Multiple sequence alignment - TraesCS1B01G038000

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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 TraesCS1B01G038000 chr1B 100.000 2966 0 0 1 2966 17886280 17883315 0.000000e+00 5478.0
1 TraesCS1B01G038000 chr1B 91.965 1842 86 25 754 2568 639427563 639429369 0.000000e+00 2525.0
2 TraesCS1B01G038000 chr1B 84.781 1071 95 35 1405 2454 627841195 627842218 0.000000e+00 1013.0
3 TraesCS1B01G038000 chr1B 88.970 689 40 10 754 1413 627828286 627828967 0.000000e+00 819.0
4 TraesCS1B01G038000 chr1B 95.210 334 10 5 2566 2899 639429730 639430057 9.420000e-145 523.0
5 TraesCS1B01G038000 chr1B 77.913 412 66 10 541 936 627827290 627827692 1.780000e-57 233.0
6 TraesCS1B01G038000 chr7A 85.532 1963 177 57 541 2454 692318389 692316485 0.000000e+00 1953.0
7 TraesCS1B01G038000 chr1D 85.950 1879 162 60 541 2382 5447903 5449716 0.000000e+00 1914.0
8 TraesCS1B01G038000 chr1D 80.344 407 44 19 567 947 5446530 5446926 2.910000e-70 276.0
9 TraesCS1B01G038000 chr1D 78.161 261 22 18 98 346 5445506 5445743 1.850000e-27 134.0
10 TraesCS1B01G038000 chr5B 100.000 34 0 0 4 37 545883375 545883342 2.470000e-06 63.9


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 TraesCS1B01G038000 chr1B 17883315 17886280 2965 True 5478.000000 5478 100.0000 1 2966 1 chr1B.!!$R1 2965
1 TraesCS1B01G038000 chr1B 639427563 639430057 2494 False 1524.000000 2525 93.5875 754 2899 2 chr1B.!!$F3 2145
2 TraesCS1B01G038000 chr1B 627841195 627842218 1023 False 1013.000000 1013 84.7810 1405 2454 1 chr1B.!!$F1 1049
3 TraesCS1B01G038000 chr1B 627827290 627828967 1677 False 526.000000 819 83.4415 541 1413 2 chr1B.!!$F2 872
4 TraesCS1B01G038000 chr7A 692316485 692318389 1904 True 1953.000000 1953 85.5320 541 2454 1 chr7A.!!$R1 1913
5 TraesCS1B01G038000 chr1D 5445506 5449716 4210 False 774.666667 1914 81.4850 98 2382 3 chr1D.!!$F1 2284

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
417 477 0.028505 CATTCCGCGGATCTTGCTTG 59.971 55.0 31.56 13.66 0.0 4.01 F
487 547 0.034089 AGGCAGGTGTTAATGGAGGC 60.034 55.0 0.00 0.00 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 3949 0.034477 GATGGTCCACCGGGTTCATT 60.034 55.0 6.32 0.0 39.43 2.57 R
1990 4118 0.106268 TTTCCCTTGGAGCAGCAACA 60.106 50.0 0.00 0.0 31.21 3.33 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
25 26 8.978564 CCCTTTTGCAAACACTTAAAATTTTT 57.021 26.923 12.39 0.00 0.00 1.94
26 27 8.858186 CCCTTTTGCAAACACTTAAAATTTTTG 58.142 29.630 12.39 4.18 0.00 2.44
27 28 9.404348 CCTTTTGCAAACACTTAAAATTTTTGT 57.596 25.926 12.39 4.85 31.19 2.83
29 30 9.950680 TTTTGCAAACACTTAAAATTTTTGTCA 57.049 22.222 12.39 0.20 31.19 3.58
30 31 9.950680 TTTGCAAACACTTAAAATTTTTGTCAA 57.049 22.222 8.05 5.90 31.19 3.18
42 43 7.665561 AAATTTTTGTCAATATTTCGGTGGG 57.334 32.000 0.00 0.00 0.00 4.61
43 44 5.793030 TTTTTGTCAATATTTCGGTGGGT 57.207 34.783 0.00 0.00 0.00 4.51
44 45 5.793030 TTTTGTCAATATTTCGGTGGGTT 57.207 34.783 0.00 0.00 0.00 4.11
45 46 5.793030 TTTGTCAATATTTCGGTGGGTTT 57.207 34.783 0.00 0.00 0.00 3.27
46 47 5.793030 TTGTCAATATTTCGGTGGGTTTT 57.207 34.783 0.00 0.00 0.00 2.43
47 48 5.793030 TGTCAATATTTCGGTGGGTTTTT 57.207 34.783 0.00 0.00 0.00 1.94
77 78 4.370364 CGAATGGAAATTTCGGTGGATT 57.630 40.909 11.95 5.23 41.62 3.01
78 79 4.743493 CGAATGGAAATTTCGGTGGATTT 58.257 39.130 11.95 0.00 41.62 2.17
79 80 5.167845 CGAATGGAAATTTCGGTGGATTTT 58.832 37.500 11.95 0.00 41.62 1.82
80 81 5.637387 CGAATGGAAATTTCGGTGGATTTTT 59.363 36.000 11.95 0.00 41.62 1.94
105 106 7.985634 TTTTTGAGAAGAAGAAATTTCGGTG 57.014 32.000 12.42 0.00 0.00 4.94
128 129 1.668101 GACGGGCCAGAACGAGAGAT 61.668 60.000 10.86 0.00 0.00 2.75
130 131 1.667154 CGGGCCAGAACGAGAGATGA 61.667 60.000 4.39 0.00 0.00 2.92
138 139 5.101628 CCAGAACGAGAGATGAAGAAAGAG 58.898 45.833 0.00 0.00 0.00 2.85
139 140 5.336372 CCAGAACGAGAGATGAAGAAAGAGT 60.336 44.000 0.00 0.00 0.00 3.24
140 141 6.155827 CAGAACGAGAGATGAAGAAAGAGTT 58.844 40.000 0.00 0.00 0.00 3.01
141 142 6.089283 CAGAACGAGAGATGAAGAAAGAGTTG 59.911 42.308 0.00 0.00 0.00 3.16
163 176 0.598680 CGAAGCCGAAGCCCATCTAG 60.599 60.000 0.00 0.00 41.25 2.43
217 230 1.082300 CGTACACAGTCGCACTCGT 60.082 57.895 0.00 0.00 36.96 4.18
218 231 1.058590 CGTACACAGTCGCACTCGTC 61.059 60.000 0.00 0.00 36.96 4.20
219 232 1.058590 GTACACAGTCGCACTCGTCG 61.059 60.000 0.00 0.00 36.96 5.12
223 236 4.702081 AGTCGCACTCGTCGCACC 62.702 66.667 0.00 0.00 36.96 5.01
224 237 4.994201 GTCGCACTCGTCGCACCA 62.994 66.667 0.00 0.00 36.96 4.17
225 238 4.994201 TCGCACTCGTCGCACCAC 62.994 66.667 0.00 0.00 36.96 4.16
