Multiple sequence alignment - TraesCS2D01G579200

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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 TraesCS2D01G579200 chr2D 100.000 2693 0 0 1 2693 641894872 641897564 0.000000e+00 4974.0
1 TraesCS2D01G579200 chr2D 96.350 1589 36 3 1122 2690 597851224 597852810 0.000000e+00 2593.0
2 TraesCS2D01G579200 chr2D 98.802 1002 12 0 1 1002 597850233 597851234 0.000000e+00 1784.0
3 TraesCS2D01G579200 chr2D 95.793 523 14 4 1636 2151 598048859 598049380 0.000000e+00 837.0
4 TraesCS2D01G579200 chr2D 95.602 523 15 5 1636 2151 598020668 598021189 0.000000e+00 832.0
5 TraesCS2D01G579200 chr2D 93.671 79 2 2 1560 1638 598020571 598020646 6.090000e-22 115.0
6 TraesCS2D01G579200 chr2D 93.671 79 2 2 1560 1638 598048762 598048837 6.090000e-22 115.0
7 TraesCS2D01G579200 chr7B 92.857 140 10 0 2554 2693 624956940 624957079 1.260000e-48 204.0
8 TraesCS2D01G579200 chr2B 85.792 183 25 1 2348 2530 263938306 263938487 2.740000e-45 193.0
9 TraesCS2D01G579200 chr2A 81.356 177 27 4 780 951 762292490 762292315 3.620000e-29 139.0
10 TraesCS2D01G579200 chr2A 95.238 42 2 0 2376 2417 652826765 652826806 1.730000e-07 67.6
11 TraesCS2D01G579200 chr4B 85.714 70 9 1 2535 2604 139634160 139634228 3.720000e-09 73.1


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 TraesCS2D01G579200 chr2D 641894872 641897564 2692 False 4974.0 4974 100.0000 1 2693 1 chr2D.!!$F1 2692
1 TraesCS2D01G579200 chr2D 597850233 597852810 2577 False 2188.5 2593 97.5760 1 2690 2 chr2D.!!$F2 2689
2 TraesCS2D01G579200 chr2D 598048762 598049380 618 False 476.0 837 94.7320 1560 2151 2 chr2D.!!$F4 591
3 TraesCS2D01G579200 chr2D 598020571 598021189 618 False 473.5 832 94.6365 1560 2151 2 chr2D.!!$F3 591

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
216 217 0.539438 TCACCCTTTGCCACCATGAC 60.539 55.0 0.00 0.0 0.00 3.06 F
817 818 0.588252 GTACCATGGCATCATCGTGC 59.412 55.0 13.04 0.0 44.31 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1042 1043 0.036732 TGTGCACCCATGAAGGACTC 59.963 55.000 15.69 0.0 41.22 3.36 R
2549 2582 1.285641 GGACAATGGCCACAACACG 59.714 57.895 8.16 0.0 0.00 4.49 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
181 182 9.955208 TGTTATCTTATTCTGCAGCATTATTTG 57.045 29.630 9.47 0.00 0.00 2.32
216 217 0.539438 TCACCCTTTGCCACCATGAC 60.539 55.000 0.00 0.00 0.00 3.06
449 450 5.588648 TCCAACTTTGACTTGGTTTACTCTG 59.411 40.000 0.00 0.00 39.48 3.35
579 580 2.676342 AGCGTTAACCCTATTTTCTGCG 59.324 45.455 0.00 0.00 0.00 5.18
614 615 2.915869 AGTTTCCCCAGATGGTGTCTA 58.084 47.619 0.00 0.00 34.69 2.59
817 818 0.588252 GTACCATGGCATCATCGTGC 59.412 55.000 13.04 0.00 44.31 5.34
