Multiple sequence alignment - TraesCS1A01G119800

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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 TraesCS1A01G119800 chr1A 100.000 3582 0 0 1 3582 132136498 132132917 0.000000e+00 6615.0
1 TraesCS1A01G119800 chr1A 97.297 37 1 0 487 523 427817056 427817092 2.990000e-06 63.9
2 TraesCS1A01G119800 chr1A 96.970 33 1 0 2176 2208 132134251 132134219 5.000000e-04 56.5
3 TraesCS1A01G119800 chr1A 96.970 33 1 0 2248 2280 132134323 132134291 5.000000e-04 56.5
4 TraesCS1A01G119800 chr1D 95.929 3193 97 15 54 3243 119406539 119403377 0.000000e+00 5145.0
5 TraesCS1A01G119800 chr1D 95.570 158 5 2 3200 3357 119403385 119403230 5.940000e-63 252.0
6 TraesCS1A01G119800 chr1D 92.553 94 6 1 3353 3445 335584718 335584625 2.240000e-27 134.0
7 TraesCS1A01G119800 chr1D 91.463 82 6 1 3275 3356 75655212 75655132 1.050000e-20 111.0
8 TraesCS1A01G119800 chr1D 84.848 99 10 5 3258 3355 73689361 73689267 1.060000e-15 95.3
9 TraesCS1A01G119800 chr1D 83.333 72 7 5 2176 2246 119404371 119404304 1.070000e-05 62.1
10 TraesCS1A01G119800 chr1D 96.970 33 1 0 2248 2280 119404443 119404411 5.000000e-04 56.5
11 TraesCS1A01G119800 chr1B 93.905 2100 73 17 58 2157 182200317 182198273 0.000000e+00 3118.0
12 TraesCS1A01G119800 chr1B 92.773 512 27 4 2470 2981 182197980 182197479 0.000000e+00 732.0
13 TraesCS1A01G119800 chr1B 92.542 295 20 2 3063 3356 182197480 182197187 4.280000e-114 422.0
14 TraesCS1A01G119800 chr1B 92.784 97 6 1 3462 3557 133441264 133441168 4.820000e-29 139.0
15 TraesCS1A01G119800 chr1B 97.297 74 2 0 2412 2485 182198068 182197995 3.750000e-25 126.0
16 TraesCS1A01G119800 chr1B 88.889 99 9 2 3340 3438 689202615 689202711 1.750000e-23 121.0
17 TraesCS1A01G119800 chr1B 91.765 85 6 1 2980 3064 380693385 380693302 2.260000e-22 117.0
18 TraesCS1A01G119800 chr1B 97.674 43 1 0 2176 2218 182198274 182198232 1.380000e-09 75.0
19 TraesCS1A01G119800 chr5D 93.814 97 6 0 3461 3557 47296137 47296041 2.880000e-31 147.0
20 TraesCS1A01G119800 chr5D 93.258 89 6 0 3350 3438 229934125 229934213 8.070000e-27 132.0
21 TraesCS1A01G119800 chr5D 93.023 86 6 0 3353 3438 575044 575129 3.750000e-25 126.0
22 TraesCS1A01G119800 chr5D 90.909 88 7 1 2976 3062 324375087 324375000 2.260000e-22 117.0
23 TraesCS1A01G119800 chr6D 96.552 87 3 0 2978 3064 230824817 230824731 1.040000e-30 145.0
24 TraesCS1A01G119800 chr6B 95.402 87 4 0 3461 3547 5911142 5911056 4.820000e-29 139.0
25 TraesCS1A01G119800 chr6B 92.941 85 6 0 2980 3064 58801734 58801818 1.350000e-24 124.0
26 TraesCS1A01G119800 chr6B 92.941 85 6 0 3354 3438 673636599 673636683 1.350000e-24 124.0
27 TraesCS1A01G119800 chr2D 95.402 87 3 1 3465 3551 615112359 615112444 1.730000e-28 137.0
28 TraesCS1A01G119800 chr7A 97.468 79 2 0 3461 3539 733344017 733344095 6.240000e-28 135.0
29 TraesCS1A01G119800 chr7A 85.859 99 10 3 3257 3355 149142824 149142730 6.330000e-18 102.0
30 TraesCS1A01G119800 chr7A 97.222 36 1 0 482 517 575926413 575926448 1.070000e-05 62.1
31 TraesCS1A01G119800 chr4D 93.407 91 5 1 3349 3438 465765344 465765254 2.240000e-27 134.0
32 TraesCS1A01G119800 chr4D 91.765 85 6 1 2980 3064 509646440 509646357 2.260000e-22 117.0
33 TraesCS1A01G119800 chr4B 94.253 87 5 0 3465 3551 645325585 645325671 2.240000e-27 134.0
34 TraesCS1A01G119800 chr4B 91.860 86 6 1 2980 3065 670403334 670403250 6.280000e-23 119.0
35 TraesCS1A01G119800 chr3D 94.253 87 5 0 3352 3438 11439966 11440052 2.240000e-27 134.0
36 TraesCS1A01G119800 chr3D 94.186 86 3 2 2980 3064 489457524 489457440 2.900000e-26 130.0
37 TraesCS1A01G119800 chr3D 85.714 105 11 4 3251 3355 37065072 37064972 1.360000e-19 108.0
38 TraesCS1A01G119800 chr3A 95.238 84 4 0 3461 3544 489304666 489304583 2.240000e-27 134.0
39 TraesCS1A01G119800 chr2B 94.186 86 5 0 3353 3438 779865600 779865685 8.070000e-27 132.0
40 TraesCS1A01G119800 chr2B 84.112 107 13 3 3249 3355 780869846 780869948 2.280000e-17 100.0
41 TraesCS1A01G119800 chr7B 90.816 98 7 2 3461 3557 5977622 5977526 2.900000e-26 130.0
42 TraesCS1A01G119800 chr7B 92.941 85 6 0 2980 3064 454616750 454616834 1.350000e-24 124.0
43 TraesCS1A01G119800 chr5B 90.426 94 9 0 3345 3438 64720354 64720447 1.350000e-24 124.0
44 TraesCS1A01G119800 chr5B 91.358 81 6 1 3275 3355 338490410 338490331 3.780000e-20 110.0
45 TraesCS1A01G119800 chr4A 93.827 81 4 1 3465 3544 614577303 614577383 1.750000e-23 121.0
