Multiple sequence alignment - TraesCS2B01G512900

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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 TraesCS2B01G512900 chr2B 100.000 6338 0 0 1 6338 708203595 708197258 0.000000e+00 11705.0
1 TraesCS2B01G512900 chr2B 84.466 1339 196 10 982 2312 756314280 756312946 0.000000e+00 1310.0
2 TraesCS2B01G512900 chr2B 84.466 1339 196 10 982 2312 756329115 756327781 0.000000e+00 1310.0
3 TraesCS2B01G512900 chr2B 84.042 1341 198 12 982 2312 756343417 756342083 0.000000e+00 1277.0
4 TraesCS2B01G512900 chr2B 80.213 1223 229 13 1095 2312 708211300 708210086 0.000000e+00 905.0
5 TraesCS2B01G512900 chr2B 86.957 483 45 8 4981 5457 708191419 708190949 1.570000e-145 527.0
6 TraesCS2B01G512900 chr2B 82.471 348 32 12 5278 5603 708187873 708188213 1.740000e-70 278.0
7 TraesCS2B01G512900 chr2B 82.471 348 32 12 5278 5603 708190164 708190504 1.740000e-70 278.0
8 TraesCS2B01G512900 chr2B 84.615 247 33 5 5038 5280 708207840 708207595 2.280000e-59 241.0
9 TraesCS2B01G512900 chr2B 87.209 172 21 1 5151 5321 708188505 708188334 1.800000e-45 195.0
10 TraesCS2B01G512900 chr2B 79.263 217 32 12 5620 5829 553655788 553655998 8.570000e-29 139.0
11 TraesCS2B01G512900 chr2D 91.744 2786 155 42 274 3019 586784944 586782194 0.000000e+00 3801.0
12 TraesCS2B01G512900 chr2D 95.171 1781 65 4 3091 4852 586779729 586777951 0.000000e+00 2793.0
13 TraesCS2B01G512900 chr2D 84.722 1224 174 9 1095 2312 618883832 618885048 0.000000e+00 1212.0
14 TraesCS2B01G512900 chr2D 91.532 496 33 5 4963 5457 586777888 586777401 0.000000e+00 675.0
15 TraesCS2B01G512900 chr2D 73.295 1393 287 63 3948 5322 618878299 618879624 3.510000e-117 433.0
16 TraesCS2B01G512900 chr2D 92.169 166 6 1 1 159 586785294 586785129 1.780000e-55 228.0
17 TraesCS2B01G512900 chr2D 93.333 120 4 3 160 276 586785089 586784971 2.350000e-39 174.0
18 TraesCS2B01G512900 chr2A 93.048 2546 128 31 274 2788 721569811 721567284 0.000000e+00 3675.0
19 TraesCS2B01G512900 chr2A 89.104 2533 150 53 3090 5574 721564643 721562189 0.000000e+00 3033.0
20 TraesCS2B01G512900 chr2A 74.522 1570 304 73 3749 5280 721589717 721588206 4.230000e-166 595.0
21 TraesCS2B01G512900 chr2A 81.071 280 26 16 21 276 721570114 721569838 1.390000e-46 198.0
22 TraesCS2B01G512900 chr5D 86.111 432 33 7 5619 6050 563205670 563205266 2.100000e-119 440.0
23 TraesCS2B01G512900 chr5D 92.248 258 13 6 6085 6338 563204983 563204729 6.040000e-95 359.0
24 TraesCS2B01G512900 chr6A 79.350 615 77 25 5665 6267 611409959 611409383 2.770000e-103 387.0
25 TraesCS2B01G512900 chrUn 82.471 348 32 12 5278 5603 333087541 333087201 1.740000e-70 278.0
26 TraesCS2B01G512900 chrUn 82.566 304 21 16 5323 5603 333086689 333086983 8.210000e-59 239.0
27 TraesCS2B01G512900 chrUn 87.209 172 21 1 5151 5321 333089200 333089371 1.800000e-45 195.0
28 TraesCS2B01G512900 chr5B 86.740 181 16 8 5983 6161 688973958 688973784 1.800000e-45 195.0
29 TraesCS2B01G512900 chr3D 81.106 217 31 8 5620 5829 569567572 569567785 1.410000e-36 165.0
30 TraesCS2B01G512900 chr4B 81.106 217 30 10 5620 5829 364038140 364038352 5.080000e-36 163.0
31 TraesCS2B01G512900 chr4D 82.065 184 29 4 5650 5829 483465370 483465553 3.060000e-33 154.0
32 TraesCS2B01G512900 chr7B 80.275 218 30 12 5620 5829 4799788 4800000 1.100000e-32 152.0
33 TraesCS2B01G512900 chr7B 78.636 220 35 9 5618 5829 623936806 623936591 1.110000e-27 135.0
34 TraesCS2B01G512900 chr5A 79.870 154 26 5 5679 5828 585636760 585636912 2.420000e-19 108.0
35 TraesCS2B01G512900 chr6D 89.062 64 6 1 5673 5735 464009784 464009721 1.890000e-10 78.7


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 TraesCS2B01G512900 chr2B 708197258 708203595 6337 True 11705.0 11705 100.0000 1 6338 1 chr2B.!!$R1 6337
1 TraesCS2B01G512900 chr2B 756312946 756314280 1334 True 1310.0 1310 84.4660 982 2312 1 chr2B.!!$R2 1330
2 TraesCS2B01G512900 chr2B 756327781 756329115 1334 True 1310.0 1310 84.4660 982 2312 1 chr2B.!!$R3 1330
3 TraesCS2B01G512900 chr2B 756342083 756343417 1334 True 1277.0 1277 84.0420 982 2312 1 chr2B.!!$R4 1330
4 TraesCS2B01G512900 chr2B 708207595 708211300 3705 True 573.0 905 82.4140 1095 5280 2 chr2B.!!$R6 4185
5 TraesCS2B01G512900 chr2B 708188334 708191419 3085 True 361.0 527 87.0830 4981 5457 2 chr2B.!!$R5 476
6 TraesCS2B01G512900 chr2B 708187873 708190504 2631 False 278.0 278 82.4710 5278 5603 2 chr2B.!!$F2 325
7 TraesCS2B01G512900 chr2D 586777401 586785294 7893 True 1534.2 3801 92.7898 1 5457 5 chr2D.!!$R1 5456
8 TraesCS2B01G512900 chr2D 618883832 618885048 1216 False 1212.0 1212 84.7220 1095 2312 1 chr2D.!!$F2 1217
9 TraesCS2B01G512900 chr2D 618878299 618879624 1325 False 433.0 433 73.2950 3948 5322 1 chr2D.!!$F1 1374
10 TraesCS2B01G512900 chr2A 721562189 721570114 7925 True 2302.0 3675 87.7410 21 5574 3 chr2A.!!$R2 5553
