Multiple sequence alignment - TraesCS2B01G120800

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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 TraesCS2B01G120800 chr2B 100.000 9344 0 0 1 9344 88432392 88423049 0.000000e+00 17256.0
1 TraesCS2B01G120800 chr2B 89.855 69 1 5 5936 6003 494265120 494265183 6.010000e-12 84.2
2 TraesCS2B01G120800 chr2B 90.625 64 2 4 5923 5984 27892521 27892460 2.160000e-11 82.4
3 TraesCS2B01G120800 chr2D 93.666 3631 146 24 151 3712 55761165 55757550 0.000000e+00 5354.0
4 TraesCS2B01G120800 chr2D 97.217 2767 71 4 5981 8743 55755146 55752382 0.000000e+00 4678.0
5 TraesCS2B01G120800 chr2D 96.634 1842 50 9 3709 5542 55757521 55755684 0.000000e+00 3048.0
6 TraesCS2B01G120800 chr2D 94.737 1843 56 10 3709 5542 39401249 39403059 0.000000e+00 2828.0
7 TraesCS2B01G120800 chr2D 97.922 770 12 1 2947 3712 39400451 39401220 0.000000e+00 1330.0
8 TraesCS2B01G120800 chr2D 88.141 624 39 14 8740 9344 55752326 55751719 0.000000e+00 710.0
9 TraesCS2B01G120800 chr2D 92.806 417 12 7 5543 5942 39403089 39403504 1.050000e-163 588.0
10 TraesCS2B01G120800 chr2D 90.465 409 12 7 5543 5948 55755652 55755268 1.800000e-141 514.0
11 TraesCS2B01G120800 chr2D 89.873 158 13 3 2317 2474 243656161 243656315 5.720000e-47 200.0
12 TraesCS2B01G120800 chr2D 94.355 124 7 0 32 155 55762125 55762002 3.440000e-44 191.0
13 TraesCS2B01G120800 chr2D 98.095 105 2 0 6008 6112 39403638 39403742 5.760000e-42 183.0
14 TraesCS2B01G120800 chr2D 89.394 66 7 0 8465 8530 39423605 39423670 6.010000e-12 84.2
15 TraesCS2B01G120800 chr2A 97.195 2816 69 7 5935 8743 57166917 57164105 0.000000e+00 4754.0
16 TraesCS2B01G120800 chr2A 93.976 2374 99 22 657 3020 57172699 57170360 0.000000e+00 3552.0
17 TraesCS2B01G120800 chr2A 95.065 1844 54 11 3709 5542 57169335 57167519 0.000000e+00 2867.0
18 TraesCS2B01G120800 chr2A 96.705 698 14 5 3018 3712 57170055 57169364 0.000000e+00 1153.0
19 TraesCS2B01G120800 chr2A 89.961 518 28 6 8740 9234 57163932 57163416 0.000000e+00 647.0
20 TraesCS2B01G120800 chr2A 93.128 422 13 2 5543 5948 57167489 57167068 1.040000e-168 604.0
21 TraesCS2B01G120800 chr1D 93.056 144 10 0 2332 2475 268963358 268963501 2.640000e-50 211.0
22 TraesCS2B01G120800 chr1D 98.077 52 0 1 5935 5986 206041030 206040980 1.290000e-13 89.8
23 TraesCS2B01G120800 chr1D 85.185 81 7 5 5935 6013 483382970 483383047 2.800000e-10 78.7
24 TraesCS2B01G120800 chr6D 93.056 144 9 1 2332 2475 210769663 210769521 9.510000e-50 209.0
25 TraesCS2B01G120800 chr4A 94.074 135 8 0 2332 2466 240371264 240371398 1.230000e-48 206.0
26 TraesCS2B01G120800 chr5D 92.908 141 9 1 2332 2472 360541995 360541856 4.420000e-48 204.0
27 TraesCS2B01G120800 chr6A 92.308 143 10 1 2332 2474 381088844 381088703 1.590000e-47 202.0
28 TraesCS2B01G120800 chr6A 94.643 56 1 2 5935 5990 58855396 58855343 1.670000e-12 86.1
29 TraesCS2B01G120800 chr6A 94.545 55 1 2 5939 5993 454654013 454654065 6.010000e-12 84.2
30 TraesCS2B01G120800 chr4D 91.724 145 10 2 2332 2476 294454442 294454584 5.720000e-47 200.0
31 TraesCS2B01G120800 chr3D 90.476 63 4 2 5939 6000 435451269 435451330 2.160000e-11 82.4
32 TraesCS2B01G120800 chr4B 89.231 65 3 4 5935 5998 652254778 652254839 2.800000e-10 78.7


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 TraesCS2B01G120800 chr2B 88423049 88432392 9343 True 17256.000000 17256 100.000000 1 9344 1 chr2B.!!$R2 9343
1 TraesCS2B01G120800 chr2D 55751719 55762125 10406 True 2415.833333 5354 93.413000 32 9344 6 chr2D.!!$R1 9312
2 TraesCS2B01G120800 chr2D 39400451 39403742 3291 False 1232.250000 2828 95.890000 2947 6112 4 chr2D.!!$F3 3165
3 TraesCS2B01G120800 chr2A 57163416 57172699 9283 True 2262.833333 4754 94.338333 657 9234 6 chr2A.!!$R1 8577

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
547 1395 0.034380 AGCAAGTGGAGCAGCATGAT 60.034 50.000 0.00 0.00 39.69 2.45 F
548 1396 0.100682 GCAAGTGGAGCAGCATGATG 59.899 55.000 6.59 6.59 39.69 3.07 F
1354 2255 0.310232 CCGTTTTTCCCGCCGTTTTA 59.690 50.000 0.00 0.00 0.00 1.52 F
1690 2595 0.037734 AAAGCTACGGGGTTTCTGGG 59.962 55.000 0.00 0.00 41.10 4.45 F
2064 2969 1.000506 CATTCAGTTTTGCCTGCAGCT 59.999 47.619 8.66 0.00 44.23 4.24 F
2069 2974 1.470098 AGTTTTGCCTGCAGCTAATCG 59.530 47.619 8.66 0.00 44.23 3.34 F
2257 3163 2.687935 TCCTTTTCCACTTTGCACAGAC 59.312 45.455 6.92 0.00 0.00 3.51 F
