Multiple sequence alignment - TraesCS2A01G373200

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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 TraesCS2A01G373200 chr2A 100.000 5437 0 0 1 5437 615522112 615527548 0.000000e+00 10041.0
1 TraesCS2A01G373200 chr2A 90.000 70 6 1 5280 5348 668538095 668538164 7.500000e-14 89.8
2 TraesCS2A01G373200 chrUn 95.353 2948 75 22 2513 5437 75458508 75455600 0.000000e+00 4628.0
3 TraesCS2A01G373200 chrUn 86.561 253 14 5 4 255 75460953 75460720 1.500000e-65 261.0
4 TraesCS2A01G373200 chrUn 100.000 116 0 0 2008 2123 75458768 75458653 1.190000e-51 215.0
5 TraesCS2A01G373200 chrUn 90.506 158 5 3 1517 1665 75460453 75460297 3.320000e-47 200.0
6 TraesCS2A01G373200 chrUn 85.507 138 0 1 2309 2446 75458653 75458536 5.720000e-25 126.0
7 TraesCS2A01G373200 chrUn 94.937 79 4 0 1695 1773 75460302 75460224 2.060000e-24 124.0
8 TraesCS2A01G373200 chrUn 97.959 49 1 0 1250 1298 1596882 1596834 9.700000e-13 86.1
9 TraesCS2A01G373200 chr2D 94.882 1778 58 11 2962 4710 473589610 473591383 0.000000e+00 2748.0
10 TraesCS2A01G373200 chr2D 89.089 834 37 17 2027 2838 473588780 473589581 0.000000e+00 987.0
11 TraesCS2A01G373200 chr2D 90.704 710 38 18 553 1252 473587296 473587987 0.000000e+00 920.0
12 TraesCS2A01G373200 chr2D 93.003 586 31 4 4694 5278 473591544 473592120 0.000000e+00 846.0
13 TraesCS2A01G373200 chr2D 92.713 247 18 0 9 255 473586758 473587004 1.860000e-94 357.0
14 TraesCS2A01G373200 chr2D 79.541 567 62 30 1306 1858 473588012 473588538 6.700000e-94 355.0
15 TraesCS2A01G373200 chr2D 87.261 157 9 3 1867 2023 473588591 473588736 9.370000e-38 169.0
16 TraesCS2A01G373200 chr2D 97.778 90 2 0 5348 5437 473592107 473592196 7.290000e-34 156.0
17 TraesCS2A01G373200 chr2D 78.261 207 21 9 251 443 473587034 473587230 1.600000e-20 111.0
18 TraesCS2A01G373200 chr2B 96.398 1527 55 0 2987 4513 553981191 553982717 0.000000e+00 2516.0
19 TraesCS2A01G373200 chr2B 86.127 865 56 28 1779 2618 553979853 553980678 0.000000e+00 874.0
20 TraesCS2A01G373200 chr2B 89.630 675 31 11 574 1235 553978757 553979405 0.000000e+00 822.0
21 TraesCS2A01G373200 chr2B 91.515 330 18 3 4546 4874 553982712 553983032 3.860000e-121 446.0
22 TraesCS2A01G373200 chr2B 83.182 440 36 14 1304 1731 553979439 553979852 8.600000e-98 368.0
23 TraesCS2A01G373200 chr2B 94.570 221 12 0 35 255 553978174 553978394 5.210000e-90 342.0
24 TraesCS2A01G373200 chr2B 89.333 75 7 1 5278 5351 617140395 617140321 5.800000e-15 93.5
25 TraesCS2A01G373200 chr6B 90.000 80 7 1 5280 5359 699610907 699610829 9.630000e-18 102.0
26 TraesCS2A01G373200 chr6B 97.959 49 1 0 1250 1298 414358003 414358051 9.700000e-13 86.1
27 TraesCS2A01G373200 chr6B 96.078 51 2 0 1251 1301 20019229 20019179 3.490000e-12 84.2
28 TraesCS2A01G373200 chr6A 91.304 69 6 0 5280 5348 559727645 559727577 1.610000e-15 95.3
29 TraesCS2A01G373200 chr5B 88.462 78 6 2 5284 5359 644311524 644311448 2.090000e-14 91.6
30 TraesCS2A01G373200 chr1A 86.747 83 8 2 5279 5359 62962986 62963067 7.500000e-14 89.8
31 TraesCS2A01G373200 chr5D 89.855 69 5 1 5279 5345 439233470 439233538 2.700000e-13 87.9
32 TraesCS2A01G373200 chr4B 96.154 52 2 0 1250 1301 228423187 228423136 9.700000e-13 86.1
33 TraesCS2A01G373200 chr4A 96.154 52 2 0 1250 1301 192618848 192618797 9.700000e-13 86.1
34 TraesCS2A01G373200 chr4A 97.959 49 1 0 1250 1298 712655671 712655719 9.700000e-13 86.1
35 TraesCS2A01G373200 chr3D 85.714 84 9 3 5278 5359 118405877 118405959 9.700000e-13 86.1
36 TraesCS2A01G373200 chr3A 94.340 53 3 0 1253 1305 621875969 621875917 1.260000e-11 82.4
37 TraesCS2A01G373200 chr1B 94.340 53 3 0 1250 1302 319975285 319975337 1.260000e-11 82.4
38 TraesCS2A01G373200 chr1D 93.878 49 3 0 1250 1298 206049544 206049592 2.100000e-09 75.0


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 TraesCS2A01G373200 chr2A 615522112 615527548 5436 False 10041.000000 10041 100.000 1 5437 1 chr2A.!!$F1 5436
1 TraesCS2A01G373200 chrUn 75455600 75460953 5353 True 925.666667 4628 92.144 4 5437 6 chrUn.!!$R2 5433
2 TraesCS2A01G373200 chr2D 473586758 473592196 5438 False 738.777778 2748 89.248 9 5437 9 chr2D.!!$F1 5428
3 TraesCS2A01G373200 chr2B 553978174 553983032 4858 False 894.666667 2516 90.237 35 4874 6 chr2B.!!$F1 4839

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
305 344 0.181350 GACCCTTGGAATGCGAGGAT 59.819 55.000 9.87 0.00 32.11 3.24 F
1511 1706 0.109723 TTGAGGTTGGTAGGTGTGGC 59.890 55.000 0.00 0.00 0.00 5.01 F
1713 1917 0.389687 GCTCTGTCTCACTCACCTGC 60.390 60.000 0.00 0.00 0.00 4.85 F
1957 2323 1.269998 ACGGTAACAGTCTGACTCAGC 59.730 52.381 7.49 5.19 0.00 4.26 F
2729 4359 0.033366 TTGCAACTGCTGACGCTAGA 59.967 50.000 0.00 0.00 42.66 2.43 F
3161 4941 0.390472 GCCTGTCAGGAGGAAGAACG 60.390 60.000 23.77 0.00 37.67 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 3661 0.033011 GAGTCTCTGGGGCTAGTCCA 60.033 60.0 16.93 10.96 36.21 4.02 R
