Multiple sequence alignment - TraesCS2A01G437600

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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 TraesCS2A01G437600 chr2A 100.000 4029 0 0 1 4029 689200630 689204658 0.000000e+00 7441.0
1 TraesCS2A01G437600 chr2A 100.000 42 0 0 3611 3652 689204197 689204238 1.200000e-10 78.7
2 TraesCS2A01G437600 chr2A 100.000 42 0 0 3568 3609 689204240 689204281 1.200000e-10 78.7
3 TraesCS2A01G437600 chr2A 94.444 36 1 1 3934 3969 102903301 102903267 2.000000e-03 54.7
4 TraesCS2A01G437600 chr2D 89.393 2206 147 35 259 2413 545854276 545852107 0.000000e+00 2697.0
5 TraesCS2A01G437600 chr2D 86.717 1069 74 25 2559 3618 545852003 545850994 0.000000e+00 1125.0
6 TraesCS2A01G437600 chr2D 88.018 434 21 7 3611 4029 545851044 545850627 6.050000e-133 484.0
7 TraesCS2A01G437600 chr2D 84.872 390 25 9 276 664 451008810 451009166 2.960000e-96 363.0
8 TraesCS2A01G437600 chr2D 80.000 285 32 9 1 261 545854652 545854369 1.910000e-43 187.0
9 TraesCS2A01G437600 chr2D 94.444 36 1 1 3934 3969 106370487 106370453 2.000000e-03 54.7
10 TraesCS2A01G437600 chr2B 89.005 1719 117 20 1 1652 652413346 652411633 0.000000e+00 2061.0
11 TraesCS2A01G437600 chr2B 86.557 729 66 14 2559 3269 652410602 652409888 0.000000e+00 774.0
12 TraesCS2A01G437600 chr2B 85.090 664 69 15 1761 2405 652411366 652410714 0.000000e+00 651.0
13 TraesCS2A01G437600 chr2B 83.295 437 27 13 3611 4029 652409592 652409184 1.060000e-95 361.0
14 TraesCS2A01G437600 chr2B 85.714 245 17 10 3380 3618 652409774 652409542 4.020000e-60 243.0
15 TraesCS2A01G437600 chr2B 94.444 36 1 1 3934 3969 155047514 155047480 2.000000e-03 54.7
16 TraesCS2A01G437600 chrUn 84.398 532 63 11 1885 2413 407129515 407129001 4.650000e-139 505.0
17 TraesCS2A01G437600 chrUn 84.023 532 64 12 1885 2413 299704291 299704804 3.620000e-135 492.0
18 TraesCS2A01G437600 chrUn 92.045 176 12 2 1704 1877 299703985 299704160 3.110000e-61 246.0
19 TraesCS2A01G437600 chrUn 92.727 110 8 0 1768 1877 352728641 352728750 4.170000e-35 159.0
20 TraesCS2A01G437600 chrUn 92.727 110 8 0 1768 1877 407129732 407129623 4.170000e-35 159.0
21 TraesCS2A01G437600 chr3D 84.211 532 64 11 1885 2413 29549793 29549279 2.160000e-137 499.0
22 TraesCS2A01G437600 chr3D 84.211 532 63 12 1885 2413 29510371 29509858 7.780000e-137 497.0
23 TraesCS2A01G437600 chr3D 92.045 176 12 2 1704 1877 29476542 29476367 3.110000e-61 246.0
24 TraesCS2A01G437600 chr3D 92.045 176 12 2 1704 1877 29510654 29510479 3.110000e-61 246.0
25 TraesCS2A01G437600 chr3D 92.045 176 12 2 1704 1877 29550076 29549901 3.110000e-61 246.0
26 TraesCS2A01G437600 chr3D 91.477 176 13 2 1704 1877 29547366 29547191 1.450000e-59 241.0
27 TraesCS2A01G437600 chr3D 94.118 51 3 0 2493 2543 579756431 579756381 1.200000e-10 78.7
28 TraesCS2A01G437600 chr7B 84.940 498 54 7 276 773 60368338 60368814 6.050000e-133 484.0
29 TraesCS2A01G437600 chr7B 83.203 512 51 14 276 773 486731305 486730815 1.720000e-118 436.0
30 TraesCS2A01G437600 chr4B 84.538 498 56 7 276 773 59871941 59871465 1.310000e-129 473.0
31 TraesCS2A01G437600 chr6D 84.314 459 51 7 272 730 14448204 14447767 2.880000e-116 429.0
32 TraesCS2A01G437600 chr6D 95.597 159 7 0 1174 1332 2958040 2957882 5.170000e-64 255.0
33 TraesCS2A01G437600 chr6D 92.157 51 4 0 2493 2543 224962342 224962292 5.590000e-09 73.1
34 TraesCS2A01G437600 chr5B 86.025 322 24 8 452 773 42945518 42945218 3.880000e-85 326.0
35 TraesCS2A01G437600 chr5B 94.118 51 3 0 2493 2543 48421177 48421127 1.200000e-10 78.7
36 TraesCS2A01G437600 chr5B 94.118 51 3 0 2493 2543 609936700 609936750 1.200000e-10 78.7
37 TraesCS2A01G437600 chr5B 88.136 59 7 0 2493 2551 383601378 383601436 2.010000e-08 71.3
38 TraesCS2A01G437600 chr7A 96.753 154 5 0 1178 1331 23331925 23331772 1.440000e-64 257.0
39 TraesCS2A01G437600 chr7D 88.479 217 17 5 1119 1331 22782268 22782056 5.170000e-64 255.0
40 TraesCS2A01G437600 chr7D 94.118 51 3 0 2493 2543 376942980 376943030 1.200000e-10 78.7
41 TraesCS2A01G437600 chr7D 91.667 48 4 0 2496 2543 556318890 556318843 2.600000e-07 67.6
42 TraesCS2A01G437600 chr4A 94.904 157 8 0 1175 1331 707036929 707037085 3.110000e-61 246.0
43 TraesCS2A01G437600 chr4A 92.157 51 4 0 2493 2543 381220543 381220593 5.590000e-09 73.1
44 TraesCS2A01G437600 chr6A 92.899 169 10 1 1164 1332 1985426 1985592 1.120000e-60 244.0
45 TraesCS2A01G437600 chr6B 94.304 158 9 0 1175 1332 6168628 6168471 4.020000e-60 243.0
46 TraesCS2A01G437600 chr3A 86.385 213 24 4 1125 1332 707465770 707465558 1.130000e-55 228.0
