Multiple sequence alignment - TraesCS7D01G496300

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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 TraesCS7D01G496300 chr7D 100.000 4688 0 0 1 4688 603159677 603154990 0.000000e+00 8658.0
1 TraesCS7D01G496300 chr7D 93.434 792 52 0 2967 3758 2151865 2151074 0.000000e+00 1175.0
2 TraesCS7D01G496300 chr7D 91.519 283 22 2 192 473 472526309 472526028 5.690000e-104 388.0
3 TraesCS7D01G496300 chr7D 92.537 67 5 0 480 546 528156215 528156149 3.860000e-16 97.1
4 TraesCS7D01G496300 chr7D 100.000 31 0 0 562 592 611459496 611459466 1.820000e-04 58.4
5 TraesCS7D01G496300 chr7D 100.000 28 0 0 565 592 611442575 611442548 8.000000e-03 52.8
6 TraesCS7D01G496300 chr7A 94.006 3620 164 24 617 4219 695880354 695876771 0.000000e+00 5433.0
7 TraesCS7D01G496300 chr7A 84.080 603 79 11 2954 3552 695849327 695848738 2.450000e-157 566.0
8 TraesCS7D01G496300 chr7A 94.382 356 19 1 4334 4688 695876720 695876365 3.190000e-151 545.0
9 TraesCS7D01G496300 chr7A 82.301 226 40 0 2686 2911 695849566 695849341 3.700000e-46 196.0
10 TraesCS7D01G496300 chr7A 95.312 64 3 0 480 543 89628592 89628655 8.300000e-18 102.0
11 TraesCS7D01G496300 chr7A 100.000 30 0 0 563 592 98094870 98094841 6.550000e-04 56.5
12 TraesCS7D01G496300 chr5B 92.938 3512 158 32 699 4174 502458541 502455084 0.000000e+00 5029.0
13 TraesCS7D01G496300 chr5B 92.975 726 45 3 3276 4001 502452276 502451557 0.000000e+00 1053.0
14 TraesCS7D01G496300 chr5B 93.478 414 21 5 4276 4688 502455026 502454618 1.120000e-170 610.0
15 TraesCS7D01G496300 chr5B 89.643 280 26 2 196 473 625040098 625039820 2.080000e-93 353.0
16 TraesCS7D01G496300 chr5B 89.643 280 26 2 196 473 628611170 628610892 2.080000e-93 353.0
17 TraesCS7D01G496300 chr5B 90.741 162 15 0 4058 4219 502451558 502451397 2.840000e-52 217.0
18 TraesCS7D01G496300 chr5B 88.000 100 4 4 617 708 502471321 502471222 1.380000e-20 111.0
19 TraesCS7D01G496300 chr5B 98.039 51 1 0 4638 4688 502384308 502384358 6.460000e-14 89.8
20 TraesCS7D01G496300 chr5A 94.840 2539 109 5 1264 3793 528363964 528366489 0.000000e+00 3943.0
21 TraesCS7D01G496300 chr5A 92.903 944 59 4 3276 4219 528370126 528371061 0.000000e+00 1365.0
22 TraesCS7D01G496300 chr5A 85.998 957 67 25 3776 4688 528366519 528367452 0.000000e+00 963.0
23 TraesCS7D01G496300 chr5A 83.150 546 33 32 729 1265 528501429 528500934 1.200000e-120 444.0
24 TraesCS7D01G496300 chr5A 92.222 270 18 3 205 473 669195912 669195645 3.420000e-101 379.0
25 TraesCS7D01G496300 chr5A 100.000 30 0 0 563 592 632142988 632143017 6.550000e-04 56.5
26 TraesCS7D01G496300 chr5D 93.458 2033 94 14 848 2880 416034139 416032146 0.000000e+00 2981.0
27 TraesCS7D01G496300 chr5D 89.191 1619 100 27 2872 4448 416000323 415998738 0.000000e+00 1951.0
28 TraesCS7D01G496300 chr5D 92.600 946 62 4 3276 4219 415986789 415985850 0.000000e+00 1352.0
29 TraesCS7D01G496300 chr5D 95.968 248 8 2 4442 4688 415989531 415989285 7.310000e-108 401.0
30 TraesCS7D01G496300 chr5D 95.312 64 3 0 482 545 262832990 262832927 8.300000e-18 102.0
31 TraesCS7D01G496300 chr5D 95.312 64 3 0 482 545 497940462 497940525 8.300000e-18 102.0
32 TraesCS7D01G496300 chr5D 95.745 47 2 0 803 849 416053209 416053163 5.030000e-10 76.8
33 TraesCS7D01G496300 chrUn 95.663 392 17 0 2720 3111 479720718 479720327 8.560000e-177 630.0
34 TraesCS7D01G496300 chr3D 86.947 475 46 10 1 473 335197864 335197404 1.930000e-143 520.0
35 TraesCS7D01G496300 chr3D 89.085 284 29 1 192 473 8939156 8939439 7.460000e-93 351.0
36 TraesCS7D01G496300 chr3D 89.085 284 29 1 192 473 113329273 113329556 7.460000e-93 351.0
37 TraesCS7D01G496300 chr3D 90.355 197 13 2 1 197 8938460 8938650 2.170000e-63 254.0
38 TraesCS7D01G496300 chr3D 91.304 69 6 0 480 548 496348452 496348384 1.390000e-15 95.3
39 TraesCS7D01G496300 chr3D 100.000 31 0 0 562 592 611018413 611018383 1.820000e-04 58.4
40 TraesCS7D01G496300 chr2B 90.210 286 24 3 192 474 749799004 749799288 2.060000e-98 370.0
41 TraesCS7D01G496300 chr2B 89.848 197 20 0 1 197 667272584 667272780 2.170000e-63 254.0
42 TraesCS7D01G496300 chr2A 89.753 283 28 1 192 473 735692401 735692119 1.240000e-95 361.0
43 TraesCS7D01G496300 chr2D 89.716 282 23 6 196 473 576275535 576275256 5.770000e-94 355.0
44 TraesCS7D01G496300 chr2D 87.745 204 17 4 1 197 455934815 455935017 1.010000e-56 231.0
45 TraesCS7D01G496300 chr2D 93.750 64 4 0 482 545 544581395 544581458 3.860000e-16 97.1
46 TraesCS7D01G496300 chr7B 91.371 197 16 1 1 197 37419580 37419385 7.730000e-68 268.0
47 TraesCS7D01G496300 chr7B 87.500 80 9 1 474 552 115567325 115567404 1.800000e-14 91.6
48 TraesCS7D01G496300 chr7B 94.595 37 2 0 556 592 86176017 86175981 1.820000e-04 58.4
49 TraesCS7D01G496300 chr6B 91.371 197 16 1 1 197 693251024 693250829 7.730000e-68 268.0
50 TraesCS7D01G496300 chr3B 88.832 197 22 0 1 197 546198885 546199081 4.690000e-60 243.0
51 TraesCS7D01G496300 chr3A 90.323 186 17 1 4 189 608180697 608180513 4.690000e-60 243.0
52 TraesCS7D01G496300 chr1D 87.817 197 24 0 1 197 479038126 479038322 1.010000e-56 231.0
53 TraesCS7D01G496300 chr1D 95.161 62 3 0 482 543 351263335 351263396 1.070000e-16 99.0
54 TraesCS7D01G496300 chr4A 95.312 64 3 0 482 545 713370560 713370623 8.300000e-18 102.0
55 TraesCS7D01G496300 chr4D 100.000 30 0 0 563 592 31804549 31804578 6.550000e-04 56.5
56 TraesCS7D01G496300 chr6D 100.000 28 0 0 562 589 2471477 2471504 8.000000e-03 52.8


