Multiple sequence alignment - TraesCS6D01G390600

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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 TraesCS6D01G390600 chr6D 100.000 4417 0 0 1 4417 465746084 465741668 0.000000e+00 8157.0
1 TraesCS6D01G390600 chr6D 87.895 2470 196 43 716 3156 465967384 465964989 0.000000e+00 2809.0
2 TraesCS6D01G390600 chr6D 88.733 1571 127 16 1826 3365 466329631 466331182 0.000000e+00 1875.0
3 TraesCS6D01G390600 chr6D 91.636 550 20 16 115 641 465967936 465967390 0.000000e+00 737.0
4 TraesCS6D01G390600 chr6D 74.335 639 124 26 2979 3597 466811951 466811333 7.390000e-58 235.0
5 TraesCS6D01G390600 chr6D 83.806 247 30 5 697 943 466621602 466621838 4.450000e-55 226.0
6 TraesCS6D01G390600 chr6D 88.202 178 17 2 307 481 466131555 466131379 4.480000e-50 209.0
7 TraesCS6D01G390600 chr6D 85.644 202 22 2 483 683 465348588 465348393 5.790000e-49 206.0
8 TraesCS6D01G390600 chr6D 96.552 116 2 2 1 115 465968108 465967994 1.620000e-44 191.0
9 TraesCS6D01G390600 chr6D 90.977 133 9 2 115 244 466131673 466131541 4.540000e-40 176.0
10 TraesCS6D01G390600 chr6D 96.296 54 1 1 383 436 466131546 466131494 2.190000e-13 87.9
11 TraesCS6D01G390600 chr6D 84.615 91 6 6 22 106 466131863 466131775 2.830000e-12 84.2
12 TraesCS6D01G390600 chr6B 92.530 3976 171 34 483 4417 710643421 710639531 0.000000e+00 5581.0
13 TraesCS6D01G390600 chr6B 87.241 1928 171 25 1462 3365 711359863 711361739 0.000000e+00 2128.0
14 TraesCS6D01G390600 chr6B 83.648 954 138 12 1826 2772 711333452 711332510 0.000000e+00 881.0
15 TraesCS6D01G390600 chr6B 81.789 950 146 18 1834 2772 710683591 710682658 0.000000e+00 771.0
16 TraesCS6D01G390600 chr6B 90.153 589 49 6 3829 4417 98829309 98828730 0.000000e+00 758.0
17 TraesCS6D01G390600 chr6B 80.684 585 58 35 483 1040 711237978 711237422 1.910000e-108 403.0
18 TraesCS6D01G390600 chr6B 89.513 267 28 0 3099 3365 711473735 711474001 5.470000e-89 339.0
19 TraesCS6D01G390600 chr6B 97.449 196 4 1 115 309 711238337 711238142 2.550000e-87 333.0
20 TraesCS6D01G390600 chr6B 93.514 185 6 3 307 485 711238188 711238004 2.020000e-68 270.0
21 TraesCS6D01G390600 chr6B 88.000 225 21 4 681 905 711709499 711709717 1.220000e-65 261.0
22 TraesCS6D01G390600 chr6B 83.588 262 23 11 928 1187 711362928 711362685 1.240000e-55 228.0
23 TraesCS6D01G390600 chr6B 84.865 185 28 0 2980 3164 711332241 711332057 2.100000e-43 187.0
24 TraesCS6D01G390600 chr6B 95.000 100 2 2 389 485 710643547 710643448 2.130000e-33 154.0
