Multiple sequence alignment - TraesCS5D01G388200

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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 TraesCS5D01G388200 chr5D 100.000 1879 0 0 1 1879 457681754 457679876 0.000000e+00 3470.0
1 TraesCS5D01G388200 chr5D 100.000 763 0 0 2083 2845 457679672 457678910 0.000000e+00 1410.0
2 TraesCS5D01G388200 chr5D 82.667 225 24 8 1465 1689 66668839 66668630 4.840000e-43 185.0
3 TraesCS5D01G388200 chr5D 73.661 224 47 9 1465 1688 498404342 498404131 3.040000e-10 76.8
4 TraesCS5D01G388200 chr5B 92.188 1920 58 40 1 1877 559780079 559778209 0.000000e+00 2630.0
5 TraesCS5D01G388200 chr5B 93.323 629 37 5 2083 2710 559778183 559777559 0.000000e+00 924.0
6 TraesCS5D01G388200 chr5B 81.333 225 27 8 1465 1689 64419321 64419530 4.870000e-38 169.0
7 TraesCS5D01G388200 chr5B 84.000 75 11 1 1614 1688 617711878 617711805 1.410000e-08 71.3
8 TraesCS5D01G388200 chr5A 87.348 1976 81 51 1 1879 575614406 575612503 0.000000e+00 2108.0
9 TraesCS5D01G388200 chr5A 94.269 349 8 3 2083 2427 575612484 575612144 9.030000e-145 523.0
10 TraesCS5D01G388200 chr5A 80.720 389 50 16 2451 2824 575612151 575611773 2.160000e-71 279.0
11 TraesCS5D01G388200 chr5A 82.667 225 24 8 1465 1689 57563479 57563688 4.840000e-43 185.0


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 TraesCS5D01G388200 chr5D 457678910 457681754 2844 True 2440 3470 100.000000 1 2845 2 chr5D.!!$R3 2844
1 TraesCS5D01G388200 chr5B 559777559 559780079 2520 True 1777 2630 92.755500 1 2710 2 chr5B.!!$R2 2709
2 TraesCS5D01G388200 chr5A 575611773 575614406 2633 True 970 2108 87.445667 1 2824 3 chr5A.!!$R1 2823

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
244 275 0.379316 GAACTGAAACCCGTTGCGTT 59.621 50.000 0.0 0.0 0.0 4.84 F
985 1073 1.133253 CACCAAGCATCTTCGCACG 59.867 57.895 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1354 0.696501 TAAGAACCCTGGCCTTGGAC 59.303 55.0 16.85 10.35 0.0 4.02 R
2450 2602 0.250124 CTGTCCACCGCACCTTAACA 60.250 55.0 0.00 0.00 0.0 2.41 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
80 84 7.505585 TCATATATCATCGCTCCATACCATACA 59.494 37.037 0.00 0.00 0.00 2.29
244 275 0.379316 GAACTGAAACCCGTTGCGTT 59.621 50.000 0.00 0.00 0.00 4.84
248 279 1.942223 GAAACCCGTTGCGTTGTGC 60.942 57.895 0.00 0.00 46.70 4.57
266 312 2.187946 GATGGACGGGGCAGACAG 59.812 66.667 0.00 0.00 0.00 3.51
