Multiple sequence alignment - TraesCS3D01G518200

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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 TraesCS3D01G518200 chr3D 100.000 3077 0 0 1 3077 600821839 600818763 0.000000e+00 5683.0
1 TraesCS3D01G518200 chr3D 91.001 1189 73 18 991 2158 600632265 600633440 0.000000e+00 1572.0
2 TraesCS3D01G518200 chr3D 81.992 472 69 12 2253 2713 151997206 151997672 1.340000e-103 387.0
3 TraesCS3D01G518200 chr3D 78.520 419 61 19 2256 2662 308801528 308801929 6.590000e-62 248.0
4 TraesCS3D01G518200 chr3D 85.938 64 9 0 1586 1649 339306434 339306497 5.510000e-08 69.4
5 TraesCS3D01G518200 chr3D 95.122 41 1 1 2715 2754 585233897 585233857 2.560000e-06 63.9
6 TraesCS3D01G518200 chr3A 91.875 1637 56 24 704 2273 730657175 730655549 0.000000e+00 2215.0
7 TraesCS3D01G518200 chr3A 90.778 1182 82 17 1014 2177 730117034 730115862 0.000000e+00 1554.0
8 TraesCS3D01G518200 chr3A 83.946 299 11 8 270 565 730659142 730658878 5.090000e-63 252.0
9 TraesCS3D01G518200 chr3A 81.860 215 27 5 2712 2914 123011218 123011004 1.470000e-38 171.0
10 TraesCS3D01G518200 chr3A 96.907 97 3 0 610 706 730657369 730657273 2.460000e-36 163.0
11 TraesCS3D01G518200 chr3B 93.352 1414 54 9 874 2273 808043816 808042429 0.000000e+00 2054.0
12 TraesCS3D01G518200 chr3B 87.374 1489 98 45 767 2177 807975618 807977094 0.000000e+00 1626.0
13 TraesCS3D01G518200 chr3B 84.857 733 45 26 24 705 808047046 808046329 0.000000e+00 678.0
14 TraesCS3D01G518200 chr3B 80.000 470 63 20 2259 2717 426837740 426837291 4.950000e-83 318.0
15 TraesCS3D01G518200 chr3B 99.291 141 1 0 704 844 808044734 808044594 3.940000e-64 255.0
16 TraesCS3D01G518200 chr3B 85.938 64 9 0 1586 1649 437914214 437914277 5.510000e-08 69.4
17 TraesCS3D01G518200 chr3B 95.349 43 2 0 235 277 808069531 808069489 5.510000e-08 69.4
18 TraesCS3D01G518200 chr6B 82.729 469 63 14 2261 2717 8291805 8291343 4.780000e-108 401.0
19 TraesCS3D01G518200 chr1B 81.102 508 70 18 2259 2751 107171223 107170727 1.730000e-102 383.0
20 TraesCS3D01G518200 chr1B 84.932 73 7 4 6 74 535360176 535360248 1.530000e-08 71.3
21 TraesCS3D01G518200 chr1B 84.722 72 8 3 6 74 535353400 535353471 5.510000e-08 69.4
22 TraesCS3D01G518200 chr6D 82.096 458 57 17 2259 2704 4212242 4211798 4.850000e-98 368.0
23 TraesCS3D01G518200 chr1D 80.000 475 68 18 2260 2717 66677288 66676824 2.960000e-85 326.0
24 TraesCS3D01G518200 chrUn 73.731 906 196 32 1112 1996 90726837 90725953 1.780000e-82 316.0
25 TraesCS3D01G518200 chrUn 73.731 906 196 32 1112 1996 90939382 90938498 1.780000e-82 316.0
26 TraesCS3D01G518200 chrUn 79.793 386 68 8 1112 1492 401026707 401026327 3.910000e-69 272.0
27 TraesCS3D01G518200 chrUn 72.958 355 70 19 2262 2603 311366082 311365741 1.950000e-17 100.0
28 TraesCS3D01G518200 chrUn 72.958 355 70 20 2262 2603 311937210 311937551 1.950000e-17 100.0
29 TraesCS3D01G518200 chrUn 72.958 355 70 19 2262 2603 337058634 337058293 1.950000e-17 100.0
30 TraesCS3D01G518200 chr2D 79.521 459 67 18 2256 2700 475503302 475503747 4.990000e-78 302.0
31 TraesCS3D01G518200 chr2D 78.571 224 44 4 1762 1983 644017110 644017331 8.890000e-31 145.0
32 TraesCS3D01G518200 chr2D 76.132 243 55 3 1769 2009 643879431 643879672 1.160000e-24 124.0
33 TraesCS3D01G518200 chr2D 89.041 73 7 1 2621 2692 11104552 11104480 4.230000e-14 89.8
34 TraesCS3D01G518200 chr7D 73.178 947 203 43 1112 2034 37234993 37234074 8.340000e-76 294.0
35 TraesCS3D01G518200 chr7D 90.769 65 6 0 2679 2743 619385148 619385084 1.520000e-13 87.9
36 TraesCS3D01G518200 chr7D 85.526 76 11 0 2303 2378 638144132 638144207 2.540000e-11 80.5
37 TraesCS3D01G518200 chr4D 89.252 214 18 5 2507 2717 503064237 503064448 2.350000e-66 263.0
38 TraesCS3D01G518200 chr4D 77.778 261 47 7 2253 2507 503063573 503063828 1.910000e-32 150.0
39 TraesCS3D01G518200 chr4D 93.506 77 4 1 2679 2754 259928069 259928145 2.510000e-21 113.0
40 TraesCS3D01G518200 chr1A 83.125 160 24 2 2260 2419 510613669 510613825 3.200000e-30 143.0
41 TraesCS3D01G518200 chr1A 92.453 53 4 0 10 62 131963586 131963638 3.290000e-10 76.8
42 TraesCS3D01G518200 chr2B 75.417 240 56 3 1772 2009 793168811 793168573 2.510000e-21 113.0
43 TraesCS3D01G518200 chr2B 75.000 248 54 7 1762 2005 793141261 793141018 1.170000e-19 108.0
44 TraesCS3D01G518200 chr2B 90.909 55 5 0 2303 2357 11514618 11514672 1.180000e-09 75.0
45 TraesCS3D01G518200 chr2B 88.889 63 3 3 3 62 548294812 548294751 1.180000e-09 75.0
46 TraesCS3D01G518200 chr7A 83.186 113 16 2 2256 2368 102051466 102051575 1.950000e-17 100.0
47 TraesCS3D01G518200 chr4A 96.000 50 2 0 4 53 658953507 658953556 7.070000e-12 82.4
48 TraesCS3D01G518200 chr7B 80.583 103 20 0 2303 2405 581003636 581003534 2.540000e-11 80.5
49 TraesCS3D01G518200 chr7B 86.567 67 8 1 12 77 535253656 535253590 4.260000e-09 73.1
