Multiple sequence alignment - TraesCS4B01G012600

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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 TraesCS4B01G012600 chr4B 100.000 5360 0 0 1 5360 8014454 8019813 0.000000e+00 9899.0
1 TraesCS4B01G012600 chr4B 95.720 5187 165 29 178 5360 8929745 8934878 0.000000e+00 8296.0
2 TraesCS4B01G012600 chr5D 96.567 3350 83 4 1410 4753 550602512 550599189 0.000000e+00 5520.0
3 TraesCS4B01G012600 chr5D 95.929 737 30 0 1 737 112079776 112080512 0.000000e+00 1195.0
4 TraesCS4B01G012600 chr5D 95.565 744 32 1 1 743 283059016 283058273 0.000000e+00 1190.0
5 TraesCS4B01G012600 chr5D 95.980 597 24 0 738 1334 550603112 550602516 0.000000e+00 970.0
6 TraesCS4B01G012600 chr5D 95.058 607 30 0 4754 5360 174179157 174178551 0.000000e+00 955.0
7 TraesCS4B01G012600 chr5D 94.634 615 31 2 4747 5360 213691355 213690742 0.000000e+00 952.0
8 TraesCS4B01G012600 chr5D 94.595 37 2 0 1329 1365 550602493 550602457 2.090000e-04 58.4
9 TraesCS4B01G012600 chr6D 96.145 3346 88 5 1410 4753 17158010 17161316 0.000000e+00 5426.0
10 TraesCS4B01G012600 chr6D 97.121 3161 88 2 1410 4568 472124803 472121644 0.000000e+00 5330.0
11 TraesCS4B01G012600 chr6D 95.387 607 28 0 4754 5360 77457744 77457138 0.000000e+00 966.0
12 TraesCS4B01G012600 chr6D 95.805 596 25 0 739 1334 17157411 17158006 0.000000e+00 963.0
13 TraesCS4B01G012600 chr6D 95.222 607 28 1 4754 5360 96679476 96680081 0.000000e+00 959.0
14 TraesCS4B01G012600 chr6D 94.966 596 30 0 739 1334 472125402 472124807 0.000000e+00 935.0
15 TraesCS4B01G012600 chr6D 100.000 31 0 0 1329 1359 17158029 17158059 2.090000e-04 58.4
16 TraesCS4B01G012600 chr6D 94.595 37 2 0 1329 1365 472124784 472124748 2.090000e-04 58.4
17 TraesCS4B01G012600 chr5B 96.809 2789 81 5 1597 4382 711409882 711407099 0.000000e+00 4650.0
18 TraesCS4B01G012600 chr6B 96.558 2789 90 3 1597 4382 674956000 674953215 0.000000e+00 4614.0
19 TraesCS4B01G012600 chr6B 97.542 1139 24 2 1597 2734 715066911 715065776 0.000000e+00 1945.0
20 TraesCS4B01G012600 chr6B 86.184 304 13 12 4454 4756 674953197 674952922 8.720000e-78 302.0
21 TraesCS4B01G012600 chr6B 96.386 166 6 0 4588 4753 715064004 715063839 1.900000e-69 274.0
22 TraesCS4B01G012600 chr7B 95.839 1610 66 1 2774 4382 578994319 578992710 0.000000e+00 2601.0
23 TraesCS4B01G012600 chr7B 94.809 732 36 1 3735 4464 66408423 66407692 0.000000e+00 1140.0
24 TraesCS4B01G012600 chr7B 93.023 602 32 3 738 1329 578995685 578995084 0.000000e+00 870.0
