Multiple sequence alignment - TraesCS4A01G072700

Loading Multiple Alignment...

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 TraesCS4A01G072700 chr4A 100.000 3923 0 0 1 3923 71121945 71125867 0.000000e+00 7245.0
1 TraesCS4A01G072700 chr4D 92.216 2518 123 28 814 3289 389480160 389482646 0.000000e+00 3496.0
2 TraesCS4A01G072700 chr4D 90.106 566 36 8 3369 3923 389482643 389483199 0.000000e+00 717.0
3 TraesCS4A01G072700 chr4D 84.277 318 28 7 524 822 389478796 389479110 1.380000e-74 291.0
4 TraesCS4A01G072700 chr4B 93.096 1767 83 17 1553 3289 479227629 479229386 0.000000e+00 2551.0
5 TraesCS4A01G072700 chr4B 93.393 787 30 5 754 1523 479226559 479227340 0.000000e+00 1146.0
6 TraesCS4A01G072700 chr4B 98.485 528 8 0 1 528 339451376 339451903 0.000000e+00 931.0
7 TraesCS4A01G072700 chr4B 93.490 553 20 7 3369 3917 479229383 479229923 0.000000e+00 808.0
8 TraesCS4A01G072700 chr4B 92.079 101 7 1 3285 3385 308049640 308049739 1.470000e-29 141.0
9 TraesCS4A01G072700 chr4B 92.000 100 7 1 3279 3377 178078908 178078809 5.290000e-29 139.0
10 TraesCS4A01G072700 chr4B 97.143 35 1 0 524 558 479216773 479216807 4.230000e-05 60.2
11 TraesCS4A01G072700 chr1B 98.295 528 9 0 1 528 524498787 524499314 0.000000e+00 926.0
12 TraesCS4A01G072700 chr1B 91.250 80 7 0 628 707 307155751 307155672 4.140000e-20 110.0
13 TraesCS4A01G072700 chr1B 83.951 81 11 2 673 753 563465850 563465928 4.200000e-10 76.8
14 TraesCS4A01G072700 chr7A 98.282 524 9 0 1 524 577673792 577673269 0.000000e+00 918.0
15 TraesCS4A01G072700 chr7A 93.617 94 6 0 3277 3370 33483184 33483277 1.470000e-29 141.0
16 TraesCS4A01G072700 chr7B 98.282 524 8 1 1 524 285271908 285272430 0.000000e+00 917.0
17 TraesCS4A01G072700 chr7B 86.066 122 13 4 3258 3377 1097794 1097675 1.140000e-25 128.0
18 TraesCS4A01G072700 chr6B 97.732 529 12 0 1 529 375446815 375446287 0.000000e+00 911.0
19 TraesCS4A01G072700 chr6B 98.084 522 10 0 1 522 182386729 182387250 0.000000e+00 909.0
20 TraesCS4A01G072700 chr2B 97.706 523 12 0 1 523 357167060 357167582 0.000000e+00 900.0
21 TraesCS4A01G072700 chr2B 97.519 524 13 0 1 524 551249433 551248910 0.000000e+00 896.0
22 TraesCS4A01G072700 chr3B 97.519 524 13 0 1 524 271826006 271826529 0.000000e+00 896.0
23 TraesCS4A01G072700 chr5D 96.552 87 3 0 3286 3372 297738342 297738428 1.140000e-30 145.0
24 TraesCS4A01G072700 chr5B 93.684 95 6 0 3286 3380 697972297 697972391 4.090000e-30 143.0
25 TraesCS4A01G072700 chr5A 93.617 94 6 0 3286 3379 38014705 38014612 1.470000e-29 141.0
26 TraesCS4A01G072700 chr1D 93.684 95 4 2 3277 3370 484555663 484555756 1.470000e-29 141.0
27 TraesCS4A01G072700 chr1D 93.617 94 5 1 3278 3370 6335601 6335508 5.290000e-29 139.0
28 TraesCS4A01G072700 chr1A 84.000 125 13 5 633 753 514027306 514027427 3.200000e-21 113.0
29 TraesCS4A01G072700 chr2A 89.655 87 9 0 664 750 654886829 654886915 1.150000e-20 111.0
30 TraesCS4A01G072700 chr2D 89.744 78 8 0 664 741 511655831 511655908 2.490000e-17 100.0