306 352 2.224670 TGCCCCACGGAATACAATATCC 60.225 50.000 0.00 0.00 0.00 2.59
468 519 6.012745 TCCATCAGCATCTATCAAGCTAGTA 58.987 40.000 0.00 0.00 36.73 1.82
470 521 7.836183 TCCATCAGCATCTATCAAGCTAGTATA 59.164 37.037 0.00 0.00 36.73 1.47
471 522 8.136800 CCATCAGCATCTATCAAGCTAGTATAG 58.863 40.741 0.00 0.00 43.09 1.31
472 523 8.685427 CATCAGCATCTATCAAGCTAGTATAGT 58.315 37.037 8.80 0.00 41.93 2.12
473 524 9.913310 ATCAGCATCTATCAAGCTAGTATAGTA 57.087 33.333 8.80 0.00 41.93 1.82
474 525 9.913310 TCAGCATCTATCAAGCTAGTATAGTAT 57.087 33.333 8.80 0.00 41.93 2.12
695 761 2.359975 GCCTAGCCACACCACACC 60.360 66.667 0.00 0.00 0.00 4.16
727 793 3.456885 CGCTGCGCTCGATCGATC 61.457 66.667 19.78 15.68 0.00 3.69
774 849 2.103538 CATTGTCAGCCCATGCGC 59.896 61.111 0.00 0.00 44.33 6.09
775 850 3.511595 ATTGTCAGCCCATGCGCG 61.512 61.111 0.00 0.00 44.33 6.86
814 889 1.209275 CTTACTCGCGATGCCCTTCG 61.209 60.000 10.36 0.00 41.99 3.79
892 980 2.490115 ACACATCGTCTTCTCCTCTCAC 59.510 50.000 0.00 0.00 0.00 3.51
960 1048 2.143122 CTTGCAAAGTTCGCTAGACCA 58.857 47.619 0.00 0.00 39.70 4.02
961 1049 2.248280 TGCAAAGTTCGCTAGACCAA 57.752 45.000 0.00 0.00 0.00 3.67
970 1058 1.639298 CGCTAGACCAAGCAAGCACC 61.639 60.000 0.00 0.00 42.91 5.01
972 1060 1.896220 CTAGACCAAGCAAGCACCAA 58.104 50.000 0.00 0.00 0.00 3.67
983 1071 3.266964 GCACCAAGCATCTTCGCA 58.733 55.556 0.00 0.00 44.79 5.10
985 1073 1.133253 CACCAAGCATCTTCGCACG 59.867 57.895 0.00 0.00 0.00 5.34
986 1074 1.301716 ACCAAGCATCTTCGCACGT 60.302 52.632 0.00 0.00 0.00 4.49
1118 1206 4.154347 GGCGACTCCCAGAGGCAG 62.154 72.222 0.00 0.00 37.60 4.85
1266 1354 7.044798 CACTACCTTATTCTTCTTCCTCCAAG 58.955 42.308 0.00 0.00 0.00 3.61
1297 1385 3.194116 CAGGGTTCTTACATGCATGCTTT 59.806 43.478 26.53 10.06 0.00 3.51
1298 1386 3.445096 AGGGTTCTTACATGCATGCTTTC 59.555 43.478 26.53 11.73 0.00 2.62
1350 1438 4.487412 CCGCCGGTGAGGTCGTAC 62.487 72.222 18.79 0.00 43.70 3.67
1351 1439 4.487412 CGCCGGTGAGGTCGTACC 62.487 72.222 10.20 0.00 43.70 3.34
1355 1443 3.685435 GGTGAGGTCGTACCGGAA 58.315 61.111 9.46 0.00 44.90 4.30
1356 1444 1.509923 GGTGAGGTCGTACCGGAAG 59.490 63.158 9.46 0.00 44.90 3.46
1357 1445 0.962356 GGTGAGGTCGTACCGGAAGA 60.962 60.000 9.46 0.37 44.90 2.87
1401 1489 0.250467 AGAGCAAGGCGAAGAAAGCA 60.250 50.000 0.00 0.00 36.08 3.91