2515 4098 0.032217 CCTCTCCTTGCTCCTCCTCT 60.032 60.0 0.00 0.00 0.00 3.69 R
2517 4100 0.118144 AACCTCTCCTTGCTCCTCCT 59.882 55.0 0.00 0.00 0.00 3.69 R
3500 5289 0.789383 GGATCACAAAAAGCGCGACG 60.789 55.0 12.10 0.00 0.00 5.12 R
3530 5319 0.835276 TCTCCATCATCAGCCACCTG 59.165 55.0 0.00 0.00 40.54 4.00 R
5099 7094 0.463654 TGTGGCACTCCTGTTGTCAC 60.464 55.0 19.83 0.12 0.00 3.67 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
31 32 8.776470 CAATTTTTACAGTGGATTCATTTGCTT 58.224 29.630 0.00 0.00 0.00 3.91
71 72 2.673775 TTCCAGATGCTCCACCAAAA 57.326 45.000 0.00 0.00 0.00 2.44
74 75 1.548582 CCAGATGCTCCACCAAAACCT 60.549 52.381 0.00 0.00 0.00 3.50
82 83 2.297033 CTCCACCAAAACCTGTTCATGG 59.703 50.000 11.26 11.26 36.27 3.66
144 145 0.598065 AAACATCAAGGAAGCACCGC 59.402 50.000 0.00 0.00 44.74 5.68
255 256 2.932261 ACAGGGACAAGGAGTTTTGAC 58.068 47.619 0.00 0.00 0.00 3.18
256 257 2.509964 ACAGGGACAAGGAGTTTTGACT 59.490 45.455 0.00 0.00 0.00 3.41
258 259 3.049344 AGGGACAAGGAGTTTTGACTCT 58.951 45.455 6.53 0.00 36.97 3.24
259 260 3.459969 AGGGACAAGGAGTTTTGACTCTT 59.540 43.478 6.53 0.00 31.09 2.85
260 261 3.815962 GGGACAAGGAGTTTTGACTCTTC 59.184 47.826 6.53 0.03 36.97 2.87
261 262 4.445019 GGGACAAGGAGTTTTGACTCTTCT 60.445 45.833 6.53 0.00 36.97 2.85
262 263 5.221661 GGGACAAGGAGTTTTGACTCTTCTA 60.222 44.000 6.53 0.00 36.97 2.10
263 264 6.289064 GGACAAGGAGTTTTGACTCTTCTAA 58.711 40.000 6.53 0.00 36.97 2.10
264 265 6.937465 GGACAAGGAGTTTTGACTCTTCTAAT 59.063 38.462 6.53 0.00 36.97 1.73
265 266 7.095017 GGACAAGGAGTTTTGACTCTTCTAATG 60.095 40.741 6.53 0.00 36.97 1.90
299 338 1.923356 TCCTTTGACCCTTGGAATGC 58.077 50.000 0.00 0.00 0.00 3.56
300 339 0.527565 CCTTTGACCCTTGGAATGCG 59.472 55.000 0.00 0.00 0.00 4.73
302 341 1.470098 CTTTGACCCTTGGAATGCGAG 59.530 52.381 0.00 0.00 0.00 5.03
304 343 1.198094 TGACCCTTGGAATGCGAGGA 61.198 55.000 9.87 0.00 32.11 3.71
305 344 0.181350 GACCCTTGGAATGCGAGGAT 59.819 55.000 9.87 0.00 32.11 3.24
308 347 1.417890 CCCTTGGAATGCGAGGATAGT 59.582 52.381 9.87 0.00 32.11 2.12
310 349 3.555168 CCCTTGGAATGCGAGGATAGTAC 60.555 52.174 9.87 0.00 32.11 2.73
311 350 3.322254 CCTTGGAATGCGAGGATAGTACT 59.678 47.826 1.20 0.00 32.11 2.73
312 351 4.551388 CTTGGAATGCGAGGATAGTACTC 58.449 47.826 0.00 0.00 0.00 2.59
313 352 2.891580 TGGAATGCGAGGATAGTACTCC 59.108 50.000 0.00 0.00 35.37 3.85
356 408 3.306156 GCATTCTCTATCCCGAGGTAACC 60.306 52.174 0.00 0.00 37.17 2.85
357 409 3.675348 TTCTCTATCCCGAGGTAACCA 57.325 47.619 0.00 0.00 37.17 3.67
361 413 1.111116 TATCCCGAGGTAACCAGCGG 61.111 60.000 7.41 7.41 41.25 5.52
384 442 0.583438 CGATGCATGATTCCGGTGAC 59.417 55.000 2.46 0.00 0.00 3.67
389 447 2.499693 TGCATGATTCCGGTGACTCTTA 59.500 45.455 0.00 0.00 0.00 2.10
398 456 2.882137 CCGGTGACTCTTATCCTCTCTC 59.118 54.545 0.00 0.00 0.00 3.20
400 458 4.202377 CCGGTGACTCTTATCCTCTCTCTA 60.202 50.000 0.00 0.00 0.00 2.43
405 463 7.174946 GGTGACTCTTATCCTCTCTCTATGAAG 59.825 44.444 0.00 0.00 0.00 3.02
410 468 8.574251 TCTTATCCTCTCTCTATGAAGTATGC 57.426 38.462 0.00 0.00 0.00 3.14
411 469 8.166726 TCTTATCCTCTCTCTATGAAGTATGCA 58.833 37.037 0.00 0.00 0.00 3.96
414 472 5.534278 TCCTCTCTCTATGAAGTATGCACTG 59.466 44.000 0.00 0.00 34.36 3.66
416 474 6.183360 CCTCTCTCTATGAAGTATGCACTGTT 60.183 42.308 0.00 0.00 34.36 3.16
423 496 9.317936 TCTATGAAGTATGCACTGTTAATCTTG 57.682 33.333 0.00 0.00 34.36 3.02
445 518 4.341806 TGTGAAATTCTGCAACAATGGAGT 59.658 37.500 0.00 0.00 44.64 3.85
450 523 0.523072 CTGCAACAATGGAGTTCCCG 59.477 55.000 0.00 0.00 39.92 5.14
457 537 1.553248 CAATGGAGTTCCCGGTCTGTA 59.447 52.381 0.00 0.00 37.93 2.74
461 541 2.291735 TGGAGTTCCCGGTCTGTATGTA 60.292 50.000 0.00 0.00 37.93 2.29
466 546 5.018809 AGTTCCCGGTCTGTATGTAAACTA 58.981 41.667 0.00 0.00 0.00 2.24
473 553 5.276868 CGGTCTGTATGTAAACTAATGCAGC 60.277 44.000 0.00 0.00 36.71 5.25
474 554 5.817816 GGTCTGTATGTAAACTAATGCAGCT 59.182 40.000 0.00 0.00 36.71 4.24
475 555 6.018669 GGTCTGTATGTAAACTAATGCAGCTC 60.019 42.308 0.00 0.00 36.71 4.09
476 556 6.758886 GTCTGTATGTAAACTAATGCAGCTCT 59.241 38.462 0.00 0.00 36.71 4.09
477 557 6.758416 TCTGTATGTAAACTAATGCAGCTCTG 59.242 38.462 0.00 0.00 36.71 3.35
490 570 2.508526 CAGCTCTGCCTAAAACTTGGT 58.491 47.619 0.00 0.00 0.00 3.67
491 571 3.674997 CAGCTCTGCCTAAAACTTGGTA 58.325 45.455 0.00 0.00 0.00 3.25
492 572 4.072131 CAGCTCTGCCTAAAACTTGGTAA 58.928 43.478 0.00 0.00 0.00 2.85
493 573 4.518970 CAGCTCTGCCTAAAACTTGGTAAA 59.481 41.667 0.00 0.00 0.00 2.01
494 574 5.009610 CAGCTCTGCCTAAAACTTGGTAAAA 59.990 40.000 0.00 0.00 0.00 1.52
495 575 5.009710 AGCTCTGCCTAAAACTTGGTAAAAC 59.990 40.000 0.00 0.00 0.00 2.43
496 576 5.221165 GCTCTGCCTAAAACTTGGTAAAACA 60.221 40.000 0.00 0.00 0.00 2.83
497 577 6.516693 GCTCTGCCTAAAACTTGGTAAAACAT 60.517 38.462 0.00 0.00 0.00 2.71
