Multiple sequence alignment - TraesCS1D01G390200

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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 TraesCS1D01G390200 chr1D 100.000 2357 0 0 1 2357 461538530 461540886 0.000000e+00 4353.0
1 TraesCS1D01G390200 chr1D 96.585 1347 43 3 631 1974 60171815 60170469 0.000000e+00 2230.0
2 TraesCS1D01G390200 chr1D 95.694 1347 51 5 631 1972 247505757 247504413 0.000000e+00 2159.0
3 TraesCS1D01G390200 chr1D 95.737 1337 49 3 631 1964 205134696 205133365 0.000000e+00 2146.0
4 TraesCS1D01G390200 chr1D 84.776 624 78 7 1 620 461752134 461752744 5.570000e-171 610.0
5 TraesCS1D01G390200 chr1D 87.003 377 42 5 204 578 461422558 461422929 3.620000e-113 418.0
6 TraesCS1D01G390200 chr2D 96.498 1342 44 2 631 1969 73126871 73125530 0.000000e+00 2215.0
7 TraesCS1D01G390200 chr2D 95.704 1350 51 6 628 1972 621748799 621750146 0.000000e+00 2165.0
8 TraesCS1D01G390200 chr3D 96.048 1341 50 2 631 1968 584701391 584700051 0.000000e+00 2180.0
9 TraesCS1D01G390200 chr7D 96.114 1338 47 4 631 1965 497560908 497562243 0.000000e+00 2178.0
10 TraesCS1D01G390200 chr7D 95.245 1346 60 3 631 1972 50081831 50080486 0.000000e+00 2128.0
11 TraesCS1D01G390200 chr6D 95.519 1339 54 3 631 1966 142136691 142135356 0.000000e+00 2135.0
12 TraesCS1D01G390200 chrUn 95.223 628 22 1 1 620 1067676 1068303 0.000000e+00 987.0
13 TraesCS1D01G390200 chrUn 93.000 100 4 2 2126 2222 1069928 1070027 2.440000e-30 143.0
14 TraesCS1D01G390200 chrUn 100.000 38 0 0 2041 2078 1069483 1069520 1.170000e-08 71.3
15 TraesCS1D01G390200 chr1B 94.872 624 27 3 1 623 634565372 634564753 0.000000e+00 970.0
16 TraesCS1D01G390200 chr1B 85.048 622 79 10 1 617 634686754 634687366 2.570000e-174 621.0
17 TraesCS1D01G390200 chr1B 87.978 366 39 3 214 578 634313326 634313687 6.020000e-116 427.0
18 TraesCS1D01G390200 chr1B 86.473 207 15 11 2029 2227 634564762 634564561 5.100000e-52 215.0
19 TraesCS1D01G390200 chr1A 85.096 624 85 5 1 620 552975953 552976572 4.270000e-177 630.0
20 TraesCS1D01G390200 chr1A 83.840 625 82 12 1 620 553046680 553047290 5.650000e-161 577.0
21 TraesCS1D01G390200 chr1A 85.372 376 52 1 203 578 552908211 552908583 1.020000e-103 387.0
22 TraesCS1D01G390200 chr1A 88.889 108 6 4 65 169 553133507 553133611 6.840000e-26 128.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G390200 chr1D 461538530 461540886 2356 False 4353.000000 4353 100.000000 1 2357 1 chr1D.!!$F2 2356
1 TraesCS1D01G390200 chr1D 60170469 60171815 1346 True 2230.000000 2230 96.585000 631 1974 1 chr1D.!!$R1 1343
2 TraesCS1D01G390200 chr1D 247504413 247505757 1344 True 2159.000000 2159 95.694000 631 1972 1 chr1D.!!$R3 1341
3 TraesCS1D01G390200 chr1D 205133365 205134696 1331 True 2146.000000 2146 95.737000 631 1964 1 chr1D.!!$R2 1333
4 TraesCS1D01G390200 chr1D 461752134 461752744 610 False 610.000000 610 84.776000 1 620 1 chr1D.!!$F3 619
5 TraesCS1D01G390200 chr2D 73125530 73126871 1341 True 2215.000000 2215 96.498000 631 1969 1 chr2D.!!$R1 1338
6 TraesCS1D01G390200 chr2D 621748799 621750146 1347 False 2165.000000 2165 95.704000 628 1972 1 chr2D.!!$F1 1344
7 TraesCS1D01G390200 chr3D 584700051 584701391 1340 True 2180.000000 2180 96.048000 631 1968 1 chr3D.!!$R1 1337
8 TraesCS1D01G390200 chr7D 497560908 497562243 1335 False 2178.000000 2178 96.114000 631 1965 1 chr7D.!!$F1 1334
9 TraesCS1D01G390200 chr7D 50080486 50081831 1345 True 2128.000000 2128 95.245000 631 1972 1 chr7D.!!$R1 1341
10 TraesCS1D01G390200 chr6D 142135356 142136691 1335 True 2135.000000 2135 95.519000 631 1966 1 chr6D.!!$R1 1335
11 TraesCS1D01G390200 chrUn 1067676 1070027 2351 False 400.433333 987 96.074333 1 2222 3 chrUn.!!$F1 2221
12 TraesCS1D01G390200 chr1B 634686754 634687366 612 False 621.000000 621 85.048000 1 617 1 chr1B.!!$F2 616
13 TraesCS1D01G390200 chr1B 634564561 634565372 811 True 592.500000 970 90.672500 1 2227 2 chr1B.!!$R1 2226
14 TraesCS1D01G390200 chr1A 552975953 552976572 619 False 630.000000 630 85.096000 1 620 1 chr1A.!!$F2 619
15 TraesCS1D01G390200 chr1A 553046680 553047290 610 False 577.000000 577 83.840000 1 620 1 chr1A.!!$F3 619

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
