Multiple sequence alignment - TraesCS7A01G051000

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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 TraesCS7A01G051000 chr7A 100.000 5973 0 0 959 6931 24586444 24592416 0.000000e+00 11031.0
1 TraesCS7A01G051000 chr7A 100.000 589 0 0 1 589 24585486 24586074 0.000000e+00 1088.0
2 TraesCS7A01G051000 chr7D 95.208 5405 128 38 1011 6331 23490373 23495730 0.000000e+00 8425.0
3 TraesCS7A01G051000 chr7D 78.918 721 92 33 2110 2803 58213545 58212858 1.070000e-117 435.0
4 TraesCS7A01G051000 chr7D 85.261 441 36 11 3 420 23488738 23489172 1.790000e-115 427.0
5 TraesCS7A01G051000 chr7D 89.888 267 22 5 6665 6930 23495916 23496178 8.610000e-89 339.0
6 TraesCS7A01G051000 chr7D 97.368 38 1 0 260 297 23488838 23488875 1.610000e-06 65.8
7 TraesCS7A01G051000 chr4A 94.036 2800 116 34 3763 6527 708325429 708322646 0.000000e+00 4198.0
8 TraesCS7A01G051000 chr4A 93.609 266 2 3 6665 6930 708322525 708322275 3.920000e-102 383.0
9 TraesCS7A01G051000 chr4A 83.333 312 45 7 5640 5947 706206057 706205749 1.470000e-71 281.0
10 TraesCS7A01G051000 chr4A 81.356 118 11 6 6549 6666 708322663 708322557 1.240000e-12 86.1
11 TraesCS7A01G051000 chr7B 88.785 321 34 1 1281 1599 318149436 318149756 6.520000e-105 392.0
12 TraesCS7A01G051000 chr3B 88.379 327 34 2 1281 1603 11383086 11383412 2.340000e-104 390.0
13 TraesCS7A01G051000 chr3B 84.314 204 25 5 2155 2353 363045766 363045565 7.090000e-45 193.0
14 TraesCS7A01G051000 chr2B 88.308 325 36 1 1281 1603 733273017 733273341 8.430000e-104 388.0
15 TraesCS7A01G051000 chr2B 87.730 326 35 2 1281 1604 326723662 326723984 6.560000e-100 375.0
16 TraesCS7A01G051000 chr2B 78.044 542 74 19 2052 2562 631365396 631364869 4.060000e-77 300.0
17 TraesCS7A01G051000 chr2B 79.747 395 41 16 2565 2947 631347066 631346699 4.150000e-62 250.0
18 TraesCS7A01G051000 chr5B 88.110 328 35 2 1281 1604 23521252 23520925 3.030000e-103 387.0
19 TraesCS7A01G051000 chr5B 84.314 204 25 5 2155 2353 140948812 140948611 7.090000e-45 193.0
20 TraesCS7A01G051000 chr5D 87.768 327 37 1 1281 1604 262396914 262396588 5.070000e-101 379.0
21 TraesCS7A01G051000 chr6B 87.117 326 40 1 1281 1604 248546198 248546523 1.100000e-97 368.0
22 TraesCS7A01G051000 chr6B 79.699 266 31 11 6665 6930 643395311 643395069 3.320000e-38 171.0
23 TraesCS7A01G051000 chr4B 86.890 328 39 2 1281 1604 658573528 658573855 1.420000e-96 364.0
24 TraesCS7A01G051000 chr4B 95.082 61 3 0 2080 2140 169934820 169934880 5.720000e-16 97.1
25 TraesCS7A01G051000 chr6D 85.294 204 23 5 2152 2350 306006148 306006349 3.280000e-48 204.0
26 TraesCS7A01G051000 chr1B 85.294 204 23 5 2155 2353 310102325 310102124 3.280000e-48 204.0
27 TraesCS7A01G051000 chr2A 88.889 162 16 2 2080 2241 19839434 19839593 1.520000e-46 198.0
28 TraesCS7A01G051000 chr1A 95.082 61 3 0 2080 2140 590829390 590829450 5.720000e-16 97.1
29 TraesCS7A01G051000 chr3A 93.443 61 4 0 2080 2140 22144517 22144577 2.660000e-14 91.6


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 TraesCS7A01G051000 chr7A 24585486 24592416 6930 False 6059.5 11031 100.00000 1 6931 2 chr7A.!!$F1 6930
1 TraesCS7A01G051000 chr7D 23488738 23496178 7440 False 2314.2 8425 91.93125 3 6930 4 chr7D.!!$F1 6927
2 TraesCS7A01G051000 chr7D 58212858 58213545 687 True 435.0 435 78.91800 2110 2803 1 chr7D.!!$R1 693
3 TraesCS7A01G051000 chr4A 708322275 708325429 3154 True 1555.7 4198 89.66700 3763 6930 3 chr4A.!!$R2 3167
4 TraesCS7A01G051000 chr2B 631364869 631365396 527 True 300.0 300 78.04400 2052 2562 1 chr2B.!!$R2 510

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
533 1386 0.041839 CACTCGTGCTTGCAGAACAC 60.042 55.000 0.00 5.92 0.00 3.32 F
572 1425 0.533085 GAGGTAGAAGAATGCGGGCC 60.533 60.000 0.00 0.00 0.00 5.80 F
574 1427 0.815615 GGTAGAAGAATGCGGGCCAG 60.816 60.000 4.39 0.00 0.00 4.85 F
1322 2187 1.075601 TTGGGTGAGCTTTCCCTGAT 58.924 50.000 22.11 0.00 43.74 2.90 F
1449 2314 1.287425 GCGGTATGGCTCAGTACAAC 58.713 55.000 0.00 0.00 0.00 3.32 F
2295 3185 1.963515 GTTCCTTTGACTGCCAATGGT 59.036 47.619 0.00 0.00 45.38 3.55 F
3202 4134 0.175760 TTGACCGTCATAGCTCTGCC 59.824 55.000 1.09 0.00 0.00 4.85 F
4311 5270 0.682292 TGACATCGCTTGTACCCACA 59.318 50.000 0.00 0.00 39.18 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 2314 0.108585 AGTACAAGTGCCACACCCAG 59.891 55.000 0.00 0.00 34.49 4.45 R
2444 3347 1.475682 GATTCTGGCCAAGCTTTCCAG 59.524 52.381 27.18 27.18 46.60 3.86 R
2446 3349 1.747924 GAGATTCTGGCCAAGCTTTCC 59.252 52.381 7.01 1.34 0.00 3.13 R
2447 3350 2.440409 TGAGATTCTGGCCAAGCTTTC 58.560 47.619 7.01 2.96 0.00 2.62 R
2790 3704 2.584791 CTCCGGAAACTGAAAATTGCG 58.415 47.619 5.23 0.00 39.64 4.85 R
3994 4953 1.735386 GCAGATGCACAGTCTCACAT 58.265 50.000 0.00 0.00 41.59 3.21 R
4893 5852 0.522180 ACTCGGCACAGAACTACTCG 59.478 55.000 0.00 0.00 0.00 4.18 R
6120 7100 0.613260 AGAAGAATACGTGCCAGGCA 59.387 50.000 11.22 11.22 35.60 4.75 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
104 105 3.535561 GTCACAGTTGATGAATCCGGAT 58.464 45.455 12.38 12.38 33.11 4.18
109 110 5.994054 CACAGTTGATGAATCCGGATATCTT 59.006 40.000 19.48 14.61 0.00 2.40
