Multiple sequence alignment - TraesCS3D01G439700

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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 TraesCS3D01G439700 chr3D 100.000 3214 0 0 1 3214 550245356 550242143 0.000000e+00 5936.0
1 TraesCS3D01G439700 chr3D 85.965 228 31 1 1 227 370531539 370531766 3.200000e-60 243.0
2 TraesCS3D01G439700 chr3B 90.123 1873 88 30 354 2163 729706703 729704865 0.000000e+00 2344.0
3 TraesCS3D01G439700 chr3B 90.029 341 17 11 2878 3207 729704052 729703718 2.960000e-115 425.0
4 TraesCS3D01G439700 chr3A 90.799 1152 50 22 1012 2126 687059108 687057976 0.000000e+00 1489.0
5 TraesCS3D01G439700 chr3A 88.783 526 47 3 1 518 687060878 687060357 4.520000e-178 634.0
6 TraesCS3D01G439700 chr3A 90.578 467 35 6 2755 3214 687057080 687056616 7.620000e-171 610.0
7 TraesCS3D01G439700 chr3A 93.664 363 8 6 510 863 687059945 687059589 2.200000e-146 529.0
8 TraesCS3D01G439700 chr3A 83.265 245 37 4 1 243 698016299 698016057 4.170000e-54 222.0
9 TraesCS3D01G439700 chr6D 86.928 306 27 5 1480 1782 424712580 424712875 6.650000e-87 331.0
10 TraesCS3D01G439700 chr6D 84.967 306 33 5 1480 1782 424745258 424745553 6.740000e-77 298.0
11 TraesCS3D01G439700 chr6D 82.258 186 24 3 1184 1369 424712400 424712576 5.550000e-33 152.0
12 TraesCS3D01G439700 chr6A 83.729 295 36 4 1482 1773 569589872 569590157 5.290000e-68 268.0
13 TraesCS3D01G439700 chr4B 86.122 245 28 6 1 243 446197649 446197889 3.180000e-65 259.0
14 TraesCS3D01G439700 chr2A 84.388 237 37 0 1 237 688410905 688410669 1.930000e-57 233.0
15 TraesCS3D01G439700 chr7B 83.673 245 38 2 1 244 579444385 579444628 2.490000e-56 230.0
16 TraesCS3D01G439700 chr1A 82.591 247 36 6 1 243 82954318 82954075 9.030000e-51 211.0
17 TraesCS3D01G439700 chr5B 83.333 222 35 2 12 233 573432617 573432398 1.510000e-48 204.0
18 TraesCS3D01G439700 chr1B 80.000 245 46 3 2 243 171046572 171046328 9.160000e-41 178.0
19 TraesCS3D01G439700 chr4D 84.524 84 11 2 274 356 509391225 509391307 7.390000e-12 82.4
20 TraesCS3D01G439700 chr1D 78.947 114 24 0 243 356 400121685 400121572 9.560000e-11 78.7
21 TraesCS3D01G439700 chr7D 83.077 65 11 0 270 334 73742752 73742816 3.460000e-05 60.2


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 TraesCS3D01G439700 chr3D 550242143 550245356 3213 True 5936.0 5936 100.000 1 3214 1 chr3D.!!$R1 3213
1 TraesCS3D01G439700 chr3B 729703718 729706703 2985 True 1384.5 2344 90.076 354 3207 2 chr3B.!!$R1 2853
2 TraesCS3D01G439700 chr3A 687056616 687060878 4262 True 815.5 1489 90.956 1 3214 4 chr3A.!!$R2 3213

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
682 1122 0.107703 CTTGTGCGATCCCCTGCTTA 60.108 55.0 0.0 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 3668 0.035439 ATGGCCGTTTAGTGGTCCAG 60.035 55.0 0.0 0.0 36.55 3.86 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
28 29 2.042435 AGCGGGAGAGGAAGGAGG 60.042 66.667 0.00 0.00 0.00 4.30
37 38 1.988982 GAGGAAGGAGGTGGATGGGC 61.989 65.000 0.00 0.00 0.00 5.36
127 128 1.506262 CGAATTTGGTCTTGGGCGG 59.494 57.895 0.00 0.00 0.00 6.13
160 161 4.695231 CCACGCGACGACGAACCT 62.695 66.667 15.93 0.00 42.66 3.50
164 165 3.164011 GCGACGACGAACCTGACG 61.164 66.667 12.29 0.00 42.66 4.35
166 167 1.369689 CGACGACGAACCTGACGTT 60.370 57.895 0.00 0.00 43.97 3.99
167 168 0.931662 CGACGACGAACCTGACGTTT 60.932 55.000 0.00 0.00 43.97 3.60
172 173 0.872881 ACGAACCTGACGTTTGTCGG 60.873 55.000 11.08 0.00 44.46 4.79
200 201 1.385528 GTTTCCAGGTGTTTCCACGT 58.614 50.000 0.00 0.00 42.80 4.49
217 218 3.311110 TGGGACCCTGTCGTCAGC 61.311 66.667 13.00 0.00 40.09 4.26
219 220 4.083862 GGACCCTGTCGTCAGCCC 62.084 72.222 3.97 1.81 40.09 5.19
259 260 1.359459 GCGTTTGAGGCCCGTCTAAG 61.359 60.000 0.00 0.00 0.00 2.18
266 267 4.222847 GCCCGTCTAAGGAGCCCG 62.223 72.222 0.00 0.00 0.00 6.13
267 268 4.222847 CCCGTCTAAGGAGCCCGC 62.223 72.222 0.00 0.00 0.00 6.13
268 269 3.458163 CCGTCTAAGGAGCCCGCA 61.458 66.667 0.00 0.00 0.00 5.69
282 283 3.792716 CCGCATGGGTCAAGAAAAC 57.207 52.632 9.14 0.00 0.00 2.43
294 295 1.004292 CAAGAAAACGTGACCGGACAC 60.004 52.381 24.55 24.55 38.78 3.67
299 300 1.389609 AACGTGACCGGACACTGACT 61.390 55.000 29.48 15.10 38.47 3.41
302 303 1.152631 TGACCGGACACTGACTGGA 60.153 57.895 9.46 0.00 37.25 3.86
304 305 1.152525 ACCGGACACTGACTGGACT 60.153 57.895 9.46 0.00 37.25 3.85
309 310 2.047844 CACTGACTGGACTGCCCG 60.048 66.667 0.00 0.00 37.93 6.13
325 326 2.025727 CGCCCGGACGTATGAGAC 59.974 66.667 0.73 0.00 0.00 3.36
340 341 1.472878 TGAGACGGATTTGAGAGGTCG 59.527 52.381 0.00 0.00 33.04 4.79
343 344 1.144057 CGGATTTGAGAGGTCGGGG 59.856 63.158 0.00 0.00 0.00 5.73
504 513 7.359014 GCGTGAAGGATTAATTCTTACCGATAC 60.359 40.741 22.33 6.75 0.00 2.24
619 1059 4.555511 GCAATCTGAACTTGTCTGAACCAC 60.556 45.833 0.00 0.00 37.70 4.16
658 1098 2.307934 AGCGAAGAGAAGAAGGCATC 57.692 50.000 0.00 0.00 0.00 3.91
682 1122 0.107703 CTTGTGCGATCCCCTGCTTA 60.108 55.000 0.00 0.00 0.00 3.09
820 1280 1.338200 GGAAGAAGAAGAAGCAGCCGA 60.338 52.381 0.00 0.00 0.00 5.54
