Multiple sequence alignment - TraesCS3D01G313900

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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 TraesCS3D01G313900 chr3D 100.000 6580 0 0 1 6580 427810327 427816906 0.000000e+00 12152
1 TraesCS3D01G313900 chr3B 91.844 3433 159 46 3179 6573 559337983 559341332 0.000000e+00 4676
2 TraesCS3D01G313900 chr3B 89.638 2268 141 33 560 2801 559335346 559337545 0.000000e+00 2800
3 TraesCS3D01G313900 chr3B 93.317 404 22 2 2 404 559334742 559335141 5.680000e-165 592
4 TraesCS3D01G313900 chr3B 88.830 376 26 9 2816 3180 559337531 559337901 1.300000e-121 448
5 TraesCS3D01G313900 chr3A 92.426 2469 126 28 2816 5250 557953541 557951100 0.000000e+00 3467
6 TraesCS3D01G313900 chr3A 92.543 1502 83 15 486 1970 557955751 557954262 0.000000e+00 2126
7 TraesCS3D01G313900 chr3A 95.437 1315 37 4 5268 6580 557951041 557949748 0.000000e+00 2074
8 TraesCS3D01G313900 chr3A 89.595 740 48 16 2082 2801 557954257 557953527 0.000000e+00 913
9 TraesCS3D01G313900 chr3A 90.191 418 29 2 2 407 557956283 557955866 9.710000e-148 534
10 TraesCS3D01G313900 chr2B 89.427 227 20 4 6348 6572 751841802 751842026 3.880000e-72 283
11 TraesCS3D01G313900 chr2D 89.908 218 18 3 6352 6565 616634858 616635075 1.810000e-70 278
12 TraesCS3D01G313900 chr2A 89.450 218 21 2 6349 6565 746851959 746852175 2.340000e-69 274
13 TraesCS3D01G313900 chrUn 88.489 139 16 0 6412 6550 98211519 98211657 1.130000e-37 169
14 TraesCS3D01G313900 chr6B 88.489 139 16 0 6412 6550 107771731 107771869 1.130000e-37 169
15 TraesCS3D01G313900 chr6A 88.489 139 16 0 6412 6550 53156743 53156881 1.130000e-37 169
16 TraesCS3D01G313900 chr5D 93.258 89 6 0 6413 6501 476462674 476462586 1.490000e-26 132


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 TraesCS3D01G313900 chr3D 427810327 427816906 6579 False 12152.0 12152 100.00000 1 6580 1 chr3D.!!$F1 6579
1 TraesCS3D01G313900 chr3B 559334742 559341332 6590 False 2129.0 4676 90.90725 2 6573 4 chr3B.!!$F1 6571
2 TraesCS3D01G313900 chr3A 557949748 557956283 6535 True 1822.8 3467 92.03840 2 6580 5 chr3A.!!$R1 6578

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
980 1087 0.105401 GGGGGAGGAGGAGAAGTAGG 60.105 65.000 0.00 0.0 0.00 3.18 F
2032 2163 0.109597 CAGGCAGAACGCAATTGACC 60.110 55.000 10.34 0.0 45.17 4.02 F
2533 2680 0.242017 GCAGCATGGAAACTGGTGAC 59.758 55.000 6.67 0.0 43.12 3.67 F
2625 2772 1.089920 CAGTACTTGCCTCATGCCAC 58.910 55.000 0.00 0.0 40.16 5.01 F
3237 3500 1.272313 ACTACCCTGCCTCTCAACGTA 60.272 52.381 0.00 0.0 0.00 3.57 F
4768 5045 1.068741 GGATGTGCGGACTAAGGGTAG 59.931 57.143 8.99 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2475 2622 0.320374 CAACTCTGGACAAGGCCGTA 59.680 55.000 0.00 0.0 0.00 4.02 R
3559 3825 0.249120 TGGCAGATTCACACCCTACG 59.751 55.000 0.00 0.0 0.00 3.51 R
4037 4310 1.613437 CGCCAGATTTGTTTCAAGGGT 59.387 47.619 0.00 0.0 0.00 4.34 R
4039 4312 1.613437 ACCGCCAGATTTGTTTCAAGG 59.387 47.619 0.00 0.0 0.00 3.61 R
4806 5083 0.546267 AGAGGCTGATCCCACACACT 60.546 55.000 0.00 0.0 34.51 3.55 R
5815 6147 1.509644 TTGCAAGCAAGCTCGTCAGG 61.510 55.000 2.89 0.0 34.99 3.86 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
21 22 4.922267 CGTGTAATTGTTTGTTGTTCCG 57.078 40.909 0.00 0.00 0.00 4.30
41 46 1.126846 GTGTTGTACATGTGAGCGAGC 59.873 52.381 9.11 0.00 0.00 5.03
42 47 0.366871 GTTGTACATGTGAGCGAGCG 59.633 55.000 9.11 0.00 0.00 5.03
43 48 0.242555 TTGTACATGTGAGCGAGCGA 59.757 50.000 9.11 0.00 0.00 4.93
44 49 0.179163 TGTACATGTGAGCGAGCGAG 60.179 55.000 9.11 0.00 0.00 5.03
95 100 3.688049 ATTAGCCCCCATTTTACTGCT 57.312 42.857 0.00 0.00 0.00 4.24
133 138 1.303282 GGCGGAGGGAGTGGAAATT 59.697 57.895 0.00 0.00 0.00 1.82
177 182 3.997021 CCTGCTAGTTTAGTCCTGTGTTG 59.003 47.826 0.00 0.00 0.00 3.33
190 195 1.140852 CTGTGTTGGGTCTGGTCTTCA 59.859 52.381 0.00 0.00 0.00 3.02
338 354 4.747108 CCTAGGACTGCTCGTTTGAATATG 59.253 45.833 1.05 0.00 0.00 1.78
339 355 2.939103 AGGACTGCTCGTTTGAATATGC 59.061 45.455 0.00 0.00 0.00 3.14
343 360 2.288666 TGCTCGTTTGAATATGCCCTC 58.711 47.619 0.00 0.00 0.00 4.30
363 380 6.374333 GCCCTCAAAATGTGAACTCATACTTA 59.626 38.462 0.00 0.00 35.22 2.24
373 390 6.152831 TGTGAACTCATACTTAGCTGCTAAGA 59.847 38.462 40.93 28.77 44.24 2.10
381 398 8.883731 TCATACTTAGCTGCTAAGAAAACAATC 58.116 33.333 40.93 0.00 44.24 2.67
383 400 7.371126 ACTTAGCTGCTAAGAAAACAATCTC 57.629 36.000 40.93 0.00 44.24 2.75
387 404 4.398247 CTGCTAAGAAAACAATCTCGTGC 58.602 43.478 0.00 0.00 0.00 5.34
394 411 5.482908 AGAAAACAATCTCGTGCAGTCTAT 58.517 37.500 0.00 0.00 0.00 1.98
395 412 5.349817 AGAAAACAATCTCGTGCAGTCTATG 59.650 40.000 0.00 0.00 0.00 2.23
407 424 0.326048 AGTCTATGACCAGCTGCCCT 60.326 55.000 8.66 0.00 32.18 5.19
408 425 0.543749 GTCTATGACCAGCTGCCCTT 59.456 55.000 8.66 2.87 0.00 3.95
409 426 0.833287 TCTATGACCAGCTGCCCTTC 59.167 55.000 8.66 2.04 0.00 3.46
