Multiple sequence alignment - TraesCS6A01G168300

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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 TraesCS6A01G168300 chr6A 100.000 2201 0 0 1 2201 172173113 172175313 0.000000e+00 4065
1 TraesCS6A01G168300 chr6A 95.639 986 40 3 1 984 162897000 162897984 0.000000e+00 1580
2 TraesCS6A01G168300 chr6A 94.900 1000 49 2 1203 2201 535313257 535314255 0.000000e+00 1563
3 TraesCS6A01G168300 chr2A 96.057 989 38 1 1 988 38895942 38896930 0.000000e+00 1609
4 TraesCS6A01G168300 chr2A 95.551 989 43 1 1 988 455874250 455873262 0.000000e+00 1581
5 TraesCS6A01G168300 chr2A 95.000 1000 49 1 1203 2201 724206507 724207506 0.000000e+00 1568
6 TraesCS6A01G168300 chr3A 95.956 989 38 2 1 988 684060273 684061260 0.000000e+00 1604
7 TraesCS6A01G168300 chr3A 95.556 990 42 2 1 988 124268057 124269046 0.000000e+00 1583
8 TraesCS6A01G168300 chr3A 94.900 1000 50 1 1203 2201 685883903 685884902 0.000000e+00 1563
9 TraesCS6A01G168300 chr3A 99.533 214 1 0 989 1202 66001142 66001355 7.370000e-105 390
10 TraesCS6A01G168300 chr4A 95.859 990 39 2 1 988 62258784 62259773 0.000000e+00 1600
11 TraesCS6A01G168300 chr4A 95.551 989 43 1 1 988 209210264 209209276 0.000000e+00 1581
12 TraesCS6A01G168300 chr4A 95.100 1000 48 1 1203 2201 146038114 146039113 0.000000e+00 1574
13 TraesCS6A01G168300 chr4A 95.000 1000 49 1 1203 2201 576488119 576489118 0.000000e+00 1568
14 TraesCS6A01G168300 chr5A 95.652 989 42 1 1 988 481802109 481803097 0.000000e+00 1587
15 TraesCS6A01G168300 chr5A 95.652 989 42 1 1 988 610311034 610312022 0.000000e+00 1587
16 TraesCS6A01G168300 chr5A 95.000 1000 49 1 1203 2201 481803098 481804097 0.000000e+00 1568
17 TraesCS6A01G168300 chr5A 94.985 997 49 1 1203 2198 281763665 281764661 0.000000e+00 1563
18 TraesCS6A01G168300 chr7A 95.100 1000 48 1 1203 2201 472332286 472331287 0.000000e+00 1574
19 TraesCS6A01G168300 chr1A 94.600 1000 53 1 1203 2201 76434279 76435278 0.000000e+00 1546
20 TraesCS6A01G168300 chrUn 99.533 214 1 0 989 1202 392770548 392770335 7.370000e-105 390
21 TraesCS6A01G168300 chr7D 99.533 214 1 0 989 1202 77233822 77234035 7.370000e-105 390
22 TraesCS6A01G168300 chr7D 99.533 214 1 0 989 1202 231570437 231570650 7.370000e-105 390
23 TraesCS6A01G168300 chr7B 99.533 214 1 0 989 1202 622433632 622433845 7.370000e-105 390
24 TraesCS6A01G168300 chr3D 99.533 214 1 0 989 1202 589259190 589259403 7.370000e-105 390
25 TraesCS6A01G168300 chr3B 99.533 214 1 0 989 1202 201543857 201543644 7.370000e-105 390
26 TraesCS6A01G168300 chr3B 99.533 214 1 0 989 1202 201547408 201547621 7.370000e-105 390
27 TraesCS6A01G168300 chr2D 99.533 214 1 0 989 1202 591990011 591989798 7.370000e-105 390


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 TraesCS6A01G168300 chr6A 172173113 172175313 2200 False 4065.0 4065 100.000 1 2201 1 chr6A.!!$F2 2200
1 TraesCS6A01G168300 chr6A 162897000 162897984 984 False 1580.0 1580 95.639 1 984 1 chr6A.!!$F1 983
2 TraesCS6A01G168300 chr6A 535313257 535314255 998 False 1563.0 1563 94.900 1203 2201 1 chr6A.!!$F3 998
3 TraesCS6A01G168300 chr2A 38895942 38896930 988 False 1609.0 1609 96.057 1 988 1 chr2A.!!$F1 987
4 TraesCS6A01G168300 chr2A 455873262 455874250 988 True 1581.0 1581 95.551 1 988 1 chr2A.!!$R1 987