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 TraesCS4A01G072700 chr4A 71121945 71125867 3922 False 7245.000000 7245 100.000000 1 3923 1 chr4A.!!$F1 3922
1 TraesCS4A01G072700 chr4D 389478796 389483199 4403 False 1501.333333 3496 88.866333 524 3923 3 chr4D.!!$F1 3399
2 TraesCS4A01G072700 chr4B 479226559 479229923 3364 False 1501.666667 2551 93.326333 754 3917 3 chr4B.!!$F4 3163
3 TraesCS4A01G072700 chr4B 339451376 339451903 527 False 931.000000 931 98.485000 1 528 1 chr4B.!!$F2 527
4 TraesCS4A01G072700 chr1B 524498787 524499314 527 False 926.000000 926 98.295000 1 528 1 chr1B.!!$F1 527
5 TraesCS4A01G072700 chr7A 577673269 577673792 523 True 918.000000 918 98.282000 1 524 1 chr7A.!!$R1 523
6 TraesCS4A01G072700 chr7B 285271908 285272430 522 False 917.000000 917 98.282000 1 524 1 chr7B.!!$F1 523
7 TraesCS4A01G072700 chr6B 375446287 375446815 528 True 911.000000 911 97.732000 1 529 1 chr6B.!!$R1 528
8 TraesCS4A01G072700 chr6B 182386729 182387250 521 False 909.000000 909 98.084000 1 522 1 chr6B.!!$F1 521
9 TraesCS4A01G072700 chr2B 357167060 357167582 522 False 900.000000 900 97.706000 1 523 1 chr2B.!!$F1 522
10 TraesCS4A01G072700 chr2B 551248910 551249433 523 True 896.000000 896 97.519000 1 524 1 chr2B.!!$R1 523
11 TraesCS4A01G072700 chr3B 271826006 271826529 523 False 896.000000 896 97.519000 1 524 1 chr3B.!!$F1 523

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
923 2000 0.393132 GGCGAAGGAAGGAAGGAAGG 60.393 60.0 0.00 0.0 0.0 3.46 F
924 2001 0.613777 GCGAAGGAAGGAAGGAAGGA 59.386 55.0 0.00 0.0 0.0 3.36 F
1665 3050 0.681175 ATGCTGTGGTTTGAAAGCCC 59.319 50.0 4.53 0.0 34.7 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 3330 1.908793 CCAGGTCAGACCGTCACCT 60.909 63.158 14.32 4.98 44.90 4.00 R
2709 4097 2.225267 TGCGATAGATGGACCTATCCCA 60.225 50.000 0.00 0.00 41.05 4.37 R
3128 4537 0.036732 GACCAGGGCACAGTTCATCA 59.963 55.000 0.00 0.00 0.00 3.07 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 81 7.060633 CGCTTTTGTCGCTTTTCTAACATATTT 59.939 33.333 0.00 0.00 0.00 1.40
445 446 0.670546 CACGGAGAAGAATGTGCGGT 60.671 55.000 0.00 0.00 38.00 5.68
552 554 2.959507 AATTTGCGGTTCCCATTAGC 57.040 45.000 0.00 0.00 0.00 3.09
558 560 1.810412 GCGGTTCCCATTAGCCACTAG 60.810 57.143 0.00 0.00 0.00 2.57
582 584 0.601046 CATCATATGCGACGGCTGGT 60.601 55.000 0.00 0.00 40.82 4.00
587 589 0.458889 TATGCGACGGCTGGTTACAC 60.459 55.000 0.00 0.00 40.82 2.90
588 590 2.356553 GCGACGGCTGGTTACACA 60.357 61.111 0.00 0.00 35.83 3.72
597 599 4.097741 ACGGCTGGTTACACACGTTATATA 59.902 41.667 0.00 0.00 32.12 0.86
601 603 5.534207 TGGTTACACACGTTATATAGGGG 57.466 43.478 0.00 0.00 0.00 4.79
602 604 5.207354 TGGTTACACACGTTATATAGGGGA 58.793 41.667 0.00 0.00 0.00 4.81
606 608 2.565834 CACACGTTATATAGGGGAGGGG 59.434 54.545 0.00 0.00 0.00 4.79
609 611 3.260128 CACGTTATATAGGGGAGGGGTTC 59.740 52.174 0.00 0.00 0.00 3.62
621 623 1.226888 GGGGTTCCGAGTTCGATCG 60.227 63.158 9.36 9.36 43.02 3.69
626 628 2.884087 TTCCGAGTTCGATCGCCTGC 62.884 60.000 11.09 0.04 41.37 4.85
