Multiple sequence alignment - TraesCS4B01G390700

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 TraesCS4B01G390700 chr4B 100.000 2570 0 0 1 2570 666613183 666610614 0.000000e+00 4747.0
1 TraesCS4B01G390700 chrUn 90.493 2009 92 36 633 2570 134314177 134312197 0.000000e+00 2560.0
2 TraesCS4B01G390700 chrUn 89.312 552 39 7 9 545 134314850 134314304 0.000000e+00 675.0
3 TraesCS4B01G390700 chrUn 75.862 203 34 12 2315 2512 134311989 134311797 3.520000e-14 89.8
4 TraesCS4B01G390700 chr5A 91.314 1842 87 30 770 2567 706020363 706022175 0.000000e+00 2447.0


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 TraesCS4B01G390700 chr4B 666610614 666613183 2569 True 4747.000000 4747 100.000000 1 2570 1 chr4B.!!$R1 2569
1 TraesCS4B01G390700 chrUn 134311797 134314850 3053 True 1108.266667 2560 85.222333 9 2570 3 chrUn.!!$R1 2561
2 TraesCS4B01G390700 chr5A 706020363 706022175 1812 False 2447.000000 2447 91.314000 770 2567 1 chr5A.!!$F1 1797

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
115 129 0.029035 CAAGCATGCTTGGCGAGATC 59.971 55.0 40.7 1.55 46.88 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 2007 1.066908 GGCAACTGCACAAACAGCTTA 59.933 47.619 3.76 0.0 44.36 3.09 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
48 49 7.222000 TGTTCATAAATACAAGGTTTGGGTC 57.778 36.000 0.00 0.00 34.12 4.46
53 54 4.396357 AATACAAGGTTTGGGTCATGGA 57.604 40.909 0.00 0.00 34.12 3.41
55 56 1.203050 ACAAGGTTTGGGTCATGGAGG 60.203 52.381 0.00 0.00 34.12 4.30
60 74 1.139498 TTTGGGTCATGGAGGGCTCA 61.139 55.000 0.00 0.00 0.00 4.26
115 129 0.029035 CAAGCATGCTTGGCGAGATC 59.971 55.000 40.70 1.55 46.88 2.75
128 142 1.656652 CGAGATCGTGGGCTTCAAAT 58.343 50.000 0.00 0.00 34.11 2.32
131 145 3.621268 CGAGATCGTGGGCTTCAAATTTA 59.379 43.478 0.00 0.00 34.11 1.40
132 146 4.273480 CGAGATCGTGGGCTTCAAATTTAT 59.727 41.667 0.00 0.00 34.11 1.40
181 196 9.847224 ATTACAAGAAAGAAAACTAGTCTTCCA 57.153 29.630 5.30 0.00 34.19 3.53
184 199 7.496263 ACAAGAAAGAAAACTAGTCTTCCACTC 59.504 37.037 5.30 0.74 34.19 3.51
196 211 8.207545 ACTAGTCTTCCACTCCATTATTTCATC 58.792 37.037 0.00 0.00 36.43 2.92
200 215 7.987458 GTCTTCCACTCCATTATTTCATCTACA 59.013 37.037 0.00 0.00 0.00 2.74
205 220 7.503566 CCACTCCATTATTTCATCTACAATGGT 59.496 37.037 10.52 0.00 43.93 3.55
226 241 1.434622 GCATGTGATCCTCCTGTGCG 61.435 60.000 0.00 0.00 0.00 5.34
