Multiple sequence alignment - TraesCS5D01G237800

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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 TraesCS5D01G237800 chr5D 100.000 5542 0 0 1 5542 345974672 345969131 0.000000e+00 10235
1 TraesCS5D01G237800 chr5B 92.603 4380 210 45 228 4553 405557464 405561783 0.000000e+00 6189
2 TraesCS5D01G237800 chr5B 94.667 375 17 1 4858 5229 405562204 405562578 3.720000e-161 579
3 TraesCS5D01G237800 chr5B 84.232 241 14 14 1 229 405557023 405557251 4.350000e-51 213
4 TraesCS5D01G237800 chr5A 93.558 3710 175 31 886 4553 445205859 445209546 0.000000e+00 5469
5 TraesCS5D01G237800 chr5A 87.176 694 40 17 4553 5229 445231745 445232406 0.000000e+00 743
6 TraesCS5D01G237800 chr5A 87.032 694 40 18 4553 5229 445209580 445210240 0.000000e+00 737
7 TraesCS5D01G237800 chr5A 87.032 694 41 17 4553 5229 445219357 445220018 0.000000e+00 737
8 TraesCS5D01G237800 chr5A 87.032 694 41 17 4553 5229 445220807 445221468 0.000000e+00 737
9 TraesCS5D01G237800 chr5A 87.032 694 41 17 4553 5229 445226276 445226937 0.000000e+00 737
10 TraesCS5D01G237800 chr5A 89.116 588 30 10 1 573 445204799 445205367 0.000000e+00 701
11 TraesCS5D01G237800 chr5A 93.846 390 13 6 12 398 445204269 445204650 1.340000e-160 577
12 TraesCS5D01G237800 chr5A 91.765 255 17 3 4553 4806 445215048 445215299 8.830000e-93 351
13 TraesCS5D01G237800 chr5A 86.190 210 18 7 602 809 445205367 445205567 3.360000e-52 217
14 TraesCS5D01G237800 chr5A 91.241 137 9 2 4555 4689 86662036 86662171 3.410000e-42 183
15 TraesCS5D01G237800 chr7D 95.625 320 7 6 5225 5542 46853888 46854202 1.780000e-139 507
16 TraesCS5D01G237800 chr7D 93.458 321 15 6 5225 5542 13070605 13070288 6.500000e-129 472
17 TraesCS5D01G237800 chr7D 90.343 321 24 6 5225 5542 37106366 37106682 1.110000e-111 414
18 TraesCS5D01G237800 chr6A 92.523 321 18 5 5225 5542 518604584 518604901 6.540000e-124 455
19 TraesCS5D01G237800 chr6A 90.491 326 16 8 5225 5542 600310712 600311030 3.090000e-112 416
20 TraesCS5D01G237800 chr3D 92.722 316 15 5 5225 5538 75964012 75964321 3.040000e-122 449
21 TraesCS5D01G237800 chr3D 91.875 320 18 5 5225 5542 99808899 99808586 1.830000e-119 440
22 TraesCS5D01G237800 chr4D 91.277 321 23 4 5225 5542 505322840 505323158 3.070000e-117 433
23 TraesCS5D01G237800 chr1D 91.139 316 25 2 5225 5539 320210016 320210329 5.130000e-115 425
24 TraesCS5D01G237800 chrUn 91.765 255 17 3 4553 4806 361785458 361785207 8.830000e-93 351
25 TraesCS5D01G237800 chrUn 93.491 169 8 2 4553 4720 366899842 366899676 1.190000e-61 248


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 TraesCS5D01G237800 chr5D 345969131 345974672 5541 True 10235.0 10235 100.000000 1 5542 1 chr5D.!!$R1 5541
1 TraesCS5D01G237800 chr5B 405557023 405562578 5555 False 2327.0 6189 90.500667 1 5229 3 chr5B.!!$F1 5228
2 TraesCS5D01G237800 chr5A 445204269 445210240 5971 False 1540.2 5469 89.948400 1 5229 5 chr5A.!!$F5 5228
3 TraesCS5D01G237800 chr5A 445231745 445232406 661 False 743.0 743 87.176000 4553 5229 1 chr5A.!!$F4 676
4 TraesCS5D01G237800 chr5A 445219357 445221468 2111 False 737.0 737 87.032000 4553 5229 2 chr5A.!!$F6 676
5 TraesCS5D01G237800 chr5A 445226276 445226937 661 False 737.0 737 87.032000 4553 5229 1 chr5A.!!$F3 676

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
972 1983 0.108329 AACGTCTAACCTCCATGCCG 60.108 55.000 0.00 0.00 0.00 5.69 F
1404 2434 0.178992 CTGGTCCACCTTGGCTTTGA 60.179 55.000 0.00 0.00 37.47 2.69 F
1961 3003 0.179037 CTATTGCCCTGCAGCAGCTA 60.179 55.000 17.81 17.54 45.13 3.32 F
1985 3027 1.212490 CGTGTTGGGCATCGCAAAT 59.788 52.632 0.00 0.00 37.99 2.32 F
2868 3916 1.418373 GTCCATTTGTCGCAAAAGGC 58.582 50.000 16.55 10.85 39.90 4.35 F
4396 5469 1.215382 CGATGCAGGAACCGTGAGA 59.785 57.895 0.00 0.00 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2425 3473 0.607489 GTCTGCCAGTTCCACTGCAT 60.607 55.000 0.00 0.0 44.63 3.96 R
2596 3644 1.271926 GGCACCCAGAAAAGCTTCCTA 60.272 52.381 0.00 0.0 31.28 2.94 R
3130 4178 1.598685 GTTCGGCGGAAAAGGGTGA 60.599 57.895 7.21 0.0 33.05 4.02 R
3141 4189 2.049156 TGTCAGCTCTGTTCGGCG 60.049 61.111 0.00 0.0 0.00 6.46 R
4424 5497 0.399833 TCAACACTAGCACCATGGCA 59.600 50.000 13.04 0.0 35.83 4.92 R
5444 8121 0.034337 TCCGCGTTTAGCCAGTTTCT 59.966 50.000 4.92 0.0 44.76 2.52 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
34 35 9.813446 ATGTAAGTAAGAAGATTAAGGTTACCG 57.187 33.333 0.00 0.00 0.00 4.02
172 733 8.440771 TCTACAGATGTATGGAGTATCTTCTGA 58.559 37.037 11.74 0.00 36.37 3.27
190 751 9.647918 ATCTTCTGACATCTTAGTTGGACTATA 57.352 33.333 0.00 0.00 29.64 1.31
346 1132 1.226746 GACTTTCAGACCAACACCGG 58.773 55.000 0.00 0.00 0.00 5.28
376 1162 4.980590 TGTGCTTACAAGAAACAACAGTG 58.019 39.130 0.00 0.00 0.00 3.66
391 1177 7.466746 AACAACAGTGCACCATTATTATCTT 57.533 32.000 14.63 0.00 0.00 2.40
392 1178 7.466746 ACAACAGTGCACCATTATTATCTTT 57.533 32.000 14.63 0.00 0.00 2.52
