Multiple sequence alignment - TraesCS2B01G530000

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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 TraesCS2B01G530000 chr2B 100.000 4268 0 0 1 4268 724751064 724746797 0.000000e+00 7882.0
1 TraesCS2B01G530000 chr2B 88.221 798 71 9 3471 4268 776869024 776869798 0.000000e+00 931.0
2 TraesCS2B01G530000 chr2B 96.063 254 8 1 3471 3722 724742606 724742353 3.070000e-111 412.0
3 TraesCS2B01G530000 chr2A 94.062 1701 79 12 909 2595 729836565 729834873 0.000000e+00 2562.0
4 TraesCS2B01G530000 chr2A 93.037 876 48 8 2609 3475 729834888 729834017 0.000000e+00 1267.0
5 TraesCS2B01G530000 chr2A 96.047 506 19 1 1 506 13794418 13793914 0.000000e+00 822.0
6 TraesCS2B01G530000 chr2A 93.833 454 21 5 503 950 729837005 729836553 0.000000e+00 676.0
7 TraesCS2B01G530000 chr2D 89.301 1888 119 41 703 2574 596197133 596195313 0.000000e+00 2290.0
8 TraesCS2B01G530000 chr2D 92.138 725 32 9 2666 3381 596195261 596194553 0.000000e+00 1000.0
9 TraesCS2B01G530000 chr5B 94.534 805 20 8 3464 4268 611961940 611961160 0.000000e+00 1221.0
10 TraesCS2B01G530000 chr5B 91.980 798 41 10 3471 4268 532452322 532453096 0.000000e+00 1098.0
11 TraesCS2B01G530000 chr5B 96.850 508 15 1 1 508 410724315 410723809 0.000000e+00 848.0
12 TraesCS2B01G530000 chr5B 96.654 508 17 0 1 508 427282831 427282324 0.000000e+00 845.0
13 TraesCS2B01G530000 chr5B 96.471 510 17 1 1 510 375645263 375644755 0.000000e+00 841.0
14 TraesCS2B01G530000 chr5B 96.471 510 17 1 1 509 541681050 541680541 0.000000e+00 841.0
15 TraesCS2B01G530000 chr5B 96.260 508 18 1 1 508 553943060 553943566 0.000000e+00 832.0
16 TraesCS2B01G530000 chr5B 93.722 223 10 4 3471 3692 611956838 611956619 8.850000e-87 331.0
17 TraesCS2B01G530000 chr5B 88.889 225 18 6 3471 3693 532457271 532457490 1.960000e-68 270.0
18 TraesCS2B01G530000 chr1B 93.890 802 31 7 3467 4268 2525963 2526746 0.000000e+00 1194.0
19 TraesCS2B01G530000 chr1B 95.370 216 8 2 3471 3686 2536872 2537085 4.090000e-90 342.0
20 TraesCS2B01G530000 chr5A 92.184 806 43 10 3465 4268 560809515 560810302 0.000000e+00 1122.0
21 TraesCS2B01G530000 chr5A 95.882 510 21 0 1 510 526390543 526391052 0.000000e+00 826.0
22 TraesCS2B01G530000 chr7A 91.855 798 45 8 3471 4268 116192960 116193737 0.000000e+00 1096.0
23 TraesCS2B01G530000 chr7B 89.348 798 63 10 3471 4268 708382349 708383124 0.000000e+00 983.0
24 TraesCS2B01G530000 chr6B 87.282 802 66 18 3471 4268 715896703 715895934 0.000000e+00 883.0
25 TraesCS2B01G530000 chr6B 97.446 509 13 0 1 509 469775207 469774699 0.000000e+00 869.0
26 TraesCS2B01G530000 chr6B 94.170 223 9 4 3471 3692 35837005 35836786 1.900000e-88 337.0