270 285 2.460918 CTTGGTTGTCGGACGCTATAG 58.539 52.381 3.34 0.00 0.00 1.31
271 286 1.466856 TGGTTGTCGGACGCTATAGT 58.533 50.000 3.34 0.00 0.00 2.12
274 289 2.034305 GGTTGTCGGACGCTATAGTCAT 59.966 50.000 3.34 0.00 42.62 3.06
291 306 5.341872 AGTCATGTTCTGGAGATCAAGAG 57.658 43.478 0.00 0.00 0.00 2.85
369 384 5.711506 TCAGTCGTACCTTGGATTACTACAA 59.288 40.000 0.00 0.00 0.00 2.41
380 395 6.681729 TGGATTACTACAACTGAAGAACCT 57.318 37.500 0.00 0.00 0.00 3.50
387 402 6.692486 ACTACAACTGAAGAACCTCATGTAG 58.308 40.000 10.61 10.61 41.02 2.74
406 421 6.806668 TGTAGAGAATGTTATGGTCATGGA 57.193 37.500 0.00 0.00 0.00 3.41
413 428 4.734398 TGTTATGGTCATGGAAAATGGC 57.266 40.909 0.00 0.00 0.00 4.40
414 429 3.450457 TGTTATGGTCATGGAAAATGGCC 59.550 43.478 0.00 0.00 43.78 5.36
455 470 1.162800 GCCGAGCCACTTCATCATCC 61.163 60.000 0.00 0.00 0.00 3.51
473 488 1.202114 TCCGCATTGATCTTGGCAAAC 59.798 47.619 0.00 0.00 0.00 2.93
517 533 1.592223 GAGCAGTCGTACAAGGCCT 59.408 57.895 0.00 0.00 0.00 5.19
519 535 1.409427 GAGCAGTCGTACAAGGCCTAT 59.591 52.381 5.16 0.00 0.00 2.57
520 536 1.831736 AGCAGTCGTACAAGGCCTATT 59.168 47.619 5.16 0.00 0.00 1.73
534 550 1.663074 CTATTCGGAGCTCGCTGCC 60.663 63.158 7.83 0.00 44.23 4.85
535 551 2.355445 CTATTCGGAGCTCGCTGCCA 62.355 60.000 7.83 0.00 44.23 4.92
545 561 0.445436 CTCGCTGCCACATTTCTGTC 59.555 55.000 0.00 0.00 31.62 3.51
546 562 0.955428 TCGCTGCCACATTTCTGTCC 60.955 55.000 0.00 0.00 31.62 4.02
547 563 0.957395 CGCTGCCACATTTCTGTCCT 60.957 55.000 0.00 0.00 31.62 3.85
548 564 0.807496 GCTGCCACATTTCTGTCCTC 59.193 55.000 0.00 0.00 31.62 3.71
549 565 1.883638 GCTGCCACATTTCTGTCCTCA 60.884 52.381 0.00 0.00 31.62 3.86
550 566 2.082231 CTGCCACATTTCTGTCCTCAG 58.918 52.381 0.00 0.00 42.54 3.35
551 567 0.807496 GCCACATTTCTGTCCTCAGC 59.193 55.000 0.00 0.00 41.10 4.26
552 568 1.883638 GCCACATTTCTGTCCTCAGCA 60.884 52.381 0.00 0.00 41.10 4.41
553 569 2.507484 CCACATTTCTGTCCTCAGCAA 58.493 47.619 0.00 0.00 41.10 3.91
554 570 2.227388 CCACATTTCTGTCCTCAGCAAC 59.773 50.000 0.00 0.00 41.10 4.17
555 571 2.880268 CACATTTCTGTCCTCAGCAACA 59.120 45.455 0.00 0.00 41.10 3.33
556 572 3.504906 CACATTTCTGTCCTCAGCAACAT 59.495 43.478 0.00 0.00 41.10 2.71
557 573 3.755378 ACATTTCTGTCCTCAGCAACATC 59.245 43.478 0.00 0.00 41.10 3.06
558 574 3.777106 TTTCTGTCCTCAGCAACATCT 57.223 42.857 0.00 0.00 41.10 2.90
559 575 3.777106 TTCTGTCCTCAGCAACATCTT 57.223 42.857 0.00 0.00 41.10 2.40