46 TraesCS1A01G119800 chr7D 83.784 111 9 7 3250 3355 111082590 111082484 2.940000e-16 97.1


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 TraesCS1A01G119800 chr1A 132132917 132136498 3581 True 2242.666667 6615 97.9800 1 3582 3 chr1A.!!$R1 3581
1 TraesCS1A01G119800 chr1D 119403230 119406539 3309 True 1378.900000 5145 92.9505 54 3357 4 chr1D.!!$R4 3303
2 TraesCS1A01G119800 chr1B 182197187 182200317 3130 True 894.600000 3118 94.8382 58 3356 5 chr1B.!!$R3 3298

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
970 982 0.034089 CCCCAGTGGTTCTTGGATCC 60.034 60.0 8.74 4.2 31.33 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2752 2856 0.032813 AGGGCATGCAGCTACCAATT 60.033 50.0 21.36 0.0 44.79 2.32 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
25 26 8.986477 CAAACTTAGGTCTTGAAAAATATGGG 57.014 34.615 0.00 0.00 0.00 4.00
26 27 6.775594 ACTTAGGTCTTGAAAAATATGGGC 57.224 37.500 0.00 0.00 0.00 5.36
27 28 5.357032 ACTTAGGTCTTGAAAAATATGGGCG 59.643 40.000 0.00 0.00 0.00 6.13
28 29 3.023832 AGGTCTTGAAAAATATGGGCGG 58.976 45.455 0.00 0.00 0.00 6.13
29 30 3.020984 GGTCTTGAAAAATATGGGCGGA 58.979 45.455 0.00 0.00 0.00 5.54
30 31 3.181490 GGTCTTGAAAAATATGGGCGGAC 60.181 47.826 0.00 0.00 0.00 4.79
31 32 3.694566 GTCTTGAAAAATATGGGCGGACT 59.305 43.478 0.00 0.00 0.00 3.85
32 33 4.879545 GTCTTGAAAAATATGGGCGGACTA 59.120 41.667 0.00 0.00 0.00 2.59
33 34 4.879545 TCTTGAAAAATATGGGCGGACTAC 59.120 41.667 0.00 0.00 0.00 2.73
34 35 4.223556 TGAAAAATATGGGCGGACTACA 57.776 40.909 0.00 0.00 0.00 2.74
35 36 4.787551 TGAAAAATATGGGCGGACTACAT 58.212 39.130 0.00 0.00 0.00 2.29
36 37 4.578516 TGAAAAATATGGGCGGACTACATG 59.421 41.667 0.00 0.00 0.00 3.21
37 38 4.431416 AAAATATGGGCGGACTACATGA 57.569 40.909 0.00 0.00 0.00 3.07
38 39 4.640771 AAATATGGGCGGACTACATGAT 57.359 40.909 0.00 0.00 0.00 2.45
39 40 3.616956 ATATGGGCGGACTACATGATG 57.383 47.619 0.00 0.00 0.00 3.07
40 41 0.397941 ATGGGCGGACTACATGATGG 59.602 55.000 0.00 0.00 0.00 3.51
41 42 0.689412 TGGGCGGACTACATGATGGA 60.689 55.000 0.00 0.00 0.00 3.41
42 43 0.468226 GGGCGGACTACATGATGGAA 59.532 55.000 0.00 0.00 0.00 3.53
43 44 1.583054 GGCGGACTACATGATGGAAC 58.417 55.000 0.00 0.00 0.00 3.62
44 45 1.209128 GCGGACTACATGATGGAACG 58.791 55.000 0.00 0.00 0.00 3.95
45 46 1.202371 GCGGACTACATGATGGAACGA 60.202 52.381 0.00 0.00 0.00 3.85
46 47 2.460918 CGGACTACATGATGGAACGAC 58.539 52.381 0.00 0.00 0.00 4.34
47 48 2.460918 GGACTACATGATGGAACGACG 58.539 52.381 0.00 0.00 0.00 5.12
48 49 2.098607 GGACTACATGATGGAACGACGA 59.901 50.000 0.00 0.00 0.00 4.20
49 50 3.364062 GACTACATGATGGAACGACGAG 58.636 50.000 0.00 0.00 0.00 4.18
50 51 3.014623 ACTACATGATGGAACGACGAGA 58.985 45.455 0.00 0.00 0.00 4.04
51 52 2.568696 ACATGATGGAACGACGAGAG 57.431 50.000 0.00 0.00 0.00 3.20
90 91 2.746904 CCAACGTGCCATGACAATCTAA 59.253 45.455 0.00 0.00 0.00 2.10
560 565 2.511600 CCAAAGCGACGCCCCTAG 60.512 66.667 17.79 2.24 0.00 3.02
577 582 2.357637 CCTAGGACGCAAGAGAGAGAAG 59.642 54.545 1.05 0.00 43.62 2.85
970 982 0.034089 CCCCAGTGGTTCTTGGATCC 60.034 60.000 8.74 4.20 31.33 3.36
993 1005 1.959085 CAGTGCTGGAATTTGGCGT 59.041 52.632 0.00 0.00 0.00 5.68
996 1008 1.412343 AGTGCTGGAATTTGGCGTTTT 59.588 42.857 0.00 0.00 0.00 2.43
1064 1076 3.701040 AGTCTGAGCCTTTCTGATCTCTC 59.299 47.826 0.00 0.00 36.35 3.20
1081 1093 2.132762 TCTCGGTTTCGTTTTCAGAGC 58.867 47.619 0.00 0.00 37.69 4.09
1125 1137 0.042581 TGATGCTGAGGAGGGTGGTA 59.957 55.000 0.00 0.00 0.00 3.25
1297 1309 4.717629 CGCCGCTCGAACACAGGA 62.718 66.667 0.00 0.00 41.67 3.86
1630 1642 0.528470 GAAGTCTGGTCCAGAGGTCG 59.472 60.000 22.46 0.00 41.46 4.79
1682 1694 3.667282 CCACTCCGTCGACCGTGT 61.667 66.667 19.48 13.66 33.66 4.49
1773 1785 0.460987 CAATGGAGGTCGAGCAGTCC 60.461 60.000 18.15 15.95 0.00 3.85
1909 1921 1.974957 TCGATGTGGACAAGGAAGGAA 59.025 47.619 0.00 0.00 0.00 3.36
2031 2043 5.050363 CGAATCTTCCATTTACCGGTATGTG 60.050 44.000 16.67 16.29 0.00 3.21
2056 2068 6.016777 GGATGCATTTACCCAGTCATCTTTAG 60.017 42.308 0.00 0.00 33.03 1.85
2057 2069 5.815581 TGCATTTACCCAGTCATCTTTAGT 58.184 37.500 0.00 0.00 0.00 2.24
2058 2070 5.647658 TGCATTTACCCAGTCATCTTTAGTG 59.352 40.000 0.00 0.00 0.00 2.74
2070 2082 9.469807 CAGTCATCTTTAGTGGTACTATTGATC 57.530 37.037 0.00 0.00 29.64 2.92
2092 2104 5.778862 TCCGAATAAGCGATGATTGTGATA 58.221 37.500 0.00 0.00 0.00 2.15
2096 2108 8.271487 CCGAATAAGCGATGATTGTGATATATG 58.729 37.037 0.00 0.00 0.00 1.78
2107 2119 8.319143 TGATTGTGATATATGTTGAGATGCAG 57.681 34.615 0.00 0.00 0.00 4.41