393 1179 7.315142 ACAACAGTGCACCATTATTATCTTTG 58.685 34.615 14.63 2.61 0.00 2.77
395 1181 7.701539 ACAGTGCACCATTATTATCTTTGAA 57.298 32.000 14.63 0.00 0.00 2.69
396 1182 8.297470 ACAGTGCACCATTATTATCTTTGAAT 57.703 30.769 14.63 0.00 0.00 2.57
397 1183 8.408601 ACAGTGCACCATTATTATCTTTGAATC 58.591 33.333 14.63 0.00 0.00 2.52
398 1184 7.864379 CAGTGCACCATTATTATCTTTGAATCC 59.136 37.037 14.63 0.00 0.00 3.01
399 1185 7.781693 AGTGCACCATTATTATCTTTGAATCCT 59.218 33.333 14.63 0.00 0.00 3.24
400 1186 7.864379 GTGCACCATTATTATCTTTGAATCCTG 59.136 37.037 5.22 0.00 0.00 3.86
401 1187 7.779326 TGCACCATTATTATCTTTGAATCCTGA 59.221 33.333 0.00 0.00 0.00 3.86
402 1188 8.632679 GCACCATTATTATCTTTGAATCCTGAA 58.367 33.333 0.00 0.00 0.00 3.02
410 1196 6.770746 ATCTTTGAATCCTGAAACAGATGG 57.229 37.500 0.00 0.00 32.44 3.51
411 1197 5.879763 TCTTTGAATCCTGAAACAGATGGA 58.120 37.500 0.00 0.00 32.44 3.41
412 1198 6.487828 TCTTTGAATCCTGAAACAGATGGAT 58.512 36.000 0.00 0.00 40.65 3.41
413 1199 6.376299 TCTTTGAATCCTGAAACAGATGGATG 59.624 38.462 0.00 0.00 39.06 3.51
448 1234 5.820947 ACTGAACAATACAGTCGACCTTTTT 59.179 36.000 13.01 0.70 43.84 1.94
490 1278 1.780309 TGGGACAGTTGGGAGAAACAT 59.220 47.619 0.00 0.00 32.21 2.71
497 1285 6.134535 ACAGTTGGGAGAAACATATGGTTA 57.865 37.500 5.84 0.00 39.29 2.85
621 1409 0.320421 TTGCCTGCTAGTTGTCCGAC 60.320 55.000 0.00 0.00 0.00 4.79
654 1442 6.110543 TGTGTTCATCTTGAATAAGCATCG 57.889 37.500 0.00 0.00 38.79 3.84
735 1523 6.074569 GCTGATTCAATCTCTTTCTAGTACGC 60.075 42.308 0.00 0.00 0.00 4.42
755 1543 4.034742 ACGCAAACTAGTCACGACAAAATT 59.965 37.500 16.21 0.00 0.00 1.82
972 1983 0.108329 AACGTCTAACCTCCATGCCG 60.108 55.000 0.00 0.00 0.00 5.69
973 1984 0.968901 ACGTCTAACCTCCATGCCGA 60.969 55.000 0.00 0.00 0.00 5.54
993 2023 6.369615 TGCCGACTCCAGTTACTAAAATTAAC 59.630 38.462 0.00 0.00 0.00 2.01
1044 2074 4.046938 TGTTCGAATAGCAGAGATGGTC 57.953 45.455 0.00 0.00 0.00 4.02
1078 2108 1.088340 CGAGGCAGCAGATGAACCTG 61.088 60.000 0.00 0.00 37.23 4.00
1167 2197 1.291877 CTCCGAAGAACTTGGCCACG 61.292 60.000 3.88 6.21 0.00 4.94
1310 2340 2.432510 GGGTCAGGGATTACAGTCTCAG 59.567 54.545 0.00 0.00 0.00 3.35
1323 2353 3.118261 ACAGTCTCAGCAAGTTCAAAGGA 60.118 43.478 0.00 0.00 0.00 3.36
1338 2368 0.471617 AAGGAGATCTGATTGCCGGG 59.528 55.000 2.18 0.00 0.00 5.73
1404 2434 0.178992 CTGGTCCACCTTGGCTTTGA 60.179 55.000 0.00 0.00 37.47 2.69
1419 2457 3.380320 GGCTTTGACCACTTAAACTGTGT 59.620 43.478 0.00 0.00 33.92 3.72
1479 2517 4.419522 TTCGAAGCTTGCTAATTTGGAC 57.580 40.909 2.10 0.00 0.00 4.02
1503 2541 3.936453 CGCAGTATGGGCTTTGTAAGTTA 59.064 43.478 0.00 0.00 43.90 2.24
1514 2552 6.174049 GGCTTTGTAAGTTACTCCTCTTGAT 58.826 40.000 14.00 0.00 0.00 2.57
1522 2560 5.241662 AGTTACTCCTCTTGATTCTGTTGC 58.758 41.667 0.00 0.00 0.00 4.17
1615 2653 3.436906 CCAGCTTCATTCCCCCATTGATA 60.437 47.826 0.00 0.00 0.00 2.15
1860 2902 4.099881 ACGTGTTGGACTAAGAGTTGGTAA 59.900 41.667 0.00 0.00 0.00 2.85
1863 2905 6.204108 CGTGTTGGACTAAGAGTTGGTAATTT 59.796 38.462 0.00 0.00 0.00 1.82
1961 3003 0.179037 CTATTGCCCTGCAGCAGCTA 60.179 55.000 17.81 17.54 45.13 3.32
1985 3027 1.212490 CGTGTTGGGCATCGCAAAT 59.788 52.632 0.00 0.00 37.99 2.32
2045 3087 4.961099 TCTGTCTGGAGATCAGTTCATCAT 59.039 41.667 0.00 0.00 43.76 2.45
2053 3095 4.040047 AGATCAGTTCATCATGGGGTACA 58.960 43.478 0.00 0.00 0.00 2.90
2111 3153 9.563748 TTTATATCTTGATCAGAACATCATGCA 57.436 29.630 0.00 0.00 34.16 3.96
2133 3175 7.259882 TGCACTGCATTTTCTGGAATTATAAG 58.740 34.615 0.00 0.00 31.71 1.73
2139 3181 9.353431 TGCATTTTCTGGAATTATAAGAGCATA 57.647 29.630 0.00 0.00 0.00 3.14
2262 3307 5.333568 GCAAGTGCTGAATTGTTTTTGGATC 60.334 40.000 0.00 0.00 38.21 3.36
2275 3320 5.047802 TGTTTTTGGATCTTTGGAGCTCATC 60.048 40.000 17.19 9.18 0.00 2.92
2294 3340 9.638176 AGCTCATCTTTATATTCATTTGGAAGT 57.362 29.630 0.00 0.00 39.30 3.01
2298 3344 7.346751 TCTTTATATTCATTTGGAAGTGGGC 57.653 36.000 0.00 0.00 39.30 5.36
2395 3441 9.037737 GTACTACTGTCTGTCTGAGTTATCTAG 57.962 40.741 0.00 0.00 0.00 2.43
2402 3450 8.979534 TGTCTGTCTGAGTTATCTAGAGTACTA 58.020 37.037 8.96 0.00 0.00 1.82
2422 3470 9.148879 AGTACTAACAAGGAGATGCTTGTATAT 57.851 33.333 18.35 7.47 42.21 0.86
2457 3505 2.559668 CTGGCAGACAATTGTGATTGGT 59.440 45.455 17.58 0.00 45.56 3.67
2493 3541 5.278315 GGTTTTCCTTCTGTTTGCGAAGTAT 60.278 40.000 0.00 0.00 36.91 2.12
2502 3550 5.975344 TCTGTTTGCGAAGTATATCGTAAGG 59.025 40.000 1.01 0.00 45.58 2.69
2506 3554 7.168637 TGTTTGCGAAGTATATCGTAAGGATTC 59.831 37.037 1.01 0.00 45.58 2.52
2507 3555 6.570672 TGCGAAGTATATCGTAAGGATTCT 57.429 37.500 0.00 0.00 44.49 2.40
2510 3558 7.381408 TGCGAAGTATATCGTAAGGATTCTTTG 59.619 37.037 0.00 0.00 44.49 2.77
2596 3644 8.360390 GTTTGATTTACACAGGGAAAGAAGAAT 58.640 33.333 0.00 0.00 0.00 2.40
2713 3761 7.969508 GGTGTTCAGATAGTAAGTGACTAAGTC 59.030 40.741 0.00 0.00 43.96 3.01
2785 3833 7.065683 GGATGAAAATTTTGTTGTCACTTGGTT 59.934 33.333 8.47 0.00 0.00 3.67
