Multiple sequence alignment - TraesCS3A01G187600

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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 TraesCS3A01G187600 chr3A 100.000 2940 0 0 1 2940 224376833 224379772 0.000000e+00 5430.0
1 TraesCS3A01G187600 chr3D 93.623 2415 99 30 563 2939 179948187 179950584 0.000000e+00 3555.0
2 TraesCS3A01G187600 chr3D 95.777 521 17 4 1 519 179947672 179948189 0.000000e+00 835.0
3 TraesCS3A01G187600 chr3D 83.529 170 25 2 2594 2760 40073253 40073422 3.920000e-34 156.0
4 TraesCS3A01G187600 chr3B 93.243 2427 97 20 559 2938 257846505 257848911 0.000000e+00 3511.0
5 TraesCS3A01G187600 chr3B 92.131 521 22 5 9 512 257845976 257846494 0.000000e+00 717.0
6 TraesCS3A01G187600 chr3B 80.734 218 32 7 2552 2760 707027181 707026965 8.430000e-36 161.0
7 TraesCS3A01G187600 chr3B 83.237 173 23 5 2594 2760 749488911 749488739 1.410000e-33 154.0
8 TraesCS3A01G187600 chr3B 86.585 82 11 0 2445 2526 372190532 372190613 1.120000e-14 91.6
9 TraesCS3A01G187600 chr5D 77.259 343 57 15 2433 2760 411155464 411155800 6.470000e-42 182.0
10 TraesCS3A01G187600 chr2D 76.524 328 62 10 2446 2760 422094037 422093712 6.520000e-37 165.0
11 TraesCS3A01G187600 chr2D 82.727 110 19 0 2444 2553 569133624 569133515 6.710000e-17 99.0
12 TraesCS3A01G187600 chr2D 81.481 108 19 1 2446 2553 80737242 80737136 1.450000e-13 87.9
13 TraesCS3A01G187600 chr6A 77.536 276 56 6 1650 1922 542430344 542430072 8.430000e-36 161.0
14 TraesCS3A01G187600 chr4A 75.831 331 65 9 2444 2760 640254766 640254437 1.410000e-33 154.0
15 TraesCS3A01G187600 chr6D 75.593 295 61 10 1650 1937 396010767 396010477 5.110000e-28 135.0
16 TraesCS3A01G187600 chr6D 79.630 108 22 0 2446 2553 365734736 365734843 8.740000e-11 78.7
17 TraesCS3A01G187600 chr1B 78.341 217 39 5 2552 2760 564574498 564574714 1.840000e-27 134.0
18 TraesCS3A01G187600 chr6B 74.242 330 70 13 2444 2760 224248004 224247677 1.110000e-24 124.0
19 TraesCS3A01G187600 chr4B 100.000 40 0 0 689 728 142674019 142674058 1.130000e-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 TraesCS3A01G187600 chr3A 224376833 224379772 2939 False 5430 5430 100.000 1 2940 1 chr3A.!!$F1 2939
1 TraesCS3A01G187600 chr3D 179947672 179950584 2912 False 2195 3555 94.700 1 2939 2 chr3D.!!$F2 2938
2 TraesCS3A01G187600 chr3B 257845976 257848911 2935 False 2114 3511 92.687 9 2938 2 chr3B.!!$F2 2929

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
20 21 0.792640 GACATCGAGTGTGTGCCTTG 59.207 55.0 5.41 0.0 42.36 3.61 F
534 553 0.871057 CACACACACACACACACACA 59.129 50.0 0.00 0.0 0.00 3.72 F
542 561 0.871057 CACACACACACACACACACA 59.129 50.0 0.00 0.0 0.00 3.72 F
548 567 0.871057 CACACACACACACACACACA 59.129 50.0 0.00 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1138 0.447801 CTGTGCGCTTACCCATTGTC 59.552 55.0 9.73 0.0 0.00 3.18 R
1554 1573 0.530744 AGCTTAAGTCACCGATGCGA 59.469 50.0 4.02 0.0 0.00 5.10 R