561 576 0.037447 GGCTGCTCCTTGTTCTTCCT 59.963 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2333 3565 0.039326 AGGCTGGCTGCTCTTCAAAT 59.961 50.0 16.14 0.0 42.39 2.32 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
298 313 4.033776 CGCAGGAAAGGGAGGCCA 62.034 66.667 5.01 0.00 0.00 5.36
334 349 3.072468 CCTCGGCCCGACAGGTTA 61.072 66.667 0.00 0.00 38.26 2.85
335 350 2.183555 CTCGGCCCGACAGGTTAC 59.816 66.667 0.00 0.00 38.26 2.50
362 377 1.201343 GAGCTCGTTATTCCAGTCGC 58.799 55.000 0.00 0.00 0.00 5.19
363 378 0.818296 AGCTCGTTATTCCAGTCGCT 59.182 50.000 0.00 0.00 0.00 4.93
364 379 0.924090 GCTCGTTATTCCAGTCGCTG 59.076 55.000 0.52 0.52 0.00 5.18
367 382 0.800683 CGTTATTCCAGTCGCTGCGA 60.801 55.000 22.24 22.24 0.00 5.10
388 403 0.802607 CGTAGCAGAAGAAGCCGGAC 60.803 60.000 5.05 0.00 0.00 4.79
445 460 4.172512 CAGAGGGCGAGCCATGCT 62.173 66.667 16.65 3.70 43.88 3.79
446 461 3.406200 AGAGGGCGAGCCATGCTT 61.406 61.111 16.65 0.00 39.88 3.91
447 462 2.439156 GAGGGCGAGCCATGCTTT 60.439 61.111 16.65 0.00 39.88 3.51
448 463 2.753043 AGGGCGAGCCATGCTTTG 60.753 61.111 16.65 0.00 39.88 2.77
457 472 4.539152 CATGCTTTGGACACGCAC 57.461 55.556 0.00 0.00 36.37 5.34
458 473 1.951510 CATGCTTTGGACACGCACT 59.048 52.632 0.00 0.00 36.37 4.40
459 474 0.311790 CATGCTTTGGACACGCACTT 59.688 50.000 0.00 0.00 36.37 3.16
460 475 0.311790 ATGCTTTGGACACGCACTTG 59.688 50.000 0.00 0.00 36.37 3.16
461 476 0.746204 TGCTTTGGACACGCACTTGA 60.746 50.000 0.00 0.00 0.00 3.02
462 477 0.380378 GCTTTGGACACGCACTTGAA 59.620 50.000 0.00 0.00 0.00 2.69
463 478 1.597937 GCTTTGGACACGCACTTGAAG 60.598 52.381 0.00 0.00 0.00 3.02
464 479 0.380378 TTTGGACACGCACTTGAAGC 59.620 50.000 0.00 0.00 0.00 3.86
471 486 2.866028 GCACTTGAAGCGGCAGAG 59.134 61.111 1.45 0.00 0.00 3.35
472 487 2.866028 CACTTGAAGCGGCAGAGC 59.134 61.111 1.45 0.00 37.41 4.09
473 488 2.740055 ACTTGAAGCGGCAGAGCG 60.740 61.111 1.45 0.00 43.00 5.03
474 489 2.433145 CTTGAAGCGGCAGAGCGA 60.433 61.111 1.45 0.00 43.00 4.93
475 490 1.812922 CTTGAAGCGGCAGAGCGAT 60.813 57.895 1.45 0.00 43.00 4.58
476 491 2.033328 CTTGAAGCGGCAGAGCGATG 62.033 60.000 1.45 0.00 43.00 3.84
477 492 2.510238 GAAGCGGCAGAGCGATGT 60.510 61.111 1.45 0.00 43.00 3.06
478 493 2.806856 GAAGCGGCAGAGCGATGTG 61.807 63.158 1.45 0.00 43.00 3.21
479 494 3.596066 AAGCGGCAGAGCGATGTGT 62.596 57.895 1.45 0.00 43.00 3.72
480 495 2.202743 GCGGCAGAGCGATGTGTA 60.203 61.111 0.00 0.00 0.00 2.90
481 496 2.233654 GCGGCAGAGCGATGTGTAG 61.234 63.158 0.00 0.00 0.00 2.74
482 497 1.589993 CGGCAGAGCGATGTGTAGG 60.590 63.158 0.00 0.00 0.00 3.18
483 498 1.227380 GGCAGAGCGATGTGTAGGG 60.227 63.158 0.00 0.00 0.00 3.53
484 499 1.884926 GCAGAGCGATGTGTAGGGC 60.885 63.158 0.00 0.00 0.00 5.19
485 500 1.517361 CAGAGCGATGTGTAGGGCA 59.483 57.895 0.00 0.00 0.00 5.36
507 522 3.522731 CGCCAGGACCTCGAGGAG 61.523 72.222 37.69 21.72 38.94 3.69
530 545 2.837291 CCTCGGGGAGGCTCTCTG 60.837 72.222 17.51 17.51 43.29 3.35
531 546 3.535962 CTCGGGGAGGCTCTCTGC 61.536 72.222 18.78 0.00 41.94 4.26
556 571 3.435186 GCCGGCTGCTCCTTGTTC 61.435 66.667 22.15 0.00 36.87 3.18
557 572 2.348998 CCGGCTGCTCCTTGTTCT 59.651 61.111 0.00 0.00 0.00 3.01
558 573 1.302832 CCGGCTGCTCCTTGTTCTT 60.303 57.895 0.00 0.00 0.00 2.52
559 574 1.301677 CCGGCTGCTCCTTGTTCTTC 61.302 60.000 0.00 0.00 0.00 2.87
560 575 1.301677 CGGCTGCTCCTTGTTCTTCC 61.302 60.000 0.00 0.00 0.00 3.46
561 576 0.037447 GGCTGCTCCTTGTTCTTCCT 59.963 55.000 0.00 0.00 0.00 3.36
562 577 1.163554 GCTGCTCCTTGTTCTTCCTG 58.836 55.000 0.00 0.00 0.00 3.86
563 578 1.818642 CTGCTCCTTGTTCTTCCTGG 58.181 55.000 0.00 0.00 0.00 4.45
564 579 1.349026 CTGCTCCTTGTTCTTCCTGGA 59.651 52.381 0.00 0.00 0.00 3.86
565 580 1.072331 TGCTCCTTGTTCTTCCTGGAC 59.928 52.381 0.00 0.00 0.00 4.02
566 581 1.611936 GCTCCTTGTTCTTCCTGGACC 60.612 57.143 0.00 0.00 0.00 4.46
567 582 1.981495 CTCCTTGTTCTTCCTGGACCT 59.019 52.381 0.00 0.00 0.00 3.85
568 583 1.978580 TCCTTGTTCTTCCTGGACCTC 59.021 52.381 0.00 0.00 0.00 3.85
569 584 1.981495 CCTTGTTCTTCCTGGACCTCT 59.019 52.381 0.00 0.00 0.00 3.69
570 585 2.373502 CCTTGTTCTTCCTGGACCTCTT 59.626 50.000 0.00 0.00 0.00 2.85
571 586 3.181439 CCTTGTTCTTCCTGGACCTCTTT 60.181 47.826 0.00 0.00 0.00 2.52
572 587 3.492102 TGTTCTTCCTGGACCTCTTTG 57.508 47.619 0.00 0.00 0.00 2.77
573 588 2.155279 GTTCTTCCTGGACCTCTTTGC 58.845 52.381 0.00 0.00 0.00 3.68
