Multiple sequence alignment - TraesCS7A01G175200

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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 TraesCS7A01G175200 chr7A 100.000 8017 0 0 1 8017 128825522 128833538 0.000000e+00 14805.0
1 TraesCS7A01G175200 chr7A 87.842 329 31 6 7319 7639 128861596 128861269 2.110000e-100 377.0
2 TraesCS7A01G175200 chr7A 81.723 383 35 15 6895 7250 128861971 128861597 3.660000e-73 287.0
3 TraesCS7A01G175200 chr7D 94.338 1978 65 15 5337 7297 128917471 128919418 0.000000e+00 2988.0
4 TraesCS7A01G175200 chr7D 91.193 2180 83 51 1 2116 128911399 128913533 0.000000e+00 2861.0
5 TraesCS7A01G175200 chr7D 97.134 1291 33 3 4040 5326 128916139 128917429 0.000000e+00 2176.0
6 TraesCS7A01G175200 chr7D 93.598 1437 42 14 2115 3543 128913560 128914954 0.000000e+00 2098.0
7 TraesCS7A01G175200 chr7D 95.728 515 16 3 3542 4050 128915112 128915626 0.000000e+00 824.0
8 TraesCS7A01G175200 chr7D 83.697 779 67 34 6895 7639 129498891 129498139 0.000000e+00 680.0
9 TraesCS7A01G175200 chr7D 95.758 330 13 1 7310 7639 128919467 128919795 1.530000e-146 531.0
10 TraesCS7A01G175200 chr7D 86.146 397 24 8 7639 8016 128919824 128920208 4.510000e-107 399.0
11 TraesCS7A01G175200 chr7B 86.959 1871 107 66 295 2116 90188937 90190719 0.000000e+00 1977.0
12 TraesCS7A01G175200 chr7B 91.276 619 39 10 6034 6642 90194130 90194743 0.000000e+00 830.0
13 TraesCS7A01G175200 chr7B 85.882 680 64 15 4575 5250 90192590 90193241 0.000000e+00 695.0
14 TraesCS7A01G175200 chr7B 87.552 482 46 8 2610 3085 90190950 90191423 5.470000e-151 545.0
15 TraesCS7A01G175200 chr7B 90.050 402 23 7 6904 7293 90194864 90195260 9.290000e-139 505.0
16 TraesCS7A01G175200 chr7B 88.372 344 30 7 4000 4333 90191894 90192237 9.690000e-109 405.0
17 TraesCS7A01G175200 chr7B 93.590 234 15 0 5800 6033 445663600 445663367 4.600000e-92 350.0
18 TraesCS7A01G175200 chr7B 89.057 265 23 3 7375 7639 90793160 90792902 2.790000e-84 324.0
19 TraesCS7A01G175200 chr7B 89.837 246 14 3 7 248 90188530 90188768 1.010000e-78 305.0
20 TraesCS7A01G175200 chr7B 84.424 321 25 9 6895 7193 90793473 90793156 7.870000e-75 292.0
21 TraesCS7A01G175200 chr7B 88.115 244 17 5 3299 3542 90191501 90191732 6.130000e-71 279.0
22 TraesCS7A01G175200 chr7B 87.556 225 20 6 4332 4549 90192309 90192532 3.710000e-63 254.0
23 TraesCS7A01G175200 chr7B 81.250 192 24 6 7296 7476 90195321 90195511 2.330000e-30 145.0
24 TraesCS7A01G175200 chr7B 85.333 75 8 3 3935 4008 397446614 397446686 3.100000e-09 75.0
25 TraesCS7A01G175200 chrUn 92.537 268 16 3 3743 4007 96301976 96302242 1.630000e-101 381.0
26 TraesCS7A01G175200 chr6B 92.549 255 16 1 3752 4003 288654874 288654620 5.910000e-96 363.0
27 TraesCS7A01G175200 chr6B 88.973 263 26 1 3743 4002 342223931 342223669 1.000000e-83 322.0
28 TraesCS7A01G175200 chr6B 89.655 87 8 1 7349 7434 40592734 40592820 8.510000e-20 110.0
29 TraesCS7A01G175200 chr6B 84.211 114 11 7 7355 7465 39192104 39191995 3.960000e-18 104.0
30 TraesCS7A01G175200 chr6B 94.872 39 1 1 6782 6820 149484472 149484435 8.690000e-05 60.2
31 TraesCS7A01G175200 chr2A 93.644 236 13 2 5799 6033 310406912 310407146 1.280000e-92 351.0
32 TraesCS7A01G175200 chr2A 93.590 234 15 0 5800 6033 449270878 449271111 4.600000e-92 350.0
33 TraesCS7A01G175200 chr2A 86.486 259 24 5 7639 7886 758386218 758385960 2.850000e-69 274.0
34 TraesCS7A01G175200 chr2A 100.000 29 0 0 6795 6823 574964290 574964262 4.000000e-03 54.7
35 TraesCS7A01G175200 chr3A 93.590 234 15 0 5800 6033 375018033 375018266 4.600000e-92 350.0
36 TraesCS7A01G175200 chr2D 93.220 236 14 2 5799 6033 249892020 249891786 5.960000e-91 346.0
37 TraesCS7A01G175200 chr2D 93.191 235 14 2 5800 6034 341699560 341699328 2.140000e-90 344.0
38 TraesCS7A01G175200 chr2D 90.234 256 21 2 3752 4003 506172287 506172032 1.670000e-86 331.0
39 TraesCS7A01G175200 chr2D 89.098 266 25 3 5801 6063 136426581 136426845 2.160000e-85 327.0
40 TraesCS7A01G175200 chr2D 80.833 120 17 5 1025 1141 355292658 355292774 1.110000e-13 89.8
41 TraesCS7A01G175200 chr1D 92.827 237 13 3 5799 6033 194467522 194467288 2.770000e-89 340.0
42 TraesCS7A01G175200 chr1D 88.973 263 26 1 3743 4002 269856932 269856670 1.000000e-83 322.0
43 TraesCS7A01G175200 chr1D 90.476 84 7 1 7350 7432 382638716 382638633 8.510000e-20 110.0
44 TraesCS7A01G175200 chr4A 88.806 268 26 2 3742 4005 12674184 12673917 7.760000e-85 326.0
45 TraesCS7A01G175200 chr4A 85.897 78 7 3 3935 4009 438615452 438615528 6.670000e-11 80.5
46 TraesCS7A01G175200 chr3D 89.804 255 23 1 3752 4003 67721290 67721036 2.790000e-84 324.0