1624 1643 0.548989 ACACCACCCTACAAAGTGCA 59.451 50.0 0.00 0.0 32.48 4.57 R
2532 2564 0.595053 CGACCGAATCCCACGAGATG 60.595 60.0 0.00 0.0 0.00 2.90 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
20 21 0.792640 GACATCGAGTGTGTGCCTTG 59.207 55.000 5.41 0.00 42.36 3.61
36 37 2.749076 GCCTTGTGTCATAGTTGCATGA 59.251 45.455 0.00 0.00 32.50 3.07
177 195 5.203528 AGCCTGCAGACATACCATTTTAAT 58.796 37.500 17.39 0.00 0.00 1.40
193 211 1.961793 TAATGGCAGCCGACATAACC 58.038 50.000 7.03 0.00 41.33 2.85
211 229 8.477419 ACATAACCATCCACTAATAAAATGGG 57.523 34.615 4.84 0.00 40.97 4.00
405 424 7.673641 ACTCCTTGATAGATGAGAAGTCAAT 57.326 36.000 0.00 0.00 35.88 2.57
440 459 8.033038 TCAGTTTGTTATTCGAGCTAACAGTAT 58.967 33.333 17.05 8.65 39.51 2.12
465 484 2.041701 GCCCATTTGCCCATGTTCTAT 58.958 47.619 0.00 0.00 0.00 1.98
512 531 9.693739 TTTCTCCTGCCAAAATATTATTCACTA 57.306 29.630 0.00 0.00 0.00 2.74
527 546 7.646446 TTATTCACTATACACACACACACAC 57.354 36.000 0.00 0.00 0.00 3.82
528 547 4.657436 TCACTATACACACACACACACA 57.343 40.909 0.00 0.00 0.00 3.72
529 548 4.364860 TCACTATACACACACACACACAC 58.635 43.478 0.00 0.00 0.00 3.82
530 549 4.116238 CACTATACACACACACACACACA 58.884 43.478 0.00 0.00 0.00 3.72
531 550 4.026062 CACTATACACACACACACACACAC 60.026 45.833 0.00 0.00 0.00 3.82
532 551 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
533 552 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
534 553 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
535 554 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
536 555 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
537 556 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
538 557 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
539 558 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
540 559 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
541 560 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
542 561 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
543 562 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
544 563 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
545 564 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
546 565 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
547 566 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
548 567 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
549 568 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
550 569 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
551 570 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
552 571 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
553 572 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
554 573 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
555 574 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
556 575 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
