Multiple sequence alignment - TraesCS4D01G340100

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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 TraesCS4D01G340100 chr4D 100.000 3223 0 0 1 3223 497497390 497494168 0.000000e+00 5952.0
1 TraesCS4D01G340100 chr4D 93.333 1200 47 14 922 2104 497467849 497466666 0.000000e+00 1742.0
2 TraesCS4D01G340100 chr4D 91.187 1146 53 14 769 1905 497562873 497561767 0.000000e+00 1513.0
3 TraesCS4D01G340100 chr4D 84.674 1181 76 37 924 2040 497515198 497514059 0.000000e+00 1081.0
4 TraesCS4D01G340100 chr4D 93.486 568 29 4 2117 2677 497445613 497445047 0.000000e+00 837.0
5 TraesCS4D01G340100 chr4D 92.661 545 38 1 2679 3223 187246429 187245887 0.000000e+00 784.0
6 TraesCS4D01G340100 chr4D 90.345 290 22 2 1452 1738 497452449 497452163 3.040000e-100 375.0
7 TraesCS4D01G340100 chr4D 92.908 141 10 0 1731 1871 497451015 497450875 4.210000e-49 206.0
8 TraesCS4D01G340100 chr4D 81.098 164 10 6 924 1072 497452911 497452754 9.450000e-21 111.0
9 TraesCS4D01G340100 chr4B 85.662 1911 155 52 98 1953 638424184 638422338 0.000000e+00 1901.0
10 TraesCS4D01G340100 chr4B 90.526 570 42 6 2117 2677 638364806 638364240 0.000000e+00 743.0
11 TraesCS4D01G340100 chr4B 83.549 772 74 24 1116 1871 638369750 638369016 0.000000e+00 673.0
12 TraesCS4D01G340100 chr4B 89.239 539 56 2 2679 3216 643576244 643576781 0.000000e+00 673.0
13 TraesCS4D01G340100 chr4B 88.399 431 40 5 2254 2677 638363534 638363107 7.980000e-141 510.0
14 TraesCS4D01G340100 chr4B 87.671 438 39 3 2254 2677 638364105 638363669 2.230000e-136 496.0
15 TraesCS4D01G340100 chr4B 81.818 165 11 4 924 1072 638369925 638369764 1.570000e-23 121.0
16 TraesCS4D01G340100 chr4B 91.071 56 4 1 2366 2421 387439528 387439582 1.240000e-09 75.0
17 TraesCS4D01G340100 chr5A 87.452 1044 43 26 815 1810 677674349 677673346 0.000000e+00 1122.0
18 TraesCS4D01G340100 chr5A 93.956 546 32 1 2679 3223 184618317 184617772 0.000000e+00 824.0
19 TraesCS4D01G340100 chr5A 83.075 969 75 46 924 1871 677778521 677777621 0.000000e+00 798.0
20 TraesCS4D01G340100 chr5A 89.180 573 49 7 2117 2677 677758294 677757723 0.000000e+00 702.0
21 TraesCS4D01G340100 chr5A 88.596 570 53 8 2117 2677 677683168 677682602 0.000000e+00 682.0
22 TraesCS4D01G340100 chr5A 81.900 779 70 29 1116 1871 677727107 677726377 2.770000e-165 592.0
23 TraesCS4D01G340100 chr5A 88.333 360 38 4 2285 2641 677682209 677681851 2.300000e-116 429.0
24 TraesCS4D01G340100 chr5A 88.312 154 11 3 1800 1953 677673317 677673171 9.190000e-41 178.0
25 TraesCS4D01G340100 chr5A 80.240 167 13 4 924 1072 677727285 677727121 1.220000e-19 108.0
26 TraesCS4D01G340100 chr6D 93.911 542 33 0 2682 3223 317516678 317516137 0.000000e+00 819.0
27 TraesCS4D01G340100 chr6D 91.575 546 44 2 2679 3223 20465112 20464568 0.000000e+00 752.0
