Multiple sequence alignment - TraesCS6D01G085200

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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 TraesCS6D01G085200 chr6D 100.000 5959 0 0 1 5959 50740141 50746099 0.000000e+00 11005.0
1 TraesCS6D01G085200 chr6A 89.040 5529 301 136 264 5655 64321471 64316111 0.000000e+00 6571.0
2 TraesCS6D01G085200 chr6A 97.927 193 4 0 5767 5959 64316050 64315858 9.570000e-88 335.0
3 TraesCS6D01G085200 chr6B 88.345 2205 147 54 25 2168 120674116 120671961 0.000000e+00 2547.0
4 TraesCS6D01G085200 chr6B 90.160 1809 97 44 2748 4491 120671479 120669687 0.000000e+00 2279.0
5 TraesCS6D01G085200 chr6B 90.244 1517 80 28 4483 5959 120668233 120666745 0.000000e+00 1919.0
6 TraesCS6D01G085200 chr6B 89.537 497 34 9 2218 2714 120671963 120671485 1.100000e-171 614.0
7 TraesCS6D01G085200 chr6B 100.000 29 0 0 1 29 12602574 12602602 3.000000e-03 54.7
8 TraesCS6D01G085200 chr2B 80.429 746 85 39 4291 5033 181699723 181700410 4.120000e-141 512.0
9 TraesCS6D01G085200 chr2B 87.200 375 39 5 5029 5395 181700444 181700817 9.240000e-113 418.0
10 TraesCS6D01G085200 chr1B 88.298 376 34 6 5029 5395 217555527 217555901 5.480000e-120 442.0
11 TraesCS6D01G085200 chr1B 84.688 320 25 13 4723 5033 217555185 217555489 1.260000e-76 298.0
12 TraesCS6D01G085200 chr3B 93.860 114 5 2 2121 2234 731134817 731134706 2.860000e-38 171.0
13 TraesCS6D01G085200 chr3B 100.000 34 0 0 99 132 755238355 755238388 4.990000e-06 63.9
14 TraesCS6D01G085200 chr7D 93.458 107 7 0 2127 2233 101395203 101395309 6.180000e-35 159.0
15 TraesCS6D01G085200 chr5B 92.661 109 5 1 2125 2230 615005129 615005021 2.880000e-33 154.0
16 TraesCS6D01G085200 chr5B 90.826 109 5 1 2127 2230 477078441 477078549 2.240000e-29 141.0
17 TraesCS6D01G085200 chr3D 92.453 106 4 1 2125 2230 349635469 349635570 1.340000e-31 148.0
18 TraesCS6D01G085200 chr2A 92.381 105 7 1 2127 2230 728548775 728548671 1.340000e-31 148.0
19 TraesCS6D01G085200 chr5D 89.655 116 10 2 2127 2241 481420988 481421102 4.810000e-31 147.0
20 TraesCS6D01G085200 chr5D 91.429 105 6 1 2127 2231 109811418 109811317 2.240000e-29 141.0
21 TraesCS6D01G085200 chr2D 89.286 84 8 1 2417 2500 465200775 465200693 2.940000e-18 104.0
22 TraesCS6D01G085200 chr4A 85.714 70 10 0 433 502 534538035 534537966 2.300000e-09 75.0
23 TraesCS6D01G085200 chr1D 85.484 62 5 3 72 132 393731930 393731988 1.790000e-05 62.1
24 TraesCS6D01G085200 chr1A 89.796 49 2 2 84 132 492131032 492130987 6.450000e-05 60.2
25 TraesCS6D01G085200 chr4D 100.000 29 0 0 1 29 75775442 75775470 3.000000e-03 54.7
26 TraesCS6D01G085200 chr7B 100.000 28 0 0 1 28 658454431 658454404 1.100000e-02 52.8
27 TraesCS6D01G085200 chr5A 100.000 28 0 0 1 28 422314975 422315002 1.100000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G085200 chr6D 50740141 50746099 5958 False 11005.00 11005 100.0000 1 5959 1 chr6D.!!$F1 5958
1 TraesCS6D01G085200 chr6A 64315858 64321471 5613 True 3453.00 6571 93.4835 264 5959 2 chr6A.!!$R1 5695
2 TraesCS6D01G085200 chr6B 120666745 120674116 7371 True 1839.75 2547 89.5715 25 5959 4 chr6B.!!$R1 5934
3 TraesCS6D01G085200 chr2B 181699723 181700817 1094 False 465.00 512 83.8145 4291 5395 2 chr2B.!!$F1 1104
4 TraesCS6D01G085200 chr1B 217555185 217555901 716 False 370.00 442 86.4930 4723 5395 2 chr1B.!!$F1 672

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
336 341 0.041312 CCTATAAACATGCGCACGCC 60.041 55.0 14.9 0.0 41.09 5.68 F
1458 1497 0.107410 TCAAAACACACTGTCGGCCT 60.107 50.0 0.0 0.0 0.00 5.19 F
1797 1846 0.463620 TCATCCATCATCGACGGCAA 59.536 50.0 0.0 0.0 0.00 4.52 F
1798 1847 0.583438 CATCCATCATCGACGGCAAC 59.417 55.0 0.0 0.0 0.00 4.17 F
2876 2992 0.871722 CGACAGTGAATTGCCCGAAA 59.128 50.0 0.0 0.0 0.00 3.46 F
3806 3976 0.107410 TGAGGCGTTGGTTTGTGACT 60.107 50.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1842 0.031178 GGCATGGATCATTCGTTGCC 59.969 55.0 0.00 0.0 40.89 4.52 R
2876 2992 0.398381 ACACAAGTGCCCCCAAACAT 60.398 50.0 0.00 0.0 0.00 2.71 R
3571 3716 0.179000 CAGCCTGCGAATCCTAGGTT 59.821 55.0 9.08 2.3 34.06 3.50 R
3721 3866 0.463620 TTGGTTGAAGGGTGCAAAGC 59.536 50.0 0.00 0.0 0.00 3.51 R
4618 6274 0.251519 CTTGCTTTGCTCCCCCTTCT 60.252 55.0 0.00 0.0 0.00 2.85 R
5752 7558 0.109532 TTCCATGGTTTGCACTCCGA 59.890 50.0 12.58 0.0 0.00 4.55 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.636231 TGGGTCGCCCTGTTGGAG 61.636 66.667 14.76 0.00 45.70 3.86
18 19 3.637273 GGGTCGCCCTGTTGGAGT 61.637 66.667 7.58 0.00 41.34 3.85
19 20 2.430367 GGTCGCCCTGTTGGAGTT 59.570 61.111 0.00 0.00 35.07 3.01
20 21 1.966451 GGTCGCCCTGTTGGAGTTG 60.966 63.158 0.00 0.00 35.07 3.16
21 22 2.281484 TCGCCCTGTTGGAGTTGC 60.281 61.111 0.00 0.00 35.07 4.17
22 23 2.281761 CGCCCTGTTGGAGTTGCT 60.282 61.111 0.00 0.00 35.39 3.91
23 24 2.328099 CGCCCTGTTGGAGTTGCTC 61.328 63.158 0.00 0.00 35.39 4.26
28 29 3.012518 CCCTGTTGGAGTTGCTCTTATG 58.987 50.000 0.00 0.00 35.39 1.90
36 37 4.721776 TGGAGTTGCTCTTATGGACCTAAT 59.278 41.667 0.00 0.00 0.00 1.73
82 83 6.552629 TCGTACTGCTTGAATACTTCTGTAG 58.447 40.000 0.00 0.00 31.51 2.74
84 85 6.807230 CGTACTGCTTGAATACTTCTGTAGTT 59.193 38.462 0.00 0.00 38.33 2.24
