Multiple sequence alignment - TraesCS6A01G125900

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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 TraesCS6A01G125900 chr6A 100.000 2386 0 0 1 2386 99406436 99408821 0.000000e+00 4407.0
1 TraesCS6A01G125900 chr6A 87.500 632 41 8 407 1028 99431027 99430424 0.000000e+00 695.0
2 TraesCS6A01G125900 chr6A 83.199 744 47 32 1106 1790 99430391 99429667 5.640000e-171 610.0
3 TraesCS6A01G125900 chr6A 85.316 395 26 12 2006 2386 99429215 99428839 1.730000e-101 379.0
4 TraesCS6A01G125900 chr6A 80.831 313 29 17 181 465 99431314 99431005 1.440000e-52 217.0
5 TraesCS6A01G125900 chr6A 92.308 91 7 0 3 93 99431540 99431450 1.920000e-26 130.0
6 TraesCS6A01G125900 chr6B 91.150 1435 48 22 409 1826 157670976 157669604 0.000000e+00 1873.0
7 TraesCS6A01G125900 chr6B 86.936 643 46 17 395 1028 157656629 157657242 0.000000e+00 688.0
8 TraesCS6A01G125900 chr6B 88.087 596 33 14 1309 1881 157657430 157658010 0.000000e+00 673.0
9 TraesCS6A01G125900 chr6B 83.878 459 29 18 1941 2386 157669122 157668696 1.720000e-106 396.0
10 TraesCS6A01G125900 chr6B 87.611 339 30 6 2 336 157671596 157671266 1.340000e-102 383.0
11 TraesCS6A01G125900 chr6B 83.632 391 33 16 2006 2386 157658069 157658438 2.940000e-89 339.0
12 TraesCS6A01G125900 chr6B 100.000 42 0 0 333 374 157671139 157671098 7.070000e-11 78.7
13 TraesCS6A01G125900 chr6D 88.665 1041 59 23 1 1015 82647972 82646965 0.000000e+00 1214.0
14 TraesCS6A01G125900 chr6D 88.821 823 43 15 1000 1810 82646783 82645998 0.000000e+00 965.0
15 TraesCS6A01G125900 chr6D 85.697 839 65 24 231 1028 82629211 82630035 0.000000e+00 833.0
16 TraesCS6A01G125900 chr6D 88.889 585 36 10 1312 1881 82630226 82630796 0.000000e+00 693.0
17 TraesCS6A01G125900 chr6D 87.430 358 15 12 2029 2386 82643847 82643520 3.720000e-103 385.0
18 TraesCS6A01G125900 chr6D 84.249 273 22 8 2015 2278 82630842 82631102 1.830000e-61 246.0
19 TraesCS6A01G125900 chr6D 88.660 97 10 1 1 97 82603927 82604022 1.500000e-22 117.0


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 TraesCS6A01G125900 chr6A 99406436 99408821 2385 False 4407.000000 4407 100.000000 1 2386 1 chr6A.!!$F1 2385
1 TraesCS6A01G125900 chr6A 99428839 99431540 2701 True 406.200000 695 85.830800 3 2386 5 chr6A.!!$R1 2383
2 TraesCS6A01G125900 chr6B 157668696 157671596 2900 True 682.675000 1873 90.659750 2 2386 4 chr6B.!!$R1 2384
3 TraesCS6A01G125900 chr6B 157656629 157658438 1809 False 566.666667 688 86.218333 395 2386 3 chr6B.!!$F1 1991
4 TraesCS6A01G125900 chr6D 82643520 82647972 4452 True 854.666667 1214 88.305333 1 2386 3 chr6D.!!$R1 2385
