Multiple sequence alignment - TraesCS7B01G072000

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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 TraesCS7B01G072000 chr7B 100.000 3365 0 0 453 3817 79310495 79307131 0.000000e+00 6215.0
1 TraesCS7B01G072000 chr7B 100.000 155 0 0 1 155 79310947 79310793 1.740000e-73 287.0
2 TraesCS7B01G072000 chr7A 94.131 1312 60 11 2514 3817 122495509 122494207 0.000000e+00 1980.0
3 TraesCS7B01G072000 chr7A 90.280 535 28 7 1990 2512 122498012 122497490 0.000000e+00 678.0
4 TraesCS7B01G072000 chr7A 92.157 459 36 0 974 1432 122531657 122531199 0.000000e+00 649.0
5 TraesCS7B01G072000 chr7A 92.105 342 24 1 1648 1989 122498704 122498366 2.670000e-131 479.0
6 TraesCS7B01G072000 chr7A 89.024 328 20 7 611 932 122678792 122678475 3.570000e-105 392.0
7 TraesCS7B01G072000 chr7A 90.323 155 9 4 1 155 122679285 122679137 8.360000e-47 198.0
8 TraesCS7B01G072000 chr7A 94.690 113 5 1 466 577 122678897 122678785 1.410000e-39 174.0
9 TraesCS7B01G072000 chr7A 84.375 96 5 7 1419 1512 122499029 122498942 6.790000e-13 86.1
10 TraesCS7B01G072000 chr7D 92.397 1210 65 13 2612 3817 118154099 118152913 0.000000e+00 1700.0
11 TraesCS7B01G072000 chr7D 90.362 1214 75 19 470 1655 118157855 118156656 0.000000e+00 1555.0
12 TraesCS7B01G072000 chr7D 85.736 659 52 17 1990 2611 118154948 118154295 0.000000e+00 658.0
13 TraesCS7B01G072000 chr7D 92.453 318 17 5 1658 1974 118155608 118155297 7.520000e-122 448.0
14 TraesCS7B01G072000 chr7D 93.284 134 5 2 16 149 118158328 118158199 1.080000e-45 195.0
15 TraesCS7B01G072000 chr4D 77.500 280 45 12 1245 1511 485481213 485480939 6.600000e-33 152.0
16 TraesCS7B01G072000 chr4B 95.455 44 2 0 1464 1507 618633819 618633776 1.900000e-08 71.3
17 TraesCS7B01G072000 chr4B 95.455 44 2 0 1464 1507 618641547 618641504 1.900000e-08 71.3


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 TraesCS7B01G072000 chr7B 79307131 79310947 3816 True 3251.000000 6215 100.000000 1 3817 2 chr7B.!!$R1 3816
1 TraesCS7B01G072000 chr7A 122494207 122499029 4822 True 805.775000 1980 90.222750 1419 3817 4 chr7A.!!$R2 2398
2 TraesCS7B01G072000 chr7A 122678475 122679285 810 True 254.666667 392 91.345667 1 932 3 chr7A.!!$R3 931
3 TraesCS7B01G072000 chr7D 118152913 118158328 5415 True 911.200000 1700 90.846400 16 3817 5 chr7D.!!$R1 3801

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
984 1014 0.323542 ACACCAACAAACCGGACCAA 60.324 50.0 9.46 0.0 0.0 3.67 F
1021 1051 0.175760 GGCGTCCAAGTCTAGCATCA 59.824 55.0 0.00 0.0 0.0 3.07 F
1635 1737 0.318762 GTGACCCTCAGAAGCGTTCT 59.681 55.0 0.00 0.0 41.7 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 3720 0.257039 AGCATGTCCATCCTTGTCCC 59.743 55.000 0.0 0.0 0.00 4.46 R
2330 3856 1.139654 GGTCACATCAGCATAGCCTCA 59.860 52.381 0.0 0.0 0.00 3.86 R
3499 7235 0.098376 GTAGGTGACACGGAGTAGCG 59.902 60.000 0.0 0.0 41.61 4.26 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
41 42 8.995027 ACAAGATGGCAAGGTTCAATATATTA 57.005 30.769 0.00 0.00 0.00 0.98