935 936 2.438021 TCTGCAGTGGTTAGTTTGGAGT 59.562 45.455 14.67 0.00 31.84 3.85
980 981 4.572389 ACTGACAGTGCTTAGTTTCAACAG 59.428 41.667 7.47 0.00 0.00 3.16
997 998 7.455641 TTCAACAGTTTTGGTTTCTGTTCTA 57.544 32.000 6.78 0.00 46.27 2.10
998 999 6.848451 TCAACAGTTTTGGTTTCTGTTCTAC 58.152 36.000 6.78 0.00 46.27 2.59
999 1000 5.830000 ACAGTTTTGGTTTCTGTTCTACC 57.170 39.130 0.00 0.00 39.00 3.18
1000 1001 5.258051 ACAGTTTTGGTTTCTGTTCTACCA 58.742 37.500 0.00 0.00 39.00 3.25
1001 1002 5.891551 ACAGTTTTGGTTTCTGTTCTACCAT 59.108 36.000 0.00 0.00 41.31 3.55
1002 1003 6.183360 ACAGTTTTGGTTTCTGTTCTACCATG 60.183 38.462 0.00 0.00 41.31 3.66
1003 1004 5.301805 AGTTTTGGTTTCTGTTCTACCATGG 59.698 40.000 11.19 11.19 41.31 3.66
1004 1005 4.447138 TTGGTTTCTGTTCTACCATGGT 57.553 40.909 23.55 23.55 41.31 3.55
1005 1006 4.447138 TGGTTTCTGTTCTACCATGGTT 57.553 40.909 25.38 7.42 37.04 3.67
1006 1007 4.141287 TGGTTTCTGTTCTACCATGGTTG 58.859 43.478 25.38 21.83 37.04 3.77
1015 1016 3.136123 CCATGGTTGGCTGCCTCG 61.136 66.667 21.03 1.70 35.85 4.63
1016 1017 3.818787 CATGGTTGGCTGCCTCGC 61.819 66.667 21.03 9.50 0.00 5.03
1024 1025 2.125147 GCTGCCTCGCCATGTGTA 60.125 61.111 0.00 0.00 0.00 2.90
1025 1026 2.464459 GCTGCCTCGCCATGTGTAC 61.464 63.158 0.00 0.00 0.00 2.90
1026 1027 2.125713 TGCCTCGCCATGTGTACG 60.126 61.111 0.00 0.00 0.00 3.67
1027 1028 2.183300 GCCTCGCCATGTGTACGA 59.817 61.111 0.00 0.00 0.00 3.43
1028 1029 1.447140 GCCTCGCCATGTGTACGAA 60.447 57.895 0.00 0.00 35.07 3.85
1029 1030 0.810031 GCCTCGCCATGTGTACGAAT 60.810 55.000 0.00 0.00 35.07 3.34
1030 1031 1.651987 CCTCGCCATGTGTACGAATT 58.348 50.000 0.00 0.00 35.07 2.17
1031 1032 1.593006 CCTCGCCATGTGTACGAATTC 59.407 52.381 0.00 0.00 35.07 2.17
1032 1033 1.593006 CTCGCCATGTGTACGAATTCC 59.407 52.381 0.00 0.00 35.07 3.01
1033 1034 1.066787 TCGCCATGTGTACGAATTCCA 60.067 47.619 0.00 0.00 31.97 3.53
1034 1035 1.939934 CGCCATGTGTACGAATTCCAT 59.060 47.619 0.00 0.00 0.00 3.41
1035 1036 3.127589 CGCCATGTGTACGAATTCCATA 58.872 45.455 0.00 0.00 0.00 2.74
1036 1037 3.745975 CGCCATGTGTACGAATTCCATAT 59.254 43.478 0.00 0.00 0.00 1.78
1037 1038 4.213270 CGCCATGTGTACGAATTCCATATT 59.787 41.667 0.00 0.00 0.00 1.28
1038 1039 5.451908 GCCATGTGTACGAATTCCATATTG 58.548 41.667 0.00 0.00 0.00 1.90
1039 1040 5.562696 GCCATGTGTACGAATTCCATATTGG 60.563 44.000 0.00 0.67 39.43 3.16
1040 1041 5.451908 CATGTGTACGAATTCCATATTGGC 58.548 41.667 0.00 0.00 37.47 4.52
1041 1042 4.518249 TGTGTACGAATTCCATATTGGCA 58.482 39.130 0.00 0.00 37.47 4.92
1042 1043 4.574421 TGTGTACGAATTCCATATTGGCAG 59.426 41.667 0.00 0.00 37.47 4.85
1043 1044 4.814234 GTGTACGAATTCCATATTGGCAGA 59.186 41.667 0.00 0.00 37.47 4.26
1044 1045 5.050091 GTGTACGAATTCCATATTGGCAGAG 60.050 44.000 0.00 0.00 37.47 3.35