25 TraesCS4B01G012600 chr7B 93.253 578 38 1 741 1318 748614527 748613951 0.000000e+00 850.0
26 TraesCS4B01G012600 chr7B 95.968 248 10 0 1410 1657 748613931 748613684 2.320000e-108 403.0
27 TraesCS4B01G012600 chr7D 97.744 1330 30 0 1410 2739 20633292 20631963 0.000000e+00 2290.0
28 TraesCS4B01G012600 chr7D 94.822 1178 33 1 3579 4756 20631965 20630816 0.000000e+00 1812.0
29 TraesCS4B01G012600 chr7D 96.201 737 28 0 1 737 396162488 396163224 0.000000e+00 1206.0
30 TraesCS4B01G012600 chr7D 95.066 608 29 1 4754 5360 372592487 372591880 0.000000e+00 955.0
31 TraesCS4B01G012600 chr7D 95.777 592 23 2 750 1339 587291436 587292027 0.000000e+00 953.0
32 TraesCS4B01G012600 chr7D 95.470 596 27 0 739 1334 20633891 20633296 0.000000e+00 952.0
33 TraesCS4B01G012600 chr7D 94.595 37 2 0 1329 1365 20633273 20633237 2.090000e-04 58.4
34 TraesCS4B01G012600 chr5A 77.463 2365 447 62 1735 4056 402917567 402919888 0.000000e+00 1336.0
35 TraesCS4B01G012600 chr2A 77.378 2365 444 66 1737 4056 37161884 37164202 0.000000e+00 1319.0
36 TraesCS4B01G012600 chr1B 95.269 782 35 2 750 1530 22641854 22641074 0.000000e+00 1238.0
37 TraesCS4B01G012600 chr1B 92.792 763 27 5 3991 4753 22641073 22640339 0.000000e+00 1079.0
38 TraesCS4B01G012600 chr3D 96.336 737 27 0 1 737 394850020 394849284 0.000000e+00 1212.0
39 TraesCS4B01G012600 chr3D 96.336 737 27 0 1 737 544732233 544732969 0.000000e+00 1212.0
40 TraesCS4B01G012600 chr2D 95.929 737 30 0 1 737 157285553 157286289 0.000000e+00 1195.0
41 TraesCS4B01G012600 chr2D 95.929 737 28 2 1 737 90271772 90271038 0.000000e+00 1194.0
42 TraesCS4B01G012600 chr2D 95.794 737 31 0 1 737 192204320 192205056 0.000000e+00 1190.0
43 TraesCS4B01G012600 chr1D 95.811 740 31 0 1 740 15814770 15814031 0.000000e+00 1195.0
44 TraesCS4B01G012600 chr1D 94.893 607 31 0 4754 5360 311732358 311731752 0.000000e+00 950.0
45 TraesCS4B01G012600 chr4D 94.893 607 31 0 4754 5360 28766294 28766900 0.000000e+00 950.0
46 TraesCS4B01G012600 chr4D 94.893 607 31 0 4754 5360 100287251 100287857 0.000000e+00 950.0
47 TraesCS4B01G012600 chr6A 93.698 603 26 5 737 1329 593440724 593441324 0.000000e+00 893.0
48 TraesCS4B01G012600 chr6A 86.333 300 13 16 4454 4753 593441739 593442010 8.720000e-78 302.0
49 TraesCS4B01G012600 chr2B 97.101 483 14 0 1410 1892 47832817 47833299 0.000000e+00 815.0
50 TraesCS4B01G012600 chr3B 86.379 301 13 11 4454 4754 710961215 710961487 2.430000e-78 303.0
51 TraesCS4B01G012600 chr3B 86.379 301 13 11 4454 4754 710973216 710973488 2.430000e-78 303.0