155 156 1.134699 GTCGGAGATGGCATGAGTTCA 60.135 52.381 3.81 0.00 40.67 3.18
240 241 4.449081 GGGGATGGGGATGAATTTATGTGA 60.449 45.833 0.00 0.00 0.00 3.58
260 261 1.692749 GGAGGGTGGGCCATAGTGA 60.693 63.158 10.70 0.00 36.17 3.41
261 262 1.527370 GAGGGTGGGCCATAGTGAC 59.473 63.158 10.70 0.00 36.17 3.67
262 263 1.229820 AGGGTGGGCCATAGTGACA 60.230 57.895 10.70 0.00 36.17 3.58
263 264 0.624500 AGGGTGGGCCATAGTGACAT 60.625 55.000 10.70 0.00 36.17 3.06
264 265 0.179018 GGGTGGGCCATAGTGACATC 60.179 60.000 10.70 0.00 36.17 3.06
265 266 0.839946 GGTGGGCCATAGTGACATCT 59.160 55.000 10.70 0.00 34.09 2.90
266 267 1.202698 GGTGGGCCATAGTGACATCTC 60.203 57.143 10.70 0.00 34.09 2.75
267 268 0.752658 TGGGCCATAGTGACATCTCG 59.247 55.000 0.00 0.00 0.00 4.04
268 269 1.040646 GGGCCATAGTGACATCTCGA 58.959 55.000 4.39 0.00 0.00 4.04
269 270 1.412710 GGGCCATAGTGACATCTCGAA 59.587 52.381 4.39 0.00 0.00 3.71
270 271 2.546795 GGGCCATAGTGACATCTCGAAG 60.547 54.545 4.39 0.00 0.00 3.79
271 272 2.101582 GGCCATAGTGACATCTCGAAGT 59.898 50.000 0.00 0.00 0.00 3.01
272 273 3.376540 GCCATAGTGACATCTCGAAGTC 58.623 50.000 5.61 5.61 35.37 3.01
273 274 3.181486 GCCATAGTGACATCTCGAAGTCA 60.181 47.826 10.02 10.02 42.06 3.41
275 276 4.336713 CCATAGTGACATCTCGAAGTCAGA 59.663 45.833 13.36 7.10 44.62 3.27
276 277 5.009510 CCATAGTGACATCTCGAAGTCAGAT 59.990 44.000 13.36 8.65 44.62 2.90
277 278 6.460814 CCATAGTGACATCTCGAAGTCAGATT 60.461 42.308 13.36 7.02 44.62 2.40
278 279 4.992688 AGTGACATCTCGAAGTCAGATTC 58.007 43.478 13.36 4.62 44.62 2.52
279 280 4.109050 GTGACATCTCGAAGTCAGATTCC 58.891 47.826 13.36 1.36 44.62 3.01
280 281 3.181496 TGACATCTCGAAGTCAGATTCCG 60.181 47.826 10.02 0.00 39.65 4.30
281 282 2.123342 CATCTCGAAGTCAGATTCCGC 58.877 52.381 0.00 0.00 0.00 5.54
282 283 1.464734 TCTCGAAGTCAGATTCCGCT 58.535 50.000 0.00 0.00 0.00 5.52
287 288 2.266554 GAAGTCAGATTCCGCTGTCTG 58.733 52.381 0.00 0.00 42.46 3.51
289 290 1.203523 AGTCAGATTCCGCTGTCTGTC 59.796 52.381 8.40 4.49 41.92 3.51
290 291 1.067565 GTCAGATTCCGCTGTCTGTCA 60.068 52.381 8.40 0.00 41.92 3.58
291 292 1.827344 TCAGATTCCGCTGTCTGTCAT 59.173 47.619 8.40 0.00 41.92 3.06
295 319 0.388520 TTCCGCTGTCTGTCATGTCG 60.389 55.000 0.00 0.00 0.00 4.35
297 321 1.080501 CGCTGTCTGTCATGTCGGT 60.081 57.895 0.00 0.00 0.00 4.69
299 323 0.244994 GCTGTCTGTCATGTCGGTCT 59.755 55.000 0.00 0.00 0.00 3.85
313 337 0.594602 CGGTCTGAACGTGTGGACTA 59.405 55.000 7.00 0.00 0.00 2.59
315 339 1.612463 GGTCTGAACGTGTGGACTACT 59.388 52.381 12.47 0.00 0.00 2.57
371 395 2.231380 AATGACTGGGGAGGCCGTT 61.231 57.895 0.00 0.00 0.00 4.44
372 396 2.484287 AATGACTGGGGAGGCCGTTG 62.484 60.000 0.00 0.00 0.00 4.10
373 397 3.637273 GACTGGGGAGGCCGTTGT 61.637 66.667 0.00 0.00 0.00 3.32
384 408 4.966787 CCGTTGTGGGGTGGGGTG 62.967 72.222 0.00 0.00 0.00 4.61
385 409 4.966787 CGTTGTGGGGTGGGGTGG 62.967 72.222 0.00 0.00 0.00 4.61
386 410 4.614036 GTTGTGGGGTGGGGTGGG 62.614 72.222 0.00 0.00 0.00 4.61
463 1316 5.774498 AAAAGAAAAAGAGACCGAAGCAT 57.226 34.783 0.00 0.00 0.00 3.79
464 1317 5.363979 AAAGAAAAAGAGACCGAAGCATC 57.636 39.130 0.00 0.00 0.00 3.91
465 1318 3.339141 AGAAAAAGAGACCGAAGCATCC 58.661 45.455 0.00 0.00 0.00 3.51
466 1319 2.859165 AAAAGAGACCGAAGCATCCA 57.141 45.000 0.00 0.00 0.00 3.41
467 1320 2.100605 AAAGAGACCGAAGCATCCAC 57.899 50.000 0.00 0.00 0.00 4.02
468 1321 0.250513 AAGAGACCGAAGCATCCACC 59.749 55.000 0.00 0.00 0.00 4.61
469 1322 0.904865 AGAGACCGAAGCATCCACCA 60.905 55.000 0.00 0.00 0.00 4.17
470 1323 0.179000 GAGACCGAAGCATCCACCAT 59.821 55.000 0.00 0.00 0.00 3.55
471 1324 0.620556 AGACCGAAGCATCCACCATT 59.379 50.000 0.00 0.00 0.00 3.16
472 1325 1.004745 AGACCGAAGCATCCACCATTT 59.995 47.619 0.00 0.00 0.00 2.32
473 1326 1.401905 GACCGAAGCATCCACCATTTC 59.598 52.381 0.00 0.00 0.00 2.17
474 1327 0.378257 CCGAAGCATCCACCATTTCG 59.622 55.000 0.00 0.00 40.03 3.46
475 1328 0.378257 CGAAGCATCCACCATTTCGG 59.622 55.000 0.00 0.00 37.55 4.30
476 1329 0.740737 GAAGCATCCACCATTTCGGG 59.259 55.000 0.00 0.00 40.22 5.14
477 1330 1.322538 AAGCATCCACCATTTCGGGC 61.323 55.000 0.00 0.00 40.22 6.13
478 1331 1.754234 GCATCCACCATTTCGGGCT 60.754 57.895 0.00 0.00 40.22 5.19
479 1332 0.465460 GCATCCACCATTTCGGGCTA 60.465 55.000 0.00 0.00 40.22 3.93
480 1333 1.308998 CATCCACCATTTCGGGCTAC 58.691 55.000 0.00 0.00 40.22 3.58
481 1334 0.916086 ATCCACCATTTCGGGCTACA 59.084 50.000 0.00 0.00 40.22 2.74
482 1335 0.693622 TCCACCATTTCGGGCTACAA 59.306 50.000 0.00 0.00 40.22 2.41
483 1336 1.074084 TCCACCATTTCGGGCTACAAA 59.926 47.619 0.00 0.00 40.22 2.83
484 1337 1.201414 CCACCATTTCGGGCTACAAAC 59.799 52.381 0.00 0.00 40.22 2.93
485 1338 1.135803 CACCATTTCGGGCTACAAACG 60.136 52.381 0.00 0.00 40.22 3.60
486 1339 0.179174 CCATTTCGGGCTACAAACGC 60.179 55.000 0.00 0.00 0.00 4.84
487 1340 0.179174 CATTTCGGGCTACAAACGCC 60.179 55.000 0.00 0.00 46.83 5.68
488 1341 0.322187 ATTTCGGGCTACAAACGCCT 60.322 50.000 0.71 0.00 46.73 5.52
489 1342 0.952010 TTTCGGGCTACAAACGCCTC 60.952 55.000 0.71 0.00 46.73 4.70
490 1343 3.186047 CGGGCTACAAACGCCTCG 61.186 66.667 0.71 0.00 46.73 4.63
491 1344 2.818274 GGGCTACAAACGCCTCGG 60.818 66.667 0.71 0.00 46.73 4.63
