Multiple sequence alignment - TraesCS3D01G492800

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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 TraesCS3D01G492800 chr3D 100.000 2339 0 0 1 2339 586419674 586422012 0.000000e+00 4320
1 TraesCS3D01G492800 chr3D 90.865 416 33 4 1 414 586568380 586567968 9.450000e-154 553
2 TraesCS3D01G492800 chr3D 85.270 482 59 5 749 1219 586567789 586567309 9.720000e-134 486
3 TraesCS3D01G492800 chr3D 95.683 139 4 1 596 732 586567909 586567771 3.030000e-54 222
4 TraesCS3D01G492800 chr3D 87.895 190 16 5 412 595 56393179 56393367 1.410000e-52 217
5 TraesCS3D01G492800 chr3D 92.553 94 7 0 1242 1335 586566117 586566024 4.050000e-28 135
6 TraesCS3D01G492800 chr7D 98.978 978 10 0 1362 2339 630435912 630434935 0.000000e+00 1751
7 TraesCS3D01G492800 chr7D 98.574 982 14 0 1358 2339 338996839 338995858 0.000000e+00 1736
8 TraesCS3D01G492800 chr7D 90.576 191 12 3 412 596 245405161 245404971 4.990000e-62 248
9 TraesCS3D01G492800 chr7D 88.947 190 14 5 412 595 619818547 619818359 6.500000e-56 228
10 TraesCS3D01G492800 chr4D 98.876 979 11 0 1361 2339 504546407 504545429 0.000000e+00 1748
11 TraesCS3D01G492800 chr4D 98.773 978 12 0 1362 2339 436872615 436871638 0.000000e+00 1740
12 TraesCS3D01G492800 chr5D 98.875 978 11 0 1362 2339 24098151 24097174 0.000000e+00 1746
13 TraesCS3D01G492800 chr5D 98.678 983 12 1 1357 2339 559970994 559970013 0.000000e+00 1742
14 TraesCS3D01G492800 chr5D 98.773 978 11 1 1362 2339 492305645 492304669 0.000000e+00 1738
15 TraesCS3D01G492800 chr5D 88.360 189 15 6 412 595 311720517 311720331 1.090000e-53 220
16 TraesCS3D01G492800 chrUn 98.773 978 12 0 1362 2339 95578542 95579519 0.000000e+00 1740
17 TraesCS3D01G492800 chr1D 98.773 978 12 0 1362 2339 361855154 361856131 0.000000e+00 1740
18 TraesCS3D01G492800 chr3B 94.346 619 27 5 749 1361 783152314 783152930 0.000000e+00 942
19 TraesCS3D01G492800 chr3B 95.726 468 18 2 895 1361 783162023 783162489 0.000000e+00 752
20 TraesCS3D01G492800 chr3B 95.513 468 19 2 895 1361 783157185 783157651 0.000000e+00 747
21 TraesCS3D01G492800 chr3B 96.119 335 12 1 1028 1361 783167250 783167584 1.580000e-151 545
22 TraesCS3D01G492800 chr3B 96.119 335 12 1 1028 1361 783172392 783172726 1.580000e-151 545
23 TraesCS3D01G492800 chr3B 91.761 352 14 7 71 413 783151660 783152005 2.100000e-130 475
24 TraesCS3D01G492800 chr3B 88.360 189 14 5 412 595 757289019 757289204 1.090000e-53 220
25 TraesCS3D01G492800 chr3B 88.108 185 20 2 412 596 454707591 454707409 3.910000e-53 219
