Multiple sequence alignment - TraesCS4B01G287300

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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 TraesCS4B01G287300 chr4B 100.000 5510 0 0 1 5510 570740792 570735283 0.000000e+00 10176.0
1 TraesCS4B01G287300 chr4B 98.137 161 3 0 1579 1739 570739054 570738894 1.170000e-71 281.0
2 TraesCS4B01G287300 chr4B 98.137 161 3 0 1739 1899 570739214 570739054 1.170000e-71 281.0
3 TraesCS4B01G287300 chr4A 94.852 2331 78 22 2378 4681 11361729 11364044 0.000000e+00 3602.0
4 TraesCS4B01G287300 chr4A 91.198 1102 51 15 1 1083 11360304 11361378 0.000000e+00 1456.0
5 TraesCS4B01G287300 chr4A 94.237 642 23 6 4762 5395 11364087 11364722 0.000000e+00 968.0
6 TraesCS4B01G287300 chr4A 90.625 192 12 3 1 189 11326992 11327180 3.300000e-62 250.0
7 TraesCS4B01G287300 chr4D 95.205 1710 68 4 2281 3978 456496486 456494779 0.000000e+00 2691.0
8 TraesCS4B01G287300 chr4D 95.881 1408 46 5 3999 5395 456494795 456493389 0.000000e+00 2268.0
9 TraesCS4B01G287300 chr4D 92.716 1112 48 16 1 1100 456497842 456496752 0.000000e+00 1574.0
10 TraesCS4B01G287300 chr4D 95.690 116 5 0 5395 5510 456493360 456493245 2.620000e-43 187.0
11 TraesCS4B01G287300 chr4D 82.759 203 19 8 1217 1405 456496715 456496515 3.410000e-37 167.0
12 TraesCS4B01G287300 chr7B 93.687 396 16 6 1856 2246 687546109 687545718 7.950000e-163 584.0
13 TraesCS4B01G287300 chr7B 91.304 299 21 3 1406 1704 687546456 687546163 2.390000e-108 403.0
14 TraesCS4B01G287300 chr7B 89.683 126 11 2 1739 1864 687546286 687546163 5.710000e-35 159.0
15 TraesCS4B01G287300 chr7B 100.000 44 0 0 1696 1739 687546109 687546066 1.270000e-11 82.4
16 TraesCS4B01G287300 chr5B 93.216 398 19 3 1857 2250 447268222 447268615 3.700000e-161 579.0
17 TraesCS4B01G287300 chr5B 92.150 293 21 1 1403 1695 447267868 447268158 3.970000e-111 412.0
18 TraesCS4B01G287300 chr5B 95.294 85 4 0 1103 1187 21154091 21154007 9.630000e-28 135.0
19 TraesCS4B01G287300 chr5B 88.350 103 12 0 1096 1198 604056368 604056470 2.080000e-24 124.0
20 TraesCS4B01G287300 chr5B 100.000 43 0 0 1697 1739 447268222 447268264 4.580000e-11 80.5
21 TraesCS4B01G287300 chr2B 92.443 397 22 4 1856 2248 136957598 136957206 1.340000e-155 560.0
22 TraesCS4B01G287300 chr2B 93.667 300 16 1 1405 1704 136957948 136957652 3.920000e-121 446.0
23 TraesCS4B01G287300 chr2B 93.333 90 4 2 1103 1192 483452954 483453041 1.250000e-26 132.0
24 TraesCS4B01G287300 chr2B 97.727 44 1 0 1696 1739 136957598 136957555 5.920000e-10 76.8
25 TraesCS4B01G287300 chr7A 91.832 404 20 6 1856 2250 735109976 735109577 8.070000e-153 551.0
26 TraesCS4B01G287300 chr7A 89.868 227 18 4 2028 2253 108748809 108748587 2.510000e-73 287.0
27 TraesCS4B01G287300 chr7A 92.063 126 10 0 1739 1864 735110155 735110030 1.580000e-40 178.0
28 TraesCS4B01G287300 chr7A 89.683 126 13 0 1739 1864 108750055 108749930 1.590000e-35 161.0
29 TraesCS4B01G287300 chr6B 91.155 407 19 6 1857 2250 62389322 62389724 2.260000e-148 536.0
30 TraesCS4B01G287300 chr6B 90.727 399 26 4 1857 2250 715710055 715709663 6.330000e-144 521.0
31 TraesCS4B01G287300 chr6B 94.483 290 14 1 1406 1695 62388972 62389259 3.920000e-121 446.0
32 TraesCS4B01G287300 chr6B 93.645 299 16 2 1406 1704 715710405 715710110 1.410000e-120 444.0
33 TraesCS4B01G287300 chr6B 93.162 117 6 1 1739 1855 62389145 62389259 2.640000e-38 171.0
34 TraesCS4B01G287300 chr6B 89.683 126 10 2 1739 1864 715710232 715710110 2.050000e-34 158.0
35 TraesCS4B01G287300 chr6B 95.238 84 4 0 1103 1186 642350237 642350320 3.460000e-27 134.0
36 TraesCS4B01G287300 chr6B 90.909 99 8 1 1100 1198 447890609 447890706 1.250000e-26 132.0
37 TraesCS4B01G287300 chr6B 97.674 43 1 0 1697 1739 62389322 62389364 2.130000e-09 75.0
38 TraesCS4B01G287300 chr6A 87.940 398 32 8 1856 2252 567344910 567345292 6.510000e-124 455.0
39 TraesCS4B01G287300 chr6A 89.831 295 25 3 1406 1695 567344552 567344846 1.870000e-99 374.0
40 TraesCS4B01G287300 chr6A 87.879 297 29 2 1409 1704 203218663 203218953 5.290000e-90 342.0
41 TraesCS4B01G287300 chr6A 88.889 126 14 0 1739 1864 203218828 203218953 7.390000e-34 156.0
42 TraesCS4B01G287300 chr3A 87.595 395 37 7 1856 2250 746320376 746320758 1.090000e-121 448.0
43 TraesCS4B01G287300 chr3A 89.384 292 31 0 1404 1695 746320023 746320314 8.720000e-98 368.0
44 TraesCS4B01G287300 chr3A 89.320 103 8 3 1093 1195 57262244 57262145 5.790000e-25 126.0
45 TraesCS4B01G287300 chr2A 87.960 299 30 1 1406 1704 126567111 126566819 1.140000e-91 348.0
46 TraesCS4B01G287300 chr2A 89.954 219 19 2 2035 2253 126566090 126565875 4.200000e-71 279.0
47 TraesCS4B01G287300 chr2A 90.476 126 12 0 1739 1864 126566944 126566819 3.410000e-37 167.0
48 TraesCS4B01G287300 chr7D 85.324 293 23 8 1856 2148 530906697 530906425 9.030000e-73 285.0
49 TraesCS4B01G287300 chr5A 91.270 126 11 0 1739 1864 642138813 642138938 7.340000e-39 172.0
50 TraesCS4B01G287300 chr1D 91.667 96 5 2 1103 1198 59867945 59868037 4.480000e-26 130.0
51 TraesCS4B01G287300 chr1D 88.889 99 5 3 1104 1201 366246135 366246228 3.490000e-22 117.0
52 TraesCS4B01G287300 chr1D 97.368 38 1 0 1700 1737 369912239 369912202 1.280000e-06 65.8
53 TraesCS4B01G287300 chr2D 90.526 95 9 0 1094 1188 208540136 208540230 5.790000e-25 126.0