633 635 3.857854 CGATCGCCTGCACTGCAC 61.858 66.667 0.26 0.00 33.79 4.57
660 662 4.485024 TTTTGCGAATTTTACACCGCTA 57.515 36.364 0.00 0.00 46.77 4.26
665 667 3.302286 GCGAATTTTACACCGCTAGCTAC 60.302 47.826 13.93 0.00 43.75 3.58
694 696 0.407528 TAATTGGCTGGCCCACTTGA 59.592 50.000 9.28 0.00 45.34 3.02
698 700 2.749441 GCTGGCCCACTTGAGCTC 60.749 66.667 6.82 6.82 0.00 4.09
704 706 4.785453 CCACTTGAGCTCCCCGCC 62.785 72.222 12.15 0.00 40.39 6.13
806 825 2.665649 GGGCTTTTGTTAAATCCCGG 57.334 50.000 0.00 0.00 39.27 5.73
868 1945 2.358737 AAGGCCCAGAAAGCGACG 60.359 61.111 0.00 0.00 0.00 5.12
921 1998 0.613777 GAGGCGAAGGAAGGAAGGAA 59.386 55.000 0.00 0.00 0.00 3.36
922 1999 0.615850 AGGCGAAGGAAGGAAGGAAG 59.384 55.000 0.00 0.00 0.00 3.46
923 2000 0.393132 GGCGAAGGAAGGAAGGAAGG 60.393 60.000 0.00 0.00 0.00 3.46
924 2001 0.613777 GCGAAGGAAGGAAGGAAGGA 59.386 55.000 0.00 0.00 0.00 3.36
1252 2340 4.760047 TTCGCCGCCTTCCAGCTC 62.760 66.667 0.00 0.00 0.00 4.09
1289 2377 4.704833 GCCTCGGCCTTGCAGTGA 62.705 66.667 0.00 0.00 34.56 3.41
1310 2411 2.930826 AAAGCTTCTCCTCGGTTCAA 57.069 45.000 0.00 0.00 0.00 2.69
1516 2621 3.199677 CCGTTTGGTTCAGTACAGTTCA 58.800 45.455 0.00 0.00 0.00 3.18
1551 2923 4.074259 TCGGTAACTGTTGCTGTAGAGTA 58.926 43.478 15.53 0.00 0.00 2.59
1589 2961 2.817844 CGGTTTGGAAGGGGACTAAAAG 59.182 50.000 0.00 0.00 42.68 2.27
1641 3021 4.640201 GCTGGATTGGTGAATTGTAGCTAA 59.360 41.667 0.00 0.00 0.00 3.09
1642 3022 5.449177 GCTGGATTGGTGAATTGTAGCTAAC 60.449 44.000 0.00 0.00 0.00 2.34
1649 3034 4.438744 GGTGAATTGTAGCTAACCACATGC 60.439 45.833 0.00 0.00 0.00 4.06
1665 3050 0.681175 ATGCTGTGGTTTGAAAGCCC 59.319 50.000 4.53 0.00 34.70 5.19
1699 3084 1.633432 TCCATGGAGGTTTAGTGGTGG 59.367 52.381 11.44 0.00 39.02 4.61
1945 3330 6.620877 ACTATGTGTGGGTGAAGATAAGAA 57.379 37.500 0.00 0.00 0.00 2.52
1953 3338 3.522553 GGTGAAGATAAGAAGGTGACGG 58.477 50.000 0.00 0.00 0.00 4.79
2015 3400 4.819630 TGTCAATGTGGGTTTCAGTTCTAC 59.180 41.667 0.00 0.00 0.00 2.59
2041 3426 9.342308 CATATTGTTCCTACCATCTTTGTACAT 57.658 33.333 0.00 0.00 0.00 2.29
2087 3472 2.892215 TGGATTGTGCAAAATCAGCAGA 59.108 40.909 27.00 6.26 43.63 4.26
2088 3473 3.057104 TGGATTGTGCAAAATCAGCAGAG 60.057 43.478 27.00 0.00 43.63 3.35
2089 3474 2.427232 TTGTGCAAAATCAGCAGAGC 57.573 45.000 0.00 0.00 43.63 4.09
2090 3475 1.612676 TGTGCAAAATCAGCAGAGCT 58.387 45.000 0.00 0.00 43.63 4.09
2168 3553 8.271458 TGCTATTCTGTTATATTGAGGTTGGAA 58.729 33.333 0.00 0.00 0.00 3.53
2240 3625 4.952460 TGCCGGTTGGTTAGATACTAATC 58.048 43.478 1.90 0.00 37.67 1.75
2272 3657 7.091443 ACTAACTCAACACATAGCTGACTTAC 58.909 38.462 0.00 0.00 0.00 2.34
2325 3710 9.736414 ATATTATCTGAAATCCTTCATCTGTGG 57.264 33.333 0.00 0.00 40.78 4.17
2547 3932 5.365619 TCTATCGTTGCTTTATTTCTCCCC 58.634 41.667 0.00 0.00 0.00 4.81
2551 3936 4.830600 TCGTTGCTTTATTTCTCCCCTTTT 59.169 37.500 0.00 0.00 0.00 2.27
2552 3937 4.923281 CGTTGCTTTATTTCTCCCCTTTTG 59.077 41.667 0.00 0.00 0.00 2.44
2553 3938 5.278758 CGTTGCTTTATTTCTCCCCTTTTGA 60.279 40.000 0.00 0.00 0.00 2.69