28 TraesCS4D01G340100 chr7A 93.578 545 35 0 2679 3223 183619641 183620185 0.000000e+00 813.0
29 TraesCS4D01G340100 chr7B 92.844 545 37 2 2679 3223 41189320 41189862 0.000000e+00 789.0
30 TraesCS4D01G340100 chr7B 90.000 60 5 1 2366 2425 509011099 509011157 3.450000e-10 76.8
31 TraesCS4D01G340100 chr5D 91.392 546 44 3 2679 3223 52957550 52958093 0.000000e+00 745.0
32 TraesCS4D01G340100 chr6B 88.170 541 64 0 2673 3213 454724176 454724716 0.000000e+00 645.0
33 TraesCS4D01G340100 chr4A 89.474 57 5 1 2366 2422 740627128 740627183 1.600000e-08 71.3
34 TraesCS4D01G340100 chr2B 80.000 90 9 8 2283 2364 7846916 7846828 1.250000e-04 58.4


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 TraesCS4D01G340100 chr4D 497494168 497497390 3222 True 5952.000000 5952 100.000000 1 3223 1 chr4D.!!$R4 3222
1 TraesCS4D01G340100 chr4D 497466666 497467849 1183 True 1742.000000 1742 93.333000 922 2104 1 chr4D.!!$R3 1182
2 TraesCS4D01G340100 chr4D 497561767 497562873 1106 True 1513.000000 1513 91.187000 769 1905 1 chr4D.!!$R6 1136
3 TraesCS4D01G340100 chr4D 497514059 497515198 1139 True 1081.000000 1081 84.674000 924 2040 1 chr4D.!!$R5 1116
4 TraesCS4D01G340100 chr4D 497445047 497445613 566 True 837.000000 837 93.486000 2117 2677 1 chr4D.!!$R2 560
5 TraesCS4D01G340100 chr4D 187245887 187246429 542 True 784.000000 784 92.661000 2679 3223 1 chr4D.!!$R1 544
6 TraesCS4D01G340100 chr4D 497450875 497452911 2036 True 230.666667 375 88.117000 924 1871 3 chr4D.!!$R7 947
7 TraesCS4D01G340100 chr4B 638422338 638424184 1846 True 1901.000000 1901 85.662000 98 1953 1 chr4B.!!$R1 1855
8 TraesCS4D01G340100 chr4B 643576244 643576781 537 False 673.000000 673 89.239000 2679 3216 1 chr4B.!!$F2 537
9 TraesCS4D01G340100 chr4B 638363107 638364806 1699 True 583.000000 743 88.865333 2117 2677 3 chr4B.!!$R2 560
10 TraesCS4D01G340100 chr4B 638369016 638369925 909 True 397.000000 673 82.683500 924 1871 2 chr4B.!!$R3 947
11 TraesCS4D01G340100 chr5A 184617772 184618317 545 True 824.000000 824 93.956000 2679 3223 1 chr5A.!!$R1 544
12 TraesCS4D01G340100 chr5A 677777621 677778521 900 True 798.000000 798 83.075000 924 1871 1 chr5A.!!$R3 947
13 TraesCS4D01G340100 chr5A 677757723 677758294 571 True 702.000000 702 89.180000 2117 2677 1 chr5A.!!$R2 560
14 TraesCS4D01G340100 chr5A 677673171 677674349 1178 True 650.000000 1122 87.882000 815 1953 2 chr5A.!!$R4 1138
15 TraesCS4D01G340100 chr5A 677681851 677683168 1317 True 555.500000 682 88.464500 2117 2677 2 chr5A.!!$R5 560
16 TraesCS4D01G340100 chr5A 677726377 677727285 908 True 350.000000 592 81.070000 924 1871 2 chr5A.!!$R6 947
17 TraesCS4D01G340100 chr6D 317516137 317516678 541 True 819.000000 819 93.911000 2682 3223 1 chr6D.!!$R2 541
