Multiple sequence alignment - TraesCS7D01G014800

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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 TraesCS7D01G014800 chr7D 100.000 8475 0 0 1 8475 6479296 6470822 0.000000e+00 15651.0
1 TraesCS7D01G014800 chr7D 80.000 305 24 19 12 313 561800635 561800905 3.120000e-44 191.0
2 TraesCS7D01G014800 chr7A 91.403 8631 405 156 23 8468 7593988 7585510 0.000000e+00 11516.0
3 TraesCS7D01G014800 chr4A 93.697 6410 274 64 1341 7674 733705630 733711985 0.000000e+00 9479.0
4 TraesCS7D01G014800 chr4A 92.298 766 32 14 7712 8464 733712150 733712901 0.000000e+00 1062.0
5 TraesCS7D01G014800 chr4A 80.235 850 98 45 51 889 733699486 733700276 7.380000e-160 575.0
6 TraesCS7D01G014800 chr4A 81.400 457 52 20 197 629 662781372 662780925 8.150000e-90 342.0
7 TraesCS7D01G014800 chr4A 95.050 101 4 1 12 111 662781495 662781395 3.170000e-34 158.0
8 TraesCS7D01G014800 chr1B 85.438 673 86 7 4218 4884 683126114 683126780 0.000000e+00 689.0
9 TraesCS7D01G014800 chr1B 84.571 350 38 3 5764 6110 683132882 683133218 4.900000e-87 333.0
10 TraesCS7D01G014800 chr1D 84.772 591 55 17 4981 5569 490421990 490422547 2.070000e-155 560.0
11 TraesCS7D01G014800 chr1D 85.203 419 43 10 4214 4616 490420863 490421278 6.120000e-111 412.0
12 TraesCS7D01G014800 chr1D 79.487 546 44 23 5675 6198 490422545 490423044 8.200000e-85 326.0
13 TraesCS7D01G014800 chr1D 86.611 239 31 1 4650 4888 490421279 490421516 6.520000e-66 263.0
14 TraesCS7D01G014800 chr4B 85.020 494 42 19 197 670 44859747 44859266 2.770000e-129 473.0
15 TraesCS7D01G014800 chr4B 83.766 462 47 17 197 637 44631285 44630831 6.120000e-111 412.0
16 TraesCS7D01G014800 chr4B 95.146 103 4 1 10 111 44631410 44631308 2.450000e-35 161.0
17 TraesCS7D01G014800 chr1A 89.241 158 14 3 3091 3246 8628974 8628818 2.410000e-45 195.0
18 TraesCS7D01G014800 chr2D 90.000 70 5 1 8106 8173 118357780 118357849 1.170000e-13 89.8


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 TraesCS7D01G014800 chr7D 6470822 6479296 8474 True 15651.00 15651 100.00000 1 8475 1 chr7D.!!$R1 8474
1 TraesCS7D01G014800 chr7A 7585510 7593988 8478 True 11516.00 11516 91.40300 23 8468 1 chr7A.!!$R1 8445
2 TraesCS7D01G014800 chr4A 733705630 733712901 7271 False 5270.50 9479 92.99750 1341 8464 2 chr4A.!!$F2 7123
3 TraesCS7D01G014800 chr4A 733699486 733700276 790 False 575.00 575 80.23500 51 889 1 chr4A.!!$F1 838
4 TraesCS7D01G014800 chr4A 662780925 662781495 570 True 250.00 342 88.22500 12 629 2 chr4A.!!$R1 617
5 TraesCS7D01G014800 chr1B 683126114 683126780 666 False 689.00 689 85.43800 4218 4884 1 chr1B.!!$F1 666
6 TraesCS7D01G014800 chr1D 490420863 490423044 2181 False 390.25 560 84.01825 4214 6198 4 chr1D.!!$F1 1984
7 TraesCS7D01G014800 chr4B 44630831 44631410 579 True 286.50 412 89.45600 10 637 2 chr4B.!!$R2 627

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
295 318 0.251209 AGTCGTCCAGTACAGCCTGA 60.251 55.000 0.00 0.0 34.23 3.86 F
1251 1358 0.038343 CGTTCGTTTTCCCCCGTCTA 60.038 55.000 0.00 0.0 0.00 2.59 F
1299 1415 0.324738 TGCAGGAGGAGGATTCTCGT 60.325 55.000 0.00 0.0 40.85 4.18 F
1672 1805 0.814010 ACGTTTGTCTGTCTGTGCCC 60.814 55.000 0.00 0.0 0.00 5.36 F
2300 2440 0.108898 TGGTTTGTGCTTGTGTGTGC 60.109 50.000 0.00 0.0 0.00 4.57 F
3858 4027 1.207089 CACTTCCATCTGGAGGCGTTA 59.793 52.381 8.17 0.0 46.36 3.18 F
4695 4881 2.037902 TGTGTTTATTCTGTCTCCGCCA 59.962 45.455 0.00 0.0 0.00 5.69 F
5367 5944 1.508088 GGCTGTTTTGGATGAGCCG 59.492 57.895 0.00 0.0 41.61 5.52 F
5680 6259 0.169672 CAAGGATGCGCCAGTTTCTG 59.830 55.000 4.18 0.0 40.02 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 1739 0.036388 GGGTTCATGTCGCAGGAAGA 60.036 55.000 7.08 0.0 34.86 2.87 R
2273 2413 0.311790 AAGCACAAACCAGCACATCG 59.688 50.000 0.00 0.0 0.00 3.84 R
2282 2422 1.139226 CGCACACACAAGCACAAACC 61.139 55.000 0.00 0.0 0.00 3.27 R
3112 3270 1.591703 CGCAGGAGCTGGTAGAACA 59.408 57.895 0.00 0.0 39.10 3.18 R
4007 4176 0.598065 ATGCGTTGCCAAAGAACTCC 59.402 50.000 0.00 0.0 0.00 3.85 R
5217 5791 0.107703 TACCAGCATGCCTGTACTGC 60.108 55.000 15.66 0.0 40.06 4.40 R
5670 6249 0.322546 ATCCCCGAACAGAAACTGGC 60.323 55.000 0.00 0.0 35.51 4.85 R
7214 7856 0.396695 TTCCTCCCCGACGAGCTATT 60.397 55.000 0.00 0.0 0.00 1.73 R
7619 8278 0.539051 ATTCCTCCCGCTCTGTTGAG 59.461 55.000 0.00 0.0 42.96 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
28 29 2.608546 CACGGTCGGAACAAGTTAACAA 59.391 45.455 8.61 0.00 0.00 2.83
60 61 8.163408 AGTAGTGCAGGGCAATATGATTAATTA 58.837 33.333 1.57 0.00 41.02 1.40
125 130 3.862877 TGGTAACAGATGGATGGATGG 57.137 47.619 0.00 0.00 46.17 3.51
126 131 3.392730 TGGTAACAGATGGATGGATGGA 58.607 45.455 0.00 0.00 46.17 3.41
129 134 4.042062 GGTAACAGATGGATGGATGGATGA 59.958 45.833 0.00 0.00 0.00 2.92
131 136 5.335028 AACAGATGGATGGATGGATGATT 57.665 39.130 0.00 0.00 0.00 2.57
133 138 6.458630 ACAGATGGATGGATGGATGATTTA 57.541 37.500 0.00 0.00 0.00 1.40
135 140 5.353400 CAGATGGATGGATGGATGATTTACG 59.647 44.000 0.00 0.00 0.00 3.18
136 141 4.972751 TGGATGGATGGATGATTTACGA 57.027 40.909 0.00 0.00 0.00 3.43