11 TraesCS2B01G512900 chr2A 721588206 721589717 1511 True 595.0 595 74.5220 3749 5280 1 chr2A.!!$R1 1531
12 TraesCS2B01G512900 chr5D 563204729 563205670 941 True 399.5 440 89.1795 5619 6338 2 chr5D.!!$R1 719
13 TraesCS2B01G512900 chr6A 611409383 611409959 576 True 387.0 387 79.3500 5665 6267 1 chr6A.!!$R1 602
14 TraesCS2B01G512900 chrUn 333086689 333089371 2682 False 217.0 239 84.8875 5151 5603 2 chrUn.!!$F1 452

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
307 389 0.478942 TCCATCTAGGGAGGAGACCG 59.521 60.0 0.00 0.00 38.24 4.79 F
345 427 1.079503 CCTCCGACTTTGCTTGTAGC 58.920 55.0 0.00 0.00 42.82 3.58 F
563 646 1.662517 TCAGTGCTGACGCTCAAAAA 58.337 45.0 0.00 0.00 33.21 1.94 F
2447 2547 0.238553 GCAGTCTTTGGCTCGGTTTC 59.761 55.0 0.00 0.00 0.00 2.78 F
3204 5764 0.623617 AATGGTACTCCCTCCACCCC 60.624 60.0 0.00 0.00 36.50 4.95 F
4802 7414 0.309302 CGTCCTGCTGGAGATACTCG 59.691 60.0 13.36 8.06 44.16 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1320 1412 0.109342 CCTGGCCGGAGCTATCAATT 59.891 55.0 15.09 0.00 39.73 2.32 R
1815 1907 0.613572 TGCTCGTGTCCCATACCAGA 60.614 55.0 0.00 0.00 0.00 3.86 R
2518 2620 0.107165 CCCCTAAGTTAGCAGCACCC 60.107 60.0 4.22 0.00 0.00 4.61 R
3384 5944 0.662970 TTGCTTCGGCGAAAATGTGC 60.663 50.0 23.81 21.56 45.37 4.57 R
5120 7976 0.036388 TAGCACCGAAAAGGCCTCAG 60.036 55.0 5.23 0.00 46.52 3.35 R
5734 11367 0.032267 GAGATAAGGGGCGGTCTTCG 59.968 60.0 0.00 0.00 42.76 3.79 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
98 109 6.700960 TGAAGCATTATTGGTTTGAACTGTTG 59.299 34.615 0.00 0.00 43.35 3.33
120 131 8.304596 TGTTGAAAGAACACTATCTATTCGAGT 58.695 33.333 0.00 0.00 0.00 4.18
149 160 4.819761 TCTGTCGATGCCAGCGCC 62.820 66.667 2.29 0.00 0.00 6.53
307 389 0.478942 TCCATCTAGGGAGGAGACCG 59.521 60.000 0.00 0.00 38.24 4.79
345 427 1.079503 CCTCCGACTTTGCTTGTAGC 58.920 55.000 0.00 0.00 42.82 3.58
371 453 7.106890 TGGTGTACCGATATTTTCATCTGAAA 58.893 34.615 1.28 1.28 39.43 2.69
409 491 2.393764 CAAACGGAATCAGTTGTTGCC 58.606 47.619 0.00 0.00 31.43 4.52
449 531 5.215160 GTTGATCAAACAGAACACCATGTC 58.785 41.667 10.35 0.00 38.75 3.06
547 630 6.096036 ACGAATGTACTGAAGAATCTGTCAG 58.904 40.000 15.74 15.74 45.59 3.51
553 636 3.922910 CTGAAGAATCTGTCAGTGCTGA 58.077 45.455 11.62 0.00 37.16 4.26
563 646 1.662517 TCAGTGCTGACGCTCAAAAA 58.337 45.000 0.00 0.00 33.21 1.94
698 789 5.261216 ACAAGTTCCTTGAAGTTTCTTCCA 58.739 37.500 10.73 0.00 43.42 3.53
700 791 3.885901 AGTTCCTTGAAGTTTCTTCCAGC 59.114 43.478 6.98 0.00 0.00 4.85
966 1057 5.695363 GCTACCTTGTTCGAGTAGTCTTTTT 59.305 40.000 9.67 0.00 36.64 1.94
1091 1183 2.185350 CTCTGCCGCGAATCCTGT 59.815 61.111 8.23 0.00 0.00 4.00
1320 1412 2.105134 TGACACGGGAAGCCTTCTTTTA 59.895 45.455 4.15 0.00 31.48 1.52
2258 2353 2.765807 CCTCATGGACCTCCGGCT 60.766 66.667 0.00 0.00 39.43 5.52
2291 2386 3.549794 GGCAAAGCCTGTATCTGAGATT 58.450 45.455 0.00 0.00 46.69 2.40
2312 2407 8.090788 AGATTAGCCAAGACAGAATTAGGTAA 57.909 34.615 0.00 0.00 0.00 2.85
2313 2408 7.988028 AGATTAGCCAAGACAGAATTAGGTAAC 59.012 37.037 0.00 0.00 0.00 2.50
2369 2466 5.965922 ACCTTTAAGACAATTAGCAATGCC 58.034 37.500 0.00 0.00 0.00 4.40
2384 2481 5.315348 AGCAATGCCATTTATTTGGTTTGT 58.685 33.333 0.00 0.00 39.11 2.83
2386 2483 5.857517 GCAATGCCATTTATTTGGTTTGTTG 59.142 36.000 0.00 0.00 39.11 3.33
2389 2486 3.190327 GCCATTTATTTGGTTTGTTGCCC 59.810 43.478 0.00 0.00 39.11 5.36
2390 2487 4.650734 CCATTTATTTGGTTTGTTGCCCT 58.349 39.130 0.00 0.00 31.74 5.19
2392 2489 6.234177 CCATTTATTTGGTTTGTTGCCCTTA 58.766 36.000 0.00 0.00 31.74 2.69
2393 2490 6.148645 CCATTTATTTGGTTTGTTGCCCTTAC 59.851 38.462 0.00 0.00 31.74 2.34
2398 2498 4.130286 TGGTTTGTTGCCCTTACAAAAG 57.870 40.909 0.00 0.00 44.42 2.27
2402 2502 2.111384 TGTTGCCCTTACAAAAGCCAA 58.889 42.857 0.00 0.00 0.00 4.52
2404 2504 1.044611 TGCCCTTACAAAAGCCAACC 58.955 50.000 0.00 0.00 0.00 3.77
2408 2508 2.632512 CCCTTACAAAAGCCAACCATGT 59.367 45.455 0.00 0.00 0.00 3.21
2410 2510 4.082245 CCCTTACAAAAGCCAACCATGTAG 60.082 45.833 0.00 0.00 0.00 2.74
2414 2514 3.004315 ACAAAAGCCAACCATGTAGTTCG 59.996 43.478 0.00 0.00 0.00 3.95
2429 2529 1.609072 AGTTCGCTTCCTCAAAAAGGC 59.391 47.619 0.00 0.00 45.78 4.35
2430 2530 1.336755 GTTCGCTTCCTCAAAAAGGCA 59.663 47.619 0.00 0.00 45.78 4.75
2433 2533 1.068954 CGCTTCCTCAAAAAGGCAGTC 60.069 52.381 0.00 0.00 45.78 3.51
2434 2534 2.234143 GCTTCCTCAAAAAGGCAGTCT 58.766 47.619 0.00 0.00 45.78 3.24
2437 2537 4.614946 CTTCCTCAAAAAGGCAGTCTTTG 58.385 43.478 0.00 0.00 44.30 2.77
2438 2538 2.958355 TCCTCAAAAAGGCAGTCTTTGG 59.042 45.455 0.00 0.00 44.30 3.28
2447 2547 0.238553 GCAGTCTTTGGCTCGGTTTC 59.761 55.000 0.00 0.00 0.00 2.78
2448 2548 1.884235 CAGTCTTTGGCTCGGTTTCT 58.116 50.000 0.00 0.00 0.00 2.52
2449 2549 1.801178 CAGTCTTTGGCTCGGTTTCTC 59.199 52.381 0.00 0.00 0.00 2.87
2475 2577 5.746307 AAAGTTGTCTCGTTTACCTTTCC 57.254 39.130 0.00 0.00 0.00 3.13