53 54 6.073765 GGTTCAATATATTAGGCACAGTGACG 60.074 42.308 4.15 0.00 0.00 4.35
54 55 6.156748 TCAATATATTAGGCACAGTGACGT 57.843 37.500 4.15 0.00 0.00 4.34
55 56 5.983118 TCAATATATTAGGCACAGTGACGTG 59.017 40.000 4.15 3.77 40.00 4.49
56 57 5.784578 ATATATTAGGCACAGTGACGTGA 57.215 39.130 4.15 0.00 39.34 4.35
57 58 4.672587 ATATTAGGCACAGTGACGTGAT 57.327 40.909 4.15 1.04 39.34 3.06
78 79 1.297664 GATGATGGCACTGACTCTGC 58.702 55.000 0.00 0.00 0.00 4.26
97 98 4.157656 TCTGCTTTTGGGGAAATAACATCG 59.842 41.667 0.00 0.00 0.00 3.84
498 522 5.180304 TGCATACACTTGACTTGCGAATAAA 59.820 36.000 0.00 0.00 36.11 1.40
530 554 3.813529 ATGCTTTGCGAAGTTACTCAC 57.186 42.857 15.22 0.00 35.25 3.51
535 559 2.513159 GCGAAGTTACTCACACGCA 58.487 52.632 16.10 0.00 45.96 5.24
536 560 1.068474 GCGAAGTTACTCACACGCAT 58.932 50.000 16.10 0.00 45.96 4.73
537 561 2.256174 GCGAAGTTACTCACACGCATA 58.744 47.619 16.10 0.00 45.96 3.14
538 562 2.279136 GCGAAGTTACTCACACGCATAG 59.721 50.000 16.10 0.00 45.96 2.23
539 563 3.499048 CGAAGTTACTCACACGCATAGT 58.501 45.455 0.00 0.00 0.00 2.12
540 564 3.918591 CGAAGTTACTCACACGCATAGTT 59.081 43.478 0.00 0.00 0.00 2.24
576 601 1.929836 TCACATGGCGCAAAAACAAAC 59.070 42.857 10.83 0.00 0.00 2.93
628 653 7.629845 GCACGTATAAACTAGCTAAAAGTTTCG 59.370 37.037 14.80 14.36 44.07 3.46
666 691 7.076842 TGACAACTTGACAAGAGAAGAAAAG 57.923 36.000 21.95 3.38 0.00 2.27
711 736 1.771565 AGGATGCCACATCAACCATG 58.228 50.000 9.60 0.00 38.64 3.66
715 740 1.992538 TGCCACATCAACCATGACAA 58.007 45.000 0.00 0.00 38.69 3.18
728 753 3.245052 ACCATGACAAGAAAAGCTAGGCT 60.245 43.478 0.00 0.00 42.56 4.58
830 855 3.303938 AGTGCACTCTAGCTCACCATAT 58.696 45.455 15.25 0.00 34.99 1.78
879 904 3.082701 GCTGGCAGCTCCTCCTCT 61.083 66.667 31.37 0.00 38.45 3.69
880 905 3.092780 GCTGGCAGCTCCTCCTCTC 62.093 68.421 31.37 0.00 38.45 3.20
881 906 1.381599 CTGGCAGCTCCTCCTCTCT 60.382 63.158 0.00 0.00 35.26 3.10
882 907 0.977108 CTGGCAGCTCCTCCTCTCTT 60.977 60.000 0.00 0.00 35.26 2.85
883 908 0.336392 TGGCAGCTCCTCCTCTCTTA 59.664 55.000 0.00 0.00 35.26 2.10
884 909 0.750249 GGCAGCTCCTCCTCTCTTAC 59.250 60.000 0.00 0.00 0.00 2.34
885 910 1.479709 GCAGCTCCTCCTCTCTTACA 58.520 55.000 0.00 0.00 0.00 2.41
886 911 2.038659 GCAGCTCCTCCTCTCTTACAT 58.961 52.381 0.00 0.00 0.00 2.29
889 914 4.692228 CAGCTCCTCCTCTCTTACATTTC 58.308 47.826 0.00 0.00 0.00 2.17
917 947 4.141505 TGGTATATATGCAGGCAAGTGTGT 60.142 41.667 0.00 0.00 0.00 3.72
933 963 2.671396 GTGTGTCCGGTATTGCTTACAG 59.329 50.000 0.00 0.00 31.99 2.74
938 968 1.014352 CGGTATTGCTTACAGCCACC 58.986 55.000 0.00 0.00 41.51 4.61
941 971 1.401905 GTATTGCTTACAGCCACCAGC 59.598 52.381 0.00 0.00 41.51 4.85
982 1012 1.232119 CTACACCAACAAACCGGACC 58.768 55.000 9.46 0.00 0.00 4.46
984 1014 0.323542 ACACCAACAAACCGGACCAA 60.324 50.000 9.46 0.00 0.00 3.67
999 1029 5.104485 ACCGGACCAAGCTAGAAAGAATAAT 60.104 40.000 9.46 0.00 0.00 1.28
1021 1051 0.175760 GGCGTCCAAGTCTAGCATCA 59.824 55.000 0.00 0.00 0.00 3.07
1025 1055 1.555075 GTCCAAGTCTAGCATCACCCA 59.445 52.381 0.00 0.00 0.00 4.51
1039 1069 4.101448 CCCACCTCCTCTTGGCCG 62.101 72.222 0.00 0.00 0.00 6.13
