Multiple sequence alignment - TraesCS3B01G465900

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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 TraesCS3B01G465900 chr3B 100.000 3301 0 0 1 3301 708502206 708505506 0.000000e+00 6096.0
1 TraesCS3B01G465900 chr3B 86.787 1945 133 62 628 2499 708912171 708910278 0.000000e+00 2054.0
2 TraesCS3B01G465900 chr3B 95.602 1046 29 4 628 1668 708496846 708497879 0.000000e+00 1661.0
3 TraesCS3B01G465900 chr3B 97.126 522 12 2 2697 3218 5133668 5133150 0.000000e+00 878.0
4 TraesCS3B01G465900 chr3B 90.374 187 16 1 2506 2690 708506526 708506340 9.150000e-61 244.0
5 TraesCS3B01G465900 chr3B 91.111 180 13 2 2506 2683 5131768 5131946 1.180000e-59 241.0
6 TraesCS3B01G465900 chr3B 77.487 382 79 7 1290 1667 708367620 708367242 4.290000e-54 222.0
7 TraesCS3B01G465900 chr3B 96.552 87 3 0 3215 3301 5132900 5132814 9.550000e-31 145.0
8 TraesCS3B01G465900 chr3D 86.583 1923 147 59 628 2477 536338871 536336987 0.000000e+00 2019.0
9 TraesCS3B01G465900 chr3D 87.915 662 58 11 2506 3164 54762288 54762930 0.000000e+00 760.0
10 TraesCS3B01G465900 chr3D 85.146 377 52 3 2507 2879 599396919 599396543 1.860000e-102 383.0
11 TraesCS3B01G465900 chr3D 78.329 383 71 10 1290 1664 536027767 536028145 1.530000e-58 237.0
12 TraesCS3B01G465900 chr3D 89.474 76 8 0 552 627 557606209 557606284 2.710000e-16 97.1
13 TraesCS3B01G465900 chr3A 89.243 1599 99 37 965 2506 671765908 671764326 0.000000e+00 1932.0
14 TraesCS3B01G465900 chr3A 89.005 191 19 1 2506 2694 671741719 671741909 5.510000e-58 235.0
15 TraesCS3B01G465900 chr3A 78.333 360 68 8 1310 1664 671697890 671697536 1.190000e-54 224.0
16 TraesCS3B01G465900 chr3A 82.807 285 14 10 628 885 671766268 671765992 4.290000e-54 222.0
17 TraesCS3B01G465900 chr3A 92.105 76 6 0 552 627 708348428 708348503 1.250000e-19 108.0
18 TraesCS3B01G465900 chr7A 99.497 795 4 0 2507 3301 158651081 158650287 0.000000e+00 1447.0
19 TraesCS3B01G465900 chr7A 95.315 555 25 1 1 554 540868980 540868426 0.000000e+00 880.0
20 TraesCS3B01G465900 chr7A 91.398 186 14 1 2507 2690 158649241 158649426 1.520000e-63 254.0
21 TraesCS3B01G465900 chr4A 99.245 795 6 0 2507 3301 610253869 610254663 0.000000e+00 1435.0
22 TraesCS3B01G465900 chr2A 98.868 795 9 0 2507 3301 377108674 377107880 0.000000e+00 1419.0
23 TraesCS3B01G465900 chr2A 91.444 187 14 1 2506 2690 377106833 377107019 4.230000e-64 255.0
