Multiple sequence alignment - TraesCS7D01G047600

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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 TraesCS7D01G047600 chr7D 100.000 1980 0 0 1 1980 24502076 24500097 0.000000e+00 3657.0
1 TraesCS7D01G047600 chr7D 100.000 428 0 0 2233 2660 24499844 24499417 0.000000e+00 791.0
2 TraesCS7D01G047600 chr7D 82.713 833 92 23 988 1814 24424653 24423867 0.000000e+00 693.0
3 TraesCS7D01G047600 chr7D 80.105 573 78 20 1248 1814 24468944 24469486 6.900000e-106 394.0
4 TraesCS7D01G047600 chr7D 88.176 296 32 3 1423 1718 24430493 24430201 1.520000e-92 350.0
5 TraesCS7D01G047600 chr7D 89.850 266 25 2 989 1253 24439317 24439581 9.120000e-90 340.0
6 TraesCS7D01G047600 chr7D 77.875 574 99 12 1037 1593 127419036 127418474 5.490000e-87 331.0
7 TraesCS7D01G047600 chr7A 93.791 1514 67 10 426 1922 24960216 24958713 0.000000e+00 2250.0
8 TraesCS7D01G047600 chr7A 82.812 832 95 26 990 1814 24926087 24925297 0.000000e+00 701.0
9 TraesCS7D01G047600 chr7A 89.486 428 40 3 1 427 24960735 24960312 1.080000e-148 536.0
10 TraesCS7D01G047600 chr7A 89.504 343 21 8 2235 2567 24958649 24958312 1.140000e-113 420.0
11 TraesCS7D01G047600 chr7A 78.087 575 96 18 1037 1593 127910044 127910606 1.180000e-88 337.0
12 TraesCS7D01G047600 chr7A 95.918 98 4 0 2563 2660 24941567 24941470 2.740000e-35 159.0
13 TraesCS7D01G047600 chr7A 88.889 99 10 1 2563 2660 24989397 24989299 1.290000e-23 121.0
14 TraesCS7D01G047600 chr7A 96.774 31 1 0 2246 2276 24958523 24958493 5.000000e-03 52.8
15 TraesCS7D01G047600 chr4A 84.254 724 79 19 988 1704 707251184 707251879 0.000000e+00 673.0
16 TraesCS7D01G047600 chr7B 78.883 573 95 14 1037 1593 88974122 88974684 5.410000e-97 364.0
17 TraesCS7D01G047600 chr7B 83.626 171 28 0 1040 1210 89207080 89206910 7.620000e-36 161.0
18 TraesCS7D01G047600 chr2A 74.737 190 47 1 3 192 31761484 31761296 1.700000e-12 84.2
19 TraesCS7D01G047600 chr4D 100.000 28 0 0 1697 1724 65836455 65836482 5.000000e-03 52.8


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 TraesCS7D01G047600 chr7D 24499417 24502076 2659 True 2224.0 3657 100.00000 1 2660 2 chr7D.!!$R4 2659
1 TraesCS7D01G047600 chr7D 24423867 24424653 786 True 693.0 693 82.71300 988 1814 1 chr7D.!!$R1 826
2 TraesCS7D01G047600 chr7D 24468944 24469486 542 False 394.0 394 80.10500 1248 1814 1 chr7D.!!$F2 566
3 TraesCS7D01G047600 chr7D 127418474 127419036 562 True 331.0 331 77.87500 1037 1593 1 chr7D.!!$R3 556
4 TraesCS7D01G047600 chr7A 24958312 24960735 2423 True 814.7 2250 92.38875 1 2567 4 chr7A.!!$R4 2566
5 TraesCS7D01G047600 chr7A 24925297 24926087 790 True 701.0 701 82.81200 990 1814 1 chr7A.!!$R1 824
6 TraesCS7D01G047600 chr7A 127910044 127910606 562 False 337.0 337 78.08700 1037 1593 1 chr7A.!!$F1 556
7 TraesCS7D01G047600 chr4A 707251184 707251879 695 False 673.0 673 84.25400 988 1704 1 chr4A.!!$F1 716
8 TraesCS7D01G047600 chr7B 88974122 88974684 562 False 364.0 364 78.88300 1037 1593 1 chr7B.!!$F1 556

