Multiple sequence alignment - TraesCS7D01G083700

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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 TraesCS7D01G083700 chr7D 100.000 2620 0 0 1 2620 50651217 50653836 0.000000e+00 4839.0
1 TraesCS7D01G083700 chr7D 80.424 802 89 32 1804 2587 50716542 50717293 1.370000e-152 549.0
2 TraesCS7D01G083700 chr7D 80.983 631 78 28 2002 2619 51667022 51666421 1.840000e-126 462.0
3 TraesCS7D01G083700 chr7D 79.749 637 87 25 1996 2619 51695972 51695365 8.670000e-115 424.0
4 TraesCS7D01G083700 chr7D 84.925 199 22 6 1821 2011 51696358 51696160 7.400000e-46 195.0
5 TraesCS7D01G083700 chr7D 81.897 116 10 4 77 181 21431239 21431124 1.290000e-13 87.9
6 TraesCS7D01G083700 chr7A 91.330 1188 53 22 1446 2620 53614913 53616063 0.000000e+00 1578.0
7 TraesCS7D01G083700 chr7A 81.662 349 36 18 184 519 22040153 22040486 5.560000e-67 265.0
8 TraesCS7D01G083700 chr7A 84.615 195 20 5 326 519 21626366 21626551 4.450000e-43 185.0
9 TraesCS7D01G083700 chr6D 98.077 520 9 1 1 520 36220880 36221398 0.000000e+00 904.0
10 TraesCS7D01G083700 chr4A 92.944 411 19 2 532 933 665450205 665450614 8.080000e-165 590.0
11 TraesCS7D01G083700 chr4A 94.315 387 18 1 1241 1627 665450606 665450988 8.080000e-165 590.0
12 TraesCS7D01G083700 chr4A 82.648 559 66 18 1808 2352 665929140 665928599 1.420000e-127 466.0
13 TraesCS7D01G083700 chr4A 80.286 629 86 23 2002 2619 665933390 665932789 8.610000e-120 440.0
14 TraesCS7D01G083700 chr4A 79.683 630 85 24 2002 2618 665934850 665934251 5.220000e-112 414.0
15 TraesCS7D01G083700 chr4A 78.630 613 90 22 1996 2595 666073002 666072418 4.120000e-98 368.0
16 TraesCS7D01G083700 chr4A 95.580 181 8 0 1 181 482874774 482874594 9.170000e-75 291.0
17 TraesCS7D01G083700 chr4A 95.580 181 8 0 1 181 507541551 507541371 9.170000e-75 291.0
18 TraesCS7D01G083700 chr4A 82.724 301 46 3 1823 2120 665969273 665968976 2.000000e-66 263.0
19 TraesCS7D01G083700 chr4A 90.659 182 14 2 2379 2558 665959841 665959661 3.370000e-59 239.0
20 TraesCS7D01G083700 chr4A 85.398 226 30 1 1810 2035 666014628 666014406 5.640000e-57 231.0
21 TraesCS7D01G083700 chr4A 86.829 205 18 4 2389 2587 665928592 665928391 1.220000e-53 220.0
22 TraesCS7D01G083700 chr4A 78.495 93 20 0 1918 2010 666073282 666073190 7.830000e-06 62.1
23 TraesCS7D01G083700 chr4B 86.378 323 12 18 1 291 559853126 559852804 9.040000e-85 324.0
24 TraesCS7D01G083700 chr4B 95.455 110 2 2 342 449 559852806 559852698 3.470000e-39 172.0
25 TraesCS7D01G083700 chr4B 92.473 93 7 0 428 520 559852599 559852507 1.640000e-27 134.0
26 TraesCS7D01G083700 chrUn 95.580 181 8 0 1 181 439879243 439879063 9.170000e-75 291.0
27 TraesCS7D01G083700 chr6A 95.580 181 8 0 1 181 105172953 105173133 9.170000e-75 291.0
28 TraesCS7D01G083700 chr3A 95.580 181 8 0 1 181 63428261 63428081 9.170000e-75 291.0


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 TraesCS7D01G083700 chr7D 50651217 50653836 2619 False 4839.00 4839 100.000000 1 2620 1 chr7D.!!$F1 2619
1 TraesCS7D01G083700 chr7D 50716542 50717293 751 False 549.00 549 80.424000 1804 2587 1 chr7D.!!$F2 783
2 TraesCS7D01G083700 chr7D 51666421 51667022 601 True 462.00 462 80.983000 2002 2619 1 chr7D.!!$R2 617
3 TraesCS7D01G083700 chr7D 51695365 51696358 993 True 309.50 424 82.337000 1821 2619 2 chr7D.!!$R3 798
4 TraesCS7D01G083700 chr7A 53614913 53616063 1150 False 1578.00 1578 91.330000 1446 2620 1 chr7A.!!$F3 1174
5 TraesCS7D01G083700 chr6D 36220880 36221398 518 False 904.00 904 98.077000 1 520 1 chr6D.!!$F1 519
6 TraesCS7D01G083700 chr4A 665450205 665450988 783 False 590.00 590 93.629500 532 1627 2 chr4A.!!$F1 1095
7 TraesCS7D01G083700 chr4A 665928391 665934850 6459 True 385.00 466 82.361500 1808 2619 4 chr4A.!!$R6 811
8 TraesCS7D01G083700 chr4A 666072418 666073282 864 True 215.05 368 78.562500 1918 2595 2 chr4A.!!$R7 677
9 TraesCS7D01G083700 chr4B 559852507 559853126 619 True 210.00 324 91.435333 1 520 3 chr4B.!!$R1 519

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
528 682 0.258774 AGTTGAACAACCCTGCCACT 59.741 50.0 13.07 0.0 42.06 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 5848 1.227853 ACGGTGGTGACAAGAAGGC 60.228 57.895 0.0 0.0 46.06 4.35 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
154 158 4.467084 GCTCGACATCGGGGCCAA 62.467 66.667 4.39 0.00 40.87 4.52
293 326 3.796844 GCTTTTGAACCACCTCTCTTTGC 60.797 47.826 0.00 0.00 0.00 3.68
404 437 4.202090 TGTGTTTTATGAATGTGCACTGCA 60.202 37.500 19.41 13.32 35.60 4.41
467 621 6.599356 TCAATAAGCTGGTACTGTCACTTA 57.401 37.500 0.00 0.00 0.00 2.24
522 676 8.098912 AGAACGTTATATAAGTTGAACAACCCT 58.901 33.333 13.07 4.97 42.06 4.34
523 677 7.605410 ACGTTATATAAGTTGAACAACCCTG 57.395 36.000 13.07 0.00 42.06 4.45