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 TraesCS4B01G287300 chr4B 570735283 570740792 5509 True 3579.333333 10176 98.758000 1 5510 3 chr4B.!!$R1 5509
1 TraesCS4B01G287300 chr4A 11360304 11364722 4418 False 2008.666667 3602 93.429000 1 5395 3 chr4A.!!$F2 5394
2 TraesCS4B01G287300 chr4D 456493245 456497842 4597 True 1377.400000 2691 92.450200 1 5510 5 chr4D.!!$R1 5509
3 TraesCS4B01G287300 chr7B 687545718 687546456 738 True 307.100000 584 93.668500 1406 2246 4 chr7B.!!$R1 840
4 TraesCS4B01G287300 chr5B 447267868 447268615 747 False 357.166667 579 95.122000 1403 2250 3 chr5B.!!$F2 847
5 TraesCS4B01G287300 chr2B 136957206 136957948 742 True 360.933333 560 94.612333 1405 2248 3 chr2B.!!$R1 843
6 TraesCS4B01G287300 chr7A 735109577 735110155 578 True 364.500000 551 91.947500 1739 2250 2 chr7A.!!$R2 511
7 TraesCS4B01G287300 chr7A 108748587 108750055 1468 True 224.000000 287 89.775500 1739 2253 2 chr7A.!!$R1 514
8 TraesCS4B01G287300 chr6B 715709663 715710405 742 True 374.333333 521 91.351667 1406 2250 3 chr6B.!!$R1 844
9 TraesCS4B01G287300 chr6B 62388972 62389724 752 False 307.000000 536 94.118500 1406 2250 4 chr6B.!!$F3 844
10 TraesCS4B01G287300 chr6A 567344552 567345292 740 False 414.500000 455 88.885500 1406 2252 2 chr6A.!!$F2 846
11 TraesCS4B01G287300 chr3A 746320023 746320758 735 False 408.000000 448 88.489500 1404 2250 2 chr3A.!!$F1 846
12 TraesCS4B01G287300 chr2A 126565875 126567111 1236 True 264.666667 348 89.463333 1406 2253 3 chr2A.!!$R1 847

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
953 985 0.108615 AGTTCGCCTGTGGATCTTCG 60.109 55.000 0.00 0.0 0.00 3.79 F
1717 1793 0.037326 AGCCGCTCACAATTCTTCGA 60.037 50.000 0.00 0.0 0.00 3.71 F
1718 1794 0.095417 GCCGCTCACAATTCTTCGAC 59.905 55.000 0.00 0.0 0.00 4.20 F
1720 1796 0.246912 CGCTCACAATTCTTCGACGC 60.247 55.000 0.00 0.0 0.00 5.19 F
1721 1797 1.071605 GCTCACAATTCTTCGACGCT 58.928 50.000 0.00 0.0 0.00 5.07 F
1722 1798 1.201855 GCTCACAATTCTTCGACGCTG 60.202 52.381 0.00 0.0 0.00 5.18 F
3583 4741 1.564348 GGGCCATGTCTCCCTTCTTTA 59.436 52.381 4.39 0.0 39.46 1.85 F
4260 5454 2.717639 ATCCTAAGAAAGGCGCACAT 57.282 45.000 10.83 0.0 46.10 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 3417 0.609681 TGCAGCATGGCATGTTCTGA 60.610 50.000 28.30 16.02 39.25 3.27 R
2609 3767 0.765135 TTTCACCTTCTGTCCGGGGA 60.765 55.000 0.00 0.00 0.00 4.81 R
2919 4077 2.275318 CTCCGTCTGAGCAGGAAAATC 58.725 52.381 0.00 0.00 33.47 2.17 R
3502 4660 2.693074 TGTTGCGATATACTCTGGAGCA 59.307 45.455 0.00 0.00 0.00 4.26 R
3613 4771 2.755103 GGAAGACCCAACATCAACATCC 59.245 50.000 0.00 0.00 34.14 3.51 R
3670 4828 3.335748 AGGTATGGGATGATTTAGGCCA 58.664 45.455 5.01 0.00 0.00 5.36 R
4416 5610 1.678970 GCCCCTCATTGGCGACTTT 60.679 57.895 0.00 0.00 39.48 2.66 R
5146 6353 5.048013 TGTCGAGAAATGAGACACACTGTAT 60.048 40.000 0.00 0.00 39.63 2.29 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
25 26 5.137551 GGCTTTAATGGGCTAAATGGAGTA 58.862 41.667 0.00 0.00 0.00 2.59
26 27 5.009710 GGCTTTAATGGGCTAAATGGAGTAC 59.990 44.000 0.00 0.00 0.00 2.73
30 31 9.349713 CTTTAATGGGCTAAATGGAGTACAATA 57.650 33.333 0.00 0.00 0.00 1.90
121 130 5.095490 CGCATACTTTTGGCTTTAAGGAAG 58.905 41.667 0.00 0.00 38.45 3.46
122 131 5.106317 CGCATACTTTTGGCTTTAAGGAAGA 60.106 40.000 0.00 0.00 37.57 2.87
123 132 6.569610 CGCATACTTTTGGCTTTAAGGAAGAA 60.570 38.462 0.00 0.00 37.57 2.52
139 148 4.452455 AGGAAGAAGTAGCAATCAACAACG 59.548 41.667 0.00 0.00 0.00 4.10
243 254 1.134401 ACCATCCAAGCGTACATCCAG 60.134 52.381 0.00 0.00 0.00 3.86
247 258 0.806102 CCAAGCGTACATCCAGACGG 60.806 60.000 0.00 0.00 39.46 4.79
266 277 1.376553 GTCTTCTCTGCACAGGGGC 60.377 63.158 0.00 0.00 0.00 5.80
273 284 1.211457 CTCTGCACAGGGGCTAAAGAT 59.789 52.381 0.00 0.00 34.04 2.40
647 677 2.197324 CGGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
648 678 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
649 679 2.520741 GAGGAGGAGGAGGAGGCG 60.521 72.222 0.00 0.00 0.00 5.52
650 680 4.150454 AGGAGGAGGAGGAGGCGG 62.150 72.222 0.00 0.00 0.00 6.13
651 681 4.144727 GGAGGAGGAGGAGGCGGA 62.145 72.222 0.00 0.00 0.00 5.54
652 682 2.520741 GAGGAGGAGGAGGCGGAG 60.521 72.222 0.00 0.00 0.00 4.63
653 683 4.150454 AGGAGGAGGAGGCGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
661 691 2.517166 GAGGCGGAGGGGATTTGC 60.517 66.667 0.00 0.00 0.00 3.68
697 727 2.398252 TCTCGCTCGTTTCTCTCCTA 57.602 50.000 0.00 0.00 0.00 2.94
746 777 2.416893 GCGGATTTTTCTCCAGTCTCAC 59.583 50.000 0.00 0.00 34.78 3.51
751 782 0.193574 TTTCTCCAGTCTCACCCCCT 59.806 55.000 0.00 0.00 0.00 4.79
781 812 2.865598 CGGCGGAGATCAGCTGGAT 61.866 63.158 15.13 6.11 39.30 3.41
953 985 0.108615 AGTTCGCCTGTGGATCTTCG 60.109 55.000 0.00 0.00 0.00 3.79
1088 1126 2.753247 CCTCTCTTACTACTTGCCCCT 58.247 52.381 0.00 0.00 0.00 4.79
1089 1127 3.912248 CCTCTCTTACTACTTGCCCCTA 58.088 50.000 0.00 0.00 0.00 3.53
1091 1129 4.902448 CCTCTCTTACTACTTGCCCCTAAT 59.098 45.833 0.00 0.00 0.00 1.73
1093 1131 6.553852 CCTCTCTTACTACTTGCCCCTAATTA 59.446 42.308 0.00 0.00 0.00 1.40
1095 1133 7.963532 TCTCTTACTACTTGCCCCTAATTATG 58.036 38.462 0.00 0.00 0.00 1.90
1097 1135 8.097791 TCTTACTACTTGCCCCTAATTATGTT 57.902 34.615 0.00 0.00 0.00 2.71
