Multiple sequence alignment - TraesCS3A01G143600

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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 TraesCS3A01G143600 chr3A 100.000 3970 0 0 1 3970 125096179 125092210 0.000000e+00 7332.0
1 TraesCS3A01G143600 chr3A 100.000 474 0 0 4312 4785 125091868 125091395 0.000000e+00 876.0
2 TraesCS3A01G143600 chr3A 94.245 417 20 3 1 416 24404829 24405242 6.760000e-178 634.0
3 TraesCS3A01G143600 chr3A 88.199 322 20 5 414 733 24405273 24405578 7.570000e-98 368.0
4 TraesCS3A01G143600 chr3A 89.558 249 18 3 723 967 24405606 24405850 4.650000e-80 309.0
5 TraesCS3A01G143600 chr3D 95.179 2759 94 10 1217 3969 116162939 116160214 0.000000e+00 4322.0
6 TraesCS3A01G143600 chr3D 98.731 394 5 0 4392 4785 116159962 116159569 0.000000e+00 701.0
7 TraesCS3A01G143600 chr3D 98.795 83 1 0 4312 4394 116160125 116160043 1.070000e-31 148.0
8 TraesCS3A01G143600 chr3B 94.242 2275 97 16 1217 3481 169835568 169833318 0.000000e+00 3445.0
9 TraesCS3A01G143600 chr3B 93.509 1818 86 7 1221 3024 169693753 169691954 0.000000e+00 2675.0
10 TraesCS3A01G143600 chr3B 99.353 773 5 0 3022 3794 169691796 169691024 0.000000e+00 1400.0
11 TraesCS3A01G143600 chr3B 96.491 456 12 4 3518 3969 169833317 169832862 0.000000e+00 750.0
12 TraesCS3A01G143600 chr3B 95.580 181 7 1 3790 3969 169690863 169690683 6.060000e-74 289.0
13 TraesCS3A01G143600 chr3B 89.899 198 18 2 4312 4509 169690509 169690314 2.210000e-63 254.0
14 TraesCS3A01G143600 chr3B 89.899 198 18 2 4312 4509 169832686 169832491 2.210000e-63 254.0
15 TraesCS3A01G143600 chr2D 97.356 416 10 1 1 416 343806755 343807169 0.000000e+00 706.0
16 TraesCS3A01G143600 chr2D 95.342 322 12 3 414 733 343807200 343807520 4.270000e-140 508.0
17 TraesCS3A01G143600 chr2D 93.701 254 11 3 723 974 343807552 343807802 4.520000e-100 375.0
18 TraesCS3A01G143600 chrUn 96.394 416 14 1 1 416 464997172 464997586 0.000000e+00 684.0
19 TraesCS3A01G143600 chrUn 95.528 246 11 0 414 659 464997617 464997862 1.250000e-105 394.0
20 TraesCS3A01G143600 chrUn 91.440 257 12 5 724 973 33359387 33359134 1.270000e-90 344.0
21 TraesCS3A01G143600 chrUn 95.385 65 3 0 661 725 33359489 33359425 2.360000e-18 104.0
22 TraesCS3A01G143600 chr6A 95.673 416 15 2 1 416 488410413 488410825 0.000000e+00 665.0
23 TraesCS3A01G143600 chr6A 94.099 322 16 3 414 733 488410856 488411176 2.000000e-133 486.0
24 TraesCS3A01G143600 chr6A 92.683 246 14 2 724 967 488411205 488411448 7.620000e-93 351.0
25 TraesCS3A01G143600 chr5D 94.575 424 13 7 1 416 85186163 85185742 0.000000e+00 647.0
26 TraesCS3A01G143600 chr5D 95.652 322 11 3 414 733 85185711 85185391 9.180000e-142 514.0
27 TraesCS3A01G143600 chr5D 93.089 246 13 2 724 967 85185362 85185119 1.640000e-94 357.0
28 TraesCS3A01G143600 chr2B 83.024 754 89 31 1 729 314672709 314673448 0.000000e+00 647.0
29 TraesCS3A01G143600 chr4A 93.062 418 26 3 1 416 294994638 294995054 4.090000e-170 608.0
30 TraesCS3A01G143600 chr4A 91.401 314 24 2 414 727 294995085 294995395 1.230000e-115 427.0
31 TraesCS3A01G143600 chr4D 88.361 421 36 10 3 416 374410107 374409693 1.200000e-135 494.0
32 TraesCS3A01G143600 chr4D 85.479 303 33 5 425 725 374409644 374409351 6.020000e-79 305.0
33 TraesCS3A01G143600 chr5B 87.648 421 39 7 3 416 441134296 441134710 1.200000e-130 477.0
34 TraesCS3A01G143600 chr5B 87.043 301 27 6 425 722 441134759 441135050 3.570000e-86 329.0
35 TraesCS3A01G143600 chr1D 85.577 312 26 13 426 729 404477492 404477192 4.650000e-80 309.0
36 TraesCS3A01G143600 chr2A 82.012 328 26 16 425 729 3355978 3356295 1.030000e-61 248.0
37 TraesCS3A01G143600 chr7A 97.826 46 1 0 929 974 339748484 339748439 3.970000e-11 80.5
38 TraesCS3A01G143600 chr7A 86.885 61 4 4 931 990 498728425 498728368 1.110000e-06 65.8
39 TraesCS3A01G143600 chr7D 92.000 50 2 2 930 979 463037701 463037748 8.590000e-08 69.4
40 TraesCS3A01G143600 chr7B 85.484 62 7 2 929 988 220968873 220968812 4.000000e-06 63.9


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 TraesCS3A01G143600 chr3A 125091395 125096179 4784 True 4104.000000 7332 100.000000 1 4785 2 chr3A.!!$R1 4784
1 TraesCS3A01G143600 chr3A 24404829 24405850 1021 False 437.000000 634 90.667333 1 967 3 chr3A.!!$F1 966
2 TraesCS3A01G143600 chr3D 116159569 116162939 3370 True 1723.666667 4322 97.568333 1217 4785 3 chr3D.!!$R1 3568
3 TraesCS3A01G143600 chr3B 169832491 169835568 3077 True 1483.000000 3445 93.544000 1217 4509 3 chr3B.!!$R2 3292
4 TraesCS3A01G143600 chr3B 169690314 169693753 3439 True 1154.500000 2675 94.585250 1221 4509 4 chr3B.!!$R1 3288
