Multiple sequence alignment - TraesCS5D01G271200

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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 TraesCS5D01G271200 chr5D 100.000 3407 0 0 1 3407 374705796 374709202 0.000000e+00 6292.0
1 TraesCS5D01G271200 chr5A 95.677 1573 51 3 969 2534 476413082 476414644 0.000000e+00 2512.0
2 TraesCS5D01G271200 chr5A 88.916 415 30 7 1 406 476410095 476410502 6.570000e-137 497.0
3 TraesCS5D01G271200 chr5A 84.868 304 22 10 526 823 476410787 476411072 5.560000e-73 285.0
4 TraesCS5D01G271200 chr5A 86.508 126 7 5 852 977 476411602 476411717 2.760000e-26 130.0
5 TraesCS5D01G271200 chr5B 93.357 1656 65 20 825 2455 447558151 447559786 0.000000e+00 2407.0
6 TraesCS5D01G271200 chr5B 91.489 470 31 6 1 464 447557195 447557661 3.710000e-179 638.0
7 TraesCS5D01G271200 chr5B 88.732 213 16 4 609 820 447557906 447558111 1.570000e-63 254.0
8 TraesCS5D01G271200 chr5B 94.382 89 3 1 2441 2529 447560654 447560740 5.930000e-28 135.0
9 TraesCS5D01G271200 chr3A 84.485 883 85 38 2532 3407 597230118 597229281 0.000000e+00 824.0
10 TraesCS5D01G271200 chr7D 88.382 680 34 26 2766 3407 22576015 22575343 0.000000e+00 776.0
11 TraesCS5D01G271200 chr7D 94.771 306 13 3 2530 2833 22576297 22575993 1.110000e-129 473.0
12 TraesCS5D01G271200 chr7D 81.602 462 82 2 1903 2361 210022305 210021844 2.480000e-101 379.0
13 TraesCS5D01G271200 chr7D 79.688 512 84 12 1138 1644 210023025 210022529 5.410000e-93 351.0
14 TraesCS5D01G271200 chr7A 85.016 634 43 26 2766 3397 131831715 131831132 6.290000e-167 597.0
15 TraesCS5D01G271200 chr7A 82.732 637 55 17 2766 3401 482766232 482765650 1.810000e-142 516.0
16 TraesCS5D01G271200 chr7A 81.474 475 85 2 1903 2374 222638540 222638066 1.480000e-103 387.0
17 TraesCS5D01G271200 chr7A 80.078 512 82 12 1138 1644 222639260 222638764 2.500000e-96 363.0
18 TraesCS5D01G271200 chr7A 87.948 307 30 6 2529 2833 482766557 482766256 4.180000e-94 355.0
19 TraesCS5D01G271200 chr7A 93.478 184 12 0 3216 3399 122745460 122745277 1.200000e-69 274.0
20 TraesCS5D01G271200 chr7B 80.632 475 71 14 1138 1606 191521111 191521570 7.000000e-92 348.0
21 TraesCS5D01G271200 chrUn 91.509 212 17 1 2925 3135 374337851 374338062 1.200000e-74 291.0
22 TraesCS5D01G271200 chrUn 91.509 212 17 1 2925 3135 382796177 382795966 1.200000e-74 291.0
