Multiple sequence alignment - TraesCS1B01G319100

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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 TraesCS1B01G319100 chr1B 100.000 4430 0 0 562 4991 543477476 543473047 0.000000e+00 8181
1 TraesCS1B01G319100 chr1B 100.000 252 0 0 1 252 543478037 543477786 2.720000e-127 466
2 TraesCS1B01G319100 chr1A 92.382 3439 178 34 863 4246 499635337 499631928 0.000000e+00 4822
3 TraesCS1B01G319100 chr1A 92.222 180 4 6 77 252 499635941 499635768 3.860000e-61 246
4 TraesCS1B01G319100 chr1A 81.544 298 33 14 562 847 499635682 499635395 5.030000e-55 226
5 TraesCS1B01G319100 chr1D 92.630 2171 125 18 2108 4262 404061442 404059291 0.000000e+00 3090
6 TraesCS1B01G319100 chr1D 91.797 1280 52 16 848 2099 404062740 404061486 0.000000e+00 1733
7 TraesCS1B01G319100 chr1D 84.314 306 32 12 565 858 404063066 404062765 8.180000e-73 285
8 TraesCS1B01G319100 chr1D 87.192 203 13 7 59 252 404063363 404063165 8.410000e-53 219
9 TraesCS1B01G319100 chr5D 82.798 1151 118 47 902 2014 393455374 393456482 0.000000e+00 955
10 TraesCS1B01G319100 chr5D 81.711 935 128 30 2524 3428 393457095 393458016 0.000000e+00 739
11 TraesCS1B01G319100 chr5D 81.070 243 40 5 2123 2362 393456509 393456748 6.600000e-44 189
12 TraesCS1B01G319100 chr5D 95.000 120 6 0 3693 3812 393458303 393458422 6.600000e-44 189
13 TraesCS1B01G319100 chr5D 76.901 355 41 25 3870 4205 393458456 393458788 4.000000e-36 163
14 TraesCS1B01G319100 chr5B 81.983 938 122 33 2523 3428 473176909 473177831 0.000000e+00 752
15 TraesCS1B01G319100 chr5B 88.601 579 54 3 4364 4930 100033316 100033894 0.000000e+00 693
16 TraesCS1B01G319100 chr5B 87.257 565 55 13 1455 2014 473175746 473176298 3.280000e-176 628
17 TraesCS1B01G319100 chr5B 81.852 540 64 16 912 1448 473175198 473175706 1.660000e-114 424
18 TraesCS1B01G319100 chr5B 81.702 235 41 2 2128 2362 473176331 473176563 1.420000e-45 195
19 TraesCS1B01G319100 chr5B 95.000 120 6 0 3693 3812 473178118 473178237 6.600000e-44 189
20 TraesCS1B01G319100 chr5B 76.630 368 40 27 3870 4217 473178271 473178612 1.440000e-35 161
21 TraesCS1B01G319100 chr4D 88.835 618 56 7 4370 4979 464374114 464373502 0.000000e+00 747
22 TraesCS1B01G319100 chr3B 77.883 1266 197 55 1596 2813 758332962 758334192 0.000000e+00 710
23 TraesCS1B01G319100 chr5A 80.835 934 139 29 2523 3428 495320950 495321871 0.000000e+00 697
24 TraesCS1B01G319100 chr5A 87.189 562 57 13 1458 2014 495319847 495320398 4.240000e-175 625
25 TraesCS1B01G319100 chr5A 81.728 602 71 22 850 1448 495319238 495319803 2.720000e-127 466
26 TraesCS1B01G319100 chr5A 77.349 415 67 17 2128 2519 495320431 495320841 2.340000e-53 220
27 TraesCS1B01G319100 chr5A 96.429 112 4 0 3701 3812 495322105 495322216 8.530000e-43 185
28 TraesCS1B01G319100 chr5A 75.741 371 39 27 3870 4217 495322250 495322592 6.740000e-29 139
29 TraesCS1B01G319100 chr6A 82.955 704 86 19 1595 2283 580184998 580185682 5.530000e-169 604
30 TraesCS1B01G319100 chr6A 81.624 702 84 25 1595 2283 333828400 333829069 1.580000e-149 540
31 TraesCS1B01G319100 chr7D 81.120 625 73 22 4365 4973 41390525 41391120 4.550000e-125 459
32 TraesCS1B01G319100 chr2A 85.714 322 31 8 4670 4991 566590999 566591305 4.820000e-85 326
33 TraesCS1B01G319100 chr2A 87.984 258 31 0 4360 4617 566590745 566591002 6.280000e-79 305
34 TraesCS1B01G319100 chr7A 92.000 75 4 2 1595 1669 684509093 684509021 2.460000e-18 104


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 TraesCS1B01G319100 chr1B 543473047 543478037 4990 True 4323.500000 8181 100.000000 1 4991 2 chr1B.!!$R1 4990
1 TraesCS1B01G319100 chr1A 499631928 499635941 4013 True 1764.666667 4822 88.716000 77 4246 3 chr1A.!!$R1 4169
2 TraesCS1B01G319100 chr1D 404059291 404063363 4072 True 1331.750000 3090 88.983250 59 4262 4 chr1D.!!$R1 4203
3 TraesCS1B01G319100 chr5D 393455374 393458788 3414 False 447.000000 955 83.496000 902 4205 5 chr5D.!!$F1 3303
4 TraesCS1B01G319100 chr5B 100033316 100033894 578 False 693.000000 693 88.601000 4364 4930 1 chr5B.!!$F1 566
5 TraesCS1B01G319100 chr5B 473175198 473178612 3414 False 391.500000 752 84.070667 912 4217 6 chr5B.!!$F2 3305
6 TraesCS1B01G319100 chr4D 464373502 464374114 612 True 747.000000 747 88.835000 4370 4979 1 chr4D.!!$R1 609
7 TraesCS1B01G319100 chr3B 758332962 758334192 1230 False 710.000000 710 77.883000 1596 2813 1 chr3B.!!$F1 1217
8 TraesCS1B01G319100 chr5A 495319238 495322592 3354 False 388.666667 697 83.211833 850 4217 6 chr5A.!!$F1 3367
9 TraesCS1B01G319100 chr6A 580184998 580185682 684 False 604.000000 604 82.955000 1595 2283 1 chr6A.!!$F2 688
10 TraesCS1B01G319100 chr6A 333828400 333829069 669 False 540.000000 540 81.624000 1595 2283 1 chr6A.!!$F1 688
11 TraesCS1B01G319100 chr7D 41390525 41391120 595 False 459.000000 459 81.120000 4365 4973 1 chr7D.!!$F1 608
12 TraesCS1B01G319100 chr2A 566590745 566591305 560 False 315.500000 326 86.849000 4360 4991 2 chr2A.!!$F1 631

