Multiple sequence alignment - TraesCS4B01G244000

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 TraesCS4B01G244000 chr4B 100.000 2306 0 0 1 2306 505279647 505281952 0.000000e+00 4259
1 TraesCS4B01G244000 chr4B 91.727 834 41 8 1489 2306 437482986 437482165 0.000000e+00 1133
2 TraesCS4B01G244000 chr4B 92.030 665 36 11 1489 2139 314971343 314972004 0.000000e+00 918
3 TraesCS4B01G244000 chr4B 96.544 463 14 1 1026 1488 272035023 272034563 0.000000e+00 765
4 TraesCS4B01G244000 chr4B 91.741 448 34 2 113 557 272035469 272035022 9.050000e-174 619
5 TraesCS4B01G244000 chr5B 93.405 834 39 4 1489 2306 140500041 140499208 0.000000e+00 1221
6 TraesCS4B01G244000 chr5B 93.165 834 40 5 1489 2306 206840848 206841680 0.000000e+00 1208
7 TraesCS4B01G244000 chr5B 92.566 834 46 4 1489 2306 397563507 397562674 0.000000e+00 1182
8 TraesCS4B01G244000 chr5B 92.821 599 28 5 1489 2072 267842082 267842680 0.000000e+00 854
9 TraesCS4B01G244000 chr3B 93.301 836 36 6 1489 2305 659646416 659647250 0.000000e+00 1216
10 TraesCS4B01G244000 chr1B 92.797 833 45 3 1489 2306 286466313 286467145 0.000000e+00 1192
11 TraesCS4B01G244000 chr1B 92.395 618 29 7 1489 2090 505303447 505304062 0.000000e+00 865
12 TraesCS4B01G244000 chr1B 89.965 568 48 7 1743 2306 101578373 101577811 0.000000e+00 725
13 TraesCS4B01G244000 chr7B 92.566 834 42 7 1489 2306 531469761 531468932 0.000000e+00 1179
14 TraesCS4B01G244000 chr7B 91.419 571 39 9 1742 2306 77329217 77329783 0.000000e+00 774
15 TraesCS4B01G244000 chr7B 86.127 173 18 4 1321 1488 655657170 655657341 5.060000e-42 182
16 TraesCS4B01G244000 chr6B 90.986 832 48 8 1489 2306 54994145 54994963 0.000000e+00 1096
17 TraesCS4B01G244000 chr6B 86.313 716 92 4 288 1000 18801582 18800870 0.000000e+00 774
18 TraesCS4B01G244000 chr6B 85.871 729 84 10 288 1000 235429956 235429231 0.000000e+00 758
19 TraesCS4B01G244000 chr6B 85.890 730 79 10 288 1000 558003703 558002981 0.000000e+00 756
20 TraesCS4B01G244000 chr6B 93.909 394 21 2 999 1390 48650611 48650219 1.970000e-165 592
21 TraesCS4B01G244000 chr6B 87.755 490 55 5 996 1482 452594979 452595466 3.320000e-158 568
22 TraesCS4B01G244000 chr6B 80.726 441 53 24 100 525 48651202 48650779 4.780000e-82 315
23 TraesCS4B01G244000 chr6B 84.239 184 19 6 1321 1496 290227000 290226819 1.100000e-38 171
24 TraesCS4B01G244000 chr2D 88.797 723 68 7 288 1000 291876027 291875308 0.000000e+00 874
