Multiple sequence alignment - TraesCS6A01G358500

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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 TraesCS6A01G358500 chr6A 100.000 5602 0 0 1 5602 588464654 588459053 0.000000e+00 10346.0
1 TraesCS6A01G358500 chr6D 91.977 3889 171 45 1292 5134 440371355 440367562 0.000000e+00 5323.0
2 TraesCS6A01G358500 chr6D 93.043 575 23 5 1 574 440372522 440371964 0.000000e+00 824.0
3 TraesCS6A01G358500 chr6D 92.553 564 34 6 718 1275 440371964 440371403 0.000000e+00 802.0
4 TraesCS6A01G358500 chr6D 91.509 212 17 1 5392 5602 440367379 440367168 1.970000e-74 291.0
5 TraesCS6A01G358500 chr6D 88.235 170 9 6 5175 5337 440367561 440367396 5.730000e-45 193.0
6 TraesCS6A01G358500 chr6B 92.512 3018 162 35 2350 5337 665514652 665511669 0.000000e+00 4263.0
7 TraesCS6A01G358500 chr6B 90.753 1568 93 21 816 2345 665516305 665514752 0.000000e+00 2045.0
8 TraesCS6A01G358500 chr6B 86.580 462 39 14 119 560 665516878 665516420 6.520000e-134 488.0
9 TraesCS6A01G358500 chr6B 91.981 212 16 1 5392 5602 665511652 665511441 4.240000e-76 296.0
10 TraesCS6A01G358500 chr3D 86.743 2874 245 60 1820 4603 346821621 346824448 0.000000e+00 3072.0
11 TraesCS6A01G358500 chr3D 83.916 143 8 8 1647 1789 346821521 346821648 7.620000e-24 122.0
12 TraesCS6A01G358500 chr3A 85.437 1133 92 16 2887 3993 456908541 456907456 0.000000e+00 1110.0
13 TraesCS6A01G358500 chr3A 84.300 1121 118 29 1820 2902 456909803 456908703 0.000000e+00 1042.0
14 TraesCS6A01G358500 chr3A 84.180 512 64 11 1277 1787 456910273 456909778 1.090000e-131 481.0
15 TraesCS6A01G358500 chr4A 76.662 647 112 23 3990 4625 356603638 356603020 7.000000e-84 322.0
16 TraesCS6A01G358500 chr4D 82.123 358 40 12 1920 2263 273541056 273541403 9.190000e-73 285.0
17 TraesCS6A01G358500 chr5D 88.889 54 4 2 1895 1947 143205918 143205970 1.300000e-06 65.8


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 TraesCS6A01G358500 chr6A 588459053 588464654 5601 True 10346.000000 10346 100.0000 1 5602 1 chr6A.!!$R1 5601
1 TraesCS6A01G358500 chr6D 440367168 440372522 5354 True 1486.600000 5323 91.4634 1 5602 5 chr6D.!!$R1 5601
2 TraesCS6A01G358500 chr6B 665511441 665516878 5437 True 1773.000000 4263 90.4565 119 5602 4 chr6B.!!$R1 5483
3 TraesCS6A01G358500 chr3D 346821521 346824448 2927 False 1597.000000 3072 85.3295 1647 4603 2 chr3D.!!$F1 2956
4 TraesCS6A01G358500 chr3A 456907456 456910273 2817 True 877.666667 1110 84.6390 1277 3993 3 chr3A.!!$R1 2716
5 TraesCS6A01G358500 chr4A 356603020 356603638 618 True 322.000000 322 76.6620 3990 4625 1 chr4A.!!$R1 635

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
584 604 0.242017 ATTTTTCACGCTGCTGCTCC 59.758 50.000 14.03 0.0 36.97 4.70 F
1022 1046 0.036388 GTGGCCATGAAGACGAAGGA 60.036 55.000 9.72 0.0 0.00 3.36 F
1154 1178 0.180406 CCCAGGTACTACCATGCCAC 59.820 60.000 8.01 0.0 41.95 5.01 F
1711 1782 1.067516 AGCATTGCAGGTTTGTGACAC 59.932 47.619 11.91 0.0 0.00 3.67 F
2551 2782 0.623723 TATTCAGTCAACAGGCCCCC 59.376 55.000 0.00 0.0 0.00 5.40 F
3200 3650 3.009723 ACTGTCCCATGCGTTCTTATTG 58.990 45.455 0.00 0.0 0.00 1.90 F
4364 4847 4.627467 CAGTTTTTGAGACCGGTGAGATAG 59.373 45.833 14.63 0.0 0.00 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1711 0.521735 GCAAGCACCTTACTTTCCGG 59.478 55.000 0.00 0.00 0.00 5.14 R
2176 2250 0.804989 GGAGACAGAAATGGTTGCCG 59.195 55.000 0.00 0.00 0.00 5.69 R
2270 2377 1.001924 TGCGGCACACAAACAATACTG 60.002 47.619 0.00 0.00 0.00 2.74 R
3200 3650 5.645497 ACAGATCTGAAATAACAGCAAGGAC 59.355 40.000 29.27 0.00 37.75 3.85 R
4515 5007 0.320374 TTCGATGCTTCTGGTTCCGT 59.680 50.000 0.00 0.00 0.00 4.69 R
4561 5054 0.179004 TCTTTTCAAAGCTCCCGGCA 60.179 50.000 0.00 0.00 44.79 5.69 R
5222 5725 0.038892 ATGCTGTTTCAGGCGCTTTG 60.039 50.000 7.64 6.75 31.21 2.77 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
36 37 7.065923 GGGATTGGACAGTTTAAAGACATAGAC 59.934 40.741 0.00 0.00 0.00 2.59
82 83 8.361139 TGCTTAGATAAGTCTTGCTCCTTATAC 58.639 37.037 0.00 0.00 34.77 1.47
91 92 6.544928 TCTTGCTCCTTATACAAGACATGA 57.455 37.500 0.00 0.00 43.55 3.07