410 427 0.179034 CTATGACCAGCTGCCCTTCC 60.179 60.000 8.66 0.00 0.00 3.46
411 428 0.913934 TATGACCAGCTGCCCTTCCA 60.914 55.000 8.66 0.00 0.00 3.53
412 429 1.792757 ATGACCAGCTGCCCTTCCAA 61.793 55.000 8.66 0.00 0.00 3.53
413 430 1.228552 GACCAGCTGCCCTTCCAAA 60.229 57.895 8.66 0.00 0.00 3.28
414 431 0.827507 GACCAGCTGCCCTTCCAAAA 60.828 55.000 8.66 0.00 0.00 2.44
415 432 0.398381 ACCAGCTGCCCTTCCAAAAA 60.398 50.000 8.66 0.00 0.00 1.94
433 450 1.986882 AAAAAGGTCTGACCAGCTGG 58.013 50.000 31.60 31.60 41.95 4.85
434 451 0.538287 AAAAGGTCTGACCAGCTGGC 60.538 55.000 33.06 24.14 41.95 4.85
435 452 1.422161 AAAGGTCTGACCAGCTGGCT 61.422 55.000 33.06 19.56 41.95 4.75
436 453 2.046507 GGTCTGACCAGCTGGCTG 60.047 66.667 33.06 25.39 43.26 4.85
437 454 2.745492 GTCTGACCAGCTGGCTGC 60.745 66.667 33.06 21.66 42.35 5.25
446 463 4.471761 GCTGGCTGCTATTCCCTC 57.528 61.111 9.31 0.00 38.95 4.30
448 465 1.704007 GCTGGCTGCTATTCCCTCCT 61.704 60.000 9.31 0.00 38.95 3.69
460 477 0.693049 TCCCTCCTTTCAACTCAGCC 59.307 55.000 0.00 0.00 0.00 4.85
465 482 3.244911 CCTCCTTTCAACTCAGCCCTAAA 60.245 47.826 0.00 0.00 0.00 1.85
517 590 9.807649 AAAATAATCACAGAAATCTAATGTGCC 57.192 29.630 0.00 0.00 43.16 5.01
615 721 2.158460 GGTTAGGCCCCATCTAATGCTT 60.158 50.000 0.00 0.00 0.00 3.91
707 813 3.000819 CCCACCTGTCGGCCACTA 61.001 66.667 2.24 0.00 0.00 2.74
974 1081 3.430497 CGGAGGGGGAGGAGGAGA 61.430 72.222 0.00 0.00 0.00 3.71
977 1084 1.707200 GAGGGGGAGGAGGAGAAGT 59.293 63.158 0.00 0.00 0.00 3.01
980 1087 0.105401 GGGGGAGGAGGAGAAGTAGG 60.105 65.000 0.00 0.00 0.00 3.18
1032 1145 2.267961 GACCGCAACCCCTTCGAT 59.732 61.111 0.00 0.00 0.00 3.59
1038 1151 0.744771 GCAACCCCTTCGATGAGGAC 60.745 60.000 5.83 0.00 39.25 3.85
1158 1271 0.175989 CTAGTCTTCGGTTCCCTGGC 59.824 60.000 0.00 0.00 0.00 4.85
1180 1293 0.523335 GCGTGGATGTCGAATTTGGC 60.523 55.000 0.00 0.00 0.00 4.52
1229 1343 1.683943 GGTTTTCGCCTATAACCCCC 58.316 55.000 0.00 0.00 36.21 5.40
1239 1353 1.411612 CTATAACCCCCTCGTTTCGCT 59.588 52.381 0.00 0.00 0.00 4.93
1269 1383 2.005960 CTCCGGTGGATCTGGTCGAC 62.006 65.000 7.13 7.13 42.90 4.20
1274 1388 0.173708 GTGGATCTGGTCGACTCACC 59.826 60.000 16.46 12.13 33.27 4.02
1431 1545 8.777865 AGAAATGATTCTTAGACACGAAATCA 57.222 30.769 0.00 0.00 43.43 2.57
1433 1547 6.595772 ATGATTCTTAGACACGAAATCAGC 57.404 37.500 0.00 0.00 0.00 4.26
1454 1568 5.865552 CAGCACTTGAACTGGGATAAATTTG 59.134 40.000 0.00 0.00 0.00 2.32
1463 1577 8.748412 TGAACTGGGATAAATTTGGTCTAATTG 58.252 33.333 0.00 0.00 0.00 2.32
1488 1602 3.116300 CGATGCGCTTTACTAGATGTGT 58.884 45.455 9.73 0.00 0.00 3.72
1613 1734 2.482316 CGTTCAGTGTGACCAGTGGTAA 60.482 50.000 16.72 4.52 41.52 2.85
1696 1821 4.438472 GGATCGTTATCTATACCGGCAGTC 60.438 50.000 0.00 0.00 32.29 3.51
1808 1935 8.310382 TGTTTGGTTGATTTTCCTAATGTATGG 58.690 33.333 0.00 0.00 0.00 2.74
1811 1938 6.127479 TGGTTGATTTTCCTAATGTATGGTGC 60.127 38.462 0.00 0.00 0.00 5.01
1937 2064 1.347707 TCTTGGTTCATCGAAGGTGCT 59.652 47.619 0.00 0.00 33.62 4.40
1953 2080 2.035066 GGTGCTTGTGCTTCAATTGAGT 59.965 45.455 8.41 0.00 40.48 3.41
1999 2130 2.991076 GCTCTGCAGCTTTGCCCAG 61.991 63.158 9.47 0.00 43.09 4.45
2022 2153 1.260544 ATTGAAAGGCCAGGCAGAAC 58.739 50.000 15.19 2.29 0.00 3.01
2032 2163 0.109597 CAGGCAGAACGCAATTGACC 60.110 55.000 10.34 0.00 45.17 4.02
2041 2172 1.959985 ACGCAATTGACCATTGACCAA 59.040 42.857 10.34 0.00 44.78 3.67
2043 2174 2.924926 CGCAATTGACCATTGACCAATG 59.075 45.455 10.34 14.10 44.78 2.82
2058 2189 2.421073 ACCAATGATGAATGCTCACACG 59.579 45.455 0.00 0.00 33.30 4.49
2071 2202 3.814842 TGCTCACACGATTCTTTGTCAAT 59.185 39.130 0.00 0.00 0.00 2.57
2074 2205 5.961843 GCTCACACGATTCTTTGTCAATATG 59.038 40.000 0.00 0.00 0.00 1.78
2075 2206 5.868257 TCACACGATTCTTTGTCAATATGC 58.132 37.500 0.00 0.00 0.00 3.14
2098 2229 7.592938 TGCTGTTGATTTCGAAATTGATTACT 58.407 30.769 23.49 0.16 0.00 2.24
2181 2320 3.701040 AGCAAAAGGAGAAAGAACTGCAA 59.299 39.130 0.00 0.00 0.00 4.08
2184 2323 5.737063 GCAAAAGGAGAAAGAACTGCAATCA 60.737 40.000 2.37 0.00 0.00 2.57
2245 2384 8.229811 GTGTCTTTTGCTTGAAACTTGAAATTT 58.770 29.630 0.00 0.00 0.00 1.82
2274 2413 7.065085 GCTTTACACTCACATCACATGTTATCT 59.935 37.037 0.00 0.00 42.70 1.98
2275 2414 7.832503 TTACACTCACATCACATGTTATCTG 57.167 36.000 0.00 0.00 42.70 2.90
2277 2416 5.871524 ACACTCACATCACATGTTATCTGAC 59.128 40.000 0.00 0.00 42.70 3.51
2337 2484 7.869937 TGTTTTGTGAATTCAGAAGTTGTTTCA 59.130 29.630 16.55 1.58 38.31 2.69
2382 2529 5.751586 TCCCCTATGCTAAAGTAAAACCTG 58.248 41.667 0.00 0.00 0.00 4.00
2390 2537 7.875327 TGCTAAAGTAAAACCTGAAGTTCTT 57.125 32.000 4.17 0.00 37.88 2.52
2401 2548 5.694995 ACCTGAAGTTCTTCTGGATGAAAA 58.305 37.500 30.82 4.95 41.04 2.29
2432 2579 3.559171 GCTTCCCAGATACTGACAAACCA 60.559 47.826 0.00 0.00 32.44 3.67
2455 2602 6.423905 CCATTGTGTTTAGATATGTAGACGGG 59.576 42.308 0.00 0.00 0.00 5.28
2469 2616 3.706600 AGACGGGTATAGCCAACAAAA 57.293 42.857 20.55 0.00 39.65 2.44