137 142 4.641396 TGGATGGATGGATGATTTACGAC 58.359 43.478 0.00 0.00 0.00 4.34
140 145 1.798813 GGATGGATGATTTACGACGCC 59.201 52.381 0.00 0.00 0.00 5.68
141 146 2.479837 GATGGATGATTTACGACGCCA 58.520 47.619 0.00 0.00 0.00 5.69
142 147 1.934589 TGGATGATTTACGACGCCAG 58.065 50.000 0.00 0.00 0.00 4.85
143 148 1.206132 TGGATGATTTACGACGCCAGT 59.794 47.619 0.00 0.00 0.00 4.00
144 149 1.593006 GGATGATTTACGACGCCAGTG 59.407 52.381 0.00 0.00 0.00 3.66
145 150 1.004927 GATGATTTACGACGCCAGTGC 60.005 52.381 0.00 0.00 0.00 4.40
204 209 4.733542 TAACCGCTGGGCCCAAGC 62.734 66.667 28.29 27.60 36.48 4.01
255 265 1.342374 GCCAAGTTCCATGGGGATTCT 60.342 52.381 13.02 0.75 44.48 2.40
263 273 4.402616 TCCATGGGGATTCTTTCAGTTT 57.597 40.909 13.02 0.00 38.64 2.66
268 278 4.575885 TGGGGATTCTTTCAGTTTAGACG 58.424 43.478 0.00 0.00 0.00 4.18
271 281 4.392138 GGGATTCTTTCAGTTTAGACGTGG 59.608 45.833 0.00 0.00 0.00 4.94
295 318 0.251209 AGTCGTCCAGTACAGCCTGA 60.251 55.000 0.00 0.00 34.23 3.86
306 329 0.329596 ACAGCCTGAGGTCCAAATCC 59.670 55.000 0.00 0.00 0.00 3.01
315 338 3.831911 TGAGGTCCAAATCCAAATCAACC 59.168 43.478 0.00 0.00 0.00 3.77
349 372 2.287909 GCCTGATGTTCTACTCTAGCCG 60.288 54.545 0.00 0.00 0.00 5.52
428 451 4.933064 GGCGAGCCGATGGACGAG 62.933 72.222 0.00 0.00 45.77 4.18
432 455 3.532155 AGCCGATGGACGAGCTCC 61.532 66.667 8.47 0.00 45.77 4.70
449 476 3.217231 CGACCAGCCGGACCTAAT 58.783 61.111 5.05 0.00 35.59 1.73
450 477 1.520666 CGACCAGCCGGACCTAATT 59.479 57.895 5.05 0.00 35.59 1.40
451 478 0.748450 CGACCAGCCGGACCTAATTA 59.252 55.000 5.05 0.00 35.59 1.40
452 479 1.137479 CGACCAGCCGGACCTAATTAA 59.863 52.381 5.05 0.00 35.59 1.40
454 481 1.134189 ACCAGCCGGACCTAATTAAGC 60.134 52.381 5.05 0.00 35.59 3.09
455 482 1.594331 CAGCCGGACCTAATTAAGCC 58.406 55.000 5.05 0.00 0.00 4.35
457 484 0.883370 GCCGGACCTAATTAAGCCCG 60.883 60.000 5.05 2.08 38.72 6.13
458 485 0.754472 CCGGACCTAATTAAGCCCGA 59.246 55.000 10.09 0.00 40.33 5.14
459 486 1.139455 CCGGACCTAATTAAGCCCGAA 59.861 52.381 10.09 0.00 40.33 4.30
480 507 1.546323 CCCAACCAGCAGACAAGACAT 60.546 52.381 0.00 0.00 0.00 3.06
506 560 3.090532 GGGTGGAGGAGGCGGAAT 61.091 66.667 0.00 0.00 0.00 3.01
507 561 2.506472 GGTGGAGGAGGCGGAATC 59.494 66.667 0.00 0.00 0.00 2.52
553 607 3.934391 CTTGTCGTGCTCCGGGTCC 62.934 68.421 0.00 0.00 37.11 4.46
691 751 3.083997 ACCCACGCCTCAGATCCC 61.084 66.667 0.00 0.00 0.00 3.85
697 781 2.206536 CGCCTCAGATCCCCTCTCC 61.207 68.421 0.00 0.00 29.16 3.71
714 798 2.972713 TCTCCCTCTCTCTCTCTCTAGC 59.027 54.545 0.00 0.00 0.00 3.42
718 802 2.439507 CCTCTCTCTCTCTCTAGCCTGT 59.560 54.545 0.00 0.00 0.00 4.00
744 834 4.280819 TGAGGAATGGAATGGAATGGAAC 58.719 43.478 0.00 0.00 0.00 3.62
745 835 4.017222 TGAGGAATGGAATGGAATGGAACT 60.017 41.667 0.00 0.00 0.00 3.01
747 837 4.231426 AGGAATGGAATGGAATGGAACTCT 59.769 41.667 0.00 0.00 0.00 3.24
773 865 2.288778 CCAGCAGCAGAGTCCTCCA 61.289 63.158 0.00 0.00 0.00 3.86
777 869 2.284995 AGCAGAGTCCTCCACCCC 60.285 66.667 0.00 0.00 0.00 4.95
779 871 2.363172 GCAGAGTCCTCCACCCCTC 61.363 68.421 0.00 0.00 0.00 4.30
780 872 1.079256 CAGAGTCCTCCACCCCTCA 59.921 63.158 0.00 0.00 0.00 3.86
781 873 1.079438 AGAGTCCTCCACCCCTCAC 59.921 63.158 0.00 0.00 0.00 3.51
784 876 2.122729 TCCTCCACCCCTCACCTG 59.877 66.667 0.00 0.00 0.00 4.00
785 877 3.721706 CCTCCACCCCTCACCTGC 61.722 72.222 0.00 0.00 0.00 4.85
786 878 3.721706 CTCCACCCCTCACCTGCC 61.722 72.222 0.00 0.00 0.00 4.85
989 1095 4.054359 TCTCTCTCCTGTTAGCTTCCTT 57.946 45.455 0.00 0.00 0.00 3.36
991 1097 3.100671 TCTCTCCTGTTAGCTTCCTTCC 58.899 50.000 0.00 0.00 0.00 3.46
992 1098 3.103742 CTCTCCTGTTAGCTTCCTTCCT 58.896 50.000 0.00 0.00 0.00 3.36
993 1099 3.100671 TCTCCTGTTAGCTTCCTTCCTC 58.899 50.000 0.00 0.00 0.00 3.71
994 1100 3.103742 CTCCTGTTAGCTTCCTTCCTCT 58.896 50.000 0.00 0.00 0.00 3.69
995 1101 2.834549 TCCTGTTAGCTTCCTTCCTCTG 59.165 50.000 0.00 0.00 0.00 3.35
996 1102 2.569404 CCTGTTAGCTTCCTTCCTCTGT 59.431 50.000 0.00 0.00 0.00 3.41
997 1103 3.368948 CCTGTTAGCTTCCTTCCTCTGTC 60.369 52.174 0.00 0.00 0.00 3.51
998 1104 3.511477 TGTTAGCTTCCTTCCTCTGTCT 58.489 45.455 0.00 0.00 0.00 3.41
999 1105 3.259374 TGTTAGCTTCCTTCCTCTGTCTG 59.741 47.826 0.00 0.00 0.00 3.51
1000 1106 2.022718 AGCTTCCTTCCTCTGTCTGT 57.977 50.000 0.00 0.00 0.00 3.41
1001 1107 1.899142 AGCTTCCTTCCTCTGTCTGTC 59.101 52.381 0.00 0.00 0.00 3.51
1002 1108 1.899142 GCTTCCTTCCTCTGTCTGTCT 59.101 52.381 0.00 0.00 0.00 3.41
1043 1149 0.113385 ATCATCCCCGTCCGATCTCT 59.887 55.000 0.00 0.00 0.00 3.10
1045 1151 1.228613 ATCCCCGTCCGATCTCTCC 60.229 63.158 0.00 0.00 0.00 3.71
1047 1153 2.196229 CCCGTCCGATCTCTCCCT 59.804 66.667 0.00 0.00 0.00 4.20
1051 1157 1.532078 GTCCGATCTCTCCCTCCCC 60.532 68.421 0.00 0.00 0.00 4.81
1053 1159 2.784654 CCGATCTCTCCCTCCCCCT 61.785 68.421 0.00 0.00 0.00 4.79
1055 1161 1.725169 CGATCTCTCCCTCCCCCTCT 61.725 65.000 0.00 0.00 0.00 3.69
1091 1197 3.508840 GAGCACCCAAATCCGCCG 61.509 66.667 0.00 0.00 0.00 6.46
1094 1200 4.114997 CACCCAAATCCGCCGCAC 62.115 66.667 0.00 0.00 0.00 5.34
1160 1266 2.593436 CGGAAAACCCAGGTGCGT 60.593 61.111 0.00 0.00 34.14 5.24