24 TraesCS3B01G465900 chr6B 96.396 555 18 2 1 554 693128014 693127461 0.000000e+00 913.0
25 TraesCS3B01G465900 chr6B 95.315 555 23 3 1 554 120807818 120807266 0.000000e+00 878.0
26 TraesCS3B01G465900 chr6B 95.315 555 23 3 1 554 679677392 679676840 0.000000e+00 878.0
27 TraesCS3B01G465900 chr1B 96.029 554 19 2 3 555 502635032 502634481 0.000000e+00 898.0
28 TraesCS3B01G465900 chr5B 95.676 555 21 3 1 554 659603832 659603280 0.000000e+00 889.0
29 TraesCS3B01G465900 chr5B 95.144 556 24 3 1 555 403154368 403154921 0.000000e+00 874.0
30 TraesCS3B01G465900 chr2B 95.660 553 23 1 3 554 90303613 90303061 0.000000e+00 887.0
31 TraesCS3B01G465900 chrUn 95.144 556 25 2 1 555 45258838 45258284 0.000000e+00 876.0
32 TraesCS3B01G465900 chr7B 90.258 349 28 4 2816 3164 592403354 592403696 5.020000e-123 451.0
33 TraesCS3B01G465900 chr5A 89.685 349 30 4 2816 3164 219244215 219243873 1.090000e-119 440.0
34 TraesCS3B01G465900 chr6A 89.157 332 31 3 2816 3147 270778959 270778633 3.070000e-110 409.0
35 TraesCS3B01G465900 chr7D 89.873 79 8 0 552 630 276127858 276127936 5.830000e-18 102.0
36 TraesCS3B01G465900 chr4D 87.342 79 9 1 552 630 428972857 428972780 4.540000e-14 89.8


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 TraesCS3B01G465900 chr3B 708502206 708505506 3300 False 6096.0 6096 100.000 1 3301 1 chr3B.!!$F3 3300
1 TraesCS3B01G465900 chr3B 708910278 708912171 1893 True 2054.0 2054 86.787 628 2499 1 chr3B.!!$R3 1871
2 TraesCS3B01G465900 chr3B 708496846 708497879 1033 False 1661.0 1661 95.602 628 1668 1 chr3B.!!$F2 1040
3 TraesCS3B01G465900 chr3B 5132814 5133668 854 True 511.5 878 96.839 2697 3301 2 chr3B.!!$R4 604
4 TraesCS3B01G465900 chr3D 536336987 536338871 1884 True 2019.0 2019 86.583 628 2477 1 chr3D.!!$R1 1849
5 TraesCS3B01G465900 chr3D 54762288 54762930 642 False 760.0 760 87.915 2506 3164 1 chr3D.!!$F1 658
6 TraesCS3B01G465900 chr3A 671764326 671766268 1942 True 1077.0 1932 86.025 628 2506 2 chr3A.!!$R2 1878
7 TraesCS3B01G465900 chr7A 158650287 158651081 794 True 1447.0 1447 99.497 2507 3301 1 chr7A.!!$R1 794
8 TraesCS3B01G465900 chr7A 540868426 540868980 554 True 880.0 880 95.315 1 554 1 chr7A.!!$R2 553
9 TraesCS3B01G465900 chr4A 610253869 610254663 794 False 1435.0 1435 99.245 2507 3301 1 chr4A.!!$F1 794
10 TraesCS3B01G465900 chr2A 377107880 377108674 794 True 1419.0 1419 98.868 2507 3301 1 chr2A.!!$R1 794
