Multiple sequence alignment - TraesCS7A01G384100

Loading Multiple Alignment...

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 TraesCS7A01G384100 chr7A 100.000 5038 0 0 1 5038 559393063 559388026 0.000000e+00 9304
1 TraesCS7A01G384100 chr7A 93.000 300 19 2 4700 4998 559362997 559362699 2.150000e-118 436
2 TraesCS7A01G384100 chr7B 91.623 4035 196 63 751 4698 522147314 522143335 0.000000e+00 5448
3 TraesCS7A01G384100 chr7B 84.091 572 52 21 1 541 522148733 522148170 2.690000e-142 516
4 TraesCS7A01G384100 chr7B 92.333 300 21 2 4700 4998 522143286 522142988 4.660000e-115 425
5 TraesCS7A01G384100 chr7B 88.110 328 35 4 4700 5025 521196025 521196350 2.200000e-103 387
6 TraesCS7A01G384100 chr7D 92.651 2395 109 30 2148 4493 493564493 493562117 0.000000e+00 3386
7 TraesCS7A01G384100 chr7D 91.458 1358 64 11 751 2076 493565861 493564524 0.000000e+00 1818
8 TraesCS7A01G384100 chr7D 84.956 565 52 21 1 541 493567147 493566592 4.440000e-150 542
9 TraesCS7A01G384100 chr7D 91.892 333 27 0 4700 5032 493561763 493561431 2.750000e-127 466
10 TraesCS7A01G384100 chr7D 88.339 283 29 4 4745 5025 491872202 491872482 2.250000e-88 337


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 TraesCS7A01G384100 chr7A 559388026 559393063 5037 True 9304.000000 9304 100.00000 1 5038 1 chr7A.!!$R2 5037
1 TraesCS7A01G384100 chr7B 522142988 522148733 5745 True 2129.666667 5448 89.34900 1 4998 3 chr7B.!!$R1 4997
2 TraesCS7A01G384100 chr7D 493561431 493567147 5716 True 1553.000000 3386 90.23925 1 5032 4 chr7D.!!$R1 5031

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
437 462 0.102844 ATGTGCGCCCATGTTATTGC 59.897 50.0 4.01 0.00 0.00 3.56 F
565 601 0.245539 TTCAGTAGTAGGGCGTGCAC 59.754 55.0 6.82 6.82 0.00 4.57 F
567 603 0.246635 CAGTAGTAGGGCGTGCACTT 59.753 55.0 16.19 0.26 0.00 3.16 F
1434 2254 0.610687 ATAGCGATTAGGGCTCCTGC 59.389 55.0 4.16 0.00 41.80 4.85 F
1860 2681 0.615331 TCCCAGGAAGCTTGCTGTAG 59.385 55.0 36.27 28.83 44.06 2.74 F
3314 4199 0.108662 CGGTGTGCTAGATCACTGCA 60.109 55.0 14.28 0.00 37.81 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 2436 1.127951 CCATTGTACGGTTGCGAACTC 59.872 52.381 0.00 0.0 0.00 3.01 R
2362 3210 1.550524 GCTATGGTGACTGGTGAGACA 59.449 52.381 0.00 0.0 0.00 3.41 R
2452 3313 7.327214 AGCAAGTTCAACAAAAACCAAGATAA 58.673 30.769 0.00 0.0 0.00 1.75 R
2883 3747 0.033601 ACACACCAGCCACTTTTCCA 60.034 50.000 0.00 0.0 0.00 3.53 R
3384 4276 0.320697 AAGTAACAGGTGAGACCGCC 59.679 55.000 0.00 0.0 44.90 6.13 R
4879 5947 0.530211 CCAGCGCTCTGAAGATCCTG 60.530 60.000 7.13 0.0 42.95 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.390340 GTCGAGCAGCAATCCAGACA 60.390 55.000 0.00 0.00 0.00 3.41
89 90 8.691797 GGATACCAAAATATTGCTTTTGAGGTA 58.308 33.333 9.72 5.81 44.97 3.08
130 131 3.897239 TCAGAAACCTTCTTTTCCTGCA 58.103 40.909 0.00 0.00 38.11 4.41
155 156 4.032703 ACTGTGTCATCAGTTTGTTTGC 57.967 40.909 3.18 0.00 44.92 3.68
174 175 4.645762 TGCTATCACTCTGATCTGACAC 57.354 45.455 0.00 0.00 38.26 3.67
176 177 4.708909 TGCTATCACTCTGATCTGACACTT 59.291 41.667 0.00 0.00 38.26 3.16
181 182 4.001652 CACTCTGATCTGACACTTGCAAT 58.998 43.478 0.00 0.00 0.00 3.56
182 183 4.093115 CACTCTGATCTGACACTTGCAATC 59.907 45.833 0.00 0.00 0.00 2.67
192 193 2.154462 CACTTGCAATCCTTCCGTTCT 58.846 47.619 0.00 0.00 0.00 3.01
214 215 4.074259 TCATTGACCAACAGGTGATGAAG 58.926 43.478 7.47 0.00 34.34 3.02
226 227 9.293404 CAACAGGTGATGAAGAATGGATATATT 57.707 33.333 0.00 0.00 0.00 1.28
259 260 2.685388 TCTCTTCCAGTCATGAGTAGCG 59.315 50.000 1.86 0.00 0.00 4.26
279 300 2.159421 CGTAGCTGAACCTGATGTACGT 60.159 50.000 0.00 0.00 0.00 3.57
286 307 0.613260 ACCTGATGTACGTGGCATGT 59.387 50.000 17.65 17.65 0.00 3.21
290 311 3.687212 CCTGATGTACGTGGCATGTAAAA 59.313 43.478 20.48 12.62 0.00 1.52
292 313 5.163663 CCTGATGTACGTGGCATGTAAAATT 60.164 40.000 20.48 2.00 0.00 1.82
293 314 6.037720 CCTGATGTACGTGGCATGTAAAATTA 59.962 38.462 20.48 12.77 0.00 1.40
307 328 6.528537 TGTAAAATTATGTGAAGCATGCCT 57.471 33.333 15.66 0.00 38.47 4.75
309 330 3.976793 AATTATGTGAAGCATGCCTCG 57.023 42.857 15.66 0.00 38.47 4.63
311 332 2.401583 TATGTGAAGCATGCCTCGTT 57.598 45.000 15.66 0.95 38.47 3.85
312 333 2.401583 ATGTGAAGCATGCCTCGTTA 57.598 45.000 15.66 1.65 36.26 3.18
313 334 1.438651 TGTGAAGCATGCCTCGTTAC 58.561 50.000 15.66 6.19 0.00 2.50
314 335 0.370273 GTGAAGCATGCCTCGTTACG 59.630 55.000 15.66 0.00 0.00 3.18
