Multiple sequence alignment - TraesCS2B01G120500

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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 TraesCS2B01G120500 chr2B 100.000 2705 0 0 1 2705 88175120 88172416 0.000000e+00 4996
1 TraesCS2B01G120500 chr2B 81.472 394 62 3 1309 1702 603691321 603691703 2.020000e-81 313
2 TraesCS2B01G120500 chr2D 90.383 967 84 7 1743 2705 158281941 158280980 0.000000e+00 1262
3 TraesCS2B01G120500 chr2D 87.088 1123 91 25 1 1098 55392155 55391062 0.000000e+00 1221
4 TraesCS2B01G120500 chr2D 86.932 528 68 1 1207 1734 315083661 315084187 2.320000e-165 592
5 TraesCS2B01G120500 chr2D 85.009 527 78 1 1208 1734 260325245 260325770 3.960000e-148 534
6 TraesCS2B01G120500 chr7A 90.021 972 88 7 1736 2705 695909263 695910227 0.000000e+00 1249
7 TraesCS2B01G120500 chr3D 89.959 966 89 8 1745 2705 581409863 581408901 0.000000e+00 1240
8 TraesCS2B01G120500 chr3D 89.866 967 86 8 1743 2705 196925843 196926801 0.000000e+00 1232
9 TraesCS2B01G120500 chr2A 89.741 965 97 2 1743 2705 676344625 676343661 0.000000e+00 1232
10 TraesCS2B01G120500 chr2A 88.117 993 77 20 1 971 56935273 56934300 0.000000e+00 1142
11 TraesCS2B01G120500 chr4D 89.845 965 87 7 1745 2705 154926811 154927768 0.000000e+00 1229
12 TraesCS2B01G120500 chr1A 89.730 964 93 3 1743 2705 173970306 173969348 0.000000e+00 1227
13 TraesCS2B01G120500 chr5A 89.659 967 92 7 1743 2705 651501556 651502518 0.000000e+00 1225
14 TraesCS2B01G120500 chr3A 89.648 966 94 5 1742 2705 323429469 323430430 0.000000e+00 1225


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 TraesCS2B01G120500 chr2B 88172416 88175120 2704 True 4996 4996 100.000 1 2705 1 chr2B.!!$R1 2704
1 TraesCS2B01G120500 chr2D 158280980 158281941 961 True 1262 1262 90.383 1743 2705 1 chr2D.!!$R2 962
2 TraesCS2B01G120500 chr2D 55391062 55392155 1093 True 1221 1221 87.088 1 1098 1 chr2D.!!$R1 1097
3 TraesCS2B01G120500 chr2D 315083661 315084187 526 False 592 592 86.932 1207 1734 1 chr2D.!!$F2 527
4 TraesCS2B01G120500 chr2D 260325245 260325770 525 False 534 534 85.009 1208 1734 1 chr2D.!!$F1 526
5 TraesCS2B01G120500 chr7A 695909263 695910227 964 False 1249 1249 90.021 1736 2705 1 chr7A.!!$F1 969
6 TraesCS2B01G120500 chr3D 581408901 581409863 962 True 1240 1240 89.959 1745 2705 1 chr3D.!!$R1 960
7 TraesCS2B01G120500 chr3D 196925843 196926801 958 False 1232 1232 89.866 1743 2705 1 chr3D.!!$F1 962
8 TraesCS2B01G120500 chr2A 676343661 676344625 964 True 1232 1232 89.741 1743 2705 1 chr2A.!!$R2 962
9 TraesCS2B01G120500 chr2A 56934300 56935273 973 True 1142 1142 88.117 1 971 1 chr2A.!!$R1 970
10 TraesCS2B01G120500 chr4D 154926811 154927768 957 False 1229 1229 89.845 1745 2705 1 chr4D.!!$F1 960
11 TraesCS2B01G120500 chr1A 173969348 173970306 958 True 1227 1227 89.730 1743 2705 1 chr1A.!!$R1 962
12 TraesCS2B01G120500 chr5A 651501556 651502518 962 False 1225 1225 89.659 1743 2705 1 chr5A.!!$F1 962
13 TraesCS2B01G120500 chr3A 323429469 323430430 961 False 1225 1225 89.648 1742 2705 1 chr3A.!!$F1 963

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
538 554 0.034089 AGCCTACTGCCCCAAATGTC 60.034 55.0 0.0 0.0 42.71 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1800 0.107017 ATGATGGTTTCGGCCTCCAG 60.107 55.0 0.0 0.0 34.62 3.86 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
53 54 0.895530 GGTTGGATCACGTGAGAGGA 59.104 55.000 24.41 7.35 0.00 3.71
120 121 8.587608 TCTTCCATTATTCATTATGCCATTTCC 58.412 33.333 0.00 0.00 0.00 3.13
124 125 3.435105 TTCATTATGCCATTTCCGTGC 57.565 42.857 0.00 0.00 0.00 5.34
128 129 1.372838 TATGCCATTTCCGTGCGTGG 61.373 55.000 0.00 0.00 34.84 4.94
143 144 5.038683 CGTGCGTGGTTAAGTAGATCATAA 58.961 41.667 0.00 0.00 0.00 1.90
204 205 4.599041 TGTTCATCCAAACCATTAGGGAG 58.401 43.478 0.00 0.00 41.15 4.30
212 213 4.941873 CCAAACCATTAGGGAGTGACTAAC 59.058 45.833 0.00 0.00 41.15 2.34
217 233 2.921834 TAGGGAGTGACTAACCTGCT 57.078 50.000 16.07 0.00 34.59 4.24
224 240 2.162681 GTGACTAACCTGCTTGGCAAT 58.837 47.619 0.00 0.00 38.41 3.56
294 310 6.334102 TCTTGGAGTGTTAGAGAAGACTTC 57.666 41.667 7.14 7.14 39.19 3.01
302 318 8.090687 AGTGTTAGAGAAGACTTCTGGCAACA 62.091 42.308 22.39 21.54 39.38 3.33
314 330 1.344438 CTGGCAACACTCCTACTGACA 59.656 52.381 0.00 0.00 46.17 3.58
317 333 1.338200 GCAACACTCCTACTGACAGGG 60.338 57.143 7.51 0.00 36.26 4.45
351 367 1.294138 CCGAGTCGGCAAAACCCTA 59.706 57.895 20.50 0.00 41.17 3.53
352 368 1.017701 CCGAGTCGGCAAAACCCTAC 61.018 60.000 20.50 0.00 41.17 3.18
364 380 0.550147 AACCCTACTCCCATGGCAGT 60.550 55.000 14.16 14.16 0.00 4.40
391 407 0.978146 CGGAGAAGGGTGATCAGGGT 60.978 60.000 0.00 0.00 0.00 4.34