11 TraesCS3B01G465900 chr6B 693127461 693128014 553 True 913.0 913 96.396 1 554 1 chr6B.!!$R3 553
12 TraesCS3B01G465900 chr6B 120807266 120807818 552 True 878.0 878 95.315 1 554 1 chr6B.!!$R1 553
13 TraesCS3B01G465900 chr6B 679676840 679677392 552 True 878.0 878 95.315 1 554 1 chr6B.!!$R2 553
14 TraesCS3B01G465900 chr1B 502634481 502635032 551 True 898.0 898 96.029 3 555 1 chr1B.!!$R1 552
15 TraesCS3B01G465900 chr5B 659603280 659603832 552 True 889.0 889 95.676 1 554 1 chr5B.!!$R1 553
16 TraesCS3B01G465900 chr5B 403154368 403154921 553 False 874.0 874 95.144 1 555 1 chr5B.!!$F1 554
17 TraesCS3B01G465900 chr2B 90303061 90303613 552 True 887.0 887 95.660 3 554 1 chr2B.!!$R1 551
18 TraesCS3B01G465900 chrUn 45258284 45258838 554 True 876.0 876 95.144 1 555 1 chrUn.!!$R1 554

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
992 1090 0.107214 GTTGATTCCATCTGCCCCGA 60.107 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 2537 0.723981 GAAGCTCGCTCGCAATCTTT 59.276 50.0 0.0 0.0 0.0 2.52 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
123 124 0.975556 TAGTCCAGGAGCGGATGCAA 60.976 55.000 0.00 0.00 46.23 4.08
210 211 1.065418 AGGTATGGTTTCCTTCTGCGG 60.065 52.381 0.00 0.00 0.00 5.69
214 215 1.375013 GGTTTCCTTCTGCGGCGTA 60.375 57.895 9.37 1.99 0.00 4.42
227 228 4.696078 GCGTATTAGTCGCGGTGA 57.304 55.556 6.13 0.00 43.94 4.02
545 547 5.972935 TGAATGAGACACGTATTACCATGT 58.027 37.500 0.00 0.00 0.00 3.21
550 552 7.821595 TGAGACACGTATTACCATGTAAAAG 57.178 36.000 0.00 0.00 0.00 2.27
555 557 9.698617 GACACGTATTACCATGTAAAAGAAATC 57.301 33.333 0.00 0.00 0.00 2.17
556 558 8.671028 ACACGTATTACCATGTAAAAGAAATCC 58.329 33.333 0.00 0.00 0.00 3.01
557 559 7.849026 CACGTATTACCATGTAAAAGAAATCCG 59.151 37.037 0.00 0.00 0.00 4.18
558 560 7.550196 ACGTATTACCATGTAAAAGAAATCCGT 59.450 33.333 0.00 0.00 0.00 4.69
559 561 9.033481 CGTATTACCATGTAAAAGAAATCCGTA 57.967 33.333 0.00 0.00 0.00 4.02
588 590 9.924650 TTTTAAGTTTTAGCACCAAACTAAACA 57.075 25.926 7.99 0.00 42.47 2.83
592 594 9.744468 AAGTTTTAGCACCAAACTAAACATTAG 57.256 29.630 7.99 0.00 42.47 1.73
593 595 9.127277 AGTTTTAGCACCAAACTAAACATTAGA 57.873 29.630 6.23 0.00 41.68 2.10
594 596 9.177304 GTTTTAGCACCAAACTAAACATTAGAC 57.823 33.333 4.24 0.00 38.87 2.59
595 597 5.607119 AGCACCAAACTAAACATTAGACG 57.393 39.130 4.24 0.00 0.00 4.18
596 598 4.083484 AGCACCAAACTAAACATTAGACGC 60.083 41.667 4.24 0.00 0.00 5.19
