Multiple sequence alignment - TraesCS5B01G495100

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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 TraesCS5B01G495100 chr5B 100.000 2463 0 0 1 2463 662941324 662943786 0.000000e+00 4549.0
1 TraesCS5B01G495100 chr5B 100.000 534 0 0 2782 3315 662944105 662944638 0.000000e+00 987.0
2 TraesCS5B01G495100 chr5B 90.262 534 48 4 2785 3315 134047624 134047092 0.000000e+00 695.0
3 TraesCS5B01G495100 chr5B 91.489 94 3 5 2372 2463 686255426 686255336 1.250000e-24 124.0
4 TraesCS5B01G495100 chr5D 91.715 1557 64 27 843 2371 526872195 526873714 0.000000e+00 2100.0
5 TraesCS5B01G495100 chr5D 90.650 492 41 5 2829 3315 509681987 509682478 0.000000e+00 649.0
6 TraesCS5B01G495100 chr5D 89.954 219 10 6 537 753 526870746 526870954 4.210000e-69 272.0
7 TraesCS5B01G495100 chr5D 92.473 93 4 3 2372 2463 197126062 197125972 2.680000e-26 130.0
8 TraesCS5B01G495100 chr5D 90.217 92 8 1 2372 2463 189973223 189973313 5.810000e-23 119.0
9 TraesCS5B01G495100 chr5D 96.491 57 1 1 756 811 526871038 526871094 3.520000e-15 93.5
10 TraesCS5B01G495100 chr5A 95.209 814 36 1 1538 2348 654074344 654075157 0.000000e+00 1284.0
11 TraesCS5B01G495100 chr5A 92.254 710 28 11 756 1456 654073559 654074250 0.000000e+00 981.0
12 TraesCS5B01G495100 chr5A 85.992 771 86 11 1540 2302 700850369 700849613 0.000000e+00 806.0
13 TraesCS5B01G495100 chr5A 85.045 448 47 14 1021 1455 700851587 700851147 3.930000e-119 438.0
14 TraesCS5B01G495100 chr5A 87.209 172 9 7 588 753 654073308 654073472 2.030000e-42 183.0
15 TraesCS5B01G495100 chr5A 76.235 324 46 19 1 298 444063636 444063318 3.450000e-30 143.0
16 TraesCS5B01G495100 chrUn 85.733 771 91 8 1540 2302 110767507 110766748 0.000000e+00 797.0
17 TraesCS5B01G495100 chrUn 84.309 427 50 11 1039 1455 110768029 110767610 5.150000e-108 401.0
18 TraesCS5B01G495100 chrUn 76.226 265 53 8 3 265 134447716 134447460 7.460000e-27 132.0
19 TraesCS5B01G495100 chr6D 90.841 535 46 3 2782 3314 445457471 445456938 0.000000e+00 713.0
20 TraesCS5B01G495100 chr6D 77.491 271 52 4 1189 1456 379339357 379339093 1.590000e-33 154.0
21 TraesCS5B01G495100 chr6D 95.181 83 3 1 2371 2453 445457605 445457524 2.680000e-26 130.0
22 TraesCS5B01G495100 chr6D 93.902 82 4 1 2372 2453 445421584 445421504 4.490000e-24 122.0
23 TraesCS5B01G495100 chr4B 84.542 731 98 9 1578 2302 660706016 660705295 0.000000e+00 710.0
24 TraesCS5B01G495100 chr4B 83.628 452 46 15 1021 1455 660707208 660706768 1.850000e-107 399.0
25 TraesCS5B01G495100 chr2D 90.280 535 48 4 2784 3315 404379299 404378766 0.000000e+00 697.0
26 TraesCS5B01G495100 chr2D 89.159 535 53 3 2786 3315 599936259 599936793 0.000000e+00 662.0
27 TraesCS5B01G495100 chr1B 92.719 467 33 1 2850 3315 593759564 593760030 0.000000e+00 673.0
28 TraesCS5B01G495100 chr4D 91.232 479 40 2 2838 3315 277000153 277000630 0.000000e+00 651.0
29 TraesCS5B01G495100 chr4D 93.103 87 6 0 2371 2457 65187216 65187302 9.650000e-26 128.0
30 TraesCS5B01G495100 chr4D 91.398 93 5 3 2372 2463 212096603 212096693 1.250000e-24 124.0
31 TraesCS5B01G495100 chr7A 90.554 487 43 3 2832 3315 722230681 722230195 2.790000e-180 641.0
32 TraesCS5B01G495100 chr7A 80.282 426 73 10 3 420 700644856 700644434 8.930000e-81 311.0
33 TraesCS5B01G495100 chr7A 80.047 426 74 10 3 420 700628135 700627713 4.150000e-79 305.0
34 TraesCS5B01G495100 chr7A 76.694 369 57 19 1 361 714575098 714575445 9.450000e-41 178.0
35 TraesCS5B01G495100 chr7B 87.759 531 63 2 2787 3315 682844704 682845234 1.310000e-173 619.0
36 TraesCS5B01G495100 chr7B 78.055 401 49 22 53 435 130581454 130581075 2.000000e-52 217.0
37 TraesCS5B01G495100 chr7B 76.163 344 66 14 3 340 674601315 674601648 2.050000e-37 167.0
38 TraesCS5B01G495100 chr2B 79.176 461 59 28 3 436 449660958 449660508 5.410000e-73 285.0
39 TraesCS5B01G495100 chr2B 82.692 156 17 7 188 336 690722801 690722649 2.680000e-26 130.0
40 TraesCS5B01G495100 chr6B 79.832 238 39 4 1189 1423 567611426 567611657 7.360000e-37 165.0
41 TraesCS5B01G495100 chr6A 78.992 238 41 4 1189 1423 521648669 521648900 1.590000e-33 154.0
42 TraesCS5B01G495100 chr3D 79.532 171 23 9 209 369 66144690 66144858 9.720000e-21 111.0
43 TraesCS5B01G495100 chr2A 92.754 69 4 1 2388 2456 22666587 22666654 7.570000e-17 99.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G495100 chr5B 662941324 662944638 3314 False 2768.000000 4549 100.000000 1 3315 2 chr5B.!!$F1 3314
1 TraesCS5B01G495100 chr5B 134047092 134047624 532 True 695.000000 695 90.262000 2785 3315 1 chr5B.!!$R1 530
2 TraesCS5B01G495100 chr5D 526870746 526873714 2968 False 821.833333 2100 92.720000 537 2371 3 chr5D.!!$F3 1834
