Multiple sequence alignment - TraesCS5A01G386800

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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 TraesCS5A01G386800 chr5A 100.000 6804 0 0 1 6804 584448643 584455446 0.000000e+00 12565.0
1 TraesCS5A01G386800 chr5A 85.068 221 31 2 592 810 559787423 559787643 2.470000e-54 224.0
2 TraesCS5A01G386800 chr5A 82.192 219 32 5 595 809 611475689 611475904 1.510000e-41 182.0
3 TraesCS5A01G386800 chr5A 96.000 50 2 0 178 227 705906126 705906175 1.570000e-11 82.4
4 TraesCS5A01G386800 chr5D 93.208 4888 213 60 1966 6804 464067604 464072421 0.000000e+00 7077.0
5 TraesCS5A01G386800 chr5D 90.062 1942 124 34 1 1911 464065707 464067610 0.000000e+00 2453.0
6 TraesCS5A01G386800 chr5D 82.648 219 34 4 595 811 438091916 438091700 2.500000e-44 191.0
7 TraesCS5A01G386800 chr5D 97.872 47 1 0 181 227 555061011 555061057 1.570000e-11 82.4
8 TraesCS5A01G386800 chr5B 92.249 4167 238 39 554 4692 570923629 570927738 0.000000e+00 5827.0
9 TraesCS5A01G386800 chr5B 91.948 1987 111 23 4844 6804 570928124 570930087 0.000000e+00 2737.0
10 TraesCS5A01G386800 chr5B 87.245 588 39 19 1 557 570905558 570906140 7.440000e-179 638.0
11 TraesCS5A01G386800 chr5B 85.340 191 14 11 4769 4955 320413653 320413833 1.170000e-42 185.0
12 TraesCS5A01G386800 chr5B 85.561 187 15 10 4776 4960 682169464 682169288 1.170000e-42 185.0
13 TraesCS5A01G386800 chr5B 96.000 50 2 0 178 227 103463318 103463367 1.570000e-11 82.4
14 TraesCS5A01G386800 chr6B 84.018 219 33 2 592 808 40071509 40071727 6.910000e-50 209.0
15 TraesCS5A01G386800 chr6B 86.264 182 14 9 4779 4958 358303033 358303205 3.240000e-43 187.0
16 TraesCS5A01G386800 chr6B 86.264 182 13 10 4779 4959 460505230 460505400 3.240000e-43 187.0
17 TraesCS5A01G386800 chr3A 84.058 207 31 2 597 801 670673989 670674195 1.500000e-46 198.0
18 TraesCS5A01G386800 chr3A 87.013 77 9 1 228 303 560130670 560130746 1.220000e-12 86.1
19 TraesCS5A01G386800 chr2D 83.256 215 31 5 597 808 160597397 160597609 6.960000e-45 193.0
20 TraesCS5A01G386800 chr2D 88.235 85 6 1 5262 5342 425742569 425742653 1.560000e-16 99.0
21 TraesCS5A01G386800 chr2D 89.474 76 6 2 228 301 644517568 644517643 2.020000e-15 95.3
22 TraesCS5A01G386800 chr2D 87.013 77 9 1 228 303 382384157 382384081 1.220000e-12 86.1
23 TraesCS5A01G386800 chr2D 96.000 50 2 0 178 227 193393251 193393202 1.570000e-11 82.4
24 TraesCS5A01G386800 chr1A 82.870 216 31 6 597 808 578473038 578473251 9.010000e-44 189.0
25 TraesCS5A01G386800 chr7A 85.417 192 14 10 4761 4947 48816419 48816601 3.240000e-43 187.0
26 TraesCS5A01G386800 chr7A 94.118 51 2 1 171 221 595198167 595198216 7.320000e-10 76.8
27 TraesCS5A01G386800 chr3B 85.946 185 14 10 4779 4961 2885353 2885179 3.240000e-43 187.0
28 TraesCS5A01G386800 chr3B 86.598 97 7 4 185 277 10286801 10286707 1.210000e-17 102.0
29 TraesCS5A01G386800 chr3B 86.905 84 8 2 5261 5341 194074855 194074772 2.610000e-14 91.6
30 TraesCS5A01G386800 chr3B 84.375 96 10 4 217 307 438579043 438579138 9.400000e-14 89.8
31 TraesCS5A01G386800 chr3B 100.000 28 0 0 544 571 705917048 705917075 1.200000e-02 52.8
32 TraesCS5A01G386800 chr2B 85.870 184 14 10 4779 4961 314771398 314771570 1.170000e-42 185.0
33 TraesCS5A01G386800 chr2B 96.774 31 1 0 544 574 104255282 104255252 1.200000e-02 52.8
34 TraesCS5A01G386800 chr3D 89.286 84 6 2 5260 5341 250931575 250931493 1.210000e-17 102.0
35 TraesCS5A01G386800 chr3D 84.884 86 10 3 224 307 549066864 549066948 4.370000e-12 84.2
36 TraesCS5A01G386800 chr6A 88.889 81 4 2 5262 5341 301951288 301951364 2.020000e-15 95.3
37 TraesCS5A01G386800 chr2A 87.805 82 8 2 228 307 769625600 769625681 2.020000e-15 95.3
38 TraesCS5A01G386800 chr6D 86.207 87 8 3 5255 5341 211444027 211443945 2.610000e-14 91.6
39 TraesCS5A01G386800 chr6D 97.872 47 1 0 181 227 323050184 323050138 1.570000e-11 82.4
40 TraesCS5A01G386800 chr6D 97.222 36 0 1 547 581 292299456 292299421 7.370000e-05 60.2
41 TraesCS5A01G386800 chr1D 87.059 85 6 4 5262 5341 279101376 279101460 2.610000e-14 91.6
42 TraesCS5A01G386800 chr1D 100.000 29 0 0 547 575 37220060 37220088 3.000000e-03 54.7
43 TraesCS5A01G386800 chr1B 86.905 84 8 3 5262 5343 539869528 539869610 2.610000e-14 91.6
