Multiple sequence alignment - TraesCS7A01G322500

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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 TraesCS7A01G322500 chr7A 100.000 2931 0 0 1 2931 466884307 466887237 0.000000e+00 5413
1 TraesCS7A01G322500 chr7B 85.821 1467 179 18 604 2057 421700240 421698790 0.000000e+00 1530
2 TraesCS7A01G322500 chr7B 85.003 1467 195 13 604 2057 420072793 420074247 0.000000e+00 1467
3 TraesCS7A01G322500 chr7B 88.777 891 88 11 2047 2931 420074271 420075155 0.000000e+00 1081
4 TraesCS7A01G322500 chr7B 88.440 891 89 11 2047 2931 421698766 421697884 0.000000e+00 1062
5 TraesCS7A01G322500 chr7B 95.158 537 21 2 1 537 421700968 421700437 0.000000e+00 843
6 TraesCS7A01G322500 chr7B 97.183 355 10 0 180 534 420072291 420072645 4.180000e-168 601
7 TraesCS7A01G322500 chr7B 93.434 198 12 1 1 198 420068772 420068968 2.860000e-75 292


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 TraesCS7A01G322500 chr7A 466884307 466887237 2930 False 5413.00 5413 100.000000 1 2931 1 chr7A.!!$F1 2930
1 TraesCS7A01G322500 chr7B 421697884 421700968 3084 True 1145.00 1530 89.806333 1 2931 3 chr7B.!!$R1 2930
2 TraesCS7A01G322500 chr7B 420068772 420075155 6383 False 860.25 1467 91.099250 1 2931 4 chr7B.!!$F1 2930

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
903 4405 0.596577 TGATACGAGGCGGTATGCTC 59.403 55.0 8.63 0.0 45.43 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2398 5938 0.109781 CAACAATGTACCCGTGCTGC 60.11 55.0 0.0 0.0 0.0 5.25 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
33 34 3.279116 GCACCGTGCACAAGAGCA 61.279 61.111 18.79 0.00 44.26 4.26
46 47 4.063689 CACAAGAGCATTGACTGAAGAGT 58.936 43.478 8.50 0.00 33.98 3.24
47 48 4.514441 CACAAGAGCATTGACTGAAGAGTT 59.486 41.667 8.50 0.00 30.16 3.01
58 59 4.654262 TGACTGAAGAGTTTACAAGGAGGT 59.346 41.667 0.00 0.00 30.16 3.85
137 138 1.153568 CTGCGAGCAATCGAGGGAA 60.154 57.895 1.17 0.00 34.64 3.97
141 142 1.401905 GCGAGCAATCGAGGGAAAAAT 59.598 47.619 1.17 0.00 34.64 1.82
146 147 3.944015 AGCAATCGAGGGAAAAATGAGAG 59.056 43.478 0.00 0.00 0.00 3.20
181 3523 2.656973 GCGTTTTTGCCACGGTGG 60.657 61.111 22.87 22.87 41.55 4.61
338 3680 3.085947 TGCCCCCTAGCTCTGCTG 61.086 66.667 1.96 0.00 40.10 4.41
375 3717 7.862512 TCAGATTTGTGGCTTTTCAATTTTT 57.137 28.000 0.00 0.00 0.00 1.94
418 3760 3.238108 TCTCAGTCTTCTCCGATTTGC 57.762 47.619 0.00 0.00 0.00 3.68
420 3762 2.670414 CTCAGTCTTCTCCGATTTGCAC 59.330 50.000 0.00 0.00 0.00 4.57
465 3807 2.704725 AACATGCCATGACGTTTCAC 57.295 45.000 12.53 0.00 33.38 3.18
495 3837 6.788243 TGTTGCTAGAATCATGCATTACAAG 58.212 36.000 0.00 0.00 36.55 3.16
544 3886 9.244799 GGCAATTATAGCATAGTTGTTTAAACC 57.755 33.333 15.59 1.33 0.00 3.27
545 3887 9.244799 GCAATTATAGCATAGTTGTTTAAACCC 57.755 33.333 15.59 6.46 0.00 4.11
548 3890 8.865420 TTATAGCATAGTTGTTTAAACCCACA 57.135 30.769 15.59 0.00 0.00 4.17
549 3891 5.705609 AGCATAGTTGTTTAAACCCACAG 57.294 39.130 15.59 7.80 0.00 3.66
550 3892 5.137551 AGCATAGTTGTTTAAACCCACAGT 58.862 37.500 15.59 3.32 0.00 3.55
551 3893 6.300703 AGCATAGTTGTTTAAACCCACAGTA 58.699 36.000 15.59 5.23 0.00 2.74
552 3894 6.773685 AGCATAGTTGTTTAAACCCACAGTAA 59.226 34.615 15.59 0.00 0.00 2.24
553 3895 7.040686 AGCATAGTTGTTTAAACCCACAGTAAG 60.041 37.037 15.59 3.65 0.00 2.34
554 3896 7.040961 GCATAGTTGTTTAAACCCACAGTAAGA 60.041 37.037 15.59 0.00 0.00 2.10
555 3897 8.842280 CATAGTTGTTTAAACCCACAGTAAGAA 58.158 33.333 15.59 0.00 0.00 2.52
556 3898 7.092137 AGTTGTTTAAACCCACAGTAAGAAC 57.908 36.000 15.59 8.84 0.00 3.01
557 3899 6.888088 AGTTGTTTAAACCCACAGTAAGAACT 59.112 34.615 15.59 10.75 35.91 3.01
590 3932 4.703575 ACATGATGGCTGGTATATGCATTC 59.296 41.667 3.54 0.00 0.00 2.67
592 3934 4.329392 TGATGGCTGGTATATGCATTCAG 58.671 43.478 3.54 9.33 0.00 3.02
637 4136 2.686405 ACATGCTTATGTCACCATGCTG 59.314 45.455 0.00 0.00 38.83 4.41
670 4172 5.779241 ATCTGGGGAAATCAAGTAGACAA 57.221 39.130 0.00 0.00 0.00 3.18
674 4176 7.872138 TCTGGGGAAATCAAGTAGACAATATT 58.128 34.615 0.00 0.00 0.00 1.28
675 4177 7.775093 TCTGGGGAAATCAAGTAGACAATATTG 59.225 37.037 14.01 14.01 0.00 1.90
725 4227 2.155279 GAGTTGCTTCTTGGGAAGGTC 58.845 52.381 7.69 0.00 46.49 3.85
727 4229 1.882623 GTTGCTTCTTGGGAAGGTCAG 59.117 52.381 7.69 0.00 46.49 3.51
793 4295 2.009051 CAGTTGTTGCTCATCGCCATA 58.991 47.619 0.00 0.00 38.05 2.74
803 4305 3.257393 CTCATCGCCATATACCTTCTGC 58.743 50.000 0.00 0.00 0.00 4.26
814 4316 4.803329 ATACCTTCTGCAATCCCATCTT 57.197 40.909 0.00 0.00 0.00 2.40
829 4331 2.219674 CCATCTTCTACAATCTTCGCGC 59.780 50.000 0.00 0.00 0.00 6.86
842 4344 1.410737 TTCGCGCTTACGATCACTGC 61.411 55.000 5.56 0.00 42.54 4.40
858 4360 1.003696 ACTGCCACCTCCTTTCTTAGC 59.996 52.381 0.00 0.00 0.00 3.09
903 4405 0.596577 TGATACGAGGCGGTATGCTC 59.403 55.000 8.63 0.00 45.43 4.26
906 4408 4.301027 CGAGGCGGTATGCTCCCC 62.301 72.222 0.00 0.00 45.43 4.81
907 4409 4.301027 GAGGCGGTATGCTCCCCG 62.301 72.222 4.46 4.46 46.90 5.73
937 4439 6.255453 TGCTCAGTTATGTTCTTTTTGTTTGC 59.745 34.615 0.00 0.00 0.00 3.68
