGCTAAGGT 59.668 50.000 0.00 0.00 0.00 3.50
3031 3317 1.472904 GGGCGAGCTAAGGTTTAGGTC 60.473 57.143 14.77 14.77 38.35 3.85
3040 3326 6.543735 AGCTAAGGTTTAGGTCACTGAAAAT 58.456 36.000 0.00 0.00 0.00 1.82
3046 3332 7.937649 AGGTTTAGGTCACTGAAAATACAAAC 58.062 34.615 0.00 0.00 0.00 2.93
3055 3341 5.977129 CACTGAAAATACAAACTGGGTCAAC 59.023 40.000 0.00 0.00 0.00 3.18
3056 3342 5.654650 ACTGAAAATACAAACTGGGTCAACA 59.345 36.000 0.00 0.00 0.00 3.33
3065 3351 6.142818 CAAACTGGGTCAACAGATTGTTTA 57.857 37.500 7.70 0.00 42.67 2.01
3071 3357 4.083484 GGGTCAACAGATTGTTTAGAACCG 60.083 45.833 1.96 0.00 38.77 4.44
3074 3360 6.134061 GTCAACAGATTGTTTAGAACCGTTC 58.866 40.000 2.81 2.81 38.77 3.95
3084 3370 2.080286 AGAACCGTTCGATGTGAAGG 57.920 50.000 5.62 0.00 41.14 3.46
3092 3378 0.892755 TCGATGTGAAGGTAACGGCT 59.107 50.000 0.00 0.00 46.39 5.52
3094 3380 2.691526 TCGATGTGAAGGTAACGGCTAT 59.308 45.455 0.00 0.00 46.39 2.97
3113 3399 3.584733 ATATGGCCTTCTTCAACCTCC 57.415 47.619 3.32 0.00 0.00 4.30
3123 3409 1.874345 TTCAACCTCCGACTCTCGCC 61.874 60.000 0.00 0.00 38.82 5.54
3147 3433 2.041620 CTCATCTTCTTCCCCCAAACCA 59.958 50.000 0.00 0.00 0.00 3.67
3169 3455 4.308458 CGACCACCGGCTGAACCA 62.308 66.667 0.00 0.00 39.03 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 73 3.427503 GCATCGGTTGGTTAGGTTTCATG 60.428 47.826 0.00 0.00 0.00 3.07
67 74 2.752903 GCATCGGTTGGTTAGGTTTCAT 59.247 45.455 0.00 0.00 0.00 2.57
191 206 4.406648 TCATACCTCATTTGCTCGACAT 57.593 40.909 0.00 0.00 0.00 3.06
217 232 2.159448 CGTCTCTCTCTCGTTGCTTCAT 60.159 50.000 0.00 0.00 0.00 2.57
330 352 1.228063 CTGTGCTTGTGCTGGGACT 60.228 57.895 0.00 0.00 40.48 3.85
333 355 4.034258 CGCTGTGCTTGTGCTGGG 62.034 66.667 0.00 0.00 40.48 4.45
342 364 0.947244 CTTGGAAGAAACGCTGTGCT 59.053 50.000 0.00 0.00 0.00 4.40
343 365 0.040067 CCTTGGAAGAAACGCTGTGC 60.040 55.000 0.00 0.00 0.00 4.57
347 369 1.168714 GATGCCTTGGAAGAAACGCT 58.831 50.000 0.00 0.00 0.00 5.07
377 399 9.856803 GTCGCTACAAACTAATACTACTACTAC 57.143 37.037 0.00 0.00 0.00 2.73
378 400 9.599866 TGTCGCTACAAACTAATACTACTACTA 57.400 33.333 0.00 0.00 30.91 1.82
379 401 8.498054 TGTCGCTACAAACTAATACTACTACT 57.502 34.615 0.00 0.00 30.91 2.57
380 402 8.394121 ACTGTCGCTACAAACTAATACTACTAC 58.606 37.037 0.00 0.00 34.49 2.73
381 403 8.498054 ACTGTCGCTACAAACTAATACTACTA 57.502 34.615 0.00 0.00 34.49 1.82