5 TraesCS6A01G168300 chr2A 724206507 724207506 999 False 1568.0 1568 95.000 1203 2201 1 chr2A.!!$F2 998
6 TraesCS6A01G168300 chr3A 684060273 684061260 987 False 1604.0 1604 95.956 1 988 1 chr3A.!!$F3 987
7 TraesCS6A01G168300 chr3A 124268057 124269046 989 False 1583.0 1583 95.556 1 988 1 chr3A.!!$F2 987
8 TraesCS6A01G168300 chr3A 685883903 685884902 999 False 1563.0 1563 94.900 1203 2201 1 chr3A.!!$F4 998
9 TraesCS6A01G168300 chr4A 62258784 62259773 989 False 1600.0 1600 95.859 1 988 1 chr4A.!!$F1 987
10 TraesCS6A01G168300 chr4A 209209276 209210264 988 True 1581.0 1581 95.551 1 988 1 chr4A.!!$R1 987
11 TraesCS6A01G168300 chr4A 146038114 146039113 999 False 1574.0 1574 95.100 1203 2201 1 chr4A.!!$F2 998
12 TraesCS6A01G168300 chr4A 576488119 576489118 999 False 1568.0 1568 95.000 1203 2201 1 chr4A.!!$F3 998
13 TraesCS6A01G168300 chr5A 610311034 610312022 988 False 1587.0 1587 95.652 1 988 1 chr5A.!!$F2 987
14 TraesCS6A01G168300 chr5A 481802109 481804097 1988 False 1577.5 1587 95.326 1 2201 2 chr5A.!!$F3 2200
15 TraesCS6A01G168300 chr5A 281763665 281764661 996 False 1563.0 1563 94.985 1203 2198 1 chr5A.!!$F1 995
16 TraesCS6A01G168300 chr7A 472331287 472332286 999 True 1574.0 1574 95.100 1203 2201 1 chr7A.!!$R1 998
17 TraesCS6A01G168300 chr1A 76434279 76435278 999 False 1546.0 1546 94.600 1203 2201 1 chr1A.!!$F1 998

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
419 422 0.681887 TTCATCCGGACGAGCACCTA 60.682 55.0 6.12 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 1707 0.035725 CCTGTTCTGCCATGAGAGCA 60.036 55.0 0.0 0.0 38.82 4.26 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 77 2.225727 GACCCTGCGTAAACCTTTCTTG 59.774 50.000 0.00 0.00 0.00 3.02
76 78 2.158726 ACCCTGCGTAAACCTTTCTTGA 60.159 45.455 0.00 0.00 0.00 3.02
85 87 6.367969 GCGTAAACCTTTCTTGATGTCTCTTA 59.632 38.462 0.00 0.00 0.00 2.10
201 203 1.619704 GGGGCTTCTTACAAAGGGCAT 60.620 52.381 0.00 0.00 32.33 4.40
243 246 7.696017 ACACCATAAAGACCAAATACCTTAGT 58.304 34.615 0.00 0.00 0.00 2.24
357 360 1.479323 TGCCTTACGTTCCGCTCTATT 59.521 47.619 0.00 0.00 0.00 1.73
419 422 0.681887 TTCATCCGGACGAGCACCTA 60.682 55.000 6.12 0.00 0.00 3.08
971 976 8.225603 TCAAGAACTTCTTCAAAATAGTGCTT 57.774 30.769 0.67 0.00 37.04 3.91
994 999 2.818132 CCACTCGGCCTCTCCATC 59.182 66.667 0.00 0.00 34.01 3.51
995 1000 2.801631 CCACTCGGCCTCTCCATCC 61.802 68.421 0.00 0.00 34.01 3.51
996 1001 2.444895 ACTCGGCCTCTCCATCCC 60.445 66.667 0.00 0.00 34.01 3.85
997 1002 3.237741 CTCGGCCTCTCCATCCCC 61.238 72.222 0.00 0.00 34.01 4.81
1000 1005 2.122989 GGCCTCTCCATCCCCGTA 60.123 66.667 0.00 0.00 34.01 4.02
1001 1006 1.536662 GGCCTCTCCATCCCCGTAT 60.537 63.158 0.00 0.00 34.01 3.06
1002 1007 1.674057 GCCTCTCCATCCCCGTATG 59.326 63.158 0.00 0.00 0.00 2.39
1003 1008 1.831652 GCCTCTCCATCCCCGTATGG 61.832 65.000 0.00 0.00 46.69 2.74
1020 1025 3.692406 GGTGGAGAACCCGTCGCT 61.692 66.667 0.00 0.00 44.02 4.93
1021 1026 2.432628 GTGGAGAACCCGTCGCTG 60.433 66.667 0.00 0.00 37.93 5.18
1022 1027 2.915659 TGGAGAACCCGTCGCTGT 60.916 61.111 0.00 0.00 37.93 4.40
1023 1028 2.126031 GGAGAACCCGTCGCTGTC 60.126 66.667 0.00 0.00 0.00 3.51
1024 1029 2.637383 GGAGAACCCGTCGCTGTCT 61.637 63.158 0.00 0.00 0.00 3.41