414 430 0.318441 CCCGTCATCATATCAGGCGT 59.682 55.000 0.00 0.00 0.00 5.68
432 448 1.168714 GTCTGCGATTCAAGCCCTTT 58.831 50.000 0.00 0.00 0.00 3.11
454 470 2.432510 GACAAAGAGATCCCAGACCGAT 59.567 50.000 0.00 0.00 0.00 4.18
505 521 7.185453 CAGTAATGAAGCTGCAAAAGATAGAC 58.815 38.462 0.00 0.00 0.00 2.59
520 536 1.030488 TAGACGAGCAAGGGACCGAG 61.030 60.000 0.00 0.00 0.00 4.63
526 542 2.359967 GCAAGGGACCGAGCCTACT 61.360 63.158 0.00 0.00 0.00 2.57
527 543 1.517832 CAAGGGACCGAGCCTACTG 59.482 63.158 0.00 0.00 0.00 2.74
530 546 3.851128 GGACCGAGCCTACTGCCC 61.851 72.222 0.00 0.00 42.71 5.36
538 554 0.034089 AGCCTACTGCCCCAAATGTC 60.034 55.000 0.00 0.00 42.71 3.06
559 575 0.512085 CGACCGAGGACGCTATACTC 59.488 60.000 0.73 0.00 38.29 2.59
565 581 2.686235 GAGGACGCTATACTCGAGCTA 58.314 52.381 13.61 4.76 37.81 3.32
593 609 0.675522 CCGCAACGGGGTAAGTCATT 60.676 55.000 0.00 0.00 44.15 2.57
595 611 1.816074 GCAACGGGGTAAGTCATTCA 58.184 50.000 0.00 0.00 0.00 2.57
597 620 2.752903 GCAACGGGGTAAGTCATTCATT 59.247 45.455 0.00 0.00 0.00 2.57
604 627 4.658901 GGGGTAAGTCATTCATTCCCTCTA 59.341 45.833 0.00 0.00 34.44 2.43
613 636 8.210265 AGTCATTCATTCCCTCTAAAGATTCTC 58.790 37.037 0.00 0.00 0.00 2.87
617 640 7.358770 TCATTCCCTCTAAAGATTCTCTGAG 57.641 40.000 0.00 0.00 0.00 3.35
618 641 6.900186 TCATTCCCTCTAAAGATTCTCTGAGT 59.100 38.462 4.32 0.00 0.00 3.41
619 642 7.401493 TCATTCCCTCTAAAGATTCTCTGAGTT 59.599 37.037 4.32 0.00 0.00 3.01
623 646 6.816140 CCCTCTAAAGATTCTCTGAGTTCAAC 59.184 42.308 4.32 0.00 0.00 3.18
624 647 6.816140 CCTCTAAAGATTCTCTGAGTTCAACC 59.184 42.308 4.32 0.00 0.00 3.77
625 648 6.390721 TCTAAAGATTCTCTGAGTTCAACCG 58.609 40.000 4.32 0.00 0.00 4.44
626 649 3.601443 AGATTCTCTGAGTTCAACCGG 57.399 47.619 0.00 0.00 0.00 5.28
627 650 2.900546 AGATTCTCTGAGTTCAACCGGT 59.099 45.455 0.00 0.00 0.00 5.28
629 652 1.410004 TCTCTGAGTTCAACCGGTGT 58.590 50.000 8.52 0.00 0.00 4.16
630 653 1.760613 TCTCTGAGTTCAACCGGTGTT 59.239 47.619 8.52 0.00 34.14 3.32
639 663 0.817634 CAACCGGTGTTGCTCCTTGA 60.818 55.000 8.52 0.00 44.86 3.02
655 679 5.426504 CTCCTTGAGCTGAGTACATCAAAT 58.573 41.667 0.00 0.00 37.52 2.32
668 694 4.669206 ACATCAAATGTTGCAGGTTTCA 57.331 36.364 0.00 0.00 41.63 2.69
796 822 3.050275 GGTTCTGTGACCAGCGGC 61.050 66.667 0.00 0.00 39.57 6.53
812 840 2.603652 GGCGGAAGGGAAGGAAGGT 61.604 63.158 0.00 0.00 0.00 3.50
816 844 0.039764 GGAAGGGAAGGAAGGTTGGG 59.960 60.000 0.00 0.00 0.00 4.12
840 868 0.670162 TTTGCTGCTCTTGGCTTGTC 59.330 50.000 0.00 0.00 42.39 3.18
847 879 2.594303 CTTGGCTTGTCCGTGGCA 60.594 61.111 0.00 0.00 37.80 4.92
851 883 2.359850 GCTTGTCCGTGGCATGGA 60.360 61.111 24.40 24.40 0.00 3.41
868 900 4.435425 CATGGATGTTGGTTATGGCTTTG 58.565 43.478 0.00 0.00 0.00 2.77
878 910 2.572333 TATGGCTTTGGGGCTCTGGC 62.572 60.000 0.00 0.00 41.48 4.85
879 911 4.372999 GGCTTTGGGGCTCTGGCT 62.373 66.667 0.00 0.00 38.73 4.75
880 912 3.066814 GCTTTGGGGCTCTGGCTG 61.067 66.667 0.00 0.00 38.73 4.85
881 913 2.362120 CTTTGGGGCTCTGGCTGG 60.362 66.667 0.00 0.00 38.73 4.85
890 923 1.919600 GCTCTGGCTGGGACCTTGAT 61.920 60.000 0.00 0.00 35.22 2.57
893 926 2.276740 GGCTGGGACCTTGATGGG 59.723 66.667 0.00 0.00 41.11 4.00
894 927 2.440980 GCTGGGACCTTGATGGGC 60.441 66.667 0.00 0.00 45.48 5.36
895 928 2.988839 GCTGGGACCTTGATGGGCT 61.989 63.158 0.00 0.00 45.52 5.19
896 929 1.077212 CTGGGACCTTGATGGGCTG 60.077 63.158 0.00 0.00 45.52 4.85
898 931 2.356278 GGACCTTGATGGGCTGCA 59.644 61.111 0.50 0.00 45.52 4.41
899 932 1.076485 GGACCTTGATGGGCTGCAT 60.076 57.895 0.50 0.00 45.52 3.96
900 933 1.105759 GGACCTTGATGGGCTGCATC 61.106 60.000 0.50 0.00 45.52 3.91
901 934 1.076485 ACCTTGATGGGCTGCATCC 60.076 57.895 0.50 0.00 41.11 3.51
911 944 3.323622 CTGCATCCCAGCCCAGTA 58.676 61.111 0.00 0.00 34.21 2.74
912 945 1.609239 CTGCATCCCAGCCCAGTAA 59.391 57.895 0.00 0.00 34.21 2.24
935 968 3.431207 CCATATTTTGAGGGCTTGCCTTG 60.431 47.826 11.71 0.00 0.00 3.61
937 970 0.760189 TTTTGAGGGCTTGCCTTGCT 60.760 50.000 11.71 0.00 0.00 3.91
938 971 0.112218 TTTGAGGGCTTGCCTTGCTA 59.888 50.000 11.71 0.00 0.00 3.49
941 974 1.076485 AGGGCTTGCCTTGCTATGG 60.076 57.895 11.71 0.00 0.00 2.74
942 975 2.129785 GGGCTTGCCTTGCTATGGG 61.130 63.158 11.71 0.00 0.00 4.00
948 981 1.228675 GCCTTGCTATGGGATGGGG 60.229 63.158 4.79 0.00 0.00 4.96
959 992 2.189499 GGATGGGGATGCTCGTTGC 61.189 63.158 0.00 0.00 43.25 4.17
969 1002 3.809832 GGATGCTCGTTGCTTGTGTATAT 59.190 43.478 5.00 0.00 43.37 0.86
970 1003 4.988540 GGATGCTCGTTGCTTGTGTATATA 59.011 41.667 5.00 0.00 43.37 0.86
971 1004 5.119279 GGATGCTCGTTGCTTGTGTATATAG 59.881 44.000 5.00 0.00 43.37 1.31
972 1005 5.006153 TGCTCGTTGCTTGTGTATATAGT 57.994 39.130 5.00 0.00 43.37 2.12