2481 2583 3.803778 GTCTCGTTTACCTTTCCGTTCAA 59.196 43.478 0.00 0.00 0.00 2.69
2492 2594 5.758924 CCTTTCCGTTCAAGGTTTAGAAAG 58.241 41.667 0.00 0.00 38.81 2.62
2516 2618 8.785329 AGTCCACTCTCTTTCAAATAAGATTC 57.215 34.615 0.00 0.00 33.89 2.52
2518 2620 6.818644 TCCACTCTCTTTCAAATAAGATTCCG 59.181 38.462 0.00 0.00 33.89 4.30
2551 2653 0.905357 TAGGGGTGCTCTTGAGAAGC 59.095 55.000 1.30 0.28 0.00 3.86
2557 2659 2.627515 TGCTCTTGAGAAGCACAAGT 57.372 45.000 1.30 0.00 43.30 3.16
2558 2660 2.216046 TGCTCTTGAGAAGCACAAGTG 58.784 47.619 1.30 0.00 43.30 3.16
2573 2675 2.294233 ACAAGTGCACAACATGGATGTC 59.706 45.455 21.04 0.00 40.80 3.06
2582 2684 3.012518 CAACATGGATGTCACCTCCTTC 58.987 50.000 0.33 0.00 40.80 3.46
2588 2690 0.898320 ATGTCACCTCCTTCCTCACG 59.102 55.000 0.00 0.00 0.00 4.35
2590 2692 1.202964 TGTCACCTCCTTCCTCACGTA 60.203 52.381 0.00 0.00 0.00 3.57
2615 2717 3.181329 TCTCCACCCATCTAGCTTTGAA 58.819 45.455 0.00 0.00 0.00 2.69
2617 2719 4.228210 TCTCCACCCATCTAGCTTTGAAAT 59.772 41.667 0.00 0.00 0.00 2.17
2622 2724 4.952335 ACCCATCTAGCTTTGAAATTGGAG 59.048 41.667 0.00 0.00 0.00 3.86
2707 2826 3.576982 TGTGTACTGTAGCAACTAAGGCT 59.423 43.478 0.00 0.00 45.18 4.58
2728 2847 8.273780 AGGCTGTCAATTCTAAAGATGTTAAG 57.726 34.615 0.00 0.00 0.00 1.85
2739 2858 2.498167 AGATGTTAAGCATGGATCGGC 58.502 47.619 0.00 0.00 38.06 5.54
2763 2882 5.220265 CGGTAATTTTGAACTTGCATGATGC 60.220 40.000 11.12 11.12 45.29 3.91
2765 2884 5.856126 AATTTTGAACTTGCATGATGCTG 57.144 34.783 19.19 13.35 45.31 4.41
2773 2892 5.648178 ACTTGCATGATGCTGTTTTCATA 57.352 34.783 19.19 0.00 45.31 2.15
2799 2923 2.380081 GACCTAATGGGCGTTGACG 58.620 57.895 0.00 0.00 39.10 4.35
2804 2928 2.073816 CTAATGGGCGTTGACGAGTTT 58.926 47.619 7.85 0.00 43.02 2.66
2819 2943 3.047280 TTTGCTAGTGGCGTGCGG 61.047 61.111 0.00 0.00 45.43 5.69
2895 3020 2.092429 TGTGCCTGGTTGTTTCTTCTCT 60.092 45.455 0.00 0.00 0.00 3.10
2925 3051 2.224066 CCATACGGGCTAGTTCCTTCTG 60.224 54.545 0.00 0.00 0.00 3.02
2993 3119 5.652744 CCGTATAGGAAATGAGGAAAACG 57.347 43.478 0.00 0.00 45.00 3.60
3007 3133 2.031683 GGAAAACGACAGGTTCAGTGTG 59.968 50.000 0.00 0.00 38.08 3.82
3016 3142 5.227569 ACAGGTTCAGTGTGAATCATACA 57.772 39.130 12.50 0.00 39.87 2.29
3019 3145 4.697352 AGGTTCAGTGTGAATCATACAAGC 59.303 41.667 12.50 8.24 39.87 4.01
3023 3149 5.178061 TCAGTGTGAATCATACAAGCGAAT 58.822 37.500 12.50 0.00 0.00 3.34
3025 3151 6.986231 TCAGTGTGAATCATACAAGCGAATAT 59.014 34.615 12.50 0.00 0.00 1.28
3026 3152 8.141268 TCAGTGTGAATCATACAAGCGAATATA 58.859 33.333 12.50 0.00 0.00 0.86
3028 3154 9.325198 AGTGTGAATCATACAAGCGAATATAAA 57.675 29.630 12.50 0.00 0.00 1.40
3029 3155 9.370126 GTGTGAATCATACAAGCGAATATAAAC 57.630 33.333 5.23 0.00 0.00 2.01
3030 3156 9.103861 TGTGAATCATACAAGCGAATATAAACA 57.896 29.630 0.00 0.00 0.00 2.83
3031 3157 9.929722 GTGAATCATACAAGCGAATATAAACAA 57.070 29.630 0.00 0.00 0.00 2.83
3051 3177 5.253330 ACAAGGTATATTTGAGGTGTGTGG 58.747 41.667 6.87 0.00 0.00 4.17
3053 3179 5.772393 AGGTATATTTGAGGTGTGTGGAA 57.228 39.130 0.00 0.00 0.00 3.53
3054 3180 5.497474 AGGTATATTTGAGGTGTGTGGAAC 58.503 41.667 0.00 0.00 37.35 3.62
3073 3199 9.337396 TGTGGAACATATATAAACCTGAACATC 57.663 33.333 0.00 0.00 45.67 3.06
3074 3200 9.337396 GTGGAACATATATAAACCTGAACATCA 57.663 33.333 0.00 0.00 44.52 3.07
3075 3201 9.337396 TGGAACATATATAAACCTGAACATCAC 57.663 33.333 0.00 0.00 0.00 3.06
3078 3204 9.679661 AACATATATAAACCTGAACATCACACA 57.320 29.630 0.00 0.00 0.00 3.72
3079 3205 9.679661 ACATATATAAACCTGAACATCACACAA 57.320 29.630 0.00 0.00 0.00 3.33
3081 3207 9.905713 ATATATAAACCTGAACATCACACAAGT 57.094 29.630 0.00 0.00 0.00 3.16
3083 3209 7.672983 ATAAACCTGAACATCACACAAGTAG 57.327 36.000 0.00 0.00 0.00 2.57
3084 3210 4.689612 ACCTGAACATCACACAAGTAGT 57.310 40.909 0.00 0.00 0.00 2.73
3085 3211 5.801531 ACCTGAACATCACACAAGTAGTA 57.198 39.130 0.00 0.00 0.00 1.82
3087 3213 6.166279 ACCTGAACATCACACAAGTAGTATG 58.834 40.000 0.00 0.00 0.00 2.39
3089 3215 6.533012 CCTGAACATCACACAAGTAGTATGAG 59.467 42.308 0.00 0.00 0.00 2.90
3175 5735 7.095695 ACAGAAGCAGTTAAAAGCAAGTAAA 57.904 32.000 3.57 0.00 0.00 2.01
3176 5736 6.972901 ACAGAAGCAGTTAAAAGCAAGTAAAC 59.027 34.615 3.57 0.00 0.00 2.01
3201 5761 4.086706 CCATAAATGGTACTCCCTCCAC 57.913 50.000 0.49 0.00 43.05 4.02
3204 5764 0.623617 AATGGTACTCCCTCCACCCC 60.624 60.000 0.00 0.00 36.50 4.95
3209 5769 2.228841 TACTCCCTCCACCCCGGTAC 62.229 65.000 0.00 0.00 35.57 3.34
3239 5799 4.492570 CGAGGTTCAAGTTTCGTATCATGC 60.493 45.833 0.00 0.00 0.00 4.06
3255 5815 0.762842 ATGCCCCATACCGCACTAGA 60.763 55.000 0.00 0.00 37.93 2.43
3297 5857 4.803098 ACTGACACATACCTCCACTAAC 57.197 45.455 0.00 0.00 0.00 2.34
3384 5944 4.154737 ACCTACATGCGCAATATAATGCAG 59.845 41.667 17.11 6.95 46.76 4.41
3404 5964 1.052287 CACATTTTCGCCGAAGCAAC 58.948 50.000 0.00 0.00 39.83 4.17
3428 5988 1.599542 GCAGAACTGTCACAGGTGAAC 59.400 52.381 10.28 0.00 41.85 3.18