2859 3907 5.379732 TTTATTTCACCGGTCCATTTGTC 57.620 39.130 2.59 0.00 0.00 3.18
2868 3916 1.418373 GTCCATTTGTCGCAAAAGGC 58.582 50.000 16.55 10.85 39.90 4.35
3130 4178 3.007940 TGCTATGTCACAACAGGTAGCTT 59.992 43.478 8.47 0.00 41.47 3.74
3140 4188 3.141767 ACAGGTAGCTTCACCCTTTTC 57.858 47.619 1.82 0.00 39.62 2.29
3141 4189 2.224793 ACAGGTAGCTTCACCCTTTTCC 60.225 50.000 1.82 0.00 39.62 3.13
3187 4235 4.406456 TGTCTGGAAAATACAGTGCCAAT 58.594 39.130 0.00 0.00 37.25 3.16
3339 4388 3.687212 CACCGCTATTCAAATACACACCA 59.313 43.478 0.00 0.00 0.00 4.17
3507 4556 2.040278 TGGCCTCTTGATTGCTGTAAGT 59.960 45.455 3.32 0.00 35.30 2.24
3513 4562 5.352569 CCTCTTGATTGCTGTAAGTACCAAG 59.647 44.000 0.00 0.00 39.25 3.61
3514 4563 4.695455 TCTTGATTGCTGTAAGTACCAAGC 59.305 41.667 0.00 0.00 38.45 4.01
3515 4564 4.014569 TGATTGCTGTAAGTACCAAGCA 57.985 40.909 5.54 5.54 43.60 3.91
3526 4577 9.113838 CTGTAAGTACCAAGCATATCTTTGATT 57.886 33.333 0.00 0.00 31.27 2.57
3622 4682 7.012704 GCAATCTCATTTGCCAAGATACTTCTA 59.987 37.037 0.00 0.00 44.94 2.10
3793 4853 5.677319 ATGTCCGAGAAAGGTAAAGATGA 57.323 39.130 0.00 0.00 0.00 2.92
4022 5084 8.547967 TTATATGTTGGTCTCAGAAGTTTCAC 57.452 34.615 0.00 0.00 0.00 3.18
4030 5092 6.483307 TGGTCTCAGAAGTTTCACACTATTTG 59.517 38.462 0.00 0.00 32.94 2.32
4059 5125 5.798132 TCAATCATTGTACTGAAGCAGTCT 58.202 37.500 2.97 0.00 41.21 3.24
4177 5243 3.007635 GGTACACCCATTCAAGCTACAC 58.992 50.000 0.00 0.00 0.00 2.90
4262 5335 2.275134 TTTGGCAGCTCATTCTGTCA 57.725 45.000 0.00 0.00 45.83 3.58
4290 5363 4.571919 TGGTTCCGTCGTCATAGAAAAAT 58.428 39.130 0.00 0.00 0.00 1.82
4340 5413 7.230108 CACATTGGAAGCAGTCATATATTCCTT 59.770 37.037 4.12 0.00 40.11 3.36
4355 5428 1.739562 CCTTGCAGTCTCTGACGCC 60.740 63.158 0.66 0.21 37.67 5.68
4396 5469 1.215382 CGATGCAGGAACCGTGAGA 59.785 57.895 0.00 0.00 0.00 3.27
4409 5482 1.467713 CCGTGAGAGAAGTAGTTCGGC 60.468 57.143 4.65 1.92 37.79 5.54
4420 5493 2.587322 TAGTTCGGCGGAATGGCTGG 62.587 60.000 7.21 0.00 42.02 4.85
4421 5494 4.028490 TTCGGCGGAATGGCTGGT 62.028 61.111 7.21 0.00 42.02 4.00
4422 5495 4.776322 TCGGCGGAATGGCTGGTG 62.776 66.667 7.21 0.00 42.02 4.17
4424 5497 4.740822 GGCGGAATGGCTGGTGGT 62.741 66.667 0.00 0.00 40.72 4.16
4425 5498 3.443045 GCGGAATGGCTGGTGGTG 61.443 66.667 0.00 0.00 0.00 4.17
4426 5499 3.443045 CGGAATGGCTGGTGGTGC 61.443 66.667 0.00 0.00 0.00 5.01
4435 5508 3.900862 TGGTGGTGCCATGGTGCT 61.901 61.111 14.67 0.00 43.61 4.40
4436 5509 2.354729 GGTGGTGCCATGGTGCTA 59.645 61.111 14.67 1.40 37.17 3.49
4454 5544 6.770785 TGGTGCTAGTGTTGAGAATAGTTTTT 59.229 34.615 0.00 0.00 0.00 1.94
4474 5564 1.833630 TGTGCTCCCTGTGATCTAAGG 59.166 52.381 7.16 7.16 0.00 2.69
4528 5618 9.295825 TGGCCAATGTAGAAACATATAATAAGG 57.704 33.333 0.61 0.00 45.79 2.69
4634 5760 5.694231 TTGTTCACTCATTTCAGTCCATG 57.306 39.130 0.00 0.00 0.00 3.66
4728 5854 4.887071 AGTGCTCCTCTACTGAGTATGAAG 59.113 45.833 0.00 0.00 38.61 3.02
4763 5889 0.911769 AACTCATGGCGGATCTTCCA 59.088 50.000 8.53 8.53 35.91 3.53
4831 5960 7.347448 GGTGCATTTCTTTTTCTTGATCAAAC 58.653 34.615 9.88 0.00 0.00 2.93
4854 5983 0.553612 AGGCCTCCCTCTCCCATTTT 60.554 55.000 0.00 0.00 36.46 1.82
4893 6104 5.479724 AGGTTCACAACTACTACTAGGGTTC 59.520 44.000 0.00 0.00 0.00 3.62
4895 6106 6.350027 GGTTCACAACTACTACTAGGGTTCTC 60.350 46.154 0.00 0.00 0.00 2.87
4937 6148 3.833070 ACTATCTTACATGACCGGGGATC 59.167 47.826 6.32 0.00 0.00 3.36
4975 6187 0.379669 GCACCTCAAAGGATCATGCG 59.620 55.000 0.00 0.00 37.67 4.73
5002 6214 4.527816 TCCCAAAATAAAAGCAGAGCACAT 59.472 37.500 0.00 0.00 0.00 3.21
5073 6285 6.734137 CAACATACAGTAGTTGGAAGCAAAA 58.266 36.000 11.95 0.00 40.97 2.44
5158 7832 0.325296 TAAGCCACCGGGATCTCAGT 60.325 55.000 6.32 0.00 35.59 3.41
5229 7906 4.373116 AACCGTCCGCACGCATCT 62.373 61.111 0.00 0.00 45.29 2.90
5230 7907 4.796231 ACCGTCCGCACGCATCTC 62.796 66.667 0.00 0.00 45.29 2.75
5232 7909 4.794439 CGTCCGCACGCATCTCCA 62.794 66.667 0.00 0.00 39.69 3.86
5233 7910 2.887568 GTCCGCACGCATCTCCAG 60.888 66.667 0.00 0.00 0.00 3.86
5234 7911 4.819761 TCCGCACGCATCTCCAGC 62.820 66.667 0.00 0.00 0.00 4.85
5238 7915 2.434884 CACGCATCTCCAGCCGTT 60.435 61.111 0.00 0.00 0.00 4.44
5239 7916 2.434884 ACGCATCTCCAGCCGTTG 60.435 61.111 0.00 0.00 0.00 4.10
5260 7937 4.055227 CCCCAGGGGCGCCTAAAA 62.055 66.667 28.56 0.00 35.35 1.52
5261 7938 2.278738 CCCAGGGGCGCCTAAAAT 59.721 61.111 28.56 4.89 0.00 1.82
5262 7939 1.828224 CCCAGGGGCGCCTAAAATC 60.828 63.158 28.56 8.16 0.00 2.17
5263 7940 2.186826 CCAGGGGCGCCTAAAATCG 61.187 63.158 28.56 8.84 0.00 3.34
5268 7945 4.607606 GCGCCTAAAATCGCCGCC 62.608 66.667 0.00 0.00 45.01 6.13
5269 7946 2.895372 CGCCTAAAATCGCCGCCT 60.895 61.111 0.00 0.00 0.00 5.52
5270 7947 2.715624 GCCTAAAATCGCCGCCTG 59.284 61.111 0.00 0.00 0.00 4.85
5271 7948 2.834618 GCCTAAAATCGCCGCCTGG 61.835 63.158 0.00 0.00 38.77 4.45
5272 7949 2.186826 CCTAAAATCGCCGCCTGGG 61.187 63.158 0.00 0.00 39.58 4.45
