Multiple sequence alignment - TraesCS2A01G561200

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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 TraesCS2A01G561200 chr2A 100.000 3732 0 0 1 3732 763027311 763023580 0.000000e+00 6892.0
1 TraesCS2A01G561200 chr2A 87.603 363 35 3 2362 2714 763052299 763052661 2.680000e-111 412.0
2 TraesCS2A01G561200 chr2A 83.473 357 25 18 1909 2258 763051701 763052030 6.060000e-78 302.0
3 TraesCS2A01G561200 chr2A 79.908 433 67 15 40 467 763049598 763050015 2.180000e-77 300.0
4 TraesCS2A01G561200 chr2A 81.188 303 36 9 2412 2714 763046396 763046677 1.350000e-54 224.0
5 TraesCS2A01G561200 chr2A 95.385 65 3 0 3031 3095 14286674 14286738 1.830000e-18 104.0
6 TraesCS2A01G561200 chr2A 95.833 48 2 0 1498 1545 763051343 763051390 1.110000e-10 78.7
7 TraesCS2A01G561200 chr2B 91.603 1179 47 15 1909 3074 794524220 794525359 0.000000e+00 1581.0
8 TraesCS2A01G561200 chr2B 90.533 845 47 11 1 837 794522824 794523643 0.000000e+00 1086.0
9 TraesCS2A01G561200 chr2B 93.096 478 15 4 1000 1462 794523733 794524207 0.000000e+00 684.0
10 TraesCS2A01G561200 chr2B 92.340 470 24 8 3067 3531 794526648 794527110 0.000000e+00 658.0
11 TraesCS2A01G561200 chr2B 81.862 827 75 37 1913 2714 794495778 794495002 8.800000e-176 627.0
12 TraesCS2A01G561200 chr2B 100.000 28 0 0 3673 3700 794527262 794527289 7.000000e-03 52.8
13 TraesCS2A01G561200 chr2D 88.093 949 63 29 2118 3041 636614062 636614985 0.000000e+00 1081.0
14 TraesCS2A01G561200 chr2D 81.468 831 101 21 1909 2714 636595446 636594644 1.890000e-177 632.0
15 TraesCS2A01G561200 chr2D 81.969 782 93 27 33 798 636597417 636596668 1.470000e-173 619.0
16 TraesCS2A01G561200 chr2D 86.228 501 34 13 79 572 636612879 636613351 9.250000e-141 510.0
17 TraesCS2A01G561200 chr2D 86.582 395 21 5 3343 3732 636645045 636645412 1.250000e-109 407.0
18 TraesCS2A01G561200 chr2D 95.031 161 5 1 1909 2066 636613904 636614064 2.230000e-62 250.0
19 TraesCS2A01G561200 chr2D 81.848 303 34 9 2412 2714 636601395 636601114 6.230000e-58 235.0
20 TraesCS2A01G561200 chr2D 94.615 130 6 1 3109 3237 636614979 636615108 2.270000e-47 200.0
21 TraesCS2A01G561200 chr2D 92.771 83 5 1 3211 3292 636644764 636644846 6.550000e-23 119.0
22 TraesCS2A01G561200 chr2D 90.909 77 5 2 3039 3114 314166605 314166530 6.590000e-18 102.0
23 TraesCS2A01G561200 chr2D 93.333 60 3 1 1050 1109 636613745 636613803 1.850000e-13 87.9
24 TraesCS2A01G561200 chr2D 93.333 60 3 1 3234 3292 636616507 636616566 1.850000e-13 87.9
25 TraesCS2A01G561200 chr3B 96.000 75 3 0 3039 3113 539670603 539670677 5.060000e-24 122.0