3 TraesCS5B01G495100 chr5A 654073308 654075157 1849 False 816.000000 1284 91.557333 588 2348 3 chr5A.!!$F1 1760
4 TraesCS5B01G495100 chr5A 700849613 700851587 1974 True 622.000000 806 85.518500 1021 2302 2 chr5A.!!$R2 1281
5 TraesCS5B01G495100 chrUn 110766748 110768029 1281 True 599.000000 797 85.021000 1039 2302 2 chrUn.!!$R2 1263
6 TraesCS5B01G495100 chr6D 445456938 445457605 667 True 421.500000 713 93.011000 2371 3314 2 chr6D.!!$R3 943
7 TraesCS5B01G495100 chr4B 660705295 660707208 1913 True 554.500000 710 84.085000 1021 2302 2 chr4B.!!$R1 1281
8 TraesCS5B01G495100 chr2D 404378766 404379299 533 True 697.000000 697 90.280000 2784 3315 1 chr2D.!!$R1 531
9 TraesCS5B01G495100 chr2D 599936259 599936793 534 False 662.000000 662 89.159000 2786 3315 1 chr2D.!!$F1 529
10 TraesCS5B01G495100 chr7B 682844704 682845234 530 False 619.000000 619 87.759000 2787 3315 1 chr7B.!!$F2 528

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
448 449 0.036010 ATTCAGCCAAGTGGTCCTCG 60.036 55.0 0.00 0.00 37.57 4.63 F
623 625 0.036010 AACCTGTTGGATCCTCGCAG 60.036 55.0 14.23 16.55 37.04 5.18 F
907 2076 0.397535 ATTGCCTCGCCATTCCCATT 60.398 50.0 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1507 3048 0.247736 GAATGAGAGCACACGGTCCT 59.752 55.000 0.00 0.0 40.69 3.85 R
1521 3062 2.473610 GCACGTGCACCTTCAGAATGA 61.474 52.381 34.52 0.0 42.34 2.57 R
2826 4795 1.175983 TTGCGGGGGTGTTGAACATC 61.176 55.000 0.00 0.0 0.00 3.06 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
40 41 9.859427 TGCTTGATTAAAAAGTTTATCTCCATG 57.141 29.630 0.00 0.00 0.00 3.66
119 120 6.998968 AAAAATTCAAATGCTTGGTCAACA 57.001 29.167 0.00 0.00 33.01 3.33
120 121 7.571080 AAAAATTCAAATGCTTGGTCAACAT 57.429 28.000 0.00 0.00 33.01 2.71
121 122 7.571080 AAAATTCAAATGCTTGGTCAACATT 57.429 28.000 0.00 0.00 35.59 2.71
122 123 7.571080 AAATTCAAATGCTTGGTCAACATTT 57.429 28.000 13.30 13.30 43.01 2.32
123 124 6.790285 ATTCAAATGCTTGGTCAACATTTC 57.210 33.333 14.86 0.00 40.94 2.17
124 125 5.534207 TCAAATGCTTGGTCAACATTTCT 57.466 34.783 14.86 2.22 40.94 2.52
125 126 5.531634 TCAAATGCTTGGTCAACATTTCTC 58.468 37.500 14.86 0.00 40.94 2.87
126 127 5.068855 TCAAATGCTTGGTCAACATTTCTCA 59.931 36.000 14.86 6.21 40.94 3.27
127 128 5.534207 AATGCTTGGTCAACATTTCTCAA 57.466 34.783 0.00 0.00 29.94 3.02
128 129 4.998671 TGCTTGGTCAACATTTCTCAAA 57.001 36.364 0.00 0.00 0.00 2.69
129 130 5.534207 TGCTTGGTCAACATTTCTCAAAT 57.466 34.783 0.00 0.00 0.00 2.32
130 131 6.647334 TGCTTGGTCAACATTTCTCAAATA 57.353 33.333 0.00 0.00 0.00 1.40
131 132 7.230849 TGCTTGGTCAACATTTCTCAAATAT 57.769 32.000 0.00 0.00 0.00 1.28
132 133 7.669427 TGCTTGGTCAACATTTCTCAAATATT 58.331 30.769 0.00 0.00 0.00 1.28
133 134 8.149647 TGCTTGGTCAACATTTCTCAAATATTT 58.850 29.630 0.00 0.00 0.00 1.40
134 135 8.437742 GCTTGGTCAACATTTCTCAAATATTTG 58.562 33.333 20.13 20.13 39.48 2.32
135 136 9.480053 CTTGGTCAACATTTCTCAAATATTTGT 57.520 29.630 23.95 5.40 39.18 2.83
136 137 9.829507 TTGGTCAACATTTCTCAAATATTTGTT 57.170 25.926 23.95 10.14 39.18 2.83
137 138 9.474920 TGGTCAACATTTCTCAAATATTTGTTC 57.525 29.630 23.95 3.48 39.18 3.18
138 139 9.474920 GGTCAACATTTCTCAAATATTTGTTCA 57.525 29.630 23.95 7.78 39.18 3.18
218 219 9.906660 ACATTTTTCATGTACGTGATAAACATT 57.093 25.926 26.05 14.20 33.82 2.71
251 252 7.556733 ACACATTTCACATTTTTCAAATGCT 57.443 28.000 8.77 0.00 39.04 3.79
252 253 7.987649 ACACATTTCACATTTTTCAAATGCTT 58.012 26.923 8.77 0.00 39.04 3.91
253 254 7.911205 ACACATTTCACATTTTTCAAATGCTTG 59.089 29.630 8.77 2.35 39.04 4.01
254 255 7.377397 CACATTTCACATTTTTCAAATGCTTGG 59.623 33.333 8.77 0.00 39.04 3.61
255 256 6.998968 TTTCACATTTTTCAAATGCTTGGT 57.001 29.167 8.77 0.00 33.01 3.67
256 257 8.557864 CATTTCACATTTTTCAAATGCTTGGTA 58.442 29.630 8.77 0.00 31.38 3.25
257 258 8.498054 TTTCACATTTTTCAAATGCTTGGTAA 57.502 26.923 8.77 0.00 33.01 2.85
258 259 7.712264 TCACATTTTTCAAATGCTTGGTAAG 57.288 32.000 8.77 0.00 33.01 2.34
274 275 7.481275 CTTGGTAAGCATTTTCACATGTTTT 57.519 32.000 0.00 0.00 30.93 2.43
275 276 7.856145 TTGGTAAGCATTTTCACATGTTTTT 57.144 28.000 0.00 0.00 30.93 1.94
276 277 8.948631 TTGGTAAGCATTTTCACATGTTTTTA 57.051 26.923 0.00 0.00 30.93 1.52
277 278 9.553064 TTGGTAAGCATTTTCACATGTTTTTAT 57.447 25.926 0.00 0.00 30.93 1.40
283 284 9.630098 AGCATTTTCACATGTTTTTATAGAGTG 57.370 29.630 0.00 0.00 0.00 3.51
284 285 9.410556 GCATTTTCACATGTTTTTATAGAGTGT 57.589 29.630 0.00 0.00 0.00 3.55
395 396 3.946242 AAAAAGGAGGTTGTGGCCT 57.054 47.368 3.32 0.00 42.53 5.19
401 402 3.168528 AGGTTGTGGCCTCCGTGT 61.169 61.111 3.32 0.00 32.39 4.49
402 403 2.203294 GGTTGTGGCCTCCGTGTT 60.203 61.111 3.32 0.00 0.00 3.32
403 404 2.258726 GGTTGTGGCCTCCGTGTTC 61.259 63.158 3.32 0.00 0.00 3.18
404 405 2.112297 TTGTGGCCTCCGTGTTCC 59.888 61.111 3.32 0.00 0.00 3.62