498 578 6.977213 TCTGCCTAAAACTTGGTAAAACATC 58.023 36.000 0.00 0.00 0.00 3.06
499 579 6.015772 TCTGCCTAAAACTTGGTAAAACATCC 60.016 38.462 0.00 0.00 0.00 3.51
500 580 5.598830 TGCCTAAAACTTGGTAAAACATCCA 59.401 36.000 0.00 0.00 0.00 3.41
501 581 6.156519 GCCTAAAACTTGGTAAAACATCCAG 58.843 40.000 0.00 0.00 35.05 3.86
502 582 6.239204 GCCTAAAACTTGGTAAAACATCCAGT 60.239 38.462 0.00 0.00 35.05 4.00
503 583 7.145323 CCTAAAACTTGGTAAAACATCCAGTG 58.855 38.462 0.00 0.00 35.05 3.66
504 584 4.584327 AACTTGGTAAAACATCCAGTGC 57.416 40.909 0.00 0.00 35.05 4.40
505 585 3.832527 ACTTGGTAAAACATCCAGTGCT 58.167 40.909 0.00 0.00 35.05 4.40
506 586 4.215109 ACTTGGTAAAACATCCAGTGCTT 58.785 39.130 0.00 0.00 35.05 3.91
507 587 4.278419 ACTTGGTAAAACATCCAGTGCTTC 59.722 41.667 0.00 0.00 35.05 3.86
508 588 4.098914 TGGTAAAACATCCAGTGCTTCT 57.901 40.909 0.00 0.00 0.00 2.85
509 589 3.820467 TGGTAAAACATCCAGTGCTTCTG 59.180 43.478 3.18 3.18 43.27 3.02
510 590 4.072131 GGTAAAACATCCAGTGCTTCTGA 58.928 43.478 10.22 0.00 46.27 3.27
511 591 4.518970 GGTAAAACATCCAGTGCTTCTGAA 59.481 41.667 10.22 0.00 46.27 3.02
512 592 4.843220 AAAACATCCAGTGCTTCTGAAG 57.157 40.909 13.02 13.02 46.27 3.02
551 681 1.000896 CCCAAGAAGCCATCCGGTT 60.001 57.895 0.00 0.00 33.99 4.44
584 726 1.164041 AAGTCGTTGGCTTCCGGTTG 61.164 55.000 0.00 0.00 0.00 3.77
598 740 1.489881 CGGTTGCTTTGCAGTTTGCC 61.490 55.000 0.00 0.00 44.23 4.52
679 821 7.309012 GGAATTCTAAAACCTCTTTAAACGCCT 60.309 37.037 5.23 0.00 0.00 5.52
680 822 8.625786 AATTCTAAAACCTCTTTAAACGCCTA 57.374 30.769 0.00 0.00 0.00 3.93
721 864 7.099764 AGCGATTCCCATGTAATATAAGAGTG 58.900 38.462 0.00 0.00 0.00 3.51
756 899 2.552315 ACTTGCACCATAGAAAACACCG 59.448 45.455 0.00 0.00 0.00 4.94
757 900 2.552599 TGCACCATAGAAAACACCGA 57.447 45.000 0.00 0.00 0.00 4.69
820 964 1.135315 CAAAGACCAATCGCAGCGG 59.865 57.895 16.42 0.32 0.00 5.52
825 969 3.853330 CCAATCGCAGCGGTCGTG 61.853 66.667 16.42 3.52 0.00 4.35
838 984 5.486706 CAGCGGTCGTGTATATAACAAAAC 58.513 41.667 0.00 0.00 40.63 2.43
893 1039 2.203584 AGGAGCCAGGAGTTGAATCAT 58.796 47.619 0.00 0.00 0.00 2.45
894 1040 2.579860 AGGAGCCAGGAGTTGAATCATT 59.420 45.455 0.00 0.00 0.00 2.57
909 1055 1.138247 CATTTTGAGCTCCTGCGCC 59.862 57.895 12.15 0.00 45.42 6.53
949 1101 1.909376 CAAAGATGCAGCATCACAGC 58.091 50.000 32.41 10.26 42.72 4.40
956 1108 2.750637 AGCATCACAGCAGCCTGC 60.751 61.111 9.13 9.13 45.46 4.85
967 1119 1.449246 CAGCCTGCTGTGCTAGACC 60.449 63.158 10.97 0.00 36.81 3.85
993 1145 1.589196 GAGCGTGGTAGCATCGGAC 60.589 63.158 15.22 3.88 40.15 4.79
1235 1397 7.038445 TCAGTCATCTTCTCTTCTTTCATTCCT 60.038 37.037 0.00 0.00 0.00 3.36
1236 1398 7.278424 CAGTCATCTTCTCTTCTTTCATTCCTC 59.722 40.741 0.00 0.00 0.00 3.71
1237 1399 6.538381 GTCATCTTCTCTTCTTTCATTCCTCC 59.462 42.308 0.00 0.00 0.00 4.30
1238 1400 6.214208 TCATCTTCTCTTCTTTCATTCCTCCA 59.786 38.462 0.00 0.00 0.00 3.86
1240 1402 6.648192 TCTTCTCTTCTTTCATTCCTCCATC 58.352 40.000 0.00 0.00 0.00 3.51
1242 1404 7.621285 TCTTCTCTTCTTTCATTCCTCCATCTA 59.379 37.037 0.00 0.00 0.00 1.98
1243 1405 7.927683 TCTCTTCTTTCATTCCTCCATCTAT 57.072 36.000 0.00 0.00 0.00 1.98
1244 1406 7.733969 TCTCTTCTTTCATTCCTCCATCTATG 58.266 38.462 0.00 0.00 0.00 2.23
1246 1408 7.865820 TCTTCTTTCATTCCTCCATCTATGTT 58.134 34.615 0.00 0.00 0.00 2.71
1252 1414 5.072329 TCATTCCTCCATCTATGTTTCCTCC 59.928 44.000 0.00 0.00 0.00 4.30
1253 1415 3.318313 TCCTCCATCTATGTTTCCTCCC 58.682 50.000 0.00 0.00 0.00 4.30
1254 1416 3.051032 TCCTCCATCTATGTTTCCTCCCT 60.051 47.826 0.00 0.00 0.00 4.20
1255 1417 3.326297 CCTCCATCTATGTTTCCTCCCTC 59.674 52.174 0.00 0.00 0.00 4.30
1258 1420 4.594920 TCCATCTATGTTTCCTCCCTCATC 59.405 45.833 0.00 0.00 0.00 2.92
1260 1422 5.782331 CCATCTATGTTTCCTCCCTCATCTA 59.218 44.000 0.00 0.00 0.00 1.98
1261 1423 6.270927 CCATCTATGTTTCCTCCCTCATCTAA 59.729 42.308 0.00 0.00 0.00 2.10
1262 1424 7.202130 CCATCTATGTTTCCTCCCTCATCTAAA 60.202 40.741 0.00 0.00 0.00 1.85
1263 1425 7.125792 TCTATGTTTCCTCCCTCATCTAAAC 57.874 40.000 0.00 0.00 0.00 2.01
1264 1426 6.903534 TCTATGTTTCCTCCCTCATCTAAACT 59.096 38.462 0.00 0.00 0.00 2.66
1265 1427 5.422214 TGTTTCCTCCCTCATCTAAACTC 57.578 43.478 0.00 0.00 0.00 3.01
1266 1428 4.225267 TGTTTCCTCCCTCATCTAAACTCC 59.775 45.833 0.00 0.00 0.00 3.85
1267 1429 3.047695 TCCTCCCTCATCTAAACTCCC 57.952 52.381 0.00 0.00 0.00 4.30
1268 1430 2.317900 TCCTCCCTCATCTAAACTCCCA 59.682 50.000 0.00 0.00 0.00 4.37
1269 1431 3.051032 TCCTCCCTCATCTAAACTCCCAT 60.051 47.826 0.00 0.00 0.00 4.00
1270 1432 3.718956 CCTCCCTCATCTAAACTCCCATT 59.281 47.826 0.00 0.00 0.00 3.16
1271 1433 4.202409 CCTCCCTCATCTAAACTCCCATTC 60.202 50.000 0.00 0.00 0.00 2.67
1272 1434 3.716872 TCCCTCATCTAAACTCCCATTCC 59.283 47.826 0.00 0.00 0.00 3.01
1273 1435 3.181439 CCCTCATCTAAACTCCCATTCCC 60.181 52.174 0.00 0.00 0.00 3.97