95 96 5.422012 TGCTCCTTATACAAGACATGAGTGA 59.578 40.000 0.00 0.00 33.20 3.41
209 210 4.714802 TGAGAATCGATCCTGTTAAGGGAA 59.285 41.667 0.00 0.00 40.79 3.97
210 211 5.366768 TGAGAATCGATCCTGTTAAGGGAAT 59.633 40.000 0.00 0.00 40.79 3.01
231 232 6.350194 GGAATACCCAAGGAATTGACTGAAAC 60.350 42.308 0.00 0.00 34.14 2.78
273 275 6.494835 ACTTCTTCTAAACCATTGAATTGCCT 59.505 34.615 0.00 0.00 0.00 4.75
275 277 6.248433 TCTTCTAAACCATTGAATTGCCTCT 58.752 36.000 0.00 0.00 0.00 3.69
296 299 4.220821 TCTGCAAGATTTCTCGTAGTCCTT 59.779 41.667 0.00 0.00 38.67 3.36
317 320 2.341846 TCTTGAACTCGGGCACTTTT 57.658 45.000 0.00 0.00 0.00 2.27
447 467 7.148689 GGTTACAAAATTGTCCGACTACTACAG 60.149 40.741 1.37 0.00 42.35 2.74
563 583 3.747099 ACGTGCATGTTGAGCTATTTC 57.253 42.857 5.51 0.00 0.00 2.17
574 594 9.003112 CATGTTGAGCTATTTCTATTTTTCACG 57.997 33.333 0.00 0.00 0.00 4.35
575 595 7.021196 TGTTGAGCTATTTCTATTTTTCACGC 58.979 34.615 0.00 0.00 0.00 5.34
576 596 6.985188 TGAGCTATTTCTATTTTTCACGCT 57.015 33.333 0.00 0.00 0.00 5.07
577 597 6.775088 TGAGCTATTTCTATTTTTCACGCTG 58.225 36.000 0.00 0.00 0.00 5.18
578 598 5.573146 AGCTATTTCTATTTTTCACGCTGC 58.427 37.500 0.00 0.00 0.00 5.25
579 599 5.355350 AGCTATTTCTATTTTTCACGCTGCT 59.645 36.000 0.00 0.00 0.00 4.24
580 600 5.453587 GCTATTTCTATTTTTCACGCTGCTG 59.546 40.000 0.00 0.00 0.00 4.41
581 601 2.900122 TCTATTTTTCACGCTGCTGC 57.100 45.000 5.34 5.34 0.00 5.25
582 602 2.426522 TCTATTTTTCACGCTGCTGCT 58.573 42.857 14.03 0.00 36.97 4.24
583 603 2.416547 TCTATTTTTCACGCTGCTGCTC 59.583 45.455 14.03 0.00 36.97 4.26
584 604 0.242017 ATTTTTCACGCTGCTGCTCC 59.758 50.000 14.03 0.00 36.97 4.70
585 605 1.795170 TTTTTCACGCTGCTGCTCCC 61.795 55.000 14.03 0.00 36.97 4.30
586 606 4.704833 TTCACGCTGCTGCTCCCC 62.705 66.667 14.03 0.00 36.97 4.81
603 623 4.493747 CGTCGCCCTCCTTCGGTC 62.494 72.222 0.00 0.00 0.00 4.79
604 624 4.144703 GTCGCCCTCCTTCGGTCC 62.145 72.222 0.00 0.00 0.00 4.46
607 627 4.144703 GCCCTCCTTCGGTCCGTC 62.145 72.222 11.88 0.00 0.00 4.79
608 628 3.823330 CCCTCCTTCGGTCCGTCG 61.823 72.222 11.88 3.39 0.00 5.12
609 629 4.493747 CCTCCTTCGGTCCGTCGC 62.494 72.222 11.88 0.00 0.00 5.19
610 630 4.493747 CTCCTTCGGTCCGTCGCC 62.494 72.222 11.88 0.00 0.00 5.54
612 632 4.796231 CCTTCGGTCCGTCGCCTG 62.796 72.222 11.88 0.00 0.00 4.85
613 633 4.052229 CTTCGGTCCGTCGCCTGT 62.052 66.667 11.88 0.00 0.00 4.00
614 634 3.966026 CTTCGGTCCGTCGCCTGTC 62.966 68.421 11.88 0.00 0.00 3.51
621 641 4.717629 CGTCGCCTGTCGCCAAGA 62.718 66.667 0.00 0.00 38.27 3.02
622 642 2.125512 GTCGCCTGTCGCCAAGAT 60.126 61.111 0.00 0.00 38.27 2.40
623 643 2.167861 GTCGCCTGTCGCCAAGATC 61.168 63.158 0.00 0.00 38.27 2.75
624 644 2.892425 CGCCTGTCGCCAAGATCC 60.892 66.667 0.00 0.00 0.00 3.36
625 645 2.892425 GCCTGTCGCCAAGATCCG 60.892 66.667 0.00 0.00 0.00 4.18
626 646 2.892425 CCTGTCGCCAAGATCCGC 60.892 66.667 0.00 0.00 0.00 5.54
627 647 2.125552 CTGTCGCCAAGATCCGCA 60.126 61.111 0.00 0.00 0.00 5.69
628 648 1.741401 CTGTCGCCAAGATCCGCAA 60.741 57.895 0.00 0.00 0.00 4.85
629 649 1.078497 TGTCGCCAAGATCCGCAAT 60.078 52.632 0.00 0.00 0.00 3.56
630 650 1.089481 TGTCGCCAAGATCCGCAATC 61.089 55.000 0.00 0.00 34.30 2.67
631 651 1.089481 GTCGCCAAGATCCGCAATCA 61.089 55.000 0.00 0.00 36.79 2.57
632 652 1.089481 TCGCCAAGATCCGCAATCAC 61.089 55.000 0.00 0.00 36.79 3.06
633 653 1.091771 CGCCAAGATCCGCAATCACT 61.092 55.000 0.00 0.00 36.79 3.41
634 654 0.659957 GCCAAGATCCGCAATCACTC 59.340 55.000 0.00 0.00 36.79 3.51
635 655 0.933097 CCAAGATCCGCAATCACTCG 59.067 55.000 0.00 0.00 36.79 4.18
636 656 0.302890 CAAGATCCGCAATCACTCGC 59.697 55.000 0.00 0.00 36.79 5.03
679 699 4.778143 GCGGCGTGGTTCCATCCT 62.778 66.667 9.37 0.00 0.00 3.24
680 700 2.511600 CGGCGTGGTTCCATCCTC 60.512 66.667 0.00 0.00 0.00 3.71
681 701 2.124695 GGCGTGGTTCCATCCTCC 60.125 66.667 0.00 0.00 0.00 4.30
682 702 2.124695 GCGTGGTTCCATCCTCCC 60.125 66.667 0.00 0.00 0.00 4.30
683 703 2.966732 GCGTGGTTCCATCCTCCCA 61.967 63.158 0.00 0.00 0.00 4.37
684 704 1.078426 CGTGGTTCCATCCTCCCAC 60.078 63.158 0.00 0.00 43.13 4.61
685 705 1.078426 GTGGTTCCATCCTCCCACG 60.078 63.158 0.00 0.00 38.14 4.94