1093 1123 0.814010 CACAGGCCCGTATTGCTACC 60.814 60.000 0.00 0.00 0.00 3.18
1095 1125 2.280592 GGCCCGTATTGCTACCCG 60.281 66.667 0.00 0.00 0.00 5.28
1112 1142 2.797278 CGGGGATGGGTCTTCCGAG 61.797 68.421 0.00 0.00 40.71 4.63
1155 1185 2.069273 GAGTATGTCGCACAGCAAACT 58.931 47.619 0.00 0.00 0.00 2.66
1162 1192 1.945662 GCACAGCAAACTTGTGGCG 60.946 57.895 7.40 0.00 44.66 5.69
1165 1195 1.369209 CAGCAAACTTGTGGCGTCG 60.369 57.895 0.00 0.00 0.00 5.12
1170 1200 1.852067 AAACTTGTGGCGTCGGCATC 61.852 55.000 25.14 17.61 40.92 3.91
1171 1201 3.853330 CTTGTGGCGTCGGCATCG 61.853 66.667 25.14 12.03 40.92 3.84
1172 1202 4.673298 TTGTGGCGTCGGCATCGT 62.673 61.111 25.14 0.00 40.92 3.73
1289 1319 0.318784 CGCTACTTCATAGGGCGGAC 60.319 60.000 0.00 0.00 41.00 4.79
1306 1336 1.571919 GACGTCTGATCCCAATTCCG 58.428 55.000 8.70 0.00 0.00 4.30
1323 1353 2.032681 GGCGTGCTCAAGGACCTT 59.967 61.111 0.00 0.00 32.36 3.50
1408 1438 1.213491 CGTGATGACCGTTCACAACA 58.787 50.000 4.62 0.00 42.90 3.33
1442 1472 5.049405 GCCTCGGTTTGGACATATAAAGATG 60.049 44.000 0.00 0.00 0.00 2.90
1539 1612 8.869109 ACAAGAATAAAGGGAATCATTTTGTGA 58.131 29.630 0.00 0.00 42.06 3.58
1577 1650 9.552114 CAACTCAATCTTTTGTTCATATGTCTC 57.448 33.333 1.90 0.00 34.32 3.36
1579 1652 7.819415 ACTCAATCTTTTGTTCATATGTCTCGA 59.181 33.333 1.90 0.00 34.32 4.04
1585 1658 8.092068 TCTTTTGTTCATATGTCTCGAGGTTTA 58.908 33.333 13.56 2.18 0.00 2.01
1596 1669 4.567159 GTCTCGAGGTTTAATAGCCTTGTG 59.433 45.833 13.56 0.00 37.50 3.33
1597 1670 4.464951 TCTCGAGGTTTAATAGCCTTGTGA 59.535 41.667 13.56 0.00 36.80 3.58
1598 1671 4.755411 TCGAGGTTTAATAGCCTTGTGAG 58.245 43.478 0.00 0.00 37.50 3.51
1635 1737 0.318762 GTGACCCTCAGAAGCGTTCT 59.681 55.000 0.00 0.00 41.70 3.01
1650 1752 6.712241 AAGCGTTCTTCGATCCATAATATG 57.288 37.500 0.00 0.00 42.86 1.78
1651 1753 5.784177 AGCGTTCTTCGATCCATAATATGT 58.216 37.500 0.00 0.00 42.86 2.29
1652 1754 5.864474 AGCGTTCTTCGATCCATAATATGTC 59.136 40.000 0.00 0.00 42.86 3.06
1654 1756 5.856986 CGTTCTTCGATCCATAATATGTCGT 59.143 40.000 11.33 0.00 42.86 4.34
1655 1757 6.032565 CGTTCTTCGATCCATAATATGTCGTC 59.967 42.308 11.33 1.63 42.86 4.20
1656 1758 5.628134 TCTTCGATCCATAATATGTCGTCG 58.372 41.667 11.33 11.00 32.59 5.12
1679 2824 7.069085 GTCGGTATATATAGGATAGCAAACCCA 59.931 40.741 0.00 0.00 0.00 4.51
1698 2843 3.491652 GCAAGAGGACGAAGCGCC 61.492 66.667 2.29 0.00 0.00 6.53
1869 3014 7.600375 TCTCGAGATATAATCCAATCAAAGCAC 59.400 37.037 12.08 0.00 0.00 4.40
1902 3047 1.754234 CCATCCCAAAAGGGCTCGG 60.754 63.158 0.00 0.00 35.67 4.63
1921 3066 2.031870 GGGCCTGGGTAAATCATTGTC 58.968 52.381 0.84 0.00 0.00 3.18
1922 3067 2.358195 GGGCCTGGGTAAATCATTGTCT 60.358 50.000 0.84 0.00 0.00 3.41
1944 3091 1.504912 AGAGATCCATGGTGACCCTG 58.495 55.000 12.58 0.00 0.00 4.45
1964 3111 4.380867 CCTGGCATACCTTTGTGATCAAAC 60.381 45.833 0.00 0.00 38.44 2.93
2009 3515 8.331022 GCCACGCATGTATGATAATTAAGATAG 58.669 37.037 0.00 0.00 0.00 2.08
2186 3710 3.298126 CACTAGTCGTGCGAGAGTG 57.702 57.895 16.78 16.78 36.72 3.51
