Multiple sequence alignment - TraesCS2D01G472300

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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 TraesCS2D01G472300 chr2D 100.000 3134 0 0 1 3134 575947213 575944080 0.000000e+00 5788.0
1 TraesCS2D01G472300 chr2D 84.658 1095 137 23 1069 2151 575969853 575968778 0.000000e+00 1062.0
2 TraesCS2D01G472300 chr2D 81.123 1086 184 15 1070 2144 575831228 575832303 0.000000e+00 850.0
3 TraesCS2D01G472300 chr2D 89.855 276 24 2 2843 3118 575833020 575833291 4.970000e-93 351.0
4 TraesCS2D01G472300 chr2D 89.313 131 9 1 2714 2839 575832445 575832575 3.240000e-35 159.0
5 TraesCS2D01G472300 chr2D 94.203 69 3 1 2170 2238 575832376 575832443 1.540000e-18 104.0
6 TraesCS2D01G472300 chr2B 91.172 1971 146 17 197 2144 692113851 692115816 0.000000e+00 2651.0
7 TraesCS2D01G472300 chr2B 88.287 683 72 4 1460 2138 692148759 692149437 0.000000e+00 811.0
8 TraesCS2D01G472300 chr2B 79.398 1097 180 32 915 1993 692128412 692129480 0.000000e+00 732.0
9 TraesCS2D01G472300 chr2B 86.167 347 37 8 2170 2513 692115889 692116227 6.390000e-97 364.0
10 TraesCS2D01G472300 chr2B 84.030 263 28 9 2419 2673 692150008 692150264 1.120000e-59 241.0
11 TraesCS2D01G472300 chr2B 84.921 252 19 4 2170 2420 692149516 692149749 1.450000e-58 237.0
12 TraesCS2D01G472300 chr2B 83.796 216 28 6 435 648 745694966 745694756 6.860000e-47 198.0
13 TraesCS2D01G472300 chr2A 97.080 822 24 0 1330 2151 714059594 714058773 0.000000e+00 1386.0
14 TraesCS2D01G472300 chr2A 90.263 760 46 9 2162 2919 714058705 714057972 0.000000e+00 968.0
15 TraesCS2D01G472300 chr2A 85.714 483 64 5 189 668 714032923 714033403 3.610000e-139 505.0
16 TraesCS2D01G472300 chr2A 81.699 153 28 0 4 156 721517545 721517393 9.120000e-26 128.0
17 TraesCS2D01G472300 chr2A 90.698 43 4 0 397 439 386009119 386009077 1.210000e-04 58.4
18 TraesCS2D01G472300 chr2A 100.000 28 0 0 398 425 4999631 4999658 6.000000e-03 52.8
19 TraesCS2D01G472300 chr7B 83.197 244 25 13 435 670 19253221 19252986 3.170000e-50 209.0
20 TraesCS2D01G472300 chr6A 82.988 241 31 9 435 670 27001293 27001058 3.170000e-50 209.0
21 TraesCS2D01G472300 chr4D 82.500 240 37 4 432 670 25461255 25461490 4.100000e-49 206.0
22 TraesCS2D01G472300 chr5A 82.500 240 33 8 435 670 91625780 91625546 5.300000e-48 202.0
23 TraesCS2D01G472300 chr5A 97.059 34 0 1 398 431 331893726 331893758 4.370000e-04 56.5
24 TraesCS2D01G472300 chr4A 83.796 216 28 6 435 648 589616154 589615944 6.860000e-47 198.0
25 TraesCS2D01G472300 chr3A 82.008 239 33 9 437 670 739741780 739742013 8.870000e-46 195.0
26 TraesCS2D01G472300 chr5D 100.000 30 0 0 78 107 285840313 285840284 4.370000e-04 56.5
27 TraesCS2D01G472300 chr1B 96.970 33 1 0 393 425 420568151 420568119 4.370000e-04 56.5


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 TraesCS2D01G472300 chr2D 575944080 575947213 3133 True 5788.000000 5788 100.0000 1 3134 1 chr2D.!!$R1 3133
1 TraesCS2D01G472300 chr2D 575968778 575969853 1075 True 1062.000000 1062 84.6580 1069 2151 1 chr2D.!!$R2 1082
2 TraesCS2D01G472300 chr2D 575831228 575833291 2063 False 366.000000 850 88.6235 1070 3118 4 chr2D.!!$F1 2048
3 TraesCS2D01G472300 chr2B 692113851 692116227 2376 False 1507.500000 2651 88.6695 197 2513 2 chr2B.!!$F2 2316
4 TraesCS2D01G472300 chr2B 692128412 692129480 1068 False 732.000000 732 79.3980 915 1993 1 chr2B.!!$F1 1078
5 TraesCS2D01G472300 chr2B 692148759 692150264 1505 False 429.666667 811 85.7460 1460 2673 3 chr2B.!!$F3 1213
6 TraesCS2D01G472300 chr2A 714057972 714059594 1622 True 1177.000000 1386 93.6715 1330 2919 2 chr2A.!!$R3 1589

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
142 143 0.103572 GAGGTAGCGGCCGTAATTGA 59.896 55.0 28.7 2.66 0.0 2.57 F
145 146 0.303796 GTAGCGGCCGTAATTGAAGC 59.696 55.0 28.7 6.14 0.0 3.86 F
512 538 0.323629 GAAGATGTTCCCGTCCACCA 59.676 55.0 0.0 0.00 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1268 1307 0.448593 GAGAGACAGGAAGACCGACG 59.551 60.000 0.00 0.00 41.83 5.12 R
1987 2037 3.386716 ATGCCCTTTTCAGGTGCAT 57.613 47.368 9.96 9.96 45.07 3.96 R
2480 2856 0.034337 TCGCTCCAAAAACGCCTAGT 59.966 50.000 0.00 0.00 0.00 2.57 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
17 18 2.811317 GAGTTGCCGACGGAGCAG 60.811 66.667 20.50 0.00 42.17 4.24
18 19 4.379243 AGTTGCCGACGGAGCAGG 62.379 66.667 20.50 0.00 42.17 4.85
19 20 4.681978 GTTGCCGACGGAGCAGGT 62.682 66.667 20.50 0.00 42.17 4.00
20 21 4.373116 TTGCCGACGGAGCAGGTC 62.373 66.667 20.50 0.00 42.17 3.85