47 TraesCS2A01G437600 chr4D 94.118 51 3 0 2493 2543 277821365 277821315 1.200000e-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 TraesCS2A01G437600 chr2A 689200630 689204658 4028 False 2532.800000 7441 100.000000 1 4029 3 chr2A.!!$F1 4028
1 TraesCS2A01G437600 chr2D 545850627 545854652 4025 True 1123.250000 2697 86.032000 1 4029 4 chr2D.!!$R2 4028
2 TraesCS2A01G437600 chr2B 652409184 652413346 4162 True 818.000000 2061 85.932200 1 4029 5 chr2B.!!$R2 4028
3 TraesCS2A01G437600 chrUn 299703985 299704804 819 False 369.000000 492 88.034000 1704 2413 2 chrUn.!!$F2 709
4 TraesCS2A01G437600 chrUn 407129001 407129732 731 True 332.000000 505 88.562500 1768 2413 2 chrUn.!!$R1 645
5 TraesCS2A01G437600 chr3D 29509858 29510654 796 True 371.500000 497 88.128000 1704 2413 2 chr3D.!!$R3 709
6 TraesCS2A01G437600 chr3D 29547191 29550076 2885 True 328.666667 499 89.244333 1704 2413 3 chr3D.!!$R4 709

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
534 664 0.179140 CGCCCAAATTGCAATAGCGT 60.179 50.000 25.5 6.7 46.23 5.07 F
989 1148 1.146485 CTCCTCCGCTCGTCTCCTA 59.854 63.158 0.0 0.0 0.00 2.94 F
1691 2061 0.240945 CACCCTTTTGCTAACTGCGG 59.759 55.000 0.0 0.0 46.63 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 1645 0.596082 CGCACCCAAACCCAAAGTAG 59.404 55.0 0.00 0.00 0.00 2.57 R
2429 2970 2.099141 TGCACAGAACTGATAGTGGC 57.901 50.0 8.87 3.48 32.80 5.01 R
3051 3606 0.035056 GATAGCAGTGGGCCACTTGT 60.035 55.0 35.95 26.39 42.59 3.16 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
59 62 5.304357 ACATCCCAAAACTCCTAACAAAAGG 59.696 40.000 0.00 0.00 38.06 3.11
70 73 6.126739 ACTCCTAACAAAAGGGAAGCCTATAG 60.127 42.308 0.00 0.00 37.24 1.31
91 104 2.614057 GCACTATCCATGCTGTAACCAC 59.386 50.000 0.00 0.00 40.08 4.16
104 117 2.873472 TGTAACCACCTGCAGTTTTACG 59.127 45.455 13.81 0.00 31.16 3.18
109 122 1.531149 CACCTGCAGTTTTACGGACAG 59.469 52.381 13.81 0.00 0.00 3.51
111 124 2.069273 CCTGCAGTTTTACGGACAGAG 58.931 52.381 13.81 0.00 0.00 3.35
122 135 2.028130 ACGGACAGAGATAGCTGGAAG 58.972 52.381 0.00 0.00 40.20 3.46
123 136 2.302260 CGGACAGAGATAGCTGGAAGA 58.698 52.381 0.00 0.00 40.20 2.87
130 143 5.814705 ACAGAGATAGCTGGAAGAAAAATCG 59.185 40.000 0.00 0.00 40.20 3.34
137 150 3.989817 GCTGGAAGAAAAATCGCACAAAT 59.010 39.130 0.00 0.00 34.07 2.32
173 198 9.071276 AGAATACCAAATATCAACATTAGCTGG 57.929 33.333 0.00 0.00 0.00 4.85
196 221 4.642429 AGCTACAAAACTACCACAGAAGG 58.358 43.478 0.00 0.00 0.00 3.46
197 222 3.188667 GCTACAAAACTACCACAGAAGGC 59.811 47.826 0.00 0.00 0.00 4.35
267 393 0.618968 AGGGCCTGACTACCTTGGAG 60.619 60.000 4.50 0.00 0.00 3.86
270 396 0.324943 GCCTGACTACCTTGGAGCAA 59.675 55.000 0.00 0.00 0.00 3.91
274 400 3.476552 CTGACTACCTTGGAGCAACAAA 58.523 45.455 0.00 0.00 0.00 2.83
281 407 4.469657 ACCTTGGAGCAACAAACTAATCA 58.530 39.130 0.00 0.00 0.00 2.57
285 411 4.072131 TGGAGCAACAAACTAATCAGGTC 58.928 43.478 0.00 0.00 0.00 3.85
313 439 1.660607 CGTACATAGCAACAGCCACTG 59.339 52.381 0.00 0.00 37.52 3.66
340 466 0.181350 GTTGGATCTACCCAGGCAGG 59.819 60.000 0.00 0.00 37.53 4.85
357 483 3.399330 GCAGGTCTACACAAGCTTACAA 58.601 45.455 0.00 0.00 0.00 2.41
387 513 2.104253 GCCCACACATTACGGACCG 61.104 63.158 13.61 13.61 0.00 4.79
534 664 0.179140 CGCCCAAATTGCAATAGCGT 60.179 50.000 25.50 6.70 46.23 5.07
567 697 1.726845 CGAATCGACGAAACGACCCG 61.727 60.000 17.64 1.63 44.84 5.28
636 766 3.215975 ACGGGAAAAGAAATCAACGGAA 58.784 40.909 0.00 0.00 0.00 4.30
689 820 1.450491 CTGACGGAGAGAGGCGAGA 60.450 63.158 0.00 0.00 0.00 4.04
798 933 2.407361 CAGACTATTTATTACGGCCGCG 59.593 50.000 28.58 1.99 0.00 6.46
887 1022 2.679639 CGAATTGGGCCTGTTAGCACTA 60.680 50.000 4.53 0.00 36.97 2.74
888 1023 3.352648 GAATTGGGCCTGTTAGCACTAA 58.647 45.455 4.53 0.00 36.97 2.24
889 1024 3.669939 ATTGGGCCTGTTAGCACTAAT 57.330 42.857 4.53 0.00 36.97 1.73
989 1148 1.146485 CTCCTCCGCTCGTCTCCTA 59.854 63.158 0.00 0.00 0.00 2.94
991 1150 1.153127 CCTCCGCTCGTCTCCTACT 60.153 63.158 0.00 0.00 0.00 2.57
1363 1536 3.195661 GTTTGGCTCGATTTCTATCCGT 58.804 45.455 0.00 0.00 0.00 4.69
1367 1540 1.614413 GCTCGATTTCTATCCGTCCCT 59.386 52.381 0.00 0.00 0.00 4.20
1371 1544 2.095364 CGATTTCTATCCGTCCCTACCG 60.095 54.545 0.00 0.00 0.00 4.02
1437 1610 1.749638 CGGTGTAGCGAGGAGGAGT 60.750 63.158 0.00 0.00 0.00 3.85
1472 1645 2.661866 AACGTGTCCTGTGAGCGC 60.662 61.111 0.00 0.00 0.00 5.92
1508 1681 0.640768 GCGAGATTGACGAGGAAACG 59.359 55.000 0.00 0.00 39.31 3.60
1592 1773 8.843262 ACACATTGTGATAATTGGATATGAGTG 58.157 33.333 23.12 0.00 36.96 3.51
1615 1796 4.156739 GCCATCTTAGGTTTCAGTTTCCAG 59.843 45.833 0.00 0.00 0.00 3.86
1629 1810 4.150627 CAGTTTCCAGTTGATGTACAGTCG 59.849 45.833 0.33 0.00 0.00 4.18
1631 1812 5.010314 AGTTTCCAGTTGATGTACAGTCGTA 59.990 40.000 0.33 0.00 0.00 3.43
1691 2061 0.240945 CACCCTTTTGCTAACTGCGG 59.759 55.000 0.00 0.00 46.63 5.69