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
582 681 0.035152 TCGGAGACCTACGTGGCTTA 60.035 55.0 0.0 0.0 40.22 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1864 0.172803 GAGGCGTGTACCACACCTAG 59.827 60.0 4.04 0.0 45.48 3.02 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
27 28 7.872138 TGGATTATGTAGAAAATCTCCCTGTT 58.128 34.615 0.00 0.00 33.50 3.16
34 35 2.080286 AAATCTCCCTGTTCGTGTCG 57.920 50.000 0.00 0.00 0.00 4.35
52 53 1.770085 CGTAGTACGCCGACTCTCCC 61.770 65.000 10.19 0.00 33.65 4.30
53 54 0.745845 GTAGTACGCCGACTCTCCCA 60.746 60.000 0.00 0.00 0.00 4.37
54 55 0.182061 TAGTACGCCGACTCTCCCAT 59.818 55.000 0.00 0.00 0.00 4.00
75 76 2.309528 TTAGGCATACCAGCGAACAG 57.690 50.000 0.00 0.00 39.06 3.16
98 99 0.321919 GCAGACACCCATCAGCTTCA 60.322 55.000 0.00 0.00 0.00 3.02
104 105 0.994247 ACCCATCAGCTTCATGTCCA 59.006 50.000 0.00 0.00 0.00 4.02
141 142 1.297893 GCTGCGGCGATGAACATTC 60.298 57.895 12.98 0.00 0.00 2.67
151 152 4.154918 GGCGATGAACATTCTGAGAAAAGT 59.845 41.667 0.00 0.00 0.00 2.66
153 154 6.456181 GGCGATGAACATTCTGAGAAAAGTAG 60.456 42.308 0.00 0.00 0.00 2.57
156 157 6.791887 TGAACATTCTGAGAAAAGTAGCTG 57.208 37.500 0.00 0.00 0.00 4.24
157 158 5.180117 TGAACATTCTGAGAAAAGTAGCTGC 59.820 40.000 0.00 0.00 0.00 5.25
158 159 4.645535 ACATTCTGAGAAAAGTAGCTGCA 58.354 39.130 4.12 0.00 0.00 4.41
159 160 4.453819 ACATTCTGAGAAAAGTAGCTGCAC 59.546 41.667 4.12 0.00 0.00 4.57
160 161 3.045601 TCTGAGAAAAGTAGCTGCACC 57.954 47.619 4.12 0.00 0.00 5.01
161 162 1.728971 CTGAGAAAAGTAGCTGCACCG 59.271 52.381 4.12 0.00 0.00 4.94
171 172 2.625906 CTGCACCGTGTTGACGTG 59.374 61.111 0.00 0.00 44.54 4.49
184 185 0.460722 TGACGTGAACGGTGAAAGGA 59.539 50.000 7.86 0.00 44.95 3.36
192 193 0.110486 ACGGTGAAAGGAACATGCCT 59.890 50.000 0.00 0.00 40.93 4.75
205 206 2.616330 ATGCCTTGCGTCGGTTGTG 61.616 57.895 0.00 0.00 0.00 3.33
206 207 2.970324 GCCTTGCGTCGGTTGTGA 60.970 61.111 0.00 0.00 0.00 3.58
232 233 2.100631 CCTACCGAGTTGCTTGGCG 61.101 63.158 2.45 0.00 38.56 5.69
262 263 6.382570 AGAACTACAGATCCTTGTAATGCTCT 59.617 38.462 0.00 0.00 33.44 4.09
272 273 0.752743 GTAATGCTCTGGCCATGGCA 60.753 55.000 36.56 27.23 44.11 4.92
338 339 2.449518 TGACCAGGAAGCCCACCA 60.450 61.111 0.00 0.00 33.88 4.17
342 343 2.765969 CAGGAAGCCCACCACCAT 59.234 61.111 0.00 0.00 33.88 3.55
349 350 2.127232 GCCCACCACCATGTATGCC 61.127 63.158 0.00 0.00 0.00 4.40
353 354 0.323269 CACCACCATGTATGCCACCA 60.323 55.000 0.00 0.00 0.00 4.17
368 369 3.957586 CCAGCACACCCTCTGCCA 61.958 66.667 0.00 0.00 35.01 4.92
374 375 2.045536 CACCCTCTGCCAGCCTTC 60.046 66.667 0.00 0.00 0.00 3.46
377 378 1.268283 ACCCTCTGCCAGCCTTCTAC 61.268 60.000 0.00 0.00 0.00 2.59
384 385 1.977854 TGCCAGCCTTCTACTTCTTGA 59.022 47.619 0.00 0.00 0.00 3.02
391 392 6.536941 CCAGCCTTCTACTTCTTGAGTATTTC 59.463 42.308 0.00 0.00 40.01 2.17
429 528 2.031037 TTGACGCAACGATTTTGAGC 57.969 45.000 0.00 0.00 0.00 4.26
456 555 5.209659 GGAAGAAGAGAGTAGGGTATTGGA 58.790 45.833 0.00 0.00 0.00 3.53
