Multiple sequence alignment - TraesCS1A01G296700

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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 TraesCS1A01G296700 chr1A 100.000 6782 0 0 1 6782 491991816 491985035 0.000000e+00 12525.0
1 TraesCS1A01G296700 chr1A 89.829 1642 107 30 4306 5916 491648512 491646900 0.000000e+00 2052.0
2 TraesCS1A01G296700 chr1A 91.405 1210 61 10 1030 2206 491651550 491650351 0.000000e+00 1618.0
3 TraesCS1A01G296700 chr1A 92.612 758 39 11 3542 4298 491895417 491894676 0.000000e+00 1074.0
4 TraesCS1A01G296700 chr1A 86.555 952 77 23 2240 3157 491649779 491648845 0.000000e+00 1002.0
5 TraesCS1A01G296700 chr1A 91.914 371 19 4 3172 3539 491648860 491648498 6.070000e-140 508.0
6 TraesCS1A01G296700 chr1A 90.050 201 15 2 5957 6152 491646815 491646615 8.730000e-64 255.0
7 TraesCS1A01G296700 chr1A 98.113 53 1 0 1 53 575006557 575006609 7.240000e-15 93.5
8 TraesCS1A01G296700 chr1B 96.045 2478 95 3 4306 6782 529209623 529207148 0.000000e+00 4030.0
9 TraesCS1A01G296700 chr1B 96.195 2260 55 9 915 3157 529212206 529209961 0.000000e+00 3668.0
10 TraesCS1A01G296700 chr1B 85.632 696 59 23 52 738 529213051 529212388 0.000000e+00 693.0
11 TraesCS1A01G296700 chr1B 97.826 368 8 0 3172 3539 529209976 529209609 2.670000e-178 636.0
12 TraesCS1A01G296700 chr1B 100.000 53 0 0 1 53 403797124 403797072 1.560000e-16 99.0
13 TraesCS1A01G296700 chr1B 98.113 53 1 0 1 53 100306983 100306931 7.240000e-15 93.5
14 TraesCS1A01G296700 chr1D 97.742 1993 42 3 4306 6297 393773093 393775083 0.000000e+00 3428.0
15 TraesCS1A01G296700 chr1D 97.065 1397 26 7 1772 3157 393771363 393772755 0.000000e+00 2338.0
16 TraesCS1A01G296700 chr1D 94.038 738 35 5 915 1648 393770630 393771362 0.000000e+00 1110.0
17 TraesCS1A01G296700 chr1D 97.808 365 8 0 3172 3536 393772740 393773104 1.240000e-176 630.0
18 TraesCS1A01G296700 chr1D 88.144 194 18 5 463 655 393770223 393770412 6.840000e-55 226.0
19 TraesCS1A01G296700 chr1D 85.246 61 1 1 686 738 393770415 393770475 1.000000e-03 56.5
20 TraesCS1A01G296700 chr6A 94.764 764 27 12 3536 4298 122423344 122424095 0.000000e+00 1177.0
21 TraesCS1A01G296700 chr6A 92.960 767 34 13 3534 4298 544634321 544635069 0.000000e+00 1099.0
22 TraesCS1A01G296700 chr6A 92.218 771 43 16 3531 4298 514030583 514031339 0.000000e+00 1075.0
23 TraesCS1A01G296700 chr4A 93.077 780 36 14 3524 4298 552872249 552873015 0.000000e+00 1125.0
24 TraesCS1A01G296700 chr5A 92.645 775 37 15 3527 4298 49938484 49939241 0.000000e+00 1098.0
25 TraesCS1A01G296700 chr5A 92.829 767 35 17 3537 4298 676953916 676953165 0.000000e+00 1094.0
26 TraesCS1A01G296700 chr2A 92.718 769 37 15 3533 4298 138113362 138112610 0.000000e+00 1092.0
27 TraesCS1A01G296700 chr2A 100.000 31 0 0 391 421 617159301 617159331 2.640000e-04 58.4
28 TraesCS1A01G296700 chr7A 92.549 765 42 14 3537 4298 543964923 543964171 0.000000e+00 1083.0
29 TraesCS1A01G296700 chr7A 98.113 53 1 0 1 53 17281926 17281874 7.240000e-15 93.5
30 TraesCS1A01G296700 chr3B 89.028 638 58 6 4306 4934 785505154 785504520 0.000000e+00 780.0
31 TraesCS1A01G296700 chr3B 87.793 426 43 4 2737 3157 785505908 785505487 2.200000e-134 490.0
32 TraesCS1A01G296700 chr3B 93.851 309 17 2 5028 5334 785504494 785504186 1.330000e-126 464.0
33 TraesCS1A01G296700 chr3B 89.785 372 25 6 3172 3539 785505502 785505140 1.330000e-126 464.0
34 TraesCS1A01G296700 chr3B 93.985 266 14 2 5070 5334 785505900 785506164 1.060000e-107 401.0
35 TraesCS1A01G296700 chr3B 98.113 53 1 0 1 53 513940777 513940725 7.240000e-15 93.5
36 TraesCS1A01G296700 chr6B 78.750 240 31 15 142 375 402200883 402201108 7.090000e-30 143.0
37 TraesCS1A01G296700 chr5B 80.625 160 24 7 139 294 709331552 709331708 4.300000e-22 117.0
38 TraesCS1A01G296700 chr5B 96.226 53 2 0 1 53 50613913 50613965 3.370000e-13 87.9
39 TraesCS1A01G296700 chr5B 94.872 39 2 0 78 116 418983631 418983669 2.040000e-05 62.1
40 TraesCS1A01G296700 chr3D 75.185 270 41 15 139 388 433733278 433733015 3.350000e-18 104.0
41 TraesCS1A01G296700 chr3D 96.364 55 2 0 1 55 502952043 502952097 2.600000e-14 91.6
42 TraesCS1A01G296700 chr4B 93.846 65 3 1 1 64 614065876 614065940 5.600000e-16 97.1
43 TraesCS1A01G296700 chr2D 81.148 122 21 2 164 284 320182346 320182466 5.600000e-16 97.1
44 TraesCS1A01G296700 chr2B 98.182 55 1 0 1 55 714737543 714737489 5.600000e-16 97.1
45 TraesCS1A01G296700 chr7B 87.097 62 5 3 144 202 509733924 509733985 4.390000e-07 67.6


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 TraesCS1A01G296700 chr1A 491985035 491991816 6781 True 12525.000000 12525 100.00000 1 6782 1 chr1A.!!$R2 6781
1 TraesCS1A01G296700 chr1A 491646615 491651550 4935 True 1087.000000 2052 89.95060 1030 6152 5 chr1A.!!$R3 5122
2 TraesCS1A01G296700 chr1A 491894676 491895417 741 True 1074.000000 1074 92.61200 3542 4298 1 chr1A.!!$R1 756
3 TraesCS1A01G296700 chr1B 529207148 529213051 5903 True 2256.750000 4030 93.92450 52 6782 4 chr1B.!!$R3 6730