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
20 21 0.107752 GCTGAGCCTTCCTCTTCCAG 60.108 60.000 0.0 0.0 41.35 3.86 F
734 749 0.179004 TGAAAACCGCATCCTGGTGT 60.179 50.000 0.0 0.0 40.35 4.16 F
735 750 0.521735 GAAAACCGCATCCTGGTGTC 59.478 55.000 0.0 0.0 40.35 3.67 F
736 751 0.179004 AAAACCGCATCCTGGTGTCA 60.179 50.000 0.0 0.0 40.35 3.58 F
737 752 0.606401 AAACCGCATCCTGGTGTCAG 60.606 55.000 0.0 0.0 40.35 3.51 F
2261 2472 1.001378 CAGGCTGCAAAAACGTAAGCT 60.001 47.619 0.0 0.0 45.62 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1701 0.600057 GCCACAGCCTGAAAAAGAGG 59.400 55.000 0.00 0.0 0.00 3.69 R
2544 2959 0.234884 GAACACCACTTACGCTGTGC 59.765 55.000 0.00 0.0 34.38 4.57 R
2554 2969 2.300723 TGGTACGCAATAGAACACCACT 59.699 45.455 0.00 0.0 31.29 4.00 R
2590 3008 2.344025 CCAAACCTGCCTAACTCGTAC 58.656 52.381 0.00 0.0 0.00 3.67 R
2793 3220 5.010213 GGGTCTGTTTGGTTAGTTGCAATTA 59.990 40.000 0.59 0.0 0.00 1.40 R
4310 4845 0.036294 GGTGCTTCTGGTACTGACCC 60.036 60.000 0.00 0.0 46.32 4.46 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
18 19 2.295904 AGCTGAGCCTTCCTCTTCC 58.704 57.895 0.00 0.00 41.35 3.46
19 20 0.546267 AGCTGAGCCTTCCTCTTCCA 60.546 55.000 0.00 0.00 41.35 3.53
20 21 0.107752 GCTGAGCCTTCCTCTTCCAG 60.108 60.000 0.00 0.00 41.35 3.86
21 22 0.540923 CTGAGCCTTCCTCTTCCAGG 59.459 60.000 0.00 0.00 45.15 4.45
23 24 2.273776 GCCTTCCTCTTCCAGGCC 59.726 66.667 0.00 0.00 46.55 5.19
24 25 2.304831 GCCTTCCTCTTCCAGGCCT 61.305 63.158 0.00 0.00 46.55 5.19
25 26 1.911471 CCTTCCTCTTCCAGGCCTC 59.089 63.158 0.00 0.00 43.08 4.70
26 27 0.620121 CCTTCCTCTTCCAGGCCTCT 60.620 60.000 0.00 0.00 43.08 3.69
27 28 0.540923 CTTCCTCTTCCAGGCCTCTG 59.459 60.000 0.00 0.00 43.08 3.35
28 29 1.557269 TTCCTCTTCCAGGCCTCTGC 61.557 60.000 0.00 0.00 43.08 4.26
39 40 1.365633 GCCTCTGCCAGTAGATCCG 59.634 63.158 0.00 0.00 0.00 4.18
40 41 1.109920 GCCTCTGCCAGTAGATCCGA 61.110 60.000 0.00 0.00 0.00 4.55
41 42 0.958091 CCTCTGCCAGTAGATCCGAG 59.042 60.000 0.00 0.00 0.00 4.63
42 43 0.313672 CTCTGCCAGTAGATCCGAGC 59.686 60.000 0.00 0.00 0.00 5.03
43 44 1.109920 TCTGCCAGTAGATCCGAGCC 61.110 60.000 0.00 0.00 0.00 4.70
44 45 2.093537 CTGCCAGTAGATCCGAGCCC 62.094 65.000 0.00 0.00 0.00 5.19
45 46 2.134287 GCCAGTAGATCCGAGCCCA 61.134 63.158 0.00 0.00 0.00 5.36
46 47 2.045280 CCAGTAGATCCGAGCCCAG 58.955 63.158 0.00 0.00 0.00 4.45
47 48 1.365633 CAGTAGATCCGAGCCCAGC 59.634 63.158 0.00 0.00 0.00 4.85
48 49 1.834822 AGTAGATCCGAGCCCAGCC 60.835 63.158 0.00 0.00 0.00 4.85
49 50 2.524394 TAGATCCGAGCCCAGCCC 60.524 66.667 0.00 0.00 0.00 5.19
50 51 3.389139 TAGATCCGAGCCCAGCCCA 62.389 63.158 0.00 0.00 0.00 5.36
51 52 4.247380 GATCCGAGCCCAGCCCAG 62.247 72.222 0.00 0.00 0.00 4.45
72 73 1.053264 CCAGCCCTCTGCCAGTAGAT 61.053 60.000 0.00 0.00 42.71 1.98
115 116 1.271656 CTCGTAGTCCAACCCGACTTT 59.728 52.381 0.00 0.00 40.23 2.66
116 117 1.000060 TCGTAGTCCAACCCGACTTTG 60.000 52.381 0.00 0.00 40.23 2.77
117 118 1.154197 GTAGTCCAACCCGACTTTGC 58.846 55.000 0.00 0.00 40.23 3.68
118 119 1.053424 TAGTCCAACCCGACTTTGCT 58.947 50.000 0.00 0.00 40.23 3.91
120 121 1.228124 TCCAACCCGACTTTGCTGG 60.228 57.895 0.00 0.00 0.00 4.85
149 157 4.154347 CGGCTGCCTCCCTGTCTC 62.154 72.222 17.92 0.00 0.00 3.36
150 158 4.154347 GGCTGCCTCCCTGTCTCG 62.154 72.222 12.43 0.00 0.00 4.04
151 159 3.071206 GCTGCCTCCCTGTCTCGA 61.071 66.667 0.00 0.00 0.00 4.04
152 160 2.888863 CTGCCTCCCTGTCTCGAC 59.111 66.667 0.00 0.00 0.00 4.20
165 173 2.812609 TCGACTCGAGTCCGACGG 60.813 66.667 33.85 21.90 41.86 4.79
628 642 0.458260 GCGGTTGGAACTTTTGGTGT 59.542 50.000 0.00 0.00 0.00 4.16
647 662 1.214367 TTCGACTGAACCTTGTTCGC 58.786 50.000 2.84 0.00 0.00 4.70
668 683 0.401395 CCCCTCCTATGTTAGGCCCA 60.401 60.000 0.00 0.00 45.82 5.36
710 725 2.015587 ACTAGCTGTACCTGTAGCGTC 58.984 52.381 0.00 0.00 44.43 5.19
733 748 0.240945 GTGAAAACCGCATCCTGGTG 59.759 55.000 0.00 0.00 40.35 4.17
734 749 0.179004 TGAAAACCGCATCCTGGTGT 60.179 50.000 0.00 0.00 40.35 4.16
735 750 0.521735 GAAAACCGCATCCTGGTGTC 59.478 55.000 0.00 0.00 40.35 3.67
736 751 0.179004 AAAACCGCATCCTGGTGTCA 60.179 50.000 0.00 0.00 40.35 3.58
737 752 0.606401 AAACCGCATCCTGGTGTCAG 60.606 55.000 0.00 0.00 40.35 3.51
748 763 3.238108 CTGGTGTCAGGTGTGATAGAC 57.762 52.381 0.00 0.00 37.36 2.59
749 764 2.828520 CTGGTGTCAGGTGTGATAGACT 59.171 50.000 0.00 0.00 37.36 3.24
750 765 4.017126 CTGGTGTCAGGTGTGATAGACTA 58.983 47.826 0.00 0.00 37.36 2.59
751 766 4.017126 TGGTGTCAGGTGTGATAGACTAG 58.983 47.826 0.00 0.00 34.36 2.57
776 791 2.450886 AGGGGAATTCCAGGTTTTCACT 59.549 45.455 25.67 0.00 37.91 3.41
837 908 3.928375 CAGATTGGTTTGCAATACAAGGC 59.072 43.478 17.62 13.21 40.06 4.35
861 967 6.615264 TCACTAATCGTAGTACATCTGTCC 57.385 41.667 0.38 0.00 38.58 4.02
967 1083 6.585695 TTCAGGAGAGAACTGTATAAACGT 57.414 37.500 0.00 0.00 37.25 3.99
988 1104 4.279659 GTTTTAGTGGTTGAAGCGACTTG 58.720 43.478 5.18 0.00 0.00 3.16
993 1109 1.412710 TGGTTGAAGCGACTTGAGTCT 59.587 47.619 9.28 0.00 42.66 3.24