27 TraesCS2B01G530000 chr4B 95.850 506 21 0 1 506 413112716 413113221 0.000000e+00 819.0
28 TraesCS2B01G530000 chr3B 86.005 786 61 23 3482 4266 758344403 758343666 0.000000e+00 797.0
29 TraesCS2B01G530000 chr3B 85.106 94 4 4 2285 2368 766325329 766325422 2.110000e-13 87.9
30 TraesCS2B01G530000 chr1D 86.957 92 2 4 2287 2368 376984773 376984864 1.260000e-15 95.3


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 TraesCS2B01G530000 chr2B 724746797 724751064 4267 True 7882.000000 7882 100.0000 1 4268 1 chr2B.!!$R2 4267
1 TraesCS2B01G530000 chr2B 776869024 776869798 774 False 931.000000 931 88.2210 3471 4268 1 chr2B.!!$F1 797
2 TraesCS2B01G530000 chr2A 729834017 729837005 2988 True 1501.666667 2562 93.6440 503 3475 3 chr2A.!!$R2 2972
3 TraesCS2B01G530000 chr2A 13793914 13794418 504 True 822.000000 822 96.0470 1 506 1 chr2A.!!$R1 505
4 TraesCS2B01G530000 chr2D 596194553 596197133 2580 True 1645.000000 2290 90.7195 703 3381 2 chr2D.!!$R1 2678
5 TraesCS2B01G530000 chr5B 611961160 611961940 780 True 1221.000000 1221 94.5340 3464 4268 1 chr5B.!!$R6 804
6 TraesCS2B01G530000 chr5B 532452322 532453096 774 False 1098.000000 1098 91.9800 3471 4268 1 chr5B.!!$F1 797
7 TraesCS2B01G530000 chr5B 410723809 410724315 506 True 848.000000 848 96.8500 1 508 1 chr5B.!!$R2 507
8 TraesCS2B01G530000 chr5B 427282324 427282831 507 True 845.000000 845 96.6540 1 508 1 chr5B.!!$R3 507
9 TraesCS2B01G530000 chr5B 375644755 375645263 508 True 841.000000 841 96.4710 1 510 1 chr5B.!!$R1 509
10 TraesCS2B01G530000 chr5B 541680541 541681050 509 True 841.000000 841 96.4710 1 509 1 chr5B.!!$R4 508
11 TraesCS2B01G530000 chr5B 553943060 553943566 506 False 832.000000 832 96.2600 1 508 1 chr5B.!!$F3 507
12 TraesCS2B01G530000 chr1B 2525963 2526746 783 False 1194.000000 1194 93.8900 3467 4268 1 chr1B.!!$F1 801
13 TraesCS2B01G530000 chr5A 560809515 560810302 787 False 1122.000000 1122 92.1840 3465 4268 1 chr5A.!!$F2 803
14 TraesCS2B01G530000 chr5A 526390543 526391052 509 False 826.000000 826 95.8820 1 510 1 chr5A.!!$F1 509
15 TraesCS2B01G530000 chr7A 116192960 116193737 777 False 1096.000000 1096 91.8550 3471 4268 1 chr7A.!!$F1 797
16 TraesCS2B01G530000 chr7B 708382349 708383124 775 False 983.000000 983 89.3480 3471 4268 1 chr7B.!!$F1 797
17 TraesCS2B01G530000 chr6B 715895934 715896703 769 True 883.000000 883 87.2820 3471 4268 1 chr6B.!!$R3 797
18 TraesCS2B01G530000 chr6B 469774699 469775207 508 True 869.000000 869 97.4460 1 509 1 chr6B.!!$R2 508
19 TraesCS2B01G530000 chr4B 413112716 413113221 505 False 819.000000 819 95.8500 1 506 1 chr4B.!!$F1 505