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 TraesCS7D01G496300 chr7D 603154990 603159677 4687 True 8658.000000 8658 100.0000 1 4688 1 chr7D.!!$R4 4687
1 TraesCS7D01G496300 chr7D 2151074 2151865 791 True 1175.000000 1175 93.4340 2967 3758 1 chr7D.!!$R1 791
2 TraesCS7D01G496300 chr7A 695876365 695880354 3989 True 2989.000000 5433 94.1940 617 4688 2 chr7A.!!$R3 4071
3 TraesCS7D01G496300 chr7A 695848738 695849566 828 True 381.000000 566 83.1905 2686 3552 2 chr7A.!!$R2 866
4 TraesCS7D01G496300 chr5B 502451397 502458541 7144 True 1727.250000 5029 92.5330 699 4688 4 chr5B.!!$R4 3989
5 TraesCS7D01G496300 chr5A 528363964 528371061 7097 False 2090.333333 3943 91.2470 1264 4688 3 chr5A.!!$F2 3424
6 TraesCS7D01G496300 chr5D 416032146 416034139 1993 True 2981.000000 2981 93.4580 848 2880 1 chr5D.!!$R3 2032
7 TraesCS7D01G496300 chr5D 415998738 416000323 1585 True 1951.000000 1951 89.1910 2872 4448 1 chr5D.!!$R2 1576
8 TraesCS7D01G496300 chr5D 415985850 415989531 3681 True 876.500000 1352 94.2840 3276 4688 2 chr5D.!!$R5 1412
9 TraesCS7D01G496300 chr3D 8938460 8939439 979 False 302.500000 351 89.7200 1 473 2 chr3D.!!$F2 472

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
487 488 0.165944 CGCAATCCTCGTTTGTCCAC 59.834 55.0 0.00 0.0 0.00 4.02 F
741 745 0.460987 TTGGCACCCAAACAAAAGCG 60.461 50.0 0.00 0.0 40.92 4.68 F
1408 1515 1.595993 CTCCCTCTTCGGCTTCGTCA 61.596 60.0 0.00 0.0 35.06 4.35 F
2979 3256 0.179089 CTGTCCGGATCCTTCTGCTG 60.179 60.0 7.81 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1703 1.022735 ACGCCATGTAGTACTCGGAG 58.977 55.000 0.00 2.83 0.00 4.63 R
2028 2285 1.139095 GAGCGTGAGGAACCCGTAG 59.861 63.158 0.00 0.00 0.00 3.51 R
3396 3676 0.313672 GATGCTGCAAACCGGTGAAA 59.686 50.000 8.52 0.00 0.00 2.69 R
4588 5016 1.203994 GGCACAGCAGCAAAATGAGAT 59.796 47.619 0.00 0.00 35.83 2.75 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
43 44 2.439701 TCCCGTCCAGGAGTAGCG 60.440 66.667 0.00 0.00 45.00 4.26
59 60 4.873129 CGCTCGATGGGTGACGGG 62.873 72.222 0.00 0.00 0.00 5.28
63 64 3.387091 CGATGGGTGACGGGTCCA 61.387 66.667 0.00 0.00 34.79 4.02
68 69 4.083862 GGTGACGGGTCCAGCTCC 62.084 72.222 0.00 0.00 0.00 4.70
89 90 1.609072 GACTTTGCTTTGACAGGGGAC 59.391 52.381 0.00 0.00 0.00 4.46
91 92 0.181587 TTTGCTTTGACAGGGGACGA 59.818 50.000 0.00 0.00 0.00 4.20
92 93 0.534203 TTGCTTTGACAGGGGACGAC 60.534 55.000 0.00 0.00 0.00 4.34
217 218 2.187946 CTTCGCTGGGGTGGCTAG 59.812 66.667 0.00 0.00 0.00 3.42
218 219 3.391665 CTTCGCTGGGGTGGCTAGG 62.392 68.421 0.00 0.00 0.00 3.02
221 222 3.339093 GCTGGGGTGGCTAGGGTT 61.339 66.667 0.00 0.00 0.00 4.11
223 224 1.000896 CTGGGGTGGCTAGGGTTTG 60.001 63.158 0.00 0.00 0.00 2.93
224 225 2.362503 GGGGTGGCTAGGGTTTGC 60.363 66.667 0.00 0.00 0.00 3.68
230 231 4.770874 GCTAGGGTTTGCCGGCGA 62.771 66.667 23.90 19.26 34.97 5.54
231 232 2.818274 CTAGGGTTTGCCGGCGAC 60.818 66.667 23.90 22.17 34.97 5.19
243 244 4.803426 GGCGACGGAGGAGCAGTG 62.803 72.222 0.00 0.00 0.00 3.66
244 245 4.057428 GCGACGGAGGAGCAGTGT 62.057 66.667 0.00 0.00 0.00 3.55
245 246 2.126307 CGACGGAGGAGCAGTGTG 60.126 66.667 0.00 0.00 0.00 3.82
246 247 2.262915 GACGGAGGAGCAGTGTGG 59.737 66.667 0.00 0.00 0.00 4.17
247 248 3.941657 GACGGAGGAGCAGTGTGGC 62.942 68.421 0.00 0.00 0.00 5.01
249 250 2.351244 CGGAGGAGCAGTGTGGCTA 61.351 63.158 0.00 0.00 45.99 3.93
250 251 1.519719 GGAGGAGCAGTGTGGCTAG 59.480 63.158 0.00 0.00 45.99 3.42
251 252 0.972983 GGAGGAGCAGTGTGGCTAGA 60.973 60.000 0.00 0.00 45.99 2.43
252 253 1.118838 GAGGAGCAGTGTGGCTAGAT 58.881 55.000 0.00 0.00 45.99 1.98
253 254 0.829333 AGGAGCAGTGTGGCTAGATG 59.171 55.000 0.00 0.00 45.99 2.90
254 255 0.179062 GGAGCAGTGTGGCTAGATGG 60.179 60.000 0.00 0.00 45.99 3.51
255 256 0.179062 GAGCAGTGTGGCTAGATGGG 60.179 60.000 0.00 0.00 45.99 4.00
256 257 1.153086 GCAGTGTGGCTAGATGGGG 60.153 63.158 0.00 0.00 0.00 4.96
257 258 1.626356 GCAGTGTGGCTAGATGGGGA 61.626 60.000 0.00 0.00 0.00 4.81
258 259 0.179000 CAGTGTGGCTAGATGGGGAC 59.821 60.000 0.00 0.00 0.00 4.46
260 261 2.063979 TGTGGCTAGATGGGGACGG 61.064 63.158 0.00 0.00 0.00 4.79
261 262 2.445845 TGGCTAGATGGGGACGGG 60.446 66.667 0.00 0.00 0.00 5.28
262 263 3.242291 GGCTAGATGGGGACGGGG 61.242 72.222 0.00 0.00 0.00 5.73
263 264 3.242291 GCTAGATGGGGACGGGGG 61.242 72.222 0.00 0.00 0.00 5.40
264 265 3.242291 CTAGATGGGGACGGGGGC 61.242 72.222 0.00 0.00 0.00 5.80
265 266 3.774336 TAGATGGGGACGGGGGCT 61.774 66.667 0.00 0.00 0.00 5.19
286 287 1.227089 CTGGAAGCGGATGAGGACG 60.227 63.158 0.00 0.00 0.00 4.79
287 288 2.107141 GGAAGCGGATGAGGACGG 59.893 66.667 0.00 0.00 0.00 4.79
310 311 2.739287 CCGCACGGTCGGCTTAAA 60.739 61.111 0.00 0.00 43.18 1.52
312 313 1.570475 CGCACGGTCGGCTTAAAAA 59.430 52.632 0.00 0.00 0.00 1.94
335 336 3.188786 GACCACCGTCGCTGATGC 61.189 66.667 0.00 0.00 0.00 3.91
353 354 2.727392 CGTGGGCCCGAGGTCATTA 61.727 63.158 19.37 0.00 0.00 1.90
354 355 1.605453 GTGGGCCCGAGGTCATTAA 59.395 57.895 19.37 0.00 0.00 1.40
355 356 0.182775 GTGGGCCCGAGGTCATTAAT 59.817 55.000 19.37 0.00 0.00 1.40
357 358 2.128535 TGGGCCCGAGGTCATTAATTA 58.871 47.619 19.37 0.00 0.00 1.40
358 359 2.510382 TGGGCCCGAGGTCATTAATTAA 59.490 45.455 19.37 0.00 0.00 1.40
359 360 3.146847 GGGCCCGAGGTCATTAATTAAG 58.853 50.000 5.69 0.00 0.00 1.85
362 363 4.036380 GGCCCGAGGTCATTAATTAAGTTG 59.964 45.833 3.94 0.00 0.00 3.16
363 364 4.879545 GCCCGAGGTCATTAATTAAGTTGA 59.120 41.667 3.94 1.01 0.00 3.18
364 365 5.220796 GCCCGAGGTCATTAATTAAGTTGAC 60.221 44.000 17.90 17.90 38.17 3.18
372 373 8.336801 GTCATTAATTAAGTTGACCAGGAAGT 57.663 34.615 16.26 0.00 33.91 3.01