237 259 4.389576 CACCACGCGCCTGCTTTC 62.390 66.667 5.73 0.00 39.65 2.62
238 260 4.626081 ACCACGCGCCTGCTTTCT 62.626 61.111 5.73 0.00 39.65 2.52
239 261 3.793144 CCACGCGCCTGCTTTCTC 61.793 66.667 5.73 0.00 39.65 2.87
240 262 2.740055 CACGCGCCTGCTTTCTCT 60.740 61.111 5.73 0.00 39.65 3.10
241 263 2.433318 ACGCGCCTGCTTTCTCTC 60.433 61.111 5.73 0.00 39.65 3.20
253 275 2.666317 CTTTCTCTCCTCCTCCTCCTC 58.334 57.143 0.00 0.00 0.00 3.71
259 281 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
261 283 2.015726 TCCTCCTCCTCCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
346 368 1.228190 GGTACCTCCTCCTCTCCTCT 58.772 60.000 4.06 0.00 0.00 3.69
347 369 1.571936 GGTACCTCCTCCTCTCCTCTT 59.428 57.143 4.06 0.00 0.00 2.85
360 400 0.496382 TCCTCTTTTCTCCCTCCCCA 59.504 55.000 0.00 0.00 0.00 4.96
361 401 1.082879 TCCTCTTTTCTCCCTCCCCAT 59.917 52.381 0.00 0.00 0.00 4.00
414 474 2.329339 GCATTCCGCGGATCTTGC 59.671 61.111 31.56 30.62 0.00 4.01
415 475 2.182842 GCATTCCGCGGATCTTGCT 61.183 57.895 33.41 14.85 0.00 3.91
416 476 1.718757 GCATTCCGCGGATCTTGCTT 61.719 55.000 33.41 13.57 0.00 3.91
417 477 0.028505 CATTCCGCGGATCTTGCTTG 59.971 55.000 31.56 13.66 0.00 4.01
418 478 0.392998 ATTCCGCGGATCTTGCTTGT 60.393 50.000 31.56 3.76 0.00 3.16
419 479 0.605319 TTCCGCGGATCTTGCTTGTT 60.605 50.000 31.56 0.00 0.00 2.83
421 481 0.240945 CCGCGGATCTTGCTTGTTTT 59.759 50.000 24.07 0.00 0.00 2.43
423 483 2.097466 CCGCGGATCTTGCTTGTTTTAT 59.903 45.455 24.07 0.00 0.00 1.40
424 484 3.354397 CGCGGATCTTGCTTGTTTTATC 58.646 45.455 0.00 0.00 0.00 1.75
425 485 3.063997 CGCGGATCTTGCTTGTTTTATCT 59.936 43.478 0.00 0.00 0.00 1.98
426 486 4.270084 CGCGGATCTTGCTTGTTTTATCTA 59.730 41.667 0.00 0.00 0.00 1.98
427 487 5.050091 CGCGGATCTTGCTTGTTTTATCTAT 60.050 40.000 0.00 0.00 0.00 1.98
431 491 7.173907 CGGATCTTGCTTGTTTTATCTATCCAT 59.826 37.037 0.00 0.00 31.51 3.41
432 492 8.510505 GGATCTTGCTTGTTTTATCTATCCATC 58.489 37.037 0.00 0.00 31.51 3.51
434 494 7.345691 TCTTGCTTGTTTTATCTATCCATCCA 58.654 34.615 0.00 0.00 0.00 3.41
435 495 7.500227 TCTTGCTTGTTTTATCTATCCATCCAG 59.500 37.037 0.00 0.00 0.00 3.86
436 496 6.662755 TGCTTGTTTTATCTATCCATCCAGT 58.337 36.000 0.00 0.00 0.00 4.00
438 498 7.283127 TGCTTGTTTTATCTATCCATCCAGTTC 59.717 37.037 0.00 0.00 0.00 3.01
439 499 7.519008 GCTTGTTTTATCTATCCATCCAGTTCG 60.519 40.741 0.00 0.00 0.00 3.95
443 503 1.688735 TCTATCCATCCAGTTCGGCTG 59.311 52.381 0.00 0.00 44.63 4.85
450 510 3.298958 CAGTTCGGCTGGCCTAGA 58.701 61.111 3.32 0.00 41.42 2.43
451 511 1.826024 CAGTTCGGCTGGCCTAGAT 59.174 57.895 3.32 0.00 41.42 1.98
452 512 0.249657 CAGTTCGGCTGGCCTAGATC 60.250 60.000 3.32 0.00 41.42 2.75
454 514 1.756950 TTCGGCTGGCCTAGATCGT 60.757 57.895 3.32 0.00 0.00 3.73
457 517 2.134287 GGCTGGCCTAGATCGTGGA 61.134 63.158 3.32 0.00 0.00 4.02
458 518 1.365633 GCTGGCCTAGATCGTGGAG 59.634 63.158 3.32 2.37 0.00 3.86
459 519 2.045280 CTGGCCTAGATCGTGGAGG 58.955 63.158 3.32 6.46 0.00 4.30
460 520 1.457643 TGGCCTAGATCGTGGAGGG 60.458 63.158 3.32 0.00 0.00 4.30
461 521 1.152525 GGCCTAGATCGTGGAGGGA 60.153 63.158 10.57 0.00 0.00 4.20
462 522 0.759436 GGCCTAGATCGTGGAGGGAA 60.759 60.000 10.57 0.00 0.00 3.97
463 523 1.120530 GCCTAGATCGTGGAGGGAAA 58.879 55.000 10.57 0.00 0.00 3.13
464 524 1.202545 GCCTAGATCGTGGAGGGAAAC 60.203 57.143 10.57 0.00 0.00 2.78
477 537 2.075837 GGAAACCCTAGGCAGGTGT 58.924 57.895 2.05 0.00 40.79 4.16
478 538 0.404426 GGAAACCCTAGGCAGGTGTT 59.596 55.000 2.05 0.00 40.79 3.32
479 539 1.631898 GGAAACCCTAGGCAGGTGTTA 59.368 52.381 2.05 0.00 40.79 2.41
480 540 2.040679 GGAAACCCTAGGCAGGTGTTAA 59.959 50.000 2.05 0.00 40.79 2.01
481 541 3.308904 GGAAACCCTAGGCAGGTGTTAAT 60.309 47.826 2.05 0.00 40.79 1.40
482 542 3.366052 AACCCTAGGCAGGTGTTAATG 57.634 47.619 2.05 0.00 40.79 1.90
483 543 1.564348 ACCCTAGGCAGGTGTTAATGG 59.436 52.381 2.05 0.00 40.79 3.16
484 544 1.843851 CCCTAGGCAGGTGTTAATGGA 59.156 52.381 2.05 0.00 40.79 3.41
485 545 2.158755 CCCTAGGCAGGTGTTAATGGAG 60.159 54.545 2.05 0.00 40.79 3.86
486 546 2.158755 CCTAGGCAGGTGTTAATGGAGG 60.159 54.545 0.00 0.00 37.15 4.30
487 547 0.034089 AGGCAGGTGTTAATGGAGGC 60.034 55.000 0.00 0.00 0.00 4.70
488 548 1.037579 GGCAGGTGTTAATGGAGGCC 61.038 60.000 0.00 0.00 0.00 5.19
489 549 1.376609 GCAGGTGTTAATGGAGGCCG 61.377 60.000 0.00 0.00 0.00 6.13
490 550 0.251916 CAGGTGTTAATGGAGGCCGA 59.748 55.000 0.00 0.00 0.00 5.54
491 551 1.134098 CAGGTGTTAATGGAGGCCGAT 60.134 52.381 0.00 0.00 0.00 4.18
492 552 1.564348 AGGTGTTAATGGAGGCCGATT 59.436 47.619 0.00 0.00 0.00 3.34
493 553 1.676006 GGTGTTAATGGAGGCCGATTG 59.324 52.381 0.00 0.00 0.00 2.67