574 589 0.693049 TCTTCCTGGACCTCTTTGCC 59.307 55.000 0.00 0.00 0.00 4.52
575 590 0.401738 CTTCCTGGACCTCTTTGCCA 59.598 55.000 0.00 0.00 0.00 4.92
576 591 1.005215 CTTCCTGGACCTCTTTGCCAT 59.995 52.381 0.00 0.00 0.00 4.40
577 592 0.620556 TCCTGGACCTCTTTGCCATC 59.379 55.000 0.00 0.00 0.00 3.51
578 593 0.745845 CCTGGACCTCTTTGCCATCG 60.746 60.000 0.00 0.00 0.00 3.84
579 594 1.372087 CTGGACCTCTTTGCCATCGC 61.372 60.000 0.00 0.00 0.00 4.58
580 595 2.115291 GGACCTCTTTGCCATCGCC 61.115 63.158 0.00 0.00 0.00 5.54
581 596 2.044946 ACCTCTTTGCCATCGCCC 60.045 61.111 0.00 0.00 0.00 6.13
582 597 2.830370 CCTCTTTGCCATCGCCCC 60.830 66.667 0.00 0.00 0.00 5.80
583 598 3.204827 CTCTTTGCCATCGCCCCG 61.205 66.667 0.00 0.00 0.00 5.73
584 599 3.976701 CTCTTTGCCATCGCCCCGT 62.977 63.158 0.00 0.00 0.00 5.28
585 600 2.124901 CTTTGCCATCGCCCCGTA 60.125 61.111 0.00 0.00 0.00 4.02
586 601 2.124901 TTTGCCATCGCCCCGTAG 60.125 61.111 0.00 0.00 0.00 3.51
587 602 4.849310 TTGCCATCGCCCCGTAGC 62.849 66.667 0.00 0.00 0.00 3.58
606 621 4.206697 GAGGAGATCCAGCCCGAT 57.793 61.111 0.92 0.00 38.89 4.18
607 622 3.365536 GAGGAGATCCAGCCCGATA 57.634 57.895 0.92 0.00 38.89 2.92
608 623 1.633774 GAGGAGATCCAGCCCGATAA 58.366 55.000 0.92 0.00 38.89 1.75
609 624 1.273886 GAGGAGATCCAGCCCGATAAC 59.726 57.143 0.92 0.00 38.89 1.89
610 625 0.038159 GGAGATCCAGCCCGATAACG 60.038 60.000 0.00 0.00 36.17 3.18
611 626 3.363589 GGAGATCCAGCCCGATAACGG 62.364 61.905 4.11 4.11 46.46 4.44
727 745 7.937394 AGCACAAAAGACCTTACAAAGTAGTAT 59.063 33.333 0.00 0.00 0.00 2.12
739 757 9.694137 CTTACAAAGTAGTATATCAGTAAGCCC 57.306 37.037 0.00 0.00 33.35 5.19
773 791 1.276421 AGGCAACATCTGTCGCTACTT 59.724 47.619 0.00 0.00 41.41 2.24
861 879 0.767375 ACATCTAATGCCGGATGCCT 59.233 50.000 5.05 0.00 41.93 4.75
984 1002 1.529010 CACAGACCTTGCCAAGCCA 60.529 57.895 0.00 0.00 0.00 4.75
1114 1179 0.804364 TGACGCGGTAGATACAACGT 59.196 50.000 12.47 8.65 40.38 3.99
1156 1221 2.267006 CATCGCCACTGCTGGAGT 59.733 61.111 0.00 0.00 40.55 3.85
1197 1262 2.632996 ACAACATCTCTCCCTCGAACAA 59.367 45.455 0.00 0.00 0.00 2.83
1568 1872 4.129737 CGATCCGACGTGGCCAGT 62.130 66.667 5.11 6.62 37.80 4.00
1574 1878 2.733593 GACGTGGCCAGTGACGAC 60.734 66.667 19.17 9.99 38.94 4.34
1691 1995 2.217038 AGCCACCACCTCACGACAT 61.217 57.895 0.00 0.00 0.00 3.06
1694 1998 1.004560 CACCACCTCACGACATGCT 60.005 57.895 0.00 0.00 0.00 3.79
1883 2562 4.664677 GCTATGGACGGCGGCGAT 62.665 66.667 38.93 22.94 0.00 4.58
1975 2656 4.129148 GAGGGGCGAGGGGCAAAT 62.129 66.667 0.00 0.00 46.16 2.32
1978 2659 1.603739 GGGGCGAGGGGCAAATATC 60.604 63.158 0.00 0.00 46.16 1.63
1982 2663 0.179018 GCGAGGGGCAAATATCTGGT 60.179 55.000 0.00 0.00 42.87 4.00
1983 2664 1.884235 CGAGGGGCAAATATCTGGTC 58.116 55.000 0.00 0.00 0.00 4.02
1984 2665 1.873903 CGAGGGGCAAATATCTGGTCG 60.874 57.143 0.00 0.00 0.00 4.79
1985 2666 1.141053 GAGGGGCAAATATCTGGTCGT 59.859 52.381 0.00 0.00 0.00 4.34
1986 2667 2.367567 GAGGGGCAAATATCTGGTCGTA 59.632 50.000 0.00 0.00 0.00 3.43
1988 2669 3.008049 AGGGGCAAATATCTGGTCGTATC 59.992 47.826 0.00 0.00 0.00 2.24
1989 2670 3.008049 GGGGCAAATATCTGGTCGTATCT 59.992 47.826 0.00 0.00 0.00 1.98
1991 2672 4.262463 GGGCAAATATCTGGTCGTATCTGA 60.262 45.833 0.00 0.00 0.00 3.27
1992 2673 5.297547 GGCAAATATCTGGTCGTATCTGAA 58.702 41.667 0.00 0.00 0.00 3.02
1994 2675 6.260050 GGCAAATATCTGGTCGTATCTGAAAA 59.740 38.462 0.00 0.00 0.00 2.29
2018 2699 5.487153 AAAAACAAATACGGGCCAAAAAC 57.513 34.783 4.39 0.00 0.00 2.43
2019 2700 2.823924 ACAAATACGGGCCAAAAACC 57.176 45.000 4.39 0.00 0.00 3.27
2020 2701 1.345089 ACAAATACGGGCCAAAAACCC 59.655 47.619 4.39 0.00 44.63 4.11
2078 2919 2.234908 CGGAATTTGGGGGTTTATTGCA 59.765 45.455 0.00 0.00 0.00 4.08
2079 2920 3.118445 CGGAATTTGGGGGTTTATTGCAT 60.118 43.478 0.00 0.00 0.00 3.96
2080 2921 4.625083 CGGAATTTGGGGGTTTATTGCATT 60.625 41.667 0.00 0.00 0.00 3.56
2081 2922 4.639755 GGAATTTGGGGGTTTATTGCATTG 59.360 41.667 0.00 0.00 0.00 2.82
2082 2923 2.777832 TTGGGGGTTTATTGCATTGC 57.222 45.000 0.46 0.46 0.00 3.56
2090 2931 0.098552 TTATTGCATTGCGCTCCGTG 59.901 50.000 9.73 3.14 43.06 4.94
2092 2933 1.865788 ATTGCATTGCGCTCCGTGTT 61.866 50.000 9.73 0.00 43.06 3.32
2104 2945 2.672996 CGTGTTCTTGGGGCTGGG 60.673 66.667 0.00 0.00 0.00 4.45
2105 2946 2.283173 GTGTTCTTGGGGCTGGGG 60.283 66.667 0.00 0.00 0.00 4.96