973 1006 4.803613 TGCTCGTTGCTTGTGTATATAGTG 59.196 41.667 5.00 0.00 43.37 2.74
974 1007 4.318121 GCTCGTTGCTTGTGTATATAGTGC 60.318 45.833 0.00 0.00 38.95 4.40
984 1017 4.037089 TGTGTATATAGTGCTACGTGGGTG 59.963 45.833 0.00 0.00 0.00 4.61
995 1028 1.893808 CGTGGGTGCTTGCTTCTGT 60.894 57.895 0.00 0.00 0.00 3.41
996 1029 1.447317 CGTGGGTGCTTGCTTCTGTT 61.447 55.000 0.00 0.00 0.00 3.16
997 1030 0.312102 GTGGGTGCTTGCTTCTGTTC 59.688 55.000 0.00 0.00 0.00 3.18
998 1031 0.183492 TGGGTGCTTGCTTCTGTTCT 59.817 50.000 0.00 0.00 0.00 3.01
999 1032 0.595095 GGGTGCTTGCTTCTGTTCTG 59.405 55.000 0.00 0.00 0.00 3.02
1009 1042 5.984695 TGCTTCTGTTCTGAGTAGTATGT 57.015 39.130 0.00 0.00 0.00 2.29
1014 1047 5.489249 TCTGTTCTGAGTAGTATGTCTCGT 58.511 41.667 0.00 0.00 33.88 4.18
1068 1104 9.331282 GCTTAGTAGAATGGACAATTTCACTAT 57.669 33.333 0.00 0.00 30.79 2.12
1071 1107 7.989826 AGTAGAATGGACAATTTCACTATTGC 58.010 34.615 0.00 0.00 38.74 3.56
1072 1108 7.831193 AGTAGAATGGACAATTTCACTATTGCT 59.169 33.333 0.00 0.00 38.74 3.91
1073 1109 9.109393 GTAGAATGGACAATTTCACTATTGCTA 57.891 33.333 0.00 0.00 38.74 3.49
1093 1129 1.694696 AGTCTGGTTCGAGCCTTTCTT 59.305 47.619 19.73 0.00 0.00 2.52
1094 1130 2.897969 AGTCTGGTTCGAGCCTTTCTTA 59.102 45.455 19.73 0.00 0.00 2.10
1095 1131 3.056465 AGTCTGGTTCGAGCCTTTCTTAG 60.056 47.826 19.73 7.27 0.00 2.18
1096 1132 3.056749 GTCTGGTTCGAGCCTTTCTTAGA 60.057 47.826 19.73 9.56 0.00 2.10
1097 1133 3.056749 TCTGGTTCGAGCCTTTCTTAGAC 60.057 47.826 19.73 0.00 0.00 2.59
1098 1134 2.897969 TGGTTCGAGCCTTTCTTAGACT 59.102 45.455 19.73 0.00 0.00 3.24
1099 1135 3.056749 TGGTTCGAGCCTTTCTTAGACTC 60.057 47.826 19.73 0.00 0.00 3.36
1101 1137 1.551145 CGAGCCTTTCTTAGACTCGC 58.449 55.000 6.97 0.00 43.02 5.03
1102 1138 1.133407 CGAGCCTTTCTTAGACTCGCT 59.867 52.381 6.97 2.16 43.02 4.93
1103 1139 2.793237 CGAGCCTTTCTTAGACTCGCTC 60.793 54.545 6.97 9.38 43.02 5.03
1104 1140 2.164624 GAGCCTTTCTTAGACTCGCTCA 59.835 50.000 14.79 0.00 40.69 4.26
1105 1141 2.763448 AGCCTTTCTTAGACTCGCTCAT 59.237 45.455 0.00 0.00 0.00 2.90
1106 1142 3.954904 AGCCTTTCTTAGACTCGCTCATA 59.045 43.478 0.00 0.00 0.00 2.15
1107 1143 4.586841 AGCCTTTCTTAGACTCGCTCATAT 59.413 41.667 0.00 0.00 0.00 1.78
1108 1144 4.683781 GCCTTTCTTAGACTCGCTCATATG 59.316 45.833 0.00 0.00 0.00 1.78
1109 1145 5.226396 CCTTTCTTAGACTCGCTCATATGG 58.774 45.833 2.13 0.00 0.00 2.74
1110 1146 5.221342 CCTTTCTTAGACTCGCTCATATGGT 60.221 44.000 2.13 0.00 0.00 3.55
1111 1147 6.016192 CCTTTCTTAGACTCGCTCATATGGTA 60.016 42.308 2.13 0.00 0.00 3.25
1112 1148 6.561737 TTCTTAGACTCGCTCATATGGTAG 57.438 41.667 2.13 0.00 0.00 3.18
1113 1149 5.622180 TCTTAGACTCGCTCATATGGTAGT 58.378 41.667 2.13 1.73 0.00 2.73
1114 1150 6.062749 TCTTAGACTCGCTCATATGGTAGTT 58.937 40.000 2.13 0.00 0.00 2.24
1115 1151 4.839668 AGACTCGCTCATATGGTAGTTC 57.160 45.455 2.13 0.00 0.00 3.01
1116 1152 3.570550 AGACTCGCTCATATGGTAGTTCC 59.429 47.826 2.13 0.00 0.00 3.62
1117 1153 3.567397 ACTCGCTCATATGGTAGTTCCT 58.433 45.455 2.13 0.00 37.07 3.36
1118 1154 4.726583 ACTCGCTCATATGGTAGTTCCTA 58.273 43.478 2.13 0.00 37.07 2.94
1119 1155 4.519730 ACTCGCTCATATGGTAGTTCCTAC 59.480 45.833 2.13 0.00 36.33 3.18
1120 1156 4.726583 TCGCTCATATGGTAGTTCCTACT 58.273 43.478 2.13 0.00 37.16 2.57
1121 1157 5.138276 TCGCTCATATGGTAGTTCCTACTT 58.862 41.667 2.13 0.00 37.16 2.24
1122 1158 6.301486 TCGCTCATATGGTAGTTCCTACTTA 58.699 40.000 2.13 0.00 37.16 2.24
1123 1159 6.946583 TCGCTCATATGGTAGTTCCTACTTAT 59.053 38.462 2.13 0.87 37.16 1.73
1124 1160 7.450634 TCGCTCATATGGTAGTTCCTACTTATT 59.549 37.037 2.13 0.00 37.16 1.40
1125 1161 8.088981 CGCTCATATGGTAGTTCCTACTTATTT 58.911 37.037 2.13 0.00 37.16 1.40
1179 1215 4.408993 TTTTTCACGATGATCTGCTGTG 57.591 40.909 0.00 0.00 0.00 3.66
1180 1216 3.317603 TTTCACGATGATCTGCTGTGA 57.682 42.857 0.00 0.57 37.76 3.58
1181 1217 2.284263 TCACGATGATCTGCTGTGAC 57.716 50.000 0.00 0.00 34.85 3.67
1182 1218 1.545582 TCACGATGATCTGCTGTGACA 59.454 47.619 0.00 0.00 34.85 3.58
1183 1219 2.029110 TCACGATGATCTGCTGTGACAA 60.029 45.455 0.00 0.00 34.85 3.18
1184 1220 2.093310 CACGATGATCTGCTGTGACAAC 59.907 50.000 0.00 0.00 32.39 3.32
1185 1221 1.322637 CGATGATCTGCTGTGACAACG 59.677 52.381 0.00 0.00 0.00 4.10
1186 1222 1.061711 GATGATCTGCTGTGACAACGC 59.938 52.381 0.00 0.00 0.00 4.84
1187 1223 0.033920 TGATCTGCTGTGACAACGCT 59.966 50.000 0.00 0.00 0.00 5.07
1188 1224 0.441533 GATCTGCTGTGACAACGCTG 59.558 55.000 0.00 0.00 0.00 5.18
1189 1225 1.572085 ATCTGCTGTGACAACGCTGC 61.572 55.000 0.00 0.00 46.45 5.25
1190 1226 3.245948 CTGCTGTGACAACGCTGCC 62.246 63.158 0.00 0.00 45.97 4.85