821 1281 1.999024 GAAGAAGAAGAAGCAGCCGAG 59.001 52.381 0.00 0.00 0.00 4.63
822 1282 0.390998 AGAAGAAGAAGCAGCCGAGC 60.391 55.000 0.00 0.00 0.00 5.03
823 1283 1.365368 GAAGAAGAAGCAGCCGAGCC 61.365 60.000 0.00 0.00 34.23 4.70
824 1284 2.046892 GAAGAAGCAGCCGAGCCA 60.047 61.111 0.00 0.00 34.23 4.75
954 1414 2.433444 TCCTTCCTCCTCCCTTTCAA 57.567 50.000 0.00 0.00 0.00 2.69
956 1416 1.004862 CCTTCCTCCTCCCTTTCAACC 59.995 57.143 0.00 0.00 0.00 3.77
1082 1874 1.665916 CACAGCGACACAGACAGGG 60.666 63.158 0.00 0.00 0.00 4.45
1089 1881 1.603172 CGACACAGACAGGGTTGAGTC 60.603 57.143 0.00 0.00 37.18 3.36
1096 1888 1.609501 CAGGGTTGAGTCGAGGGGA 60.610 63.158 0.00 0.00 0.00 4.81
1537 2359 2.021068 ATGATGCACGAGGAGTCCGG 62.021 60.000 2.76 0.00 0.00 5.14
1661 2483 4.719369 GTCGACGCGGACCAGCTT 62.719 66.667 12.47 0.00 34.40 3.74
1664 2486 4.373116 GACGCGGACCAGCTTGGA 62.373 66.667 12.47 0.00 40.96 3.53
1736 2561 4.705519 CTGCGCCGCCAAAACCAG 62.706 66.667 6.63 0.00 0.00 4.00
1738 2563 4.700365 GCGCCGCCAAAACCAGAC 62.700 66.667 0.00 0.00 0.00 3.51
1798 2623 2.480555 GGCGTGCCGATGAAGTTG 59.519 61.111 0.00 0.00 0.00 3.16
1803 2628 0.727398 GTGCCGATGAAGTTGCCTAC 59.273 55.000 0.00 0.00 0.00 3.18
1806 2631 0.541863 CCGATGAAGTTGCCTACCCT 59.458 55.000 0.00 0.00 0.00 4.34
1864 2695 1.434696 CATGATTGCTTGGACGGGC 59.565 57.895 0.00 0.00 0.00 6.13
1938 2773 1.078426 GTGTCGGGGGACAGGAATG 60.078 63.158 0.00 0.00 35.54 2.67
1939 2774 2.297895 TGTCGGGGGACAGGAATGG 61.298 63.158 0.00 0.00 0.00 3.16
1940 2775 1.993391 GTCGGGGGACAGGAATGGA 60.993 63.158 0.00 0.00 0.00 3.41
1941 2776 1.229690 TCGGGGGACAGGAATGGAA 60.230 57.895 0.00 0.00 0.00 3.53
1942 2777 0.623324 TCGGGGGACAGGAATGGAAT 60.623 55.000 0.00 0.00 0.00 3.01
1951 2786 2.201732 CAGGAATGGAATACGTCGTGG 58.798 52.381 8.47 0.00 0.00 4.94
2067 2902 9.665719 TCTTCTTTTTCTGCATGTATGTATGTA 57.334 29.630 0.00 0.00 0.00 2.29
2070 2905 9.394767 TCTTTTTCTGCATGTATGTATGTATGT 57.605 29.630 0.00 0.00 0.00 2.29
2091 2929 3.865745 GTCAGTGTAAAGATGTGGATCGG 59.134 47.826 0.00 0.00 33.34 4.18
2112 2950 4.566070 CGGGTCCTGGATGGTTTTTAGTTA 60.566 45.833 0.00 0.00 37.07 2.24
2120 2958 5.073965 TGGATGGTTTTTAGTTACTGGGACT 59.926 40.000 0.00 0.00 0.00 3.85
2126 2964 8.713036 TGGTTTTTAGTTACTGGGACTAAGTAA 58.287 33.333 0.00 0.00 39.83 2.24
2134 2972 9.152327 AGTTACTGGGACTAAGTAAAGTTTACT 57.848 33.333 20.34 20.34 40.75 2.24
2135 2973 9.770097 GTTACTGGGACTAAGTAAAGTTTACTT 57.230 33.333 32.73 32.73 40.75 2.24
2137 2975 8.672823 ACTGGGACTAAGTAAAGTTTACTTTG 57.327 34.615 34.39 32.62 45.01 2.77
2138 2976 7.228108 ACTGGGACTAAGTAAAGTTTACTTTGC 59.772 37.037 34.39 26.87 45.01 3.68
2139 2977 7.055378 TGGGACTAAGTAAAGTTTACTTTGCA 58.945 34.615 34.39 24.56 46.47 4.08
2140 2978 7.722285 TGGGACTAAGTAAAGTTTACTTTGCAT 59.278 33.333 34.39 22.06 46.47 3.96
2181 3054 6.801539 TGTGTGGTTACTCTTGATCAATTC 57.198 37.500 8.96 0.00 0.00 2.17
2195 3068 9.374838 TCTTGATCAATTCATATGTATCATCCG 57.625 33.333 8.96 0.00 33.34 4.18
2196 3069 7.543947 TGATCAATTCATATGTATCATCCGC 57.456 36.000 1.90 0.00 0.00 5.54
2197 3070 7.333323 TGATCAATTCATATGTATCATCCGCT 58.667 34.615 1.90 0.00 0.00 5.52
2198 3071 7.493645 TGATCAATTCATATGTATCATCCGCTC 59.506 37.037 1.90 0.00 0.00 5.03
2199 3072 5.807011 TCAATTCATATGTATCATCCGCTCG 59.193 40.000 1.90 0.00 0.00 5.03
2200 3073 3.150848 TCATATGTATCATCCGCTCGC 57.849 47.619 1.90 0.00 0.00 5.03
2201 3074 2.491693 TCATATGTATCATCCGCTCGCA 59.508 45.455 1.90 0.00 0.00 5.10
2202 3075 3.056891 TCATATGTATCATCCGCTCGCAA 60.057 43.478 1.90 0.00 0.00 4.85
2203 3076 2.238942 ATGTATCATCCGCTCGCAAA 57.761 45.000 0.00 0.00 0.00 3.68
2204 3077 2.017138 TGTATCATCCGCTCGCAAAA 57.983 45.000 0.00 0.00 0.00 2.44
2205 3078 2.351455 TGTATCATCCGCTCGCAAAAA 58.649 42.857 0.00 0.00 0.00 1.94
2294 3222 7.013942 AGTCAAAGGGTAAATGTGTTTAAGGTC 59.986 37.037 0.00 0.00 31.94 3.85
2295 3223 6.265876 TCAAAGGGTAAATGTGTTTAAGGTCC 59.734 38.462 0.00 0.00 31.94 4.46
2300 3228 7.346175 AGGGTAAATGTGTTTAAGGTCCTTTTT 59.654 33.333 10.04 5.03 31.94 1.94
2301 3229 7.654520 GGGTAAATGTGTTTAAGGTCCTTTTTC 59.345 37.037 10.04 1.39 31.94 2.29
2308 3455 6.859508 GTGTTTAAGGTCCTTTTTCCAATACG 59.140 38.462 10.04 0.00 0.00 3.06
2322 3469 3.932710 TCCAATACGAGAAAGATGCACAC 59.067 43.478 0.00 0.00 0.00 3.82
2325 3472 2.238942 ACGAGAAAGATGCACACACA 57.761 45.000 0.00 0.00 0.00 3.72
2326 3473 2.771089 ACGAGAAAGATGCACACACAT 58.229 42.857 0.00 0.00 0.00 3.21
2327 3474 2.481568 ACGAGAAAGATGCACACACATG 59.518 45.455 0.00 0.00 0.00 3.21
2328 3475 2.738314 CGAGAAAGATGCACACACATGA 59.262 45.455 0.00 0.00 0.00 3.07
2329 3476 3.181523 CGAGAAAGATGCACACACATGAG 60.182 47.826 0.00 0.00 0.00 2.90
2330 3477 2.486982 AGAAAGATGCACACACATGAGC 59.513 45.455 0.00 0.00 42.25 4.26
2334 3481 3.325902 TGCACACACATGAGCATGA 57.674 47.368 16.70 0.00 45.95 3.07
2335 3482 1.606903 TGCACACACATGAGCATGAA 58.393 45.000 16.70 0.00 45.95 2.57
2337 3484 2.361438 TGCACACACATGAGCATGAAAA 59.639 40.909 16.70 0.00 45.95 2.29