50 TraesCS3D01G518200 chr7B 89.474 57 4 2 7 62 60869977 60869922 1.530000e-08 71.3
51 TraesCS3D01G518200 chr7B 100.000 28 0 0 2875 2902 718153691 718153664 6.000000e-03 52.8
52 TraesCS3D01G518200 chr4B 95.652 46 2 0 8 53 670388299 670388344 1.180000e-09 75.0


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 TraesCS3D01G518200 chr3D 600818763 600821839 3076 True 5683.000000 5683 100.000000 1 3077 1 chr3D.!!$R2 3076
1 TraesCS3D01G518200 chr3D 600632265 600633440 1175 False 1572.000000 1572 91.001000 991 2158 1 chr3D.!!$F4 1167
2 TraesCS3D01G518200 chr3A 730115862 730117034 1172 True 1554.000000 1554 90.778000 1014 2177 1 chr3A.!!$R2 1163
3 TraesCS3D01G518200 chr3A 730655549 730659142 3593 True 876.666667 2215 90.909333 270 2273 3 chr3A.!!$R3 2003
4 TraesCS3D01G518200 chr3B 807975618 807977094 1476 False 1626.000000 1626 87.374000 767 2177 1 chr3B.!!$F2 1410
5 TraesCS3D01G518200 chr3B 808042429 808047046 4617 True 995.666667 2054 92.500000 24 2273 3 chr3B.!!$R3 2249
6 TraesCS3D01G518200 chrUn 90725953 90726837 884 True 316.000000 316 73.731000 1112 1996 1 chrUn.!!$R1 884
7 TraesCS3D01G518200 chrUn 90938498 90939382 884 True 316.000000 316 73.731000 1112 1996 1 chrUn.!!$R2 884
8 TraesCS3D01G518200 chr7D 37234074 37234993 919 True 294.000000 294 73.178000 1112 2034 1 chr7D.!!$R1 922
9 TraesCS3D01G518200 chr4D 503063573 503064448 875 False 206.500000 263 83.515000 2253 2717 2 chr4D.!!$F2 464

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
530 553 0.036732 CCCTGCCTGTTCTAACTGCA 59.963 55.0 9.27 9.27 36.48 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2440 6409 0.110486 ATTTTGAGGCCTCCGTGTGT 59.89 50.0 29.95 8.39 0.0 3.72 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
40 41 7.549488 CCCCCTATGTAAAGAAATATAAGAGCG 59.451 40.741 0.00 0.00 0.00 5.03
41 42 8.095169 CCCCTATGTAAAGAAATATAAGAGCGT 58.905 37.037 0.00 0.00 0.00 5.07
116 117 5.287674 AGTATTGCATCTAGTCAGCACAT 57.712 39.130 6.11 6.45 38.11 3.21
119 120 8.127150 AGTATTGCATCTAGTCAGCACATATA 57.873 34.615 6.11 1.30 38.11 0.86
125 126 6.034363 GCATCTAGTCAGCACATATATTGTCG 59.966 42.308 0.00 0.00 36.00 4.35
128 129 8.161699 TCTAGTCAGCACATATATTGTCGTTA 57.838 34.615 0.00 0.00 36.00 3.18
146 147 4.525487 TCGTTAGCTAGAGAAAAAGGTGGA 59.475 41.667 0.00 0.00 0.00 4.02
207 208 0.953727 TGATCTTGTGGCAAGCACAC 59.046 50.000 4.16 6.69 39.26 3.82
208 209 0.953727 GATCTTGTGGCAAGCACACA 59.046 50.000 10.80 10.80 46.22 3.72
213 214 0.107459 TGTGGCAAGCACACACACTA 60.107 50.000 10.80 0.00 43.35 2.74
228 229 5.934625 ACACACACTAGCCAATTAAGAAGAG 59.065 40.000 0.00 0.00 0.00 2.85
296 297 5.622770 CTTTTAAGCACGGGTGAATTAGT 57.377 39.130 2.38 0.00 0.00 2.24
306 307 4.611310 GGGTGAATTAGTTAAAGCCGAC 57.389 45.455 0.00 0.00 0.00 4.79
307 308 3.063045 GGGTGAATTAGTTAAAGCCGACG 59.937 47.826 0.00 0.00 0.00 5.12
362 363 7.203255 ACAAATTTCTAACGGAAGAGAAAGG 57.797 36.000 3.73 0.00 43.11 3.11
363 364 6.771267 ACAAATTTCTAACGGAAGAGAAAGGT 59.229 34.615 3.73 0.25 43.11 3.50
364 365 6.803154 AATTTCTAACGGAAGAGAAAGGTG 57.197 37.500 3.73 0.00 43.11 4.00
365 366 3.314541 TCTAACGGAAGAGAAAGGTGC 57.685 47.619 0.00 0.00 0.00 5.01
366 367 2.631062 TCTAACGGAAGAGAAAGGTGCA 59.369 45.455 0.00 0.00 0.00 4.57
367 368 1.884235 AACGGAAGAGAAAGGTGCAG 58.116 50.000 0.00 0.00 0.00 4.41
393 394 2.894257 ATGGTCAGTGCAAGCGGGA 61.894 57.895 0.00 0.00 0.00 5.14
397 398 2.210013 TCAGTGCAAGCGGGAGAGT 61.210 57.895 0.00 0.00 0.00 3.24
398 399 2.031516 CAGTGCAAGCGGGAGAGTG 61.032 63.158 0.00 0.00 0.00 3.51
401 402 1.301716 TGCAAGCGGGAGAGTGAAC 60.302 57.895 0.00 0.00 0.00 3.18
407 408 1.478510 AGCGGGAGAGTGAACACATAG 59.521 52.381 7.68 0.00 0.00 2.23
413 414 5.652518 GGGAGAGTGAACACATAGAAGTAC 58.347 45.833 7.68 0.00 0.00 2.73
414 415 5.419471 GGGAGAGTGAACACATAGAAGTACT 59.581 44.000 7.68 0.00 0.00 2.73
450 454 5.458891 CGTAGCAAGGCGAGTATTATAGTT 58.541 41.667 0.00 0.00 0.00 2.24
527 550 2.912956 TCAATCCCTGCCTGTTCTAACT 59.087 45.455 0.00 0.00 0.00 2.24
528 551 3.012518 CAATCCCTGCCTGTTCTAACTG 58.987 50.000 0.00 0.00 0.00 3.16
529 552 0.324943 TCCCTGCCTGTTCTAACTGC 59.675 55.000 0.00 0.00 0.00 4.40
530 553 0.036732 CCCTGCCTGTTCTAACTGCA 59.963 55.000 9.27 9.27 36.48 4.41
607 936 2.557056 CGATCTCCGCCCTGTATAAGAA 59.443 50.000 0.00 0.00 0.00 2.52
608 937 3.193691 CGATCTCCGCCCTGTATAAGAAT 59.806 47.826 0.00 0.00 0.00 2.40
617 2104 5.621193 GCCCTGTATAAGAATTAAGAGGCA 58.379 41.667 0.00 0.00 32.17 4.75
622 2109 9.566432 CCTGTATAAGAATTAAGAGGCATCTTT 57.434 33.333 19.98 0.45 43.45 2.52
1984 5936 1.613630 AACCAGGGTCAGATCCGCT 60.614 57.895 0.00 0.00 0.00 5.52
2144 6107 2.566833 TGGTTTGGACTCTGGATGTG 57.433 50.000 0.00 0.00 0.00 3.21
2154 6117 2.687425 ACTCTGGATGTGAGAGTGATCG 59.313 50.000 0.00 0.00 46.80 3.69
2209 6174 1.520787 GTGGCCCTCGTGTAATCGG 60.521 63.158 0.00 0.00 0.00 4.18