2470 2617 3.606687 AGACGGGTATAGCCAACAAAAG 58.393 45.455 20.55 5.14 39.65 2.27
2473 2620 3.504520 ACGGGTATAGCCAACAAAAGTTG 59.495 43.478 20.55 3.06 39.65 3.16
2474 2621 3.754323 CGGGTATAGCCAACAAAAGTTGA 59.246 43.478 20.55 0.00 39.65 3.18
2475 2622 4.398044 CGGGTATAGCCAACAAAAGTTGAT 59.602 41.667 20.55 1.53 39.65 2.57
2476 2623 5.587043 CGGGTATAGCCAACAAAAGTTGATA 59.413 40.000 20.55 3.51 39.65 2.15
2477 2624 6.457799 CGGGTATAGCCAACAAAAGTTGATAC 60.458 42.308 20.55 9.17 39.65 2.24
2533 2680 0.242017 GCAGCATGGAAACTGGTGAC 59.758 55.000 6.67 0.00 43.12 3.67
2577 2724 1.974236 CAGGCTCCCCTATAGTCCTTG 59.026 57.143 0.00 0.00 40.33 3.61
2625 2772 1.089920 CAGTACTTGCCTCATGCCAC 58.910 55.000 0.00 0.00 40.16 5.01
2643 2801 2.489329 CCACAGTGAGCTAAAACCATGG 59.511 50.000 11.19 11.19 0.00 3.66
2644 2802 2.489329 CACAGTGAGCTAAAACCATGGG 59.511 50.000 18.09 0.00 0.00 4.00
2645 2803 2.375174 ACAGTGAGCTAAAACCATGGGA 59.625 45.455 18.09 0.00 0.00 4.37
2646 2804 3.010584 ACAGTGAGCTAAAACCATGGGAT 59.989 43.478 18.09 0.78 0.00 3.85
2647 2805 3.629398 CAGTGAGCTAAAACCATGGGATC 59.371 47.826 18.09 6.47 0.00 3.36
2648 2806 3.525199 AGTGAGCTAAAACCATGGGATCT 59.475 43.478 18.09 3.85 0.00 2.75
2649 2807 3.879892 GTGAGCTAAAACCATGGGATCTC 59.120 47.826 18.09 12.99 0.00 2.75
2650 2808 3.782523 TGAGCTAAAACCATGGGATCTCT 59.217 43.478 18.09 5.55 0.00 3.10
2651 2809 4.968719 TGAGCTAAAACCATGGGATCTCTA 59.031 41.667 18.09 0.00 0.00 2.43
2652 2810 5.163301 TGAGCTAAAACCATGGGATCTCTAC 60.163 44.000 18.09 2.61 0.00 2.59
2653 2811 4.058817 GCTAAAACCATGGGATCTCTACG 58.941 47.826 18.09 0.00 0.00 3.51
2654 2812 4.202223 GCTAAAACCATGGGATCTCTACGA 60.202 45.833 18.09 0.00 0.00 3.43
2655 2813 5.511545 GCTAAAACCATGGGATCTCTACGAT 60.512 44.000 18.09 0.00 34.25 3.73
2659 2817 2.893489 CCATGGGATCTCTACGATGACA 59.107 50.000 2.85 0.00 30.84 3.58
2675 2833 5.538813 ACGATGACACTTATAGCCCTATGAA 59.461 40.000 0.00 0.00 0.00 2.57
2689 2847 2.169769 CCTATGAAGTGAAGGGCGGTTA 59.830 50.000 0.00 0.00 0.00 2.85
2705 2863 2.095263 CGGTTATGCTTGTGGAAACTGG 60.095 50.000 0.00 0.00 0.00 4.00
2797 2958 9.612066 TCTTAACATGAATGTACAATATGCTGA 57.388 29.630 0.00 0.36 40.80 4.26
2801 2962 8.687292 ACATGAATGTACAATATGCTGAATCT 57.313 30.769 0.00 0.00 39.68 2.40
2802 2963 9.128404 ACATGAATGTACAATATGCTGAATCTT 57.872 29.630 0.00 0.00 39.68 2.40
2803 2964 9.961265 CATGAATGTACAATATGCTGAATCTTT 57.039 29.630 0.00 0.00 0.00 2.52
2805 2966 9.791820 TGAATGTACAATATGCTGAATCTTTTG 57.208 29.630 0.00 0.00 0.00 2.44
2806 2967 9.793252 GAATGTACAATATGCTGAATCTTTTGT 57.207 29.630 0.00 0.00 0.00 2.83
2808 2969 8.969121 TGTACAATATGCTGAATCTTTTGTTG 57.031 30.769 0.00 0.00 0.00 3.33
2809 2970 8.791675 TGTACAATATGCTGAATCTTTTGTTGA 58.208 29.630 0.00 0.00 0.00 3.18
2810 2971 9.793252 GTACAATATGCTGAATCTTTTGTTGAT 57.207 29.630 0.00 0.00 0.00 2.57
2811 2972 8.922058 ACAATATGCTGAATCTTTTGTTGATC 57.078 30.769 0.00 0.00 0.00 2.92
2812 2973 8.525316 ACAATATGCTGAATCTTTTGTTGATCA 58.475 29.630 0.00 0.00 0.00 2.92
2813 2974 9.529325 CAATATGCTGAATCTTTTGTTGATCAT 57.471 29.630 0.00 0.00 0.00 2.45
2830 2991 8.570488 TGTTGATCATAACAATATGCTGAATCC 58.430 33.333 0.00 0.00 39.04 3.01
2847 3008 4.202461 TGAATCCAGAGTTAGCAGTGGTTT 60.202 41.667 0.00 0.00 0.00 3.27
2850 3011 5.499004 TCCAGAGTTAGCAGTGGTTTTAT 57.501 39.130 0.00 0.00 0.00 1.40
2873 3034 7.611213 ATGTAATCAGTAAAACCTTTCTCGG 57.389 36.000 0.00 0.00 0.00 4.63
2877 3038 4.394729 TCAGTAAAACCTTTCTCGGCAAT 58.605 39.130 0.00 0.00 0.00 3.56
2884 3045 3.157087 ACCTTTCTCGGCAATGTTTCAT 58.843 40.909 0.00 0.00 0.00 2.57
2887 3048 4.155826 CCTTTCTCGGCAATGTTTCATACA 59.844 41.667 0.00 0.00 41.97 2.29
2894 3062 2.923020 GCAATGTTTCATACAAAGCCCG 59.077 45.455 0.00 0.00 40.89 6.13
3034 3204 8.705594 AGTTCTTCCTATAGCTAATGCAGTTAA 58.294 33.333 0.00 0.00 42.74 2.01
3070 3241 6.452757 TCTAGCCATGATATTGATGGGAAA 57.547 37.500 13.81 0.00 40.80 3.13
3085 3259 7.308450 TGATGGGAAAGAGGTAGATAAGATG 57.692 40.000 0.00 0.00 0.00 2.90
3087 3261 8.010697 TGATGGGAAAGAGGTAGATAAGATGTA 58.989 37.037 0.00 0.00 0.00 2.29
3091 3269 8.652290 GGGAAAGAGGTAGATAAGATGTACAAT 58.348 37.037 0.00 0.00 31.17 2.71
3128 3306 7.001073 GGATATTTATCTGGAAGCTTGTTCCT 58.999 38.462 2.10 0.00 39.31 3.36
3137 3315 3.381590 GGAAGCTTGTTCCTGTCAACTTT 59.618 43.478 2.10 0.00 35.73 2.66
3173 3351 7.707624 TGAATGATTCAGTGAAAGGCTATTT 57.292 32.000 10.14 0.00 34.08 1.40
3237 3500 1.272313 ACTACCCTGCCTCTCAACGTA 60.272 52.381 0.00 0.00 0.00 3.57
3241 3504 2.835764 ACCCTGCCTCTCAACGTAATAA 59.164 45.455 0.00 0.00 0.00 1.40
3273 3536 4.870123 TTCATTTGCAGCTGGTATTGTT 57.130 36.364 17.12 0.00 0.00 2.83
3297 3560 1.407618 GAAACGAAAAACTGGCCACCT 59.592 47.619 0.00 0.00 0.00 4.00
3395 3658 5.255710 TGTTCATTGTTGGGTAAGTGTTG 57.744 39.130 0.00 0.00 0.00 3.33
3488 3754 3.694566 GCAAACACTATTCTTACTGGGGG 59.305 47.826 0.00 0.00 0.00 5.40