597 599 4.319911 GCACCAAACTAAACATTAGACGCA 60.320 41.667 4.24 0.00 0.00 5.24
598 600 5.753744 CACCAAACTAAACATTAGACGCAA 58.246 37.500 4.24 0.00 0.00 4.85
614 616 2.404215 CGCAAGTTATATGACTCCGGG 58.596 52.381 0.00 0.91 0.00 5.73
615 617 2.223971 CGCAAGTTATATGACTCCGGGT 60.224 50.000 0.00 0.00 0.00 5.28
616 618 3.131396 GCAAGTTATATGACTCCGGGTG 58.869 50.000 0.00 0.00 0.00 4.61
617 619 3.181469 GCAAGTTATATGACTCCGGGTGA 60.181 47.826 0.00 0.00 0.00 4.02
618 620 4.503296 GCAAGTTATATGACTCCGGGTGAT 60.503 45.833 0.00 0.44 0.00 3.06
619 621 5.279306 GCAAGTTATATGACTCCGGGTGATA 60.279 44.000 0.00 3.01 0.00 2.15
620 622 6.574465 GCAAGTTATATGACTCCGGGTGATAT 60.574 42.308 15.44 15.44 38.12 1.63
621 623 7.386851 CAAGTTATATGACTCCGGGTGATATT 58.613 38.462 16.03 2.16 36.43 1.28
622 624 8.528643 CAAGTTATATGACTCCGGGTGATATTA 58.471 37.037 16.03 8.10 36.43 0.98
623 625 8.064336 AGTTATATGACTCCGGGTGATATTAC 57.936 38.462 16.03 16.18 36.43 1.89
624 626 5.934402 ATATGACTCCGGGTGATATTACC 57.066 43.478 8.16 8.16 32.24 2.85
625 627 3.323774 TGACTCCGGGTGATATTACCT 57.676 47.619 15.69 0.00 40.66 3.08
626 628 3.228453 TGACTCCGGGTGATATTACCTC 58.772 50.000 15.69 6.32 40.66 3.85
634 636 4.523173 CGGGTGATATTACCTCTAAGCTCA 59.477 45.833 15.69 0.00 40.66 4.26
647 649 0.669932 AAGCTCAGCTGCGAGAGTTG 60.670 55.000 20.23 2.38 39.62 3.16
687 698 2.815211 GCGCGCCTTGATCTGTCA 60.815 61.111 23.24 0.00 0.00 3.58
710 724 0.463654 TGATTACGGGCAGCCATGTC 60.464 55.000 15.19 4.26 0.00 3.06
743 757 2.348888 CGGACCTGGCTACGACCTT 61.349 63.158 0.00 0.00 0.00 3.50
916 976 0.391661 GAGGCCAATCAGCGTCAAGA 60.392 55.000 5.01 0.00 44.90 3.02
990 1088 1.728490 GCGTTGATTCCATCTGCCCC 61.728 60.000 0.00 0.00 0.00 5.80
991 1089 1.439353 CGTTGATTCCATCTGCCCCG 61.439 60.000 0.00 0.00 0.00 5.73
992 1090 0.107214 GTTGATTCCATCTGCCCCGA 60.107 55.000 0.00 0.00 0.00 5.14
993 1091 0.107214 TTGATTCCATCTGCCCCGAC 60.107 55.000 0.00 0.00 0.00 4.79
994 1092 1.271127 TGATTCCATCTGCCCCGACA 61.271 55.000 0.00 0.00 0.00 4.35
995 1093 0.109342 GATTCCATCTGCCCCGACAT 59.891 55.000 0.00 0.00 0.00 3.06
1035 1133 4.643387 AACACCCAGCACTCGCCC 62.643 66.667 0.00 0.00 39.83 6.13
1149 1247 3.844090 GAGCTCACTCCTCGGGGC 61.844 72.222 9.40 0.00 36.90 5.80
1254 1364 1.395635 TCGGCCGTTGCTATCTAGAA 58.604 50.000 27.15 0.00 37.74 2.10
1648 1761 0.627451 TCCTCCTCGGCTACAACCTA 59.373 55.000 0.00 0.00 0.00 3.08
1684 1802 2.118683 CGTCGCCATTGCCATTATTTG 58.881 47.619 0.00 0.00 0.00 2.32