382 404 7.388460 ACTGTCGCTACAAACTAATACTACT 57.612 36.000 0.00 0.00 34.49 2.57
383 405 7.854916 CCTACTGTCGCTACAAACTAATACTAC 59.145 40.741 0.00 0.00 34.49 2.73
384 406 7.770433 TCCTACTGTCGCTACAAACTAATACTA 59.230 37.037 0.00 0.00 34.49 1.82
385 407 6.600822 TCCTACTGTCGCTACAAACTAATACT 59.399 38.462 0.00 0.00 34.49 2.12
445 476 6.992715 GGATGGGCCTGATTATACATATGTAC 59.007 42.308 17.69 6.04 32.72 2.90
446 477 6.101150 GGGATGGGCCTGATTATACATATGTA 59.899 42.308 17.65 17.65 36.66 2.29
447 478 5.103940 GGGATGGGCCTGATTATACATATGT 60.104 44.000 13.93 13.93 36.66 2.29
448 479 5.103982 TGGGATGGGCCTGATTATACATATG 60.104 44.000 4.53 0.00 36.66 1.78
449 480 5.045831 TGGGATGGGCCTGATTATACATAT 58.954 41.667 4.53 0.00 36.66 1.78
450 481 4.443658 TGGGATGGGCCTGATTATACATA 58.556 43.478 4.53 0.00 36.66 2.29
451 482 3.268146 TGGGATGGGCCTGATTATACAT 58.732 45.455 4.53 0.00 36.66 2.29
474 505 2.799917 CGAGGTGACGGGAGATTTGATC 60.800 54.545 0.00 0.00 0.00 2.92
476 507 0.530744 CGAGGTGACGGGAGATTTGA 59.469 55.000 0.00 0.00 0.00 2.69
488 524 2.355363 CGCCAACGAACGAGGTGA 60.355 61.111 14.55 0.00 43.93 4.02
522 558 2.125512 GCAGCGGACGGAACAGAT 60.126 61.111 0.00 0.00 0.00 2.90
551 587 1.318158 ACGATCGGGAAACTAGCGGT 61.318 55.000 20.98 0.00 31.16 5.68
555 630 3.372954 CAAGCTACGATCGGGAAACTAG 58.627 50.000 20.98 11.54 0.00 2.57
557 632 1.739371 GCAAGCTACGATCGGGAAACT 60.739 52.381 20.98 6.33 0.00 2.66
582 657 0.838987 AGGCCCAGAAACGGACCTAA 60.839 55.000 0.00 0.00 0.00 2.69
586 661 2.626780 GCAAGGCCCAGAAACGGAC 61.627 63.158 0.00 0.00 0.00 4.79
615 690 1.405526 GCATCCGCAAGACAAGTCCTA 60.406 52.381 0.00 0.00 43.02 2.94
616 691 0.674895 GCATCCGCAAGACAAGTCCT 60.675 55.000 0.00 0.00 43.02 3.85
650 725 3.058846 CCATGAGATGAGAGGTACGTACG 60.059 52.174 18.98 15.01 0.00 3.67
714 789 1.065199 TCTCTGAAATTCAGCGGGCAT 60.065 47.619 17.58 0.00 43.95 4.40
729 804 0.810426 TCCGGACGATCGAGTCTCTG 60.810 60.000 24.34 13.44 40.76 3.35
749 831 0.247974 CTAGCGTACGTGTTCCGGAG 60.248 60.000 17.90 0.00 42.24 4.63
750 832 1.796151 CTAGCGTACGTGTTCCGGA 59.204 57.895 17.90 0.00 42.24 5.14
751 833 1.870901 GCTAGCGTACGTGTTCCGG 60.871 63.158 17.90 0.00 42.24 5.14
752 834 1.870901 GGCTAGCGTACGTGTTCCG 60.871 63.158 17.90 0.00 44.03 4.30
753 835 0.801067 CAGGCTAGCGTACGTGTTCC 60.801 60.000 17.90 13.00 0.00 3.62
754 836 1.411493 GCAGGCTAGCGTACGTGTTC 61.411 60.000 17.90 0.00 0.00 3.18