2106 2947 4.299796 TGTTCTTGGGGCTGGGGC 62.300 66.667 0.00 0.00 37.82 5.80
2107 2948 3.984732 GTTCTTGGGGCTGGGGCT 61.985 66.667 0.00 0.00 38.73 5.19
2222 3454 1.274167 GGAGTGTGACACGTATTCCCA 59.726 52.381 10.41 0.00 39.64 4.37
2225 3457 3.399330 AGTGTGACACGTATTCCCAAAG 58.601 45.455 10.41 0.00 39.64 2.77
2227 3459 2.105134 TGTGACACGTATTCCCAAAGGT 59.895 45.455 0.22 0.00 0.00 3.50
2228 3460 2.740447 GTGACACGTATTCCCAAAGGTC 59.260 50.000 0.00 0.00 0.00 3.85
2229 3461 2.369203 TGACACGTATTCCCAAAGGTCA 59.631 45.455 0.00 0.00 0.00 4.02
2230 3462 2.740447 GACACGTATTCCCAAAGGTCAC 59.260 50.000 0.00 0.00 0.00 3.67
2231 3463 1.730064 CACGTATTCCCAAAGGTCACG 59.270 52.381 0.00 0.00 38.09 4.35
2232 3464 1.619827 ACGTATTCCCAAAGGTCACGA 59.380 47.619 0.00 0.00 36.68 4.35
2233 3465 2.037511 ACGTATTCCCAAAGGTCACGAA 59.962 45.455 0.00 0.00 36.68 3.85
2234 3466 2.414138 CGTATTCCCAAAGGTCACGAAC 59.586 50.000 0.00 0.00 35.86 3.95
2242 3474 3.308705 GGTCACGAACCCCTCCGT 61.309 66.667 0.00 0.00 42.85 4.69
2243 3475 2.260743 GTCACGAACCCCTCCGTC 59.739 66.667 0.00 0.00 36.83 4.79
2244 3476 2.116772 TCACGAACCCCTCCGTCT 59.883 61.111 0.00 0.00 36.83 4.18
2245 3477 1.975407 TCACGAACCCCTCCGTCTC 60.975 63.158 0.00 0.00 36.83 3.36
2246 3478 1.977544 CACGAACCCCTCCGTCTCT 60.978 63.158 0.00 0.00 36.83 3.10
2247 3479 1.678300 ACGAACCCCTCCGTCTCTC 60.678 63.158 0.00 0.00 33.23 3.20
2248 3480 1.378778 CGAACCCCTCCGTCTCTCT 60.379 63.158 0.00 0.00 0.00 3.10
2249 3481 1.378124 CGAACCCCTCCGTCTCTCTC 61.378 65.000 0.00 0.00 0.00 3.20
2250 3482 0.323542 GAACCCCTCCGTCTCTCTCA 60.324 60.000 0.00 0.00 0.00 3.27
2251 3483 0.612453 AACCCCTCCGTCTCTCTCAC 60.612 60.000 0.00 0.00 0.00 3.51
2252 3484 1.000771 CCCCTCCGTCTCTCTCACA 60.001 63.158 0.00 0.00 0.00 3.58
2253 3485 0.396417 CCCCTCCGTCTCTCTCACAT 60.396 60.000 0.00 0.00 0.00 3.21
2254 3486 1.479709 CCCTCCGTCTCTCTCACATT 58.520 55.000 0.00 0.00 0.00 2.71
2255 3487 2.656002 CCCTCCGTCTCTCTCACATTA 58.344 52.381 0.00 0.00 0.00 1.90
2256 3488 2.621055 CCCTCCGTCTCTCTCACATTAG 59.379 54.545 0.00 0.00 0.00 1.73
2257 3489 3.283751 CCTCCGTCTCTCTCACATTAGT 58.716 50.000 0.00 0.00 0.00 2.24
2258 3490 3.697045 CCTCCGTCTCTCTCACATTAGTT 59.303 47.826 0.00 0.00 0.00 2.24
2259 3491 4.158764 CCTCCGTCTCTCTCACATTAGTTT 59.841 45.833 0.00 0.00 0.00 2.66
2260 3492 5.357314 CCTCCGTCTCTCTCACATTAGTTTA 59.643 44.000 0.00 0.00 0.00 2.01
2261 3493 6.039941 CCTCCGTCTCTCTCACATTAGTTTAT 59.960 42.308 0.00 0.00 0.00 1.40
2262 3494 6.796426 TCCGTCTCTCTCACATTAGTTTATG 58.204 40.000 0.00 0.00 0.00 1.90
2263 3495 6.377429 TCCGTCTCTCTCACATTAGTTTATGT 59.623 38.462 0.00 0.00 39.27 2.29
2264 3496 7.555195 TCCGTCTCTCTCACATTAGTTTATGTA 59.445 37.037 0.00 0.00 36.64 2.29
2265 3497 8.188799 CCGTCTCTCTCACATTAGTTTATGTAA 58.811 37.037 0.00 0.00 36.64 2.41
2266 3498 9.737427 CGTCTCTCTCACATTAGTTTATGTAAT 57.263 33.333 0.00 0.00 36.64 1.89
2286 3518 8.388319 TGTAATGTGTTTTATAAAGATTGCGC 57.612 30.769 0.00 0.00 0.00 6.09
2287 3519 6.885735 AATGTGTTTTATAAAGATTGCGCC 57.114 33.333 4.18 0.00 0.00 6.53
2288 3520 5.378292 TGTGTTTTATAAAGATTGCGCCA 57.622 34.783 4.18 0.00 0.00 5.69
2289 3521 5.773575 TGTGTTTTATAAAGATTGCGCCAA 58.226 33.333 4.18 0.00 0.00 4.52
2290 3522 6.216569 TGTGTTTTATAAAGATTGCGCCAAA 58.783 32.000 4.18 0.00 0.00 3.28
2291 3523 6.364706 TGTGTTTTATAAAGATTGCGCCAAAG 59.635 34.615 4.18 0.00 0.00 2.77
2292 3524 5.866633 TGTTTTATAAAGATTGCGCCAAAGG 59.133 36.000 4.18 0.00 0.00 3.11
2293 3525 5.652994 TTTATAAAGATTGCGCCAAAGGT 57.347 34.783 4.18 0.00 0.00 3.50
2294 3526 3.782889 ATAAAGATTGCGCCAAAGGTC 57.217 42.857 4.18 0.00 0.00 3.85
2295 3527 0.603065 AAAGATTGCGCCAAAGGTCC 59.397 50.000 4.18 0.00 0.00 4.46
2296 3528 0.251341 AAGATTGCGCCAAAGGTCCT 60.251 50.000 4.18 0.00 0.00 3.85
2297 3529 0.678048 AGATTGCGCCAAAGGTCCTC 60.678 55.000 4.18 0.00 0.00 3.71
2298 3530 0.960364 GATTGCGCCAAAGGTCCTCA 60.960 55.000 4.18 0.00 0.00 3.86
2299 3531 0.323725 ATTGCGCCAAAGGTCCTCAT 60.324 50.000 4.18 0.00 0.00 2.90
2300 3532 0.326595 TTGCGCCAAAGGTCCTCATA 59.673 50.000 4.18 0.00 0.00 2.15
2301 3533 0.326595 TGCGCCAAAGGTCCTCATAA 59.673 50.000 4.18 0.00 0.00 1.90
2302 3534 1.271652 TGCGCCAAAGGTCCTCATAAA 60.272 47.619 4.18 0.00 0.00 1.40
2303 3535 1.132453 GCGCCAAAGGTCCTCATAAAC 59.868 52.381 0.00 0.00 0.00 2.01