85 86 7.966753 CGTACTGCTTGAATACTTCTGTAGTTA 59.033 37.037 0.00 0.00 38.33 2.24
86 87 9.074443 GTACTGCTTGAATACTTCTGTAGTTAC 57.926 37.037 0.00 0.00 38.33 2.50
87 88 7.897864 ACTGCTTGAATACTTCTGTAGTTACT 58.102 34.615 0.00 0.00 38.33 2.24
88 89 9.021807 ACTGCTTGAATACTTCTGTAGTTACTA 57.978 33.333 0.00 0.00 38.33 1.82
89 90 9.291664 CTGCTTGAATACTTCTGTAGTTACTAC 57.708 37.037 14.99 14.99 38.33 2.73
90 91 8.248945 TGCTTGAATACTTCTGTAGTTACTACC 58.751 37.037 18.49 3.10 38.33 3.18
95 96 9.401058 GAATACTTCTGTAGTTACTACCCACTA 57.599 37.037 18.49 0.26 38.33 2.74
96 97 9.933240 AATACTTCTGTAGTTACTACCCACTAT 57.067 33.333 18.49 5.79 38.33 2.12
138 139 9.750125 ATGTTCTAACCTTTTTCTGAATTTGAC 57.250 29.630 0.00 0.00 0.00 3.18
145 146 9.594478 AACCTTTTTCTGAATTTGACGTATTTT 57.406 25.926 0.00 0.00 0.00 1.82
154 155 7.870826 TGAATTTGACGTATTTTGACAGATGT 58.129 30.769 0.00 0.00 0.00 3.06
174 175 3.862845 TGTCGACATACATGCACATACAC 59.137 43.478 15.76 0.00 0.00 2.90
180 181 8.952278 TCGACATACATGCACATACACTATATA 58.048 33.333 0.00 0.00 0.00 0.86
220 221 5.643379 TTTGAATTGGTTAGACAGATGCC 57.357 39.130 0.00 0.00 0.00 4.40
221 222 3.620488 TGAATTGGTTAGACAGATGCCC 58.380 45.455 0.00 0.00 0.00 5.36
225 228 1.915489 TGGTTAGACAGATGCCCACAT 59.085 47.619 0.00 0.00 39.98 3.21
227 230 3.118408 TGGTTAGACAGATGCCCACATAC 60.118 47.826 0.00 0.00 36.35 2.39
231 234 2.009774 GACAGATGCCCACATACACAC 58.990 52.381 0.00 0.00 36.35 3.82
240 243 6.987403 TGCCCACATACACACTATATAAGA 57.013 37.500 0.00 0.00 0.00 2.10
241 244 7.553504 TGCCCACATACACACTATATAAGAT 57.446 36.000 0.00 0.00 0.00 2.40
242 245 7.386059 TGCCCACATACACACTATATAAGATG 58.614 38.462 0.00 0.00 0.00 2.90
243 246 7.016170 TGCCCACATACACACTATATAAGATGT 59.984 37.037 0.00 0.00 34.11 3.06
244 247 7.878127 GCCCACATACACACTATATAAGATGTT 59.122 37.037 0.00 0.00 32.61 2.71
245 248 9.424319 CCCACATACACACTATATAAGATGTTC 57.576 37.037 0.00 0.00 32.61 3.18
325 330 6.479001 ACGCACATACACTCATTCCTATAAAC 59.521 38.462 0.00 0.00 0.00 2.01
326 331 6.478673 CGCACATACACTCATTCCTATAAACA 59.521 38.462 0.00 0.00 0.00 2.83
328 333 8.285394 GCACATACACTCATTCCTATAAACATG 58.715 37.037 0.00 0.00 0.00 3.21
336 341 0.041312 CCTATAAACATGCGCACGCC 60.041 55.000 14.90 0.00 41.09 5.68
339 344 1.992233 ATAAACATGCGCACGCCCAG 61.992 55.000 14.90 0.73 41.09 4.45
347 352 1.154035 CGCACGCCCAGGAAAATTC 60.154 57.895 0.00 0.00 0.00 2.17
350 355 1.669795 GCACGCCCAGGAAAATTCAAG 60.670 52.381 0.00 0.00 0.00 3.02
354 359 1.344114 GCCCAGGAAAATTCAAGCACA 59.656 47.619 0.00 0.00 0.00 4.57
355 360 2.027837 GCCCAGGAAAATTCAAGCACAT 60.028 45.455 0.00 0.00 0.00 3.21
390 395 8.494433 TCTAATACTTGAACTTTGATGGCCTAT 58.506 33.333 3.32 0.00 0.00 2.57
400 411 4.314522 TTGATGGCCTATCACAAGGAAA 57.685 40.909 14.94 0.16 45.22 3.13
411 422 7.338449 GCCTATCACAAGGAAACTAACCATTTA 59.662 37.037 0.00 0.00 42.68 1.40
430 451 7.394359 ACCATTTAAGTTATGCTCAGTTCACAT 59.606 33.333 0.00 0.00 0.00 3.21
462 483 4.576463 GTGTTTGTTCACTCCATTCAGTCT 59.424 41.667 0.00 0.00 35.68 3.24
470 491 8.977412 TGTTCACTCCATTCAGTCTGTATATAA 58.023 33.333 0.00 0.00 0.00 0.98
570 594 7.944729 AACTAACTATGAAAACAGCCATGAT 57.055 32.000 0.00 0.00 0.00 2.45
571 595 9.461312 AAACTAACTATGAAAACAGCCATGATA 57.539 29.630 0.00 0.00 0.00 2.15
696 720 3.130693 ACCAACGAACTCTACCTAGCATC 59.869 47.826 0.00 0.00 0.00 3.91
810 842 0.800683 TGTCGATCCGTGTGAATCGC 60.801 55.000 0.00 0.00 36.58 4.58
857 889 2.154462 CAGGAAACTAACTGGTGGCAG 58.846 52.381 0.00 0.00 40.21 4.85
858 890 0.881796 GGAAACTAACTGGTGGCAGC 59.118 55.000 10.30 10.30 0.00 5.25
878 910 4.114997 CCGGCGGTGGTTGATTGC 62.115 66.667 19.97 0.00 0.00 3.56
896 932 4.269523 TCAGGTGGTGGTGCAGCC 62.270 66.667 14.36 5.89 37.90 4.85
960 996 0.386100 CTAGCCGGTGTGATCGATCG 60.386 60.000 20.03 9.36 0.00 3.69
1359 1398 0.324614 TGTGGTCCGACATGCTCAAT 59.675 50.000 0.00 0.00 0.00 2.57
1407 1446 2.554806 TCATGGAAGTACGTAGCGTG 57.445 50.000 0.00 0.00 41.39 5.34
1424 1463 1.668419 GTGGCGTGCTCCATTAGATT 58.332 50.000 0.00 0.00 38.57 2.40
1425 1464 2.801699 CGTGGCGTGCTCCATTAGATTA 60.802 50.000 0.00 0.00 38.57 1.75
1426 1465 3.403038 GTGGCGTGCTCCATTAGATTAT 58.597 45.455 0.00 0.00 38.57 1.28
1427 1466 3.815401 GTGGCGTGCTCCATTAGATTATT 59.185 43.478 0.00 0.00 38.57 1.40
1429 1468 4.515191 TGGCGTGCTCCATTAGATTATTTC 59.485 41.667 0.00 0.00 0.00 2.17
1430 1469 4.515191 GGCGTGCTCCATTAGATTATTTCA 59.485 41.667 0.00 0.00 0.00 2.69
1431 1470 5.182001 GGCGTGCTCCATTAGATTATTTCAT 59.818 40.000 0.00 0.00 0.00 2.57
1432 1471 6.310197 GCGTGCTCCATTAGATTATTTCATC 58.690 40.000 0.00 0.00 0.00 2.92
1433 1472 6.621596 GCGTGCTCCATTAGATTATTTCATCC 60.622 42.308 0.00 0.00 0.00 3.51
1434 1473 6.401474 CGTGCTCCATTAGATTATTTCATCCG 60.401 42.308 0.00 0.00 0.00 4.18
1435 1474 6.428159 GTGCTCCATTAGATTATTTCATCCGT 59.572 38.462 0.00 0.00 0.00 4.69
1437 1476 6.183360 GCTCCATTAGATTATTTCATCCGTCG 60.183 42.308 0.00 0.00 0.00 5.12
1438 1477 6.988522 TCCATTAGATTATTTCATCCGTCGA 58.011 36.000 0.00 0.00 0.00 4.20
1441 1480 7.545615 CCATTAGATTATTTCATCCGTCGATCA 59.454 37.037 0.00 0.00 0.00 2.92
1442 1481 8.925700 CATTAGATTATTTCATCCGTCGATCAA 58.074 33.333 0.00 0.00 0.00 2.57
1443 1482 8.880878 TTAGATTATTTCATCCGTCGATCAAA 57.119 30.769 0.00 0.00 0.00 2.69