1011 1127 6.711277 TGAGTCTTTAACCATGAGTAGCATT 58.289 36.000 0.00 0.00 34.15 3.56
1044 1160 2.104111 TGATCTGTCCGTCACCACTTTT 59.896 45.455 0.00 0.00 0.00 2.27
1148 1266 5.360591 TGTTTTCTTGACCTTCTCTGTCTC 58.639 41.667 0.00 0.00 33.83 3.36
1236 1354 4.755411 TGGAATTGTCCTCGTAAGTGATC 58.245 43.478 0.00 0.00 45.22 2.92
1238 1356 5.104941 TGGAATTGTCCTCGTAAGTGATCAT 60.105 40.000 0.00 0.00 45.22 2.45
1239 1357 5.817816 GGAATTGTCCTCGTAAGTGATCATT 59.182 40.000 0.00 0.00 41.24 2.57
1275 1393 6.894339 ACTTTTACTCAAATGGGGTGTTAG 57.106 37.500 0.00 0.00 0.00 2.34
1276 1394 6.370453 ACTTTTACTCAAATGGGGTGTTAGT 58.630 36.000 0.00 0.00 0.00 2.24
1277 1395 6.264518 ACTTTTACTCAAATGGGGTGTTAGTG 59.735 38.462 0.00 0.00 0.00 2.74
1278 1396 3.876309 ACTCAAATGGGGTGTTAGTGT 57.124 42.857 0.00 0.00 0.00 3.55
1279 1397 4.178956 ACTCAAATGGGGTGTTAGTGTT 57.821 40.909 0.00 0.00 0.00 3.32
1280 1398 5.313280 ACTCAAATGGGGTGTTAGTGTTA 57.687 39.130 0.00 0.00 0.00 2.41
1285 1403 6.270463 TCAAATGGGGTGTTAGTGTTACTCTA 59.730 38.462 0.00 0.00 0.00 2.43
1309 1427 6.072112 TGCTTCTTTTGTGTGATAACCTTC 57.928 37.500 0.00 0.00 0.00 3.46
1348 1466 2.271800 GGTGTGGAGAAGCTGATAACG 58.728 52.381 0.00 0.00 0.00 3.18
1464 1617 6.012508 CAGGGTGGTTGGGATATATATTCTGT 60.013 42.308 0.95 0.00 0.00 3.41
1466 1619 7.742213 AGGGTGGTTGGGATATATATTCTGTAA 59.258 37.037 0.95 0.00 0.00 2.41
1481 1634 5.705609 TTCTGTAATGTTCCCTTTCTTGC 57.294 39.130 0.00 0.00 0.00 4.01
1497 1650 6.035975 CCTTTCTTGCCTTTTTATAATTGCCG 59.964 38.462 0.00 0.00 0.00 5.69
1546 1701 9.573133 CATTTGGTAATGAAGTTAATTCCTGTC 57.427 33.333 0.00 0.00 43.12 3.51
1642 1798 9.294030 CAGCCAATTATGAAAAGTGAGAATTAC 57.706 33.333 0.00 0.00 0.00 1.89
1684 1842 9.214957 TCATACCAAATGTTTGTAGAACTGTAG 57.785 33.333 4.92 0.00 36.45 2.74
1815 1976 4.393371 GGTAAGGCAGTCAAGATGTTCTTC 59.607 45.833 0.00 0.00 33.78 2.87
1816 1977 4.363991 AAGGCAGTCAAGATGTTCTTCT 57.636 40.909 0.00 0.00 33.78 2.85
1817 1978 4.363991 AGGCAGTCAAGATGTTCTTCTT 57.636 40.909 0.00 0.00 33.78 2.52
1886 2047 5.305585 TGATAACACTTCAAACTCCTGTCC 58.694 41.667 0.00 0.00 0.00 4.02
1996 2159 9.247126 CATATGTGAGTTCTCAATCTAAGACAG 57.753 37.037 3.99 0.00 0.00 3.51
2261 2472 1.001378 CAGGCTGCAAAAACGTAAGCT 60.001 47.619 0.00 0.00 45.62 3.74
2262 2473 1.001378 AGGCTGCAAAAACGTAAGCTG 60.001 47.619 0.50 0.00 45.62 4.24
2315 2527 4.415596 TGATTCCTGTAGTGGCCATTTTT 58.584 39.130 9.72 0.00 0.00 1.94
2355 2567 2.008268 GCATGGCTAAAGCATGGCGT 62.008 55.000 4.07 0.00 44.36 5.68
2376 2599 7.328493 TGGCGTATTCATGAATCGTTCTTATAG 59.672 37.037 23.95 5.47 32.50 1.31
2422 2664 8.435982 AGTAGATCTTTAGGAATAAGCATGCTT 58.564 33.333 33.70 33.70 39.83 3.91
2452 2702 5.045012 TCTTAAAGCTGCTCATCATCCAT 57.955 39.130 1.00 0.00 0.00 3.41
2465 2715 7.095229 TGCTCATCATCCATATTTAGCGTTTAC 60.095 37.037 0.00 0.00 0.00 2.01
2483 2733 5.405797 GTTTACGCAGGTACTAGTTTAGCT 58.594 41.667 0.00 0.00 36.02 3.32
2517 2771 6.469410 TCAACGGGTGAATACACTCTTATTT 58.531 36.000 0.00 0.00 44.55 1.40
2521 2936 6.817140 ACGGGTGAATACACTCTTATTTCTTC 59.183 38.462 0.00 0.00 44.55 2.87
2531 2946 8.608844 ACACTCTTATTTCTTCTGTTAGGTTG 57.391 34.615 0.00 0.00 0.00 3.77
2544 2959 1.568504 TAGGTTGGCCACTACCAGAG 58.431 55.000 25.30 0.00 43.77 3.35
2551 2966 1.446792 CCACTACCAGAGCACAGCG 60.447 63.158 0.00 0.00 0.00 5.18
2554 2969 1.067846 CACTACCAGAGCACAGCGTAA 60.068 52.381 0.00 0.00 0.00 3.18
2570 2988 2.222729 GCGTAAGTGGTGTTCTATTGCG 60.223 50.000 0.00 0.00 41.68 4.85
2590 3008 3.306166 GCGTACCACAGTTTGCTACATAG 59.694 47.826 0.00 0.00 0.00 2.23
2640 3061 5.332280 GCTCGTATTTGTTTCTTTGCCAAAC 60.332 40.000 0.00 0.00 34.79 2.93
2787 3214 7.920682 ACACTTCTCGCACAAATTTTAGAAAAT 59.079 29.630 0.00 0.00 40.15 1.82
2830 3263 3.618690 ACAGACCCTCAGTTTAGCATC 57.381 47.619 0.00 0.00 0.00 3.91
2978 3415 3.181519 ACGTACTAGATCATAGATGCGCG 60.182 47.826 0.00 0.00 0.00 6.86
2994 3431 2.857748 TGCGCGTCATTTACATAGTCTG 59.142 45.455 8.43 0.00 0.00 3.51
3101 3538 7.784470 AAGACTTGGTCTGTATCTACTTTCT 57.216 36.000 0.74 0.00 42.59 2.52
3129 3568 4.154737 GCAGCTTTGTAGTCATTGATGTGA 59.845 41.667 0.00 0.00 0.00 3.58
3322 3761 8.090831 TGGTTCTCCATTCTAATTCATCTATCG 58.909 37.037 0.00 0.00 39.03 2.92
3549 4004 4.944930 AGACAGCCAGTAGTTACTAGTCAG 59.055 45.833 0.00 1.33 34.13 3.51
3580 4039 4.569943 TGGATTTTCTCTCAGAAGGAACG 58.430 43.478 0.00 0.00 35.37 3.95
3624 4131 2.173782 TGGTTTTACTCCCACAAGCAGA 59.826 45.455 0.00 0.00 0.00 4.26
3673 4180 6.760770 ACAAATTGCCATACCCGAAATAATTG 59.239 34.615 0.00 0.00 0.00 2.32
3675 4182 2.625790 TGCCATACCCGAAATAATTGCC 59.374 45.455 0.00 0.00 0.00 4.52
4025 4537 4.411013 AGCTCTGCTTCCCATTTACTTTT 58.589 39.130 0.00 0.00 33.89 2.27
4035 4549 2.095668 CCATTTACTTTTACGTGCGGCA 60.096 45.455 0.00 0.00 0.00 5.69
4066 4585 0.591659 GGAGTGGAGCGGTTTGTTTC 59.408 55.000 0.00 0.00 0.00 2.78
4105 4626 2.192861 CAGGGCGTTGTTGCTTCCA 61.193 57.895 0.00 0.00 34.52 3.53
4138 4659 1.414181 CATCCCAGTCGAGGTAGCAAT 59.586 52.381 0.00 0.00 0.00 3.56
4147 4670 2.166459 TCGAGGTAGCAATCAGGTTCTG 59.834 50.000 0.00 0.00 0.00 3.02