686 706 2.124695 GGTTCCATCCTCCCACGC 60.125 66.667 0.00 0.00 0.00 5.34
687 707 2.124695 GTTCCATCCTCCCACGCC 60.125 66.667 0.00 0.00 0.00 5.68
688 708 3.781307 TTCCATCCTCCCACGCCG 61.781 66.667 0.00 0.00 0.00 6.46
691 711 4.530857 CATCCTCCCACGCCGGTC 62.531 72.222 1.90 0.00 0.00 4.79
710 730 3.522731 CCGGTCGCCTCTCTCCTG 61.523 72.222 0.00 0.00 0.00 3.86
711 731 4.200283 CGGTCGCCTCTCTCCTGC 62.200 72.222 0.00 0.00 0.00 4.85
712 732 3.844090 GGTCGCCTCTCTCCTGCC 61.844 72.222 0.00 0.00 0.00 4.85
713 733 3.071206 GTCGCCTCTCTCCTGCCA 61.071 66.667 0.00 0.00 0.00 4.92
714 734 2.042537 TCGCCTCTCTCCTGCCAT 60.043 61.111 0.00 0.00 0.00 4.40
766 786 1.831652 CGGCTCTTCAACCTCCACCT 61.832 60.000 0.00 0.00 0.00 4.00
943 967 0.636932 TCCCTTCCCTCCTCCCCTAT 60.637 60.000 0.00 0.00 0.00 2.57
954 978 3.996124 CCCCTATCGCCGCTCCTG 61.996 72.222 0.00 0.00 0.00 3.86
1022 1046 0.036388 GTGGCCATGAAGACGAAGGA 60.036 55.000 9.72 0.00 0.00 3.36
1143 1167 3.834799 CGCCTCGACCCCAGGTAC 61.835 72.222 0.00 0.00 35.25 3.34
1150 1174 0.750850 CGACCCCAGGTACTACCATG 59.249 60.000 8.01 3.44 41.95 3.66
1154 1178 0.180406 CCCAGGTACTACCATGCCAC 59.820 60.000 8.01 0.00 41.95 5.01
1163 1187 1.505151 TACCATGCCACACCCCATGT 61.505 55.000 0.00 0.00 44.81 3.21
1165 1189 2.053865 CATGCCACACCCCATGTCC 61.054 63.158 0.00 0.00 40.64 4.02
1170 1194 3.249189 ACACCCCATGTCCGTGCT 61.249 61.111 4.47 0.00 36.54 4.40
1182 1206 1.128692 GTCCGTGCTGTGCAGTATTTC 59.871 52.381 0.00 0.00 40.08 2.17
1211 1236 3.777478 CAATGGCCTGCTGAATTTGTAG 58.223 45.455 3.32 0.00 0.00 2.74
1216 1241 2.440409 CCTGCTGAATTTGTAGTGCCT 58.560 47.619 0.00 0.00 0.00 4.75
1232 1257 3.817647 AGTGCCTGAGTCTTCAATTTGAC 59.182 43.478 0.00 0.00 31.69 3.18
1235 1264 4.036734 TGCCTGAGTCTTCAATTTGACAAC 59.963 41.667 0.00 0.79 35.81 3.32
1285 1342 4.081198 AGCTTCTTGTGCTGCTACTAGAAT 60.081 41.667 19.75 10.44 40.07 2.40
1336 1401 4.821260 TGTTCAATGTCATGTGCACTAGTT 59.179 37.500 19.41 1.82 0.00 2.24
1346 1411 6.018262 GTCATGTGCACTAGTTGTTTCACTTA 60.018 38.462 19.41 0.00 33.44 2.24
1364 1429 9.872757 TTTCACTTACTTTACATGTTCGATTTC 57.127 29.630 2.30 0.00 0.00 2.17
1381 1446 5.346822 TCGATTTCGTCTACTTTGTTTAGCC 59.653 40.000 0.00 0.00 40.80 3.93
1391 1456 8.557029 GTCTACTTTGTTTAGCCGCATATTAAT 58.443 33.333 0.00 0.00 0.00 1.40
1398 1463 7.316640 TGTTTAGCCGCATATTAATTTTGTGT 58.683 30.769 0.00 0.00 0.00 3.72
1423 1488 4.789095 TTAACTCTGCACAAACGTCTTC 57.211 40.909 0.00 0.00 0.00 2.87
1538 1609 1.068541 GTTTCGACATGGCTGGAAACC 60.069 52.381 16.92 4.23 41.29 3.27
1601 1672 1.644786 CGACTGGATCCGGCAAAACC 61.645 60.000 21.17 2.48 0.00 3.27
1637 1708 3.258872 TGCCTATTGTGCAAATGCTTTCT 59.741 39.130 6.97 0.00 42.66 2.52
1640 1711 5.343249 CCTATTGTGCAAATGCTTTCTACC 58.657 41.667 6.97 0.00 42.66 3.18
1709 1780 3.641437 TTAGCATTGCAGGTTTGTGAC 57.359 42.857 11.91 0.00 0.00 3.67
1711 1782 1.067516 AGCATTGCAGGTTTGTGACAC 59.932 47.619 11.91 0.00 0.00 3.67
2027 2101 6.356556 TCTGATCAAGAAGTCCAAACAAGAA 58.643 36.000 0.00 0.00 29.54 2.52
2141 2215 9.294030 GATCATATCAACATGACAAAAGGTTTC 57.706 33.333 0.00 0.00 37.74 2.78
2171 2245 6.922136 GGAGCATCTTCAATACCTGGTAGGT 61.922 48.000 12.78 5.74 43.81 3.08
2241 2325 7.064371 GGATGACTGAGTTCATATATGATGTGC 59.936 40.741 16.06 7.43 36.30 4.57
2270 2377 5.914033 TGTCCTGTTATACATAGTTGAGGC 58.086 41.667 0.00 0.00 0.00 4.70
2324 2448 2.420022 GTCGAACAGTATGCTGGCAATT 59.580 45.455 15.65 0.00 46.62 2.32
2391 2620 3.057033 CCAGATAGCAGCATATTTTGGCC 60.057 47.826 0.00 0.00 0.00 5.36
2429 2658 7.004086 ACTAGAACAATTTTCCAGATTCACCA 58.996 34.615 0.00 0.00 0.00 4.17
2506 2737 2.093553 AGTTGCAACAAGTTTGGCATGT 60.094 40.909 30.11 2.79 35.98 3.21
2547 2778 9.691362 TTTTAAAGAATTATTCAGTCAACAGGC 57.309 29.630 7.74 0.00 0.00 4.85
2551 2782 0.623723 TATTCAGTCAACAGGCCCCC 59.376 55.000 0.00 0.00 0.00 5.40
2634 2865 8.731275 TTGTGCATATTAGTATTAGTGTTGCT 57.269 30.769 0.00 0.00 0.00 3.91
2655 2895 9.797473 GTTGCTTACTTGCTTTTGATTTATTTC 57.203 29.630 0.00 0.00 0.00 2.17
2850 3090 7.484035 AAGCCTTGTTCTACGATATCAATTC 57.516 36.000 3.12 0.00 0.00 2.17