26 TraesCS3D01G492800 chr3B 96.429 112 3 1 893 1004 783170522 783170632 1.430000e-42 183
27 TraesCS3D01G492800 chr3B 92.308 104 6 1 631 732 783152229 783152332 1.870000e-31 147
28 TraesCS3D01G492800 chr3B 94.805 77 3 1 1286 1361 783179003 783179079 4.080000e-23 119
29 TraesCS3D01G492800 chr6B 95.597 159 5 2 412 569 126608589 126608432 1.070000e-63 254
30 TraesCS3D01G492800 chr4A 90.576 191 12 3 412 597 615701174 615701363 4.990000e-62 248
31 TraesCS3D01G492800 chr5B 89.947 189 12 4 412 594 476814133 476814320 1.080000e-58 237


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 TraesCS3D01G492800 chr3D 586419674 586422012 2338 False 4320.000000 4320 100.000000 1 2339 1 chr3D.!!$F2 2338
1 TraesCS3D01G492800 chr3D 586566024 586568380 2356 True 349.000000 553 91.092750 1 1335 4 chr3D.!!$R1 1334
2 TraesCS3D01G492800 chr7D 630434935 630435912 977 True 1751.000000 1751 98.978000 1362 2339 1 chr7D.!!$R4 977
3 TraesCS3D01G492800 chr7D 338995858 338996839 981 True 1736.000000 1736 98.574000 1358 2339 1 chr7D.!!$R2 981
4 TraesCS3D01G492800 chr4D 504545429 504546407 978 True 1748.000000 1748 98.876000 1361 2339 1 chr4D.!!$R2 978
5 TraesCS3D01G492800 chr4D 436871638 436872615 977 True 1740.000000 1740 98.773000 1362 2339 1 chr4D.!!$R1 977
6 TraesCS3D01G492800 chr5D 24097174 24098151 977 True 1746.000000 1746 98.875000 1362 2339 1 chr5D.!!$R1 977
7 TraesCS3D01G492800 chr5D 559970013 559970994 981 True 1742.000000 1742 98.678000 1357 2339 1 chr5D.!!$R4 982
8 TraesCS3D01G492800 chr5D 492304669 492305645 976 True 1738.000000 1738 98.773000 1362 2339 1 chr5D.!!$R3 977
9 TraesCS3D01G492800 chrUn 95578542 95579519 977 False 1740.000000 1740 98.773000 1362 2339 1 chrUn.!!$F1 977
10 TraesCS3D01G492800 chr1D 361855154 361856131 977 False 1740.000000 1740 98.773000 1362 2339 1 chr1D.!!$F1 977
11 TraesCS3D01G492800 chr3B 783151660 783152930 1270 False 521.333333 942 92.805000 71 1361 3 chr3B.!!$F5 1290
12 TraesCS3D01G492800 chr3B 783167250 783172726 5476 False 424.333333 545 96.222333 893 1361 3 chr3B.!!$F6 468

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
526 536 0.040067 CGCCACTCAAAAAGGTCAGC 60.04 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 7301 1.1959 GTTCGCATTTGCCACTACGAA 59.804 47.619 0.0 0.0 37.21 3.85 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
49 50 1.537202 GAAGCTGGTGCGTGAAAGAAT 59.463 47.619 0.00 0.00 45.42 2.40
69 70 3.643398 GGTCTGCCGGTCCCTATT 58.357 61.111 1.90 0.00 0.00 1.73
100 101 5.069781 AGCCAATCTACTCATGGTAAGAGAC 59.930 44.000 0.00 0.00 36.57 3.36