1025 1030 1.153997 GAGAACCCGTCGCTGTCTC 60.154 63.158 2.74 2.74 0.00 3.36
1026 1031 2.504244 GAACCCGTCGCTGTCTCG 60.504 66.667 0.00 0.00 0.00 4.04
1027 1032 3.966026 GAACCCGTCGCTGTCTCGG 62.966 68.421 0.00 0.00 43.30 4.63
1031 1036 4.406173 CGTCGCTGTCTCGGCTGT 62.406 66.667 0.00 0.00 32.89 4.40
1032 1037 2.807045 GTCGCTGTCTCGGCTGTG 60.807 66.667 0.00 0.00 32.89 3.66
1033 1038 2.983592 TCGCTGTCTCGGCTGTGA 60.984 61.111 0.00 0.00 32.89 3.58
1034 1039 2.182791 CGCTGTCTCGGCTGTGAT 59.817 61.111 0.00 0.00 32.89 3.06
1035 1040 1.029947 TCGCTGTCTCGGCTGTGATA 61.030 55.000 0.00 0.00 32.89 2.15
1036 1041 0.867753 CGCTGTCTCGGCTGTGATAC 60.868 60.000 0.00 0.00 32.89 2.24
1037 1042 0.528684 GCTGTCTCGGCTGTGATACC 60.529 60.000 0.00 0.00 32.24 2.73
1053 1058 3.863606 CCGGAGGCTCTAGGGAAG 58.136 66.667 15.23 0.00 46.14 3.46
1054 1059 1.075896 CCGGAGGCTCTAGGGAAGT 60.076 63.158 15.23 0.00 46.14 3.01
1055 1060 1.110518 CCGGAGGCTCTAGGGAAGTC 61.111 65.000 15.23 0.00 46.14 3.01
1056 1061 1.448922 CGGAGGCTCTAGGGAAGTCG 61.449 65.000 15.23 1.94 0.00 4.18
1057 1062 1.110518 GGAGGCTCTAGGGAAGTCGG 61.111 65.000 15.23 0.00 0.00 4.79
1058 1063 0.106619 GAGGCTCTAGGGAAGTCGGA 60.107 60.000 7.40 0.00 0.00 4.55
1059 1064 0.106419 AGGCTCTAGGGAAGTCGGAG 60.106 60.000 0.00 0.00 0.00 4.63
1060 1065 1.110518 GGCTCTAGGGAAGTCGGAGG 61.111 65.000 0.00 0.00 0.00 4.30
1061 1066 0.106619 GCTCTAGGGAAGTCGGAGGA 60.107 60.000 0.00 0.00 0.00 3.71
1062 1067 1.975660 CTCTAGGGAAGTCGGAGGAG 58.024 60.000 0.00 0.00 0.00 3.69
1063 1068 1.491332 CTCTAGGGAAGTCGGAGGAGA 59.509 57.143 0.00 0.00 0.00 3.71
1064 1069 1.491332 TCTAGGGAAGTCGGAGGAGAG 59.509 57.143 0.00 0.00 0.00 3.20
1065 1070 1.491332 CTAGGGAAGTCGGAGGAGAGA 59.509 57.143 0.00 0.00 0.00 3.10
1066 1071 0.257616 AGGGAAGTCGGAGGAGAGAG 59.742 60.000 0.00 0.00 0.00 3.20
1067 1072 1.388837 GGGAAGTCGGAGGAGAGAGC 61.389 65.000 0.00 0.00 0.00 4.09
1068 1073 0.681564 GGAAGTCGGAGGAGAGAGCA 60.682 60.000 0.00 0.00 0.00 4.26
1069 1074 0.454196 GAAGTCGGAGGAGAGAGCAC 59.546 60.000 0.00 0.00 0.00 4.40
1070 1075 0.039035 AAGTCGGAGGAGAGAGCACT 59.961 55.000 0.00 0.00 0.00 4.40
1071 1076 0.393808 AGTCGGAGGAGAGAGCACTC 60.394 60.000 2.51 2.51 42.90 3.51
1072 1077 0.678366 GTCGGAGGAGAGAGCACTCA 60.678 60.000 13.86 0.00 44.79 3.41
1073 1078 0.257328 TCGGAGGAGAGAGCACTCAT 59.743 55.000 13.86 3.31 44.79 2.90
1074 1079 0.667993 CGGAGGAGAGAGCACTCATC 59.332 60.000 13.86 11.77 44.79 2.92
1075 1080 1.750332 CGGAGGAGAGAGCACTCATCT 60.750 57.143 13.86 9.57 44.00 2.90
1076 1081 2.387757 GGAGGAGAGAGCACTCATCTT 58.612 52.381 13.86 4.72 44.00 2.40
1077 1082 2.101249 GGAGGAGAGAGCACTCATCTTG 59.899 54.545 13.86 0.00 44.00 3.02
1078 1083 2.101249 GAGGAGAGAGCACTCATCTTGG 59.899 54.545 13.86 0.00 44.79 3.61
1079 1084 1.138661 GGAGAGAGCACTCATCTTGGG 59.861 57.143 13.86 0.00 44.79 4.12
1080 1085 1.138661 GAGAGAGCACTCATCTTGGGG 59.861 57.143 13.86 0.00 44.79 4.96
1081 1086 0.908198 GAGAGCACTCATCTTGGGGT 59.092 55.000 6.25 0.00 42.21 4.95
1082 1087 0.617413 AGAGCACTCATCTTGGGGTG 59.383 55.000 0.00 0.00 0.00 4.61
1083 1088 0.393537 GAGCACTCATCTTGGGGTGG 60.394 60.000 0.00 0.00 0.00 4.61
1084 1089 1.379044 GCACTCATCTTGGGGTGGG 60.379 63.158 0.00 0.00 0.00 4.61
1085 1090 1.379044 CACTCATCTTGGGGTGGGC 60.379 63.158 0.00 0.00 0.00 5.36