18 TraesCS4D01G340100 chr6D 20464568 20465112 544 True 752.000000 752 91.575000 2679 3223 1 chr6D.!!$R1 544
19 TraesCS4D01G340100 chr7A 183619641 183620185 544 False 813.000000 813 93.578000 2679 3223 1 chr7A.!!$F1 544
20 TraesCS4D01G340100 chr7B 41189320 41189862 542 False 789.000000 789 92.844000 2679 3223 1 chr7B.!!$F1 544
21 TraesCS4D01G340100 chr5D 52957550 52958093 543 False 745.000000 745 91.392000 2679 3223 1 chr5D.!!$F1 544
22 TraesCS4D01G340100 chr6B 454724176 454724716 540 False 645.000000 645 88.170000 2673 3213 1 chr6B.!!$F1 540

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
745 751 0.037326 ACGAACGATCATGCAGTGGT 60.037 50.0 0.14 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2637 4689 0.396435 ACCATGACCATGTGACACGT 59.604 50.0 8.93 0.0 37.11 4.49 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
20 21 4.524318 GCAGGGCGCGGCTACTTA 62.524 66.667 32.30 0.00 0.00 2.24
21 22 2.185867 CAGGGCGCGGCTACTTAA 59.814 61.111 32.30 0.00 0.00 1.85
22 23 1.448893 CAGGGCGCGGCTACTTAAA 60.449 57.895 32.30 0.00 0.00 1.52
23 24 1.449070 AGGGCGCGGCTACTTAAAC 60.449 57.895 32.30 12.90 0.00 2.01
24 25 1.449070 GGGCGCGGCTACTTAAACT 60.449 57.895 32.30 0.00 0.00 2.66
25 26 1.702491 GGGCGCGGCTACTTAAACTG 61.702 60.000 32.30 0.00 0.00 3.16
26 27 1.702491 GGCGCGGCTACTTAAACTGG 61.702 60.000 27.05 0.00 0.00 4.00
27 28 1.017701 GCGCGGCTACTTAAACTGGT 61.018 55.000 8.83 0.00 0.00 4.00
28 29 0.719465 CGCGGCTACTTAAACTGGTG 59.281 55.000 0.00 0.00 0.00 4.17
29 30 1.804601 GCGGCTACTTAAACTGGTGT 58.195 50.000 0.00 0.00 0.00 4.16
30 31 2.148768 GCGGCTACTTAAACTGGTGTT 58.851 47.619 0.00 0.00 38.16 3.32
31 32 2.551032 GCGGCTACTTAAACTGGTGTTT 59.449 45.455 0.00 0.00 46.74 2.83
32 33 3.004002 GCGGCTACTTAAACTGGTGTTTT 59.996 43.478 0.00 0.00 43.13 2.43
33 34 4.498513 GCGGCTACTTAAACTGGTGTTTTT 60.499 41.667 0.00 0.00 43.13 1.94
54 55 4.722203 TTTTTGCATGTTTTATGTGCCG 57.278 36.364 0.00 0.00 38.06 5.69
55 56 2.360553 TTGCATGTTTTATGTGCCGG 57.639 45.000 0.00 0.00 38.06 6.13
56 57 1.252175 TGCATGTTTTATGTGCCGGT 58.748 45.000 1.90 0.00 38.06 5.28
57 58 1.067985 TGCATGTTTTATGTGCCGGTG 60.068 47.619 1.90 0.00 38.06 4.94
58 59 1.067915 GCATGTTTTATGTGCCGGTGT 60.068 47.619 1.90 0.00 32.88 4.16
59 60 2.609244 GCATGTTTTATGTGCCGGTGTT 60.609 45.455 1.90 0.00 32.88 3.32
60 61 3.648009 CATGTTTTATGTGCCGGTGTTT 58.352 40.909 1.90 0.00 0.00 2.83
61 62 4.799678 CATGTTTTATGTGCCGGTGTTTA 58.200 39.130 1.90 0.00 0.00 2.01
62 63 5.406649 CATGTTTTATGTGCCGGTGTTTAT 58.593 37.500 1.90 0.00 0.00 1.40
63 64 5.455056 TGTTTTATGTGCCGGTGTTTATT 57.545 34.783 1.90 0.00 0.00 1.40
64 65 6.570672 TGTTTTATGTGCCGGTGTTTATTA 57.429 33.333 1.90 0.00 0.00 0.98
65 66 6.613233 TGTTTTATGTGCCGGTGTTTATTAG 58.387 36.000 1.90 0.00 0.00 1.73
