Multiple sequence alignment - TraesCS1B01G319700

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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 TraesCS1B01G319700 chr1B 100.000 3405 0 0 1 3405 543742089 543738685 0.000000e+00 6288.0
1 TraesCS1B01G319700 chr1B 84.192 1689 130 48 686 2310 543581575 543579960 0.000000e+00 1513.0
2 TraesCS1B01G319700 chr1B 92.000 125 8 2 193 317 543581876 543581754 1.260000e-39 174.0
3 TraesCS1B01G319700 chr1B 90.840 131 8 2 323 449 582869038 582869168 4.520000e-39 172.0
4 TraesCS1B01G319700 chr1D 84.299 1675 145 58 684 2310 404240345 404238741 0.000000e+00 1528.0
5 TraesCS1B01G319700 chr1D 83.955 1608 145 46 684 2254 404261380 404259849 0.000000e+00 1435.0
6 TraesCS1B01G319700 chr1D 83.871 372 56 2 3037 3405 55406116 55405746 5.410000e-93 351.0
7 TraesCS1B01G319700 chr1D 83.598 378 55 5 3033 3405 410067195 410067570 6.990000e-92 348.0
8 TraesCS1B01G319700 chr1D 83.377 379 54 8 3033 3405 348003932 348003557 3.250000e-90 342.0
9 TraesCS1B01G319700 chr1D 93.814 194 9 3 1 194 404262023 404261833 4.300000e-74 289.0
10 TraesCS1B01G319700 chr1D 82.210 371 25 22 2328 2691 404238584 404238248 7.190000e-72 281.0
11 TraesCS1B01G319700 chr1D 84.053 301 24 7 1 300 404241078 404240801 5.600000e-68 268.0
12 TraesCS1B01G319700 chr1D 86.928 153 12 5 2545 2691 404259659 404259509 7.560000e-37 165.0
13 TraesCS1B01G319700 chr1D 82.443 131 20 3 34 162 404234525 404234396 9.990000e-21 111.0
14 TraesCS1B01G319700 chr1D 95.385 65 3 0 518 582 404240419 404240355 1.670000e-18 104.0
15 TraesCS1B01G319700 chr1D 95.385 65 3 0 518 582 404261454 404261390 1.670000e-18 104.0
16 TraesCS1B01G319700 chr1D 94.118 51 3 0 2824 2874 469018736 469018686 1.010000e-10 78.7
17 TraesCS1B01G319700 chr1D 100.000 33 0 0 2278 2310 404259846 404259814 1.020000e-05 62.1
18 TraesCS1B01G319700 chr1D 100.000 28 0 0 786 813 404240205 404240178 6.000000e-03 52.8
19 TraesCS1B01G319700 chr1D 100.000 28 0 0 786 813 404261226 404261199 6.000000e-03 52.8
20 TraesCS1B01G319700 chr1A 82.294 1683 178 65 686 2303 499928030 499926403 0.000000e+00 1347.0
21 TraesCS1B01G319700 chr1A 84.540 1119 104 32 686 1766 499809509 499808422 0.000000e+00 1044.0
22 TraesCS1B01G319700 chr1A 88.270 503 30 10 1811 2310 499808282 499807806 2.950000e-160 575.0
23 TraesCS1B01G319700 chr1A 82.000 550 60 19 2869 3405 499923147 499922624 6.750000e-117 431.0
24 TraesCS1B01G319700 chr1A 85.934 391 26 12 2306 2691 499926336 499925970 1.150000e-104 390.0
25 TraesCS1B01G319700 chr1A 92.553 188 12 2 7 194 499928967 499928782 5.600000e-68 268.0
26 TraesCS1B01G319700 chr1A 88.000 125 14 1 193 317 499809840 499809717 2.740000e-31 147.0
27 TraesCS1B01G319700 chr1A 90.909 88 8 0 2732 2819 499923232 499923145 5.970000e-23 119.0
28 TraesCS1B01G319700 chr1A 100.000 28 0 0 786 813 499809357 499809330 6.000000e-03 52.8
29 TraesCS1B01G319700 chr6B 83.289 377 58 3 3033 3405 484006853 484006478 3.250000e-90 342.0
30 TraesCS1B01G319700 chr6B 90.722 97 7 2 574 670 481696410 481696504 9.920000e-26 128.0
31 TraesCS1B01G319700 chr2D 83.113 379 61 1 3030 3405 572206376 572206754 3.250000e-90 342.0
32 TraesCS1B01G319700 chr2D 83.069 378 57 5 3033 3405 11667675 11667300 1.510000e-88 337.0
33 TraesCS1B01G319700 chr2D 88.172 186 14 5 325 503 43474043 43474227 7.400000e-52 215.0
34 TraesCS1B01G319700 chr2D 88.060 67 6 2 2824 2889 451299459 451299394 1.010000e-10 78.7
35 TraesCS1B01G319700 chr3D 83.069 378 61 1 3031 3405 104387717 104387340 1.170000e-89 340.0
36 TraesCS1B01G319700 chr3D 94.118 51 3 0 2824 2874 614292132 614292182 1.010000e-10 78.7
37 TraesCS1B01G319700 chr5A 82.979 376 61 2 3033 3405 681859300 681859675 1.510000e-88 337.0
38 TraesCS1B01G319700 chr5A 87.317 205 14 7 323 516 119033226 119033429 1.230000e-54 224.0
39 TraesCS1B01G319700 chr6D 82.677 381 62 2 3029 3405 457662904 457662524 5.440000e-88 335.0
40 TraesCS1B01G319700 chr4D 90.374 187 11 4 325 504 478743613 478743799 4.390000e-59 239.0
41 TraesCS1B01G319700 chr4D 89.894 188 11 5 325 504 478744414 478744601 5.680000e-58 235.0
42 TraesCS1B01G319700 chr4D 87.374 198 18 4 325 515 61155019 61154822 1.590000e-53 220.0
43 TraesCS1B01G319700 chr4D 95.455 88 3 1 578 665 437508982 437508896 4.580000e-29 139.0
44 TraesCS1B01G319700 chr5B 87.000 200 17 5 323 515 546559627 546559824 2.060000e-52 217.0
45 TraesCS1B01G319700 chr5B 85.500 200 20 5 323 515 547585820 547586017 2.070000e-47 200.0
46 TraesCS1B01G319700 chr7B 91.603 131 7 2 323 449 630611034 630611164 9.710000e-41 178.0
47 TraesCS1B01G319700 chr7B 93.182 44 2 1 486 528 468952121 468952164 2.840000e-06 63.9
48 TraesCS1B01G319700 chr4A 94.681 94 4 1 576 669 95187468 95187560 9.850000e-31 145.0
49 TraesCS1B01G319700 chr4A 96.000 50 2 0 2824 2873 187572300 187572349 7.830000e-12 82.4
50 TraesCS1B01G319700 chr6A 94.565 92 4 1 578 669 15768236 15768146 1.270000e-29 141.0
51 TraesCS1B01G319700 chr6A 95.349 86 3 1 580 665 607959947 607960031 5.930000e-28 135.0
52 TraesCS1B01G319700 chr6A 88.136 59 7 0 2824 2882 22432920 22432862 1.700000e-08 71.3
53 TraesCS1B01G319700 chr2B 91.753 97 6 2 573 668 478114467 478114372 2.130000e-27 134.0
54 TraesCS1B01G319700 chr2B 91.579 95 7 1 572 666 694516880 694516787 2.760000e-26 130.0
55 TraesCS1B01G319700 chr2B 82.308 130 15 7 401 525 414955826 414955952 4.650000e-19 106.0