2132 2144 6.205464 GTGACCATCTTCATTCAGTTCTTCAA 59.795 38.462 0.00 0.00 0.00 2.69
2284 2296 5.910355 TCAGATGGAATGATGGATTGGTA 57.090 39.130 0.00 0.00 0.00 3.25
2341 2353 6.420903 GGATTGTTGCTGTTCTTTCTTTAACC 59.579 38.462 0.00 0.00 0.00 2.85
2589 2693 0.737715 GTGCTGACATGACCTCCGTC 60.738 60.000 0.00 0.00 39.66 4.79
2720 2824 7.491048 AGTTTGCTGGTTTTTGTAAGTTATGTG 59.509 33.333 0.00 0.00 0.00 3.21
2752 2856 6.264771 TGAGATATTGGGTGGAATTGATGA 57.735 37.500 0.00 0.00 0.00 2.92
2758 2862 3.788933 TGGGTGGAATTGATGAATTGGT 58.211 40.909 0.00 0.00 31.58 3.67
2785 2889 1.975660 TGCCCTGTAGTTTTGGTCAC 58.024 50.000 0.00 0.00 0.00 3.67
2864 2968 2.462503 GCAGCCATGGCAATGTTTG 58.537 52.632 37.18 25.55 44.88 2.93
2881 2985 0.820074 TTGCGTGGTGTAAGTTGGGG 60.820 55.000 0.00 0.00 0.00 4.96
2897 3001 2.170166 TGGGGCAATTTGATGAGACAC 58.830 47.619 0.00 0.00 0.00 3.67
2900 3004 2.083774 GGCAATTTGATGAGACACCGA 58.916 47.619 0.00 0.00 0.00 4.69
2925 3029 2.819019 TGAGCTCGAAAATGCCAAATGA 59.181 40.909 9.64 0.00 0.00 2.57
2934 3038 1.755179 ATGCCAAATGAAGACCGAGG 58.245 50.000 0.00 0.00 0.00 4.63
2942 3046 0.252057 TGAAGACCGAGGTCCATGGA 60.252 55.000 11.44 11.44 45.59 3.41
2964 3068 6.072175 TGGAGGTCGTATTTTGAAAAATCCAG 60.072 38.462 4.34 0.00 39.24 3.86
3026 3130 5.357032 AGACGTTTTTGGAGTTCAAAGTGAT 59.643 36.000 0.00 0.00 45.00 3.06
3036 3140 5.460091 GGAGTTCAAAGTGATCTGCAAAAAC 59.540 40.000 0.00 0.00 35.47 2.43
3108 3212 7.164122 AGAAATATGCATGTATCGGAGACATT 58.836 34.615 15.13 4.80 42.51 2.71
3163 3267 5.726397 TGCGTTAAAAGGAGAGCTACATAA 58.274 37.500 0.00 0.00 0.00 1.90
3235 3339 4.377839 TGGTTTCGATTTCTTTGTGCAA 57.622 36.364 0.00 0.00 0.00 4.08
3236 3374 4.942852 TGGTTTCGATTTCTTTGTGCAAT 58.057 34.783 0.00 0.00 0.00 3.56
3279 3418 8.174733 TCTCAAAGCTCATGATTTTCTTTTCT 57.825 30.769 0.00 0.00 28.28 2.52
3309 3448 3.432252 AGTTCGCAAGTCAAGGTATTTCG 59.568 43.478 0.00 0.00 39.48 3.46
3357 3496 9.764363 CACATTACATCCTTGTATACATGTACT 57.236 33.333 7.96 8.32 36.12 2.73
3360 3499 9.998106 ATTACATCCTTGTATACATGTACTTCC 57.002 33.333 7.96 0.00 38.12 3.46
3361 3500 7.676683 ACATCCTTGTATACATGTACTTCCT 57.323 36.000 7.96 0.00 33.16 3.36
3362 3501 7.727181 ACATCCTTGTATACATGTACTTCCTC 58.273 38.462 7.96 0.00 33.16 3.71
3363 3502 7.565398 ACATCCTTGTATACATGTACTTCCTCT 59.435 37.037 7.96 0.00 33.16 3.69
3364 3503 7.348080 TCCTTGTATACATGTACTTCCTCTG 57.652 40.000 7.96 0.00 0.00 3.35
3365 3504 6.895756 TCCTTGTATACATGTACTTCCTCTGT 59.104 38.462 7.96 0.00 0.00 3.41
3366 3505 8.057011 TCCTTGTATACATGTACTTCCTCTGTA 58.943 37.037 7.96 0.00 0.00 2.74
3367 3506 8.692710 CCTTGTATACATGTACTTCCTCTGTAA 58.307 37.037 7.96 0.00 0.00 2.41
3369 3508 9.865321 TTGTATACATGTACTTCCTCTGTAAAC 57.135 33.333 7.96 0.00 0.00 2.01
3370 3509 9.251440 TGTATACATGTACTTCCTCTGTAAACT 57.749 33.333 7.96 0.00 0.00 2.66
3382 3521 9.400638 CTTCCTCTGTAAACTAATATAGAAGCG 57.599 37.037 0.00 0.00 0.00 4.68
3383 3522 8.461249 TCCTCTGTAAACTAATATAGAAGCGT 57.539 34.615 0.00 0.00 0.00 5.07
3384 3523 8.910944 TCCTCTGTAAACTAATATAGAAGCGTT 58.089 33.333 0.00 0.00 0.00 4.84
3385 3524 9.530633 CCTCTGTAAACTAATATAGAAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
3398 3537 9.900710 ATATAGAAGCGTTTAGATCACTACTTG 57.099 33.333 0.00 0.00 0.00 3.16
3399 3538 6.268825 AGAAGCGTTTAGATCACTACTTGA 57.731 37.500 0.00 0.00 39.11 3.02
3400 3539 6.326375 AGAAGCGTTTAGATCACTACTTGAG 58.674 40.000 0.00 0.00 37.77 3.02
3401 3540 5.646577 AGCGTTTAGATCACTACTTGAGT 57.353 39.130 0.00 0.00 37.77 3.41
3402 3541 6.754702 AGCGTTTAGATCACTACTTGAGTA 57.245 37.500 0.00 0.00 37.77 2.59
3403 3542 7.336161 AGCGTTTAGATCACTACTTGAGTAT 57.664 36.000 0.00 0.00 37.77 2.12
3404 3543 7.773149 AGCGTTTAGATCACTACTTGAGTATT 58.227 34.615 0.00 0.00 37.77 1.89
3405 3544 7.916450 AGCGTTTAGATCACTACTTGAGTATTC 59.084 37.037 0.00 0.00 37.77 1.75
3406 3545 7.916450 GCGTTTAGATCACTACTTGAGTATTCT 59.084 37.037 0.00 0.00 37.77 2.40
3412 3551 7.916450 AGATCACTACTTGAGTATTCTAAACGC 59.084 37.037 0.00 0.00 37.77 4.84
3413 3552 7.154435 TCACTACTTGAGTATTCTAAACGCT 57.846 36.000 0.00 0.00 35.64 5.07
3414 3553 7.249147 TCACTACTTGAGTATTCTAAACGCTC 58.751 38.462 0.00 0.00 35.64 5.03
3415 3554 7.120873 TCACTACTTGAGTATTCTAAACGCTCT 59.879 37.037 0.00 0.00 35.64 4.09
3416 3555 7.755822 CACTACTTGAGTATTCTAAACGCTCTT 59.244 37.037 0.00 0.00 35.64 2.85
3417 3556 8.954350 ACTACTTGAGTATTCTAAACGCTCTTA 58.046 33.333 0.00 0.00 36.27 2.10