151 154 3.032265 AGACAGCCTTTCTTGGGTTTT 57.968 42.857 0.00 0.00 35.37 2.43
200 210 5.965334 CCTATGTTGCACTGTTAAAATAGCG 59.035 40.000 0.00 0.00 0.00 4.26
220 230 3.787476 GCGTCATTGTATTTGCCCTTACG 60.787 47.826 0.00 0.00 0.00 3.18
414 424 0.108615 GCGAGCTCTTCCAAGCAGTA 60.109 55.000 12.85 0.00 45.00 2.74
416 426 2.898705 CGAGCTCTTCCAAGCAGTAAT 58.101 47.619 12.85 0.00 45.00 1.89
418 428 3.686726 CGAGCTCTTCCAAGCAGTAATTT 59.313 43.478 12.85 0.00 45.00 1.82
420 430 5.335191 CGAGCTCTTCCAAGCAGTAATTTTT 60.335 40.000 12.85 0.00 45.00 1.94
422 432 4.853743 GCTCTTCCAAGCAGTAATTTTTCG 59.146 41.667 0.00 0.00 42.05 3.46
423 433 5.371115 TCTTCCAAGCAGTAATTTTTCGG 57.629 39.130 0.00 0.00 0.00 4.30
424 434 5.067273 TCTTCCAAGCAGTAATTTTTCGGA 58.933 37.500 0.00 0.00 0.00 4.55
426 436 5.560966 TCCAAGCAGTAATTTTTCGGATC 57.439 39.130 0.00 0.00 0.00 3.36
427 437 5.007034 TCCAAGCAGTAATTTTTCGGATCA 58.993 37.500 0.00 0.00 0.00 2.92
428 438 5.095490 CCAAGCAGTAATTTTTCGGATCAC 58.905 41.667 0.00 0.00 0.00 3.06
429 439 4.965119 AGCAGTAATTTTTCGGATCACC 57.035 40.909 0.00 0.00 0.00 4.02
430 440 3.694566 AGCAGTAATTTTTCGGATCACCC 59.305 43.478 0.00 0.00 0.00 4.61
439 449 4.832608 GGATCACCCGGGTGCGAC 62.833 72.222 43.20 33.00 45.04 5.19
456 466 2.278857 CGCTGGCTAGGCGTGTAG 60.279 66.667 12.19 4.40 46.37 2.74
468 478 1.801913 CGTGTAGCGCCTGTCAGTC 60.802 63.158 2.29 0.00 0.00 3.51
469 479 1.289066 GTGTAGCGCCTGTCAGTCA 59.711 57.895 2.29 0.00 0.00 3.41
478 488 3.871248 CTGTCAGTCAGGCGCTGCA 62.871 63.158 7.64 0.00 40.23 4.41
480 490 3.927548 TCAGTCAGGCGCTGCACA 61.928 61.111 7.64 0.00 34.21 4.57
481 491 3.420606 CAGTCAGGCGCTGCACAG 61.421 66.667 7.64 0.00 0.00 3.66
482 492 3.933722 AGTCAGGCGCTGCACAGT 61.934 61.111 7.64 0.00 0.00 3.55
484 494 4.240103 TCAGGCGCTGCACAGTGT 62.240 61.111 7.64 0.00 40.84 3.55
485 495 2.357396 CAGGCGCTGCACAGTGTA 60.357 61.111 7.64 0.00 40.84 2.90
486 496 2.047844 AGGCGCTGCACAGTGTAG 60.048 61.111 14.02 14.02 40.84 2.74
488 498 2.671177 GGCGCTGCACAGTGTAGTG 61.671 63.158 23.67 23.67 42.30 2.74
491 501 1.560004 CGCTGCACAGTGTAGTGTGG 61.560 60.000 20.70 5.64 46.73 4.17
493 503 1.560004 CTGCACAGTGTAGTGTGGCG 61.560 60.000 18.52 6.77 46.73 5.69
494 504 2.954753 GCACAGTGTAGTGTGGCGC 61.955 63.158 18.52 0.00 46.73 6.53
496 506 2.343758 CAGTGTAGTGTGGCGCCT 59.656 61.111 29.70 9.99 0.00 5.52
497 507 1.301716 CAGTGTAGTGTGGCGCCTT 60.302 57.895 29.70 13.03 0.00 4.35
498 508 1.004918 AGTGTAGTGTGGCGCCTTC 60.005 57.895 29.70 20.58 0.00 3.46
499 509 2.048597 TGTAGTGTGGCGCCTTCG 60.049 61.111 29.70 0.00 39.07 3.79