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 TraesCS4B01G012600 chr4B 8014454 8019813 5359 False 9899.000000 9899 100.000000 1 5360 1 chr4B.!!$F1 5359
1 TraesCS4B01G012600 chr4B 8929745 8934878 5133 False 8296.000000 8296 95.720000 178 5360 1 chr4B.!!$F2 5182
2 TraesCS4B01G012600 chr5D 550599189 550603112 3923 True 2182.800000 5520 95.714000 738 4753 3 chr5D.!!$R4 4015
3 TraesCS4B01G012600 chr5D 112079776 112080512 736 False 1195.000000 1195 95.929000 1 737 1 chr5D.!!$F1 736
4 TraesCS4B01G012600 chr5D 283058273 283059016 743 True 1190.000000 1190 95.565000 1 743 1 chr5D.!!$R3 742
5 TraesCS4B01G012600 chr5D 174178551 174179157 606 True 955.000000 955 95.058000 4754 5360 1 chr5D.!!$R1 606
6 TraesCS4B01G012600 chr5D 213690742 213691355 613 True 952.000000 952 94.634000 4747 5360 1 chr5D.!!$R2 613
7 TraesCS4B01G012600 chr6D 17157411 17161316 3905 False 2149.133333 5426 97.316667 739 4753 3 chr6D.!!$F2 4014
8 TraesCS4B01G012600 chr6D 472121644 472125402 3758 True 2107.800000 5330 95.560667 739 4568 3 chr6D.!!$R2 3829
9 TraesCS4B01G012600 chr6D 77457138 77457744 606 True 966.000000 966 95.387000 4754 5360 1 chr6D.!!$R1 606
10 TraesCS4B01G012600 chr6D 96679476 96680081 605 False 959.000000 959 95.222000 4754 5360 1 chr6D.!!$F1 606
11 TraesCS4B01G012600 chr5B 711407099 711409882 2783 True 4650.000000 4650 96.809000 1597 4382 1 chr5B.!!$R1 2785
12 TraesCS4B01G012600 chr6B 674952922 674956000 3078 True 2458.000000 4614 91.371000 1597 4756 2 chr6B.!!$R1 3159
13 TraesCS4B01G012600 chr6B 715063839 715066911 3072 True 1109.500000 1945 96.964000 1597 4753 2 chr6B.!!$R2 3156
14 TraesCS4B01G012600 chr7B 578992710 578995685 2975 True 1735.500000 2601 94.431000 738 4382 2 chr7B.!!$R2 3644
15 TraesCS4B01G012600 chr7B 66407692 66408423 731 True 1140.000000 1140 94.809000 3735 4464 1 chr7B.!!$R1 729
16 TraesCS4B01G012600 chr7B 748613684 748614527 843 True 626.500000 850 94.610500 741 1657 2 chr7B.!!$R3 916
17 TraesCS4B01G012600 chr7D 20630816 20633891 3075 True 1278.100000 2290 95.657750 739 4756 4 chr7D.!!$R2 4017
18 TraesCS4B01G012600 chr7D 396162488 396163224 736 False 1206.000000 1206 96.201000 1 737 1 chr7D.!!$F1 736
19 TraesCS4B01G012600 chr7D 372591880 372592487 607 True 955.000000 955 95.066000 4754 5360 1 chr7D.!!$R1 606
20 TraesCS4B01G012600 chr7D 587291436 587292027 591 False 953.000000 953 95.777000 750 1339 1 chr7D.!!$F2 589
21 TraesCS4B01G012600 chr5A 402917567 402919888 2321 False 1336.000000 1336 77.463000 1735 4056 1 chr5A.!!$F1 2321