373 374 8.451748 GTCATTAATTAAGTTGACCAGGAAGTC 58.548 37.037 16.26 0.00 33.91 3.01
375 376 3.396260 TTAAGTTGACCAGGAAGTCCG 57.604 47.619 0.00 0.00 42.08 4.79
376 377 0.250338 AAGTTGACCAGGAAGTCCGC 60.250 55.000 0.00 0.00 42.08 5.54
377 378 2.027625 GTTGACCAGGAAGTCCGCG 61.028 63.158 0.00 0.00 42.08 6.46
379 380 4.452733 GACCAGGAAGTCCGCGGG 62.453 72.222 27.83 8.96 42.08 6.13
385 386 3.423154 GAAGTCCGCGGGCAGTTG 61.423 66.667 34.17 0.12 0.00 3.16
396 397 4.980805 GCAGTTGGACGACCGCCA 62.981 66.667 0.00 2.39 39.42 5.69
397 398 2.738521 CAGTTGGACGACCGCCAG 60.739 66.667 0.00 0.00 39.42 4.85
398 399 2.915659 AGTTGGACGACCGCCAGA 60.916 61.111 0.00 0.00 39.42 3.86
399 400 2.264794 GTTGGACGACCGCCAGAT 59.735 61.111 0.00 0.00 39.42 2.90
401 402 3.309436 TTGGACGACCGCCAGATGG 62.309 63.158 0.00 0.00 39.42 3.51
402 403 4.530857 GGACGACCGCCAGATGGG 62.531 72.222 0.12 0.00 40.85 4.00
446 447 2.474266 CATGGCGTCCGTTTCGTG 59.526 61.111 0.00 0.00 0.00 4.35
449 450 3.408851 GGCGTCCGTTTCGTGTCC 61.409 66.667 0.00 0.00 0.00 4.02
450 451 3.759828 GCGTCCGTTTCGTGTCCG 61.760 66.667 0.00 0.00 0.00 4.79
451 452 3.759828 CGTCCGTTTCGTGTCCGC 61.760 66.667 0.00 0.00 0.00 5.54
452 453 3.759828 GTCCGTTTCGTGTCCGCG 61.760 66.667 0.00 0.00 0.00 6.46
462 463 4.673298 TGTCCGCGCCGACACATT 62.673 61.111 24.54 0.00 37.85 2.71
463 464 3.419759 GTCCGCGCCGACACATTT 61.420 61.111 21.55 0.00 32.74 2.32
464 465 3.418913 TCCGCGCCGACACATTTG 61.419 61.111 0.00 0.00 0.00 2.32
465 466 3.722295 CCGCGCCGACACATTTGT 61.722 61.111 0.00 0.00 39.32 2.83
475 476 2.740668 CACATTTGTGGCGCAATCC 58.259 52.632 15.06 0.00 42.10 3.01
477 478 0.527565 ACATTTGTGGCGCAATCCTC 59.472 50.000 15.06 0.00 36.89 3.71
478 479 0.523968 CATTTGTGGCGCAATCCTCG 60.524 55.000 15.06 0.00 36.89 4.63
480 481 1.169661 TTTGTGGCGCAATCCTCGTT 61.170 50.000 15.06 0.00 36.89 3.85
482 483 1.154225 GTGGCGCAATCCTCGTTTG 60.154 57.895 10.83 0.00 0.00 2.93
483 484 1.599518 TGGCGCAATCCTCGTTTGT 60.600 52.632 10.83 0.00 0.00 2.83
484 485 1.134694 GGCGCAATCCTCGTTTGTC 59.865 57.895 10.83 0.00 0.00 3.18
485 486 1.134694 GCGCAATCCTCGTTTGTCC 59.865 57.895 0.30 0.00 0.00 4.02
486 487 1.573829 GCGCAATCCTCGTTTGTCCA 61.574 55.000 0.30 0.00 0.00 4.02
487 488 0.165944 CGCAATCCTCGTTTGTCCAC 59.834 55.000 0.00 0.00 0.00 4.02
488 489 0.165944 GCAATCCTCGTTTGTCCACG 59.834 55.000 0.00 0.00 41.78 4.94
492 493 2.355363 CTCGTTTGTCCACGCCGA 60.355 61.111 0.00 0.00 40.14 5.54
493 494 2.654912 CTCGTTTGTCCACGCCGAC 61.655 63.158 0.00 0.00 40.14 4.79
494 495 3.708734 CGTTTGTCCACGCCGACC 61.709 66.667 0.00 0.00 32.43 4.79
495 496 3.351416 GTTTGTCCACGCCGACCC 61.351 66.667 0.00 0.00 31.35 4.46
496 497 3.862991 TTTGTCCACGCCGACCCA 61.863 61.111 0.00 0.00 31.35 4.51
498 499 2.888464 TTTGTCCACGCCGACCCAAA 62.888 55.000 0.00 0.00 31.35 3.28
499 500 3.351416 GTCCACGCCGACCCAAAC 61.351 66.667 0.00 0.00 0.00 2.93
500 501 4.973055 TCCACGCCGACCCAAACG 62.973 66.667 0.00 0.00 0.00 3.60
524 525 3.486263 GGCAGACGAAATGGGTCG 58.514 61.111 0.00 0.00 46.54 4.79
526 527 1.359459 GGCAGACGAAATGGGTCGAC 61.359 60.000 7.13 7.13 43.86 4.20
527 528 1.359459 GCAGACGAAATGGGTCGACC 61.359 60.000 27.04 27.04 43.86 4.79
539 540 0.521735 GGTCGACCCATTGAAGTTGC 59.478 55.000 24.75 0.00 0.00 4.17
541 542 1.464997 GTCGACCCATTGAAGTTGCTC 59.535 52.381 3.51 0.00 0.00 4.26
542 543 1.347707 TCGACCCATTGAAGTTGCTCT 59.652 47.619 0.00 0.00 0.00 4.09
543 544 2.154462 CGACCCATTGAAGTTGCTCTT 58.846 47.619 0.00 0.00 39.32 2.85
544 545 3.007506 TCGACCCATTGAAGTTGCTCTTA 59.992 43.478 0.00 0.00 36.40 2.10
545 546 3.941483 CGACCCATTGAAGTTGCTCTTAT 59.059 43.478 0.00 0.00 36.40 1.73
547 548 4.273318 ACCCATTGAAGTTGCTCTTATCC 58.727 43.478 0.00 0.00 36.40 2.59
548 549 4.263905 ACCCATTGAAGTTGCTCTTATCCA 60.264 41.667 0.00 0.00 36.40 3.41
549 550 4.891756 CCCATTGAAGTTGCTCTTATCCAT 59.108 41.667 0.00 0.00 36.40 3.41
550 551 6.064060 CCCATTGAAGTTGCTCTTATCCATA 58.936 40.000 0.00 0.00 36.40 2.74
551 552 6.547141 CCCATTGAAGTTGCTCTTATCCATAA 59.453 38.462 0.00 0.00 36.40 1.90
552 553 7.232127 CCCATTGAAGTTGCTCTTATCCATAAT 59.768 37.037 0.00 0.00 36.40 1.28
553 554 8.636213 CCATTGAAGTTGCTCTTATCCATAATT 58.364 33.333 0.00 0.00 36.40 1.40
554 555 9.459640 CATTGAAGTTGCTCTTATCCATAATTG 57.540 33.333 0.00 0.00 36.40 2.32
555 556 8.806429 TTGAAGTTGCTCTTATCCATAATTGA 57.194 30.769 0.00 0.00 36.40 2.57
556 557 8.806429 TGAAGTTGCTCTTATCCATAATTGAA 57.194 30.769 0.00 0.00 36.40 2.69
557 558 8.677300 TGAAGTTGCTCTTATCCATAATTGAAC 58.323 33.333 0.00 0.00 36.40 3.18
559 560 8.218338 AGTTGCTCTTATCCATAATTGAACAG 57.782 34.615 0.00 0.00 0.00 3.16
560 561 7.831193 AGTTGCTCTTATCCATAATTGAACAGT 59.169 33.333 0.00 0.00 0.00 3.55
561 562 7.558161 TGCTCTTATCCATAATTGAACAGTG 57.442 36.000 0.00 0.00 0.00 3.66
562 563 6.038603 TGCTCTTATCCATAATTGAACAGTGC 59.961 38.462 0.00 0.00 0.00 4.40
563 564 6.603237 TCTTATCCATAATTGAACAGTGCG 57.397 37.500 0.00 0.00 0.00 5.34
564 565 5.527214 TCTTATCCATAATTGAACAGTGCGG 59.473 40.000 0.00 0.00 0.00 5.69
565 566 1.742831 TCCATAATTGAACAGTGCGGC 59.257 47.619 0.00 0.00 0.00 6.53
566 567 1.472082 CCATAATTGAACAGTGCGGCA 59.528 47.619 0.00 0.00 0.00 5.69
567 568 2.478370 CCATAATTGAACAGTGCGGCAG 60.478 50.000 1.18 0.00 0.00 4.85
568 569 1.164411 TAATTGAACAGTGCGGCAGG 58.836 50.000 1.18 0.72 0.00 4.85
569 570 2.146073 AATTGAACAGTGCGGCAGGC 62.146 55.000 1.18 0.00 43.96 4.85
581 582 3.058160 GCAGGCGTGGTGAGCAAT 61.058 61.111 8.72 0.00 36.08 3.56
582 583 3.044059 GCAGGCGTGGTGAGCAATC 62.044 63.158 8.72 0.00 36.08 2.67