938 4440 6.292328 GCTCAGTTATGTTCTTTTTGTTTGCC 60.292 38.462 0.00 0.00 0.00 4.52
1014 4516 2.360726 CAGATGGCTGCTGCACCA 60.361 61.111 20.68 20.68 41.91 4.17
1038 4540 2.113860 CCTTCTCGGCTCATTTGGAA 57.886 50.000 0.00 0.00 0.00 3.53
1041 4543 3.255642 CCTTCTCGGCTCATTTGGAAAAA 59.744 43.478 0.00 0.00 0.00 1.94
1051 4553 5.289434 GCTCATTTGGAAAAATGGATCGTTC 59.711 40.000 10.40 0.00 39.84 3.95
1058 4560 4.406943 GAAAAATGGATCGTTCAGCAGAC 58.593 43.478 0.00 0.00 0.00 3.51
1059 4561 2.029838 AATGGATCGTTCAGCAGACC 57.970 50.000 0.00 0.00 0.00 3.85
1062 4564 1.338105 TGGATCGTTCAGCAGACCAAG 60.338 52.381 0.00 0.00 0.00 3.61
1071 4573 3.114606 TCAGCAGACCAAGGATTCCATA 58.885 45.455 5.29 0.00 0.00 2.74
1103 4605 8.772250 TGTGAATATCTCTCCTAATTTGGACTT 58.228 33.333 4.36 0.00 31.94 3.01
1107 4609 9.844257 AATATCTCTCCTAATTTGGACTTCAAG 57.156 33.333 4.36 0.00 36.62 3.02
1108 4610 6.935240 TCTCTCCTAATTTGGACTTCAAGA 57.065 37.500 4.36 0.00 36.62 3.02
1109 4611 6.940739 TCTCTCCTAATTTGGACTTCAAGAG 58.059 40.000 4.36 8.93 36.62 2.85
1110 4612 6.498651 TCTCTCCTAATTTGGACTTCAAGAGT 59.501 38.462 15.28 0.00 42.70 3.24
1111 4613 7.674348 TCTCTCCTAATTTGGACTTCAAGAGTA 59.326 37.037 15.28 5.36 39.19 2.59
1113 4615 8.656806 TCTCCTAATTTGGACTTCAAGAGTAAA 58.343 33.333 4.36 0.00 39.19 2.01
1114 4616 8.617290 TCCTAATTTGGACTTCAAGAGTAAAC 57.383 34.615 4.36 0.00 39.19 2.01
1130 4632 7.979786 AGAGTAAACTGGAAGATCTTATGGA 57.020 36.000 8.25 0.00 37.43 3.41
1131 4633 8.017418 AGAGTAAACTGGAAGATCTTATGGAG 57.983 38.462 8.25 4.64 37.43 3.86
1132 4634 7.841729 AGAGTAAACTGGAAGATCTTATGGAGA 59.158 37.037 8.25 0.00 36.54 3.71
1133 4635 8.380742 AGTAAACTGGAAGATCTTATGGAGAA 57.619 34.615 8.25 0.00 35.92 2.87
1134 4636 8.826765 AGTAAACTGGAAGATCTTATGGAGAAA 58.173 33.333 8.25 0.00 35.92 2.52
1136 4638 5.679601 ACTGGAAGATCTTATGGAGAAAGC 58.320 41.667 8.25 0.00 35.92 3.51
1137 4639 5.041191 TGGAAGATCTTATGGAGAAAGCC 57.959 43.478 8.25 1.78 38.06 4.35
1146 4648 5.241506 TCTTATGGAGAAAGCCAAAACTGTG 59.758 40.000 0.00 0.00 42.16 3.66
1153 4655 1.067916 GCCAAAACTGTGCCAGTGG 59.932 57.895 4.20 4.20 44.62 4.00
1154 4656 1.741525 CCAAAACTGTGCCAGTGGG 59.258 57.895 12.15 7.33 44.62 4.61
1156 4658 1.457455 AAAACTGTGCCAGTGGGGG 60.457 57.895 12.15 0.00 44.62 5.40
1163 4665 2.361737 GCCAGTGGGGGAAAGAGC 60.362 66.667 12.15 0.00 37.04 4.09
1169 4671 2.273776 GGGGGAAAGAGCAGAGGC 59.726 66.667 0.00 0.00 41.61 4.70
1181 4683 3.298958 AGAGGCGCTGAATCCGAA 58.701 55.556 7.64 0.00 0.00 4.30
1183 4685 0.460987 AGAGGCGCTGAATCCGAAAG 60.461 55.000 7.64 0.00 0.00 2.62
1206 4708 0.889186 AATGTGCCGGGTCTGTTGTC 60.889 55.000 2.18 0.00 0.00 3.18
1208 4710 3.228017 TGCCGGGTCTGTTGTCGA 61.228 61.111 2.18 0.00 0.00 4.20
1214 4716 2.325761 CGGGTCTGTTGTCGAAGTTAG 58.674 52.381 0.00 0.00 0.00 2.34
1216 4718 3.551454 CGGGTCTGTTGTCGAAGTTAGAA 60.551 47.826 0.00 0.00 0.00 2.10
1217 4719 3.739810 GGGTCTGTTGTCGAAGTTAGAAC 59.260 47.826 0.00 0.00 0.00 3.01
1219 4721 4.807304 GGTCTGTTGTCGAAGTTAGAACAA 59.193 41.667 0.00 0.00 0.00 2.83
1220 4722 5.050972 GGTCTGTTGTCGAAGTTAGAACAAG 60.051 44.000 0.00 0.00 0.00 3.16
1221 4723 5.047847 TCTGTTGTCGAAGTTAGAACAAGG 58.952 41.667 0.00 0.00 0.00 3.61
1224 4726 4.252971 TGTCGAAGTTAGAACAAGGGAG 57.747 45.455 0.00 0.00 0.00 4.30
1229 4731 5.422331 TCGAAGTTAGAACAAGGGAGATCAT 59.578 40.000 0.00 0.00 0.00 2.45
1230 4732 6.070767 TCGAAGTTAGAACAAGGGAGATCATT 60.071 38.462 0.00 0.00 0.00 2.57
1234 4736 8.560124 AGTTAGAACAAGGGAGATCATTATCT 57.440 34.615 0.00 0.00 45.46 1.98
1254 4756 4.711399 TCTTATCAAGTGCCCATCTCATG 58.289 43.478 0.00 0.00 0.00 3.07
1278 4780 5.008613 GGAGCATGTCTACACAGTTTCAAAA 59.991 40.000 0.00 0.00 35.41 2.44
1281 4783 5.221048 GCATGTCTACACAGTTTCAAAACCT 60.221 40.000 2.08 0.00 39.71 3.50
1282 4784 6.430451 CATGTCTACACAGTTTCAAAACCTC 58.570 40.000 2.08 0.00 39.71 3.85
1287 4789 7.065923 GTCTACACAGTTTCAAAACCTCTTTCT 59.934 37.037 2.08 0.00 39.71 2.52
1294 4796 5.479716 TTCAAAACCTCTTTCTGTTCGTC 57.520 39.130 0.00 0.00 0.00 4.20
1295 4797 4.766375 TCAAAACCTCTTTCTGTTCGTCT 58.234 39.130 0.00 0.00 0.00 4.18
1296 4798 5.183228 TCAAAACCTCTTTCTGTTCGTCTT 58.817 37.500 0.00 0.00 0.00 3.01
1302 4804 3.275143 TCTTTCTGTTCGTCTTGCCAAA 58.725 40.909 0.00 0.00 0.00 3.28
1312 4814 3.058777 TCGTCTTGCCAAAACGTATTTCC 60.059 43.478 2.92 0.00 37.64 3.13
1323 4825 7.186804 CCAAAACGTATTTCCATACAGATGTC 58.813 38.462 0.00 0.00 35.81 3.06
1329 4831 6.538742 CGTATTTCCATACAGATGTCCTTTGT 59.461 38.462 0.00 0.00 35.81 2.83
1332 4834 4.832248 TCCATACAGATGTCCTTTGTGAC 58.168 43.478 0.00 0.00 35.77 3.67
1343 4845 3.008049 GTCCTTTGTGACCACTATGAGGT 59.992 47.826 1.62 0.00 43.46 3.85
1354 4856 6.038997 ACCACTATGAGGTTAGTTTCAGTC 57.961 41.667 0.00 0.00 35.33 3.51
1355 4857 5.103000 CCACTATGAGGTTAGTTTCAGTCG 58.897 45.833 0.00 0.00 29.93 4.18
1366 4868 0.534203 TTTCAGTCGACCTGGGCAAC 60.534 55.000 13.01 0.00 41.83 4.17
1367 4869 1.691195 TTCAGTCGACCTGGGCAACA 61.691 55.000 13.01 0.00 41.83 3.33
1368 4870 1.003355 CAGTCGACCTGGGCAACAT 60.003 57.895 13.01 0.00 37.54 2.71
