Multiple sequence alignment - TraesCS4B01G069500

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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 TraesCS4B01G069500 chr4B 100.000 3893 0 0 1 3893 63232673 63228781 0.000000e+00 7190
1 TraesCS4B01G069500 chr4A 91.276 1811 74 39 2059 3835 556538651 556540411 0.000000e+00 2392
2 TraesCS4B01G069500 chr4A 85.957 2058 121 79 1 1969 556536606 556538584 0.000000e+00 2045
3 TraesCS4B01G069500 chr4A 94.898 98 5 0 3796 3893 556540411 556540508 1.870000e-33 154
4 TraesCS4B01G069500 chr4D 93.694 1348 66 12 2059 3393 43555187 43556528 0.000000e+00 2001
5 TraesCS4B01G069500 chr4D 95.594 976 40 2 997 1969 43554142 43555117 0.000000e+00 1561
6 TraesCS4B01G069500 chr4D 87.187 999 62 31 1 947 43553139 43554123 0.000000e+00 1075


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 TraesCS4B01G069500 chr4B 63228781 63232673 3892 True 7190.000000 7190 100.000000 1 3893 1 chr4B.!!$R1 3892
1 TraesCS4B01G069500 chr4A 556536606 556540508 3902 False 1530.333333 2392 90.710333 1 3893 3 chr4A.!!$F1 3892
2 TraesCS4B01G069500 chr4D 43553139 43556528 3389 False 1545.666667 2001 92.158333 1 3393 3 chr4D.!!$F1 3392

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
973 1068 0.034896 TTCACGGAAGGACTGCTTCC 59.965 55.0 17.4 17.4 46.33 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2934 3073 0.81401 GTCTGTCAACAAGTGCCGGT 60.814 55.0 1.9 0.0 0.0 5.28 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
59 61 2.086869 AGGAGCAATGGTCAACAATCG 58.913 47.619 14.70 0.00 0.00 3.34
61 63 0.527565 AGCAATGGTCAACAATCGCC 59.472 50.000 0.00 0.00 0.00 5.54
64 77 0.251564 AATGGTCAACAATCGCCCCA 60.252 50.000 0.00 0.00 0.00 4.96
79 92 1.526887 CCCACACACCACACTGACT 59.473 57.895 0.00 0.00 0.00 3.41
83 96 0.179111 ACACACCACACTGACTGACG 60.179 55.000 0.00 0.00 0.00 4.35
84 97 0.102300 CACACCACACTGACTGACGA 59.898 55.000 0.00 0.00 0.00 4.20
85 98 0.102481 ACACCACACTGACTGACGAC 59.898 55.000 0.00 0.00 0.00 4.34
86 99 0.597637 CACCACACTGACTGACGACC 60.598 60.000 0.00 0.00 0.00 4.79
87 100 1.006102 CCACACTGACTGACGACCC 60.006 63.158 0.00 0.00 0.00 4.46
88 101 1.739667 CACACTGACTGACGACCCA 59.260 57.895 0.00 0.00 0.00 4.51
89 102 0.318441 CACACTGACTGACGACCCAT 59.682 55.000 0.00 0.00 0.00 4.00
90 103 0.318441 ACACTGACTGACGACCCATG 59.682 55.000 0.00 0.00 0.00 3.66
134 148 1.345838 ACCCCATCATCCCATCTCACT 60.346 52.381 0.00 0.00 0.00 3.41
135 149 1.350351 CCCCATCATCCCATCTCACTC 59.650 57.143 0.00 0.00 0.00 3.51
136 150 2.052468 CCCATCATCCCATCTCACTCA 58.948 52.381 0.00 0.00 0.00 3.41
137 151 2.224475 CCCATCATCCCATCTCACTCAC 60.224 54.545 0.00 0.00 0.00 3.51
138 152 2.224475 CCATCATCCCATCTCACTCACC 60.224 54.545 0.00 0.00 0.00 4.02
139 153 1.114627 TCATCCCATCTCACTCACCG 58.885 55.000 0.00 0.00 0.00 4.94
169 184 6.899075 ACTAAACTAAAACCCTTCCCAAAAGT 59.101 34.615 0.00 0.00 0.00 2.66
175 194 1.202891 ACCCTTCCCAAAAGTTCTCCG 60.203 52.381 0.00 0.00 0.00 4.63
182 201 1.666872 AAAAGTTCTCCGGCCGTCG 60.667 57.895 26.12 14.66 38.88 5.12
186 205 2.439701 TTCTCCGGCCGTCGATCT 60.440 61.111 26.12 0.00 42.43 2.75
