Multiple sequence alignment - TraesCS4D01G312600

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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 TraesCS4D01G312600 chr4D 100.000 3300 0 0 1 3300 478675701 478672402 0.000000e+00 6095
1 TraesCS4D01G312600 chr4D 76.457 875 78 43 1686 2486 478668289 478667469 1.130000e-94 357
2 TraesCS4D01G312600 chr4D 84.553 123 12 3 1021 1138 99207614 99207494 7.480000e-22 115
3 TraesCS4D01G312600 chr4B 94.341 2050 84 14 1274 3300 605279885 605277845 0.000000e+00 3114
4 TraesCS4D01G312600 chr4B 95.124 964 35 8 56 1014 605281104 605280148 0.000000e+00 1509
5 TraesCS4D01G312600 chr4A 91.636 1901 81 30 1182 3034 685309717 685307847 0.000000e+00 2558
6 TraesCS4D01G312600 chr4A 88.783 945 52 17 61 956 685310657 685309718 0.000000e+00 1109
7 TraesCS4D01G312600 chr4A 93.310 284 15 1 3021 3300 685306882 685306599 1.830000e-112 416
8 TraesCS4D01G312600 chr4A 79.136 671 49 31 1686 2313 685302024 685301402 2.400000e-101 379
9 TraesCS4D01G312600 chr4A 85.484 124 11 5 1020 1138 483958721 483958600 4.470000e-24 122
10 TraesCS4D01G312600 chr1A 92.857 98 7 0 1691 1788 158493627 158493530 3.430000e-30 143
11 TraesCS4D01G312600 chr1D 91.837 98 8 0 1691 1788 131412501 131412404 1.600000e-28 137
12 TraesCS4D01G312600 chr6B 84.000 125 15 2 1019 1138 279005963 279006087 7.480000e-22 115
13 TraesCS4D01G312600 chr1B 84.127 126 12 4 1019 1139 619104467 619104589 7.480000e-22 115
14 TraesCS4D01G312600 chr7B 82.812 128 16 4 1018 1139 52367473 52367600 3.480000e-20 110
15 TraesCS4D01G312600 chr7B 83.200 125 15 4 1020 1139 624471102 624470979 3.480000e-20 110
16 TraesCS4D01G312600 chr6A 83.065 124 15 4 1020 1138 23493153 23493031 1.250000e-19 108
17 TraesCS4D01G312600 chr6D 82.400 125 16 4 1021 1139 380820843 380820967 1.620000e-18 104
18 TraesCS4D01G312600 chr5B 82.927 123 14 5 1022 1139 491603994 491603874 1.620000e-18 104


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 TraesCS4D01G312600 chr4D 478672402 478675701 3299 True 6095.0 6095 100.0000 1 3300 1 chr4D.!!$R3 3299
1 TraesCS4D01G312600 chr4D 478667469 478668289 820 True 357.0 357 76.4570 1686 2486 1 chr4D.!!$R2 800
2 TraesCS4D01G312600 chr4B 605277845 605281104 3259 True 2311.5 3114 94.7325 56 3300 2 chr4B.!!$R1 3244
3 TraesCS4D01G312600 chr4A 685306599 685310657 4058 True 1361.0 2558 91.2430 61 3300 3 chr4A.!!$R3 3239
4 TraesCS4D01G312600 chr4A 685301402 685302024 622 True 379.0 379 79.1360 1686 2313 1 chr4A.!!$R2 627

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
52 53 0.039180 TGGTTCCGTCTGCTCCTCTA 59.961 55.0 0.00 0.0 0.0 2.43 F
967 1020 0.249911 GGCCGGCTCAATGGTACTAG 60.250 60.0 28.56 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1102 1155 0.317938 GCGTCGCTAGGTGGTCTATG 60.318 60.000 10.68 0.0 0.0 2.23 R
2910 3231 1.406069 GCGAAGAGGCTCATTGAGGAA 60.406 52.381 18.26 0.0 0.0 3.36 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
25 26 3.948735 TTTTTAGGCTCCACCGAGG 57.051 52.632 0.00 0.00 46.52 4.63
26 27 0.326927 TTTTTAGGCTCCACCGAGGG 59.673 55.000 0.00 0.00 46.52 4.30
27 28 2.193087 TTTTAGGCTCCACCGAGGGC 62.193 60.000 0.00 0.00 46.52 5.19