26 TraesCS2A01G561200 chr3B 92.105 76 1 3 3039 3114 754970268 754970338 6.590000e-18 102.0
27 TraesCS2A01G561200 chr1B 94.667 75 4 0 3040 3114 480850624 480850550 2.360000e-22 117.0
28 TraesCS2A01G561200 chr1B 77.465 142 5 8 1569 1699 9376264 9376389 4.030000e-05 60.2
29 TraesCS2A01G561200 chr1B 100.000 30 0 0 1569 1598 9291028 9291057 5.210000e-04 56.5
30 TraesCS2A01G561200 chr1B 100.000 30 0 0 1569 1598 9321530 9321559 5.210000e-04 56.5
31 TraesCS2A01G561200 chr3D 91.358 81 5 1 3038 3116 225684872 225684792 3.940000e-20 110.0
32 TraesCS2A01G561200 chr7D 90.789 76 7 0 3039 3114 23509201 23509276 6.590000e-18 102.0
33 TraesCS2A01G561200 chr1A 89.610 77 6 1 3039 3113 555640269 555640345 3.070000e-16 97.1
34 TraesCS2A01G561200 chr1A 100.000 30 0 0 1569 1598 8501202 8501231 5.210000e-04 56.5
35 TraesCS2A01G561200 chr1A 100.000 29 0 0 1569 1597 8559700 8559728 2.000000e-03 54.7
36 TraesCS2A01G561200 chr4D 78.761 113 18 3 2099 2211 24259395 24259289 1.860000e-08 71.3
37 TraesCS2A01G561200 chr6D 97.059 34 1 0 3238 3271 62887587 62887620 1.450000e-04 58.4
38 TraesCS2A01G561200 chr1D 100.000 30 0 0 1569 1598 6976725 6976754 5.210000e-04 56.5


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 TraesCS2A01G561200 chr2A 763023580 763027311 3731 True 6892.000000 6892 100.000000 1 3732 1 chr2A.!!$R1 3731
1 TraesCS2A01G561200 chr2A 763046396 763052661 6265 False 263.340000 412 85.601000 40 2714 5 chr2A.!!$F2 2674
2 TraesCS2A01G561200 chr2B 794522824 794527289 4465 False 812.360000 1581 93.514400 1 3700 5 chr2B.!!$F1 3699
3 TraesCS2A01G561200 chr2B 794495002 794495778 776 True 627.000000 627 81.862000 1913 2714 1 chr2B.!!$R1 801
4 TraesCS2A01G561200 chr2D 636594644 636601395 6751 True 495.333333 632 81.761667 33 2714 3 chr2D.!!$R2 2681
5 TraesCS2A01G561200 chr2D 636612879 636616566 3687 False 369.466667 1081 91.772167 79 3292 6 chr2D.!!$F1 3213
6 TraesCS2A01G561200 chr2D 636644764 636645412 648 False 263.000000 407 89.676500 3211 3732 2 chr2D.!!$F2 521

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
838 5722 0.034896 ACCAACAGCGACCGAGAATT 59.965 50.0 0.00 0.0 0.0 2.17 F
1561 6710 0.107263 TGCTGCCTGTGTCACTGAAA 60.107 50.0 11.17 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 7226 0.675083 TTCATGCAGGTGCTGTTTGG 59.325 50.0 3.18 0.0 42.66 3.28 R
3555 12298 0.110486 TCCAAGGACTTCCACCAAGC 59.890 55.0 0.00 0.0 38.89 4.01 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
66 4418 1.933949 GCTAAGAGCGCGGGGTATAAC 60.934 57.143 8.83 0.00 0.00 1.89
168 4536 2.530177 CGAAGAGCTCATGCGAGTAAA 58.470 47.619 17.77 0.00 45.42 2.01