22 23 4.148825 GCCGACGGAGCAGGTCAT 62.149 66.667 20.50 0.00 34.04 3.06
23 24 2.105128 CCGACGGAGCAGGTCATC 59.895 66.667 8.64 0.00 34.04 2.92
24 25 2.105128 CGACGGAGCAGGTCATCC 59.895 66.667 1.20 0.00 34.04 3.51
25 26 2.418910 CGACGGAGCAGGTCATCCT 61.419 63.158 1.20 0.00 46.37 3.24
26 27 1.439644 GACGGAGCAGGTCATCCTC 59.560 63.158 1.20 0.00 43.07 3.71
27 28 1.000993 ACGGAGCAGGTCATCCTCT 59.999 57.895 1.20 0.00 43.07 3.69
28 29 1.326213 ACGGAGCAGGTCATCCTCTG 61.326 60.000 1.20 0.00 43.07 3.35
31 32 2.895680 GCAGGTCATCCTCTGCGA 59.104 61.111 0.00 0.00 45.31 5.10
32 33 1.227205 GCAGGTCATCCTCTGCGAG 60.227 63.158 0.00 0.00 45.31 5.03
41 42 2.185350 CTCTGCGAGGACGGCAAT 59.815 61.111 0.00 0.00 40.15 3.56
42 43 1.880340 CTCTGCGAGGACGGCAATC 60.880 63.158 0.00 0.00 40.15 2.67
43 44 2.892425 CTGCGAGGACGGCAATCC 60.892 66.667 0.00 0.00 40.15 3.01
53 54 4.963878 GGCAATCCGGATGACACT 57.036 55.556 19.95 0.00 0.00 3.55
54 55 2.695314 GGCAATCCGGATGACACTC 58.305 57.895 19.95 3.66 0.00 3.51
55 56 0.815615 GGCAATCCGGATGACACTCC 60.816 60.000 19.95 9.19 0.00 3.85
61 62 4.368003 GGATGACACTCCGGGGTA 57.632 61.111 6.68 0.00 0.00 3.69
62 63 1.821258 GGATGACACTCCGGGGTAC 59.179 63.158 6.68 5.08 0.00 3.34
76 77 1.145377 GGTACCACATGGCCCTACG 59.855 63.158 7.15 0.00 39.32 3.51
77 78 1.145377 GTACCACATGGCCCTACGG 59.855 63.158 0.00 0.00 39.32 4.02
87 88 4.157120 CCCTACGGGCGTTGGAGG 62.157 72.222 0.00 3.47 42.22 4.30
88 89 4.832608 CCTACGGGCGTTGGAGGC 62.833 72.222 0.00 0.00 42.22 4.70
116 117 3.123620 GCAGCGGCTGTGAGGAAG 61.124 66.667 28.88 3.61 36.96 3.46
117 118 2.435586 CAGCGGCTGTGAGGAAGG 60.436 66.667 21.60 0.00 0.00 3.46
118 119 4.400961 AGCGGCTGTGAGGAAGGC 62.401 66.667 0.00 0.00 36.89 4.35
125 126 4.821589 GTGAGGAAGGCCGCCGAG 62.822 72.222 3.05 0.00 39.96 4.63
128 129 4.772231 AGGAAGGCCGCCGAGGTA 62.772 66.667 3.05 0.00 43.70 3.08
129 130 4.222847 GGAAGGCCGCCGAGGTAG 62.223 72.222 3.05 0.00 43.70 3.18
130 131 4.893601 GAAGGCCGCCGAGGTAGC 62.894 72.222 3.05 0.00 43.70 3.58
138 139 3.520862 CCGAGGTAGCGGCCGTAA 61.521 66.667 28.70 12.69 45.38 3.18
139 140 2.726274 CGAGGTAGCGGCCGTAAT 59.274 61.111 28.70 15.79 0.00 1.89
140 141 1.066918 CGAGGTAGCGGCCGTAATT 59.933 57.895 28.70 12.68 0.00 1.40
141 142 1.213094 CGAGGTAGCGGCCGTAATTG 61.213 60.000 28.70 8.80 0.00 2.32
142 143 0.103572 GAGGTAGCGGCCGTAATTGA 59.896 55.000 28.70 2.66 0.00 2.57
143 144 0.538118 AGGTAGCGGCCGTAATTGAA 59.462 50.000 28.70 1.36 0.00 2.69
144 145 0.935196 GGTAGCGGCCGTAATTGAAG 59.065 55.000 28.70 0.00 0.00 3.02
145 146 0.303796 GTAGCGGCCGTAATTGAAGC 59.696 55.000 28.70 6.14 0.00 3.86
146 147 1.149361 TAGCGGCCGTAATTGAAGCG 61.149 55.000 28.70 0.00 0.00 4.68
150 151 2.707039 CCGTAATTGAAGCGGCCG 59.293 61.111 24.05 24.05 38.99 6.13
151 152 2.022762 CGTAATTGAAGCGGCCGC 59.977 61.111 42.34 42.34 42.33 6.53
168 169 4.233635 CGGCGATTGCTGCAGAGC 62.234 66.667 20.43 13.38 46.44 4.09
185 186 2.269978 GCAGGCAGCAAAATCTCCA 58.730 52.632 0.00 0.00 44.79 3.86
186 187 0.604578 GCAGGCAGCAAAATCTCCAA 59.395 50.000 0.00 0.00 44.79 3.53
187 188 1.670967 GCAGGCAGCAAAATCTCCAAC 60.671 52.381 0.00 0.00 44.79 3.77
188 189 0.883833 AGGCAGCAAAATCTCCAACG 59.116 50.000 0.00 0.00 0.00 4.10
189 190 0.881118 GGCAGCAAAATCTCCAACGA 59.119 50.000 0.00 0.00 0.00 3.85
190 191 1.135575 GGCAGCAAAATCTCCAACGAG 60.136 52.381 0.00 0.00 37.48 4.18
191 192 1.537202 GCAGCAAAATCTCCAACGAGT 59.463 47.619 0.00 0.00 37.40 4.18
192 193 2.742053 GCAGCAAAATCTCCAACGAGTA 59.258 45.455 0.00 0.00 37.40 2.59
193 194 3.181516 GCAGCAAAATCTCCAACGAGTAG 60.182 47.826 0.00 0.00 37.40 2.57
194 195 3.997021 CAGCAAAATCTCCAACGAGTAGT 59.003 43.478 0.00 0.00 37.40 2.73
195 196 5.168569 CAGCAAAATCTCCAACGAGTAGTA 58.831 41.667 0.00 0.00 37.40 1.82
196 197 5.812642 CAGCAAAATCTCCAACGAGTAGTAT 59.187 40.000 0.00 0.00 37.40 2.12
197 198 6.978659 CAGCAAAATCTCCAACGAGTAGTATA 59.021 38.462 0.00 0.00 37.40 1.47
198 199 7.168302 CAGCAAAATCTCCAACGAGTAGTATAG 59.832 40.741 0.00 0.00 37.40 1.31
243 244 4.603131 AGTGGGTAAATCTTGTGATGCAT 58.397 39.130 0.00 0.00 32.44 3.96
248 249 5.506317 GGGTAAATCTTGTGATGCATGCTAC 60.506 44.000 20.33 15.18 32.44 3.58
250 251 6.483307 GGTAAATCTTGTGATGCATGCTACTA 59.517 38.462 20.33 11.00 32.44 1.82
251 252 5.998454 AATCTTGTGATGCATGCTACTAC 57.002 39.130 20.33 12.76 32.44 2.73
282 283 6.978674 TGAGGTCTAATATGAGGTACTTGG 57.021 41.667 0.00 0.00 41.55 3.61
283 284 6.441222 TGAGGTCTAATATGAGGTACTTGGT 58.559 40.000 0.00 0.00 41.55 3.67
285 286 7.125792 AGGTCTAATATGAGGTACTTGGTTG 57.874 40.000 0.00 0.00 41.55 3.77
