Multiple sequence alignment - TraesCS1D01G222400

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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 TraesCS1D01G222400 chr1D 100.000 3288 0 0 1 3288 309985846 309982559 0.000000e+00 6072.0
1 TraesCS1D01G222400 chr2D 96.507 1603 51 3 630 2231 114668275 114666677 0.000000e+00 2645.0
2 TraesCS1D01G222400 chr2D 88.176 888 97 5 2252 3132 518292378 518293264 0.000000e+00 1051.0
3 TraesCS1D01G222400 chr5D 96.442 1602 56 1 630 2231 363005537 363007137 0.000000e+00 2641.0
4 TraesCS1D01G222400 chr3D 96.130 1602 59 1 630 2231 579163365 579164963 0.000000e+00 2612.0
5 TraesCS1D01G222400 chr7D 96.060 1599 59 2 630 2228 604446522 604448116 0.000000e+00 2601.0
6 TraesCS1D01G222400 chr7D 95.415 916 33 3 2225 3132 604461632 604462546 0.000000e+00 1450.0
7 TraesCS1D01G222400 chr4B 95.737 1595 64 3 636 2227 525388701 525387108 0.000000e+00 2566.0
8 TraesCS1D01G222400 chr4B 95.443 1602 68 4 630 2228 525305947 525307546 0.000000e+00 2549.0
9 TraesCS1D01G222400 chr5A 95.443 1602 72 1 630 2231 524632949 524631349 0.000000e+00 2553.0
10 TraesCS1D01G222400 chr5A 95.504 645 22 1 2233 2870 524630979 524630335 0.000000e+00 1024.0
11 TraesCS1D01G222400 chr1A 95.217 1610 68 4 630 2231 50971193 50969585 0.000000e+00 2538.0
12 TraesCS1D01G222400 chr1A 91.331 646 21 7 1 633 389830055 389829432 0.000000e+00 850.0
13 TraesCS1D01G222400 chr1A 78.286 175 15 16 3128 3288 389829438 389829273 1.260000e-14 91.6
14 TraesCS1D01G222400 chr2A 95.131 1602 75 1 630 2231 676711115 676712713 0.000000e+00 2523.0
15 TraesCS1D01G222400 chr2B 91.676 913 64 8 2229 3132 629028337 629027428 0.000000e+00 1254.0
16 TraesCS1D01G222400 chr2B 91.196 920 69 6 2225 3135 71596544 71597460 0.000000e+00 1240.0
17 TraesCS1D01G222400 chr2B 91.000 900 70 5 2242 3132 90462876 90463773 0.000000e+00 1203.0
18 TraesCS1D01G222400 chr5B 91.218 911 71 6 2225 3132 514923687 514924591 0.000000e+00 1230.0
19 TraesCS1D01G222400 chr5B 87.879 924 97 9 2225 3135 709363588 709362667 0.000000e+00 1072.0
20 TraesCS1D01G222400 chr5B 87.391 920 97 9 2225 3132 121638704 121637792 0.000000e+00 1038.0
21 TraesCS1D01G222400 chr6B 90.747 897 71 6 2243 3130 332423590 332424483 0.000000e+00 1186.0
22 TraesCS1D01G222400 chr3A 92.476 638 22 3 1 633 128543569 128544185 0.000000e+00 889.0
23 TraesCS1D01G222400 chr3A 80.142 141 10 9 3131 3257 128544182 128544318 4.520000e-14 89.8
24 TraesCS1D01G222400 chr1B 92.160 625 28 8 1 610 419972358 419972976 0.000000e+00 863.0


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 TraesCS1D01G222400 chr1D 309982559 309985846 3287 True 6072.0 6072 100.0000 1 3288 1 chr1D.!!$R1 3287