466 565 0.396811 GGGTATTGGATGGAGACCGG 59.603 60.000 0.00 0.00 0.00 5.28
491 590 4.384318 GGGATGGAAGAAGAAAGTAGGGTC 60.384 50.000 0.00 0.00 0.00 4.46
501 600 0.109723 AAGTAGGGTCTTTTGCCGCA 59.890 50.000 0.00 0.00 0.00 5.69
502 601 0.109723 AGTAGGGTCTTTTGCCGCAA 59.890 50.000 0.38 0.38 0.00 4.85
518 617 1.617740 GCAAAAATAGTGCGACTGGC 58.382 50.000 0.00 0.00 43.96 4.85
528 627 1.069906 GTGCGACTGGCTACAAAAGTG 60.070 52.381 0.00 0.00 44.05 3.16
535 634 1.524008 GGCTACAAAAGTGCGGGCTT 61.524 55.000 0.00 0.00 0.00 4.35
582 681 0.035152 TCGGAGACCTACGTGGCTTA 60.035 55.000 0.00 0.00 40.22 3.09
589 688 2.102588 GACCTACGTGGCTTATGTCCAT 59.897 50.000 0.00 0.00 40.22 3.41
590 689 3.302161 ACCTACGTGGCTTATGTCCATA 58.698 45.455 0.00 0.00 40.22 2.74
601 700 5.063880 GCTTATGTCCATACTCCGGAAAAT 58.936 41.667 5.23 0.00 33.29 1.82
603 702 3.553828 TGTCCATACTCCGGAAAATCC 57.446 47.619 5.23 0.00 33.29 3.01
606 705 1.774856 CCATACTCCGGAAAATCCCCT 59.225 52.381 5.23 0.00 31.13 4.79
608 707 3.214328 CATACTCCGGAAAATCCCCTTG 58.786 50.000 5.23 0.00 31.13 3.61
614 715 1.275010 CGGAAAATCCCCTTGGTTTGG 59.725 52.381 0.00 0.00 31.13 3.28
617 718 3.495983 GGAAAATCCCCTTGGTTTGGTTG 60.496 47.826 0.00 0.00 0.00 3.77
667 768 2.892425 CCGCGGACAGATTGGAGC 60.892 66.667 24.07 0.00 0.00 4.70
677 778 2.035626 ATTGGAGCCGGTGTTGGG 59.964 61.111 1.90 0.00 0.00 4.12
716 825 2.955342 AGTAGGTACTCCCTCCGATC 57.045 55.000 0.00 0.00 44.81 3.69
727 836 3.515502 CTCCCTCCGATCCATAATAAGCA 59.484 47.826 0.00 0.00 0.00 3.91
792 901 0.606401 ACACTTGGCCGTTGGATCAG 60.606 55.000 0.00 0.00 0.00 2.90
800 909 1.808133 GCCGTTGGATCAGGATCTGTC 60.808 57.143 9.01 0.34 37.92 3.51
802 911 1.405463 CGTTGGATCAGGATCTGTCGA 59.595 52.381 9.01 0.00 37.92 4.20
868 977 6.331061 CCTAGTCGCTCCCATAAATACATAC 58.669 44.000 0.00 0.00 0.00 2.39
875 984 2.027929 CCCATAAATACATACCGCGGGA 60.028 50.000 31.76 24.91 32.60 5.14
937 1046 1.186030 GCCACGAACGTAGTACATCG 58.814 55.000 18.69 18.69 45.00 3.84
985 1097 5.920903 AGTTACTAGCAAGTACACCAAACA 58.079 37.500 0.00 0.00 37.94 2.83
1452 1573 2.125961 GGAGGACCTACCGATGCGT 61.126 63.158 0.00 0.00 44.74 5.24
1762 1910 3.207778 AGACTGTAGTAGGCTCGATGAC 58.792 50.000 0.00 0.00 42.87 3.06
1814 1963 5.641636 TGAGTATTTGCGCTGAATTAACTCA 59.358 36.000 23.55 23.55 0.00 3.41
1815 1964 6.316140 TGAGTATTTGCGCTGAATTAACTCAT 59.684 34.615 23.55 2.87 0.00 2.90
1816 1965 7.494298 TGAGTATTTGCGCTGAATTAACTCATA 59.506 33.333 23.55 12.52 0.00 2.15
1817 1966 8.383318 AGTATTTGCGCTGAATTAACTCATAT 57.617 30.769 9.73 0.00 0.00 1.78
1818 1967 8.285394 AGTATTTGCGCTGAATTAACTCATATG 58.715 33.333 9.73 0.00 0.00 1.78
1819 1968 6.676237 TTTGCGCTGAATTAACTCATATGA 57.324 33.333 9.73 5.07 0.00 2.15
1820 1969 6.676237 TTGCGCTGAATTAACTCATATGAA 57.324 33.333 9.73 0.00 0.00 2.57
1821 1970 6.866010 TGCGCTGAATTAACTCATATGAAT 57.134 33.333 9.73 0.00 0.00 2.57
1852 2001 3.312697 TCTGATTCTCTACCGTGTCGATG 59.687 47.826 0.00 0.00 0.00 3.84