5 TraesCS6A01G125900 chr6D 82629211 82631102 1891 False 590.666667 833 86.278333 231 2278 3 chr6D.!!$F2 2047

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
810 1179 0.038744 CCACATGTTTGAGGGAGCCT 59.961 55.0 0.0 0.0 36.03 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2996 0.036483 TTCGTTCTGCATGCCTAGCA 60.036 50.0 16.68 0.0 44.86 3.49 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.890424 ACCTTTCCGGTTACATACATTTG 57.110 39.130 0.00 0.00 46.37 2.32
88 93 3.512033 AGCTCGTCCATACTCAAGAAC 57.488 47.619 0.00 0.00 0.00 3.01
93 98 2.418746 CGTCCATACTCAAGAACAGGGG 60.419 54.545 0.00 0.00 0.00 4.79
97 102 3.264450 CCATACTCAAGAACAGGGGAACT 59.736 47.826 0.00 0.00 0.00 3.01
99 104 5.045869 CCATACTCAAGAACAGGGGAACTTA 60.046 44.000 0.00 0.00 0.00 2.24
108 113 6.086775 AGAACAGGGGAACTTAGTACCTAAA 58.913 40.000 6.09 0.00 0.00 1.85
128 134 8.688151 ACCTAAACATACTCATAGTTCTCTGTC 58.312 37.037 0.00 0.00 0.00 3.51
131 137 6.366315 ACATACTCATAGTTCTCTGTCGAC 57.634 41.667 9.11 9.11 0.00 4.20
141 147 6.432607 AGTTCTCTGTCGACGTATCAATTA 57.567 37.500 11.62 0.00 0.00 1.40
201 261 4.646492 AGGTTTGCTGGGTATCATTCATTC 59.354 41.667 0.00 0.00 0.00 2.67
230 290 6.056090 TGGTACTGCTGTAATATTTCCACA 57.944 37.500 4.88 0.00 0.00 4.17
260 328 7.761651 TTGAATGAGATTACTGACAGAATCG 57.238 36.000 10.08 0.00 37.19 3.34
291 362 3.746045 TCCTGTAGTCACACCAAAGTC 57.254 47.619 0.00 0.00 0.00 3.01
292 363 3.305720 TCCTGTAGTCACACCAAAGTCT 58.694 45.455 0.00 0.00 0.00 3.24
319 393 8.857098 GGATATGTATGTTCAACCTCACTAGTA 58.143 37.037 0.00 0.00 0.00 1.82
320 394 9.900710 GATATGTATGTTCAACCTCACTAGTAG 57.099 37.037 0.00 0.00 0.00 2.57
321 395 7.719871 ATGTATGTTCAACCTCACTAGTAGT 57.280 36.000 0.00 0.00 0.00 2.73
374 578 3.703001 TTTGGCTCCTCAGGTTTCTAG 57.297 47.619 0.00 0.00 0.00 2.43
375 579 2.327325 TGGCTCCTCAGGTTTCTAGT 57.673 50.000 0.00 0.00 0.00 2.57
376 580 2.621070 TGGCTCCTCAGGTTTCTAGTT 58.379 47.619 0.00 0.00 0.00 2.24
387 673 7.041303 CCTCAGGTTTCTAGTTCTTTTTACCAC 60.041 40.741 0.00 0.00 0.00 4.16
441 781 7.421530 TTTACTGTTCATCTGTTGCTACTTC 57.578 36.000 0.00 0.00 0.00 3.01
465 805 9.491675 TTCGTTACTTTCCATTTACTGTTCATA 57.508 29.630 0.00 0.00 0.00 2.15
687 1046 1.081641 CAAGGCTTGCTGTTGCTCG 60.082 57.895 15.25 0.00 40.48 5.03
724 1084 1.613317 ATCGTTGGGGATCGTGCTCA 61.613 55.000 0.00 0.00 0.00 4.26
799 1168 1.852157 TGCCCTCCTCCCACATGTT 60.852 57.895 0.00 0.00 0.00 2.71
800 1169 1.384191 GCCCTCCTCCCACATGTTT 59.616 57.895 0.00 0.00 0.00 2.83
804 1173 1.340405 CCTCCTCCCACATGTTTGAGG 60.340 57.143 25.10 25.10 44.69 3.86
809 1178 2.571548 CCACATGTTTGAGGGAGCC 58.428 57.895 0.00 0.00 30.58 4.70
810 1179 0.038744 CCACATGTTTGAGGGAGCCT 59.961 55.000 0.00 0.00 36.03 4.58