583 584 1.376424 CAGGCGTGGTGAGCAATCT 60.376 57.895 0.00 0.00 36.08 2.40
585 586 0.674895 AGGCGTGGTGAGCAATCTTC 60.675 55.000 0.00 0.00 36.08 2.87
586 587 0.955428 GGCGTGGTGAGCAATCTTCA 60.955 55.000 0.00 0.00 36.08 3.02
587 588 0.874390 GCGTGGTGAGCAATCTTCAA 59.126 50.000 0.00 0.00 34.19 2.69
588 589 1.266718 GCGTGGTGAGCAATCTTCAAA 59.733 47.619 0.00 0.00 34.19 2.69
589 590 2.095059 GCGTGGTGAGCAATCTTCAAAT 60.095 45.455 0.00 0.00 34.19 2.32
590 591 3.751621 CGTGGTGAGCAATCTTCAAATC 58.248 45.455 0.00 0.00 0.00 2.17
591 592 3.189080 CGTGGTGAGCAATCTTCAAATCA 59.811 43.478 0.00 0.00 0.00 2.57
592 593 4.320421 CGTGGTGAGCAATCTTCAAATCAA 60.320 41.667 0.00 0.00 0.00 2.57
593 594 5.531634 GTGGTGAGCAATCTTCAAATCAAA 58.468 37.500 0.00 0.00 0.00 2.69
594 595 6.161381 GTGGTGAGCAATCTTCAAATCAAAT 58.839 36.000 0.00 0.00 0.00 2.32
595 596 6.309737 GTGGTGAGCAATCTTCAAATCAAATC 59.690 38.462 0.00 0.00 0.00 2.17
596 597 6.015265 TGGTGAGCAATCTTCAAATCAAATCA 60.015 34.615 0.00 0.00 0.00 2.57
597 598 6.309737 GGTGAGCAATCTTCAAATCAAATCAC 59.690 38.462 0.00 0.00 33.24 3.06
599 600 7.597743 GTGAGCAATCTTCAAATCAAATCACTT 59.402 33.333 0.00 0.00 31.75 3.16
600 601 8.795513 TGAGCAATCTTCAAATCAAATCACTTA 58.204 29.630 0.00 0.00 0.00 2.24
601 602 9.286946 GAGCAATCTTCAAATCAAATCACTTAG 57.713 33.333 0.00 0.00 0.00 2.18
602 603 9.017509 AGCAATCTTCAAATCAAATCACTTAGA 57.982 29.630 0.00 0.00 0.00 2.10
617 618 6.169557 TCACTTAGAAAAAGTAGTGAGGCA 57.830 37.500 0.00 0.00 41.34 4.75
618 619 6.769512 TCACTTAGAAAAAGTAGTGAGGCAT 58.230 36.000 0.00 0.00 41.34 4.40
619 620 7.903145 TCACTTAGAAAAAGTAGTGAGGCATA 58.097 34.615 0.00 0.00 41.34 3.14
620 621 8.372459 TCACTTAGAAAAAGTAGTGAGGCATAA 58.628 33.333 0.00 0.00 41.34 1.90
621 622 9.167311 CACTTAGAAAAAGTAGTGAGGCATAAT 57.833 33.333 0.00 0.00 40.24 1.28
622 623 9.384764 ACTTAGAAAAAGTAGTGAGGCATAATC 57.615 33.333 0.00 0.00 0.00 1.75
623 624 9.606631 CTTAGAAAAAGTAGTGAGGCATAATCT 57.393 33.333 0.00 0.00 0.00 2.40
624 625 9.959721 TTAGAAAAAGTAGTGAGGCATAATCTT 57.040 29.630 0.00 0.00 0.00 2.40
625 626 8.499403 AGAAAAAGTAGTGAGGCATAATCTTC 57.501 34.615 0.00 0.00 0.00 2.87
631 632 7.568349 AGTAGTGAGGCATAATCTTCAAATCA 58.432 34.615 0.00 0.00 0.00 2.57
649 650 9.734620 TTCAAATCATTCAAAAAGAGTAGTGTG 57.265 29.630 0.00 0.00 0.00 3.82
650 651 7.862372 TCAAATCATTCAAAAAGAGTAGTGTGC 59.138 33.333 0.00 0.00 0.00 4.57
651 652 5.342806 TCATTCAAAAAGAGTAGTGTGCG 57.657 39.130 0.00 0.00 0.00 5.34
659 660 2.285083 AGAGTAGTGTGCGCAAACAAA 58.715 42.857 31.30 16.87 0.00 2.83
660 661 2.680841 AGAGTAGTGTGCGCAAACAAAA 59.319 40.909 31.30 14.30 0.00 2.44
663 664 1.476074 AGTGTGCGCAAACAAAATCG 58.524 45.000 31.30 0.00 0.00 3.34
664 665 1.196200 GTGTGCGCAAACAAAATCGT 58.804 45.000 25.77 0.00 0.00 3.73
671 672 4.439449 TGCGCAAACAAAATCGTTAAGAAG 59.561 37.500 8.16 0.00 0.00 2.85
672 673 4.673311 GCGCAAACAAAATCGTTAAGAAGA 59.327 37.500 0.30 0.00 0.00 2.87
682 683 8.779561 CAAAATCGTTAAGAAGATTCATCGTTG 58.220 33.333 0.00 0.00 36.20 4.10
692 693 4.978099 AGATTCATCGTTGCTTCCCATAT 58.022 39.130 0.00 0.00 0.00 1.78
694 695 5.934625 AGATTCATCGTTGCTTCCCATATAC 59.065 40.000 0.00 0.00 0.00 1.47
696 697 4.631131 TCATCGTTGCTTCCCATATACAG 58.369 43.478 0.00 0.00 0.00 2.74
739 743 1.134965 TCGTTGGCACCCAAACAAAAG 60.135 47.619 0.00 0.00 45.73 2.27
740 744 1.013596 GTTGGCACCCAAACAAAAGC 58.986 50.000 0.00 0.00 45.73 3.51
741 745 0.460987 TTGGCACCCAAACAAAAGCG 60.461 50.000 0.00 0.00 40.92 4.68
832 837 2.943653 GCCGGACAAAACAGACCG 59.056 61.111 5.05 0.00 44.44 4.79
1035 1066 4.527583 CTCTGCCTCGCCTGCCTC 62.528 72.222 0.00 0.00 0.00 4.70
1200 1231 2.043852 TCCTCGCTGGACCTCCTC 60.044 66.667 0.00 0.00 40.56 3.71
1408 1515 1.595993 CTCCCTCTTCGGCTTCGTCA 61.596 60.000 0.00 0.00 35.06 4.35
1444 1551 4.796231 CCACCTCCGACGCGAAGG 62.796 72.222 15.93 16.13 36.21 3.46
1921 2178 2.554636 TACGACGTGGCGGTCAACT 61.555 57.895 11.56 0.00 36.73 3.16
1932 2189 2.047179 GTCAACTCCACGAGGGGC 60.047 66.667 0.00 0.00 39.93 5.80
2269 2526 2.572284 CGGTCACCTTCTCCGTCC 59.428 66.667 0.00 0.00 39.51 4.79
2733 3010 2.990479 GGGAAGGACGGCATGAGT 59.010 61.111 0.00 0.00 0.00 3.41
2748 3025 1.734477 GAGTGTGCACGAGACGCAT 60.734 57.895 13.13 0.00 42.32 4.73
2958 3235 1.367471 CTCTGTCACCAGCAACCGA 59.633 57.895 0.00 0.00 38.66 4.69
2979 3256 0.179089 CTGTCCGGATCCTTCTGCTG 60.179 60.000 7.81 0.00 0.00 4.41
2986 3263 0.463474 GATCCTTCTGCTGAGTGGCC 60.463 60.000 0.00 0.00 0.00 5.36
3222 3499 3.057526 GGGGTTTCTCTTTCAAATCCACG 60.058 47.826 0.00 0.00 35.91 4.94
3225 3502 3.896648 TTCTCTTTCAAATCCACGCAC 57.103 42.857 0.00 0.00 0.00 5.34
3468 3748 4.108570 AGGGACTTACATGTGGATTGGTA 58.891 43.478 9.11 0.00 27.25 3.25
3471 3751 5.497474 GGACTTACATGTGGATTGGTAGTT 58.503 41.667 9.11 0.00 0.00 2.24
3514 3796 1.472188 GGTGGCTTACCTCGAGTACT 58.528 55.000 12.31 0.00 46.51 2.73
3614 3896 1.066573 AGTTGATCTTCTGCAGTCCGG 60.067 52.381 14.67 0.00 0.00 5.14
3669 3951 1.216122 GATCGATGGAAGTGCAGCTC 58.784 55.000 0.54 0.00 0.00 4.09
3871 4201 2.544721 TCCTCTTTGACTGCAGGAGAT 58.455 47.619 19.93 0.00 31.10 2.75
3874 4204 4.100653 TCCTCTTTGACTGCAGGAGATATG 59.899 45.833 19.93 3.19 31.10 1.78
3882 4212 1.694150 TGCAGGAGATATGTAGGTGCC 59.306 52.381 0.00 0.00 0.00 5.01
3886 4216 2.090494 AGGAGATATGTAGGTGCCCTGT 60.090 50.000 4.16 0.00 34.61 4.00
3890 4220 5.193099 AGATATGTAGGTGCCCTGTTTTT 57.807 39.130 4.16 0.00 34.61 1.94
3891 4221 5.193679 AGATATGTAGGTGCCCTGTTTTTC 58.806 41.667 4.16 0.00 34.61 2.29