44 TraesCS5A01G386800 chr4B 100.000 28 0 0 548 575 668813811 668813838 1.200000e-02 52.8


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 TraesCS5A01G386800 chr5A 584448643 584455446 6803 False 12565 12565 100.0000 1 6804 1 chr5A.!!$F2 6803
1 TraesCS5A01G386800 chr5D 464065707 464072421 6714 False 4765 7077 91.6350 1 6804 2 chr5D.!!$F2 6803
2 TraesCS5A01G386800 chr5B 570923629 570930087 6458 False 4282 5827 92.0985 554 6804 2 chr5B.!!$F4 6250
3 TraesCS5A01G386800 chr5B 570905558 570906140 582 False 638 638 87.2450 1 557 1 chr5B.!!$F3 556

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
897 934 0.179040 GATGGGGATTACGGGCGAAA 60.179 55.000 0.0 0.0 0.00 3.46 F
1666 1709 1.135603 CCAAACGTGGTGCATGATGAG 60.136 52.381 0.0 0.0 40.42 2.90 F
2070 2129 0.103937 GCTAGTGCCTACTGCCTCTG 59.896 60.000 0.0 0.0 40.16 3.35 F
3829 3895 0.042131 ACCAATACCTCCCCTCACGA 59.958 55.000 0.0 0.0 0.00 4.35 F
4785 4874 0.034089 GAACATGGGGGAAGGACAGG 60.034 60.000 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 1757 1.444383 CGTGCAGAGACTAAGCGCA 60.444 57.895 11.47 0.0 38.61 6.09 R
3128 3188 1.469079 GCAAATGCATGTACCGGGAAC 60.469 52.381 6.32 4.0 41.59 3.62 R
3944 4010 0.045008 TGATAGGCCACAGGGGGTAA 59.955 55.000 5.01 0.0 37.04 2.85 R
4918 5237 0.321671 GTGCTAGAAGCTCCCACACA 59.678 55.000 0.00 0.0 42.97 3.72 R
6540 6902 0.187851 CCCCCGGACTACTACTCCAT 59.812 60.000 0.73 0.0 0.00 3.41 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
112 117 9.083422 TGGATAAGTTTCACCATTGTATTTCAA 57.917 29.630 0.00 0.00 40.53 2.69
148 153 7.610305 TCTTATGAACTTGACCCCTTTTGATAC 59.390 37.037 0.00 0.00 0.00 2.24
198 204 7.500992 TGTGCTCCCTCTGTTTCTAAATATAG 58.499 38.462 0.00 0.00 0.00 1.31
280 312 9.170734 CATATGTAGTCCATATTGAAATCCCTG 57.829 37.037 0.00 0.00 42.87 4.45
283 315 4.467769 AGTCCATATTGAAATCCCTGCAG 58.532 43.478 6.78 6.78 0.00 4.41
387 420 3.819564 TGTGCGCTTCTACCTATGATT 57.180 42.857 9.73 0.00 0.00 2.57
389 422 4.513442 TGTGCGCTTCTACCTATGATTTT 58.487 39.130 9.73 0.00 0.00 1.82
446 479 4.163458 TGCAGCACAATTTGTCATAGTG 57.837 40.909 0.00 0.00 0.00 2.74
480 513 6.468484 CATTACGCCAAATGTTGCTTTTATG 58.532 36.000 0.00 0.00 33.11 1.90
484 517 4.142859 CGCCAAATGTTGCTTTTATGCATT 60.143 37.500 3.54 0.00 42.96 3.56
531 564 6.809196 AGTTGCTAGAGTCGATTTTGTTAGAG 59.191 38.462 0.00 0.00 0.00 2.43
538 571 7.862648 AGAGTCGATTTTGTTAGAGAAAAACC 58.137 34.615 0.00 0.00 0.00 3.27
545 578 2.514582 TGTTAGAGAAAAACCACCCCCA 59.485 45.455 0.00 0.00 0.00 4.96
563 596 4.315803 CCCCACGACAAGTAATATGGATC 58.684 47.826 0.00 0.00 0.00 3.36
615 648 6.658849 TCAGGATTTATTTCAGGATTTCCGA 58.341 36.000 0.00 0.00 42.08 4.55
617 650 5.828328 AGGATTTATTTCAGGATTTCCGACC 59.172 40.000 0.00 0.00 42.08 4.79
636 669 3.240134 ATGCGCGTTCAGTGGGAGT 62.240 57.895 8.43 0.00 0.00 3.85
647 680 1.616865 CAGTGGGAGTAGACGTTTCCA 59.383 52.381 10.26 0.00 32.50 3.53
701 734 1.693606 TCTCAAGATGATATGCCGGCA 59.306 47.619 34.80 34.80 0.00 5.69
705 738 0.604780 AGATGATATGCCGGCACAGC 60.605 55.000 35.50 26.67 0.00 4.40
736 770 9.099071 AGAGATGCTCATAAAGTTAGGATATGT 57.901 33.333 0.00 0.00 32.06 2.29
754 788 3.388345 TGTGTGTGTGCGTTTATAGGA 57.612 42.857 0.00 0.00 0.00 2.94
791 825 4.330347 TGTTTATATGAGCGCTTGCGTTTA 59.670 37.500 13.26 7.80 45.69 2.01
795 829 1.003851 TGAGCGCTTGCGTTTATACC 58.996 50.000 13.26 0.00 45.69 2.73
829 865 2.788786 AGCAACAAAATCAGCGAAAACG 59.211 40.909 0.00 0.00 0.00 3.60
894 931 2.032071 GGATGGGGATTACGGGCG 59.968 66.667 0.00 0.00 0.00 6.13
895 932 2.513259 GGATGGGGATTACGGGCGA 61.513 63.158 0.00 0.00 0.00 5.54
896 933 1.448497 GATGGGGATTACGGGCGAA 59.552 57.895 0.00 0.00 0.00 4.70
897 934 0.179040 GATGGGGATTACGGGCGAAA 60.179 55.000 0.00 0.00 0.00 3.46
925 962 1.956629 CTTCCATCGTACGGCCCAGT 61.957 60.000 16.52 0.00 0.00 4.00
982 1019 9.436957 ACCAGATTAATGACGTAATAATCATCC 57.563 33.333 20.53 4.28 38.11 3.51
983 1020 9.435688 CCAGATTAATGACGTAATAATCATCCA 57.564 33.333 20.53 0.80 38.11 3.41
985 1022 9.436957 AGATTAATGACGTAATAATCATCCACC 57.563 33.333 20.53 3.06 38.11 4.61
986 1023 7.646446 TTAATGACGTAATAATCATCCACCG 57.354 36.000 0.00 0.00 34.41 4.94
1159 1198 3.440872 ACGACTACTTGGAGTGTGAGATC 59.559 47.826 0.00 0.00 0.00 2.75
1209 1248 1.591183 CATTCGGGGTGCTTTTGGG 59.409 57.895 0.00 0.00 0.00 4.12