1 TraesCS1D01G222400 chr2D 114666677 114668275 1598 True 2645.0 2645 96.5070 630 2231 1 chr2D.!!$R1 1601
2 TraesCS1D01G222400 chr2D 518292378 518293264 886 False 1051.0 1051 88.1760 2252 3132 1 chr2D.!!$F1 880
3 TraesCS1D01G222400 chr5D 363005537 363007137 1600 False 2641.0 2641 96.4420 630 2231 1 chr5D.!!$F1 1601
4 TraesCS1D01G222400 chr3D 579163365 579164963 1598 False 2612.0 2612 96.1300 630 2231 1 chr3D.!!$F1 1601
5 TraesCS1D01G222400 chr7D 604446522 604448116 1594 False 2601.0 2601 96.0600 630 2228 1 chr7D.!!$F1 1598
6 TraesCS1D01G222400 chr7D 604461632 604462546 914 False 1450.0 1450 95.4150 2225 3132 1 chr7D.!!$F2 907
7 TraesCS1D01G222400 chr4B 525387108 525388701 1593 True 2566.0 2566 95.7370 636 2227 1 chr4B.!!$R1 1591
8 TraesCS1D01G222400 chr4B 525305947 525307546 1599 False 2549.0 2549 95.4430 630 2228 1 chr4B.!!$F1 1598
9 TraesCS1D01G222400 chr5A 524630335 524632949 2614 True 1788.5 2553 95.4735 630 2870 2 chr5A.!!$R1 2240
10 TraesCS1D01G222400 chr1A 50969585 50971193 1608 True 2538.0 2538 95.2170 630 2231 1 chr1A.!!$R1 1601
11 TraesCS1D01G222400 chr1A 389829273 389830055 782 True 470.8 850 84.8085 1 3288 2 chr1A.!!$R2 3287
12 TraesCS1D01G222400 chr2A 676711115 676712713 1598 False 2523.0 2523 95.1310 630 2231 1 chr2A.!!$F1 1601
13 TraesCS1D01G222400 chr2B 629027428 629028337 909 True 1254.0 1254 91.6760 2229 3132 1 chr2B.!!$R1 903
14 TraesCS1D01G222400 chr2B 71596544 71597460 916 False 1240.0 1240 91.1960 2225 3135 1 chr2B.!!$F1 910
15 TraesCS1D01G222400 chr2B 90462876 90463773 897 False 1203.0 1203 91.0000 2242 3132 1 chr2B.!!$F2 890
16 TraesCS1D01G222400 chr5B 514923687 514924591 904 False 1230.0 1230 91.2180 2225 3132 1 chr5B.!!$F1 907
17 TraesCS1D01G222400 chr5B 709362667 709363588 921 True 1072.0 1072 87.8790 2225 3135 1 chr5B.!!$R2 910
18 TraesCS1D01G222400 chr5B 121637792 121638704 912 True 1038.0 1038 87.3910 2225 3132 1 chr5B.!!$R1 907
19 TraesCS1D01G222400 chr6B 332423590 332424483 893 False 1186.0 1186 90.7470 2243 3130 1 chr6B.!!$F1 887
20 TraesCS1D01G222400 chr3A 128543569 128544318 749 False 489.4 889 86.3090 1 3257 2 chr3A.!!$F1 3256
21 TraesCS1D01G222400 chr1B 419972358 419972976 618 False 863.0 863 92.1600 1 610 1 chr1B.!!$F1 609

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
603 629 0.094216 CGTGATTGCTCAAGTCGCAG 59.906 55.0 0.0 0.0 38.8 5.18 F
848 875 0.112412 AACTCCCGCCACCATTCTTT 59.888 50.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 2662 0.924363 GTCATCGTCATCGTCGTCGG 60.924 60.0 1.55 0.0 38.33 4.79 R