2554 3939 5.722021 TGCTTTATTTCTCCCCTTTTGAC 57.278 39.130 0.00 0.00 0.00 3.18
2789 4177 1.129437 GTTGAGAAGCGCATCAAGGAC 59.871 52.381 19.06 8.34 36.16 3.85
2836 4224 5.408604 GGTGAGTTATTGAACACGACTCAAT 59.591 40.000 6.12 13.20 45.64 2.57
2851 4240 5.643348 ACGACTCAATGCATTATCAGTTGAA 59.357 36.000 25.55 4.01 0.00 2.69
2872 4261 7.197071 TGAATTAGACAATGCGTTTACAAGT 57.803 32.000 0.00 0.00 0.00 3.16
2960 4349 9.630098 TGCACTTGAATCATAAGATTTTTCTTC 57.370 29.630 0.00 0.00 44.30 2.87
2996 4385 6.711277 TGATGTGCTTAAAGGAGTAGACATT 58.289 36.000 0.00 0.00 0.00 2.71
3013 4402 4.038402 AGACATTGCTAAATAATGCTGGGC 59.962 41.667 0.00 0.00 38.72 5.36
3033 4422 2.868839 GCCGTGCTACACTGGAACTTAA 60.869 50.000 11.13 0.00 32.71 1.85
3082 4490 7.812690 TGTAACTCACTAACTCTGTGAAGTA 57.187 36.000 0.00 0.00 42.85 2.24
3084 4492 8.350722 TGTAACTCACTAACTCTGTGAAGTAAG 58.649 37.037 0.00 0.00 42.85 2.34
3086 4494 5.834204 ACTCACTAACTCTGTGAAGTAAGGT 59.166 40.000 0.00 0.00 42.85 3.50
3165 4574 5.649395 CCTGGTCTGATTGATTTTGCTAAGA 59.351 40.000 0.00 0.00 0.00 2.10
3217 4626 2.517959 TGATGCCTGCCTAAATATGCC 58.482 47.619 0.00 0.00 0.00 4.40
3223 4632 2.930040 CCTGCCTAAATATGCCGATACG 59.070 50.000 0.00 0.00 0.00 3.06
3244 4653 2.813754 GCAATCCACTGTGTGCTTAGAA 59.186 45.455 12.88 0.00 34.13 2.10
3288 4697 9.905713 TCCTCTAATGTTTGCTTTATTGATACT 57.094 29.630 0.00 0.00 0.00 2.12
3291 4700 9.120538 TCTAATGTTTGCTTTATTGATACTCCC 57.879 33.333 0.00 0.00 0.00 4.30
3292 4701 7.961326 AATGTTTGCTTTATTGATACTCCCT 57.039 32.000 0.00 0.00 0.00 4.20
3293 4702 7.573968 ATGTTTGCTTTATTGATACTCCCTC 57.426 36.000 0.00 0.00 0.00 4.30
3294 4703 5.885912 TGTTTGCTTTATTGATACTCCCTCC 59.114 40.000 0.00 0.00 0.00 4.30
3295 4704 4.336889 TGCTTTATTGATACTCCCTCCG 57.663 45.455 0.00 0.00 0.00 4.63
3296 4705 3.067833 GCTTTATTGATACTCCCTCCGC 58.932 50.000 0.00 0.00 0.00 5.54
3297 4706 3.665190 CTTTATTGATACTCCCTCCGCC 58.335 50.000 0.00 0.00 0.00 6.13
3298 4707 1.640917 TATTGATACTCCCTCCGCCC 58.359 55.000 0.00 0.00 0.00 6.13
3299 4708 1.128188 ATTGATACTCCCTCCGCCCC 61.128 60.000 0.00 0.00 0.00 5.80
3300 4709 2.122989 GATACTCCCTCCGCCCCA 60.123 66.667 0.00 0.00 0.00 4.96
3301 4710 1.536662 GATACTCCCTCCGCCCCAT 60.537 63.158 0.00 0.00 0.00 4.00
3302 4711 0.252103 GATACTCCCTCCGCCCCATA 60.252 60.000 0.00 0.00 0.00 2.74
3303 4712 0.192566 ATACTCCCTCCGCCCCATAA 59.807 55.000 0.00 0.00 0.00 1.90
3304 4713 0.192566 TACTCCCTCCGCCCCATAAT 59.807 55.000 0.00 0.00 0.00 1.28
3305 4714 1.376466 CTCCCTCCGCCCCATAATG 59.624 63.158 0.00 0.00 0.00 1.90
3306 4715 1.385347 TCCCTCCGCCCCATAATGT 60.385 57.895 0.00 0.00 0.00 2.71
3307 4716 0.104882 TCCCTCCGCCCCATAATGTA 60.105 55.000 0.00 0.00 0.00 2.29
3308 4717 0.768622 CCCTCCGCCCCATAATGTAA 59.231 55.000 0.00 0.00 0.00 2.41
3309 4718 1.271379 CCCTCCGCCCCATAATGTAAG 60.271 57.143 0.00 0.00 0.00 2.34
3310 4719 1.697432 CCTCCGCCCCATAATGTAAGA 59.303 52.381 0.00 0.00 0.00 2.10
3311 4720 2.550208 CCTCCGCCCCATAATGTAAGAC 60.550 54.545 0.00 0.00 0.00 3.01