3200 3650 3.009723 ACTGTCCCATGCGTTCTTATTG 58.990 45.455 0.00 0.00 0.00 1.90
3726 4179 5.998454 AAATAGATGTTCTCATTGGCTCG 57.002 39.130 0.00 0.00 34.06 5.03
3903 4356 9.646336 GAGGTAATACGCTGTTTAACAATAATG 57.354 33.333 0.00 0.00 0.00 1.90
3954 4414 6.514541 GCTGTGGTTGATTGATTCCATGATAG 60.515 42.308 0.00 0.00 32.45 2.08
3964 4424 9.445878 GATTGATTCCATGATAGTGTACATGAT 57.554 33.333 0.00 0.00 44.28 2.45
4092 4563 7.560262 TGCTGTAGATAACTGTTACTATCAGGT 59.440 37.037 20.93 0.00 37.25 4.00
4158 4629 8.646004 TGAATCACCTTGATATTTGTTTTGGAA 58.354 29.630 0.00 0.00 35.76 3.53
4364 4847 4.627467 CAGTTTTTGAGACCGGTGAGATAG 59.373 45.833 14.63 0.00 0.00 2.08
4515 5007 7.010160 ACTGAAAGATAAATTGAAAGGGTCCA 58.990 34.615 0.00 0.00 37.43 4.02
4561 5054 3.581332 TCCAACAAGTCGGGAGATAAAGT 59.419 43.478 0.00 0.00 43.27 2.66
4659 5157 3.598299 TGTAAACGTCTTAAATCCCCGG 58.402 45.455 0.00 0.00 0.00 5.73
4683 5181 6.240060 GGCTGGTACATATATTTGGGGAACTA 60.240 42.308 0.00 0.00 38.20 2.24
4699 5197 4.379290 GGGAACTATACTATCCGAAGACGC 60.379 50.000 0.00 0.00 38.29 5.19
4700 5198 4.214971 GGAACTATACTATCCGAAGACGCA 59.785 45.833 0.00 0.00 38.29 5.24
4701 5199 5.359716 AACTATACTATCCGAAGACGCAG 57.640 43.478 0.00 0.00 38.29 5.18
4736 5235 7.054124 CCCCTGTTTGCTTTTCTATATGTAGA 58.946 38.462 0.00 0.00 35.17 2.59
4738 5237 8.398665 CCCTGTTTGCTTTTCTATATGTAGAAC 58.601 37.037 11.11 2.15 44.47 3.01
4827 5326 6.265196 TGGCTGATTTAGTCTGAACATTTGTT 59.735 34.615 0.00 0.00 41.64 2.83
4876 5375 5.130519 CGTCACAGTAATTTTTCGTGTCTG 58.869 41.667 0.00 0.00 0.00 3.51
4949 5448 4.814234 TGTTCAAATGCTACAAGTCGAAGT 59.186 37.500 0.00 0.00 0.00 3.01
4986 5485 3.213206 TCAGAGTTGTCAGTGGCATTT 57.787 42.857 0.00 0.00 0.00 2.32
4987 5486 3.554934 TCAGAGTTGTCAGTGGCATTTT 58.445 40.909 0.00 0.00 0.00 1.82
4988 5487 3.953612 TCAGAGTTGTCAGTGGCATTTTT 59.046 39.130 0.00 0.00 0.00 1.94
5048 5551 3.777478 TCTTCACCGGATCACGTAATTC 58.223 45.455 9.46 0.00 42.24 2.17
5088 5591 9.064706 CATGGCTTAATATCTTGAGTTCTTGAT 57.935 33.333 0.00 0.00 0.00 2.57
5100 5603 4.121317 GAGTTCTTGATGCTCTGAGGATG 58.879 47.826 16.76 2.66 0.00 3.51
5101 5604 3.518705 AGTTCTTGATGCTCTGAGGATGT 59.481 43.478 16.76 0.00 0.00 3.06
5133 5636 0.327924 TGTTACCACCTGCATCCCAG 59.672 55.000 0.00 0.00 41.41 4.45
5166 5669 2.510594 GCATTTCGCGCATGGCTTG 61.511 57.895 8.75 0.00 40.44 4.01
5167 5670 1.137194 CATTTCGCGCATGGCTTGA 59.863 52.632 8.75 0.00 40.44 3.02
5186 5689 5.347907 GCTTGACAGTAAACGCACTATAACT 59.652 40.000 0.00 0.00 0.00 2.24
5208 5711 0.543749 AGGTTATCTGACTGGCTGGC 59.456 55.000 0.00 0.00 0.00 4.85
5210 5713 1.661341 GTTATCTGACTGGCTGGCTG 58.339 55.000 6.56 6.56 0.00 4.85
5222 5725 1.376037 CTGGCTGTCCGGGAAGAAC 60.376 63.158 0.00 0.00 35.00 3.01
5224 5727 1.072505 GGCTGTCCGGGAAGAACAA 59.927 57.895 0.00 0.00 0.00 2.83
5225 5728 0.536460 GGCTGTCCGGGAAGAACAAA 60.536 55.000 0.00 0.00 0.00 2.83
5228 5731 0.882927 TGTCCGGGAAGAACAAAGCG 60.883 55.000 0.00 0.00 0.00 4.68
5229 5732 1.964373 TCCGGGAAGAACAAAGCGC 60.964 57.895 0.00 0.00 0.00 5.92
5230 5733 2.561373 CGGGAAGAACAAAGCGCC 59.439 61.111 2.29 0.00 0.00 6.53
5231 5734 1.966451 CGGGAAGAACAAAGCGCCT 60.966 57.895 2.29 0.00 0.00 5.52
5232 5735 1.581447 GGGAAGAACAAAGCGCCTG 59.419 57.895 2.29 4.31 0.00 4.85
5262 5766 3.721706 CTCCCCTGGCTCCCACAC 61.722 72.222 0.00 0.00 0.00 3.82
5304 5812 3.382865 TGTTGACCAGCTTTGCATTTGTA 59.617 39.130 0.00 0.00 0.00 2.41
5337 5845 5.710613 AAAACAACTTTGCATTTGTACCG 57.289 34.783 8.75 0.00 34.82 4.02
5338 5846 4.379339 AACAACTTTGCATTTGTACCGT 57.621 36.364 8.75 0.00 34.82 4.83
5339 5847 4.379339 ACAACTTTGCATTTGTACCGTT 57.621 36.364 6.99 0.00 34.12 4.44
5341 5849 4.564769 ACAACTTTGCATTTGTACCGTTTG 59.435 37.500 6.99 0.00 34.12 2.93
5343 5851 4.749976 ACTTTGCATTTGTACCGTTTGTT 58.250 34.783 0.00 0.00 0.00 2.83
5344 5852 4.564769 ACTTTGCATTTGTACCGTTTGTTG 59.435 37.500 0.00 0.00 0.00 3.33
5345 5853 3.784701 TGCATTTGTACCGTTTGTTGT 57.215 38.095 0.00 0.00 0.00 3.32
5346 5854 3.696898 TGCATTTGTACCGTTTGTTGTC 58.303 40.909 0.00 0.00 0.00 3.18
5348 5856 4.575236 TGCATTTGTACCGTTTGTTGTCTA 59.425 37.500 0.00 0.00 0.00 2.59