494 554 1.676006 GTGTTAATGGAGGCCGATTGG 59.324 52.381 0.00 0.00 38.77 3.16
510 570 4.512914 GGCTGCCCTGGATCCACC 62.513 72.222 11.44 5.62 39.54 4.61
518 578 1.614317 CCCTGGATCCACCTTGTTGAC 60.614 57.143 11.44 0.00 39.86 3.18
537 597 1.758440 CGGGTGTGATGGATCCGGAT 61.758 60.000 19.21 19.21 37.35 4.18
538 598 0.474184 GGGTGTGATGGATCCGGATT 59.526 55.000 20.22 1.73 0.00 3.01
554 614 2.169352 CGGATTGGTTCTCTGGACTCAT 59.831 50.000 0.00 0.00 0.00 2.90
562 1187 4.813697 GGTTCTCTGGACTCATATTGAAGC 59.186 45.833 0.00 0.00 0.00 3.86
563 1188 5.423015 GTTCTCTGGACTCATATTGAAGCA 58.577 41.667 0.00 0.00 0.00 3.91
565 1190 6.244552 TCTCTGGACTCATATTGAAGCAAT 57.755 37.500 0.00 0.00 37.80 3.56
581 1206 6.957150 TGAAGCAATTTAAATGTTTTGCCTG 58.043 32.000 16.73 4.75 44.21 4.85
590 1217 4.339872 AATGTTTTGCCTGCTGAATTCA 57.660 36.364 8.12 8.12 0.00 2.57
621 1248 8.190326 TGTTAATCTAGTGTTTCTCTTCCTGA 57.810 34.615 0.00 0.00 0.00 3.86
631 1258 5.760253 TGTTTCTCTTCCTGACAATCTGAAC 59.240 40.000 0.00 0.00 0.00 3.18
644 1271 5.689819 ACAATCTGAACGTTGCTGAATAAC 58.310 37.500 5.00 0.00 0.00 1.89
647 1274 5.342806 TCTGAACGTTGCTGAATAACAAG 57.657 39.130 5.00 0.00 0.00 3.16
651 1278 6.734137 TGAACGTTGCTGAATAACAAGAATT 58.266 32.000 5.00 0.00 0.00 2.17
672 1299 8.918116 AGAATTTAAAGTTTGGAGCTTCTCTTT 58.082 29.630 12.42 12.42 0.00 2.52
716 1343 2.955660 TGGTTTGGGCCATAATCGAATC 59.044 45.455 7.26 0.00 32.81 2.52
717 1344 2.296190 GGTTTGGGCCATAATCGAATCC 59.704 50.000 7.26 0.00 0.00 3.01
728 1355 6.326375 CCATAATCGAATCCAGTACTAGCTC 58.674 44.000 0.00 0.00 0.00 4.09
740 1367 0.889306 ACTAGCTCGTGTCCTGGTTC 59.111 55.000 0.00 0.00 0.00 3.62
743 1370 2.261671 CTCGTGTCCTGGTTCGGG 59.738 66.667 0.00 0.00 0.00 5.14
747 1374 1.666872 GTGTCCTGGTTCGGGTTCG 60.667 63.158 0.00 0.00 37.82 3.95
780 1407 3.946558 GCTTGATCTTTTGCTCTGGATCT 59.053 43.478 0.00 0.00 36.51 2.75
782 1409 4.564782 TGATCTTTTGCTCTGGATCTGT 57.435 40.909 0.00 0.00 36.51 3.41
783 1410 4.259356 TGATCTTTTGCTCTGGATCTGTG 58.741 43.478 0.00 0.00 36.51 3.66
784 1411 2.430465 TCTTTTGCTCTGGATCTGTGC 58.570 47.619 0.00 0.00 0.00 4.57
796 1423 3.871006 TGGATCTGTGCGAATAACATGAC 59.129 43.478 0.00 0.00 0.00 3.06
801 1428 2.682352 TGTGCGAATAACATGACCATGG 59.318 45.455 11.19 11.19 42.91 3.66
912 1561 4.281657 GTTCATCCTTTAGGGCCTTGATT 58.718 43.478 13.45 0.00 35.41 2.57
922 1571 1.688735 GGGCCTTGATTTATGGAAGCC 59.311 52.381 0.84 0.00 0.00 4.35
961 3086 5.601662 TGCTAATACATGCTGTTAGTCCTC 58.398 41.667 11.61 0.57 0.00 3.71
971 3096 3.119424 GCTGTTAGTCCTCGAAGCTTACT 60.119 47.826 0.00 0.85 0.00 2.24
991 3116 4.246458 ACTGTCTCTTTGGCGATTCTTAC 58.754 43.478 0.00 0.00 0.00 2.34
1149 3277 2.294512 CCTCAAAAGGAACACTTGCTCC 59.705 50.000 0.00 0.00 46.67 4.70
1188 3316 0.527565 TTGAGTACGACCCTAACCGC 59.472 55.000 0.00 0.00 0.00 5.68
1278 3406 1.267532 CGTGCGCCTGTCAATTACATC 60.268 52.381 4.18 0.00 37.50 3.06
1383 3511 1.471119 CTGCCCACAATGCTGATTCT 58.529 50.000 0.00 0.00 0.00 2.40
1427 3555 2.968206 CAAGGCCAGCCAAGAAGC 59.032 61.111 12.03 0.00 38.92 3.86
1658 3786 1.918293 TGGTCAAGGAGTCGGCCAT 60.918 57.895 2.24 0.00 0.00 4.40
1740 3868 1.226974 CATCGGCGTCGTCTCCAAT 60.227 57.895 10.18 0.00 37.69 3.16
1741 3869 1.226974 ATCGGCGTCGTCTCCAATG 60.227 57.895 10.18 0.00 37.69 2.82
1779 3907 3.801997 CTGAGGAAGGCGGGGCAT 61.802 66.667 0.00 0.00 0.00 4.40
1821 3949 4.634133 GTCGTCCGTGGTGTCGCA 62.634 66.667 0.00 0.00 0.00 5.10
1990 4118 1.833630 TGATCTTCATGGAAGCCGTCT 59.166 47.619 1.14 0.00 39.29 4.18
2018 4146 2.437413 CTCCAAGGGAAAGGTAGCAAC 58.563 52.381 0.00 0.00 0.00 4.17
2105 4237 0.524392 TGCAAACGGTTTCTGTTGCG 60.524 50.000 2.51 0.00 0.00 4.85
2113 4245 1.477105 GTTTCTGTTGCGGCACTTTC 58.523 50.000 0.05 0.00 0.00 2.62
2125 4260 4.273005 CGGCACTTTCGCTTTATTATGT 57.727 40.909 0.00 0.00 0.00 2.29
2126 4261 5.398176 CGGCACTTTCGCTTTATTATGTA 57.602 39.130 0.00 0.00 0.00 2.29
2127 4262 5.195379 CGGCACTTTCGCTTTATTATGTAC 58.805 41.667 0.00 0.00 0.00 2.90
2128 4263 5.006358 CGGCACTTTCGCTTTATTATGTACT 59.994 40.000 0.00 0.00 0.00 2.73
2129 4264 6.199531 CGGCACTTTCGCTTTATTATGTACTA 59.800 38.462 0.00 0.00 0.00 1.82
2130 4265 7.342942 GGCACTTTCGCTTTATTATGTACTAC 58.657 38.462 0.00 0.00 0.00 2.73
2233 4370 5.868043 TGAGTATGTTGCTTGTGATTGAG 57.132 39.130 0.00 0.00 0.00 3.02
2244 4381 5.010314 TGCTTGTGATTGAGAATTTGCTCTT 59.990 36.000 0.00 0.00 35.91 2.85
2245 4382 5.345202 GCTTGTGATTGAGAATTTGCTCTTG 59.655 40.000 0.00 0.00 35.91 3.02
2246 4383 6.395426 TTGTGATTGAGAATTTGCTCTTGT 57.605 33.333 0.00 0.00 35.91 3.16
2247 4384 6.005583 TGTGATTGAGAATTTGCTCTTGTC 57.994 37.500 0.00 0.00 35.91 3.18