25 TraesCS4B01G244000 chr2B 89.045 712 44 14 1620 2306 65959649 65960351 0.000000e+00 852
26 TraesCS4B01G244000 chr2B 92.063 504 24 3 1819 2306 377193098 377193601 0.000000e+00 695
27 TraesCS4B01G244000 chr5D 93.448 580 23 3 1742 2306 261306116 261305537 0.000000e+00 846
28 TraesCS4B01G244000 chr5D 84.049 163 15 8 1338 1490 55583931 55584092 1.850000e-31 147
29 TraesCS4B01G244000 chr1D 87.967 723 74 7 288 1000 416348488 416349207 0.000000e+00 841
30 TraesCS4B01G244000 chr1D 93.399 409 23 3 999 1404 476375519 476375112 9.110000e-169 603
31 TraesCS4B01G244000 chr4A 86.712 730 79 7 288 1000 645863136 645863864 0.000000e+00 795
32 TraesCS4B01G244000 chr4A 85.437 515 51 9 996 1488 645865804 645866316 4.390000e-142 514
33 TraesCS4B01G244000 chr6A 91.566 581 33 4 1742 2306 96102539 96103119 0.000000e+00 787
34 TraesCS4B01G244000 chr5A 86.401 728 81 12 288 1000 39308540 39309264 0.000000e+00 780
35 TraesCS4B01G244000 chr5A 86.692 526 47 9 996 1499 39311167 39311691 1.550000e-156 562
36 TraesCS4B01G244000 chr5A 86.207 174 17 4 1321 1488 129059576 129059748 5.060000e-42 182
37 TraesCS4B01G244000 chr7A 86.050 724 85 10 288 1000 391446479 391445761 0.000000e+00 763
38 TraesCS4B01G244000 chr7A 90.000 520 28 5 999 1494 671136602 671136083 0.000000e+00 651
39 TraesCS4B01G244000 chr6D 86.415 714 77 11 290 1000 407034397 407033701 0.000000e+00 763
40 TraesCS4B01G244000 chr6D 84.091 176 20 6 1321 1489 454667648 454667822 1.830000e-36 163
41 TraesCS4B01G244000 chr2A 87.476 519 34 7 999 1488 28468888 28468372 9.240000e-159 569
42 TraesCS4B01G244000 chr2A 80.401 449 42 30 100 525 28469481 28469056 1.340000e-77 300
43 TraesCS4B01G244000 chr7D 87.375 499 53 5 999 1488 35835175 35834678 4.300000e-157 564
44 TraesCS4B01G244000 chr3A 84.615 312 32 6 287 595 645949057 645948759 1.730000e-76 296
45 TraesCS4B01G244000 chrUn 87.079 178 16 4 1321 1492 30346084 30346260 6.500000e-46 195


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 TraesCS4B01G244000 chr4B 505279647 505281952 2305 False 4259.0 4259 100.0000 1 2306 1 chr4B.!!$F2 2305
1 TraesCS4B01G244000 chr4B 437482165 437482986 821 True 1133.0 1133 91.7270 1489 2306 1 chr4B.!!$R1 817
2 TraesCS4B01G244000 chr4B 314971343 314972004 661 False 918.0 918 92.0300 1489 2139 1 chr4B.!!$F1 650
3 TraesCS4B01G244000 chr4B 272034563 272035469 906 True 692.0 765 94.1425 113 1488 2 chr4B.!!$R2 1375
4 TraesCS4B01G244000 chr5B 140499208 140500041 833 True 1221.0 1221 93.4050 1489 2306 1 chr5B.!!$R1 817