368 393 2.928416 GAACTGGGTTCCTTCCGTG 58.072 57.895 0.00 0.00 36.65 4.94
369 394 0.605589 GAACTGGGTTCCTTCCGTGG 60.606 60.000 0.00 0.00 36.65 4.94
383 408 5.424252 TCCTTCCGTGGTCTCTGTAAATATT 59.576 40.000 0.00 0.00 0.00 1.28
386 411 7.599245 CCTTCCGTGGTCTCTGTAAATATTATC 59.401 40.741 0.00 0.00 0.00 1.75
426 451 5.168526 TCAACTAATTAATCATGTGCGCC 57.831 39.130 4.18 0.00 0.00 6.53
427 452 4.036262 TCAACTAATTAATCATGTGCGCCC 59.964 41.667 4.18 0.00 0.00 6.13
428 453 3.550820 ACTAATTAATCATGTGCGCCCA 58.449 40.909 4.18 0.00 0.00 5.36
429 454 4.144297 ACTAATTAATCATGTGCGCCCAT 58.856 39.130 4.18 0.56 0.00 4.00
430 455 3.374220 AATTAATCATGTGCGCCCATG 57.626 42.857 24.64 24.64 42.89 3.66
431 456 1.761449 TTAATCATGTGCGCCCATGT 58.239 45.000 28.12 15.38 42.29 3.21
432 457 1.761449 TAATCATGTGCGCCCATGTT 58.239 45.000 28.12 22.63 42.29 2.71
433 458 1.761449 AATCATGTGCGCCCATGTTA 58.239 45.000 28.12 13.80 42.29 2.41
435 460 1.761449 TCATGTGCGCCCATGTTATT 58.239 45.000 28.12 0.00 42.29 1.40
436 461 1.404748 TCATGTGCGCCCATGTTATTG 59.595 47.619 28.12 7.59 42.29 1.90
437 462 0.102844 ATGTGCGCCCATGTTATTGC 59.897 50.000 4.01 0.00 0.00 3.56
438 463 1.226945 GTGCGCCCATGTTATTGCC 60.227 57.895 4.18 0.00 0.00 4.52
439 464 2.026014 GCGCCCATGTTATTGCCG 59.974 61.111 0.00 0.00 0.00 5.69
441 466 1.063972 CGCCCATGTTATTGCCGTG 59.936 57.895 0.00 0.00 0.00 4.94
442 467 1.437160 GCCCATGTTATTGCCGTGG 59.563 57.895 0.00 0.00 38.48 4.94
443 468 1.319614 GCCCATGTTATTGCCGTGGT 61.320 55.000 0.00 0.00 37.29 4.16
444 469 1.181786 CCCATGTTATTGCCGTGGTT 58.818 50.000 0.00 0.00 37.29 3.67
445 470 1.548269 CCCATGTTATTGCCGTGGTTT 59.452 47.619 0.00 0.00 37.29 3.27
446 471 2.028567 CCCATGTTATTGCCGTGGTTTT 60.029 45.455 0.00 0.00 37.29 2.43
447 472 2.992543 CCATGTTATTGCCGTGGTTTTG 59.007 45.455 0.00 0.00 34.82 2.44
448 473 3.553922 CCATGTTATTGCCGTGGTTTTGT 60.554 43.478 0.00 0.00 34.82 2.83
449 474 3.802948 TGTTATTGCCGTGGTTTTGTT 57.197 38.095 0.00 0.00 0.00 2.83
450 475 4.124851 TGTTATTGCCGTGGTTTTGTTT 57.875 36.364 0.00 0.00 0.00 2.83
457 482 2.025898 CCGTGGTTTTGTTTACCCTGT 58.974 47.619 0.00 0.00 34.66 4.00
483 519 1.072965 ACCTTCTTTGGCTGTCAGGAG 59.927 52.381 1.14 0.00 0.00 3.69
492 528 1.280421 GGCTGTCAGGAGACCTTGAAT 59.720 52.381 1.14 0.00 44.33 2.57
493 529 2.354259 GCTGTCAGGAGACCTTGAATG 58.646 52.381 1.14 0.00 44.33 2.67
511 547 7.278424 CCTTGAATGATAATTCCGTGCAAAATT 59.722 33.333 0.00 0.00 0.00 1.82
521 557 4.865776 TCCGTGCAAAATTAAACTCCTTG 58.134 39.130 0.00 0.00 0.00 3.61
532 568 7.530426 AATTAAACTCCTTGCATTCTGAGTT 57.470 32.000 12.28 12.28 46.88 3.01
536 572 0.529378 CCTTGCATTCTGAGTTGGCC 59.471 55.000 0.00 0.00 0.00 5.36
540 576 2.037901 TGCATTCTGAGTTGGCCAAAA 58.962 42.857 22.47 11.20 0.00 2.44
541 577 2.433604 TGCATTCTGAGTTGGCCAAAAA 59.566 40.909 22.47 10.12 0.00 1.94
563 599 2.311124 AATTCAGTAGTAGGGCGTGC 57.689 50.000 0.00 0.00 0.00 5.34
564 600 1.191535 ATTCAGTAGTAGGGCGTGCA 58.808 50.000 0.00 0.00 0.00 4.57
565 601 0.245539 TTCAGTAGTAGGGCGTGCAC 59.754 55.000 6.82 6.82 0.00 4.57
566 602 0.611062 TCAGTAGTAGGGCGTGCACT 60.611 55.000 16.19 0.73 0.00 4.40
567 603 0.246635 CAGTAGTAGGGCGTGCACTT 59.753 55.000 16.19 0.26 0.00 3.16
568 604 0.246635 AGTAGTAGGGCGTGCACTTG 59.753 55.000 16.19 0.69 0.00 3.16
580 1120 2.031191 CGTGCACTTGTTTTTAGGTCGT 59.969 45.455 16.19 0.00 0.00 4.34
595 1135 9.887406 TTTTTAGGTCGTTGATTTTGACTAATC 57.113 29.630 0.00 0.00 35.54 1.75
596 1136 7.605410 TTAGGTCGTTGATTTTGACTAATCC 57.395 36.000 0.00 0.00 34.34 3.01
599 1139 6.488683 AGGTCGTTGATTTTGACTAATCCAAA 59.511 34.615 0.00 0.00 34.34 3.28
601 1141 7.326063 GGTCGTTGATTTTGACTAATCCAAAAG 59.674 37.037 0.00 0.00 43.83 2.27
603 1143 7.860373 TCGTTGATTTTGACTAATCCAAAAGTG 59.140 33.333 0.00 0.00 43.83 3.16
604 1144 7.647715 CGTTGATTTTGACTAATCCAAAAGTGT 59.352 33.333 0.00 0.00 43.83 3.55
607 1261 9.959749 TGATTTTGACTAATCCAAAAGTGTAAC 57.040 29.630 0.00 0.00 43.83 2.50
640 1294 6.129062 CGAATACGAATCCAGTGATTAGCTTC 60.129 42.308 0.00 0.00 41.30 3.86
642 1296 4.437239 ACGAATCCAGTGATTAGCTTCTG 58.563 43.478 0.00 0.00 41.30 3.02
649 1365 5.053145 CCAGTGATTAGCTTCTGATGGTAC 58.947 45.833 0.00 0.00 0.00 3.34
667 1383 6.233905 TGGTACATAATACATGTGCTCAGT 57.766 37.500 9.11 4.55 35.44 3.41
679 1400 1.215647 GCTCAGTACACCTGACCGG 59.784 63.158 0.00 0.00 45.34 5.28
680 1401 1.248785 GCTCAGTACACCTGACCGGA 61.249 60.000 9.46 0.00 45.34 5.14