4 TraesCS1A01G296700 chr1D 393770223 393775083 4860 False 1298.083333 3428 93.34050 463 6297 6 chr1D.!!$F1 5834
5 TraesCS1A01G296700 chr6A 122423344 122424095 751 False 1177.000000 1177 94.76400 3536 4298 1 chr6A.!!$F1 762
6 TraesCS1A01G296700 chr6A 544634321 544635069 748 False 1099.000000 1099 92.96000 3534 4298 1 chr6A.!!$F3 764
7 TraesCS1A01G296700 chr6A 514030583 514031339 756 False 1075.000000 1075 92.21800 3531 4298 1 chr6A.!!$F2 767
8 TraesCS1A01G296700 chr4A 552872249 552873015 766 False 1125.000000 1125 93.07700 3524 4298 1 chr4A.!!$F1 774
9 TraesCS1A01G296700 chr5A 49938484 49939241 757 False 1098.000000 1098 92.64500 3527 4298 1 chr5A.!!$F1 771
10 TraesCS1A01G296700 chr5A 676953165 676953916 751 True 1094.000000 1094 92.82900 3537 4298 1 chr5A.!!$R1 761
11 TraesCS1A01G296700 chr2A 138112610 138113362 752 True 1092.000000 1092 92.71800 3533 4298 1 chr2A.!!$R1 765
12 TraesCS1A01G296700 chr7A 543964171 543964923 752 True 1083.000000 1083 92.54900 3537 4298 1 chr7A.!!$R2 761
13 TraesCS1A01G296700 chr3B 785504186 785505908 1722 True 549.500000 780 90.11425 2737 5334 4 chr3B.!!$R2 2597

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
904 1016 0.039618 TCTCAACTCCCAAATGCCCC 59.960 55.000 0.00 0.00 0.00 5.80 F
905 1017 0.040204 CTCAACTCCCAAATGCCCCT 59.960 55.000 0.00 0.00 0.00 4.79 F
1089 1211 0.322546 GGAAGACCACAAAGGCGGAT 60.323 55.000 0.00 0.00 43.14 4.18 F
1373 1495 1.557651 GACGAGCGGTCTTACCAATC 58.442 55.000 13.48 0.00 42.62 2.67 F
3044 3757 1.981495 CTCCTCTTCTGTTTGTCCCCT 59.019 52.381 0.00 0.00 0.00 4.79 F
3160 3875 0.035630 ATCAGACACTCAGGCTTGCC 60.036 55.000 2.97 2.97 27.44 4.52 F
4368 5108 0.598065 GCCACTGGATGTGTTTGGTC 59.402 55.000 0.00 0.00 44.81 4.02 F
4436 5176 0.811281 AGCGCAAAAGGGATAACTGC 59.189 50.000 11.47 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2275 0.040067 CGAGCAAAGCTTCCACAACC 60.040 55.000 0.00 0.00 39.88 3.77 R
2736 3446 3.752747 GGATTGAAGGTTTGCCCAATTTG 59.247 43.478 0.00 0.00 30.29 2.32 R
3015 3728 7.118535 GGACAAACAGAAGAGGAGAAATTCTAC 59.881 40.741 0.00 0.00 32.16 2.59 R
3141 3856 0.035630 GGCAAGCCTGAGTGTCTGAT 60.036 55.000 3.29 0.00 0.00 2.90 R
4368 5108 0.247460 TCATCCCTCACAGCAACGAG 59.753 55.000 0.00 0.00 0.00 4.18 R
5106 5881 1.108776 GATCCTGCATGCAACACCAT 58.891 50.000 22.88 8.86 0.00 3.55 R
5469 6245 0.036952 CCCTCATGTGACTGACGCTT 60.037 55.000 0.00 0.00 0.00 4.68 R
6393 7251 0.321298 CCCTCCCGTAGTTGTGGTTG 60.321 60.000 0.00 0.00 0.00 3.77 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
27 28 7.042797 TCTTAATTAATGGATGAGGCAAAGC 57.957 36.000 0.00 0.00 0.00 3.51
28 29 6.835488 TCTTAATTAATGGATGAGGCAAAGCT 59.165 34.615 0.00 0.00 0.00 3.74
29 30 5.945144 AATTAATGGATGAGGCAAAGCTT 57.055 34.783 0.00 0.00 0.00 3.74
30 31 5.945144 ATTAATGGATGAGGCAAAGCTTT 57.055 34.783 5.69 5.69 0.00 3.51
31 32 5.743636 TTAATGGATGAGGCAAAGCTTTT 57.256 34.783 9.53 0.00 0.00 2.27
32 33 3.604875 ATGGATGAGGCAAAGCTTTTG 57.395 42.857 9.53 6.62 0.00 2.44
47 48 4.591998 GCTTTTGCCTTCGTTTCAAAAA 57.408 36.364 0.00 0.00 38.65 1.94
70 71 1.578583 AAGATACATTGTACGGGCGC 58.421 50.000 0.00 0.00 0.00 6.53
76 77 2.760159 ATTGTACGGGCGCACATGC 61.760 57.895 11.77 0.00 37.78 4.06
94 95 0.739112 GCCGGAAGTGCTCTTCTCAG 60.739 60.000 23.63 16.19 46.47 3.35
97 98 1.337635 CGGAAGTGCTCTTCTCAGCTT 60.338 52.381 23.63 0.00 46.47 3.74
129 130 8.491152 CACATGAGCTCGGATAAATAGTAAAAG 58.509 37.037 9.64 0.00 0.00 2.27
133 134 9.832445 TGAGCTCGGATAAATAGTAAAAGAAAT 57.168 29.630 9.64 0.00 0.00 2.17
214 218 6.321181 TGCAAAGTTTCATTAGGGGATGATAC 59.679 38.462 0.00 0.00 37.89 2.24
231 235 5.845391 TGATACTCATGGAATACGTGACA 57.155 39.130 0.00 0.00 40.12 3.58
293 298 4.886579 ACATTGTTGGAGCCTCAATTTTC 58.113 39.130 0.00 0.00 30.74 2.29
297 302 5.200368 TGTTGGAGCCTCAATTTTCTTTC 57.800 39.130 0.00 0.00 0.00 2.62
305 310 4.559153 CCTCAATTTTCTTTCGCCATGTT 58.441 39.130 0.00 0.00 0.00 2.71
307 312 5.466393 CCTCAATTTTCTTTCGCCATGTTTT 59.534 36.000 0.00 0.00 0.00 2.43
308 313 6.018016 CCTCAATTTTCTTTCGCCATGTTTTT 60.018 34.615 0.00 0.00 0.00 1.94
317 322 4.052159 TCGCCATGTTTTTCACAAATGT 57.948 36.364 0.00 0.00 39.50 2.71
333 341 7.587629 TCACAAATGTCAGATGATGAAACTTC 58.412 34.615 0.00 0.00 40.43 3.01
345 353 3.921119 TGAAACTTCGCAAGCAATCAT 57.079 38.095 0.00 0.00 37.18 2.45
353 361 5.801947 ACTTCGCAAGCAATCATAACATTTC 59.198 36.000 0.00 0.00 37.18 2.17
359 367 7.514591 CGCAAGCAATCATAACATTTCTCAATG 60.515 37.037 0.00 0.00 44.90 2.82
461 469 2.818751 TTTTCGCAACCCCATATCCT 57.181 45.000 0.00 0.00 0.00 3.24
467 475 5.160607 TCGCAACCCCATATCCTATTAAG 57.839 43.478 0.00 0.00 0.00 1.85
519 527 3.014604 GCTCGAGCTCATATTAACCGT 57.985 47.619 29.88 0.00 38.21 4.83
529 538 4.341935 TCATATTAACCGTGTCACGTACG 58.658 43.478 23.01 15.01 40.58 3.67
563 572 5.877012 TCTTCTTTTTAGTAGAGCATGCAGG 59.123 40.000 21.98 0.00 0.00 4.85