3499 3765 1.622607 TACTGGGGGCCTCACATTCG 61.623 60.000 0.00 0.00 0.00 3.34
3504 3770 1.322538 GGGGCCTCACATTCGCATTT 61.323 55.000 0.84 0.00 0.00 2.32
3532 3798 5.001232 TGTCCAACTAATGCACTTACTTCC 58.999 41.667 0.00 0.00 0.00 3.46
3558 3824 3.693085 GGATCAATGCGATTGCCATATCT 59.307 43.478 1.50 0.00 41.78 1.98
3559 3825 4.201891 GGATCAATGCGATTGCCATATCTC 60.202 45.833 1.50 0.00 41.78 2.75
3560 3826 2.738314 TCAATGCGATTGCCATATCTCG 59.262 45.455 1.50 0.00 41.78 4.04
3601 3870 2.369860 TGTCTTCTGAGAAGTGGCATGT 59.630 45.455 20.59 0.00 32.66 3.21
3609 3878 3.316029 TGAGAAGTGGCATGTGAAAACAG 59.684 43.478 0.00 0.00 0.00 3.16
3610 3879 3.554934 AGAAGTGGCATGTGAAAACAGA 58.445 40.909 0.00 0.00 0.00 3.41
3626 3896 8.265998 GTGAAAACAGAATGGTATTTCAAAACG 58.734 33.333 0.00 0.00 43.57 3.60
3638 3908 7.599245 TGGTATTTCAAAACGTCAACAAACTTT 59.401 29.630 0.00 0.00 0.00 2.66
3641 3911 4.159857 TCAAAACGTCAACAAACTTTCCG 58.840 39.130 0.00 0.00 0.00 4.30
3672 3942 8.251750 TGACAATCTGTACTTTGTAACTATGC 57.748 34.615 8.67 0.00 36.25 3.14
3673 3943 8.094548 TGACAATCTGTACTTTGTAACTATGCT 58.905 33.333 8.67 0.00 36.25 3.79
3676 3946 9.546909 CAATCTGTACTTTGTAACTATGCTTTG 57.453 33.333 0.00 0.00 0.00 2.77
3681 3951 8.776470 TGTACTTTGTAACTATGCTTTGTTACC 58.224 33.333 23.93 13.70 44.45 2.85
3775 4048 4.462483 GGCTTAAACTTCCAATGGTCATGA 59.538 41.667 0.00 0.00 0.00 3.07
3804 4077 5.794687 TGTCCAACAAATGCTAGTAATCG 57.205 39.130 0.00 0.00 0.00 3.34
3805 4078 4.634004 TGTCCAACAAATGCTAGTAATCGG 59.366 41.667 0.00 0.00 0.00 4.18
3831 4104 3.415087 GGGCCCAGATGGTCAGCT 61.415 66.667 19.95 0.00 42.20 4.24
3868 4141 5.008217 AGGAGATTCGAGTCTAAGATTGTCG 59.992 44.000 10.78 0.00 0.00 4.35
3898 4171 3.380637 GCACAGATTCCTGATTTCTGCAT 59.619 43.478 0.00 0.00 43.02 3.96
3923 4196 1.341187 TGATGCCATGCAGGATTGACA 60.341 47.619 0.00 0.00 43.65 3.58
4033 4306 2.502947 TGTGGATCAACTGCTATCTGCT 59.497 45.455 1.02 0.00 43.37 4.24
4037 4310 3.069300 GGATCAACTGCTATCTGCTCTGA 59.931 47.826 0.00 0.00 43.37 3.27
4039 4312 2.167281 TCAACTGCTATCTGCTCTGACC 59.833 50.000 0.00 0.00 43.37 4.02
4041 4314 1.342874 ACTGCTATCTGCTCTGACCCT 60.343 52.381 0.00 0.00 43.37 4.34
4148 4421 3.007506 CCTATGTGTTATGGTATCGGCCA 59.992 47.826 2.24 0.00 43.48 5.36
4192 4465 5.698832 TGTGTACATGCTTATGCTTTTGTC 58.301 37.500 0.00 0.67 40.48 3.18
4420 4693 6.183360 CGTGACGAGCTAATATTCCATTCATC 60.183 42.308 0.00 0.00 0.00 2.92
4594 4867 8.946085 CCATGCGTAAATATGGTAGTTATTCAT 58.054 33.333 0.00 0.00 39.18 2.57
4607 4880 9.555727 TGGTAGTTATTCATTTATTCTGGCTAC 57.444 33.333 0.00 0.00 0.00 3.58
4619 4892 4.377471 GGCTACGCCGCAAAATTC 57.623 55.556 0.00 0.00 39.62 2.17
4628 4901 3.086161 CGCAAAATTCGGACACACC 57.914 52.632 0.00 0.00 0.00 4.16
4688 4961 7.676004 TCTTCAGTATCTTGACCATACACAAA 58.324 34.615 0.00 0.00 0.00 2.83
4691 4964 8.942338 TCAGTATCTTGACCATACACAAATAC 57.058 34.615 0.00 0.00 0.00 1.89
4697 4970 9.959721 ATCTTGACCATACACAAATACTTACTT 57.040 29.630 0.00 0.00 0.00 2.24
4713 4986 4.939439 ACTTACTTATAAAAGGCACCACCG 59.061 41.667 2.75 0.00 46.52 4.94
4756 5033 2.871633 TGTTACATATGCTGGATGTGCG 59.128 45.455 1.58 0.00 38.03 5.34
4768 5045 1.068741 GGATGTGCGGACTAAGGGTAG 59.931 57.143 8.99 0.00 0.00 3.18
4836 5113 4.384940 GGATCAGCCTCTACCAAAGATTC 58.615 47.826 0.00 0.00 32.41 2.52
4848 5125 4.398319 ACCAAAGATTCCGATTGACAGTT 58.602 39.130 0.00 0.00 0.00 3.16
4854 5131 2.357327 TCCGATTGACAGTTGGTACG 57.643 50.000 4.26 0.00 0.00 3.67
4920 5197 3.192844 ACCACCTACTCAGTACATTGTCG 59.807 47.826 0.00 0.00 0.00 4.35
4922 5199 2.823747 ACCTACTCAGTACATTGTCGCA 59.176 45.455 0.00 0.00 0.00 5.10
5079 5356 8.336235 TCTTTTCAAATCATAGATAGGTGGGTT 58.664 33.333 0.00 0.00 0.00 4.11
5129 5408 6.472016 TCACATTATCTAACTTTGCCTGTCA 58.528 36.000 0.00 0.00 0.00 3.58
5217 5498 6.126883 TGTGGGGGTAAGTATTTCTGTCTATG 60.127 42.308 0.00 0.00 0.00 2.23
5221 5502 6.224584 GGGTAAGTATTTCTGTCTATGGAGC 58.775 44.000 0.00 0.00 0.00 4.70
5250 5531 1.538687 ATGGCTGCTTTTCTGGGTGC 61.539 55.000 0.00 0.00 0.00 5.01
5251 5532 2.202395 GGCTGCTTTTCTGGGTGCA 61.202 57.895 0.00 0.00 0.00 4.57
5253 5534 0.108945 GCTGCTTTTCTGGGTGCATC 60.109 55.000 0.00 0.00 34.79 3.91
5254 5535 0.529378 CTGCTTTTCTGGGTGCATCC 59.471 55.000 9.82 9.82 34.79 3.51
5305 5627 7.677454 TGACTAGTCATTTACGTTGTCTCTA 57.323 36.000 21.74 0.00 34.14 2.43
5306 5628 7.524912 TGACTAGTCATTTACGTTGTCTCTAC 58.475 38.462 21.74 0.00 34.14 2.59
5307 5629 7.389884 TGACTAGTCATTTACGTTGTCTCTACT 59.610 37.037 21.74 0.00 34.14 2.57
5308 5630 8.108551 ACTAGTCATTTACGTTGTCTCTACTT 57.891 34.615 0.00 0.00 0.00 2.24
5309 5631 9.224267 ACTAGTCATTTACGTTGTCTCTACTTA 57.776 33.333 0.00 0.00 0.00 2.24
5312 5634 9.754382 AGTCATTTACGTTGTCTCTACTTAAAA 57.246 29.630 0.00 0.00 0.00 1.52
5408 5730 1.084289 GGTGATCCAGGTGCGTTTAC 58.916 55.000 0.00 0.00 0.00 2.01
5652 5974 3.472652 TGGCGTCTTGTCTTTGTACATT 58.527 40.909 0.00 0.00 0.00 2.71
5815 6147 6.821388 AGATACAACTTCCACCATCACTATC 58.179 40.000 0.00 0.00 0.00 2.08
