Multiple sequence alignment - TraesCS5A01G177300

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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 TraesCS5A01G177300 chr5A 100.000 5636 0 0 1 5636 374650186 374644551 0.000000e+00 10408.0
1 TraesCS5A01G177300 chr5D 93.133 5388 225 51 2 5328 282156619 282151316 0.000000e+00 7766.0
2 TraesCS5A01G177300 chr5D 88.785 107 8 4 5339 5445 282151270 282151168 1.650000e-25 128.0
3 TraesCS5A01G177300 chr5B 93.317 4878 225 41 7 4834 320156990 320152164 0.000000e+00 7108.0
4 TraesCS5A01G177300 chr5B 90.892 527 29 8 4843 5354 320152039 320151517 0.000000e+00 689.0
5 TraesCS5A01G177300 chr5B 79.070 172 30 3 5470 5636 487452683 487452853 4.610000e-21 113.0
6 TraesCS5A01G177300 chr3A 79.608 765 145 8 3633 4393 64281497 64282254 6.430000e-149 538.0
7 TraesCS5A01G177300 chr3B 79.161 763 152 6 3633 4393 82625575 82626332 6.470000e-144 521.0
8 TraesCS5A01G177300 chr3B 78.530 694 140 8 3641 4331 443806253 443806940 1.110000e-121 448.0
9 TraesCS5A01G177300 chr7D 79.882 169 29 4 5473 5636 554197291 554197123 9.920000e-23 119.0
10 TraesCS5A01G177300 chr7D 79.389 131 20 5 5512 5636 391260339 391260468 1.010000e-12 86.1
11 TraesCS5A01G177300 chr7D 84.000 75 10 1 5564 5636 448760925 448760851 2.820000e-08 71.3


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G177300 chr5A 374644551 374650186 5635 True 10408.0 10408 100.0000 1 5636 1 chr5A.!!$R1 5635
1 TraesCS5A01G177300 chr5D 282151168 282156619 5451 True 3947.0 7766 90.9590 2 5445 2 chr5D.!!$R1 5443
2 TraesCS5A01G177300 chr5B 320151517 320156990 5473 True 3898.5 7108 92.1045 7 5354 2 chr5B.!!$R1 5347
3 TraesCS5A01G177300 chr3A 64281497 64282254 757 False 538.0 538 79.6080 3633 4393 1 chr3A.!!$F1 760
4 TraesCS5A01G177300 chr3B 82625575 82626332 757 False 521.0 521 79.1610 3633 4393 1 chr3B.!!$F1 760
5 TraesCS5A01G177300 chr3B 443806253 443806940 687 False 448.0 448 78.5300 3641 4331 1 chr3B.!!$F2 690

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
497 555 0.028770 TGCTTCTTGGTTTCGTTGCG 59.971 50.000 0.00 0.00 0.00 4.85 F
549 607 0.258774 AGGTTGCAACTGGACTTGGT 59.741 50.000 27.64 0.67 0.00 3.67 F
1003 1080 0.391661 CACAGGACCCGAAGACATGG 60.392 60.000 0.00 0.00 0.00 3.66 F
2386 2475 0.250124 CAACTACCTCAACGGCACCA 60.250 55.000 0.00 0.00 35.61 4.17 F
3513 3602 1.001487 CTCTCGCTGCTCATACTCCTG 60.001 57.143 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 1922 0.250553 TTAGGCCGTTGTTGGACCAG 60.251 55.000 0.00 0.0 38.01 4.00 R
2146 2235 0.534203 GCCACAAAGTCACCGGAGAA 60.534 55.000 9.46 0.0 0.00 2.87 R
2638 2727 2.430921 CGACAGCGACACCCAGAC 60.431 66.667 0.00 0.0 40.82 3.51 R
3554 3643 0.382515 CGTTCTGATCTCCTCGGTCC 59.617 60.000 0.00 0.0 0.00 4.46 R
5225 5452 0.032952 GTGGTGCTACTGTCCACGAA 59.967 55.000 1.24 0.0 41.37 3.85 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
44 45 0.033090 CGAGGGCGAGTAATTACCCC 59.967 60.000 16.65 16.65 43.96 4.95
79 91 0.730840 CCTCCCGCGAATAAACAACC 59.269 55.000 8.23 0.00 0.00 3.77
208 221 2.766229 GGAGCTCTGTCCCTCCCC 60.766 72.222 14.64 0.00 41.42 4.81
209 222 2.366570 GAGCTCTGTCCCTCCCCT 59.633 66.667 6.43 0.00 0.00 4.79
210 223 2.040278 AGCTCTGTCCCTCCCCTG 59.960 66.667 0.00 0.00 0.00 4.45
213 226 1.311403 CTCTGTCCCTCCCCTGCTA 59.689 63.158 0.00 0.00 0.00 3.49
215 228 1.002274 CTGTCCCTCCCCTGCTACT 59.998 63.158 0.00 0.00 0.00 2.57
217 230 0.714180 TGTCCCTCCCCTGCTACTTA 59.286 55.000 0.00 0.00 0.00 2.24
218 231 1.079825 TGTCCCTCCCCTGCTACTTAA 59.920 52.381 0.00 0.00 0.00 1.85
229 257 7.963532 TCCCCTGCTACTTAATAAATAGTCAG 58.036 38.462 6.19 6.19 0.00 3.51
257 285 1.227943 TGTGTGTGCTTCCTCTGCC 60.228 57.895 0.00 0.00 0.00 4.85
258 286 1.072159 GTGTGTGCTTCCTCTGCCT 59.928 57.895 0.00 0.00 0.00 4.75
259 287 0.952984 GTGTGTGCTTCCTCTGCCTC 60.953 60.000 0.00 0.00 0.00 4.70
260 288 1.123861 TGTGTGCTTCCTCTGCCTCT 61.124 55.000 0.00 0.00 0.00 3.69
261 289 0.673022 GTGTGCTTCCTCTGCCTCTG 60.673 60.000 0.00 0.00 0.00 3.35
262 290 1.744741 GTGCTTCCTCTGCCTCTGC 60.745 63.158 0.00 0.00 38.26 4.26
299 327 1.227205 CTCGTCCAGCAGCATCTCC 60.227 63.158 0.00 0.00 0.00 3.71
334 369 2.978000 TCGCCTGCGATTCTTGGA 59.022 55.556 10.61 0.00 44.01 3.53
464 522 1.214992 AATCTTTCCGGGCTCCCCTT 61.215 55.000 0.00 0.00 42.67 3.95
465 523 1.636769 ATCTTTCCGGGCTCCCCTTC 61.637 60.000 0.00 0.00 42.67 3.46
466 524 2.204090 TTTCCGGGCTCCCCTTCT 60.204 61.111 0.00 0.00 42.67 2.85
467 525 2.258748 CTTTCCGGGCTCCCCTTCTC 62.259 65.000 0.00 0.00 42.67 2.87
469 527 3.474570 CCGGGCTCCCCTTCTCTG 61.475 72.222 0.00 0.00 42.67 3.35
473 531 1.052617 GGGCTCCCCTTCTCTGTATC 58.947 60.000 0.00 0.00 41.34 2.24
497 555 0.028770 TGCTTCTTGGTTTCGTTGCG 59.971 50.000 0.00 0.00 0.00 4.85
539 597 1.205893 TGGTGGTTTGAAGGTTGCAAC 59.794 47.619 21.59 21.59 0.00 4.17
547 605 2.023673 TGAAGGTTGCAACTGGACTTG 58.976 47.619 27.64 0.00 0.00 3.16
548 606 1.338020 GAAGGTTGCAACTGGACTTGG 59.662 52.381 27.64 0.00 0.00 3.61