3312 4721 1.069513 TCCGCCCCATAATGTAAGACG 59.930 52.381 0.00 0.00 0.00 4.18
3313 4722 1.202604 CCGCCCCATAATGTAAGACGT 60.203 52.381 0.00 0.00 0.00 4.34
3314 4723 2.557317 CGCCCCATAATGTAAGACGTT 58.443 47.619 0.00 0.00 0.00 3.99
3315 4724 2.940410 CGCCCCATAATGTAAGACGTTT 59.060 45.455 0.00 0.00 0.00 3.60
3316 4725 3.375922 CGCCCCATAATGTAAGACGTTTT 59.624 43.478 0.00 0.00 0.00 2.43
3317 4726 4.142556 CGCCCCATAATGTAAGACGTTTTT 60.143 41.667 0.00 0.00 0.00 1.94
3361 4770 6.693315 AAAACATCTTACATTATGGGACGG 57.307 37.500 0.00 0.00 0.00 4.79
3362 4771 5.623956 AACATCTTACATTATGGGACGGA 57.376 39.130 0.00 0.00 0.00 4.69
3363 4772 5.215252 ACATCTTACATTATGGGACGGAG 57.785 43.478 0.00 0.00 0.00 4.63
3364 4773 4.040461 ACATCTTACATTATGGGACGGAGG 59.960 45.833 0.00 0.00 0.00 4.30
3365 4774 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3366 4775 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3367 4776 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3433 4845 2.225019 GCCATTCATGATCGGACATGTC 59.775 50.000 17.91 17.91 45.21 3.06
3445 4857 7.614494 TGATCGGACATGTCAACATATGATAT 58.386 34.615 26.47 5.06 40.16 1.63
3609 5029 1.553248 ACCTGCGCTAGTTTCATGGTA 59.447 47.619 9.73 0.00 0.00 3.25
3629 5049 1.312371 GCAGAATTTGCGGCCAGGTA 61.312 55.000 2.24 0.00 44.09 3.08
3668 5088 9.219603 TCTAATTATTCAGGAACAGACAAACAG 57.780 33.333 0.00 0.00 0.00 3.16
3670 5090 3.281727 TTCAGGAACAGACAAACAGCT 57.718 42.857 0.00 0.00 0.00 4.24
3917 5339 4.336433 CGCAGATGGATTTTGTGGTATTCT 59.664 41.667 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 4.824537 TGTTGTGCTAATAAGTTTGCCAGA 59.175 37.500 0.00 0.00 35.59 3.86
486 487 1.410517 TGCGTTGCAATGGGAGAAAAA 59.589 42.857 19.93 0.00 34.76 1.94
542 543 1.490490 CCTGCTAGTGGCTAATGGGAA 59.510 52.381 0.00 0.00 42.39 3.97
543 544 1.131638 CCTGCTAGTGGCTAATGGGA 58.868 55.000 0.00 0.00 42.39 4.37
569 571 1.740296 GTGTAACCAGCCGTCGCAT 60.740 57.895 0.00 0.00 37.52 4.73
572 574 2.369629 CGTGTGTAACCAGCCGTCG 61.370 63.158 0.00 0.00 34.36 5.12
574 576 0.388659 TAACGTGTGTAACCAGCCGT 59.611 50.000 0.00 0.00 34.36 5.68
582 584 4.834496 CCCTCCCCTATATAACGTGTGTAA 59.166 45.833 0.00 0.00 0.00 2.41
587 589 2.898662 ACCCCTCCCCTATATAACGTG 58.101 52.381 0.00 0.00 0.00 4.49
588 590 3.514539 GAACCCCTCCCCTATATAACGT 58.485 50.000 0.00 0.00 0.00 3.99
597 599 3.189770 AACTCGGAACCCCTCCCCT 62.190 63.158 0.00 0.00 41.87 4.79
601 603 0.102663 GATCGAACTCGGAACCCCTC 59.897 60.000 0.00 0.00 40.29 4.30
602 604 1.664321 CGATCGAACTCGGAACCCCT 61.664 60.000 10.26 0.00 40.29 4.79
606 608 1.139095 AGGCGATCGAACTCGGAAC 59.861 57.895 21.57 0.00 39.05 3.62
609 611 2.956964 GCAGGCGATCGAACTCGG 60.957 66.667 21.57 6.29 39.05 4.63
612 614 1.446792 CAGTGCAGGCGATCGAACT 60.447 57.895 21.57 13.24 0.00 3.01
660 662 3.118371 GCCAATTAGGTGGTACTGTAGCT 60.118 47.826 16.93 0.00 41.12 3.32
665 667 2.643551 CCAGCCAATTAGGTGGTACTG 58.356 52.381 13.24 0.00 41.12 2.74
709 711 3.081133 CAGATTGGCGGACGTTCG 58.919 61.111 13.13 13.13 0.00 3.95
729 731 3.782244 CTGTCTGCCGCTCGTTGC 61.782 66.667 0.00 0.00 38.57 4.17