3418 3557 9.953697 CTACTTGAGTATTCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
3433 3572 8.530269 AACGCTCTTATATTAATTTACGGAGG 57.470 34.615 0.00 0.00 0.00 4.30
3434 3573 7.889469 ACGCTCTTATATTAATTTACGGAGGA 58.111 34.615 0.00 0.00 0.00 3.71
3435 3574 8.362639 ACGCTCTTATATTAATTTACGGAGGAA 58.637 33.333 0.00 0.00 0.00 3.36
3436 3575 8.861101 CGCTCTTATATTAATTTACGGAGGAAG 58.139 37.037 0.00 0.00 0.00 3.46
3437 3576 9.708092 GCTCTTATATTAATTTACGGAGGAAGT 57.292 33.333 0.00 0.00 0.00 3.01
3439 3578 9.991906 TCTTATATTAATTTACGGAGGAAGTGG 57.008 33.333 0.00 0.00 0.00 4.00
3440 3579 8.611654 TTATATTAATTTACGGAGGAAGTGGC 57.388 34.615 0.00 0.00 0.00 5.01
3441 3580 4.563140 TTAATTTACGGAGGAAGTGGCT 57.437 40.909 0.00 0.00 0.00 4.75
3442 3581 3.434940 AATTTACGGAGGAAGTGGCTT 57.565 42.857 0.00 0.00 0.00 4.35
3443 3582 2.943036 TTTACGGAGGAAGTGGCTTT 57.057 45.000 0.00 0.00 0.00 3.51
3444 3583 2.943036 TTACGGAGGAAGTGGCTTTT 57.057 45.000 0.00 0.00 0.00 2.27
3445 3584 2.178912 TACGGAGGAAGTGGCTTTTG 57.821 50.000 0.00 0.00 0.00 2.44
3446 3585 0.182775 ACGGAGGAAGTGGCTTTTGT 59.817 50.000 0.00 0.00 0.00 2.83
3447 3586 0.875059 CGGAGGAAGTGGCTTTTGTC 59.125 55.000 0.00 0.00 0.00 3.18
3448 3587 1.813862 CGGAGGAAGTGGCTTTTGTCA 60.814 52.381 0.00 0.00 0.00 3.58
3449 3588 2.306847 GGAGGAAGTGGCTTTTGTCAA 58.693 47.619 0.00 0.00 34.92 3.18
3450 3589 2.893489 GGAGGAAGTGGCTTTTGTCAAT 59.107 45.455 0.00 0.00 34.92 2.57
3451 3590 3.321968 GGAGGAAGTGGCTTTTGTCAATT 59.678 43.478 0.00 0.00 45.43 2.32
3452 3591 4.522789 GGAGGAAGTGGCTTTTGTCAATTA 59.477 41.667 0.00 0.00 42.67 1.40
3453 3592 5.010617 GGAGGAAGTGGCTTTTGTCAATTAA 59.989 40.000 0.00 0.00 42.67 1.40
3454 3593 6.462347 GGAGGAAGTGGCTTTTGTCAATTAAA 60.462 38.462 0.00 0.00 42.67 1.52
3455 3594 7.066307 AGGAAGTGGCTTTTGTCAATTAAAT 57.934 32.000 0.00 0.00 42.67 1.40
3456 3595 8.189119 AGGAAGTGGCTTTTGTCAATTAAATA 57.811 30.769 0.00 0.00 42.67 1.40
3457 3596 8.306761 AGGAAGTGGCTTTTGTCAATTAAATAG 58.693 33.333 0.00 0.00 42.67 1.73
3458 3597 8.088365 GGAAGTGGCTTTTGTCAATTAAATAGT 58.912 33.333 0.00 0.00 42.67 2.12
3459 3598 9.476202 GAAGTGGCTTTTGTCAATTAAATAGTT 57.524 29.630 0.00 0.00 42.67 2.24
3460 3599 9.476202 AAGTGGCTTTTGTCAATTAAATAGTTC 57.524 29.630 0.00 0.00 40.73 3.01
3461 3600 8.860088 AGTGGCTTTTGTCAATTAAATAGTTCT 58.140 29.630 0.00 0.00 34.92 3.01
3462 3601 9.129209 GTGGCTTTTGTCAATTAAATAGTTCTC 57.871 33.333 0.00 0.00 34.92 2.87
3463 3602 8.303876 TGGCTTTTGTCAATTAAATAGTTCTCC 58.696 33.333 0.00 0.00 0.00 3.71
3464 3603 7.759886 GGCTTTTGTCAATTAAATAGTTCTCCC 59.240 37.037 0.00 0.00 0.00 4.30
3465 3604 7.759886 GCTTTTGTCAATTAAATAGTTCTCCCC 59.240 37.037 0.00 0.00 0.00 4.81
3466 3605 7.712204 TTTGTCAATTAAATAGTTCTCCCCC 57.288 36.000 0.00 0.00 0.00 5.40
3467 3606 6.652205 TGTCAATTAAATAGTTCTCCCCCT 57.348 37.500 0.00 0.00 0.00 4.79
3468 3607 6.659824 TGTCAATTAAATAGTTCTCCCCCTC 58.340 40.000 0.00 0.00 0.00 4.30
3469 3608 6.062749 GTCAATTAAATAGTTCTCCCCCTCC 58.937 44.000 0.00 0.00 0.00 4.30
3470 3609 5.133830 TCAATTAAATAGTTCTCCCCCTCCC 59.866 44.000 0.00 0.00 0.00 4.30
3471 3610 1.508256 AAATAGTTCTCCCCCTCCCG 58.492 55.000 0.00 0.00 0.00 5.14
3472 3611 0.640495 AATAGTTCTCCCCCTCCCGA 59.360 55.000 0.00 0.00 0.00 5.14
3473 3612 0.188834 ATAGTTCTCCCCCTCCCGAG 59.811 60.000 0.00 0.00 0.00 4.63
3474 3613 2.584873 TAGTTCTCCCCCTCCCGAGC 62.585 65.000 0.00 0.00 0.00 5.03
3475 3614 4.798682 TTCTCCCCCTCCCGAGCC 62.799 72.222 0.00 0.00 0.00 4.70
3513 3652 2.451294 GGAGGCCCCAGATCCCAT 60.451 66.667 0.00 0.00 34.14 4.00
3514 3653 2.533463 GGAGGCCCCAGATCCCATC 61.533 68.421 0.00 0.00 34.14 3.51
3515 3654 2.851102 AGGCCCCAGATCCCATCG 60.851 66.667 0.00 0.00 0.00 3.84
3516 3655 3.958860 GGCCCCAGATCCCATCGG 61.959 72.222 0.00 0.00 0.00 4.18
3517 3656 4.650377 GCCCCAGATCCCATCGGC 62.650 72.222 0.00 0.00 0.00 5.54
3518 3657 3.958860 CCCCAGATCCCATCGGCC 61.959 72.222 0.00 0.00 0.00 6.13
3519 3658 4.320456 CCCAGATCCCATCGGCCG 62.320 72.222 22.12 22.12 0.00 6.13
3520 3659 4.320456 CCAGATCCCATCGGCCGG 62.320 72.222 27.83 10.29 0.00 6.13
3521 3660 3.233980 CAGATCCCATCGGCCGGA 61.234 66.667 27.83 15.37 0.00 5.14
3522 3661 3.234730 AGATCCCATCGGCCGGAC 61.235 66.667 27.83 0.00 0.00 4.79
3523 3662 4.315941 GATCCCATCGGCCGGACC 62.316 72.222 27.83 4.99 0.00 4.46
3524 3663 4.880426 ATCCCATCGGCCGGACCT 62.880 66.667 27.83 4.82 35.61 3.85
3535 3674 4.400251 CGGACCTCCCCCACTCCT 62.400 72.222 0.00 0.00 0.00 3.69
3536 3675 2.365768 GGACCTCCCCCACTCCTC 60.366 72.222 0.00 0.00 0.00 3.71