1444 1483 7.786178 AGATTATTTCATCCGTCGATCAAAA 57.214 32.000 0.00 0.00 0.00 2.44
1446 1485 6.729391 TTATTTCATCCGTCGATCAAAACA 57.271 33.333 0.00 0.00 0.00 2.83
1447 1486 4.398549 TTTCATCCGTCGATCAAAACAC 57.601 40.909 0.00 0.00 0.00 3.32
1448 1487 3.033368 TCATCCGTCGATCAAAACACA 57.967 42.857 0.00 0.00 0.00 3.72
1449 1488 2.734606 TCATCCGTCGATCAAAACACAC 59.265 45.455 0.00 0.00 0.00 3.82
1450 1489 2.519377 TCCGTCGATCAAAACACACT 57.481 45.000 0.00 0.00 0.00 3.55
1451 1490 2.131972 TCCGTCGATCAAAACACACTG 58.868 47.619 0.00 0.00 0.00 3.66
1452 1491 1.864711 CCGTCGATCAAAACACACTGT 59.135 47.619 0.00 0.00 0.00 3.55
1453 1492 2.096909 CCGTCGATCAAAACACACTGTC 60.097 50.000 0.00 0.00 0.00 3.51
1454 1493 2.408487 CGTCGATCAAAACACACTGTCG 60.408 50.000 0.00 0.00 0.00 4.35
1455 1494 2.096909 GTCGATCAAAACACACTGTCGG 60.097 50.000 0.00 0.00 0.00 4.79
1456 1495 1.398451 CGATCAAAACACACTGTCGGC 60.398 52.381 0.00 0.00 0.00 5.54
1457 1496 0.951558 ATCAAAACACACTGTCGGCC 59.048 50.000 0.00 0.00 0.00 6.13
1458 1497 0.107410 TCAAAACACACTGTCGGCCT 60.107 50.000 0.00 0.00 0.00 5.19
1459 1498 0.738389 CAAAACACACTGTCGGCCTT 59.262 50.000 0.00 0.00 0.00 4.35
1460 1499 1.134175 CAAAACACACTGTCGGCCTTT 59.866 47.619 0.00 0.00 0.00 3.11
1462 1501 2.335316 AACACACTGTCGGCCTTTAA 57.665 45.000 0.00 0.00 0.00 1.52
1463 1502 2.561478 ACACACTGTCGGCCTTTAAT 57.439 45.000 0.00 0.00 0.00 1.40
1465 1504 3.219281 ACACACTGTCGGCCTTTAATTT 58.781 40.909 0.00 0.00 0.00 1.82
1466 1505 3.252458 ACACACTGTCGGCCTTTAATTTC 59.748 43.478 0.00 0.00 0.00 2.17
1467 1506 3.502211 CACACTGTCGGCCTTTAATTTCT 59.498 43.478 0.00 0.00 0.00 2.52
1469 1508 4.215613 ACACTGTCGGCCTTTAATTTCTTC 59.784 41.667 0.00 0.00 0.00 2.87
1470 1509 4.455877 CACTGTCGGCCTTTAATTTCTTCT 59.544 41.667 0.00 0.00 0.00 2.85
1476 1517 7.280205 TGTCGGCCTTTAATTTCTTCTCTATTC 59.720 37.037 0.00 0.00 0.00 1.75
1644 1693 1.878522 CAGCATGGACCGCTACGTC 60.879 63.158 0.00 0.00 37.72 4.34
1770 1819 4.209911 GTCTCCGGCGTGGTAATTAATTAC 59.790 45.833 24.31 24.31 41.38 1.89
1787 1836 4.987963 ATTACCTGCTCATCATCCATCA 57.012 40.909 0.00 0.00 0.00 3.07
1788 1837 4.987963 TTACCTGCTCATCATCCATCAT 57.012 40.909 0.00 0.00 0.00 2.45
1789 1838 3.420300 ACCTGCTCATCATCCATCATC 57.580 47.619 0.00 0.00 0.00 2.92
1790 1839 2.289506 ACCTGCTCATCATCCATCATCG 60.290 50.000 0.00 0.00 0.00 3.84
1792 1841 2.994578 CTGCTCATCATCCATCATCGAC 59.005 50.000 0.00 0.00 0.00 4.20
1793 1842 1.991264 GCTCATCATCCATCATCGACG 59.009 52.381 0.00 0.00 0.00 5.12
1795 1844 1.073964 CATCATCCATCATCGACGGC 58.926 55.000 0.00 0.00 0.00 5.68
1797 1846 0.463620 TCATCCATCATCGACGGCAA 59.536 50.000 0.00 0.00 0.00 4.52
1798 1847 0.583438 CATCCATCATCGACGGCAAC 59.417 55.000 0.00 0.00 0.00 4.17
2172 2277 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
2173 2278 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2187 2292 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
2188 2293 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
2189 2294 8.305317 ACTACTTTAGTGATCTAAACGCTCTTT 58.695 33.333 0.00 0.00 40.05 2.52
2190 2295 9.784680 CTACTTTAGTGATCTAAACGCTCTTTA 57.215 33.333 0.00 0.00 40.05 1.85
2191 2296 8.690680 ACTTTAGTGATCTAAACGCTCTTTAG 57.309 34.615 0.00 4.97 40.05 1.85
2192 2297 8.305317 ACTTTAGTGATCTAAACGCTCTTTAGT 58.695 33.333 9.42 0.00 40.05 2.24
2193 2298 8.462143 TTTAGTGATCTAAACGCTCTTTAGTG 57.538 34.615 9.42 0.00 40.05 2.74
2194 2299 6.268825 AGTGATCTAAACGCTCTTTAGTGA 57.731 37.500 9.42 0.00 36.68 3.41
2195 2300 6.868622 AGTGATCTAAACGCTCTTTAGTGAT 58.131 36.000 9.42 0.00 36.68 3.06
2196 2301 6.975772 AGTGATCTAAACGCTCTTTAGTGATC 59.024 38.462 9.42 0.00 36.68 2.92
2197 2302 6.975772 GTGATCTAAACGCTCTTTAGTGATCT 59.024 38.462 9.42 0.00 36.68 2.75
2198 2303 8.129840 GTGATCTAAACGCTCTTTAGTGATCTA 58.870 37.037 9.42 0.00 36.68 1.98
2199 2304 8.683615 TGATCTAAACGCTCTTTAGTGATCTAA 58.316 33.333 9.42 0.00 36.68 2.10
2200 2305 9.517609 GATCTAAACGCTCTTTAGTGATCTAAA 57.482 33.333 9.42 0.00 41.87 1.85
2201 2306 8.684973 TCTAAACGCTCTTTAGTGATCTAAAC 57.315 34.615 9.42 0.00 40.05 2.01
2202 2307 6.390987 AAACGCTCTTTAGTGATCTAAACG 57.609 37.500 0.00 0.00 40.05 3.60
2203 2308 3.858238 ACGCTCTTTAGTGATCTAAACGC 59.142 43.478 0.00 0.00 40.05 4.84
2204 2309 4.106197 CGCTCTTTAGTGATCTAAACGCT 58.894 43.478 0.00 0.00 40.05 5.07
2205 2310 4.205385 CGCTCTTTAGTGATCTAAACGCTC 59.795 45.833 0.00 0.00 40.05 5.03
2206 2311 5.344884 GCTCTTTAGTGATCTAAACGCTCT 58.655 41.667 0.00 0.00 40.05 4.09
2207 2312 5.808030 GCTCTTTAGTGATCTAAACGCTCTT 59.192 40.000 0.00 0.00 40.05 2.85
2208 2313 6.973474 GCTCTTTAGTGATCTAAACGCTCTTA 59.027 38.462 0.00 0.00 40.05 2.10
2209 2314 7.650104 GCTCTTTAGTGATCTAAACGCTCTTAT 59.350 37.037 0.00 0.00 40.05 1.73
2216 2321 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
2280 2385 5.591099 CCTGTTTTGTTAGCAGATTTGTGT 58.409 37.500 0.00 0.00 32.39 3.72
2293 2398 5.535333 CAGATTTGTGTGCTCCAAGAAAAT 58.465 37.500 0.00 0.00 0.00 1.82
2294 2399 5.987347 CAGATTTGTGTGCTCCAAGAAAATT 59.013 36.000 0.00 0.00 0.00 1.82
2466 2575 2.485302 CCTGTGCCGGATGTTCATCATA 60.485 50.000 5.05 0.00 36.83 2.15
2559 2668 5.559148 AGATCCATGTAACCCATCTCTTC 57.441 43.478 0.00 0.00 0.00 2.87
2601 2710 5.048434 TCAGTCAGTCATCGGCTAATCTATG 60.048 44.000 0.00 0.00 0.00 2.23