47 TraesCS7A01G175200 chr3B 89.272 261 24 2 3746 4003 687075680 687075939 2.790000e-84 324.0
48 TraesCS7A01G175200 chr6D 90.050 201 17 3 988 1186 403976041 403975842 2.870000e-64 257.0
49 TraesCS7A01G175200 chr6A 91.444 187 16 0 1000 1186 550643622 550643436 2.870000e-64 257.0
50 TraesCS7A01G175200 chr6A 89.773 88 7 2 7349 7434 23259566 23259479 2.370000e-20 111.0
51 TraesCS7A01G175200 chr5D 85.915 213 21 8 3801 4008 291081718 291081510 1.350000e-52 219.0
52 TraesCS7A01G175200 chr5D 93.617 47 3 0 2344 2390 162440961 162440915 4.010000e-08 71.3
53 TraesCS7A01G175200 chr5B 95.745 47 2 0 2344 2390 180023076 180023122 8.630000e-10 76.8
54 TraesCS7A01G175200 chr5A 93.617 47 3 0 2344 2390 260689496 260689450 4.010000e-08 71.3


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 TraesCS7A01G175200 chr7A 128825522 128833538 8016 False 14805.000000 14805 100.000000 1 8017 1 chr7A.!!$F1 8016
1 TraesCS7A01G175200 chr7A 128861269 128861971 702 True 332.000000 377 84.782500 6895 7639 2 chr7A.!!$R1 744
2 TraesCS7A01G175200 chr7D 128911399 128920208 8809 False 1696.714286 2988 93.413571 1 8016 7 chr7D.!!$F1 8015
3 TraesCS7A01G175200 chr7D 129498139 129498891 752 True 680.000000 680 83.697000 6895 7639 1 chr7D.!!$R1 744
4 TraesCS7A01G175200 chr7B 90188530 90195511 6981 False 594.000000 1977 87.684900 7 7476 10 chr7B.!!$F2 7469
5 TraesCS7A01G175200 chr7B 90792902 90793473 571 True 308.000000 324 86.740500 6895 7639 2 chr7B.!!$R2 744

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
386 513 0.249489 CGCCGGAACAGGGAATCTAG 60.249 60.000 5.05 0.0 0.00 2.43 F
1204 1349 0.748729 CGTACCTTCGCCTCTCCTCT 60.749 60.000 0.00 0.0 0.00 3.69 F
1205 1350 1.026584 GTACCTTCGCCTCTCCTCTC 58.973 60.000 0.00 0.0 0.00 3.20 F
2517 2787 1.324383 GTTTTGCCGAGGAAAAGGGA 58.676 50.000 4.13 0.0 0.00 4.20 F
2740 3014 1.332375 GTTTTGTCGCTTGGTGCTGTA 59.668 47.619 0.00 0.0 40.11 2.74 F
3774 4217 3.117663 TCCTTCCCAAAATATAAGGCGCT 60.118 43.478 7.64 0.0 38.70 5.92 F
3974 4420 1.873591 AGACCGTGCAAAGTCAATCAC 59.126 47.619 17.12 0.0 35.38 3.06 F
5551 6695 3.120269 GCTGATTGCTGAACTCTCAAGTG 60.120 47.826 0.00 0.0 35.65 3.16 F
6575 8143 1.405526 GCAGTACATTCGGGAAGCTCA 60.406 52.381 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1765 0.678684 TCGATCTGGTACTGTGCCGA 60.679 55.000 10.39 10.47 0.00 5.54 R
2427 2697 0.810648 TTCGGCTCCAACATGAATGC 59.189 50.000 0.00 0.00 0.00 3.56 R
3144 3425 1.268625 GCACAGTTACTTTTTCCCCGG 59.731 52.381 0.00 0.00 0.00 5.73 R
3769 4212 1.135575 CCAGAAAAGTCAATCAGCGCC 60.136 52.381 2.29 0.00 0.00 6.53 R
3974 4420 3.821033 CCTCCTTCCCAAAATATAAGGCG 59.179 47.826 0.00 0.00 38.70 5.52 R
5183 6275 1.675641 GAATTGCCGGTCCTGCAGT 60.676 57.895 13.81 2.63 40.35 4.40 R
5808 7366 1.555533 GGTCTACCCCAACCTCTCTTG 59.444 57.143 0.00 0.00 32.54 3.02 R
6830 8441 0.102120 GCTGTCAGACTCATCTCCGG 59.898 60.000 3.32 0.00 30.42 5.14 R
7908 9702 0.179100 CTGTATGTCCAGGTCCAGCG 60.179 60.000 0.00 0.00 0.00 5.18 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
63 64 3.866582 CCCGCACAGAGATCCCCC 61.867 72.222 0.00 0.00 0.00 5.40
108 113 1.889530 CTCCTGTTCCCTCCACGACC 61.890 65.000 0.00 0.00 0.00 4.79
144 149 1.077787 TCCCATCAATCGGCACCAC 60.078 57.895 0.00 0.00 0.00 4.16
146 151 2.120909 CCATCAATCGGCACCACCC 61.121 63.158 0.00 0.00 33.26 4.61
147 152 1.378382 CATCAATCGGCACCACCCA 60.378 57.895 0.00 0.00 33.26 4.51
155 160 2.601367 GCACCACCCAACAGGCAT 60.601 61.111 0.00 0.00 40.58 4.40
164 169 2.578021 ACCCAACAGGCATGAGATTAGT 59.422 45.455 4.84 0.00 40.58 2.24
248 253 4.368808 CCGCAACTGTTCACGGCG 62.369 66.667 15.91 14.89 46.61 6.46
250 255 2.248431 GCAACTGTTCACGGCGAC 59.752 61.111 16.62 1.03 0.00 5.19
263 268 2.022129 GGCGACGATGATAAGCCCG 61.022 63.158 0.00 0.00 41.81 6.13
264 269 2.022129 GCGACGATGATAAGCCCGG 61.022 63.158 0.00 0.00 0.00 5.73
266 271 1.668151 GACGATGATAAGCCCGGGC 60.668 63.158 39.29 39.29 42.33 6.13
267 272 2.358737 CGATGATAAGCCCGGGCC 60.359 66.667 41.72 26.48 43.17 5.80
268 273 2.836154 GATGATAAGCCCGGGCCA 59.164 61.111 41.72 31.29 43.17 5.36
269 274 1.150536 GATGATAAGCCCGGGCCAA 59.849 57.895 41.72 29.97 43.17 4.52
270 275 0.890996 GATGATAAGCCCGGGCCAAG 60.891 60.000 41.72 5.97 43.17 3.61
271 276 2.907407 GATAAGCCCGGGCCAAGC 60.907 66.667 41.72 28.40 43.17 4.01
272 277 3.420482 ATAAGCCCGGGCCAAGCT 61.420 61.111 41.72 21.28 43.17 3.74
273 278 3.721370 ATAAGCCCGGGCCAAGCTG 62.721 63.158 41.72 3.29 43.17 4.24
386 513 0.249489 CGCCGGAACAGGGAATCTAG 60.249 60.000 5.05 0.00 0.00 2.43
444 571 3.384532 TACTGTTCCGACCCGCCC 61.385 66.667 0.00 0.00 0.00 6.13
519 648 2.021106 CCGTCGTCGTCGTAGCTC 59.979 66.667 10.76 0.00 38.33 4.09