2250 6215 2.834549 TGCTAACTTGGGAGGAGAAGAG 59.165 50.000 0.00 0.00 0.00 2.85
2251 6216 2.419436 GCTAACTTGGGAGGAGAAGAGC 60.419 54.545 0.00 0.00 0.00 4.09
2274 6239 9.336171 GAGCTCTCTTGTCCATCTTTTTAATAT 57.664 33.333 6.43 0.00 0.00 1.28
2302 6267 9.587772 TTTCTTCTCAAGTAATCTATACAGTGC 57.412 33.333 0.00 0.00 0.00 4.40
2305 6270 9.891828 CTTCTCAAGTAATCTATACAGTGCTAG 57.108 37.037 0.00 0.00 0.00 3.42
2306 6271 9.628500 TTCTCAAGTAATCTATACAGTGCTAGA 57.372 33.333 0.00 5.71 0.00 2.43
2341 6306 3.360867 TGTTTTTCAACAGAAGCTCCCA 58.639 40.909 0.00 0.00 38.03 4.37
2342 6307 3.766591 TGTTTTTCAACAGAAGCTCCCAA 59.233 39.130 0.00 0.00 38.03 4.12
2378 6343 2.120232 CGCTGATGTATGTCGAAGGTC 58.880 52.381 0.00 0.00 0.00 3.85
2384 6349 4.402474 TGATGTATGTCGAAGGTCAGATGT 59.598 41.667 0.00 0.00 0.00 3.06
2385 6350 5.592688 TGATGTATGTCGAAGGTCAGATGTA 59.407 40.000 0.00 0.00 0.00 2.29
2393 6358 6.485313 TGTCGAAGGTCAGATGTAAATTGTTT 59.515 34.615 0.00 0.00 0.00 2.83
2399 6364 6.374333 AGGTCAGATGTAAATTGTTTGCGTAT 59.626 34.615 0.00 0.00 0.00 3.06
2400 6365 6.468956 GGTCAGATGTAAATTGTTTGCGTATG 59.531 38.462 2.36 2.36 35.64 2.39
2401 6366 6.468956 GTCAGATGTAAATTGTTTGCGTATGG 59.531 38.462 7.25 0.00 35.24 2.74
2407 6372 0.529833 TTGTTTGCGTATGGCCATGG 59.470 50.000 29.04 20.03 42.61 3.66
2414 6379 1.071471 GTATGGCCATGGACGGAGG 59.929 63.158 29.04 0.00 0.00 4.30
2417 6382 3.728373 GGCCATGGACGGAGGGTT 61.728 66.667 18.40 0.00 0.00 4.11
2422 6387 0.739813 CATGGACGGAGGGTTTCGAC 60.740 60.000 0.00 0.00 0.00 4.20
2423 6388 1.189524 ATGGACGGAGGGTTTCGACA 61.190 55.000 0.00 0.00 0.00 4.35
2424 6389 1.189524 TGGACGGAGGGTTTCGACAT 61.190 55.000 0.00 0.00 0.00 3.06
2425 6390 0.819582 GGACGGAGGGTTTCGACATA 59.180 55.000 0.00 0.00 0.00 2.29
2426 6391 1.470458 GGACGGAGGGTTTCGACATAC 60.470 57.143 0.00 0.00 0.00 2.39
2427 6392 1.475682 GACGGAGGGTTTCGACATACT 59.524 52.381 0.00 0.00 0.00 2.12
2428 6393 1.475682 ACGGAGGGTTTCGACATACTC 59.524 52.381 0.00 0.00 0.00 2.59
2429 6394 1.475280 CGGAGGGTTTCGACATACTCA 59.525 52.381 8.17 0.00 0.00 3.41
2430 6395 2.479730 CGGAGGGTTTCGACATACTCAG 60.480 54.545 8.17 1.84 0.00 3.35
2431 6396 2.758979 GGAGGGTTTCGACATACTCAGA 59.241 50.000 8.17 0.00 0.00 3.27
2432 6397 3.429135 GGAGGGTTTCGACATACTCAGAC 60.429 52.174 8.17 0.00 0.00 3.51
2440 6409 5.959618 TCGACATACTCAGACTTCTCAAA 57.040 39.130 0.00 0.00 0.00 2.69
2443 6412 5.343593 CGACATACTCAGACTTCTCAAACAC 59.656 44.000 0.00 0.00 0.00 3.32
2445 6414 5.986135 ACATACTCAGACTTCTCAAACACAC 59.014 40.000 0.00 0.00 0.00 3.82
2461 6430 0.400213 ACACGGAGGCCTCAAAATCA 59.600 50.000 33.29 0.00 0.00 2.57
2462 6431 1.202879 ACACGGAGGCCTCAAAATCAA 60.203 47.619 33.29 0.00 0.00 2.57
2469 6438 4.019174 GAGGCCTCAAAATCAAAGGATGA 58.981 43.478 28.43 0.00 43.67 2.92
2476 6446 7.442062 GCCTCAAAATCAAAGGATGAAGAAAAA 59.558 33.333 0.00 0.00 42.54 1.94
2520 6899 0.924090 TGGAGACCGGTGGATCTCTA 59.076 55.000 14.63 7.52 41.05 2.43
2533 6912 5.188555 GGTGGATCTCTATGCTCCATAATGA 59.811 44.000 0.00 0.00 42.20 2.57
2535 6914 6.817641 GTGGATCTCTATGCTCCATAATGAAG 59.182 42.308 0.00 0.00 42.20 3.02
2537 6916 7.093421 TGGATCTCTATGCTCCATAATGAAGAG 60.093 40.741 0.00 0.00 36.18 2.85
2541 6920 5.846164 TCTATGCTCCATAATGAAGAGGGAA 59.154 40.000 0.00 0.00 0.00 3.97
2543 6922 3.782523 TGCTCCATAATGAAGAGGGAAGT 59.217 43.478 0.00 0.00 0.00 3.01
2544 6923 4.228210 TGCTCCATAATGAAGAGGGAAGTT 59.772 41.667 0.00 0.00 0.00 2.66
2545 6924 5.196695 GCTCCATAATGAAGAGGGAAGTTT 58.803 41.667 0.00 0.00 0.00 2.66
2584 6964 6.975949 ACTATTTTCCTGAGAGAGAGGAGTA 58.024 40.000 0.00 0.00 40.79 2.59
2586 6966 3.943671 TTCCTGAGAGAGAGGAGTAGG 57.056 52.381 0.00 0.00 40.79 3.18
2662 7044 5.927115 GCTAGTAGTGGTTACCTTATGATGC 59.073 44.000 2.07 0.00 32.37 3.91
2670 7052 8.880244 AGTGGTTACCTTATGATGCTCATTATA 58.120 33.333 2.07 0.00 38.26 0.98
2675 7057 9.929180 TTACCTTATGATGCTCATTATAGTGAC 57.071 33.333 4.35 0.00 38.26 3.67
2677 7059 8.600668 ACCTTATGATGCTCATTATAGTGACAT 58.399 33.333 10.75 10.75 38.26 3.06
2678 7060 8.880750 CCTTATGATGCTCATTATAGTGACATG 58.119 37.037 13.85 0.00 38.26 3.21
2726 7108 9.618890 AATGAGTTGTTATATCATTGCTACTGT 57.381 29.630 0.00 0.00 41.03 3.55
2784 7166 9.555727 TGAAATGAAATAAGGTATAGTAGTGGC 57.444 33.333 0.00 0.00 0.00 5.01
2785 7167 8.603242 AAATGAAATAAGGTATAGTAGTGGCG 57.397 34.615 0.00 0.00 0.00 5.69
2786 7168 5.535333 TGAAATAAGGTATAGTAGTGGCGC 58.465 41.667 0.00 0.00 0.00 6.53
2787 7169 3.844577 ATAAGGTATAGTAGTGGCGCG 57.155 47.619 0.00 0.00 0.00 6.86
2788 7170 0.672342 AAGGTATAGTAGTGGCGCGG 59.328 55.000 8.83 0.00 0.00 6.46
2789 7171 1.177256 AGGTATAGTAGTGGCGCGGG 61.177 60.000 8.83 0.00 0.00 6.13
2790 7172 1.288127 GTATAGTAGTGGCGCGGGG 59.712 63.158 8.83 0.00 0.00 5.73
2791 7173 1.152694 TATAGTAGTGGCGCGGGGT 60.153 57.895 8.83 0.00 0.00 4.95
2792 7174 0.110295 TATAGTAGTGGCGCGGGGTA 59.890 55.000 8.83 0.00 0.00 3.69