525 679 6.457799 CGTTATATAAGTTGAACAACCCTGCC 60.458 42.308 13.07 0.00 42.06 4.85
526 680 2.738587 TAAGTTGAACAACCCTGCCA 57.261 45.000 13.07 0.00 42.06 4.92
528 682 0.258774 AGTTGAACAACCCTGCCACT 59.741 50.000 13.07 0.00 42.06 4.00
529 683 1.493022 AGTTGAACAACCCTGCCACTA 59.507 47.619 13.07 0.00 42.06 2.74
530 684 1.880027 GTTGAACAACCCTGCCACTAG 59.120 52.381 6.43 0.00 35.36 2.57
564 718 4.434520 AGCTCTACGCCTAGTTCAATTTC 58.565 43.478 0.00 0.00 40.39 2.17
655 809 1.939980 AGACTAGAAGGGCGAAACCT 58.060 50.000 0.00 0.00 44.56 3.50
663 817 1.353091 AGGGCGAAACCTCTTCTCTT 58.647 50.000 0.00 0.00 35.43 2.85
703 857 4.020839 ACTTGCATTTCCCTCCAAAATCTG 60.021 41.667 0.00 0.00 0.00 2.90
749 903 4.512944 GCGGTAGTTCATCATGATCACATT 59.487 41.667 4.86 0.00 34.15 2.71
819 973 4.771590 TCAATCAATTGCTCACCAGTTC 57.228 40.909 0.00 0.00 37.68 3.01
847 1010 5.240121 TCATCATCATCATCACATAACCCG 58.760 41.667 0.00 0.00 0.00 5.28
851 1014 6.768483 TCATCATCATCACATAACCCGTAAT 58.232 36.000 0.00 0.00 0.00 1.89
879 1042 3.438087 CGTCATCTTGTCAGCCAAATTCT 59.562 43.478 0.00 0.00 31.20 2.40
883 1046 4.572985 TCTTGTCAGCCAAATTCTGTTG 57.427 40.909 0.00 0.00 33.48 3.33
884 1047 2.798976 TGTCAGCCAAATTCTGTTGC 57.201 45.000 0.00 0.00 33.48 4.17
921 1084 1.293924 CGCTCCAGTTCATCACCATC 58.706 55.000 0.00 0.00 0.00 3.51
924 1087 2.877168 GCTCCAGTTCATCACCATCATC 59.123 50.000 0.00 0.00 0.00 2.92
925 1088 3.129109 CTCCAGTTCATCACCATCATCG 58.871 50.000 0.00 0.00 0.00 3.84
926 1089 1.600957 CCAGTTCATCACCATCATCGC 59.399 52.381 0.00 0.00 0.00 4.58
927 1090 2.282407 CAGTTCATCACCATCATCGCA 58.718 47.619 0.00 0.00 0.00 5.10
929 1092 2.876550 AGTTCATCACCATCATCGCATG 59.123 45.455 0.00 0.00 0.00 4.06
930 1093 2.874086 GTTCATCACCATCATCGCATGA 59.126 45.455 0.00 2.05 44.55 3.07
931 1094 2.486918 TCATCACCATCATCGCATGAC 58.513 47.619 0.00 0.00 43.01 3.06
932 1095 1.534163 CATCACCATCATCGCATGACC 59.466 52.381 0.00 0.00 43.01 4.02
937 1100 1.162698 CATCATCGCATGACCCATCC 58.837 55.000 0.00 0.00 43.01 3.51
938 1101 0.766752 ATCATCGCATGACCCATCCA 59.233 50.000 0.00 0.00 43.01 3.41
940 1103 0.664761 CATCGCATGACCCATCCAAC 59.335 55.000 0.00 0.00 0.00 3.77
941 1104 0.815213 ATCGCATGACCCATCCAACG 60.815 55.000 0.00 0.00 0.00 4.10
942 1105 1.449423 CGCATGACCCATCCAACGA 60.449 57.895 0.00 0.00 0.00 3.85
943 1106 1.024046 CGCATGACCCATCCAACGAA 61.024 55.000 0.00 0.00 0.00 3.85
944 1107 0.451783 GCATGACCCATCCAACGAAC 59.548 55.000 0.00 0.00 0.00 3.95
946 1109 1.468520 CATGACCCATCCAACGAACAC 59.531 52.381 0.00 0.00 0.00 3.32
947 1110 0.470341 TGACCCATCCAACGAACACA 59.530 50.000 0.00 0.00 0.00 3.72
948 1111 0.872388 GACCCATCCAACGAACACAC 59.128 55.000 0.00 0.00 0.00 3.82
949 1112 0.536460 ACCCATCCAACGAACACACC 60.536 55.000 0.00 0.00 0.00 4.16
950 1113 1.241315 CCCATCCAACGAACACACCC 61.241 60.000 0.00 0.00 0.00 4.61
951 1114 1.573829 CCATCCAACGAACACACCCG 61.574 60.000 0.00 0.00 0.00 5.28
952 1115 1.964373 ATCCAACGAACACACCCGC 60.964 57.895 0.00 0.00 0.00 6.13
953 1116 3.656045 CCAACGAACACACCCGCC 61.656 66.667 0.00 0.00 0.00 6.13
954 1117 2.897846 CAACGAACACACCCGCCA 60.898 61.111 0.00 0.00 0.00 5.69
955 1118 2.112297 AACGAACACACCCGCCAT 59.888 55.556 0.00 0.00 0.00 4.40
957 1120 1.512156 AACGAACACACCCGCCATTC 61.512 55.000 0.00 0.00 0.00 2.67
958 1121 1.671054 CGAACACACCCGCCATTCT 60.671 57.895 0.00 0.00 0.00 2.40
959 1122 1.875963 GAACACACCCGCCATTCTG 59.124 57.895 0.00 0.00 0.00 3.02
960 1123 2.200170 GAACACACCCGCCATTCTGC 62.200 60.000 0.00 0.00 0.00 4.26
961 1124 3.443045 CACACCCGCCATTCTGCC 61.443 66.667 0.00 0.00 0.00 4.85
962 1125 3.965258 ACACCCGCCATTCTGCCA 61.965 61.111 0.00 0.00 0.00 4.92
963 1126 3.136123 CACCCGCCATTCTGCCAG 61.136 66.667 0.00 0.00 0.00 4.85
967 1130 2.768492 CCGCCATTCTGCCAGCTTC 61.768 63.158 0.00 0.00 0.00 3.86
968 1131 2.042259 CGCCATTCTGCCAGCTTCA 61.042 57.895 0.00 0.00 0.00 3.02
969 1132 1.381928 CGCCATTCTGCCAGCTTCAT 61.382 55.000 0.00 0.00 0.00 2.57
970 1133 0.822164 GCCATTCTGCCAGCTTCATT 59.178 50.000 0.00 0.00 0.00 2.57
971 1134 1.206371 GCCATTCTGCCAGCTTCATTT 59.794 47.619 0.00 0.00 0.00 2.32
972 1135 2.737679 GCCATTCTGCCAGCTTCATTTC 60.738 50.000 0.00 0.00 0.00 2.17
973 1136 2.479049 CCATTCTGCCAGCTTCATTTCG 60.479 50.000 0.00 0.00 0.00 3.46
974 1137 0.523072 TTCTGCCAGCTTCATTTCGC 59.477 50.000 0.00 0.00 0.00 4.70
976 1139 1.303561 TGCCAGCTTCATTTCGCCT 60.304 52.632 0.00 0.00 0.00 5.52
977 1140 1.308069 TGCCAGCTTCATTTCGCCTC 61.308 55.000 0.00 0.00 0.00 4.70
979 1142 1.743772 GCCAGCTTCATTTCGCCTCTA 60.744 52.381 0.00 0.00 0.00 2.43
980 1143 1.936547 CCAGCTTCATTTCGCCTCTAC 59.063 52.381 0.00 0.00 0.00 2.59
981 1144 2.419297 CCAGCTTCATTTCGCCTCTACT 60.419 50.000 0.00 0.00 0.00 2.57
982 1145 2.863137 CAGCTTCATTTCGCCTCTACTC 59.137 50.000 0.00 0.00 0.00 2.59