1685 1803 2.479389 CGTCGCCATTGCCATTATTTGT 60.479 45.455 0.00 0.00 0.00 2.83
1686 1804 3.520569 GTCGCCATTGCCATTATTTGTT 58.479 40.909 0.00 0.00 0.00 2.83
1737 1859 0.097325 GTCGATCGACGTGCTCTCTT 59.903 55.000 30.46 0.00 43.13 2.85
1762 1887 5.258456 TCTCCGTTAGAAATAATCGTGCT 57.742 39.130 0.00 0.00 0.00 4.40
1776 1901 1.666189 TCGTGCTGACATCTCTCTACG 59.334 52.381 0.00 0.00 0.00 3.51
2304 2447 2.861935 GGCAAGTGCATACATTGATTGC 59.138 45.455 5.52 8.11 44.36 3.56
2306 2449 4.178540 GCAAGTGCATACATTGATTGCTT 58.821 39.130 13.75 2.48 41.59 3.91
2307 2450 4.266976 GCAAGTGCATACATTGATTGCTTC 59.733 41.667 13.75 8.84 41.59 3.86
2326 2469 4.866486 GCTTCATTTGTTCATTGATGGGAC 59.134 41.667 0.00 0.00 0.00 4.46
2330 2484 3.364460 TTGTTCATTGATGGGACCGAT 57.636 42.857 0.00 0.00 0.00 4.18
2334 2503 0.392706 CATTGATGGGACCGATCGGA 59.607 55.000 39.55 18.68 38.96 4.55
2351 2520 5.291858 CGATCGGAATTGTTCATTGAGAGAA 59.708 40.000 7.38 0.00 0.00 2.87
2367 2536 0.327924 AGAAACCGATGGTGCATGGA 59.672 50.000 0.00 0.00 35.34 3.41
2368 2537 1.173043 GAAACCGATGGTGCATGGAA 58.827 50.000 0.00 0.00 35.34 3.53
2422 2591 2.290367 CTGTGTTTCGCCATTCTGTTCA 59.710 45.455 0.00 0.00 0.00 3.18
2423 2592 2.884012 TGTGTTTCGCCATTCTGTTCAT 59.116 40.909 0.00 0.00 0.00 2.57
2424 2593 4.068599 TGTGTTTCGCCATTCTGTTCATA 58.931 39.130 0.00 0.00 0.00 2.15
2760 2939 0.115349 GCATAGCCCCCTCTCCTCTA 59.885 60.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 1.731613 CGCTGGAGCAAACGTCGTA 60.732 57.895 0.00 0.00 42.21 3.43
123 124 1.078709 CGTCGATGCAGACCACAATT 58.921 50.000 0.00 0.00 37.85 2.32
214 215 0.172803 GACACCTCACCGCGACTAAT 59.827 55.000 8.23 0.00 0.00 1.73
227 228 3.632333 TCGAACTCCAGATATGACACCT 58.368 45.455 0.00 0.00 0.00 4.00
273 274 4.181578 CCTTACCGTTGAACGAATCAGAT 58.818 43.478 20.47 0.00 46.05 2.90
325 326 0.309922 CTGATATGCAGCTTTGCGGG 59.690 55.000 0.00 0.00 37.90 6.13
388 389 1.081175 GCAGCCACCGAAGAAAAGC 60.081 57.895 0.00 0.00 0.00 3.51
562 564 9.924650 TGTTTAGTTTGGTGCTAAAACTTAAAA 57.075 25.926 14.31 9.04 43.60 1.52
566 568 9.744468 CTAATGTTTAGTTTGGTGCTAAAACTT 57.256 29.630 14.31 2.54 43.60 2.66
567 569 9.127277 TCTAATGTTTAGTTTGGTGCTAAAACT 57.873 29.630 13.79 13.79 46.72 2.66
568 570 9.177304 GTCTAATGTTTAGTTTGGTGCTAAAAC 57.823 33.333 0.00 2.47 39.29 2.43
569 571 8.071368 CGTCTAATGTTTAGTTTGGTGCTAAAA 58.929 33.333 0.00 0.00 39.29 1.52