1161 1267 2.903547 CGGAAAACCCAGGTGCGTG 61.904 63.158 0.00 0.00 34.14 5.34
1162 1268 2.335011 GAAAACCCAGGTGCGTGC 59.665 61.111 0.00 0.00 0.00 5.34
1215 1322 3.235355 GATTCGCCTCGGAATCGC 58.765 61.111 0.13 0.00 41.88 4.58
1221 1328 4.951963 CCTCGGAATCGCGAGGCC 62.952 72.222 21.02 17.11 44.06 5.19
1222 1329 4.951963 CTCGGAATCGCGAGGCCC 62.952 72.222 16.66 14.14 36.13 5.80
1242 1349 0.110956 GCGGTTCCTCGTTCGTTTTC 60.111 55.000 0.00 0.00 0.00 2.29
1247 1354 2.030958 CCTCGTTCGTTTTCCCCCG 61.031 63.158 0.00 0.00 0.00 5.73
1248 1355 1.301165 CTCGTTCGTTTTCCCCCGT 60.301 57.895 0.00 0.00 0.00 5.28
1249 1356 1.287041 CTCGTTCGTTTTCCCCCGTC 61.287 60.000 0.00 0.00 0.00 4.79
1250 1357 1.301165 CGTTCGTTTTCCCCCGTCT 60.301 57.895 0.00 0.00 0.00 4.18
1251 1358 0.038343 CGTTCGTTTTCCCCCGTCTA 60.038 55.000 0.00 0.00 0.00 2.59
1253 1360 1.800586 GTTCGTTTTCCCCCGTCTAAC 59.199 52.381 0.00 0.00 0.00 2.34
1254 1361 1.341080 TCGTTTTCCCCCGTCTAACT 58.659 50.000 0.00 0.00 0.00 2.24
1255 1362 1.273327 TCGTTTTCCCCCGTCTAACTC 59.727 52.381 0.00 0.00 0.00 3.01
1256 1363 1.274447 CGTTTTCCCCCGTCTAACTCT 59.726 52.381 0.00 0.00 0.00 3.24
1257 1364 2.696506 GTTTTCCCCCGTCTAACTCTG 58.303 52.381 0.00 0.00 0.00 3.35
1258 1365 0.611714 TTTCCCCCGTCTAACTCTGC 59.388 55.000 0.00 0.00 0.00 4.26
1296 1412 0.619832 TGCTGCAGGAGGAGGATTCT 60.620 55.000 17.12 0.00 33.18 2.40
1299 1415 0.324738 TGCAGGAGGAGGATTCTCGT 60.325 55.000 0.00 0.00 40.85 4.18
1386 1504 2.548920 CCGTGGGATGAGCTAGATTTCC 60.549 54.545 0.00 0.00 0.00 3.13
1393 1511 3.802948 TGAGCTAGATTTCCTTCGACC 57.197 47.619 0.00 0.00 0.00 4.79
1394 1512 3.366396 TGAGCTAGATTTCCTTCGACCT 58.634 45.455 0.00 0.00 0.00 3.85
1395 1513 4.533815 TGAGCTAGATTTCCTTCGACCTA 58.466 43.478 0.00 0.00 0.00 3.08
1528 1659 1.227031 TTGCTGTTGCTGTTGCTGC 60.227 52.632 0.00 0.00 40.48 5.25
1559 1692 1.908483 GAGGCCCCCAAGTGAGTAG 59.092 63.158 0.00 0.00 0.00 2.57
1560 1693 0.910088 GAGGCCCCCAAGTGAGTAGT 60.910 60.000 0.00 0.00 0.00 2.73
1595 1728 3.352222 GCGCTGTCTGTTGCTGCT 61.352 61.111 0.00 0.00 0.00 4.24
1606 1739 3.177194 TTGCTGCTAGTGTGCCGGT 62.177 57.895 1.90 0.00 0.00 5.28
1672 1805 0.814010 ACGTTTGTCTGTCTGTGCCC 60.814 55.000 0.00 0.00 0.00 5.36
1698 1831 2.509166 ACATGAGGACGGTCTACTCA 57.491 50.000 16.10 16.10 44.44 3.41
1941 2076 2.181021 CAGTACACGACGCCCCTC 59.819 66.667 0.00 0.00 0.00 4.30
2149 2284 2.191128 AGCTCTGGGAACATGTGAAC 57.809 50.000 0.00 0.00 41.51 3.18
2158 2297 4.081365 TGGGAACATGTGAACGATTAGCTA 60.081 41.667 0.00 0.00 33.40 3.32
2159 2298 4.873827 GGGAACATGTGAACGATTAGCTAA 59.126 41.667 8.99 8.99 0.00 3.09
2160 2299 5.527582 GGGAACATGTGAACGATTAGCTAAT 59.472 40.000 18.92 18.92 0.00 1.73
2161 2300 6.704493 GGGAACATGTGAACGATTAGCTAATA 59.296 38.462 18.87 2.19 0.00 0.98
2162 2301 7.307219 GGGAACATGTGAACGATTAGCTAATAC 60.307 40.741 18.87 13.11 0.00 1.89
2163 2302 7.307219 GGAACATGTGAACGATTAGCTAATACC 60.307 40.741 18.87 6.99 0.00 2.73
2164 2303 5.690409 ACATGTGAACGATTAGCTAATACCG 59.310 40.000 18.87 19.63 0.00 4.02
2165 2304 4.613944 TGTGAACGATTAGCTAATACCGG 58.386 43.478 23.56 14.74 0.00 5.28
2166 2305 3.985925 GTGAACGATTAGCTAATACCGGG 59.014 47.826 23.56 12.89 0.00 5.73
2173 2312 6.886459 ACGATTAGCTAATACCGGGAATAGTA 59.114 38.462 23.56 0.00 0.00 1.82
2178 2317 9.759473 TTAGCTAATACCGGGAATAGTAGTTAT 57.241 33.333 10.56 0.00 0.00 1.89
2182 2321 9.635520 CTAATACCGGGAATAGTAGTTATGTTG 57.364 37.037 6.32 0.00 0.00 3.33
2183 2322 7.844493 ATACCGGGAATAGTAGTTATGTTGA 57.156 36.000 6.32 0.00 0.00 3.18
2220 2359 3.822735 CCACTCTGTGTTGGTGAAATGAT 59.177 43.478 0.00 0.00 33.32 2.45
2240 2380 6.751514 TGATATTTTTGTTGCGTATCAGGT 57.248 33.333 0.00 0.00 30.63 4.00
2241 2381 7.851387 TGATATTTTTGTTGCGTATCAGGTA 57.149 32.000 0.00 0.00 30.63 3.08
2253 2393 6.694447 TGCGTATCAGGTACTTTTTACTCTT 58.306 36.000 0.00 0.00 34.60 2.85
2282 2422 3.369546 AAAAAGAAACCCGATGTGCTG 57.630 42.857 0.00 0.00 0.00 4.41
2299 2439 1.912001 CTGGTTTGTGCTTGTGTGTG 58.088 50.000 0.00 0.00 0.00 3.82
2300 2440 0.108898 TGGTTTGTGCTTGTGTGTGC 60.109 50.000 0.00 0.00 0.00 4.57
2305 2447 2.202810 TGCTTGTGTGTGCGTCGA 60.203 55.556 0.00 0.00 0.00 4.20
2359 2501 9.935682 GTCAATTAATTACATGGTCATACTGTG 57.064 33.333 0.00 0.00 0.00 3.66
2405 2549 6.753913 TCTCTCCTGTGCATCCTAATTTAT 57.246 37.500 0.00 0.00 0.00 1.40
2616 2768 2.669569 GCGCCTCAGCCAAACAGA 60.670 61.111 0.00 0.00 34.57 3.41
2971 3129 7.851228 TGAGGAAAGAGCAACATAAATCTCTA 58.149 34.615 0.00 0.00 35.08 2.43
3112 3270 9.388506 CATCAAGATACCACTAAAACATCTTCT 57.611 33.333 0.00 0.00 34.53 2.85
3359 3517 9.520515 AAATTAGTTTACTGAACCATCACATCT 57.479 29.630 0.00 0.00 39.13 2.90
3360 3518 9.520515 AATTAGTTTACTGAACCATCACATCTT 57.479 29.630 0.00 0.00 39.13 2.40
3361 3519 8.547967 TTAGTTTACTGAACCATCACATCTTC 57.452 34.615 0.00 0.00 39.13 2.87
3379 3537 9.159364 CACATCTTCTTCTCTGTGATCAAAATA 57.841 33.333 0.00 0.00 41.11 1.40
3386 3544 9.035890 TCTTCTCTGTGATCAAAATAGGTCTAA 57.964 33.333 0.00 0.00 0.00 2.10
3429 3587 6.019318 GCTGACAGTTTTTACTCGTGTCTAAA 60.019 38.462 3.99 0.00 38.67 1.85