3489 6049 0.328258 GTAACAGTGCCCCTGGTCAT 59.672 55.000 5.58 0.00 46.06 3.06
3591 6173 9.988815 AATCTCAACTATATAGACACATTGGTC 57.011 33.333 16.79 0.00 38.08 4.02
3665 6248 3.916989 AGTAGACAATCCTCCAAGGGTTT 59.083 43.478 0.00 0.00 34.28 3.27
3677 6260 4.479158 TCCAAGGGTTTTAGACAATGCTT 58.521 39.130 0.00 0.00 0.00 3.91
4235 6841 4.804868 TTGGTAATCACTGCATTGCATT 57.195 36.364 12.53 3.33 38.13 3.56
4278 6884 4.170292 ACATGTAGAAACGCGTAAGACT 57.830 40.909 14.46 12.12 43.02 3.24
4304 6910 9.733556 TCAACTTGCTATTCCTATCTGTTTTTA 57.266 29.630 0.00 0.00 0.00 1.52
4383 6989 3.057596 TGAATTGGGCGCAAAGAGTAAAG 60.058 43.478 20.86 0.00 0.00 1.85
4455 7061 5.014123 AGTCATTCACAGGGATCTAAAACCA 59.986 40.000 0.00 0.00 0.00 3.67
4653 7265 8.686334 GCTATGGATATTTCTTTTCCTGTTTCA 58.314 33.333 0.00 0.00 0.00 2.69
4688 7300 6.540551 GGAGAGACCTCAATTAACTCCATTTC 59.459 42.308 0.00 0.00 41.20 2.17
4693 7305 8.797438 AGACCTCAATTAACTCCATTTCTTTTC 58.203 33.333 0.00 0.00 0.00 2.29
4767 7379 2.679837 CCCTGACATACAAGTGTGATGC 59.320 50.000 3.91 0.00 31.16 3.91
4787 7399 0.739561 ATACAGCTTCGGAGTCGTCC 59.260 55.000 0.00 0.00 39.88 4.79
4799 7411 1.335496 GAGTCGTCCTGCTGGAGATAC 59.665 57.143 13.36 11.07 44.16 2.24
4802 7414 0.309302 CGTCCTGCTGGAGATACTCG 59.691 60.000 13.36 8.06 44.16 4.18
4852 7473 4.586001 ACGTTCCTTCCTCAAGTAAGTACA 59.414 41.667 0.00 0.00 0.00 2.90
4853 7474 4.922103 CGTTCCTTCCTCAAGTAAGTACAC 59.078 45.833 0.00 0.00 0.00 2.90
4854 7475 4.778534 TCCTTCCTCAAGTAAGTACACG 57.221 45.455 0.00 0.00 0.00 4.49
4855 7476 4.147321 TCCTTCCTCAAGTAAGTACACGT 58.853 43.478 0.00 0.00 0.00 4.49
4856 7477 4.217118 TCCTTCCTCAAGTAAGTACACGTC 59.783 45.833 0.00 0.00 0.00 4.34
4857 7478 4.217983 CCTTCCTCAAGTAAGTACACGTCT 59.782 45.833 0.00 0.00 0.00 4.18
4859 7480 4.649692 TCCTCAAGTAAGTACACGTCTCT 58.350 43.478 0.00 0.00 0.00 3.10
4860 7481 5.798132 TCCTCAAGTAAGTACACGTCTCTA 58.202 41.667 0.00 0.00 0.00 2.43
4861 7482 6.233434 TCCTCAAGTAAGTACACGTCTCTAA 58.767 40.000 0.00 0.00 0.00 2.10
4930 7576 3.125607 CGGGTGCCGCTGACTATA 58.874 61.111 0.00 0.00 41.17 1.31
4934 7580 0.928229 GGTGCCGCTGACTATAAACG 59.072 55.000 0.00 0.00 0.00 3.60
4944 7590 6.142480 CCGCTGACTATAAACGAGTAATCTTG 59.858 42.308 0.00 0.00 0.00 3.02
4953 7599 3.589988 ACGAGTAATCTTGGTTCAGCTG 58.410 45.455 7.63 7.63 0.00 4.24
4956 7602 2.040278 AGTAATCTTGGTTCAGCTGGCA 59.960 45.455 15.13 0.00 0.00 4.92
4959 7605 1.165907 TCTTGGTTCAGCTGGCAACG 61.166 55.000 15.13 0.00 42.51 4.10
4975 7622 1.543802 CAACGCAATACCCCAACACAT 59.456 47.619 0.00 0.00 0.00 3.21
5033 7680 2.931386 GCGACGCTGTATGATGGC 59.069 61.111 13.73 0.00 0.00 4.40
5064 7917 2.108075 TCTTTTGCAGGTCTGGGAATCA 59.892 45.455 0.00 0.00 0.00 2.57
5120 7976 0.954452 CAAGTGGGTGAACCTGAAGC 59.046 55.000 0.00 0.00 41.11 3.86
5133 7989 0.801251 CTGAAGCTGAGGCCTTTTCG 59.199 55.000 6.77 0.00 39.73 3.46
5236 10839 1.582610 AATGCTAACCAACACCGGCG 61.583 55.000 0.00 0.00 0.00 6.46
5237 10840 2.667199 GCTAACCAACACCGGCGT 60.667 61.111 6.01 0.00 0.00 5.68
5238 10841 2.961669 GCTAACCAACACCGGCGTG 61.962 63.158 6.01 7.05 46.11 5.34
5285 10889 1.757306 CCAATATCGGAGCTGGCCT 59.243 57.895 3.32 0.00 0.00 5.19
5289 10893 0.683973 ATATCGGAGCTGGCCTTCAG 59.316 55.000 3.32 0.03 46.03 3.02
5348 10959 2.731571 CCCGGTGACCATCCATCGT 61.732 63.158 1.11 0.00 38.88 3.73
5386 10997 7.645340 GTGATATCTTGGGACGAAAATGAAATG 59.355 37.037 3.98 0.00 0.00 2.32
5391 11002 4.954875 TGGGACGAAAATGAAATGCTTTT 58.045 34.783 0.00 0.00 0.00 2.27
5411 11024 0.759346 AAGTTTGAGTGCCTCGTCCT 59.241 50.000 0.00 0.00 32.35 3.85
5412 11025 0.318762 AGTTTGAGTGCCTCGTCCTC 59.681 55.000 0.00 0.00 32.35 3.71
5413 11026 0.670854 GTTTGAGTGCCTCGTCCTCC 60.671 60.000 0.00 0.00 32.35 4.30
5414 11027 1.118965 TTTGAGTGCCTCGTCCTCCA 61.119 55.000 0.00 0.00 32.35 3.86
5415 11028 0.904865 TTGAGTGCCTCGTCCTCCAT 60.905 55.000 0.00 0.00 32.35 3.41
5499 11130 2.346099 TGCGGCATTTCTAACTTTGC 57.654 45.000 0.00 0.00 0.00 3.68
5522 11153 2.028476 TCTTAACACTGGACGGGATGTG 60.028 50.000 0.00 0.00 36.59 3.21
5541 11172 3.504520 TGTGGCCTTCGTTTATCCTTTTC 59.495 43.478 3.32 0.00 0.00 2.29
5543 11174 3.245122 TGGCCTTCGTTTATCCTTTTCCT 60.245 43.478 3.32 0.00 0.00 3.36
5546 11177 5.161358 GCCTTCGTTTATCCTTTTCCTTTG 58.839 41.667 0.00 0.00 0.00 2.77
5547 11178 5.048294 GCCTTCGTTTATCCTTTTCCTTTGA 60.048 40.000 0.00 0.00 0.00 2.69
5548 11179 6.612306 CCTTCGTTTATCCTTTTCCTTTGAG 58.388 40.000 0.00 0.00 0.00 3.02
5567 11198 6.978343 TTGAGAGGGTATGTGTTTAAATCG 57.022 37.500 0.00 0.00 0.00 3.34
5574 11205 5.195379 GGTATGTGTTTAAATCGCGACATC 58.805 41.667 12.93 2.99 0.00 3.06
5578 11209 4.088648 GTGTTTAAATCGCGACATCCTTG 58.911 43.478 12.93 0.00 0.00 3.61
5604 11235 4.981806 TTTGTGAGGCAAATGCTATACC 57.018 40.909 5.25 0.00 41.68 2.73
5605 11236 3.643199 TGTGAGGCAAATGCTATACCA 57.357 42.857 5.25 0.00 41.70 3.25