521 650 2.451167 CGTCGTCGTCGTAGCTCCT 61.451 63.158 3.67 0.00 38.33 3.69
584 713 2.370849 GGAGATTTTCCGGGCCTGTATA 59.629 50.000 11.58 0.00 35.91 1.47
585 714 3.557264 GGAGATTTTCCGGGCCTGTATAG 60.557 52.174 11.58 0.00 35.91 1.31
586 715 6.614347 GGAGATTTTCCGGGCCTGTATAGG 62.614 54.167 11.58 0.10 40.81 2.57
587 716 1.587066 TTTTCCGGGCCTGTATAGGT 58.413 50.000 11.58 0.00 46.41 3.08
589 718 2.708037 TTCCGGGCCTGTATAGGTAT 57.292 50.000 11.58 0.00 46.41 2.73
590 719 3.831642 TTCCGGGCCTGTATAGGTATA 57.168 47.619 11.58 0.00 46.41 1.47
591 720 3.091633 TCCGGGCCTGTATAGGTATAC 57.908 52.381 11.58 0.00 46.41 1.47
592 721 2.105766 CCGGGCCTGTATAGGTATACC 58.894 57.143 14.54 14.54 46.41 2.73
784 923 1.826487 GAGCGAGACCTCTCCCTCC 60.826 68.421 5.89 0.00 40.35 4.30
859 1001 2.417339 ATATACTAGGCGCACACACG 57.583 50.000 10.83 0.00 0.00 4.49
1191 1336 2.283966 AGCTCCAGGCACGTACCT 60.284 61.111 0.00 0.00 44.79 3.08
1201 1346 1.139095 CACGTACCTTCGCCTCTCC 59.861 63.158 0.00 0.00 0.00 3.71
1202 1347 1.001145 ACGTACCTTCGCCTCTCCT 60.001 57.895 0.00 0.00 0.00 3.69
1203 1348 1.031029 ACGTACCTTCGCCTCTCCTC 61.031 60.000 0.00 0.00 0.00 3.71
1204 1349 0.748729 CGTACCTTCGCCTCTCCTCT 60.749 60.000 0.00 0.00 0.00 3.69
1205 1350 1.026584 GTACCTTCGCCTCTCCTCTC 58.973 60.000 0.00 0.00 0.00 3.20
1289 1434 7.176589 TCTACCTTCTCCATTCTCTCTTTTC 57.823 40.000 0.00 0.00 0.00 2.29
1293 1438 6.070824 ACCTTCTCCATTCTCTCTTTTCTCTC 60.071 42.308 0.00 0.00 0.00 3.20
1296 1441 8.657387 TTCTCCATTCTCTCTTTTCTCTCTTA 57.343 34.615 0.00 0.00 0.00 2.10
1298 1443 7.893302 TCTCCATTCTCTCTTTTCTCTCTTACT 59.107 37.037 0.00 0.00 0.00 2.24
1299 1444 8.062065 TCCATTCTCTCTTTTCTCTCTTACTC 57.938 38.462 0.00 0.00 0.00 2.59
1300 1445 7.123547 TCCATTCTCTCTTTTCTCTCTTACTCC 59.876 40.741 0.00 0.00 0.00 3.85
1344 1489 3.515687 CGACTCGATGCGGATTCG 58.484 61.111 0.00 0.00 37.94 3.34
1362 1507 1.817099 GGGATCCTCTTGCTGCACG 60.817 63.158 12.58 0.00 0.00 5.34
1369 1514 3.503363 CTTGCTGCACGGGCTAGC 61.503 66.667 22.09 22.09 41.49 3.42
1376 1521 2.732619 GCACGGGCTAGCTAGGGTT 61.733 63.158 22.10 0.00 36.96 4.11
1377 1522 1.442148 CACGGGCTAGCTAGGGTTC 59.558 63.158 22.10 5.27 0.00 3.62
1378 1523 1.761271 ACGGGCTAGCTAGGGTTCC 60.761 63.158 22.10 13.84 0.00 3.62
1379 1524 2.508751 CGGGCTAGCTAGGGTTCCC 61.509 68.421 22.10 20.51 0.00 3.97
1380 1525 2.148052 GGGCTAGCTAGGGTTCCCC 61.148 68.421 22.10 18.32 45.90 4.81
1485 1656 2.096013 GCTACGAAGAGCCACCATTTTC 59.904 50.000 0.00 0.00 36.38 2.29
1486 1657 2.568623 ACGAAGAGCCACCATTTTCT 57.431 45.000 0.00 0.00 0.00 2.52
1487 1658 3.695830 ACGAAGAGCCACCATTTTCTA 57.304 42.857 0.00 0.00 0.00 2.10
1493 1664 4.775236 AGAGCCACCATTTTCTACTCATC 58.225 43.478 0.00 0.00 0.00 2.92
1494 1665 4.225942 AGAGCCACCATTTTCTACTCATCA 59.774 41.667 0.00 0.00 0.00 3.07
1498 1669 4.037208 CCACCATTTTCTACTCATCATGGC 59.963 45.833 0.00 0.00 35.52 4.40
1499 1670 4.885907 CACCATTTTCTACTCATCATGGCT 59.114 41.667 0.00 0.00 35.52 4.75
1500 1671 6.057533 CACCATTTTCTACTCATCATGGCTA 58.942 40.000 0.00 0.00 35.52 3.93
1528 1700 4.697756 CGGCCTCCGTCCTTTGCA 62.698 66.667 0.00 0.00 42.73 4.08
1788 1975 2.256764 CGTCTCTGCAGCTCGTGT 59.743 61.111 9.47 0.00 0.00 4.49
1862 2051 2.866028 CCTGCGTGCAAAGAGCTC 59.134 61.111 5.27 5.27 45.94 4.09
1863 2052 2.684843 CCTGCGTGCAAAGAGCTCC 61.685 63.158 10.93 0.00 45.94 4.70
1864 2053 2.669569 TGCGTGCAAAGAGCTCCC 60.670 61.111 10.93 0.00 45.94 4.30
1865 2054 3.435186 GCGTGCAAAGAGCTCCCC 61.435 66.667 10.93 0.00 45.94 4.81
2238 2508 9.635915 CTGTAAGCTTGTACAATGCAAGATGCA 62.636 40.741 23.12 7.57 44.29 3.96
2287 2557 8.814038 AATGATCTGATTTTACTTAAGCACCT 57.186 30.769 1.29 0.00 0.00 4.00
2288 2558 9.905713 AATGATCTGATTTTACTTAAGCACCTA 57.094 29.630 1.29 0.00 0.00 3.08
2324 2594 2.809010 GGACGCTAGGCACCTCTC 59.191 66.667 0.00 0.00 0.00 3.20
2332 2602 6.249911 ACGCTAGGCACCTCTCTATATATA 57.750 41.667 0.00 0.00 0.00 0.86
2424 2694 5.044558 GGAACGGTTTGTGCAATTCTTTTA 58.955 37.500 0.00 0.00 0.00 1.52
2425 2695 5.694458 GGAACGGTTTGTGCAATTCTTTTAT 59.306 36.000 0.00 0.00 0.00 1.40
2427 2697 4.987912 ACGGTTTGTGCAATTCTTTTATGG 59.012 37.500 0.00 0.00 0.00 2.74
2475 2745 4.952957 TGTTGGGATTTGTTTGAGTGAGAA 59.047 37.500 0.00 0.00 0.00 2.87
2517 2787 1.324383 GTTTTGCCGAGGAAAAGGGA 58.676 50.000 4.13 0.00 0.00 4.20
2570 2842 3.010027 TGATGGAAGTGCTTATGGAACCA 59.990 43.478 0.00 0.00 0.00 3.67
2651 2924 3.915536 ACTAGTCGAAGAAGAAAGGCAC 58.084 45.455 0.00 0.00 39.69 5.01
2740 3014 1.332375 GTTTTGTCGCTTGGTGCTGTA 59.668 47.619 0.00 0.00 40.11 2.74
3040 3320 8.697507 ATTCTATAAAAGTGCCCCTAATTGAG 57.302 34.615 0.00 0.00 0.00 3.02