681 1402 0.811915 CTCAGTACACCTGACCGGAG 59.188 60.000 9.46 0.00 45.34 4.63
682 1403 1.215647 CAGTACACCTGACCGGAGC 59.784 63.158 9.46 0.00 44.49 4.70
683 1404 2.181021 GTACACCTGACCGGAGCG 59.819 66.667 9.46 0.00 36.31 5.03
684 1405 2.034532 TACACCTGACCGGAGCGA 59.965 61.111 9.46 0.00 36.31 4.93
685 1406 2.044555 TACACCTGACCGGAGCGAG 61.045 63.158 9.46 0.00 36.31 5.03
686 1407 4.803426 CACCTGACCGGAGCGAGC 62.803 72.222 9.46 0.00 36.31 5.03
688 1409 4.504916 CCTGACCGGAGCGAGCTG 62.505 72.222 9.46 0.00 33.16 4.24
689 1410 4.504916 CTGACCGGAGCGAGCTGG 62.505 72.222 9.46 0.66 40.29 4.85
696 1417 1.302511 GGAGCGAGCTGGGTTTGAA 60.303 57.895 0.84 0.00 0.00 2.69
729 1450 5.241949 ACCAACATTTAAGACGCCAAATACA 59.758 36.000 0.00 0.00 0.00 2.29
730 1451 6.071616 ACCAACATTTAAGACGCCAAATACAT 60.072 34.615 0.00 0.00 0.00 2.29
731 1452 7.121463 ACCAACATTTAAGACGCCAAATACATA 59.879 33.333 0.00 0.00 0.00 2.29
732 1453 8.134895 CCAACATTTAAGACGCCAAATACATAT 58.865 33.333 0.00 0.00 0.00 1.78
773 1560 6.385649 GTCAAACAGACTTGTTGGGATAAA 57.614 37.500 0.00 0.00 46.54 1.40
833 1623 6.211584 AGTGCTCCAAGTTCTTGATAAGACTA 59.788 38.462 13.29 0.00 37.23 2.59
861 1652 1.962547 CGACTGCACAAAACGAAATCG 59.037 47.619 0.48 0.48 46.33 3.34
870 1661 5.713281 CACAAAACGAAATCGAAAACCAAG 58.287 37.500 10.16 0.00 43.02 3.61
873 1664 3.701532 ACGAAATCGAAAACCAAGCAA 57.298 38.095 10.16 0.00 43.02 3.91
884 1675 2.371658 ACCAAGCAAAAGAAGCTCCT 57.628 45.000 0.00 0.00 42.53 3.69
1110 1925 2.603652 GGTGGTGAAGGGGAGGTCC 61.604 68.421 0.00 0.00 0.00 4.46
1210 2025 1.614241 CCCCCAAGGTCGAAGATCGT 61.614 60.000 0.00 0.00 46.28 3.73
1217 2032 4.847516 TCGAAGATCGTGCCCGCG 62.848 66.667 0.00 0.00 41.35 6.46
1278 2097 2.093447 TGCTTGCTTTAGGGTCTCTAGC 60.093 50.000 0.00 0.00 0.00 3.42
1343 2162 2.134630 CTGTGCCCCCTGAGCTTTCT 62.135 60.000 0.00 0.00 0.00 2.52
1406 2226 2.407210 CACACACGCACCAACCAC 59.593 61.111 0.00 0.00 0.00 4.16
1419 2239 1.152963 AACCACGGGGATGCATAGC 60.153 57.895 12.96 0.00 38.05 2.97
1434 2254 0.610687 ATAGCGATTAGGGCTCCTGC 59.389 55.000 4.16 0.00 41.80 4.85
1470 2290 0.696501 GGTACCCATTCCCACACACT 59.303 55.000 0.00 0.00 0.00 3.55
1510 2330 0.807496 GCAACTCATGTCTTCAGGGC 59.193 55.000 0.00 0.00 0.00 5.19
1599 2419 2.490509 GTTTCCCCATTCCGTTAGTTGG 59.509 50.000 0.00 0.00 0.00 3.77
1616 2436 3.632145 AGTTGGTTAACAGAGGCAAACAG 59.368 43.478 8.10 0.00 39.30 3.16
1649 2469 5.160641 CCGTACAATGGGAAAACATGAAAG 58.839 41.667 0.00 0.00 0.00 2.62
1656 2476 4.238669 TGGGAAAACATGAAAGGGGAAAT 58.761 39.130 0.00 0.00 0.00 2.17
1657 2477 4.041444 TGGGAAAACATGAAAGGGGAAATG 59.959 41.667 0.00 0.00 0.00 2.32
1784 2605 2.364324 ACATCCCATACTGACGCGTAAT 59.636 45.455 13.97 2.61 0.00 1.89
1832 2653 6.071840 ACCAATCAATCTAGTAGGCTATCGAC 60.072 42.308 0.00 0.00 0.00 4.20
1860 2681 0.615331 TCCCAGGAAGCTTGCTGTAG 59.385 55.000 36.27 28.83 44.06 2.74
1865 2686 3.406764 CAGGAAGCTTGCTGTAGAAGTT 58.593 45.455 32.91 2.35 41.12 2.66
1959 2780 5.132897 ACTCTTCAGAGCAGTACAAGAAG 57.867 43.478 3.58 0.00 45.79 2.85
1984 2813 5.959527 GTCACTGCATTTATGTCATTACGTG 59.040 40.000 0.00 0.00 0.00 4.49
2024 2853 4.657013 TGTTGAGTTTATATGTGCCACCA 58.343 39.130 0.00 0.00 0.00 4.17
2064 2893 5.702670 CACAAGGACAATTGAGTGTATGAGT 59.297 40.000 13.59 0.00 34.20 3.41
2137 2981 3.134623 CACAGTATTAGGTCAGGGCATCA 59.865 47.826 0.00 0.00 0.00 3.07
2452 3313 7.418337 ACTTTTGGGTTGACTTGTTTTATCT 57.582 32.000 0.00 0.00 0.00 1.98
2603 3464 8.824756 TCCATATACCTAGATGACAAGGATAC 57.175 38.462 0.00 0.00 36.66 2.24
2779 3642 6.460123 GGGAATTATGCTGTCTGTTTATGGTG 60.460 42.308 0.00 0.00 0.00 4.17
2782 3645 6.978343 TTATGCTGTCTGTTTATGGTGTAC 57.022 37.500 0.00 0.00 0.00 2.90
2787 3650 4.062293 TGTCTGTTTATGGTGTACACTGC 58.938 43.478 24.55 10.37 0.00 4.40
2832 3695 7.436933 CAGGCATAGTCTATGACAGTTGATTA 58.563 38.462 24.69 0.00 46.85 1.75
2882 3746 6.984474 TGCAAGCCTAGTTCTGTATTATGTAC 59.016 38.462 0.00 0.00 0.00 2.90
2883 3747 7.147724 TGCAAGCCTAGTTCTGTATTATGTACT 60.148 37.037 0.00 0.00 0.00 2.73
2884 3748 7.169982 GCAAGCCTAGTTCTGTATTATGTACTG 59.830 40.741 0.00 0.00 0.00 2.74
2898 3764 1.493022 TGTACTGGAAAAGTGGCTGGT 59.507 47.619 0.00 0.00 40.26 4.00
2990 3861 2.338577 ATCACAGTAGGAATGCTGGC 57.661 50.000 0.00 0.00 37.07 4.85
3065 3936 5.459762 CCATTATTATTGAAACTGCTTGGCG 59.540 40.000 0.00 0.00 0.00 5.69