501 511 2.048597 TAGTGTGGCGCCTTCGTG 60.049 61.111 29.70 0.00 38.14 4.35
502 512 2.863346 TAGTGTGGCGCCTTCGTGT 61.863 57.895 29.70 9.85 38.14 4.49
503 513 2.372040 TAGTGTGGCGCCTTCGTGTT 62.372 55.000 29.70 9.15 38.14 3.32
505 515 1.666553 TGTGGCGCCTTCGTGTTAG 60.667 57.895 29.70 0.00 38.14 2.34
506 516 1.373748 GTGGCGCCTTCGTGTTAGA 60.374 57.895 29.70 0.00 38.14 2.10
507 517 1.373748 TGGCGCCTTCGTGTTAGAC 60.374 57.895 29.70 0.00 38.14 2.59
516 526 3.188773 CGTGTTAGACGCCACTCAA 57.811 52.632 0.00 0.00 42.21 3.02
517 527 1.493772 CGTGTTAGACGCCACTCAAA 58.506 50.000 0.00 0.00 42.21 2.69
520 530 3.603857 CGTGTTAGACGCCACTCAAAAAG 60.604 47.826 0.00 0.00 42.21 2.27
521 531 2.875933 TGTTAGACGCCACTCAAAAAGG 59.124 45.455 0.00 0.00 0.00 3.11
522 532 2.876550 GTTAGACGCCACTCAAAAAGGT 59.123 45.455 0.00 0.00 0.00 3.50
526 536 0.040067 CGCCACTCAAAAAGGTCAGC 60.040 55.000 0.00 0.00 0.00 4.26
528 538 1.000938 GCCACTCAAAAAGGTCAGCTG 60.001 52.381 7.63 7.63 0.00 4.24
529 539 2.575532 CCACTCAAAAAGGTCAGCTGA 58.424 47.619 13.74 13.74 0.00 4.26
530 540 2.551459 CCACTCAAAAAGGTCAGCTGAG 59.449 50.000 18.89 3.30 39.53 3.35
531 541 3.209410 CACTCAAAAAGGTCAGCTGAGT 58.791 45.455 18.89 4.41 45.81 3.41
532 542 3.209410 ACTCAAAAAGGTCAGCTGAGTG 58.791 45.455 18.89 8.68 43.81 3.51
533 543 3.118261 ACTCAAAAAGGTCAGCTGAGTGA 60.118 43.478 18.89 12.32 43.81 3.41
535 545 4.464008 TCAAAAAGGTCAGCTGAGTGATT 58.536 39.130 18.89 7.77 0.00 2.57
538 548 5.859205 AAAAGGTCAGCTGAGTGATTTTT 57.141 34.783 18.89 15.27 0.00 1.94
560 570 6.917217 TTTTTAAGGGCAGTTCATTTTGTG 57.083 33.333 0.00 0.00 0.00 3.33
561 571 5.860941 TTTAAGGGCAGTTCATTTTGTGA 57.139 34.783 0.00 0.00 34.25 3.58
577 587 5.611796 TTTGTGAAATGATTCAGAGGTCG 57.388 39.130 0.00 0.00 45.88 4.79
580 590 5.304778 TGTGAAATGATTCAGAGGTCGAAA 58.695 37.500 0.00 0.00 45.88 3.46
582 592 6.430925 TGTGAAATGATTCAGAGGTCGAAATT 59.569 34.615 0.00 0.00 45.88 1.82
583 593 6.744537 GTGAAATGATTCAGAGGTCGAAATTG 59.255 38.462 0.00 0.00 45.88 2.32
584 594 6.430925 TGAAATGATTCAGAGGTCGAAATTGT 59.569 34.615 0.00 0.00 40.59 2.71
585 595 6.824305 AATGATTCAGAGGTCGAAATTGTT 57.176 33.333 0.00 0.00 0.00 2.83
586 596 7.921786 AATGATTCAGAGGTCGAAATTGTTA 57.078 32.000 0.00 0.00 0.00 2.41
588 598 7.737972 TGATTCAGAGGTCGAAATTGTTAAA 57.262 32.000 0.00 0.00 0.00 1.52
589 599 8.335532 TGATTCAGAGGTCGAAATTGTTAAAT 57.664 30.769 0.00 0.00 0.00 1.40
590 600 8.792633 TGATTCAGAGGTCGAAATTGTTAAATT 58.207 29.630 0.00 0.00 37.61 1.82
591 601 9.626045 GATTCAGAGGTCGAAATTGTTAAATTT 57.374 29.630 0.00 0.00 46.37 1.82