2347 3253 3.774766 TGCTCTAAAGAACTAGCCATGGA 59.225 43.478 18.40 0.00 33.99 3.41 F
4533 5796 0.472925 TGCACTTCCCTGGTCCTACA 60.473 55.000 0.00 0.00 0.00 2.74 F
5609 6922 1.824230 GTTCATGGCAATTGGCTGGTA 59.176 47.619 29.53 12.45 44.01 3.25 F
7476 8967 0.533951 GTATCCGGTCTCCGTTTGGT 59.466 55.000 0.00 0.00 46.80 3.67 F
8277 9768 0.737715 GGCACGAGAACGATCTTGCT 60.738 55.000 16.06 0.70 40.28 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 2446 0.107361 AGCCGAAATCTAAACGGGGG 60.107 55.000 0.00 0.0 45.66 5.40 R
1690 2595 0.240945 CAACATGGCCAAAGTCCGTC 59.759 55.000 10.96 0.0 0.00 4.79 R
2226 3132 2.143925 GTGGAAAAGGAGTCGGAACAG 58.856 52.381 0.00 0.0 0.00 3.16 R
3549 4767 1.978580 AGGTGGTACAAGAAGTCCTGG 59.021 52.381 0.00 0.0 44.16 4.45 R
3917 5170 4.513198 ACTAAGCAGTCAGAAGTCAGTC 57.487 45.455 0.00 0.0 0.00 3.51 R
4333 5594 5.582689 ACTGTTTAATTCAATGCTAGCCC 57.417 39.130 13.29 0.0 0.00 5.19 R
4493 5756 5.132648 TGCAGGGGTGAATTGAGAAGTATAT 59.867 40.000 0.00 0.0 0.00 0.86 R
4785 6050 8.477419 ACAAGACCTTAAGGAATTTTGATTGA 57.523 30.769 28.52 0.0 38.94 2.57 R
6520 8009 1.619654 TTGCAACTTGATGGACAGGG 58.380 50.000 0.00 0.0 0.00 4.45 R
7491 8982 0.178995 TTTGGATGAGCTGTGCCACA 60.179 50.000 0.00 0.0 0.00 4.17 R
8280 9771 0.653636 CTCCTCGCTCGAGTAGTGAC 59.346 60.000 15.13 0.0 39.84 3.67 R
9247 10943 2.257207 TGGTTCCTGGACTTGGACTAG 58.743 52.381 0.00 0.0 32.65 2.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.458951 GCATGTGAAAGTATAAGAGGCG 57.541 45.455 0.00 0.00 0.00 5.52
22 23 3.871594 GCATGTGAAAGTATAAGAGGCGT 59.128 43.478 0.00 0.00 0.00 5.68
23 24 4.025647 GCATGTGAAAGTATAAGAGGCGTC 60.026 45.833 0.00 0.00 0.00 5.19
24 25 4.119442 TGTGAAAGTATAAGAGGCGTCC 57.881 45.455 2.06 0.00 0.00 4.79
25 26 3.512329 TGTGAAAGTATAAGAGGCGTCCA 59.488 43.478 2.06 0.00 0.00 4.02
26 27 4.113354 GTGAAAGTATAAGAGGCGTCCAG 58.887 47.826 2.06 0.00 0.00 3.86
27 28 4.021229 TGAAAGTATAAGAGGCGTCCAGA 58.979 43.478 2.06 0.00 0.00 3.86
28 29 4.464951 TGAAAGTATAAGAGGCGTCCAGAA 59.535 41.667 2.06 0.00 0.00 3.02
29 30 5.046878 TGAAAGTATAAGAGGCGTCCAGAAA 60.047 40.000 2.06 0.00 0.00 2.52
30 31 4.657436 AGTATAAGAGGCGTCCAGAAAG 57.343 45.455 2.06 0.00 0.00 2.62
37 38 0.586802 GGCGTCCAGAAAGAACACAC 59.413 55.000 0.00 0.00 0.00 3.82
75 76 9.781834 CATACCAAATCAAAACGATTAAAGCTA 57.218 29.630 0.00 0.00 43.83 3.32
114 115 2.568956 TCAAGATGGTGGTCTCAGAAGG 59.431 50.000 0.00 0.00 0.00 3.46
125 126 5.940470 GTGGTCTCAGAAGGTTATTCATGTT 59.060 40.000 0.00 0.00 0.00 2.71
145 146 2.785562 TGTTGATTACCTCGGGGTTTG 58.214 47.619 15.04 0.00 44.73 2.93
164 1006 5.684184 GGTTTGAGGTTTAACGATTGTTGAC 59.316 40.000 8.70 7.04 39.12 3.18
173 1015 7.166142 GGTTTAACGATTGTTGACGATTTTCAA 59.834 33.333 8.70 0.00 39.12 2.69
202 1044 1.308047 GCATTGCCATGGTGACGATA 58.692 50.000 14.67 0.00 0.00 2.92
209 1051 2.297315 GCCATGGTGACGATAGAGATCA 59.703 50.000 14.67 0.00 41.38 2.92
213 1055 5.047448 CCATGGTGACGATAGAGATCAGATT 60.047 44.000 2.57 0.00 41.38 2.40
217 1059 8.863872 TGGTGACGATAGAGATCAGATTTATA 57.136 34.615 0.00 0.00 41.38 0.98
218 1060 8.731605 TGGTGACGATAGAGATCAGATTTATAC 58.268 37.037 0.00 0.00 41.38 1.47
219 1061 7.906010 GGTGACGATAGAGATCAGATTTATACG 59.094 40.741 0.00 0.00 41.38 3.06
220 1062 7.427030 GTGACGATAGAGATCAGATTTATACGC 59.573 40.741 0.00 0.00 41.38 4.42
221 1063 7.119262 TGACGATAGAGATCAGATTTATACGCA 59.881 37.037 0.00 0.00 41.38 5.24
241 1083 2.101249 CACCCCAACATAATGCATGGAC 59.899 50.000 0.00 0.00 39.13 4.02
245 1087 2.945008 CCAACATAATGCATGGACGAGT 59.055 45.455 0.00 0.00 39.13 4.18
246 1088 3.242837 CCAACATAATGCATGGACGAGTG 60.243 47.826 0.00 0.00 39.13 3.51
248 1090 4.400529 ACATAATGCATGGACGAGTGTA 57.599 40.909 0.00 0.00 39.13 2.90
256 1098 3.677700 GCATGGACGAGTGTATGTGGTTA 60.678 47.826 0.00 0.00 0.00 2.85
258 1100 2.494471 TGGACGAGTGTATGTGGTTAGG 59.506 50.000 0.00 0.00 0.00 2.69
266 1108 2.105766 GTATGTGGTTAGGAGGACGGT 58.894 52.381 0.00 0.00 0.00 4.83
267 1109 1.192428 ATGTGGTTAGGAGGACGGTC 58.808 55.000 0.00 0.00 0.00 4.79
297 1139 6.531948 GGCGTCGCTTAAATGATTCTATCTAT 59.468 38.462 18.11 0.00 0.00 1.98
318 1160 1.740025 GCTTTAGTCCATGCCAGACAC 59.260 52.381 3.83 0.00 36.68 3.67
349 1191 4.615912 GCTTGCATCTACATTCCGTGTTTT 60.616 41.667 0.00 0.00 42.29 2.43
373 1215 7.681939 TCCATGTATTGTAGTTTCTTCAACC 57.318 36.000 0.00 0.00 35.77 3.77