5 TraesCS3A01G143600 chr2D 343806755 343807802 1047 False 529.666667 706 95.466333 1 974 3 chr2D.!!$F1 973
6 TraesCS3A01G143600 chrUn 464997172 464997862 690 False 539.000000 684 95.961000 1 659 2 chrUn.!!$F1 658
7 TraesCS3A01G143600 chr6A 488410413 488411448 1035 False 500.666667 665 94.151667 1 967 3 chr6A.!!$F1 966
8 TraesCS3A01G143600 chr5D 85185119 85186163 1044 True 506.000000 647 94.438667 1 967 3 chr5D.!!$R1 966
9 TraesCS3A01G143600 chr2B 314672709 314673448 739 False 647.000000 647 83.024000 1 729 1 chr2B.!!$F1 728
10 TraesCS3A01G143600 chr4A 294994638 294995395 757 False 517.500000 608 92.231500 1 727 2 chr4A.!!$F1 726
11 TraesCS3A01G143600 chr4D 374409351 374410107 756 True 399.500000 494 86.920000 3 725 2 chr4D.!!$R1 722
12 TraesCS3A01G143600 chr5B 441134296 441135050 754 False 403.000000 477 87.345500 3 722 2 chr5B.!!$F1 719

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
967 1077 1.134340 ACGCACGGGCATATTTCCTAA 60.134 47.619 11.77 0.0 41.24 2.69 F
1108 1218 0.034089 GGGGATCAGGGGAAACAGTG 60.034 60.000 0.00 0.0 0.00 3.66 F
1109 1219 0.034089 GGGATCAGGGGAAACAGTGG 60.034 60.000 0.00 0.0 0.00 4.00 F
1124 1234 0.034896 AGTGGATTCGTTTCACGCCT 59.965 50.000 0.00 0.0 42.21 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2893 3033 0.546122 TTGACCCCATTCATCTCGGG 59.454 55.000 0.00 0.0 41.71 5.14 R
2967 3107 2.596452 AGACATGCGTGTTCGTCTAAG 58.404 47.619 13.92 0.0 39.09 2.18 R
3027 3331 6.449698 CAACAAGCTACATCAACCTTCAAAT 58.550 36.000 0.00 0.0 0.00 2.32 R
3824 4295 2.163818 TGAGGTTTACAGCGGTTCAG 57.836 50.000 0.00 0.0 0.00 3.02 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
131 135 9.264719 TCTGCATACATTATTGACATCTTACAG 57.735 33.333 0.00 0.00 0.00 2.74
195 199 6.240894 TGGTGATCTGCAATAGTTCTTTCTT 58.759 36.000 0.00 0.00 0.00 2.52
302 308 8.611051 AAGGAGTATACTAGGACACTCATTTT 57.389 34.615 15.32 3.84 38.47 1.82
396 414 7.220740 TGTGGATCGCATATAGGATTTGTAAA 58.779 34.615 0.00 0.00 0.00 2.01
477 535 8.409371 TCTACTTGAGTCTTTGCATCTATAGTG 58.591 37.037 0.00 0.00 0.00 2.74
483 541 9.029368 TGAGTCTTTGCATCTATAGTGCTATAT 57.971 33.333 20.56 8.35 42.92 0.86
527 585 8.012957 TCTCCATAGCTTTTTAGGTCTTAGAG 57.987 38.462 0.00 0.00 0.00 2.43
556 616 7.832187 TCTCCTTCCGTTTCCAAAAATACATAT 59.168 33.333 0.00 0.00 0.00 1.78
859 965 7.066284 CAGAACTGATGGGGTAATACTGAAAAG 59.934 40.741 0.00 0.00 0.00 2.27
903 1013 5.188359 GTGTGTGGGAGTAGAGGGTTATAAA 59.812 44.000 0.00 0.00 0.00 1.40
967 1077 1.134340 ACGCACGGGCATATTTCCTAA 60.134 47.619 11.77 0.00 41.24 2.69
974 1084 7.095774 CGCACGGGCATATTTCCTAATATATAC 60.096 40.741 11.77 0.00 41.24 1.47
975 1085 7.172703 GCACGGGCATATTTCCTAATATATACC 59.827 40.741 3.77 0.00 40.72 2.73
976 1086 8.429641 CACGGGCATATTTCCTAATATATACCT 58.570 37.037 0.00 0.00 35.28 3.08
977 1087 9.664777 ACGGGCATATTTCCTAATATATACCTA 57.335 33.333 0.00 0.00 35.28 3.08
996 1106 6.944234 ACCTAATATAAGGCAAAGAACAGC 57.056 37.500 0.00 0.00 40.62 4.40
1002 1112 4.181051 GCAAAGAACAGCCACCCT 57.819 55.556 0.00 0.00 0.00 4.34
1003 1113 1.959848 GCAAAGAACAGCCACCCTC 59.040 57.895 0.00 0.00 0.00 4.30
1004 1114 1.856265 GCAAAGAACAGCCACCCTCG 61.856 60.000 0.00 0.00 0.00 4.63
1005 1115 0.535102 CAAAGAACAGCCACCCTCGT 60.535 55.000 0.00 0.00 0.00 4.18
1006 1116 0.250338 AAAGAACAGCCACCCTCGTC 60.250 55.000 0.00 0.00 0.00 4.20
1007 1117 1.122019 AAGAACAGCCACCCTCGTCT 61.122 55.000 0.00 0.00 0.00 4.18
1008 1118 1.122019 AGAACAGCCACCCTCGTCTT 61.122 55.000 0.00 0.00 0.00 3.01
1009 1119 0.951040 GAACAGCCACCCTCGTCTTG 60.951 60.000 0.00 0.00 0.00 3.02
1010 1120 1.696097 AACAGCCACCCTCGTCTTGT 61.696 55.000 0.00 0.00 0.00 3.16
1011 1121 1.071471 CAGCCACCCTCGTCTTGTT 59.929 57.895 0.00 0.00 0.00 2.83
1012 1122 0.951040 CAGCCACCCTCGTCTTGTTC 60.951 60.000 0.00 0.00 0.00 3.18
1013 1123 1.671379 GCCACCCTCGTCTTGTTCC 60.671 63.158 0.00 0.00 0.00 3.62
1014 1124 1.003718 CCACCCTCGTCTTGTTCCC 60.004 63.158 0.00 0.00 0.00 3.97
1015 1125 1.374252 CACCCTCGTCTTGTTCCCG 60.374 63.158 0.00 0.00 0.00 5.14
1016 1126 1.532316 ACCCTCGTCTTGTTCCCGA 60.532 57.895 0.00 0.00 0.00 5.14
1017 1127 1.080025 CCCTCGTCTTGTTCCCGAC 60.080 63.158 0.00 0.00 0.00 4.79
1018 1128 1.080025 CCTCGTCTTGTTCCCGACC 60.080 63.158 0.00 0.00 0.00 4.79
1019 1129 1.080025 CTCGTCTTGTTCCCGACCC 60.080 63.158 0.00 0.00 0.00 4.46
1020 1130 1.812686 CTCGTCTTGTTCCCGACCCA 61.813 60.000 0.00 0.00 0.00 4.51
1021 1131 1.070105 CGTCTTGTTCCCGACCCAA 59.930 57.895 0.00 0.00 0.00 4.12
1022 1132 1.226030 CGTCTTGTTCCCGACCCAAC 61.226 60.000 0.00 0.00 0.00 3.77