2248 4385 5.766670 TGTGATTGAGAATTTGCTCTTGTCT 59.233 36.000 0.00 0.00 35.91 3.41
2249 4386 6.084925 GTGATTGAGAATTTGCTCTTGTCTG 58.915 40.000 0.00 0.00 35.91 3.51
2252 4389 2.751806 GAGAATTTGCTCTTGTCTGGGG 59.248 50.000 0.00 0.00 32.16 4.96
2362 4510 8.923683 CATGTGCTGAGCTGCATATATATATAC 58.076 37.037 5.83 0.67 45.23 1.47
2363 4511 8.010733 TGTGCTGAGCTGCATATATATATACA 57.989 34.615 5.83 5.33 45.23 2.29
2470 4640 7.418368 CCATTCATACATAGACATAGGGCCTAG 60.418 44.444 19.74 13.07 0.00 3.02
2473 4643 7.063593 TCATACATAGACATAGGGCCTAGATC 58.936 42.308 19.74 17.46 0.00 2.75
2474 4644 4.274147 ACATAGACATAGGGCCTAGATCG 58.726 47.826 19.74 9.64 0.00 3.69
2475 4645 4.018324 ACATAGACATAGGGCCTAGATCGA 60.018 45.833 19.74 14.47 0.00 3.59
2476 4646 3.748645 AGACATAGGGCCTAGATCGAT 57.251 47.619 19.74 0.00 0.00 3.59
2486 4656 2.670414 GCCTAGATCGATACTGCAATGC 59.330 50.000 0.00 0.00 0.00 3.56
2522 4692 3.057315 CCTGGTGGTTTTGCTATTCAGTG 60.057 47.826 0.00 0.00 0.00 3.66
2528 4698 3.004734 GGTTTTGCTATTCAGTGCACACT 59.995 43.478 21.04 0.00 43.61 3.55
2560 4730 2.159114 TCCTGCCAAGTTTTGTTTGCTC 60.159 45.455 0.00 0.00 0.00 4.26
2605 5138 3.013921 ACTGACCGAGCTAGAAAGAGAG 58.986 50.000 0.00 0.00 0.00 3.20
2606 5139 3.275143 CTGACCGAGCTAGAAAGAGAGA 58.725 50.000 0.00 0.00 0.00 3.10
2620 5153 5.598005 AGAAAGAGAGACCAGAGATGTATGG 59.402 44.000 1.21 1.21 41.28 2.74
2644 5177 1.619332 TGTCATTGTGCATTGCATGGT 59.381 42.857 15.49 0.73 41.91 3.55
2650 5183 2.737544 TGTGCATTGCATGGTCCTAAT 58.262 42.857 15.49 0.00 41.91 1.73
2756 5289 3.659183 ACATCTTGATGGGGAAGAAGG 57.341 47.619 14.18 0.00 33.22 3.46
2765 5298 1.228154 GGGAAGAAGGCAACGGTGT 60.228 57.895 0.66 0.00 46.39 4.16
2766 5299 0.822121 GGGAAGAAGGCAACGGTGTT 60.822 55.000 0.66 0.00 46.39 3.32
2811 5344 5.339611 CGTGGTTCGAGACATTTCATTTTTC 59.660 40.000 0.00 0.00 42.86 2.29
2812 5345 5.339611 GTGGTTCGAGACATTTCATTTTTCG 59.660 40.000 0.00 0.00 0.00 3.46
2899 5432 0.877071 GAGACAACTGGTGCACATGG 59.123 55.000 20.43 10.12 0.00 3.66
2900 5433 1.174712 AGACAACTGGTGCACATGGC 61.175 55.000 20.43 13.55 45.13 4.40
2901 5434 1.152694 ACAACTGGTGCACATGGCT 60.153 52.632 20.43 0.00 45.15 4.75
2902 5435 1.174712 ACAACTGGTGCACATGGCTC 61.175 55.000 20.43 0.00 45.15 4.70
2903 5436 1.151221 AACTGGTGCACATGGCTCA 59.849 52.632 20.43 5.06 45.15 4.26
2904 5437 0.251474 AACTGGTGCACATGGCTCAT 60.251 50.000 20.43 0.00 45.15 2.90
2905 5438 0.963856 ACTGGTGCACATGGCTCATG 60.964 55.000 20.43 12.06 46.18 3.07
2906 5439 2.279502 CTGGTGCACATGGCTCATGC 62.280 60.000 20.43 0.00 44.80 4.06
2907 5440 2.344981 GGTGCACATGGCTCATGCA 61.345 57.895 20.43 3.97 44.80 3.96
2908 5441 4.098847 TGCACATGGCTCATGCAA 57.901 50.000 13.19 0.00 45.96 4.08
2909 5442 2.585876 TGCACATGGCTCATGCAAT 58.414 47.368 13.19 0.00 45.96 3.56
2910 5443 0.899019 TGCACATGGCTCATGCAATT 59.101 45.000 13.19 0.00 45.96 2.32
2911 5444 1.276705 TGCACATGGCTCATGCAATTT 59.723 42.857 13.19 0.00 45.96 1.82
2912 5445 2.496470 TGCACATGGCTCATGCAATTTA 59.504 40.909 13.19 0.00 45.96 1.40
2913 5446 3.133183 TGCACATGGCTCATGCAATTTAT 59.867 39.130 13.19 0.00 45.96 1.40
2914 5447 4.124238 GCACATGGCTCATGCAATTTATT 58.876 39.130 13.19 0.00 44.80 1.40
2915 5448 4.210537 GCACATGGCTCATGCAATTTATTC 59.789 41.667 13.19 0.00 44.80 1.75
2916 5449 5.353111 CACATGGCTCATGCAATTTATTCA 58.647 37.500 13.19 0.00 44.80 2.57
2917 5450 5.233476 CACATGGCTCATGCAATTTATTCAC 59.767 40.000 13.19 0.00 44.80 3.18
2918 5451 4.031418 TGGCTCATGCAATTTATTCACG 57.969 40.909 0.00 0.00 41.91 4.35
2919 5452 3.693578 TGGCTCATGCAATTTATTCACGA 59.306 39.130 0.00 0.00 41.91 4.35
2920 5453 4.201940 TGGCTCATGCAATTTATTCACGAG 60.202 41.667 0.00 0.00 41.91 4.18
2921 5454 4.201950 GGCTCATGCAATTTATTCACGAGT 60.202 41.667 0.00 0.00 41.91 4.18
2922 5455 5.007626 GGCTCATGCAATTTATTCACGAGTA 59.992 40.000 0.00 0.00 41.91 2.59
2923 5456 6.132056 GCTCATGCAATTTATTCACGAGTAG 58.868 40.000 0.00 0.00 39.41 2.57
2924 5457 6.048073 TCATGCAATTTATTCACGAGTAGC 57.952 37.500 0.00 0.00 0.00 3.58
2925 5458 5.817296 TCATGCAATTTATTCACGAGTAGCT 59.183 36.000 0.00 0.00 0.00 3.32
2926 5459 6.316140 TCATGCAATTTATTCACGAGTAGCTT 59.684 34.615 0.00 0.00 0.00 3.74
2927 5460 6.494893 TGCAATTTATTCACGAGTAGCTTT 57.505 33.333 0.00 0.00 0.00 3.51
2928 5461 6.908825 TGCAATTTATTCACGAGTAGCTTTT 58.091 32.000 0.00 0.00 0.00 2.27
2929 5462 6.801377 TGCAATTTATTCACGAGTAGCTTTTG 59.199 34.615 0.00 0.00 0.00 2.44
2930 5463 6.801862 GCAATTTATTCACGAGTAGCTTTTGT 59.198 34.615 0.00 0.00 0.00 2.83
2931 5464 7.960738 GCAATTTATTCACGAGTAGCTTTTGTA 59.039 33.333 0.00 0.00 0.00 2.41
2932 5465 9.478019 CAATTTATTCACGAGTAGCTTTTGTAG 57.522 33.333 0.00 0.00 0.00 2.74