492 1345 3.497031 GGCTACAAACGCCTCGGC 61.497 66.667 0.00 0.00 44.17 5.54
493 1346 2.740826 GCTACAAACGCCTCGGCA 60.741 61.111 8.87 0.00 42.06 5.69
494 1347 2.106683 GCTACAAACGCCTCGGCAT 61.107 57.895 8.87 0.00 42.06 4.40
495 1348 1.715585 CTACAAACGCCTCGGCATG 59.284 57.895 8.87 6.32 42.06 4.06
496 1349 1.705337 CTACAAACGCCTCGGCATGG 61.705 60.000 8.87 0.00 42.06 3.66
497 1350 3.814268 CAAACGCCTCGGCATGGG 61.814 66.667 8.87 0.00 42.06 4.00
508 1361 4.511246 GCATGGGCCAGCCAGCTA 62.511 66.667 13.78 0.00 37.98 3.32
509 1362 2.519441 CATGGGCCAGCCAGCTAT 59.481 61.111 13.78 0.00 37.98 2.97
510 1363 1.602888 CATGGGCCAGCCAGCTATC 60.603 63.158 13.78 0.00 37.98 2.08
511 1364 2.838467 ATGGGCCAGCCAGCTATCC 61.838 63.158 13.78 0.00 37.98 2.59
512 1365 4.277009 GGGCCAGCCAGCTATCCC 62.277 72.222 11.50 11.27 37.98 3.85
513 1366 4.277009 GGCCAGCCAGCTATCCCC 62.277 72.222 3.12 0.00 35.81 4.81
514 1367 4.277009 GCCAGCCAGCTATCCCCC 62.277 72.222 0.00 0.00 0.00 5.40
515 1368 2.773918 CCAGCCAGCTATCCCCCA 60.774 66.667 0.00 0.00 0.00 4.96
516 1369 2.512896 CAGCCAGCTATCCCCCAC 59.487 66.667 0.00 0.00 0.00 4.61
517 1370 2.074948 CAGCCAGCTATCCCCCACT 61.075 63.158 0.00 0.00 0.00 4.00
518 1371 1.768077 AGCCAGCTATCCCCCACTC 60.768 63.158 0.00 0.00 0.00 3.51
519 1372 3.142393 CCAGCTATCCCCCACTCG 58.858 66.667 0.00 0.00 0.00 4.18
520 1373 1.762460 CCAGCTATCCCCCACTCGT 60.762 63.158 0.00 0.00 0.00 4.18
521 1374 1.443407 CAGCTATCCCCCACTCGTG 59.557 63.158 0.00 0.00 0.00 4.35
522 1375 2.109181 GCTATCCCCCACTCGTGC 59.891 66.667 0.00 0.00 0.00 5.34
523 1376 2.435693 GCTATCCCCCACTCGTGCT 61.436 63.158 0.00 0.00 0.00 4.40
524 1377 1.972660 GCTATCCCCCACTCGTGCTT 61.973 60.000 0.00 0.00 0.00 3.91
525 1378 0.179073 CTATCCCCCACTCGTGCTTG 60.179 60.000 0.00 0.00 0.00 4.01
526 1379 2.252072 TATCCCCCACTCGTGCTTGC 62.252 60.000 0.00 0.00 0.00 4.01
527 1380 4.641645 CCCCCACTCGTGCTTGCA 62.642 66.667 0.00 0.00 0.00 4.08
528 1381 3.052082 CCCCACTCGTGCTTGCAG 61.052 66.667 0.00 0.00 0.00 4.41
529 1382 2.031012 CCCACTCGTGCTTGCAGA 59.969 61.111 0.00 0.00 0.00 4.26
530 1383 1.597854 CCCACTCGTGCTTGCAGAA 60.598 57.895 0.00 0.00 0.00 3.02
531 1384 1.571460 CCACTCGTGCTTGCAGAAC 59.429 57.895 0.00 0.00 0.00 3.01
532 1385 1.159713 CCACTCGTGCTTGCAGAACA 61.160 55.000 0.00 0.00 0.00 3.18
533 1386 0.041839 CACTCGTGCTTGCAGAACAC 60.042 55.000 0.00 5.92 0.00 3.32
536 1389 2.050985 GTGCTTGCAGAACACGGC 60.051 61.111 0.00 0.00 0.00 5.68
537 1390 2.515757 TGCTTGCAGAACACGGCA 60.516 55.556 0.00 0.00 38.46 5.69
538 1391 2.253452 GCTTGCAGAACACGGCAG 59.747 61.111 0.00 0.00 41.68 4.85
539 1392 2.949106 CTTGCAGAACACGGCAGG 59.051 61.111 0.00 0.00 41.68 4.85
540 1393 3.259425 CTTGCAGAACACGGCAGGC 62.259 63.158 0.00 0.00 41.68 4.85
543 1396 4.641645 CAGAACACGGCAGGCCCA 62.642 66.667 0.00 0.00 0.00 5.36
544 1397 3.884774 AGAACACGGCAGGCCCAA 61.885 61.111 0.00 0.00 0.00 4.12
545 1398 3.670377 GAACACGGCAGGCCCAAC 61.670 66.667 0.00 0.00 0.00 3.77
568 1421 2.208074 CGCGAGGTAGAAGAATGCG 58.792 57.895 0.00 0.00 38.04 4.73
569 1422 1.209275 CGCGAGGTAGAAGAATGCGG 61.209 60.000 0.00 0.00 40.36 5.69
570 1423 0.876342 GCGAGGTAGAAGAATGCGGG 60.876 60.000 0.00 0.00 0.00 6.13
571 1424 0.876342 CGAGGTAGAAGAATGCGGGC 60.876 60.000 0.00 0.00 0.00 6.13
572 1425 0.533085 GAGGTAGAAGAATGCGGGCC 60.533 60.000 0.00 0.00 0.00 5.80
573 1426 1.223487 GGTAGAAGAATGCGGGCCA 59.777 57.895 4.39 0.00 0.00 5.36
574 1427 0.815615 GGTAGAAGAATGCGGGCCAG 60.816 60.000 4.39 0.00 0.00 4.85
575 1428 1.153168 TAGAAGAATGCGGGCCAGC 60.153 57.895 22.10 22.10 37.71 4.85
576 1429 2.923426 TAGAAGAATGCGGGCCAGCG 62.923 60.000 23.18 10.38 40.67 5.18
577 1430 4.408821 AAGAATGCGGGCCAGCGA 62.409 61.111 23.18 12.53 40.67 4.93
578 1431 3.918253 AAGAATGCGGGCCAGCGAA 62.918 57.895 23.18 6.89 40.67 4.70
579 1432 3.880846 GAATGCGGGCCAGCGAAG 61.881 66.667 23.18 0.00 40.67 3.79
1002 1855 4.838152 CTCGCCCCCACGACCATG 62.838 72.222 0.00 0.00 37.09 3.66
1322 2187 1.075601 TTGGGTGAGCTTTCCCTGAT 58.924 50.000 22.11 0.00 43.74 2.90
1449 2314 1.287425 GCGGTATGGCTCAGTACAAC 58.713 55.000 0.00 0.00 0.00 3.32
1475 2340 3.435671 GTGTGGCACTTGTACTGTAATCC 59.564 47.826 19.83 0.00 0.00 3.01
1585 2450 3.803368 GCTAAATGTGGTGGCAAAAGCTT 60.803 43.478 0.00 0.00 0.00 3.74
1672 2537 6.065976 TCAGATCACCATTCACCTGTTATT 57.934 37.500 0.00 0.00 0.00 1.40
1801 2666 6.721318 TGGACTCTTTAAGCATACAGGATTT 58.279 36.000 0.00 0.00 0.00 2.17
1878 2743 7.672239 TCCTTGGTGCCTAATTACAAAGTAATT 59.328 33.333 16.52 16.52 0.00 1.40
2116 3001 6.360370 TCAGAAAGCTTATGAGGTACTTGT 57.640 37.500 0.00 0.00 41.55 3.16
2148 3033 2.733227 GCGTGGATGCTCAATTTCAAGG 60.733 50.000 0.00 0.00 0.00 3.61
2295 3185 1.963515 GTTCCTTTGACTGCCAATGGT 59.036 47.619 0.00 0.00 45.38 3.55
2409 3303 4.865776 TGTTTGCCTACACTATTTGCAAC 58.134 39.130 0.00 0.00 41.21 4.17
2410 3304 4.339530 TGTTTGCCTACACTATTTGCAACA 59.660 37.500 0.00 0.00 41.21 3.33
2419 3313 6.389830 ACACTATTTGCAACAGTCATCAAA 57.610 33.333 9.43 0.00 33.64 2.69
2447 3350 9.554395 AATTAAAACACCAACCTTTTATTCTGG 57.446 29.630 0.00 0.00 0.00 3.86
2499 3402 8.408601 ACATGGAATCTACATTGATAACTTTGC 58.591 33.333 0.00 0.00 0.00 3.68
