Multiple sequence alignment - TraesCS5A01G173400

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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 TraesCS5A01G173400 chr5A 100.000 3160 0 0 1 3160 366717948 366714789 0.000000e+00 5836
1 TraesCS5A01G173400 chr5A 100.000 2435 0 0 4784 7218 366713165 366710731 0.000000e+00 4497
2 TraesCS5A01G173400 chr5A 100.000 1249 0 0 3329 4577 366714620 366713372 0.000000e+00 2307
3 TraesCS5A01G173400 chr5A 86.774 620 60 15 6599 7218 451130206 451129609 0.000000e+00 671
4 TraesCS5A01G173400 chr5A 82.312 571 97 4 6620 7188 537376190 537376758 6.510000e-135 492
5 TraesCS5A01G173400 chr5B 94.706 1719 67 16 4784 6498 315810750 315809052 0.000000e+00 2649
6 TraesCS5A01G173400 chr5B 92.928 1612 88 11 1566 3158 315813661 315812057 0.000000e+00 2322
7 TraesCS5A01G173400 chr5B 89.679 1618 89 30 1 1566 315815300 315813709 0.000000e+00 1991
8 TraesCS5A01G173400 chr5B 94.889 1174 53 7 3403 4574 315811996 315810828 0.000000e+00 1829
9 TraesCS5A01G173400 chr5D 93.719 1608 75 17 1566 3160 277624444 277622850 0.000000e+00 2386
10 TraesCS5A01G173400 chr5D 92.654 1579 77 16 1 1568 277626050 277624500 0.000000e+00 2237
11 TraesCS5A01G173400 chr5D 95.589 1247 38 5 3329 4574 277622849 277621619 0.000000e+00 1982
12 TraesCS5A01G173400 chr5D 92.107 1267 63 13 4784 6026 277621536 277620283 0.000000e+00 1751
13 TraesCS5A01G173400 chr5D 80.066 602 107 7 6590 7189 32755646 32755056 1.110000e-117 435
14 TraesCS5A01G173400 chr5D 97.368 76 1 1 6423 6497 277619762 277619687 2.110000e-25 128
15 TraesCS5A01G173400 chr7A 87.859 626 73 1 6596 7218 679793978 679794603 0.000000e+00 732
16 TraesCS5A01G173400 chr2D 95.294 340 15 1 6880 7218 480779445 480779784 8.240000e-149 538
17 TraesCS5A01G173400 chr2D 79.000 600 120 1 6590 7189 522706762 522706169 8.720000e-109 405
18 TraesCS5A01G173400 chr2A 81.135 599 103 2 6599 7188 186398987 186398390 8.480000e-129 472
19 TraesCS5A01G173400 chr6D 80.936 577 106 4 6616 7190 55426139 55425565 3.070000e-123 453
20 TraesCS5A01G173400 chr6D 81.644 523 94 2 6667 7188 24938242 24938763 4.000000e-117 433


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 TraesCS5A01G173400 chr5A 366710731 366717948 7217 True 4213.333333 5836 100.0000 1 7218 3 chr5A.!!$R2 7217
1 TraesCS5A01G173400 chr5A 451129609 451130206 597 True 671.000000 671 86.7740 6599 7218 1 chr5A.!!$R1 619
2 TraesCS5A01G173400 chr5A 537376190 537376758 568 False 492.000000 492 82.3120 6620 7188 1 chr5A.!!$F1 568
3 TraesCS5A01G173400 chr5B 315809052 315815300 6248 True 2197.750000 2649 93.0505 1 6498 4 chr5B.!!$R1 6497
4 TraesCS5A01G173400 chr5D 277619687 277626050 6363 True 1696.800000 2386 94.2874 1 6497 5 chr5D.!!$R2 6496
5 TraesCS5A01G173400 chr5D 32755056 32755646 590 True 435.000000 435 80.0660 6590 7189 1 chr5D.!!$R1 599
6 TraesCS5A01G173400 chr7A 679793978 679794603 625 False 732.000000 732 87.8590 6596 7218 1 chr7A.!!$F1 622
7 TraesCS5A01G173400 chr2D 522706169 522706762 593 True 405.000000 405 79.0000 6590 7189 1 chr2D.!!$R1 599
8 TraesCS5A01G173400 chr2A 186398390 186398987 597 True 472.000000 472 81.1350 6599 7188 1 chr2A.!!$R1 589
9 TraesCS5A01G173400 chr6D 55425565 55426139 574 True 453.000000 453 80.9360 6616 7190 1 chr6D.!!$R1 574
10 TraesCS5A01G173400 chr6D 24938242 24938763 521 False 433.000000 433 81.6440 6667 7188 1 chr6D.!!$F1 521

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
473 540 0.036164 TAATGTTGGGCAGACTGCGT 59.964 50.000 20.82 3.12 46.21 5.24 F
2049 2186 0.324183 CCTCTCAGCTGGAGGTCTGA 60.324 60.000 29.25 12.08 43.77 3.27 F
2926 3080 0.178990 GTGGCCTGGGAAACTTCACT 60.179 55.000 3.32 0.00 0.00 3.41 F
3426 3584 1.153208 GTCCCTGCTGGAGATGCTG 60.153 63.158 11.88 0.00 46.38 4.41 F
4915 5076 1.535028 TGCGTGCTGGAGTATGTTTTG 59.465 47.619 0.00 0.00 0.00 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 2471 0.388520 TAGCAGCTGTACAGTGTGCG 60.389 55.0 30.39 16.05 41.97 5.34 R
3370 3528 0.264955 TGGTTTTGGCTTACCCCCAA 59.735 50.0 0.00 0.00 40.43 4.12 R
4128 4289 0.108138 AATACACGAGCTCCCTGCAC 60.108 55.0 8.47 0.00 45.94 4.57 R
5363 5527 0.034337 TAACAAGCCGGACACCTGAC 59.966 55.0 5.05 0.00 0.00 3.51 R
6577 6928 0.036388 AGAGCGAGCCGAAAATCCAA 60.036 50.0 0.00 0.00 0.00 3.53 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
130 143 6.696411 AGCTATTCTAGAGAAATCGGGAATG 58.304 40.000 0.00 0.00 37.61 2.67
299 317 6.571925 GCTTGCTTGGATTCATCTTCTTTTCT 60.572 38.462 0.00 0.00 0.00 2.52
396 463 7.892778 TCAATTCATTGAAACAATCCACATG 57.107 32.000 2.68 0.00 43.26 3.21
400 467 1.265236 TGAAACAATCCACATGCCCC 58.735 50.000 0.00 0.00 0.00 5.80
401 468 0.173255 GAAACAATCCACATGCCCCG 59.827 55.000 0.00 0.00 0.00 5.73
402 469 0.541764 AAACAATCCACATGCCCCGT 60.542 50.000 0.00 0.00 0.00 5.28