5996 6328 8.408601 CAAATGAAAATGGGAGACGAATCTATT 58.591 33.333 0.00 0.00 34.34 1.73
6006 6338 7.176865 TGGGAGACGAATCTATTATAACTCTGG 59.823 40.741 0.00 0.00 34.34 3.86
6013 6345 5.707242 TCTATTATAACTCTGGCGTGAGG 57.293 43.478 11.14 0.00 38.32 3.86
6016 6348 0.537188 ATAACTCTGGCGTGAGGTGG 59.463 55.000 7.93 0.00 38.32 4.61
6063 6397 2.411904 CCTCTCTATTTGCCGCTCATC 58.588 52.381 0.00 0.00 0.00 2.92
6267 6601 2.283966 ACCACCTCCTCGTCCTGG 60.284 66.667 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.203361 CACGGAACAACAAACAATTACACG 59.797 41.667 0.00 0.00 0.00 4.49
21 22 1.126846 GCTCGCTCACATGTACAACAC 59.873 52.381 0.00 0.00 0.00 3.32
41 46 2.581953 GCCAAGCTCTCTCGCTCG 60.582 66.667 0.00 0.00 39.86 5.03
42 47 1.519013 CAGCCAAGCTCTCTCGCTC 60.519 63.158 0.00 0.00 39.86 5.03
43 48 1.825281 AACAGCCAAGCTCTCTCGCT 61.825 55.000 0.00 0.00 43.31 4.93
44 49 1.357991 GAACAGCCAAGCTCTCTCGC 61.358 60.000 0.00 0.00 36.40 5.03
116 121 2.413310 TTAATTTCCACTCCCTCCGC 57.587 50.000 0.00 0.00 0.00 5.54
130 135 7.065683 GGCGTTTTTCCCATTCATTCATTAATT 59.934 33.333 0.00 0.00 0.00 1.40
133 138 5.186797 AGGCGTTTTTCCCATTCATTCATTA 59.813 36.000 0.00 0.00 0.00 1.90
177 182 3.503748 CACAGAAAATGAAGACCAGACCC 59.496 47.826 0.00 0.00 0.00 4.46
190 195 2.223711 GCGAACCAACACCACAGAAAAT 60.224 45.455 0.00 0.00 0.00 1.82
231 236 6.261826 AGAGATGGTTGTCTTCAAAACTTCTG 59.738 38.462 0.00 0.00 35.20 3.02
338 354 4.702131 AGTATGAGTTCACATTTTGAGGGC 59.298 41.667 0.00 0.00 34.94 5.19
339 355 6.824305 AAGTATGAGTTCACATTTTGAGGG 57.176 37.500 0.00 0.00 34.94 4.30
343 360 6.744537 GCAGCTAAGTATGAGTTCACATTTTG 59.255 38.462 0.00 0.00 0.00 2.44
363 380 4.153117 CACGAGATTGTTTTCTTAGCAGCT 59.847 41.667 0.00 0.00 0.00 4.24
373 390 5.120830 GTCATAGACTGCACGAGATTGTTTT 59.879 40.000 0.00 0.00 0.00 2.43
381 398 1.800655 GCTGGTCATAGACTGCACGAG 60.801 57.143 0.00 0.00 34.40 4.18
383 400 0.174389 AGCTGGTCATAGACTGCACG 59.826 55.000 14.20 0.00 35.70 5.34
387 404 0.179062 GGGCAGCTGGTCATAGACTG 60.179 60.000 17.12 0.00 32.47 3.51
394 411 2.005606 TTTGGAAGGGCAGCTGGTCA 62.006 55.000 17.12 0.00 0.00 4.02
395 412 0.827507 TTTTGGAAGGGCAGCTGGTC 60.828 55.000 17.12 0.00 0.00 4.02
414 431 1.986882 CCAGCTGGTCAGACCTTTTT 58.013 50.000 25.53 1.17 39.58 1.94
415 432 0.538287 GCCAGCTGGTCAGACCTTTT 60.538 55.000 32.81 2.97 39.58 2.27
416 433 1.073897 GCCAGCTGGTCAGACCTTT 59.926 57.895 32.81 3.33 39.58 3.11
417 434 1.845205 AGCCAGCTGGTCAGACCTT 60.845 57.895 32.81 6.58 39.58 3.50
418 435 2.203907 AGCCAGCTGGTCAGACCT 60.204 61.111 32.81 17.80 39.58 3.85
419 436 2.046507 CAGCCAGCTGGTCAGACC 60.047 66.667 32.81 13.35 40.17 3.85
420 437 2.745492 GCAGCCAGCTGGTCAGAC 60.745 66.667 32.81 16.47 43.77 3.51
429 446 1.228094 GGAGGGAATAGCAGCCAGC 60.228 63.158 0.00 0.00 46.19 4.85
430 447 0.842635 AAGGAGGGAATAGCAGCCAG 59.157 55.000 0.00 0.00 0.00 4.85
431 448 1.212935 GAAAGGAGGGAATAGCAGCCA 59.787 52.381 0.00 0.00 0.00 4.75
432 449 1.212935 TGAAAGGAGGGAATAGCAGCC 59.787 52.381 0.00 0.00 0.00 4.85
433 450 2.685388 GTTGAAAGGAGGGAATAGCAGC 59.315 50.000 0.00 0.00 0.00 5.25
434 451 4.195416 GAGTTGAAAGGAGGGAATAGCAG 58.805 47.826 0.00 0.00 0.00 4.24
435 452 3.587061 TGAGTTGAAAGGAGGGAATAGCA 59.413 43.478 0.00 0.00 0.00 3.49
436 453 4.195416 CTGAGTTGAAAGGAGGGAATAGC 58.805 47.826 0.00 0.00 0.00 2.97
437 454 4.195416 GCTGAGTTGAAAGGAGGGAATAG 58.805 47.826 0.00 0.00 0.00 1.73
438 455 3.054361 GGCTGAGTTGAAAGGAGGGAATA 60.054 47.826 0.00 0.00 0.00 1.75
439 456 2.291217 GGCTGAGTTGAAAGGAGGGAAT 60.291 50.000 0.00 0.00 0.00 3.01
440 457 1.073923 GGCTGAGTTGAAAGGAGGGAA 59.926 52.381 0.00 0.00 0.00 3.97
441 458 0.693049 GGCTGAGTTGAAAGGAGGGA 59.307 55.000 0.00 0.00 0.00 4.20
442 459 0.322906 GGGCTGAGTTGAAAGGAGGG 60.323 60.000 0.00 0.00 0.00 4.30
470 487 2.708037 TACACTTACACAGGGTCCCT 57.292 50.000 3.85 3.85 39.03 4.20
534 607 9.787532 CAAGAAATGTTTGGATTACGTGATTAT 57.212 29.630 0.00 0.00 0.00 1.28
535 608 8.240682 CCAAGAAATGTTTGGATTACGTGATTA 58.759 33.333 0.00 0.00 46.42 1.75
537 610 6.620678 CCAAGAAATGTTTGGATTACGTGAT 58.379 36.000 0.00 0.00 46.42 3.06
538 611 5.563867 GCCAAGAAATGTTTGGATTACGTGA 60.564 40.000 8.13 0.00 46.42 4.35
539 612 4.621034 GCCAAGAAATGTTTGGATTACGTG 59.379 41.667 8.13 0.00 46.42 4.49
540 613 4.614993 CGCCAAGAAATGTTTGGATTACGT 60.615 41.667 8.13 0.00 46.42 3.57
541 614 3.851403 CGCCAAGAAATGTTTGGATTACG 59.149 43.478 8.13 0.00 46.42 3.18
542 615 4.805219 ACGCCAAGAAATGTTTGGATTAC 58.195 39.130 8.13 0.00 46.42 1.89
543 616 5.461032 AACGCCAAGAAATGTTTGGATTA 57.539 34.783 8.13 0.00 46.42 1.75
548 621 3.452474 TGGAAACGCCAAGAAATGTTTG 58.548 40.909 0.00 0.00 45.87 2.93
615 721 1.146774 TGGCATTCAGGGACAAAAGGA 59.853 47.619 0.00 0.00 0.00 3.36
707 813 1.291184 GGTTTAGCGCGTACGGGTTT 61.291 55.000 29.58 21.14 40.57 3.27
784 890 4.901849 TGGGTTTGGAATGTGGATTTGTTA 59.098 37.500 0.00 0.00 0.00 2.41