2843 3274 0.976073 ACCTAGCACACCTACGCCAT 60.976 55.0 0.00 0.0 0.00 4.40 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
517 539 1.790387 GCACTGCGGCAGAGTAAAG 59.210 57.895 34.70 17.06 35.18 1.85
564 590 2.125552 CATGGCTTCGACTCCGCA 60.126 61.111 0.00 0.00 35.37 5.69
565 591 2.169789 CATGGCTTCGACTCCGCAG 61.170 63.158 0.00 0.00 35.37 5.18
574 600 1.578206 CGACTCCGCAGTGTCTCTCA 61.578 60.000 0.00 0.00 34.93 3.27
593 619 1.221840 CTGGCCCTACGTGATTGCT 59.778 57.895 0.00 0.00 0.00 3.91
594 620 0.811616 CTGGCCCTACGTGATTGCTC 60.812 60.000 0.00 0.00 0.00 4.26
595 621 1.220749 GGCCCTACGTGATTGCTCA 59.779 57.895 0.00 0.00 0.00 4.26
596 622 0.392461 GGCCCTACGTGATTGCTCAA 60.392 55.000 0.00 0.00 31.85 3.02
597 623 1.009829 GCCCTACGTGATTGCTCAAG 58.990 55.000 0.00 0.00 36.98 3.02
598 624 1.676014 GCCCTACGTGATTGCTCAAGT 60.676 52.381 0.00 0.64 44.66 3.16
599 625 2.271800 CCCTACGTGATTGCTCAAGTC 58.728 52.381 0.00 0.00 42.15 3.01
600 626 1.920574 CCTACGTGATTGCTCAAGTCG 59.079 52.381 0.00 0.00 42.15 4.18
601 627 1.321743 CTACGTGATTGCTCAAGTCGC 59.678 52.381 0.00 0.00 42.15 5.19
602 628 0.599991 ACGTGATTGCTCAAGTCGCA 60.600 50.000 0.00 0.00 39.49 5.10
603 629 0.094216 CGTGATTGCTCAAGTCGCAG 59.906 55.000 0.00 0.00 38.80 5.18
604 630 1.151668 GTGATTGCTCAAGTCGCAGT 58.848 50.000 0.00 0.00 38.80 4.40
605 631 2.337583 GTGATTGCTCAAGTCGCAGTA 58.662 47.619 0.00 0.00 38.80 2.74
606 632 2.736721 GTGATTGCTCAAGTCGCAGTAA 59.263 45.455 0.00 0.00 38.80 2.24
607 633 2.995939 TGATTGCTCAAGTCGCAGTAAG 59.004 45.455 0.00 0.00 38.80 2.34
608 634 2.526304 TTGCTCAAGTCGCAGTAAGT 57.474 45.000 0.00 0.00 38.80 2.24
609 635 2.065993 TGCTCAAGTCGCAGTAAGTC 57.934 50.000 0.00 0.00 32.80 3.01
610 636 0.985549 GCTCAAGTCGCAGTAAGTCG 59.014 55.000 0.00 0.00 0.00 4.18
611 637 1.666311 GCTCAAGTCGCAGTAAGTCGT 60.666 52.381 0.00 0.00 0.00 4.34
612 638 2.413765 GCTCAAGTCGCAGTAAGTCGTA 60.414 50.000 0.00 0.00 0.00 3.43
613 639 3.162068 CTCAAGTCGCAGTAAGTCGTAC 58.838 50.000 0.00 0.00 0.00 3.67
614 640 2.810274 TCAAGTCGCAGTAAGTCGTACT 59.190 45.455 0.00 0.00 44.33 2.73
621 647 0.531200 AGTAAGTCGTACTGCTGGCC 59.469 55.000 0.00 0.00 41.75 5.36
622 648 0.245539 GTAAGTCGTACTGCTGGCCA 59.754 55.000 4.71 4.71 0.00 5.36
623 649 0.245539 TAAGTCGTACTGCTGGCCAC 59.754 55.000 0.00 0.00 0.00 5.01
624 650 1.472662 AAGTCGTACTGCTGGCCACT 61.473 55.000 0.00 0.00 0.00 4.00
625 651 1.446272 GTCGTACTGCTGGCCACTC 60.446 63.158 0.00 0.00 0.00 3.51
626 652 2.507102 CGTACTGCTGGCCACTCG 60.507 66.667 0.00 0.00 0.00 4.18
627 653 2.815647 GTACTGCTGGCCACTCGC 60.816 66.667 0.00 4.52 0.00 5.03