744 746 1.153939 CACTCGCGAAGACCTCCTG 60.154 63.158 11.33 0.00 0.00 3.86
830 1907 2.100584 TGCGATGGTTCCATTAATTGGC 59.899 45.455 5.77 0.00 46.01 4.52
835 1912 1.748493 GCCTTGCGATGGTTCCATTAA 59.252 47.619 5.77 2.38 0.00 1.40
870 1947 1.273887 GTCGGCAAGCGATTCGATG 59.726 57.895 10.88 8.93 34.13 3.84
921 1998 3.432588 CAGTCGCGTCGGTCTCCT 61.433 66.667 5.77 0.00 0.00 3.69
922 1999 1.915614 TAACAGTCGCGTCGGTCTCC 61.916 60.000 9.60 0.00 0.00 3.71
923 2000 0.098376 ATAACAGTCGCGTCGGTCTC 59.902 55.000 9.60 0.00 0.00 3.36
924 2001 0.098376 GATAACAGTCGCGTCGGTCT 59.902 55.000 9.60 0.97 0.00 3.85
1049 2137 1.601663 GCTGGATCGATCGAAGTGGAG 60.602 57.143 23.50 14.00 0.00 3.86
1287 2375 2.930826 ACCGAGGAGAAGCTTTTTCA 57.069 45.000 0.00 0.00 0.00 2.69
1289 2377 3.208747 TGAACCGAGGAGAAGCTTTTT 57.791 42.857 0.00 0.00 0.00 1.94
1310 2411 2.099921 ACGCAAATCTATCGTCAGAGCT 59.900 45.455 0.00 0.00 0.00 4.09
1336 2437 5.446860 AGATATCTACACACGAGAGGGAAA 58.553 41.667 2.53 0.00 38.45 3.13
1475 2576 3.308866 CGGCAGAAAACCCTAGAAATACG 59.691 47.826 0.00 0.00 0.00 3.06
1476 2577 4.259356 ACGGCAGAAAACCCTAGAAATAC 58.741 43.478 0.00 0.00 0.00 1.89
1526 2631 4.890088 TCTACAGCAACAGTTACCGATTT 58.110 39.130 0.00 0.00 0.00 2.17
1551 2923 3.051081 ACCGAAGACGTGTACTCTACT 57.949 47.619 0.00 0.00 37.88 2.57
1649 3034 1.200020 GATCGGGCTTTCAAACCACAG 59.800 52.381 0.00 0.00 0.00 3.66
1699 3084 8.218338 ACATCATATCAAATTGAAGACCAGAC 57.782 34.615 0.00 0.00 0.00 3.51
1790 3175 6.016276 CAGGCCATTTTAGTAACAACAGAACT 60.016 38.462 5.01 0.00 0.00 3.01
1791 3176 6.016610 TCAGGCCATTTTAGTAACAACAGAAC 60.017 38.462 5.01 0.00 0.00 3.01
1882 3267 9.479549 AATGGAAATAGGTGATGTGTTTAGATT 57.520 29.630 0.00 0.00 0.00 2.40
1887 3272 8.109634 ACTAGAATGGAAATAGGTGATGTGTTT 58.890 33.333 0.00 0.00 0.00 2.83
1904 3289 9.436957 ACACATAGTTACTTCAAACTAGAATGG 57.563 33.333 0.00 0.00 43.32 3.16
1926 3311 3.650942 ACCTTCTTATCTTCACCCACACA 59.349 43.478 0.00 0.00 0.00 3.72
1945 3330 1.908793 CCAGGTCAGACCGTCACCT 60.909 63.158 14.32 4.98 44.90 4.00
1953 3338 5.416271 TCCACTAATTTACCAGGTCAGAC 57.584 43.478 0.00 0.00 0.00 3.51
2015 3400 8.731275 TGTACAAAGATGGTAGGAACAATATG 57.269 34.615 0.00 0.00 0.00 1.78
2041 3426 6.712095 AGCTGCAAATGGATATCTTCGATTTA 59.288 34.615 1.02 0.00 39.79 1.40
2087 3472 6.956202 AAAATTATAAGAGCATGCTCAGCT 57.044 33.333 40.91 28.72 46.82 4.24
2088 3473 9.339492 GATAAAAATTATAAGAGCATGCTCAGC 57.661 33.333 40.91 21.69 44.99 4.26
2091 3476 9.339492 GCAGATAAAAATTATAAGAGCATGCTC 57.661 33.333 35.57 35.57 43.03 4.26
2105 3490 8.295288 CAGTTTCAGAGTGAGCAGATAAAAATT 58.705 33.333 0.00 0.00 0.00 1.82
2240 3625 2.387185 TGTGTTGAGTTAGTACGTGCG 58.613 47.619 0.00 0.00 0.00 5.34
2272 3657 8.682936 ATAATAAGAAGGTAGGATGCAAGTTG 57.317 34.615 0.00 0.00 0.00 3.16
2299 3684 9.736414 CCACAGATGAAGGATTTCAGATAATAT 57.264 33.333 0.00 0.00 45.89 1.28
2304 3689 5.682659 CTCCACAGATGAAGGATTTCAGAT 58.317 41.667 0.00 0.00 45.89 2.90
2322 3707 7.483307 ACAAATTGATTATACACATGCTCCAC 58.517 34.615 0.00 0.00 0.00 4.02