833 940 1.600485 GGACTTCCGCTTTTTCGACAA 59.400 47.619 0.00 0.00 0.00 3.18
954 1061 2.040606 CCTCCTCCCCCTCCGAAA 59.959 66.667 0.00 0.00 0.00 3.46
956 1063 3.430497 CTCCTCCTCCCCCTCCGA 61.430 72.222 0.00 0.00 0.00 4.55
963 1070 1.571936 ACTCCTACTTCTCCTCCTCCC 59.428 57.143 0.00 0.00 0.00 4.30
974 1081 1.860906 CCTCCCTCCCTACTCCTACTT 59.139 57.143 0.00 0.00 0.00 2.24
977 1084 1.702901 CCTCCTCCCTCCCTACTCCTA 60.703 61.905 0.00 0.00 0.00 2.94
980 1087 1.152419 GCCTCCTCCCTCCCTACTC 60.152 68.421 0.00 0.00 0.00 2.59
1032 1145 2.567497 GGGGTTGACGTCGTCCTCA 61.567 63.158 22.05 1.82 0.00 3.86
1038 1151 3.110178 GCGAAGGGGTTGACGTCG 61.110 66.667 11.62 0.00 41.57 5.12
1068 1181 3.519579 GGGTAGAAAGTAGAAACGGAGC 58.480 50.000 0.00 0.00 0.00 4.70
1135 1248 1.553706 GGGAACCGAAGACTAGGTGA 58.446 55.000 3.59 0.00 40.86 4.02
1158 1271 0.999406 AAATTCGACATCCACGCGAG 59.001 50.000 15.93 4.16 35.31 5.03
1165 1278 1.724582 CCGGGCCAAATTCGACATCC 61.725 60.000 4.39 0.00 0.00 3.51
1229 1343 0.600255 ACCCAGAACAGCGAAACGAG 60.600 55.000 0.00 0.00 0.00 4.18
1239 1353 2.847234 ACCGGAGCACCCAGAACA 60.847 61.111 9.46 0.00 34.14 3.18
1286 1400 2.570752 CCATCCATCGAATCCCTCTGAT 59.429 50.000 0.00 0.00 34.22 2.90
1287 1401 1.973515 CCATCCATCGAATCCCTCTGA 59.026 52.381 0.00 0.00 0.00 3.27
1288 1402 1.973515 TCCATCCATCGAATCCCTCTG 59.026 52.381 0.00 0.00 0.00 3.35
1431 1545 5.047092 CCAAATTTATCCCAGTTCAAGTGCT 60.047 40.000 0.00 0.00 0.00 4.40
1433 1547 6.209391 AGACCAAATTTATCCCAGTTCAAGTG 59.791 38.462 0.00 0.00 0.00 3.16
1463 1577 1.924524 TCTAGTAAAGCGCATCGTTGC 59.075 47.619 11.47 8.44 45.78 4.17
1474 1588 7.548097 TCCAAAGCTCTACACATCTAGTAAAG 58.452 38.462 0.00 0.00 0.00 1.85
1488 1602 1.280710 TCGCCCAATTCCAAAGCTCTA 59.719 47.619 0.00 0.00 0.00 2.43
1690 1815 2.045926 ACAGCAATCCGGACTGCC 60.046 61.111 32.60 15.93 39.47 4.85
1696 1821 1.526575 AAGTTGGCACAGCAATCCGG 61.527 55.000 0.00 0.00 43.86 5.14
1789 1916 7.067372 CAGAGCACCATACATTAGGAAAATCAA 59.933 37.037 0.00 0.00 0.00 2.57
1799 1926 2.158769 CCCTGCAGAGCACCATACATTA 60.159 50.000 17.39 0.00 33.79 1.90
1808 1935 2.583520 CTCCTCCCTGCAGAGCAC 59.416 66.667 17.39 0.00 33.79 4.40
1811 1938 0.324738 TACACCTCCTCCCTGCAGAG 60.325 60.000 17.39 0.39 0.00 3.35
1937 2064 5.321959 TGACAAACTCAATTGAAGCACAA 57.678 34.783 9.88 0.00 42.95 3.33
1953 2080 9.897744 CATCTTGCTAAGTAAAGAATTGACAAA 57.102 29.630 0.00 0.00 36.09 2.83
1987 2118 1.614903 TCAATTCACTGGGCAAAGCTG 59.385 47.619 0.00 0.00 0.00 4.24
1988 2119 1.999648 TCAATTCACTGGGCAAAGCT 58.000 45.000 0.00 0.00 0.00 3.74
1989 2120 2.818130 TTCAATTCACTGGGCAAAGC 57.182 45.000 0.00 0.00 0.00 3.51
1990 2121 3.656559 CCTTTCAATTCACTGGGCAAAG 58.343 45.455 0.00 0.00 0.00 2.77
1991 2122 2.224257 GCCTTTCAATTCACTGGGCAAA 60.224 45.455 0.00 0.00 38.16 3.68
1999 2130 0.968405 TGCCTGGCCTTTCAATTCAC 59.032 50.000 17.53 0.00 0.00 3.18
2022 2153 2.721274 TTGGTCAATGGTCAATTGCG 57.279 45.000 0.00 0.00 44.63 4.85
2032 2163 5.257082 TGAGCATTCATCATTGGTCAATG 57.743 39.130 15.38 15.38 44.68 2.82
2041 2172 4.449131 AGAATCGTGTGAGCATTCATCAT 58.551 39.130 0.00 0.00 35.39 2.45
2043 2174 4.871993 AAGAATCGTGTGAGCATTCATC 57.128 40.909 0.00 0.00 35.39 2.92
2051 2182 5.961843 GCATATTGACAAAGAATCGTGTGAG 59.038 40.000 0.00 0.00 0.00 3.51
2054 2185 5.412594 ACAGCATATTGACAAAGAATCGTGT 59.587 36.000 0.00 0.00 0.00 4.49
2058 2189 8.922058 AATCAACAGCATATTGACAAAGAATC 57.078 30.769 0.00 0.00 38.84 2.52
2071 2202 9.502145 GTAATCAATTTCGAAATCAACAGCATA 57.498 29.630 22.93 6.89 0.00 3.14
2074 2205 7.750458 TCAGTAATCAATTTCGAAATCAACAGC 59.250 33.333 22.93 12.49 0.00 4.40
2075 2206 9.611284 TTCAGTAATCAATTTCGAAATCAACAG 57.389 29.630 22.93 13.07 0.00 3.16
2098 2229 2.220824 CGACACGCTGTGAAAGAATTCA 59.779 45.455 8.44 0.00 43.18 2.57
2181 2320 3.009473 TGTTAAGCTCAGCCTCCTTTGAT 59.991 43.478 0.00 0.00 0.00 2.57
2184 2323 3.508845 TTGTTAAGCTCAGCCTCCTTT 57.491 42.857 0.00 0.00 0.00 3.11
2245 2384 4.335400 TGTGATGTGAGTGTAAAGCTGA 57.665 40.909 0.00 0.00 0.00 4.26
2274 2413 9.628746 CAAATCAATAACTCAAATGACATGTCA 57.371 29.630 29.67 29.67 44.59 3.58
2275 2414 9.630098 ACAAATCAATAACTCAAATGACATGTC 57.370 29.630 19.27 19.27 0.00 3.06
2337 2484 8.645110 GGGGATTTTGATCACTGAATGAATTAT 58.355 33.333 0.00 0.00 41.93 1.28
2382 2529 8.137437 TCACAAATTTTCATCCAGAAGAACTTC 58.863 33.333 6.46 6.46 37.57 3.01
2390 2537 6.409524 AAGCTTCACAAATTTTCATCCAGA 57.590 33.333 0.00 0.00 0.00 3.86
2401 2548 4.946157 CAGTATCTGGGAAGCTTCACAAAT 59.054 41.667 30.22 25.47 40.65 2.32
2432 2579 7.120923 ACCCGTCTACATATCTAAACACAAT 57.879 36.000 0.00 0.00 0.00 2.71
2438 2585 7.177184 TGGCTATACCCGTCTACATATCTAAA 58.823 38.462 0.00 0.00 37.83 1.85
2469 2616 0.981183 TGGACAAGGCCGTATCAACT 59.019 50.000 0.00 0.00 0.00 3.16
2470 2617 1.066430 TCTGGACAAGGCCGTATCAAC 60.066 52.381 0.00 0.00 0.00 3.18
2473 2620 0.824759 ACTCTGGACAAGGCCGTATC 59.175 55.000 0.00 0.00 0.00 2.24