983 1146 2.497675 AGCTTCATTTCGCCTCTACTCA 59.502 45.455 0.00 0.00 0.00 3.41
984 1147 3.133721 AGCTTCATTTCGCCTCTACTCAT 59.866 43.478 0.00 0.00 0.00 2.90
986 1149 4.739137 GCTTCATTTCGCCTCTACTCATCT 60.739 45.833 0.00 0.00 0.00 2.90
988 1151 4.211125 TCATTTCGCCTCTACTCATCTCT 58.789 43.478 0.00 0.00 0.00 3.10
989 1152 4.277174 TCATTTCGCCTCTACTCATCTCTC 59.723 45.833 0.00 0.00 0.00 3.20
991 1154 3.120321 TCGCCTCTACTCATCTCTCTC 57.880 52.381 0.00 0.00 0.00 3.20
992 1155 2.436173 TCGCCTCTACTCATCTCTCTCA 59.564 50.000 0.00 0.00 0.00 3.27
993 1156 2.807967 CGCCTCTACTCATCTCTCTCAG 59.192 54.545 0.00 0.00 0.00 3.35
994 1157 3.744214 CGCCTCTACTCATCTCTCTCAGT 60.744 52.174 0.00 0.00 0.00 3.41
995 1158 4.502431 CGCCTCTACTCATCTCTCTCAGTA 60.502 50.000 0.00 0.00 0.00 2.74
996 1159 4.997395 GCCTCTACTCATCTCTCTCAGTAG 59.003 50.000 0.00 0.00 39.77 2.57
1001 1164 5.435686 ACTCATCTCTCTCAGTAGTCAGT 57.564 43.478 0.00 0.00 0.00 3.41
1004 1167 8.257602 ACTCATCTCTCTCAGTAGTCAGTATA 57.742 38.462 0.00 0.00 0.00 1.47
1005 1168 8.880244 ACTCATCTCTCTCAGTAGTCAGTATAT 58.120 37.037 0.00 0.00 0.00 0.86
1027 1190 2.798834 ACATACGTGTATGCAAACGC 57.201 45.000 17.62 0.00 45.06 4.84
1029 1192 2.480802 ACATACGTGTATGCAAACGCAA 59.519 40.909 17.62 8.37 45.06 4.85
1030 1193 2.865556 TACGTGTATGCAAACGCAAG 57.134 45.000 16.85 7.07 44.09 4.01
1031 1194 0.385473 ACGTGTATGCAAACGCAAGC 60.385 50.000 16.85 0.00 44.09 4.01
1032 1195 1.065031 CGTGTATGCAAACGCAAGCC 61.065 55.000 6.96 0.00 44.09 4.35
1033 1196 0.732538 GTGTATGCAAACGCAAGCCC 60.733 55.000 0.00 0.00 44.09 5.19
1034 1197 1.175347 TGTATGCAAACGCAAGCCCA 61.175 50.000 0.00 0.00 44.09 5.36
1036 1199 0.038709 TATGCAAACGCAAGCCCAAC 60.039 50.000 0.00 0.00 44.09 3.77
1037 1200 1.747325 ATGCAAACGCAAGCCCAACT 61.747 50.000 0.00 0.00 44.09 3.16
1039 1202 1.732917 CAAACGCAAGCCCAACTCA 59.267 52.632 0.00 0.00 45.62 3.41
1040 1203 0.594796 CAAACGCAAGCCCAACTCAC 60.595 55.000 0.00 0.00 45.62 3.51
1041 1204 1.034838 AAACGCAAGCCCAACTCACA 61.035 50.000 0.00 0.00 45.62 3.58
1043 1206 1.283793 CGCAAGCCCAACTCACAAG 59.716 57.895 0.00 0.00 0.00 3.16
1045 1208 0.031178 GCAAGCCCAACTCACAAGTG 59.969 55.000 0.00 0.00 35.36 3.16
1046 1209 0.031178 CAAGCCCAACTCACAAGTGC 59.969 55.000 0.00 0.00 35.36 4.40
1048 1211 0.820891 AGCCCAACTCACAAGTGCAG 60.821 55.000 0.00 0.00 35.36 4.41
1049 1212 1.103398 GCCCAACTCACAAGTGCAGT 61.103 55.000 0.00 0.00 35.36 4.40
1051 1214 0.029834 CCAACTCACAAGTGCAGTGC 59.970 55.000 8.58 8.58 35.36 4.40
1053 1216 1.003116 CAACTCACAAGTGCAGTGCTC 60.003 52.381 17.60 13.26 35.36 4.26
1054 1217 0.533755 ACTCACAAGTGCAGTGCTCC 60.534 55.000 17.60 6.96 36.93 4.70
1056 1219 0.815213 TCACAAGTGCAGTGCTCCAC 60.815 55.000 17.60 6.30 36.93 4.02
1057 1220 0.816825 CACAAGTGCAGTGCTCCACT 60.817 55.000 17.60 8.78 46.51 4.00
1059 1222 1.072159 AAGTGCAGTGCTCCACTCC 59.928 57.895 17.60 0.00 43.43 3.85
1060 1223 1.699054 AAGTGCAGTGCTCCACTCCA 61.699 55.000 17.60 0.00 43.43 3.86
1061 1224 1.963338 GTGCAGTGCTCCACTCCAC 60.963 63.158 17.60 3.92 44.24 4.02
1062 1225 2.359230 GCAGTGCTCCACTCCACC 60.359 66.667 8.18 0.00 43.43 4.61
1063 1226 3.150949 CAGTGCTCCACTCCACCA 58.849 61.111 0.00 0.00 43.43 4.17
1064 1227 1.004080 CAGTGCTCCACTCCACCAG 60.004 63.158 0.00 0.00 43.43 4.00
1065 1228 1.152247 AGTGCTCCACTCCACCAGA 60.152 57.895 0.00 0.00 41.21 3.86
1066 1229 1.190833 AGTGCTCCACTCCACCAGAG 61.191 60.000 0.00 0.00 41.21 3.35
1067 1230 1.156095 TGCTCCACTCCACCAGAGA 59.844 57.895 0.00 0.00 46.50 3.10
1068 1231 0.471780 TGCTCCACTCCACCAGAGAA 60.472 55.000 0.00 0.00 46.50 2.87
1069 1232 0.248843 GCTCCACTCCACCAGAGAAG 59.751 60.000 0.00 0.00 46.50 2.85
1070 1233 1.930251 CTCCACTCCACCAGAGAAGA 58.070 55.000 0.00 0.00 46.50 2.87
1071 1234 2.251818 CTCCACTCCACCAGAGAAGAA 58.748 52.381 0.00 0.00 46.50 2.52
1072 1235 2.634940 CTCCACTCCACCAGAGAAGAAA 59.365 50.000 0.00 0.00 46.50 2.52
1074 1237 3.458118 TCCACTCCACCAGAGAAGAAAAA 59.542 43.478 0.00 0.00 46.50 1.94
1091 1254 3.446310 AAAAACCAACCAACGTCCATC 57.554 42.857 0.00 0.00 0.00 3.51
1092 1255 2.060050 AAACCAACCAACGTCCATCA 57.940 45.000 0.00 0.00 0.00 3.07
1094 1257 2.286365 ACCAACCAACGTCCATCAAT 57.714 45.000 0.00 0.00 0.00 2.57
1095 1258 1.885887 ACCAACCAACGTCCATCAATG 59.114 47.619 0.00 0.00 0.00 2.82
1104 1267 2.404789 CCATCAATGGCGTCGTGC 59.595 61.111 0.00 0.00 41.75 5.34
1120 1283 3.715097 GCAGCCAGCACCTCCTCT 61.715 66.667 0.00 0.00 44.79 3.69
1121 1284 2.583520 CAGCCAGCACCTCCTCTC 59.416 66.667 0.00 0.00 0.00 3.20
1122 1285 2.121385 AGCCAGCACCTCCTCTCA 59.879 61.111 0.00 0.00 0.00 3.27
1123 1286 1.988956 AGCCAGCACCTCCTCTCAG 60.989 63.158 0.00 0.00 0.00 3.35
1124 1287 2.583520 CCAGCACCTCCTCTCAGC 59.416 66.667 0.00 0.00 0.00 4.26
1125 1288 2.583520 CAGCACCTCCTCTCAGCC 59.416 66.667 0.00 0.00 0.00 4.85