31 32 4.699522 GCTCCACCGAGGGCGTTT 62.700 66.667 0.00 0.00 36.55 3.60
32 33 2.742372 CTCCACCGAGGGCGTTTG 60.742 66.667 0.00 0.00 38.24 2.93
33 34 3.530910 CTCCACCGAGGGCGTTTGT 62.531 63.158 0.00 0.00 38.24 2.83
34 35 3.353836 CCACCGAGGGCGTTTGTG 61.354 66.667 0.00 3.85 35.23 3.33
35 36 3.353836 CACCGAGGGCGTTTGTGG 61.354 66.667 0.00 0.00 35.23 4.17
36 37 3.868985 ACCGAGGGCGTTTGTGGT 61.869 61.111 0.00 0.00 35.23 4.16
37 38 2.593436 CCGAGGGCGTTTGTGGTT 60.593 61.111 0.00 0.00 35.23 3.67
38 39 2.613506 CCGAGGGCGTTTGTGGTTC 61.614 63.158 0.00 0.00 35.23 3.62
39 40 2.613506 CGAGGGCGTTTGTGGTTCC 61.614 63.158 0.00 0.00 0.00 3.62
40 41 2.593436 AGGGCGTTTGTGGTTCCG 60.593 61.111 0.00 0.00 0.00 4.30
41 42 2.903350 GGGCGTTTGTGGTTCCGT 60.903 61.111 0.00 0.00 0.00 4.69
42 43 2.635338 GGCGTTTGTGGTTCCGTC 59.365 61.111 0.00 0.00 0.00 4.79
43 44 1.890510 GGCGTTTGTGGTTCCGTCT 60.891 57.895 0.00 0.00 0.00 4.18
44 45 1.278637 GCGTTTGTGGTTCCGTCTG 59.721 57.895 0.00 0.00 0.00 3.51
45 46 1.278637 CGTTTGTGGTTCCGTCTGC 59.721 57.895 0.00 0.00 0.00 4.26
46 47 1.157870 CGTTTGTGGTTCCGTCTGCT 61.158 55.000 0.00 0.00 0.00 4.24
47 48 0.586802 GTTTGTGGTTCCGTCTGCTC 59.413 55.000 0.00 0.00 0.00 4.26
48 49 0.534203 TTTGTGGTTCCGTCTGCTCC 60.534 55.000 0.00 0.00 0.00 4.70
49 50 1.407656 TTGTGGTTCCGTCTGCTCCT 61.408 55.000 0.00 0.00 0.00 3.69
50 51 1.079750 GTGGTTCCGTCTGCTCCTC 60.080 63.158 0.00 0.00 0.00 3.71
51 52 1.228894 TGGTTCCGTCTGCTCCTCT 60.229 57.895 0.00 0.00 0.00 3.69
52 53 0.039180 TGGTTCCGTCTGCTCCTCTA 59.961 55.000 0.00 0.00 0.00 2.43
53 54 0.741915 GGTTCCGTCTGCTCCTCTAG 59.258 60.000 0.00 0.00 0.00 2.43
54 55 1.682394 GGTTCCGTCTGCTCCTCTAGA 60.682 57.143 0.00 0.00 0.00 2.43
213 228 0.317603 ATGTTACGTAGCTAGCGCCG 60.318 55.000 22.12 22.12 36.60 6.46
264 281 1.481772 ACATTATGTTGGCATGGGCAC 59.518 47.619 0.00 0.00 43.71 5.01
265 282 1.481363 CATTATGTTGGCATGGGCACA 59.519 47.619 0.00 0.00 43.71 4.57
303 320 3.495434 TGACAATTGGTAAGTTCCCGT 57.505 42.857 10.83 0.00 0.00 5.28
486 529 3.131223 GTGAGTGAGTGGCTAGCTGATTA 59.869 47.826 15.72 0.00 0.00 1.75
488 531 4.406972 TGAGTGAGTGGCTAGCTGATTATT 59.593 41.667 15.72 0.00 0.00 1.40
489 532 5.598417 TGAGTGAGTGGCTAGCTGATTATTA 59.402 40.000 15.72 0.00 0.00 0.98
725 772 1.164411 CACTTGCAGGCGATTAACCA 58.836 50.000 0.00 0.00 0.00 3.67
769 816 7.973944 AGACAAAATAAGGCGGAAAAATATCAC 59.026 33.333 0.00 0.00 0.00 3.06
831 878 0.730834 CTTGAGACGCGACCTGTCTG 60.731 60.000 15.93 0.00 46.29 3.51
860 907 1.071471 CCATCCTCCCATACACGCC 59.929 63.158 0.00 0.00 0.00 5.68
929 980 9.715123 TTATGTGTGATAGTGCAATTAATTTCG 57.285 29.630 0.00 0.00 0.00 3.46
964 1017 2.516225 GGGCCGGCTCAATGGTAC 60.516 66.667 28.56 5.59 0.00 3.34
966 1019 1.692173 GGGCCGGCTCAATGGTACTA 61.692 60.000 28.56 0.00 0.00 1.82
967 1020 0.249911 GGCCGGCTCAATGGTACTAG 60.250 60.000 28.56 0.00 0.00 2.57
968 1021 0.464452 GCCGGCTCAATGGTACTAGT 59.536 55.000 22.15 0.00 0.00 2.57
969 1022 1.684983 GCCGGCTCAATGGTACTAGTA 59.315 52.381 22.15 0.00 0.00 1.82
970 1023 2.299297 GCCGGCTCAATGGTACTAGTAT 59.701 50.000 22.15 0.00 0.00 2.12
971 1024 3.508793 GCCGGCTCAATGGTACTAGTATA 59.491 47.826 22.15 0.00 0.00 1.47