374 1216 7.227873 TCCATGTATTGTAGTTTCTTCAACCA 58.772 34.615 0.00 0.00 35.77 3.67
376 1218 8.023128 CCATGTATTGTAGTTTCTTCAACCAAG 58.977 37.037 0.00 0.00 35.77 3.61
389 1231 5.412594 TCTTCAACCAAGAAATCGATGAAGG 59.587 40.000 15.72 9.41 41.44 3.46
390 1232 4.651778 TCAACCAAGAAATCGATGAAGGT 58.348 39.130 0.00 0.35 0.00 3.50
396 1238 5.391310 CCAAGAAATCGATGAAGGTGTCTTG 60.391 44.000 0.00 2.98 40.12 3.02
416 1258 6.016276 GTCTTGTCAAAAACCCACATGATAGT 60.016 38.462 0.00 0.00 29.82 2.12
423 1265 4.927267 AACCCACATGATAGTTCCTTCA 57.073 40.909 0.00 0.00 0.00 3.02
425 1267 3.198068 CCCACATGATAGTTCCTTCACG 58.802 50.000 0.00 0.00 0.00 4.35
453 1295 2.932614 ACTTTGACTAGCACGATGATGC 59.067 45.455 0.00 0.00 46.50 3.91
467 1309 1.227380 GATGCCGAGCGTCCTTCAT 60.227 57.895 6.79 0.00 38.50 2.57
481 1323 2.061773 CCTTCATACGACGCCATGATC 58.938 52.381 12.05 0.00 31.50 2.92
490 1332 2.076100 GACGCCATGATCTGTGAACAA 58.924 47.619 0.00 0.00 0.00 2.83
534 1382 1.423161 AGAGGCAAGGAAGAAGCAAGT 59.577 47.619 0.00 0.00 0.00 3.16
541 1389 1.163554 GGAAGAAGCAAGTGGAGCAG 58.836 55.000 0.00 0.00 0.00 4.24
547 1395 0.034380 AGCAAGTGGAGCAGCATGAT 60.034 50.000 0.00 0.00 39.69 2.45
548 1396 0.100682 GCAAGTGGAGCAGCATGATG 59.899 55.000 6.59 6.59 39.69 3.07
556 1404 0.599466 AGCAGCATGATGATCGACCG 60.599 55.000 16.67 0.00 39.69 4.79
579 1427 5.671493 GGTTAGCATACACCTGATACAGTT 58.329 41.667 0.00 0.00 0.00 3.16
583 1431 4.049186 GCATACACCTGATACAGTTACCG 58.951 47.826 0.00 0.00 0.00 4.02
584 1432 4.441079 GCATACACCTGATACAGTTACCGT 60.441 45.833 0.00 0.00 0.00 4.83
585 1433 5.657474 CATACACCTGATACAGTTACCGTT 58.343 41.667 0.00 0.00 0.00 4.44
586 1434 4.612264 ACACCTGATACAGTTACCGTTT 57.388 40.909 0.00 0.00 0.00 3.60
590 1438 5.291128 CACCTGATACAGTTACCGTTTCATC 59.709 44.000 0.00 0.00 0.00 2.92
635 1490 3.200593 GCCATGCGCTGTCCTGAG 61.201 66.667 9.73 0.00 0.00 3.35
636 1491 2.580815 CCATGCGCTGTCCTGAGA 59.419 61.111 9.73 0.00 0.00 3.27
638 1493 0.463295 CCATGCGCTGTCCTGAGAAT 60.463 55.000 9.73 0.00 0.00 2.40
706 1580 1.089481 GGCAATTCGTCTCATCGCCA 61.089 55.000 0.00 0.00 37.98 5.69
708 1582 1.926561 CAATTCGTCTCATCGCCAGA 58.073 50.000 0.00 0.00 0.00 3.86
709 1583 1.590238 CAATTCGTCTCATCGCCAGAC 59.410 52.381 0.00 0.00 37.51 3.51
712 1586 2.181777 GTCTCATCGCCAGACGCA 59.818 61.111 0.00 0.00 43.23 5.24
713 1587 1.446099 GTCTCATCGCCAGACGCAA 60.446 57.895 0.00 0.00 43.23 4.85
774 1668 4.454554 GGTACGACTGCGACAGAC 57.545 61.111 12.77 6.56 41.64 3.51
817 1711 1.815817 GCCCCACGCCAAAACAGAAT 61.816 55.000 0.00 0.00 0.00 2.40
836 1730 2.123251 ATCCGACGGCCCAGATCT 60.123 61.111 9.66 0.00 0.00 2.75
842 1736 4.888325 CGGCCCAGATCTCCCCCT 62.888 72.222 0.00 0.00 0.00 4.79
868 1763 1.301623 CCCCGGCTCATAAACCACA 59.698 57.895 0.00 0.00 0.00 4.17
875 1770 3.065371 CGGCTCATAAACCACATTCTTCC 59.935 47.826 0.00 0.00 0.00 3.46
1151 2052 3.984749 GGAGATCTCCCGCCTCGC 61.985 72.222 28.84 3.09 43.94 5.03
1354 2255 0.310232 CCGTTTTTCCCGCCGTTTTA 59.690 50.000 0.00 0.00 0.00 1.52
1445 2346 2.103736 GCGTACCGGCTGTACCTC 59.896 66.667 12.72 2.76 45.89 3.85
1474 2375 2.280592 GGGCAACGTCACGTCCTT 60.281 61.111 1.67 0.00 39.99 3.36
1484 2385 1.797933 CACGTCCTTCTCGCTGTCG 60.798 63.158 0.00 0.00 0.00 4.35
1514 2415 2.798499 CGGGCCTAATCGTGACAAGTAG 60.798 54.545 0.84 0.00 0.00 2.57
1539 2440 5.413499 GGTTCAGCTATGCAATGTTTGAAT 58.587 37.500 0.00 0.00 32.41 2.57
1541 2442 4.426416 TCAGCTATGCAATGTTTGAATGC 58.574 39.130 0.00 0.00 40.45 3.56
1544 2445 3.484649 GCTATGCAATGTTTGAATGCGAG 59.515 43.478 0.00 0.00 42.91 5.03
1545 2446 1.700523 TGCAATGTTTGAATGCGAGC 58.299 45.000 0.00 0.00 42.91 5.03
1549 2450 1.322538 ATGTTTGAATGCGAGCCCCC 61.323 55.000 0.00 0.00 0.00 5.40
1553 2454 2.750237 GAATGCGAGCCCCCGTTT 60.750 61.111 0.00 0.00 0.00 3.60
1561 2462 1.296727 GAGCCCCCGTTTAGATTTCG 58.703 55.000 0.00 0.00 0.00 3.46
1581 2482 3.057245 TCGGCTATCAGTGATCTGTATGC 60.057 47.826 9.42 5.87 41.91 3.14
1582 2483 3.056962 CGGCTATCAGTGATCTGTATGCT 60.057 47.826 9.42 0.00 41.91 3.79
1583 2484 4.244066 GGCTATCAGTGATCTGTATGCTG 58.756 47.826 9.42 0.00 41.91 4.41
1584 2485 3.679025 GCTATCAGTGATCTGTATGCTGC 59.321 47.826 9.42 0.00 41.91 5.25
1625 2530 4.963276 TGCTCATACATGGTTACTTTGC 57.037 40.909 0.00 0.00 0.00 3.68
1639 2544 1.992557 ACTTTGCCTCCCAGGATAACA 59.007 47.619 0.00 0.00 37.67 2.41
