Multiple sequence alignment - TraesCS5B01G075200

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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 TraesCS5B01G075200 chr5B 100.000 5635 0 0 1 5635 89639525 89633891 0.000000e+00 10406.0
1 TraesCS5B01G075200 chr5B 97.440 625 11 3 1 623 205864756 205865377 0.000000e+00 1061.0
2 TraesCS5B01G075200 chr5B 87.580 628 52 17 1 621 349091394 349090786 0.000000e+00 704.0
3 TraesCS5B01G075200 chr5A 93.231 5008 220 52 693 5633 77095997 77091042 0.000000e+00 7260.0
4 TraesCS5B01G075200 chr5D 94.968 4213 126 33 1458 5634 80709299 80705137 0.000000e+00 6527.0
5 TraesCS5B01G075200 chr5D 95.953 593 22 2 873 1464 80709919 80709328 0.000000e+00 961.0
6 TraesCS5B01G075200 chr5D 88.776 98 9 1 3367 3464 34445610 34445515 9.920000e-23 119.0
7 TraesCS5B01G075200 chr5D 86.735 98 8 2 3363 3457 526884339 526884244 2.780000e-18 104.0
8 TraesCS5B01G075200 chr3B 98.077 624 8 3 1 623 227832294 227831674 0.000000e+00 1083.0
9 TraesCS5B01G075200 chr3B 97.753 623 12 2 1 623 29784628 29784008 0.000000e+00 1072.0
10 TraesCS5B01G075200 chr4B 97.913 623 9 3 1 623 67846797 67847415 0.000000e+00 1075.0
11 TraesCS5B01G075200 chr6B 97.592 623 11 3 1 623 572115250 572114632 0.000000e+00 1064.0
12 TraesCS5B01G075200 chr6B 98.182 440 5 2 1 440 22930904 22931340 0.000000e+00 765.0
13 TraesCS5B01G075200 chr6B 96.552 145 3 1 481 623 572114125 572113981 7.300000e-59 239.0
14 TraesCS5B01G075200 chr6B 83.036 112 15 2 3357 3464 340545161 340545272 1.290000e-16 99.0
15 TraesCS5B01G075200 chr6B 96.875 32 1 0 633 664 647361567 647361536 3.000000e-03 54.7
16 TraesCS5B01G075200 chr2B 95.520 625 8 3 1 625 221929235 221928631 0.000000e+00 981.0
17 TraesCS5B01G075200 chr7B 94.245 556 23 8 3 555 448002511 448001962 0.000000e+00 841.0
18 TraesCS5B01G075200 chr7B 100.000 29 0 0 633 661 34056987 34056959 3.000000e-03 54.7
19 TraesCS5B01G075200 chr7A 89.103 624 51 10 1 618 42132299 42132911 0.000000e+00 760.0
20 TraesCS5B01G075200 chr1D 81.186 388 34 17 3499 3856 490397462 490397084 5.560000e-70 276.0
21 TraesCS5B01G075200 chr1D 82.624 282 29 11 3487 3751 460552271 460551993 1.220000e-56 231.0
22 TraesCS5B01G075200 chr1D 82.946 258 24 11 2084 2328 490397796 490397546 1.230000e-51 215.0
23 TraesCS5B01G075200 chr1D 79.876 323 27 12 5096 5394 460549285 460548977 9.570000e-48 202.0
24 TraesCS5B01G075200 chr1B 86.735 98 9 3 3366 3462 546690443 546690349 7.720000e-19 106.0
25 TraesCS5B01G075200 chr7D 86.000 100 10 4 3368 3464 635566502 635566600 2.780000e-18 104.0
26 TraesCS5B01G075200 chr4D 84.615 104 12 3 3363 3465 312567486 312567386 3.590000e-17 100.0
27 TraesCS5B01G075200 chr4D 83.036 112 15 2 3357 3464 312648910 312649021 1.290000e-16 99.0


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 TraesCS5B01G075200 chr5B 89633891 89639525 5634 True 10406.0 10406 100.0000 1 5635 1 chr5B.!!$R1 5634