811 1180 1.548582 CCACATGTTTGAGGGAGCCTT 60.549 52.381 0.00 0.00 31.76 4.35
812 1181 2.242043 CACATGTTTGAGGGAGCCTTT 58.758 47.619 0.00 0.00 31.76 3.11
813 1182 2.029649 CACATGTTTGAGGGAGCCTTTG 60.030 50.000 0.00 0.00 31.76 2.77
814 1183 1.547372 CATGTTTGAGGGAGCCTTTGG 59.453 52.381 0.00 0.00 31.76 3.28
815 1184 0.178964 TGTTTGAGGGAGCCTTTGGG 60.179 55.000 0.00 0.00 31.76 4.12
816 1185 0.178961 GTTTGAGGGAGCCTTTGGGT 60.179 55.000 0.00 0.00 31.76 4.51
817 1186 0.560688 TTTGAGGGAGCCTTTGGGTT 59.439 50.000 0.00 0.00 31.76 4.11
818 1187 0.112412 TTGAGGGAGCCTTTGGGTTC 59.888 55.000 0.00 0.00 41.34 3.62
997 1580 7.998580 TGATTAAACTATGAATCTGCAATGCA 58.001 30.769 7.99 7.99 36.92 3.96
998 1581 8.468399 TGATTAAACTATGAATCTGCAATGCAA 58.532 29.630 9.92 0.73 38.41 4.08
1081 1665 4.022935 TGCAGGAAAGCTGTTGTTTATCTG 60.023 41.667 0.00 0.00 34.99 2.90
1082 1666 4.616835 GCAGGAAAGCTGTTGTTTATCTGG 60.617 45.833 0.00 0.00 0.00 3.86
1083 1667 4.761739 CAGGAAAGCTGTTGTTTATCTGGA 59.238 41.667 0.00 0.00 0.00 3.86
1084 1668 5.241506 CAGGAAAGCTGTTGTTTATCTGGAA 59.758 40.000 0.00 0.00 0.00 3.53
1085 1669 5.241728 AGGAAAGCTGTTGTTTATCTGGAAC 59.758 40.000 0.00 0.00 0.00 3.62
1086 1670 5.453567 AAAGCTGTTGTTTATCTGGAACC 57.546 39.130 0.00 0.00 0.00 3.62
1087 1671 3.074412 AGCTGTTGTTTATCTGGAACCG 58.926 45.455 0.00 0.00 0.00 4.44
1088 1672 2.161609 GCTGTTGTTTATCTGGAACCGG 59.838 50.000 0.00 0.00 0.00 5.28
1089 1673 2.156098 TGTTGTTTATCTGGAACCGGC 58.844 47.619 0.00 0.00 0.00 6.13
1090 1674 2.224670 TGTTGTTTATCTGGAACCGGCT 60.225 45.455 0.00 0.00 0.00 5.52
1091 1675 2.396590 TGTTTATCTGGAACCGGCTC 57.603 50.000 0.00 0.00 0.00 4.70
1092 1676 1.065709 TGTTTATCTGGAACCGGCTCC 60.066 52.381 17.45 17.45 35.88 4.70
1093 1677 1.209747 GTTTATCTGGAACCGGCTCCT 59.790 52.381 24.04 7.38 36.35 3.69
1094 1678 1.120530 TTATCTGGAACCGGCTCCTC 58.879 55.000 24.04 5.22 36.35 3.71
1095 1679 0.261991 TATCTGGAACCGGCTCCTCT 59.738 55.000 24.04 11.25 36.35 3.69
1096 1680 0.261991 ATCTGGAACCGGCTCCTCTA 59.738 55.000 24.04 10.22 36.35 2.43
1097 1681 0.683504 TCTGGAACCGGCTCCTCTAC 60.684 60.000 24.04 0.00 36.35 2.59
1098 1682 1.677637 CTGGAACCGGCTCCTCTACC 61.678 65.000 24.04 6.22 36.35 3.18
1103 1687 4.208686 CGGCTCCTCTACCGTGCC 62.209 72.222 0.00 0.00 44.46 5.01
1108 1692 0.962489 CTCCTCTACCGTGCCCTATG 59.038 60.000 0.00 0.00 0.00 2.23
1210 1800 5.870978 GCAAGGCACATTCTACATCAAAAAT 59.129 36.000 0.00 0.00 0.00 1.82
1304 1928 3.549625 GCAAGTGTCAGGAAGCAAAAGAG 60.550 47.826 0.00 0.00 0.00 2.85
1439 2075 3.203716 GGTTTGCTCCTACTAATTCCCG 58.796 50.000 0.00 0.00 0.00 5.14
1451 2091 4.767478 ACTAATTCCCGTAGAGCTTTTCC 58.233 43.478 0.00 0.00 0.00 3.13