592 602 8.795786 TTCAGAGGTCGAAATTGTTAAATTTG 57.204 30.769 0.00 0.00 44.27 2.32
593 603 6.861055 TCAGAGGTCGAAATTGTTAAATTTGC 59.139 34.615 0.00 0.00 44.27 3.68
594 604 6.089417 CAGAGGTCGAAATTGTTAAATTTGCC 59.911 38.462 0.00 2.28 44.27 4.52
598 608 6.183359 GGTCGAAATTGTTAAATTTGCCGTAC 60.183 38.462 0.00 0.00 44.27 3.67
715 854 2.260434 GCGCAGAAGTACCCGACA 59.740 61.111 0.30 0.00 0.00 4.35
716 855 1.373748 GCGCAGAAGTACCCGACAA 60.374 57.895 0.30 0.00 0.00 3.18
717 856 0.739813 GCGCAGAAGTACCCGACAAT 60.740 55.000 0.30 0.00 0.00 2.71
719 858 1.671850 CGCAGAAGTACCCGACAATGT 60.672 52.381 0.00 0.00 0.00 2.71
720 859 2.416296 CGCAGAAGTACCCGACAATGTA 60.416 50.000 0.00 0.00 0.00 2.29
721 860 2.928116 GCAGAAGTACCCGACAATGTAC 59.072 50.000 0.00 0.00 38.06 2.90
723 862 2.821969 AGAAGTACCCGACAATGTACGT 59.178 45.455 0.00 0.00 41.67 3.57
724 863 2.927553 AGTACCCGACAATGTACGTC 57.072 50.000 0.00 0.00 41.67 4.34
725 864 2.440409 AGTACCCGACAATGTACGTCT 58.560 47.619 0.00 0.00 41.67 4.18
726 865 3.609853 AGTACCCGACAATGTACGTCTA 58.390 45.455 0.00 0.00 41.67 2.59
727 866 2.927553 ACCCGACAATGTACGTCTAC 57.072 50.000 0.00 0.00 0.00 2.59
729 868 2.095059 ACCCGACAATGTACGTCTACAC 60.095 50.000 0.00 0.00 35.63 2.90
740 879 2.060326 CGTCTACACGCTTCCTCAAA 57.940 50.000 0.00 0.00 39.69 2.69
742 881 2.798283 CGTCTACACGCTTCCTCAAAAA 59.202 45.455 0.00 0.00 39.69 1.94
769 910 6.377327 AAAATGATTACTTCTACGCCCATG 57.623 37.500 0.00 0.00 0.00 3.66
771 912 2.434336 TGATTACTTCTACGCCCATGCT 59.566 45.455 0.00 0.00 34.43 3.79
817 958 0.641783 GCTGCATTGCATGTAAACGC 59.358 50.000 12.53 6.41 38.13 4.84
833 974 2.405892 ACGCACAAAAGATCTTGCAC 57.594 45.000 9.17 0.00 34.49 4.57
835 976 2.287188 ACGCACAAAAGATCTTGCACTG 60.287 45.455 9.17 7.09 34.49 3.66
836 977 2.669364 GCACAAAAGATCTTGCACTGG 58.331 47.619 9.17 0.00 34.97 4.00
837 978 2.294233 GCACAAAAGATCTTGCACTGGA 59.706 45.455 9.17 0.00 34.97 3.86
839 980 4.293415 CACAAAAGATCTTGCACTGGAAC 58.707 43.478 9.17 0.00 0.00 3.62
906 3287 0.469917 CATGAGAGGTGCCCCGTAAT 59.530 55.000 0.00 0.00 35.12 1.89
1052 5169 3.545481 CGCGCTTGTACTGCTCGG 61.545 66.667 5.56 0.33 35.39 4.63
1143 5266 1.374252 GGTGATGCCAACGTCGTCT 60.374 57.895 0.00 0.00 37.17 4.18
1161 5284 1.115467 CTATCAAGCTGGAGGACGGT 58.885 55.000 0.00 0.00 0.00 4.83
1231 6523 2.507102 ACATCGGCAAGAGCGTCG 60.507 61.111 0.00 0.00 43.41 5.12
1240 6532 2.979197 AAGAGCGTCGACGACAGGG 61.979 63.158 39.74 11.89 43.02 4.45
1248 6540 1.300620 CGACGACAGGGACAAGCAA 60.301 57.895 0.00 0.00 0.00 3.91
1368 6661 3.118738 GCCAGCACTACATACCACTAGTT 60.119 47.826 0.00 0.00 0.00 2.24