286 287 5.758784 GGTCTAATATGAGGTACTTGGTTGC 59.241 44.000 0.00 0.00 41.55 4.17
287 288 6.346096 GTCTAATATGAGGTACTTGGTTGCA 58.654 40.000 0.00 0.00 41.55 4.08
288 289 6.821665 GTCTAATATGAGGTACTTGGTTGCAA 59.178 38.462 0.00 0.00 41.55 4.08
289 290 5.897377 AATATGAGGTACTTGGTTGCAAC 57.103 39.130 21.59 21.59 41.55 4.17
290 291 2.719531 TGAGGTACTTGGTTGCAACA 57.280 45.000 29.55 13.95 41.55 3.33
316 317 3.103080 AGGAGAGAAGTGACCGGTTAT 57.897 47.619 9.42 0.00 0.00 1.89
329 330 3.352648 ACCGGTTATTGTCCAGATTTGG 58.647 45.455 0.00 0.00 46.49 3.28
340 341 3.008049 GTCCAGATTTGGTATATCCGGCT 59.992 47.826 0.00 0.00 45.26 5.52
342 343 2.744202 CAGATTTGGTATATCCGGCTGC 59.256 50.000 0.00 0.00 39.52 5.25
349 350 1.066573 GTATATCCGGCTGCAGATGCT 60.067 52.381 20.43 0.00 42.66 3.79
354 355 1.440893 CGGCTGCAGATGCTCTAGT 59.559 57.895 20.43 0.00 42.66 2.57
355 356 0.670706 CGGCTGCAGATGCTCTAGTA 59.329 55.000 20.43 0.00 42.66 1.82
356 357 1.601663 CGGCTGCAGATGCTCTAGTAC 60.602 57.143 20.43 0.00 42.66 2.73
357 358 1.270041 GGCTGCAGATGCTCTAGTACC 60.270 57.143 20.43 0.00 42.66 3.34
358 359 1.686052 GCTGCAGATGCTCTAGTACCT 59.314 52.381 20.43 0.00 42.66 3.08
365 366 6.375736 TGCAGATGCTCTAGTACCTATACATC 59.624 42.308 6.35 7.39 42.66 3.06
366 367 6.601613 GCAGATGCTCTAGTACCTATACATCT 59.398 42.308 10.77 10.77 42.68 2.90
398 399 1.676006 ACAAAAGTCGTTGGGCTGAAG 59.324 47.619 0.00 0.00 32.50 3.02
399 400 0.668535 AAAAGTCGTTGGGCTGAAGC 59.331 50.000 0.00 0.00 41.14 3.86
407 433 0.539438 TTGGGCTGAAGCGAACCAAT 60.539 50.000 7.24 0.00 43.26 3.16
408 434 0.326595 TGGGCTGAAGCGAACCAATA 59.673 50.000 0.00 0.00 43.26 1.90
413 439 2.677836 GCTGAAGCGAACCAATATGTGA 59.322 45.455 0.00 0.00 0.00 3.58
429 455 3.260475 TGTGATTGGATGGTTACGAGG 57.740 47.619 0.00 0.00 0.00 4.63
430 456 2.093181 TGTGATTGGATGGTTACGAGGG 60.093 50.000 0.00 0.00 0.00 4.30
431 457 1.134220 TGATTGGATGGTTACGAGGGC 60.134 52.381 0.00 0.00 0.00 5.19
438 464 1.277579 TGGTTACGAGGGCATTGGTA 58.722 50.000 0.00 0.00 0.00 3.25
451 477 4.202111 GGGCATTGGTACTCGCATTATTTT 60.202 41.667 0.00 0.00 0.00 1.82
452 478 5.348164 GGCATTGGTACTCGCATTATTTTT 58.652 37.500 0.00 0.00 0.00 1.94
453 479 5.231991 GGCATTGGTACTCGCATTATTTTTG 59.768 40.000 0.00 0.00 0.00 2.44
454 480 5.231991 GCATTGGTACTCGCATTATTTTTGG 59.768 40.000 0.00 0.00 0.00 3.28
486 512 1.005984 TTCCGGCGATGTTCGTTCA 60.006 52.632 9.30 0.00 42.81 3.18
490 516 1.787847 GGCGATGTTCGTTCAGTGG 59.212 57.895 0.00 0.00 42.81 4.00
492 518 1.635663 GCGATGTTCGTTCAGTGGGG 61.636 60.000 0.00 0.00 42.81 4.96
498 524 1.003233 GTTCGTTCAGTGGGGGAAGAT 59.997 52.381 0.00 0.00 0.00 2.40
502 528 2.437413 GTTCAGTGGGGGAAGATGTTC 58.563 52.381 0.00 0.00 0.00 3.18
511 537 0.392595 GGAAGATGTTCCCGTCCACC 60.393 60.000 10.58 0.00 46.11 4.61
512 538 0.323629 GAAGATGTTCCCGTCCACCA 59.676 55.000 0.00 0.00 0.00 4.17
526 552 2.167219 CACCACGAGGCGCATGTAG 61.167 63.158 10.83 0.00 39.06 2.74
534 560 0.458543 AGGCGCATGTAGTGACTTCG 60.459 55.000 10.83 0.00 46.28 3.79
541 567 5.481472 CGCATGTAGTGACTTCGTAAAATC 58.519 41.667 0.00 0.00 0.00 2.17
557 583 8.282124 TCGTAAAATCTTAAGATGCTATGACG 57.718 34.615 18.61 19.00 34.49 4.35
561 587 3.629058 TCTTAAGATGCTATGACGTCGC 58.371 45.455 11.62 9.03 0.00 5.19
564 590 0.747255 AGATGCTATGACGTCGCCTT 59.253 50.000 11.62 0.00 0.00 4.35
566 592 2.030717 AGATGCTATGACGTCGCCTTAG 60.031 50.000 11.62 10.10 0.00 2.18
572 598 1.085091 TGACGTCGCCTTAGTCTCTC 58.915 55.000 11.62 0.00 36.01 3.20
573 599 1.085091 GACGTCGCCTTAGTCTCTCA 58.915 55.000 0.00 0.00 32.58 3.27
585 611 6.568869 CCTTAGTCTCTCAAAGGTACTCATG 58.431 44.000 0.00 0.00 38.49 3.07
595 622 1.129058 GGTACTCATGGGGTAGGGTG 58.871 60.000 0.00 0.00 0.00 4.61
605 632 1.959226 GGTAGGGTGTGCGTGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
616 643 0.372334 GCGTGTGTGCGTTTATAGGG 59.628 55.000 0.00 0.00 0.00 3.53
649 676 4.534168 GCTCGTATATGTGAGCGACTTTA 58.466 43.478 13.23 0.00 47.00 1.85
656 683 7.097128 CGTATATGTGAGCGACTTTAAGTGTAC 60.097 40.741 0.93 0.00 0.00 2.90
657 684 3.645884 TGTGAGCGACTTTAAGTGTACC 58.354 45.455 0.93 0.00 0.00 3.34
660 687 2.660236 GAGCGACTTTAAGTGTACCGTG 59.340 50.000 0.93 0.00 0.00 4.94
688 717 6.493189 AAAAATTCTTTAGGCTGAACCCAA 57.507 33.333 0.00 0.00 40.58 4.12
693 722 3.826157 TCTTTAGGCTGAACCCAACAATG 59.174 43.478 0.00 0.00 40.58 2.82
697 726 1.000274 GGCTGAACCCAACAATGACAC 60.000 52.381 0.00 0.00 0.00 3.67
743 772 5.006386 AGCCAGGATCAGTTTGTAGAAAAG 58.994 41.667 0.00 0.00 0.00 2.27
744 773 5.003804 GCCAGGATCAGTTTGTAGAAAAGA 58.996 41.667 0.00 0.00 0.00 2.52
