Multiple sequence alignment - TraesCS6A01G310100

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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 TraesCS6A01G310100 chr6A 100.000 4306 0 0 1 4306 546480972 546476667 0.000000e+00 7952.0
1 TraesCS6A01G310100 chr6D 94.997 1879 73 8 1557 3423 400540089 400538220 0.000000e+00 2929.0
2 TraesCS6A01G310100 chr6D 96.190 945 31 4 390 1331 400541338 400540396 0.000000e+00 1541.0
3 TraesCS6A01G310100 chr6D 90.465 409 30 6 3797 4201 400471042 400470639 8.200000e-147 531.0
4 TraesCS6A01G310100 chr6D 89.423 416 24 6 1 397 400542552 400542138 1.380000e-139 507.0
5 TraesCS6A01G310100 chr6D 87.402 254 20 8 3419 3670 400537887 400537644 9.120000e-72 281.0
6 TraesCS6A01G310100 chr6D 91.018 167 5 1 1334 1490 126435126 126435292 2.610000e-52 217.0
7 TraesCS6A01G310100 chr6D 97.143 105 3 0 4201 4305 400462895 400462791 1.230000e-40 178.0
8 TraesCS6A01G310100 chr6D 95.652 69 3 0 3712 3780 400537337 400537269 1.270000e-20 111.0
9 TraesCS6A01G310100 chr6B 92.950 1078 55 11 2374 3445 599401227 599400165 0.000000e+00 1550.0
10 TraesCS6A01G310100 chr6B 94.913 806 30 5 1585 2388 599408511 599407715 0.000000e+00 1251.0
11 TraesCS6A01G310100 chr6B 89.960 757 49 8 6 737 599410225 599409471 0.000000e+00 952.0
12 TraesCS6A01G310100 chr6B 94.992 599 18 7 736 1325 599409347 599408752 0.000000e+00 929.0
13 TraesCS6A01G310100 chr6B 94.568 405 20 2 3797 4201 599399779 599399377 3.660000e-175 625.0
14 TraesCS6A01G310100 chr6B 91.813 171 12 2 1162 1331 644936828 644936997 2.000000e-58 237.0
15 TraesCS6A01G310100 chr6B 90.419 167 6 2 1334 1490 224871659 224871825 1.210000e-50 211.0
16 TraesCS6A01G310100 chr6B 94.286 105 6 0 4201 4305 599398761 599398657 1.240000e-35 161.0
17 TraesCS6A01G310100 chr6B 98.507 67 1 0 3712 3778 599399917 599399851 7.560000e-23 119.0
18 TraesCS6A01G310100 chr5D 89.803 304 30 1 3898 4201 378475348 378475046 5.220000e-104 388.0
19 TraesCS6A01G310100 chr2B 90.116 172 6 3 1334 1495 18927252 18927082 3.370000e-51 213.0
20 TraesCS6A01G310100 chr3A 89.222 167 8 1 1334 1490 573979298 573979464 2.630000e-47 200.0
21 TraesCS6A01G310100 chr3D 88.024 167 10 4 1334 1490 479627565 479627399 5.680000e-44 189.0
22 TraesCS6A01G310100 chr5B 87.135 171 10 6 1332 1490 432709905 432709735 2.640000e-42 183.0
23 TraesCS6A01G310100 chr5B 87.234 141 11 4 1337 1476 55182837 55182971 2.070000e-33 154.0
24 TraesCS6A01G310100 chr1A 90.141 142 11 3 1334 1472 181768797 181768938 9.510000e-42 182.0
25 TraesCS6A01G310100 chr2A 91.339 127 8 2 1353 1479 205493209 205493332 2.060000e-38 171.0
26 TraesCS6A01G310100 chr7B 87.591 137 11 2 1334 1470 541688141 541688271 2.070000e-33 154.0
27 TraesCS6A01G310100 chr4B 84.672 137 12 6 1360 1496 27932242 27932369 1.260000e-25 128.0
28 TraesCS6A01G310100 chr4B 80.597 134 24 2 4012 4144 8416306 8416174 7.620000e-18 102.0
29 TraesCS6A01G310100 chr4B 76.243 181 39 4 3966 4144 7744717 7744895 4.580000e-15 93.5
30 TraesCS6A01G310100 chr4B 75.936 187 37 8 3965 4144 8366596 8366781 5.930000e-14 89.8
31 TraesCS6A01G310100 chr4A 78.333 180 37 2 3966 4144 598607914 598608092 9.780000e-22 115.0
32 TraesCS6A01G310100 chr3B 80.537 149 8 7 1334 1472 629288886 629288749 1.270000e-15 95.3


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 TraesCS6A01G310100 chr6A 546476667 546480972 4305 True 7952.00 7952 100.000000 1 4306 1 chr6A.!!$R1 4305
1 TraesCS6A01G310100 chr6D 400537269 400542552 5283 True 1073.80 2929 92.732800 1 3780 5 chr6D.!!$R3 3779
2 TraesCS6A01G310100 chr6B 599407715 599410225 2510 True 1044.00 1251 93.288333 6 2388 3 chr6B.!!$R2 2382
3 TraesCS6A01G310100 chr6B 599398657 599401227 2570 True 613.75 1550 95.077750 2374 4305 4 chr6B.!!$R1 1931

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
454 1285 1.102978 GACTGGGAGAGAGAGTGAGC 58.897 60.000 0.00 0.0 0.00 4.26 F
1461 2425 0.037046 TTTTTCCGAGTCGCTACCCC 60.037 55.000 7.12 0.0 0.00 4.95 F
1473 2437 0.824759 GCTACCCCAGAACGACTCAT 59.175 55.000 0.00 0.0 0.00 2.90 F
1524 2488 0.914417 ATGTGTGAGTAGGGGGTGGG 60.914 60.000 0.00 0.0 0.00 4.61 F
2490 3540 1.132881 TCTGGGCCTTCCACCAAAAAT 60.133 47.619 4.53 0.0 41.46 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 3406 0.036164 ATCAGCTTGCCACACGGTTA 59.964 50.000 0.00 0.0 33.28 2.85 R
2360 3407 1.228245 ATCAGCTTGCCACACGGTT 60.228 52.632 0.00 0.0 33.28 4.44 R
2361 3408 1.968017 CATCAGCTTGCCACACGGT 60.968 57.895 0.00 0.0 33.28 4.83 R
2539 3589 2.035066 AGCATCCTCACTTGTTTTGTGC 59.965 45.455 0.00 0.0 35.58 4.57 R
3899 5640 0.447801 ATGCATTCGCGTTCTTGGTC 59.552 50.000 5.77 0.0 42.97 4.02 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
53 55 1.907222 GATCCCCTCCCCGTTTTCGT 61.907 60.000 0.00 0.00 42.35 3.85
81 83 2.587194 CGCAATCTGGAGCCCGAG 60.587 66.667 0.00 0.00 0.00 4.63
112 114 2.456119 GGACGCCAAGTGCTGATCG 61.456 63.158 0.00 0.00 38.25 3.69