2933 5466 8.773404 ATTTATTCACGAGTAGCTTTTGTAGT 57.227 30.769 0.00 0.00 0.00 2.73
2934 5467 9.865321 ATTTATTCACGAGTAGCTTTTGTAGTA 57.135 29.630 0.00 0.00 0.00 1.82
2935 5468 9.695526 TTTATTCACGAGTAGCTTTTGTAGTAA 57.304 29.630 0.00 0.00 0.00 2.24
2936 5469 6.998258 TTCACGAGTAGCTTTTGTAGTAAC 57.002 37.500 0.00 0.00 0.00 2.50
2937 5470 6.323203 TCACGAGTAGCTTTTGTAGTAACT 57.677 37.500 0.00 0.00 0.00 2.24
2938 5471 6.742109 TCACGAGTAGCTTTTGTAGTAACTT 58.258 36.000 0.00 0.00 0.00 2.66
2939 5472 7.205297 TCACGAGTAGCTTTTGTAGTAACTTT 58.795 34.615 0.00 0.00 0.00 2.66
2940 5473 7.707893 TCACGAGTAGCTTTTGTAGTAACTTTT 59.292 33.333 0.00 0.00 0.00 2.27
2941 5474 7.792508 CACGAGTAGCTTTTGTAGTAACTTTTG 59.207 37.037 0.00 0.00 0.00 2.44
2942 5475 6.790825 CGAGTAGCTTTTGTAGTAACTTTTGC 59.209 38.462 0.00 0.00 0.00 3.68
2943 5476 7.517734 CGAGTAGCTTTTGTAGTAACTTTTGCA 60.518 37.037 0.00 0.00 0.00 4.08
2944 5477 7.992008 AGTAGCTTTTGTAGTAACTTTTGCAA 58.008 30.769 0.00 0.00 0.00 4.08
2945 5478 8.463607 AGTAGCTTTTGTAGTAACTTTTGCAAA 58.536 29.630 8.05 8.05 0.00 3.68
2946 5479 9.078753 GTAGCTTTTGTAGTAACTTTTGCAAAA 57.921 29.630 22.61 22.61 35.45 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.858186 CAAAAATTTTAAGTGTTTGCAAAAGGG 58.142 29.630 14.67 0.00 0.00 3.95
1 2 9.404348 ACAAAAATTTTAAGTGTTTGCAAAAGG 57.596 25.926 14.67 0.00 33.46 3.11
3 4 9.950680 TGACAAAAATTTTAAGTGTTTGCAAAA 57.049 22.222 14.67 1.61 33.46 2.44
4 5 9.950680 TTGACAAAAATTTTAAGTGTTTGCAAA 57.049 22.222 8.05 8.05 33.46 3.68
16 17 9.209175 CCCACCGAAATATTGACAAAAATTTTA 57.791 29.630 3.34 0.00 0.00 1.52
17 18 7.717436 ACCCACCGAAATATTGACAAAAATTTT 59.283 29.630 11.19 0.00 0.00 1.82
18 19 7.220740 ACCCACCGAAATATTGACAAAAATTT 58.779 30.769 10.16 10.16 0.00 1.82
19 20 6.764379 ACCCACCGAAATATTGACAAAAATT 58.236 32.000 0.00 0.00 0.00 1.82
20 21 6.353404 ACCCACCGAAATATTGACAAAAAT 57.647 33.333 0.00 0.00 0.00 1.82
21 22 5.793030 ACCCACCGAAATATTGACAAAAA 57.207 34.783 0.00 0.00 0.00 1.94
22 23 5.793030 AACCCACCGAAATATTGACAAAA 57.207 34.783 0.00 0.00 0.00 2.44
23 24 5.793030 AAACCCACCGAAATATTGACAAA 57.207 34.783 0.00 0.00 0.00 2.83
24 25 5.793030 AAAACCCACCGAAATATTGACAA 57.207 34.783 0.00 0.00 0.00 3.18
25 26 5.793030 AAAAACCCACCGAAATATTGACA 57.207 34.783 0.00 0.00 0.00 3.58
45 46 9.130312 CCGAAATTTCCATTCGTATGTTAAAAA 57.870 29.630 12.54 0.00 46.11 1.94
46 47 8.298140 ACCGAAATTTCCATTCGTATGTTAAAA 58.702 29.630 12.54 0.30 46.11 1.52
47 48 7.751348 CACCGAAATTTCCATTCGTATGTTAAA 59.249 33.333 12.54 2.49 46.11 1.52
48 49 7.244898 CACCGAAATTTCCATTCGTATGTTAA 58.755 34.615 12.54 0.00 46.11 2.01
49 50 6.183360 CCACCGAAATTTCCATTCGTATGTTA 60.183 38.462 12.54 0.00 46.11 2.41
50 51 5.392595 CCACCGAAATTTCCATTCGTATGTT 60.393 40.000 12.54 0.00 46.11 2.71
51 52 4.095782 CCACCGAAATTTCCATTCGTATGT 59.904 41.667 12.54 0.00 46.11 2.29
52 53 4.334203 TCCACCGAAATTTCCATTCGTATG 59.666 41.667 12.54 0.00 46.11 2.39
53 54 4.519213 TCCACCGAAATTTCCATTCGTAT 58.481 39.130 12.54 0.00 46.11 3.06
54 55 3.940319 TCCACCGAAATTTCCATTCGTA 58.060 40.909 12.54 0.00 46.11 3.43
55 56 2.785562 TCCACCGAAATTTCCATTCGT 58.214 42.857 12.54 0.00 46.11 3.85
56 57 4.370364 AATCCACCGAAATTTCCATTCG 57.630 40.909 12.54 1.02 46.86 3.34
81 82 6.978080 CCACCGAAATTTCTTCTTCTCAAAAA 59.022 34.615 15.92 0.00 0.00 1.94
82 83 6.096282 ACCACCGAAATTTCTTCTTCTCAAAA 59.904 34.615 15.92 0.00 0.00 2.44
83 84 5.592688 ACCACCGAAATTTCTTCTTCTCAAA 59.407 36.000 15.92 0.00 0.00 2.69
84 85 5.130350 ACCACCGAAATTTCTTCTTCTCAA 58.870 37.500 15.92 0.00 0.00 3.02
85 86 4.714632 ACCACCGAAATTTCTTCTTCTCA 58.285 39.130 15.92 0.00 0.00 3.27
86 87 6.091034 GTCTACCACCGAAATTTCTTCTTCTC 59.909 42.308 15.92 0.00 0.00 2.87
87 88 5.932883 GTCTACCACCGAAATTTCTTCTTCT 59.067 40.000 15.92 0.00 0.00 2.85
88 89 5.163982 CGTCTACCACCGAAATTTCTTCTTC 60.164 44.000 15.92 0.00 0.00 2.87
89 90 4.689345 CGTCTACCACCGAAATTTCTTCTT 59.311 41.667 15.92 0.00 0.00 2.52
90 91 4.243270 CGTCTACCACCGAAATTTCTTCT 58.757 43.478 15.92 0.00 0.00 2.85
91 92 3.370061 CCGTCTACCACCGAAATTTCTTC 59.630 47.826 15.92 0.00 0.00 2.87
92 93 3.332034 CCGTCTACCACCGAAATTTCTT 58.668 45.455 15.92 0.21 0.00 2.52
93 94 2.354403 CCCGTCTACCACCGAAATTTCT 60.354 50.000 15.92 0.00 0.00 2.52
94 95 2.004733 CCCGTCTACCACCGAAATTTC 58.995 52.381 8.20 8.20 0.00 2.17
95 96 1.947212 GCCCGTCTACCACCGAAATTT 60.947 52.381 0.00 0.00 0.00 1.82
96 97 0.392060 GCCCGTCTACCACCGAAATT 60.392 55.000 0.00 0.00 0.00 1.82
104 105 2.642254 CGTTCTGGCCCGTCTACCA 61.642 63.158 0.00 0.00 0.00 3.25
105 106 2.183555 CGTTCTGGCCCGTCTACC 59.816 66.667 0.00 0.00 0.00 3.18