748 777 7.862873 CCAGGATCAGTTTGTAGAAAAGAAAAC 59.137 37.037 0.00 0.00 33.65 2.43
749 778 8.405531 CAGGATCAGTTTGTAGAAAAGAAAACA 58.594 33.333 0.00 0.00 35.46 2.83
750 779 8.624776 AGGATCAGTTTGTAGAAAAGAAAACAG 58.375 33.333 0.00 0.00 35.46 3.16
751 780 8.406297 GGATCAGTTTGTAGAAAAGAAAACAGT 58.594 33.333 0.00 0.00 35.46 3.55
754 783 9.974980 TCAGTTTGTAGAAAAGAAAACAGTTTT 57.025 25.926 11.22 11.22 35.46 2.43
807 836 4.082136 ACTGTTACGGAAAGCCTCTTCTAG 60.082 45.833 0.00 0.00 0.00 2.43
808 837 3.188492 GTTACGGAAAGCCTCTTCTAGC 58.812 50.000 0.00 0.00 0.00 3.42
812 841 2.737039 CGGAAAGCCTCTTCTAGCAGTC 60.737 54.545 0.00 0.00 0.00 3.51
813 842 2.535331 GAAAGCCTCTTCTAGCAGTCG 58.465 52.381 0.00 0.00 0.00 4.18
819 848 2.685388 CCTCTTCTAGCAGTCGATGTCA 59.315 50.000 0.00 0.00 0.00 3.58
836 865 3.169908 TGTCACCCTACAAGTCAGCATA 58.830 45.455 0.00 0.00 0.00 3.14
840 869 4.081642 TCACCCTACAAGTCAGCATACTTC 60.082 45.833 1.05 0.00 37.61 3.01
845 874 5.809562 CCTACAAGTCAGCATACTTCTTCTG 59.190 44.000 1.05 0.00 37.61 3.02
851 880 6.529220 AGTCAGCATACTTCTTCTGTTTTCT 58.471 36.000 0.00 0.00 0.00 2.52
865 894 1.961394 GTTTTCTTGGGTGGGGAAGTC 59.039 52.381 0.00 0.00 0.00 3.01
866 895 0.481128 TTTCTTGGGTGGGGAAGTCC 59.519 55.000 0.00 0.00 0.00 3.85
906 935 0.743097 ATAGGGACTCACGTTACGGC 59.257 55.000 10.20 0.00 41.75 5.68
909 938 1.217244 GGACTCACGTTACGGCCAT 59.783 57.895 10.20 0.00 0.00 4.40
910 939 1.082117 GGACTCACGTTACGGCCATG 61.082 60.000 10.20 0.00 0.00 3.66
922 951 2.489971 ACGGCCATGGATATAAACGTG 58.510 47.619 18.40 0.00 31.60 4.49
1034 1073 2.507992 CTGCTCTTCGGTCAGGCG 60.508 66.667 0.00 0.00 0.00 5.52
1268 1307 1.661112 GGAGCACAAATCTGTCTACGC 59.339 52.381 0.00 0.00 31.64 4.42
1456 1495 5.004440 GGCTTTGAAAAGTTTGTCGAGAAAC 59.996 40.000 25.96 25.96 38.28 2.78
1816 1863 4.707448 ACTTCATCTACACGGATTCTCTGT 59.293 41.667 0.00 0.00 36.16 3.41
1987 2037 2.591429 CGGAGCAACACCACTGCA 60.591 61.111 0.00 0.00 42.48 4.41
2056 2106 2.287788 CGCCAAGCTGTCAAAGAAACAT 60.288 45.455 0.00 0.00 0.00 2.71
2138 2188 3.140895 CCTCCCCCACAATCCTGAATATT 59.859 47.826 0.00 0.00 0.00 1.28
2162 2261 7.706100 TGGTATATAGCATAATGACACCGTA 57.294 36.000 10.55 0.00 0.00 4.02
2163 2262 8.124808 TGGTATATAGCATAATGACACCGTAA 57.875 34.615 10.55 0.00 0.00 3.18
2167 2266 8.932945 ATATAGCATAATGACACCGTAATGAG 57.067 34.615 0.00 0.00 0.00 2.90
2168 2267 3.809832 AGCATAATGACACCGTAATGAGC 59.190 43.478 0.00 0.00 0.00 4.26
2178 2285 4.180817 CACCGTAATGAGCTAATGACACA 58.819 43.478 0.00 0.00 0.00 3.72
2223 2331 9.312904 AGATTATCCAATTTTTGTTCCTTCTCA 57.687 29.630 0.00 0.00 0.00 3.27
2260 2370 5.705905 GGTATCTGTAACTTTTCTTGTGGCT 59.294 40.000 0.00 0.00 0.00 4.75
2327 2437 4.659111 ATTCCATGTATTCGTCGTGGTA 57.341 40.909 0.00 0.00 41.28 3.25
2329 2439 4.659111 TCCATGTATTCGTCGTGGTAAT 57.341 40.909 0.00 0.00 41.28 1.89
2455 2831 3.210227 TGCTGGTCATCGAAGAAAAACA 58.790 40.909 0.00 0.00 43.58 2.83
2480 2856 3.402110 TGTTAGAAGTCAGACGTCCGTA 58.598 45.455 13.01 0.00 0.00 4.02
2530 2908 1.273606 CCTCGTTGGATCTGACACACT 59.726 52.381 0.00 0.00 38.35 3.55
2577 2955 1.863454 GTCTGCAGCAGATATGGTTCG 59.137 52.381 27.86 0.00 42.73 3.95
2586 2964 2.285220 CAGATATGGTTCGCTCCAAACG 59.715 50.000 2.80 0.00 41.09 3.60
2591 2969 2.031465 TTCGCTCCAAACGGGGAC 59.969 61.111 0.00 0.00 37.22 4.46
2635 3013 3.350219 TTCCCATTTTCCTTCTCTCCG 57.650 47.619 0.00 0.00 0.00 4.63
2660 3038 6.017605 GCTCACTCAAAATCACTCTTCTTCAA 60.018 38.462 0.00 0.00 0.00 2.69
2663 3041 6.914757 CACTCAAAATCACTCTTCTTCAAACC 59.085 38.462 0.00 0.00 0.00 3.27
2667 3045 7.445402 TCAAAATCACTCTTCTTCAAACCCTAG 59.555 37.037 0.00 0.00 0.00 3.02
2687 3065 5.804473 CCTAGATATAGCATTGAGAAGCACG 59.196 44.000 0.00 0.00 0.00 5.34
2696 3074 4.443266 AGAAGCACGGAGGCGCTC 62.443 66.667 7.64 2.45 39.45 5.03
2710 3088 3.403558 GCTCCCCTCTGTCCACCC 61.404 72.222 0.00 0.00 0.00 4.61
2711 3089 2.122729 CTCCCCTCTGTCCACCCA 59.877 66.667 0.00 0.00 0.00 4.51
2712 3090 1.307343 CTCCCCTCTGTCCACCCAT 60.307 63.158 0.00 0.00 0.00 4.00
2731 3109 2.829003 CCGTGCGCTCTCCTCCTA 60.829 66.667 9.73 0.00 0.00 2.94
2756 3134 2.734175 CGAGCAACCTAGCACGTGAATA 60.734 50.000 22.23 10.22 42.33 1.75
2796 3174 0.250727 CAAGGGTGTTGTCGTCCCAT 60.251 55.000 0.00 0.00 43.31 4.00
2802 3180 4.015406 TTGTCGTCCCATGCGGCT 62.015 61.111 0.00 0.00 34.76 5.52
2839 3222 2.202878 GCAACTCGCCGCATCCTA 60.203 61.111 0.00 0.00 32.94 2.94
2840 3223 1.595382 GCAACTCGCCGCATCCTAT 60.595 57.895 0.00 0.00 32.94 2.57
2851 3675 2.365617 CCGCATCCTATACAACCTCTGT 59.634 50.000 0.00 0.00 42.47 3.41