2474 2621 1.066143 CAACTCTGGACAAGGCCGTAT 60.066 52.381 0.00 0.00 0.00 3.06
2475 2622 0.320374 CAACTCTGGACAAGGCCGTA 59.680 55.000 0.00 0.00 0.00 4.02
2476 2623 1.071471 CAACTCTGGACAAGGCCGT 59.929 57.895 0.00 0.00 0.00 5.68
2477 2624 0.535102 AACAACTCTGGACAAGGCCG 60.535 55.000 0.00 0.00 0.00 6.13
2533 2680 5.694995 AGGTAAATCCATGTCAACCATAGG 58.305 41.667 0.00 0.00 39.02 2.57
2577 2724 6.453943 TGATCTGATCAATAGTTAGAGCAGC 58.546 40.000 17.56 0.00 45.26 5.25
2625 2772 3.071874 TCCCATGGTTTTAGCTCACTG 57.928 47.619 11.73 0.00 0.00 3.66
2643 2801 6.403855 GGCTATAAGTGTCATCGTAGAGATCC 60.404 46.154 0.00 0.00 43.63 3.36
2644 2802 6.403855 GGGCTATAAGTGTCATCGTAGAGATC 60.404 46.154 0.00 0.00 43.63 2.75
2645 2803 5.416326 GGGCTATAAGTGTCATCGTAGAGAT 59.584 44.000 0.00 0.00 43.63 2.75
2646 2804 4.760715 GGGCTATAAGTGTCATCGTAGAGA 59.239 45.833 0.00 0.00 43.63 3.10
2647 2805 4.762765 AGGGCTATAAGTGTCATCGTAGAG 59.237 45.833 0.00 0.00 43.63 2.43
2648 2806 4.726583 AGGGCTATAAGTGTCATCGTAGA 58.273 43.478 0.00 0.00 45.75 2.59
2649 2807 6.374613 TCATAGGGCTATAAGTGTCATCGTAG 59.625 42.308 0.00 0.00 0.00 3.51
2650 2808 6.243148 TCATAGGGCTATAAGTGTCATCGTA 58.757 40.000 0.00 0.00 0.00 3.43
2651 2809 5.077564 TCATAGGGCTATAAGTGTCATCGT 58.922 41.667 0.00 0.00 0.00 3.73
2652 2810 5.644977 TCATAGGGCTATAAGTGTCATCG 57.355 43.478 0.00 0.00 0.00 3.84
2653 2811 6.870965 CACTTCATAGGGCTATAAGTGTCATC 59.129 42.308 0.00 0.00 41.21 2.92
2654 2812 6.554982 TCACTTCATAGGGCTATAAGTGTCAT 59.445 38.462 11.88 0.00 44.60 3.06
2655 2813 5.897250 TCACTTCATAGGGCTATAAGTGTCA 59.103 40.000 11.88 0.00 44.60 3.58
2659 2817 5.308237 CCCTTCACTTCATAGGGCTATAAGT 59.692 44.000 0.00 0.00 42.04 2.24
2675 2833 0.328258 AAGCATAACCGCCCTTCACT 59.672 50.000 0.00 0.00 0.00 3.41
2684 2842 2.095263 CCAGTTTCCACAAGCATAACCG 60.095 50.000 0.00 0.00 0.00 4.44
2689 2847 2.584835 TAGCCAGTTTCCACAAGCAT 57.415 45.000 0.00 0.00 0.00 3.79
2776 2937 8.687292 AGATTCAGCATATTGTACATTCATGT 57.313 30.769 0.00 0.00 44.48 3.21
2777 2938 9.961265 AAAGATTCAGCATATTGTACATTCATG 57.039 29.630 0.00 2.05 0.00 3.07
2779 2940 9.791820 CAAAAGATTCAGCATATTGTACATTCA 57.208 29.630 0.00 0.00 0.00 2.57
2780 2941 9.793252 ACAAAAGATTCAGCATATTGTACATTC 57.207 29.630 0.00 0.00 0.00 2.67
2782 2943 9.577110 CAACAAAAGATTCAGCATATTGTACAT 57.423 29.630 0.00 0.00 0.00 2.29
2783 2944 8.791675 TCAACAAAAGATTCAGCATATTGTACA 58.208 29.630 0.00 0.00 0.00 2.90
2784 2945 9.793252 ATCAACAAAAGATTCAGCATATTGTAC 57.207 29.630 0.00 0.00 0.00 2.90
2786 2947 8.525316 TGATCAACAAAAGATTCAGCATATTGT 58.475 29.630 0.00 0.00 0.00 2.71
2787 2948 8.920509 TGATCAACAAAAGATTCAGCATATTG 57.079 30.769 0.00 0.00 0.00 1.90
2791 2952 8.525316 TGTTATGATCAACAAAAGATTCAGCAT 58.475 29.630 0.00 0.00 35.53 3.79
2792 2953 7.884257 TGTTATGATCAACAAAAGATTCAGCA 58.116 30.769 0.00 0.00 35.53 4.41
2793 2954 8.746922 TTGTTATGATCAACAAAAGATTCAGC 57.253 30.769 9.95 0.00 43.53 4.26
2804 2965 8.570488 GGATTCAGCATATTGTTATGATCAACA 58.430 33.333 0.00 0.00 37.94 3.33
2805 2966 8.570488 TGGATTCAGCATATTGTTATGATCAAC 58.430 33.333 0.00 0.00 37.94 3.18
2806 2967 8.694581 TGGATTCAGCATATTGTTATGATCAA 57.305 30.769 0.00 0.00 37.94 2.57
2807 2968 8.158789 TCTGGATTCAGCATATTGTTATGATCA 58.841 33.333 0.00 0.00 40.69 2.92
2808 2969 8.557592 TCTGGATTCAGCATATTGTTATGATC 57.442 34.615 0.00 0.00 40.69 2.92
2809 2970 8.162085 ACTCTGGATTCAGCATATTGTTATGAT 58.838 33.333 0.00 0.00 40.69 2.45
2810 2971 7.512130 ACTCTGGATTCAGCATATTGTTATGA 58.488 34.615 0.00 0.00 40.69 2.15
2811 2972 7.741027 ACTCTGGATTCAGCATATTGTTATG 57.259 36.000 0.00 0.00 40.69 1.90
2812 2973 9.499479 CTAACTCTGGATTCAGCATATTGTTAT 57.501 33.333 0.00 0.00 40.69 1.89
2813 2974 7.442364 GCTAACTCTGGATTCAGCATATTGTTA 59.558 37.037 0.00 0.00 40.69 2.41
2814 2975 6.261826 GCTAACTCTGGATTCAGCATATTGTT 59.738 38.462 0.00 0.00 40.69 2.83
2830 2991 7.667043 TTACATAAAACCACTGCTAACTCTG 57.333 36.000 0.00 0.00 0.00 3.35
2847 3008 9.158233 CCGAGAAAGGTTTTACTGATTACATAA 57.842 33.333 0.00 0.00 0.00 1.90
2850 3011 5.410439 GCCGAGAAAGGTTTTACTGATTACA 59.590 40.000 0.00 0.00 0.00 2.41
2873 3034 2.923020 CGGGCTTTGTATGAAACATTGC 59.077 45.455 0.00 0.00 38.10 3.56
2877 3038 2.570415 TCCGGGCTTTGTATGAAACA 57.430 45.000 0.00 0.00 35.88 2.83
2884 3045 0.392461 GAGCACATCCGGGCTTTGTA 60.392 55.000 0.00 0.00 41.22 2.41
2887 3048 1.033746 CATGAGCACATCCGGGCTTT 61.034 55.000 0.00 0.00 41.22 3.51
3119 3297 5.500645 AACTAAAGTTGACAGGAACAAGC 57.499 39.130 0.00 0.00 36.80 4.01
3128 3306 8.836413 CATTCAAGGTCTTAACTAAAGTTGACA 58.164 33.333 5.62 0.00 38.90 3.58
3137 3315 8.593679 TCACTGAATCATTCAAGGTCTTAACTA 58.406 33.333 0.75 0.00 39.58 2.24
3173 3351 7.870509 AGAGCATAATGACAAAATTAGCTGA 57.129 32.000 0.00 0.00 32.01 4.26
3185 3445 5.874810 TGGACTGTAACAAGAGCATAATGAC 59.125 40.000 0.00 0.00 0.00 3.06
3237 3500 9.538508 GCTGCAAATGAAAAGGAAGATATTATT 57.461 29.630 0.00 0.00 0.00 1.40