1496 2136 1.938585 TCCAGATCGACTCCCTTTGT 58.061 50.000 0.00 0.00 0.00 2.83
1577 2217 3.118775 TGTCCTTTATCCACCACATCTCG 60.119 47.826 0.00 0.00 0.00 4.04
1618 2258 2.004733 GGCTTTTCATCTTTGGCATGC 58.995 47.619 9.90 9.90 0.00 4.06
1619 2259 2.613474 GGCTTTTCATCTTTGGCATGCA 60.613 45.455 21.36 2.54 0.00 3.96
1620 2260 3.267483 GCTTTTCATCTTTGGCATGCAT 58.733 40.909 21.36 0.00 0.00 3.96
1621 2261 3.063452 GCTTTTCATCTTTGGCATGCATG 59.937 43.478 22.70 22.70 0.00 4.06
1674 2314 3.055240 TGGTTGGGATCCATTCAAAATGC 60.055 43.478 15.23 0.00 31.53 3.56
1727 2375 9.878599 GTCAACCATATGTATGTAATTTGCTAC 57.121 33.333 1.24 0.00 31.82 3.58
1728 2376 9.062524 TCAACCATATGTATGTAATTTGCTACC 57.937 33.333 1.24 0.00 31.82 3.18
1773 2435 4.174009 ACCGATGTGTGAGATTAAAGACG 58.826 43.478 0.00 0.00 0.00 4.18
1784 2446 5.419788 TGAGATTAAAGACGCCTACAGGTTA 59.580 40.000 0.00 0.00 37.57 2.85
1886 2896 6.319658 ACATTGCGGACTGATCAAGAAATATT 59.680 34.615 0.24 0.00 0.00 1.28
1919 2929 8.376270 GGGCTAATCCAGTATGTAATTTCTAGT 58.624 37.037 0.00 0.00 36.21 2.57
1920 2930 9.780186 GGCTAATCCAGTATGTAATTTCTAGTT 57.220 33.333 0.00 0.00 34.01 2.24
1952 2986 6.571605 TGCTATATAATGCTGAGCTGATCTC 58.428 40.000 5.83 0.00 42.23 2.75
1953 2987 5.686841 GCTATATAATGCTGAGCTGATCTCG 59.313 44.000 5.83 0.00 44.86 4.04
1955 2989 6.765915 ATATAATGCTGAGCTGATCTCGTA 57.234 37.500 5.83 0.00 44.86 3.43
1956 2990 5.657826 ATAATGCTGAGCTGATCTCGTAT 57.342 39.130 5.83 0.00 44.86 3.06
1957 2991 6.765915 ATAATGCTGAGCTGATCTCGTATA 57.234 37.500 5.83 0.00 44.86 1.47
1959 2993 6.765915 AATGCTGAGCTGATCTCGTATATA 57.234 37.500 5.83 0.00 44.86 0.86
1960 2994 6.765915 ATGCTGAGCTGATCTCGTATATAA 57.234 37.500 5.83 0.00 44.86 0.98
1962 2996 7.163001 TGCTGAGCTGATCTCGTATATAATT 57.837 36.000 5.83 0.00 44.86 1.40
1963 2997 7.031975 TGCTGAGCTGATCTCGTATATAATTG 58.968 38.462 5.83 0.00 44.86 2.32
1964 2998 6.019961 GCTGAGCTGATCTCGTATATAATTGC 60.020 42.308 0.00 0.00 44.86 3.56
1965 2999 7.163001 TGAGCTGATCTCGTATATAATTGCT 57.837 36.000 0.00 0.00 44.86 3.91
1966 3000 8.281212 TGAGCTGATCTCGTATATAATTGCTA 57.719 34.615 0.00 0.00 44.86 3.49
1967 3001 8.401709 TGAGCTGATCTCGTATATAATTGCTAG 58.598 37.037 0.00 0.00 44.86 3.42
1968 3002 7.711846 AGCTGATCTCGTATATAATTGCTAGG 58.288 38.462 0.00 0.00 0.00 3.02
1969 3003 6.419413 GCTGATCTCGTATATAATTGCTAGGC 59.581 42.308 0.00 0.00 0.00 3.93
1970 3004 7.404671 TGATCTCGTATATAATTGCTAGGCA 57.595 36.000 0.00 0.00 36.47 4.75
1971 3005 8.011844 TGATCTCGTATATAATTGCTAGGCAT 57.988 34.615 0.00 0.00 38.76 4.40
1978 3012 4.843220 ATAATTGCTAGGCATGCAGAAC 57.157 40.909 21.36 6.55 41.71 3.01
1990 3024 2.668280 GCAGAACGAACCGTCTGGC 61.668 63.158 15.19 7.06 39.99 4.85