1045 1046 4.156455 ACGAATTCCATATTGGCAGAGT 57.844 40.909 0.00 0.00 37.47 3.24
1046 1047 4.130118 ACGAATTCCATATTGGCAGAGTC 58.870 43.478 0.00 0.00 37.47 3.36
1047 1048 3.499918 CGAATTCCATATTGGCAGAGTCC 59.500 47.826 0.00 0.00 37.47 3.85
1048 1049 4.723309 GAATTCCATATTGGCAGAGTCCT 58.277 43.478 0.00 0.00 37.47 3.85
1049 1050 4.803329 ATTCCATATTGGCAGAGTCCTT 57.197 40.909 0.00 0.00 37.47 3.36
1050 1051 3.845781 TCCATATTGGCAGAGTCCTTC 57.154 47.619 0.00 0.00 37.47 3.46
1051 1052 3.114606 TCCATATTGGCAGAGTCCTTCA 58.885 45.455 0.00 0.00 37.47 3.02
1052 1053 3.718434 TCCATATTGGCAGAGTCCTTCAT 59.282 43.478 0.00 0.00 37.47 2.57
1053 1054 3.819337 CCATATTGGCAGAGTCCTTCATG 59.181 47.826 0.00 0.00 0.00 3.07
1054 1055 2.431954 ATTGGCAGAGTCCTTCATGG 57.568 50.000 0.00 0.00 37.10 3.66
1055 1056 0.329261 TTGGCAGAGTCCTTCATGGG 59.671 55.000 0.00 0.00 36.20 4.00
1056 1057 0.842030 TGGCAGAGTCCTTCATGGGT 60.842 55.000 0.00 0.00 36.20 4.51
1057 1058 0.393537 GGCAGAGTCCTTCATGGGTG 60.394 60.000 0.00 0.00 36.20 4.61
1058 1059 1.028868 GCAGAGTCCTTCATGGGTGC 61.029 60.000 0.00 0.00 36.20 5.01
1059 1060 0.325933 CAGAGTCCTTCATGGGTGCA 59.674 55.000 0.00 0.00 36.20 4.57
1060 1061 0.326264 AGAGTCCTTCATGGGTGCAC 59.674 55.000 8.80 8.80 36.20 4.57
1061 1062 0.036732 GAGTCCTTCATGGGTGCACA 59.963 55.000 20.43 0.00 36.20 4.57
1062 1063 0.700564 AGTCCTTCATGGGTGCACAT 59.299 50.000 20.43 0.81 36.20 3.21
1063 1064 1.076024 AGTCCTTCATGGGTGCACATT 59.924 47.619 20.43 0.00 36.20 2.71
1064 1065 1.895131 GTCCTTCATGGGTGCACATTT 59.105 47.619 20.43 0.00 36.20 2.32
1065 1066 1.894466 TCCTTCATGGGTGCACATTTG 59.106 47.619 20.43 12.11 36.20 2.32
1066 1067 1.894466 CCTTCATGGGTGCACATTTGA 59.106 47.619 20.43 14.27 0.00 2.69
1067 1068 2.353011 CCTTCATGGGTGCACATTTGAC 60.353 50.000 20.43 0.00 0.00 3.18
1068 1069 1.992538 TCATGGGTGCACATTTGACA 58.007 45.000 20.43 7.54 0.00 3.58
1069 1070 1.887854 TCATGGGTGCACATTTGACAG 59.112 47.619 20.43 0.00 0.00 3.51
1070 1071 1.067425 CATGGGTGCACATTTGACAGG 60.067 52.381 20.43 5.28 0.00 4.00
1071 1072 0.106268 TGGGTGCACATTTGACAGGT 60.106 50.000 20.43 0.00 0.00 4.00
1072 1073 1.143889 TGGGTGCACATTTGACAGGTA 59.856 47.619 20.43 0.00 0.00 3.08
1073 1074 1.539827 GGGTGCACATTTGACAGGTAC 59.460 52.381 20.43 0.00 0.00 3.34
1074 1075 2.226330 GGTGCACATTTGACAGGTACA 58.774 47.619 20.43 0.00 0.00 2.90
1075 1076 2.819608 GGTGCACATTTGACAGGTACAT 59.180 45.455 20.43 0.00 0.00 2.29
1076 1077 3.366273 GGTGCACATTTGACAGGTACATG 60.366 47.826 20.43 5.87 0.00 3.21
1077 1078 2.228582 TGCACATTTGACAGGTACATGC 59.771 45.455 7.57 1.22 0.00 4.06
1078 1079 2.228582 GCACATTTGACAGGTACATGCA 59.771 45.455 7.57 4.02 0.00 3.96