4148 4671 2.093973 CGAGGTAGCAATCAGGTTCTGT 60.094 50.000 0.00 0.00 32.61 3.41
4149 4672 3.265791 GAGGTAGCAATCAGGTTCTGTG 58.734 50.000 0.00 0.00 32.61 3.66
4150 4673 2.639839 AGGTAGCAATCAGGTTCTGTGT 59.360 45.455 0.00 0.00 32.61 3.72
4262 4797 1.320344 ATCACGCGTGGCCTAAGAGA 61.320 55.000 36.41 16.29 0.00 3.10
4263 4798 1.141881 CACGCGTGGCCTAAGAGAT 59.858 57.895 31.15 0.00 0.00 2.75
4264 4799 0.384309 CACGCGTGGCCTAAGAGATA 59.616 55.000 31.15 0.00 0.00 1.98
4265 4800 0.384669 ACGCGTGGCCTAAGAGATAC 59.615 55.000 12.93 0.00 0.00 2.24
4266 4801 0.384309 CGCGTGGCCTAAGAGATACA 59.616 55.000 3.32 0.00 0.00 2.29
4267 4802 1.000163 CGCGTGGCCTAAGAGATACAT 60.000 52.381 3.32 0.00 0.00 2.29
4268 4803 2.228103 CGCGTGGCCTAAGAGATACATA 59.772 50.000 3.32 0.00 0.00 2.29
4269 4804 3.119459 CGCGTGGCCTAAGAGATACATAT 60.119 47.826 3.32 0.00 0.00 1.78
4270 4805 4.177026 GCGTGGCCTAAGAGATACATATG 58.823 47.826 3.32 0.00 0.00 1.78
4271 4806 4.748892 CGTGGCCTAAGAGATACATATGG 58.251 47.826 3.32 0.00 0.00 2.74
4272 4807 4.462834 CGTGGCCTAAGAGATACATATGGA 59.537 45.833 3.32 0.00 0.00 3.41
4273 4808 5.047306 CGTGGCCTAAGAGATACATATGGAA 60.047 44.000 3.32 0.00 0.00 3.53
4274 4809 6.518369 CGTGGCCTAAGAGATACATATGGAAA 60.518 42.308 3.32 0.00 0.00 3.13
4275 4810 7.398024 GTGGCCTAAGAGATACATATGGAAAT 58.602 38.462 3.32 0.00 0.00 2.17
4276 4811 7.550906 GTGGCCTAAGAGATACATATGGAAATC 59.449 40.741 3.32 7.19 0.00 2.17
4277 4812 7.051000 GGCCTAAGAGATACATATGGAAATCC 58.949 42.308 7.80 0.00 0.00 3.01
4278 4813 7.051000 GCCTAAGAGATACATATGGAAATCCC 58.949 42.308 7.80 0.00 34.29 3.85
4295 4830 8.257306 TGGAAATCCCATGTCTTTTAATTTAGC 58.743 33.333 0.00 0.00 40.82 3.09
4296 4831 8.478066 GGAAATCCCATGTCTTTTAATTTAGCT 58.522 33.333 0.00 0.00 34.14 3.32
4297 4832 9.305925 GAAATCCCATGTCTTTTAATTTAGCTG 57.694 33.333 0.00 0.00 0.00 4.24
4298 4833 6.207691 TCCCATGTCTTTTAATTTAGCTGC 57.792 37.500 0.00 0.00 0.00 5.25
4299 4834 5.127031 TCCCATGTCTTTTAATTTAGCTGCC 59.873 40.000 0.00 0.00 0.00 4.85
4300 4835 5.036737 CCATGTCTTTTAATTTAGCTGCCG 58.963 41.667 0.00 0.00 0.00 5.69
4301 4836 4.091453 TGTCTTTTAATTTAGCTGCCGC 57.909 40.909 0.00 0.00 0.00 6.53
4302 4837 3.119637 TGTCTTTTAATTTAGCTGCCGCC 60.120 43.478 0.00 0.00 36.60 6.13
4303 4838 3.128764 GTCTTTTAATTTAGCTGCCGCCT 59.871 43.478 0.00 0.00 36.60 5.52
4304 4839 4.334481 GTCTTTTAATTTAGCTGCCGCCTA 59.666 41.667 0.00 0.00 36.60 3.93
4305 4840 4.944930 TCTTTTAATTTAGCTGCCGCCTAA 59.055 37.500 0.00 0.00 36.60 2.69
4306 4841 4.625972 TTTAATTTAGCTGCCGCCTAAC 57.374 40.909 0.00 0.00 36.60 2.34
4307 4842 2.420058 AATTTAGCTGCCGCCTAACT 57.580 45.000 0.00 0.00 36.60 2.24
4308 4843 3.553828 AATTTAGCTGCCGCCTAACTA 57.446 42.857 0.00 0.00 36.60 2.24
4309 4844 3.553828 ATTTAGCTGCCGCCTAACTAA 57.446 42.857 0.00 0.00 36.60 2.24
4310 4845 2.596904 TTAGCTGCCGCCTAACTAAG 57.403 50.000 0.00 0.00 36.60 2.18
4312 4847 1.523938 GCTGCCGCCTAACTAAGGG 60.524 63.158 0.00 0.00 46.65 3.95
4313 4848 1.905512 CTGCCGCCTAACTAAGGGT 59.094 57.895 0.00 0.00 46.65 4.34
4314 4849 0.179081 CTGCCGCCTAACTAAGGGTC 60.179 60.000 0.00 0.00 46.65 4.46
4315 4850 0.905809 TGCCGCCTAACTAAGGGTCA 60.906 55.000 0.00 0.00 46.65 4.02
4316 4851 0.179081 GCCGCCTAACTAAGGGTCAG 60.179 60.000 0.00 0.00 46.65 3.51
4317 4852 1.192428 CCGCCTAACTAAGGGTCAGT 58.808 55.000 0.00 0.00 46.65 3.41
4318 4853 2.381911 CCGCCTAACTAAGGGTCAGTA 58.618 52.381 0.00 0.00 46.65 2.74
4319 4854 2.100418 CCGCCTAACTAAGGGTCAGTAC 59.900 54.545 0.00 0.00 46.65 2.73
4320 4855 2.100418 CGCCTAACTAAGGGTCAGTACC 59.900 54.545 0.00 0.00 46.65 3.34
4329 4864 3.534721 GGTCAGTACCAGAAGCACC 57.465 57.895 0.00 0.00 45.98 5.01
4330 4865 0.036294 GGTCAGTACCAGAAGCACCC 60.036 60.000 0.00 0.00 45.98 4.61
4331 4866 0.977395 GTCAGTACCAGAAGCACCCT 59.023 55.000 0.00 0.00 0.00 4.34
4332 4867 1.348036 GTCAGTACCAGAAGCACCCTT 59.652 52.381 0.00 0.00 0.00 3.95
4333 4868 2.054799 TCAGTACCAGAAGCACCCTTT 58.945 47.619 0.00 0.00 0.00 3.11
4334 4869 3.007614 GTCAGTACCAGAAGCACCCTTTA 59.992 47.826 0.00 0.00 0.00 1.85
4335 4870 3.844211 TCAGTACCAGAAGCACCCTTTAT 59.156 43.478 0.00 0.00 0.00 1.40
4336 4871 4.288626 TCAGTACCAGAAGCACCCTTTATT 59.711 41.667 0.00 0.00 0.00 1.40
4337 4872 5.486063 TCAGTACCAGAAGCACCCTTTATTA 59.514 40.000 0.00 0.00 0.00 0.98
4338 4873 5.585047 CAGTACCAGAAGCACCCTTTATTAC 59.415 44.000 0.00 0.00 0.00 1.89
4339 4874 4.929146 ACCAGAAGCACCCTTTATTACT 57.071 40.909 0.00 0.00 0.00 2.24
4340 4875 5.256806 ACCAGAAGCACCCTTTATTACTT 57.743 39.130 0.00 0.00 0.00 2.24
4341 4876 5.641155 ACCAGAAGCACCCTTTATTACTTT 58.359 37.500 0.00 0.00 0.00 2.66
4342 4877 6.786122 ACCAGAAGCACCCTTTATTACTTTA 58.214 36.000 0.00 0.00 0.00 1.85
4343 4878 6.884836 ACCAGAAGCACCCTTTATTACTTTAG 59.115 38.462 0.00 0.00 0.00 1.85
4344 4879 7.110155 CCAGAAGCACCCTTTATTACTTTAGA 58.890 38.462 0.00 0.00 0.00 2.10
4345 4880 7.610305 CCAGAAGCACCCTTTATTACTTTAGAA 59.390 37.037 0.00 0.00 0.00 2.10
4346 4881 8.451748 CAGAAGCACCCTTTATTACTTTAGAAC 58.548 37.037 0.00 0.00 0.00 3.01