56 TraesCS1B01G319700 chr2B 84.685 111 10 6 410 516 17217337 17217230 1.670000e-18 104.0
57 TraesCS1B01G319700 chr3B 91.579 95 7 1 574 668 551052701 551052608 2.760000e-26 130.0
58 TraesCS1B01G319700 chr7A 89.320 103 9 2 566 668 431991002 431990902 9.920000e-26 128.0
59 TraesCS1B01G319700 chr7D 97.917 48 1 0 2824 2871 275790264 275790311 2.180000e-12 84.2
60 TraesCS1B01G319700 chr2A 96.000 50 2 0 2824 2873 78848867 78848818 7.830000e-12 82.4
61 TraesCS1B01G319700 chr3A 94.118 51 3 0 2824 2874 600026577 600026527 1.010000e-10 78.7
62 TraesCS1B01G319700 chr3A 92.593 54 3 1 2824 2876 86366667 86366614 3.640000e-10 76.8


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 TraesCS1B01G319700 chr1B 543738685 543742089 3404 True 6288.000000 6288 100.0000 1 3405 1 chr1B.!!$R1 3404
1 TraesCS1B01G319700 chr1B 543579960 543581876 1916 True 843.500000 1513 88.0960 193 2310 2 chr1B.!!$R2 2117
2 TraesCS1B01G319700 chr1D 404234396 404241078 6682 True 390.800000 1528 88.0650 1 2691 6 chr1D.!!$R4 2690
3 TraesCS1B01G319700 chr1D 404259509 404262023 2514 True 351.316667 1435 93.3470 1 2691 6 chr1D.!!$R5 2690
4 TraesCS1B01G319700 chr1A 499922624 499928967 6343 True 511.000000 1347 86.7380 7 3405 5 chr1A.!!$R2 3398
5 TraesCS1B01G319700 chr1A 499807806 499809840 2034 True 454.700000 1044 90.2025 193 2310 4 chr1A.!!$R1 2117
6 TraesCS1B01G319700 chr4D 478743613 478744601 988 False 237.000000 239 90.1340 325 504 2 chr4D.!!$F1 179

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
381 1020 0.896923 ATTCAACCGTGGCAATGCAT 59.103 45.0 7.79 0.0 0.0 3.96 F
1071 1898 0.031716 TCCCACTCCCCTCAGATCAG 60.032 60.0 0.00 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 3421 0.608640 ACTCACTCACGAATCCACCC 59.391 55.0 0.00 0.0 0.0 4.61 R
2991 8940 0.037303 AGAATGGGCCGCTCATATGG 59.963 55.0 6.06 0.0 0.0 2.74 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
124 126 3.983044 AGCACCGAGATTTTAAGAGGT 57.017 42.857 0.00 0.00 0.00 3.85
133 135 6.149474 CCGAGATTTTAAGAGGTTGATGTGTT 59.851 38.462 0.00 0.00 0.00 3.32
178 180 9.604626 GGAAAGAATAATGCAAATCTTATCTCG 57.395 33.333 0.00 0.00 32.13 4.04
184 186 6.932356 AATGCAAATCTTATCTCGTCACAT 57.068 33.333 0.00 0.00 0.00 3.21
219 512 1.457346 AGGTGTTCGGTACCGTAGAG 58.543 55.000 32.16 5.76 43.06 2.43
225 518 3.438087 TGTTCGGTACCGTAGAGAAGAAG 59.562 47.826 32.16 1.28 40.74 2.85
277 732 5.018539 TGGACAGAAATATAACTCCACGG 57.981 43.478 0.00 0.00 0.00 4.94
302 757 9.243637 GGCAATTAAATTTACTATTCGCATGAA 57.756 29.630 0.00 0.00 38.76 2.57
377 1016 3.631250 AGGATAATTCAACCGTGGCAAT 58.369 40.909 0.00 0.00 0.00 3.56
378 1017 3.381272 AGGATAATTCAACCGTGGCAATG 59.619 43.478 0.00 0.00 0.00 2.82
381 1020 0.896923 ATTCAACCGTGGCAATGCAT 59.103 45.000 7.79 0.00 0.00 3.96
426 1068 5.682943 TGAGGACCTAATTTCAACGTTTG 57.317 39.130 0.00 0.00 0.00 2.93
437 1079 9.825972 CTAATTTCAACGTTTGTCATACTTGAT 57.174 29.630 0.00 1.04 33.56 2.57
456 1101 6.151144 ACTTGATTATAAGTGGAGTTTGGCAC 59.849 38.462 0.00 0.00 39.33 5.01
473 1118 1.859998 GCACGTGAAGCAGGTTTTGTC 60.860 52.381 22.23 0.00 29.69 3.18
504 1284 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
505 1285 2.669910 TTGCAACGCACGGGCATA 60.670 55.556 11.77 0.00 38.71 3.14
507 1287 2.024588 GCAACGCACGGGCATATG 59.975 61.111 11.77 6.17 41.24 1.78
509 1289 1.433053 GCAACGCACGGGCATATGTA 61.433 55.000 11.77 0.00 41.24 2.29
516 1296 3.119602 CGCACGGGCATATGTACTAGTAT 60.120 47.826 11.77 0.00 41.24 2.12
520 1300 6.039493 GCACGGGCATATGTACTAGTATATCT 59.961 42.308 14.69 3.82 40.72 1.98
593 1379 3.957591 AAAAACTACTCCCTCCGTCTC 57.042 47.619 0.00 0.00 0.00 3.36
594 1380 2.599408 AAACTACTCCCTCCGTCTCA 57.401 50.000 0.00 0.00 0.00 3.27
595 1381 2.830651 AACTACTCCCTCCGTCTCAT 57.169 50.000 0.00 0.00 0.00 2.90
596 1382 3.947612 AACTACTCCCTCCGTCTCATA 57.052 47.619 0.00 0.00 0.00 2.15
597 1383 3.947612 ACTACTCCCTCCGTCTCATAA 57.052 47.619 0.00 0.00 0.00 1.90
598 1384 4.456662 ACTACTCCCTCCGTCTCATAAT 57.543 45.455 0.00 0.00 0.00 1.28
599 1385 5.579753 ACTACTCCCTCCGTCTCATAATA 57.420 43.478 0.00 0.00 0.00 0.98
600 1386 5.315348 ACTACTCCCTCCGTCTCATAATAC 58.685 45.833 0.00 0.00 0.00 1.89
601 1387 4.180377 ACTCCCTCCGTCTCATAATACA 57.820 45.455 0.00 0.00 0.00 2.29
602 1388 4.145807 ACTCCCTCCGTCTCATAATACAG 58.854 47.826 0.00 0.00 0.00 2.74
603 1389 3.497332 TCCCTCCGTCTCATAATACAGG 58.503 50.000 0.00 0.00 0.00 4.00
604 1390 3.139584 TCCCTCCGTCTCATAATACAGGA 59.860 47.826 0.00 0.00 0.00 3.86
605 1391 3.256136 CCCTCCGTCTCATAATACAGGAC 59.744 52.174 0.00 0.00 0.00 3.85
606 1392 3.058155 CCTCCGTCTCATAATACAGGACG 60.058 52.174 0.00 0.00 45.92 4.79
607 1393 3.548770 TCCGTCTCATAATACAGGACGT 58.451 45.455 11.70 0.00 45.22 4.34
608 1394 3.949754 TCCGTCTCATAATACAGGACGTT 59.050 43.478 11.70 0.00 45.22 3.99
609 1395 4.400251 TCCGTCTCATAATACAGGACGTTT 59.600 41.667 11.70 0.00 45.22 3.60
610 1396 5.105635 TCCGTCTCATAATACAGGACGTTTT 60.106 40.000 11.70 0.00 45.22 2.43
611 1397 5.579511 CCGTCTCATAATACAGGACGTTTTT 59.420 40.000 11.70 0.00 45.22 1.94
658 1444 8.480643 AAAAAGTCTTACATTATGAGACGGAG 57.519 34.615 0.00 0.00 46.23 4.63
659 1445 5.776173 AGTCTTACATTATGAGACGGAGG 57.224 43.478 0.00 0.00 46.23 4.30
660 1446 4.585162 AGTCTTACATTATGAGACGGAGGG 59.415 45.833 0.00 0.00 46.23 4.30
661 1447 4.583489 GTCTTACATTATGAGACGGAGGGA 59.417 45.833 0.00 0.00 34.53 4.20