1696 2066 1.606668 CTTTTGCTAACTGCGGGTCAA 59.393 47.619 0.00 0.00 46.63 3.18
1699 2069 0.948678 TGCTAACTGCGGGTCAAAAC 59.051 50.000 0.00 0.00 46.63 2.43
1847 2225 2.025981 TCTGTGATCCTTTGGTGATGGG 60.026 50.000 0.00 0.00 0.00 4.00
1871 2249 7.147742 GGGTATATTGGTTCATGGACATTGTTT 60.148 37.037 6.44 0.00 0.00 2.83
1893 2394 5.895636 TTTTGTTCATGGGTATGCTACTG 57.104 39.130 0.00 0.00 34.21 2.74
2014 2515 7.589395 TGTTTGGCATATACTACTTGTTTGTG 58.411 34.615 0.00 0.00 0.00 3.33
2044 2545 8.031864 TGTTCAGTAGCTAATCTGAAGAGAAAG 58.968 37.037 21.12 0.00 46.62 2.62
2045 2546 7.710676 TCAGTAGCTAATCTGAAGAGAAAGT 57.289 36.000 10.74 0.00 37.69 2.66
2046 2547 8.128322 TCAGTAGCTAATCTGAAGAGAAAGTT 57.872 34.615 10.74 0.00 37.69 2.66
2047 2548 8.589338 TCAGTAGCTAATCTGAAGAGAAAGTTT 58.411 33.333 10.74 0.00 37.69 2.66
2049 2550 6.493449 AGCTAATCTGAAGAGAAAGTTTGC 57.507 37.500 0.00 0.00 0.00 3.68
2050 2551 6.237154 AGCTAATCTGAAGAGAAAGTTTGCT 58.763 36.000 0.00 0.00 0.00 3.91
2054 2555 9.985318 CTAATCTGAAGAGAAAGTTTGCTATTG 57.015 33.333 0.00 0.00 0.00 1.90
2055 2556 8.627208 AATCTGAAGAGAAAGTTTGCTATTGA 57.373 30.769 0.00 0.00 0.00 2.57
2059 2560 8.539770 TGAAGAGAAAGTTTGCTATTGACTAG 57.460 34.615 0.00 0.00 0.00 2.57
2273 2777 5.091552 AGAACAAGGACTATGGTGGTAAGA 58.908 41.667 0.00 0.00 0.00 2.10
2287 2791 8.766994 ATGGTGGTAAGATTATTGCTTATGTT 57.233 30.769 0.00 0.00 31.22 2.71
2292 2796 9.547753 TGGTAAGATTATTGCTTATGTTCTCTC 57.452 33.333 0.00 0.00 31.22 3.20
2308 2812 7.452880 TGTTCTCTCTATTCCATTGTTTTGG 57.547 36.000 0.00 0.00 38.18 3.28
2311 2815 4.331968 TCTCTATTCCATTGTTTTGGCGT 58.668 39.130 0.00 0.00 36.66 5.68
2315 2819 7.122055 TCTCTATTCCATTGTTTTGGCGTATTT 59.878 33.333 0.00 0.00 36.66 1.40
2354 2867 4.166144 AGCTGTTGGTAGGCCATACTTTAT 59.834 41.667 5.01 0.00 45.56 1.40
2359 2872 6.545666 TGTTGGTAGGCCATACTTTATGATTG 59.454 38.462 5.01 0.00 45.56 2.67
2365 2879 5.829924 AGGCCATACTTTATGATTGTCCTTG 59.170 40.000 5.01 0.00 38.45 3.61
2399 2913 6.484288 TGGTCAATCAGATTTGTGATACCTT 58.516 36.000 9.69 0.00 36.85 3.50
2401 2915 8.106462 TGGTCAATCAGATTTGTGATACCTTAA 58.894 33.333 9.69 0.00 36.85 1.85
2407 2921 9.699410 ATCAGATTTGTGATACCTTAATCCAAA 57.301 29.630 0.00 0.00 35.30 3.28
2449 2990 2.238144 AGCCACTATCAGTTCTGTGCAT 59.762 45.455 0.00 0.00 0.00 3.96
2456 2998 4.696899 ATCAGTTCTGTGCATTGATGTG 57.303 40.909 0.00 0.00 0.00 3.21
2461 3003 1.808343 TCTGTGCATTGATGTGCTCAC 59.192 47.619 0.00 0.00 45.27 3.51
2483 3025 7.751732 TCACTGCACAGTTTGATTCAATATAC 58.248 34.615 0.00 0.00 40.20 1.47
2485 3027 7.907045 CACTGCACAGTTTGATTCAATATACTC 59.093 37.037 0.00 0.00 40.20 2.59
2488 3030 6.543831 GCACAGTTTGATTCAATATACTCCCT 59.456 38.462 0.00 0.00 0.00 4.20
2490 3032 7.227512 CACAGTTTGATTCAATATACTCCCTCC 59.772 40.741 0.00 0.00 0.00 4.30
2491 3033 6.425114 CAGTTTGATTCAATATACTCCCTCCG 59.575 42.308 0.00 0.00 0.00 4.63
2492 3034 6.099845 AGTTTGATTCAATATACTCCCTCCGT 59.900 38.462 0.00 0.00 0.00 4.69
2493 3035 7.289317 AGTTTGATTCAATATACTCCCTCCGTA 59.711 37.037 0.00 0.00 0.00 4.02
2494 3036 6.835819 TGATTCAATATACTCCCTCCGTAG 57.164 41.667 0.00 0.00 0.00 3.51
2496 3038 7.182760 TGATTCAATATACTCCCTCCGTAGAT 58.817 38.462 0.00 0.00 0.00 1.98
2497 3039 8.333984 TGATTCAATATACTCCCTCCGTAGATA 58.666 37.037 0.00 0.00 0.00 1.98
2498 3040 7.934855 TTCAATATACTCCCTCCGTAGATAC 57.065 40.000 0.00 0.00 0.00 2.24
2499 3041 7.024345 TCAATATACTCCCTCCGTAGATACA 57.976 40.000 0.00 0.00 0.00 2.29
2500 3042 7.640313 TCAATATACTCCCTCCGTAGATACAT 58.360 38.462 0.00 0.00 0.00 2.29
2501 3043 8.114102 TCAATATACTCCCTCCGTAGATACATT 58.886 37.037 0.00 0.00 0.00 2.71
2502 3044 8.407064 CAATATACTCCCTCCGTAGATACATTC 58.593 40.741 0.00 0.00 0.00 2.67
2503 3045 3.147629 ACTCCCTCCGTAGATACATTCG 58.852 50.000 0.00 0.00 0.00 3.34
2504 3046 3.147629 CTCCCTCCGTAGATACATTCGT 58.852 50.000 0.00 0.00 0.00 3.85
2505 3047 4.202398 ACTCCCTCCGTAGATACATTCGTA 60.202 45.833 0.00 0.00 0.00 3.43
2506 3048 4.914983 TCCCTCCGTAGATACATTCGTAT 58.085 43.478 0.00 0.00 41.16 3.06
2507 3049 4.698780 TCCCTCCGTAGATACATTCGTATG 59.301 45.833 0.00 0.00 38.48 2.39
2508 3050 4.458295 CCCTCCGTAGATACATTCGTATGT 59.542 45.833 12.50 12.50 46.49 2.29
2523 3065 9.517609 ACATTCGTATGTAGACAAATCTAAGAC 57.482 33.333 5.81 0.00 43.12 3.01
2524 3066 9.516314 CATTCGTATGTAGACAAATCTAAGACA 57.484 33.333 0.00 0.00 39.20 3.41
2526 3068 9.569167 TTCGTATGTAGACAAATCTAAGACAAG 57.431 33.333 0.00 0.00 39.20 3.16
2527 3069 7.701078 TCGTATGTAGACAAATCTAAGACAAGC 59.299 37.037 0.00 0.00 39.20 4.01
2528 3070 7.702772 CGTATGTAGACAAATCTAAGACAAGCT 59.297 37.037 0.00 0.00 39.20 3.74
2529 3071 9.372369 GTATGTAGACAAATCTAAGACAAGCTT 57.628 33.333 0.00 0.00 39.20 3.74