128 129 2.494059 CTTCGGCCAACTCTTTCTTCA 58.506 47.619 2.24 0.00 0.00 3.02
130 131 1.239347 GCTTCGGCCAACTCTTTCTT 58.761 50.000 2.24 0.00 34.32 2.52
159 172 2.231529 GCCTCCTCGTTCTATGCTAGA 58.768 52.381 0.00 0.00 0.00 2.43
163 176 1.069935 GGGCCTCCTCGTTCTATGC 59.930 63.158 0.84 0.00 0.00 3.14
199 212 1.058590 GACGAGTGCGACTGTGTACG 61.059 60.000 0.00 0.00 41.64 3.67
200 213 1.058590 CGACGAGTGCGACTGTGTAC 61.059 60.000 0.00 0.00 41.64 2.90
201 214 1.205820 CGACGAGTGCGACTGTGTA 59.794 57.895 0.00 0.00 41.64 2.90
223 236 2.734673 GAGAGAAAGCAGGCGCGTG 61.735 63.158 24.99 24.99 45.49 5.34
224 237 2.433318 GAGAGAAAGCAGGCGCGT 60.433 61.111 8.43 0.00 45.49 6.01
225 238 3.191539 GGAGAGAAAGCAGGCGCG 61.192 66.667 0.00 0.00 45.49 6.86
237 259 0.478507 GAGGAGGAGGAGGAGGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
238 260 0.996762 GGAGGAGGAGGAGGAGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
239 261 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
240 262 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
241 263 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
300 322 3.967335 GACGGAGGGATCGGAGCG 61.967 72.222 0.00 0.00 0.00 5.03
301 323 3.607661 GGACGGAGGGATCGGAGC 61.608 72.222 0.00 0.00 0.00 4.70
302 324 3.288290 CGGACGGAGGGATCGGAG 61.288 72.222 0.00 0.00 0.00 4.63
346 368 1.596496 GAGGATGGGGAGGGAGAAAA 58.404 55.000 0.00 0.00 0.00 2.29
347 369 0.327576 GGAGGATGGGGAGGGAGAAA 60.328 60.000 0.00 0.00 0.00 2.52
403 463 2.892373 TAAAACAAGCAAGATCCGCG 57.108 45.000 0.00 0.00 0.00 6.46
406 466 7.807977 TGGATAGATAAAACAAGCAAGATCC 57.192 36.000 0.00 0.00 0.00 3.36
407 467 8.510505 GGATGGATAGATAAAACAAGCAAGATC 58.489 37.037 0.00 0.00 0.00 2.75
408 468 8.000709 TGGATGGATAGATAAAACAAGCAAGAT 58.999 33.333 0.00 0.00 0.00 2.40
409 469 7.345691 TGGATGGATAGATAAAACAAGCAAGA 58.654 34.615 0.00 0.00 0.00 3.02
410 470 7.284034 ACTGGATGGATAGATAAAACAAGCAAG 59.716 37.037 0.00 0.00 0.00 4.01
411 471 7.118723 ACTGGATGGATAGATAAAACAAGCAA 58.881 34.615 0.00 0.00 0.00 3.91
412 472 6.662755 ACTGGATGGATAGATAAAACAAGCA 58.337 36.000 0.00 0.00 0.00 3.91
413 473 7.519008 CGAACTGGATGGATAGATAAAACAAGC 60.519 40.741 0.00 0.00 0.00 4.01
414 474 7.041780 CCGAACTGGATGGATAGATAAAACAAG 60.042 40.741 0.00 0.00 42.00 3.16
415 475 6.765989 CCGAACTGGATGGATAGATAAAACAA 59.234 38.462 0.00 0.00 42.00 2.83
416 476 6.288294 CCGAACTGGATGGATAGATAAAACA 58.712 40.000 0.00 0.00 42.00 2.83
417 477 5.179555 GCCGAACTGGATGGATAGATAAAAC 59.820 44.000 0.00 0.00 42.00 2.43
418 478 5.071788 AGCCGAACTGGATGGATAGATAAAA 59.928 40.000 0.00 0.00 42.00 1.52
419 479 4.593206 AGCCGAACTGGATGGATAGATAAA 59.407 41.667 0.00 0.00 42.00 1.40
421 481 3.779444 AGCCGAACTGGATGGATAGATA 58.221 45.455 0.00 0.00 42.00 1.98
423 483 2.088104 AGCCGAACTGGATGGATAGA 57.912 50.000 0.00 0.00 42.00 1.98
434 494 1.739338 CGATCTAGGCCAGCCGAACT 61.739 60.000 5.01 0.00 41.95 3.01
435 495 1.300233 CGATCTAGGCCAGCCGAAC 60.300 63.158 5.01 0.00 41.95 3.95
436 496 1.756950 ACGATCTAGGCCAGCCGAA 60.757 57.895 5.01 0.00 41.95 4.30
438 498 2.028190 CACGATCTAGGCCAGCCG 59.972 66.667 5.01 9.84 41.95 5.52
439 499 2.093537 CTCCACGATCTAGGCCAGCC 62.094 65.000 5.01 0.00 0.00 4.85
443 503 0.759436 TTCCCTCCACGATCTAGGCC 60.759 60.000 0.00 0.00 0.00 5.19
445 505 1.413077 GGTTTCCCTCCACGATCTAGG 59.587 57.143 0.00 0.00 0.00 3.02
446 506 1.413077 GGGTTTCCCTCCACGATCTAG 59.587 57.143 0.00 0.00 41.34 2.43
448 508 2.297937 GGGTTTCCCTCCACGATCT 58.702 57.895 0.00 0.00 41.34 2.75
449 509 4.957164 GGGTTTCCCTCCACGATC 57.043 61.111 0.00 0.00 41.34 3.69
466 526 2.746472 GCCTCCATTAACACCTGCCTAG 60.746 54.545 0.00 0.00 0.00 3.02
467 527 1.211949 GCCTCCATTAACACCTGCCTA 59.788 52.381 0.00 0.00 0.00 3.93
468 528 0.034089 GCCTCCATTAACACCTGCCT 60.034 55.000 0.00 0.00 0.00 4.75
469 529 1.037579 GGCCTCCATTAACACCTGCC 61.038 60.000 0.00 0.00 0.00 4.85
470 530 1.376609 CGGCCTCCATTAACACCTGC 61.377 60.000 0.00 0.00 0.00 4.85
471 531 0.251916 TCGGCCTCCATTAACACCTG 59.748 55.000 0.00 0.00 0.00 4.00
472 532 1.213296 ATCGGCCTCCATTAACACCT 58.787 50.000 0.00 0.00 0.00 4.00
473 533 1.676006 CAATCGGCCTCCATTAACACC 59.324 52.381 0.00 0.00 0.00 4.16
474 534 1.676006 CCAATCGGCCTCCATTAACAC 59.324 52.381 0.00 0.00 0.00 3.32
475 535 2.051334 CCAATCGGCCTCCATTAACA 57.949 50.000 0.00 0.00 0.00 2.41
487 547 3.426309 ATCCAGGGCAGCCAATCGG 62.426 63.158 15.19 7.56 0.00 4.18
488 548 1.895707 GATCCAGGGCAGCCAATCG 60.896 63.158 15.19 0.00 0.00 3.34
489 549 1.530183 GGATCCAGGGCAGCCAATC 60.530 63.158 15.19 9.98 0.00 2.67
490 550 2.318966 TGGATCCAGGGCAGCCAAT 61.319 57.895 11.44 0.00 0.00 3.16