549 607 0.258774 AGGTTGCAACTGGACTTGGT 59.741 50.000 27.64 0.67 0.00 3.67
550 608 1.111277 GGTTGCAACTGGACTTGGTT 58.889 50.000 27.64 0.00 0.00 3.67
551 609 1.480545 GGTTGCAACTGGACTTGGTTT 59.519 47.619 27.64 0.00 0.00 3.27
552 610 2.481276 GGTTGCAACTGGACTTGGTTTC 60.481 50.000 27.64 3.83 0.00 2.78
553 611 2.136298 TGCAACTGGACTTGGTTTCA 57.864 45.000 0.00 0.00 0.00 2.69
554 612 2.665165 TGCAACTGGACTTGGTTTCAT 58.335 42.857 0.00 0.00 0.00 2.57
555 613 2.361757 TGCAACTGGACTTGGTTTCATG 59.638 45.455 0.00 0.00 0.00 3.07
556 614 2.288395 GCAACTGGACTTGGTTTCATGG 60.288 50.000 0.00 0.00 0.00 3.66
557 615 1.620822 ACTGGACTTGGTTTCATGGC 58.379 50.000 0.00 0.00 0.00 4.40
558 616 0.890683 CTGGACTTGGTTTCATGGCC 59.109 55.000 0.00 0.00 44.19 5.36
559 617 0.482446 TGGACTTGGTTTCATGGCCT 59.518 50.000 3.32 0.00 44.23 5.19
604 662 1.003331 TGTTTGTGATTTGCGTCCGAC 60.003 47.619 0.00 0.00 0.00 4.79
623 681 3.186613 CGACTTGGAGCTTGTTTCTTACC 59.813 47.826 0.00 0.00 0.00 2.85
648 706 4.202367 GGATTCGTTCCATGGGTTCTATCT 60.202 45.833 13.02 0.00 44.74 1.98
649 707 4.402056 TTCGTTCCATGGGTTCTATCTC 57.598 45.455 13.02 0.00 0.00 2.75
650 708 3.643237 TCGTTCCATGGGTTCTATCTCT 58.357 45.455 13.02 0.00 0.00 3.10
653 711 4.709250 GTTCCATGGGTTCTATCTCTTCC 58.291 47.826 13.02 0.00 0.00 3.46
654 712 2.965831 TCCATGGGTTCTATCTCTTCCG 59.034 50.000 13.02 0.00 0.00 4.30
695 753 4.342665 GGGGTTTAGTGTGTTGAATTTGGA 59.657 41.667 0.00 0.00 0.00 3.53
697 755 4.973663 GGTTTAGTGTGTTGAATTTGGACG 59.026 41.667 0.00 0.00 0.00 4.79
699 757 5.666969 TTAGTGTGTTGAATTTGGACGAG 57.333 39.130 0.00 0.00 0.00 4.18
706 764 5.983118 GTGTTGAATTTGGACGAGGAATTTT 59.017 36.000 0.00 0.00 0.00 1.82
800 871 1.506262 CGAGCAAATTGTTCGGGGG 59.494 57.895 21.57 0.00 45.30 5.40
883 954 1.831736 ACCCAAATCTTCTCCGTCGAT 59.168 47.619 0.00 0.00 0.00 3.59
891 962 4.288670 TCTTCTCCGTCGATATGTGAAC 57.711 45.455 0.00 0.00 0.00 3.18
950 1022 3.497879 CGGGCATCTCCGTTTTCC 58.502 61.111 0.00 0.00 44.60 3.13
964 1041 2.287608 CGTTTTCCCTCCTTGCAAGAAC 60.288 50.000 28.05 18.99 0.00 3.01
998 1075 2.915659 ACGCACAGGACCCGAAGA 60.916 61.111 0.00 0.00 0.00 2.87
1003 1080 0.391661 CACAGGACCCGAAGACATGG 60.392 60.000 0.00 0.00 0.00 3.66
1253 1342 2.032528 CCTCAACCTCAGCGGCAA 59.967 61.111 1.45 0.00 35.61 4.52
1633 1722 2.154798 CTCCGCCAACCTCTTCACGA 62.155 60.000 0.00 0.00 0.00 4.35
1830 1919 3.050275 GGCAACCTGACGGTGCTC 61.050 66.667 0.00 0.00 44.73 4.26
1833 1922 2.022129 CAACCTGACGGTGCTCGAC 61.022 63.158 7.01 1.91 44.73 4.20
1845 1934 0.531974 TGCTCGACTGGTCCAACAAC 60.532 55.000 0.00 0.00 0.00 3.32
1864 1953 2.820037 GCCTAAGCAGCACCGGAC 60.820 66.667 9.46 0.00 39.53 4.79
1866 1955 1.956629 GCCTAAGCAGCACCGGACTA 61.957 60.000 9.46 0.00 39.53 2.59
1889 1978 4.329545 GGGTCTCGCCAACTGCCA 62.330 66.667 0.00 0.00 39.65 4.92
1890 1979 3.050275 GGTCTCGCCAACTGCCAC 61.050 66.667 0.00 0.00 36.24 5.01
1953 2042 2.987232 GGCTCAATACCGACCTTCTTT 58.013 47.619 0.00 0.00 0.00 2.52
1962 2051 3.157087 ACCGACCTTCTTTACCGAACTA 58.843 45.455 0.00 0.00 0.00 2.24
2050 2139 2.434185 TGTGCGGCAGAATCGTCC 60.434 61.111 1.18 0.00 0.00 4.79
2053 2142 1.078497 TGCGGCAGAATCGTCCATT 60.078 52.632 0.00 0.00 0.00 3.16
2055 2144 0.451783 GCGGCAGAATCGTCCATTTT 59.548 50.000 0.00 0.00 0.00 1.82
2106 2195 2.126734 CCGGCGAGCTTTGCAAAG 60.127 61.111 30.70 30.70 39.03 2.77
2146 2235 1.867919 CGACCTCAGAGCGAACCAGT 61.868 60.000 0.00 0.00 0.00 4.00
2290 2379 1.899534 GAGGAGATCGACCTCGGGG 60.900 68.421 20.29 0.00 43.25 5.73
2331 2420 4.457496 ATGCCGGACCTGTGCTCG 62.457 66.667 5.05 0.00 0.00 5.03
2386 2475 0.250124 CAACTACCTCAACGGCACCA 60.250 55.000 0.00 0.00 35.61 4.17
2388 2477 1.563924 ACTACCTCAACGGCACCATA 58.436 50.000 0.00 0.00 35.61 2.74
2638 2727 1.956170 ACAAGCTGCGTGAACCTCG 60.956 57.895 21.97 0.00 0.00 4.63
2745 2834 1.743252 CAAGAACCAGCTCTCCGGC 60.743 63.158 0.00 0.00 0.00 6.13
2949 3038 2.601804 GGACTGCTCTTCGAGTTCTTC 58.398 52.381 0.00 0.00 31.39 2.87
3015 3104 3.399181 TGCCCGGTCACCAGGATC 61.399 66.667 0.00 0.00 0.00 3.36
3020 3109 1.414158 CCGGTCACCAGGATCTACAT 58.586 55.000 0.00 0.00 0.00 2.29
3237 3326 2.480419 CCTGTCAAACAATCACCTCGTC 59.520 50.000 0.00 0.00 0.00 4.20
3513 3602 1.001487 CTCTCGCTGCTCATACTCCTG 60.001 57.143 0.00 0.00 0.00 3.86
3573 3662 0.382515 GGACCGAGGAGATCAGAACG 59.617 60.000 0.00 0.00 0.00 3.95
3596 3685 0.110678 TACATCGAGAGCCTCCCGAT 59.889 55.000 5.19 5.19 42.88 4.18
3989 4081 2.050714 GCTCCACGACAACGACGA 60.051 61.111 0.00 0.00 42.66 4.20
4266 4358 3.114616 CAGAGCTTCCGGTGCACG 61.115 66.667 20.41 6.23 43.80 5.34
4419 4511 1.224722 GCGGCGAGATCTTTGATCCC 61.225 60.000 12.98 0.00 0.00 3.85
4467 4559 0.589223 CCGAGCTCGATCAGTACCTC 59.411 60.000 36.59 0.00 43.02 3.85
4643 4735 7.545965 AGAGAAATCATCGTCGTAATGTTTTCT 59.454 33.333 21.27 21.27 46.12 2.52
4644 4736 7.456253 AGAAATCATCGTCGTAATGTTTTCTG 58.544 34.615 20.85 0.00 44.08 3.02
4645 4737 6.721571 AATCATCGTCGTAATGTTTTCTGT 57.278 33.333 0.00 0.00 0.00 3.41