25 TraesCS6D01G390600 chr6B 80.693 202 20 9 989 1187 711359566 711359751 5.960000e-29 139.0
26 TraesCS6D01G390600 chr6A 88.374 1574 137 25 1826 3365 612291770 612293331 0.000000e+00 1851.0
27 TraesCS6D01G390600 chr6A 85.584 1748 193 31 1452 3157 612300128 612301858 0.000000e+00 1777.0
28 TraesCS6D01G390600 chr6A 85.181 965 120 17 1826 2782 611902361 611903310 0.000000e+00 968.0
29 TraesCS6D01G390600 chr6A 84.182 746 102 12 1826 2564 125260593 125261329 0.000000e+00 710.0
30 TraesCS6D01G390600 chr6A 91.768 413 29 3 478 889 612110043 612109635 1.780000e-158 569.0
31 TraesCS6D01G390600 chr6A 89.104 413 29 2 478 889 613078798 613079195 2.370000e-137 499.0
32 TraesCS6D01G390600 chr6A 90.164 366 33 3 515 879 125259253 125259616 1.440000e-129 473.0
33 TraesCS6D01G390600 chr6A 87.805 410 42 6 889 1297 612299656 612300058 1.440000e-129 473.0
34 TraesCS6D01G390600 chr6A 89.941 338 33 1 551 888 611901233 611901569 6.780000e-118 435.0
35 TraesCS6D01G390600 chr6A 80.438 593 65 22 2595 3156 125261328 125261900 5.320000e-109 405.0
36 TraesCS6D01G390600 chr6A 94.694 245 7 3 115 353 612110617 612110373 4.170000e-100 375.0
37 TraesCS6D01G390600 chr6A 95.154 227 7 3 263 485 612110329 612110103 5.430000e-94 355.0
38 TraesCS6D01G390600 chr6A 80.272 441 69 12 2900 3328 612676653 612677087 2.560000e-82 316.0
39 TraesCS6D01G390600 chr6A 79.167 360 40 14 389 717 612299211 612299566 2.680000e-52 217.0
40 TraesCS6D01G390600 chr6A 79.612 309 40 12 2871 3156 611903362 611903670 2.690000e-47 200.0
41 TraesCS6D01G390600 chr6A 94.215 121 7 0 307 427 612126118 612125998 7.540000e-43 185.0
42 TraesCS6D01G390600 chr6A 93.162 117 5 3 1 115 612110790 612110675 7.600000e-38 169.0
43 TraesCS6D01G390600 chr6A 86.207 145 5 2 115 244 612126248 612126104 4.610000e-30 143.0
44 TraesCS6D01G390600 chr6A 91.579 95 4 3 263 353 612110375 612110281 1.290000e-25 128.0
45 TraesCS6D01G390600 chr6A 91.579 95 4 3 263 353 612110421 612110327 1.290000e-25 128.0
46 TraesCS6D01G390600 chr6A 94.444 54 2 1 383 436 612126109 612126057 1.020000e-11 82.4
47 TraesCS6D01G390600 chr7B 89.552 670 42 8 3753 4412 664958098 664958749 0.000000e+00 824.0
48 TraesCS6D01G390600 chr7B 90.492 589 45 6 3829 4417 604770903 604770326 0.000000e+00 767.0
49 TraesCS6D01G390600 chr7B 90.339 590 45 6 3829 4412 68226856 68226273 0.000000e+00 763.0
50 TraesCS6D01G390600 chr7B 89.983 589 52 2 3829 4417 323757731 323758312 0.000000e+00 754.0