557 576 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
589 608 5.103000 ACGTATCTTCTCTGAAATGTTCCG 58.897 41.667 0.00 0.00 0.00 4.30
624 643 2.719705 AGGTGGGACTAACCATTGGAAA 59.280 45.455 10.37 0.00 43.59 3.13
731 750 4.989168 ACGTGGACTTTACTTCTCACAATC 59.011 41.667 0.00 0.00 0.00 2.67
884 903 4.645136 ACGGTAAGCAGTAGATGAGATGAA 59.355 41.667 0.00 0.00 0.00 2.57
941 960 4.580580 ACTTTGTTCTCTCCTGCGATTTTT 59.419 37.500 0.00 0.00 0.00 1.94
962 981 5.531122 TTGGCTGTATCGATTAACTAGCT 57.469 39.130 1.71 0.00 0.00 3.32
1551 1570 2.220479 GTACAGAAGGTACCCATCGC 57.780 55.000 8.74 0.00 45.43 4.58
1552 1571 1.479323 GTACAGAAGGTACCCATCGCA 59.521 52.381 8.74 0.00 45.43 5.10
1553 1572 1.204146 ACAGAAGGTACCCATCGCAT 58.796 50.000 8.74 0.00 0.00 4.73
1554 1573 1.559682 ACAGAAGGTACCCATCGCATT 59.440 47.619 8.74 0.00 0.00 3.56
1555 1574 2.213499 CAGAAGGTACCCATCGCATTC 58.787 52.381 8.74 3.92 0.00 2.67
1556 1575 1.202533 AGAAGGTACCCATCGCATTCG 60.203 52.381 8.74 0.00 0.00 3.34
1569 1588 1.286501 GCATTCGCATCGGTGACTTA 58.713 50.000 0.00 0.00 38.36 2.24
1583 1602 2.593336 GTGACTTAAGCTCTAACGCGTC 59.407 50.000 14.44 0.00 34.40 5.19
1584 1603 2.486982 TGACTTAAGCTCTAACGCGTCT 59.513 45.455 14.44 0.70 34.40 4.18
1588 1607 2.837371 AAGCTCTAACGCGTCTGCCC 62.837 60.000 14.44 1.10 38.08 5.36
1624 1643 8.033038 TCTCGAGCTAACATGTAGTATTTGTTT 58.967 33.333 7.81 0.00 35.37 2.83
1920 1939 2.665603 GAGCTTCGGCCAGACCTT 59.334 61.111 2.24 0.00 43.01 3.50
1969 1992 2.546795 CGACCACTGCAGAAGTCTCTTT 60.547 50.000 26.71 1.36 36.83 2.52
1980 2003 8.813643 TGCAGAAGTCTCTTTACTTTTACTAC 57.186 34.615 0.00 0.00 39.78 2.73
1981 2004 8.639761 TGCAGAAGTCTCTTTACTTTTACTACT 58.360 33.333 0.00 0.00 39.78 2.57
2077 2100 1.145803 GTGGTGAGGTTACGCACTTC 58.854 55.000 6.87 0.00 45.32 3.01
2310 2334 5.126869 TGGAATGTGTTTTGAGAGCTTGAAA 59.873 36.000 0.00 0.00 0.00 2.69
2348 2372 4.066490 TGCTTGGCCAATTCTTTCATTTG 58.934 39.130 20.85 3.42 0.00 2.32
2365 2397 6.335471 TCATTTGTCATGTCAAGCTTCAAT 57.665 33.333 0.00 0.00 0.00 2.57
2366 2398 6.751157 TCATTTGTCATGTCAAGCTTCAATT 58.249 32.000 0.00 0.00 0.00 2.32
2474 2506 2.764547 GTTCTCCCCGCCTAGCCT 60.765 66.667 0.00 0.00 0.00 4.58
2495 2527 3.682885 TCCCAACGGCGCGTCTAA 61.683 61.111 9.90 0.00 39.99 2.10
2502 2534 2.793946 GGCGCGTCTAACCTCGTA 59.206 61.111 8.43 0.00 0.00 3.43
2506 2538 0.942962 CGCGTCTAACCTCGTAGGAT 59.057 55.000 0.00 0.00 37.67 3.24
2508 2540 1.945394 GCGTCTAACCTCGTAGGATGA 59.055 52.381 7.76 1.34 37.67 2.92
2520 2552 2.372264 GTAGGATGACGTGTGGAGGTA 58.628 52.381 0.00 0.00 0.00 3.08
2532 2564 2.159099 TGTGGAGGTATGTCTTCATCGC 60.159 50.000 0.00 0.00 35.70 4.58
2537 2569 4.233789 GAGGTATGTCTTCATCGCATCTC 58.766 47.826 0.00 0.00 35.70 2.75
2555 2613 1.299926 CGTGGGATTCGGTCGGATC 60.300 63.158 3.19 3.19 0.00 3.36
2609 2673 3.450817 TCTGCAATCCTTCCAATCTACGA 59.549 43.478 0.00 0.00 0.00 3.43
2627 2691 2.030523 CGATTCTCTTCATCGACGACG 58.969 52.381 0.00 0.00 45.30 5.12