2304 3536 1.743394 CGCCAAAGGTCCTCATAAACC 59.257 52.381 0.00 0.00 35.69 3.27
2305 3537 1.743394 GCCAAAGGTCCTCATAAACCG 59.257 52.381 0.00 0.00 40.63 4.44
2306 3538 2.878526 GCCAAAGGTCCTCATAAACCGT 60.879 50.000 0.00 0.00 40.63 4.83
2307 3539 3.620472 GCCAAAGGTCCTCATAAACCGTA 60.620 47.826 0.00 0.00 40.63 4.02
2308 3540 4.777463 CCAAAGGTCCTCATAAACCGTAT 58.223 43.478 0.00 0.00 40.63 3.06
2309 3541 4.574828 CCAAAGGTCCTCATAAACCGTATG 59.425 45.833 0.00 0.00 40.63 2.39
2310 3542 5.424757 CAAAGGTCCTCATAAACCGTATGA 58.575 41.667 0.00 0.00 40.63 2.15
2311 3543 5.687166 AAGGTCCTCATAAACCGTATGAA 57.313 39.130 0.00 0.00 40.63 2.57
2312 3544 5.687166 AGGTCCTCATAAACCGTATGAAA 57.313 39.130 0.00 0.00 40.63 2.69
2313 3545 6.248569 AGGTCCTCATAAACCGTATGAAAT 57.751 37.500 0.00 0.00 40.63 2.17
2314 3546 6.659824 AGGTCCTCATAAACCGTATGAAATT 58.340 36.000 0.00 0.00 40.63 1.82
2315 3547 6.542370 AGGTCCTCATAAACCGTATGAAATTG 59.458 38.462 0.00 0.00 40.63 2.32
2316 3548 6.540914 GGTCCTCATAAACCGTATGAAATTGA 59.459 38.462 0.00 0.00 34.00 2.57
2317 3549 7.228706 GGTCCTCATAAACCGTATGAAATTGAT 59.771 37.037 0.00 0.00 34.00 2.57
2318 3550 8.283291 GTCCTCATAAACCGTATGAAATTGATC 58.717 37.037 0.00 0.00 34.00 2.92
2319 3551 8.210946 TCCTCATAAACCGTATGAAATTGATCT 58.789 33.333 0.00 0.00 34.00 2.75
2320 3552 8.840321 CCTCATAAACCGTATGAAATTGATCTT 58.160 33.333 0.00 0.00 34.00 2.40
2323 3555 9.878599 CATAAACCGTATGAAATTGATCTTACC 57.121 33.333 0.00 0.00 30.27 2.85
2324 3556 9.847224 ATAAACCGTATGAAATTGATCTTACCT 57.153 29.630 0.00 0.00 30.27 3.08
2325 3557 7.553881 AACCGTATGAAATTGATCTTACCTG 57.446 36.000 0.00 0.00 30.27 4.00
2326 3558 6.884832 ACCGTATGAAATTGATCTTACCTGA 58.115 36.000 0.00 0.00 30.27 3.86
2327 3559 7.509546 ACCGTATGAAATTGATCTTACCTGAT 58.490 34.615 0.00 0.00 30.27 2.90
2328 3560 8.647796 ACCGTATGAAATTGATCTTACCTGATA 58.352 33.333 0.00 0.00 30.27 2.15
2329 3561 9.658799 CCGTATGAAATTGATCTTACCTGATAT 57.341 33.333 0.00 0.00 30.27 1.63
2343 3575 9.935241 TCTTACCTGATATCATATTTGAAGAGC 57.065 33.333 5.72 0.00 34.96 4.09
2344 3576 9.716531 CTTACCTGATATCATATTTGAAGAGCA 57.283 33.333 5.72 0.00 34.96 4.26
2345 3577 9.716531 TTACCTGATATCATATTTGAAGAGCAG 57.283 33.333 5.72 8.68 36.12 4.24
2346 3578 6.654161 ACCTGATATCATATTTGAAGAGCAGC 59.346 38.462 5.72 0.00 35.53 5.25
2347 3579 6.093771 CCTGATATCATATTTGAAGAGCAGCC 59.906 42.308 5.72 0.00 35.53 4.85
2348 3580 6.536447 TGATATCATATTTGAAGAGCAGCCA 58.464 36.000 0.00 0.00 34.96 4.75
2349 3581 6.653740 TGATATCATATTTGAAGAGCAGCCAG 59.346 38.462 0.00 0.00 34.96 4.85
2350 3582 2.947652 TCATATTTGAAGAGCAGCCAGC 59.052 45.455 0.00 0.00 46.19 4.85
2351 3583 5.526714 ATCATATTTGAAGAGCAGCCAGCC 61.527 45.833 0.00 0.00 38.76 4.85
2352 3584 7.684769 ATCATATTTGAAGAGCAGCCAGCCT 62.685 44.000 0.00 0.00 38.76 4.58
2353 3585 9.756656 TATCATATTTGAAGAGCAGCCAGCCTT 62.757 40.741 0.00 0.00 38.76 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
322 337 1.447314 CTTCCGTAACCTGTCGGGC 60.447 63.158 0.00 0.00 45.79 6.13
334 349 1.664321 ATAACGAGCTCCGCTTCCGT 61.664 55.000 8.47 0.00 39.98 4.69
335 350 0.527817 AATAACGAGCTCCGCTTCCG 60.528 55.000 8.47 0.00 39.88 4.30
340 355 0.179108 ACTGGAATAACGAGCTCCGC 60.179 55.000 8.47 0.00 43.32 5.54
351 366 1.226974 GCTCGCAGCGACTGGAATA 60.227 57.895 15.11 0.00 31.21 1.75
352 367 2.510238 GCTCGCAGCGACTGGAAT 60.510 61.111 15.11 0.00 31.21 3.01
363 378 0.456824 CTTCTTCTGCTACGCTCGCA 60.457 55.000 0.00 0.00 35.80 5.10
364 379 1.747686 GCTTCTTCTGCTACGCTCGC 61.748 60.000 0.00 0.00 0.00 5.03
367 382 1.153745 CGGCTTCTTCTGCTACGCT 60.154 57.895 0.00 0.00 0.00 5.07
376 391 2.436824 GCCCTGTCCGGCTTCTTC 60.437 66.667 0.00 0.00 46.10 2.87
443 458 0.380378 TTCAAGTGCGTGTCCAAAGC 59.620 50.000 0.00 0.00 0.00 3.51
444 459 1.597937 GCTTCAAGTGCGTGTCCAAAG 60.598 52.381 0.00 0.00 0.00 2.77
445 460 0.380378 GCTTCAAGTGCGTGTCCAAA 59.620 50.000 0.00 0.00 0.00 3.28
446 461 2.021722 GCTTCAAGTGCGTGTCCAA 58.978 52.632 0.00 0.00 0.00 3.53
447 462 3.731136 GCTTCAAGTGCGTGTCCA 58.269 55.556 0.00 0.00 0.00 4.02
454 469 2.866028 CTCTGCCGCTTCAAGTGC 59.134 61.111 0.00 0.00 0.00 4.40
455 470 2.866028 GCTCTGCCGCTTCAAGTG 59.134 61.111 0.00 0.00 0.00 3.16
456 471 2.513026 ATCGCTCTGCCGCTTCAAGT 62.513 55.000 0.00 0.00 0.00 3.16
457 472 1.812922 ATCGCTCTGCCGCTTCAAG 60.813 57.895 0.00 0.00 0.00 3.02