2530 3072 8.854614 ATGTAGACAAATCTAAGACAAGCTTT 57.145 30.769 0.00 0.00 39.20 3.51
2531 3073 8.677148 TGTAGACAAATCTAAGACAAGCTTTT 57.323 30.769 0.00 0.00 39.20 2.27
2532 3074 9.120538 TGTAGACAAATCTAAGACAAGCTTTTT 57.879 29.630 0.00 0.00 39.20 1.94
2553 3095 6.610075 TTTTGGACGGAGGTAATAGTTACT 57.390 37.500 0.00 0.00 36.39 2.24
2554 3096 7.716799 TTTTGGACGGAGGTAATAGTTACTA 57.283 36.000 0.00 0.00 36.39 1.82
2555 3097 6.699575 TTGGACGGAGGTAATAGTTACTAC 57.300 41.667 0.00 0.00 36.39 2.73
2556 3098 5.754782 TGGACGGAGGTAATAGTTACTACA 58.245 41.667 0.00 0.00 36.39 2.74
2557 3099 6.367983 TGGACGGAGGTAATAGTTACTACAT 58.632 40.000 0.00 0.00 36.39 2.29
2633 3175 7.793948 AGTCAGTGTTAAGGTTATAGTCCTT 57.206 36.000 13.36 13.36 45.72 3.36
2666 3208 6.040842 CCTTTTGGAAAGACTGATCCTTCAAA 59.959 38.462 8.57 0.00 44.07 2.69
2677 3219 5.244402 ACTGATCCTTCAAACATGATTTGCA 59.756 36.000 0.00 0.00 0.00 4.08
2732 3275 1.002888 ACTGTTCACATGCCTCCTGAG 59.997 52.381 0.00 0.00 0.00 3.35
2739 3282 0.107703 CATGCCTCCTGAGCCGTTAA 60.108 55.000 0.00 0.00 0.00 2.01
2810 3365 5.699915 CCTATGCATACTTCTGTTCTCCATG 59.300 44.000 1.16 0.00 0.00 3.66
2829 3384 7.449395 TCTCCATGAAGAACATTTCTCACAAAT 59.551 33.333 0.00 0.00 39.61 2.32
2859 3414 4.718940 ATTTGTCCCGGATTTTCATCAC 57.281 40.909 0.73 0.00 0.00 3.06
3045 3600 2.920912 ACATGTCCCCGTCGGTGT 60.921 61.111 11.06 4.50 0.00 4.16
3075 3630 2.280457 GCCCACTGCTATCGCTCC 60.280 66.667 0.00 0.00 36.87 4.70
3187 3746 5.130292 TCTTCACGAACTGTAGGTTAAGG 57.870 43.478 0.00 0.00 38.41 2.69
3205 3764 3.876274 AGGACTGCATGTACTACTGTG 57.124 47.619 0.00 0.00 38.27 3.66
3289 3848 2.634453 TCATGTGTTTGGAGCTCTGAGA 59.366 45.455 14.64 0.00 0.00 3.27
3290 3849 3.262660 TCATGTGTTTGGAGCTCTGAGAT 59.737 43.478 14.64 0.55 0.00 2.75
3291 3850 3.777106 TGTGTTTGGAGCTCTGAGATT 57.223 42.857 14.64 0.00 0.00 2.40
3292 3851 4.890158 TGTGTTTGGAGCTCTGAGATTA 57.110 40.909 14.64 0.00 0.00 1.75
3293 3852 5.426689 TGTGTTTGGAGCTCTGAGATTAT 57.573 39.130 14.64 0.00 0.00 1.28
3294 3853 5.809001 TGTGTTTGGAGCTCTGAGATTATT 58.191 37.500 14.64 0.00 0.00 1.40
3295 3854 6.240894 TGTGTTTGGAGCTCTGAGATTATTT 58.759 36.000 14.64 0.00 0.00 1.40
3296 3855 6.716628 TGTGTTTGGAGCTCTGAGATTATTTT 59.283 34.615 14.64 0.00 0.00 1.82
3297 3856 7.094634 TGTGTTTGGAGCTCTGAGATTATTTTC 60.095 37.037 14.64 0.00 0.00 2.29
3298 3857 6.942005 TGTTTGGAGCTCTGAGATTATTTTCA 59.058 34.615 14.64 0.00 0.00 2.69
3299 3858 6.992063 TTGGAGCTCTGAGATTATTTTCAC 57.008 37.500 14.64 0.00 0.00 3.18
3300 3859 6.305272 TGGAGCTCTGAGATTATTTTCACT 57.695 37.500 14.64 0.00 0.00 3.41
3301 3860 6.344500 TGGAGCTCTGAGATTATTTTCACTC 58.656 40.000 14.64 1.30 0.00 3.51
3302 3861 5.461737 GGAGCTCTGAGATTATTTTCACTCG 59.538 44.000 14.64 0.00 32.81 4.18
3303 3862 5.971763 AGCTCTGAGATTATTTTCACTCGT 58.028 37.500 9.28 0.00 32.81 4.18
3304 3863 5.809562 AGCTCTGAGATTATTTTCACTCGTG 59.190 40.000 9.28 0.00 32.81 4.35
3305 3864 5.807520 GCTCTGAGATTATTTTCACTCGTGA 59.192 40.000 9.28 0.00 37.91 4.35
3313 3872 9.334947 AGATTATTTTCACTCGTGATGATGAAT 57.665 29.630 0.00 0.00 39.64 2.57
3321 3880 3.829026 CTCGTGATGATGAATCCTCCCTA 59.171 47.826 0.00 0.00 34.00 3.53
3340 3899 3.199946 CCTACCCTGTTTCAGCTCCATTA 59.800 47.826 0.00 0.00 0.00 1.90
3341 3900 3.806949 ACCCTGTTTCAGCTCCATTAA 57.193 42.857 0.00 0.00 0.00 1.40
3342 3901 4.322057 ACCCTGTTTCAGCTCCATTAAT 57.678 40.909 0.00 0.00 0.00 1.40
3343 3902 4.677182 ACCCTGTTTCAGCTCCATTAATT 58.323 39.130 0.00 0.00 0.00 1.40
3421 4962 5.878669 TCAGAAATCATCCATCTCTGTGTTG 59.121 40.000 0.00 0.00 35.93 3.33
3457 5001 4.742201 CAGTGACCACGGGAGGCG 62.742 72.222 0.00 0.00 36.20 5.52
3585 5259 2.741092 ACGTGCAGGTCCGTGATT 59.259 55.556 6.15 0.00 35.69 2.57
3586 5260 1.667830 ACGTGCAGGTCCGTGATTG 60.668 57.895 6.15 0.00 35.69 2.67
3587 5261 2.390599 CGTGCAGGTCCGTGATTGG 61.391 63.158 0.00 0.00 0.00 3.16
3589 5263 2.045926 GCAGGTCCGTGATTGGCT 60.046 61.111 0.00 0.00 0.00 4.75
3590 5264 2.401766 GCAGGTCCGTGATTGGCTG 61.402 63.158 0.00 0.00 0.00 4.85
3591 5265 2.045926 AGGTCCGTGATTGGCTGC 60.046 61.111 0.00 0.00 0.00 5.25
3593 5267 2.045926 GTCCGTGATTGGCTGCCT 60.046 61.111 21.03 0.00 0.00 4.75
3596 5270 0.546122 TCCGTGATTGGCTGCCTTAT 59.454 50.000 21.03 13.08 0.00 1.73
3598 5272 0.947244 CGTGATTGGCTGCCTTATCC 59.053 55.000 21.03 13.88 0.00 2.59
3600 5274 0.819259 TGATTGGCTGCCTTATCCGC 60.819 55.000 21.03 3.07 0.00 5.54
3602 5276 4.545706 TGGCTGCCTTATCCGCCG 62.546 66.667 21.03 0.00 45.36 6.46
3603 5277 4.235762 GGCTGCCTTATCCGCCGA 62.236 66.667 12.43 0.00 32.22 5.54
3604 5278 2.203015 GCTGCCTTATCCGCCGAA 60.203 61.111 0.00 0.00 0.00 4.30
3605 5279 1.598130 GCTGCCTTATCCGCCGAAT 60.598 57.895 0.00 0.00 0.00 3.34