1100 1138 7.404671 ACTACTTGCCCCTAATTATGTTTTG 57.595 36.000 0.00 0.00 0.00 2.44
1101 1139 7.179269 ACTACTTGCCCCTAATTATGTTTTGA 58.821 34.615 0.00 0.00 0.00 2.69
1102 1140 6.926630 ACTTGCCCCTAATTATGTTTTGAA 57.073 33.333 0.00 0.00 0.00 2.69
1103 1141 6.697395 ACTTGCCCCTAATTATGTTTTGAAC 58.303 36.000 0.00 0.00 0.00 3.18
1104 1142 6.496911 ACTTGCCCCTAATTATGTTTTGAACT 59.503 34.615 0.00 0.00 0.00 3.01
1105 1143 6.524101 TGCCCCTAATTATGTTTTGAACTC 57.476 37.500 0.00 0.00 0.00 3.01
1106 1144 6.013379 TGCCCCTAATTATGTTTTGAACTCA 58.987 36.000 0.00 0.00 0.00 3.41
1107 1145 6.071616 TGCCCCTAATTATGTTTTGAACTCAC 60.072 38.462 0.00 0.00 0.00 3.51
1108 1146 6.152831 GCCCCTAATTATGTTTTGAACTCACT 59.847 38.462 0.00 0.00 0.00 3.41
1109 1147 7.628580 GCCCCTAATTATGTTTTGAACTCACTC 60.629 40.741 0.00 0.00 0.00 3.51
1110 1148 7.611855 CCCCTAATTATGTTTTGAACTCACTCT 59.388 37.037 0.00 0.00 0.00 3.24
1111 1149 8.454106 CCCTAATTATGTTTTGAACTCACTCTG 58.546 37.037 0.00 0.00 0.00 3.35
1112 1150 9.003658 CCTAATTATGTTTTGAACTCACTCTGT 57.996 33.333 0.00 0.00 0.00 3.41
1117 1155 9.607988 TTATGTTTTGAACTCACTCTGTAAAGA 57.392 29.630 0.00 0.00 0.00 2.52
1118 1156 7.539712 TGTTTTGAACTCACTCTGTAAAGAG 57.460 36.000 8.50 8.50 41.45 2.85
1119 1157 7.327975 TGTTTTGAACTCACTCTGTAAAGAGA 58.672 34.615 17.23 0.00 39.14 3.10
1120 1158 7.987458 TGTTTTGAACTCACTCTGTAAAGAGAT 59.013 33.333 17.23 0.00 39.14 2.75
1121 1159 9.477484 GTTTTGAACTCACTCTGTAAAGAGATA 57.523 33.333 17.23 3.15 39.14 1.98
1128 1166 8.846211 ACTCACTCTGTAAAGAGATATAAGAGC 58.154 37.037 17.23 0.00 39.14 4.09
1129 1167 7.866729 TCACTCTGTAAAGAGATATAAGAGCG 58.133 38.462 17.23 0.00 39.14 5.03
1130 1168 7.499563 TCACTCTGTAAAGAGATATAAGAGCGT 59.500 37.037 17.23 0.00 39.14 5.07
1131 1169 8.132362 CACTCTGTAAAGAGATATAAGAGCGTT 58.868 37.037 17.23 0.00 39.14 4.84
1132 1170 8.688151 ACTCTGTAAAGAGATATAAGAGCGTTT 58.312 33.333 17.23 0.00 39.14 3.60
1139 1177 9.685828 AAAGAGATATAAGAGCGTTTAGATCAC 57.314 33.333 15.45 11.24 37.82 3.06
1140 1178 8.397575 AGAGATATAAGAGCGTTTAGATCACA 57.602 34.615 15.45 0.00 37.82 3.58
1141 1179 8.851145 AGAGATATAAGAGCGTTTAGATCACAA 58.149 33.333 15.45 0.00 37.82 3.33
1142 1180 8.804688 AGATATAAGAGCGTTTAGATCACAAC 57.195 34.615 15.45 0.00 37.82 3.32
1143 1181 8.634444 AGATATAAGAGCGTTTAGATCACAACT 58.366 33.333 15.45 0.00 37.82 3.16
1144 1182 9.250624 GATATAAGAGCGTTTAGATCACAACTT 57.749 33.333 10.86 0.00 37.82 2.66
1145 1183 7.907214 ATAAGAGCGTTTAGATCACAACTTT 57.093 32.000 0.00 0.00 37.82 2.66
1146 1184 8.997621 ATAAGAGCGTTTAGATCACAACTTTA 57.002 30.769 0.00 0.00 37.82 1.85
1147 1185 6.952935 AGAGCGTTTAGATCACAACTTTAG 57.047 37.500 0.00 0.00 37.82 1.85
1148 1186 6.456501 AGAGCGTTTAGATCACAACTTTAGT 58.543 36.000 0.00 0.00 37.82 2.24
1149 1187 6.366332 AGAGCGTTTAGATCACAACTTTAGTG 59.634 38.462 0.00 0.00 37.82 2.74
1161 1199 8.181487 TCACAACTTTAGTGATCTATAAACGC 57.819 34.615 0.00 0.00 40.80 4.84
1162 1200 8.033038 TCACAACTTTAGTGATCTATAAACGCT 58.967 33.333 0.00 0.00 40.80 5.07
1163 1201 8.321716 CACAACTTTAGTGATCTATAAACGCTC 58.678 37.037 0.00 0.00 39.30 5.03
1164 1202 8.251721 ACAACTTTAGTGATCTATAAACGCTCT 58.748 33.333 0.00 0.00 0.00 4.09
1165 1203 9.088512 CAACTTTAGTGATCTATAAACGCTCTT 57.911 33.333 0.00 0.00 0.00 2.85
1182 1220 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
1183 1221 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
1184 1222 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
1185 1223 7.596995 CGCTCTTATATTTCTTTACAGAGGGAG 59.403 40.741 4.76 0.00 40.49 4.30
1186 1224 8.425703 GCTCTTATATTTCTTTACAGAGGGAGT 58.574 37.037 0.00 0.00 0.00 3.85
1250 1299 2.360483 TCGATTGCTTTGGCTGTTTTGA 59.640 40.909 0.00 0.00 39.59 2.69
1256 1305 7.360269 CGATTGCTTTGGCTGTTTTGATTATTT 60.360 33.333 0.00 0.00 39.59 1.40
1258 1307 5.049543 TGCTTTGGCTGTTTTGATTATTTGC 60.050 36.000 0.00 0.00 39.59 3.68
1266 1330 7.041848 GGCTGTTTTGATTATTTGCAGTTCTTT 60.042 33.333 0.00 0.00 0.00 2.52
1273 1337 8.020861 TGATTATTTGCAGTTCTTTGATTTGC 57.979 30.769 0.00 0.00 35.42 3.68
1301 1368 4.081365 TGTTGAATTGAGAGGCGTACCATA 60.081 41.667 0.00 0.00 39.06 2.74
1321 1390 6.949352 CATATCTGGGGCAAATATGGATAC 57.051 41.667 0.00 0.00 32.27 2.24
1350 1422 9.665719 TGTTATGCATCTTACACTTCTATTTCA 57.334 29.630 0.19 0.00 0.00 2.69
1372 1444 9.538508 TTTCAGTCACTAGTTTTTACCTACTTC 57.461 33.333 0.00 0.00 0.00 3.01
1449 1523 7.894376 ATTAAGTTCGTCGGAGTTTGATTAA 57.106 32.000 0.00 0.00 0.00 1.40
1604 1680 3.442625 CGGCCCATAACTATCTACATCGA 59.557 47.826 0.00 0.00 0.00 3.59
1652 1728 2.816958 AACTCATCAGGCAGCGCG 60.817 61.111 0.00 0.00 0.00 6.86
1670 1746 3.081409 GCCGCCTCCTCAACCCTA 61.081 66.667 0.00 0.00 0.00 3.53
1671 1747 2.444256 GCCGCCTCCTCAACCCTAT 61.444 63.158 0.00 0.00 0.00 2.57
1672 1748 1.447643 CCGCCTCCTCAACCCTATG 59.552 63.158 0.00 0.00 0.00 2.23
1673 1749 1.227674 CGCCTCCTCAACCCTATGC 60.228 63.158 0.00 0.00 0.00 3.14
1674 1750 1.227674 GCCTCCTCAACCCTATGCG 60.228 63.158 0.00 0.00 0.00 4.73
1675 1751 1.686325 GCCTCCTCAACCCTATGCGA 61.686 60.000 0.00 0.00 0.00 5.10
1676 1752 1.051812 CCTCCTCAACCCTATGCGAT 58.948 55.000 0.00 0.00 0.00 4.58
1677 1753 1.270518 CCTCCTCAACCCTATGCGATG 60.271 57.143 0.00 0.00 0.00 3.84
1678 1754 1.688735 CTCCTCAACCCTATGCGATGA 59.311 52.381 0.00 0.00 0.00 2.92