2325 3710 7.645340 GTGGACAAATTGATTATACACATGCTC 59.355 37.037 0.00 0.00 0.00 4.26
2529 3914 4.783764 AAAGGGGAGAAATAAAGCAACG 57.216 40.909 0.00 0.00 0.00 4.10
2547 3932 6.365789 TCTGCACAAGAAACAAAAGTCAAAAG 59.634 34.615 0.00 0.00 29.54 2.27
2551 3936 5.581126 ATCTGCACAAGAAACAAAAGTCA 57.419 34.783 0.00 0.00 38.79 3.41
2552 3937 6.892310 AAATCTGCACAAGAAACAAAAGTC 57.108 33.333 0.00 0.00 38.79 3.01
2553 3938 6.873076 TGAAAATCTGCACAAGAAACAAAAGT 59.127 30.769 0.00 0.00 38.79 2.66
2554 3939 7.293402 TGAAAATCTGCACAAGAAACAAAAG 57.707 32.000 0.00 0.00 38.79 2.27
2709 4097 2.225267 TGCGATAGATGGACCTATCCCA 60.225 50.000 0.00 0.00 41.05 4.37
2789 4177 5.980116 CCACAAACTAGGATGATTCTACTCG 59.020 44.000 4.26 0.00 0.00 4.18
2851 4240 7.661127 TGTACTTGTAAACGCATTGTCTAAT 57.339 32.000 0.00 0.00 0.00 1.73
2917 4306 6.767902 TCAAGTGCACAAGTAAATCTTCTCTT 59.232 34.615 21.04 0.00 33.63 2.85
2921 4310 7.362662 TGATTCAAGTGCACAAGTAAATCTTC 58.637 34.615 21.04 3.24 33.63 2.87
2960 4349 1.800586 AGCACATCAACGCACACTAAG 59.199 47.619 0.00 0.00 0.00 2.18
2996 4385 1.317613 CGGCCCAGCATTATTTAGCA 58.682 50.000 0.00 0.00 0.00 3.49
3013 4402 2.736144 TAAGTTCCAGTGTAGCACGG 57.264 50.000 0.00 0.00 39.64 4.94
3033 4422 4.081752 TGCAGGAATTTGCCGAACATTATT 60.082 37.500 0.00 0.00 43.43 1.40
3082 4490 6.605594 TGAATCAAAAGTGTCCAAGTTACCTT 59.394 34.615 0.00 0.00 0.00 3.50
3084 4492 6.385649 TGAATCAAAAGTGTCCAAGTTACC 57.614 37.500 0.00 0.00 0.00 2.85
3086 4494 6.378564 TGGTTGAATCAAAAGTGTCCAAGTTA 59.621 34.615 0.00 0.00 0.00 2.24
3128 4537 0.036732 GACCAGGGCACAGTTCATCA 59.963 55.000 0.00 0.00 0.00 3.07
3165 4574 8.896744 CAAGTCATGTCCAGATGTTTGTAATAT 58.103 33.333 0.00 0.00 0.00 1.28
3217 4626 1.324435 CACACAGTGGATTGCGTATCG 59.676 52.381 5.31 0.00 33.82 2.92
3223 4632 2.426522 TCTAAGCACACAGTGGATTGC 58.573 47.619 5.31 6.01 33.64 3.56
3262 4671 9.905713 AGTATCAATAAAGCAAACATTAGAGGA 57.094 29.630 0.00 0.00 0.00 3.71
3285 4694 0.192566 ATTATGGGGCGGAGGGAGTA 59.807 55.000 0.00 0.00 0.00 2.59
3286 4695 1.073706 ATTATGGGGCGGAGGGAGT 60.074 57.895 0.00 0.00 0.00 3.85
3287 4696 1.376466 CATTATGGGGCGGAGGGAG 59.624 63.158 0.00 0.00 0.00 4.30
3288 4697 0.104882 TACATTATGGGGCGGAGGGA 60.105 55.000 0.00 0.00 0.00 4.20
3289 4698 0.768622 TTACATTATGGGGCGGAGGG 59.231 55.000 0.00 0.00 0.00 4.30
3290 4699 1.697432 TCTTACATTATGGGGCGGAGG 59.303 52.381 0.00 0.00 0.00 4.30
3291 4700 2.767505 GTCTTACATTATGGGGCGGAG 58.232 52.381 0.00 0.00 0.00 4.63
3292 4701 1.069513 CGTCTTACATTATGGGGCGGA 59.930 52.381 0.00 0.00 0.00 5.54
3293 4702 1.202604 ACGTCTTACATTATGGGGCGG 60.203 52.381 11.76 0.00 0.00 6.13
3294 4703 2.234300 ACGTCTTACATTATGGGGCG 57.766 50.000 0.00 2.66 0.00 6.13
3295 4704 4.976224 AAAACGTCTTACATTATGGGGC 57.024 40.909 0.00 0.00 0.00 5.80
3337 4746 6.887545 TCCGTCCCATAATGTAAGATGTTTTT 59.112 34.615 0.00 0.00 0.00 1.94
3338 4747 6.419791 TCCGTCCCATAATGTAAGATGTTTT 58.580 36.000 0.00 0.00 0.00 2.43
3339 4748 5.996644 TCCGTCCCATAATGTAAGATGTTT 58.003 37.500 0.00 0.00 0.00 2.83