3537 3676 2.365768 GACCTCCCCCACTCCTCC 60.366 72.222 0.00 0.00 0.00 4.30
3538 3677 2.876858 ACCTCCCCCACTCCTCCT 60.877 66.667 0.00 0.00 0.00 3.69
3539 3678 2.456840 CCTCCCCCACTCCTCCTT 59.543 66.667 0.00 0.00 0.00 3.36
3540 3679 1.690985 CCTCCCCCACTCCTCCTTC 60.691 68.421 0.00 0.00 0.00 3.46
3541 3680 1.394151 CTCCCCCACTCCTCCTTCT 59.606 63.158 0.00 0.00 0.00 2.85
3542 3681 0.689412 CTCCCCCACTCCTCCTTCTC 60.689 65.000 0.00 0.00 0.00 2.87
3543 3682 1.690985 CCCCCACTCCTCCTTCTCC 60.691 68.421 0.00 0.00 0.00 3.71
3544 3683 1.394151 CCCCACTCCTCCTTCTCCT 59.606 63.158 0.00 0.00 0.00 3.69
3545 3684 0.689412 CCCCACTCCTCCTTCTCCTC 60.689 65.000 0.00 0.00 0.00 3.71
3546 3685 0.689412 CCCACTCCTCCTTCTCCTCC 60.689 65.000 0.00 0.00 0.00 4.30
3547 3686 0.689412 CCACTCCTCCTTCTCCTCCC 60.689 65.000 0.00 0.00 0.00 4.30
3548 3687 0.338120 CACTCCTCCTTCTCCTCCCT 59.662 60.000 0.00 0.00 0.00 4.20
3549 3688 0.634465 ACTCCTCCTTCTCCTCCCTC 59.366 60.000 0.00 0.00 0.00 4.30
3550 3689 0.467290 CTCCTCCTTCTCCTCCCTCG 60.467 65.000 0.00 0.00 0.00 4.63
3551 3690 1.215679 TCCTCCTTCTCCTCCCTCGT 61.216 60.000 0.00 0.00 0.00 4.18
3552 3691 0.753848 CCTCCTTCTCCTCCCTCGTC 60.754 65.000 0.00 0.00 0.00 4.20
3553 3692 0.033991 CTCCTTCTCCTCCCTCGTCA 60.034 60.000 0.00 0.00 0.00 4.35
3554 3693 0.323542 TCCTTCTCCTCCCTCGTCAC 60.324 60.000 0.00 0.00 0.00 3.67
3555 3694 1.324005 CCTTCTCCTCCCTCGTCACC 61.324 65.000 0.00 0.00 0.00 4.02
3556 3695 1.658686 CTTCTCCTCCCTCGTCACCG 61.659 65.000 0.00 0.00 0.00 4.94
3557 3696 3.141488 CTCCTCCCTCGTCACCGG 61.141 72.222 0.00 0.00 33.95 5.28
3581 3720 4.444081 CGGGGTCTCGGGTCCTCT 62.444 72.222 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.545615 GCCCATATTTTTCAAGACCTAAGTTTG 59.454 37.037 0.00 0.00 0.00 2.93
1 2 7.576856 CGCCCATATTTTTCAAGACCTAAGTTT 60.577 37.037 0.00 0.00 0.00 2.66
3 4 5.357032 CGCCCATATTTTTCAAGACCTAAGT 59.643 40.000 0.00 0.00 0.00 2.24
4 5 5.221048 CCGCCCATATTTTTCAAGACCTAAG 60.221 44.000 0.00 0.00 0.00 2.18
5 6 4.642885 CCGCCCATATTTTTCAAGACCTAA 59.357 41.667 0.00 0.00 0.00 2.69
6 7 4.080243 TCCGCCCATATTTTTCAAGACCTA 60.080 41.667 0.00 0.00 0.00 3.08
7 8 3.023832 CCGCCCATATTTTTCAAGACCT 58.976 45.455 0.00 0.00 0.00 3.85
8 9 3.020984 TCCGCCCATATTTTTCAAGACC 58.979 45.455 0.00 0.00 0.00 3.85
9 10 3.694566 AGTCCGCCCATATTTTTCAAGAC 59.305 43.478 0.00 0.00 0.00 3.01
10 11 3.963129 AGTCCGCCCATATTTTTCAAGA 58.037 40.909 0.00 0.00 0.00 3.02
11 12 4.638421 TGTAGTCCGCCCATATTTTTCAAG 59.362 41.667 0.00 0.00 0.00 3.02
12 13 4.590918 TGTAGTCCGCCCATATTTTTCAA 58.409 39.130 0.00 0.00 0.00 2.69
13 14 4.223556 TGTAGTCCGCCCATATTTTTCA 57.776 40.909 0.00 0.00 0.00 2.69
14 15 4.819630 TCATGTAGTCCGCCCATATTTTTC 59.180 41.667 0.00 0.00 0.00 2.29
15 16 4.787551 TCATGTAGTCCGCCCATATTTTT 58.212 39.130 0.00 0.00 0.00 1.94
16 17 4.431416 TCATGTAGTCCGCCCATATTTT 57.569 40.909 0.00 0.00 0.00 1.82
17 18 4.326826 CATCATGTAGTCCGCCCATATTT 58.673 43.478 0.00 0.00 0.00 1.40
18 19 3.307691 CCATCATGTAGTCCGCCCATATT 60.308 47.826 0.00 0.00 0.00 1.28
19 20 2.237143 CCATCATGTAGTCCGCCCATAT 59.763 50.000 0.00 0.00 0.00 1.78
20 21 1.623311 CCATCATGTAGTCCGCCCATA 59.377 52.381 0.00 0.00 0.00 2.74
21 22 0.397941 CCATCATGTAGTCCGCCCAT 59.602 55.000 0.00 0.00 0.00 4.00
22 23 0.689412 TCCATCATGTAGTCCGCCCA 60.689 55.000 0.00 0.00 0.00 5.36
23 24 0.468226 TTCCATCATGTAGTCCGCCC 59.532 55.000 0.00 0.00 0.00 6.13
24 25 1.583054 GTTCCATCATGTAGTCCGCC 58.417 55.000 0.00 0.00 0.00 6.13
25 26 1.202371 TCGTTCCATCATGTAGTCCGC 60.202 52.381 0.00 0.00 0.00 5.54
26 27 2.460918 GTCGTTCCATCATGTAGTCCG 58.539 52.381 0.00 0.00 0.00 4.79
27 28 2.098607 TCGTCGTTCCATCATGTAGTCC 59.901 50.000 0.00 0.00 0.00 3.85
28 29 3.064958 TCTCGTCGTTCCATCATGTAGTC 59.935 47.826 0.00 0.00 0.00 2.59
29 30 3.014623 TCTCGTCGTTCCATCATGTAGT 58.985 45.455 0.00 0.00 0.00 2.73
30 31 3.065510 ACTCTCGTCGTTCCATCATGTAG 59.934 47.826 0.00 0.00 0.00 2.74
31 32 3.014623 ACTCTCGTCGTTCCATCATGTA 58.985 45.455 0.00 0.00 0.00 2.29
32 33 1.819288 ACTCTCGTCGTTCCATCATGT 59.181 47.619 0.00 0.00 0.00 3.21
33 34 2.568696 ACTCTCGTCGTTCCATCATG 57.431 50.000 0.00 0.00 0.00 3.07
34 35 3.542648 TCTACTCTCGTCGTTCCATCAT 58.457 45.455 0.00 0.00 0.00 2.45
35 36 2.981898 TCTACTCTCGTCGTTCCATCA 58.018 47.619 0.00 0.00 0.00 3.07
36 37 4.555348 AATCTACTCTCGTCGTTCCATC 57.445 45.455 0.00 0.00 0.00 3.51
37 38 4.985538 AAATCTACTCTCGTCGTTCCAT 57.014 40.909 0.00 0.00 0.00 3.41