2249 3775 2.303022 TCTTTTCCTCATGAGTCGCCTT 59.697 45.455 21.11 0.00 0.00 4.35
2271 3797 7.331026 CCTTGAAGATAGTTCTCATGTTACCA 58.669 38.462 0.00 0.00 0.00 3.25
2329 3855 6.753913 ATTGCCTAAGATCATCACCTTCTA 57.246 37.500 0.00 0.00 0.00 2.10
2330 3856 6.753913 TTGCCTAAGATCATCACCTTCTAT 57.246 37.500 0.00 0.00 0.00 1.98
2334 3860 6.574073 GCCTAAGATCATCACCTTCTATGAGG 60.574 46.154 0.00 0.00 42.75 3.86
2338 3864 6.262980 AGATCATCACCTTCTATGAGGCTAT 58.737 40.000 0.00 0.00 40.65 2.97
2339 3865 5.735285 TCATCACCTTCTATGAGGCTATG 57.265 43.478 0.00 0.00 40.65 2.23
2461 4003 6.273071 CACGATGTATCTATTGTCTCCAACA 58.727 40.000 0.00 0.00 35.59 3.33
2462 4004 6.199154 CACGATGTATCTATTGTCTCCAACAC 59.801 42.308 0.00 0.00 37.70 3.32
2489 4031 2.487625 CCTTTCGAACACCACCCCTTTA 60.488 50.000 0.00 0.00 0.00 1.85
2499 4041 4.283212 ACACCACCCCTTTATTTGTCATTG 59.717 41.667 0.00 0.00 0.00 2.82
2526 6049 5.682049 CGACTTCGTGGTACTTCATAAAG 57.318 43.478 0.00 0.00 35.10 1.85
2529 6052 6.092955 ACTTCGTGGTACTTCATAAAGTCA 57.907 37.500 0.00 0.00 44.64 3.41
2553 6076 5.026462 GCAGTGAATCAATCTTCGACAATG 58.974 41.667 0.00 0.00 0.00 2.82
2555 6078 4.696877 AGTGAATCAATCTTCGACAATGCA 59.303 37.500 0.00 0.00 0.00 3.96
2668 6386 2.588464 TTTCCTTCATTTACCCCGCA 57.412 45.000 0.00 0.00 0.00 5.69
2738 6456 0.322975 GAGGTGCAGTCTCCACATGT 59.677 55.000 0.00 0.00 34.94 3.21
2843 6565 2.407090 GCCAGCATTTCACCAAAACTC 58.593 47.619 0.00 0.00 0.00 3.01
2845 6567 3.493176 GCCAGCATTTCACCAAAACTCTT 60.493 43.478 0.00 0.00 0.00 2.85
2846 6568 4.261994 GCCAGCATTTCACCAAAACTCTTA 60.262 41.667 0.00 0.00 0.00 2.10
2847 6569 5.567423 GCCAGCATTTCACCAAAACTCTTAT 60.567 40.000 0.00 0.00 0.00 1.73
2848 6570 6.095377 CCAGCATTTCACCAAAACTCTTATC 58.905 40.000 0.00 0.00 0.00 1.75
2849 6571 6.071728 CCAGCATTTCACCAAAACTCTTATCT 60.072 38.462 0.00 0.00 0.00 1.98
2882 6606 7.700022 AAGAAAATCTTGATTCAGGAAGAGG 57.300 36.000 2.30 0.00 34.98 3.69
3012 6745 6.313744 AGACAACAATAAAGCCTACACAAC 57.686 37.500 0.00 0.00 0.00 3.32
3093 6828 8.659527 TCACTATATGAGCAATCCTAATTTGGA 58.340 33.333 11.15 11.15 35.10 3.53
3101 6836 8.494433 TGAGCAATCCTAATTTGGAGTAACTAT 58.506 33.333 14.05 0.00 39.78 2.12
3142 6878 7.252612 TCTGTAGATAACCTTTGAACCATCA 57.747 36.000 0.00 0.00 0.00 3.07
3169 6905 7.660208 CCAAGACTATTACAGGTTACAACAAGT 59.340 37.037 0.00 0.00 0.00 3.16
3182 6918 2.195922 CAACAAGTTGAGGCTGTTTGC 58.804 47.619 10.54 0.00 42.93 3.68
3183 6919 1.473258 ACAAGTTGAGGCTGTTTGCA 58.527 45.000 10.54 0.00 45.15 4.08
3198 6934 2.044946 GCACCCCCACATCTCACC 60.045 66.667 0.00 0.00 0.00 4.02
3211 6947 6.183360 CCCACATCTCACCATCTTGTTATTTC 60.183 42.308 0.00 0.00 0.00 2.17
3212 6948 6.600822 CCACATCTCACCATCTTGTTATTTCT 59.399 38.462 0.00 0.00 0.00 2.52
3213 6949 7.121759 CCACATCTCACCATCTTGTTATTTCTT 59.878 37.037 0.00 0.00 0.00 2.52
3214 6950 8.517878 CACATCTCACCATCTTGTTATTTCTTT 58.482 33.333 0.00 0.00 0.00 2.52
3221 6957 9.410556 CACCATCTTGTTATTTCTTTTTACCAG 57.589 33.333 0.00 0.00 0.00 4.00
3222 6958 8.088365 ACCATCTTGTTATTTCTTTTTACCAGC 58.912 33.333 0.00 0.00 0.00 4.85