662 1448 4.827835 TCTTACATTATGAGACGGAGGGAG 59.172 45.833 0.00 0.00 0.00 4.30
663 1449 3.033659 ACATTATGAGACGGAGGGAGT 57.966 47.619 0.00 0.00 0.00 3.85
664 1450 4.180377 ACATTATGAGACGGAGGGAGTA 57.820 45.455 0.00 0.00 0.00 2.59
665 1451 3.890147 ACATTATGAGACGGAGGGAGTAC 59.110 47.826 0.00 0.00 0.00 2.73
666 1452 3.947612 TTATGAGACGGAGGGAGTACT 57.052 47.619 0.00 0.00 0.00 2.73
667 1453 5.163120 ACATTATGAGACGGAGGGAGTACTA 60.163 44.000 0.00 0.00 0.00 1.82
668 1454 5.579753 TTATGAGACGGAGGGAGTACTAT 57.420 43.478 0.00 0.00 0.00 2.12
669 1455 3.210232 TGAGACGGAGGGAGTACTATG 57.790 52.381 0.00 0.00 0.00 2.23
670 1456 1.881324 GAGACGGAGGGAGTACTATGC 59.119 57.143 0.00 0.00 0.00 3.14
671 1457 1.214673 AGACGGAGGGAGTACTATGCA 59.785 52.381 0.00 0.00 0.00 3.96
672 1458 2.029623 GACGGAGGGAGTACTATGCAA 58.970 52.381 0.00 0.00 0.00 4.08
673 1459 1.755380 ACGGAGGGAGTACTATGCAAC 59.245 52.381 0.00 0.00 0.00 4.17
674 1460 1.068741 CGGAGGGAGTACTATGCAACC 59.931 57.143 0.00 0.00 0.00 3.77
675 1461 1.068741 GGAGGGAGTACTATGCAACCG 59.931 57.143 0.00 0.00 0.00 4.44
676 1462 1.755380 GAGGGAGTACTATGCAACCGT 59.245 52.381 0.00 0.00 0.00 4.83
677 1463 1.755380 AGGGAGTACTATGCAACCGTC 59.245 52.381 0.00 0.00 0.00 4.79
678 1464 1.479323 GGGAGTACTATGCAACCGTCA 59.521 52.381 0.00 0.00 0.00 4.35
679 1465 2.093869 GGGAGTACTATGCAACCGTCAA 60.094 50.000 0.00 0.00 0.00 3.18
680 1466 3.592059 GGAGTACTATGCAACCGTCAAA 58.408 45.455 0.00 0.00 0.00 2.69
681 1467 3.998341 GGAGTACTATGCAACCGTCAAAA 59.002 43.478 0.00 0.00 0.00 2.44
682 1468 4.453136 GGAGTACTATGCAACCGTCAAAAA 59.547 41.667 0.00 0.00 0.00 1.94
718 1504 2.093152 GCGATCAAAATGGCAAAAGCTG 59.907 45.455 0.00 0.00 36.68 4.24
730 1516 2.290641 GCAAAAGCTGTATATGACCGGG 59.709 50.000 6.32 0.00 0.00 5.73
752 1540 3.486108 GCATATGACTCTAACAACGACGG 59.514 47.826 6.97 0.00 0.00 4.79
796 1584 1.675641 CGGAGGAAAAGGTGGCCAG 60.676 63.158 5.11 0.00 0.00 4.85
825 1614 5.930837 TTGTCCAAAAGTTCACCATTTCT 57.069 34.783 0.00 0.00 0.00 2.52
859 1648 3.053828 GCCAGCTGCCACATTGTT 58.946 55.556 8.66 0.00 0.00 2.83
871 1660 4.404073 TGCCACATTGTTCAAAACCTTACT 59.596 37.500 0.00 0.00 0.00 2.24
960 1785 2.205152 ACGCGTACCACCACCTTCT 61.205 57.895 11.67 0.00 0.00 2.85
997 1822 1.659233 CAGCAAACCACGGCATGAA 59.341 52.632 0.00 0.00 0.00 2.57
1028 1853 1.502163 GCACAGCTCGCAAGTTCACT 61.502 55.000 0.00 0.00 39.48 3.41
1046 1871 3.229156 TAGTCACAACACCGGCCGG 62.229 63.158 42.17 42.17 42.03 6.13
1071 1898 0.031716 TCCCACTCCCCTCAGATCAG 60.032 60.000 0.00 0.00 0.00 2.90
1136 1979 1.299620 CGGTGACCGTCTTCGTTGT 60.300 57.895 17.28 0.00 42.73 3.32
1142 1985 2.019951 CCGTCTTCGTTGTGGTCGG 61.020 63.158 0.00 0.00 35.01 4.79
1214 2057 2.048127 GCTCGTGGACCAGTGGAC 60.048 66.667 18.40 10.15 0.00 4.02
1216 2059 2.920912 TCGTGGACCAGTGGACCC 60.921 66.667 25.26 20.02 36.73 4.46
1253 2096 2.499205 CGCGCTGGGTATCTGGAA 59.501 61.111 5.56 0.00 0.00 3.53
1341 2196 1.148273 GTGAGTGAGGCCACACCAA 59.852 57.895 27.17 14.59 45.54 3.67
1389 2253 3.211865 TCTGTCGTATATTCTGGACGCT 58.788 45.455 0.00 0.00 36.54 5.07
1428 2301 6.071616 CCGATTTTCAATAGGGGTTTCTTTGA 60.072 38.462 0.00 0.00 0.00 2.69
1433 2306 6.387192 TCAATAGGGGTTTCTTTGATCTGA 57.613 37.500 0.00 0.00 0.00 3.27
1434 2307 6.973642 TCAATAGGGGTTTCTTTGATCTGAT 58.026 36.000 0.00 0.00 0.00 2.90
1438 2311 6.642733 AGGGGTTTCTTTGATCTGATAGAA 57.357 37.500 0.00 0.00 0.00 2.10
1439 2312 7.032598 AGGGGTTTCTTTGATCTGATAGAAA 57.967 36.000 9.08 9.08 35.04 2.52
1482 2355 3.764466 CCTCTGTCGCCGGAGCTT 61.764 66.667 5.05 0.00 41.94 3.74
1542 2419 2.206576 AACCCATCTGTTTCTGCCTC 57.793 50.000 0.00 0.00 0.00 4.70
1545 2422 3.118531 ACCCATCTGTTTCTGCCTCTAT 58.881 45.455 0.00 0.00 0.00 1.98
1546 2423 3.525199 ACCCATCTGTTTCTGCCTCTATT 59.475 43.478 0.00 0.00 0.00 1.73
1554 2435 7.394016 TCTGTTTCTGCCTCTATTGATTGTTA 58.606 34.615 0.00 0.00 0.00 2.41
1556 2437 7.168219 TGTTTCTGCCTCTATTGATTGTTACT 58.832 34.615 0.00 0.00 0.00 2.24
1559 2440 7.849804 TCTGCCTCTATTGATTGTTACTTTC 57.150 36.000 0.00 0.00 0.00 2.62
1560 2441 6.823689 TCTGCCTCTATTGATTGTTACTTTCC 59.176 38.462 0.00 0.00 0.00 3.13
1561 2442 6.721318 TGCCTCTATTGATTGTTACTTTCCT 58.279 36.000 0.00 0.00 0.00 3.36
1562 2443 7.175104 TGCCTCTATTGATTGTTACTTTCCTT 58.825 34.615 0.00 0.00 0.00 3.36
1567 2448 8.092068 TCTATTGATTGTTACTTTCCTTGACGA 58.908 33.333 0.00 0.00 0.00 4.20
1635 2542 4.080015 TGGACCAATATCCAAGGAACGATT 60.080 41.667 0.00 0.00 46.08 3.34
1650 2557 0.826715 CGATTCCTGAAGAGCTGGGA 59.173 55.000 0.00 0.00 36.34 4.37
1668 2575 3.140144 TGGGAAACTTGGAGAACCTGAAT 59.860 43.478 0.00 0.00 37.04 2.57
1698 2605 2.857186 TGCACAACAATAGCCTCTCA 57.143 45.000 0.00 0.00 0.00 3.27
1754 2661 1.143305 CTGAAACAGCTGTGAGTCCG 58.857 55.000 22.49 10.86 0.00 4.79
1755 2662 0.464036 TGAAACAGCTGTGAGTCCGT 59.536 50.000 22.49 0.00 0.00 4.69
1756 2663 1.140816 GAAACAGCTGTGAGTCCGTC 58.859 55.000 22.49 5.81 0.00 4.79
1809 2882 2.417339 TGTTCTGCTCGTACAGTGAC 57.583 50.000 0.00 7.94 38.84 3.67
1887 3001 1.444119 GCACCTTCAACAGAACCGCA 61.444 55.000 0.00 0.00 0.00 5.69
1953 3067 2.287427 ACGAGTGTGTAAGTTGGACGAG 60.287 50.000 0.00 0.00 0.00 4.18
2008 3122 6.039382 TCTCTCTCGACGATCAATTAATCCAA 59.961 38.462 0.00 0.00 0.00 3.53
2034 3148 5.932619 TCTTCATCTCTATCGTTTTCCCA 57.067 39.130 0.00 0.00 0.00 4.37
2039 3153 6.075315 TCATCTCTATCGTTTTCCCATCCTA 58.925 40.000 0.00 0.00 0.00 2.94