2615 2724 7.540400 CGGCTAATCTATGTACTTGATCAAGAG 59.460 40.741 36.15 23.78 40.79 2.85
2644 2753 9.635404 ATGATCCCTTTTTATTTACGGTTCATA 57.365 29.630 0.00 0.00 31.29 2.15
2716 2825 2.378208 TCATTGATCCCAGGTTTGTCCA 59.622 45.455 0.00 0.00 39.02 4.02
2725 2834 3.555966 CCAGGTTTGTCCAAGAAGTTCT 58.444 45.455 0.00 0.00 39.02 3.01
2726 2835 3.954258 CCAGGTTTGTCCAAGAAGTTCTT 59.046 43.478 12.50 12.50 37.14 2.52
2788 2898 4.558095 GCAGCACTGACAATTCAAATGAGT 60.558 41.667 0.81 0.00 0.00 3.41
2805 2916 8.306038 TCAAATGAGTTTGCTTTGCATAGTATT 58.694 29.630 6.03 0.00 43.47 1.89
2831 2942 2.351157 GCATGCTGAAGTTGAACTCACC 60.351 50.000 11.37 0.00 0.00 4.02
2836 2947 4.096382 TGCTGAAGTTGAACTCACCTTTTC 59.904 41.667 0.00 0.00 28.37 2.29
2842 2958 4.640647 AGTTGAACTCACCTTTTCTGTTCC 59.359 41.667 0.00 0.00 36.98 3.62
2876 2992 0.871722 CGACAGTGAATTGCCCGAAA 59.128 50.000 0.00 0.00 0.00 3.46
2878 2994 2.728846 CGACAGTGAATTGCCCGAAATG 60.729 50.000 0.00 0.00 0.00 2.32
3011 3130 4.795469 TCATACATGATGCAAGGGAATGT 58.205 39.130 0.00 0.00 35.29 2.71
3076 3201 4.141914 GCTATACTACAGCTGAACCCACTT 60.142 45.833 23.35 0.00 36.07 3.16
3084 3209 1.517242 CTGAACCCACTTCTGAGCAC 58.483 55.000 0.00 0.00 31.03 4.40
3203 3328 1.666054 AGACTATCACCGAGGACGAC 58.334 55.000 0.00 0.00 42.66 4.34
3238 3363 2.568623 AAGGTTGCCACGAGATTTCT 57.431 45.000 0.00 0.00 0.00 2.52
3243 3368 3.751698 GGTTGCCACGAGATTTCTTACTT 59.248 43.478 0.00 0.00 0.00 2.24
3247 3372 7.254353 GGTTGCCACGAGATTTCTTACTTATAC 60.254 40.741 0.00 0.00 0.00 1.47
3377 3507 3.712881 GGTGGCGCACGACAAGAC 61.713 66.667 10.83 0.00 33.39 3.01
3427 3557 3.349927 CATGAGGTGCCAAATGAAGAGA 58.650 45.455 0.00 0.00 0.00 3.10
3452 3582 5.523916 CCAAGGTGAAGGAATATGTCTAACG 59.476 44.000 0.00 0.00 0.00 3.18
3460 3600 4.528596 AGGAATATGTCTAACGCCTAGCAT 59.471 41.667 0.00 0.00 32.55 3.79
3526 3669 4.341520 GTCCCTTCCATGGTAGTAGTAGTG 59.658 50.000 16.36 0.39 0.00 2.74
3548 3693 6.757010 AGTGAGTACTAACTTGACTTTGTGTG 59.243 38.462 7.11 0.00 35.56 3.82
3560 3705 2.558359 ACTTTGTGTGGCCTAATTCTGC 59.442 45.455 3.32 0.00 0.00 4.26
3571 3716 3.743584 GCCTAATTCTGCTGCATCTCTGA 60.744 47.826 1.31 0.00 0.00 3.27
3746 3894 5.359194 TTGCACCCTTCAACCAAATAAAA 57.641 34.783 0.00 0.00 0.00 1.52
3769 3917 4.978099 ACTCCATGAAAAAGCAGAGAGAA 58.022 39.130 0.00 0.00 0.00 2.87
3804 3974 1.606668 GAATGAGGCGTTGGTTTGTGA 59.393 47.619 0.00 0.00 0.00 3.58
3805 3975 0.951558 ATGAGGCGTTGGTTTGTGAC 59.048 50.000 0.00 0.00 0.00 3.67
3806 3976 0.107410 TGAGGCGTTGGTTTGTGACT 60.107 50.000 0.00 0.00 0.00 3.41
3807 3977 1.021968 GAGGCGTTGGTTTGTGACTT 58.978 50.000 0.00 0.00 0.00 3.01
3808 3978 1.404035 GAGGCGTTGGTTTGTGACTTT 59.596 47.619 0.00 0.00 0.00 2.66
3809 3979 1.134175 AGGCGTTGGTTTGTGACTTTG 59.866 47.619 0.00 0.00 0.00 2.77
3810 3980 1.135228 GGCGTTGGTTTGTGACTTTGT 60.135 47.619 0.00 0.00 0.00 2.83
3828 3998 2.912771 TGTGTGTGGTTCTGAACGAAT 58.087 42.857 13.89 0.00 33.45 3.34
3833 4003 4.202172 TGTGTGGTTCTGAACGAATAGTGA 60.202 41.667 13.89 0.00 33.45 3.41
4051 4222 1.004560 CAGAACCGCAAGCTCCTGA 60.005 57.895 0.00 0.00 0.00 3.86
4167 4341 4.035102 GAGAAGGTGGCCGCCCTT 62.035 66.667 32.01 26.97 44.98 3.95
4291 4478 4.406648 GTGAGGACCACATGACATGATA 57.593 45.455 22.19 0.00 45.03 2.15
4299 4487 4.223700 ACCACATGACATGATACAGACACT 59.776 41.667 22.19 0.00 0.00 3.55
4301 4489 4.807834 CACATGACATGATACAGACACTCC 59.192 45.833 22.19 0.00 0.00 3.85
4309 4497 5.139435 TGATACAGACACTCCTTCTTGTG 57.861 43.478 0.00 0.00 39.80 3.33
4315 4503 3.007398 AGACACTCCTTCTTGTGTGATCC 59.993 47.826 3.41 0.00 45.94 3.36
4319 4507 2.568956 CTCCTTCTTGTGTGATCCTGGA 59.431 50.000 0.00 0.00 0.00 3.86
4438 4629 2.515901 GGATGGTAAGGCCGGCAT 59.484 61.111 30.85 21.35 41.21 4.40
4450 4641 0.674895 GCCGGCATTCTCACTCACTT 60.675 55.000 24.80 0.00 0.00 3.16
4491 4682 2.637872 TGGTACTGTTAGGCTCAAGCTT 59.362 45.455 0.00 0.00 41.70 3.74
4662 6336 7.718753 AGAAAGAGAAAGAGAGAAAAATGCAGA 59.281 33.333 0.00 0.00 0.00 4.26
4665 6339 7.873910 AGAGAAAGAGAGAAAAATGCAGAAAG 58.126 34.615 0.00 0.00 0.00 2.62
4686 6376 8.982723 AGAAAGAAGGATACATACATACACACT 58.017 33.333 0.00 0.00 41.41 3.55
4692 6382 9.595823 AAGGATACATACATACACACTTACAAC 57.404 33.333 0.00 0.00 41.41 3.32
4721 6418 2.822764 CCGAGGCTGAATTGTAGTACC 58.177 52.381 0.00 0.00 0.00 3.34
4837 6535 0.533032 GGTCCTAGCTATGCCGATCC 59.467 60.000 0.00 0.00 0.00 3.36
4846 6544 0.828022 TATGCCGATCCCGTCTTGTT 59.172 50.000 0.00 0.00 0.00 2.83
4897 6606 7.830739 AGAATTGTAAGGCCTTTGTCTTTATG 58.169 34.615 26.08 0.00 37.63 1.90
4931 6641 2.336554 TTTGCGCTTCTGAAGAATGC 57.663 45.000 21.06 18.86 36.48 3.56
4944 6654 5.466728 TCTGAAGAATGCTGTGTAACTGAAC 59.533 40.000 0.00 0.00 38.12 3.18
5047 6819 2.876581 ACAATGGTCTTGTTTCCCCTC 58.123 47.619 0.00 0.00 0.00 4.30
5072 6844 6.346598 CGTTATTTGCATCCTATGGAACTACG 60.347 42.308 0.00 1.74 40.40 3.51
5073 6845 4.746535 TTTGCATCCTATGGAACTACGA 57.253 40.909 0.00 0.00 40.40 3.43
5103 6880 2.030363 GCTAGAGCTGCATATCGTCAGT 60.030 50.000 1.02 0.00 38.21 3.41
5168 6950 1.867233 CAGAACCAAGACAGGTCAACG 59.133 52.381 1.84 0.00 42.25 4.10
5170 6952 2.169769 AGAACCAAGACAGGTCAACGAA 59.830 45.455 1.84 0.00 42.25 3.85