3430 3588 7.307219 GCTGACAGTTTTTACTCGTGTCTAAAT 60.307 37.037 3.99 0.00 38.67 1.40
3431 3589 8.068893 TGACAGTTTTTACTCGTGTCTAAATC 57.931 34.615 0.00 0.00 38.67 2.17
3432 3590 7.924412 TGACAGTTTTTACTCGTGTCTAAATCT 59.076 33.333 0.00 0.00 38.67 2.40
3447 3613 7.169982 GTGTCTAAATCTAATCGGTTCATCTGG 59.830 40.741 0.00 0.00 0.00 3.86
3587 3755 9.125026 GATGTGTTCATCAGTATAAAGGGAATT 57.875 33.333 3.72 0.00 46.78 2.17
3736 3905 5.363005 AGGATAAGTTACCGACTATTGTGCT 59.637 40.000 0.00 0.00 37.72 4.40
3807 3976 4.953940 AGCAACAAAAAGAAGGGCATTA 57.046 36.364 0.00 0.00 0.00 1.90
3815 3984 5.712152 AAAAGAAGGGCATTACTGACAAG 57.288 39.130 0.00 0.00 28.82 3.16
3858 4027 1.207089 CACTTCCATCTGGAGGCGTTA 59.793 52.381 8.17 0.00 46.36 3.18
3905 4074 6.641169 AAAATTCTGAAAGGAACTGAGGAC 57.359 37.500 0.00 0.00 40.86 3.85
3950 4119 9.383519 GATGATAAGTACTCCATTGAGAAACAA 57.616 33.333 0.00 0.00 41.42 2.83
3980 4149 2.908688 AAAATGGTGGTTCAGTTGGC 57.091 45.000 0.00 0.00 0.00 4.52
4007 4176 6.602406 AGGACAATTCAATCTCAATCTTGGAG 59.398 38.462 0.00 0.00 0.00 3.86
4324 4494 4.661993 TTTATGCTGTTCATGTCGTCAC 57.338 40.909 0.00 0.00 36.63 3.67
4343 4513 3.006752 TCACAAAATGCCAATGGGTCTTC 59.993 43.478 0.00 0.00 36.17 2.87
4695 4881 2.037902 TGTGTTTATTCTGTCTCCGCCA 59.962 45.455 0.00 0.00 0.00 5.69
4833 5019 5.733676 TGTGTCATATGCTATGTGTCAGTT 58.266 37.500 0.00 0.00 0.00 3.16
4845 5031 8.414003 TGCTATGTGTCAGTTAATAGAAGTAGG 58.586 37.037 0.00 0.00 0.00 3.18
4916 5473 2.314549 TCCCCCTTTCCAGTATGCAAAT 59.685 45.455 0.00 0.00 31.97 2.32
5068 5642 6.814043 TCCATGATTGTGAACAATGACAAAA 58.186 32.000 13.21 0.00 45.72 2.44
5191 5765 5.191722 TCAAGGCTACTACCATTTCCATCTT 59.808 40.000 0.00 0.00 0.00 2.40
5367 5944 1.508088 GGCTGTTTTGGATGAGCCG 59.492 57.895 0.00 0.00 41.61 5.52
5516 6095 4.940046 ACAGAGTTCTGATGTAAATGCCAG 59.060 41.667 15.63 0.00 46.59 4.85
5631 6210 3.119495 GCGTGACCTTGGAAGCATTATTT 60.119 43.478 0.00 0.00 0.00 1.40
5670 6249 0.465097 AGCTCCATTCCAAGGATGCG 60.465 55.000 0.00 0.00 35.69 4.73
5680 6259 0.169672 CAAGGATGCGCCAGTTTCTG 59.830 55.000 4.18 0.00 40.02 3.02
5797 6387 7.349412 ACTGGAATAGAGTACAGGAATACAC 57.651 40.000 0.00 0.00 35.34 2.90
6036 6630 1.807142 GAACCTGCTCAAGTACTTGGC 59.193 52.381 30.35 29.05 40.78 4.52
6360 6961 0.538287 AAGGCTTGCCAAGAGGTGTC 60.538 55.000 9.04 0.00 37.19 3.67
6474 7075 1.003580 GGAGACTTTGGACTGATGCCA 59.996 52.381 0.00 0.00 0.00 4.92
6503 7104 7.873505 AGGTAAGAGTCTGTACAAGTTCATTTC 59.126 37.037 0.00 0.00 0.00 2.17
6537 7138 5.856126 TTACTTGCAGTTTATTCCGTCAG 57.144 39.130 0.00 0.00 0.00 3.51
6543 7144 4.336993 TGCAGTTTATTCCGTCAGTGTTTT 59.663 37.500 0.00 0.00 0.00 2.43
6550 7151 3.479505 TCCGTCAGTGTTTTGTTTGTG 57.520 42.857 0.00 0.00 0.00 3.33
6638 7245 6.814506 ACTTCCAAAATCTGACATCTCTTG 57.185 37.500 0.00 0.00 0.00 3.02
6644 7251 7.173218 TCCAAAATCTGACATCTCTTGTTACAC 59.827 37.037 0.00 0.00 39.18 2.90
6658 7265 5.298276 TCTTGTTACACTCCACAAAATCCAC 59.702 40.000 0.00 0.00 32.53 4.02
6659 7266 4.787551 TGTTACACTCCACAAAATCCACT 58.212 39.130 0.00 0.00 0.00 4.00
6660 7267 4.819630 TGTTACACTCCACAAAATCCACTC 59.180 41.667 0.00 0.00 0.00 3.51
6661 7268 2.494059 ACACTCCACAAAATCCACTCG 58.506 47.619 0.00 0.00 0.00 4.18
6662 7269 2.104111 ACACTCCACAAAATCCACTCGA 59.896 45.455 0.00 0.00 0.00 4.04
6744 7354 3.632604 TGCGTCTTTTTGGTGGTTATGAA 59.367 39.130 0.00 0.00 0.00 2.57
6748 7358 5.912955 CGTCTTTTTGGTGGTTATGAACTTC 59.087 40.000 0.00 0.00 0.00 3.01
6750 7360 4.839668 TTTTGGTGGTTATGAACTTCCG 57.160 40.909 0.00 0.00 0.00 4.30
6875 7485 4.805719 GGCTTCTTGTTTTTCCAGTTTGAG 59.194 41.667 0.00 0.00 0.00 3.02
6888 7505 3.123621 CCAGTTTGAGTTATCAGACACGC 59.876 47.826 2.33 0.00 41.79 5.34
6922 7539 8.757164 AACCGTTCAATTTTATCCTGAATTTC 57.243 30.769 0.00 0.00 32.08 2.17
6945 7568 8.553459 TTCTTATGATCCAACTCTGTTTTCTC 57.447 34.615 0.00 0.00 0.00 2.87
6946 7569 7.911651 TCTTATGATCCAACTCTGTTTTCTCT 58.088 34.615 0.00 0.00 0.00 3.10
7130 7754 5.250235 TGAGATACAGATGAAGAACGACC 57.750 43.478 0.00 0.00 0.00 4.79
7145 7769 1.148273 GACCCTGTTGTGCCTGTCA 59.852 57.895 0.00 0.00 0.00 3.58
7152 7790 1.271325 TGTTGTGCCTGTCATACCCAG 60.271 52.381 0.00 0.00 0.00 4.45
7214 7856 4.611807 CGTTTGCGGTTGCTACAAGATAAA 60.612 41.667 0.00 0.00 43.34 1.40
7320 7966 3.008157 GCTGATGATGATCTGGTGAGGAT 59.992 47.826 1.53 0.00 0.00 3.24
7336 7982 1.556561 GATGGAGGGAGGGAGGGAT 59.443 63.158 0.00 0.00 0.00 3.85
7388 8034 1.676014 GCCACATCTGTACCTGTGTCC 60.676 57.143 15.16 6.22 40.89 4.02
7402 8052 0.597637 GTGTCCGTGTCTGTGTCTGG 60.598 60.000 0.00 0.00 0.00 3.86
7478 8129 3.723325 ACATATTTGCATTTGGTCCCCT 58.277 40.909 0.00 0.00 0.00 4.79
7479 8130 3.706086 ACATATTTGCATTTGGTCCCCTC 59.294 43.478 0.00 0.00 0.00 4.30
7480 8131 2.629017 ATTTGCATTTGGTCCCCTCT 57.371 45.000 0.00 0.00 0.00 3.69
7481 8132 1.631405 TTTGCATTTGGTCCCCTCTG 58.369 50.000 0.00 0.00 0.00 3.35
7482 8133 0.776810 TTGCATTTGGTCCCCTCTGA 59.223 50.000 0.00 0.00 0.00 3.27
7483 8134 0.038166 TGCATTTGGTCCCCTCTGAC 59.962 55.000 0.00 0.00 34.42 3.51
7484 8135 1.026718 GCATTTGGTCCCCTCTGACG 61.027 60.000 0.00 0.00 36.07 4.35