4347 4882 6.980051 AGCACCCTTTATTACTTTAGAACG 57.020 37.500 0.00 0.00 0.00 3.95
4348 4883 5.878669 AGCACCCTTTATTACTTTAGAACGG 59.121 40.000 0.00 0.00 0.00 4.44
4349 4884 5.876460 GCACCCTTTATTACTTTAGAACGGA 59.124 40.000 0.00 0.00 0.00 4.69
4350 4885 6.541278 GCACCCTTTATTACTTTAGAACGGAT 59.459 38.462 0.00 0.00 0.00 4.18
4351 4886 7.712205 GCACCCTTTATTACTTTAGAACGGATA 59.288 37.037 0.00 0.00 0.00 2.59
4352 4887 9.257651 CACCCTTTATTACTTTAGAACGGATAG 57.742 37.037 0.00 0.00 0.00 2.08
4353 4888 8.427276 ACCCTTTATTACTTTAGAACGGATAGG 58.573 37.037 0.00 0.00 0.00 2.57
4354 4889 8.645110 CCCTTTATTACTTTAGAACGGATAGGA 58.355 37.037 0.00 0.00 0.00 2.94
4361 4896 9.947433 TTACTTTAGAACGGATAGGATTTTGAA 57.053 29.630 0.00 0.00 0.00 2.69
4362 4897 8.857694 ACTTTAGAACGGATAGGATTTTGAAA 57.142 30.769 0.00 0.00 0.00 2.69
4390 4925 0.323957 GGCTCGTTTGGTAAGAGGGT 59.676 55.000 0.00 0.00 32.96 4.34
4484 5019 2.037367 GGGGTTTGGAGGAAGGGC 59.963 66.667 0.00 0.00 0.00 5.19
4600 5141 2.293184 TGAAAGAGTATGGGAGGAGGCT 60.293 50.000 0.00 0.00 0.00 4.58
4650 5203 1.913762 CCGGTGTCCCTTCTCCAGT 60.914 63.158 0.00 0.00 0.00 4.00
4672 5225 1.004918 CAAACCGGTCCTTCTCGCT 60.005 57.895 8.04 0.00 0.00 4.93
4674 5227 0.971386 AAACCGGTCCTTCTCGCTAA 59.029 50.000 8.04 0.00 0.00 3.09
4680 5233 2.361438 CGGTCCTTCTCGCTAAAGGTAT 59.639 50.000 9.27 0.00 43.22 2.73
4689 5242 1.067212 CGCTAAAGGTATGTCTCCGCT 59.933 52.381 0.00 0.00 0.00 5.52
4710 5263 1.221213 CCCCTTTCCCCTCATTCCCA 61.221 60.000 0.00 0.00 0.00 4.37
4746 5299 0.844661 ACCTTCACCCACCATGGCTA 60.845 55.000 13.04 0.00 35.79 3.93
4748 5301 0.620556 CTTCACCCACCATGGCTACT 59.379 55.000 13.04 0.00 35.79 2.57
4800 5356 2.926242 TCCTCCCCGGCGAACTTT 60.926 61.111 9.30 0.00 0.00 2.66
4878 5434 2.913060 GTCGCCGCCCTCCTAGAT 60.913 66.667 0.00 0.00 0.00 1.98
4886 5442 0.547712 GCCCTCCTAGATGCCCCATA 60.548 60.000 0.00 0.00 0.00 2.74
4894 5450 1.675641 GATGCCCCATATCCACCGC 60.676 63.158 0.00 0.00 0.00 5.68
4908 5464 0.317160 CACCGCGGCATCTCCTAATA 59.683 55.000 28.58 0.00 0.00 0.98
4958 5523 8.752005 TTTATTGGTCTGCATATAGCTTCTTT 57.248 30.769 0.00 0.00 45.94 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.546267 TGGAAGAGGAAGGCTCAGCT 60.546 55.000 0.00 0.00 0.00 4.24
1 2 0.107752 CTGGAAGAGGAAGGCTCAGC 60.108 60.000 0.00 0.00 34.07 4.26
2 3 0.540923 CCTGGAAGAGGAAGGCTCAG 59.459 60.000 0.00 0.00 46.33 3.35
7 8 0.620121 AGAGGCCTGGAAGAGGAAGG 60.620 60.000 12.00 0.00 46.33 3.46
8 9 0.540923 CAGAGGCCTGGAAGAGGAAG 59.459 60.000 12.00 0.00 46.33 3.46
9 10 1.557269 GCAGAGGCCTGGAAGAGGAA 61.557 60.000 12.00 0.00 46.33 3.36
10 11 1.992277 GCAGAGGCCTGGAAGAGGA 60.992 63.158 12.00 0.00 46.33 3.71
11 12 2.588989 GCAGAGGCCTGGAAGAGG 59.411 66.667 12.00 0.00 46.13 3.69
21 22 1.109920 TCGGATCTACTGGCAGAGGC 61.110 60.000 23.66 9.63 40.13 4.70
22 23 0.958091 CTCGGATCTACTGGCAGAGG 59.042 60.000 23.66 12.96 0.00 3.69
23 24 0.313672 GCTCGGATCTACTGGCAGAG 59.686 60.000 23.66 14.02 0.00 3.35
24 25 1.109920 GGCTCGGATCTACTGGCAGA 61.110 60.000 23.66 0.00 0.00 4.26
25 26 1.365633 GGCTCGGATCTACTGGCAG 59.634 63.158 14.16 14.16 0.00 4.85
26 27 2.134287 GGGCTCGGATCTACTGGCA 61.134 63.158 0.00 0.00 0.00 4.92
27 28 2.093537 CTGGGCTCGGATCTACTGGC 62.094 65.000 0.00 0.00 0.00 4.85
28 29 2.045280 CTGGGCTCGGATCTACTGG 58.955 63.158 0.00 0.00 0.00 4.00
29 30 1.365633 GCTGGGCTCGGATCTACTG 59.634 63.158 0.00 0.00 0.00 2.74
30 31 1.834822 GGCTGGGCTCGGATCTACT 60.835 63.158 0.00 0.00 0.00 2.57
31 32 2.737830 GGCTGGGCTCGGATCTAC 59.262 66.667 0.00 0.00 0.00 2.59
32 33 2.524394 GGGCTGGGCTCGGATCTA 60.524 66.667 0.00 0.00 0.00 1.98
33 34 4.804420 TGGGCTGGGCTCGGATCT 62.804 66.667 0.00 0.00 0.00 2.75
34 35 4.247380 CTGGGCTGGGCTCGGATC 62.247 72.222 0.00 0.00 37.67 3.36
52 53 2.688666 TACTGGCAGAGGGCTGGG 60.689 66.667 23.66 0.00 42.53 4.45
53 54 1.053264 ATCTACTGGCAGAGGGCTGG 61.053 60.000 23.66 0.00 42.53 4.85
54 55 0.392336 GATCTACTGGCAGAGGGCTG 59.608 60.000 23.66 4.35 45.13 4.85
55 56 0.762461 GGATCTACTGGCAGAGGGCT 60.762 60.000 23.66 0.00 44.01 5.19
56 57 1.751563 GGATCTACTGGCAGAGGGC 59.248 63.158 23.66 6.07 43.74 5.19
57 58 0.468214 TCGGATCTACTGGCAGAGGG 60.468 60.000 23.66 10.39 0.00 4.30
62 63 2.134287 GGGCTCGGATCTACTGGCA 61.134 63.158 0.00 0.00 0.00 4.92
149 157 3.862402 CCCGTCGGACTCGAGTCG 61.862 72.222 33.07 27.52 46.91 4.18
150 158 4.176851 GCCCGTCGGACTCGAGTC 62.177 72.222 32.96 32.96 46.91 3.36
152 160 4.477975 GTGCCCGTCGGACTCGAG 62.478 72.222 14.39 11.84 46.91 4.04
576 590 1.801913 CACGACAGACTGTAGCGGC 60.802 63.158 17.81 0.00 0.00 6.53
616 630 4.609691 TTCAGTCGAACACCAAAAGTTC 57.390 40.909 0.00 0.00 41.41 3.01
628 642 1.214367 GCGAACAAGGTTCAGTCGAA 58.786 50.000 9.50 0.00 0.00 3.71
665 680 3.721706 GGTGGCTCCAGGAGTGGG 61.722 72.222 18.37 0.00 45.11 4.61
700 715 0.666274 TTTCACTGCGACGCTACAGG 60.666 55.000 22.08 8.35 38.25 4.00
733 748 4.270834 TGGTCTAGTCTATCACACCTGAC 58.729 47.826 0.00 0.00 0.00 3.51