3041 3321 7.208064 TCTATAAAAGTGCCCCTAATTGAGT 57.792 36.000 0.00 0.00 0.00 3.41
3042 3322 7.280356 TCTATAAAAGTGCCCCTAATTGAGTC 58.720 38.462 0.00 0.00 0.00 3.36
3043 3323 4.388577 AAAAGTGCCCCTAATTGAGTCT 57.611 40.909 0.00 0.00 0.00 3.24
3098 3379 9.113876 CAGAAATTTGTTTACGTACCATCTTTC 57.886 33.333 0.00 7.65 0.00 2.62
3246 3527 9.217278 CATTCACATCTCTAGCTTTAAGCATAT 57.783 33.333 19.63 0.88 45.56 1.78
3317 3598 9.868277 CAGCCTCCAATTATTTTATTGTTGTTA 57.132 29.630 0.00 0.00 34.42 2.41
3335 3616 8.121305 TGTTGTTATTGGCTTGAGAATACAAT 57.879 30.769 0.00 0.00 36.00 2.71
3363 3644 6.384258 TGTTTCAGATCGAACCATTCAAAA 57.616 33.333 0.00 0.00 31.73 2.44
3376 3657 5.187687 ACCATTCAAAATCCATCCATTTGC 58.812 37.500 0.00 0.00 34.77 3.68
3423 3704 9.923143 AAATAGCTTGAACATAACCCTTTTTAC 57.077 29.630 0.00 0.00 0.00 2.01
3424 3705 8.879427 ATAGCTTGAACATAACCCTTTTTACT 57.121 30.769 0.00 0.00 0.00 2.24
3425 3706 7.597288 AGCTTGAACATAACCCTTTTTACTT 57.403 32.000 0.00 0.00 0.00 2.24
3426 3707 8.700439 AGCTTGAACATAACCCTTTTTACTTA 57.300 30.769 0.00 0.00 0.00 2.24
3595 4038 9.529823 AAATCCTCATTTCTATGCATGTGATAT 57.470 29.630 10.16 5.66 0.00 1.63
3749 4192 7.907841 TGCAGGTTATTCCTCTTATGTACTA 57.092 36.000 0.00 0.00 46.24 1.82
3750 4193 7.952671 TGCAGGTTATTCCTCTTATGTACTAG 58.047 38.462 0.00 0.00 46.24 2.57
3769 4212 8.429641 TGTACTAGCTCCTTCCCAAAATATAAG 58.570 37.037 0.00 0.00 0.00 1.73
3774 4217 3.117663 TCCTTCCCAAAATATAAGGCGCT 60.118 43.478 7.64 0.00 38.70 5.92
3974 4420 1.873591 AGACCGTGCAAAGTCAATCAC 59.126 47.619 17.12 0.00 35.38 3.06
4101 5076 7.404671 ACCTTCAAACACTTTTGTACAGAAT 57.595 32.000 0.00 0.00 42.51 2.40
4110 5085 6.095440 ACACTTTTGTACAGAATCTTGCTTGT 59.905 34.615 0.00 0.00 32.60 3.16
4195 5173 3.555547 GTGATTTTGGTTTGGTGAACAGC 59.444 43.478 0.00 0.00 40.13 4.40
4475 5531 5.988561 TGTCCTTTGCCAATCATTTGTAAAC 59.011 36.000 0.00 0.00 0.00 2.01
4943 6035 7.503566 CCATCCTGGATTTGTGTGATTAACTAT 59.496 37.037 6.42 0.00 40.96 2.12
5228 6324 5.519722 CAACAAATTAGTGACCTCCAACAC 58.480 41.667 0.00 0.00 37.30 3.32
5255 6351 8.324191 AGGTGAGGAATGATCTCTATTGTTTA 57.676 34.615 0.00 0.00 32.78 2.01
5326 6439 8.673711 TGTATGTCAGGCAAATTATCAAACTAC 58.326 33.333 0.00 0.00 0.00 2.73
5328 6441 7.759489 TGTCAGGCAAATTATCAAACTACTT 57.241 32.000 0.00 0.00 0.00 2.24
5329 6442 8.856153 TGTCAGGCAAATTATCAAACTACTTA 57.144 30.769 0.00 0.00 0.00 2.24
5331 6444 8.726988 GTCAGGCAAATTATCAAACTACTTACA 58.273 33.333 0.00 0.00 0.00 2.41
5332 6445 8.726988 TCAGGCAAATTATCAAACTACTTACAC 58.273 33.333 0.00 0.00 0.00 2.90
5333 6446 8.511321 CAGGCAAATTATCAAACTACTTACACA 58.489 33.333 0.00 0.00 0.00 3.72
5447 6591 8.655970 GGCATGTAGGAAATTAATTGTTTGAAC 58.344 33.333 0.39 0.00 0.00 3.18
5551 6695 3.120269 GCTGATTGCTGAACTCTCAAGTG 60.120 47.826 0.00 0.00 35.65 3.16
5674 6835 5.820404 TGCACAGAGATGGAGAATGATAT 57.180 39.130 0.00 0.00 0.00 1.63
5688 7245 9.895138 TGGAGAATGATATGAATATACATGTGG 57.105 33.333 9.11 0.00 0.00 4.17
5715 7272 8.409358 AGTAGTAGATATGTGCATGTCATGTA 57.591 34.615 14.26 7.11 32.21 2.29
5931 7489 4.769688 TGTGGAAGCTTACTATCCATGTG 58.230 43.478 10.74 0.00 44.55 3.21
5933 7491 3.142174 GGAAGCTTACTATCCATGTGCC 58.858 50.000 0.00 0.00 33.30 5.01
5957 7515 3.678056 ACTATGAGTTGGTTGCGAGAA 57.322 42.857 0.00 0.00 0.00 2.87
6168 7728 6.788598 TGCTCCCTGATTGCATTATTTTTA 57.211 33.333 0.00 0.00 0.00 1.52
6398 7959 5.772825 ATAAGAAGTGCAGCTTGAACAAA 57.227 34.783 6.31 0.00 37.59 2.83
6415 7977 9.364989 CTTGAACAAAAGTCCAATAAAAGTTGA 57.635 29.630 0.00 0.00 0.00 3.18
6575 8143 1.405526 GCAGTACATTCGGGAAGCTCA 60.406 52.381 0.00 0.00 0.00 4.26
6673 8269 8.891985 TCTTTATCCTGATCATATGCTAGTCT 57.108 34.615 0.00 0.00 0.00 3.24
6680 8276 7.876582 TCCTGATCATATGCTAGTCTCAAAATG 59.123 37.037 0.00 0.00 0.00 2.32
6686 8282 4.019792 TGCTAGTCTCAAAATGCCTTCA 57.980 40.909 0.00 0.00 0.00 3.02
6694 8290 7.344913 AGTCTCAAAATGCCTTCATAGAATCT 58.655 34.615 0.00 0.00 31.46 2.40
6697 8293 4.825546 AAATGCCTTCATAGAATCTGCG 57.174 40.909 0.00 0.00 31.46 5.18
6702 8298 3.186001 GCCTTCATAGAATCTGCGACATG 59.814 47.826 0.00 0.00 0.00 3.21
6762 8364 8.340757 TCCCAAATTGTATATTTTGTACTCCCT 58.659 33.333 0.00 0.00 32.23 4.20
6764 8366 9.408648 CCAAATTGTATATTTTGTACTCCCTCT 57.591 33.333 0.00 0.00 32.23 3.69
6766 8368 9.975218 AAATTGTATATTTTGTACTCCCTCTGT 57.025 29.630 0.00 0.00 0.00 3.41
6769 8371 8.834004 TGTATATTTTGTACTCCCTCTGTACT 57.166 34.615 0.00 0.00 40.44 2.73
6782 8384 6.266080 TCCCTCTGTACTTATACTTTTGGGA 58.734 40.000 0.00 0.00 36.19 4.37
6783 8385 6.155737 TCCCTCTGTACTTATACTTTTGGGAC 59.844 42.308 0.00 0.00 34.96 4.46