66 67 6.207025 TGTTTTATGTGCCGGTGTTTATTAGT 59.793 34.615 1.90 0.00 0.00 2.24
67 68 6.821031 TTTATGTGCCGGTGTTTATTAGTT 57.179 33.333 1.90 0.00 0.00 2.24
68 69 6.821031 TTATGTGCCGGTGTTTATTAGTTT 57.179 33.333 1.90 0.00 0.00 2.66
69 70 5.715434 ATGTGCCGGTGTTTATTAGTTTT 57.285 34.783 1.90 0.00 0.00 2.43
70 71 5.517322 TGTGCCGGTGTTTATTAGTTTTT 57.483 34.783 1.90 0.00 0.00 1.94
71 72 5.521544 TGTGCCGGTGTTTATTAGTTTTTC 58.478 37.500 1.90 0.00 0.00 2.29
72 73 5.299782 TGTGCCGGTGTTTATTAGTTTTTCT 59.700 36.000 1.90 0.00 0.00 2.52
73 74 6.183360 TGTGCCGGTGTTTATTAGTTTTTCTT 60.183 34.615 1.90 0.00 0.00 2.52
74 75 6.698329 GTGCCGGTGTTTATTAGTTTTTCTTT 59.302 34.615 1.90 0.00 0.00 2.52
75 76 7.223193 GTGCCGGTGTTTATTAGTTTTTCTTTT 59.777 33.333 1.90 0.00 0.00 2.27
76 77 7.435784 TGCCGGTGTTTATTAGTTTTTCTTTTC 59.564 33.333 1.90 0.00 0.00 2.29
77 78 7.435784 GCCGGTGTTTATTAGTTTTTCTTTTCA 59.564 33.333 1.90 0.00 0.00 2.69
78 79 9.471084 CCGGTGTTTATTAGTTTTTCTTTTCAT 57.529 29.630 0.00 0.00 0.00 2.57
109 110 6.989155 TTTCTGTACTAGTTTCCTTCAGGA 57.011 37.500 0.00 0.00 43.73 3.86
182 183 9.727627 TTCAATACATTTGTTTTCCATTTTTGC 57.272 25.926 0.00 0.00 0.00 3.68
189 190 4.583871 TGTTTTCCATTTTTGCACACCTT 58.416 34.783 0.00 0.00 0.00 3.50
282 283 8.014517 ACACAATTTTTCAAACACACATTGAAC 58.985 29.630 1.48 0.00 44.14 3.18
283 284 8.013947 CACAATTTTTCAAACACACATTGAACA 58.986 29.630 1.48 0.00 44.14 3.18
400 401 6.966435 AGTGTGAAGTTTTGTTTCAAATGG 57.034 33.333 0.00 0.00 36.41 3.16
433 434 8.635765 ATGTTTGAGTGGTGTGAAATATAGTT 57.364 30.769 0.00 0.00 0.00 2.24
462 463 9.590088 GATTTACGTGGTAGTTTCTTTAACTTG 57.410 33.333 0.00 0.00 44.73 3.16
478 479 8.640291 TCTTTAACTTGTTTTTAAGTTTGCACG 58.360 29.630 8.91 0.00 45.85 5.34
479 480 8.516811 TTTAACTTGTTTTTAAGTTTGCACGA 57.483 26.923 8.91 0.00 45.85 4.35
480 481 8.516811 TTAACTTGTTTTTAAGTTTGCACGAA 57.483 26.923 8.91 0.00 45.85 3.85
481 482 6.384178 ACTTGTTTTTAAGTTTGCACGAAC 57.616 33.333 0.00 0.00 37.62 3.95
482 483 5.921408 ACTTGTTTTTAAGTTTGCACGAACA 59.079 32.000 4.19 0.00 37.62 3.18
483 484 6.588373 ACTTGTTTTTAAGTTTGCACGAACAT 59.412 30.769 4.19 0.00 37.62 2.71
484 485 6.952935 TGTTTTTAAGTTTGCACGAACATT 57.047 29.167 4.19 0.00 31.94 2.71
485 486 7.352719 TGTTTTTAAGTTTGCACGAACATTT 57.647 28.000 4.19 0.00 31.94 2.32
581 582 4.202111 ACTTGCGGACAAAACTTTTATGCT 60.202 37.500 0.00 0.00 34.74 3.79
583 584 2.408368 GCGGACAAAACTTTTATGCTGC 59.592 45.455 0.00 0.00 0.00 5.25
593 594 6.689178 AACTTTTATGCTGCGTTAACATTG 57.311 33.333 6.39 0.00 0.00 2.82
595 596 6.212955 ACTTTTATGCTGCGTTAACATTGTT 58.787 32.000 7.30 7.30 0.00 2.83
596 597 6.362283 ACTTTTATGCTGCGTTAACATTGTTC 59.638 34.615 5.07 0.00 0.00 3.18
597 598 5.621197 TTATGCTGCGTTAACATTGTTCT 57.379 34.783 5.07 0.00 0.00 3.01
599 600 5.621197 ATGCTGCGTTAACATTGTTCTAA 57.379 34.783 5.07 0.00 0.00 2.10