125 127 2.102084 TGCTGATCGAGAATCCTCCTTG 59.898 50.000 0.00 0.00 36.04 3.61
128 130 1.691434 GATCGAGAATCCTCCTTGCCT 59.309 52.381 0.00 0.00 36.04 4.75
291 293 1.692042 ATGAGGCAGAGGAGGTGGG 60.692 63.158 0.00 0.00 0.00 4.61
433 1264 2.033602 TGCTGCTGCTGCTGTGAT 59.966 55.556 27.67 0.00 39.81 3.06
449 1280 4.136796 CTGTGATAGACTGGGAGAGAGAG 58.863 52.174 0.00 0.00 0.00 3.20
454 1285 1.102978 GACTGGGAGAGAGAGTGAGC 58.897 60.000 0.00 0.00 0.00 4.26
478 1309 2.492012 GCTTCGGCTGAGATGAATGAT 58.508 47.619 0.00 0.00 38.08 2.45
574 1407 2.883888 GCTCTCCCAAACATGGCCTAAA 60.884 50.000 3.32 0.00 0.00 1.85
833 1791 6.575942 GCATGCTGCAAAGATTTAACAAAAAG 59.424 34.615 11.37 0.00 44.26 2.27
850 1808 8.757164 AACAAAAAGAGTAAAACTTCTGTTGG 57.243 30.769 0.00 0.00 34.79 3.77
854 1812 5.986004 AGAGTAAAACTTCTGTTGGAACG 57.014 39.130 0.00 0.00 36.39 3.95
904 1862 4.276183 TGCAACTAAAGCGTAATCAAACCA 59.724 37.500 0.00 0.00 33.85 3.67
971 1929 8.864087 AGTCATGCACTCAGTAATTCTCATATA 58.136 33.333 0.00 0.00 0.00 0.86
1262 2220 4.260985 TGAGGCCATGTGTATGTGTTTAG 58.739 43.478 5.01 0.00 32.21 1.85
1343 2307 5.088068 CACATGTGTGTATCATGGTTTTCG 58.912 41.667 18.03 0.00 44.57 3.46
1344 2308 5.000591 ACATGTGTGTATCATGGTTTTCGA 58.999 37.500 0.00 0.00 44.57 3.71
1345 2309 5.122239 ACATGTGTGTATCATGGTTTTCGAG 59.878 40.000 0.00 0.00 44.57 4.04
1346 2310 4.637276 TGTGTGTATCATGGTTTTCGAGT 58.363 39.130 0.00 0.00 0.00 4.18
1347 2311 4.688879 TGTGTGTATCATGGTTTTCGAGTC 59.311 41.667 0.00 0.00 0.00 3.36
1348 2312 3.924073 TGTGTATCATGGTTTTCGAGTCG 59.076 43.478 6.09 6.09 0.00 4.18
1349 2313 2.927477 TGTATCATGGTTTTCGAGTCGC 59.073 45.455 7.92 0.00 0.00 5.19
1350 2314 0.999406 ATCATGGTTTTCGAGTCGCG 59.001 50.000 7.92 0.00 42.69 5.87
1351 2315 0.319211 TCATGGTTTTCGAGTCGCGT 60.319 50.000 7.92 0.00 41.80 6.01
1352 2316 0.179250 CATGGTTTTCGAGTCGCGTG 60.179 55.000 7.92 1.19 41.80 5.34
1353 2317 0.319211 ATGGTTTTCGAGTCGCGTGA 60.319 50.000 7.92 0.00 41.80 4.35
1354 2318 1.210545 TGGTTTTCGAGTCGCGTGAC 61.211 55.000 21.32 21.32 45.86 3.67
1362 2326 4.339565 GTCGCGTGACTAGTCGTC 57.660 61.111 21.55 12.14 42.08 4.20
1363 2327 1.577117 GTCGCGTGACTAGTCGTCG 60.577 63.158 25.46 25.46 45.87 5.12
1364 2328 1.734117 TCGCGTGACTAGTCGTCGA 60.734 57.895 30.45 26.21 45.87 4.20
1365 2329 1.577117 CGCGTGACTAGTCGTCGAC 60.577 63.158 30.45 17.70 45.87 4.20
1366 2330 1.786582 GCGTGACTAGTCGTCGACT 59.213 57.895 30.45 29.25 45.87 4.18
1367 2331 0.994995 GCGTGACTAGTCGTCGACTA 59.005 55.000 30.45 28.43 45.87 2.59
1405 2369 4.749245 AAAATGGCGACTCAACTTAGTG 57.251 40.909 0.00 0.00 0.00 2.74
1406 2370 3.402628 AATGGCGACTCAACTTAGTGT 57.597 42.857 0.00 0.00 0.00 3.55
1407 2371 2.433868 TGGCGACTCAACTTAGTGTC 57.566 50.000 0.00 0.00 0.00 3.67
1413 2377 4.485024 GACTCAACTTAGTGTCGACTCA 57.515 45.455 17.92 1.57 33.21 3.41
1414 2378 5.049398 GACTCAACTTAGTGTCGACTCAT 57.951 43.478 17.92 5.07 33.21 2.90
1415 2379 4.799678 ACTCAACTTAGTGTCGACTCATG 58.200 43.478 17.92 9.57 33.21 3.07
1416 2380 4.519350 ACTCAACTTAGTGTCGACTCATGA 59.481 41.667 17.92 11.95 33.21 3.07
1417 2381 4.795268 TCAACTTAGTGTCGACTCATGAC 58.205 43.478 17.92 5.97 36.88 3.06
1418 2382 4.519350 TCAACTTAGTGTCGACTCATGACT 59.481 41.667 17.92 13.44 37.26 3.41
1419 2383 4.688511 ACTTAGTGTCGACTCATGACTC 57.311 45.455 17.92 0.00 37.26 3.36
1420 2384 3.125487 ACTTAGTGTCGACTCATGACTCG 59.875 47.826 17.92 15.98 37.26 4.18
1421 2385 1.809684 AGTGTCGACTCATGACTCGA 58.190 50.000 19.46 19.46 37.26 4.04
1422 2386 1.735018 AGTGTCGACTCATGACTCGAG 59.265 52.381 22.57 11.84 39.51 4.04
1423 2387 1.465387 GTGTCGACTCATGACTCGAGT 59.535 52.381 22.57 20.18 46.32 4.18
1432 2396 2.574736 GACTCGAGTCGCGACTGC 60.575 66.667 43.61 30.66 45.59 4.40
1433 2397 3.310253 GACTCGAGTCGCGACTGCA 62.310 63.158 43.61 27.73 45.59 4.41
1434 2398 2.575525 CTCGAGTCGCGACTGCAG 60.576 66.667 43.61 31.86 45.59 4.41
1435 2399 4.103103 TCGAGTCGCGACTGCAGG 62.103 66.667 43.61 27.82 45.59 4.85
1437 2401 4.427661 GAGTCGCGACTGCAGGCT 62.428 66.667 43.61 20.63 42.66 4.58
1438 2402 3.923563 GAGTCGCGACTGCAGGCTT 62.924 63.158 43.61 19.81 42.66 4.35
1439 2403 3.782244 GTCGCGACTGCAGGCTTG 61.782 66.667 31.12 9.96 42.97 4.01
1440 2404 3.989787 TCGCGACTGCAGGCTTGA 61.990 61.111 19.55 12.44 42.97 3.02
1441 2405 3.782244 CGCGACTGCAGGCTTGAC 61.782 66.667 19.55 3.21 42.97 3.18
1442 2406 2.358003 GCGACTGCAGGCTTGACT 60.358 61.111 19.55 0.00 42.15 3.41
1443 2407 1.963338 GCGACTGCAGGCTTGACTT 60.963 57.895 19.55 0.00 42.15 3.01
1444 2408 1.510480 GCGACTGCAGGCTTGACTTT 61.510 55.000 19.55 0.00 42.15 2.66
1445 2409 0.947244 CGACTGCAGGCTTGACTTTT 59.053 50.000 19.55 0.00 0.00 2.27
1446 2410 1.334869 CGACTGCAGGCTTGACTTTTT 59.665 47.619 19.55 0.00 0.00 1.94
1447 2411 2.603173 CGACTGCAGGCTTGACTTTTTC 60.603 50.000 19.55 0.00 0.00 2.29
1448 2412 1.683385 ACTGCAGGCTTGACTTTTTCC 59.317 47.619 19.93 0.00 0.00 3.13
1449 2413 0.667993 TGCAGGCTTGACTTTTTCCG 59.332 50.000 0.00 0.00 0.00 4.30