20 TraesCS2B01G530000 chr3B 758343666 758344403 737 True 797.000000 797 86.0050 3482 4266 1 chr3B.!!$R1 784

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
482 484 0.399376 TCTATTTAGGCGCCCTGGGA 60.399 55.0 26.15 11.55 34.61 4.37 F
1792 1851 0.109412 CGTACGAGAACGAGGCCTTT 60.109 55.0 10.44 0.00 45.68 3.11 F
2599 2665 0.036765 AATTAACCGCGCTCACCTCA 60.037 50.0 5.56 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 1991 0.386858 CGCGTTCTCGAACTCTGGAA 60.387 55.0 0.0 0.0 39.08 3.53 R
2882 2955 0.373024 CTCTCGTCGAACTCCCGTAC 59.627 60.0 0.0 0.0 0.00 3.67 R
3459 3545 0.518636 CGTTTCACACCCATCAGCAG 59.481 55.0 0.0 0.0 0.00 4.24 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
85 86 3.610791 CTGAACGAGCTGCCGACGA 62.611 63.158 15.53 0.69 0.00 4.20
150 151 3.917760 GCCTCTACATCGCCGCCT 61.918 66.667 0.00 0.00 0.00 5.52
348 349 1.335506 GGATTTGCGGCGTCTTTTGAA 60.336 47.619 9.37 0.00 0.00 2.69
482 484 0.399376 TCTATTTAGGCGCCCTGGGA 60.399 55.000 26.15 11.55 34.61 4.37
512 517 2.639839 GGCTGGAGATGCCCTAAGATAA 59.360 50.000 0.00 0.00 44.32 1.75
522 527 6.995091 AGATGCCCTAAGATAAATGAAGTGAC 59.005 38.462 0.00 0.00 0.00 3.67
525 530 6.116126 GCCCTAAGATAAATGAAGTGACTGT 58.884 40.000 0.00 0.00 0.00 3.55
526 531 6.599638 GCCCTAAGATAAATGAAGTGACTGTT 59.400 38.462 0.00 0.00 0.00 3.16
598 606 2.005451 CTGCTTCCTTCACTGAATCGG 58.995 52.381 0.00 0.00 0.00 4.18
611 619 7.857734 TCACTGAATCGGCTAATTCAAATTA 57.142 32.000 13.00 0.00 43.22 1.40
653 661 5.236478 CGTCCAGTAAAACTGTTGATCAACT 59.764 40.000 32.57 18.44 44.50 3.16
657 665 6.483307 CCAGTAAAACTGTTGATCAACTGAGA 59.517 38.462 37.21 20.06 44.50 3.27
690 698 8.041323 AGATTCCGTTTACTTGTCACTATTGAT 58.959 33.333 0.00 0.00 33.11 2.57
741 751 6.462207 GCCTCTAGAGAGCACTATCAATTCAA 60.462 42.308 21.76 0.00 40.75 2.69
815 826 1.977293 GACAGGGACCCATCTGCTCC 61.977 65.000 14.60 0.00 34.57 4.70
832 843 3.243367 TGCTCCGAAAACCACATGAAAAG 60.243 43.478 0.00 0.00 0.00 2.27
863 874 9.710900 AGAATAAACAATTCAAGATTTCCCAAC 57.289 29.630 1.01 0.00 45.58 3.77
1005 1053 2.318908 TCTTTGCCACAAGCCAGAAAT 58.681 42.857 0.00 0.00 42.71 2.17
1017 1065 5.993441 ACAAGCCAGAAATTTTCAATCCAAG 59.007 36.000 11.53 0.00 0.00 3.61
1037 1085 6.012858 TCCAAGGTTAACCACAGATAATCAGT 60.013 38.462 26.26 0.00 38.89 3.41
1060 1108 4.558226 ATCCTCAGCAGACATACAAACA 57.442 40.909 0.00 0.00 0.00 2.83
1062 1110 4.713553 TCCTCAGCAGACATACAAACAAA 58.286 39.130 0.00 0.00 0.00 2.83
1075 1123 9.185192 GACATACAAACAAAAGAAATCAGAAGG 57.815 33.333 0.00 0.00 0.00 3.46
1077 1125 5.976458 ACAAACAAAAGAAATCAGAAGGCA 58.024 33.333 0.00 0.00 0.00 4.75
1175 1225 2.016318 TGTAGCGCCCAAAGAATCATG 58.984 47.619 2.29 0.00 0.00 3.07
