Multiple sequence alignment - TraesCS4B01G271100

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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 TraesCS4B01G271100 chr4B 100.000 2980 0 0 1 2980 547183500 547186479 0.000000e+00 5504.0
1 TraesCS4B01G271100 chr4D 91.691 2407 120 37 629 2980 441117609 441119990 0.000000e+00 3264.0
2 TraesCS4B01G271100 chr4D 93.506 154 7 2 405 558 441114776 441114926 2.990000e-55 226.0
3 TraesCS4B01G271100 chr4D 72.592 737 164 33 1259 1971 441132113 441132835 1.080000e-49 207.0
4 TraesCS4B01G271100 chr4D 92.308 65 2 1 2 63 441114699 441114763 4.090000e-14 89.8
5 TraesCS4B01G271100 chr5A 97.093 344 10 0 63 406 640903959 640904302 5.540000e-162 580.0
6 TraesCS4B01G271100 chr5A 94.186 344 20 0 63 406 568153806 568154149 2.630000e-145 525.0
7 TraesCS4B01G271100 chr5A 95.652 46 2 0 1106 1151 623504412 623504367 1.150000e-09 75.0
8 TraesCS4B01G271100 chr5A 97.674 43 1 0 1106 1148 653717282 653717240 1.150000e-09 75.0
9 TraesCS4B01G271100 chr3D 95.942 345 13 1 66 409 281325124 281325468 2.590000e-155 558.0
10 TraesCS4B01G271100 chr3D 95.640 344 15 0 63 406 281309488 281309831 1.210000e-153 553.0
11 TraesCS4B01G271100 chr3D 94.828 348 17 1 63 409 281309143 281309490 2.610000e-150 542.0
12 TraesCS4B01G271100 chr3D 78.947 323 55 12 1257 1577 451885579 451885890 1.080000e-49 207.0
13 TraesCS4B01G271100 chr1D 95.072 345 16 1 63 406 203251364 203251708 2.610000e-150 542.0
14 TraesCS4B01G271100 chr1D 94.477 344 18 1 63 406 492362187 492361845 2.030000e-146 529.0
15 TraesCS4B01G271100 chr1D 92.063 63 5 0 1086 1148 191733746 191733808 4.090000e-14 89.8
16 TraesCS4B01G271100 chr2A 94.767 344 18 0 63 406 100541553 100541896 1.220000e-148 536.0
17 TraesCS4B01G271100 chr2A 100.000 28 0 0 2529 2556 503475411 503475384 5.000000e-03 52.8
18 TraesCS4B01G271100 chr6A 94.186 344 20 0 63 406 121079379 121079036 2.630000e-145 525.0
19 TraesCS4B01G271100 chr4A 92.513 187 13 1 406 591 26461538 26461352 1.760000e-67 267.0
20 TraesCS4B01G271100 chr4A 78.358 268 53 5 1265 1531 26413805 26413542 5.110000e-38 169.0
21 TraesCS4B01G271100 chr7D 79.091 330 64 4 1258 1583 501116276 501116604 3.870000e-54 222.0
22 TraesCS4B01G271100 chr3A 79.385 325 54 9 1255 1577 594492469 594492782 1.800000e-52 217.0
23 TraesCS4B01G271100 chr3B 79.365 315 53 8 1255 1567 593541303 593541607 8.370000e-51 211.0
24 TraesCS4B01G271100 chr1A 78.679 333 54 13 1255 1583 495192933 495192614 3.890000e-49 206.0
25 TraesCS4B01G271100 chr1A 76.984 126 23 6 2714 2837 533045292 533045413 1.920000e-07 67.6
26 TraesCS4B01G271100 chr1B 77.846 325 63 9 1257 1578 264763400 264763718 3.030000e-45 193.0
27 TraesCS4B01G271100 chr5D 95.745 47 2 0 1106 1152 526572236 526572190 3.190000e-10 76.8
28 TraesCS4B01G271100 chr5D 92.453 53 2 2 1106 1157 499246703 499246652 1.150000e-09 75.0
29 TraesCS4B01G271100 chr5B 95.745 47 2 0 1106 1152 662037033 662036987 3.190000e-10 76.8