1274 1436 3.181439 CCTCATCTAAACTCCCATTCCCC 60.181 52.174 0.00 0.00 0.00 4.81
1275 1437 3.718956 CTCATCTAAACTCCCATTCCCCT 59.281 47.826 0.00 0.00 0.00 4.79
1276 1438 4.119155 TCATCTAAACTCCCATTCCCCTT 58.881 43.478 0.00 0.00 0.00 3.95
1277 1439 4.166144 TCATCTAAACTCCCATTCCCCTTC 59.834 45.833 0.00 0.00 0.00 3.46
1278 1440 2.850568 TCTAAACTCCCATTCCCCTTCC 59.149 50.000 0.00 0.00 0.00 3.46
1279 1441 0.710588 AAACTCCCATTCCCCTTCCC 59.289 55.000 0.00 0.00 0.00 3.97
1280 1442 0.479589 AACTCCCATTCCCCTTCCCA 60.480 55.000 0.00 0.00 0.00 4.37
1281 1443 0.479589 ACTCCCATTCCCCTTCCCAA 60.480 55.000 0.00 0.00 0.00 4.12
1282 1444 0.709992 CTCCCATTCCCCTTCCCAAA 59.290 55.000 0.00 0.00 0.00 3.28
1283 1445 1.291939 CTCCCATTCCCCTTCCCAAAT 59.708 52.381 0.00 0.00 0.00 2.32
1284 1446 2.517980 CTCCCATTCCCCTTCCCAAATA 59.482 50.000 0.00 0.00 0.00 1.40
1285 1447 3.142787 CTCCCATTCCCCTTCCCAAATAT 59.857 47.826 0.00 0.00 0.00 1.28
1286 1448 3.539832 TCCCATTCCCCTTCCCAAATATT 59.460 43.478 0.00 0.00 0.00 1.28
1287 1449 3.647590 CCCATTCCCCTTCCCAAATATTG 59.352 47.826 0.00 0.00 0.00 1.90
1288 1450 3.071457 CCATTCCCCTTCCCAAATATTGC 59.929 47.826 0.00 0.00 0.00 3.56
1289 1451 2.470057 TCCCCTTCCCAAATATTGCC 57.530 50.000 0.00 0.00 0.00 4.52
1290 1452 1.648568 TCCCCTTCCCAAATATTGCCA 59.351 47.619 0.00 0.00 0.00 4.92
1291 1453 2.045047 TCCCCTTCCCAAATATTGCCAA 59.955 45.455 0.00 0.00 0.00 4.52
1292 1454 2.843113 CCCCTTCCCAAATATTGCCAAA 59.157 45.455 0.00 0.00 0.00 3.28
1293 1455 3.370421 CCCCTTCCCAAATATTGCCAAAC 60.370 47.826 0.00 0.00 0.00 2.93
1294 1456 3.262915 CCCTTCCCAAATATTGCCAAACA 59.737 43.478 0.00 0.00 0.00 2.83
1295 1457 4.252878 CCTTCCCAAATATTGCCAAACAC 58.747 43.478 0.00 0.00 0.00 3.32
1296 1458 3.584406 TCCCAAATATTGCCAAACACG 57.416 42.857 0.00 0.00 0.00 4.49
1297 1459 1.999024 CCCAAATATTGCCAAACACGC 59.001 47.619 0.00 0.00 0.00 5.34
1298 1460 1.999024 CCAAATATTGCCAAACACGCC 59.001 47.619 0.00 0.00 0.00 5.68
1299 1461 1.653114 CAAATATTGCCAAACACGCCG 59.347 47.619 0.00 0.00 0.00 6.46
1300 1462 0.885196 AATATTGCCAAACACGCCGT 59.115 45.000 0.00 0.00 0.00 5.68
1301 1463 0.170116 ATATTGCCAAACACGCCGTG 59.830 50.000 16.94 16.94 39.75 4.94
1302 1464 0.885150 TATTGCCAAACACGCCGTGA 60.885 50.000 25.94 0.00 36.96 4.35
1319 1487 3.522553 CGTGAGGATCCAACCTTAGTTC 58.477 50.000 15.82 0.00 40.73 3.01
1320 1488 3.195825 CGTGAGGATCCAACCTTAGTTCT 59.804 47.826 15.82 0.00 40.73 3.01
1338 1506 2.587194 CTGCTCGGGGAGAATGCG 60.587 66.667 0.00 0.00 32.36 4.73
1340 1508 2.586357 GCTCGGGGAGAATGCGTC 60.586 66.667 0.00 0.00 0.00 5.19
1382 1550 1.200020 GAAGGGGTTCGAATGTTGCTG 59.800 52.381 0.00 0.00 0.00 4.41
1386 1554 0.874390 GGTTCGAATGTTGCTGAGCA 59.126 50.000 1.40 1.40 36.47 4.26
1405 1573 3.682315 GTCACGCGATCATCGGCG 61.682 66.667 15.93 18.24 40.84 6.46
1414 1586 1.653094 GATCATCGGCGGGCACAAAA 61.653 55.000 7.21 0.00 0.00 2.44
1452 1632 6.285224 TGTAGCTTAGCAAGAAACTGTTGTA 58.715 36.000 7.07 0.00 0.00 2.41
1475 1655 4.171878 TGAGGATCGGAGTAGAGAACAT 57.828 45.455 0.00 0.00 38.61 2.71
1476 1656 4.537751 TGAGGATCGGAGTAGAGAACATT 58.462 43.478 0.00 0.00 38.61 2.71
1477 1657 4.339530 TGAGGATCGGAGTAGAGAACATTG 59.660 45.833 0.00 0.00 38.61 2.82
1505 1700 1.281867 TGGCAGATTGAGGTTGGTAGG 59.718 52.381 0.00 0.00 0.00 3.18
1506 1701 1.282157 GGCAGATTGAGGTTGGTAGGT 59.718 52.381 0.00 0.00 0.00 3.08
1510 1705 2.305927 AGATTGAGGTTGGTAGGTGTGG 59.694 50.000 0.00 0.00 0.00 4.17
1511 1706 0.109723 TTGAGGTTGGTAGGTGTGGC 59.890 55.000 0.00 0.00 0.00 5.01
1512 1707 1.002502 GAGGTTGGTAGGTGTGGCC 60.003 63.158 0.00 0.00 37.58 5.36
1673 1877 1.242076 AGTGGCATCTGCACTGAAAC 58.758 50.000 4.33 0.00 44.36 2.78
1674 1878 1.202855 AGTGGCATCTGCACTGAAACT 60.203 47.619 4.33 0.00 44.36 2.66
1675 1879 2.038952 AGTGGCATCTGCACTGAAACTA 59.961 45.455 4.33 0.00 44.36 2.24
1676 1880 2.417933 GTGGCATCTGCACTGAAACTAG 59.582 50.000 4.33 0.00 44.36 2.57
1677 1881 2.038952 TGGCATCTGCACTGAAACTAGT 59.961 45.455 4.33 0.00 44.36 2.57
1678 1882 3.260632 TGGCATCTGCACTGAAACTAGTA 59.739 43.478 4.33 0.00 44.36 1.82
1679 1883 3.619038 GGCATCTGCACTGAAACTAGTAC 59.381 47.826 4.33 0.00 44.36 2.73
1680 1884 4.499183 GCATCTGCACTGAAACTAGTACT 58.501 43.478 0.00 0.00 41.59 2.73
1681 1885 5.394224 GGCATCTGCACTGAAACTAGTACTA 60.394 44.000 1.89 1.89 44.36 1.82
1713 1917 0.389687 GCTCTGTCTCACTCACCTGC 60.390 60.000 0.00 0.00 0.00 4.85
1756 1960 2.767566 GCAAATCGCATTTTTCACCG 57.232 45.000 0.00 0.00 41.79 4.94
1779 1983 4.574599 GCTATCTGGCCTTTACCATTTG 57.425 45.455 3.32 0.00 39.54 2.32
1864 2230 7.968246 ACGATCTACATCACTCAAATTTTCAG 58.032 34.615 0.00 0.00 0.00 3.02
1883 2249 7.566760 TTTCAGAAACTTGAAATAGCTGACA 57.433 32.000 0.00 0.00 40.95 3.58
1891 2257 5.634020 ACTTGAAATAGCTGACAACGTAGAC 59.366 40.000 0.00 0.00 0.00 2.59
1892 2258 4.163552 TGAAATAGCTGACAACGTAGACG 58.836 43.478 0.00 0.00 46.33 4.18