1023 1133 1.070105 TCTTGTTCCCGACCCAACG 59.930 57.895 0.00 0.00 0.00 4.10
1024 1134 2.592287 TTGTTCCCGACCCAACGC 60.592 61.111 0.00 0.00 0.00 4.84
1025 1135 4.973055 TGTTCCCGACCCAACGCG 62.973 66.667 3.53 3.53 0.00 6.01
1064 1174 2.850404 GCGTTGCGATGTCGTCAA 59.150 55.556 4.20 6.28 42.22 3.18
1065 1175 1.507096 GCGTTGCGATGTCGTCAAC 60.507 57.895 21.50 21.50 44.58 3.18
1066 1176 4.698496 GTTGCGATGTCGTCAACG 57.302 55.556 18.96 7.87 41.93 4.10
1067 1177 1.129809 GTTGCGATGTCGTCAACGG 59.870 57.895 18.96 0.00 41.93 4.44
1068 1178 1.007154 TTGCGATGTCGTCAACGGA 60.007 52.632 13.34 8.30 39.59 4.69
1069 1179 1.006825 TTGCGATGTCGTCAACGGAG 61.007 55.000 13.34 0.00 40.45 4.63
1070 1180 1.154093 GCGATGTCGTCAACGGAGA 60.154 57.895 13.34 0.00 39.59 3.71
1071 1181 0.525668 GCGATGTCGTCAACGGAGAT 60.526 55.000 13.34 0.00 39.59 2.75
1072 1182 1.191944 CGATGTCGTCAACGGAGATG 58.808 55.000 4.52 0.00 40.29 2.90
1073 1183 0.924090 GATGTCGTCAACGGAGATGC 59.076 55.000 2.31 0.00 40.29 3.91
1074 1184 0.246360 ATGTCGTCAACGGAGATGCA 59.754 50.000 2.31 0.00 40.29 3.96
1075 1185 0.388520 TGTCGTCAACGGAGATGCAG 60.389 55.000 2.31 0.00 40.29 4.41
1076 1186 0.109272 GTCGTCAACGGAGATGCAGA 60.109 55.000 2.31 0.00 40.29 4.26
1077 1187 0.817654 TCGTCAACGGAGATGCAGAT 59.182 50.000 2.31 0.00 40.29 2.90
1078 1188 0.926155 CGTCAACGGAGATGCAGATG 59.074 55.000 0.00 0.00 35.37 2.90
1079 1189 0.654683 GTCAACGGAGATGCAGATGC 59.345 55.000 0.00 0.00 42.50 3.91
1080 1190 0.807275 TCAACGGAGATGCAGATGCG 60.807 55.000 12.30 12.30 45.83 4.73
1081 1191 0.807275 CAACGGAGATGCAGATGCGA 60.807 55.000 19.22 0.00 45.83 5.10
1082 1192 0.105593 AACGGAGATGCAGATGCGAT 59.894 50.000 19.22 6.80 45.83 4.58
1083 1193 0.105593 ACGGAGATGCAGATGCGATT 59.894 50.000 19.22 0.00 45.83 3.34
1084 1194 0.788995 CGGAGATGCAGATGCGATTC 59.211 55.000 8.86 0.00 45.83 2.52
1085 1195 1.604947 CGGAGATGCAGATGCGATTCT 60.605 52.381 8.86 2.72 45.83 2.40
1086 1196 1.799403 GGAGATGCAGATGCGATTCTG 59.201 52.381 9.88 9.88 45.83 3.02
1090 1200 3.327148 CAGATGCGATTCTGCCGG 58.673 61.111 0.00 0.00 36.96 6.13
1091 1201 2.109799 AGATGCGATTCTGCCGGG 59.890 61.111 2.18 0.00 0.00 5.73
1092 1202 2.974698 GATGCGATTCTGCCGGGG 60.975 66.667 2.18 0.00 0.00 5.73
1093 1203 3.460672 GATGCGATTCTGCCGGGGA 62.461 63.158 2.18 0.00 0.00 4.81
1094 1204 2.738213 GATGCGATTCTGCCGGGGAT 62.738 60.000 2.18 0.00 0.00 3.85
1095 1205 2.666526 GCGATTCTGCCGGGGATC 60.667 66.667 2.18 0.00 0.00 3.36
1096 1206 2.821685 CGATTCTGCCGGGGATCA 59.178 61.111 2.18 0.00 0.00 2.92
1097 1207 1.301244 CGATTCTGCCGGGGATCAG 60.301 63.158 2.18 1.28 0.00 2.90
1098 1208 1.072159 GATTCTGCCGGGGATCAGG 59.928 63.158 2.18 0.00 0.00 3.86
1099 1209 2.403132 GATTCTGCCGGGGATCAGGG 62.403 65.000 2.18 0.00 0.00 4.45
1102 1212 4.750695 TGCCGGGGATCAGGGGAA 62.751 66.667 2.18 0.00 0.00 3.97
1103 1213 3.416880 GCCGGGGATCAGGGGAAA 61.417 66.667 2.18 0.00 0.00 3.13
1104 1214 2.595655 CCGGGGATCAGGGGAAAC 59.404 66.667 0.00 0.00 0.00 2.78
1105 1215 2.305607 CCGGGGATCAGGGGAAACA 61.306 63.158 0.00 0.00 0.00 2.83
1106 1216 1.224592 CGGGGATCAGGGGAAACAG 59.775 63.158 0.00 0.00 0.00 3.16
1107 1217 1.562672 CGGGGATCAGGGGAAACAGT 61.563 60.000 0.00 0.00 0.00 3.55
1108 1218 0.034089 GGGGATCAGGGGAAACAGTG 60.034 60.000 0.00 0.00 0.00 3.66
1109 1219 0.034089 GGGATCAGGGGAAACAGTGG 60.034 60.000 0.00 0.00 0.00 4.00
1110 1220 0.991920 GGATCAGGGGAAACAGTGGA 59.008 55.000 0.00 0.00 0.00 4.02
1111 1221 1.566231 GGATCAGGGGAAACAGTGGAT 59.434 52.381 0.00 0.00 0.00 3.41
1112 1222 2.024941 GGATCAGGGGAAACAGTGGATT 60.025 50.000 0.00 0.00 0.00 3.01
1113 1223 2.879103 TCAGGGGAAACAGTGGATTC 57.121 50.000 0.00 0.00 0.00 2.52
1114 1224 1.003118 TCAGGGGAAACAGTGGATTCG 59.997 52.381 0.00 0.00 0.00 3.34
1115 1225 1.064825 AGGGGAAACAGTGGATTCGT 58.935 50.000 0.00 0.00 0.00 3.85
1116 1226 1.423921 AGGGGAAACAGTGGATTCGTT 59.576 47.619 0.00 0.00 0.00 3.85
1117 1227 2.158519 AGGGGAAACAGTGGATTCGTTT 60.159 45.455 0.00 0.00 35.63 3.60
1118 1228 2.228103 GGGGAAACAGTGGATTCGTTTC 59.772 50.000 0.00 0.00 44.93 2.78
1119 1229 2.882137 GGGAAACAGTGGATTCGTTTCA 59.118 45.455 14.17 0.00 46.59 2.69
1120 1230 3.304458 GGGAAACAGTGGATTCGTTTCAC 60.304 47.826 14.17 8.31 46.59 3.18
1121 1231 3.541711 GAAACAGTGGATTCGTTTCACG 58.458 45.455 8.86 0.00 44.98 4.35
1122 1232 0.865769 ACAGTGGATTCGTTTCACGC 59.134 50.000 0.00 0.00 42.21 5.34
1123 1233 0.165944 CAGTGGATTCGTTTCACGCC 59.834 55.000 0.00 0.00 42.21 5.68
1124 1234 0.034896 AGTGGATTCGTTTCACGCCT 59.965 50.000 0.00 0.00 42.21 5.52