240 4612 4.517285 AGGCTTGATTGTGATAACGTCAT 58.483 39.130 0.00 0.00 39.48 3.06
278 4650 1.227002 CCCGCGCTCTTAGTTCTCC 60.227 63.158 5.56 0.00 0.00 3.71
297 4675 0.158928 CGTGACGTTTCAAGTCGCTC 59.841 55.000 0.00 0.00 44.35 5.03
353 4732 1.153353 CTAAACTTTCCCGCGCTTCA 58.847 50.000 5.56 0.00 0.00 3.02
411 4790 1.369448 CGCTCTGATCCGTCGTAGC 60.369 63.158 0.00 0.00 0.00 3.58
412 4791 1.008309 GCTCTGATCCGTCGTAGCC 60.008 63.158 0.00 0.00 0.00 3.93
420 4801 2.478890 CCGTCGTAGCCCTCATCGT 61.479 63.158 0.00 0.00 0.00 3.73
473 4861 0.618393 CCATGGCTGTCCCCCAAATT 60.618 55.000 0.00 0.00 35.67 1.82
474 4862 0.538118 CATGGCTGTCCCCCAAATTG 59.462 55.000 0.00 0.00 35.67 2.32
477 4865 1.347062 GGCTGTCCCCCAAATTGAAA 58.653 50.000 0.00 0.00 0.00 2.69
479 4867 2.093500 GGCTGTCCCCCAAATTGAAATC 60.093 50.000 0.00 0.00 0.00 2.17
480 4868 2.417243 GCTGTCCCCCAAATTGAAATCG 60.417 50.000 0.00 0.00 0.00 3.34
481 4869 3.088532 CTGTCCCCCAAATTGAAATCGA 58.911 45.455 0.00 0.00 0.00 3.59
482 4870 3.501349 TGTCCCCCAAATTGAAATCGAA 58.499 40.909 0.00 0.00 0.00 3.71
483 4871 3.509575 TGTCCCCCAAATTGAAATCGAAG 59.490 43.478 0.00 0.00 0.00 3.79
628 5019 4.408596 AGAGCCTCTCCTTATCCTCTTTTG 59.591 45.833 0.00 0.00 0.00 2.44
677 5181 6.435430 TGTCATTCTTGTATGGTATTGTGC 57.565 37.500 0.00 0.00 0.00 4.57
680 5184 4.937696 TTCTTGTATGGTATTGTGCGTG 57.062 40.909 0.00 0.00 0.00 5.34
701 5513 6.801862 GCGTGTTATTAGTGAGAAAAATTGCT 59.198 34.615 0.00 0.00 0.00 3.91
744 5610 3.640967 CTCCATTACTTCTCCCCTCTCTG 59.359 52.174 0.00 0.00 0.00 3.35
783 5667 2.685897 CTCTCTCTCTCTAAACACCGGG 59.314 54.545 6.32 0.00 0.00 5.73
799 5683 1.429463 CGGGGAGAAACAGAAGAACG 58.571 55.000 0.00 0.00 0.00 3.95
813 5697 3.255149 AGAAGAACGGAGCGAGTAGAAAA 59.745 43.478 0.00 0.00 0.00 2.29
814 5698 3.219052 AGAACGGAGCGAGTAGAAAAG 57.781 47.619 0.00 0.00 0.00 2.27
821 5705 3.503891 GAGCGAGTAGAAAAGACAGACC 58.496 50.000 0.00 0.00 0.00 3.85
823 5707 3.321111 AGCGAGTAGAAAAGACAGACCAA 59.679 43.478 0.00 0.00 0.00 3.67
825 5709 4.617959 CGAGTAGAAAAGACAGACCAACA 58.382 43.478 0.00 0.00 0.00 3.33
826 5710 4.681942 CGAGTAGAAAAGACAGACCAACAG 59.318 45.833 0.00 0.00 0.00 3.16
837 5721 0.389948 GACCAACAGCGACCGAGAAT 60.390 55.000 0.00 0.00 0.00 2.40
838 5722 0.034896 ACCAACAGCGACCGAGAATT 59.965 50.000 0.00 0.00 0.00 2.17
839 5723 1.156736 CCAACAGCGACCGAGAATTT 58.843 50.000 0.00 0.00 0.00 1.82
840 5724 1.535462 CCAACAGCGACCGAGAATTTT 59.465 47.619 0.00 0.00 0.00 1.82
841 5725 2.031157 CCAACAGCGACCGAGAATTTTT 60.031 45.455 0.00 0.00 0.00 1.94
842 5726 3.226347 CAACAGCGACCGAGAATTTTTC 58.774 45.455 0.00 0.00 0.00 2.29
843 5727 2.489971 ACAGCGACCGAGAATTTTTCA 58.510 42.857 0.00 0.00 0.00 2.69