23 TraesCS5D01G271200 chrUn 91.509 212 17 1 2925 3135 382885717 382885928 1.200000e-74 291.0
24 TraesCS5D01G271200 chrUn 91.509 212 17 1 2925 3135 458597883 458598094 1.200000e-74 291.0
25 TraesCS5D01G271200 chrUn 94.245 139 8 0 3266 3404 374338062 374338200 2.660000e-51 213.0
26 TraesCS5D01G271200 chrUn 93.662 142 9 0 3266 3407 382795966 382795825 2.660000e-51 213.0
27 TraesCS5D01G271200 chrUn 94.245 139 8 0 3266 3404 382885928 382886066 2.660000e-51 213.0
28 TraesCS5D01G271200 chrUn 94.245 139 8 0 3266 3404 458598094 458598232 2.660000e-51 213.0
29 TraesCS5D01G271200 chr2A 86.979 192 22 3 2530 2720 688579974 688579785 2.660000e-51 213.0
30 TraesCS5D01G271200 chr1A 84.000 175 22 6 2529 2700 111589231 111589402 2.720000e-36 163.0
31 TraesCS5D01G271200 chr1A 91.304 69 4 2 2530 2597 577822810 577822743 3.620000e-15 93.5
32 TraesCS5D01G271200 chr1D 89.873 79 5 3 2523 2600 333492992 333493068 7.780000e-17 99.0
33 TraesCS5D01G271200 chr3B 89.855 69 5 2 2529 2596 325874406 325874473 1.680000e-13 87.9
34 TraesCS5D01G271200 chr4B 89.394 66 5 2 2532 2596 636772427 636772363 7.840000e-12 82.4
35 TraesCS5D01G271200 chr6D 75.532 188 29 9 2528 2713 22972770 22972942 3.650000e-10 76.8


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 TraesCS5D01G271200 chr5D 374705796 374709202 3406 False 6292.0 6292 100.00000 1 3407 1 chr5D.!!$F1 3406
1 TraesCS5D01G271200 chr5A 476410095 476414644 4549 False 856.0 2512 88.99225 1 2534 4 chr5A.!!$F1 2533
2 TraesCS5D01G271200 chr5B 447557195 447560740 3545 False 858.5 2407 91.99000 1 2529 4 chr5B.!!$F1 2528
3 TraesCS5D01G271200 chr3A 597229281 597230118 837 True 824.0 824 84.48500 2532 3407 1 chr3A.!!$R1 875
4 TraesCS5D01G271200 chr7D 22575343 22576297 954 True 624.5 776 91.57650 2530 3407 2 chr7D.!!$R1 877
5 TraesCS5D01G271200 chr7D 210021844 210023025 1181 True 365.0 379 80.64500 1138 2361 2 chr7D.!!$R2 1223
6 TraesCS5D01G271200 chr7A 131831132 131831715 583 True 597.0 597 85.01600 2766 3397 1 chr7A.!!$R2 631
7 TraesCS5D01G271200 chr7A 482765650 482766557 907 True 435.5 516 85.34000 2529 3401 2 chr7A.!!$R4 872
8 TraesCS5D01G271200 chr7A 222638066 222639260 1194 True 375.0 387 80.77600 1138 2374 2 chr7A.!!$R3 1236

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
869 1798 0.109504 GACTGACTGACTGACGAGGC 60.110 60.000 0.00 0.0 0.0 4.70 F