734 749 4.527944 CTGGTCTAGTCTATCACACCTGA 58.472 47.826 0.00 0.00 0.00 3.86
735 750 3.634448 CCTGGTCTAGTCTATCACACCTG 59.366 52.174 0.00 0.00 0.00 4.00
736 751 3.373220 CCCTGGTCTAGTCTATCACACCT 60.373 52.174 0.00 0.00 0.00 4.00
737 752 2.959707 CCCTGGTCTAGTCTATCACACC 59.040 54.545 0.00 0.00 0.00 4.16
738 753 2.959707 CCCCTGGTCTAGTCTATCACAC 59.040 54.545 0.00 0.00 0.00 3.82
739 754 2.856864 TCCCCTGGTCTAGTCTATCACA 59.143 50.000 0.00 0.00 0.00 3.58
740 755 3.596940 TCCCCTGGTCTAGTCTATCAC 57.403 52.381 0.00 0.00 0.00 3.06
741 756 4.834406 ATTCCCCTGGTCTAGTCTATCA 57.166 45.455 0.00 0.00 0.00 2.15
742 757 4.528987 GGAATTCCCCTGGTCTAGTCTATC 59.471 50.000 14.03 0.00 0.00 2.08
743 758 4.077982 TGGAATTCCCCTGGTCTAGTCTAT 60.078 45.833 21.90 0.00 34.29 1.98
744 759 3.273886 TGGAATTCCCCTGGTCTAGTCTA 59.726 47.826 21.90 0.00 34.29 2.59
745 760 2.045885 TGGAATTCCCCTGGTCTAGTCT 59.954 50.000 21.90 0.00 34.29 3.24
746 761 2.436173 CTGGAATTCCCCTGGTCTAGTC 59.564 54.545 21.90 0.00 34.29 2.59
747 762 2.482494 CTGGAATTCCCCTGGTCTAGT 58.518 52.381 21.90 0.00 34.29 2.57
748 763 1.771255 CCTGGAATTCCCCTGGTCTAG 59.229 57.143 21.90 9.37 39.61 2.43
749 764 1.893315 CCTGGAATTCCCCTGGTCTA 58.107 55.000 21.90 0.00 39.61 2.59
750 765 2.715295 CCTGGAATTCCCCTGGTCT 58.285 57.895 21.90 0.00 39.61 3.85
805 876 4.072131 GCAAACCAATCTGAGGTCTGTTA 58.928 43.478 0.00 0.00 38.76 2.41
837 908 6.564312 CGGACAGATGTACTACGATTAGTGAG 60.564 46.154 0.00 0.00 39.06 3.51
861 967 4.023450 ACAAGCATATGCAGGAATCATTCG 60.023 41.667 28.62 9.33 45.16 3.34
967 1083 4.193090 TCAAGTCGCTTCAACCACTAAAA 58.807 39.130 0.00 0.00 0.00 1.52
988 1104 6.037610 CCAATGCTACTCATGGTTAAAGACTC 59.962 42.308 0.00 0.00 35.13 3.36
993 1109 5.417580 GGTTCCAATGCTACTCATGGTTAAA 59.582 40.000 0.00 0.00 35.13 1.52
1011 1127 1.760613 GACAGATCATACCCGGTTCCA 59.239 52.381 0.00 0.00 0.00 3.53
1148 1266 5.404366 CCAAAGTTTCATCATGAAGTTGCAG 59.596 40.000 0.00 0.00 37.70 4.41
1260 1378 5.072600 AGAGTAACACTAACACCCCATTTGA 59.927 40.000 0.00 0.00 0.00 2.69
1263 1381 6.650120 CATAGAGTAACACTAACACCCCATT 58.350 40.000 0.00 0.00 0.00 3.16
1275 1393 7.042051 TCACACAAAAGAAGCATAGAGTAACAC 60.042 37.037 0.00 0.00 0.00 3.32
1276 1394 6.989759 TCACACAAAAGAAGCATAGAGTAACA 59.010 34.615 0.00 0.00 0.00 2.41
1277 1395 7.421530 TCACACAAAAGAAGCATAGAGTAAC 57.578 36.000 0.00 0.00 0.00 2.50
1278 1396 9.719355 TTATCACACAAAAGAAGCATAGAGTAA 57.281 29.630 0.00 0.00 0.00 2.24
1279 1397 9.151471 GTTATCACACAAAAGAAGCATAGAGTA 57.849 33.333 0.00 0.00 0.00 2.59
1280 1398 7.119846 GGTTATCACACAAAAGAAGCATAGAGT 59.880 37.037 0.00 0.00 0.00 3.24
1285 1403 6.491403 AGAAGGTTATCACACAAAAGAAGCAT 59.509 34.615 0.00 0.00 0.00 3.79
1309 1427 7.234782 TCCACACCCTGTAGACCAATATATTAG 59.765 40.741 0.00 0.00 0.00 1.73
1325 1443 0.617413 ATCAGCTTCTCCACACCCTG 59.383 55.000 0.00 0.00 0.00 4.45
1348 1466 3.126831 CCCAGCAAGTATCATCTTCGAC 58.873 50.000 0.00 0.00 0.00 4.20
1464 1617 6.493189 AAAAAGGCAAGAAAGGGAACATTA 57.507 33.333 0.00 0.00 0.00 1.90
1466 1619 6.686484 ATAAAAAGGCAAGAAAGGGAACAT 57.314 33.333 0.00 0.00 0.00 2.71
1478 1631 6.031751 AGAACGGCAATTATAAAAAGGCAA 57.968 33.333 8.64 0.00 0.00 4.52
1481 1634 7.883229 AACAAGAACGGCAATTATAAAAAGG 57.117 32.000 0.00 0.00 0.00 3.11
1497 1650 5.049954 TGCAATCCGTTACAGTAACAAGAAC 60.050 40.000 20.99 11.86 38.57 3.01
1546 1701 0.600057 GCCACAGCCTGAAAAAGAGG 59.400 55.000 0.00 0.00 0.00 3.69
1642 1798 9.918630 ATTTGGTATGAAAATCAAAAGTCTCAG 57.081 29.630 0.00 0.00 33.62 3.35
1815 1976 6.442513 AACACCTTCTTCTTCTTGAACAAG 57.557 37.500 8.09 8.09 39.71 3.16
1816 1977 5.357032 GGAACACCTTCTTCTTCTTGAACAA 59.643 40.000 0.00 0.00 0.00 2.83
1817 1978 4.881850 GGAACACCTTCTTCTTCTTGAACA 59.118 41.667 0.00 0.00 0.00 3.18
1835 1996 7.474222 ACTATCAAGTAACATGTTGGAGGAACA 60.474 37.037 21.42 0.00 40.72 3.18
1836 1997 6.879458 ACTATCAAGTAACATGTTGGAGGAAC 59.121 38.462 21.42 9.89 32.84 3.62
1837 1998 7.016153 ACTATCAAGTAACATGTTGGAGGAA 57.984 36.000 21.42 0.00 32.84 3.36
1838 1999 6.620877 ACTATCAAGTAACATGTTGGAGGA 57.379 37.500 21.42 13.16 32.84 3.71
1868 2029 1.843851 TGGGACAGGAGTTTGAAGTGT 59.156 47.619 0.00 0.00 0.00 3.55
1886 2047 2.576832 CCACAGCCAAAAGGCCTGG 61.577 63.158 5.69 5.34 36.99 4.45
1996 2159 4.259356 ACGGCAAAATAGAAGAACTACCC 58.741 43.478 0.00 0.00 33.62 3.69
2029 2192 2.618045 CCAACTTATCCCTTGCTCGGTT 60.618 50.000 0.00 0.00 0.00 4.44
2070 2233 1.476833 GCCCAGTCACTGACAGGAAAA 60.477 52.381 19.64 0.00 40.93 2.29
2315 2527 5.907207 TGCTAGTGGTTTGCAACAAAATAA 58.093 33.333 0.00 0.00 34.59 1.40
2339 2551 1.946768 GAATACGCCATGCTTTAGCCA 59.053 47.619 0.00 0.00 41.18 4.75
2422 2664 6.207221 TGATGAGCAGCTTTAAGAACATCAAA 59.793 34.615 15.03 0.00 39.44 2.69
2465 2715 3.505464 ACAGCTAAACTAGTACCTGCG 57.495 47.619 0.00 0.00 0.00 5.18
2483 2733 4.022413 TTCACCCGTTGAATATGGAACA 57.978 40.909 0.00 0.00 40.82 3.18
2505 2755 9.706691 CAACCTAACAGAAGAAATAAGAGTGTA 57.293 33.333 0.00 0.00 0.00 2.90
2507 2757 7.361286 GCCAACCTAACAGAAGAAATAAGAGTG 60.361 40.741 0.00 0.00 0.00 3.51