1127 1290 3.386237 GCACCTCCTCTCAGCCGT 61.386 66.667 0.00 0.00 0.00 5.68
1128 1291 2.888863 CACCTCCTCTCAGCCGTC 59.111 66.667 0.00 0.00 0.00 4.79
1129 1292 2.752238 ACCTCCTCTCAGCCGTCG 60.752 66.667 0.00 0.00 0.00 5.12
1131 1294 4.200283 CTCCTCTCAGCCGTCGCC 62.200 72.222 0.00 0.00 34.57 5.54
1133 1296 3.842923 CCTCTCAGCCGTCGCCAT 61.843 66.667 0.00 0.00 34.57 4.40
1135 1298 2.755876 TCTCAGCCGTCGCCATCT 60.756 61.111 0.00 0.00 34.57 2.90
1136 1299 2.185350 CTCAGCCGTCGCCATCTT 59.815 61.111 0.00 0.00 34.57 2.40
1137 1300 1.880340 CTCAGCCGTCGCCATCTTC 60.880 63.158 0.00 0.00 34.57 2.87
1139 1302 1.880340 CAGCCGTCGCCATCTTCTC 60.880 63.158 0.00 0.00 34.57 2.87
1140 1303 2.586357 GCCGTCGCCATCTTCTCC 60.586 66.667 0.00 0.00 0.00 3.71
1141 1304 2.278857 CCGTCGCCATCTTCTCCG 60.279 66.667 0.00 0.00 0.00 4.63
1143 1306 1.586564 CGTCGCCATCTTCTCCGTC 60.587 63.158 0.00 0.00 0.00 4.79
1144 1307 1.227002 GTCGCCATCTTCTCCGTCC 60.227 63.158 0.00 0.00 0.00 4.79
1145 1308 1.379977 TCGCCATCTTCTCCGTCCT 60.380 57.895 0.00 0.00 0.00 3.85
1146 1309 1.227089 CGCCATCTTCTCCGTCCTG 60.227 63.158 0.00 0.00 0.00 3.86
1147 1310 1.144936 GCCATCTTCTCCGTCCTGG 59.855 63.158 0.00 0.00 40.09 4.45
1148 1311 1.144936 CCATCTTCTCCGTCCTGGC 59.855 63.158 0.00 0.00 37.80 4.85
1150 1313 2.427245 ATCTTCTCCGTCCTGGCCG 61.427 63.158 0.00 0.00 37.80 6.13
1151 1314 4.821589 CTTCTCCGTCCTGGCCGC 62.822 72.222 0.00 0.00 37.80 6.53
1172 1335 4.467084 CGCCACCGCCACCAGTAT 62.467 66.667 0.00 0.00 0.00 2.12
1173 1336 2.824041 GCCACCGCCACCAGTATG 60.824 66.667 0.00 0.00 0.00 2.39
1175 1338 1.901820 CCACCGCCACCAGTATGTA 59.098 57.895 0.00 0.00 0.00 2.29
1176 1339 0.461339 CCACCGCCACCAGTATGTAC 60.461 60.000 0.00 0.00 0.00 2.90
1177 1340 0.248012 CACCGCCACCAGTATGTACA 59.752 55.000 0.00 0.00 0.00 2.90
1178 1341 0.248289 ACCGCCACCAGTATGTACAC 59.752 55.000 0.00 0.00 0.00 2.90
1179 1342 0.461339 CCGCCACCAGTATGTACACC 60.461 60.000 0.00 0.00 0.00 4.16
1180 1343 0.535335 CGCCACCAGTATGTACACCT 59.465 55.000 0.00 0.00 0.00 4.00
1181 1344 1.739035 CGCCACCAGTATGTACACCTG 60.739 57.143 14.59 14.59 0.00 4.00
1182 1345 2.012051 GCCACCAGTATGTACACCTGC 61.012 57.143 15.66 4.45 0.00 4.85
1183 1346 1.555075 CCACCAGTATGTACACCTGCT 59.445 52.381 15.66 0.74 0.00 4.24
1184 1347 2.764010 CCACCAGTATGTACACCTGCTA 59.236 50.000 15.66 0.00 0.00 3.49
1185 1348 3.430374 CCACCAGTATGTACACCTGCTAC 60.430 52.174 15.66 7.05 0.00 3.58
1186 1349 2.426024 ACCAGTATGTACACCTGCTACG 59.574 50.000 15.66 7.47 0.00 3.51
1187 1350 2.686405 CCAGTATGTACACCTGCTACGA 59.314 50.000 15.66 0.00 0.00 3.43
1189 1352 4.352039 CAGTATGTACACCTGCTACGAAG 58.648 47.826 10.49 0.00 0.00 3.79
1190 1353 2.961526 ATGTACACCTGCTACGAAGG 57.038 50.000 0.00 0.00 40.93 3.46
1191 1354 0.892755 TGTACACCTGCTACGAAGGG 59.107 55.000 0.00 0.00 39.30 3.95
1192 1355 0.175073 GTACACCTGCTACGAAGGGG 59.825 60.000 0.00 0.00 44.45 4.79
1194 1357 1.079127 CACCTGCTACGAAGGGGTG 60.079 63.158 0.00 0.00 39.30 4.61
1195 1358 2.291043 ACCTGCTACGAAGGGGTGG 61.291 63.158 0.00 0.00 39.30 4.61
1196 1359 2.584608 CTGCTACGAAGGGGTGGG 59.415 66.667 0.00 0.00 0.00 4.61
1197 1360 3.682292 CTGCTACGAAGGGGTGGGC 62.682 68.421 0.00 0.00 0.00 5.36
1198 1361 4.484872 GCTACGAAGGGGTGGGCC 62.485 72.222 0.00 0.00 0.00 5.80
1199 1362 2.687566 CTACGAAGGGGTGGGCCT 60.688 66.667 4.53 0.00 34.45 5.19
1200 1363 2.686106 TACGAAGGGGTGGGCCTC 60.686 66.667 4.53 0.00 34.70 4.70
1229 1392 3.402681 GCTCCAGGGCTGCCACTA 61.403 66.667 22.05 1.44 0.00 2.74
1230 1393 2.586792 CTCCAGGGCTGCCACTAC 59.413 66.667 22.05 2.38 0.00 2.73
1231 1394 1.992277 CTCCAGGGCTGCCACTACT 60.992 63.158 22.05 5.07 0.00 2.57
1232 1395 0.687757 CTCCAGGGCTGCCACTACTA 60.688 60.000 22.05 0.00 0.00 1.82
1235 1398 1.305046 AGGGCTGCCACTACTACGT 60.305 57.895 22.05 0.00 0.00 3.57
1236 1399 1.153628 GGGCTGCCACTACTACGTG 60.154 63.158 22.05 0.00 34.71 4.49
1237 1400 1.601419 GGGCTGCCACTACTACGTGA 61.601 60.000 22.05 0.00 37.06 4.35
1238 1401 0.458025 GGCTGCCACTACTACGTGAC 60.458 60.000 15.17 0.00 37.06 3.67
1275 1438 3.064324 GTGCCGCTGCTCCCAATT 61.064 61.111 0.70 0.00 38.71 2.32
1278 1441 2.768492 GCCGCTGCTCCCAATTGAG 61.768 63.158 7.12 0.00 35.40 3.02
1292 1455 2.679837 CAATTGAGGTGATGAAGGACCG 59.320 50.000 0.00 0.00 37.32 4.79
1323 1486 4.899239 CTGGCCGCCATCTCGTCC 62.899 72.222 13.86 0.00 30.82 4.79
1549 1712 5.156355 CGCTAGCTTGTTCATGAAAACATT 58.844 37.500 10.35 0.00 38.83 2.71
1567 1730 9.624697 GAAAACATTGTGTGAATGAATAAGCTA 57.375 29.630 0.00 0.00 0.00 3.32
1569 1732 6.789262 ACATTGTGTGAATGAATAAGCTAGC 58.211 36.000 6.62 6.62 0.00 3.42
1576 1739 5.008415 GTGAATGAATAAGCTAGCAGCATGT 59.992 40.000 18.83 0.00 45.56 3.21
1602 1773 1.142870 CCGTGGATGGGTGATATGGTT 59.857 52.381 0.00 0.00 0.00 3.67