2080 3194 0.884704 AAACAACGATCTGTGCGGCT 60.885 50.000 0.00 0.00 0.00 5.52
2206 3352 5.488341 GGAGTGAAGAATAAACTGGCAGTA 58.512 41.667 22.37 6.57 0.00 2.74
2207 3353 5.351740 GGAGTGAAGAATAAACTGGCAGTAC 59.648 44.000 22.37 11.78 0.00 2.73
2208 3354 6.115448 AGTGAAGAATAAACTGGCAGTACT 57.885 37.500 22.37 13.97 0.00 2.73
2225 3371 6.989169 GGCAGTACTACTACTACTACTAGCAA 59.011 42.308 0.00 0.00 31.46 3.91
2265 3411 1.165907 CGCCCGGTTCATGCATGTAT 61.166 55.000 25.43 0.00 0.00 2.29
2271 3421 4.261155 CCCGGTTCATGCATGTATTACTTG 60.261 45.833 25.43 14.46 0.00 3.16
2312 3573 0.740737 AATTTAGCTGCGTGCCATCC 59.259 50.000 0.00 0.00 44.23 3.51
2404 3727 6.363357 CGATCGAATATATTCACAGAGTTGCA 59.637 38.462 22.22 0.00 36.61 4.08
2410 3733 3.844577 ATTCACAGAGTTGCATTGCTC 57.155 42.857 10.49 3.43 0.00 4.26
2432 3755 3.833706 GTGCTTGAGTTGACTGCAC 57.166 52.632 8.65 8.65 45.23 4.57
2456 3779 1.315690 TCGTTCTCTGTTCCTGTCGT 58.684 50.000 0.00 0.00 0.00 4.34
2457 3780 1.001706 TCGTTCTCTGTTCCTGTCGTG 60.002 52.381 0.00 0.00 0.00 4.35
2458 3781 1.140816 GTTCTCTGTTCCTGTCGTGC 58.859 55.000 0.00 0.00 0.00 5.34
2459 3782 0.318699 TTCTCTGTTCCTGTCGTGCG 60.319 55.000 0.00 0.00 0.00 5.34
2460 3783 1.007271 CTCTGTTCCTGTCGTGCGT 60.007 57.895 0.00 0.00 0.00 5.24
2461 3784 0.597637 CTCTGTTCCTGTCGTGCGTT 60.598 55.000 0.00 0.00 0.00 4.84
2462 3785 0.596600 TCTGTTCCTGTCGTGCGTTC 60.597 55.000 0.00 0.00 0.00 3.95
2463 3786 0.874175 CTGTTCCTGTCGTGCGTTCA 60.874 55.000 0.00 0.00 0.00 3.18
2464 3787 0.874175 TGTTCCTGTCGTGCGTTCAG 60.874 55.000 10.45 10.45 0.00 3.02
2465 3788 0.596600 GTTCCTGTCGTGCGTTCAGA 60.597 55.000 15.77 5.23 0.00 3.27
2466 3789 0.103390 TTCCTGTCGTGCGTTCAGAA 59.897 50.000 15.77 8.98 0.00 3.02
2467 3790 0.596600 TCCTGTCGTGCGTTCAGAAC 60.597 55.000 2.85 2.85 0.00 3.01
2468 3791 0.874175 CCTGTCGTGCGTTCAGAACA 60.874 55.000 13.82 0.00 0.00 3.18
2469 3792 0.504384 CTGTCGTGCGTTCAGAACAG 59.496 55.000 13.82 7.33 32.82 3.16
2470 3793 1.201825 GTCGTGCGTTCAGAACAGC 59.798 57.895 13.82 16.18 0.00 4.40
2471 3794 1.067416 TCGTGCGTTCAGAACAGCT 59.933 52.632 22.27 0.00 33.95 4.24
2472 3795 0.529773 TCGTGCGTTCAGAACAGCTT 60.530 50.000 22.27 0.00 33.95 3.74
2639 3985 1.134401 CCTCAACGGTGTGGATGCTAT 60.134 52.381 16.62 0.00 40.28 2.97
2657 4003 3.118371 GCTATTTGGCAGTACAGTACCCT 60.118 47.826 7.13 0.00 0.00 4.34
2662 4008 2.706723 TGGCAGTACAGTACCCTTTTGA 59.293 45.455 7.13 0.00 0.00 2.69
2663 4009 3.244422 TGGCAGTACAGTACCCTTTTGAG 60.244 47.826 7.13 0.00 0.00 3.02
2664 4010 3.007614 GGCAGTACAGTACCCTTTTGAGA 59.992 47.826 7.13 0.00 0.00 3.27
2714 5891 5.060662 TGTGAATCAGTCGAGTCCTAAAG 57.939 43.478 0.00 0.00 35.34 1.85
2719 5896 3.650139 TCAGTCGAGTCCTAAAGTTTGC 58.350 45.455 0.00 0.00 0.00 3.68
2740 5917 5.869579 TGCTGTGAAAAGAGTAAGGAAGAT 58.130 37.500 0.00 0.00 0.00 2.40
2743 5920 6.428159 GCTGTGAAAAGAGTAAGGAAGATGAA 59.572 38.462 0.00 0.00 0.00 2.57
2754 8695 1.135286 GGAAGATGAAAAGCAAGGCCG 60.135 52.381 0.00 0.00 0.00 6.13
2785 8726 4.092279 CTGTGGCATAGAGAGGATGGATA 58.908 47.826 5.14 0.00 0.00 2.59
2819 8760 7.362662 CACTGTGCAATTATTCAACAACTACT 58.637 34.615 0.00 0.00 0.00 2.57
2820 8761 7.535258 CACTGTGCAATTATTCAACAACTACTC 59.465 37.037 0.00 0.00 0.00 2.59
2821 8762 6.908825 TGTGCAATTATTCAACAACTACTCC 58.091 36.000 0.00 0.00 0.00 3.85
2822 8763 6.072175 TGTGCAATTATTCAACAACTACTCCC 60.072 38.462 0.00 0.00 0.00 4.30
2823 8764 6.151144 GTGCAATTATTCAACAACTACTCCCT 59.849 38.462 0.00 0.00 0.00 4.20
2824 8765 6.374333 TGCAATTATTCAACAACTACTCCCTC 59.626 38.462 0.00 0.00 0.00 4.30
2825 8766 6.183360 GCAATTATTCAACAACTACTCCCTCC 60.183 42.308 0.00 0.00 0.00 4.30
2826 8767 3.611766 ATTCAACAACTACTCCCTCCG 57.388 47.619 0.00 0.00 0.00 4.63
2827 8768 2.005370 TCAACAACTACTCCCTCCGT 57.995 50.000 0.00 0.00 0.00 4.69
2828 8769 2.322658 TCAACAACTACTCCCTCCGTT 58.677 47.619 0.00 0.00 0.00 4.44
2829 8770 2.701951 TCAACAACTACTCCCTCCGTTT 59.298 45.455 0.00 0.00 0.00 3.60
2830 8771 3.135167 TCAACAACTACTCCCTCCGTTTT 59.865 43.478 0.00 0.00 0.00 2.43
2831 8772 4.344679 TCAACAACTACTCCCTCCGTTTTA 59.655 41.667 0.00 0.00 0.00 1.52
2832 8773 5.012354 TCAACAACTACTCCCTCCGTTTTAT 59.988 40.000 0.00 0.00 0.00 1.40
2833 8774 5.082251 ACAACTACTCCCTCCGTTTTATC 57.918 43.478 0.00 0.00 0.00 1.75
2834 8775 4.081254 ACAACTACTCCCTCCGTTTTATCC 60.081 45.833 0.00 0.00 0.00 2.59
2835 8776 3.716431 ACTACTCCCTCCGTTTTATCCA 58.284 45.455 0.00 0.00 0.00 3.41
2836 8777 4.296056 ACTACTCCCTCCGTTTTATCCAT 58.704 43.478 0.00 0.00 0.00 3.41
2837 8778 4.720273 ACTACTCCCTCCGTTTTATCCATT 59.280 41.667 0.00 0.00 0.00 3.16
2838 8779 4.586306 ACTCCCTCCGTTTTATCCATTT 57.414 40.909 0.00 0.00 0.00 2.32
2839 8780 4.524053 ACTCCCTCCGTTTTATCCATTTC 58.476 43.478 0.00 0.00 0.00 2.17
2840 8781 4.227527 ACTCCCTCCGTTTTATCCATTTCT 59.772 41.667 0.00 0.00 0.00 2.52
2841 8782 5.427481 ACTCCCTCCGTTTTATCCATTTCTA 59.573 40.000 0.00 0.00 0.00 2.10
2842 8783 5.925509 TCCCTCCGTTTTATCCATTTCTAG 58.074 41.667 0.00 0.00 0.00 2.43
2843 8784 5.063880 CCCTCCGTTTTATCCATTTCTAGG 58.936 45.833 0.00 0.00 0.00 3.02
2844 8785 5.163237 CCCTCCGTTTTATCCATTTCTAGGA 60.163 44.000 0.00 0.00 39.97 2.94
2845 8786 5.758784 CCTCCGTTTTATCCATTTCTAGGAC 59.241 44.000 0.00 0.00 38.13 3.85
2846 8787 6.302535 TCCGTTTTATCCATTTCTAGGACA 57.697 37.500 0.00 0.00 38.13 4.02
2847 8788 6.713276 TCCGTTTTATCCATTTCTAGGACAA 58.287 36.000 0.00 0.00 38.13 3.18