405 406 2.448582 TTGTGGCCTCCGTGTTCCT 61.449 57.895 3.32 0.00 0.00 3.36
406 407 2.358737 GTGGCCTCCGTGTTCCTG 60.359 66.667 3.32 0.00 0.00 3.86
407 408 3.636231 TGGCCTCCGTGTTCCTGG 61.636 66.667 3.32 0.00 0.00 4.45
408 409 4.410400 GGCCTCCGTGTTCCTGGG 62.410 72.222 0.00 0.00 0.00 4.45
410 411 4.410400 CCTCCGTGTTCCTGGGCC 62.410 72.222 0.00 0.00 0.00 5.80
411 412 4.760047 CTCCGTGTTCCTGGGCCG 62.760 72.222 0.00 0.00 0.00 6.13
425 426 4.115199 GCCGGCCCATCTTGGTCT 62.115 66.667 18.11 0.00 35.17 3.85
426 427 2.677228 CCGGCCCATCTTGGTCTT 59.323 61.111 0.00 0.00 35.17 3.01
427 428 1.452108 CCGGCCCATCTTGGTCTTC 60.452 63.158 0.00 0.00 35.17 2.87
428 429 1.452108 CGGCCCATCTTGGTCTTCC 60.452 63.158 0.00 0.00 35.17 3.46
429 430 1.691219 GGCCCATCTTGGTCTTCCA 59.309 57.895 0.00 0.00 42.66 3.53
430 431 0.259938 GGCCCATCTTGGTCTTCCAT 59.740 55.000 0.00 0.00 43.91 3.41
431 432 1.342374 GGCCCATCTTGGTCTTCCATT 60.342 52.381 0.00 0.00 43.91 3.16
432 433 2.027385 GCCCATCTTGGTCTTCCATTC 58.973 52.381 0.00 0.00 43.91 2.67
433 434 2.621407 GCCCATCTTGGTCTTCCATTCA 60.621 50.000 0.00 0.00 43.91 2.57
434 435 3.285484 CCCATCTTGGTCTTCCATTCAG 58.715 50.000 0.00 0.00 43.91 3.02
435 436 2.686915 CCATCTTGGTCTTCCATTCAGC 59.313 50.000 0.00 0.00 43.91 4.26
436 437 2.496899 TCTTGGTCTTCCATTCAGCC 57.503 50.000 0.00 0.00 43.91 4.85
437 438 1.704628 TCTTGGTCTTCCATTCAGCCA 59.295 47.619 0.00 0.00 43.91 4.75
438 439 2.108075 TCTTGGTCTTCCATTCAGCCAA 59.892 45.455 0.00 0.00 43.91 4.52
439 440 2.205022 TGGTCTTCCATTCAGCCAAG 57.795 50.000 0.00 0.00 39.03 3.61
440 441 1.425066 TGGTCTTCCATTCAGCCAAGT 59.575 47.619 0.00 0.00 39.03 3.16
441 442 1.815003 GGTCTTCCATTCAGCCAAGTG 59.185 52.381 0.00 0.00 0.00 3.16
442 443 1.815003 GTCTTCCATTCAGCCAAGTGG 59.185 52.381 0.00 0.00 38.53 4.00
443 444 1.425066 TCTTCCATTCAGCCAAGTGGT 59.575 47.619 0.00 0.00 37.57 4.16
444 445 1.815003 CTTCCATTCAGCCAAGTGGTC 59.185 52.381 0.00 0.00 37.57 4.02
445 446 0.038166 TCCATTCAGCCAAGTGGTCC 59.962 55.000 0.00 0.00 37.57 4.46
446 447 0.038744 CCATTCAGCCAAGTGGTCCT 59.961 55.000 0.00 0.00 37.57 3.85
447 448 1.457346 CATTCAGCCAAGTGGTCCTC 58.543 55.000 0.00 0.00 37.57 3.71
448 449 0.036010 ATTCAGCCAAGTGGTCCTCG 60.036 55.000 0.00 0.00 37.57 4.63
449 450 2.046892 CAGCCAAGTGGTCCTCGG 60.047 66.667 0.00 0.00 37.57 4.63
450 451 4.021925 AGCCAAGTGGTCCTCGGC 62.022 66.667 0.00 2.53 43.31 5.54
451 452 4.021925 GCCAAGTGGTCCTCGGCT 62.022 66.667 0.00 0.00 39.73 5.52
452 453 2.266055 CCAAGTGGTCCTCGGCTC 59.734 66.667 0.00 0.00 0.00 4.70
453 454 2.583441 CCAAGTGGTCCTCGGCTCA 61.583 63.158 0.00 0.00 0.00 4.26
454 455 1.371183 CAAGTGGTCCTCGGCTCAA 59.629 57.895 0.00 0.00 0.00 3.02
455 456 0.951040 CAAGTGGTCCTCGGCTCAAC 60.951 60.000 0.00 0.00 0.00 3.18
456 457 2.432628 GTGGTCCTCGGCTCAACG 60.433 66.667 0.00 0.00 0.00 4.10
457 458 2.599281 TGGTCCTCGGCTCAACGA 60.599 61.111 0.00 0.00 41.13 3.85
463 464 3.759544 TCGGCTCAACGAGTGTCT 58.240 55.556 0.00 0.00 38.06 3.41
464 465 1.285950 TCGGCTCAACGAGTGTCTG 59.714 57.895 0.00 0.00 38.06 3.51
465 466 1.170290 TCGGCTCAACGAGTGTCTGA 61.170 55.000 0.00 0.00 38.06 3.27
466 467 0.109086 CGGCTCAACGAGTGTCTGAT 60.109 55.000 0.00 0.00 35.47 2.90
467 468 1.634702 GGCTCAACGAGTGTCTGATC 58.365 55.000 0.00 0.00 31.39 2.92
468 469 1.067565 GGCTCAACGAGTGTCTGATCA 60.068 52.381 0.00 0.00 31.39 2.92
469 470 2.610479 GGCTCAACGAGTGTCTGATCAA 60.610 50.000 0.00 0.00 31.39 2.57
470 471 3.257393 GCTCAACGAGTGTCTGATCAAT 58.743 45.455 0.00 0.00 31.39 2.57
471 472 3.061831 GCTCAACGAGTGTCTGATCAATG 59.938 47.826 0.00 0.00 31.39 2.82
472 473 3.588955 TCAACGAGTGTCTGATCAATGG 58.411 45.455 0.00 0.00 0.00 3.16
473 474 2.015736 ACGAGTGTCTGATCAATGGC 57.984 50.000 0.00 0.00 0.00 4.40
474 475 1.276138 ACGAGTGTCTGATCAATGGCA 59.724 47.619 0.00 0.00 0.00 4.92
475 476 1.931841 CGAGTGTCTGATCAATGGCAG 59.068 52.381 0.00 0.00 0.00 4.85
476 477 2.286872 GAGTGTCTGATCAATGGCAGG 58.713 52.381 0.00 0.00 33.05 4.85
477 478 1.632409 AGTGTCTGATCAATGGCAGGT 59.368 47.619 0.00 0.00 33.05 4.00
478 479 1.741706 GTGTCTGATCAATGGCAGGTG 59.258 52.381 0.00 0.00 33.05 4.00
479 480 0.737219 GTCTGATCAATGGCAGGTGC 59.263 55.000 0.00 0.00 41.14 5.01
480 481 0.745486 TCTGATCAATGGCAGGTGCG 60.745 55.000 0.00 0.00 43.26 5.34
481 482 1.721664 CTGATCAATGGCAGGTGCGG 61.722 60.000 0.00 0.00 43.26 5.69
482 483 3.129913 GATCAATGGCAGGTGCGGC 62.130 63.158 0.00 0.00 43.26 6.53
496 497 3.680786 CGGCGTGTGGGAGAGACA 61.681 66.667 0.00 0.00 0.00 3.41
497 498 2.982130 GGCGTGTGGGAGAGACAT 59.018 61.111 0.00 0.00 0.00 3.06
498 499 1.663379 CGGCGTGTGGGAGAGACATA 61.663 60.000 0.00 0.00 0.00 2.29
499 500 0.103208 GGCGTGTGGGAGAGACATAG 59.897 60.000 0.00 0.00 0.00 2.23