942 1871 1.268743 GGCCGCTCTGTTTCAATATGC 60.269 52.381 0.00 0.0 0.0 3.14 F
1836 4256 0.037447 AGCTCAAGAAGGCCAAGTCC 59.963 55.000 5.01 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 4228 0.603975 GGCCTTCTTGAGCTTGTCGT 60.604 55.000 0.00 0.0 0.00 4.34 R
2376 4799 1.227089 CAAGGACTCTGGCGATCCG 60.227 63.158 0.00 0.0 37.60 4.18 R
3288 6752 0.034767 TGCCTTCCATGAGCAAGGAG 60.035 55.000 17.65 0.0 41.74 3.69 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
27 28 2.461110 CGCCGCCAGCTTAATTCGT 61.461 57.895 0.00 0.00 40.39 3.85
42 43 2.123988 TTCGTGGGTCGTGCAAATGC 62.124 55.000 0.00 0.00 40.80 3.56
46 47 2.268076 GGGTCGTGCAAATGCTGGT 61.268 57.895 6.97 0.00 42.66 4.00
64 65 1.279846 GGTTCCCGGTCAATGGTCTTA 59.720 52.381 0.00 0.00 0.00 2.10
65 66 2.353323 GTTCCCGGTCAATGGTCTTAC 58.647 52.381 0.00 0.00 0.00 2.34
82 83 3.367630 TCTTACCGAAAACGTAATTCCGC 59.632 43.478 8.05 0.00 0.00 5.54
121 125 4.335037 TCATCATGCATTTACGCAGCTTTA 59.665 37.500 0.00 0.00 46.99 1.85
122 126 4.693538 TCATGCATTTACGCAGCTTTAA 57.306 36.364 0.00 0.00 46.99 1.52
365 377 1.164411 GGATGTTCCGTTGCATCACA 58.836 50.000 10.86 0.00 42.22 3.58
384 396 4.080975 TCACAGTCACATGATTGATGCCTA 60.081 41.667 10.96 0.00 35.63 3.93
421 666 7.781548 ATTTTCTATCCATTTGAATGCTTGC 57.218 32.000 0.00 0.00 35.08 4.01
423 668 2.589798 ATCCATTTGAATGCTTGCCG 57.410 45.000 0.00 0.00 35.08 5.69
446 691 6.205784 CGAGTCTCTGAAACAATATCCTCTC 58.794 44.000 0.00 0.00 0.00 3.20
464 709 5.771666 TCCTCTCATTCTTGCAGTCAAAATT 59.228 36.000 0.00 0.00 0.00 1.82
465 710 6.266103 TCCTCTCATTCTTGCAGTCAAAATTT 59.734 34.615 0.00 0.00 0.00 1.82
466 711 7.448161 TCCTCTCATTCTTGCAGTCAAAATTTA 59.552 33.333 0.00 0.00 0.00 1.40
467 712 8.084073 CCTCTCATTCTTGCAGTCAAAATTTAA 58.916 33.333 0.00 0.00 0.00 1.52
469 714 9.814899 TCTCATTCTTGCAGTCAAAATTTAAAA 57.185 25.926 0.00 0.00 0.00 1.52
478 723 9.598517 TGCAGTCAAAATTTAAAATATCCATCC 57.401 29.630 0.00 0.00 0.00 3.51
479 724 8.755018 GCAGTCAAAATTTAAAATATCCATCCG 58.245 33.333 0.00 0.00 0.00 4.18
487 732 6.817765 TTAAAATATCCATCCGATTCCTGC 57.182 37.500 0.00 0.00 31.92 4.85
488 733 4.647564 AAATATCCATCCGATTCCTGCT 57.352 40.909 0.00 0.00 31.92 4.24
489 734 5.762179 AAATATCCATCCGATTCCTGCTA 57.238 39.130 0.00 0.00 31.92 3.49
490 735 5.965033 AATATCCATCCGATTCCTGCTAT 57.035 39.130 0.00 0.00 31.92 2.97
491 736 3.623906 ATCCATCCGATTCCTGCTATG 57.376 47.619 0.00 0.00 0.00 2.23