3196 4080 3.432252 CACGTAACTAAACAAGCTCCAGG 59.568 47.826 0.00 0.00 0.00 4.45
3299 4184 0.673644 CTCCAAAGCCTACCACGGTG 60.674 60.000 0.00 0.00 0.00 4.94
3314 4199 0.108662 CGGTGTGCTAGATCACTGCA 60.109 55.000 14.28 0.00 37.81 4.41
3408 4300 4.097589 GCGGTCTCACCTGTTACTTATAGT 59.902 45.833 0.00 0.00 35.66 2.12
3432 4328 7.389053 AGTCTGTTAATGAAGAATTGAGTGGAC 59.611 37.037 0.00 0.00 0.00 4.02
3461 4357 1.910819 GTTGCATCGTTGGTTATTGCG 59.089 47.619 0.00 0.00 36.11 4.85
3472 4369 4.364415 TGGTTATTGCGTGATTAAAGCC 57.636 40.909 0.00 0.00 0.00 4.35
3494 4391 5.971792 GCCGCCAAATCTTATTCTTAAAGTC 59.028 40.000 0.00 0.00 0.00 3.01
3515 4412 5.009010 AGTCAATTTTGCCACAGTAGACAAG 59.991 40.000 0.00 0.00 0.00 3.16
3536 4433 5.904362 AGCAATACAGAAAATGTTCCCTC 57.096 39.130 0.00 0.00 39.96 4.30
3578 4476 6.168389 AGGTACTTTAATTAACTCACGGTGG 58.832 40.000 8.50 1.73 27.25 4.61
3655 4553 1.341209 CGCCTATATCTCAGTGTGCCA 59.659 52.381 0.00 0.00 0.00 4.92
3665 4563 4.973168 TCTCAGTGTGCCAGAAACTAAAT 58.027 39.130 0.00 0.00 0.00 1.40
3673 4571 9.830975 AGTGTGCCAGAAACTAAATTTATTTTT 57.169 25.926 13.01 9.02 0.00 1.94
3694 4592 9.902196 ATTTTTACGTTGGTTAATAAGACTTGG 57.098 29.630 0.00 0.00 0.00 3.61
3859 4757 8.458573 TGCTCTTTTGGTTTAAACTCTAATCA 57.541 30.769 17.50 3.70 0.00 2.57
3869 4767 7.393515 GGTTTAAACTCTAATCAAGTCCATGGT 59.606 37.037 17.50 0.00 0.00 3.55
3894 4792 4.861210 TGCATCGAATTTTAACAAACGGT 58.139 34.783 0.00 0.00 0.00 4.83
3908 4806 4.429108 ACAAACGGTGAATTTTCAACTGG 58.571 39.130 6.76 0.00 42.66 4.00
3956 4854 2.594592 GTGGCCAGTGGTGTGGTC 60.595 66.667 5.11 0.00 43.11 4.02
3972 4870 5.242838 GGTGTGGTCAGGAACATGAATAAAA 59.757 40.000 0.00 0.00 0.00 1.52
4059 4957 4.545208 AACCTAGCTCTTGTTCTCCTTC 57.455 45.455 0.00 0.00 0.00 3.46
4114 5013 6.295123 GGAGCATGTAATCTATTACTTCCGGA 60.295 42.308 0.00 0.00 42.32 5.14
4121 5020 5.776173 ATCTATTACTTCCGGAGACACTG 57.224 43.478 3.34 0.00 0.00 3.66
4125 5024 4.373116 TTCCGGAGACACTGGCGC 62.373 66.667 3.34 0.00 44.31 6.53
4155 5054 0.603707 TCGCTTGGTTTCTGAGGCTG 60.604 55.000 0.00 0.00 0.00 4.85
4174 5073 1.168714 GTGGCTGGGATTTCACTGTC 58.831 55.000 0.00 0.00 0.00 3.51
4217 5116 3.200522 GGCTGTTGTATGCCTGCC 58.799 61.111 0.00 0.00 45.26 4.85
4219 5118 1.660560 GGCTGTTGTATGCCTGCCTG 61.661 60.000 0.00 0.00 45.26 4.85
4220 5119 0.962356 GCTGTTGTATGCCTGCCTGT 60.962 55.000 0.00 0.00 0.00 4.00
4221 5120 1.538047 CTGTTGTATGCCTGCCTGTT 58.462 50.000 0.00 0.00 0.00 3.16
4224 5123 2.035704 TGTTGTATGCCTGCCTGTTTTG 59.964 45.455 0.00 0.00 0.00 2.44
4226 5125 1.202989 TGTATGCCTGCCTGTTTTGGA 60.203 47.619 0.00 0.00 0.00 3.53
4227 5126 2.102578 GTATGCCTGCCTGTTTTGGAT 58.897 47.619 0.00 0.00 0.00 3.41
4230 5129 1.260544 GCCTGCCTGTTTTGGATTCT 58.739 50.000 0.00 0.00 0.00 2.40
4233 5132 2.611224 CCTGCCTGTTTTGGATTCTTGC 60.611 50.000 0.00 0.00 0.00 4.01
4330 5229 9.454585 CAATGTATAGGATGCAATGTAACAAAG 57.545 33.333 0.00 0.00 0.00 2.77
4338 5237 8.408601 AGGATGCAATGTAACAAAGCTATAAAG 58.591 33.333 0.00 0.00 0.00 1.85
4421 5321 0.978907 ATTTGGCTTCCTTTGCTGGG 59.021 50.000 0.00 0.00 0.00 4.45
4453 5353 3.266510 TCATGGCAGTGTCTTGGTATC 57.733 47.619 10.41 0.00 0.00 2.24
4456 5356 1.696884 TGGCAGTGTCTTGGTATCACA 59.303 47.619 0.00 0.00 34.94 3.58
4466 5366 5.119694 GTCTTGGTATCACAGAGGAAATCC 58.880 45.833 0.00 0.00 0.00 3.01
4634 5647 4.785511 ATTTACTACAGTCGTGTGAGCT 57.214 40.909 0.00 0.00 37.52 4.09
4670 5683 8.682710 GCTCATCAATTTTGGGTACAAGTATAA 58.317 33.333 0.00 0.00 37.97 0.98
4758 5826 0.896940 TTCTCCCAGACGGCGTAGTT 60.897 55.000 14.74 0.00 0.00 2.24
4783 5851 4.063967 TGCGCCGAGGTCACGAAT 62.064 61.111 4.18 0.00 35.09 3.34
4810 5878 3.599285 GATCACGGCCCCAACGTCA 62.599 63.158 0.00 0.00 43.58 4.35
4851 5919 1.079127 CCACCTTGCCGTCGATCTT 60.079 57.895 0.00 0.00 0.00 2.40
4879 5947 3.195698 GCGTCCCCTTCGTGCATC 61.196 66.667 0.00 0.00 0.00 3.91
4891 5959 2.102578 TCGTGCATCAGGATCTTCAGA 58.897 47.619 0.00 0.00 0.00 3.27
4897 5965 0.459078 TCAGGATCTTCAGAGCGCTG 59.541 55.000 18.48 11.71 43.67 5.18
4916 5984 2.030412 TCGCTGTGATGCCGTTGT 59.970 55.556 0.00 0.00 0.00 3.32
4936 6004 1.599047 CTTCCTGATCGCCACCAGT 59.401 57.895 0.00 0.00 0.00 4.00
4948 6016 3.381983 ACCAGTGCCGCGATCTCA 61.382 61.111 8.23 0.00 0.00 3.27
4953 6021 1.953138 GTGCCGCGATCTCATCCTG 60.953 63.158 8.23 0.00 0.00 3.86
4954 6022 2.127232 TGCCGCGATCTCATCCTGA 61.127 57.895 8.23 0.00 0.00 3.86