2339 3486 3.427528 GCACACACATGAGCATGAAAAAG 59.572 43.478 16.70 5.36 41.60 2.27
2341 3488 3.006110 ACACACATGAGCATGAAAAAGGG 59.994 43.478 16.70 5.27 41.20 3.95
2342 3489 2.564062 ACACATGAGCATGAAAAAGGGG 59.436 45.455 16.70 0.00 41.20 4.79
2344 3491 3.763360 CACATGAGCATGAAAAAGGGGTA 59.237 43.478 16.70 0.00 41.20 3.69
2346 3493 4.403432 ACATGAGCATGAAAAAGGGGTATG 59.597 41.667 16.70 0.00 41.20 2.39
2347 3494 4.314522 TGAGCATGAAAAAGGGGTATGA 57.685 40.909 0.00 0.00 0.00 2.15
2349 3496 4.706476 TGAGCATGAAAAAGGGGTATGAAG 59.294 41.667 0.00 0.00 0.00 3.02
2352 3499 2.815158 TGAAAAAGGGGTATGAAGGGC 58.185 47.619 0.00 0.00 0.00 5.19
2353 3500 2.108168 GAAAAAGGGGTATGAAGGGCC 58.892 52.381 0.00 0.00 0.00 5.80
2354 3501 0.338467 AAAAGGGGTATGAAGGGCCC 59.662 55.000 16.46 16.46 41.62 5.80
2355 3502 0.555117 AAAGGGGTATGAAGGGCCCT 60.555 55.000 22.28 22.28 42.01 5.19
2359 3506 1.068352 GGGTATGAAGGGCCCTCCAT 61.068 60.000 28.37 28.37 39.31 3.41
2361 3508 0.846693 GTATGAAGGGCCCTCCATGT 59.153 55.000 32.53 13.95 38.24 3.21
2362 3509 2.054799 GTATGAAGGGCCCTCCATGTA 58.945 52.381 32.53 11.94 38.24 2.29
2363 3510 1.143813 ATGAAGGGCCCTCCATGTAG 58.856 55.000 24.95 0.00 38.24 2.74
2364 3511 0.988145 TGAAGGGCCCTCCATGTAGG 60.988 60.000 28.84 0.00 38.24 3.18
2372 3519 1.295020 CCTCCATGTAGGGTTGGGAA 58.705 55.000 0.00 0.00 38.24 3.97
2373 3520 1.212935 CCTCCATGTAGGGTTGGGAAG 59.787 57.143 0.00 0.00 38.24 3.46
2374 3521 2.196595 CTCCATGTAGGGTTGGGAAGA 58.803 52.381 0.00 0.00 38.24 2.87
2375 3522 2.171448 CTCCATGTAGGGTTGGGAAGAG 59.829 54.545 0.00 0.00 38.24 2.85
2378 3525 3.434167 CCATGTAGGGTTGGGAAGAGATG 60.434 52.174 0.00 0.00 0.00 2.90
2380 3527 3.256704 TGTAGGGTTGGGAAGAGATGTT 58.743 45.455 0.00 0.00 0.00 2.71
2381 3528 3.655777 TGTAGGGTTGGGAAGAGATGTTT 59.344 43.478 0.00 0.00 0.00 2.83
2382 3529 3.903530 AGGGTTGGGAAGAGATGTTTT 57.096 42.857 0.00 0.00 0.00 2.43
2383 3530 5.311121 TGTAGGGTTGGGAAGAGATGTTTTA 59.689 40.000 0.00 0.00 0.00 1.52
2386 3533 3.444034 GGTTGGGAAGAGATGTTTTAGGC 59.556 47.826 0.00 0.00 0.00 3.93
2391 3550 4.440663 GGGAAGAGATGTTTTAGGCATTGC 60.441 45.833 0.00 0.00 0.00 3.56
2394 3553 6.442513 AAGAGATGTTTTAGGCATTGCTAC 57.557 37.500 8.82 0.85 0.00 3.58
2396 3555 6.183347 AGAGATGTTTTAGGCATTGCTACTT 58.817 36.000 8.82 0.00 0.00 2.24
2405 3564 4.796606 AGGCATTGCTACTTGGAATATGT 58.203 39.130 8.82 0.00 34.89 2.29
2443 3602 3.992260 TTTTGTGTGAAACGGGTATGG 57.008 42.857 0.00 0.00 42.39 2.74
2444 3603 2.932855 TTGTGTGAAACGGGTATGGA 57.067 45.000 0.00 0.00 42.39 3.41
2445 3604 3.426787 TTGTGTGAAACGGGTATGGAT 57.573 42.857 0.00 0.00 42.39 3.41
2446 3605 2.980568 TGTGTGAAACGGGTATGGATC 58.019 47.619 0.00 0.00 42.39 3.36
2447 3606 2.569853 TGTGTGAAACGGGTATGGATCT 59.430 45.455 0.00 0.00 42.39 2.75
2448 3607 3.770388 TGTGTGAAACGGGTATGGATCTA 59.230 43.478 0.00 0.00 42.39 1.98
2449 3608 4.407621 TGTGTGAAACGGGTATGGATCTAT 59.592 41.667 0.00 0.00 42.39 1.98
2450 3609 5.104693 TGTGTGAAACGGGTATGGATCTATT 60.105 40.000 0.00 0.00 42.39 1.73
2451 3610 6.098552 TGTGTGAAACGGGTATGGATCTATTA 59.901 38.462 0.00 0.00 42.39 0.98
2452 3611 7.159372 GTGTGAAACGGGTATGGATCTATTAT 58.841 38.462 0.00 0.00 42.39 1.28
2453 3612 8.308931 GTGTGAAACGGGTATGGATCTATTATA 58.691 37.037 0.00 0.00 42.39 0.98
2454 3613 8.872134 TGTGAAACGGGTATGGATCTATTATAA 58.128 33.333 0.00 0.00 42.39 0.98
2455 3614 9.715121 GTGAAACGGGTATGGATCTATTATAAA 57.285 33.333 0.00 0.00 0.00 1.40
2460 3619 9.939802 ACGGGTATGGATCTATTATAAAAGTTC 57.060 33.333 0.00 0.00 0.00 3.01
2461 3620 9.938280 CGGGTATGGATCTATTATAAAAGTTCA 57.062 33.333 0.00 0.00 0.00 3.18
2471 3630 9.547753 TCTATTATAAAAGTTCATCAGGAGTGC 57.452 33.333 0.00 0.00 0.00 4.40
2472 3631 9.330063 CTATTATAAAAGTTCATCAGGAGTGCA 57.670 33.333 0.00 0.00 0.00 4.57
2473 3632 7.994425 TTATAAAAGTTCATCAGGAGTGCAA 57.006 32.000 0.00 0.00 0.00 4.08
2474 3633 6.899393 ATAAAAGTTCATCAGGAGTGCAAA 57.101 33.333 0.00 0.00 0.00 3.68
2475 3634 5.796424 AAAAGTTCATCAGGAGTGCAAAT 57.204 34.783 0.00 0.00 0.00 2.32
2476 3635 5.382618 AAAGTTCATCAGGAGTGCAAATC 57.617 39.130 0.00 0.00 0.00 2.17
2477 3636 4.025040 AGTTCATCAGGAGTGCAAATCA 57.975 40.909 0.00 0.00 28.43 2.57
2478 3637 4.597004 AGTTCATCAGGAGTGCAAATCAT 58.403 39.130 0.00 0.00 28.43 2.45
2479 3638 4.639310 AGTTCATCAGGAGTGCAAATCATC 59.361 41.667 0.00 0.00 28.43 2.92
2480 3639 4.498894 TCATCAGGAGTGCAAATCATCT 57.501 40.909 0.00 0.00 28.43 2.90
2481 3640 4.449131 TCATCAGGAGTGCAAATCATCTC 58.551 43.478 0.00 0.00 28.43 2.75
2482 3641 3.986996 TCAGGAGTGCAAATCATCTCA 57.013 42.857 0.00 0.00 28.43 3.27
2483 3642 4.290711 TCAGGAGTGCAAATCATCTCAA 57.709 40.909 0.00 0.00 28.43 3.02
2484 3643 4.654915 TCAGGAGTGCAAATCATCTCAAA 58.345 39.130 0.00 0.00 28.43 2.69
2485 3644 4.456911 TCAGGAGTGCAAATCATCTCAAAC 59.543 41.667 0.00 0.00 28.43 2.93
2486 3645 4.216902 CAGGAGTGCAAATCATCTCAAACA 59.783 41.667 0.00 0.00 28.43 2.83
2487 3646 5.014858 AGGAGTGCAAATCATCTCAAACAT 58.985 37.500 0.00 0.00 28.43 2.71