2848 8789 6.821665 TCCGTTTTATCCATTTCTAGGACAAG 59.178 38.462 0.00 0.00 38.13 3.16
2849 8790 6.598064 CCGTTTTATCCATTTCTAGGACAAGT 59.402 38.462 0.00 0.00 38.13 3.16
2850 8791 7.767198 CCGTTTTATCCATTTCTAGGACAAGTA 59.233 37.037 0.00 0.00 38.13 2.24
2851 8792 9.326413 CGTTTTATCCATTTCTAGGACAAGTAT 57.674 33.333 0.00 0.00 38.13 2.12
2855 8796 9.847224 TTATCCATTTCTAGGACAAGTATTTCC 57.153 33.333 0.00 0.00 38.13 3.13
2856 8797 6.346096 TCCATTTCTAGGACAAGTATTTCCG 58.654 40.000 0.00 0.00 36.95 4.30
2857 8798 5.527582 CCATTTCTAGGACAAGTATTTCCGG 59.472 44.000 0.00 0.00 36.95 5.14
2858 8799 6.346096 CATTTCTAGGACAAGTATTTCCGGA 58.654 40.000 0.00 0.00 36.95 5.14
2859 8800 4.996788 TCTAGGACAAGTATTTCCGGAC 57.003 45.455 1.83 0.00 36.95 4.79
2860 8801 2.667473 AGGACAAGTATTTCCGGACG 57.333 50.000 1.83 0.00 36.95 4.79
2861 8802 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
2862 8803 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
2863 8804 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2864 8805 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2865 8806 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2866 8807 0.325016 AGTATTTCCGGACGGAGGGT 60.325 55.000 13.64 6.69 46.06 4.34
2867 8808 0.179092 GTATTTCCGGACGGAGGGTG 60.179 60.000 13.64 0.00 46.06 4.61
2868 8809 0.615544 TATTTCCGGACGGAGGGTGT 60.616 55.000 13.64 2.76 46.06 4.16
2869 8810 0.615544 ATTTCCGGACGGAGGGTGTA 60.616 55.000 13.64 0.00 46.06 2.90
2870 8811 1.535204 TTTCCGGACGGAGGGTGTAC 61.535 60.000 13.64 0.00 46.06 2.90
2884 8825 5.511545 GGAGGGTGTACATATTCATCAGGAC 60.512 48.000 0.00 0.00 0.00 3.85
2889 8830 7.819900 GGGTGTACATATTCATCAGGACTAATC 59.180 40.741 0.00 0.00 0.00 1.75
2943 8884 9.859692 GTACTAAAAATACCAAGTTATCATCGC 57.140 33.333 0.00 0.00 0.00 4.58
2958 8899 0.818040 ATCGCATTAAACCCCGAGCC 60.818 55.000 0.00 0.00 32.86 4.70
2965 8906 1.455248 TAAACCCCGAGCCAATTTCG 58.545 50.000 0.00 0.00 37.78 3.46
2971 8912 1.705337 CCGAGCCAATTTCGCACGAT 61.705 55.000 13.44 0.00 41.93 3.73
2983 8932 3.118454 CACGATCGCGGGTTTGCT 61.118 61.111 16.60 0.00 43.17 3.91
3016 9544 0.753111 GAGCGGCCCATTCTCCAAAT 60.753 55.000 0.00 0.00 0.00 2.32
3117 9673 9.554395 TGACAACAATAACAGAGATTCAACTAA 57.446 29.630 0.00 0.00 0.00 2.24
3163 9719 7.923344 AGATGAATAGATGAAACCTAAGACACG 59.077 37.037 0.00 0.00 0.00 4.49
3173 9729 4.780275 ACCTAAGACACGGACTAGAAAC 57.220 45.455 0.00 0.00 0.00 2.78
3227 9783 4.680110 GTCATAATTACGTACGATGCAGCT 59.320 41.667 24.41 0.00 0.00 4.24
3237 9793 1.429927 CGATGCAGCTGGAGCAGAAG 61.430 60.000 23.47 2.90 46.36 2.85
3239 9795 3.132801 GCAGCTGGAGCAGAAGCC 61.133 66.667 17.12 0.00 45.16 4.35
3253 9809 1.280421 AGAAGCCCTGGAGTTGATGTC 59.720 52.381 0.00 0.00 0.00 3.06
3257 9813 1.450312 CCTGGAGTTGATGTCGGCC 60.450 63.158 0.00 0.00 0.00 6.13
3258 9814 1.296392 CTGGAGTTGATGTCGGCCA 59.704 57.895 2.24 0.00 0.00 5.36
3259 9815 0.107508 CTGGAGTTGATGTCGGCCAT 60.108 55.000 2.24 0.00 36.13 4.40
3260 9816 0.392863 TGGAGTTGATGTCGGCCATG 60.393 55.000 2.24 0.00 32.56 3.66
3261 9817 0.392998 GGAGTTGATGTCGGCCATGT 60.393 55.000 2.24 0.00 32.56 3.21
3262 9818 1.009829 GAGTTGATGTCGGCCATGTC 58.990 55.000 2.24 0.00 32.56 3.06
3265 9821 1.745087 GTTGATGTCGGCCATGTCATT 59.255 47.619 2.24 0.00 32.56 2.57
3304 9860 2.159462 GGTCGGATAAGAAGTCGTCGTT 60.159 50.000 0.00 0.00 0.00 3.85
3305 9861 2.844804 GTCGGATAAGAAGTCGTCGTTG 59.155 50.000 0.00 0.00 0.00 4.10
3306 9862 2.159476 TCGGATAAGAAGTCGTCGTTGG 60.159 50.000 0.00 0.00 0.00 3.77
3307 9863 2.415090 CGGATAAGAAGTCGTCGTTGGT 60.415 50.000 0.00 0.00 0.00 3.67
3309 9865 3.366679 GGATAAGAAGTCGTCGTTGGTGA 60.367 47.826 0.00 0.00 0.00 4.02
3310 9866 2.589798 AAGAAGTCGTCGTTGGTGAA 57.410 45.000 0.00 0.00 0.00 3.18
3311 9867 2.135664 AGAAGTCGTCGTTGGTGAAG 57.864 50.000 0.00 0.00 0.00 3.02
3312 9868 1.407979 AGAAGTCGTCGTTGGTGAAGT 59.592 47.619 0.00 0.00 0.00 3.01
3314 9870 0.317603 AGTCGTCGTTGGTGAAGTCG 60.318 55.000 0.00 0.00 0.00 4.18
3315 9871 0.593263 GTCGTCGTTGGTGAAGTCGT 60.593 55.000 0.00 0.00 0.00 4.34
3316 9872 0.101040 TCGTCGTTGGTGAAGTCGTT 59.899 50.000 0.00 0.00 0.00 3.85
3320 9876 1.067364 TCGTTGGTGAAGTCGTTGCTA 59.933 47.619 0.00 0.00 0.00 3.49
3335 9891 4.476410 CTACCAGCAGTCGCGCGA 62.476 66.667 31.40 31.40 45.49 5.87
3336 9892 3.964221 CTACCAGCAGTCGCGCGAA 62.964 63.158 36.57 15.67 45.49 4.70
3358 9914 5.649782 ATGCGATCCCCAAAAATATGATC 57.350 39.130 0.00 0.00 0.00 2.92
3375 9931 2.658321 ATCGCCCCTCTCCCGTACAT 62.658 60.000 0.00 0.00 0.00 2.29
3382 9938 2.031870 CCTCTCCCGTACATGATCACA 58.968 52.381 0.00 0.00 0.00 3.58
3390 9946 2.479560 CGTACATGATCACAAGAGGCGA 60.480 50.000 0.00 0.00 0.00 5.54
3392 9948 1.134580 ACATGATCACAAGAGGCGAGG 60.135 52.381 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 86 0.840617 TGGCCACCTGTAGTTTGTGA 59.159 50.000 0.00 0.00 31.66 3.58
124 126 6.533367 GCTAACTTTTTCAACCAACACATCAA 59.467 34.615 0.00 0.00 0.00 2.57
133 135 7.057894 TCTTTCCTAGCTAACTTTTTCAACCA 58.942 34.615 0.00 0.00 0.00 3.67
202 495 2.744202 TCTTCTCTACGGTACCGAACAC 59.256 50.000 39.52 0.00 42.83 3.32
219 512 7.377766 TGGTCAAATGCATAGTAACTTCTTC 57.622 36.000 0.00 0.00 0.00 2.87
310 800 2.306805 TGAGAAGCCAGAATCCACACAT 59.693 45.455 0.00 0.00 0.00 3.21
311 801 1.699083 TGAGAAGCCAGAATCCACACA 59.301 47.619 0.00 0.00 0.00 3.72
312 802 2.079925 GTGAGAAGCCAGAATCCACAC 58.920 52.381 0.00 0.00 0.00 3.82