403 470 1.250154 AACAATCCACATGCCCCGTG 61.250 55.000 0.00 0.00 0.00 4.94
404 471 2.755469 AATCCACATGCCCCGTGC 60.755 61.111 0.00 0.00 41.77 5.34
405 472 4.820744 ATCCACATGCCCCGTGCC 62.821 66.667 0.00 0.00 40.16 5.01
447 514 0.178967 TGTGCAATCCCCTCAGCAAA 60.179 50.000 0.00 0.00 38.91 3.68
452 519 0.332972 AATCCCCTCAGCAAAGTCCC 59.667 55.000 0.00 0.00 0.00 4.46
453 520 1.575447 ATCCCCTCAGCAAAGTCCCC 61.575 60.000 0.00 0.00 0.00 4.81
454 521 2.234296 CCCCTCAGCAAAGTCCCCT 61.234 63.158 0.00 0.00 0.00 4.79
455 522 0.914417 CCCCTCAGCAAAGTCCCCTA 60.914 60.000 0.00 0.00 0.00 3.53
456 523 0.991920 CCCTCAGCAAAGTCCCCTAA 59.008 55.000 0.00 0.00 0.00 2.69
458 525 2.648059 CCTCAGCAAAGTCCCCTAATG 58.352 52.381 0.00 0.00 0.00 1.90
473 540 0.036164 TAATGTTGGGCAGACTGCGT 59.964 50.000 20.82 3.12 46.21 5.24
478 545 4.082523 GGGCAGACTGCGTGGCTA 62.083 66.667 20.82 0.00 46.21 3.93
479 546 2.510238 GGCAGACTGCGTGGCTAG 60.510 66.667 20.82 0.00 46.21 3.42
480 547 2.262915 GCAGACTGCGTGGCTAGT 59.737 61.111 12.53 0.00 31.71 2.57
481 548 2.097038 GCAGACTGCGTGGCTAGTG 61.097 63.158 12.53 0.00 31.71 2.74
482 549 2.097038 CAGACTGCGTGGCTAGTGC 61.097 63.158 0.00 0.00 38.76 4.40
530 599 5.527214 GCAAGTTGGGAGCATTTTAACTTTT 59.473 36.000 4.75 0.00 38.96 2.27
537 606 7.678837 TGGGAGCATTTTAACTTTTGATTGAT 58.321 30.769 0.00 0.00 0.00 2.57
611 680 4.186856 TGCCATTTTAGCTAAAGTTGGC 57.813 40.909 37.89 37.89 45.99 4.52
614 683 4.494484 CCATTTTAGCTAAAGTTGGCACC 58.506 43.478 25.30 0.00 37.10 5.01
632 701 1.337074 ACCGCGGTTCGAAATACTTCA 60.337 47.619 28.70 0.00 41.67 3.02
690 767 4.383118 CCAGAGGTTACACATCCTAACCAG 60.383 50.000 9.46 0.71 43.98 4.00
694 771 4.020485 AGGTTACACATCCTAACCAGTGTC 60.020 45.833 9.46 0.00 43.98 3.67
724 801 7.042523 GCATTAAATTACTGATTTGATGGGTGC 60.043 37.037 14.20 2.81 45.11 5.01
734 811 1.199615 TGATGGGTGCGACTATGGAA 58.800 50.000 0.00 0.00 0.00 3.53
738 815 2.639065 TGGGTGCGACTATGGAATTTC 58.361 47.619 0.00 0.00 0.00 2.17
744 821 5.527582 GGTGCGACTATGGAATTTCTGTAAT 59.472 40.000 0.00 0.00 0.00 1.89
772 849 6.127253 GCTTCCTACTTGTAATAGTGGTACCA 60.127 42.308 11.60 11.60 0.00 3.25
791 868 7.624478 TGGTACCACTAATTAATACCTTCCTGA 59.376 37.037 11.60 0.00 36.93 3.86
802 879 9.872684 ATTAATACCTTCCTGATCAATGATTGT 57.127 29.630 4.93 0.41 0.00 2.71
840 917 2.750948 TGTTTCGTAAGTGAGCACCTC 58.249 47.619 0.00 0.00 39.48 3.85
858 935 5.016173 CACCTCAAAGGGGATGTGAATTTA 58.984 41.667 0.00 0.00 43.10 1.40
860 937 5.222337 ACCTCAAAGGGGATGTGAATTTAGT 60.222 40.000 0.00 0.00 40.58 2.24
904 981 2.722094 AGTGTTGCTCAAAGTTGGACA 58.278 42.857 0.00 0.00 0.00 4.02
914 991 3.876914 TCAAAGTTGGACACTTGTAGCTG 59.123 43.478 0.00 0.00 45.77 4.24
928 1005 3.329386 TGTAGCTGAACTGCTTCATCAC 58.671 45.455 11.02 4.56 43.74 3.06
936 1013 1.143684 ACTGCTTCATCACCAACCTGT 59.856 47.619 0.00 0.00 0.00 4.00
974 1051 2.923020 CGCTTTGTCACTTTGTTTGCTT 59.077 40.909 0.00 0.00 0.00 3.91
1020 1097 7.067129 GCAGCAATGGATATAGATGATGTGATT 59.933 37.037 0.00 0.00 30.56 2.57
1041 1118 0.457681 GCAACTTGCGTGTTGTTGGT 60.458 50.000 18.47 0.00 46.33 3.67
1188 1265 1.270041 GGCGAGAACCTCAGATGGATC 60.270 57.143 0.00 0.00 0.00 3.36
1189 1266 1.270041 GCGAGAACCTCAGATGGATCC 60.270 57.143 4.20 4.20 30.30 3.36
1360 1438 8.450578 TCGCTGTTATATTTGGATCTGAAATT 57.549 30.769 8.08 2.03 0.00 1.82
1484 1562 0.462047 CAGACCATGGGCCGTAGAAC 60.462 60.000 16.13 0.00 0.00 3.01
1486 1564 2.234913 GACCATGGGCCGTAGAACGT 62.235 60.000 18.09 0.00 40.58 3.99
1683 1819 1.070577 GTGTCACGATATGGATTGCGC 60.071 52.381 0.00 0.00 0.00 6.09
1696 1832 2.806244 GGATTGCGCGTAGGTGATAATT 59.194 45.455 8.43 0.00 0.00 1.40
1817 1953 3.465871 GAGGCAGAAGCAGAGAAATAGG 58.534 50.000 0.00 0.00 44.61 2.57
1822 1958 5.455326 GGCAGAAGCAGAGAAATAGGGATTA 60.455 44.000 0.00 0.00 44.61 1.75
1855 1991 9.236006 AGACTTTGTAGCTTGATTCATAACAAT 57.764 29.630 0.00 0.00 0.00 2.71
1860 1996 6.883756 TGTAGCTTGATTCATAACAATGGTGA 59.116 34.615 0.00 0.00 0.00 4.02
1902 2038 5.428253 GTTGGCCTTACTCATATGACTCAA 58.572 41.667 3.32 0.00 0.00 3.02
1905 2041 5.880332 TGGCCTTACTCATATGACTCAAAAC 59.120 40.000 3.32 0.00 0.00 2.43
1976 2113 3.248024 ACACCATTAGGACAAGGACTCA 58.752 45.455 0.00 0.00 38.69 3.41
2015 2152 2.159240 TCATGCTGCAACCGAGTAGTAG 60.159 50.000 6.36 0.00 0.00 2.57
2049 2186 0.324183 CCTCTCAGCTGGAGGTCTGA 60.324 60.000 29.25 12.08 43.77 3.27
2062 2199 0.895100 GGTCTGAAAGCATGGTGCCA 60.895 55.000 0.00 0.00 46.52 4.92
2068 2205 0.610232 AAAGCATGGTGCCACCTCTC 60.610 55.000 16.23 3.66 46.52 3.20
2120 2257 1.389555 ATTTTTCCGATTCCGCCCTC 58.610 50.000 0.00 0.00 0.00 4.30
2124 2261 4.918201 CCGATTCCGCCCTCCTGC 62.918 72.222 0.00 0.00 0.00 4.85
2139 2277 2.616842 CTCCTGCGTACCTTTTTGTGTT 59.383 45.455 0.00 0.00 0.00 3.32