492 737 1.625315 TCCATCCGATTCCTGCTATGG 59.375 52.381 0.00 0.00 36.11 2.74
493 738 1.349026 CCATCCGATTCCTGCTATGGT 59.651 52.381 0.00 0.00 31.28 3.55
494 739 2.613977 CCATCCGATTCCTGCTATGGTC 60.614 54.545 0.00 0.00 31.28 4.02
495 740 1.048601 TCCGATTCCTGCTATGGTCC 58.951 55.000 0.00 0.00 0.00 4.46
496 741 0.758734 CCGATTCCTGCTATGGTCCA 59.241 55.000 0.00 0.00 0.00 4.02
497 742 1.541233 CCGATTCCTGCTATGGTCCAC 60.541 57.143 0.00 0.00 0.00 4.02
498 743 1.138859 CGATTCCTGCTATGGTCCACA 59.861 52.381 0.00 0.00 0.00 4.17
499 744 2.565841 GATTCCTGCTATGGTCCACAC 58.434 52.381 0.00 0.00 0.00 3.82
500 745 0.249120 TTCCTGCTATGGTCCACACG 59.751 55.000 0.00 0.00 0.00 4.49
501 746 0.902984 TCCTGCTATGGTCCACACGT 60.903 55.000 0.00 0.00 0.00 4.49
502 747 0.821517 CCTGCTATGGTCCACACGTA 59.178 55.000 0.00 0.00 0.00 3.57
503 748 1.470979 CCTGCTATGGTCCACACGTAC 60.471 57.143 0.00 0.00 0.00 3.67
504 749 1.476891 CTGCTATGGTCCACACGTACT 59.523 52.381 0.00 0.00 0.00 2.73
505 750 2.686405 CTGCTATGGTCCACACGTACTA 59.314 50.000 0.00 0.00 0.00 1.82
506 751 3.293337 TGCTATGGTCCACACGTACTAT 58.707 45.455 0.00 0.00 0.00 2.12
507 752 4.463070 TGCTATGGTCCACACGTACTATA 58.537 43.478 0.00 0.00 0.00 1.31
508 753 4.517832 TGCTATGGTCCACACGTACTATAG 59.482 45.833 12.68 12.68 39.11 1.31
509 754 4.518211 GCTATGGTCCACACGTACTATAGT 59.482 45.833 16.31 10.87 38.63 2.12
510 755 5.702670 GCTATGGTCCACACGTACTATAGTA 59.297 44.000 16.31 8.59 38.63 1.82
511 756 6.348050 GCTATGGTCCACACGTACTATAGTAC 60.348 46.154 26.67 26.67 45.47 2.73
559 804 3.119849 CGCCCTTCTTCGAACAATTCATT 60.120 43.478 0.00 0.00 0.00 2.57
575 820 8.836268 ACAATTCATTTGCATCAACTGTTTAT 57.164 26.923 0.00 0.00 39.03 1.40
586 831 9.123902 TGCATCAACTGTTTATATATTTCTGCT 57.876 29.630 0.00 0.00 0.00 4.24
591 836 9.443283 CAACTGTTTATATATTTCTGCTCAAGC 57.557 33.333 0.00 0.00 42.50 4.01
627 1023 2.030540 TCAGAAGTAAGTGGACGAACGG 60.031 50.000 0.00 0.00 0.00 4.44
635 1031 4.084888 GGACGAACGGCGCCAAAG 62.085 66.667 28.98 16.59 46.04 2.77
672 1068 1.338674 CCGGACTGTTGCTGTAATCCA 60.339 52.381 0.00 0.00 0.00 3.41
709 1105 3.996825 CAACTTTGCCGCCTATGAC 57.003 52.632 0.00 0.00 0.00 3.06
710 1106 1.453155 CAACTTTGCCGCCTATGACT 58.547 50.000 0.00 0.00 0.00 3.41
711 1107 2.627945 CAACTTTGCCGCCTATGACTA 58.372 47.619 0.00 0.00 0.00 2.59
712 1108 3.206150 CAACTTTGCCGCCTATGACTAT 58.794 45.455 0.00 0.00 0.00 2.12