3931 4308 7.652909 TGTTTTTCATCTTTTTGAGCATAGGTG 59.347 33.333 0.00 0.00 0.00 4.00
4094 4474 5.815233 ATCTTAACATCGGTCCATGAGAT 57.185 39.130 0.00 4.30 0.00 2.75
4130 4510 8.383619 CAGTAATGTGAAGCTGTTAACATAGAC 58.616 37.037 9.13 3.04 36.81 2.59
4132 4512 6.974932 ATGTGAAGCTGTTAACATAGACAG 57.025 37.500 9.13 0.00 44.67 3.51
4135 4515 6.866770 TGTGAAGCTGTTAACATAGACAGTAC 59.133 38.462 9.13 2.73 43.94 2.73
4140 4520 7.763356 AGCTGTTAACATAGACAGTACAGTAG 58.237 38.462 9.13 0.00 43.94 2.57
4164 4544 6.016943 AGCCGAGTACTATTGTCAGATTACTC 60.017 42.308 0.00 0.00 0.00 2.59
4186 4599 4.925068 CACTTTTGTGCTCTTATATGCCC 58.075 43.478 0.00 0.00 44.07 5.36
4188 4601 5.822519 CACTTTTGTGCTCTTATATGCCCTA 59.177 40.000 0.00 0.00 44.07 3.53
4189 4602 5.823045 ACTTTTGTGCTCTTATATGCCCTAC 59.177 40.000 0.00 0.00 0.00 3.18
4190 4603 5.630415 TTTGTGCTCTTATATGCCCTACT 57.370 39.130 0.00 0.00 0.00 2.57
4191 4604 5.630415 TTGTGCTCTTATATGCCCTACTT 57.370 39.130 0.00 0.00 0.00 2.24
4194 4607 5.822519 TGTGCTCTTATATGCCCTACTTTTG 59.177 40.000 0.00 0.00 0.00 2.44
4195 4608 6.055588 GTGCTCTTATATGCCCTACTTTTGA 58.944 40.000 0.00 0.00 0.00 2.69
4196 4609 6.017852 GTGCTCTTATATGCCCTACTTTTGAC 60.018 42.308 0.00 0.00 0.00 3.18
4197 4610 5.470437 GCTCTTATATGCCCTACTTTTGACC 59.530 44.000 0.00 0.00 0.00 4.02
4198 4611 5.937111 TCTTATATGCCCTACTTTTGACCC 58.063 41.667 0.00 0.00 0.00 4.46
4199 4612 5.670361 TCTTATATGCCCTACTTTTGACCCT 59.330 40.000 0.00 0.00 0.00 4.34
4200 4613 4.881157 ATATGCCCTACTTTTGACCCTT 57.119 40.909 0.00 0.00 0.00 3.95
4203 4616 4.456662 TGCCCTACTTTTGACCCTTTTA 57.543 40.909 0.00 0.00 0.00 1.52
4204 4617 4.805744 TGCCCTACTTTTGACCCTTTTAA 58.194 39.130 0.00 0.00 0.00 1.52
4205 4618 5.209659 TGCCCTACTTTTGACCCTTTTAAA 58.790 37.500 0.00 0.00 0.00 1.52
4206 4619 5.841783 TGCCCTACTTTTGACCCTTTTAAAT 59.158 36.000 0.00 0.00 0.00 1.40
4207 4620 6.327887 TGCCCTACTTTTGACCCTTTTAAATT 59.672 34.615 0.00 0.00 0.00 1.82
4208 4621 7.147461 TGCCCTACTTTTGACCCTTTTAAATTT 60.147 33.333 0.00 0.00 0.00 1.82
4209 4622 7.717875 GCCCTACTTTTGACCCTTTTAAATTTT 59.282 33.333 0.00 0.00 0.00 1.82
4210 4623 9.621629 CCCTACTTTTGACCCTTTTAAATTTTT 57.378 29.630 0.00 0.00 0.00 1.94
4245 4658 8.721133 AATATGTCCTACTTTTGACCCTTTTT 57.279 30.769 0.00 0.00 0.00 1.94
4288 4715 3.964031 TGTCCTACTTTTGGCAATTTGGT 59.036 39.130 0.00 0.65 0.00 3.67
4305 4732 1.493022 TGGTACCAACAGAAGCTGGTT 59.507 47.619 13.60 0.00 41.35 3.67
4308 4735 2.435372 ACCAACAGAAGCTGGTTCAA 57.565 45.000 20.36 0.00 41.35 2.69
4311 4738 2.033801 CCAACAGAAGCTGGTTCAAGTG 59.966 50.000 20.36 12.72 37.67 3.16
4325 4752 1.275010 TCAAGTGTTAGGCTGATCGCA 59.725 47.619 0.00 0.00 41.67 5.10
4349 4776 4.442192 CCCTGATAAGCCTACTCAACAGAC 60.442 50.000 0.00 0.00 0.00 3.51
4386 4813 9.528018 GATAACCAATTACACCAAATAACCATG 57.472 33.333 0.00 0.00 0.00 3.66
4564 4992 0.615331 TGGACATCCTCTGCTCCAAC 59.385 55.000 0.00 0.00 34.30 3.77
4588 5016 5.416326 CCAAACCAAATCAGGTACCGAAATA 59.584 40.000 6.18 0.00 42.25 1.40
4593 5021 6.126883 ACCAAATCAGGTACCGAAATATCTCA 60.127 38.462 6.18 0.00 40.98 3.27
4622 5050 4.703897 TGCTGTGCCCTTACTATATTGTC 58.296 43.478 0.00 0.00 0.00 3.18
4668 5096 6.607198 ACTGCATGTTAGGCCTATTGTTTTAT 59.393 34.615 14.74 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.718210 GACCCGTCACCCATCGAGC 62.718 68.421 0.00 0.00 0.00 5.03
59 60 0.603975 AAGCAAAGTCGGAGCTGGAC 60.604 55.000 0.00 0.00 38.86 4.02
63 64 1.230324 GTCAAAGCAAAGTCGGAGCT 58.770 50.000 0.00 0.00 41.03 4.09
68 69 0.593128 CCCCTGTCAAAGCAAAGTCG 59.407 55.000 0.00 0.00 0.00 4.18
72 73 0.181587 TCGTCCCCTGTCAAAGCAAA 59.818 50.000 0.00 0.00 0.00 3.68
73 74 0.534203 GTCGTCCCCTGTCAAAGCAA 60.534 55.000 0.00 0.00 0.00 3.91
156 157 2.776913 CGGTCGAGGAAGAGGAGGC 61.777 68.421 0.00 0.00 0.00 4.70
204 205 2.919096 AAACCCTAGCCACCCCAGC 61.919 63.158 0.00 0.00 0.00 4.85
205 206 1.000896 CAAACCCTAGCCACCCCAG 60.001 63.158 0.00 0.00 0.00 4.45
206 207 3.176297 CAAACCCTAGCCACCCCA 58.824 61.111 0.00 0.00 0.00 4.96
207 208 2.362503 GCAAACCCTAGCCACCCC 60.363 66.667 0.00 0.00 0.00 4.95
214 215 2.818274 GTCGCCGGCAAACCCTAG 60.818 66.667 28.98 7.38 0.00 3.02
215 216 4.745751 CGTCGCCGGCAAACCCTA 62.746 66.667 28.98 0.00 0.00 3.53
226 227 4.803426 CACTGCTCCTCCGTCGCC 62.803 72.222 0.00 0.00 0.00 5.54
227 228 4.057428 ACACTGCTCCTCCGTCGC 62.057 66.667 0.00 0.00 0.00 5.19
228 229 2.126307 CACACTGCTCCTCCGTCG 60.126 66.667 0.00 0.00 0.00 5.12
229 230 2.262915 CCACACTGCTCCTCCGTC 59.737 66.667 0.00 0.00 0.00 4.79
230 231 4.008933 GCCACACTGCTCCTCCGT 62.009 66.667 0.00 0.00 0.00 4.69
231 232 2.290122 CTAGCCACACTGCTCCTCCG 62.290 65.000 0.00 0.00 41.68 4.63
232 233 0.972983 TCTAGCCACACTGCTCCTCC 60.973 60.000 0.00 0.00 41.68 4.30
234 235 0.829333 CATCTAGCCACACTGCTCCT 59.171 55.000 0.00 0.00 41.68 3.69
235 236 0.179062 CCATCTAGCCACACTGCTCC 60.179 60.000 0.00 0.00 41.68 4.70
236 237 0.179062 CCCATCTAGCCACACTGCTC 60.179 60.000 0.00 0.00 41.68 4.26
237 238 1.630126 CCCCATCTAGCCACACTGCT 61.630 60.000 0.00 0.00 45.38 4.24
239 240 0.179000 GTCCCCATCTAGCCACACTG 59.821 60.000 0.00 0.00 0.00 3.66
241 242 1.144057 CGTCCCCATCTAGCCACAC 59.856 63.158 0.00 0.00 0.00 3.82
243 244 2.808206 CCCGTCCCCATCTAGCCAC 61.808 68.421 0.00 0.00 0.00 5.01
244 245 2.445845 CCCGTCCCCATCTAGCCA 60.446 66.667 0.00 0.00 0.00 4.75
245 246 3.242291 CCCCGTCCCCATCTAGCC 61.242 72.222 0.00 0.00 0.00 3.93
246 247 3.242291 CCCCCGTCCCCATCTAGC 61.242 72.222 0.00 0.00 0.00 3.42
247 248 3.242291 GCCCCCGTCCCCATCTAG 61.242 72.222 0.00 0.00 0.00 2.43