1633 1804 7.805071 GCATAAGTGCGCAATAAAGAGAATAAT 59.195 33.333 14.00 0.00 42.28 1.28
1634 1805 9.322776 CATAAGTGCGCAATAAAGAGAATAATC 57.677 33.333 14.00 0.00 0.00 1.75
1635 1806 7.559590 AAGTGCGCAATAAAGAGAATAATCT 57.440 32.000 14.00 0.00 39.10 2.40
1636 1807 7.559590 AGTGCGCAATAAAGAGAATAATCTT 57.440 32.000 14.00 0.00 41.31 2.40
1637 1808 7.634522 AGTGCGCAATAAAGAGAATAATCTTC 58.365 34.615 14.00 0.00 38.59 2.87
1639 1810 6.074005 GCGCAATAAAGAGAATAATCTTCCG 58.926 40.000 0.30 0.00 38.59 4.30
1641 1812 7.360438 GCGCAATAAAGAGAATAATCTTCCGAT 60.360 37.037 0.30 0.00 38.59 4.18
1642 1813 7.954248 CGCAATAAAGAGAATAATCTTCCGATG 59.046 37.037 0.00 0.00 38.59 3.84
1643 1814 8.233190 GCAATAAAGAGAATAATCTTCCGATGG 58.767 37.037 0.00 0.00 38.59 3.51
1644 1815 9.277783 CAATAAAGAGAATAATCTTCCGATGGT 57.722 33.333 0.00 0.00 38.59 3.55
1645 1816 9.853177 AATAAAGAGAATAATCTTCCGATGGTT 57.147 29.630 0.00 0.00 38.59 3.67
1648 1819 7.130681 AGAGAATAATCTTCCGATGGTTCTT 57.869 36.000 0.00 0.00 35.78 2.52
1650 1821 8.705594 AGAGAATAATCTTCCGATGGTTCTTAA 58.294 33.333 0.00 0.00 35.78 1.85
1652 1823 9.110502 AGAATAATCTTCCGATGGTTCTTAAAC 57.889 33.333 0.00 0.00 33.74 2.01
1653 1824 9.110502 GAATAATCTTCCGATGGTTCTTAAACT 57.889 33.333 0.00 0.00 35.61 2.66
1655 1826 6.743575 ATCTTCCGATGGTTCTTAAACTTG 57.256 37.500 0.00 0.00 35.61 3.16
1656 1827 5.860611 TCTTCCGATGGTTCTTAAACTTGA 58.139 37.500 0.00 0.00 35.61 3.02
1657 1828 5.699458 TCTTCCGATGGTTCTTAAACTTGAC 59.301 40.000 0.00 0.00 35.61 3.18
1658 1829 4.320870 TCCGATGGTTCTTAAACTTGACC 58.679 43.478 0.00 0.00 35.61 4.02
1659 1830 4.069304 CCGATGGTTCTTAAACTTGACCA 58.931 43.478 0.00 0.00 35.61 4.02
1660 1831 4.154195 CCGATGGTTCTTAAACTTGACCAG 59.846 45.833 0.00 0.00 35.61 4.00
1661 1832 4.994852 CGATGGTTCTTAAACTTGACCAGA 59.005 41.667 0.00 0.00 35.61 3.86
1662 1833 5.468746 CGATGGTTCTTAAACTTGACCAGAA 59.531 40.000 0.00 0.00 35.61 3.02
1664 1835 5.502079 TGGTTCTTAAACTTGACCAGAACA 58.498 37.500 11.39 0.00 43.45 3.18
1665 1836 5.588648 TGGTTCTTAAACTTGACCAGAACAG 59.411 40.000 11.39 0.00 43.45 3.16
1666 1837 5.505819 GGTTCTTAAACTTGACCAGAACAGC 60.506 44.000 11.39 0.00 43.45 4.40
1690 1861 4.749245 AAATACTTGACCAAGAACAGCG 57.251 40.909 15.84 0.00 40.79 5.18
1754 1925 2.931713 GATCACTGCCGACCGTACCG 62.932 65.000 0.00 0.00 0.00 4.02
1776 1947 2.630098 TCCTCACTCATATACAGCCAGC 59.370 50.000 0.00 0.00 0.00 4.85
1777 1948 2.366590 CCTCACTCATATACAGCCAGCA 59.633 50.000 0.00 0.00 0.00 4.41
1778 1949 3.554544 CCTCACTCATATACAGCCAGCAG 60.555 52.174 0.00 0.00 0.00 4.24
1850 5751 0.036010 CCCCGAGAACTGTCTGCAAT 60.036 55.000 0.00 0.00 32.80 3.56
1966 5874 1.070786 GTCACCACCGTCCATGTGT 59.929 57.895 0.00 0.00 31.71 3.72
2353 6483 0.249398 GGTACCTCAGTCCGCATGTT 59.751 55.000 4.06 0.00 0.00 2.71
2359 6489 3.119101 ACCTCAGTCCGCATGTTTACTAG 60.119 47.826 0.00 0.00 0.00 2.57
2568 6719 1.270839 TGGCTCTGGCTACAAGACAAC 60.271 52.381 0.00 0.00 29.23 3.32
2572 6723 3.803715 GCTCTGGCTACAAGACAACAAGA 60.804 47.826 0.00 0.00 29.23 3.02
2574 6725 4.380531 TCTGGCTACAAGACAACAAGAAG 58.619 43.478 0.00 0.00 29.23 2.85
2575 6726 2.878406 TGGCTACAAGACAACAAGAAGC 59.122 45.455 0.00 0.00 23.92 3.86
2576 6727 2.226674 GGCTACAAGACAACAAGAAGCC 59.773 50.000 0.00 0.00 41.27 4.35
2577 6728 2.096218 GCTACAAGACAACAAGAAGCCG 60.096 50.000 0.00 0.00 0.00 5.52
2578 6729 1.308998 ACAAGACAACAAGAAGCCGG 58.691 50.000 0.00 0.00 0.00 6.13
2579 6730 1.134220 ACAAGACAACAAGAAGCCGGA 60.134 47.619 5.05 0.00 0.00 5.14
2598 6750 4.034048 CCGGACAAGTCAATATAACAGCAC 59.966 45.833 0.00 0.00 0.00 4.40
2614 6766 3.284617 CAGCACTCATCATTCCCATTGA 58.715 45.455 0.00 0.00 0.00 2.57
2615 6767 3.889538 CAGCACTCATCATTCCCATTGAT 59.110 43.478 0.00 0.00 34.15 2.57
2617 6769 5.533528 CAGCACTCATCATTCCCATTGATTA 59.466 40.000 0.00 0.00 31.50 1.75
2619 6771 6.040166 AGCACTCATCATTCCCATTGATTAAC 59.960 38.462 0.00 0.00 31.50 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 158 4.318618 CGCGTCGATAAGTATGTAGAGTGT 60.319 45.833 0.00 0.00 0.00 3.55
293 326 2.703416 TGCAGCCTAAATGACTGACTG 58.297 47.619 0.00 0.00 33.10 3.51
404 437 6.112058 ACAACAGTAAAAATGCATTGTTGGT 58.888 32.000 29.38 20.04 45.74 3.67
452 606 3.576982 TCCAACCTAAGTGACAGTACCAG 59.423 47.826 0.00 0.00 0.00 4.00
467 621 2.165998 GAAAGCAGAGCAATCCAACCT 58.834 47.619 0.00 0.00 0.00 3.50
564 718 5.308825 AGGACATTAACAGACAAGACAAGG 58.691 41.667 0.00 0.00 0.00 3.61
663 817 1.971167 GTTGGGCATTGCGTGAGGA 60.971 57.895 1.91 0.00 0.00 3.71
703 857 6.536688 GCACAATTGATTAATTTGTTGGAGC 58.463 36.000 13.59 6.49 34.34 4.70
799 953 4.508461 TGAACTGGTGAGCAATTGATTG 57.492 40.909 10.34 0.00 40.66 2.67
803 957 4.157105 TGATGATGAACTGGTGAGCAATTG 59.843 41.667 0.00 0.00 0.00 2.32
819 973 8.398665 GGTTATGTGATGATGATGATGATGATG 58.601 37.037 0.00 0.00 0.00 3.07