51 TraesCS6D01G390600 chr2B 91.032 591 42 7 3829 4417 325640724 325640143 0.000000e+00 787.0
52 TraesCS6D01G390600 chr1B 90.832 589 46 4 3829 4417 157940161 157940741 0.000000e+00 782.0
53 TraesCS6D01G390600 chr3B 87.372 681 70 6 3748 4417 6581102 6580427 0.000000e+00 767.0
54 TraesCS6D01G390600 chr2A 89.848 591 50 6 3829 4417 761071705 761071123 0.000000e+00 750.0
55 TraesCS6D01G390600 chr5B 81.460 685 70 27 3745 4407 375650932 375651581 3.940000e-140 508.0
56 TraesCS6D01G390600 chr5B 74.603 630 92 41 3745 4347 491941383 491941971 9.620000e-52 215.0
57 TraesCS6D01G390600 chr4A 88.124 421 42 3 483 899 594050330 594049914 1.100000e-135 494.0
58 TraesCS6D01G390600 chr1D 82.593 270 26 13 923 1187 447556960 447557213 7.440000e-53 219.0
59 TraesCS6D01G390600 chr1D 86.047 172 21 3 1270 1440 447557208 447557377 9.760000e-42 182.0
60 TraesCS6D01G390600 chr1A 92.308 52 2 2 3750 3801 492130464 492130415 6.130000e-09 73.1
61 TraesCS6D01G390600 chr1A 95.556 45 2 0 1299 1343 543641691 543641735 6.130000e-09 73.1


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 TraesCS6D01G390600 chr6D 465741668 465746084 4416 True 8157.000000 8157 100.000000 1 4417 1 chr6D.!!$R2 4416
1 TraesCS6D01G390600 chr6D 466329631 466331182 1551 False 1875.000000 1875 88.733000 1826 3365 1 chr6D.!!$F1 1539
2 TraesCS6D01G390600 chr6D 465964989 465968108 3119 True 1245.666667 2809 92.027667 1 3156 3 chr6D.!!$R4 3155
3 TraesCS6D01G390600 chr6D 466811333 466811951 618 True 235.000000 235 74.335000 2979 3597 1 chr6D.!!$R3 618
4 TraesCS6D01G390600 chr6B 710639531 710643547 4016 True 2867.500000 5581 93.765000 389 4417 2 chr6B.!!$R4 4028
5 TraesCS6D01G390600 chr6B 711359566 711361739 2173 False 1133.500000 2128 83.967000 989 3365 2 chr6B.!!$F3 2376
6 TraesCS6D01G390600 chr6B 710682658 710683591 933 True 771.000000 771 81.789000 1834 2772 1 chr6B.!!$R2 938
7 TraesCS6D01G390600 chr6B 98828730 98829309 579 True 758.000000 758 90.153000 3829 4417 1 chr6B.!!$R1 588
8 TraesCS6D01G390600 chr6B 711332057 711333452 1395 True 534.000000 881 84.256500 1826 3164 2 chr6B.!!$R6 1338
9 TraesCS6D01G390600 chr6B 711237422 711238337 915 True 335.333333 403 90.549000 115 1040 3 chr6B.!!$R5 925
10 TraesCS6D01G390600 chr6A 612291770 612293331 1561 False 1851.000000 1851 88.374000 1826 3365 1 chr6A.!!$F1 1539
11 TraesCS6D01G390600 chr6A 612299211 612301858 2647 False 822.333333 1777 84.185333 389 3157 3 chr6A.!!$F6 2768