5290 7967 3.972276 GGTGAGCCGGCGCAAAAA 61.972 61.111 34.87 9.47 37.52 1.94
5304 7981 4.111967 AAAAATGGCCCTGGGACG 57.888 55.556 19.27 0.00 29.56 4.79
5305 7982 1.462928 AAAAATGGCCCTGGGACGA 59.537 52.632 19.27 4.85 29.56 4.20
5306 7983 0.611896 AAAAATGGCCCTGGGACGAG 60.612 55.000 19.27 0.00 29.56 4.18
5307 7984 1.789576 AAAATGGCCCTGGGACGAGT 61.790 55.000 19.27 0.00 29.56 4.18
5308 7985 1.789576 AAATGGCCCTGGGACGAGTT 61.790 55.000 19.27 7.44 29.56 3.01
5309 7986 2.484287 AATGGCCCTGGGACGAGTTG 62.484 60.000 19.27 0.00 29.56 3.16
5310 7987 4.410400 GGCCCTGGGACGAGTTGG 62.410 72.222 19.27 0.00 0.00 3.77
5311 7988 3.637273 GCCCTGGGACGAGTTGGT 61.637 66.667 19.27 0.00 0.00 3.67
5312 7989 2.663196 CCCTGGGACGAGTTGGTC 59.337 66.667 7.01 0.00 36.18 4.02
5318 7995 2.047179 GACGAGTTGGTCCCCAGC 60.047 66.667 0.00 0.00 33.81 4.85
5319 7996 3.607370 GACGAGTTGGTCCCCAGCC 62.607 68.421 0.00 0.00 35.27 4.85
5320 7997 4.760047 CGAGTTGGTCCCCAGCCG 62.760 72.222 0.00 0.00 35.27 5.52
5352 8029 3.366915 GCCCCAGGCGCGTTTAAA 61.367 61.111 8.43 0.00 39.62 1.52
5353 8030 2.921797 GCCCCAGGCGCGTTTAAAA 61.922 57.895 8.43 0.00 39.62 1.52
5354 8031 1.660917 CCCCAGGCGCGTTTAAAAA 59.339 52.632 8.43 0.00 0.00 1.94
5379 8056 7.581011 AAAGGCAAAAATATAGCAAAGTTCG 57.419 32.000 0.00 0.00 0.00 3.95
5380 8057 5.650543 AGGCAAAAATATAGCAAAGTTCGG 58.349 37.500 0.00 0.00 0.00 4.30
5381 8058 4.267690 GGCAAAAATATAGCAAAGTTCGGC 59.732 41.667 0.00 0.00 0.00 5.54
5382 8059 4.027702 GCAAAAATATAGCAAAGTTCGGCG 60.028 41.667 0.00 0.00 34.54 6.46
5383 8060 5.328691 CAAAAATATAGCAAAGTTCGGCGA 58.671 37.500 4.99 4.99 34.54 5.54
5384 8061 5.554822 AAAATATAGCAAAGTTCGGCGAA 57.445 34.783 19.83 19.83 34.54 4.70
5385 8062 4.795970 AATATAGCAAAGTTCGGCGAAG 57.204 40.909 24.41 12.45 34.54 3.79
5386 8063 2.094762 ATAGCAAAGTTCGGCGAAGT 57.905 45.000 24.41 23.86 34.54 3.01
5387 8064 1.873698 TAGCAAAGTTCGGCGAAGTT 58.126 45.000 31.04 31.04 36.85 2.66
5388 8065 0.586802 AGCAAAGTTCGGCGAAGTTC 59.413 50.000 34.76 25.35 34.57 3.01
5389 8066 0.721483 GCAAAGTTCGGCGAAGTTCG 60.721 55.000 34.76 27.94 43.89 3.95
5390 8067 0.110823 CAAAGTTCGGCGAAGTTCGG 60.111 55.000 34.76 26.83 40.84 4.30
5402 8079 5.779806 GCGAAGTTCGGCATATATTACAT 57.220 39.130 25.55 0.00 40.84 2.29
5403 8080 6.880822 GCGAAGTTCGGCATATATTACATA 57.119 37.500 25.55 0.00 40.84 2.29
5404 8081 7.285783 GCGAAGTTCGGCATATATTACATAA 57.714 36.000 25.55 0.00 40.84 1.90
5405 8082 7.906160 GCGAAGTTCGGCATATATTACATAAT 58.094 34.615 25.55 0.00 40.84 1.28
5406 8083 9.027129 GCGAAGTTCGGCATATATTACATAATA 57.973 33.333 25.55 0.00 40.84 0.98
5410 8087 9.731819 AGTTCGGCATATATTACATAATAGTCG 57.268 33.333 0.00 0.00 32.24 4.18
5411 8088 8.477709 GTTCGGCATATATTACATAATAGTCGC 58.522 37.037 0.00 0.85 32.24 5.19
5412 8089 6.854381 TCGGCATATATTACATAATAGTCGCG 59.146 38.462 0.00 0.00 32.24 5.87
5413 8090 6.087687 CGGCATATATTACATAATAGTCGCGG 59.912 42.308 6.13 0.00 32.24 6.46
5414 8091 7.143340 GGCATATATTACATAATAGTCGCGGA 58.857 38.462 6.13 0.00 32.24 5.54
5415 8092 7.813148 GGCATATATTACATAATAGTCGCGGAT 59.187 37.037 6.13 0.00 32.24 4.18
5416 8093 9.193133 GCATATATTACATAATAGTCGCGGATT 57.807 33.333 6.13 6.66 32.24 3.01
5425 8102 9.263538 ACATAATAGTCGCGGATTTTTATTACA 57.736 29.630 6.13 0.00 0.00 2.41
5459 8136 9.887406 TCTAATTAAAAAGAAACTGGCTAAACG 57.113 29.630 0.00 0.00 0.00 3.60
5460 8137 7.402811 AATTAAAAAGAAACTGGCTAAACGC 57.597 32.000 0.00 0.00 38.13 4.84
5461 8138 2.681152 AAAGAAACTGGCTAAACGCG 57.319 45.000 3.53 3.53 40.44 6.01
5462 8139 0.872388 AAGAAACTGGCTAAACGCGG 59.128 50.000 12.47 0.00 40.44 6.46
5463 8140 0.034337 AGAAACTGGCTAAACGCGGA 59.966 50.000 12.47 0.00 40.44 5.54
5464 8141 0.442699 GAAACTGGCTAAACGCGGAG 59.557 55.000 12.47 5.75 40.44 4.63
5465 8142 0.250166 AAACTGGCTAAACGCGGAGT 60.250 50.000 12.47 0.00 40.44 3.85
5466 8143 0.604578 AACTGGCTAAACGCGGAGTA 59.395 50.000 12.47 0.00 40.44 2.59
5467 8144 0.172803 ACTGGCTAAACGCGGAGTAG 59.827 55.000 12.47 9.80 40.44 2.57
5468 8145 0.172803 CTGGCTAAACGCGGAGTAGT 59.827 55.000 12.47 0.00 40.44 2.73
5469 8146 0.171903 TGGCTAAACGCGGAGTAGTC 59.828 55.000 12.47 10.75 40.44 2.59
5470 8147 0.864797 GGCTAAACGCGGAGTAGTCG 60.865 60.000 12.47 0.00 40.44 4.18
5478 8155 2.402787 GGAGTAGTCGCCGTCGTC 59.597 66.667 0.00 0.00 36.96 4.20
5479 8156 2.021106 GAGTAGTCGCCGTCGTCG 59.979 66.667 0.00 0.00 36.96 5.12
5480 8157 4.157958 AGTAGTCGCCGTCGTCGC 62.158 66.667 0.00 0.00 36.96 5.19
5501 8178 4.592192 CATCCTCGCCGCCGTCAT 62.592 66.667 0.00 0.00 35.54 3.06
5502 8179 4.286320 ATCCTCGCCGCCGTCATC 62.286 66.667 0.00 0.00 35.54 2.92
5513 8190 4.175489 CGTCATCGTCGTCGGGCT 62.175 66.667 1.55 0.00 37.69 5.19
5514 8191 2.181021 GTCATCGTCGTCGGGCTT 59.819 61.111 1.55 0.00 37.69 4.35
5515 8192 1.872679 GTCATCGTCGTCGGGCTTC 60.873 63.158 1.55 0.00 37.69 3.86
5516 8193 2.044555 TCATCGTCGTCGGGCTTCT 61.045 57.895 1.55 0.00 37.69 2.85