1 TraesCS5B01G075200 chr5B 205864756 205865377 621 False 1061.0 1061 97.4400 1 623 1 chr5B.!!$F1 622
2 TraesCS5B01G075200 chr5B 349090786 349091394 608 True 704.0 704 87.5800 1 621 1 chr5B.!!$R2 620
3 TraesCS5B01G075200 chr5A 77091042 77095997 4955 True 7260.0 7260 93.2310 693 5633 1 chr5A.!!$R1 4940
4 TraesCS5B01G075200 chr5D 80705137 80709919 4782 True 3744.0 6527 95.4605 873 5634 2 chr5D.!!$R3 4761
5 TraesCS5B01G075200 chr3B 227831674 227832294 620 True 1083.0 1083 98.0770 1 623 1 chr3B.!!$R2 622
6 TraesCS5B01G075200 chr3B 29784008 29784628 620 True 1072.0 1072 97.7530 1 623 1 chr3B.!!$R1 622
7 TraesCS5B01G075200 chr4B 67846797 67847415 618 False 1075.0 1075 97.9130 1 623 1 chr4B.!!$F1 622
8 TraesCS5B01G075200 chr6B 572113981 572115250 1269 True 651.5 1064 97.0720 1 623 2 chr6B.!!$R2 622
9 TraesCS5B01G075200 chr2B 221928631 221929235 604 True 981.0 981 95.5200 1 625 1 chr2B.!!$R1 624
10 TraesCS5B01G075200 chr7B 448001962 448002511 549 True 841.0 841 94.2450 3 555 1 chr7B.!!$R2 552
11 TraesCS5B01G075200 chr7A 42132299 42132911 612 False 760.0 760 89.1030 1 618 1 chr7A.!!$F1 617
12 TraesCS5B01G075200 chr1D 490397084 490397796 712 True 245.5 276 82.0660 2084 3856 2 chr1D.!!$R2 1772
13 TraesCS5B01G075200 chr1D 460548977 460552271 3294 True 216.5 231 81.2500 3487 5394 2 chr1D.!!$R1 1907

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
661 1329 0.178068 GCCGAATAGGAACCAGCTGA 59.822 55.0 17.39 0.0 45.00 4.26 F
774 1442 0.248907 ACGACAGACTGAACCGTGTG 60.249 55.0 10.08 0.0 34.64 3.82 F
1304 1983 0.395686 CCTGCATCATCTCCATCGGT 59.604 55.0 0.00 0.0 0.00 4.69 F
1371 2050 0.746923 GCCCCCGTTTGGTATCTGTC 60.747 60.0 0.00 0.0 0.00 3.51 F
3262 3992 0.035820 CACCTGCCGGTTAGCCTTAA 60.036 55.0 1.90 0.0 42.13 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2818 1.453155 AAAGCACAGTTATCAGCGGG 58.547 50.000 0.00 0.0 0.0 6.13 R
2700 3429 4.551702 ACAAAATGCATAAGGGGGAAAC 57.448 40.909 0.00 0.0 0.0 2.78 R
3014 3743 0.099968 CAAATGCGGCAGTCTGGATG 59.900 55.000 9.25 0.0 29.5 3.51 R
3330 4060 3.386402 TGTGATGTGTACTGAGTTGACCA 59.614 43.478 0.00 0.0 0.0 4.02 R
5040 7392 0.523966 GTCAGTCAGTCAGGTCTCCG 59.476 60.000 0.00 0.0 0.0 4.63 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
464 470 3.639099 CAACATGGAGGTGCAGAGT 57.361 52.632 0.00 0.00 0.00 3.24
471 477 2.176045 TGGAGGTGCAGAGTTCGAATA 58.824 47.619 0.00 0.00 0.00 1.75
635 1303 4.553144 TTCCCTAGGAACCACGCT 57.447 55.556 11.48 0.00 36.71 5.07
636 1304 1.980052 TTCCCTAGGAACCACGCTG 59.020 57.895 11.48 0.00 36.71 5.18
637 1305 0.543410 TTCCCTAGGAACCACGCTGA 60.543 55.000 11.48 0.00 36.71 4.26
638 1306 0.970937 TCCCTAGGAACCACGCTGAG 60.971 60.000 11.48 0.00 0.00 3.35
639 1307 1.517832 CCTAGGAACCACGCTGAGG 59.482 63.158 1.05 0.00 0.00 3.86
640 1308 1.517832 CTAGGAACCACGCTGAGGG 59.482 63.158 0.00 0.00 0.00 4.30
641 1309 2.579684 CTAGGAACCACGCTGAGGGC 62.580 65.000 0.00 0.00 37.64 5.19
650 1318 2.663188 GCTGAGGGCGCCGAATAG 60.663 66.667 22.54 16.53 0.00 1.73