1176 1226 2.017049 GTAGCGCCCAAAGAATCATGT 58.983 47.619 2.29 0.00 0.00 3.21
1177 1227 2.418368 AGCGCCCAAAGAATCATGTA 57.582 45.000 2.29 0.00 0.00 2.29
1178 1228 2.017049 AGCGCCCAAAGAATCATGTAC 58.983 47.619 2.29 0.00 0.00 2.90
1179 1229 2.017049 GCGCCCAAAGAATCATGTACT 58.983 47.619 0.00 0.00 0.00 2.73
1205 1255 2.336809 CGACCCGCTCTCCATAGC 59.663 66.667 0.00 0.00 39.21 2.97
1207 1257 2.041922 ACCCGCTCTCCATAGCCA 60.042 61.111 0.00 0.00 39.43 4.75
1213 1263 1.165284 GCTCTCCATAGCCAGCAAGC 61.165 60.000 0.00 0.00 36.45 4.01
1215 1265 1.890979 CTCCATAGCCAGCAAGCCG 60.891 63.158 0.00 0.00 0.00 5.52
1351 1402 2.602267 TTCTCGCCCAAGGTCGGA 60.602 61.111 0.00 0.00 0.00 4.55
1429 1480 1.078848 CGCCCTCTTCCTCAACCTG 60.079 63.158 0.00 0.00 0.00 4.00
1445 1496 3.214253 TGCTCCTGCAGATCCTCG 58.786 61.111 17.39 0.00 45.31 4.63
1598 1657 2.158841 GCTGCAATGCAAACTGAAATGG 59.841 45.455 9.92 0.00 38.41 3.16
1604 1663 4.778534 ATGCAAACTGAAATGGACTCTG 57.221 40.909 0.00 0.00 0.00 3.35
1691 1750 3.758088 CTGACGGGGCTCATCGACG 62.758 68.421 0.00 0.00 0.00 5.12
1715 1774 0.980231 AGTGGATCTGGACAGGAGCC 60.980 60.000 0.00 0.05 39.45 4.70
1792 1851 0.109412 CGTACGAGAACGAGGCCTTT 60.109 55.000 10.44 0.00 45.68 3.11
1832 1891 1.078918 CGCTGGCAGATGGAGTTCA 60.079 57.895 20.86 0.00 0.00 3.18
1865 1924 2.699954 ACTGCTGGAACGGTAATCAAG 58.300 47.619 0.00 0.00 36.83 3.02
1878 1937 4.564769 CGGTAATCAAGAGAACTCTTCTGC 59.435 45.833 13.26 5.96 46.13 4.26
1883 1942 0.965439 AGAGAACTCTTCTGCGTGCT 59.035 50.000 0.00 0.00 40.87 4.40
1886 1945 1.066914 GAACTCTTCTGCGTGCTCAG 58.933 55.000 0.00 0.00 35.46 3.35
1888 1947 1.373873 CTCTTCTGCGTGCTCAGCA 60.374 57.895 0.00 0.00 42.99 4.41
1889 1948 0.740164 CTCTTCTGCGTGCTCAGCAT 60.740 55.000 0.54 0.00 44.26 3.79
1892 1951 1.078201 TTCTGCGTGCTCAGCATACG 61.078 55.000 0.54 3.44 44.26 3.06
1893 1952 1.807165 CTGCGTGCTCAGCATACGT 60.807 57.895 0.54 0.00 44.26 3.57
1894 1953 2.017458 CTGCGTGCTCAGCATACGTG 62.017 60.000 0.54 0.00 44.26 4.49
1895 1954 2.802667 GCGTGCTCAGCATACGTGG 61.803 63.158 0.54 0.00 41.91 4.94
1904 1969 1.933181 CAGCATACGTGGGTGTGTATG 59.067 52.381 0.00 7.76 46.77 2.39
1906 1971 2.761767 AGCATACGTGGGTGTGTATGTA 59.238 45.455 12.38 0.00 46.11 2.29
1908 1973 3.307782 GCATACGTGGGTGTGTATGTAAC 59.692 47.826 12.38 0.00 46.11 2.50
1909 1974 2.068837 ACGTGGGTGTGTATGTAACG 57.931 50.000 0.00 0.00 35.78 3.18
1926 1991 1.729484 CGTGATGCGTGTCGACTGT 60.729 57.895 17.92 0.00 35.54 3.55
1941 2006 2.031069 CGACTGTTCCAGAGTTCGAGAA 60.031 50.000 0.00 0.00 32.00 2.87
1977 2042 1.482955 CGTTCGTGTTCTGCGACAG 59.517 57.895 0.00 0.00 38.14 3.51
2332 2397 1.602771 GTACCACAGGGAGAAGGCC 59.397 63.158 0.00 0.00 38.05 5.19