187 206 2.478890 TTCTCCGGCCGTCGATCTC 61.479 63.158 26.12 0.00 42.43 2.75
188 207 3.967335 CTCCGGCCGTCGATCTCC 61.967 72.222 26.12 0.00 42.43 3.71
189 208 4.501285 TCCGGCCGTCGATCTCCT 62.501 66.667 26.12 0.00 42.43 3.69
190 209 3.967335 CCGGCCGTCGATCTCCTC 61.967 72.222 26.12 0.00 42.43 3.71
217 236 2.044946 GCTCCAACGGCCCAGATT 60.045 61.111 0.00 0.00 0.00 2.40
219 238 1.299648 CTCCAACGGCCCAGATTCA 59.700 57.895 0.00 0.00 0.00 2.57
224 243 2.075355 AACGGCCCAGATTCACCCAA 62.075 55.000 0.00 0.00 0.00 4.12
314 368 2.360483 TCGGCTGCAAGAAAACAAATGA 59.640 40.909 0.50 0.00 34.07 2.57
345 402 7.525158 AGAATTACTAATTTCTTCTCCCCCA 57.475 36.000 0.00 0.00 0.00 4.96
347 404 6.910259 ATTACTAATTTCTTCTCCCCCACT 57.090 37.500 0.00 0.00 0.00 4.00
348 405 4.576330 ACTAATTTCTTCTCCCCCACTG 57.424 45.455 0.00 0.00 0.00 3.66
351 408 0.772124 TTTCTTCTCCCCCACTGCCT 60.772 55.000 0.00 0.00 0.00 4.75
352 409 1.492133 TTCTTCTCCCCCACTGCCTG 61.492 60.000 0.00 0.00 0.00 4.85
402 463 1.623811 TCACACCTTCTTCCACTAGCC 59.376 52.381 0.00 0.00 0.00 3.93
573 658 2.456948 GGGCGAGCGCTTCTTTCTC 61.457 63.158 13.26 0.00 41.60 2.87
864 954 0.529378 CAGCCATGGTGAGCTTTTCC 59.471 55.000 14.67 0.00 37.18 3.13
875 965 3.932089 GTGAGCTTTTCCTGAGATCTGAC 59.068 47.826 0.00 0.00 31.12 3.51
916 1006 0.174389 TGCTCTTCAGATCTGCCGTC 59.826 55.000 18.36 6.39 0.00 4.79
929 1024 4.056125 CCGTCGTGAGAGCTGCCA 62.056 66.667 0.00 0.00 43.49 4.92
953 1048 4.544689 CGAGGTGCTCGCGAGGAG 62.545 72.222 35.10 18.35 46.75 3.69
954 1049 3.444805 GAGGTGCTCGCGAGGAGT 61.445 66.667 35.10 23.44 45.03 3.85
958 1053 2.089349 GTGCTCGCGAGGAGTTCAC 61.089 63.158 35.10 27.88 45.03 3.18
960 1055 2.202492 CTCGCGAGGAGTTCACGG 60.202 66.667 28.40 0.00 38.02 4.94
964 1059 1.446272 GCGAGGAGTTCACGGAAGG 60.446 63.158 0.00 0.00 0.00 3.46
966 1061 0.109226 CGAGGAGTTCACGGAAGGAC 60.109 60.000 0.00 0.00 0.00 3.85
967 1062 1.258676 GAGGAGTTCACGGAAGGACT 58.741 55.000 0.00 0.00 0.00 3.85
968 1063 0.969894 AGGAGTTCACGGAAGGACTG 59.030 55.000 0.00 0.00 0.00 3.51
969 1064 0.670854 GGAGTTCACGGAAGGACTGC 60.671 60.000 0.00 0.00 0.00 4.40
970 1065 0.318762 GAGTTCACGGAAGGACTGCT 59.681 55.000 0.00 0.00 0.00 4.24
971 1066 0.759346 AGTTCACGGAAGGACTGCTT 59.241 50.000 0.00 0.00 0.00 3.91
972 1067 1.149148 GTTCACGGAAGGACTGCTTC 58.851 55.000 1.70 1.70 0.00 3.86
973 1068 0.034896 TTCACGGAAGGACTGCTTCC 59.965 55.000 17.40 17.40 46.33 3.46
989 1084 2.337532 CCGTTCCGGTGTCGTTCT 59.662 61.111 0.00 0.00 42.73 3.01
990 1085 2.019951 CCGTTCCGGTGTCGTTCTG 61.020 63.158 0.00 0.00 42.73 3.02
991 1086 2.654912 CGTTCCGGTGTCGTTCTGC 61.655 63.158 0.00 0.00 33.95 4.26
992 1087 2.355363 TTCCGGTGTCGTTCTGCG 60.355 61.111 0.00 0.00 43.01 5.18
993 1088 3.851845 TTCCGGTGTCGTTCTGCGG 62.852 63.158 0.00 0.00 41.72 5.69
994 1089 4.657824 CCGGTGTCGTTCTGCGGT 62.658 66.667 0.00 0.00 41.72 5.68
995 1090 3.403057 CGGTGTCGTTCTGCGGTG 61.403 66.667 0.00 0.00 41.72 4.94
996 1091 2.028484 GGTGTCGTTCTGCGGTGA 59.972 61.111 0.00 0.00 41.72 4.02
997 1092 1.593209 GGTGTCGTTCTGCGGTGAA 60.593 57.895 0.00 0.00 41.72 3.18