1992 3026 2.029964 GAACGAACCGTCTGGCCA 59.970 61.111 4.71 4.71 39.99 5.36
1997 3031 1.671742 GAACCGTCTGGCCAGAAGA 59.328 57.895 39.93 18.85 38.88 2.87
2002 3036 1.649664 CGTCTGGCCAGAAGAAGATG 58.350 55.000 36.73 17.56 38.88 2.90
2013 3442 5.182760 GCCAGAAGAAGATGAAGACATTGTT 59.817 40.000 0.00 0.00 36.82 2.83
2025 4786 8.970691 ATGAAGACATTGTTTACTAATTGCAC 57.029 30.769 0.00 0.00 32.21 4.57
2038 4799 6.327279 ACTAATTGCACTGGGAGTAAAAAC 57.673 37.500 0.00 0.00 0.00 2.43
2063 4824 0.176680 GATGTGATGAGGGCGACAGT 59.823 55.000 0.00 0.00 0.00 3.55
2120 4881 1.468520 GCACGGCAATAAAGAAGCTCA 59.531 47.619 0.00 0.00 0.00 4.26
2123 4884 3.624861 CACGGCAATAAAGAAGCTCATCT 59.375 43.478 0.00 0.00 0.00 2.90
2166 4936 5.294306 TCAAACTATGTGCTCGATCAATTCC 59.706 40.000 0.00 0.00 0.00 3.01
2193 4963 0.731514 GCACATGCATGCATATCGCC 60.732 55.000 31.73 14.92 45.39 5.54
2194 4964 0.453782 CACATGCATGCATATCGCCG 60.454 55.000 31.73 20.40 41.33 6.46
2195 4965 1.135939 CATGCATGCATATCGCCGG 59.864 57.895 31.73 14.61 41.33 6.13
2196 4966 2.693762 ATGCATGCATATCGCCGGC 61.694 57.895 31.35 19.07 41.33 6.13
2244 5014 0.833834 AGGCTCGGACTCCCATATGG 60.834 60.000 15.41 15.41 0.00 2.74
2245 5015 1.004440 GCTCGGACTCCCATATGGC 60.004 63.158 16.97 2.25 0.00 4.40
2246 5016 1.674057 CTCGGACTCCCATATGGCC 59.326 63.158 16.97 10.89 0.00 5.36
2247 5017 1.074850 TCGGACTCCCATATGGCCA 60.075 57.895 16.97 8.56 0.00 5.36
2248 5018 0.473694 TCGGACTCCCATATGGCCAT 60.474 55.000 24.45 24.45 0.00 4.40
2249 5019 1.203250 TCGGACTCCCATATGGCCATA 60.203 52.381 27.36 27.36 0.00 2.74
2250 5020 1.839994 CGGACTCCCATATGGCCATAT 59.160 52.381 29.24 29.24 34.50 1.78
2251 5021 2.420547 CGGACTCCCATATGGCCATATG 60.421 54.545 41.29 41.29 46.31 1.78
2252 5022 2.648059 GACTCCCATATGGCCATATGC 58.352 52.381 42.24 30.48 45.72 3.14
2253 5023 2.240667 GACTCCCATATGGCCATATGCT 59.759 50.000 42.24 29.31 45.72 3.79
2281 5065 5.048154 GCTAGCATGACACTATCTCAGATGA 60.048 44.000 10.63 0.00 0.00 2.92
2304 5088 4.237349 TGATGATCATCATTGTGCATGC 57.763 40.909 30.27 11.82 42.42 4.06
2305 5089 3.634448 TGATGATCATCATTGTGCATGCA 59.366 39.130 30.27 18.46 42.42 3.96
2306 5090 4.280677 TGATGATCATCATTGTGCATGCAT 59.719 37.500 30.27 4.77 42.42 3.96
2307 5091 3.976169 TGATCATCATTGTGCATGCATG 58.024 40.909 25.64 22.70 32.13 4.06
2308 5092 5.092799 ATGATCATCATTGTGCATGCATGC 61.093 41.667 38.71 38.71 43.48 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 104 9.924010 AGAGAACTATGAGTATGTTTAGGTACT 57.076 33.333 0.00 0.00 46.37 2.73
108 113 5.006844 CGTCGACAGAGAACTATGAGTATGT 59.993 44.000 17.16 0.00 0.00 2.29
128 134 7.853377 ATCATGTGTAGTAATTGATACGTCG 57.147 36.000 0.00 0.00 39.62 5.12