560 576 3.777106 TCTGTCCTCAGCAACATCTTT 57.223 42.857 0.00 0.00 41.10 2.52
561 577 4.890158 TCTGTCCTCAGCAACATCTTTA 57.110 40.909 0.00 0.00 41.10 1.85
562 578 5.227569 TCTGTCCTCAGCAACATCTTTAA 57.772 39.130 0.00 0.00 41.10 1.52
563 579 4.997395 TCTGTCCTCAGCAACATCTTTAAC 59.003 41.667 0.00 0.00 41.10 2.01
564 580 4.973168 TGTCCTCAGCAACATCTTTAACT 58.027 39.130 0.00 0.00 0.00 2.24
565 581 4.997395 TGTCCTCAGCAACATCTTTAACTC 59.003 41.667 0.00 0.00 0.00 3.01
566 582 4.997395 GTCCTCAGCAACATCTTTAACTCA 59.003 41.667 0.00 0.00 0.00 3.41
567 583 5.470098 GTCCTCAGCAACATCTTTAACTCAA 59.530 40.000 0.00 0.00 0.00 3.02
568 584 6.017109 GTCCTCAGCAACATCTTTAACTCAAA 60.017 38.462 0.00 0.00 0.00 2.69
569 585 6.205464 TCCTCAGCAACATCTTTAACTCAAAG 59.795 38.462 0.00 0.00 44.36 2.77
579 595 5.966742 CTTTAACTCAAAGAAAGAGGGGG 57.033 43.478 0.00 0.00 45.62 5.40
600 616 3.844090 GGCCTGCCCGAGAGAGTC 61.844 72.222 0.00 0.00 0.00 3.36
601 617 3.071206 GCCTGCCCGAGAGAGTCA 61.071 66.667 0.00 0.00 0.00 3.41
602 618 2.430610 GCCTGCCCGAGAGAGTCAT 61.431 63.158 0.00 0.00 0.00 3.06
603 619 1.739049 CCTGCCCGAGAGAGTCATC 59.261 63.158 0.00 0.00 0.00 2.92
604 620 1.358402 CTGCCCGAGAGAGTCATCG 59.642 63.158 10.00 10.00 38.65 3.84
609 625 1.278337 CGAGAGAGTCATCGGCTCG 59.722 63.158 9.29 0.00 43.51 5.03
610 626 1.008995 GAGAGAGTCATCGGCTCGC 60.009 63.158 0.00 0.00 37.99 5.03
611 627 1.719725 GAGAGAGTCATCGGCTCGCA 61.720 60.000 2.28 0.00 37.99 5.10
612 628 1.106351 AGAGAGTCATCGGCTCGCAT 61.106 55.000 2.28 0.00 37.99 4.73
613 629 0.249238 GAGAGTCATCGGCTCGCATT 60.249 55.000 0.00 0.00 37.99 3.56
614 630 0.529337 AGAGTCATCGGCTCGCATTG 60.529 55.000 0.00 0.00 37.99 2.82
615 631 1.493950 GAGTCATCGGCTCGCATTGG 61.494 60.000 0.00 0.00 0.00 3.16
616 632 1.815421 GTCATCGGCTCGCATTGGT 60.815 57.895 0.00 0.00 0.00 3.67
617 633 1.815003 TCATCGGCTCGCATTGGTG 60.815 57.895 0.00 0.00 0.00 4.17
618 634 2.514592 ATCGGCTCGCATTGGTGG 60.515 61.111 0.00 0.00 0.00 4.61
619 635 4.776322 TCGGCTCGCATTGGTGGG 62.776 66.667 0.00 0.00 39.47 4.61
692 748 1.678101 GGCTTTGGGCTGTGCTTATAG 59.322 52.381 0.00 0.00 41.46 1.31
700 756 3.118223 GGGCTGTGCTTATAGAAAGTCCT 60.118 47.826 0.00 0.00 0.00 3.85
709 765 2.822707 TAGAAAGTCCTAGCCCGAGT 57.177 50.000 0.00 0.00 0.00 4.18
714 770 2.043248 TCCTAGCCCGAGTCCACC 60.043 66.667 0.00 0.00 0.00 4.61
726 782 4.639726 TCCACCCGGGAGATATGG 57.360 61.111 32.02 24.40 42.15 2.74