22 TraesCS4B01G012600 chr2A 37161884 37164202 2318 False 1319.000000 1319 77.378000 1737 4056 1 chr2A.!!$F1 2319
23 TraesCS4B01G012600 chr1B 22640339 22641854 1515 True 1158.500000 1238 94.030500 750 4753 2 chr1B.!!$R1 4003
24 TraesCS4B01G012600 chr3D 394849284 394850020 736 True 1212.000000 1212 96.336000 1 737 1 chr3D.!!$R1 736
25 TraesCS4B01G012600 chr3D 544732233 544732969 736 False 1212.000000 1212 96.336000 1 737 1 chr3D.!!$F1 736
26 TraesCS4B01G012600 chr2D 157285553 157286289 736 False 1195.000000 1195 95.929000 1 737 1 chr2D.!!$F1 736
27 TraesCS4B01G012600 chr2D 90271038 90271772 734 True 1194.000000 1194 95.929000 1 737 1 chr2D.!!$R1 736
28 TraesCS4B01G012600 chr2D 192204320 192205056 736 False 1190.000000 1190 95.794000 1 737 1 chr2D.!!$F2 736
29 TraesCS4B01G012600 chr1D 15814031 15814770 739 True 1195.000000 1195 95.811000 1 740 1 chr1D.!!$R1 739
30 TraesCS4B01G012600 chr1D 311731752 311732358 606 True 950.000000 950 94.893000 4754 5360 1 chr1D.!!$R2 606
31 TraesCS4B01G012600 chr4D 28766294 28766900 606 False 950.000000 950 94.893000 4754 5360 1 chr4D.!!$F1 606
32 TraesCS4B01G012600 chr4D 100287251 100287857 606 False 950.000000 950 94.893000 4754 5360 1 chr4D.!!$F2 606
33 TraesCS4B01G012600 chr6A 593440724 593442010 1286 False 597.500000 893 90.015500 737 4753 2 chr6A.!!$F1 4016

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
934 937 1.617850 TCCAAAATGAAACCGCTGCAT 59.382 42.857 0.0 0.0 0.00 3.96 F
1688 1713 0.035439 ACCCTGCGTGGAAGTATTGG 60.035 55.000 0.0 0.0 38.35 3.16 F
2981 3192 0.681564 TGGAAAGGTGTTGGCGTTGT 60.682 50.000 0.0 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 2283 0.831307 AGTAGGCCCATCGGAGTTTC 59.169 55.000 0.00 0.0 0.00 2.78 R
3262 3473 2.104967 CCTTGTGATGCAATGGACCAT 58.895 47.619 0.00 0.0 36.36 3.55 R
4719 5989 0.107848 GCCCGCTAAACCTCTTAGCA 60.108 55.000 14.86 0.0 45.63 3.49 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
150 151 1.690219 CGAGGCTTATGGAGGGCACT 61.690 60.000 0.00 0.00 0.00 4.40
191 192 3.253188 CACATAAGGTATTGCAATCCGGG 59.747 47.826 16.86 10.96 0.00 5.73
531 533 4.648762 TGACTGATGGTGGTTCACATTTTT 59.351 37.500 0.38 0.00 35.86 1.94
571 573 7.148918 CCGTAAAATGCTTGCTAAATATGATGC 60.149 37.037 0.00 0.00 0.00 3.91
730 732 5.582950 TTATGGGCCTATAGAACTGCATT 57.417 39.130 8.99 0.00 0.00 3.56
934 937 1.617850 TCCAAAATGAAACCGCTGCAT 59.382 42.857 0.00 0.00 0.00 3.96
1009 1021 0.122435 AAACCCTATCCCCACTCCCA 59.878 55.000 0.00 0.00 0.00 4.37