5517 8194 1.586564 CATCGTCGTCGGGCTTCTC 60.587 63.158 1.55 0.00 37.69 2.87
5518 8195 2.772691 ATCGTCGTCGGGCTTCTCC 61.773 63.158 1.55 0.00 37.69 3.71
5519 8196 3.441290 CGTCGTCGGGCTTCTCCT 61.441 66.667 0.00 0.00 34.39 3.69
5520 8197 2.490685 GTCGTCGGGCTTCTCCTC 59.509 66.667 0.00 0.00 34.39 3.71
5521 8198 2.754658 TCGTCGGGCTTCTCCTCC 60.755 66.667 0.00 0.00 34.39 4.30
5522 8199 2.756283 CGTCGGGCTTCTCCTCCT 60.756 66.667 0.00 0.00 34.39 3.69
5523 8200 2.352032 CGTCGGGCTTCTCCTCCTT 61.352 63.158 0.00 0.00 34.39 3.36
5524 8201 1.219393 GTCGGGCTTCTCCTCCTTG 59.781 63.158 0.00 0.00 34.39 3.61
5525 8202 1.078528 TCGGGCTTCTCCTCCTTGA 59.921 57.895 0.00 0.00 34.39 3.02
5526 8203 1.219393 CGGGCTTCTCCTCCTTGAC 59.781 63.158 0.00 0.00 34.39 3.18
5527 8204 1.219393 GGGCTTCTCCTCCTTGACG 59.781 63.158 0.00 0.00 34.39 4.35
5528 8205 1.448717 GGCTTCTCCTCCTTGACGC 60.449 63.158 0.00 0.00 0.00 5.19
5529 8206 1.807573 GCTTCTCCTCCTTGACGCG 60.808 63.158 3.53 3.53 0.00 6.01
5530 8207 1.153745 CTTCTCCTCCTTGACGCGG 60.154 63.158 12.47 0.00 0.00 6.46
5531 8208 3.296709 TTCTCCTCCTTGACGCGGC 62.297 63.158 12.47 8.67 0.00 6.53
5532 8209 4.821589 CTCCTCCTTGACGCGGCC 62.822 72.222 10.82 0.56 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.860898 TTCGGTAACCTTAATCTTCTTACTTAC 57.139 33.333 0.00 0.00 0.00 2.34
12 13 9.955102 AATTCGGTAACCTTAATCTTCTTACTT 57.045 29.630 0.00 0.00 0.00 2.24
13 14 9.955102 AAATTCGGTAACCTTAATCTTCTTACT 57.045 29.630 0.00 0.00 0.00 2.24
99 649 3.072944 AGAGCAGACAGATGAACAAAGC 58.927 45.455 0.00 0.00 0.00 3.51
102 652 3.243873 ACGAAGAGCAGACAGATGAACAA 60.244 43.478 0.00 0.00 0.00 2.83
166 727 9.906660 GATATAGTCCAACTAAGATGTCAGAAG 57.093 37.037 0.00 0.00 33.89 2.85
172 733 6.784969 AGGCTGATATAGTCCAACTAAGATGT 59.215 38.462 0.00 0.00 33.89 3.06
190 751 2.040278 TCAAGTTTGTGCCTAGGCTGAT 59.960 45.455 33.07 11.44 42.51 2.90
376 1162 8.169977 TCAGGATTCAAAGATAATAATGGTGC 57.830 34.615 0.00 0.00 0.00 5.01
391 1177 5.573219 ACATCCATCTGTTTCAGGATTCAA 58.427 37.500 0.00 0.00 38.77 2.69
392 1178 5.183530 ACATCCATCTGTTTCAGGATTCA 57.816 39.130 0.00 0.00 38.77 2.57
393 1179 5.649395 TGAACATCCATCTGTTTCAGGATTC 59.351 40.000 0.00 0.00 39.40 2.52
395 1181 4.946157 GTGAACATCCATCTGTTTCAGGAT 59.054 41.667 0.00 0.00 39.40 3.24
396 1182 4.202451 TGTGAACATCCATCTGTTTCAGGA 60.202 41.667 0.00 0.00 39.40 3.86
397 1183 4.074259 TGTGAACATCCATCTGTTTCAGG 58.926 43.478 0.00 0.00 39.40 3.86
398 1184 4.758674 AGTGTGAACATCCATCTGTTTCAG 59.241 41.667 0.00 0.00 39.40 3.02
399 1185 4.516321 CAGTGTGAACATCCATCTGTTTCA 59.484 41.667 0.00 0.00 39.40 2.69
400 1186 4.756642 TCAGTGTGAACATCCATCTGTTTC 59.243 41.667 0.00 0.00 39.40 2.78
401 1187 4.717877 TCAGTGTGAACATCCATCTGTTT 58.282 39.130 0.00 0.00 39.40 2.83
402 1188 4.356405 TCAGTGTGAACATCCATCTGTT 57.644 40.909 0.00 0.00 41.92 3.16
403 1189 4.356405 TTCAGTGTGAACATCCATCTGT 57.644 40.909 0.00 0.00 30.26 3.41
448 1234 9.643735 TCCCATTCTAACAGTAAAAGGTAAAAA 57.356 29.630 0.00 0.00 0.00 1.94
454 1240 6.743575 CTGTCCCATTCTAACAGTAAAAGG 57.256 41.667 0.00 0.00 36.50 3.11
462 1250 2.983192 TCCCAACTGTCCCATTCTAACA 59.017 45.455 0.00 0.00 0.00 2.41
558 1346 8.893219 CTAAGAATAGCAACAGTGAATCCATA 57.107 34.615 0.00 0.00 0.00 2.74
593 1381 4.584325 ACAACTAGCAGGCAAATCTTTTCA 59.416 37.500 0.00 0.00 0.00 2.69
621 1409 5.491070 TCAAGATGAACACATACCTTGAGG 58.509 41.667 0.00 0.00 36.21 3.86
631 1419 5.447683 GCGATGCTTATTCAAGATGAACACA 60.448 40.000 0.00 0.00 39.45 3.72
654 1442 6.445357 TTTCGTTTTGGGAGAAATATAGGC 57.555 37.500 0.00 0.00 0.00 3.93
694 1482 1.742761 CAGCAGTATGTTGGTGGAGG 58.257 55.000 3.37 0.00 44.15 4.30
928 1938 6.885735 ACAGTACTTCAACATTGCAAAAAC 57.114 33.333 1.71 0.00 0.00 2.43
943 1954 5.536161 TGGAGGTTAGACGTTTACAGTACTT 59.464 40.000 0.00 0.00 0.00 2.24
993 2023 5.551233 TGTTATCCTGGAGAAACAGTTGAG 58.449 41.667 18.41 0.00 36.75 3.02
1028 2058 4.613925 TGATGGACCATCTCTGCTATTC 57.386 45.455 30.11 6.73 41.06 1.75
1030 2060 8.011883 AGATATATGATGGACCATCTCTGCTAT 58.988 37.037 30.11 18.48 41.06 2.97
1044 2074 4.680702 CTGCCTCGTCAGATATATGATGG 58.319 47.826 17.33 13.65 36.93 3.51
1078 2108 1.237285 GGTGTCTGTGTGGTGATGCC 61.237 60.000 0.00 0.00 37.90 4.40
1167 2197 7.117092 GTCTCTCTCAATGTTTCTGTAAACTCC 59.883 40.741 3.01 0.00 44.44 3.85
1292 2322 2.820178 TGCTGAGACTGTAATCCCTGA 58.180 47.619 0.00 0.00 0.00 3.86
1293 2323 3.055530 ACTTGCTGAGACTGTAATCCCTG 60.056 47.826 0.00 0.00 0.00 4.45
1310 2340 5.638783 CAATCAGATCTCCTTTGAACTTGC 58.361 41.667 0.00 0.00 0.00 4.01
1323 2353 0.911769 TCAACCCGGCAATCAGATCT 59.088 50.000 0.00 0.00 0.00 2.75
1338 2368 0.674895 AGAGGCTTGCGATGGTCAAC 60.675 55.000 0.00 0.00 0.00 3.18
1387 2417 1.179174 GGTCAAAGCCAAGGTGGACC 61.179 60.000 0.00 0.00 40.96 4.46
1404 2434 4.481368 TGTCAGACACAGTTTAAGTGGT 57.519 40.909 0.00 0.00 41.21 4.16
1419 2457 5.233083 AGAGTCCAACATTCAATGTCAGA 57.767 39.130 2.74 0.81 44.07 3.27
1503 2541 2.613977 CCGCAACAGAATCAAGAGGAGT 60.614 50.000 0.00 0.00 0.00 3.85