573 583 5.819901 AGTAGAGCATGCAGGATTACTTTTC 59.180 40.000 21.98 3.65 0.00 2.29
575 585 5.994250 AGAGCATGCAGGATTACTTTTCTA 58.006 37.500 21.98 0.00 0.00 2.10
584 594 6.199342 GCAGGATTACTTTTCTAAGCTACTCG 59.801 42.308 0.00 0.00 34.60 4.18
590 600 2.257974 TTCTAAGCTACTCGTGCACG 57.742 50.000 32.76 32.76 41.45 5.34
603 613 2.984471 TCGTGCACGATTACTGTCTTTC 59.016 45.455 36.40 0.00 44.22 2.62
626 637 4.439057 TCTAGTGGAAATGCACGATTACC 58.561 43.478 0.00 0.00 0.00 2.85
630 641 4.156008 AGTGGAAATGCACGATTACCTTTC 59.844 41.667 0.00 0.00 0.00 2.62
633 644 5.095490 GGAAATGCACGATTACCTTTCTTG 58.905 41.667 0.00 0.00 0.00 3.02
634 645 5.335661 GGAAATGCACGATTACCTTTCTTGT 60.336 40.000 0.00 0.00 0.00 3.16
635 646 5.705609 AATGCACGATTACCTTTCTTGTT 57.294 34.783 0.00 0.00 0.00 2.83
637 648 5.856126 TGCACGATTACCTTTCTTGTTAG 57.144 39.130 0.00 0.00 0.00 2.34
638 649 5.543714 TGCACGATTACCTTTCTTGTTAGA 58.456 37.500 0.00 0.00 0.00 2.10
639 650 6.170506 TGCACGATTACCTTTCTTGTTAGAT 58.829 36.000 0.00 0.00 0.00 1.98
640 651 6.092122 TGCACGATTACCTTTCTTGTTAGATG 59.908 38.462 0.00 0.00 0.00 2.90
642 653 6.092122 CACGATTACCTTTCTTGTTAGATGCA 59.908 38.462 0.00 0.00 0.00 3.96
643 654 6.092259 ACGATTACCTTTCTTGTTAGATGCAC 59.908 38.462 0.00 0.00 0.00 4.57
644 655 5.856126 TTACCTTTCTTGTTAGATGCACG 57.144 39.130 0.00 0.00 0.00 5.34
645 656 4.002906 ACCTTTCTTGTTAGATGCACGA 57.997 40.909 0.00 0.00 0.00 4.35
646 657 4.579869 ACCTTTCTTGTTAGATGCACGAT 58.420 39.130 0.00 0.00 0.00 3.73
647 658 5.003804 ACCTTTCTTGTTAGATGCACGATT 58.996 37.500 0.00 0.00 0.00 3.34
648 659 6.170506 ACCTTTCTTGTTAGATGCACGATTA 58.829 36.000 0.00 0.00 0.00 1.75
649 660 6.092259 ACCTTTCTTGTTAGATGCACGATTAC 59.908 38.462 0.00 0.00 0.00 1.89
650 661 6.417191 TTTCTTGTTAGATGCACGATTACC 57.583 37.500 0.00 0.00 0.00 2.85
651 662 5.339008 TCTTGTTAGATGCACGATTACCT 57.661 39.130 0.00 0.00 0.00 3.08
652 663 5.730550 TCTTGTTAGATGCACGATTACCTT 58.269 37.500 0.00 0.00 0.00 3.50
653 664 6.170506 TCTTGTTAGATGCACGATTACCTTT 58.829 36.000 0.00 0.00 0.00 3.11
654 665 6.653320 TCTTGTTAGATGCACGATTACCTTTT 59.347 34.615 0.00 0.00 0.00 2.27
655 666 6.811253 TGTTAGATGCACGATTACCTTTTT 57.189 33.333 0.00 0.00 0.00 1.94
683 694 7.530010 AGGACATTGATGAACGATTACTTTTG 58.470 34.615 0.00 0.00 0.00 2.44
738 757 4.142049 ACGAGGAAATCAAGAGAGATCACC 60.142 45.833 0.00 0.00 0.00 4.02
739 758 4.702831 GAGGAAATCAAGAGAGATCACCC 58.297 47.826 0.00 0.00 0.00 4.61
740 759 4.369872 AGGAAATCAAGAGAGATCACCCT 58.630 43.478 0.00 0.00 0.00 4.34
741 760 4.787534 AGGAAATCAAGAGAGATCACCCTT 59.212 41.667 0.00 0.00 0.00 3.95
742 761 5.252630 AGGAAATCAAGAGAGATCACCCTTT 59.747 40.000 0.00 0.00 0.00 3.11
743 762 5.948758 GGAAATCAAGAGAGATCACCCTTTT 59.051 40.000 0.00 0.00 0.00 2.27
744 763 6.435591 GGAAATCAAGAGAGATCACCCTTTTT 59.564 38.462 0.00 0.00 0.00 1.94
802 821 3.557228 ATCAAGAGAGATCACCTTGGC 57.443 47.619 16.46 0.00 38.19 4.52
805 824 0.324738 AGAGAGATCACCTTGGCCGA 60.325 55.000 0.00 0.00 0.00 5.54
826 845 6.035217 CCGACCCGTTTTTCTTTTCTTTTTA 58.965 36.000 0.00 0.00 0.00 1.52
847 932 0.322098 AATCATGTCGGCCCGTTTCA 60.322 50.000 1.63 1.76 0.00 2.69
848 933 0.107214 ATCATGTCGGCCCGTTTCAT 60.107 50.000 1.63 4.25 0.00 2.57
860 945 2.227865 CCCGTTTCATATTTATGGGCCG 59.772 50.000 0.00 0.00 34.50 6.13
878 990 1.202687 CCGCTCATCAGGCTAAATGGA 60.203 52.381 8.65 0.00 0.00 3.41
891 1003 2.100605 AAATGGACGAGCCTCTCAAC 57.899 50.000 0.00 0.00 37.63 3.18
892 1004 1.270907 AATGGACGAGCCTCTCAACT 58.729 50.000 0.00 0.00 37.63 3.16
893 1005 0.820871 ATGGACGAGCCTCTCAACTC 59.179 55.000 0.00 0.00 37.63 3.01
894 1006 1.251527 TGGACGAGCCTCTCAACTCC 61.252 60.000 0.00 0.00 37.63 3.85
895 1007 1.513622 GACGAGCCTCTCAACTCCC 59.486 63.158 0.00 0.00 0.00 4.30
896 1008 1.228894 ACGAGCCTCTCAACTCCCA 60.229 57.895 0.00 0.00 0.00 4.37
897 1009 0.832135 ACGAGCCTCTCAACTCCCAA 60.832 55.000 0.00 0.00 0.00 4.12
898 1010 0.321671 CGAGCCTCTCAACTCCCAAA 59.678 55.000 0.00 0.00 0.00 3.28
899 1011 1.065854 CGAGCCTCTCAACTCCCAAAT 60.066 52.381 0.00 0.00 0.00 2.32
900 1012 2.363683 GAGCCTCTCAACTCCCAAATG 58.636 52.381 0.00 0.00 0.00 2.32
901 1013 0.813821 GCCTCTCAACTCCCAAATGC 59.186 55.000 0.00 0.00 0.00 3.56
902 1014 1.467920 CCTCTCAACTCCCAAATGCC 58.532 55.000 0.00 0.00 0.00 4.40
903 1015 1.467920 CTCTCAACTCCCAAATGCCC 58.532 55.000 0.00 0.00 0.00 5.36
904 1016 0.039618 TCTCAACTCCCAAATGCCCC 59.960 55.000 0.00 0.00 0.00 5.80
905 1017 0.040204 CTCAACTCCCAAATGCCCCT 59.960 55.000 0.00 0.00 0.00 4.79
906 1018 1.284785 CTCAACTCCCAAATGCCCCTA 59.715 52.381 0.00 0.00 0.00 3.53
907 1019 1.713647 TCAACTCCCAAATGCCCCTAA 59.286 47.619 0.00 0.00 0.00 2.69
908 1020 2.110899 TCAACTCCCAAATGCCCCTAAA 59.889 45.455 0.00 0.00 0.00 1.85
909 1021 2.903135 CAACTCCCAAATGCCCCTAAAA 59.097 45.455 0.00 0.00 0.00 1.52
910 1022 2.820178 ACTCCCAAATGCCCCTAAAAG 58.180 47.619 0.00 0.00 0.00 2.27
911 1023 2.381961 ACTCCCAAATGCCCCTAAAAGA 59.618 45.455 0.00 0.00 0.00 2.52