1957 2323 1.269998 ACGGTAACAGTCTGACTCAGC 59.730 52.381 7.49 5.19 0.00 4.26
1983 2383 3.726517 CAGTCCTGTTTGCCGGCG 61.727 66.667 23.90 6.63 0.00 6.46
2123 3645 1.683629 CGAACTCTAGCCCCAGAGACT 60.684 57.143 13.03 1.99 44.11 3.24
2124 3646 2.462723 GAACTCTAGCCCCAGAGACTT 58.537 52.381 13.03 0.38 44.11 3.01
2125 3647 2.632763 ACTCTAGCCCCAGAGACTTT 57.367 50.000 13.03 0.00 44.11 2.66
2126 3648 2.909217 ACTCTAGCCCCAGAGACTTTT 58.091 47.619 13.03 0.00 44.11 2.27
2127 3649 3.252351 ACTCTAGCCCCAGAGACTTTTT 58.748 45.455 13.03 0.00 44.11 1.94
2215 3737 6.017400 TCACTCGAAAAGGAAACGTACTAT 57.983 37.500 0.00 0.00 0.00 2.12
2222 3744 6.471519 CGAAAAGGAAACGTACTATGGAGTAG 59.528 42.308 0.00 0.00 38.88 2.57
2223 3745 5.848833 AAGGAAACGTACTATGGAGTAGG 57.151 43.478 0.00 3.85 45.53 3.18
2224 3746 5.121380 AGGAAACGTACTATGGAGTAGGA 57.879 43.478 10.79 0.00 43.69 2.94
2729 4359 0.033366 TTGCAACTGCTGACGCTAGA 59.967 50.000 0.00 0.00 42.66 2.43
2740 4370 3.797039 CTGACGCTAGATTTTCATCCCA 58.203 45.455 0.00 0.00 0.00 4.37
2783 4418 6.509418 TTTATTCTCAGCCAACACCATAAC 57.491 37.500 0.00 0.00 0.00 1.89
2811 4446 3.861569 AGAGAAAACTTCGAAACTGCG 57.138 42.857 0.00 0.00 34.02 5.18
2843 4606 6.258727 AGTTAAGACCATGTTATCTTGATGCG 59.741 38.462 12.17 0.00 35.91 4.73
2929 4703 5.356190 TCCGGAACATGACTAGTGTACTTAG 59.644 44.000 0.00 0.00 0.00 2.18
3101 4875 3.257393 CATCACCGAGTTTCAGGAAGAG 58.743 50.000 0.00 0.00 0.00 2.85
3161 4941 0.390472 GCCTGTCAGGAGGAAGAACG 60.390 60.000 23.77 0.00 37.67 3.95
3401 5186 1.358787 TGCATCAACTTGGGGATCCTT 59.641 47.619 12.58 0.00 0.00 3.36
3500 5289 1.519455 CCCGTCTGTCTTCATCGGC 60.519 63.158 0.00 0.00 38.54 5.54
3530 5319 3.162154 GTGATCCCGGAGTCCCCC 61.162 72.222 0.73 0.00 0.00 5.40
3566 5355 1.480545 GAGAAGAGAGTTCCAGAGGCC 59.519 57.143 0.00 0.00 0.00 5.19
3638 5427 3.092851 GGCTGAGATTGAGGAAGCC 57.907 57.895 0.00 0.00 46.04 4.35
4298 6087 1.577468 TTGTGTACTTCTGTGTGCCG 58.423 50.000 0.00 0.00 0.00 5.69
4355 6144 1.691196 TGTTTGAAGGTGGCAAGGAG 58.309 50.000 0.00 0.00 0.00 3.69
4497 6311 2.507992 CAGCCTCGTCCTGCTTCG 60.508 66.667 0.00 0.00 35.12 3.79
4636 6453 7.568199 AAAGTACTCCATTATGCAACCATAC 57.432 36.000 0.00 0.00 33.79 2.39
4669 6486 2.271800 GTAGAAGGAGGACACAATGCG 58.728 52.381 0.00 0.00 0.00 4.73
5090 7085 8.020819 CGAAGAATTAGCCAAAAGAACACATTA 58.979 33.333 0.00 0.00 0.00 1.90
5164 7159 1.134907 GTGCTGCCCATTGAAATCTGG 60.135 52.381 0.00 0.00 0.00 3.86
5165 7160 0.179092 GCTGCCCATTGAAATCTGGC 60.179 55.000 6.27 6.27 42.49 4.85
5174 7169 5.421277 CCATTGAAATCTGGCATGCTTTTA 58.579 37.500 18.92 4.08 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.517614 TGAATCCACTGTAAAAATTGCACTA 57.482 32.000 0.00 0.00 0.00 2.74
1 2 6.403866 TGAATCCACTGTAAAAATTGCACT 57.596 33.333 0.00 0.00 0.00 4.40
2 3 7.656707 AATGAATCCACTGTAAAAATTGCAC 57.343 32.000 0.00 0.00 0.00 4.57
6 7 8.907222 AAGCAAATGAATCCACTGTAAAAATT 57.093 26.923 0.00 0.00 0.00 1.82
45 46 1.340405 TGGAGCATCTGGAAAGGAAGC 60.340 52.381 0.00 0.00 33.73 3.86
54 55 0.890683 GGTTTTGGTGGAGCATCTGG 59.109 55.000 0.00 0.00 33.73 3.86
71 72 1.599047 CGGCTCTCCATGAACAGGT 59.401 57.895 0.00 0.00 0.00 4.00
74 75 2.268920 GCCGGCTCTCCATGAACA 59.731 61.111 22.15 0.00 0.00 3.18
144 145 2.040278 TCAGATGTTTCACCTCCTTGGG 59.960 50.000 0.00 0.00 41.11 4.12
233 234 4.351111 AGTCAAAACTCCTTGTCCCTGTAT 59.649 41.667 0.00 0.00 0.00 2.29
265 266 1.580845 AAGGATCGCTTGCTGTGTGC 61.581 55.000 0.00 0.00 43.25 4.57
278 317 2.428530 GCATTCCAAGGGTCAAAGGATC 59.571 50.000 0.00 0.00 0.00 3.36
310 349 8.150945 TGCTAGTGGCTAATTAAGATTAAGGAG 58.849 37.037 0.00 0.00 42.39 3.69
311 350 8.029782 TGCTAGTGGCTAATTAAGATTAAGGA 57.970 34.615 0.00 0.00 42.39 3.36
312 351 8.854614 ATGCTAGTGGCTAATTAAGATTAAGG 57.145 34.615 0.00 0.00 42.39 2.69
327 375 2.353208 CGGGATAGAGAATGCTAGTGGC 60.353 54.545 0.00 0.00 42.22 5.01
356 408 2.055310 ATCATGCATCGCAACCGCTG 62.055 55.000 0.00 0.00 43.62 5.18
357 409 1.378882 AATCATGCATCGCAACCGCT 61.379 50.000 0.00 0.00 43.62 5.52
361 413 0.317269 CCGGAATCATGCATCGCAAC 60.317 55.000 0.00 0.00 43.62 4.17
384 442 8.677300 GCATACTTCATAGAGAGAGGATAAGAG 58.323 40.741 0.00 0.00 0.00 2.85
389 447 6.209192 CAGTGCATACTTCATAGAGAGAGGAT 59.791 42.308 0.00 0.00 34.07 3.24
398 456 9.102757 ACAAGATTAACAGTGCATACTTCATAG 57.897 33.333 0.00 0.00 34.07 2.23
400 458 7.607607 TCACAAGATTAACAGTGCATACTTCAT 59.392 33.333 0.00 0.00 34.07 2.57
405 463 8.970691 AATTTCACAAGATTAACAGTGCATAC 57.029 30.769 0.00 0.00 32.25 2.39
410 468 7.140705 TGCAGAATTTCACAAGATTAACAGTG 58.859 34.615 0.00 0.00 0.00 3.66
411 469 7.275888 TGCAGAATTTCACAAGATTAACAGT 57.724 32.000 0.00 0.00 0.00 3.55
414 472 7.928908 TGTTGCAGAATTTCACAAGATTAAC 57.071 32.000 0.00 0.00 0.00 2.01
416 474 7.599621 CCATTGTTGCAGAATTTCACAAGATTA 59.400 33.333 4.40 0.00 0.00 1.75
423 496 4.874970 ACTCCATTGTTGCAGAATTTCAC 58.125 39.130 0.00 0.00 0.00 3.18