1191 1227 2.974698 GCTGTGACAACGCTGCCT 60.975 61.111 0.00 0.00 42.66 4.75
1192 1228 2.959357 GCTGTGACAACGCTGCCTC 61.959 63.158 0.00 0.00 42.66 4.70
1193 1229 1.595109 CTGTGACAACGCTGCCTCA 60.595 57.895 0.00 0.00 0.00 3.86
1194 1230 1.153269 TGTGACAACGCTGCCTCAA 60.153 52.632 0.00 0.00 0.00 3.02
1195 1231 1.279840 GTGACAACGCTGCCTCAAC 59.720 57.895 0.00 0.00 0.00 3.18
1196 1232 1.153269 TGACAACGCTGCCTCAACA 60.153 52.632 0.00 0.00 0.00 3.33
1197 1233 1.279840 GACAACGCTGCCTCAACAC 59.720 57.895 0.00 0.00 0.00 3.32
1198 1234 2.117941 GACAACGCTGCCTCAACACC 62.118 60.000 0.00 0.00 0.00 4.16
1199 1235 2.594592 AACGCTGCCTCAACACCC 60.595 61.111 0.00 0.00 0.00 4.61
1200 1236 3.120086 AACGCTGCCTCAACACCCT 62.120 57.895 0.00 0.00 0.00 4.34
1201 1237 3.052082 CGCTGCCTCAACACCCTG 61.052 66.667 0.00 0.00 0.00 4.45
1202 1238 3.368571 GCTGCCTCAACACCCTGC 61.369 66.667 0.00 0.00 0.00 4.85
1203 1239 2.674380 CTGCCTCAACACCCTGCC 60.674 66.667 0.00 0.00 0.00 4.85
1204 1240 4.284550 TGCCTCAACACCCTGCCC 62.285 66.667 0.00 0.00 0.00 5.36
1205 1241 3.971702 GCCTCAACACCCTGCCCT 61.972 66.667 0.00 0.00 0.00 5.19
1230 1266 1.092345 GGCTTCCTCTGACGGCAATC 61.092 60.000 0.00 0.00 35.64 2.67
1241 1277 2.885113 GGCAATCGAAGCCCAACC 59.115 61.111 18.63 0.00 46.50 3.77
1254 1290 0.679002 CCCAACCTGTGATGCTGGAG 60.679 60.000 0.00 0.00 39.25 3.86
1257 1293 1.064906 CAACCTGTGATGCTGGAGGAT 60.065 52.381 0.00 0.00 39.25 3.24
1269 1305 0.755079 TGGAGGATGAAGATGAGGCG 59.245 55.000 0.00 0.00 0.00 5.52
1278 1314 3.782443 GATGAGGCGGACCCGGTT 61.782 66.667 10.70 0.00 40.19 4.44
1315 1351 0.770557 TGTTGGGAAGGTACTGGCCT 60.771 55.000 3.32 0.00 40.86 5.19
1320 1356 0.919710 GGAAGGTACTGGCCTCCAAT 59.080 55.000 3.32 0.00 40.86 3.16
1402 1438 3.655211 AGCTCCACCTTGCAGGGG 61.655 66.667 20.34 12.74 40.58 4.79
1417 1453 4.016444 TGCAGGGGATAACATCTTTGTTC 58.984 43.478 0.00 0.00 42.43 3.18
1428 1464 5.473066 ACATCTTTGTTCCTGAATTTGGG 57.527 39.130 0.00 0.00 29.55 4.12
1437 1473 0.454957 CTGAATTTGGGTCGCAAGCG 60.455 55.000 8.36 8.36 41.35 4.68
1440 1476 1.862602 AATTTGGGTCGCAAGCGGAC 61.863 55.000 14.98 10.88 40.25 4.79
1461 1497 1.442769 GTGCTCGTGTGATGAATGGT 58.557 50.000 0.00 0.00 0.00 3.55
1497 1533 2.749621 GGGGAAACATGCTGTACTTCTG 59.250 50.000 0.00 0.00 0.00 3.02
1515 1551 2.226437 TCTGAAGCTTTTTGATGCGGAC 59.774 45.455 0.00 0.00 0.00 4.79
1529 1565 4.329545 GGACACCCAGCCGCTTCA 62.330 66.667 0.00 0.00 0.00 3.02
1533 1569 4.021925 ACCCAGCCGCTTCAGGTC 62.022 66.667 0.00 0.00 0.00 3.85
1537 1573 1.004560 CAGCCGCTTCAGGTCAAGA 60.005 57.895 0.00 0.00 0.00 3.02
1539 1575 0.326264 AGCCGCTTCAGGTCAAGATT 59.674 50.000 0.00 0.00 0.00 2.40
1545 1581 3.063180 CGCTTCAGGTCAAGATTGATCAC 59.937 47.826 8.46 0.00 40.76 3.06
1551 1587 2.356535 GGTCAAGATTGATCACCTGGCT 60.357 50.000 0.00 0.00 38.20 4.75
1552 1588 2.681848 GTCAAGATTGATCACCTGGCTG 59.318 50.000 0.00 0.00 39.73 4.85
1553 1589 1.404391 CAAGATTGATCACCTGGCTGC 59.596 52.381 0.00 0.00 0.00 5.25
1566 1602 1.303155 GGCTGCATGGGCTAGGATC 60.303 63.158 0.50 0.00 41.91 3.36
1569 1605 1.349026 GCTGCATGGGCTAGGATCTTA 59.651 52.381 0.00 0.00 41.91 2.10
1578 1614 2.700897 GGCTAGGATCTTAGCACTTCCA 59.299 50.000 30.91 0.00 46.21 3.53
1587 1623 4.326826 TCTTAGCACTTCCACCAAGATTG 58.673 43.478 0.00 0.00 35.82 2.67
1593 1629 4.022068 GCACTTCCACCAAGATTGATGAAA 60.022 41.667 0.00 0.00 35.82 2.69
1595 1631 5.242393 CACTTCCACCAAGATTGATGAAAGT 59.758 40.000 0.00 0.00 35.82 2.66
1604 1640 8.423349 ACCAAGATTGATGAAAGTGAAATTTGA 58.577 29.630 0.00 0.00 0.00 2.69
1674 1710 1.380246 TGATGGCTGATGTTGGGGC 60.380 57.895 0.00 0.00 0.00 5.80
1679 1715 2.361610 CTGATGTTGGGGCGCCTT 60.362 61.111 28.56 4.23 0.00 4.35
1680 1716 1.978617 CTGATGTTGGGGCGCCTTT 60.979 57.895 28.56 4.63 0.00 3.11
1692 1728 3.098555 GCCTTTATGCGTGTCCGG 58.901 61.111 0.00 0.00 33.68 5.14
1694 1730 2.469516 CCTTTATGCGTGTCCGGGC 61.470 63.158 0.00 0.00 33.68 6.13
1695 1731 1.449601 CTTTATGCGTGTCCGGGCT 60.450 57.895 7.97 0.00 33.68 5.19
1702 1738 1.813859 CGTGTCCGGGCTGAGATTA 59.186 57.895 7.97 0.00 0.00 1.75
1710 1746 1.331756 CGGGCTGAGATTAATGTGCAC 59.668 52.381 10.75 10.75 0.00 4.57
1713 1749 2.677836 GGCTGAGATTAATGTGCACGAA 59.322 45.455 13.13 6.73 0.00 3.85
1720 1756 1.518325 TAATGTGCACGAACCTGTGG 58.482 50.000 13.13 0.00 40.26 4.17
1723 1759 0.178301 TGTGCACGAACCTGTGGTTA 59.822 50.000 13.13 0.00 46.95 2.85
1725 1761 0.250124 TGCACGAACCTGTGGTTAGG 60.250 55.000 12.72 6.53 46.95 2.69
1734 1770 3.973206 CCTGTGGTTAGGTATGTGACA 57.027 47.619 0.00 0.00 32.99 3.58
1773 1809 5.230942 CAACTTAGTATTATCTGGAGGCCG 58.769 45.833 0.00 0.00 0.00 6.13
1776 1812 5.601313 ACTTAGTATTATCTGGAGGCCGAAA 59.399 40.000 0.00 0.00 0.00 3.46