2664 2728 0.249911 CTGGTCCTATGCGGCCTTAC 60.250 60.000 0.00 0.00 32.24 2.34
2668 2732 0.978667 TCCTATGCGGCCTTACCACA 60.979 55.000 0.00 0.00 39.03 4.17
2676 2740 1.002087 CGGCCTTACCACAAGACTTCT 59.998 52.381 0.00 0.00 39.03 2.85
2682 2746 2.802787 ACCACAAGACTTCTCGACTG 57.197 50.000 0.00 0.00 0.00 3.51
2687 2751 4.378978 CCACAAGACTTCTCGACTGTCTAG 60.379 50.000 6.21 4.58 39.78 2.43
2705 2775 0.912486 AGTAAGATTTGCCCGGCTCT 59.088 50.000 11.61 2.06 0.00 4.09
2716 2786 0.976073 CCCGGCTCTGTTAAGGGAGA 60.976 60.000 0.00 0.00 44.70 3.71
2720 2790 0.905357 GCTCTGTTAAGGGAGAGGCA 59.095 55.000 8.33 0.00 36.91 4.75
2730 2800 2.892425 GAGAGGCAATGACGGCGG 60.892 66.667 13.24 0.00 36.37 6.13
2753 2823 2.415608 CCTTCGGCTCGCTCCAGTA 61.416 63.158 0.00 0.00 0.00 2.74
2760 2830 2.737359 CGGCTCGCTCCAGTAATTGTAA 60.737 50.000 0.00 0.00 0.00 2.41
2765 2835 4.901868 TCGCTCCAGTAATTGTAACCTTT 58.098 39.130 0.00 0.00 0.00 3.11
2831 2901 8.591114 ATTCTTTGAGAAGGTGAATGAATGAT 57.409 30.769 0.00 0.00 37.69 2.45
2868 2939 0.758310 TTTGTTGTGGCATGGGCTCA 60.758 50.000 0.00 0.00 40.87 4.26
2910 2981 9.195411 TCTTAGCATTTGCATTCACTTTAAAAG 57.805 29.630 5.20 0.00 45.16 2.27
2916 2987 8.776470 CATTTGCATTCACTTTAAAAGATTGGT 58.224 29.630 0.00 0.00 0.00 3.67
2939 3010 9.635404 TGGTAAAGAAAAGACTGGAAAATAGAA 57.365 29.630 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 9.440761 AATATACCAGAGACTCCAAGAATTAGT 57.559 33.333 0.00 0.00 0.00 2.24
42 43 5.777449 TGGAATATACCAGAGACTCCAAGA 58.223 41.667 0.00 0.00 34.77 3.02
91 92 9.027202 TGGGAAAGGTAAAAGGTTAAATATGTC 57.973 33.333 0.00 0.00 0.00 3.06
102 103 4.651962 TGGAAAACTGGGAAAGGTAAAAGG 59.348 41.667 0.00 0.00 0.00 3.11
103 104 5.362717 ACTGGAAAACTGGGAAAGGTAAAAG 59.637 40.000 0.00 0.00 0.00 2.27
177 195 0.463654 GATGGTTATGTCGGCTGCCA 60.464 55.000 20.29 2.90 0.00 4.92
211 229 7.910304 AGTTTTGCTTATCACGAGATCATTAC 58.090 34.615 0.00 0.00 35.67 1.89
405 424 6.745116 TCGAATAACAAACTGAGAGAAGACA 58.255 36.000 0.00 0.00 0.00 3.41
512 531 2.675844 GTGTGTGTGTGTGTGTGTGTAT 59.324 45.455 0.00 0.00 0.00 2.29
514 533 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
515 534 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
517 536 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
519 538 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
521 540 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
522 541 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
523 542 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
524 543 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
525 544 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
526 545 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
527 546 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
528 547 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
529 548 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