445 518 5.999205 TTAGTTTACATACAGACCGGGAA 57.001 39.130 6.32 0.00 0.00 3.97
450 523 5.817816 AGCTGCATTAGTTTACATACAGACC 59.182 40.000 1.02 0.00 0.00 3.85
473 553 6.385649 TGTTTTACCAAGTTTTAGGCAGAG 57.614 37.500 0.00 0.00 0.00 3.35
474 554 6.015772 GGATGTTTTACCAAGTTTTAGGCAGA 60.016 38.462 0.00 0.00 0.00 4.26
475 555 6.156519 GGATGTTTTACCAAGTTTTAGGCAG 58.843 40.000 0.00 0.00 0.00 4.85
476 556 5.598830 TGGATGTTTTACCAAGTTTTAGGCA 59.401 36.000 0.00 0.00 32.93 4.75
477 557 6.091718 TGGATGTTTTACCAAGTTTTAGGC 57.908 37.500 0.00 0.00 32.93 3.93
478 558 7.145323 CACTGGATGTTTTACCAAGTTTTAGG 58.855 38.462 0.00 0.00 35.67 2.69
479 559 6.640907 GCACTGGATGTTTTACCAAGTTTTAG 59.359 38.462 0.00 0.00 35.67 1.85
480 560 6.322712 AGCACTGGATGTTTTACCAAGTTTTA 59.677 34.615 0.00 0.00 35.67 1.52
481 561 5.128663 AGCACTGGATGTTTTACCAAGTTTT 59.871 36.000 0.00 0.00 35.67 2.43
482 562 4.649218 AGCACTGGATGTTTTACCAAGTTT 59.351 37.500 0.00 0.00 35.67 2.66
483 563 4.215109 AGCACTGGATGTTTTACCAAGTT 58.785 39.130 0.00 0.00 35.67 2.66
484 564 3.832527 AGCACTGGATGTTTTACCAAGT 58.167 40.909 0.00 0.00 35.67 3.16
485 565 4.520492 AGAAGCACTGGATGTTTTACCAAG 59.480 41.667 0.00 0.00 35.67 3.61
486 566 4.278170 CAGAAGCACTGGATGTTTTACCAA 59.722 41.667 3.48 0.00 42.39 3.67
487 567 3.820467 CAGAAGCACTGGATGTTTTACCA 59.180 43.478 3.48 0.00 42.39 3.25
488 568 4.072131 TCAGAAGCACTGGATGTTTTACC 58.928 43.478 10.23 0.00 45.76 2.85
489 569 5.689383 TTCAGAAGCACTGGATGTTTTAC 57.311 39.130 10.23 0.00 45.76 2.01
490 570 5.947228 CTTCAGAAGCACTGGATGTTTTA 57.053 39.130 10.23 0.00 45.76 1.52
491 571 4.843220 CTTCAGAAGCACTGGATGTTTT 57.157 40.909 10.23 0.00 45.76 2.43
504 584 1.093159 GCACTGGATGGCTTCAGAAG 58.907 55.000 5.72 5.72 35.20 2.85
505 585 0.694771 AGCACTGGATGGCTTCAGAA 59.305 50.000 2.60 0.00 36.92 3.02
506 586 0.694771 AAGCACTGGATGGCTTCAGA 59.305 50.000 2.60 0.00 46.82 3.27
507 587 3.261250 AAGCACTGGATGGCTTCAG 57.739 52.632 2.60 2.21 46.82 3.02
530 660 1.452108 CGGATGGCTTCTTGGGTCC 60.452 63.158 0.07 0.00 0.00 4.46
551 681 5.007332 GCCAACGACTTTTTCTAACTCAAGA 59.993 40.000 0.00 0.00 0.00 3.02
598 740 6.999272 TCTAGACTAGACTAATAGCAAGTGGG 59.001 42.308 8.17 0.00 0.00 4.61
679 821 3.483421 TCGCTATCAAGATTCCGGTCTA 58.517 45.455 0.00 0.00 0.00 2.59
680 822 2.307768 TCGCTATCAAGATTCCGGTCT 58.692 47.619 0.00 0.00 0.00 3.85
769 912 2.738521 CCACGTTCACGGCAGGAG 60.739 66.667 4.07 0.00 44.95 3.69
820 964 8.889849 ATGCTTTGTTTTGTTATATACACGAC 57.110 30.769 0.00 0.00 36.21 4.34
838 984 6.293626 GCTTGGGTCTATGTATGTATGCTTTG 60.294 42.308 0.00 0.00 0.00 2.77
893 1039 3.049674 CGGCGCAGGAGCTCAAAA 61.050 61.111 17.19 0.00 39.10 2.44
909 1055 2.649516 CTTCTCTTCAGATCTAGCGCG 58.350 52.381 0.00 0.00 0.00 6.86
956 1108 1.895798 TCAAGGACTGGTCTAGCACAG 59.104 52.381 10.74 10.74 40.48 3.66
967 1119 0.737715 GCTACCACGCTCAAGGACTG 60.738 60.000 0.00 0.00 0.00 3.51
993 1145 0.823769 TCATCCCCGTCATCTCCGAG 60.824 60.000 0.00 0.00 0.00 4.63
1235 1397 4.007581 TGAGGGAGGAAACATAGATGGA 57.992 45.455 0.00 0.00 0.00 3.41
1236 1398 4.596643 AGATGAGGGAGGAAACATAGATGG 59.403 45.833 0.00 0.00 0.00 3.51
1237 1399 5.822132 AGATGAGGGAGGAAACATAGATG 57.178 43.478 0.00 0.00 0.00 2.90
1238 1400 7.570607 AGTTTAGATGAGGGAGGAAACATAGAT 59.429 37.037 0.00 0.00 30.89 1.98
1240 1402 7.130681 AGTTTAGATGAGGGAGGAAACATAG 57.869 40.000 0.00 0.00 30.89 2.23
1242 1404 5.104318 GGAGTTTAGATGAGGGAGGAAACAT 60.104 44.000 0.00 0.00 30.89 2.71
1243 1405 4.225267 GGAGTTTAGATGAGGGAGGAAACA 59.775 45.833 0.00 0.00 30.89 2.83
1244 1406 4.384318 GGGAGTTTAGATGAGGGAGGAAAC 60.384 50.000 0.00 0.00 0.00 2.78
1246 1408 3.246350 TGGGAGTTTAGATGAGGGAGGAA 60.246 47.826 0.00 0.00 0.00 3.36
1252 1414 3.181439 GGGGAATGGGAGTTTAGATGAGG 60.181 52.174 0.00 0.00 0.00 3.86
1253 1415 3.718956 AGGGGAATGGGAGTTTAGATGAG 59.281 47.826 0.00 0.00 0.00 2.90
1254 1416 3.747852 AGGGGAATGGGAGTTTAGATGA 58.252 45.455 0.00 0.00 0.00 2.92
1255 1417 4.464947 GAAGGGGAATGGGAGTTTAGATG 58.535 47.826 0.00 0.00 0.00 2.90
1258 1420 2.091830 GGGAAGGGGAATGGGAGTTTAG 60.092 54.545 0.00 0.00 0.00 1.85
1260 1422 0.710588 GGGAAGGGGAATGGGAGTTT 59.289 55.000 0.00 0.00 0.00 2.66
1261 1423 0.479589 TGGGAAGGGGAATGGGAGTT 60.480 55.000 0.00 0.00 0.00 3.01
1262 1424 0.479589 TTGGGAAGGGGAATGGGAGT 60.480 55.000 0.00 0.00 0.00 3.85
1263 1425 0.709992 TTTGGGAAGGGGAATGGGAG 59.290 55.000 0.00 0.00 0.00 4.30
1264 1426 1.403089 ATTTGGGAAGGGGAATGGGA 58.597 50.000 0.00 0.00 0.00 4.37
1265 1427 3.636018 ATATTTGGGAAGGGGAATGGG 57.364 47.619 0.00 0.00 0.00 4.00
1266 1428 3.071457 GCAATATTTGGGAAGGGGAATGG 59.929 47.826 0.00 0.00 0.00 3.16
1267 1429 3.071457 GGCAATATTTGGGAAGGGGAATG 59.929 47.826 0.00 0.00 0.00 2.67
1268 1430 3.311252 TGGCAATATTTGGGAAGGGGAAT 60.311 43.478 0.00 0.00 0.00 3.01
1269 1431 2.045047 TGGCAATATTTGGGAAGGGGAA 59.955 45.455 0.00 0.00 0.00 3.97