2709 3620 4.252878 CAGTTTGGTGGTTTTGCTTCTTT 58.747 39.130 0.00 0.00 0.00 2.52
2770 3684 5.582550 TGACTCAGCAGAAATAGTATCGTG 58.417 41.667 0.00 0.00 0.00 4.35
2780 3694 7.011482 GCAGAAATAGTATCGTGTGGAAAATCT 59.989 37.037 0.00 0.00 0.00 2.40
2790 3704 6.668323 TCGTGTGGAAAATCTTTTCATCTTC 58.332 36.000 15.24 1.21 46.34 2.87
2806 3720 5.460646 TCATCTTCGCAATTTTCAGTTTCC 58.539 37.500 0.00 0.00 0.00 3.13
2937 3851 4.080863 ACCCTCTTATGTCACAGATGGTTC 60.081 45.833 5.45 0.00 35.21 3.62
2938 3852 4.446371 CCTCTTATGTCACAGATGGTTCC 58.554 47.826 0.00 0.00 0.00 3.62
2939 3853 4.163078 CCTCTTATGTCACAGATGGTTCCT 59.837 45.833 0.00 0.00 0.00 3.36
2940 3854 5.344743 TCTTATGTCACAGATGGTTCCTC 57.655 43.478 0.00 0.00 0.00 3.71
2941 3855 5.026121 TCTTATGTCACAGATGGTTCCTCT 58.974 41.667 0.00 0.00 0.00 3.69
2942 3856 3.902881 ATGTCACAGATGGTTCCTCTC 57.097 47.619 0.00 0.00 0.00 3.20
2943 3857 2.894731 TGTCACAGATGGTTCCTCTCT 58.105 47.619 0.00 0.00 0.00 3.10
2944 3858 2.828520 TGTCACAGATGGTTCCTCTCTC 59.171 50.000 0.00 0.00 0.00 3.20
2945 3859 3.096092 GTCACAGATGGTTCCTCTCTCT 58.904 50.000 0.00 0.00 0.00 3.10
2946 3860 3.130340 GTCACAGATGGTTCCTCTCTCTC 59.870 52.174 0.00 0.00 0.00 3.20
3090 4022 7.908827 AGCATATTTAATCTGATCTCTGCTG 57.091 36.000 0.00 0.00 35.13 4.41
3202 4134 0.175760 TTGACCGTCATAGCTCTGCC 59.824 55.000 1.09 0.00 0.00 4.85
3334 4266 4.116961 TGCGAAACCTGCAGTATGTATAC 58.883 43.478 13.81 0.00 39.31 1.47
3350 4282 8.131100 AGTATGTATACGCACGTGTATTTTACT 58.869 33.333 18.38 11.00 38.28 2.24
3398 4330 7.955864 GGTAACTAAATGTCGTCTTTGAATCAC 59.044 37.037 0.00 0.00 0.00 3.06
3508 4440 4.101119 AGGGGTTCTGGATATGTTAGTTCG 59.899 45.833 0.00 0.00 0.00 3.95
3512 4444 5.163437 GGTTCTGGATATGTTAGTTCGTCCT 60.163 44.000 0.00 0.00 0.00 3.85
3519 4451 1.899814 TGTTAGTTCGTCCTCCAGCAT 59.100 47.619 0.00 0.00 0.00 3.79
3679 4617 6.341316 GCAAGACTGTAAAGGTGAGATATCA 58.659 40.000 5.32 0.00 0.00 2.15
3721 4679 3.127548 AGCTTTCCGATGTAGCACATTTG 59.872 43.478 0.00 1.27 39.27 2.32
3734 4692 1.888512 CACATTTGCTGTACCAAGCCT 59.111 47.619 2.98 0.00 42.83 4.58
3740 4698 1.075374 TGCTGTACCAAGCCTCCAATT 59.925 47.619 2.98 0.00 42.83 2.32
3748 4706 6.667414 TGTACCAAGCCTCCAATTAATCATTT 59.333 34.615 0.00 0.00 0.00 2.32
3964 4923 9.646336 GTGTACTTTTTAGTGTGTACTGATTTG 57.354 33.333 0.00 0.00 37.78 2.32
3994 4953 6.620877 ACCAGGTGACTAGAATAAATGTCA 57.379 37.500 0.00 0.00 40.21 3.58
4038 4997 9.277783 GCATCTTCCTATCATACATTACTGTTT 57.722 33.333 0.00 0.00 36.79 2.83
4070 5029 8.408601 GTGAATGTTGCTTCCTATCATACATTT 58.591 33.333 0.00 0.00 35.55 2.32
4311 5270 0.682292 TGACATCGCTTGTACCCACA 59.318 50.000 0.00 0.00 39.18 4.17
4478 5437 1.951602 TCAGTCGTCTTCTCGTTTGGA 59.048 47.619 0.00 0.00 0.00 3.53
4490 5449 5.418310 TCTCGTTTGGAATTTCTGTTGTC 57.582 39.130 0.00 0.00 0.00 3.18
4693 5652 6.238842 GGGACAGTTAAAGGAAAGTGGTAAAC 60.239 42.308 0.00 0.00 34.66 2.01
4718 5677 3.518992 TCCCCCTTCTTCGAAATTGTT 57.481 42.857 0.00 0.00 0.00 2.83
4836 5795 4.459852 AATGCTATTAGCTTCCCCATGT 57.540 40.909 16.29 0.00 42.97 3.21
5204 6170 6.248433 TCTGAGAGGAAAAGGTAAATTGCAT 58.752 36.000 0.00 0.00 0.00 3.96
5273 6239 9.635520 GCATATACGGTGACATAGTTTATAGTT 57.364 33.333 0.00 0.00 0.00 2.24
5458 6424 4.381411 AGAGACAAAGTTTGTAGCACCTC 58.619 43.478 20.90 19.99 45.52 3.85
5539 6505 6.389906 AGAAAATGCCAGGATTCGTTTTTAG 58.610 36.000 0.00 0.00 33.17 1.85
5606 6572 9.701098 ATGATTTATGTATGGCATCACATTTTC 57.299 29.630 20.07 15.88 38.94 2.29
5607 6573 8.693625 TGATTTATGTATGGCATCACATTTTCA 58.306 29.630 20.07 17.31 38.94 2.69
5608 6574 9.188588 GATTTATGTATGGCATCACATTTTCAG 57.811 33.333 20.07 0.00 38.94 3.02
5609 6575 7.878547 TTATGTATGGCATCACATTTTCAGA 57.121 32.000 20.07 6.13 38.94 3.27
5651 6627 6.071391 AGGAAAACGGAATAACTGATGCATTT 60.071 34.615 0.00 0.00 0.00 2.32
5699 6677 3.840831 TCCTGCAGGAATCAAGACG 57.159 52.632 33.41 2.70 42.18 4.18
5912 6890 0.251341 ACAAGGATGCGGAAAAGGCT 60.251 50.000 0.00 0.00 0.00 4.58
5918 6896 2.985847 GCGGAAAAGGCTGCTGGT 60.986 61.111 0.00 0.00 37.20 4.00
6120 7100 3.555966 GGAAATAATGCTACACCCTGCT 58.444 45.455 0.00 0.00 0.00 4.24
6234 7224 2.108976 CACACGGTGCCACTGTCT 59.891 61.111 6.28 0.00 35.04 3.41
6252 7242 3.056179 TGTCTTATTCATGTCGCTGGTCA 60.056 43.478 0.00 0.00 0.00 4.02
6258 7248 1.827344 TCATGTCGCTGGTCAGAAGAT 59.173 47.619 1.65 0.00 0.00 2.40
6263 7253 2.808543 GTCGCTGGTCAGAAGATTTTGT 59.191 45.455 1.65 0.00 0.00 2.83
6270 7260 4.523943 TGGTCAGAAGATTTTGTCATTGGG 59.476 41.667 0.00 0.00 0.00 4.12
6290 7280 3.507622 GGGAACAATTTTGCTAGCTCTGT 59.492 43.478 17.23 8.82 0.00 3.41
6296 7286 5.979517 ACAATTTTGCTAGCTCTGTTTTCAC 59.020 36.000 17.23 0.00 0.00 3.18
6299 7289 3.475566 TGCTAGCTCTGTTTTCACTGT 57.524 42.857 17.23 0.00 0.00 3.55
6312 7302 8.141268 TCTGTTTTCACTGTTTTTGAGAGTTTT 58.859 29.630 0.00 0.00 27.48 2.43
6320 7310 9.023967 CACTGTTTTTGAGAGTTTTGATTTAGG 57.976 33.333 0.00 0.00 27.48 2.69
6321 7311 8.966868 ACTGTTTTTGAGAGTTTTGATTTAGGA 58.033 29.630 0.00 0.00 0.00 2.94
6322 7312 9.237846 CTGTTTTTGAGAGTTTTGATTTAGGAC 57.762 33.333 0.00 0.00 0.00 3.85
6323 7313 8.744652 TGTTTTTGAGAGTTTTGATTTAGGACA 58.255 29.630 0.00 0.00 0.00 4.02