2153 2293 8.635328 ACCTTTTTGTGTTTATAGTTTGGTAGG 58.365 33.333 0.00 0.00 0.00 3.18
2178 2318 9.998106 GGAAGTACCAAGTATATGTGAATATGT 57.002 33.333 0.00 0.00 38.79 2.29
2202 2342 9.683069 TGTTTAGAATTCTTCAAAAAGCAGATC 57.317 29.630 14.36 0.00 32.18 2.75
2331 2471 0.605319 TGAAATCGGTGTCCTGTGGC 60.605 55.000 0.00 0.00 0.00 5.01
2451 2591 9.443283 CTAAATTAATTGTACTGCTGAATCTGC 57.557 33.333 0.39 5.11 0.00 4.26
2501 2641 6.791775 GCAACACAAAAATAGTTAGCATTTGC 59.208 34.615 0.00 0.00 42.49 3.68
2606 2746 4.094739 CACTGGATCAATTATGTCGCACAA 59.905 41.667 0.00 0.00 0.00 3.33
2703 2843 7.801893 TGATGTTTCCTCTTAGTTTACCCTA 57.198 36.000 0.00 0.00 0.00 3.53
2715 2855 9.268282 TCTTAGTTTACCCTATTTCATCTGTCT 57.732 33.333 0.00 0.00 0.00 3.41
2736 2876 8.547967 TGTCTGGAAAGTAAACATGATAAGTC 57.452 34.615 0.00 0.00 0.00 3.01
2819 2972 4.633565 GTGGTCTTGATCCTTAAAGCTGAG 59.366 45.833 0.00 0.00 0.00 3.35
2899 3052 0.754957 TTTGTGCCCCCAGTGACAAG 60.755 55.000 0.00 0.00 30.37 3.16
2911 3065 2.679837 CAGTGACAAGTATCATGGTGGC 59.320 50.000 0.00 0.00 0.00 5.01
2926 3080 0.178990 GTGGCCTGGGAAACTTCACT 60.179 55.000 3.32 0.00 0.00 3.41
3148 3306 1.546029 CTTGCTTTTTAGCTGGGGGTC 59.454 52.381 0.00 0.00 35.49 4.46
3391 3549 1.344087 TGGGGGTAAGCCAAAACCAAA 60.344 47.619 0.00 0.00 37.51 3.28
3426 3584 1.153208 GTCCCTGCTGGAGATGCTG 60.153 63.158 11.88 0.00 46.38 4.41
3475 3633 8.630054 AGTAACTGTTGGCAGATTTAAATGTA 57.370 30.769 5.17 0.00 45.28 2.29
3515 3673 9.460019 TTGAATGTATGTTTTGAGGTGATATCA 57.540 29.630 0.00 0.00 0.00 2.15
3518 3676 7.263100 TGTATGTTTTGAGGTGATATCATGC 57.737 36.000 9.02 2.33 0.00 4.06
3665 3823 2.639347 TGTCCATCTTCTGTCCACATGT 59.361 45.455 0.00 0.00 0.00 3.21
3726 3884 5.246307 ACATACTAGACTGAAACTTTGGGC 58.754 41.667 0.00 0.00 0.00 5.36
3781 3941 4.547671 AGGTTCTCAGAATCGGATAGGAA 58.452 43.478 0.00 0.00 0.00 3.36
3806 3966 5.113383 TGTATGGTAAGATCGCAAATCGTT 58.887 37.500 0.00 0.00 39.67 3.85
3827 3988 7.552459 TCGTTGGATCATAACTGTTAGAATCA 58.448 34.615 18.72 11.04 0.00 2.57
3873 4034 4.866508 ATCAGTTTAGACCGTGAAGTCA 57.133 40.909 0.00 0.00 39.34 3.41
3932 4093 6.392354 TGATTAGTGACCGTAACTTAAGGTG 58.608 40.000 10.77 0.00 40.70 4.00
4327 4488 6.420903 GGTTTCTTCAGTTGGCAAAATAGAAC 59.579 38.462 0.00 1.92 0.00 3.01
4426 4587 5.069119 AGTGTCATGCGATCTAATAAGTGGA 59.931 40.000 0.00 0.00 0.00 4.02
4430 4591 6.646653 GTCATGCGATCTAATAAGTGGAATCA 59.353 38.462 0.00 0.00 0.00 2.57
4437 4598 8.607459 CGATCTAATAAGTGGAATCAATATGGC 58.393 37.037 0.00 0.00 0.00 4.40
4443 4604 5.343307 AGTGGAATCAATATGGCCAAAAC 57.657 39.130 10.96 0.00 0.00 2.43
4531 4692 5.886960 ACTTTATGGTTAGAAGCTGCAAG 57.113 39.130 1.02 0.00 0.00 4.01
4571 4732 8.154649 ACTTGTCTATTGGTTTTACTGAGTTG 57.845 34.615 0.00 0.00 0.00 3.16
4574 4735 7.276658 TGTCTATTGGTTTTACTGAGTTGTGA 58.723 34.615 0.00 0.00 0.00 3.58
4575 4736 7.771361 TGTCTATTGGTTTTACTGAGTTGTGAA 59.229 33.333 0.00 0.00 0.00 3.18
4576 4737 8.068380 GTCTATTGGTTTTACTGAGTTGTGAAC 58.932 37.037 0.00 0.00 0.00 3.18
4915 5076 1.535028 TGCGTGCTGGAGTATGTTTTG 59.465 47.619 0.00 0.00 0.00 2.44
4924 5085 9.503427 GTGCTGGAGTATGTTTTGATTATAAAC 57.497 33.333 0.00 0.00 36.32 2.01
4926 5087 8.609176 GCTGGAGTATGTTTTGATTATAAACGA 58.391 33.333 0.00 0.00 38.11 3.85
4954 5115 1.977854 TGGAGACATTGCAGTACAGGT 59.022 47.619 0.00 0.00 33.40 4.00
4955 5116 2.371841 TGGAGACATTGCAGTACAGGTT 59.628 45.455 0.00 0.00 33.40 3.50
4956 5117 3.181445 TGGAGACATTGCAGTACAGGTTT 60.181 43.478 0.00 0.00 33.40 3.27
5028 5191 3.757493 CAGCTTCTGATCTTCAGCCTTTT 59.243 43.478 6.89 0.00 43.95 2.27
5044 5207 3.507622 GCCTTTTATCATGTAGGCCCATC 59.492 47.826 0.00 0.00 45.87 3.51
5267 5431 1.613928 TTGGGGCGGAGGACATGTA 60.614 57.895 0.00 0.00 0.00 2.29
5306 5470 3.211865 ACCTCAGAACGGTTTCTTTTCC 58.788 45.455 0.00 0.00 40.34 3.13
5517 5681 1.202099 TCCGGTTGATTGGTAGGCCA 61.202 55.000 5.01 0.00 44.38 5.36
5538 5702 5.104900 GCCACCTACTTCCATCTCTCTTTTA 60.105 44.000 0.00 0.00 0.00 1.52
5613 5777 5.305585 AGTCTGAAATCTTTTTCTGCGGTA 58.694 37.500 0.00 0.00 41.54 4.02
5823 5987 9.362151 TGAGAAATTAAGGTATGGACAACTTTT 57.638 29.630 0.00 0.00 0.00 2.27
5845 6009 4.799564 TTTTGGGCTCATATTGGTGTTC 57.200 40.909 0.00 0.00 0.00 3.18
5901 6065 0.251608 CCAGTACAAAAGGGGGTGGG 60.252 60.000 0.00 0.00 0.00 4.61
5904 6068 1.389093 TACAAAAGGGGGTGGGGGT 60.389 57.895 0.00 0.00 0.00 4.95
5905 6069 0.103499 TACAAAAGGGGGTGGGGGTA 60.103 55.000 0.00 0.00 0.00 3.69
5906 6070 1.005566 ACAAAAGGGGGTGGGGGTAA 61.006 55.000 0.00 0.00 0.00 2.85
5919 6106 4.779489 GGTGGGGGTAAGAGAGTACTTAAA 59.221 45.833 0.00 0.00 34.74 1.52
5921 6108 5.483231 GTGGGGGTAAGAGAGTACTTAAACT 59.517 44.000 0.00 0.00 34.74 2.66
6035 6222 3.810941 ACGGAAATGAGACGTTGCTTTTA 59.189 39.130 0.00 0.00 37.61 1.52
6047 6234 8.597662 AGACGTTGCTTTTATGTCTACTAAAA 57.402 30.769 0.00 0.00 39.46 1.52