4646 4738 6.721571 ATCATCGTCGTAATGTTTTCTGTT 57.278 33.333 0.00 0.00 0.00 3.16
4647 4739 6.533819 TCATCGTCGTAATGTTTTCTGTTT 57.466 33.333 0.00 0.00 0.00 2.83
4648 4740 6.586751 TCATCGTCGTAATGTTTTCTGTTTC 58.413 36.000 0.00 0.00 0.00 2.78
4649 4741 6.422701 TCATCGTCGTAATGTTTTCTGTTTCT 59.577 34.615 0.00 0.00 0.00 2.52
4650 4742 6.592798 TCGTCGTAATGTTTTCTGTTTCTT 57.407 33.333 0.00 0.00 0.00 2.52
4651 4743 6.415702 TCGTCGTAATGTTTTCTGTTTCTTG 58.584 36.000 0.00 0.00 0.00 3.02
4661 4753 8.655651 TGTTTTCTGTTTCTTGTTTCTTGTTT 57.344 26.923 0.00 0.00 0.00 2.83
4662 4754 8.760569 TGTTTTCTGTTTCTTGTTTCTTGTTTC 58.239 29.630 0.00 0.00 0.00 2.78
4755 4847 2.618053 CGTAGTGTCCTCCAATTCACC 58.382 52.381 0.00 0.00 0.00 4.02
4769 4861 1.196104 TTCACCGGGGGAGGTTGTAG 61.196 60.000 2.42 0.00 43.00 2.74
4796 4888 7.914427 TTGTGGTTCCACTCTCTGTATATAT 57.086 36.000 20.48 0.00 37.78 0.86
4797 4889 9.429109 TTTGTGGTTCCACTCTCTGTATATATA 57.571 33.333 20.48 0.00 37.78 0.86
4804 4896 7.166167 TCCACTCTCTGTATATATAAGCGTCA 58.834 38.462 0.00 0.00 0.00 4.35
4923 5131 5.618056 TTTCAGTTGCATGTCTCAGATTC 57.382 39.130 0.00 0.00 0.00 2.52
4928 5136 5.354513 CAGTTGCATGTCTCAGATTCTCATT 59.645 40.000 0.00 0.00 0.00 2.57
4932 5140 5.123344 TGCATGTCTCAGATTCTCATTTGTG 59.877 40.000 0.00 0.00 0.00 3.33
4942 5150 6.805271 CAGATTCTCATTTGTGCTTTTACCTG 59.195 38.462 0.00 0.00 0.00 4.00
4944 5152 4.144297 TCTCATTTGTGCTTTTACCTGCT 58.856 39.130 0.00 0.00 0.00 4.24
4960 5168 8.506168 TTTACCTGCTAGAATCAGTTATTTGG 57.494 34.615 0.00 0.00 0.00 3.28
4961 5169 6.313519 ACCTGCTAGAATCAGTTATTTGGA 57.686 37.500 0.00 0.00 0.00 3.53
4962 5170 6.721318 ACCTGCTAGAATCAGTTATTTGGAA 58.279 36.000 0.00 0.00 0.00 3.53
5029 5237 1.985473 TGATTGACACTTTGCAGGCT 58.015 45.000 0.00 0.00 0.00 4.58
5033 5244 2.340210 TGACACTTTGCAGGCTGTAA 57.660 45.000 14.27 14.27 0.00 2.41
5043 5254 4.662468 TGCAGGCTGTAATGAACAAAAA 57.338 36.364 17.16 0.00 37.74 1.94
5044 5255 4.619973 TGCAGGCTGTAATGAACAAAAAG 58.380 39.130 17.16 0.00 37.74 2.27
5045 5256 4.340666 TGCAGGCTGTAATGAACAAAAAGA 59.659 37.500 17.16 0.00 37.74 2.52
5046 5257 4.919754 GCAGGCTGTAATGAACAAAAAGAG 59.080 41.667 17.16 0.00 37.74 2.85
5153 5380 7.913297 CGTCTTTCCTTGACAAAACAAAATCTA 59.087 33.333 0.00 0.00 34.37 1.98
5166 5393 4.389374 ACAAAATCTATAGCCGATGGTGG 58.611 43.478 0.00 0.00 0.00 4.61
5171 5398 4.042271 TCTATAGCCGATGGTGGTGATA 57.958 45.455 0.00 0.00 0.00 2.15
5181 5408 2.470990 TGGTGGTGATATCAGTGAGCT 58.529 47.619 5.42 0.00 0.00 4.09
5216 5443 1.613437 CAGGGCGTTGAAAAATCCAGT 59.387 47.619 0.00 0.00 0.00 4.00
5225 5452 5.648092 CGTTGAAAAATCCAGTCCCTAGATT 59.352 40.000 0.00 0.00 0.00 2.40
5227 5454 7.539436 GTTGAAAAATCCAGTCCCTAGATTTC 58.461 38.462 0.00 0.00 38.85 2.17
5306 5538 0.528924 TGCTGAATGATTGCTGTGGC 59.471 50.000 0.00 0.00 39.26 5.01
5310 5542 0.099436 GAATGATTGCTGTGGCGACC 59.901 55.000 0.00 0.00 42.25 4.79
5411 5685 3.668386 GCTTTTGCAGCGGGTAGT 58.332 55.556 0.00 0.00 46.58 2.73
5422 5696 0.872388 GCGGGTAGTTTGTGGACAAG 59.128 55.000 0.00 0.00 37.15 3.16
5445 5719 4.399004 TGAAGAGCAGAGAAGATAAGGC 57.601 45.455 0.00 0.00 0.00 4.35
5446 5720 3.133721 TGAAGAGCAGAGAAGATAAGGCC 59.866 47.826 0.00 0.00 0.00 5.19
5447 5721 2.756907 AGAGCAGAGAAGATAAGGCCA 58.243 47.619 5.01 0.00 0.00 5.36
5448 5722 3.110705 AGAGCAGAGAAGATAAGGCCAA 58.889 45.455 5.01 0.00 0.00 4.52
5449 5723 3.118445 AGAGCAGAGAAGATAAGGCCAAC 60.118 47.826 5.01 0.00 0.00 3.77
5450 5724 2.843113 AGCAGAGAAGATAAGGCCAACT 59.157 45.455 5.01 0.00 0.00 3.16
5451 5725 3.265479 AGCAGAGAAGATAAGGCCAACTT 59.735 43.478 5.01 4.37 43.28 2.66
5452 5726 3.625313 GCAGAGAAGATAAGGCCAACTTC 59.375 47.826 5.01 13.56 40.64 3.01
5453 5727 4.836825 CAGAGAAGATAAGGCCAACTTCA 58.163 43.478 22.95 0.00 40.47 3.02
5454 5728 5.248640 CAGAGAAGATAAGGCCAACTTCAA 58.751 41.667 22.95 0.00 40.47 2.69
5455 5729 5.123027 CAGAGAAGATAAGGCCAACTTCAAC 59.877 44.000 22.95 18.05 40.47 3.18
5456 5730 4.003648 AGAAGATAAGGCCAACTTCAACG 58.996 43.478 22.95 0.00 40.47 4.10
5457 5731 2.084546 AGATAAGGCCAACTTCAACGC 58.915 47.619 5.01 0.00 40.64 4.84
5458 5732 0.802494 ATAAGGCCAACTTCAACGCG 59.198 50.000 5.01 3.53 40.64 6.01
5459 5733 1.847890 TAAGGCCAACTTCAACGCGC 61.848 55.000 5.73 0.00 40.64 6.86
5460 5734 4.700365 GGCCAACTTCAACGCGCC 62.700 66.667 5.73 0.00 0.00 6.53
5461 5735 4.700365 GCCAACTTCAACGCGCCC 62.700 66.667 5.73 0.00 0.00 6.13
5462 5736 3.283684 CCAACTTCAACGCGCCCA 61.284 61.111 5.73 0.00 0.00 5.36
5463 5737 2.051345 CAACTTCAACGCGCCCAC 60.051 61.111 5.73 0.00 0.00 4.61
5464 5738 2.203153 AACTTCAACGCGCCCACT 60.203 55.556 5.73 0.00 0.00 4.00
5465 5739 1.070105 AACTTCAACGCGCCCACTA 59.930 52.632 5.73 0.00 0.00 2.74
5466 5740 0.533308 AACTTCAACGCGCCCACTAA 60.533 50.000 5.73 0.00 0.00 2.24
5467 5741 0.533308 ACTTCAACGCGCCCACTAAA 60.533 50.000 5.73 0.00 0.00 1.85
5468 5742 0.589223 CTTCAACGCGCCCACTAAAA 59.411 50.000 5.73 0.00 0.00 1.52
5469 5743 0.308376 TTCAACGCGCCCACTAAAAC 59.692 50.000 5.73 0.00 0.00 2.43