530 549 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
531 550 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
532 551 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
533 552 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
534 553 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
535 554 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
536 555 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
537 556 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
538 557 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
539 558 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
540 559 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
541 560 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
542 561 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
543 562 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
544 563 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
545 564 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
546 565 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
547 566 2.315011 GTTTGTGTGTGTGTGTGTGTG 58.685 47.619 0.00 0.00 0.00 3.82
548 567 1.069568 CGTTTGTGTGTGTGTGTGTGT 60.070 47.619 0.00 0.00 0.00 3.72
549 568 1.069568 ACGTTTGTGTGTGTGTGTGTG 60.070 47.619 0.00 0.00 0.00 3.82
550 569 1.231221 ACGTTTGTGTGTGTGTGTGT 58.769 45.000 0.00 0.00 0.00 3.72
551 570 3.308595 AGATACGTTTGTGTGTGTGTGTG 59.691 43.478 0.00 0.00 0.00 3.82
552 571 3.527533 AGATACGTTTGTGTGTGTGTGT 58.472 40.909 0.00 0.00 0.00 3.72
553 572 4.270084 AGAAGATACGTTTGTGTGTGTGTG 59.730 41.667 0.00 0.00 0.00 3.82
554 573 4.439057 AGAAGATACGTTTGTGTGTGTGT 58.561 39.130 0.00 0.00 0.00 3.72
555 574 4.745125 AGAGAAGATACGTTTGTGTGTGTG 59.255 41.667 0.00 0.00 0.00 3.82
556 575 4.745125 CAGAGAAGATACGTTTGTGTGTGT 59.255 41.667 0.00 0.00 0.00 3.72
557 576 4.982295 TCAGAGAAGATACGTTTGTGTGTG 59.018 41.667 0.00 0.00 0.00 3.82
624 643 7.938140 AATAGTGCATGTTGGTTACTGTAAT 57.062 32.000 3.23 0.00 0.00 1.89
683 702 1.798223 CACTGCGAACCGATCTTGAAA 59.202 47.619 0.00 0.00 0.00 2.69
684 703 1.428448 CACTGCGAACCGATCTTGAA 58.572 50.000 0.00 0.00 0.00 2.69
860 879 4.036852 TCATCTCATCTACTGCTTACCGTG 59.963 45.833 0.00 0.00 0.00 4.94
918 937 3.409026 AATCGCAGGAGAGAACAAAGT 57.591 42.857 0.00 0.00 0.00 2.66
919 938 4.756084 AAAATCGCAGGAGAGAACAAAG 57.244 40.909 0.00 0.00 0.00 2.77
920 939 4.261572 CCAAAAATCGCAGGAGAGAACAAA 60.262 41.667 0.00 0.00 0.00 2.83
921 940 3.253188 CCAAAAATCGCAGGAGAGAACAA 59.747 43.478 0.00 0.00 0.00 2.83
941 960 4.583073 TGAGCTAGTTAATCGATACAGCCA 59.417 41.667 0.00 4.68 0.00 4.75
962 981 3.727726 TCTGAAAATCAGCAACGAGTGA 58.272 40.909 2.48 0.00 43.95 3.41
1062 1081 1.457346 CATTGCTCCAGGTTGAGTCC 58.543 55.000 0.00 0.00 34.74 3.85
1119 1138 0.447801 CTGTGCGCTTACCCATTGTC 59.552 55.000 9.73 0.00 0.00 3.18
1409 1428 2.813908 GGGAGTGCGTAGTTGGCG 60.814 66.667 0.00 0.00 0.00 5.69