2793 7175 0.756442 ATAGTAGTGGCGCGGGGTAA 60.756 55.000 8.83 0.00 0.00 2.85
2794 7176 0.756442 TAGTAGTGGCGCGGGGTAAT 60.756 55.000 8.83 0.00 0.00 1.89
2795 7177 0.756442 AGTAGTGGCGCGGGGTAATA 60.756 55.000 8.83 0.00 0.00 0.98
2796 7178 0.598419 GTAGTGGCGCGGGGTAATAC 60.598 60.000 8.83 0.00 0.00 1.89
2797 7179 1.747325 TAGTGGCGCGGGGTAATACC 61.747 60.000 8.83 0.00 37.60 2.73
2809 7191 2.835027 GGTAATACCCAGCACTACTGC 58.165 52.381 0.00 0.00 45.78 4.40
2834 7216 2.987752 GCAATAGCGTGGGTCCTAC 58.012 57.895 0.00 0.00 0.00 3.18
2835 7217 0.532196 GCAATAGCGTGGGTCCTACC 60.532 60.000 0.00 0.00 37.60 3.18
2845 7227 2.460027 GGTCCTACCCCACACAACT 58.540 57.895 0.00 0.00 30.04 3.16
2846 7228 1.648116 GGTCCTACCCCACACAACTA 58.352 55.000 0.00 0.00 30.04 2.24
2847 7229 1.277273 GGTCCTACCCCACACAACTAC 59.723 57.143 0.00 0.00 30.04 2.73
2848 7230 2.254508 GTCCTACCCCACACAACTACT 58.745 52.381 0.00 0.00 0.00 2.57
2849 7231 2.028385 GTCCTACCCCACACAACTACTG 60.028 54.545 0.00 0.00 0.00 2.74
2850 7232 2.158279 TCCTACCCCACACAACTACTGA 60.158 50.000 0.00 0.00 0.00 3.41
2851 7233 2.233922 CCTACCCCACACAACTACTGAG 59.766 54.545 0.00 0.00 0.00 3.35
2852 7234 2.097110 ACCCCACACAACTACTGAGA 57.903 50.000 0.00 0.00 0.00 3.27
2853 7235 2.404559 ACCCCACACAACTACTGAGAA 58.595 47.619 0.00 0.00 0.00 2.87
2854 7236 2.775384 ACCCCACACAACTACTGAGAAA 59.225 45.455 0.00 0.00 0.00 2.52
2855 7237 3.394606 ACCCCACACAACTACTGAGAAAT 59.605 43.478 0.00 0.00 0.00 2.17
2856 7238 4.141251 ACCCCACACAACTACTGAGAAATT 60.141 41.667 0.00 0.00 0.00 1.82
2857 7239 4.827284 CCCCACACAACTACTGAGAAATTT 59.173 41.667 0.00 0.00 0.00 1.82
2858 7240 6.001460 CCCCACACAACTACTGAGAAATTTA 58.999 40.000 0.00 0.00 0.00 1.40
2859 7241 6.149474 CCCCACACAACTACTGAGAAATTTAG 59.851 42.308 0.00 0.00 0.00 1.85
2860 7242 6.710744 CCCACACAACTACTGAGAAATTTAGT 59.289 38.462 0.00 0.00 0.00 2.24
2861 7243 7.876068 CCCACACAACTACTGAGAAATTTAGTA 59.124 37.037 0.00 0.00 0.00 1.82
2862 7244 8.926710 CCACACAACTACTGAGAAATTTAGTAG 58.073 37.037 18.75 18.75 45.81 2.57
2863 7245 8.436200 CACACAACTACTGAGAAATTTAGTAGC 58.564 37.037 19.70 0.00 44.79 3.58
2864 7246 8.148351 ACACAACTACTGAGAAATTTAGTAGCA 58.852 33.333 19.70 3.32 44.79 3.49
2865 7247 8.651588 CACAACTACTGAGAAATTTAGTAGCAG 58.348 37.037 19.70 15.91 44.79 4.24
2866 7248 8.368668 ACAACTACTGAGAAATTTAGTAGCAGT 58.631 33.333 19.70 16.35 44.79 4.40
2867 7249 9.856488 CAACTACTGAGAAATTTAGTAGCAGTA 57.144 33.333 19.70 16.13 44.79 2.74
2868 7250 9.857957 AACTACTGAGAAATTTAGTAGCAGTAC 57.142 33.333 19.70 0.00 44.79 2.73
2869 7251 8.468399 ACTACTGAGAAATTTAGTAGCAGTACC 58.532 37.037 19.70 0.00 44.79 3.34
2870 7252 6.641474 ACTGAGAAATTTAGTAGCAGTACCC 58.359 40.000 0.00 0.00 33.78 3.69
2871 7253 6.440965 ACTGAGAAATTTAGTAGCAGTACCCT 59.559 38.462 0.00 0.00 33.78 4.34
2872 7254 6.875076 TGAGAAATTTAGTAGCAGTACCCTC 58.125 40.000 0.00 0.00 0.00 4.30
2873 7255 6.668283 TGAGAAATTTAGTAGCAGTACCCTCT 59.332 38.462 0.00 0.00 0.00 3.69
2874 7256 7.180408 TGAGAAATTTAGTAGCAGTACCCTCTT 59.820 37.037 0.00 0.00 0.00 2.85
2875 7257 7.331791 AGAAATTTAGTAGCAGTACCCTCTTG 58.668 38.462 0.00 0.00 0.00 3.02
2876 7258 4.467198 TTTAGTAGCAGTACCCTCTTGC 57.533 45.455 0.00 0.00 0.00 4.01
2877 7259 2.239681 AGTAGCAGTACCCTCTTGCT 57.760 50.000 10.90 10.90 39.36 3.91
2878 7260 3.383698 AGTAGCAGTACCCTCTTGCTA 57.616 47.619 9.11 9.11 37.08 3.49
2879 7261 3.439895 GTAGCAGTACCCTCTTGCTAC 57.560 52.381 21.38 21.38 46.88 3.58
2880 7262 2.239681 AGCAGTACCCTCTTGCTACT 57.760 50.000 4.85 0.00 33.70 2.57
2881 7263 3.383698 AGCAGTACCCTCTTGCTACTA 57.616 47.619 4.85 0.00 33.70 1.82
2882 7264 3.025262 AGCAGTACCCTCTTGCTACTAC 58.975 50.000 4.85 0.00 33.70 2.73
2883 7265 3.025262 GCAGTACCCTCTTGCTACTACT 58.975 50.000 0.00 0.00 0.00 2.57
2884 7266 4.079901 AGCAGTACCCTCTTGCTACTACTA 60.080 45.833 4.85 0.00 33.70 1.82
2885 7267 4.643784 GCAGTACCCTCTTGCTACTACTAA 59.356 45.833 0.00 0.00 0.00 2.24
2886 7268 5.126707 GCAGTACCCTCTTGCTACTACTAAA 59.873 44.000 0.00 0.00 0.00 1.85
2887 7269 6.350780 GCAGTACCCTCTTGCTACTACTAAAA 60.351 42.308 0.00 0.00 0.00 1.52
2888 7270 7.259161 CAGTACCCTCTTGCTACTACTAAAAG 58.741 42.308 0.00 0.00 0.00 2.27
2889 7271 6.952938 AGTACCCTCTTGCTACTACTAAAAGT 59.047 38.462 0.00 0.00 0.00 2.66
2890 7272 6.683312 ACCCTCTTGCTACTACTAAAAGTT 57.317 37.500 0.00 0.00 0.00 2.66
2891 7273 7.787623 ACCCTCTTGCTACTACTAAAAGTTA 57.212 36.000 0.00 0.00 0.00 2.24
2892 7274 7.838884 ACCCTCTTGCTACTACTAAAAGTTAG 58.161 38.462 0.00 0.00 0.00 2.34
2893 7275 6.757478 CCCTCTTGCTACTACTAAAAGTTAGC 59.243 42.308 4.53 4.53 31.94 3.09
2894 7276 7.363968 CCCTCTTGCTACTACTAAAAGTTAGCT 60.364 40.741 10.50 0.00 32.25 3.32
2895 7277 7.489757 CCTCTTGCTACTACTAAAAGTTAGCTG 59.510 40.741 0.00 5.70 32.25 4.24
2896 7278 6.812160 TCTTGCTACTACTAAAAGTTAGCTGC 59.188 38.462 0.00 0.00 32.25 5.25