651 1319 2.029666 CTGAGGGCGCCGAATAGG 59.970 66.667 22.54 4.29 44.97 2.57
652 1320 2.443203 TGAGGGCGCCGAATAGGA 60.443 61.111 22.54 0.00 45.00 2.94
653 1321 2.028125 CTGAGGGCGCCGAATAGGAA 62.028 60.000 22.54 0.00 45.00 3.36
654 1322 1.594564 GAGGGCGCCGAATAGGAAC 60.595 63.158 22.54 2.36 45.00 3.62
655 1323 2.590859 GGGCGCCGAATAGGAACC 60.591 66.667 22.54 0.00 45.00 3.62
656 1324 2.188469 GGCGCCGAATAGGAACCA 59.812 61.111 12.58 0.00 45.00 3.67
657 1325 1.887707 GGCGCCGAATAGGAACCAG 60.888 63.158 12.58 0.00 45.00 4.00
658 1326 2.534903 GCGCCGAATAGGAACCAGC 61.535 63.158 0.00 0.00 45.00 4.85
659 1327 1.144057 CGCCGAATAGGAACCAGCT 59.856 57.895 0.00 0.00 45.00 4.24
660 1328 1.154205 CGCCGAATAGGAACCAGCTG 61.154 60.000 6.78 6.78 45.00 4.24
661 1329 0.178068 GCCGAATAGGAACCAGCTGA 59.822 55.000 17.39 0.00 45.00 4.26
662 1330 1.808133 GCCGAATAGGAACCAGCTGAG 60.808 57.143 17.39 8.04 45.00 3.35
663 1331 1.202580 CCGAATAGGAACCAGCTGAGG 60.203 57.143 17.39 0.81 45.00 3.86
664 1332 1.808133 CGAATAGGAACCAGCTGAGGC 60.808 57.143 17.39 3.02 39.06 4.70
684 1352 1.442148 GGCCAAGCCTAGTAGTCGG 59.558 63.158 0.00 0.00 46.69 4.79
685 1353 1.041447 GGCCAAGCCTAGTAGTCGGA 61.041 60.000 0.00 0.00 46.69 4.55
686 1354 0.822164 GCCAAGCCTAGTAGTCGGAA 59.178 55.000 0.00 0.00 0.00 4.30
687 1355 1.471153 GCCAAGCCTAGTAGTCGGAAC 60.471 57.143 0.00 0.00 0.00 3.62
688 1356 2.100989 CCAAGCCTAGTAGTCGGAACT 58.899 52.381 0.00 0.00 39.66 3.01
689 1357 2.496470 CCAAGCCTAGTAGTCGGAACTT 59.504 50.000 0.00 0.00 36.92 2.66
690 1358 3.512680 CAAGCCTAGTAGTCGGAACTTG 58.487 50.000 0.00 0.00 36.92 3.16
691 1359 2.100989 AGCCTAGTAGTCGGAACTTGG 58.899 52.381 6.10 6.10 41.18 3.61
736 1404 2.351276 GGCCCATGGTATAGCCCG 59.649 66.667 16.66 0.00 39.60 6.13
757 1425 2.401766 GCCCATGTTCAGCCTGACG 61.402 63.158 0.00 0.00 0.00 4.35
774 1442 0.248907 ACGACAGACTGAACCGTGTG 60.249 55.000 10.08 0.00 34.64 3.82
893 1569 1.475034 GCCAACGAGCCCATCATCTAA 60.475 52.381 0.00 0.00 0.00 2.10
896 1572 3.313526 CCAACGAGCCCATCATCTAAAAG 59.686 47.826 0.00 0.00 0.00 2.27
906 1582 6.338146 CCCATCATCTAAAAGTCGTTACAGA 58.662 40.000 0.00 0.00 0.00 3.41
1078 1757 1.675219 TGGAACTTCCAGGTACCGC 59.325 57.895 6.39 0.00 42.67 5.68
1286 1965 5.240403 CAGGCCAAGAGCTTATCTTAAATCC 59.760 44.000 5.01 0.00 46.91 3.01
1304 1983 0.395686 CCTGCATCATCTCCATCGGT 59.604 55.000 0.00 0.00 0.00 4.69
1371 2050 0.746923 GCCCCCGTTTGGTATCTGTC 60.747 60.000 0.00 0.00 0.00 3.51
1420 2099 7.973388 TGCTCTTAATTTTTGTATGCGCTATTT 59.027 29.630 9.73 0.00 0.00 1.40
1425 2104 6.966435 ATTTTTGTATGCGCTATTTTGCTT 57.034 29.167 9.73 0.00 0.00 3.91
1440 2119 7.068226 GCTATTTTGCTTAATTCCCTCCAACTA 59.932 37.037 0.00 0.00 0.00 2.24
1446 2127 5.703130 GCTTAATTCCCTCCAACTATAGCAG 59.297 44.000 0.00 0.00 0.00 4.24
1489 2205 5.067954 GTGGGAATGTGTAACTTACCTGTT 58.932 41.667 0.00 0.00 38.04 3.16
1490 2206 6.183361 TGTGGGAATGTGTAACTTACCTGTTA 60.183 38.462 0.00 0.00 38.04 2.41