998 1093 0.949105 GGTGTCGTTCTGCGGTGAAT 60.949 55.000 0.00 0.00 41.72 2.57
1008 1103 2.503765 TCTGCGGTGAATAATGGAGGAA 59.496 45.455 0.00 0.00 0.00 3.36
1066 1161 2.033141 GAGTGCTTGGCCTGCTCA 59.967 61.111 19.10 3.61 0.00 4.26
1146 1241 1.754201 GCCAAGTTCAGGAAGGTGGTT 60.754 52.381 10.84 0.00 31.40 3.67
1305 1415 2.507992 CCTTCGACCAGCTCTGCG 60.508 66.667 0.00 0.00 0.00 5.18
1328 1441 4.684485 GCAGGTGTATCCTAGAAACAGCAT 60.684 45.833 17.60 6.05 46.24 3.79
1329 1442 5.431765 CAGGTGTATCCTAGAAACAGCATT 58.568 41.667 17.60 2.50 46.24 3.56
1330 1443 5.882557 CAGGTGTATCCTAGAAACAGCATTT 59.117 40.000 17.60 0.00 46.24 2.32
1410 1529 1.705337 CGCATTTCCAGTTCGGCGAT 61.705 55.000 11.76 0.00 46.65 4.58
1491 1613 3.501445 AGATGTTCAAGAGAAGCAACAGC 59.499 43.478 0.00 0.00 35.78 4.40
1611 1733 0.250234 TGGATGCCAAGTCTTCCTCG 59.750 55.000 0.00 0.00 33.03 4.63
1626 1748 0.657840 CCTCGTTCCATTTGATCGGC 59.342 55.000 0.00 0.00 36.92 5.54
1656 1778 3.950794 GAGCGACCCGGTGAATGCA 62.951 63.158 0.00 0.00 37.83 3.96
1665 1787 1.975407 GGTGAATGCACAGCAGGCT 60.975 57.895 6.08 0.00 46.96 4.58
1674 1796 1.537397 ACAGCAGGCTCCAAGGAGA 60.537 57.895 19.99 0.00 44.53 3.71
1675 1797 1.130054 ACAGCAGGCTCCAAGGAGAA 61.130 55.000 19.99 0.00 44.53 2.87
1780 1902 4.997395 TCTGCTATCTTTGGTGTTTCTGAC 59.003 41.667 0.00 0.00 0.00 3.51
1787 1909 6.834168 TCTTTGGTGTTTCTGACTCTTTTT 57.166 33.333 0.00 0.00 0.00 1.94
1805 1927 7.549488 ACTCTTTTTATTCAAGATAGGACACCG 59.451 37.037 0.00 0.00 29.78 4.94
1978 2110 9.413734 CTCATCCCAGGTATTCTAATTTTTCTT 57.586 33.333 0.00 0.00 0.00 2.52
1985 2117 8.915654 CAGGTATTCTAATTTTTCTTGTTGTGC 58.084 33.333 0.00 0.00 0.00 4.57
1986 2118 8.637986 AGGTATTCTAATTTTTCTTGTTGTGCA 58.362 29.630 0.00 0.00 0.00 4.57
1987 2119 9.255304 GGTATTCTAATTTTTCTTGTTGTGCAA 57.745 29.630 0.00 0.00 35.50 4.08
1997 2129 8.770438 TTTTCTTGTTGTGCAAATAAAGAAGT 57.230 26.923 12.03 0.00 36.53 3.01
1998 2130 7.754069 TTCTTGTTGTGCAAATAAAGAAGTG 57.246 32.000 9.40 0.00 36.53 3.16
1999 2131 5.748152 TCTTGTTGTGCAAATAAAGAAGTGC 59.252 36.000 0.00 0.00 36.53 4.40
2020 2152 3.549997 AACTGCACGTTCAACATGC 57.450 47.368 0.46 0.46 39.88 4.06
2022 2154 1.024271 ACTGCACGTTCAACATGCTT 58.976 45.000 10.38 0.00 40.13 3.91
2023 2155 1.002468 ACTGCACGTTCAACATGCTTC 60.002 47.619 10.38 0.00 40.13 3.86
2025 2157 1.403323 TGCACGTTCAACATGCTTCAA 59.597 42.857 10.38 0.00 40.13 2.69
2026 2158 1.780860 GCACGTTCAACATGCTTCAAC 59.219 47.619 0.16 0.00 36.40 3.18
2027 2159 2.541588 GCACGTTCAACATGCTTCAACT 60.542 45.455 0.16 0.00 36.40 3.16
2029 2161 4.788201 GCACGTTCAACATGCTTCAACTTA 60.788 41.667 0.16 0.00 36.40 2.24
2033 2165 5.396362 CGTTCAACATGCTTCAACTTAGTTG 59.604 40.000 18.12 18.12 43.99 3.16
2034 2166 5.437289 TCAACATGCTTCAACTTAGTTGG 57.563 39.130 22.82 10.51 42.99 3.77
2035 2167 3.923017 ACATGCTTCAACTTAGTTGGC 57.077 42.857 22.82 19.04 42.99 4.52
2036 2168 3.490348 ACATGCTTCAACTTAGTTGGCT 58.510 40.909 22.82 8.32 42.99 4.75
2038 2170 5.070001 ACATGCTTCAACTTAGTTGGCTTA 58.930 37.500 22.82 9.65 42.99 3.09
2039 2171 5.534654 ACATGCTTCAACTTAGTTGGCTTAA 59.465 36.000 22.82 10.30 42.99 1.85