3223 6959 8.087750 CCATCTTGTTATTTCTTTTTACCAGCA 58.912 33.333 0.00 0.00 0.00 4.41
3247 6983 5.012239 AGACATGCTTCAGCCTTTTATTGA 58.988 37.500 0.00 0.00 41.18 2.57
3249 6985 6.154021 AGACATGCTTCAGCCTTTTATTGATT 59.846 34.615 0.00 0.00 41.18 2.57
3250 6986 6.704310 ACATGCTTCAGCCTTTTATTGATTT 58.296 32.000 0.00 0.00 41.18 2.17
3251 6987 7.839907 ACATGCTTCAGCCTTTTATTGATTTA 58.160 30.769 0.00 0.00 41.18 1.40
3373 7109 2.947532 CGCAGCCTCTCCACCTCAA 61.948 63.158 0.00 0.00 0.00 3.02
3382 7118 0.034059 CTCCACCTCAACTTCAGCGT 59.966 55.000 0.00 0.00 0.00 5.07
3385 7121 2.103432 TCCACCTCAACTTCAGCGTTTA 59.897 45.455 0.00 0.00 0.00 2.01
3386 7122 2.223377 CCACCTCAACTTCAGCGTTTAC 59.777 50.000 0.00 0.00 0.00 2.01
3468 7204 3.070018 GTCTGAGGTTGACAATGGACTG 58.930 50.000 0.00 0.00 34.80 3.51
3499 7235 9.995003 AGAGAATGTTGGTATTCTGATTAGATC 57.005 33.333 5.80 0.00 45.00 2.75
3653 7389 5.425217 TCTCATAACTCCAGAATGCACCTAA 59.575 40.000 0.00 0.00 31.97 2.69
3791 7527 2.392662 TCTCCTGTTCCTGGATAGCAG 58.607 52.381 13.26 13.26 31.33 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.576463 CCTTGCCATCTTGTACTCCATAAC 59.424 45.833 0.00 0.00 0.00 1.89
13 14 3.788227 TGAACCTTGCCATCTTGTACT 57.212 42.857 0.00 0.00 0.00 2.73
22 23 5.534654 GTGCCTAATATATTGAACCTTGCCA 59.465 40.000 8.28 0.00 0.00 4.92
41 42 0.392706 TCAATCACGTCACTGTGCCT 59.607 50.000 2.12 0.00 39.73 4.75
53 54 3.276857 AGTCAGTGCCATCATCAATCAC 58.723 45.455 0.00 0.00 0.00 3.06
54 55 3.199289 AGAGTCAGTGCCATCATCAATCA 59.801 43.478 0.00 0.00 0.00 2.57
55 56 3.560481 CAGAGTCAGTGCCATCATCAATC 59.440 47.826 0.00 0.00 0.00 2.67
56 57 3.542648 CAGAGTCAGTGCCATCATCAAT 58.457 45.455 0.00 0.00 0.00 2.57
57 58 2.938314 GCAGAGTCAGTGCCATCATCAA 60.938 50.000 0.00 0.00 34.67 2.57
78 79 6.019779 TGTTCGATGTTATTTCCCCAAAAG 57.980 37.500 0.00 0.00 0.00 2.27
97 98 3.575965 AGCCCATTTCGTTTGATGTTC 57.424 42.857 0.00 0.00 0.00 3.18
452 453 5.463724 GCATACAGATAGGCTACAACTCAAC 59.536 44.000 0.00 0.00 35.19 3.18
453 454 5.128663 TGCATACAGATAGGCTACAACTCAA 59.871 40.000 0.00 0.00 38.92 3.02
454 455 4.649218 TGCATACAGATAGGCTACAACTCA 59.351 41.667 0.00 0.00 38.92 3.41
455 456 5.201713 TGCATACAGATAGGCTACAACTC 57.798 43.478 0.00 0.00 38.92 3.01
456 457 5.815233 ATGCATACAGATAGGCTACAACT 57.185 39.130 0.00 0.00 38.92 3.16
457 458 6.366332 GTGTATGCATACAGATAGGCTACAAC 59.634 42.308 34.29 17.00 43.32 3.32
458 459 6.267699 AGTGTATGCATACAGATAGGCTACAA 59.732 38.462 34.29 9.79 43.32 2.41
459 460 5.775195 AGTGTATGCATACAGATAGGCTACA 59.225 40.000 34.29 12.50 43.32 2.74
460 461 6.274157 AGTGTATGCATACAGATAGGCTAC 57.726 41.667 34.29 20.85 43.32 3.58
461 462 6.493458 TCAAGTGTATGCATACAGATAGGCTA 59.507 38.462 34.29 13.54 43.32 3.93
462 463 5.305386 TCAAGTGTATGCATACAGATAGGCT 59.695 40.000 34.29 24.32 43.32 4.58
463 464 5.406780 GTCAAGTGTATGCATACAGATAGGC 59.593 44.000 34.29 22.83 43.32 3.93
464 465 6.753180 AGTCAAGTGTATGCATACAGATAGG 58.247 40.000 34.29 22.48 43.32 2.57
498 522 6.203338 ACTTCGCAAAGCATTGATTTTCAAAT 59.797 30.769 5.73 0.00 36.60 2.32
530 554 6.529463 TCATGTGATAATCAACTATGCGTG 57.471 37.500 0.00 0.00 0.00 5.34