847 1010 5.175856 GCTGACAAGATGACGGATGTATTAC 59.824 44.000 0.00 0.00 0.00 1.89
851 1014 2.159099 GGCTGACAAGATGACGGATGTA 60.159 50.000 0.00 0.00 0.00 2.29
879 1042 5.051173 CGCAGTTGATTAATTTGTTGCAACA 60.051 36.000 27.96 27.96 38.37 3.33
883 1046 3.674753 AGCGCAGTTGATTAATTTGTTGC 59.325 39.130 11.47 0.00 0.00 4.17
884 1047 4.324402 GGAGCGCAGTTGATTAATTTGTTG 59.676 41.667 11.47 0.00 0.00 3.33
921 1084 0.664761 GTTGGATGGGTCATGCGATG 59.335 55.000 0.00 0.00 34.93 3.84
924 1087 1.024046 TTCGTTGGATGGGTCATGCG 61.024 55.000 0.00 0.00 34.93 4.73
925 1088 0.451783 GTTCGTTGGATGGGTCATGC 59.548 55.000 0.00 0.00 32.81 4.06
926 1089 1.468520 GTGTTCGTTGGATGGGTCATG 59.531 52.381 0.00 0.00 0.00 3.07
927 1090 1.073125 TGTGTTCGTTGGATGGGTCAT 59.927 47.619 0.00 0.00 0.00 3.06
929 1092 0.872388 GTGTGTTCGTTGGATGGGTC 59.128 55.000 0.00 0.00 0.00 4.46
930 1093 0.536460 GGTGTGTTCGTTGGATGGGT 60.536 55.000 0.00 0.00 0.00 4.51
931 1094 1.241315 GGGTGTGTTCGTTGGATGGG 61.241 60.000 0.00 0.00 0.00 4.00
932 1095 1.573829 CGGGTGTGTTCGTTGGATGG 61.574 60.000 0.00 0.00 0.00 3.51
937 1100 1.791103 AATGGCGGGTGTGTTCGTTG 61.791 55.000 0.00 0.00 0.00 4.10
938 1101 1.512156 GAATGGCGGGTGTGTTCGTT 61.512 55.000 0.00 0.00 0.00 3.85
940 1103 1.671054 AGAATGGCGGGTGTGTTCG 60.671 57.895 0.00 0.00 0.00 3.95
941 1104 1.875963 CAGAATGGCGGGTGTGTTC 59.124 57.895 0.00 0.00 0.00 3.18
942 1105 2.268076 GCAGAATGGCGGGTGTGTT 61.268 57.895 0.00 0.00 35.86 3.32
943 1106 2.672996 GCAGAATGGCGGGTGTGT 60.673 61.111 0.00 0.00 35.86 3.72
952 1115 2.479049 CGAAATGAAGCTGGCAGAATGG 60.479 50.000 20.86 0.00 35.86 3.16
953 1116 2.793933 CGAAATGAAGCTGGCAGAATG 58.206 47.619 20.86 0.00 40.87 2.67
954 1117 1.133790 GCGAAATGAAGCTGGCAGAAT 59.866 47.619 20.86 5.27 0.00 2.40
955 1118 0.523072 GCGAAATGAAGCTGGCAGAA 59.477 50.000 20.86 0.00 0.00 3.02
957 1120 1.138247 GGCGAAATGAAGCTGGCAG 59.862 57.895 10.94 10.94 0.00 4.85
958 1121 1.303561 AGGCGAAATGAAGCTGGCA 60.304 52.632 0.00 0.00 0.00 4.92
959 1122 1.028868 AGAGGCGAAATGAAGCTGGC 61.029 55.000 0.00 0.00 0.00 4.85
960 1123 1.936547 GTAGAGGCGAAATGAAGCTGG 59.063 52.381 0.00 0.00 0.00 4.85
961 1124 2.863137 GAGTAGAGGCGAAATGAAGCTG 59.137 50.000 0.00 0.00 0.00 4.24
962 1125 2.497675 TGAGTAGAGGCGAAATGAAGCT 59.502 45.455 0.00 0.00 0.00 3.74
963 1126 2.893637 TGAGTAGAGGCGAAATGAAGC 58.106 47.619 0.00 0.00 0.00 3.86
967 1130 4.278170 AGAGAGATGAGTAGAGGCGAAATG 59.722 45.833 0.00 0.00 0.00 2.32
968 1131 4.469657 AGAGAGATGAGTAGAGGCGAAAT 58.530 43.478 0.00 0.00 0.00 2.17
969 1132 3.880490 GAGAGAGATGAGTAGAGGCGAAA 59.120 47.826 0.00 0.00 0.00 3.46
970 1133 3.118223 TGAGAGAGATGAGTAGAGGCGAA 60.118 47.826 0.00 0.00 0.00 4.70
971 1134 2.436173 TGAGAGAGATGAGTAGAGGCGA 59.564 50.000 0.00 0.00 0.00 5.54
972 1135 2.807967 CTGAGAGAGATGAGTAGAGGCG 59.192 54.545 0.00 0.00 0.00 5.52
973 1136 3.820557 ACTGAGAGAGATGAGTAGAGGC 58.179 50.000 0.00 0.00 0.00 4.70
974 1137 6.174720 ACTACTGAGAGAGATGAGTAGAGG 57.825 45.833 11.09 0.00 40.17 3.69
976 1139 6.382859 ACTGACTACTGAGAGAGATGAGTAGA 59.617 42.308 11.09 0.00 40.17 2.59
977 1140 6.582636 ACTGACTACTGAGAGAGATGAGTAG 58.417 44.000 0.00 0.00 42.40 2.57
979 1142 5.435686 ACTGACTACTGAGAGAGATGAGT 57.564 43.478 0.00 0.00 0.00 3.41
1008 1171 2.798834 GCGTTTGCATACACGTATGT 57.201 45.000 16.43 0.00 43.57 2.29
1020 1183 1.661509 GAGTTGGGCTTGCGTTTGC 60.662 57.895 0.00 0.00 43.20 3.68
1021 1184 0.594796 GTGAGTTGGGCTTGCGTTTG 60.595 55.000 0.00 0.00 0.00 2.93
1022 1185 1.034838 TGTGAGTTGGGCTTGCGTTT 61.035 50.000 0.00 0.00 0.00 3.60
1024 1187 1.447317 CTTGTGAGTTGGGCTTGCGT 61.447 55.000 0.00 0.00 0.00 5.24
1025 1188 1.283793 CTTGTGAGTTGGGCTTGCG 59.716 57.895 0.00 0.00 0.00 4.85
1026 1189 0.031178 CACTTGTGAGTTGGGCTTGC 59.969 55.000 0.00 0.00 32.54 4.01
1027 1190 0.031178 GCACTTGTGAGTTGGGCTTG 59.969 55.000 4.79 0.00 32.54 4.01
1029 1192 0.820891 CTGCACTTGTGAGTTGGGCT 60.821 55.000 4.79 0.00 32.54 5.19
1030 1193 1.103398 ACTGCACTTGTGAGTTGGGC 61.103 55.000 4.79 0.00 32.54 5.36
1031 1194 0.664761 CACTGCACTTGTGAGTTGGG 59.335 55.000 4.79 0.00 37.60 4.12
1032 1195 0.029834 GCACTGCACTTGTGAGTTGG 59.970 55.000 8.64 0.00 37.60 3.77
1033 1196 1.003116 GAGCACTGCACTTGTGAGTTG 60.003 52.381 8.64 0.00 37.60 3.16
1034 1197 1.303309 GAGCACTGCACTTGTGAGTT 58.697 50.000 8.64 0.00 37.60 3.01
1036 1199 0.533531 TGGAGCACTGCACTTGTGAG 60.534 55.000 8.64 2.46 37.60 3.51
1037 1200 0.815213 GTGGAGCACTGCACTTGTGA 60.815 55.000 14.26 0.00 46.49 3.58
1039 1202 4.147701 GTGGAGCACTGCACTTGT 57.852 55.556 14.26 0.00 46.49 3.16
1046 1209 1.004080 CTGGTGGAGTGGAGCACTG 60.004 63.158 0.00 0.00 45.44 3.66
1048 1211 1.188219 TCTCTGGTGGAGTGGAGCAC 61.188 60.000 0.00 0.00 42.40 4.40
1049 1212 0.471780 TTCTCTGGTGGAGTGGAGCA 60.472 55.000 0.00 0.00 42.40 4.26