1690 2595 0.037734 AAAGCTACGGGGTTTCTGGG 59.962 55.000 0.00 0.00 41.10 4.45
1702 2607 2.747686 TCTGGGACGGACTTTGGC 59.252 61.111 0.00 0.00 39.80 4.52
1750 2655 6.823182 TGATTGTTATCACCAAACTGATCGAT 59.177 34.615 0.00 0.00 35.87 3.59
1752 2657 6.421377 TGTTATCACCAAACTGATCGATTG 57.579 37.500 0.00 0.00 32.86 2.67
1753 2658 5.937540 TGTTATCACCAAACTGATCGATTGT 59.062 36.000 0.00 0.00 32.86 2.71
1771 2676 3.512516 GTGCTGGAGGATTGCGGC 61.513 66.667 0.00 0.00 46.29 6.53
1789 2694 2.684374 CGGCATTTCATCTGGAATGACA 59.316 45.455 15.67 0.00 34.91 3.58
1815 2720 3.235200 AGCAGGAGAGTGTATATCCCAC 58.765 50.000 0.00 0.00 40.46 4.61
1913 2818 2.132762 GTCGAAAGAACACCGTCATGT 58.867 47.619 0.00 0.00 45.01 3.21
1978 2883 3.344904 GCATTTCTGCGCTTGATATGT 57.655 42.857 23.05 5.06 38.92 2.29
1993 2898 7.337718 GCTTGATATGTCTTAACATGTACGTG 58.662 38.462 13.64 13.64 45.72 4.49
2064 2969 1.000506 CATTCAGTTTTGCCTGCAGCT 59.999 47.619 8.66 0.00 44.23 4.24
2069 2974 1.470098 AGTTTTGCCTGCAGCTAATCG 59.530 47.619 8.66 0.00 44.23 3.34
2085 2990 4.556699 GCTAATCGTCATATTTTGGCACCC 60.557 45.833 0.00 0.00 0.00 4.61
2126 3031 4.392940 CATGTGAGGATAAGGGGACAATC 58.607 47.826 0.00 0.00 0.00 2.67
2182 3088 7.116075 ACGGAGTAGGCACAAGTATTATAAA 57.884 36.000 0.00 0.00 41.94 1.40
2226 3132 3.181496 GGTAAAGCTGCATTTCTGTAGGC 60.181 47.826 1.02 0.00 35.80 3.93
2257 3163 2.687935 TCCTTTTCCACTTTGCACAGAC 59.312 45.455 6.92 0.00 0.00 3.51
2313 3219 9.463443 CCATTAGCTATTCCCTTTTTATTTTCG 57.537 33.333 0.00 0.00 0.00 3.46
2347 3253 3.774766 TGCTCTAAAGAACTAGCCATGGA 59.225 43.478 18.40 0.00 33.99 3.41
2580 3487 6.966435 AAAAACAACTTGTCAGTCCATTTG 57.034 33.333 0.00 0.00 30.45 2.32
3061 4275 7.550906 AGTGTCTGAAGAGCTTTTTACATATCC 59.449 37.037 0.00 0.00 0.00 2.59
3549 4767 5.824624 TCTCTTCAGGATTTGGTGCAATATC 59.175 40.000 0.00 0.00 0.00 1.63
3740 4991 9.965824 CTGAGGTTACTATTTGTGACAATTTTT 57.034 29.630 0.00 0.00 36.95 1.94
3775 5026 6.600882 ATCTGTCTTGGCATTTCTGAAAAT 57.399 33.333 6.95 0.00 35.43 1.82
3842 5093 6.569179 TCCCTGTACTTCTTTTAACAATGC 57.431 37.500 0.00 0.00 0.00 3.56
3908 5161 6.157904 TGTGCTATCAATTTGGTCATGTTTG 58.842 36.000 0.00 0.00 0.00 2.93
3917 5170 8.356657 TCAATTTGGTCATGTTTGGTAAACTAG 58.643 33.333 6.07 0.00 41.90 2.57
3939 5192 5.317808 AGACTGACTTCTGACTGCTTAGTA 58.682 41.667 0.00 0.00 0.00 1.82
4349 5610 7.912778 AATTTTAGGGGCTAGCATTGAATTA 57.087 32.000 18.24 0.00 0.00 1.40
4442 5705 5.977129 AGCGAAGTTAAAACACATTTCTTGG 59.023 36.000 0.00 0.00 32.27 3.61
4533 5796 0.472925 TGCACTTCCCTGGTCCTACA 60.473 55.000 0.00 0.00 0.00 2.74
4776 6041 8.997323 CCAATTTGCCATGAAAAATTACAAGTA 58.003 29.630 14.26 0.00 34.92 2.24
4811 6076 9.581289 TCAATCAAAATTCCTTAAGGTCTTGTA 57.419 29.630 21.04 10.20 36.34 2.41
4861 6126 4.707934 TGATCTCCACAACAGTATACGGAA 59.292 41.667 10.15 0.00 0.00 4.30
5208 6475 2.570302 GGAGTAGTTTTCTGGGGCTACA 59.430 50.000 0.00 0.00 37.02 2.74
5516 6784 9.590451 CTGTAATATTCTTGCAACAATCCATTT 57.410 29.630 2.98 0.00 0.00 2.32
5602 6915 2.163010 AGAAGCGAGTTCATGGCAATTG 59.837 45.455 0.00 0.00 37.67 2.32
5609 6922 1.824230 GTTCATGGCAATTGGCTGGTA 59.176 47.619 29.53 12.45 44.01 3.25
5670 6983 8.816640 AACTACATTGTTTAGCAAATTCCAAG 57.183 30.769 0.00 0.00 40.91 3.61
5778 7091 5.611796 TTTATGTCCGCATGCAATATCTC 57.388 39.130 19.57 1.09 36.58 2.75
5779 7092 2.618442 TGTCCGCATGCAATATCTCA 57.382 45.000 19.57 3.75 0.00 3.27
5904 7220 4.207891 TCTGTTCTAAGACTTGATGGCC 57.792 45.455 0.00 0.00 0.00 5.36
5986 7473 9.903682 TTATATTTCTTTACGAAGGGAGTATCG 57.096 33.333 0.00 0.00 44.33 2.92
6112 7601 3.264193 TCATACAGGTTCCAGATGTTGCT 59.736 43.478 0.00 0.00 0.00 3.91
6368 7857 6.765989 CCGTATTGAGTTCCCAAATTCATCTA 59.234 38.462 0.00 0.00 31.98 1.98
6520 8009 4.846779 TTCTGGACTTGGCAATACAAAC 57.153 40.909 0.00 0.00 0.00 2.93
6776 8265 2.022195 GCCGAGACATGACTACCAGTA 58.978 52.381 0.00 0.00 0.00 2.74
6931 8420 4.320788 GCTTCTCTTGCTGCAATTGTTAGT 60.321 41.667 16.38 0.00 0.00 2.24
7089 8578 2.031870 TCACAGCTGCTATCCACGTAT 58.968 47.619 15.27 0.00 0.00 3.06
7172 8661 4.015084 CCTTCAGGTTTTCAGCATCATCT 58.985 43.478 0.00 0.00 0.00 2.90
7208 8699 6.199557 TGCCCCAATATCTTTATTGCTCTA 57.800 37.500 1.11 0.00 42.21 2.43
7209 8700 6.793478 TGCCCCAATATCTTTATTGCTCTAT 58.207 36.000 1.11 0.00 42.21 1.98
7476 8967 0.533951 GTATCCGGTCTCCGTTTGGT 59.466 55.000 0.00 0.00 46.80 3.67
7491 8982 3.997021 CGTTTGGTAGAGACAAAGATGCT 59.003 43.478 0.00 0.00 38.38 3.79