458 473 2.102438 CATCGCTCTGCCGCTTCAA 61.102 57.895 0.00 0.00 0.00 2.69
459 474 2.510012 CATCGCTCTGCCGCTTCA 60.510 61.111 0.00 0.00 0.00 3.02
460 475 2.510238 ACATCGCTCTGCCGCTTC 60.510 61.111 0.00 0.00 0.00 3.86
461 476 2.225791 TACACATCGCTCTGCCGCTT 62.226 55.000 0.00 0.00 0.00 4.68
462 477 2.619840 CTACACATCGCTCTGCCGCT 62.620 60.000 0.00 0.00 0.00 5.52
463 478 2.202743 TACACATCGCTCTGCCGC 60.203 61.111 0.00 0.00 0.00 6.53
464 479 1.589993 CCTACACATCGCTCTGCCG 60.590 63.158 0.00 0.00 0.00 5.69
465 480 1.227380 CCCTACACATCGCTCTGCC 60.227 63.158 0.00 0.00 0.00 4.85
466 481 1.884926 GCCCTACACATCGCTCTGC 60.885 63.158 0.00 0.00 0.00 4.26
467 482 1.517361 TGCCCTACACATCGCTCTG 59.483 57.895 0.00 0.00 0.00 3.35
468 483 4.034246 TGCCCTACACATCGCTCT 57.966 55.556 0.00 0.00 0.00 4.09
490 505 3.522731 CTCCTCGAGGTCCTGGCG 61.523 72.222 30.17 2.90 36.34 5.69
491 506 3.151022 CCTCCTCGAGGTCCTGGC 61.151 72.222 30.17 0.00 44.25 4.85
514 529 3.535962 GCAGAGAGCCTCCCCGAG 61.536 72.222 0.00 0.00 37.23 4.63
539 554 3.435186 GAACAAGGAGCAGCCGGC 61.435 66.667 21.89 21.89 43.43 6.13
540 555 1.301677 GAAGAACAAGGAGCAGCCGG 61.302 60.000 0.00 0.00 43.43 6.13
541 556 1.301677 GGAAGAACAAGGAGCAGCCG 61.302 60.000 0.00 0.00 43.43 5.52
542 557 0.037447 AGGAAGAACAAGGAGCAGCC 59.963 55.000 0.00 0.00 0.00 4.85
543 558 1.163554 CAGGAAGAACAAGGAGCAGC 58.836 55.000 0.00 0.00 0.00 5.25
544 559 1.349026 TCCAGGAAGAACAAGGAGCAG 59.651 52.381 0.00 0.00 0.00 4.24
545 560 1.072331 GTCCAGGAAGAACAAGGAGCA 59.928 52.381 0.00 0.00 0.00 4.26
546 561 1.611936 GGTCCAGGAAGAACAAGGAGC 60.612 57.143 0.00 0.00 39.35 4.70
547 562 1.981495 AGGTCCAGGAAGAACAAGGAG 59.019 52.381 0.00 0.00 0.00 3.69
548 563 1.978580 GAGGTCCAGGAAGAACAAGGA 59.021 52.381 0.00 0.00 0.00 3.36
549 564 1.981495 AGAGGTCCAGGAAGAACAAGG 59.019 52.381 0.00 0.00 0.00 3.61
550 565 3.778954 AAGAGGTCCAGGAAGAACAAG 57.221 47.619 0.00 0.00 0.00 3.16
551 566 3.820557 CAAAGAGGTCCAGGAAGAACAA 58.179 45.455 0.00 0.00 0.00 2.83
552 567 2.487265 GCAAAGAGGTCCAGGAAGAACA 60.487 50.000 0.00 0.00 0.00 3.18
553 568 2.155279 GCAAAGAGGTCCAGGAAGAAC 58.845 52.381 0.00 0.00 0.00 3.01
554 569 1.073923 GGCAAAGAGGTCCAGGAAGAA 59.926 52.381 0.00 0.00 0.00 2.52
555 570 0.693049 GGCAAAGAGGTCCAGGAAGA 59.307 55.000 0.00 0.00 0.00 2.87
556 571 0.401738 TGGCAAAGAGGTCCAGGAAG 59.598 55.000 0.00 0.00 0.00 3.46
557 572 1.004745 GATGGCAAAGAGGTCCAGGAA 59.995 52.381 0.00 0.00 32.78 3.36
558 573 0.620556 GATGGCAAAGAGGTCCAGGA 59.379 55.000 0.00 0.00 32.78 3.86
559 574 0.745845 CGATGGCAAAGAGGTCCAGG 60.746 60.000 0.00 0.00 32.78 4.45
560 575 1.372087 GCGATGGCAAAGAGGTCCAG 61.372 60.000 0.00 0.00 39.62 3.86
561 576 1.377202 GCGATGGCAAAGAGGTCCA 60.377 57.895 0.00 0.00 39.62 4.02
562 577 2.115291 GGCGATGGCAAAGAGGTCC 61.115 63.158 1.01 0.00 42.47 4.46
563 578 2.115291 GGGCGATGGCAAAGAGGTC 61.115 63.158 1.01 0.00 42.47 3.85
564 579 2.044946 GGGCGATGGCAAAGAGGT 60.045 61.111 1.01 0.00 42.47 3.85
565 580 2.830370 GGGGCGATGGCAAAGAGG 60.830 66.667 1.01 0.00 42.47 3.69
566 581 2.587322 TACGGGGCGATGGCAAAGAG 62.587 60.000 1.01 0.00 42.47 2.85
567 582 2.587322 CTACGGGGCGATGGCAAAGA 62.587 60.000 1.01 0.00 42.47 2.52
568 583 2.124901 TACGGGGCGATGGCAAAG 60.125 61.111 1.01 0.00 42.47 2.77
569 584 2.124901 CTACGGGGCGATGGCAAA 60.125 61.111 1.01 0.00 42.47 3.68
570 585 4.849310 GCTACGGGGCGATGGCAA 62.849 66.667 1.01 0.00 42.47 4.52
588 603 0.251832 TATCGGGCTGGATCTCCTCC 60.252 60.000 0.00 0.00 45.19 4.30
589 604 1.273886 GTTATCGGGCTGGATCTCCTC 59.726 57.143 0.00 0.00 36.82 3.71
590 605 1.343069 GTTATCGGGCTGGATCTCCT 58.657 55.000 0.00 0.00 36.82 3.69
591 606 0.038159 CGTTATCGGGCTGGATCTCC 60.038 60.000 0.00 0.00 0.00 3.71
592 607 3.498676 CGTTATCGGGCTGGATCTC 57.501 57.895 0.00 0.00 0.00 2.75
617 632 4.413800 AAAAACATCCGCCGCCGC 62.414 61.111 0.00 0.00 0.00 6.53
727 745 1.491668 TGGCTTCGGGCTTACTGATA 58.508 50.000 1.83 0.00 41.46 2.15
773 791 0.911769 CACTGCATCAAGGGGGTAGA 59.088 55.000 0.00 0.00 0.00 2.59
802 820 3.516300 TCTGTTTGGTATTAGGCTCGGAA 59.484 43.478 0.00 0.00 0.00 4.30
861 879 1.338107 CCGGTATGTGGCTAGGATGA 58.662 55.000 0.00 0.00 0.00 2.92
964 982 1.900498 GCTTGGCAAGGTCTGTGCT 60.900 57.895 27.25 0.00 41.88 4.40
1114 1179 4.947147 GGTTGCCAGGTGGTGCGA 62.947 66.667 0.00 0.00 37.57 5.10