3606 5280 1.569479 GCTGCCTTATCCGCCGAATC 61.569 60.000 0.00 0.00 0.00 2.52
3607 5281 0.951040 CTGCCTTATCCGCCGAATCC 60.951 60.000 0.00 0.00 0.00 3.01
3608 5282 1.371558 GCCTTATCCGCCGAATCCT 59.628 57.895 0.00 0.00 0.00 3.24
3610 5284 1.672145 GCCTTATCCGCCGAATCCTAC 60.672 57.143 0.00 0.00 0.00 3.18
3611 5285 1.616865 CCTTATCCGCCGAATCCTACA 59.383 52.381 0.00 0.00 0.00 2.74
3612 5286 2.609737 CCTTATCCGCCGAATCCTACAC 60.610 54.545 0.00 0.00 0.00 2.90
3613 5287 0.594602 TATCCGCCGAATCCTACACG 59.405 55.000 0.00 0.00 0.00 4.49
3614 5288 1.389609 ATCCGCCGAATCCTACACGT 61.390 55.000 0.00 0.00 0.00 4.49
3615 5289 1.876714 CCGCCGAATCCTACACGTG 60.877 63.158 15.48 15.48 0.00 4.49
3617 5291 1.447140 GCCGAATCCTACACGTGCA 60.447 57.895 17.22 0.49 0.00 4.57
3618 5292 1.421410 GCCGAATCCTACACGTGCAG 61.421 60.000 17.22 12.81 0.00 4.41
3619 5293 0.806102 CCGAATCCTACACGTGCAGG 60.806 60.000 26.33 26.33 0.00 4.85
3620 5294 0.108804 CGAATCCTACACGTGCAGGT 60.109 55.000 29.64 15.24 33.37 4.00
3629 5303 1.667830 ACGTGCAGGTCCGTGATTG 60.668 57.895 6.15 0.00 35.69 2.67
3661 5335 2.109799 CGAATCCTCCCGCTGCAT 59.890 61.111 0.00 0.00 0.00 3.96
3662 5336 2.249535 CGAATCCTCCCGCTGCATG 61.250 63.158 0.00 0.00 0.00 4.06
3663 5337 2.517875 AATCCTCCCGCTGCATGC 60.518 61.111 11.82 11.82 38.57 4.06
3664 5338 4.575973 ATCCTCCCGCTGCATGCC 62.576 66.667 16.68 0.00 38.78 4.40
3668 5342 4.488136 TCCCGCTGCATGCCGAAT 62.488 61.111 16.68 0.00 38.78 3.34
3743 5417 3.060663 GCGAGCGCTCAAGTCGAAC 62.061 63.158 34.69 7.57 35.70 3.95
3779 5453 3.453679 GGCGCGACCTTCCTCTCT 61.454 66.667 12.10 0.00 34.51 3.10
3854 5537 1.597663 GCACACGTATGTATGCTTCCC 59.402 52.381 11.12 0.00 36.72 3.97
3860 5543 3.069016 ACGTATGTATGCTTCCCGATTCA 59.931 43.478 0.00 0.00 0.00 2.57
3864 5547 2.158957 TGTATGCTTCCCGATTCAGACC 60.159 50.000 0.00 0.00 0.00 3.85
3878 5561 3.519930 GACCGCGAGTCCCCTCTC 61.520 72.222 8.23 0.00 39.84 3.20
3879 5562 4.361971 ACCGCGAGTCCCCTCTCA 62.362 66.667 8.23 0.00 35.43 3.27
3882 5565 2.107953 GCGAGTCCCCTCTCATGC 59.892 66.667 0.00 0.00 35.43 4.06
3884 5567 1.109920 GCGAGTCCCCTCTCATGCTA 61.110 60.000 0.00 0.00 35.43 3.49
3885 5568 1.403814 CGAGTCCCCTCTCATGCTAA 58.596 55.000 0.00 0.00 35.43 3.09
3886 5569 1.339610 CGAGTCCCCTCTCATGCTAAG 59.660 57.143 0.00 0.00 35.43 2.18
3887 5570 2.393646 GAGTCCCCTCTCATGCTAAGT 58.606 52.381 0.00 0.00 34.69 2.24
3888 5571 2.769095 GAGTCCCCTCTCATGCTAAGTT 59.231 50.000 0.00 0.00 34.69 2.66
3889 5572 3.961408 GAGTCCCCTCTCATGCTAAGTTA 59.039 47.826 0.00 0.00 34.69 2.24
3890 5573 4.362677 AGTCCCCTCTCATGCTAAGTTAA 58.637 43.478 0.00 0.00 0.00 2.01
3891 5574 4.162509 AGTCCCCTCTCATGCTAAGTTAAC 59.837 45.833 0.00 0.00 0.00 2.01
3931 5628 3.677648 GTGTGCTGCCAGGCCAAG 61.678 66.667 9.64 0.87 0.00 3.61
3932 5629 4.208403 TGTGCTGCCAGGCCAAGT 62.208 61.111 9.64 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.717436 TGTTATGTGACATTCTGTGTTTTAGGA 59.283 33.333 2.29 0.00 42.36 2.94
12 13 7.870826 TGTTATGTGACATTCTGTGTTTTAGG 58.129 34.615 2.29 0.00 42.36 2.69
15 16 7.370383 GGATGTTATGTGACATTCTGTGTTTT 58.630 34.615 2.29 0.00 42.36 2.43
21 22 6.513806 TTTGGGATGTTATGTGACATTCTG 57.486 37.500 2.29 0.00 40.21 3.02
59 62 4.764172 CATGGATAGTGCTATAGGCTTCC 58.236 47.826 1.04 0.00 42.39 3.46
70 73 2.614057 GTGGTTACAGCATGGATAGTGC 59.386 50.000 0.00 0.00 43.62 4.40
82 85 3.059188 CGTAAAACTGCAGGTGGTTACAG 60.059 47.826 20.81 12.52 32.89 2.74
89 102 1.531149 CTGTCCGTAAAACTGCAGGTG 59.469 52.381 19.93 0.00 0.00 4.00
91 104 2.069273 CTCTGTCCGTAAAACTGCAGG 58.931 52.381 19.93 0.00 0.00 4.85
104 117 4.744795 TTTCTTCCAGCTATCTCTGTCC 57.255 45.455 0.00 0.00 32.32 4.02
109 122 4.572389 TGCGATTTTTCTTCCAGCTATCTC 59.428 41.667 0.00 0.00 0.00 2.75
111 124 4.094887 TGTGCGATTTTTCTTCCAGCTATC 59.905 41.667 0.00 0.00 0.00 2.08
169 185 2.742589 GTGGTAGTTTTGTAGCTCCAGC 59.257 50.000 0.00 0.00 42.49 4.85
173 198 4.691216 CCTTCTGTGGTAGTTTTGTAGCTC 59.309 45.833 0.00 0.00 0.00 4.09
251 282 0.324943 TTGCTCCAAGGTAGTCAGGC 59.675 55.000 0.00 0.00 0.00 4.85
254 285 3.118038 AGTTTGTTGCTCCAAGGTAGTCA 60.118 43.478 0.00 0.00 0.00 3.41
255 286 3.477530 AGTTTGTTGCTCCAAGGTAGTC 58.522 45.455 0.00 0.00 0.00 2.59
267 393 7.062255 GCTAAATTGACCTGATTAGTTTGTTGC 59.938 37.037 0.00 0.00 0.00 4.17
270 396 6.430000 ACGCTAAATTGACCTGATTAGTTTGT 59.570 34.615 0.00 0.00 0.00 2.83
274 400 6.636705 TGTACGCTAAATTGACCTGATTAGT 58.363 36.000 0.00 0.00 0.00 2.24
281 407 5.018539 TGCTATGTACGCTAAATTGACCT 57.981 39.130 0.00 0.00 0.00 3.85
285 411 4.963953 GCTGTTGCTATGTACGCTAAATTG 59.036 41.667 0.00 0.00 36.03 2.32
313 439 4.503991 CCTGGGTAGATCCAACTATTCTGC 60.504 50.000 0.00 0.00 36.21 4.26
