Multiple sequence alignment - TraesCS2D01G080000

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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 TraesCS2D01G080000 chr2D 100.000 5456 0 0 1 5456 34227021 34232476 0.000000e+00 10076.0
1 TraesCS2D01G080000 chr2A 90.812 2253 120 34 450 2654 37084562 37086775 0.000000e+00 2933.0
2 TraesCS2D01G080000 chr2A 92.764 1382 49 14 3425 4787 37087437 37088786 0.000000e+00 1951.0
3 TraesCS2D01G080000 chr2A 94.436 683 19 5 2735 3401 37086765 37087444 0.000000e+00 1033.0
4 TraesCS2D01G080000 chr2A 87.074 557 27 13 4911 5447 37089053 37089584 6.090000e-164 588.0
5 TraesCS2D01G080000 chr2A 86.997 323 26 9 110 420 37084018 37084336 3.130000e-92 350.0
6 TraesCS2D01G080000 chr2A 80.374 214 22 11 2368 2581 37085799 37085992 1.580000e-30 145.0
7 TraesCS2D01G080000 chr2A 97.531 81 2 0 1 81 37083814 37083894 7.370000e-29 139.0
8 TraesCS2D01G080000 chr2A 89.655 58 1 3 3029 3083 37086356 37086411 9.810000e-08 69.4
9 TraesCS2D01G080000 chr2B 90.069 1873 97 50 1 1822 56516863 56518697 0.000000e+00 2346.0
10 TraesCS2D01G080000 chr2B 87.341 1335 101 36 3479 4766 56520390 56521703 0.000000e+00 1467.0
11 TraesCS2D01G080000 chr2B 82.820 617 47 15 4846 5456 56521841 56522404 1.060000e-136 497.0
12 TraesCS2D01G080000 chr2B 83.725 510 55 16 2869 3357 56519597 56520099 1.790000e-124 457.0
13 TraesCS2D01G080000 chr2B 78.411 491 68 26 2893 3350 523779690 523779205 8.940000e-73 285.0
14 TraesCS2D01G080000 chr2B 76.891 238 18 19 1859 2068 56518697 56518925 3.480000e-17 100.0
15 TraesCS2D01G080000 chr1A 77.731 952 105 56 2893 3764 168550483 168551407 8.220000e-133 484.0
16 TraesCS2D01G080000 chr1A 86.301 219 21 6 5238 5447 582061056 582060838 4.250000e-56 230.0
17 TraesCS2D01G080000 chr7D 85.874 269 13 9 5194 5443 450003554 450003292 4.190000e-66 263.0
18 TraesCS2D01G080000 chr4D 87.556 225 16 5 5200 5415 434801288 434801509 3.260000e-62 250.0
19 TraesCS2D01G080000 chr4D 94.366 142 8 0 5200 5341 148416051 148416192 9.200000e-53 219.0
20 TraesCS2D01G080000 chr1B 84.871 271 16 10 5192 5443 566763881 566763617 3.260000e-62 250.0
21 TraesCS2D01G080000 chr3A 86.603 209 19 5 5248 5447 642605288 642605496 7.110000e-54 222.0
22 TraesCS2D01G080000 chr4A 76.866 402 77 15 996 1387 120569780 120570175 4.280000e-51 213.0
23 TraesCS2D01G080000 chr4A 90.244 123 10 2 2458 2579 701630008 701630129 5.660000e-35 159.0
24 TraesCS2D01G080000 chr4A 89.474 114 12 0 2466 2579 672126798 672126911 1.580000e-30 145.0
25 TraesCS2D01G080000 chr6A 84.932 219 22 7 5238 5447 15396905 15397121 1.540000e-50 211.0
26 TraesCS2D01G080000 chr6D 91.870 123 8 2 2458 2579 443864739 443864618 2.610000e-38 171.0
27 TraesCS2D01G080000 chr6B 90.984 122 11 0 2458 2579 75275056 75274935 1.220000e-36 165.0
28 TraesCS2D01G080000 chr3D 91.057 123 9 2 2458 2579 124116753 124116632 1.220000e-36 165.0
29 TraesCS2D01G080000 chr7B 91.509 106 9 0 2474 2579 126627353 126627248 4.400000e-31 147.0


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 TraesCS2D01G080000 chr2D 34227021 34232476 5455 False 10076.00 10076 100.000000 1 5456 1 chr2D.!!$F1 5455
1 TraesCS2D01G080000 chr2A 37083814 37089584 5770 False 901.05 2933 89.955375 1 5447 8 chr2A.!!$F1 5446
2 TraesCS2D01G080000 chr2B 56516863 56522404 5541 False 973.40 2346 84.169200 1 5456 5 chr2B.!!$F1 5455
3 TraesCS2D01G080000 chr1A 168550483 168551407 924 False 484.00 484 77.731000 2893 3764 1 chr1A.!!$F1 871

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
151 261 0.040067 GGTAGTGTTGCTGCTGTTGC 60.040 55.000 0.00 0.00 40.20 4.17 F
156 266 0.179020 TGTTGCTGCTGTTGCCTAGT 60.179 50.000 0.00 0.00 38.71 2.57 F
243 357 0.181350 GATGGCGATGGGTCCTCTTT 59.819 55.000 0.00 0.00 0.00 2.52 F
620 938 0.391597 TCCCCTAGCGAAAATAGCCG 59.608 55.000 0.00 0.00 34.64 5.52 F
736 1055 1.135517 CAAATTACCCAAACGCCCTCG 60.136 52.381 0.00 0.00 42.43 4.63 F
2452 2866 1.132453 CAATAGTGACGACAGGCTCGA 59.868 52.381 2.96 0.00 46.14 4.04 F
3525 4407 0.681887 TCAATGCTGGACCATGCCTG 60.682 55.000 11.80 9.66 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 2131 0.100325 TCACAGCAACAAACAAGCCG 59.900 50.000 0.00 0.00 0.00 5.52 R
1999 2364 0.673437 ACATCAAAACAGCAACCCCG 59.327 50.000 0.00 0.00 0.00 5.73 R
2015 2380 5.072329 CCCTCTTAATCTACCATGGTCACAT 59.928 44.000 23.76 9.03 37.99 3.21 R
2427 2841 2.094700 GCCTGTCGTCACTATTGTCTCA 60.095 50.000 0.00 0.00 0.00 3.27 R
2646 3060 2.824936 CACCAAAGCATAACATGGACCA 59.175 45.455 0.00 0.00 36.75 4.02 R
4388 5291 1.417890 AGGCATGGATTTACTCTCCCG 59.582 52.381 0.00 0.00 31.32 5.14 R
4887 6068 0.167470 CTGTCTTGCTTGCCACGATG 59.833 55.000 0.00 0.00 0.00 3.84 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
101 103 4.248859 CCCGATCCTACATGAATGATCAC 58.751 47.826 17.07 0.00 38.69 3.06
104 106 4.984785 CGATCCTACATGAATGATCACGTT 59.015 41.667 17.07 0.00 38.69 3.99
105 107 6.149633 CGATCCTACATGAATGATCACGTTA 58.850 40.000 17.07 0.00 38.69 3.18
106 108 6.306596 CGATCCTACATGAATGATCACGTTAG 59.693 42.308 17.07 0.00 38.69 2.34
107 109 5.842907 TCCTACATGAATGATCACGTTAGG 58.157 41.667 0.00 3.17 38.69 2.69
151 261 0.040067 GGTAGTGTTGCTGCTGTTGC 60.040 55.000 0.00 0.00 40.20 4.17