2521 2586 2.023673 CATTTCCTGCATTTCGGGCTA 58.976 47.619 0.00 0.00 41.21 3.93
2546 2611 0.450983 CCACTTCGACGTCTCCTACC 59.549 60.000 14.70 0.00 0.00 3.18
2571 2637 4.290711 TCAAGGTGATCATTGAGCTTCA 57.709 40.909 7.51 0.00 39.03 3.02
2595 2661 0.717224 TCGAAATTAACCGCGCTCAC 59.283 50.000 5.56 0.00 0.00 3.51
2596 2662 0.247537 CGAAATTAACCGCGCTCACC 60.248 55.000 5.56 0.00 0.00 4.02
2597 2663 1.084289 GAAATTAACCGCGCTCACCT 58.916 50.000 5.56 0.00 0.00 4.00
2598 2664 1.062148 GAAATTAACCGCGCTCACCTC 59.938 52.381 5.56 0.00 0.00 3.85
2599 2665 0.036765 AATTAACCGCGCTCACCTCA 60.037 50.000 5.56 0.00 0.00 3.86
2600 2666 0.036765 ATTAACCGCGCTCACCTCAA 60.037 50.000 5.56 0.00 0.00 3.02
2601 2667 0.249953 TTAACCGCGCTCACCTCAAA 60.250 50.000 5.56 0.00 0.00 2.69
2602 2668 0.249953 TAACCGCGCTCACCTCAAAA 60.250 50.000 5.56 0.00 0.00 2.44
2603 2669 1.098712 AACCGCGCTCACCTCAAAAA 61.099 50.000 5.56 0.00 0.00 1.94
2642 2708 4.453819 GCTCATGCTCTTAGTTGAAGTTGT 59.546 41.667 0.00 0.00 36.45 3.32
2643 2709 5.049129 GCTCATGCTCTTAGTTGAAGTTGTT 60.049 40.000 0.00 0.00 36.45 2.83
2791 2864 5.360144 GCCAAGTCTTACTAGATACCTCACA 59.640 44.000 0.00 0.00 31.86 3.58
2848 2921 4.137849 TCACGTACACTCGTAAACTGAG 57.862 45.455 0.00 0.00 42.27 3.35
2858 2931 6.208994 ACACTCGTAAACTGAGGAGATAAACT 59.791 38.462 0.50 0.00 37.79 2.66
2872 2945 4.451900 AGATAAACTAAATGTGGCCGAGG 58.548 43.478 0.00 0.00 0.00 4.63
2875 2948 0.392998 ACTAAATGTGGCCGAGGCAG 60.393 55.000 16.65 5.21 44.11 4.85
2895 2968 1.746615 CGGAGGTACGGGAGTTCGA 60.747 63.158 0.00 0.00 43.33 3.71
3017 3098 1.071299 TGCTCGTGCAGGTGTTCAT 59.929 52.632 8.30 0.00 45.31 2.57
3155 3236 2.405522 TACTTCCGGGAAGGGTGGGT 62.406 60.000 33.73 18.87 43.25 4.51
3301 3382 0.921896 AGCCATGGCCTTGACTATGT 59.078 50.000 33.14 7.61 43.17 2.29
3319 3400 9.057089 TGACTATGTGATGTGATGTACTACTAG 57.943 37.037 0.00 0.00 0.00 2.57
3320 3401 8.982091 ACTATGTGATGTGATGTACTACTAGT 57.018 34.615 0.00 0.00 0.00 2.57
3459 3545 0.391130 TAGTTGTGTGATCCGCCTGC 60.391 55.000 0.00 0.00 0.00 4.85
3468 3554 3.769369 ATCCGCCTGCTGCTGATGG 62.769 63.158 8.20 9.02 41.69 3.51
3547 3634 3.525221 GGCAATGCCGTGGCTTAT 58.475 55.556 9.14 0.00 39.62 1.73
3580 3673 3.544440 CGAGAGAGAACGATCGTTACAGG 60.544 52.174 31.79 14.27 38.60 4.00
3581 3674 3.607741 AGAGAGAACGATCGTTACAGGA 58.392 45.455 31.79 0.00 38.60 3.86
3582 3675 4.008330 AGAGAGAACGATCGTTACAGGAA 58.992 43.478 31.79 0.00 38.60 3.36
3583 3676 4.458295 AGAGAGAACGATCGTTACAGGAAA 59.542 41.667 31.79 0.00 38.60 3.13
3584 3677 4.483311 AGAGAACGATCGTTACAGGAAAC 58.517 43.478 31.79 17.17 38.60 2.78
3607 3700 3.003394 TCGGTACAGGAGGATTACGAA 57.997 47.619 0.00 0.00 0.00 3.85