2488 3647 5.479375 AGGAGTGCAAATCATCTCAAACATT 59.521 36.000 0.00 0.00 28.43 2.71
2489 3648 6.660521 AGGAGTGCAAATCATCTCAAACATTA 59.339 34.615 0.00 0.00 28.43 1.90
2490 3649 7.177216 AGGAGTGCAAATCATCTCAAACATTAA 59.823 33.333 0.00 0.00 28.43 1.40
2491 3650 7.814107 GGAGTGCAAATCATCTCAAACATTAAA 59.186 33.333 0.00 0.00 28.43 1.52
2492 3651 9.195411 GAGTGCAAATCATCTCAAACATTAAAA 57.805 29.630 0.00 0.00 0.00 1.52
2493 3652 9.545105 AGTGCAAATCATCTCAAACATTAAAAA 57.455 25.926 0.00 0.00 0.00 1.94
2513 3672 5.489792 AAAAGTACATCAAGCTCTCTGGA 57.510 39.130 0.00 0.00 0.00 3.86
2514 3673 4.464069 AAGTACATCAAGCTCTCTGGAC 57.536 45.455 0.00 0.00 0.00 4.02
2515 3674 2.763448 AGTACATCAAGCTCTCTGGACC 59.237 50.000 0.00 0.00 0.00 4.46
2516 3675 1.649321 ACATCAAGCTCTCTGGACCA 58.351 50.000 0.00 0.00 0.00 4.02
2517 3676 1.277557 ACATCAAGCTCTCTGGACCAC 59.722 52.381 0.00 0.00 0.00 4.16
2518 3677 1.554160 CATCAAGCTCTCTGGACCACT 59.446 52.381 0.00 0.00 0.00 4.00
2519 3678 2.604912 TCAAGCTCTCTGGACCACTA 57.395 50.000 0.00 0.00 0.00 2.74
2520 3679 2.889512 TCAAGCTCTCTGGACCACTAA 58.110 47.619 0.00 0.00 0.00 2.24
2521 3680 3.239449 TCAAGCTCTCTGGACCACTAAA 58.761 45.455 0.00 0.00 0.00 1.85
2522 3681 3.006967 TCAAGCTCTCTGGACCACTAAAC 59.993 47.826 0.00 0.00 0.00 2.01
2523 3682 1.546476 AGCTCTCTGGACCACTAAACG 59.454 52.381 0.00 0.00 0.00 3.60
2524 3683 1.404315 GCTCTCTGGACCACTAAACGG 60.404 57.143 0.00 0.00 0.00 4.44
2525 3684 0.606604 TCTCTGGACCACTAAACGGC 59.393 55.000 0.00 0.00 0.00 5.68
2526 3685 0.391263 CTCTGGACCACTAAACGGCC 60.391 60.000 0.00 0.00 0.00 6.13
2527 3686 1.122632 TCTGGACCACTAAACGGCCA 61.123 55.000 2.24 0.00 0.00 5.36
2528 3687 0.035439 CTGGACCACTAAACGGCCAT 60.035 55.000 2.24 0.00 31.90 4.40
2529 3688 0.402504 TGGACCACTAAACGGCCATT 59.597 50.000 2.24 0.00 0.00 3.16
2530 3689 1.629353 TGGACCACTAAACGGCCATTA 59.371 47.619 2.24 0.05 0.00 1.90
2531 3690 2.011947 GGACCACTAAACGGCCATTAC 58.988 52.381 2.24 0.00 0.00 1.89
2532 3691 2.011947 GACCACTAAACGGCCATTACC 58.988 52.381 2.24 0.00 0.00 2.85
2543 3702 1.940613 GGCCATTACCGATGTCAGAAC 59.059 52.381 0.00 0.00 33.71 3.01
2544 3703 1.940613 GCCATTACCGATGTCAGAACC 59.059 52.381 0.00 0.00 33.71 3.62
2547 3706 4.199310 CCATTACCGATGTCAGAACCATT 58.801 43.478 0.00 0.00 33.71 3.16
2564 3723 8.124199 CAGAACCATTGAAATTTTGGAAACTTG 58.876 33.333 13.22 2.64 34.52 3.16
2570 3729 6.245890 TGAAATTTTGGAAACTTGGGTCAT 57.754 33.333 0.00 0.00 0.00 3.06
2574 3733 5.683876 TTTTGGAAACTTGGGTCATTTCA 57.316 34.783 0.00 0.00 34.63 2.69
2575 3734 5.683876 TTTGGAAACTTGGGTCATTTCAA 57.316 34.783 0.00 0.00 34.63 2.69
2576 3735 5.885449 TTGGAAACTTGGGTCATTTCAAT 57.115 34.783 0.00 0.00 34.63 2.57
2577 3736 6.985653 TTGGAAACTTGGGTCATTTCAATA 57.014 33.333 0.00 0.00 34.63 1.90
2578 3737 6.588719 TGGAAACTTGGGTCATTTCAATAG 57.411 37.500 0.00 0.00 34.63 1.73
2579 3738 6.310941 TGGAAACTTGGGTCATTTCAATAGA 58.689 36.000 0.00 0.00 34.63 1.98
2581 3740 8.112822 TGGAAACTTGGGTCATTTCAATAGATA 58.887 33.333 0.00 0.00 34.63 1.98
2582 3741 8.406297 GGAAACTTGGGTCATTTCAATAGATAC 58.594 37.037 0.00 0.00 34.63 2.24
2585 3744 7.056635 ACTTGGGTCATTTCAATAGATACTGG 58.943 38.462 0.00 0.00 0.00 4.00
2607 3766 8.624701 CTGGAATAATTACATTGCAGTGAAAG 57.375 34.615 16.98 0.00 44.68 2.62
2675 3849 8.783093 TGAAGTGTCAAAATACTTAGTTGGATG 58.217 33.333 0.00 0.00 37.01 3.51
2696 3870 8.369424 TGGATGTCAATCAAATTCAAGTGAAAT 58.631 29.630 0.00 0.00 34.51 2.17
2705 3879 7.563906 TCAAATTCAAGTGAAATTTTGGGTCT 58.436 30.769 15.19 0.00 35.94 3.85
2706 3880 8.046107 TCAAATTCAAGTGAAATTTTGGGTCTT 58.954 29.630 15.19 0.00 35.94 3.01
2707 3881 8.337532 CAAATTCAAGTGAAATTTTGGGTCTTC 58.662 33.333 10.35 0.00 37.61 2.87
2709 3883 7.889873 TTCAAGTGAAATTTTGGGTCTTCTA 57.110 32.000 0.00 0.00 0.00 2.10
2711 3885 7.060421 TCAAGTGAAATTTTGGGTCTTCTAGT 58.940 34.615 0.00 0.00 0.00 2.57
2720 3894 5.677319 TTGGGTCTTCTAGTCGAAATGAT 57.323 39.130 0.00 0.00 0.00 2.45
2730 3904 7.605410 TCTAGTCGAAATGATAACCAAAACC 57.395 36.000 0.00 0.00 0.00 3.27
2732 3906 6.834168 AGTCGAAATGATAACCAAAACCAT 57.166 33.333 0.00 0.00 0.00 3.55
2733 3907 7.227049 AGTCGAAATGATAACCAAAACCATT 57.773 32.000 0.00 0.00 0.00 3.16
2734 3908 7.090173 AGTCGAAATGATAACCAAAACCATTG 58.910 34.615 0.00 0.00 0.00 2.82
2735 3909 7.040062 AGTCGAAATGATAACCAAAACCATTGA 60.040 33.333 0.00 0.00 0.00 2.57
2738 3912 8.434661 CGAAATGATAACCAAAACCATTGAAAG 58.565 33.333 0.00 0.00 0.00 2.62
2741 4085 3.810310 AACCAAAACCATTGAAAGCGA 57.190 38.095 0.00 0.00 0.00 4.93
2744 4088 5.461032 ACCAAAACCATTGAAAGCGATAA 57.539 34.783 0.00 0.00 0.00 1.75
2747 4091 6.368516 ACCAAAACCATTGAAAGCGATAAATG 59.631 34.615 0.00 0.00 0.00 2.32
2750 4094 5.070770 ACCATTGAAAGCGATAAATGCAA 57.929 34.783 0.00 0.00 33.85 4.08
2752 4096 5.577945 ACCATTGAAAGCGATAAATGCAAAG 59.422 36.000 0.00 0.00 33.85 2.77
2758 4105 8.393395 TGAAAGCGATAAATGCAAAGAATAAC 57.607 30.769 0.00 0.00 33.85 1.89
2763 4110 9.109393 AGCGATAAATGCAAAGAATAACTAGAA 57.891 29.630 0.00 0.00 33.85 2.10