156 266 0.179020 TGTTGCTGCTGTTGCCTAGT 60.179 50.000 0.00 0.00 38.71 2.57
161 271 1.952367 GCTGCTGTTGCCTAGTGGAAT 60.952 52.381 0.00 0.00 38.71 3.01
166 276 2.489329 CTGTTGCCTAGTGGAATTGTGG 59.511 50.000 0.00 0.00 34.57 4.17
167 277 1.818674 GTTGCCTAGTGGAATTGTGGG 59.181 52.381 0.00 0.00 34.57 4.61
240 354 2.029666 CGATGGCGATGGGTCCTC 59.970 66.667 0.00 0.00 40.82 3.71
243 357 0.181350 GATGGCGATGGGTCCTCTTT 59.819 55.000 0.00 0.00 0.00 2.52
271 385 2.541588 CGTGGCTGAAACTTGAAAGGTG 60.542 50.000 0.00 0.00 0.00 4.00
304 422 0.825425 TTGGGCGATGTTGGCTTGAA 60.825 50.000 0.00 0.00 34.31 2.69
384 502 1.421268 TGGATCGGAATGAGATTGGGG 59.579 52.381 0.00 0.00 0.00 4.96
420 538 0.748005 AATCTGCCGGGGAATCGTTG 60.748 55.000 2.18 0.00 0.00 4.10
421 539 1.622607 ATCTGCCGGGGAATCGTTGA 61.623 55.000 2.18 0.00 0.00 3.18
424 542 0.542333 TGCCGGGGAATCGTTGATTA 59.458 50.000 2.18 0.00 31.89 1.75
425 543 0.942252 GCCGGGGAATCGTTGATTAC 59.058 55.000 2.18 0.00 31.89 1.89
427 573 1.937899 CCGGGGAATCGTTGATTACAC 59.062 52.381 0.00 0.00 34.75 2.90
433 579 6.872020 CGGGGAATCGTTGATTACACTAATAT 59.128 38.462 2.75 0.00 34.33 1.28
434 580 8.030692 CGGGGAATCGTTGATTACACTAATATA 58.969 37.037 2.75 0.00 34.33 0.86
598 915 2.874245 TCCACTCCCTCCTCCCCA 60.874 66.667 0.00 0.00 0.00 4.96
620 938 0.391597 TCCCCTAGCGAAAATAGCCG 59.608 55.000 0.00 0.00 34.64 5.52
736 1055 1.135517 CAAATTACCCAAACGCCCTCG 60.136 52.381 0.00 0.00 42.43 4.63
870 1190 4.803908 CCAGAAGCTTCCGGCCCC 62.804 72.222 22.81 0.00 43.05 5.80
910 1230 2.187946 CAGTGGCCTCCATCGTCC 59.812 66.667 3.32 0.00 35.28 4.79
914 1234 2.060383 TGGCCTCCATCGTCCTCAG 61.060 63.158 3.32 0.00 0.00 3.35
936 1257 4.444081 CTCCTCCTCCCCGTCCGT 62.444 72.222 0.00 0.00 0.00 4.69
949 1270 2.764547 TCCGTCCCCACACACACA 60.765 61.111 0.00 0.00 0.00 3.72
1044 1369 3.450115 AGCGACGAGTACCTGGCC 61.450 66.667 0.00 0.00 0.00 5.36
1107 1432 4.643387 AAGAACTGCGCGCCCCTT 62.643 61.111 30.77 21.44 0.00 3.95
1169 1499 2.123640 CTCCCCTCCCTCGTCTCC 60.124 72.222 0.00 0.00 0.00 3.71
1189 1519 4.643733 CCGATCTGATCTGACGGC 57.356 61.111 21.26 8.78 37.32 5.68
1190 1520 1.371022 CCGATCTGATCTGACGGCG 60.371 63.158 21.26 4.80 37.32 6.46
1192 1522 1.361993 GATCTGATCTGACGGCGCT 59.638 57.895 6.90 0.00 0.00 5.92
1197 1528 1.315981 TGATCTGACGGCGCTCTCTT 61.316 55.000 6.90 0.00 0.00 2.85
1708 2045 7.817478 TCAACGTGTATTATTGACTTGAGTGAT 59.183 33.333 0.00 0.00 0.00 3.06
1712 2049 7.513660 CGTGTATTATTGACTTGAGTGATGACG 60.514 40.741 0.00 0.00 0.00 4.35
1730 2067 3.119065 TGACGGATGCGGTATTGTTTAGA 60.119 43.478 12.44 0.00 0.00 2.10
1757 2094 3.591527 TGGTTGGAATAGTTGGTCCAGAT 59.408 43.478 0.00 0.00 44.61 2.90
1785 2122 5.181690 TGTTTATAGAATGGCGATTTGGC 57.818 39.130 0.00 0.00 45.12 4.52
1793 2131 3.092081 GGCGATTTGGCGAATATGC 57.908 52.632 13.24 13.24 0.00 3.14
1803 2141 1.191096 GCGAATATGCGGCTTGTTTG 58.809 50.000 4.99 4.94 0.00 2.93
1816 2154 2.129607 CTTGTTTGTTGCTGTGATGGC 58.870 47.619 0.00 0.00 0.00 4.40
1851 2189 1.600957 CTATTGCGGCTTCATGAGTGG 59.399 52.381 0.00 0.00 0.00 4.00
1853 2191 2.825836 GCGGCTTCATGAGTGGGG 60.826 66.667 0.00 0.00 0.00 4.96
1885 2223 5.573219 TGTTCCATCCAATGTCTGATTCTT 58.427 37.500 0.00 0.00 0.00 2.52
1893 2231 9.286170 CATCCAATGTCTGATTCTTATCTGATT 57.714 33.333 0.00 0.00 39.81 2.57
1896 2234 9.117183 CCAATGTCTGATTCTTATCTGATTTGA 57.883 33.333 0.00 0.00 39.81 2.69
1924 2262 9.826574 ATATAGCCATAACTACGAAAAAGAACA 57.173 29.630 0.00 0.00 0.00 3.18
1925 2263 8.732746 ATAGCCATAACTACGAAAAAGAACAT 57.267 30.769 0.00 0.00 0.00 2.71
1926 2264 7.073342 AGCCATAACTACGAAAAAGAACATC 57.927 36.000 0.00 0.00 0.00 3.06
1927 2265 5.957796 GCCATAACTACGAAAAAGAACATCG 59.042 40.000 0.00 0.00 42.05 3.84
1964 2303 4.431416 TTCTAGTCCATGTGTTGGTGTT 57.569 40.909 0.00 0.00 46.52 3.32
1967 2306 2.575532 AGTCCATGTGTTGGTGTTCTG 58.424 47.619 0.00 0.00 46.52 3.02
1979 2343 5.700832 TGTTGGTGTTCTGATGATCAAGTAC 59.299 40.000 0.00 0.00 0.00 2.73
1999 2364 7.959689 AGTACTGATGATTGAATCTATGTGC 57.040 36.000 6.73 4.48 0.00 4.57
2010 2375 1.377202 CTATGTGCGGGGTTGCTGT 60.377 57.895 0.00 0.00 35.36 4.40
2015 2380 1.754621 TGCGGGGTTGCTGTTTTGA 60.755 52.632 0.00 0.00 35.36 2.69
2040 2405 3.973973 TGACCATGGTAGATTAAGAGGGG 59.026 47.826 19.80 0.00 0.00 4.79
2214 2626 7.882791 TGTTATGAAAAGTATGTGTGTCCTCAT 59.117 33.333 0.00 0.00 0.00 2.90
2222 2634 6.810911 AGTATGTGTGTCCTCATATTCTCAC 58.189 40.000 0.00 0.00 31.70 3.51
2396 2810 4.217767 ACTTTAGTGACGACAGATGCAGTA 59.782 41.667 0.00 0.00 0.00 2.74
2412 2826 7.283127 CAGATGCAGTATTGTTTAGTTGGGTAT 59.717 37.037 0.00 0.00 0.00 2.73
2425 2839 8.799367 GTTTAGTTGGGTATTTGGAATAGTTGT 58.201 33.333 0.00 0.00 0.00 3.32
2427 2841 7.849322 AGTTGGGTATTTGGAATAGTTGTTT 57.151 32.000 0.00 0.00 0.00 2.83
2444 2858 5.900339 TTGTTTGAGACAATAGTGACGAC 57.100 39.130 0.00 0.00 43.13 4.34
2445 2859 4.939271 TGTTTGAGACAATAGTGACGACA 58.061 39.130 0.00 0.00 34.69 4.35
2446 2860 4.982295 TGTTTGAGACAATAGTGACGACAG 59.018 41.667 0.00 0.00 34.69 3.51
2447 2861 3.850122 TGAGACAATAGTGACGACAGG 57.150 47.619 0.00 0.00 0.00 4.00
2448 2862 2.094700 TGAGACAATAGTGACGACAGGC 60.095 50.000 0.00 0.00 0.00 4.85
2449 2863 2.164624 GAGACAATAGTGACGACAGGCT 59.835 50.000 0.00 0.00 0.00 4.58