1125 1235 0.442699 GTGGATTCGTTTCACGCCTC 59.557 55.000 0.00 0.00 42.21 4.70
1126 1236 0.672401 TGGATTCGTTTCACGCCTCC 60.672 55.000 8.98 8.98 42.21 4.30
1127 1237 1.366854 GGATTCGTTTCACGCCTCCC 61.367 60.000 5.95 0.00 42.21 4.30
1128 1238 1.693083 GATTCGTTTCACGCCTCCCG 61.693 60.000 0.00 0.00 42.21 5.14
1131 1241 2.263540 GTTTCACGCCTCCCGCTA 59.736 61.111 0.00 0.00 41.76 4.26
1132 1242 2.098831 GTTTCACGCCTCCCGCTAC 61.099 63.158 0.00 0.00 41.76 3.58
1133 1243 3.305177 TTTCACGCCTCCCGCTACC 62.305 63.158 0.00 0.00 41.76 3.18
1145 1255 3.015145 GCTACCCCAGCCCTTCCA 61.015 66.667 0.00 0.00 45.23 3.53
1146 1256 2.998949 CTACCCCAGCCCTTCCAC 59.001 66.667 0.00 0.00 0.00 4.02
1147 1257 3.006728 TACCCCAGCCCTTCCACG 61.007 66.667 0.00 0.00 0.00 4.94
1150 1260 4.101448 CCCAGCCCTTCCACGGAG 62.101 72.222 0.00 0.00 0.00 4.63
1151 1261 4.101448 CCAGCCCTTCCACGGAGG 62.101 72.222 0.00 0.00 39.47 4.30
1165 1275 2.203126 GAGGATCCGGCTTGCCTG 60.203 66.667 5.98 3.29 0.00 4.85
1166 1276 4.496336 AGGATCCGGCTTGCCTGC 62.496 66.667 5.98 0.00 0.00 4.85
1167 1277 4.496336 GGATCCGGCTTGCCTGCT 62.496 66.667 10.12 0.00 0.00 4.24
1168 1278 2.899339 GATCCGGCTTGCCTGCTC 60.899 66.667 10.12 0.76 0.00 4.26
1169 1279 4.496336 ATCCGGCTTGCCTGCTCC 62.496 66.667 10.12 0.00 0.00 4.70
1187 1297 4.803426 CTCGCCGTGCTCCCACTC 62.803 72.222 0.00 0.00 39.86 3.51
1190 1300 4.101448 GCCGTGCTCCCACTCCAT 62.101 66.667 0.00 0.00 39.86 3.41
1191 1301 2.187946 CCGTGCTCCCACTCCATC 59.812 66.667 0.00 0.00 39.86 3.51
1192 1302 2.187946 CGTGCTCCCACTCCATCC 59.812 66.667 0.00 0.00 39.86 3.51
1193 1303 2.362369 CGTGCTCCCACTCCATCCT 61.362 63.158 0.00 0.00 39.86 3.24
1194 1304 1.043116 CGTGCTCCCACTCCATCCTA 61.043 60.000 0.00 0.00 39.86 2.94
1195 1305 0.466124 GTGCTCCCACTCCATCCTAC 59.534 60.000 0.00 0.00 38.93 3.18
1196 1306 1.043116 TGCTCCCACTCCATCCTACG 61.043 60.000 0.00 0.00 0.00 3.51
1197 1307 1.742768 CTCCCACTCCATCCTACGC 59.257 63.158 0.00 0.00 0.00 4.42
1198 1308 0.757188 CTCCCACTCCATCCTACGCT 60.757 60.000 0.00 0.00 0.00 5.07
1199 1309 0.325296 TCCCACTCCATCCTACGCTT 60.325 55.000 0.00 0.00 0.00 4.68
1200 1310 0.105039 CCCACTCCATCCTACGCTTC 59.895 60.000 0.00 0.00 0.00 3.86
1201 1311 0.105039 CCACTCCATCCTACGCTTCC 59.895 60.000 0.00 0.00 0.00 3.46
1202 1312 0.824109 CACTCCATCCTACGCTTCCA 59.176 55.000 0.00 0.00 0.00 3.53
1203 1313 0.824759 ACTCCATCCTACGCTTCCAC 59.175 55.000 0.00 0.00 0.00 4.02
1204 1314 0.249073 CTCCATCCTACGCTTCCACG 60.249 60.000 0.00 0.00 39.50 4.94
1205 1315 1.227263 CCATCCTACGCTTCCACGG 60.227 63.158 0.00 0.00 37.37 4.94
1206 1316 1.672854 CCATCCTACGCTTCCACGGA 61.673 60.000 0.00 0.00 37.37 4.69
1207 1317 0.249073 CATCCTACGCTTCCACGGAG 60.249 60.000 0.00 0.00 43.90 4.63
1229 1339 3.525862 GACCTAGGGGATCTCCATGATT 58.474 50.000 15.83 0.00 37.91 2.57
1269 1379 1.304630 TCGAACTCGACCCCCATGA 60.305 57.895 0.00 0.00 44.22 3.07
1317 1427 2.159653 CGTATGCTTTGCACACTCCTTC 60.160 50.000 0.00 0.00 43.04 3.46
1322 1432 2.099756 GCTTTGCACACTCCTTCACTTT 59.900 45.455 0.00 0.00 0.00 2.66
1324 1434 4.022849 GCTTTGCACACTCCTTCACTTTAT 60.023 41.667 0.00 0.00 0.00 1.40
1325 1435 5.437289 TTTGCACACTCCTTCACTTTATG 57.563 39.130 0.00 0.00 0.00 1.90
1347 1466 0.676782 CGCTCCATCGGGAAGGTTTT 60.677 55.000 0.00 0.00 44.38 2.43
1448 1567 1.671379 GGACCTCAAGTTCCCACGC 60.671 63.158 0.00 0.00 0.00 5.34
1538 1661 5.987019 AAGATTGCCCAGGTACCTATTTA 57.013 39.130 15.80 0.00 0.00 1.40
1542 1665 6.561070 AGATTGCCCAGGTACCTATTTATACA 59.439 38.462 15.80 3.56 0.00 2.29
1543 1666 6.773583 TTGCCCAGGTACCTATTTATACAT 57.226 37.500 15.80 0.00 0.00 2.29
1572 1695 5.799827 TCAATTTCCCCGAAATTTCAACT 57.200 34.783 17.99 0.00 46.07 3.16
1576 1699 6.850752 ATTTCCCCGAAATTTCAACTATGT 57.149 33.333 17.99 0.00 38.89 2.29
1577 1700 6.658188 TTTCCCCGAAATTTCAACTATGTT 57.342 33.333 17.99 0.00 0.00 2.71
1648 1771 4.970662 TCGATAGCGATGATGATGATGA 57.029 40.909 0.00 0.00 42.51 2.92
1649 1772 5.511234 TCGATAGCGATGATGATGATGAT 57.489 39.130 0.00 0.00 42.51 2.45
1650 1773 5.279384 TCGATAGCGATGATGATGATGATG 58.721 41.667 0.00 0.00 42.51 3.07
1651 1774 5.066893 TCGATAGCGATGATGATGATGATGA 59.933 40.000 0.00 0.00 42.51 2.92
1652 1775 5.173492 CGATAGCGATGATGATGATGATGAC 59.827 44.000 0.00 0.00 40.82 3.06
1653 1776 3.251571 AGCGATGATGATGATGATGACG 58.748 45.455 0.00 0.00 0.00 4.35
1654 1777 3.057033 AGCGATGATGATGATGATGACGA 60.057 43.478 0.00 0.00 0.00 4.20
1655 1778 3.060496 GCGATGATGATGATGATGACGAC 59.940 47.826 0.00 0.00 0.00 4.34
1656 1779 3.300066 CGATGATGATGATGATGACGACG 59.700 47.826 0.00 0.00 0.00 5.12
1657 1780 3.988379 TGATGATGATGATGACGACGA 57.012 42.857 0.00 0.00 0.00 4.20