1450 2414 0.951558 GCAGGCTTGACTTTTTCCGA 59.048 50.000 0.00 0.00 0.00 4.55
1451 2415 1.068954 GCAGGCTTGACTTTTTCCGAG 60.069 52.381 0.00 0.00 0.00 4.63
1452 2416 2.222027 CAGGCTTGACTTTTTCCGAGT 58.778 47.619 0.00 0.00 0.00 4.18
1453 2417 2.224314 CAGGCTTGACTTTTTCCGAGTC 59.776 50.000 0.00 0.00 42.98 3.36
1454 2418 1.194772 GGCTTGACTTTTTCCGAGTCG 59.805 52.381 5.29 5.29 45.05 4.18
1455 2419 1.398578 GCTTGACTTTTTCCGAGTCGC 60.399 52.381 7.12 0.00 45.05 5.19
1456 2420 2.135933 CTTGACTTTTTCCGAGTCGCT 58.864 47.619 7.12 0.00 45.05 4.93
1457 2421 3.314553 CTTGACTTTTTCCGAGTCGCTA 58.685 45.455 7.12 0.00 45.05 4.26
1458 2422 2.669364 TGACTTTTTCCGAGTCGCTAC 58.331 47.619 7.12 0.00 45.05 3.58
1459 2423 1.991264 GACTTTTTCCGAGTCGCTACC 59.009 52.381 7.12 0.00 34.76 3.18
1460 2424 1.337541 ACTTTTTCCGAGTCGCTACCC 60.338 52.381 7.12 0.00 0.00 3.69
1461 2425 0.037046 TTTTTCCGAGTCGCTACCCC 60.037 55.000 7.12 0.00 0.00 4.95
1462 2426 1.186917 TTTTCCGAGTCGCTACCCCA 61.187 55.000 7.12 0.00 0.00 4.96
1463 2427 1.601419 TTTCCGAGTCGCTACCCCAG 61.601 60.000 7.12 0.00 0.00 4.45
1464 2428 2.439701 CCGAGTCGCTACCCCAGA 60.440 66.667 7.12 0.00 0.00 3.86
1465 2429 2.050350 CCGAGTCGCTACCCCAGAA 61.050 63.158 7.12 0.00 0.00 3.02
1466 2430 1.139095 CGAGTCGCTACCCCAGAAC 59.861 63.158 0.00 0.00 0.00 3.01
1467 2431 1.139095 GAGTCGCTACCCCAGAACG 59.861 63.158 0.00 0.00 0.00 3.95
1468 2432 1.303888 AGTCGCTACCCCAGAACGA 60.304 57.895 0.00 0.00 0.00 3.85
1469 2433 1.153881 GTCGCTACCCCAGAACGAC 60.154 63.158 0.00 0.00 45.10 4.34
1470 2434 1.303888 TCGCTACCCCAGAACGACT 60.304 57.895 0.00 0.00 0.00 4.18
1471 2435 1.139095 CGCTACCCCAGAACGACTC 59.861 63.158 0.00 0.00 0.00 3.36
1472 2436 1.592400 CGCTACCCCAGAACGACTCA 61.592 60.000 0.00 0.00 0.00 3.41
1473 2437 0.824759 GCTACCCCAGAACGACTCAT 59.175 55.000 0.00 0.00 0.00 2.90
1474 2438 1.202428 GCTACCCCAGAACGACTCATC 60.202 57.143 0.00 0.00 0.00 2.92
1489 2453 4.962693 GACTCATCGACTTGAAAACCATG 58.037 43.478 0.00 0.00 0.00 3.66
1490 2454 3.753272 ACTCATCGACTTGAAAACCATGG 59.247 43.478 11.19 11.19 0.00 3.66
1491 2455 3.750371 TCATCGACTTGAAAACCATGGT 58.250 40.909 13.00 13.00 0.00 3.55
1492 2456 3.501828 TCATCGACTTGAAAACCATGGTG 59.498 43.478 20.60 7.17 0.00 4.17
1493 2457 2.925724 TCGACTTGAAAACCATGGTGT 58.074 42.857 20.60 10.88 0.00 4.16
1494 2458 2.616376 TCGACTTGAAAACCATGGTGTG 59.384 45.455 20.60 3.00 0.00 3.82
1495 2459 2.357637 CGACTTGAAAACCATGGTGTGT 59.642 45.455 20.60 6.83 0.00 3.72
1496 2460 3.562141 CGACTTGAAAACCATGGTGTGTA 59.438 43.478 20.60 2.37 0.00 2.90
1497 2461 4.215399 CGACTTGAAAACCATGGTGTGTAT 59.785 41.667 20.60 0.00 0.00 2.29
1498 2462 5.616866 CGACTTGAAAACCATGGTGTGTATC 60.617 44.000 20.60 8.30 0.00 2.24
1499 2463 5.136828 ACTTGAAAACCATGGTGTGTATCA 58.863 37.500 20.60 11.15 0.00 2.15
1500 2464 5.774690 ACTTGAAAACCATGGTGTGTATCAT 59.225 36.000 20.60 0.00 0.00 2.45
1501 2465 5.641783 TGAAAACCATGGTGTGTATCATG 57.358 39.130 20.60 0.00 43.61 3.07
1502 2466 5.076182 TGAAAACCATGGTGTGTATCATGT 58.924 37.500 20.60 0.00 42.66 3.21
1503 2467 5.048154 TGAAAACCATGGTGTGTATCATGTG 60.048 40.000 20.60 0.00 42.66 3.21
1504 2468 3.719268 ACCATGGTGTGTATCATGTGT 57.281 42.857 18.99 0.00 42.66 3.72
1505 2469 4.835284 ACCATGGTGTGTATCATGTGTA 57.165 40.909 18.99 0.00 42.66 2.90
1506 2470 5.372343 ACCATGGTGTGTATCATGTGTAT 57.628 39.130 18.99 0.00 42.66 2.29
1507 2471 5.125356 ACCATGGTGTGTATCATGTGTATG 58.875 41.667 18.99 0.00 42.66 2.39
1508 2472 5.125356 CCATGGTGTGTATCATGTGTATGT 58.875 41.667 2.57 0.00 42.66 2.29
1509 2473 5.007921 CCATGGTGTGTATCATGTGTATGTG 59.992 44.000 2.57 0.00 42.66 3.21
1510 2474 5.159273 TGGTGTGTATCATGTGTATGTGT 57.841 39.130 0.00 0.00 35.73 3.72
1511 2475 4.934602 TGGTGTGTATCATGTGTATGTGTG 59.065 41.667 0.00 0.00 35.73 3.82
1512 2476 5.175127 GGTGTGTATCATGTGTATGTGTGA 58.825 41.667 0.00 0.00 35.73 3.58
1513 2477 5.291858 GGTGTGTATCATGTGTATGTGTGAG 59.708 44.000 0.00 0.00 35.73 3.51
1514 2478 5.869344 GTGTGTATCATGTGTATGTGTGAGT 59.131 40.000 0.00 0.00 35.73 3.41
1515 2479 7.033185 GTGTGTATCATGTGTATGTGTGAGTA 58.967 38.462 0.00 0.00 35.73 2.59
1516 2480 7.220875 GTGTGTATCATGTGTATGTGTGAGTAG 59.779 40.741 0.00 0.00 35.73 2.57
1517 2481 6.697455 GTGTATCATGTGTATGTGTGAGTAGG 59.303 42.308 0.00 0.00 35.73 3.18
1518 2482 4.736126 TCATGTGTATGTGTGAGTAGGG 57.264 45.455 0.00 0.00 35.73 3.53
1519 2483 3.450817 TCATGTGTATGTGTGAGTAGGGG 59.549 47.826 0.00 0.00 35.73 4.79
1520 2484 2.184533 TGTGTATGTGTGAGTAGGGGG 58.815 52.381 0.00 0.00 0.00 5.40
1521 2485 2.185387 GTGTATGTGTGAGTAGGGGGT 58.815 52.381 0.00 0.00 0.00 4.95
1522 2486 2.093658 GTGTATGTGTGAGTAGGGGGTG 60.094 54.545 0.00 0.00 0.00 4.61
1523 2487 1.485066 GTATGTGTGAGTAGGGGGTGG 59.515 57.143 0.00 0.00 0.00 4.61
1524 2488 0.914417 ATGTGTGAGTAGGGGGTGGG 60.914 60.000 0.00 0.00 0.00 4.61
1525 2489 2.124085 TGTGAGTAGGGGGTGGGG 59.876 66.667 0.00 0.00 0.00 4.96