5470 5744 0.814410 TCAACGCGCCCACTAAAACA 60.814 50.000 5.73 0.00 0.00 2.83
5471 5745 0.385473 CAACGCGCCCACTAAAACAG 60.385 55.000 5.73 0.00 0.00 3.16
5472 5746 1.512156 AACGCGCCCACTAAAACAGG 61.512 55.000 5.73 0.00 0.00 4.00
5473 5747 2.566529 GCGCCCACTAAAACAGGC 59.433 61.111 0.00 0.00 42.18 4.85
5474 5748 1.971695 GCGCCCACTAAAACAGGCT 60.972 57.895 0.00 0.00 43.48 4.58
5475 5749 1.524008 GCGCCCACTAAAACAGGCTT 61.524 55.000 0.00 0.00 43.48 4.35
5476 5750 0.958822 CGCCCACTAAAACAGGCTTT 59.041 50.000 0.00 0.00 43.48 3.51
5477 5751 1.335872 CGCCCACTAAAACAGGCTTTG 60.336 52.381 0.00 0.00 43.48 2.77
5478 5752 1.686587 GCCCACTAAAACAGGCTTTGT 59.313 47.619 0.00 0.00 42.34 2.83
5479 5753 2.288213 GCCCACTAAAACAGGCTTTGTC 60.288 50.000 0.00 0.00 42.34 3.18
5480 5754 2.296190 CCCACTAAAACAGGCTTTGTCC 59.704 50.000 0.00 0.00 39.73 4.02
5481 5755 2.955660 CCACTAAAACAGGCTTTGTCCA 59.044 45.455 0.00 0.00 39.73 4.02
5482 5756 3.573967 CCACTAAAACAGGCTTTGTCCAT 59.426 43.478 0.00 0.00 39.73 3.41
5483 5757 4.039124 CCACTAAAACAGGCTTTGTCCATT 59.961 41.667 0.00 0.00 39.73 3.16
5484 5758 5.453198 CCACTAAAACAGGCTTTGTCCATTT 60.453 40.000 0.00 0.00 39.73 2.32
5485 5759 6.048509 CACTAAAACAGGCTTTGTCCATTTT 58.951 36.000 0.00 0.00 39.73 1.82
5486 5760 6.538381 CACTAAAACAGGCTTTGTCCATTTTT 59.462 34.615 0.00 0.00 39.73 1.94
5505 5779 3.479505 TTTGTATGTTTGAATCGGCCG 57.520 42.857 22.12 22.12 0.00 6.13
5506 5780 2.388310 TGTATGTTTGAATCGGCCGA 57.612 45.000 33.12 33.12 0.00 5.54
5507 5781 2.004017 TGTATGTTTGAATCGGCCGAC 58.996 47.619 33.75 20.13 0.00 4.79
5508 5782 2.277084 GTATGTTTGAATCGGCCGACT 58.723 47.619 33.75 23.15 0.00 4.18
5509 5783 1.086696 ATGTTTGAATCGGCCGACTG 58.913 50.000 33.75 0.00 0.00 3.51
5510 5784 1.134694 GTTTGAATCGGCCGACTGC 59.865 57.895 33.75 22.47 40.16 4.40
5511 5785 1.003839 TTTGAATCGGCCGACTGCT 60.004 52.632 33.75 15.70 40.92 4.24
5512 5786 1.019278 TTTGAATCGGCCGACTGCTC 61.019 55.000 33.75 23.47 40.92 4.26
5513 5787 2.956964 GAATCGGCCGACTGCTCG 60.957 66.667 33.75 0.00 40.92 5.03
5514 5788 3.701604 GAATCGGCCGACTGCTCGT 62.702 63.158 33.75 10.25 38.32 4.18
5515 5789 3.701604 AATCGGCCGACTGCTCGTC 62.702 63.158 33.75 0.00 38.32 4.20
5517 5791 4.498520 CGGCCGACTGCTCGTCAT 62.499 66.667 24.07 0.00 42.98 3.06
5518 5792 2.125512 GGCCGACTGCTCGTCATT 60.126 61.111 7.35 0.00 42.98 2.57
5519 5793 2.167861 GGCCGACTGCTCGTCATTC 61.168 63.158 7.35 0.00 42.98 2.67
5520 5794 2.508891 GCCGACTGCTCGTCATTCG 61.509 63.158 11.06 11.06 44.39 3.34
5521 5795 1.154016 CCGACTGCTCGTCATTCGT 60.154 57.895 14.66 0.00 43.61 3.85
5522 5796 0.732880 CCGACTGCTCGTCATTCGTT 60.733 55.000 14.66 0.00 43.61 3.85
5523 5797 1.060713 CGACTGCTCGTCATTCGTTT 58.939 50.000 10.25 0.00 42.98 3.60
5524 5798 1.455786 CGACTGCTCGTCATTCGTTTT 59.544 47.619 10.25 0.00 42.98 2.43
5525 5799 2.470781 CGACTGCTCGTCATTCGTTTTC 60.471 50.000 10.25 0.00 42.98 2.29
5526 5800 2.731976 GACTGCTCGTCATTCGTTTTCT 59.268 45.455 2.46 0.00 42.37 2.52
5527 5801 3.131396 ACTGCTCGTCATTCGTTTTCTT 58.869 40.909 0.00 0.00 40.80 2.52
5528 5802 3.560068 ACTGCTCGTCATTCGTTTTCTTT 59.440 39.130 0.00 0.00 40.80 2.52
5529 5803 4.035208 ACTGCTCGTCATTCGTTTTCTTTT 59.965 37.500 0.00 0.00 40.80 2.27
5530 5804 4.278858 TGCTCGTCATTCGTTTTCTTTTG 58.721 39.130 0.00 0.00 40.80 2.44
5531 5805 4.201871 TGCTCGTCATTCGTTTTCTTTTGT 60.202 37.500 0.00 0.00 40.80 2.83
5532 5806 4.144731 GCTCGTCATTCGTTTTCTTTTGTG 59.855 41.667 0.00 0.00 40.80 3.33
5533 5807 5.224562 TCGTCATTCGTTTTCTTTTGTGT 57.775 34.783 0.00 0.00 40.80 3.72
5534 5808 5.632959 TCGTCATTCGTTTTCTTTTGTGTT 58.367 33.333 0.00 0.00 40.80 3.32
5535 5809 6.087522 TCGTCATTCGTTTTCTTTTGTGTTT 58.912 32.000 0.00 0.00 40.80 2.83
5536 5810 6.032985 TCGTCATTCGTTTTCTTTTGTGTTTG 59.967 34.615 0.00 0.00 40.80 2.93
5537 5811 6.465978 GTCATTCGTTTTCTTTTGTGTTTGG 58.534 36.000 0.00 0.00 0.00 3.28
5538 5812 5.578727 TCATTCGTTTTCTTTTGTGTTTGGG 59.421 36.000 0.00 0.00 0.00 4.12
5539 5813 4.522722 TCGTTTTCTTTTGTGTTTGGGT 57.477 36.364 0.00 0.00 0.00 4.51
5540 5814 4.487019 TCGTTTTCTTTTGTGTTTGGGTC 58.513 39.130 0.00 0.00 0.00 4.46
5541 5815 3.302170 CGTTTTCTTTTGTGTTTGGGTCG 59.698 43.478 0.00 0.00 0.00 4.79
5542 5816 4.487019 GTTTTCTTTTGTGTTTGGGTCGA 58.513 39.130 0.00 0.00 0.00 4.20
5543 5817 4.993029 TTTCTTTTGTGTTTGGGTCGAT 57.007 36.364 0.00 0.00 0.00 3.59
5544 5818 4.561735 TTCTTTTGTGTTTGGGTCGATC 57.438 40.909 0.00 0.00 0.00 3.69
5545 5819 2.546368 TCTTTTGTGTTTGGGTCGATCG 59.454 45.455 9.36 9.36 0.00 3.69
5546 5820 1.956297 TTTGTGTTTGGGTCGATCGT 58.044 45.000 15.94 0.00 0.00 3.73
5547 5821 1.222300 TTGTGTTTGGGTCGATCGTG 58.778 50.000 15.94 0.00 0.00 4.35
5548 5822 1.225376 TGTGTTTGGGTCGATCGTGC 61.225 55.000 15.94 9.31 0.00 5.34
5549 5823 1.069935 TGTTTGGGTCGATCGTGCA 59.930 52.632 15.94 0.00 0.00 4.57
5550 5824 1.225376 TGTTTGGGTCGATCGTGCAC 61.225 55.000 15.94 6.82 0.00 4.57
5551 5825 0.949105 GTTTGGGTCGATCGTGCACT 60.949 55.000 16.19 0.00 0.00 4.40
5552 5826 0.669318 TTTGGGTCGATCGTGCACTC 60.669 55.000 16.19 6.68 0.00 3.51