12 TraesCS6D01G390600 chr6A 611901233 611903670 2437 False 534.333333 968 84.911333 551 3156 3 chr6A.!!$F5 2605
13 TraesCS6D01G390600 chr6A 125259253 125261900 2647 False 529.333333 710 84.928000 515 3156 3 chr6A.!!$F4 2641
14 TraesCS6D01G390600 chr6A 612109635 612110790 1155 True 287.333333 569 92.989333 1 889 6 chr6A.!!$R1 888
15 TraesCS6D01G390600 chr7B 664958098 664958749 651 False 824.000000 824 89.552000 3753 4412 1 chr7B.!!$F2 659
16 TraesCS6D01G390600 chr7B 604770326 604770903 577 True 767.000000 767 90.492000 3829 4417 1 chr7B.!!$R2 588
17 TraesCS6D01G390600 chr7B 68226273 68226856 583 True 763.000000 763 90.339000 3829 4412 1 chr7B.!!$R1 583
18 TraesCS6D01G390600 chr7B 323757731 323758312 581 False 754.000000 754 89.983000 3829 4417 1 chr7B.!!$F1 588
19 TraesCS6D01G390600 chr2B 325640143 325640724 581 True 787.000000 787 91.032000 3829 4417 1 chr2B.!!$R1 588
20 TraesCS6D01G390600 chr1B 157940161 157940741 580 False 782.000000 782 90.832000 3829 4417 1 chr1B.!!$F1 588
21 TraesCS6D01G390600 chr3B 6580427 6581102 675 True 767.000000 767 87.372000 3748 4417 1 chr3B.!!$R1 669
22 TraesCS6D01G390600 chr2A 761071123 761071705 582 True 750.000000 750 89.848000 3829 4417 1 chr2A.!!$R1 588
23 TraesCS6D01G390600 chr5B 375650932 375651581 649 False 508.000000 508 81.460000 3745 4407 1 chr5B.!!$F1 662
24 TraesCS6D01G390600 chr5B 491941383 491941971 588 False 215.000000 215 74.603000 3745 4347 1 chr5B.!!$F2 602

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
855 1181 2.656560 ATTCAGTCTCCGAGTTTCCG 57.343 50.0 0.0 0.0 0.00 4.30 F
1487 2061 0.108424 ACCAAAGCTGCGTTTTTGCA 60.108 45.0 0.0 0.0 43.95 4.08 F
2298 2995 0.165944 GCCGTTTTGACATGGTCGAG 59.834 55.0 0.0 0.0 34.95 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2613 3315 1.004628 TGCTGGAACACATATGCCTGT 59.995 47.619 1.58 0.00 0.00 4.00 R
3365 4165 0.912486 AGTTAGCTCCCATGACACCC 59.088 55.000 0.00 0.00 0.00 4.61 R
3864 4734 0.102481 ATATGGGACGCGTGTCTGAC 59.898 55.000 26.79 17.77 44.83 3.51 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
52 53 5.208463 ACTTTGAAATACCATTTTGGCGT 57.792 34.783 0.00 0.00 42.67 5.68
855 1181 2.656560 ATTCAGTCTCCGAGTTTCCG 57.343 50.000 0.00 0.00 0.00 4.30
891 1312 7.524863 GCAACCCGGCAGCTGTATATATATATA 60.525 40.741 16.64 8.16 0.00 0.86
894 1315 9.937876 ACCCGGCAGCTGTATATATATATATAT 57.062 33.333 22.83 22.83 38.90 0.86
1487 2061 0.108424 ACCAAAGCTGCGTTTTTGCA 60.108 45.000 0.00 0.00 43.95 4.08