7490 8141 1.621814 TGGTCCCCTCTGACGTTTTAG 59.378 52.381 0.00 0.00 36.07 1.85
7491 8142 1.622312 GGTCCCCTCTGACGTTTTAGT 59.378 52.381 0.00 0.00 36.07 2.24
7495 8146 4.577693 GTCCCCTCTGACGTTTTAGTTTTT 59.422 41.667 0.00 0.00 0.00 1.94
7542 8196 3.131046 CACATCAACTGGGATAAAAGGCC 59.869 47.826 0.00 0.00 0.00 5.19
7559 8213 2.616842 AGGCCGTGACACAAAGTTAAAG 59.383 45.455 6.37 0.00 0.00 1.85
7561 8215 3.181494 GGCCGTGACACAAAGTTAAAGTT 60.181 43.478 6.37 0.00 0.00 2.66
7565 8219 5.510323 CCGTGACACAAAGTTAAAGTTCAAC 59.490 40.000 6.37 0.00 0.00 3.18
7613 8272 6.530019 GGATTTCATCCCTACACAATGTTT 57.470 37.500 0.00 0.00 43.88 2.83
7616 8275 7.545615 GGATTTCATCCCTACACAATGTTTTTC 59.454 37.037 0.00 0.00 43.88 2.29
7619 8278 4.846779 TCCCTACACAATGTTTTTCAGC 57.153 40.909 0.00 0.00 0.00 4.26
7626 8290 5.104374 ACACAATGTTTTTCAGCTCAACAG 58.896 37.500 0.00 0.00 34.00 3.16
7635 8299 2.125350 GCTCAACAGAGCGGGAGG 60.125 66.667 1.33 0.00 44.62 4.30
7644 8308 4.115199 AGCGGGAGGAATGCACCC 62.115 66.667 0.00 0.00 40.17 4.61
7666 8330 3.006110 CCATGCTGAACTTGATGGTGTTT 59.994 43.478 0.00 0.00 32.20 2.83
7693 8470 7.493743 TCAGTTTGTTGCGGTAAAATACTTA 57.506 32.000 0.00 0.00 0.00 2.24
7701 8478 8.569641 TGTTGCGGTAAAATACTTACTGAAATT 58.430 29.630 7.50 0.00 32.91 1.82
7705 8482 9.058424 GCGGTAAAATACTTACTGAAATTTGTC 57.942 33.333 0.00 0.00 34.10 3.18
7714 8491 8.394971 ACTTACTGAAATTTGTCACATGATCA 57.605 30.769 0.00 0.00 0.00 2.92
7716 8493 9.850628 CTTACTGAAATTTGTCACATGATCATT 57.149 29.630 5.16 0.00 0.00 2.57
7727 8517 7.764331 TGTCACATGATCATTACAAATCCAAG 58.236 34.615 5.16 0.00 0.00 3.61
7742 8532 8.606040 ACAAATCCAAGATTTGTATGTTTTGG 57.394 30.769 26.22 7.02 46.63 3.28
7766 8560 9.959749 TGGTCAATCTTAAAGAACAAATGTTAC 57.040 29.630 0.00 0.00 38.56 2.50
7790 8584 7.667557 ACCTTATAACCAAGAAAAGAAAAGGC 58.332 34.615 0.00 0.00 34.46 4.35
7791 8585 7.509318 ACCTTATAACCAAGAAAAGAAAAGGCT 59.491 33.333 0.00 0.00 34.46 4.58
7866 8662 0.320247 CTGAACTCTGAAGCAGCGGT 60.320 55.000 0.00 0.00 0.00 5.68
7879 8675 1.004918 AGCGGTACTGTGTTGGAGC 60.005 57.895 3.10 0.00 0.00 4.70
7891 8688 1.134340 TGTTGGAGCGTAGTGTGGTTT 60.134 47.619 0.00 0.00 0.00 3.27
7894 8691 0.320697 GGAGCGTAGTGTGGTTTCCT 59.679 55.000 0.00 0.00 0.00 3.36
7951 8757 4.770874 GAAACCCTAGCCGCCGCA 62.771 66.667 0.00 0.00 37.52 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.309950 GTTCCGACCGTGTGGCCT 62.310 66.667 3.32 0.00 39.70 5.19
2 3 4.612412 TGTTCCGACCGTGTGGCC 62.612 66.667 0.00 0.00 39.70 5.36
3 4 2.589442 TTGTTCCGACCGTGTGGC 60.589 61.111 0.00 0.00 39.70 5.01
4 5 0.812412 AACTTGTTCCGACCGTGTGG 60.812 55.000 0.00 0.00 42.84 4.17
5 6 1.855513 TAACTTGTTCCGACCGTGTG 58.144 50.000 0.00 0.00 0.00 3.82
6 7 2.204237 GTTAACTTGTTCCGACCGTGT 58.796 47.619 0.00 0.00 0.00 4.49
7 8 2.203401 TGTTAACTTGTTCCGACCGTG 58.797 47.619 7.22 0.00 0.00 4.94
8 9 2.600470 TGTTAACTTGTTCCGACCGT 57.400 45.000 7.22 0.00 0.00 4.83
14 15 7.908601 CACTACTTCACTTTGTTAACTTGTTCC 59.091 37.037 7.22 0.00 0.00 3.62
28 29 0.764890 TGCCCTGCACTACTTCACTT 59.235 50.000 0.00 0.00 31.71 3.16
68 69 9.606631 GGCCATTTACATTTGATTTTTACCATA 57.393 29.630 0.00 0.00 0.00 2.74
112 117 5.249163 TCGTAAATCATCCATCCATCCATCT 59.751 40.000 0.00 0.00 0.00 2.90
125 130 1.004927 GCACTGGCGTCGTAAATCATC 60.005 52.381 0.00 0.00 0.00 2.92
126 131 1.006832 GCACTGGCGTCGTAAATCAT 58.993 50.000 0.00 0.00 0.00 2.45
146 151 0.875908 TGCTATGCTCGATGCGGAAC 60.876 55.000 0.00 0.00 46.63 3.62
147 152 0.033920 ATGCTATGCTCGATGCGGAA 59.966 50.000 0.00 0.00 46.63 4.30
148 153 0.389037 GATGCTATGCTCGATGCGGA 60.389 55.000 0.00 0.00 46.63 5.54
194 199 2.931105 TTAGGACGCTTGGGCCCA 60.931 61.111 24.45 24.45 34.44 5.36
195 200 2.124695 CTTAGGACGCTTGGGCCC 60.125 66.667 17.59 17.59 34.44 5.80
204 209 2.625790 CAGGATCTCTTCCCTTAGGACG 59.374 54.545 0.00 0.00 46.81 4.79
255 265 2.361757 TCGTCCCACGTCTAAACTGAAA 59.638 45.455 0.00 0.00 43.14 2.69
263 273 1.004560 ACGACTCGTCCCACGTCTA 60.005 57.895 0.00 0.00 43.14 2.59
275 285 0.171455 CAGGCTGTACTGGACGACTC 59.829 60.000 6.28 0.00 34.84 3.36
283 293 0.976641 TTGGACCTCAGGCTGTACTG 59.023 55.000 15.27 4.24 39.84 2.74
295 318 3.834231 CTGGTTGATTTGGATTTGGACCT 59.166 43.478 0.00 0.00 0.00 3.85
306 329 0.245539 CTGCCTGCCTGGTTGATTTG 59.754 55.000 0.00 0.00 38.35 2.32
331 354 2.656002 AGCGGCTAGAGTAGAACATCA 58.344 47.619 0.00 0.00 0.00 3.07
432 455 0.748450 TAATTAGGTCCGGCTGGTCG 59.252 55.000 12.43 0.00 36.30 4.79
449 476 0.250989 CTGGTTGGGTTCGGGCTTAA 60.251 55.000 0.00 0.00 0.00 1.85
450 477 1.377229 CTGGTTGGGTTCGGGCTTA 59.623 57.895 0.00 0.00 0.00 3.09
451 478 2.115266 CTGGTTGGGTTCGGGCTT 59.885 61.111 0.00 0.00 0.00 4.35
452 479 4.660938 GCTGGTTGGGTTCGGGCT 62.661 66.667 0.00 0.00 0.00 5.19
454 481 2.672996 CTGCTGGTTGGGTTCGGG 60.673 66.667 0.00 0.00 0.00 5.14
455 482 1.966451 GTCTGCTGGTTGGGTTCGG 60.966 63.158 0.00 0.00 0.00 4.30
457 484 0.954452 CTTGTCTGCTGGTTGGGTTC 59.046 55.000 0.00 0.00 0.00 3.62
458 485 0.550914 TCTTGTCTGCTGGTTGGGTT 59.449 50.000 0.00 0.00 0.00 4.11
459 486 0.179018 GTCTTGTCTGCTGGTTGGGT 60.179 55.000 0.00 0.00 0.00 4.51