1270 1432 1.648568 TGGCAATATTTGGGAAGGGGA 59.351 47.619 0.00 0.00 0.00 4.81
1271 1433 2.173126 TGGCAATATTTGGGAAGGGG 57.827 50.000 0.00 0.00 0.00 4.79
1272 1434 3.262915 TGTTTGGCAATATTTGGGAAGGG 59.737 43.478 0.00 0.00 0.00 3.95
1273 1435 4.252878 GTGTTTGGCAATATTTGGGAAGG 58.747 43.478 0.00 0.00 0.00 3.46
1274 1436 3.925913 CGTGTTTGGCAATATTTGGGAAG 59.074 43.478 0.00 0.00 0.00 3.46
1275 1437 3.862642 GCGTGTTTGGCAATATTTGGGAA 60.863 43.478 0.00 0.00 0.00 3.97
1276 1438 2.353208 GCGTGTTTGGCAATATTTGGGA 60.353 45.455 0.00 0.00 0.00 4.37
1277 1439 1.999024 GCGTGTTTGGCAATATTTGGG 59.001 47.619 0.00 0.00 0.00 4.12
1278 1440 1.999024 GGCGTGTTTGGCAATATTTGG 59.001 47.619 0.00 0.00 0.00 3.28
1279 1441 1.653114 CGGCGTGTTTGGCAATATTTG 59.347 47.619 0.00 0.00 0.00 2.32
1280 1442 1.271102 ACGGCGTGTTTGGCAATATTT 59.729 42.857 13.76 0.00 0.00 1.40
1281 1443 0.885196 ACGGCGTGTTTGGCAATATT 59.115 45.000 13.76 0.00 0.00 1.28
1282 1444 0.170116 CACGGCGTGTTTGGCAATAT 59.830 50.000 30.56 0.00 0.00 1.28
1283 1445 0.885150 TCACGGCGTGTTTGGCAATA 60.885 50.000 35.65 13.72 34.79 1.90
1284 1446 2.128853 CTCACGGCGTGTTTGGCAAT 62.129 55.000 35.65 0.00 34.79 3.56
1285 1447 2.824489 TCACGGCGTGTTTGGCAA 60.824 55.556 35.65 15.23 34.79 4.52
1286 1448 3.276091 CTCACGGCGTGTTTGGCA 61.276 61.111 35.65 17.31 34.79 4.92
1287 1449 4.025401 CCTCACGGCGTGTTTGGC 62.025 66.667 35.65 0.00 34.79 4.52
1288 1450 1.635663 GATCCTCACGGCGTGTTTGG 61.636 60.000 35.65 31.55 34.79 3.28
1289 1451 1.635663 GGATCCTCACGGCGTGTTTG 61.636 60.000 35.65 25.61 34.79 2.93
1290 1452 1.375523 GGATCCTCACGGCGTGTTT 60.376 57.895 35.65 20.31 34.79 2.83
1291 1453 2.107041 TTGGATCCTCACGGCGTGTT 62.107 55.000 35.65 20.64 34.79 3.32
1292 1454 2.579657 TTGGATCCTCACGGCGTGT 61.580 57.895 35.65 19.72 34.79 4.49
1293 1455 2.100631 GTTGGATCCTCACGGCGTG 61.101 63.158 32.75 32.75 34.45 5.34
1294 1456 2.264794 GTTGGATCCTCACGGCGT 59.735 61.111 14.23 6.77 0.00 5.68
1295 1457 2.511600 GGTTGGATCCTCACGGCG 60.512 66.667 14.23 4.80 0.00 6.46
1296 1458 0.539986 TAAGGTTGGATCCTCACGGC 59.460 55.000 14.23 0.00 36.74 5.68
1297 1459 1.831736 ACTAAGGTTGGATCCTCACGG 59.168 52.381 14.23 4.23 36.74 4.94
1298 1460 3.195825 AGAACTAAGGTTGGATCCTCACG 59.804 47.826 14.23 0.16 36.74 4.35
1299 1461 4.468153 AGAGAACTAAGGTTGGATCCTCAC 59.532 45.833 14.23 9.62 36.74 3.51
1300 1462 4.467795 CAGAGAACTAAGGTTGGATCCTCA 59.532 45.833 14.23 0.00 36.74 3.86
1301 1463 4.682050 GCAGAGAACTAAGGTTGGATCCTC 60.682 50.000 14.23 6.14 36.74 3.71
1302 1464 3.198853 GCAGAGAACTAAGGTTGGATCCT 59.801 47.826 14.23 0.00 39.84 3.24
1319 1487 1.227497 GCATTCTCCCCGAGCAGAG 60.227 63.158 0.00 0.00 0.00 3.35
1320 1488 2.903357 GCATTCTCCCCGAGCAGA 59.097 61.111 0.00 0.00 0.00 4.26
1338 1506 0.656205 AAACAACGTTGCGATGCGAC 60.656 50.000 27.61 0.00 39.38 5.19
1340 1508 1.760160 CAAACAACGTTGCGATGCG 59.240 52.632 27.61 7.21 33.06 4.73
1351 1519 2.754472 GAACCCCTTCATGCAAACAAC 58.246 47.619 0.00 0.00 0.00 3.32
1364 1532 0.400213 TCAGCAACATTCGAACCCCT 59.600 50.000 0.00 0.00 0.00 4.79
1382 1550 1.802300 GATGATCGCGTGACGTGCTC 61.802 60.000 14.41 14.48 44.19 4.26
1386 1554 2.277949 CCGATGATCGCGTGACGT 60.278 61.111 9.74 0.00 44.19 4.34
1405 1573 2.279186 GCCACGTGTTTTGTGCCC 60.279 61.111 15.65 0.00 36.01 5.36
1414 1586 1.954146 CTACAGCAACGCCACGTGT 60.954 57.895 15.65 0.00 39.99 4.49
1452 1632 4.537751 TGTTCTCTACTCCGATCCTCAAT 58.462 43.478 0.00 0.00 0.00 2.57
1475 1655 2.290367 CTCAATCTGCCAAACACGACAA 59.710 45.455 0.00 0.00 0.00 3.18
1476 1656 1.872952 CTCAATCTGCCAAACACGACA 59.127 47.619 0.00 0.00 0.00 4.35
1477 1657 1.197721 CCTCAATCTGCCAAACACGAC 59.802 52.381 0.00 0.00 0.00 4.34
1510 1705 4.767255 CAGAGGCTCCCACACGGC 62.767 72.222 11.71 0.00 0.00 5.68
1511 1706 2.997315 TCAGAGGCTCCCACACGG 60.997 66.667 11.71 0.00 0.00 4.94
1512 1707 2.262915 GTCAGAGGCTCCCACACG 59.737 66.667 11.71 0.00 0.00 4.49
1676 1880 6.039616 ACAGAGCTGTAGTACTACGTAGTAC 58.960 44.000 40.22 40.22 45.34 2.73
1677 1881 6.096141 AGACAGAGCTGTAGTACTACGTAGTA 59.904 42.308 27.51 27.51 45.05 1.82
1678 1882 5.083533 ACAGAGCTGTAGTACTACGTAGT 57.916 43.478 29.62 29.62 43.81 2.73
1679 1883 5.350633 AGACAGAGCTGTAGTACTACGTAG 58.649 45.833 24.36 20.97 45.05 3.51
1680 1884 5.105595 TGAGACAGAGCTGTAGTACTACGTA 60.106 44.000 24.36 10.12 45.05 3.57
1681 1885 4.183101 GAGACAGAGCTGTAGTACTACGT 58.817 47.826 24.36 16.15 45.05 3.57
1689 1893 2.163412 GGTGAGTGAGACAGAGCTGTAG 59.837 54.545 2.65 0.00 45.05 2.74
1713 1917 2.106683 GGCCGGATTGACGAGTTGG 61.107 63.158 5.05 0.00 35.47 3.77
1830 2079 6.321435 TGAGTGATGTAGATCGTTCCTGTTAT 59.679 38.462 0.00 0.00 0.00 1.89
1864 2230 5.748592 ACGTTGTCAGCTATTTCAAGTTTC 58.251 37.500 0.00 0.00 0.00 2.78
1891 2257 7.023575 AGTAATTTACACGGTGTAGAACTACG 58.976 38.462 19.29 0.00 38.85 3.51