600 601 5.621197 TGCTGCGTTAACATTGTTCTAAT 57.379 34.783 5.07 0.00 0.00 1.73
601 602 6.729391 TGCTGCGTTAACATTGTTCTAATA 57.271 33.333 5.07 0.00 0.00 0.98
602 603 6.539324 TGCTGCGTTAACATTGTTCTAATAC 58.461 36.000 5.07 0.00 0.00 1.89
603 604 6.370442 TGCTGCGTTAACATTGTTCTAATACT 59.630 34.615 5.07 0.00 0.00 2.12
604 605 7.546316 TGCTGCGTTAACATTGTTCTAATACTA 59.454 33.333 5.07 0.00 0.00 1.82
605 606 8.548721 GCTGCGTTAACATTGTTCTAATACTAT 58.451 33.333 5.07 0.00 0.00 2.12
727 733 8.483218 GCTAATGAAAAAGCAGAGAAGAAAAAC 58.517 33.333 0.00 0.00 38.63 2.43
742 748 3.498397 AGAAAAACGAACGATCATGCAGT 59.502 39.130 0.14 0.00 0.00 4.40
743 749 2.880822 AAACGAACGATCATGCAGTG 57.119 45.000 0.14 0.00 0.00 3.66
744 750 1.078709 AACGAACGATCATGCAGTGG 58.921 50.000 0.14 0.00 0.00 4.00
745 751 0.037326 ACGAACGATCATGCAGTGGT 60.037 50.000 0.14 0.00 0.00 4.16
746 752 0.371301 CGAACGATCATGCAGTGGTG 59.629 55.000 0.00 0.00 0.00 4.17
747 753 1.442769 GAACGATCATGCAGTGGTGT 58.557 50.000 0.00 0.00 0.00 4.16
748 754 1.129251 GAACGATCATGCAGTGGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
801 807 1.891933 TCCCCATGTATGCTTCTGGA 58.108 50.000 0.00 0.00 0.00 3.86
837 845 1.521681 GCTCGATTTGGCTAGCGGT 60.522 57.895 9.00 0.00 0.00 5.68
1321 1447 3.465403 CCTCCTCCCCTGCGACTG 61.465 72.222 0.00 0.00 0.00 3.51
1322 1448 4.154347 CTCCTCCCCTGCGACTGC 62.154 72.222 0.00 0.00 43.20 4.40
1396 1579 0.107993 ATCACCAGTCGGCATCACAG 60.108 55.000 0.00 0.00 34.57 3.66
1438 1621 0.107410 TGGTTGTCAGCCTTGTCGTT 60.107 50.000 7.30 0.00 0.00 3.85
1734 1935 2.299013 GTCCATGACGCCATCCACTATA 59.701 50.000 0.00 0.00 0.00 1.31
1798 3179 1.371337 ATGCACACGCGCTCATTCAT 61.371 50.000 5.73 0.00 42.97 2.57
1905 3370 9.504708 TTTCTAAATCCGTGACAGGTTAAATAA 57.495 29.630 0.00 0.00 0.00 1.40
2081 3549 6.904626 AGTATTAGTTTACGGAGGGAGTAGA 58.095 40.000 0.00 0.00 0.00 2.59
2082 3550 6.997476 AGTATTAGTTTACGGAGGGAGTAGAG 59.003 42.308 0.00 0.00 0.00 2.43
2084 3552 4.851639 AGTTTACGGAGGGAGTAGAGTA 57.148 45.455 0.00 0.00 0.00 2.59
2085 3553 5.184892 AGTTTACGGAGGGAGTAGAGTAA 57.815 43.478 0.00 0.00 0.00 2.24
2086 3554 4.946772 AGTTTACGGAGGGAGTAGAGTAAC 59.053 45.833 0.00 0.00 0.00 2.50
2205 3678 7.132128 ACTAAACACCAAATATCCATGGGAAT 58.868 34.615 13.02 0.91 41.17 3.01
2375 3849 2.329379 GCTCTTTGCTATCGTATCCCG 58.671 52.381 0.00 0.00 38.95 5.14
2559 4611 1.219522 CTCCACAACGGGAACACGAC 61.220 60.000 2.83 0.00 36.27 4.34
2561 4613 2.109593 ACAACGGGAACACGACCC 59.890 61.111 2.83 0.00 43.57 4.46
2637 4689 3.450817 TCTTGAAAGATACCGGCTGATCA 59.549 43.478 0.00 0.00 0.00 2.92
2644 4701 1.245376 TACCGGCTGATCACGTGTCA 61.245 55.000 16.51 16.43 0.00 3.58
2677 4734 4.443034 GGTGCCGTGAGAGTAGGATTTAAT 60.443 45.833 0.00 0.00 0.00 1.40
2686 4743 9.367444 GTGAGAGTAGGATTTAATCGAAAAAGA 57.633 33.333 0.00 0.00 0.00 2.52