1791 1828 6.121776 AGGCCGAAACCATCATATATACAA 57.878 37.500 0.00 0.00 0.00 2.41
1812 1849 9.778741 ATACAAGTACAAGAGAATGTCAAAAGA 57.221 29.630 0.00 0.00 34.75 2.52
1913 1954 3.561725 CACTGAGTTTGGAGAGGTGAAAC 59.438 47.826 0.00 0.00 0.00 2.78
1936 1977 1.185618 TGTTGCGCTCTAGTCTGGGT 61.186 55.000 9.73 0.00 0.00 4.51
1960 2001 3.076621 TCGTGAAGAAGTCCGCTAACTA 58.923 45.455 0.00 0.00 0.00 2.24
1968 2009 5.121811 AGAAGTCCGCTAACTATAACTCGA 58.878 41.667 0.00 0.00 0.00 4.04
1981 2022 6.505272 ACTATAACTCGAAAGGCACATACTC 58.495 40.000 0.00 0.00 0.00 2.59
2000 2041 4.392047 ACTCAAGAGCAACAACATGATCA 58.608 39.130 0.00 0.00 38.17 2.92
2007 2048 3.006003 AGCAACAACATGATCATGCACAA 59.994 39.130 31.17 0.00 42.39 3.33
2008 2049 3.930229 GCAACAACATGATCATGCACAAT 59.070 39.130 31.17 12.22 42.39 2.71
2013 2054 3.208594 ACATGATCATGCACAATAGCGT 58.791 40.909 31.17 8.72 42.39 5.07
2026 2067 6.072948 TGCACAATAGCGTGTACAAAATAAGT 60.073 34.615 0.00 0.00 39.19 2.24
2088 2129 1.217001 CCGCGCAATACTGATAGCAA 58.783 50.000 8.75 0.00 0.00 3.91
2094 2135 4.270084 GCGCAATACTGATAGCAACTGTAA 59.730 41.667 0.30 0.00 0.00 2.41
2108 2149 4.307432 CAACTGTAATGTCGGACAAGAGT 58.693 43.478 15.72 10.56 0.00 3.24
2156 2197 0.824759 AGTCCTCCAGTAACCATCGC 59.175 55.000 0.00 0.00 0.00 4.58
2219 2260 2.811317 GCCTCTGCACTCGAACGG 60.811 66.667 0.00 0.00 37.47 4.44
2243 2284 5.841957 AAACTGCAGTCTGTTTCTTCATT 57.158 34.783 21.95 2.75 39.22 2.57
2249 2290 5.126869 TGCAGTCTGTTTCTTCATTTTCCAA 59.873 36.000 0.93 0.00 0.00 3.53
2270 2311 1.815003 GCAATGAGAGAACCACCAAGG 59.185 52.381 0.00 0.00 45.67 3.61
2284 2325 3.317993 CCACCAAGGAAAACACAGTAAGG 59.682 47.826 0.00 0.00 41.22 2.69
2295 2336 7.013369 GGAAAACACAGTAAGGAGAAAGTGAAT 59.987 37.037 0.00 0.00 0.00 2.57
2342 2383 1.618837 GTAGCATCCGAATAGGCCTGA 59.381 52.381 17.99 3.29 40.77 3.86
2392 2435 3.176336 CGATGAGAGATCGTGCCAG 57.824 57.895 0.00 0.00 36.84 4.85
2433 2476 5.029014 CGAAGAAGGTGACTATAGTGAACG 58.971 45.833 10.90 0.00 42.68 3.95
2462 2505 5.104693 TGGGAGTAGAAACAAACTGACTCAA 60.105 40.000 0.00 0.00 35.98 3.02
2491 2534 8.800515 ATGGACATGATATGAGATATCTGGAT 57.199 34.615 10.74 4.59 41.69 3.41
2523 2566 4.177026 CAAGATAGACAAGACTCCCAACG 58.823 47.826 0.00 0.00 0.00 4.10
2571 2614 1.817099 GGGCTCACCATCAGAAGCG 60.817 63.158 0.00 0.00 39.85 4.68
2589 2632 0.443869 CGCGAAGGTGAACATTGAGG 59.556 55.000 0.00 0.00 0.00 3.86
2595 2638 3.356529 AGGTGAACATTGAGGTCCATC 57.643 47.619 0.00 0.00 30.86 3.51
2596 2639 2.644299 AGGTGAACATTGAGGTCCATCA 59.356 45.455 0.00 0.00 30.86 3.07
2650 2693 0.539051 ACGAGCAAGAAGATCCTGGG 59.461 55.000 0.00 0.00 0.00 4.45
2656 2699 3.322254 AGCAAGAAGATCCTGGGTATACG 59.678 47.826 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 6.847421 AAGCTCTTCTTTTATTGGCTTCAT 57.153 33.333 0.00 0.00 34.09 2.57
120 121 2.871133 TGATCTACTTAACCACGCACG 58.129 47.619 0.00 0.00 0.00 5.34
124 125 7.043325 GCTGAAGTTATGATCTACTTAACCACG 60.043 40.741 7.96 0.00 38.83 4.94
128 129 9.974750 GTTTGCTGAAGTTATGATCTACTTAAC 57.025 33.333 7.96 0.00 38.54 2.01
143 144 2.158871 TGGTTCCTACGTTTGCTGAAGT 60.159 45.455 0.00 0.00 0.00 3.01
170 171 6.350445 GGTTTGGATGAACATACAATGAGCTT 60.350 38.462 12.37 0.00 40.99 3.74
204 205 1.604604 TTGCCAAGCAGGTTAGTCAC 58.395 50.000 0.00 0.00 40.61 3.67
217 233 3.119673 CGTATGTTACCTGCAATTGCCAA 60.120 43.478 26.94 12.88 41.18 4.52
224 240 5.877564 TGATCATTTCGTATGTTACCTGCAA 59.122 36.000 0.00 0.00 0.00 4.08
294 310 1.344438 TGTCAGTAGGAGTGTTGCCAG 59.656 52.381 0.00 0.00 0.00 4.85
302 318 0.324830 GGAGCCCTGTCAGTAGGAGT 60.325 60.000 0.00 0.00 40.42 3.85
317 333 3.376918 GGCTGTTTGGGCAGGAGC 61.377 66.667 0.00 0.00 37.00 4.70
352 368 3.915575 GCTTCACTGCCATGGGAG 58.084 61.111 29.94 29.94 39.56 4.30
364 380 3.009115 CCCTTCTCCGGGGCTTCA 61.009 66.667 0.00 0.00 40.75 3.02
372 388 0.978146 ACCCTGATCACCCTTCTCCG 60.978 60.000 0.00 0.00 0.00 4.63
391 407 1.970640 CCTGATATGATGACGGGGTCA 59.029 52.381 0.38 0.38 46.90 4.02
414 430 1.167851 CAAAGGGCTTGAATCGCAGA 58.832 50.000 0.00 0.00 38.04 4.26
432 448 1.550524 CGGTCTGGGATCTCTTTGTCA 59.449 52.381 0.00 0.00 0.00 3.58
454 470 2.224159 GGCAGGGAGTGGAGTTCCA 61.224 63.158 0.00 0.00 45.30 3.53
505 521 4.821589 GGCTCGGTCCCTTGCTCG 62.822 72.222 0.00 0.00 0.00 5.03
520 536 1.376609 CGACATTTGGGGCAGTAGGC 61.377 60.000 0.00 0.00 43.74 3.93
526 542 3.053291 GTCGCGACATTTGGGGCA 61.053 61.111 33.09 0.00 0.00 5.36
527 543 3.810896 GGTCGCGACATTTGGGGC 61.811 66.667 37.26 16.08 0.00 5.80
530 546 2.452813 CCTCGGTCGCGACATTTGG 61.453 63.158 37.26 27.39 0.00 3.28
604 627 9.950159 AACACCGGTTGAACTCAGAGAATCTTT 62.950 40.741 2.97 0.00 38.84 2.52