730 786 2.603473 CCCGGGAGATATGGCCGA 60.603 66.667 18.48 0.00 0.00 5.54
800 856 0.104304 CCAGATTTAGGACCCGGACG 59.896 60.000 0.73 0.00 0.00 4.79
838 895 1.029681 GAGGACCAAACCGCAAAACT 58.970 50.000 0.00 0.00 34.73 2.66
839 896 1.001706 GAGGACCAAACCGCAAAACTC 60.002 52.381 0.00 0.00 34.73 3.01
840 897 0.031585 GGACCAAACCGCAAAACTCC 59.968 55.000 0.00 0.00 0.00 3.85
841 898 0.031585 GACCAAACCGCAAAACTCCC 59.968 55.000 0.00 0.00 0.00 4.30
848 905 2.907179 CGCAAAACTCCCCTCCCCT 61.907 63.158 0.00 0.00 0.00 4.79
849 906 1.000771 GCAAAACTCCCCTCCCCTC 60.001 63.158 0.00 0.00 0.00 4.30
866 927 4.338710 CCCCGTCGGCCAAGGAAA 62.339 66.667 5.50 0.00 0.00 3.13
896 968 1.065701 CATCGGAAGTCTACTCCCACG 59.934 57.143 0.00 0.00 0.00 4.94
1035 1129 2.654079 CGTCCTGCTGCTCCTCCTT 61.654 63.158 0.00 0.00 0.00 3.36
1405 1514 2.822399 CCGCCTCCATGTACCTCC 59.178 66.667 0.00 0.00 0.00 4.30
1472 1581 1.360194 CTCTACAGCGAGGACGACGT 61.360 60.000 0.00 0.00 42.66 4.34
1473 1582 1.226046 CTACAGCGAGGACGACGTG 60.226 63.158 4.58 0.00 42.66 4.49
1474 1583 1.909141 CTACAGCGAGGACGACGTGT 61.909 60.000 4.58 0.00 42.66 4.49
1575 1696 2.223665 CGCCGGTAAGAACTAACTAGGG 60.224 54.545 1.90 0.00 0.00 3.53
1576 1697 2.482664 GCCGGTAAGAACTAACTAGGGC 60.483 54.545 1.90 0.00 0.00 5.19
1577 1698 3.029570 CCGGTAAGAACTAACTAGGGCT 58.970 50.000 0.00 0.00 0.00 5.19
1613 1737 2.550101 GCAGGCAGATGATTCGGGC 61.550 63.158 0.00 0.00 41.85 6.13
1653 1777 9.747293 GGAATTGTGGAGTACTCTTATTACTAC 57.253 37.037 21.88 4.13 31.74 2.73
1695 1821 0.961857 TGCGCCTGTCTACCGTTCTA 60.962 55.000 4.18 0.00 0.00 2.10
1706 1838 5.648960 TGTCTACCGTTCTATATGTGTGTGA 59.351 40.000 0.00 0.00 0.00 3.58
1717 1851 0.692476 TGTGTGTGATTGGGGAGGAG 59.308 55.000 0.00 0.00 0.00 3.69
1799 1933 6.127925 CCCAAACATGATTATGTATCCATCCG 60.128 42.308 3.20 0.00 46.54 4.18
1838 1972 4.465886 TGGTTTCTGCTGCCTAGTAAAAA 58.534 39.130 0.00 0.00 0.00 1.94
1873 2007 2.031120 CAACCTGTGGTGAATTGTGGT 58.969 47.619 0.00 0.00 35.34 4.16
1891 2029 2.098934 TGGTAAGCTGTTTGTGCAGTTG 59.901 45.455 0.00 0.00 38.65 3.16
1892 2030 2.119457 GTAAGCTGTTTGTGCAGTTGC 58.881 47.619 0.00 0.00 38.65 4.17
1904 2042 1.807981 CAGTTGCCGTCGCCGAATA 60.808 57.895 0.00 0.00 35.63 1.75
1956 2094 2.551355 ATCAGTCGAGTGATGTGTCG 57.449 50.000 30.26 0.00 35.76 4.35
1959 2097 2.159517 TCAGTCGAGTGATGTGTCGATG 60.160 50.000 18.99 0.00 46.22 3.84