2450 2864 2.164624 AGACAATAGTGACGACAGGCTC 59.835 50.000 0.00 0.00 0.00 4.70
2452 2866 1.132453 CAATAGTGACGACAGGCTCGA 59.868 52.381 2.96 0.00 46.14 4.04
2453 2867 1.460504 ATAGTGACGACAGGCTCGAA 58.539 50.000 2.96 0.00 46.14 3.71
2454 2868 1.460504 TAGTGACGACAGGCTCGAAT 58.539 50.000 2.96 0.00 46.14 3.34
2455 2869 1.460504 AGTGACGACAGGCTCGAATA 58.539 50.000 2.96 0.00 46.14 1.75
2456 2870 1.402259 AGTGACGACAGGCTCGAATAG 59.598 52.381 2.96 0.00 46.14 1.73
2471 2885 8.421784 AGGCTCGAATAGTTGTTTATAGAATGA 58.578 33.333 0.00 0.00 0.00 2.57
2619 3033 5.590530 AAAAGAAATGTGTTGGTGTGCTA 57.409 34.783 0.00 0.00 0.00 3.49
2622 3036 3.003275 AGAAATGTGTTGGTGTGCTAACG 59.997 43.478 0.00 0.00 38.69 3.18
2624 3038 2.025589 TGTGTTGGTGTGCTAACGAA 57.974 45.000 0.00 0.00 38.69 3.85
2642 3056 3.073356 ACGAAAGTTCAGGGGAAATGGTA 59.927 43.478 0.00 0.00 46.40 3.25
2643 3057 4.263771 ACGAAAGTTCAGGGGAAATGGTAT 60.264 41.667 0.00 0.00 46.40 2.73
2644 3058 4.705023 CGAAAGTTCAGGGGAAATGGTATT 59.295 41.667 0.00 0.00 34.13 1.89
2645 3059 5.163652 CGAAAGTTCAGGGGAAATGGTATTC 60.164 44.000 0.00 0.00 34.13 1.75
2646 3060 5.536497 AAGTTCAGGGGAAATGGTATTCT 57.464 39.130 0.00 0.00 34.13 2.40
2647 3061 4.860022 AGTTCAGGGGAAATGGTATTCTG 58.140 43.478 0.00 0.00 34.13 3.02
2648 3062 3.951563 TCAGGGGAAATGGTATTCTGG 57.048 47.619 0.00 0.00 0.00 3.86
2649 3063 3.197983 TCAGGGGAAATGGTATTCTGGT 58.802 45.455 0.00 0.00 0.00 4.00
2650 3064 3.202151 TCAGGGGAAATGGTATTCTGGTC 59.798 47.826 0.00 0.00 0.00 4.02
2651 3065 2.514160 AGGGGAAATGGTATTCTGGTCC 59.486 50.000 0.00 0.00 0.00 4.46
2652 3066 2.243736 GGGGAAATGGTATTCTGGTCCA 59.756 50.000 0.00 0.00 35.64 4.02
2653 3067 3.117131 GGGGAAATGGTATTCTGGTCCAT 60.117 47.826 0.00 0.00 42.82 3.41
2654 3068 3.891366 GGGAAATGGTATTCTGGTCCATG 59.109 47.826 0.00 0.00 41.12 3.66
2655 3069 4.536765 GGAAATGGTATTCTGGTCCATGT 58.463 43.478 0.00 0.00 41.12 3.21
2656 3070 4.956075 GGAAATGGTATTCTGGTCCATGTT 59.044 41.667 0.00 0.00 41.12 2.71
2657 3071 6.126409 GGAAATGGTATTCTGGTCCATGTTA 58.874 40.000 0.00 0.00 41.12 2.41
2658 3072 6.777580 GGAAATGGTATTCTGGTCCATGTTAT 59.222 38.462 0.00 0.00 41.12 1.89
2659 3073 7.255590 GGAAATGGTATTCTGGTCCATGTTATG 60.256 40.741 0.00 0.00 41.12 1.90
2660 3074 4.460263 TGGTATTCTGGTCCATGTTATGC 58.540 43.478 0.00 0.00 0.00 3.14
2661 3075 4.165950 TGGTATTCTGGTCCATGTTATGCT 59.834 41.667 0.00 0.00 0.00 3.79
2662 3076 5.133221 GGTATTCTGGTCCATGTTATGCTT 58.867 41.667 0.00 0.00 0.00 3.91
2663 3077 5.594317 GGTATTCTGGTCCATGTTATGCTTT 59.406 40.000 0.00 0.00 0.00 3.51
2664 3078 5.587388 ATTCTGGTCCATGTTATGCTTTG 57.413 39.130 0.00 0.00 0.00 2.77
2665 3079 3.355378 TCTGGTCCATGTTATGCTTTGG 58.645 45.455 0.00 0.00 0.00 3.28
2666 3080 3.091545 CTGGTCCATGTTATGCTTTGGT 58.908 45.455 0.00 0.00 0.00 3.67
2667 3081 2.824936 TGGTCCATGTTATGCTTTGGTG 59.175 45.455 0.00 0.00 0.00 4.17
2668 3082 2.825532 GGTCCATGTTATGCTTTGGTGT 59.174 45.455 0.00 0.00 0.00 4.16
2669 3083 3.367292 GGTCCATGTTATGCTTTGGTGTG 60.367 47.826 0.00 0.00 0.00 3.82
2670 3084 3.505680 GTCCATGTTATGCTTTGGTGTGA 59.494 43.478 0.00 0.00 0.00 3.58
2671 3085 3.505680 TCCATGTTATGCTTTGGTGTGAC 59.494 43.478 0.00 0.00 0.00 3.67
2672 3086 3.367292 CCATGTTATGCTTTGGTGTGACC 60.367 47.826 0.00 0.00 39.22 4.02
2684 3098 4.632327 TGGTGTGACCATGTTAGATTGA 57.368 40.909 0.00 0.00 44.79 2.57
2685 3099 4.578871 TGGTGTGACCATGTTAGATTGAG 58.421 43.478 0.00 0.00 44.79 3.02
2686 3100 4.285775 TGGTGTGACCATGTTAGATTGAGA 59.714 41.667 0.00 0.00 44.79 3.27
2687 3101 4.631813 GGTGTGACCATGTTAGATTGAGAC 59.368 45.833 0.00 0.00 38.42 3.36
2688 3102 4.327357 GTGTGACCATGTTAGATTGAGACG 59.673 45.833 0.00 0.00 0.00 4.18
2689 3103 4.219725 TGTGACCATGTTAGATTGAGACGA 59.780 41.667 0.00 0.00 0.00 4.20
2690 3104 5.105351 TGTGACCATGTTAGATTGAGACGAT 60.105 40.000 0.00 0.00 0.00 3.73
2691 3105 5.812642 GTGACCATGTTAGATTGAGACGATT 59.187 40.000 0.00 0.00 0.00 3.34
2692 3106 6.978659 GTGACCATGTTAGATTGAGACGATTA 59.021 38.462 0.00 0.00 0.00 1.75
2693 3107 7.653713 GTGACCATGTTAGATTGAGACGATTAT 59.346 37.037 0.00 0.00 0.00 1.28
2694 3108 7.653311 TGACCATGTTAGATTGAGACGATTATG 59.347 37.037 0.00 0.00 0.00 1.90
2695 3109 7.500992 ACCATGTTAGATTGAGACGATTATGT 58.499 34.615 0.00 0.00 0.00 2.29
2696 3110 8.638873 ACCATGTTAGATTGAGACGATTATGTA 58.361 33.333 0.00 0.00 0.00 2.29
2697 3111 9.133627 CCATGTTAGATTGAGACGATTATGTAG 57.866 37.037 0.00 0.00 0.00 2.74
2698 3112 8.642885 CATGTTAGATTGAGACGATTATGTAGC 58.357 37.037 0.00 0.00 0.00 3.58
2699 3113 7.941919 TGTTAGATTGAGACGATTATGTAGCT 58.058 34.615 0.00 0.00 0.00 3.32
2700 3114 9.063615 TGTTAGATTGAGACGATTATGTAGCTA 57.936 33.333 0.00 0.00 0.00 3.32
2701 3115 9.894783 GTTAGATTGAGACGATTATGTAGCTAA 57.105 33.333 0.00 0.00 0.00 3.09
2704 3118 9.988815 AGATTGAGACGATTATGTAGCTAATTT 57.011 29.630 0.00 0.00 0.00 1.82
2706 3120 9.764363 ATTGAGACGATTATGTAGCTAATTTGA 57.236 29.630 0.00 0.00 0.00 2.69
2707 3121 9.764363 TTGAGACGATTATGTAGCTAATTTGAT 57.236 29.630 0.00 0.00 0.00 2.57
2708 3122 9.411801 TGAGACGATTATGTAGCTAATTTGATC 57.588 33.333 0.00 0.00 0.00 2.92
2709 3123 9.632807 GAGACGATTATGTAGCTAATTTGATCT 57.367 33.333 0.00 0.00 0.00 2.75
2710 3124 9.988815 AGACGATTATGTAGCTAATTTGATCTT 57.011 29.630 0.00 0.00 0.00 2.40