1863 2012 1.714794 GTGTCGATGGAGTTGTGAGG 58.285 55.000 0.00 0.00 0.00 3.86
1968 2117 2.672714 GTTGATTTTTCAACCTCGCCC 58.327 47.619 7.46 0.00 42.88 6.13
1969 2118 1.253100 TGATTTTTCAACCTCGCCCC 58.747 50.000 0.00 0.00 0.00 5.80
1970 2119 1.203001 TGATTTTTCAACCTCGCCCCT 60.203 47.619 0.00 0.00 0.00 4.79
1973 2122 0.538746 TTTTCAACCTCGCCCCTTCC 60.539 55.000 0.00 0.00 0.00 3.46
1974 2123 2.420466 TTTCAACCTCGCCCCTTCCC 62.420 60.000 0.00 0.00 0.00 3.97
1975 2124 4.426313 CAACCTCGCCCCTTCCCC 62.426 72.222 0.00 0.00 0.00 4.81
1976 2125 4.995058 AACCTCGCCCCTTCCCCA 62.995 66.667 0.00 0.00 0.00 4.96
1979 2128 3.411517 CTCGCCCCTTCCCCACAT 61.412 66.667 0.00 0.00 0.00 3.21
2371 2520 9.482627 TTTGTCCGCAAAATATTTATTTTCAGT 57.517 25.926 0.01 0.00 42.26 3.41
2389 2538 6.554334 TTCAGTAATGAATAATTAGGGCGC 57.446 37.500 0.56 0.00 31.22 6.53
2390 2539 5.865085 TCAGTAATGAATAATTAGGGCGCT 58.135 37.500 7.64 8.86 31.22 5.92
2391 2540 6.999950 TCAGTAATGAATAATTAGGGCGCTA 58.000 36.000 7.64 6.37 31.22 4.26
2392 2541 7.620880 TCAGTAATGAATAATTAGGGCGCTAT 58.379 34.615 11.75 0.00 31.22 2.97
2567 2725 0.181587 TTCTGCCACCCGTCAGAAAA 59.818 50.000 2.57 0.00 43.79 2.29
2568 2726 0.181587 TCTGCCACCCGTCAGAAAAA 59.818 50.000 0.00 0.00 36.50 1.94
2569 2727 0.310854 CTGCCACCCGTCAGAAAAAC 59.689 55.000 0.00 0.00 32.26 2.43
2570 2728 0.394488 TGCCACCCGTCAGAAAAACA 60.394 50.000 0.00 0.00 0.00 2.83
2571 2729 0.030235 GCCACCCGTCAGAAAAACAC 59.970 55.000 0.00 0.00 0.00 3.32
2572 2730 1.675552 CCACCCGTCAGAAAAACACT 58.324 50.000 0.00 0.00 0.00 3.55
2573 2731 2.841215 CCACCCGTCAGAAAAACACTA 58.159 47.619 0.00 0.00 0.00 2.74
2574 2732 2.806244 CCACCCGTCAGAAAAACACTAG 59.194 50.000 0.00 0.00 0.00 2.57
2575 2733 3.463944 CACCCGTCAGAAAAACACTAGT 58.536 45.455 0.00 0.00 0.00 2.57
2576 2734 4.501915 CCACCCGTCAGAAAAACACTAGTA 60.502 45.833 0.00 0.00 0.00 1.82
2577 2735 5.235516 CACCCGTCAGAAAAACACTAGTAT 58.764 41.667 0.00 0.00 0.00 2.12
2578 2736 5.699458 CACCCGTCAGAAAAACACTAGTATT 59.301 40.000 0.00 0.00 0.00 1.89
2579 2737 6.869913 CACCCGTCAGAAAAACACTAGTATTA 59.130 38.462 0.00 0.00 0.00 0.98
2580 2738 7.548075 CACCCGTCAGAAAAACACTAGTATTAT 59.452 37.037 0.00 0.00 0.00 1.28
2581 2739 8.098912 ACCCGTCAGAAAAACACTAGTATTATT 58.901 33.333 0.00 0.00 0.00 1.40
2582 2740 8.388103 CCCGTCAGAAAAACACTAGTATTATTG 58.612 37.037 0.00 0.00 0.00 1.90
2583 2741 9.146984 CCGTCAGAAAAACACTAGTATTATTGA 57.853 33.333 0.00 0.00 0.00 2.57
2594 2752 9.757227 ACACTAGTATTATTGAGAAGATTGCTC 57.243 33.333 0.00 0.00 0.00 4.26
2595 2753 9.755804 CACTAGTATTATTGAGAAGATTGCTCA 57.244 33.333 0.00 0.00 40.41 4.26
2604 2762 7.926674 TTGAGAAGATTGCTCAATACAATGA 57.073 32.000 0.00 0.00 44.81 2.57
2605 2763 7.982224 TTGAGAAGATTGCTCAATACAATGAG 58.018 34.615 0.00 0.02 44.81 2.90
2619 2777 9.836864 TCAATACAATGAGACATAACAAGCTAT 57.163 29.630 0.00 0.00 0.00 2.97
2636 2794 9.938280 AACAAGCTATTTAATAGTACACACTGA 57.062 29.630 12.82 0.00 36.14 3.41
2637 2795 9.367444 ACAAGCTATTTAATAGTACACACTGAC 57.633 33.333 12.82 0.00 36.14 3.51