2782 4129 8.135382 ACTAGAACTGTATTTTCCTCTTAGCA 57.865 34.615 0.00 0.00 0.00 3.49
2783 4130 8.254508 ACTAGAACTGTATTTTCCTCTTAGCAG 58.745 37.037 0.00 0.00 0.00 4.24
2785 4132 6.213600 AGAACTGTATTTTCCTCTTAGCAGGA 59.786 38.462 0.00 0.00 41.16 3.86
2795 4145 2.413453 CTCTTAGCAGGAAAACGCAGTC 59.587 50.000 0.00 0.00 45.00 3.51
2807 4157 3.455469 GCAGTCCCCCTTGCATGC 61.455 66.667 11.82 11.82 40.02 4.06
2808 4158 2.357836 CAGTCCCCCTTGCATGCT 59.642 61.111 20.33 0.00 0.00 3.79
2817 4167 2.557056 CCCCTTGCATGCTTGATGATAG 59.443 50.000 20.33 3.44 33.31 2.08
2821 4171 4.760204 CCTTGCATGCTTGATGATAGATGA 59.240 41.667 20.33 0.00 33.31 2.92
2918 4301 0.370273 CAGTATTGTTCGCTCCGCAC 59.630 55.000 0.00 0.00 0.00 5.34
2936 4319 1.817099 CCTTCCATCGGACAGCAGC 60.817 63.158 0.00 0.00 0.00 5.25
3013 4397 0.742990 CAACGAGCAGCCCCGATTTA 60.743 55.000 11.28 0.00 0.00 1.40
3084 4468 5.838529 GTGCCCACACATAAAAAGTAAGTT 58.161 37.500 0.00 0.00 46.61 2.66
3162 4550 0.534427 GCTACCTAATCCGGGGCAAC 60.534 60.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.377760 TTCCTCTCCCGCTCCGGT 62.378 66.667 0.00 0.00 46.80 5.28
28 29 2.187946 CAGTCCGAGCCCATCCAC 59.812 66.667 0.00 0.00 0.00 4.02
54 55 1.127343 CCATCCACCTCCCTTCTCTC 58.873 60.000 0.00 0.00 0.00 3.20
60 61 0.327576 CCTAACCCATCCACCTCCCT 60.328 60.000 0.00 0.00 0.00 4.20
111 112 2.635443 CGCCGCCCAAGACCAAATT 61.635 57.895 0.00 0.00 0.00 1.82
150 151 0.179129 ACAAACGTCAGGTTCGTCGT 60.179 50.000 0.00 0.00 40.69 4.34
160 161 2.659244 GCGGTCCGACAAACGTCA 60.659 61.111 17.49 0.00 40.78 4.35
176 177 1.802337 GAAACACCTGGAAACCCGGC 61.802 60.000 0.00 0.00 0.00 6.13
177 178 1.176619 GGAAACACCTGGAAACCCGG 61.177 60.000 0.00 0.00 35.41 5.73
200 201 3.311110 GCTGACGACAGGGTCCCA 61.311 66.667 16.41 0.00 43.62 4.37
266 267 1.606668 TCACGTTTTCTTGACCCATGC 59.393 47.619 0.00 0.00 0.00 4.06
267 268 3.268013 GTCACGTTTTCTTGACCCATG 57.732 47.619 0.00 0.00 41.34 3.66
277 278 0.580104 CAGTGTCCGGTCACGTTTTC 59.420 55.000 23.14 1.71 42.40 2.29
282 283 1.371758 CAGTCAGTGTCCGGTCACG 60.372 63.158 23.14 18.12 42.40 4.35
289 290 1.004440 GGCAGTCCAGTCAGTGTCC 60.004 63.158 0.00 0.00 0.00 4.02
294 295 4.767255 GGCGGGCAGTCCAGTCAG 62.767 72.222 0.00 0.00 32.15 3.51
309 310 2.025727 CGTCTCATACGTCCGGGC 59.974 66.667 0.00 0.00 46.72 6.13
325 326 1.144057 CCCCGACCTCTCAAATCCG 59.856 63.158 0.00 0.00 0.00 4.18
332 333 1.819903 GCATCTATACCCCGACCTCTC 59.180 57.143 0.00 0.00 0.00 3.20
334 335 1.819903 GAGCATCTATACCCCGACCTC 59.180 57.143 0.00 0.00 0.00 3.85
504 513 6.978659 TGGATGAATGCTTCGTTAACTACTAG 59.021 38.462 3.71 0.00 0.00 2.57
619 1059 0.539051 ATCCTTCTGACCTTGCTCCG 59.461 55.000 0.00 0.00 0.00 4.63
658 1098 2.401766 GGGGATCGCACAAGCACAG 61.402 63.158 12.32 0.00 42.27 3.66
820 1280 2.602568 CCTTGGCTTGGCTTGGCT 60.603 61.111 5.64 0.00 0.00 4.75
821 1281 4.383861 GCCTTGGCTTGGCTTGGC 62.384 66.667 12.74 12.69 46.38 4.52
930 1390 0.725133 AGGGAGGAGGAAGGAATGGA 59.275 55.000 0.00 0.00 0.00 3.41
954 1414 2.755686 GGTATATATAGGCACGGGGGT 58.244 52.381 0.00 0.00 0.00 4.95
956 1416 1.684983 CCGGTATATATAGGCACGGGG 59.315 57.143 13.33 0.10 36.45 5.73
987 1447 2.676471 AATGTGGAGTTGGGCCGC 60.676 61.111 0.00 0.00 36.47 6.53
989 1449 1.470996 TTGCAATGTGGAGTTGGGCC 61.471 55.000 0.00 0.00 0.00 5.80
996 1456 0.452987 CGGTGGATTGCAATGTGGAG 59.547 55.000 18.59 1.50 0.00 3.86
1034 1826 0.529773 TCTGTTCTGTCCGTGTGTGC 60.530 55.000 0.00 0.00 0.00 4.57
1043 1835 2.230266 GTCCCTGACTCTCTGTTCTGTC 59.770 54.545 0.00 0.00 0.00 3.51
1044 1836 2.243810 GTCCCTGACTCTCTGTTCTGT 58.756 52.381 0.00 0.00 0.00 3.41
1046 1838 2.243810 GTGTCCCTGACTCTCTGTTCT 58.756 52.381 0.00 0.00 33.15 3.01
1082 1874 0.685660 ACCTTTCCCCTCGACTCAAC 59.314 55.000 0.00 0.00 0.00 3.18
1089 1881 1.217244 CGTACCACCTTTCCCCTCG 59.783 63.158 0.00 0.00 0.00 4.63
1096 1888 1.337447 CCATGTCGTCGTACCACCTTT 60.337 52.381 0.00 0.00 0.00 3.11
1146 1938 2.908015 CAGGTACCCCCACATCCG 59.092 66.667 8.74 0.00 34.66 4.18
1652 2474 3.672295 CTCGCCTCCAAGCTGGTCC 62.672 68.421 0.00 0.00 39.03 4.46
1730 2555 3.553095 GAGCAGCCCGGTCTGGTTT 62.553 63.158 19.40 0.00 43.94 3.27
1751 2576 1.705873 CGGCTTCCTGGAGGTAGTAT 58.294 55.000 7.71 0.00 35.33 2.12
1803 2628 2.511600 GGACAATGCCGTCGAGGG 60.512 66.667 19.82 19.82 41.48 4.30
1938 2773 3.790177 GTGCCCACGACGTATTCC 58.210 61.111 0.00 0.00 0.00 3.01
2027 2862 2.338577 AGAAGAGGGTACATGCATGC 57.661 50.000 26.53 11.82 0.00 4.06
2028 2863 5.416952 AGAAAAAGAAGAGGGTACATGCATG 59.583 40.000 25.09 25.09 0.00 4.06
2029 2864 5.416952 CAGAAAAAGAAGAGGGTACATGCAT 59.583 40.000 0.00 0.00 0.00 3.96
2030 2865 4.761739 CAGAAAAAGAAGAGGGTACATGCA 59.238 41.667 0.00 0.00 0.00 3.96
2067 2902 5.111989 CGATCCACATCTTTACACTGACAT 58.888 41.667 0.00 0.00 0.00 3.06
2068 2903 4.494484 CGATCCACATCTTTACACTGACA 58.506 43.478 0.00 0.00 0.00 3.58
2069 2904 3.865745 CCGATCCACATCTTTACACTGAC 59.134 47.826 0.00 0.00 0.00 3.51
2070 2905 3.118775 CCCGATCCACATCTTTACACTGA 60.119 47.826 0.00 0.00 0.00 3.41