1110 1122 3.706373 GCCTTCCTCGCCACTCCA 61.706 66.667 0.00 0.00 0.00 3.86
1133 1153 1.684734 AGCGACGGGGTATTCCACT 60.685 57.895 0.00 0.00 34.37 4.00
1276 1297 0.685131 CCATGAGCCAGCAAATCCCA 60.685 55.000 0.00 0.00 0.00 4.37
1318 1339 8.458573 TCTATCCTCTGTTATCTCTTCTTGTC 57.541 38.462 0.00 0.00 0.00 3.18
1389 1410 7.059448 TGCTCAAGATTTGTGTTTTTCAAAC 57.941 32.000 0.00 0.00 37.56 2.93
1391 1412 6.034470 GCTCAAGATTTGTGTTTTTCAAACGA 59.966 34.615 0.00 0.00 37.56 3.85
1407 1428 2.065993 ACGATGGACTCAGTTCAACG 57.934 50.000 13.95 13.95 41.87 4.10
1448 1469 4.198530 TGAATGCTCCAGATTCGCAATAA 58.801 39.130 0.00 0.00 37.20 1.40
1514 1536 8.306038 AGATGCATTGAAAGTTTATTTGCTACA 58.694 29.630 0.00 0.12 0.00 2.74
1629 1654 1.601759 GGCTCAAGCACTGCCTCAA 60.602 57.895 4.13 0.00 44.36 3.02
1644 1669 2.928334 CCTCAATAGCAGCACCTTCAT 58.072 47.619 0.00 0.00 0.00 2.57
1688 1713 0.035439 ACCCTGCGTGGAAGTATTGG 60.035 55.000 0.00 0.00 38.35 3.16
1942 1967 4.705023 TGTTGACTTAGATCACTCCGATGA 59.295 41.667 0.00 0.00 33.17 2.92
2296 2322 3.966006 ACTGCATATGAGATGAGTGGACT 59.034 43.478 6.97 0.00 0.00 3.85
2480 2507 7.300320 TCTTGAATTCAGTTGATTGTTCATCG 58.700 34.615 8.41 0.00 34.08 3.84
2566 2594 3.541632 ACAAAGTCGTTCAAGTGGTGAT 58.458 40.909 0.00 0.00 35.70 3.06
2747 2843 6.228258 AGTAACGGTGTTCTTGTATTCACAT 58.772 36.000 0.00 0.00 33.76 3.21
2981 3192 0.681564 TGGAAAGGTGTTGGCGTTGT 60.682 50.000 0.00 0.00 0.00 3.32
3020 3231 4.038402 GCCAATGGCTAATGTGCTAAGAAT 59.962 41.667 18.47 0.00 46.69 2.40
3185 3396 2.151202 CAAGTCGCCACTACATTTGGT 58.849 47.619 0.00 0.00 36.40 3.67
3201 3412 5.659079 ACATTTGGTTGGGTACTTTCTGAAA 59.341 36.000 2.44 2.44 0.00 2.69
3254 3465 7.038729 TGTGATAGAGAGGGATGGATCATTTAC 60.039 40.741 0.00 0.00 0.00 2.01
3256 3467 7.513781 TGATAGAGAGGGATGGATCATTTACAA 59.486 37.037 0.00 0.00 0.00 2.41
3257 3468 6.776887 AGAGAGGGATGGATCATTTACAAT 57.223 37.500 0.00 0.00 0.00 2.71
3262 3473 7.293299 AGAGGGATGGATCATTTACAATAGTCA 59.707 37.037 0.00 0.00 0.00 3.41
3483 4039 5.823045 CCCCTCTTTGTACTTGCCTAAATAG 59.177 44.000 0.00 0.00 0.00 1.73
3513 4075 5.921976 TGTTTCAATGTCTTAATGCAGCAAG 59.078 36.000 0.00 0.00 0.00 4.01
3523 4085 0.256752 ATGCAGCAAGATGGTGGCTA 59.743 50.000 0.00 0.00 45.26 3.93
3729 4310 9.729023 CATACTTGATTTTGTTCACTTACACAA 57.271 29.630 0.00 0.00 0.00 3.33
3870 4451 6.483307 AGAAGACAATCGTTGATGTTCTTGAA 59.517 34.615 7.51 0.00 29.61 2.69
3919 4500 6.019640 CGGCATTGTTGGAAATGATAATGTTC 60.020 38.462 1.22 0.00 39.46 3.18