1476 1564 1.270358 GGCTCCTTCGTCAAAGTGAGT 60.270 52.381 0.00 0.00 35.95 3.41
1497 1585 2.517875 GACGGAGCGCCCTACCTA 60.518 66.667 2.29 0.00 0.00 3.08
1671 1762 1.137872 GACCTCATGCTTGTCGGAGAT 59.862 52.381 14.33 0.00 40.67 2.75
1689 1780 2.093973 AGATGTGCCCTTCGAGTAAGTG 60.094 50.000 0.00 0.00 32.89 3.16
1752 1869 5.414360 TGTGAAGCAGTGACTTATGATCTC 58.586 41.667 0.00 0.00 0.00 2.75
1852 1969 5.184671 GCCTGGGATCCAAATAATGAAGATC 59.815 44.000 15.23 0.00 30.80 2.75
1861 1978 7.341030 TCCAAATAATGAAGATCTGAGAAGCA 58.659 34.615 0.00 0.00 0.00 3.91
2341 2458 2.706952 CTTCCGGTTTCCCCTTGGCA 62.707 60.000 0.00 0.00 0.00 4.92
2366 2487 6.804677 TGTGCTTTTGTATTCAAGTTGTCAT 58.195 32.000 2.11 0.00 34.88 3.06
2385 2506 7.755582 TGTCATAGTCACTTTATCATCAACG 57.244 36.000 0.00 0.00 0.00 4.10
2387 2508 6.255670 GTCATAGTCACTTTATCATCAACGCA 59.744 38.462 0.00 0.00 0.00 5.24
2427 2579 2.293122 TGTGAGCACCACTTGTTTATGC 59.707 45.455 10.03 0.00 45.86 3.14
2428 2580 1.535028 TGAGCACCACTTGTTTATGCG 59.465 47.619 0.00 0.00 41.23 4.73
2429 2581 1.535462 GAGCACCACTTGTTTATGCGT 59.465 47.619 0.00 0.00 41.23 5.24
2430 2582 1.953686 AGCACCACTTGTTTATGCGTT 59.046 42.857 0.00 0.00 41.23 4.84
2431 2583 2.031157 AGCACCACTTGTTTATGCGTTC 60.031 45.455 0.00 0.00 41.23 3.95
2432 2584 2.031157 GCACCACTTGTTTATGCGTTCT 60.031 45.455 0.00 0.00 0.00 3.01
2433 2585 3.810373 CACCACTTGTTTATGCGTTCTC 58.190 45.455 0.00 0.00 0.00 2.87
2434 2586 3.249799 CACCACTTGTTTATGCGTTCTCA 59.750 43.478 0.00 0.00 0.00 3.27
2435 2587 3.498397 ACCACTTGTTTATGCGTTCTCAG 59.502 43.478 0.00 0.00 0.00 3.35
2436 2588 3.498397 CCACTTGTTTATGCGTTCTCAGT 59.502 43.478 0.00 0.00 0.00 3.41
2437 2589 4.024048 CCACTTGTTTATGCGTTCTCAGTT 60.024 41.667 0.00 0.00 0.00 3.16
2438 2590 5.140177 CACTTGTTTATGCGTTCTCAGTTC 58.860 41.667 0.00 0.00 0.00 3.01
2439 2591 4.084537 ACTTGTTTATGCGTTCTCAGTTCG 60.085 41.667 0.00 0.00 0.00 3.95
2440 2592 3.644823 TGTTTATGCGTTCTCAGTTCGA 58.355 40.909 0.00 0.00 0.00 3.71
2441 2593 3.673338 TGTTTATGCGTTCTCAGTTCGAG 59.327 43.478 0.00 0.00 43.80 4.04
2442 2594 3.570926 TTATGCGTTCTCAGTTCGAGT 57.429 42.857 0.00 0.00 42.88 4.18
2443 2595 1.983972 ATGCGTTCTCAGTTCGAGTC 58.016 50.000 0.00 0.00 42.88 3.36
2444 2596 0.039437 TGCGTTCTCAGTTCGAGTCC 60.039 55.000 0.00 0.00 42.88 3.85
2445 2597 0.039437 GCGTTCTCAGTTCGAGTCCA 60.039 55.000 0.00 0.00 42.88 4.02