1086 1091 1.542375 ACTCATCTTGGGGTGGGCT 60.542 57.895 0.00 0.00 0.00 5.19
1087 1092 1.142688 ACTCATCTTGGGGTGGGCTT 61.143 55.000 0.00 0.00 0.00 4.35
1088 1093 0.918983 CTCATCTTGGGGTGGGCTTA 59.081 55.000 0.00 0.00 0.00 3.09
1089 1094 0.623723 TCATCTTGGGGTGGGCTTAC 59.376 55.000 0.00 0.00 0.00 2.34
1090 1095 0.625849 CATCTTGGGGTGGGCTTACT 59.374 55.000 0.00 0.00 0.00 2.24
1091 1096 1.843851 CATCTTGGGGTGGGCTTACTA 59.156 52.381 0.00 0.00 0.00 1.82
1092 1097 1.282382 TCTTGGGGTGGGCTTACTAC 58.718 55.000 0.00 0.00 0.00 2.73
1093 1098 1.203389 TCTTGGGGTGGGCTTACTACT 60.203 52.381 0.00 0.00 0.00 2.57
1094 1099 1.633945 CTTGGGGTGGGCTTACTACTT 59.366 52.381 0.00 0.00 0.00 2.24
1095 1100 2.645951 TGGGGTGGGCTTACTACTTA 57.354 50.000 0.00 0.00 0.00 2.24
1096 1101 3.139606 TGGGGTGGGCTTACTACTTAT 57.860 47.619 0.00 0.00 0.00 1.73
1097 1102 4.283798 TGGGGTGGGCTTACTACTTATA 57.716 45.455 0.00 0.00 0.00 0.98
1098 1103 4.834852 TGGGGTGGGCTTACTACTTATAT 58.165 43.478 0.00 0.00 0.00 0.86
1099 1104 4.595781 TGGGGTGGGCTTACTACTTATATG 59.404 45.833 0.00 0.00 0.00 1.78
1100 1105 4.565028 GGGGTGGGCTTACTACTTATATGC 60.565 50.000 0.00 0.00 0.00 3.14
1101 1106 4.286291 GGGTGGGCTTACTACTTATATGCT 59.714 45.833 0.00 0.00 0.00 3.79
1102 1107 5.221864 GGGTGGGCTTACTACTTATATGCTT 60.222 44.000 0.00 0.00 0.00 3.91
1103 1108 6.296803 GGTGGGCTTACTACTTATATGCTTT 58.703 40.000 0.00 0.00 0.00 3.51
1104 1109 6.427242 GGTGGGCTTACTACTTATATGCTTTC 59.573 42.308 0.00 0.00 0.00 2.62
1105 1110 6.990349 GTGGGCTTACTACTTATATGCTTTCA 59.010 38.462 0.00 0.00 0.00 2.69
1106 1111 7.171678 GTGGGCTTACTACTTATATGCTTTCAG 59.828 40.741 0.00 0.00 0.00 3.02
1107 1112 6.147985 GGGCTTACTACTTATATGCTTTCAGC 59.852 42.308 0.00 0.00 42.82 4.26
1120 1125 3.202097 GCTTTCAGCAGTTATCCTCTCC 58.798 50.000 0.00 0.00 41.89 3.71
1121 1126 3.452474 CTTTCAGCAGTTATCCTCTCCG 58.548 50.000 0.00 0.00 0.00 4.63
1122 1127 0.747255 TCAGCAGTTATCCTCTCCGC 59.253 55.000 0.00 0.00 0.00 5.54
1123 1128 0.461548 CAGCAGTTATCCTCTCCGCA 59.538 55.000 0.00 0.00 0.00 5.69
1124 1129 0.461961 AGCAGTTATCCTCTCCGCAC 59.538 55.000 0.00 0.00 0.00 5.34
1125 1130 0.461961 GCAGTTATCCTCTCCGCACT 59.538 55.000 0.00 0.00 0.00 4.40
1126 1131 1.134670 GCAGTTATCCTCTCCGCACTT 60.135 52.381 0.00 0.00 0.00 3.16
1127 1132 2.544685 CAGTTATCCTCTCCGCACTTG 58.455 52.381 0.00 0.00 0.00 3.16
1128 1133 1.482593 AGTTATCCTCTCCGCACTTGG 59.517 52.381 0.00 0.00 0.00 3.61
1129 1134 0.178068 TTATCCTCTCCGCACTTGGC 59.822 55.000 0.00 0.00 39.90 4.52
1130 1135 0.687757 TATCCTCTCCGCACTTGGCT 60.688 55.000 0.00 0.00 41.67 4.75
1131 1136 0.687757 ATCCTCTCCGCACTTGGCTA 60.688 55.000 0.00 0.00 41.67 3.93
1132 1137 1.153549 CCTCTCCGCACTTGGCTAC 60.154 63.158 0.00 0.00 41.67 3.58
1133 1138 1.153549 CTCTCCGCACTTGGCTACC 60.154 63.158 0.00 0.00 41.67 3.18
1134 1139 2.125106 CTCCGCACTTGGCTACCC 60.125 66.667 0.00 0.00 41.67 3.69
1135 1140 2.925706 TCCGCACTTGGCTACCCA 60.926 61.111 0.00 0.00 41.67 4.51
1136 1141 2.436646 CCGCACTTGGCTACCCAG 60.437 66.667 0.00 0.00 43.37 4.45
1145 1150 3.790177 GCTACCCAGCGTTTACCG 58.210 61.111 0.00 0.00 38.22 4.02
1146 1151 1.079612 GCTACCCAGCGTTTACCGT 60.080 57.895 0.00 0.00 38.22 4.83
1147 1152 0.173255 GCTACCCAGCGTTTACCGTA 59.827 55.000 0.00 0.00 38.22 4.02
1148 1153 1.800286 GCTACCCAGCGTTTACCGTAG 60.800 57.143 0.00 0.00 38.22 3.51