2955 3779 0.329039 TCCTCTAGCTCCCTCCTCCT 60.329 60.000 0.00 0.00 0.00 3.69
2956 3780 0.112412 CCTCTAGCTCCCTCCTCCTC 59.888 65.000 0.00 0.00 0.00 3.71
2957 3781 0.112412 CTCTAGCTCCCTCCTCCTCC 59.888 65.000 0.00 0.00 0.00 4.30
2958 3782 0.627768 TCTAGCTCCCTCCTCCTCCA 60.628 60.000 0.00 0.00 0.00 3.86
2959 3783 0.486879 CTAGCTCCCTCCTCCTCCAT 59.513 60.000 0.00 0.00 0.00 3.41
2960 3784 0.189574 TAGCTCCCTCCTCCTCCATG 59.810 60.000 0.00 0.00 0.00 3.66
2961 3785 2.817056 GCTCCCTCCTCCTCCATGC 61.817 68.421 0.00 0.00 0.00 4.06
2962 3786 2.444706 TCCCTCCTCCTCCATGCG 60.445 66.667 0.00 0.00 0.00 4.73
2963 3787 2.765807 CCCTCCTCCTCCATGCGT 60.766 66.667 0.00 0.00 0.00 5.24
2968 3792 2.110967 CCTCCTCCATGCGTTGCAG 61.111 63.158 0.00 0.00 43.65 4.41
3006 3830 4.715130 CTGTGGAGGGACCGGGGA 62.715 72.222 6.32 0.00 42.61 4.81
3035 3859 0.033405 TCCGTTAGAGGGAGGAGTGG 60.033 60.000 0.00 0.00 0.00 4.00
3040 3864 0.555369 TAGAGGGAGGAGTGGAGGGT 60.555 60.000 0.00 0.00 0.00 4.34
3046 3870 0.543174 GAGGAGTGGAGGGTGTCACT 60.543 60.000 2.35 0.00 45.70 3.41
3052 3876 0.178906 TGGAGGGTGTCACTGATGGA 60.179 55.000 2.35 0.00 0.00 3.41
3054 3878 1.561542 GGAGGGTGTCACTGATGGAAT 59.438 52.381 2.35 0.00 0.00 3.01
3063 3887 4.074970 GTCACTGATGGAATTGTTGGAGT 58.925 43.478 0.00 0.00 0.00 3.85
3118 3942 2.872557 CAAGGTGTGGATGCGCAG 59.127 61.111 18.32 0.00 0.00 5.18
3119 3943 1.672030 CAAGGTGTGGATGCGCAGA 60.672 57.895 18.32 0.00 0.00 4.26
3120 3944 1.376424 AAGGTGTGGATGCGCAGAG 60.376 57.895 18.32 0.00 0.00 3.35
3132 3956 3.706373 GCAGAGCGGGAAGGGTGA 61.706 66.667 0.00 0.00 0.00 4.02
3133 3957 2.581354 CAGAGCGGGAAGGGTGAG 59.419 66.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.811317 CTGCTCCGTCGGCAACTC 60.811 66.667 6.34 0.00 39.30 3.01
2 3 4.681978 ACCTGCTCCGTCGGCAAC 62.682 66.667 6.34 0.00 39.30 4.17
5 6 4.148825 ATGACCTGCTCCGTCGGC 62.149 66.667 6.34 0.00 32.68 5.54
6 7 2.105128 GATGACCTGCTCCGTCGG 59.895 66.667 4.39 4.39 32.68 4.79
7 8 2.105128 GGATGACCTGCTCCGTCG 59.895 66.667 0.00 0.00 32.68 5.12
8 9 3.622514 AGGATGACCTGCTCCGTC 58.377 61.111 0.00 0.00 45.92 4.79
25 26 2.184322 GATTGCCGTCCTCGCAGA 59.816 61.111 0.00 0.00 35.54 4.26
26 27 2.892425 GGATTGCCGTCCTCGCAG 60.892 66.667 0.00 0.00 35.32 5.18
36 37 0.815615 GGAGTGTCATCCGGATTGCC 60.816 60.000 16.19 6.00 0.00 4.52
37 38 2.695314 GGAGTGTCATCCGGATTGC 58.305 57.895 16.19 11.13 0.00 3.56
44 45 1.683418 GGTACCCCGGAGTGTCATCC 61.683 65.000 0.73 0.00 35.88 3.51
45 46 0.974010 TGGTACCCCGGAGTGTCATC 60.974 60.000 10.07 0.00 0.00 2.92
46 47 1.079621 TGGTACCCCGGAGTGTCAT 59.920 57.895 10.07 0.00 0.00 3.06
47 48 1.909781 GTGGTACCCCGGAGTGTCA 60.910 63.158 10.07 0.00 0.00 3.58
48 49 1.262640 ATGTGGTACCCCGGAGTGTC 61.263 60.000 10.07 0.00 0.00 3.67
49 50 1.229400 ATGTGGTACCCCGGAGTGT 60.229 57.895 10.07 0.00 0.00 3.55
50 51 1.220749 CATGTGGTACCCCGGAGTG 59.779 63.158 10.07 0.00 0.00 3.51
51 52 1.993391 CCATGTGGTACCCCGGAGT 60.993 63.158 10.07 0.00 0.00 3.85
52 53 2.908015 CCATGTGGTACCCCGGAG 59.092 66.667 10.07 0.00 0.00 4.63
53 54 3.404438 GCCATGTGGTACCCCGGA 61.404 66.667 10.07 0.00 37.57 5.14
54 55 4.499633 GGCCATGTGGTACCCCGG 62.500 72.222 10.07 5.54 37.57 5.73
55 56 4.499633 GGGCCATGTGGTACCCCG 62.500 72.222 10.07 0.00 37.57 5.73
56 57 1.694882 TAGGGCCATGTGGTACCCC 60.695 63.158 10.07 0.00 38.00 4.95
57 58 1.530283 GTAGGGCCATGTGGTACCC 59.470 63.158 10.07 6.63 37.66 3.69
58 59 1.145377 CGTAGGGCCATGTGGTACC 59.855 63.158 6.18 4.43 37.57 3.34
59 60 4.848685 CGTAGGGCCATGTGGTAC 57.151 61.111 6.18 0.00 37.57 3.34
99 100 3.123620 CTTCCTCACAGCCGCTGC 61.124 66.667 20.56 0.00 34.37 5.25
100 101 2.435586 CCTTCCTCACAGCCGCTG 60.436 66.667 19.08 19.08 37.52 5.18
101 102 4.400961 GCCTTCCTCACAGCCGCT 62.401 66.667 0.00 0.00 0.00 5.52
108 109 4.821589 CTCGGCGGCCTTCCTCAC 62.822 72.222 18.34 0.00 0.00 3.51
111 112 4.772231 TACCTCGGCGGCCTTCCT 62.772 66.667 18.34 0.00 35.61 3.36
112 113 4.222847 CTACCTCGGCGGCCTTCC 62.223 72.222 18.34 0.11 35.61 3.46
113 114 4.893601 GCTACCTCGGCGGCCTTC 62.894 72.222 18.34 0.00 35.61 3.46
122 123 1.066918 AATTACGGCCGCTACCTCG 59.933 57.895 28.58 0.00 0.00 4.63
123 124 0.103572 TCAATTACGGCCGCTACCTC 59.896 55.000 28.58 0.00 0.00 3.85
124 125 0.538118 TTCAATTACGGCCGCTACCT 59.462 50.000 28.58 7.96 0.00 3.08
125 126 0.935196 CTTCAATTACGGCCGCTACC 59.065 55.000 28.58 0.00 0.00 3.18
126 127 0.303796 GCTTCAATTACGGCCGCTAC 59.696 55.000 28.58 0.18 0.00 3.58
127 128 1.149361 CGCTTCAATTACGGCCGCTA 61.149 55.000 28.58 14.53 0.00 4.26
128 129 2.461110 CGCTTCAATTACGGCCGCT 61.461 57.895 28.58 15.49 0.00 5.52