771 1168 2.027653 TGTTATCCACGGTGCTCAATGA 60.028 45.455 1.68 0.00 0.00 2.57
772 1169 3.006940 GTTATCCACGGTGCTCAATGAA 58.993 45.455 1.68 0.00 0.00 2.57
777 1174 2.384382 CACGGTGCTCAATGAAACAAC 58.616 47.619 0.00 0.00 0.00 3.32
800 1197 9.143631 CAACAAATTCTCAAATTAGGTCCAATC 57.856 33.333 0.00 0.00 33.93 2.67
803 1200 6.705863 ATTCTCAAATTAGGTCCAATCAGC 57.294 37.500 0.00 0.00 0.00 4.26
804 1201 4.526970 TCTCAAATTAGGTCCAATCAGCC 58.473 43.478 0.00 0.00 0.00 4.85
805 1202 4.018506 TCTCAAATTAGGTCCAATCAGCCA 60.019 41.667 0.00 0.00 0.00 4.75
844 1282 6.490566 GAGTAACTTTCTCGGGCATAAAAA 57.509 37.500 0.00 0.00 0.00 1.94
869 1798 0.109504 GACTGACTGACTGACGAGGC 60.110 60.000 0.00 0.00 0.00 4.70
911 1840 2.540101 GAGACACCAACGAAACTCTGTG 59.460 50.000 0.00 0.00 0.00 3.66
941 1870 2.016318 TGGCCGCTCTGTTTCAATATG 58.984 47.619 0.00 0.00 0.00 1.78
942 1871 1.268743 GGCCGCTCTGTTTCAATATGC 60.269 52.381 0.00 0.00 0.00 3.14
944 1873 2.033801 GCCGCTCTGTTTCAATATGCAT 59.966 45.455 3.79 3.79 0.00 3.96
947 1876 3.484649 CGCTCTGTTTCAATATGCATTGC 59.515 43.478 3.54 0.46 41.21 3.56
948 1877 4.426416 GCTCTGTTTCAATATGCATTGCA 58.574 39.130 14.72 14.72 44.86 4.08
986 3288 3.887335 GACAAACTACGCCGGCCCA 62.887 63.158 23.46 7.79 0.00 5.36
1312 3658 2.524394 AGGTGTCCGTGCTGTCCT 60.524 61.111 0.00 0.00 0.00 3.85
1836 4256 0.037447 AGCTCAAGAAGGCCAAGTCC 59.963 55.000 5.01 0.00 0.00 3.85
2202 4622 3.146828 AAGGCTGGGCTTTTCCGGT 62.147 57.895 0.00 0.00 35.63 5.28
2259 4679 2.345991 GTGGCGTGGGACTTGCTA 59.654 61.111 0.00 0.00 0.00 3.49
2322 4745 4.015406 ATTGTGGCGTGCGAGGGA 62.015 61.111 0.00 0.00 0.00 4.20
2413 4836 0.318784 GCCAGAGTTCTGACGTTCGT 60.319 55.000 10.64 0.00 46.59 3.85
2431 4854 2.481185 TCGTTCGTTATTTTCACCTGCC 59.519 45.455 0.00 0.00 0.00 4.85
2540 5844 9.941664 GTAAATATACGACACTAAGAGCAACTA 57.058 33.333 0.00 0.00 0.00 2.24
2542 5846 3.572604 ACGACACTAAGAGCAACTACC 57.427 47.619 0.00 0.00 0.00 3.18
2544 5848 3.319972 ACGACACTAAGAGCAACTACCAA 59.680 43.478 0.00 0.00 0.00 3.67
2545 5849 3.673809 CGACACTAAGAGCAACTACCAAC 59.326 47.826 0.00 0.00 0.00 3.77
2634 5938 1.603326 GTCCGCTTTTTCGTTTGGGTA 59.397 47.619 0.00 0.00 0.00 3.69
2987 6420 3.833176 GAACACGTCAACACCGCGC 62.833 63.158 0.00 0.00 0.00 6.86
3192 6642 2.613026 TCAGCCAACGAACAAGAAGA 57.387 45.000 0.00 0.00 0.00 2.87