500 501 1.103803 GCGTGTGGGAGAGACATAGA 58.896 55.000 0.00 0.00 0.00 1.98
501 502 1.683917 GCGTGTGGGAGAGACATAGAT 59.316 52.381 0.00 0.00 0.00 1.98
502 503 2.544694 GCGTGTGGGAGAGACATAGATG 60.545 54.545 0.00 0.00 0.00 2.90
503 504 2.952310 CGTGTGGGAGAGACATAGATGA 59.048 50.000 0.00 0.00 0.00 2.92
504 505 3.243234 CGTGTGGGAGAGACATAGATGAC 60.243 52.174 0.00 0.00 0.00 3.06
505 506 3.068873 GTGTGGGAGAGACATAGATGACC 59.931 52.174 0.00 0.00 0.00 4.02
506 507 3.052566 TGTGGGAGAGACATAGATGACCT 60.053 47.826 0.00 0.00 0.00 3.85
507 508 3.572255 GTGGGAGAGACATAGATGACCTC 59.428 52.174 0.00 3.13 34.12 3.85
508 509 3.205282 TGGGAGAGACATAGATGACCTCA 59.795 47.826 14.36 0.00 35.31 3.86
509 510 4.219115 GGGAGAGACATAGATGACCTCAA 58.781 47.826 14.36 0.00 35.31 3.02
510 511 4.651503 GGGAGAGACATAGATGACCTCAAA 59.348 45.833 14.36 0.00 35.31 2.69
511 512 5.129485 GGGAGAGACATAGATGACCTCAAAA 59.871 44.000 14.36 0.00 35.31 2.44
512 513 6.183361 GGGAGAGACATAGATGACCTCAAAAT 60.183 42.308 14.36 0.79 35.31 1.82
513 514 7.278875 GGAGAGACATAGATGACCTCAAAATT 58.721 38.462 14.36 0.00 35.31 1.82
514 515 7.772757 GGAGAGACATAGATGACCTCAAAATTT 59.227 37.037 14.36 0.00 35.31 1.82
515 516 8.729805 AGAGACATAGATGACCTCAAAATTTC 57.270 34.615 14.36 0.00 35.31 2.17
516 517 7.772757 AGAGACATAGATGACCTCAAAATTTCC 59.227 37.037 14.36 0.00 35.31 3.13
517 518 7.405292 AGACATAGATGACCTCAAAATTTCCA 58.595 34.615 0.00 0.00 0.00 3.53
518 519 8.057623 AGACATAGATGACCTCAAAATTTCCAT 58.942 33.333 0.00 0.00 0.00 3.41
519 520 9.342308 GACATAGATGACCTCAAAATTTCCATA 57.658 33.333 0.00 0.00 0.00 2.74
520 521 9.872684 ACATAGATGACCTCAAAATTTCCATAT 57.127 29.630 0.00 0.00 0.00 1.78
527 528 8.757877 TGACCTCAAAATTTCCATATTTTAGGG 58.242 33.333 1.04 0.00 35.98 3.53
528 529 8.909423 ACCTCAAAATTTCCATATTTTAGGGA 57.091 30.769 13.83 0.00 35.98 4.20
529 530 9.332713 ACCTCAAAATTTCCATATTTTAGGGAA 57.667 29.630 13.83 0.00 45.87 3.97
541 542 1.874129 TTAGGGAAAGATGGCCTCGA 58.126 50.000 3.32 0.00 0.00 4.04
542 543 1.874129 TAGGGAAAGATGGCCTCGAA 58.126 50.000 3.32 0.00 0.00 3.71
568 569 9.480053 AATGTTTATCAATTTGTGAAGAACCAG 57.520 29.630 0.00 0.00 40.50 4.00
620 622 1.550524 TCAGAACCTGTTGGATCCTCG 59.449 52.381 14.23 0.00 35.96 4.63
621 623 0.250513 AGAACCTGTTGGATCCTCGC 59.749 55.000 14.23 3.62 35.96 5.03
622 624 0.036388 GAACCTGTTGGATCCTCGCA 60.036 55.000 14.23 8.17 37.04 5.10
623 625 0.036010 AACCTGTTGGATCCTCGCAG 60.036 55.000 14.23 16.55 37.04 5.18
624 626 1.194781 ACCTGTTGGATCCTCGCAGT 61.195 55.000 14.23 2.36 37.04 4.40
625 627 0.460987 CCTGTTGGATCCTCGCAGTC 60.461 60.000 14.23 0.00 34.57 3.51
626 628 0.803768 CTGTTGGATCCTCGCAGTCG 60.804 60.000 14.23 0.00 0.00 4.18
663 665 4.442052 CCTGAGATCGGTATCTTCTGCAAA 60.442 45.833 0.00 0.00 42.73 3.68
734 741 4.648626 GCTGTGGGCTGGCTGTGA 62.649 66.667 0.00 0.00 38.06 3.58
740 747 2.356278 GGCTGGCTGTGATGGGAA 59.644 61.111 0.00 0.00 0.00 3.97
811 903 7.335422 TGGCATAGAGAAGAGAAGAAAACAATC 59.665 37.037 0.00 0.00 0.00 2.67
836 928 4.996122 GTGAGCCAATCATCCTCTATCAAG 59.004 45.833 0.00 0.00 40.92 3.02
837 929 4.041321 TGAGCCAATCATCCTCTATCAAGG 59.959 45.833 0.00 0.00 33.31 3.61
903 2072 0.749454 AGTGATTGCCTCGCCATTCC 60.749 55.000 0.00 0.00 34.78 3.01
907 2076 0.397535 ATTGCCTCGCCATTCCCATT 60.398 50.000 0.00 0.00 0.00 3.16
908 2077 1.037030 TTGCCTCGCCATTCCCATTC 61.037 55.000 0.00 0.00 0.00 2.67
968 2137 4.053295 GCACAATCAAACTCAAATGCACT 58.947 39.130 0.00 0.00 0.00 4.40
969 2138 4.149396 GCACAATCAAACTCAAATGCACTC 59.851 41.667 0.00 0.00 0.00 3.51
970 2139 5.526115 CACAATCAAACTCAAATGCACTCT 58.474 37.500 0.00 0.00 0.00 3.24
971 2140 5.628193 CACAATCAAACTCAAATGCACTCTC 59.372 40.000 0.00 0.00 0.00 3.20
972 2141 5.159209 CAATCAAACTCAAATGCACTCTCC 58.841 41.667 0.00 0.00 0.00 3.71
991 2160 2.983192 TCCACTGAATAACTCCCCACAA 59.017 45.455 0.00 0.00 0.00 3.33
1004 2173 2.304761 TCCCCACAAGTAGAACCATGAC 59.695 50.000 0.00 0.00 0.00 3.06
1005 2174 2.618045 CCCCACAAGTAGAACCATGACC 60.618 54.545 0.00 0.00 0.00 4.02
1006 2175 2.039746 CCCACAAGTAGAACCATGACCA 59.960 50.000 0.00 0.00 0.00 4.02
1007 2176 3.308402 CCCACAAGTAGAACCATGACCAT 60.308 47.826 0.00 0.00 0.00 3.55
1008 2177 3.691118 CCACAAGTAGAACCATGACCATG 59.309 47.826 0.00 3.11 38.51 3.66
1009 2178 4.565444 CCACAAGTAGAACCATGACCATGA 60.565 45.833 11.28 0.00 41.20 3.07
1010 2179 4.633126 CACAAGTAGAACCATGACCATGAG 59.367 45.833 11.28 4.65 41.20 2.90
1011 2180 4.194640 CAAGTAGAACCATGACCATGAGG 58.805 47.826 11.28 0.00 41.20 3.86
1045 2238 2.268920 GCAGATGCTTCGTCCCCA 59.731 61.111 0.00 0.00 38.21 4.96
1095 2288 3.435186 GCGGCTTCCAACCTGCTC 61.435 66.667 0.00 0.00 0.00 4.26
1096 2289 2.747855 CGGCTTCCAACCTGCTCC 60.748 66.667 0.00 0.00 0.00 4.70