1162 1167 2.910688 CCGTAGGCATGATAACTGGT 57.089 50.000 0.00 0.00 46.14 4.00
1164 1169 3.650139 CCGTAGGCATGATAACTGGTAC 58.350 50.000 0.00 0.00 46.14 3.34
1165 1170 3.069016 CCGTAGGCATGATAACTGGTACA 59.931 47.826 0.00 0.00 46.14 2.90
1166 1171 4.049186 CGTAGGCATGATAACTGGTACAC 58.951 47.826 0.00 0.00 0.00 2.90
1167 1172 3.560636 AGGCATGATAACTGGTACACC 57.439 47.619 0.00 0.00 0.00 4.16
1168 1173 2.843730 AGGCATGATAACTGGTACACCA 59.156 45.455 0.00 0.28 45.30 4.17
1188 1193 4.754667 GGTGCGTCCTTCCCGGTC 62.755 72.222 0.00 0.00 0.00 4.79
1189 1194 4.754667 GTGCGTCCTTCCCGGTCC 62.755 72.222 0.00 0.00 0.00 4.46
1191 1196 4.144703 GCGTCCTTCCCGGTCCTC 62.145 72.222 0.00 0.00 0.00 3.71
1192 1197 2.362632 CGTCCTTCCCGGTCCTCT 60.363 66.667 0.00 0.00 0.00 3.69
1193 1198 2.416432 CGTCCTTCCCGGTCCTCTC 61.416 68.421 0.00 0.00 0.00 3.20
1194 1199 2.044252 TCCTTCCCGGTCCTCTCG 60.044 66.667 0.00 0.00 0.00 4.04
1195 1200 2.362632 CCTTCCCGGTCCTCTCGT 60.363 66.667 0.00 0.00 0.00 4.18
1196 1201 1.077212 CCTTCCCGGTCCTCTCGTA 60.077 63.158 0.00 0.00 0.00 3.43
1197 1202 1.382692 CCTTCCCGGTCCTCTCGTAC 61.383 65.000 0.00 0.00 0.00 3.67
1198 1203 0.394080 CTTCCCGGTCCTCTCGTACT 60.394 60.000 0.00 0.00 0.00 2.73
1199 1204 0.911769 TTCCCGGTCCTCTCGTACTA 59.088 55.000 0.00 0.00 0.00 1.82
1200 1205 0.467384 TCCCGGTCCTCTCGTACTAG 59.533 60.000 0.00 0.00 0.00 2.57
1201 1206 0.534652 CCCGGTCCTCTCGTACTAGG 60.535 65.000 0.00 0.00 0.00 3.02
1248 1253 2.574018 TAGCATCCATCTCCGCCCG 61.574 63.158 0.00 0.00 0.00 6.13
1398 1403 5.738909 CTTTTCCGGCCATAGATGATCTAT 58.261 41.667 9.11 9.11 40.13 1.98
1413 1418 2.748209 TCTATGACGGACCTCATGGA 57.252 50.000 12.70 12.70 36.20 3.41
1448 1453 2.214376 ATTGAGTTCGGCCCATTCAA 57.786 45.000 9.26 9.26 32.90 2.69
1508 1513 1.569479 GAACTGCGACCAGAACAGCC 61.569 60.000 0.00 0.00 41.77 4.85
1555 1560 2.986311 GAAGTATTCGGCCGCATCA 58.014 52.632 23.51 0.00 34.17 3.07
1584 1589 0.179045 GCCGCCAAGTCCAGATATGT 60.179 55.000 0.00 0.00 0.00 2.29
1702 1707 4.455606 CTTCACACAGTTCCTCCTTCTTT 58.544 43.478 0.00 0.00 0.00 2.52
1823 1828 4.429108 GGCAGTGTCTTTTAACTTTGCAA 58.571 39.130 0.00 0.00 33.65 4.08
1869 1874 4.120331 GCAATGCGCCGCCTTCTT 62.120 61.111 6.63 0.00 32.94 2.52
1883 1888 3.911661 CCTTCTTGGCTTTGAACTCTG 57.088 47.619 0.00 0.00 0.00 3.35
1926 1931 4.436050 CGCATTACTACTCCTTGCTTGTTG 60.436 45.833 0.00 0.00 0.00 3.33
1945 1950 2.836154 TTGGCTCGGGCAAGTTCT 59.164 55.556 10.74 0.00 42.98 3.01
2014 2020 2.698855 AAGATACTGGCATCACGCTT 57.301 45.000 0.00 0.00 41.91 4.68
2032 2038 5.457148 CACGCTTCTCTTACTATGTGACATC 59.543 44.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 87 4.594920 AGAATCCGAGGGATGTGTATCAAT 59.405 41.667 0.00 0.00 42.27 2.57
201 203 2.228925 GTGTAAACCGGGCCTAAACAA 58.771 47.619 6.32 0.00 0.00 2.83
357 360 4.408821 CTGGTGCCGCCTTAGCCA 62.409 66.667 0.00 0.00 38.35 4.75
419 422 4.750598 GTCAGTTTTCGGCTTTCTCTACTT 59.249 41.667 0.00 0.00 0.00 2.24
540 543 4.188702 CGAATTCGGGGTGCGTAA 57.811 55.556 20.16 0.00 35.37 3.18
1003 1008 3.692406 AGCGACGGGTTCTCCACC 61.692 66.667 0.00 0.00 46.46 4.61
1004 1009 2.432628 CAGCGACGGGTTCTCCAC 60.433 66.667 0.00 0.00 34.36 4.02
1005 1010 2.915659 ACAGCGACGGGTTCTCCA 60.916 61.111 0.00 0.00 34.36 3.86