998 1051 0.591170 GCAACACCAGAAGCGCTAAA 59.409 50.000 12.05 0.00 0.00 1.85
1005 1058 3.684788 CACCAGAAGCGCTAAACATAACT 59.315 43.478 12.05 0.00 0.00 2.24
1014 1067 3.485877 CGCTAAACATAACTGGAGCAAGC 60.486 47.826 0.00 0.00 30.99 4.01
1016 1069 4.082787 GCTAAACATAACTGGAGCAAGCAA 60.083 41.667 0.00 0.00 30.99 3.91
1017 1070 3.923017 AACATAACTGGAGCAAGCAAC 57.077 42.857 0.00 0.00 0.00 4.17
1018 1071 3.146104 ACATAACTGGAGCAAGCAACT 57.854 42.857 0.00 0.00 0.00 3.16
1020 1073 3.891366 ACATAACTGGAGCAAGCAACTTT 59.109 39.130 0.00 0.00 0.00 2.66
1021 1074 4.342092 ACATAACTGGAGCAAGCAACTTTT 59.658 37.500 0.00 0.00 0.00 2.27
1045 1098 6.702716 TTTTTACGGGAAAACTGTTGATCT 57.297 33.333 0.00 0.00 39.94 2.75
1046 1099 7.804843 TTTTTACGGGAAAACTGTTGATCTA 57.195 32.000 0.00 0.00 39.94 1.98
1047 1100 7.989416 TTTTACGGGAAAACTGTTGATCTAT 57.011 32.000 0.00 0.00 39.94 1.98
1048 1101 7.989416 TTTACGGGAAAACTGTTGATCTATT 57.011 32.000 0.00 0.00 39.94 1.73
1049 1102 7.605410 TTACGGGAAAACTGTTGATCTATTC 57.395 36.000 0.00 0.00 39.94 1.75
1050 1103 5.556915 ACGGGAAAACTGTTGATCTATTCA 58.443 37.500 0.00 0.00 34.09 2.57
1051 1104 6.180472 ACGGGAAAACTGTTGATCTATTCAT 58.820 36.000 0.00 0.00 34.09 2.57
1052 1105 6.316390 ACGGGAAAACTGTTGATCTATTCATC 59.684 38.462 0.00 0.00 34.09 2.92
1053 1106 6.540189 CGGGAAAACTGTTGATCTATTCATCT 59.460 38.462 0.00 0.00 33.34 2.90
1054 1107 7.254590 CGGGAAAACTGTTGATCTATTCATCTC 60.255 40.741 0.00 0.00 33.34 2.75
1055 1108 7.012799 GGGAAAACTGTTGATCTATTCATCTCC 59.987 40.741 0.00 0.00 33.34 3.71
1056 1109 7.554118 GGAAAACTGTTGATCTATTCATCTCCA 59.446 37.037 0.00 0.00 33.34 3.86
1057 1110 8.868522 AAAACTGTTGATCTATTCATCTCCAA 57.131 30.769 0.00 0.00 33.34 3.53
1058 1111 8.503458 AAACTGTTGATCTATTCATCTCCAAG 57.497 34.615 0.00 0.00 33.34 3.61
1059 1112 6.054295 ACTGTTGATCTATTCATCTCCAAGC 58.946 40.000 0.00 0.00 33.34 4.01
1060 1113 5.993055 TGTTGATCTATTCATCTCCAAGCA 58.007 37.500 0.00 0.00 33.34 3.91
1061 1114 6.598503 TGTTGATCTATTCATCTCCAAGCAT 58.401 36.000 0.00 0.00 33.34 3.79
1062 1115 7.058525 TGTTGATCTATTCATCTCCAAGCATT 58.941 34.615 0.00 0.00 33.34 3.56
1063 1116 8.212995 TGTTGATCTATTCATCTCCAAGCATTA 58.787 33.333 0.00 0.00 33.34 1.90
1064 1117 8.502387 GTTGATCTATTCATCTCCAAGCATTAC 58.498 37.037 0.00 0.00 33.34 1.89
1065 1118 7.738847 TGATCTATTCATCTCCAAGCATTACA 58.261 34.615 0.00 0.00 0.00 2.41
1066 1119 8.212995 TGATCTATTCATCTCCAAGCATTACAA 58.787 33.333 0.00 0.00 0.00 2.41
1067 1120 7.792374 TCTATTCATCTCCAAGCATTACAAC 57.208 36.000 0.00 0.00 0.00 3.32
1068 1121 4.944962 TTCATCTCCAAGCATTACAACG 57.055 40.909 0.00 0.00 0.00 4.10
1069 1122 4.200838 TCATCTCCAAGCATTACAACGA 57.799 40.909 0.00 0.00 0.00 3.85
1070 1123 4.574892 TCATCTCCAAGCATTACAACGAA 58.425 39.130 0.00 0.00 0.00 3.85
1071 1124 4.391830 TCATCTCCAAGCATTACAACGAAC 59.608 41.667 0.00 0.00 0.00 3.95
1072 1125 3.734463 TCTCCAAGCATTACAACGAACA 58.266 40.909 0.00 0.00 0.00 3.18
1073 1126 4.323417 TCTCCAAGCATTACAACGAACAT 58.677 39.130 0.00 0.00 0.00 2.71
1074 1127 4.391830 TCTCCAAGCATTACAACGAACATC 59.608 41.667 0.00 0.00 0.00 3.06
1075 1128 4.068599 TCCAAGCATTACAACGAACATCA 58.931 39.130 0.00 0.00 0.00 3.07