1229 1268 3.165058 GCCTTTTGCCCTTATTACTGC 57.835 47.619 0.00 0.00 0.00 4.40
1230 1269 2.760650 GCCTTTTGCCCTTATTACTGCT 59.239 45.455 0.00 0.00 0.00 4.24
1231 1270 3.195610 GCCTTTTGCCCTTATTACTGCTT 59.804 43.478 0.00 0.00 0.00 3.91
1232 1271 4.678044 GCCTTTTGCCCTTATTACTGCTTC 60.678 45.833 0.00 0.00 0.00 3.86
1335 1375 2.419021 CCCATGGTGATGATTTTGCCAC 60.419 50.000 11.73 0.00 31.47 5.01
1336 1376 2.498481 CCATGGTGATGATTTTGCCACT 59.502 45.455 2.57 0.00 31.47 4.00
1338 1378 3.159213 TGGTGATGATTTTGCCACTCT 57.841 42.857 0.00 0.00 0.00 3.24
1412 1454 3.967332 AAAAGGCATTGTGGAGAATGG 57.033 42.857 0.00 0.00 34.42 3.16
1417 1459 3.703052 AGGCATTGTGGAGAATGGATTTC 59.297 43.478 0.00 0.00 34.42 2.17
1423 1465 3.191162 TGTGGAGAATGGATTTCGCTTTG 59.809 43.478 0.00 0.00 39.46 2.77
1428 1470 3.698040 AGAATGGATTTCGCTTTGCATCT 59.302 39.130 0.00 0.00 39.46 2.90
1430 1472 5.357878 AGAATGGATTTCGCTTTGCATCTTA 59.642 36.000 0.00 0.00 39.46 2.10
1435 1477 5.163713 GGATTTCGCTTTGCATCTTAACTCT 60.164 40.000 0.00 0.00 0.00 3.24
1465 1507 1.476085 TGGCCATGCTTTAATTGTCGG 59.524 47.619 0.00 0.00 0.00 4.79
1487 1529 1.475280 CCCGAGATATAATCCCGCGAA 59.525 52.381 8.23 0.00 0.00 4.70
1494 1536 2.169832 ATAATCCCGCGAATGACAGG 57.830 50.000 8.23 0.00 0.00 4.00
1618 1661 5.456921 AAGGGCAGATCAAATTTCTCCTA 57.543 39.130 0.00 0.00 0.00 2.94
1666 1709 1.135603 CCAAACGTGGTGCATGATGAG 60.136 52.381 0.00 0.00 40.42 2.90
1681 1724 2.159043 TGATGAGAATGCCTCGGAGAAC 60.159 50.000 6.58 0.00 44.92 3.01
1696 1739 3.366476 CGGAGAACATGACGAGGGATATC 60.366 52.174 0.00 0.00 0.00 1.63
1714 1757 5.940470 GGATATCGAAAATAGCCAGGACAAT 59.060 40.000 0.00 0.00 30.83 2.71
1969 2019 3.181476 ACAACAGCTTGCTTTTAACCTGG 60.181 43.478 0.00 0.00 0.00 4.45
1989 2039 3.181429 TGGTTCTGCTTCCTTCCTTCAAT 60.181 43.478 0.00 0.00 0.00 2.57
2068 2127 1.066587 CGCTAGTGCCTACTGCCTC 59.933 63.158 0.00 0.00 40.16 4.70
2070 2129 0.103937 GCTAGTGCCTACTGCCTCTG 59.896 60.000 0.00 0.00 40.16 3.35
2071 2130 0.749649 CTAGTGCCTACTGCCTCTGG 59.250 60.000 0.00 0.00 40.16 3.86
2170 2229 8.200364 TGTACCAAACTTTAGACTTTGTACAC 57.800 34.615 0.00 0.00 29.21 2.90
2247 2306 6.615088 CCAGACAAAACAGATAAAGATGTGG 58.385 40.000 0.00 0.00 30.51 4.17
2349 2409 8.259049 ACAAATTATTCAGCACCATGAAATTG 57.741 30.769 0.00 1.26 42.21 2.32
2406 2466 3.123804 GCCTGGTATTACTCGTGTGATG 58.876 50.000 5.26 0.00 0.00 3.07
2410 2470 5.067413 CCTGGTATTACTCGTGTGATGTACT 59.933 44.000 5.26 0.00 0.00 2.73
2417 2477 2.753452 CTCGTGTGATGTACTACCCAGT 59.247 50.000 0.00 0.00 38.91 4.00
2422 2482 5.061179 GTGTGATGTACTACCCAGTTGTTT 58.939 41.667 0.00 0.00 36.14 2.83
2464 2524 4.584325 AGAAGCCTAACACAAGATGCAAAA 59.416 37.500 0.00 0.00 0.00 2.44
2725 2785 5.991606 GCAAGGTATAAGCAGTGATGTCATA 59.008 40.000 0.00 0.00 0.00 2.15
3139 3199 4.764050 ATATGTTCATGTTCCCGGTACA 57.236 40.909 8.85 8.85 0.00 2.90
3269 3330 9.520204 CTTGTGACAATGAGAATGTAAGTTTTT 57.480 29.630 0.00 0.00 0.00 1.94
3307 3368 7.441017 AGTGATGCCTTATCTTCTGAGTTATC 58.559 38.462 0.00 0.00 36.71 1.75
3437 3498 1.057275 TGTGGCTGGACTGGTGGTTA 61.057 55.000 0.00 0.00 0.00 2.85
3532 3597 0.986019 AGGATGTAACATCGGGCCCA 60.986 55.000 24.92 9.77 0.00 5.36
3533 3598 0.535102 GGATGTAACATCGGGCCCAG 60.535 60.000 24.92 15.19 0.00 4.45
3567 3632 4.201802 GCTTGCTTGCATTCTCTAGAACTC 60.202 45.833 0.00 0.00 36.80 3.01
3568 3633 4.541973 TGCTTGCATTCTCTAGAACTCA 57.458 40.909 0.00 0.00 36.80 3.41
3636 3702 5.046910 TCTGCATTTTACAAGCTAACAGC 57.953 39.130 0.00 0.00 42.84 4.40
3661 3727 5.424121 AATAGAATTAGTGGTCAATGCGC 57.576 39.130 0.00 0.00 0.00 6.09
3667 3733 0.537143 AGTGGTCAATGCGCTGGAAA 60.537 50.000 9.73 0.00 0.00 3.13
3672 3738 3.066380 GGTCAATGCGCTGGAAATTTTT 58.934 40.909 9.73 0.00 0.00 1.94
3707 3773 4.931002 TCCGGTACAGTTTAAAGGAATTCG 59.069 41.667 0.00 0.00 0.00 3.34
3760 3826 4.862641 AGCCTAGTGGTACAATTTCCAT 57.137 40.909 0.00 0.00 44.16 3.41
3766 3832 8.474831 GCCTAGTGGTACAATTTCCATAATTTT 58.525 33.333 0.00 0.00 44.16 1.82
3795 3861 8.568617 ACCTTTCTGATACCCTGTTCTATTAT 57.431 34.615 0.00 0.00 0.00 1.28
3822 3888 4.993705 TCCATTATCACCAATACCTCCC 57.006 45.455 0.00 0.00 0.00 4.30
3829 3895 0.042131 ACCAATACCTCCCCTCACGA 59.958 55.000 0.00 0.00 0.00 4.35