2298 2995 0.165944 GCCGTTTTGACATGGTCGAG 59.834 55.000 0.00 0.00 34.95 4.04
2340 3037 0.671251 CCTGGCTGGCGTTTTTGTTA 59.329 50.000 0.00 0.00 0.00 2.41
2348 3045 5.393243 GGCTGGCGTTTTTGTTATGGTTATA 60.393 40.000 0.00 0.00 0.00 0.98
2352 3049 8.001881 TGGCGTTTTTGTTATGGTTATATCAT 57.998 30.769 0.00 0.00 0.00 2.45
2354 3051 7.096230 GGCGTTTTTGTTATGGTTATATCATGC 60.096 37.037 0.00 0.00 0.00 4.06
2420 3117 3.479489 TGAGACTTTCAAATGCTGCTCA 58.521 40.909 0.00 0.00 31.34 4.26
2450 3147 4.024048 CCACAAAAACGTCAAGCTGAGTAT 60.024 41.667 0.00 0.00 0.00 2.12
2484 3181 1.202952 ACCTCTGTTCGAGACCTGACT 60.203 52.381 0.00 0.00 42.62 3.41
2548 3246 2.297701 TGTTCTGGCTTCACTTGTTCC 58.702 47.619 0.00 0.00 0.00 3.62
2572 3271 6.393990 CCTACTCATCCTATCACATGCTTAC 58.606 44.000 0.00 0.00 0.00 2.34
2581 3283 2.153645 TCACATGCTTACTGTTGCAGG 58.846 47.619 14.99 14.99 45.01 4.85
2613 3315 2.771943 ACCAGAGTGTTTGACCAGAAGA 59.228 45.455 0.00 0.00 0.00 2.87
2915 3679 7.095649 GGAGTGCAAAATTAACCTGTTTCATTC 60.096 37.037 0.00 0.00 0.00 2.67
3084 3878 4.832248 TCAAGCTAAAGACTACATGGTGG 58.168 43.478 0.00 0.00 0.00 4.61
3146 3940 6.656632 CAGGATGTGTACCTGTATGATAGT 57.343 41.667 0.00 0.00 46.71 2.12
3248 4048 3.199946 TGAATCTGCCGATAAAGTTCCCT 59.800 43.478 0.00 0.00 0.00 4.20
3324 4124 2.293122 TCACTTGCCAAAATCCACTTCG 59.707 45.455 0.00 0.00 0.00 3.79
3358 4158 0.179100 ATGAGGGCTGAACATCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
3365 4165 1.590238 GCTGAACATCGTCGAAGGATG 59.410 52.381 20.36 20.36 43.82 3.51
3368 4168 0.902531 AACATCGTCGAAGGATGGGT 59.097 50.000 23.78 13.27 42.85 4.51
3370 4170 0.175760 CATCGTCGAAGGATGGGTGT 59.824 55.000 16.23 0.00 36.98 4.16
3372 4172 0.896479 TCGTCGAAGGATGGGTGTCA 60.896 55.000 0.00 0.00 0.00 3.58
3373 4173 0.175760 CGTCGAAGGATGGGTGTCAT 59.824 55.000 0.00 0.00 39.13 3.06
3374 4174 1.656652 GTCGAAGGATGGGTGTCATG 58.343 55.000 0.00 0.00 35.97 3.07
3376 4188 0.464373 CGAAGGATGGGTGTCATGGG 60.464 60.000 0.00 0.00 35.97 4.00
3379 4191 1.152881 GGATGGGTGTCATGGGAGC 60.153 63.158 0.00 0.00 35.97 4.70
3404 4216 0.105039 GGATGTTGTCGAGGCTAGGG 59.895 60.000 0.00 0.00 0.00 3.53
3441 4253 2.317609 CCAGTCGGTTGGAGTTGCG 61.318 63.158 0.35 0.00 40.87 4.85
3453 4270 1.068954 GGAGTTGCGAGCTTTTCTTGG 60.069 52.381 0.00 0.00 0.00 3.61
3567 4386 7.749126 CGATACAACCAGTTAAAATTTGAGACC 59.251 37.037 0.00 0.00 0.00 3.85
3684 4540 2.778299 AGCATGTAATTGGTCACGTGT 58.222 42.857 16.51 0.00 34.75 4.49