201 261 9.301153 GGAAATATTACAGCAGTACCATTTTTG 57.699 33.333 8.01 0.00 30.14 2.44
230 290 8.262933 TCTGTCAGTAATCTCATTCAATCATGT 58.737 33.333 0.00 0.00 0.00 3.21
260 328 3.433615 GTGACTACAGGAAGTTGCATGTC 59.566 47.826 0.00 0.37 34.33 3.06
291 362 6.586344 AGTGAGGTTGAACATACATATCCAG 58.414 40.000 0.00 0.00 0.00 3.86
292 363 6.560003 AGTGAGGTTGAACATACATATCCA 57.440 37.500 0.00 0.00 0.00 3.41
319 393 7.891561 TGCAGTAAAATATTTTTAGTGGCACT 58.108 30.769 25.34 25.34 36.39 4.40
320 394 8.594687 CATGCAGTAAAATATTTTTAGTGGCAC 58.405 33.333 18.14 10.29 36.39 5.01
321 395 8.310382 ACATGCAGTAAAATATTTTTAGTGGCA 58.690 29.630 18.14 18.51 36.39 4.92
374 578 1.951602 AGGGTGCGTGGTAAAAAGAAC 59.048 47.619 0.00 0.00 0.00 3.01
375 579 2.351706 AGGGTGCGTGGTAAAAAGAA 57.648 45.000 0.00 0.00 0.00 2.52
376 580 1.950909 CAAGGGTGCGTGGTAAAAAGA 59.049 47.619 0.00 0.00 0.00 2.52
404 708 9.003658 AGATGAACAGTAAATGGAAAGTAACAG 57.996 33.333 0.00 0.00 0.00 3.16
465 805 6.977244 ATTAGAAACCAGCTGGGGATATAT 57.023 37.500 35.42 18.61 42.91 0.86
467 807 5.134339 TGAATTAGAAACCAGCTGGGGATAT 59.866 40.000 35.42 20.12 42.91 1.63
469 809 3.269381 TGAATTAGAAACCAGCTGGGGAT 59.731 43.478 35.42 21.15 42.91 3.85
470 810 2.647299 TGAATTAGAAACCAGCTGGGGA 59.353 45.455 35.42 14.93 42.91 4.81
687 1046 4.077188 GCTCGGAAGTGCGTGCAC 62.077 66.667 16.91 16.91 46.50 4.57
708 1068 2.109126 GCTGAGCACGATCCCCAAC 61.109 63.158 0.00 0.00 0.00 3.77
710 1070 3.002583 TGCTGAGCACGATCCCCA 61.003 61.111 1.40 0.00 31.71 4.96
799 1168 0.112412 GAACCCAAAGGCTCCCTCAA 59.888 55.000 0.00 0.00 36.11 3.02
800 1169 1.767692 GAACCCAAAGGCTCCCTCA 59.232 57.895 0.00 0.00 36.11 3.86
805 1174 0.609406 GTCCAGGAACCCAAAGGCTC 60.609 60.000 0.00 0.00 36.11 4.70
806 1175 1.460699 GTCCAGGAACCCAAAGGCT 59.539 57.895 0.00 0.00 36.11 4.58
807 1176 1.606601 GGTCCAGGAACCCAAAGGC 60.607 63.158 0.00 0.00 36.11 4.35
808 1177 1.303317 CGGTCCAGGAACCCAAAGG 60.303 63.158 0.00 0.00 35.79 3.11
809 1178 1.971695 GCGGTCCAGGAACCCAAAG 60.972 63.158 0.00 0.00 35.79 2.77
810 1179 2.114411 GCGGTCCAGGAACCCAAA 59.886 61.111 0.00 0.00 35.79 3.28
811 1180 3.961414 GGCGGTCCAGGAACCCAA 61.961 66.667 0.00 0.00 35.79 4.12
812 1181 4.974438 AGGCGGTCCAGGAACCCA 62.974 66.667 13.08 0.00 35.79 4.51
813 1182 4.097361 GAGGCGGTCCAGGAACCC 62.097 72.222 0.00 1.05 35.79 4.11
814 1183 4.097361 GGAGGCGGTCCAGGAACC 62.097 72.222 0.00 0.00 46.10 3.62
911 1297 7.280876 TCAAATAATCATGGACTGCTTCAGTAC 59.719 37.037 2.33 2.33 45.44 2.73
916 1302 7.268199 TCATCAAATAATCATGGACTGCTTC 57.732 36.000 0.00 0.00 0.00 3.86
997 1580 1.972795 ACCATGTTGCAGAGCCATTTT 59.027 42.857 0.00 0.00 0.00 1.82