5 TraesCS4B01G244000 chr5B 206840848 206841680 832 False 1208.0 1208 93.1650 1489 2306 1 chr5B.!!$F1 817
6 TraesCS4B01G244000 chr5B 397562674 397563507 833 True 1182.0 1182 92.5660 1489 2306 1 chr5B.!!$R2 817
7 TraesCS4B01G244000 chr5B 267842082 267842680 598 False 854.0 854 92.8210 1489 2072 1 chr5B.!!$F2 583
8 TraesCS4B01G244000 chr3B 659646416 659647250 834 False 1216.0 1216 93.3010 1489 2305 1 chr3B.!!$F1 816
9 TraesCS4B01G244000 chr1B 286466313 286467145 832 False 1192.0 1192 92.7970 1489 2306 1 chr1B.!!$F1 817
10 TraesCS4B01G244000 chr1B 505303447 505304062 615 False 865.0 865 92.3950 1489 2090 1 chr1B.!!$F2 601
11 TraesCS4B01G244000 chr1B 101577811 101578373 562 True 725.0 725 89.9650 1743 2306 1 chr1B.!!$R1 563
12 TraesCS4B01G244000 chr7B 531468932 531469761 829 True 1179.0 1179 92.5660 1489 2306 1 chr7B.!!$R1 817
13 TraesCS4B01G244000 chr7B 77329217 77329783 566 False 774.0 774 91.4190 1742 2306 1 chr7B.!!$F1 564
14 TraesCS4B01G244000 chr6B 54994145 54994963 818 False 1096.0 1096 90.9860 1489 2306 1 chr6B.!!$F1 817
15 TraesCS4B01G244000 chr6B 18800870 18801582 712 True 774.0 774 86.3130 288 1000 1 chr6B.!!$R1 712
16 TraesCS4B01G244000 chr6B 235429231 235429956 725 True 758.0 758 85.8710 288 1000 1 chr6B.!!$R2 712
17 TraesCS4B01G244000 chr6B 558002981 558003703 722 True 756.0 756 85.8900 288 1000 1 chr6B.!!$R4 712
18 TraesCS4B01G244000 chr6B 48650219 48651202 983 True 453.5 592 87.3175 100 1390 2 chr6B.!!$R5 1290
19 TraesCS4B01G244000 chr2D 291875308 291876027 719 True 874.0 874 88.7970 288 1000 1 chr2D.!!$R1 712
20 TraesCS4B01G244000 chr2B 65959649 65960351 702 False 852.0 852 89.0450 1620 2306 1 chr2B.!!$F1 686
21 TraesCS4B01G244000 chr2B 377193098 377193601 503 False 695.0 695 92.0630 1819 2306 1 chr2B.!!$F2 487
22 TraesCS4B01G244000 chr5D 261305537 261306116 579 True 846.0 846 93.4480 1742 2306 1 chr5D.!!$R1 564
23 TraesCS4B01G244000 chr1D 416348488 416349207 719 False 841.0 841 87.9670 288 1000 1 chr1D.!!$F1 712
24 TraesCS4B01G244000 chr4A 645863136 645866316 3180 False 654.5 795 86.0745 288 1488 2 chr4A.!!$F1 1200
25 TraesCS4B01G244000 chr6A 96102539 96103119 580 False 787.0 787 91.5660 1742 2306 1 chr6A.!!$F1 564
26 TraesCS4B01G244000 chr5A 39308540 39311691 3151 False 671.0 780 86.5465 288 1499 2 chr5A.!!$F2 1211
27 TraesCS4B01G244000 chr7A 391445761 391446479 718 True 763.0 763 86.0500 288 1000 1 chr7A.!!$R1 712