6785 8387 5.969423 TCTGTACTTATACTTTTGGGACGG 58.031 41.667 0.00 0.00 32.00 4.79
6786 8388 5.716228 TCTGTACTTATACTTTTGGGACGGA 59.284 40.000 0.00 0.00 32.00 4.69
6789 8391 3.199289 ACTTATACTTTTGGGACGGAGGG 59.801 47.826 0.00 0.00 0.00 4.30
6790 8392 1.961133 ATACTTTTGGGACGGAGGGA 58.039 50.000 0.00 0.00 0.00 4.20
6799 8410 1.962100 GGGACGGAGGGAGTACTATTG 59.038 57.143 0.00 0.00 0.00 1.90
6830 8441 5.242171 GGAGGGAGTAGTTAGCTCTGATAAC 59.758 48.000 0.00 0.00 34.08 1.89
6831 8442 5.141910 AGGGAGTAGTTAGCTCTGATAACC 58.858 45.833 0.00 0.00 34.34 2.85
6848 8459 1.468985 ACCGGAGATGAGTCTGACAG 58.531 55.000 9.46 0.00 33.97 3.51
6874 8485 6.434596 TCTAATTTCAATGTGTGTTTGTCGG 58.565 36.000 0.00 0.00 0.00 4.79
6880 8491 5.950883 TCAATGTGTGTTTGTCGGTTTTTA 58.049 33.333 0.00 0.00 0.00 1.52
6882 8493 7.036220 TCAATGTGTGTTTGTCGGTTTTTATT 58.964 30.769 0.00 0.00 0.00 1.40
6883 8494 7.545965 TCAATGTGTGTTTGTCGGTTTTTATTT 59.454 29.630 0.00 0.00 0.00 1.40
6884 8495 7.835634 ATGTGTGTTTGTCGGTTTTTATTTT 57.164 28.000 0.00 0.00 0.00 1.82
6893 8504 6.274579 TGTCGGTTTTTATTTTTGAGGGAAC 58.725 36.000 0.00 0.00 0.00 3.62
6933 8545 4.511826 CCTGACTGAGTTACCAACAGTTTC 59.488 45.833 0.00 0.00 43.49 2.78
6965 8577 7.394077 TCAATTCTGAAATGTGGCAGATTCTTA 59.606 33.333 10.57 0.00 40.51 2.10
6972 8584 6.446781 AATGTGGCAGATTCTTATTCACTG 57.553 37.500 3.70 0.00 0.00 3.66
7007 8625 0.908180 AAGTAAGGACCGTGGGGAGG 60.908 60.000 0.00 0.00 36.97 4.30
7053 8688 5.374921 AGAGAAGATGTGAAATGCTATGGG 58.625 41.667 0.00 0.00 0.00 4.00
7075 8710 3.495806 GGAATCACTCCAAGATAGGCTGG 60.496 52.174 0.00 0.00 44.67 4.85
7141 8780 3.059044 CGAGTTGTCGTTTTATGTCTCCG 59.941 47.826 0.00 0.00 41.57 4.63
7177 8816 2.081787 TCCACCTTTGTGCCTGGGA 61.082 57.895 0.00 0.00 41.35 4.37
7205 8844 4.459685 AGTCACTGAACTTGTAGCGTATCT 59.540 41.667 0.00 0.00 0.00 1.98
7263 8914 3.016031 CAAACTATGTATGTGCCTGCCA 58.984 45.455 0.00 0.00 0.00 4.92
7426 9174 1.207089 GTGATAGCCAGCTACACCACA 59.793 52.381 16.94 6.22 31.12 4.17
7439 9187 6.150307 CAGCTACACCACAACACCATAATTAA 59.850 38.462 0.00 0.00 0.00 1.40
7444 9192 8.825667 ACACCACAACACCATAATTAATTTTC 57.174 30.769 5.91 0.00 0.00 2.29
7525 9276 7.695480 ACACATGATCTACTTATCGAGCTAT 57.305 36.000 0.00 0.00 0.00 2.97
7665 9450 5.581085 TCTCGCTAAGCTTTTATTCAACCTC 59.419 40.000 3.20 0.00 0.00 3.85
7686 9480 6.599638 ACCTCCATAATGTTTACTTGAAGCTC 59.400 38.462 0.00 0.00 0.00 4.09
7689 9483 7.624549 TCCATAATGTTTACTTGAAGCTCTCT 58.375 34.615 0.00 0.00 0.00 3.10
7712 9506 1.611977 GTTGACCTAACCAAACAGGGC 59.388 52.381 0.00 0.00 43.89 5.19
7733 9527 3.132925 CGACCAAACCCGAGAGTTAAAA 58.867 45.455 0.00 0.00 0.00 1.52
7754 9548 3.482156 AATGCCTAGCGAGATTGTGAT 57.518 42.857 0.00 0.00 0.00 3.06
7807 9601 6.131544 ACGATATTACAATCAGCAAAACCC 57.868 37.500 0.00 0.00 0.00 4.11
7815 9609 2.004583 TCAGCAAAACCCGTAGATCG 57.995 50.000 0.00 0.00 39.52 3.69
7830 9624 6.919687 CGTAGATCGGTCTATGATTTCTTG 57.080 41.667 18.43 0.00 43.65 3.02
7831 9625 6.439599 CGTAGATCGGTCTATGATTTCTTGT 58.560 40.000 18.43 0.00 43.65 3.16
7832 9626 7.582352 CGTAGATCGGTCTATGATTTCTTGTA 58.418 38.462 18.43 0.00 43.65 2.41
7834 9628 6.439599 AGATCGGTCTATGATTTCTTGTACG 58.560 40.000 0.00 0.00 31.36 3.67
7835 9629 5.823209 TCGGTCTATGATTTCTTGTACGA 57.177 39.130 0.00 0.00 0.00 3.43
7836 9630 6.387041 TCGGTCTATGATTTCTTGTACGAT 57.613 37.500 0.00 0.00 0.00 3.73
7838 9632 7.582352 TCGGTCTATGATTTCTTGTACGATAG 58.418 38.462 0.00 0.00 46.19 2.08
7871 9665 4.297510 CCACGAAATTTTGCTTGATGTCA 58.702 39.130 5.27 0.00 0.00 3.58
7886 9680 2.631160 TGTCATTCACCACCGTCTTT 57.369 45.000 0.00 0.00 0.00 2.52
7910 9704 2.932498 TCACTTGCAATGTGAATTCGC 58.068 42.857 21.65 12.17 46.37 4.70
7911 9705 2.553602 TCACTTGCAATGTGAATTCGCT 59.446 40.909 21.65 3.20 46.37 4.93
7912 9706 2.659757 CACTTGCAATGTGAATTCGCTG 59.340 45.455 19.21 11.46 44.01 5.18
7913 9707 2.256174 CTTGCAATGTGAATTCGCTGG 58.744 47.619 19.21 9.94 0.00 4.85
7914 9708 1.532523 TGCAATGTGAATTCGCTGGA 58.467 45.000 19.21 9.15 0.00 3.86
7915 9709 1.199789 TGCAATGTGAATTCGCTGGAC 59.800 47.619 19.21 7.87 0.00 4.02
7987 9789 1.218316 CGAGGGTAGTTGGGTCTGC 59.782 63.158 0.00 0.00 0.00 4.26
8016 9818 7.840342 AATCTGAATATAACCGATGATGCTC 57.160 36.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 2.525248 CGATGGATTCGTGGGTGCG 61.525 63.158 0.00 0.00 43.01 5.34
108 113 4.373116 CGTGGTGGAGTGGGACGG 62.373 72.222 0.00 0.00 0.00 4.79
144 149 3.287867 ACTAATCTCATGCCTGTTGGG 57.712 47.619 0.00 0.00 38.36 4.12
146 151 7.492524 TCTTACTACTAATCTCATGCCTGTTG 58.507 38.462 0.00 0.00 0.00 3.33
147 152 7.661536 TCTTACTACTAATCTCATGCCTGTT 57.338 36.000 0.00 0.00 0.00 3.16