30 TraesCS4B01G271100 chr5B 95.652 46 2 0 1106 1151 619927317 619927272 1.150000e-09 75.0


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 TraesCS4B01G271100 chr4B 547183500 547186479 2979 False 5504.000000 5504 100.000000 1 2980 1 chr4B.!!$F1 2979
1 TraesCS4B01G271100 chr4D 441114699 441119990 5291 False 1193.266667 3264 92.501667 2 2980 3 chr4D.!!$F2 2978
2 TraesCS4B01G271100 chr4D 441132113 441132835 722 False 207.000000 207 72.592000 1259 1971 1 chr4D.!!$F1 712
3 TraesCS4B01G271100 chr3D 281309143 281309831 688 False 547.500000 553 95.234000 63 409 2 chr3D.!!$F3 346

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
963 3942 0.031043 TCACGTTTCACCGATCACGT 59.969 50.0 1.22 1.22 46.45 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2852 5942 0.177141 GTGCCCTTGTGCTATACGGA 59.823 55.0 0.0 0.0 0.0 4.69 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
86 90 1.003851 CACGTTGTCGCGGGAATATT 58.996 50.000 6.13 0.00 37.48 1.28
272 621 5.725325 TTCATGCAGGTTTCATGATGAAA 57.275 34.783 16.04 16.04 46.54 2.69
275 624 5.419471 TCATGCAGGTTTCATGATGAAATGA 59.581 36.000 21.91 16.87 46.55 2.57
316 665 2.170607 ACATATGGTAGTGAGTGTGGGC 59.829 50.000 7.80 0.00 0.00 5.36
347 696 2.229302 TGCATGTTGTGTGATGATGTGG 59.771 45.455 0.00 0.00 0.00 4.17
383 732 4.595986 TGAGAAAAATAGTTAGTGGGGGC 58.404 43.478 0.00 0.00 0.00 5.80
384 733 4.043561 TGAGAAAAATAGTTAGTGGGGGCA 59.956 41.667 0.00 0.00 0.00 5.36
416 765 9.843704 TTTAGATATAGAAGATCCCAGGATTCA 57.156 33.333 0.00 0.00 34.60 2.57
424 773 3.909364 AGATCCCAGGATTCATCTTCTCC 59.091 47.826 0.00 0.00 34.60 3.71
434 783 7.656948 CAGGATTCATCTTCTCCTTCTTATCAC 59.343 40.741 0.00 0.00 37.30 3.06
435 784 6.934083 GGATTCATCTTCTCCTTCTTATCACC 59.066 42.308 0.00 0.00 0.00 4.02
436 785 6.874278 TTCATCTTCTCCTTCTTATCACCA 57.126 37.500 0.00 0.00 0.00 4.17
466 815 1.026182 TCCTTGTGTGGCATCGCATC 61.026 55.000 0.00 0.00 35.69 3.91
473 822 1.089920 GTGGCATCGCATCTCAACTT 58.910 50.000 0.00 0.00 0.00 2.66
474 823 1.470098 GTGGCATCGCATCTCAACTTT 59.530 47.619 0.00 0.00 0.00 2.66
523 872 0.892755 ATGACAAGTTCGCCGTCCTA 59.107 50.000 0.00 0.00 0.00 2.94
569 3444 5.240183 CAGCTAATCATCCCATTGTCGAATT 59.760 40.000 0.00 0.00 0.00 2.17
595 3470 1.745087 GAGCAAGATTCATGGCGGAAA 59.255 47.619 0.00 0.00 0.00 3.13
596 3471 1.474077 AGCAAGATTCATGGCGGAAAC 59.526 47.619 0.00 0.00 0.00 2.78
597 3472 1.202114 GCAAGATTCATGGCGGAAACA 59.798 47.619 0.00 0.00 0.00 2.83
598 3473 2.159198 GCAAGATTCATGGCGGAAACAT 60.159 45.455 0.00 0.00 0.00 2.71
599 3474 3.441163 CAAGATTCATGGCGGAAACATG 58.559 45.455 0.00 0.00 45.39 3.21
600 3475 1.406539 AGATTCATGGCGGAAACATGC 59.593 47.619 0.00 0.00 44.07 4.06
603 3478 0.322366 TCATGGCGGAAACATGCAGA 60.322 50.000 0.00 0.00 44.07 4.26
604 3479 0.099968 CATGGCGGAAACATGCAGAG 59.900 55.000 0.00 0.00 39.23 3.35
606 3481 0.250684 TGGCGGAAACATGCAGAGAA 60.251 50.000 0.00 0.00 0.00 2.87
608 3483 1.401539 GGCGGAAACATGCAGAGAAAC 60.402 52.381 0.00 0.00 0.00 2.78