628 654 2.997315 TACTGCTGGCCACTCGCT 60.997 61.111 15.70 0.30 37.74 4.93
701 727 3.483869 GAAGCAGGGGAGGGCGAT 61.484 66.667 0.00 0.00 34.54 4.58
777 803 1.847328 AAAATCGGCGGGAGGATTTT 58.153 45.000 7.21 8.71 44.02 1.82
848 875 0.112412 AACTCCCGCCACCATTCTTT 59.888 50.000 0.00 0.00 0.00 2.52
1074 1102 1.467920 GCTGCAGCTAGGGTTTGATT 58.532 50.000 31.33 0.00 38.21 2.57
1099 1127 2.722094 TGCATGGTTGATTAGTGGTCC 58.278 47.619 0.00 0.00 0.00 4.46
1146 1174 5.881777 TGCTATGTTGCGGTTACAATTTA 57.118 34.783 0.00 0.00 35.36 1.40
1420 1448 1.004185 CTATGCTCACTGTCAATGCGC 60.004 52.381 0.00 0.00 0.00 6.09
1469 1497 1.827969 ACGCAAGATCTTAGTCAGGCT 59.172 47.619 7.86 0.00 43.62 4.58
1508 1536 2.988493 CCAATTTGCTCCATCGTTTGTG 59.012 45.455 0.00 0.00 0.00 3.33
1607 1638 0.391228 TCGTTGAGCCAACTACTGCA 59.609 50.000 13.76 0.00 41.62 4.41
1612 1655 0.321122 GAGCCAACTACTGCAGCTGT 60.321 55.000 15.27 10.14 32.97 4.40
1754 1797 2.258109 GGAGTTAGGACTGACAAGGGT 58.742 52.381 0.00 0.00 35.88 4.34
1872 1916 2.837591 TGGAGAAGTCGATGGATCCAAA 59.162 45.455 20.67 4.50 34.02 3.28
1976 2020 0.736325 ATGTCGCGGTTAGCTCACAC 60.736 55.000 6.13 0.00 45.59 3.82
2026 2070 2.159099 TGCCTACTCCTAATCGCAACTG 60.159 50.000 0.00 0.00 0.00 3.16
2053 2097 7.285401 ACAACACTTGTGTTTCATTCTTAGGAT 59.715 33.333 15.46 0.00 43.48 3.24
2086 2130 1.202698 GCTGAGTTCCTCAACACACCT 60.203 52.381 0.00 0.00 40.18 4.00
2098 2142 5.129485 CCTCAACACACCTATCCAGAACTAT 59.871 44.000 0.00 0.00 0.00 2.12
2288 2700 4.609947 TGACGACGTACATTTTGTGTAGT 58.390 39.130 0.00 0.00 43.70 2.73
2440 2852 4.161102 AGGTAGTGCTAGGAAGAACTTGT 58.839 43.478 0.00 0.00 38.62 3.16
2525 2943 2.229784 GCTTGCTACTTGTGCTCCATTT 59.770 45.455 0.00 0.00 0.00 2.32
2843 3274 2.535012 TCGTCACCATTGCTGTGTTA 57.465 45.000 0.00 0.00 35.25 2.41
2850 3281 2.013400 CCATTGCTGTGTTATGGCGTA 58.987 47.619 0.00 0.00 33.08 4.42
2877 3308 2.292267 CTAGGTGTGATCATTGTGGGC 58.708 52.381 0.00 0.00 0.00 5.36
2997 3428 5.371115 ACAAAATGCACTTGCGTATTACT 57.629 34.783 9.70 0.00 45.83 2.24
2998 3429 6.489127 ACAAAATGCACTTGCGTATTACTA 57.511 33.333 9.70 0.00 45.83 1.82
2999 3430 6.542852 ACAAAATGCACTTGCGTATTACTAG 58.457 36.000 9.70 0.00 45.83 2.57
3077 3508 1.408702 GTTTTTGCTCAACCAGGCTGA 59.591 47.619 17.94 0.00 0.00 4.26
3086 3517 2.172505 TCAACCAGGCTGAGTTGAGAAA 59.827 45.455 30.61 18.36 45.53 2.52
3088 3519 4.041567 TCAACCAGGCTGAGTTGAGAAATA 59.958 41.667 30.61 17.62 45.53 1.40
3092 3523 5.189736 ACCAGGCTGAGTTGAGAAATACATA 59.810 40.000 17.94 0.00 0.00 2.29
3101 3532 6.573434 AGTTGAGAAATACATACGATGCAGA 58.427 36.000 0.00 0.00 0.00 4.26