5606 11237 3.278574 TGTGAGGCAAATGCTATACCAC 58.721 45.455 5.25 7.14 41.70 4.16
5607 11238 3.278574 GTGAGGCAAATGCTATACCACA 58.721 45.455 5.25 0.00 41.70 4.17
5608 11239 3.313526 GTGAGGCAAATGCTATACCACAG 59.686 47.826 5.25 0.00 41.70 3.66
5609 11240 2.880890 GAGGCAAATGCTATACCACAGG 59.119 50.000 5.25 0.00 41.70 4.00
5610 11241 2.242196 AGGCAAATGCTATACCACAGGT 59.758 45.455 5.25 0.00 41.70 4.00
5611 11242 3.023832 GGCAAATGCTATACCACAGGTT 58.976 45.455 5.25 0.00 41.70 3.50
5612 11243 4.080015 AGGCAAATGCTATACCACAGGTTA 60.080 41.667 5.25 0.00 41.70 2.85
5613 11244 4.642885 GGCAAATGCTATACCACAGGTTAA 59.357 41.667 5.25 0.00 41.70 2.01
5614 11245 5.221048 GGCAAATGCTATACCACAGGTTAAG 60.221 44.000 5.25 0.00 41.70 1.85
5615 11246 5.733373 GCAAATGCTATACCACAGGTTAAGC 60.733 44.000 12.76 12.76 40.40 3.09
5616 11247 5.373812 AATGCTATACCACAGGTTAAGCT 57.626 39.130 17.67 0.12 40.53 3.74
5617 11248 4.837093 TGCTATACCACAGGTTAAGCTT 57.163 40.909 17.67 3.48 40.53 3.74
5621 11252 4.650972 ATACCACAGGTTAAGCTTTGGA 57.349 40.909 35.03 22.84 37.09 3.53
5632 11263 5.980715 GGTTAAGCTTTGGAAATCGTTTGAA 59.019 36.000 3.20 0.00 0.00 2.69
5643 11274 2.353030 GTTTGAAAACGGCGCGCT 60.353 55.556 32.29 10.98 0.00 5.92
5647 11278 1.570347 TTGAAAACGGCGCGCTGTAT 61.570 50.000 42.57 33.50 34.70 2.29
5651 11282 1.366111 AAACGGCGCGCTGTATGAAT 61.366 50.000 42.57 26.06 34.70 2.57
5658 11289 1.062002 CGCGCTGTATGAATTTTCCGT 59.938 47.619 5.56 0.00 0.00 4.69
5734 11367 1.161843 CGTGTATTTGGTGGACCCAC 58.838 55.000 10.61 10.61 45.19 4.61
5736 11369 1.057471 TGTATTTGGTGGACCCACGA 58.943 50.000 12.54 6.45 45.19 4.35
5749 11382 2.652095 CCACGAAGACCGCCCCTTA 61.652 63.158 0.00 0.00 43.32 2.69
5750 11383 1.520666 CACGAAGACCGCCCCTTAT 59.479 57.895 0.00 0.00 43.32 1.73
5754 11387 1.415200 GAAGACCGCCCCTTATCTCT 58.585 55.000 0.00 0.00 0.00 3.10
5757 11390 1.763545 AGACCGCCCCTTATCTCTTTC 59.236 52.381 0.00 0.00 0.00 2.62
5758 11391 0.837940 ACCGCCCCTTATCTCTTTCC 59.162 55.000 0.00 0.00 0.00 3.13
5761 11394 2.326428 CGCCCCTTATCTCTTTCCCTA 58.674 52.381 0.00 0.00 0.00 3.53
5762 11395 2.037381 CGCCCCTTATCTCTTTCCCTAC 59.963 54.545 0.00 0.00 0.00 3.18
5763 11396 2.372504 GCCCCTTATCTCTTTCCCTACC 59.627 54.545 0.00 0.00 0.00 3.18
5764 11397 2.633481 CCCCTTATCTCTTTCCCTACCG 59.367 54.545 0.00 0.00 0.00 4.02
5766 11399 2.698797 CCTTATCTCTTTCCCTACCGCA 59.301 50.000 0.00 0.00 0.00 5.69
5923 11560 1.893808 CCACAAGTTGAGCAGCGGT 60.894 57.895 10.54 0.00 0.00 5.68
5927 11564 1.153168 AAGTTGAGCAGCGGTGTGT 60.153 52.632 17.07 3.70 0.00 3.72
5944 11581 0.671251 TGTTGGAACCATGGCGAAAC 59.329 50.000 13.04 11.97 0.00 2.78
6032 11669 4.209866 GCACCCCCAGGCCATAGG 62.210 72.222 5.01 3.25 36.11 2.57
6057 11694 1.757682 TTTGCTGTAATAAGGGGGCG 58.242 50.000 0.00 0.00 0.00 6.13
6059 11696 2.251642 GCTGTAATAAGGGGGCGCG 61.252 63.158 0.00 0.00 0.00 6.86
6064 11701 1.096416 TAATAAGGGGGCGCGTTTTG 58.904 50.000 14.68 0.00 0.00 2.44
6117 12000 2.945668 GGCGAGGAATTTTGCTACATCT 59.054 45.455 0.00 0.00 0.00 2.90
6119 12002 3.623060 GCGAGGAATTTTGCTACATCTGA 59.377 43.478 0.00 0.00 0.00 3.27
6139 12022 5.302568 TCTGATGTCTGTTTTTGCTGGAAAT 59.697 36.000 0.00 0.00 0.00 2.17
6146 12029 3.243670 TGTTTTTGCTGGAAATCATCGCA 60.244 39.130 0.00 0.00 0.00 5.10
6153 12036 5.904941 TGCTGGAAATCATCGCATTTTTAT 58.095 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 127 1.067283 ACAGATTCTCCAGCACACTCG 60.067 52.381 0.00 0.00 0.00 4.18
120 131 1.256812 TCGACAGATTCTCCAGCACA 58.743 50.000 0.00 0.00 0.00 4.57
149 160 2.487762 TCATTGGTTTAGCCTTTGAGCG 59.512 45.455 0.00 0.00 38.35 5.03
282 364 1.476007 CCTCCCTAGATGGAAGGCCG 61.476 65.000 0.00 0.00 38.35 6.13
307 389 5.066593 GGAGGTTTGAATATGTCCTGATCC 58.933 45.833 0.00 0.00 0.00 3.36
345 427 6.280643 TCAGATGAAAATATCGGTACACCAG 58.719 40.000 0.00 0.00 35.14 4.00
371 453 4.559153 GTTTGCTGCATTTTGTATGACCT 58.441 39.130 1.84 0.00 0.00 3.85
409 491 1.721389 CAACAGATCACCGAACGACTG 59.279 52.381 0.00 0.00 0.00 3.51
449 531 2.178890 GCTCGCTTCATGCCAGGAG 61.179 63.158 0.00 0.00 38.78 3.69
553 636 2.754472 GGGCAAGAAATTTTTGAGCGT 58.246 42.857 13.72 0.00 0.00 5.07
700 791 1.614903 TGAATGGTTCTTGCAAGGCTG 59.385 47.619 25.73 1.45 0.00 4.85
1198 1290 3.877508 GAGAACCAAATCCCAAGGTATCG 59.122 47.826 0.00 0.00 34.63 2.92
1320 1412 0.109342 CCTGGCCGGAGCTATCAATT 59.891 55.000 15.09 0.00 39.73 2.32
1815 1907 0.613572 TGCTCGTGTCCCATACCAGA 60.614 55.000 0.00 0.00 0.00 3.86
2291 2386 5.724854 AGGTTACCTAATTCTGTCTTGGCTA 59.275 40.000 0.15 0.00 28.47 3.93
2352 2449 8.885722 CAAATAAATGGCATTGCTAATTGTCTT 58.114 29.630 14.47 0.00 0.00 3.01
2354 2451 7.280652 ACCAAATAAATGGCATTGCTAATTGTC 59.719 33.333 14.47 0.00 44.75 3.18
2369 2466 6.708054 TGTAAGGGCAACAAACCAAATAAATG 59.292 34.615 0.00 0.00 39.74 2.32
2384 2481 1.414550 GGTTGGCTTTTGTAAGGGCAA 59.585 47.619 6.46 6.46 41.84 4.52
2386 2483 1.044611 TGGTTGGCTTTTGTAAGGGC 58.955 50.000 0.00 0.00 31.76 5.19