491 551 2.940467 TGGATCCAGGGCAGCCAA 60.940 61.111 11.44 0.00 0.00 4.52
492 552 3.731728 GTGGATCCAGGGCAGCCA 61.732 66.667 16.81 0.00 0.00 4.75
493 553 4.512914 GGTGGATCCAGGGCAGCC 62.513 72.222 16.81 7.99 35.97 4.85
494 554 2.988839 AAGGTGGATCCAGGGCAGC 61.989 63.158 16.81 1.85 39.02 5.25
510 570 0.874390 CCATCACACCCGTCAACAAG 59.126 55.000 0.00 0.00 0.00 3.16
518 578 1.758440 ATCCGGATCCATCACACCCG 61.758 60.000 12.38 0.00 39.85 5.28
537 597 6.373005 TTCAATATGAGTCCAGAGAACCAA 57.627 37.500 0.00 0.00 0.00 3.67
538 598 5.627735 GCTTCAATATGAGTCCAGAGAACCA 60.628 44.000 0.00 0.00 0.00 3.67
554 614 9.282569 AGGCAAAACATTTAAATTGCTTCAATA 57.717 25.926 18.68 0.00 45.60 1.90
562 1187 6.542574 TCAGCAGGCAAAACATTTAAATTG 57.457 33.333 0.00 0.00 0.00 2.32
563 1188 7.748691 ATTCAGCAGGCAAAACATTTAAATT 57.251 28.000 0.00 0.00 0.00 1.82
565 1190 6.765036 TGAATTCAGCAGGCAAAACATTTAAA 59.235 30.769 3.38 0.00 0.00 1.52
590 1217 8.854614 AGAGAAACACTAGATTAACAATTGCT 57.145 30.769 5.05 0.00 0.00 3.91
597 1224 8.088981 TGTCAGGAAGAGAAACACTAGATTAAC 58.911 37.037 0.00 0.00 0.00 2.01
599 1226 7.776618 TGTCAGGAAGAGAAACACTAGATTA 57.223 36.000 0.00 0.00 0.00 1.75
600 1227 6.672266 TGTCAGGAAGAGAAACACTAGATT 57.328 37.500 0.00 0.00 0.00 2.40
601 1228 6.672266 TTGTCAGGAAGAGAAACACTAGAT 57.328 37.500 0.00 0.00 0.00 1.98
602 1229 6.495181 AGATTGTCAGGAAGAGAAACACTAGA 59.505 38.462 0.00 0.00 32.74 2.43
603 1230 6.589523 CAGATTGTCAGGAAGAGAAACACTAG 59.410 42.308 0.00 0.00 32.74 2.57
621 1248 5.238432 TGTTATTCAGCAACGTTCAGATTGT 59.762 36.000 0.00 0.00 0.00 2.71
631 1258 9.180678 ACTTTAAATTCTTGTTATTCAGCAACG 57.819 29.630 0.00 0.00 0.00 4.10
644 1271 8.355913 AGAGAAGCTCCAAACTTTAAATTCTTG 58.644 33.333 0.00 0.00 0.00 3.02
647 1274 9.534565 AAAAGAGAAGCTCCAAACTTTAAATTC 57.465 29.630 0.00 0.00 0.00 2.17
663 1290 3.854240 GCGGCAAGATTTAAAAGAGAAGC 59.146 43.478 0.00 0.00 0.00 3.86
672 1299 6.272318 CAATAAGATTGGCGGCAAGATTTAA 58.728 36.000 28.83 12.39 0.00 1.52
674 1301 4.441913 CCAATAAGATTGGCGGCAAGATTT 60.442 41.667 28.83 22.32 32.18 2.17
678 1305 1.750778 ACCAATAAGATTGGCGGCAAG 59.249 47.619 28.83 15.15 43.23 4.01
716 1343 1.402259 CAGGACACGAGCTAGTACTGG 59.598 57.143 14.80 3.15 41.89 4.00
717 1344 1.402259 CCAGGACACGAGCTAGTACTG 59.598 57.143 15.40 15.40 44.54 2.74
728 1355 1.666872 GAACCCGAACCAGGACACG 60.667 63.158 0.00 0.00 0.00 4.49
743 1370 2.413837 TCAAGCAGCTTAGGTTCGAAC 58.586 47.619 20.14 20.14 0.00 3.95
747 1374 5.397326 CAAAAGATCAAGCAGCTTAGGTTC 58.603 41.667 7.52 1.58 0.00 3.62
780 1407 2.682352 CCATGGTCATGTTATTCGCACA 59.318 45.455 2.57 0.00 37.11 4.57
782 1409 2.682352 CACCATGGTCATGTTATTCGCA 59.318 45.455 16.53 0.00 37.11 5.10
783 1410 2.682856 ACACCATGGTCATGTTATTCGC 59.317 45.455 16.53 0.00 37.11 4.70
784 1411 4.963276 AACACCATGGTCATGTTATTCG 57.037 40.909 16.53 1.79 34.84 3.34
796 1423 9.191995 GTTTACTGATTAAAAGAAACACCATGG 57.808 33.333 11.19 11.19 31.22 3.66
850 1492 5.638596 TCAACAGAAAGTAGCGAGATACA 57.361 39.130 1.28 0.00 0.00 2.29
851 1493 6.975772 AGAATCAACAGAAAGTAGCGAGATAC 59.024 38.462 0.00 0.00 0.00 2.24
853 1495 5.971763 AGAATCAACAGAAAGTAGCGAGAT 58.028 37.500 0.00 0.00 0.00 2.75
854 1496 5.392767 AGAATCAACAGAAAGTAGCGAGA 57.607 39.130 0.00 0.00 0.00 4.04
855 1497 6.073548 ACAAAGAATCAACAGAAAGTAGCGAG 60.074 38.462 0.00 0.00 0.00 5.03
912 1561 5.221722 CCAGCAAGTAGATAGGCTTCCATAA 60.222 44.000 0.00 0.00 33.60 1.90
961 3086 2.413453 GCCAAAGAGACAGTAAGCTTCG 59.587 50.000 0.00 0.00 0.00 3.79
971 3096 3.250744 CGTAAGAATCGCCAAAGAGACA 58.749 45.455 0.00 0.00 43.02 3.41
1005 3133 1.691196 TGGCCAAGGTCTTGAACTTG 58.309 50.000 18.50 18.50 42.93 3.16
1149 3277 0.958091 TCCTTTCCACAATGCCAACG 59.042 50.000 0.00 0.00 0.00 4.10
1188 3316 1.946768 AGAAGAGCGATCCGAGAAGAG 59.053 52.381 0.00 0.00 0.00 2.85
1427 3555 4.521062 CAGCGCCCTCCTCTTCGG 62.521 72.222 2.29 0.00 0.00 4.30
1729 3857 1.745489 GGGTGGCATTGGAGACGAC 60.745 63.158 0.00 0.00 0.00 4.34
1821 3949 0.034477 GATGGTCCACCGGGTTCATT 60.034 55.000 6.32 0.00 39.43 2.57
1990 4118 0.106268 TTTCCCTTGGAGCAGCAACA 60.106 50.000 0.00 0.00 31.21 3.33
2018 4146 3.409570 CATAGCCACATCAAGATCCTGG 58.590 50.000 0.00 0.00 0.00 4.45
2083 4211 2.413453 GCAACAGAAACCGTTTGCAAAA 59.587 40.909 14.67 0.00 0.00 2.44
2105 4237 6.359480 AGTACATAATAAAGCGAAAGTGCC 57.641 37.500 0.00 0.00 34.65 5.01
2233 4370 2.519013 ACCCCAGACAAGAGCAAATTC 58.481 47.619 0.00 0.00 0.00 2.17
2244 4381 1.281867 CCAGATTGCTTACCCCAGACA 59.718 52.381 0.00 0.00 0.00 3.41
2245 4382 1.408822 CCCAGATTGCTTACCCCAGAC 60.409 57.143 0.00 0.00 0.00 3.51