313 803 1.699083 TGTGAGAAGCCAGAATCCACA 59.301 47.619 0.00 0.00 0.00 4.17
314 804 2.479566 TGTGAGAAGCCAGAATCCAC 57.520 50.000 0.00 0.00 0.00 4.02
315 805 2.573009 TCATGTGAGAAGCCAGAATCCA 59.427 45.455 0.00 0.00 0.00 3.41
316 806 3.272574 TCATGTGAGAAGCCAGAATCC 57.727 47.619 0.00 0.00 0.00 3.01
317 807 4.005650 TGTTCATGTGAGAAGCCAGAATC 58.994 43.478 0.00 0.00 0.00 2.52
318 808 3.755378 GTGTTCATGTGAGAAGCCAGAAT 59.245 43.478 0.00 0.00 0.00 2.40
319 809 3.141398 GTGTTCATGTGAGAAGCCAGAA 58.859 45.455 0.00 0.00 0.00 3.02
320 810 2.369860 AGTGTTCATGTGAGAAGCCAGA 59.630 45.455 0.00 0.00 0.00 3.86
321 811 2.775890 AGTGTTCATGTGAGAAGCCAG 58.224 47.619 0.00 0.00 0.00 4.85
322 812 2.936919 AGTGTTCATGTGAGAAGCCA 57.063 45.000 0.00 0.00 0.00 4.75
437 1079 3.749088 CACGTGCCAAACTCCACTTATAA 59.251 43.478 0.82 0.00 0.00 0.98
439 1081 2.151202 CACGTGCCAAACTCCACTTAT 58.849 47.619 0.82 0.00 0.00 1.73
450 1092 1.034838 AAACCTGCTTCACGTGCCAA 61.035 50.000 11.67 0.00 0.00 4.52
456 1101 2.842208 TTGACAAAACCTGCTTCACG 57.158 45.000 0.00 0.00 0.00 4.35
520 1300 8.379428 AGTCATGCACCATGGTAGATATATAA 57.621 34.615 19.28 0.00 41.66 0.98
583 1369 3.256136 GTCCTGTATTATGAGACGGAGGG 59.744 52.174 0.00 0.00 0.00 4.30
585 1371 4.148563 CGTCCTGTATTATGAGACGGAG 57.851 50.000 3.08 0.00 44.86 4.63
633 1419 7.549488 CCTCCGTCTCATAATGTAAGACTTTTT 59.451 37.037 0.00 0.00 37.79 1.94
634 1420 7.042335 CCTCCGTCTCATAATGTAAGACTTTT 58.958 38.462 0.00 0.00 37.79 2.27
635 1421 6.407074 CCCTCCGTCTCATAATGTAAGACTTT 60.407 42.308 0.00 0.00 37.79 2.66
636 1422 5.069251 CCCTCCGTCTCATAATGTAAGACTT 59.931 44.000 0.00 0.00 37.79 3.01
637 1423 4.585162 CCCTCCGTCTCATAATGTAAGACT 59.415 45.833 0.00 0.00 37.79 3.24
638 1424 4.583489 TCCCTCCGTCTCATAATGTAAGAC 59.417 45.833 0.00 0.00 36.82 3.01
639 1425 4.800023 TCCCTCCGTCTCATAATGTAAGA 58.200 43.478 0.00 0.00 0.00 2.10
640 1426 4.585162 ACTCCCTCCGTCTCATAATGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
641 1427 4.543689 ACTCCCTCCGTCTCATAATGTAA 58.456 43.478 0.00 0.00 0.00 2.41
642 1428 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
643 1429 3.033659 ACTCCCTCCGTCTCATAATGT 57.966 47.619 0.00 0.00 0.00 2.71
644 1430 4.145807 AGTACTCCCTCCGTCTCATAATG 58.854 47.826 0.00 0.00 0.00 1.90
645 1431 4.456662 AGTACTCCCTCCGTCTCATAAT 57.543 45.455 0.00 0.00 0.00 1.28
646 1432 3.947612 AGTACTCCCTCCGTCTCATAA 57.052 47.619 0.00 0.00 0.00 1.90
647 1433 4.806625 GCATAGTACTCCCTCCGTCTCATA 60.807 50.000 0.00 0.00 0.00 2.15
648 1434 3.757270 CATAGTACTCCCTCCGTCTCAT 58.243 50.000 0.00 0.00 0.00 2.90
649 1435 2.748798 GCATAGTACTCCCTCCGTCTCA 60.749 54.545 0.00 0.00 0.00 3.27
650 1436 1.881324 GCATAGTACTCCCTCCGTCTC 59.119 57.143 0.00 0.00 0.00 3.36
651 1437 1.214673 TGCATAGTACTCCCTCCGTCT 59.785 52.381 0.00 0.00 0.00 4.18
652 1438 1.688772 TGCATAGTACTCCCTCCGTC 58.311 55.000 0.00 0.00 0.00 4.79
653 1439 1.755380 GTTGCATAGTACTCCCTCCGT 59.245 52.381 0.00 0.00 0.00 4.69
654 1440 1.068741 GGTTGCATAGTACTCCCTCCG 59.931 57.143 0.00 0.00 0.00 4.63
655 1441 1.068741 CGGTTGCATAGTACTCCCTCC 59.931 57.143 0.00 0.00 0.00 4.30
656 1442 1.755380 ACGGTTGCATAGTACTCCCTC 59.245 52.381 0.00 0.00 0.00 4.30
657 1443 1.755380 GACGGTTGCATAGTACTCCCT 59.245 52.381 0.00 0.00 0.00 4.20
658 1444 1.479323 TGACGGTTGCATAGTACTCCC 59.521 52.381 0.00 0.00 0.00 4.30
659 1445 2.953466 TGACGGTTGCATAGTACTCC 57.047 50.000 0.00 0.00 0.00 3.85
660 1446 5.600908 TTTTTGACGGTTGCATAGTACTC 57.399 39.130 0.00 0.00 0.00 2.59
718 1504 4.402793 AGAGTCATATGCCCGGTCATATAC 59.597 45.833 17.17 14.61 37.50 1.47
730 1516 3.486108 CCGTCGTTGTTAGAGTCATATGC 59.514 47.826 0.00 0.00 0.00 3.14
752 1540 4.216902 ACTGCCGGTTTAATTTGGACTTAC 59.783 41.667 1.90 0.00 0.00 2.34
796 1584 2.224018 TGAACTTTTGGACAATGGCAGC 60.224 45.455 0.00 0.00 0.00 5.25
825 1614 2.562298 CTGGCCACCTTTGAAATGCTAA 59.438 45.455 0.00 0.00 0.00 3.09
853 1642 8.925161 TCAAGAAAGTAAGGTTTTGAACAATG 57.075 30.769 0.00 0.00 0.00 2.82
854 1643 7.706607 GCTCAAGAAAGTAAGGTTTTGAACAAT 59.293 33.333 0.00 0.00 0.00 2.71
859 1648 5.221048 GCTGCTCAAGAAAGTAAGGTTTTGA 60.221 40.000 0.00 0.00 0.00 2.69
871 1660 1.682323 TGCAATGTGCTGCTCAAGAAA 59.318 42.857 8.59 0.00 45.31 2.52
960 1785 1.639628 TGCGGGGTTTTATAGGGGAAA 59.360 47.619 0.00 0.00 0.00 3.13
997 1822 2.641305 GAGCTGTGCTTTGGATGATCT 58.359 47.619 0.00 0.00 39.88 2.75
1028 1853 2.340809 CGGCCGGTGTTGTGACTA 59.659 61.111 20.10 0.00 0.00 2.59
1201 2044 4.699522 GCGGGTCCACTGGTCCAC 62.700 72.222 12.79 1.53 32.60 4.02
1205 2048 3.001406 GTAGGCGGGTCCACTGGT 61.001 66.667 0.00 0.00 37.29 4.00
1208 2051 2.683933 CCTGTAGGCGGGTCCACT 60.684 66.667 0.00 0.00 36.39 4.00
1210 2053 2.682494 GTCCTGTAGGCGGGTCCA 60.682 66.667 0.00 0.00 41.89 4.02
1214 2057 3.470888 CAGGGTCCTGTAGGCGGG 61.471 72.222 8.78 0.00 42.59 6.13
1216 2059 2.893398 GTCAGGGTCCTGTAGGCG 59.107 66.667 15.77 0.00 43.96 5.52
1243 2086 1.049289 AGCTCCGGGTTCCAGATACC 61.049 60.000 0.00 0.00 34.82 2.73
1247 2090 1.984570 CTCAGCTCCGGGTTCCAGA 60.985 63.158 0.00 0.00 0.00 3.86
1341 2196 1.952621 TGGAAGGGAAGAAGGATCGT 58.047 50.000 0.00 0.00 0.00 3.73
1389 2253 3.887621 AAATCGGATGAAGAGGACGAA 57.112 42.857 0.00 0.00 37.11 3.85
1428 2301 4.217118 GCATGGCCGATTTTTCTATCAGAT 59.783 41.667 0.00 0.00 0.00 2.90
1433 2306 2.571212 TCGCATGGCCGATTTTTCTAT 58.429 42.857 0.00 0.00 31.36 1.98