1526 2490 2.691252 GTGAGTAGGGGGTGGGGG 60.691 72.222 0.00 0.00 0.00 5.40
1540 2504 4.779486 GGGGGATGGAGTGGGGGT 62.779 72.222 0.00 0.00 0.00 4.95
1541 2505 3.420482 GGGGATGGAGTGGGGGTG 61.420 72.222 0.00 0.00 0.00 4.61
1542 2506 3.420482 GGGATGGAGTGGGGGTGG 61.420 72.222 0.00 0.00 0.00 4.61
1543 2507 3.420482 GGATGGAGTGGGGGTGGG 61.420 72.222 0.00 0.00 0.00 4.61
1544 2508 3.420482 GATGGAGTGGGGGTGGGG 61.420 72.222 0.00 0.00 0.00 4.96
1677 2723 1.739466 CCTCCATTTGTGACATGGACG 59.261 52.381 3.87 0.00 44.50 4.79
1732 2778 8.703604 TTCTCATGTGACTATGCTAGTAAAAC 57.296 34.615 0.00 0.00 39.59 2.43
1894 2940 8.519799 ACATGTTAATAACTGGACCCTTAATG 57.480 34.615 4.67 0.00 0.00 1.90
1917 2963 3.270877 GTTACTGACAAGTAGGCATGGG 58.729 50.000 0.00 0.00 40.02 4.00
1934 2980 1.213182 TGGGTAGCAAAACACCAGTCA 59.787 47.619 0.00 0.00 36.48 3.41
1947 2993 5.413309 ACACCAGTCAAGGAGAAATAGAG 57.587 43.478 0.00 0.00 0.00 2.43
1968 3014 5.994668 AGAGGAAAGTGAACATGAACTCTTC 59.005 40.000 0.00 6.92 29.18 2.87
2005 3051 6.466308 TGTTTATCGTGAAGTGAACATGAG 57.534 37.500 0.00 0.00 36.85 2.90
2027 3073 2.489938 TGTGTAGGCCACCTGATTTC 57.510 50.000 5.01 0.00 43.85 2.17
2036 3082 3.703052 GGCCACCTGATTTCATTTCTCAT 59.297 43.478 0.00 0.00 0.00 2.90
2078 3124 5.061808 GTCAATGAAGTTTTCTGATGCATGC 59.938 40.000 11.82 11.82 0.00 4.06
2080 3126 3.159472 TGAAGTTTTCTGATGCATGCCT 58.841 40.909 16.68 4.84 0.00 4.75
2282 3329 1.508088 GAAGATGCCCAAACCTGCG 59.492 57.895 0.00 0.00 0.00 5.18
2490 3540 1.132881 TCTGGGCCTTCCACCAAAAAT 60.133 47.619 4.53 0.00 41.46 1.82
2539 3589 3.976793 AATGAGCAACAACAGACACAG 57.023 42.857 0.00 0.00 0.00 3.66
2560 3610 2.035066 GCACAAAACAAGTGAGGATGCT 59.965 45.455 0.00 0.00 39.30 3.79
2659 3709 0.826715 AGCCGTACTGTCAGCATCAT 59.173 50.000 0.00 0.00 0.00 2.45
2660 3710 0.933097 GCCGTACTGTCAGCATCATG 59.067 55.000 0.00 0.00 0.00 3.07
2813 3870 4.936891 AGCTTAAGTTCAACTGGCAAAAG 58.063 39.130 4.02 3.86 0.00 2.27
2866 3923 3.879295 AGATGACCAACTTGTGACACTTG 59.121 43.478 7.20 3.26 0.00 3.16
2885 3942 4.400251 ACTTGGTATGATTTGTGCATCTGG 59.600 41.667 0.00 0.00 0.00 3.86
3179 4236 2.531206 GCGTACAAGAAGAGCTCGAAT 58.469 47.619 8.37 0.00 0.00 3.34
3301 4358 2.064762 GAGTATGCAGGACGATGATGC 58.935 52.381 0.00 0.00 40.40 3.91
3362 4419 5.889289 ACTTTGCCTTTTGTTGGAGTACTTA 59.111 36.000 0.00 0.00 0.00 2.24
3388 4448 7.067981 AGTGGAGATTCTTTTGAGATAAATGGC 59.932 37.037 0.00 0.00 0.00 4.40
3409 4469 5.123186 TGGCAAAGACGTTATTTCATCGATT 59.877 36.000 0.00 0.00 0.00 3.34
3450 4847 3.079578 CAGCTGGTCAATGTGAGTGATT 58.920 45.455 5.57 0.00 0.00 2.57
3454 4851 4.330250 CTGGTCAATGTGAGTGATTTCCT 58.670 43.478 0.00 0.00 0.00 3.36
3527 4924 7.423844 AATGGGTTTCTCAATCCTTTATTCC 57.576 36.000 0.00 0.00 33.67 3.01
3535 4932 5.667626 TCTCAATCCTTTATTCCTACCTGCT 59.332 40.000 0.00 0.00 0.00 4.24
3543 4940 2.634639 TTCCTACCTGCTAGGGTTGA 57.365 50.000 7.06 1.25 42.51 3.18
3558 4955 7.094377 TGCTAGGGTTGATAACATTTCTGAAAC 60.094 37.037 4.73 0.00 0.00 2.78
3560 4957 7.219484 AGGGTTGATAACATTTCTGAAACTG 57.781 36.000 4.73 7.77 0.00 3.16
3637 5034 5.505173 TCTTTTTCTGAACAAGGCTTCAG 57.495 39.130 14.40 8.14 45.94 3.02
3646 5043 4.889409 TGAACAAGGCTTCAGATCAAAGTT 59.111 37.500 0.00 0.00 0.00 2.66
3677 5313 6.735678 TGCAAGTATGTATTACAACACCAG 57.264 37.500 0.00 0.29 32.87 4.00
3678 5314 6.234920 TGCAAGTATGTATTACAACACCAGT 58.765 36.000 0.00 0.00 32.87 4.00
3681 5317 7.762615 GCAAGTATGTATTACAACACCAGTAGA 59.237 37.037 0.00 0.00 32.87 2.59
3693 5329 5.632034 ACACCAGTAGAGAAGGAAAAAGT 57.368 39.130 0.00 0.00 0.00 2.66
3697 5333 6.017852 CACCAGTAGAGAAGGAAAAAGTTCAC 60.018 42.308 0.00 0.00 35.25 3.18
3700 5336 6.144724 CAGTAGAGAAGGAAAAAGTTCACTCG 59.855 42.308 0.00 0.00 36.25 4.18
3701 5337 5.024785 AGAGAAGGAAAAAGTTCACTCGT 57.975 39.130 0.00 0.00 36.25 4.18
3702 5338 5.429130 AGAGAAGGAAAAAGTTCACTCGTT 58.571 37.500 0.00 0.00 36.25 3.85
3704 5340 7.046033 AGAGAAGGAAAAAGTTCACTCGTTTA 58.954 34.615 0.00 0.00 36.25 2.01
3705 5341 7.224949 AGAGAAGGAAAAAGTTCACTCGTTTAG 59.775 37.037 0.00 0.00 36.25 1.85
3706 5342 7.046033 AGAAGGAAAAAGTTCACTCGTTTAGA 58.954 34.615 0.00 0.00 35.25 2.10
3836 5577 4.451900 ACCCTTGTGAATCGGATCAATAC 58.548 43.478 0.00 0.00 0.00 1.89
3855 5596 3.426787 ACAACCATAAACACCGGATCA 57.573 42.857 9.46 0.00 0.00 2.92
3891 5632 4.927782 AGCGCACGCAAGACCCAA 62.928 61.111 18.24 0.00 44.88 4.12
3898 5639 2.199652 CGCAAGACCCAAGGCCAAA 61.200 57.895 5.01 0.00 43.02 3.28
3899 5640 1.667722 GCAAGACCCAAGGCCAAAG 59.332 57.895 5.01 0.00 0.00 2.77
3900 5641 0.827507 GCAAGACCCAAGGCCAAAGA 60.828 55.000 5.01 0.00 0.00 2.52
3902 5643 0.178961 AAGACCCAAGGCCAAAGACC 60.179 55.000 5.01 0.00 0.00 3.85
3903 5644 1.152830 GACCCAAGGCCAAAGACCA 59.847 57.895 5.01 0.00 0.00 4.02
3904 5645 0.469144 GACCCAAGGCCAAAGACCAA 60.469 55.000 5.01 0.00 0.00 3.67
3905 5646 0.469892 ACCCAAGGCCAAAGACCAAG 60.470 55.000 5.01 0.00 0.00 3.61
3906 5647 0.178964 CCCAAGGCCAAAGACCAAGA 60.179 55.000 5.01 0.00 0.00 3.02