912 1024 3.181412 ACTCCCAAATGCCCCTAAAAGAA 60.181 43.478 0.00 0.00 0.00 2.52
913 1025 3.440127 TCCCAAATGCCCCTAAAAGAAG 58.560 45.455 0.00 0.00 0.00 2.85
955 1073 2.665165 CAGAGTCTAGGTCAGGAGCAT 58.335 52.381 0.00 0.00 0.00 3.79
1067 1186 2.987985 GGGGGAGTAGGAGAACGTT 58.012 57.895 0.00 0.00 0.00 3.99
1076 1195 3.506844 AGTAGGAGAACGTTGAGGAAGAC 59.493 47.826 5.00 0.00 0.00 3.01
1084 1206 1.873591 CGTTGAGGAAGACCACAAAGG 59.126 52.381 0.00 0.00 45.27 3.11
1089 1211 0.322546 GGAAGACCACAAAGGCGGAT 60.323 55.000 0.00 0.00 43.14 4.18
1107 1229 2.417719 GATTATCCATCGGTGCTGGAC 58.582 52.381 0.00 0.00 45.27 4.02
1335 1457 4.199310 CAAGACTGGAGTTGGAGAAAACA 58.801 43.478 0.00 0.00 32.21 2.83
1373 1495 1.557651 GACGAGCGGTCTTACCAATC 58.442 55.000 13.48 0.00 42.62 2.67
1556 1683 6.481313 GCTTAGCATCATGTCAGATCTGTTTA 59.519 38.462 21.92 10.19 0.00 2.01
1603 1730 8.389603 TCAAGCAAAAACAGCTGAAATTTAAAG 58.610 29.630 23.35 12.09 42.53 1.85
1905 2056 6.995686 TGATGCTACTTTCTGTAAACCTTCAA 59.004 34.615 0.00 0.00 0.00 2.69
2063 2214 5.837829 TCAAGCCCCAAATAGGTTTATCTT 58.162 37.500 0.00 0.00 34.66 2.40
2124 2275 5.288804 CCTGGTGGTTTGTCAGTTTAAATG 58.711 41.667 0.00 0.00 0.00 2.32
2451 3145 8.664669 TCATCCTGCATAAGGTTGATAGTATA 57.335 34.615 1.80 0.00 45.85 1.47
2452 3146 9.271921 TCATCCTGCATAAGGTTGATAGTATAT 57.728 33.333 1.80 0.00 45.85 0.86
2624 3324 8.186821 CACATTTCACTAAATCCTTGATTCTCC 58.813 37.037 0.00 0.00 32.87 3.71
3015 3728 4.333649 TCTGCAACTTCTTGTTCAGAACTG 59.666 41.667 14.51 7.54 38.54 3.16
3044 3757 1.981495 CTCCTCTTCTGTTTGTCCCCT 59.019 52.381 0.00 0.00 0.00 4.79
3149 3864 9.640963 ACAAAGTGTTTCTACTATATCAGACAC 57.359 33.333 0.00 0.00 37.12 3.67
3150 3865 9.862371 CAAAGTGTTTCTACTATATCAGACACT 57.138 33.333 0.00 0.00 45.81 3.55
3152 3867 8.809468 AGTGTTTCTACTATATCAGACACTCA 57.191 34.615 0.00 0.00 41.69 3.41
3153 3868 8.898761 AGTGTTTCTACTATATCAGACACTCAG 58.101 37.037 0.00 0.00 41.69 3.35
3154 3869 8.132362 GTGTTTCTACTATATCAGACACTCAGG 58.868 40.741 0.00 0.00 34.79 3.86
3155 3870 6.885952 TTCTACTATATCAGACACTCAGGC 57.114 41.667 0.00 0.00 0.00 4.85
3156 3871 6.194285 TCTACTATATCAGACACTCAGGCT 57.806 41.667 0.00 0.00 33.98 4.58
3157 3872 6.606069 TCTACTATATCAGACACTCAGGCTT 58.394 40.000 0.00 0.00 27.44 4.35
3158 3873 5.528043 ACTATATCAGACACTCAGGCTTG 57.472 43.478 0.00 0.00 27.44 4.01
3159 3874 2.680312 TATCAGACACTCAGGCTTGC 57.320 50.000 0.00 0.00 27.44 4.01
3160 3875 0.035630 ATCAGACACTCAGGCTTGCC 60.036 55.000 2.97 2.97 27.44 4.52
3161 3876 1.123861 TCAGACACTCAGGCTTGCCT 61.124 55.000 8.56 8.56 27.44 4.75
3162 3877 0.610174 CAGACACTCAGGCTTGCCTA 59.390 55.000 14.35 2.68 27.44 3.93
3163 3878 1.002430 CAGACACTCAGGCTTGCCTAA 59.998 52.381 14.35 0.00 27.44 2.69
3164 3879 1.699634 AGACACTCAGGCTTGCCTAAA 59.300 47.619 14.35 4.91 20.59 1.85
3165 3880 2.106511 AGACACTCAGGCTTGCCTAAAA 59.893 45.455 14.35 2.44 20.59 1.52
3166 3881 2.884639 GACACTCAGGCTTGCCTAAAAA 59.115 45.455 14.35 0.02 0.00 1.94
3306 4021 5.043903 GCGTCTCTTCTTGCTGTATATTCA 58.956 41.667 0.00 0.00 0.00 2.57
3452 4171 1.985614 TGCCACTACATGCAGCTCT 59.014 52.632 0.00 0.00 32.77 4.09
3591 4310 5.092259 GCCCTAGTCTAATATACACCCCTT 58.908 45.833 0.00 0.00 0.00 3.95
3603 4322 8.577164 AATATACACCCCTTAACTCCAATACT 57.423 34.615 0.00 0.00 0.00 2.12
4060 4795 2.233271 CTCAGGTGTCCAAACATGCTT 58.767 47.619 0.00 0.00 37.81 3.91
4276 5016 5.402997 GGGGGTGTATATTAGACTAGTGC 57.597 47.826 0.00 0.00 0.00 4.40
4277 5017 5.085219 GGGGGTGTATATTAGACTAGTGCT 58.915 45.833 0.00 0.00 0.00 4.40
4278 5018 6.251471 GGGGGTGTATATTAGACTAGTGCTA 58.749 44.000 0.00 0.00 0.00 3.49
4305 5045 3.577805 GGGGGTGTAATATGCACTTCT 57.422 47.619 9.60 0.00 37.07 2.85
4306 5046 3.477530 GGGGGTGTAATATGCACTTCTC 58.522 50.000 9.60 1.75 37.07 2.87
4307 5047 3.136626 GGGGGTGTAATATGCACTTCTCT 59.863 47.826 9.60 0.00 37.07 3.10
4308 5048 4.381411 GGGGTGTAATATGCACTTCTCTC 58.619 47.826 9.60 0.00 37.07 3.20
4309 5049 4.101741 GGGGTGTAATATGCACTTCTCTCT 59.898 45.833 9.60 0.00 37.07 3.10
4310 5050 5.396884 GGGGTGTAATATGCACTTCTCTCTT 60.397 44.000 9.60 0.00 37.07 2.85
4311 5051 6.116126 GGGTGTAATATGCACTTCTCTCTTT 58.884 40.000 9.60 0.00 37.07 2.52
4352 5092 2.864885 ATGGGGATTTACATTGGCCA 57.135 45.000 0.00 0.00 0.00 5.36
4368 5108 0.598065 GCCACTGGATGTGTTTGGTC 59.402 55.000 0.00 0.00 44.81 4.02
4436 5176 0.811281 AGCGCAAAAGGGATAACTGC 59.189 50.000 11.47 0.00 0.00 4.40
4463 5203 6.478512 ACTCTCAATGAGGAGGTTCTTATC 57.521 41.667 10.71 0.00 46.72 1.75
4794 5542 5.183140 ACGCATTTAGGCTAATGTTTTCTGT 59.817 36.000 7.96 0.00 37.72 3.41
5007 5781 6.204688 TGTTGTGCCACAGATTTCTAGTTTAG 59.795 38.462 0.00 0.00 0.00 1.85
5214 5990 3.780925 GCTGAAAGTGAAGCGCATT 57.219 47.368 11.47 0.00 35.30 3.56
5289 6065 6.270156 TGCAAGTCAATCAATTATCAAGCA 57.730 33.333 0.00 0.00 0.00 3.91
5336 6112 4.210447 CGTGAGCAGCCAAAAACG 57.790 55.556 0.00 0.00 0.00 3.60