38 39 4.778534 AAAATCTACTCTCGTCGTTCCA 57.221 40.909 0.00 0.00 0.00 3.53
62 63 1.557371 TCATGGCACGTTGGATCCTAA 59.443 47.619 14.23 2.83 0.00 2.69
69 70 1.167851 AGATTGTCATGGCACGTTGG 58.832 50.000 0.00 0.00 0.00 3.77
73 74 2.615447 AGCATTAGATTGTCATGGCACG 59.385 45.455 0.00 0.00 0.00 5.34
90 91 6.029607 CACACAAATAGAAAATACGCAGCAT 58.970 36.000 0.00 0.00 0.00 3.79
123 126 2.239654 CCTACTGGACATCCACACCATT 59.760 50.000 0.00 0.00 42.01 3.16
124 127 1.839994 CCTACTGGACATCCACACCAT 59.160 52.381 0.00 0.00 42.01 3.55
125 128 1.275666 CCTACTGGACATCCACACCA 58.724 55.000 0.00 0.00 42.01 4.17
126 129 0.107654 GCCTACTGGACATCCACACC 60.108 60.000 0.00 0.00 42.01 4.16
235 239 4.498009 CGTGCAGACTCTTTTTCCACAATT 60.498 41.667 0.00 0.00 0.00 2.32
236 240 3.003689 CGTGCAGACTCTTTTTCCACAAT 59.996 43.478 0.00 0.00 0.00 2.71
237 241 2.354510 CGTGCAGACTCTTTTTCCACAA 59.645 45.455 0.00 0.00 0.00 3.33
319 323 7.491372 GCAAAATCTGTACTGCATGTAGTAGTA 59.509 37.037 22.15 13.88 41.71 1.82
320 324 6.313905 GCAAAATCTGTACTGCATGTAGTAGT 59.686 38.462 22.15 10.71 45.62 2.73
321 325 6.313658 TGCAAAATCTGTACTGCATGTAGTAG 59.686 38.462 22.15 14.39 39.77 2.57
331 335 5.391950 GGTGGTACATGCAAAATCTGTACTG 60.392 44.000 20.97 1.95 44.52 2.74
386 391 2.534349 GTGTAGCCACGTCGTATCAATG 59.466 50.000 0.00 0.00 0.00 2.82
499 504 4.486503 GAGCAGGAGCAGGGGCAG 62.487 72.222 0.00 0.00 45.49 4.85
560 565 0.800300 CGCTTCTCTCTCTTGCGTCC 60.800 60.000 0.00 0.00 41.45 4.79
730 736 2.725450 CGATCGCTCTCGCTCAGC 60.725 66.667 0.26 0.00 30.92 4.26
731 737 1.082821 CTCGATCGCTCTCGCTCAG 60.083 63.158 11.09 0.00 38.52 3.35
732 738 2.538448 CCTCGATCGCTCTCGCTCA 61.538 63.158 11.09 0.00 38.52 4.26
850 861 0.600557 CGGATGAGGAGGAATCTCGG 59.399 60.000 0.00 0.00 40.85 4.63
851 862 0.600557 CCGGATGAGGAGGAATCTCG 59.399 60.000 0.00 0.00 40.85 4.04
996 1008 5.527951 ACTAAAAAGCAATCACGCATCAAA 58.472 33.333 0.00 0.00 0.00 2.69
1064 1076 0.721483 GCGCTCTGAAAACGAAACCG 60.721 55.000 0.00 0.00 0.00 4.44
1290 1302 3.637273 GCGGGGAAGGTCCTGTGT 61.637 66.667 0.00 0.00 36.57 3.72
1630 1642 1.664965 GAGCACCACTGGACACGAC 60.665 63.158 0.71 0.00 0.00 4.34
1682 1694 1.374947 CCGGAAGCAGGGAACTTGA 59.625 57.895 0.00 0.00 40.21 3.02
1773 1785 0.817654 TGATGCAGGTGTAGTCCTCG 59.182 55.000 0.00 0.00 35.37 4.63
1909 1921 1.344763 GACCAGCCAGTACAACTCAGT 59.655 52.381 0.00 0.00 0.00 3.41
2031 2043 3.825328 AGATGACTGGGTAAATGCATCC 58.175 45.455 0.00 0.00 34.26 3.51
2056 2068 5.345202 CGCTTATTCGGATCAATAGTACCAC 59.655 44.000 0.00 0.00 0.00 4.16
2057 2069 5.242171 TCGCTTATTCGGATCAATAGTACCA 59.758 40.000 0.00 0.00 0.00 3.25
2058 2070 5.706916 TCGCTTATTCGGATCAATAGTACC 58.293 41.667 0.00 0.00 0.00 3.34
2070 2082 4.997905 ATCACAATCATCGCTTATTCGG 57.002 40.909 0.00 0.00 0.00 4.30
2092 2104 4.492494 TGGTCACTGCATCTCAACATAT 57.508 40.909 0.00 0.00 0.00 1.78
2096 2108 2.983229 AGATGGTCACTGCATCTCAAC 58.017 47.619 0.00 0.00 30.63 3.18
2107 2119 5.702670 TGAAGAACTGAATGAAGATGGTCAC 59.297 40.000 0.00 0.00 0.00 3.67
2132 2144 5.754782 TGTATGTAGGTGATGCAAATTCCT 58.245 37.500 0.00 0.00 0.00 3.36
2250 2262 7.506328 TCATTCCATCTGAAGAGCAATTATG 57.494 36.000 0.00 0.00 36.14 1.90
2341 2353 6.347321 GCCCATTTCATTTTTAACTTGGTTCG 60.347 38.462 0.00 0.00 0.00 3.95
2589 2693 1.565390 TTGGTCAGGCATCAGGGGAG 61.565 60.000 0.00 0.00 0.00 4.30
2720 2824 3.624861 CACCCAATATCTCAACTGCTGAC 59.375 47.826 0.00 0.00 0.00 3.51
2752 2856 0.032813 AGGGCATGCAGCTACCAATT 60.033 50.000 21.36 0.00 44.79 2.32
2758 2862 0.911769 AACTACAGGGCATGCAGCTA 59.088 50.000 21.36 1.85 44.79 3.32
2785 2889 3.119531 TCATAATCGCCAAAACTGCCTTG 60.120 43.478 0.00 0.00 0.00 3.61
2864 2968 2.622962 GCCCCAACTTACACCACGC 61.623 63.158 0.00 0.00 0.00 5.34
2869 2973 4.021544 TCATCAAATTGCCCCAACTTACAC 60.022 41.667 0.00 0.00 0.00 2.90
2881 2985 2.483877 TGTCGGTGTCTCATCAAATTGC 59.516 45.455 0.00 0.00 0.00 3.56
2897 3001 2.789092 GCATTTTCGAGCTCAATGTCGG 60.789 50.000 20.35 2.40 36.81 4.79
2900 3004 2.161855 TGGCATTTTCGAGCTCAATGT 58.838 42.857 20.35 0.00 31.60 2.71
2925 3029 0.978146 CCTCCATGGACCTCGGTCTT 60.978 60.000 11.44 1.74 44.04 3.01
2934 3038 3.869065 TCAAAATACGACCTCCATGGAC 58.131 45.455 11.44 0.00 39.71 4.02
2942 3046 7.519032 TTCTGGATTTTTCAAAATACGACCT 57.481 32.000 3.32 0.00 41.20 3.85
2991 3095 9.675464 AACTCCAAAAACGTCTTATATTATGGA 57.325 29.630 0.00 0.00 0.00 3.41
2999 3103 7.066525 TCACTTTGAACTCCAAAAACGTCTTAT 59.933 33.333 0.00 0.00 43.50 1.73
3026 3130 6.348950 CCCATAATGTAAGACGTTTTTGCAGA 60.349 38.462 0.00 0.00 0.00 4.26