1076 1129 4.154015 TCCAAGCATTACAACGAACATCAG 59.846 41.667 0.00 0.00 0.00 2.90
1077 1130 4.154015 CCAAGCATTACAACGAACATCAGA 59.846 41.667 0.00 0.00 0.00 3.27
1078 1131 5.334802 CCAAGCATTACAACGAACATCAGAA 60.335 40.000 0.00 0.00 0.00 3.02
1079 1132 5.940192 AGCATTACAACGAACATCAGAAA 57.060 34.783 0.00 0.00 0.00 2.52
1080 1133 6.500684 AGCATTACAACGAACATCAGAAAT 57.499 33.333 0.00 0.00 0.00 2.17
1081 1134 7.609760 AGCATTACAACGAACATCAGAAATA 57.390 32.000 0.00 0.00 0.00 1.40
1082 1135 8.039603 AGCATTACAACGAACATCAGAAATAA 57.960 30.769 0.00 0.00 0.00 1.40
1083 1136 8.677300 AGCATTACAACGAACATCAGAAATAAT 58.323 29.630 0.00 0.00 0.00 1.28
1084 1137 9.929722 GCATTACAACGAACATCAGAAATAATA 57.070 29.630 0.00 0.00 0.00 0.98
1117 1170 5.707242 TTAGATTCATAGACCACCTAGCG 57.293 43.478 0.00 0.00 0.00 4.26
1118 1171 3.833732 AGATTCATAGACCACCTAGCGA 58.166 45.455 0.00 0.00 0.00 4.93
1119 1172 3.570550 AGATTCATAGACCACCTAGCGAC 59.429 47.826 0.00 0.00 0.00 5.19
1120 1173 1.306148 TCATAGACCACCTAGCGACG 58.694 55.000 0.00 0.00 0.00 5.12
1121 1174 0.317938 CATAGACCACCTAGCGACGC 60.318 60.000 13.03 13.03 0.00 5.19
1122 1175 0.465824 ATAGACCACCTAGCGACGCT 60.466 55.000 27.45 27.45 43.41 5.07
1123 1176 0.679002 TAGACCACCTAGCGACGCTT 60.679 55.000 29.54 8.67 40.44 4.68
1124 1177 0.679002 AGACCACCTAGCGACGCTTA 60.679 55.000 29.54 12.76 40.44 3.09
1125 1178 0.384669 GACCACCTAGCGACGCTTAT 59.615 55.000 29.54 11.05 40.44 1.73
1126 1179 1.605710 GACCACCTAGCGACGCTTATA 59.394 52.381 29.54 9.37 40.44 0.98
1127 1180 2.026641 ACCACCTAGCGACGCTTATAA 58.973 47.619 29.54 8.95 40.44 0.98
1128 1181 2.034305 ACCACCTAGCGACGCTTATAAG 59.966 50.000 29.54 18.54 40.44 1.73
1143 1196 4.470462 CTTATAAGCATTGAAGCATCGCC 58.530 43.478 0.00 0.00 36.85 5.54
1144 1197 1.024271 TAAGCATTGAAGCATCGCCC 58.976 50.000 0.00 0.00 36.85 6.13
1145 1198 1.669999 AAGCATTGAAGCATCGCCCC 61.670 55.000 0.00 0.00 36.85 5.80
1146 1199 2.123428 GCATTGAAGCATCGCCCCT 61.123 57.895 0.00 0.00 0.00 4.79
1147 1200 2.028130 CATTGAAGCATCGCCCCTC 58.972 57.895 0.00 0.00 0.00 4.30
1148 1201 1.152881 ATTGAAGCATCGCCCCTCC 60.153 57.895 0.00 0.00 0.00 4.30
1149 1202 2.631012 ATTGAAGCATCGCCCCTCCC 62.631 60.000 0.00 0.00 0.00 4.30
1150 1203 3.483869 GAAGCATCGCCCCTCCCT 61.484 66.667 0.00 0.00 0.00 4.20
1151 1204 3.468326 GAAGCATCGCCCCTCCCTC 62.468 68.421 0.00 0.00 0.00 4.30
1213 1266 9.790389 GTGATGATGCCTGTACTAGTATTATAC 57.210 37.037 5.75 0.00 0.00 1.47
1214 1267 9.755122 TGATGATGCCTGTACTAGTATTATACT 57.245 33.333 9.96 9.96 42.68 2.12
1216 1269 8.935614 TGATGCCTGTACTAGTATTATACTGT 57.064 34.615 14.53 12.17 39.81 3.55
1261 1314 2.175878 TTTCAGAGTGAAGCAGCTCC 57.824 50.000 0.00 0.00 37.70 4.70
1262 1315 1.051008 TTCAGAGTGAAGCAGCTCCA 58.949 50.000 0.00 0.00 31.83 3.86
1296 1475 1.913778 TTTTCCCCGAGTAAAAGCCC 58.086 50.000 0.00 0.00 0.00 5.19
1494 1682 1.610673 TCACTGTCCCCCAGCTCTC 60.611 63.158 0.00 0.00 45.68 3.20
1573 1765 1.839994 TCCCCACAGATCCTCATTCAC 59.160 52.381 0.00 0.00 0.00 3.18
1816 2020 2.182030 GACGTCAGCTTCCCGGAG 59.818 66.667 11.55 0.00 0.00 4.63
2030 2240 2.598394 TGCTTGCAACTGGGCCTC 60.598 61.111 4.53 0.00 0.00 4.70
2250 2544 7.992180 ATTACTTCAGTTCTTTTGTTGCTTG 57.008 32.000 0.00 0.00 0.00 4.01