28 TraesCS4B01G244000 chr7A 671136083 671136602 519 True 651.0 651 90.0000 999 1494 1 chr7A.!!$R2 495
29 TraesCS4B01G244000 chr6D 407033701 407034397 696 True 763.0 763 86.4150 290 1000 1 chr6D.!!$R1 710
30 TraesCS4B01G244000 chr2A 28468372 28469481 1109 True 434.5 569 83.9385 100 1488 2 chr2A.!!$R1 1388

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
228 229 0.036952 TTACGTCGACTCCTCGTCCT 60.037 55.0 14.7 0.0 41.02 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 5816 1.167851 CTTGCATCACGGTGGTTGAT 58.832 50.0 8.5 0.0 0.0 2.57 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
17 18 2.441348 TAGCGACCAGGCCATCGA 60.441 61.111 23.49 5.10 40.86 3.59
18 19 2.490148 TAGCGACCAGGCCATCGAG 61.490 63.158 23.49 5.81 40.86 4.04
21 22 4.899239 GACCAGGCCATCGAGCGG 62.899 72.222 5.01 0.00 0.00 5.52
24 25 4.473520 CAGGCCATCGAGCGGGTT 62.474 66.667 5.01 0.00 0.00 4.11
25 26 2.762459 AGGCCATCGAGCGGGTTA 60.762 61.111 5.01 0.00 0.00 2.85
26 27 2.140792 AGGCCATCGAGCGGGTTAT 61.141 57.895 5.01 0.00 0.00 1.89
27 28 1.668151 GGCCATCGAGCGGGTTATC 60.668 63.158 0.00 0.00 0.00 1.75
28 29 1.668151 GCCATCGAGCGGGTTATCC 60.668 63.158 5.85 0.00 0.00 2.59
29 30 2.050269 CCATCGAGCGGGTTATCCT 58.950 57.895 0.00 0.00 0.00 3.24
30 31 0.393077 CCATCGAGCGGGTTATCCTT 59.607 55.000 0.00 0.00 0.00 3.36
31 32 1.202651 CCATCGAGCGGGTTATCCTTT 60.203 52.381 0.00 0.00 0.00 3.11
32 33 2.561569 CATCGAGCGGGTTATCCTTTT 58.438 47.619 0.00 0.00 0.00 2.27
33 34 2.773993 TCGAGCGGGTTATCCTTTTT 57.226 45.000 0.00 0.00 0.00 1.94
61 62 3.577649 CGTGGATCGCTATGTTATCCT 57.422 47.619 0.00 0.00 39.97 3.24
62 63 4.696899 CGTGGATCGCTATGTTATCCTA 57.303 45.455 0.00 0.00 39.97 2.94
63 64 5.055642 CGTGGATCGCTATGTTATCCTAA 57.944 43.478 0.00 0.00 39.97 2.69
64 65 5.466819 CGTGGATCGCTATGTTATCCTAAA 58.533 41.667 0.00 0.00 39.97 1.85
65 66 5.924254 CGTGGATCGCTATGTTATCCTAAAA 59.076 40.000 0.00 0.00 39.97 1.52
66 67 6.422701 CGTGGATCGCTATGTTATCCTAAAAA 59.577 38.462 0.00 0.00 39.97 1.94
88 89 8.723942 AAAAAGAAACTAGATCGCTACATGAT 57.276 30.769 0.00 0.00 0.00 2.45
89 90 7.938563 AAAGAAACTAGATCGCTACATGATC 57.061 36.000 0.00 0.00 42.04 2.92
90 91 5.694816 AGAAACTAGATCGCTACATGATCG 58.305 41.667 0.00 0.00 45.44 3.69
91 92 5.470437 AGAAACTAGATCGCTACATGATCGA 59.530 40.000 0.00 5.42 45.44 3.59
92 93 4.937696 ACTAGATCGCTACATGATCGAG 57.062 45.455 0.00 10.30 45.48 4.04
93 94 4.570930 ACTAGATCGCTACATGATCGAGA 58.429 43.478 16.46 0.00 43.87 4.04