2040 2172 6.209391 ACATGCTTCAACTTAGTTGGCTTAAT 59.791 34.615 22.82 8.12 42.99 1.40
2042 2174 5.767665 TGCTTCAACTTAGTTGGCTTAATCA 59.232 36.000 22.82 10.11 42.99 2.57
2043 2175 6.086871 GCTTCAACTTAGTTGGCTTAATCAC 58.913 40.000 22.82 2.09 42.99 3.06
2044 2176 6.569179 TTCAACTTAGTTGGCTTAATCACC 57.431 37.500 22.82 0.00 42.99 4.02
2045 2177 5.626142 TCAACTTAGTTGGCTTAATCACCA 58.374 37.500 22.82 0.00 42.99 4.17
2046 2178 6.245408 TCAACTTAGTTGGCTTAATCACCAT 58.755 36.000 22.82 0.00 42.99 3.55
2047 2179 7.398829 TCAACTTAGTTGGCTTAATCACCATA 58.601 34.615 22.82 0.00 42.99 2.74
2048 2180 7.885922 TCAACTTAGTTGGCTTAATCACCATAA 59.114 33.333 22.82 0.00 42.99 1.90
2049 2181 7.625828 ACTTAGTTGGCTTAATCACCATAAC 57.374 36.000 0.00 0.00 35.42 1.89
2050 2182 7.172342 ACTTAGTTGGCTTAATCACCATAACA 58.828 34.615 0.00 0.00 35.42 2.41
2051 2183 5.897377 AGTTGGCTTAATCACCATAACAC 57.103 39.130 0.00 0.00 35.42 3.32
2052 2184 5.321102 AGTTGGCTTAATCACCATAACACA 58.679 37.500 0.00 0.00 35.42 3.72
2053 2185 5.772672 AGTTGGCTTAATCACCATAACACAA 59.227 36.000 0.00 0.00 35.42 3.33
2054 2186 6.437162 AGTTGGCTTAATCACCATAACACAAT 59.563 34.615 0.00 0.00 35.42 2.71
2055 2187 6.206395 TGGCTTAATCACCATAACACAATG 57.794 37.500 0.00 0.00 0.00 2.82
2056 2188 5.948758 TGGCTTAATCACCATAACACAATGA 59.051 36.000 0.00 0.00 0.00 2.57
2057 2189 6.095300 TGGCTTAATCACCATAACACAATGAG 59.905 38.462 0.00 0.00 0.00 2.90
2337 2469 3.002348 GGTGTCGATGCCTTAATTGCTAC 59.998 47.826 0.00 0.00 0.00 3.58
2380 2512 5.622914 CGTGGATGATGCCATTCTTTCTTTT 60.623 40.000 0.00 0.00 40.68 2.27
2386 2518 7.104043 TGATGCCATTCTTTCTTTTCTATGG 57.896 36.000 0.00 0.00 36.47 2.74
2400 2532 7.560368 TCTTTTCTATGGCACTTTTGGAAAAA 58.440 30.769 10.11 2.12 33.08 1.94
2404 2536 9.434420 TTTCTATGGCACTTTTGGAAAAATATG 57.566 29.630 0.00 0.00 0.00 1.78
2480 2612 6.327279 TCGTGATTCACTTACTCTTTCTCA 57.673 37.500 14.54 0.00 31.34 3.27
2503 2637 9.658799 CTCACACCATATAATAATCCTAACCAG 57.341 37.037 0.00 0.00 0.00 4.00
2631 2769 7.592903 GCACAGATCTTTTCCTCTTTTTAACAG 59.407 37.037 0.00 0.00 0.00 3.16
2636 2774 7.931578 TCTTTTCCTCTTTTTAACAGACACA 57.068 32.000 0.00 0.00 0.00 3.72
2656 2794 5.130975 ACACAGGATATAGAAACATGGCTCA 59.869 40.000 0.00 0.00 0.00 4.26
2671 2809 7.325660 ACATGGCTCATTGTACTTCTATTTG 57.674 36.000 0.00 0.00 0.00 2.32
2769 2908 1.401905 GGGTACTACAAATGCAGCAGC 59.598 52.381 0.00 0.00 42.57 5.25
2934 3073 4.214310 TCTTTTCAGGAAATGCCAACTCA 58.786 39.130 0.00 0.00 40.02 3.41
3197 3337 7.703755 AGAGTTGGAAGGGAAGATAGAAATTT 58.296 34.615 0.00 0.00 0.00 1.82
3285 3425 2.027285 AGTGCACAAAAAGGCTGGTTTT 60.027 40.909 21.04 0.00 0.00 2.43
3347 3492 3.181434 ACATTGGTGTGTTGTACCTCCAT 60.181 43.478 0.00 0.00 39.01 3.41
3395 3540 8.331730 ACCAAGTTAAATATCTTGTGTGTACC 57.668 34.615 9.31 0.00 39.25 3.34
3396 3541 7.940137 ACCAAGTTAAATATCTTGTGTGTACCA 59.060 33.333 9.31 0.00 39.25 3.25
3397 3542 8.788806 CCAAGTTAAATATCTTGTGTGTACCAA 58.211 33.333 9.31 0.00 39.25 3.67
3511 3681 8.754991 TTTTCTAGAGAATCCTACTACCTCTG 57.245 38.462 0.00 0.00 35.93 3.35
3519 3689 7.133483 AGAATCCTACTACCTCTGTACCAAAT 58.867 38.462 0.00 0.00 0.00 2.32