1434 2307 2.031258 TCGCATGGCCGATTTTTCTA 57.969 45.000 0.00 0.00 31.36 2.10
1438 2311 0.965363 AGGTTCGCATGGCCGATTTT 60.965 50.000 0.00 0.00 37.06 1.82
1439 2312 1.378514 AGGTTCGCATGGCCGATTT 60.379 52.632 0.00 0.00 37.06 2.17
1542 2419 8.251750 TCGTCAAGGAAAGTAACAATCAATAG 57.748 34.615 0.00 0.00 0.00 1.73
1545 2422 6.539649 CTCGTCAAGGAAAGTAACAATCAA 57.460 37.500 0.00 0.00 0.00 2.57
1560 2441 6.369890 CCATATAATCCATCAACCTCGTCAAG 59.630 42.308 0.00 0.00 0.00 3.02
1561 2442 6.230472 CCATATAATCCATCAACCTCGTCAA 58.770 40.000 0.00 0.00 0.00 3.18
1562 2443 5.793817 CCATATAATCCATCAACCTCGTCA 58.206 41.667 0.00 0.00 0.00 4.35
1567 2448 6.398655 AGATGCCATATAATCCATCAACCT 57.601 37.500 10.55 0.00 37.21 3.50
1635 2542 1.734655 AGTTTCCCAGCTCTTCAGGA 58.265 50.000 0.00 0.00 0.00 3.86
1650 2557 4.803452 TGGAATTCAGGTTCTCCAAGTTT 58.197 39.130 7.93 0.00 35.02 2.66
1698 2605 2.872388 CGATGCGGGTATCTGCCCT 61.872 63.158 3.85 0.00 46.47 5.19
1754 2661 1.967066 ACATCGGGAGGAGATCATGAC 59.033 52.381 0.00 0.00 0.00 3.06
1755 2662 2.388526 ACATCGGGAGGAGATCATGA 57.611 50.000 0.00 0.00 0.00 3.07
1756 2663 3.482156 AAACATCGGGAGGAGATCATG 57.518 47.619 0.00 0.00 0.00 3.07
1809 2882 5.879223 AGCCAGACTTGTTTTATCATGAGAG 59.121 40.000 0.09 0.00 0.00 3.20
1953 3067 5.147162 CAACTGGAATTAACGCTGAGAAAC 58.853 41.667 0.00 0.00 0.00 2.78
2008 3122 7.158021 GGGAAAACGATAGAGATGAAGATCAT 58.842 38.462 0.00 0.00 38.98 2.45
2022 3136 6.126409 AGCAAAATAGGATGGGAAAACGATA 58.874 36.000 0.00 0.00 0.00 2.92
2034 3148 5.264395 AGGTTACTGCAAGCAAAATAGGAT 58.736 37.500 0.00 0.00 37.60 3.24
2039 3153 4.144297 TGAGAGGTTACTGCAAGCAAAAT 58.856 39.130 0.00 0.00 37.60 1.82
2080 3194 1.406341 GGGACCATTTGTCGGAATCGA 60.406 52.381 0.00 0.00 45.46 3.59
2092 3206 4.387026 TGATGTTCTTGAAGGGACCATT 57.613 40.909 0.00 0.00 0.00 3.16
2206 3352 5.528320 GCTGCTTGCTAGTAGTAGTAGTAGT 59.472 44.000 17.20 0.00 36.58 2.73
2207 3353 5.049267 GGCTGCTTGCTAGTAGTAGTAGTAG 60.049 48.000 13.97 13.24 42.39 2.57
2208 3354 4.820716 GGCTGCTTGCTAGTAGTAGTAGTA 59.179 45.833 13.97 6.34 42.39 1.82
2225 3371 2.906458 CCCGATTCTCTGGCTGCT 59.094 61.111 0.00 0.00 0.00 4.24
2265 3411 2.635915 ACTCACGAATCCACCCAAGTAA 59.364 45.455 0.00 0.00 0.00 2.24
2271 3421 0.608640 ACTCACTCACGAATCCACCC 59.391 55.000 0.00 0.00 0.00 4.61
2350 3673 1.593006 AGCAACTTAATCGCGATTCCG 59.407 47.619 35.57 27.46 39.16 4.30
2404 3727 0.403271 ACTCAAGCACCCAGAGCAAT 59.597 50.000 0.00 0.00 32.71 3.56
2410 3733 1.233019 CAGTCAACTCAAGCACCCAG 58.767 55.000 0.00 0.00 0.00 4.45
2432 3755 2.287668 ACAGGAACAGAGAACGAACGAG 60.288 50.000 0.14 0.00 0.00 4.18
2456 3779 0.249280 TCGAAGCTGTTCTGAACGCA 60.249 50.000 26.57 12.38 34.79 5.24
2457 3780 0.161870 GTCGAAGCTGTTCTGAACGC 59.838 55.000 21.32 21.32 0.00 4.84
2458 3781 0.431233 CGTCGAAGCTGTTCTGAACG 59.569 55.000 15.18 11.01 0.00 3.95
2459 3782 0.161870 GCGTCGAAGCTGTTCTGAAC 59.838 55.000 16.42 13.49 0.00 3.18
2460 3783 2.517598 GCGTCGAAGCTGTTCTGAA 58.482 52.632 16.42 0.00 0.00 3.02
2461 3784 4.245054 GCGTCGAAGCTGTTCTGA 57.755 55.556 16.42 0.00 0.00 3.27
2469 3792 3.565516 TCATATATGTCAGCGTCGAAGC 58.434 45.455 15.94 15.94 37.41 3.86
2470 3793 5.284897 GTGATCATATATGTCAGCGTCGAAG 59.715 44.000 12.42 0.00 0.00 3.79
2471 3794 5.154222 GTGATCATATATGTCAGCGTCGAA 58.846 41.667 12.42 0.00 0.00 3.71
2472 3795 4.215399 TGTGATCATATATGTCAGCGTCGA 59.785 41.667 12.42 0.00 0.00 4.20
2517 3857 8.089115 ACTAATTTTCTGTTCTGAAGTACTGC 57.911 34.615 0.00 0.00 0.00 4.40
2608 3953 4.335315 CACACCGTTGAGGCATGTAATTAT 59.665 41.667 0.00 0.00 46.52 1.28
2639 3985 3.868619 AAAGGGTACTGTACTGCCAAA 57.131 42.857 16.79 0.00 0.00 3.28
2714 5891 5.751243 TCCTTACTCTTTTCACAGCAAAC 57.249 39.130 0.00 0.00 0.00 2.93
2719 5896 7.969536 TTCATCTTCCTTACTCTTTTCACAG 57.030 36.000 0.00 0.00 0.00 3.66
2740 5917 2.563798 CCAGCGGCCTTGCTTTTCA 61.564 57.895 1.89 0.00 44.46 2.69
2754 8695 3.680620 TATGCCACAGGACGCCAGC 62.681 63.158 0.00 0.00 0.00 4.85
2785 8726 6.602803 TGAATAATTGCACAGTGGACATATGT 59.397 34.615 8.43 8.43 0.00 2.29
2795 8736 7.308589 GGAGTAGTTGTTGAATAATTGCACAGT 60.309 37.037 0.00 0.00 0.00 3.55
2797 8738 6.072175 GGGAGTAGTTGTTGAATAATTGCACA 60.072 38.462 0.00 0.00 0.00 4.57
2819 8760 4.855298 AGAAATGGATAAAACGGAGGGA 57.145 40.909 0.00 0.00 0.00 4.20
2820 8761 5.063880 CCTAGAAATGGATAAAACGGAGGG 58.936 45.833 0.00 0.00 0.00 4.30
2821 8762 5.758784 GTCCTAGAAATGGATAAAACGGAGG 59.241 44.000 0.00 0.00 35.87 4.30
2822 8763 6.346096 TGTCCTAGAAATGGATAAAACGGAG 58.654 40.000 0.00 0.00 35.87 4.63
2823 8764 6.302535 TGTCCTAGAAATGGATAAAACGGA 57.697 37.500 0.00 0.00 35.87 4.69
2824 8765 6.598064 ACTTGTCCTAGAAATGGATAAAACGG 59.402 38.462 0.00 0.00 34.98 4.44
2825 8766 7.611213 ACTTGTCCTAGAAATGGATAAAACG 57.389 36.000 0.00 0.00 34.98 3.60
2829 8770 9.847224 GGAAATACTTGTCCTAGAAATGGATAA 57.153 33.333 0.00 0.00 35.87 1.75
2830 8771 8.148351 CGGAAATACTTGTCCTAGAAATGGATA 58.852 37.037 0.00 0.00 35.87 2.59
2831 8772 6.992715 CGGAAATACTTGTCCTAGAAATGGAT 59.007 38.462 0.00 0.00 35.87 3.41
2832 8773 6.346096 CGGAAATACTTGTCCTAGAAATGGA 58.654 40.000 0.00 0.00 0.00 3.41
2833 8774 5.527582 CCGGAAATACTTGTCCTAGAAATGG 59.472 44.000 0.00 0.00 0.00 3.16
2834 8775 6.258068 GTCCGGAAATACTTGTCCTAGAAATG 59.742 42.308 5.23 0.00 0.00 2.32
2835 8776 6.346896 GTCCGGAAATACTTGTCCTAGAAAT 58.653 40.000 5.23 0.00 0.00 2.17