2446 2598 1.602165 GCGTTCTCAGTTCGAGTCCAA 60.602 52.381 0.00 0.00 42.88 3.53
2447 2599 2.927014 GCGTTCTCAGTTCGAGTCCAAT 60.927 50.000 0.00 0.00 42.88 3.16
2448 2600 2.663602 CGTTCTCAGTTCGAGTCCAATG 59.336 50.000 0.00 0.00 42.88 2.82
2449 2601 3.611766 CGTTCTCAGTTCGAGTCCAATGA 60.612 47.826 0.00 0.00 42.88 2.57
2450 2602 4.499183 GTTCTCAGTTCGAGTCCAATGAT 58.501 43.478 0.00 0.00 42.88 2.45
2451 2603 4.115401 TCTCAGTTCGAGTCCAATGATG 57.885 45.455 0.00 0.00 42.88 3.07
2452 2604 3.511540 TCTCAGTTCGAGTCCAATGATGT 59.488 43.478 0.00 0.00 42.88 3.06
2453 2605 4.021104 TCTCAGTTCGAGTCCAATGATGTT 60.021 41.667 0.00 0.00 42.88 2.71
2454 2606 5.185056 TCTCAGTTCGAGTCCAATGATGTTA 59.815 40.000 0.00 0.00 42.88 2.41
2455 2607 5.789521 TCAGTTCGAGTCCAATGATGTTAA 58.210 37.500 0.00 0.00 0.00 2.01
2456 2608 5.869344 TCAGTTCGAGTCCAATGATGTTAAG 59.131 40.000 0.00 0.00 0.00 1.85
2457 2609 5.063944 CAGTTCGAGTCCAATGATGTTAAGG 59.936 44.000 0.00 0.00 0.00 2.69
2472 2624 2.107041 TAAGGTGCGGTGGACAGTGG 62.107 60.000 0.00 0.00 0.00 4.00
2476 2628 0.533491 GTGCGGTGGACAGTGGTATA 59.467 55.000 0.00 0.00 0.00 1.47
2513 2665 5.443693 GCATTTCGACAATGTTTTGATCTGC 60.444 40.000 16.39 0.00 36.64 4.26
2517 2669 4.994217 TCGACAATGTTTTGATCTGCTGTA 59.006 37.500 0.00 0.00 36.64 2.74
2520 2672 7.495606 TCGACAATGTTTTGATCTGCTGTATAT 59.504 33.333 0.00 0.00 36.64 0.86
2579 2738 3.669023 GCTAAGACTGCAAACACAGATGC 60.669 47.826 0.00 0.00 40.25 3.91
2587 2746 4.799419 GCAAACACAGATGCAAAACATT 57.201 36.364 0.00 0.00 39.84 2.71
2628 2788 4.567971 TGCAACATTTTAGGGCATCTTTG 58.432 39.130 0.00 0.00 0.00 2.77
2641 2801 4.498682 GGGCATCTTTGATCGAAGGAATTG 60.499 45.833 20.44 14.14 0.00 2.32
2657 2817 7.701924 CGAAGGAATTGCAAACATATTGTGTAT 59.298 33.333 1.71 0.00 41.14 2.29
2720 2886 7.112779 AGAAACCTTTTGGATATCACCTACAG 58.887 38.462 4.83 0.00 44.07 2.74
2722 2888 6.831664 ACCTTTTGGATATCACCTACAGAT 57.168 37.500 4.83 0.00 44.07 2.90
2744 2910 8.865090 CAGATTGATATGTAGGACTAGAAACCT 58.135 37.037 0.00 4.98 39.95 3.50
2747 2913 8.783660 TTGATATGTAGGACTAGAAACCTGAT 57.216 34.615 14.54 10.25 37.68 2.90
2748 2914 9.877222 TTGATATGTAGGACTAGAAACCTGATA 57.123 33.333 14.54 11.48 37.68 2.15
2749 2915 9.298250 TGATATGTAGGACTAGAAACCTGATAC 57.702 37.037 14.54 8.17 37.68 2.24
2750 2916 6.636562 ATGTAGGACTAGAAACCTGATACG 57.363 41.667 14.54 0.00 37.68 3.06