3520 3690 6.732896 ATCCTACTACCTCTGTACCAAATG 57.267 41.667 0.00 0.00 0.00 2.32
3532 3703 7.341445 TCTGTACCAAATGTAAGCTGTTTTT 57.659 32.000 0.00 0.00 0.00 1.94
3604 3775 9.444600 GGGAGTACAAAGTAAATAAATGACTGA 57.555 33.333 0.00 0.00 0.00 3.41
3647 3821 2.103941 TGGAAAGCCATTGACCCAAAAC 59.896 45.455 0.00 0.00 39.92 2.43
3653 3827 1.069500 CCATTGACCCAAAACGTCGTC 60.069 52.381 0.00 0.00 32.68 4.20
3696 3870 1.959085 CTGTTTGGATTGCAGCCGT 59.041 52.632 3.59 0.00 0.00 5.68
3756 3930 0.321919 AGGCTTCGCTTGAATCAGCA 60.322 50.000 5.75 0.00 40.09 4.41
3761 3935 1.136147 CGCTTGAATCAGCACCAGC 59.864 57.895 5.75 0.65 40.09 4.85
3767 3941 1.661341 GAATCAGCACCAGCGATTCT 58.339 50.000 18.50 0.13 45.87 2.40
3768 3942 1.329906 GAATCAGCACCAGCGATTCTG 59.670 52.381 18.50 0.00 45.87 3.02
3769 3943 2.997224 GAATCAGCACCAGCGATTCTGA 60.997 50.000 18.50 0.00 45.87 3.27
3770 3944 4.477784 GAATCAGCACCAGCGATTCTGAA 61.478 47.826 18.50 0.00 45.87 3.02
3771 3945 6.482503 GAATCAGCACCAGCGATTCTGAAC 62.483 50.000 18.50 0.00 45.87 3.18
3772 3946 1.796796 GCACCAGCGATTCTGAACC 59.203 57.895 0.00 0.00 45.72 3.62
3773 3947 0.955428 GCACCAGCGATTCTGAACCA 60.955 55.000 0.00 0.00 45.72 3.67
3774 3948 0.798776 CACCAGCGATTCTGAACCAC 59.201 55.000 0.00 0.00 45.72 4.16
3779 3953 1.787847 CGATTCTGAACCACGCCAC 59.212 57.895 0.00 0.00 0.00 5.01
3804 3978 1.123928 TGGTTGCCCCGTTCAATTTT 58.876 45.000 0.00 0.00 35.15 1.82
3812 3986 2.234908 CCCCGTTCAATTTTTATGCCCA 59.765 45.455 0.00 0.00 0.00 5.36
3853 4066 2.387757 GGCAGAATCCTTGGCCAAATA 58.612 47.619 20.91 10.85 45.70 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 61 2.906897 CAGTGTGGTGTGTGGGGC 60.907 66.667 0.00 0.00 0.00 5.80
61 63 0.815213 CAGTCAGTGTGGTGTGTGGG 60.815 60.000 0.00 0.00 0.00 4.61
64 77 0.179111 CGTCAGTCAGTGTGGTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
79 92 1.987855 GGAGGGACATGGGTCGTCA 60.988 63.158 0.00 0.00 45.28 4.35
83 96 0.991920 TCAAAGGAGGGACATGGGTC 59.008 55.000 0.00 0.00 43.55 4.46
84 97 0.698818 GTCAAAGGAGGGACATGGGT 59.301 55.000 0.00 0.00 34.22 4.51
85 98 0.392998 CGTCAAAGGAGGGACATGGG 60.393 60.000 0.00 0.00 33.66 4.00
86 99 0.324943 ACGTCAAAGGAGGGACATGG 59.675 55.000 0.00 0.00 33.66 3.66
87 100 2.185004 AACGTCAAAGGAGGGACATG 57.815 50.000 0.00 0.00 33.66 3.21
88 101 2.884639 CAAAACGTCAAAGGAGGGACAT 59.115 45.455 0.00 0.00 33.66 3.06
89 102 2.092861 TCAAAACGTCAAAGGAGGGACA 60.093 45.455 0.00 0.00 33.66 4.02
90 103 2.289820 GTCAAAACGTCAAAGGAGGGAC 59.710 50.000 0.00 0.00 33.26 4.46
134 148 5.469760 GGGTTTTAGTTTAGTTTAGCGGTGA 59.530 40.000 0.00 0.00 0.00 4.02
135 149 5.471116 AGGGTTTTAGTTTAGTTTAGCGGTG 59.529 40.000 0.00 0.00 0.00 4.94
136 150 5.624159 AGGGTTTTAGTTTAGTTTAGCGGT 58.376 37.500 0.00 0.00 0.00 5.68
137 151 6.348786 GGAAGGGTTTTAGTTTAGTTTAGCGG 60.349 42.308 0.00 0.00 0.00 5.52
138 152 6.348786 GGGAAGGGTTTTAGTTTAGTTTAGCG 60.349 42.308 0.00 0.00 0.00 4.26
139 153 6.491062 TGGGAAGGGTTTTAGTTTAGTTTAGC 59.509 38.462 0.00 0.00 0.00 3.09
169 184 2.439701 AGATCGACGGCCGGAGAA 60.440 61.111 31.76 12.37 39.14 2.87