3618 3712 6.435904 CAGGAGGATTACGAAGGAGAGATAAT 59.564 42.308 0.00 0.00 0.00 1.28
3652 3746 8.380742 AGATAGAGAAGGGTACAAGATTTGAA 57.619 34.615 0.00 0.00 0.00 2.69
3653 3747 8.826765 AGATAGAGAAGGGTACAAGATTTGAAA 58.173 33.333 0.00 0.00 0.00 2.69
3654 3748 9.103861 GATAGAGAAGGGTACAAGATTTGAAAG 57.896 37.037 0.00 0.00 0.00 2.62
3655 3749 7.079451 AGAGAAGGGTACAAGATTTGAAAGA 57.921 36.000 0.00 0.00 0.00 2.52
3656 3750 7.694093 AGAGAAGGGTACAAGATTTGAAAGAT 58.306 34.615 0.00 0.00 0.00 2.40
3657 3751 8.826765 AGAGAAGGGTACAAGATTTGAAAGATA 58.173 33.333 0.00 0.00 0.00 1.98
3658 3752 9.620259 GAGAAGGGTACAAGATTTGAAAGATAT 57.380 33.333 0.00 0.00 0.00 1.63
3659 3753 9.620259 AGAAGGGTACAAGATTTGAAAGATATC 57.380 33.333 0.00 0.00 0.00 1.63
3660 3754 9.620259 GAAGGGTACAAGATTTGAAAGATATCT 57.380 33.333 0.00 0.00 0.00 1.98
3726 3821 6.838382 ACTAACCAACTATTTCAACACTCCT 58.162 36.000 0.00 0.00 0.00 3.69
3955 4051 0.543749 GGCTGAGAGGTAGGTTGCAT 59.456 55.000 0.00 0.00 0.00 3.96
4029 4125 7.673504 AGCTCATAGAGTAATGTCTGTATCCAT 59.326 37.037 0.00 0.00 31.39 3.41
4084 4180 7.041098 CCTTGTATTCAGCTTTTGTACTTGACT 60.041 37.037 0.00 0.00 0.00 3.41
4228 4324 5.724328 CAGTAACAAGCATAGAAGAGGACA 58.276 41.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
348 349 0.464916 AAACTTGGTCGTTCCCGCTT 60.465 50.000 0.00 0.00 34.77 4.68
526 531 1.458588 GGGGGTGCAGGTGGAAAAA 60.459 57.895 0.00 0.00 0.00 1.94
653 661 8.717821 CAAGTAAACGGAATCTAATGTTTCTCA 58.282 33.333 0.00 0.00 36.14 3.27
657 665 8.287503 GTGACAAGTAAACGGAATCTAATGTTT 58.712 33.333 0.00 0.00 38.10 2.83
690 698 7.027778 TCGACGATTGAGAAATAGAGATTGA 57.972 36.000 0.00 0.00 0.00 2.57
700 708 2.231478 AGAGGCTTCGACGATTGAGAAA 59.769 45.455 0.00 0.00 0.00 2.52
815 826 6.491394 TCTTACACTTTTCATGTGGTTTTCG 58.509 36.000 0.00 0.00 39.52 3.46
888 900 2.936919 ACATGCTTGTCACAAGAGGA 57.063 45.000 22.30 4.29 0.00 3.71
1005 1053 5.894393 TCTGTGGTTAACCTTGGATTGAAAA 59.106 36.000 24.78 0.00 36.82 2.29
1017 1065 8.211629 AGGATAACTGATTATCTGTGGTTAACC 58.788 37.037 18.27 18.27 44.29 2.85
1037 1085 6.048732 TGTTTGTATGTCTGCTGAGGATAA 57.951 37.500 0.00 0.00 0.00 1.75
1060 1108 3.638160 TGCTGTGCCTTCTGATTTCTTTT 59.362 39.130 0.00 0.00 0.00 2.27
1062 1110 2.867624 TGCTGTGCCTTCTGATTTCTT 58.132 42.857 0.00 0.00 0.00 2.52
1075 1123 0.318445 CTCACTGGCTTTTGCTGTGC 60.318 55.000 0.00 0.00 46.54 4.57
1077 1125 2.057137 TTCTCACTGGCTTTTGCTGT 57.943 45.000 0.00 0.00 46.54 4.40
1128 1176 4.944048 AGTTTAGTTGCAAAGGCGATTTT 58.056 34.783 0.00 0.00 45.35 1.82
1129 1177 4.584327 AGTTTAGTTGCAAAGGCGATTT 57.416 36.364 0.00 0.00 45.35 2.17
1148 1196 0.109723 TTTGGGCGCTACAGGAAAGT 59.890 50.000 7.64 0.00 0.00 2.66