357 483 1.997311 TGTGGGCATCTAGCTGGCT 60.997 57.895 18.26 0.00 44.79 4.75
387 513 2.819608 TGGATTTGCAGTTTGAGGTAGC 59.180 45.455 0.00 0.00 0.00 3.58
534 664 0.031314 GATTCGATCCTGCTCGCTCA 59.969 55.000 0.00 0.00 38.52 4.26
678 808 4.211986 GAGTCGTCTCGCCTCTCT 57.788 61.111 0.00 0.00 0.00 3.10
689 820 0.594602 TTCCACGTGATTCGAGTCGT 59.405 50.000 19.30 0.00 42.86 4.34
777 908 2.407361 CGCGGCCGTAATAAATAGTCTG 59.593 50.000 28.70 0.00 0.00 3.51
798 933 3.603770 GCACAAGACAACGATACAATTGC 59.396 43.478 5.05 0.00 0.00 3.56
871 1006 3.118038 CCTTATTAGTGCTAACAGGCCCA 60.118 47.826 0.00 0.00 0.00 5.36
1281 1454 3.573598 GATGTAGCAGTCGATCATCTGG 58.426 50.000 13.56 0.26 34.12 3.86
1342 1515 3.195661 ACGGATAGAAATCGAGCCAAAC 58.804 45.455 0.00 0.00 32.44 2.93
1367 1540 2.356075 CGCGAAACACCCACGGTA 60.356 61.111 0.00 0.00 32.11 4.02
1371 1544 1.209127 CATTCCGCGAAACACCCAC 59.791 57.895 8.23 0.00 0.00 4.61
1378 1551 2.325583 ATTAGCCTCATTCCGCGAAA 57.674 45.000 8.23 0.00 0.00 3.46
1437 1610 4.008330 ACGTTGTAGATCCTCTTCTTCGA 58.992 43.478 0.00 0.00 0.00 3.71
1472 1645 0.596082 CGCACCCAAACCCAAAGTAG 59.404 55.000 0.00 0.00 0.00 2.57
1508 1681 2.561478 TACCTTCCAGCTTGTTGGAC 57.439 50.000 5.70 0.00 46.61 4.02
1550 1723 8.531622 CACAATGTGTGCTTAAATATGGAAAA 57.468 30.769 5.00 0.00 41.89 2.29
1574 1755 7.024345 AGATGGCACTCATATCCAATTATCA 57.976 36.000 0.00 0.00 35.97 2.15
1586 1767 4.018960 ACTGAAACCTAAGATGGCACTCAT 60.019 41.667 0.00 0.00 39.13 2.90
1589 1770 4.373156 AACTGAAACCTAAGATGGCACT 57.627 40.909 0.00 0.00 0.00 4.40
1590 1771 4.082733 GGAAACTGAAACCTAAGATGGCAC 60.083 45.833 0.00 0.00 0.00 5.01
1592 1773 4.079253 TGGAAACTGAAACCTAAGATGGC 58.921 43.478 0.00 0.00 0.00 4.40
1615 1796 6.946229 ACTGAAATACGACTGTACATCAAC 57.054 37.500 0.00 0.00 31.74 3.18
1674 2044 0.893727 ACCCGCAGTTAGCAAAAGGG 60.894 55.000 0.00 0.00 46.13 3.95
1691 2061 5.793026 TTTGCACTTGAAATGTTTTGACC 57.207 34.783 0.00 0.00 0.00 4.02
1699 2069 5.970140 TCACACATTTTGCACTTGAAATG 57.030 34.783 16.43 16.43 44.68 2.32
1847 2225 9.651913 AAAAACAATGTCCATGAACCAATATAC 57.348 29.630 0.00 0.00 0.00 1.47
1871 2249 4.157656 GCAGTAGCATACCCATGAACAAAA 59.842 41.667 0.00 0.00 44.47 2.44
1893 2394 3.252458 ACCATCAACGAAGGTAAAAGTGC 59.748 43.478 0.00 0.00 31.49 4.40
1901 2402 3.369471 CCTGATACACCATCAACGAAGGT 60.369 47.826 0.00 0.00 43.15 3.50
2002 2503 6.377327 ACTGAACATTCCACAAACAAGTAG 57.623 37.500 0.00 0.00 0.00 2.57
2003 2504 6.017440 GCTACTGAACATTCCACAAACAAGTA 60.017 38.462 0.00 0.00 0.00 2.24
2004 2505 5.221048 GCTACTGAACATTCCACAAACAAGT 60.221 40.000 0.00 0.00 0.00 3.16
2014 2515 7.268586 TCTTCAGATTAGCTACTGAACATTCC 58.731 38.462 18.18 0.00 44.59 3.01
2044 2545 6.035112 GCTGTACTCACTAGTCAATAGCAAAC 59.965 42.308 0.00 0.00 37.15 2.93
2045 2546 6.071334 AGCTGTACTCACTAGTCAATAGCAAA 60.071 38.462 12.86 0.00 37.15 3.68
2046 2547 5.419155 AGCTGTACTCACTAGTCAATAGCAA 59.581 40.000 12.86 0.00 37.15 3.91
2047 2548 4.950475 AGCTGTACTCACTAGTCAATAGCA 59.050 41.667 12.86 1.21 37.15 3.49
2049 2550 7.089770 TGAAGCTGTACTCACTAGTCAATAG 57.910 40.000 0.00 0.00 37.15 1.73
2050 2551 6.659668 ACTGAAGCTGTACTCACTAGTCAATA 59.340 38.462 0.00 0.00 37.15 1.90
2054 2555 4.216687 ACACTGAAGCTGTACTCACTAGTC 59.783 45.833 0.00 0.00 37.15 2.59
2055 2556 4.145807 ACACTGAAGCTGTACTCACTAGT 58.854 43.478 0.00 0.00 39.91 2.57
2059 2560 4.627467 CCATAACACTGAAGCTGTACTCAC 59.373 45.833 0.00 0.00 0.00 3.51
2180 2684 6.266558 AGGCCTGTATATTGAAAACACAAACA 59.733 34.615 3.11 0.00 33.44 2.83
2287 2791 4.635765 CGCCAAAACAATGGAATAGAGAGA 59.364 41.667 0.00 0.00 43.54 3.10
2292 2796 7.826260 AAAATACGCCAAAACAATGGAATAG 57.174 32.000 0.00 0.00 43.54 1.73
2308 2812 7.376072 AGCTAGCATAAAATTCGAAAAATACGC 59.624 33.333 18.83 1.74 0.00 4.42
2315 2819 6.072175 ACCAACAGCTAGCATAAAATTCGAAA 60.072 34.615 18.83 0.00 0.00 3.46
2354 2867 6.542821 ACCAATTCTACTTCAAGGACAATCA 58.457 36.000 0.00 0.00 0.00 2.57
2359 2872 6.655003 TGATTGACCAATTCTACTTCAAGGAC 59.345 38.462 0.00 0.00 30.07 3.85
2365 2879 8.734386 ACAAATCTGATTGACCAATTCTACTTC 58.266 33.333 3.22 0.00 34.38 3.01
2407 2921 7.497249 GTGGCTCATTAAGTAGAATCAAGTCAT 59.503 37.037 0.00 0.00 0.00 3.06
2429 2970 2.099141 TGCACAGAACTGATAGTGGC 57.901 50.000 8.87 3.48 32.80 5.01
2456 2998 2.291465 TGAATCAAACTGTGCAGTGAGC 59.709 45.455 5.53 0.00 41.58 4.26
2461 3003 7.412853 GGAGTATATTGAATCAAACTGTGCAG 58.587 38.462 0.00 0.00 0.00 4.41
2475 3017 7.024345 TGTATCTACGGAGGGAGTATATTGA 57.976 40.000 0.00 0.00 0.00 2.57
2483 3025 3.147629 ACGAATGTATCTACGGAGGGAG 58.852 50.000 0.00 0.00 0.00 4.30
2485 3027 4.458295 ACATACGAATGTATCTACGGAGGG 59.542 45.833 0.00 0.00 44.66 4.30
2488 3030 6.930722 TGTCTACATACGAATGTATCTACGGA 59.069 38.462 0.00 0.00 45.33 4.69