1658 1781 3.632189 TGATGATGATGATGACGACGAC 58.368 45.455 0.00 0.00 0.00 4.34
1675 1798 0.859232 GACGACGACAACTGCAATGT 59.141 50.000 0.00 4.57 0.00 2.71
1676 1799 1.260561 GACGACGACAACTGCAATGTT 59.739 47.619 0.00 0.00 0.00 2.71
1736 1859 8.917414 AGATAATCTGCCCAGGTATCTAATTA 57.083 34.615 15.04 4.33 35.91 1.40
1865 1998 2.220313 GAGCTGGAATGGATTGAGAGC 58.780 52.381 0.00 0.00 0.00 4.09
1893 2026 1.967066 AGCAGATGGGAGAATACTCGG 59.033 52.381 0.00 0.00 43.44 4.63
1936 2069 1.595357 GGGAGGACCACGACGATTT 59.405 57.895 0.00 0.00 39.85 2.17
2000 2133 5.763698 CACAACATCTCTATGCTTCATGGAT 59.236 40.000 0.00 0.00 36.50 3.41
2063 2196 1.816835 TCTACCAGTAAGTGCCACTCG 59.183 52.381 0.00 0.00 0.00 4.18
2079 2217 4.734108 GCCACTCGTTCCTAGTAATCTGTC 60.734 50.000 0.00 0.00 0.00 3.51
2090 2228 5.934625 CCTAGTAATCTGTCTTTGTGCTGTT 59.065 40.000 0.00 0.00 0.00 3.16
2107 2245 4.157656 TGCTGTTTGCTTAACAACTCACTT 59.842 37.500 6.46 0.00 45.69 3.16
2119 2257 6.391227 AACAACTCACTTTGGTTCCTAATG 57.609 37.500 0.00 0.00 0.00 1.90
2123 2261 7.174946 ACAACTCACTTTGGTTCCTAATGTATG 59.825 37.037 0.00 0.00 0.00 2.39
2133 2271 5.335127 GTTCCTAATGTATGTTTGCAGCTG 58.665 41.667 10.11 10.11 0.00 4.24
2159 2297 1.202417 ACTCTTGGATATCGCACACCG 60.202 52.381 0.00 0.00 38.61 4.94
2573 2713 8.946935 CACATTAGTTTTTATATGATGTGCGTG 58.053 33.333 0.00 0.00 37.26 5.34
2606 2746 6.040247 TGTACATACAAATCGTCATCTGGTC 58.960 40.000 0.00 0.00 32.40 4.02
2616 2756 9.476202 CAAATCGTCATCTGGTCAATATACTTA 57.524 33.333 0.00 0.00 0.00 2.24
2680 2820 4.083164 TGACTGCTTGTGTGCATTAAGATG 60.083 41.667 10.55 5.66 42.48 2.90
2724 2864 1.544691 ACTAGGCGTCTGTGGTTACTG 59.455 52.381 0.00 0.00 0.00 2.74
2739 2879 5.242838 GTGGTTACTGATTGTGATTTTCCCA 59.757 40.000 0.00 0.00 0.00 4.37
2967 3107 5.047377 TGCTTCCTTTCACCCAATATTTGAC 60.047 40.000 0.00 0.00 0.00 3.18
2991 3131 4.365899 AGACGAACACGCATGTCTTATA 57.634 40.909 0.00 0.00 38.48 0.98
2994 3134 4.678622 ACGAACACGCATGTCTTATATGA 58.321 39.130 0.00 0.00 38.45 2.15
2995 3135 4.740205 ACGAACACGCATGTCTTATATGAG 59.260 41.667 0.00 0.00 38.45 2.90
2996 3136 4.740205 CGAACACGCATGTCTTATATGAGT 59.260 41.667 0.00 0.00 38.45 3.41
2997 3137 5.232202 CGAACACGCATGTCTTATATGAGTT 59.768 40.000 0.00 0.00 38.45 3.01
3824 4295 5.817816 AGCATTATAGTCCAGTGTGTTAAGC 59.182 40.000 0.00 0.00 0.00 3.09
3923 4396 0.037882 CAGTGGTCGTGATGCTGTCT 60.038 55.000 0.00 0.00 0.00 3.41
3969 4442 2.137523 CCAATTTGGTCAGCACAAAGC 58.862 47.619 7.31 0.00 40.70 3.51
4534 5090 2.224793 GGTATGGGATAGGCAAGAACCC 60.225 54.545 0.00 0.00 40.79 4.11
4550 5106 0.475044 ACCCACTTTTGCCGACCTAA 59.525 50.000 0.00 0.00 0.00 2.69
4589 5145 6.101296 ACCGAGATTCCAAATTAGGGTATCTT 59.899 38.462 15.08 2.90 33.52 2.40
4617 5173 2.159572 CGTTCATCAAATCGGACAACCC 60.160 50.000 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.830975 TTTAGCATGTATATGAGCAAAGTTAGA 57.169 29.630 3.28 0.00 36.36 2.10
51 54 6.815641 CCCTCTCGTTGGAATATAAGATGATG 59.184 42.308 0.00 0.00 0.00 3.07
131 135 6.418057 TGGCCATGATCCCAAATATAAAAC 57.582 37.500 0.00 0.00 0.00 2.43
195 199 3.139957 ACCATATACCACCCATTGCATCA 59.860 43.478 0.00 0.00 0.00 3.07
302 308 4.825634 AGCTCACGTGCATAGTACCTATTA 59.174 41.667 11.67 0.00 34.99 0.98
416 434 8.121305 AGCATATCCATTTTCACTACAACAAA 57.879 30.769 0.00 0.00 0.00 2.83
417 435 7.701539 AGCATATCCATTTTCACTACAACAA 57.298 32.000 0.00 0.00 0.00 2.83
437 495 9.142014 AGACTCAAGTAGAATCTACAATAGCAT 57.858 33.333 21.04 5.72 29.49 3.79
477 535 8.103948 AGGCAAATCACTTACATGAATATAGC 57.896 34.615 0.00 0.00 30.82 2.97
483 541 4.943705 GGAGAGGCAAATCACTTACATGAA 59.056 41.667 0.00 0.00 30.82 2.57
527 585 4.642445 TTTTGGAAACGGAAGGAGAAAC 57.358 40.909 0.00 0.00 0.00 2.78
652 713 3.025262 GGTAAATTTTGGTGCGGGGATA 58.975 45.455 0.00 0.00 0.00 2.59
755 861 4.476628 TCAGCACTCTCAAGATATGCAA 57.523 40.909 15.06 4.35 38.07 4.08
796 902 9.258629 TCTTTCCATTGAGTTCAATATTGGATT 57.741 29.630 15.36 3.29 44.10 3.01
903 1013 9.931698 ATGGCCATATAACTCAATAATCATGAT 57.068 29.630 19.18 1.18 0.00 2.45
921 1031 2.900546 ACGGGAAAAACAAATGGCCATA 59.099 40.909 21.15 0.00 0.00 2.74
922 1032 1.696884 ACGGGAAAAACAAATGGCCAT 59.303 42.857 14.09 14.09 0.00 4.40
923 1033 1.123928 ACGGGAAAAACAAATGGCCA 58.876 45.000 8.56 8.56 0.00 5.36
924 1034 1.870402 CAACGGGAAAAACAAATGGCC 59.130 47.619 0.00 0.00 0.00 5.36
925 1035 1.262950 GCAACGGGAAAAACAAATGGC 59.737 47.619 0.00 0.00 0.00 4.40
974 1084 6.319141 GGCTGTTCTTTGCCTTATATTAGG 57.681 41.667 3.26 3.26 45.26 2.69
985 1095 1.856265 CGAGGGTGGCTGTTCTTTGC 61.856 60.000 0.00 0.00 0.00 3.68