2091 2929 5.414765 CAGTAACTAAAAACCATCCAGGACC 59.585 44.000 0.00 0.00 41.22 4.46
2096 2934 5.073965 AGTCCCAGTAACTAAAAACCATCCA 59.926 40.000 0.00 0.00 0.00 3.41
2112 2950 7.228108 GCAAAGTAAACTTTACTTAGTCCCAGT 59.772 37.037 21.88 6.35 43.72 4.00
2147 2985 9.599866 CAAGAGTAACCACACATAGAATGAATA 57.400 33.333 0.00 0.00 0.00 1.75
2152 2990 7.851228 TGATCAAGAGTAACCACACATAGAAT 58.149 34.615 0.00 0.00 0.00 2.40
2155 2993 8.498054 AATTGATCAAGAGTAACCACACATAG 57.502 34.615 14.54 0.00 0.00 2.23
2159 2997 6.801539 TGAATTGATCAAGAGTAACCACAC 57.198 37.500 14.54 0.00 34.30 3.82
2181 3054 2.879826 TGCGAGCGGATGATACATATG 58.120 47.619 0.00 0.00 0.00 1.78
2252 3156 9.884814 ACCCTTTGACTTATACTACTATCTCAT 57.115 33.333 0.00 0.00 0.00 2.90
2260 3164 9.662947 ACACATTTACCCTTTGACTTATACTAC 57.337 33.333 0.00 0.00 0.00 2.73
2266 3170 8.852135 CCTTAAACACATTTACCCTTTGACTTA 58.148 33.333 0.00 0.00 29.77 2.24
2289 3217 5.237236 TCTCGTATTGGAAAAAGGACCTT 57.763 39.130 0.00 0.00 0.00 3.50
2291 3219 5.704053 TCTTTCTCGTATTGGAAAAAGGACC 59.296 40.000 0.00 0.00 32.17 4.46
2294 3222 6.030228 GCATCTTTCTCGTATTGGAAAAAGG 58.970 40.000 0.00 0.00 32.17 3.11
2295 3223 6.524586 GTGCATCTTTCTCGTATTGGAAAAAG 59.475 38.462 0.00 0.00 32.17 2.27
2300 3228 3.932710 GTGTGCATCTTTCTCGTATTGGA 59.067 43.478 0.00 0.00 0.00 3.53
2301 3229 3.684305 TGTGTGCATCTTTCTCGTATTGG 59.316 43.478 0.00 0.00 0.00 3.16
2308 3455 3.425892 GCTCATGTGTGTGCATCTTTCTC 60.426 47.826 0.00 0.00 42.75 2.87
2322 3469 2.564062 ACCCCTTTTTCATGCTCATGTG 59.436 45.455 9.41 0.00 39.72 3.21
2325 3472 4.870636 TCATACCCCTTTTTCATGCTCAT 58.129 39.130 0.00 0.00 0.00 2.90
2326 3473 4.314522 TCATACCCCTTTTTCATGCTCA 57.685 40.909 0.00 0.00 0.00 4.26
2327 3474 4.098501 CCTTCATACCCCTTTTTCATGCTC 59.901 45.833 0.00 0.00 0.00 4.26
2328 3475 4.026052 CCTTCATACCCCTTTTTCATGCT 58.974 43.478 0.00 0.00 0.00 3.79
2329 3476 3.132824 CCCTTCATACCCCTTTTTCATGC 59.867 47.826 0.00 0.00 0.00 4.06
2330 3477 3.132824 GCCCTTCATACCCCTTTTTCATG 59.867 47.826 0.00 0.00 0.00 3.07
2332 3479 2.558800 GGCCCTTCATACCCCTTTTTCA 60.559 50.000 0.00 0.00 0.00 2.69
2334 3481 1.273609 GGGCCCTTCATACCCCTTTTT 60.274 52.381 17.04 0.00 37.70 1.94
2335 3482 0.338467 GGGCCCTTCATACCCCTTTT 59.662 55.000 17.04 0.00 37.70 2.27
2337 3484 1.086757 AGGGCCCTTCATACCCCTT 59.913 57.895 22.28 0.00 45.49 3.95
2339 3486 2.461739 GGAGGGCCCTTCATACCCC 61.462 68.421 29.39 17.37 45.48 4.95
2341 3488 0.111253 CATGGAGGGCCCTTCATACC 59.889 60.000 40.33 29.12 40.10 2.73
2342 3489 0.846693 ACATGGAGGGCCCTTCATAC 59.153 55.000 40.33 21.39 40.10 2.39
2344 3491 1.143813 CTACATGGAGGGCCCTTCAT 58.856 55.000 36.84 36.84 42.66 2.57
2346 3493 1.839894 CCTACATGGAGGGCCCTTC 59.160 63.158 29.39 27.16 38.35 3.46
2347 3494 4.089839 CCTACATGGAGGGCCCTT 57.910 61.111 29.39 12.73 38.35 3.95
2353 3500 1.212935 CTTCCCAACCCTACATGGAGG 59.787 57.143 18.13 18.13 39.12 4.30
2354 3501 2.171448 CTCTTCCCAACCCTACATGGAG 59.829 54.545 0.00 0.00 39.12 3.86
2355 3502 2.196595 CTCTTCCCAACCCTACATGGA 58.803 52.381 0.00 0.00 39.12 3.41
2359 3506 2.915869 ACATCTCTTCCCAACCCTACA 58.084 47.619 0.00 0.00 0.00 2.74
2361 3508 5.045140 CCTAAAACATCTCTTCCCAACCCTA 60.045 44.000 0.00 0.00 0.00 3.53
2362 3509 3.903530 AAAACATCTCTTCCCAACCCT 57.096 42.857 0.00 0.00 0.00 4.34
2363 3510 4.017126 CCTAAAACATCTCTTCCCAACCC 58.983 47.826 0.00 0.00 0.00 4.11
2364 3511 3.444034 GCCTAAAACATCTCTTCCCAACC 59.556 47.826 0.00 0.00 0.00 3.77
2365 3512 4.079253 TGCCTAAAACATCTCTTCCCAAC 58.921 43.478 0.00 0.00 0.00 3.77
2366 3513 4.380843 TGCCTAAAACATCTCTTCCCAA 57.619 40.909 0.00 0.00 0.00 4.12
2368 3515 4.440663 GCAATGCCTAAAACATCTCTTCCC 60.441 45.833 0.00 0.00 0.00 3.97
2369 3516 4.400567 AGCAATGCCTAAAACATCTCTTCC 59.599 41.667 0.00 0.00 0.00 3.46
2370 3517 5.573337 AGCAATGCCTAAAACATCTCTTC 57.427 39.130 0.00 0.00 0.00 2.87
2372 3519 5.749462 AGTAGCAATGCCTAAAACATCTCT 58.251 37.500 0.00 0.00 0.00 3.10
2373 3520 6.261118 CAAGTAGCAATGCCTAAAACATCTC 58.739 40.000 0.00 0.00 0.00 2.75
2374 3521 5.126061 CCAAGTAGCAATGCCTAAAACATCT 59.874 40.000 0.00 0.00 0.00 2.90
2375 3522 5.125417 TCCAAGTAGCAATGCCTAAAACATC 59.875 40.000 0.00 0.00 0.00 3.06
2378 3525 5.385509 TTCCAAGTAGCAATGCCTAAAAC 57.614 39.130 0.00 0.00 0.00 2.43
2380 3527 6.833416 ACATATTCCAAGTAGCAATGCCTAAA 59.167 34.615 0.00 0.00 0.00 1.85
2381 3528 6.364701 ACATATTCCAAGTAGCAATGCCTAA 58.635 36.000 0.00 0.00 0.00 2.69
2382 3529 5.940617 ACATATTCCAAGTAGCAATGCCTA 58.059 37.500 0.00 0.00 0.00 3.93
2383 3530 4.796606 ACATATTCCAAGTAGCAATGCCT 58.203 39.130 0.00 0.00 0.00 4.75
2422 3581 3.952323 TCCATACCCGTTTCACACAAAAA 59.048 39.130 0.00 0.00 0.00 1.94
2423 3582 3.552875 TCCATACCCGTTTCACACAAAA 58.447 40.909 0.00 0.00 0.00 2.44
2424 3583 3.210232 TCCATACCCGTTTCACACAAA 57.790 42.857 0.00 0.00 0.00 2.83
2425 3584 2.932855 TCCATACCCGTTTCACACAA 57.067 45.000 0.00 0.00 0.00 3.33
2426 3585 2.569853 AGATCCATACCCGTTTCACACA 59.430 45.455 0.00 0.00 0.00 3.72
2427 3586 3.261981 AGATCCATACCCGTTTCACAC 57.738 47.619 0.00 0.00 0.00 3.82