1079 1080 3.825308 CACATTTGACAGGTACATGCAC 58.175 45.455 7.57 2.95 0.00 4.57
1080 1081 2.819608 ACATTTGACAGGTACATGCACC 59.180 45.455 7.05 7.05 39.02 5.01
1081 1082 1.518325 TTTGACAGGTACATGCACCG 58.482 50.000 9.53 7.33 43.84 4.94
1082 1083 0.321210 TTGACAGGTACATGCACCGG 60.321 55.000 13.14 13.14 43.84 5.28
1083 1084 3.478780 ACAGGTACATGCACCGGT 58.521 55.556 14.46 14.46 43.84 5.28
1084 1085 1.003839 ACAGGTACATGCACCGGTG 60.004 57.895 30.66 30.66 44.08 4.94
1097 1098 3.499737 CGGTGCTTTAGCGGCTGG 61.500 66.667 13.86 3.97 45.98 4.85
1098 1099 2.359975 GGTGCTTTAGCGGCTGGT 60.360 61.111 13.86 1.35 45.83 4.00
1099 1100 2.690778 GGTGCTTTAGCGGCTGGTG 61.691 63.158 13.86 3.22 45.83 4.17
1100 1101 1.966451 GTGCTTTAGCGGCTGGTGT 60.966 57.895 13.86 0.00 45.83 4.16
1101 1102 1.965930 TGCTTTAGCGGCTGGTGTG 60.966 57.895 13.86 0.00 45.83 3.82
1102 1103 2.690778 GCTTTAGCGGCTGGTGTGG 61.691 63.158 13.86 0.00 0.00 4.17
1103 1104 1.302511 CTTTAGCGGCTGGTGTGGT 60.303 57.895 13.86 0.00 0.00 4.16
1104 1105 1.298859 CTTTAGCGGCTGGTGTGGTC 61.299 60.000 13.86 0.00 0.00 4.02
1105 1106 1.764571 TTTAGCGGCTGGTGTGGTCT 61.765 55.000 13.86 0.00 0.00 3.85
1106 1107 2.449031 TTAGCGGCTGGTGTGGTCTG 62.449 60.000 13.86 0.00 0.00 3.51
1109 1110 4.269523 GGCTGGTGTGGTCTGGCA 62.270 66.667 0.00 0.00 0.00 4.92
1110 1111 2.034687 GCTGGTGTGGTCTGGCAT 59.965 61.111 0.00 0.00 0.00 4.40
1111 1112 1.299648 GCTGGTGTGGTCTGGCATA 59.700 57.895 0.00 0.00 0.00 3.14
1112 1113 0.107017 GCTGGTGTGGTCTGGCATAT 60.107 55.000 0.00 0.00 0.00 1.78
1113 1114 1.140852 GCTGGTGTGGTCTGGCATATA 59.859 52.381 0.00 0.00 0.00 0.86
1114 1115 2.838736 CTGGTGTGGTCTGGCATATAC 58.161 52.381 0.00 0.00 0.00 1.47
1115 1116 1.138069 TGGTGTGGTCTGGCATATACG 59.862 52.381 0.00 0.00 0.00 3.06
1116 1117 1.138266 GGTGTGGTCTGGCATATACGT 59.862 52.381 0.00 0.00 0.00 3.57
1117 1118 2.363038 GGTGTGGTCTGGCATATACGTA 59.637 50.000 0.00 0.00 0.00 3.57
1118 1119 3.378339 GTGTGGTCTGGCATATACGTAC 58.622 50.000 0.00 0.00 0.00 3.67
1119 1120 3.025262 TGTGGTCTGGCATATACGTACA 58.975 45.455 0.00 0.00 0.00 2.90
1120 1121 3.447944 TGTGGTCTGGCATATACGTACAA 59.552 43.478 0.00 0.00 0.00 2.41
1121 1122 4.100344 TGTGGTCTGGCATATACGTACAAT 59.900 41.667 0.00 0.00 0.00 2.71
1122 1123 4.447724 GTGGTCTGGCATATACGTACAATG 59.552 45.833 13.06 13.06 0.00 2.82
1123 1124 4.100344 TGGTCTGGCATATACGTACAATGT 59.900 41.667 16.81 0.00 0.00 2.71
1124 1125 5.054477 GGTCTGGCATATACGTACAATGTT 58.946 41.667 16.81 0.00 0.00 2.71
1125 1126 6.183360 TGGTCTGGCATATACGTACAATGTTA 60.183 38.462 16.81 8.64 0.00 2.41
1126 1127 6.702723 GGTCTGGCATATACGTACAATGTTAA 59.297 38.462 16.81 6.40 0.00 2.01
1371 1372 4.832823 TGCCGATTATCATCCTAGACTCAA 59.167 41.667 0.00 0.00 0.00 3.02