2897 7279 6.032956 TGCTACTACTAAAAGTTAGCTGCA 57.967 37.500 1.02 0.00 32.25 4.41
2898 7280 6.100004 TGCTACTACTAAAAGTTAGCTGCAG 58.900 40.000 10.11 10.11 32.25 4.41
2899 7281 5.005875 GCTACTACTAAAAGTTAGCTGCAGC 59.994 44.000 31.53 31.53 42.49 5.25
2911 7293 3.603365 TGCAGCGCTCTAGCAGTA 58.397 55.556 16.09 0.00 42.21 2.74
2912 7294 1.435105 TGCAGCGCTCTAGCAGTAG 59.565 57.895 16.09 0.00 42.21 2.57
2913 7295 1.948635 GCAGCGCTCTAGCAGTAGC 60.949 63.158 7.13 0.00 42.21 3.58
2914 7296 1.435105 CAGCGCTCTAGCAGTAGCA 59.565 57.895 7.13 0.00 45.49 3.49
2915 7297 0.869454 CAGCGCTCTAGCAGTAGCAC 60.869 60.000 7.13 0.00 45.49 4.40
2916 7298 1.941734 GCGCTCTAGCAGTAGCACG 60.942 63.158 0.00 0.00 45.49 5.34
2917 7299 1.722082 CGCTCTAGCAGTAGCACGA 59.278 57.895 2.44 0.00 45.49 4.35
2918 7300 0.309302 CGCTCTAGCAGTAGCACGAT 59.691 55.000 2.44 0.00 45.49 3.73
2919 7301 1.661743 CGCTCTAGCAGTAGCACGATC 60.662 57.143 2.44 0.00 45.49 3.69
2920 7302 1.335506 GCTCTAGCAGTAGCACGATCC 60.336 57.143 0.00 0.00 45.49 3.36
2921 7303 1.268352 CTCTAGCAGTAGCACGATCCC 59.732 57.143 0.00 0.00 45.49 3.85
2922 7304 1.133761 TCTAGCAGTAGCACGATCCCT 60.134 52.381 0.00 0.00 45.49 4.20
2923 7305 1.000827 CTAGCAGTAGCACGATCCCTG 60.001 57.143 0.00 0.00 45.49 4.45
2924 7306 0.684479 AGCAGTAGCACGATCCCTGA 60.684 55.000 0.00 0.00 45.49 3.86
2925 7307 0.175760 GCAGTAGCACGATCCCTGAA 59.824 55.000 0.00 0.00 41.58 3.02
2926 7308 1.927895 CAGTAGCACGATCCCTGAAC 58.072 55.000 0.00 0.00 0.00 3.18
2927 7309 0.824759 AGTAGCACGATCCCTGAACC 59.175 55.000 0.00 0.00 0.00 3.62
2928 7310 0.527817 GTAGCACGATCCCTGAACCG 60.528 60.000 0.00 0.00 0.00 4.44
2929 7311 0.968901 TAGCACGATCCCTGAACCGT 60.969 55.000 0.00 0.00 35.46 4.83
2930 7312 1.375523 GCACGATCCCTGAACCGTT 60.376 57.895 0.00 0.00 32.50 4.44
2931 7313 0.953960 GCACGATCCCTGAACCGTTT 60.954 55.000 0.00 0.00 32.50 3.60
2932 7314 1.519408 CACGATCCCTGAACCGTTTT 58.481 50.000 0.00 0.00 32.50 2.43
2933 7315 1.877443 CACGATCCCTGAACCGTTTTT 59.123 47.619 0.00 0.00 32.50 1.94
3051 7433 8.696410 TTTTAGTTTGCGAAAATCTTTGAAGT 57.304 26.923 0.00 0.00 0.00 3.01
3052 7434 8.696410 TTTAGTTTGCGAAAATCTTTGAAGTT 57.304 26.923 0.00 0.00 0.00 2.66
3053 7435 6.812481 AGTTTGCGAAAATCTTTGAAGTTC 57.188 33.333 0.00 0.00 0.00 3.01
3054 7436 5.748630 AGTTTGCGAAAATCTTTGAAGTTCC 59.251 36.000 0.00 0.00 0.00 3.62
3055 7437 4.237349 TGCGAAAATCTTTGAAGTTCCC 57.763 40.909 0.00 0.00 0.00 3.97
3056 7438 3.005367 TGCGAAAATCTTTGAAGTTCCCC 59.995 43.478 0.00 0.00 0.00 4.81
3057 7439 3.255888 GCGAAAATCTTTGAAGTTCCCCT 59.744 43.478 0.00 0.00 0.00 4.79
3058 7440 4.262036 GCGAAAATCTTTGAAGTTCCCCTT 60.262 41.667 0.00 0.00 35.59 3.95
3059 7441 5.739070 GCGAAAATCTTTGAAGTTCCCCTTT 60.739 40.000 0.00 0.00 32.03 3.11
3060 7442 6.280643 CGAAAATCTTTGAAGTTCCCCTTTT 58.719 36.000 0.00 0.33 32.03 2.27
3061 7443 6.761242 CGAAAATCTTTGAAGTTCCCCTTTTT 59.239 34.615 0.00 1.15 32.03 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.383947 GCTCTTATATTTCTTTACATAGGGGGT 58.616 37.037 0.00 0.00 0.00 4.95
14 15 7.549488 CGCTCTTATATTTCTTTACATAGGGGG 59.451 40.741 0.00 0.00 0.00 5.40
15 16 8.095169 ACGCTCTTATATTTCTTTACATAGGGG 58.905 37.037 0.00 0.00 0.00 4.79
16 17 9.490379 AACGCTCTTATATTTCTTTACATAGGG 57.510 33.333 0.00 0.00 0.00 3.53
63 64 4.112634 TGGGGAGACACATAAGCTTTTT 57.887 40.909 3.20 0.00 40.38 1.94
73 74 1.451504 CACTTGCTGGGGAGACACA 59.548 57.895 0.00 0.00 45.84 3.72
74 75 1.302832 CCACTTGCTGGGGAGACAC 60.303 63.158 0.00 0.00 43.63 3.67
75 76 1.461268 TCCACTTGCTGGGGAGACA 60.461 57.895 0.00 0.00 44.85 3.41
76 77 3.483587 TCCACTTGCTGGGGAGAC 58.516 61.111 0.00 0.00 44.85 3.36
83 84 3.693085 AGATGCAATACTTCCACTTGCTG 59.307 43.478 7.85 0.00 44.29 4.41
101 102 7.087007 ACGACAATATATGTGCTGACTAGATG 58.913 38.462 0.00 0.00 44.12 2.90
105 106 6.861572 GCTAACGACAATATATGTGCTGACTA 59.138 38.462 0.00 0.00 44.12 2.59
110 111 7.175119 TCTCTAGCTAACGACAATATATGTGCT 59.825 37.037 0.00 0.00 44.12 4.40
111 112 7.306213 TCTCTAGCTAACGACAATATATGTGC 58.694 38.462 0.00 0.00 44.12 4.57
116 117 9.745880 CCTTTTTCTCTAGCTAACGACAATATA 57.254 33.333 0.00 0.00 0.00 0.86
119 120 6.369065 CACCTTTTTCTCTAGCTAACGACAAT 59.631 38.462 0.00 0.00 0.00 2.71
125 126 5.548406 TGTCCACCTTTTTCTCTAGCTAAC 58.452 41.667 0.00 0.00 0.00 2.34
128 129 4.917906 ATGTCCACCTTTTTCTCTAGCT 57.082 40.909 0.00 0.00 0.00 3.32
146 147 3.020984 ACAAAGGAACACGACCAAATGT 58.979 40.909 0.00 0.00 0.00 2.71
156 157 3.066621 TCATGCACTCAACAAAGGAACAC 59.933 43.478 0.00 0.00 0.00 3.32
159 160 3.068024 GGTTCATGCACTCAACAAAGGAA 59.932 43.478 0.00 0.00 0.00 3.36
207 208 9.817809 TTATACTCTTCTTAATTGGCTAGTGTG 57.182 33.333 0.00 0.00 0.00 3.82
213 214 7.272978 TCGCTTTATACTCTTCTTAATTGGCT 58.727 34.615 0.00 0.00 0.00 4.75
228 229 2.030091 GCACGGGTTCTTCGCTTTATAC 59.970 50.000 0.00 0.00 0.00 1.47
296 297 0.034337 AAGGCAGTCGTCGGCTTTAA 59.966 50.000 0.00 0.00 46.09 1.52