5173 6955 1.070134 CCAAGACAGGTCAACGAAGGA 59.930 52.381 1.84 0.00 0.00 3.36
5195 6978 5.506982 GGAATTCTGCTGCAATCCTGTATTC 60.507 44.000 3.02 6.70 0.00 1.75
5253 7037 8.008844 CAGCGCAAAAACACATTTATTTATGTT 58.991 29.630 11.47 0.00 36.64 2.71
5284 7070 5.882040 TCTGTCCATTTACAAACCCATGTA 58.118 37.500 0.00 0.00 34.75 2.29
5363 7149 0.755079 CCATCTCCGGCATCTCAGAA 59.245 55.000 0.00 0.00 0.00 3.02
5398 7191 1.040339 CAAGGGGGTCTCTCTCCTCG 61.040 65.000 0.00 0.00 36.78 4.63
5399 7192 1.511316 AAGGGGGTCTCTCTCCTCGT 61.511 60.000 0.00 0.00 36.78 4.18
5400 7193 1.454295 GGGGGTCTCTCTCCTCGTC 60.454 68.421 0.00 0.00 36.78 4.20
5401 7194 1.454295 GGGGTCTCTCTCCTCGTCC 60.454 68.421 0.00 0.00 32.92 4.79
5456 7251 3.685139 TTCTGCAACAGGAAGGTAGAG 57.315 47.619 0.00 0.00 31.51 2.43
5563 7368 2.163818 TCCTGTCAACGTAAGCAAGG 57.836 50.000 0.00 0.00 45.62 3.61
5572 7377 1.275573 ACGTAAGCAAGGAGTTCCTCC 59.724 52.381 0.22 1.90 47.00 4.30
5613 7418 3.118629 TGCAGAGCCTAGATGAATTTCGT 60.119 43.478 0.00 0.00 0.00 3.85
5655 7461 7.819900 GTGACAAGTACTGACCTTCTCAATTAT 59.180 37.037 0.00 0.00 0.00 1.28
5690 7496 2.722094 TGCAACAAGTTCTGAAGTGGT 58.278 42.857 0.00 0.00 0.00 4.16
5763 7570 3.972950 TTTTCGAAATCGGAGTGCAAA 57.027 38.095 12.12 0.00 40.29 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.617274 GCAACTCCAACAGGGCGAC 61.617 63.158 0.00 0.00 36.21 5.19
5 6 2.281761 AGCAACTCCAACAGGGCG 60.282 61.111 0.00 0.00 36.21 6.13
6 7 0.538287 AAGAGCAACTCCAACAGGGC 60.538 55.000 0.00 0.00 36.21 5.19
7 8 2.859165 TAAGAGCAACTCCAACAGGG 57.141 50.000 0.00 0.00 38.37 4.45
8 9 3.012518 CCATAAGAGCAACTCCAACAGG 58.987 50.000 0.00 0.00 0.00 4.00
9 10 3.686726 GTCCATAAGAGCAACTCCAACAG 59.313 47.826 0.00 0.00 0.00 3.16
10 11 3.559171 GGTCCATAAGAGCAACTCCAACA 60.559 47.826 0.00 0.00 42.81 3.33
11 12 3.010420 GGTCCATAAGAGCAACTCCAAC 58.990 50.000 0.00 0.00 42.81 3.77
12 13 2.912956 AGGTCCATAAGAGCAACTCCAA 59.087 45.455 0.00 0.00 45.87 3.53
13 14 2.551270 AGGTCCATAAGAGCAACTCCA 58.449 47.619 0.00 0.00 45.87 3.86
14 15 4.755266 TTAGGTCCATAAGAGCAACTCC 57.245 45.455 0.00 0.00 45.87 3.85
15 16 7.501844 AGTAATTAGGTCCATAAGAGCAACTC 58.498 38.462 0.00 0.00 45.87 3.01
16 17 7.439108 AGTAATTAGGTCCATAAGAGCAACT 57.561 36.000 0.00 0.00 45.87 3.16
17 18 8.507524 AAAGTAATTAGGTCCATAAGAGCAAC 57.492 34.615 0.00 0.00 45.87 4.17
28 29 6.978659 GGCTGCAAAATAAAGTAATTAGGTCC 59.021 38.462 0.50 0.00 0.00 4.46
36 37 7.822658 ACGAATTAGGCTGCAAAATAAAGTAA 58.177 30.769 0.50 0.00 0.00 2.24
66 67 8.746530 TGGGTAGTAACTACAGAAGTATTCAAG 58.253 37.037 0.00 0.00 40.69 3.02
82 83 7.916914 ATTTGTGAACATAGTGGGTAGTAAC 57.083 36.000 0.00 0.00 0.00 2.50
130 131 7.214449 CGACATCTGTCAAAATACGTCAAATTC 59.786 37.037 10.69 0.00 44.99 2.17
132 133 6.367695 TCGACATCTGTCAAAATACGTCAAAT 59.632 34.615 10.69 0.00 44.99 2.32
134 135 5.118050 GTCGACATCTGTCAAAATACGTCAA 59.882 40.000 11.55 0.00 44.99 3.18
135 136 4.619760 GTCGACATCTGTCAAAATACGTCA 59.380 41.667 11.55 0.00 44.99 4.35
138 139 5.702622 ATGTCGACATCTGTCAAAATACG 57.297 39.130 25.18 0.00 44.99 3.06
145 146 3.119173 TGCATGTATGTCGACATCTGTCA 60.119 43.478 33.11 24.95 44.99 3.58
148 149 3.189285 TGTGCATGTATGTCGACATCTG 58.811 45.455 33.11 26.38 37.99 2.90
154 155 4.385358 AGTGTATGTGCATGTATGTCGA 57.615 40.909 0.00 0.00 0.00 4.20
195 196 7.099120 GGCATCTGTCTAACCAATTCAAAAAT 58.901 34.615 0.00 0.00 0.00 1.82
199 200 4.016444 GGGCATCTGTCTAACCAATTCAA 58.984 43.478 0.00 0.00 0.00 2.69
205 206 1.357137 TGTGGGCATCTGTCTAACCA 58.643 50.000 0.00 0.00 0.00 3.67
208 209 3.517500 TGTGTATGTGGGCATCTGTCTAA 59.482 43.478 0.00 0.00 36.58 2.10
210 211 1.908619 TGTGTATGTGGGCATCTGTCT 59.091 47.619 0.00 0.00 36.58 3.41
211 212 2.009774 GTGTGTATGTGGGCATCTGTC 58.990 52.381 0.00 0.00 36.58 3.51
215 216 7.611770 TCTTATATAGTGTGTATGTGGGCATC 58.388 38.462 0.00 0.00 36.58 3.91
216 217 7.553504 TCTTATATAGTGTGTATGTGGGCAT 57.446 36.000 0.00 0.00 39.03 4.40
217 218 6.987403 TCTTATATAGTGTGTATGTGGGCA 57.013 37.500 0.00 0.00 0.00 5.36
218 219 7.386851 ACATCTTATATAGTGTGTATGTGGGC 58.613 38.462 0.00 0.00 0.00 5.36
293 296 2.267426 GAGTGTATGTGCGTGTATGCA 58.733 47.619 0.00 0.00 43.95 3.96
294 297 2.267426 TGAGTGTATGTGCGTGTATGC 58.733 47.619 0.00 0.00 0.00 3.14
328 333 3.281359 AATTTTCCTGGGCGTGCGC 62.281 57.895 8.17 8.17 41.06 6.09
336 341 3.991773 CACATGTGCTTGAATTTTCCTGG 59.008 43.478 13.94 0.00 0.00 4.45
347 352 7.788585 AGTATTAGACTTGGCACATGTGCTTG 61.789 42.308 40.86 31.96 46.89 4.01
350 355 3.941483 AGTATTAGACTTGGCACATGTGC 59.059 43.478 37.29 37.29 46.89 4.57
368 373 6.543831 GTGATAGGCCATCAAAGTTCAAGTAT 59.456 38.462 16.37 0.00 45.28 2.12
369 374 5.880332 GTGATAGGCCATCAAAGTTCAAGTA 59.120 40.000 16.37 0.00 45.28 2.24
378 383 4.314522 TTCCTTGTGATAGGCCATCAAA 57.685 40.909 16.37 10.59 45.28 2.69
390 395 8.528044 AACTTAAATGGTTAGTTTCCTTGTGA 57.472 30.769 0.00 0.00 0.00 3.58
400 411 8.863872 AACTGAGCATAACTTAAATGGTTAGT 57.136 30.769 8.59 8.59 46.96 2.24
430 451 7.867305 TGGAGTGAACAAACACACTAAAATA 57.133 32.000 0.00 0.00 45.54 1.40
505 526 7.987649 ACCTTACTATTTACTCTCTCTGTTCG 58.012 38.462 0.00 0.00 0.00 3.95
549 573 8.217111 TGGATATCATGGCTGTTTTCATAGTTA 58.783 33.333 4.83 0.00 0.00 2.24
570 594 5.188359 ACCGCTCCTAACTTTAACTTGGATA 59.812 40.000 0.00 0.00 0.00 2.59