2712 3126 9.764363 ACGATTATGTAGCTAATTTGATCTTCA 57.236 29.630 0.00 0.00 0.00 3.02
2728 3142 9.499479 TTTGATCTTCAATCTAGATTCTATGCC 57.501 33.333 15.24 5.02 36.11 4.40
2729 3143 8.433249 TGATCTTCAATCTAGATTCTATGCCT 57.567 34.615 15.24 0.00 32.64 4.75
2730 3144 8.312564 TGATCTTCAATCTAGATTCTATGCCTG 58.687 37.037 15.24 2.88 32.64 4.85
2731 3145 7.846101 TCTTCAATCTAGATTCTATGCCTGA 57.154 36.000 15.24 5.28 0.00 3.86
2732 3146 8.255111 TCTTCAATCTAGATTCTATGCCTGAA 57.745 34.615 15.24 12.30 0.00 3.02
2733 3147 8.708378 TCTTCAATCTAGATTCTATGCCTGAAA 58.292 33.333 15.24 3.59 0.00 2.69
2768 3182 5.771469 TCACATTGTTTCTTAGGCAACATG 58.229 37.500 0.00 0.00 41.41 3.21
2784 3198 5.106555 GGCAACATGGTATGCATATGTCTAC 60.107 44.000 10.16 6.45 44.32 2.59
2792 3206 7.840931 TGGTATGCATATGTCTACAATCTAGG 58.159 38.462 10.16 0.00 0.00 3.02
2799 3213 7.095439 GCATATGTCTACAATCTAGGTGCTTTC 60.095 40.741 4.29 0.00 0.00 2.62
2847 3276 3.876309 TTAACTCAAACTTGCCTCCCT 57.124 42.857 0.00 0.00 0.00 4.20
2851 3280 4.489306 ACTCAAACTTGCCTCCCTATAC 57.511 45.455 0.00 0.00 0.00 1.47
3207 3884 4.021016 CCTGATGCTACCCAAGGTACTATC 60.021 50.000 0.00 0.00 38.49 2.08
3209 3886 1.684983 TGCTACCCAAGGTACTATCGC 59.315 52.381 0.00 0.00 38.49 4.58
3367 4083 8.479313 TCATAGTGCTATCAACTGTTAGTTTG 57.521 34.615 0.00 0.00 36.03 2.93
3524 4406 0.682209 GTCAATGCTGGACCATGCCT 60.682 55.000 11.80 1.86 0.00 4.75
3525 4407 0.681887 TCAATGCTGGACCATGCCTG 60.682 55.000 11.80 9.66 0.00 4.85
3527 4409 0.682209 AATGCTGGACCATGCCTGTC 60.682 55.000 11.80 0.00 0.00 3.51
3560 4442 5.394993 GCTTCTATAGTCAGGGTTAAACGGT 60.395 44.000 0.00 0.00 0.00 4.83
3584 4466 8.487176 GGTTTATGCTTGTCTGTTTGTTTTATG 58.513 33.333 0.00 0.00 0.00 1.90
3797 4688 1.661341 CCATGCTTGTCTGTAGGCTC 58.339 55.000 0.00 0.00 0.00 4.70
3815 4706 2.413371 GCTCGATTGAAAGGTTGTGCTC 60.413 50.000 0.00 0.00 0.00 4.26
4159 5059 1.336056 GCGGTACATCCTCGATCCTTC 60.336 57.143 0.00 0.00 0.00 3.46
4197 5097 3.743521 TCTCACAGTGTTCATCTTTGGG 58.256 45.455 0.00 0.00 0.00 4.12
4391 5294 0.523072 CTTGTGCAAACATCCTCGGG 59.477 55.000 0.00 0.00 0.00 5.14
4406 5309 2.910688 TCGGGAGAGTAAATCCATGC 57.089 50.000 0.00 0.00 38.70 4.06
4407 5310 1.416401 TCGGGAGAGTAAATCCATGCC 59.584 52.381 0.00 0.00 38.70 4.40
4409 5312 2.632996 CGGGAGAGTAAATCCATGCCTA 59.367 50.000 0.00 0.00 38.70 3.93
4412 5315 4.534103 GGGAGAGTAAATCCATGCCTATCT 59.466 45.833 0.00 0.00 38.70 1.98
4522 5434 7.498239 TCATGAAGAAGAAGAGCAATAAGGATG 59.502 37.037 0.00 0.00 0.00 3.51
4523 5435 6.715280 TGAAGAAGAAGAGCAATAAGGATGT 58.285 36.000 0.00 0.00 0.00 3.06
4524 5436 6.596888 TGAAGAAGAAGAGCAATAAGGATGTG 59.403 38.462 0.00 0.00 0.00 3.21
4525 5437 6.059787 AGAAGAAGAGCAATAAGGATGTGT 57.940 37.500 0.00 0.00 0.00 3.72
4526 5438 6.479884 AGAAGAAGAGCAATAAGGATGTGTT 58.520 36.000 0.00 0.00 0.00 3.32
4527 5439 6.373774 AGAAGAAGAGCAATAAGGATGTGTTG 59.626 38.462 0.00 0.00 0.00 3.33
4528 5440 4.946157 AGAAGAGCAATAAGGATGTGTTGG 59.054 41.667 0.00 0.00 0.00 3.77
4529 5441 3.019564 AGAGCAATAAGGATGTGTTGGC 58.980 45.455 0.00 0.00 0.00 4.52
4530 5442 2.099756 GAGCAATAAGGATGTGTTGGCC 59.900 50.000 0.00 0.00 0.00 5.36
4531 5443 2.102578 GCAATAAGGATGTGTTGGCCT 58.897 47.619 3.32 0.00 0.00 5.19
4532 5444 2.159198 GCAATAAGGATGTGTTGGCCTG 60.159 50.000 3.32 0.00 31.06 4.85
4533 5445 1.767759 ATAAGGATGTGTTGGCCTGC 58.232 50.000 3.32 0.00 31.06 4.85
4534 5446 0.676466 TAAGGATGTGTTGGCCTGCG 60.676 55.000 3.32 0.00 31.06 5.18
4535 5447 3.443045 GGATGTGTTGGCCTGCGG 61.443 66.667 3.32 0.00 0.00 5.69
4574 5511 4.080299 GTCTGGACTTGGATTAGATGGGTT 60.080 45.833 0.00 0.00 0.00 4.11
4605 5542 3.242706 GGGTGTTGCATTGTTTTGCTTTC 60.243 43.478 0.00 0.00 43.18 2.62
4617 5554 2.733593 GCTTTCGACGCCTCGTGT 60.734 61.111 5.03 0.00 41.37 4.49
4618 5555 2.717809 GCTTTCGACGCCTCGTGTC 61.718 63.158 5.03 0.00 41.37 3.67
4619 5556 1.371267 CTTTCGACGCCTCGTGTCA 60.371 57.895 5.03 0.00 42.42 3.58
4644 5581 2.000447 GTGATGGGCGTTCTTGTAGTC 59.000 52.381 0.00 0.00 0.00 2.59
4725 5662 3.812053 CGAAATGAAAATTTGGTTGCCCA 59.188 39.130 0.00 0.00 39.65 5.36
4740 5686 1.693640 CCCACATTTGGCCCTCTCT 59.306 57.895 0.00 0.00 42.35 3.10
4766 5712 2.634600 TGTTTTACCAGCTTGTCGTGT 58.365 42.857 0.00 0.00 0.00 4.49
4769 5715 2.319136 TTACCAGCTTGTCGTGTTGT 57.681 45.000 0.00 0.00 0.00 3.32
4770 5716 2.319136 TACCAGCTTGTCGTGTTGTT 57.681 45.000 0.00 0.00 0.00 2.83
4775 5721 2.080693 AGCTTGTCGTGTTGTTTGTCA 58.919 42.857 0.00 0.00 0.00 3.58
4802 5891 6.795098 AGTTTTGTATCATCGTTTGCTGTA 57.205 33.333 0.00 0.00 0.00 2.74
4810 5899 1.225855 TCGTTTGCTGTAGGCTGTTG 58.774 50.000 0.00 0.00 42.39 3.33
4811 5900 0.385974 CGTTTGCTGTAGGCTGTTGC 60.386 55.000 0.00 0.00 42.39 4.17
4812 5901 0.667993 GTTTGCTGTAGGCTGTTGCA 59.332 50.000 0.00 1.24 42.39 4.08
4813 5902 1.270550 GTTTGCTGTAGGCTGTTGCAT 59.729 47.619 0.00 0.00 42.39 3.96
4814 5903 1.167851 TTGCTGTAGGCTGTTGCATC 58.832 50.000 0.00 0.00 42.39 3.91
4815 5904 1.020861 TGCTGTAGGCTGTTGCATCG 61.021 55.000 0.00 0.00 42.39 3.84
4816 5905 0.740868 GCTGTAGGCTGTTGCATCGA 60.741 55.000 0.00 0.00 41.91 3.59
4817 5906 1.284657 CTGTAGGCTGTTGCATCGAG 58.715 55.000 0.00 0.00 41.91 4.04
4818 5907 0.608130 TGTAGGCTGTTGCATCGAGT 59.392 50.000 0.00 0.00 41.91 4.18