2488 2801 3.261580 TGATCCAATAGCACGTGAACTG 58.738 45.455 22.23 9.89 0.00 3.16
2545 2866 8.437742 GGATAAATGCAGTGACAAAGAAATTTG 58.562 33.333 0.00 0.00 37.89 2.32
2819 3140 6.102897 TCTCAAGGAACTACAAGGAGAAAG 57.897 41.667 0.00 0.00 38.49 2.62
2823 3144 3.258622 AGGAACTACAAGGAGAAAGACCG 59.741 47.826 0.00 0.00 36.02 4.79
2828 3149 2.322658 ACAAGGAGAAAGACCGTACCA 58.677 47.619 0.00 0.00 0.00 3.25
2871 3192 7.976175 TGCGTCATTTGATAGATCATAGGTATC 59.024 37.037 0.00 0.00 36.56 2.24
2910 3231 3.334881 ACCTCCATTTCCAACCTCAATCT 59.665 43.478 0.00 0.00 0.00 2.40
2994 3315 5.156355 CAATATCACCACTTGTCTTTGTGC 58.844 41.667 0.00 0.00 33.26 4.57
3075 4374 1.516110 CTCATCCCCTCATCCCAACT 58.484 55.000 0.00 0.00 0.00 3.16
3112 4411 2.535012 TTCAATACACCGCTGACACA 57.465 45.000 0.00 0.00 0.00 3.72
3233 4540 2.114616 CCCAGAGTAATCAGTGGAGCT 58.885 52.381 0.33 0.00 31.04 4.09
3235 4542 3.706594 CCCAGAGTAATCAGTGGAGCTAA 59.293 47.826 0.33 0.00 31.04 3.09
3266 4573 4.223032 AGATTTACCATCAAGACGGTGACT 59.777 41.667 0.00 0.00 36.69 3.41
3288 4595 2.373169 GGAATGCCACTCCATATCCAGA 59.627 50.000 0.00 0.00 32.77 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.326927 CCCTCGGTGGAGCCTAAAAA 59.673 55.000 0.00 0.00 39.06 1.94
8 9 1.988015 CCCTCGGTGGAGCCTAAAA 59.012 57.895 0.00 0.00 39.06 1.52
9 10 2.666098 GCCCTCGGTGGAGCCTAAA 61.666 63.158 0.00 0.00 39.06 1.85
10 11 3.081409 GCCCTCGGTGGAGCCTAA 61.081 66.667 0.00 0.00 39.06 2.69
14 15 4.699522 AAACGCCCTCGGTGGAGC 62.700 66.667 0.00 0.00 39.06 4.70
15 16 2.742372 CAAACGCCCTCGGTGGAG 60.742 66.667 0.00 0.00 40.69 3.86
16 17 3.552384 ACAAACGCCCTCGGTGGA 61.552 61.111 0.00 0.00 40.69 4.02
17 18 3.353836 CACAAACGCCCTCGGTGG 61.354 66.667 0.00 0.00 40.69 4.61
18 19 3.353836 CCACAAACGCCCTCGGTG 61.354 66.667 0.00 0.00 40.69 4.94
19 20 3.409605 AACCACAAACGCCCTCGGT 62.410 57.895 0.00 0.00 40.69 4.69
20 21 2.593436 AACCACAAACGCCCTCGG 60.593 61.111 0.00 0.00 40.69 4.63
21 22 2.613506 GGAACCACAAACGCCCTCG 61.614 63.158 0.00 0.00 42.43 4.63
22 23 2.613506 CGGAACCACAAACGCCCTC 61.614 63.158 0.00 0.00 0.00 4.30
23 24 2.593436 CGGAACCACAAACGCCCT 60.593 61.111 0.00 0.00 0.00 5.19
24 25 2.900167 GACGGAACCACAAACGCCC 61.900 63.158 0.00 0.00 0.00 6.13
25 26 1.890510 AGACGGAACCACAAACGCC 60.891 57.895 0.00 0.00 0.00 5.68
26 27 1.278637 CAGACGGAACCACAAACGC 59.721 57.895 0.00 0.00 0.00 4.84
27 28 1.157870 AGCAGACGGAACCACAAACG 61.158 55.000 0.00 0.00 0.00 3.60
28 29 0.586802 GAGCAGACGGAACCACAAAC 59.413 55.000 0.00 0.00 0.00 2.93
29 30 0.534203 GGAGCAGACGGAACCACAAA 60.534 55.000 0.00 0.00 0.00 2.83
30 31 1.070786 GGAGCAGACGGAACCACAA 59.929 57.895 0.00 0.00 0.00 3.33
31 32 1.816863 GAGGAGCAGACGGAACCACA 61.817 60.000 0.00 0.00 0.00 4.17
32 33 1.079750 GAGGAGCAGACGGAACCAC 60.080 63.158 0.00 0.00 0.00 4.16
33 34 0.039180 TAGAGGAGCAGACGGAACCA 59.961 55.000 0.00 0.00 0.00 3.67
34 35 0.741915 CTAGAGGAGCAGACGGAACC 59.258 60.000 0.00 0.00 0.00 3.62
35 36 1.673920 CTCTAGAGGAGCAGACGGAAC 59.326 57.143 12.27 0.00 35.08 3.62
36 37 2.045561 CTCTAGAGGAGCAGACGGAA 57.954 55.000 12.27 0.00 35.08 4.30
37 38 3.790691 CTCTAGAGGAGCAGACGGA 57.209 57.895 12.27 0.00 35.08 4.69