986 1096 0.535102 ACGAGGGTGGCTGTTCTTTG 60.535 55.000 0.00 0.00 0.00 2.77
987 1097 0.250338 GACGAGGGTGGCTGTTCTTT 60.250 55.000 0.00 0.00 0.00 2.52
988 1098 1.122019 AGACGAGGGTGGCTGTTCTT 61.122 55.000 0.00 0.00 0.00 2.52
989 1099 1.122019 AAGACGAGGGTGGCTGTTCT 61.122 55.000 0.00 0.00 0.00 3.01
990 1100 0.951040 CAAGACGAGGGTGGCTGTTC 60.951 60.000 0.00 0.00 0.00 3.18
991 1101 1.071471 CAAGACGAGGGTGGCTGTT 59.929 57.895 0.00 0.00 0.00 3.16
992 1102 1.696097 AACAAGACGAGGGTGGCTGT 61.696 55.000 0.00 0.00 0.00 4.40
993 1103 0.951040 GAACAAGACGAGGGTGGCTG 60.951 60.000 0.00 0.00 0.00 4.85
994 1104 1.371558 GAACAAGACGAGGGTGGCT 59.628 57.895 0.00 0.00 0.00 4.75
995 1105 1.671379 GGAACAAGACGAGGGTGGC 60.671 63.158 0.00 0.00 0.00 5.01
996 1106 1.003718 GGGAACAAGACGAGGGTGG 60.004 63.158 0.00 0.00 0.00 4.61
997 1107 1.374252 CGGGAACAAGACGAGGGTG 60.374 63.158 0.00 0.00 0.00 4.61
998 1108 1.532316 TCGGGAACAAGACGAGGGT 60.532 57.895 0.00 0.00 32.29 4.34
999 1109 1.080025 GTCGGGAACAAGACGAGGG 60.080 63.158 0.00 0.00 37.30 4.30
1000 1110 1.080025 GGTCGGGAACAAGACGAGG 60.080 63.158 0.00 0.00 38.16 4.63
1001 1111 1.080025 GGGTCGGGAACAAGACGAG 60.080 63.158 0.00 0.00 38.16 4.18
1002 1112 1.401318 TTGGGTCGGGAACAAGACGA 61.401 55.000 0.00 0.00 38.16 4.20
1003 1113 1.070105 TTGGGTCGGGAACAAGACG 59.930 57.895 0.00 0.00 38.16 4.18
1004 1114 1.226030 CGTTGGGTCGGGAACAAGAC 61.226 60.000 0.00 0.00 36.93 3.01
1005 1115 1.070105 CGTTGGGTCGGGAACAAGA 59.930 57.895 0.00 0.00 0.00 3.02
1006 1116 2.613506 GCGTTGGGTCGGGAACAAG 61.614 63.158 0.00 0.00 0.00 3.16
1007 1117 2.592287 GCGTTGGGTCGGGAACAA 60.592 61.111 0.00 0.00 0.00 2.83
1008 1118 4.973055 CGCGTTGGGTCGGGAACA 62.973 66.667 0.00 0.00 44.40 3.18
1047 1157 1.507096 GTTGACGACATCGCAACGC 60.507 57.895 18.62 5.26 41.93 4.84
1048 1158 4.698496 GTTGACGACATCGCAACG 57.302 55.556 18.62 0.00 41.93 4.10
1049 1159 1.129809 CCGTTGACGACATCGCAAC 59.870 57.895 21.25 21.25 44.58 4.17
1050 1160 1.006825 CTCCGTTGACGACATCGCAA 61.007 55.000 11.89 4.33 44.43 4.85
1051 1161 1.443702 CTCCGTTGACGACATCGCA 60.444 57.895 11.89 0.00 44.43 5.10
1052 1162 0.525668 ATCTCCGTTGACGACATCGC 60.526 55.000 11.89 0.00 44.43 4.58
1053 1163 1.191944 CATCTCCGTTGACGACATCG 58.808 55.000 10.66 10.66 43.02 3.84
1054 1164 0.924090 GCATCTCCGTTGACGACATC 59.076 55.000 4.91 0.00 43.02 3.06
1055 1165 0.246360 TGCATCTCCGTTGACGACAT 59.754 50.000 4.91 0.00 43.02 3.06
1056 1166 0.388520 CTGCATCTCCGTTGACGACA 60.389 55.000 4.91 0.00 43.02 4.35
1057 1167 0.109272 TCTGCATCTCCGTTGACGAC 60.109 55.000 4.91 0.00 43.02 4.34
1058 1168 0.817654 ATCTGCATCTCCGTTGACGA 59.182 50.000 4.91 0.00 43.02 4.20
1059 1169 0.926155 CATCTGCATCTCCGTTGACG 59.074 55.000 0.00 0.00 39.44 4.35
1060 1170 0.654683 GCATCTGCATCTCCGTTGAC 59.345 55.000 0.00 0.00 41.59 3.18
1061 1171 0.807275 CGCATCTGCATCTCCGTTGA 60.807 55.000 2.72 0.00 42.21 3.18
1062 1172 0.807275 TCGCATCTGCATCTCCGTTG 60.807 55.000 2.72 0.00 42.21 4.10
1063 1173 0.105593 ATCGCATCTGCATCTCCGTT 59.894 50.000 2.72 0.00 42.21 4.44
1064 1174 0.105593 AATCGCATCTGCATCTCCGT 59.894 50.000 2.72 0.00 42.21 4.69
1065 1175 0.788995 GAATCGCATCTGCATCTCCG 59.211 55.000 2.72 0.00 42.21 4.63
1066 1176 1.799403 CAGAATCGCATCTGCATCTCC 59.201 52.381 2.72 0.00 40.31 3.71
1074 1184 2.109799 CCCGGCAGAATCGCATCT 59.890 61.111 0.00 0.00 0.00 2.90
1075 1185 2.738213 ATCCCCGGCAGAATCGCATC 62.738 60.000 0.00 0.00 0.00 3.91
1076 1186 2.738213 GATCCCCGGCAGAATCGCAT 62.738 60.000 0.00 0.00 0.00 4.73
1077 1187 3.460672 GATCCCCGGCAGAATCGCA 62.461 63.158 0.00 0.00 0.00 5.10
1078 1188 2.666526 GATCCCCGGCAGAATCGC 60.667 66.667 0.00 0.00 0.00 4.58
1079 1189 1.301244 CTGATCCCCGGCAGAATCG 60.301 63.158 0.00 0.00 34.06 3.34
1080 1190 1.072159 CCTGATCCCCGGCAGAATC 59.928 63.158 8.24 3.10 34.06 2.52
1081 1191 2.455565 CCCTGATCCCCGGCAGAAT 61.456 63.158 8.24 0.00 34.06 2.40
1082 1192 3.089874 CCCTGATCCCCGGCAGAA 61.090 66.667 8.24 0.00 34.06 3.02
1085 1195 4.750695 TTCCCCTGATCCCCGGCA 62.751 66.667 0.00 0.00 0.00 5.69
1086 1196 3.416880 TTTCCCCTGATCCCCGGC 61.417 66.667 0.00 0.00 0.00 6.13
1087 1197 2.270874 CTGTTTCCCCTGATCCCCGG 62.271 65.000 0.00 0.00 0.00 5.73
1088 1198 1.224592 CTGTTTCCCCTGATCCCCG 59.775 63.158 0.00 0.00 0.00 5.73
1089 1199 0.034089 CACTGTTTCCCCTGATCCCC 60.034 60.000 0.00 0.00 0.00 4.81
1090 1200 0.034089 CCACTGTTTCCCCTGATCCC 60.034 60.000 0.00 0.00 0.00 3.85
1091 1201 0.991920 TCCACTGTTTCCCCTGATCC 59.008 55.000 0.00 0.00 0.00 3.36
1092 1202 3.282885 GAATCCACTGTTTCCCCTGATC 58.717 50.000 0.00 0.00 0.00 2.92