3036 3140 4.099573 ACCTCTGTCCCATAATGTAAGACG 59.900 45.833 0.00 0.00 0.00 4.18
3084 3188 6.974932 ATGTCTCCGATACATGCATATTTC 57.025 37.500 0.00 0.00 36.24 2.17
3090 3194 4.990426 CACATAATGTCTCCGATACATGCA 59.010 41.667 0.47 0.00 37.62 3.96
3095 3199 3.425525 CGTGCACATAATGTCTCCGATAC 59.574 47.826 18.64 0.00 0.00 2.24
3108 3212 7.708752 TCATGAAGATTTACATACGTGCACATA 59.291 33.333 18.64 6.32 0.00 2.29
3235 3339 4.082625 TGAGAATGAACTTGCATTGCGAAT 60.083 37.500 3.84 0.00 38.53 3.34
3236 3374 3.252944 TGAGAATGAACTTGCATTGCGAA 59.747 39.130 3.84 0.00 38.53 4.70
3309 3448 6.799441 TGTGTATGCGTGTAAAATTTCATGAC 59.201 34.615 0.00 0.00 0.00 3.06
3357 3496 8.910944 ACGCTTCTATATTAGTTTACAGAGGAA 58.089 33.333 0.00 0.00 0.00 3.36
3358 3497 8.461249 ACGCTTCTATATTAGTTTACAGAGGA 57.539 34.615 0.00 0.00 0.00 3.71
3359 3498 9.530633 AAACGCTTCTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
3372 3511 9.900710 CAAGTAGTGATCTAAACGCTTCTATAT 57.099 33.333 0.00 0.00 0.00 0.86
3373 3512 9.117183 TCAAGTAGTGATCTAAACGCTTCTATA 57.883 33.333 0.00 0.00 0.00 1.31
3374 3513 7.997482 TCAAGTAGTGATCTAAACGCTTCTAT 58.003 34.615 0.00 0.00 0.00 1.98
3375 3514 7.120873 ACTCAAGTAGTGATCTAAACGCTTCTA 59.879 37.037 0.00 0.00 36.93 2.10
3376 3515 6.071840 ACTCAAGTAGTGATCTAAACGCTTCT 60.072 38.462 0.00 0.00 36.93 2.85
3377 3516 6.094061 ACTCAAGTAGTGATCTAAACGCTTC 58.906 40.000 0.00 0.00 36.93 3.86
3378 3517 6.026947 ACTCAAGTAGTGATCTAAACGCTT 57.973 37.500 0.00 0.00 36.93 4.68
3379 3518 5.646577 ACTCAAGTAGTGATCTAAACGCT 57.353 39.130 0.00 0.00 36.93 5.07
3380 3519 7.916450 AGAATACTCAAGTAGTGATCTAAACGC 59.084 37.037 0.00 0.00 39.39 4.84
3386 3525 7.916450 GCGTTTAGAATACTCAAGTAGTGATCT 59.084 37.037 0.00 0.34 39.39 2.75
3387 3526 7.916450 AGCGTTTAGAATACTCAAGTAGTGATC 59.084 37.037 0.00 0.00 39.39 2.92
3388 3527 7.773149 AGCGTTTAGAATACTCAAGTAGTGAT 58.227 34.615 0.00 0.00 39.39 3.06
3389 3528 7.120873 AGAGCGTTTAGAATACTCAAGTAGTGA 59.879 37.037 0.00 0.00 39.39 3.41
3390 3529 7.251994 AGAGCGTTTAGAATACTCAAGTAGTG 58.748 38.462 0.00 0.00 39.39 2.74
3391 3530 7.393841 AGAGCGTTTAGAATACTCAAGTAGT 57.606 36.000 0.00 0.00 42.62 2.73
3392 3531 9.953697 ATAAGAGCGTTTAGAATACTCAAGTAG 57.046 33.333 0.00 0.00 33.52 2.57
3407 3546 8.985805 CCTCCGTAAATTAATATAAGAGCGTTT 58.014 33.333 0.00 0.00 0.00 3.60
3408 3547 8.362639 TCCTCCGTAAATTAATATAAGAGCGTT 58.637 33.333 0.00 0.00 0.00 4.84
3409 3548 7.889469 TCCTCCGTAAATTAATATAAGAGCGT 58.111 34.615 0.00 0.00 0.00 5.07
3410 3549 8.752766 TTCCTCCGTAAATTAATATAAGAGCG 57.247 34.615 0.00 0.00 0.00 5.03
3411 3550 9.708092 ACTTCCTCCGTAAATTAATATAAGAGC 57.292 33.333 0.00 0.00 0.00 4.09
3413 3552 9.991906 CCACTTCCTCCGTAAATTAATATAAGA 57.008 33.333 0.00 0.00 0.00 2.10
3414 3553 8.718734 GCCACTTCCTCCGTAAATTAATATAAG 58.281 37.037 0.00 0.00 0.00 1.73
3415 3554 8.434392 AGCCACTTCCTCCGTAAATTAATATAA 58.566 33.333 0.00 0.00 0.00 0.98
3416 3555 7.970102 AGCCACTTCCTCCGTAAATTAATATA 58.030 34.615 0.00 0.00 0.00 0.86
3417 3556 6.838382 AGCCACTTCCTCCGTAAATTAATAT 58.162 36.000 0.00 0.00 0.00 1.28
3418 3557 6.243216 AGCCACTTCCTCCGTAAATTAATA 57.757 37.500 0.00 0.00 0.00 0.98
3419 3558 5.112129 AGCCACTTCCTCCGTAAATTAAT 57.888 39.130 0.00 0.00 0.00 1.40
3420 3559 4.563140 AGCCACTTCCTCCGTAAATTAA 57.437 40.909 0.00 0.00 0.00 1.40
3421 3560 4.563140 AAGCCACTTCCTCCGTAAATTA 57.437 40.909 0.00 0.00 0.00 1.40
3422 3561 3.434940 AAGCCACTTCCTCCGTAAATT 57.565 42.857 0.00 0.00 0.00 1.82
3423 3562 3.434940 AAAGCCACTTCCTCCGTAAAT 57.565 42.857 0.00 0.00 0.00 1.40
3424 3563 2.882137 CAAAAGCCACTTCCTCCGTAAA 59.118 45.455 0.00 0.00 0.00 2.01
3425 3564 2.158726 ACAAAAGCCACTTCCTCCGTAA 60.159 45.455 0.00 0.00 0.00 3.18
3426 3565 1.418637 ACAAAAGCCACTTCCTCCGTA 59.581 47.619 0.00 0.00 0.00 4.02
3427 3566 0.182775 ACAAAAGCCACTTCCTCCGT 59.817 50.000 0.00 0.00 0.00 4.69
3428 3567 0.875059 GACAAAAGCCACTTCCTCCG 59.125 55.000 0.00 0.00 0.00 4.63
3429 3568 1.981256 TGACAAAAGCCACTTCCTCC 58.019 50.000 0.00 0.00 0.00 4.30
3430 3569 4.590850 AATTGACAAAAGCCACTTCCTC 57.409 40.909 0.00 0.00 0.00 3.71
3431 3570 6.478512 TTTAATTGACAAAAGCCACTTCCT 57.521 33.333 0.00 0.00 0.00 3.36
3432 3571 8.088365 ACTATTTAATTGACAAAAGCCACTTCC 58.912 33.333 0.00 0.00 0.00 3.46
3433 3572 9.476202 AACTATTTAATTGACAAAAGCCACTTC 57.524 29.630 0.00 0.00 0.00 3.01
3434 3573 9.476202 GAACTATTTAATTGACAAAAGCCACTT 57.524 29.630 0.00 0.00 0.00 3.16
3435 3574 8.860088 AGAACTATTTAATTGACAAAAGCCACT 58.140 29.630 0.00 0.00 0.00 4.00