262 263 4.496336 ATCCGCTTCCAGCCAGCC 62.496 66.667 0.00 0.00 38.18 4.85
263 264 3.207669 CATCCGCTTCCAGCCAGC 61.208 66.667 0.00 0.00 38.18 4.85
264 265 1.523258 CTCATCCGCTTCCAGCCAG 60.523 63.158 0.00 0.00 38.18 4.85
265 266 2.586245 CTCATCCGCTTCCAGCCA 59.414 61.111 0.00 0.00 38.18 4.75
266 267 2.203126 CCTCATCCGCTTCCAGCC 60.203 66.667 0.00 0.00 38.18 4.85
267 268 1.522580 GTCCTCATCCGCTTCCAGC 60.523 63.158 0.00 0.00 38.02 4.85
270 271 2.107141 CCGTCCTCATCCGCTTCC 59.893 66.667 0.00 0.00 0.00 3.46
271 272 2.586357 GCCGTCCTCATCCGCTTC 60.586 66.667 0.00 0.00 0.00 3.86
272 273 4.162690 GGCCGTCCTCATCCGCTT 62.163 66.667 0.00 0.00 0.00 4.68
335 336 2.246761 TTAATGACCTCGGGCCCACG 62.247 60.000 24.92 11.84 0.00 4.94
336 337 0.182775 ATTAATGACCTCGGGCCCAC 59.817 55.000 24.92 7.77 0.00 4.61
337 338 0.923358 AATTAATGACCTCGGGCCCA 59.077 50.000 24.92 8.28 0.00 5.36
338 339 2.943036 TAATTAATGACCTCGGGCCC 57.057 50.000 13.57 13.57 0.00 5.80
339 340 3.816994 ACTTAATTAATGACCTCGGGCC 58.183 45.455 0.00 0.00 0.00 5.80
340 341 4.879545 TCAACTTAATTAATGACCTCGGGC 59.120 41.667 0.00 0.00 0.00 6.13
341 342 6.359480 GTCAACTTAATTAATGACCTCGGG 57.641 41.667 16.26 0.00 36.94 5.14
347 348 8.336801 ACTTCCTGGTCAACTTAATTAATGAC 57.663 34.615 17.90 17.90 41.06 3.06
349 350 7.414098 CGGACTTCCTGGTCAACTTAATTAATG 60.414 40.741 0.00 0.00 37.91 1.90
350 351 6.598064 CGGACTTCCTGGTCAACTTAATTAAT 59.402 38.462 0.00 0.00 37.91 1.40
351 352 5.935789 CGGACTTCCTGGTCAACTTAATTAA 59.064 40.000 0.00 0.00 37.91 1.40
353 354 4.324267 CGGACTTCCTGGTCAACTTAATT 58.676 43.478 0.00 0.00 37.91 1.40
354 355 3.868754 GCGGACTTCCTGGTCAACTTAAT 60.869 47.826 0.00 0.00 37.91 1.40
355 356 2.549349 GCGGACTTCCTGGTCAACTTAA 60.549 50.000 0.00 0.00 37.91 1.85
357 358 0.250338 GCGGACTTCCTGGTCAACTT 60.250 55.000 0.00 0.00 37.91 2.66
358 359 1.371558 GCGGACTTCCTGGTCAACT 59.628 57.895 0.00 0.00 37.91 3.16
359 360 2.027625 CGCGGACTTCCTGGTCAAC 61.028 63.158 0.00 0.00 37.91 3.18
362 363 4.452733 CCCGCGGACTTCCTGGTC 62.453 72.222 30.73 0.00 35.66 4.02
367 368 4.699522 AACTGCCCGCGGACTTCC 62.700 66.667 30.73 9.73 0.00 3.46
368 369 3.423154 CAACTGCCCGCGGACTTC 61.423 66.667 30.73 13.17 0.00 3.01
381 382 2.283529 ATCTGGCGGTCGTCCAACT 61.284 57.895 0.00 0.00 32.41 3.16
382 383 2.100631 CATCTGGCGGTCGTCCAAC 61.101 63.158 0.00 0.00 32.41 3.77
383 384 2.264480 CATCTGGCGGTCGTCCAA 59.736 61.111 0.00 1.85 32.41 3.53
385 386 4.530857 CCCATCTGGCGGTCGTCC 62.531 72.222 0.00 0.00 0.00 4.79
386 387 4.530857 CCCCATCTGGCGGTCGTC 62.531 72.222 0.00 0.00 0.00 4.20
389 390 4.530857 CGTCCCCATCTGGCGGTC 62.531 72.222 0.00 0.00 0.00 4.79
428 429 3.419759 ACGAAACGGACGCCATGC 61.420 61.111 0.00 0.00 0.00 4.06
429 430 2.222953 GACACGAAACGGACGCCATG 62.223 60.000 0.00 0.00 0.00 3.66
430 431 2.025418 GACACGAAACGGACGCCAT 61.025 57.895 0.00 0.00 0.00 4.40
431 432 2.659244 GACACGAAACGGACGCCA 60.659 61.111 0.00 0.00 0.00 5.69
433 434 3.759828 CGGACACGAAACGGACGC 61.760 66.667 0.00 0.00 44.60 5.19
434 435 3.759828 GCGGACACGAAACGGACG 61.760 66.667 0.00 0.00 44.60 4.79
435 436 3.759828 CGCGGACACGAAACGGAC 61.760 66.667 0.00 0.00 44.60 4.79
446 447 3.419759 AAATGTGTCGGCGCGGAC 61.420 61.111 33.62 33.62 37.45 4.79
449 450 2.499520 CACAAATGTGTCGGCGCG 60.500 61.111 0.00 0.00 40.96 6.86
450 451 2.126888 CCACAAATGTGTCGGCGC 60.127 61.111 12.21 0.00 44.21 6.53
451 452 2.126888 GCCACAAATGTGTCGGCG 60.127 61.111 12.21 0.00 44.21 6.46
452 453 2.126888 CGCCACAAATGTGTCGGC 60.127 61.111 15.64 15.64 42.78 5.54
453 454 2.126888 GCGCCACAAATGTGTCGG 60.127 61.111 17.19 2.02 46.01 4.79
455 456 1.339711 GATTGCGCCACAAATGTGTC 58.660 50.000 4.18 0.00 42.86 3.67
456 457 0.038343 GGATTGCGCCACAAATGTGT 60.038 50.000 4.18 0.00 42.86 3.72
457 458 0.244450 AGGATTGCGCCACAAATGTG 59.756 50.000 4.18 6.57 42.86 3.21
458 459 0.527565 GAGGATTGCGCCACAAATGT 59.472 50.000 4.18 0.00 42.86 2.71
459 460 0.523968 CGAGGATTGCGCCACAAATG 60.524 55.000 4.18 0.00 42.86 2.32
460 461 0.960364 ACGAGGATTGCGCCACAAAT 60.960 50.000 4.18 0.00 42.86 2.32
462 463 1.169661 AAACGAGGATTGCGCCACAA 61.170 50.000 4.18 0.00 44.01 3.33
463 464 1.599518 AAACGAGGATTGCGCCACA 60.600 52.632 4.18 0.00 0.00 4.17
464 465 1.154225 CAAACGAGGATTGCGCCAC 60.154 57.895 4.18 0.00 0.00 5.01
465 466 1.573829 GACAAACGAGGATTGCGCCA 61.574 55.000 4.18 0.00 0.00 5.69
466 467 1.134694 GACAAACGAGGATTGCGCC 59.865 57.895 4.18 0.00 0.00 6.53
468 469 0.165944 GTGGACAAACGAGGATTGCG 59.834 55.000 0.00 0.00 0.00 4.85
469 470 0.165944 CGTGGACAAACGAGGATTGC 59.834 55.000 0.00 0.00 46.49 3.56
471 472 0.953960 GGCGTGGACAAACGAGGATT 60.954 55.000 0.17 0.00 46.49 3.01
473 474 2.029964 GGCGTGGACAAACGAGGA 59.970 61.111 0.17 0.00 46.49 3.71
474 475 3.411351 CGGCGTGGACAAACGAGG 61.411 66.667 0.00 0.00 46.49 4.63
475 476 2.355363 TCGGCGTGGACAAACGAG 60.355 61.111 6.85 0.00 46.49 4.18
477 478 3.708734 GGTCGGCGTGGACAAACG 61.709 66.667 6.85 0.00 46.30 3.60
478 479 3.351416 GGGTCGGCGTGGACAAAC 61.351 66.667 6.85 0.00 38.70 2.93
480 481 3.402095 TTTGGGTCGGCGTGGACAA 62.402 57.895 6.85 5.90 38.70 3.18
482 483 3.351416 GTTTGGGTCGGCGTGGAC 61.351 66.667 6.85 0.00 36.18 4.02
483 484 4.973055 CGTTTGGGTCGGCGTGGA 62.973 66.667 6.85 0.00 0.00 4.02
485 486 4.973055 TCCGTTTGGGTCGGCGTG 62.973 66.667 6.85 0.00 46.49 5.34
486 487 4.974989 GTCCGTTTGGGTCGGCGT 62.975 66.667 6.85 0.00 46.49 5.68
501 502 2.813908 ATTTCGTCTGCCGCCGTC 60.814 61.111 0.00 0.00 36.19 4.79
502 503 3.118454 CATTTCGTCTGCCGCCGT 61.118 61.111 0.00 0.00 36.19 5.68