2389 2486 5.705609 ACTACATGGTTGGCTTTTGTAAG 57.294 39.130 0.00 0.00 34.36 2.34
2390 2487 5.278071 CGAACTACATGGTTGGCTTTTGTAA 60.278 40.000 0.00 0.00 0.00 2.41
2392 2489 3.004315 CGAACTACATGGTTGGCTTTTGT 59.996 43.478 0.00 0.00 0.00 2.83
2393 2490 3.564511 CGAACTACATGGTTGGCTTTTG 58.435 45.455 0.00 0.00 0.00 2.44
2398 2498 1.130561 GAAGCGAACTACATGGTTGGC 59.869 52.381 11.92 11.92 46.27 4.52
2402 2502 1.899814 TGAGGAAGCGAACTACATGGT 59.100 47.619 0.00 0.00 0.00 3.55
2404 2504 5.356882 TTTTTGAGGAAGCGAACTACATG 57.643 39.130 0.00 0.00 0.00 3.21
2429 2529 1.801178 GAGAAACCGAGCCAAAGACTG 59.199 52.381 0.00 0.00 0.00 3.51
2430 2530 1.416401 TGAGAAACCGAGCCAAAGACT 59.584 47.619 0.00 0.00 0.00 3.24
2433 2533 3.708563 TTTTGAGAAACCGAGCCAAAG 57.291 42.857 0.00 0.00 0.00 2.77
2461 2563 3.185797 CCTTGAACGGAAAGGTAAACGAG 59.814 47.826 0.00 0.00 39.55 4.18
2475 2577 4.814771 AGTGGACTTTCTAAACCTTGAACG 59.185 41.667 0.00 0.00 0.00 3.95
2481 2583 6.099845 TGAAAGAGAGTGGACTTTCTAAACCT 59.900 38.462 16.64 0.00 46.66 3.50
2492 2594 7.201565 CGGAATCTTATTTGAAAGAGAGTGGAC 60.202 40.741 0.00 0.00 38.81 4.02
2516 2618 0.462047 CCTAAGTTAGCAGCACCCGG 60.462 60.000 4.22 0.00 0.00 5.73
2518 2620 0.107165 CCCCTAAGTTAGCAGCACCC 60.107 60.000 4.22 0.00 0.00 4.61
2551 2653 2.034939 ACATCCATGTTGTGCACTTGTG 59.965 45.455 19.41 11.15 37.90 3.33
2556 2658 1.068333 GGTGACATCCATGTTGTGCAC 60.068 52.381 10.75 10.75 41.95 4.57
2557 2659 1.202915 AGGTGACATCCATGTTGTGCA 60.203 47.619 3.47 0.00 41.95 4.57
2558 2660 1.470098 GAGGTGACATCCATGTTGTGC 59.530 52.381 3.47 0.00 41.95 4.57
2559 2661 2.086869 GGAGGTGACATCCATGTTGTG 58.913 52.381 11.95 0.00 41.95 3.33
2560 2662 1.988107 AGGAGGTGACATCCATGTTGT 59.012 47.619 19.28 0.00 41.95 3.32
2561 2663 2.795231 AGGAGGTGACATCCATGTTG 57.205 50.000 19.28 0.00 41.95 3.33
2562 2664 2.025887 GGAAGGAGGTGACATCCATGTT 60.026 50.000 19.28 3.90 41.95 2.71
2563 2665 1.561542 GGAAGGAGGTGACATCCATGT 59.438 52.381 19.28 2.84 45.16 3.21
2565 2667 2.122768 GAGGAAGGAGGTGACATCCAT 58.877 52.381 19.28 6.35 39.47 3.41
2566 2668 1.203300 TGAGGAAGGAGGTGACATCCA 60.203 52.381 19.28 0.00 39.47 3.41
2567 2669 1.208293 GTGAGGAAGGAGGTGACATCC 59.792 57.143 8.46 8.46 37.07 3.51
2568 2670 1.134965 CGTGAGGAAGGAGGTGACATC 60.135 57.143 0.00 0.00 0.00 3.06
2569 2671 0.898320 CGTGAGGAAGGAGGTGACAT 59.102 55.000 0.00 0.00 0.00 3.06
2573 2675 2.100197 TCATACGTGAGGAAGGAGGTG 58.900 52.381 0.00 0.00 0.00 4.00
2582 2684 1.341531 GGGTGGAGATCATACGTGAGG 59.658 57.143 0.00 0.00 37.87 3.86
2588 2690 4.093011 AGCTAGATGGGTGGAGATCATAC 58.907 47.826 0.00 0.00 0.00 2.39
2590 2692 3.272716 AGCTAGATGGGTGGAGATCAT 57.727 47.619 0.00 0.00 0.00 2.45
2641 2743 9.717942 AGTTAAATGCTGGAGTTCTATATGATC 57.282 33.333 0.00 0.00 0.00 2.92
2687 2806 3.576982 ACAGCCTTAGTTGCTACAGTACA 59.423 43.478 0.13 0.00 36.81 2.90
2688 2807 4.174762 GACAGCCTTAGTTGCTACAGTAC 58.825 47.826 0.13 0.00 36.81 2.73
2707 2826 8.461222 CCATGCTTAACATCTTTAGAATTGACA 58.539 33.333 0.00 0.00 36.64 3.58
2728 2847 0.951558 AAATTACCGCCGATCCATGC 59.048 50.000 0.00 0.00 0.00 4.06
2739 2858 5.220265 GCATCATGCAAGTTCAAAATTACCG 60.220 40.000 4.20 0.00 44.26 4.02
2765 2884 7.148239 CCCATTAGGTCTGTTGTCTATGAAAAC 60.148 40.741 0.00 0.00 30.98 2.43
2773 2892 1.066143 CGCCCATTAGGTCTGTTGTCT 60.066 52.381 0.00 0.00 38.26 3.41
2799 2923 1.497722 GCACGCCACTAGCAAACTC 59.502 57.895 0.00 0.00 44.04 3.01
2872 2996 1.748493 GAAGAAACAACCAGGCACACA 59.252 47.619 0.00 0.00 0.00 3.72
2895 3020 7.016858 AGGAACTAGCCCGTATGGAAATTTATA 59.983 37.037 1.27 0.00 36.02 0.98
2909 3034 0.175989 GACCAGAAGGAACTAGCCCG 59.824 60.000 0.00 0.00 38.49 6.13
2950 3076 3.715871 TGAAGCGTTTCATGGGTCA 57.284 47.368 10.92 0.00 38.37 4.02
2971 3097 5.233689 GTCGTTTTCCTCATTTCCTATACGG 59.766 44.000 0.00 0.00 0.00 4.02
2976 3102 4.041198 ACCTGTCGTTTTCCTCATTTCCTA 59.959 41.667 0.00 0.00 0.00 2.94
2993 3119 5.237815 TGTATGATTCACACTGAACCTGTC 58.762 41.667 0.00 0.00 39.45 3.51
3007 3133 9.599322 CCTTGTTTATATTCGCTTGTATGATTC 57.401 33.333 0.00 0.00 0.00 2.52
3025 3151 7.392113 CCACACACCTCAAATATACCTTGTTTA 59.608 37.037 0.00 0.00 0.00 2.01
3026 3152 6.208599 CCACACACCTCAAATATACCTTGTTT 59.791 38.462 0.00 0.00 0.00 2.83
3028 3154 5.013704 TCCACACACCTCAAATATACCTTGT 59.986 40.000 0.00 0.00 0.00 3.16
3029 3155 5.496556 TCCACACACCTCAAATATACCTTG 58.503 41.667 0.00 0.00 0.00 3.61
3030 3156 5.772393 TCCACACACCTCAAATATACCTT 57.228 39.130 0.00 0.00 0.00 3.50
3031 3157 5.013704 TGTTCCACACACCTCAAATATACCT 59.986 40.000 0.00 0.00 0.00 3.08
3037 3163 9.693739 TTTATATATGTTCCACACACCTCAAAT 57.306 29.630 0.00 0.00 38.61 2.32
3040 3166 7.051623 GGTTTATATATGTTCCACACACCTCA 58.948 38.462 0.00 0.00 38.61 3.86
3042 3168 7.054124 CAGGTTTATATATGTTCCACACACCT 58.946 38.462 0.00 0.00 38.61 4.00
3044 3170 8.395633 GTTCAGGTTTATATATGTTCCACACAC 58.604 37.037 0.00 0.00 38.61 3.82