623 646 3.972227 CTCAAGGAGCAACACCGG 58.028 61.111 0.00 0.00 0.00 5.28
634 657 4.940046 ACATTTGATGTACTCAGCTCAAGG 59.060 41.667 0.00 0.00 42.78 3.61
639 663 4.074259 TGCAACATTTGATGTACTCAGCT 58.926 39.130 0.00 0.00 44.07 4.24
646 670 5.781210 TGAAACCTGCAACATTTGATGTA 57.219 34.783 0.00 0.00 44.07 2.29
648 672 5.106869 CCAATGAAACCTGCAACATTTGATG 60.107 40.000 0.00 0.00 31.85 3.07
649 673 4.998672 CCAATGAAACCTGCAACATTTGAT 59.001 37.500 0.00 0.00 31.85 2.57
650 674 4.100653 TCCAATGAAACCTGCAACATTTGA 59.899 37.500 0.00 0.00 31.85 2.69
651 675 4.378774 TCCAATGAAACCTGCAACATTTG 58.621 39.130 0.00 0.00 31.85 2.32
652 676 4.503643 CCTCCAATGAAACCTGCAACATTT 60.504 41.667 0.00 0.00 31.85 2.32
655 679 1.962807 CCTCCAATGAAACCTGCAACA 59.037 47.619 0.00 0.00 0.00 3.33
668 694 1.079127 CTTGACGGCGTCCTCCAAT 60.079 57.895 34.28 0.00 0.00 3.16
796 822 0.322546 CCAACCTTCCTTCCCTTCCG 60.323 60.000 0.00 0.00 0.00 4.30
812 840 2.203818 AGCAGCAAATGGCCCCAA 60.204 55.556 0.00 0.00 46.50 4.12
816 844 1.217244 CCAAGAGCAGCAAATGGCC 59.783 57.895 0.00 0.00 46.50 5.36
840 868 1.250154 AACCAACATCCATGCCACGG 61.250 55.000 0.00 0.00 0.00 4.94
847 879 3.451902 CCAAAGCCATAACCAACATCCAT 59.548 43.478 0.00 0.00 0.00 3.41
851 883 2.187100 CCCCAAAGCCATAACCAACAT 58.813 47.619 0.00 0.00 0.00 2.71
878 910 1.077212 CAGCCCATCAAGGTCCCAG 60.077 63.158 0.00 0.00 34.66 4.45
879 911 3.089838 CAGCCCATCAAGGTCCCA 58.910 61.111 0.00 0.00 34.66 4.37
880 912 2.440980 GCAGCCCATCAAGGTCCC 60.441 66.667 0.00 0.00 34.66 4.46
881 913 1.076485 ATGCAGCCCATCAAGGTCC 60.076 57.895 0.00 0.00 34.66 4.46
893 926 2.556840 TTACTGGGCTGGGATGCAGC 62.557 60.000 0.00 0.00 44.38 5.25
894 927 0.749454 GTTACTGGGCTGGGATGCAG 60.749 60.000 0.00 0.00 34.04 4.41
895 928 1.302949 GTTACTGGGCTGGGATGCA 59.697 57.895 0.00 0.00 34.04 3.96
896 929 1.453928 GGTTACTGGGCTGGGATGC 60.454 63.158 0.00 0.00 0.00 3.91
898 931 2.206322 TATGGTTACTGGGCTGGGAT 57.794 50.000 0.00 0.00 0.00 3.85
899 932 2.206322 ATATGGTTACTGGGCTGGGA 57.794 50.000 0.00 0.00 0.00 4.37
900 933 3.312736 AAATATGGTTACTGGGCTGGG 57.687 47.619 0.00 0.00 0.00 4.45
901 934 4.277476 TCAAAATATGGTTACTGGGCTGG 58.723 43.478 0.00 0.00 0.00 4.85
904 937 3.636764 CCCTCAAAATATGGTTACTGGGC 59.363 47.826 0.00 0.00 0.00 5.36
911 944 2.501316 GGCAAGCCCTCAAAATATGGTT 59.499 45.455 0.00 0.00 0.00 3.67
912 945 2.110578 GGCAAGCCCTCAAAATATGGT 58.889 47.619 0.00 0.00 0.00 3.55
935 968 0.034670 GAGCATCCCCATCCCATAGC 60.035 60.000 0.00 0.00 0.00 2.97
937 970 0.473694 ACGAGCATCCCCATCCCATA 60.474 55.000 0.00 0.00 0.00 2.74
938 971 1.355718 AACGAGCATCCCCATCCCAT 61.356 55.000 0.00 0.00 0.00 4.00
941 974 2.189499 GCAACGAGCATCCCCATCC 61.189 63.158 0.00 0.00 44.79 3.51
942 975 3.425422 GCAACGAGCATCCCCATC 58.575 61.111 0.00 0.00 44.79 3.51
959 992 5.220381 CCCACGTAGCACTATATACACAAG 58.780 45.833 0.00 0.00 0.00 3.16
969 1002 0.037697 CAAGCACCCACGTAGCACTA 60.038 55.000 0.00 0.00 0.00 2.74
970 1003 1.301716 CAAGCACCCACGTAGCACT 60.302 57.895 0.00 0.00 0.00 4.40
971 1004 2.966309 GCAAGCACCCACGTAGCAC 61.966 63.158 0.00 0.00 0.00 4.40
972 1005 2.668212 GCAAGCACCCACGTAGCA 60.668 61.111 0.00 0.00 0.00 3.49
973 1006 1.912371 GAAGCAAGCACCCACGTAGC 61.912 60.000 0.00 0.00 0.00 3.58
974 1007 0.320771 AGAAGCAAGCACCCACGTAG 60.321 55.000 0.00 0.00 0.00 3.51
984 1017 3.658709 ACTACTCAGAACAGAAGCAAGC 58.341 45.455 0.00 0.00 0.00 4.01
995 1028 5.173664 TCGAACGAGACATACTACTCAGAA 58.826 41.667 0.00 0.00 33.86 3.02
996 1029 4.752146 TCGAACGAGACATACTACTCAGA 58.248 43.478 0.00 0.00 33.86 3.27
997 1030 5.466432 TTCGAACGAGACATACTACTCAG 57.534 43.478 0.00 0.00 33.86 3.35
998 1031 4.331992 CCTTCGAACGAGACATACTACTCA 59.668 45.833 0.00 0.00 33.86 3.41
999 1032 4.332268 ACCTTCGAACGAGACATACTACTC 59.668 45.833 0.00 0.00 0.00 2.59
1009 1042 2.486982 CCTTGAGTACCTTCGAACGAGA 59.513 50.000 0.00 0.00 0.00 4.04
1014 1047 3.893200 TCACTTCCTTGAGTACCTTCGAA 59.107 43.478 0.00 0.00 0.00 3.71
1068 1104 0.246635 GGCTCGAACCAGACTAGCAA 59.753 55.000 0.00 0.00 34.85 3.91
1069 1105 0.612174 AGGCTCGAACCAGACTAGCA 60.612 55.000 7.76 0.00 34.85 3.49
1070 1106 0.533032 AAGGCTCGAACCAGACTAGC 59.467 55.000 7.76 0.00 28.36 3.42
1071 1107 2.494073 AGAAAGGCTCGAACCAGACTAG 59.506 50.000 7.76 0.00 28.36 2.57
1072 1108 2.526432 AGAAAGGCTCGAACCAGACTA 58.474 47.619 7.76 0.00 28.36 2.59
1073 1109 1.343069 AGAAAGGCTCGAACCAGACT 58.657 50.000 7.76 0.02 30.40 3.24
1093 1129 4.760715 GGAACTACCATATGAGCGAGTCTA 59.239 45.833 3.65 0.00 38.79 2.59
1094 1130 3.570550 GGAACTACCATATGAGCGAGTCT 59.429 47.826 3.65 0.00 38.79 3.24
1095 1131 3.570550 AGGAACTACCATATGAGCGAGTC 59.429 47.826 3.65 0.00 42.04 3.36