1679 1755 2.103094 CTCCTCAACCCTATGCGATGAA 59.897 50.000 0.00 0.00 0.00 2.57
1680 1756 2.705658 TCCTCAACCCTATGCGATGAAT 59.294 45.455 0.00 0.00 0.00 2.57
1681 1757 3.136443 TCCTCAACCCTATGCGATGAATT 59.864 43.478 0.00 0.00 0.00 2.17
1682 1758 3.499918 CCTCAACCCTATGCGATGAATTC 59.500 47.826 0.00 0.00 0.00 2.17
1683 1759 4.129380 CTCAACCCTATGCGATGAATTCA 58.871 43.478 11.26 11.26 0.00 2.57
1684 1760 4.717877 TCAACCCTATGCGATGAATTCAT 58.282 39.130 20.85 20.85 39.70 2.57
1685 1761 4.756642 TCAACCCTATGCGATGAATTCATC 59.243 41.667 30.57 30.57 46.93 2.92
1696 1772 1.672363 TGAATTCATCATCTGGTGCGC 59.328 47.619 3.38 0.00 31.50 6.09
1697 1773 1.945394 GAATTCATCATCTGGTGCGCT 59.055 47.619 9.73 0.00 0.00 5.92
1698 1774 2.916702 ATTCATCATCTGGTGCGCTA 57.083 45.000 9.73 0.00 0.00 4.26
1699 1775 2.229675 TTCATCATCTGGTGCGCTAG 57.770 50.000 9.73 3.91 0.00 3.42
1700 1776 0.249615 TCATCATCTGGTGCGCTAGC 60.250 55.000 9.73 4.06 45.41 3.42
1701 1777 1.070445 ATCATCTGGTGCGCTAGCC 59.930 57.895 9.73 9.18 44.33 3.93
1702 1778 2.705934 ATCATCTGGTGCGCTAGCCG 62.706 60.000 9.73 5.65 44.33 5.52
1711 1787 3.799753 CGCTAGCCGCTCACAATT 58.200 55.556 9.66 0.00 36.13 2.32
1712 1788 1.638467 CGCTAGCCGCTCACAATTC 59.362 57.895 9.66 0.00 36.13 2.17
1713 1789 0.807667 CGCTAGCCGCTCACAATTCT 60.808 55.000 9.66 0.00 36.13 2.40
1714 1790 1.373570 GCTAGCCGCTCACAATTCTT 58.626 50.000 2.29 0.00 35.14 2.52
1715 1791 1.328986 GCTAGCCGCTCACAATTCTTC 59.671 52.381 2.29 0.00 35.14 2.87
1716 1792 1.590238 CTAGCCGCTCACAATTCTTCG 59.410 52.381 0.00 0.00 0.00 3.79
1717 1793 0.037326 AGCCGCTCACAATTCTTCGA 60.037 50.000 0.00 0.00 0.00 3.71
1718 1794 0.095417 GCCGCTCACAATTCTTCGAC 59.905 55.000 0.00 0.00 0.00 4.20
1719 1795 0.366871 CCGCTCACAATTCTTCGACG 59.633 55.000 0.00 0.00 0.00 5.12
1720 1796 0.246912 CGCTCACAATTCTTCGACGC 60.247 55.000 0.00 0.00 0.00 5.19
1721 1797 1.071605 GCTCACAATTCTTCGACGCT 58.928 50.000 0.00 0.00 0.00 5.07
1722 1798 1.201855 GCTCACAATTCTTCGACGCTG 60.202 52.381 0.00 0.00 0.00 5.18
1723 1799 2.061773 CTCACAATTCTTCGACGCTGT 58.938 47.619 0.00 0.00 0.00 4.40
1724 1800 2.476619 CTCACAATTCTTCGACGCTGTT 59.523 45.455 0.00 0.00 0.00 3.16
1725 1801 2.869801 TCACAATTCTTCGACGCTGTTT 59.130 40.909 0.00 0.00 0.00 2.83
1726 1802 3.059868 TCACAATTCTTCGACGCTGTTTC 60.060 43.478 0.00 0.00 0.00 2.78
1727 1803 3.059597 CACAATTCTTCGACGCTGTTTCT 60.060 43.478 0.00 0.00 0.00 2.52
1728 1804 4.149922 CACAATTCTTCGACGCTGTTTCTA 59.850 41.667 0.00 0.00 0.00 2.10
1729 1805 4.748102 ACAATTCTTCGACGCTGTTTCTAA 59.252 37.500 0.00 0.00 0.00 2.10
1730 1806 5.408604 ACAATTCTTCGACGCTGTTTCTAAT 59.591 36.000 0.00 0.00 0.00 1.73
1731 1807 5.704217 ATTCTTCGACGCTGTTTCTAATC 57.296 39.130 0.00 0.00 0.00 1.75
1732 1808 4.436242 TCTTCGACGCTGTTTCTAATCT 57.564 40.909 0.00 0.00 0.00 2.40
1733 1809 4.413087 TCTTCGACGCTGTTTCTAATCTC 58.587 43.478 0.00 0.00 0.00 2.75
1734 1810 4.156190 TCTTCGACGCTGTTTCTAATCTCT 59.844 41.667 0.00 0.00 0.00 3.10
1735 1811 4.017380 TCGACGCTGTTTCTAATCTCTC 57.983 45.455 0.00 0.00 0.00 3.20
1736 1812 3.109619 CGACGCTGTTTCTAATCTCTCC 58.890 50.000 0.00 0.00 0.00 3.71
1737 1813 3.427638 CGACGCTGTTTCTAATCTCTCCA 60.428 47.826 0.00 0.00 0.00 3.86
1770 1846 5.243060 CCATAACTATCTACATCGGTCCACA 59.757 44.000 0.00 0.00 0.00 4.17
1812 1893 2.816958 AACTCATCAGGCAGCGCG 60.817 61.111 0.00 0.00 0.00 6.86
1831 1912 2.444256 GCCGCCTCCTCAACCCTAT 61.444 63.158 0.00 0.00 0.00 2.57
1907 3022 9.958180 TGTTTCTAATCTCTCCATTGTCAATAA 57.042 29.630 0.00 0.00 0.00 1.40
1973 3094 8.255206 TCGTAGCAAATCCTACAGAAAAATAGA 58.745 33.333 0.00 0.00 38.03 1.98
2000 3125 3.057174 CGACATCTAGCACCTAAGGATCC 60.057 52.174 2.48 2.48 0.00 3.36
2059 3186 2.045561 TCTCTCTCGTGGAGTGATCC 57.954 55.000 7.71 0.00 42.40 3.36
2083 3217 3.570975 TCAGTATGTGTTCCGTGTGTAGT 59.429 43.478 0.00 0.00 37.40 2.73
2091 3225 5.123661 TGTGTTCCGTGTGTAGTAATCGATA 59.876 40.000 0.00 0.00 0.00 2.92
2134 3276 4.220602 CGTGGGATCTTTTTCATTTTCCCT 59.779 41.667 7.29 0.00 42.74 4.20
2274 3417 7.959152 TCCTATTTTTGTCCCCCTTTCTTATTT 59.041 33.333 0.00 0.00 0.00 1.40
2275 3418 8.258007 CCTATTTTTGTCCCCCTTTCTTATTTC 58.742 37.037 0.00 0.00 0.00 2.17
2276 3419 7.625498 ATTTTTGTCCCCCTTTCTTATTTCA 57.375 32.000 0.00 0.00 0.00 2.69
2278 3421 5.592587 TTGTCCCCCTTTCTTATTTCAGA 57.407 39.130 0.00 0.00 0.00 3.27
2326 3484 9.372369 AGAACATTAATTTCTTCTTAGGTCTCG 57.628 33.333 6.92 0.00 28.36 4.04
2342 3500 9.460906 CTTAGGTCTCGTATACTTCAAATTACC 57.539 37.037 0.56 0.00 0.00 2.85
2345 3503 6.460123 GGTCTCGTATACTTCAAATTACCCGA 60.460 42.308 0.56 0.00 0.00 5.14
2346 3504 6.636044 GTCTCGTATACTTCAAATTACCCGAG 59.364 42.308 0.56 0.00 39.38 4.63
2349 3507 6.319658 TCGTATACTTCAAATTACCCGAGAGT 59.680 38.462 0.56 0.00 0.00 3.24
2359 3517 8.658609 TCAAATTACCCGAGAGTAAATAAAACG 58.341 33.333 0.00 0.00 35.90 3.60
2360 3518 7.543947 AATTACCCGAGAGTAAATAAAACGG 57.456 36.000 0.00 0.00 35.90 4.44
2363 3521 4.931601 ACCCGAGAGTAAATAAAACGGAAC 59.068 41.667 0.00 0.00 41.09 3.62
2409 3567 2.093553 GCAGAGAGCTCCTTCAGTTCAT 60.094 50.000 10.93 0.00 41.15 2.57
2412 3570 5.531634 CAGAGAGCTCCTTCAGTTCATATC 58.468 45.833 10.93 0.00 34.79 1.63
2419 3577 6.070309 AGCTCCTTCAGTTCATATCTTCAGTT 60.070 38.462 0.00 0.00 0.00 3.16