1370 4872 0.249398 AGTCGACCTGGGCAACATAC 59.751 55.000 13.01 0.00 39.74 2.39
1376 4878 2.943033 GACCTGGGCAACATACACATAC 59.057 50.000 0.00 0.00 39.74 2.39
1378 4880 3.778075 ACCTGGGCAACATACACATACTA 59.222 43.478 0.00 0.00 39.74 1.82
1384 4886 5.883673 GGGCAACATACACATACTAAAAGGA 59.116 40.000 0.00 0.00 39.74 3.36
1421 4923 7.720957 AGCTACAATTATTGGCATAGATTGTGA 59.279 33.333 22.36 12.00 40.16 3.58
1446 4948 0.534412 ACTTGCTCCTCATCTCCGTG 59.466 55.000 0.00 0.00 0.00 4.94
1459 4961 1.078759 CTCCGTGCCACGAGTGAATC 61.079 60.000 20.57 0.00 46.05 2.52
1461 4963 1.354337 CCGTGCCACGAGTGAATCTG 61.354 60.000 20.57 0.00 46.05 2.90
1463 4965 1.795768 GTGCCACGAGTGAATCTGAA 58.204 50.000 4.59 0.00 0.00 3.02
1472 4974 4.039245 ACGAGTGAATCTGAAGAACTTGGA 59.961 41.667 0.00 0.00 0.00 3.53
1473 4975 5.174395 CGAGTGAATCTGAAGAACTTGGAT 58.826 41.667 0.00 0.00 0.00 3.41
1476 4978 7.251321 AGTGAATCTGAAGAACTTGGATAGT 57.749 36.000 0.00 0.00 39.32 2.12
1477 4979 7.102346 AGTGAATCTGAAGAACTTGGATAGTG 58.898 38.462 0.00 0.00 37.12 2.74
1479 4981 7.064016 GTGAATCTGAAGAACTTGGATAGTGAC 59.936 40.741 0.00 0.00 37.12 3.67
1484 4986 4.199432 AGAACTTGGATAGTGACTGCAG 57.801 45.455 13.48 13.48 37.12 4.41
1485 4987 2.393271 ACTTGGATAGTGACTGCAGC 57.607 50.000 15.27 7.45 35.19 5.25
1487 4989 0.608130 TTGGATAGTGACTGCAGCGT 59.392 50.000 15.27 0.00 0.00 5.07
1490 4992 1.554392 GATAGTGACTGCAGCGTCAG 58.446 55.000 15.27 6.70 43.94 3.51
1491 4993 0.459237 ATAGTGACTGCAGCGTCAGC 60.459 55.000 15.27 7.03 43.94 4.26
1520 5022 3.835395 CCTCTTACCTTCAGTTCAGTCCT 59.165 47.826 0.00 0.00 0.00 3.85
1524 5026 2.695585 ACCTTCAGTTCAGTCCTTCCT 58.304 47.619 0.00 0.00 0.00 3.36
1543 5045 3.070878 TCCTGTGCAACTTGATGAGTGTA 59.929 43.478 0.00 0.00 39.00 2.90
1551 5053 6.375174 TGCAACTTGATGAGTGTATTATGCTT 59.625 34.615 0.00 0.00 39.00 3.91
1563 5065 0.618458 TTATGCTTTCGTGGCCTCCT 59.382 50.000 3.32 0.00 0.00 3.69
1569 5071 0.753479 TTTCGTGGCCTCCTTTGCAA 60.753 50.000 3.32 0.00 0.00 4.08
1587 5089 2.290464 CAACACCGGACTGTGGTTAAA 58.710 47.619 9.46 0.00 40.62 1.52
1596 5098 5.337813 CCGGACTGTGGTTAAAGGTAGTATT 60.338 44.000 0.00 0.00 0.00 1.89
1605 5107 8.789762 GTGGTTAAAGGTAGTATTTGTCACATT 58.210 33.333 0.00 0.00 0.00 2.71
1606 5108 9.357161 TGGTTAAAGGTAGTATTTGTCACATTT 57.643 29.630 0.00 0.00 0.00 2.32
1607 5109 9.836076 GGTTAAAGGTAGTATTTGTCACATTTC 57.164 33.333 0.00 0.00 0.00 2.17
1633 5135 7.652524 AGAGCACTCTATGATTTAGTGAAGA 57.347 36.000 10.04 0.00 42.59 2.87
1636 5138 7.846066 AGCACTCTATGATTTAGTGAAGAAGT 58.154 34.615 10.04 0.00 42.59 3.01
1637 5139 8.317679 AGCACTCTATGATTTAGTGAAGAAGTT 58.682 33.333 10.04 0.00 42.59 2.66
1639 5141 8.877779 CACTCTATGATTTAGTGAAGAAGTTGG 58.122 37.037 0.00 0.00 42.59 3.77
1664 5166 2.645838 CCTGTTGGGTATGGGATGAG 57.354 55.000 0.00 0.00 0.00 2.90
1665 5167 1.143684 CCTGTTGGGTATGGGATGAGG 59.856 57.143 0.00 0.00 0.00 3.86
1669 5171 0.768221 TGGGTATGGGATGAGGCTCC 60.768 60.000 12.86 0.00 34.31 4.70
1679 5181 2.284190 GATGAGGCTCCTGCAAGTAAC 58.716 52.381 12.86 0.00 41.91 2.50
1680 5182 1.055849 TGAGGCTCCTGCAAGTAACA 58.944 50.000 12.86 0.00 41.91 2.41
1692 5194 2.156891 GCAAGTAACAATCGCGAGTGAA 59.843 45.455 39.19 24.54 0.00 3.18
1695 5197 4.385244 AGTAACAATCGCGAGTGAAAAC 57.615 40.909 39.19 29.60 0.00 2.43
1725 5227 1.614525 AGCTCCACTGCTGGATGGA 60.615 57.895 0.00 0.00 46.18 3.41
1728 5230 0.907486 CTCCACTGCTGGATGGAAGA 59.093 55.000 4.78 0.00 46.18 2.87
1734 5236 2.026449 ACTGCTGGATGGAAGAGGAAAG 60.026 50.000 0.00 0.00 0.00 2.62
1737 5239 2.682269 GCTGGATGGAAGAGGAAAGGTC 60.682 54.545 0.00 0.00 0.00 3.85
1743 5245 2.986019 TGGAAGAGGAAAGGTCATTGGA 59.014 45.455 0.00 0.00 0.00 3.53
1767 5269 1.335132 TACATGGAGGTTCGGGAGGC 61.335 60.000 0.00 0.00 0.00 4.70
1786 5288 3.330701 AGGCCCATTCTCTTACTTTGTCA 59.669 43.478 0.00 0.00 0.00 3.58
1787 5289 4.079253 GGCCCATTCTCTTACTTTGTCAA 58.921 43.478 0.00 0.00 0.00 3.18
1791 5293 5.474876 CCCATTCTCTTACTTTGTCAAGCTT 59.525 40.000 0.00 0.00 32.57 3.74
1796 5298 4.689071 TCTTACTTTGTCAAGCTTCGTCA 58.311 39.130 0.00 0.00 32.57 4.35
1800 5302 3.248602 ACTTTGTCAAGCTTCGTCACATC 59.751 43.478 0.00 0.00 32.57 3.06
1801 5303 2.524569 TGTCAAGCTTCGTCACATCA 57.475 45.000 0.00 0.00 0.00 3.07
1814 5316 3.187700 GTCACATCATACCGTTCCTGAC 58.812 50.000 0.00 0.00 0.00 3.51
1851 5353 4.671880 TGCGCGTAAGTTATCACATTTT 57.328 36.364 8.43 0.00 41.68 1.82
1927 5429 4.165950 TGTGCATAATATTCAGGTCAGGGT 59.834 41.667 0.00 0.00 0.00 4.34
1932 5434 6.428159 GCATAATATTCAGGTCAGGGTTAGTG 59.572 42.308 0.00 0.00 0.00 2.74
1935 5437 4.762289 ATTCAGGTCAGGGTTAGTGATC 57.238 45.455 0.00 0.00 0.00 2.92
1936 5438 2.467880 TCAGGTCAGGGTTAGTGATCC 58.532 52.381 0.00 0.00 0.00 3.36
1937 5439 2.187958 CAGGTCAGGGTTAGTGATCCA 58.812 52.381 0.00 0.00 0.00 3.41
1944 5446 3.392285 CAGGGTTAGTGATCCATCCATGA 59.608 47.826 0.00 0.00 0.00 3.07
1950 5452 6.718454 GGTTAGTGATCCATCCATGATCATTT 59.282 38.462 5.16 0.00 37.62 2.32
1955 5457 5.768164 TGATCCATCCATGATCATTTCTGTG 59.232 40.000 5.16 1.36 31.26 3.66