1096 1132 3.567397 AGGAACTACCATATGAGCGAGT 58.433 45.455 3.65 0.00 42.04 4.18
1158 1194 4.064388 TCACAGCAGATCATCGTGAAAAA 58.936 39.130 0.00 0.00 33.86 1.94
1159 1195 3.433274 GTCACAGCAGATCATCGTGAAAA 59.567 43.478 8.32 0.00 38.26 2.29
1160 1196 2.995939 GTCACAGCAGATCATCGTGAAA 59.004 45.455 8.32 0.00 38.26 2.69
1161 1197 2.029110 TGTCACAGCAGATCATCGTGAA 60.029 45.455 8.32 0.00 38.26 3.18
1162 1198 1.545582 TGTCACAGCAGATCATCGTGA 59.454 47.619 0.00 0.00 34.37 4.35
1163 1199 2.000429 TGTCACAGCAGATCATCGTG 58.000 50.000 0.00 0.00 0.00 4.35
1164 1200 2.341257 GTTGTCACAGCAGATCATCGT 58.659 47.619 0.00 0.00 0.00 3.73
1165 1201 1.322637 CGTTGTCACAGCAGATCATCG 59.677 52.381 0.00 0.00 0.00 3.84
1166 1202 1.061711 GCGTTGTCACAGCAGATCATC 59.938 52.381 0.00 0.00 0.00 2.92
1167 1203 1.081892 GCGTTGTCACAGCAGATCAT 58.918 50.000 0.00 0.00 0.00 2.45
1168 1204 0.033920 AGCGTTGTCACAGCAGATCA 59.966 50.000 0.00 0.00 0.00 2.92
1169 1205 0.441533 CAGCGTTGTCACAGCAGATC 59.558 55.000 0.00 0.00 0.00 2.75
1170 1206 1.572085 GCAGCGTTGTCACAGCAGAT 61.572 55.000 0.00 0.00 0.00 2.90
1171 1207 2.246739 GCAGCGTTGTCACAGCAGA 61.247 57.895 0.00 0.00 0.00 4.26
1172 1208 2.250485 GCAGCGTTGTCACAGCAG 59.750 61.111 0.00 0.00 0.00 4.24
1173 1209 3.279116 GGCAGCGTTGTCACAGCA 61.279 61.111 0.00 0.00 0.00 4.41
1174 1210 2.959357 GAGGCAGCGTTGTCACAGC 61.959 63.158 6.64 0.00 0.00 4.40
1175 1211 1.159713 TTGAGGCAGCGTTGTCACAG 61.160 55.000 6.64 0.00 31.25 3.66
1176 1212 1.153269 TTGAGGCAGCGTTGTCACA 60.153 52.632 6.64 2.72 0.00 3.58
1177 1213 1.279840 GTTGAGGCAGCGTTGTCAC 59.720 57.895 6.64 0.00 0.00 3.67
1178 1214 1.153269 TGTTGAGGCAGCGTTGTCA 60.153 52.632 6.64 0.00 0.00 3.58
1179 1215 1.279840 GTGTTGAGGCAGCGTTGTC 59.720 57.895 0.00 0.00 0.00 3.18
1180 1216 2.186826 GGTGTTGAGGCAGCGTTGT 61.187 57.895 0.00 0.00 0.00 3.32
1181 1217 2.639286 GGTGTTGAGGCAGCGTTG 59.361 61.111 0.00 0.00 0.00 4.10
1182 1218 2.594592 GGGTGTTGAGGCAGCGTT 60.595 61.111 0.00 0.00 37.71 4.84
1183 1219 3.560251 AGGGTGTTGAGGCAGCGT 61.560 61.111 0.00 0.00 37.71 5.07
1184 1220 3.052082 CAGGGTGTTGAGGCAGCG 61.052 66.667 0.00 0.00 37.71 5.18
1185 1221 3.368571 GCAGGGTGTTGAGGCAGC 61.369 66.667 0.00 0.00 36.26 5.25
1186 1222 2.674380 GGCAGGGTGTTGAGGCAG 60.674 66.667 0.00 0.00 0.00 4.85
1187 1223 4.284550 GGGCAGGGTGTTGAGGCA 62.285 66.667 0.00 0.00 0.00 4.75
1188 1224 3.971702 AGGGCAGGGTGTTGAGGC 61.972 66.667 0.00 0.00 0.00 4.70
1189 1225 2.034687 CAGGGCAGGGTGTTGAGG 59.965 66.667 0.00 0.00 0.00 3.86
1190 1226 2.034687 CCAGGGCAGGGTGTTGAG 59.965 66.667 0.00 0.00 0.00 3.02
1191 1227 1.650242 TTTCCAGGGCAGGGTGTTGA 61.650 55.000 0.00 0.00 0.00 3.18
1192 1228 1.152567 TTTCCAGGGCAGGGTGTTG 60.153 57.895 0.00 0.00 0.00 3.33
1193 1229 1.153756 CTTTCCAGGGCAGGGTGTT 59.846 57.895 0.00 0.00 0.00 3.32
1194 1230 2.845345 CCTTTCCAGGGCAGGGTGT 61.845 63.158 0.00 0.00 36.36 4.16
1195 1231 2.036256 CCTTTCCAGGGCAGGGTG 59.964 66.667 0.00 0.00 36.36 4.61
1217 1253 1.424493 GGCTTCGATTGCCGTCAGAG 61.424 60.000 13.07 0.00 41.03 3.35
1218 1254 1.447838 GGCTTCGATTGCCGTCAGA 60.448 57.895 13.07 0.00 41.03 3.27
1219 1255 3.093278 GGCTTCGATTGCCGTCAG 58.907 61.111 13.07 0.00 41.03 3.51
1230 1266 1.926511 GCATCACAGGTTGGGCTTCG 61.927 60.000 0.00 0.00 0.00 3.79
1241 1277 2.169978 TCTTCATCCTCCAGCATCACAG 59.830 50.000 0.00 0.00 0.00 3.66
1254 1290 0.250081 GGTCCGCCTCATCTTCATCC 60.250 60.000 0.00 0.00 0.00 3.51
1257 1293 2.721167 CGGGTCCGCCTCATCTTCA 61.721 63.158 0.00 0.00 34.45 3.02
1308 1344 1.425066 TGAAGAACATTGGAGGCCAGT 59.575 47.619 5.01 0.00 33.81 4.00
1309 1345 1.815003 GTGAAGAACATTGGAGGCCAG 59.185 52.381 5.01 0.00 33.81 4.85
1320 1356 5.954752 AGAGATAGTCTGGATGTGAAGAACA 59.045 40.000 0.00 0.00 37.38 3.18
1382 1418 3.060615 CTGCAAGGTGGAGCTGCC 61.061 66.667 1.53 0.00 35.13 4.85
1394 1430 4.046286 ACAAAGATGTTATCCCCTGCAA 57.954 40.909 0.00 0.00 35.91 4.08
1417 1453 0.109132 GCTTGCGACCCAAATTCAGG 60.109 55.000 0.00 0.00 31.94 3.86
1437 1473 2.094659 CATCACACGAGCACGGTCC 61.095 63.158 8.74 0.00 44.46 4.46
1440 1476 0.371301 CATTCATCACACGAGCACGG 59.629 55.000 8.74 0.00 44.46 4.94
1446 1482 2.301583 TGGAGAACCATTCATCACACGA 59.698 45.455 0.00 0.00 41.77 4.35
1461 1497 2.297895 CCCCACCGTCCATGGAGAA 61.298 63.158 16.81 0.00 39.87 2.87
1472 1508 3.277133 CAGCATGTTTCCCCACCG 58.723 61.111 0.00 0.00 0.00 4.94
1497 1533 2.319472 GTGTCCGCATCAAAAAGCTTC 58.681 47.619 0.00 0.00 0.00 3.86
1515 1551 4.335647 ACCTGAAGCGGCTGGGTG 62.336 66.667 17.62 5.33 0.00 4.61
1527 1563 3.054875 CCAGGTGATCAATCTTGACCTGA 60.055 47.826 21.75 2.12 45.96 3.86
1529 1565 2.356535 GCCAGGTGATCAATCTTGACCT 60.357 50.000 0.00 0.00 40.49 3.85
1533 1569 1.404391 GCAGCCAGGTGATCAATCTTG 59.596 52.381 0.00 0.00 0.00 3.02