570 572 7.577979 CGTCTAATGTTTAGTTTGGTGCTAAA 58.422 34.615 0.00 0.00 36.44 1.85
571 573 6.347888 GCGTCTAATGTTTAGTTTGGTGCTAA 60.348 38.462 0.00 0.00 0.00 3.09
572 574 5.121142 GCGTCTAATGTTTAGTTTGGTGCTA 59.879 40.000 0.00 0.00 0.00 3.49
573 575 4.083484 GCGTCTAATGTTTAGTTTGGTGCT 60.083 41.667 0.00 0.00 0.00 4.40
574 576 4.156182 GCGTCTAATGTTTAGTTTGGTGC 58.844 43.478 0.00 0.00 0.00 5.01
575 577 5.351233 TGCGTCTAATGTTTAGTTTGGTG 57.649 39.130 0.00 0.00 0.00 4.17
576 578 5.529800 ACTTGCGTCTAATGTTTAGTTTGGT 59.470 36.000 0.00 0.00 0.00 3.67
577 579 5.997385 ACTTGCGTCTAATGTTTAGTTTGG 58.003 37.500 0.00 0.00 0.00 3.28
581 583 9.811995 TCATATAACTTGCGTCTAATGTTTAGT 57.188 29.630 0.00 0.00 0.00 2.24
583 585 9.811995 AGTCATATAACTTGCGTCTAATGTTTA 57.188 29.630 0.00 0.00 0.00 2.01
584 586 8.718102 AGTCATATAACTTGCGTCTAATGTTT 57.282 30.769 0.00 0.00 0.00 2.83
585 587 7.438459 GGAGTCATATAACTTGCGTCTAATGTT 59.562 37.037 0.00 0.00 0.00 2.71
586 588 6.924060 GGAGTCATATAACTTGCGTCTAATGT 59.076 38.462 0.00 0.00 0.00 2.71
587 589 6.088217 CGGAGTCATATAACTTGCGTCTAATG 59.912 42.308 0.00 0.00 0.00 1.90
588 590 6.150318 CGGAGTCATATAACTTGCGTCTAAT 58.850 40.000 0.00 0.00 0.00 1.73
589 591 5.506815 CCGGAGTCATATAACTTGCGTCTAA 60.507 44.000 0.00 0.00 0.00 2.10
590 592 4.023450 CCGGAGTCATATAACTTGCGTCTA 60.023 45.833 0.00 0.00 0.00 2.59
591 593 3.243434 CCGGAGTCATATAACTTGCGTCT 60.243 47.826 0.00 0.00 0.00 4.18
592 594 3.050619 CCGGAGTCATATAACTTGCGTC 58.949 50.000 0.00 0.00 0.00 5.19
593 595 2.223971 CCCGGAGTCATATAACTTGCGT 60.224 50.000 0.73 0.00 0.00 5.24
594 596 2.223971 ACCCGGAGTCATATAACTTGCG 60.224 50.000 0.73 0.00 0.00 4.85
595 597 3.131396 CACCCGGAGTCATATAACTTGC 58.869 50.000 0.73 0.00 0.00 4.01
596 598 4.665833 TCACCCGGAGTCATATAACTTG 57.334 45.455 0.73 0.00 0.00 3.16
597 599 7.554959 AATATCACCCGGAGTCATATAACTT 57.445 36.000 0.73 0.00 0.00 2.66
598 600 7.123847 GGTAATATCACCCGGAGTCATATAACT 59.876 40.741 0.73 0.00 31.91 2.24
599 601 7.123847 AGGTAATATCACCCGGAGTCATATAAC 59.876 40.741 0.73 0.00 39.62 1.89
600 602 7.186972 AGGTAATATCACCCGGAGTCATATAA 58.813 38.462 0.73 0.00 39.62 0.98
601 603 6.738635 AGGTAATATCACCCGGAGTCATATA 58.261 40.000 0.73 0.00 39.62 0.86
602 604 5.590818 AGGTAATATCACCCGGAGTCATAT 58.409 41.667 0.73 0.00 39.62 1.78
603 605 5.006896 AGGTAATATCACCCGGAGTCATA 57.993 43.478 0.73 0.00 39.62 2.15
604 606 3.833070 GAGGTAATATCACCCGGAGTCAT 59.167 47.826 0.73 0.00 39.62 3.06