1492 1493 6.338146 CGACCATTCTGGACTATGTTTTCTA 58.662 40.000 0.00 0.00 40.96 2.10
1563 1564 0.676782 AGGTTGCTGTTGCGGTATCC 60.677 55.000 0.00 0.00 43.34 2.59
1767 1792 5.473846 TGACTATGCCGGTTTTGAATTGTAA 59.526 36.000 1.90 0.00 0.00 2.41
1828 1853 5.353394 TCACTTACTCCAAAAGTCTGTGT 57.647 39.130 0.00 0.00 39.90 3.72
1949 1974 2.558359 TGCGAGAGAAGTTCATCAGTGA 59.442 45.455 5.50 0.00 0.00 3.41
2222 2255 2.990774 AATGCTCGTGCGTTATTACG 57.009 45.000 14.84 0.00 45.56 3.18
2246 2279 5.230182 GGCTCATAACATGATCATGACGTA 58.770 41.667 36.37 24.71 41.20 3.57
2378 2411 1.470890 TGCGTTGCTATGGGTTTAAGC 59.529 47.619 0.00 0.00 36.77 3.09
2417 2450 1.340658 CGTGTGACTGATTGTCCTCG 58.659 55.000 0.00 0.00 44.75 4.63
2467 2500 1.921230 GAGAGCTTTCGATCGTCAACC 59.079 52.381 15.94 1.35 0.00 3.77
2475 2508 1.076533 CGATCGTCAACCCTTGGTCG 61.077 60.000 7.03 0.00 33.12 4.79
2580 2613 0.244450 ATTGTCCATGTTGGCAAGCG 59.756 50.000 0.00 0.00 37.12 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 3.409026 AGGCAAGGACTTACAAGACTG 57.591 47.619 0.00 0.00 0.00 3.51
181 182 6.466885 AAGGGTGACATATAGTACACTGTC 57.533 41.667 0.00 3.16 38.74 3.51
449 450 6.889301 ATTGTCATCACATATGGTTCATCC 57.111 37.500 7.80 0.00 30.55 3.51
579 580 3.056536 GGGAAACTTGGAATTCAGCTTCC 60.057 47.826 15.06 15.06 44.23 3.46
614 615 5.047306 TGGAAGATCGTATGAAGTTGACACT 60.047 40.000 0.00 0.00 33.11 3.55
670 671 2.012673 GACTTGATCAATGGCTTCGCT 58.987 47.619 8.96 0.00 0.00 4.93
817 818 4.092968 GGAAACATGTGGTAGTAAGAAGCG 59.907 45.833 0.00 0.00 0.00 4.68
867 868 5.567138 AAAGATGTTATAGGCAGCAACAC 57.433 39.130 0.00 0.00 35.17 3.32
935 936 3.517296 TCCCACCACTCAAAATGCTTA 57.483 42.857 0.00 0.00 0.00 3.09
980 981 5.068591 ACCATGGTAGAACAGAAACCAAAAC 59.931 40.000 18.10 0.00 45.91 2.43
999 1000 3.818787 GCGAGGCAGCCAACCATG 61.819 66.667 15.80 0.00 0.00 3.66
1007 1008 2.125147 TACACATGGCGAGGCAGC 60.125 61.111 5.43 0.00 0.00 5.25
1008 1009 2.167219 CGTACACATGGCGAGGCAG 61.167 63.158 5.43 0.67 0.00 4.85
1009 1010 2.125713 CGTACACATGGCGAGGCA 60.126 61.111 0.88 0.88 0.00 4.75
1010 1011 0.810031 ATTCGTACACATGGCGAGGC 60.810 55.000 0.00 0.00 36.00 4.70
1011 1012 1.593006 GAATTCGTACACATGGCGAGG 59.407 52.381 0.00 0.00 36.00 4.63
1012 1013 1.593006 GGAATTCGTACACATGGCGAG 59.407 52.381 0.00 0.00 36.00 5.03
1013 1014 1.066787 TGGAATTCGTACACATGGCGA 60.067 47.619 0.00 0.00 0.00 5.54
1014 1015 1.364721 TGGAATTCGTACACATGGCG 58.635 50.000 0.00 0.00 0.00 5.69
1015 1016 5.451908 CAATATGGAATTCGTACACATGGC 58.548 41.667 0.00 0.00 0.00 4.40
1016 1017 5.562696 GCCAATATGGAATTCGTACACATGG 60.563 44.000 0.00 3.60 40.96 3.66
1017 1018 5.008514 TGCCAATATGGAATTCGTACACATG 59.991 40.000 0.00 0.00 40.96 3.21