3201 6651 6.071463 CCAACGAACAAGAAGAAAACGATAG 58.929 40.000 0.00 0.00 46.19 2.08
3224 6674 0.029035 GACAACGCGCTAGCTAGCTA 59.971 55.000 36.02 22.85 46.85 3.32
3252 6702 0.811281 GTGTACCATGGCTTCTTGGC 59.189 55.000 13.04 0.00 38.77 4.52
3276 6726 1.064134 CGACATCGACGCTGGATGA 59.936 57.895 15.28 0.00 43.07 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.062525 CACGAATTAAGCTGGCGGC 59.937 57.895 11.19 11.19 42.19 6.53
27 28 2.267351 CCAGCATTTGCACGACCCA 61.267 57.895 5.20 0.00 45.16 4.51
46 47 1.279846 GGTAAGACCATTGACCGGGAA 59.720 52.381 6.32 0.00 38.42 3.97
82 83 5.459768 CATGATGATGAAGTAGTCCTCGAG 58.540 45.833 5.13 5.13 0.00 4.04
121 125 1.081641 CTGCAGTCGACGTACCGTT 60.082 57.895 10.46 0.00 41.37 4.44
122 126 1.789078 AACTGCAGTCGACGTACCGT 61.789 55.000 21.95 0.00 45.10 4.83
135 140 4.772624 AGTACTGGATGAACTCTAACTGCA 59.227 41.667 0.00 0.00 0.00 4.41
365 377 4.767578 ACTAGGCATCAATCATGTGACT 57.232 40.909 0.00 0.00 34.56 3.41
421 666 5.068460 AGAGGATATTGTTTCAGAGACTCGG 59.932 44.000 0.00 0.00 0.00 4.63
423 668 7.106439 TGAGAGGATATTGTTTCAGAGACTC 57.894 40.000 0.00 0.00 0.00 3.36
464 709 6.542821 AGCAGGAATCGGATGGATATTTTAA 58.457 36.000 0.00 0.00 34.08 1.52
465 710 6.126863 AGCAGGAATCGGATGGATATTTTA 57.873 37.500 0.00 0.00 34.08 1.52
466 711 4.990526 AGCAGGAATCGGATGGATATTTT 58.009 39.130 0.00 0.00 34.08 1.82
467 712 4.647564 AGCAGGAATCGGATGGATATTT 57.352 40.909 0.00 0.00 34.08 1.40
469 714 4.102210 CCATAGCAGGAATCGGATGGATAT 59.898 45.833 0.00 0.00 36.71 1.63
470 715 3.452264 CCATAGCAGGAATCGGATGGATA 59.548 47.826 0.00 0.00 36.71 2.59
473 718 1.349026 ACCATAGCAGGAATCGGATGG 59.651 52.381 0.00 0.00 39.80 3.51
474 719 2.613977 GGACCATAGCAGGAATCGGATG 60.614 54.545 0.00 0.00 0.00 3.51
475 720 1.625818 GGACCATAGCAGGAATCGGAT 59.374 52.381 0.00 0.00 0.00 4.18
476 721 1.048601 GGACCATAGCAGGAATCGGA 58.951 55.000 0.00 0.00 0.00 4.55
477 722 0.758734 TGGACCATAGCAGGAATCGG 59.241 55.000 0.00 0.00 0.00 4.18
478 723 1.138859 TGTGGACCATAGCAGGAATCG 59.861 52.381 0.00 0.00 0.00 3.34
479 724 2.565841 GTGTGGACCATAGCAGGAATC 58.434 52.381 0.00 0.00 0.00 2.52
480 725 1.134401 CGTGTGGACCATAGCAGGAAT 60.134 52.381 0.00 0.00 0.00 3.01
481 726 0.249120 CGTGTGGACCATAGCAGGAA 59.751 55.000 0.00 0.00 0.00 3.36
482 727 0.902984 ACGTGTGGACCATAGCAGGA 60.903 55.000 0.00 0.00 0.00 3.86
483 728 0.821517 TACGTGTGGACCATAGCAGG 59.178 55.000 0.00 0.00 0.00 4.85