2508 2758 6.655425 GCCAACCTAACAGAAGAAATAAGAGT 59.345 38.462 0.00 0.00 0.00 3.24
2509 2759 6.094186 GGCCAACCTAACAGAAGAAATAAGAG 59.906 42.308 0.00 0.00 0.00 2.85
2510 2760 5.944007 GGCCAACCTAACAGAAGAAATAAGA 59.056 40.000 0.00 0.00 0.00 2.10
2517 2771 2.054799 AGTGGCCAACCTAACAGAAGA 58.945 47.619 7.24 0.00 36.63 2.87
2521 2936 1.349688 TGGTAGTGGCCAACCTAACAG 59.650 52.381 24.02 0.00 36.67 3.16
2531 2946 1.078848 CTGTGCTCTGGTAGTGGCC 60.079 63.158 0.00 0.00 0.00 5.36
2544 2959 0.234884 GAACACCACTTACGCTGTGC 59.765 55.000 0.00 0.00 34.38 4.57
2551 2966 4.328169 GGTACGCAATAGAACACCACTTAC 59.672 45.833 0.00 0.00 0.00 2.34
2554 2969 2.300723 TGGTACGCAATAGAACACCACT 59.699 45.455 0.00 0.00 31.29 4.00
2590 3008 2.344025 CCAAACCTGCCTAACTCGTAC 58.656 52.381 0.00 0.00 0.00 3.67
2790 3217 8.301002 GGTCTGTTTGGTTAGTTGCAATTATTA 58.699 33.333 0.59 0.00 0.00 0.98
2793 3220 5.010213 GGGTCTGTTTGGTTAGTTGCAATTA 59.990 40.000 0.59 0.00 0.00 1.40
2856 3289 8.893727 AGTTCTGGTACAATATTTCTGTTATGC 58.106 33.333 0.00 0.00 38.70 3.14
3079 3516 6.378848 AGGAGAAAGTAGATACAGACCAAGTC 59.621 42.308 0.00 0.00 0.00 3.01
3101 3538 2.928801 TGACTACAAAGCTGCAAGGA 57.071 45.000 1.02 0.00 0.00 3.36
3177 3616 4.576216 ACAACATATTGAACCGCACAAA 57.424 36.364 0.00 0.00 39.30 2.83
3185 3624 7.865706 AGGGACATTCTACAACATATTGAAC 57.134 36.000 0.00 0.00 39.30 3.18
3322 3761 7.952671 TCTATCTCCCTGTATGACAACATTAC 58.047 38.462 0.00 0.00 37.87 1.89
3529 3984 5.183331 TGTTCTGACTAGTAACTACTGGCTG 59.817 44.000 0.00 0.00 38.22 4.85
3530 3985 5.322754 TGTTCTGACTAGTAACTACTGGCT 58.677 41.667 0.00 0.00 38.22 4.75
3580 4039 5.902613 TGATTTGGAGGATCAACAATGTC 57.097 39.130 0.00 0.00 36.25 3.06
3624 4131 9.019656 TGTAATAGAGTATTGCAACCACAAATT 57.980 29.630 0.00 6.94 37.73 1.82
3690 4198 4.763793 CCATAAATTCTGCATGTAGAGGGG 59.236 45.833 13.45 6.80 0.00 4.79
3691 4199 5.240183 CACCATAAATTCTGCATGTAGAGGG 59.760 44.000 13.45 11.37 0.00 4.30
3825 4333 3.049344 GAGTTCCAAGGGAGGTGGATAT 58.951 50.000 0.00 0.00 44.62 1.63
3826 4334 2.478292 GAGTTCCAAGGGAGGTGGATA 58.522 52.381 0.00 0.00 44.62 2.59
3827 4335 1.290134 GAGTTCCAAGGGAGGTGGAT 58.710 55.000 0.00 0.00 44.62 3.41
3828 4336 0.840722 GGAGTTCCAAGGGAGGTGGA 60.841 60.000 0.00 0.00 43.57 4.02
3829 4337 1.133809 TGGAGTTCCAAGGGAGGTGG 61.134 60.000 0.00 0.00 44.35 4.61
3830 4338 2.463441 TGGAGTTCCAAGGGAGGTG 58.537 57.895 0.00 0.00 44.35 4.00
4025 4537 2.099427 TGTATCTGTTATGCCGCACGTA 59.901 45.455 0.00 0.00 0.00 3.57
4035 4549 3.319405 CGCTCCACTCCTGTATCTGTTAT 59.681 47.826 0.00 0.00 0.00 1.89
4138 4659 2.291930 ACCCCAAAAACACAGAACCTGA 60.292 45.455 0.45 0.00 35.18 3.86
4147 4670 2.099427 TCGCTACAAACCCCAAAAACAC 59.901 45.455 0.00 0.00 0.00 3.32
4148 4671 2.376109 TCGCTACAAACCCCAAAAACA 58.624 42.857 0.00 0.00 0.00 2.83
4149 4672 3.439895 TTCGCTACAAACCCCAAAAAC 57.560 42.857 0.00 0.00 0.00 2.43
4150 4673 3.304794 CGATTCGCTACAAACCCCAAAAA 60.305 43.478 0.00 0.00 0.00 1.94
4216 4751 6.406370 AGATCTGTGACAAATATGTTCGGAA 58.594 36.000 0.00 0.00 40.74 4.30
4226 4761 5.220472 CGCGTGATTAAGATCTGTGACAAAT 60.220 40.000 0.00 0.00 33.28 2.32
4270 4805 8.478066 AGCTAAATTAAAAGACATGGGATTTCC 58.522 33.333 0.00 0.00 0.00 3.13
4271 4806 9.305925 CAGCTAAATTAAAAGACATGGGATTTC 57.694 33.333 0.00 0.00 0.00 2.17
4272 4807 7.765819 GCAGCTAAATTAAAAGACATGGGATTT 59.234 33.333 0.00 0.00 0.00 2.17
4273 4808 7.267857 GCAGCTAAATTAAAAGACATGGGATT 58.732 34.615 0.00 0.00 0.00 3.01
4274 4809 6.183360 GGCAGCTAAATTAAAAGACATGGGAT 60.183 38.462 0.00 0.00 0.00 3.85
4275 4810 5.127031 GGCAGCTAAATTAAAAGACATGGGA 59.873 40.000 0.00 0.00 0.00 4.37
4276 4811 5.351458 GGCAGCTAAATTAAAAGACATGGG 58.649 41.667 0.00 0.00 0.00 4.00
4277 4812 5.036737 CGGCAGCTAAATTAAAAGACATGG 58.963 41.667 0.00 0.00 0.00 3.66
4278 4813 4.500477 GCGGCAGCTAAATTAAAAGACATG 59.500 41.667 0.00 0.00 41.01 3.21
4279 4814 4.440112 GGCGGCAGCTAAATTAAAAGACAT 60.440 41.667 9.17 0.00 44.37 3.06
4280 4815 3.119637 GGCGGCAGCTAAATTAAAAGACA 60.120 43.478 9.17 0.00 44.37 3.41
4281 4816 3.128764 AGGCGGCAGCTAAATTAAAAGAC 59.871 43.478 13.08 0.00 44.37 3.01
4282 4817 3.352648 AGGCGGCAGCTAAATTAAAAGA 58.647 40.909 13.08 0.00 44.37 2.52
4283 4818 3.782889 AGGCGGCAGCTAAATTAAAAG 57.217 42.857 13.08 0.00 44.37 2.27
4284 4819 4.703093 AGTTAGGCGGCAGCTAAATTAAAA 59.297 37.500 13.08 0.00 44.37 1.52
4285 4820 4.266714 AGTTAGGCGGCAGCTAAATTAAA 58.733 39.130 13.08 0.00 44.37 1.52
4286 4821 3.881220 AGTTAGGCGGCAGCTAAATTAA 58.119 40.909 13.08 0.00 44.37 1.40
4287 4822 3.553828 AGTTAGGCGGCAGCTAAATTA 57.446 42.857 13.08 0.00 44.37 1.40
4288 4823 2.420058 AGTTAGGCGGCAGCTAAATT 57.580 45.000 13.08 0.00 44.37 1.82
4289 4824 3.467803 CTTAGTTAGGCGGCAGCTAAAT 58.532 45.455 13.08 7.39 44.37 1.40
4290 4825 2.419574 CCTTAGTTAGGCGGCAGCTAAA 60.420 50.000 13.08 0.35 44.37 1.85
4291 4826 1.138266 CCTTAGTTAGGCGGCAGCTAA 59.862 52.381 13.08 14.46 44.37 3.09
4292 4827 0.750850 CCTTAGTTAGGCGGCAGCTA 59.249 55.000 13.08 7.40 44.37 3.32