2490 3648 3.535280 TTCCTTTGTTTCTTGTTGGGC 57.465 42.857 0.00 0.00 0.00 5.36
2603 3761 4.448537 GCCATCTATAAGAGATCGCAGT 57.551 45.455 0.00 0.00 45.36 4.40
2609 3767 1.769026 TAAGAGATCGCAGTGAGCCT 58.231 50.000 0.00 0.00 41.38 4.58
2612 3770 2.107953 GATCGCAGTGAGCCTCCC 59.892 66.667 0.00 0.00 41.38 4.30
2624 3782 2.284699 CCTCCCCGGACAGAAGGT 60.285 66.667 0.73 0.00 33.16 3.50
2690 3848 7.156876 TGATCTTAAAAATGCGACCAAGAAT 57.843 32.000 0.00 0.00 0.00 2.40
2919 4077 7.063780 GCTATTTTTCATGTTTCCTGATGGTTG 59.936 37.037 0.00 0.00 34.23 3.77
2999 4157 5.945784 TGTTAAGCTCATTGGTTATTGCTCT 59.054 36.000 0.00 0.00 38.27 4.09
3085 4243 9.436957 TCTGTTCAGAAGTATGTTCTTTAATCC 57.563 33.333 0.00 0.00 0.00 3.01
3318 4476 5.694910 TCAAACATTCTTCTTGACTCGGTAC 59.305 40.000 0.00 0.00 0.00 3.34
3579 4737 1.649271 ATGGGGCCATGTCTCCCTTC 61.649 60.000 4.39 2.10 42.25 3.46
3583 4741 1.564348 GGGCCATGTCTCCCTTCTTTA 59.436 52.381 4.39 0.00 39.46 1.85
3611 4769 5.237127 GTCATGTGACATCAGTTCTGACAAA 59.763 40.000 8.22 0.00 44.18 2.83
3612 4770 5.999600 TCATGTGACATCAGTTCTGACAAAT 59.000 36.000 4.58 0.00 0.00 2.32
3613 4771 5.678132 TGTGACATCAGTTCTGACAAATG 57.322 39.130 4.58 2.65 0.00 2.32
3634 4792 2.755103 GGATGTTGATGTTGGGTCTTCC 59.245 50.000 0.00 0.00 0.00 3.46
3708 4888 5.487488 CCATACCTATGGTGAAGCCCTATTA 59.513 44.000 3.44 0.00 46.42 0.98
3919 5102 9.931210 CACTTTATTCCTATTAAATTCGACACC 57.069 33.333 0.00 0.00 0.00 4.16
4001 5184 6.500684 ACTGTGCATAAGAAATGAACGAAT 57.499 33.333 6.39 0.00 30.09 3.34
4002 5185 7.609760 ACTGTGCATAAGAAATGAACGAATA 57.390 32.000 6.39 0.00 30.09 1.75
4003 5186 8.213518 ACTGTGCATAAGAAATGAACGAATAT 57.786 30.769 6.39 0.00 30.09 1.28
4005 5188 9.507280 CTGTGCATAAGAAATGAACGAATATTT 57.493 29.630 0.00 0.00 30.09 1.40
4260 5454 2.717639 ATCCTAAGAAAGGCGCACAT 57.282 45.000 10.83 0.00 46.10 3.21
4372 5566 7.448469 AGCTCCAAGACTCTAAAAGCAATTTAA 59.552 33.333 8.42 0.00 33.20 1.52
4416 5610 0.979187 GGACCTCCAATACCGTCCCA 60.979 60.000 0.00 0.00 39.13 4.37
4526 5720 7.531955 TGCACTAGAAGCACACCTTAGAAGG 62.532 48.000 6.77 6.77 43.76 3.46
4616 5810 3.507622 GCTTCTTGCTCATTTGTAGGGTT 59.492 43.478 0.00 0.00 38.95 4.11
4669 5865 7.986320 TGATGAATTGTTTTTCACCAAATCTGT 59.014 29.630 0.00 0.00 38.37 3.41
4735 5931 1.017387 GCCGGGTTTATCTTCTGCAG 58.983 55.000 7.63 7.63 0.00 4.41
4736 5932 1.406887 GCCGGGTTTATCTTCTGCAGA 60.407 52.381 13.74 13.74 35.33 4.26
4737 5933 2.280628 CCGGGTTTATCTTCTGCAGAC 58.719 52.381 18.03 3.09 32.83 3.51
4738 5934 2.354704 CCGGGTTTATCTTCTGCAGACA 60.355 50.000 18.03 6.45 32.83 3.41
4739 5935 3.535561 CGGGTTTATCTTCTGCAGACAT 58.464 45.455 18.03 13.92 32.83 3.06
4742 5941 5.128919 GGGTTTATCTTCTGCAGACATGAT 58.871 41.667 18.03 20.57 32.83 2.45
4753 5952 4.891260 TGCAGACATGATACTGGATGATC 58.109 43.478 0.00 0.00 35.05 2.92
4754 5953 4.252073 GCAGACATGATACTGGATGATCC 58.748 47.826 4.05 4.05 36.96 3.36
4755 5954 4.829968 CAGACATGATACTGGATGATCCC 58.170 47.826 9.36 0.00 35.03 3.85
4782 5981 3.134623 TGACATGACAGAAACTGTGGACT 59.865 43.478 9.15 0.00 45.44 3.85
4791 5990 0.037303 AACTGTGGACTGGGAGCATG 59.963 55.000 0.00 0.00 0.00 4.06
5029 6236 6.189859 TGAGCCTTGAATTTCAGGAATGTAT 58.810 36.000 9.88 0.00 0.00 2.29
5115 6322 3.188460 GGAGAACAAAAACAGCAGCGATA 59.812 43.478 0.00 0.00 0.00 2.92
5146 6353 2.325583 CTGCTAAGGCGGGTAAATGA 57.674 50.000 0.00 0.00 40.90 2.57
5307 6514 5.349061 ACATCAGACAATCATACAGCTCA 57.651 39.130 0.00 0.00 0.00 4.26
5311 6518 4.467438 TCAGACAATCATACAGCTCAGGAA 59.533 41.667 0.00 0.00 0.00 3.36
5315 6522 7.660617 CAGACAATCATACAGCTCAGGAATAAT 59.339 37.037 0.00 0.00 0.00 1.28
5326 6533 6.320672 CAGCTCAGGAATAATTTGGTCAAGAT 59.679 38.462 0.00 0.00 0.00 2.40
5489 6725 6.777580 AGTTGTATGAGGTTTCATTTTCTGGT 59.222 34.615 0.00 0.00 41.24 4.00
5501 6737 8.696410 TTTCATTTTCTGGTGAAACTTTGTAC 57.304 30.769 0.00 0.00 41.34 2.90
5506 6742 5.092554 TCTGGTGAAACTTTGTACTGTGA 57.907 39.130 0.00 0.00 36.74 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.972568 TCCTATTGTACTCCATTTAGCCCA 59.027 41.667 0.00 0.00 0.00 5.36
11 12 5.562298 TCCTATTGTACTCCATTTAGCCC 57.438 43.478 0.00 0.00 0.00 5.19
121 130 6.370593 TGAATTCGTTGTTGATTGCTACTTC 58.629 36.000 0.04 0.00 0.00 3.01
122 131 6.312399 TGAATTCGTTGTTGATTGCTACTT 57.688 33.333 0.04 0.00 0.00 2.24
123 132 5.940192 TGAATTCGTTGTTGATTGCTACT 57.060 34.783 0.04 0.00 0.00 2.57
139 148 6.200286 CAGTCAATATGCTTTGCCATGAATTC 59.800 38.462 0.00 0.00 0.00 2.17
243 254 0.389166 CTGTGCAGAGAAGACCCGTC 60.389 60.000 4.50 0.00 0.00 4.79
247 258 1.298014 CCCCTGTGCAGAGAAGACC 59.702 63.158 13.38 0.00 0.00 3.85
266 277 8.331022 CGATATGTTTGAGTGTTCCATCTTTAG 58.669 37.037 0.00 0.00 0.00 1.85
273 284 4.020573 ACCTCGATATGTTTGAGTGTTCCA 60.021 41.667 0.00 0.00 34.41 3.53
289 300 2.449031 TTTGCGTGCAGGACCTCGAT 62.449 55.000 11.29 0.00 0.00 3.59
438 449 2.291043 GGGAGGAGGAGCAACGGAA 61.291 63.158 0.00 0.00 0.00 4.30
645 675 2.616458 AAGCAAATCCCCTCCGCCT 61.616 57.895 0.00 0.00 0.00 5.52
646 676 2.043953 AAGCAAATCCCCTCCGCC 60.044 61.111 0.00 0.00 0.00 6.13
647 677 1.378514 TCAAGCAAATCCCCTCCGC 60.379 57.895 0.00 0.00 0.00 5.54
648 678 0.035056 AGTCAAGCAAATCCCCTCCG 60.035 55.000 0.00 0.00 0.00 4.63
649 679 2.222227 AAGTCAAGCAAATCCCCTCC 57.778 50.000 0.00 0.00 0.00 4.30