6091 6278 4.870991 CCTTTCTTTTACGGTCTCCTGATC 59.129 45.833 0.00 0.00 0.00 2.92
6102 6290 9.542462 TTACGGTCTCCTGATCTATTTATTTTG 57.458 33.333 0.00 0.00 0.00 2.44
6112 6300 8.207521 TGATCTATTTATTTTGTGTGCATCGA 57.792 30.769 0.00 0.00 0.00 3.59
6113 6301 8.839343 TGATCTATTTATTTTGTGTGCATCGAT 58.161 29.630 0.00 0.00 0.00 3.59
6157 6345 1.963515 AGGGAACATTTGGTTGAGCAC 59.036 47.619 0.00 0.00 40.63 4.40
6173 6361 1.000283 AGCACGGAGACTCTGAACTTG 60.000 52.381 18.40 6.76 0.00 3.16
6199 6387 5.337009 GGAAATGCACATGGTTGAAGAGATT 60.337 40.000 0.00 0.00 0.00 2.40
6226 6414 0.455005 AAGCCGGTTAGACTCGTAGC 59.545 55.000 1.90 0.00 0.00 3.58
6239 6427 0.594028 TCGTAGCGAATCGATGTGGC 60.594 55.000 6.91 2.85 31.06 5.01
6278 6466 6.506147 GCCATACACATTGATTCAAGCATTA 58.494 36.000 5.21 0.00 0.00 1.90
6299 6487 7.456253 CATTAGCGCTGTTGTATTATATCACC 58.544 38.462 22.90 0.00 0.00 4.02
6362 6550 2.104111 TGGTCTCCCAAGTGTGTAACAG 59.896 50.000 0.00 0.00 43.54 3.16
6497 6848 8.572828 CACAACTTGTGCTTTATATTGTTCAA 57.427 30.769 8.97 0.00 41.89 2.69
6498 6849 9.029243 CACAACTTGTGCTTTATATTGTTCAAA 57.971 29.630 8.97 0.00 41.89 2.69
6499 6850 9.762933 ACAACTTGTGCTTTATATTGTTCAAAT 57.237 25.926 0.00 0.00 0.00 2.32
6501 6852 9.762933 AACTTGTGCTTTATATTGTTCAAATGT 57.237 25.926 0.00 0.00 0.00 2.71
6502 6853 9.762933 ACTTGTGCTTTATATTGTTCAAATGTT 57.237 25.926 0.00 0.00 0.00 2.71
6504 6855 9.539825 TTGTGCTTTATATTGTTCAAATGTTGT 57.460 25.926 0.00 0.00 0.00 3.32
6505 6856 9.539825 TGTGCTTTATATTGTTCAAATGTTGTT 57.460 25.926 0.00 0.00 0.00 2.83
6507 6858 9.755804 TGCTTTATATTGTTCAAATGTTGTTCA 57.244 25.926 0.00 0.00 0.00 3.18
6512 6863 6.907206 ATTGTTCAAATGTTGTTCAGGTTG 57.093 33.333 0.00 0.00 0.00 3.77
6513 6864 4.753233 TGTTCAAATGTTGTTCAGGTTGG 58.247 39.130 0.00 0.00 0.00 3.77
6514 6865 3.451141 TCAAATGTTGTTCAGGTTGGC 57.549 42.857 0.00 0.00 0.00 4.52
6515 6866 2.126467 CAAATGTTGTTCAGGTTGGCG 58.874 47.619 0.00 0.00 0.00 5.69
6516 6867 1.398692 AATGTTGTTCAGGTTGGCGT 58.601 45.000 0.00 0.00 0.00 5.68
6517 6868 0.667993 ATGTTGTTCAGGTTGGCGTG 59.332 50.000 0.00 0.00 0.00 5.34
6518 6869 1.358759 GTTGTTCAGGTTGGCGTGG 59.641 57.895 0.00 0.00 0.00 4.94
6519 6870 1.077357 TTGTTCAGGTTGGCGTGGT 60.077 52.632 0.00 0.00 0.00 4.16
6520 6871 0.681564 TTGTTCAGGTTGGCGTGGTT 60.682 50.000 0.00 0.00 0.00 3.67
6521 6872 0.681564 TGTTCAGGTTGGCGTGGTTT 60.682 50.000 0.00 0.00 0.00 3.27
6522 6873 1.310904 GTTCAGGTTGGCGTGGTTTA 58.689 50.000 0.00 0.00 0.00 2.01
6523 6874 1.883926 GTTCAGGTTGGCGTGGTTTAT 59.116 47.619 0.00 0.00 0.00 1.40
6524 6875 1.816074 TCAGGTTGGCGTGGTTTATC 58.184 50.000 0.00 0.00 0.00 1.75
6525 6876 1.072489 TCAGGTTGGCGTGGTTTATCA 59.928 47.619 0.00 0.00 0.00 2.15
6526 6877 2.091541 CAGGTTGGCGTGGTTTATCAT 58.908 47.619 0.00 0.00 0.00 2.45
6527 6878 3.055021 TCAGGTTGGCGTGGTTTATCATA 60.055 43.478 0.00 0.00 0.00 2.15
6528 6879 3.064820 CAGGTTGGCGTGGTTTATCATAC 59.935 47.826 0.00 0.00 0.00 2.39
6529 6880 3.011119 GGTTGGCGTGGTTTATCATACA 58.989 45.455 0.00 0.00 0.00 2.29
6530 6881 3.630312 GGTTGGCGTGGTTTATCATACAT 59.370 43.478 0.00 0.00 0.00 2.29
6531 6882 4.097286 GGTTGGCGTGGTTTATCATACATT 59.903 41.667 0.00 0.00 0.00 2.71
6532 6883 5.393678 GGTTGGCGTGGTTTATCATACATTT 60.394 40.000 0.00 0.00 0.00 2.32
6533 6884 5.242069 TGGCGTGGTTTATCATACATTTG 57.758 39.130 0.00 0.00 0.00 2.32
6534 6885 4.944317 TGGCGTGGTTTATCATACATTTGA 59.056 37.500 0.00 0.00 0.00 2.69
6535 6886 5.416013 TGGCGTGGTTTATCATACATTTGAA 59.584 36.000 0.00 0.00 0.00 2.69
6536 6887 6.071896 TGGCGTGGTTTATCATACATTTGAAA 60.072 34.615 0.00 0.00 0.00 2.69
6537 6888 6.978080 GGCGTGGTTTATCATACATTTGAAAT 59.022 34.615 0.00 0.00 0.00 2.17
6538 6889 7.491048 GGCGTGGTTTATCATACATTTGAAATT 59.509 33.333 0.00 0.00 0.00 1.82
6539 6890 8.531530 GCGTGGTTTATCATACATTTGAAATTC 58.468 33.333 0.00 0.00 0.00 2.17
6540 6891 9.566530 CGTGGTTTATCATACATTTGAAATTCA 57.433 29.630 0.00 0.00 0.00 2.57
6552 6903 8.697846 ACATTTGAAATTCATGCTGAATACTG 57.302 30.769 10.51 4.57 45.57 2.74
6553 6904 7.762615 ACATTTGAAATTCATGCTGAATACTGG 59.237 33.333 10.51 3.04 45.57 4.00
6554 6905 6.839124 TTGAAATTCATGCTGAATACTGGT 57.161 33.333 10.51 0.00 45.57 4.00
6555 6906 6.198650 TGAAATTCATGCTGAATACTGGTG 57.801 37.500 10.51 0.00 45.57 4.17
6556 6907 5.945191 TGAAATTCATGCTGAATACTGGTGA 59.055 36.000 10.51 0.00 45.57 4.02
6557 6908 6.433716 TGAAATTCATGCTGAATACTGGTGAA 59.566 34.615 10.51 0.00 45.57 3.18
6558 6909 6.446781 AATTCATGCTGAATACTGGTGAAG 57.553 37.500 10.51 0.00 45.57 3.02
6559 6910 3.877559 TCATGCTGAATACTGGTGAAGG 58.122 45.455 0.00 0.00 0.00 3.46
6560 6911 3.519107 TCATGCTGAATACTGGTGAAGGA 59.481 43.478 0.00 0.00 0.00 3.36
6561 6912 4.019411 TCATGCTGAATACTGGTGAAGGAA 60.019 41.667 0.00 0.00 0.00 3.36