1156 1221 1.335132 GGATGGTGGGCTCCGAGTAA 61.335 60.000 0.00 0.00 0.00 2.24
1197 1262 2.058675 CCGTCTTGGGAGGAACTGT 58.941 57.895 0.00 0.00 41.55 3.55
1862 2185 4.910585 CCGCCGTCCATAGCACCC 62.911 72.222 0.00 0.00 0.00 4.61
1883 2562 2.328589 CCTCCTCCTCTCCCCCTCA 61.329 68.421 0.00 0.00 0.00 3.86
1996 2677 4.335874 GGTTTTTGGCCCGTATTTGTTTTT 59.664 37.500 0.00 0.00 0.00 1.94
1997 2678 3.878103 GGTTTTTGGCCCGTATTTGTTTT 59.122 39.130 0.00 0.00 0.00 2.43
1999 2680 2.224329 GGGTTTTTGGCCCGTATTTGTT 60.224 45.455 0.00 0.00 36.30 2.83
2000 2681 1.345089 GGGTTTTTGGCCCGTATTTGT 59.655 47.619 0.00 0.00 36.30 2.83
2001 2682 2.087501 GGGTTTTTGGCCCGTATTTG 57.912 50.000 0.00 0.00 36.30 2.32
2008 2689 1.338294 CCGTATTTGGGTTTTTGGCCC 60.338 52.381 0.00 0.00 46.26 5.80
2009 2690 1.338294 CCCGTATTTGGGTTTTTGGCC 60.338 52.381 0.00 0.00 44.76 5.36
2010 2691 2.087501 CCCGTATTTGGGTTTTTGGC 57.912 50.000 0.00 0.00 44.76 4.52
2029 2710 2.049433 AGATACATACGCCGCCGC 60.049 61.111 0.00 0.00 38.22 6.53
2031 2712 1.726791 CATTCAGATACATACGCCGCC 59.273 52.381 0.00 0.00 0.00 6.13
2032 2713 2.404215 ACATTCAGATACATACGCCGC 58.596 47.619 0.00 0.00 0.00 6.53
2033 2714 5.444613 GCATAACATTCAGATACATACGCCG 60.445 44.000 0.00 0.00 0.00 6.46
2034 2715 5.444613 CGCATAACATTCAGATACATACGCC 60.445 44.000 0.00 0.00 0.00 5.68
2078 2919 1.577328 CCAAGAACACGGAGCGCAAT 61.577 55.000 11.47 0.00 0.00 3.56
2079 2920 2.250939 CCAAGAACACGGAGCGCAA 61.251 57.895 11.47 0.00 0.00 4.85
2080 2921 2.664851 CCAAGAACACGGAGCGCA 60.665 61.111 11.47 0.00 0.00 6.09
2081 2922 3.423154 CCCAAGAACACGGAGCGC 61.423 66.667 0.00 0.00 0.00 5.92
2082 2923 2.742372 CCCCAAGAACACGGAGCG 60.742 66.667 0.00 0.00 0.00 5.03
2090 2931 3.946126 GAGCCCCAGCCCCAAGAAC 62.946 68.421 0.00 0.00 41.25 3.01
2109 2950 7.792383 ACGTTGTATTTCCGAGAATATATCG 57.208 36.000 3.81 3.81 39.86 2.92
2111 2952 7.386848 CCCAACGTTGTATTTCCGAGAATATAT 59.613 37.037 25.63 0.00 0.00 0.86
2112 2953 6.702723 CCCAACGTTGTATTTCCGAGAATATA 59.297 38.462 25.63 0.00 0.00 0.86
2113 2954 5.526111 CCCAACGTTGTATTTCCGAGAATAT 59.474 40.000 25.63 0.00 0.00 1.28
2196 3426 1.621992 ACGTGTCACACTCCATCTCT 58.378 50.000 6.33 0.00 31.34 3.10
2227 3459 1.975407 GAGACGGAGGGGTTCGTGA 60.975 63.158 0.00 0.00 39.88 4.35
2228 3460 1.935327 GAGAGACGGAGGGGTTCGTG 61.935 65.000 0.00 0.00 39.88 4.35
2229 3461 1.678300 GAGAGACGGAGGGGTTCGT 60.678 63.158 0.00 0.00 42.67 3.85
2230 3462 1.378124 GAGAGAGACGGAGGGGTTCG 61.378 65.000 0.00 0.00 0.00 3.95
2231 3463 0.323542 TGAGAGAGACGGAGGGGTTC 60.324 60.000 0.00 0.00 0.00 3.62
2232 3464 0.612453 GTGAGAGAGACGGAGGGGTT 60.612 60.000 0.00 0.00 0.00 4.11
2233 3465 1.000646 GTGAGAGAGACGGAGGGGT 60.001 63.158 0.00 0.00 0.00 4.95
2234 3466 0.396417 ATGTGAGAGAGACGGAGGGG 60.396 60.000 0.00 0.00 0.00 4.79
2235 3467 1.479709 AATGTGAGAGAGACGGAGGG 58.520 55.000 0.00 0.00 0.00 4.30
2236 3468 3.283751 ACTAATGTGAGAGAGACGGAGG 58.716 50.000 0.00 0.00 0.00 4.30
2237 3469 4.974368 AACTAATGTGAGAGAGACGGAG 57.026 45.455 0.00 0.00 0.00 4.63
2238 3470 6.377429 ACATAAACTAATGTGAGAGAGACGGA 59.623 38.462 0.00 0.00 38.65 4.69
2239 3471 6.565234 ACATAAACTAATGTGAGAGAGACGG 58.435 40.000 0.00 0.00 38.65 4.79
2240 3472 9.737427 ATTACATAAACTAATGTGAGAGAGACG 57.263 33.333 0.00 0.00 40.29 4.18
2260 3492 9.019764 GCGCAATCTTTATAAAACACATTACAT 57.980 29.630 0.30 0.00 0.00 2.29
2261 3493 7.486551 GGCGCAATCTTTATAAAACACATTACA 59.513 33.333 10.83 0.00 0.00 2.41
2262 3494 7.486551 TGGCGCAATCTTTATAAAACACATTAC 59.513 33.333 10.83 0.00 0.00 1.89
2263 3495 7.539436 TGGCGCAATCTTTATAAAACACATTA 58.461 30.769 10.83 0.00 0.00 1.90
2264 3496 6.393990 TGGCGCAATCTTTATAAAACACATT 58.606 32.000 10.83 0.00 0.00 2.71
2265 3497 5.960113 TGGCGCAATCTTTATAAAACACAT 58.040 33.333 10.83 0.00 0.00 3.21
2266 3498 5.378292 TGGCGCAATCTTTATAAAACACA 57.622 34.783 10.83 0.00 0.00 3.72
2267 3499 6.183360 CCTTTGGCGCAATCTTTATAAAACAC 60.183 38.462 10.83 0.00 0.00 3.32
2268 3500 5.866633 CCTTTGGCGCAATCTTTATAAAACA 59.133 36.000 10.83 0.00 0.00 2.83
2269 3501 5.867174 ACCTTTGGCGCAATCTTTATAAAAC 59.133 36.000 10.83 0.00 0.00 2.43
2270 3502 6.031751 ACCTTTGGCGCAATCTTTATAAAA 57.968 33.333 10.83 0.00 0.00 1.52
2271 3503 5.393678 GGACCTTTGGCGCAATCTTTATAAA 60.394 40.000 10.83 0.00 0.00 1.40
2272 3504 4.097286 GGACCTTTGGCGCAATCTTTATAA 59.903 41.667 10.83 0.00 0.00 0.98