3135 3566 1.517832 CAACCAAACACGCCCCAAA 59.482 52.632 0.00 0.00 0.00 3.28
3136 3567 0.529555 CAACCAAACACGCCCCAAAG 60.530 55.000 0.00 0.00 0.00 2.77
3137 3568 0.973496 AACCAAACACGCCCCAAAGT 60.973 50.000 0.00 0.00 0.00 2.66
3138 3569 0.973496 ACCAAACACGCCCCAAAGTT 60.973 50.000 0.00 0.00 0.00 2.66
3139 3570 0.176910 CCAAACACGCCCCAAAGTTT 59.823 50.000 0.00 0.00 34.78 2.66
3140 3571 1.406205 CCAAACACGCCCCAAAGTTTT 60.406 47.619 0.00 0.00 32.34 2.43
3141 3572 2.351455 CAAACACGCCCCAAAGTTTTT 58.649 42.857 0.00 0.00 32.34 1.94
3142 3573 2.303163 AACACGCCCCAAAGTTTTTC 57.697 45.000 0.00 0.00 0.00 2.29
3187 3635 6.412362 AGTGGCTGTAATATTCTACTCCAG 57.588 41.667 0.00 0.00 30.90 3.86
3188 3636 5.900123 AGTGGCTGTAATATTCTACTCCAGT 59.100 40.000 0.00 0.00 30.90 4.00
3189 3637 7.067421 AGTGGCTGTAATATTCTACTCCAGTA 58.933 38.462 0.00 0.00 32.24 2.74
3251 3699 3.074999 GCAGCTCCCGGTCAGAGAG 62.075 68.421 10.08 5.43 32.86 3.20
3260 3708 3.366629 GTCAGAGAGACGCCACCA 58.633 61.111 0.00 0.00 37.53 4.17
3261 3709 1.893786 GTCAGAGAGACGCCACCAT 59.106 57.895 0.00 0.00 37.53 3.55
3262 3710 0.179124 GTCAGAGAGACGCCACCATC 60.179 60.000 0.00 0.00 37.53 3.51
3263 3711 0.611896 TCAGAGAGACGCCACCATCA 60.612 55.000 0.00 0.00 0.00 3.07
3269 3717 4.697756 ACGCCACCATCACCACGG 62.698 66.667 0.00 0.00 0.00 4.94
3285 3733 0.251653 ACGGCTACTCCAAGTCTCCA 60.252 55.000 0.00 0.00 34.01 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
282 297 1.360931 GCCACGCCGTATTAAACCGT 61.361 55.000 0.00 0.00 0.00 4.83
352 367 0.895559 TCTTCCTCTGCGACTCTGCA 60.896 55.000 0.00 0.00 43.95 4.41
359 375 1.468985 CTCTTCCTCTTCCTCTGCGA 58.531 55.000 0.00 0.00 0.00 5.10
509 531 0.685097 TTGCTCGTGCCCTTTACTCT 59.315 50.000 7.05 0.00 38.71 3.24
517 539 3.567473 GAGTTCTTGCTCGTGCCC 58.433 61.111 7.05 0.00 38.71 5.36
574 600 1.078426 GCAATCACGTAGGGCCAGT 60.078 57.895 6.18 0.00 0.00 4.00
576 602 1.220749 GAGCAATCACGTAGGGCCA 59.779 57.895 6.18 0.00 0.00 5.36
593 619 2.810274 AGTACGACTTACTGCGACTTGA 59.190 45.455 0.00 0.00 39.78 3.02
594 620 3.198863 AGTACGACTTACTGCGACTTG 57.801 47.619 0.00 0.00 39.78 3.16
602 628 0.531200 GGCCAGCAGTACGACTTACT 59.469 55.000 0.00 0.00 42.23 2.24
603 629 0.245539 TGGCCAGCAGTACGACTTAC 59.754 55.000 0.00 0.00 0.00 2.34
604 630 0.245539 GTGGCCAGCAGTACGACTTA 59.754 55.000 5.11 0.00 0.00 2.24
605 631 1.004918 GTGGCCAGCAGTACGACTT 60.005 57.895 5.11 0.00 0.00 3.01
606 632 1.878656 GAGTGGCCAGCAGTACGACT 61.879 60.000 5.11 0.00 0.00 4.18
607 633 1.446272 GAGTGGCCAGCAGTACGAC 60.446 63.158 5.11 0.00 0.00 4.34
608 634 2.970639 GAGTGGCCAGCAGTACGA 59.029 61.111 5.11 0.00 0.00 3.43