504 558 1.137872 CGCTCCTCCTGTAAGCAGATT 59.862 52.381 0.00 0.00 45.28 2.40
505 559 0.749649 CGCTCCTCCTGTAAGCAGAT 59.250 55.000 0.00 0.00 45.28 2.90
506 560 1.949847 GCGCTCCTCCTGTAAGCAGA 61.950 60.000 0.00 0.00 45.28 4.26
507 561 1.520342 GCGCTCCTCCTGTAAGCAG 60.520 63.158 0.00 0.00 42.22 4.24
645 705 2.441348 TGATGGAGTCGGCGGCTA 60.441 61.111 16.64 0.00 0.00 3.93
646 706 4.148825 GTGATGGAGTCGGCGGCT 62.149 66.667 16.62 16.62 0.00 5.52
691 751 2.412591 AGAGAGAGAGAGAGGGAGAGG 58.587 57.143 0.00 0.00 0.00 3.69
697 781 2.439507 ACAGGCTAGAGAGAGAGAGAGG 59.560 54.545 0.00 0.00 0.00 3.69
714 798 3.635373 CCATTCCATTCCTCATCAACAGG 59.365 47.826 0.00 0.00 0.00 4.00
718 802 4.897076 CCATTCCATTCCATTCCTCATCAA 59.103 41.667 0.00 0.00 0.00 2.57
793 885 4.796231 CGTCTCGCCTTCCCCACG 62.796 72.222 0.00 0.00 0.00 4.94
794 886 3.358076 CTCGTCTCGCCTTCCCCAC 62.358 68.421 0.00 0.00 0.00 4.61
795 887 3.068691 CTCGTCTCGCCTTCCCCA 61.069 66.667 0.00 0.00 0.00 4.96
796 888 3.839432 CCTCGTCTCGCCTTCCCC 61.839 72.222 0.00 0.00 0.00 4.81
797 889 2.754658 TCCTCGTCTCGCCTTCCC 60.755 66.667 0.00 0.00 0.00 3.97
890 982 0.250901 TGCTTTTCAGTCCCTGGAGC 60.251 55.000 0.00 0.00 35.03 4.70
892 984 2.746279 TTTGCTTTTCAGTCCCTGGA 57.254 45.000 0.00 0.00 31.51 3.86
894 986 3.670627 GCGTATTTGCTTTTCAGTCCCTG 60.671 47.826 0.00 0.00 0.00 4.45
895 987 2.488153 GCGTATTTGCTTTTCAGTCCCT 59.512 45.455 0.00 0.00 0.00 4.20
898 990 2.158841 TCCGCGTATTTGCTTTTCAGTC 59.841 45.455 4.92 0.00 0.00 3.51
899 991 2.147958 TCCGCGTATTTGCTTTTCAGT 58.852 42.857 4.92 0.00 0.00 3.41
901 993 1.135803 GCTCCGCGTATTTGCTTTTCA 60.136 47.619 4.92 0.00 0.00 2.69
902 994 1.135803 TGCTCCGCGTATTTGCTTTTC 60.136 47.619 4.92 0.00 0.00 2.29
904 996 0.168128 GTGCTCCGCGTATTTGCTTT 59.832 50.000 4.92 0.00 0.00 3.51
905 997 1.794222 GTGCTCCGCGTATTTGCTT 59.206 52.632 4.92 0.00 0.00 3.91
906 998 2.452813 CGTGCTCCGCGTATTTGCT 61.453 57.895 4.92 0.00 32.40 3.91
949 1044 4.281941 AGAGAAAACATTTTGGAGAAGGGC 59.718 41.667 0.00 0.00 0.00 5.19
989 1095 3.181329 AGAGAGAGAGACAGACAGAGGA 58.819 50.000 0.00 0.00 0.00 3.71
991 1097 4.478206 AGAGAGAGAGAGACAGACAGAG 57.522 50.000 0.00 0.00 0.00 3.35
992 1098 4.323485 GGAAGAGAGAGAGAGACAGACAGA 60.323 50.000 0.00 0.00 0.00 3.41
993 1099 3.941483 GGAAGAGAGAGAGAGACAGACAG 59.059 52.174 0.00 0.00 0.00 3.51
994 1100 3.587061 AGGAAGAGAGAGAGAGACAGACA 59.413 47.826 0.00 0.00 0.00 3.41
995 1101 4.192317 GAGGAAGAGAGAGAGAGACAGAC 58.808 52.174 0.00 0.00 0.00 3.51
996 1102 3.118775 CGAGGAAGAGAGAGAGAGACAGA 60.119 52.174 0.00 0.00 0.00 3.41
997 1103 3.198068 CGAGGAAGAGAGAGAGAGACAG 58.802 54.545 0.00 0.00 0.00 3.51
998 1104 2.679639 GCGAGGAAGAGAGAGAGAGACA 60.680 54.545 0.00 0.00 0.00 3.41
999 1105 1.940613 GCGAGGAAGAGAGAGAGAGAC 59.059 57.143 0.00 0.00 0.00 3.36
1000 1106 1.134220 GGCGAGGAAGAGAGAGAGAGA 60.134 57.143 0.00 0.00 0.00 3.10
1001 1107 1.308998 GGCGAGGAAGAGAGAGAGAG 58.691 60.000 0.00 0.00 0.00 3.20
1002 1108 0.621082 TGGCGAGGAAGAGAGAGAGA 59.379 55.000 0.00 0.00 0.00 3.10
1045 1151 4.862823 GGTCGGGAGAGGGGGAGG 62.863 77.778 0.00 0.00 41.26 4.30
1221 1328 4.712425 ACGAACGAGGAACCGCGG 62.712 66.667 26.86 26.86 43.22 6.46
1222 1329 1.824272 AAAACGAACGAGGAACCGCG 61.824 55.000 14.63 14.63 44.41 6.46
1231 1338 1.300853 GACGGGGGAAAACGAACGA 60.301 57.895 0.14 0.00 0.00 3.85
1236 1343 1.274447 AGAGTTAGACGGGGGAAAACG 59.726 52.381 0.00 0.00 0.00 3.60
1242 1349 2.732619 GGGCAGAGTTAGACGGGGG 61.733 68.421 0.00 0.00 0.00 5.40
1247 1354 1.804372 CGCATCAGGGCAGAGTTAGAC 60.804 57.143 0.00 0.00 0.00 2.59
1248 1355 0.461548 CGCATCAGGGCAGAGTTAGA 59.538 55.000 0.00 0.00 0.00 2.10
1249 1356 0.531532 CCGCATCAGGGCAGAGTTAG 60.532 60.000 0.00 0.00 0.00 2.34
1250 1357 1.522092 CCGCATCAGGGCAGAGTTA 59.478 57.895 0.00 0.00 0.00 2.24
1251 1358 2.270205 CCGCATCAGGGCAGAGTT 59.730 61.111 0.00 0.00 0.00 3.01
1338 1454 1.002502 GAAACCCAACTCCCTCCGG 60.003 63.158 0.00 0.00 0.00 5.14
1365 1483 2.548920 GGAAATCTAGCTCATCCCACGG 60.549 54.545 0.00 0.00 0.00 4.94
1386 1504 1.267261 CGCCATCCTAGTAGGTCGAAG 59.733 57.143 16.02 3.17 36.53 3.79
1393 1511 2.651361 CGGCCGCCATCCTAGTAG 59.349 66.667 14.67 0.00 0.00 2.57
1394 1512 3.612681 GCGGCCGCCATCCTAGTA 61.613 66.667 39.89 0.00 34.56 1.82
1559 1692 0.388649 CAGGGCACACTGACGAGTAC 60.389 60.000 0.00 0.00 40.97 2.73
1560 1693 1.964448 CAGGGCACACTGACGAGTA 59.036 57.895 0.00 0.00 40.97 2.59
1595 1728 1.972198 CAGGAAGACCGGCACACTA 59.028 57.895 0.00 0.00 41.83 2.74
1606 1739 0.036388 GGGTTCATGTCGCAGGAAGA 60.036 55.000 7.08 0.00 34.86 2.87
1646 1779 3.242739 ACAGACAGACAAACGTGCAAATC 60.243 43.478 0.00 0.00 0.00 2.17
1647 1780 2.682856 ACAGACAGACAAACGTGCAAAT 59.317 40.909 0.00 0.00 0.00 2.32
1648 1781 2.080693 ACAGACAGACAAACGTGCAAA 58.919 42.857 0.00 0.00 0.00 3.68
1653 1786 0.814010 GGGCACAGACAGACAAACGT 60.814 55.000 0.00 0.00 0.00 3.99
1654 1787 1.831389 CGGGCACAGACAGACAAACG 61.831 60.000 0.00 0.00 0.00 3.60
1672 1805 1.811266 CCGTCCTCATGTTCCTGCG 60.811 63.158 0.00 0.00 0.00 5.18
2001 2136 2.574399 GAGCGAGTGTCCCACCTC 59.426 66.667 0.00 0.00 34.49 3.85
2031 2166 2.517484 GAAAGTCCCCTTCCCGGTCG 62.517 65.000 0.00 0.00 0.00 4.79