6562 6913 3.674997 TGCTGAATACTGGTGAAGGAAC 58.325 45.455 0.00 0.00 0.00 3.62
6563 6914 3.072330 TGCTGAATACTGGTGAAGGAACA 59.928 43.478 0.00 0.00 0.00 3.18
6564 6915 4.072131 GCTGAATACTGGTGAAGGAACAA 58.928 43.478 0.00 0.00 0.00 2.83
6565 6916 4.154918 GCTGAATACTGGTGAAGGAACAAG 59.845 45.833 0.00 0.00 0.00 3.16
6566 6917 5.304686 TGAATACTGGTGAAGGAACAAGT 57.695 39.130 0.00 0.00 38.00 3.16
6567 6918 6.428083 TGAATACTGGTGAAGGAACAAGTA 57.572 37.500 0.00 0.00 40.15 2.24
6568 6919 6.464222 TGAATACTGGTGAAGGAACAAGTAG 58.536 40.000 0.00 0.00 39.42 2.57
6569 6920 6.042781 TGAATACTGGTGAAGGAACAAGTAGT 59.957 38.462 0.00 0.00 39.42 2.73
6570 6921 4.772886 ACTGGTGAAGGAACAAGTAGTT 57.227 40.909 0.00 0.00 44.93 2.24
6571 6922 4.451900 ACTGGTGAAGGAACAAGTAGTTG 58.548 43.478 8.81 8.81 41.51 3.16
6572 6923 3.815401 CTGGTGAAGGAACAAGTAGTTGG 59.185 47.826 14.69 0.00 41.51 3.77
6573 6924 3.146847 GGTGAAGGAACAAGTAGTTGGG 58.853 50.000 14.69 0.00 41.51 4.12
6574 6925 3.434596 GGTGAAGGAACAAGTAGTTGGGT 60.435 47.826 14.69 2.05 41.51 4.51
6575 6926 3.564225 GTGAAGGAACAAGTAGTTGGGTG 59.436 47.826 14.69 0.00 41.51 4.61
6576 6927 3.456644 TGAAGGAACAAGTAGTTGGGTGA 59.543 43.478 14.69 0.00 41.51 4.02
6577 6928 4.104102 TGAAGGAACAAGTAGTTGGGTGAT 59.896 41.667 14.69 0.00 41.51 3.06
6578 6929 4.724279 AGGAACAAGTAGTTGGGTGATT 57.276 40.909 14.69 0.00 41.51 2.57
6579 6930 4.398319 AGGAACAAGTAGTTGGGTGATTG 58.602 43.478 14.69 0.00 41.51 2.67
6580 6931 3.506067 GGAACAAGTAGTTGGGTGATTGG 59.494 47.826 14.69 0.00 41.51 3.16
6581 6932 4.394729 GAACAAGTAGTTGGGTGATTGGA 58.605 43.478 14.69 0.00 41.51 3.53
6582 6933 4.657814 ACAAGTAGTTGGGTGATTGGAT 57.342 40.909 14.69 0.00 38.07 3.41
6583 6934 4.998051 ACAAGTAGTTGGGTGATTGGATT 58.002 39.130 14.69 0.00 38.07 3.01
6584 6935 5.393866 ACAAGTAGTTGGGTGATTGGATTT 58.606 37.500 14.69 0.00 38.07 2.17
6585 6936 5.838521 ACAAGTAGTTGGGTGATTGGATTTT 59.161 36.000 14.69 0.00 38.07 1.82
6586 6937 6.015434 ACAAGTAGTTGGGTGATTGGATTTTC 60.015 38.462 14.69 0.00 38.07 2.29
6587 6938 4.700213 AGTAGTTGGGTGATTGGATTTTCG 59.300 41.667 0.00 0.00 0.00 3.46
6588 6939 2.825532 AGTTGGGTGATTGGATTTTCGG 59.174 45.455 0.00 0.00 0.00 4.30
6614 6965 2.960659 CGCATGCCTCTCGCTCTG 60.961 66.667 13.15 0.00 38.78 3.35
6775 7138 1.489649 TCTACGAGAGATTCCCCGAGT 59.510 52.381 0.00 0.00 0.00 4.18
6827 7190 1.556911 AGTTCTCATGGCGACCAGATT 59.443 47.619 4.90 0.00 36.75 2.40
6909 7272 4.020617 CAGGAGTGGAAGGCGGCA 62.021 66.667 13.08 0.00 0.00 5.69
7073 7436 2.123726 GATGCCCCCATTTCCGCT 60.124 61.111 0.00 0.00 0.00 5.52
7077 7440 2.998097 CCCCCATTTCCGCTCTCA 59.002 61.111 0.00 0.00 0.00 3.27
7079 7442 1.299648 CCCCATTTCCGCTCTCACA 59.700 57.895 0.00 0.00 0.00 3.58
7084 7447 2.172483 ATTTCCGCTCTCACAGCCGT 62.172 55.000 0.00 0.00 46.74 5.68
7128 7491 1.518572 GGAGGCGAAATCGAGCGAA 60.519 57.895 7.06 0.00 43.02 4.70
7176 7539 2.676608 CTGGGTATGCTGCCACCA 59.323 61.111 18.67 10.90 36.48 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 203 1.377725 CAATCTCGCTGCCTTGGGT 60.378 57.895 0.00 0.00 0.00 4.51
299 317 2.435938 GGCCGCCGAAATGACAGA 60.436 61.111 0.00 0.00 0.00 3.41
405 472 4.647615 CAGATACTCGGGGGCGCG 62.648 72.222 0.00 0.00 0.00 6.86
406 473 2.100879 AATCAGATACTCGGGGGCGC 62.101 60.000 0.00 0.00 0.00 6.53
407 474 0.038159 GAATCAGATACTCGGGGGCG 60.038 60.000 0.00 0.00 0.00 6.13
408 475 1.343069 AGAATCAGATACTCGGGGGC 58.657 55.000 0.00 0.00 0.00 5.80
409 476 2.700897 ACAAGAATCAGATACTCGGGGG 59.299 50.000 0.00 0.00 0.00 5.40
410 477 3.722147 CACAAGAATCAGATACTCGGGG 58.278 50.000 0.00 0.00 0.00 5.73
411 478 3.126831 GCACAAGAATCAGATACTCGGG 58.873 50.000 0.00 0.00 0.00 5.14
412 479 3.785486 TGCACAAGAATCAGATACTCGG 58.215 45.455 0.00 0.00 0.00 4.63
413 480 5.050499 GGATTGCACAAGAATCAGATACTCG 60.050 44.000 0.00 0.00 32.34 4.18
416 483 4.276926 GGGGATTGCACAAGAATCAGATAC 59.723 45.833 0.00 0.00 32.34 2.24
452 519 1.098050 GCAGTCTGCCCAACATTAGG 58.902 55.000 14.27 0.00 37.42 2.69
453 520 0.729116 CGCAGTCTGCCCAACATTAG 59.271 55.000 19.14 0.00 41.12 1.73
454 521 0.036164 ACGCAGTCTGCCCAACATTA 59.964 50.000 19.14 0.00 41.12 1.90
455 522 1.228245 ACGCAGTCTGCCCAACATT 60.228 52.632 19.14 0.00 41.12 2.71
456 523 1.968017 CACGCAGTCTGCCCAACAT 60.968 57.895 19.14 0.00 41.61 2.71
458 525 3.357079 CCACGCAGTCTGCCCAAC 61.357 66.667 19.14 0.00 41.61 3.77
478 545 2.100879 GAGACCCTGTTGACGGCACT 62.101 60.000 0.00 0.00 0.00 4.40
479 546 1.668151 GAGACCCTGTTGACGGCAC 60.668 63.158 0.00 0.00 0.00 5.01
480 547 2.099652 CTGAGACCCTGTTGACGGCA 62.100 60.000 0.00 0.00 0.00 5.69
481 548 1.374758 CTGAGACCCTGTTGACGGC 60.375 63.158 0.00 0.00 0.00 5.68
482 549 0.393077 AACTGAGACCCTGTTGACGG 59.607 55.000 0.00 0.00 35.90 4.79
483 550 2.240493 AAACTGAGACCCTGTTGACG 57.760 50.000 0.00 0.00 37.08 4.35