3969 4550 4.679373 TCAACAAGAGAGAGCTTCAACT 57.321 40.909 0.00 0.00 0.00 3.16
4025 4606 0.470341 GCGCCCCCTAGAAAGAAGAT 59.530 55.000 0.00 0.00 0.00 2.40
4029 4610 3.181450 CGCCCCCTAGAAAGAAGATGAAT 60.181 47.826 0.00 0.00 0.00 2.57
4060 4641 6.544928 TGCAATCTCTCCTTAATAGTGTCA 57.455 37.500 0.00 0.00 0.00 3.58
4097 4678 4.522022 ACTTTCTGCCTCTTCCAATTCTTG 59.478 41.667 0.00 0.00 0.00 3.02
4104 4685 4.065088 CCTCTTCCAATTCTTGTTCGTCA 58.935 43.478 0.00 0.00 0.00 4.35
4287 4868 9.691362 GTTGATGTACCACTTTTGTTATTCAAT 57.309 29.630 0.00 0.00 35.84 2.57
4314 4895 3.780804 TGGTGGTATGTTGCTAGTTGT 57.219 42.857 0.00 0.00 0.00 3.32
4334 4915 3.005684 TGTTATGCCAAACTTTGCTCTGG 59.994 43.478 0.00 0.00 0.00 3.86
4431 5090 9.982651 GCATTATGACTATGAGTTTAGGACTTA 57.017 33.333 0.00 0.00 39.19 2.24
4543 5811 5.360591 ACTTGGCTGTATGCTAGTTGATAC 58.639 41.667 0.00 0.00 42.39 2.24
4668 5938 0.455815 CTGAAACGCTAAATGGGGCC 59.544 55.000 0.00 0.00 0.00 5.80
4716 5986 3.439857 TTCATAGCTTTTGGTCAGGCT 57.560 42.857 0.00 0.00 38.62 4.58
4719 5989 3.054139 TCATAGCTTTTGGTCAGGCTGAT 60.054 43.478 21.84 4.24 36.40 2.90
4729 5999 1.484240 GTCAGGCTGATGCTAAGAGGT 59.516 52.381 21.84 0.00 39.59 3.85
4783 6054 4.888239 CCCTATGGGTATGTCTCCGTATAG 59.112 50.000 0.00 0.00 38.25 1.31
4800 6071 9.284968 CTCCGTATAGAATGGTTTATGGAAAAT 57.715 33.333 0.00 0.00 35.53 1.82
4848 6119 5.955961 ACATAAGGCTTATTGGGCAATTT 57.044 34.783 16.95 0.00 32.50 1.82
4881 6152 2.192664 TGATTTCAAGCTTGCCGGTA 57.807 45.000 21.99 0.56 0.00 4.02
4968 6239 9.805966 CCAAGTTGTTTAAAGAAAAAGTCAAAC 57.194 29.630 0.00 0.00 0.00 2.93
5000 6272 2.986479 CAAAAGGATACAAAAGCGTGGC 59.014 45.455 0.00 0.00 41.41 5.01
5189 6461 9.869844 GGTCAAAGAATCAAACATTATATCTCG 57.130 33.333 0.00 0.00 0.00 4.04
5267 6539 5.825593 ACATAAGAGACACTTCCCAGAAA 57.174 39.130 0.00 0.00 39.72 2.52
5314 6586 5.480073 AGGTATGTGGTACGGTAAGTAAACA 59.520 40.000 0.00 0.00 38.05 2.83
5339 6611 4.018960 ACTCCAGAACAGTTCTAATGGCAT 60.019 41.667 15.73 0.00 38.11 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 0.318360 TGCTCAGGTACACAACGTCG 60.318 55.000 0.00 0.00 0.00 5.12
150 151 2.099263 GTGCAGTTCTATCTCCAGCGTA 59.901 50.000 0.00 0.00 0.00 4.42
191 192 6.094186 CCTTGAAGAGAGTAGGCCAATAAAAC 59.906 42.308 5.01 0.00 0.00 2.43
255 256 8.467963 TGACGTCTACTAATATTACCAATCCA 57.532 34.615 17.92 0.00 0.00 3.41
306 307 6.939163 CCCCAAACATCAAATGGTTCAATAAA 59.061 34.615 0.00 0.00 38.32 1.40
399 401 7.567622 TGGAATAGCTTCTACCCACTTAGTAAT 59.432 37.037 0.00 0.00 0.00 1.89