5553 5827 1.811645 TTGGGTCGATCGTGCACTCA 61.812 55.000 16.19 9.53 0.00 3.41
5554 5828 1.080093 GGGTCGATCGTGCACTCAA 60.080 57.895 16.19 0.13 0.00 3.02
5555 5829 1.352156 GGGTCGATCGTGCACTCAAC 61.352 60.000 16.19 1.69 0.00 3.18
5556 5830 1.674611 GGTCGATCGTGCACTCAACG 61.675 60.000 16.19 14.47 0.00 4.10
5557 5831 2.086426 TCGATCGTGCACTCAACGC 61.086 57.895 16.19 0.00 0.00 4.84
5558 5832 2.391821 GATCGTGCACTCAACGCG 59.608 61.111 16.19 3.53 42.18 6.01
5559 5833 2.355837 ATCGTGCACTCAACGCGT 60.356 55.556 16.19 5.58 41.56 6.01
5560 5834 2.267227 GATCGTGCACTCAACGCGTC 62.267 60.000 14.44 0.00 41.56 5.19
5561 5835 4.059459 CGTGCACTCAACGCGTCC 62.059 66.667 14.44 0.00 36.34 4.79
5562 5836 3.712881 GTGCACTCAACGCGTCCC 61.713 66.667 14.44 0.00 0.00 4.46
5563 5837 4.228567 TGCACTCAACGCGTCCCA 62.229 61.111 14.44 0.44 0.00 4.37
5564 5838 2.742372 GCACTCAACGCGTCCCAT 60.742 61.111 14.44 0.00 0.00 4.00
5565 5839 2.325082 GCACTCAACGCGTCCCATT 61.325 57.895 14.44 0.00 0.00 3.16
5566 5840 1.852067 GCACTCAACGCGTCCCATTT 61.852 55.000 14.44 0.00 0.00 2.32
5567 5841 0.591170 CACTCAACGCGTCCCATTTT 59.409 50.000 14.44 0.00 0.00 1.82
5568 5842 0.872388 ACTCAACGCGTCCCATTTTC 59.128 50.000 14.44 0.00 0.00 2.29
5569 5843 0.179225 CTCAACGCGTCCCATTTTCG 60.179 55.000 14.44 0.00 0.00 3.46
5570 5844 1.795962 CAACGCGTCCCATTTTCGC 60.796 57.895 14.44 0.00 45.28 4.70
5571 5845 1.964373 AACGCGTCCCATTTTCGCT 60.964 52.632 14.44 0.00 46.31 4.93
5572 5846 1.908066 AACGCGTCCCATTTTCGCTC 61.908 55.000 14.44 0.00 46.31 5.03
5573 5847 2.100631 CGCGTCCCATTTTCGCTCT 61.101 57.895 0.00 0.00 46.31 4.09
5574 5848 1.716172 GCGTCCCATTTTCGCTCTC 59.284 57.895 0.00 0.00 45.29 3.20
5575 5849 1.999051 CGTCCCATTTTCGCTCTCG 59.001 57.895 0.00 0.00 0.00 4.04
5576 5850 1.716172 GTCCCATTTTCGCTCTCGC 59.284 57.895 0.00 0.00 35.26 5.03
5598 5872 2.338620 GGCCTGCCGTGGTTTTTC 59.661 61.111 0.00 0.00 0.00 2.29
5599 5873 2.494530 GGCCTGCCGTGGTTTTTCA 61.495 57.895 0.00 0.00 0.00 2.69
5600 5874 1.439644 GCCTGCCGTGGTTTTTCAA 59.560 52.632 0.00 0.00 0.00 2.69
5601 5875 0.179097 GCCTGCCGTGGTTTTTCAAA 60.179 50.000 0.00 0.00 0.00 2.69
5602 5876 1.566404 CCTGCCGTGGTTTTTCAAAC 58.434 50.000 0.00 0.00 0.00 2.93
5603 5877 1.134965 CCTGCCGTGGTTTTTCAAACA 60.135 47.619 2.00 0.00 0.00 2.83
5604 5878 2.482839 CCTGCCGTGGTTTTTCAAACAT 60.483 45.455 2.00 0.00 30.24 2.71
5605 5879 3.243569 CCTGCCGTGGTTTTTCAAACATA 60.244 43.478 2.00 0.00 30.24 2.29
5606 5880 4.363999 CTGCCGTGGTTTTTCAAACATAA 58.636 39.130 2.00 0.00 30.24 1.90
5607 5881 4.950050 TGCCGTGGTTTTTCAAACATAAT 58.050 34.783 2.00 0.00 30.24 1.28
5608 5882 5.360591 TGCCGTGGTTTTTCAAACATAATT 58.639 33.333 2.00 0.00 30.24 1.40
5609 5883 5.463724 TGCCGTGGTTTTTCAAACATAATTC 59.536 36.000 2.00 0.00 30.24 2.17
5610 5884 5.463724 GCCGTGGTTTTTCAAACATAATTCA 59.536 36.000 2.00 0.00 30.24 2.57
5611 5885 6.018669 GCCGTGGTTTTTCAAACATAATTCAA 60.019 34.615 2.00 0.00 30.24 2.69
5612 5886 7.466050 GCCGTGGTTTTTCAAACATAATTCAAA 60.466 33.333 2.00 0.00 30.24 2.69
5613 5887 8.555361 CCGTGGTTTTTCAAACATAATTCAAAT 58.445 29.630 2.00 0.00 30.24 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.108041 GGGCTGGATGCAAATGGTTG 60.108 55.000 0.00 0.00 45.15 3.77
210 223 9.694137 CCTACACCTGACTATTTATTAAGTAGC 57.306 37.037 6.01 1.58 0.00 3.58
213 226 7.347485 AGGCCTACACCTGACTATTTATTAAGT 59.653 37.037 1.29 0.00 39.13 2.24
215 228 7.685849 AGGCCTACACCTGACTATTTATTAA 57.314 36.000 1.29 0.00 39.13 1.40
229 257 1.966451 GCACACACAGGCCTACACC 60.966 63.158 3.98 0.00 0.00 4.16
257 285 1.733360 GAAGCAGAAGCAGAAGCAGAG 59.267 52.381 0.00 0.00 45.49 3.35
258 286 1.347050 AGAAGCAGAAGCAGAAGCAGA 59.653 47.619 0.00 0.00 45.49 4.26
259 287 1.810959 AGAAGCAGAAGCAGAAGCAG 58.189 50.000 0.00 0.00 45.49 4.24
260 288 2.149578 GAAGAAGCAGAAGCAGAAGCA 58.850 47.619 0.00 0.00 45.49 3.91
261 289 1.468127 GGAAGAAGCAGAAGCAGAAGC 59.532 52.381 0.00 0.00 45.49 3.86
262 290 3.002102 GAGGAAGAAGCAGAAGCAGAAG 58.998 50.000 0.00 0.00 45.49 2.85
299 327 0.621082 GAGGACAAGGGAAGGGAAGG 59.379 60.000 0.00 0.00 0.00 3.46
333 368 2.102252 CAGGTGGAGAATCTAGGTGCTC 59.898 54.545 1.79 1.79 33.73 4.26
334 369 2.114616 CAGGTGGAGAATCTAGGTGCT 58.885 52.381 0.00 0.00 33.73 4.40
436 494 2.932261 CCCGGAAAGATTAGGAAAGGG 58.068 52.381 0.73 0.00 0.00 3.95
464 522 5.181009 CCAAGAAGCAACATGATACAGAGA 58.819 41.667 0.00 0.00 0.00 3.10
465 523 4.940046 ACCAAGAAGCAACATGATACAGAG 59.060 41.667 0.00 0.00 0.00 3.35
466 524 4.910195 ACCAAGAAGCAACATGATACAGA 58.090 39.130 0.00 0.00 0.00 3.41
467 525 5.633830 AACCAAGAAGCAACATGATACAG 57.366 39.130 0.00 0.00 0.00 2.74
469 527 5.088739 CGAAACCAAGAAGCAACATGATAC 58.911 41.667 0.00 0.00 0.00 2.24
473 531 3.354089 ACGAAACCAAGAAGCAACATG 57.646 42.857 0.00 0.00 0.00 3.21
514 572 3.530535 CAACCTTCAAACCACCAAAAGG 58.469 45.455 0.00 0.00 41.81 3.11
539 597 0.890683 GGCCATGAAACCAAGTCCAG 59.109 55.000 0.00 0.00 0.00 3.86
570 628 4.735369 TCACAAACATGTCCCAGGTAATT 58.265 39.130 0.00 0.00 0.00 1.40