1514 2552 2.162208 GCATCAAATCTCCGCAACAGAA 59.838 45.455 0.00 0.00 0.00 3.02
1522 2560 3.680642 ATGTTTCGCATCAAATCTCCG 57.319 42.857 0.00 0.00 30.67 4.63
1615 2653 2.107031 TGAGCTACCCATTGCAGCATAT 59.893 45.455 0.00 0.00 37.78 1.78
1786 2824 7.817418 TGTTTGCATATACCTTAGAAATCCC 57.183 36.000 0.00 0.00 0.00 3.85
1869 2911 6.509386 ACTCTATAAGGAACCCTAACCTGAA 58.491 40.000 0.00 0.00 36.56 3.02
1961 3003 1.135517 GCGATGCCCAACACGTATTTT 60.136 47.619 0.00 0.00 0.00 1.82
1985 3027 7.571080 AACTATGTCGGTTTTCCTTGTAAAA 57.429 32.000 0.00 0.00 37.95 1.52
2045 3087 8.119891 TGCTAAGTATATGAGATATGTACCCCA 58.880 37.037 0.00 0.00 0.00 4.96
2096 3138 2.718563 TGCAGTGCATGATGTTCTGAT 58.281 42.857 15.37 0.00 31.71 2.90
2111 3153 7.340232 TGCTCTTATAATTCCAGAAAATGCAGT 59.660 33.333 0.00 0.00 0.00 4.40
2275 3320 7.111247 TGCCCACTTCCAAATGAATATAAAG 57.889 36.000 0.00 0.00 31.06 1.85
2294 3340 1.337118 GGAACAAATTCACCTGCCCA 58.663 50.000 0.00 0.00 36.46 5.36
2362 3408 8.760735 ACTCAGACAGACAGTAGTACTATCTTA 58.239 37.037 8.42 0.00 27.62 2.10
2422 3470 2.771372 TCTGCCAGTTCCACTGCATATA 59.229 45.455 0.00 0.00 44.63 0.86
2423 3471 1.561076 TCTGCCAGTTCCACTGCATAT 59.439 47.619 0.00 0.00 44.63 1.78
2424 3472 0.983467 TCTGCCAGTTCCACTGCATA 59.017 50.000 0.00 0.00 44.63 3.14
2425 3473 0.607489 GTCTGCCAGTTCCACTGCAT 60.607 55.000 0.00 0.00 44.63 3.96
2457 3505 6.003950 CAGAAGGAAAACCAGGAAAGATACA 58.996 40.000 0.00 0.00 0.00 2.29
2502 3550 8.161699 TGTAAAGGTACAAGGAACAAAGAATC 57.838 34.615 0.00 0.00 37.29 2.52
2574 3622 8.047310 TCCTATTCTTCTTTCCCTGTGTAAATC 58.953 37.037 0.00 0.00 0.00 2.17
2596 3644 1.271926 GGCACCCAGAAAAGCTTCCTA 60.272 52.381 0.00 0.00 31.28 2.94
2713 3761 5.009010 ACACAACTGAGCCTGAATTTTACTG 59.991 40.000 0.00 0.00 0.00 2.74
2785 3833 5.647658 CCTGTTCAATGTGCTTTACCTGATA 59.352 40.000 0.00 0.00 0.00 2.15
2868 3916 3.300009 GCAAACAACACCGATCTTGAAG 58.700 45.455 0.00 0.00 0.00 3.02
3130 4178 1.598685 GTTCGGCGGAAAAGGGTGA 60.599 57.895 7.21 0.00 33.05 4.02
3140 4188 2.811317 GTCAGCTCTGTTCGGCGG 60.811 66.667 7.21 0.00 0.00 6.13
3141 4189 2.049156 TGTCAGCTCTGTTCGGCG 60.049 61.111 0.00 0.00 0.00 6.46
3339 4388 3.136443 TGATCGACCCTAGGATTGCATTT 59.864 43.478 11.48 0.00 0.00 2.32
3539 4590 2.290367 CTCCGCAAAAAGACATGACACA 59.710 45.455 0.00 0.00 0.00 3.72
3540 4591 2.548057 TCTCCGCAAAAAGACATGACAC 59.452 45.455 0.00 0.00 0.00 3.67
3556 4608 6.872670 GAACAAGTTCTACTTATGTCTCCG 57.127 41.667 5.72 0.00 36.03 4.63
3613 4673 6.403878 TGGCCTTGTTACTTGTAGAAGTATC 58.596 40.000 12.81 12.32 42.92 2.24
3622 4682 2.092103 TGTCCTTGGCCTTGTTACTTGT 60.092 45.455 3.32 0.00 0.00 3.16
3655 4715 2.671963 GTGGTGCCGGGAAGGTTC 60.672 66.667 2.18 0.00 43.70 3.62
3772 4832 5.677319 ATCATCTTTACCTTTCTCGGACA 57.323 39.130 0.00 0.00 0.00 4.02
3838 4900 3.988379 ACTGAATTCATGTGTGCGTTT 57.012 38.095 8.96 0.00 0.00 3.60
3839 4901 4.515191 AGTTACTGAATTCATGTGTGCGTT 59.485 37.500 8.96 0.00 0.00 4.84
3840 4902 4.065088 AGTTACTGAATTCATGTGTGCGT 58.935 39.130 8.96 4.11 0.00 5.24
3841 4903 4.668576 AGTTACTGAATTCATGTGTGCG 57.331 40.909 8.96 0.00 0.00 5.34
3842 4904 6.000891 TGAAGTTACTGAATTCATGTGTGC 57.999 37.500 8.96 2.33 0.00 4.57
3843 4905 6.082338 GCTGAAGTTACTGAATTCATGTGTG 58.918 40.000 8.96 0.00 32.82 3.82
3949 5011 5.705609 TCAAGGAACTGATTTTAGGCAAC 57.294 39.130 0.00 0.00 40.86 4.17
4052 5118 2.295349 CAGCATTTTTCACCAGACTGCT 59.705 45.455 0.00 0.00 38.93 4.24
4059 5125 3.984838 GCACCAGCATTTTTCACCA 57.015 47.368 0.00 0.00 41.58 4.17
4209 5280 2.814805 ACAACATTATCAGCTGCCCT 57.185 45.000 9.47 0.00 0.00 5.19
4262 5335 0.682852 TGACGACGGAACCAGGATTT 59.317 50.000 0.00 0.00 0.00 2.17
4290 5363 0.518636 GTGAGCTTCGATGCTTGCAA 59.481 50.000 24.71 10.20 44.17 4.08
4340 5413 3.295273 ACGGCGTCAGAGACTGCA 61.295 61.111 6.77 0.00 35.22 4.41
4355 5428 0.519792 TCGTCGTACAGAATCGCACG 60.520 55.000 0.00 0.00 34.64 5.34
4396 5469 1.134788 CCATTCCGCCGAACTACTTCT 60.135 52.381 0.00 0.00 0.00 2.85
4409 5482 3.443045 GCACCACCAGCCATTCCG 61.443 66.667 0.00 0.00 0.00 4.30
4420 5493 1.002134 ACTAGCACCATGGCACCAC 60.002 57.895 13.04 0.00 35.83 4.16
4421 5494 1.002257 CACTAGCACCATGGCACCA 60.002 57.895 13.04 0.00 35.83 4.17
4422 5495 0.609131 AACACTAGCACCATGGCACC 60.609 55.000 13.04 0.00 35.83 5.01
4423 5496 0.523072 CAACACTAGCACCATGGCAC 59.477 55.000 13.04 3.68 35.83 5.01
4424 5497 0.399833 TCAACACTAGCACCATGGCA 59.600 50.000 13.04 0.00 35.83 4.92
4425 5498 1.089920 CTCAACACTAGCACCATGGC 58.910 55.000 13.04 0.00 0.00 4.40
4426 5499 2.768253 TCTCAACACTAGCACCATGG 57.232 50.000 11.19 11.19 0.00 3.66
4427 5500 5.423015 ACTATTCTCAACACTAGCACCATG 58.577 41.667 0.00 0.00 0.00 3.66
4428 5501 5.683876 ACTATTCTCAACACTAGCACCAT 57.316 39.130 0.00 0.00 0.00 3.55
4429 5502 5.483685 AACTATTCTCAACACTAGCACCA 57.516 39.130 0.00 0.00 0.00 4.17
4430 5503 6.803154 AAAACTATTCTCAACACTAGCACC 57.197 37.500 0.00 0.00 0.00 5.01