164 169 7.327761 GGTCGCGCTGATTAATTAATCTTACTA 59.672 37.037 29.37 14.42 41.93 1.82
198 203 2.107950 TTAATCACTCGGCTGGTTGG 57.892 50.000 0.00 0.00 0.00 3.77
208 213 5.297029 GGGTGGTTAGCTTGATTAATCACTC 59.703 44.000 17.76 11.92 40.38 3.51
209 214 5.193679 GGGTGGTTAGCTTGATTAATCACT 58.806 41.667 17.76 14.39 40.38 3.41
210 215 4.035208 CGGGTGGTTAGCTTGATTAATCAC 59.965 45.833 17.76 7.73 40.01 3.06
211 216 4.196193 CGGGTGGTTAGCTTGATTAATCA 58.804 43.478 14.23 14.23 34.44 2.57
248 253 1.668151 GCCCGGGCTTATCATCGTC 60.668 63.158 38.76 4.09 38.26 4.20
250 255 2.358737 GGCCCGGGCTTATCATCG 60.359 66.667 42.70 3.74 41.60 3.84
251 256 0.890996 CTTGGCCCGGGCTTATCATC 60.891 60.000 42.70 25.58 41.60 2.92
255 260 3.420482 AGCTTGGCCCGGGCTTAT 61.420 61.111 42.70 22.54 41.60 1.73
263 268 3.357079 CACGTCACAGCTTGGCCC 61.357 66.667 0.00 0.00 0.00 5.80
264 269 4.030452 GCACGTCACAGCTTGGCC 62.030 66.667 0.00 0.00 0.00 5.36
266 271 0.100325 TTTTGCACGTCACAGCTTGG 59.900 50.000 0.00 0.00 0.00 3.61
267 272 1.906757 TTTTTGCACGTCACAGCTTG 58.093 45.000 0.00 0.00 0.00 4.01
519 648 1.691823 GTCCTTTTCCTCCCCCAGG 59.308 63.158 0.00 0.00 45.15 4.45
521 650 2.228480 CGGTCCTTTTCCTCCCCCA 61.228 63.158 0.00 0.00 0.00 4.96
566 695 2.779506 CCTATACAGGCCCGGAAAATC 58.220 52.381 0.73 0.00 34.35 2.17
606 736 3.404707 CGCGCCGGTCGTTGTTTA 61.405 61.111 17.38 0.00 41.07 2.01
660 799 0.171679 CGGTTAAACAAATCGGGGGC 59.828 55.000 0.00 0.00 38.07 5.80
784 923 1.900545 GACGGGAAAGGTGAGGGAGG 61.901 65.000 0.00 0.00 0.00 4.30
903 1045 5.728255 CACGAACAAACAAACAAACAAACA 58.272 33.333 0.00 0.00 0.00 2.83
1191 1336 1.187087 GGAAAGAGAGGAGAGGCGAA 58.813 55.000 0.00 0.00 0.00 4.70
1201 1346 2.736826 GGGCGGGGAGGAAAGAGAG 61.737 68.421 0.00 0.00 0.00 3.20
1202 1347 2.687566 GGGCGGGGAGGAAAGAGA 60.688 66.667 0.00 0.00 0.00 3.10
1203 1348 2.689034 AGGGCGGGGAGGAAAGAG 60.689 66.667 0.00 0.00 0.00 2.85
1204 1349 2.687566 GAGGGCGGGGAGGAAAGA 60.688 66.667 0.00 0.00 0.00 2.52
1205 1350 2.689034 AGAGGGCGGGGAGGAAAG 60.689 66.667 0.00 0.00 0.00 2.62
1289 1434 3.563808 CGGACAGATCTGGAGTAAGAGAG 59.436 52.174 26.08 0.00 34.19 3.20
1293 1438 3.697045 AGAACGGACAGATCTGGAGTAAG 59.303 47.826 26.08 13.03 35.26 2.34
1296 1441 2.223803 AGAACGGACAGATCTGGAGT 57.776 50.000 26.08 18.48 35.26 3.85
1298 1443 2.755655 GAGAAGAACGGACAGATCTGGA 59.244 50.000 26.08 0.00 35.26 3.86
1299 1444 2.478709 CGAGAAGAACGGACAGATCTGG 60.479 54.545 26.08 11.41 35.26 3.86
1300 1445 2.162608 ACGAGAAGAACGGACAGATCTG 59.837 50.000 21.37 21.37 37.24 2.90
1344 1489 1.817099 CGTGCAGCAAGAGGATCCC 60.817 63.158 8.55 0.00 33.66 3.85
1353 1498 2.578163 CTAGCTAGCCCGTGCAGCAA 62.578 60.000 12.13 0.00 41.27 3.91
1354 1499 3.074369 TAGCTAGCCCGTGCAGCA 61.074 61.111 12.13 0.00 41.27 4.41
1401 1546 1.452108 GGAGGAAATCAGGCCGGTG 60.452 63.158 1.90 0.00 0.00 4.94
1405 1550 1.147153 CGGAGGAGGAAATCAGGCC 59.853 63.158 0.00 0.00 0.00 5.19
1485 1656 6.014755 TGAGGATCTTTAGCCATGATGAGTAG 60.015 42.308 0.00 0.00 34.92 2.57
1486 1657 5.840693 TGAGGATCTTTAGCCATGATGAGTA 59.159 40.000 0.00 0.00 34.92 2.59
1487 1658 4.657504 TGAGGATCTTTAGCCATGATGAGT 59.342 41.667 0.00 0.00 34.92 3.41
1543 1715 1.541233 CCCCATTTCTCCGGAATCGAG 60.541 57.143 5.23 0.00 39.00 4.04
1582 1765 0.678684 TCGATCTGGTACTGTGCCGA 60.679 55.000 10.39 10.47 0.00 5.54
1788 1975 1.376683 ACAGGTACGTACGGGCGTA 60.377 57.895 21.06 9.16 45.06 4.42
1968 2164 2.500504 AGCAACAACCTAGTAGTAGCCC 59.499 50.000 0.00 0.00 0.00 5.19
2197 2456 9.284968 ACAAGCTTACAGAAAGTACATACAATT 57.715 29.630 0.00 0.00 37.53 2.32
2238 2508 2.104451 CACAAGCATCTCCTCTAGGCAT 59.896 50.000 0.00 0.00 34.44 4.40
2240 2510 1.759445 TCACAAGCATCTCCTCTAGGC 59.241 52.381 0.00 0.00 34.44 3.93
2241 2511 4.478206 TTTCACAAGCATCTCCTCTAGG 57.522 45.455 0.00 0.00 0.00 3.02
2242 2512 6.111382 TCATTTTCACAAGCATCTCCTCTAG 58.889 40.000 0.00 0.00 0.00 2.43
2243 2513 6.053632 TCATTTTCACAAGCATCTCCTCTA 57.946 37.500 0.00 0.00 0.00 2.43
2244 2514 4.914983 TCATTTTCACAAGCATCTCCTCT 58.085 39.130 0.00 0.00 0.00 3.69
2245 2515 5.589452 AGATCATTTTCACAAGCATCTCCTC 59.411 40.000 0.00 0.00 0.00 3.71
2246 2516 5.357314 CAGATCATTTTCACAAGCATCTCCT 59.643 40.000 0.00 0.00 0.00 3.69
2247 2517 5.356190 TCAGATCATTTTCACAAGCATCTCC 59.644 40.000 0.00 0.00 0.00 3.71
2287 2557 7.922278 AGCGTCCGTGTTATACAAATAAGAATA 59.078 33.333 0.00 0.00 0.00 1.75
2288 2558 6.759827 AGCGTCCGTGTTATACAAATAAGAAT 59.240 34.615 0.00 0.00 0.00 2.40
2360 2630 5.755861 TGCAAGGTGCTTGTAAAAATAAACC 59.244 36.000 1.43 0.00 45.31 3.27
2424 2694 1.117150 GGCTCCAACATGAATGCCAT 58.883 50.000 0.00 0.00 40.04 4.40