2726 4783 1.681538 TAAAGCAAACCGCCACAGAA 58.318 45.000 0.00 0.00 44.04 3.02
2843 5132 0.325272 AAAAGAGAAGAGTCGGGGGC 59.675 55.000 0.00 0.00 0.00 5.80
2859 5148 0.324275 GGGCCCCAACAAGCATCTAA 60.324 55.000 12.23 0.00 0.00 2.10
2946 5235 1.522580 GAAGGCAGAGATGGCGTCC 60.523 63.158 2.37 0.00 37.01 4.79
3024 5313 1.452953 TAGCGTCAGTAGCCCATCGG 61.453 60.000 0.00 0.00 34.64 4.18
3149 5687 1.482593 CTGGAGTTCCGAATACAGGCT 59.517 52.381 0.00 0.00 39.43 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.524318 TAAGTAGCCGCGCCCTGC 62.524 66.667 0.00 1.75 41.47 4.85
4 5 1.448893 TTTAAGTAGCCGCGCCCTG 60.449 57.895 0.00 0.00 0.00 4.45
5 6 1.449070 GTTTAAGTAGCCGCGCCCT 60.449 57.895 0.00 0.87 0.00 5.19
6 7 1.449070 AGTTTAAGTAGCCGCGCCC 60.449 57.895 0.00 0.00 0.00 6.13
7 8 1.702491 CCAGTTTAAGTAGCCGCGCC 61.702 60.000 0.00 0.00 0.00 6.53
8 9 1.017701 ACCAGTTTAAGTAGCCGCGC 61.018 55.000 0.00 0.00 0.00 6.86
9 10 0.719465 CACCAGTTTAAGTAGCCGCG 59.281 55.000 0.00 0.00 0.00 6.46
10 11 1.804601 ACACCAGTTTAAGTAGCCGC 58.195 50.000 0.00 0.00 0.00 6.53
11 12 4.823790 AAAACACCAGTTTAAGTAGCCG 57.176 40.909 0.00 0.00 46.79 5.52
33 34 3.496130 CCGGCACATAAAACATGCAAAAA 59.504 39.130 0.00 0.00 41.27 1.94
34 35 3.062763 CCGGCACATAAAACATGCAAAA 58.937 40.909 0.00 0.00 41.27 2.44
35 36 2.036475 ACCGGCACATAAAACATGCAAA 59.964 40.909 0.00 0.00 41.27 3.68
36 37 1.615883 ACCGGCACATAAAACATGCAA 59.384 42.857 0.00 0.00 41.27 4.08
37 38 1.067985 CACCGGCACATAAAACATGCA 60.068 47.619 0.00 0.00 41.27 3.96
38 39 1.067915 ACACCGGCACATAAAACATGC 60.068 47.619 0.00 0.00 38.68 4.06
39 40 3.296322 AACACCGGCACATAAAACATG 57.704 42.857 0.00 0.00 0.00 3.21
40 41 5.652994 ATAAACACCGGCACATAAAACAT 57.347 34.783 0.00 0.00 0.00 2.71
41 42 5.455056 AATAAACACCGGCACATAAAACA 57.545 34.783 0.00 0.00 0.00 2.83
42 43 6.614160 ACTAATAAACACCGGCACATAAAAC 58.386 36.000 0.00 0.00 0.00 2.43
43 44 6.821031 ACTAATAAACACCGGCACATAAAA 57.179 33.333 0.00 0.00 0.00 1.52
44 45 6.821031 AACTAATAAACACCGGCACATAAA 57.179 33.333 0.00 0.00 0.00 1.40
45 46 6.821031 AAACTAATAAACACCGGCACATAA 57.179 33.333 0.00 0.00 0.00 1.90
46 47 6.821031 AAAACTAATAAACACCGGCACATA 57.179 33.333 0.00 0.00 0.00 2.29
47 48 5.715434 AAAACTAATAAACACCGGCACAT 57.285 34.783 0.00 0.00 0.00 3.21
48 49 5.299782 AGAAAAACTAATAAACACCGGCACA 59.700 36.000 0.00 0.00 0.00 4.57
49 50 5.765176 AGAAAAACTAATAAACACCGGCAC 58.235 37.500 0.00 0.00 0.00 5.01
50 51 6.394025 AAGAAAAACTAATAAACACCGGCA 57.606 33.333 0.00 0.00 0.00 5.69
51 52 7.435784 TGAAAAGAAAAACTAATAAACACCGGC 59.564 33.333 0.00 0.00 0.00 6.13
52 53 8.859517 TGAAAAGAAAAACTAATAAACACCGG 57.140 30.769 0.00 0.00 0.00 5.28
82 83 8.750298 CCTGAAGGAAACTAGTACAGAAATCTA 58.250 37.037 0.00 0.00 42.68 1.98