2002 2140 4.673061 GCGTAGATAATCCTGGAGTGATCG 60.673 50.000 6.96 5.92 0.00 3.69
2067 2205 7.410174 TGTATCATTTCCCACTAAAACCTGAT 58.590 34.615 0.00 0.00 0.00 2.90
2075 2213 3.370953 CCACTAAAACCTGATCCCTGAGG 60.371 52.174 0.00 0.00 35.26 3.86
2077 2215 0.332972 AAAACCTGATCCCTGAGGGC 59.667 55.000 14.20 0.00 43.94 5.19
2152 2290 2.194271 GCAGTGCACCGACTATCTAAC 58.806 52.381 14.63 0.00 0.00 2.34
2197 2335 5.890419 ACTGATTTCTGATCCCCTTGAATTC 59.110 40.000 0.00 0.00 0.00 2.17
2242 2380 5.001232 CGGAACCTACTCCTGAAATGAAAA 58.999 41.667 0.00 0.00 32.82 2.29
2309 2455 4.661709 ACCCCTGACCCATATTAATAACGT 59.338 41.667 0.00 0.00 0.00 3.99
2323 2469 2.676632 TAACGTTATGGCACCGACAT 57.323 45.000 3.29 0.00 34.61 3.06
2342 2488 5.872617 CGACATTCTAACACATTGGTTCCTA 59.127 40.000 0.00 0.00 32.29 2.94
2443 2589 8.414003 TGTCTAATGTTCTCTATGTGTATGGTC 58.586 37.037 0.00 0.00 0.00 4.02
2444 2590 8.634444 GTCTAATGTTCTCTATGTGTATGGTCT 58.366 37.037 0.00 0.00 0.00 3.85
2448 2594 4.536295 TCTCTATGTGTATGGTCTGGGA 57.464 45.455 0.00 0.00 0.00 4.37
2507 2653 7.092079 TGCATATGGTCATTTTCAAACTGAAG 58.908 34.615 4.56 0.00 37.70 3.02
2536 2682 2.374504 AGTATCCATCCTGAAGCATGGG 59.625 50.000 0.37 0.00 40.21 4.00
2542 2688 0.842030 TCCTGAAGCATGGGACCTGT 60.842 55.000 0.00 0.00 0.00 4.00
2555 2701 2.616510 GGGACCTGTTGGATTCTGTCTG 60.617 54.545 0.00 0.00 37.04 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.334171 ACATTGCTTTGAATAAATAAAGTGGGC 59.666 33.333 0.00 0.00 36.52 5.36
1 2 8.776376 ACATTGCTTTGAATAAATAAAGTGGG 57.224 30.769 0.00 0.00 36.52 4.61
32 33 4.344104 CTCCATGACCCAAACCTTGTATT 58.656 43.478 0.00 0.00 0.00 1.89
33 34 3.309121 CCTCCATGACCCAAACCTTGTAT 60.309 47.826 0.00 0.00 0.00 2.29
48 49 0.251297 TTGGTTGTGAGCCCTCCATG 60.251 55.000 0.00 0.00 0.00 3.66
53 54 2.969821 TATGTTTGGTTGTGAGCCCT 57.030 45.000 0.00 0.00 0.00 5.19
55 56 4.485163 GTCATTATGTTTGGTTGTGAGCC 58.515 43.478 0.00 0.00 0.00 4.70
60 74 7.346471 AGCTATAGGTCATTATGTTTGGTTGT 58.654 34.615 0.00 0.00 0.00 3.32
100 114 1.640069 CACGATCTCGCCAAGCATG 59.360 57.895 0.00 0.00 44.43 4.06
103 117 2.892425 CCCACGATCTCGCCAAGC 60.892 66.667 0.00 0.00 44.43 4.01
107 121 2.586357 GAAGCCCACGATCTCGCC 60.586 66.667 0.00 0.00 44.43 5.54
115 129 6.852664 AGAAACTATAAATTTGAAGCCCACG 58.147 36.000 0.00 0.00 0.00 4.94
131 145 9.744468 AATTTTGTTTTCAAGCGTAGAAACTAT 57.256 25.926 9.97 2.03 41.09 2.12