7743 9234 1.202627 TCCCACAAACTTGCAAATGGC 60.203 47.619 0.00 0.00 45.13 4.40
7902 9393 1.617947 ATGAGGAGACCTTGCCGACC 61.618 60.000 0.00 0.00 31.76 4.79
7958 9449 3.914579 CTGGACCAGTGGCCAGCAG 62.915 68.421 28.51 12.08 39.03 4.24
8266 9757 0.944311 GCTTCGAAGTTGGCACGAGA 60.944 55.000 25.24 0.00 37.36 4.04
8277 9768 0.737715 GGCACGAGAACGATCTTGCT 60.738 55.000 16.06 0.70 40.28 3.91
8280 9771 1.916651 CACGAGAACGATCTTGCTCTG 59.083 52.381 9.72 2.42 40.28 3.35
8353 9844 4.883585 CCTTGCTACAATGATCTTGCCTTA 59.116 41.667 0.00 0.00 0.00 2.69
8356 9847 4.823442 TGCTACAATGATCTTGCCTTATGG 59.177 41.667 0.00 0.00 0.00 2.74
8414 9906 2.617532 GCAGTCTCAAGCCTGAATTCCT 60.618 50.000 2.27 0.00 0.00 3.36
8453 9945 3.525537 CCAGCAGATAGTCGTGTTCATT 58.474 45.455 0.00 0.00 0.00 2.57
8460 9952 4.929808 AGATAGTCGTGTTCATTTGTGGAC 59.070 41.667 0.00 0.00 0.00 4.02
8469 9961 4.814234 TGTTCATTTGTGGACTAGTGTCAC 59.186 41.667 15.35 15.35 44.61 3.67
8484 9976 1.202256 TGTCACGTCATCTCGTATGGC 60.202 52.381 0.00 0.00 42.27 4.40
8502 9994 1.067354 GGCCTCTTTGCTGGATGTTTG 60.067 52.381 0.00 0.00 0.00 2.93
8520 10012 9.431887 GGATGTTTGACTGAAGTATGTAAGTTA 57.568 33.333 0.00 0.00 0.00 2.24
8559 10051 5.160607 TGACAAGTATCCTGGGTAAAGTG 57.839 43.478 0.00 0.00 0.00 3.16
8600 10094 4.127171 GTGTAATATAGTGGGGCACTGTG 58.873 47.826 2.76 2.76 45.01 3.66
8604 10098 2.124507 ATAGTGGGGCACTGTGCGTT 62.125 55.000 24.86 11.45 46.21 4.84
8613 10107 3.488489 GGCACTGTGCGTTTACAATTAG 58.512 45.455 24.86 0.00 46.21 1.73
8622 10116 3.065786 GCGTTTACAATTAGTTAGCCCCC 59.934 47.826 0.00 0.00 0.00 5.40
8649 10143 3.165071 TCCAAGAAAATTTGGCCCTCTC 58.835 45.455 0.00 0.00 45.83 3.20
8651 10145 2.819608 CAAGAAAATTTGGCCCTCTCGA 59.180 45.455 0.00 0.00 0.00 4.04
8661 10155 0.103390 GCCCTCTCGAAGGCTTAGAC 59.897 60.000 5.92 0.00 46.14 2.59
8727 10221 6.489361 GCTCTGAATCTTTGGGATATCATTGT 59.511 38.462 4.83 0.00 33.71 2.71
8733 10227 7.823745 ATCTTTGGGATATCATTGTGGTAAC 57.176 36.000 4.83 0.00 32.04 2.50
8738 10232 6.361433 TGGGATATCATTGTGGTAACGAATT 58.639 36.000 4.83 0.00 42.51 2.17
8753 10425 9.104965 TGGTAACGAATTTGTTATCTCCTTATG 57.895 33.333 23.40 0.00 36.58 1.90
8915 10591 5.213891 TGAGACAGTTCTTCATGTAAGCA 57.786 39.130 0.00 0.00 34.97 3.91
8982 10658 5.004448 TGAACCTGGTATTATTTTGCGTCA 58.996 37.500 0.00 0.00 0.00 4.35
9012 10688 8.039538 ACATAATACTAGATCGACGAGGATACA 58.960 37.037 3.01 0.00 41.41 2.29
9013 10689 9.047371 CATAATACTAGATCGACGAGGATACAT 57.953 37.037 3.01 0.00 41.41 2.29
9014 10690 6.912203 ATACTAGATCGACGAGGATACATG 57.088 41.667 3.01 0.00 41.41 3.21
9015 10691 4.895961 ACTAGATCGACGAGGATACATGA 58.104 43.478 3.01 0.00 41.41 3.07
9037 10714 4.331968 AGAGTGGTTTGTGACTTTGTGAA 58.668 39.130 0.00 0.00 0.00 3.18
9047 10724 8.921670 GTTTGTGACTTTGTGAACAAGTTTTAT 58.078 29.630 0.00 0.00 37.15 1.40
9177 10872 5.299949 AGAACAAAGGATTTTGGCATCAAC 58.700 37.500 5.17 0.00 46.33 3.18
9204 10900 3.370421 GCAATTTATTGGTGGAAAGGGGG 60.370 47.826 4.76 0.00 38.21 5.40
9213 10909 4.769050 TGGTGGAAAGGGGGAAAATAAAT 58.231 39.130 0.00 0.00 0.00 1.40
9256 10952 4.739137 GCTGAAGGTAGCATCTAGTCCAAG 60.739 50.000 0.00 0.00 43.17 3.61
9293 10989 4.289410 TCAAGTTGGAATGAGGATGGAGAA 59.711 41.667 2.34 0.00 0.00 2.87
9328 11024 3.616379 CCAAAAAGTCAACACGTGCAAAT 59.384 39.130 17.22 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.871594 ACGCCTCTTATACTTTCACATGC 59.128 43.478 0.00 0.00 0.00 4.06
1 2 4.508124 GGACGCCTCTTATACTTTCACATG 59.492 45.833 0.00 0.00 0.00 3.21
2 3 4.161565 TGGACGCCTCTTATACTTTCACAT 59.838 41.667 0.00 0.00 0.00 3.21
3 4 3.512329 TGGACGCCTCTTATACTTTCACA 59.488 43.478 0.00 0.00 0.00 3.58
4 5 4.113354 CTGGACGCCTCTTATACTTTCAC 58.887 47.826 0.00 0.00 0.00 3.18
5 6 4.021229 TCTGGACGCCTCTTATACTTTCA 58.979 43.478 0.00 0.00 0.00 2.69
6 7 4.650754 TCTGGACGCCTCTTATACTTTC 57.349 45.455 0.00 0.00 0.00 2.62
7 8 5.187186 TCTTTCTGGACGCCTCTTATACTTT 59.813 40.000 0.00 0.00 0.00 2.66
8 9 4.710375 TCTTTCTGGACGCCTCTTATACTT 59.290 41.667 0.00 0.00 0.00 2.24
9 10 4.279145 TCTTTCTGGACGCCTCTTATACT 58.721 43.478 0.00 0.00 0.00 2.12
10 11 4.650754 TCTTTCTGGACGCCTCTTATAC 57.349 45.455 0.00 0.00 0.00 1.47
11 12 4.464951 TGTTCTTTCTGGACGCCTCTTATA 59.535 41.667 0.00 0.00 0.00 0.98
12 13 3.260884 TGTTCTTTCTGGACGCCTCTTAT 59.739 43.478 0.00 0.00 0.00 1.73