1491 2207 6.370718 GTGGGAATGTGTAACTTACCTGTTAG 59.629 42.308 0.00 0.00 38.04 2.34
1752 2468 2.587522 AGAGAAACAGGAGGGTTTTGC 58.412 47.619 0.00 0.00 40.85 3.68
1854 2570 6.061441 TCCATGACTTGTTGTACAAACTGAT 58.939 36.000 10.51 0.00 37.69 2.90
2700 3429 3.792956 GCTCAATGCACGATTTTGTATGG 59.207 43.478 0.00 0.00 42.31 2.74
2741 3470 3.689161 TGTTGAGGTCTTGCATTAATCCG 59.311 43.478 0.00 0.00 0.00 4.18
3014 3743 6.091986 CCTTCTCTCAGTCAAAGTATGCTTTC 59.908 42.308 5.74 0.00 42.54 2.62
3034 3763 1.660560 ATCCAGACTGCCGCATTTGC 61.661 55.000 0.00 0.00 37.78 3.68
3039 3768 0.179179 GACTGCCGCATTTGCTTCTC 60.179 55.000 0.00 0.00 39.32 2.87
3260 3990 2.064242 AACACCTGCCGGTTAGCCTT 62.064 55.000 1.90 0.00 42.13 4.35
3262 3992 0.035820 CACCTGCCGGTTAGCCTTAA 60.036 55.000 1.90 0.00 42.13 1.85
3308 4038 7.934855 ATATCAACTCATTCACTCAGCTTTT 57.065 32.000 0.00 0.00 0.00 2.27
3316 4046 8.940952 ACTCATTCACTCAGCTTTTAAAGTATC 58.059 33.333 6.57 0.00 0.00 2.24
3323 4053 8.656849 CACTCAGCTTTTAAAGTATCGTGTATT 58.343 33.333 6.57 0.00 0.00 1.89
3352 4082 3.386402 TGGTCAACTCAGTACACATCACA 59.614 43.478 0.00 0.00 0.00 3.58
3353 4083 3.741344 GGTCAACTCAGTACACATCACAC 59.259 47.826 0.00 0.00 0.00 3.82
3681 4429 6.010219 ACCATTTAGACTACAAAATGCTGGT 58.990 36.000 4.32 0.00 40.27 4.00
3967 5922 2.297597 CAGTGACGAAGAAGAAGACCCT 59.702 50.000 0.00 0.00 0.00 4.34
4025 5980 3.416277 CGTGCAGGTTATTGTTGAATCG 58.584 45.455 0.00 0.00 0.00 3.34
4068 6023 2.360726 TCACTGCCTGCCATGCTG 60.361 61.111 0.00 0.00 0.00 4.41
4111 6068 8.780846 TTTCTTTGTCTGTTGTCACTTACTAA 57.219 30.769 0.00 0.00 0.00 2.24
4223 6183 1.279496 TATCACAAGTGCAGGGCTCT 58.721 50.000 0.00 0.00 33.65 4.09
4238 6198 1.074752 GCTCTGTGTGCTCAGCTTAC 58.925 55.000 0.00 0.00 35.63 2.34
4274 6234 4.962362 ACAAAACCAAAGTTCTCCCATCTT 59.038 37.500 0.00 0.00 34.19 2.40
4345 6305 3.869272 GAGCAACATCGGCCAGCG 61.869 66.667 2.24 0.00 0.00 5.18
4370 6330 0.456221 AGATCCTCAGTAACCACGCG 59.544 55.000 3.53 3.53 0.00 6.01
4550 6696 4.667935 TGGGGCTTCGGGAGGGAA 62.668 66.667 0.00 0.00 0.00 3.97
4591 6737 0.692476 CACCTGTCCAAGATGGTCCA 59.308 55.000 0.00 0.00 39.03 4.02
4594 6740 0.321671 CTGTCCAAGATGGTCCACGT 59.678 55.000 0.00 0.00 39.03 4.49
4647 6943 2.029290 TCTGACTAAAACCTGACTCGGC 60.029 50.000 0.00 0.00 0.00 5.54
4654 6950 2.052782 AACCTGACTCGGCTTTGTTT 57.947 45.000 0.00 0.00 0.00 2.83
4675 7004 1.550976 TGTGTGCGGGACATACATACA 59.449 47.619 5.42 0.00 44.48 2.29
4678 7007 2.159156 TGTGCGGGACATACATACAGTC 60.159 50.000 0.00 0.00 0.00 3.51
4707 7036 1.204704 GTAGGATGTTTTTGCTGGGCC 59.795 52.381 0.00 0.00 0.00 5.80
4714 7043 2.290577 TGTTTTTGCTGGGCCAAAACTT 60.291 40.909 24.40 0.00 46.85 2.66
4715 7044 2.323968 TTTTGCTGGGCCAAAACTTC 57.676 45.000 8.04 0.00 39.14 3.01
4726 7055 3.998341 GGCCAAAACTTCTGTGATACGTA 59.002 43.478 0.00 0.00 0.00 3.57
4757 7093 3.054503 GGTGCAGCAGCTGTGGAG 61.055 66.667 23.60 4.09 42.74 3.86
4778 7114 6.551227 TGGAGTATTCTCATGCATGTACTACT 59.449 38.462 25.94 24.12 42.05 2.57