1097 2290 2.436109 GGCTTCCAACCTGCTCCA 59.564 61.111 0.00 0.00 0.00 3.86
1137 2333 1.132640 GCGCGCGTTTTCTTCTCAT 59.867 52.632 32.35 0.00 0.00 2.90
1501 3042 7.969690 ATACTATAATGATCAGGAGGTGAGG 57.030 40.000 0.09 0.00 39.07 3.86
1503 3044 6.015918 ACTATAATGATCAGGAGGTGAGGAG 58.984 44.000 0.09 0.00 39.07 3.69
1505 3046 1.010795 TGATCAGGAGGTGAGGAGGA 58.989 55.000 0.00 0.00 39.07 3.71
1507 3048 0.712979 ATCAGGAGGTGAGGAGGACA 59.287 55.000 0.00 0.00 39.07 4.02
1512 3053 0.973496 GAGGTGAGGAGGACAGGACC 60.973 65.000 0.00 0.00 0.00 4.46
1514 3055 1.606889 GTGAGGAGGACAGGACCGT 60.607 63.158 0.00 0.00 34.73 4.83
1515 3056 1.606601 TGAGGAGGACAGGACCGTG 60.607 63.158 0.00 0.00 34.73 4.94
1516 3057 1.606889 GAGGAGGACAGGACCGTGT 60.607 63.158 0.00 0.00 34.73 4.49
1517 3058 1.878656 GAGGAGGACAGGACCGTGTG 61.879 65.000 0.00 0.00 34.73 3.82
1518 3059 2.048127 GAGGACAGGACCGTGTGC 60.048 66.667 6.29 6.29 38.97 4.57
1521 3062 2.574955 GGACAGGACCGTGTGCTCT 61.575 63.158 7.02 0.00 35.97 4.09
1524 3065 1.188219 ACAGGACCGTGTGCTCTCAT 61.188 55.000 0.00 0.00 30.21 2.90
1525 3066 0.036952 CAGGACCGTGTGCTCTCATT 60.037 55.000 0.00 0.00 30.21 2.57
1527 3068 0.247736 GGACCGTGTGCTCTCATTCT 59.752 55.000 0.00 0.00 0.00 2.40
1528 3069 1.354040 GACCGTGTGCTCTCATTCTG 58.646 55.000 0.00 0.00 0.00 3.02
1529 3070 0.969149 ACCGTGTGCTCTCATTCTGA 59.031 50.000 0.00 0.00 0.00 3.27
1531 3072 1.998315 CCGTGTGCTCTCATTCTGAAG 59.002 52.381 0.00 0.00 0.00 3.02
1532 3073 1.998315 CGTGTGCTCTCATTCTGAAGG 59.002 52.381 0.00 0.00 0.00 3.46
1535 3492 1.736681 GTGCTCTCATTCTGAAGGTGC 59.263 52.381 1.70 6.30 0.00 5.01
1536 3493 1.348696 TGCTCTCATTCTGAAGGTGCA 59.651 47.619 12.73 12.73 0.00 4.57
2402 4371 2.356535 GGAGAGAGGGATTGTGTGCATT 60.357 50.000 0.00 0.00 0.00 3.56
2407 4376 4.858850 AGAGGGATTGTGTGCATTGATAA 58.141 39.130 0.00 0.00 0.00 1.75
2416 4385 8.867112 ATTGTGTGCATTGATAATTCTCATTC 57.133 30.769 0.00 0.00 0.00 2.67
2427 4396 4.611310 AATTCTCATTCATCGTGCACTG 57.389 40.909 16.19 7.56 0.00 3.66
2453 4422 5.488341 CACATATATAGGTACAAGGGGTGC 58.512 45.833 0.00 0.00 0.00 5.01
2455 4424 0.754472 TATAGGTACAAGGGGTGCGC 59.246 55.000 0.00 0.00 32.16 6.09
2456 4425 1.979619 ATAGGTACAAGGGGTGCGCC 61.980 60.000 8.12 8.12 32.16 6.53
2802 4771 0.231279 CGACAGGTGCAACGTACAAC 59.769 55.000 0.00 0.00 38.12 3.32
2816 4785 5.051891 ACGTACAACACACAGACCTATAC 57.948 43.478 0.00 0.00 0.00 1.47
2826 4795 6.037940 ACACACAGACCTATACACGTATGTAG 59.962 42.308 0.00 0.00 44.51 2.74
2845 4816 1.152652 ATGTTCAACACCCCCGCAA 60.153 52.632 0.00 0.00 0.00 4.85
2964 4935 1.654105 GGTACATGCAAGACTCGAACG 59.346 52.381 0.00 0.00 0.00 3.95
2967 4938 2.730672 ATGCAAGACTCGAACGCGC 61.731 57.895 5.73 0.00 37.46 6.86
3037 5008 0.875908 CGTCCGGCGATGATGAACAT 60.876 55.000 9.30 0.00 44.77 2.71
3055 5026 1.134280 CATGGTTGGCAGAGAGGTAGG 60.134 57.143 0.00 0.00 0.00 3.18
3057 5028 1.553690 GGTTGGCAGAGAGGTAGGCA 61.554 60.000 0.00 0.00 35.94 4.75
3059 5030 0.545309 TTGGCAGAGAGGTAGGCAGT 60.545 55.000 0.00 0.00 39.08 4.40
3095 5066 0.392461 TAGACAATCGTGGCCTTGGC 60.392 55.000 3.32 1.35 30.22 4.52
3129 5100 1.178276 ACTCCTGAAGTAGCTGTCGG 58.822 55.000 0.00 0.00 36.07 4.79
3180 5155 3.138798 GCCTGTACTCGGCCTCGA 61.139 66.667 13.72 0.00 41.73 4.04
3199 5175 1.007336 ACACTCGATCGTGAAACCGC 61.007 55.000 22.80 0.00 38.27 5.68
3206 5182 4.676586 CGTGAAACCGCGGGTTGC 62.677 66.667 37.08 24.05 46.20 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.859427 CATGGAGATAAACTTTTTAATCAAGCA 57.141 29.630 0.00 0.00 0.00 3.91
96 97 6.998968 TGTTGACCAAGCATTTGAATTTTT 57.001 29.167 0.00 0.00 36.36 1.94
97 98 7.571080 AATGTTGACCAAGCATTTGAATTTT 57.429 28.000 0.00 0.00 36.36 1.82
98 99 7.499895 AGAAATGTTGACCAAGCATTTGAATTT 59.500 29.630 18.56 0.00 41.24 1.82
99 100 6.993902 AGAAATGTTGACCAAGCATTTGAATT 59.006 30.769 18.56 0.00 41.24 2.17
100 101 6.527423 AGAAATGTTGACCAAGCATTTGAAT 58.473 32.000 18.56 8.95 41.24 2.57
101 102 5.916318 AGAAATGTTGACCAAGCATTTGAA 58.084 33.333 18.56 0.00 41.24 2.69
102 103 5.068855 TGAGAAATGTTGACCAAGCATTTGA 59.931 36.000 18.56 7.81 41.24 2.69
103 104 5.291178 TGAGAAATGTTGACCAAGCATTTG 58.709 37.500 18.56 0.00 41.24 2.32
104 105 5.534207 TGAGAAATGTTGACCAAGCATTT 57.466 34.783 15.91 15.91 43.06 2.32
105 106 5.534207 TTGAGAAATGTTGACCAAGCATT 57.466 34.783 0.00 0.00 34.69 3.56
106 107 5.534207 TTTGAGAAATGTTGACCAAGCAT 57.466 34.783 0.00 0.00 0.00 3.79
107 108 4.998671 TTTGAGAAATGTTGACCAAGCA 57.001 36.364 0.00 0.00 0.00 3.91
108 109 8.437742 CAAATATTTGAGAAATGTTGACCAAGC 58.562 33.333 21.35 0.00 40.55 4.01
109 110 9.480053 ACAAATATTTGAGAAATGTTGACCAAG 57.520 29.630 30.18 2.18 40.55 3.61
110 111 9.829507 AACAAATATTTGAGAAATGTTGACCAA 57.170 25.926 30.18 0.00 40.55 3.67