1006 1011 2.126031 GACAGCGACGGGTTCTCC 60.126 66.667 0.00 0.00 0.00 3.71
1007 1012 1.153997 GAGACAGCGACGGGTTCTC 60.154 63.158 0.00 0.00 0.00 2.87
1008 1013 2.963371 GAGACAGCGACGGGTTCT 59.037 61.111 0.00 0.00 0.00 3.01
1009 1014 2.504244 CGAGACAGCGACGGGTTC 60.504 66.667 0.00 0.00 0.00 3.62
1010 1015 4.052229 CCGAGACAGCGACGGGTT 62.052 66.667 0.00 0.00 42.48 4.11
1014 1019 4.406173 ACAGCCGAGACAGCGACG 62.406 66.667 0.00 0.00 34.64 5.12
1015 1020 2.549611 ATCACAGCCGAGACAGCGAC 62.550 60.000 0.00 0.00 34.64 5.19
1016 1021 1.029947 TATCACAGCCGAGACAGCGA 61.030 55.000 0.00 0.00 34.64 4.93
1017 1022 0.867753 GTATCACAGCCGAGACAGCG 60.868 60.000 0.00 0.00 34.64 5.18
1018 1023 0.528684 GGTATCACAGCCGAGACAGC 60.529 60.000 0.00 0.00 0.00 4.40
1019 1024 3.650409 GGTATCACAGCCGAGACAG 57.350 57.895 0.00 0.00 0.00 3.51
1025 1030 2.417516 CCTCCGGTATCACAGCCG 59.582 66.667 0.00 0.00 46.80 5.52
1026 1031 2.109181 GCCTCCGGTATCACAGCC 59.891 66.667 0.00 0.00 0.00 4.85
1027 1032 1.068250 GAGCCTCCGGTATCACAGC 59.932 63.158 0.00 0.00 0.00 4.40
1028 1033 1.883275 CTAGAGCCTCCGGTATCACAG 59.117 57.143 0.00 0.00 0.00 3.66
1029 1034 1.478837 CCTAGAGCCTCCGGTATCACA 60.479 57.143 0.00 0.00 0.00 3.58
1030 1035 1.249407 CCTAGAGCCTCCGGTATCAC 58.751 60.000 0.00 0.00 0.00 3.06
1031 1036 0.112606 CCCTAGAGCCTCCGGTATCA 59.887 60.000 0.00 0.00 0.00 2.15
1032 1037 0.404812 TCCCTAGAGCCTCCGGTATC 59.595 60.000 0.00 0.00 0.00 2.24
1033 1038 0.858369 TTCCCTAGAGCCTCCGGTAT 59.142 55.000 0.00 0.00 0.00 2.73
1034 1039 0.185416 CTTCCCTAGAGCCTCCGGTA 59.815 60.000 0.00 0.00 0.00 4.02
1035 1040 1.075896 CTTCCCTAGAGCCTCCGGT 60.076 63.158 0.00 0.00 0.00 5.28
1036 1041 1.075896 ACTTCCCTAGAGCCTCCGG 60.076 63.158 0.00 0.00 0.00 5.14
1037 1042 1.448922 CGACTTCCCTAGAGCCTCCG 61.449 65.000 0.00 0.00 0.00 4.63
1038 1043 1.110518 CCGACTTCCCTAGAGCCTCC 61.111 65.000 0.00 0.00 0.00 4.30
1039 1044 0.106619 TCCGACTTCCCTAGAGCCTC 60.107 60.000 0.00 0.00 0.00 4.70
1040 1045 0.106419 CTCCGACTTCCCTAGAGCCT 60.106 60.000 0.00 0.00 0.00 4.58
1041 1046 1.110518 CCTCCGACTTCCCTAGAGCC 61.111 65.000 0.00 0.00 0.00 4.70
1042 1047 0.106619 TCCTCCGACTTCCCTAGAGC 60.107 60.000 0.00 0.00 0.00 4.09
1043 1048 1.491332 TCTCCTCCGACTTCCCTAGAG 59.509 57.143 0.00 0.00 0.00 2.43
1044 1049 1.491332 CTCTCCTCCGACTTCCCTAGA 59.509 57.143 0.00 0.00 0.00 2.43
1045 1050 1.491332 TCTCTCCTCCGACTTCCCTAG 59.509 57.143 0.00 0.00 0.00 3.02
1046 1051 1.491332 CTCTCTCCTCCGACTTCCCTA 59.509 57.143 0.00 0.00 0.00 3.53
1047 1052 0.257616 CTCTCTCCTCCGACTTCCCT 59.742 60.000 0.00 0.00 0.00 4.20
1048 1053 1.388837 GCTCTCTCCTCCGACTTCCC 61.389 65.000 0.00 0.00 0.00 3.97
1049 1054 0.681564 TGCTCTCTCCTCCGACTTCC 60.682 60.000 0.00 0.00 0.00 3.46
1050 1055 0.454196 GTGCTCTCTCCTCCGACTTC 59.546 60.000 0.00 0.00 0.00 3.01
1051 1056 0.039035 AGTGCTCTCTCCTCCGACTT 59.961 55.000 0.00 0.00 0.00 3.01
1052 1057 0.393808 GAGTGCTCTCTCCTCCGACT 60.394 60.000 8.54 0.00 37.68 4.18
1053 1058 0.678366 TGAGTGCTCTCTCCTCCGAC 60.678 60.000 16.23 0.00 40.98 4.79
1054 1059 0.257328 ATGAGTGCTCTCTCCTCCGA 59.743 55.000 16.23 0.00 40.98 4.55
1055 1060 0.667993 GATGAGTGCTCTCTCCTCCG 59.332 60.000 16.23 0.00 40.98 4.63
1056 1061 2.071778 AGATGAGTGCTCTCTCCTCC 57.928 55.000 16.23 2.38 40.98 4.30