2638 2796 9.587772 CAAGCTATTTAATAGTACACACTGACT 57.412 33.333 12.82 0.00 36.14 3.41
2651 2809 9.731819 AGTACACACTGACTAATATTTGTATCG 57.268 33.333 2.41 0.00 32.25 2.92
2652 2810 9.726232 GTACACACTGACTAATATTTGTATCGA 57.274 33.333 2.41 0.00 0.00 3.59
2653 2811 8.630278 ACACACTGACTAATATTTGTATCGAC 57.370 34.615 2.41 0.00 0.00 4.20
2654 2812 7.705325 ACACACTGACTAATATTTGTATCGACC 59.295 37.037 2.41 0.00 0.00 4.79
2655 2813 7.704899 CACACTGACTAATATTTGTATCGACCA 59.295 37.037 2.41 0.00 0.00 4.02
2656 2814 8.255206 ACACTGACTAATATTTGTATCGACCAA 58.745 33.333 2.41 0.00 0.00 3.67
2657 2815 8.540492 CACTGACTAATATTTGTATCGACCAAC 58.460 37.037 2.41 0.00 0.00 3.77
2658 2816 8.255206 ACTGACTAATATTTGTATCGACCAACA 58.745 33.333 2.41 0.00 0.00 3.33
2659 2817 9.093970 CTGACTAATATTTGTATCGACCAACAA 57.906 33.333 2.41 5.88 33.92 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.879765 ACTACGACACGAACAGGGAG 59.120 55.000 0.00 0.00 0.00 4.30
23 24 1.245224 GCGTACTACGACACGAACAG 58.755 55.000 12.87 0.00 46.05 3.16
34 35 0.745845 TGGGAGAGTCGGCGTACTAC 60.746 60.000 6.85 5.62 0.00 2.73
52 53 3.376859 TGTTCGCTGGTATGCCTAAAATG 59.623 43.478 0.16 0.00 35.27 2.32
53 54 3.616219 TGTTCGCTGGTATGCCTAAAAT 58.384 40.909 0.16 0.00 35.27 1.82
54 55 3.006940 CTGTTCGCTGGTATGCCTAAAA 58.993 45.455 0.16 0.00 35.27 1.52
75 76 1.812922 CTGATGGGTGTCTGCTCGC 60.813 63.158 0.00 0.00 0.00 5.03
78 79 3.817508 AGCTGATGGGTGTCTGCT 58.182 55.556 2.96 2.96 45.07 4.24
83 84 1.340405 GGACATGAAGCTGATGGGTGT 60.340 52.381 0.00 0.21 0.00 4.16
98 99 1.005394 GGACACGGACGTTGGACAT 60.005 57.895 0.00 0.00 0.00 3.06
141 142 1.728971 CGGTGCAGCTACTTTTCTCAG 59.271 52.381 14.92 0.00 0.00 3.35
151 152 1.663388 CGTCAACACGGTGCAGCTA 60.663 57.895 14.92 0.00 42.73 3.32
161 162 1.000884 TTCACCGTTCACGTCAACAC 58.999 50.000 2.50 0.00 37.74 3.32
171 172 1.068541 GGCATGTTCCTTTCACCGTTC 60.069 52.381 0.00 0.00 0.00 3.95
192 193 1.069935 TCCATCACAACCGACGCAA 59.930 52.632 0.00 0.00 0.00 4.85
193 194 1.666553 GTCCATCACAACCGACGCA 60.667 57.895 0.00 0.00 0.00 5.24
205 206 0.824759 AACTCGGTAGGCAGTCCATC 59.175 55.000 0.00 0.00 33.74 3.51
206 207 0.537188 CAACTCGGTAGGCAGTCCAT 59.463 55.000 0.00 0.00 33.74 3.41
232 233 5.662674 ACAAGGATCTGTAGTTCTACACC 57.337 43.478 8.38 8.69 0.00 4.16
262 263 2.034532 CAGACACTGCCATGGCCA 59.965 61.111 33.44 19.88 41.09 5.36
272 273 4.664677 GCCGACGGTGCAGACACT 62.665 66.667 16.73 0.00 46.57 3.55
277 278 0.027979 CATATTTGCCGACGGTGCAG 59.972 55.000 16.73 0.00 40.35 4.41
283 284 2.551912 GGCCCCATATTTGCCGACG 61.552 63.158 0.00 0.00 35.08 5.12
315 316 2.432628 GCTTCCTGGTCACGGACG 60.433 66.667 0.00 0.00 32.65 4.79
338 339 4.664062 GCTGGTGGCATACATGGT 57.336 55.556 0.00 0.00 41.35 3.55
349 350 2.670934 GCAGAGGGTGTGCTGGTG 60.671 66.667 0.00 0.00 37.96 4.17
353 354 4.341783 GCTGGCAGAGGGTGTGCT 62.342 66.667 20.86 0.00 40.97 4.40
357 358 1.267574 TAGAAGGCTGGCAGAGGGTG 61.268 60.000 20.86 0.00 0.00 4.61