13 14 2.631062 TGTTCTTTCTGGACGCCTCTTA 59.369 45.455 0.00 0.00 0.00 2.10
14 15 1.416401 TGTTCTTTCTGGACGCCTCTT 59.584 47.619 0.00 0.00 0.00 2.85
15 16 1.048601 TGTTCTTTCTGGACGCCTCT 58.951 50.000 0.00 0.00 0.00 3.69
16 17 1.149148 GTGTTCTTTCTGGACGCCTC 58.851 55.000 0.00 0.00 0.00 4.70
17 18 0.468226 TGTGTTCTTTCTGGACGCCT 59.532 50.000 0.00 0.00 0.00 5.52
18 19 0.586802 GTGTGTTCTTTCTGGACGCC 59.413 55.000 0.00 0.00 0.00 5.68
19 20 1.261619 CAGTGTGTTCTTTCTGGACGC 59.738 52.381 0.00 0.00 0.00 5.19
20 21 2.821546 TCAGTGTGTTCTTTCTGGACG 58.178 47.619 0.00 0.00 0.00 4.79
21 22 5.352569 CCATATCAGTGTGTTCTTTCTGGAC 59.647 44.000 0.00 0.00 0.00 4.02
22 23 5.013079 ACCATATCAGTGTGTTCTTTCTGGA 59.987 40.000 0.00 0.00 0.00 3.86
23 24 5.248640 ACCATATCAGTGTGTTCTTTCTGG 58.751 41.667 0.00 0.00 0.00 3.86
24 25 6.605849 CAACCATATCAGTGTGTTCTTTCTG 58.394 40.000 0.00 0.00 0.00 3.02
25 26 5.182001 GCAACCATATCAGTGTGTTCTTTCT 59.818 40.000 0.00 0.00 0.00 2.52
26 27 5.048782 TGCAACCATATCAGTGTGTTCTTTC 60.049 40.000 0.00 0.00 0.00 2.62
27 28 4.826733 TGCAACCATATCAGTGTGTTCTTT 59.173 37.500 0.00 0.00 0.00 2.52
28 29 4.397420 TGCAACCATATCAGTGTGTTCTT 58.603 39.130 0.00 0.00 0.00 2.52
29 30 4.019792 TGCAACCATATCAGTGTGTTCT 57.980 40.909 0.00 0.00 0.00 3.01
30 31 4.970662 ATGCAACCATATCAGTGTGTTC 57.029 40.909 0.00 0.00 0.00 3.18
60 61 6.708285 TCCTTCCTCTAGCTTTAATCGTTTT 58.292 36.000 0.00 0.00 0.00 2.43
64 65 5.523438 ACTCCTTCCTCTAGCTTTAATCG 57.477 43.478 0.00 0.00 0.00 3.34
75 76 5.090139 TCTTGAATCTCAACTCCTTCCTCT 58.910 41.667 0.00 0.00 32.21 3.69
114 115 7.186804 CCGAGGTAATCAACAACATGAATAAC 58.813 38.462 0.00 0.00 32.06 1.89
145 146 4.977741 TCGTCAACAATCGTTAAACCTC 57.022 40.909 0.00 0.00 32.75 3.85
164 1006 3.976169 TGCCCTTTTCTGTTGAAAATCG 58.024 40.909 4.71 0.75 46.90 3.34
192 1034 7.767250 ATAAATCTGATCTCTATCGTCACCA 57.233 36.000 0.00 0.00 34.60 4.17
202 1044 4.021016 GGGGTGCGTATAAATCTGATCTCT 60.021 45.833 0.00 0.00 0.00 3.10
209 1051 3.637911 TGTTGGGGTGCGTATAAATCT 57.362 42.857 0.00 0.00 0.00 2.40
213 1055 3.566322 GCATTATGTTGGGGTGCGTATAA 59.434 43.478 0.00 0.00 0.00 0.98
217 1059 0.610509 TGCATTATGTTGGGGTGCGT 60.611 50.000 0.00 0.00 38.58 5.24
218 1060 0.746063 ATGCATTATGTTGGGGTGCG 59.254 50.000 0.00 0.00 38.58 5.34
219 1061 1.202557 CCATGCATTATGTTGGGGTGC 60.203 52.381 0.00 0.00 34.87 5.01
220 1062 2.101249 GTCCATGCATTATGTTGGGGTG 59.899 50.000 13.55 0.00 34.87 4.61
221 1063 2.387757 GTCCATGCATTATGTTGGGGT 58.612 47.619 13.55 0.00 34.87 4.95
241 1083 3.021695 TCCTCCTAACCACATACACTCG 58.978 50.000 0.00 0.00 0.00 4.18
245 1087 2.104967 CCGTCCTCCTAACCACATACA 58.895 52.381 0.00 0.00 0.00 2.29
246 1088 2.100418 GACCGTCCTCCTAACCACATAC 59.900 54.545 0.00 0.00 0.00 2.39
248 1090 1.192428 GACCGTCCTCCTAACCACAT 58.808 55.000 0.00 0.00 0.00 3.21
256 1098 2.362632 CCTTCGGACCGTCCTCCT 60.363 66.667 14.79 0.00 33.30 3.69
258 1100 4.493747 CGCCTTCGGACCGTCCTC 62.494 72.222 14.79 1.55 33.30 3.71
297 1139 1.350684 TGTCTGGCATGGACTAAAGCA 59.649 47.619 8.17 0.00 35.04 3.91
308 1150 3.402681 CCCCTCCGTGTCTGGCAT 61.403 66.667 0.00 0.00 0.00 4.40
318 1160 2.443394 TAGATGCAAGCCCCCTCCG 61.443 63.158 0.00 0.00 0.00 4.63
349 1191 7.227873 TGGTTGAAGAAACTACAATACATGGA 58.772 34.615 0.00 0.00 38.92 3.41
373 1215 5.180117 ACAAGACACCTTCATCGATTTCTTG 59.820 40.000 0.00 7.95 42.80 3.02
374 1216 5.308825 ACAAGACACCTTCATCGATTTCTT 58.691 37.500 0.00 0.00 0.00 2.52
376 1218 4.690748 TGACAAGACACCTTCATCGATTTC 59.309 41.667 0.00 0.00 0.00 2.17
389 1231 3.859411 TGTGGGTTTTTGACAAGACAC 57.141 42.857 6.24 3.48 0.00 3.67
390 1232 4.019858 TCATGTGGGTTTTTGACAAGACA 58.980 39.130 0.00 0.00 0.00 3.41
396 1238 5.476945 AGGAACTATCATGTGGGTTTTTGAC 59.523 40.000 0.00 0.00 36.02 3.18
416 1258 4.809426 GTCAAAGTCTTTCTCGTGAAGGAA 59.191 41.667 12.79 0.00 39.46 3.36
423 1265 4.299978 GTGCTAGTCAAAGTCTTTCTCGT 58.700 43.478 0.00 0.00 0.00 4.18
425 1267 4.547532 TCGTGCTAGTCAAAGTCTTTCTC 58.452 43.478 0.00 0.00 0.00 2.87
453 1295 0.591741 GTCGTATGAAGGACGCTCGG 60.592 60.000 0.00 0.00 40.14 4.63
467 1309 1.099689 TCACAGATCATGGCGTCGTA 58.900 50.000 0.00 0.00 0.00 3.43
481 1323 6.563422 TCCTCTTTGAAAACATTGTTCACAG 58.437 36.000 1.83 0.86 34.78 3.66
534 1382 0.754472 TCGATCATCATGCTGCTCCA 59.246 50.000 0.00 0.00 0.00 3.86
541 1389 2.061773 CTAACCGGTCGATCATCATGC 58.938 52.381 8.04 0.00 0.00 4.06