3833 3899 1.192428 ATACCTCCCCTCACGACAAC 58.808 55.000 0.00 0.00 0.00 3.32
3838 3904 1.893801 CTCCCCTCACGACAACTAACT 59.106 52.381 0.00 0.00 0.00 2.24
3843 3909 5.359009 TCCCCTCACGACAACTAACTATTAG 59.641 44.000 0.00 0.00 39.18 1.73
3960 4026 0.717801 TACTTACCCCCTGTGGCCTA 59.282 55.000 3.32 0.00 0.00 3.93
3970 4036 3.364549 CCCTGTGGCCTATCAAATTGAA 58.635 45.455 3.32 0.00 0.00 2.69
3975 4041 5.189928 TGTGGCCTATCAAATTGAATACGT 58.810 37.500 3.32 0.00 0.00 3.57
3987 4053 8.175069 TCAAATTGAATACGTCTCTTTACATGC 58.825 33.333 0.00 0.00 0.00 4.06
4024 4090 6.268566 GGACTCTGAATTTTTATGATGCACC 58.731 40.000 0.00 0.00 0.00 5.01
4035 4101 7.433708 TTTTATGATGCACCGGATACTATTG 57.566 36.000 9.46 0.00 0.00 1.90
4157 4223 3.564053 TCATGTGCAATGCTCTATGGA 57.436 42.857 6.82 0.00 0.00 3.41
4178 4244 6.504398 TGGACTATGCTAGAAACTACAATCG 58.496 40.000 0.00 0.00 0.00 3.34
4265 4348 0.874390 TTGAAGTGCCGATGCTTGTC 59.126 50.000 0.00 0.00 38.71 3.18
4313 4397 8.612619 GTTTGTTATATGAACGTCATCCATCTT 58.387 33.333 4.15 0.00 38.26 2.40
4396 4480 1.227556 GTGCGTTGGTCTGACACCT 60.228 57.895 10.38 0.00 46.98 4.00
4402 4486 1.947456 GTTGGTCTGACACCTGAAACC 59.053 52.381 10.38 0.00 46.98 3.27
4481 4565 7.280356 TCTCCTAAATTGGTAAGAGGCAATAC 58.720 38.462 0.00 0.00 0.00 1.89
4490 4574 4.163649 GGTAAGAGGCAATACTACCAACCT 59.836 45.833 0.00 0.00 0.00 3.50
4603 4687 8.416485 ACCGTGTTATAAGCAAGTAGTAATTC 57.584 34.615 0.00 0.00 0.00 2.17
4608 4692 9.378551 TGTTATAAGCAAGTAGTAATTCCACAG 57.621 33.333 0.00 0.00 0.00 3.66
4655 4740 6.147000 GTGCAAACTTTCCTTTTCAGAAAACA 59.853 34.615 4.06 0.00 33.06 2.83
4656 4741 6.708054 TGCAAACTTTCCTTTTCAGAAAACAA 59.292 30.769 4.06 0.00 33.06 2.83
4688 4773 4.927425 TCGTCCTTCAAAACCTCGAAATAG 59.073 41.667 0.00 0.00 0.00 1.73
4696 4781 3.538634 AACCTCGAAATAGCCCTACAC 57.461 47.619 0.00 0.00 0.00 2.90
4697 4782 2.748388 ACCTCGAAATAGCCCTACACT 58.252 47.619 0.00 0.00 0.00 3.55
4698 4783 3.907221 ACCTCGAAATAGCCCTACACTA 58.093 45.455 0.00 0.00 0.00 2.74
4699 4784 3.635836 ACCTCGAAATAGCCCTACACTAC 59.364 47.826 0.00 0.00 0.00 2.73
4700 4785 3.635373 CCTCGAAATAGCCCTACACTACA 59.365 47.826 0.00 0.00 0.00 2.74
4701 4786 4.098960 CCTCGAAATAGCCCTACACTACAA 59.901 45.833 0.00 0.00 0.00 2.41
4702 4787 5.394883 CCTCGAAATAGCCCTACACTACAAA 60.395 44.000 0.00 0.00 0.00 2.83
4703 4788 6.229936 TCGAAATAGCCCTACACTACAAAT 57.770 37.500 0.00 0.00 0.00 2.32
4704 4789 7.350744 TCGAAATAGCCCTACACTACAAATA 57.649 36.000 0.00 0.00 0.00 1.40
4705 4790 7.959175 TCGAAATAGCCCTACACTACAAATAT 58.041 34.615 0.00 0.00 0.00 1.28
4706 4791 7.870954 TCGAAATAGCCCTACACTACAAATATG 59.129 37.037 0.00 0.00 0.00 1.78
4785 4874 0.034089 GAACATGGGGGAAGGACAGG 60.034 60.000 0.00 0.00 0.00 4.00
4811 4900 1.475682 CGTAGTGGTGAAGTACTCCCC 59.524 57.143 0.00 0.00 33.16 4.81
4816 4905 1.697432 TGGTGAAGTACTCCCCACTTG 59.303 52.381 17.10 0.00 36.38 3.16
4827 4916 1.151450 CCCACTTGTGCCAAGAGGT 59.849 57.895 21.11 2.99 37.19 3.85
4836 4925 1.002011 GCCAAGAGGTCCTGGGTTC 60.002 63.158 0.00 0.00 38.32 3.62
4839 4928 0.905357 CAAGAGGTCCTGGGTTCGAT 59.095 55.000 0.00 0.00 0.00 3.59
4885 5204 3.624959 GCAGGGGTAAGGCACTAAGATTT 60.625 47.826 0.00 0.00 38.49 2.17
4913 5232 6.030082 TCATATAATCCTTCCCTAGAACCCC 58.970 44.000 0.00 0.00 0.00 4.95
4918 5237 1.670059 CTTCCCTAGAACCCCACCTT 58.330 55.000 0.00 0.00 0.00 3.50
4949 5268 1.927487 TCTAGCACCGGGTCTGTTTA 58.073 50.000 6.32 0.00 0.00 2.01
4954 5273 4.023726 AGCACCGGGTCTGTTTATTTTA 57.976 40.909 6.32 0.00 0.00 1.52
4979 5300 1.330655 ACATGTAGCTCGTGGGGAGG 61.331 60.000 0.00 0.00 43.36 4.30
5032 5354 3.990318 AGCAAAGGCAGAAGTTTGTAC 57.010 42.857 0.00 0.00 44.61 2.90
5093 5415 9.717942 ATTAAGCTTATCCAGAGACATATCAAC 57.282 33.333 7.08 0.00 0.00 3.18
5165 5487 7.147976 GCAATTTCACATAAAAGGCCCTATAG 58.852 38.462 0.00 0.00 0.00 1.31
5177 5499 5.997384 AGGCCCTATAGTTAATTACCGAG 57.003 43.478 0.00 0.00 0.00 4.63
5281 5603 2.667473 ACTCCCTCCGTATCAAAACG 57.333 50.000 0.00 0.00 42.49 3.60
5294 5616 7.799447 TCCGTATCAAAACGTAAGACATTTTTG 59.201 33.333 0.00 0.00 41.27 2.44
5295 5617 7.799447 CCGTATCAAAACGTAAGACATTTTTGA 59.201 33.333 9.46 9.46 46.50 2.69
5296 5618 8.615585 CGTATCAAAACGTAAGACATTTTTGAC 58.384 33.333 9.29 0.36 45.74 3.18