1956 5458 5.120054 TCCATCCATGATCATTTCTGTGT 57.880 39.130 5.16 0.00 0.00 3.72
1964 5466 6.407865 CCATGATCATTTCTGTGTAGAGGACT 60.408 42.308 5.16 0.00 33.70 3.85
1970 5472 1.895798 TCTGTGTAGAGGACTTGCCAG 59.104 52.381 0.00 0.00 40.02 4.85
1971 5473 0.976641 TGTGTAGAGGACTTGCCAGG 59.023 55.000 0.00 0.00 40.02 4.45
1972 5474 0.977395 GTGTAGAGGACTTGCCAGGT 59.023 55.000 0.00 0.00 40.02 4.00
1985 5487 1.209504 TGCCAGGTCCACTACTATTGC 59.790 52.381 0.00 0.00 0.00 3.56
2000 5502 8.150945 CACTACTATTGCTGGTAAGTTATCCAT 58.849 37.037 5.13 0.00 33.01 3.41
2010 5512 7.224949 GCTGGTAAGTTATCCATGTCTTCTTAC 59.775 40.741 12.40 12.40 36.68 2.34
2012 5514 6.990939 GGTAAGTTATCCATGTCTTCTTACCC 59.009 42.308 20.75 11.24 44.45 3.69
2013 5515 6.893020 AAGTTATCCATGTCTTCTTACCCT 57.107 37.500 0.00 0.00 0.00 4.34
2014 5516 6.240549 AGTTATCCATGTCTTCTTACCCTG 57.759 41.667 0.00 0.00 0.00 4.45
2015 5517 3.567478 ATCCATGTCTTCTTACCCTGC 57.433 47.619 0.00 0.00 0.00 4.85
2016 5518 2.265367 TCCATGTCTTCTTACCCTGCA 58.735 47.619 0.00 0.00 0.00 4.41
2021 5525 2.642311 TGTCTTCTTACCCTGCAATCCA 59.358 45.455 0.00 0.00 0.00 3.41
2053 5557 6.115448 ACATGTGGCTAGGTATTCCTATTC 57.885 41.667 0.00 0.00 44.30 1.75
2057 5561 6.621394 TGTGGCTAGGTATTCCTATTCTAGT 58.379 40.000 0.00 0.00 44.30 2.57
2058 5562 7.073854 TGTGGCTAGGTATTCCTATTCTAGTT 58.926 38.462 0.00 0.00 44.30 2.24
2059 5563 7.567622 TGTGGCTAGGTATTCCTATTCTAGTTT 59.432 37.037 0.00 0.00 44.30 2.66
2060 5564 7.873505 GTGGCTAGGTATTCCTATTCTAGTTTG 59.126 40.741 0.00 0.00 44.30 2.93
2062 5566 7.256368 GGCTAGGTATTCCTATTCTAGTTTGCT 60.256 40.741 0.00 0.00 44.30 3.91
2063 5567 7.815549 GCTAGGTATTCCTATTCTAGTTTGCTC 59.184 40.741 0.00 0.00 44.30 4.26
2064 5568 7.922699 AGGTATTCCTATTCTAGTTTGCTCT 57.077 36.000 0.00 0.00 43.12 4.09
2065 5569 8.325477 AGGTATTCCTATTCTAGTTTGCTCTT 57.675 34.615 0.00 0.00 43.12 2.85
2066 5570 8.773216 AGGTATTCCTATTCTAGTTTGCTCTTT 58.227 33.333 0.00 0.00 43.12 2.52
2067 5571 9.047371 GGTATTCCTATTCTAGTTTGCTCTTTC 57.953 37.037 0.00 0.00 0.00 2.62
2068 5572 9.047371 GTATTCCTATTCTAGTTTGCTCTTTCC 57.953 37.037 0.00 0.00 0.00 3.13
2086 5624 7.542130 GCTCTTTCCTTATGTTGTTAATTGGTG 59.458 37.037 0.00 0.00 0.00 4.17
2093 5631 8.527810 CCTTATGTTGTTAATTGGTGGTGTTAT 58.472 33.333 0.00 0.00 0.00 1.89
2196 5734 1.385528 GGGAACCGTGTGAACACTTT 58.614 50.000 11.55 4.80 44.34 2.66
2207 5745 1.610038 TGAACACTTTGCTGCAGATGG 59.390 47.619 20.43 6.38 0.00 3.51
2246 5784 5.411781 ACTTAGTTCTGTCGATCATCCAAC 58.588 41.667 0.00 0.00 0.00 3.77
2256 5794 7.231519 TCTGTCGATCATCCAACATAGAGTAAT 59.768 37.037 0.00 0.00 0.00 1.89
2295 5833 4.518970 TGTTATGTTCCCTTGAAAGCTGAC 59.481 41.667 0.00 0.00 30.79 3.51
2301 5839 0.169672 CCTTGAAAGCTGACATGGCG 59.830 55.000 10.70 0.00 34.52 5.69
2308 5846 1.965930 GCTGACATGGCGGTGACAA 60.966 57.895 9.70 0.00 0.00 3.18
2309 5847 1.514678 GCTGACATGGCGGTGACAAA 61.515 55.000 9.70 0.00 0.00 2.83
2314 5854 3.570125 TGACATGGCGGTGACAAAATAAA 59.430 39.130 0.00 0.00 0.00 1.40
2350 5890 9.890629 ATACAGCTCAGAGTGAACATAATAAAA 57.109 29.630 0.00 0.00 0.00 1.52
2351 5891 8.261492 ACAGCTCAGAGTGAACATAATAAAAG 57.739 34.615 0.00 0.00 0.00 2.27
2354 5894 6.823689 GCTCAGAGTGAACATAATAAAAGGGA 59.176 38.462 0.00 0.00 0.00 4.20
2398 5938 8.171196 GTGATTGATATACGATTGCAATACCTG 58.829 37.037 12.97 5.46 30.06 4.00
2417 5957 0.109781 GCAGCACGGGTACATTGTTG 60.110 55.000 0.00 0.00 0.00 3.33
2427 5967 3.552068 GGGTACATTGTTGTTGCCAGTTC 60.552 47.826 0.00 0.00 37.28 3.01
2434 5974 3.348119 TGTTGTTGCCAGTTCTACACAA 58.652 40.909 0.00 0.00 0.00 3.33
2454 5996 4.118410 CAACATTTTGCAAAGCAGTGGTA 58.882 39.130 12.41 0.00 40.61 3.25
2456 5998 4.764172 ACATTTTGCAAAGCAGTGGTAAA 58.236 34.783 12.41 0.00 40.61 2.01
2458 6000 5.821995 ACATTTTGCAAAGCAGTGGTAAAAT 59.178 32.000 12.41 7.42 40.61 1.82
2459 6001 6.989169 ACATTTTGCAAAGCAGTGGTAAAATA 59.011 30.769 12.41 0.00 40.61 1.40
2502 6044 7.810766 TTTGAGTTTAAACTTTGCACTTGAG 57.189 32.000 21.40 0.00 39.88 3.02
2515 6059 3.307691 TGCACTTGAGCTATAAGGCAACT 60.308 43.478 16.66 0.00 42.64 3.16
2532 6076 4.346129 GCAACTGATCATCCTAAAAAGCG 58.654 43.478 0.00 0.00 0.00 4.68
2544 6088 3.689649 CCTAAAAAGCGTATCAAGCCTGT 59.310 43.478 0.00 0.00 34.64 4.00
2545 6089 4.873827 CCTAAAAAGCGTATCAAGCCTGTA 59.126 41.667 0.00 0.00 34.64 2.74
2548 6092 3.444703 AAGCGTATCAAGCCTGTAGAG 57.555 47.619 0.00 0.00 34.64 2.43
2549 6093 2.656002 AGCGTATCAAGCCTGTAGAGA 58.344 47.619 0.00 0.00 34.64 3.10
2550 6094 3.024547 AGCGTATCAAGCCTGTAGAGAA 58.975 45.455 0.00 0.00 34.64 2.87
2551 6095 3.447586 AGCGTATCAAGCCTGTAGAGAAA 59.552 43.478 0.00 0.00 34.64 2.52
2552 6096 4.081642 AGCGTATCAAGCCTGTAGAGAAAA 60.082 41.667 0.00 0.00 34.64 2.29
2553 6097 4.630069 GCGTATCAAGCCTGTAGAGAAAAA 59.370 41.667 0.00 0.00 0.00 1.94
2562 6107 9.010029 CAAGCCTGTAGAGAAAAATTAAAGGTA 57.990 33.333 0.00 0.00 0.00 3.08
2579 6124 5.843019 AAGGTAGAGAAAAGATTCACCCA 57.157 39.130 0.00 0.00 38.06 4.51
2597 6142 9.620259 ATTCACCCATATTAGAGAAGAAAAGTC 57.380 33.333 0.00 0.00 0.00 3.01