547 1395 2.025898 TGTATGCTAACCGGTCGATCA 58.974 47.619 8.04 4.22 0.00 2.92
548 1396 2.391879 GTGTATGCTAACCGGTCGATC 58.608 52.381 8.04 0.00 0.00 3.69
556 1404 5.277857 ACTGTATCAGGTGTATGCTAACC 57.722 43.478 1.90 0.00 35.51 2.85
583 1431 2.171635 GGCCTGACCGTGATGAAAC 58.828 57.895 0.00 0.00 0.00 2.78
584 1432 4.713946 GGCCTGACCGTGATGAAA 57.286 55.556 0.00 0.00 0.00 2.69
627 1482 1.354368 GACCCCCAAATTCTCAGGACA 59.646 52.381 0.00 0.00 0.00 4.02
628 1483 1.636003 AGACCCCCAAATTCTCAGGAC 59.364 52.381 0.00 0.00 0.00 3.85
630 1485 2.041620 TGAAGACCCCCAAATTCTCAGG 59.958 50.000 0.00 0.00 0.00 3.86
631 1486 3.439857 TGAAGACCCCCAAATTCTCAG 57.560 47.619 0.00 0.00 0.00 3.35
672 1546 4.488879 GAATTGCCCATTGTGTCTTCTTC 58.511 43.478 0.00 0.00 0.00 2.87
710 1584 1.398022 GAATGACGTGTGCGCATTGC 61.398 55.000 15.91 6.02 41.29 3.56
712 1586 1.501741 GGAATGACGTGTGCGCATT 59.498 52.632 15.91 0.25 42.64 3.56
713 1587 2.739704 CGGAATGACGTGTGCGCAT 61.740 57.895 15.91 0.00 42.83 4.73
817 1711 2.443952 ATCTGGGCCGTCGGATCA 60.444 61.111 17.49 11.01 0.00 2.92
855 1750 3.381590 GGGGAAGAATGTGGTTTATGAGC 59.618 47.826 0.00 0.00 0.00 4.26
1354 2255 3.561143 AGTCACTCTCGCATATCCTTCT 58.439 45.455 0.00 0.00 0.00 2.85
1379 2280 2.354539 CTGCAAAAACCACCGCCG 60.355 61.111 0.00 0.00 0.00 6.46
1445 2346 2.359107 TTGCCCTTCAGCAGCTCG 60.359 61.111 0.00 0.00 45.13 5.03
1514 2415 1.767759 ACATTGCATAGCTGAACCCC 58.232 50.000 0.00 0.00 0.00 4.95
1539 2440 1.906105 AATCTAAACGGGGGCTCGCA 61.906 55.000 0.00 0.00 0.00 5.10
1541 2442 1.296727 GAAATCTAAACGGGGGCTCG 58.703 55.000 0.00 0.00 0.00 5.03
1544 2445 1.721664 GCCGAAATCTAAACGGGGGC 61.722 60.000 0.00 0.00 45.66 5.80
1545 2446 0.107361 AGCCGAAATCTAAACGGGGG 60.107 55.000 0.00 0.00 45.66 5.40
1549 2450 5.041287 TCACTGATAGCCGAAATCTAAACG 58.959 41.667 0.00 0.00 0.00 3.60
1553 2454 5.536538 ACAGATCACTGATAGCCGAAATCTA 59.463 40.000 0.00 0.00 46.03 1.98
1561 2462 4.244066 CAGCATACAGATCACTGATAGCC 58.756 47.826 0.00 0.00 46.03 3.93
1625 2530 4.249638 TGGATTTTGTTATCCTGGGAGG 57.750 45.455 0.00 0.00 43.75 4.30
1639 2544 1.009829 GAGCAGCGTCGATGGATTTT 58.990 50.000 13.06 0.00 0.00 1.82
1690 2595 0.240945 CAACATGGCCAAAGTCCGTC 59.759 55.000 10.96 0.00 0.00 4.79
1702 2607 3.318839 ACACAAACAGGATGACAACATGG 59.681 43.478 2.39 0.00 39.69 3.66
1750 2655 1.236616 CGCAATCCTCCAGCACACAA 61.237 55.000 0.00 0.00 0.00 3.33
1752 2657 2.401766 CCGCAATCCTCCAGCACAC 61.402 63.158 0.00 0.00 0.00 3.82
1753 2658 2.046023 CCGCAATCCTCCAGCACA 60.046 61.111 0.00 0.00 0.00 4.57
1771 2676 4.945543 TCCTGTGTCATTCCAGATGAAATG 59.054 41.667 0.00 0.00 36.33 2.32
1789 2694 2.541233 ATACACTCTCCTGCTCCTGT 57.459 50.000 0.00 0.00 0.00 4.00
1913 2818 5.125900 CCATGATATGCAACACTTCCAAAGA 59.874 40.000 0.00 0.00 0.00 2.52
1978 2883 6.905544 TTGTTCAACACGTACATGTTAAGA 57.094 33.333 7.04 0.00 40.89 2.10
2064 2969 3.562141 CGGGTGCCAAAATATGACGATTA 59.438 43.478 0.00 0.00 0.00 1.75
2069 2974 3.181494 GGTAACGGGTGCCAAAATATGAC 60.181 47.826 0.00 0.00 0.00 3.06
2085 2990 2.848691 TGGTAACCCAACAAGGTAACG 58.151 47.619 0.00 0.00 40.05 3.18
2226 3132 2.143925 GTGGAAAAGGAGTCGGAACAG 58.856 52.381 0.00 0.00 0.00 3.16
2313 3219 7.588512 AGTTCTTTAGAGCATGTTCACAAATC 58.411 34.615 12.41 5.77 0.00 2.17
2524 3430 3.947910 AGGCAAGGTGATGTGAATTTG 57.052 42.857 0.00 0.00 0.00 2.32
2580 3487 7.041372 TGTTGATTCTTAGCTACACCAAAGAAC 60.041 37.037 8.83 5.22 39.89 3.01
2754 3661 5.618863 GCTCACTCTCCAGATATACATCACG 60.619 48.000 0.00 0.00 33.21 4.35
3061 4275 3.953766 ACTATATCAAGACGACAGCACG 58.046 45.455 0.00 0.00 39.31 5.34
3549 4767 1.978580 AGGTGGTACAAGAAGTCCTGG 59.021 52.381 0.00 0.00 44.16 4.45
3705 4923 8.883731 CACAAATAGTAACCTCAGTGAATAAGG 58.116 37.037 0.00 0.00 36.21 2.69
3740 4991 4.576053 GCCAAGACAGATTGCATATACACA 59.424 41.667 0.00 0.00 0.00 3.72
3775 5026 5.826601 TCACAAATACTCACAAGCAACAA 57.173 34.783 0.00 0.00 0.00 2.83
3891 5144 7.118496 AGTTTACCAAACATGACCAAATTGA 57.882 32.000 0.00 0.00 43.79 2.57
3908 5161 6.383415 CAGTCAGAAGTCAGTCTAGTTTACC 58.617 44.000 0.00 0.00 0.00 2.85
3917 5170 4.513198 ACTAAGCAGTCAGAAGTCAGTC 57.487 45.455 0.00 0.00 0.00 3.51
4333 5594 5.582689 ACTGTTTAATTCAATGCTAGCCC 57.417 39.130 13.29 0.00 0.00 5.19
4368 5629 5.699097 AAACTGCTTTAAAATACTCGGCA 57.301 34.783 0.00 0.00 0.00 5.69
4493 5756 5.132648 TGCAGGGGTGAATTGAGAAGTATAT 59.867 40.000 0.00 0.00 0.00 0.86