3048 3174 9.337396 TGATGTTCAGGTTTATATATGTTCCAC 57.663 33.333 0.00 0.00 0.00 4.02
3049 3175 9.337396 GTGATGTTCAGGTTTATATATGTTCCA 57.663 33.333 0.00 0.00 0.00 3.53
3053 3179 9.679661 TTGTGTGATGTTCAGGTTTATATATGT 57.320 29.630 0.00 0.00 0.00 2.29
3055 3181 9.905713 ACTTGTGTGATGTTCAGGTTTATATAT 57.094 29.630 0.00 0.00 0.00 0.86
3058 3184 8.372459 ACTACTTGTGTGATGTTCAGGTTTATA 58.628 33.333 0.00 0.00 0.00 0.98
3059 3185 7.224297 ACTACTTGTGTGATGTTCAGGTTTAT 58.776 34.615 0.00 0.00 0.00 1.40
3061 3187 5.437060 ACTACTTGTGTGATGTTCAGGTTT 58.563 37.500 0.00 0.00 0.00 3.27
3062 3188 5.036117 ACTACTTGTGTGATGTTCAGGTT 57.964 39.130 0.00 0.00 0.00 3.50
3063 3189 4.689612 ACTACTTGTGTGATGTTCAGGT 57.310 40.909 0.00 0.00 0.00 4.00
3064 3190 6.398095 TCATACTACTTGTGTGATGTTCAGG 58.602 40.000 0.00 0.00 40.96 3.86
3065 3191 7.315890 TCTCATACTACTTGTGTGATGTTCAG 58.684 38.462 0.00 0.00 43.96 3.02
3066 3192 7.227049 TCTCATACTACTTGTGTGATGTTCA 57.773 36.000 0.00 0.00 43.96 3.18
3067 3193 8.534333 TTTCTCATACTACTTGTGTGATGTTC 57.466 34.615 0.00 0.00 43.96 3.18
3069 3195 7.931407 TGTTTTCTCATACTACTTGTGTGATGT 59.069 33.333 0.00 0.00 43.96 3.06
3070 3196 8.310406 TGTTTTCTCATACTACTTGTGTGATG 57.690 34.615 0.00 0.00 43.96 3.07
3089 3215 9.161629 CCCCCAAAATGAAAGTTATATGTTTTC 57.838 33.333 0.00 0.00 0.00 2.29
3111 5671 5.479027 ACTTATTACACAAATTGTCACCCCC 59.521 40.000 0.00 0.00 39.91 5.40
3152 5712 6.972328 TGTTTACTTGCTTTTAACTGCTTCTG 59.028 34.615 1.38 0.00 0.00 3.02
3200 5760 0.248289 CTCGAAATGTGTACCGGGGT 59.752 55.000 6.32 0.00 0.00 4.95
3201 5761 0.461339 CCTCGAAATGTGTACCGGGG 60.461 60.000 6.32 0.00 36.25 5.73
3204 5764 2.679450 TGAACCTCGAAATGTGTACCG 58.321 47.619 0.00 0.00 0.00 4.02
3209 5769 4.211389 CGAAACTTGAACCTCGAAATGTG 58.789 43.478 0.00 0.00 33.13 3.21
3239 5799 1.825474 CCTATCTAGTGCGGTATGGGG 59.175 57.143 0.00 0.00 0.00 4.96
3297 5857 7.837202 AAACCAGATTTAATCATGCACATTG 57.163 32.000 7.74 0.00 0.00 2.82
3384 5944 0.662970 TTGCTTCGGCGAAAATGTGC 60.663 50.000 23.81 21.56 45.37 4.57
3404 5964 2.031420 CACCTGTGACAGTTCTGCATTG 60.031 50.000 12.15 0.00 0.00 2.82
3489 6049 5.023533 AGCAACGAGAGCCAGAATAATAA 57.976 39.130 0.00 0.00 0.00 1.40
3591 6173 1.640428 TCCTTCTTCGCAATGCTACG 58.360 50.000 2.94 0.00 0.00 3.51
3665 6248 4.469657 ACAACCCTTGAAGCATTGTCTAA 58.530 39.130 6.50 0.00 0.00 2.10
3677 6260 3.659786 CGACATTGTCTACAACCCTTGA 58.340 45.455 14.54 0.00 38.86 3.02
4278 6884 8.635765 AAAAACAGATAGGAATAGCAAGTTGA 57.364 30.769 7.16 0.00 0.00 3.18
4304 6910 1.541233 GCTAATAGGCGTGTGAGGCAT 60.541 52.381 0.00 0.00 39.37 4.40
4383 6989 1.068474 CGGCGATCCCACGAATTATC 58.932 55.000 0.00 0.00 35.09 1.75
4455 7061 6.653020 TGTGTCATTCAGAAGTATATTGCCT 58.347 36.000 0.00 0.00 0.00 4.75
4653 7265 2.433646 AGGTCTCTCCTGGACGCAGT 62.434 60.000 0.00 0.00 46.43 4.40
4767 7379 1.534175 GGACGACTCCGAAGCTGTATG 60.534 57.143 0.00 0.00 39.50 2.39
4787 7399 0.387202 CCACCGAGTATCTCCAGCAG 59.613 60.000 0.00 0.00 0.00 4.24
4873 7494 0.748729 AAGACGTGTCCCCGCAAAAA 60.749 50.000 0.00 0.00 0.00 1.94
4874 7495 1.153127 AAGACGTGTCCCCGCAAAA 60.153 52.632 0.00 0.00 0.00 2.44
4875 7496 1.595929 GAAGACGTGTCCCCGCAAA 60.596 57.895 0.00 0.00 0.00 3.68
4876 7497 1.180456 TAGAAGACGTGTCCCCGCAA 61.180 55.000 0.00 0.00 0.00 4.85
4877 7498 1.180456 TTAGAAGACGTGTCCCCGCA 61.180 55.000 0.00 0.00 0.00 5.69
4878 7499 0.175073 ATTAGAAGACGTGTCCCCGC 59.825 55.000 0.00 0.00 0.00 6.13
4879 7500 2.667473 AATTAGAAGACGTGTCCCCG 57.333 50.000 0.00 0.00 0.00 5.73
4880 7501 4.203654 AGAAATTAGAAGACGTGTCCCC 57.796 45.455 0.00 0.00 0.00 4.81
4881 7502 5.480205 AGAAGAAATTAGAAGACGTGTCCC 58.520 41.667 0.00 0.00 0.00 4.46
4882 7503 6.089685 GTGAGAAGAAATTAGAAGACGTGTCC 59.910 42.308 0.00 0.00 0.00 4.02
4883 7504 6.864165 AGTGAGAAGAAATTAGAAGACGTGTC 59.136 38.462 0.00 0.00 0.00 3.67
4930 7576 4.452455 CAGCTGAACCAAGATTACTCGTTT 59.548 41.667 8.42 0.00 0.00 3.60
4934 7580 2.680339 GCCAGCTGAACCAAGATTACTC 59.320 50.000 17.39 0.00 0.00 2.59
4944 7590 2.146073 ATTGCGTTGCCAGCTGAACC 62.146 55.000 17.39 7.44 35.28 3.62
4953 7599 1.214325 GTTGGGGTATTGCGTTGCC 59.786 57.895 0.00 0.00 0.00 4.52
4956 7602 1.543802 CATGTGTTGGGGTATTGCGTT 59.456 47.619 0.00 0.00 0.00 4.84
4959 7605 2.094234 GGAACATGTGTTGGGGTATTGC 60.094 50.000 0.00 0.00 38.56 3.56
5033 7680 3.383761 ACCTGCAAAAGAAAGAAATGCG 58.616 40.909 0.00 0.00 39.81 4.73
5064 7917 1.224075 CGATCTCGCATTGCTTCCAT 58.776 50.000 7.12 0.00 0.00 3.41
5120 7976 0.036388 TAGCACCGAAAAGGCCTCAG 60.036 55.000 5.23 0.00 46.52 3.35
5133 7989 1.821332 GATGCACCTGGCTAGCACC 60.821 63.158 18.24 0.00 45.15 5.01
5236 10839 4.746309 TGGCATGGGGAGCTGCAC 62.746 66.667 7.79 3.19 40.18 4.57
5237 10840 3.949885 CTTGGCATGGGGAGCTGCA 62.950 63.158 7.79 0.00 40.18 4.41
5238 10841 3.145551 CTTGGCATGGGGAGCTGC 61.146 66.667 0.00 0.00 37.66 5.25
5285 10889 2.026729 TCCGATATTGGTTGTGCCTGAA 60.027 45.455 8.94 0.00 38.35 3.02