6324 7314 9.237846 GTTTTTGAGAGTTTTGATTTAGGACAG 57.762 33.333 0.00 0.00 0.00 3.51
6326 7316 7.496529 TTGAGAGTTTTGATTTAGGACAGTG 57.503 36.000 0.00 0.00 0.00 3.66
6337 7327 2.564721 GGACAGTGTTTGCTGGGCC 61.565 63.158 0.00 0.00 40.59 5.80
6408 7398 6.491403 ACTTGCTTGGTCTTCTGTAAAATCAT 59.509 34.615 0.00 0.00 0.00 2.45
6410 7400 7.288810 TGCTTGGTCTTCTGTAAAATCATTT 57.711 32.000 0.00 0.00 0.00 2.32
6412 7402 8.203485 TGCTTGGTCTTCTGTAAAATCATTTTT 58.797 29.630 0.00 0.00 38.56 1.94
6436 7426 4.222366 TGTTGGCTGCATTTTCATGGATAA 59.778 37.500 0.50 0.00 28.97 1.75
6437 7427 4.659111 TGGCTGCATTTTCATGGATAAG 57.341 40.909 0.50 0.00 28.97 1.73
6445 7456 7.430441 TGCATTTTCATGGATAAGATGTCATG 58.570 34.615 0.00 0.00 38.54 3.07
6477 7488 4.670896 AGTTTTGCCAATTTGCAGTAGT 57.329 36.364 4.22 0.00 43.21 2.73
6480 7491 6.758254 AGTTTTGCCAATTTGCAGTAGTAAT 58.242 32.000 4.22 0.00 43.21 1.89
6491 7502 5.371115 TGCAGTAGTAATTGTGCCTTTTC 57.629 39.130 0.00 0.00 34.91 2.29
6497 7508 9.507280 CAGTAGTAATTGTGCCTTTTCATATTG 57.493 33.333 0.00 0.00 0.00 1.90
6518 7529 4.490743 TGCAATTGAGCAATGTTGAGATG 58.509 39.130 10.34 0.00 42.46 2.90
6519 7530 4.218852 TGCAATTGAGCAATGTTGAGATGA 59.781 37.500 10.34 0.00 42.46 2.92
6520 7531 4.798907 GCAATTGAGCAATGTTGAGATGAG 59.201 41.667 10.34 0.00 0.00 2.90
6521 7532 4.634184 ATTGAGCAATGTTGAGATGAGC 57.366 40.909 0.00 0.00 0.00 4.26
6522 7533 3.062122 TGAGCAATGTTGAGATGAGCA 57.938 42.857 0.00 0.00 0.00 4.26
6523 7534 3.414269 TGAGCAATGTTGAGATGAGCAA 58.586 40.909 0.00 0.00 0.00 3.91
6524 7535 3.189910 TGAGCAATGTTGAGATGAGCAAC 59.810 43.478 0.00 0.00 44.40 4.17
6533 7544 5.522456 GTTGAGATGAGCAACATTGTTTCA 58.478 37.500 0.00 2.91 43.77 2.69
6534 7545 5.771153 TGAGATGAGCAACATTGTTTCAA 57.229 34.783 7.74 0.00 39.56 2.69
6535 7546 6.146601 TGAGATGAGCAACATTGTTTCAAA 57.853 33.333 7.74 0.00 39.56 2.69
6536 7547 6.571605 TGAGATGAGCAACATTGTTTCAAAA 58.428 32.000 7.74 0.00 39.56 2.44
6537 7548 7.040494 TGAGATGAGCAACATTGTTTCAAAAA 58.960 30.769 7.74 0.00 39.56 1.94
6538 7549 7.711772 TGAGATGAGCAACATTGTTTCAAAAAT 59.288 29.630 7.74 0.00 39.56 1.82
6539 7550 9.195411 GAGATGAGCAACATTGTTTCAAAAATA 57.805 29.630 7.74 0.00 39.56 1.40
6540 7551 9.545105 AGATGAGCAACATTGTTTCAAAAATAA 57.455 25.926 7.74 0.00 39.56 1.40
6578 7589 0.675633 GCAACATGAACAGGCCTTGT 59.324 50.000 0.00 0.48 43.45 3.16
6589 7600 0.314935 AGGCCTTGTTGTTGCAATCG 59.685 50.000 0.00 0.00 0.00 3.34
6602 7613 1.135431 TGCAATCGTTGTAATGGCTGC 60.135 47.619 0.00 0.00 0.00 5.25
6609 7620 2.419673 CGTTGTAATGGCTGCATTCTCA 59.580 45.455 0.50 0.00 0.00 3.27
6618 7629 5.245584 TGGCTGCATTCTCATGGATATTA 57.754 39.130 0.50 0.00 28.97 0.98
6627 7638 7.415318 GCATTCTCATGGATATTAATGCTCCTG 60.415 40.741 15.85 12.38 43.53 3.86
6632 7643 4.645535 TGGATATTAATGCTCCTGACTGC 58.354 43.478 15.85 0.00 0.00 4.40
6634 7645 4.453819 GGATATTAATGCTCCTGACTGCAC 59.546 45.833 10.25 0.00 42.26 4.57
6635 7646 3.641434 ATTAATGCTCCTGACTGCACT 57.359 42.857 0.00 0.00 42.26 4.40
6652 7663 3.812609 TGCACTTTCTTGTAATTCAGCGA 59.187 39.130 0.00 0.00 0.00 4.93
6766 7824 7.764443 TCTCCTCCTTGTACGAGAATAATTTTG 59.236 37.037 12.02 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.750888 GGAGATGACGGTTTGCGCC 61.751 63.158 4.18 0.00 0.00 6.53
47 48 1.827969 CTTGAGGAGGAGATGACGGTT 59.172 52.381 0.00 0.00 0.00 4.44
104 105 4.160439 ACAGCGGAATCTGACTTCAAGATA 59.840 41.667 0.00 0.00 37.51 1.98
109 110 1.895798 AGACAGCGGAATCTGACTTCA 59.104 47.619 0.00 0.00 36.06 3.02
147 148 3.679389 AGCTTTTCACCGATGAACTCAT 58.321 40.909 0.00 0.00 44.66 2.90
148 149 3.126001 AGCTTTTCACCGATGAACTCA 57.874 42.857 0.00 0.00 44.66 3.41
155 156 0.546598 CCCCCTAGCTTTTCACCGAT 59.453 55.000 0.00 0.00 0.00 4.18
240 241 2.039405 CTATGGCCCACCCTCCCT 60.039 66.667 0.00 0.00 33.59 4.20
260 261 2.480416 GCGGAATCTGACTTCGAGATGT 60.480 50.000 0.00 0.00 30.30 3.06
261 262 2.123342 GCGGAATCTGACTTCGAGATG 58.877 52.381 0.00 0.00 30.30 2.90
262 263 2.028130 AGCGGAATCTGACTTCGAGAT 58.972 47.619 0.00 0.00 0.00 2.75
263 264 1.133216 CAGCGGAATCTGACTTCGAGA 59.867 52.381 0.00 0.00 36.19 4.04
264 265 1.135257 ACAGCGGAATCTGACTTCGAG 60.135 52.381 0.00 0.00 37.51 4.04
265 266 0.888619 ACAGCGGAATCTGACTTCGA 59.111 50.000 0.00 0.00 37.51 3.71
266 267 1.135257 AGACAGCGGAATCTGACTTCG 60.135 52.381 0.00 0.00 36.06 3.79
267 268 2.266554 CAGACAGCGGAATCTGACTTC 58.733 52.381 0.00 0.00 44.32 3.01
268 269 1.620819 ACAGACAGCGGAATCTGACTT 59.379 47.619 10.66 0.00 44.32 3.01
269 270 1.203523 GACAGACAGCGGAATCTGACT 59.796 52.381 10.66 0.00 44.32 3.41
270 271 1.067565 TGACAGACAGCGGAATCTGAC 60.068 52.381 10.66 5.91 44.32 3.51
271 272 1.256812 TGACAGACAGCGGAATCTGA 58.743 50.000 10.66 0.00 44.32 3.27
272 273 1.931841 CATGACAGACAGCGGAATCTG 59.068 52.381 3.45 3.45 46.49 2.90
273 274 1.552337 ACATGACAGACAGCGGAATCT 59.448 47.619 0.00 0.00 0.00 2.40
275 276 1.737029 CGACATGACAGACAGCGGAAT 60.737 52.381 0.00 0.00 0.00 3.01
276 277 0.388520 CGACATGACAGACAGCGGAA 60.389 55.000 0.00 0.00 0.00 4.30
277 278 1.212751 CGACATGACAGACAGCGGA 59.787 57.895 0.00 0.00 0.00 5.54
278 279 1.807165 CCGACATGACAGACAGCGG 60.807 63.158 0.00 0.00 36.14 5.52
279 280 1.073216 GACCGACATGACAGACAGCG 61.073 60.000 0.00 0.00 0.00 5.18