571 629 4.380843 TCACAAACATGTCCCAGGTAAT 57.619 40.909 0.00 0.00 0.00 1.89
574 632 2.978156 ATCACAAACATGTCCCAGGT 57.022 45.000 0.00 0.00 0.00 4.00
604 662 3.503748 CCTGGTAAGAAACAAGCTCCAAG 59.496 47.826 0.00 0.00 0.00 3.61
648 706 0.754472 ACCCAAAACGTCTCGGAAGA 59.246 50.000 0.00 0.00 39.12 2.87
649 707 1.589803 AACCCAAAACGTCTCGGAAG 58.410 50.000 0.00 0.00 0.00 3.46
650 708 2.041251 AAACCCAAAACGTCTCGGAA 57.959 45.000 0.00 0.00 0.00 4.30
653 711 1.268845 CCCAAAACCCAAAACGTCTCG 60.269 52.381 0.00 0.00 0.00 4.04
654 712 1.067974 CCCCAAAACCCAAAACGTCTC 59.932 52.381 0.00 0.00 0.00 3.36
695 753 3.578688 GAGCAAATGCAAAATTCCTCGT 58.421 40.909 8.28 0.00 45.16 4.18
697 755 3.264947 GGGAGCAAATGCAAAATTCCTC 58.735 45.455 8.28 0.00 45.16 3.71
699 757 2.001872 CGGGAGCAAATGCAAAATTCC 58.998 47.619 8.28 5.22 45.16 3.01
706 764 0.313672 GAACAACGGGAGCAAATGCA 59.686 50.000 8.28 0.00 45.16 3.96
778 840 1.662876 CCCGAACAATTTGCTCGTGTG 60.663 52.381 17.94 5.91 34.48 3.82
799 870 0.328258 TAGGGAAACAAGCTCAGCCC 59.672 55.000 0.00 0.00 35.79 5.19
800 871 1.003696 ACTAGGGAAACAAGCTCAGCC 59.996 52.381 0.00 0.00 0.00 4.85
802 873 3.685139 TCACTAGGGAAACAAGCTCAG 57.315 47.619 0.00 0.00 0.00 3.35
803 874 3.646162 TCTTCACTAGGGAAACAAGCTCA 59.354 43.478 9.13 0.00 0.00 4.26
804 875 4.273148 TCTTCACTAGGGAAACAAGCTC 57.727 45.455 9.13 0.00 0.00 4.09
883 954 2.443632 TGTTCTTGGGTGGGTTCACATA 59.556 45.455 0.00 0.00 45.32 2.29
891 962 2.983592 GCCGTGTTCTTGGGTGGG 60.984 66.667 0.00 0.00 0.00 4.61
934 1005 0.748367 GAGGGAAAACGGAGATGCCC 60.748 60.000 0.00 0.00 35.79 5.36
950 1022 1.291877 CGTCGGTTCTTGCAAGGAGG 61.292 60.000 25.73 15.80 0.00 4.30
964 1041 2.813474 TCAATTCGCAGCCGTCGG 60.813 61.111 6.99 6.99 35.54 4.79
986 1063 1.450312 GCCATGTCTTCGGGTCCTG 60.450 63.158 0.00 0.00 0.00 3.86
1019 1096 1.719600 CACGAGCAAGAAGGAGAAGG 58.280 55.000 0.00 0.00 0.00 3.46
1137 1226 2.048127 GACACCCAGGTCGTGAGC 60.048 66.667 3.02 0.00 35.17 4.26
1602 1691 1.255667 TGGCGGAGAGGTTGAGGTAC 61.256 60.000 0.00 0.00 0.00 3.34
1830 1919 2.604174 GCCGTTGTTGGACCAGTCG 61.604 63.158 0.00 0.00 0.00 4.18
1833 1922 0.250553 TTAGGCCGTTGTTGGACCAG 60.251 55.000 0.00 0.00 38.01 4.00
1889 1978 4.421479 CGAGCGTCTCAAGGCGGT 62.421 66.667 8.62 8.62 41.16 5.68
1890 1979 4.116328 TCGAGCGTCTCAAGGCGG 62.116 66.667 6.12 0.00 41.16 6.13
1953 2042 4.914983 TCTTCAGAGAAGGTAGTTCGGTA 58.085 43.478 6.89 0.00 40.49 4.02
2050 2139 2.350772 GGTTGCTCGACAGGTCAAAATG 60.351 50.000 0.00 0.00 0.00 2.32
2053 2142 0.878523 CGGTTGCTCGACAGGTCAAA 60.879 55.000 0.00 0.00 0.00 2.69
2055 2144 2.338620 CGGTTGCTCGACAGGTCA 59.661 61.111 0.00 0.00 0.00 4.02
2106 2195 3.386237 ACCTCGAGGGAGCTGCAC 61.386 66.667 34.04 0.00 39.06 4.57
2146 2235 0.534203 GCCACAAAGTCACCGGAGAA 60.534 55.000 9.46 0.00 0.00 2.87
2290 2379 4.415332 TCCGTCGAGCTCGTTGGC 62.415 66.667 33.33 20.50 40.80 4.52
2331 2420 3.393089 TTCTTCAGAGAAGGCAGTGAC 57.607 47.619 6.89 0.00 36.99 3.67
2528 2617 2.826128 GAGCATAGGATGTCCGGTATCA 59.174 50.000 18.51 10.37 42.08 2.15
2638 2727 2.430921 CGACAGCGACACCCAGAC 60.431 66.667 0.00 0.00 40.82 3.51
3003 3092 1.417890 CCCATGTAGATCCTGGTGACC 59.582 57.143 0.00 0.00 31.26 4.02
3015 3104 1.745115 CACCGTGGTGCCCATGTAG 60.745 63.158 6.03 1.98 38.76 2.74
3033 3122 2.223433 GCCATTGCTGCTGAATGAGTAC 60.223 50.000 12.68 0.00 33.36 2.73
3037 3126 0.815095 CTGCCATTGCTGCTGAATGA 59.185 50.000 12.68 0.00 38.71 2.57
3108 3197 4.925861 GCCATGCTCCCGAGGCTC 62.926 72.222 3.87 3.87 43.70 4.70
3237 3326 4.609018 CCTGAGGGTATGCCGCCG 62.609 72.222 0.00 0.00 34.97 6.46
3422 3511 4.722535 AGCTTCCTCCCCCGCTCA 62.723 66.667 0.00 0.00 0.00 4.26
3499 3588 0.464870 AGCAGCAGGAGTATGAGCAG 59.535 55.000 0.00 0.00 0.00 4.24
3507 3596 1.123861 TGACCAAGAGCAGCAGGAGT 61.124 55.000 0.00 0.00 0.00 3.85
3513 3602 2.358003 AGCGTGACCAAGAGCAGC 60.358 61.111 0.00 0.00 0.00 5.25
3554 3643 0.382515 CGTTCTGATCTCCTCGGTCC 59.617 60.000 0.00 0.00 0.00 4.46
3573 3662 1.465200 GGAGGCTCTCGATGTACCCC 61.465 65.000 15.23 0.00 0.00 4.95
3989 4081 0.610232 GAGCTTCACCATGGCCTTGT 60.610 55.000 13.04 2.29 0.00 3.16
4266 4358 1.153881 GTAGACGTCGCCCTTGGTC 60.154 63.158 10.46 0.00 0.00 4.02
4399 4491 0.249657 GGATCAAAGATCTCGCCGCT 60.250 55.000 0.00 0.00 0.00 5.52
4419 4511 2.279851 TTGGTGTCGGTCAGCGTG 60.280 61.111 0.00 0.00 46.24 5.34
4467 4559 1.880340 GCACTCGGAGGCGATCTTG 60.880 63.158 10.23 0.00 0.00 3.02
4554 4646 1.512310 GAAGTCGCTGTCGGAGTCG 60.512 63.158 0.00 0.00 36.13 4.18
4680 4772 3.300388 TCTCGCTGTTCTATCCTTCCAT 58.700 45.455 0.00 0.00 0.00 3.41
4681 4773 2.735151 TCTCGCTGTTCTATCCTTCCA 58.265 47.619 0.00 0.00 0.00 3.53
4682 4774 4.617298 GCTATCTCGCTGTTCTATCCTTCC 60.617 50.000 0.00 0.00 0.00 3.46
4683 4775 4.217550 AGCTATCTCGCTGTTCTATCCTTC 59.782 45.833 0.00 0.00 39.16 3.46
4684 4776 4.148838 AGCTATCTCGCTGTTCTATCCTT 58.851 43.478 0.00 0.00 39.16 3.36
4685 4777 3.756434 GAGCTATCTCGCTGTTCTATCCT 59.244 47.826 0.00 0.00 41.08 3.24