5349 5857 4.907582 GCATTTGTACCGTTTGTTGTCTAC 59.092 41.667 0.00 0.00 0.00 2.59
5350 5858 5.277634 GCATTTGTACCGTTTGTTGTCTACT 60.278 40.000 0.00 0.00 0.00 2.57
5352 5860 4.652421 TGTACCGTTTGTTGTCTACTCA 57.348 40.909 0.00 0.00 0.00 3.41
5353 5861 5.008619 TGTACCGTTTGTTGTCTACTCAA 57.991 39.130 0.00 0.00 0.00 3.02
5354 5862 5.417811 TGTACCGTTTGTTGTCTACTCAAA 58.582 37.500 0.00 0.00 0.00 2.69
5355 5863 5.873712 TGTACCGTTTGTTGTCTACTCAAAA 59.126 36.000 0.00 0.00 33.80 2.44
5356 5864 5.225899 ACCGTTTGTTGTCTACTCAAAAC 57.774 39.130 0.00 0.00 33.80 2.43
5357 5865 4.939439 ACCGTTTGTTGTCTACTCAAAACT 59.061 37.500 0.00 0.00 33.80 2.66
5358 5866 5.413523 ACCGTTTGTTGTCTACTCAAAACTT 59.586 36.000 0.00 0.00 33.80 2.66
5359 5867 6.072342 ACCGTTTGTTGTCTACTCAAAACTTT 60.072 34.615 0.00 0.00 33.80 2.66
5360 5868 6.250527 CCGTTTGTTGTCTACTCAAAACTTTG 59.749 38.462 0.00 0.00 39.48 2.77
5361 5869 6.250527 CGTTTGTTGTCTACTCAAAACTTTGG 59.749 38.462 2.49 0.00 38.66 3.28
5362 5870 6.827586 TTGTTGTCTACTCAAAACTTTGGT 57.172 33.333 2.49 2.84 38.66 3.67
5363 5871 7.925043 TTGTTGTCTACTCAAAACTTTGGTA 57.075 32.000 2.49 3.72 38.66 3.25
5364 5872 8.514330 TTGTTGTCTACTCAAAACTTTGGTAT 57.486 30.769 2.49 0.00 38.66 2.73
5365 5873 8.514330 TGTTGTCTACTCAAAACTTTGGTATT 57.486 30.769 2.49 0.00 38.66 1.89
5366 5874 8.962679 TGTTGTCTACTCAAAACTTTGGTATTT 58.037 29.630 2.49 0.00 38.66 1.40
5367 5875 9.797556 GTTGTCTACTCAAAACTTTGGTATTTT 57.202 29.630 2.49 0.00 38.66 1.82
5372 5880 9.940166 CTACTCAAAACTTTGGTATTTTTACGT 57.060 29.630 0.00 0.00 38.66 3.57
5374 5882 9.292846 ACTCAAAACTTTGGTATTTTTACGTTC 57.707 29.630 0.00 0.00 38.66 3.95
5375 5883 9.291664 CTCAAAACTTTGGTATTTTTACGTTCA 57.708 29.630 0.00 0.00 38.66 3.18
5376 5884 9.291664 TCAAAACTTTGGTATTTTTACGTTCAG 57.708 29.630 0.00 0.00 38.66 3.02
5377 5885 9.291664 CAAAACTTTGGTATTTTTACGTTCAGA 57.708 29.630 0.00 0.00 34.59 3.27
5378 5886 9.857957 AAAACTTTGGTATTTTTACGTTCAGAA 57.142 25.926 0.00 0.00 0.00 3.02
5379 5887 9.857957 AAACTTTGGTATTTTTACGTTCAGAAA 57.142 25.926 0.00 0.00 0.00 2.52
5380 5888 9.857957 AACTTTGGTATTTTTACGTTCAGAAAA 57.142 25.926 0.00 0.00 0.00 2.29
5381 5889 9.511144 ACTTTGGTATTTTTACGTTCAGAAAAG 57.489 29.630 0.00 0.00 0.00 2.27
5382 5890 9.724839 CTTTGGTATTTTTACGTTCAGAAAAGA 57.275 29.630 0.00 0.00 0.00 2.52
5385 5893 9.505995 TGGTATTTTTACGTTCAGAAAAGAAAC 57.494 29.630 0.00 0.00 0.00 2.78
5386 5894 9.726232 GGTATTTTTACGTTCAGAAAAGAAACT 57.274 29.630 0.00 0.00 0.00 2.66
5390 5898 9.680315 TTTTTACGTTCAGAAAAGAAACTTTGA 57.320 25.926 0.00 0.00 0.00 2.69
5403 5911 9.463443 AAAAGAAACTTTGATATTTTGGACTCG 57.537 29.630 0.00 0.00 0.00 4.18
5405 5913 4.600012 ACTTTGATATTTTGGACTCGCG 57.400 40.909 0.00 0.00 0.00 5.87
5421 5929 5.333416 GGACTCGCGATAAATTTGATTCCTC 60.333 44.000 10.36 0.00 0.00 3.71
5424 5932 6.018669 ACTCGCGATAAATTTGATTCCTCTTC 60.019 38.462 10.36 0.00 0.00 2.87
5431 5939 9.298774 GATAAATTTGATTCCTCTTCAGCTTTG 57.701 33.333 0.00 0.00 0.00 2.77
5433 5941 5.443185 TTTGATTCCTCTTCAGCTTTGTG 57.557 39.130 0.00 0.00 0.00 3.33
5434 5942 2.816087 TGATTCCTCTTCAGCTTTGTGC 59.184 45.455 0.00 0.00 43.29 4.57
5464 5972 3.302092 CGAACGACAGCTCAGCAATAATC 60.302 47.826 0.00 0.00 0.00 1.75
5468 5976 4.093998 ACGACAGCTCAGCAATAATCTTTG 59.906 41.667 0.00 0.00 0.00 2.77
5549 6058 9.447157 GAGATATTAGAAGAAAGGCTATTGCAT 57.553 33.333 0.66 0.00 41.91 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.015519 TGTCTTTAAACTGTCCAATCCCATTG 60.016 38.462 0.00 0.00 39.94 2.82
9 10 5.055265 TGTCTTTAAACTGTCCAATCCCA 57.945 39.130 0.00 0.00 0.00 4.37
10 11 7.065923 GTCTATGTCTTTAAACTGTCCAATCCC 59.934 40.741 0.00 0.00 0.00 3.85
82 83 4.261072 GCAATGCCTATCACTCATGTCTTG 60.261 45.833 0.00 0.00 0.00 3.02
95 96 5.175161 TCATGTCAATGTGGCAATGCCTAT 61.175 41.667 25.93 16.33 40.01 2.57
107 108 5.649395 AGGACGAATGAATTCATGTCAATGT 59.351 36.000 27.24 17.77 36.56 2.71
112 113 7.308782 ACTAAAGGACGAATGAATTCATGTC 57.691 36.000 21.39 21.79 36.56 3.06
113 114 8.425577 CTACTAAAGGACGAATGAATTCATGT 57.574 34.615 21.39 15.41 36.56 3.21
162 163 4.125703 GACTTCATGGACCAAGCTCATAG 58.874 47.826 0.00 0.00 0.00 2.23