111 112 9.474920 GAACAAATATTTGAGAAATGTTGACCA 57.525 29.630 30.18 0.00 40.55 4.02
112 113 9.474920 TGAACAAATATTTGAGAAATGTTGACC 57.525 29.630 30.18 6.27 40.55 4.02
192 193 9.906660 AATGTTTATCACGTACATGAAAAATGT 57.093 25.926 0.00 0.00 33.10 2.71
225 226 9.275398 AGCATTTGAAAAATGTGAAATGTGTAT 57.725 25.926 12.82 0.00 37.85 2.29
226 227 8.659925 AGCATTTGAAAAATGTGAAATGTGTA 57.340 26.923 12.82 0.00 37.85 2.90
227 228 7.556733 AGCATTTGAAAAATGTGAAATGTGT 57.443 28.000 12.82 0.00 37.85 3.72
228 229 7.377397 CCAAGCATTTGAAAAATGTGAAATGTG 59.623 33.333 12.82 0.00 37.85 3.21
229 230 7.067251 ACCAAGCATTTGAAAAATGTGAAATGT 59.933 29.630 12.82 3.17 37.85 2.71
230 231 7.419204 ACCAAGCATTTGAAAAATGTGAAATG 58.581 30.769 12.82 0.00 38.35 2.32
231 232 7.571080 ACCAAGCATTTGAAAAATGTGAAAT 57.429 28.000 12.82 0.00 36.36 2.17
232 233 6.998968 ACCAAGCATTTGAAAAATGTGAAA 57.001 29.167 12.82 0.00 36.36 2.69
233 234 8.140677 CTTACCAAGCATTTGAAAAATGTGAA 57.859 30.769 12.82 0.00 36.36 3.18
234 235 7.712264 CTTACCAAGCATTTGAAAAATGTGA 57.288 32.000 12.82 0.00 36.36 3.58
250 251 7.481275 AAAACATGTGAAAATGCTTACCAAG 57.519 32.000 0.00 0.00 0.00 3.61
251 252 7.856145 AAAAACATGTGAAAATGCTTACCAA 57.144 28.000 0.00 0.00 0.00 3.67
257 258 9.630098 CACTCTATAAAAACATGTGAAAATGCT 57.370 29.630 0.00 0.00 0.00 3.79
258 259 9.410556 ACACTCTATAAAAACATGTGAAAATGC 57.589 29.630 0.00 0.00 0.00 3.56
377 378 3.946242 AGGCCACAACCTCCTTTTT 57.054 47.368 5.01 0.00 33.62 1.94
384 385 2.676163 GAACACGGAGGCCACAACCT 62.676 60.000 5.01 0.00 45.04 3.50
385 386 2.203294 AACACGGAGGCCACAACC 60.203 61.111 5.01 1.45 0.00 3.77
386 387 2.258726 GGAACACGGAGGCCACAAC 61.259 63.158 5.01 0.00 0.00 3.32
387 388 2.112297 GGAACACGGAGGCCACAA 59.888 61.111 5.01 0.00 0.00 3.33
388 389 2.847234 AGGAACACGGAGGCCACA 60.847 61.111 5.01 0.00 0.00 4.17
389 390 2.358737 CAGGAACACGGAGGCCAC 60.359 66.667 5.01 0.00 0.00 5.01
390 391 3.636231 CCAGGAACACGGAGGCCA 61.636 66.667 5.01 0.00 0.00 5.36
391 392 4.410400 CCCAGGAACACGGAGGCC 62.410 72.222 0.00 0.00 0.00 5.19
393 394 4.410400 GGCCCAGGAACACGGAGG 62.410 72.222 0.00 0.00 0.00 4.30
394 395 4.760047 CGGCCCAGGAACACGGAG 62.760 72.222 0.00 0.00 0.00 4.63
421 422 1.815003 CACTTGGCTGAATGGAAGACC 59.185 52.381 0.00 0.00 0.00 3.85
422 423 1.815003 CCACTTGGCTGAATGGAAGAC 59.185 52.381 0.00 0.00 33.80 3.01
423 424 1.425066 ACCACTTGGCTGAATGGAAGA 59.575 47.619 0.00 0.00 39.32 2.87
424 425 1.815003 GACCACTTGGCTGAATGGAAG 59.185 52.381 0.00 0.00 39.32 3.46
425 426 1.547675 GGACCACTTGGCTGAATGGAA 60.548 52.381 0.00 0.00 39.32 3.53
426 427 0.038166 GGACCACTTGGCTGAATGGA 59.962 55.000 0.00 0.00 39.32 3.41
427 428 0.038744 AGGACCACTTGGCTGAATGG 59.961 55.000 0.00 0.00 39.32 3.16
428 429 1.457346 GAGGACCACTTGGCTGAATG 58.543 55.000 0.00 0.00 39.32 2.67
429 430 0.036010 CGAGGACCACTTGGCTGAAT 60.036 55.000 0.00 0.00 39.32 2.57
430 431 1.371183 CGAGGACCACTTGGCTGAA 59.629 57.895 0.00 0.00 39.32 3.02
431 432 2.583441 CCGAGGACCACTTGGCTGA 61.583 63.158 0.00 0.00 43.78 4.26
432 433 2.046892 CCGAGGACCACTTGGCTG 60.047 66.667 0.00 0.00 43.78 4.85
436 437 0.951040 GTTGAGCCGAGGACCACTTG 60.951 60.000 0.00 0.00 0.00 3.16
437 438 1.371558 GTTGAGCCGAGGACCACTT 59.628 57.895 0.00 0.00 0.00 3.16
438 439 2.932234 CGTTGAGCCGAGGACCACT 61.932 63.158 0.00 0.00 0.00 4.00
439 440 2.432628 CGTTGAGCCGAGGACCAC 60.433 66.667 0.00 0.00 0.00 4.16
440 441 2.599281 TCGTTGAGCCGAGGACCA 60.599 61.111 0.00 0.00 32.18 4.02
446 447 1.170290 TCAGACACTCGTTGAGCCGA 61.170 55.000 0.00 0.00 32.04 5.54
447 448 0.109086 ATCAGACACTCGTTGAGCCG 60.109 55.000 0.00 0.00 32.04 5.52
448 449 1.067565 TGATCAGACACTCGTTGAGCC 60.068 52.381 0.00 0.00 32.04 4.70
449 450 2.354109 TGATCAGACACTCGTTGAGC 57.646 50.000 0.00 0.00 32.04 4.26
450 451 3.615937 CCATTGATCAGACACTCGTTGAG 59.384 47.826 0.00 0.00 35.52 3.02
451 452 3.588955 CCATTGATCAGACACTCGTTGA 58.411 45.455 0.00 0.00 0.00 3.18
452 453 2.094894 GCCATTGATCAGACACTCGTTG 59.905 50.000 0.00 0.00 0.00 4.10
453 454 2.289631 TGCCATTGATCAGACACTCGTT 60.290 45.455 0.00 0.00 0.00 3.85
454 455 1.276138 TGCCATTGATCAGACACTCGT 59.724 47.619 0.00 0.00 0.00 4.18
455 456 1.931841 CTGCCATTGATCAGACACTCG 59.068 52.381 0.00 0.00 32.26 4.18
456 457 2.286872 CCTGCCATTGATCAGACACTC 58.713 52.381 0.00 0.00 32.26 3.51
457 458 1.632409 ACCTGCCATTGATCAGACACT 59.368 47.619 0.00 0.00 32.26 3.55
458 459 1.741706 CACCTGCCATTGATCAGACAC 59.258 52.381 0.00 0.00 32.26 3.67
459 460 1.951895 GCACCTGCCATTGATCAGACA 60.952 52.381 0.00 0.00 34.31 3.41
460 461 0.737219 GCACCTGCCATTGATCAGAC 59.263 55.000 0.00 0.00 34.31 3.51
461 462 0.745486 CGCACCTGCCATTGATCAGA 60.745 55.000 0.00 0.00 37.91 3.27
462 463 1.721664 CCGCACCTGCCATTGATCAG 61.722 60.000 0.00 0.00 37.91 2.90