2428 3587 5.623956 AATAGATCCATACCCGTTTCACA 57.376 39.130 0.00 0.00 0.00 3.58
2429 3588 9.715121 TTTATAATAGATCCATACCCGTTTCAC 57.285 33.333 0.00 0.00 0.00 3.18
2434 3593 9.939802 GAACTTTTATAATAGATCCATACCCGT 57.060 33.333 9.58 0.00 0.00 5.28
2435 3594 9.938280 TGAACTTTTATAATAGATCCATACCCG 57.062 33.333 9.58 0.00 0.00 5.28
2445 3604 9.547753 GCACTCCTGATGAACTTTTATAATAGA 57.452 33.333 9.58 0.00 0.00 1.98
2446 3605 9.330063 TGCACTCCTGATGAACTTTTATAATAG 57.670 33.333 1.79 1.79 0.00 1.73
2447 3606 9.679661 TTGCACTCCTGATGAACTTTTATAATA 57.320 29.630 0.00 0.00 0.00 0.98
2448 3607 8.579850 TTGCACTCCTGATGAACTTTTATAAT 57.420 30.769 0.00 0.00 0.00 1.28
2449 3608 7.994425 TTGCACTCCTGATGAACTTTTATAA 57.006 32.000 0.00 0.00 0.00 0.98
2450 3609 7.994425 TTTGCACTCCTGATGAACTTTTATA 57.006 32.000 0.00 0.00 0.00 0.98
2451 3610 6.899393 TTTGCACTCCTGATGAACTTTTAT 57.101 33.333 0.00 0.00 0.00 1.40
2452 3611 6.489700 TGATTTGCACTCCTGATGAACTTTTA 59.510 34.615 0.00 0.00 0.00 1.52
2453 3612 5.302568 TGATTTGCACTCCTGATGAACTTTT 59.697 36.000 0.00 0.00 0.00 2.27
2454 3613 4.828939 TGATTTGCACTCCTGATGAACTTT 59.171 37.500 0.00 0.00 0.00 2.66
2455 3614 4.401022 TGATTTGCACTCCTGATGAACTT 58.599 39.130 0.00 0.00 0.00 2.66
2456 3615 4.025040 TGATTTGCACTCCTGATGAACT 57.975 40.909 0.00 0.00 0.00 3.01
2457 3616 4.639310 AGATGATTTGCACTCCTGATGAAC 59.361 41.667 0.00 0.00 0.00 3.18
2458 3617 4.851843 AGATGATTTGCACTCCTGATGAA 58.148 39.130 0.00 0.00 0.00 2.57
2459 3618 4.080751 TGAGATGATTTGCACTCCTGATGA 60.081 41.667 0.00 0.00 0.00 2.92
2460 3619 4.196971 TGAGATGATTTGCACTCCTGATG 58.803 43.478 0.00 0.00 0.00 3.07
2461 3620 4.498894 TGAGATGATTTGCACTCCTGAT 57.501 40.909 0.00 0.00 0.00 2.90
2462 3621 3.986996 TGAGATGATTTGCACTCCTGA 57.013 42.857 0.00 0.00 0.00 3.86
2463 3622 4.216902 TGTTTGAGATGATTTGCACTCCTG 59.783 41.667 0.00 0.00 0.00 3.86
2464 3623 4.401022 TGTTTGAGATGATTTGCACTCCT 58.599 39.130 0.00 0.00 0.00 3.69
2465 3624 4.771590 TGTTTGAGATGATTTGCACTCC 57.228 40.909 0.00 0.00 0.00 3.85
2466 3625 8.746922 TTTAATGTTTGAGATGATTTGCACTC 57.253 30.769 0.00 0.00 0.00 3.51
2467 3626 9.545105 TTTTTAATGTTTGAGATGATTTGCACT 57.455 25.926 0.00 0.00 0.00 4.40
2490 3649 5.703130 GTCCAGAGAGCTTGATGTACTTTTT 59.297 40.000 0.00 0.00 0.00 1.94
2491 3650 5.241662 GTCCAGAGAGCTTGATGTACTTTT 58.758 41.667 0.00 0.00 0.00 2.27
2492 3651 4.323104 GGTCCAGAGAGCTTGATGTACTTT 60.323 45.833 0.00 0.00 37.53 2.66
2493 3652 3.196685 GGTCCAGAGAGCTTGATGTACTT 59.803 47.826 0.00 0.00 37.53 2.24
2494 3653 2.763448 GGTCCAGAGAGCTTGATGTACT 59.237 50.000 0.00 0.00 37.53 2.73
2495 3654 2.497675 TGGTCCAGAGAGCTTGATGTAC 59.502 50.000 0.00 0.00 41.26 2.90
2496 3655 2.497675 GTGGTCCAGAGAGCTTGATGTA 59.502 50.000 0.00 0.00 41.26 2.29
2497 3656 1.277557 GTGGTCCAGAGAGCTTGATGT 59.722 52.381 0.00 0.00 41.26 3.06
2498 3657 1.554160 AGTGGTCCAGAGAGCTTGATG 59.446 52.381 0.00 0.00 41.26 3.07
2499 3658 1.949799 AGTGGTCCAGAGAGCTTGAT 58.050 50.000 0.00 0.00 41.26 2.57
2500 3659 2.604912 TAGTGGTCCAGAGAGCTTGA 57.395 50.000 0.00 0.00 41.26 3.02
2501 3660 3.330267 GTTTAGTGGTCCAGAGAGCTTG 58.670 50.000 0.00 0.00 41.26 4.01
2502 3661 2.028930 CGTTTAGTGGTCCAGAGAGCTT 60.029 50.000 0.00 0.00 41.26 3.74
2503 3662 1.546476 CGTTTAGTGGTCCAGAGAGCT 59.454 52.381 0.00 0.00 41.26 4.09
2504 3663 1.404315 CCGTTTAGTGGTCCAGAGAGC 60.404 57.143 0.00 0.00 41.06 4.09
2505 3664 1.404315 GCCGTTTAGTGGTCCAGAGAG 60.404 57.143 0.00 0.00 0.00 3.20
2506 3665 0.606604 GCCGTTTAGTGGTCCAGAGA 59.393 55.000 0.00 0.00 0.00 3.10
2507 3666 0.391263 GGCCGTTTAGTGGTCCAGAG 60.391 60.000 0.00 0.00 0.00 3.35
2508 3667 1.122632 TGGCCGTTTAGTGGTCCAGA 61.123 55.000 0.00 0.00 31.75 3.86
2509 3668 0.035439 ATGGCCGTTTAGTGGTCCAG 60.035 55.000 0.00 0.00 36.55 3.86
2510 3669 0.402504 AATGGCCGTTTAGTGGTCCA 59.597 50.000 3.71 0.00 37.18 4.02
2511 3670 2.011947 GTAATGGCCGTTTAGTGGTCC 58.988 52.381 17.09 0.00 0.00 4.46
2512 3671 2.011947 GGTAATGGCCGTTTAGTGGTC 58.988 52.381 17.09 0.00 0.00 4.02
2513 3672 1.676615 CGGTAATGGCCGTTTAGTGGT 60.677 52.381 17.09 0.00 46.11 4.16
2514 3673 1.011333 CGGTAATGGCCGTTTAGTGG 58.989 55.000 17.09 0.00 46.11 4.00
2523 3682 1.940613 GTTCTGACATCGGTAATGGCC 59.059 52.381 0.00 0.00 43.47 5.36
2524 3683 1.940613 GGTTCTGACATCGGTAATGGC 59.059 52.381 0.00 0.00 44.48 4.40
2525 3684 3.260475 TGGTTCTGACATCGGTAATGG 57.740 47.619 0.00 0.00 39.90 3.16
2526 3685 4.875536 TCAATGGTTCTGACATCGGTAATG 59.124 41.667 0.00 0.00 41.48 1.90
2527 3686 5.097742 TCAATGGTTCTGACATCGGTAAT 57.902 39.130 0.00 0.00 0.00 1.89
2528 3687 4.545208 TCAATGGTTCTGACATCGGTAA 57.455 40.909 0.00 0.00 0.00 2.85
2529 3688 4.545208 TTCAATGGTTCTGACATCGGTA 57.455 40.909 0.00 0.00 0.00 4.02
2530 3689 3.417069 TTCAATGGTTCTGACATCGGT 57.583 42.857 0.00 0.00 0.00 4.69
2531 3690 4.970662 ATTTCAATGGTTCTGACATCGG 57.029 40.909 0.00 0.00 0.00 4.18
2532 3691 6.089820 CCAAAATTTCAATGGTTCTGACATCG 59.910 38.462 0.00 0.00 0.00 3.84
2533 3692 7.153985 TCCAAAATTTCAATGGTTCTGACATC 58.846 34.615 7.17 0.00 35.66 3.06