4734 4826 2.618053 GTGAATTGGAGGACACTACGG 58.382 52.381 0.00 0.00 0.00 4.02
4755 4847 1.202842 ACAAAACTACAACCTCCCCCG 60.203 52.381 0.00 0.00 0.00 5.73
4796 4888 5.046878 TCCCTCTTCATACTTTTGACGCTTA 60.047 40.000 0.00 0.00 0.00 3.09
4797 4889 4.003648 CCCTCTTCATACTTTTGACGCTT 58.996 43.478 0.00 0.00 0.00 4.68
4804 4896 6.183347 CCTTCATGTCCCTCTTCATACTTTT 58.817 40.000 0.00 0.00 0.00 2.27
4923 5131 4.510038 AGCAGGTAAAAGCACAAATGAG 57.490 40.909 0.00 0.00 0.00 2.90
4928 5136 5.312895 TGATTCTAGCAGGTAAAAGCACAA 58.687 37.500 0.00 0.00 0.00 3.33
4932 5140 7.793927 ATAACTGATTCTAGCAGGTAAAAGC 57.206 36.000 0.00 0.00 38.87 3.51
4942 5150 8.723942 TCTTCTTCCAAATAACTGATTCTAGC 57.276 34.615 0.00 0.00 0.00 3.42
4960 5168 7.020914 AGAACAACACAGTCAATTCTTCTTC 57.979 36.000 0.00 0.00 0.00 2.87
4961 5169 7.121168 TCAAGAACAACACAGTCAATTCTTCTT 59.879 33.333 0.00 0.00 34.90 2.52
4962 5170 6.599244 TCAAGAACAACACAGTCAATTCTTCT 59.401 34.615 0.00 0.00 34.90 2.85
5029 5237 9.429359 GATCTCTCTCTCTTTTTGTTCATTACA 57.571 33.333 0.00 0.00 34.12 2.41
5033 5244 7.013823 TGGATCTCTCTCTCTTTTTGTTCAT 57.986 36.000 0.00 0.00 0.00 2.57
5043 5254 3.493334 CATCTGCTGGATCTCTCTCTCT 58.507 50.000 0.00 0.00 31.27 3.10
5044 5255 3.928727 CATCTGCTGGATCTCTCTCTC 57.071 52.381 0.00 0.00 31.27 3.20
5102 5328 3.055719 CGCCCGGTCAAGCACATT 61.056 61.111 0.00 0.00 0.00 2.71
5122 5349 5.124776 TGTTTTGTCAAGGAAAGACGACAAT 59.875 36.000 4.81 0.00 45.09 2.71
5153 5380 3.173151 TGATATCACCACCATCGGCTAT 58.827 45.455 0.00 0.00 0.00 2.97
5166 5393 4.662468 TTCCTGAGCTCACTGATATCAC 57.338 45.455 13.74 0.00 0.00 3.06
5171 5398 1.134159 GGCATTCCTGAGCTCACTGAT 60.134 52.381 13.74 3.71 0.00 2.90
5181 5408 2.586245 CTGAGCCGGCATTCCTGA 59.414 61.111 31.54 0.00 0.00 3.86
5216 5443 2.816411 ACTGTCCACGAAATCTAGGGA 58.184 47.619 0.00 0.00 0.00 4.20
5225 5452 0.032952 GTGGTGCTACTGTCCACGAA 59.967 55.000 1.24 0.00 41.37 3.85
5227 5454 4.261888 GTGGTGCTACTGTCCACG 57.738 61.111 1.24 0.00 41.37 4.94
5248 5480 3.317149 CCTGGCAAAGTACATCCATGATG 59.683 47.826 0.00 2.62 44.71 3.07
5306 5538 0.601046 TCTGTTGCTCAGCTTGGTCG 60.601 55.000 0.00 0.00 43.32 4.79
5310 5542 6.864685 TCATTTTATTTCTGTTGCTCAGCTTG 59.135 34.615 0.00 0.00 43.32 4.01
5357 5631 2.030363 GCTACATCCATCCGTCTCAGAG 60.030 54.545 0.00 0.00 0.00 3.35
5358 5632 1.957177 GCTACATCCATCCGTCTCAGA 59.043 52.381 0.00 0.00 0.00 3.27
5405 5679 1.880027 CAGCTTGTCCACAAACTACCC 59.120 52.381 0.00 0.00 35.15 3.69
5409 5683 3.209410 CTCTTCAGCTTGTCCACAAACT 58.791 45.455 0.00 0.00 35.15 2.66
5411 5685 1.949525 GCTCTTCAGCTTGTCCACAAA 59.050 47.619 0.00 0.00 43.09 2.83
5435 5709 3.426292 GCGTTGAAGTTGGCCTTATCTTC 60.426 47.826 3.32 12.63 37.42 2.87
5436 5710 2.488153 GCGTTGAAGTTGGCCTTATCTT 59.512 45.455 3.32 3.08 32.03 2.40
5438 5712 1.202031 CGCGTTGAAGTTGGCCTTATC 60.202 52.381 3.32 0.00 32.03 1.75
5440 5714 1.847890 GCGCGTTGAAGTTGGCCTTA 61.848 55.000 8.43 0.00 32.03 2.69
5441 5715 3.030652 CGCGTTGAAGTTGGCCTT 58.969 55.556 3.32 0.00 35.59 4.35
5442 5716 3.660111 GCGCGTTGAAGTTGGCCT 61.660 61.111 8.43 0.00 0.00 5.19
5443 5717 4.700365 GGCGCGTTGAAGTTGGCC 62.700 66.667 8.43 0.00 0.00 5.36
5444 5718 4.700365 GGGCGCGTTGAAGTTGGC 62.700 66.667 8.43 0.00 0.00 4.52
5445 5719 3.283684 TGGGCGCGTTGAAGTTGG 61.284 61.111 8.43 0.00 0.00 3.77
5446 5720 1.225376 TAGTGGGCGCGTTGAAGTTG 61.225 55.000 8.43 0.00 0.00 3.16
5447 5721 0.533308 TTAGTGGGCGCGTTGAAGTT 60.533 50.000 8.43 0.00 0.00 2.66
5448 5722 0.533308 TTTAGTGGGCGCGTTGAAGT 60.533 50.000 8.43 0.00 0.00 3.01
5449 5723 0.589223 TTTTAGTGGGCGCGTTGAAG 59.411 50.000 8.43 0.00 0.00 3.02
5450 5724 0.308376 GTTTTAGTGGGCGCGTTGAA 59.692 50.000 8.43 0.00 0.00 2.69
5451 5725 0.814410 TGTTTTAGTGGGCGCGTTGA 60.814 50.000 8.43 0.00 0.00 3.18
5452 5726 0.385473 CTGTTTTAGTGGGCGCGTTG 60.385 55.000 8.43 0.00 0.00 4.10
5453 5727 1.512156 CCTGTTTTAGTGGGCGCGTT 61.512 55.000 8.43 0.00 0.00 4.84
5454 5728 1.964373 CCTGTTTTAGTGGGCGCGT 60.964 57.895 8.43 0.00 0.00 6.01
5455 5729 2.867472 CCTGTTTTAGTGGGCGCG 59.133 61.111 0.00 0.00 0.00 6.86
5456 5730 2.566529 GCCTGTTTTAGTGGGCGC 59.433 61.111 0.00 0.00 35.08 6.53
5458 5732 1.686587 ACAAAGCCTGTTTTAGTGGGC 59.313 47.619 0.00 0.00 44.38 5.36
5459 5733 2.296190 GGACAAAGCCTGTTTTAGTGGG 59.704 50.000 0.00 0.00 38.84 4.61
5460 5734 2.955660 TGGACAAAGCCTGTTTTAGTGG 59.044 45.455 0.00 0.00 38.84 4.00
5461 5735 4.853924 ATGGACAAAGCCTGTTTTAGTG 57.146 40.909 0.00 0.00 38.84 2.74
5462 5736 5.869649 AAATGGACAAAGCCTGTTTTAGT 57.130 34.783 0.00 0.00 38.84 2.24
5483 5757 4.023107 TCGGCCGATTCAAACATACAAAAA 60.023 37.500 27.28 0.00 0.00 1.94
5484 5758 3.502595 TCGGCCGATTCAAACATACAAAA 59.497 39.130 27.28 0.00 0.00 2.44
5485 5759 3.075148 TCGGCCGATTCAAACATACAAA 58.925 40.909 27.28 0.00 0.00 2.83
5486 5760 2.417239 GTCGGCCGATTCAAACATACAA 59.583 45.455 33.58 0.00 0.00 2.41
5487 5761 2.004017 GTCGGCCGATTCAAACATACA 58.996 47.619 33.58 0.00 0.00 2.29
5488 5762 2.030457 CAGTCGGCCGATTCAAACATAC 59.970 50.000 33.58 14.87 0.00 2.39