536 560 9.485206 CATGTGAGATCATGTGATAATCAACTA 57.515 33.333 10.32 3.99 39.93 2.24
537 561 7.444487 CCATGTGAGATCATGTGATAATCAACT 59.556 37.037 10.32 0.00 42.29 3.16
538 562 7.582352 CCATGTGAGATCATGTGATAATCAAC 58.418 38.462 10.32 7.23 42.29 3.18
539 563 6.206048 GCCATGTGAGATCATGTGATAATCAA 59.794 38.462 10.32 4.67 42.29 2.57
540 564 5.704053 GCCATGTGAGATCATGTGATAATCA 59.296 40.000 0.00 1.55 42.29 2.57
576 601 9.072294 CAAACCTTGTTAAAACTAACAACAGAG 57.928 33.333 6.40 0.00 42.82 3.35
628 653 2.484264 AGTTGTCATCGGTGCTTAAAGC 59.516 45.455 0.00 0.00 42.82 3.51
666 691 1.133025 CTTTCGAACCATGTGGCATCC 59.867 52.381 0.00 0.00 39.32 3.51
711 736 2.960819 TCGAGCCTAGCTTTTCTTGTC 58.039 47.619 0.00 0.00 39.88 3.18
715 740 2.482839 GCTGATCGAGCCTAGCTTTTCT 60.483 50.000 5.81 0.00 42.54 2.52
728 753 5.941948 TTGAGATATTCGTAGCTGATCGA 57.058 39.130 0.00 0.97 0.00 3.59
830 855 7.979537 ACTAAATCTGTTGTGCTATATGACGAA 59.020 33.333 0.00 0.00 0.00 3.85
872 897 5.068987 CCAGAGAGAAATGTAAGAGAGGAGG 59.931 48.000 0.00 0.00 0.00 4.30
875 900 5.930837 ACCAGAGAGAAATGTAAGAGAGG 57.069 43.478 0.00 0.00 0.00 3.69
882 907 8.753133 CCTGCATATATACCAGAGAGAAATGTA 58.247 37.037 11.83 0.00 0.00 2.29
883 908 7.619050 CCTGCATATATACCAGAGAGAAATGT 58.381 38.462 11.83 0.00 0.00 2.71
884 909 6.538021 GCCTGCATATATACCAGAGAGAAATG 59.462 42.308 11.83 0.00 0.00 2.32
885 910 6.214208 TGCCTGCATATATACCAGAGAGAAAT 59.786 38.462 11.83 0.00 0.00 2.17
886 911 5.543790 TGCCTGCATATATACCAGAGAGAAA 59.456 40.000 11.83 0.00 0.00 2.52
889 914 5.046735 ACTTGCCTGCATATATACCAGAGAG 60.047 44.000 11.83 9.21 0.00 3.20
907 932 0.802494 CAATACCGGACACACTTGCC 59.198 55.000 9.46 0.00 0.00 4.52
933 963 3.969802 GTGCACTGTGCTGGTGGC 61.970 66.667 30.43 11.89 45.31 5.01
938 968 1.096967 TGAGGTTGTGCACTGTGCTG 61.097 55.000 30.43 0.00 45.31 4.41
941 971 1.667236 TCTTGAGGTTGTGCACTGTG 58.333 50.000 19.41 2.76 0.00 3.66
942 972 2.418368 TTCTTGAGGTTGTGCACTGT 57.582 45.000 19.41 0.00 0.00 3.55
953 983 5.449999 GGTTTGTTGGTGTAGTTTCTTGAGG 60.450 44.000 0.00 0.00 0.00 3.86
982 1012 7.360438 GGACGCCATATTATTCTTTCTAGCTTG 60.360 40.741 0.00 0.00 0.00 4.01
984 1014 6.166982 GGACGCCATATTATTCTTTCTAGCT 58.833 40.000 0.00 0.00 0.00 3.32
999 1029 1.480789 TGCTAGACTTGGACGCCATA 58.519 50.000 0.00 0.00 31.53 2.74
1021 1051 2.936032 GGCCAAGAGGAGGTGGGT 60.936 66.667 0.00 0.00 36.89 4.51
1039 1069 4.131088 GACGGAGACCAGGACGGC 62.131 72.222 0.00 0.00 39.03 5.68
1083 1113 0.036306 CCATCCCCGGGTAGCAATAC 59.964 60.000 21.85 0.00 0.00 1.89
1093 1123 3.861797 CGGAAGACCCATCCCCGG 61.862 72.222 0.00 0.00 37.71 5.73
1095 1125 3.108288 GCTCGGAAGACCCATCCCC 62.108 68.421 0.00 0.00 35.39 4.81
1112 1142 2.985847 AGCCTTCAAGCGGGTTGC 60.986 61.111 14.76 3.60 46.98 4.17
1155 1185 4.673298 ACGATGCCGACGCCACAA 62.673 61.111 0.00 0.00 39.50 3.33
1209 1239 1.817099 CTTGCAGCACCGATCCCTC 60.817 63.158 0.00 0.00 0.00 4.30
1266 1296 0.880718 GCCCTATGAAGTAGCGCACC 60.881 60.000 11.47 0.00 34.90 5.01
1289 1319 1.160329 GCCGGAATTGGGATCAGACG 61.160 60.000 5.05 0.00 0.00 4.18