2149 2284 6.205101 ACTATTCCCGGTATTAGCTAATCG 57.795 41.667 22.09 18.92 0.00 3.34
2158 2297 8.146412 GTCAACATAACTACTATTCCCGGTATT 58.854 37.037 0.00 0.00 0.00 1.89
2159 2298 7.256083 GGTCAACATAACTACTATTCCCGGTAT 60.256 40.741 0.00 0.00 0.00 2.73
2160 2299 6.040842 GGTCAACATAACTACTATTCCCGGTA 59.959 42.308 0.00 0.00 0.00 4.02
2161 2300 5.163374 GGTCAACATAACTACTATTCCCGGT 60.163 44.000 0.00 0.00 0.00 5.28
2162 2301 5.070047 AGGTCAACATAACTACTATTCCCGG 59.930 44.000 0.00 0.00 0.00 5.73
2163 2302 6.158023 AGGTCAACATAACTACTATTCCCG 57.842 41.667 0.00 0.00 0.00 5.14
2164 2303 8.803397 AAAAGGTCAACATAACTACTATTCCC 57.197 34.615 0.00 0.00 0.00 3.97
2165 2304 8.601476 CGAAAAGGTCAACATAACTACTATTCC 58.399 37.037 0.00 0.00 0.00 3.01
2166 2305 9.362539 TCGAAAAGGTCAACATAACTACTATTC 57.637 33.333 0.00 0.00 0.00 1.75
2173 2312 7.280205 GGTCATATCGAAAAGGTCAACATAACT 59.720 37.037 0.00 0.00 0.00 2.24
2178 2317 4.693566 GTGGTCATATCGAAAAGGTCAACA 59.306 41.667 0.00 0.00 0.00 3.33
2182 2321 4.806247 CAGAGTGGTCATATCGAAAAGGTC 59.194 45.833 0.00 0.00 0.00 3.85
2183 2322 4.223032 ACAGAGTGGTCATATCGAAAAGGT 59.777 41.667 0.00 0.00 0.00 3.50
2220 2359 7.675962 AAGTACCTGATACGCAACAAAAATA 57.324 32.000 0.00 0.00 38.97 1.40
2273 2413 0.311790 AAGCACAAACCAGCACATCG 59.688 50.000 0.00 0.00 0.00 3.84
2282 2422 1.139226 CGCACACACAAGCACAAACC 61.139 55.000 0.00 0.00 0.00 3.27
2300 2440 3.874706 ACTATTCTTAGCGACATCGACG 58.125 45.455 5.26 0.00 43.02 5.12
2305 2447 8.414003 TCATCTGTTTACTATTCTTAGCGACAT 58.586 33.333 0.00 0.00 0.00 3.06
2369 2511 6.986817 TGCACAGGAGAGAAAATTAGTATAGC 59.013 38.462 0.00 0.00 0.00 2.97
2405 2549 6.349280 GCCAGTTGACATTTCTAATAAGTGCA 60.349 38.462 0.00 0.00 0.00 4.57
2418 2562 6.888632 AGATAAGAAGAATGCCAGTTGACATT 59.111 34.615 0.00 0.00 39.16 2.71
2695 2849 9.787435 ATTCACTAAACAATTGTAGTTGACCTA 57.213 29.630 12.39 0.00 33.37 3.08
2697 2851 9.821662 GTATTCACTAAACAATTGTAGTTGACC 57.178 33.333 12.39 0.79 33.37 4.02
2866 3022 9.655769 CAGCAGAAACAACATACATTATATGTC 57.344 33.333 0.27 0.00 43.67 3.06
2971 3129 4.455606 CAGGACCAGTCTTCTTTTCTTGT 58.544 43.478 0.00 0.00 0.00 3.16
2985 3143 4.285260 TCATGATATCATCACCAGGACCAG 59.715 45.833 15.49 0.54 43.01 4.00
3112 3270 1.591703 CGCAGGAGCTGGTAGAACA 59.408 57.895 0.00 0.00 39.10 3.18
3359 3517 7.911651 AGACCTATTTTGATCACAGAGAAGAA 58.088 34.615 0.00 0.00 0.00 2.52
3360 3518 7.487822 AGACCTATTTTGATCACAGAGAAGA 57.512 36.000 0.00 0.00 0.00 2.87
3361 3519 9.658799 TTTAGACCTATTTTGATCACAGAGAAG 57.341 33.333 0.00 0.00 0.00 2.85
3429 3587 9.877178 GATATAAACCAGATGAACCGATTAGAT 57.123 33.333 0.00 0.00 0.00 1.98
3430 3588 9.090103 AGATATAAACCAGATGAACCGATTAGA 57.910 33.333 0.00 0.00 0.00 2.10
3431 3589 9.712305 AAGATATAAACCAGATGAACCGATTAG 57.288 33.333 0.00 0.00 0.00 1.73
3436 3602 9.326413 AGTAAAAGATATAAACCAGATGAACCG 57.674 33.333 0.00 0.00 0.00 4.44
3587 3755 3.869912 GCAACTAGAATCCCAAGAGTGCA 60.870 47.826 0.00 0.00 0.00 4.57
3641 3809 5.178061 CAGTGTCACATTGGCAGATAGTAA 58.822 41.667 5.62 0.00 29.65 2.24
3642 3810 4.222810 ACAGTGTCACATTGGCAGATAGTA 59.777 41.667 5.16 0.00 29.65 1.82
3643 3811 3.008375 ACAGTGTCACATTGGCAGATAGT 59.992 43.478 5.16 0.00 29.65 2.12
3736 3905 7.147602 GGTTTCCCTCTACTTGGCTACTAAATA 60.148 40.741 0.00 0.00 0.00 1.40
3807 3976 5.227569 TGATGTACACCAATCTTGTCAGT 57.772 39.130 0.00 0.00 0.00 3.41
3815 3984 4.917415 GTGTGCTTTTGATGTACACCAATC 59.083 41.667 2.77 0.00 42.42 2.67
3858 4027 5.136105 AGGAACAAATTCAGTTGAAGAGCT 58.864 37.500 0.74 0.00 37.48 4.09
3905 4074 0.744874 CCATTGCATCAGCTTCCCAG 59.255 55.000 0.00 0.00 42.74 4.45
3980 4149 7.033791 CCAAGATTGAGATTGAATTGTCCTTG 58.966 38.462 0.00 0.00 0.00 3.61
4007 4176 0.598065 ATGCGTTGCCAAAGAACTCC 59.402 50.000 0.00 0.00 0.00 3.85
4082 4251 6.699575 AAGAGTGAGCACAACAAAATAAGT 57.300 33.333 3.19 0.00 0.00 2.24
4126 4295 4.961099 AGATGACAGAGATCCACATGAGAA 59.039 41.667 0.00 0.00 0.00 2.87
4203 4372 3.055094 GGTCCATGTCACAGGTCATAACT 60.055 47.826 0.00 0.00 0.00 2.24
4324 4494 2.568509 AGGAAGACCCATTGGCATTTTG 59.431 45.455 0.00 0.00 37.41 2.44
4373 4544 4.148838 TCATCCCCAGAAACAAAAATCGT 58.851 39.130 0.00 0.00 0.00 3.73
4374 4545 4.782019 TCATCCCCAGAAACAAAAATCG 57.218 40.909 0.00 0.00 0.00 3.34
4833 5019 6.022958 TGGCATGGCTATCCTACTTCTATTA 58.977 40.000 21.08 0.00 0.00 0.98
4845 5031 4.992951 GGAAATTTTCATGGCATGGCTATC 59.007 41.667 26.15 16.11 0.00 2.08
4884 5070 5.548056 ACTGGAAAGGGGGATATGTATACAG 59.452 44.000 11.91 0.00 0.00 2.74
4994 5568 7.878127 CCTCTGAAGGTTTTGAATCTACAGTAA 59.122 37.037 0.00 0.00 37.94 2.24
5068 5642 1.203050 AGCTATGTTTTGTGGGCCTGT 60.203 47.619 4.53 0.00 0.00 4.00
5217 5791 0.107703 TACCAGCATGCCTGTACTGC 60.108 55.000 15.66 0.00 40.06 4.40
5367 5944 1.648467 CTACTTTCTGCTTGGCGGCC 61.648 60.000 13.32 13.32 34.49 6.13
5484 6063 3.303881 TCAGAACTCTGTGGTTCATCG 57.696 47.619 6.61 6.56 45.52 3.84
5631 6210 2.960384 CTCATTCATAAATGCAGCCCCA 59.040 45.455 0.00 0.00 41.76 4.96
5670 6249 0.322546 ATCCCCGAACAGAAACTGGC 60.323 55.000 0.00 0.00 35.51 4.85
5680 6259 1.689273 ACTAGATGCAGATCCCCGAAC 59.311 52.381 0.00 0.00 0.00 3.95