182 201 2.107953 GGTGCAGGCGAGGAGATC 59.892 66.667 0.00 0.00 0.00 2.75
205 224 2.075355 TTGGGTGAATCTGGGCCGTT 62.075 55.000 0.00 0.00 0.00 4.44
213 232 0.609131 CTTGGCCGTTGGGTGAATCT 60.609 55.000 0.00 0.00 34.97 2.40
217 236 2.203280 CACTTGGCCGTTGGGTGA 60.203 61.111 0.00 0.00 34.97 4.02
267 321 3.581755 GCCGGTCTGTATAATATTGCGA 58.418 45.455 1.90 0.00 0.00 5.10
314 368 8.080363 AGAAGAAATTAGTAATTCTCCGTCCT 57.920 34.615 8.56 0.00 0.00 3.85
573 658 2.757124 CCCTCCCAAGATTCCCCCG 61.757 68.421 0.00 0.00 0.00 5.73
840 930 2.113433 GCTCACCATGGCTGCTCTG 61.113 63.158 13.04 0.85 0.00 3.35
841 931 1.849975 AAGCTCACCATGGCTGCTCT 61.850 55.000 21.72 12.36 38.91 4.09
864 954 6.271488 AGAGAAAACTCAGTCAGATCTCAG 57.729 41.667 0.00 0.00 34.78 3.35
875 965 4.699257 CAGGAAATGGGAGAGAAAACTCAG 59.301 45.833 0.00 0.00 38.51 3.35
916 1006 1.080995 GCTACTTGGCAGCTCTCACG 61.081 60.000 0.00 0.00 36.07 4.35
947 1042 0.109226 GTCCTTCCGTGAACTCCTCG 60.109 60.000 0.00 0.00 0.00 4.63
951 1046 0.318762 AGCAGTCCTTCCGTGAACTC 59.681 55.000 0.00 0.00 0.00 3.01
953 1048 1.149148 GAAGCAGTCCTTCCGTGAAC 58.851 55.000 0.00 0.00 43.39 3.18
954 1049 3.606886 GAAGCAGTCCTTCCGTGAA 57.393 52.632 0.00 0.00 43.39 3.18
974 1069 3.241177 GCAGAACGACACCGGAAC 58.759 61.111 9.46 0.00 40.78 3.62
984 1079 2.276201 TCCATTATTCACCGCAGAACG 58.724 47.619 0.00 0.00 43.15 3.95
985 1080 2.614057 CCTCCATTATTCACCGCAGAAC 59.386 50.000 0.00 0.00 0.00 3.01
986 1081 2.503765 TCCTCCATTATTCACCGCAGAA 59.496 45.455 0.00 0.00 0.00 3.02
987 1082 2.115427 TCCTCCATTATTCACCGCAGA 58.885 47.619 0.00 0.00 0.00 4.26
988 1083 2.620251 TCCTCCATTATTCACCGCAG 57.380 50.000 0.00 0.00 0.00 5.18
989 1084 2.238646 ACTTCCTCCATTATTCACCGCA 59.761 45.455 0.00 0.00 0.00 5.69
990 1085 2.614057 CACTTCCTCCATTATTCACCGC 59.386 50.000 0.00 0.00 0.00 5.68
991 1086 3.118408 TCCACTTCCTCCATTATTCACCG 60.118 47.826 0.00 0.00 0.00 4.94
992 1087 4.455606 CTCCACTTCCTCCATTATTCACC 58.544 47.826 0.00 0.00 0.00 4.02
993 1088 4.164221 TCCTCCACTTCCTCCATTATTCAC 59.836 45.833 0.00 0.00 0.00 3.18
994 1089 4.370776 TCCTCCACTTCCTCCATTATTCA 58.629 43.478 0.00 0.00 0.00 2.57
995 1090 4.202409 CCTCCTCCACTTCCTCCATTATTC 60.202 50.000 0.00 0.00 0.00 1.75
996 1091 3.718956 CCTCCTCCACTTCCTCCATTATT 59.281 47.826 0.00 0.00 0.00 1.40
997 1092 3.321950 CCTCCTCCACTTCCTCCATTAT 58.678 50.000 0.00 0.00 0.00 1.28
998 1093 2.764269 CCTCCTCCACTTCCTCCATTA 58.236 52.381 0.00 0.00 0.00 1.90
1008 1103 2.227036 CCTGTTGGCCTCCTCCACT 61.227 63.158 3.32 0.00 35.50 4.00
1048 1143 3.123620 GAGCAGGCCAAGCACTCG 61.124 66.667 20.51 0.00 0.00 4.18
1188 1298 1.874562 GCTCACAAGCTTGGCTCTG 59.125 57.895 29.18 18.28 45.55 3.35
1328 1441 1.861542 CGCGGGCTGTGAATCCAAAA 61.862 55.000 0.00 0.00 0.00 2.44
1329 1442 2.331893 CGCGGGCTGTGAATCCAAA 61.332 57.895 0.00 0.00 0.00 3.28
1330 1443 2.745884 CGCGGGCTGTGAATCCAA 60.746 61.111 0.00 0.00 0.00 3.53
1383 1502 0.960364 ACTGGAAATGCGCGGACAAT 60.960 50.000 8.83 0.00 0.00 2.71
1410 1529 3.365832 GAACTGATTATACCGCGACGAA 58.634 45.455 8.23 0.00 0.00 3.85
1491 1613 3.563808 TGTCAAACTTCAAGTTGATCCCG 59.436 43.478 2.78 0.00 38.66 5.14