1175 1225 2.098117 AGCGGGTCGTGTATGTTAGTAC 59.902 50.000 0.00 0.00 0.00 2.73
1176 1226 2.355756 GAGCGGGTCGTGTATGTTAGTA 59.644 50.000 0.00 0.00 0.00 1.82
1177 1227 1.133790 GAGCGGGTCGTGTATGTTAGT 59.866 52.381 0.00 0.00 0.00 2.24
1178 1228 1.404391 AGAGCGGGTCGTGTATGTTAG 59.596 52.381 0.96 0.00 0.00 2.34
1179 1229 1.402968 GAGAGCGGGTCGTGTATGTTA 59.597 52.381 0.96 0.00 0.00 2.41
1213 1263 0.311790 AATCAACTGTTGCTGCACGG 59.688 50.000 15.52 5.68 0.00 4.94
1215 1265 1.067516 ACCAATCAACTGTTGCTGCAC 59.932 47.619 15.52 0.00 0.00 4.57
1304 1355 3.692406 GAGGTCGAACGGGCTGGT 61.692 66.667 0.00 0.00 0.00 4.00
1429 1480 1.067250 GACGAGGATCTGCAGGAGC 59.933 63.158 15.13 3.28 42.57 4.70
1493 1544 2.430244 GACGAGGTTGAGCGCGAA 60.430 61.111 12.10 0.00 0.00 4.70
1559 1618 3.283684 CAAGACGGGCGCCAAACA 61.284 61.111 30.85 0.00 0.00 2.83
1598 1657 0.798776 CAATCAACCACGGCAGAGTC 59.201 55.000 0.00 0.00 0.00 3.36
1604 1663 1.288752 CCAACCAATCAACCACGGC 59.711 57.895 0.00 0.00 0.00 5.68
1691 1750 2.303549 CTGTCCAGATCCACTCGCCC 62.304 65.000 0.00 0.00 0.00 6.13
1699 1758 1.743321 CGAGGCTCCTGTCCAGATCC 61.743 65.000 9.32 0.00 0.00 3.36
1792 1851 2.486504 GTGACCACGTCGCGGATA 59.513 61.111 6.13 0.00 34.95 2.59
1832 1891 4.623932 TCCAGCAGTTGTAGAACTTGAT 57.376 40.909 1.81 0.00 40.68 2.57
1865 1924 1.336332 TGAGCACGCAGAAGAGTTCTC 60.336 52.381 0.00 0.00 38.06 2.87
1878 1937 2.167219 CCCACGTATGCTGAGCACG 61.167 63.158 10.33 13.01 43.04 5.34
1883 1942 1.258676 TACACACCCACGTATGCTGA 58.741 50.000 0.00 0.00 0.00 4.26
1886 1945 2.018542 ACATACACACCCACGTATGC 57.981 50.000 8.96 0.00 45.79 3.14
1888 1947 3.193267 ACGTTACATACACACCCACGTAT 59.807 43.478 0.00 0.00 37.61 3.06
1889 1948 2.556189 ACGTTACATACACACCCACGTA 59.444 45.455 0.00 0.00 37.61 3.57
1892 1951 3.029320 TCACGTTACATACACACCCAC 57.971 47.619 0.00 0.00 0.00 4.61
1893 1952 3.591023 CATCACGTTACATACACACCCA 58.409 45.455 0.00 0.00 0.00 4.51
1894 1953 2.350498 GCATCACGTTACATACACACCC 59.650 50.000 0.00 0.00 0.00 4.61
1895 1954 2.028763 CGCATCACGTTACATACACACC 59.971 50.000 0.00 0.00 36.87 4.16
1909 1974 0.435008 GAACAGTCGACACGCATCAC 59.565 55.000 19.50 0.00 0.00 3.06
1926 1991 0.386858 CGCGTTCTCGAACTCTGGAA 60.387 55.000 0.00 0.00 39.08 3.53
2321 2386 2.370445 CCATCACGGCCTTCTCCCT 61.370 63.158 0.00 0.00 0.00 4.20
2521 2586 1.215647 GACGTCGAAGTGGAGGCAT 59.784 57.895 9.23 0.00 0.00 4.40
2571 2637 1.392510 GCGCGGTTAATTTCGAGAAGT 59.607 47.619 8.83 0.00 0.00 3.01
2619 2685 4.453819 ACAACTTCAACTAAGAGCATGAGC 59.546 41.667 0.00 0.00 38.67 4.26
2620 2686 6.551385 AACAACTTCAACTAAGAGCATGAG 57.449 37.500 0.00 0.00 38.67 2.90