3340 4749 5.454755 CCTCCGTCCCATAATGTAAGATGTT 60.455 44.000 0.00 0.00 0.00 2.71
3341 4750 4.040461 CCTCCGTCCCATAATGTAAGATGT 59.960 45.833 0.00 0.00 0.00 3.06
3342 4751 4.563580 CCCTCCGTCCCATAATGTAAGATG 60.564 50.000 0.00 0.00 0.00 2.90
3343 4752 3.583086 CCCTCCGTCCCATAATGTAAGAT 59.417 47.826 0.00 0.00 0.00 2.40
3344 4753 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3345 4754 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3346 4755 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3347 4756 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3348 4757 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3349 4758 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3350 4759 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3351 4760 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3352 4761 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3353 4762 1.145325 CTAGTACTCCCTCCGTCCCAT 59.855 57.143 0.00 0.00 0.00 4.00
3354 4763 0.549950 CTAGTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
3355 4764 0.550432 ACTAGTACTCCCTCCGTCCC 59.450 60.000 0.00 0.00 0.00 4.46
3356 4765 2.433662 AACTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
3357 4766 3.876320 CACTAACTAGTACTCCCTCCGTC 59.124 52.174 0.00 0.00 34.13 4.79
3358 4767 3.883669 CACTAACTAGTACTCCCTCCGT 58.116 50.000 0.00 0.00 34.13 4.69
3359 4768 2.617774 GCACTAACTAGTACTCCCTCCG 59.382 54.545 0.00 0.00 34.13 4.63
3360 4769 3.884693 GAGCACTAACTAGTACTCCCTCC 59.115 52.174 0.00 0.00 39.64 4.30
3361 4770 4.525024 TGAGCACTAACTAGTACTCCCTC 58.475 47.826 12.55 1.02 43.10 4.30
3362 4771 4.587976 TGAGCACTAACTAGTACTCCCT 57.412 45.455 12.55 0.00 43.10 4.20
3363 4772 4.098196 CCTTGAGCACTAACTAGTACTCCC 59.902 50.000 12.55 0.00 43.10 4.30
3364 4773 4.948621 TCCTTGAGCACTAACTAGTACTCC 59.051 45.833 12.55 0.00 43.10 3.85
3365 4774 6.702716 ATCCTTGAGCACTAACTAGTACTC 57.297 41.667 0.00 9.37 43.72 2.59
3366 4775 6.663953 TCAATCCTTGAGCACTAACTAGTACT 59.336 38.462 0.00 0.00 34.08 2.73
3367 4776 6.864342 TCAATCCTTGAGCACTAACTAGTAC 58.136 40.000 0.00 0.00 34.08 2.73
3389 4798 7.555914 TGGCATGTTCAAGCTTTACTATAATCA 59.444 33.333 0.00 0.00 0.00 2.57
3411 4822 2.223745 CATGTCCGATCATGAATGGCA 58.776 47.619 0.00 7.68 45.41 4.92
3445 4857 6.070021 CCATCACCAATAGGAGAAGGCATATA 60.070 42.308 0.00 0.00 36.74 0.86
3496 4916 2.408271 TTGGAATTCATCAGCTCGCT 57.592 45.000 7.93 0.00 0.00 4.93
3499 4919 4.082354 GGGCATATTGGAATTCATCAGCTC 60.082 45.833 7.93 0.00 0.00 4.09
3668 5088 6.059484 ACATCTAGTCTAGAAGTCAGGTAGC 58.941 44.000 13.58 0.00 38.50 3.58
3670 5090 8.550280 TCTACATCTAGTCTAGAAGTCAGGTA 57.450 38.462 18.57 10.85 37.79 3.08
3795 5216 9.778741 TGAAAGTAGAACAAATGAGTAATGAGT 57.221 29.630 0.00 0.00 0.00 3.41
3888 5310 4.487948 CACAAAATCCATCTGCGTCAATT 58.512 39.130 0.00 0.00 0.00 2.32
3890 5312 2.228582 CCACAAAATCCATCTGCGTCAA 59.771 45.455 0.00 0.00 0.00 3.18
3894 5316 4.336433 AGAATACCACAAAATCCATCTGCG 59.664 41.667 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.