1892 2258 7.486232 GGAGTAATTTACACGGTGTAGAACTAC 59.514 40.741 19.29 18.26 33.92 2.73
1894 2260 6.393171 GGAGTAATTTACACGGTGTAGAACT 58.607 40.000 19.29 18.80 33.92 3.01
1939 2305 3.386768 TTGCTGAGTCAGACTGTTACC 57.613 47.619 24.55 3.83 32.44 2.85
1940 2306 5.715070 ACTATTGCTGAGTCAGACTGTTAC 58.285 41.667 24.55 4.57 32.44 2.50
1941 2307 5.392057 CGACTATTGCTGAGTCAGACTGTTA 60.392 44.000 24.55 6.46 42.97 2.41
1957 2323 2.159653 GCAAACAGGACTGCGACTATTG 60.160 50.000 0.00 0.00 0.00 1.90
2130 3652 0.891904 GGGCTAGTCCACCGCAAAAA 60.892 55.000 9.01 0.00 36.21 1.94
2131 3653 1.302993 GGGCTAGTCCACCGCAAAA 60.303 57.895 9.01 0.00 36.21 2.44
2132 3654 2.349755 GGGCTAGTCCACCGCAAA 59.650 61.111 9.01 0.00 36.21 3.68
2133 3655 3.712907 GGGGCTAGTCCACCGCAA 61.713 66.667 16.93 0.00 38.68 4.85
2135 3657 4.162690 CTGGGGCTAGTCCACCGC 62.163 72.222 16.93 4.96 37.50 5.68
2136 3658 2.363795 TCTGGGGCTAGTCCACCG 60.364 66.667 16.93 2.41 37.50 4.94
2137 3659 1.001760 TCTCTGGGGCTAGTCCACC 59.998 63.158 16.93 9.21 37.50 4.61
2138 3660 0.324830 AGTCTCTGGGGCTAGTCCAC 60.325 60.000 16.93 7.12 39.32 4.02
2139 3661 0.033011 GAGTCTCTGGGGCTAGTCCA 60.033 60.000 16.93 10.96 36.21 4.02
2140 3662 1.104577 CGAGTCTCTGGGGCTAGTCC 61.105 65.000 4.21 4.21 0.00 3.85
2141 3663 1.730451 GCGAGTCTCTGGGGCTAGTC 61.730 65.000 0.00 0.00 0.00 2.59
2142 3664 1.755008 GCGAGTCTCTGGGGCTAGT 60.755 63.158 0.00 0.00 0.00 2.57
2215 3737 4.081087 GCCAAGATTTGTACTCCTACTCCA 60.081 45.833 0.00 0.00 0.00 3.86
2222 3744 3.010420 GAGGTGCCAAGATTTGTACTCC 58.990 50.000 0.00 0.00 0.00 3.85
2223 3745 2.673368 CGAGGTGCCAAGATTTGTACTC 59.327 50.000 0.00 0.00 0.00 2.59
2224 3746 2.699954 CGAGGTGCCAAGATTTGTACT 58.300 47.619 0.00 0.00 0.00 2.73
2507 4090 3.213402 CTCCTCCTCTCGGACGCC 61.213 72.222 0.00 0.00 34.92 5.68
2508 4091 3.894947 GCTCCTCCTCTCGGACGC 61.895 72.222 0.00 0.00 34.92 5.19
2509 4092 1.999071 CTTGCTCCTCCTCTCGGACG 61.999 65.000 0.00 0.00 34.92 4.79
2510 4093 1.671901 CCTTGCTCCTCCTCTCGGAC 61.672 65.000 0.00 0.00 34.92 4.79
2511 4094 1.380515 CCTTGCTCCTCCTCTCGGA 60.381 63.158 0.00 0.00 37.82 4.55
2512 4095 1.380515 TCCTTGCTCCTCCTCTCGG 60.381 63.158 0.00 0.00 0.00 4.63
2513 4096 0.395036 TCTCCTTGCTCCTCCTCTCG 60.395 60.000 0.00 0.00 0.00 4.04
2514 4097 1.402787 CTCTCCTTGCTCCTCCTCTC 58.597 60.000 0.00 0.00 0.00 3.20
2515 4098 0.032217 CCTCTCCTTGCTCCTCCTCT 60.032 60.000 0.00 0.00 0.00 3.69
2516 4099 0.325203 ACCTCTCCTTGCTCCTCCTC 60.325 60.000 0.00 0.00 0.00 3.71
2517 4100 0.118144 AACCTCTCCTTGCTCCTCCT 59.882 55.000 0.00 0.00 0.00 3.69
2518 4101 0.539518 GAACCTCTCCTTGCTCCTCC 59.460 60.000 0.00 0.00 0.00 4.30
2519 4102 0.174617 CGAACCTCTCCTTGCTCCTC 59.825 60.000 0.00 0.00 0.00 3.71
2520 4103 0.543174 ACGAACCTCTCCTTGCTCCT 60.543 55.000 0.00 0.00 0.00 3.69
2521 4104 0.390472 CACGAACCTCTCCTTGCTCC 60.390 60.000 0.00 0.00 0.00 4.70
2522 4105 0.318762 ACACGAACCTCTCCTTGCTC 59.681 55.000 0.00 0.00 0.00 4.26
2618 4201 6.127310 ACAAGCCATTTCTATTCGTAGACTCT 60.127 38.462 0.00 0.00 34.32 3.24
2729 4359 4.588899 TCACTCGTGAATGGGATGAAAAT 58.411 39.130 0.00 0.00 36.53 1.82
2783 4418 6.256757 AGTTTCGAAGTTTTCTCTTCAGTCTG 59.743 38.462 0.00 0.00 42.53 3.51
2811 4446 8.723942 AGATAACATGGTCTTAACTTCATGTC 57.276 34.615 8.03 0.00 46.27 3.06
2897 4671 2.083774 GTCATGTTCCGGATGCTGAAA 58.916 47.619 4.15 0.00 0.00 2.69
2929 4703 2.237066 GCACGGCAGCCACAAAAAC 61.237 57.895 13.30 0.00 0.00 2.43
3101 4875 4.192317 CACTTAGGCAACCAACTAGGATC 58.808 47.826 0.00 0.00 41.22 3.36
3401 5186 2.754946 AATTGGAAACGTAGCCGAGA 57.245 45.000 0.00 0.00 37.88 4.04
3500 5289 0.789383 GGATCACAAAAAGCGCGACG 60.789 55.000 12.10 0.00 0.00 5.12
3530 5319 0.835276 TCTCCATCATCAGCCACCTG 59.165 55.000 0.00 0.00 40.54 4.00
3638 5427 4.536364 AACCGACTTCATGATATTTGCG 57.464 40.909 0.00 0.00 0.00 4.85
4298 6087 5.382616 TCCAGAGTTTTCCCTTTAGTTTCC 58.617 41.667 0.00 0.00 0.00 3.13
4355 6144 1.376037 CTCGCCACCTCCTTTCCAC 60.376 63.158 0.00 0.00 0.00 4.02
4497 6311 5.909477 TCATCATTTTTCAATCTGATGCCC 58.091 37.500 6.52 0.00 42.91 5.36
4627 6444 3.063452 CGTGATACTTGTGGTATGGTTGC 59.937 47.826 0.00 0.00 40.82 4.17
4636 6453 4.440250 CCTCCTTCTACGTGATACTTGTGG 60.440 50.000 0.00 0.00 0.00 4.17
4669 6486 3.369576 GGAAGAGACCACCAGATACAACC 60.370 52.174 0.00 0.00 0.00 3.77
5031 7026 6.246163 TCGATACTAGGGCTATGATTCAGAA 58.754 40.000 0.00 0.00 0.00 3.02
5090 7085 3.117888 ACTCCTGTTGTCACAAGGAACAT 60.118 43.478 0.00 0.00 32.82 2.71
5099 7094 0.463654 TGTGGCACTCCTGTTGTCAC 60.464 55.000 19.83 0.12 0.00 3.67
5164 7159 7.699812 CCTTCTTATTCTGTCTTAAAAGCATGC 59.300 37.037 10.51 10.51 0.00 4.06
5165 7160 7.699812 GCCTTCTTATTCTGTCTTAAAAGCATG 59.300 37.037 0.00 0.00 0.00 4.06
5174 7169 2.681097 GCGGGCCTTCTTATTCTGTCTT 60.681 50.000 0.84 0.00 0.00 3.01
5221 7216 8.985315 TCTTGAAGATGCAAAACCTATCATAT 57.015 30.769 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.