755 837 1.445582 GCAGGCTAGCGTACGTGTT 60.446 57.895 17.90 5.75 0.00 3.32
814 896 3.252964 CGTTTCCATCAGCGCACA 58.747 55.556 11.47 0.00 0.00 4.57
890 972 1.642037 CGACTGATTGCCACCAGCTG 61.642 60.000 6.78 6.78 44.23 4.24
891 973 1.376424 CGACTGATTGCCACCAGCT 60.376 57.895 0.00 0.00 44.23 4.24
892 974 2.401766 CCGACTGATTGCCACCAGC 61.402 63.158 0.00 0.00 44.14 4.85
893 975 0.606401 AACCGACTGATTGCCACCAG 60.606 55.000 0.00 0.00 36.53 4.00
894 976 0.179004 AAACCGACTGATTGCCACCA 60.179 50.000 0.00 0.00 0.00 4.17
895 977 1.467342 GTAAACCGACTGATTGCCACC 59.533 52.381 0.00 0.00 0.00 4.61
896 978 1.467342 GGTAAACCGACTGATTGCCAC 59.533 52.381 0.00 0.00 0.00 5.01
897 979 1.072489 TGGTAAACCGACTGATTGCCA 59.928 47.619 0.00 0.00 36.63 4.92
962 1044 7.504924 ACTGGATTTCAATCGACTAAAAACA 57.495 32.000 0.00 0.00 36.27 2.83
1020 1105 0.391661 ACTCTAATGGCGTGTGCAGG 60.392 55.000 0.00 0.00 45.35 4.85
1033 1118 1.666553 CGGGCACGTTGCACTCTAA 60.667 57.895 0.00 0.00 46.59 2.10
1075 1160 3.060615 CCAGGAAGCTGCAGCACC 61.061 66.667 38.24 35.26 45.16 5.01
1160 1250 1.677637 GGCTACTTGGCTAGCGAGGT 61.678 60.000 18.09 18.09 40.21 3.85
1180 1272 1.146930 CAGTGTGTGTGACTGGCCT 59.853 57.895 3.32 0.00 37.72 5.19
1193 1285 0.038251 TTGATTCTCGAGCGCAGTGT 60.038 50.000 11.47 0.00 0.00 3.55
1194 1286 0.644331 CTTGATTCTCGAGCGCAGTG 59.356 55.000 11.47 4.24 0.00 3.66
1199 1291 1.517257 ACGCCTTGATTCTCGAGCG 60.517 57.895 7.81 8.80 35.25 5.03
1216 1308 1.606350 CGAGGTGTCGTCGCTTTCAC 61.606 60.000 0.00 0.00 41.57 3.18
1247 1339 1.284982 CTTCGACTTGGCAGTGTCCG 61.285 60.000 14.22 10.60 31.22 4.79
1251 1343 2.064762 CTCTTCTTCGACTTGGCAGTG 58.935 52.381 0.00 0.00 31.22 3.66
1261 1353 1.550976 GGCCTTCTTCCTCTTCTTCGA 59.449 52.381 0.00 0.00 0.00 3.71
1290 1382 1.508088 GCAGCCAAAGATGAACCCG 59.492 57.895 0.00 0.00 0.00 5.28
1340 1432 0.462581 TGCCATCGTGGAGAGATTGC 60.463 55.000 8.04 0.00 40.96 3.56
1840 1935 3.197790 CTTCTGCATGGGGTCGCG 61.198 66.667 0.00 0.00 0.00 5.87
1841 1936 3.512516 GCTTCTGCATGGGGTCGC 61.513 66.667 0.00 0.00 39.41 5.19
1842 1937 2.046023 TGCTTCTGCATGGGGTCG 60.046 61.111 0.00 0.00 45.31 4.79
1848 1943 5.801379 GCTTCTGCTTCTGCTTCTGCATG 62.801 52.174 0.00 0.00 41.50 4.06
1853 1948 1.297456 GCGCTTCTGCTTCTGCTTCT 61.297 55.000 0.00 0.00 40.48 2.85
1872 1967 2.352805 GCAGGGGAGACAACAGGG 59.647 66.667 0.00 0.00 0.00 4.45