94 95 5.182487 ACTAGATCGCTACATGATCGAGAT 58.818 41.667 16.46 0.00 43.87 2.75
95 96 4.614555 AGATCGCTACATGATCGAGATC 57.385 45.455 0.00 9.13 45.44 2.75
96 97 2.882742 TCGCTACATGATCGAGATCG 57.117 50.000 0.00 0.00 40.63 3.69
97 98 2.143925 TCGCTACATGATCGAGATCGT 58.856 47.619 0.00 5.40 40.63 3.73
101 102 3.881953 CATGATCGAGATCGTGGCT 57.118 52.632 21.52 0.00 46.11 4.75
102 103 2.997485 CATGATCGAGATCGTGGCTA 57.003 50.000 21.52 0.36 46.11 3.93
103 104 2.590073 CATGATCGAGATCGTGGCTAC 58.410 52.381 21.52 0.00 46.11 3.58
117 118 1.081892 GGCTACGCGTATAGGATCGA 58.918 55.000 20.91 0.00 0.00 3.59
157 158 2.613223 GCTACAGGAAAAGAACGCCTCT 60.613 50.000 0.00 0.00 35.13 3.69
228 229 0.036952 TTACGTCGACTCCTCGTCCT 60.037 55.000 14.70 0.00 41.02 3.85
241 242 4.021925 GTCCTGCCTGACCGCCTT 62.022 66.667 0.00 0.00 0.00 4.35
269 307 2.798499 CGGAATTCGGACTAAGCGACAT 60.798 50.000 7.20 0.00 34.75 3.06
358 398 2.161808 ACGTCGTCTCGTCAGATTGATT 59.838 45.455 0.00 0.00 40.04 2.57
364 404 1.590238 CTCGTCAGATTGATTCGGTGC 59.410 52.381 0.00 0.00 0.00 5.01
366 406 1.740380 CGTCAGATTGATTCGGTGCCT 60.740 52.381 0.00 0.00 0.00 4.75
373 413 0.532573 TGATTCGGTGCCTGACTCTC 59.467 55.000 4.03 0.00 0.00 3.20
375 415 0.976641 ATTCGGTGCCTGACTCTCAA 59.023 50.000 0.00 0.00 0.00 3.02
390 430 4.583871 ACTCTCAATTTCAGGTGCTTAGG 58.416 43.478 0.00 0.00 0.00 2.69
415 455 7.119262 GGGAGTCATTCTTTTCGATTAACTTCA 59.881 37.037 0.00 0.00 0.00 3.02
475 525 3.057734 GGCGGATCGTTACTTCATTAGG 58.942 50.000 0.00 0.00 0.00 2.69
513 577 4.466370 TCCTCGGTTAAAGATCACATGACT 59.534 41.667 0.00 0.00 0.00 3.41
681 746 2.770164 AACATCAGTCTGGTGCCTAC 57.230 50.000 13.25 0.00 29.79 3.18
759 840 7.812669 GGTGGTATGGACAGATTTGTTAAAAAG 59.187 37.037 0.00 0.00 37.76 2.27
760 841 8.573035 GTGGTATGGACAGATTTGTTAAAAAGA 58.427 33.333 0.00 0.00 37.76 2.52
793 877 5.336150 AGTGTCATCTGGTAATCAGTCTG 57.664 43.478 0.00 0.00 43.76 3.51
847 931 9.551734 TTGTTCCATACAATGATTCTAGAGATG 57.448 33.333 0.00 0.00 41.73 2.90
850 934 7.674120 TCCATACAATGATTCTAGAGATGGTG 58.326 38.462 0.00 0.00 34.28 4.17
853 937 6.805016 ACAATGATTCTAGAGATGGTGAGT 57.195 37.500 0.00 0.00 0.00 3.41
859 943 4.163441 TCTAGAGATGGTGAGTCAGAGG 57.837 50.000 0.00 0.00 0.00 3.69
870 954 6.314917 TGGTGAGTCAGAGGCAGATAATATA 58.685 40.000 0.00 0.00 0.00 0.86
873 957 7.148086 GGTGAGTCAGAGGCAGATAATATAGAG 60.148 44.444 0.00 0.00 0.00 2.43
917 1001 9.832445 TGATATTAACTTGAATAGTTCACCTCC 57.168 33.333 0.00 0.00 43.67 4.30