609 3484 1.266718 GCGGAAACATGCAGAGAAACA 59.733 47.619 0.00 0.00 0.00 2.83
610 3485 2.095059 GCGGAAACATGCAGAGAAACAT 60.095 45.455 0.00 0.00 0.00 2.71
612 3487 3.671433 CGGAAACATGCAGAGAAACATGG 60.671 47.826 7.78 0.00 46.35 3.66
613 3488 3.507233 GGAAACATGCAGAGAAACATGGA 59.493 43.478 7.78 0.00 46.35 3.41
616 3491 2.089201 CATGCAGAGAAACATGGAGCA 58.911 47.619 0.00 0.00 39.98 4.26
617 3492 2.275134 TGCAGAGAAACATGGAGCAA 57.725 45.000 0.00 0.00 0.00 3.91
618 3493 2.799017 TGCAGAGAAACATGGAGCAAT 58.201 42.857 0.00 0.00 0.00 3.56
619 3494 3.159472 TGCAGAGAAACATGGAGCAATT 58.841 40.909 0.00 0.00 0.00 2.32
620 3495 3.192001 TGCAGAGAAACATGGAGCAATTC 59.808 43.478 0.00 0.00 0.00 2.17
621 3496 3.730061 GCAGAGAAACATGGAGCAATTCG 60.730 47.826 0.00 0.00 0.00 3.34
622 3497 3.686241 CAGAGAAACATGGAGCAATTCGA 59.314 43.478 0.00 0.00 0.00 3.71
623 3498 3.686726 AGAGAAACATGGAGCAATTCGAC 59.313 43.478 0.00 0.00 0.00 4.20
624 3499 2.749621 AGAAACATGGAGCAATTCGACC 59.250 45.455 0.00 0.00 0.00 4.79
625 3500 1.086696 AACATGGAGCAATTCGACCG 58.913 50.000 0.00 0.00 0.00 4.79
627 3502 0.652592 CATGGAGCAATTCGACCGAC 59.347 55.000 0.00 0.00 0.00 4.79
639 3600 0.170561 CGACCGACGATCAGGAGTTT 59.829 55.000 0.00 0.00 45.77 2.66
688 3649 5.011329 TGGAAGCTAAACTACGAGGAAAGAA 59.989 40.000 0.00 0.00 0.00 2.52
689 3650 5.930569 GGAAGCTAAACTACGAGGAAAGAAA 59.069 40.000 0.00 0.00 0.00 2.52
690 3651 6.128607 GGAAGCTAAACTACGAGGAAAGAAAC 60.129 42.308 0.00 0.00 0.00 2.78
699 3667 2.417933 CGAGGAAAGAAACATGGAGCAG 59.582 50.000 0.00 0.00 0.00 4.24
700 3668 2.163211 GAGGAAAGAAACATGGAGCAGC 59.837 50.000 0.00 0.00 0.00 5.25
723 3691 1.951130 CCGACGATCCAATCTGCGG 60.951 63.158 0.00 0.00 0.00 5.69
761 3729 0.107945 GCTGAGCGATCCAGTTTCCT 60.108 55.000 0.00 0.00 34.29 3.36
775 3743 2.139917 GTTTCCTGTGCACGTGTCATA 58.860 47.619 18.38 12.54 0.00 2.15
785 3753 2.433491 GTGTCATACGCGCCACCA 60.433 61.111 5.73 0.00 0.00 4.17
790 3758 1.011242 CATACGCGCCACCAATTCG 60.011 57.895 5.73 0.00 0.00 3.34
802 3770 4.722700 AATTCGCTGCACCGGCCT 62.723 61.111 0.00 0.00 40.13 5.19
811 3779 4.028490 CACCGGCCTGCAGGGTTA 62.028 66.667 33.46 0.00 35.57 2.85
852 3820 2.777109 CGATCGATCGCTCACTCAC 58.223 57.895 32.34 0.00 43.84 3.51
853 3821 0.306228 CGATCGATCGCTCACTCACT 59.694 55.000 32.34 0.00 43.84 3.41
854 3822 1.658931 CGATCGATCGCTCACTCACTC 60.659 57.143 32.34 0.00 43.84 3.51
879 3847 5.276536 CCGCTACTTATTTAAACTACCGTGC 60.277 44.000 0.00 0.00 0.00 5.34
890 3858 2.086869 ACTACCGTGCGTACAGTGTAT 58.913 47.619 6.21 0.00 0.00 2.29
898 3877 3.611113 GTGCGTACAGTGTATGTTGTAGG 59.389 47.826 20.87 0.51 39.96 3.18
900 3879 4.103357 GCGTACAGTGTATGTTGTAGGAG 58.897 47.826 20.87 0.18 39.96 3.69
902 3881 5.163723 GCGTACAGTGTATGTTGTAGGAGTA 60.164 44.000 20.87 0.00 39.96 2.59
903 3882 6.484540 CGTACAGTGTATGTTGTAGGAGTAG 58.515 44.000 13.47 0.00 39.96 2.57
906 3885 7.627298 ACAGTGTATGTTGTAGGAGTAGTAG 57.373 40.000 0.00 0.00 39.96 2.57
924 3903 4.282496 AGTAGTAGAGTGGATCACTTGGG 58.718 47.826 1.90 0.00 45.44 4.12