1877 1972 3.650950 GGCCTGCAGGGGAGACAA 61.651 66.667 33.46 0.00 35.18 3.18
1937 2032 1.948104 AGTTAACTTGTCAGTGCGCA 58.052 45.000 5.66 5.66 31.60 6.09
1990 2089 1.595093 GCAACAATTCCCGAGGGTGG 61.595 60.000 8.20 0.00 36.47 4.61
1991 2090 1.595093 GGCAACAATTCCCGAGGGTG 61.595 60.000 8.20 1.88 36.47 4.61
1992 2091 1.304134 GGCAACAATTCCCGAGGGT 60.304 57.895 8.20 0.00 36.47 4.34
1993 2092 2.406616 CGGCAACAATTCCCGAGGG 61.407 63.158 0.65 0.65 44.55 4.30
2034 2133 1.442520 CTGAAAACCATGCACGCGG 60.443 57.895 12.47 0.00 0.00 6.46
2042 2141 1.541147 CATCACGGCACTGAAAACCAT 59.459 47.619 0.00 0.00 0.00 3.55
2096 2201 1.478510 GGAGAGAACTGATTCAGGCGA 59.521 52.381 17.66 0.00 37.29 5.54
2097 2202 1.480137 AGGAGAGAACTGATTCAGGCG 59.520 52.381 17.66 0.00 37.29 5.52
2148 2253 3.242903 CGCAATATTCACGGGCAATGTAA 60.243 43.478 0.41 0.00 0.00 2.41
2155 2264 4.996113 CACGCAATATTCACGGGC 57.004 55.556 11.06 0.00 0.00 6.13
2230 2450 4.974989 ACGTTTGCCCGACCGACC 62.975 66.667 0.00 0.00 0.00 4.79
2231 2451 3.708734 CACGTTTGCCCGACCGAC 61.709 66.667 0.00 0.00 0.00 4.79
2232 2452 4.973055 CCACGTTTGCCCGACCGA 62.973 66.667 0.00 0.00 0.00 4.69
2293 2520 0.977627 ACTCGGCCTCATGATGGTCA 60.978 55.000 13.82 3.55 0.00 4.02
2462 2697 5.473066 TCAATCAATCAGTCAGTCAGTCA 57.527 39.130 0.00 0.00 0.00 3.41
2463 2698 5.873712 ACATCAATCAATCAGTCAGTCAGTC 59.126 40.000 0.00 0.00 0.00 3.51
2464 2699 5.642491 CACATCAATCAATCAGTCAGTCAGT 59.358 40.000 0.00 0.00 0.00 3.41
2465 2700 5.873164 TCACATCAATCAATCAGTCAGTCAG 59.127 40.000 0.00 0.00 0.00 3.51
2466 2701 5.797051 TCACATCAATCAATCAGTCAGTCA 58.203 37.500 0.00 0.00 0.00 3.41
2467 2702 5.220624 GCTCACATCAATCAATCAGTCAGTC 60.221 44.000 0.00 0.00 0.00 3.51
2468 2703 4.634883 GCTCACATCAATCAATCAGTCAGT 59.365 41.667 0.00 0.00 0.00 3.41
2469 2704 4.876679 AGCTCACATCAATCAATCAGTCAG 59.123 41.667 0.00 0.00 0.00 3.51
2477 2712 1.733912 GACGCAGCTCACATCAATCAA 59.266 47.619 0.00 0.00 0.00 2.57
2629 2872 1.454653 GTAAAGAACACGGACGTCAGC 59.545 52.381 18.91 0.00 0.00 4.26
2636 2879 2.546373 CCGGACAAGTAAAGAACACGGA 60.546 50.000 0.00 0.00 41.13 4.69
2642 2885 2.102925 ACGAACCCGGACAAGTAAAGAA 59.897 45.455 0.73 0.00 40.78 2.52
2644 2887 1.796459 CACGAACCCGGACAAGTAAAG 59.204 52.381 0.73 0.00 40.78 1.85
2645 2888 1.868469 CACGAACCCGGACAAGTAAA 58.132 50.000 0.73 0.00 40.78 2.01