4431 5504 7.587757 CACAAAAACTATTCTCAACACTAGCAC 59.412 37.037 0.00 0.00 0.00 4.40
4432 5505 7.639039 CACAAAAACTATTCTCAACACTAGCA 58.361 34.615 0.00 0.00 0.00 3.49
4433 5506 6.578919 GCACAAAAACTATTCTCAACACTAGC 59.421 38.462 0.00 0.00 0.00 3.42
4434 5507 7.865707 AGCACAAAAACTATTCTCAACACTAG 58.134 34.615 0.00 0.00 0.00 2.57
4435 5508 7.041372 GGAGCACAAAAACTATTCTCAACACTA 60.041 37.037 0.00 0.00 0.00 2.74
4436 5509 6.238759 GGAGCACAAAAACTATTCTCAACACT 60.239 38.462 0.00 0.00 0.00 3.55
4454 5544 1.833630 CCTTAGATCACAGGGAGCACA 59.166 52.381 0.00 0.00 33.23 4.57
4474 5564 2.117156 ATCATCTTGCGCTGCCCAC 61.117 57.895 9.73 0.00 0.00 4.61
4498 5588 4.519540 ATGTTTCTACATTGGCCACAAC 57.480 40.909 3.88 0.59 42.29 3.32
4528 5618 1.306148 GGCTCCCGTAATTGCCTTAC 58.694 55.000 0.00 0.00 41.92 2.34
4610 5736 5.499139 TGGACTGAAATGAGTGAACAAAC 57.501 39.130 0.00 0.00 0.00 2.93
4728 5854 6.368791 GCCATGAGTTCCAAAAATTTACTTCC 59.631 38.462 0.00 0.00 0.00 3.46
4739 5865 1.281867 AGATCCGCCATGAGTTCCAAA 59.718 47.619 0.00 0.00 0.00 3.28
4740 5866 0.911769 AGATCCGCCATGAGTTCCAA 59.088 50.000 0.00 0.00 0.00 3.53
4854 5983 7.996644 AGTTGTGAACCTTGGTTTCTCTTAATA 59.003 33.333 6.49 0.00 0.00 0.98
4893 6104 0.665369 GTCGTGTGTGGGGTAACGAG 60.665 60.000 0.00 0.00 44.83 4.18
4895 6106 0.320073 ATGTCGTGTGTGGGGTAACG 60.320 55.000 0.00 0.00 37.38 3.18
4975 6187 5.126061 TGCTCTGCTTTTATTTTGGGATCTC 59.874 40.000 0.00 0.00 0.00 2.75
5002 6214 3.712907 GCCCCGGTTCAGCTGGTA 61.713 66.667 15.13 0.00 42.20 3.25
5073 6285 5.989477 TGCTTTAGCTATGATGTGTTAGGT 58.011 37.500 3.10 0.00 42.66 3.08
5217 7894 4.819761 GCTGGAGATGCGTGCGGA 62.820 66.667 0.00 0.00 0.00 5.54
5244 7921 1.828224 GATTTTAGGCGCCCCTGGG 60.828 63.158 26.15 5.50 42.90 4.45
5245 7922 2.186826 CGATTTTAGGCGCCCCTGG 61.187 63.158 26.15 1.98 42.90 4.45
5246 7923 2.834618 GCGATTTTAGGCGCCCCTG 61.835 63.158 26.15 7.46 46.93 4.45
5247 7924 2.516225 GCGATTTTAGGCGCCCCT 60.516 61.111 26.15 8.44 46.93 4.79
5253 7930 2.715624 CAGGCGGCGATTTTAGGC 59.284 61.111 12.98 0.00 0.00 3.93
5254 7931 2.186826 CCCAGGCGGCGATTTTAGG 61.187 63.158 12.98 2.42 0.00 2.69
5255 7932 2.186826 CCCCAGGCGGCGATTTTAG 61.187 63.158 12.98 0.00 0.00 1.85
5256 7933 2.124487 CCCCAGGCGGCGATTTTA 60.124 61.111 12.98 0.00 0.00 1.52
5273 7950 3.972276 TTTTTGCGCCGGCTCACC 61.972 61.111 26.68 10.54 40.82 4.02
5287 7964 0.611896 CTCGTCCCAGGGCCATTTTT 60.612 55.000 6.18 0.00 0.00 1.94
5288 7965 1.000896 CTCGTCCCAGGGCCATTTT 60.001 57.895 6.18 0.00 0.00 1.82
5289 7966 1.789576 AACTCGTCCCAGGGCCATTT 61.790 55.000 6.18 0.00 0.00 2.32
5290 7967 2.231380 AACTCGTCCCAGGGCCATT 61.231 57.895 6.18 0.00 0.00 3.16
5291 7968 2.610859 AACTCGTCCCAGGGCCAT 60.611 61.111 6.18 0.00 0.00 4.40
5292 7969 3.636231 CAACTCGTCCCAGGGCCA 61.636 66.667 6.18 0.00 0.00 5.36
5293 7970 4.410400 CCAACTCGTCCCAGGGCC 62.410 72.222 0.00 0.00 0.00 5.80
5294 7971 3.607370 GACCAACTCGTCCCAGGGC 62.607 68.421 0.00 0.00 0.00 5.19
5295 7972 2.663196 GACCAACTCGTCCCAGGG 59.337 66.667 0.00 0.00 0.00 4.45
5296 7973 2.663196 GGACCAACTCGTCCCAGG 59.337 66.667 0.00 0.00 45.72 4.45
5335 8012 2.423290 TTTTTAAACGCGCCTGGGGC 62.423 55.000 24.41 24.41 46.75 5.80
5336 8013 1.660917 TTTTTAAACGCGCCTGGGG 59.339 52.632 5.73 6.36 0.00 4.96
5353 8030 8.495148 CGAACTTTGCTATATTTTTGCCTTTTT 58.505 29.630 0.00 0.00 0.00 1.94
5354 8031 7.117667 CCGAACTTTGCTATATTTTTGCCTTTT 59.882 33.333 0.00 0.00 0.00 2.27
5355 8032 6.589907 CCGAACTTTGCTATATTTTTGCCTTT 59.410 34.615 0.00 0.00 0.00 3.11
5356 8033 6.099341 CCGAACTTTGCTATATTTTTGCCTT 58.901 36.000 0.00 0.00 0.00 4.35
5357 8034 5.650543 CCGAACTTTGCTATATTTTTGCCT 58.349 37.500 0.00 0.00 0.00 4.75
5358 8035 4.267690 GCCGAACTTTGCTATATTTTTGCC 59.732 41.667 0.00 0.00 0.00 4.52
5359 8036 4.027702 CGCCGAACTTTGCTATATTTTTGC 60.028 41.667 0.00 0.00 0.00 3.68
5360 8037 5.328691 TCGCCGAACTTTGCTATATTTTTG 58.671 37.500 0.00 0.00 0.00 2.44
5361 8038 5.554822 TCGCCGAACTTTGCTATATTTTT 57.445 34.783 0.00 0.00 0.00 1.94
5362 8039 5.123344 ACTTCGCCGAACTTTGCTATATTTT 59.877 36.000 0.00 0.00 0.00 1.82
5363 8040 4.634443 ACTTCGCCGAACTTTGCTATATTT 59.366 37.500 0.00 0.00 0.00 1.40
5364 8041 4.189231 ACTTCGCCGAACTTTGCTATATT 58.811 39.130 0.00 0.00 0.00 1.28
5365 8042 3.793559 ACTTCGCCGAACTTTGCTATAT 58.206 40.909 0.00 0.00 0.00 0.86
5366 8043 3.241067 ACTTCGCCGAACTTTGCTATA 57.759 42.857 0.00 0.00 0.00 1.31
5367 8044 2.094762 ACTTCGCCGAACTTTGCTAT 57.905 45.000 0.00 0.00 0.00 2.97
5368 8045 1.796459 GAACTTCGCCGAACTTTGCTA 59.204 47.619 0.00 0.00 0.00 3.49
5369 8046 0.586802 GAACTTCGCCGAACTTTGCT 59.413 50.000 0.00 0.00 0.00 3.91
5370 8047 0.721483 CGAACTTCGCCGAACTTTGC 60.721 55.000 0.00 0.00 31.14 3.68
5371 8048 0.110823 CCGAACTTCGCCGAACTTTG 60.111 55.000 5.61 0.00 38.82 2.77
5372 8049 1.838568 GCCGAACTTCGCCGAACTTT 61.839 55.000 5.61 0.00 38.82 2.66
5373 8050 2.315386 GCCGAACTTCGCCGAACTT 61.315 57.895 5.61 0.00 38.82 2.66