5347 6123 3.003275 CAGCCAAAAACGTAGAAGCAAGA 59.997 43.478 0.00 0.00 0.00 3.02
5381 6157 1.202222 GCTGACATGTGGCATTGTAGC 60.202 52.381 1.15 10.68 29.25 3.58
5421 6197 2.248280 TCAGTGTGCGTATTGTTGGT 57.752 45.000 0.00 0.00 0.00 3.67
5469 6245 0.955428 GGTTCATTGCCTCGACTGCA 60.955 55.000 0.86 0.86 36.84 4.41
5499 6275 2.371841 TCACATGAGGGTGTTACTGCTT 59.628 45.455 0.00 0.00 39.76 3.91
5635 6411 3.991999 GCAGCCAGCAGATTGACA 58.008 55.556 0.00 0.00 44.79 3.58
5650 6426 5.991606 CAGATTGACAGTGAGGTGTTCTTTA 59.008 40.000 0.00 0.00 0.00 1.85
5750 6526 5.596772 CCCTTTTTCCGTTATGTTATCCCAT 59.403 40.000 0.00 0.00 0.00 4.00
5960 6815 1.665679 GGCATGTTATGAGTCGTGGTG 59.334 52.381 0.00 0.00 0.00 4.17
6066 6924 5.069648 TGTGAGGATAAGTTAGATCTGCTGG 59.930 44.000 5.18 0.00 0.00 4.85
6083 6941 9.774742 GATCTGCTGGTTTAATTAACTGTTTAG 57.225 33.333 0.00 0.00 36.93 1.85
6190 7048 1.678101 GTGCTGGATTAATGTGAGGGC 59.322 52.381 0.00 0.00 0.00 5.19
6193 7051 2.295349 GCTGGATTAATGTGAGGGCATG 59.705 50.000 0.00 0.00 0.00 4.06
6206 7064 2.694628 GAGGGCATGCAAATGAACCATA 59.305 45.455 21.36 0.00 0.00 2.74
6207 7065 3.311091 AGGGCATGCAAATGAACCATAT 58.689 40.909 21.36 0.00 0.00 1.78
6219 7077 5.999205 ATGAACCATATTTTTGCTGGTCA 57.001 34.783 0.00 0.00 42.38 4.02
6233 7091 2.615912 GCTGGTCATGCACTTCCTTATC 59.384 50.000 0.00 0.00 0.00 1.75
6273 7131 7.286313 TGCTTGTAAATGGAAAAGGGAAAAAT 58.714 30.769 0.00 0.00 0.00 1.82
6317 7175 3.140707 TGCCATGATAATCAAGGGGTCAT 59.859 43.478 0.00 0.00 35.87 3.06
6360 7218 4.036734 TGAAGACAATCTTGAAAGTGGCAC 59.963 41.667 10.29 10.29 36.73 5.01
6362 7220 2.548057 GACAATCTTGAAAGTGGCACGA 59.452 45.455 12.71 2.31 0.00 4.35
6381 7239 5.348451 GCACGAATTCAAAGTGGCAAATATT 59.652 36.000 6.22 0.00 36.48 1.28
6392 7250 8.991026 CAAAGTGGCAAATATTCAATTTTCTCA 58.009 29.630 0.00 0.00 0.00 3.27
6393 7251 8.538409 AAGTGGCAAATATTCAATTTTCTCAC 57.462 30.769 0.00 0.00 0.00 3.51
6407 7265 2.519377 TCTCACAACCACAACTACGG 57.481 50.000 0.00 0.00 0.00 4.02
6424 7282 1.420138 ACGGGAGGGCTATTATTGGTG 59.580 52.381 0.00 0.00 0.00 4.17
6465 7323 4.277593 CCTAGCTCTGGCGGCTCG 62.278 72.222 11.43 0.98 44.37 5.03
6489 7347 2.838813 GGAAACCTAACCTCCTGTAGCT 59.161 50.000 0.00 0.00 0.00 3.32
6502 7360 2.448542 TAGCTGGCCCTCCCCATC 60.449 66.667 0.00 0.00 33.64 3.51
6508 7366 2.444895 GCCCTCCCCATCGACTCT 60.445 66.667 0.00 0.00 0.00 3.24
6510 7368 1.826024 CCCTCCCCATCGACTCTTG 59.174 63.158 0.00 0.00 0.00 3.02
6512 7370 1.333636 CCTCCCCATCGACTCTTGCT 61.334 60.000 0.00 0.00 0.00 3.91
6517 7375 1.134580 CCCATCGACTCTTGCTGTCAT 60.135 52.381 0.00 0.00 34.37 3.06
6524 7382 1.270518 ACTCTTGCTGTCATCGCTGTT 60.271 47.619 0.00 0.00 0.00 3.16
6535 7393 3.429141 CGCTGTTGCTGGCTCCTG 61.429 66.667 0.00 0.00 36.97 3.86
6581 7439 2.642807 TCGAAAGAGGGTGGGAATCTTT 59.357 45.455 0.00 0.00 43.96 2.52
6587 7445 0.037734 GGGTGGGAATCTTTGGTCGT 59.962 55.000 0.00 0.00 0.00 4.34
6632 7490 3.595758 GGCGCAACTTGGTGCTGT 61.596 61.111 10.83 0.00 43.61 4.40
6636 7494 2.859981 GCAACTTGGTGCTGTGGGG 61.860 63.158 3.07 0.00 41.51 4.96
6683 7541 1.841556 GACCTGGGTGTGGACCTCA 60.842 63.158 0.00 0.00 42.66 3.86
6689 7547 1.073025 GGTGTGGACCTCATGTGCA 59.927 57.895 0.00 0.00 43.74 4.57
6737 7595 3.838271 GGGCGGATCGACAGCTGA 61.838 66.667 23.35 0.00 36.10 4.26
6747 7605 1.447643 GACAGCTGAGTGTGGTGGT 59.552 57.895 23.35 0.00 37.25 4.16
6752 7610 1.302033 CTGAGTGTGGTGGTGGCTC 60.302 63.158 0.00 0.00 0.00 4.70
6756 7614 4.927782 TGTGGTGGTGGCTCGTGC 62.928 66.667 0.00 0.00 38.76 5.34
6764 7622 4.641645 TGGCTCGTGCAGGTTGGG 62.642 66.667 12.07 0.00 41.91 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.945144 AAGCTTTGCCTCATCCATTAATT 57.055 34.783 0.00 0.00 0.00 1.40
8 9 5.945144 AAAGCTTTGCCTCATCCATTAAT 57.055 34.783 11.80 0.00 0.00 1.40
9 10 5.481105 CAAAAGCTTTGCCTCATCCATTAA 58.519 37.500 13.54 0.00 0.00 1.40
10 11 4.621274 GCAAAAGCTTTGCCTCATCCATTA 60.621 41.667 13.54 0.00 39.38 1.90
11 12 3.867216 GCAAAAGCTTTGCCTCATCCATT 60.867 43.478 13.54 0.00 39.38 3.16
12 13 2.354403 GCAAAAGCTTTGCCTCATCCAT 60.354 45.455 13.54 0.00 39.38 3.41
13 14 1.001181 GCAAAAGCTTTGCCTCATCCA 59.999 47.619 13.54 0.00 39.38 3.41
14 15 1.718396 GCAAAAGCTTTGCCTCATCC 58.282 50.000 13.54 0.00 39.38 3.51
21 22 1.570813 AACGAAGGCAAAAGCTTTGC 58.429 45.000 13.54 17.13 44.22 3.68
22 23 3.186119 TGAAACGAAGGCAAAAGCTTTG 58.814 40.909 13.54 8.26 0.00 2.77
23 24 3.518634 TGAAACGAAGGCAAAAGCTTT 57.481 38.095 5.69 5.69 0.00 3.51
24 25 3.518634 TTGAAACGAAGGCAAAAGCTT 57.481 38.095 0.00 0.00 0.00 3.74
25 26 3.518634 TTTGAAACGAAGGCAAAAGCT 57.481 38.095 0.00 0.00 0.00 3.74
26 27 4.591998 TTTTTGAAACGAAGGCAAAAGC 57.408 36.364 0.00 0.00 41.02 3.51
48 49 3.181504 GCGCCCGTACAATGTATCTTTTT 60.182 43.478 0.00 0.00 0.00 1.94
49 50 2.353579 GCGCCCGTACAATGTATCTTTT 59.646 45.455 0.00 0.00 0.00 2.27
50 51 1.937899 GCGCCCGTACAATGTATCTTT 59.062 47.619 0.00 0.00 0.00 2.52
70 71 0.957395 AAGAGCACTTCCGGCATGTG 60.957 55.000 14.19 14.19 34.01 3.21