5010 6078 9.844790 CTACAAATCATTGAAGCAACAATTCTA 57.155 29.630 5.80 0.00 38.25 2.10
5036 6104 9.880157 AAGTTTCCTGAATGAATAAATGAATGG 57.120 29.630 0.00 0.00 0.00 3.16
5037 6105 9.039165 AGTTTCCTGAATGAATAAATGAATGGT 57.961 29.630 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.141053 GGGTTATTCATCGAGCCCTGT 59.859 52.381 0.00 0.00 33.58 4.00
89 90 2.765689 AGCTGAGTGATAGGTAGCCT 57.234 50.000 0.00 0.00 37.71 4.58
105 106 4.582240 CAGGAAAAGAAGGTTTCTGAAGCT 59.418 41.667 4.26 0.00 45.04 3.74
155 156 5.042593 GCAAGTGTCAGATCAGAGTGATAG 58.957 45.833 0.00 0.00 37.20 2.08
174 175 2.426522 TGAGAACGGAAGGATTGCAAG 58.573 47.619 4.94 0.00 35.47 4.01
176 177 2.749076 CAATGAGAACGGAAGGATTGCA 59.251 45.455 0.00 0.00 35.47 4.08
181 182 1.974957 TGGTCAATGAGAACGGAAGGA 59.025 47.619 0.00 0.00 36.45 3.36
182 183 2.472695 TGGTCAATGAGAACGGAAGG 57.527 50.000 0.00 0.00 36.45 3.46
192 193 3.786368 TCATCACCTGTTGGTCAATGA 57.214 42.857 0.00 0.00 46.60 2.57
214 215 5.938125 AGTAACGGTGGCAATATATCCATTC 59.062 40.000 0.00 0.00 34.47 2.67
226 227 0.606604 GGAAGAGAGTAACGGTGGCA 59.393 55.000 0.00 0.00 0.00 4.92
259 260 3.179830 CACGTACATCAGGTTCAGCTAC 58.820 50.000 0.00 0.00 0.00 3.58
263 264 1.337728 TGCCACGTACATCAGGTTCAG 60.338 52.381 0.00 0.00 0.00 3.02
264 265 0.682292 TGCCACGTACATCAGGTTCA 59.318 50.000 0.00 0.00 0.00 3.18
265 266 1.665679 CATGCCACGTACATCAGGTTC 59.334 52.381 0.47 0.00 0.00 3.62
266 267 1.003118 ACATGCCACGTACATCAGGTT 59.997 47.619 0.47 0.00 0.00 3.50
279 300 6.278172 TGCTTCACATAATTTTACATGCCA 57.722 33.333 0.00 0.00 0.00 4.92
286 307 5.356751 ACGAGGCATGCTTCACATAATTTTA 59.643 36.000 27.01 0.00 36.64 1.52
290 311 2.923121 ACGAGGCATGCTTCACATAAT 58.077 42.857 27.01 4.56 36.64 1.28
292 313 2.401583 AACGAGGCATGCTTCACATA 57.598 45.000 27.01 0.00 36.64 2.29
293 314 2.009774 GTAACGAGGCATGCTTCACAT 58.990 47.619 27.01 15.39 40.66 3.21
312 333 9.101655 GTGGAATATACAGGTTAATTTACACGT 57.898 33.333 0.00 0.00 0.00 4.49
313 334 9.321562 AGTGGAATATACAGGTTAATTTACACG 57.678 33.333 0.00 0.00 30.97 4.49
334 359 3.007940 CCAGTTCCTGTACAATGAGTGGA 59.992 47.826 15.70 7.41 0.00 4.02
356 381 0.037232 CAGAGACCACGGAAGGAACC 60.037 60.000 0.00 0.00 0.00 3.62
363 388 6.014840 GGGATAATATTTACAGAGACCACGGA 60.015 42.308 0.00 0.00 0.00 4.69
364 389 6.164176 GGGATAATATTTACAGAGACCACGG 58.836 44.000 0.00 0.00 0.00 4.94
365 390 6.755206 TGGGATAATATTTACAGAGACCACG 58.245 40.000 0.00 0.00 0.00 4.94
368 393 8.598041 AGTGATGGGATAATATTTACAGAGACC 58.402 37.037 0.00 0.00 0.00 3.85
421 446 2.769539 CGGCAATAACATGGGCGCA 61.770 57.895 10.83 5.70 43.46 6.09
422 447 2.026014 CGGCAATAACATGGGCGC 59.974 61.111 0.00 0.00 43.46 6.53
424 449 1.319614 ACCACGGCAATAACATGGGC 61.320 55.000 0.00 0.00 34.56 5.36
426 451 2.992543 CAAAACCACGGCAATAACATGG 59.007 45.455 0.00 0.00 36.46 3.66
427 452 3.648009 ACAAAACCACGGCAATAACATG 58.352 40.909 0.00 0.00 0.00 3.21
428 453 4.329462 AACAAAACCACGGCAATAACAT 57.671 36.364 0.00 0.00 0.00 2.71
429 454 3.802948 AACAAAACCACGGCAATAACA 57.197 38.095 0.00 0.00 0.00 2.41
430 455 4.445052 GGTAAACAAAACCACGGCAATAAC 59.555 41.667 0.00 0.00 36.96 1.89
431 456 4.501058 GGGTAAACAAAACCACGGCAATAA 60.501 41.667 0.00 0.00 38.87 1.40
432 457 3.005578 GGGTAAACAAAACCACGGCAATA 59.994 43.478 0.00 0.00 38.87 1.90
433 458 2.224090 GGGTAAACAAAACCACGGCAAT 60.224 45.455 0.00 0.00 38.87 3.56
435 460 0.745468 GGGTAAACAAAACCACGGCA 59.255 50.000 0.00 0.00 38.87 5.69
436 461 1.034356 AGGGTAAACAAAACCACGGC 58.966 50.000 0.00 0.00 38.87 5.68
437 462 2.025898 ACAGGGTAAACAAAACCACGG 58.974 47.619 0.00 0.00 38.87 4.94
438 463 3.626670 TGTACAGGGTAAACAAAACCACG 59.373 43.478 0.00 0.00 38.87 4.94
439 464 4.398673 TGTGTACAGGGTAAACAAAACCAC 59.601 41.667 0.00 0.00 38.87 4.16
441 466 5.342433 GTTGTGTACAGGGTAAACAAAACC 58.658 41.667 12.37 0.00 35.99 3.27
442 467 5.125900 AGGTTGTGTACAGGGTAAACAAAAC 59.874 40.000 12.37 9.38 39.55 2.43
443 468 5.262804 AGGTTGTGTACAGGGTAAACAAAA 58.737 37.500 12.37 0.00 32.92 2.44
444 469 4.857679 AGGTTGTGTACAGGGTAAACAAA 58.142 39.130 12.37 0.00 32.92 2.83
445 470 4.506937 AGGTTGTGTACAGGGTAAACAA 57.493 40.909 7.80 7.80 0.00 2.83
446 471 4.164604 AGAAGGTTGTGTACAGGGTAAACA 59.835 41.667 0.00 0.00 0.00 2.83
447 472 4.711399 AGAAGGTTGTGTACAGGGTAAAC 58.289 43.478 0.00 0.00 0.00 2.01
448 473 5.376756 AAGAAGGTTGTGTACAGGGTAAA 57.623 39.130 0.00 0.00 0.00 2.01
449 474 5.127491 CAAAGAAGGTTGTGTACAGGGTAA 58.873 41.667 0.00 0.00 0.00 2.85