180 195 8.455903 ACCATTGTAGATGAAATAATGGAGTG 57.544 34.615 18.14 0.00 46.71 3.51
181 196 8.906867 CAACCATTGTAGATGAAATAATGGAGT 58.093 33.333 18.14 5.67 46.71 3.85
196 211 3.949754 AGGATCACATGCAACCATTGTAG 59.050 43.478 0.00 0.00 0.00 2.74
200 215 2.024655 AGGAGGATCACATGCAACCATT 60.025 45.455 0.00 0.00 36.25 3.16
205 220 1.951895 GCACAGGAGGATCACATGCAA 60.952 52.381 0.00 0.00 36.25 4.08
226 241 4.142600 GGGTAGTGAATGACATTCTTGTGC 60.143 45.833 24.80 14.13 39.96 4.57
270 285 3.870419 GCTCTTGATCTCCAGAACATGAC 59.130 47.826 0.00 0.00 31.31 3.06
271 286 3.516700 TGCTCTTGATCTCCAGAACATGA 59.483 43.478 0.00 3.43 32.77 3.07
274 289 4.511527 GAATGCTCTTGATCTCCAGAACA 58.488 43.478 0.00 0.00 0.00 3.18
291 306 1.517694 CAATGGCACTGGCGAATGC 60.518 57.895 0.00 0.00 42.47 3.56
369 384 6.212388 ACATTCTCTACATGAGGTTCTTCAGT 59.788 38.462 0.00 0.00 42.86 3.41
380 395 7.071071 TCCATGACCATAACATTCTCTACATGA 59.929 37.037 0.00 0.00 35.09 3.07
387 402 7.205297 CCATTTTCCATGACCATAACATTCTC 58.795 38.462 0.00 0.00 0.00 2.87
402 417 2.120909 CGGAGCGGCCATTTTCCAT 61.121 57.895 2.24 0.00 35.94 3.41
403 418 2.550699 ATCGGAGCGGCCATTTTCCA 62.551 55.000 2.24 0.00 35.94 3.53
406 421 1.823899 GGATCGGAGCGGCCATTTT 60.824 57.895 2.24 0.00 35.94 1.82
413 428 2.341543 CATGGAGGATCGGAGCGG 59.658 66.667 0.00 0.00 34.37 5.52
414 429 2.356793 GCATGGAGGATCGGAGCG 60.357 66.667 0.00 0.00 34.37 5.03
455 470 2.350899 TGTTTGCCAAGATCAATGCG 57.649 45.000 0.00 0.00 0.00 4.73
496 511 0.179134 GCCTTGTACGACTGCTCGAT 60.179 55.000 1.98 0.00 43.06 3.59
510 525 0.598680 CGAGCTCCGAATAGGCCTTG 60.599 60.000 12.58 0.00 41.76 3.61
517 533 2.417516 GGCAGCGAGCTCCGAATA 59.582 61.111 8.47 0.00 44.79 1.75
519 535 4.742201 GTGGCAGCGAGCTCCGAA 62.742 66.667 8.47 0.00 44.79 4.30
534 550 2.880268 TGTTGCTGAGGACAGAAATGTG 59.120 45.455 0.00 0.00 42.77 3.21
535 551 3.213206 TGTTGCTGAGGACAGAAATGT 57.787 42.857 0.00 0.00 42.77 2.71
545 561 5.947228 TTGAGTTAAAGATGTTGCTGAGG 57.053 39.130 0.00 0.00 0.00 3.86
557 573 5.966742 CCCCCTCTTTCTTTGAGTTAAAG 57.033 43.478 1.00 1.00 45.77 1.85
583 599 3.844090 GACTCTCTCGGGCAGGCC 61.844 72.222 1.81 1.81 0.00 5.19
584 600 2.362329 GATGACTCTCTCGGGCAGGC 62.362 65.000 0.00 0.00 0.00 4.85
585 601 1.739049 GATGACTCTCTCGGGCAGG 59.261 63.158 0.00 0.00 0.00 4.85
586 602 1.358402 CGATGACTCTCTCGGGCAG 59.642 63.158 0.00 0.00 0.00 4.85
587 603 3.514417 CGATGACTCTCTCGGGCA 58.486 61.111 0.00 0.00 0.00 5.36