4779 7115 7.087639 GGAGTATTCTCATGCATGTACTACTC 58.912 42.308 29.07 29.07 42.05 2.59
4781 7117 3.990318 TCTCATGCATGTACTACTCCG 57.010 47.619 25.43 0.00 0.00 4.63
4782 7118 2.034685 TCTCATGCATGTACTACTCCGC 59.965 50.000 25.43 0.00 0.00 5.54
4783 7119 2.031870 TCATGCATGTACTACTCCGCT 58.968 47.619 25.43 0.00 0.00 5.52
4784 7120 2.430694 TCATGCATGTACTACTCCGCTT 59.569 45.455 25.43 0.00 0.00 4.68
4828 7164 4.148825 ATCTGGCGTGCGAGGGTC 62.149 66.667 4.01 0.00 0.00 4.46
4850 7192 2.462889 GTTTTGTGATGCATATGCCCG 58.537 47.619 24.54 0.00 41.18 6.13
4951 7302 4.683400 GCTTGGATCCAGATCTCCGTTTTA 60.683 45.833 15.53 0.00 37.92 1.52
4967 7318 7.219372 TCCGTTTTATTTTCCGTTGTTTTTC 57.781 32.000 0.00 0.00 0.00 2.29
4973 7324 7.933728 TTATTTTCCGTTGTTTTTCTAAGGC 57.066 32.000 0.00 0.00 0.00 4.35
5040 7392 3.008485 AGAGAAGGGAAACTGATGTGGAC 59.992 47.826 0.00 0.00 0.00 4.02
5053 7405 1.179174 TGTGGACGGAGACCTGACTG 61.179 60.000 0.00 0.00 44.19 3.51
5055 7407 0.894184 TGGACGGAGACCTGACTGAC 60.894 60.000 0.00 0.00 44.19 3.51
5056 7408 0.609681 GGACGGAGACCTGACTGACT 60.610 60.000 0.00 0.00 39.76 3.41
5101 7455 3.106242 TGGCGTATGAGTATTGCGAAT 57.894 42.857 0.00 0.00 0.00 3.34
5395 7781 1.478510 AGGCGAGACATACAAGACAGG 59.521 52.381 0.00 0.00 0.00 4.00
5396 7782 1.204941 GGCGAGACATACAAGACAGGT 59.795 52.381 0.00 0.00 0.00 4.00
5407 7793 4.402056 ACAAGACAGGTTCGAAAAGAGA 57.598 40.909 0.00 0.00 0.00 3.10
5466 7856 4.822896 AGCTAGTCATCGTTAGAGGTTAGG 59.177 45.833 0.00 0.00 0.00 2.69
5505 7897 0.101579 GGCAGGAGCTCGAGAGTAAC 59.898 60.000 18.75 0.00 41.70 2.50
5513 7905 2.648102 CGAGAGTAACGAGCGCCG 60.648 66.667 15.25 15.25 45.44 6.46
5549 7941 0.390340 CGCCAGTGTGAGCATGTACT 60.390 55.000 0.00 0.00 0.00 2.73
5550 7942 1.363744 GCCAGTGTGAGCATGTACTC 58.636 55.000 0.00 0.00 37.19 2.59
5551 7943 2.009042 GCCAGTGTGAGCATGTACTCC 61.009 57.143 0.00 0.00 35.72 3.85
5552 7944 1.552337 CCAGTGTGAGCATGTACTCCT 59.448 52.381 0.00 0.00 35.72 3.69
5572 7973 6.119240 TCCTTCAGTTCATCACAGAGAATT 57.881 37.500 0.00 0.00 0.00 2.17
5580 7981 0.391661 TCACAGAGAATTGAGCCGGC 60.392 55.000 21.89 21.89 0.00 6.13
5630 8033 0.519961 GGGTGTTTCGTGTGCCATAC 59.480 55.000 0.00 0.00 0.00 2.39
5634 8037 3.687698 GGTGTTTCGTGTGCCATACTAAT 59.312 43.478 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
633 1301 2.663188 CTATTCGGCGCCCTCAGC 60.663 66.667 23.46 0.00 38.52 4.26
634 1302 2.028125 TTCCTATTCGGCGCCCTCAG 62.028 60.000 23.46 12.78 0.00 3.35
635 1303 2.061578 TTCCTATTCGGCGCCCTCA 61.062 57.895 23.46 4.83 0.00 3.86
636 1304 1.594564 GTTCCTATTCGGCGCCCTC 60.595 63.158 23.46 0.00 0.00 4.30
637 1305 2.504519 GTTCCTATTCGGCGCCCT 59.495 61.111 23.46 8.60 0.00 5.19
638 1306 2.590859 GGTTCCTATTCGGCGCCC 60.591 66.667 23.46 2.37 0.00 6.13
639 1307 1.887707 CTGGTTCCTATTCGGCGCC 60.888 63.158 19.07 19.07 0.00 6.53
640 1308 2.534903 GCTGGTTCCTATTCGGCGC 61.535 63.158 0.00 0.00 0.00 6.53
641 1309 1.144057 AGCTGGTTCCTATTCGGCG 59.856 57.895 0.00 0.00 37.81 6.46