1057 1062 2.101249 CCAAGATGAGTGCTCTCTCCTC 59.899 54.545 16.23 10.33 40.98 3.71
1058 1063 2.109774 CCAAGATGAGTGCTCTCTCCT 58.890 52.381 16.23 10.17 40.98 3.69
1059 1064 1.138661 CCCAAGATGAGTGCTCTCTCC 59.861 57.143 16.23 8.25 40.98 3.71
1060 1065 1.138661 CCCCAAGATGAGTGCTCTCTC 59.861 57.143 16.23 11.01 40.98 3.20
1061 1066 1.202330 CCCCAAGATGAGTGCTCTCT 58.798 55.000 16.23 2.84 40.98 3.10
1062 1067 0.908198 ACCCCAAGATGAGTGCTCTC 59.092 55.000 8.86 8.86 40.79 3.20
1063 1068 0.617413 CACCCCAAGATGAGTGCTCT 59.383 55.000 0.68 0.00 0.00 4.09
1064 1069 0.393537 CCACCCCAAGATGAGTGCTC 60.394 60.000 0.00 0.00 0.00 4.26
1065 1070 1.687612 CCACCCCAAGATGAGTGCT 59.312 57.895 0.00 0.00 0.00 4.40
1066 1071 1.379044 CCCACCCCAAGATGAGTGC 60.379 63.158 0.00 0.00 0.00 4.40
1067 1072 1.379044 GCCCACCCCAAGATGAGTG 60.379 63.158 0.00 0.00 0.00 3.51
1068 1073 1.142688 AAGCCCACCCCAAGATGAGT 61.143 55.000 0.00 0.00 0.00 3.41
1069 1074 0.918983 TAAGCCCACCCCAAGATGAG 59.081 55.000 0.00 0.00 0.00 2.90
1070 1075 0.623723 GTAAGCCCACCCCAAGATGA 59.376 55.000 0.00 0.00 0.00 2.92
1071 1076 0.625849 AGTAAGCCCACCCCAAGATG 59.374 55.000 0.00 0.00 0.00 2.90
1072 1077 1.844497 GTAGTAAGCCCACCCCAAGAT 59.156 52.381 0.00 0.00 0.00 2.40
1073 1078 1.203389 AGTAGTAAGCCCACCCCAAGA 60.203 52.381 0.00 0.00 0.00 3.02
1074 1079 1.286248 AGTAGTAAGCCCACCCCAAG 58.714 55.000 0.00 0.00 0.00 3.61
1075 1080 1.750022 AAGTAGTAAGCCCACCCCAA 58.250 50.000 0.00 0.00 0.00 4.12
1076 1081 2.645951 TAAGTAGTAAGCCCACCCCA 57.354 50.000 0.00 0.00 0.00 4.96
1077 1082 4.565028 GCATATAAGTAGTAAGCCCACCCC 60.565 50.000 0.00 0.00 0.00 4.95
1078 1083 4.286291 AGCATATAAGTAGTAAGCCCACCC 59.714 45.833 0.00 0.00 0.00 4.61
1079 1084 5.485209 AGCATATAAGTAGTAAGCCCACC 57.515 43.478 0.00 0.00 0.00 4.61
1080 1085 6.990349 TGAAAGCATATAAGTAGTAAGCCCAC 59.010 38.462 0.00 0.00 0.00 4.61
1081 1086 7.131907 TGAAAGCATATAAGTAGTAAGCCCA 57.868 36.000 0.00 0.00 0.00 5.36
1082 1087 7.659652 CTGAAAGCATATAAGTAGTAAGCCC 57.340 40.000 0.00 0.00 0.00 5.19
1100 1105 3.452474 CGGAGAGGATAACTGCTGAAAG 58.548 50.000 0.00 0.00 0.00 2.62
1101 1106 2.418746 GCGGAGAGGATAACTGCTGAAA 60.419 50.000 0.00 0.00 33.73 2.69
1102 1107 1.137086 GCGGAGAGGATAACTGCTGAA 59.863 52.381 0.00 0.00 33.73 3.02
1103 1108 0.747255 GCGGAGAGGATAACTGCTGA 59.253 55.000 0.00 0.00 33.73 4.26
1104 1109 0.461548 TGCGGAGAGGATAACTGCTG 59.538 55.000 0.00 0.00 36.92 4.41
1105 1110 0.461961 GTGCGGAGAGGATAACTGCT 59.538 55.000 0.00 0.00 36.92 4.24
1106 1111 0.461961 AGTGCGGAGAGGATAACTGC 59.538 55.000 0.00 0.00 36.58 4.40
1107 1112 2.544685 CAAGTGCGGAGAGGATAACTG 58.455 52.381 0.00 0.00 0.00 3.16
1108 1113 1.482593 CCAAGTGCGGAGAGGATAACT 59.517 52.381 0.00 0.00 0.00 2.24
1109 1114 1.941325 CCAAGTGCGGAGAGGATAAC 58.059 55.000 0.00 0.00 0.00 1.89
1110 1115 0.178068 GCCAAGTGCGGAGAGGATAA 59.822 55.000 0.00 0.00 0.00 1.75
1111 1116 1.823295 GCCAAGTGCGGAGAGGATA 59.177 57.895 0.00 0.00 0.00 2.59
1112 1117 2.586792 GCCAAGTGCGGAGAGGAT 59.413 61.111 0.00 0.00 0.00 3.24
1128 1133 3.790177 CGGTAAACGCTGGGTAGC 58.210 61.111 0.00 0.00 46.62 3.58
1138 1143 4.510340 CCAGTTATCATGCCTACGGTAAAC 59.490 45.833 0.00 0.00 0.00 2.01
1139 1144 4.162698 ACCAGTTATCATGCCTACGGTAAA 59.837 41.667 0.00 0.00 0.00 2.01
1140 1145 3.707611 ACCAGTTATCATGCCTACGGTAA 59.292 43.478 0.00 0.00 0.00 2.85