305 306 2.930040 CGTCATGATTAAAGGCAGTCGT 59.070 45.455 0.00 0.00 0.00 4.34
306 307 3.000322 GTCGTCATGATTAAAGGCAGTCG 60.000 47.826 0.00 0.00 0.00 4.18
307 308 3.000322 CGTCGTCATGATTAAAGGCAGTC 60.000 47.826 0.00 0.00 0.00 3.51
365 366 0.170339 CACTGACCATGCATGCACTG 59.830 55.000 25.37 20.62 0.00 3.66
366 367 1.592400 GCACTGACCATGCATGCACT 61.592 55.000 25.37 8.45 42.88 4.40
367 368 1.153901 GCACTGACCATGCATGCAC 60.154 57.895 25.37 16.22 42.88 4.57
378 379 1.739562 CTCTCCCGCTTGCACTGAC 60.740 63.158 0.00 0.00 0.00 3.51
389 390 3.193691 ACTTCTATGTGTTCACTCTCCCG 59.806 47.826 4.59 0.00 0.00 5.14
397 398 8.982091 AGCTAGATAGTACTTCTATGTGTTCA 57.018 34.615 0.00 0.00 39.22 3.18
401 402 8.455682 GCCTTAGCTAGATAGTACTTCTATGTG 58.544 40.741 0.00 0.00 36.40 3.21
407 408 5.945466 ACGCCTTAGCTAGATAGTACTTC 57.055 43.478 0.00 0.00 36.60 3.01
450 454 6.114187 ACAATCATCACACAACTCTCCTAA 57.886 37.500 0.00 0.00 0.00 2.69
1066 4999 1.445754 CGGCTGACACAGAGCTCAG 60.446 63.158 17.77 11.05 37.55 3.35
1067 5000 2.653115 CGGCTGACACAGAGCTCA 59.347 61.111 17.77 0.00 36.63 4.26
1068 5001 2.813042 GCGGCTGACACAGAGCTC 60.813 66.667 5.27 5.27 36.63 4.09
1069 5002 4.731612 CGCGGCTGACACAGAGCT 62.732 66.667 0.00 0.00 35.62 4.09
1314 5266 4.394078 CGGAGCGTGACGTTCGGA 62.394 66.667 21.03 0.00 39.00 4.55
1866 5818 2.113139 CTGGTGACCACGGGCTTT 59.887 61.111 0.00 0.00 0.00 3.51
2144 6107 2.177977 CTTACACACGCGATCACTCTC 58.822 52.381 15.93 0.00 0.00 3.20
2153 6116 2.624766 CTTGACAAACTTACACACGCG 58.375 47.619 3.53 3.53 0.00 6.01
2154 6117 2.223157 TGCTTGACAAACTTACACACGC 60.223 45.455 0.00 0.00 0.00 5.34
2209 6174 4.641989 AGCACAACCATGTATTTCTGGATC 59.358 41.667 0.00 0.00 37.82 3.36
2278 6243 8.526667 AGCACTGTATAGATTACTTGAGAAGA 57.473 34.615 0.00 0.00 0.00 2.87
2279 6244 9.891828 CTAGCACTGTATAGATTACTTGAGAAG 57.108 37.037 0.00 0.00 0.00 2.85
2281 6246 9.800572 ATCTAGCACTGTATAGATTACTTGAGA 57.199 33.333 8.25 0.00 35.66 3.27
2314 6279 7.970614 GGGAGCTTCTGTTGAAAAACATAATAG 59.029 37.037 0.00 0.00 31.47 1.73
2316 6281 6.267471 TGGGAGCTTCTGTTGAAAAACATAAT 59.733 34.615 0.00 0.00 31.47 1.28
2318 6283 5.136828 TGGGAGCTTCTGTTGAAAAACATA 58.863 37.500 0.00 0.00 31.47 2.29
2324 6289 4.214310 TCATTTGGGAGCTTCTGTTGAAA 58.786 39.130 0.00 0.00 0.00 2.69
2331 6296 3.508793 CACAACATCATTTGGGAGCTTCT 59.491 43.478 0.00 0.00 30.79 2.85
2335 6300 1.404583 GGCACAACATCATTTGGGAGC 60.405 52.381 0.00 0.00 30.79 4.70
2338 6303 1.205417 GGAGGCACAACATCATTTGGG 59.795 52.381 0.00 0.00 32.58 4.12
2341 6306 0.527565 GCGGAGGCACAACATCATTT 59.472 50.000 0.00 0.00 39.62 2.32
2342 6307 0.322816 AGCGGAGGCACAACATCATT 60.323 50.000 0.00 0.00 43.41 2.57
2378 6343 5.229887 GCCATACGCAAACAATTTACATCTG 59.770 40.000 0.00 0.00 37.47 2.90
2384 6349 4.428209 CATGGCCATACGCAAACAATTTA 58.572 39.130 20.30 0.00 40.31 1.40
2385 6350 3.260740 CATGGCCATACGCAAACAATTT 58.739 40.909 20.30 0.00 40.31 1.82
2393 6358 2.203001 CGTCCATGGCCATACGCA 60.203 61.111 24.02 4.75 40.31 5.24
2400 6365 3.282374 AAACCCTCCGTCCATGGCC 62.282 63.158 6.96 0.00 0.00 5.36
2401 6366 1.749258 GAAACCCTCCGTCCATGGC 60.749 63.158 6.96 0.96 0.00 4.40
2407 6372 1.475682 AGTATGTCGAAACCCTCCGTC 59.524 52.381 0.00 0.00 0.00 4.79
2414 6379 5.061920 AGAAGTCTGAGTATGTCGAAACC 57.938 43.478 0.00 0.00 0.00 3.27
2417 6382 5.959618 TTGAGAAGTCTGAGTATGTCGAA 57.040 39.130 0.00 0.00 0.00 3.71
2422 6387 5.117745 CGTGTGTTTGAGAAGTCTGAGTATG 59.882 44.000 0.00 0.00 0.00 2.39
2423 6388 5.223382 CGTGTGTTTGAGAAGTCTGAGTAT 58.777 41.667 0.00 0.00 0.00 2.12
2424 6389 4.499188 CCGTGTGTTTGAGAAGTCTGAGTA 60.499 45.833 0.00 0.00 0.00 2.59
2425 6390 3.448686 CGTGTGTTTGAGAAGTCTGAGT 58.551 45.455 0.00 0.00 0.00 3.41
2426 6391 2.797156 CCGTGTGTTTGAGAAGTCTGAG 59.203 50.000 0.00 0.00 0.00 3.35
2427 6392 2.429250 TCCGTGTGTTTGAGAAGTCTGA 59.571 45.455 0.00 0.00 0.00 3.27
2428 6393 2.797156 CTCCGTGTGTTTGAGAAGTCTG 59.203 50.000 0.00 0.00 0.00 3.51
2429 6394 2.224066 CCTCCGTGTGTTTGAGAAGTCT 60.224 50.000 0.00 0.00 0.00 3.24
2430 6395 2.135933 CCTCCGTGTGTTTGAGAAGTC 58.864 52.381 0.00 0.00 0.00 3.01
2431 6396 1.810412 GCCTCCGTGTGTTTGAGAAGT 60.810 52.381 0.00 0.00 0.00 3.01
2432 6397 0.868406 GCCTCCGTGTGTTTGAGAAG 59.132 55.000 0.00 0.00 0.00 2.85
2440 6409 0.110486 ATTTTGAGGCCTCCGTGTGT 59.890 50.000 29.95 8.39 0.00 3.72
2443 6412 1.533625 TTGATTTTGAGGCCTCCGTG 58.466 50.000 29.95 0.00 0.00 4.94
2445 6414 1.474077 CCTTTGATTTTGAGGCCTCCG 59.526 52.381 29.95 6.70 0.00 4.63
2476 6446 4.002797 GCCTTCGCCCAGTCAATT 57.997 55.556 0.00 0.00 0.00 2.32
2486 6456 2.485122 CCAATTCGTGGCCTTCGC 59.515 61.111 3.32 0.00 41.72 4.70
2496 6466 0.178068 ATCCACCGGTCTCCAATTCG 59.822 55.000 2.59 0.00 0.00 3.34
2497 6467 1.486726 AGATCCACCGGTCTCCAATTC 59.513 52.381 2.59 0.00 0.00 2.17
2501 6471 0.924090 TAGAGATCCACCGGTCTCCA 59.076 55.000 15.43 1.69 41.36 3.86