605 607 3.117246 AGAGGTAATATCACCCGGAGTCA 60.117 47.826 0.73 0.00 39.62 3.41
606 608 3.498334 AGAGGTAATATCACCCGGAGTC 58.502 50.000 0.73 0.00 39.62 3.36
607 609 3.614568 AGAGGTAATATCACCCGGAGT 57.385 47.619 0.73 0.00 39.62 3.85
608 610 4.082136 GCTTAGAGGTAATATCACCCGGAG 60.082 50.000 0.73 0.00 39.62 4.63
609 611 3.830755 GCTTAGAGGTAATATCACCCGGA 59.169 47.826 0.73 0.00 39.62 5.14
610 612 3.833070 AGCTTAGAGGTAATATCACCCGG 59.167 47.826 0.00 0.00 39.62 5.73
611 613 4.523173 TGAGCTTAGAGGTAATATCACCCG 59.477 45.833 0.00 0.00 39.62 5.28
612 614 5.567823 GCTGAGCTTAGAGGTAATATCACCC 60.568 48.000 10.16 0.00 39.62 4.61
613 615 5.245075 AGCTGAGCTTAGAGGTAATATCACC 59.755 44.000 10.16 0.00 33.89 4.02
614 616 6.155827 CAGCTGAGCTTAGAGGTAATATCAC 58.844 44.000 8.42 0.00 36.40 3.06
615 617 5.279206 GCAGCTGAGCTTAGAGGTAATATCA 60.279 44.000 20.43 0.00 36.40 2.15
616 618 5.167845 GCAGCTGAGCTTAGAGGTAATATC 58.832 45.833 20.43 0.00 36.40 1.63
617 619 4.321601 CGCAGCTGAGCTTAGAGGTAATAT 60.322 45.833 20.43 0.00 36.40 1.28
618 620 3.004839 CGCAGCTGAGCTTAGAGGTAATA 59.995 47.826 20.43 0.00 36.40 0.98
619 621 2.223923 CGCAGCTGAGCTTAGAGGTAAT 60.224 50.000 20.43 0.00 36.40 1.89
620 622 1.135139 CGCAGCTGAGCTTAGAGGTAA 59.865 52.381 20.43 0.00 36.40 2.85
621 623 0.741326 CGCAGCTGAGCTTAGAGGTA 59.259 55.000 20.43 0.00 36.40 3.08
622 624 0.967887 TCGCAGCTGAGCTTAGAGGT 60.968 55.000 20.43 0.00 36.40 3.85
623 625 0.248990 CTCGCAGCTGAGCTTAGAGG 60.249 60.000 20.43 6.26 36.40 3.69
624 626 0.737804 TCTCGCAGCTGAGCTTAGAG 59.262 55.000 20.43 22.52 39.39 2.43
625 627 0.737804 CTCTCGCAGCTGAGCTTAGA 59.262 55.000 20.43 12.34 36.40 2.10
626 628 0.455410 ACTCTCGCAGCTGAGCTTAG 59.545 55.000 20.43 14.09 36.40 2.18
634 636 0.038709 GTCTCACAACTCTCGCAGCT 60.039 55.000 0.00 0.00 0.00 4.24
647 649 0.036732 TGGTCATGGCCAAGTCTCAC 59.963 55.000 18.92 0.00 35.25 3.51
687 698 0.037590 TGGCTGCCCGTAATCAAACT 59.962 50.000 17.53 0.00 0.00 2.66
711 725 1.168407 GGTCCGATGCCATCCACATG 61.168 60.000 0.00 0.00 0.00 3.21
712 726 1.149174 GGTCCGATGCCATCCACAT 59.851 57.895 0.00 0.00 0.00 3.21
713 727 1.995066 AGGTCCGATGCCATCCACA 60.995 57.895 0.00 0.00 0.00 4.17
714 728 1.524621 CAGGTCCGATGCCATCCAC 60.525 63.158 0.00 0.00 0.00 4.02
715 729 2.745308 CCAGGTCCGATGCCATCCA 61.745 63.158 0.00 0.00 0.00 3.41
916 976 2.158608 ACTACCAGCAAGCCTGACTTTT 60.159 45.455 0.00 0.00 44.64 2.27