3907 5648 1.703411 CCAAGGCCAAAGACCAAGAA 58.297 50.000 5.01 0.00 0.00 2.52
3908 5649 1.341209 CCAAGGCCAAAGACCAAGAAC 59.659 52.381 5.01 0.00 0.00 3.01
3909 5650 1.001378 CAAGGCCAAAGACCAAGAACG 60.001 52.381 5.01 0.00 0.00 3.95
3910 5651 1.172812 AGGCCAAAGACCAAGAACGC 61.173 55.000 5.01 0.00 0.00 4.84
3913 5654 0.941542 CCAAAGACCAAGAACGCGAA 59.058 50.000 15.93 0.00 0.00 4.70
3914 5655 1.535462 CCAAAGACCAAGAACGCGAAT 59.465 47.619 15.93 0.00 0.00 3.34
3915 5656 2.574322 CAAAGACCAAGAACGCGAATG 58.426 47.619 15.93 5.63 0.00 2.67
3916 5657 0.517316 AAGACCAAGAACGCGAATGC 59.483 50.000 15.93 0.00 37.91 3.56
3917 5658 0.602638 AGACCAAGAACGCGAATGCA 60.603 50.000 15.93 0.00 42.97 3.96
3918 5659 0.447801 GACCAAGAACGCGAATGCAT 59.552 50.000 15.93 0.00 42.97 3.96
3936 5677 1.948145 CATTCCATCTCAAGCTGAGCC 59.052 52.381 0.00 0.00 43.95 4.70
3941 5682 0.183014 ATCTCAAGCTGAGCCATGGG 59.817 55.000 15.13 0.25 43.95 4.00
3942 5683 1.203441 TCTCAAGCTGAGCCATGGGT 61.203 55.000 18.33 18.33 43.95 4.51
4172 5913 3.744719 CGGCGACTTGGACCTCGA 61.745 66.667 0.00 0.00 31.24 4.04
4204 6561 4.101448 CCACGGAGGGCCCTTCAG 62.101 72.222 30.44 23.25 0.00 3.02
4237 6594 0.103026 CTGCAGATCCGGATCGTTCA 59.897 55.000 33.24 28.17 42.48 3.18
4238 6595 0.179111 TGCAGATCCGGATCGTTCAC 60.179 55.000 33.24 22.80 42.48 3.18
4253 6610 0.389817 TTCACGGCTCGTTCATGGAG 60.390 55.000 0.00 0.00 38.32 3.86
4256 6613 1.519455 CGGCTCGTTCATGGAGGAC 60.519 63.158 0.00 0.00 32.10 3.85
4305 6662 2.202824 CCAAATGCAGCATGGCGG 60.203 61.111 9.18 6.12 35.86 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 114 1.140652 CTGGAGGCAAGGAGGATTCTC 59.859 57.143 0.00 0.00 39.25 2.87
273 275 1.692042 CCCACCTCCTCTGCCTCAT 60.692 63.158 0.00 0.00 0.00 2.90
274 276 2.284921 CCCACCTCCTCTGCCTCA 60.285 66.667 0.00 0.00 0.00 3.86
433 1264 2.092646 GCTCACTCTCTCTCCCAGTCTA 60.093 54.545 0.00 0.00 0.00 2.59
454 1285 2.103143 ATCTCAGCCGAAGCGTCG 59.897 61.111 15.45 15.45 46.67 5.12
566 1399 6.719370 AGTTCTGTATTTCAACATTTAGGCCA 59.281 34.615 5.01 0.00 0.00 5.36
664 1497 7.799583 AGGTCTTATATTTTGATAGGGAGGGAA 59.200 37.037 0.00 0.00 0.00 3.97
753 1711 5.882557 CAGAGTAGTGCCCATAAACAGAAAT 59.117 40.000 0.00 0.00 0.00 2.17
833 1791 5.729974 ACGTTCCAACAGAAGTTTTACTC 57.270 39.130 0.00 0.00 35.28 2.59
893 1851 7.532682 ACAACAATGTTTGTGGTTTGATTAC 57.467 32.000 0.00 0.00 45.34 1.89
971 1929 4.044065 TGGACCCTGGAATTGACATAAACT 59.956 41.667 0.00 0.00 0.00 2.66
984 1942 0.918983 CCATAGCTTTGGACCCTGGA 59.081 55.000 17.55 0.00 39.25 3.86
1191 2149 6.396829 AGCTAGAAACAAACTGAAGCAATT 57.603 33.333 0.00 0.00 0.00 2.32
1262 2220 3.003480 CTGCCACAAGCTTAGTACCTTC 58.997 50.000 0.00 0.00 44.23 3.46
1331 2295 0.999406 CGCGACTCGAAAACCATGAT 59.001 50.000 0.00 0.00 41.67 2.45
1333 2297 0.179250 CACGCGACTCGAAAACCATG 60.179 55.000 15.93 0.00 41.67 3.66
1334 2298 0.319211 TCACGCGACTCGAAAACCAT 60.319 50.000 15.93 0.00 41.67 3.55
1335 2299 1.066093 TCACGCGACTCGAAAACCA 59.934 52.632 15.93 0.00 41.67 3.67
1336 2300 1.485943 GTCACGCGACTCGAAAACC 59.514 57.895 15.93 0.00 41.67 3.27
1383 2347 4.578928 ACACTAAGTTGAGTCGCCATTTTT 59.421 37.500 0.00 0.00 0.00 1.94
1384 2348 4.134563 ACACTAAGTTGAGTCGCCATTTT 58.865 39.130 0.00 0.00 0.00 1.82
1385 2349 3.740115 ACACTAAGTTGAGTCGCCATTT 58.260 40.909 0.00 0.00 0.00 2.32
1386 2350 3.326747 GACACTAAGTTGAGTCGCCATT 58.673 45.455 0.00 0.00 0.00 3.16
1387 2351 2.671351 CGACACTAAGTTGAGTCGCCAT 60.671 50.000 11.69 0.00 45.68 4.40
1388 2352 1.335597 CGACACTAAGTTGAGTCGCCA 60.336 52.381 11.69 0.00 45.68 5.69
1389 2353 1.337821 CGACACTAAGTTGAGTCGCC 58.662 55.000 11.69 0.00 45.68 5.54
1393 2357 4.519350 TCATGAGTCGACACTAAGTTGAGT 59.481 41.667 19.50 0.00 45.19 3.41
1394 2358 4.854291 GTCATGAGTCGACACTAAGTTGAG 59.146 45.833 19.50 0.00 41.31 3.02
1395 2359 4.519350 AGTCATGAGTCGACACTAAGTTGA 59.481 41.667 19.50 7.66 38.33 3.18
1396 2360 4.799678 AGTCATGAGTCGACACTAAGTTG 58.200 43.478 19.50 5.44 35.77 3.16
1397 2361 5.049398 GAGTCATGAGTCGACACTAAGTT 57.951 43.478 19.50 0.00 35.77 2.66
1398 2362 4.688511 GAGTCATGAGTCGACACTAAGT 57.311 45.455 19.50 4.30 35.77 2.24
1410 2374 1.716172 TCGCGACTCGAGTCATGAG 59.284 57.895 37.14 25.74 44.99 2.90
1411 2375 3.884900 TCGCGACTCGAGTCATGA 58.115 55.556 37.14 30.71 44.99 3.07
1418 2382 4.103103 CCTGCAGTCGCGACTCGA 62.103 66.667 37.41 24.72 46.29 4.04
1420 2384 3.923563 AAGCCTGCAGTCGCGACTC 62.924 63.158 37.41 29.03 42.97 3.36
1421 2385 3.996124 AAGCCTGCAGTCGCGACT 61.996 61.111 34.98 34.98 42.97 4.18
1422 2386 3.782244 CAAGCCTGCAGTCGCGAC 61.782 66.667 31.30 31.30 42.97 5.19
1423 2387 3.989787 TCAAGCCTGCAGTCGCGA 61.990 61.111 13.81 3.71 42.97 5.87
1424 2388 3.782244 GTCAAGCCTGCAGTCGCG 61.782 66.667 13.81 0.00 42.97 5.87
1425 2389 1.510480 AAAGTCAAGCCTGCAGTCGC 61.510 55.000 13.81 10.03 39.24 5.19
1426 2390 0.947244 AAAAGTCAAGCCTGCAGTCG 59.053 50.000 13.81 0.00 0.00 4.18