450 475 4.445162 CCAAAGAAGGTTGTGTACAGGGTA 60.445 45.833 0.00 0.00 0.00 3.69
483 519 4.335315 TGCACGGAATTATCATTCAAGGTC 59.665 41.667 2.21 0.00 40.77 3.85
492 528 7.757624 GGAGTTTAATTTTGCACGGAATTATCA 59.242 33.333 8.90 0.43 30.36 2.15
493 529 7.973944 AGGAGTTTAATTTTGCACGGAATTATC 59.026 33.333 8.90 5.55 30.36 1.75
511 547 4.761739 CCAACTCAGAATGCAAGGAGTTTA 59.238 41.667 17.57 0.00 45.52 2.01
521 557 2.818130 TTTTGGCCAACTCAGAATGC 57.182 45.000 20.35 0.00 34.76 3.56
541 577 3.439129 GCACGCCCTACTACTGAATTTTT 59.561 43.478 0.00 0.00 0.00 1.94
542 578 3.007635 GCACGCCCTACTACTGAATTTT 58.992 45.455 0.00 0.00 0.00 1.82
545 581 1.134788 GTGCACGCCCTACTACTGAAT 60.135 52.381 0.00 0.00 0.00 2.57
546 582 0.245539 GTGCACGCCCTACTACTGAA 59.754 55.000 0.00 0.00 0.00 3.02
547 583 0.611062 AGTGCACGCCCTACTACTGA 60.611 55.000 12.01 0.00 0.00 3.41
548 584 0.246635 AAGTGCACGCCCTACTACTG 59.753 55.000 12.01 0.00 0.00 2.74
550 586 0.037605 ACAAGTGCACGCCCTACTAC 60.038 55.000 12.01 0.00 0.00 2.73
552 588 0.179029 AAACAAGTGCACGCCCTACT 60.179 50.000 12.01 0.00 0.00 2.57
553 589 0.666374 AAAACAAGTGCACGCCCTAC 59.334 50.000 12.01 0.00 0.00 3.18
556 592 1.601914 CCTAAAAACAAGTGCACGCCC 60.602 52.381 12.01 0.00 0.00 6.13
557 593 1.066454 ACCTAAAAACAAGTGCACGCC 59.934 47.619 12.01 0.00 0.00 5.68
558 594 2.381589 GACCTAAAAACAAGTGCACGC 58.618 47.619 12.01 0.00 0.00 5.34
559 595 2.031191 ACGACCTAAAAACAAGTGCACG 59.969 45.455 12.01 0.00 0.00 5.34
560 596 3.685836 ACGACCTAAAAACAAGTGCAC 57.314 42.857 9.40 9.40 0.00 4.57
563 599 7.486551 TCAAAATCAACGACCTAAAAACAAGTG 59.513 33.333 0.00 0.00 0.00 3.16
564 600 7.486870 GTCAAAATCAACGACCTAAAAACAAGT 59.513 33.333 0.00 0.00 0.00 3.16
565 601 7.700656 AGTCAAAATCAACGACCTAAAAACAAG 59.299 33.333 0.00 0.00 0.00 3.16
566 602 7.540299 AGTCAAAATCAACGACCTAAAAACAA 58.460 30.769 0.00 0.00 0.00 2.83
567 603 7.090953 AGTCAAAATCAACGACCTAAAAACA 57.909 32.000 0.00 0.00 0.00 2.83
568 604 9.673454 ATTAGTCAAAATCAACGACCTAAAAAC 57.327 29.630 0.00 0.00 0.00 2.43
599 1139 7.467557 TCGTATTCGAACAAAAGTTACACTT 57.532 32.000 0.00 0.00 43.34 3.16
615 1269 5.223382 AGCTAATCACTGGATTCGTATTCG 58.777 41.667 0.00 0.00 42.66 3.34
621 1275 4.686972 TCAGAAGCTAATCACTGGATTCG 58.313 43.478 0.00 0.00 42.66 3.34
629 1283 8.839310 ATTATGTACCATCAGAAGCTAATCAC 57.161 34.615 0.00 0.00 0.00 3.06
634 1288 8.870116 ACATGTATTATGTACCATCAGAAGCTA 58.130 33.333 0.00 0.00 0.00 3.32
635 1289 7.658982 CACATGTATTATGTACCATCAGAAGCT 59.341 37.037 0.00 0.00 0.00 3.74
640 1294 6.930722 TGAGCACATGTATTATGTACCATCAG 59.069 38.462 0.00 0.00 0.00 2.90
642 1296 6.931281 ACTGAGCACATGTATTATGTACCATC 59.069 38.462 0.00 0.00 0.00 3.51
649 1365 6.283694 AGGTGTACTGAGCACATGTATTATG 58.716 40.000 0.00 0.00 38.51 1.90
652 1368 4.826274 AGGTGTACTGAGCACATGTATT 57.174 40.909 0.00 0.00 38.51 1.89
665 1381 2.341101 CGCTCCGGTCAGGTGTACT 61.341 63.158 0.00 0.00 41.99 2.73
667 1383 2.034532 TCGCTCCGGTCAGGTGTA 59.965 61.111 0.00 0.00 41.99 2.90
679 1400 0.320771 TCTTCAAACCCAGCTCGCTC 60.321 55.000 0.00 0.00 0.00 5.03
680 1401 0.108585 TTCTTCAAACCCAGCTCGCT 59.891 50.000 0.00 0.00 0.00 4.93
681 1402 0.951558 TTTCTTCAAACCCAGCTCGC 59.048 50.000 0.00 0.00 0.00 5.03
682 1403 3.708563 TTTTTCTTCAAACCCAGCTCG 57.291 42.857 0.00 0.00 0.00 5.03
706 1427 5.704888 TGTATTTGGCGTCTTAAATGTTGG 58.295 37.500 0.00 0.00 0.00 3.77
764 1551 5.843673 TCGCATATTGCTTTTTATCCCAA 57.156 34.783 0.00 0.00 42.25 4.12
765 1552 5.359576 ACTTCGCATATTGCTTTTTATCCCA 59.640 36.000 0.00 0.00 42.25 4.37
766 1553 5.831997 ACTTCGCATATTGCTTTTTATCCC 58.168 37.500 0.00 0.00 42.25 3.85
767 1554 7.639945 AGTACTTCGCATATTGCTTTTTATCC 58.360 34.615 0.00 0.00 42.25 2.59
771 1558 9.289303 CAAATAGTACTTCGCATATTGCTTTTT 57.711 29.630 0.00 0.00 42.25 1.94
772 1559 8.673711 TCAAATAGTACTTCGCATATTGCTTTT 58.326 29.630 0.00 0.00 42.25 2.27
773 1560 8.208718 TCAAATAGTACTTCGCATATTGCTTT 57.791 30.769 0.00 0.00 42.25 3.51
785 1572 5.727434 TCCCTCCGTTTCAAATAGTACTTC 58.273 41.667 0.00 0.00 0.00 3.01
795 1585 0.034896 GAGCACTCCCTCCGTTTCAA 59.965 55.000 0.00 0.00 0.00 2.69
818 1608 6.757010 TCGCCAGAATTAGTCTTATCAAGAAC 59.243 38.462 0.00 0.00 39.67 3.01
833 1623 1.317613 TTTGTGCAGTCGCCAGAATT 58.682 45.000 0.00 0.00 37.32 2.17
861 1652 3.804325 GGAGCTTCTTTTGCTTGGTTTTC 59.196 43.478 0.00 0.00 41.30 2.29