503 504 3.864686 CCATTTCGTCTGCCGCCG 61.865 66.667 0.00 0.00 36.19 6.46
504 505 3.508840 CCCATTTCGTCTGCCGCC 61.509 66.667 0.00 0.00 36.19 6.13
505 506 2.746277 ACCCATTTCGTCTGCCGC 60.746 61.111 0.00 0.00 36.19 6.53
506 507 2.452813 CGACCCATTTCGTCTGCCG 61.453 63.158 0.00 0.00 34.16 5.69
507 508 1.079405 TCGACCCATTTCGTCTGCC 60.079 57.895 0.00 0.00 40.07 4.85
508 509 1.359459 GGTCGACCCATTTCGTCTGC 61.359 60.000 24.75 0.00 40.07 4.26
520 521 0.521735 GCAACTTCAATGGGTCGACC 59.478 55.000 27.04 27.04 40.81 4.79
521 522 1.464997 GAGCAACTTCAATGGGTCGAC 59.535 52.381 7.13 7.13 0.00 4.20
523 524 1.813513 AGAGCAACTTCAATGGGTCG 58.186 50.000 0.00 0.00 33.29 4.79
524 525 4.336713 GGATAAGAGCAACTTCAATGGGTC 59.663 45.833 0.00 0.00 39.72 4.46
526 527 4.272489 TGGATAAGAGCAACTTCAATGGG 58.728 43.478 0.00 0.00 39.72 4.00
527 528 7.572523 TTATGGATAAGAGCAACTTCAATGG 57.427 36.000 0.00 0.00 39.72 3.16
528 529 9.459640 CAATTATGGATAAGAGCAACTTCAATG 57.540 33.333 0.00 0.00 39.72 2.82
529 530 9.412460 TCAATTATGGATAAGAGCAACTTCAAT 57.588 29.630 0.00 0.00 39.72 2.57
530 531 8.806429 TCAATTATGGATAAGAGCAACTTCAA 57.194 30.769 0.00 0.00 39.72 2.69
531 532 8.677300 GTTCAATTATGGATAAGAGCAACTTCA 58.323 33.333 0.00 0.00 39.72 3.02
533 534 8.579850 TGTTCAATTATGGATAAGAGCAACTT 57.420 30.769 2.10 2.10 42.04 2.66
534 535 7.831193 ACTGTTCAATTATGGATAAGAGCAACT 59.169 33.333 0.00 0.00 0.00 3.16
535 536 7.912250 CACTGTTCAATTATGGATAAGAGCAAC 59.088 37.037 0.00 0.00 0.00 4.17
537 538 6.038603 GCACTGTTCAATTATGGATAAGAGCA 59.961 38.462 0.00 0.00 0.00 4.26
539 540 6.293081 CCGCACTGTTCAATTATGGATAAGAG 60.293 42.308 0.00 0.00 0.00 2.85
541 542 5.751680 CCGCACTGTTCAATTATGGATAAG 58.248 41.667 0.00 0.00 0.00 1.73
542 543 4.036262 GCCGCACTGTTCAATTATGGATAA 59.964 41.667 0.00 0.00 0.00 1.75
543 544 3.563808 GCCGCACTGTTCAATTATGGATA 59.436 43.478 0.00 0.00 0.00 2.59
544 545 2.358898 GCCGCACTGTTCAATTATGGAT 59.641 45.455 0.00 0.00 0.00 3.41
545 546 1.742831 GCCGCACTGTTCAATTATGGA 59.257 47.619 0.00 0.00 0.00 3.41
547 548 2.478370 CCTGCCGCACTGTTCAATTATG 60.478 50.000 0.00 0.00 0.00 1.90
548 549 1.745087 CCTGCCGCACTGTTCAATTAT 59.255 47.619 0.00 0.00 0.00 1.28
549 550 1.164411 CCTGCCGCACTGTTCAATTA 58.836 50.000 0.00 0.00 0.00 1.40
550 551 1.959085 CCTGCCGCACTGTTCAATT 59.041 52.632 0.00 0.00 0.00 2.32
551 552 2.629656 GCCTGCCGCACTGTTCAAT 61.630 57.895 0.00 0.00 37.47 2.57
552 553 3.286751 GCCTGCCGCACTGTTCAA 61.287 61.111 0.00 0.00 37.47 2.69
564 565 3.044059 GATTGCTCACCACGCCTGC 62.044 63.158 0.00 0.00 0.00 4.85
565 566 0.957395 AAGATTGCTCACCACGCCTG 60.957 55.000 0.00 0.00 0.00 4.85
566 567 0.674895 GAAGATTGCTCACCACGCCT 60.675 55.000 0.00 0.00 0.00 5.52
567 568 0.955428 TGAAGATTGCTCACCACGCC 60.955 55.000 0.00 0.00 0.00 5.68
568 569 0.874390 TTGAAGATTGCTCACCACGC 59.126 50.000 0.00 0.00 0.00 5.34
569 570 3.189080 TGATTTGAAGATTGCTCACCACG 59.811 43.478 0.00 0.00 0.00 4.94
570 571 4.771590 TGATTTGAAGATTGCTCACCAC 57.228 40.909 0.00 0.00 0.00 4.16
571 572 5.787953 TTTGATTTGAAGATTGCTCACCA 57.212 34.783 0.00 0.00 0.00 4.17
572 573 6.309737 GTGATTTGATTTGAAGATTGCTCACC 59.690 38.462 0.00 0.00 0.00 4.02
573 574 7.088905 AGTGATTTGATTTGAAGATTGCTCAC 58.911 34.615 0.00 0.00 0.00 3.51
575 576 9.286946 CTAAGTGATTTGATTTGAAGATTGCTC 57.713 33.333 0.00 0.00 0.00 4.26
576 577 9.017509 TCTAAGTGATTTGATTTGAAGATTGCT 57.982 29.630 0.00 0.00 0.00 3.91
577 578 9.630098 TTCTAAGTGATTTGATTTGAAGATTGC 57.370 29.630 0.00 0.00 0.00 3.56
589 590 9.273016 CCTCACTACTTTTTCTAAGTGATTTGA 57.727 33.333 4.64 0.00 45.26 2.69
590 591 8.017946 GCCTCACTACTTTTTCTAAGTGATTTG 58.982 37.037 4.64 0.00 45.26 2.32
591 592 7.719633 TGCCTCACTACTTTTTCTAAGTGATTT 59.280 33.333 4.64 0.00 45.26 2.17
592 593 7.224297 TGCCTCACTACTTTTTCTAAGTGATT 58.776 34.615 4.64 0.00 45.26 2.57
593 594 6.769512 TGCCTCACTACTTTTTCTAAGTGAT 58.230 36.000 4.64 0.00 45.26 3.06
594 595 6.169557 TGCCTCACTACTTTTTCTAAGTGA 57.830 37.500 4.18 4.18 44.47 3.41
595 596 8.547967 TTATGCCTCACTACTTTTTCTAAGTG 57.452 34.615 0.00 0.00 40.54 3.16
596 597 9.384764 GATTATGCCTCACTACTTTTTCTAAGT 57.615 33.333 0.00 0.00 0.00 2.24
597 598 9.606631 AGATTATGCCTCACTACTTTTTCTAAG 57.393 33.333 0.00 0.00 0.00 2.18
599 600 9.601217 GAAGATTATGCCTCACTACTTTTTCTA 57.399 33.333 0.00 0.00 0.00 2.10
600 601 8.103305 TGAAGATTATGCCTCACTACTTTTTCT 58.897 33.333 0.00 0.00 0.00 2.52
601 602 8.268850 TGAAGATTATGCCTCACTACTTTTTC 57.731 34.615 0.00 0.00 0.00 2.29
602 603 8.635765 TTGAAGATTATGCCTCACTACTTTTT 57.364 30.769 0.00 0.00 0.00 1.94
604 605 8.814038 ATTTGAAGATTATGCCTCACTACTTT 57.186 30.769 0.00 0.00 0.00 2.66
609 610 7.558807 TGAATGATTTGAAGATTATGCCTCACT 59.441 33.333 0.00 0.00 0.00 3.41
622 623 9.956720 ACACTACTCTTTTTGAATGATTTGAAG 57.043 29.630 0.00 0.00 0.00 3.02
623 624 9.734620 CACACTACTCTTTTTGAATGATTTGAA 57.265 29.630 0.00 0.00 0.00 2.69
624 625 7.862372 GCACACTACTCTTTTTGAATGATTTGA 59.138 33.333 0.00 0.00 0.00 2.69
625 626 7.149080 CGCACACTACTCTTTTTGAATGATTTG 60.149 37.037 0.00 0.00 0.00 2.32
631 632 3.563808 TGCGCACACTACTCTTTTTGAAT 59.436 39.130 5.66 0.00 0.00 2.57
645 646 1.196200 ACGATTTTGTTTGCGCACAC 58.804 45.000 19.53 19.53 0.00 3.82
649 650 4.673311 TCTTCTTAACGATTTTGTTTGCGC 59.327 37.500 0.00 0.00 33.32 6.09
650 651 6.911484 ATCTTCTTAACGATTTTGTTTGCG 57.089 33.333 0.00 0.00 33.32 4.85
651 652 8.280909 TGAATCTTCTTAACGATTTTGTTTGC 57.719 30.769 0.00 0.00 33.32 3.68
659 660 6.313905 AGCAACGATGAATCTTCTTAACGATT 59.686 34.615 0.00 0.00 32.86 3.34
660 661 5.812642 AGCAACGATGAATCTTCTTAACGAT 59.187 36.000 0.00 0.00 0.00 3.73