2490 3032 8.998558 TTTGTCTACATACGAATGTATCTACG 57.001 34.615 0.00 0.00 45.33 3.51
2498 3040 9.516314 TGTCTTAGATTTGTCTACATACGAATG 57.484 33.333 0.00 0.00 34.30 2.67
2500 3042 9.569167 CTTGTCTTAGATTTGTCTACATACGAA 57.431 33.333 0.00 0.00 0.00 3.85
2501 3043 7.701078 GCTTGTCTTAGATTTGTCTACATACGA 59.299 37.037 0.00 0.00 0.00 3.43
2502 3044 7.702772 AGCTTGTCTTAGATTTGTCTACATACG 59.297 37.037 0.00 0.00 0.00 3.06
2503 3045 8.934507 AGCTTGTCTTAGATTTGTCTACATAC 57.065 34.615 0.00 0.00 0.00 2.39
2504 3046 9.944376 AAAGCTTGTCTTAGATTTGTCTACATA 57.056 29.630 0.00 0.00 32.91 2.29
2505 3047 8.854614 AAAGCTTGTCTTAGATTTGTCTACAT 57.145 30.769 0.00 0.00 32.91 2.29
2506 3048 8.677148 AAAAGCTTGTCTTAGATTTGTCTACA 57.323 30.769 0.00 0.00 34.28 2.74
2529 3071 7.008021 AGTAACTATTACCTCCGTCCAAAAA 57.992 36.000 0.00 0.00 36.81 1.94
2530 3072 6.610075 AGTAACTATTACCTCCGTCCAAAA 57.390 37.500 0.00 0.00 36.81 2.44
2531 3073 6.663093 TGTAGTAACTATTACCTCCGTCCAAA 59.337 38.462 0.00 0.00 36.81 3.28
2532 3074 6.186957 TGTAGTAACTATTACCTCCGTCCAA 58.813 40.000 0.00 0.00 36.81 3.53
2533 3075 5.754782 TGTAGTAACTATTACCTCCGTCCA 58.245 41.667 0.00 0.00 36.81 4.02
2534 3076 6.890979 ATGTAGTAACTATTACCTCCGTCC 57.109 41.667 0.00 0.00 36.81 4.79
2535 3077 8.840321 TGTAATGTAGTAACTATTACCTCCGTC 58.160 37.037 0.00 0.00 36.78 4.79
2536 3078 8.752005 TGTAATGTAGTAACTATTACCTCCGT 57.248 34.615 0.00 0.00 36.78 4.69
2537 3079 9.622004 CATGTAATGTAGTAACTATTACCTCCG 57.378 37.037 0.00 0.00 40.20 4.63
2549 3091 9.391006 GGTTTCCTCAATCATGTAATGTAGTAA 57.609 33.333 0.00 0.00 46.80 2.24
2550 3092 8.768397 AGGTTTCCTCAATCATGTAATGTAGTA 58.232 33.333 0.00 0.00 46.80 1.82
2551 3093 7.633789 AGGTTTCCTCAATCATGTAATGTAGT 58.366 34.615 0.00 0.00 46.80 2.73
2552 3094 8.511604 AAGGTTTCCTCAATCATGTAATGTAG 57.488 34.615 0.00 0.00 38.22 2.74
2554 3096 9.479549 AATAAGGTTTCCTCAATCATGTAATGT 57.520 29.630 0.00 0.00 38.22 2.71
2591 3133 9.243105 ACACTGACTAATAAATTAATGCACCTT 57.757 29.630 0.00 0.00 0.00 3.50
2592 3134 8.807948 ACACTGACTAATAAATTAATGCACCT 57.192 30.769 0.00 0.00 0.00 4.00
2625 3167 9.768215 TTTCCAAAAGGATCATTTAAGGACTAT 57.232 29.630 20.18 0.00 30.58 2.12
2626 3168 9.243105 CTTTCCAAAAGGATCATTTAAGGACTA 57.757 33.333 20.18 13.25 30.58 2.59
2633 3175 8.884124 ATCAGTCTTTCCAAAAGGATCATTTA 57.116 30.769 5.67 0.00 0.00 1.40
2677 3219 7.505923 GGTATAAACCCTTGAATAGAAAGCCAT 59.494 37.037 0.00 0.00 40.21 4.40
2732 3275 3.546002 TGCACTTGTACAATTAACGGC 57.454 42.857 9.13 4.07 0.00 5.68
2739 3282 6.594788 AAGGATCAATTGCACTTGTACAAT 57.405 33.333 15.50 2.97 38.11 2.71
2829 3384 4.705110 ATCCGGGACAAATATGATCACA 57.295 40.909 0.00 0.00 0.00 3.58
2835 3390 6.208644 GTGATGAAAATCCGGGACAAATATG 58.791 40.000 0.00 0.00 0.00 1.78
2838 3393 3.128589 CGTGATGAAAATCCGGGACAAAT 59.871 43.478 0.00 0.00 0.00 2.32
3045 3600 3.561241 TGGGCCACTTGTGCGGTA 61.561 61.111 0.00 0.00 0.00 4.02
3050 3605 0.322816 ATAGCAGTGGGCCACTTGTG 60.323 55.000 35.95 25.86 42.59 3.33
3051 3606 0.035056 GATAGCAGTGGGCCACTTGT 60.035 55.000 35.95 26.39 42.59 3.16
3075 3630 3.999663 GCAGTTGCTATATCTAGGGCAAG 59.000 47.826 0.00 0.00 43.76 4.01
3187 3746 4.082733 TCACTCACAGTAGTACATGCAGTC 60.083 45.833 2.52 0.00 0.00 3.51
3205 3764 4.095610 CAAAACAACGGAACAAGTCACTC 58.904 43.478 0.00 0.00 0.00 3.51
3289 3848 8.562892 GGATTCATCATCACGAGTGAAAATAAT 58.437 33.333 10.15 6.89 43.58 1.28
3290 3849 7.770433 AGGATTCATCATCACGAGTGAAAATAA 59.230 33.333 10.15 2.68 43.58 1.40
3291 3850 7.275183 AGGATTCATCATCACGAGTGAAAATA 58.725 34.615 10.15 0.00 43.58 1.40
3292 3851 6.118170 AGGATTCATCATCACGAGTGAAAAT 58.882 36.000 10.15 4.26 43.58 1.82
3293 3852 5.491070 AGGATTCATCATCACGAGTGAAAA 58.509 37.500 10.15 2.03 43.58 2.29
3294 3853 5.089970 AGGATTCATCATCACGAGTGAAA 57.910 39.130 10.15 2.38 43.58 2.69
3295 3854 4.442052 GGAGGATTCATCATCACGAGTGAA 60.442 45.833 10.15 0.00 43.58 3.18
3296 3855 3.068732 GGAGGATTCATCATCACGAGTGA 59.931 47.826 8.48 8.48 44.59 3.41
3297 3856 3.388308 GGAGGATTCATCATCACGAGTG 58.612 50.000 4.00 0.00 39.21 3.51
3298 3857 2.366916 GGGAGGATTCATCATCACGAGT 59.633 50.000 4.00 0.00 39.21 4.18
3299 3858 2.632028 AGGGAGGATTCATCATCACGAG 59.368 50.000 4.00 0.00 45.03 4.18
3300 3859 2.682594 AGGGAGGATTCATCATCACGA 58.317 47.619 4.00 0.00 45.03 4.35
3301 3860 3.306364 GGTAGGGAGGATTCATCATCACG 60.306 52.174 4.00 0.00 45.03 4.35
3302 3861 3.008485 GGGTAGGGAGGATTCATCATCAC 59.992 52.174 4.00 0.00 41.05 3.06
3303 3862 3.116199 AGGGTAGGGAGGATTCATCATCA 60.116 47.826 4.00 0.00 39.21 3.07
3304 3863 3.262915 CAGGGTAGGGAGGATTCATCATC 59.737 52.174 0.25 0.00 36.91 2.92
3305 3864 3.254960 CAGGGTAGGGAGGATTCATCAT 58.745 50.000 0.25 0.00 0.00 2.45