280 281 0.244994 AGACCGACATGACAGACAGC 59.755 55.000 0.00 0.00 0.00 4.40
281 282 1.541588 TCAGACCGACATGACAGACAG 59.458 52.381 0.00 0.00 0.00 3.51
282 283 1.616159 TCAGACCGACATGACAGACA 58.384 50.000 0.00 0.00 0.00 3.41
287 288 1.060713 CACGTTCAGACCGACATGAC 58.939 55.000 0.00 0.00 0.00 3.06
289 290 0.784178 CACACGTTCAGACCGACATG 59.216 55.000 0.00 0.00 0.00 3.21
290 291 0.319555 CCACACGTTCAGACCGACAT 60.320 55.000 0.00 0.00 0.00 3.06
291 292 1.066752 CCACACGTTCAGACCGACA 59.933 57.895 0.00 0.00 0.00 4.35
295 319 1.612463 AGTAGTCCACACGTTCAGACC 59.388 52.381 5.27 0.00 0.00 3.85
297 321 3.382227 TGAAAGTAGTCCACACGTTCAGA 59.618 43.478 0.00 0.00 38.76 3.27
299 323 3.491964 CCTGAAAGTAGTCCACACGTTCA 60.492 47.826 4.30 4.30 40.49 3.18
313 337 2.154462 CTCAAACGGATGCCTGAAAGT 58.846 47.619 0.00 0.00 0.00 2.66
315 339 1.879380 CACTCAAACGGATGCCTGAAA 59.121 47.619 0.00 0.00 0.00 2.69
392 416 4.387598 AGCATCTACAAGCCATGAATCTC 58.612 43.478 0.00 0.00 0.00 2.75
463 1316 0.693622 TTGTAGCCCGAAATGGTGGA 59.306 50.000 0.00 0.00 35.15 4.02
464 1317 1.201414 GTTTGTAGCCCGAAATGGTGG 59.799 52.381 0.00 0.00 35.15 4.61
465 1318 1.135803 CGTTTGTAGCCCGAAATGGTG 60.136 52.381 0.00 0.00 35.15 4.17
466 1319 1.161843 CGTTTGTAGCCCGAAATGGT 58.838 50.000 0.00 0.00 35.15 3.55
467 1320 0.179174 GCGTTTGTAGCCCGAAATGG 60.179 55.000 0.00 0.00 37.55 3.16
468 1321 3.306206 GCGTTTGTAGCCCGAAATG 57.694 52.632 0.00 0.00 0.00 2.32
476 1329 2.106683 ATGCCGAGGCGTTTGTAGC 61.107 57.895 9.78 0.00 45.51 3.58
477 1330 1.705337 CCATGCCGAGGCGTTTGTAG 61.705 60.000 6.03 0.00 45.51 2.74
478 1331 1.743623 CCATGCCGAGGCGTTTGTA 60.744 57.895 6.03 0.00 45.51 2.41
479 1332 3.055719 CCATGCCGAGGCGTTTGT 61.056 61.111 6.03 0.00 45.51 2.83
480 1333 3.814268 CCCATGCCGAGGCGTTTG 61.814 66.667 6.03 5.43 45.51 2.93
491 1344 3.804638 ATAGCTGGCTGGCCCATGC 62.805 63.158 9.28 10.50 44.33 4.06
492 1345 1.602888 GATAGCTGGCTGGCCCATG 60.603 63.158 9.28 1.07 44.33 3.66
493 1346 2.838467 GGATAGCTGGCTGGCCCAT 61.838 63.158 9.28 0.00 44.33 4.00
494 1347 3.492353 GGATAGCTGGCTGGCCCA 61.492 66.667 9.28 0.00 42.79 5.36
495 1348 4.277009 GGGATAGCTGGCTGGCCC 62.277 72.222 15.22 15.22 34.96 5.80
496 1349 4.277009 GGGGATAGCTGGCTGGCC 62.277 72.222 4.43 4.43 0.00 5.36
497 1350 4.277009 GGGGGATAGCTGGCTGGC 62.277 72.222 5.25 0.00 0.00 4.85
498 1351 2.773918 TGGGGGATAGCTGGCTGG 60.774 66.667 5.25 0.00 0.00 4.85
499 1352 2.049627 GAGTGGGGGATAGCTGGCTG 62.050 65.000 5.25 0.00 0.00 4.85
500 1353 1.768077 GAGTGGGGGATAGCTGGCT 60.768 63.158 0.00 0.00 0.00 4.75
501 1354 2.832498 GAGTGGGGGATAGCTGGC 59.168 66.667 0.00 0.00 0.00 4.85
502 1355 1.762460 ACGAGTGGGGGATAGCTGG 60.762 63.158 0.00 0.00 0.00 4.85
503 1356 1.443407 CACGAGTGGGGGATAGCTG 59.557 63.158 0.00 0.00 0.00 4.24
504 1357 2.435693 GCACGAGTGGGGGATAGCT 61.436 63.158 5.32 0.00 0.00 3.32
505 1358 1.972660 AAGCACGAGTGGGGGATAGC 61.973 60.000 5.32 0.00 0.00 2.97
506 1359 0.179073 CAAGCACGAGTGGGGGATAG 60.179 60.000 5.32 0.00 0.00 2.08
507 1360 1.904771 CAAGCACGAGTGGGGGATA 59.095 57.895 5.32 0.00 0.00 2.59
508 1361 2.671070 CAAGCACGAGTGGGGGAT 59.329 61.111 5.32 0.00 0.00 3.85
509 1362 4.329545 GCAAGCACGAGTGGGGGA 62.330 66.667 5.32 0.00 0.00 4.81
510 1363 4.641645 TGCAAGCACGAGTGGGGG 62.642 66.667 5.32 0.00 0.00 5.40
511 1364 3.052082 CTGCAAGCACGAGTGGGG 61.052 66.667 5.32 0.00 0.00 4.96
512 1365 1.597854 TTCTGCAAGCACGAGTGGG 60.598 57.895 5.32 0.00 0.00 4.61
513 1366 1.159713 TGTTCTGCAAGCACGAGTGG 61.160 55.000 5.32 0.00 30.59 4.00
514 1367 0.041839 GTGTTCTGCAAGCACGAGTG 60.042 55.000 0.00 0.00 30.59 3.51
515 1368 2.311294 GTGTTCTGCAAGCACGAGT 58.689 52.632 0.00 0.00 30.59 4.18
519 1372 2.050985 GCCGTGTTCTGCAAGCAC 60.051 61.111 0.00 5.25 0.00 4.40
520 1373 2.515757 TGCCGTGTTCTGCAAGCA 60.516 55.556 0.00 0.00 36.61 3.91
521 1374 2.253452 CTGCCGTGTTCTGCAAGC 59.747 61.111 0.00 0.00 36.98 4.01
522 1375 2.949106 CCTGCCGTGTTCTGCAAG 59.051 61.111 0.00 0.00 36.98 4.01
523 1376 3.286751 GCCTGCCGTGTTCTGCAA 61.287 61.111 0.00 0.00 36.98 4.08
526 1379 4.641645 TGGGCCTGCCGTGTTCTG 62.642 66.667 4.53 0.00 36.85 3.02
527 1380 3.884774 TTGGGCCTGCCGTGTTCT 61.885 61.111 4.53 0.00 36.85 3.01
528 1381 3.670377 GTTGGGCCTGCCGTGTTC 61.670 66.667 4.53 0.00 36.85 3.18
545 1398 4.570663 CTTCTACCTCGCGGCCCG 62.571 72.222 6.13 0.00 38.61 6.13
546 1399 2.029307 ATTCTTCTACCTCGCGGCCC 62.029 60.000 6.13 0.00 0.00 5.80
547 1400 0.876342 CATTCTTCTACCTCGCGGCC 60.876 60.000 6.13 0.00 0.00 6.13
548 1401 1.491505 GCATTCTTCTACCTCGCGGC 61.492 60.000 6.13 0.00 0.00 6.53
549 1402 1.209275 CGCATTCTTCTACCTCGCGG 61.209 60.000 6.13 0.00 37.72 6.46
550 1403 1.209275 CCGCATTCTTCTACCTCGCG 61.209 60.000 0.00 0.00 40.83 5.87
551 1404 0.876342 CCCGCATTCTTCTACCTCGC 60.876 60.000 0.00 0.00 0.00 5.03
552 1405 0.876342 GCCCGCATTCTTCTACCTCG 60.876 60.000 0.00 0.00 0.00 4.63
553 1406 0.533085 GGCCCGCATTCTTCTACCTC 60.533 60.000 0.00 0.00 0.00 3.85
554 1407 1.271840 TGGCCCGCATTCTTCTACCT 61.272 55.000 0.00 0.00 0.00 3.08
555 1408 0.815615 CTGGCCCGCATTCTTCTACC 60.816 60.000 0.00 0.00 0.00 3.18
556 1409 1.440145 GCTGGCCCGCATTCTTCTAC 61.440 60.000 15.08 0.00 0.00 2.59