2751 2917 5.503927 TGTAGGACTAGAAACCTGATACGT 58.496 41.667 14.54 0.00 37.68 3.57
2757 2923 6.262720 GGACTAGAAACCTGATACGTAGATGT 59.737 42.308 0.08 0.00 0.00 3.06
2763 2929 7.974501 AGAAACCTGATACGTAGATGTTACTTG 59.025 37.037 0.08 0.00 0.00 3.16
2768 2934 6.263344 TGATACGTAGATGTTACTTGTGAGC 58.737 40.000 0.08 0.00 0.00 4.26
2772 2938 3.059352 AGATGTTACTTGTGAGCCACC 57.941 47.619 3.33 0.00 32.73 4.61
2775 2941 2.047061 TGTTACTTGTGAGCCACCTCT 58.953 47.619 3.33 0.00 38.93 3.69
2792 2958 3.005897 ACCTCTCATCCGATACCAAATCG 59.994 47.826 0.51 0.51 40.86 3.34
2798 2964 6.765989 TCTCATCCGATACCAAATCGAAATTT 59.234 34.615 8.86 0.00 43.59 1.82
2804 2970 6.636850 CCGATACCAAATCGAAATTTCCATTC 59.363 38.462 12.54 0.00 43.59 2.67
2824 2990 7.176690 TCCATTCGAGAGTTCATATGCTATGTA 59.823 37.037 0.00 0.00 0.00 2.29
2825 2991 7.814587 CCATTCGAGAGTTCATATGCTATGTAA 59.185 37.037 0.00 0.00 0.00 2.41
2826 2992 9.196552 CATTCGAGAGTTCATATGCTATGTAAA 57.803 33.333 0.00 0.00 0.00 2.01
2827 2993 9.764363 ATTCGAGAGTTCATATGCTATGTAAAA 57.236 29.630 0.00 0.00 0.00 1.52
2828 2994 9.594478 TTCGAGAGTTCATATGCTATGTAAAAA 57.406 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 64 4.763073 CATGTATGGTATGGAGCGATGAT 58.237 43.478 0.00 0.00 0.00 2.45
61 65 3.617288 GCATGTATGGTATGGAGCGATGA 60.617 47.826 0.00 0.00 0.00 2.92
80 84 0.178984 TGGGCCGATGAATCATGCAT 60.179 50.000 0.00 0.00 0.00 3.96
248 279 3.723235 CTGTCTGCCCCGTCCATCG 62.723 68.421 0.00 0.00 39.52 3.84
266 312 0.748005 ACATGGCATGTCTAACGGGC 60.748 55.000 26.78 0.00 39.92 6.13
374 425 0.036875 TCGAGAGCTGGACTGACTGA 59.963 55.000 0.00 0.00 0.00 3.41
375 426 1.102154 ATCGAGAGCTGGACTGACTG 58.898 55.000 0.00 0.00 0.00 3.51
376 427 1.476085 CAATCGAGAGCTGGACTGACT 59.524 52.381 0.00 0.00 0.00 3.41
377 428 1.203523 ACAATCGAGAGCTGGACTGAC 59.796 52.381 0.00 0.00 0.00 3.51
474 525 4.712238 TCGGCCTGGCTGTACGATAGTA 62.712 54.545 25.92 1.40 41.59 1.82
476 527 1.007271 CGGCCTGGCTGTACGATAG 60.007 63.158 19.55 0.00 46.19 2.08
477 528 0.826256 ATCGGCCTGGCTGTACGATA 60.826 55.000 25.92 7.09 41.83 2.92
523 574 2.635338 CATGTGCCGATGCCGATG 59.365 61.111 0.00 0.00 38.22 3.84
524 575 2.592574 CCATGTGCCGATGCCGAT 60.593 61.111 0.00 0.00 38.22 4.18
725 791 0.952280 ACGTAGGTGCATCGATCGAT 59.048 50.000 24.60 24.60 34.81 3.59
726 792 0.028902 CACGTAGGTGCATCGATCGA 59.971 55.000 21.86 21.86 37.35 3.59