609 635 2.507102 CGAGTGGCCAGCAGTACG 60.507 66.667 5.11 1.95 0.00 3.67
610 636 2.815647 GCGAGTGGCCAGCAGTAC 60.816 66.667 5.11 0.00 34.80 2.73
611 637 2.997315 AGCGAGTGGCCAGCAGTA 60.997 61.111 16.94 0.00 45.17 2.74
612 638 4.694233 CAGCGAGTGGCCAGCAGT 62.694 66.667 16.94 0.00 45.17 4.40
620 646 4.767255 GGGTCTGGCAGCGAGTGG 62.767 72.222 10.34 0.00 0.00 4.00
621 647 3.947132 CTGGGTCTGGCAGCGAGTG 62.947 68.421 10.34 0.00 0.00 3.51
622 648 3.699894 CTGGGTCTGGCAGCGAGT 61.700 66.667 10.34 0.00 0.00 4.18
623 649 4.463879 CCTGGGTCTGGCAGCGAG 62.464 72.222 10.34 3.37 0.00 5.03
701 727 2.048222 CACGAGGGAAGAAGCGCA 60.048 61.111 11.47 0.00 0.00 6.09
752 778 1.004799 TCCCGCCGATTTTTCGACA 60.005 52.632 0.00 0.00 34.64 4.35
848 875 2.431942 GGAAAGCGCGAACGGAGA 60.432 61.111 12.10 0.00 40.57 3.71
1074 1102 5.754782 ACCACTAATCAACCATGCATCTAA 58.245 37.500 0.00 0.00 0.00 2.10
1099 1127 3.657015 ACCATATCAGCTCACAGATCG 57.343 47.619 0.00 0.00 0.00 3.69
1146 1174 3.181450 GCTTGAACATCTAGCCCTACCAT 60.181 47.826 2.94 0.00 38.90 3.55
1208 1236 4.793678 GCATGATTCAACACAAGCACAAGA 60.794 41.667 0.00 0.00 32.24 3.02
1420 1448 3.043586 GTCATGTCCTACAATCGTAGCG 58.956 50.000 0.00 0.00 43.33 4.26
1486 1514 2.627699 ACAAACGATGGAGCAAATTGGT 59.372 40.909 0.00 0.00 0.00 3.67
1508 1536 1.365633 CATAGGCTGCGAGTCCTCC 59.634 63.158 0.00 0.00 34.02 4.30
1754 1797 2.727123 TCAAGTGCACCTCCTTGAAA 57.273 45.000 14.63 0.00 42.92 2.69
1872 1916 1.949799 AGGTCTCTCAGCTTGGACAT 58.050 50.000 0.00 0.00 0.00 3.06
1953 1997 2.511600 GCTAACCGCGACATGGCT 60.512 61.111 8.23 0.00 0.00 4.75
1976 2020 4.518249 GACAGTATGAAAAGGAAGAGGGG 58.482 47.826 0.00 0.00 39.69 4.79
2053 2097 2.525629 TCAGCGTCCCTTGGGTGA 60.526 61.111 5.51 0.00 38.24 4.02
2086 2130 6.519043 GCTGCATCTGGTTATAGTTCTGGATA 60.519 42.308 0.00 0.00 0.00 2.59
2250 2662 0.924363 GTCATCGTCATCGTCGTCGG 60.924 60.000 1.55 0.00 38.33 4.79
2288 2700 6.723977 ACCATCAAATAGTTTTTGAGCCCTAA 59.276 34.615 13.15 0.00 41.13 2.69
2360 2772 0.981183 TCCTACCACCGCAAGTTCAT 59.019 50.000 0.00 0.00 0.00 2.57
2440 2852 5.240121 AGCATGCATGATCATACGACATAA 58.760 37.500 30.64 0.00 0.00 1.90
2525 2943 3.822735 AGCAAGAGTTGAAGCAGCAAATA 59.177 39.130 0.00 0.00 0.00 1.40
2843 3274 0.976073 ACCTAGCACACCTACGCCAT 60.976 55.000 0.00 0.00 0.00 4.40
2850 3281 1.644509 TGATCACACCTAGCACACCT 58.355 50.000 0.00 0.00 0.00 4.00
2877 3308 2.301870 TGTACCCTAGTTGGTGAGCTTG 59.698 50.000 1.21 0.00 39.53 4.01
2997 3428 2.894731 CATCCCTAGTCCCTGCATCTA 58.105 52.381 0.00 0.00 0.00 1.98
2998 3429 1.727062 CATCCCTAGTCCCTGCATCT 58.273 55.000 0.00 0.00 0.00 2.90
2999 3430 0.036022 GCATCCCTAGTCCCTGCATC 59.964 60.000 0.00 0.00 33.13 3.91