484 729 1.476891 AGTACGTGTGGACCATAGCAG 59.523 52.381 0.00 0.00 0.00 4.24
485 730 1.552578 AGTACGTGTGGACCATAGCA 58.447 50.000 0.00 0.00 0.00 3.49
486 731 4.518211 ACTATAGTACGTGTGGACCATAGC 59.482 45.833 2.75 0.00 0.00 2.97
487 732 7.126726 GTACTATAGTACGTGTGGACCATAG 57.873 44.000 23.65 0.00 41.06 2.23
500 745 5.843360 GCGAGCTTTACACGTACTATAGTAC 59.157 44.000 26.67 26.67 45.47 2.73
501 746 5.755375 AGCGAGCTTTACACGTACTATAGTA 59.245 40.000 8.59 8.59 34.56 1.82
502 747 4.574013 AGCGAGCTTTACACGTACTATAGT 59.426 41.667 10.87 10.87 34.56 2.12
503 748 5.050227 AGAGCGAGCTTTACACGTACTATAG 60.050 44.000 0.00 0.00 34.56 1.31
504 749 4.813161 AGAGCGAGCTTTACACGTACTATA 59.187 41.667 0.00 0.00 34.56 1.31
505 750 3.626670 AGAGCGAGCTTTACACGTACTAT 59.373 43.478 0.00 0.00 34.56 2.12
506 751 3.005554 AGAGCGAGCTTTACACGTACTA 58.994 45.455 0.00 0.00 34.56 1.82
507 752 1.811359 AGAGCGAGCTTTACACGTACT 59.189 47.619 0.00 0.00 34.56 2.73
508 753 2.259505 AGAGCGAGCTTTACACGTAC 57.740 50.000 0.00 0.00 34.56 3.67
509 754 2.227149 TCAAGAGCGAGCTTTACACGTA 59.773 45.455 0.00 0.00 34.56 3.57
510 755 1.000607 TCAAGAGCGAGCTTTACACGT 60.001 47.619 0.00 0.00 34.56 4.49
511 756 1.651138 CTCAAGAGCGAGCTTTACACG 59.349 52.381 0.00 0.00 35.25 4.49
559 804 9.734620 GCAGAAATATATAAACAGTTGATGCAA 57.265 29.630 0.00 0.00 0.00 4.08
586 831 0.250081 TACGTGTGCATGGTGCTTGA 60.250 50.000 0.00 0.00 45.31 3.02
591 836 2.008752 TCTGATACGTGTGCATGGTG 57.991 50.000 0.00 0.00 0.00 4.17
607 1002 2.325761 CCGTTCGTCCACTTACTTCTG 58.674 52.381 0.00 0.00 0.00 3.02
672 1068 0.538287 GCAAGGCCAGTCCTCACTTT 60.538 55.000 5.01 0.00 46.94 2.66
707 1103 9.355215 TCGAGAGAAGTTGAATTGTTTATAGTC 57.645 33.333 0.00 0.00 37.03 2.59
771 1168 8.482128 TGGACCTAATTTGAGAATTTGTTGTTT 58.518 29.630 0.00 0.00 36.82 2.83
772 1169 8.017418 TGGACCTAATTTGAGAATTTGTTGTT 57.983 30.769 0.00 0.00 36.82 2.83
777 1174 7.490402 GCTGATTGGACCTAATTTGAGAATTTG 59.510 37.037 0.00 0.00 36.82 2.32
793 1190 2.093235 AGCTAGAGTTGGCTGATTGGAC 60.093 50.000 0.00 0.00 39.96 4.02
794 1191 2.191400 AGCTAGAGTTGGCTGATTGGA 58.809 47.619 0.00 0.00 39.96 3.53
803 1200 0.037326 TCGTGCCAAGCTAGAGTTGG 60.037 55.000 16.47 16.47 46.36 3.77
804 1201 1.337260 ACTCGTGCCAAGCTAGAGTTG 60.337 52.381 10.25 0.00 40.62 3.16
805 1202 0.969894 ACTCGTGCCAAGCTAGAGTT 59.030 50.000 10.25 0.00 40.62 3.01