571 595 4.019591 ACCGCTCCTAACTTTAACTTGGAT 60.020 41.667 0.00 0.00 0.00 3.41
612 636 1.269309 CGAGGCTCTCCCACTATTTCG 60.269 57.143 13.50 0.00 35.39 3.46
753 784 1.987855 TACCAGGGAGACGGCCTTG 60.988 63.158 0.00 0.00 34.99 3.61
754 785 1.988406 GTACCAGGGAGACGGCCTT 60.988 63.158 0.00 0.00 0.00 4.35
755 786 2.363925 GTACCAGGGAGACGGCCT 60.364 66.667 0.00 0.00 0.00 5.19
810 842 6.800543 TCGATGGAGAAGAGATAACAAGAAG 58.199 40.000 0.00 0.00 0.00 2.85
876 908 3.480679 CTGCACCACCACCTGAGCA 62.481 63.158 0.00 0.00 32.10 4.26
878 910 2.670934 GCTGCACCACCACCTGAG 60.671 66.667 0.00 0.00 0.00 3.35
960 996 0.564767 CGTCGTCGCCTTATTTCGTC 59.435 55.000 0.00 0.00 0.00 4.20
1359 1398 2.668212 CCGAACTCCTTGCGCCAA 60.668 61.111 4.18 0.00 0.00 4.52
1407 1446 4.515191 TGAAATAATCTAATGGAGCACGCC 59.485 41.667 0.00 0.00 0.00 5.68
1424 1463 5.639931 TGTGTTTTGATCGACGGATGAAATA 59.360 36.000 0.00 0.00 36.00 1.40
1425 1464 4.454161 TGTGTTTTGATCGACGGATGAAAT 59.546 37.500 0.00 0.00 36.00 2.17
1426 1465 3.810386 TGTGTTTTGATCGACGGATGAAA 59.190 39.130 0.00 0.00 34.57 2.69
1427 1466 3.185594 GTGTGTTTTGATCGACGGATGAA 59.814 43.478 0.00 0.00 31.51 2.57
1429 1468 2.736721 AGTGTGTTTTGATCGACGGATG 59.263 45.455 0.00 0.00 31.51 3.51
1430 1469 2.736721 CAGTGTGTTTTGATCGACGGAT 59.263 45.455 0.00 0.00 34.96 4.18
1431 1470 2.131972 CAGTGTGTTTTGATCGACGGA 58.868 47.619 0.00 0.00 0.00 4.69
1432 1471 1.864711 ACAGTGTGTTTTGATCGACGG 59.135 47.619 0.00 0.00 0.00 4.79
1433 1472 2.408487 CGACAGTGTGTTTTGATCGACG 60.408 50.000 0.00 0.00 0.00 5.12
1434 1473 2.096909 CCGACAGTGTGTTTTGATCGAC 60.097 50.000 0.00 0.00 0.00 4.20
1435 1474 2.131972 CCGACAGTGTGTTTTGATCGA 58.868 47.619 0.00 0.00 0.00 3.59
1437 1476 1.069227 GGCCGACAGTGTGTTTTGATC 60.069 52.381 0.00 0.00 0.00 2.92
1438 1477 0.951558 GGCCGACAGTGTGTTTTGAT 59.048 50.000 0.00 0.00 0.00 2.57
1441 1480 1.470051 AAAGGCCGACAGTGTGTTTT 58.530 45.000 0.00 0.00 0.00 2.43
1442 1481 2.335316 TAAAGGCCGACAGTGTGTTT 57.665 45.000 0.00 0.00 0.00 2.83
1443 1482 2.335316 TTAAAGGCCGACAGTGTGTT 57.665 45.000 0.00 0.00 0.00 3.32
1444 1483 2.561478 ATTAAAGGCCGACAGTGTGT 57.439 45.000 0.00 0.00 0.00 3.72
1446 1485 3.751518 AGAAATTAAAGGCCGACAGTGT 58.248 40.909 0.00 0.00 0.00 3.55
1447 1486 4.455877 AGAAGAAATTAAAGGCCGACAGTG 59.544 41.667 0.00 0.00 0.00 3.66
1448 1487 4.652822 AGAAGAAATTAAAGGCCGACAGT 58.347 39.130 0.00 0.00 0.00 3.55
1449 1488 4.938226 AGAGAAGAAATTAAAGGCCGACAG 59.062 41.667 0.00 0.00 0.00 3.51
1450 1489 4.906618 AGAGAAGAAATTAAAGGCCGACA 58.093 39.130 0.00 0.00 0.00 4.35
1451 1490 7.516943 CGAATAGAGAAGAAATTAAAGGCCGAC 60.517 40.741 0.00 0.00 0.00 4.79
1452 1491 6.479001 CGAATAGAGAAGAAATTAAAGGCCGA 59.521 38.462 0.00 0.00 0.00 5.54
1453 1492 6.479001 TCGAATAGAGAAGAAATTAAAGGCCG 59.521 38.462 0.00 0.00 0.00 6.13
1454 1493 7.516943 CGTCGAATAGAGAAGAAATTAAAGGCC 60.517 40.741 0.00 0.00 0.00 5.19
1455 1494 7.010275 ACGTCGAATAGAGAAGAAATTAAAGGC 59.990 37.037 0.00 0.00 0.00 4.35
1456 1495 8.408743 ACGTCGAATAGAGAAGAAATTAAAGG 57.591 34.615 0.00 0.00 0.00 3.11
1458 1497 9.003112 CGTACGTCGAATAGAGAAGAAATTAAA 57.997 33.333 7.22 0.00 42.86 1.52
1459 1498 8.177663 ACGTACGTCGAATAGAGAAGAAATTAA 58.822 33.333 16.72 0.00 42.86 1.40
1460 1499 7.688372 ACGTACGTCGAATAGAGAAGAAATTA 58.312 34.615 16.72 0.00 42.86 1.40
1462 1501 6.116680 ACGTACGTCGAATAGAGAAGAAAT 57.883 37.500 16.72 0.00 42.86 2.17
1463 1502 5.536554 ACGTACGTCGAATAGAGAAGAAA 57.463 39.130 16.72 0.00 42.86 2.52
1465 1504 4.205181 CGTACGTACGTCGAATAGAGAAGA 59.795 45.833 33.95 0.00 44.13 2.87
1466 1505 4.432209 CGTACGTACGTCGAATAGAGAAG 58.568 47.826 33.95 2.19 44.13 2.85
1467 1506 4.422997 CGTACGTACGTCGAATAGAGAA 57.577 45.455 33.95 0.00 44.13 2.87
1644 1693 0.898789 ACTCCCTCACGTGGTACCTG 60.899 60.000 17.00 8.33 0.00 4.00
1770 1819 2.028385 TCGATGATGGATGATGAGCAGG 60.028 50.000 0.00 0.00 0.00 4.85
1780 1829 0.875908 CGTTGCCGTCGATGATGGAT 60.876 55.000 6.11 0.00 40.94 3.41
1787 1836 1.209128 GATCATTCGTTGCCGTCGAT 58.791 50.000 0.00 0.00 37.18 3.59
1788 1837 0.804544 GGATCATTCGTTGCCGTCGA 60.805 55.000 0.00 0.00 35.50 4.20
1789 1838 1.081556 TGGATCATTCGTTGCCGTCG 61.082 55.000 0.00 0.00 35.01 5.12
1790 1839 1.003545 CATGGATCATTCGTTGCCGTC 60.004 52.381 0.00 0.00 35.01 4.79
1792 1841 0.317269 GCATGGATCATTCGTTGCCG 60.317 55.000 0.00 0.00 0.00 5.69
1793 1842 0.031178 GGCATGGATCATTCGTTGCC 59.969 55.000 0.00 0.00 40.89 4.52
1795 1844 2.225019 GCTAGGCATGGATCATTCGTTG 59.775 50.000 0.00 0.00 0.00 4.10
1797 1846 1.696336 AGCTAGGCATGGATCATTCGT 59.304 47.619 0.00 0.00 0.00 3.85
1798 1847 2.469274 AGCTAGGCATGGATCATTCG 57.531 50.000 0.00 0.00 0.00 3.34
1799 1848 4.550076 ACTAGCTAGGCATGGATCATTC 57.450 45.455 24.35 0.00 0.00 2.67
1800 1849 4.989875 AACTAGCTAGGCATGGATCATT 57.010 40.909 24.35 3.10 0.00 2.57
1801 1850 4.596643 AGAAACTAGCTAGGCATGGATCAT 59.403 41.667 24.35 0.00 0.00 2.45
1873 1927 1.926511 GCCCTGAGACATGCCAAACG 61.927 60.000 0.00 0.00 0.00 3.60
2168 2273 8.301720 TCACTAAAGAGCGTTTAGATCACTAAA 58.698 33.333 21.60 0.00 43.52 1.85
2169 2274 7.823665 TCACTAAAGAGCGTTTAGATCACTAA 58.176 34.615 21.60 0.00 37.82 2.24
2170 2275 7.387119 TCACTAAAGAGCGTTTAGATCACTA 57.613 36.000 21.60 4.56 37.82 2.74