129 130 2.022762 CGCTTCAATTACGGCCGC 59.977 61.111 28.58 3.86 0.00 6.53
130 131 2.707039 CCGCTTCAATTACGGCCG 59.293 61.111 26.86 26.86 40.55 6.13
134 135 2.022762 GCGGCCGCTTCAATTACG 59.977 61.111 41.71 4.32 38.26 3.18
135 136 2.022762 CGCGGCCGCTTCAATTAC 59.977 61.111 43.60 15.84 39.32 1.89
136 137 3.199190 CCGCGGCCGCTTCAATTA 61.199 61.111 43.60 0.00 39.32 1.40
150 151 4.233635 CTCTGCAGCAATCGCCGC 62.234 66.667 9.47 0.00 42.19 6.53
151 152 4.233635 GCTCTGCAGCAATCGCCG 62.234 66.667 9.47 0.00 46.06 6.46
161 162 1.183030 ATTTTGCTGCCTGCTCTGCA 61.183 50.000 0.00 0.00 43.37 4.41
162 163 0.458025 GATTTTGCTGCCTGCTCTGC 60.458 55.000 0.00 0.00 43.37 4.26
163 164 1.132643 GAGATTTTGCTGCCTGCTCTG 59.867 52.381 0.00 0.00 43.37 3.35
164 165 1.461559 GAGATTTTGCTGCCTGCTCT 58.538 50.000 0.00 0.00 43.37 4.09
165 166 0.455005 GGAGATTTTGCTGCCTGCTC 59.545 55.000 0.00 0.00 43.37 4.26
166 167 0.251474 TGGAGATTTTGCTGCCTGCT 60.251 50.000 0.00 0.00 43.37 4.24
167 168 0.604578 TTGGAGATTTTGCTGCCTGC 59.395 50.000 0.00 0.00 43.25 4.85
168 169 1.401931 CGTTGGAGATTTTGCTGCCTG 60.402 52.381 0.00 0.00 0.00 4.85
169 170 0.883833 CGTTGGAGATTTTGCTGCCT 59.116 50.000 0.00 0.00 0.00 4.75
170 171 0.881118 TCGTTGGAGATTTTGCTGCC 59.119 50.000 0.00 0.00 0.00 4.85
171 172 1.537202 ACTCGTTGGAGATTTTGCTGC 59.463 47.619 0.00 0.00 43.27 5.25
172 173 3.997021 ACTACTCGTTGGAGATTTTGCTG 59.003 43.478 0.00 0.00 43.27 4.41
173 174 4.273148 ACTACTCGTTGGAGATTTTGCT 57.727 40.909 0.00 0.00 43.27 3.91
174 175 6.421202 CCTATACTACTCGTTGGAGATTTTGC 59.579 42.308 0.00 0.00 43.27 3.68
175 176 6.421202 GCCTATACTACTCGTTGGAGATTTTG 59.579 42.308 0.00 0.00 43.27 2.44
176 177 6.324254 AGCCTATACTACTCGTTGGAGATTTT 59.676 38.462 0.00 0.00 43.27 1.82
177 178 5.834204 AGCCTATACTACTCGTTGGAGATTT 59.166 40.000 0.00 0.00 43.27 2.17
178 179 5.386924 AGCCTATACTACTCGTTGGAGATT 58.613 41.667 0.00 0.00 43.27 2.40
179 180 4.988029 AGCCTATACTACTCGTTGGAGAT 58.012 43.478 0.00 0.00 43.27 2.75
180 181 4.434545 AGCCTATACTACTCGTTGGAGA 57.565 45.455 0.00 0.00 43.27 3.71
181 182 5.307204 ACTAGCCTATACTACTCGTTGGAG 58.693 45.833 0.00 0.00 46.13 3.86
182 183 5.301835 ACTAGCCTATACTACTCGTTGGA 57.698 43.478 0.00 0.00 0.00 3.53
183 184 6.388435 AAACTAGCCTATACTACTCGTTGG 57.612 41.667 0.00 0.00 0.00 3.77
184 185 7.590689 GCTAAAACTAGCCTATACTACTCGTTG 59.409 40.741 0.00 0.00 37.11 4.10
185 186 7.501892 AGCTAAAACTAGCCTATACTACTCGTT 59.498 37.037 0.58 0.00 43.81 3.85
186 187 6.997476 AGCTAAAACTAGCCTATACTACTCGT 59.003 38.462 0.58 0.00 43.81 4.18
187 188 7.437793 AGCTAAAACTAGCCTATACTACTCG 57.562 40.000 0.58 0.00 43.81 4.18
193 194 9.771915 CGTAGATAAGCTAAAACTAGCCTATAC 57.228 37.037 0.58 0.00 43.81 1.47
194 195 9.512588 ACGTAGATAAGCTAAAACTAGCCTATA 57.487 33.333 0.58 0.00 43.81 1.31
195 196 8.406730 ACGTAGATAAGCTAAAACTAGCCTAT 57.593 34.615 0.58 0.00 43.81 2.57
196 197 7.814264 ACGTAGATAAGCTAAAACTAGCCTA 57.186 36.000 0.58 0.00 43.81 3.93
197 198 6.712179 ACGTAGATAAGCTAAAACTAGCCT 57.288 37.500 0.58 0.00 43.81 4.58
198 199 7.590689 CACTACGTAGATAAGCTAAAACTAGCC 59.409 40.741 28.74 0.00 43.81 3.93
210 211 8.411683 ACAAGATTTACCCACTACGTAGATAAG 58.588 37.037 28.74 15.47 0.00 1.73
218 219 4.034048 GCATCACAAGATTTACCCACTACG 59.966 45.833 0.00 0.00 30.20 3.51
243 244 4.716784 AGACCTCAAATCCATGTAGTAGCA 59.283 41.667 0.00 0.00 0.00 3.49
248 249 9.650539 CTCATATTAGACCTCAAATCCATGTAG 57.349 37.037 0.00 0.00 0.00 2.74
250 251 7.072961 ACCTCATATTAGACCTCAAATCCATGT 59.927 37.037 0.00 0.00 0.00 3.21
251 252 7.456725 ACCTCATATTAGACCTCAAATCCATG 58.543 38.462 0.00 0.00 0.00 3.66
258 259 6.901300 ACCAAGTACCTCATATTAGACCTCAA 59.099 38.462 0.00 0.00 0.00 3.02
297 298 3.056035 ACAATAACCGGTCACTTCTCTCC 60.056 47.826 8.04 0.00 0.00 3.71
298 299 4.174762 GACAATAACCGGTCACTTCTCTC 58.825 47.826 8.04 0.00 34.22 3.20
300 301 3.259902 GGACAATAACCGGTCACTTCTC 58.740 50.000 8.04 0.00 35.74 2.87
304 305 2.253610 TCTGGACAATAACCGGTCACT 58.746 47.619 8.04 0.00 35.74 3.41
329 330 1.066573 AGCATCTGCAGCCGGATATAC 60.067 52.381 9.47 0.00 45.16 1.47
354 355 8.663167 TGTTAGCTAGGTACAGATGTATAGGTA 58.337 37.037 0.00 7.80 30.83 3.08
355 356 7.524290 TGTTAGCTAGGTACAGATGTATAGGT 58.476 38.462 0.00 9.20 32.18 3.08
356 357 7.997773 TGTTAGCTAGGTACAGATGTATAGG 57.002 40.000 0.00 0.00 32.54 2.57
365 366 5.467705 ACGACTTTTGTTAGCTAGGTACAG 58.532 41.667 0.00 0.00 0.00 2.74
366 367 5.458041 ACGACTTTTGTTAGCTAGGTACA 57.542 39.130 0.00 0.98 0.00 2.90
384 385 1.959226 TTCGCTTCAGCCCAACGAC 60.959 57.895 0.00 0.00 37.91 4.34