870 1661 6.743575 TTATTCAGTAGGAGCTTCTTTTGC 57.256 37.500 0.00 0.00 0.00 3.68
873 1664 5.351740 GCGTTTATTCAGTAGGAGCTTCTTT 59.648 40.000 0.00 0.00 0.00 2.52
884 1675 2.901249 GCCTCTGGCGTTTATTCAGTA 58.099 47.619 0.00 0.00 39.62 2.74
915 1706 2.820037 GAGGGGGCTTCGCTTTCG 60.820 66.667 0.00 0.00 38.88 3.46
929 1720 0.256464 AGAGACTGTAGACGGGGAGG 59.744 60.000 0.00 0.00 0.00 4.30
935 1726 0.097325 GCGTGGAGAGACTGTAGACG 59.903 60.000 0.00 0.00 0.00 4.18
936 1727 0.097325 CGCGTGGAGAGACTGTAGAC 59.903 60.000 0.00 0.00 0.00 2.59
1217 2032 0.539518 GAAGAGAGGAGGAAGGTGGC 59.460 60.000 0.00 0.00 0.00 5.01
1223 2038 3.598782 AGGGTAAGAGAAGAGAGGAGGAA 59.401 47.826 0.00 0.00 0.00 3.36
1343 2162 2.596851 GCAGAACAGGGAGCCCAGA 61.597 63.158 8.53 0.00 38.92 3.86
1388 2208 3.513438 TGGTTGGTGCGTGTGTGC 61.513 61.111 0.00 0.00 0.00 4.57
1406 2226 1.645034 CTAATCGCTATGCATCCCCG 58.355 55.000 0.19 4.75 0.00 5.73
1419 2239 1.144057 AACGCAGGAGCCCTAATCG 59.856 57.895 0.00 1.97 37.52 3.34
1452 2272 2.093128 CCTAGTGTGTGGGAATGGGTAC 60.093 54.545 0.00 0.00 0.00 3.34
1470 2290 3.758554 GCAATCAAGGTGCTTTCTTCCTA 59.241 43.478 0.00 0.00 39.00 2.94
1510 2330 8.060679 TGTTAACATTGCAATTTTGTCGAATTG 58.939 29.630 18.80 4.16 45.42 2.32
1549 2369 4.217550 GCCACAATACAGCTTAGTTTCCAA 59.782 41.667 0.00 0.00 0.00 3.53
1599 2419 4.318831 CGAACTCTGTTTGCCTCTGTTAAC 60.319 45.833 0.00 0.00 0.00 2.01
1616 2436 1.127951 CCATTGTACGGTTGCGAACTC 59.872 52.381 0.00 0.00 0.00 3.01
1649 2469 2.123726 ATGCCGAGCCATTTCCCC 60.124 61.111 0.00 0.00 0.00 4.81
1700 2521 5.584253 TTTCGTCCAATTGTCTTTTTCCA 57.416 34.783 4.43 0.00 0.00 3.53
1784 2605 6.374333 GGTAGAATTCTTTTGTGGCACTGATA 59.626 38.462 19.83 0.00 0.00 2.15
1832 2653 2.053244 AGCTTCCTGGGATCTGTATGG 58.947 52.381 0.00 0.00 0.00 2.74
1860 2681 7.674471 AAATGGCAGTAGTAGAGAAAACTTC 57.326 36.000 0.00 0.00 0.00 3.01
1865 2686 7.241042 ACACTAAATGGCAGTAGTAGAGAAA 57.759 36.000 11.95 0.00 0.00 2.52
1959 2780 5.064707 ACGTAATGACATAAATGCAGTGACC 59.935 40.000 0.00 0.00 0.00 4.02
1984 2813 5.728471 TCAACAGAAGATCCAGAATCTGAC 58.272 41.667 12.53 3.13 44.26 3.51
2024 2853 2.746279 TGTGTGGTTCCCAGAACATT 57.254 45.000 9.50 0.00 32.34 2.71
2103 2947 9.295825 TGACCTAATACTGTGTTTCAATGAAAT 57.704 29.630 11.87 0.00 33.97 2.17
2117 2961 4.422073 TTGATGCCCTGACCTAATACTG 57.578 45.455 0.00 0.00 0.00 2.74
2347 3195 6.406370 TGGTGAGACAATAAATCCAGTGTAG 58.594 40.000 0.00 0.00 0.00 2.74
2362 3210 1.550524 GCTATGGTGACTGGTGAGACA 59.449 52.381 0.00 0.00 0.00 3.41
2452 3313 7.327214 AGCAAGTTCAACAAAAACCAAGATAA 58.673 30.769 0.00 0.00 0.00 1.75
2603 3464 3.374042 TCTCTCCCTTCACTGTAGAGG 57.626 52.381 0.00 3.19 35.47 3.69
2733 3596 3.119743 CCATGCACATTAAGTCACACTGG 60.120 47.826 0.00 0.00 0.00 4.00
2779 3642 3.505464 AAGACGACCTATGCAGTGTAC 57.495 47.619 0.00 0.00 0.00 2.90
2782 3645 3.784701 ACTAAGACGACCTATGCAGTG 57.215 47.619 0.00 0.00 0.00 3.66
2787 3650 5.392165 GCCTGCTATACTAAGACGACCTATG 60.392 48.000 0.00 0.00 0.00 2.23
2882 3746 0.670162 CACACCAGCCACTTTTCCAG 59.330 55.000 0.00 0.00 0.00 3.86
2883 3747 0.033601 ACACACCAGCCACTTTTCCA 60.034 50.000 0.00 0.00 0.00 3.53
2884 3748 1.067060 GAACACACCAGCCACTTTTCC 59.933 52.381 0.00 0.00 0.00 3.13
2890 3756 1.959085 CCATGAACACACCAGCCAC 59.041 57.895 0.00 0.00 0.00 5.01
3039 3910 6.256321 GCCAAGCAGTTTCAATAATAATGGTG 59.744 38.462 0.00 0.00 0.00 4.17
3041 3912 5.459762 CGCCAAGCAGTTTCAATAATAATGG 59.540 40.000 0.00 0.00 0.00 3.16
3042 3913 6.264832 TCGCCAAGCAGTTTCAATAATAATG 58.735 36.000 0.00 0.00 0.00 1.90
3179 4063 3.118038 TGTGACCTGGAGCTTGTTTAGTT 60.118 43.478 0.00 0.00 0.00 2.24
3282 4167 1.072505 ACACCGTGGTAGGCTTTGG 59.927 57.895 3.03 0.00 33.69 3.28
3299 4184 2.093764 ACCTCTTGCAGTGATCTAGCAC 60.094 50.000 6.77 0.00 38.11 4.40
3314 4199 2.038952 TGTGACATGCTAAGCACCTCTT 59.961 45.455 0.00 0.00 43.04 2.85
3384 4276 0.320697 AAGTAACAGGTGAGACCGCC 59.679 55.000 0.00 0.00 44.90 6.13
3385 4277 3.521947 ATAAGTAACAGGTGAGACCGC 57.478 47.619 0.00 0.00 44.90 5.68
3408 4300 7.223584 TGTCCACTCAATTCTTCATTAACAGA 58.776 34.615 0.00 0.00 0.00 3.41
3423 4319 3.191162 GCAACATTAGCATGTCCACTCAA 59.809 43.478 0.00 0.00 43.34 3.02
3461 4357 3.782889 AGATTTGGCGGCTTTAATCAC 57.217 42.857 23.22 7.98 31.12 3.06
3472 4369 9.573133 AATTGACTTTAAGAATAAGATTTGGCG 57.427 29.630 0.00 0.00 0.00 5.69
3494 4391 3.983344 GCTTGTCTACTGTGGCAAAATTG 59.017 43.478 0.00 0.00 0.00 2.32