1306 1336 2.032681 AAGGTCCTTGAGCACGCC 59.967 61.111 2.38 0.00 31.89 5.68
1408 1438 1.205460 AAACCGAGGCAGTATGGGGT 61.205 55.000 0.00 0.00 35.86 4.95
1442 1472 5.417266 TCATTCATGAGAGACGGATCTATCC 59.583 44.000 0.00 0.00 41.70 2.59
1455 1485 6.829811 TGGAACATGCTTATTCATTCATGAGA 59.170 34.615 7.90 0.00 38.77 3.27
1577 1650 4.504858 ACTCACAAGGCTATTAAACCTCG 58.495 43.478 0.00 0.00 34.31 4.63
1579 1652 7.439108 AGATACTCACAAGGCTATTAAACCT 57.561 36.000 0.00 0.00 38.14 3.50
1596 1669 7.254932 GGGTCACAAGCAATGAATAAGATACTC 60.255 40.741 0.00 0.00 0.00 2.59
1597 1670 6.543831 GGGTCACAAGCAATGAATAAGATACT 59.456 38.462 0.00 0.00 0.00 2.12
1598 1671 6.543831 AGGGTCACAAGCAATGAATAAGATAC 59.456 38.462 0.00 0.00 0.00 2.24
1630 1732 5.856986 ACGACATATTATGGATCGAAGAACG 59.143 40.000 18.24 0.00 35.14 3.95
1635 1737 4.216902 ACCGACGACATATTATGGATCGAA 59.783 41.667 18.24 0.00 36.03 3.71
1646 1748 9.381033 GCTATCCTATATATACCGACGACATAT 57.619 37.037 0.00 1.57 0.00 1.78
1647 1749 8.370182 TGCTATCCTATATATACCGACGACATA 58.630 37.037 0.00 0.00 0.00 2.29
1648 1750 7.222161 TGCTATCCTATATATACCGACGACAT 58.778 38.462 0.00 0.00 0.00 3.06
1650 1752 7.488187 TTGCTATCCTATATATACCGACGAC 57.512 40.000 0.00 0.00 0.00 4.34
1651 1753 7.012704 GGTTTGCTATCCTATATATACCGACGA 59.987 40.741 0.00 0.00 0.00 4.20
1652 1754 7.137426 GGTTTGCTATCCTATATATACCGACG 58.863 42.308 0.00 0.00 0.00 5.12
1654 1756 7.127405 TGGGTTTGCTATCCTATATATACCGA 58.873 38.462 0.00 0.00 0.00 4.69
1655 1757 7.356089 TGGGTTTGCTATCCTATATATACCG 57.644 40.000 0.00 0.00 0.00 4.02
1656 1758 7.661847 GCATGGGTTTGCTATCCTATATATACC 59.338 40.741 0.00 0.00 39.57 2.73
1679 2824 2.103042 GCGCTTCGTCCTCTTGCAT 61.103 57.895 0.00 0.00 0.00 3.96
1698 2843 1.468985 TGGTTGTGTTGAACCTGGTG 58.531 50.000 0.00 0.00 45.07 4.17
1902 3047 2.952310 GAGACAATGATTTACCCAGGCC 59.048 50.000 0.00 0.00 0.00 5.19
1921 3066 2.896685 GGGTCACCATGGATCTCTAGAG 59.103 54.545 21.47 13.98 36.50 2.43
1922 3067 2.520120 AGGGTCACCATGGATCTCTAGA 59.480 50.000 21.47 1.45 40.13 2.43
1944 3091 4.782019 TGTTTGATCACAAAGGTATGCC 57.218 40.909 0.00 0.00 44.97 4.40
1964 3111 7.594386 TGCGTGGCAATAATTATATGTGATTTG 59.406 33.333 0.00 0.00 34.76 2.32
1974 3121 6.816134 TCATACATGCGTGGCAATAATTAT 57.184 33.333 11.36 0.00 43.62 1.28
1975 3122 6.816134 ATCATACATGCGTGGCAATAATTA 57.184 33.333 11.36 0.00 43.62 1.40
1978 3125 6.816134 ATTATCATACATGCGTGGCAATAA 57.184 33.333 11.36 8.85 43.62 1.40
1984 3131 8.820933 CCTATCTTAATTATCATACATGCGTGG 58.179 37.037 11.36 0.00 0.00 4.94
2029 3535 7.925993 TCTTCAATTTGTGAACGAATAAGTGT 58.074 30.769 0.00 0.00 41.47 3.55
2032 3538 9.778993 ATCATCTTCAATTTGTGAACGAATAAG 57.221 29.630 0.00 0.00 41.47 1.73
2118 3631 5.141182 TCTAGACACTCTTTGGTTGTCTCT 58.859 41.667 6.74 0.00 40.00 3.10
2186 3710 2.663196 CTTGTCCCCCGAGTGTCC 59.337 66.667 0.00 0.00 0.00 4.02
2193 3717 1.635817 ATGTCCATCCTTGTCCCCCG 61.636 60.000 0.00 0.00 0.00 5.73
2196 3720 0.257039 AGCATGTCCATCCTTGTCCC 59.743 55.000 0.00 0.00 0.00 4.46
2271 3797 4.595781 TCTTTACACATGTTGACCCCTACT 59.404 41.667 0.00 0.00 0.00 2.57