925 3904 3.474798 AGTAGAGTGGATCACTTGGGA 57.525 47.619 1.90 0.00 45.44 4.37
926 3905 3.370104 AGTAGAGTGGATCACTTGGGAG 58.630 50.000 1.90 0.00 45.44 4.30
927 3906 0.908198 AGAGTGGATCACTTGGGAGC 59.092 55.000 1.90 0.00 45.44 4.70
928 3907 0.908198 GAGTGGATCACTTGGGAGCT 59.092 55.000 1.90 0.00 45.44 4.09
929 3908 0.617413 AGTGGATCACTTGGGAGCTG 59.383 55.000 0.00 0.00 42.59 4.24
930 3909 0.326264 GTGGATCACTTGGGAGCTGT 59.674 55.000 0.00 0.00 0.00 4.40
931 3910 0.615331 TGGATCACTTGGGAGCTGTC 59.385 55.000 0.00 0.00 0.00 3.51
940 3919 1.965414 TGGGAGCTGTCTGGGATTAA 58.035 50.000 0.00 0.00 0.00 1.40
962 3941 1.133407 TTCACGTTTCACCGATCACG 58.867 50.000 0.00 0.00 38.62 4.35
963 3942 0.031043 TCACGTTTCACCGATCACGT 59.969 50.000 1.22 1.22 46.45 4.49
964 3943 1.266446 TCACGTTTCACCGATCACGTA 59.734 47.619 6.36 0.00 43.79 3.57
965 3944 1.384409 CACGTTTCACCGATCACGTAC 59.616 52.381 6.36 0.00 43.79 3.67
984 3967 1.610673 ACCGGCCATCACTCTCACT 60.611 57.895 0.00 0.00 0.00 3.41
1000 3983 5.010112 ACTCTCACTGACGATCTTGAGAAAA 59.990 40.000 10.98 0.00 42.96 2.29
1001 3984 6.030548 TCTCACTGACGATCTTGAGAAAAT 57.969 37.500 8.44 0.00 41.16 1.82
1007 3990 5.171476 TGACGATCTTGAGAAAATGGAGAC 58.829 41.667 0.00 0.00 0.00 3.36
1010 3993 2.337583 TCTTGAGAAAATGGAGACGCG 58.662 47.619 3.53 3.53 0.00 6.01
1045 4031 0.373716 CTTTATGCTGTTCGCCGTCC 59.626 55.000 0.00 0.00 38.05 4.79
1153 4139 1.366111 CGGCACCATGGGTAAGTTCG 61.366 60.000 18.09 6.13 32.11 3.95
1154 4140 1.654023 GGCACCATGGGTAAGTTCGC 61.654 60.000 18.09 5.04 32.11 4.70
1155 4141 1.654023 GCACCATGGGTAAGTTCGCC 61.654 60.000 18.09 0.00 32.11 5.54
1156 4142 1.078708 ACCATGGGTAAGTTCGCCG 60.079 57.895 18.09 0.00 32.11 6.46
1189 4175 3.929610 CACTGCTAGCCTCTGTTTACTTC 59.070 47.826 13.29 0.00 0.00 3.01
1201 4193 3.926616 TGTTTACTTCAGAGCTACCAGC 58.073 45.455 0.00 0.00 42.84 4.85
1226 4218 1.160137 CAGTGGAGTGGTTAAGCAGC 58.840 55.000 7.79 3.30 0.00 5.25
1228 4220 1.160137 GTGGAGTGGTTAAGCAGCAG 58.840 55.000 7.79 0.00 31.97 4.24
1229 4221 1.055849 TGGAGTGGTTAAGCAGCAGA 58.944 50.000 7.79 0.00 31.97 4.26
1232 4224 0.393077 AGTGGTTAAGCAGCAGACGT 59.607 50.000 7.79 0.00 31.97 4.34
1367 4359 4.697756 GTGCGGGCAGTGCTACCA 62.698 66.667 16.11 6.55 0.00 3.25
1586 4578 2.398252 GTGCTCTACCAAAGGTACCC 57.602 55.000 8.74 0.00 37.09 3.69
1587 4579 1.626825 GTGCTCTACCAAAGGTACCCA 59.373 52.381 8.74 0.00 37.09 4.51
1588 4580 1.626825 TGCTCTACCAAAGGTACCCAC 59.373 52.381 8.74 0.00 37.09 4.61
1589 4581 1.907255 GCTCTACCAAAGGTACCCACT 59.093 52.381 8.74 0.00 37.09 4.00
1590 4582 3.102204 GCTCTACCAAAGGTACCCACTA 58.898 50.000 8.74 0.00 37.09 2.74
1591 4583 3.118847 GCTCTACCAAAGGTACCCACTAC 60.119 52.174 8.74 0.00 37.09 2.73
1592 4584 4.091549 CTCTACCAAAGGTACCCACTACA 58.908 47.826 8.74 0.00 37.09 2.74
1601 4593 2.081462 GTACCCACTACACACCATTGC 58.919 52.381 0.00 0.00 0.00 3.56
1623 4615 0.608035 GGGCGGTTTGACTTGGATGA 60.608 55.000 0.00 0.00 0.00 2.92
1629 4621 5.298276 GGCGGTTTGACTTGGATGAATATTA 59.702 40.000 0.00 0.00 0.00 0.98