2171 2276 6.268825 TCACTAAAGAGCGTTTAGATCACT 57.731 37.500 21.60 3.42 37.82 3.41
2172 2277 6.975772 AGATCACTAAAGAGCGTTTAGATCAC 59.024 38.462 21.60 12.83 37.82 3.06
2173 2278 7.101652 AGATCACTAAAGAGCGTTTAGATCA 57.898 36.000 21.60 9.77 37.82 2.92
2174 2279 9.517609 TTTAGATCACTAAAGAGCGTTTAGATC 57.482 33.333 21.60 16.18 41.71 2.75
2175 2280 9.303537 GTTTAGATCACTAAAGAGCGTTTAGAT 57.696 33.333 21.60 10.52 45.42 1.98
2176 2281 7.484007 CGTTTAGATCACTAAAGAGCGTTTAGA 59.516 37.037 21.60 7.12 45.42 2.10
2177 2282 7.601775 CGTTTAGATCACTAAAGAGCGTTTAG 58.398 38.462 15.99 15.99 45.42 1.85
2178 2283 6.034256 GCGTTTAGATCACTAAAGAGCGTTTA 59.966 38.462 0.00 0.00 45.42 2.01
2179 2284 5.163982 GCGTTTAGATCACTAAAGAGCGTTT 60.164 40.000 0.00 0.00 45.42 3.60
2180 2285 4.326548 GCGTTTAGATCACTAAAGAGCGTT 59.673 41.667 0.00 0.00 45.42 4.84
2181 2286 3.858238 GCGTTTAGATCACTAAAGAGCGT 59.142 43.478 0.00 0.00 45.42 5.07
2182 2287 4.106197 AGCGTTTAGATCACTAAAGAGCG 58.894 43.478 16.38 11.92 46.12 5.03
2183 2288 5.344884 AGAGCGTTTAGATCACTAAAGAGC 58.655 41.667 15.46 15.46 45.42 4.09
2190 2295 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
2195 2300 8.810427 CCGTAAACAAATATAAGAGCGTTTAGA 58.190 33.333 0.00 0.00 31.53 2.10
2196 2301 8.810427 TCCGTAAACAAATATAAGAGCGTTTAG 58.190 33.333 0.00 0.00 31.53 1.85
2197 2302 8.700722 TCCGTAAACAAATATAAGAGCGTTTA 57.299 30.769 0.00 0.00 0.00 2.01
2198 2303 7.201582 CCTCCGTAAACAAATATAAGAGCGTTT 60.202 37.037 0.00 0.00 0.00 3.60
2199 2304 6.257193 CCTCCGTAAACAAATATAAGAGCGTT 59.743 38.462 0.00 0.00 0.00 4.84
2200 2305 5.751990 CCTCCGTAAACAAATATAAGAGCGT 59.248 40.000 0.00 0.00 0.00 5.07
2201 2306 5.176958 CCCTCCGTAAACAAATATAAGAGCG 59.823 44.000 0.00 0.00 0.00 5.03
2202 2307 6.285990 TCCCTCCGTAAACAAATATAAGAGC 58.714 40.000 0.00 0.00 0.00 4.09
2203 2308 7.498443 ACTCCCTCCGTAAACAAATATAAGAG 58.502 38.462 0.00 0.00 0.00 2.85
2204 2309 7.427989 ACTCCCTCCGTAAACAAATATAAGA 57.572 36.000 0.00 0.00 0.00 2.10
2205 2310 8.419442 AGTACTCCCTCCGTAAACAAATATAAG 58.581 37.037 0.00 0.00 0.00 1.73
2206 2311 8.310122 AGTACTCCCTCCGTAAACAAATATAA 57.690 34.615 0.00 0.00 0.00 0.98
2207 2312 7.902920 AGTACTCCCTCCGTAAACAAATATA 57.097 36.000 0.00 0.00 0.00 0.86
2208 2313 6.803366 AGTACTCCCTCCGTAAACAAATAT 57.197 37.500 0.00 0.00 0.00 1.28
2209 2314 6.610075 AAGTACTCCCTCCGTAAACAAATA 57.390 37.500 0.00 0.00 0.00 1.40
2210 2315 5.494390 AAGTACTCCCTCCGTAAACAAAT 57.506 39.130 0.00 0.00 0.00 2.32
2211 2316 4.961438 AAGTACTCCCTCCGTAAACAAA 57.039 40.909 0.00 0.00 0.00 2.83
2212 2317 4.961438 AAAGTACTCCCTCCGTAAACAA 57.039 40.909 0.00 0.00 0.00 2.83
2213 2318 4.961438 AAAAGTACTCCCTCCGTAAACA 57.039 40.909 0.00 0.00 0.00 2.83
2214 2319 7.277319 CAGATAAAAAGTACTCCCTCCGTAAAC 59.723 40.741 0.00 0.00 0.00 2.01
2215 2320 7.038799 ACAGATAAAAAGTACTCCCTCCGTAAA 60.039 37.037 0.00 0.00 0.00 2.01
2216 2321 6.438425 ACAGATAAAAAGTACTCCCTCCGTAA 59.562 38.462 0.00 0.00 0.00 3.18
2217 2322 5.954150 ACAGATAAAAAGTACTCCCTCCGTA 59.046 40.000 0.00 0.00 0.00 4.02
2218 2323 4.776308 ACAGATAAAAAGTACTCCCTCCGT 59.224 41.667 0.00 0.00 0.00 4.69
2219 2324 5.127356 AGACAGATAAAAAGTACTCCCTCCG 59.873 44.000 0.00 0.00 0.00 4.63
2466 2575 1.376812 GAATCCCTGACCGGCGTTT 60.377 57.895 6.01 0.00 0.00 3.60
2559 2668 6.401394 TGACTGATAAAGGACATGAACTGAG 58.599 40.000 0.00 0.00 0.00 3.35
2615 2724 9.726232 GAACCGTAAATAAAAAGGGATCATAAC 57.274 33.333 0.00 0.00 0.00 1.89
2620 2729 8.347771 GGTATGAACCGTAAATAAAAAGGGATC 58.652 37.037 0.00 0.00 35.62 3.36
2736 2845 6.892658 TGCAAAATCCTTTTAGAGTTGCTA 57.107 33.333 6.97 0.00 39.61 3.49
2788 2898 5.125257 TGCTGCTAATACTATGCAAAGCAAA 59.875 36.000 0.00 0.00 43.62 3.68
2831 2942 2.031682 CCGCAGAACAGGAACAGAAAAG 60.032 50.000 0.00 0.00 0.00 2.27
2836 2947 1.672356 CCCCGCAGAACAGGAACAG 60.672 63.158 0.00 0.00 0.00 3.16
2842 2958 2.027625 GTCGAACCCCGCAGAACAG 61.028 63.158 0.00 0.00 38.37 3.16
2876 2992 0.398381 ACACAAGTGCCCCCAAACAT 60.398 50.000 0.00 0.00 0.00 2.71
2878 2994 1.272212 CATACACAAGTGCCCCCAAAC 59.728 52.381 0.00 0.00 0.00 2.93
3076 3201 1.937191 TCATGGTACCTGTGCTCAGA 58.063 50.000 17.19 0.00 43.76 3.27
3084 3209 4.280677 ACCACAAAATGTTCATGGTACCTG 59.719 41.667 14.36 9.10 41.90 4.00
3238 3363 8.898761 CCATGTAAAACCTGCATGTATAAGTAA 58.101 33.333 0.00 0.00 44.29 2.24
3243 3368 4.582656 GGCCATGTAAAACCTGCATGTATA 59.417 41.667 0.00 0.00 44.29 1.47
3247 3372 1.826720 AGGCCATGTAAAACCTGCATG 59.173 47.619 5.01 0.00 45.09 4.06
3280 3410 3.118645 CGTCAGAGATGCGAACGATAATG 59.881 47.826 0.00 0.00 0.00 1.90
3281 3411 3.003378 TCGTCAGAGATGCGAACGATAAT 59.997 43.478 0.00 0.00 0.00 1.28
3377 3507 4.823419 TATGCGGCGGGTGTTCGG 62.823 66.667 9.78 0.00 0.00 4.30
3427 3557 6.415573 GTTAGACATATTCCTTCACCTTGGT 58.584 40.000 0.00 0.00 0.00 3.67
3452 3582 3.438360 CAAATCCGACAAAATGCTAGGC 58.562 45.455 0.00 0.00 0.00 3.93
3460 3600 5.856126 CTACTGTAGCAAATCCGACAAAA 57.144 39.130 1.26 0.00 0.00 2.44
3526 3669 5.050295 GCCACACAAAGTCAAGTTAGTACTC 60.050 44.000 0.00 0.00 31.99 2.59
3548 3693 1.878734 GAGATGCAGCAGAATTAGGCC 59.121 52.381 4.07 0.00 0.00 5.19
3560 3705 4.630111 GAATCCTAGGTTCAGAGATGCAG 58.370 47.826 9.08 0.00 0.00 4.41