1402 6695 1.971357 CCATACGCCTCCATTAGTCCT 59.029 52.381 0.00 0.00 0.00 3.85
1420 6713 3.621715 GTCCTCAAAATAATCGAACCGCT 59.378 43.478 0.00 0.00 0.00 5.52
1440 6733 4.648651 GCTACAAAAGGGGTCTTTAGTCA 58.351 43.478 0.00 0.00 41.92 3.41
1441 6734 5.254115 GCTACAAAAGGGGTCTTTAGTCAT 58.746 41.667 0.00 0.00 41.92 3.06
2008 7301 5.617252 TCACTACGGGTTTGAAAGATTTCT 58.383 37.500 6.84 0.00 38.02 2.52
2054 7347 6.183347 AGCAGCAAGGTTTTATTATCTGTCT 58.817 36.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 6.560003 TGAGTAGATTGGCTCAAGGAAATA 57.440 37.500 0.00 0.00 38.61 1.40
67 68 5.441718 TGAGTAGATTGGCTCAAGGAAAT 57.558 39.130 0.00 0.00 38.61 2.17
68 69 4.908601 TGAGTAGATTGGCTCAAGGAAA 57.091 40.909 0.00 0.00 38.61 3.13
69 70 4.774124 CATGAGTAGATTGGCTCAAGGAA 58.226 43.478 0.00 0.00 43.79 3.36
151 154 7.437862 GGATAAATGTTGAAGTGCAGAAAACAA 59.562 33.333 7.89 0.00 34.67 2.83
200 210 5.329493 GTTCGTAAGGGCAAATACAATGAC 58.671 41.667 0.00 0.00 38.47 3.06
440 450 2.586357 GCTACACGCCTAGCCAGC 60.586 66.667 1.26 0.00 34.16 4.85
441 451 2.278857 CGCTACACGCCTAGCCAG 60.279 66.667 6.41 0.00 36.53 4.85
451 461 0.734253 CTGACTGACAGGCGCTACAC 60.734 60.000 7.64 0.00 42.39 2.90
453 463 4.485554 CTGACTGACAGGCGCTAC 57.514 61.111 7.64 0.00 42.39 3.58
465 475 3.933722 ACTGTGCAGCGCCTGACT 61.934 61.111 2.29 0.00 32.44 3.41
468 478 2.357396 TACACTGTGCAGCGCCTG 60.357 61.111 2.29 2.69 34.12 4.85
469 479 2.047844 CTACACTGTGCAGCGCCT 60.048 61.111 2.29 0.00 0.00 5.52
474 484 1.560004 CGCCACACTACACTGTGCAG 61.560 60.000 7.90 7.13 40.33 4.41
475 485 1.594021 CGCCACACTACACTGTGCA 60.594 57.895 7.90 0.00 40.33 4.57
476 486 2.954753 GCGCCACACTACACTGTGC 61.955 63.158 7.90 0.00 40.33 4.57
478 488 2.030562 GGCGCCACACTACACTGT 59.969 61.111 24.80 0.00 0.00 3.55
480 490 1.004918 GAAGGCGCCACACTACACT 60.005 57.895 31.54 0.00 0.00 3.55
481 491 2.380410 CGAAGGCGCCACACTACAC 61.380 63.158 31.54 8.98 0.00 2.90
482 492 2.048597 CGAAGGCGCCACACTACA 60.049 61.111 31.54 0.00 0.00 2.74
484 494 2.048597 CACGAAGGCGCCACACTA 60.049 61.111 31.54 0.00 42.48 2.74
485 495 2.372040 TAACACGAAGGCGCCACACT 62.372 55.000 31.54 9.96 42.48 3.55
486 496 1.897398 CTAACACGAAGGCGCCACAC 61.897 60.000 31.54 17.81 42.48 3.82
488 498 1.373748 TCTAACACGAAGGCGCCAC 60.374 57.895 31.54 20.88 42.48 5.01
490 500 3.471399 GTCTAACACGAAGGCGCC 58.529 61.111 21.89 21.89 42.48 6.53
499 509 3.303791 CCTTTTTGAGTGGCGTCTAACAC 60.304 47.826 0.00 0.00 37.86 3.32
501 511 2.876550 ACCTTTTTGAGTGGCGTCTAAC 59.123 45.455 0.00 0.00 0.00 2.34
502 512 3.135994 GACCTTTTTGAGTGGCGTCTAA 58.864 45.455 0.00 0.00 0.00 2.10