2621 2687 6.942532 AAACAACTTCAACTAAGAGCATGA 57.057 33.333 0.00 0.00 38.67 3.07
2622 2688 7.992180 AAAAACAACTTCAACTAAGAGCATG 57.008 32.000 0.00 0.00 38.67 4.06
2649 2715 1.202879 TGTTCACCGGGCAGAAATTCT 60.203 47.619 6.32 0.00 0.00 2.40
2662 2728 2.804931 GCGCGCCAATTGTTCACC 60.805 61.111 23.24 0.00 0.00 4.02
2663 2729 2.501607 TACGCGCGCCAATTGTTCAC 62.502 55.000 32.58 0.00 0.00 3.18
2745 2818 4.301628 CAGGTTTTGGCATGAGAAAAGAC 58.698 43.478 0.00 0.00 0.00 3.01
2791 2864 5.937540 TGTGACCTTACATCGTCAATGATTT 59.062 36.000 0.00 0.00 40.53 2.17
2828 2901 3.058708 TCCTCAGTTTACGAGTGTACGTG 60.059 47.826 0.00 0.00 46.02 4.49
2848 2921 4.448210 TCGGCCACATTTAGTTTATCTCC 58.552 43.478 2.24 0.00 0.00 3.71
2858 2931 1.748879 GCTGCCTCGGCCACATTTA 60.749 57.895 2.24 0.00 41.09 1.40
2875 2948 3.073101 AACTCCCGTACCTCCGGC 61.073 66.667 0.00 0.00 46.71 6.13
2882 2955 0.373024 CTCTCGTCGAACTCCCGTAC 59.627 60.000 0.00 0.00 0.00 3.67
2895 2968 1.745320 AACAGTTCGGTGGCTCTCGT 61.745 55.000 0.00 0.00 0.00 4.18
3017 3098 1.826921 GTCTCGCCCGGTATCTCCA 60.827 63.158 0.00 0.00 35.57 3.86
3301 3382 9.761504 GTAGTAGACTAGTAGTACATCACATCA 57.238 37.037 1.88 0.00 31.54 3.07
3319 3400 3.522553 ACACGTACGGGTAGTAGTAGAC 58.477 50.000 24.11 0.00 35.72 2.59
3320 3401 3.430374 GGACACGTACGGGTAGTAGTAGA 60.430 52.174 25.47 0.00 35.72 2.59
3459 3545 0.518636 CGTTTCACACCCATCAGCAG 59.481 55.000 0.00 0.00 0.00 4.24
3468 3554 4.671766 GCTTCCACAATATCGTTTCACACC 60.672 45.833 0.00 0.00 0.00 4.16
3547 3634 3.797796 CGTTCTCTCTCGATCTCGTCTTA 59.202 47.826 0.00 0.00 40.80 2.10
3580 3673 1.747355 TCCTCCTGTACCGATCGTTTC 59.253 52.381 15.09 0.00 0.00 2.78
3581 3674 1.843368 TCCTCCTGTACCGATCGTTT 58.157 50.000 15.09 2.86 0.00 3.60
3582 3675 2.068834 ATCCTCCTGTACCGATCGTT 57.931 50.000 15.09 1.36 0.00 3.85
3583 3676 2.068834 AATCCTCCTGTACCGATCGT 57.931 50.000 15.09 4.92 0.00 3.73
3584 3677 2.095869 CGTAATCCTCCTGTACCGATCG 60.096 54.545 8.51 8.51 0.00 3.69
3585 3678 3.144506 TCGTAATCCTCCTGTACCGATC 58.855 50.000 0.00 0.00 0.00 3.69
3618 3712 8.103660 TGTACCCTTCTCTATCTCTTCTTCTA 57.896 38.462 0.00 0.00 0.00 2.10
3658 3752 9.937458 AGGGATAGATATCTGTATAGGGATAGA 57.063 37.037 15.79 0.00 33.28 1.98
3726 3821 9.807921 AAAGTTTCATAAGGTTTAGATTGAGGA 57.192 29.630 0.00 0.00 0.00 3.71
3955 4051 7.777440 TGCAAGGTTATGGTGTGATAATATTGA 59.223 33.333 0.00 0.00 0.00 2.57
4029 4125 4.142403 GCAAATGCCACAGCTGAAGTAATA 60.142 41.667 23.35 0.00 40.80 0.98
4084 4180 5.835113 AGAAAGCAAGCAACTGTTTCTAA 57.165 34.783 4.93 0.00 36.05 2.10
4228 4324 2.173569 GACTTGGGCTCCAGATTACCAT 59.826 50.000 0.00 0.00 33.81 3.55


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

AutoCloner maintained by Alex Coulton.