45 46 2.123683 TGGCCGGCTCTAGAGGAG 60.124 66.667 28.56 0.00 44.49 3.69
46 47 2.442272 GTGGCCGGCTCTAGAGGA 60.442 66.667 28.56 0.00 0.00 3.71
47 48 3.541713 GGTGGCCGGCTCTAGAGG 61.542 72.222 28.56 7.01 0.00 3.69
48 49 3.905678 CGGTGGCCGGCTCTAGAG 61.906 72.222 28.56 15.85 44.15 2.43
264 281 3.274586 CCGCATGCTCGTCCCATG 61.275 66.667 17.13 7.86 42.23 3.66
265 282 3.329542 AACCGCATGCTCGTCCCAT 62.330 57.895 17.13 0.00 0.00 4.00
303 320 1.496060 AGTAGCATCCACATTCCGGA 58.504 50.000 0.00 0.00 36.84 5.14
579 625 5.326069 TGTAGGTTGAGCTCTTCTCTACTT 58.674 41.667 23.59 11.13 43.82 2.24
597 643 1.279271 CCTTGTCCCTGTCCTTGTAGG 59.721 57.143 0.00 0.00 36.46 3.18
725 772 2.115266 CCCTGCGTTTGGACCCTT 59.885 61.111 0.00 0.00 0.00 3.95
769 816 3.432252 ACCTGCGACGTTTCTTATTTGAG 59.568 43.478 0.00 0.00 0.00 3.02
831 878 3.412624 GAGGATGGGCACAGGGCTC 62.413 68.421 0.00 0.00 46.04 4.70
929 980 2.510948 CTGCATGCGTAGGATCGAC 58.489 57.895 14.09 0.00 35.32 4.20
964 1017 7.886338 TCTGGTGTTGCTGTCATATATACTAG 58.114 38.462 0.00 0.00 0.00 2.57
966 1019 6.731292 TCTGGTGTTGCTGTCATATATACT 57.269 37.500 0.00 0.00 0.00 2.12
967 1020 6.073548 GCTTCTGGTGTTGCTGTCATATATAC 60.074 42.308 0.00 0.00 0.00 1.47
968 1021 5.991606 GCTTCTGGTGTTGCTGTCATATATA 59.008 40.000 0.00 0.00 0.00 0.86
969 1022 4.818546 GCTTCTGGTGTTGCTGTCATATAT 59.181 41.667 0.00 0.00 0.00 0.86
970 1023 4.191544 GCTTCTGGTGTTGCTGTCATATA 58.808 43.478 0.00 0.00 0.00 0.86
971 1024 3.012518 GCTTCTGGTGTTGCTGTCATAT 58.987 45.455 0.00 0.00 0.00 1.78
998 1051 3.146104 AGTTGCTTGCTCCAGTTATGT 57.854 42.857 0.00 0.00 0.00 2.29
1023 1076 7.989416 ATAGATCAACAGTTTTCCCGTAAAA 57.011 32.000 0.00 0.00 34.66 1.52
1025 1078 7.162761 TGAATAGATCAACAGTTTTCCCGTAA 58.837 34.615 0.00 0.00 34.30 3.18
1026 1079 6.703319 TGAATAGATCAACAGTTTTCCCGTA 58.297 36.000 0.00 0.00 34.30 4.02
1029 1082 7.012799 GGAGATGAATAGATCAACAGTTTTCCC 59.987 40.741 0.00 0.00 42.54 3.97
1031 1084 8.498054 TGGAGATGAATAGATCAACAGTTTTC 57.502 34.615 0.00 0.00 42.54 2.29
1032 1085 8.868522 TTGGAGATGAATAGATCAACAGTTTT 57.131 30.769 0.00 0.00 42.54 2.43
1033 1086 7.066766 GCTTGGAGATGAATAGATCAACAGTTT 59.933 37.037 0.00 0.00 42.54 2.66
1036 1089 6.053650 TGCTTGGAGATGAATAGATCAACAG 58.946 40.000 0.00 0.00 42.54 3.16
1037 1090 5.993055 TGCTTGGAGATGAATAGATCAACA 58.007 37.500 0.00 0.00 42.54 3.33
1038 1091 7.507733 AATGCTTGGAGATGAATAGATCAAC 57.492 36.000 0.00 0.00 42.54 3.18
1039 1092 8.212995 TGTAATGCTTGGAGATGAATAGATCAA 58.787 33.333 0.00 0.00 42.54 2.57
1040 1093 7.738847 TGTAATGCTTGGAGATGAATAGATCA 58.261 34.615 0.00 0.00 43.67 2.92
1041 1094 8.502387 GTTGTAATGCTTGGAGATGAATAGATC 58.498 37.037 0.00 0.00 0.00 2.75
1042 1095 7.172190 CGTTGTAATGCTTGGAGATGAATAGAT 59.828 37.037 0.00 0.00 0.00 1.98
1043 1096 6.479990 CGTTGTAATGCTTGGAGATGAATAGA 59.520 38.462 0.00 0.00 0.00 1.98
1044 1097 6.479990 TCGTTGTAATGCTTGGAGATGAATAG 59.520 38.462 0.00 0.00 0.00 1.73
1045 1098 6.345298 TCGTTGTAATGCTTGGAGATGAATA 58.655 36.000 0.00 0.00 0.00 1.75
1046 1099 5.185454 TCGTTGTAATGCTTGGAGATGAAT 58.815 37.500 0.00 0.00 0.00 2.57
1047 1100 4.574892 TCGTTGTAATGCTTGGAGATGAA 58.425 39.130 0.00 0.00 0.00 2.57