1427 2391 2.287849 GGAAAAAGTCAAGCCTGCAGTC 60.288 50.000 13.81 0.00 0.00 3.51
1428 2392 1.683385 GGAAAAAGTCAAGCCTGCAGT 59.317 47.619 13.81 0.00 0.00 4.40
1429 2393 1.335324 CGGAAAAAGTCAAGCCTGCAG 60.335 52.381 6.78 6.78 0.00 4.41
1430 2394 0.667993 CGGAAAAAGTCAAGCCTGCA 59.332 50.000 0.00 0.00 0.00 4.41
1431 2395 0.951558 TCGGAAAAAGTCAAGCCTGC 59.048 50.000 0.00 0.00 0.00 4.85
1432 2396 2.222027 ACTCGGAAAAAGTCAAGCCTG 58.778 47.619 0.00 0.00 0.00 4.85
1433 2397 2.495084 GACTCGGAAAAAGTCAAGCCT 58.505 47.619 0.00 0.00 42.23 4.58
1434 2398 1.194772 CGACTCGGAAAAAGTCAAGCC 59.805 52.381 4.36 0.00 42.68 4.35
1435 2399 1.398578 GCGACTCGGAAAAAGTCAAGC 60.399 52.381 0.00 0.00 42.68 4.01
1436 2400 2.135933 AGCGACTCGGAAAAAGTCAAG 58.864 47.619 0.00 0.00 42.68 3.02
1437 2401 2.234300 AGCGACTCGGAAAAAGTCAA 57.766 45.000 0.00 0.00 42.68 3.18
1438 2402 2.608752 GGTAGCGACTCGGAAAAAGTCA 60.609 50.000 0.00 0.00 42.68 3.41
1439 2403 1.991264 GGTAGCGACTCGGAAAAAGTC 59.009 52.381 0.00 0.00 39.82 3.01
1440 2404 1.337541 GGGTAGCGACTCGGAAAAAGT 60.338 52.381 0.00 0.00 0.00 2.66
1441 2405 1.356938 GGGTAGCGACTCGGAAAAAG 58.643 55.000 0.00 0.00 0.00 2.27
1442 2406 0.037046 GGGGTAGCGACTCGGAAAAA 60.037 55.000 0.00 0.00 0.00 1.94
1443 2407 1.186917 TGGGGTAGCGACTCGGAAAA 61.187 55.000 0.00 0.00 0.00 2.29
1444 2408 1.601419 CTGGGGTAGCGACTCGGAAA 61.601 60.000 0.00 0.00 0.00 3.13
1445 2409 2.036098 TGGGGTAGCGACTCGGAA 59.964 61.111 0.00 0.00 0.00 4.30
1446 2410 2.439701 CTGGGGTAGCGACTCGGA 60.440 66.667 0.00 0.00 0.00 4.55
1447 2411 2.050350 TTCTGGGGTAGCGACTCGG 61.050 63.158 0.00 0.00 0.00 4.63
1448 2412 1.139095 GTTCTGGGGTAGCGACTCG 59.861 63.158 0.00 0.00 0.00 4.18
1449 2413 1.139095 CGTTCTGGGGTAGCGACTC 59.861 63.158 0.00 0.00 0.00 3.36
1450 2414 1.303888 TCGTTCTGGGGTAGCGACT 60.304 57.895 0.00 0.00 0.00 4.18
1451 2415 1.153881 GTCGTTCTGGGGTAGCGAC 60.154 63.158 0.00 0.00 43.53 5.19
1452 2416 1.303888 AGTCGTTCTGGGGTAGCGA 60.304 57.895 0.00 0.00 0.00 4.93
1453 2417 1.139095 GAGTCGTTCTGGGGTAGCG 59.861 63.158 0.00 0.00 0.00 4.26
1454 2418 0.824759 ATGAGTCGTTCTGGGGTAGC 59.175 55.000 0.00 0.00 0.00 3.58
1455 2419 1.065701 CGATGAGTCGTTCTGGGGTAG 59.934 57.143 0.00 0.00 42.78 3.18
1456 2420 1.100510 CGATGAGTCGTTCTGGGGTA 58.899 55.000 0.00 0.00 42.78 3.69
1457 2421 1.890894 CGATGAGTCGTTCTGGGGT 59.109 57.895 0.00 0.00 42.78 4.95
1458 2422 4.814900 CGATGAGTCGTTCTGGGG 57.185 61.111 0.00 0.00 42.78 4.96
1467 2431 4.142816 CCATGGTTTTCAAGTCGATGAGTC 60.143 45.833 2.57 0.00 0.00 3.36
1468 2432 3.753272 CCATGGTTTTCAAGTCGATGAGT 59.247 43.478 2.57 0.00 0.00 3.41
1469 2433 3.753272 ACCATGGTTTTCAAGTCGATGAG 59.247 43.478 13.00 0.00 0.00 2.90
1470 2434 3.501828 CACCATGGTTTTCAAGTCGATGA 59.498 43.478 16.84 0.00 0.00 2.92
1471 2435 3.253188 ACACCATGGTTTTCAAGTCGATG 59.747 43.478 16.84 1.19 0.00 3.84
1472 2436 3.253188 CACACCATGGTTTTCAAGTCGAT 59.747 43.478 16.84 0.00 0.00 3.59
1473 2437 2.616376 CACACCATGGTTTTCAAGTCGA 59.384 45.455 16.84 0.00 0.00 4.20
1474 2438 2.357637 ACACACCATGGTTTTCAAGTCG 59.642 45.455 16.84 2.75 0.00 4.18
1475 2439 5.240623 TGATACACACCATGGTTTTCAAGTC 59.759 40.000 16.84 8.41 0.00 3.01
1476 2440 5.136828 TGATACACACCATGGTTTTCAAGT 58.863 37.500 16.84 6.00 0.00 3.16
1477 2441 5.703978 TGATACACACCATGGTTTTCAAG 57.296 39.130 16.84 5.24 0.00 3.02
1478 2442 5.538053 ACATGATACACACCATGGTTTTCAA 59.462 36.000 16.84 0.00 43.16 2.69
1479 2443 5.048154 CACATGATACACACCATGGTTTTCA 60.048 40.000 16.84 12.36 43.16 2.69
1480 2444 5.048083 ACACATGATACACACCATGGTTTTC 60.048 40.000 16.84 6.60 43.16 2.29
1481 2445 4.832266 ACACATGATACACACCATGGTTTT 59.168 37.500 16.84 1.50 43.16 2.43
1482 2446 4.406456 ACACATGATACACACCATGGTTT 58.594 39.130 16.84 6.07 43.16 3.27
1483 2447 4.032960 ACACATGATACACACCATGGTT 57.967 40.909 16.84 3.22 43.16 3.67
1484 2448 3.719268 ACACATGATACACACCATGGT 57.281 42.857 13.00 13.00 43.16 3.55
1485 2449 5.007921 CACATACACATGATACACACCATGG 59.992 44.000 11.19 11.19 43.16 3.66
1486 2450 5.585844 ACACATACACATGATACACACCATG 59.414 40.000 0.00 0.00 44.12 3.66
1487 2451 5.585844 CACACATACACATGATACACACCAT 59.414 40.000 0.00 0.00 35.96 3.55
1488 2452 4.934602 CACACATACACATGATACACACCA 59.065 41.667 0.00 0.00 35.96 4.17
1489 2453 5.175127 TCACACATACACATGATACACACC 58.825 41.667 0.00 0.00 35.96 4.16
1490 2454 5.869344 ACTCACACATACACATGATACACAC 59.131 40.000 0.00 0.00 35.96 3.82
1491 2455 6.036577 ACTCACACATACACATGATACACA 57.963 37.500 0.00 0.00 35.96 3.72
1492 2456 6.697455 CCTACTCACACATACACATGATACAC 59.303 42.308 0.00 0.00 35.96 2.90
1493 2457 6.183360 CCCTACTCACACATACACATGATACA 60.183 42.308 0.00 0.00 35.96 2.29
1494 2458 6.216569 CCCTACTCACACATACACATGATAC 58.783 44.000 0.00 0.00 35.96 2.24
1495 2459 5.304357 CCCCTACTCACACATACACATGATA 59.696 44.000 0.00 0.00 35.96 2.15
1496 2460 4.101585 CCCCTACTCACACATACACATGAT 59.898 45.833 0.00 0.00 35.96 2.45