3436 3575 9.129209 GAGAACTATTTAATTGACAAAAGCCAC 57.871 33.333 0.00 0.00 0.00 5.01
3437 3576 8.303876 GGAGAACTATTTAATTGACAAAAGCCA 58.696 33.333 0.00 0.00 0.00 4.75
3438 3577 7.759886 GGGAGAACTATTTAATTGACAAAAGCC 59.240 37.037 0.00 0.00 0.00 4.35
3439 3578 7.759886 GGGGAGAACTATTTAATTGACAAAAGC 59.240 37.037 0.00 0.00 0.00 3.51
3440 3579 8.251026 GGGGGAGAACTATTTAATTGACAAAAG 58.749 37.037 0.00 0.00 0.00 2.27
3441 3580 7.953493 AGGGGGAGAACTATTTAATTGACAAAA 59.047 33.333 0.00 0.00 0.00 2.44
3442 3581 7.475299 AGGGGGAGAACTATTTAATTGACAAA 58.525 34.615 0.00 0.00 0.00 2.83
3443 3582 7.039722 AGGGGGAGAACTATTTAATTGACAA 57.960 36.000 0.00 0.00 0.00 3.18
3444 3583 6.353602 GGAGGGGGAGAACTATTTAATTGACA 60.354 42.308 0.00 0.00 0.00 3.58
3445 3584 6.062749 GGAGGGGGAGAACTATTTAATTGAC 58.937 44.000 0.00 0.00 0.00 3.18
3446 3585 5.133830 GGGAGGGGGAGAACTATTTAATTGA 59.866 44.000 0.00 0.00 0.00 2.57
3447 3586 5.386060 GGGAGGGGGAGAACTATTTAATTG 58.614 45.833 0.00 0.00 0.00 2.32
3448 3587 4.104261 CGGGAGGGGGAGAACTATTTAATT 59.896 45.833 0.00 0.00 0.00 1.40
3449 3588 3.651423 CGGGAGGGGGAGAACTATTTAAT 59.349 47.826 0.00 0.00 0.00 1.40
3450 3589 3.043418 CGGGAGGGGGAGAACTATTTAA 58.957 50.000 0.00 0.00 0.00 1.52
3451 3590 2.248160 TCGGGAGGGGGAGAACTATTTA 59.752 50.000 0.00 0.00 0.00 1.40
3452 3591 1.009183 TCGGGAGGGGGAGAACTATTT 59.991 52.381 0.00 0.00 0.00 1.40
3453 3592 0.640495 TCGGGAGGGGGAGAACTATT 59.360 55.000 0.00 0.00 0.00 1.73
3454 3593 0.188834 CTCGGGAGGGGGAGAACTAT 59.811 60.000 0.00 0.00 31.90 2.12
3455 3594 1.619143 CTCGGGAGGGGGAGAACTA 59.381 63.158 0.00 0.00 31.90 2.24
3456 3595 2.364961 CTCGGGAGGGGGAGAACT 59.635 66.667 0.00 0.00 31.90 3.01
3457 3596 3.471806 GCTCGGGAGGGGGAGAAC 61.472 72.222 0.00 0.00 31.90 3.01
3458 3597 4.798682 GGCTCGGGAGGGGGAGAA 62.799 72.222 0.00 0.00 31.90 2.87
3496 3635 2.451294 ATGGGATCTGGGGCCTCC 60.451 66.667 0.00 0.00 0.00 4.30
3497 3636 2.888447 CGATGGGATCTGGGGCCTC 61.888 68.421 0.84 0.00 0.00 4.70
3498 3637 2.851102 CGATGGGATCTGGGGCCT 60.851 66.667 0.84 0.00 0.00 5.19
3499 3638 3.958860 CCGATGGGATCTGGGGCC 61.959 72.222 0.00 0.00 34.06 5.80
3500 3639 4.650377 GCCGATGGGATCTGGGGC 62.650 72.222 0.00 0.00 34.06 5.80
3501 3640 3.958860 GGCCGATGGGATCTGGGG 61.959 72.222 0.00 0.00 34.06 4.96
3502 3641 4.320456 CGGCCGATGGGATCTGGG 62.320 72.222 24.07 0.00 34.06 4.45
3503 3642 4.320456 CCGGCCGATGGGATCTGG 62.320 72.222 30.73 0.44 34.06 3.86
3504 3643 3.233980 TCCGGCCGATGGGATCTG 61.234 66.667 30.73 6.27 34.06 2.90
3505 3644 3.234730 GTCCGGCCGATGGGATCT 61.235 66.667 30.73 0.00 34.25 2.75
3506 3645 4.315941 GGTCCGGCCGATGGGATC 62.316 72.222 30.73 12.23 34.25 3.36
3507 3646 4.880426 AGGTCCGGCCGATGGGAT 62.880 66.667 30.73 3.94 43.70 3.85
3518 3657 4.400251 AGGAGTGGGGGAGGTCCG 62.400 72.222 0.00 0.00 36.71 4.79
3519 3658 2.365768 GAGGAGTGGGGGAGGTCC 60.366 72.222 0.00 0.00 0.00 4.46
3520 3659 2.365768 GGAGGAGTGGGGGAGGTC 60.366 72.222 0.00 0.00 0.00 3.85
3521 3660 2.478722 GAAGGAGGAGTGGGGGAGGT 62.479 65.000 0.00 0.00 0.00 3.85
3522 3661 1.690985 GAAGGAGGAGTGGGGGAGG 60.691 68.421 0.00 0.00 0.00 4.30
3523 3662 0.689412 GAGAAGGAGGAGTGGGGGAG 60.689 65.000 0.00 0.00 0.00 4.30
3524 3663 1.392534 GAGAAGGAGGAGTGGGGGA 59.607 63.158 0.00 0.00 0.00 4.81
3525 3664 1.690985 GGAGAAGGAGGAGTGGGGG 60.691 68.421 0.00 0.00 0.00 5.40
3526 3665 0.689412 GAGGAGAAGGAGGAGTGGGG 60.689 65.000 0.00 0.00 0.00 4.96
3527 3666 0.689412 GGAGGAGAAGGAGGAGTGGG 60.689 65.000 0.00 0.00 0.00 4.61
3528 3667 0.689412 GGGAGGAGAAGGAGGAGTGG 60.689 65.000 0.00 0.00 0.00 4.00
3529 3668 0.338120 AGGGAGGAGAAGGAGGAGTG 59.662 60.000 0.00 0.00 0.00 3.51
3530 3669 0.634465 GAGGGAGGAGAAGGAGGAGT 59.366 60.000 0.00 0.00 0.00 3.85
3531 3670 0.467290 CGAGGGAGGAGAAGGAGGAG 60.467 65.000 0.00 0.00 0.00 3.69
3532 3671 1.215679 ACGAGGGAGGAGAAGGAGGA 61.216 60.000 0.00 0.00 0.00 3.71
3533 3672 0.753848 GACGAGGGAGGAGAAGGAGG 60.754 65.000 0.00 0.00 0.00 4.30
3534 3673 0.033991 TGACGAGGGAGGAGAAGGAG 60.034 60.000 0.00 0.00 0.00 3.69
3535 3674 0.323542 GTGACGAGGGAGGAGAAGGA 60.324 60.000 0.00 0.00 0.00 3.36
3536 3675 1.324005 GGTGACGAGGGAGGAGAAGG 61.324 65.000 0.00 0.00 0.00 3.46
3537 3676 2.194460 GGTGACGAGGGAGGAGAAG 58.806 63.158 0.00 0.00 0.00 2.85
3538 3677 4.436368 GGTGACGAGGGAGGAGAA 57.564 61.111 0.00 0.00 0.00 2.87
3564 3703 4.444081 AGAGGACCCGAGACCCCG 62.444 72.222 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.