209 210 4.700213 CGTTTCAGTCAATTCCTTGGGTAT 59.300 41.667 0.00 0.00 32.95 2.73
210 211 4.069304 CGTTTCAGTCAATTCCTTGGGTA 58.931 43.478 0.00 0.00 32.95 3.69
273 275 3.764434 AGGACTACGAGAAATCTTGCAGA 59.236 43.478 5.13 0.00 0.00 4.26
275 277 4.537135 AAGGACTACGAGAAATCTTGCA 57.463 40.909 0.00 0.00 0.00 4.08
296 299 2.341846 AAGTGCCCGAGTTCAAGAAA 57.658 45.000 0.00 0.00 0.00 2.52
317 320 2.685388 CACTAGGCGAGTCTGAGATTGA 59.315 50.000 0.00 0.00 35.64 2.57
550 570 7.021196 GCGTGAAAAATAGAAATAGCTCAACA 58.979 34.615 0.00 0.00 0.00 3.33
559 579 4.168760 GCAGCAGCGTGAAAAATAGAAAT 58.831 39.130 0.00 0.00 0.00 2.17
596 616 3.966026 GACAGGCGACGGACCGAAG 62.966 68.421 23.38 14.66 0.00 3.79
597 617 4.047059 GACAGGCGACGGACCGAA 62.047 66.667 23.38 0.00 0.00 4.30
608 628 2.892425 CGGATCTTGGCGACAGGC 60.892 66.667 0.00 0.00 44.54 4.85
609 629 2.892425 GCGGATCTTGGCGACAGG 60.892 66.667 0.00 0.00 44.54 4.00
610 630 1.091771 ATTGCGGATCTTGGCGACAG 61.092 55.000 0.00 0.00 44.54 3.51
611 631 1.078497 ATTGCGGATCTTGGCGACA 60.078 52.632 0.00 0.00 39.83 4.35
612 632 1.089481 TGATTGCGGATCTTGGCGAC 61.089 55.000 0.00 0.00 35.69 5.19
613 633 1.089481 GTGATTGCGGATCTTGGCGA 61.089 55.000 0.00 0.00 35.69 5.54
614 634 1.091771 AGTGATTGCGGATCTTGGCG 61.092 55.000 0.00 0.00 35.69 5.69
615 635 0.659957 GAGTGATTGCGGATCTTGGC 59.340 55.000 0.00 0.00 35.69 4.52
616 636 0.933097 CGAGTGATTGCGGATCTTGG 59.067 55.000 0.00 0.00 35.69 3.61
617 637 0.302890 GCGAGTGATTGCGGATCTTG 59.697 55.000 0.00 0.00 35.69 3.02
618 638 2.682893 GCGAGTGATTGCGGATCTT 58.317 52.632 0.00 0.00 35.69 2.40
619 639 4.427394 GCGAGTGATTGCGGATCT 57.573 55.556 0.00 0.00 35.69 2.75
662 682 4.778143 AGGATGGAACCACGCCGC 62.778 66.667 0.00 0.00 0.00 6.53
663 683 2.511600 GAGGATGGAACCACGCCG 60.512 66.667 0.00 0.00 0.00 6.46
693 713 3.522731 CAGGAGAGAGGCGACCGG 61.523 72.222 0.00 0.00 0.00 5.28
694 714 4.200283 GCAGGAGAGAGGCGACCG 62.200 72.222 0.00 0.00 0.00 4.79
695 715 3.844090 GGCAGGAGAGAGGCGACC 61.844 72.222 0.00 0.00 0.00 4.79
696 716 2.362329 GATGGCAGGAGAGAGGCGAC 62.362 65.000 0.00 0.00 0.00 5.19
697 717 2.042537 ATGGCAGGAGAGAGGCGA 60.043 61.111 0.00 0.00 0.00 5.54
698 718 2.420890 GATGGCAGGAGAGAGGCG 59.579 66.667 0.00 0.00 0.00 5.52
699 719 2.420890 CGATGGCAGGAGAGAGGC 59.579 66.667 0.00 0.00 0.00 4.70
700 720 2.420890 GCGATGGCAGGAGAGAGG 59.579 66.667 0.00 0.00 39.62 3.69
701 721 1.684386 AAGGCGATGGCAGGAGAGAG 61.684 60.000 1.01 0.00 42.47 3.20
702 722 1.680522 GAAGGCGATGGCAGGAGAGA 61.681 60.000 1.01 0.00 42.47 3.10
703 723 1.227497 GAAGGCGATGGCAGGAGAG 60.227 63.158 1.01 0.00 42.47 3.20
704 724 1.680522 GAGAAGGCGATGGCAGGAGA 61.681 60.000 1.01 0.00 42.47 3.71
705 725 1.227497 GAGAAGGCGATGGCAGGAG 60.227 63.158 1.01 0.00 42.47 3.69
706 726 2.735772 GGAGAAGGCGATGGCAGGA 61.736 63.158 1.01 0.00 42.47 3.86
707 727 2.203126 GGAGAAGGCGATGGCAGG 60.203 66.667 1.01 0.00 42.47 4.85
708 728 2.203126 GGGAGAAGGCGATGGCAG 60.203 66.667 1.01 0.00 42.47 4.85
709 729 3.797353 GGGGAGAAGGCGATGGCA 61.797 66.667 1.01 0.00 42.47 4.92
710 730 3.049080 AAGGGGAGAAGGCGATGGC 62.049 63.158 0.00 0.00 38.90 4.40
711 731 1.153086 CAAGGGGAGAAGGCGATGG 60.153 63.158 0.00 0.00 0.00 3.51
712 732 1.153086 CCAAGGGGAGAAGGCGATG 60.153 63.158 0.00 0.00 35.59 3.84
713 733 1.616628 ACCAAGGGGAGAAGGCGAT 60.617 57.895 0.00 0.00 38.05 4.58
714 734 2.203938 ACCAAGGGGAGAAGGCGA 60.204 61.111 0.00 0.00 38.05 5.54
870 892 2.417787 CGGAACAGAGTGCTGATGATGA 60.418 50.000 0.00 0.00 45.17 2.92
1143 1167 0.752743 CATGGGGTGTGGCATGGTAG 60.753 60.000 0.00 0.00 0.00 3.18
1150 1174 4.344865 ACGGACATGGGGTGTGGC 62.345 66.667 0.00 0.00 42.36 5.01
1154 1178 2.747460 CAGCACGGACATGGGGTG 60.747 66.667 0.00 3.14 34.85 4.61
1163 1187 1.001974 AGAAATACTGCACAGCACGGA 59.998 47.619 0.00 0.00 33.79 4.69
1165 1189 2.515641 CAGAAATACTGCACAGCACG 57.484 50.000 0.00 0.00 39.86 5.34
1182 1206 3.064987 GCAGGCCATTGCTGAGCAG 62.065 63.158 7.39 0.00 40.61 4.24
1190 1215 2.754946 ACAAATTCAGCAGGCCATTG 57.245 45.000 5.01 0.00 0.00 2.82
1191 1216 3.194116 CACTACAAATTCAGCAGGCCATT 59.806 43.478 5.01 0.00 0.00 3.16