2534 3693 7.065120 TCCAAAATTTCAATGGTTCTGACAT 57.935 32.000 7.17 0.00 35.66 3.06
2535 3694 6.477053 TCCAAAATTTCAATGGTTCTGACA 57.523 33.333 7.17 0.00 35.66 3.58
2538 3697 7.790823 AGTTTCCAAAATTTCAATGGTTCTG 57.209 32.000 7.17 0.00 35.66 3.02
2540 3699 7.416817 CCAAGTTTCCAAAATTTCAATGGTTC 58.583 34.615 7.17 1.26 35.66 3.62
2543 3702 5.827267 ACCCAAGTTTCCAAAATTTCAATGG 59.173 36.000 1.52 1.52 35.49 3.16
2544 3703 6.541641 TGACCCAAGTTTCCAAAATTTCAATG 59.458 34.615 0.00 0.00 0.00 2.82
2547 3706 5.683876 TGACCCAAGTTTCCAAAATTTCA 57.316 34.783 0.00 0.00 0.00 2.69
2564 3723 9.793259 TTATTCCAGTATCTATTGAAATGACCC 57.207 33.333 0.00 0.00 0.00 4.46
2577 3736 9.060347 CACTGCAATGTAATTATTCCAGTATCT 57.940 33.333 0.00 0.00 32.46 1.98
2578 3737 9.056005 TCACTGCAATGTAATTATTCCAGTATC 57.944 33.333 0.00 0.00 32.46 2.24
2579 3738 8.978874 TCACTGCAATGTAATTATTCCAGTAT 57.021 30.769 0.00 0.00 32.46 2.12
2581 3740 7.701539 TTCACTGCAATGTAATTATTCCAGT 57.298 32.000 0.00 0.00 32.46 4.00
2582 3741 8.246180 ACTTTCACTGCAATGTAATTATTCCAG 58.754 33.333 0.00 0.00 32.46 3.86
2603 3762 9.990360 TTTTACCCCAATTCTTGAAATACTTTC 57.010 29.630 0.00 0.00 40.08 2.62
2650 3824 8.784043 ACATCCAACTAAGTATTTTGACACTTC 58.216 33.333 0.00 0.00 36.44 3.01
2653 3827 8.094798 TGACATCCAACTAAGTATTTTGACAC 57.905 34.615 0.00 0.00 0.00 3.67
2654 3828 8.684386 TTGACATCCAACTAAGTATTTTGACA 57.316 30.769 0.00 0.00 0.00 3.58
2655 3829 9.774742 GATTGACATCCAACTAAGTATTTTGAC 57.225 33.333 0.00 0.00 37.63 3.18
2662 3836 9.513906 TGAATTTGATTGACATCCAACTAAGTA 57.486 29.630 0.00 0.00 37.63 2.24
2663 3837 8.408043 TGAATTTGATTGACATCCAACTAAGT 57.592 30.769 0.00 0.00 37.63 2.24
2664 3838 9.350357 CTTGAATTTGATTGACATCCAACTAAG 57.650 33.333 0.00 0.00 37.63 2.18
2665 3839 8.859090 ACTTGAATTTGATTGACATCCAACTAA 58.141 29.630 0.00 0.00 37.63 2.24
2666 3840 8.298854 CACTTGAATTTGATTGACATCCAACTA 58.701 33.333 0.00 0.00 37.63 2.24
2675 3849 9.654417 CCAAAATTTCACTTGAATTTGATTGAC 57.346 29.630 15.15 0.00 36.71 3.18
2696 3870 5.860611 TCATTTCGACTAGAAGACCCAAAA 58.139 37.500 0.00 0.00 40.40 2.44
2699 3873 6.406624 GGTTATCATTTCGACTAGAAGACCCA 60.407 42.308 0.00 0.00 40.40 4.51
2700 3874 5.984323 GGTTATCATTTCGACTAGAAGACCC 59.016 44.000 0.00 0.00 40.40 4.46
2705 3879 7.662258 TGGTTTTGGTTATCATTTCGACTAGAA 59.338 33.333 0.00 0.00 37.01 2.10
2706 3880 7.162761 TGGTTTTGGTTATCATTTCGACTAGA 58.837 34.615 0.00 0.00 0.00 2.43
2707 3881 7.372451 TGGTTTTGGTTATCATTTCGACTAG 57.628 36.000 0.00 0.00 0.00 2.57
2709 3883 6.834168 ATGGTTTTGGTTATCATTTCGACT 57.166 33.333 0.00 0.00 0.00 4.18
2711 3885 7.220741 TCAATGGTTTTGGTTATCATTTCGA 57.779 32.000 0.00 0.00 0.00 3.71
2720 3894 4.920640 TCGCTTTCAATGGTTTTGGTTA 57.079 36.364 0.00 0.00 0.00 2.85
2730 3904 6.874297 TCTTTGCATTTATCGCTTTCAATG 57.126 33.333 0.00 0.00 0.00 2.82
2732 3906 8.859156 GTTATTCTTTGCATTTATCGCTTTCAA 58.141 29.630 0.00 0.00 0.00 2.69
2733 3907 8.243426 AGTTATTCTTTGCATTTATCGCTTTCA 58.757 29.630 0.00 0.00 0.00 2.69
2734 3908 8.620533 AGTTATTCTTTGCATTTATCGCTTTC 57.379 30.769 0.00 0.00 0.00 2.62
2735 3909 9.722056 CTAGTTATTCTTTGCATTTATCGCTTT 57.278 29.630 0.00 0.00 0.00 3.51
2738 3912 9.159470 GTTCTAGTTATTCTTTGCATTTATCGC 57.841 33.333 0.00 0.00 0.00 4.58
2758 4105 7.708752 CCTGCTAAGAGGAAAATACAGTTCTAG 59.291 40.741 0.00 0.00 34.69 2.43
2774 4121 2.413453 GACTGCGTTTTCCTGCTAAGAG 59.587 50.000 0.00 0.00 0.00 2.85
2778 4125 0.321298 GGGACTGCGTTTTCCTGCTA 60.321 55.000 0.00 0.00 31.90 3.49
2779 4126 1.600916 GGGACTGCGTTTTCCTGCT 60.601 57.895 0.00 0.00 31.90 4.24
2780 4127 2.626780 GGGGACTGCGTTTTCCTGC 61.627 63.158 0.00 0.00 31.90 4.85
2781 4128 1.971695 GGGGGACTGCGTTTTCCTG 60.972 63.158 0.00 0.00 31.90 3.86
2782 4129 1.716028 AAGGGGGACTGCGTTTTCCT 61.716 55.000 0.00 0.00 31.90 3.36
2783 4130 1.228459 AAGGGGGACTGCGTTTTCC 60.228 57.895 0.00 0.00 0.00 3.13
2785 4132 2.200337 GCAAGGGGGACTGCGTTTT 61.200 57.895 0.00 0.00 0.00 2.43
2790 4140 3.455469 GCATGCAAGGGGGACTGC 61.455 66.667 14.21 0.00 0.00 4.40
2795 4145 0.685131 TCATCAAGCATGCAAGGGGG 60.685 55.000 21.98 4.69 31.70 5.40
2853 4206 5.068636 ACAGTGCAGATGAAGAGAACATTT 58.931 37.500 5.87 0.00 0.00 2.32
2857 4210 2.999355 GGACAGTGCAGATGAAGAGAAC 59.001 50.000 5.87 0.00 0.00 3.01
2859 4212 2.495270 GAGGACAGTGCAGATGAAGAGA 59.505 50.000 5.87 0.00 0.00 3.10
2860 4213 2.496871 AGAGGACAGTGCAGATGAAGAG 59.503 50.000 5.87 0.00 0.00 2.85
2918 4301 1.817099 GCTGCTGTCCGATGGAAGG 60.817 63.158 0.00 0.00 31.38 3.46
2936 4319 1.864711 CCACCAAACGACAGTACTGTG 59.135 52.381 32.51 24.02 45.05 3.66
3013 4397 1.145738 CAGCTGGCCTGGGGTTTATAT 59.854 52.381 12.06 0.00 37.93 0.86
3070 4454 9.760660 GTGCAGTAGATCAACTTACTTTTTATG 57.239 33.333 0.00 0.00 0.00 1.90
3084 4468 4.576053 GTGCCAATTATGTGCAGTAGATCA 59.424 41.667 0.00 0.00 34.72 2.92
3162 4550 3.476031 ATTATGGTGGCTCCGCGGG 62.476 63.158 27.83 17.41 39.52 6.13


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

AutoCloner maintained by Alex Coulton.