503 513 2.103432 TGACCTTTTTGAGTGGCGTCTA 59.897 45.455 0.00 0.00 0.00 2.59
505 515 1.264288 CTGACCTTTTTGAGTGGCGTC 59.736 52.381 0.00 0.00 0.00 5.19
506 516 1.308998 CTGACCTTTTTGAGTGGCGT 58.691 50.000 0.00 0.00 0.00 5.68
507 517 0.040067 GCTGACCTTTTTGAGTGGCG 60.040 55.000 0.00 0.00 0.00 5.69
508 518 1.000938 CAGCTGACCTTTTTGAGTGGC 60.001 52.381 8.42 0.00 0.00 5.01
509 519 2.551459 CTCAGCTGACCTTTTTGAGTGG 59.449 50.000 13.74 0.00 32.60 4.00
510 520 3.209410 ACTCAGCTGACCTTTTTGAGTG 58.791 45.455 13.74 0.60 44.80 3.51
511 521 3.118261 TCACTCAGCTGACCTTTTTGAGT 60.118 43.478 13.74 2.70 46.77 3.41
512 522 3.470709 TCACTCAGCTGACCTTTTTGAG 58.529 45.455 13.74 1.98 40.73 3.02
513 523 3.558931 TCACTCAGCTGACCTTTTTGA 57.441 42.857 13.74 5.87 0.00 2.69
514 524 4.843220 AATCACTCAGCTGACCTTTTTG 57.157 40.909 13.74 3.60 0.00 2.44
516 526 5.859205 AAAAATCACTCAGCTGACCTTTT 57.141 34.783 13.74 12.51 0.00 2.27
538 548 6.227298 TCACAAAATGAACTGCCCTTAAAA 57.773 33.333 0.00 0.00 33.02 1.52
553 563 6.430925 TCGACCTCTGAATCATTTCACAAAAT 59.569 34.615 0.00 0.00 36.94 1.82
554 564 5.762711 TCGACCTCTGAATCATTTCACAAAA 59.237 36.000 0.00 0.00 36.94 2.44
555 565 5.304778 TCGACCTCTGAATCATTTCACAAA 58.695 37.500 0.00 0.00 36.94 2.83
556 566 4.893608 TCGACCTCTGAATCATTTCACAA 58.106 39.130 0.00 0.00 36.94 3.33
558 568 5.862924 TTTCGACCTCTGAATCATTTCAC 57.137 39.130 0.00 0.00 36.94 3.18
560 570 6.846350 ACAATTTCGACCTCTGAATCATTTC 58.154 36.000 0.00 0.00 0.00 2.17
561 571 6.824305 ACAATTTCGACCTCTGAATCATTT 57.176 33.333 0.00 0.00 0.00 2.32
565 575 9.626045 AAATTTAACAATTTCGACCTCTGAATC 57.374 29.630 0.00 0.00 38.02 2.52
567 577 7.381139 GCAAATTTAACAATTTCGACCTCTGAA 59.619 33.333 0.00 0.00 40.09 3.02
568 578 6.861055 GCAAATTTAACAATTTCGACCTCTGA 59.139 34.615 0.00 0.00 40.09 3.27
569 579 6.089417 GGCAAATTTAACAATTTCGACCTCTG 59.911 38.462 0.00 0.00 40.09 3.35
570 580 6.156519 GGCAAATTTAACAATTTCGACCTCT 58.843 36.000 0.00 0.00 40.09 3.69
571 581 5.060446 CGGCAAATTTAACAATTTCGACCTC 59.940 40.000 0.00 0.00 40.09 3.85
572 582 4.920927 CGGCAAATTTAACAATTTCGACCT 59.079 37.500 0.00 0.00 40.09 3.85
573 583 4.682401 ACGGCAAATTTAACAATTTCGACC 59.318 37.500 7.92 2.83 40.09 4.79
574 584 5.815964 ACGGCAAATTTAACAATTTCGAC 57.184 34.783 7.92 0.00 40.09 4.20
575 585 6.436261 TGTACGGCAAATTTAACAATTTCGA 58.564 32.000 7.92 0.00 40.09 3.71
576 586 6.677027 TGTACGGCAAATTTAACAATTTCG 57.323 33.333 0.00 0.00 40.09 3.46
580 590 9.677567 GATGATATGTACGGCAAATTTAACAAT 57.322 29.630 0.00 0.00 0.00 2.71