83 84 7.455008 TCCTGAAGGAAACTAGTACAGAAATCT 59.545 37.037 0.00 0.00 42.68 2.40
84 85 7.612677 TCCTGAAGGAAACTAGTACAGAAATC 58.387 38.462 0.00 0.00 42.68 2.17
85 86 7.554959 TCCTGAAGGAAACTAGTACAGAAAT 57.445 36.000 0.00 0.00 42.68 2.17
86 87 6.989155 TCCTGAAGGAAACTAGTACAGAAA 57.011 37.500 0.00 0.00 42.68 2.52
167 168 4.213564 AGGTGTGCAAAAATGGAAAACA 57.786 36.364 0.00 0.00 0.00 2.83
168 169 4.633565 TCAAGGTGTGCAAAAATGGAAAAC 59.366 37.500 0.00 0.00 0.00 2.43
172 173 3.703556 TCTTCAAGGTGTGCAAAAATGGA 59.296 39.130 0.00 0.00 0.00 3.41
174 175 6.607735 AAATCTTCAAGGTGTGCAAAAATG 57.392 33.333 0.00 0.00 0.00 2.32
175 176 7.121020 ACAAAAATCTTCAAGGTGTGCAAAAAT 59.879 29.630 0.00 0.00 0.00 1.82
177 178 5.936956 ACAAAAATCTTCAAGGTGTGCAAAA 59.063 32.000 0.00 0.00 0.00 2.44
181 182 7.865385 TGTATAACAAAAATCTTCAAGGTGTGC 59.135 33.333 0.00 0.00 0.00 4.57
182 183 9.180678 GTGTATAACAAAAATCTTCAAGGTGTG 57.819 33.333 0.00 0.00 0.00 3.82
373 374 9.662545 CATTTGAAACAAAACTTCACACTTTTT 57.337 25.926 0.00 0.00 32.61 1.94
377 378 5.351189 GCCATTTGAAACAAAACTTCACACT 59.649 36.000 0.00 0.00 32.61 3.55
378 379 5.121454 TGCCATTTGAAACAAAACTTCACAC 59.879 36.000 0.00 0.00 32.61 3.82
400 401 5.353956 TCACACCACTCAAACATATATGTGC 59.646 40.000 18.94 0.00 41.61 4.57
410 411 9.180678 CAAAACTATATTTCACACCACTCAAAC 57.819 33.333 0.00 0.00 0.00 2.93
433 434 9.934190 GTTAAAGAAACTACCACGTAAATCAAA 57.066 29.630 0.00 0.00 35.05 2.69
462 463 8.648422 AAAAATGTTCGTGCAAACTTAAAAAC 57.352 26.923 3.11 0.00 0.00 2.43
519 520 9.410556 GTTGATAGCATTAAAACAATGTTCACT 57.589 29.630 0.00 0.00 0.00 3.41
520 521 9.190858 TGTTGATAGCATTAAAACAATGTTCAC 57.809 29.630 0.00 0.00 0.00 3.18
549 550 5.355910 AGTTTTGTCCGCAAGTCTTTTAGAA 59.644 36.000 0.00 0.00 35.82 2.10
558 559 4.048504 GCATAAAAGTTTTGTCCGCAAGT 58.951 39.130 11.18 0.00 35.82 3.16
695 696 6.006449 TCTCTGCTTTTTCATTAGCTCCTTT 58.994 36.000 0.00 0.00 38.22 3.11
696 697 5.564550 TCTCTGCTTTTTCATTAGCTCCTT 58.435 37.500 0.00 0.00 38.22 3.36
698 699 5.645497 TCTTCTCTGCTTTTTCATTAGCTCC 59.355 40.000 0.00 0.00 38.22 4.70
699 700 6.734104 TCTTCTCTGCTTTTTCATTAGCTC 57.266 37.500 0.00 0.00 38.22 4.09
701 702 8.483218 GTTTTTCTTCTCTGCTTTTTCATTAGC 58.517 33.333 0.00 0.00 37.89 3.09
710 716 4.331717 TCGTTCGTTTTTCTTCTCTGCTTT 59.668 37.500 0.00 0.00 0.00 3.51
727 733 0.371301 CACCACTGCATGATCGTTCG 59.629 55.000 0.00 0.00 0.00 3.95
752 758 2.638330 AATACATGGGGTCCGTCGCG 62.638 60.000 0.00 0.00 0.00 5.87
754 760 0.462375 TCAATACATGGGGTCCGTCG 59.538 55.000 0.00 0.00 0.00 5.12
755 761 1.474498 GGTCAATACATGGGGTCCGTC 60.474 57.143 0.00 0.00 0.00 4.79
756 762 0.544697 GGTCAATACATGGGGTCCGT 59.455 55.000 0.00 0.00 0.00 4.69
757 763 0.531974 CGGTCAATACATGGGGTCCG 60.532 60.000 0.00 0.00 0.00 4.79
760 766 1.406341 CGTTCGGTCAATACATGGGGT 60.406 52.381 0.00 0.00 0.00 4.95