591 607 1.278337 CGAGCCGATGACTCTCTCG 59.722 63.158 0.00 0.00 36.53 4.04
592 608 1.008995 GCGAGCCGATGACTCTCTC 60.009 63.158 0.00 0.00 31.71 3.20
593 609 1.106351 ATGCGAGCCGATGACTCTCT 61.106 55.000 0.00 0.00 31.71 3.10
594 610 0.249238 AATGCGAGCCGATGACTCTC 60.249 55.000 0.00 0.00 31.71 3.20
595 611 0.529337 CAATGCGAGCCGATGACTCT 60.529 55.000 0.00 0.00 31.71 3.24
596 612 1.493950 CCAATGCGAGCCGATGACTC 61.494 60.000 0.00 0.00 0.00 3.36
597 613 1.522355 CCAATGCGAGCCGATGACT 60.522 57.895 0.00 0.00 0.00 3.41
598 614 1.815421 ACCAATGCGAGCCGATGAC 60.815 57.895 0.00 0.00 0.00 3.06
599 615 1.815003 CACCAATGCGAGCCGATGA 60.815 57.895 0.00 0.00 0.00 2.92
600 616 2.711311 CACCAATGCGAGCCGATG 59.289 61.111 0.00 0.00 0.00 3.84
601 617 2.514592 CCACCAATGCGAGCCGAT 60.515 61.111 0.00 0.00 0.00 4.18
602 618 4.776322 CCCACCAATGCGAGCCGA 62.776 66.667 0.00 0.00 0.00 5.54
649 704 2.708325 GCCCAGATTGAGACCTCCTATT 59.292 50.000 0.00 0.00 0.00 1.73
650 705 2.334023 GCCCAGATTGAGACCTCCTAT 58.666 52.381 0.00 0.00 0.00 2.57
651 706 1.692762 GGCCCAGATTGAGACCTCCTA 60.693 57.143 0.00 0.00 0.00 2.94
652 707 0.985490 GGCCCAGATTGAGACCTCCT 60.985 60.000 0.00 0.00 0.00 3.69
653 708 1.529309 GGCCCAGATTGAGACCTCC 59.471 63.158 0.00 0.00 0.00 4.30
654 709 1.144936 CGGCCCAGATTGAGACCTC 59.855 63.158 0.00 0.00 0.00 3.85
692 748 0.460722 GGACTCGGGCTAGGACTTTC 59.539 60.000 0.00 0.00 0.00 2.62
709 765 1.841556 GCCATATCTCCCGGGTGGA 60.842 63.158 27.06 22.45 42.41 4.02
714 770 2.657237 GTCGGCCATATCTCCCGG 59.343 66.667 2.24 0.00 42.18 5.73
730 786 1.539124 GAAGAGGGTCAGGGTGGGT 60.539 63.158 0.00 0.00 0.00 4.51
735 791 2.038975 TCCGGAAGAGGGTCAGGG 59.961 66.667 0.00 0.00 34.01 4.45
807 863 0.902531 TGGTCCTCGGAGATGTTTCC 59.097 55.000 6.58 0.67 33.89 3.13
814 870 2.939261 GCGGTTTGGTCCTCGGAGA 61.939 63.158 6.58 0.00 0.00 3.71
849 906 3.853698 TTTTCCTTGGCCGACGGGG 62.854 63.158 17.22 8.36 39.58 5.73
896 968 1.370051 GTTTGTTTGACTCGGCGCC 60.370 57.895 19.07 19.07 0.00 6.53
962 1043 4.875713 CGGATTTGGGGAGGGCGG 62.876 72.222 0.00 0.00 0.00 6.13
1019 1113 2.964310 GCAAGGAGGAGCAGCAGGA 61.964 63.158 0.00 0.00 0.00 3.86
1405 1514 3.827898 GGCGACGAGGGACCAGAG 61.828 72.222 0.00 0.00 0.00 3.35
1476 1585 4.808238 GAGGCGTCGTCGTCGTCC 62.808 72.222 12.62 13.38 46.96 4.79
1477 1586 4.808238 GGAGGCGTCGTCGTCGTC 62.808 72.222 8.41 8.41 46.96 4.20