5489 5763 2.276201 CAGTCGGCCGATTCAAACATA 58.724 47.619 33.58 0.18 0.00 2.29
5490 5764 1.086696 CAGTCGGCCGATTCAAACAT 58.913 50.000 33.58 7.17 0.00 2.71
5491 5765 1.573829 GCAGTCGGCCGATTCAAACA 61.574 55.000 33.58 2.05 36.11 2.83
5492 5766 1.134694 GCAGTCGGCCGATTCAAAC 59.865 57.895 33.58 18.14 36.11 2.93
5493 5767 1.003839 AGCAGTCGGCCGATTCAAA 60.004 52.632 33.58 3.94 46.50 2.69
5494 5768 1.447838 GAGCAGTCGGCCGATTCAA 60.448 57.895 33.58 4.89 46.50 2.69
5495 5769 2.184322 GAGCAGTCGGCCGATTCA 59.816 61.111 33.58 5.39 46.50 2.57
5496 5770 2.956964 CGAGCAGTCGGCCGATTC 60.957 66.667 33.58 23.28 46.50 2.52
5506 5780 2.755650 AGAAAACGAATGACGAGCAGT 58.244 42.857 0.00 0.00 45.77 4.40
5507 5781 3.795561 AAGAAAACGAATGACGAGCAG 57.204 42.857 0.00 0.00 45.77 4.24
5508 5782 4.201871 ACAAAAGAAAACGAATGACGAGCA 60.202 37.500 0.00 0.00 45.77 4.26
5509 5783 4.144731 CACAAAAGAAAACGAATGACGAGC 59.855 41.667 0.00 0.00 45.77 5.03
5510 5784 5.263185 ACACAAAAGAAAACGAATGACGAG 58.737 37.500 0.00 0.00 45.77 4.18
5511 5785 5.224562 ACACAAAAGAAAACGAATGACGA 57.775 34.783 0.00 0.00 45.77 4.20
5513 5787 6.454981 CCCAAACACAAAAGAAAACGAATGAC 60.455 38.462 0.00 0.00 0.00 3.06
5514 5788 5.578727 CCCAAACACAAAAGAAAACGAATGA 59.421 36.000 0.00 0.00 0.00 2.57
5515 5789 5.350091 ACCCAAACACAAAAGAAAACGAATG 59.650 36.000 0.00 0.00 0.00 2.67
5516 5790 5.483811 ACCCAAACACAAAAGAAAACGAAT 58.516 33.333 0.00 0.00 0.00 3.34
5517 5791 4.884247 ACCCAAACACAAAAGAAAACGAA 58.116 34.783 0.00 0.00 0.00 3.85
5518 5792 4.487019 GACCCAAACACAAAAGAAAACGA 58.513 39.130 0.00 0.00 0.00 3.85
5519 5793 3.302170 CGACCCAAACACAAAAGAAAACG 59.698 43.478 0.00 0.00 0.00 3.60
5520 5794 4.487019 TCGACCCAAACACAAAAGAAAAC 58.513 39.130 0.00 0.00 0.00 2.43
5521 5795 4.785511 TCGACCCAAACACAAAAGAAAA 57.214 36.364 0.00 0.00 0.00 2.29
5522 5796 4.496673 CGATCGACCCAAACACAAAAGAAA 60.497 41.667 10.26 0.00 0.00 2.52
5523 5797 3.002862 CGATCGACCCAAACACAAAAGAA 59.997 43.478 10.26 0.00 0.00 2.52
5524 5798 2.546368 CGATCGACCCAAACACAAAAGA 59.454 45.455 10.26 0.00 0.00 2.52
5525 5799 2.289547 ACGATCGACCCAAACACAAAAG 59.710 45.455 24.34 0.00 0.00 2.27
5526 5800 2.032302 CACGATCGACCCAAACACAAAA 59.968 45.455 24.34 0.00 0.00 2.44
5527 5801 1.600013 CACGATCGACCCAAACACAAA 59.400 47.619 24.34 0.00 0.00 2.83
5528 5802 1.222300 CACGATCGACCCAAACACAA 58.778 50.000 24.34 0.00 0.00 3.33
5529 5803 1.225376 GCACGATCGACCCAAACACA 61.225 55.000 24.34 0.00 0.00 3.72
5530 5804 1.225376 TGCACGATCGACCCAAACAC 61.225 55.000 24.34 0.53 0.00 3.32
5531 5805 1.069935 TGCACGATCGACCCAAACA 59.930 52.632 24.34 5.78 0.00 2.83
5532 5806 0.949105 AGTGCACGATCGACCCAAAC 60.949 55.000 24.34 10.56 0.00 2.93
5533 5807 0.669318 GAGTGCACGATCGACCCAAA 60.669 55.000 24.34 0.00 0.00 3.28
5534 5808 1.080093 GAGTGCACGATCGACCCAA 60.080 57.895 24.34 0.00 0.00 4.12
5535 5809 1.811645 TTGAGTGCACGATCGACCCA 61.812 55.000 24.34 12.24 0.00 4.51
5536 5810 1.080093 TTGAGTGCACGATCGACCC 60.080 57.895 24.34 9.65 0.00 4.46
5537 5811 1.674611 CGTTGAGTGCACGATCGACC 61.675 60.000 24.34 12.27 0.00 4.79
5538 5812 1.696644 CGTTGAGTGCACGATCGAC 59.303 57.895 24.34 13.17 0.00 4.20
5539 5813 2.086426 GCGTTGAGTGCACGATCGA 61.086 57.895 24.34 10.47 0.00 3.59
5540 5814 2.391821 GCGTTGAGTGCACGATCG 59.608 61.111 14.88 14.88 0.00 3.69
5541 5815 2.267227 GACGCGTTGAGTGCACGATC 62.267 60.000 15.53 5.07 0.00 3.69
5542 5816 2.355837 ACGCGTTGAGTGCACGAT 60.356 55.556 5.58 0.00 0.00 3.73
5543 5817 3.028019 GACGCGTTGAGTGCACGA 61.028 61.111 15.53 0.00 0.00 4.35
5544 5818 4.059459 GGACGCGTTGAGTGCACG 62.059 66.667 15.53 0.00 0.00 5.34
5545 5819 3.712881 GGGACGCGTTGAGTGCAC 61.713 66.667 15.53 9.40 0.00 4.57
5546 5820 3.529341 ATGGGACGCGTTGAGTGCA 62.529 57.895 15.53 0.00 0.00 4.57
5547 5821 1.852067 AAATGGGACGCGTTGAGTGC 61.852 55.000 15.53 0.00 0.00 4.40
5548 5822 0.591170 AAAATGGGACGCGTTGAGTG 59.409 50.000 15.53 0.00 0.00 3.51
5549 5823 0.872388 GAAAATGGGACGCGTTGAGT 59.128 50.000 15.53 0.00 0.00 3.41
5550 5824 0.179225 CGAAAATGGGACGCGTTGAG 60.179 55.000 15.53 0.00 0.00 3.02
5551 5825 1.863491 CGAAAATGGGACGCGTTGA 59.137 52.632 15.53 0.00 0.00 3.18
5552 5826 1.795962 GCGAAAATGGGACGCGTTG 60.796 57.895 15.53 0.00 42.65 4.10
5553 5827 2.559330 GCGAAAATGGGACGCGTT 59.441 55.556 15.53 0.00 42.65 4.84
5557 5831 1.999051 CGAGAGCGAAAATGGGACG 59.001 57.895 0.00 0.00 40.82 4.79
5581 5855 2.022240 TTGAAAAACCACGGCAGGCC 62.022 55.000 0.00 0.00 0.00 5.19
5582 5856 0.179097 TTTGAAAAACCACGGCAGGC 60.179 50.000 0.00 0.00 0.00 4.85
5583 5857 1.134965 TGTTTGAAAAACCACGGCAGG 60.135 47.619 0.71 0.00 0.00 4.85
5584 5858 2.285827 TGTTTGAAAAACCACGGCAG 57.714 45.000 0.71 0.00 0.00 4.85
5585 5859 2.969628 ATGTTTGAAAAACCACGGCA 57.030 40.000 0.71 0.00 0.00 5.69
5586 5860 5.463724 TGAATTATGTTTGAAAAACCACGGC 59.536 36.000 0.71 0.00 0.00 5.68
5587 5861 7.470289 TTGAATTATGTTTGAAAAACCACGG 57.530 32.000 0.71 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.