2649 2925 3.047877 GGCACGAACCCGGACAAG 61.048 66.667 0.73 0.00 40.78 3.16
2664 2940 1.153208 CAGACAGAGAGGCATGGGC 60.153 63.158 0.00 0.00 40.13 5.36
2676 2952 0.038251 TGTCAAGCGCCTACAGACAG 60.038 55.000 2.29 0.00 34.59 3.51
2730 3008 2.620367 GGTATTTGTCAGGCACCCATGA 60.620 50.000 0.00 0.00 0.00 3.07
2733 3011 0.774276 TGGTATTTGTCAGGCACCCA 59.226 50.000 0.00 0.00 0.00 4.51
2753 3031 9.607285 CCATATGAACCGCTTAATTTGTTATAC 57.393 33.333 3.65 0.00 0.00 1.47
2825 3103 4.034975 GCTTCCAGTCAATCAGCTTATCAC 59.965 45.833 0.00 0.00 0.00 3.06
2830 3108 1.446907 CGCTTCCAGTCAATCAGCTT 58.553 50.000 0.00 0.00 0.00 3.74
2894 3172 2.185867 CATCCACCCACCGTACGG 59.814 66.667 32.22 32.22 42.03 4.02
2895 3173 2.510691 GCATCCACCCACCGTACG 60.511 66.667 8.69 8.69 0.00 3.67
2896 3174 1.095228 CATGCATCCACCCACCGTAC 61.095 60.000 0.00 0.00 0.00 3.67
2897 3175 1.223211 CATGCATCCACCCACCGTA 59.777 57.895 0.00 0.00 0.00 4.02
2898 3176 2.045045 CATGCATCCACCCACCGT 60.045 61.111 0.00 0.00 0.00 4.83
2899 3177 3.520862 GCATGCATCCACCCACCG 61.521 66.667 14.21 0.00 0.00 4.94
3004 3285 1.272480 ACCTTAGCTCGCCCCATTTTT 60.272 47.619 0.00 0.00 0.00 1.94
3016 3297 5.562298 TTTCAGTGACCTAAACCTTAGCT 57.438 39.130 0.00 0.00 0.00 3.32
3024 3305 7.013846 CCCAGTTTGTATTTTCAGTGACCTAAA 59.986 37.037 0.00 0.00 0.00 1.85
3031 3317 5.766150 TGACCCAGTTTGTATTTTCAGTG 57.234 39.130 0.00 0.00 0.00 3.66
3040 3326 4.787551 ACAATCTGTTGACCCAGTTTGTA 58.212 39.130 13.19 0.00 46.10 2.41
3046 3332 5.048713 GGTTCTAAACAATCTGTTGACCCAG 60.049 44.000 0.00 0.00 40.14 4.45
3055 3341 5.120208 ACATCGAACGGTTCTAAACAATCTG 59.880 40.000 17.94 4.30 0.00 2.90
3056 3342 5.120208 CACATCGAACGGTTCTAAACAATCT 59.880 40.000 17.94 0.00 0.00 2.40
3065 3351 1.343465 ACCTTCACATCGAACGGTTCT 59.657 47.619 17.94 0.00 33.77 3.01
3071 3357 1.392510 GCCGTTACCTTCACATCGAAC 59.607 52.381 0.00 0.00 0.00 3.95
3074 3360 2.572191 TAGCCGTTACCTTCACATCG 57.428 50.000 0.00 0.00 0.00 3.84
3092 3378 3.071023 CGGAGGTTGAAGAAGGCCATATA 59.929 47.826 5.01 0.00 0.00 0.86
3094 3380 1.209504 CGGAGGTTGAAGAAGGCCATA 59.790 52.381 5.01 0.00 0.00 2.74
3104 3390 1.585006 GCGAGAGTCGGAGGTTGAA 59.415 57.895 0.00 0.00 40.84 2.69
3113 3399 1.299014 GATGAGCAGGCGAGAGTCG 60.299 63.158 0.00 0.00 43.49 4.18
3123 3409 0.914644 TGGGGGAAGAAGATGAGCAG 59.085 55.000 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.