1018 1019 5.129634 TGCCAATATGGAATTCGTACACAT 58.870 37.500 0.00 0.00 40.96 3.21
1019 1020 4.518249 TGCCAATATGGAATTCGTACACA 58.482 39.130 0.00 0.00 40.96 3.72
1020 1021 4.814234 TCTGCCAATATGGAATTCGTACAC 59.186 41.667 0.00 0.00 40.96 2.90
1021 1022 5.029807 TCTGCCAATATGGAATTCGTACA 57.970 39.130 0.00 0.00 40.96 2.90
1022 1023 5.057149 ACTCTGCCAATATGGAATTCGTAC 58.943 41.667 0.00 0.00 40.96 3.67
1023 1024 5.290493 ACTCTGCCAATATGGAATTCGTA 57.710 39.130 0.00 0.00 40.96 3.43
1024 1025 4.130118 GACTCTGCCAATATGGAATTCGT 58.870 43.478 0.00 0.00 40.96 3.85
1025 1026 3.499918 GGACTCTGCCAATATGGAATTCG 59.500 47.826 0.00 0.00 40.96 3.34
1026 1027 4.723309 AGGACTCTGCCAATATGGAATTC 58.277 43.478 0.00 0.00 40.96 2.17
1027 1028 4.803329 AGGACTCTGCCAATATGGAATT 57.197 40.909 0.00 0.00 40.96 2.17
1028 1029 4.166725 TGAAGGACTCTGCCAATATGGAAT 59.833 41.667 0.00 0.00 40.96 3.01
1029 1030 3.523157 TGAAGGACTCTGCCAATATGGAA 59.477 43.478 0.00 0.00 40.96 3.53
1030 1031 3.114606 TGAAGGACTCTGCCAATATGGA 58.885 45.455 0.00 0.00 40.96 3.41
1031 1032 3.565764 TGAAGGACTCTGCCAATATGG 57.434 47.619 0.00 0.00 41.55 2.74
1032 1033 3.819337 CCATGAAGGACTCTGCCAATATG 59.181 47.826 0.00 0.00 41.22 1.78
1033 1034 3.181436 CCCATGAAGGACTCTGCCAATAT 60.181 47.826 0.00 0.00 41.22 1.28
1034 1035 2.173356 CCCATGAAGGACTCTGCCAATA 59.827 50.000 0.00 0.00 41.22 1.90
1035 1036 1.064166 CCCATGAAGGACTCTGCCAAT 60.064 52.381 0.00 0.00 41.22 3.16
1036 1037 0.329261 CCCATGAAGGACTCTGCCAA 59.671 55.000 0.00 0.00 41.22 4.52
1037 1038 0.842030 ACCCATGAAGGACTCTGCCA 60.842 55.000 0.00 0.00 41.22 4.92
1038 1039 0.393537 CACCCATGAAGGACTCTGCC 60.394 60.000 0.00 0.00 41.22 4.85
1039 1040 1.028868 GCACCCATGAAGGACTCTGC 61.029 60.000 0.00 0.00 41.22 4.26
1040 1041 0.325933 TGCACCCATGAAGGACTCTG 59.674 55.000 0.00 0.00 41.22 3.35
1041 1042 0.326264 GTGCACCCATGAAGGACTCT 59.674 55.000 5.22 0.00 41.22 3.24
1042 1043 0.036732 TGTGCACCCATGAAGGACTC 59.963 55.000 15.69 0.00 41.22 3.36
1043 1044 0.700564 ATGTGCACCCATGAAGGACT 59.299 50.000 15.69 0.00 41.22 3.85
1044 1045 1.549203 AATGTGCACCCATGAAGGAC 58.451 50.000 15.69 0.00 41.22 3.85
1045 1046 1.894466 CAAATGTGCACCCATGAAGGA 59.106 47.619 15.69 0.00 41.22 3.36
1046 1047 1.894466 TCAAATGTGCACCCATGAAGG 59.106 47.619 15.69 0.00 37.03 3.46
1047 1048 2.296752 TGTCAAATGTGCACCCATGAAG 59.703 45.455 15.69 0.00 0.00 3.02
1048 1049 2.296752 CTGTCAAATGTGCACCCATGAA 59.703 45.455 15.69 0.00 0.00 2.57
1049 1050 1.887854 CTGTCAAATGTGCACCCATGA 59.112 47.619 15.69 12.54 0.00 3.07
1050 1051 1.067425 CCTGTCAAATGTGCACCCATG 60.067 52.381 15.69 10.30 0.00 3.66
1051 1052 1.259609 CCTGTCAAATGTGCACCCAT 58.740 50.000 15.69 0.00 0.00 4.00
1052 1053 0.106268 ACCTGTCAAATGTGCACCCA 60.106 50.000 15.69 0.00 0.00 4.51