1048 1101 4.200838 TCGTTGTAATGCTTGGAGATGA 57.799 40.909 0.00 0.00 0.00 2.92
1049 1102 4.154015 TGTTCGTTGTAATGCTTGGAGATG 59.846 41.667 0.00 0.00 0.00 2.90
1050 1103 4.323417 TGTTCGTTGTAATGCTTGGAGAT 58.677 39.130 0.00 0.00 0.00 2.75
1051 1104 3.734463 TGTTCGTTGTAATGCTTGGAGA 58.266 40.909 0.00 0.00 0.00 3.71
1052 1105 4.154015 TGATGTTCGTTGTAATGCTTGGAG 59.846 41.667 0.00 0.00 0.00 3.86
1053 1106 4.068599 TGATGTTCGTTGTAATGCTTGGA 58.931 39.130 0.00 0.00 0.00 3.53
1054 1107 4.154015 TCTGATGTTCGTTGTAATGCTTGG 59.846 41.667 0.00 0.00 0.00 3.61
1055 1108 5.281693 TCTGATGTTCGTTGTAATGCTTG 57.718 39.130 0.00 0.00 0.00 4.01
1056 1109 5.940192 TTCTGATGTTCGTTGTAATGCTT 57.060 34.783 0.00 0.00 0.00 3.91
1057 1110 5.940192 TTTCTGATGTTCGTTGTAATGCT 57.060 34.783 0.00 0.00 0.00 3.79
1058 1111 8.841444 ATTATTTCTGATGTTCGTTGTAATGC 57.159 30.769 0.00 0.00 0.00 3.56
1091 1144 8.470805 CGCTAGGTGGTCTATGAATCTAAATAT 58.529 37.037 0.00 0.00 0.00 1.28
1092 1145 7.668469 TCGCTAGGTGGTCTATGAATCTAAATA 59.332 37.037 0.00 0.00 0.00 1.40
1093 1146 6.493802 TCGCTAGGTGGTCTATGAATCTAAAT 59.506 38.462 0.00 0.00 0.00 1.40
1094 1147 5.831525 TCGCTAGGTGGTCTATGAATCTAAA 59.168 40.000 0.00 0.00 0.00 1.85
1095 1148 5.241064 GTCGCTAGGTGGTCTATGAATCTAA 59.759 44.000 0.00 0.00 0.00 2.10
1096 1149 4.760715 GTCGCTAGGTGGTCTATGAATCTA 59.239 45.833 0.00 0.00 0.00 1.98
1097 1150 3.570550 GTCGCTAGGTGGTCTATGAATCT 59.429 47.826 0.00 0.00 0.00 2.40
1098 1151 3.609644 CGTCGCTAGGTGGTCTATGAATC 60.610 52.174 0.00 0.00 0.00 2.52
1099 1152 2.293677 CGTCGCTAGGTGGTCTATGAAT 59.706 50.000 0.00 0.00 0.00 2.57
1100 1153 1.674441 CGTCGCTAGGTGGTCTATGAA 59.326 52.381 0.00 0.00 0.00 2.57
1101 1154 1.306148 CGTCGCTAGGTGGTCTATGA 58.694 55.000 0.00 0.00 0.00 2.15
1102 1155 0.317938 GCGTCGCTAGGTGGTCTATG 60.318 60.000 10.68 0.00 0.00 2.23
1103 1156 0.465824 AGCGTCGCTAGGTGGTCTAT 60.466 55.000 20.25 0.00 36.99 1.98
1104 1157 0.679002 AAGCGTCGCTAGGTGGTCTA 60.679 55.000 22.04 0.00 38.25 2.59
1105 1158 0.679002 TAAGCGTCGCTAGGTGGTCT 60.679 55.000 22.04 4.45 38.25 3.85
1106 1159 0.384669 ATAAGCGTCGCTAGGTGGTC 59.615 55.000 22.04 0.00 38.25 4.02
1107 1160 1.683943 TATAAGCGTCGCTAGGTGGT 58.316 50.000 22.04 6.09 38.25 4.16
1108 1161 2.662700 CTTATAAGCGTCGCTAGGTGG 58.337 52.381 22.04 7.55 38.25 4.61
1109 1162 2.052157 GCTTATAAGCGTCGCTAGGTG 58.948 52.381 22.04 10.99 42.88 4.00
1110 1163 2.418983 GCTTATAAGCGTCGCTAGGT 57.581 50.000 22.04 11.83 42.88 3.08
1121 1174 4.470462 GGCGATGCTTCAATGCTTATAAG 58.530 43.478 8.20 8.20 0.00 1.73
1122 1175 3.253188 GGGCGATGCTTCAATGCTTATAA 59.747 43.478 0.08 0.00 0.00 0.98
1123 1176 2.813754 GGGCGATGCTTCAATGCTTATA 59.186 45.455 0.08 0.00 0.00 0.98
1124 1177 1.610522 GGGCGATGCTTCAATGCTTAT 59.389 47.619 0.08 0.00 0.00 1.73
1125 1178 1.024271 GGGCGATGCTTCAATGCTTA 58.976 50.000 0.08 0.00 0.00 3.09
1126 1179 1.669999 GGGGCGATGCTTCAATGCTT 61.670 55.000 0.08 0.00 0.00 3.91
1127 1180 2.123428 GGGGCGATGCTTCAATGCT 61.123 57.895 0.08 0.00 0.00 3.79
1128 1181 2.068277 GAGGGGCGATGCTTCAATGC 62.068 60.000 0.08 0.00 0.00 3.56
1129 1182 1.450531 GGAGGGGCGATGCTTCAATG 61.451 60.000 0.08 0.00 0.00 2.82
1130 1183 1.152881 GGAGGGGCGATGCTTCAAT 60.153 57.895 0.08 0.00 0.00 2.57