358 359 1.081092 TAGAAGGCTGGCAGAGGGT 59.919 57.895 20.86 0.00 0.00 4.34
368 369 6.628398 CGGAAATACTCAAGAAGTAGAAGGCT 60.628 42.308 0.00 0.00 43.64 4.58
374 375 5.012328 AGGCGGAAATACTCAAGAAGTAG 57.988 43.478 0.00 0.00 43.64 2.57
377 378 4.455877 ACAAAGGCGGAAATACTCAAGAAG 59.544 41.667 0.00 0.00 0.00 2.85
406 407 3.358775 TCAAAATCGTTGCGTCAAAGTG 58.641 40.909 5.72 0.00 0.00 3.16
407 408 3.617669 CTCAAAATCGTTGCGTCAAAGT 58.382 40.909 5.72 0.00 0.00 2.66
412 414 0.162933 TCGCTCAAAATCGTTGCGTC 59.837 50.000 0.00 0.00 45.69 5.19
429 528 2.303175 CCCTACTCTCTTCTTCCCTCG 58.697 57.143 0.00 0.00 0.00 4.63
456 555 1.460305 CCATCCCTCCGGTCTCCAT 60.460 63.158 0.00 0.00 0.00 3.41
466 565 4.141597 CCCTACTTTCTTCTTCCATCCCTC 60.142 50.000 0.00 0.00 0.00 4.30
491 590 3.438373 GCACTATTTTTGCGGCAAAAG 57.562 42.857 31.92 25.34 42.91 2.27
501 600 3.670625 TGTAGCCAGTCGCACTATTTTT 58.329 40.909 0.00 0.00 41.38 1.94
502 601 3.328382 TGTAGCCAGTCGCACTATTTT 57.672 42.857 0.00 0.00 41.38 1.82
513 612 0.889186 CCCGCACTTTTGTAGCCAGT 60.889 55.000 0.00 0.00 0.00 4.00
515 614 2.265182 GCCCGCACTTTTGTAGCCA 61.265 57.895 0.00 0.00 0.00 4.75
516 615 1.524008 AAGCCCGCACTTTTGTAGCC 61.524 55.000 0.00 0.00 0.00 3.93
518 617 0.165944 CGAAGCCCGCACTTTTGTAG 59.834 55.000 0.00 0.00 0.00 2.74
535 634 1.508808 GCCCACCAAAACTAACGCGA 61.509 55.000 15.93 0.00 0.00 5.87
539 638 1.275010 CCCATGCCCACCAAAACTAAC 59.725 52.381 0.00 0.00 0.00 2.34
543 642 1.841103 ACCCCATGCCCACCAAAAC 60.841 57.895 0.00 0.00 0.00 2.43
565 664 1.755380 ACATAAGCCACGTAGGTCTCC 59.245 52.381 0.00 0.00 40.61 3.71
582 681 3.181443 GGGATTTTCCGGAGTATGGACAT 60.181 47.826 3.34 0.00 37.43 3.06
589 688 1.562475 CCAAGGGGATTTTCCGGAGTA 59.438 52.381 3.34 0.00 37.43 2.59
590 689 0.331616 CCAAGGGGATTTTCCGGAGT 59.668 55.000 3.34 0.00 37.43 3.85
601 700 1.234529 CCCAACCAAACCAAGGGGA 59.765 57.895 0.00 0.00 37.80 4.81
603 702 1.053835 AAGCCCAACCAAACCAAGGG 61.054 55.000 0.00 0.00 42.55 3.95
606 705 0.107459 GCAAAGCCCAACCAAACCAA 60.107 50.000 0.00 0.00 0.00 3.67
608 707 0.532640 CAGCAAAGCCCAACCAAACC 60.533 55.000 0.00 0.00 0.00 3.27
614 715 3.627123 ACAATTTTTCAGCAAAGCCCAAC 59.373 39.130 0.00 0.00 0.00 3.77
617 718 2.549329 CCACAATTTTTCAGCAAAGCCC 59.451 45.455 0.00 0.00 0.00 5.19
651 752 2.892425 GGCTCCAATCTGTCCGCG 60.892 66.667 0.00 0.00 0.00 6.46
653 754 2.202932 CCGGCTCCAATCTGTCCG 60.203 66.667 0.00 0.00 39.79 4.79
658 759 1.002134 CCAACACCGGCTCCAATCT 60.002 57.895 0.00 0.00 0.00 2.40
667 768 2.608368 TACCTCCCCCAACACCGG 60.608 66.667 0.00 0.00 0.00 5.28
755 864 6.238897 CCAAGTGTGGCAGTTTTAAACTATGA 60.239 38.462 10.21 0.00 37.86 2.15
757 866 6.084326 CCAAGTGTGGCAGTTTTAAACTAT 57.916 37.500 10.21 0.00 37.86 2.12
772 881 0.888736 TGATCCAACGGCCAAGTGTG 60.889 55.000 2.24 0.00 0.00 3.82
792 901 1.035923 TGCTCTCCATCGACAGATCC 58.964 55.000 0.00 0.00 34.23 3.36
800 909 0.392193 AGCCACTTTGCTCTCCATCG 60.392 55.000 0.00 0.00 36.75 3.84
802 911 0.694771 TCAGCCACTTTGCTCTCCAT 59.305 50.000 0.00 0.00 40.32 3.41