642 1310 0.178068 TCAGCTGGTTCCTATTCGGC 59.822 55.000 15.13 0.00 0.00 5.54
643 1311 1.202580 CCTCAGCTGGTTCCTATTCGG 60.203 57.143 15.13 0.00 0.00 4.30
644 1312 1.808133 GCCTCAGCTGGTTCCTATTCG 60.808 57.143 15.13 0.00 35.50 3.34
645 1313 1.960417 GCCTCAGCTGGTTCCTATTC 58.040 55.000 15.13 0.00 35.50 1.75
667 1335 0.822164 TTCCGACTACTAGGCTTGGC 59.178 55.000 0.00 0.00 0.00 4.52
668 1336 2.100989 AGTTCCGACTACTAGGCTTGG 58.899 52.381 0.00 0.00 33.32 3.61
669 1337 3.512680 CAAGTTCCGACTACTAGGCTTG 58.487 50.000 0.00 0.00 34.21 4.01
670 1338 2.496470 CCAAGTTCCGACTACTAGGCTT 59.504 50.000 0.00 0.00 34.21 4.35
671 1339 2.100989 CCAAGTTCCGACTACTAGGCT 58.899 52.381 0.00 0.00 34.21 4.58
672 1340 1.823610 ACCAAGTTCCGACTACTAGGC 59.176 52.381 0.00 0.00 34.21 3.93
673 1341 2.165845 CCACCAAGTTCCGACTACTAGG 59.834 54.545 0.00 0.00 34.21 3.02
674 1342 2.416972 GCCACCAAGTTCCGACTACTAG 60.417 54.545 0.00 0.00 34.21 2.57
675 1343 1.547372 GCCACCAAGTTCCGACTACTA 59.453 52.381 0.00 0.00 34.21 1.82
676 1344 0.320697 GCCACCAAGTTCCGACTACT 59.679 55.000 0.00 0.00 34.21 2.57
677 1345 0.034337 TGCCACCAAGTTCCGACTAC 59.966 55.000 0.00 0.00 34.21 2.73
678 1346 0.320374 CTGCCACCAAGTTCCGACTA 59.680 55.000 0.00 0.00 34.21 2.59
679 1347 1.071471 CTGCCACCAAGTTCCGACT 59.929 57.895 0.00 0.00 37.87 4.18
680 1348 0.951040 CTCTGCCACCAAGTTCCGAC 60.951 60.000 0.00 0.00 0.00 4.79
681 1349 1.118965 TCTCTGCCACCAAGTTCCGA 61.119 55.000 0.00 0.00 0.00 4.55
682 1350 0.671781 CTCTCTGCCACCAAGTTCCG 60.672 60.000 0.00 0.00 0.00 4.30
683 1351 0.322008 CCTCTCTGCCACCAAGTTCC 60.322 60.000 0.00 0.00 0.00 3.62
684 1352 0.957888 GCCTCTCTGCCACCAAGTTC 60.958 60.000 0.00 0.00 0.00 3.01
685 1353 1.073897 GCCTCTCTGCCACCAAGTT 59.926 57.895 0.00 0.00 0.00 2.66
686 1354 1.845205 AGCCTCTCTGCCACCAAGT 60.845 57.895 0.00 0.00 0.00 3.16
687 1355 1.376942 CAGCCTCTCTGCCACCAAG 60.377 63.158 0.00 0.00 35.78 3.61
688 1356 2.752358 CAGCCTCTCTGCCACCAA 59.248 61.111 0.00 0.00 35.78 3.67
689 1357 3.324930 CCAGCCTCTCTGCCACCA 61.325 66.667 0.00 0.00 41.50 4.17
690 1358 3.325753 ACCAGCCTCTCTGCCACC 61.326 66.667 0.00 0.00 41.50 4.61
691 1359 2.046507 CACCAGCCTCTCTGCCAC 60.047 66.667 0.00 0.00 41.50 5.01
736 1404 4.066139 AGGCTGAACATGGGCCCC 62.066 66.667 22.27 3.07 46.31 5.80
752 1420 0.311165 ACGGTTCAGTCTGTCGTCAG 59.689 55.000 3.03 3.03 42.54 3.51
757 1425 1.222115 GCCACACGGTTCAGTCTGTC 61.222 60.000 0.00 0.00 33.28 3.51
886 1562 5.093457 CGCTCTGTAACGACTTTTAGATGA 58.907 41.667 0.00 0.00 0.00 2.92
893 1569 1.699343 GCTCGCTCTGTAACGACTTT 58.301 50.000 0.00 0.00 34.08 2.66
896 1572 0.858135 CTCGCTCGCTCTGTAACGAC 60.858 60.000 0.00 0.00 34.08 4.34
924 1600 1.484240 AGCCGGAGAAGAAGAAGATGG 59.516 52.381 5.05 0.00 0.00 3.51
970 1649 3.680786 CTCACGGGGACTGCGTGA 61.681 66.667 0.00 0.00 46.98 4.35
1078 1757 1.017701 GGTTTAGGGTGTCGCGAAGG 61.018 60.000 12.06 0.00 0.00 3.46
1081 1760 0.611618 TAGGGTTTAGGGTGTCGCGA 60.612 55.000 3.71 3.71 0.00 5.87