3054 3485 1.408702 GCCTGGTTGAGCAAAAACAGA 59.591 47.619 15.80 0.00 45.95 3.41
3077 3508 6.573434 TCTGCATCGTATGTATTTCTCAACT 58.427 36.000 0.00 0.00 0.00 3.16
3086 3517 6.036083 GTGAACAGTTTCTGCATCGTATGTAT 59.964 38.462 0.00 0.00 34.37 2.29
3088 3519 4.152402 GTGAACAGTTTCTGCATCGTATGT 59.848 41.667 0.00 0.00 34.37 2.29
3092 3523 2.560504 TGTGAACAGTTTCTGCATCGT 58.439 42.857 0.00 0.00 34.37 3.73
3101 3532 1.135228 GGTTGCCGTTGTGAACAGTTT 60.135 47.619 0.00 0.00 0.00 2.66
3135 3566 8.441312 TCGGAAAGTTTATACAGTGAAAAACT 57.559 30.769 13.01 13.01 42.40 2.66
3136 3567 7.322938 GCTCGGAAAGTTTATACAGTGAAAAAC 59.677 37.037 0.00 4.52 33.11 2.43
3137 3568 7.357303 GCTCGGAAAGTTTATACAGTGAAAAA 58.643 34.615 0.00 0.00 0.00 1.94
3138 3569 6.347079 CGCTCGGAAAGTTTATACAGTGAAAA 60.347 38.462 0.00 0.00 0.00 2.29
3139 3570 5.119588 CGCTCGGAAAGTTTATACAGTGAAA 59.880 40.000 0.00 0.00 0.00 2.69
3140 3571 4.624024 CGCTCGGAAAGTTTATACAGTGAA 59.376 41.667 0.00 0.00 0.00 3.18
3141 3572 4.082625 TCGCTCGGAAAGTTTATACAGTGA 60.083 41.667 0.00 0.00 0.00 3.41
3142 3573 4.171005 TCGCTCGGAAAGTTTATACAGTG 58.829 43.478 0.00 0.00 0.00 3.66
3199 3647 7.771826 AGCTTCTTCTAGAATTCTACGTACTCT 59.228 37.037 11.24 1.73 33.13 3.24
3200 3648 7.853929 CAGCTTCTTCTAGAATTCTACGTACTC 59.146 40.741 11.24 0.00 33.13 2.59
3201 3649 7.680113 GCAGCTTCTTCTAGAATTCTACGTACT 60.680 40.741 11.24 0.91 33.13 2.73
3202 3650 6.415573 GCAGCTTCTTCTAGAATTCTACGTAC 59.584 42.308 11.24 0.00 33.13 3.67
3203 3651 6.095021 TGCAGCTTCTTCTAGAATTCTACGTA 59.905 38.462 11.24 0.00 33.13 3.57
3204 3652 5.105716 TGCAGCTTCTTCTAGAATTCTACGT 60.106 40.000 11.24 0.00 33.13 3.57
3205 3653 5.231147 GTGCAGCTTCTTCTAGAATTCTACG 59.769 44.000 11.24 8.07 33.13 3.51
3241 3689 2.179517 GTGGCGTCTCTCTGACCG 59.820 66.667 0.00 0.00 42.49 4.79
3242 3690 1.608717 ATGGTGGCGTCTCTCTGACC 61.609 60.000 0.00 0.00 42.49 4.02
3251 3699 3.118454 CGTGGTGATGGTGGCGTC 61.118 66.667 0.00 0.00 0.00 5.19
3257 3705 1.614241 GGAGTAGCCGTGGTGATGGT 61.614 60.000 0.00 0.00 0.00 3.55
3258 3706 1.144057 GGAGTAGCCGTGGTGATGG 59.856 63.158 0.00 0.00 0.00 3.51
3259 3707 0.249120 TTGGAGTAGCCGTGGTGATG 59.751 55.000 0.00 0.00 40.66 3.07
3260 3708 0.537188 CTTGGAGTAGCCGTGGTGAT 59.463 55.000 0.00 0.00 40.66 3.06
3261 3709 0.830444 ACTTGGAGTAGCCGTGGTGA 60.830 55.000 0.00 0.00 40.66 4.02
3262 3710 0.389948 GACTTGGAGTAGCCGTGGTG 60.390 60.000 0.00 0.00 40.66 4.17
3263 3711 0.542232 AGACTTGGAGTAGCCGTGGT 60.542 55.000 0.00 0.00 40.66 4.16


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

AutoCloner maintained by Alex Coulton.