398 399 4.539870 CATCCAATCACATATTGGTTCGC 58.460 43.478 14.66 0.00 46.47 4.70
399 400 4.580167 ACCATCCAATCACATATTGGTTCG 59.420 41.667 14.66 4.37 46.47 3.95
407 433 4.202315 CCCTCGTAACCATCCAATCACATA 60.202 45.833 0.00 0.00 0.00 2.29
408 434 3.433598 CCCTCGTAACCATCCAATCACAT 60.434 47.826 0.00 0.00 0.00 3.21
413 439 0.916086 TGCCCTCGTAACCATCCAAT 59.084 50.000 0.00 0.00 0.00 3.16
417 443 1.308998 CCAATGCCCTCGTAACCATC 58.691 55.000 0.00 0.00 0.00 3.51
425 451 4.420143 CGAGTACCAATGCCCTCG 57.580 61.111 0.00 0.00 40.54 4.63
429 455 4.568152 AAATAATGCGAGTACCAATGCC 57.432 40.909 0.00 0.00 0.00 4.40
430 456 5.231991 CCAAAAATAATGCGAGTACCAATGC 59.768 40.000 0.00 0.00 0.00 3.56
431 457 6.559810 TCCAAAAATAATGCGAGTACCAATG 58.440 36.000 0.00 0.00 0.00 2.82
438 464 9.868277 TGAAATAAATCCAAAAATAATGCGAGT 57.132 25.926 0.00 0.00 0.00 4.18
451 477 5.474825 GCCGGAAGTTTGAAATAAATCCAA 58.525 37.500 5.05 0.00 0.00 3.53
452 478 4.380023 CGCCGGAAGTTTGAAATAAATCCA 60.380 41.667 5.05 0.00 0.00 3.41
453 479 4.102649 CGCCGGAAGTTTGAAATAAATCC 58.897 43.478 5.05 0.00 0.00 3.01
454 480 4.976987 TCGCCGGAAGTTTGAAATAAATC 58.023 39.130 5.05 0.00 0.00 2.17
465 491 0.601841 AACGAACATCGCCGGAAGTT 60.602 50.000 5.05 2.85 45.12 2.66
470 496 1.736645 ACTGAACGAACATCGCCGG 60.737 57.895 0.00 0.00 45.12 6.13
492 518 0.392595 GGTGGACGGGAACATCTTCC 60.393 60.000 0.00 0.00 45.04 3.46
508 534 2.125713 TACATGCGCCTCGTGGTG 60.126 61.111 12.66 12.66 46.17 4.17
511 537 1.153842 TCACTACATGCGCCTCGTG 60.154 57.895 4.18 5.50 37.70 4.35
512 538 1.153823 GTCACTACATGCGCCTCGT 60.154 57.895 4.18 1.11 0.00 4.18
516 542 0.736325 ACGAAGTCACTACATGCGCC 60.736 55.000 4.18 0.00 29.74 6.53
526 552 7.965045 AGCATCTTAAGATTTTACGAAGTCAC 58.035 34.615 15.49 0.00 35.39 3.67
534 560 8.208560 CGACGTCATAGCATCTTAAGATTTTAC 58.791 37.037 15.49 5.93 31.21 2.01
541 567 2.726760 GGCGACGTCATAGCATCTTAAG 59.273 50.000 17.16 0.00 0.00 1.85
557 583 2.882324 CCTTTGAGAGACTAAGGCGAC 58.118 52.381 0.00 0.00 42.41 5.19
564 590 4.956700 CCCATGAGTACCTTTGAGAGACTA 59.043 45.833 0.00 0.00 0.00 2.59
566 592 3.118592 CCCCATGAGTACCTTTGAGAGAC 60.119 52.174 0.00 0.00 0.00 3.36
572 598 2.172717 CCCTACCCCATGAGTACCTTTG 59.827 54.545 0.00 0.00 0.00 2.77
573 599 2.226065 ACCCTACCCCATGAGTACCTTT 60.226 50.000 0.00 0.00 0.00 3.11
585 611 3.633116 ACACGCACACCCTACCCC 61.633 66.667 0.00 0.00 0.00 4.95
595 622 1.201877 CCTATAAACGCACACACGCAC 60.202 52.381 0.00 0.00 36.19 5.34
605 632 4.389077 GCATACACTCATCCCTATAAACGC 59.611 45.833 0.00 0.00 0.00 4.84
616 643 6.612306 TCACATATACGAGCATACACTCATC 58.388 40.000 0.00 0.00 36.42 2.92
670 699 3.586470 TGTTGGGTTCAGCCTAAAGAA 57.414 42.857 0.00 0.00 39.52 2.52
688 717 1.667830 CGAGCCACCGTGTCATTGT 60.668 57.895 0.00 0.00 0.00 2.71
693 722 2.202756 GATCCGAGCCACCGTGTC 60.203 66.667 0.00 0.00 0.00 3.67
697 726 1.067582 GTTAGGATCCGAGCCACCG 59.932 63.158 5.98 0.00 0.00 4.94
743 772 8.080417 GGATCCCTACTAAACAAAACTGTTTTC 58.920 37.037 15.17 0.19 41.58 2.29
744 773 7.562088 TGGATCCCTACTAAACAAAACTGTTTT 59.438 33.333 12.50 12.50 41.58 2.43
748 777 7.703058 ATTGGATCCCTACTAAACAAAACTG 57.297 36.000 9.90 0.00 0.00 3.16
749 778 9.462606 CTTATTGGATCCCTACTAAACAAAACT 57.537 33.333 9.90 0.00 0.00 2.66
750 779 9.457436 TCTTATTGGATCCCTACTAAACAAAAC 57.543 33.333 9.90 0.00 0.00 2.43
751 780 9.681062 CTCTTATTGGATCCCTACTAAACAAAA 57.319 33.333 9.90 0.00 0.00 2.44
753 782 8.388656 ACTCTTATTGGATCCCTACTAAACAA 57.611 34.615 9.90 0.00 0.00 2.83
754 783 7.070821 GGACTCTTATTGGATCCCTACTAAACA 59.929 40.741 9.90 0.00 0.00 2.83
755 784 7.070821 TGGACTCTTATTGGATCCCTACTAAAC 59.929 40.741 9.90 0.00 0.00 2.01
761 790 6.447084 AGTTTTGGACTCTTATTGGATCCCTA 59.553 38.462 9.90 0.00 31.20 3.53
807 836 0.530744 TGTAGGGTGACATCGACTGC 59.469 55.000 0.00 0.00 0.00 4.40
808 837 2.231478 ACTTGTAGGGTGACATCGACTG 59.769 50.000 0.00 0.00 0.00 3.51
812 841 2.881074 CTGACTTGTAGGGTGACATCG 58.119 52.381 0.00 0.00 0.00 3.84
813 842 2.028112 TGCTGACTTGTAGGGTGACATC 60.028 50.000 0.00 0.00 0.00 3.06
819 848 4.097418 AGAAGTATGCTGACTTGTAGGGT 58.903 43.478 8.33 0.00 39.79 4.34
836 865 3.954258 CCACCCAAGAAAACAGAAGAAGT 59.046 43.478 0.00 0.00 0.00 3.01
840 869 1.963515 CCCCACCCAAGAAAACAGAAG 59.036 52.381 0.00 0.00 0.00 2.85
845 874 1.961394 GACTTCCCCACCCAAGAAAAC 59.039 52.381 0.00 0.00 0.00 2.43
906 935 4.351874 AGGGACACGTTTATATCCATGG 57.648 45.455 4.97 4.97 32.45 3.66
909 938 3.775866 TGGAAGGGACACGTTTATATCCA 59.224 43.478 0.00 0.00 32.45 3.41
910 939 4.377897 CTGGAAGGGACACGTTTATATCC 58.622 47.826 0.00 0.00 0.00 2.59