6155 6749 2.202566 GCTGACTCCTATTACCAACGC 58.797 52.381 0.00 0.00 0.00 4.84
6360 6961 1.451567 CACAGGCTGAGATGGCAGG 60.452 63.158 23.66 0.00 36.41 4.85
6474 7075 4.481072 ACTTGTACAGACTCTTACCTGGT 58.519 43.478 4.05 4.05 34.85 4.00
6537 7138 7.402640 TCAAAACTTTGACACAAACAAAACAC 58.597 30.769 0.69 0.00 41.88 3.32
6638 7245 4.084013 CGAGTGGATTTTGTGGAGTGTAAC 60.084 45.833 0.00 0.00 0.00 2.50
6644 7251 2.996621 GAGTCGAGTGGATTTTGTGGAG 59.003 50.000 0.00 0.00 0.00 3.86
6658 7265 2.158449 GGCACAACTTGAATGAGTCGAG 59.842 50.000 0.00 0.00 42.85 4.04
6659 7266 2.143122 GGCACAACTTGAATGAGTCGA 58.857 47.619 0.00 0.00 0.00 4.20
6660 7267 2.096069 CAGGCACAACTTGAATGAGTCG 60.096 50.000 0.00 0.00 0.00 4.18
6661 7268 3.141398 TCAGGCACAACTTGAATGAGTC 58.859 45.455 0.00 0.00 0.00 3.36
6662 7269 3.213206 TCAGGCACAACTTGAATGAGT 57.787 42.857 0.00 0.00 0.00 3.41
6710 7317 3.795561 AAAGACGCAGAATTCAACTCG 57.204 42.857 8.44 7.55 0.00 4.18
6748 7358 3.323243 ACAGTAAATGAAGTTCCGACGG 58.677 45.455 7.84 7.84 0.00 4.79
6750 7360 7.319615 CGTTTTAACAGTAAATGAAGTTCCGAC 59.680 37.037 0.00 0.00 0.00 4.79
6847 7457 5.744171 ACTGGAAAAACAAGAAGCCATTTT 58.256 33.333 0.00 0.00 0.00 1.82
6854 7464 9.237846 GATAACTCAAACTGGAAAAACAAGAAG 57.762 33.333 0.00 0.00 0.00 2.85
6875 7485 1.852895 GGATGTCGCGTGTCTGATAAC 59.147 52.381 5.77 0.00 0.00 1.89
6888 7505 3.552604 AATTGAACGGTTTGGATGTCG 57.447 42.857 0.00 0.00 0.00 4.35
6922 7539 8.558973 AAGAGAAAACAGAGTTGGATCATAAG 57.441 34.615 0.00 0.00 0.00 1.73
6945 7568 4.141574 TGGACCCGATGGACCTAAATAAAG 60.142 45.833 2.02 0.00 45.57 1.85
6946 7569 3.781407 TGGACCCGATGGACCTAAATAAA 59.219 43.478 2.02 0.00 45.57 1.40
7128 7752 1.064003 TATGACAGGCACAACAGGGT 58.936 50.000 0.00 0.00 0.00 4.34
7130 7754 1.453155 GGTATGACAGGCACAACAGG 58.547 55.000 0.00 0.00 0.00 4.00
7145 7769 2.378547 ACATGGTGGTTTGTCTGGGTAT 59.621 45.455 0.00 0.00 0.00 2.73
7152 7790 2.687935 ACACAGAACATGGTGGTTTGTC 59.312 45.455 0.00 0.00 39.31 3.18
7214 7856 0.396695 TTCCTCCCCGACGAGCTATT 60.397 55.000 0.00 0.00 0.00 1.73
7320 7966 2.705410 CATCCCTCCCTCCCTCCA 59.295 66.667 0.00 0.00 0.00 3.86
7336 7982 1.212688 CAGCACCCAATGTATCCTCCA 59.787 52.381 0.00 0.00 0.00 3.86
7388 8034 2.370281 AATAGCCAGACACAGACACG 57.630 50.000 0.00 0.00 0.00 4.49
7495 8146 8.307483 TGAATGGTTAGTTTTTCTTCACACAAA 58.693 29.630 0.00 0.00 0.00 2.83
7498 8149 7.254852 TGTGAATGGTTAGTTTTTCTTCACAC 58.745 34.615 10.24 0.00 43.37 3.82
7500 8154 8.134895 TGATGTGAATGGTTAGTTTTTCTTCAC 58.865 33.333 0.00 0.00 40.67 3.18
7504 8158 8.137437 CAGTTGATGTGAATGGTTAGTTTTTCT 58.863 33.333 0.00 0.00 0.00 2.52
7542 8196 6.081049 TGTTGAACTTTAACTTTGTGTCACG 58.919 36.000 0.00 0.00 0.00 4.35
7559 8213 9.744468 ATGTACTGGTCTTTTTATTTGTTGAAC 57.256 29.630 0.00 0.00 0.00 3.18
7561 8215 8.356657 CCATGTACTGGTCTTTTTATTTGTTGA 58.643 33.333 0.00 0.00 40.49 3.18
7565 8219 7.975616 CCATCCATGTACTGGTCTTTTTATTTG 59.024 37.037 10.08 0.00 46.08 2.32
7594 8253 6.516527 GCTGAAAAACATTGTGTAGGGATGAA 60.517 38.462 0.00 0.00 0.00 2.57
7601 8260 6.264832 TGTTGAGCTGAAAAACATTGTGTAG 58.735 36.000 0.00 0.00 0.00 2.74
7619 8278 0.539051 ATTCCTCCCGCTCTGTTGAG 59.461 55.000 0.00 0.00 42.96 3.02
7626 8290 2.514824 GGTGCATTCCTCCCGCTC 60.515 66.667 0.00 0.00 0.00 5.03
7629 8293 3.060614 ATGGGGTGCATTCCTCCCG 62.061 63.158 3.40 0.00 46.27 5.14
7644 8308 2.165167 ACACCATCAAGTTCAGCATGG 58.835 47.619 0.00 0.00 41.52 3.66
7666 8330 7.259161 AGTATTTTACCGCAACAAACTGAAAA 58.741 30.769 0.00 0.00 0.00 2.29
7669 8333 6.380095 AAGTATTTTACCGCAACAAACTGA 57.620 33.333 0.00 0.00 0.00 3.41
7670 8334 7.322699 CAGTAAGTATTTTACCGCAACAAACTG 59.677 37.037 0.00 0.00 0.00 3.16
7675 8452 7.493743 TTTCAGTAAGTATTTTACCGCAACA 57.506 32.000 0.00 0.00 0.00 3.33
7689 8466 8.394971 TGATCATGTGACAAATTTCAGTAAGT 57.605 30.769 0.00 0.00 0.00 2.24
7693 8470 8.795513 TGTAATGATCATGTGACAAATTTCAGT 58.204 29.630 9.46 0.00 0.00 3.41
7701 8478 7.700022 TGGATTTGTAATGATCATGTGACAA 57.300 32.000 19.55 19.55 0.00 3.18
7705 8482 9.811995 AAATCTTGGATTTGTAATGATCATGTG 57.188 29.630 9.46 0.00 0.00 3.21
7722 8512 6.968263 TGACCAAAACATACAAATCTTGGA 57.032 33.333 5.69 0.00 37.38 3.53
7735 8525 9.883142 ATTTGTTCTTTAAGATTGACCAAAACA 57.117 25.926 0.00 0.00 0.00 2.83
7740 8530 9.959749 GTAACATTTGTTCTTTAAGATTGACCA 57.040 29.630 0.00 0.00 39.31 4.02
7766 8560 7.814587 CAGCCTTTTCTTTTCTTGGTTATAAGG 59.185 37.037 0.00 0.00 33.33 2.69
7775 8569 3.126073 GGCACAGCCTTTTCTTTTCTTG 58.874 45.455 0.00 0.00 46.69 3.02
7791 8585 8.949339 CACAAAAACAGAGTGAAAAATGGCACA 61.949 37.037 0.00 0.00 38.01 4.57
7807 8601 5.296748 CCCATTTTACCCTCACAAAAACAG 58.703 41.667 0.00 0.00 0.00 3.16
7866 8662 1.958579 ACACTACGCTCCAACACAGTA 59.041 47.619 0.00 0.00 0.00 2.74
7879 8675 1.798813 GCTGAAGGAAACCACACTACG 59.201 52.381 0.00 0.00 0.00 3.51
7891 8688 2.268920 GCGACCATGGCTGAAGGA 59.731 61.111 13.04 0.00 0.00 3.36
7894 8691 2.747460 GCTGCGACCATGGCTGAA 60.747 61.111 13.04 0.00 0.00 3.02
8208 9025 2.031516 CAGCAGCAGGTCGAGGTTG 61.032 63.158 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.