4293 4828 1.522569 CCTTAGTTAGGCGGCAGCT 59.477 57.895 13.08 8.47 44.37 4.24
4294 4829 1.523938 CCCTTAGTTAGGCGGCAGC 60.524 63.158 13.08 0.00 43.27 5.25
4295 4830 0.179081 GACCCTTAGTTAGGCGGCAG 60.179 60.000 13.08 0.00 43.27 4.85
4296 4831 0.905809 TGACCCTTAGTTAGGCGGCA 60.906 55.000 13.08 0.00 43.27 5.69
4297 4832 0.179081 CTGACCCTTAGTTAGGCGGC 60.179 60.000 0.00 0.00 43.27 6.53
4298 4833 1.192428 ACTGACCCTTAGTTAGGCGG 58.808 55.000 0.00 0.00 43.27 6.13
4299 4834 2.100418 GGTACTGACCCTTAGTTAGGCG 59.900 54.545 0.00 0.00 43.27 5.52
4300 4835 3.102204 TGGTACTGACCCTTAGTTAGGC 58.898 50.000 0.00 0.00 46.32 3.93
4301 4836 4.607239 TCTGGTACTGACCCTTAGTTAGG 58.393 47.826 0.00 0.00 46.32 2.69
4302 4837 5.394333 GCTTCTGGTACTGACCCTTAGTTAG 60.394 48.000 0.00 0.00 46.32 2.34
4303 4838 4.465305 GCTTCTGGTACTGACCCTTAGTTA 59.535 45.833 0.00 0.00 46.32 2.24
4304 4839 3.261137 GCTTCTGGTACTGACCCTTAGTT 59.739 47.826 0.00 0.00 46.32 2.24
4305 4840 2.832733 GCTTCTGGTACTGACCCTTAGT 59.167 50.000 0.00 0.00 46.32 2.24
4306 4841 2.832129 TGCTTCTGGTACTGACCCTTAG 59.168 50.000 0.00 0.00 46.32 2.18
4307 4842 2.565834 GTGCTTCTGGTACTGACCCTTA 59.434 50.000 0.00 0.00 46.32 2.69
4308 4843 1.348036 GTGCTTCTGGTACTGACCCTT 59.652 52.381 0.00 0.00 46.32 3.95
4309 4844 0.977395 GTGCTTCTGGTACTGACCCT 59.023 55.000 0.00 0.00 46.32 4.34
4310 4845 0.036294 GGTGCTTCTGGTACTGACCC 60.036 60.000 0.00 0.00 46.32 4.46
4312 4847 0.977395 AGGGTGCTTCTGGTACTGAC 59.023 55.000 0.00 0.00 35.62 3.51
4313 4848 1.729586 AAGGGTGCTTCTGGTACTGA 58.270 50.000 0.00 0.00 33.53 3.41
4314 4849 2.568623 AAAGGGTGCTTCTGGTACTG 57.431 50.000 0.00 0.00 0.00 2.74
4315 4850 4.929146 AATAAAGGGTGCTTCTGGTACT 57.071 40.909 0.00 0.00 0.00 2.73
4316 4851 5.742063 AGTAATAAAGGGTGCTTCTGGTAC 58.258 41.667 0.00 0.00 0.00 3.34
4317 4852 6.382919 AAGTAATAAAGGGTGCTTCTGGTA 57.617 37.500 0.00 0.00 0.00 3.25
4318 4853 4.929146 AGTAATAAAGGGTGCTTCTGGT 57.071 40.909 0.00 0.00 0.00 4.00
4319 4854 7.110155 TCTAAAGTAATAAAGGGTGCTTCTGG 58.890 38.462 0.00 0.00 0.00 3.86
4320 4855 8.451748 GTTCTAAAGTAATAAAGGGTGCTTCTG 58.548 37.037 0.00 0.00 0.00 3.02
4321 4856 7.333672 CGTTCTAAAGTAATAAAGGGTGCTTCT 59.666 37.037 0.00 0.00 0.00 2.85
4322 4857 7.413767 CCGTTCTAAAGTAATAAAGGGTGCTTC 60.414 40.741 0.00 0.00 0.00 3.86
4323 4858 6.373495 CCGTTCTAAAGTAATAAAGGGTGCTT 59.627 38.462 0.00 0.00 0.00 3.91
4324 4859 5.878669 CCGTTCTAAAGTAATAAAGGGTGCT 59.121 40.000 0.00 0.00 0.00 4.40
4325 4860 5.876460 TCCGTTCTAAAGTAATAAAGGGTGC 59.124 40.000 0.00 0.00 0.00 5.01
4326 4861 9.257651 CTATCCGTTCTAAAGTAATAAAGGGTG 57.742 37.037 0.00 0.00 0.00 4.61
4327 4862 8.427276 CCTATCCGTTCTAAAGTAATAAAGGGT 58.573 37.037 0.00 0.00 0.00 4.34
4328 4863 8.645110 TCCTATCCGTTCTAAAGTAATAAAGGG 58.355 37.037 0.00 0.00 0.00 3.95
4335 4870 9.947433 TTCAAAATCCTATCCGTTCTAAAGTAA 57.053 29.630 0.00 0.00 0.00 2.24
4336 4871 9.947433 TTTCAAAATCCTATCCGTTCTAAAGTA 57.053 29.630 0.00 0.00 0.00 2.24
4337 4872 8.727910 GTTTCAAAATCCTATCCGTTCTAAAGT 58.272 33.333 0.00 0.00 0.00 2.66
4338 4873 8.182227 GGTTTCAAAATCCTATCCGTTCTAAAG 58.818 37.037 0.00 0.00 0.00 1.85
4339 4874 7.121611 GGGTTTCAAAATCCTATCCGTTCTAAA 59.878 37.037 0.00 0.00 36.23 1.85
4340 4875 6.600427 GGGTTTCAAAATCCTATCCGTTCTAA 59.400 38.462 0.00 0.00 36.23 2.10
4341 4876 6.117488 GGGTTTCAAAATCCTATCCGTTCTA 58.883 40.000 0.00 0.00 36.23 2.10
4342 4877 4.948004 GGGTTTCAAAATCCTATCCGTTCT 59.052 41.667 0.00 0.00 36.23 3.01
4343 4878 5.244785 GGGTTTCAAAATCCTATCCGTTC 57.755 43.478 0.00 0.00 36.23 3.95
4390 4925 1.413808 CCCCTGAAAACCTCCCCAAAA 60.414 52.381 0.00 0.00 0.00 2.44
4490 5025 0.183731 GGGGATTCCAGGGATCACAC 59.816 60.000 12.58 0.00 35.00 3.82
4519 5054 0.821711 CTCGGGGCTTCAAAACCACA 60.822 55.000 0.00 0.00 0.00 4.17
4630 5183 3.003763 GGAGAAGGGACACCGGCT 61.004 66.667 0.00 0.00 43.47 5.52
4650 5203 1.542915 CGAGAAGGACCGGTTTGTCTA 59.457 52.381 9.42 0.00 35.54 2.59
4672 5225 1.138266 GGCAGCGGAGACATACCTTTA 59.862 52.381 0.00 0.00 0.00 1.85
4674 5227 1.522569 GGCAGCGGAGACATACCTT 59.477 57.895 0.00 0.00 0.00 3.50
4680 5233 3.249189 AAAGGGGCAGCGGAGACA 61.249 61.111 0.00 0.00 0.00 3.41
4689 5242 1.697297 GAATGAGGGGAAAGGGGCA 59.303 57.895 0.00 0.00 0.00 5.36
4701 5254 2.412591 ACCCTAGGTGATGGGAATGAG 58.587 52.381 8.29 0.00 46.15 2.90
4702 5255 2.587060 ACCCTAGGTGATGGGAATGA 57.413 50.000 8.29 0.00 46.15 2.57
4764 5317 2.354259 GACGAGGAGAACGAAGGTCTA 58.646 52.381 0.00 0.00 34.70 2.59
4771 5327 1.378250 GGGAGGACGAGGAGAACGA 60.378 63.158 0.00 0.00 34.70 3.85
4800 5356 0.975556 TAGGAGATGGCGTGCTTGGA 60.976 55.000 0.00 0.00 0.00 3.53
4878 5434 4.248842 CGCGGTGGATATGGGGCA 62.249 66.667 0.00 0.00 0.00 5.36
4886 5442 4.241555 GGAGATGCCGCGGTGGAT 62.242 66.667 28.70 16.43 42.00 3.41
4894 5450 7.604164 ACAAAATACTCATATTAGGAGATGCCG 59.396 37.037 12.05 0.00 33.96 5.69
4939 5495 8.624776 ACATTTTAAAGAAGCTATATGCAGACC 58.375 33.333 0.00 0.00 45.94 3.85


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

AutoCloner maintained by Alex Coulton.