531 533 4.920640 TTTTACGGAAAGCACCATGAAA 57.079 36.364 0.00 0.00 0.00 2.69
1009 1021 3.588842 TGGTTCCTGTTTGAGATGAGGAT 59.411 43.478 0.00 0.00 34.53 3.24
1049 1061 1.302431 CTGTCGCCATGGTTGGTCA 60.302 57.895 14.67 6.49 45.57 4.02
1093 1105 2.932130 GATGGAGTGGCGAGGAAGGC 62.932 65.000 0.00 0.00 37.19 4.35
1244 1265 1.976132 CTCATGGTCGCCTGGTGGAT 61.976 60.000 7.51 0.00 34.57 3.41
1276 1297 5.843421 AGGATAGATGAGCTTACCTGTTGAT 59.157 40.000 0.00 0.00 32.40 2.57
1318 1339 4.808077 ATCTTGAGCATTACAAGCATCG 57.192 40.909 0.00 0.00 42.76 3.84
1359 1380 7.846644 AAAACACAAATCTTGAGCATTCAAA 57.153 28.000 0.00 0.00 42.48 2.69
1360 1381 7.548427 TGAAAAACACAAATCTTGAGCATTCAA 59.452 29.630 0.00 0.00 40.92 2.69
1389 1410 1.350193 CCGTTGAACTGAGTCCATCG 58.650 55.000 0.00 0.00 0.00 3.84
1391 1412 0.324943 CCCCGTTGAACTGAGTCCAT 59.675 55.000 0.00 0.00 0.00 3.41
1407 1428 3.631250 TCAGCTATTCACCATTTTCCCC 58.369 45.455 0.00 0.00 0.00 4.81
1514 1536 9.871238 AAGTACGTGATAGAAAAATGTACATCT 57.129 29.630 9.23 5.36 38.30 2.90
1579 1604 5.117592 CCTATGCAAAAAGAAGCGAACAAAG 59.882 40.000 0.00 0.00 0.00 2.77
1629 1654 1.849039 AGGGAATGAAGGTGCTGCTAT 59.151 47.619 0.00 0.00 0.00 2.97
1644 1669 3.146066 CCGAATCAACAACTTGAGGGAA 58.854 45.455 0.00 0.00 39.83 3.97
1942 1967 8.566260 CATCTTCTTCATCAGTTTCTTGTTCTT 58.434 33.333 0.00 0.00 0.00 2.52
2179 2204 2.338577 ATGTGGGATGCTAGCTTCAC 57.661 50.000 26.51 24.65 0.00 3.18
2257 2283 0.831307 AGTAGGCCCATCGGAGTTTC 59.169 55.000 0.00 0.00 0.00 2.78
2480 2507 5.146010 TGTATTTGCCATTTTTCTGGACC 57.854 39.130 0.00 0.00 38.69 4.46
2566 2594 3.925379 ACATTGACACTAGCATTGTCGA 58.075 40.909 4.79 4.79 45.44 4.20
2747 2843 3.706594 CCTCATCAGAGCTAACACCCTTA 59.293 47.826 0.00 0.00 40.68 2.69
2981 3192 4.278170 CCATTGGCTCAAAGTAGTTGACAA 59.722 41.667 0.00 0.00 41.47 3.18
3020 3231 2.549992 GCGGGCACATCACTATCCATTA 60.550 50.000 0.00 0.00 0.00 1.90
3089 3300 6.595326 ACTCTCATCATTATCAAAACTCGCAA 59.405 34.615 0.00 0.00 0.00 4.85
3159 3370 3.188159 TGTAGTGGCGACTTGAGTTTT 57.812 42.857 6.71 0.00 33.21 2.43
3201 3412 9.010767 ACCTTGTTTGGATAATAATAGTAGGGT 57.989 33.333 0.00 0.00 0.00 4.34
3254 3465 4.581409 TGATGCAATGGACCATGACTATTG 59.419 41.667 8.02 17.50 38.57 1.90
3256 3467 4.139786 GTGATGCAATGGACCATGACTAT 58.860 43.478 8.02 0.70 0.00 2.12
3257 3468 3.054508 TGTGATGCAATGGACCATGACTA 60.055 43.478 8.02 0.00 0.00 2.59
3262 3473 2.104967 CCTTGTGATGCAATGGACCAT 58.895 47.619 0.00 0.00 36.36 3.55
3483 4039 8.741101 TGCATTAAGACATTGAAACATTGTAC 57.259 30.769 0.00 0.00 29.78 2.90