3241 3504 6.406624 CCAGCTGCAAATGAAAAGGAAGATAT 60.407 38.462 8.66 0.00 0.00 1.63
3273 3536 4.500035 GGTGGCCAGTTTTTCGTTTCAATA 60.500 41.667 5.11 0.00 0.00 1.90
3297 3560 6.324254 TGTCATGATGAATGATGGGCATAAAA 59.676 34.615 0.00 0.00 46.90 1.52
3395 3658 4.969484 TGAGGAGAGGTAAAACAAGAACC 58.031 43.478 0.00 0.00 0.00 3.62
3447 3713 9.631639 GTGTTTGCAATATTTGAACAAAAGTAC 57.368 29.630 0.00 0.00 31.74 2.73
3478 3744 0.625849 AATGTGAGGCCCCCAGTAAG 59.374 55.000 0.00 0.00 0.00 2.34
3488 3754 2.420022 AGTGTAAATGCGAATGTGAGGC 59.580 45.455 0.00 0.00 0.00 4.70
3499 3765 5.095490 GCATTAGTTGGACAGTGTAAATGC 58.905 41.667 14.57 14.57 40.56 3.56
3532 3798 0.313043 GCAATCGCATTGATCCAGGG 59.687 55.000 11.52 0.00 42.83 4.45
3558 3824 0.535335 GGCAGATTCACACCCTACGA 59.465 55.000 0.00 0.00 0.00 3.43
3559 3825 0.249120 TGGCAGATTCACACCCTACG 59.751 55.000 0.00 0.00 0.00 3.51
3560 3826 2.684881 CAATGGCAGATTCACACCCTAC 59.315 50.000 0.00 0.00 0.00 3.18
3601 3870 7.976734 ACGTTTTGAAATACCATTCTGTTTTCA 59.023 29.630 0.00 0.00 35.23 2.69
3609 3878 7.687005 TTGTTGACGTTTTGAAATACCATTC 57.313 32.000 0.00 0.00 0.00 2.67
3610 3879 7.762159 AGTTTGTTGACGTTTTGAAATACCATT 59.238 29.630 0.00 0.00 0.00 3.16
3638 3908 5.654603 AGTACAGATTGTCAACATACGGA 57.345 39.130 0.00 0.00 0.00 4.69
3641 3911 9.807386 GTTACAAAGTACAGATTGTCAACATAC 57.193 33.333 12.98 0.00 40.14 2.39
3789 4062 7.361201 CCACCATTATCCGATTACTAGCATTTG 60.361 40.741 0.00 0.00 0.00 2.32
3898 4171 4.650131 TCAATCCTGCATGGCATCAAAATA 59.350 37.500 0.00 0.00 38.13 1.40
3923 4196 7.270047 CAATGATGTTCCAAAAGAGGCATAAT 58.730 34.615 0.00 0.00 0.00 1.28
3987 4260 8.958506 CAAGATGTAGACAGTAAGGTACTACTT 58.041 37.037 0.00 0.00 38.49 2.24
4033 4306 4.144297 CCAGATTTGTTTCAAGGGTCAGA 58.856 43.478 0.00 0.00 0.00 3.27
4037 4310 1.613437 CGCCAGATTTGTTTCAAGGGT 59.387 47.619 0.00 0.00 0.00 4.34
4039 4312 1.613437 ACCGCCAGATTTGTTTCAAGG 59.387 47.619 0.00 0.00 0.00 3.61
4041 4314 2.035321 GGAACCGCCAGATTTGTTTCAA 59.965 45.455 0.00 0.00 36.34 2.69
4148 4421 7.895759 ACACAAACCTCATTGCATTATAAAGT 58.104 30.769 0.00 0.00 33.52 2.66
4192 4465 8.629986 CATACAAAGAAGCGACTTGTAAAAATG 58.370 33.333 7.48 1.34 0.00 2.32
4343 4616 4.412796 TGCATCAAAAATGTGGAAACCA 57.587 36.364 0.00 0.00 0.00 3.67
4344 4617 5.945466 AATGCATCAAAAATGTGGAAACC 57.055 34.783 0.00 0.00 0.00 3.27
4390 4663 5.870433 TGGAATATTAGCTCGTCACGAAAAA 59.130 36.000 0.00 0.00 34.74 1.94
4397 4670 5.863935 CGATGAATGGAATATTAGCTCGTCA 59.136 40.000 0.00 0.00 0.00 4.35
4420 4693 1.972872 AGGGGCAAAGATCATTAGCG 58.027 50.000 0.00 0.00 0.00 4.26
4655 4928 9.911788 ATGGTCAAGATACTGAAGAATAACAAT 57.088 29.630 0.00 0.00 0.00 2.71
4688 4961 6.764560 CGGTGGTGCCTTTTATAAGTAAGTAT 59.235 38.462 0.00 0.00 34.25 2.12
4691 4964 4.201881 GCGGTGGTGCCTTTTATAAGTAAG 60.202 45.833 0.00 0.00 34.25 2.34
4768 5045 7.609532 TCTCAGTTTAGTAAGTAGTAGGGTGTC 59.390 40.741 0.00 0.00 0.00 3.67
4806 5083 0.546267 AGAGGCTGATCCCACACACT 60.546 55.000 0.00 0.00 34.51 3.55
4836 5113 0.719465 GCGTACCAACTGTCAATCGG 59.281 55.000 0.00 0.00 0.00 4.18
4854 5131 1.463674 ACCTGGATCAATTCGGTTGC 58.536 50.000 0.00 0.00 37.74 4.17
4920 5197 2.547211 CAGTGCTGGAAGTGCTATATGC 59.453 50.000 0.00 0.00 43.25 3.14
4922 5199 4.970860 ATCAGTGCTGGAAGTGCTATAT 57.029 40.909 0.00 0.00 35.30 0.86
4967 5244 6.098409 ACCGAATTGATCCAGACAATACTACT 59.902 38.462 0.00 0.00 37.04 2.57
4977 5254 2.358957 CAGCAACCGAATTGATCCAGA 58.641 47.619 3.81 0.00 41.23 3.86
5079 5356 8.774546 ATGAGTTGTAGATAAGAGGAGATGAA 57.225 34.615 0.00 0.00 0.00 2.57
5129 5408 5.710099 CCCACTGTAACACCAGAAACAATAT 59.290 40.000 0.00 0.00 36.30 1.28
5217 5498 1.068127 CAGCCATGCCAAATTAGCTCC 59.932 52.381 0.00 0.00 0.00 4.70
5250 5531 2.202932 CGCGGGTCTGGAAGGATG 60.203 66.667 0.00 0.00 0.00 3.51
5251 5532 2.683933 ACGCGGGTCTGGAAGGAT 60.684 61.111 12.47 0.00 0.00 3.24
5312 5634 9.783081 AAATATCTGCCAGAAGAAAATGTTTTT 57.217 25.926 0.00 0.00 0.00 1.94
5313 5635 9.783081 AAAATATCTGCCAGAAGAAAATGTTTT 57.217 25.926 0.00 0.00 0.00 2.43
5315 5637 9.860898 GTAAAATATCTGCCAGAAGAAAATGTT 57.139 29.630 0.00 0.00 0.00 2.71
5325 5647 6.945435 TCCAACAAAGTAAAATATCTGCCAGA 59.055 34.615 0.00 0.00 0.00 3.86
5408 5730 1.613270 GCACGGAAAAAGGTTATGCG 58.387 50.000 0.00 0.00 0.00 4.73
5421 5743 0.472471 AAGGAAACAGAAGGCACGGA 59.528 50.000 0.00 0.00 0.00 4.69
5652 5974 3.838317 GCCACCCACAGATATGTATAGGA 59.162 47.826 9.61 0.00 0.00 2.94
5726 6058 4.331168 CCTAGGAAAGAAATGAAGCACTCG 59.669 45.833 1.05 0.00 0.00 4.18
5815 6147 1.509644 TTGCAAGCAAGCTCGTCAGG 61.510 55.000 2.89 0.00 34.99 3.86
5996 6328 1.754803 CCACCTCACGCCAGAGTTATA 59.245 52.381 0.07 0.00 33.75 0.98
6006 6338 1.940613 GTATGAAATCCCACCTCACGC 59.059 52.381 0.00 0.00 0.00 5.34
6013 6345 7.148069 CCCAAAAAGTAGAGTATGAAATCCCAC 60.148 40.741 0.00 0.00 0.00 4.61
6016 6348 6.183360 GCCCCAAAAAGTAGAGTATGAAATCC 60.183 42.308 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.