5297 5619 9.440784 GTATCAAAACGTAAGACATTTTTGACA 57.559 29.630 9.29 0.00 45.74 3.58
5298 5620 7.962934 TCAAAACGTAAGACATTTTTGACAG 57.037 32.000 4.18 0.00 41.01 3.51
5300 5622 4.483476 ACGTAAGACATTTTTGACAGCC 57.517 40.909 0.00 0.00 43.62 4.85
5376 5703 2.859538 CGCCGCATGCTTTAATCATTTT 59.140 40.909 17.13 0.00 38.05 1.82
5407 5734 0.710567 CTGCAGTCGCGTTCAAGTAG 59.289 55.000 5.77 3.56 42.97 2.57
5457 5784 3.311596 CGGGATAATTCTTGGGTCGTTTC 59.688 47.826 0.00 0.00 0.00 2.78
5534 5861 4.052229 CGAGCGGTTCCAGTCGGT 62.052 66.667 0.00 0.00 39.89 4.69
5546 5873 3.967715 GTCGGTCCAGACTTTGCC 58.032 61.111 6.61 0.00 38.09 4.52
5570 5897 2.158769 ACATGCAGGACTCTTCAACACA 60.159 45.455 4.84 0.00 0.00 3.72
5638 5965 5.539955 ACATGTTTCAATTTGTAAGGAGGCT 59.460 36.000 0.00 0.00 0.00 4.58
5688 6015 8.664669 TGGTAATAATGTATATGCTGGAGAGA 57.335 34.615 0.00 0.00 0.00 3.10
5747 6074 5.729454 GCGTGTTCTGTTGTTGTATCTTGTT 60.729 40.000 0.00 0.00 0.00 2.83
5750 6077 5.356751 TGTTCTGTTGTTGTATCTTGTTGCT 59.643 36.000 0.00 0.00 0.00 3.91
5756 6083 5.199024 TGTTGTATCTTGTTGCTGCAAAT 57.801 34.783 17.80 9.47 0.00 2.32
5762 6089 7.252708 TGTATCTTGTTGCTGCAAATAATCTG 58.747 34.615 17.80 4.68 0.00 2.90
5773 6100 6.603237 TGCAAATAATCTGTCATAGTTCCG 57.397 37.500 0.00 0.00 0.00 4.30
5775 6102 5.758296 GCAAATAATCTGTCATAGTTCCGGA 59.242 40.000 0.00 0.00 0.00 5.14
5779 6106 4.592485 ATCTGTCATAGTTCCGGATGTC 57.408 45.455 4.15 0.00 0.00 3.06
5780 6107 3.361786 TCTGTCATAGTTCCGGATGTCA 58.638 45.455 4.15 3.61 0.00 3.58
5789 6116 1.933021 TCCGGATGTCAGTAACCTGT 58.067 50.000 0.00 0.00 39.82 4.00
5790 6117 3.090210 TCCGGATGTCAGTAACCTGTA 57.910 47.619 0.00 0.00 39.82 2.74
5873 6211 1.281287 ACCATTGTCTGCTGCATCTCT 59.719 47.619 1.31 0.00 0.00 3.10
5890 6231 0.469494 TCTGTTGAGCTGAAGGTGCA 59.531 50.000 0.00 0.00 0.00 4.57
5966 6307 2.170187 CTGCAAAGCCTACTGATCTCCT 59.830 50.000 0.00 0.00 0.00 3.69
6038 6387 9.264719 CTGCAGTATTATCTACAAATGATGTGA 57.735 33.333 5.25 0.00 43.77 3.58
6107 6456 2.735772 CCCATGCCACGTAGCTCCT 61.736 63.158 7.64 0.00 0.00 3.69
6220 6569 0.331954 TACAGCTCCTCGAACCCTCT 59.668 55.000 0.00 0.00 0.00 3.69
6310 6672 8.862550 ATCAGTTTTTCAGTTCAGTTTTGATC 57.137 30.769 0.00 0.00 32.27 2.92
6311 6673 8.055279 TCAGTTTTTCAGTTCAGTTTTGATCT 57.945 30.769 0.00 0.00 34.46 2.75
6312 6674 8.522830 TCAGTTTTTCAGTTCAGTTTTGATCTT 58.477 29.630 0.00 0.00 32.36 2.40
6313 6675 9.143631 CAGTTTTTCAGTTCAGTTTTGATCTTT 57.856 29.630 0.00 0.00 32.36 2.52
6314 6676 9.358872 AGTTTTTCAGTTCAGTTTTGATCTTTC 57.641 29.630 0.00 0.00 32.36 2.62
6315 6677 9.139174 GTTTTTCAGTTCAGTTTTGATCTTTCA 57.861 29.630 0.00 0.00 32.36 2.69
6316 6678 9.874205 TTTTTCAGTTCAGTTTTGATCTTTCAT 57.126 25.926 0.00 0.00 32.36 2.57
6342 6704 5.987347 CCTTCTTCAGTTTTGCATTTGTCAT 59.013 36.000 0.00 0.00 0.00 3.06
6541 6903 4.552365 CTGCGGGGATGACGGCAT 62.552 66.667 1.48 1.48 44.10 4.40
6542 6904 4.854924 TGCGGGGATGACGGCATG 62.855 66.667 9.52 0.00 41.00 4.06
6544 6906 3.860605 CGGGGATGACGGCATGGA 61.861 66.667 9.52 0.00 34.11 3.41
6557 6922 0.674534 GCATGGAGTAGTAGTCCGGG 59.325 60.000 17.51 13.16 40.67 5.73
6725 7090 1.056464 CGTTCGTCACCGTGTACTCG 61.056 60.000 10.28 10.28 35.01 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 7.648142 TGGATGCTTAGTTTCAAAGTAAACAG 58.352 34.615 6.89 0.00 40.97 3.16
112 117 4.067896 CAAGTTCATAAGACACTGCCACT 58.932 43.478 0.00 0.00 0.00 4.00
148 153 9.419737 CAAATAACGACAATTTTTCACCAAAAG 57.580 29.630 0.00 0.00 37.79 2.27
165 170 2.301870 ACAGAGGGAGCACAAATAACGA 59.698 45.455 0.00 0.00 0.00 3.85
280 312 5.390567 CCCGTTTCTAAACATAAGTGTCTGC 60.391 44.000 6.41 0.00 37.67 4.26
283 315 4.393990 CCCCCGTTTCTAAACATAAGTGTC 59.606 45.833 6.41 0.00 37.67 3.67
415 448 2.206815 TTGTGCTGCATTCAACACAC 57.793 45.000 5.27 0.00 45.65 3.82
446 479 2.516225 GCGTAATGCCCACTCCCC 60.516 66.667 0.00 0.00 37.76 4.81
513 546 7.497909 TGGTTTTTCTCTAACAAAATCGACTCT 59.502 33.333 0.00 0.00 0.00 3.24
531 564 0.752376 TGTCGTGGGGGTGGTTTTTC 60.752 55.000 0.00 0.00 0.00 2.29
538 571 3.202906 CATATTACTTGTCGTGGGGGTG 58.797 50.000 0.00 0.00 0.00 4.61
545 578 4.022242 CCTCCGATCCATATTACTTGTCGT 60.022 45.833 0.00 0.00 0.00 4.34
563 596 1.664151 GCGATTTTTGTAGTCCCTCCG 59.336 52.381 0.00 0.00 0.00 4.63
615 648 3.049674 CCACTGAACGCGCATGGT 61.050 61.111 5.73 0.00 0.00 3.55