868 977 3.708220 GAGAGAAGCACTCCCGCGG 62.708 68.421 21.04 21.04 45.96 6.46
875 984 3.678252 CGTGAATGATGGAGAGAAGCACT 60.678 47.826 0.00 0.00 0.00 4.40
937 1046 4.296690 AGCCAACGATCGTTATAACTAGC 58.703 43.478 31.27 22.38 36.46 3.42
985 1097 2.165234 CGGCCATCTGATCTCGATGTAT 59.835 50.000 18.12 0.00 37.22 2.29
1216 1328 0.104304 ACGAACTTGAGCGACACCTT 59.896 50.000 0.00 0.00 0.00 3.50
1718 1862 1.590147 GCGTGTACCACACCTAGCT 59.410 57.895 3.97 0.00 45.93 3.32
1719 1863 1.447314 GGCGTGTACCACACCTAGC 60.447 63.158 3.97 2.25 45.93 3.42
1720 1864 0.172803 GAGGCGTGTACCACACCTAG 59.827 60.000 4.04 0.00 45.48 3.02
1734 1882 1.874872 GCCTACTACAGTCTAGAGGCG 59.125 57.143 5.39 0.00 40.07 5.52
1762 1910 2.126888 GCATCAAACGTGCACGGG 60.127 61.111 39.21 27.97 44.95 5.28
1818 1967 9.413048 CGGTAGAGAATCAGAAAAGGTATATTC 57.587 37.037 0.00 0.00 37.82 1.75
1819 1968 8.925338 ACGGTAGAGAATCAGAAAAGGTATATT 58.075 33.333 0.00 0.00 37.82 1.28
1820 1969 8.361139 CACGGTAGAGAATCAGAAAAGGTATAT 58.639 37.037 0.00 0.00 37.82 0.86
1821 1970 7.341256 ACACGGTAGAGAATCAGAAAAGGTATA 59.659 37.037 0.00 0.00 37.82 1.47
1951 2100 1.545841 AGGGGCGAGGTTGAAAAATC 58.454 50.000 0.00 0.00 0.00 2.17
1956 2105 2.754375 GGAAGGGGCGAGGTTGAA 59.246 61.111 0.00 0.00 0.00 2.69
1957 2106 3.327404 GGGAAGGGGCGAGGTTGA 61.327 66.667 0.00 0.00 0.00 3.18
1958 2107 4.426313 GGGGAAGGGGCGAGGTTG 62.426 72.222 0.00 0.00 0.00 3.77
1959 2108 4.995058 TGGGGAAGGGGCGAGGTT 62.995 66.667 0.00 0.00 0.00 3.50
1962 2111 3.411517 ATGTGGGGAAGGGGCGAG 61.412 66.667 0.00 0.00 0.00 5.03
2232 2381 5.465056 CGTTGGATTAAACCTTGTTGCAATT 59.535 36.000 0.59 0.00 0.00 2.32
2233 2382 4.987912 CGTTGGATTAAACCTTGTTGCAAT 59.012 37.500 0.59 0.00 0.00 3.56
2327 2476 7.382218 GCGGACAAAATATGAATTTTAGGATGG 59.618 37.037 0.00 0.00 42.18 3.51
2364 2513 7.284489 AGCGCCCTAATTATTCATTACTGAAAA 59.716 33.333 2.29 0.00 44.29 2.29
2366 2515 6.296026 AGCGCCCTAATTATTCATTACTGAA 58.704 36.000 2.29 0.00 45.15 3.02
2367 2516 5.865085 AGCGCCCTAATTATTCATTACTGA 58.135 37.500 2.29 0.00 0.00 3.41
2368 2517 7.549134 TCATAGCGCCCTAATTATTCATTACTG 59.451 37.037 2.29 0.00 0.00 2.74
2370 2519 7.549488 ACTCATAGCGCCCTAATTATTCATTAC 59.451 37.037 2.29 0.00 0.00 1.89
2371 2520 7.620880 ACTCATAGCGCCCTAATTATTCATTA 58.379 34.615 2.29 0.00 0.00 1.90
2372 2521 6.476378 ACTCATAGCGCCCTAATTATTCATT 58.524 36.000 2.29 0.00 0.00 2.57
2373 2522 6.054860 ACTCATAGCGCCCTAATTATTCAT 57.945 37.500 2.29 0.00 0.00 2.57
2375 2524 6.803154 AAACTCATAGCGCCCTAATTATTC 57.197 37.500 2.29 0.00 0.00 1.75
2376 2525 7.068226 ACAAAAACTCATAGCGCCCTAATTATT 59.932 33.333 2.29 0.00 0.00 1.40
2377 2526 6.546034 ACAAAAACTCATAGCGCCCTAATTAT 59.454 34.615 2.29 0.00 0.00 1.28
2378 2527 5.883673 ACAAAAACTCATAGCGCCCTAATTA 59.116 36.000 2.29 0.00 0.00 1.40
2379 2528 4.705023 ACAAAAACTCATAGCGCCCTAATT 59.295 37.500 2.29 0.00 0.00 1.40
2381 2530 3.681593 ACAAAAACTCATAGCGCCCTAA 58.318 40.909 2.29 0.00 0.00 2.69