2425 2695 1.314534 CGGCTCCAACATGAATGCCA 61.315 55.000 0.00 0.00 40.27 4.92
2427 2697 0.810648 TTCGGCTCCAACATGAATGC 59.189 50.000 0.00 0.00 0.00 3.56
2570 2842 6.796785 AAGTTTGGCAAAGGAATAGCATAT 57.203 33.333 13.94 0.00 0.00 1.78
2837 3113 8.369424 GGTTAGGGTTTGTTTAATTTGGTACAT 58.631 33.333 0.00 0.00 39.30 2.29
2847 3123 6.490721 ACATGATTCGGTTAGGGTTTGTTTAA 59.509 34.615 0.00 0.00 0.00 1.52
2848 3124 6.005198 ACATGATTCGGTTAGGGTTTGTTTA 58.995 36.000 0.00 0.00 0.00 2.01
2849 3125 4.830600 ACATGATTCGGTTAGGGTTTGTTT 59.169 37.500 0.00 0.00 0.00 2.83
2850 3126 4.403734 ACATGATTCGGTTAGGGTTTGTT 58.596 39.130 0.00 0.00 0.00 2.83
2851 3127 4.028993 ACATGATTCGGTTAGGGTTTGT 57.971 40.909 0.00 0.00 0.00 2.83
2892 3169 2.949644 GGTACAGCCACAAACTCAAAGT 59.050 45.455 0.00 0.00 37.17 2.66
3098 3379 9.645059 TTACTTCTGAGAAAGTAATGTCATCAG 57.355 33.333 10.88 4.42 43.39 2.90
3144 3425 1.268625 GCACAGTTACTTTTTCCCCGG 59.731 52.381 0.00 0.00 0.00 5.73
3191 3472 2.939460 AAAGTGAAATACATGGCCGC 57.061 45.000 0.00 0.00 0.00 6.53
3311 3592 8.986477 AATTGTATTCTCAAGCCAATAACAAC 57.014 30.769 0.00 0.00 0.00 3.32
3317 3598 7.844009 ACATGAAATTGTATTCTCAAGCCAAT 58.156 30.769 0.00 0.00 0.00 3.16
3363 3644 4.028131 ACATCTTGTGCAAATGGATGGAT 58.972 39.130 18.53 3.03 38.33 3.41
3568 4011 7.268199 TCACATGCATAGAAATGAGGATTTC 57.732 36.000 0.00 0.00 45.50 2.17
3631 4074 6.761714 ACTTGTTCAGAACTGATAAACTCGTT 59.238 34.615 14.51 0.00 39.64 3.85
3682 4125 6.565234 AGTAGTGAATTGTCCAGAAGTATCG 58.435 40.000 0.00 0.00 0.00 2.92
3749 4192 4.474394 GCCTTATATTTTGGGAAGGAGCT 58.526 43.478 3.71 0.00 40.88 4.09
3750 4193 3.253432 CGCCTTATATTTTGGGAAGGAGC 59.747 47.826 3.71 0.00 40.88 4.70
3769 4212 1.135575 CCAGAAAAGTCAATCAGCGCC 60.136 52.381 2.29 0.00 0.00 6.53
3774 4217 4.703897 ACGAAGACCAGAAAAGTCAATCA 58.296 39.130 0.00 0.00 36.68 2.57
3927 4370 8.520835 TGATGCACGACTTTGACTAATATATC 57.479 34.615 0.00 0.00 0.00 1.63
3974 4420 3.821033 CCTCCTTCCCAAAATATAAGGCG 59.179 47.826 0.00 0.00 38.70 5.52
4195 5173 5.791367 ACTTGTCAATGATCTCGTTCATG 57.209 39.130 0.00 0.00 36.48 3.07
4439 5495 7.665561 TTGGCAAAGGACATTTTTAATTAGC 57.334 32.000 0.00 0.00 0.00 3.09
4717 5809 6.035843 GTGCAATGTTAAATTGGACGATCAT 58.964 36.000 4.08 0.00 39.74 2.45
4723 5815 8.190122 TGAGATATGTGCAATGTTAAATTGGAC 58.810 33.333 12.02 12.02 46.20 4.02
5183 6275 1.675641 GAATTGCCGGTCCTGCAGT 60.676 57.895 13.81 2.63 40.35 4.40
5213 6309 2.104111 CACCTTGTGTTGGAGGTCACTA 59.896 50.000 0.00 0.00 44.28 2.74
5228 6324 6.590068 ACAATAGAGATCATTCCTCACCTTG 58.410 40.000 0.00 0.00 33.25 3.61
5255 6351 2.528564 TCTGCTGCCAAAAGCCTAAAT 58.471 42.857 0.00 0.00 42.83 1.40
5329 6442 8.768397 TCCCTCTGTAAAGAAATATACATGTGT 58.232 33.333 9.11 4.04 32.02 3.72
5331 6444 8.993424 ACTCCCTCTGTAAAGAAATATACATGT 58.007 33.333 2.69 2.69 32.02 3.21
5379 6523 3.616219 CCATAAAACCCATTCGACTCCA 58.384 45.455 0.00 0.00 0.00 3.86
5415 6559 3.874392 AATTTCCTACATGCCTGCAAC 57.126 42.857 0.00 0.00 0.00 4.17
5422 6566 9.423061 AGTTCAAACAATTAATTTCCTACATGC 57.577 29.630 0.00 0.00 0.00 4.06
5461 6605 7.441760 TCTTAGCATGCAACATTTTCAAACAAT 59.558 29.630 21.98 0.00 0.00 2.71
5652 6813 5.306160 TCATATCATTCTCCATCTCTGTGCA 59.694 40.000 0.00 0.00 0.00 4.57
5688 7245 7.869937 ACATGACATGCACATATCTACTACTTC 59.130 37.037 15.49 0.00 0.00 3.01
5715 7272 7.151976 GCCAATTTTAGGTATTGACTTGTTGT 58.848 34.615 0.00 0.00 35.49 3.32
5808 7366 1.555533 GGTCTACCCCAACCTCTCTTG 59.444 57.143 0.00 0.00 32.54 3.02
5931 7489 2.162408 GCAACCAACTCATAGTTCTGGC 59.838 50.000 0.00 0.00 36.03 4.85
5933 7491 3.325870 TCGCAACCAACTCATAGTTCTG 58.674 45.455 0.00 0.00 36.03 3.02
6129 7689 2.498167 GAGCAACTCCATTGACTGTGT 58.502 47.619 0.00 0.00 41.23 3.72
6173 7733 7.981225 AGTCAATTTTGTGTTGCTGAATAGTTT 59.019 29.630 0.00 0.00 0.00 2.66
6225 7785 8.212312 TCACCTTGTAGAAGTACACCAAAAATA 58.788 33.333 0.00 0.00 38.95 1.40
6398 7959 4.280929 GCCACCTCAACTTTTATTGGACTT 59.719 41.667 0.00 0.00 0.00 3.01
6415 7977 0.178981 AAATGTGTGCTCTGCCACCT 60.179 50.000 8.05 0.00 34.85 4.00
6575 8143 2.303022 AGAACCGTCATCATTGTCCTGT 59.697 45.455 0.00 0.00 0.00 4.00
6673 8269 5.220912 CGCAGATTCTATGAAGGCATTTTGA 60.221 40.000 0.00 0.00 35.94 2.69
6680 8276 2.826428 TGTCGCAGATTCTATGAAGGC 58.174 47.619 0.00 0.00 40.67 4.35
6726 8328 1.271926 ACAATTTGGGAACGGAGGGAG 60.272 52.381 0.78 0.00 0.00 4.30
6729 8331 6.709018 AAATATACAATTTGGGAACGGAGG 57.291 37.500 0.78 0.00 0.00 4.30
6733 8335 9.498307 GAGTACAAAATATACAATTTGGGAACG 57.502 33.333 0.78 0.00 40.09 3.95
6762 8364 5.716228 TCCGTCCCAAAAGTATAAGTACAGA 59.284 40.000 0.00 0.00 33.09 3.41