1215 1894 0.892755 GGTACAGGACGTCCATGTCA 59.107 55.000 35.00 19.31 40.72 3.58
1286 1965 2.141517 GAACCGATGGAGATGATGCAG 58.858 52.381 0.00 0.00 30.11 4.41
1304 1983 3.728076 AAGCAGTGTGACTAAGACGAA 57.272 42.857 0.00 0.00 0.00 3.85
1371 2050 5.061808 CACAAGTAAATTACCTCGAGAACCG 59.938 44.000 15.71 0.00 40.25 4.44
1420 2099 6.062095 GCTATAGTTGGAGGGAATTAAGCAA 58.938 40.000 0.84 0.00 0.00 3.91
1425 2104 5.665812 ACACTGCTATAGTTGGAGGGAATTA 59.334 40.000 0.84 0.00 37.60 1.40
1440 2119 3.005554 GCATCTTGTCACACACTGCTAT 58.994 45.455 0.00 0.00 30.27 2.97
1446 2127 2.358898 ACAAAGGCATCTTGTCACACAC 59.641 45.455 0.00 0.00 32.75 3.82
1489 2205 7.273712 TGTACACAACCACTGACAAAATACTA 58.726 34.615 0.00 0.00 0.00 1.82
1490 2206 6.116806 TGTACACAACCACTGACAAAATACT 58.883 36.000 0.00 0.00 0.00 2.12
1491 2207 6.366315 TGTACACAACCACTGACAAAATAC 57.634 37.500 0.00 0.00 0.00 1.89
1752 2468 8.850026 GCACAAGCAATCCAAAACAACATTGG 62.850 42.308 0.00 0.00 43.61 3.16
1854 2570 5.816777 GCTTTGGCAATTTAAATATGCTCCA 59.183 36.000 22.83 15.72 39.94 3.86
2101 2818 1.453155 AAAGCACAGTTATCAGCGGG 58.547 50.000 0.00 0.00 0.00 6.13
2680 3409 5.384063 AACCATACAAAATCGTGCATTGA 57.616 34.783 4.06 0.00 0.00 2.57
2700 3429 4.551702 ACAAAATGCATAAGGGGGAAAC 57.448 40.909 0.00 0.00 0.00 2.78
3014 3743 0.099968 CAAATGCGGCAGTCTGGATG 59.900 55.000 9.25 0.00 29.50 3.51
3039 3768 9.900710 ACATCTAATCGTACTAGAATAAAGCAG 57.099 33.333 0.00 0.00 0.00 4.24
3087 3816 4.095483 CACAGAATATGTTCCTGCCTGTTC 59.905 45.833 0.00 0.00 41.41 3.18
3323 4053 7.867305 TGTGTACTGAGTTGACCAATAAAAA 57.133 32.000 0.00 0.00 0.00 1.94
3330 4060 3.386402 TGTGATGTGTACTGAGTTGACCA 59.614 43.478 0.00 0.00 0.00 4.02
3342 4072 7.966339 ACTTTATAGTAGGGTGTGATGTGTA 57.034 36.000 0.00 0.00 31.21 2.90
3352 4082 5.457342 CGGAGGGAGTACTTTATAGTAGGGT 60.457 48.000 0.00 0.00 37.53 4.34
3353 4083 5.008980 CGGAGGGAGTACTTTATAGTAGGG 58.991 50.000 0.00 0.00 37.53 3.53
3675 4423 1.896660 GTTTGAAGCCGGACCAGCA 60.897 57.895 5.05 0.00 0.00 4.41
3681 4429 1.271108 TGTGCTATGTTTGAAGCCGGA 60.271 47.619 5.05 0.00 37.97 5.14
3967 5922 5.630121 ACCACCAATGATTCAACAGAGTAA 58.370 37.500 0.00 0.00 0.00 2.24
4025 5980 9.833917 AGAATTAAATGGACTACTAGGCTTAAC 57.166 33.333 0.00 0.00 0.00 2.01
4068 6023 7.276438 ACAAAGAAAGAACTCAAGCAACAATTC 59.724 33.333 0.00 0.00 0.00 2.17
4165 6125 6.279882 CCACCTGTGTCAACAAATTTACATT 58.720 36.000 0.00 0.00 35.37 2.71
4177 6137 1.302431 CGATGCCCACCTGTGTCAA 60.302 57.895 0.00 0.00 0.00 3.18
4223 6183 1.605457 CCTTCGTAAGCTGAGCACACA 60.605 52.381 7.39 0.00 37.18 3.72
4250 6210 4.342092 AGATGGGAGAACTTTGGTTTTGTG 59.658 41.667 0.00 0.00 35.58 3.33
4274 6234 2.836154 GGGCAGGGTGACACTGAA 59.164 61.111 20.78 0.00 38.20 3.02
4345 6305 0.595310 GTTACTGAGGATCTCGCCGC 60.595 60.000 0.00 0.00 34.92 6.53
4370 6330 1.304464 CTTTGGCTGGGTTCCCTCC 60.304 63.158 9.43 10.35 0.00 4.30
4433 6393 3.760035 AGGACCGCGTTGCTCGAT 61.760 61.111 4.92 0.00 42.86 3.59