2623 6168 4.766373 TCTTGATGAGGCATTACAGCAAAA 59.234 37.500 0.00 0.00 40.80 2.44
2624 6169 5.243507 TCTTGATGAGGCATTACAGCAAAAA 59.756 36.000 0.00 0.00 40.80 1.94
2636 6181 2.425312 ACAGCAAAAACGTTGTGGATGA 59.575 40.909 17.89 0.00 0.00 2.92
2649 6194 4.356405 TGTGGATGAGTGTCACAAAGAT 57.644 40.909 5.62 0.00 38.30 2.40
2659 6204 4.703575 AGTGTCACAAAGATATGCAATGCT 59.296 37.500 6.82 0.00 0.00 3.79
2677 6222 4.128925 TGCTCTGACCTAAATGCTACAG 57.871 45.455 0.00 0.00 0.00 2.74
2691 6236 1.151899 TACAGCCCTCAACCCAGGT 60.152 57.895 0.00 0.00 0.00 4.00
2704 6249 6.889722 CCTCAACCCAGGTTTAATCATCTTTA 59.110 38.462 0.00 0.00 36.00 1.85
2706 6251 8.893563 TCAACCCAGGTTTAATCATCTTTAAT 57.106 30.769 0.00 0.00 36.00 1.40
2805 6350 6.638468 GTCAATTCTGGATTGTTCAAACTGAC 59.362 38.462 8.47 0.00 44.46 3.51
2848 6393 0.463833 GGGAGCGGTTTCCATACCTG 60.464 60.000 0.00 0.00 39.09 4.00
2864 6409 5.704515 CCATACCTGATTTCCTTCTGCTATG 59.295 44.000 0.00 0.00 0.00 2.23
2865 6410 4.162040 ACCTGATTTCCTTCTGCTATGG 57.838 45.455 0.00 0.00 0.00 2.74
2867 6412 2.883386 CTGATTTCCTTCTGCTATGGCC 59.117 50.000 0.00 0.00 37.74 5.36
2892 6437 2.029073 CAGCGTGTCCCGTCAGTT 59.971 61.111 0.00 0.00 39.32 3.16
2911 6456 4.646945 CAGTTAGAGCAGAGAATAGGGTGA 59.353 45.833 0.00 0.00 0.00 4.02
2925 6470 1.587054 GGTGACGCTGTAGAGTGCT 59.413 57.895 0.00 0.00 32.44 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.183361 ACCTCCTTGTAAACTCTTCAGTCAAT 60.183 38.462 0.00 0.00 29.93 2.57
34 35 5.130477 ACCTCCTTGTAAACTCTTCAGTCAA 59.870 40.000 0.00 0.00 29.93 3.18
35 36 4.654262 ACCTCCTTGTAAACTCTTCAGTCA 59.346 41.667 0.00 0.00 29.93 3.41
46 47 1.669760 CGCGCCACCTCCTTGTAAA 60.670 57.895 0.00 0.00 0.00 2.01
47 48 2.047655 CGCGCCACCTCCTTGTAA 60.048 61.111 0.00 0.00 0.00 2.41
91 92 1.631388 TCCGCCAAACCCTAGATTGAA 59.369 47.619 0.00 0.00 0.00 2.69
137 138 1.303282 GTCGGCCCCCTCTCATTTT 59.697 57.895 0.00 0.00 0.00 1.82
181 3523 0.811616 CTGGTCGCTACTGCAATCCC 60.812 60.000 0.00 0.00 39.64 3.85
290 3632 2.090775 ACAGGAAAAGGGATGGTTTGGT 60.091 45.455 0.00 0.00 0.00 3.67
403 3745 1.126846 CACGTGCAAATCGGAGAAGAC 59.873 52.381 0.82 0.00 43.58 3.01
418 3760 6.330278 TCTTATATGAAAGAGTGGACACGTG 58.670 40.000 15.48 15.48 36.20 4.49
420 3762 6.980978 ACATCTTATATGAAAGAGTGGACACG 59.019 38.462 0.00 0.00 38.81 4.49
465 3807 3.550233 GCATGATTCTAGCAACATGGCAG 60.550 47.826 13.03 0.00 39.96 4.85
534 3876 7.090953 CAGTTCTTACTGTGGGTTTAAACAA 57.909 36.000 19.57 4.87 45.46 2.83
548 3890 7.055667 TCATGTGTTCTTCTCAGTTCTTACT 57.944 36.000 0.00 0.00 34.00 2.24
549 3891 7.148507 CCATCATGTGTTCTTCTCAGTTCTTAC 60.149 40.741 0.00 0.00 0.00 2.34
550 3892 6.875726 CCATCATGTGTTCTTCTCAGTTCTTA 59.124 38.462 0.00 0.00 0.00 2.10
551 3893 5.704515 CCATCATGTGTTCTTCTCAGTTCTT 59.295 40.000 0.00 0.00 0.00 2.52
552 3894 5.243981 CCATCATGTGTTCTTCTCAGTTCT 58.756 41.667 0.00 0.00 0.00 3.01
553 3895 4.142730 GCCATCATGTGTTCTTCTCAGTTC 60.143 45.833 0.00 0.00 0.00 3.01
554 3896 3.755378 GCCATCATGTGTTCTTCTCAGTT 59.245 43.478 0.00 0.00 0.00 3.16
555 3897 3.008813 AGCCATCATGTGTTCTTCTCAGT 59.991 43.478 0.00 0.00 0.00 3.41
556 3898 3.374367 CAGCCATCATGTGTTCTTCTCAG 59.626 47.826 0.00 0.00 0.00 3.35
557 3899 3.340928 CAGCCATCATGTGTTCTTCTCA 58.659 45.455 0.00 0.00 0.00 3.27
558 3900 2.681848 CCAGCCATCATGTGTTCTTCTC 59.318 50.000 0.00 0.00 0.00 2.87
559 3901 2.040813 ACCAGCCATCATGTGTTCTTCT 59.959 45.455 0.00 0.00 0.00 2.85
560 3902 2.440409 ACCAGCCATCATGTGTTCTTC 58.560 47.619 0.00 0.00 0.00 2.87
561 3903 2.592102 ACCAGCCATCATGTGTTCTT 57.408 45.000 0.00 0.00 0.00 2.52
562 3904 3.939740 ATACCAGCCATCATGTGTTCT 57.060 42.857 0.00 0.00 0.00 3.01
637 4136 7.020827 TGATTTCCCCAGATATAAGACATCC 57.979 40.000 0.00 0.00 0.00 3.51
674 4176 8.173542 ACAGCATTGCAAGAATATATCAATCA 57.826 30.769 11.91 0.00 0.00 2.57
678 4180 9.123902 AGTTAACAGCATTGCAAGAATATATCA 57.876 29.630 11.91 0.00 0.00 2.15
725 4227 7.614674 GACAAAAAGTCATAAACAGAAGCTG 57.385 36.000 0.00 0.00 46.77 4.24
793 4295 4.414846 AGAAGATGGGATTGCAGAAGGTAT 59.585 41.667 0.00 0.00 0.00 2.73
803 4305 5.049818 GCGAAGATTGTAGAAGATGGGATTG 60.050 44.000 0.00 0.00 0.00 2.67
814 4316 2.096335 TCGTAAGCGCGAAGATTGTAGA 59.904 45.455 12.10 0.00 37.99 2.59
829 4331 1.471676 GGAGGTGGCAGTGATCGTAAG 60.472 57.143 0.00 0.00 0.00 2.34
842 4344 1.680249 GCTGGCTAAGAAAGGAGGTGG 60.680 57.143 0.00 0.00 0.00 4.61
873 4375 2.881074 CCTCGTATCAGACAACCACAG 58.119 52.381 0.00 0.00 0.00 3.66
903 4405 2.158900 ACATAACTGAGCAGATTCGGGG 60.159 50.000 4.21 0.00 0.00 5.73
906 4408 6.414408 AAAGAACATAACTGAGCAGATTCG 57.586 37.500 4.21 0.00 0.00 3.34
907 4409 8.078596 ACAAAAAGAACATAACTGAGCAGATTC 58.921 33.333 4.21 1.03 0.00 2.52
937 4439 9.778741 ACACTATGTTTAATATGATGTACAGGG 57.221 33.333 0.33 0.00 0.00 4.45
972 4474 2.959030 ACAGGAAAAAGGAAAGACAGCC 59.041 45.455 0.00 0.00 0.00 4.85
973 4475 4.363138 CAACAGGAAAAAGGAAAGACAGC 58.637 43.478 0.00 0.00 0.00 4.40
974 4476 4.363138 GCAACAGGAAAAAGGAAAGACAG 58.637 43.478 0.00 0.00 0.00 3.51