2836 8777 5.622914 CGTCCGGAAATACTTGTCCTAGAAA 60.623 44.000 5.23 0.00 0.00 2.52
2837 8778 4.142315 CGTCCGGAAATACTTGTCCTAGAA 60.142 45.833 5.23 0.00 0.00 2.10
2838 8779 3.379372 CGTCCGGAAATACTTGTCCTAGA 59.621 47.826 5.23 0.00 0.00 2.43
2839 8780 3.490419 CCGTCCGGAAATACTTGTCCTAG 60.490 52.174 5.23 0.00 37.50 3.02
2840 8781 2.428171 CCGTCCGGAAATACTTGTCCTA 59.572 50.000 5.23 0.00 37.50 2.94
2841 8782 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
2842 8783 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
2843 8784 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2844 8785 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2845 8786 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2846 8787 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2847 8788 0.325016 ACCCTCCGTCCGGAAATACT 60.325 55.000 5.23 0.00 44.66 2.12
2848 8789 0.179092 CACCCTCCGTCCGGAAATAC 60.179 60.000 5.23 0.00 44.66 1.89
2849 8790 0.615544 ACACCCTCCGTCCGGAAATA 60.616 55.000 5.23 0.00 44.66 1.40
2850 8791 0.615544 TACACCCTCCGTCCGGAAAT 60.616 55.000 5.23 0.00 44.66 2.17
2851 8792 1.228831 TACACCCTCCGTCCGGAAA 60.229 57.895 5.23 0.00 44.66 3.13
2852 8793 1.978617 GTACACCCTCCGTCCGGAA 60.979 63.158 5.23 0.00 44.66 4.30
2853 8794 2.361610 GTACACCCTCCGTCCGGA 60.362 66.667 0.00 0.00 42.90 5.14
2854 8795 0.752743 TATGTACACCCTCCGTCCGG 60.753 60.000 0.00 0.00 0.00 5.14
2855 8796 1.325355 ATATGTACACCCTCCGTCCG 58.675 55.000 0.00 0.00 0.00 4.79
2856 8797 2.696707 TGAATATGTACACCCTCCGTCC 59.303 50.000 0.00 0.00 0.00 4.79
2857 8798 4.038763 TGATGAATATGTACACCCTCCGTC 59.961 45.833 0.00 0.00 0.00 4.79
2858 8799 3.964688 TGATGAATATGTACACCCTCCGT 59.035 43.478 0.00 0.00 0.00 4.69
2859 8800 4.560128 CTGATGAATATGTACACCCTCCG 58.440 47.826 0.00 0.00 0.00 4.63
2860 8801 4.593206 TCCTGATGAATATGTACACCCTCC 59.407 45.833 0.00 0.00 0.00 4.30
2861 8802 5.305644 AGTCCTGATGAATATGTACACCCTC 59.694 44.000 0.00 0.00 0.00 4.30
2862 8803 5.219739 AGTCCTGATGAATATGTACACCCT 58.780 41.667 0.00 0.00 0.00 4.34
2863 8804 5.552870 AGTCCTGATGAATATGTACACCC 57.447 43.478 0.00 0.00 0.00 4.61
2864 8805 8.367911 TGATTAGTCCTGATGAATATGTACACC 58.632 37.037 0.00 0.00 0.00 4.16
2865 8806 9.197694 GTGATTAGTCCTGATGAATATGTACAC 57.802 37.037 0.00 0.00 0.00 2.90
2866 8807 8.923270 TGTGATTAGTCCTGATGAATATGTACA 58.077 33.333 0.00 0.00 0.00 2.90
2867 8808 9.935241 ATGTGATTAGTCCTGATGAATATGTAC 57.065 33.333 0.00 0.00 0.00 2.90
2917 8858 9.859692 GCGATGATAACTTGGTATTTTTAGTAC 57.140 33.333 0.00 0.00 0.00 2.73
2936 8877 2.494059 CTCGGGGTTTAATGCGATGAT 58.506 47.619 0.00 0.00 0.00 2.45
2943 8884 3.733684 CGAAATTGGCTCGGGGTTTAATG 60.734 47.826 0.00 0.00 32.62 1.90
2965 8906 4.811761 GCAAACCCGCGATCGTGC 62.812 66.667 22.93 16.00 0.00 5.34
2991 8940 0.037303 AGAATGGGCCGCTCATATGG 59.963 55.000 6.06 0.00 0.00 2.74
3110 9666 5.270893 TGCTAGTCCGCATAATTAGTTGA 57.729 39.130 0.00 0.00 34.44 3.18
3123 9679 7.851387 TCTATTCATCTACTATGCTAGTCCG 57.149 40.000 0.00 0.00 40.14 4.79
3153 9709 4.380655 CCTGTTTCTAGTCCGTGTCTTAGG 60.381 50.000 0.00 0.00 0.00 2.69
3159 9715 4.618920 AATTCCTGTTTCTAGTCCGTGT 57.381 40.909 0.00 0.00 0.00 4.49
3162 9718 6.421202 GTGCTATAATTCCTGTTTCTAGTCCG 59.579 42.308 0.00 0.00 0.00 4.79
3163 9719 7.272978 TGTGCTATAATTCCTGTTTCTAGTCC 58.727 38.462 0.00 0.00 0.00 3.85
3205 9761 4.679654 CAGCTGCATCGTACGTAATTATGA 59.320 41.667 16.05 0.00 0.00 2.15
3206 9762 4.143326 CCAGCTGCATCGTACGTAATTATG 60.143 45.833 16.05 11.97 0.00 1.90
3227 9783 2.203983 TCCAGGGCTTCTGCTCCA 60.204 61.111 2.74 0.00 41.57 3.86
3237 9793 1.450312 CCGACATCAACTCCAGGGC 60.450 63.158 0.00 0.00 0.00 5.19
3239 9795 1.450312 GGCCGACATCAACTCCAGG 60.450 63.158 0.00 0.00 0.00 4.45
3253 9809 2.289820 CTCTTCATCAATGACATGGCCG 59.710 50.000 0.00 0.00 36.36 6.13
3257 9813 4.439700 GGCAACCTCTTCATCAATGACATG 60.440 45.833 0.00 0.00 36.36 3.21
3258 9814 3.698040 GGCAACCTCTTCATCAATGACAT 59.302 43.478 0.00 0.00 36.36 3.06
3259 9815 3.084039 GGCAACCTCTTCATCAATGACA 58.916 45.455 0.00 0.00 36.36 3.58
3260 9816 2.096496 CGGCAACCTCTTCATCAATGAC 59.904 50.000 0.00 0.00 36.36 3.06
3261 9817 2.027285 TCGGCAACCTCTTCATCAATGA 60.027 45.455 0.00 0.00 34.44 2.57
3262 9818 2.353889 CTCGGCAACCTCTTCATCAATG 59.646 50.000 0.00 0.00 0.00 2.82
3265 9821 0.250234 CCTCGGCAACCTCTTCATCA 59.750 55.000 0.00 0.00 0.00 3.07
3290 9846 3.067180 ACTTCACCAACGACGACTTCTTA 59.933 43.478 0.00 0.00 0.00 2.10
3304 9860 0.753867 TGGTAGCAACGACTTCACCA 59.246 50.000 0.00 0.00 33.78 4.17
3305 9861 1.429463 CTGGTAGCAACGACTTCACC 58.571 55.000 0.00 0.00 0.00 4.02
3306 9862 0.790814 GCTGGTAGCAACGACTTCAC 59.209 55.000 0.00 0.00 41.89 3.18
3307 9863 3.210857 GCTGGTAGCAACGACTTCA 57.789 52.632 0.00 0.00 41.89 3.02
3320 9876 4.742201 ATTCGCGCGACTGCTGGT 62.742 61.111 35.02 9.60 39.65 4.00
3335 9891 5.335897 CGATCATATTTTTGGGGATCGCATT 60.336 40.000 12.32 0.00 46.94 3.56
3336 9892 4.156556 CGATCATATTTTTGGGGATCGCAT 59.843 41.667 12.32 0.00 46.94 4.73
3341 9897 3.165071 GGGCGATCATATTTTTGGGGAT 58.835 45.455 0.00 0.00 0.00 3.85
3358 9914 2.838225 ATGTACGGGAGAGGGGCG 60.838 66.667 0.00 0.00 0.00 6.13
3359 9915 1.122019 ATCATGTACGGGAGAGGGGC 61.122 60.000 0.00 0.00 0.00 5.80
3375 9931 0.976641 AACCTCGCCTCTTGTGATCA 59.023 50.000 0.00 0.00 31.86 2.92
3382 9938 2.283676 TCCGGAACCTCGCCTCTT 60.284 61.111 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.