4819 5908 1.002366 GTAGGCTGTTGCATCGAGTG 58.998 55.000 0.00 0.00 41.91 3.51
4820 5909 0.108186 TAGGCTGTTGCATCGAGTGG 60.108 55.000 0.00 0.00 41.91 4.00
4821 5910 1.672356 GGCTGTTGCATCGAGTGGT 60.672 57.895 0.00 0.00 41.91 4.16
4822 5911 1.639298 GGCTGTTGCATCGAGTGGTC 61.639 60.000 0.00 0.00 41.91 4.02
4823 5912 1.959899 GCTGTTGCATCGAGTGGTCG 61.960 60.000 0.00 0.00 42.55 4.79
4824 5913 1.354337 CTGTTGCATCGAGTGGTCGG 61.354 60.000 0.00 0.00 46.80 4.79
4825 5914 2.434185 TTGCATCGAGTGGTCGGC 60.434 61.111 0.00 0.00 46.80 5.54
4826 5915 2.942796 TTGCATCGAGTGGTCGGCT 61.943 57.895 0.00 0.00 46.80 5.52
4827 5916 2.887568 GCATCGAGTGGTCGGCTG 60.888 66.667 0.00 0.00 46.80 4.85
4828 5917 2.573869 CATCGAGTGGTCGGCTGT 59.426 61.111 0.00 0.00 46.80 4.40
4829 5918 1.807165 CATCGAGTGGTCGGCTGTG 60.807 63.158 0.00 0.00 46.80 3.66
4830 5919 3.649277 ATCGAGTGGTCGGCTGTGC 62.649 63.158 0.00 0.00 46.80 4.57
4831 5920 4.662961 CGAGTGGTCGGCTGTGCA 62.663 66.667 0.00 0.00 42.87 4.57
4832 5921 2.046892 GAGTGGTCGGCTGTGCAT 60.047 61.111 0.00 0.00 0.00 3.96
4833 5922 2.046892 AGTGGTCGGCTGTGCATC 60.047 61.111 0.00 0.00 0.00 3.91
4834 5923 3.490759 GTGGTCGGCTGTGCATCG 61.491 66.667 0.00 0.00 0.00 3.84
4835 5924 4.758251 TGGTCGGCTGTGCATCGG 62.758 66.667 0.00 0.00 0.00 4.18
4898 6079 4.170062 CGGCAGCATCGTGGCAAG 62.170 66.667 0.00 0.00 43.10 4.01
4899 6080 4.487412 GGCAGCATCGTGGCAAGC 62.487 66.667 0.00 6.84 42.50 4.01
4900 6081 3.740397 GCAGCATCGTGGCAAGCA 61.740 61.111 0.00 0.00 37.14 3.91
4901 6082 2.956194 CAGCATCGTGGCAAGCAA 59.044 55.556 0.00 0.00 35.83 3.91
4902 6083 1.154093 CAGCATCGTGGCAAGCAAG 60.154 57.895 0.00 0.00 35.83 4.01
4903 6084 1.302752 AGCATCGTGGCAAGCAAGA 60.303 52.632 0.00 0.00 35.83 3.02
4904 6085 1.154150 GCATCGTGGCAAGCAAGAC 60.154 57.895 0.00 0.00 0.00 3.01
4909 6091 0.512952 CGTGGCAAGCAAGACAGTAC 59.487 55.000 0.00 0.00 0.00 2.73
4921 6104 4.960354 GCAAGACAGTACTACATACGTACG 59.040 45.833 15.01 15.01 41.51 3.67
4922 6105 5.220472 GCAAGACAGTACTACATACGTACGA 60.220 44.000 24.41 6.04 41.51 3.43
4932 6115 3.609853 ACATACGTACGACCTACTCCAA 58.390 45.455 24.41 0.00 0.00 3.53
5005 6189 4.985413 TCGAGCTGCAAAAATGGAATTAG 58.015 39.130 1.02 0.00 33.67 1.73
5055 6239 1.977009 GGAAGGGCCGGAAAACCAG 60.977 63.158 5.05 0.00 0.00 4.00
5056 6240 2.600470 AAGGGCCGGAAAACCAGC 60.600 61.111 5.05 0.00 0.00 4.85
5057 6241 3.444818 AAGGGCCGGAAAACCAGCA 62.445 57.895 5.05 0.00 0.00 4.41
5058 6242 2.915137 GGGCCGGAAAACCAGCAA 60.915 61.111 5.05 0.00 0.00 3.91
5059 6243 2.650778 GGCCGGAAAACCAGCAAG 59.349 61.111 5.05 0.00 0.00 4.01
5060 6244 2.650778 GCCGGAAAACCAGCAAGG 59.349 61.111 5.05 0.00 45.67 3.61
5061 6245 2.931068 GCCGGAAAACCAGCAAGGG 61.931 63.158 5.05 0.00 43.89 3.95
5062 6246 2.650778 CGGAAAACCAGCAAGGGC 59.349 61.111 0.04 0.00 43.89 5.19
5097 6281 2.780693 CTCCCTCCCTCCACTCCA 59.219 66.667 0.00 0.00 0.00 3.86
5101 6285 3.077556 CTCCCTCCACTCCACCCG 61.078 72.222 0.00 0.00 0.00 5.28
5191 6377 2.107546 CACCATACCCCGTACCGC 59.892 66.667 0.00 0.00 0.00 5.68
5211 6397 2.759114 CACCAGTCCACCATGGCT 59.241 61.111 13.04 0.00 40.45 4.75
5385 6583 4.047059 GACGGCGAGGACAACGGA 62.047 66.667 16.62 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 91 5.333645 GCTAAGCCTAACGTGATCATTCATG 60.334 44.000 0.00 0.00 43.33 3.07
135 245 0.179020 TAGGCAACAGCAGCAACACT 60.179 50.000 0.00 0.00 41.41 3.55
143 253 2.161855 CAATTCCACTAGGCAACAGCA 58.838 47.619 0.00 0.00 41.41 4.41
151 261 2.301346 GCATCCCACAATTCCACTAGG 58.699 52.381 0.00 0.00 0.00 3.02
156 266 0.258484 ATCCGCATCCCACAATTCCA 59.742 50.000 0.00 0.00 0.00 3.53
161 271 0.392863 CACTCATCCGCATCCCACAA 60.393 55.000 0.00 0.00 0.00 3.33
166 276 0.176680 ACACTCACTCATCCGCATCC 59.823 55.000 0.00 0.00 0.00 3.51
167 277 1.284657 CACACTCACTCATCCGCATC 58.715 55.000 0.00 0.00 0.00 3.91
240 354 1.827315 TTCAGCCACGAACGCGAAAG 61.827 55.000 15.93 5.40 41.64 2.62
243 357 2.279584 TTTCAGCCACGAACGCGA 60.280 55.556 15.93 0.00 41.64 5.87
271 385 1.809207 CCCAATCAATCACACGCCC 59.191 57.895 0.00 0.00 0.00 6.13
378 496 7.845537 TTAGATCCATGGTATAATCCCCAAT 57.154 36.000 12.58 0.00 33.66 3.16
384 502 6.703607 CGGCAGATTAGATCCATGGTATAATC 59.296 42.308 23.91 23.91 34.51 1.75
519 835 2.439701 CATCTGGCTGCCCCACTG 60.440 66.667 17.53 4.77 39.18 3.66
571 888 2.620112 GGGAGTGGACGACGACGAA 61.620 63.158 15.32 0.00 42.66 3.85
598 915 1.416772 GCTATTTTCGCTAGGGGAGGT 59.583 52.381 6.99 0.00 0.00 3.85
620 938 0.455972 GTCAGTCTGTCAGAGCGCTC 60.456 60.000 30.01 30.01 0.00 5.03
632 950 2.281345 ACGTCGGTCGGTCAGTCT 60.281 61.111 0.00 0.00 44.69 3.24
751 1070 2.342648 GACGGTTCTGCCCTCGTT 59.657 61.111 0.00 0.00 35.91 3.85
870 1190 2.506865 CCTCTCGCGCTTATATACACG 58.493 52.381 5.56 0.28 0.00 4.49
910 1230 3.535962 GAGGAGGAGCGGGCTGAG 61.536 72.222 0.00 0.00 0.00 3.35
931 1252 2.280592 GTGTGTGTGGGGACGGAC 60.281 66.667 0.00 0.00 0.00 4.79
932 1253 2.764547 TGTGTGTGTGGGGACGGA 60.765 61.111 0.00 0.00 0.00 4.69
934 1255 2.964925 CGTGTGTGTGTGGGGACG 60.965 66.667 0.00 0.00 0.00 4.79
935 1256 3.276846 GCGTGTGTGTGTGGGGAC 61.277 66.667 0.00 0.00 0.00 4.46
936 1257 3.787001 TGCGTGTGTGTGTGGGGA 61.787 61.111 0.00 0.00 0.00 4.81