941 1026 6.376299 CCTGAGGATGTTGATGATTCTTTTCA 59.624 38.462 0.00 0.00 0.00 2.69
979 1064 7.334090 TGATCCAAGAAACTAGGATTCTCTTG 58.666 38.462 11.96 11.72 42.03 3.02
1012 4949 9.144298 AGAAGATTGATATCATGCCAAAAGAAT 57.856 29.630 6.17 0.00 32.95 2.40
1130 5067 5.466728 TGACAGTTGCATCAGTAGAAAGAAC 59.533 40.000 0.00 0.00 0.00 3.01
1272 5214 7.934457 AGGGTATGATTGAAGATTTCATTTCG 58.066 34.615 0.00 0.00 39.84 3.46
1301 5243 9.553064 GAATACTACAAGAATGAGGATGTTCAT 57.447 33.333 0.00 0.00 39.42 2.57
1466 5435 4.966787 GTTTCGCACAGGGCCCCA 62.967 66.667 21.43 0.00 40.31 4.96
1617 5589 9.436957 GGTGAAAGACATTTTTGAGTCTATAGA 57.563 33.333 0.00 0.00 43.88 1.98
1755 5744 1.005924 CTTAGCACCCCCTTGACCATT 59.994 52.381 0.00 0.00 0.00 3.16
1825 5816 2.187958 ACCGGATGAATGACTCCAAGA 58.812 47.619 9.46 0.00 0.00 3.02
2113 6123 3.886123 ACCTATGTTACTCCCAATGTGC 58.114 45.455 0.00 0.00 0.00 4.57
2114 6124 3.214328 CCTATGTTACTCCCAATGTGCC 58.786 50.000 0.00 0.00 0.00 5.01
2119 6129 3.270877 GTTACTCCCAATGTGCCTAGTG 58.729 50.000 0.00 0.00 0.00 2.74
2130 6140 6.753279 CCAATGTGCCTAGTGTCATAATTTTG 59.247 38.462 0.00 0.00 0.00 2.44
2242 6256 1.895020 GACTGGGGACGCACCATGTA 61.895 60.000 1.19 0.00 41.20 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.441348 TCGATGGCCTGGTCGCTA 60.441 61.111 17.22 2.96 37.74 4.26
1 2 3.842923 CTCGATGGCCTGGTCGCT 61.843 66.667 17.22 0.00 37.74 4.93
4 5 4.899239 CCGCTCGATGGCCTGGTC 62.899 72.222 3.32 0.00 0.00 4.02
8 9 2.100879 GATAACCCGCTCGATGGCCT 62.101 60.000 3.32 0.00 0.00 5.19
9 10 1.668151 GATAACCCGCTCGATGGCC 60.668 63.158 0.00 0.00 0.00 5.36
10 11 1.668151 GGATAACCCGCTCGATGGC 60.668 63.158 0.00 0.00 0.00 4.40
12 13 2.240493 AAAGGATAACCCGCTCGATG 57.760 50.000 0.00 0.00 40.87 3.84
13 14 3.277142 AAAAAGGATAACCCGCTCGAT 57.723 42.857 0.00 0.00 40.87 3.59
14 15 2.773993 AAAAAGGATAACCCGCTCGA 57.226 45.000 0.00 0.00 40.87 4.04
41 42 3.577649 AGGATAACATAGCGATCCACG 57.422 47.619 3.15 0.00 41.48 4.94
42 43 7.724305 TTTTTAGGATAACATAGCGATCCAC 57.276 36.000 3.15 0.00 41.48 4.02
63 64 8.723942 ATCATGTAGCGATCTAGTTTCTTTTT 57.276 30.769 0.00 0.00 0.00 1.94
64 65 7.168302 CGATCATGTAGCGATCTAGTTTCTTTT 59.832 37.037 0.00 0.00 40.11 2.27
65 66 6.638873 CGATCATGTAGCGATCTAGTTTCTTT 59.361 38.462 0.00 0.00 40.11 2.52
66 67 6.017026 TCGATCATGTAGCGATCTAGTTTCTT 60.017 38.462 2.17 0.00 41.97 2.52
67 68 5.470437 TCGATCATGTAGCGATCTAGTTTCT 59.530 40.000 2.17 0.00 41.97 2.52