617 650 2.741985 TCCCACTGAACGCGCATG 60.742 61.111 5.73 0.00 0.00 4.06
636 669 3.261580 TCGTAGTCGATGGAAACGTCTA 58.738 45.455 11.75 0.00 44.51 2.59
647 680 0.098376 GTGGACGCTTCGTAGTCGAT 59.902 55.000 11.42 0.00 45.65 3.59
658 691 0.892755 TAGAAATCACCGTGGACGCT 59.107 50.000 0.00 0.00 38.18 5.07
662 695 5.800296 TGAGATTTTAGAAATCACCGTGGA 58.200 37.500 13.92 0.00 0.00 4.02
664 697 7.364522 TCTTGAGATTTTAGAAATCACCGTG 57.635 36.000 13.92 0.00 0.00 4.94
672 705 8.777413 CGGCATATCATCTTGAGATTTTAGAAA 58.223 33.333 0.00 0.00 31.21 2.52
701 734 0.616964 TGAGCATCTCTGAGGGCTGT 60.617 55.000 23.07 6.60 36.59 4.40
705 738 4.686191 ACTTTATGAGCATCTCTGAGGG 57.314 45.455 4.59 0.00 34.92 4.30
736 770 3.006003 TCACTCCTATAAACGCACACACA 59.994 43.478 0.00 0.00 0.00 3.72
754 788 6.569780 TCATATAAACACGCATACACTCACT 58.430 36.000 0.00 0.00 0.00 3.41
809 843 3.140281 CGTTTTCGCTGATTTTGTTGC 57.860 42.857 0.00 0.00 36.22 4.17
850 886 4.640647 GGCTCACTCTATTTTAAACTGGGG 59.359 45.833 0.00 0.00 0.00 4.96
894 931 3.279434 ACGATGGAAGCCCTGTATTTTC 58.721 45.455 0.00 0.00 0.00 2.29
895 932 3.366052 ACGATGGAAGCCCTGTATTTT 57.634 42.857 0.00 0.00 0.00 1.82
896 933 3.740141 CGTACGATGGAAGCCCTGTATTT 60.740 47.826 10.44 0.00 0.00 1.40
897 934 2.223971 CGTACGATGGAAGCCCTGTATT 60.224 50.000 10.44 0.00 0.00 1.89
1002 1041 1.452108 GGGTGGGGAAATCTCGCTG 60.452 63.158 0.00 0.00 34.94 5.18
1159 1198 2.577763 GAAACAAATCGGAGCCGGCG 62.578 60.000 23.20 7.22 40.25 6.46
1209 1248 2.760650 AGCAGTAATAAGGGCAAAAGGC 59.239 45.455 0.00 0.00 43.74 4.35
1223 1262 3.155093 GGAACGATACGGAAGCAGTAA 57.845 47.619 0.00 0.00 0.00 2.24
1225 1264 3.735181 GGAACGATACGGAAGCAGT 57.265 52.632 0.00 0.00 0.00 4.40
1397 1439 3.699067 CGAAATCCATTCTCCACAATGC 58.301 45.455 0.00 0.00 35.79 3.56
1409 1451 5.126061 AGTTAAGATGCAAAGCGAAATCCAT 59.874 36.000 0.00 0.00 0.00 3.41
1412 1454 5.736358 CAGAGTTAAGATGCAAAGCGAAATC 59.264 40.000 0.00 0.00 0.00 2.17
1417 1459 4.627467 ACTACAGAGTTAAGATGCAAAGCG 59.373 41.667 0.00 0.00 28.61 4.68
1423 1465 6.422400 GCCAGATTACTACAGAGTTAAGATGC 59.578 42.308 0.00 0.00 37.10 3.91
1428 1470 6.582636 CATGGCCAGATTACTACAGAGTTAA 58.417 40.000 13.05 0.00 37.10 2.01
1430 1472 4.684485 GCATGGCCAGATTACTACAGAGTT 60.684 45.833 13.05 0.00 37.10 3.01
1435 1477 3.931907 AAGCATGGCCAGATTACTACA 57.068 42.857 13.05 0.00 0.00 2.74
1487 1529 1.136329 AACAGCCAGTCCCCTGTCAT 61.136 55.000 0.00 0.00 41.16 3.06
1494 1536 3.838244 TCATATACAACAGCCAGTCCC 57.162 47.619 0.00 0.00 0.00 4.46
1666 1709 1.936547 GTCATGTTCTCCGAGGCATTC 59.063 52.381 0.00 0.00 0.00 2.67
1681 1724 5.289675 GCTATTTTCGATATCCCTCGTCATG 59.710 44.000 0.00 0.00 39.62 3.07
1696 1739 2.539547 CGCATTGTCCTGGCTATTTTCG 60.540 50.000 0.00 0.00 0.00 3.46
1714 1757 1.444383 CGTGCAGAGACTAAGCGCA 60.444 57.895 11.47 0.00 38.61 6.09
1953 2003 3.642705 CAGAACCAGGTTAAAAGCAAGC 58.357 45.455 4.25 0.00 0.00 4.01
1957 2007 3.305403 GGAAGCAGAACCAGGTTAAAAGC 60.305 47.826 4.25 7.21 0.00 3.51
1969 2019 5.221322 ACAAATTGAAGGAAGGAAGCAGAAC 60.221 40.000 0.00 0.00 0.00 3.01
1989 2039 5.414454 GTCCATTATGTTGCAGGACTACAAA 59.586 40.000 10.85 0.44 44.10 2.83
2068 2127 9.369904 CCACCAGAAATTAAATTAAATGTCCAG 57.630 33.333 0.00 0.00 0.00 3.86
2070 2129 9.719355 AACCACCAGAAATTAAATTAAATGTCC 57.281 29.630 0.00 0.00 0.00 4.02
2202 2261 7.715249 GTCTGGCATTTAATATGTTACTCTGGA 59.285 37.037 0.00 0.00 0.00 3.86
2204 2263 8.437360 TGTCTGGCATTTAATATGTTACTCTG 57.563 34.615 0.00 0.00 0.00 3.35
2205 2264 9.461312 TTTGTCTGGCATTTAATATGTTACTCT 57.539 29.630 0.00 0.00 0.00 3.24
2208 2267 9.632807 TGTTTTGTCTGGCATTTAATATGTTAC 57.367 29.630 0.00 0.00 0.00 2.50
2406 2466 7.733402 TGACAATTAAACAACTGGGTAGTAC 57.267 36.000 0.00 0.00 35.69 2.73
2410 2470 9.521841 TCAATATGACAATTAAACAACTGGGTA 57.478 29.630 0.00 0.00 0.00 3.69
2422 2482 7.340232 AGGCTTCTTGCTTCAATATGACAATTA 59.660 33.333 0.00 0.00 42.39 1.40
2464 2524 8.512138 GTTGCATTGTTAATTACAGAGTTAGGT 58.488 33.333 0.00 0.00 38.19 3.08
2500 2560 7.201794 CGACTACCCTTCTGTATTTCTATGTCA 60.202 40.741 0.00 0.00 0.00 3.58
2501 2561 7.013083 TCGACTACCCTTCTGTATTTCTATGTC 59.987 40.741 0.00 0.00 0.00 3.06
2739 2799 8.307483 TGAAGATTCGATACTGGATTCCTAATC 58.693 37.037 3.95 3.79 37.17 1.75