1206 1231 4.623932 ATTGAAGACTCAGGCACTACAA 57.376 40.909 0.00 0.00 36.02 2.41
1211 1236 3.565482 TGTCAAATTGAAGACTCAGGCAC 59.435 43.478 0.00 0.00 35.81 5.01
1216 1241 5.049474 CCATCGTTGTCAAATTGAAGACTCA 60.049 40.000 0.00 0.00 35.81 3.41
1309 1374 5.045215 AGTGCACATGACATTGAACAAAAG 58.955 37.500 21.04 0.00 0.00 2.27
1336 1401 7.773864 TCGAACATGTAAAGTAAGTGAAACA 57.226 32.000 0.00 0.00 41.43 2.83
1346 1411 7.088905 AGTAGACGAAATCGAACATGTAAAGT 58.911 34.615 10.16 0.00 43.02 2.66
1381 1446 9.567848 AGTTAAAGGACACAAAATTAATATGCG 57.432 29.630 0.00 0.00 0.00 4.73
1391 1456 4.702612 TGTGCAGAGTTAAAGGACACAAAA 59.297 37.500 0.00 0.00 33.94 2.44
1398 1463 3.537580 ACGTTTGTGCAGAGTTAAAGGA 58.462 40.909 0.00 0.00 0.00 3.36
1423 1488 4.260784 GCCCTCTGTTACATGCTATTTTCG 60.261 45.833 0.00 0.00 0.00 3.46
1472 1543 3.127533 ATCCGCTGCAACGCTTCC 61.128 61.111 3.43 0.00 0.00 3.46
1538 1609 1.962807 TGAAAAGCACCAGGACCAATG 59.037 47.619 0.00 0.00 0.00 2.82
1601 1672 2.057137 TAGGCAAGGCATAAGCAAGG 57.943 50.000 0.00 0.00 44.61 3.61
1637 1708 1.648116 AGCACCTTACTTTCCGGGTA 58.352 50.000 0.00 0.00 0.00 3.69
1640 1711 0.521735 GCAAGCACCTTACTTTCCGG 59.478 55.000 0.00 0.00 0.00 5.14
2141 2215 4.125703 GGTATTGAAGATGCTCCAGACTG 58.874 47.826 0.00 0.00 0.00 3.51
2171 2245 2.028130 ACAGAAATGGTTGCCGACAAA 58.972 42.857 0.00 0.00 37.58 2.83
2174 2248 1.464997 GAGACAGAAATGGTTGCCGAC 59.535 52.381 0.00 0.00 0.00 4.79
2176 2250 0.804989 GGAGACAGAAATGGTTGCCG 59.195 55.000 0.00 0.00 0.00 5.69
2270 2377 1.001924 TGCGGCACACAAACAATACTG 60.002 47.619 0.00 0.00 0.00 2.74
2372 2591 2.892852 TGGGCCAAAATATGCTGCTATC 59.107 45.455 2.13 0.00 0.00 2.08
2391 2620 6.780457 ATTGTTCTAGTCATCCCAAAATGG 57.220 37.500 0.00 0.00 37.25 3.16
2408 2637 6.089249 AGTGGTGAATCTGGAAAATTGTTC 57.911 37.500 0.00 0.00 0.00 3.18
2429 2658 6.711277 TCCATAGCAAGTGTCTAAATGAAGT 58.289 36.000 0.00 0.00 0.00 3.01
2523 2754 7.093945 GGGCCTGTTGACTGAATAATTCTTTAA 60.094 37.037 0.84 0.00 0.00 1.52
2524 2755 6.377146 GGGCCTGTTGACTGAATAATTCTTTA 59.623 38.462 0.84 0.00 0.00 1.85
2617 2848 9.449719 AAGCAAGTAAGCAACACTAATACTAAT 57.550 29.630 0.00 0.00 36.85 1.73
2619 2850 8.842358 AAAGCAAGTAAGCAACACTAATACTA 57.158 30.769 0.00 0.00 36.85 1.82
2620 2851 7.745620 AAAGCAAGTAAGCAACACTAATACT 57.254 32.000 0.00 0.00 36.85 2.12
2621 2852 8.073768 TCAAAAGCAAGTAAGCAACACTAATAC 58.926 33.333 0.00 0.00 36.85 1.89
2850 3090 7.693969 AAAAGAGGACAAGAATAACATGAGG 57.306 36.000 0.00 0.00 0.00 3.86
3125 3574 5.835257 TCAGGCATAAGCATTGATAAAAGC 58.165 37.500 0.00 0.00 44.61 3.51
3200 3650 5.645497 ACAGATCTGAAATAACAGCAAGGAC 59.355 40.000 29.27 0.00 37.75 3.85
3726 4179 6.222038 TGTATTCCTCGAGCCATTATATCC 57.778 41.667 6.99 0.00 0.00 2.59
3840 4293 2.807967 CGTGAAGCAAGAACCAGATTCA 59.192 45.455 0.00 0.00 40.09 2.57
4068 4539 9.344772 AGACCTGATAGTAACAGTTATCTACAG 57.655 37.037 6.67 5.26 34.04 2.74
4224 4699 3.213206 TGACATTTGACTCAGCAACCT 57.787 42.857 0.00 0.00 0.00 3.50
4364 4847 7.617041 AGTAATCTGATTAAAACAGGACTGC 57.383 36.000 11.46 0.00 36.22 4.40
4515 5007 0.320374 TTCGATGCTTCTGGTTCCGT 59.680 50.000 0.00 0.00 0.00 4.69
4561 5054 0.179004 TCTTTTCAAAGCTCCCGGCA 60.179 50.000 0.00 0.00 44.79 5.69
4659 5157 5.631119 AGTTCCCCAAATATATGTACCAGC 58.369 41.667 0.00 0.00 0.00 4.85
4683 5181 2.287668 GCACTGCGTCTTCGGATAGTAT 60.288 50.000 0.00 0.00 36.72 2.12
4736 5235 3.555117 TCAGTAGGGGTAACAGAGGTT 57.445 47.619 0.00 0.00 41.06 3.50
4738 5237 3.643237 TGATCAGTAGGGGTAACAGAGG 58.357 50.000 0.00 0.00 39.74 3.69
4827 5326 5.475564 GCACCTAGAATTTTCAGGTTTACCA 59.524 40.000 1.13 0.00 36.93 3.25
4876 5375 2.154074 AGGTGGGGGTCAGTTGGAC 61.154 63.158 0.00 0.00 46.20 4.02
4917 5416 2.676748 AGCATTTGAACAAGGGGAACA 58.323 42.857 0.00 0.00 0.00 3.18
4949 5448 4.202398 ACTCTGATGAACAAGGAGAAGCAA 60.202 41.667 0.00 0.00 0.00 3.91
5048 5551 1.133598 AGCCATGATGTTTGATGCGTG 59.866 47.619 0.00 0.00 0.00 5.34
5088 5591 6.156949 AGGTTAATTAGAACATCCTCAGAGCA 59.843 38.462 0.00 0.00 0.00 4.26
5142 5645 0.247655 CATGCGCGAAATGCTTACGT 60.248 50.000 12.10 0.00 43.27 3.57
5166 5669 7.543520 ACCTTAAGTTATAGTGCGTTTACTGTC 59.456 37.037 0.97 0.00 32.19 3.51