1533 1655 2.181021 GACCTCGCGGACGACATT 59.819 61.111 6.13 0.00 45.12 2.71
1611 1733 1.727467 CCCGCCGATCAAATGGAAC 59.273 57.895 0.00 0.00 0.00 3.62
1656 1778 1.130054 TTCTCCTTGGAGCCTGCTGT 61.130 55.000 11.61 0.00 0.00 4.40
1665 1787 0.826715 CCGAGCATCTTCTCCTTGGA 59.173 55.000 0.00 0.00 32.82 3.53
1674 1796 2.579201 CCACGTCCCGAGCATCTT 59.421 61.111 0.00 0.00 0.00 2.40
1675 1797 3.461773 CCCACGTCCCGAGCATCT 61.462 66.667 0.00 0.00 0.00 2.90
1737 1859 7.327214 AGCAGATTTACTACCTTCTCTTTGAG 58.673 38.462 0.00 0.00 0.00 3.02
1740 1862 9.207868 AGATAGCAGATTTACTACCTTCTCTTT 57.792 33.333 0.00 0.00 0.00 2.52
1780 1902 7.549488 ACGGTGTCCTATCTTGAATAAAAAGAG 59.451 37.037 0.00 0.00 37.10 2.85
1787 1909 7.591421 TTATCACGGTGTCCTATCTTGAATA 57.409 36.000 8.17 0.00 0.00 1.75
1805 1927 9.832445 TGAAATAGGGTAGAGAACAATTATCAC 57.168 33.333 0.00 0.00 0.00 3.06
1833 1955 1.275291 CTCTTCACCCGCAACTTCCTA 59.725 52.381 0.00 0.00 0.00 2.94
1978 2110 5.003692 TGCACTTCTTTATTTGCACAACA 57.996 34.783 0.00 0.00 40.01 3.33
1985 2117 5.522456 TGCAGTTCTGCACTTCTTTATTTG 58.478 37.500 21.30 0.00 40.23 2.32
1986 2118 5.772825 TGCAGTTCTGCACTTCTTTATTT 57.227 34.783 21.30 0.00 40.23 1.40
2010 2142 5.687285 CCAACTAAGTTGAAGCATGTTGAAC 59.313 40.000 0.00 0.00 45.28 3.18
2013 2145 3.983344 GCCAACTAAGTTGAAGCATGTTG 59.017 43.478 0.00 0.00 45.28 3.33
2014 2146 3.891366 AGCCAACTAAGTTGAAGCATGTT 59.109 39.130 0.00 0.00 45.28 2.71
2016 2148 4.510038 AAGCCAACTAAGTTGAAGCATG 57.490 40.909 0.00 0.00 45.28 4.06
2018 2150 5.767665 TGATTAAGCCAACTAAGTTGAAGCA 59.232 36.000 0.00 0.00 45.28 3.91
2019 2151 6.086871 GTGATTAAGCCAACTAAGTTGAAGC 58.913 40.000 0.00 0.00 45.28 3.86
2020 2152 6.206634 TGGTGATTAAGCCAACTAAGTTGAAG 59.793 38.462 0.00 0.00 45.28 3.02
2022 2154 5.626142 TGGTGATTAAGCCAACTAAGTTGA 58.374 37.500 0.00 0.00 45.28 3.18
2023 2155 5.957842 TGGTGATTAAGCCAACTAAGTTG 57.042 39.130 0.00 0.00 42.49 3.16
2025 2157 7.120726 GTGTTATGGTGATTAAGCCAACTAAGT 59.879 37.037 1.15 0.00 38.38 2.24
2026 2158 7.120579 TGTGTTATGGTGATTAAGCCAACTAAG 59.879 37.037 1.15 0.00 38.38 2.18
2027 2159 6.943146 TGTGTTATGGTGATTAAGCCAACTAA 59.057 34.615 1.15 0.00 38.38 2.24
2029 2161 5.321102 TGTGTTATGGTGATTAAGCCAACT 58.679 37.500 1.15 0.00 38.38 3.16
2033 2165 6.095440 ACTCATTGTGTTATGGTGATTAAGCC 59.905 38.462 0.00 0.00 0.00 4.35
2034 2166 7.088589 ACTCATTGTGTTATGGTGATTAAGC 57.911 36.000 0.00 0.00 0.00 3.09
2035 2167 9.988350 GTTACTCATTGTGTTATGGTGATTAAG 57.012 33.333 0.00 0.00 0.00 1.85
2036 2168 9.508642 TGTTACTCATTGTGTTATGGTGATTAA 57.491 29.630 0.00 0.00 0.00 1.40
2038 2170 7.994425 TGTTACTCATTGTGTTATGGTGATT 57.006 32.000 0.00 0.00 0.00 2.57
2039 2171 8.579850 AATGTTACTCATTGTGTTATGGTGAT 57.420 30.769 0.00 0.00 44.06 3.06
2040 2172 7.994425 AATGTTACTCATTGTGTTATGGTGA 57.006 32.000 0.00 0.00 44.06 4.02
2086 2218 7.093771 TGGTGATTATAGCATCATCACGACTAT 60.094 37.037 12.90 0.00 45.29 2.12
2092 2224 8.446273 GTGTTATGGTGATTATAGCATCATCAC 58.554 37.037 3.05 4.66 45.16 3.06
2337 2469 9.580916 CATCCACGAAGTAATTATTTAATGTCG 57.419 33.333 0.00 0.00 41.61 4.35