1673 4740 6.322712 TGATGTTTTATTTATGTAGGGTGGCC 59.677 38.462 0.00 0.00 0.00 5.36
1678 4745 0.978667 TTATGTAGGGTGGCCTGCGA 60.979 55.000 3.32 0.00 0.00 5.10
1754 4821 3.066190 ATCTCGAACGTGGCCGGA 61.066 61.111 5.05 0.00 38.78 5.14
1757 4824 4.668118 TCGAACGTGGCCGGAACC 62.668 66.667 5.05 0.00 38.78 3.62
1988 5055 0.107116 TCTCCTACTGACTCCTCCGC 60.107 60.000 0.00 0.00 0.00 5.54
2009 5076 0.108992 GTACATTCAGCGGTCGGACA 60.109 55.000 10.76 0.00 0.00 4.02
2030 5097 1.202313 CGAGATCGACTTCCCTGGTTC 60.202 57.143 0.00 0.00 43.02 3.62
2044 5111 3.491652 GTTCGCTTGGAGGCTCGC 61.492 66.667 8.69 5.60 0.00 5.03
2057 5126 3.006967 GGAGGCTCGCTTCATCCTATTTA 59.993 47.826 8.69 0.00 0.00 1.40
2060 5129 3.991121 GGCTCGCTTCATCCTATTTAGTC 59.009 47.826 0.00 0.00 0.00 2.59
2117 5186 1.009829 GTGGAAATGAGGCTAGCGTG 58.990 55.000 15.88 0.00 0.00 5.34
2245 5314 2.910994 CGGAGTAGGCCTACCGGG 60.911 72.222 34.54 21.46 42.76 5.73
2261 5330 2.073117 CGGGGGTTTCGGAATTTTTG 57.927 50.000 0.00 0.00 0.00 2.44
2262 5331 1.341852 CGGGGGTTTCGGAATTTTTGT 59.658 47.619 0.00 0.00 0.00 2.83
2343 5413 7.834181 AGGTAACATATTAAGGCAACAGACATT 59.166 33.333 0.00 0.00 38.30 2.71
2488 5560 5.062809 TGTTTGCGAGTTTCAAAAACATTCC 59.937 36.000 5.46 0.00 36.20 3.01
2599 5689 3.503363 AGCAATGCTCACGAATTCAAAGA 59.497 39.130 0.00 0.00 30.62 2.52
2775 5865 9.900710 AAAAGGAAAAACACAAAATAAAACCAC 57.099 25.926 0.00 0.00 0.00 4.16
2852 5942 1.342374 GGAAATCCTGAATGGGCCAGT 60.342 52.381 13.78 10.20 36.20 4.00
2855 5945 1.987807 ATCCTGAATGGGCCAGTCCG 61.988 60.000 29.17 23.07 36.20 4.79
2874 5964 1.134818 CGTATAGCACAAGGGCACTCA 60.135 52.381 0.00 0.00 35.83 3.41
2877 5967 0.035317 TAGCACAAGGGCACTCACAG 59.965 55.000 0.00 0.00 35.83 3.66
2907 5998 2.605837 TGGTGCACGTTTGTCTCTAA 57.394 45.000 11.45 0.00 0.00 2.10
2928 6019 1.451387 CCTGTGGTATGCGGGGAAC 60.451 63.158 0.00 0.00 0.00 3.62
2942 6033 3.886123 CGGGGAACTGGAACAATCTATT 58.114 45.455 0.00 0.00 38.70 1.73
2968 6059 2.284258 AGAACTGCTCGCTCCCCT 60.284 61.111 0.00 0.00 0.00 4.79
2975 6066 4.560856 CTCGCTCCCCTTCGCTCG 62.561 72.222 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 79 7.095397 TGAGATATGTTACAAAATATTCCCGCG 60.095 37.037 0.00 0.00 0.00 6.46
228 577 5.551760 AAAAAGACCTATCTCAACATGCG 57.448 39.130 0.00 0.00 32.34 4.73
289 638 2.290916 ACTCACTACCATATGTCTCGCG 59.709 50.000 0.00 0.00 0.00 5.87
302 651 2.152016 GAAAAGGCCCACACTCACTAC 58.848 52.381 0.00 0.00 0.00 2.73
316 665 2.033299 ACACAACATGCACGAGAAAAGG 59.967 45.455 0.00 0.00 0.00 3.11
366 715 3.096852 GCTTGCCCCCACTAACTATTTT 58.903 45.455 0.00 0.00 0.00 1.82
416 765 5.104318 GGGTTGGTGATAAGAAGGAGAAGAT 60.104 44.000 0.00 0.00 0.00 2.40
424 773 2.017113 GCCGGGGTTGGTGATAAGAAG 61.017 57.143 2.18 0.00 0.00 2.85
435 784 4.740822 CAAGGAGGGCCGGGGTTG 62.741 72.222 2.18 0.00 39.96 3.77
473 822 8.754991 TCCTGAGTTGTTAGTTTATTTTCCAA 57.245 30.769 0.00 0.00 0.00 3.53
474 823 7.447238 CCTCCTGAGTTGTTAGTTTATTTTCCA 59.553 37.037 0.00 0.00 0.00 3.53