1482 1591 4.813526 CTGTCGGAGGCGTCGTCG 62.814 72.222 0.00 0.00 40.37 5.12
1490 1599 2.527951 CTTCTTGGGGCTGTCGGAGG 62.528 65.000 0.00 0.00 0.00 4.30
1592 1716 2.249535 CGAATCATCTGCCTGCCGG 61.250 63.158 0.00 0.00 0.00 6.13
1604 1728 2.169561 TGTAGTTATGCAGCCCGAATCA 59.830 45.455 0.00 0.00 0.00 2.57
1613 1737 5.589855 TCCACAATTCCATGTAGTTATGCAG 59.410 40.000 0.00 0.00 30.84 4.41
1653 1777 4.237724 ACACGATATCATAGGTGCGAATG 58.762 43.478 3.12 0.00 33.81 2.67
1695 1821 3.122480 TCCTCCCCAATCACACACATAT 58.878 45.455 0.00 0.00 0.00 1.78
1706 1838 4.044571 TCTTCACAATTTCTCCTCCCCAAT 59.955 41.667 0.00 0.00 0.00 3.16
1717 1851 9.727627 GATAGGAATCACATTCTTCACAATTTC 57.272 33.333 0.00 0.00 39.24 2.17
1873 2007 1.066908 GGCAACTGCACAAACAGCTTA 59.933 47.619 3.76 0.00 44.36 3.09
1904 2042 2.827921 GTGAGGGGTGAAAATTCTGCAT 59.172 45.455 0.00 0.00 0.00 3.96
1933 2071 3.007635 ACACATCACTCGACTGATACGA 58.992 45.455 7.17 0.00 38.11 3.43
1934 2072 3.355270 GACACATCACTCGACTGATACG 58.645 50.000 7.17 4.84 29.28 3.06
1935 2073 3.063588 TCGACACATCACTCGACTGATAC 59.936 47.826 7.17 1.04 34.04 2.24
1936 2074 3.267483 TCGACACATCACTCGACTGATA 58.733 45.455 7.17 0.00 34.04 2.15
1937 2075 2.084546 TCGACACATCACTCGACTGAT 58.915 47.619 2.10 2.10 34.04 2.90
1980 2118 4.142578 CCGATCACTCCAGGATTATCTACG 60.143 50.000 0.00 0.00 0.00 3.51
2002 2140 2.030946 GTCGCTATGCAGACAAATGACC 59.969 50.000 0.00 0.00 34.30 4.02
2075 2213 4.144703 GGAGGTTCCGGAGTCGCC 62.145 72.222 3.34 8.70 34.56 5.54
2077 2215 1.215647 CAAGGAGGTTCCGGAGTCG 59.784 63.158 3.34 0.00 42.75 4.18
2152 2290 8.867112 TCAGTTTATTACTAGAAACCATAGCG 57.133 34.615 0.00 0.00 36.39 4.26
2197 2335 4.440250 CGTGATTAAGTAGTGGAGTGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2242 2380 7.201884 CCATCCAAGAGCTCACATTTCATAAAT 60.202 37.037 17.77 0.00 0.00 1.40
2309 2455 3.936453 GTGTTAGAATGTCGGTGCCATAA 59.064 43.478 0.00 0.00 0.00 1.90
2342 2488 7.570607 AGGGGATCAGAAATCAGTCTATTACTT 59.429 37.037 0.00 0.00 35.76 2.24
2443 2589 6.319658 AGCACATATACAATTTCTTGTCCCAG 59.680 38.462 0.00 0.00 44.43 4.45
2444 2590 6.186957 AGCACATATACAATTTCTTGTCCCA 58.813 36.000 0.00 0.00 44.43 4.37
2507 2653 4.277515 TCAGGATGGATACTAAGCATGC 57.722 45.455 10.51 10.51 36.16 4.06
2536 2682 2.079925 GCAGACAGAATCCAACAGGTC 58.920 52.381 0.00 0.00 0.00 3.85
2542 2688 2.373169 AGAACCAGCAGACAGAATCCAA 59.627 45.455 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.