2380 2512 8.133024 ACATATTTTTCCAAAAGTGCCATAGA 57.867 30.769 0.00 0.00 0.00 1.98
2386 2518 8.309163 TGATTGACATATTTTTCCAAAAGTGC 57.691 30.769 0.00 0.00 0.00 4.40
2424 2556 7.001099 TCTCGGTTAAATTAAGAAGTGGTCT 57.999 36.000 0.00 0.00 38.69 3.85
2440 2572 3.818773 TCACGATAGCATGATCTCGGTTA 59.181 43.478 20.62 5.09 42.67 2.85
2480 2612 9.166222 TCACTGGTTAGGATTATTATATGGTGT 57.834 33.333 0.00 0.00 0.00 4.16
2499 2633 1.719063 ATGGTGGGCAAGTCACTGGT 61.719 55.000 0.00 0.00 35.61 4.00
2503 2637 1.589716 GAGCATGGTGGGCAAGTCAC 61.590 60.000 0.00 0.00 34.61 3.67
2556 2692 9.307121 GATTGCCATTACTGTATACTAGCTATG 57.693 37.037 4.17 7.15 0.00 2.23
2631 2769 5.615289 AGCCATGTTTCTATATCCTGTGTC 58.385 41.667 0.00 0.00 0.00 3.67
2636 2774 6.845908 ACAATGAGCCATGTTTCTATATCCT 58.154 36.000 0.00 0.00 0.00 3.24
2671 2809 9.191995 CTTAGAAACATGTTGGGTTTGAAATAC 57.808 33.333 12.82 0.00 38.50 1.89
2934 3073 0.814010 GTCTGTCAACAAGTGCCGGT 60.814 55.000 1.90 0.00 0.00 5.28
3197 3337 5.708736 ACTTTACACACATATCATCCCCA 57.291 39.130 0.00 0.00 0.00 4.96
3347 3492 3.010200 TGTCTCTGATGAGCTAGAGCA 57.990 47.619 6.39 5.61 45.16 4.26
3476 3641 8.855804 AGGATTCTCTAGAAAATACTGGGTTA 57.144 34.615 2.50 0.00 37.61 2.85
3477 3642 7.757242 AGGATTCTCTAGAAAATACTGGGTT 57.243 36.000 2.50 0.00 37.61 4.11
3478 3643 8.068733 AGTAGGATTCTCTAGAAAATACTGGGT 58.931 37.037 13.06 0.00 37.61 4.51
3479 3644 8.485578 AGTAGGATTCTCTAGAAAATACTGGG 57.514 38.462 13.06 0.00 37.61 4.45
3575 3746 9.668497 GTCATTTATTTACTTTGTACTCCCTCT 57.332 33.333 0.00 0.00 0.00 3.69
3647 3821 0.924363 CGCTGGAATCTACGACGACG 60.924 60.000 5.58 5.58 45.75 5.12
3653 3827 3.736252 CCTTACATTCGCTGGAATCTACG 59.264 47.826 0.00 0.00 40.90 3.51
3696 3870 0.178975 AAAATCGGTTGGGTGAGCCA 60.179 50.000 0.00 0.00 36.17 4.75
3721 3895 0.465460 GCCTGTGGGAACAGTCAACA 60.465 55.000 5.24 0.00 44.46 3.33
3756 3930 0.670546 CGTGGTTCAGAATCGCTGGT 60.671 55.000 5.44 0.00 44.98 4.00
3761 3935 0.670546 AGTGGCGTGGTTCAGAATCG 60.671 55.000 0.00 0.00 0.00 3.34
3762 3936 2.380084 TAGTGGCGTGGTTCAGAATC 57.620 50.000 0.00 0.00 0.00 2.52
3763 3937 3.350219 AATAGTGGCGTGGTTCAGAAT 57.650 42.857 0.00 0.00 0.00 2.40
3764 3938 2.851263 AATAGTGGCGTGGTTCAGAA 57.149 45.000 0.00 0.00 0.00 3.02
3765 3939 2.811431 CAAAATAGTGGCGTGGTTCAGA 59.189 45.455 0.00 0.00 0.00 3.27
3766 3940 2.095263 CCAAAATAGTGGCGTGGTTCAG 60.095 50.000 0.00 0.00 0.00 3.02
3767 3941 1.883275 CCAAAATAGTGGCGTGGTTCA 59.117 47.619 0.00 0.00 0.00 3.18
3768 3942 1.883926 ACCAAAATAGTGGCGTGGTTC 59.116 47.619 0.00 0.00 43.00 3.62
3769 3943 1.989706 ACCAAAATAGTGGCGTGGTT 58.010 45.000 0.00 0.00 43.00 3.67
3770 3944 1.611491 CAACCAAAATAGTGGCGTGGT 59.389 47.619 0.00 0.00 44.47 4.16
3771 3945 1.668628 GCAACCAAAATAGTGGCGTGG 60.669 52.381 0.00 0.00 43.00 4.94
3772 3946 1.668628 GGCAACCAAAATAGTGGCGTG 60.669 52.381 0.00 0.00 43.00 5.34
3773 3947 0.601057 GGCAACCAAAATAGTGGCGT 59.399 50.000 0.00 0.00 43.00 5.68
3774 3948 3.416955 GGCAACCAAAATAGTGGCG 57.583 52.632 0.00 0.00 43.00 5.69


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

AutoCloner maintained by Alex Coulton.