727 793 2.495633 CACGTAGGTGCATCGATCG 58.504 57.895 9.36 9.36 37.35 3.69
814 889 0.313987 GCCCATGTTTTATAGGCGGC 59.686 55.000 0.00 0.00 33.18 6.53
909 997 2.195922 TGCGATGTGAATGACGAGATG 58.804 47.619 0.00 0.00 0.00 2.90
952 1040 0.606401 TGGTGCTTGCTTGGTCTAGC 60.606 55.000 0.00 0.00 41.59 3.42
953 1041 1.808945 CTTGGTGCTTGCTTGGTCTAG 59.191 52.381 0.00 0.00 0.00 2.43
954 1042 1.896220 CTTGGTGCTTGCTTGGTCTA 58.104 50.000 0.00 0.00 0.00 2.59
955 1043 1.458639 GCTTGGTGCTTGCTTGGTCT 61.459 55.000 0.00 0.00 38.95 3.85
956 1044 1.006922 GCTTGGTGCTTGCTTGGTC 60.007 57.895 0.00 0.00 38.95 4.02
957 1045 1.117142 ATGCTTGGTGCTTGCTTGGT 61.117 50.000 0.00 0.00 43.37 3.67
958 1046 0.389426 GATGCTTGGTGCTTGCTTGG 60.389 55.000 0.00 0.00 43.37 3.61
960 1048 1.271656 GAAGATGCTTGGTGCTTGCTT 59.728 47.619 0.00 0.00 43.37 3.91
961 1049 0.886563 GAAGATGCTTGGTGCTTGCT 59.113 50.000 0.00 0.00 43.37 3.91
970 1058 0.023732 CGTACGTGCGAAGATGCTTG 59.976 55.000 21.98 0.00 35.36 4.01
972 1060 0.797249 GACGTACGTGCGAAGATGCT 60.797 55.000 32.30 7.99 35.36 3.79
975 1063 0.455633 GTGGACGTACGTGCGAAGAT 60.456 55.000 32.30 10.04 39.39 2.40
976 1064 1.081906 GTGGACGTACGTGCGAAGA 60.082 57.895 32.30 13.80 39.39 2.87
978 1066 1.370778 CAGTGGACGTACGTGCGAA 60.371 57.895 32.30 14.87 39.39 4.70
981 1069 0.598158 TTTCCAGTGGACGTACGTGC 60.598 55.000 30.07 30.07 36.97 5.34
982 1070 1.724623 CATTTCCAGTGGACGTACGTG 59.275 52.381 28.16 10.90 0.00 4.49
983 1071 1.337447 CCATTTCCAGTGGACGTACGT 60.337 52.381 23.04 23.04 39.12 3.57
985 1073 2.754946 TCCATTTCCAGTGGACGTAC 57.245 50.000 12.69 0.00 40.72 3.67
986 1074 2.614481 GCTTCCATTTCCAGTGGACGTA 60.614 50.000 12.69 0.27 45.05 3.57
1266 1354 0.696501 TAAGAACCCTGGCCTTGGAC 59.303 55.000 16.85 10.35 0.00 4.02
1297 1385 1.599606 GCCCTGCGAGAGTTGAGAGA 61.600 60.000 0.00 0.00 0.00 3.10
1298 1386 1.153667 GCCCTGCGAGAGTTGAGAG 60.154 63.158 0.00 0.00 0.00 3.20
1346 1434 0.802607 GAAGCAGCTCTTCCGGTACG 60.803 60.000 0.00 0.00 44.22 3.67
1347 1435 3.052181 GAAGCAGCTCTTCCGGTAC 57.948 57.895 0.00 0.00 44.22 3.34
1354 1442 2.046507 CGCCTGGAAGCAGCTCTT 60.047 61.111 0.00 0.00 37.83 2.85
1355 1443 4.093291 CCGCCTGGAAGCAGCTCT 62.093 66.667 0.00 0.00 37.49 4.09
1401 1489 3.630013 TTGCTGCTGGCCTCGTCT 61.630 61.111 3.32 0.00 40.92 4.18
1497 1585 1.938585 TCCTCATGTCGACCTTCCTT 58.061 50.000 14.12 0.00 0.00 3.36