2246 4383 0.918983 CCCAGATTGCTTACCCCAGA 59.081 55.000 0.00 0.00 0.00 3.86
2247 4384 0.106519 CCCCAGATTGCTTACCCCAG 60.107 60.000 0.00 0.00 0.00 4.45
2248 4385 1.580066 CCCCCAGATTGCTTACCCCA 61.580 60.000 0.00 0.00 0.00 4.96
2249 4386 1.230212 CCCCCAGATTGCTTACCCC 59.770 63.158 0.00 0.00 0.00 4.95
2252 4389 1.035139 CATGCCCCCAGATTGCTTAC 58.965 55.000 0.00 0.00 0.00 2.34
2386 4552 7.461182 TGGATTTACACCAACAGAAATTAGG 57.539 36.000 0.00 0.00 34.25 2.69
2387 4553 8.739039 TGATGGATTTACACCAACAGAAATTAG 58.261 33.333 0.00 0.00 40.93 1.73
2470 4640 2.735663 CAGAGGCATTGCAGTATCGATC 59.264 50.000 11.39 0.00 0.00 3.69
2473 4643 1.202568 TCCAGAGGCATTGCAGTATCG 60.203 52.381 11.39 0.00 0.00 2.92
2474 4644 2.158842 ACTCCAGAGGCATTGCAGTATC 60.159 50.000 11.39 2.90 0.00 2.24
2475 4645 1.842562 ACTCCAGAGGCATTGCAGTAT 59.157 47.619 11.39 0.00 0.00 2.12
2476 4646 1.279496 ACTCCAGAGGCATTGCAGTA 58.721 50.000 11.39 0.00 0.00 2.74
2560 4730 3.063510 TCTTGAGCAAATGTCTCCTGG 57.936 47.619 0.00 0.00 0.00 4.45
2605 5138 3.034635 ACAGACCCATACATCTCTGGTC 58.965 50.000 0.00 0.00 44.64 4.02
2606 5139 3.034635 GACAGACCCATACATCTCTGGT 58.965 50.000 0.00 0.00 35.43 4.00
2620 5153 1.270274 TGCAATGCACAATGACAGACC 59.730 47.619 2.72 0.00 31.71 3.85
2644 5177 2.298729 GTTGTGGCTGGCAAAATTAGGA 59.701 45.455 10.23 0.00 0.00 2.94
2650 5183 1.687146 TGGGTTGTGGCTGGCAAAA 60.687 52.632 5.14 3.57 0.00 2.44
2744 5277 1.000896 CCGTTGCCTTCTTCCCCAT 60.001 57.895 0.00 0.00 0.00 4.00
2756 5289 2.173964 GCGAATCATTAACACCGTTGC 58.826 47.619 0.00 0.00 0.00 4.17
2789 5322 5.237561 TCGAAAAATGAAATGTCTCGAACCA 59.762 36.000 0.00 0.00 0.00 3.67
2811 5344 7.009357 TGTTTAACTTTTTGGATTCGGTTTTCG 59.991 33.333 0.00 0.00 40.90 3.46
2812 5345 8.111836 GTGTTTAACTTTTTGGATTCGGTTTTC 58.888 33.333 0.00 0.00 0.00 2.29
2823 5356 2.532317 CCGCACGTGTTTAACTTTTTGG 59.468 45.455 18.38 0.00 0.00 3.28
2861 5394 7.745620 TGTCTCCATTAGAGGTTTTCTTTTC 57.254 36.000 0.00 0.00 43.44 2.29
2862 5395 7.780271 AGTTGTCTCCATTAGAGGTTTTCTTTT 59.220 33.333 0.00 0.00 43.44 2.27
2866 5399 5.412904 CCAGTTGTCTCCATTAGAGGTTTTC 59.587 44.000 0.00 0.00 43.44 2.29
2870 5403 3.261897 CACCAGTTGTCTCCATTAGAGGT 59.738 47.826 0.00 0.00 43.44 3.85
2899 5432 4.913376 ACTCGTGAATAAATTGCATGAGC 58.087 39.130 0.00 0.00 45.17 4.26
2900 5433 6.018425 AGCTACTCGTGAATAAATTGCATGAG 60.018 38.462 0.00 0.00 46.15 2.90
2901 5434 5.817296 AGCTACTCGTGAATAAATTGCATGA 59.183 36.000 0.00 0.00 0.00 3.07
2902 5435 6.052840 AGCTACTCGTGAATAAATTGCATG 57.947 37.500 0.00 0.00 0.00 4.06
2903 5436 6.683974 AAGCTACTCGTGAATAAATTGCAT 57.316 33.333 0.00 0.00 0.00 3.96
2904 5437 6.494893 AAAGCTACTCGTGAATAAATTGCA 57.505 33.333 0.00 0.00 0.00 4.08
2905 5438 6.801862 ACAAAAGCTACTCGTGAATAAATTGC 59.198 34.615 0.00 0.00 0.00 3.56
2906 5439 9.478019 CTACAAAAGCTACTCGTGAATAAATTG 57.522 33.333 0.00 0.00 0.00 2.32
2907 5440 9.216117 ACTACAAAAGCTACTCGTGAATAAATT 57.784 29.630 0.00 0.00 0.00 1.82
2908 5441 8.773404 ACTACAAAAGCTACTCGTGAATAAAT 57.227 30.769 0.00 0.00 0.00 1.40
2909 5442 9.695526 TTACTACAAAAGCTACTCGTGAATAAA 57.304 29.630 0.00 0.00 0.00 1.40
2910 5443 9.132521 GTTACTACAAAAGCTACTCGTGAATAA 57.867 33.333 0.00 0.00 0.00 1.40
2911 5444 8.517878 AGTTACTACAAAAGCTACTCGTGAATA 58.482 33.333 0.00 0.00 0.00 1.75
2912 5445 7.376615 AGTTACTACAAAAGCTACTCGTGAAT 58.623 34.615 0.00 0.00 0.00 2.57
2913 5446 6.742109 AGTTACTACAAAAGCTACTCGTGAA 58.258 36.000 0.00 0.00 0.00 3.18
2914 5447 6.323203 AGTTACTACAAAAGCTACTCGTGA 57.677 37.500 0.00 0.00 0.00 4.35
2915 5448 7.404139 AAAGTTACTACAAAAGCTACTCGTG 57.596 36.000 0.00 0.00 0.00 4.35
2916 5449 7.517893 GCAAAAGTTACTACAAAAGCTACTCGT 60.518 37.037 0.00 0.00 0.00 4.18
2917 5450 6.790825 GCAAAAGTTACTACAAAAGCTACTCG 59.209 38.462 0.00 0.00 0.00 4.18
2918 5451 7.636326 TGCAAAAGTTACTACAAAAGCTACTC 58.364 34.615 0.00 0.00 0.00 2.59
2919 5452 7.562454 TGCAAAAGTTACTACAAAAGCTACT 57.438 32.000 0.00 0.00 0.00 2.57
2920 5453 8.623310 TTTGCAAAAGTTACTACAAAAGCTAC 57.377 30.769 10.02 0.00 0.00 3.58
2921 5454 9.296400 CTTTTGCAAAAGTTACTACAAAAGCTA 57.704 29.630 33.98 5.69 43.76 3.32
2922 5455 7.277760 CCTTTTGCAAAAGTTACTACAAAAGCT 59.722 33.333 37.05 0.00 46.28 3.74
2923 5456 7.398746 CCTTTTGCAAAAGTTACTACAAAAGC 58.601 34.615 37.05 9.60 46.28 3.51
2924 5457 7.398746 GCCTTTTGCAAAAGTTACTACAAAAG 58.601 34.615 37.05 23.52 46.78 2.27
2925 5458 7.297229 GCCTTTTGCAAAAGTTACTACAAAA 57.703 32.000 37.05 10.42 42.92 2.44
2926 5459 6.895607 GCCTTTTGCAAAAGTTACTACAAA 57.104 33.333 37.05 10.60 42.92 2.83


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

AutoCloner maintained by Alex Coulton.