2273 3505 3.630312 GGACCTTTGGCGCAATCTTTATA 59.370 43.478 10.83 0.00 0.00 0.98
2274 3506 2.427095 GGACCTTTGGCGCAATCTTTAT 59.573 45.455 10.83 0.00 0.00 1.40
2275 3507 1.816224 GGACCTTTGGCGCAATCTTTA 59.184 47.619 10.83 0.00 0.00 1.85
2276 3508 0.603065 GGACCTTTGGCGCAATCTTT 59.397 50.000 10.83 0.00 0.00 2.52
2277 3509 0.251341 AGGACCTTTGGCGCAATCTT 60.251 50.000 10.83 0.00 0.00 2.40
2278 3510 0.678048 GAGGACCTTTGGCGCAATCT 60.678 55.000 10.83 0.00 0.00 2.40
2279 3511 0.960364 TGAGGACCTTTGGCGCAATC 60.960 55.000 10.83 0.00 0.00 2.67
2280 3512 0.323725 ATGAGGACCTTTGGCGCAAT 60.324 50.000 10.83 0.00 0.00 3.56
2281 3513 0.326595 TATGAGGACCTTTGGCGCAA 59.673 50.000 10.83 0.00 0.00 4.85
2282 3514 0.326595 TTATGAGGACCTTTGGCGCA 59.673 50.000 10.83 0.00 0.00 6.09
2283 3515 1.132453 GTTTATGAGGACCTTTGGCGC 59.868 52.381 0.00 0.00 0.00 6.53
2284 3516 1.743394 GGTTTATGAGGACCTTTGGCG 59.257 52.381 0.00 0.00 33.08 5.69
2285 3517 1.743394 CGGTTTATGAGGACCTTTGGC 59.257 52.381 0.00 0.00 33.69 4.52
2286 3518 3.067684 ACGGTTTATGAGGACCTTTGG 57.932 47.619 0.00 0.00 33.69 3.28
2287 3519 5.424757 TCATACGGTTTATGAGGACCTTTG 58.575 41.667 0.00 0.00 33.69 2.77
2288 3520 5.687166 TCATACGGTTTATGAGGACCTTT 57.313 39.130 0.00 0.00 33.69 3.11
2289 3521 5.687166 TTCATACGGTTTATGAGGACCTT 57.313 39.130 0.00 0.00 35.62 3.50
2290 3522 5.687166 TTTCATACGGTTTATGAGGACCT 57.313 39.130 0.00 0.00 35.62 3.85
2291 3523 6.540914 TCAATTTCATACGGTTTATGAGGACC 59.459 38.462 0.00 0.00 35.62 4.46
2292 3524 7.548196 TCAATTTCATACGGTTTATGAGGAC 57.452 36.000 0.00 0.00 35.62 3.85
2293 3525 8.210946 AGATCAATTTCATACGGTTTATGAGGA 58.789 33.333 0.00 0.00 35.62 3.71
2294 3526 8.383318 AGATCAATTTCATACGGTTTATGAGG 57.617 34.615 0.00 0.00 35.62 3.86
2297 3529 9.878599 GGTAAGATCAATTTCATACGGTTTATG 57.121 33.333 0.00 0.00 0.00 1.90
2298 3530 9.847224 AGGTAAGATCAATTTCATACGGTTTAT 57.153 29.630 0.00 0.00 0.00 1.40
2299 3531 9.104965 CAGGTAAGATCAATTTCATACGGTTTA 57.895 33.333 0.00 0.00 0.00 2.01
2300 3532 7.827236 TCAGGTAAGATCAATTTCATACGGTTT 59.173 33.333 0.00 0.00 0.00 3.27
2301 3533 7.335627 TCAGGTAAGATCAATTTCATACGGTT 58.664 34.615 0.00 0.00 0.00 4.44
2302 3534 6.884832 TCAGGTAAGATCAATTTCATACGGT 58.115 36.000 0.00 0.00 0.00 4.83
2303 3535 7.969536 ATCAGGTAAGATCAATTTCATACGG 57.030 36.000 0.00 0.00 0.00 4.02
2317 3549 9.935241 GCTCTTCAAATATGATATCAGGTAAGA 57.065 33.333 11.78 11.78 34.96 2.10
2318 3550 9.716531 TGCTCTTCAAATATGATATCAGGTAAG 57.283 33.333 11.78 8.59 34.96 2.34
2319 3551 9.716531 CTGCTCTTCAAATATGATATCAGGTAA 57.283 33.333 11.78 0.00 34.96 2.85
2320 3552 7.821359 GCTGCTCTTCAAATATGATATCAGGTA 59.179 37.037 11.78 0.00 34.96 3.08
2321 3553 6.654161 GCTGCTCTTCAAATATGATATCAGGT 59.346 38.462 11.78 0.00 34.96 4.00
2322 3554 6.093771 GGCTGCTCTTCAAATATGATATCAGG 59.906 42.308 11.78 0.00 34.96 3.86
2323 3555 6.653740 TGGCTGCTCTTCAAATATGATATCAG 59.346 38.462 11.78 0.00 34.96 2.90
2324 3556 6.536447 TGGCTGCTCTTCAAATATGATATCA 58.464 36.000 8.10 8.10 34.96 2.15
2325 3557 6.403418 GCTGGCTGCTCTTCAAATATGATATC 60.403 42.308 9.31 0.00 38.95 1.63
2326 3558 5.415077 GCTGGCTGCTCTTCAAATATGATAT 59.585 40.000 9.31 0.00 38.95 1.63
2327 3559 4.758674 GCTGGCTGCTCTTCAAATATGATA 59.241 41.667 9.31 0.00 38.95 2.15
2328 3560 3.568853 GCTGGCTGCTCTTCAAATATGAT 59.431 43.478 9.31 0.00 38.95 2.45
2329 3561 2.947652 GCTGGCTGCTCTTCAAATATGA 59.052 45.455 9.31 0.00 38.95 2.15
2330 3562 2.034305 GGCTGGCTGCTCTTCAAATATG 59.966 50.000 16.14 0.00 42.39 1.78
2331 3563 2.091994 AGGCTGGCTGCTCTTCAAATAT 60.092 45.455 16.14 0.00 42.39 1.28
2332 3564 1.283029 AGGCTGGCTGCTCTTCAAATA 59.717 47.619 16.14 0.00 42.39 1.40
2333 3565 0.039326 AGGCTGGCTGCTCTTCAAAT 59.961 50.000 16.14 0.00 42.39 2.32
2334 3566 0.178981 AAGGCTGGCTGCTCTTCAAA 60.179 50.000 16.14 0.00 42.39 2.69
2335 3567 0.178981 AAAGGCTGGCTGCTCTTCAA 60.179 50.000 16.14 0.00 42.39 2.69
2336 3568 0.892358 CAAAGGCTGGCTGCTCTTCA 60.892 55.000 16.14 0.00 42.39 3.02
2337 3569 0.892814 ACAAAGGCTGGCTGCTCTTC 60.893 55.000 16.14 0.00 42.39 2.87
2338 3570 1.152368 ACAAAGGCTGGCTGCTCTT 59.848 52.632 16.14 13.79 42.39 2.85
2339 3571 2.842058 ACAAAGGCTGGCTGCTCT 59.158 55.556 16.14 8.69 42.39 4.09


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

AutoCloner maintained by Alex Coulton.