463 464 1.750018 CCGCACCTGCCATTGATCA 60.750 57.895 0.00 0.00 37.91 2.92
464 465 3.113745 CCGCACCTGCCATTGATC 58.886 61.111 0.00 0.00 37.91 2.92
465 466 3.142838 GCCGCACCTGCCATTGAT 61.143 61.111 0.00 0.00 37.91 2.57
479 480 1.663379 TATGTCTCTCCCACACGCCG 61.663 60.000 0.00 0.00 0.00 6.46
480 481 0.103208 CTATGTCTCTCCCACACGCC 59.897 60.000 0.00 0.00 0.00 5.68
481 482 1.103803 TCTATGTCTCTCCCACACGC 58.896 55.000 0.00 0.00 0.00 5.34
482 483 2.952310 TCATCTATGTCTCTCCCACACG 59.048 50.000 0.00 0.00 0.00 4.49
483 484 3.068873 GGTCATCTATGTCTCTCCCACAC 59.931 52.174 0.00 0.00 0.00 3.82
484 485 3.052566 AGGTCATCTATGTCTCTCCCACA 60.053 47.826 0.00 0.00 0.00 4.17
485 486 3.571590 AGGTCATCTATGTCTCTCCCAC 58.428 50.000 0.00 0.00 0.00 4.61
486 487 3.205282 TGAGGTCATCTATGTCTCTCCCA 59.795 47.826 13.11 0.00 33.68 4.37
487 488 3.838565 TGAGGTCATCTATGTCTCTCCC 58.161 50.000 13.11 0.00 33.68 4.30
488 489 5.860941 TTTGAGGTCATCTATGTCTCTCC 57.139 43.478 13.11 0.00 33.68 3.71
489 490 8.729805 AAATTTTGAGGTCATCTATGTCTCTC 57.270 34.615 13.11 8.87 33.68 3.20
490 491 7.772757 GGAAATTTTGAGGTCATCTATGTCTCT 59.227 37.037 0.00 2.03 33.68 3.10
491 492 7.554118 TGGAAATTTTGAGGTCATCTATGTCTC 59.446 37.037 0.00 8.21 33.39 3.36
492 493 7.405292 TGGAAATTTTGAGGTCATCTATGTCT 58.595 34.615 0.00 0.00 0.00 3.41
493 494 7.630242 TGGAAATTTTGAGGTCATCTATGTC 57.370 36.000 0.00 0.00 0.00 3.06
494 495 9.872684 ATATGGAAATTTTGAGGTCATCTATGT 57.127 29.630 0.00 0.00 0.00 2.29
501 502 8.757877 CCCTAAAATATGGAAATTTTGAGGTCA 58.242 33.333 5.12 0.00 38.98 4.02
502 503 8.977412 TCCCTAAAATATGGAAATTTTGAGGTC 58.023 33.333 5.12 0.00 38.98 3.85
503 504 8.909423 TCCCTAAAATATGGAAATTTTGAGGT 57.091 30.769 5.12 0.00 38.98 3.85
510 511 8.432013 GCCATCTTTCCCTAAAATATGGAAATT 58.568 33.333 15.23 0.00 46.86 1.82
511 512 7.016563 GGCCATCTTTCCCTAAAATATGGAAAT 59.983 37.037 15.23 0.00 46.86 2.17
512 513 6.326323 GGCCATCTTTCCCTAAAATATGGAAA 59.674 38.462 15.23 6.48 46.86 3.13
513 514 5.838521 GGCCATCTTTCCCTAAAATATGGAA 59.161 40.000 15.23 0.00 46.86 3.53
514 515 5.136048 AGGCCATCTTTCCCTAAAATATGGA 59.864 40.000 5.01 0.00 46.86 3.41
515 516 5.397360 AGGCCATCTTTCCCTAAAATATGG 58.603 41.667 5.01 9.40 46.73 2.74
516 517 5.182001 CGAGGCCATCTTTCCCTAAAATATG 59.818 44.000 5.01 0.00 33.44 1.78
517 518 5.073144 TCGAGGCCATCTTTCCCTAAAATAT 59.927 40.000 5.01 0.00 0.00 1.28
518 519 4.410883 TCGAGGCCATCTTTCCCTAAAATA 59.589 41.667 5.01 0.00 0.00 1.40
519 520 3.202151 TCGAGGCCATCTTTCCCTAAAAT 59.798 43.478 5.01 0.00 0.00 1.82
520 521 2.574369 TCGAGGCCATCTTTCCCTAAAA 59.426 45.455 5.01 0.00 0.00 1.52
521 522 2.193127 TCGAGGCCATCTTTCCCTAAA 58.807 47.619 5.01 0.00 0.00 1.85
522 523 1.874129 TCGAGGCCATCTTTCCCTAA 58.126 50.000 5.01 0.00 0.00 2.69
523 524 1.874129 TTCGAGGCCATCTTTCCCTA 58.126 50.000 5.01 0.00 0.00 3.53
524 525 0.991920 TTTCGAGGCCATCTTTCCCT 59.008 50.000 5.01 0.00 0.00 4.20
525 526 1.678101 CATTTCGAGGCCATCTTTCCC 59.322 52.381 5.01 0.00 0.00 3.97
526 527 2.369394 ACATTTCGAGGCCATCTTTCC 58.631 47.619 5.01 0.00 0.00 3.13
527 528 4.440839 AAACATTTCGAGGCCATCTTTC 57.559 40.909 5.01 0.00 0.00 2.62
528 529 5.652014 TGATAAACATTTCGAGGCCATCTTT 59.348 36.000 5.01 0.00 0.00 2.52
529 530 5.192927 TGATAAACATTTCGAGGCCATCTT 58.807 37.500 5.01 0.00 0.00 2.40
530 531 4.780815 TGATAAACATTTCGAGGCCATCT 58.219 39.130 5.01 0.00 0.00 2.90
531 532 5.499139 TTGATAAACATTTCGAGGCCATC 57.501 39.130 5.01 0.00 0.00 3.51
532 533 6.469782 AATTGATAAACATTTCGAGGCCAT 57.530 33.333 5.01 0.00 0.00 4.40
533 534 5.913137 AATTGATAAACATTTCGAGGCCA 57.087 34.783 5.01 0.00 0.00 5.36
534 535 6.034898 CACAAATTGATAAACATTTCGAGGCC 59.965 38.462 0.00 0.00 0.00 5.19
535 536 6.806249 TCACAAATTGATAAACATTTCGAGGC 59.194 34.615 0.00 0.00 0.00 4.70
541 542 9.829507 TGGTTCTTCACAAATTGATAAACATTT 57.170 25.926 0.00 0.00 33.57 2.32
542 543 9.480053 CTGGTTCTTCACAAATTGATAAACATT 57.520 29.630 0.00 0.00 33.57 2.71
602 603 0.250513 GCGAGGATCCAACAGGTTCT 59.749 55.000 15.82 0.00 0.00 3.01
620 622 1.661112 GATTGAACTACCTGCGACTGC 59.339 52.381 0.00 0.00 43.20 4.40
621 623 2.093973 AGGATTGAACTACCTGCGACTG 60.094 50.000 0.00 0.00 32.39 3.51
622 624 2.093973 CAGGATTGAACTACCTGCGACT 60.094 50.000 0.00 0.00 43.32 4.18
623 625 2.271800 CAGGATTGAACTACCTGCGAC 58.728 52.381 0.00 0.00 43.32 5.19
624 626 2.672961 CAGGATTGAACTACCTGCGA 57.327 50.000 0.00 0.00 43.32 5.10
663 665 5.012328 AGTTCACGACAGAAGAGTCTTTT 57.988 39.130 6.88 0.00 36.38 2.27
679 683 3.618690 ACCATAGCCTCAAGAGTTCAC 57.381 47.619 0.00 0.00 0.00 3.18
747 754 1.091537 GGGCTGCGCACACTAATTAA 58.908 50.000 5.66 0.00 0.00 1.40
811 903 4.040095 TGATAGAGGATGATTGGCTCACTG 59.960 45.833 0.00 0.00 36.48 3.66