557 1410 1.153168 GCTGGCCCGCATTCTTCTA 60.153 57.895 15.08 0.00 0.00 2.10
558 1411 2.439156 GCTGGCCCGCATTCTTCT 60.439 61.111 15.08 0.00 0.00 2.85
559 1412 3.880846 CGCTGGCCCGCATTCTTC 61.881 66.667 19.88 0.00 0.00 2.87
560 1413 3.918253 TTCGCTGGCCCGCATTCTT 62.918 57.895 19.88 0.00 0.00 2.52
561 1414 4.408821 TTCGCTGGCCCGCATTCT 62.409 61.111 19.88 0.00 0.00 2.40
562 1415 3.880846 CTTCGCTGGCCCGCATTC 61.881 66.667 19.88 0.00 0.00 2.67
985 1838 4.838152 CATGGTCGTGGGGGCGAG 62.838 72.222 0.00 0.00 41.85 5.03
1240 2105 1.807573 GAAGAACCTGCTCGGCGAG 60.808 63.158 31.40 31.40 35.61 5.03
1322 2187 4.544047 TGCACGCAGCCACAGACA 62.544 61.111 0.00 0.00 44.83 3.41
1351 2216 2.118732 TAGTCCCTCACCGCCACA 59.881 61.111 0.00 0.00 0.00 4.17
1449 2314 0.108585 AGTACAAGTGCCACACCCAG 59.891 55.000 0.00 0.00 34.49 4.45
1475 2340 7.426410 TCAAGTTCAGTCTTAGACAACACTAG 58.574 38.462 15.23 0.14 34.60 2.57
1585 2450 7.924288 GAGCGATGATTCGATTTCTAAGCACA 61.924 42.308 0.00 0.00 45.41 4.57
1608 2473 7.550551 ACACATGATGAACTAATAACAGGTGAG 59.449 37.037 14.61 0.00 40.67 3.51
1672 2537 7.001674 ACAAAACTCAGACAATATTACCACCA 58.998 34.615 0.00 0.00 0.00 4.17
1801 2666 3.798515 TCCTAAGGCCCTTTACTTCTGA 58.201 45.455 0.00 0.00 0.00 3.27
1878 2743 9.166173 GCCACAGATATGATATAATAACTTGCA 57.834 33.333 0.00 0.00 0.00 4.08
1927 2792 9.809395 ATGAACTATCTTACAGTGTAGCCTATA 57.191 33.333 2.68 0.69 0.00 1.31
1928 2793 8.713708 ATGAACTATCTTACAGTGTAGCCTAT 57.286 34.615 2.68 0.00 0.00 2.57
1929 2794 9.064706 GTATGAACTATCTTACAGTGTAGCCTA 57.935 37.037 2.68 0.00 36.62 3.93
2181 3070 5.844004 AGTCTACAGAGAAGAAGCGAAAAA 58.156 37.500 0.00 0.00 31.96 1.94
2409 3303 8.327429 GTTGGTGTTTTAATTGTTTGATGACTG 58.673 33.333 0.00 0.00 0.00 3.51
2410 3304 7.494298 GGTTGGTGTTTTAATTGTTTGATGACT 59.506 33.333 0.00 0.00 0.00 3.41
2444 3347 1.475682 GATTCTGGCCAAGCTTTCCAG 59.524 52.381 27.18 27.18 46.60 3.86
2446 3349 1.747924 GAGATTCTGGCCAAGCTTTCC 59.252 52.381 7.01 1.34 0.00 3.13
2447 3350 2.440409 TGAGATTCTGGCCAAGCTTTC 58.560 47.619 7.01 2.96 0.00 2.62
2663 3574 8.625786 TGGGACCTAAAATAAAAACAGTAGAC 57.374 34.615 0.00 0.00 0.00 2.59
2709 3620 9.906660 AATAATGCTAAAAACGTGAGATTTGAA 57.093 25.926 0.00 0.00 36.17 2.69
2752 3663 4.682787 TCCACACGATACTATTTCTGCTG 58.317 43.478 0.00 0.00 0.00 4.41
2770 3684 5.460646 TGCGAAGATGAAAAGATTTTCCAC 58.539 37.500 13.89 8.74 44.48 4.02
2780 3694 7.042791 GGAAACTGAAAATTGCGAAGATGAAAA 60.043 33.333 0.00 0.00 0.00 2.29
2790 3704 2.584791 CTCCGGAAACTGAAAATTGCG 58.415 47.619 5.23 0.00 39.64 4.85
2937 3851 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
2938 3852 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2939 3853 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2940 3854 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2941 3855 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2942 3856 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
2943 3857 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
2944 3858 5.564455 CGATGAGAGAGAGAGAGAGAGAGAG 60.564 52.000 0.00 0.00 0.00 3.20
2945 3859 4.279420 CGATGAGAGAGAGAGAGAGAGAGA 59.721 50.000 0.00 0.00 0.00 3.10
2946 3860 4.279420 TCGATGAGAGAGAGAGAGAGAGAG 59.721 50.000 0.00 0.00 0.00 3.20
3073 4005 6.705302 ACAAAGACAGCAGAGATCAGATTAA 58.295 36.000 0.00 0.00 0.00 1.40
3082 4014 2.615447 CAGCAAACAAAGACAGCAGAGA 59.385 45.455 0.00 0.00 0.00 3.10
3090 4022 4.105486 GGAACTTCACAGCAAACAAAGAC 58.895 43.478 0.00 0.00 0.00 3.01
3191 4123 3.490419 GCAATTCAAAGGGCAGAGCTATG 60.490 47.826 3.34 3.34 0.00 2.23
3202 4134 8.819974 GGATTACATGTAATTGCAATTCAAAGG 58.180 33.333 27.28 17.23 38.34 3.11
3334 4266 6.991655 TGGTAAATAGTAAAATACACGTGCG 58.008 36.000 17.22 0.00 0.00 5.34
3398 4330 9.309516 CATGATGTTATCAGAAAAGGGAAAATG 57.690 33.333 0.00 0.00 43.53 2.32
3679 4617 8.863872 AAAGCTGATAGTTGGTATTACAAAGT 57.136 30.769 0.00 0.00 31.17 2.66
3690 4628 3.535561 ACATCGGAAAGCTGATAGTTGG 58.464 45.455 0.00 0.00 38.05 3.77
3721 4679 1.839424 AATTGGAGGCTTGGTACAGC 58.161 50.000 0.00 0.00 42.39 4.40
3740 4698 7.040062 ACGAATGGTCAACTTTCCAAATGATTA 60.040 33.333 0.00 0.00 37.27 1.75
3748 4706 4.517453 CCTTAACGAATGGTCAACTTTCCA 59.483 41.667 0.00 0.00 38.14 3.53
3830 4789 8.814931 TGGTCATCTGGTTGAAAATAAATCAAT 58.185 29.630 0.00 0.00 38.89 2.57
3831 4790 8.187913 TGGTCATCTGGTTGAAAATAAATCAA 57.812 30.769 0.00 0.00 34.56 2.57
3842 4801 5.887598 CCATTTATTCTGGTCATCTGGTTGA 59.112 40.000 0.00 0.00 0.00 3.18
3994 4953 1.735386 GCAGATGCACAGTCTCACAT 58.265 50.000 0.00 0.00 41.59 3.21
4038 4997 9.797642 ATGATAGGAAGCAACATTCACATTATA 57.202 29.630 0.00 0.00 0.00 0.98
4039 4998 8.701908 ATGATAGGAAGCAACATTCACATTAT 57.298 30.769 0.00 0.00 0.00 1.28
4070 5029 7.239763 TCATCAGTCTTCACATTAACCAGTA 57.760 36.000 0.00 0.00 0.00 2.74
4270 5229 3.595190 AAACTTGGAAGCTTACCAGGT 57.405 42.857 19.78 19.78 46.85 4.00
4478 5437 3.057033 GCCATCAGCTGACAACAGAAATT 60.057 43.478 20.97 0.00 46.03 1.82
4667 5626 3.154710 CCACTTTCCTTTAACTGTCCCC 58.845 50.000 0.00 0.00 0.00 4.81
4693 5652 3.350219 TTTCGAAGAAGGGGGATCAAG 57.650 47.619 0.00 0.00 45.90 3.02