5167 5670 7.381323 ACCTTAAGTTATAGTGCGTTTACTGT 58.619 34.615 0.97 0.00 32.19 3.55
5186 5689 3.370527 GCCAGCCAGTCAGATAACCTTAA 60.371 47.826 0.00 0.00 0.00 1.85
5208 5711 0.875059 GCTTTGTTCTTCCCGGACAG 59.125 55.000 0.73 0.00 0.00 3.51
5210 5713 1.866925 CGCTTTGTTCTTCCCGGAC 59.133 57.895 0.73 0.00 0.00 4.79
5222 5725 0.038892 ATGCTGTTTCAGGCGCTTTG 60.039 50.000 7.64 6.75 31.21 2.77
5224 5727 1.402968 CATATGCTGTTTCAGGCGCTT 59.597 47.619 7.64 0.00 31.21 4.68
5225 5728 1.019673 CATATGCTGTTTCAGGCGCT 58.980 50.000 7.64 0.00 31.21 5.92
5248 5752 2.032860 CTATCGTGTGGGAGCCAGGG 62.033 65.000 0.00 0.00 32.34 4.45
5262 5766 8.122952 GTCAACAAATTGGAAGATAACCTATCG 58.877 37.037 0.00 0.00 37.06 2.92
5304 5812 6.872920 TGCAAAGTTGTTTTTCATAGAAGGT 58.127 32.000 0.00 0.00 0.00 3.50
5337 5845 7.088272 ACCAAAGTTTTGAGTAGACAACAAAC 58.912 34.615 6.18 0.00 40.55 2.93
5338 5846 7.222000 ACCAAAGTTTTGAGTAGACAACAAA 57.778 32.000 6.18 0.00 40.55 2.83
5339 5847 6.827586 ACCAAAGTTTTGAGTAGACAACAA 57.172 33.333 6.18 0.00 40.55 2.83
5341 5849 9.797556 AAAATACCAAAGTTTTGAGTAGACAAC 57.202 29.630 6.18 0.00 40.55 3.32
5346 5854 9.940166 ACGTAAAAATACCAAAGTTTTGAGTAG 57.060 29.630 6.18 0.00 40.55 2.57
5348 5856 9.292846 GAACGTAAAAATACCAAAGTTTTGAGT 57.707 29.630 6.18 5.38 40.55 3.41
5349 5857 9.291664 TGAACGTAAAAATACCAAAGTTTTGAG 57.708 29.630 6.18 0.00 40.55 3.02
5350 5858 9.291664 CTGAACGTAAAAATACCAAAGTTTTGA 57.708 29.630 6.18 0.00 40.55 2.69
5352 5860 9.857957 TTCTGAACGTAAAAATACCAAAGTTTT 57.142 25.926 0.00 0.00 0.00 2.43
5353 5861 9.857957 TTTCTGAACGTAAAAATACCAAAGTTT 57.142 25.926 0.00 0.00 0.00 2.66
5354 5862 9.857957 TTTTCTGAACGTAAAAATACCAAAGTT 57.142 25.926 0.00 0.00 0.00 2.66
5355 5863 9.511144 CTTTTCTGAACGTAAAAATACCAAAGT 57.489 29.630 0.00 0.00 0.00 2.66
5356 5864 9.724839 TCTTTTCTGAACGTAAAAATACCAAAG 57.275 29.630 0.00 0.00 0.00 2.77
5359 5867 9.505995 GTTTCTTTTCTGAACGTAAAAATACCA 57.494 29.630 0.00 0.00 0.00 3.25
5360 5868 9.726232 AGTTTCTTTTCTGAACGTAAAAATACC 57.274 29.630 0.00 0.00 0.00 2.73
5364 5872 9.680315 TCAAAGTTTCTTTTCTGAACGTAAAAA 57.320 25.926 0.00 0.00 0.00 1.94
5365 5873 9.849166 ATCAAAGTTTCTTTTCTGAACGTAAAA 57.151 25.926 0.00 0.00 0.00 1.52
5377 5885 9.463443 CGAGTCCAAAATATCAAAGTTTCTTTT 57.537 29.630 0.00 0.00 0.00 2.27
5378 5886 7.595130 GCGAGTCCAAAATATCAAAGTTTCTTT 59.405 33.333 0.00 0.00 0.00 2.52
5379 5887 7.084486 GCGAGTCCAAAATATCAAAGTTTCTT 58.916 34.615 0.00 0.00 0.00 2.52
5380 5888 6.612306 GCGAGTCCAAAATATCAAAGTTTCT 58.388 36.000 0.00 0.00 0.00 2.52
5381 5889 5.508224 CGCGAGTCCAAAATATCAAAGTTTC 59.492 40.000 0.00 0.00 0.00 2.78
5382 5890 5.180492 TCGCGAGTCCAAAATATCAAAGTTT 59.820 36.000 3.71 0.00 0.00 2.66
5383 5891 4.693566 TCGCGAGTCCAAAATATCAAAGTT 59.306 37.500 3.71 0.00 0.00 2.66
5384 5892 4.250464 TCGCGAGTCCAAAATATCAAAGT 58.750 39.130 3.71 0.00 0.00 2.66
5385 5893 4.857871 TCGCGAGTCCAAAATATCAAAG 57.142 40.909 3.71 0.00 0.00 2.77
5386 5894 6.912203 TTATCGCGAGTCCAAAATATCAAA 57.088 33.333 16.66 0.00 0.00 2.69
5387 5895 6.912203 TTTATCGCGAGTCCAAAATATCAA 57.088 33.333 16.66 0.00 0.00 2.57
5388 5896 7.490962 AATTTATCGCGAGTCCAAAATATCA 57.509 32.000 16.66 0.00 0.00 2.15
5389 5897 8.067784 TCAAATTTATCGCGAGTCCAAAATATC 58.932 33.333 16.66 0.00 0.00 1.63
5390 5898 7.925993 TCAAATTTATCGCGAGTCCAAAATAT 58.074 30.769 16.66 0.00 0.00 1.28
5399 5907 5.360591 AGAGGAATCAAATTTATCGCGAGT 58.639 37.500 16.66 5.59 0.00 4.18
5403 5911 5.911838 GCTGAAGAGGAATCAAATTTATCGC 59.088 40.000 0.00 0.00 0.00 4.58
5405 5913 9.298774 CAAAGCTGAAGAGGAATCAAATTTATC 57.701 33.333 0.00 0.00 0.00 1.75
5421 5929 3.111098 GTCTTGTTGCACAAAGCTGAAG 58.889 45.455 3.17 0.00 45.94 3.02
5424 5932 1.063912 TCGTCTTGTTGCACAAAGCTG 59.936 47.619 3.17 0.00 45.94 4.24
5431 5939 0.648441 TGTCGTTCGTCTTGTTGCAC 59.352 50.000 0.00 0.00 0.00 4.57
5433 5941 0.383124 GCTGTCGTTCGTCTTGTTGC 60.383 55.000 0.00 0.00 0.00 4.17
5434 5942 1.190323 GAGCTGTCGTTCGTCTTGTTG 59.810 52.381 0.00 0.00 0.00 3.33
5442 5950 1.629013 TATTGCTGAGCTGTCGTTCG 58.371 50.000 5.83 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.