991 1089 3.576356 CACCGCCATGCCGATGTC 61.576 66.667 0.00 0.00 0.00 3.06
992 1090 4.094646 TCACCGCCATGCCGATGT 62.095 61.111 0.00 0.00 0.00 3.06
993 1091 3.274586 CTCACCGCCATGCCGATG 61.275 66.667 0.00 0.00 0.00 3.84
1035 1133 3.358076 GAGGAGGAAGGTGACCGCG 62.358 68.421 0.00 0.00 0.00 6.46
1254 1364 3.320359 CCGTTGGGGTCTGGCTAT 58.680 61.111 0.00 0.00 0.00 2.97
1648 1761 2.050351 CGACGTGCCGTGAAGAGT 60.050 61.111 4.94 0.00 41.37 3.24
1686 1804 9.599866 GAAAGAAGGAAAGAAAGGATTGAAAAA 57.400 29.630 0.00 0.00 0.00 1.94
1691 1813 5.335976 CCCGAAAGAAGGAAAGAAAGGATTG 60.336 44.000 0.00 0.00 0.00 2.67
1692 1814 4.767409 CCCGAAAGAAGGAAAGAAAGGATT 59.233 41.667 0.00 0.00 0.00 3.01
1693 1815 4.042934 TCCCGAAAGAAGGAAAGAAAGGAT 59.957 41.667 0.00 0.00 0.00 3.24
1699 1821 1.690352 ACGTCCCGAAAGAAGGAAAGA 59.310 47.619 0.00 0.00 32.81 2.52
1700 1822 2.067013 GACGTCCCGAAAGAAGGAAAG 58.933 52.381 3.51 0.00 32.81 2.62
1718 1840 0.097325 AAGAGAGCACGTCGATCGAC 59.903 55.000 33.22 33.22 42.86 4.20
1737 1859 5.690409 GCACGATTATTTCTAACGGAGATCA 59.310 40.000 0.00 0.00 32.88 2.92
1762 1887 1.208776 TCGGTCCGTAGAGAGATGTCA 59.791 52.381 11.88 0.00 0.00 3.58
1776 1901 3.966026 CTCGTCAACGCCTCGGTCC 62.966 68.421 0.00 0.00 39.60 4.46
1862 2005 1.134901 GCTCGACGTCGTGATGTCT 59.865 57.895 35.91 0.00 43.36 3.41
2072 2215 0.956902 TGTCGACGAACCTGATCCGA 60.957 55.000 11.62 0.00 0.00 4.55
2279 2422 2.025981 TCAATGTATGCACTTGCCTCCT 60.026 45.455 0.00 0.00 41.18 3.69
2304 2447 5.413499 GGTCCCATCAATGAACAAATGAAG 58.587 41.667 0.00 0.00 0.00 3.02
2306 2449 3.443329 CGGTCCCATCAATGAACAAATGA 59.557 43.478 0.00 0.00 0.00 2.57
2307 2450 3.443329 TCGGTCCCATCAATGAACAAATG 59.557 43.478 0.00 0.00 0.00 2.32
2326 2469 3.871006 TCTCAATGAACAATTCCGATCGG 59.129 43.478 28.62 28.62 0.00 4.18
2330 2484 5.181245 GGTTTCTCTCAATGAACAATTCCGA 59.819 40.000 0.00 0.00 0.00 4.55
2334 2503 6.349611 CCATCGGTTTCTCTCAATGAACAATT 60.350 38.462 0.00 0.00 0.00 2.32
2351 2520 1.545582 CTTTTCCATGCACCATCGGTT 59.454 47.619 0.00 0.00 31.02 4.44
2367 2536 1.129437 GAAGCTCGCTCGCAATCTTTT 59.871 47.619 0.00 0.00 0.00 2.27
2368 2537 0.723981 GAAGCTCGCTCGCAATCTTT 59.276 50.000 0.00 0.00 0.00 2.52
2445 2614 6.291067 AGAAATATATCATGTGTGCGTGTG 57.709 37.500 0.00 0.00 33.51 3.82
2500 2675 3.680196 GCCAGTGTCATTTACTCTCCCTC 60.680 52.174 0.00 0.00 29.46 4.30
2760 2939 4.592485 AGAACACGAACAGACAGAGAAT 57.408 40.909 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.