2385 2534 3.121025 GCAAAACAAAAACTCATAGCGCC 60.121 43.478 2.29 0.00 0.00 6.53
2386 2535 3.489047 TGCAAAACAAAAACTCATAGCGC 59.511 39.130 0.00 0.00 0.00 5.92
2387 2536 5.005203 TGTTGCAAAACAAAAACTCATAGCG 59.995 36.000 0.00 0.00 40.82 4.26
2388 2537 6.343226 TGTTGCAAAACAAAAACTCATAGC 57.657 33.333 0.00 0.00 40.82 2.97
2389 2538 9.848172 GTATTGTTGCAAAACAAAAACTCATAG 57.152 29.630 7.98 0.00 44.70 2.23
2390 2539 8.821894 GGTATTGTTGCAAAACAAAAACTCATA 58.178 29.630 7.98 0.00 44.70 2.15
2391 2540 7.335422 TGGTATTGTTGCAAAACAAAAACTCAT 59.665 29.630 7.98 0.00 44.70 2.90
2392 2541 6.650807 TGGTATTGTTGCAAAACAAAAACTCA 59.349 30.769 7.98 7.30 44.70 3.41
2543 2701 2.009774 CTGACGGGTGGCAGAATTAAG 58.990 52.381 0.00 0.00 34.06 1.85
2568 2726 9.757227 GAGCAATCTTCTCAATAATACTAGTGT 57.243 33.333 5.39 0.00 0.00 3.55
2569 2727 9.755804 TGAGCAATCTTCTCAATAATACTAGTG 57.244 33.333 5.39 0.00 37.61 2.74
2581 2739 7.279536 GTCTCATTGTATTGAGCAATCTTCTCA 59.720 37.037 0.00 0.00 42.37 3.27
2582 2740 7.279536 TGTCTCATTGTATTGAGCAATCTTCTC 59.720 37.037 0.00 0.00 42.37 2.87
2583 2741 7.108194 TGTCTCATTGTATTGAGCAATCTTCT 58.892 34.615 0.00 0.00 42.37 2.85
2584 2742 7.312657 TGTCTCATTGTATTGAGCAATCTTC 57.687 36.000 0.00 0.00 42.37 2.87
2585 2743 7.876936 ATGTCTCATTGTATTGAGCAATCTT 57.123 32.000 0.00 0.00 42.37 2.40
2586 2744 8.834465 GTTATGTCTCATTGTATTGAGCAATCT 58.166 33.333 0.00 0.00 42.37 2.40
2587 2745 8.615211 TGTTATGTCTCATTGTATTGAGCAATC 58.385 33.333 0.00 0.00 42.37 2.67
2588 2746 8.510243 TGTTATGTCTCATTGTATTGAGCAAT 57.490 30.769 0.97 0.97 42.37 3.56
2589 2747 7.920160 TGTTATGTCTCATTGTATTGAGCAA 57.080 32.000 0.00 0.00 42.37 3.91
2590 2748 7.414429 GCTTGTTATGTCTCATTGTATTGAGCA 60.414 37.037 0.00 0.12 42.37 4.26
2591 2749 6.909357 GCTTGTTATGTCTCATTGTATTGAGC 59.091 38.462 0.00 0.00 42.37 4.26
2592 2750 8.206325 AGCTTGTTATGTCTCATTGTATTGAG 57.794 34.615 0.00 0.00 43.70 3.02
2593 2751 9.836864 ATAGCTTGTTATGTCTCATTGTATTGA 57.163 29.630 0.00 0.00 0.00 2.57
2610 2768 9.938280 TCAGTGTGTACTATTAAATAGCTTGTT 57.062 29.630 0.00 0.00 36.30 2.83
2611 2769 9.367444 GTCAGTGTGTACTATTAAATAGCTTGT 57.633 33.333 0.00 0.00 36.30 3.16
2612 2770 9.587772 AGTCAGTGTGTACTATTAAATAGCTTG 57.412 33.333 0.00 0.00 36.30 4.01
2625 2783 9.731819 CGATACAAATATTAGTCAGTGTGTACT 57.268 33.333 0.00 0.00 37.75 2.73
2626 2784 9.726232 TCGATACAAATATTAGTCAGTGTGTAC 57.274 33.333 0.00 0.00 0.00 2.90
2627 2785 9.726232 GTCGATACAAATATTAGTCAGTGTGTA 57.274 33.333 0.00 0.00 0.00 2.90
2628 2786 7.705325 GGTCGATACAAATATTAGTCAGTGTGT 59.295 37.037 0.00 0.00 0.00 3.72
2629 2787 7.704899 TGGTCGATACAAATATTAGTCAGTGTG 59.295 37.037 0.00 0.00 0.00 3.82
2630 2788 7.778083 TGGTCGATACAAATATTAGTCAGTGT 58.222 34.615 0.00 0.00 0.00 3.55
2631 2789 8.540492 GTTGGTCGATACAAATATTAGTCAGTG 58.460 37.037 7.02 0.00 0.00 3.66
2632 2790 8.255206 TGTTGGTCGATACAAATATTAGTCAGT 58.745 33.333 7.02 0.00 0.00 3.41
2633 2791 8.642908 TGTTGGTCGATACAAATATTAGTCAG 57.357 34.615 7.02 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.