4785 6050 8.477419 ACAAGACCTTAAGGAATTTTGATTGA 57.523 30.769 28.52 0.00 38.94 2.57
4811 6076 9.705290 ACTCGCCAAAAATCACTAAATATTTTT 57.295 25.926 5.91 0.00 42.88 1.94
4861 6126 7.776969 AGCATGGACAAGTCAACTCAATATTAT 59.223 33.333 2.29 0.00 0.00 1.28
5208 6475 1.603802 CATTTCCGTGTGCTCACAAGT 59.396 47.619 18.23 1.12 43.77 3.16
5516 6784 5.419155 TCCGCCACCAATTTCATATGTTAAA 59.581 36.000 1.90 0.00 0.00 1.52
5670 6983 2.095364 CACTGAGGCATTGTTCAAGCTC 60.095 50.000 0.00 0.00 0.00 4.09
5758 7071 4.248058 CTGAGATATTGCATGCGGACATA 58.752 43.478 14.09 7.14 33.67 2.29
5779 7092 5.913137 TTGAAAATGACACAACAGGAACT 57.087 34.783 0.00 0.00 43.88 3.01
5904 7220 3.807622 TCAAAACCTACAGAGCAACTTCG 59.192 43.478 0.00 0.00 0.00 3.79
6112 7601 1.814394 CAGAGTGGCATTAAAGCTGCA 59.186 47.619 1.02 0.00 41.47 4.41
6368 7857 4.883006 GCTGCCAGAGTTAGTACTAGTAGT 59.117 45.833 14.57 14.57 33.84 2.73
6520 8009 1.619654 TTGCAACTTGATGGACAGGG 58.380 50.000 0.00 0.00 0.00 4.45
6931 8420 6.452242 TCGTGTAATTTCTGCTGAGAAGTAA 58.548 36.000 0.00 0.00 39.44 2.24
7089 8578 6.247229 TGCATAAGAATAGGAAGCAGGTTA 57.753 37.500 0.00 0.00 0.00 2.85
7172 8661 3.287867 TTGGGGCAAATTTTCTGCAAA 57.712 38.095 3.19 0.00 41.78 3.68
7227 8718 3.569701 CACCACCTGCAAGAGTAAAATGT 59.430 43.478 0.00 0.00 34.07 2.71
7476 8967 2.302733 TGCCACAGCATCTTTGTCTCTA 59.697 45.455 0.00 0.00 46.52 2.43
7491 8982 0.178995 TTTGGATGAGCTGTGCCACA 60.179 50.000 0.00 0.00 0.00 4.17
7768 9259 1.004595 GGCGGTCGACCTGATTTTAC 58.995 55.000 30.92 10.93 0.00 2.01
7902 9393 2.591923 TCCTGAGCTGATAGCAGTAGG 58.408 52.381 10.15 14.28 45.56 3.18
7958 9449 2.099756 GCCATGGCATAACCTTGAAGTC 59.900 50.000 32.08 0.00 44.61 3.01
8266 9757 3.508012 AGTAGTGACAGAGCAAGATCGTT 59.492 43.478 0.00 0.00 0.00 3.85
8277 9768 1.360820 CTCGCTCGAGTAGTGACAGA 58.639 55.000 15.13 0.88 39.84 3.41
8280 9771 0.653636 CTCCTCGCTCGAGTAGTGAC 59.346 60.000 15.13 0.00 39.84 3.67
8375 9866 2.161855 TGCAATGGCTCCTACAAGTTG 58.838 47.619 0.00 0.00 41.91 3.16
8438 9930 4.929808 AGTCCACAAATGAACACGACTATC 59.070 41.667 0.00 0.00 0.00 2.08
8453 9945 2.025898 TGACGTGACACTAGTCCACAA 58.974 47.619 19.26 6.74 44.33 3.33
8460 9952 4.519147 CATACGAGATGACGTGACACTAG 58.481 47.826 3.68 0.00 46.02 2.57
8469 9961 0.955178 AGAGGCCATACGAGATGACG 59.045 55.000 5.01 0.00 39.31 4.35
8484 9976 3.057736 CAGTCAAACATCCAGCAAAGAGG 60.058 47.826 0.00 0.00 0.00 3.69
8520 10012 3.942829 TGTCATCGGCTCTGAGAATTTT 58.057 40.909 9.28 0.00 0.00 1.82
8559 10051 2.358898 CACATGTTATTACAGCTGGGGC 59.641 50.000 19.93 2.52 37.77 5.80
8588 10080 1.894756 TAAACGCACAGTGCCCCAC 60.895 57.895 20.16 0.00 41.12 4.61
8600 10094 3.065786 GGGGGCTAACTAATTGTAAACGC 59.934 47.826 0.00 0.00 0.00 4.84
8630 10124 2.819608 TCGAGAGGGCCAAATTTTCTTG 59.180 45.455 6.18 2.43 0.00 3.02
8727 10221 9.104965 CATAAGGAGATAACAAATTCGTTACCA 57.895 33.333 0.00 0.00 34.31 3.25
8807 10480 5.994054 TCATCAACTCTTTTTCTGAGTGAGG 59.006 40.000 0.00 0.00 43.16 3.86
8915 10591 6.756299 AAGTTTGAACATTTTTGCCACATT 57.244 29.167 0.00 0.00 0.00 2.71
8959 10635 5.004448 TGACGCAAAATAATACCAGGTTCA 58.996 37.500 0.00 0.00 0.00 3.18
8973 10649 8.710835 TCTAGTATTATGTTGATGACGCAAAA 57.289 30.769 0.00 0.00 0.00 2.44
8982 10658 7.606839 TCCTCGTCGATCTAGTATTATGTTGAT 59.393 37.037 0.00 0.00 0.00 2.57
8993 10669 4.895961 TCATGTATCCTCGTCGATCTAGT 58.104 43.478 0.00 0.00 0.00 2.57
9012 10688 4.336433 CACAAAGTCACAAACCACTCTCAT 59.664 41.667 0.00 0.00 0.00 2.90
9013 10689 3.689161 CACAAAGTCACAAACCACTCTCA 59.311 43.478 0.00 0.00 0.00 3.27
9014 10690 3.938963 TCACAAAGTCACAAACCACTCTC 59.061 43.478 0.00 0.00 0.00 3.20
9015 10691 3.950397 TCACAAAGTCACAAACCACTCT 58.050 40.909 0.00 0.00 0.00 3.24
9037 10714 2.106857 TCCGTGGGGTCATAAAACTTGT 59.893 45.455 0.00 0.00 33.83 3.16
9047 10724 1.305129 TATCCGTTCCGTGGGGTCA 60.305 57.895 0.00 0.00 33.83 4.02
9177 10872 4.448537 TTCCACCAATAAATTGCCTTCG 57.551 40.909 0.00 0.00 36.48 3.79
9235 10931 4.353777 ACTTGGACTAGATGCTACCTTCA 58.646 43.478 0.00 0.00 0.00 3.02
9247 10943 2.257207 TGGTTCCTGGACTTGGACTAG 58.743 52.381 0.00 0.00 32.65 2.57
9256 10952 2.640316 ACTTGAGTTGGTTCCTGGAC 57.360 50.000 0.00 0.00 0.00 4.02
9293 10989 5.212745 TGACTTTTTGGGGTAAAATCCACT 58.787 37.500 0.00 0.00 38.03 4.00


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

AutoCloner maintained by Alex Coulton.