650 680 4.039124 TCAAAAAGTCAAGCAAATCCCCTC 59.961 41.667 0.00 0.00 0.00 4.30
651 681 3.966665 TCAAAAAGTCAAGCAAATCCCCT 59.033 39.130 0.00 0.00 0.00 4.79
652 682 4.335400 TCAAAAAGTCAAGCAAATCCCC 57.665 40.909 0.00 0.00 0.00 4.81
653 683 4.212004 GCTTCAAAAAGTCAAGCAAATCCC 59.788 41.667 0.00 0.00 41.87 3.85
661 691 3.971240 GCGAGAAGCTTCAAAAAGTCAAG 59.029 43.478 27.57 5.63 44.04 3.02
685 715 0.992802 GCAACGCTAGGAGAGAAACG 59.007 55.000 0.00 0.00 0.00 3.60
746 777 2.356667 GCCACTTGAAGGAGGGGG 59.643 66.667 7.83 0.00 40.75 5.40
751 782 4.697756 CCGCCGCCACTTGAAGGA 62.698 66.667 0.00 0.00 0.00 3.36
781 812 0.179004 TTTCTGGCGAGGCTTTTGGA 60.179 50.000 0.00 0.00 0.00 3.53
893 925 1.856265 CGGGTCAAGTCAGCAAAGCC 61.856 60.000 0.00 0.00 0.00 4.35
919 951 1.404851 CGAACTCTGCTCCTCTTTCCC 60.405 57.143 0.00 0.00 0.00 3.97
953 985 2.954989 GGATGAATGAGCTTCCTTTCCC 59.045 50.000 0.00 0.00 32.49 3.97
1091 1129 9.607988 TCTTTACAGAGTGAGTTCAAAACATAA 57.392 29.630 0.00 0.00 0.00 1.90
1093 1131 7.987458 TCTCTTTACAGAGTGAGTTCAAAACAT 59.013 33.333 5.82 0.00 46.24 2.71
1095 1133 7.772332 TCTCTTTACAGAGTGAGTTCAAAAC 57.228 36.000 5.82 0.00 46.24 2.43
1102 1140 8.846211 GCTCTTATATCTCTTTACAGAGTGAGT 58.154 37.037 5.82 0.00 46.24 3.41
1103 1141 8.015087 CGCTCTTATATCTCTTTACAGAGTGAG 58.985 40.741 5.82 6.61 46.24 3.51
1104 1142 7.499563 ACGCTCTTATATCTCTTTACAGAGTGA 59.500 37.037 12.51 0.00 46.24 3.41
1105 1143 7.644490 ACGCTCTTATATCTCTTTACAGAGTG 58.356 38.462 5.82 0.00 46.24 3.51
1106 1144 7.811117 ACGCTCTTATATCTCTTTACAGAGT 57.189 36.000 5.82 0.00 46.24 3.24
1113 1151 9.685828 GTGATCTAAACGCTCTTATATCTCTTT 57.314 33.333 0.00 0.00 0.00 2.52
1114 1152 8.851145 TGTGATCTAAACGCTCTTATATCTCTT 58.149 33.333 0.00 0.00 0.00 2.85
1115 1153 8.397575 TGTGATCTAAACGCTCTTATATCTCT 57.602 34.615 0.00 0.00 0.00 3.10
1116 1154 8.907685 GTTGTGATCTAAACGCTCTTATATCTC 58.092 37.037 0.00 0.00 0.00 2.75
1117 1155 8.634444 AGTTGTGATCTAAACGCTCTTATATCT 58.366 33.333 0.00 0.00 0.00 1.98
1118 1156 8.804688 AGTTGTGATCTAAACGCTCTTATATC 57.195 34.615 0.00 0.00 0.00 1.63
1119 1157 9.601217 AAAGTTGTGATCTAAACGCTCTTATAT 57.399 29.630 0.00 0.00 0.00 0.86
1120 1158 8.997621 AAAGTTGTGATCTAAACGCTCTTATA 57.002 30.769 0.00 0.00 0.00 0.98
1121 1159 7.907214 AAAGTTGTGATCTAAACGCTCTTAT 57.093 32.000 0.00 0.00 0.00 1.73
1122 1160 8.086522 ACTAAAGTTGTGATCTAAACGCTCTTA 58.913 33.333 0.00 0.00 0.00 2.10
1123 1161 6.929606 ACTAAAGTTGTGATCTAAACGCTCTT 59.070 34.615 0.00 0.00 0.00 2.85
1124 1162 6.366332 CACTAAAGTTGTGATCTAAACGCTCT 59.634 38.462 0.00 0.00 37.60 4.09
1125 1163 6.365247 TCACTAAAGTTGTGATCTAAACGCTC 59.635 38.462 0.00 0.00 39.23 5.03
1126 1164 6.220930 TCACTAAAGTTGTGATCTAAACGCT 58.779 36.000 0.00 0.00 39.23 5.07
1127 1165 6.462073 TCACTAAAGTTGTGATCTAAACGC 57.538 37.500 0.00 0.00 39.23 4.84
1136 1174 8.033038 AGCGTTTATAGATCACTAAAGTTGTGA 58.967 33.333 0.00 0.00 46.58 3.58
1137 1175 8.186178 AGCGTTTATAGATCACTAAAGTTGTG 57.814 34.615 0.00 0.00 36.82 3.33
1138 1176 8.251721 AGAGCGTTTATAGATCACTAAAGTTGT 58.748 33.333 0.00 0.00 32.04 3.32
1139 1177 8.635877 AGAGCGTTTATAGATCACTAAAGTTG 57.364 34.615 0.00 0.00 32.04 3.16
1156 1194 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
1157 1195 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
1158 1196 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
1159 1197 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
1160 1198 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
1167 1205 9.710818 ACATACTACTCCCTCTGTAAAGAAATA 57.289 33.333 0.00 0.00 0.00 1.40
1168 1206 8.611051 ACATACTACTCCCTCTGTAAAGAAAT 57.389 34.615 0.00 0.00 0.00 2.17
1169 1207 9.710818 ATACATACTACTCCCTCTGTAAAGAAA 57.289 33.333 0.00 0.00 0.00 2.52
1170 1208 9.710818 AATACATACTACTCCCTCTGTAAAGAA 57.289 33.333 0.00 0.00 0.00 2.52
1171 1209 9.710818 AAATACATACTACTCCCTCTGTAAAGA 57.289 33.333 0.00 0.00 0.00 2.52
1172 1210 9.751542 CAAATACATACTACTCCCTCTGTAAAG 57.248 37.037 0.00 0.00 0.00 1.85
1173 1211 9.263446 ACAAATACATACTACTCCCTCTGTAAA 57.737 33.333 0.00 0.00 0.00 2.01
1174 1212 8.834004 ACAAATACATACTACTCCCTCTGTAA 57.166 34.615 0.00 0.00 0.00 2.41
1175 1213 8.057011 TGACAAATACATACTACTCCCTCTGTA 58.943 37.037 0.00 0.00 0.00 2.74
1176 1214 6.895756 TGACAAATACATACTACTCCCTCTGT 59.104 38.462 0.00 0.00 0.00 3.41
1177 1215 7.068839 ACTGACAAATACATACTACTCCCTCTG 59.931 40.741 0.00 0.00 0.00 3.35
1178 1216 7.126733 ACTGACAAATACATACTACTCCCTCT 58.873 38.462 0.00 0.00 0.00 3.69
1179 1217 7.349412 ACTGACAAATACATACTACTCCCTC 57.651 40.000 0.00 0.00 0.00 4.30
1180 1218 7.735326 AACTGACAAATACATACTACTCCCT 57.265 36.000 0.00 0.00 0.00 4.20
1181 1219 8.258708 AGAAACTGACAAATACATACTACTCCC 58.741 37.037 0.00 0.00 0.00 4.30
1190 1228 9.436957 CAGGTAAGTAGAAACTGACAAATACAT 57.563 33.333 0.00 0.00 38.70 2.29
1239 1288 5.212532 ACTGCAAATAATCAAAACAGCCA 57.787 34.783 0.00 0.00 0.00 4.75
1250 1299 8.611654 AAGCAAATCAAAGAACTGCAAATAAT 57.388 26.923 0.00 0.00 35.44 1.28
1256 1305 4.567558 CACAAAGCAAATCAAAGAACTGCA 59.432 37.500 0.00 0.00 35.44 4.41
1258 1307 6.310956 TCAACACAAAGCAAATCAAAGAACTG 59.689 34.615 0.00 0.00 0.00 3.16
1266 1330 6.571605 TCTCAATTCAACACAAAGCAAATCA 58.428 32.000 0.00 0.00 0.00 2.57