3515 4412 5.643379 TGAGGGAACATTTTCTGTATTGC 57.357 39.130 0.00 0.00 36.98 3.56
3572 4469 1.450211 CAGTTCCTCCAACCACCGT 59.550 57.895 0.00 0.00 35.28 4.83
3578 4476 4.019231 ACTTTAGGATCCAGTTCCTCCAAC 60.019 45.833 15.82 0.00 42.71 3.77
3673 4571 6.996509 AGACCAAGTCTTATTAACCAACGTA 58.003 36.000 0.00 0.00 40.28 3.57
3694 4592 5.164233 TCATCACATCTTTCTCGTGAAGAC 58.836 41.667 0.00 0.00 42.53 3.01
3745 4643 9.617523 TGCAATGTTATCAAGATAAGAAGATGA 57.382 29.630 2.88 0.00 34.27 2.92
3746 4644 9.880064 CTGCAATGTTATCAAGATAAGAAGATG 57.120 33.333 2.88 5.12 34.27 2.90
3747 4645 8.566260 GCTGCAATGTTATCAAGATAAGAAGAT 58.434 33.333 2.88 0.00 34.27 2.40
3748 4646 7.772292 AGCTGCAATGTTATCAAGATAAGAAGA 59.228 33.333 1.02 0.00 34.27 2.87
3749 4647 7.928103 AGCTGCAATGTTATCAAGATAAGAAG 58.072 34.615 1.02 1.86 34.27 2.85
3750 4648 7.870509 AGCTGCAATGTTATCAAGATAAGAA 57.129 32.000 1.02 0.00 34.27 2.52
3751 4649 8.206867 AGTAGCTGCAATGTTATCAAGATAAGA 58.793 33.333 4.12 2.76 34.27 2.10
3754 4652 7.500141 TGAGTAGCTGCAATGTTATCAAGATA 58.500 34.615 4.12 0.00 0.00 1.98
3859 4757 2.513753 TCGATGCAAAACCATGGACTT 58.486 42.857 21.47 8.46 0.00 3.01
3869 4767 6.255887 ACCGTTTGTTAAAATTCGATGCAAAA 59.744 30.769 0.00 0.00 0.00 2.44
3894 4792 3.295093 TGCAGGTCCAGTTGAAAATTCA 58.705 40.909 0.00 0.00 34.92 2.57
3908 4806 3.340814 TTCCTCTGAAATCTGCAGGTC 57.659 47.619 15.13 9.76 34.20 3.85
3956 4854 7.174107 AGTCCCAATTTTATTCATGTTCCTG 57.826 36.000 0.00 0.00 0.00 3.86
4059 4957 9.844257 ATTTTTCTCTATTCTACTCCAGGATTG 57.156 33.333 0.00 0.00 0.00 2.67
4114 5013 1.599606 CTACTCCTGCGCCAGTGTCT 61.600 60.000 4.18 0.00 0.00 3.41
4155 5054 1.168714 GACAGTGAAATCCCAGCCAC 58.831 55.000 0.00 0.00 0.00 5.01
4174 5073 1.394917 GCGTTAGGCATGAACTGACAG 59.605 52.381 0.00 0.00 42.87 3.51
4216 5115 3.007182 ACATGGCAAGAATCCAAAACAGG 59.993 43.478 0.00 0.00 37.13 4.00
4217 5116 4.261578 ACATGGCAAGAATCCAAAACAG 57.738 40.909 0.00 0.00 37.13 3.16
4219 5118 3.996363 GGAACATGGCAAGAATCCAAAAC 59.004 43.478 12.19 0.00 37.13 2.43
4220 5119 3.903090 AGGAACATGGCAAGAATCCAAAA 59.097 39.130 17.00 0.00 37.13 2.44
4221 5120 3.509442 AGGAACATGGCAAGAATCCAAA 58.491 40.909 17.00 0.00 37.13 3.28
4224 5123 3.368739 CCAAAGGAACATGGCAAGAATCC 60.369 47.826 10.02 10.02 31.21 3.01
4226 5125 3.242011 ACCAAAGGAACATGGCAAGAAT 58.758 40.909 0.00 0.00 40.58 2.40
4227 5126 2.676748 ACCAAAGGAACATGGCAAGAA 58.323 42.857 0.00 0.00 40.58 2.52
4230 5129 3.420893 CTCTACCAAAGGAACATGGCAA 58.579 45.455 0.00 0.00 40.58 4.52
4233 5132 2.025887 AGGCTCTACCAAAGGAACATGG 60.026 50.000 0.00 0.00 43.14 3.66
4267 5166 2.486951 ATGAAGATCGCATTGCAAGC 57.513 45.000 9.69 8.00 0.00 4.01
4330 5229 5.278218 GGCAAAAGATGAGCTCCTTTATAGC 60.278 44.000 12.15 16.50 40.40 2.97
4338 5237 4.641989 TCAAATAGGCAAAAGATGAGCTCC 59.358 41.667 12.15 0.00 0.00 4.70
4400 5299 1.619827 CCAGCAAAGGAAGCCAAATGA 59.380 47.619 0.00 0.00 0.00 2.57
4421 5321 5.723295 ACACTGCCATGAATCCAAATAAAC 58.277 37.500 0.00 0.00 0.00 2.01
4453 5353 8.792830 TTACTGAAAATAGGATTTCCTCTGTG 57.207 34.615 1.47 0.00 44.77 3.66
4478 5378 3.119495 GCCGGCATGACAGTTTTTCTAAT 60.119 43.478 24.80 0.00 0.00 1.73
4480 5380 1.810151 GCCGGCATGACAGTTTTTCTA 59.190 47.619 24.80 0.00 0.00 2.10
4612 5625 5.892160 AGCTCACACGACTGTAGTAAATA 57.108 39.130 0.00 0.00 0.00 1.40
4634 5647 6.483307 CCCAAAATTGATGAGCTCTACGAATA 59.517 38.462 16.19 0.00 0.00 1.75
4732 5800 2.579738 GTCTGGGAGAAGACCGGC 59.420 66.667 0.00 0.00 40.66 6.13
4798 5866 1.451387 CAGGTATGACGTTGGGGCC 60.451 63.158 0.00 0.00 0.00 5.80
4804 5872 0.612732 TCGGGTCCAGGTATGACGTT 60.613 55.000 0.00 0.00 33.46 3.99
4810 5878 2.040178 GTGAAGATCGGGTCCAGGTAT 58.960 52.381 0.00 0.00 0.00 2.73
4879 5947 0.530211 CCAGCGCTCTGAAGATCCTG 60.530 60.000 7.13 0.00 42.95 3.86
4897 5965 2.742372 AACGGCATCACAGCGACC 60.742 61.111 0.00 0.00 34.64 4.79
4903 5971 1.514678 GGAAGCACAACGGCATCACA 61.515 55.000 0.00 0.00 33.39 3.58
4916 5984 2.268920 GGTGGCGATCAGGAAGCA 59.731 61.111 0.00 0.00 0.00 3.91
4936 6004 2.127232 TCAGGATGAGATCGCGGCA 61.127 57.895 6.13 0.00 42.56 5.69
4953 6021 3.006859 CCATTTCTTCAACCTGGGGTTTC 59.993 47.826 0.00 0.00 44.33 2.78
4954 6022 2.972021 CCATTTCTTCAACCTGGGGTTT 59.028 45.455 0.00 0.00 44.33 3.27
5010 6078 9.880157 CCATTCATTTATTCATTCAGGAAACTT 57.120 29.630 0.00 0.00 40.21 2.66


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

AutoCloner maintained by Alex Coulton.