1141 1146 3.302161 ACCAGTTATCATGCCTACGGTA 58.698 45.455 0.00 0.00 0.00 4.02
1142 1147 2.116238 ACCAGTTATCATGCCTACGGT 58.884 47.619 0.00 0.00 0.00 4.83
1143 1148 2.910688 ACCAGTTATCATGCCTACGG 57.089 50.000 0.00 0.00 0.00 4.02
1144 1149 4.049186 GTGTACCAGTTATCATGCCTACG 58.951 47.826 0.00 0.00 0.00 3.51
1145 1150 4.141801 TGGTGTACCAGTTATCATGCCTAC 60.142 45.833 0.00 0.00 42.01 3.18
1146 1151 4.034410 TGGTGTACCAGTTATCATGCCTA 58.966 43.478 0.00 0.00 42.01 3.93
1147 1152 2.843730 TGGTGTACCAGTTATCATGCCT 59.156 45.455 0.00 0.00 42.01 4.75
1148 1153 3.275617 TGGTGTACCAGTTATCATGCC 57.724 47.619 0.00 0.00 42.01 4.40
1171 1176 4.754667 GACCGGGAAGGACGCACC 62.755 72.222 6.32 0.00 45.00 5.01
1172 1177 4.754667 GGACCGGGAAGGACGCAC 62.755 72.222 6.32 0.00 45.00 5.34
1174 1179 4.144703 GAGGACCGGGAAGGACGC 62.145 72.222 6.32 0.00 45.00 5.19
1175 1180 2.362632 AGAGGACCGGGAAGGACG 60.363 66.667 6.32 0.00 45.00 4.79
1176 1181 2.416432 CGAGAGGACCGGGAAGGAC 61.416 68.421 6.32 0.00 45.00 3.85
1177 1182 1.565390 TACGAGAGGACCGGGAAGGA 61.565 60.000 6.32 0.00 45.00 3.36
1179 1184 2.105124 GTACGAGAGGACCGGGAAG 58.895 63.158 6.32 0.00 39.75 3.46
1180 1185 4.326255 GTACGAGAGGACCGGGAA 57.674 61.111 6.32 0.00 39.75 3.97
1186 1191 1.881324 GCCATCCTAGTACGAGAGGAC 59.119 57.143 14.21 2.04 44.64 3.85
1187 1192 1.202903 GGCCATCCTAGTACGAGAGGA 60.203 57.143 14.26 14.26 45.88 3.71
1188 1193 1.249407 GGCCATCCTAGTACGAGAGG 58.751 60.000 4.34 4.96 0.00 3.69
1189 1194 0.875728 CGGCCATCCTAGTACGAGAG 59.124 60.000 2.24 0.00 0.00 3.20
1190 1195 0.471191 TCGGCCATCCTAGTACGAGA 59.529 55.000 2.24 0.00 0.00 4.04
1191 1196 1.001597 GTTCGGCCATCCTAGTACGAG 60.002 57.143 2.24 0.00 0.00 4.18
1192 1197 1.027357 GTTCGGCCATCCTAGTACGA 58.973 55.000 2.24 0.00 0.00 3.43
1193 1198 0.031721 GGTTCGGCCATCCTAGTACG 59.968 60.000 2.24 0.00 37.17 3.67
1194 1199 0.391966 GGGTTCGGCCATCCTAGTAC 59.608 60.000 2.24 0.00 39.65 2.73
1195 1200 0.263765 AGGGTTCGGCCATCCTAGTA 59.736 55.000 2.24 0.00 39.65 1.82
1196 1201 1.003051 AGGGTTCGGCCATCCTAGT 59.997 57.895 2.24 0.00 39.65 2.57
1197 1202 1.447643 CAGGGTTCGGCCATCCTAG 59.552 63.158 2.24 0.00 39.65 3.02
1198 1203 2.742116 GCAGGGTTCGGCCATCCTA 61.742 63.158 2.24 0.00 39.65 2.94
1199 1204 4.115199 GCAGGGTTCGGCCATCCT 62.115 66.667 2.24 0.00 39.65 3.24
1248 1253 0.958382 TGCCCGTGTCAAAGCATACC 60.958 55.000 0.00 0.00 0.00 2.73
1320 1325 3.505790 TTCCTTGGTGCGGTGCCAT 62.506 57.895 0.00 0.00 35.71 4.40
1398 1403 1.275291 GACTTTCCATGAGGTCCGTCA 59.725 52.381 0.00 0.00 35.89 4.35
1413 1418 3.326880 ACTCAATAGGTTGTCCGGACTTT 59.673 43.478 33.39 18.49 39.05 2.66
1448 1453 2.388735 TCCATTGACCGATCAGCTAGT 58.611 47.619 0.00 0.00 35.83 2.57
1508 1513 0.898320 ACAGATCGGGAAGTGGACAG 59.102 55.000 0.00 0.00 0.00 3.51
1584 1589 3.220999 CTGTGGAGTTCGGCGGACA 62.221 63.158 22.14 6.82 0.00 4.02
1702 1707 0.035725 CCTGTTCTGCCATGAGAGCA 60.036 55.000 0.00 0.00 38.82 4.26
1823 1828 3.463048 AGAGAAAATGGCCAAGATGGT 57.537 42.857 10.96 0.00 40.46 3.55
1869 1874 2.260869 GCCGCAGAGTTCAAAGCCA 61.261 57.895 0.00 0.00 0.00 4.75
1926 1931 1.172812 AGAACTTGCCCGAGCCAAAC 61.173 55.000 0.00 0.00 38.69 2.93
2032 2038 5.590259 CAGGGTAAGTGATATTTTCTGGTGG 59.410 44.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.