663 664 6.251549 GGAAGCAACGATGAATCTTCTTAAC 58.748 40.000 0.00 0.00 34.98 2.01
664 665 5.354234 GGGAAGCAACGATGAATCTTCTTAA 59.646 40.000 0.00 0.00 34.98 1.85
671 672 5.700832 TGTATATGGGAAGCAACGATGAATC 59.299 40.000 0.00 0.00 0.00 2.52
672 673 5.620206 TGTATATGGGAAGCAACGATGAAT 58.380 37.500 0.00 0.00 0.00 2.57
682 683 3.142174 GCTGTTCCTGTATATGGGAAGC 58.858 50.000 8.90 7.06 41.55 3.86
692 693 1.372499 GCACGTCGCTGTTCCTGTA 60.372 57.895 0.00 0.00 37.77 2.74
694 695 2.661537 TGCACGTCGCTGTTCCTG 60.662 61.111 10.54 0.00 43.06 3.86
696 697 4.059459 CGTGCACGTCGCTGTTCC 62.059 66.667 30.50 0.00 43.06 3.62
752 756 4.364409 GAACGAACGTGCGTGGGC 62.364 66.667 24.81 11.71 44.86 5.36
1027 1058 3.160748 GAGGAGGAGGAGGCAGGC 61.161 72.222 0.00 0.00 0.00 4.85
1028 1059 2.837291 CGAGGAGGAGGAGGCAGG 60.837 72.222 0.00 0.00 0.00 4.85
1575 1703 1.022735 ACGCCATGTAGTACTCGGAG 58.977 55.000 0.00 2.83 0.00 4.63
1624 1752 1.154205 CCGATCATGGAGACGTTGGC 61.154 60.000 0.00 0.00 0.00 4.52
1809 1937 1.507141 GCCTGGTGTTGTTGACGGAG 61.507 60.000 0.00 0.00 0.00 4.63
1921 2178 3.399181 GGTCATGCCCCTCGTGGA 61.399 66.667 4.76 0.00 35.39 4.02
1932 2189 1.524621 GGCCCAGATGACGGTCATG 60.525 63.158 27.11 15.53 37.20 3.07
2028 2285 1.139095 GAGCGTGAGGAACCCGTAG 59.861 63.158 0.00 0.00 0.00 3.51
2094 2351 2.982130 CCCTGGTCCTCCTTGTCG 59.018 66.667 0.00 0.00 34.23 4.35
2634 2911 2.918345 GCTGTTCACCATTGCGCCA 61.918 57.895 4.18 0.00 0.00 5.69
2733 3010 1.734117 CTCATGCGTCTCGTGCACA 60.734 57.895 18.64 3.15 46.57 4.57
2748 3025 3.165875 CCTCTTGTAGGTGAGGTTCTCA 58.834 50.000 0.00 0.00 43.49 3.27
2958 3235 1.617947 GCAGAAGGATCCGGACAGGT 61.618 60.000 6.12 0.00 41.99 4.00
3096 3373 2.686915 GAGATCCCCTTTGACATGCTTG 59.313 50.000 0.00 0.00 0.00 4.01
3396 3676 0.313672 GATGCTGCAAACCGGTGAAA 59.686 50.000 8.52 0.00 0.00 2.69
3468 3748 1.340991 ACAGCACTCACAACCCAAACT 60.341 47.619 0.00 0.00 0.00 2.66
3471 3751 2.884012 CAATACAGCACTCACAACCCAA 59.116 45.455 0.00 0.00 0.00 4.12
3514 3796 5.209818 TCTCTTCTTCGCTTAACCTTCAA 57.790 39.130 0.00 0.00 0.00 2.69
3614 3896 5.476614 AGTCCATTTTACTGTCGAACCTAC 58.523 41.667 0.00 0.00 0.00 3.18
3669 3951 1.734465 GTTCATCCTTTGAGTGGCTCG 59.266 52.381 0.00 0.00 35.27 5.03
3882 4212 5.006386 AGAGCACCTATTCTGAAAAACAGG 58.994 41.667 0.00 2.08 45.76 4.00
3886 4216 6.959639 AAACAGAGCACCTATTCTGAAAAA 57.040 33.333 8.35 0.00 42.67 1.94
3890 4220 5.620206 TGAAAAACAGAGCACCTATTCTGA 58.380 37.500 8.35 0.00 42.67 3.27
3891 4221 5.947228 TGAAAAACAGAGCACCTATTCTG 57.053 39.130 0.27 0.27 44.93 3.02
4094 4474 8.040727 ACAGCTTCACATTACTGTATGTCATAA 58.959 33.333 0.00 0.00 41.41 1.90
4130 4510 5.296283 ACAATAGTACTCGGCTACTGTACTG 59.704 44.000 0.00 0.00 44.25 2.74
4132 4512 5.295292 TGACAATAGTACTCGGCTACTGTAC 59.705 44.000 0.00 0.00 30.39 2.90
4135 4515 4.575236 TCTGACAATAGTACTCGGCTACTG 59.425 45.833 0.00 0.00 0.00 2.74
4140 4520 6.074544 AGTAATCTGACAATAGTACTCGGC 57.925 41.667 0.00 0.00 0.00 5.54
4164 4544 4.641989 AGGGCATATAAGAGCACAAAAGTG 59.358 41.667 0.00 0.00 36.38 3.16
4174 4587 5.998363 GGGTCAAAAGTAGGGCATATAAGAG 59.002 44.000 0.00 0.00 0.00 2.85
4181 4594 3.542969 AAAGGGTCAAAAGTAGGGCAT 57.457 42.857 0.00 0.00 0.00 4.40
4182 4595 3.322191 AAAAGGGTCAAAAGTAGGGCA 57.678 42.857 0.00 0.00 0.00 5.36
4183 4596 5.794726 TTTAAAAGGGTCAAAAGTAGGGC 57.205 39.130 0.00 0.00 0.00 5.19
4184 4597 9.621629 AAAAATTTAAAAGGGTCAAAAGTAGGG 57.378 29.630 0.00 0.00 0.00 3.53
4213 4626 9.178758 GGTCAAAAGTAGGACATATTTCTGAAT 57.821 33.333 0.00 0.00 35.74 2.57
4214 4627 7.610305 GGGTCAAAAGTAGGACATATTTCTGAA 59.390 37.037 0.00 0.00 35.74 3.02
4215 4628 7.037586 AGGGTCAAAAGTAGGACATATTTCTGA 60.038 37.037 0.00 0.00 35.74 3.27
4216 4629 7.112779 AGGGTCAAAAGTAGGACATATTTCTG 58.887 38.462 0.00 0.00 35.74 3.02
4217 4630 7.272144 AGGGTCAAAAGTAGGACATATTTCT 57.728 36.000 0.00 0.00 35.74 2.52
4218 4631 7.939784 AAGGGTCAAAAGTAGGACATATTTC 57.060 36.000 0.00 0.00 35.74 2.17
4219 4632 8.721133 AAAAGGGTCAAAAGTAGGACATATTT 57.279 30.769 0.00 0.00 35.74 1.40
4220 4633 8.721133 AAAAAGGGTCAAAAGTAGGACATATT 57.279 30.769 0.00 0.00 35.74 1.28
4221 4634 9.816787 TTAAAAAGGGTCAAAAGTAGGACATAT 57.183 29.630 0.00 0.00 35.74 1.78
4262 4675 7.038373 ACCAAATTGCCAAAAGTAGGACATATT 60.038 33.333 0.00 0.00 0.00 1.28
4263 4676 6.440328 ACCAAATTGCCAAAAGTAGGACATAT 59.560 34.615 0.00 0.00 0.00 1.78
4267 4680 4.600692 ACCAAATTGCCAAAAGTAGGAC 57.399 40.909 0.00 0.00 0.00 3.85
4268 4681 4.525100 GGTACCAAATTGCCAAAAGTAGGA 59.475 41.667 7.15 0.00 0.00 2.94
4269 4682 4.282195 TGGTACCAAATTGCCAAAAGTAGG 59.718 41.667 13.60 0.00 0.00 3.18
4270 4683 5.461032 TGGTACCAAATTGCCAAAAGTAG 57.539 39.130 13.60 0.00 0.00 2.57
4271 4684 5.128827 TGTTGGTACCAAATTGCCAAAAGTA 59.871 36.000 28.67 0.00 41.89 2.24
4272 4685 4.080863 TGTTGGTACCAAATTGCCAAAAGT 60.081 37.500 28.67 0.00 41.89 2.66
4274 4687 4.162320 TCTGTTGGTACCAAATTGCCAAAA 59.838 37.500 28.67 10.14 41.89 2.44
4305 4732 2.010145 GCGATCAGCCTAACACTTGA 57.990 50.000 0.00 0.00 40.81 3.02
4325 4752 3.450904 TGTTGAGTAGGCTTATCAGGGT 58.549 45.455 0.00 0.00 0.00 4.34
4386 4813 5.745769 GCTTAACCTGAAGCTAAATGCATTC 59.254 40.000 13.38 0.00 46.85 2.67
4564 4992 2.785562 TCGGTACCTGATTTGGTTTGG 58.214 47.619 10.90 0.00 41.22 3.28
4588 5016 1.203994 GGCACAGCAGCAAAATGAGAT 59.796 47.619 0.00 0.00 35.83 2.75
4593 5021 1.273327 GTAAGGGCACAGCAGCAAAAT 59.727 47.619 0.00 0.00 35.83 1.82
4622 5050 3.931468 GTCTGATGTCCATGTCACTGAAG 59.069 47.826 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.