4550 6696 1.406065 CGCCCATGTCCTCCATCTCT 61.406 60.000 0.00 0.00 0.00 3.10
4591 6737 2.424302 CCTCGGGGTGAAACACGT 59.576 61.111 0.00 0.00 45.55 4.49
4647 6943 1.135257 TGTCCCGCACACAAAACAAAG 60.135 47.619 0.00 0.00 0.00 2.77
4654 6950 2.028020 TGTATGTATGTCCCGCACACAA 60.028 45.455 0.00 0.00 38.10 3.33
4675 7004 0.743688 CATCCTACAGCAGCTCGACT 59.256 55.000 0.00 0.00 0.00 4.18
4678 7007 2.015736 AAACATCCTACAGCAGCTCG 57.984 50.000 0.00 0.00 0.00 5.03
4707 7036 6.529125 ACCGTATACGTATCACAGAAGTTTTG 59.471 38.462 22.87 4.84 37.74 2.44
4714 7043 3.807553 TCCACCGTATACGTATCACAGA 58.192 45.455 22.87 7.68 37.74 3.41
4715 7044 4.023450 ACATCCACCGTATACGTATCACAG 60.023 45.833 22.87 8.93 37.74 3.66
4726 7055 1.223487 GCACCCACATCCACCGTAT 59.777 57.895 0.00 0.00 0.00 3.06
4757 7093 5.859114 CGGAGTAGTACATGCATGAGAATAC 59.141 44.000 32.75 27.20 0.00 1.89
4828 7164 2.462889 GGCATATGCATCACAAAACCG 58.537 47.619 28.07 0.00 44.36 4.44
4850 7192 3.131396 CTGAGATAATACCAACGGCCAC 58.869 50.000 2.24 0.00 0.00 5.01
4951 7302 5.908341 TGCCTTAGAAAAACAACGGAAAAT 58.092 33.333 0.00 0.00 0.00 1.82
4973 7324 1.139163 GAAACCGCATTGGCAACTTG 58.861 50.000 0.00 0.00 43.94 3.16
5015 7366 2.641815 ACATCAGTTTCCCTTCTCTGCT 59.358 45.455 0.00 0.00 0.00 4.24
5040 7392 0.523966 GTCAGTCAGTCAGGTCTCCG 59.476 60.000 0.00 0.00 0.00 4.63
5053 7405 4.453819 CCTCTGAAATTTGACAGGTCAGTC 59.546 45.833 0.00 1.03 41.13 3.51
5055 7407 3.755378 CCCTCTGAAATTTGACAGGTCAG 59.245 47.826 0.00 0.00 41.13 3.51
5056 7408 3.754965 CCCTCTGAAATTTGACAGGTCA 58.245 45.455 0.00 0.00 37.91 4.02
5101 7455 3.181477 CCATGCTCCACAACAGTCAAAAA 60.181 43.478 0.00 0.00 0.00 1.94
5153 7514 3.255642 CGGGCCAATTTAATCATACAGGG 59.744 47.826 4.39 0.00 0.00 4.45
5274 7651 2.924290 GTTCTTGTACGCAGACAGATCC 59.076 50.000 0.00 0.00 0.00 3.36
5395 7781 7.648112 AGGTGCTTTATTTTTCTCTTTTCGAAC 59.352 33.333 0.00 0.00 0.00 3.95
5396 7782 7.712797 AGGTGCTTTATTTTTCTCTTTTCGAA 58.287 30.769 0.00 0.00 0.00 3.71
5407 7793 5.047092 CCATGACAGGAGGTGCTTTATTTTT 60.047 40.000 0.00 0.00 0.00 1.94
5466 7856 0.460987 CTCTTCCCCGTGTCTCATGC 60.461 60.000 0.00 0.00 0.00 4.06
5505 7897 0.509499 TTAAGAAAACACGGCGCTCG 59.491 50.000 6.90 12.33 45.88 5.03
5509 7901 3.594312 GATCGATTAAGAAAACACGGCG 58.406 45.455 4.80 4.80 0.00 6.46
5513 7905 4.092968 ACTGGCGATCGATTAAGAAAACAC 59.907 41.667 21.57 0.00 0.00 3.32
5549 7941 5.752036 ATTCTCTGTGATGAACTGAAGGA 57.248 39.130 0.00 0.00 36.43 3.36
5550 7942 5.936372 TCAATTCTCTGTGATGAACTGAAGG 59.064 40.000 0.00 0.00 36.43 3.46
5551 7943 6.402334 GCTCAATTCTCTGTGATGAACTGAAG 60.402 42.308 0.00 0.00 36.43 3.02
5552 7944 5.410746 GCTCAATTCTCTGTGATGAACTGAA 59.589 40.000 0.00 0.00 36.43 3.02
5572 7973 0.392327 TGAATTCATTCGCCGGCTCA 60.392 50.000 26.68 15.86 39.62 4.26
5580 7981 0.301687 CGTCGGGCTGAATTCATTCG 59.698 55.000 8.96 12.71 39.62 3.34


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

AutoCloner maintained by Alex Coulton.