1671 1762 1.045407 ACACTTACTCGAAGGGCACA 58.955 50.000 0.00 0.00 43.02 4.57
1752 1869 2.529151 ACTGCAAAAACGCAAGAACAG 58.471 42.857 0.00 0.00 42.45 3.16
1852 1969 6.149640 CCCATGATATCATCTTTGCTTCTCAG 59.850 42.308 15.49 0.09 33.61 3.35
2341 2458 6.804677 TGACAACTTGAATACAAAAGCACAT 58.195 32.000 0.00 0.00 35.49 3.21
2366 2487 7.609760 AATTGCGTTGATGATAAAGTGACTA 57.390 32.000 0.00 0.00 0.00 2.59
2385 2506 6.036517 TCACAAACAACAACCAACATAATTGC 59.963 34.615 0.00 0.00 0.00 3.56
2387 2508 6.257630 GCTCACAAACAACAACCAACATAATT 59.742 34.615 0.00 0.00 0.00 1.40
2432 2584 3.961480 ACATCATTGGACTCGAACTGA 57.039 42.857 0.00 0.00 0.00 3.41
2433 2585 5.063944 CCTTAACATCATTGGACTCGAACTG 59.936 44.000 0.00 0.00 0.00 3.16
2434 2586 5.178797 CCTTAACATCATTGGACTCGAACT 58.821 41.667 0.00 0.00 0.00 3.01
2435 2587 4.935808 ACCTTAACATCATTGGACTCGAAC 59.064 41.667 0.00 0.00 0.00 3.95
2436 2588 4.935205 CACCTTAACATCATTGGACTCGAA 59.065 41.667 0.00 0.00 0.00 3.71
2437 2589 4.503910 CACCTTAACATCATTGGACTCGA 58.496 43.478 0.00 0.00 0.00 4.04
2438 2590 3.063997 GCACCTTAACATCATTGGACTCG 59.936 47.826 0.00 0.00 0.00 4.18
2439 2591 3.063997 CGCACCTTAACATCATTGGACTC 59.936 47.826 0.00 0.00 0.00 3.36
2440 2592 3.009723 CGCACCTTAACATCATTGGACT 58.990 45.455 0.00 0.00 0.00 3.85
2441 2593 2.097466 CCGCACCTTAACATCATTGGAC 59.903 50.000 0.00 0.00 0.00 4.02
2442 2594 2.290641 ACCGCACCTTAACATCATTGGA 60.291 45.455 0.00 0.00 0.00 3.53
2443 2595 2.091541 ACCGCACCTTAACATCATTGG 58.908 47.619 0.00 0.00 0.00 3.16
2444 2596 2.159393 CCACCGCACCTTAACATCATTG 60.159 50.000 0.00 0.00 0.00 2.82
2445 2597 2.091541 CCACCGCACCTTAACATCATT 58.908 47.619 0.00 0.00 0.00 2.57
2446 2598 1.280710 TCCACCGCACCTTAACATCAT 59.719 47.619 0.00 0.00 0.00 2.45
2447 2599 0.687920 TCCACCGCACCTTAACATCA 59.312 50.000 0.00 0.00 0.00 3.07
2448 2600 1.084289 GTCCACCGCACCTTAACATC 58.916 55.000 0.00 0.00 0.00 3.06
2449 2601 0.398696 TGTCCACCGCACCTTAACAT 59.601 50.000 0.00 0.00 0.00 2.71
2450 2602 0.250124 CTGTCCACCGCACCTTAACA 60.250 55.000 0.00 0.00 0.00 2.41
2451 2603 0.250166 ACTGTCCACCGCACCTTAAC 60.250 55.000 0.00 0.00 0.00 2.01
2452 2604 0.250124 CACTGTCCACCGCACCTTAA 60.250 55.000 0.00 0.00 0.00 1.85
2453 2605 1.369692 CACTGTCCACCGCACCTTA 59.630 57.895 0.00 0.00 0.00 2.69
2454 2606 2.111043 CACTGTCCACCGCACCTT 59.889 61.111 0.00 0.00 0.00 3.50