998 1581 1.636148 ACCATGTTGCAGAGCCATTT 58.364 45.000 0.00 0.00 0.00 2.32
1081 1665 2.783288 CGGTAGAGGAGCCGGTTCC 61.783 68.421 28.69 28.69 43.85 3.62
1082 1666 2.806237 CGGTAGAGGAGCCGGTTC 59.194 66.667 10.28 10.28 43.85 3.62
1087 1671 2.923634 TAGGGCACGGTAGAGGAGCC 62.924 65.000 0.00 0.00 44.48 4.70
1088 1672 0.828343 ATAGGGCACGGTAGAGGAGC 60.828 60.000 0.00 0.00 0.00 4.70
1089 1673 0.962489 CATAGGGCACGGTAGAGGAG 59.038 60.000 0.00 0.00 0.00 3.69
1090 1674 0.554305 TCATAGGGCACGGTAGAGGA 59.446 55.000 0.00 0.00 0.00 3.71
1091 1675 1.633774 ATCATAGGGCACGGTAGAGG 58.366 55.000 0.00 0.00 0.00 3.69
1092 1676 4.017126 TGATATCATAGGGCACGGTAGAG 58.983 47.826 0.00 0.00 0.00 2.43
1093 1677 4.042271 TGATATCATAGGGCACGGTAGA 57.958 45.455 0.00 0.00 0.00 2.59
1094 1678 4.402474 TGATGATATCATAGGGCACGGTAG 59.598 45.833 18.19 0.00 36.57 3.18
1095 1679 4.159693 GTGATGATATCATAGGGCACGGTA 59.840 45.833 18.19 0.00 42.04 4.02
1096 1680 3.055819 GTGATGATATCATAGGGCACGGT 60.056 47.826 18.19 0.00 42.04 4.83
1097 1681 3.196469 AGTGATGATATCATAGGGCACGG 59.804 47.826 18.19 0.00 42.04 4.94
1098 1682 4.179298 CAGTGATGATATCATAGGGCACG 58.821 47.826 18.19 12.94 42.04 5.34
1099 1683 5.157940 ACAGTGATGATATCATAGGGCAC 57.842 43.478 18.19 19.29 42.04 5.01
1100 1684 5.554070 CAACAGTGATGATATCATAGGGCA 58.446 41.667 18.19 9.20 42.04 5.36
1101 1685 4.394300 GCAACAGTGATGATATCATAGGGC 59.606 45.833 18.19 11.04 42.04 5.19
1102 1686 4.940046 GGCAACAGTGATGATATCATAGGG 59.060 45.833 18.19 10.55 42.04 3.53
1103 1687 5.554070 TGGCAACAGTGATGATATCATAGG 58.446 41.667 18.19 10.24 46.17 2.57
1210 1800 9.778741 CTTGGCCTGTAGTCTTATATAATGAAA 57.221 33.333 3.32 0.00 0.00 2.69
1304 1928 2.841044 CAATCCAGGCATGCCCCC 60.841 66.667 33.14 8.89 36.58 5.40
1577 2217 4.870991 GCCTAATGGTAGAATATTCTCGGC 59.129 45.833 21.17 16.56 38.70 5.54
1618 2258 4.201950 GCAAAAGATGTGGTAGTAGGCATG 60.202 45.833 0.00 0.00 0.00 4.06
1619 2259 3.947834 GCAAAAGATGTGGTAGTAGGCAT 59.052 43.478 0.00 0.00 0.00 4.40
1620 2260 3.343617 GCAAAAGATGTGGTAGTAGGCA 58.656 45.455 0.00 0.00 0.00 4.75
1621 2261 2.683362 GGCAAAAGATGTGGTAGTAGGC 59.317 50.000 0.00 0.00 0.00 3.93
1674 2314 2.697751 AGTAACTAGAGCCTGCATCCAG 59.302 50.000 0.00 0.00 38.85 3.86
1722 2368 6.826741 GGATGTTTAGACCTTTATTGGTAGCA 59.173 38.462 0.00 0.00 41.00 3.49
1727 2375 9.503399 GGTATAGGATGTTTAGACCTTTATTGG 57.497 37.037 0.00 0.00 35.52 3.16
1728 2376 9.204570 CGGTATAGGATGTTTAGACCTTTATTG 57.795 37.037 0.00 0.00 35.52 1.90
1844 2512 4.883585 GCAATGTGATAATCAAGTCCCTCA 59.116 41.667 0.00 0.00 0.00 3.86
1860 2528 2.349590 TCTTGATCAGTCCGCAATGTG 58.650 47.619 0.00 0.00 0.00 3.21
1920 2930 9.730705 AGCTCAGCATTATATAGCAGAATTAAA 57.269 29.630 0.00 0.00 35.63 1.52