6764 8366 5.105228 CCTCCGTCCCAAAAGTATAAGTACA 60.105 44.000 0.00 0.00 33.09 2.90
6765 8367 5.354767 CCTCCGTCCCAAAAGTATAAGTAC 58.645 45.833 0.00 0.00 0.00 2.73
6766 8368 4.406649 CCCTCCGTCCCAAAAGTATAAGTA 59.593 45.833 0.00 0.00 0.00 2.24
6767 8369 3.199289 CCCTCCGTCCCAAAAGTATAAGT 59.801 47.826 0.00 0.00 0.00 2.24
6768 8370 3.453353 TCCCTCCGTCCCAAAAGTATAAG 59.547 47.826 0.00 0.00 0.00 1.73
6769 8371 3.452878 TCCCTCCGTCCCAAAAGTATAA 58.547 45.455 0.00 0.00 0.00 0.98
6782 8384 2.385803 CCACAATAGTACTCCCTCCGT 58.614 52.381 0.00 0.00 0.00 4.69
6783 8385 1.687123 CCCACAATAGTACTCCCTCCG 59.313 57.143 0.00 0.00 0.00 4.63
6785 8387 2.361438 CGTCCCACAATAGTACTCCCTC 59.639 54.545 0.00 0.00 0.00 4.30
6786 8388 2.385803 CGTCCCACAATAGTACTCCCT 58.614 52.381 0.00 0.00 0.00 4.20
6789 8391 2.361438 CCTCCGTCCCACAATAGTACTC 59.639 54.545 0.00 0.00 0.00 2.59
6790 8392 2.385803 CCTCCGTCCCACAATAGTACT 58.614 52.381 0.00 0.00 0.00 2.73
6799 8410 0.614134 AACTACTCCCTCCGTCCCAC 60.614 60.000 0.00 0.00 0.00 4.61
6830 8441 0.102120 GCTGTCAGACTCATCTCCGG 59.898 60.000 3.32 0.00 30.42 5.14
6831 8442 1.065401 GAGCTGTCAGACTCATCTCCG 59.935 57.143 3.32 0.00 30.42 4.63
6848 8459 6.086765 CGACAAACACACATTGAAATTAGAGC 59.913 38.462 0.00 0.00 0.00 4.09
6874 8485 8.341903 CACATTGGTTCCCTCAAAAATAAAAAC 58.658 33.333 0.00 0.00 0.00 2.43
6880 8491 4.408596 ACACACATTGGTTCCCTCAAAAAT 59.591 37.500 0.00 0.00 0.00 1.82
6882 8493 3.370104 ACACACATTGGTTCCCTCAAAA 58.630 40.909 0.00 0.00 0.00 2.44
6883 8494 3.025322 ACACACATTGGTTCCCTCAAA 57.975 42.857 0.00 0.00 0.00 2.69
6884 8495 2.746279 ACACACATTGGTTCCCTCAA 57.254 45.000 0.00 0.00 0.00 3.02
6933 8545 7.012989 TCTGCCACATTTCAGAATTGATGATAG 59.987 37.037 11.27 7.71 36.50 2.08
6965 8577 4.104102 TCCAAGGTAACCTGTTCAGTGAAT 59.896 41.667 9.18 0.00 32.13 2.57
6972 8584 5.001874 CCTTACTTCCAAGGTAACCTGTTC 58.998 45.833 0.00 0.00 40.29 3.18
7053 8688 3.495806 CCAGCCTATCTTGGAGTGATTCC 60.496 52.174 0.00 0.00 46.98 3.01
7075 8710 5.486526 CTTCTACTATGGGATCATTCCAGC 58.513 45.833 0.00 0.00 44.60 4.85
7263 8914 8.988934 CATCATAAAATAAGTACACATAGCCGT 58.011 33.333 0.00 0.00 0.00 5.68
7313 9051 2.330254 TTTTTGCCCTGTCTCAGCG 58.670 52.632 0.00 0.00 0.00 5.18
7665 9450 7.856145 AGAGAGCTTCAAGTAAACATTATGG 57.144 36.000 0.00 0.00 0.00 2.74
7707 9501 4.323477 TCGGGTTTGGTCGCCCTG 62.323 66.667 0.00 0.00 42.67 4.45
7709 9503 3.952628 CTCTCGGGTTTGGTCGCCC 62.953 68.421 0.00 0.00 41.45 6.13
7712 9506 2.443887 TTAACTCTCGGGTTTGGTCG 57.556 50.000 0.00 0.00 0.00 4.79
7733 9527 3.266510 TCACAATCTCGCTAGGCATTT 57.733 42.857 0.00 0.00 0.00 2.32
7742 9536 2.209838 TTCGAGGATCACAATCTCGC 57.790 50.000 11.94 0.00 34.93 5.03
7807 9601 6.439599 ACAAGAAATCATAGACCGATCTACG 58.560 40.000 0.00 0.00 40.32 3.51
7825 9619 8.252417 TGGCAAAGTAATACTATCGTACAAGAA 58.748 33.333 0.00 0.00 0.00 2.52
7826 9620 7.703621 GTGGCAAAGTAATACTATCGTACAAGA 59.296 37.037 0.00 0.00 0.00 3.02
7828 9622 6.473131 CGTGGCAAAGTAATACTATCGTACAA 59.527 38.462 0.00 0.00 0.00 2.41
7829 9623 5.972973 CGTGGCAAAGTAATACTATCGTACA 59.027 40.000 0.00 0.00 0.00 2.90
7830 9624 6.201517 TCGTGGCAAAGTAATACTATCGTAC 58.798 40.000 0.00 0.00 0.00 3.67
7831 9625 6.375945 TCGTGGCAAAGTAATACTATCGTA 57.624 37.500 0.00 0.00 0.00 3.43
7832 9626 5.252969 TCGTGGCAAAGTAATACTATCGT 57.747 39.130 0.00 0.00 0.00 3.73
7834 9628 9.783256 AAAATTTCGTGGCAAAGTAATACTATC 57.217 29.630 0.00 0.00 0.00 2.08
7835 9629 9.567848 CAAAATTTCGTGGCAAAGTAATACTAT 57.432 29.630 0.00 0.00 0.00 2.12
7836 9630 7.539366 GCAAAATTTCGTGGCAAAGTAATACTA 59.461 33.333 0.00 0.00 0.00 1.82
7838 9632 6.364976 AGCAAAATTTCGTGGCAAAGTAATAC 59.635 34.615 0.00 0.00 0.00 1.89
7839 9633 6.451393 AGCAAAATTTCGTGGCAAAGTAATA 58.549 32.000 0.00 0.00 0.00 0.98
7840 9634 5.296748 AGCAAAATTTCGTGGCAAAGTAAT 58.703 33.333 0.00 0.00 0.00 1.89
7841 9635 4.688021 AGCAAAATTTCGTGGCAAAGTAA 58.312 34.783 0.00 0.00 0.00 2.24
7847 9641 2.879002 TCAAGCAAAATTTCGTGGCA 57.121 40.000 0.00 0.00 0.00 4.92
7851 9645 6.144402 GTGAATGACATCAAGCAAAATTTCGT 59.856 34.615 0.00 0.00 0.00 3.85
7854 9648 6.203338 GTGGTGAATGACATCAAGCAAAATTT 59.797 34.615 4.34 0.00 41.58 1.82
7871 9665 2.104111 TGACTGAAAGACGGTGGTGAAT 59.896 45.455 0.00 0.00 38.34 2.57
7886 9680 4.319694 CGAATTCACATTGCAAGTGACTGA 60.320 41.667 22.90 13.95 44.95 3.41
7908 9702 0.179100 CTGTATGTCCAGGTCCAGCG 60.179 60.000 0.00 0.00 0.00 5.18
7934 9728 0.312102 GTGAAGGACAAGCACTTGCC 59.688 55.000 10.26 11.83 44.03 4.52
7970 9764 0.690762 TTGCAGACCCAACTACCCTC 59.309 55.000 0.00 0.00 0.00 4.30
7987 9789 9.603298 CATCATCGGTTATATTCAGATTTGTTG 57.397 33.333 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.