2455 2607 3.941188 CCACTGTCCACCGCACCT 61.941 66.667 0.00 0.00 0.00 4.00
2456 2608 2.180159 ATACCACTGTCCACCGCACC 62.180 60.000 0.00 0.00 0.00 5.01
2457 2609 0.533491 TATACCACTGTCCACCGCAC 59.467 55.000 0.00 0.00 0.00 5.34
2472 2624 2.242769 TGCTCGATCGTCGCATATAC 57.757 50.000 23.62 4.22 40.21 1.47
2476 2628 0.855349 GAAATGCTCGATCGTCGCAT 59.145 50.000 28.65 28.65 45.50 4.73
2501 2653 7.334858 TGTACCATATACAGCAGATCAAAACA 58.665 34.615 0.00 0.00 0.00 2.83
2506 2658 5.365314 TGGTTGTACCATATACAGCAGATCA 59.635 40.000 0.00 0.00 44.79 2.92
2582 2741 7.224557 GCAGTGATACAAAAGAAACCAAATGTT 59.775 33.333 0.00 0.00 39.43 2.71
2587 2746 5.843673 TGCAGTGATACAAAAGAAACCAA 57.156 34.783 0.00 0.00 0.00 3.67
2606 2765 4.282957 TCAAAGATGCCCTAAAATGTTGCA 59.717 37.500 0.00 0.00 36.23 4.08
2628 2788 6.974622 ACAATATGTTTGCAATTCCTTCGATC 59.025 34.615 0.00 0.00 0.00 3.69
2690 2850 7.780271 AGGTGATATCCAAAAGGTTTCTTATCC 59.220 37.037 0.00 0.00 32.01 2.59
2695 2855 7.027874 TGTAGGTGATATCCAAAAGGTTTCT 57.972 36.000 0.00 0.00 0.00 2.52
2720 2886 8.861086 TCAGGTTTCTAGTCCTACATATCAATC 58.139 37.037 4.24 0.00 32.26 2.67
2722 2888 8.783660 ATCAGGTTTCTAGTCCTACATATCAA 57.216 34.615 4.24 0.00 32.26 2.57
2735 2901 8.838365 AGTAACATCTACGTATCAGGTTTCTAG 58.162 37.037 9.24 0.00 0.00 2.43
2744 2910 6.263344 GCTCACAAGTAACATCTACGTATCA 58.737 40.000 0.00 0.00 0.00 2.15
2747 2913 4.460034 TGGCTCACAAGTAACATCTACGTA 59.540 41.667 0.00 0.00 0.00 3.57
2748 2914 3.257375 TGGCTCACAAGTAACATCTACGT 59.743 43.478 0.00 0.00 0.00 3.57
2749 2915 3.612860 GTGGCTCACAAGTAACATCTACG 59.387 47.826 1.01 0.00 34.08 3.51
2750 2916 3.933332 GGTGGCTCACAAGTAACATCTAC 59.067 47.826 7.49 0.00 35.86 2.59
2751 2917 3.838317 AGGTGGCTCACAAGTAACATCTA 59.162 43.478 7.49 0.00 35.86 1.98
2757 2923 2.325484 TGAGAGGTGGCTCACAAGTAA 58.675 47.619 7.49 0.00 39.84 2.24
2763 2929 1.142748 CGGATGAGAGGTGGCTCAC 59.857 63.158 0.00 0.00 46.72 3.51
2768 2934 1.704641 TGGTATCGGATGAGAGGTGG 58.295 55.000 0.00 0.00 0.00 4.61
2772 2938 4.505313 TCGATTTGGTATCGGATGAGAG 57.495 45.455 0.00 0.00 41.45 3.20
2775 2941 6.017440 GGAAATTTCGATTTGGTATCGGATGA 60.017 38.462 11.95 0.00 41.45 2.92
2792 2958 7.589221 GCATATGAACTCTCGAATGGAAATTTC 59.411 37.037 9.83 9.83 0.00 2.17
2798 2964 4.944619 AGCATATGAACTCTCGAATGGA 57.055 40.909 6.97 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.