1921 2931 9.159364 CAGCTCAGCATTATATAGCAGAATTAA 57.841 33.333 0.00 0.00 35.63 1.40
1922 2932 8.534496 TCAGCTCAGCATTATATAGCAGAATTA 58.466 33.333 0.00 0.00 35.63 1.40
1952 2986 5.812127 TCTGCATGCCTAGCAATTATATACG 59.188 40.000 16.68 0.00 43.62 3.06
1953 2987 7.467623 GTTCTGCATGCCTAGCAATTATATAC 58.532 38.462 16.68 0.00 43.62 1.47
1955 2989 5.122869 CGTTCTGCATGCCTAGCAATTATAT 59.877 40.000 16.68 0.00 43.62 0.86
1956 2990 4.452114 CGTTCTGCATGCCTAGCAATTATA 59.548 41.667 16.68 0.00 43.62 0.98
1957 2991 3.251729 CGTTCTGCATGCCTAGCAATTAT 59.748 43.478 16.68 0.00 43.62 1.28
1959 2993 1.402968 CGTTCTGCATGCCTAGCAATT 59.597 47.619 16.68 0.00 43.62 2.32
1960 2994 1.019673 CGTTCTGCATGCCTAGCAAT 58.980 50.000 16.68 0.00 43.62 3.56
1962 2996 0.036483 TTCGTTCTGCATGCCTAGCA 60.036 50.000 16.68 0.00 44.86 3.49
1963 2997 0.375106 GTTCGTTCTGCATGCCTAGC 59.625 55.000 16.68 4.15 0.00 3.42
1964 2998 1.009829 GGTTCGTTCTGCATGCCTAG 58.990 55.000 16.68 7.00 0.00 3.02
1965 2999 0.739462 CGGTTCGTTCTGCATGCCTA 60.739 55.000 16.68 0.00 0.00 3.93
1966 3000 2.034879 CGGTTCGTTCTGCATGCCT 61.035 57.895 16.68 0.00 0.00 4.75
1967 3001 2.240612 GACGGTTCGTTCTGCATGCC 62.241 60.000 16.68 0.00 41.37 4.40
1968 3002 1.132640 GACGGTTCGTTCTGCATGC 59.867 57.895 11.82 11.82 41.37 4.06
1969 3003 0.439985 CAGACGGTTCGTTCTGCATG 59.560 55.000 0.00 0.00 41.37 4.06
1970 3004 0.670546 CCAGACGGTTCGTTCTGCAT 60.671 55.000 11.47 0.00 41.37 3.96
1971 3005 1.300620 CCAGACGGTTCGTTCTGCA 60.301 57.895 11.47 0.00 41.37 4.41
1978 3012 1.738099 CTTCTGGCCAGACGGTTCG 60.738 63.158 35.26 14.74 37.14 3.95
1990 3024 6.814506 AACAATGTCTTCATCTTCTTCTGG 57.185 37.500 0.00 0.00 32.56 3.86
1997 3031 9.846248 GCAATTAGTAAACAATGTCTTCATCTT 57.154 29.630 0.00 0.00 32.56 2.40
2002 3036 7.538678 CCAGTGCAATTAGTAAACAATGTCTTC 59.461 37.037 0.00 0.00 0.00 2.87
2013 3442 7.308109 CGTTTTTACTCCCAGTGCAATTAGTAA 60.308 37.037 8.60 8.60 0.00 2.24
2025 4786 5.120830 CACATCTTCTCGTTTTTACTCCCAG 59.879 44.000 0.00 0.00 0.00 4.45
2038 4799 1.863267 GCCCTCATCACATCTTCTCG 58.137 55.000 0.00 0.00 0.00 4.04
2120 4881 8.469309 TTGAGAAAGAATGAAAAAGACCAGAT 57.531 30.769 0.00 0.00 0.00 2.90
2123 4884 8.066612 AGTTTGAGAAAGAATGAAAAAGACCA 57.933 30.769 0.00 0.00 0.00 4.02
2152 4922 1.203237 TCCCTGGAATTGATCGAGCA 58.797 50.000 0.00 0.00 32.89 4.26
2251 5021 2.021355 AGTGTCATGCTAGCTCAAGC 57.979 50.000 17.23 1.26 43.08 4.01
2252 5022 5.199024 AGATAGTGTCATGCTAGCTCAAG 57.801 43.478 17.23 3.19 30.34 3.02
2253 5023 5.193663 GAGATAGTGTCATGCTAGCTCAA 57.806 43.478 17.23 0.00 45.80 3.02


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

AutoCloner maintained by Alex Coulton.