101 102 5.777802 ACTATTTATCCGAGCTCATGTGAG 58.222 41.667 15.40 5.66 44.75 3.51
179 183 7.814107 CCTAATGAAACTTTGCAAGCTATCAAA 59.186 33.333 0.00 11.35 0.00 2.69
269 273 4.961438 AATTGAGGCTCCAACAATGTTT 57.039 36.364 12.86 0.00 35.00 2.83
286 290 6.628461 GTGAAAAACATGGCGAAAGAAAATTG 59.372 34.615 0.00 0.00 0.00 2.32
287 291 6.314896 TGTGAAAAACATGGCGAAAGAAAATT 59.685 30.769 0.00 0.00 32.36 1.82
293 298 5.006552 ACATTTGTGAAAAACATGGCGAAAG 59.993 36.000 0.00 0.00 38.99 2.62
297 302 3.801050 TGACATTTGTGAAAAACATGGCG 59.199 39.130 0.00 0.00 38.99 5.69
305 310 8.415553 AGTTTCATCATCTGACATTTGTGAAAA 58.584 29.630 6.15 0.00 36.47 2.29
307 312 7.514784 AGTTTCATCATCTGACATTTGTGAA 57.485 32.000 0.00 0.00 32.17 3.18
308 313 7.514784 AAGTTTCATCATCTGACATTTGTGA 57.485 32.000 0.00 0.00 32.17 3.58
317 322 3.125829 GCTTGCGAAGTTTCATCATCTGA 59.874 43.478 0.00 0.00 0.00 3.27
333 341 5.334319 TGAGAAATGTTATGATTGCTTGCG 58.666 37.500 0.00 0.00 0.00 4.85
396 404 4.583073 AGCTCGGGTGAACAGTAAAATTTT 59.417 37.500 8.75 8.75 0.00 1.82
399 407 3.335579 GAGCTCGGGTGAACAGTAAAAT 58.664 45.455 0.00 0.00 0.00 1.82
403 411 1.880894 CGAGCTCGGGTGAACAGTA 59.119 57.895 28.40 0.00 35.37 2.74
445 453 4.595781 ACTTAATAGGATATGGGGTTGCGA 59.404 41.667 0.00 0.00 0.00 5.10
446 454 4.695455 CACTTAATAGGATATGGGGTTGCG 59.305 45.833 0.00 0.00 0.00 4.85
447 455 5.876357 TCACTTAATAGGATATGGGGTTGC 58.124 41.667 0.00 0.00 0.00 4.17
448 456 8.760980 TTTTCACTTAATAGGATATGGGGTTG 57.239 34.615 0.00 0.00 0.00 3.77
450 458 9.367160 CATTTTTCACTTAATAGGATATGGGGT 57.633 33.333 0.00 0.00 0.00 4.95
451 459 8.806146 CCATTTTTCACTTAATAGGATATGGGG 58.194 37.037 0.00 0.00 0.00 4.96
467 475 6.867816 TGCACAGATGTATTTCCATTTTTCAC 59.132 34.615 0.00 0.00 0.00 3.18
529 538 7.584987 TCTACTAAAAAGAAGAAAGCATGCAC 58.415 34.615 21.98 10.82 0.00 4.57
563 572 6.530534 TGCACGAGTAGCTTAGAAAAGTAATC 59.469 38.462 0.00 0.00 34.99 1.75
573 583 3.990546 TCGTGCACGAGTAGCTTAG 57.009 52.632 36.40 6.27 44.22 2.18
584 594 4.238514 AGAGAAAGACAGTAATCGTGCAC 58.761 43.478 6.82 6.82 0.00 4.57
590 600 9.092876 CATTTCCACTAGAGAAAGACAGTAATC 57.907 37.037 14.80 0.00 36.71 1.75
603 613 4.508124 GGTAATCGTGCATTTCCACTAGAG 59.492 45.833 0.00 0.00 33.12 2.43
626 637 6.313905 AGGTAATCGTGCATCTAACAAGAAAG 59.686 38.462 0.00 0.00 0.00 2.62
630 641 6.422776 AAAGGTAATCGTGCATCTAACAAG 57.577 37.500 0.00 0.00 0.00 3.16
653 664 9.226606 AGTAATCGTTCATCAATGTCCTAAAAA 57.773 29.630 0.00 0.00 0.00 1.94
654 665 8.786826 AGTAATCGTTCATCAATGTCCTAAAA 57.213 30.769 0.00 0.00 0.00 1.52
655 666 8.786826 AAGTAATCGTTCATCAATGTCCTAAA 57.213 30.769 0.00 0.00 0.00 1.85
656 667 8.786826 AAAGTAATCGTTCATCAATGTCCTAA 57.213 30.769 0.00 0.00 0.00 2.69
657 668 8.664798 CAAAAGTAATCGTTCATCAATGTCCTA 58.335 33.333 0.00 0.00 0.00 2.94
658 669 7.174946 ACAAAAGTAATCGTTCATCAATGTCCT 59.825 33.333 0.00 0.00 0.00 3.85
659 670 7.305474 ACAAAAGTAATCGTTCATCAATGTCC 58.695 34.615 0.00 0.00 0.00 4.02
660 671 8.728088 AACAAAAGTAATCGTTCATCAATGTC 57.272 30.769 0.00 0.00 0.00 3.06
661 672 9.528018 AAAACAAAAGTAATCGTTCATCAATGT 57.472 25.926 0.00 0.00 0.00 2.71
692 703 2.213499 CAGTAAATCGTGGATCCTGCC 58.787 52.381 14.23 0.00 0.00 4.85
774 793 9.224267 CAAGGTGATCTCTCTTGATTCTAAAAA 57.776 33.333 15.28 0.00 39.97 1.94
775 794 7.826252 CCAAGGTGATCTCTCTTGATTCTAAAA 59.174 37.037 19.16 0.00 39.97 1.52
776 795 7.334090 CCAAGGTGATCTCTCTTGATTCTAAA 58.666 38.462 19.16 0.00 39.97 1.85
777 796 6.631314 GCCAAGGTGATCTCTCTTGATTCTAA 60.631 42.308 19.16 0.00 39.97 2.10
778 797 5.163364 GCCAAGGTGATCTCTCTTGATTCTA 60.163 44.000 19.16 0.00 39.97 2.10
779 798 4.383989 GCCAAGGTGATCTCTCTTGATTCT 60.384 45.833 19.16 0.00 39.97 2.40
780 799 3.876320 GCCAAGGTGATCTCTCTTGATTC 59.124 47.826 19.16 9.84 39.97 2.52
781 800 3.371380 GGCCAAGGTGATCTCTCTTGATT 60.371 47.826 19.16 0.00 39.97 2.57
782 801 2.172293 GGCCAAGGTGATCTCTCTTGAT 59.828 50.000 19.16 0.00 39.97 2.57
783 802 1.556911 GGCCAAGGTGATCTCTCTTGA 59.443 52.381 19.16 0.00 39.97 3.02
784 803 1.741732 CGGCCAAGGTGATCTCTCTTG 60.742 57.143 2.24 14.19 38.01 3.02
785 804 0.539051 CGGCCAAGGTGATCTCTCTT 59.461 55.000 2.24 0.00 0.00 2.85
786 805 0.324738 TCGGCCAAGGTGATCTCTCT 60.325 55.000 2.24 0.00 0.00 3.10
787 806 0.179097 GTCGGCCAAGGTGATCTCTC 60.179 60.000 2.24 0.00 0.00 3.20
788 807 1.617947 GGTCGGCCAAGGTGATCTCT 61.618 60.000 0.00 0.00 34.09 3.10
789 808 1.153349 GGTCGGCCAAGGTGATCTC 60.153 63.158 0.00 0.00 34.09 2.75
790 809 2.670148 GGGTCGGCCAAGGTGATCT 61.670 63.158 9.07 0.00 36.17 2.75
791 810 2.124695 GGGTCGGCCAAGGTGATC 60.125 66.667 9.07 0.00 36.17 2.92
792 811 4.096003 CGGGTCGGCCAAGGTGAT 62.096 66.667 9.07 0.00 36.17 3.06
794 813 4.636435 AACGGGTCGGCCAAGGTG 62.636 66.667 9.07 0.00 36.17 4.00
795 814 2.914756 AAAAACGGGTCGGCCAAGGT 62.915 55.000 9.07 0.00 36.17 3.50
796 815 2.137425 GAAAAACGGGTCGGCCAAGG 62.137 60.000 9.07 0.00 36.17 3.61
797 816 1.170290 AGAAAAACGGGTCGGCCAAG 61.170 55.000 9.07 3.26 36.17 3.61