1169 1499 1.371022 CGTCAGATCAGATCGGCGG 60.371 63.158 16.58 4.54 31.11 6.13
1189 1519 1.807573 GCGGAGGACAAAGAGAGCG 60.808 63.158 0.00 0.00 0.00 5.03
1190 1520 0.739112 CTGCGGAGGACAAAGAGAGC 60.739 60.000 0.00 0.00 0.00 4.09
1192 1522 0.832135 ACCTGCGGAGGACAAAGAGA 60.832 55.000 31.46 0.00 42.93 3.10
1197 1528 4.329545 GCCACCTGCGGAGGACAA 62.330 66.667 31.46 0.00 42.93 3.18
1397 1728 4.057428 GCGAGATCGGATCGGGGG 62.057 72.222 12.08 4.68 40.50 5.40
1708 2045 2.102070 AAACAATACCGCATCCGTCA 57.898 45.000 0.00 0.00 0.00 4.35
1712 2049 3.502211 CCCATCTAAACAATACCGCATCC 59.498 47.826 0.00 0.00 0.00 3.51
1730 2067 2.381961 ACCAACTATTCCAACCACCCAT 59.618 45.455 0.00 0.00 0.00 4.00
1785 2122 2.542766 ACAAACAAGCCGCATATTCG 57.457 45.000 0.00 0.00 0.00 3.34
1793 2131 0.100325 TCACAGCAACAAACAAGCCG 59.900 50.000 0.00 0.00 0.00 5.52
1816 2154 4.271049 CCGCAATAGTTGTCTTGGATGTAG 59.729 45.833 0.00 0.00 0.00 2.74
1830 2168 2.283298 CACTCATGAAGCCGCAATAGT 58.717 47.619 0.00 0.00 0.00 2.12
1831 2169 1.600957 CCACTCATGAAGCCGCAATAG 59.399 52.381 0.00 0.00 0.00 1.73
1913 2251 6.367421 TGGAATACAACGATGTTCTTTTTCG 58.633 36.000 2.83 0.00 41.05 3.46
1925 2263 9.321562 GGACTAGAATTTTATGGAATACAACGA 57.678 33.333 0.00 0.00 0.00 3.85
1926 2264 9.104965 TGGACTAGAATTTTATGGAATACAACG 57.895 33.333 0.00 0.00 0.00 4.10
1964 2303 8.015185 TCAATCATCAGTACTTGATCATCAGA 57.985 34.615 9.90 3.72 44.76 3.27
1967 2306 9.491675 AGATTCAATCATCAGTACTTGATCATC 57.508 33.333 9.90 11.08 44.76 2.92
1979 2343 4.153655 CCCGCACATAGATTCAATCATCAG 59.846 45.833 0.00 0.00 0.00 2.90
1999 2364 0.673437 ACATCAAAACAGCAACCCCG 59.327 50.000 0.00 0.00 0.00 5.73
2010 2375 8.106462 TCTTAATCTACCATGGTCACATCAAAA 58.894 33.333 23.76 6.18 34.35 2.44
2015 2380 5.072329 CCCTCTTAATCTACCATGGTCACAT 59.928 44.000 23.76 9.03 37.99 3.21
2214 2626 7.044181 CAGATTTTAGACAGCCTGTGAGAATA 58.956 38.462 0.00 0.00 0.00 1.75
2222 2634 6.183360 CCATGTAACAGATTTTAGACAGCCTG 60.183 42.308 0.00 0.00 0.00 4.85
2380 2794 3.592898 ACAATACTGCATCTGTCGTCA 57.407 42.857 0.00 0.00 0.00 4.35
2383 2797 6.243551 CAACTAAACAATACTGCATCTGTCG 58.756 40.000 0.00 0.00 0.00 4.35
2396 2810 9.541884 ACTATTCCAAATACCCAACTAAACAAT 57.458 29.630 0.00 0.00 0.00 2.71
2425 2839 4.556233 CCTGTCGTCACTATTGTCTCAAA 58.444 43.478 0.00 0.00 0.00 2.69
2427 2841 2.094700 GCCTGTCGTCACTATTGTCTCA 60.095 50.000 0.00 0.00 0.00 3.27
2442 2856 7.201145 TCTATAAACAACTATTCGAGCCTGTC 58.799 38.462 0.00 0.00 0.00 3.51
2443 2857 7.108841 TCTATAAACAACTATTCGAGCCTGT 57.891 36.000 0.00 0.00 0.00 4.00
2444 2858 8.491152 CATTCTATAAACAACTATTCGAGCCTG 58.509 37.037 0.00 0.00 0.00 4.85
2445 2859 8.421784 TCATTCTATAAACAACTATTCGAGCCT 58.578 33.333 0.00 0.00 0.00 4.58
2446 2860 8.589335 TCATTCTATAAACAACTATTCGAGCC 57.411 34.615 0.00 0.00 0.00 4.70
2471 2885 6.323739 ACAAGCCCGATATTTCACCAAATTAT 59.676 34.615 0.00 0.00 33.95 1.28
2473 2887 4.466015 ACAAGCCCGATATTTCACCAAATT 59.534 37.500 0.00 0.00 33.95 1.82
2619 3033 2.890945 CCATTTCCCCTGAACTTTCGTT 59.109 45.455 0.00 0.00 35.68 3.85
2622 3036 5.952347 AGAATACCATTTCCCCTGAACTTTC 59.048 40.000 0.00 0.00 0.00 2.62
2624 3038 5.264395 CAGAATACCATTTCCCCTGAACTT 58.736 41.667 0.00 0.00 0.00 2.66
2642 3056 4.403432 CCAAAGCATAACATGGACCAGAAT 59.597 41.667 0.00 0.00 34.82 2.40
2643 3057 3.763360 CCAAAGCATAACATGGACCAGAA 59.237 43.478 0.00 0.00 34.82 3.02
2644 3058 3.245229 ACCAAAGCATAACATGGACCAGA 60.245 43.478 0.00 0.00 36.75 3.86
2645 3059 3.091545 ACCAAAGCATAACATGGACCAG 58.908 45.455 0.00 0.00 36.75 4.00
2646 3060 2.824936 CACCAAAGCATAACATGGACCA 59.175 45.455 0.00 0.00 36.75 4.02
2647 3061 2.825532 ACACCAAAGCATAACATGGACC 59.174 45.455 0.00 0.00 36.75 4.46
2648 3062 3.505680 TCACACCAAAGCATAACATGGAC 59.494 43.478 0.00 0.00 36.75 4.02
2649 3063 3.505680 GTCACACCAAAGCATAACATGGA 59.494 43.478 0.00 0.00 36.75 3.41
2650 3064 3.367292 GGTCACACCAAAGCATAACATGG 60.367 47.826 0.00 0.00 38.42 3.66
2651 3065 3.836949 GGTCACACCAAAGCATAACATG 58.163 45.455 0.00 0.00 38.42 3.21
2664 3078 4.631813 GTCTCAATCTAACATGGTCACACC 59.368 45.833 0.00 0.00 39.22 4.16
2665 3079 4.327357 CGTCTCAATCTAACATGGTCACAC 59.673 45.833 0.00 0.00 0.00 3.82
2666 3080 4.219725 TCGTCTCAATCTAACATGGTCACA 59.780 41.667 0.00 0.00 0.00 3.58
2667 3081 4.744570 TCGTCTCAATCTAACATGGTCAC 58.255 43.478 0.00 0.00 0.00 3.67
2668 3082 5.598416 ATCGTCTCAATCTAACATGGTCA 57.402 39.130 0.00 0.00 0.00 4.02
2669 3083 7.653713 ACATAATCGTCTCAATCTAACATGGTC 59.346 37.037 0.00 0.00 0.00 4.02
2670 3084 7.500992 ACATAATCGTCTCAATCTAACATGGT 58.499 34.615 0.00 0.00 0.00 3.55
2671 3085 7.953158 ACATAATCGTCTCAATCTAACATGG 57.047 36.000 0.00 0.00 0.00 3.66
2672 3086 8.642885 GCTACATAATCGTCTCAATCTAACATG 58.357 37.037 0.00 0.00 0.00 3.21
2673 3087 8.580720 AGCTACATAATCGTCTCAATCTAACAT 58.419 33.333 0.00 0.00 0.00 2.71
2674 3088 7.941919 AGCTACATAATCGTCTCAATCTAACA 58.058 34.615 0.00 0.00 0.00 2.41
2675 3089 9.894783 TTAGCTACATAATCGTCTCAATCTAAC 57.105 33.333 0.00 0.00 0.00 2.34
2678 3092 9.988815 AAATTAGCTACATAATCGTCTCAATCT 57.011 29.630 0.00 0.00 0.00 2.40
2680 3094 9.764363 TCAAATTAGCTACATAATCGTCTCAAT 57.236 29.630 0.00 0.00 0.00 2.57
2681 3095 9.764363 ATCAAATTAGCTACATAATCGTCTCAA 57.236 29.630 0.00 0.00 0.00 3.02