3685 4541 2.742053 AGCATGTAATTGGTCACGTGTC 59.258 45.455 16.51 10.16 34.75 3.67
3686 4542 2.159572 GCATGTAATTGGTCACGTGTCC 60.160 50.000 22.81 22.81 34.75 4.02
3687 4543 2.172851 TGTAATTGGTCACGTGTCCC 57.827 50.000 25.73 21.00 0.00 4.46
3688 4544 1.270947 TGTAATTGGTCACGTGTCCCC 60.271 52.381 25.73 18.78 0.00 4.81
3689 4545 1.002773 GTAATTGGTCACGTGTCCCCT 59.997 52.381 25.73 14.02 0.00 4.79
3690 4546 0.476771 AATTGGTCACGTGTCCCCTT 59.523 50.000 25.73 16.88 0.00 3.95
3691 4547 0.476771 ATTGGTCACGTGTCCCCTTT 59.523 50.000 25.73 7.96 0.00 3.11
3692 4548 0.464735 TTGGTCACGTGTCCCCTTTG 60.465 55.000 25.73 0.00 0.00 2.77
3693 4549 1.147600 GGTCACGTGTCCCCTTTGT 59.852 57.895 19.61 0.00 0.00 2.83
3694 4550 0.883370 GGTCACGTGTCCCCTTTGTC 60.883 60.000 19.61 0.00 0.00 3.18
3695 4551 0.179067 GTCACGTGTCCCCTTTGTCA 60.179 55.000 16.51 0.00 0.00 3.58
3696 4552 0.542333 TCACGTGTCCCCTTTGTCAA 59.458 50.000 16.51 0.00 0.00 3.18
3697 4553 0.661020 CACGTGTCCCCTTTGTCAAC 59.339 55.000 7.58 0.00 0.00 3.18
3698 4554 0.464916 ACGTGTCCCCTTTGTCAACC 60.465 55.000 0.00 0.00 0.00 3.77
3699 4555 1.503818 CGTGTCCCCTTTGTCAACCG 61.504 60.000 0.00 0.00 0.00 4.44
3700 4556 0.464916 GTGTCCCCTTTGTCAACCGT 60.465 55.000 0.00 0.00 0.00 4.83
3701 4557 1.129917 TGTCCCCTTTGTCAACCGTA 58.870 50.000 0.00 0.00 0.00 4.02
3702 4558 1.700739 TGTCCCCTTTGTCAACCGTAT 59.299 47.619 0.00 0.00 0.00 3.06
3703 4559 2.905085 TGTCCCCTTTGTCAACCGTATA 59.095 45.455 0.00 0.00 0.00 1.47
3704 4560 3.327172 TGTCCCCTTTGTCAACCGTATAA 59.673 43.478 0.00 0.00 0.00 0.98
3705 4561 4.019141 TGTCCCCTTTGTCAACCGTATAAT 60.019 41.667 0.00 0.00 0.00 1.28
3706 4562 4.945543 GTCCCCTTTGTCAACCGTATAATT 59.054 41.667 0.00 0.00 0.00 1.40
3707 4563 4.944930 TCCCCTTTGTCAACCGTATAATTG 59.055 41.667 0.00 0.00 0.00 2.32
3708 4564 4.439563 CCCCTTTGTCAACCGTATAATTGC 60.440 45.833 0.00 0.00 0.00 3.56
3709 4565 4.398044 CCCTTTGTCAACCGTATAATTGCT 59.602 41.667 0.00 0.00 0.00 3.91
3710 4566 5.331902 CCTTTGTCAACCGTATAATTGCTG 58.668 41.667 0.00 0.00 0.00 4.41
3728 4584 2.030562 CAGCACGGAACTCGGGTT 59.969 61.111 0.00 0.00 45.61 4.11
3859 4729 2.038329 CCCAGGTGTCGTCCCCTA 59.962 66.667 0.00 0.00 0.00 3.53
3860 4730 1.611261 CCCAGGTGTCGTCCCCTAA 60.611 63.158 0.00 0.00 0.00 2.69
3861 4731 1.614241 CCCAGGTGTCGTCCCCTAAG 61.614 65.000 0.00 0.00 0.00 2.18
3862 4732 1.614241 CCAGGTGTCGTCCCCTAAGG 61.614 65.000 0.00 0.00 0.00 2.69
3863 4733 1.988406 AGGTGTCGTCCCCTAAGGC 60.988 63.158 0.00 0.00 34.51 4.35