2520 6899 4.414846 ACTTCCCTCTTCATTATGGAGCAT 59.585 41.667 0.00 0.00 0.00 3.79
2584 6964 4.097418 AGCACATGAAAGTACTAGGACCT 58.903 43.478 0.00 0.00 0.00 3.85
2589 6969 6.868622 ACTTCCTAGCACATGAAAGTACTAG 58.131 40.000 0.00 1.10 35.94 2.57
2700 7082 9.618890 ACAGTAGCAATGATATAACAACTCATT 57.381 29.630 0.00 0.00 39.55 2.57
2758 7140 9.555727 GCCACTACTATACCTTATTTCATTTCA 57.444 33.333 0.00 0.00 0.00 2.69
2759 7141 8.709646 CGCCACTACTATACCTTATTTCATTTC 58.290 37.037 0.00 0.00 0.00 2.17
2760 7142 7.172703 GCGCCACTACTATACCTTATTTCATTT 59.827 37.037 0.00 0.00 0.00 2.32
2761 7143 6.649557 GCGCCACTACTATACCTTATTTCATT 59.350 38.462 0.00 0.00 0.00 2.57
2762 7144 6.164176 GCGCCACTACTATACCTTATTTCAT 58.836 40.000 0.00 0.00 0.00 2.57
2763 7145 5.535333 GCGCCACTACTATACCTTATTTCA 58.465 41.667 0.00 0.00 0.00 2.69
2764 7146 4.620184 CGCGCCACTACTATACCTTATTTC 59.380 45.833 0.00 0.00 0.00 2.17
2765 7147 4.553323 CGCGCCACTACTATACCTTATTT 58.447 43.478 0.00 0.00 0.00 1.40
2766 7148 3.057033 CCGCGCCACTACTATACCTTATT 60.057 47.826 0.00 0.00 0.00 1.40
2767 7149 2.490903 CCGCGCCACTACTATACCTTAT 59.509 50.000 0.00 0.00 0.00 1.73
2768 7150 1.881973 CCGCGCCACTACTATACCTTA 59.118 52.381 0.00 0.00 0.00 2.69
2769 7151 0.672342 CCGCGCCACTACTATACCTT 59.328 55.000 0.00 0.00 0.00 3.50
2770 7152 1.177256 CCCGCGCCACTACTATACCT 61.177 60.000 0.00 0.00 0.00 3.08
2771 7153 1.288127 CCCGCGCCACTACTATACC 59.712 63.158 0.00 0.00 0.00 2.73
2772 7154 1.288127 CCCCGCGCCACTACTATAC 59.712 63.158 0.00 0.00 0.00 1.47
2773 7155 0.110295 TACCCCGCGCCACTACTATA 59.890 55.000 0.00 0.00 0.00 1.31
2774 7156 0.756442 TTACCCCGCGCCACTACTAT 60.756 55.000 0.00 0.00 0.00 2.12
2775 7157 0.756442 ATTACCCCGCGCCACTACTA 60.756 55.000 0.00 0.00 0.00 1.82
2776 7158 0.756442 TATTACCCCGCGCCACTACT 60.756 55.000 0.00 0.00 0.00 2.57
2777 7159 0.598419 GTATTACCCCGCGCCACTAC 60.598 60.000 0.00 0.00 0.00 2.73
2778 7160 1.741525 GTATTACCCCGCGCCACTA 59.258 57.895 0.00 0.00 0.00 2.74
2779 7161 2.502577 GTATTACCCCGCGCCACT 59.497 61.111 0.00 0.00 0.00 4.00
2780 7162 2.589724 GGTATTACCCCGCGCCAC 60.590 66.667 0.00 0.00 30.04 5.01
2809 7191 3.746492 GGACCCACGCTATTGCTAAATAG 59.254 47.826 0.00 1.85 45.56 1.73
2810 7192 3.389983 AGGACCCACGCTATTGCTAAATA 59.610 43.478 0.00 0.00 36.97 1.40
2811 7193 2.172717 AGGACCCACGCTATTGCTAAAT 59.827 45.455 0.00 0.00 36.97 1.40
2812 7194 1.557832 AGGACCCACGCTATTGCTAAA 59.442 47.619 0.00 0.00 36.97 1.85
2813 7195 1.200519 AGGACCCACGCTATTGCTAA 58.799 50.000 0.00 0.00 36.97 3.09
2814 7196 1.684983 GTAGGACCCACGCTATTGCTA 59.315 52.381 0.00 0.00 36.97 3.49
2815 7197 0.464452 GTAGGACCCACGCTATTGCT 59.536 55.000 0.00 0.00 36.97 3.91
2816 7198 0.532196 GGTAGGACCCACGCTATTGC 60.532 60.000 0.00 0.00 30.04 3.56
2817 7199 3.680842 GGTAGGACCCACGCTATTG 57.319 57.895 0.00 0.00 30.04 1.90
2827 7209 1.277273 GTAGTTGTGTGGGGTAGGACC 59.723 57.143 0.00 0.00 37.60 4.46
2828 7210 2.028385 CAGTAGTTGTGTGGGGTAGGAC 60.028 54.545 0.00 0.00 0.00 3.85
2829 7211 2.158279 TCAGTAGTTGTGTGGGGTAGGA 60.158 50.000 0.00 0.00 0.00 2.94
2830 7212 2.233922 CTCAGTAGTTGTGTGGGGTAGG 59.766 54.545 0.00 0.00 0.00 3.18
2831 7213 3.162666 TCTCAGTAGTTGTGTGGGGTAG 58.837 50.000 0.00 0.00 0.00 3.18
2832 7214 3.247948 TCTCAGTAGTTGTGTGGGGTA 57.752 47.619 0.00 0.00 0.00 3.69
2833 7215 2.097110 TCTCAGTAGTTGTGTGGGGT 57.903 50.000 0.00 0.00 0.00 4.95
2834 7216 3.485463 TTTCTCAGTAGTTGTGTGGGG 57.515 47.619 0.00 0.00 0.00 4.96
2835 7217 6.710744 ACTAAATTTCTCAGTAGTTGTGTGGG 59.289 38.462 0.00 0.00 0.00 4.61
2836 7218 7.730364 ACTAAATTTCTCAGTAGTTGTGTGG 57.270 36.000 0.00 0.00 0.00 4.17
2837 7219 8.436200 GCTACTAAATTTCTCAGTAGTTGTGTG 58.564 37.037 20.23 3.46 42.40 3.82
2838 7220 8.148351 TGCTACTAAATTTCTCAGTAGTTGTGT 58.852 33.333 20.23 0.00 42.40 3.72
2839 7221 8.534333 TGCTACTAAATTTCTCAGTAGTTGTG 57.466 34.615 20.23 4.48 42.40 3.33
2840 7222 8.368668 ACTGCTACTAAATTTCTCAGTAGTTGT 58.631 33.333 20.23 16.91 42.40 3.32
2841 7223 8.764524 ACTGCTACTAAATTTCTCAGTAGTTG 57.235 34.615 20.23 16.50 42.40 3.16
2842 7224 9.857957 GTACTGCTACTAAATTTCTCAGTAGTT 57.142 33.333 20.23 11.97 42.40 2.24
2843 7225 8.468399 GGTACTGCTACTAAATTTCTCAGTAGT 58.532 37.037 20.23 17.89 42.40 2.73
2844 7226 7.921745 GGGTACTGCTACTAAATTTCTCAGTAG 59.078 40.741 17.08 17.08 42.99 2.57
2845 7227 7.618512 AGGGTACTGCTACTAAATTTCTCAGTA 59.381 37.037 0.00 4.27 35.31 2.74
2846 7228 6.440965 AGGGTACTGCTACTAAATTTCTCAGT 59.559 38.462 0.00 5.17 37.17 3.41
2847 7229 6.879400 AGGGTACTGCTACTAAATTTCTCAG 58.121 40.000 0.00 0.00 0.00 3.35
2848 7230 6.668283 AGAGGGTACTGCTACTAAATTTCTCA 59.332 38.462 0.00 0.00 0.00 3.27
2849 7231 7.114866 AGAGGGTACTGCTACTAAATTTCTC 57.885 40.000 0.00 0.00 0.00 2.87
2850 7232 7.331791 CAAGAGGGTACTGCTACTAAATTTCT 58.668 38.462 0.00 0.00 0.00 2.52
2851 7233 6.037281 GCAAGAGGGTACTGCTACTAAATTTC 59.963 42.308 0.00 0.00 0.00 2.17