2682 3096 9.411801 GATCAAATTAGCTACATAATCGTCTCA 57.588 33.333 0.00 0.00 0.00 3.27
2683 3097 9.632807 AGATCAAATTAGCTACATAATCGTCTC 57.367 33.333 0.00 0.00 0.00 3.36
2684 3098 9.988815 AAGATCAAATTAGCTACATAATCGTCT 57.011 29.630 0.00 0.00 0.00 4.18
2686 3100 9.764363 TGAAGATCAAATTAGCTACATAATCGT 57.236 29.630 0.00 0.00 0.00 3.73
2702 3116 9.499479 GGCATAGAATCTAGATTGAAGATCAAA 57.501 33.333 22.61 0.80 40.12 2.69
2703 3117 8.878211 AGGCATAGAATCTAGATTGAAGATCAA 58.122 33.333 22.61 0.00 41.09 2.57
2704 3118 8.312564 CAGGCATAGAATCTAGATTGAAGATCA 58.687 37.037 22.61 0.54 32.48 2.92
2705 3119 8.530311 TCAGGCATAGAATCTAGATTGAAGATC 58.470 37.037 22.61 7.19 32.48 2.75
2706 3120 8.433249 TCAGGCATAGAATCTAGATTGAAGAT 57.567 34.615 22.61 7.31 35.17 2.40
2707 3121 7.846101 TCAGGCATAGAATCTAGATTGAAGA 57.154 36.000 22.61 5.33 0.00 2.87
2708 3122 8.899427 TTTCAGGCATAGAATCTAGATTGAAG 57.101 34.615 22.61 10.33 0.00 3.02
2709 3123 9.857656 AATTTCAGGCATAGAATCTAGATTGAA 57.142 29.630 22.61 14.09 0.00 2.69
2710 3124 9.499479 GAATTTCAGGCATAGAATCTAGATTGA 57.501 33.333 22.61 10.53 0.00 2.57
2711 3125 9.504708 AGAATTTCAGGCATAGAATCTAGATTG 57.495 33.333 22.61 10.02 0.00 2.67
2713 3127 9.504708 CAAGAATTTCAGGCATAGAATCTAGAT 57.495 33.333 0.00 0.00 0.00 1.98
2714 3128 8.489489 ACAAGAATTTCAGGCATAGAATCTAGA 58.511 33.333 0.00 0.00 0.00 2.43
2715 3129 8.674263 ACAAGAATTTCAGGCATAGAATCTAG 57.326 34.615 0.00 0.00 0.00 2.43
2716 3130 7.716998 GGACAAGAATTTCAGGCATAGAATCTA 59.283 37.037 0.00 0.00 0.00 1.98
2717 3131 6.545298 GGACAAGAATTTCAGGCATAGAATCT 59.455 38.462 0.00 0.00 0.00 2.40
2718 3132 6.319658 TGGACAAGAATTTCAGGCATAGAATC 59.680 38.462 0.00 0.00 0.00 2.52
2719 3133 6.189859 TGGACAAGAATTTCAGGCATAGAAT 58.810 36.000 0.00 0.00 0.00 2.40
2720 3134 5.569355 TGGACAAGAATTTCAGGCATAGAA 58.431 37.500 0.00 0.00 0.00 2.10
2721 3135 5.178096 TGGACAAGAATTTCAGGCATAGA 57.822 39.130 0.00 0.00 0.00 1.98
2722 3136 6.095860 TGAATGGACAAGAATTTCAGGCATAG 59.904 38.462 0.00 0.00 0.00 2.23
2723 3137 5.951148 TGAATGGACAAGAATTTCAGGCATA 59.049 36.000 0.00 0.00 0.00 3.14
2724 3138 4.773674 TGAATGGACAAGAATTTCAGGCAT 59.226 37.500 0.00 0.00 0.00 4.40
2725 3139 4.022068 GTGAATGGACAAGAATTTCAGGCA 60.022 41.667 0.00 0.00 0.00 4.75
2726 3140 4.022068 TGTGAATGGACAAGAATTTCAGGC 60.022 41.667 0.00 0.00 0.00 4.85
2727 3141 5.710513 TGTGAATGGACAAGAATTTCAGG 57.289 39.130 0.00 0.00 0.00 3.86
2728 3142 7.149973 ACAATGTGAATGGACAAGAATTTCAG 58.850 34.615 0.00 0.00 0.00 3.02
2729 3143 7.053316 ACAATGTGAATGGACAAGAATTTCA 57.947 32.000 0.00 0.00 0.00 2.69
2730 3144 7.951530 AACAATGTGAATGGACAAGAATTTC 57.048 32.000 0.00 0.00 0.00 2.17
2731 3145 8.206189 AGAAACAATGTGAATGGACAAGAATTT 58.794 29.630 0.00 0.00 0.00 1.82
2732 3146 7.729116 AGAAACAATGTGAATGGACAAGAATT 58.271 30.769 0.00 0.00 0.00 2.17
2733 3147 7.294017 AGAAACAATGTGAATGGACAAGAAT 57.706 32.000 0.00 0.00 0.00 2.40
2768 3182 7.761704 CACCTAGATTGTAGACATATGCATACC 59.238 40.741 8.99 1.57 0.00 2.73
2784 3198 3.679389 ACTGTGGAAAGCACCTAGATTG 58.321 45.455 0.00 0.00 0.00 2.67
2792 3206 6.426937 TCAAAGTAGATAACTGTGGAAAGCAC 59.573 38.462 0.00 0.00 42.90 4.40
2799 3213 8.783093 TGATGTTTTCAAAGTAGATAACTGTGG 58.217 33.333 0.00 0.00 42.90 4.17
2851 3280 8.833231 ATGAAGATAAACGGTGACCTAATATG 57.167 34.615 0.00 0.00 0.00 1.78
3207 3884 2.599659 TGATATAGAAGATGCTGCGCG 58.400 47.619 0.00 0.00 0.00 6.86
3209 3886 4.746611 TGTGTTGATATAGAAGATGCTGCG 59.253 41.667 0.00 0.00 0.00 5.18
3350 4038 7.872993 TCCTCTTGTCAAACTAACAGTTGATAG 59.127 37.037 0.00 0.00 38.66 2.08
3367 4083 6.899114 ACGAATTTAATTGTGTCCTCTTGTC 58.101 36.000 0.00 0.00 0.00 3.18
3435 4309 8.203681 AGGTACACCTAAACTAAGAGAAATGT 57.796 34.615 0.00 0.00 46.48 2.71
3462 4344 7.881232 ACCGAGACATAAAACTTAAGAATTCCA 59.119 33.333 10.09 0.00 0.00 3.53
3524 4406 5.185828 TGACTATAGAAGCAGAGCAAAGACA 59.814 40.000 6.78 0.00 0.00 3.41
3525 4407 5.655488 TGACTATAGAAGCAGAGCAAAGAC 58.345 41.667 6.78 0.00 0.00 3.01
3527 4409 5.049167 CCTGACTATAGAAGCAGAGCAAAG 58.951 45.833 6.78 0.00 33.64 2.77
3560 4442 7.925483 AGCATAAAACAAACAGACAAGCATAAA 59.075 29.630 0.00 0.00 0.00 1.40
3584 4466 3.081061 TCCACACACCATAAATCACAGC 58.919 45.455 0.00 0.00 0.00 4.40
3797 4688 2.662791 CGTGAGCACAACCTTTCAATCG 60.663 50.000 1.20 0.00 0.00 3.34
3815 4706 3.811722 TCAGACAATTAAAGCTGCGTG 57.188 42.857 0.00 0.00 0.00 5.34
4022 4922 5.226194 AGCTCACTGTCAAGAGAAGAAAT 57.774 39.130 6.22 0.00 33.74 2.17
4159 5059 4.038763 TGTGAGAACCCATAATAGGCTACG 59.961 45.833 0.00 0.00 0.00 3.51
4197 5097 6.596106 TCACACACATTACATTGGTATGGTAC 59.404 38.462 5.58 0.00 36.01 3.34
4212 5115 2.355513 GGCCTCTCAGATCACACACATT 60.356 50.000 0.00 0.00 0.00 2.71
4388 5291 1.417890 AGGCATGGATTTACTCTCCCG 59.582 52.381 0.00 0.00 31.32 5.14
4391 5294 8.317679 ACAATAGATAGGCATGGATTTACTCTC 58.682 37.037 0.00 0.00 0.00 3.20
4406 5309 7.645340 CGCCAAATCTGAAAAACAATAGATAGG 59.355 37.037 0.00 0.00 32.50 2.57
4407 5310 8.397906 TCGCCAAATCTGAAAAACAATAGATAG 58.602 33.333 0.00 0.00 30.19 2.08
4409 5312 7.156876 TCGCCAAATCTGAAAAACAATAGAT 57.843 32.000 0.00 0.00 0.00 1.98
4412 5315 5.708948 CCTCGCCAAATCTGAAAAACAATA 58.291 37.500 0.00 0.00 0.00 1.90
4530 5442 1.588824 AACACATGACATGGCCGCAG 61.589 55.000 19.39 4.91 33.60 5.18