68 69 5.690816 TCGATCATGTAGCGATCTAGTTTC 58.309 41.667 2.17 0.00 41.97 2.78
69 70 5.470437 TCTCGATCATGTAGCGATCTAGTTT 59.530 40.000 6.08 0.00 46.40 2.66
70 71 4.998033 TCTCGATCATGTAGCGATCTAGTT 59.002 41.667 6.08 0.00 46.40 2.24
71 72 4.570930 TCTCGATCATGTAGCGATCTAGT 58.429 43.478 6.08 0.00 46.40 2.57
72 73 5.556194 CGATCTCGATCATGTAGCGATCTAG 60.556 48.000 7.59 0.00 46.40 2.43
73 74 4.268884 CGATCTCGATCATGTAGCGATCTA 59.731 45.833 7.59 0.00 46.40 1.98
74 75 3.063316 CGATCTCGATCATGTAGCGATCT 59.937 47.826 7.59 0.00 46.40 2.75
75 76 3.181515 ACGATCTCGATCATGTAGCGATC 60.182 47.826 6.60 6.78 46.40 3.69
76 77 2.744741 ACGATCTCGATCATGTAGCGAT 59.255 45.455 6.60 0.00 46.40 4.58
77 78 2.096218 CACGATCTCGATCATGTAGCGA 60.096 50.000 6.60 5.61 45.25 4.93
78 79 2.237526 CACGATCTCGATCATGTAGCG 58.762 52.381 6.60 0.00 43.02 4.26
79 80 2.590073 CCACGATCTCGATCATGTAGC 58.410 52.381 6.60 0.00 43.02 3.58
80 81 2.227626 AGCCACGATCTCGATCATGTAG 59.772 50.000 6.60 0.00 43.02 2.74
81 82 2.230660 AGCCACGATCTCGATCATGTA 58.769 47.619 6.60 0.00 43.02 2.29
82 83 1.035923 AGCCACGATCTCGATCATGT 58.964 50.000 6.60 0.00 43.02 3.21
83 84 2.590073 GTAGCCACGATCTCGATCATG 58.410 52.381 6.60 2.22 43.02 3.07
84 85 2.999507 GTAGCCACGATCTCGATCAT 57.000 50.000 6.60 0.00 43.02 2.45
98 99 6.302593 GATCTCGATCCTATACGCGTAGCC 62.303 54.167 24.78 8.38 40.53 3.93
99 100 3.302610 GATCTCGATCCTATACGCGTAGC 60.303 52.174 24.78 4.47 40.34 3.58
100 101 3.061073 CGATCTCGATCCTATACGCGTAG 60.061 52.174 24.78 13.61 43.02 3.51
101 102 2.856557 CGATCTCGATCCTATACGCGTA 59.143 50.000 22.94 22.94 43.02 4.42
102 103 1.659601 CGATCTCGATCCTATACGCGT 59.340 52.381 19.17 19.17 43.02 6.01
103 104 1.659601 ACGATCTCGATCCTATACGCG 59.340 52.381 3.53 3.53 43.02 6.01
104 105 2.223066 CCACGATCTCGATCCTATACGC 60.223 54.545 6.60 0.00 43.02 4.42
105 106 2.223066 GCCACGATCTCGATCCTATACG 60.223 54.545 6.60 0.00 43.02 3.06
106 107 3.011119 AGCCACGATCTCGATCCTATAC 58.989 50.000 6.60 0.00 43.02 1.47
107 108 3.351794 AGCCACGATCTCGATCCTATA 57.648 47.619 6.60 0.00 43.02 1.31
108 109 2.208132 AGCCACGATCTCGATCCTAT 57.792 50.000 6.60 0.00 43.02 2.57
109 110 2.424557 GTAGCCACGATCTCGATCCTA 58.575 52.381 6.60 1.07 43.02 2.94
110 111 1.240256 GTAGCCACGATCTCGATCCT 58.760 55.000 6.60 1.95 43.02 3.24
135 136 1.071699 AGGCGTTCTTTTCCTGTAGCA 59.928 47.619 0.00 0.00 0.00 3.49
194 195 1.673808 CGTAAGGCGGTAAGGGCTCT 61.674 60.000 0.00 0.00 42.70 4.09