484 551 4.083271 GCATAAAACTGAGACCCTGTTGAC 60.083 45.833 0.00 0.00 37.08 3.18
485 552 4.072131 GCATAAAACTGAGACCCTGTTGA 58.928 43.478 0.00 0.00 37.08 3.18
486 553 3.820467 TGCATAAAACTGAGACCCTGTTG 59.180 43.478 0.00 0.00 37.08 3.33
487 554 4.098914 TGCATAAAACTGAGACCCTGTT 57.901 40.909 0.00 0.00 38.37 3.16
488 555 3.788227 TGCATAAAACTGAGACCCTGT 57.212 42.857 0.00 0.00 0.00 4.00
489 556 4.074970 ACTTGCATAAAACTGAGACCCTG 58.925 43.478 0.00 0.00 0.00 4.45
490 557 4.373156 ACTTGCATAAAACTGAGACCCT 57.627 40.909 0.00 0.00 0.00 4.34
594 663 3.366985 GCGGTGCCAACTTTAGCTAAAAT 60.367 43.478 19.10 7.39 0.00 1.82
611 680 1.060122 GAAGTATTTCGAACCGCGGTG 59.940 52.381 34.95 21.24 41.33 4.94
614 683 3.443054 TTTGAAGTATTTCGAACCGCG 57.557 42.857 0.00 0.00 42.69 6.46
632 701 7.013942 GCCCCCAAAATAATACTACGATCTTTT 59.986 37.037 0.00 0.00 0.00 2.27
720 797 3.270877 ACAGAAATTCCATAGTCGCACC 58.729 45.455 0.00 0.00 0.00 5.01
724 801 8.594881 AGCTTATTACAGAAATTCCATAGTCG 57.405 34.615 0.00 0.00 0.00 4.18
744 821 7.729124 ACCACTATTACAAGTAGGAAGCTTA 57.271 36.000 0.00 0.00 0.00 3.09
782 859 8.599624 AATTTACAATCATTGATCAGGAAGGT 57.400 30.769 3.79 4.04 0.00 3.50
840 917 5.047092 AGCAACTAAATTCACATCCCCTTTG 60.047 40.000 0.00 0.00 0.00 2.77
858 935 2.281761 CCGGCACAGGAAGCAACT 60.282 61.111 0.00 0.00 0.00 3.16
860 937 2.058125 TTACCCGGCACAGGAAGCAA 62.058 55.000 0.00 0.00 0.00 3.91
904 981 3.475566 TGAAGCAGTTCAGCTACAAGT 57.524 42.857 0.00 0.00 45.89 3.16
914 991 2.227388 CAGGTTGGTGATGAAGCAGTTC 59.773 50.000 0.00 0.00 37.63 3.01
928 1005 4.341235 TGAGGACGAATCTATACAGGTTGG 59.659 45.833 0.00 0.00 0.00 3.77
936 1013 5.009710 ACAAAGCGATGAGGACGAATCTATA 59.990 40.000 0.00 0.00 0.00 1.31
974 1051 2.805099 GCCGGTTCATCAAATGCAAAAA 59.195 40.909 1.90 0.00 0.00 1.94
992 1069 3.865446 TCATCTATATCCATTGCTGCCG 58.135 45.455 0.00 0.00 0.00 5.69
994 1071 5.878669 TCACATCATCTATATCCATTGCTGC 59.121 40.000 0.00 0.00 0.00 5.25
1041 1118 0.472044 TAGCACTCTTGGTTGGCACA 59.528 50.000 0.00 0.00 34.50 4.57
1188 1265 0.031043 CACGGCCACATGCAATATGG 59.969 55.000 2.24 9.35 43.89 2.74
1189 1266 0.595567 GCACGGCCACATGCAATATG 60.596 55.000 16.64 0.00 43.89 1.78
1209 1286 0.461870 AAACGACTGCAGCAGTGTGA 60.462 50.000 33.03 0.00 45.44 3.58
1360 1438 9.613428 CATCAGGGATAATAACTCAACTACAAA 57.387 33.333 0.00 0.00 0.00 2.83
1484 1562 1.931841 CAAGAGTGCTCATGGATGACG 59.068 52.381 1.82 0.00 32.50 4.35
1683 1819 5.538118 TGCCTATCACAATTATCACCTACG 58.462 41.667 0.00 0.00 0.00 3.51
1817 1953 8.821894 CAAGCTACAAAGTCTAATCACTAATCC 58.178 37.037 0.00 0.00 0.00 3.01
1822 1958 8.097038 TGAATCAAGCTACAAAGTCTAATCACT 58.903 33.333 0.00 0.00 0.00 3.41
1855 1991 4.466827 TCTATATAACGAGGCAGTCACCA 58.533 43.478 0.00 0.00 0.00 4.17
1902 2038 5.104067 AGAGTCCTAAGTCCAACTTTGGTTT 60.104 40.000 16.31 6.78 46.50 3.27
1937 2073 2.662156 GTGTCTTAGTAGCTGCACGTTC 59.338 50.000 4.12 0.00 0.00 3.95
1976 2113 2.191400 TGACCTAGATGCCTTCAGCTT 58.809 47.619 0.00 0.00 44.23 3.74
2015 2152 1.418264 GAGAGGGCCAAGGAATCCTAC 59.582 57.143 6.18 0.00 31.13 3.18
2049 2186 0.610232 GAGAGGTGGCACCATGCTTT 60.610 55.000 36.28 16.57 44.28 3.51
2062 2199 6.550938 TCAGAATGTCATGTTATGAGAGGT 57.449 37.500 0.00 0.00 40.53 3.85
2120 2257 3.430333 AAACACAAAAAGGTACGCAGG 57.570 42.857 0.00 0.00 0.00 4.85
2124 2261 8.130469 ACCAAACTATAAACACAAAAAGGTACG 58.870 33.333 0.00 0.00 0.00 3.67
2301 2441 3.945285 ACACCGATTTCACAAACTCAGTT 59.055 39.130 0.00 0.00 0.00 3.16
2331 2471 0.388520 TAGCAGCTGTACAGTGTGCG 60.389 55.000 30.39 16.05 41.97 5.34
2451 2591 4.010349 GTTGGTTCTCAATCTACAAGGGG 58.990 47.826 0.00 0.00 37.73 4.79
2606 2746 6.471233 TCGGTCTCATGAATCTACTTGAAT 57.529 37.500 0.00 0.00 0.00 2.57
2703 2843 8.517878 CATGTTTACTTTCCAGACAGATGAAAT 58.482 33.333 0.00 0.00 0.00 2.17
2736 2876 8.672823 ATGTATCTATGCATATAGTTGGCATG 57.327 34.615 6.92 0.00 46.82 4.06
2777 2918 7.343357 AGACCACGAGGGATTTGAATAAATAA 58.657 34.615 3.29 0.00 41.15 1.40
2819 2972 7.938563 TGAGTATTGTTTAAACATTTGGTGC 57.061 32.000 21.17 9.23 38.95 5.01
2899 3052 0.550914 TTCCCAGGCCACCATGATAC 59.449 55.000 5.01 0.00 0.00 2.24
2911 3065 4.261614 GCAAACTAAGTGAAGTTTCCCAGG 60.262 45.833 0.00 0.00 45.59 4.45
3003 3157 1.720781 AAAAGCACTTTCAGGGGCAT 58.279 45.000 0.00 0.00 31.45 4.40
3361 3519 2.798445 CTTACCCCCAAGTTGCCCCC 62.798 65.000 0.00 0.00 0.00 5.40
3362 3520 1.304962 CTTACCCCCAAGTTGCCCC 60.305 63.158 0.00 0.00 0.00 5.80
3363 3521 1.982395 GCTTACCCCCAAGTTGCCC 60.982 63.158 0.00 0.00 0.00 5.36
3364 3522 1.982395 GGCTTACCCCCAAGTTGCC 60.982 63.158 0.00 0.00 33.27 4.52
3365 3523 0.830023 TTGGCTTACCCCCAAGTTGC 60.830 55.000 0.00 0.00 37.43 4.17
3366 3524 1.710816 TTTGGCTTACCCCCAAGTTG 58.289 50.000 0.00 0.00 42.80 3.16
3367 3525 2.043992 GTTTTGGCTTACCCCCAAGTT 58.956 47.619 0.00 0.00 42.80 2.66