1053 1054 1.539827 GTACCTGTCAAATGTGCACCC 59.460 52.381 15.69 0.00 0.00 4.61
1054 1055 2.226330 TGTACCTGTCAAATGTGCACC 58.774 47.619 15.69 0.00 0.00 5.01
1055 1056 3.825308 CATGTACCTGTCAAATGTGCAC 58.175 45.455 10.75 10.75 0.00 4.57
1056 1057 2.228582 GCATGTACCTGTCAAATGTGCA 59.771 45.455 0.00 0.00 0.00 4.57
1057 1058 2.228582 TGCATGTACCTGTCAAATGTGC 59.771 45.455 0.00 0.00 0.00 4.57
1058 1059 3.366273 GGTGCATGTACCTGTCAAATGTG 60.366 47.826 24.21 0.00 37.74 3.21
1059 1060 2.819608 GGTGCATGTACCTGTCAAATGT 59.180 45.455 24.21 0.00 37.74 2.71
1060 1061 2.159531 CGGTGCATGTACCTGTCAAATG 60.160 50.000 27.51 8.39 38.62 2.32
1061 1062 2.083774 CGGTGCATGTACCTGTCAAAT 58.916 47.619 27.51 0.00 38.62 2.32
1062 1063 1.518325 CGGTGCATGTACCTGTCAAA 58.482 50.000 27.51 0.00 38.62 2.69
1063 1064 0.321210 CCGGTGCATGTACCTGTCAA 60.321 55.000 27.51 0.00 38.62 3.18
1064 1065 1.295101 CCGGTGCATGTACCTGTCA 59.705 57.895 27.51 0.00 38.62 3.58
1065 1066 1.019278 CACCGGTGCATGTACCTGTC 61.019 60.000 27.51 4.78 36.22 3.51
1066 1067 1.003839 CACCGGTGCATGTACCTGT 60.004 57.895 27.51 24.44 38.50 4.00
1067 1068 3.889227 CACCGGTGCATGTACCTG 58.111 61.111 27.51 23.81 38.62 4.00
1077 1078 3.799755 GCCGCTAAAGCACCGGTG 61.800 66.667 30.66 30.66 43.70 4.94
1078 1079 4.016706 AGCCGCTAAAGCACCGGT 62.017 61.111 0.00 0.00 43.70 5.28
1079 1080 3.499737 CAGCCGCTAAAGCACCGG 61.500 66.667 0.00 0.00 44.58 5.28
1080 1081 3.499737 CCAGCCGCTAAAGCACCG 61.500 66.667 2.44 0.00 42.21 4.94
1081 1082 2.359975 ACCAGCCGCTAAAGCACC 60.360 61.111 2.44 0.00 42.21 5.01
1082 1083 1.966451 ACACCAGCCGCTAAAGCAC 60.966 57.895 2.44 0.00 42.21 4.40
1083 1084 1.965930 CACACCAGCCGCTAAAGCA 60.966 57.895 2.44 0.00 42.21 3.91
1084 1085 2.690778 CCACACCAGCCGCTAAAGC 61.691 63.158 0.00 0.00 37.78 3.51
1085 1086 1.298859 GACCACACCAGCCGCTAAAG 61.299 60.000 0.00 0.00 0.00 1.85
1086 1087 1.302192 GACCACACCAGCCGCTAAA 60.302 57.895 0.00 0.00 0.00 1.85
1087 1088 2.214216 AGACCACACCAGCCGCTAA 61.214 57.895 0.00 0.00 0.00 3.09
1088 1089 2.603473 AGACCACACCAGCCGCTA 60.603 61.111 0.00 0.00 0.00 4.26
1089 1090 4.320456 CAGACCACACCAGCCGCT 62.320 66.667 0.00 0.00 0.00 5.52
1092 1093 2.196997 TATGCCAGACCACACCAGCC 62.197 60.000 0.00 0.00 0.00 4.85
1093 1094 0.107017 ATATGCCAGACCACACCAGC 60.107 55.000 0.00 0.00 0.00 4.85
1094 1095 2.803133 CGTATATGCCAGACCACACCAG 60.803 54.545 0.00 0.00 0.00 4.00
1095 1096 1.138069 CGTATATGCCAGACCACACCA 59.862 52.381 0.00 0.00 0.00 4.17
1096 1097 1.138266 ACGTATATGCCAGACCACACC 59.862 52.381 0.00 0.00 0.00 4.16
1097 1098 2.596904 ACGTATATGCCAGACCACAC 57.403 50.000 0.00 0.00 0.00 3.82
1098 1099 3.025262 TGTACGTATATGCCAGACCACA 58.975 45.455 0.00 0.00 0.00 4.17