3864 4734 2.183555 GTGTCGTCCCCTAAGGCG 59.816 66.667 0.00 0.00 36.75 5.52
3865 4735 2.283388 TGTCGTCCCCTAAGGCGT 60.283 61.111 0.00 0.00 36.77 5.68
4145 5055 4.803426 GCTGGGCGTCACGGAGAG 62.803 72.222 0.00 0.00 0.00 3.20
4217 5150 0.179081 GCCGGTATCAGGTTCAGGAC 60.179 60.000 1.90 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
654 938 2.043980 GGATCGCCGCTCCCAAAAA 61.044 57.895 0.00 0.00 0.00 1.94
686 970 1.743252 GGTTGCAGCTCGGAGAAGG 60.743 63.158 9.69 0.00 34.09 3.46
688 972 2.048222 CGGTTGCAGCTCGGAGAA 60.048 61.111 9.69 0.00 34.09 2.87
761 1087 4.606210 GGATTAGCCACTAAAAAGGGGAA 58.394 43.478 0.00 0.00 36.34 3.97
1171 1612 4.035208 CCAGTTTCGATTATGGTTGCTACC 59.965 45.833 10.70 10.70 45.26 3.18
1188 1629 3.702548 GGTTAGGTTTTGTCCACCAGTTT 59.297 43.478 0.00 0.00 36.67 2.66
1455 2026 3.191371 CAGCTTTGGTTTGGCTAAGGTAG 59.809 47.826 0.00 0.00 34.71 3.18
1458 2029 1.337167 GCAGCTTTGGTTTGGCTAAGG 60.337 52.381 0.00 0.00 34.71 2.69
1469 2043 1.005340 TTGCAAAAACGCAGCTTTGG 58.995 45.000 0.00 0.00 44.14 3.28
1852 2541 3.418068 GTGTGCCAGCGTGCTCTC 61.418 66.667 0.00 0.00 0.00 3.20
2298 2995 1.072505 TTTCGGAACCCAGGTGAGC 59.927 57.895 0.00 0.00 0.00 4.26
2340 3037 6.936900 GTGGTAGTTCTGCATGATATAACCAT 59.063 38.462 0.00 0.00 0.00 3.55
2348 3045 3.261643 TGACAGTGGTAGTTCTGCATGAT 59.738 43.478 0.00 0.00 35.37 2.45
2352 3049 2.039418 AGTGACAGTGGTAGTTCTGCA 58.961 47.619 0.00 0.00 35.37 4.41
2354 3051 2.289072 CCCAGTGACAGTGGTAGTTCTG 60.289 54.545 24.64 6.80 36.97 3.02
2420 3117 5.067283 AGCTTGACGTTTTTGTGGAAACTAT 59.933 36.000 0.00 0.00 37.37 2.12
2450 3147 3.242867 ACAGAGGTCTCATGGAGAAACA 58.757 45.455 0.00 0.00 40.59 2.83
2484 3181 6.314899 ACCTTTTCACATTTAAACCCCAAA 57.685 33.333 0.00 0.00 0.00 3.28
2548 3246 5.480642 AAGCATGTGATAGGATGAGTAGG 57.519 43.478 0.00 0.00 0.00 3.18
2572 3271 1.110442 TGAACCCAAACCTGCAACAG 58.890 50.000 0.00 0.00 0.00 3.16
2581 3283 2.375146 ACACTCTGGTTGAACCCAAAC 58.625 47.619 12.53 0.00 40.35 2.93
2613 3315 1.004628 TGCTGGAACACATATGCCTGT 59.995 47.619 1.58 0.00 0.00 4.00
2782 3509 3.731089 CCACGTGGTAAAACAACTCCTA 58.269 45.455 26.95 0.00 0.00 2.94
3084 3878 2.103042 GGACACGCCTGACATGAGC 61.103 63.158 0.00 0.00 0.00 4.26
3248 4048 2.224426 ACGCTGGTCCTCATTTGTACAA 60.224 45.455 3.59 3.59 0.00 2.41
3324 4124 3.879892 GCCCTCATTTCCTTAGATGTCAC 59.120 47.826 0.00 0.00 0.00 3.67
3358 4158 0.918983 TCCCATGACACCCATCCTTC 59.081 55.000 0.00 0.00 31.94 3.46
3365 4165 0.912486 AGTTAGCTCCCATGACACCC 59.088 55.000 0.00 0.00 0.00 4.61