3128 3188 1.469079 GCAAATGCATGTACCGGGAAC 60.469 52.381 6.32 4.00 41.59 3.62
3269 3330 5.567037 AGGCATCACTAATTAGCACCATA 57.433 39.130 12.54 0.00 0.00 2.74
3270 3331 4.443978 AGGCATCACTAATTAGCACCAT 57.556 40.909 12.54 0.00 0.00 3.55
3271 3332 3.931907 AGGCATCACTAATTAGCACCA 57.068 42.857 12.54 0.00 0.00 4.17
3273 3334 7.659390 AGAAGATAAGGCATCACTAATTAGCAC 59.341 37.037 12.54 0.00 35.96 4.40
3280 3341 6.798427 ACTCAGAAGATAAGGCATCACTAA 57.202 37.500 0.00 0.00 35.96 2.24
3307 3368 3.627577 ACACACAAGCTAAACTTCCACAG 59.372 43.478 0.00 0.00 36.04 3.66
3351 3412 8.491134 TCTAAAGCATTACTTAGGCCTGATAAA 58.509 33.333 17.99 4.74 37.75 1.40
3398 3459 5.425398 CACAACATCATTGTTCAAAAAGCG 58.575 37.500 0.00 0.00 44.24 4.68
3611 3676 6.633500 TGTTAGCTTGTAAAATGCAGAACT 57.367 33.333 0.00 0.00 32.62 3.01
3614 3679 4.378356 CGCTGTTAGCTTGTAAAATGCAGA 60.378 41.667 0.00 0.00 39.60 4.26
3628 3694 5.177696 CCACTAATTCTATTCCGCTGTTAGC 59.822 44.000 0.00 0.00 38.02 3.09
3636 3702 5.333339 CGCATTGACCACTAATTCTATTCCG 60.333 44.000 0.00 0.00 0.00 4.30
3661 3727 7.968405 CGGAGGAATTACAGTAAAAATTTCCAG 59.032 37.037 19.21 10.37 28.73 3.86
3707 3773 8.640291 GCTACGCTATGACTTAATTCTATGAAC 58.360 37.037 0.00 0.00 0.00 3.18
3766 3832 6.500336 AGAACAGGGTATCAGAAAGGTACTA 58.500 40.000 0.00 0.00 38.49 1.82
3768 3834 5.678955 AGAACAGGGTATCAGAAAGGTAC 57.321 43.478 0.00 0.00 0.00 3.34
3769 3835 7.989947 AATAGAACAGGGTATCAGAAAGGTA 57.010 36.000 0.00 0.00 0.00 3.08
3770 3836 6.893020 AATAGAACAGGGTATCAGAAAGGT 57.107 37.500 0.00 0.00 0.00 3.50
3771 3837 8.432805 ACATAATAGAACAGGGTATCAGAAAGG 58.567 37.037 0.00 0.00 0.00 3.11
3772 3838 9.838339 AACATAATAGAACAGGGTATCAGAAAG 57.162 33.333 0.00 0.00 0.00 2.62
3795 3861 7.942341 GGAGGTATTGGTGATAATGGATAAACA 59.058 37.037 0.00 0.00 0.00 2.83
3802 3868 3.657727 AGGGGAGGTATTGGTGATAATGG 59.342 47.826 0.00 0.00 0.00 3.16
3819 3885 2.005370 AGTTAGTTGTCGTGAGGGGA 57.995 50.000 0.00 0.00 0.00 4.81
3838 3904 8.192110 GCGGGGATTTGTAAAATGAAACTAATA 58.808 33.333 0.00 0.00 0.00 0.98
3843 3909 3.930229 GGCGGGGATTTGTAAAATGAAAC 59.070 43.478 0.00 0.00 0.00 2.78
3888 3954 5.823861 TGCTAGGGCAGATATTTGTGATA 57.176 39.130 0.00 0.00 44.28 2.15
3944 4010 0.045008 TGATAGGCCACAGGGGGTAA 59.955 55.000 5.01 0.00 37.04 2.85
3945 4011 0.045008 TTGATAGGCCACAGGGGGTA 59.955 55.000 5.01 0.00 37.04 3.69
3970 4036 6.985188 AACATTGCATGTAAAGAGACGTAT 57.015 33.333 5.76 0.00 44.07 3.06
3975 4041 6.127925 CCAAGCTAACATTGCATGTAAAGAGA 60.128 38.462 5.76 0.00 44.07 3.10
3987 4053 3.942829 TCAGAGTCCCAAGCTAACATTG 58.057 45.455 0.00 0.00 0.00 2.82
4035 4101 8.626526 TGTGAAGGTTTCTTTATCTGTTTTACC 58.373 33.333 0.00 0.00 32.52 2.85
4102 4168 6.696411 TGATGCACCAATATGATATACGACA 58.304 36.000 0.00 0.00 0.00 4.35
4157 4223 5.290386 GGCGATTGTAGTTTCTAGCATAGT 58.710 41.667 0.00 0.00 40.38 2.12
4178 4244 7.488150 CCTTTTATCTAATGTTTTTCCTTCGGC 59.512 37.037 0.00 0.00 0.00 5.54
4247 4330 0.250252 TGACAAGCATCGGCACTTCA 60.250 50.000 0.00 0.00 44.61 3.02
4265 4348 8.806634 CAAACCCAAAATGTAAATCATACGATG 58.193 33.333 0.00 0.00 35.48 3.84
4313 4397 9.116067 AGCATATAAAAAGTTAGCAATCGGTAA 57.884 29.630 0.00 0.00 32.78 2.85
4396 4480 5.011943 CCATTTCCCTTTGAATCTGGTTTCA 59.988 40.000 0.00 0.00 34.08 2.69
4402 4486 5.179929 GCAAAACCATTTCCCTTTGAATCTG 59.820 40.000 0.00 0.00 31.77 2.90
4481 4565 9.720769 TTTCTACAGATTTAAAGAGGTTGGTAG 57.279 33.333 0.00 0.00 0.00 3.18
4533 4617 4.400251 CAGGAAGATGAGCTTTATTTGGCA 59.600 41.667 0.00 0.00 36.83 4.92
4666 4751 4.435651 GCTATTTCGAGGTTTTGAAGGACG 60.436 45.833 0.00 0.00 0.00 4.79
4688 4773 3.146847 GGGCATATTTGTAGTGTAGGGC 58.853 50.000 0.00 0.00 0.00 5.19
4714 4799 2.976185 TGAAGTGTGTGTATTGGGGAGA 59.024 45.455 0.00 0.00 0.00 3.71
4770 4859 3.023735 GCCCTGTCCTTCCCCCAT 61.024 66.667 0.00 0.00 0.00 4.00
4785 4874 1.741770 CTTCACCACTACGCCAGCC 60.742 63.158 0.00 0.00 0.00 4.85
4816 4905 2.069165 AACCCAGGACCTCTTGGCAC 62.069 60.000 0.00 0.00 41.31 5.01
4827 4916 2.268920 GCTGCATCGAACCCAGGA 59.731 61.111 10.91 0.00 0.00 3.86
4885 5204 5.915628 TCTAGGGAAGGATTATATGAGGCA 58.084 41.667 0.00 0.00 0.00 4.75
4918 5237 0.321671 GTGCTAGAAGCTCCCACACA 59.678 55.000 0.00 0.00 42.97 3.72
4949 5268 8.188139 CCCACGAGCTACATGTAAAAATAAAAT 58.812 33.333 7.06 0.00 0.00 1.82