3368 3526 1.712056 GTTTTGGCTTACCCCCAAGT 58.288 50.000 0.00 0.00 42.80 3.16
3369 3527 0.973632 GGTTTTGGCTTACCCCCAAG 59.026 55.000 0.00 0.00 42.80 3.61
3370 3528 0.264955 TGGTTTTGGCTTACCCCCAA 59.735 50.000 0.00 0.00 40.43 4.12
3371 3529 0.264955 TTGGTTTTGGCTTACCCCCA 59.735 50.000 0.00 0.00 33.34 4.96
3391 3549 0.323087 GACCCTTAACACGGCCCATT 60.323 55.000 0.00 0.00 0.00 3.16
3475 3633 8.225603 ACATACATTCAAAAACAGAGTCAGTT 57.774 30.769 0.00 0.00 0.00 3.16
3491 3649 9.888878 CATGATATCACCTCAAAACATACATTC 57.111 33.333 7.78 0.00 0.00 2.67
3726 3884 1.225855 TGACAAAGCTAGCACCAACG 58.774 50.000 18.83 1.29 0.00 4.10
3781 3941 4.745125 CGATTTGCGATCTTACCATACAGT 59.255 41.667 0.00 0.00 44.57 3.55
3873 4034 6.312918 ACAGCGATTTTGTTGTACGATTCTAT 59.687 34.615 0.00 0.00 31.08 1.98
4128 4289 0.108138 AATACACGAGCTCCCTGCAC 60.108 55.000 8.47 0.00 45.94 4.57
4327 4488 5.277058 GGTTAGCTCGTCATAAATCAAGCTG 60.277 44.000 5.01 0.00 40.15 4.24
4393 4554 5.605534 AGATCGCATGACACTAAGCTAAAT 58.394 37.500 0.00 0.00 0.00 1.40
4426 4587 5.760484 AACTGGTTTTGGCCATATTGATT 57.240 34.783 6.09 0.00 37.96 2.57
4443 4604 9.559958 CAGTGATTTAAGTAATAGCAAAACTGG 57.440 33.333 0.00 0.00 0.00 4.00
4531 4692 8.612619 CAATAGACAAGTCATGGTGTTAATACC 58.387 37.037 14.13 14.13 41.24 2.73
4915 5076 8.826710 TGTCTCCAAATGATGTCGTTTATAATC 58.173 33.333 0.25 0.00 33.66 1.75
4924 5085 3.127376 TGCAATGTCTCCAAATGATGTCG 59.873 43.478 0.00 0.00 0.00 4.35
4926 5087 4.084287 ACTGCAATGTCTCCAAATGATGT 58.916 39.130 0.00 0.00 0.00 3.06
4954 5115 6.183360 GCTTTCAAAAGAACATGCTCCAAAAA 60.183 34.615 6.67 0.00 38.28 1.94
4955 5116 5.294060 GCTTTCAAAAGAACATGCTCCAAAA 59.706 36.000 6.67 0.00 38.28 2.44
4956 5117 4.810491 GCTTTCAAAAGAACATGCTCCAAA 59.190 37.500 6.67 0.00 38.28 3.28
5028 5191 8.860517 ATAGAAATAGATGGGCCTACATGATA 57.139 34.615 4.53 0.00 0.00 2.15
5069 5232 4.649218 GTCCCCATGTATACCTGCAAAATT 59.351 41.667 0.00 0.00 0.00 1.82
5255 5419 1.443407 CTGGCCTACATGTCCTCCG 59.557 63.158 0.00 0.00 0.00 4.63
5273 5437 3.635268 CTGAGGTCCAAGCCCCAGC 62.635 68.421 0.00 0.00 40.32 4.85
5306 5470 1.143305 CGGATCCATTAAGAGCGCAG 58.857 55.000 11.47 0.00 0.00 5.18
5363 5527 0.034337 TAACAAGCCGGACACCTGAC 59.966 55.000 5.05 0.00 0.00 3.51
5517 5681 7.621683 ACTCATAAAAGAGAGATGGAAGTAGGT 59.378 37.037 0.00 0.00 38.98 3.08
5538 5702 9.507329 AAGAATAGTTACACATTTCACACTCAT 57.493 29.630 0.00 0.00 0.00 2.90
5613 5777 2.834549 CTCACCTCTCCAACACACCTAT 59.165 50.000 0.00 0.00 0.00 2.57
5823 5987 4.837860 AGAACACCAATATGAGCCCAAAAA 59.162 37.500 0.00 0.00 0.00 1.94
5828 5992 2.684881 CACAGAACACCAATATGAGCCC 59.315 50.000 0.00 0.00 0.00 5.19
5839 6003 1.609208 ATTCAGCCACACAGAACACC 58.391 50.000 0.00 0.00 0.00 4.16
5845 6009 2.159421 GCATGAGAATTCAGCCACACAG 60.159 50.000 8.44 0.00 36.61 3.66
5901 6065 8.751242 AGATTGAGTTTAAGTACTCTCTTACCC 58.249 37.037 9.87 0.00 43.92 3.69
5919 6106 4.910195 TGGCTCACACAAATAGATTGAGT 58.090 39.130 0.00 0.00 42.57 3.41
5921 6108 6.839124 AATTGGCTCACACAAATAGATTGA 57.161 33.333 0.00 0.00 41.85 2.57
6091 6278 8.619146 AACATCGATGCACACAAAATAAATAG 57.381 30.769 25.11 0.00 0.00 1.73
6102 6290 7.376866 CCAATAATAAGAAACATCGATGCACAC 59.623 37.037 25.11 13.61 0.00 3.82
6112 6300 8.789825 TGCAAAATGCCAATAATAAGAAACAT 57.210 26.923 0.00 0.00 44.23 2.71
6113 6301 7.333921 CCTGCAAAATGCCAATAATAAGAAACA 59.666 33.333 0.00 0.00 44.23 2.83
6157 6345 1.613925 TCCACAAGTTCAGAGTCTCCG 59.386 52.381 0.00 0.00 0.00 4.63
6173 6361 3.005684 TCTTCAACCATGTGCATTTCCAC 59.994 43.478 0.00 0.00 36.28 4.02
6226 6414 1.889105 CCAGGGCCACATCGATTCG 60.889 63.158 6.18 0.00 0.00 3.34
6239 6427 0.684153 ATGGCGAAATGGAACCAGGG 60.684 55.000 0.00 0.00 35.20 4.45
6278 6466 3.987868 CGGTGATATAATACAACAGCGCT 59.012 43.478 2.64 2.64 43.13 5.92
6294 6482 3.350219 ACAATTGCTACTTCCGGTGAT 57.650 42.857 5.05 0.00 0.00 3.06
6362 6550 0.902516 ACACAGAGCCTCCACTCCTC 60.903 60.000 0.00 0.00 37.39 3.71
6490 6841 5.174395 CCAACCTGAACAACATTTGAACAA 58.826 37.500 0.00 0.00 0.00 2.83
6497 6848 1.066908 CACGCCAACCTGAACAACATT 59.933 47.619 0.00 0.00 0.00 2.71
6498 6849 0.667993 CACGCCAACCTGAACAACAT 59.332 50.000 0.00 0.00 0.00 2.71
6499 6850 1.380403 CCACGCCAACCTGAACAACA 61.380 55.000 0.00 0.00 0.00 3.33
6500 6851 1.358759 CCACGCCAACCTGAACAAC 59.641 57.895 0.00 0.00 0.00 3.32
6501 6852 0.681564 AACCACGCCAACCTGAACAA 60.682 50.000 0.00 0.00 0.00 2.83
6502 6853 0.681564 AAACCACGCCAACCTGAACA 60.682 50.000 0.00 0.00 0.00 3.18
6503 6854 1.310904 TAAACCACGCCAACCTGAAC 58.689 50.000 0.00 0.00 0.00 3.18
6504 6855 2.156098 GATAAACCACGCCAACCTGAA 58.844 47.619 0.00 0.00 0.00 3.02
6505 6856 1.072489 TGATAAACCACGCCAACCTGA 59.928 47.619 0.00 0.00 0.00 3.86
6506 6857 1.529226 TGATAAACCACGCCAACCTG 58.471 50.000 0.00 0.00 0.00 4.00