1051 1214 1.930251 TCTTCTCTGGTGGAGTGGAG 58.070 55.000 0.00 0.00 42.40 3.86
1053 1216 3.492102 TTTTCTTCTCTGGTGGAGTGG 57.508 47.619 0.00 0.00 42.40 4.00
1071 1234 2.761208 TGATGGACGTTGGTTGGTTTTT 59.239 40.909 0.00 0.00 0.00 1.94
1072 1235 2.379972 TGATGGACGTTGGTTGGTTTT 58.620 42.857 0.00 0.00 0.00 2.43
1074 1237 2.060050 TTGATGGACGTTGGTTGGTT 57.940 45.000 0.00 0.00 0.00 3.67
1075 1238 1.885887 CATTGATGGACGTTGGTTGGT 59.114 47.619 0.00 0.00 0.00 3.67
1076 1239 2.634982 CATTGATGGACGTTGGTTGG 57.365 50.000 0.00 0.00 0.00 3.77
1088 1251 1.061411 CTGCACGACGCCATTGATG 59.939 57.895 0.00 0.00 41.33 3.07
1090 1253 3.422303 GCTGCACGACGCCATTGA 61.422 61.111 0.00 0.00 41.33 2.57
1091 1254 4.465512 GGCTGCACGACGCCATTG 62.466 66.667 9.69 0.00 45.59 2.82
1103 1266 3.678951 GAGAGGAGGTGCTGGCTGC 62.679 68.421 9.67 9.67 43.25 5.25
1104 1267 2.241479 CTGAGAGGAGGTGCTGGCTG 62.241 65.000 0.00 0.00 0.00 4.85
1105 1268 1.988956 CTGAGAGGAGGTGCTGGCT 60.989 63.158 0.00 0.00 0.00 4.75
1106 1269 2.583520 CTGAGAGGAGGTGCTGGC 59.416 66.667 0.00 0.00 0.00 4.85
1107 1270 2.583520 GCTGAGAGGAGGTGCTGG 59.416 66.667 0.00 0.00 0.00 4.85
1108 1271 2.583520 GGCTGAGAGGAGGTGCTG 59.416 66.667 0.00 0.00 0.00 4.41
1109 1272 3.073735 CGGCTGAGAGGAGGTGCT 61.074 66.667 0.00 0.00 0.00 4.40
1111 1274 2.888863 GACGGCTGAGAGGAGGTG 59.111 66.667 0.00 0.00 0.00 4.00
1113 1276 4.200283 GCGACGGCTGAGAGGAGG 62.200 72.222 0.00 0.00 35.83 4.30
1114 1277 4.200283 GGCGACGGCTGAGAGGAG 62.200 72.222 15.00 0.00 39.81 3.69
1116 1279 3.781770 GATGGCGACGGCTGAGAGG 62.782 68.421 22.70 0.00 39.81 3.69
1117 1280 2.279120 GATGGCGACGGCTGAGAG 60.279 66.667 22.70 0.00 39.81 3.20
1118 1281 2.284798 GAAGATGGCGACGGCTGAGA 62.285 60.000 22.70 1.89 39.81 3.27
1119 1282 1.880340 GAAGATGGCGACGGCTGAG 60.880 63.158 22.70 0.00 39.81 3.35
1120 1283 2.184322 GAAGATGGCGACGGCTGA 59.816 61.111 22.70 3.12 39.81 4.26
1121 1284 1.880340 GAGAAGATGGCGACGGCTG 60.880 63.158 22.70 0.00 39.81 4.85
1122 1285 2.496817 GAGAAGATGGCGACGGCT 59.503 61.111 22.70 7.99 39.81 5.52
1123 1286 2.586357 GGAGAAGATGGCGACGGC 60.586 66.667 15.43 15.43 38.90 5.68
1124 1287 2.278857 CGGAGAAGATGGCGACGG 60.279 66.667 0.00 0.00 0.00 4.79
1125 1288 1.586564 GACGGAGAAGATGGCGACG 60.587 63.158 0.00 0.00 0.00 5.12
1127 1290 1.379977 AGGACGGAGAAGATGGCGA 60.380 57.895 0.00 0.00 0.00 5.54
1128 1291 1.227089 CAGGACGGAGAAGATGGCG 60.227 63.158 0.00 0.00 0.00 5.69
1129 1292 1.144936 CCAGGACGGAGAAGATGGC 59.855 63.158 0.00 0.00 36.56 4.40
1131 1294 1.144936 GGCCAGGACGGAGAAGATG 59.855 63.158 0.00 0.00 36.56 2.90
1133 1296 3.068691 CGGCCAGGACGGAGAAGA 61.069 66.667 6.89 0.00 36.56 2.87
1155 1318 4.467084 ATACTGGTGGCGGTGGCG 62.467 66.667 0.00 0.00 41.24 5.69
1156 1319 2.246761 TACATACTGGTGGCGGTGGC 62.247 60.000 0.00 0.00 38.90 5.01
1157 1320 0.461339 GTACATACTGGTGGCGGTGG 60.461 60.000 0.00 0.00 0.00 4.61
1158 1321 0.248012 TGTACATACTGGTGGCGGTG 59.752 55.000 0.00 0.00 0.00 4.94
1160 1323 0.461339 GGTGTACATACTGGTGGCGG 60.461 60.000 0.00 0.00 0.00 6.13
1162 1325 2.012051 GCAGGTGTACATACTGGTGGC 61.012 57.143 23.56 11.51 32.98 5.01
1163 1326 1.555075 AGCAGGTGTACATACTGGTGG 59.445 52.381 24.97 7.48 40.96 4.61
1165 1328 2.426024 CGTAGCAGGTGTACATACTGGT 59.574 50.000 27.08 27.08 44.23 4.00
1166 1329 2.686405 TCGTAGCAGGTGTACATACTGG 59.314 50.000 23.56 12.39 32.98 4.00
1167 1330 4.352039 CTTCGTAGCAGGTGTACATACTG 58.648 47.826 20.17 20.17 35.40 2.74
1168 1331 3.380637 CCTTCGTAGCAGGTGTACATACT 59.619 47.826 0.00 0.00 0.00 2.12
1169 1332 3.490419 CCCTTCGTAGCAGGTGTACATAC 60.490 52.174 0.00 0.00 0.00 2.39
1170 1333 2.691526 CCCTTCGTAGCAGGTGTACATA 59.308 50.000 0.00 0.00 0.00 2.29
1171 1334 1.480954 CCCTTCGTAGCAGGTGTACAT 59.519 52.381 0.00 0.00 0.00 2.29
1172 1335 0.892755 CCCTTCGTAGCAGGTGTACA 59.107 55.000 0.00 0.00 0.00 2.90
1173 1336 0.175073 CCCCTTCGTAGCAGGTGTAC 59.825 60.000 0.00 0.00 0.00 2.90
1175 1338 1.535687 ACCCCTTCGTAGCAGGTGT 60.536 57.895 1.91 0.00 0.00 4.16
1176 1339 1.079127 CACCCCTTCGTAGCAGGTG 60.079 63.158 12.77 12.77 37.70 4.00
1177 1340 2.291043 CCACCCCTTCGTAGCAGGT 61.291 63.158 0.00 0.00 0.00 4.00
1178 1341 2.584608 CCACCCCTTCGTAGCAGG 59.415 66.667 0.00 0.00 0.00 4.85
1179 1342 2.584608 CCCACCCCTTCGTAGCAG 59.415 66.667 0.00 0.00 0.00 4.24
1180 1343 3.712907 GCCCACCCCTTCGTAGCA 61.713 66.667 0.00 0.00 0.00 3.49
1181 1344 4.484872 GGCCCACCCCTTCGTAGC 62.485 72.222 0.00 0.00 0.00 3.58
1182 1345 2.687566 AGGCCCACCCCTTCGTAG 60.688 66.667 0.00 0.00 36.11 3.51
1183 1346 2.686106 GAGGCCCACCCCTTCGTA 60.686 66.667 0.00 0.00 34.69 3.43
1212 1375 3.402681 TAGTGGCAGCCCTGGAGC 61.403 66.667 9.64 0.00 0.00 4.70
1213 1376 0.687757 TAGTAGTGGCAGCCCTGGAG 60.688 60.000 9.64 0.00 0.00 3.86