3571 3716 0.179000 CAGCCTGCGAATCCTAGGTT 59.821 55.000 9.08 2.30 34.06 3.50
3721 3866 0.463620 TTGGTTGAAGGGTGCAAAGC 59.536 50.000 0.00 0.00 0.00 3.51
3746 3894 4.978099 TCTCTCTGCTTTTTCATGGAGTT 58.022 39.130 0.00 0.00 0.00 3.01
3769 3917 4.202346 GCCTCATTCCATTAGCTCTCTCTT 60.202 45.833 0.00 0.00 0.00 2.85
3804 3974 2.418628 CGTTCAGAACCACACACAAAGT 59.581 45.455 7.76 0.00 0.00 2.66
3805 3975 2.675844 TCGTTCAGAACCACACACAAAG 59.324 45.455 7.76 0.00 0.00 2.77
3806 3976 2.701107 TCGTTCAGAACCACACACAAA 58.299 42.857 7.76 0.00 0.00 2.83
3807 3977 2.388310 TCGTTCAGAACCACACACAA 57.612 45.000 7.76 0.00 0.00 3.33
3808 3978 2.388310 TTCGTTCAGAACCACACACA 57.612 45.000 7.76 0.00 33.14 3.72
3809 3979 4.056050 ACTATTCGTTCAGAACCACACAC 58.944 43.478 7.76 0.00 42.39 3.82
3810 3980 4.055360 CACTATTCGTTCAGAACCACACA 58.945 43.478 7.76 0.00 42.39 3.72
3828 3998 3.758023 CCATGCCAAACACATTCTCACTA 59.242 43.478 0.00 0.00 0.00 2.74
3833 4003 1.619827 CCACCATGCCAAACACATTCT 59.380 47.619 0.00 0.00 0.00 2.40
4033 4204 0.603707 TTCAGGAGCTTGCGGTTCTG 60.604 55.000 0.00 0.00 44.05 3.02
4272 4446 4.100035 TCTGTATCATGTCATGTGGTCCTC 59.900 45.833 12.54 0.00 0.00 3.71
4275 4449 4.568359 GTGTCTGTATCATGTCATGTGGTC 59.432 45.833 12.54 3.61 0.00 4.02
4276 4450 4.223700 AGTGTCTGTATCATGTCATGTGGT 59.776 41.667 12.54 3.56 0.00 4.16
4277 4451 4.763073 AGTGTCTGTATCATGTCATGTGG 58.237 43.478 12.54 1.04 0.00 4.17
4291 4478 2.766263 TCACACAAGAAGGAGTGTCTGT 59.234 45.455 0.00 0.00 46.44 3.41
4299 4487 2.619931 TCCAGGATCACACAAGAAGGA 58.380 47.619 0.00 0.00 0.00 3.36
4301 4489 5.604758 TCTATCCAGGATCACACAAGAAG 57.395 43.478 4.75 0.00 0.00 2.85
4309 4497 6.013379 TCCACCATTAATCTATCCAGGATCAC 60.013 42.308 4.75 0.00 0.00 3.06
4315 4503 6.378661 TGGATCCACCATTAATCTATCCAG 57.621 41.667 11.44 0.00 44.64 3.86
4438 4629 3.396560 CAGACATGCAAGTGAGTGAGAA 58.603 45.455 0.00 0.00 0.00 2.87
4483 4674 2.977405 GTGCTTACCACAAGCTTGAG 57.023 50.000 32.50 24.08 44.06 3.02
4618 6274 0.251519 CTTGCTTTGCTCCCCCTTCT 60.252 55.000 0.00 0.00 0.00 2.85
4665 6339 9.811995 TTGTAAGTGTGTATGTATGTATCCTTC 57.188 33.333 0.00 0.00 0.00 3.46
4686 6376 1.339631 CCTCGGCATTCCAGGTTGTAA 60.340 52.381 0.00 0.00 0.00 2.41
4692 6382 2.515523 CAGCCTCGGCATTCCAGG 60.516 66.667 11.02 0.00 44.88 4.45
4721 6418 2.198827 TCTTGTGGCCTAATGTGGTG 57.801 50.000 3.32 0.00 0.00 4.17
4837 6535 7.113404 CACAGAAAATATGTTTCAACAAGACGG 59.887 37.037 0.00 0.00 43.03 4.79
4897 6606 2.156697 GCGCAAAACTGAGAGAGTCTTC 59.843 50.000 0.30 0.00 31.73 2.87
4931 6641 4.055360 TCAATCACGGTTCAGTTACACAG 58.945 43.478 0.00 0.00 0.00 3.66
5011 6741 4.342951 ACCATTGTTGATAGGGCATCATTG 59.657 41.667 0.00 0.00 43.26 2.82
5021 6751 5.105756 GGGGAAACAAGACCATTGTTGATAG 60.106 44.000 6.74 0.00 41.30 2.08
5047 6819 6.346598 CGTAGTTCCATAGGATGCAAATAACG 60.347 42.308 0.00 0.00 0.00 3.18
5093 6870 4.122776 GCTTTCACCATGACTGACGATAT 58.877 43.478 0.00 0.00 0.00 1.63
5103 6880 0.319986 TACACGCGCTTTCACCATGA 60.320 50.000 5.73 0.00 0.00 3.07
5168 6950 3.022406 AGGATTGCAGCAGAATTCCTTC 58.978 45.455 0.65 0.00 0.00 3.46
5170 6952 2.291411 ACAGGATTGCAGCAGAATTCCT 60.291 45.455 0.65 10.82 0.00 3.36
5173 6955 4.951715 TGAATACAGGATTGCAGCAGAATT 59.048 37.500 0.00 0.00 0.00 2.17
5195 6978 2.408271 TTCAGCCTGCCTGTCTTATG 57.592 50.000 0.00 0.00 42.38 1.90
5253 7037 7.177744 GGGTTTGTAAATGGACAGAAAATCCTA 59.822 37.037 0.00 0.00 37.13 2.94
5284 7070 6.713762 TCCTGACAAATGTGAAAAAGACAT 57.286 33.333 0.00 0.00 0.00 3.06
5363 7149 4.080582 CCCCCTTGGTTCAGTTTTCTTTTT 60.081 41.667 0.00 0.00 0.00 1.94
5398 7191 2.089980 TGTCTTGCTACTAGGACGGAC 58.910 52.381 0.00 0.00 0.00 4.79
5399 7192 2.502142 TGTCTTGCTACTAGGACGGA 57.498 50.000 0.00 0.00 0.00 4.69
5400 7193 2.287069 CGATGTCTTGCTACTAGGACGG 60.287 54.545 0.00 0.00 0.00 4.79
5401 7194 2.287069 CCGATGTCTTGCTACTAGGACG 60.287 54.545 0.00 0.00 0.00 4.79
5456 7251 6.592994 TCTTGATCTGTTTCTCATGTGTCATC 59.407 38.462 0.00 0.00 0.00 2.92
5572 7377 0.749649 ACGAGGCTCTTATCAGGCAG 59.250 55.000 13.50 0.00 41.49 4.85
5613 7418 4.359434 TGTCACTTACCCTGTGCATTTA 57.641 40.909 0.00 0.00 35.58 1.40
5663 7469 8.081633 CCACTTCAGAACTTGTTGCATATTTTA 58.918 33.333 0.00 0.00 0.00 1.52
5666 7472 5.536161 ACCACTTCAGAACTTGTTGCATATT 59.464 36.000 0.00 0.00 0.00 1.28
5667 7473 5.048504 CACCACTTCAGAACTTGTTGCATAT 60.049 40.000 0.00 0.00 0.00 1.78
5707 7513 1.671261 GCTGCTCACTGTGTCACTAGG 60.671 57.143 7.79 0.00 0.00 3.02
5711 7517 0.585357 CTTGCTGCTCACTGTGTCAC 59.415 55.000 7.79 0.00 0.00 3.67
5715 7521 1.241990 ATGGCTTGCTGCTCACTGTG 61.242 55.000 0.17 0.17 42.39 3.66
5747 7553 0.871722 TGGTTTGCACTCCGATTTCG 59.128 50.000 0.00 0.00 39.44 3.46
5748 7554 2.415893 CCATGGTTTGCACTCCGATTTC 60.416 50.000 2.57 0.00 0.00 2.17
5749 7555 1.545582 CCATGGTTTGCACTCCGATTT 59.454 47.619 2.57 0.00 0.00 2.17
5752 7558 0.109532 TTCCATGGTTTGCACTCCGA 59.890 50.000 12.58 0.00 0.00 4.55
5753 7559 1.176527 ATTCCATGGTTTGCACTCCG 58.823 50.000 12.58 0.00 0.00 4.63
5754 7560 3.119137 GGTAATTCCATGGTTTGCACTCC 60.119 47.826 12.58 2.31 35.97 3.85
5763 7570 6.150474 CGTAACAAAGAAGGTAATTCCATGGT 59.850 38.462 12.58 0.00 38.84 3.55


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

AutoCloner maintained by Alex Coulton.