1273 1337 3.003689 ACGCCTCTCAATTCAACACAAAG 59.996 43.478 0.00 0.00 0.00 2.77
1301 1368 3.662148 TGGTATCCATATTTGCCCCAGAT 59.338 43.478 0.00 0.00 0.00 2.90
1314 1383 7.391554 GTGTAAGATGCATAACATGGTATCCAT 59.608 37.037 6.90 6.90 46.37 3.41
1321 1390 6.932356 AGAAGTGTAAGATGCATAACATGG 57.068 37.500 0.00 0.00 39.84 3.66
1350 1422 7.282332 ACGAAGTAGGTAAAAACTAGTGACT 57.718 36.000 0.00 0.00 41.94 3.41
1372 1444 0.951040 GAAGGTGCACCAGAGGAACG 60.951 60.000 36.39 0.00 38.89 3.95
1449 1523 9.788960 GTCAAGAAGAAATCAACTTTGTAGTTT 57.211 29.630 0.00 0.00 41.85 2.66
1576 1652 3.511477 AGATAGTTATGGGCCGATCACT 58.489 45.455 17.39 17.39 0.00 3.41
1604 1680 2.180276 GGTATAGATGGAGGCGTGGAT 58.820 52.381 0.00 0.00 0.00 3.41
1663 1739 5.039480 GATGAATTCATCGCATAGGGTTG 57.961 43.478 27.90 0.00 42.66 3.77
1676 1752 1.672363 GCGCACCAGATGATGAATTCA 59.328 47.619 11.26 11.26 39.12 2.57
1677 1753 1.945394 AGCGCACCAGATGATGAATTC 59.055 47.619 11.47 0.00 0.00 2.17
1678 1754 2.048444 AGCGCACCAGATGATGAATT 57.952 45.000 11.47 0.00 0.00 2.17
1679 1755 2.763933 CTAGCGCACCAGATGATGAAT 58.236 47.619 11.47 0.00 0.00 2.57
1680 1756 1.807755 GCTAGCGCACCAGATGATGAA 60.808 52.381 11.47 0.00 35.78 2.57
1681 1757 0.249615 GCTAGCGCACCAGATGATGA 60.250 55.000 11.47 0.00 35.78 2.92
1682 1758 1.226686 GGCTAGCGCACCAGATGATG 61.227 60.000 11.47 0.00 38.10 3.07
1683 1759 1.070445 GGCTAGCGCACCAGATGAT 59.930 57.895 11.47 0.00 38.10 2.45
1684 1760 2.501128 GGCTAGCGCACCAGATGA 59.499 61.111 11.47 0.00 38.10 2.92
1685 1761 2.963854 CGGCTAGCGCACCAGATG 60.964 66.667 11.47 0.00 38.10 2.90
1686 1762 4.899239 GCGGCTAGCGCACCAGAT 62.899 66.667 21.32 0.00 38.10 2.90
1696 1772 1.590238 CGAAGAATTGTGAGCGGCTAG 59.410 52.381 0.60 0.00 0.00 3.42
1697 1773 1.203758 TCGAAGAATTGTGAGCGGCTA 59.796 47.619 0.60 0.00 0.00 3.93
1698 1774 0.037326 TCGAAGAATTGTGAGCGGCT 60.037 50.000 0.00 0.00 0.00 5.52
1699 1775 0.095417 GTCGAAGAATTGTGAGCGGC 59.905 55.000 0.00 0.00 39.69 6.53
1700 1776 0.366871 CGTCGAAGAATTGTGAGCGG 59.633 55.000 0.00 0.00 39.69 5.52
1701 1777 0.246912 GCGTCGAAGAATTGTGAGCG 60.247 55.000 1.37 0.00 39.69 5.03
1702 1778 1.071605 AGCGTCGAAGAATTGTGAGC 58.928 50.000 1.37 0.00 39.69 4.26
1703 1779 2.061773 ACAGCGTCGAAGAATTGTGAG 58.938 47.619 1.37 0.00 39.69 3.51
1704 1780 2.148916 ACAGCGTCGAAGAATTGTGA 57.851 45.000 1.37 0.00 39.69 3.58
1705 1781 2.949714 AACAGCGTCGAAGAATTGTG 57.050 45.000 1.37 0.00 39.69 3.33
1706 1782 3.131396 AGAAACAGCGTCGAAGAATTGT 58.869 40.909 1.37 0.24 39.69 2.71
1707 1783 3.795561 AGAAACAGCGTCGAAGAATTG 57.204 42.857 1.37 0.00 39.69 2.32
1708 1784 5.869888 AGATTAGAAACAGCGTCGAAGAATT 59.130 36.000 1.37 0.00 39.69 2.17
1709 1785 5.411781 AGATTAGAAACAGCGTCGAAGAAT 58.588 37.500 1.37 0.00 39.69 2.40
1710 1786 4.806330 AGATTAGAAACAGCGTCGAAGAA 58.194 39.130 1.37 0.00 39.69 2.52
1711 1787 4.156190 AGAGATTAGAAACAGCGTCGAAGA 59.844 41.667 1.37 0.00 0.00 2.87
1712 1788 4.416620 AGAGATTAGAAACAGCGTCGAAG 58.583 43.478 0.00 0.00 0.00 3.79
1713 1789 4.413087 GAGAGATTAGAAACAGCGTCGAA 58.587 43.478 0.00 0.00 0.00 3.71
1714 1790 3.181499 GGAGAGATTAGAAACAGCGTCGA 60.181 47.826 0.00 0.00 0.00 4.20
1715 1791 3.109619 GGAGAGATTAGAAACAGCGTCG 58.890 50.000 0.00 0.00 0.00 5.12
1716 1792 4.111375 TGGAGAGATTAGAAACAGCGTC 57.889 45.455 0.00 0.00 0.00 5.19
1717 1793 4.160439 TCATGGAGAGATTAGAAACAGCGT 59.840 41.667 0.00 0.00 0.00 5.07
1718 1794 4.686972 TCATGGAGAGATTAGAAACAGCG 58.313 43.478 0.00 0.00 0.00 5.18
1719 1795 5.404968 CGATCATGGAGAGATTAGAAACAGC 59.595 44.000 0.00 0.00 0.00 4.40
1720 1796 5.925397 CCGATCATGGAGAGATTAGAAACAG 59.075 44.000 0.00 0.00 0.00 3.16
1721 1797 5.740224 GCCGATCATGGAGAGATTAGAAACA 60.740 44.000 0.00 0.00 0.00 2.83
1722 1798 4.688413 GCCGATCATGGAGAGATTAGAAAC 59.312 45.833 0.00 0.00 0.00 2.78
1723 1799 4.262635 GGCCGATCATGGAGAGATTAGAAA 60.263 45.833 0.00 0.00 0.00 2.52
1724 1800 3.259374 GGCCGATCATGGAGAGATTAGAA 59.741 47.826 0.00 0.00 0.00 2.10
1725 1801 2.828520 GGCCGATCATGGAGAGATTAGA 59.171 50.000 0.00 0.00 0.00 2.10
1726 1802 2.093764 GGGCCGATCATGGAGAGATTAG 60.094 54.545 0.00 0.00 0.00 1.73
1727 1803 1.902508 GGGCCGATCATGGAGAGATTA 59.097 52.381 0.00 0.00 0.00 1.75
1728 1804 0.689623 GGGCCGATCATGGAGAGATT 59.310 55.000 0.00 0.00 0.00 2.40
1729 1805 0.472543 TGGGCCGATCATGGAGAGAT 60.473 55.000 0.00 0.00 0.00 2.75
1730 1806 0.472543 ATGGGCCGATCATGGAGAGA 60.473 55.000 0.00 0.00 0.00 3.10
1731 1807 1.269958 TATGGGCCGATCATGGAGAG 58.730 55.000 2.36 0.00 0.00 3.20
1732 1808 1.347707 GTTATGGGCCGATCATGGAGA 59.652 52.381 2.36 0.00 0.00 3.71
1733 1809 1.349026 AGTTATGGGCCGATCATGGAG 59.651 52.381 2.36 0.00 0.00 3.86
1734 1810 1.434188 AGTTATGGGCCGATCATGGA 58.566 50.000 2.36 0.00 0.00 3.41
1735 1811 3.198635 AGATAGTTATGGGCCGATCATGG 59.801 47.826 2.36 0.00 0.00 3.66
1736 1812 4.478206 AGATAGTTATGGGCCGATCATG 57.522 45.455 2.36 0.00 0.00 3.07
1737 1813 5.023452 TGTAGATAGTTATGGGCCGATCAT 58.977 41.667 2.36 0.09 0.00 2.45
1770 1846 2.379226 ACGGCTAGGTATAGATGGAGGT 59.621 50.000 0.00 0.00 0.00 3.85
1831 1912 2.204237 CCAGATGATGAATTCGTCGCA 58.796 47.619 20.10 7.25 43.90 5.10
1973 3094 0.747255 AGGTGCTAGATGTCGCGATT 59.253 50.000 14.06 2.40 0.00 3.34
2059 3186 3.325870 ACACACGGAACACATACTGATG 58.674 45.455 0.00 0.00 39.16 3.07