5374 8051 2.737376 GCCGAACTTCGCCGAACT 60.737 61.111 5.61 0.00 38.82 3.01
5375 8052 1.079875 TATGCCGAACTTCGCCGAAC 61.080 55.000 5.61 0.00 38.82 3.95
5376 8053 0.179094 ATATGCCGAACTTCGCCGAA 60.179 50.000 5.61 0.00 38.82 4.30
5377 8054 0.669619 TATATGCCGAACTTCGCCGA 59.330 50.000 5.61 0.00 38.82 5.54
5378 8055 1.710013 ATATATGCCGAACTTCGCCG 58.290 50.000 5.61 0.00 38.82 6.46
5379 8056 3.991773 TGTAATATATGCCGAACTTCGCC 59.008 43.478 5.61 0.00 38.82 5.54
5380 8057 5.779806 ATGTAATATATGCCGAACTTCGC 57.220 39.130 5.61 2.62 38.82 4.70
5384 8061 9.731819 CGACTATTATGTAATATATGCCGAACT 57.268 33.333 0.00 0.00 0.00 3.01
5385 8062 8.477709 GCGACTATTATGTAATATATGCCGAAC 58.522 37.037 0.00 0.00 0.00 3.95
5386 8063 7.377662 CGCGACTATTATGTAATATATGCCGAA 59.622 37.037 0.00 0.00 0.00 4.30
5387 8064 6.854381 CGCGACTATTATGTAATATATGCCGA 59.146 38.462 0.00 0.00 0.00 5.54
5388 8065 6.087687 CCGCGACTATTATGTAATATATGCCG 59.912 42.308 8.23 0.00 0.00 5.69
5389 8066 7.143340 TCCGCGACTATTATGTAATATATGCC 58.857 38.462 8.23 0.00 0.00 4.40
5390 8067 8.744008 ATCCGCGACTATTATGTAATATATGC 57.256 34.615 8.23 0.00 0.00 3.14
5399 8076 9.263538 TGTAATAAAAATCCGCGACTATTATGT 57.736 29.630 8.23 0.00 0.00 2.29
5433 8110 9.887406 CGTTTAGCCAGTTTCTTTTTAATTAGA 57.113 29.630 0.00 0.00 0.00 2.10
5434 8111 8.635983 GCGTTTAGCCAGTTTCTTTTTAATTAG 58.364 33.333 0.00 0.00 40.81 1.73
5435 8112 7.324135 CGCGTTTAGCCAGTTTCTTTTTAATTA 59.676 33.333 0.00 0.00 44.76 1.40
5436 8113 6.143278 CGCGTTTAGCCAGTTTCTTTTTAATT 59.857 34.615 0.00 0.00 44.76 1.40
5437 8114 5.627780 CGCGTTTAGCCAGTTTCTTTTTAAT 59.372 36.000 0.00 0.00 44.76 1.40
5438 8115 4.971220 CGCGTTTAGCCAGTTTCTTTTTAA 59.029 37.500 0.00 0.00 44.76 1.52
5439 8116 4.529446 CGCGTTTAGCCAGTTTCTTTTTA 58.471 39.130 0.00 0.00 44.76 1.52
5440 8117 3.368495 CGCGTTTAGCCAGTTTCTTTTT 58.632 40.909 0.00 0.00 44.76 1.94
5441 8118 2.287368 CCGCGTTTAGCCAGTTTCTTTT 60.287 45.455 4.92 0.00 44.76 2.27
5442 8119 1.265905 CCGCGTTTAGCCAGTTTCTTT 59.734 47.619 4.92 0.00 44.76 2.52
5443 8120 0.872388 CCGCGTTTAGCCAGTTTCTT 59.128 50.000 4.92 0.00 44.76 2.52
5444 8121 0.034337 TCCGCGTTTAGCCAGTTTCT 59.966 50.000 4.92 0.00 44.76 2.52
5445 8122 0.442699 CTCCGCGTTTAGCCAGTTTC 59.557 55.000 4.92 0.00 44.76 2.78
5446 8123 0.250166 ACTCCGCGTTTAGCCAGTTT 60.250 50.000 4.92 0.00 44.76 2.66
5447 8124 0.604578 TACTCCGCGTTTAGCCAGTT 59.395 50.000 4.92 0.00 44.76 3.16
5448 8125 0.172803 CTACTCCGCGTTTAGCCAGT 59.827 55.000 4.92 0.00 44.76 4.00
5449 8126 0.172803 ACTACTCCGCGTTTAGCCAG 59.827 55.000 4.92 3.53 44.76 4.85
5450 8127 0.171903 GACTACTCCGCGTTTAGCCA 59.828 55.000 4.92 0.00 44.76 4.75
5451 8128 0.864797 CGACTACTCCGCGTTTAGCC 60.865 60.000 4.92 0.00 44.76 3.93
5452 8129 1.469912 GCGACTACTCCGCGTTTAGC 61.470 60.000 4.92 0.00 43.28 3.09
5453 8130 2.563614 GCGACTACTCCGCGTTTAG 58.436 57.895 4.92 4.83 43.28 1.85
5454 8131 4.771684 GCGACTACTCCGCGTTTA 57.228 55.556 4.92 0.00 43.28 2.01
5459 8136 4.883300 CGACGGCGACTACTCCGC 62.883 72.222 16.62 0.00 46.67 5.54
5461 8138 2.402787 GACGACGGCGACTACTCC 59.597 66.667 22.49 0.00 41.64 3.85
5462 8139 2.021106 CGACGACGGCGACTACTC 59.979 66.667 22.49 1.83 41.64 2.59
5463 8140 4.157958 GCGACGACGGCGACTACT 62.158 66.667 30.26 0.00 41.64 2.57
5484 8161 4.592192 ATGACGGCGGCGAGGATG 62.592 66.667 38.93 8.23 0.00 3.51
5485 8162 4.286320 GATGACGGCGGCGAGGAT 62.286 66.667 38.93 24.06 0.00 3.24
5496 8173 3.678717 AAGCCCGACGACGATGACG 62.679 63.158 9.28 1.79 42.66 4.35
5497 8174 1.872679 GAAGCCCGACGACGATGAC 60.873 63.158 9.28 0.00 42.66 3.06
5498 8175 1.989966 GAGAAGCCCGACGACGATGA 61.990 60.000 9.28 0.00 42.66 2.92
5499 8176 1.586564 GAGAAGCCCGACGACGATG 60.587 63.158 9.28 0.49 42.66 3.84
5500 8177 2.772691 GGAGAAGCCCGACGACGAT 61.773 63.158 9.28 0.00 42.66 3.73
5501 8178 3.437795 GGAGAAGCCCGACGACGA 61.438 66.667 9.28 0.00 42.66 4.20
5502 8179 3.398353 GAGGAGAAGCCCGACGACG 62.398 68.421 0.00 0.00 37.37 5.12
5503 8180 2.490685 GAGGAGAAGCCCGACGAC 59.509 66.667 0.00 0.00 37.37 4.34
5504 8181 2.754658 GGAGGAGAAGCCCGACGA 60.755 66.667 0.00 0.00 37.37 4.20
5505 8182 2.352032 AAGGAGGAGAAGCCCGACG 61.352 63.158 0.00 0.00 37.37 5.12
5506 8183 1.219393 CAAGGAGGAGAAGCCCGAC 59.781 63.158 0.00 0.00 37.37 4.79
5507 8184 1.078528 TCAAGGAGGAGAAGCCCGA 59.921 57.895 0.00 0.00 37.37 5.14
5508 8185 1.219393 GTCAAGGAGGAGAAGCCCG 59.781 63.158 0.00 0.00 37.37 6.13
5509 8186 1.219393 CGTCAAGGAGGAGAAGCCC 59.781 63.158 0.00 0.00 37.37 5.19
5510 8187 1.448717 GCGTCAAGGAGGAGAAGCC 60.449 63.158 0.00 0.00 33.96 4.35
5511 8188 1.807573 CGCGTCAAGGAGGAGAAGC 60.808 63.158 0.00 0.00 36.19 3.86
5512 8189 1.153745 CCGCGTCAAGGAGGAGAAG 60.154 63.158 4.92 0.00 0.00 2.85
5513 8190 2.970639 CCGCGTCAAGGAGGAGAA 59.029 61.111 4.92 0.00 0.00 2.87
5514 8191 3.760035 GCCGCGTCAAGGAGGAGA 61.760 66.667 4.92 0.00 0.00 3.71
5515 8192 4.821589 GGCCGCGTCAAGGAGGAG 62.822 72.222 4.92 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.