4954 5273 3.945285 CCCCACGAGCTACATGTAAAAAT 59.055 43.478 7.06 0.00 0.00 1.82
4988 5309 4.717629 GCGCGTCCCCTTTTTGGC 62.718 66.667 8.43 0.00 0.00 4.52
5032 5354 2.260869 CGGTGCCTTGGGTCTGTTG 61.261 63.158 0.00 0.00 0.00 3.33
5129 5451 7.503521 TTATGTGAAATTGCAGTGAGTGTTA 57.496 32.000 0.00 0.00 0.00 2.41
5135 5457 5.229423 GCCTTTTATGTGAAATTGCAGTGA 58.771 37.500 0.00 0.00 0.00 3.41
5177 5499 6.036470 GGGTGTTTTTCTCAATAGCTTATGC 58.964 40.000 0.00 0.00 40.05 3.14
5281 5603 5.215160 CACTGGCTGTCAAAAATGTCTTAC 58.785 41.667 0.00 0.00 0.00 2.34
5376 5703 1.202348 CGACTGCAGGTACATGTGAGA 59.798 52.381 19.93 0.00 0.00 3.27
5407 5734 2.035442 GGCTGACTTCAAGGGACGC 61.035 63.158 0.00 0.00 0.00 5.19
5500 5827 1.672030 CGCCTCATCAACACTGGCA 60.672 57.895 0.00 0.00 43.38 4.92
5534 5861 1.619654 CATGTTGGGCAAAGTCTGGA 58.380 50.000 0.00 0.00 0.00 3.86
5544 5871 0.610232 AAGAGTCCTGCATGTTGGGC 60.610 55.000 3.07 3.07 0.00 5.36
5546 5873 2.189594 TGAAGAGTCCTGCATGTTGG 57.810 50.000 0.00 0.00 0.00 3.77
5570 5897 3.786368 AGAAAAGCTTCTGAGAGCCTT 57.214 42.857 0.00 0.00 43.74 4.35
5688 6015 3.131396 CCTTCTACAGAACAGTTGCGTT 58.869 45.455 0.00 0.00 0.00 4.84
5702 6029 4.659088 GCCAAGCGTTTTTATCCTTCTAC 58.341 43.478 0.00 0.00 0.00 2.59
5703 6030 4.957759 GCCAAGCGTTTTTATCCTTCTA 57.042 40.909 0.00 0.00 0.00 2.10
5747 6074 6.038603 GGAACTATGACAGATTATTTGCAGCA 59.961 38.462 0.00 0.00 0.00 4.41
5750 6077 5.527214 CCGGAACTATGACAGATTATTTGCA 59.473 40.000 0.00 0.00 0.00 4.08
5756 6083 5.596772 TGACATCCGGAACTATGACAGATTA 59.403 40.000 9.01 0.00 0.00 1.75
5762 6089 3.802948 ACTGACATCCGGAACTATGAC 57.197 47.619 9.01 2.91 0.00 3.06
5780 6107 8.983702 TCAAAGTAAATGGTTTACAGGTTACT 57.016 30.769 13.27 0.00 46.11 2.24
5789 6116 6.401688 CGCTCACGATCAAAGTAAATGGTTTA 60.402 38.462 0.00 0.00 43.93 2.01
5790 6117 5.616866 CGCTCACGATCAAAGTAAATGGTTT 60.617 40.000 0.00 0.00 43.93 3.27
5873 6211 3.011085 CTGCACCTTCAGCTCAACA 57.989 52.632 0.00 0.00 0.00 3.33
6008 6349 8.681486 TCATTTGTAGATAATACTGCAGCAAT 57.319 30.769 15.27 4.81 34.42 3.56
6038 6387 3.649981 AGGCATAGCTTGTCTGGATGTAT 59.350 43.478 0.00 0.00 39.37 2.29
6092 6441 2.903357 CCAGGAGCTACGTGGCAT 59.097 61.111 26.36 11.00 45.45 4.40
6284 6635 9.305925 GATCAAAACTGAACTGAAAAACTGATT 57.694 29.630 0.00 0.00 0.00 2.57
6300 6662 8.355169 TGAAGAAGGAATGAAAGATCAAAACTG 58.645 33.333 0.00 0.00 39.49 3.16
6301 6663 8.469309 TGAAGAAGGAATGAAAGATCAAAACT 57.531 30.769 0.00 0.00 39.49 2.66
6304 6666 8.469309 AACTGAAGAAGGAATGAAAGATCAAA 57.531 30.769 0.00 0.00 39.49 2.69
6305 6667 8.469309 AAACTGAAGAAGGAATGAAAGATCAA 57.531 30.769 0.00 0.00 39.49 2.57
6306 6668 8.355169 CAAAACTGAAGAAGGAATGAAAGATCA 58.645 33.333 0.00 0.00 40.57 2.92
6307 6669 7.328005 GCAAAACTGAAGAAGGAATGAAAGATC 59.672 37.037 0.00 0.00 0.00 2.75
6308 6670 7.150640 GCAAAACTGAAGAAGGAATGAAAGAT 58.849 34.615 0.00 0.00 0.00 2.40
6309 6671 6.096705 TGCAAAACTGAAGAAGGAATGAAAGA 59.903 34.615 0.00 0.00 0.00 2.52
6310 6672 6.275335 TGCAAAACTGAAGAAGGAATGAAAG 58.725 36.000 0.00 0.00 0.00 2.62
6311 6673 6.219417 TGCAAAACTGAAGAAGGAATGAAA 57.781 33.333 0.00 0.00 0.00 2.69
6312 6674 5.850557 TGCAAAACTGAAGAAGGAATGAA 57.149 34.783 0.00 0.00 0.00 2.57
6313 6675 6.409524 AATGCAAAACTGAAGAAGGAATGA 57.590 33.333 0.00 0.00 0.00 2.57
6314 6676 6.480981 ACAAATGCAAAACTGAAGAAGGAATG 59.519 34.615 0.00 0.00 0.00 2.67
6315 6677 6.585416 ACAAATGCAAAACTGAAGAAGGAAT 58.415 32.000 0.00 0.00 0.00 3.01
6316 6678 5.976458 ACAAATGCAAAACTGAAGAAGGAA 58.024 33.333 0.00 0.00 0.00 3.36
6342 6704 0.609957 ACCGTCATCGACAGGGTACA 60.610 55.000 8.48 0.00 39.71 2.90
6533 6895 2.022195 GACTACTACTCCATGCCGTCA 58.978 52.381 0.00 0.00 0.00 4.35
6540 6902 0.187851 CCCCCGGACTACTACTCCAT 59.812 60.000 0.73 0.00 0.00 3.41
6541 6903 1.616921 CCCCCGGACTACTACTCCA 59.383 63.158 0.73 0.00 0.00 3.86
6542 6904 4.595031 CCCCCGGACTACTACTCC 57.405 66.667 0.73 0.00 0.00 3.85
6557 6922 1.144936 CGAGTTCAGCATCCTCCCC 59.855 63.158 0.00 0.00 0.00 4.81
6560 6925 0.532573 TGTCCGAGTTCAGCATCCTC 59.467 55.000 0.00 0.00 0.00 3.71
6718 7083 4.111016 CGCTGGCGTCCGAGTACA 62.111 66.667 6.83 0.00 34.35 2.90


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

AutoCloner maintained by Alex Coulton.