1038 4540 2.749621 GGTCTGCTGAACGATCCATTTT 59.250 45.455 0.00 0.00 0.00 1.82
1041 4543 0.904649 TGGTCTGCTGAACGATCCAT 59.095 50.000 4.03 0.00 31.14 3.41
1051 4553 2.431954 ATGGAATCCTTGGTCTGCTG 57.568 50.000 0.00 0.00 0.00 4.41
1084 4586 7.181845 ACTCTTGAAGTCCAAATTAGGAGAGAT 59.818 37.037 0.00 0.00 38.64 2.75
1088 4590 8.722394 GTTTACTCTTGAAGTCCAAATTAGGAG 58.278 37.037 0.00 0.00 38.64 3.69
1092 4594 8.215050 TCCAGTTTACTCTTGAAGTCCAAATTA 58.785 33.333 0.00 0.00 39.55 1.40
1095 4597 5.996644 TCCAGTTTACTCTTGAAGTCCAAA 58.003 37.500 0.00 0.00 39.55 3.28
1103 4605 8.260818 CCATAAGATCTTCCAGTTTACTCTTGA 58.739 37.037 12.24 0.00 0.00 3.02
1107 4609 8.012957 TCTCCATAAGATCTTCCAGTTTACTC 57.987 38.462 12.24 0.00 0.00 2.59
1108 4610 7.979786 TCTCCATAAGATCTTCCAGTTTACT 57.020 36.000 12.24 0.00 0.00 2.24
1109 4611 9.103861 CTTTCTCCATAAGATCTTCCAGTTTAC 57.896 37.037 12.24 0.00 32.82 2.01
1110 4612 7.770897 GCTTTCTCCATAAGATCTTCCAGTTTA 59.229 37.037 12.24 0.00 32.82 2.01
1111 4613 6.601217 GCTTTCTCCATAAGATCTTCCAGTTT 59.399 38.462 12.24 0.00 32.82 2.66
1113 4615 5.397334 GGCTTTCTCCATAAGATCTTCCAGT 60.397 44.000 12.24 0.00 32.82 4.00
1114 4616 5.062528 GGCTTTCTCCATAAGATCTTCCAG 58.937 45.833 12.24 4.07 32.82 3.86
1120 4622 6.151817 ACAGTTTTGGCTTTCTCCATAAGATC 59.848 38.462 0.00 0.00 35.77 2.75
1130 4632 1.484038 TGGCACAGTTTTGGCTTTCT 58.516 45.000 0.00 0.00 42.50 2.52
1146 4648 2.361737 GCTCTTTCCCCCACTGGC 60.362 66.667 0.00 0.00 0.00 4.85
1153 4655 2.124942 CGCCTCTGCTCTTTCCCC 60.125 66.667 0.00 0.00 34.43 4.81
1154 4656 2.821810 GCGCCTCTGCTCTTTCCC 60.822 66.667 0.00 0.00 34.43 3.97
1156 4658 0.671781 TTCAGCGCCTCTGCTCTTTC 60.672 55.000 2.29 0.00 45.23 2.62
1163 4665 0.740868 TTTCGGATTCAGCGCCTCTG 60.741 55.000 2.29 1.21 44.21 3.35
1169 4671 0.521291 TTTGCCTTTCGGATTCAGCG 59.479 50.000 0.00 0.00 0.00 5.18
1185 4687 0.039256 CAACAGACCCGGCACATTTG 60.039 55.000 0.00 0.00 0.00 2.32
1186 4688 0.467290 ACAACAGACCCGGCACATTT 60.467 50.000 0.00 0.00 0.00 2.32
1187 4689 0.889186 GACAACAGACCCGGCACATT 60.889 55.000 0.00 0.00 0.00 2.71
1188 4690 1.302511 GACAACAGACCCGGCACAT 60.303 57.895 0.00 0.00 0.00 3.21
1189 4691 2.110213 GACAACAGACCCGGCACA 59.890 61.111 0.00 0.00 0.00 4.57
1191 4693 2.709125 CTTCGACAACAGACCCGGCA 62.709 60.000 0.00 0.00 0.00 5.69
1192 4694 2.027625 CTTCGACAACAGACCCGGC 61.028 63.158 0.00 0.00 0.00 6.13
1194 4696 2.030540 TCTAACTTCGACAACAGACCCG 60.031 50.000 0.00 0.00 0.00 5.28
1197 4699 5.050972 CCTTGTTCTAACTTCGACAACAGAC 60.051 44.000 0.00 0.00 0.00 3.51
1206 4708 5.073311 TGATCTCCCTTGTTCTAACTTCG 57.927 43.478 0.00 0.00 0.00 3.79
1208 4710 8.997734 AGATAATGATCTCCCTTGTTCTAACTT 58.002 33.333 0.00 0.00 38.01 2.66
1214 4716 9.784531 TTGATAAGATAATGATCTCCCTTGTTC 57.215 33.333 0.00 0.00 41.87 3.18
1216 4718 8.943085 ACTTGATAAGATAATGATCTCCCTTGT 58.057 33.333 0.00 0.00 41.87 3.16
1217 4719 9.217278 CACTTGATAAGATAATGATCTCCCTTG 57.783 37.037 0.00 0.00 41.87 3.61
1219 4721 7.393216 GCACTTGATAAGATAATGATCTCCCT 58.607 38.462 0.00 0.00 41.87 4.20
1220 4722 6.597280 GGCACTTGATAAGATAATGATCTCCC 59.403 42.308 0.00 0.00 41.87 4.30
1221 4723 6.597280 GGGCACTTGATAAGATAATGATCTCC 59.403 42.308 0.00 0.00 41.87 3.71
1224 4726 7.828223 AGATGGGCACTTGATAAGATAATGATC 59.172 37.037 0.00 0.00 0.00 2.92
1229 4731 6.499106 TGAGATGGGCACTTGATAAGATAA 57.501 37.500 0.00 0.00 0.00 1.75
1230 4732 6.470278 CATGAGATGGGCACTTGATAAGATA 58.530 40.000 0.00 0.00 0.00 1.98
1234 4736 3.824133 CCATGAGATGGGCACTTGATAA 58.176 45.455 0.00 0.00 46.86 1.75
1254 4756 3.664107 TGAAACTGTGTAGACATGCTCC 58.336 45.455 0.00 0.00 0.00 4.70
1265 4767 5.476945 ACAGAAAGAGGTTTTGAAACTGTGT 59.523 36.000 6.57 0.00 38.89 3.72
1278 4780 2.484889 GCAAGACGAACAGAAAGAGGT 58.515 47.619 0.00 0.00 0.00 3.85
1281 4783 2.613026 TGGCAAGACGAACAGAAAGA 57.387 45.000 0.00 0.00 0.00 2.52
1282 4784 3.691049 TTTGGCAAGACGAACAGAAAG 57.309 42.857 0.00 0.00 0.00 2.62
1287 4789 1.088306 ACGTTTTGGCAAGACGAACA 58.912 45.000 38.78 5.86 39.85 3.18
1294 4796 5.704888 TGTATGGAAATACGTTTTGGCAAG 58.295 37.500 0.00 0.00 0.00 4.01
1295 4797 5.473846 TCTGTATGGAAATACGTTTTGGCAA 59.526 36.000 0.00 0.00 0.00 4.52
1296 4798 5.004448 TCTGTATGGAAATACGTTTTGGCA 58.996 37.500 0.00 0.00 0.00 4.92
1302 4804 6.235231 AGGACATCTGTATGGAAATACGTT 57.765 37.500 0.00 0.00 37.43 3.99
1312 4814 4.393062 GTGGTCACAAAGGACATCTGTATG 59.607 45.833 0.00 0.00 39.59 2.39
1323 4825 3.703001 ACCTCATAGTGGTCACAAAGG 57.297 47.619 3.82 6.69 31.03 3.11
1329 4831 5.542635 ACTGAAACTAACCTCATAGTGGTCA 59.457 40.000 0.00 0.00 36.28 4.02
1332 4834 5.103000 CGACTGAAACTAACCTCATAGTGG 58.897 45.833 0.00 0.00 36.28 4.00
1354 4856 0.321210 TGTGTATGTTGCCCAGGTCG 60.321 55.000 0.00 0.00 0.00 4.79
1355 4857 2.128771 ATGTGTATGTTGCCCAGGTC 57.871 50.000 0.00 0.00 0.00 3.85
1376 4878 4.775236 AGCTGAGGCATACTTCCTTTTAG 58.225 43.478 0.00 0.00 41.70 1.85
1378 4880 3.728385 AGCTGAGGCATACTTCCTTTT 57.272 42.857 0.00 0.00 41.70 2.27
1384 4886 6.488006 CCAATAATTGTAGCTGAGGCATACTT 59.512 38.462 0.00 0.00 41.70 2.24