506 855 0.243095 ACTAGGACGGCGAACTTGTC 59.757 55.000 16.62 0.00 0.00 3.18
523 872 6.478512 TGGAATTGTTTGCCTTTTCTTACT 57.521 33.333 0.00 0.00 0.00 2.24
569 3444 2.640184 CCATGAATCTTGCTCAGCTCA 58.360 47.619 0.00 0.00 0.00 4.26
595 3470 2.089980 GCTCCATGTTTCTCTGCATGT 58.910 47.619 0.00 0.00 40.42 3.21
596 3471 2.089201 TGCTCCATGTTTCTCTGCATG 58.911 47.619 0.00 0.00 41.37 4.06
597 3472 2.502142 TGCTCCATGTTTCTCTGCAT 57.498 45.000 0.00 0.00 0.00 3.96
598 3473 2.275134 TTGCTCCATGTTTCTCTGCA 57.725 45.000 0.00 0.00 0.00 4.41
599 3474 3.730061 CGAATTGCTCCATGTTTCTCTGC 60.730 47.826 0.00 0.00 0.00 4.26
600 3475 3.686241 TCGAATTGCTCCATGTTTCTCTG 59.314 43.478 0.00 0.00 0.00 3.35
603 3478 2.749621 GGTCGAATTGCTCCATGTTTCT 59.250 45.455 0.00 0.00 0.00 2.52
604 3479 2.476185 CGGTCGAATTGCTCCATGTTTC 60.476 50.000 0.00 0.00 0.00 2.78
606 3481 1.086696 CGGTCGAATTGCTCCATGTT 58.913 50.000 0.00 0.00 0.00 2.71
608 3483 0.652592 GTCGGTCGAATTGCTCCATG 59.347 55.000 0.00 0.00 0.00 3.66
609 3484 0.806102 CGTCGGTCGAATTGCTCCAT 60.806 55.000 0.00 0.00 42.86 3.41
610 3485 1.445410 CGTCGGTCGAATTGCTCCA 60.445 57.895 0.00 0.00 42.86 3.86
611 3486 1.153901 TCGTCGGTCGAATTGCTCC 60.154 57.895 0.00 0.00 45.98 4.70
612 3487 4.470876 TCGTCGGTCGAATTGCTC 57.529 55.556 0.00 0.00 45.98 4.26
620 3495 0.170561 AAACTCCTGATCGTCGGTCG 59.829 55.000 0.21 0.00 41.41 4.79
621 3496 2.365408 AAAACTCCTGATCGTCGGTC 57.635 50.000 0.00 0.00 0.00 4.79
622 3497 2.833631 AAAAACTCCTGATCGTCGGT 57.166 45.000 0.00 0.00 0.00 4.69
645 3606 6.571731 GCTTCCATGTACAGTACAGTGTTAGA 60.572 42.308 18.30 6.35 42.77 2.10
646 3607 5.577164 GCTTCCATGTACAGTACAGTGTTAG 59.423 44.000 18.30 12.07 42.77 2.34
649 3610 3.578716 AGCTTCCATGTACAGTACAGTGT 59.421 43.478 18.30 0.00 42.77 3.55
650 3611 4.193826 AGCTTCCATGTACAGTACAGTG 57.806 45.455 18.30 14.97 42.77 3.66
651 3612 5.995565 TTAGCTTCCATGTACAGTACAGT 57.004 39.130 18.30 4.96 42.77 3.55
652 3613 6.398918 AGTTTAGCTTCCATGTACAGTACAG 58.601 40.000 18.30 10.42 42.77 2.74
653 3614 6.354794 AGTTTAGCTTCCATGTACAGTACA 57.645 37.500 15.90 15.90 43.80 2.90
654 3615 6.471519 CGTAGTTTAGCTTCCATGTACAGTAC 59.528 42.308 0.33 3.49 0.00 2.73
655 3616 6.375174 TCGTAGTTTAGCTTCCATGTACAGTA 59.625 38.462 0.33 0.00 0.00 2.74
660 3621 4.951715 TCCTCGTAGTTTAGCTTCCATGTA 59.048 41.667 0.00 0.00 0.00 2.29
688 3649 1.078848 GGTCGAGCTGCTCCATGTT 60.079 57.895 22.97 0.00 0.00 2.71
689 3650 2.581354 GGTCGAGCTGCTCCATGT 59.419 61.111 22.97 0.00 0.00 3.21
690 3651 2.584418 CGGTCGAGCTGCTCCATG 60.584 66.667 22.97 10.12 0.00 3.66
723 3691 1.822250 CTAGAATTCCGCGCGCTTCC 61.822 60.000 30.48 11.72 0.00 3.46
730 3698 1.543941 CGCTCAGCTAGAATTCCGCG 61.544 60.000 0.00 0.00 31.18 6.46
734 3702 3.243704 ACTGGATCGCTCAGCTAGAATTC 60.244 47.826 0.00 0.00 35.78 2.17
736 3704 2.315176 ACTGGATCGCTCAGCTAGAAT 58.685 47.619 0.00 0.00 35.78 2.40
785 3753 4.722700 AGGCCGGTGCAGCGAATT 62.723 61.111 37.48 19.47 40.13 2.17