3368 4168 1.951209 TCCAGTTAGCTCCCATGACA 58.049 50.000 0.00 0.00 0.00 3.58
3370 4170 2.481441 ACATCCAGTTAGCTCCCATGA 58.519 47.619 0.00 0.00 0.00 3.07
3372 4172 2.578021 ACAACATCCAGTTAGCTCCCAT 59.422 45.455 0.00 0.00 38.74 4.00
3373 4173 1.985159 ACAACATCCAGTTAGCTCCCA 59.015 47.619 0.00 0.00 38.74 4.37
3374 4174 2.633488 GACAACATCCAGTTAGCTCCC 58.367 52.381 0.00 0.00 38.74 4.30
3376 4188 3.182967 CTCGACAACATCCAGTTAGCTC 58.817 50.000 0.00 0.00 38.74 4.09
3379 4191 2.093973 AGCCTCGACAACATCCAGTTAG 60.094 50.000 0.00 0.00 38.74 2.34
3453 4270 2.860136 GCAACCACAAAAGAAGAGCAAC 59.140 45.455 0.00 0.00 0.00 4.17
3684 4540 4.847990 ATTATACGGTTGACAAAGGGGA 57.152 40.909 0.00 0.00 0.00 4.81
3685 4541 4.439563 GCAATTATACGGTTGACAAAGGGG 60.440 45.833 0.00 0.00 0.00 4.79
3686 4542 4.398044 AGCAATTATACGGTTGACAAAGGG 59.602 41.667 0.00 0.00 0.00 3.95
3687 4543 5.331902 CAGCAATTATACGGTTGACAAAGG 58.668 41.667 0.00 0.00 0.00 3.11
3688 4544 4.793216 GCAGCAATTATACGGTTGACAAAG 59.207 41.667 0.00 0.00 0.00 2.77
3689 4545 4.216472 TGCAGCAATTATACGGTTGACAAA 59.784 37.500 0.00 0.00 0.00 2.83
3690 4546 3.753797 TGCAGCAATTATACGGTTGACAA 59.246 39.130 0.00 0.00 0.00 3.18
3691 4547 3.339141 TGCAGCAATTATACGGTTGACA 58.661 40.909 0.00 0.00 0.00 3.58
3692 4548 3.788797 GCTGCAGCAATTATACGGTTGAC 60.789 47.826 33.36 0.00 41.59 3.18
3693 4549 2.354510 GCTGCAGCAATTATACGGTTGA 59.645 45.455 33.36 0.00 41.59 3.18
3694 4550 2.719798 GCTGCAGCAATTATACGGTTG 58.280 47.619 33.36 0.00 41.59 3.77
3707 4563 3.782244 CGAGTTCCGTGCTGCAGC 61.782 66.667 31.89 31.89 42.50 5.25
3708 4564 3.114616 CCGAGTTCCGTGCTGCAG 61.115 66.667 10.11 10.11 36.31 4.41
3709 4565 4.680237 CCCGAGTTCCGTGCTGCA 62.680 66.667 0.00 0.00 36.31 4.41
3710 4566 4.681978 ACCCGAGTTCCGTGCTGC 62.682 66.667 0.00 0.00 36.31 5.25
3728 4584 6.475504 TGCTCTAAGAATTCAGTCAAATGGA 58.524 36.000 8.44 0.00 0.00 3.41
3729 4585 6.748333 TGCTCTAAGAATTCAGTCAAATGG 57.252 37.500 8.44 0.00 0.00 3.16
3850 4720 2.036098 TGACGCCTTAGGGGACGA 59.964 61.111 22.36 4.35 39.07 4.20
3855 4725 1.153823 CGTGTCTGACGCCTTAGGG 60.154 63.158 15.13 0.00 42.21 3.53
3856 4726 4.478195 CGTGTCTGACGCCTTAGG 57.522 61.111 15.13 0.00 42.21 2.69
3864 4734 0.102481 ATATGGGACGCGTGTCTGAC 59.898 55.000 26.79 17.77 44.83 3.51
3865 4735 0.821517 AATATGGGACGCGTGTCTGA 59.178 50.000 26.79 14.84 44.83 3.27


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

AutoCloner maintained by Alex Coulton.