2083 3217 7.677454 ACACAGGTCGTATACATATCGATTA 57.323 36.000 1.71 0.00 36.08 1.75
2091 3225 3.691118 ACGTGTACACAGGTCGTATACAT 59.309 43.478 24.98 0.00 40.49 2.29
2134 3276 6.392625 AGCGTAAGAGATGATTAGTGCTAA 57.607 37.500 0.00 0.00 43.02 3.09
2253 3396 6.841755 TCTGAAATAAGAAAGGGGGACAAAAA 59.158 34.615 0.00 0.00 0.00 1.94
2254 3397 6.377912 TCTGAAATAAGAAAGGGGGACAAAA 58.622 36.000 0.00 0.00 0.00 2.44
2255 3398 5.959512 TCTGAAATAAGAAAGGGGGACAAA 58.040 37.500 0.00 0.00 0.00 2.83
2256 3399 5.592587 TCTGAAATAAGAAAGGGGGACAA 57.407 39.130 0.00 0.00 0.00 3.18
2257 3400 5.163034 TGTTCTGAAATAAGAAAGGGGGACA 60.163 40.000 0.00 0.00 37.90 4.02
2258 3401 5.321927 TGTTCTGAAATAAGAAAGGGGGAC 58.678 41.667 0.00 0.00 37.90 4.46
2274 3417 0.609681 TGCAGCATGGCATGTTCTGA 60.610 50.000 28.30 16.02 39.25 3.27
2275 3418 1.887301 TGCAGCATGGCATGTTCTG 59.113 52.632 26.94 24.69 39.25 3.02
2276 3419 4.426971 TGCAGCATGGCATGTTCT 57.573 50.000 26.94 14.69 39.25 3.01
2323 3481 6.732154 TCTCGGGTAATTTGAAGTATACGAG 58.268 40.000 15.06 15.06 38.10 4.18
2325 3483 6.501781 ACTCTCGGGTAATTTGAAGTATACG 58.498 40.000 0.00 0.00 0.00 3.06
2326 3484 9.807649 TTTACTCTCGGGTAATTTGAAGTATAC 57.192 33.333 0.00 0.00 32.64 1.47
2340 3498 4.806640 TCCGTTTTATTTACTCTCGGGT 57.193 40.909 0.00 0.00 37.54 5.28
2342 3500 6.716898 AAGTTCCGTTTTATTTACTCTCGG 57.283 37.500 0.00 0.00 38.16 4.63
2354 3512 9.917129 AATTCCGAATTAAATAAGTTCCGTTTT 57.083 25.926 4.46 0.00 0.00 2.43
2398 3556 7.912056 TGAAACTGAAGATATGAACTGAAGG 57.088 36.000 0.00 0.00 0.00 3.46
2409 3567 9.567776 TTCAGGTTTACAATGAAACTGAAGATA 57.432 29.630 11.95 0.00 38.97 1.98
2412 3570 7.930217 TCTTCAGGTTTACAATGAAACTGAAG 58.070 34.615 26.75 26.75 38.97 3.02
2490 3648 3.806521 GTCACTTTCGATGGATCTGATGG 59.193 47.826 0.00 0.00 0.00 3.51
2603 3761 3.539593 TTCTGTCCGGGGAGGCTCA 62.540 63.158 17.69 0.00 40.77 4.26
2609 3767 0.765135 TTTCACCTTCTGTCCGGGGA 60.765 55.000 0.00 0.00 0.00 4.81
2612 3770 2.744202 CAAGATTTCACCTTCTGTCCGG 59.256 50.000 0.00 0.00 0.00 5.14
2624 3782 4.556233 AGTTCGACGATGACAAGATTTCA 58.444 39.130 0.00 0.00 0.00 2.69
2919 4077 2.275318 CTCCGTCTGAGCAGGAAAATC 58.725 52.381 0.00 0.00 33.47 2.17
2999 4157 4.532126 ACCAGAAGTCTGTTATCACCATCA 59.468 41.667 7.51 0.00 42.27 3.07
3318 4476 8.196802 TCAGAGTCAACATTATATTTCAACCG 57.803 34.615 0.00 0.00 0.00 4.44
3502 4660 2.693074 TGTTGCGATATACTCTGGAGCA 59.307 45.455 0.00 0.00 0.00 4.26
3604 4762 5.165676 CCAACATCAACATCCATTTGTCAG 58.834 41.667 0.00 0.00 0.00 3.51
3611 4769 3.744940 AGACCCAACATCAACATCCAT 57.255 42.857 0.00 0.00 0.00 3.41
3612 4770 3.420893 GAAGACCCAACATCAACATCCA 58.579 45.455 0.00 0.00 0.00 3.41
3613 4771 2.755103 GGAAGACCCAACATCAACATCC 59.245 50.000 0.00 0.00 34.14 3.51
3634 4792 8.475639 TCAACTTAGGTTTAGCTAATACAGAGG 58.524 37.037 7.08 4.15 32.73 3.69
3662 4820 6.623329 TGGGATGATTTAGGCCAGAAAATAT 58.377 36.000 5.01 4.05 0.00 1.28
3670 4828 3.335748 AGGTATGGGATGATTTAGGCCA 58.664 45.455 5.01 0.00 0.00 5.36
3972 5155 9.935682 CGTTCATTTCTTATGCACAGTATAATT 57.064 29.630 0.00 0.00 0.00 1.40
3975 5158 8.710835 TTCGTTCATTTCTTATGCACAGTATA 57.289 30.769 0.00 0.00 0.00 1.47
3979 5162 9.507280 AAATATTCGTTCATTTCTTATGCACAG 57.493 29.630 0.00 0.00 0.00 3.66
4191 5385 1.667830 GTACAGCCTGCGCTTGTCA 60.668 57.895 9.73 0.00 45.55 3.58
4359 5553 3.854809 GCGGCGACATTAAATTGCTTTTA 59.145 39.130 12.98 0.00 0.00 1.52
4372 5566 2.742372 GTCAACCTGCGGCGACAT 60.742 61.111 12.98 0.00 31.33 3.06
4407 5601 1.756408 TTGGCGACTTTGGGACGGTA 61.756 55.000 0.00 0.00 0.00 4.02
4416 5610 1.678970 GCCCCTCATTGGCGACTTT 60.679 57.895 0.00 0.00 39.48 2.66
4517 5711 3.238597 CATCTCTCTCCCCCTTCTAAGG 58.761 54.545 1.47 1.47 46.06 2.69
4526 5720 2.296073 ACGGATACATCTCTCTCCCC 57.704 55.000 0.00 0.00 0.00 4.81
4616 5810 2.482316 CCGTAGTCATATTCCGTGCCAA 60.482 50.000 0.00 0.00 0.00 4.52
4735 5931 5.221803 ACAAGGGATCATCCAGTATCATGTC 60.222 44.000 5.89 0.00 38.64 3.06
4736 5932 4.662179 ACAAGGGATCATCCAGTATCATGT 59.338 41.667 5.89 0.00 38.64 3.21
4737 5933 5.238624 ACAAGGGATCATCCAGTATCATG 57.761 43.478 5.89 0.00 38.64 3.07
4738 5934 5.370584 TCAACAAGGGATCATCCAGTATCAT 59.629 40.000 5.89 0.00 38.64 2.45
4739 5935 4.721274 TCAACAAGGGATCATCCAGTATCA 59.279 41.667 5.89 0.00 38.64 2.15
4742 5941 3.843619 TGTCAACAAGGGATCATCCAGTA 59.156 43.478 5.89 0.00 38.64 2.74
4753 5952 3.885297 AGTTTCTGTCATGTCAACAAGGG 59.115 43.478 0.00 0.00 0.00 3.95
4754 5953 4.336433 ACAGTTTCTGTCATGTCAACAAGG 59.664 41.667 0.00 0.00 41.21 3.61
4755 5954 5.268544 CACAGTTTCTGTCATGTCAACAAG 58.731 41.667 0.00 0.00 43.43 3.16
4782 5981 2.202236 GAAGCCTGGACATGCTCCCA 62.202 60.000 0.00 6.83 38.49 4.37
4791 5990 2.092323 GGTAACCAATGAAGCCTGGAC 58.908 52.381 0.00 0.00 36.49 4.02
4895 6101 1.829222 AGGAATTGCAATTGCCTGAGG 59.171 47.619 32.26 0.00 41.18 3.86
5029 6236 8.225416 ACCCAAGAGACATACATCTAGTACATA 58.775 37.037 0.00 0.00 35.05 2.29
5146 6353 5.048013 TGTCGAGAAATGAGACACACTGTAT 60.048 40.000 0.00 0.00 39.63 2.29
5326 6533 7.872138 AGGATTCAAGGTTTATCATTGGTCTA 58.128 34.615 0.00 0.00 38.23 2.59
5434 6670 7.391148 AATCAACTGAGTACAAAGTGTTGTT 57.609 32.000 0.00 0.00 46.01 2.83
5439 6675 6.483307 TCTGGAAATCAACTGAGTACAAAGTG 59.517 38.462 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.