582 592 8.445275 AGATGATATGTACGGCAAATTTAACA 57.555 30.769 0.00 0.00 0.00 2.41
583 593 9.382244 GAAGATGATATGTACGGCAAATTTAAC 57.618 33.333 0.00 0.00 0.00 2.01
584 594 8.279800 CGAAGATGATATGTACGGCAAATTTAA 58.720 33.333 0.00 0.00 0.00 1.52
585 595 7.570507 GCGAAGATGATATGTACGGCAAATTTA 60.571 37.037 0.00 0.00 0.00 1.40
586 596 6.658831 CGAAGATGATATGTACGGCAAATTT 58.341 36.000 0.00 0.00 0.00 1.82
588 598 4.152402 GCGAAGATGATATGTACGGCAAAT 59.848 41.667 0.00 0.00 0.00 2.32
589 599 3.493129 GCGAAGATGATATGTACGGCAAA 59.507 43.478 0.00 0.00 0.00 3.68
590 600 3.057019 GCGAAGATGATATGTACGGCAA 58.943 45.455 0.00 0.00 0.00 4.52
591 601 2.296190 AGCGAAGATGATATGTACGGCA 59.704 45.455 0.00 0.00 0.00 5.69
592 602 2.917971 GAGCGAAGATGATATGTACGGC 59.082 50.000 0.00 0.00 0.00 5.68
593 603 3.502920 GGAGCGAAGATGATATGTACGG 58.497 50.000 0.00 0.00 0.00 4.02
594 604 3.502920 GGGAGCGAAGATGATATGTACG 58.497 50.000 0.00 0.00 0.00 3.67
740 879 9.797556 GGGCGTAGAAGTAATCATTTTTATTTT 57.202 29.630 0.00 0.00 0.00 1.82
742 881 8.514330 TGGGCGTAGAAGTAATCATTTTTATT 57.486 30.769 0.00 0.00 0.00 1.40
744 883 7.468084 GCATGGGCGTAGAAGTAATCATTTTTA 60.468 37.037 0.00 0.00 0.00 1.52
745 884 6.680378 GCATGGGCGTAGAAGTAATCATTTTT 60.680 38.462 0.00 0.00 0.00 1.94
746 885 5.221048 GCATGGGCGTAGAAGTAATCATTTT 60.221 40.000 0.00 0.00 0.00 1.82
769 910 0.678048 ATTTGCTCTGGTTCCCGAGC 60.678 55.000 22.28 22.28 44.23 5.03
771 912 3.343617 CTTAATTTGCTCTGGTTCCCGA 58.656 45.455 0.00 0.00 0.00 5.14
817 958 4.202040 TGTTCCAGTGCAAGATCTTTTGTG 60.202 41.667 4.86 0.00 0.00 3.33
906 3287 5.884322 TGGCTTATAGTAGATCGAGGGTTA 58.116 41.667 0.00 0.00 0.00 2.85
1143 5266 0.824109 CACCGTCCTCCAGCTTGATA 59.176 55.000 0.00 0.00 0.00 2.15
1206 5329 1.136774 CTTGCCGATGTCGACGAGA 59.863 57.895 11.62 0.00 43.02 4.04
1231 6523 1.557443 CGTTGCTTGTCCCTGTCGTC 61.557 60.000 0.00 0.00 0.00 4.20
1248 6540 0.250166 ACGGAGTTTTAAGGCAGCGT 60.250 50.000 0.00 0.00 37.78 5.07
1368 6661 2.747446 GCGTATGGAAGCCTCTTTTTCA 59.253 45.455 0.00 0.00 0.00 2.69
1402 6695 6.483385 TTTGTAGCGGTTCGATTATTTTGA 57.517 33.333 0.00 0.00 0.00 2.69
1420 6713 5.073965 ACCATGACTAAAGACCCCTTTTGTA 59.926 40.000 0.00 0.00 44.30 2.41
1440 6733 1.689582 GGGTCTCCTCCCGAACCAT 60.690 63.158 0.00 0.00 38.17 3.55
1441 6734 2.284405 GGGTCTCCTCCCGAACCA 60.284 66.667 0.00 0.00 38.17 3.67
2008 7301 1.195900 GTTCGCATTTGCCACTACGAA 59.804 47.619 0.00 0.00 37.21 3.85
2054 7347 6.530019 TCTGATTCTTACAGACAGCACATA 57.470 37.500 0.00 0.00 39.10 2.29


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

AutoCloner maintained by Alex Coulton.