283 321 4.715523 CAACGATGGCACCGGGGT 62.716 66.667 6.07 0.00 0.00 4.95
358 398 0.976641 AATTGAGAGTCAGGCACCGA 59.023 50.000 0.00 0.00 0.00 4.69
366 406 3.777106 AGCACCTGAAATTGAGAGTCA 57.223 42.857 0.00 0.00 0.00 3.41
373 413 3.690460 ACTCCCTAAGCACCTGAAATTG 58.310 45.455 0.00 0.00 0.00 2.32
375 415 2.912956 TGACTCCCTAAGCACCTGAAAT 59.087 45.455 0.00 0.00 0.00 2.17
390 430 8.029642 TGAAGTTAATCGAAAAGAATGACTCC 57.970 34.615 0.00 0.00 0.00 3.85
513 577 7.414222 AACCGTCTAACTCACCTAATATTCA 57.586 36.000 0.00 0.00 0.00 2.57
681 746 1.268692 TGTGCTTTTCTCTTGCGCTTG 60.269 47.619 9.73 0.65 37.98 4.01
793 877 3.010420 GTGCAAGGGTAGAAGGATCAAC 58.990 50.000 0.00 0.00 0.00 3.18
828 912 8.489676 ACTCACCATCTCTAGAATCATTGTAT 57.510 34.615 0.00 0.00 0.00 2.29
847 931 5.736951 ATATTATCTGCCTCTGACTCACC 57.263 43.478 0.00 0.00 0.00 4.02
850 934 6.889722 ACCTCTATATTATCTGCCTCTGACTC 59.110 42.308 0.00 0.00 0.00 3.36
853 937 8.164057 TCTACCTCTATATTATCTGCCTCTGA 57.836 38.462 0.00 0.00 0.00 3.27
859 943 9.640952 ATCTTCCTCTACCTCTATATTATCTGC 57.359 37.037 0.00 0.00 0.00 4.26
917 1001 7.120873 ACTGAAAAGAATCATCAACATCCTCAG 59.879 37.037 0.00 0.00 0.00 3.35
968 1053 9.835389 CAATCTTCTTAGAATCAAGAGAATCCT 57.165 33.333 0.00 0.00 35.99 3.24
979 1064 9.445878 TGGCATGATATCAATCTTCTTAGAATC 57.554 33.333 9.99 0.00 33.20 2.52
1012 4949 7.119709 TCAGAATTTCAACAGGTCCGATATA 57.880 36.000 0.00 0.00 0.00 0.86
1272 5214 9.606631 AACATCCTCATTCTTGTAGTATTCTTC 57.393 33.333 0.00 0.00 0.00 2.87
1421 5390 2.252714 TGGGGCCCTATTTCACAAAAC 58.747 47.619 25.93 0.00 0.00 2.43
1517 5486 6.370442 GCCATGTCATATTTTATGCCTACGTA 59.630 38.462 0.00 0.00 0.00 3.57
1537 5506 8.498054 TCTCTCTTCTTAATTAACTTGCCATG 57.502 34.615 0.00 0.00 0.00 3.66
1617 5589 9.305925 GTTGCTAAGCTTGCTTCATTTAATTAT 57.694 29.630 9.86 0.00 0.00 1.28
1825 5816 1.167851 CTTGCATCACGGTGGTTGAT 58.832 50.000 8.50 0.00 0.00 2.57
1890 5884 5.962031 AGTCTATGTTACTACCCATTGTGGA 59.038 40.000 0.00 0.00 40.96 4.02
2113 6123 5.580691 TGACGAGCAAAATTATGACACTAGG 59.419 40.000 0.00 0.00 0.00 3.02
2114 6124 6.647212 TGACGAGCAAAATTATGACACTAG 57.353 37.500 0.00 0.00 0.00 2.57
2119 6129 6.849811 CAGATGATGACGAGCAAAATTATGAC 59.150 38.462 0.00 0.00 0.00 3.06
2130 6140 3.812609 TCTAGACTCAGATGATGACGAGC 59.187 47.826 0.00 0.00 33.22 5.03
2242 6256 2.599578 ACGTACGGAGTGCCCACT 60.600 61.111 21.06 0.00 45.73 4.00


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

AutoCloner maintained by Alex Coulton.