1017 1056 2.507992 CGCCTGACCGAAGAGCAG 60.508 66.667 0.00 0.00 0.00 4.24
1034 1073 1.534729 CTTCTTTGGTGGGTACTGCC 58.465 55.000 0.00 0.00 0.00 4.85
1159 1198 1.761198 GAGGAACTTACCGGCACCTAT 59.239 52.381 0.00 0.00 41.55 2.57
1170 1209 2.314071 TTCCCGACCTGAGGAACTTA 57.686 50.000 4.99 0.00 41.55 2.24
1268 1307 0.448593 GAGAGACAGGAAGACCGACG 59.551 60.000 0.00 0.00 41.83 5.12
1696 1743 3.569701 CCAAAGAGCTCAGCCTTAAACAA 59.430 43.478 17.77 0.00 0.00 2.83
1987 2037 3.386716 ATGCCCTTTTCAGGTGCAT 57.613 47.368 9.96 9.96 45.07 3.96
2056 2106 5.912892 TGTTACGAGATGCTTGAATCCATA 58.087 37.500 0.00 0.00 0.00 2.74
2138 2188 6.599356 ACGGTGTCATTATGCTATATACCA 57.401 37.500 0.00 0.00 0.00 3.25
2151 2201 5.523916 GTCATTAGCTCATTACGGTGTCATT 59.476 40.000 0.00 0.00 0.00 2.57
2152 2202 5.050490 GTCATTAGCTCATTACGGTGTCAT 58.950 41.667 0.00 0.00 0.00 3.06
2154 2204 4.267928 GTGTCATTAGCTCATTACGGTGTC 59.732 45.833 0.00 0.00 0.00 3.67
2155 2205 4.181578 GTGTCATTAGCTCATTACGGTGT 58.818 43.478 0.00 0.00 0.00 4.16
2156 2206 4.180817 TGTGTCATTAGCTCATTACGGTG 58.819 43.478 0.00 0.00 0.00 4.94
2157 2207 4.081642 ACTGTGTCATTAGCTCATTACGGT 60.082 41.667 0.00 0.00 0.00 4.83
2158 2208 4.433615 ACTGTGTCATTAGCTCATTACGG 58.566 43.478 0.00 0.00 0.00 4.02
2159 2209 7.275779 AGTTTACTGTGTCATTAGCTCATTACG 59.724 37.037 0.00 0.00 0.00 3.18
2162 2261 7.390027 AGAGTTTACTGTGTCATTAGCTCATT 58.610 34.615 0.00 0.00 0.00 2.57
2163 2262 6.940739 AGAGTTTACTGTGTCATTAGCTCAT 58.059 36.000 0.00 0.00 0.00 2.90
2167 2266 9.582431 TTATGTAGAGTTTACTGTGTCATTAGC 57.418 33.333 0.00 0.00 0.00 3.09
2327 2437 9.836864 AAGGTGCAAAGAAAAAGAATAGAAATT 57.163 25.926 0.00 0.00 0.00 1.82
2329 2439 7.710475 CCAAGGTGCAAAGAAAAAGAATAGAAA 59.290 33.333 0.00 0.00 0.00 2.52
2435 2806 3.896648 TGTTTTTCTTCGATGACCAGC 57.103 42.857 0.00 0.00 0.00 4.85
2455 2831 4.684703 CGGACGTCTGACTTCTAACATTTT 59.315 41.667 20.01 0.00 0.00 1.82
2480 2856 0.034337 TCGCTCCAAAAACGCCTAGT 59.966 50.000 0.00 0.00 0.00 2.57
2586 2964 2.597903 GCATTCCCTCTGGTCCCC 59.402 66.667 0.00 0.00 0.00 4.81
2591 2969 1.002134 ACGTTGGCATTCCCTCTGG 60.002 57.895 0.00 0.00 0.00 3.86
2593 2971 1.079127 CGACGTTGGCATTCCCTCT 60.079 57.895 0.00 0.00 0.00 3.69
2594 2972 0.953960 AACGACGTTGGCATTCCCTC 60.954 55.000 13.38 0.00 0.00 4.30
2603 2981 4.408694 GAAAATGGGAATAACGACGTTGG 58.591 43.478 23.00 0.00 0.00 3.77
2635 3013 5.468072 TGAAGAAGAGTGATTTTGAGTGAGC 59.532 40.000 0.00 0.00 0.00 4.26
2660 3038 6.270927 TGCTTCTCAATGCTATATCTAGGGTT 59.729 38.462 0.00 0.00 0.00 4.11
2663 3041 5.804473 CGTGCTTCTCAATGCTATATCTAGG 59.196 44.000 0.00 0.00 0.00 3.02
2667 3045 4.560128 TCCGTGCTTCTCAATGCTATATC 58.440 43.478 0.00 0.00 0.00 1.63
2696 3074 3.001514 CATGGGTGGACAGAGGGG 58.998 66.667 0.00 0.00 0.00 4.79
2719 3097 1.448922 CTCGGGTTAGGAGGAGAGCG 61.449 65.000 0.00 0.00 0.00 5.03
2731 3109 1.003718 GTGCTAGGTTGCTCGGGTT 60.004 57.895 0.00 0.00 0.00 4.11
2756 3134 1.295915 TGCCCCCTCCATTAGCCAAT 61.296 55.000 0.00 0.00 0.00 3.16
2796 3174 3.043713 CTTGACGCTTCAGCCGCA 61.044 61.111 0.00 0.00 37.91 5.69
2839 3222 2.834549 CTGGAGGTCACAGAGGTTGTAT 59.165 50.000 0.00 0.00 38.16 2.29
2840 3223 2.248248 CTGGAGGTCACAGAGGTTGTA 58.752 52.381 0.00 0.00 38.16 2.41
2919 3743 0.249489 GGAGCGCTATCATCGTTGGT 60.249 55.000 11.50 0.00 0.00 3.67
2922 3746 1.323412 AGAGGAGCGCTATCATCGTT 58.677 50.000 11.50 0.00 35.22 3.85
2957 3781 4.465512 GACGCCCTGCAACGCATG 62.466 66.667 5.60 0.00 38.13 4.06
2962 3786 4.980805 TCGTGGACGCCCTGCAAC 62.981 66.667 0.00 0.00 39.60 4.17
2963 3787 4.980805 GTCGTGGACGCCCTGCAA 62.981 66.667 0.00 0.00 39.60 4.08
2968 3792 3.296709 ATCACAGTCGTGGACGCCC 62.297 63.158 0.00 0.00 43.79 6.13
3016 3840 0.033405 CCACTCCTCCCTCTAACGGA 60.033 60.000 0.00 0.00 0.00 4.69
3020 3844 0.637195 CCCTCCACTCCTCCCTCTAA 59.363 60.000 0.00 0.00 0.00 2.10
3027 3851 0.543174 AGTGACACCCTCCACTCCTC 60.543 60.000 0.84 0.00 39.19 3.71
3030 3854 1.066573 CATCAGTGACACCCTCCACTC 60.067 57.143 0.84 0.00 41.26 3.51
3032 3856 0.036010 CCATCAGTGACACCCTCCAC 60.036 60.000 0.84 0.00 0.00 4.02
3035 3859 3.012518 CAATTCCATCAGTGACACCCTC 58.987 50.000 0.84 0.00 0.00 4.30
3040 3864 4.074259 CTCCAACAATTCCATCAGTGACA 58.926 43.478 0.00 0.00 0.00 3.58
3046 3870 4.567537 CCACCTACTCCAACAATTCCATCA 60.568 45.833 0.00 0.00 0.00 3.07
3052 3876 2.615493 CGCTCCACCTACTCCAACAATT 60.615 50.000 0.00 0.00 0.00 2.32
3054 3878 0.320374 CGCTCCACCTACTCCAACAA 59.680 55.000 0.00 0.00 0.00 2.83
3063 3887 3.390521 CCACTGCCGCTCCACCTA 61.391 66.667 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.