1497 2461 3.450817 CCCCTACTCACACATACACATGA 59.549 47.826 0.00 0.00 35.96 3.07
1498 2462 3.432186 CCCCCTACTCACACATACACATG 60.432 52.174 0.00 0.00 38.21 3.21
1499 2463 2.771943 CCCCCTACTCACACATACACAT 59.228 50.000 0.00 0.00 0.00 3.21
1500 2464 2.184533 CCCCCTACTCACACATACACA 58.815 52.381 0.00 0.00 0.00 3.72
1501 2465 2.093658 CACCCCCTACTCACACATACAC 60.094 54.545 0.00 0.00 0.00 2.90
1502 2466 2.184533 CACCCCCTACTCACACATACA 58.815 52.381 0.00 0.00 0.00 2.29
1503 2467 1.485066 CCACCCCCTACTCACACATAC 59.515 57.143 0.00 0.00 0.00 2.39
1504 2468 1.624113 CCCACCCCCTACTCACACATA 60.624 57.143 0.00 0.00 0.00 2.29
1505 2469 0.914417 CCCACCCCCTACTCACACAT 60.914 60.000 0.00 0.00 0.00 3.21
1506 2470 1.537889 CCCACCCCCTACTCACACA 60.538 63.158 0.00 0.00 0.00 3.72
1507 2471 2.298661 CCCCACCCCCTACTCACAC 61.299 68.421 0.00 0.00 0.00 3.82
1508 2472 2.124085 CCCCACCCCCTACTCACA 59.876 66.667 0.00 0.00 0.00 3.58
1509 2473 2.691252 CCCCCACCCCCTACTCAC 60.691 72.222 0.00 0.00 0.00 3.51
1523 2487 4.779486 ACCCCCACTCCATCCCCC 62.779 72.222 0.00 0.00 0.00 5.40
1524 2488 3.420482 CACCCCCACTCCATCCCC 61.420 72.222 0.00 0.00 0.00 4.81
1525 2489 3.420482 CCACCCCCACTCCATCCC 61.420 72.222 0.00 0.00 0.00 3.85
1526 2490 3.420482 CCCACCCCCACTCCATCC 61.420 72.222 0.00 0.00 0.00 3.51
1527 2491 3.420482 CCCCACCCCCACTCCATC 61.420 72.222 0.00 0.00 0.00 3.51
1530 2494 4.358181 TACCCCCACCCCCACTCC 62.358 72.222 0.00 0.00 0.00 3.85
1531 2495 2.691252 CTACCCCCACCCCCACTC 60.691 72.222 0.00 0.00 0.00 3.51
1532 2496 3.213245 TCTACCCCCACCCCCACT 61.213 66.667 0.00 0.00 0.00 4.00
1533 2497 2.691252 CTCTACCCCCACCCCCAC 60.691 72.222 0.00 0.00 0.00 4.61
1534 2498 4.752594 GCTCTACCCCCACCCCCA 62.753 72.222 0.00 0.00 0.00 4.96
1535 2499 3.964484 AAGCTCTACCCCCACCCCC 62.964 68.421 0.00 0.00 0.00 5.40
1536 2500 2.286197 AAGCTCTACCCCCACCCC 60.286 66.667 0.00 0.00 0.00 4.95
1537 2501 1.615424 TCAAGCTCTACCCCCACCC 60.615 63.158 0.00 0.00 0.00 4.61
1538 2502 0.910088 ACTCAAGCTCTACCCCCACC 60.910 60.000 0.00 0.00 0.00 4.61
1539 2503 0.250513 CACTCAAGCTCTACCCCCAC 59.749 60.000 0.00 0.00 0.00 4.61
1540 2504 0.116342 TCACTCAAGCTCTACCCCCA 59.884 55.000 0.00 0.00 0.00 4.96
1541 2505 1.501582 ATCACTCAAGCTCTACCCCC 58.498 55.000 0.00 0.00 0.00 5.40
1542 2506 2.769095 AGAATCACTCAAGCTCTACCCC 59.231 50.000 0.00 0.00 0.00 4.95
1543 2507 3.196685 ACAGAATCACTCAAGCTCTACCC 59.803 47.826 0.00 0.00 0.00 3.69
1544 2508 4.464069 ACAGAATCACTCAAGCTCTACC 57.536 45.455 0.00 0.00 0.00 3.18
1545 2509 5.719173 AGAACAGAATCACTCAAGCTCTAC 58.281 41.667 0.00 0.00 0.00 2.59
1677 2723 5.163874 GCTAAAGCTGCATATCAGATAGCAC 60.164 44.000 1.02 6.21 45.72 4.40
1894 2940 3.684788 CCATGCCTACTTGTCAGTAACAC 59.315 47.826 0.00 0.00 37.70 3.32
1917 2963 3.211045 TCCTTGACTGGTGTTTTGCTAC 58.789 45.455 0.00 0.00 0.00 3.58
1934 2980 7.079451 TGTTCACTTTCCTCTATTTCTCCTT 57.921 36.000 0.00 0.00 0.00 3.36
1947 2993 6.625873 AAGAAGAGTTCATGTTCACTTTCC 57.374 37.500 0.00 0.00 33.63 3.13
2049 3095 8.525316 TGCATCAGAAAACTTCATTGACATATT 58.475 29.630 0.00 0.00 0.00 1.28
2069 3115 1.270274 GTTCAACACAGGCATGCATCA 59.730 47.619 21.36 0.00 0.00 3.07
2078 3124 3.119531 TGCTGTCAAAAGTTCAACACAGG 60.120 43.478 6.99 0.00 33.33 4.00
2080 3126 3.505680 ACTGCTGTCAAAAGTTCAACACA 59.494 39.130 0.00 0.00 0.00 3.72
2216 3263 2.481969 CCACATATCCTCCACACGTGAG 60.482 54.545 25.01 15.20 0.00 3.51
2282 3329 4.479619 CTGCTGTTTTGAGCTTAACCATC 58.520 43.478 0.00 0.00 39.90 3.51
2357 3404 0.040425 CAGCTTGCCACACGGTTAAC 60.040 55.000 0.00 0.00 33.28 2.01
2358 3405 0.179043 TCAGCTTGCCACACGGTTAA 60.179 50.000 0.00 0.00 33.28 2.01
2359 3406 0.036164 ATCAGCTTGCCACACGGTTA 59.964 50.000 0.00 0.00 33.28 2.85
2360 3407 1.228245 ATCAGCTTGCCACACGGTT 60.228 52.632 0.00 0.00 33.28 4.44
2361 3408 1.968017 CATCAGCTTGCCACACGGT 60.968 57.895 0.00 0.00 33.28 4.83
2490 3540 3.159472 ACTTGATCATTTGCAGAAGCCA 58.841 40.909 0.00 0.00 41.13 4.75
2539 3589 2.035066 AGCATCCTCACTTGTTTTGTGC 59.965 45.455 0.00 0.00 35.58 4.57
2677 3727 7.597386 AGATGGAAGCTTCACTTGAATTTAAC 58.403 34.615 27.02 6.21 39.29 2.01
2682 3732 7.765695 TTTTAGATGGAAGCTTCACTTGAAT 57.234 32.000 27.02 10.51 39.29 2.57
2768 3825 5.209818 ACTCTACAAGAATGAACACGGAA 57.790 39.130 0.00 0.00 0.00 4.30
2813 3870 2.396590 TATCAGGGTCGTTCCAAAGC 57.603 50.000 2.42 0.00 38.11 3.51
2851 3908 5.947228 ATCATACCAAGTGTCACAAGTTG 57.053 39.130 5.62 0.00 0.00 3.16
2866 3923 4.202050 GGAACCAGATGCACAAATCATACC 60.202 45.833 0.00 0.00 0.00 2.73
2899 3956 9.000486 GGGTCATACAAAACTAGAATATTAGCC 58.000 37.037 0.00 0.00 0.00 3.93
3179 4236 2.688446 CGACTGCCTATCAAGGTACTGA 59.312 50.000 0.00 0.00 45.64 3.41
3245 4302 2.663520 ATCAACGACAACCGCGCA 60.664 55.556 8.75 0.00 43.32 6.09
3278 4335 2.654863 TCATCGTCCTGCATACTCTCA 58.345 47.619 0.00 0.00 0.00 3.27
3301 4358 5.334724 AGCAATTTTCATCAAAGCCTAGG 57.665 39.130 3.67 3.67 0.00 3.02
3362 4419 7.067981 GCCATTTATCTCAAAAGAATCTCCACT 59.932 37.037 0.00 0.00 34.49 4.00