1537 1573 1.399714 CATGCAGCCAGGTGATCAAT 58.600 50.000 0.00 0.00 0.00 2.57
1539 1575 1.077285 CCATGCAGCCAGGTGATCA 60.077 57.895 0.04 0.00 0.00 2.92
1545 1581 2.203308 CTAGCCCATGCAGCCAGG 60.203 66.667 0.00 0.00 41.13 4.45
1551 1587 1.349026 GCTAAGATCCTAGCCCATGCA 59.651 52.381 11.68 0.00 38.72 3.96
1552 1588 1.349026 TGCTAAGATCCTAGCCCATGC 59.651 52.381 18.56 0.00 43.13 4.06
1553 1589 2.636893 AGTGCTAAGATCCTAGCCCATG 59.363 50.000 18.56 0.00 43.13 3.66
1566 1602 4.326826 TCAATCTTGGTGGAAGTGCTAAG 58.673 43.478 0.00 0.00 32.90 2.18
1569 1605 2.957402 TCAATCTTGGTGGAAGTGCT 57.043 45.000 0.00 0.00 32.90 4.40
1575 1611 4.984295 TCACTTTCATCAATCTTGGTGGA 58.016 39.130 3.49 0.00 39.72 4.02
1578 1614 8.423349 TCAAATTTCACTTTCATCAATCTTGGT 58.577 29.630 0.00 0.00 0.00 3.67
1587 1623 8.822652 ACTCCATTTCAAATTTCACTTTCATC 57.177 30.769 0.00 0.00 0.00 2.92
1593 1629 6.585416 AGCAAACTCCATTTCAAATTTCACT 58.415 32.000 0.00 0.00 0.00 3.41
1595 1631 7.171337 GCTTAGCAAACTCCATTTCAAATTTCA 59.829 33.333 0.00 0.00 0.00 2.69
1604 1640 5.240121 CAATTGGCTTAGCAAACTCCATTT 58.760 37.500 6.53 0.00 0.00 2.32
1631 1667 5.473846 GCATCTGATTCCACATGAATGATCT 59.526 40.000 0.00 0.00 43.81 2.75
1635 1671 4.578928 TCAGCATCTGATTCCACATGAATG 59.421 41.667 0.00 0.00 43.81 2.67
1662 1698 0.679640 TAAAGGCGCCCCAACATCAG 60.680 55.000 26.15 0.00 0.00 2.90
1679 1715 2.125310 CAGCCCGGACACGCATAA 60.125 61.111 0.73 0.00 39.22 1.90
1680 1716 3.071837 TCAGCCCGGACACGCATA 61.072 61.111 0.73 0.00 39.22 3.14
1692 1728 2.279741 TCGTGCACATTAATCTCAGCC 58.720 47.619 18.64 0.00 0.00 4.85
1694 1730 3.935203 AGGTTCGTGCACATTAATCTCAG 59.065 43.478 18.64 0.00 0.00 3.35
1695 1731 3.684305 CAGGTTCGTGCACATTAATCTCA 59.316 43.478 18.64 0.00 0.00 3.27
1702 1738 0.465460 ACCACAGGTTCGTGCACATT 60.465 50.000 18.64 0.00 35.47 2.71
1756 1792 3.071167 GGTTTCGGCCTCCAGATAATACT 59.929 47.826 0.00 0.00 0.00 2.12
1757 1793 3.181458 TGGTTTCGGCCTCCAGATAATAC 60.181 47.826 0.00 0.00 0.00 1.89
1764 1800 0.107017 ATGATGGTTTCGGCCTCCAG 60.107 55.000 0.00 0.00 34.62 3.86
1765 1801 1.208706 TATGATGGTTTCGGCCTCCA 58.791 50.000 0.00 4.67 35.64 3.86
1805 1842 6.013725 TGGCCTCTTGTATTCTAGTCTTTTGA 60.014 38.462 3.32 0.00 0.00 2.69
1812 1849 4.626529 GCCTTTGGCCTCTTGTATTCTAGT 60.627 45.833 3.32 0.00 44.06 2.57
1864 1901 1.741028 TCCACCATGAGTTTGAGGGA 58.259 50.000 0.00 0.00 0.00 4.20
1888 1929 3.964688 TCACCTCTCCAAACTCAGTGTTA 59.035 43.478 0.00 0.00 38.03 2.41
1913 1954 0.176680 AGACTAGAGCGCAACATGGG 59.823 55.000 11.47 0.00 0.00 4.00
1957 1998 6.096423 TGAGTATGTGCCTTTCGAGTTATAGT 59.904 38.462 0.00 0.00 0.00 2.12
1960 2001 5.339008 TGAGTATGTGCCTTTCGAGTTAT 57.661 39.130 0.00 0.00 0.00 1.89
1968 2009 3.423539 TGCTCTTGAGTATGTGCCTTT 57.576 42.857 0.00 0.00 0.00 3.11
1981 2022 3.857665 GCATGATCATGTTGTTGCTCTTG 59.142 43.478 31.09 8.42 40.80 3.02
2000 2041 4.757799 TTTTGTACACGCTATTGTGCAT 57.242 36.364 0.00 0.00 41.08 3.96
2007 2048 9.373603 TGTTGATACTTATTTTGTACACGCTAT 57.626 29.630 0.00 0.00 0.00 2.97
2008 2049 8.649841 GTGTTGATACTTATTTTGTACACGCTA 58.350 33.333 0.00 0.00 0.00 4.26
2088 2129 3.321111 ACACTCTTGTCCGACATTACAGT 59.679 43.478 1.09 0.00 0.00 3.55
2094 2135 1.048601 ACCACACTCTTGTCCGACAT 58.951 50.000 1.09 0.00 31.66 3.06
2108 2149 5.363292 TGTTTCTGTTACTACACCTACCACA 59.637 40.000 0.00 0.00 0.00 4.17
2138 2179 0.535335 TGCGATGGTTACTGGAGGAC 59.465 55.000 0.00 0.00 0.00 3.85
2156 2197 1.230635 CGGCAGAGGTGACTTGGTTG 61.231 60.000 0.00 0.00 44.43 3.77
2241 2282 4.834496 TGGTTCTCTCATTGCTTGGAAAAT 59.166 37.500 0.00 0.00 0.00 1.82
2243 2284 3.569701 GTGGTTCTCTCATTGCTTGGAAA 59.430 43.478 0.00 0.00 0.00 3.13
2249 2290 2.553904 CCTTGGTGGTTCTCTCATTGCT 60.554 50.000 0.00 0.00 0.00 3.91
2270 2311 6.920569 TCACTTTCTCCTTACTGTGTTTTC 57.079 37.500 0.00 0.00 0.00 2.29
2284 2325 3.770666 TCGGATCGTCATTCACTTTCTC 58.229 45.455 0.00 0.00 0.00 2.87
2392 2435 7.596995 CCTTCTTCGTGTTCTATGATATCTTCC 59.403 40.741 3.98 0.00 0.00 3.46
2433 2476 4.515567 CAGTTTGTTTCTACTCCCACTTCC 59.484 45.833 0.00 0.00 0.00 3.46
2444 2487 9.567776 TCCATATTTTGAGTCAGTTTGTTTCTA 57.432 29.630 0.00 0.00 0.00 2.10
2491 2534 6.040955 AGTCTTGTCTATCTTGTTGTCACTCA 59.959 38.462 0.00 0.00 0.00 3.41
2571 2614 1.464997 GACCTCAATGTTCACCTTCGC 59.535 52.381 0.00 0.00 0.00 4.70
2589 2632 3.583806 CACTGTTGAGACTCTGATGGAC 58.416 50.000 3.68 0.00 0.00 4.02
2595 2638 0.319383 AGCGCACTGTTGAGACTCTG 60.319 55.000 11.47 0.00 0.00 3.35
2596 2639 0.038709 GAGCGCACTGTTGAGACTCT 60.039 55.000 11.47 0.00 0.00 3.24
2677 2720 1.546029 GGTTTCCTCCACCTTTGATGC 59.454 52.381 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.