1093 1203 2.356125 CGAATCCACTGTTTCCCCTGAT 60.356 50.000 0.00 0.00 0.00 2.90
1094 1204 1.003118 CGAATCCACTGTTTCCCCTGA 59.997 52.381 0.00 0.00 0.00 3.86
1095 1205 1.271379 ACGAATCCACTGTTTCCCCTG 60.271 52.381 0.00 0.00 0.00 4.45
1096 1206 1.064825 ACGAATCCACTGTTTCCCCT 58.935 50.000 0.00 0.00 0.00 4.79
1097 1207 1.905637 AACGAATCCACTGTTTCCCC 58.094 50.000 0.00 0.00 0.00 4.81
1098 1208 2.882137 TGAAACGAATCCACTGTTTCCC 59.118 45.455 12.80 0.00 46.75 3.97
1099 1209 3.885358 GTGAAACGAATCCACTGTTTCC 58.115 45.455 12.80 3.32 46.75 3.13
1129 1239 2.998949 GTGGAAGGGCTGGGGTAG 59.001 66.667 0.00 0.00 0.00 3.18
1130 1240 3.006728 CGTGGAAGGGCTGGGGTA 61.007 66.667 0.00 0.00 0.00 3.69
1133 1243 4.101448 CTCCGTGGAAGGGCTGGG 62.101 72.222 0.00 0.00 42.91 4.45
1134 1244 4.101448 CCTCCGTGGAAGGGCTGG 62.101 72.222 0.00 0.00 42.91 4.85
1135 1245 3.003173 TCCTCCGTGGAAGGGCTG 61.003 66.667 0.00 0.00 42.91 4.85
1147 1257 3.483869 AGGCAAGCCGGATCCTCC 61.484 66.667 5.05 0.15 41.95 4.30
1148 1258 2.203126 CAGGCAAGCCGGATCCTC 60.203 66.667 5.05 1.17 41.95 3.71
1149 1259 4.496336 GCAGGCAAGCCGGATCCT 62.496 66.667 15.46 0.00 41.95 3.24
1150 1260 4.496336 AGCAGGCAAGCCGGATCC 62.496 66.667 15.46 0.00 41.95 3.36
1151 1261 2.899339 GAGCAGGCAAGCCGGATC 60.899 66.667 15.46 14.32 39.23 3.36
1152 1262 4.496336 GGAGCAGGCAAGCCGGAT 62.496 66.667 15.46 8.74 41.95 4.18
1170 1280 4.803426 GAGTGGGAGCACGGCGAG 62.803 72.222 16.62 7.03 0.00 5.03
1173 1283 4.101448 ATGGAGTGGGAGCACGGC 62.101 66.667 0.00 0.00 0.00 5.68
1174 1284 2.187946 GATGGAGTGGGAGCACGG 59.812 66.667 0.00 0.00 0.00 4.94
1175 1285 1.043116 TAGGATGGAGTGGGAGCACG 61.043 60.000 0.00 0.00 0.00 5.34
1176 1286 0.466124 GTAGGATGGAGTGGGAGCAC 59.534 60.000 0.00 0.00 0.00 4.40
1177 1287 1.043116 CGTAGGATGGAGTGGGAGCA 61.043 60.000 0.00 0.00 0.00 4.26
1178 1288 1.742768 CGTAGGATGGAGTGGGAGC 59.257 63.158 0.00 0.00 0.00 4.70
1179 1289 0.757188 AGCGTAGGATGGAGTGGGAG 60.757 60.000 0.00 0.00 0.00 4.30
1180 1290 0.325296 AAGCGTAGGATGGAGTGGGA 60.325 55.000 0.00 0.00 0.00 4.37
1181 1291 0.105039 GAAGCGTAGGATGGAGTGGG 59.895 60.000 0.00 0.00 0.00 4.61
1182 1292 0.105039 GGAAGCGTAGGATGGAGTGG 59.895 60.000 0.00 0.00 0.00 4.00
1183 1293 0.824109 TGGAAGCGTAGGATGGAGTG 59.176 55.000 0.00 0.00 0.00 3.51
1184 1294 0.824759 GTGGAAGCGTAGGATGGAGT 59.175 55.000 0.00 0.00 0.00 3.85
1185 1295 0.249073 CGTGGAAGCGTAGGATGGAG 60.249 60.000 0.00 0.00 0.00 3.86
1186 1296 1.672854 CCGTGGAAGCGTAGGATGGA 61.673 60.000 0.00 0.00 0.00 3.41
1187 1297 1.227263 CCGTGGAAGCGTAGGATGG 60.227 63.158 0.00 0.00 0.00 3.51
1188 1298 0.249073 CTCCGTGGAAGCGTAGGATG 60.249 60.000 0.00 0.00 0.00 3.51
1189 1299 1.392710 CCTCCGTGGAAGCGTAGGAT 61.393 60.000 0.00 0.00 39.86 3.24
1190 1300 2.050350 CCTCCGTGGAAGCGTAGGA 61.050 63.158 0.00 0.00 39.86 2.94
1191 1301 2.050350 TCCTCCGTGGAAGCGTAGG 61.050 63.158 0.00 0.00 42.94 3.18
1192 1302 3.599584 TCCTCCGTGGAAGCGTAG 58.400 61.111 0.00 0.00 42.94 3.51
1199 1309 2.687902 CCCTAGGTCCTCCGTGGA 59.312 66.667 8.29 0.00 43.86 4.02
1200 1310 2.313749 ATCCCCTAGGTCCTCCGTGG 62.314 65.000 8.29 0.00 39.05 4.94
1201 1311 0.828343 GATCCCCTAGGTCCTCCGTG 60.828 65.000 8.29 0.00 39.05 4.94
1202 1312 1.000041 AGATCCCCTAGGTCCTCCGT 61.000 60.000 8.29 0.00 39.05 4.69
1203 1313 0.251430 GAGATCCCCTAGGTCCTCCG 60.251 65.000 8.29 0.00 39.05 4.63
1204 1314 0.115547 GGAGATCCCCTAGGTCCTCC 59.884 65.000 8.29 13.01 41.81 4.30
1205 1315 0.861155 TGGAGATCCCCTAGGTCCTC 59.139 60.000 14.68 11.10 34.26 3.71
1206 1316 1.150986 CATGGAGATCCCCTAGGTCCT 59.849 57.143 14.68 0.00 34.29 3.85
1207 1317 1.150135 TCATGGAGATCCCCTAGGTCC 59.850 57.143 8.29 8.23 34.29 4.46
1208 1318 2.704190 TCATGGAGATCCCCTAGGTC 57.296 55.000 8.29 0.00 34.29 3.85
1209 1319 3.525862 GAATCATGGAGATCCCCTAGGT 58.474 50.000 8.29 0.00 35.39 3.08
1210 1320 2.499289 CGAATCATGGAGATCCCCTAGG 59.501 54.545 0.06 0.06 35.39 3.02
1211 1321 2.093764 GCGAATCATGGAGATCCCCTAG 60.094 54.545 0.00 0.00 35.39 3.02
1212 1322 1.902508 GCGAATCATGGAGATCCCCTA 59.097 52.381 0.00 0.00 35.39 3.53
1213 1323 0.689623 GCGAATCATGGAGATCCCCT 59.310 55.000 0.00 0.00 35.39 4.79
1214 1324 0.689623 AGCGAATCATGGAGATCCCC 59.310 55.000 0.00 0.00 35.39 4.81
1215 1325 1.610102 CCAGCGAATCATGGAGATCCC 60.610 57.143 0.00 0.00 39.02 3.85
1229 1339 2.060383 CATCCACCTCCTCCAGCGA 61.060 63.158 0.00 0.00 0.00 4.93
1291 1401 4.395519 TGCAAAGCATACGCACCT 57.604 50.000 0.00 0.00 42.27 4.00
1301 1411 1.312815 AGTGAAGGAGTGTGCAAAGC 58.687 50.000 0.00 0.00 0.00 3.51