3513 4075 3.636300 TGTGCCATAATTTAGCCACCATC 59.364 43.478 0.00 0.00 0.00 3.51
3606 4168 6.815089 ACTTGTTCAAATGCTGACCAATTTA 58.185 32.000 0.00 0.00 36.05 1.40
3729 4310 3.563808 TGCTGCGTTTCTTTGTATGAACT 59.436 39.130 0.00 0.00 0.00 3.01
3799 4380 6.609876 TCTCTCTCTTATGCTTCATCCTAGT 58.390 40.000 0.00 0.00 0.00 2.57
3870 4451 3.945921 TGATGAACTCGTTATCCTCGTCT 59.054 43.478 0.00 0.00 0.00 4.18
3919 4500 5.694231 TCTTCATCACCAACATGTTCAAG 57.306 39.130 8.48 3.16 0.00 3.02
3969 4550 6.435904 TCTTCTTTTTCCCTTGTTCTTGTGAA 59.564 34.615 0.00 0.00 0.00 3.18
4060 4641 5.131809 AGGCAGAAAGTATAGCTTCCTCATT 59.868 40.000 0.00 0.00 36.17 2.57
4097 4678 5.406649 ACTCATCTTCTGATTCTGACGAAC 58.593 41.667 4.29 0.00 32.10 3.95
4104 4685 4.882559 AGGGAGACTCATCTTCTGATTCT 58.117 43.478 4.53 0.00 44.19 2.40
4141 4722 4.080975 CACCCAACCATGCAATTAATCCTT 60.081 41.667 0.00 0.00 0.00 3.36
4142 4723 3.451902 CACCCAACCATGCAATTAATCCT 59.548 43.478 0.00 0.00 0.00 3.24
4287 4868 1.678627 GCAACATACCACCAACACACA 59.321 47.619 0.00 0.00 0.00 3.72
4314 4895 3.230134 ACCAGAGCAAAGTTTGGCATAA 58.770 40.909 17.11 0.00 33.98 1.90
4334 4915 8.562892 CAGGAGATGGTTCAATTCATTACATAC 58.437 37.037 0.00 0.00 0.00 2.39
4383 5040 5.163099 TGCAAAGAACAGCCCCATATAGTAT 60.163 40.000 0.00 0.00 0.00 2.12
4451 5110 4.082787 GCAAACAGCCACATAACATAGTGT 60.083 41.667 0.00 0.00 37.23 3.55
4593 5861 9.538508 CATAGAATCAGTCATCAACTTGACATA 57.461 33.333 7.28 0.00 46.81 2.29
4594 5862 8.045507 ACATAGAATCAGTCATCAACTTGACAT 58.954 33.333 7.28 0.00 46.81 3.06
4595 5863 7.389232 ACATAGAATCAGTCATCAACTTGACA 58.611 34.615 7.28 0.00 46.81 3.58
4716 5986 2.158957 CCCGCTAAACCTCTTAGCATCA 60.159 50.000 14.86 0.00 45.63 3.07
4719 5989 0.107848 GCCCGCTAAACCTCTTAGCA 60.108 55.000 14.86 0.00 45.63 3.49
4729 5999 6.174760 TCAAAGTTTTAGATAGCCCGCTAAA 58.825 36.000 0.00 0.00 35.45 1.85
4736 6006 9.582431 GGGTTTTTATCAAAGTTTTAGATAGCC 57.418 33.333 0.00 0.00 0.00 3.93
4783 6054 8.253113 AGTGACATGATTTTCCATAAACCATTC 58.747 33.333 0.00 0.00 0.00 2.67
4800 6071 4.079970 AGTTCGAGAGGTAAGTGACATGA 58.920 43.478 0.00 0.00 0.00 3.07
4881 6152 8.103305 TGAGCTAATGTCAAATAACCTCTTCTT 58.897 33.333 0.00 0.00 0.00 2.52
4968 6239 3.627123 TGTATCCTTTTGTCATGCCATCG 59.373 43.478 0.00 0.00 0.00 3.84
5267 6539 4.417426 TTCCTTTTCGGAGTCTGAAACT 57.583 40.909 23.81 0.00 44.28 2.66
5314 6586 4.323104 GCCATTAGAACTGTTCTGGAGTCT 60.323 45.833 28.46 7.17 40.94 3.24


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

AutoCloner maintained by Alex Coulton.