3313 3872 1.952621 CTGAAACAGGGTAGGGAGGA 58.047 55.000 0.00 0.00 0.00 3.71
3321 3880 3.806949 TTAATGGAGCTGAAACAGGGT 57.193 42.857 0.00 0.00 31.21 4.34
3340 3899 2.084546 GCTTGTTACAGAGGGCGAATT 58.915 47.619 0.00 0.00 0.00 2.17
3341 3900 1.739067 GCTTGTTACAGAGGGCGAAT 58.261 50.000 0.00 0.00 0.00 3.34
3342 3901 0.669318 CGCTTGTTACAGAGGGCGAA 60.669 55.000 14.69 0.00 44.36 4.70
3343 3902 1.080093 CGCTTGTTACAGAGGGCGA 60.080 57.895 14.69 0.00 44.36 5.54
3421 4962 3.009140 CATCATGGCTCGTGCGAC 58.991 61.111 3.02 0.00 40.82 5.19
3457 5001 0.167251 CATTGTTACCGAACCGTGCC 59.833 55.000 0.00 0.00 34.38 5.01
3459 5003 1.195900 CCACATTGTTACCGAACCGTG 59.804 52.381 0.00 0.00 34.38 4.94
3461 5005 1.798283 TCCACATTGTTACCGAACCG 58.202 50.000 0.00 0.00 34.38 4.44
3462 5006 2.095415 GCTTCCACATTGTTACCGAACC 60.095 50.000 0.00 0.00 34.38 3.62
3463 5007 2.095415 GGCTTCCACATTGTTACCGAAC 60.095 50.000 0.00 0.00 36.00 3.95
3464 5008 2.156098 GGCTTCCACATTGTTACCGAA 58.844 47.619 0.00 0.00 0.00 4.30
3522 5193 2.098443 CCACACGTTTGCTGGTAAAACT 59.902 45.455 0.00 0.00 35.75 2.66
3577 5251 0.546122 ATAAGGCAGCCAATCACGGA 59.454 50.000 15.80 0.00 0.00 4.69
3578 5252 0.947244 GATAAGGCAGCCAATCACGG 59.053 55.000 15.80 0.00 0.00 4.94
3579 5253 0.947244 GGATAAGGCAGCCAATCACG 59.053 55.000 22.12 0.00 30.82 4.35
3580 5254 0.947244 CGGATAAGGCAGCCAATCAC 59.053 55.000 22.12 13.52 30.82 3.06
3581 5255 0.819259 GCGGATAAGGCAGCCAATCA 60.819 55.000 22.12 3.48 30.82 2.57
3582 5256 1.518903 GGCGGATAAGGCAGCCAATC 61.519 60.000 15.80 15.60 46.54 2.67
3583 5257 1.529244 GGCGGATAAGGCAGCCAAT 60.529 57.895 15.80 6.61 46.54 3.16
3584 5258 2.124320 GGCGGATAAGGCAGCCAA 60.124 61.111 15.80 0.63 46.54 4.52
3586 5260 3.750373 TTCGGCGGATAAGGCAGCC 62.750 63.158 7.21 1.84 44.31 4.85
3587 5261 1.569479 GATTCGGCGGATAAGGCAGC 61.569 60.000 7.21 0.00 36.37 5.25
3589 5263 1.070786 GGATTCGGCGGATAAGGCA 59.929 57.895 7.21 0.00 36.37 4.75
3590 5264 0.606604 TAGGATTCGGCGGATAAGGC 59.393 55.000 7.21 0.00 0.00 4.35
3591 5265 1.616865 TGTAGGATTCGGCGGATAAGG 59.383 52.381 7.21 0.00 0.00 2.69
3593 5267 1.001048 CGTGTAGGATTCGGCGGATAA 60.001 52.381 7.21 0.00 0.00 1.75
3596 5270 2.048023 ACGTGTAGGATTCGGCGGA 61.048 57.895 7.21 0.00 0.00 5.54
3598 5272 2.514013 GCACGTGTAGGATTCGGCG 61.514 63.158 18.38 0.00 0.00 6.46
3600 5274 2.665777 CTGCACGTGTAGGATTCGG 58.334 57.895 24.15 3.72 0.00 4.30
3607 5281 2.649034 ACGGACCTGCACGTGTAG 59.351 61.111 24.79 24.79 42.39 2.74
3611 5285 1.667830 CAATCACGGACCTGCACGT 60.668 57.895 0.00 0.00 45.25 4.49
3612 5286 2.390599 CCAATCACGGACCTGCACG 61.391 63.158 0.00 0.00 0.00 5.34
3613 5287 2.690778 GCCAATCACGGACCTGCAC 61.691 63.158 0.00 0.00 0.00 4.57
3614 5288 2.359850 GCCAATCACGGACCTGCA 60.360 61.111 0.00 0.00 0.00 4.41
3615 5289 2.045926 AGCCAATCACGGACCTGC 60.046 61.111 0.00 0.00 0.00 4.85
3617 5291 2.045926 GCAGCCAATCACGGACCT 60.046 61.111 0.00 0.00 0.00 3.85
3618 5292 3.134127 GGCAGCCAATCACGGACC 61.134 66.667 6.55 0.00 0.00 4.46
3619 5293 0.392461 TAAGGCAGCCAATCACGGAC 60.392 55.000 15.80 0.00 0.00 4.79
3620 5294 0.546122 ATAAGGCAGCCAATCACGGA 59.454 50.000 15.80 0.00 0.00 4.69
3629 5303 3.750373 TTCGGCGGATAAGGCAGCC 62.750 63.158 7.21 1.84 44.31 4.85
3708 5382 4.415332 CACGGTCTCGGTCACGGG 62.415 72.222 0.00 0.00 43.55 5.28
3743 5417 1.815421 CGCCATTTCCCTCACTCCG 60.815 63.158 0.00 0.00 0.00 4.63
3854 5537 1.586564 GGACTCGCGGTCTGAATCG 60.587 63.158 21.54 0.00 43.97 3.34
3872 5555 3.873952 GCTGTTAACTTAGCATGAGAGGG 59.126 47.826 11.89 0.00 39.67 4.30
3875 5558 6.467677 AGAAAGCTGTTAACTTAGCATGAGA 58.532 36.000 17.40 0.00 42.29 3.27
3876 5559 6.183360 GGAGAAAGCTGTTAACTTAGCATGAG 60.183 42.308 17.40 1.63 42.29 2.90
3877 5560 5.643777 GGAGAAAGCTGTTAACTTAGCATGA 59.356 40.000 17.40 0.00 42.29 3.07
3878 5561 5.446473 CGGAGAAAGCTGTTAACTTAGCATG 60.446 44.000 17.40 0.00 42.29 4.06
3879 5562 4.631813 CGGAGAAAGCTGTTAACTTAGCAT 59.368 41.667 17.40 5.48 42.29 3.79
3882 5565 4.143094 GCACGGAGAAAGCTGTTAACTTAG 60.143 45.833 7.22 0.00 0.00 2.18
3884 5567 2.548480 GCACGGAGAAAGCTGTTAACTT 59.452 45.455 7.22 0.00 0.00 2.66
3885 5568 2.143925 GCACGGAGAAAGCTGTTAACT 58.856 47.619 7.22 0.00 0.00 2.24
3886 5569 1.871039 TGCACGGAGAAAGCTGTTAAC 59.129 47.619 0.00 0.00 0.00 2.01
3887 5570 2.143122 CTGCACGGAGAAAGCTGTTAA 58.857 47.619 0.00 0.00 0.00 2.01
3888 5571 1.343142 TCTGCACGGAGAAAGCTGTTA 59.657 47.619 0.00 0.00 0.00 2.41
3889 5572 0.106708 TCTGCACGGAGAAAGCTGTT 59.893 50.000 0.00 0.00 0.00 3.16
3890 5573 0.322975 ATCTGCACGGAGAAAGCTGT 59.677 50.000 0.00 0.00 0.00 4.40
3891 5574 1.396301 GAATCTGCACGGAGAAAGCTG 59.604 52.381 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.