802 821 3.703286 AAGAAAAGAAAAACGGGTCGG 57.297 42.857 0.00 0.00 0.00 4.79
805 824 9.309516 GATTCTAAAAAGAAAAGAAAAACGGGT 57.690 29.630 0.00 0.00 33.26 5.28
826 845 0.035439 AAACGGGCCGACATGATTCT 60.035 50.000 35.78 2.80 0.00 2.40
847 932 3.614092 CTGATGAGCGGCCCATAAATAT 58.386 45.455 0.00 0.00 0.00 1.28
848 933 2.290260 CCTGATGAGCGGCCCATAAATA 60.290 50.000 0.00 0.00 0.00 1.40
860 945 1.869767 CGTCCATTTAGCCTGATGAGC 59.130 52.381 0.00 0.00 0.00 4.26
878 990 0.832135 TTGGGAGTTGAGAGGCTCGT 60.832 55.000 9.22 0.00 32.35 4.18
891 1003 3.100207 TCTTTTAGGGGCATTTGGGAG 57.900 47.619 0.00 0.00 0.00 4.30
892 1004 3.440127 CTTCTTTTAGGGGCATTTGGGA 58.560 45.455 0.00 0.00 0.00 4.37
893 1005 2.093500 GCTTCTTTTAGGGGCATTTGGG 60.093 50.000 0.00 0.00 0.00 4.12
894 1006 2.833943 AGCTTCTTTTAGGGGCATTTGG 59.166 45.455 0.00 0.00 0.00 3.28
895 1007 3.118992 GGAGCTTCTTTTAGGGGCATTTG 60.119 47.826 0.00 0.00 0.00 2.32
896 1008 3.099905 GGAGCTTCTTTTAGGGGCATTT 58.900 45.455 0.00 0.00 0.00 2.32
897 1009 2.624293 GGGAGCTTCTTTTAGGGGCATT 60.624 50.000 0.00 0.00 0.00 3.56
898 1010 1.063642 GGGAGCTTCTTTTAGGGGCAT 60.064 52.381 0.00 0.00 0.00 4.40
899 1011 0.331616 GGGAGCTTCTTTTAGGGGCA 59.668 55.000 0.00 0.00 0.00 5.36
900 1012 0.331616 TGGGAGCTTCTTTTAGGGGC 59.668 55.000 0.00 0.00 0.00 5.80
901 1013 2.899303 TTGGGAGCTTCTTTTAGGGG 57.101 50.000 0.00 0.00 0.00 4.79
902 1014 3.118992 GCATTTGGGAGCTTCTTTTAGGG 60.119 47.826 0.00 0.00 0.00 3.53
903 1015 3.118992 GGCATTTGGGAGCTTCTTTTAGG 60.119 47.826 0.00 0.00 0.00 2.69
904 1016 3.428045 CGGCATTTGGGAGCTTCTTTTAG 60.428 47.826 0.00 0.00 0.00 1.85
905 1017 2.491693 CGGCATTTGGGAGCTTCTTTTA 59.508 45.455 0.00 0.00 0.00 1.52
906 1018 1.273327 CGGCATTTGGGAGCTTCTTTT 59.727 47.619 0.00 0.00 0.00 2.27
907 1019 0.890683 CGGCATTTGGGAGCTTCTTT 59.109 50.000 0.00 0.00 0.00 2.52
908 1020 0.038166 TCGGCATTTGGGAGCTTCTT 59.962 50.000 0.00 0.00 0.00 2.52
909 1021 0.038166 TTCGGCATTTGGGAGCTTCT 59.962 50.000 0.00 0.00 0.00 2.85
910 1022 0.171231 GTTCGGCATTTGGGAGCTTC 59.829 55.000 0.00 0.00 0.00 3.86
911 1023 1.586154 CGTTCGGCATTTGGGAGCTT 61.586 55.000 0.00 0.00 0.00 3.74
912 1024 2.040544 CGTTCGGCATTTGGGAGCT 61.041 57.895 0.00 0.00 0.00 4.09
913 1025 1.022451 TACGTTCGGCATTTGGGAGC 61.022 55.000 0.00 0.00 0.00 4.70
989 1107 2.586245 CCTCCATCTCGGCAAGCA 59.414 61.111 0.00 0.00 33.14 3.91
1067 1186 0.250295 CGCCTTTGTGGTCTTCCTCA 60.250 55.000 0.00 0.00 38.35 3.86
1076 1195 2.051334 TGGATAATCCGCCTTTGTGG 57.949 50.000 0.00 0.00 40.17 4.17
1084 1206 0.320771 AGCACCGATGGATAATCCGC 60.321 55.000 0.00 0.00 40.17 5.54
1107 1229 2.662857 ATCGCGGCATCCATCACG 60.663 61.111 6.13 0.00 0.00 4.35
1335 1457 2.116238 TCGGGATCCTTCTTCGGATTT 58.884 47.619 12.58 0.00 43.71 2.17
1373 1495 2.164624 CACTCCCAGTTCTCTCGGTAAG 59.835 54.545 0.00 0.00 0.00 2.34
1542 1669 2.555325 ACCGTCGTAAACAGATCTGACA 59.445 45.455 29.27 10.34 0.00 3.58
1543 1670 3.213249 ACCGTCGTAAACAGATCTGAC 57.787 47.619 29.27 15.50 0.00 3.51
1544 1671 3.752747 TGTACCGTCGTAAACAGATCTGA 59.247 43.478 29.27 3.89 0.00 3.27
1545 1672 4.087510 TGTACCGTCGTAAACAGATCTG 57.912 45.455 21.37 21.37 0.00 2.90
1546 1673 4.201990 GGATGTACCGTCGTAAACAGATCT 60.202 45.833 0.00 0.00 0.00 2.75
1556 1683 1.830279 TTCTCAGGATGTACCGTCGT 58.170 50.000 0.00 0.00 44.74 4.34
1603 1730 3.378427 CCTGCAATACTTGGCTAAACCTC 59.622 47.826 0.00 0.00 40.22 3.85
1905 2056 2.831526 GGGAATTTACAATGCTGGGTGT 59.168 45.455 0.00 0.00 0.00 4.16
2063 2214 4.398988 GCATACAACAGTGGGATCAAATGA 59.601 41.667 0.00 0.00 0.00 2.57
2113 2264 4.892934 AGCTTCCACAACCATTTAAACTGA 59.107 37.500 0.00 0.00 0.00 3.41
2124 2275 0.040067 CGAGCAAAGCTTCCACAACC 60.040 55.000 0.00 0.00 39.88 3.77
2206 2357 5.072464 GCCTAATGGAAAGGAGAGGTCTTAT 59.928 44.000 0.00 0.00 36.08 1.73
2440 3134 7.807687 ACAATACGCGGAATATACTATCAAC 57.192 36.000 12.47 0.00 0.00 3.18
2441 3135 8.186163 CCTACAATACGCGGAATATACTATCAA 58.814 37.037 12.47 0.00 0.00 2.57
2451 3145 5.916661 ATCTATCCTACAATACGCGGAAT 57.083 39.130 12.47 0.00 0.00 3.01
2452 3146 5.124457 GGTATCTATCCTACAATACGCGGAA 59.876 44.000 12.47 0.00 0.00 4.30
2624 3324 9.787626 CGACAGAATTTTCTTTTTCATTTCATG 57.212 29.630 0.00 0.00 34.74 3.07
2736 3446 3.752747 GGATTGAAGGTTTGCCCAATTTG 59.247 43.478 0.00 0.00 30.29 2.32
3015 3728 7.118535 GGACAAACAGAAGAGGAGAAATTCTAC 59.881 40.741 0.00 0.00 32.16 2.59
3141 3856 0.035630 GGCAAGCCTGAGTGTCTGAT 60.036 55.000 3.29 0.00 0.00 2.90
3142 3857 1.123861 AGGCAAGCCTGAGTGTCTGA 61.124 55.000 13.80 0.00 46.22 3.27
3143 3858 1.374190 AGGCAAGCCTGAGTGTCTG 59.626 57.895 13.80 0.00 46.22 3.51
3144 3859 3.897856 AGGCAAGCCTGAGTGTCT 58.102 55.556 13.80 0.00 46.22 3.41
3167 3882 3.893813 AGCAGCCTGAGTTTCTGATTTTT 59.106 39.130 0.00 0.00 0.00 1.94
3168 3883 3.494332 AGCAGCCTGAGTTTCTGATTTT 58.506 40.909 0.00 0.00 0.00 1.82
3169 3884 3.151912 AGCAGCCTGAGTTTCTGATTT 57.848 42.857 0.00 0.00 0.00 2.17