4531 5443 1.177895 AAACACATGACATGGCCGCA 61.178 50.000 19.39 0.00 33.60 5.69
4532 5444 0.733566 CAAACACATGACATGGCCGC 60.734 55.000 19.39 0.00 33.60 6.53
4533 5445 0.597568 ACAAACACATGACATGGCCG 59.402 50.000 19.39 9.78 33.60 6.13
4534 5446 1.888512 AGACAAACACATGACATGGCC 59.111 47.619 19.39 0.00 33.60 5.36
4535 5447 2.352030 CCAGACAAACACATGACATGGC 60.352 50.000 19.39 0.00 33.60 4.40
4536 5448 3.058016 GTCCAGACAAACACATGACATGG 60.058 47.826 19.39 10.68 33.60 3.66
4537 5449 3.817084 AGTCCAGACAAACACATGACATG 59.183 43.478 14.02 14.02 0.00 3.21
4538 5450 4.090761 AGTCCAGACAAACACATGACAT 57.909 40.909 0.00 0.00 0.00 3.06
4539 5451 3.558931 AGTCCAGACAAACACATGACA 57.441 42.857 0.00 0.00 0.00 3.58
4574 5511 2.033448 GCAACACCCCATCGACCA 59.967 61.111 0.00 0.00 0.00 4.02
4619 5556 2.086869 CAAGAACGCCCATCACAAGAT 58.913 47.619 0.00 0.00 33.87 2.40
4635 5572 5.302059 ACACTTAGCAGTTCAGACTACAAGA 59.698 40.000 0.00 0.00 33.90 3.02
4644 5581 7.063544 GGAACTACATAACACTTAGCAGTTCAG 59.936 40.741 11.82 0.00 41.39 3.02
4725 5662 0.773644 ACACAGAGAGGGCCAAATGT 59.226 50.000 6.18 1.63 0.00 2.71
4735 5672 4.576463 AGCTGGTAAAACAAACACAGAGAG 59.424 41.667 0.00 0.00 0.00 3.20
4740 5686 4.673061 CGACAAGCTGGTAAAACAAACACA 60.673 41.667 0.00 0.00 0.00 3.72
4766 5712 7.561021 TGATACAAAACTAGCTGACAAACAA 57.439 32.000 0.00 0.00 0.00 2.83
4769 5715 6.649141 ACGATGATACAAAACTAGCTGACAAA 59.351 34.615 0.00 0.00 0.00 2.83
4770 5716 6.163476 ACGATGATACAAAACTAGCTGACAA 58.837 36.000 0.00 0.00 0.00 3.18
4775 5721 5.643777 AGCAAACGATGATACAAAACTAGCT 59.356 36.000 0.00 0.00 0.00 3.32
4802 5891 1.376424 CCACTCGATGCAACAGCCT 60.376 57.895 0.00 0.00 0.00 4.58
4810 5899 2.887568 CAGCCGACCACTCGATGC 60.888 66.667 0.00 0.00 43.06 3.91
4811 5900 1.807165 CACAGCCGACCACTCGATG 60.807 63.158 0.00 0.00 43.06 3.84
4812 5901 2.573869 CACAGCCGACCACTCGAT 59.426 61.111 0.00 0.00 43.06 3.59
4813 5902 4.357947 GCACAGCCGACCACTCGA 62.358 66.667 0.00 0.00 43.06 4.04
4814 5903 3.939837 ATGCACAGCCGACCACTCG 62.940 63.158 0.00 0.00 39.83 4.18
4815 5904 2.046892 ATGCACAGCCGACCACTC 60.047 61.111 0.00 0.00 0.00 3.51
4816 5905 2.046892 GATGCACAGCCGACCACT 60.047 61.111 0.00 0.00 0.00 4.00
4817 5906 3.490759 CGATGCACAGCCGACCAC 61.491 66.667 0.00 0.00 0.00 4.16
4818 5907 4.758251 CCGATGCACAGCCGACCA 62.758 66.667 0.00 0.00 0.00 4.02
4836 5925 1.731700 CATCAAATGCTGGCTCCGG 59.268 57.895 0.00 0.00 0.00 5.14
4843 5932 7.822303 ACAGATGTGTTCGCATCAAATGCTG 62.822 44.000 22.54 15.11 43.98 4.41
4844 5933 5.871477 ACAGATGTGTTCGCATCAAATGCT 61.871 41.667 22.54 4.14 43.98 3.79
4859 5948 1.497278 CACGGCCGAAACAGATGTG 59.503 57.895 35.90 12.72 0.00 3.21
4861 5950 1.647545 ATGCACGGCCGAAACAGATG 61.648 55.000 35.90 19.16 0.00 2.90
4862 6043 1.369091 GATGCACGGCCGAAACAGAT 61.369 55.000 35.90 14.06 0.00 2.90
4883 6064 3.271706 TTGCTTGCCACGATGCTGC 62.272 57.895 0.00 0.00 34.01 5.25
4884 6065 1.154093 CTTGCTTGCCACGATGCTG 60.154 57.895 0.00 0.00 0.00 4.41
4885 6066 1.302752 TCTTGCTTGCCACGATGCT 60.303 52.632 0.00 0.00 0.00 3.79
4886 6067 1.154150 GTCTTGCTTGCCACGATGC 60.154 57.895 0.00 0.00 0.00 3.91
4887 6068 0.167470 CTGTCTTGCTTGCCACGATG 59.833 55.000 0.00 0.00 0.00 3.84
4888 6069 0.250467 ACTGTCTTGCTTGCCACGAT 60.250 50.000 0.00 0.00 0.00 3.73
4889 6070 0.391228 TACTGTCTTGCTTGCCACGA 59.609 50.000 0.00 0.00 0.00 4.35
4891 6072 1.884235 AGTACTGTCTTGCTTGCCAC 58.116 50.000 0.00 0.00 0.00 5.01
4892 6073 2.367241 TGTAGTACTGTCTTGCTTGCCA 59.633 45.455 5.39 0.00 0.00 4.92
4898 6079 4.960354 CGTACGTATGTAGTACTGTCTTGC 59.040 45.833 7.22 0.53 41.51 4.01
4899 6080 6.181255 GTCGTACGTATGTAGTACTGTCTTG 58.819 44.000 16.05 0.00 41.51 3.02
4900 6081 5.292101 GGTCGTACGTATGTAGTACTGTCTT 59.708 44.000 16.05 0.08 41.51 3.01
4901 6082 4.806247 GGTCGTACGTATGTAGTACTGTCT 59.194 45.833 16.05 0.00 41.51 3.41
4902 6083 4.806247 AGGTCGTACGTATGTAGTACTGTC 59.194 45.833 16.05 0.00 41.51 3.51
4903 6084 4.759782 AGGTCGTACGTATGTAGTACTGT 58.240 43.478 16.05 0.00 41.51 3.55
4904 6085 5.980116 AGTAGGTCGTACGTATGTAGTACTG 59.020 44.000 16.05 0.00 41.51 2.74
4909 6091 4.371786 TGGAGTAGGTCGTACGTATGTAG 58.628 47.826 16.05 0.00 36.66 2.74
5014 6198 4.450053 CATTGGTTGGTGTTTGGTGATTT 58.550 39.130 0.00 0.00 0.00 2.17
5072 6256 3.767044 GAGGGAGGGAGGGAGAGCC 62.767 73.684 0.00 0.00 0.00 4.70
5073 6257 2.123033 GAGGGAGGGAGGGAGAGC 60.123 72.222 0.00 0.00 0.00 4.09
5074 6258 2.328589 TGGAGGGAGGGAGGGAGAG 61.329 68.421 0.00 0.00 0.00 3.20
5075 6259 2.204624 TGGAGGGAGGGAGGGAGA 60.205 66.667 0.00 0.00 0.00 3.71
5076 6260 2.041405 GTGGAGGGAGGGAGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
5077 6261 2.540910 AGTGGAGGGAGGGAGGGA 60.541 66.667 0.00 0.00 0.00 4.20
5078 6262 2.041405 GAGTGGAGGGAGGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
5079 6263 2.041405 GGAGTGGAGGGAGGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
5097 6281 3.339253 AAACTTATAAACGAGGCGGGT 57.661 42.857 0.00 0.00 0.00 5.28
5101 6285 6.025896 GGCTTGTTAAACTTATAAACGAGGC 58.974 40.000 11.10 11.10 46.47 4.70
5191 6377 1.303561 CCATGGTGGACTGGTGGTG 60.304 63.158 2.57 0.00 40.96 4.17
5367 6562 4.351938 CCGTTGTCCTCGCCGTCA 62.352 66.667 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.