1214 1377 0.976073 GTAGTAGTGGCAGCCCTGGA 60.976 60.000 9.64 0.00 0.00 3.86
1215 1378 1.522569 GTAGTAGTGGCAGCCCTGG 59.477 63.158 9.64 0.00 0.00 4.45
1216 1379 1.141881 CGTAGTAGTGGCAGCCCTG 59.858 63.158 9.64 0.00 0.00 4.45
1217 1380 1.305046 ACGTAGTAGTGGCAGCCCT 60.305 57.895 9.64 8.36 41.94 5.19
1218 1381 1.153628 CACGTAGTAGTGGCAGCCC 60.154 63.158 9.64 0.00 41.61 5.19
1219 1382 0.458025 GTCACGTAGTAGTGGCAGCC 60.458 60.000 3.66 3.66 45.32 4.85
1220 1383 3.031660 GTCACGTAGTAGTGGCAGC 57.968 57.895 0.00 0.00 45.32 5.25
1225 1388 0.800631 TGCGAGGTCACGTAGTAGTG 59.199 55.000 0.00 0.00 41.61 2.74
1226 1389 1.085091 CTGCGAGGTCACGTAGTAGT 58.915 55.000 0.00 0.00 41.61 2.73
1227 1390 1.062294 GTCTGCGAGGTCACGTAGTAG 59.938 57.143 0.00 0.00 41.61 2.57
1228 1391 1.081892 GTCTGCGAGGTCACGTAGTA 58.918 55.000 0.00 0.00 41.61 1.82
1230 1393 1.136984 GGTCTGCGAGGTCACGTAG 59.863 63.158 0.00 0.00 44.64 3.51
1231 1394 1.303074 AGGTCTGCGAGGTCACGTA 60.303 57.895 0.00 0.00 35.59 3.57
1232 1395 2.597805 AGGTCTGCGAGGTCACGT 60.598 61.111 0.00 0.00 35.59 4.49
1258 1421 3.064324 AATTGGGAGCAGCGGCAC 61.064 61.111 12.44 4.33 44.61 5.01
1272 1435 2.356125 CCGGTCCTTCATCACCTCAATT 60.356 50.000 0.00 0.00 0.00 2.32
1275 1438 0.544357 ACCGGTCCTTCATCACCTCA 60.544 55.000 0.00 0.00 0.00 3.86
1278 1441 1.745489 GCACCGGTCCTTCATCACC 60.745 63.158 2.59 0.00 0.00 4.02
1549 1712 4.333649 GCTGCTAGCTTATTCATTCACACA 59.666 41.667 17.23 0.00 38.45 3.72
1567 1730 1.297689 ACGGATGTGACATGCTGCT 59.702 52.632 15.02 0.00 0.00 4.24
1633 1804 5.699458 GTCAAGTTTAAGAACCATCGGAAGA 59.301 40.000 0.00 0.00 39.76 2.87
1634 1805 5.106673 GGTCAAGTTTAAGAACCATCGGAAG 60.107 44.000 0.00 0.00 36.39 3.46
1635 1806 4.758165 GGTCAAGTTTAAGAACCATCGGAA 59.242 41.667 0.00 0.00 36.39 4.30
1636 1807 4.202377 TGGTCAAGTTTAAGAACCATCGGA 60.202 41.667 0.00 0.00 36.39 4.55
1637 1808 4.069304 TGGTCAAGTTTAAGAACCATCGG 58.931 43.478 0.00 0.00 36.39 4.18
1639 1810 6.262273 TGTTCTGGTCAAGTTTAAGAACCATC 59.738 38.462 10.42 0.00 43.87 3.51
1641 1812 5.502079 TGTTCTGGTCAAGTTTAAGAACCA 58.498 37.500 10.42 0.00 43.87 3.67
1642 1813 5.505819 GCTGTTCTGGTCAAGTTTAAGAACC 60.506 44.000 10.42 0.00 43.87 3.62
1643 1814 5.065988 TGCTGTTCTGGTCAAGTTTAAGAAC 59.934 40.000 6.86 6.86 44.45 3.01
1644 1815 5.189928 TGCTGTTCTGGTCAAGTTTAAGAA 58.810 37.500 0.00 0.00 0.00 2.52
1645 1816 4.776349 TGCTGTTCTGGTCAAGTTTAAGA 58.224 39.130 0.00 0.00 0.00 2.10
1648 1819 5.906113 TTTTGCTGTTCTGGTCAAGTTTA 57.094 34.783 0.00 0.00 0.00 2.01
1650 1821 4.799564 TTTTTGCTGTTCTGGTCAAGTT 57.200 36.364 0.00 0.00 0.00 2.66
1652 1823 6.076981 AGTATTTTTGCTGTTCTGGTCAAG 57.923 37.500 0.00 0.00 0.00 3.02
1653 1824 6.096141 TCAAGTATTTTTGCTGTTCTGGTCAA 59.904 34.615 0.00 0.00 0.00 3.18
1655 1826 5.915196 GTCAAGTATTTTTGCTGTTCTGGTC 59.085 40.000 0.00 0.00 0.00 4.02
1656 1827 5.221244 GGTCAAGTATTTTTGCTGTTCTGGT 60.221 40.000 0.00 0.00 0.00 4.00
1657 1828 5.221224 TGGTCAAGTATTTTTGCTGTTCTGG 60.221 40.000 0.00 0.00 0.00 3.86
1658 1829 5.830912 TGGTCAAGTATTTTTGCTGTTCTG 58.169 37.500 0.00 0.00 0.00 3.02
1659 1830 6.321181 TCTTGGTCAAGTATTTTTGCTGTTCT 59.679 34.615 10.10 0.00 39.38 3.01
1660 1831 6.503524 TCTTGGTCAAGTATTTTTGCTGTTC 58.496 36.000 10.10 0.00 39.38 3.18
1661 1832 6.463995 TCTTGGTCAAGTATTTTTGCTGTT 57.536 33.333 10.10 0.00 39.38 3.16
1662 1833 6.127479 TGTTCTTGGTCAAGTATTTTTGCTGT 60.127 34.615 10.10 0.00 39.38 4.40
1664 1835 6.463995 TGTTCTTGGTCAAGTATTTTTGCT 57.536 33.333 10.10 0.00 39.38 3.91
1665 1836 5.175673 GCTGTTCTTGGTCAAGTATTTTTGC 59.824 40.000 10.10 4.60 39.38 3.68
1666 1837 5.399301 CGCTGTTCTTGGTCAAGTATTTTTG 59.601 40.000 10.10 0.00 39.38 2.44
1754 1925 3.553922 GCTGGCTGTATATGAGTGAGGAC 60.554 52.174 0.00 0.00 0.00 3.85
1776 1947 4.708177 TGTTTCTGAAGAGAAGAACCCTG 58.292 43.478 0.00 0.00 39.44 4.45
1777 1948 5.373812 TTGTTTCTGAAGAGAAGAACCCT 57.626 39.130 0.00 0.00 39.44 4.34
1778 1949 5.590663 AGTTTGTTTCTGAAGAGAAGAACCC 59.409 40.000 0.00 0.00 39.44 4.11
1940 5848 1.227853 ACGGTGGTGACAAGAAGGC 60.228 57.895 0.00 0.00 46.06 4.35
2311 6441 5.300792 CCAGCCTTAAGTAACCTGAAAACAA 59.699 40.000 0.97 0.00 0.00 2.83
2568 6719 1.593196 TTGACTTGTCCGGCTTCTTG 58.407 50.000 0.00 0.00 0.00 3.02
2572 6723 4.839121 TGTTATATTGACTTGTCCGGCTT 58.161 39.130 0.00 0.00 0.00 4.35
2574 6725 3.002348 GCTGTTATATTGACTTGTCCGGC 59.998 47.826 0.00 0.00 0.00 6.13
2575 6726 4.034048 GTGCTGTTATATTGACTTGTCCGG 59.966 45.833 0.00 0.00 0.00 5.14
2576 6727 4.870426 AGTGCTGTTATATTGACTTGTCCG 59.130 41.667 0.00 0.00 0.00 4.79
2577 6728 5.874810 TGAGTGCTGTTATATTGACTTGTCC 59.125 40.000 0.00 0.00 0.00 4.02
2578 6729 6.968131 TGAGTGCTGTTATATTGACTTGTC 57.032 37.500 0.00 0.00 0.00 3.18
2579 6730 7.105588 TGATGAGTGCTGTTATATTGACTTGT 58.894 34.615 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.