802 3770 7.397892 TCGATTTCATAATTTTAACCCTGCA 57.602 32.000 0.00 0.00 0.00 4.41
811 3779 8.208718 TCGAGTGGAATCGATTTCATAATTTT 57.791 30.769 21.75 4.65 46.20 1.82
851 3819 6.577103 GGTAGTTTAAATAAGTAGCGGGAGT 58.423 40.000 0.00 0.00 0.00 3.85
852 3820 5.689068 CGGTAGTTTAAATAAGTAGCGGGAG 59.311 44.000 13.27 0.00 32.44 4.30
853 3821 5.127031 ACGGTAGTTTAAATAAGTAGCGGGA 59.873 40.000 20.86 0.00 38.55 5.14
854 3822 5.232838 CACGGTAGTTTAAATAAGTAGCGGG 59.767 44.000 20.86 16.14 38.55 6.13
879 3847 5.306532 ACTCCTACAACATACACTGTACG 57.693 43.478 0.00 0.00 36.98 3.67
890 3858 6.214208 TCCACTCTACTACTACTCCTACAACA 59.786 42.308 0.00 0.00 0.00 3.33
898 3877 6.261381 CCAAGTGATCCACTCTACTACTACTC 59.739 46.154 0.00 0.00 44.62 2.59
900 3879 5.299782 CCCAAGTGATCCACTCTACTACTAC 59.700 48.000 0.00 0.00 44.62 2.73
902 3881 4.017407 TCCCAAGTGATCCACTCTACTACT 60.017 45.833 0.00 0.00 44.62 2.57
903 3882 4.279145 TCCCAAGTGATCCACTCTACTAC 58.721 47.826 0.00 0.00 44.62 2.73
906 3885 2.159028 GCTCCCAAGTGATCCACTCTAC 60.159 54.545 0.00 0.00 44.62 2.59
924 3903 4.393371 GTGAAAGTTAATCCCAGACAGCTC 59.607 45.833 0.00 0.00 0.00 4.09
925 3904 4.327680 GTGAAAGTTAATCCCAGACAGCT 58.672 43.478 0.00 0.00 0.00 4.24
926 3905 3.125316 CGTGAAAGTTAATCCCAGACAGC 59.875 47.826 0.00 0.00 0.00 4.40
927 3906 4.315803 ACGTGAAAGTTAATCCCAGACAG 58.684 43.478 0.00 0.00 0.00 3.51
928 3907 4.345859 ACGTGAAAGTTAATCCCAGACA 57.654 40.909 0.00 0.00 0.00 3.41
929 3908 5.237779 TGAAACGTGAAAGTTAATCCCAGAC 59.762 40.000 0.00 0.00 33.41 3.51
930 3909 5.237779 GTGAAACGTGAAAGTTAATCCCAGA 59.762 40.000 0.00 0.00 33.41 3.86
931 3910 5.449304 GTGAAACGTGAAAGTTAATCCCAG 58.551 41.667 0.00 0.00 33.41 4.45
940 3919 2.542595 GTGATCGGTGAAACGTGAAAGT 59.457 45.455 0.00 0.00 38.12 2.66
962 3941 0.179108 GAGAGTGATGGCCGGTGTAC 60.179 60.000 1.90 0.00 0.00 2.90
963 3942 0.613572 TGAGAGTGATGGCCGGTGTA 60.614 55.000 1.90 0.00 0.00 2.90
964 3943 1.913262 TGAGAGTGATGGCCGGTGT 60.913 57.895 1.90 0.00 0.00 4.16
965 3944 1.448540 GTGAGAGTGATGGCCGGTG 60.449 63.158 1.90 0.00 0.00 4.94
984 3967 5.171476 GTCTCCATTTTCTCAAGATCGTCA 58.829 41.667 0.00 0.00 0.00 4.35
1000 3983 3.842923 CCTGCTCCGCGTCTCCAT 61.843 66.667 4.92 0.00 0.00 3.41
1010 3993 2.850828 AAAGCTCCATGGCCTGCTCC 62.851 60.000 21.17 1.03 34.38 4.70
1014 3997 0.672342 GCATAAAGCTCCATGGCCTG 59.328 55.000 6.96 0.00 41.15 4.85
1166 4152 2.003301 GTAAACAGAGGCTAGCAGTGC 58.997 52.381 18.24 7.13 0.00 4.40
1198 4190 0.036952 CCACTCCACTGTACCTGCTG 60.037 60.000 0.00 0.00 0.00 4.41
1201 4193 3.864921 GCTTAACCACTCCACTGTACCTG 60.865 52.174 0.00 0.00 0.00 4.00
1205 4197 2.289444 GCTGCTTAACCACTCCACTGTA 60.289 50.000 0.00 0.00 0.00 2.74
1208 4200 0.764890 TGCTGCTTAACCACTCCACT 59.235 50.000 0.00 0.00 0.00 4.00
1212 4204 1.071605 CGTCTGCTGCTTAACCACTC 58.928 55.000 0.00 0.00 0.00 3.51
1226 4218 2.192463 CGCGTTGAAAACTACGTCTG 57.808 50.000 0.00 0.00 46.99 3.51
1232 4224 1.069568 CCATGCACGCGTTGAAAACTA 60.070 47.619 10.22 0.00 46.99 2.24