1391 4893 6.233434 TCTATGCCAATAATTGTAGCTGAGG 58.767 40.000 0.00 0.00 0.00 3.86
1393 4895 7.720957 ACAATCTATGCCAATAATTGTAGCTGA 59.279 33.333 0.00 0.00 38.43 4.26
1446 4948 2.370281 TCTTCAGATTCACTCGTGGC 57.630 50.000 0.00 0.00 0.00 5.01
1459 4961 4.629200 GCAGTCACTATCCAAGTTCTTCAG 59.371 45.833 0.00 0.00 35.76 3.02
1461 4963 4.569943 TGCAGTCACTATCCAAGTTCTTC 58.430 43.478 0.00 0.00 35.76 2.87
1463 4965 3.618507 GCTGCAGTCACTATCCAAGTTCT 60.619 47.826 16.64 0.00 35.76 3.01
1472 4974 0.459237 GCTGACGCTGCAGTCACTAT 60.459 55.000 16.64 0.00 45.18 2.12
1473 4975 1.080501 GCTGACGCTGCAGTCACTA 60.081 57.895 16.64 0.00 45.18 2.74
1477 4979 2.435586 ATGGCTGACGCTGCAGTC 60.436 61.111 16.64 7.40 40.82 3.51
1479 4981 3.200593 GGATGGCTGACGCTGCAG 61.201 66.667 10.11 10.11 38.91 4.41
1484 4986 1.965754 AAGAGGAGGATGGCTGACGC 61.966 60.000 0.00 0.00 0.00 5.19
1485 4987 1.067821 GTAAGAGGAGGATGGCTGACG 59.932 57.143 0.00 0.00 0.00 4.35
1487 4989 1.292242 AGGTAAGAGGAGGATGGCTGA 59.708 52.381 0.00 0.00 0.00 4.26
1490 4992 2.103941 CTGAAGGTAAGAGGAGGATGGC 59.896 54.545 0.00 0.00 0.00 4.40
1491 4993 3.379452 ACTGAAGGTAAGAGGAGGATGG 58.621 50.000 0.00 0.00 0.00 3.51
1520 5022 2.880268 CACTCATCAAGTTGCACAGGAA 59.120 45.455 0.00 0.00 35.45 3.36
1524 5026 6.403527 GCATAATACACTCATCAAGTTGCACA 60.404 38.462 0.00 0.00 35.34 4.57
1543 5045 1.212935 AGGAGGCCACGAAAGCATAAT 59.787 47.619 5.01 0.00 0.00 1.28
1551 5053 1.152860 TTGCAAAGGAGGCCACGAA 60.153 52.632 5.01 0.00 0.00 3.85
1563 5065 1.380403 CCACAGTCCGGTGTTGCAAA 61.380 55.000 0.00 0.00 37.06 3.68
1569 5071 1.202722 CCTTTAACCACAGTCCGGTGT 60.203 52.381 0.00 0.00 36.67 4.16
1587 5089 7.119846 GCTCTTGAAATGTGACAAATACTACCT 59.880 37.037 0.00 0.00 0.00 3.08
1596 5098 4.454678 AGAGTGCTCTTGAAATGTGACAA 58.545 39.130 0.00 0.00 36.31 3.18
1605 5107 7.840931 TCACTAAATCATAGAGTGCTCTTGAA 58.159 34.615 7.05 0.00 40.35 2.69
1606 5108 7.410120 TCACTAAATCATAGAGTGCTCTTGA 57.590 36.000 7.05 10.63 40.35 3.02
1607 5109 7.978414 TCTTCACTAAATCATAGAGTGCTCTTG 59.022 37.037 7.05 6.15 40.35 3.02
1633 5135 1.687996 CCCAACAGGGTTGTCCAACTT 60.688 52.381 9.79 0.00 40.94 2.66
1664 5166 1.398390 CGATTGTTACTTGCAGGAGCC 59.602 52.381 1.40 0.00 41.13 4.70
1665 5167 1.202076 GCGATTGTTACTTGCAGGAGC 60.202 52.381 1.40 0.00 42.57 4.70
1669 5171 1.726791 ACTCGCGATTGTTACTTGCAG 59.273 47.619 10.36 0.00 0.00 4.41
1679 5181 0.179225 CCCGTTTTCACTCGCGATTG 60.179 55.000 19.35 19.35 0.00 2.67
1680 5182 0.320073 TCCCGTTTTCACTCGCGATT 60.320 50.000 10.36 0.00 0.00 3.34
1716 5218 1.283321 ACCTTTCCTCTTCCATCCAGC 59.717 52.381 0.00 0.00 0.00 4.85
1717 5219 2.573462 TGACCTTTCCTCTTCCATCCAG 59.427 50.000 0.00 0.00 0.00 3.86
1725 5227 4.293368 AGGATTCCAATGACCTTTCCTCTT 59.707 41.667 5.29 0.00 0.00 2.85
1728 5230 4.540099 TGTAGGATTCCAATGACCTTTCCT 59.460 41.667 5.29 0.00 36.21 3.36
1734 5236 4.437682 TCCATGTAGGATTCCAATGACC 57.562 45.455 5.29 0.00 43.07 4.02
1767 5269 5.006386 AGCTTGACAAAGTAAGAGAATGGG 58.994 41.667 0.00 0.00 35.69 4.00
1786 5288 2.094182 ACGGTATGATGTGACGAAGCTT 60.094 45.455 0.00 0.00 0.00 3.74
1787 5289 1.476891 ACGGTATGATGTGACGAAGCT 59.523 47.619 0.00 0.00 0.00 3.74
1791 5293 2.097036 AGGAACGGTATGATGTGACGA 58.903 47.619 0.00 0.00 0.00 4.20
1796 5298 3.973206 TTGTCAGGAACGGTATGATGT 57.027 42.857 0.00 0.00 0.00 3.06
1800 5302 4.379394 CCATGTTTTGTCAGGAACGGTATG 60.379 45.833 0.00 0.00 0.00 2.39
1801 5303 3.756434 CCATGTTTTGTCAGGAACGGTAT 59.244 43.478 0.00 0.00 0.00 2.73
1829 5331 4.671880 AAATGTGATAACTTACGCGCAA 57.328 36.364 5.73 0.00 0.00 4.85
1831 5333 4.849383 ACAAAAATGTGATAACTTACGCGC 59.151 37.500 5.73 0.00 0.00 6.86
1890 5392 6.832520 ATTATGCACAGGTTATTGTCAACA 57.167 33.333 0.00 0.00 0.00 3.33
1891 5393 9.450807 GAATATTATGCACAGGTTATTGTCAAC 57.549 33.333 0.00 0.00 0.00 3.18
1922 5424 3.392285 TCATGGATGGATCACTAACCCTG 59.608 47.826 0.00 0.00 0.00 4.45
1923 5425 3.668821 TCATGGATGGATCACTAACCCT 58.331 45.455 0.00 0.00 0.00 4.34
1932 5434 5.768662 ACACAGAAATGATCATGGATGGATC 59.231 40.000 9.46 0.00 41.20 3.36
1935 5437 6.293698 TCTACACAGAAATGATCATGGATGG 58.706 40.000 9.46 1.26 0.00 3.51
1936 5438 6.427242 CCTCTACACAGAAATGATCATGGATG 59.573 42.308 9.46 10.41 0.00 3.51
1937 5439 6.328410 TCCTCTACACAGAAATGATCATGGAT 59.672 38.462 9.46 0.00 0.00 3.41
1944 5446 5.181748 GCAAGTCCTCTACACAGAAATGAT 58.818 41.667 0.00 0.00 0.00 2.45
1950 5452 1.895798 CTGGCAAGTCCTCTACACAGA 59.104 52.381 0.00 0.00 35.26 3.41
1964 5466 2.355716 GCAATAGTAGTGGACCTGGCAA 60.356 50.000 0.00 0.00 0.00 4.52
1970 5472 4.161754 ACTTACCAGCAATAGTAGTGGACC 59.838 45.833 0.00 0.00 33.95 4.46
1971 5473 5.340439 ACTTACCAGCAATAGTAGTGGAC 57.660 43.478 0.00 0.00 33.95 4.02
1972 5474 7.201974 GGATAACTTACCAGCAATAGTAGTGGA 60.202 40.741 0.00 0.00 33.95 4.02
1978 5480 6.900194 ACATGGATAACTTACCAGCAATAGT 58.100 36.000 0.00 0.00 39.62 2.12
1985 5487 8.649973 GTAAGAAGACATGGATAACTTACCAG 57.350 38.462 14.86 0.00 39.62 4.00
2000 5502 2.642311 TGGATTGCAGGGTAAGAAGACA 59.358 45.455 0.00 0.00 0.00 3.41