3170 3885 2.875094 AGCAGCCTGAGTTTCTGATT 57.125 45.000 0.00 0.00 0.00 2.57
3285 4000 8.654230 TGATTGAATATACAGCAAGAAGAGAC 57.346 34.615 0.00 0.00 0.00 3.36
3452 4171 1.075212 TGAAACACATGGCTGGGATCA 59.925 47.619 0.00 0.00 0.00 2.92
3591 4310 9.880157 GGTGTATTTTAGACAGTATTGGAGTTA 57.120 33.333 0.00 0.00 0.00 2.24
3742 4467 9.447157 TGGAACTTTCTGAATTTTGTCAAAAAT 57.553 25.926 14.47 6.57 45.81 1.82
4013 4747 3.688272 TCGAGATGTCCGTAAATTCGAC 58.312 45.455 0.00 0.00 31.54 4.20
4296 5036 6.995091 ACTTTAACTGAAAGAGAGAAGTGCAT 59.005 34.615 4.14 0.00 46.57 3.96
4297 5037 6.349300 ACTTTAACTGAAAGAGAGAAGTGCA 58.651 36.000 4.14 0.00 46.57 4.57
4298 5038 6.852858 ACTTTAACTGAAAGAGAGAAGTGC 57.147 37.500 4.14 0.00 46.57 4.40
4299 5039 8.425577 TCAACTTTAACTGAAAGAGAGAAGTG 57.574 34.615 4.14 0.00 46.57 3.16
4300 5040 7.713073 CCTCAACTTTAACTGAAAGAGAGAAGT 59.287 37.037 17.55 0.00 46.57 3.01
4301 5041 7.928706 TCCTCAACTTTAACTGAAAGAGAGAAG 59.071 37.037 17.55 8.53 46.57 2.85
4302 5042 7.792032 TCCTCAACTTTAACTGAAAGAGAGAA 58.208 34.615 17.55 3.88 46.57 2.87
4303 5043 7.361457 TCCTCAACTTTAACTGAAAGAGAGA 57.639 36.000 17.55 7.62 46.57 3.10
4304 5044 8.438676 TTTCCTCAACTTTAACTGAAAGAGAG 57.561 34.615 4.14 9.55 46.57 3.20
4305 5045 8.980481 ATTTCCTCAACTTTAACTGAAAGAGA 57.020 30.769 4.14 1.70 46.57 3.10
4311 5051 9.627123 CCCATATATTTCCTCAACTTTAACTGA 57.373 33.333 0.00 0.00 0.00 3.41
4352 5092 1.416401 ACGAGACCAAACACATCCAGT 59.584 47.619 0.00 0.00 0.00 4.00
4368 5108 0.247460 TCATCCCTCACAGCAACGAG 59.753 55.000 0.00 0.00 0.00 4.18
4436 5176 3.710209 ACCTCCTCATTGAGAGTTTGG 57.290 47.619 15.36 10.84 43.12 3.28
4484 5224 5.574891 TTGTTGCAGAGCTAGAAACAAAA 57.425 34.783 18.08 2.27 37.68 2.44
4571 5311 8.426489 ACACATACTAGAGGTTGTGAAGTAAAA 58.574 33.333 18.71 0.00 38.75 1.52
4702 5450 9.234827 TGCACATATAGCTCAAAGCATATTAAT 57.765 29.630 0.00 0.00 45.56 1.40
4794 5542 3.635836 TGTGAGGTGCAAACAAATGATGA 59.364 39.130 0.00 0.00 0.00 2.92
5106 5881 1.108776 GATCCTGCATGCAACACCAT 58.891 50.000 22.88 8.86 0.00 3.55
5289 6065 1.597461 GGCGCACTCTCCCTTACTT 59.403 57.895 10.83 0.00 0.00 2.24
5336 6112 4.201891 CCAATGTGCTCATCTTGCTTCTAC 60.202 45.833 1.01 0.00 32.56 2.59
5347 6123 1.003928 TGTCAGCTCCAATGTGCTCAT 59.996 47.619 0.00 0.00 39.21 2.90
5421 6197 2.863383 ATCCATCTGGCCAGGACCCA 62.863 60.000 32.23 13.54 33.57 4.51
5469 6245 0.036952 CCCTCATGTGACTGACGCTT 60.037 55.000 0.00 0.00 0.00 4.68
5499 6275 7.399191 ACAGGCGTATCCTTATCTCCAATATTA 59.601 37.037 0.00 0.00 44.75 0.98
5635 6411 7.514721 TCTAATGGTTTAAAGAACACCTCACT 58.485 34.615 0.00 0.00 0.00 3.41
5750 6526 1.979308 TGGGTGAAGGAATACGGTCAA 59.021 47.619 0.00 0.00 0.00 3.18
5960 6815 3.323751 AATGCCATTTCAGAAGCAACC 57.676 42.857 0.05 0.00 38.99 3.77
6083 6941 6.017605 CCCTGAGAATGTGCAAGTATAATGTC 60.018 42.308 0.00 0.00 0.00 3.06
6206 7064 3.555586 GGAAGTGCATGACCAGCAAAAAT 60.556 43.478 0.00 0.00 44.64 1.82
6207 7065 2.224018 GGAAGTGCATGACCAGCAAAAA 60.224 45.455 0.00 0.00 44.64 1.94
6219 7077 5.809001 TGTCTTCAAGATAAGGAAGTGCAT 58.191 37.500 0.00 0.00 40.98 3.96
6297 7155 4.989277 TCATGACCCCTTGATTATCATGG 58.011 43.478 17.23 17.23 44.39 3.66
6307 7165 1.077212 CCCAGCTCATGACCCCTTG 60.077 63.158 0.00 0.00 0.00 3.61
6317 7175 0.680618 CAAAATTGCCACCCAGCTCA 59.319 50.000 0.00 0.00 0.00 4.26
6360 7218 7.579589 TTGAATATTTGCCACTTTGAATTCG 57.420 32.000 0.04 0.00 0.00 3.34
6381 7239 5.913137 AGTTGTGGTTGTGAGAAAATTGA 57.087 34.783 0.00 0.00 0.00 2.57
6392 7250 0.395312 CCTCCCGTAGTTGTGGTTGT 59.605 55.000 0.00 0.00 0.00 3.32
6393 7251 0.321298 CCCTCCCGTAGTTGTGGTTG 60.321 60.000 0.00 0.00 0.00 3.77
6407 7265 1.882352 CGCCACCAATAATAGCCCTCC 60.882 57.143 0.00 0.00 0.00 4.30
6465 7323 0.624254 CAGGAGGTTAGGTTTCCCCC 59.376 60.000 0.00 0.00 0.00 5.40
6489 7347 4.414956 AGTCGATGGGGAGGGCCA 62.415 66.667 6.18 0.00 35.15 5.36
6502 7360 0.457509 AGCGATGACAGCAAGAGTCG 60.458 55.000 0.00 0.00 38.83 4.18
6508 7366 0.886043 AGCAACAGCGATGACAGCAA 60.886 50.000 8.12 0.00 37.01 3.91
6510 7368 1.134075 CAGCAACAGCGATGACAGC 59.866 57.895 8.12 8.21 0.00 4.40
6512 7370 2.327343 GCCAGCAACAGCGATGACA 61.327 57.895 8.12 0.00 0.00 3.58
6517 7375 3.630013 AGGAGCCAGCAACAGCGA 61.630 61.111 0.00 0.00 0.00 4.93
6550 7408 3.327404 TCTTTCGAGGGTGGGGCC 61.327 66.667 0.00 0.00 0.00 5.80
6561 7419 2.749621 CAAAGATTCCCACCCTCTTTCG 59.250 50.000 0.00 0.00 37.17 3.46
6581 7439 4.938074 TTCCCCCACGGACGACCA 62.938 66.667 4.48 0.00 41.83 4.02
6618 7476 2.730094 CCCACAGCACCAAGTTGC 59.270 61.111 0.00 0.00 43.34 4.17
6666 7524 1.151810 ATGAGGTCCACACCCAGGT 60.152 57.895 0.00 0.00 45.12 4.00
6721 7579 2.279120 CTCAGCTGTCGATCCGCC 60.279 66.667 14.67 0.00 0.00 6.13
6737 7595 3.161450 ACGAGCCACCACCACACT 61.161 61.111 0.00 0.00 0.00 3.55
6747 7605 4.641645 CCCAACCTGCACGAGCCA 62.642 66.667 1.39 0.00 41.13 4.75


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

AutoCloner maintained by Alex Coulton.