1237 4229 1.501292 CATCCATGCACGCGTTGAA 59.499 52.632 10.22 0.00 0.00 2.69
1367 4359 4.640855 CGTGGTCGCACGTCACCT 62.641 66.667 7.32 0.00 42.91 4.00
1405 4397 2.358737 CACCGACTTCCCTGGCAC 60.359 66.667 0.00 0.00 0.00 5.01
1585 4577 2.925578 CATGCAATGGTGTGTAGTGG 57.074 50.000 0.00 0.00 41.79 4.00
1601 4593 0.893270 TCCAAGTCAAACCGCCCATG 60.893 55.000 0.00 0.00 0.00 3.66
1673 4740 2.103934 CCTCCTCGCTTCTCGCAG 59.896 66.667 0.00 0.00 39.08 5.18
1678 4745 3.394836 GCACCCCTCCTCGCTTCT 61.395 66.667 0.00 0.00 0.00 2.85
1685 4752 3.637273 GTGAACCGCACCCCTCCT 61.637 66.667 0.00 0.00 41.78 3.69
1754 4821 2.355115 GCCTTGATGTCCCCGGTT 59.645 61.111 0.00 0.00 0.00 4.44
1757 4824 4.096003 ACCGCCTTGATGTCCCCG 62.096 66.667 0.00 0.00 0.00 5.73
1983 5050 3.706140 GCTGAATGTACGGCGGAG 58.294 61.111 13.24 0.00 32.46 4.63
2009 5076 0.323542 ACCAGGGAAGTCGATCTCGT 60.324 55.000 0.00 0.00 40.80 4.18
2030 5097 3.191539 GAAGCGAGCCTCCAAGCG 61.192 66.667 0.00 0.00 38.01 4.68
2044 5111 4.344102 TGGACGGGACTAAATAGGATGAAG 59.656 45.833 0.00 0.00 0.00 3.02
2057 5126 1.408266 GCACCATTATTGGACGGGACT 60.408 52.381 10.62 0.00 46.92 3.85
2060 5129 1.024271 CTGCACCATTATTGGACGGG 58.976 55.000 10.62 0.00 46.92 5.28
2117 5186 2.462255 TTCGACCACACGACTACGCC 62.462 60.000 0.00 0.00 41.97 5.68
2139 5208 8.768957 TTCTCTCAATCTTCTGTTCACATTAG 57.231 34.615 0.00 0.00 0.00 1.73
2245 5314 6.367695 CCAAGAATACAAAAATTCCGAAACCC 59.632 38.462 0.00 0.00 36.68 4.11
2259 5328 3.886505 ACGAGGCAAAACCAAGAATACAA 59.113 39.130 0.00 0.00 43.14 2.41
2260 5329 3.482436 ACGAGGCAAAACCAAGAATACA 58.518 40.909 0.00 0.00 43.14 2.29
2261 5330 4.215613 AGAACGAGGCAAAACCAAGAATAC 59.784 41.667 0.00 0.00 43.14 1.89
2262 5331 4.215399 CAGAACGAGGCAAAACCAAGAATA 59.785 41.667 0.00 0.00 43.14 1.75
2292 5361 5.959527 CACGGAAAAATATTCACTGACATCG 59.040 40.000 0.00 0.00 0.00 3.84
2319 5389 8.673711 TCAATGTCTGTTGCCTTAATATGTTAC 58.326 33.333 0.00 0.00 0.00 2.50
2325 5395 6.658816 ACATGTCAATGTCTGTTGCCTTAATA 59.341 34.615 0.00 0.00 43.85 0.98
2343 5413 7.496747 TGATATTTCCGTGAGATTACATGTCA 58.503 34.615 0.00 0.00 0.00 3.58
2570 5660 1.275010 TCGTGAGCATTGCTGGAAGTA 59.725 47.619 17.51 0.00 39.88 2.24
2662 5752 9.853555 GGAACAGTTTTTGAAATTTGGAAAAAT 57.146 25.926 15.44 9.99 32.71 1.82
2666 5756 7.390027 TCAGGAACAGTTTTTGAAATTTGGAA 58.610 30.769 0.00 0.00 0.00 3.53
2667 5757 6.940739 TCAGGAACAGTTTTTGAAATTTGGA 58.059 32.000 0.00 0.00 0.00 3.53
2770 5860 7.441836 AGAACACTTTCTTTCTTTTTGTGGTT 58.558 30.769 0.00 0.00 39.17 3.67
2801 5891 5.374071 GAGTTTTGGGAAGGTTCTAGAACA 58.626 41.667 31.30 11.77 42.85 3.18
2848 5938 1.202533 CCCTTGTGCTATACGGACTGG 60.203 57.143 0.00 0.00 34.66 4.00
2852 5942 0.177141 GTGCCCTTGTGCTATACGGA 59.823 55.000 0.00 0.00 0.00 4.69
2855 5945 2.280628 GTGAGTGCCCTTGTGCTATAC 58.719 52.381 0.00 0.00 0.00 1.47
2942 6033 1.404717 GCGAGCAGTTCTCTTGGATCA 60.405 52.381 0.00 0.00 39.70 2.92


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

AutoCloner maintained by Alex Coulton.