844 5728 2.223377 ACAGCGACCGAGAATTTTTCAC 59.777 45.455 0.00 0.00 0.00 3.18
845 5729 2.480419 CAGCGACCGAGAATTTTTCACT 59.520 45.455 0.00 0.00 0.00 3.41
846 5730 3.058914 CAGCGACCGAGAATTTTTCACTT 60.059 43.478 0.00 0.00 0.00 3.16
847 5731 3.058914 AGCGACCGAGAATTTTTCACTTG 60.059 43.478 0.00 0.00 0.00 3.16
848 5732 3.059188 GCGACCGAGAATTTTTCACTTGA 60.059 43.478 0.00 0.00 0.00 3.02
849 5733 4.702392 CGACCGAGAATTTTTCACTTGAG 58.298 43.478 0.00 0.00 0.00 3.02
850 5734 4.447724 CGACCGAGAATTTTTCACTTGAGA 59.552 41.667 0.00 0.00 0.00 3.27
851 5735 5.120830 CGACCGAGAATTTTTCACTTGAGAT 59.879 40.000 0.00 0.00 0.00 2.75
852 5736 6.246420 ACCGAGAATTTTTCACTTGAGATG 57.754 37.500 0.00 0.00 0.00 2.90
853 5737 5.182001 ACCGAGAATTTTTCACTTGAGATGG 59.818 40.000 0.00 0.00 0.00 3.51
854 5738 5.392380 CCGAGAATTTTTCACTTGAGATGGG 60.392 44.000 0.00 0.00 0.00 4.00
855 5739 5.397142 AGAATTTTTCACTTGAGATGGGC 57.603 39.130 0.00 0.00 0.00 5.36
856 5740 4.834496 AGAATTTTTCACTTGAGATGGGCA 59.166 37.500 0.00 0.00 0.00 5.36
857 5741 4.796038 ATTTTTCACTTGAGATGGGCAG 57.204 40.909 0.00 0.00 0.00 4.85
858 5742 2.957402 TTTCACTTGAGATGGGCAGT 57.043 45.000 0.00 0.00 0.00 4.40
859 5743 2.189594 TTCACTTGAGATGGGCAGTG 57.810 50.000 0.00 0.00 0.00 3.66
868 5805 3.258872 TGAGATGGGCAGTGGAATTTTTG 59.741 43.478 0.00 0.00 0.00 2.44
921 5862 4.008539 GATTCGTTGTTGAATCTGCCTC 57.991 45.455 8.76 0.00 46.87 4.70
925 5866 1.075601 TTGTTGAATCTGCCTCCCCT 58.924 50.000 0.00 0.00 0.00 4.79
926 5867 0.620556 TGTTGAATCTGCCTCCCCTC 59.379 55.000 0.00 0.00 0.00 4.30
954 5925 2.116736 CTCGGCGTTGCTTTGCTTCA 62.117 55.000 6.85 0.00 0.00 3.02
959 5930 0.662374 CGTTGCTTTGCTTCAGCTGG 60.662 55.000 15.13 0.00 42.66 4.85
974 5953 0.820871 GCTGGGTGTTTTGTTGGTGA 59.179 50.000 0.00 0.00 0.00 4.02
993 5972 1.131315 GATTGGTTGAAGAAGAGCGGC 59.869 52.381 0.00 0.00 0.00 6.53
994 5973 0.108585 TTGGTTGAAGAAGAGCGGCT 59.891 50.000 0.00 0.00 0.00 5.52
995 5974 0.108585 TGGTTGAAGAAGAGCGGCTT 59.891 50.000 2.97 0.00 40.25 4.35
996 5975 0.519077 GGTTGAAGAAGAGCGGCTTG 59.481 55.000 2.97 0.00 36.83 4.01
1054 6049 3.745480 CGGAATCATGGGTAAGCATCTGT 60.745 47.826 0.00 0.00 0.00 3.41
1061 6146 2.912956 TGGGTAAGCATCTGTTTCTCCT 59.087 45.455 0.00 0.00 0.00 3.69
1135 6246 6.271488 TCAAATCTTGCCCAATTCTTGTAG 57.729 37.500 0.00 0.00 0.00 2.74
1211 6347 1.672356 CCCCAAGACAACTCTGCGG 60.672 63.158 0.00 0.00 0.00 5.69
1231 6367 0.247736 CCGCTCTCAAGCCTGTACTT 59.752 55.000 0.00 0.00 46.34 2.24
1378 6527 6.019779 ACTGTCATCTGAAACTACTGTCTC 57.980 41.667 0.00 0.00 0.00 3.36
1381 6530 5.047731 TGTCATCTGAAACTACTGTCTCCAG 60.048 44.000 0.00 0.00 44.68 3.86