1131 1184 2.272146 GGAGGGGCGATGCTTCAA 59.728 61.111 0.08 0.00 0.00 2.69
1132 1185 3.797353 GGGAGGGGCGATGCTTCA 61.797 66.667 0.08 0.00 0.00 3.02
1133 1186 3.468326 GAGGGAGGGGCGATGCTTC 62.468 68.421 0.00 0.00 0.00 3.86
1134 1187 3.483869 GAGGGAGGGGCGATGCTT 61.484 66.667 0.00 0.00 0.00 3.91
1153 1206 1.202879 TCTTACCACAACAGCCTTGGG 60.203 52.381 0.00 0.00 34.41 4.12
1154 1207 2.270352 TCTTACCACAACAGCCTTGG 57.730 50.000 0.00 0.00 36.39 3.61
1155 1208 3.120199 CGATTCTTACCACAACAGCCTTG 60.120 47.826 0.00 0.00 0.00 3.61
1156 1209 3.074412 CGATTCTTACCACAACAGCCTT 58.926 45.455 0.00 0.00 0.00 4.35
1157 1210 2.301870 TCGATTCTTACCACAACAGCCT 59.698 45.455 0.00 0.00 0.00 4.58
1158 1211 2.695359 TCGATTCTTACCACAACAGCC 58.305 47.619 0.00 0.00 0.00 4.85
1159 1212 3.932710 TGATCGATTCTTACCACAACAGC 59.067 43.478 0.00 0.00 0.00 4.40
1160 1213 5.062683 CACTGATCGATTCTTACCACAACAG 59.937 44.000 0.00 0.00 0.00 3.16
1161 1214 4.929211 CACTGATCGATTCTTACCACAACA 59.071 41.667 0.00 0.00 0.00 3.33
1162 1215 4.929808 ACACTGATCGATTCTTACCACAAC 59.070 41.667 0.00 0.00 0.00 3.32
1163 1216 5.147330 ACACTGATCGATTCTTACCACAA 57.853 39.130 0.00 0.00 0.00 3.33
1164 1217 4.801330 ACACTGATCGATTCTTACCACA 57.199 40.909 0.00 0.00 0.00 4.17
1165 1218 5.744345 CACTACACTGATCGATTCTTACCAC 59.256 44.000 0.00 0.00 0.00 4.16
1166 1219 5.650703 TCACTACACTGATCGATTCTTACCA 59.349 40.000 0.00 0.00 0.00 3.25
1167 1220 6.132791 TCACTACACTGATCGATTCTTACC 57.867 41.667 0.00 0.00 0.00 2.85
1222 1275 8.542926 TCTGAAATCTGAAATATCCTCTTGTGA 58.457 33.333 0.00 0.00 0.00 3.58
1281 1460 0.679960 CCTTGGGCTTTTACTCGGGG 60.680 60.000 0.00 0.00 0.00 5.73
1282 1461 1.313091 GCCTTGGGCTTTTACTCGGG 61.313 60.000 0.80 0.00 46.69 5.14
1296 1475 3.378427 GGTATGTAGAAAAGCTGGCCTTG 59.622 47.826 3.32 0.00 33.01 3.61
1494 1682 2.375146 GCCGGGGGCTAATATATTTGG 58.625 52.381 2.18 0.00 46.69 3.28
1516 1708 2.660258 GAAGTGCGTGTGTGAGGGGT 62.660 60.000 0.00 0.00 0.00 4.95
2030 2240 3.136123 CTGCTTCCATGGCACCGG 61.136 66.667 6.96 0.00 35.71 5.28
2372 2675 2.982470 CGAATCAAAACAAGAGCCAAGC 59.018 45.455 0.00 0.00 0.00 4.01
2526 2847 3.456280 GGCAAATTTCTTTGTCACTGCA 58.544 40.909 0.00 0.00 44.60 4.41
2545 2866 6.223852 TCATTTGCAGTACTATTAGCTAGGC 58.776 40.000 0.00 0.00 0.00 3.93
2819 3140 6.730960 TTCATAAGTTGAAATGGTACGGTC 57.269 37.500 0.00 0.00 41.38 4.79
2871 3192 7.687941 ATGGAGGTGTCATAAACTAAACTTG 57.312 36.000 0.00 0.00 0.00 3.16
2910 3231 1.406069 GCGAAGAGGCTCATTGAGGAA 60.406 52.381 18.26 0.00 0.00 3.36
2994 3315 4.574013 AGATTGAAGAAGATTTGCCGCTAG 59.426 41.667 0.00 0.00 0.00 3.42
3075 4374 6.713762 ATTGAATGACAACAAAGTCTTCCA 57.286 33.333 0.00 0.00 41.52 3.53
3086 4385 3.435327 TCAGCGGTGTATTGAATGACAAC 59.565 43.478 15.22 0.00 41.52 3.32
3087 4386 3.435327 GTCAGCGGTGTATTGAATGACAA 59.565 43.478 15.22 0.00 42.95 3.18
3112 4411 0.905357 AGACTAGGAGCACCGCAATT 59.095 50.000 0.00 0.00 41.83 2.32
3233 4540 8.956426 GTCTTGATGGTAAATCTTCCAACATTA 58.044 33.333 0.00 0.00 36.63 1.90
3235 4542 6.094048 CGTCTTGATGGTAAATCTTCCAACAT 59.906 38.462 0.00 0.00 36.63 2.71


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

AutoCloner maintained by Alex Coulton.