2010 5512 1.033746 AAGCGTGATGGATTGCAGGG 61.034 55.000 0.00 0.00 0.00 4.45
2011 5513 1.331756 GTAAGCGTGATGGATTGCAGG 59.668 52.381 0.00 0.00 0.00 4.85
2012 5514 2.009051 TGTAAGCGTGATGGATTGCAG 58.991 47.619 0.00 0.00 0.00 4.41
2013 5515 2.106477 TGTAAGCGTGATGGATTGCA 57.894 45.000 0.00 0.00 0.00 4.08
2014 5516 2.355756 ACATGTAAGCGTGATGGATTGC 59.644 45.455 0.00 0.00 35.65 3.56
2015 5517 3.242837 CCACATGTAAGCGTGATGGATTG 60.243 47.826 0.00 0.00 36.13 2.67
2016 5518 2.945008 CCACATGTAAGCGTGATGGATT 59.055 45.455 0.00 0.00 36.13 3.01
2021 5525 2.483714 CCTAGCCACATGTAAGCGTGAT 60.484 50.000 12.85 0.90 35.02 3.06
2053 5557 7.440523 ACAACATAAGGAAAGAGCAAACTAG 57.559 36.000 0.00 0.00 0.00 2.57
2057 5561 9.474920 CAATTAACAACATAAGGAAAGAGCAAA 57.525 29.630 0.00 0.00 0.00 3.68
2058 5562 8.087750 CCAATTAACAACATAAGGAAAGAGCAA 58.912 33.333 0.00 0.00 0.00 3.91
2059 5563 7.232534 ACCAATTAACAACATAAGGAAAGAGCA 59.767 33.333 0.00 0.00 0.00 4.26
2060 5564 7.542130 CACCAATTAACAACATAAGGAAAGAGC 59.458 37.037 0.00 0.00 0.00 4.09
2062 5566 7.507616 ACCACCAATTAACAACATAAGGAAAGA 59.492 33.333 0.00 0.00 0.00 2.52
2063 5567 7.598493 CACCACCAATTAACAACATAAGGAAAG 59.402 37.037 0.00 0.00 0.00 2.62
2064 5568 7.070074 ACACCACCAATTAACAACATAAGGAAA 59.930 33.333 0.00 0.00 0.00 3.13
2065 5569 6.551601 ACACCACCAATTAACAACATAAGGAA 59.448 34.615 0.00 0.00 0.00 3.36
2066 5570 6.071984 ACACCACCAATTAACAACATAAGGA 58.928 36.000 0.00 0.00 0.00 3.36
2067 5571 6.339587 ACACCACCAATTAACAACATAAGG 57.660 37.500 0.00 0.00 0.00 2.69
2161 5699 0.184933 TCCCCTCAAACACAAGGTGG 59.815 55.000 1.07 0.00 37.94 4.61
2162 5700 1.681264 GTTCCCCTCAAACACAAGGTG 59.319 52.381 0.00 0.00 39.75 4.00
2196 5734 2.093816 CAGTTCTAGTCCATCTGCAGCA 60.094 50.000 9.47 0.00 0.00 4.41
2233 5771 6.587990 CCATTACTCTATGTTGGATGATCGAC 59.412 42.308 0.00 0.00 30.06 4.20
2273 5811 4.518970 TGTCAGCTTTCAAGGGAACATAAC 59.481 41.667 0.00 0.00 31.35 1.89
2274 5812 4.724399 TGTCAGCTTTCAAGGGAACATAA 58.276 39.130 0.00 0.00 31.35 1.90
2275 5813 4.365514 TGTCAGCTTTCAAGGGAACATA 57.634 40.909 0.00 0.00 31.35 2.29
2287 5825 1.073025 TCACCGCCATGTCAGCTTT 59.927 52.632 0.00 0.00 0.00 3.51
2295 5833 5.868801 AGAAATTTATTTTGTCACCGCCATG 59.131 36.000 0.00 0.00 0.00 3.66
2314 5854 8.526667 TCACTCTGAGCTGTATAGTAAGAAAT 57.473 34.615 4.19 0.00 0.00 2.17
2398 5938 0.109781 CAACAATGTACCCGTGCTGC 60.110 55.000 0.00 0.00 0.00 5.25
2417 5957 4.568152 AATGTTGTGTAGAACTGGCAAC 57.432 40.909 0.00 0.00 39.62 4.17
2427 5967 4.805192 ACTGCTTTGCAAAATGTTGTGTAG 59.195 37.500 13.84 10.52 38.41 2.74
2434 5974 2.985957 ACCACTGCTTTGCAAAATGT 57.014 40.000 13.84 9.14 38.41 2.71
2458 6000 9.485206 ACTCAAAAAGTTCTACGCTAAAGAATA 57.515 29.630 0.00 0.00 35.53 1.75
2459 6001 8.379457 ACTCAAAAAGTTCTACGCTAAAGAAT 57.621 30.769 0.00 0.00 35.53 2.40
2491 6033 3.684908 TGCCTTATAGCTCAAGTGCAAA 58.315 40.909 15.51 2.20 31.01 3.68
2497 6039 5.363101 TGATCAGTTGCCTTATAGCTCAAG 58.637 41.667 0.00 0.00 0.00 3.02
2502 6044 4.904241 AGGATGATCAGTTGCCTTATAGC 58.096 43.478 0.09 0.00 0.00 2.97
2515 6059 6.017934 GCTTGATACGCTTTTTAGGATGATCA 60.018 38.462 0.00 0.00 0.00 2.92
2519 6063 4.576463 AGGCTTGATACGCTTTTTAGGATG 59.424 41.667 0.00 0.00 0.00 3.51
2528 6072 3.024547 TCTCTACAGGCTTGATACGCTT 58.975 45.455 1.40 0.00 0.00 4.68
2552 6096 9.244292 GGGTGAATCTTTTCTCTACCTTTAATT 57.756 33.333 0.00 0.00 30.09 1.40
2553 6097 8.390921 TGGGTGAATCTTTTCTCTACCTTTAAT 58.609 33.333 0.00 0.00 30.09 1.40
2562 6107 9.218525 TCTCTAATATGGGTGAATCTTTTCTCT 57.781 33.333 0.00 0.00 32.78 3.10
2587 6132 5.106752 GCCTCATCAAGAGTGACTTTTCTTC 60.107 44.000 0.00 0.00 43.12 2.87
2597 6142 3.311871 GCTGTAATGCCTCATCAAGAGTG 59.688 47.826 0.00 0.00 43.12 3.51
2623 6168 2.210116 GTGACACTCATCCACAACGTT 58.790 47.619 0.00 0.00 0.00 3.99
2624 6169 1.138069 TGTGACACTCATCCACAACGT 59.862 47.619 7.20 0.00 37.80 3.99
2636 6181 4.703575 AGCATTGCATATCTTTGTGACACT 59.296 37.500 11.91 0.00 0.00 3.55
2649 6194 4.276678 GCATTTAGGTCAGAGCATTGCATA 59.723 41.667 11.91 0.00 0.00 3.14
2659 6204 2.170607 GGGCTGTAGCATTTAGGTCAGA 59.829 50.000 6.18 0.00 44.36 3.27
2677 6222 2.100197 GATTAAACCTGGGTTGAGGGC 58.900 52.381 7.38 0.00 38.47 5.19
2771 6316 7.636150 ACAATCCAGAATTGACTTCCTAATG 57.364 36.000 4.86 0.00 46.54 1.90
2777 6322 7.380602 CAGTTTGAACAATCCAGAATTGACTTC 59.619 37.037 4.86 0.80 46.54 3.01
2789 6334 7.672983 TCTCTAATGTCAGTTTGAACAATCC 57.327 36.000 0.00 0.00 0.00 3.01
2805 6350 8.313292 CCCTCTTCCTCATCTTTATCTCTAATG 58.687 40.741 0.00 0.00 0.00 1.90
2848 6393 2.234143 GGGCCATAGCAGAAGGAAATC 58.766 52.381 4.39 0.00 42.56 2.17
2864 6409 3.443045 CACGCTGTCAATGGGGCC 61.443 66.667 0.00 0.00 0.00 5.80
2865 6410 2.672996 ACACGCTGTCAATGGGGC 60.673 61.111 0.00 0.00 0.00 5.80
2883 6428 1.464734 TCTCTGCTCTAACTGACGGG 58.535 55.000 0.00 0.00 0.00 5.28
2892 6437 3.215151 CGTCACCCTATTCTCTGCTCTA 58.785 50.000 0.00 0.00 0.00 2.43
2911 6456 0.898320 ATCCAAGCACTCTACAGCGT 59.102 50.000 0.00 0.00 35.48 5.07


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

AutoCloner maintained by Alex Coulton.