2852 7234 5.880887 GCAAGAGGGTACTGCTACTAAATTT 59.119 40.000 0.00 0.00 0.00 1.82
2853 7235 5.189934 AGCAAGAGGGTACTGCTACTAAATT 59.810 40.000 4.85 0.00 33.70 1.82
2854 7236 4.717280 AGCAAGAGGGTACTGCTACTAAAT 59.283 41.667 4.85 0.00 33.70 1.40
2855 7237 4.094476 AGCAAGAGGGTACTGCTACTAAA 58.906 43.478 4.85 0.00 33.70 1.85
2856 7238 3.709587 AGCAAGAGGGTACTGCTACTAA 58.290 45.455 4.85 0.00 33.70 2.24
2857 7239 3.383698 AGCAAGAGGGTACTGCTACTA 57.616 47.619 4.85 0.00 33.70 1.82
2858 7240 2.239681 AGCAAGAGGGTACTGCTACT 57.760 50.000 4.85 0.00 33.70 2.57
2859 7241 3.439895 GTAGCAAGAGGGTACTGCTAC 57.560 52.381 21.38 21.38 46.88 3.58
2866 7248 7.787623 AACTTTTAGTAGTAGCAAGAGGGTA 57.212 36.000 5.87 0.00 0.00 3.69
2867 7249 6.683312 AACTTTTAGTAGTAGCAAGAGGGT 57.317 37.500 5.87 0.00 0.00 4.34
2868 7250 6.757478 GCTAACTTTTAGTAGTAGCAAGAGGG 59.243 42.308 5.92 0.00 31.21 4.30
2869 7251 7.489757 CAGCTAACTTTTAGTAGTAGCAAGAGG 59.510 40.741 11.17 0.00 32.25 3.69
2870 7252 7.009723 GCAGCTAACTTTTAGTAGTAGCAAGAG 59.990 40.741 11.17 2.81 32.25 2.85
2871 7253 6.812160 GCAGCTAACTTTTAGTAGTAGCAAGA 59.188 38.462 11.17 0.00 32.25 3.02
2872 7254 6.590292 TGCAGCTAACTTTTAGTAGTAGCAAG 59.410 38.462 11.17 6.20 32.25 4.01
2873 7255 6.460781 TGCAGCTAACTTTTAGTAGTAGCAA 58.539 36.000 11.17 0.00 32.25 3.91
2874 7256 6.032956 TGCAGCTAACTTTTAGTAGTAGCA 57.967 37.500 11.17 0.00 32.25 3.49
2875 7257 5.005875 GCTGCAGCTAACTTTTAGTAGTAGC 59.994 44.000 31.33 0.00 38.21 3.58
2876 7258 5.230306 CGCTGCAGCTAACTTTTAGTAGTAG 59.770 44.000 34.22 10.29 39.32 2.57
2877 7259 5.100259 CGCTGCAGCTAACTTTTAGTAGTA 58.900 41.667 34.22 0.00 39.32 1.82
2878 7260 3.927142 CGCTGCAGCTAACTTTTAGTAGT 59.073 43.478 34.22 0.00 39.32 2.73
2879 7261 3.242123 GCGCTGCAGCTAACTTTTAGTAG 60.242 47.826 34.22 16.00 39.32 2.57
2880 7262 2.671396 GCGCTGCAGCTAACTTTTAGTA 59.329 45.455 34.22 0.00 39.32 1.82
2881 7263 1.464997 GCGCTGCAGCTAACTTTTAGT 59.535 47.619 34.22 0.00 39.32 2.24
2882 7264 2.165282 GCGCTGCAGCTAACTTTTAG 57.835 50.000 34.22 17.42 39.32 1.85
2892 7274 3.263422 CTGCTAGAGCGCTGCAGC 61.263 66.667 28.36 29.12 45.76 5.25
2894 7276 1.435105 CTACTGCTAGAGCGCTGCA 59.565 57.895 18.48 18.51 45.83 4.41
2895 7277 1.948635 GCTACTGCTAGAGCGCTGC 60.949 63.158 18.48 13.95 45.83 5.25
2896 7278 0.869454 GTGCTACTGCTAGAGCGCTG 60.869 60.000 18.48 0.22 44.12 5.18
2897 7279 1.435515 GTGCTACTGCTAGAGCGCT 59.564 57.895 11.27 11.27 44.12 5.92
2898 7280 1.941734 CGTGCTACTGCTAGAGCGC 60.942 63.158 0.00 0.00 45.83 5.92
2899 7281 0.309302 ATCGTGCTACTGCTAGAGCG 59.691 55.000 0.00 0.00 45.83 5.03
2900 7282 1.335506 GGATCGTGCTACTGCTAGAGC 60.336 57.143 0.00 0.00 40.48 4.09
2901 7283 1.268352 GGGATCGTGCTACTGCTAGAG 59.732 57.143 0.00 0.00 40.48 2.43
2902 7284 1.133761 AGGGATCGTGCTACTGCTAGA 60.134 52.381 0.00 0.00 40.48 2.43
2903 7285 1.000827 CAGGGATCGTGCTACTGCTAG 60.001 57.143 0.00 0.00 40.48 3.42
2904 7286 1.032794 CAGGGATCGTGCTACTGCTA 58.967 55.000 0.00 0.00 40.48 3.49
2905 7287 0.684479 TCAGGGATCGTGCTACTGCT 60.684 55.000 0.00 0.00 40.48 4.24
2906 7288 0.175760 TTCAGGGATCGTGCTACTGC 59.824 55.000 0.00 0.00 40.20 4.40
2907 7289 1.471676 GGTTCAGGGATCGTGCTACTG 60.472 57.143 0.00 0.00 0.00 2.74
2908 7290 0.824759 GGTTCAGGGATCGTGCTACT 59.175 55.000 0.00 0.00 0.00 2.57
2909 7291 0.527817 CGGTTCAGGGATCGTGCTAC 60.528 60.000 0.00 0.00 0.00 3.58
2910 7292 0.968901 ACGGTTCAGGGATCGTGCTA 60.969 55.000 0.00 0.00 34.40 3.49
2911 7293 1.827399 AACGGTTCAGGGATCGTGCT 61.827 55.000 0.00 0.00 35.93 4.40
2912 7294 0.953960 AAACGGTTCAGGGATCGTGC 60.954 55.000 0.00 0.00 35.93 5.34
2913 7295 1.519408 AAAACGGTTCAGGGATCGTG 58.481 50.000 0.00 0.00 35.93 4.35
2914 7296 2.265589 AAAAACGGTTCAGGGATCGT 57.734 45.000 0.00 0.00 37.45 3.73
3025 7407 9.145865 ACTTCAAAGATTTTCGCAAACTAAAAA 57.854 25.926 0.00 0.00 0.00 1.94
3026 7408 8.696410 ACTTCAAAGATTTTCGCAAACTAAAA 57.304 26.923 0.00 0.00 0.00 1.52
3027 7409 8.696410 AACTTCAAAGATTTTCGCAAACTAAA 57.304 26.923 0.00 0.00 0.00 1.85
3028 7410 7.434013 GGAACTTCAAAGATTTTCGCAAACTAA 59.566 33.333 0.00 0.00 0.00 2.24
3029 7411 6.915843 GGAACTTCAAAGATTTTCGCAAACTA 59.084 34.615 0.00 0.00 0.00 2.24
3030 7412 5.748630 GGAACTTCAAAGATTTTCGCAAACT 59.251 36.000 0.00 0.00 0.00 2.66
3031 7413 5.051039 GGGAACTTCAAAGATTTTCGCAAAC 60.051 40.000 0.00 0.00 0.00 2.93
3032 7414 5.047188 GGGAACTTCAAAGATTTTCGCAAA 58.953 37.500 0.00 0.00 0.00 3.68
3033 7415 4.500716 GGGGAACTTCAAAGATTTTCGCAA 60.501 41.667 0.00 0.00 32.36 4.85
3034 7416 3.005367 GGGGAACTTCAAAGATTTTCGCA 59.995 43.478 0.00 0.00 32.36 5.10
3035 7417 3.255888 AGGGGAACTTCAAAGATTTTCGC 59.744 43.478 0.00 0.00 0.00 4.70
3036 7418 5.453567 AAGGGGAACTTCAAAGATTTTCG 57.546 39.130 0.00 0.00 32.85 3.46


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

AutoCloner maintained by Alex Coulton.