2320 3846 3.323115 CAGCATAGCCTCATAGAAGGTGA 59.677 47.826 0.00 0.00 38.79 4.02
2329 3855 2.224475 GGTCACATCAGCATAGCCTCAT 60.224 50.000 0.00 0.00 0.00 2.90
2330 3856 1.139654 GGTCACATCAGCATAGCCTCA 59.860 52.381 0.00 0.00 0.00 3.86
2334 3860 4.065321 AGTTAGGTCACATCAGCATAGC 57.935 45.455 0.00 0.00 0.00 2.97
2338 3864 4.623932 AGAAAGTTAGGTCACATCAGCA 57.376 40.909 0.00 0.00 0.00 4.41
2339 3865 5.525378 CCATAGAAAGTTAGGTCACATCAGC 59.475 44.000 0.00 0.00 0.00 4.26
2372 3898 7.328249 ACGTGAATTGGCATTTTACAAAGTATG 59.672 33.333 14.66 2.65 0.00 2.39
2461 4003 1.616865 TGGTGTTCGAAAGGATCTCGT 59.383 47.619 0.00 0.00 37.56 4.18
2462 4004 1.993370 GTGGTGTTCGAAAGGATCTCG 59.007 52.381 0.00 0.00 37.66 4.04
2525 6048 3.931468 CGAAGATTGATTCACTGCTGACT 59.069 43.478 0.00 0.00 0.00 3.41
2526 6049 3.928992 TCGAAGATTGATTCACTGCTGAC 59.071 43.478 0.00 0.00 0.00 3.51
2529 6052 3.930336 TGTCGAAGATTGATTCACTGCT 58.070 40.909 0.00 0.00 40.67 4.24
2860 6584 7.175641 TGTTCCTCTTCCTGAATCAAGATTTTC 59.824 37.037 0.00 0.00 0.00 2.29
2882 6606 7.315890 CACTTAAGAATTGGATTTCCCTGTTC 58.684 38.462 10.09 0.00 35.38 3.18
2964 6696 9.817809 CTTGTAAATATGGAAGCAGTACTCTAA 57.182 33.333 0.00 0.00 0.00 2.10
2965 6697 9.197306 TCTTGTAAATATGGAAGCAGTACTCTA 57.803 33.333 0.00 0.00 0.00 2.43
2966 6698 7.982354 GTCTTGTAAATATGGAAGCAGTACTCT 59.018 37.037 0.00 0.00 0.00 3.24
2967 6699 7.764443 TGTCTTGTAAATATGGAAGCAGTACTC 59.236 37.037 0.00 0.00 0.00 2.59
2968 6700 7.620880 TGTCTTGTAAATATGGAAGCAGTACT 58.379 34.615 0.00 0.00 0.00 2.73
2969 6701 7.843490 TGTCTTGTAAATATGGAAGCAGTAC 57.157 36.000 0.00 0.00 0.00 2.73
2970 6702 7.880713 TGTTGTCTTGTAAATATGGAAGCAGTA 59.119 33.333 0.00 0.00 0.00 2.74
3126 6862 4.825085 GTCTTGGTGATGGTTCAAAGGTTA 59.175 41.667 0.00 0.00 32.48 2.85
3142 6878 7.069877 TGTTGTAACCTGTAATAGTCTTGGT 57.930 36.000 0.00 0.00 0.00 3.67
3182 6918 0.107017 GATGGTGAGATGTGGGGGTG 60.107 60.000 0.00 0.00 0.00 4.61
3183 6919 0.253347 AGATGGTGAGATGTGGGGGT 60.253 55.000 0.00 0.00 0.00 4.95
3198 6934 9.474920 TTGCTGGTAAAAAGAAATAACAAGATG 57.525 29.630 0.00 0.00 0.00 2.90
3222 6958 3.655276 AAAAGGCTGAAGCATGTCTTG 57.345 42.857 4.43 0.00 44.36 3.02
3223 6959 5.477984 TCAATAAAAGGCTGAAGCATGTCTT 59.522 36.000 4.43 0.00 44.36 3.01
3247 6983 6.995511 TGAAGCGGCTACTTTGTAATAAAT 57.004 33.333 1.35 0.00 0.00 1.40
3249 6985 5.233476 CGATGAAGCGGCTACTTTGTAATAA 59.767 40.000 1.35 0.00 0.00 1.40
3250 6986 4.743151 CGATGAAGCGGCTACTTTGTAATA 59.257 41.667 1.35 0.00 0.00 0.98
3251 6987 3.555956 CGATGAAGCGGCTACTTTGTAAT 59.444 43.478 1.35 0.00 0.00 1.89
3373 7109 2.817844 GGGGAAATGTAAACGCTGAAGT 59.182 45.455 0.00 0.00 0.00 3.01
3406 7142 9.806448 ATTGGCATTTCACCTTGTATATATGTA 57.194 29.630 0.00 0.00 0.00 2.29
3468 7204 5.877012 TCAGAATACCAACATTCTCTTGAGC 59.123 40.000 0.00 0.00 42.14 4.26
3499 7235 0.098376 GTAGGTGACACGGAGTAGCG 59.902 60.000 0.00 0.00 41.61 4.26
3585 7321 4.883585 GCATCACATGAAGTCATTAGGGAA 59.116 41.667 0.00 0.00 33.61 3.97


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

AutoCloner maintained by Alex Coulton.