837 1275 7.386025 TCAGTCAGTCAGTCAGTCATTTTTATG 59.614 37.037 0.00 0.00 0.00 1.90
844 1282 2.227626 CGTCAGTCAGTCAGTCAGTCAT 59.772 50.000 0.00 0.00 0.00 3.06
869 1798 2.353376 CGTGGCACTGGCGTTTTG 60.353 61.111 16.72 0.00 42.47 2.44
941 1870 0.461339 CTTCCCCTGCAATGCAATGC 60.461 55.000 19.99 19.99 46.58 3.56
942 1871 0.461339 GCTTCCCCTGCAATGCAATG 60.461 55.000 9.92 3.27 38.41 2.82
944 1873 2.638354 CGCTTCCCCTGCAATGCAA 61.638 57.895 9.92 0.00 38.41 4.08
947 1876 1.078214 TCTCGCTTCCCCTGCAATG 60.078 57.895 0.00 0.00 0.00 2.82
948 1877 1.078143 GTCTCGCTTCCCCTGCAAT 60.078 57.895 0.00 0.00 0.00 3.56
986 3288 3.244561 CGTGCTCATATAAAGGTGGGGAT 60.245 47.826 0.00 0.00 0.00 3.85
1158 3492 1.603455 CAGGAACACCGTGCCCATT 60.603 57.895 11.73 0.00 29.51 3.16
1290 3636 3.314331 AGCACGGACACCTCCCAG 61.314 66.667 0.00 0.00 31.93 4.45
1518 3864 2.499685 GGCTTGAGGTCGCGGTAT 59.500 61.111 6.13 0.00 0.00 2.73
1811 4228 0.603975 GGCCTTCTTGAGCTTGTCGT 60.604 55.000 0.00 0.00 0.00 4.34
2322 4745 3.492137 GGAAGTAATCTACCACGCCGAAT 60.492 47.826 0.00 0.00 0.00 3.34
2376 4799 1.227089 CAAGGACTCTGGCGATCCG 60.227 63.158 0.00 0.00 37.60 4.18
2413 4836 3.823873 ACATGGCAGGTGAAAATAACGAA 59.176 39.130 3.00 0.00 0.00 3.85
2431 4854 4.800993 TGCAAAACGGTAAAAACTGACATG 59.199 37.500 0.00 0.00 0.00 3.21
2668 5972 2.690778 GCTGGAACGGACATGCACC 61.691 63.158 0.00 0.00 36.31 5.01
2955 6388 4.011517 GTTCCACCGCTTCCCCGA 62.012 66.667 0.00 0.00 0.00 5.14
2976 6409 2.970324 GTCCTTGCGCGGTGTTGA 60.970 61.111 8.83 0.00 0.00 3.18
2978 6411 4.595538 TCGTCCTTGCGCGGTGTT 62.596 61.111 8.83 0.00 0.00 3.32
3025 6459 3.849951 CAGCACCCGTCCGGCTAT 61.850 66.667 0.00 0.00 35.82 2.97
3192 6642 2.339400 CGCGTTGTCGTACTATCGTTTT 59.661 45.455 0.00 0.00 39.49 2.43
3201 6651 0.247814 TAGCTAGCGCGTTGTCGTAC 60.248 55.000 9.55 0.00 42.32 3.67
3287 6751 1.382692 GCCTTCCATGAGCAAGGAGC 61.383 60.000 17.65 4.30 41.74 4.70
3288 6752 0.034767 TGCCTTCCATGAGCAAGGAG 60.035 55.000 17.65 0.00 41.74 3.69
3289 6753 0.034767 CTGCCTTCCATGAGCAAGGA 60.035 55.000 17.65 0.00 41.74 3.36
3290 6754 1.035932 CCTGCCTTCCATGAGCAAGG 61.036 60.000 11.73 11.73 42.05 3.61
3291 6755 1.664321 GCCTGCCTTCCATGAGCAAG 61.664 60.000 0.00 0.00 35.79 4.01
3292 6756 1.679977 GCCTGCCTTCCATGAGCAA 60.680 57.895 0.00 0.00 35.79 3.91


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

AutoCloner maintained by Alex Coulton.