1099 1100 3.720949 TGTACGTATATGCCAGACCAC 57.279 47.619 0.00 0.00 0.00 4.16
1100 1101 4.100344 ACATTGTACGTATATGCCAGACCA 59.900 41.667 16.19 0.00 0.00 4.02
1101 1102 4.628074 ACATTGTACGTATATGCCAGACC 58.372 43.478 16.19 0.00 0.00 3.85
1102 1103 7.703298 TTAACATTGTACGTATATGCCAGAC 57.297 36.000 16.19 0.00 0.00 3.51
1103 1104 7.042321 GCTTTAACATTGTACGTATATGCCAGA 60.042 37.037 16.19 4.16 0.00 3.86
1104 1105 7.069569 GCTTTAACATTGTACGTATATGCCAG 58.930 38.462 16.19 10.25 0.00 4.85
1105 1106 6.539103 TGCTTTAACATTGTACGTATATGCCA 59.461 34.615 16.19 0.58 0.00 4.92
1106 1107 6.950545 TGCTTTAACATTGTACGTATATGCC 58.049 36.000 16.19 0.00 0.00 4.40
1107 1108 9.445786 AAATGCTTTAACATTGTACGTATATGC 57.554 29.630 16.19 6.19 40.12 3.14
1113 1114 9.997482 CCTATAAAATGCTTTAACATTGTACGT 57.003 29.630 0.00 0.00 40.12 3.57
1117 1118 9.950680 CGATCCTATAAAATGCTTTAACATTGT 57.049 29.630 0.00 0.00 40.12 2.71
1118 1119 9.950680 ACGATCCTATAAAATGCTTTAACATTG 57.049 29.630 0.00 0.00 40.12 2.82
1120 1121 9.561069 AGACGATCCTATAAAATGCTTTAACAT 57.439 29.630 0.00 0.00 30.87 2.71
1121 1122 8.958119 AGACGATCCTATAAAATGCTTTAACA 57.042 30.769 0.00 0.00 30.87 2.41
1124 1125 9.832445 AGAAAGACGATCCTATAAAATGCTTTA 57.168 29.630 0.00 0.00 0.00 1.85
1125 1126 8.738645 AGAAAGACGATCCTATAAAATGCTTT 57.261 30.769 0.00 0.00 0.00 3.51
1126 1127 8.738645 AAGAAAGACGATCCTATAAAATGCTT 57.261 30.769 0.00 0.00 0.00 3.91
1215 1216 8.255905 AGAGATTAAAAGATTGAATTTGGCAGG 58.744 33.333 0.00 0.00 0.00 4.85
1492 1493 2.903375 AGAGGAGAAACGTAGAGGGT 57.097 50.000 0.00 0.00 0.00 4.34
1528 1529 4.519437 CTGCAGCGGCGAGGATCA 62.519 66.667 12.98 0.00 45.35 2.92
1563 1564 1.726853 GGAAGGTCAACCATGAGACG 58.273 55.000 1.33 0.00 35.88 4.18
1767 1792 7.181125 ACAGATCCTCTCAGTTATAGGTTGTTT 59.819 37.037 0.00 0.00 0.00 2.83
1791 1816 6.182507 AGTAAGTGAGGTCCAAAATACACA 57.817 37.500 0.00 0.00 0.00 3.72
1828 1853 9.485206 GTCACTTGTTAATTTCTACCAAGTCTA 57.515 33.333 0.00 0.00 42.68 2.59
2217 2250 5.227569 TGATCATGTTATGAGCCCGTAAT 57.772 39.130 4.80 0.00 44.67 1.89
2222 2255 3.434641 CGTCATGATCATGTTATGAGCCC 59.565 47.826 30.01 10.64 44.67 5.19
2288 2321 3.623906 TCATCCTCTTTTCTGAGCCTG 57.376 47.619 0.00 0.00 33.02 4.85
2359 2392 1.470890 TGCTTAAACCCATAGCAACGC 59.529 47.619 0.00 0.00 41.57 4.84
2378 2411 7.540400 TCACACGCCATCACTTTTTAAATATTG 59.460 33.333 0.00 0.00 0.00 1.90
2417 2450 3.040147 TCAAAGACGATGGTGAAGACC 57.960 47.619 0.00 0.00 43.48 3.85
2467 2500 2.182030 GCTCGAGGACGACCAAGG 59.818 66.667 15.58 0.00 43.81 3.61
2475 2508 2.287849 TGATGATCATTCGCTCGAGGAC 60.288 50.000 15.58 0.00 0.00 3.85
2549 2582 1.285641 GGACAATGGCCACAACACG 59.714 57.895 8.16 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.