3388 4448 7.005062 AGGAATCGATGAAATAACGTCTTTG 57.995 36.000 0.00 0.00 0.00 2.77
3409 4469 7.933577 CCAGCTGAATGTATAATAAGACAAGGA 59.066 37.037 17.39 0.00 29.04 3.36
3427 4824 2.104622 TCACTCACATTGACCAGCTGAA 59.895 45.455 17.39 1.24 0.00 3.02
3476 4873 4.433615 TCTTCTTCATTAGCGCTCGATTT 58.566 39.130 16.34 0.00 0.00 2.17
3477 4874 4.046938 TCTTCTTCATTAGCGCTCGATT 57.953 40.909 16.34 0.00 0.00 3.34
3478 4875 3.551863 CCTCTTCTTCATTAGCGCTCGAT 60.552 47.826 16.34 6.81 0.00 3.59
3479 4876 2.223595 CCTCTTCTTCATTAGCGCTCGA 60.224 50.000 16.34 6.60 0.00 4.04
3480 4877 2.123342 CCTCTTCTTCATTAGCGCTCG 58.877 52.381 16.34 3.66 0.00 5.03
3486 4883 4.952335 ACCCATTTGCCTCTTCTTCATTAG 59.048 41.667 0.00 0.00 0.00 1.73
3527 4924 5.552870 ATGTTATCAACCCTAGCAGGTAG 57.447 43.478 0.00 0.00 40.05 3.18
3535 4932 7.094377 GCAGTTTCAGAAATGTTATCAACCCTA 60.094 37.037 0.00 0.00 33.58 3.53
3543 4940 5.106555 CCTGTCGCAGTTTCAGAAATGTTAT 60.107 40.000 0.00 0.00 33.58 1.89
3558 4955 4.087892 CCCTGGGTCCTGTCGCAG 62.088 72.222 3.97 0.00 44.38 5.18
3606 5003 8.730680 GCCTTGTTCAGAAAAAGAATCATAGTA 58.269 33.333 14.03 0.00 0.00 1.82
3607 5004 7.449704 AGCCTTGTTCAGAAAAAGAATCATAGT 59.550 33.333 14.03 0.00 0.00 2.12
3608 5005 7.824672 AGCCTTGTTCAGAAAAAGAATCATAG 58.175 34.615 14.03 0.00 0.00 2.23
3610 5007 6.661304 AGCCTTGTTCAGAAAAAGAATCAT 57.339 33.333 14.03 0.00 0.00 2.45
3611 5008 6.096705 TGAAGCCTTGTTCAGAAAAAGAATCA 59.903 34.615 14.03 11.39 32.54 2.57
3612 5009 6.507023 TGAAGCCTTGTTCAGAAAAAGAATC 58.493 36.000 14.03 9.34 32.54 2.52
3613 5010 6.469782 TGAAGCCTTGTTCAGAAAAAGAAT 57.530 33.333 14.03 0.18 32.54 2.40
3625 5022 6.959639 TTAACTTTGATCTGAAGCCTTGTT 57.040 33.333 8.68 0.00 0.00 2.83
3626 5023 6.959639 TTTAACTTTGATCTGAAGCCTTGT 57.040 33.333 8.68 0.00 0.00 3.16
3627 5024 7.592903 GTCTTTTAACTTTGATCTGAAGCCTTG 59.407 37.037 8.68 0.00 0.00 3.61
3637 5034 9.334693 CATACTTGCAGTCTTTTAACTTTGATC 57.665 33.333 0.00 0.00 0.00 2.92
3663 5060 7.166691 TCCTTCTCTACTGGTGTTGTAATAC 57.833 40.000 0.00 0.00 0.00 1.89
3677 5313 5.984323 ACGAGTGAACTTTTTCCTTCTCTAC 59.016 40.000 0.00 0.00 0.00 2.59
3678 5314 6.158023 ACGAGTGAACTTTTTCCTTCTCTA 57.842 37.500 0.00 0.00 0.00 2.43
3681 5317 7.046033 TCTAAACGAGTGAACTTTTTCCTTCT 58.954 34.615 0.00 0.00 0.00 2.85
3693 5329 9.447040 CGAATATACAATCTCTAAACGAGTGAA 57.553 33.333 0.00 0.00 40.75 3.18
3697 5333 7.368833 ACCCGAATATACAATCTCTAAACGAG 58.631 38.462 0.00 0.00 41.30 4.18
3704 5340 8.707796 TCTCTAAACCCGAATATACAATCTCT 57.292 34.615 0.00 0.00 0.00 3.10
3705 5341 9.930693 AATCTCTAAACCCGAATATACAATCTC 57.069 33.333 0.00 0.00 0.00 2.75
3706 5342 9.712305 CAATCTCTAAACCCGAATATACAATCT 57.288 33.333 0.00 0.00 0.00 2.40
3707 5343 9.490379 ACAATCTCTAAACCCGAATATACAATC 57.510 33.333 0.00 0.00 0.00 2.67
3709 5345 9.754382 GTACAATCTCTAAACCCGAATATACAA 57.246 33.333 0.00 0.00 0.00 2.41
3710 5346 9.139734 AGTACAATCTCTAAACCCGAATATACA 57.860 33.333 0.00 0.00 0.00 2.29
3718 5406 6.164176 ACTTGAAGTACAATCTCTAAACCCG 58.836 40.000 0.00 0.00 37.88 5.28
3819 5560 4.837972 TGGTTGTATTGATCCGATTCACA 58.162 39.130 0.00 0.00 0.00 3.58
3836 5577 4.199310 AGATGATCCGGTGTTTATGGTTG 58.801 43.478 0.00 0.00 0.00 3.77
3855 5596 5.586643 TGCGCTGATCGATATAAGTAGAGAT 59.413 40.000 9.73 0.00 41.67 2.75
3891 5632 1.172812 GCGTTCTTGGTCTTTGGCCT 61.173 55.000 3.32 0.00 0.00 5.19
3898 5639 0.602638 TGCATTCGCGTTCTTGGTCT 60.603 50.000 5.77 0.00 42.97 3.85
3899 5640 0.447801 ATGCATTCGCGTTCTTGGTC 59.552 50.000 5.77 0.00 42.97 4.02
3900 5641 0.881118 AATGCATTCGCGTTCTTGGT 59.119 45.000 5.99 0.00 44.15 3.67
3907 5648 0.940126 GAGATGGAATGCATTCGCGT 59.060 50.000 28.38 22.40 42.97 6.01
3908 5649 0.939419 TGAGATGGAATGCATTCGCG 59.061 50.000 28.38 0.00 42.97 5.87
3909 5650 2.857489 GCTTGAGATGGAATGCATTCGC 60.857 50.000 28.38 21.97 37.67 4.70
3910 5651 2.617308 AGCTTGAGATGGAATGCATTCG 59.383 45.455 28.38 15.57 37.67 3.34
3913 5654 3.292492 TCAGCTTGAGATGGAATGCAT 57.708 42.857 0.00 0.00 31.33 3.96
3914 5655 2.793288 TCAGCTTGAGATGGAATGCA 57.207 45.000 0.00 0.00 31.33 3.96
4062 5803 4.101448 CTGGCCTTGAGGTCGGGG 62.101 72.222 3.32 0.00 44.44 5.73
4076 5817 2.422479 CAGAATGTGACCTTGATGCTGG 59.578 50.000 0.00 0.00 0.00 4.85
4114 5855 1.226717 CGCAGAAGTAGGAGACGCC 60.227 63.158 0.00 0.00 0.00 5.68
4154 5895 4.052229 CGAGGTCCAAGTCGCCGT 62.052 66.667 0.00 0.00 0.00 5.68
4157 5898 2.126031 GGTCGAGGTCCAAGTCGC 60.126 66.667 0.00 0.00 36.11 5.19
4204 6561 2.747855 GCAGCTGGGTGTAGTGGC 60.748 66.667 17.12 0.00 0.00 5.01
4207 6564 0.539051 GATCTGCAGCTGGGTGTAGT 59.461 55.000 17.12 5.58 32.42 2.73
4237 6594 1.982395 TCCTCCATGAACGAGCCGT 60.982 57.895 0.00 0.00 43.97 5.68
4238 6595 1.519455 GTCCTCCATGAACGAGCCG 60.519 63.158 0.00 0.00 0.00 5.52
4256 6613 1.226974 ATCGAATGTGACGGCTCCG 60.227 57.895 6.79 6.79 46.03 4.63


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

AutoCloner maintained by Alex Coulton.