1551 1570 2.285834 GCTTAAGTCACCGATGCGAATG 60.286 50.000 4.02 0.00 0.00 2.67
1552 1571 1.933853 GCTTAAGTCACCGATGCGAAT 59.066 47.619 4.02 0.00 0.00 3.34
1553 1572 1.067142 AGCTTAAGTCACCGATGCGAA 60.067 47.619 4.02 0.00 0.00 4.70
1554 1573 0.530744 AGCTTAAGTCACCGATGCGA 59.469 50.000 4.02 0.00 0.00 5.10
1555 1574 0.924090 GAGCTTAAGTCACCGATGCG 59.076 55.000 4.02 0.00 0.00 4.73
1556 1575 2.301577 AGAGCTTAAGTCACCGATGC 57.698 50.000 4.02 0.00 0.00 3.91
1569 1588 1.446272 GGCAGACGCGTTAGAGCTT 60.446 57.895 15.53 0.00 39.92 3.74
1584 1603 4.357947 GAGACGCACTGACGGGCA 62.358 66.667 0.00 0.00 37.37 5.36
1588 1607 1.967597 TAGCTCGAGACGCACTGACG 61.968 60.000 18.75 0.00 39.50 4.35
1624 1643 0.548989 ACACCACCCTACAAAGTGCA 59.451 50.000 0.00 0.00 32.48 4.57
1920 1939 1.378911 TAGAACTGGCTACCGGCGA 60.379 57.895 9.30 0.00 42.94 5.54
1980 2003 4.593157 GCTGACACTCTACACGAAGATAG 58.407 47.826 0.00 0.00 0.00 2.08
1981 2004 3.063588 CGCTGACACTCTACACGAAGATA 59.936 47.826 0.00 0.00 0.00 1.98
1982 2005 2.159503 CGCTGACACTCTACACGAAGAT 60.160 50.000 0.00 0.00 0.00 2.40
2077 2100 1.268625 GAGCAAAAACGGTAACCCCAG 59.731 52.381 0.00 0.00 0.00 4.45
2310 2334 4.082125 CCAAGCAAAGGTAGAACAATCCT 58.918 43.478 0.00 0.00 0.00 3.24
2409 2441 5.344128 GCTTGTGTTAGCTGAATGACATTTG 59.656 40.000 1.39 0.37 38.15 2.32
2495 2527 0.809385 CACACGTCATCCTACGAGGT 59.191 55.000 3.10 0.00 45.68 3.85
2502 2534 1.757118 CATACCTCCACACGTCATCCT 59.243 52.381 0.00 0.00 0.00 3.24
2506 2538 1.919240 AGACATACCTCCACACGTCA 58.081 50.000 0.00 0.00 0.00 4.35
2508 2540 2.244695 TGAAGACATACCTCCACACGT 58.755 47.619 0.00 0.00 0.00 4.49
2520 2552 2.467838 CACGAGATGCGATGAAGACAT 58.532 47.619 0.00 0.00 44.57 3.06
2532 2564 0.595053 CGACCGAATCCCACGAGATG 60.595 60.000 0.00 0.00 0.00 2.90
2537 2569 1.299926 GATCCGACCGAATCCCACG 60.300 63.158 0.00 0.00 0.00 4.94
2555 2613 1.461317 CGCATACGAACGACGACTGG 61.461 60.000 0.00 0.00 45.77 4.00
2609 2673 1.743958 ACCGTCGTCGATGAAGAGAAT 59.256 47.619 20.29 2.24 39.71 2.40
2627 2691 0.536006 AGCTCACCAGAACAGCAACC 60.536 55.000 0.00 0.00 35.46 3.77
2664 2728 2.294791 AGACAGTCGAGAAGTCTTGTGG 59.705 50.000 8.15 0.00 39.45 4.17
2668 2732 6.465948 TCTTACTAGACAGTCGAGAAGTCTT 58.534 40.000 16.88 5.75 42.25 3.01
2676 2740 4.142227 GGGCAAATCTTACTAGACAGTCGA 60.142 45.833 0.00 0.00 36.14 4.20
2682 2746 2.158943 AGCCGGGCAAATCTTACTAGAC 60.159 50.000 23.09 0.00 31.99 2.59
2687 2751 1.017387 CAGAGCCGGGCAAATCTTAC 58.983 55.000 23.09 2.00 0.00 2.34
2705 2775 2.354704 CGTCATTGCCTCTCCCTTAACA 60.355 50.000 0.00 0.00 0.00 2.41
2753 2823 7.049133 GGTTTTGGTGGTTAAAGGTTACAATT 58.951 34.615 0.00 0.00 0.00 2.32
2760 2830 4.098155 AGTTGGTTTTGGTGGTTAAAGGT 58.902 39.130 0.00 0.00 0.00 3.50
2765 2835 5.941555 ATGAAAGTTGGTTTTGGTGGTTA 57.058 34.783 0.00 0.00 0.00 2.85
2906 2977 8.533569 TCCAGTCTTTTCTTTACCAATCTTTT 57.466 30.769 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.