6507 6858 2.507407 ATGATAAACCACGCCAACCT 57.493 45.000 0.00 0.00 0.00 3.50
6508 6859 3.011119 TGTATGATAAACCACGCCAACC 58.989 45.455 0.00 0.00 0.00 3.77
6509 6860 4.893424 ATGTATGATAAACCACGCCAAC 57.107 40.909 0.00 0.00 0.00 3.77
6510 6861 5.416013 TCAAATGTATGATAAACCACGCCAA 59.584 36.000 0.00 0.00 0.00 4.52
6511 6862 4.944317 TCAAATGTATGATAAACCACGCCA 59.056 37.500 0.00 0.00 0.00 5.69
6512 6863 5.493133 TCAAATGTATGATAAACCACGCC 57.507 39.130 0.00 0.00 0.00 5.68
6513 6864 7.985634 ATTTCAAATGTATGATAAACCACGC 57.014 32.000 0.00 0.00 0.00 5.34
6514 6865 9.566530 TGAATTTCAAATGTATGATAAACCACG 57.433 29.630 0.00 0.00 0.00 4.94
6539 6890 3.877559 TCCTTCACCAGTATTCAGCATG 58.122 45.455 0.00 0.00 37.54 4.06
6540 6891 4.263462 TGTTCCTTCACCAGTATTCAGCAT 60.263 41.667 0.00 0.00 0.00 3.79
6541 6892 3.072330 TGTTCCTTCACCAGTATTCAGCA 59.928 43.478 0.00 0.00 0.00 4.41
6542 6893 3.674997 TGTTCCTTCACCAGTATTCAGC 58.325 45.455 0.00 0.00 0.00 4.26
6543 6894 5.308825 ACTTGTTCCTTCACCAGTATTCAG 58.691 41.667 0.00 0.00 0.00 3.02
6544 6895 5.304686 ACTTGTTCCTTCACCAGTATTCA 57.695 39.130 0.00 0.00 0.00 2.57
6545 6896 6.465084 ACTACTTGTTCCTTCACCAGTATTC 58.535 40.000 0.00 0.00 27.63 1.75
6546 6897 6.435292 ACTACTTGTTCCTTCACCAGTATT 57.565 37.500 0.00 0.00 27.63 1.89
6547 6898 6.231211 CAACTACTTGTTCCTTCACCAGTAT 58.769 40.000 0.00 0.00 36.63 2.12
6548 6899 5.454187 CCAACTACTTGTTCCTTCACCAGTA 60.454 44.000 0.00 0.00 36.63 2.74
6549 6900 4.451900 CAACTACTTGTTCCTTCACCAGT 58.548 43.478 0.00 0.00 36.63 4.00
6550 6901 3.815401 CCAACTACTTGTTCCTTCACCAG 59.185 47.826 0.00 0.00 36.63 4.00
6551 6902 3.434453 CCCAACTACTTGTTCCTTCACCA 60.434 47.826 0.00 0.00 36.63 4.17
6552 6903 3.146847 CCCAACTACTTGTTCCTTCACC 58.853 50.000 0.00 0.00 36.63 4.02
6553 6904 3.564225 CACCCAACTACTTGTTCCTTCAC 59.436 47.826 0.00 0.00 36.63 3.18
6554 6905 3.456644 TCACCCAACTACTTGTTCCTTCA 59.543 43.478 0.00 0.00 36.63 3.02
6555 6906 4.081322 TCACCCAACTACTTGTTCCTTC 57.919 45.455 0.00 0.00 36.63 3.46
6556 6907 4.724279 ATCACCCAACTACTTGTTCCTT 57.276 40.909 0.00 0.00 36.63 3.36
6557 6908 4.398319 CAATCACCCAACTACTTGTTCCT 58.602 43.478 0.00 0.00 36.63 3.36
6558 6909 3.506067 CCAATCACCCAACTACTTGTTCC 59.494 47.826 0.00 0.00 36.63 3.62
6559 6910 4.394729 TCCAATCACCCAACTACTTGTTC 58.605 43.478 0.00 0.00 36.63 3.18
6560 6911 4.447138 TCCAATCACCCAACTACTTGTT 57.553 40.909 0.00 0.00 39.92 2.83
6561 6912 4.657814 ATCCAATCACCCAACTACTTGT 57.342 40.909 0.00 0.00 0.00 3.16
6562 6913 5.982890 AAATCCAATCACCCAACTACTTG 57.017 39.130 0.00 0.00 0.00 3.16
6563 6914 5.183140 CGAAAATCCAATCACCCAACTACTT 59.817 40.000 0.00 0.00 0.00 2.24
6564 6915 4.700213 CGAAAATCCAATCACCCAACTACT 59.300 41.667 0.00 0.00 0.00 2.57
6565 6916 4.142469 CCGAAAATCCAATCACCCAACTAC 60.142 45.833 0.00 0.00 0.00 2.73
6566 6917 4.013728 CCGAAAATCCAATCACCCAACTA 58.986 43.478 0.00 0.00 0.00 2.24
6567 6918 2.825532 CCGAAAATCCAATCACCCAACT 59.174 45.455 0.00 0.00 0.00 3.16
6568 6919 2.673893 GCCGAAAATCCAATCACCCAAC 60.674 50.000 0.00 0.00 0.00 3.77
6569 6920 1.548269 GCCGAAAATCCAATCACCCAA 59.452 47.619 0.00 0.00 0.00 4.12
6570 6921 1.181786 GCCGAAAATCCAATCACCCA 58.818 50.000 0.00 0.00 0.00 4.51
6571 6922 1.405463 GAGCCGAAAATCCAATCACCC 59.595 52.381 0.00 0.00 0.00 4.61
6572 6923 1.064060 CGAGCCGAAAATCCAATCACC 59.936 52.381 0.00 0.00 0.00 4.02
6573 6924 1.531883 GCGAGCCGAAAATCCAATCAC 60.532 52.381 0.00 0.00 0.00 3.06
6574 6925 0.732571 GCGAGCCGAAAATCCAATCA 59.267 50.000 0.00 0.00 0.00 2.57
6575 6926 1.003438 GAGCGAGCCGAAAATCCAATC 60.003 52.381 0.00 0.00 0.00 2.67
6576 6927 1.017387 GAGCGAGCCGAAAATCCAAT 58.983 50.000 0.00 0.00 0.00 3.16
6577 6928 0.036388 AGAGCGAGCCGAAAATCCAA 60.036 50.000 0.00 0.00 0.00 3.53
6578 6929 0.460284 GAGAGCGAGCCGAAAATCCA 60.460 55.000 0.00 0.00 0.00 3.41
6579 6930 1.483424 CGAGAGCGAGCCGAAAATCC 61.483 60.000 0.00 0.00 40.82 3.01
6580 6931 1.920762 CGAGAGCGAGCCGAAAATC 59.079 57.895 0.00 0.00 40.82 2.17
6581 6932 4.094684 CGAGAGCGAGCCGAAAAT 57.905 55.556 0.00 0.00 40.82 1.82
6715 7078 4.525028 TGGGGGAGGTGTGGGTGT 62.525 66.667 0.00 0.00 0.00 4.16
6775 7138 1.205655 CGGAGAGATCAGCCACAGAAA 59.794 52.381 0.00 0.00 0.00 2.52
6846 7209 4.770362 TCCCGGATCCTGGTCGCA 62.770 66.667 20.59 0.00 0.00 5.10
6870 7233 1.144057 GCACCGGATCCACTCGAAT 59.856 57.895 9.46 0.00 0.00 3.34
7013 7376 2.125552 CCTCGAAGATGCACCGCA 60.126 61.111 0.00 0.00 44.86 5.69
7073 7436 1.863662 GAACTCCGACGGCTGTGAGA 61.864 60.000 17.49 6.98 0.00 3.27
7077 7440 3.292936 ACGAACTCCGACGGCTGT 61.293 61.111 9.66 7.80 41.76 4.40
7079 7442 1.874345 AATCACGAACTCCGACGGCT 61.874 55.000 9.66 0.00 41.76 5.52
7084 7447 0.672401 GCCCAAATCACGAACTCCGA 60.672 55.000 0.00 0.00 41.76 4.55
7152 7515 1.815421 CAGCATACCCAGGACGCAC 60.815 63.158 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.