1302 1412 5.455392 CATAAAGTGAAGGAGTGTGCAAAG 58.545 41.667 0.00 0.00 0.00 2.77
1304 1414 3.253188 GCATAAAGTGAAGGAGTGTGCAA 59.747 43.478 0.00 0.00 0.00 4.08
1317 1427 1.004610 CGATGGAGCGTGCATAAAGTG 60.005 52.381 0.00 0.00 0.00 3.16
1322 1432 1.681486 TTCCCGATGGAGCGTGCATA 61.681 55.000 0.00 0.00 43.07 3.14
1324 1434 3.664025 CTTCCCGATGGAGCGTGCA 62.664 63.158 0.00 0.00 43.07 4.57
1325 1435 2.892425 CTTCCCGATGGAGCGTGC 60.892 66.667 0.00 0.00 43.07 5.34
1347 1466 4.984295 TCAACTCAAACAAGATCCATCCA 58.016 39.130 0.00 0.00 0.00 3.41
1392 1511 4.613925 TCTGACCAGGATCTGAATATGC 57.386 45.455 0.00 0.00 32.44 3.14
1448 1567 1.021202 AGTCTGATTCGCTCTCCTCG 58.979 55.000 0.00 0.00 0.00 4.63
1497 1616 1.195115 TTCTCCTCCCCGTCAATCAG 58.805 55.000 0.00 0.00 0.00 2.90
1538 1661 7.316393 TCGGGGAAATTGAATCTAGATGTAT 57.684 36.000 5.86 0.00 0.00 2.29
1587 1710 4.102681 AGAATTAGTGTAGAATTCCGGGGG 59.897 45.833 0.00 0.00 42.03 5.40
1588 1711 5.291905 AGAATTAGTGTAGAATTCCGGGG 57.708 43.478 0.00 0.00 42.03 5.73
1594 1717 9.401058 CATTCCCTGAAGAATTAGTGTAGAATT 57.599 33.333 0.00 0.00 34.19 2.17
1644 1767 0.025898 TCGTCGTCGTCGTCATCATC 59.974 55.000 11.41 0.00 38.33 2.92
1645 1768 0.247576 GTCGTCGTCGTCGTCATCAT 60.248 55.000 11.41 0.00 38.33 2.45
1646 1769 1.131218 GTCGTCGTCGTCGTCATCA 59.869 57.895 11.41 0.00 38.33 3.07
1647 1770 0.451628 TTGTCGTCGTCGTCGTCATC 60.452 55.000 11.58 3.50 38.33 2.92
1648 1771 0.723790 GTTGTCGTCGTCGTCGTCAT 60.724 55.000 11.58 0.00 38.33 3.06
1649 1772 1.368019 GTTGTCGTCGTCGTCGTCA 60.368 57.895 11.41 9.42 38.33 4.35
1650 1773 1.083144 AGTTGTCGTCGTCGTCGTC 60.083 57.895 11.41 6.94 38.33 4.20
1651 1774 1.368493 CAGTTGTCGTCGTCGTCGT 60.368 57.895 11.41 0.00 38.33 4.34
1652 1775 2.694615 GCAGTTGTCGTCGTCGTCG 61.695 63.158 5.50 5.50 38.33 5.12
1653 1776 1.204228 TTGCAGTTGTCGTCGTCGTC 61.204 55.000 1.33 0.00 38.33 4.20
1654 1777 0.596600 ATTGCAGTTGTCGTCGTCGT 60.597 50.000 1.33 0.00 38.33 4.34
1655 1778 0.179275 CATTGCAGTTGTCGTCGTCG 60.179 55.000 0.00 0.00 38.55 5.12
1656 1779 0.859232 ACATTGCAGTTGTCGTCGTC 59.141 50.000 0.00 0.00 0.00 4.20
1657 1780 1.260561 GAACATTGCAGTTGTCGTCGT 59.739 47.619 5.00 0.00 0.00 4.34
1658 1781 1.260297 TGAACATTGCAGTTGTCGTCG 59.740 47.619 5.00 0.00 0.00 5.12
1675 1798 3.713858 TGTCCTCGTAAACGACTTGAA 57.286 42.857 0.14 0.00 44.22 2.69
1676 1799 3.713858 TTGTCCTCGTAAACGACTTGA 57.286 42.857 0.14 0.00 44.22 3.02
1699 1822 3.487544 GCAGATTATCTTCGTGTTTGGGC 60.488 47.826 0.00 0.00 0.00 5.36
1700 1823 3.065371 GGCAGATTATCTTCGTGTTTGGG 59.935 47.826 0.00 0.00 0.00 4.12
1736 1859 8.621286 ACGAGTTTTGTTTTCAACTGAATAGAT 58.379 29.630 0.00 0.00 39.73 1.98
1763 1896 1.340405 GCAGATGATCTGTGGGTGGTT 60.340 52.381 22.23 0.00 45.94 3.67
1865 1998 1.483827 TCTCCCATCTGCTTGCAGTAG 59.516 52.381 20.20 14.01 0.00 2.57
1893 2026 4.479619 GCCAGAATGTCATCAAACAGTTC 58.520 43.478 0.00 0.00 31.50 3.01
1936 2069 5.578157 AGGAAAAGGAGGCAAAGTAGTAA 57.422 39.130 0.00 0.00 0.00 2.24
2063 2196 6.091441 CAGCACAAAGACAGATTACTAGGAAC 59.909 42.308 0.00 0.00 0.00 3.62
2090 2228 5.393678 GGAACCAAAGTGAGTTGTTAAGCAA 60.394 40.000 0.00 0.00 34.16 3.91
2107 2245 5.336372 GCTGCAAACATACATTAGGAACCAA 60.336 40.000 0.00 0.00 0.00 3.67
2133 2271 3.059325 GTGCGATATCCAAGAGTTGATGC 60.059 47.826 0.00 0.00 0.00 3.91
2573 2713 8.974408 TGACGATTTGTATGTACATGTATTAGC 58.026 33.333 18.81 0.00 35.89 3.09
2630 2770 8.778358 ACTCATGACTTGTGAAAAGAAATAGAC 58.222 33.333 0.00 0.00 0.00 2.59
2724 2864 7.886338 AGTTTAAGACTGGGAAAATCACAATC 58.114 34.615 0.00 0.00 37.17 2.67
2739 2879 5.526479 GTCTCGTTCCCAAAAGTTTAAGACT 59.474 40.000 0.00 0.00 41.47 3.24
2893 3033 0.546122 TTGACCCCATTCATCTCGGG 59.454 55.000 0.00 0.00 41.71 5.14
2967 3107 2.596452 AGACATGCGTGTTCGTCTAAG 58.404 47.619 13.92 0.00 39.09 2.18
3025 3329 7.145932 ACAAGCTACATCAACCTTCAAATAC 57.854 36.000 0.00 0.00 0.00 1.89
3027 3331 6.449698 CAACAAGCTACATCAACCTTCAAAT 58.550 36.000 0.00 0.00 0.00 2.32
3824 4295 2.163818 TGAGGTTTACAGCGGTTCAG 57.836 50.000 0.00 0.00 0.00 3.02
3923 4396 1.483827 TGTGCATGCCAAGGTTTCAAA 59.516 42.857 16.68 0.00 0.00 2.69
4326 4799 4.569966 CACAGAACTTAGAGCATGATCACC 59.430 45.833 14.38 0.00 0.00 4.02
4534 5090 4.083003 TGCTAAATTAGGTCGGCAAAAGTG 60.083 41.667 1.88 0.00 0.00 3.16
4550 5106 5.066505 GGAATCTCGGTTTGACATGCTAAAT 59.933 40.000 0.00 0.00 0.00 1.40
4589 5145 2.097304 CCGATTTGATGAACGGCATTGA 59.903 45.455 0.00 0.00 37.34 2.57
4617 5173 3.021788 CGTGCCCGCAAACGTTTG 61.022 61.111 31.76 31.76 41.03 2.93


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

AutoCloner maintained by Alex Coulton.