4740 5699 2.751166 TCAGTGGCTTAGAACAGAGC 57.249 50.000 0.00 0.00 38.17 4.09
4836 5795 4.365514 TGGTACTTGCTCATTCAAAGGA 57.634 40.909 0.00 0.00 0.00 3.36
4893 5852 0.522180 ACTCGGCACAGAACTACTCG 59.478 55.000 0.00 0.00 0.00 4.18
5204 6170 4.819630 ACGAGCAAAAGATAAACAGTCCAA 59.180 37.500 0.00 0.00 0.00 3.53
5273 6239 6.714810 AGATGTACTTCAACATAAAAGCACCA 59.285 34.615 11.02 0.00 40.17 4.17
5458 6424 4.341366 AGGCAAAAGGAGACAATTTTGG 57.659 40.909 11.16 0.00 43.42 3.28
5539 6505 2.338577 ATGTTCACCTAGATGCCAGC 57.661 50.000 0.00 0.00 0.00 4.85
5668 6645 3.009723 CCTGCAGGACACGATGTTTATT 58.990 45.455 29.88 0.00 37.39 1.40
5699 6677 6.864165 GGTCTCCATATGAATACGAGTTTCTC 59.136 42.308 3.65 0.00 0.00 2.87
5858 6836 3.085533 CTCTTCCTTCTCGAACTCCTCA 58.914 50.000 0.00 0.00 0.00 3.86
5900 6878 2.985282 CCAGCAGCCTTTTCCGCA 60.985 61.111 0.00 0.00 0.00 5.69
5918 6896 0.760567 AGACCGGCTATCCTGATGCA 60.761 55.000 0.00 0.00 0.00 3.96
6120 7100 0.613260 AGAAGAATACGTGCCAGGCA 59.387 50.000 11.22 11.22 35.60 4.75
6234 7224 3.885724 TCTGACCAGCGACATGAATAA 57.114 42.857 0.00 0.00 0.00 1.40
6252 7242 6.729690 TTGTTCCCAATGACAAAATCTTCT 57.270 33.333 0.00 0.00 33.19 2.85
6258 7248 5.884792 AGCAAAATTGTTCCCAATGACAAAA 59.115 32.000 0.00 0.00 40.42 2.44
6263 7253 4.527816 AGCTAGCAAAATTGTTCCCAATGA 59.472 37.500 18.83 0.00 40.42 2.57
6270 7260 6.697019 TGAAAACAGAGCTAGCAAAATTGTTC 59.303 34.615 18.83 11.84 0.00 3.18
6283 7273 5.415701 TCTCAAAAACAGTGAAAACAGAGCT 59.584 36.000 0.00 0.00 0.00 4.09
6290 7280 9.487790 AATCAAAACTCTCAAAAACAGTGAAAA 57.512 25.926 0.00 0.00 0.00 2.29
6296 7286 9.237846 GTCCTAAATCAAAACTCTCAAAAACAG 57.762 33.333 0.00 0.00 0.00 3.16
6299 7289 8.966868 ACTGTCCTAAATCAAAACTCTCAAAAA 58.033 29.630 0.00 0.00 0.00 1.94
6312 7302 3.820467 CCAGCAAACACTGTCCTAAATCA 59.180 43.478 0.00 0.00 35.83 2.57
6318 7308 1.529244 GCCCAGCAAACACTGTCCT 60.529 57.895 0.00 0.00 35.83 3.85
6320 7310 2.908073 CGGCCCAGCAAACACTGTC 61.908 63.158 0.00 0.00 35.83 3.51
6321 7311 2.902423 TTCGGCCCAGCAAACACTGT 62.902 55.000 0.00 0.00 35.83 3.55
6322 7312 2.192861 TTCGGCCCAGCAAACACTG 61.193 57.895 0.00 0.00 37.42 3.66
6323 7313 2.193536 GTTCGGCCCAGCAAACACT 61.194 57.895 0.00 0.00 0.00 3.55
6324 7314 2.335011 GTTCGGCCCAGCAAACAC 59.665 61.111 0.00 0.00 0.00 3.32
6326 7316 4.700365 GCGTTCGGCCCAGCAAAC 62.700 66.667 0.00 0.00 34.80 2.93
6410 7400 3.564644 CCATGAAAATGCAGCCAACAAAA 59.435 39.130 0.00 0.00 0.00 2.44
6412 7402 2.367894 TCCATGAAAATGCAGCCAACAA 59.632 40.909 0.00 0.00 0.00 2.83
6414 7404 2.747396 TCCATGAAAATGCAGCCAAC 57.253 45.000 0.00 0.00 0.00 3.77
6415 7405 4.710865 TCTTATCCATGAAAATGCAGCCAA 59.289 37.500 0.00 0.00 0.00 4.52
6418 7408 5.839621 ACATCTTATCCATGAAAATGCAGC 58.160 37.500 0.00 0.00 0.00 5.25
6421 7411 7.381408 CACATGACATCTTATCCATGAAAATGC 59.619 37.037 0.00 0.00 38.83 3.56
6422 7412 8.410912 ACACATGACATCTTATCCATGAAAATG 58.589 33.333 0.00 0.00 38.83 2.32
6436 7426 9.467258 CAAAACTTTGAATTACACATGACATCT 57.533 29.630 0.00 0.00 40.55 2.90
6437 7427 8.216453 GCAAAACTTTGAATTACACATGACATC 58.784 33.333 0.00 0.00 40.55 3.06
6445 7456 7.165647 GCAAATTGGCAAAACTTTGAATTACAC 59.834 33.333 22.40 5.29 40.55 2.90
6477 7488 8.666573 CAATTGCAATATGAAAAGGCACAATTA 58.333 29.630 13.39 0.00 34.45 1.40
6480 7491 6.228995 TCAATTGCAATATGAAAAGGCACAA 58.771 32.000 13.39 0.00 33.66 3.33
6497 7508 4.740268 TCATCTCAACATTGCTCAATTGC 58.260 39.130 0.00 0.00 0.00 3.56
6549 7560 4.379186 CCTGTTCATGTTGCTCATCTCAAC 60.379 45.833 0.00 0.00 42.91 3.18
6550 7561 3.754850 CCTGTTCATGTTGCTCATCTCAA 59.245 43.478 0.00 0.00 34.09 3.02
6551 7562 3.340928 CCTGTTCATGTTGCTCATCTCA 58.659 45.455 0.00 0.00 34.09 3.27
6552 7563 2.097142 GCCTGTTCATGTTGCTCATCTC 59.903 50.000 0.00 0.00 34.09 2.75
6553 7564 2.089980 GCCTGTTCATGTTGCTCATCT 58.910 47.619 0.00 0.00 34.09 2.90
6554 7565 1.133790 GGCCTGTTCATGTTGCTCATC 59.866 52.381 0.00 0.00 34.09 2.92
6555 7566 1.180029 GGCCTGTTCATGTTGCTCAT 58.820 50.000 0.00 0.00 37.22 2.90
6556 7567 0.111061 AGGCCTGTTCATGTTGCTCA 59.889 50.000 3.11 0.00 0.00 4.26
6578 7589 3.005261 AGCCATTACAACGATTGCAACAA 59.995 39.130 0.00 0.00 0.00 2.83
6589 7600 4.357142 CATGAGAATGCAGCCATTACAAC 58.643 43.478 0.00 0.00 41.60 3.32
6602 7613 7.827729 TCAGGAGCATTAATATCCATGAGAATG 59.172 37.037 17.08 7.99 35.45 2.67
6609 7620 5.221986 TGCAGTCAGGAGCATTAATATCCAT 60.222 40.000 17.08 4.34 35.51 3.41
6618 7629 2.157738 GAAAGTGCAGTCAGGAGCATT 58.842 47.619 0.00 0.00 43.44 3.56
6627 7638 5.149977 GCTGAATTACAAGAAAGTGCAGTC 58.850 41.667 0.00 0.00 0.00 3.51
6632 7643 5.669848 GCTCTCGCTGAATTACAAGAAAGTG 60.670 44.000 0.00 0.00 0.00 3.16
6634 7645 4.389992 TGCTCTCGCTGAATTACAAGAAAG 59.610 41.667 0.00 0.00 36.97 2.62
6635 7646 4.314961 TGCTCTCGCTGAATTACAAGAAA 58.685 39.130 0.00 0.00 36.97 2.52
6652 7663 6.944862 ACAGAATAGGTTCTCAAAATTGCTCT 59.055 34.615 0.00 0.00 42.73 4.09
6766 7824 2.237643 ACCACCAACCAAAAAGGAAACC 59.762 45.455 0.00 0.00 41.22 3.27
6807 7866 1.953017 CATCCTCCTCCTCTACGCG 59.047 63.158 3.53 3.53 0.00 6.01
6813 7872 1.757423 GCCTCAGCATCCTCCTCCTC 61.757 65.000 0.00 0.00 39.53 3.71


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

AutoCloner maintained by Alex Coulton.