5289 10893 2.290641 GTCATCCGATATTGGTTGTGCC 59.709 50.000 16.55 5.95 37.90 5.01
5333 10944 2.107950 TCAAACGATGGATGGTCACC 57.892 50.000 0.00 0.00 0.00 4.02
5348 10959 6.775142 TCCCAAGATATCACAAACTGTTCAAA 59.225 34.615 5.32 0.00 0.00 2.69
5431 11044 3.118956 CCCTGATAAGCTGAAACGAGACT 60.119 47.826 0.00 0.00 0.00 3.24
5432 11045 3.190874 CCCTGATAAGCTGAAACGAGAC 58.809 50.000 0.00 0.00 0.00 3.36
5434 11047 2.932614 CACCCTGATAAGCTGAAACGAG 59.067 50.000 0.00 0.00 0.00 4.18
5435 11048 2.565391 TCACCCTGATAAGCTGAAACGA 59.435 45.455 0.00 0.00 0.00 3.85
5477 11108 4.420168 GCAAAGTTAGAAATGCCGCAATA 58.580 39.130 0.00 0.00 32.73 1.90
5499 11130 1.263356 TCCCGTCCAGTGTTAAGAGG 58.737 55.000 0.00 0.00 0.00 3.69
5522 11153 3.353557 AGGAAAAGGATAAACGAAGGCC 58.646 45.455 0.00 0.00 0.00 5.19
5541 11172 7.414098 CGATTTAAACACATACCCTCTCAAAGG 60.414 40.741 0.00 0.00 45.77 3.11
5543 11174 6.128117 GCGATTTAAACACATACCCTCTCAAA 60.128 38.462 0.00 0.00 0.00 2.69
5546 11177 4.025979 CGCGATTTAAACACATACCCTCTC 60.026 45.833 0.00 0.00 0.00 3.20
5547 11178 3.869246 CGCGATTTAAACACATACCCTCT 59.131 43.478 0.00 0.00 0.00 3.69
5548 11179 3.866910 TCGCGATTTAAACACATACCCTC 59.133 43.478 3.71 0.00 0.00 4.30
5567 11198 3.496884 TCACAAACTTACAAGGATGTCGC 59.503 43.478 0.00 0.00 41.05 5.19
5574 11205 4.647424 TTTGCCTCACAAACTTACAAGG 57.353 40.909 0.00 0.00 43.35 3.61
5603 11234 4.615912 CGATTTCCAAAGCTTAACCTGTGG 60.616 45.833 0.00 2.32 40.91 4.17
5604 11235 4.023193 ACGATTTCCAAAGCTTAACCTGTG 60.023 41.667 0.00 0.00 0.00 3.66
5605 11236 4.142038 ACGATTTCCAAAGCTTAACCTGT 58.858 39.130 0.00 0.00 0.00 4.00
5606 11237 4.766404 ACGATTTCCAAAGCTTAACCTG 57.234 40.909 0.00 0.00 0.00 4.00
5607 11238 5.300792 TCAAACGATTTCCAAAGCTTAACCT 59.699 36.000 0.00 0.00 0.00 3.50
5608 11239 5.525199 TCAAACGATTTCCAAAGCTTAACC 58.475 37.500 0.00 0.00 0.00 2.85
5609 11240 7.458038 TTTCAAACGATTTCCAAAGCTTAAC 57.542 32.000 0.00 0.00 0.00 2.01
5610 11241 7.901002 GTTTTCAAACGATTTCCAAAGCTTAA 58.099 30.769 0.00 0.00 0.00 1.85
5611 11242 7.458038 GTTTTCAAACGATTTCCAAAGCTTA 57.542 32.000 0.00 0.00 0.00 3.09
5612 11243 6.344572 GTTTTCAAACGATTTCCAAAGCTT 57.655 33.333 0.00 0.00 0.00 3.74
5613 11244 5.966636 GTTTTCAAACGATTTCCAAAGCT 57.033 34.783 0.00 0.00 0.00 3.74
5632 11263 1.366111 ATTCATACAGCGCGCCGTTT 61.366 50.000 30.33 16.86 0.00 3.60
5639 11270 2.705154 GACGGAAAATTCATACAGCGC 58.295 47.619 0.00 0.00 0.00 5.92
5640 11271 2.285602 CCGACGGAAAATTCATACAGCG 60.286 50.000 8.64 0.00 0.00 5.18
5643 11274 3.680937 GTGTCCGACGGAAAATTCATACA 59.319 43.478 20.26 6.67 31.38 2.29
5647 11278 1.141645 CGTGTCCGACGGAAAATTCA 58.858 50.000 20.26 9.24 44.85 2.57
5734 11367 0.032267 GAGATAAGGGGCGGTCTTCG 59.968 60.000 0.00 0.00 42.76 3.79
5736 11369 1.880941 AAGAGATAAGGGGCGGTCTT 58.119 50.000 0.00 0.00 0.00 3.01
5749 11382 0.460311 CGTGCGGTAGGGAAAGAGAT 59.540 55.000 0.00 0.00 0.00 2.75
5750 11383 1.888018 CGTGCGGTAGGGAAAGAGA 59.112 57.895 0.00 0.00 0.00 3.10
5754 11387 2.357760 GTGCGTGCGGTAGGGAAA 60.358 61.111 0.00 0.00 0.00 3.13
5757 11390 4.814294 GGAGTGCGTGCGGTAGGG 62.814 72.222 0.00 0.00 0.00 3.53
5758 11391 3.371097 ATGGAGTGCGTGCGGTAGG 62.371 63.158 0.00 0.00 0.00 3.18
5761 11394 4.760047 GGATGGAGTGCGTGCGGT 62.760 66.667 0.00 0.00 0.00 5.68
5764 11397 3.918253 TTGGGGATGGAGTGCGTGC 62.918 63.158 0.00 0.00 0.00 5.34
5766 11399 2.351276 GTTGGGGATGGAGTGCGT 59.649 61.111 0.00 0.00 0.00 5.24
5851 11485 0.938168 GCAGCTGAAGTGTGCTTTGC 60.938 55.000 20.43 0.00 37.44 3.68
5923 11560 0.466372 TTCGCCATGGTTCCAACACA 60.466 50.000 14.67 0.00 0.00 3.72
5927 11564 1.339610 CAAGTTTCGCCATGGTTCCAA 59.660 47.619 14.67 0.00 0.00 3.53
6043 11680 0.035247 AAACGCGCCCCCTTATTACA 60.035 50.000 5.73 0.00 0.00 2.41
6044 11681 1.097232 AAAACGCGCCCCCTTATTAC 58.903 50.000 5.73 0.00 0.00 1.89
6045 11682 1.096416 CAAAACGCGCCCCCTTATTA 58.904 50.000 5.73 0.00 0.00 0.98
6057 11694 1.950630 CTGGTTGCAGCCAAAACGC 60.951 57.895 23.45 0.00 38.18 4.84
6059 11696 4.032356 GCTGGTTGCAGCCAAAAC 57.968 55.556 23.45 11.95 42.05 2.43
6076 11714 0.802494 GGTTCCAACATACACCGCAG 59.198 55.000 0.00 0.00 0.00 5.18
6080 11718 1.641123 CGCCGGTTCCAACATACACC 61.641 60.000 1.90 0.00 0.00 4.16
6117 12000 4.998671 TTTCCAGCAAAAACAGACATCA 57.001 36.364 0.00 0.00 0.00 3.07
6119 12002 5.534207 TGATTTCCAGCAAAAACAGACAT 57.466 34.783 0.00 0.00 0.00 3.06
6139 12022 9.284594 GTAGTAGCAAAAATAAAAATGCGATGA 57.715 29.630 0.00 0.00 43.39 2.92
6146 12029 9.423061 CAAGCTGGTAGTAGCAAAAATAAAAAT 57.577 29.630 3.25 0.00 46.07 1.82
6153 12036 4.204012 ACACAAGCTGGTAGTAGCAAAAA 58.796 39.130 3.25 0.00 46.07 1.94
6180 12065 2.424842 AATTGGCTGCGGGTTCCAGA 62.425 55.000 0.00 0.00 32.03 3.86
6315 12203 0.846401 CAGTAATGCGATGACGACGG 59.154 55.000 0.00 0.00 42.66 4.79


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

AutoCloner maintained by Alex Coulton.