836 928 3.644884 ATCTTGATCCATCGTACGTCC 57.355 47.619 16.05 0.36 0.00 4.79
837 929 4.083217 AGCTATCTTGATCCATCGTACGTC 60.083 45.833 16.05 5.49 0.00 4.34
839 931 4.162072 CAGCTATCTTGATCCATCGTACG 58.838 47.826 9.53 9.53 0.00 3.67
840 932 3.923461 GCAGCTATCTTGATCCATCGTAC 59.077 47.826 0.00 0.00 0.00 3.67
841 933 3.829026 AGCAGCTATCTTGATCCATCGTA 59.171 43.478 0.00 0.00 0.00 3.43
903 2072 5.415701 TGATGATGATCATGCATGAGAATGG 59.584 40.000 31.36 3.52 37.20 3.16
907 2076 9.494271 CATATATGATGATGATCATGCATGAGA 57.506 33.333 31.36 21.59 46.83 3.27
908 2077 8.725148 CCATATATGATGATGATCATGCATGAG 58.275 37.037 31.36 13.58 46.83 2.90
968 2137 2.838202 GTGGGGAGTTATTCAGTGGAGA 59.162 50.000 0.00 0.00 0.00 3.71
969 2138 2.571653 TGTGGGGAGTTATTCAGTGGAG 59.428 50.000 0.00 0.00 0.00 3.86
970 2139 2.626785 TGTGGGGAGTTATTCAGTGGA 58.373 47.619 0.00 0.00 0.00 4.02
971 2140 3.244911 ACTTGTGGGGAGTTATTCAGTGG 60.245 47.826 0.00 0.00 0.00 4.00
972 2141 4.021102 ACTTGTGGGGAGTTATTCAGTG 57.979 45.455 0.00 0.00 0.00 3.66
991 2160 2.774234 CCCTCATGGTCATGGTTCTACT 59.226 50.000 10.61 0.00 39.24 2.57
1004 2173 0.465097 GCTCACATGGACCCTCATGG 60.465 60.000 9.25 0.12 46.33 3.66
1006 2175 0.545171 CTGCTCACATGGACCCTCAT 59.455 55.000 0.00 0.00 0.00 2.90
1007 2176 1.985614 CTGCTCACATGGACCCTCA 59.014 57.895 0.00 0.00 0.00 3.86
1008 2177 1.451028 GCTGCTCACATGGACCCTC 60.451 63.158 0.00 0.00 0.00 4.30
1009 2178 2.194388 CTGCTGCTCACATGGACCCT 62.194 60.000 0.00 0.00 0.00 4.34
1010 2179 1.748122 CTGCTGCTCACATGGACCC 60.748 63.158 0.00 0.00 0.00 4.46
1011 2180 2.404995 GCTGCTGCTCACATGGACC 61.405 63.158 8.53 0.00 36.03 4.46
1045 2238 0.689080 AGGAGCATGAGGGACACGAT 60.689 55.000 0.00 0.00 0.00 3.73
1095 2288 1.528309 GTGTGGGAAGGTGGTGTGG 60.528 63.158 0.00 0.00 0.00 4.17
1096 2289 1.528309 GGTGTGGGAAGGTGGTGTG 60.528 63.158 0.00 0.00 0.00 3.82
1097 2290 2.763645 GGGTGTGGGAAGGTGGTGT 61.764 63.158 0.00 0.00 0.00 4.16
1137 2333 1.335597 GGTCGTGATCGTGTGTGAAGA 60.336 52.381 0.00 0.00 38.33 2.87
1491 3032 1.149782 TCCTGTCCTCCTCACCTCCT 61.150 60.000 0.00 0.00 0.00 3.69
1493 3034 0.973496 GGTCCTGTCCTCCTCACCTC 60.973 65.000 0.00 0.00 0.00 3.85
1494 3035 1.079438 GGTCCTGTCCTCCTCACCT 59.921 63.158 0.00 0.00 0.00 4.00
1495 3036 2.352032 CGGTCCTGTCCTCCTCACC 61.352 68.421 0.00 0.00 0.00 4.02
1496 3037 1.606889 ACGGTCCTGTCCTCCTCAC 60.607 63.158 0.00 0.00 0.00 3.51
1497 3038 1.606601 CACGGTCCTGTCCTCCTCA 60.607 63.158 0.00 0.00 0.00 3.86
1498 3039 1.606889 ACACGGTCCTGTCCTCCTC 60.607 63.158 0.00 0.00 0.00 3.71
1499 3040 1.908793 CACACGGTCCTGTCCTCCT 60.909 63.158 0.00 0.00 0.00 3.69
1500 3041 2.657237 CACACGGTCCTGTCCTCC 59.343 66.667 0.00 0.00 0.00 4.30
1501 3042 2.048127 GCACACGGTCCTGTCCTC 60.048 66.667 0.00 0.00 0.00 3.71
1503 3044 2.048127 GAGCACACGGTCCTGTCC 60.048 66.667 0.00 0.00 33.34 4.02
1505 3046 1.188219 ATGAGAGCACACGGTCCTGT 61.188 55.000 0.00 0.00 40.69 4.00
1507 3048 0.247736 GAATGAGAGCACACGGTCCT 59.752 55.000 0.00 0.00 40.69 3.85
1521 3062 2.473610 GCACGTGCACCTTCAGAATGA 61.474 52.381 34.52 0.00 42.34 2.57
1524 3065 3.731136 GCACGTGCACCTTCAGAA 58.269 55.556 34.52 0.00 41.59 3.02
2037 3994 3.986116 AAGCCCTCGACCCTCCTCC 62.986 68.421 0.00 0.00 0.00 4.30
2290 4256 7.839680 TTATGTAGAGTTGAGCATATGGAGA 57.160 36.000 4.56 0.00 0.00 3.71
2356 4325 3.914312 ACTTACAACAGTCACCAGATCG 58.086 45.455 0.00 0.00 0.00 3.69
2361 4330 3.054287 TCCCAAACTTACAACAGTCACCA 60.054 43.478 0.00 0.00 0.00 4.17
2402 4371 6.018507 CAGTGCACGATGAATGAGAATTATCA 60.019 38.462 12.01 5.04 0.00 2.15
2407 4376 2.941064 CCAGTGCACGATGAATGAGAAT 59.059 45.455 12.01 0.00 0.00 2.40
2427 4396 4.080526 CCCCTTGTACCTATATATGTGCCC 60.081 50.000 0.00 0.00 0.00 5.36
2802 4771 5.244785 ACATACGTGTATAGGTCTGTGTG 57.755 43.478 0.00 0.00 36.63 3.82
2816 4785 4.328983 GGGTGTTGAACATCTACATACGTG 59.671 45.833 8.65 0.00 34.89 4.49
2826 4795 1.175983 TTGCGGGGGTGTTGAACATC 61.176 55.000 0.00 0.00 0.00 3.06
2941 4912 1.831106 TCGAGTCTTGCATGTACCCAT 59.169 47.619 0.00 0.00 0.00 4.00
2964 4935 4.980903 CACGTTGCACTTGGGCGC 62.981 66.667 0.00 0.00 36.28 6.53
3037 5008 1.553690 GCCTACCTCTCTGCCAACCA 61.554 60.000 0.00 0.00 0.00 3.67
3055 5026 0.529773 TGTGACAACGTCTCCACTGC 60.530 55.000 12.98 0.00 33.15 4.40
3057 5028 1.112113 ACTGTGACAACGTCTCCACT 58.888 50.000 12.98 0.00 33.15 4.00
3059 5030 2.292569 GTCTACTGTGACAACGTCTCCA 59.707 50.000 0.00 0.00 36.97 3.86
3095 5066 3.005554 CAGGAGTTGCTATGTGAGGTTG 58.994 50.000 0.00 0.00 0.00 3.77
3129 5100 2.817396 GCGGAGTGCTCTTGGCTC 60.817 66.667 0.00 0.00 42.39 4.70
3180 5155 1.007336 GCGGTTTCACGATCGAGTGT 61.007 55.000 24.34 0.00 42.40 3.55


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

AutoCloner maintained by Alex Coulton.