763 769 2.350498 GGAACGTTCGGTCAATACATGG 59.650 50.000 21.34 0.00 0.00 3.66
765 771 2.624636 GGGAACGTTCGGTCAATACAT 58.375 47.619 21.34 0.00 0.00 2.29
766 772 1.338011 GGGGAACGTTCGGTCAATACA 60.338 52.381 21.34 0.00 0.00 2.29
767 773 1.338011 TGGGGAACGTTCGGTCAATAC 60.338 52.381 21.34 5.38 0.00 1.89
837 845 1.871039 CATGATCATGCATGCTCGTGA 59.129 47.619 34.01 19.22 40.52 4.35
1059 1134 1.302511 GCCACCCGAAGAAGAAGCA 60.303 57.895 0.00 0.00 0.00 3.91
1248 1338 0.101759 GCATCGTCTACTACCGGCAA 59.898 55.000 0.00 0.00 0.00 4.52
1417 1600 0.813610 CGACAAGGCTGACAACCACA 60.814 55.000 0.00 0.00 0.00 4.17
1734 1935 1.344763 ACTTACGCTGGACTTCTTGCT 59.655 47.619 0.00 0.00 0.00 3.91
1798 3179 8.054152 TGAAATTACTCATTAATCAGCAAGCA 57.946 30.769 0.00 0.00 29.39 3.91
1905 3370 8.799367 GTGTTTTTGTAATATACAGAAGGGGTT 58.201 33.333 0.00 0.00 40.24 4.11
1919 3387 6.017770 TCTCCAAATCGTCGTGTTTTTGTAAT 60.018 34.615 0.00 0.00 0.00 1.89
1920 3388 5.293814 TCTCCAAATCGTCGTGTTTTTGTAA 59.706 36.000 0.00 0.00 0.00 2.41
1994 3462 6.262193 TGTTTTGTAGGCTAAAACTATGGC 57.738 37.500 20.45 1.24 44.34 4.40
1995 3463 8.281212 AGATGTTTTGTAGGCTAAAACTATGG 57.719 34.615 20.45 0.00 44.34 2.74
2138 3607 4.610333 GGAAATTTTCCTACTGACCCCAT 58.390 43.478 19.01 0.00 46.57 4.00
2183 3656 7.147567 GGTTATTCCCATGGATATTTGGTGTTT 60.148 37.037 15.22 0.00 0.00 2.83
2205 3678 4.780554 TGAAGGTCAGGACATACATGGTTA 59.219 41.667 0.00 0.00 0.00 2.85
2249 3722 4.023980 TGGGAATAATCTGAGTGACTCGT 58.976 43.478 8.23 0.00 32.35 4.18
2320 3794 2.224719 ACTGAAGCTCTGCAAAGGTGAT 60.225 45.455 0.00 0.00 0.00 3.06
2328 3802 5.362143 AGTCATATAAGACTGAAGCTCTGCA 59.638 40.000 9.75 0.00 46.58 4.41
2375 3849 5.852738 ATTGACTCATAATGTAGCATCGC 57.147 39.130 0.00 0.00 0.00 4.58
2429 3910 3.119101 AGACGCTCCTGTGTAATTCGATT 60.119 43.478 0.00 0.00 37.00 3.34
2430 3911 2.427453 AGACGCTCCTGTGTAATTCGAT 59.573 45.455 0.00 0.00 37.00 3.59
2488 4539 0.595053 CGATGGCGACGCTAGTTCAT 60.595 55.000 20.77 13.76 40.82 2.57
2559 4611 5.483685 TCATAGTAAATCGGGATTCTGGG 57.516 43.478 0.00 0.00 0.00 4.45
2561 4613 7.761704 CCACTATCATAGTAAATCGGGATTCTG 59.238 40.741 0.00 0.00 37.23 3.02
2637 4689 0.396435 ACCATGACCATGTGACACGT 59.604 50.000 8.93 0.00 37.11 4.49
2644 4701 1.675310 CACGGCACCATGACCATGT 60.675 57.895 8.93 0.00 37.11 3.21
2726 4783 5.738619 TGAACTAGTCCATGTATGTGTGT 57.261 39.130 0.00 0.00 0.00 3.72
2843 5132 1.949525 CCGATTAGATGCTTGTTGGGG 59.050 52.381 0.00 0.00 0.00 4.96
2879 5168 4.974438 TGTCTCCACCGCCCCCTT 62.974 66.667 0.00 0.00 0.00 3.95
2976 5265 1.534595 CTGTCTGGTTTCTTGCAGCTC 59.465 52.381 0.00 0.00 0.00 4.09
3024 5313 1.067250 GATCCAGCGTGCTCCTCTC 59.933 63.158 0.00 0.00 0.00 3.20
3149 5687 2.197324 GCCACACCAACTTCCCCA 59.803 61.111 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.