1422 6571 8.890718 CACTTATTCAGAAACTGTCATCATCAT 58.109 33.333 0.00 0.00 32.61 2.45
1423 6572 9.107177 ACTTATTCAGAAACTGTCATCATCATC 57.893 33.333 0.00 0.00 32.61 2.92
1424 6573 9.106070 CTTATTCAGAAACTGTCATCATCATCA 57.894 33.333 0.00 0.00 32.61 3.07
1430 6579 6.539103 AGAAACTGTCATCATCATCATCTGTG 59.461 38.462 0.00 0.00 0.00 3.66
1439 6588 4.334481 TCATCATCATCTGTGTGCACATTC 59.666 41.667 24.69 11.88 41.01 2.67
1449 6598 4.905429 TGTGTGCACATTCCTAACAGTAT 58.095 39.130 24.69 0.00 36.21 2.12
1468 6617 5.919141 CAGTATGTACTAACAGTTATCCGGC 59.081 44.000 0.00 0.00 39.49 6.13
1469 6618 5.595542 AGTATGTACTAACAGTTATCCGGCA 59.404 40.000 0.00 0.00 39.49 5.69
1470 6619 4.380841 TGTACTAACAGTTATCCGGCAG 57.619 45.455 0.00 0.00 0.00 4.85
1471 6620 2.311124 ACTAACAGTTATCCGGCAGC 57.689 50.000 0.00 0.00 0.00 5.25
1472 6621 1.553248 ACTAACAGTTATCCGGCAGCA 59.447 47.619 0.00 0.00 0.00 4.41
1473 6622 2.027561 ACTAACAGTTATCCGGCAGCAA 60.028 45.455 0.00 0.00 0.00 3.91
1474 6623 1.165270 AACAGTTATCCGGCAGCAAC 58.835 50.000 0.00 0.00 0.00 4.17
1475 6624 0.324943 ACAGTTATCCGGCAGCAACT 59.675 50.000 0.00 0.00 0.00 3.16
1476 6625 1.553248 ACAGTTATCCGGCAGCAACTA 59.447 47.619 0.00 0.00 30.31 2.24
1477 6626 2.027561 ACAGTTATCCGGCAGCAACTAA 60.028 45.455 0.00 0.00 30.31 2.24
1478 6627 3.206150 CAGTTATCCGGCAGCAACTAAT 58.794 45.455 0.00 0.00 30.31 1.73
1479 6628 3.002656 CAGTTATCCGGCAGCAACTAATG 59.997 47.826 0.00 0.00 30.31 1.90
1480 6629 2.943033 GTTATCCGGCAGCAACTAATGT 59.057 45.455 0.00 0.00 0.00 2.71
1481 6630 2.128771 ATCCGGCAGCAACTAATGTT 57.871 45.000 0.00 0.00 36.75 2.71
1482 6631 1.904287 TCCGGCAGCAACTAATGTTT 58.096 45.000 0.00 0.00 33.52 2.83
1483 6632 1.539388 TCCGGCAGCAACTAATGTTTG 59.461 47.619 0.00 0.00 33.52 2.93
1484 6633 1.269448 CCGGCAGCAACTAATGTTTGT 59.731 47.619 0.00 0.00 33.52 2.83
1485 6634 2.486203 CCGGCAGCAACTAATGTTTGTA 59.514 45.455 0.00 0.00 33.52 2.41
1486 6635 3.426159 CCGGCAGCAACTAATGTTTGTAG 60.426 47.826 0.00 0.00 33.52 2.74
1487 6636 3.426159 CGGCAGCAACTAATGTTTGTAGG 60.426 47.826 0.00 0.00 33.52 3.18
1488 6637 3.756434 GGCAGCAACTAATGTTTGTAGGA 59.244 43.478 0.00 0.00 33.52 2.94
1489 6638 4.379499 GGCAGCAACTAATGTTTGTAGGAC 60.379 45.833 0.00 0.00 33.52 3.85
1490 6639 4.215399 GCAGCAACTAATGTTTGTAGGACA 59.785 41.667 0.00 0.00 33.52 4.02
1491 6640 5.617751 GCAGCAACTAATGTTTGTAGGACAG 60.618 44.000 0.00 0.00 33.52 3.51
1492 6641 5.470098 CAGCAACTAATGTTTGTAGGACAGT 59.530 40.000 0.00 0.00 33.52 3.55
1493 6642 6.649141 CAGCAACTAATGTTTGTAGGACAGTA 59.351 38.462 0.00 0.00 33.52 2.74
1494 6643 6.649557 AGCAACTAATGTTTGTAGGACAGTAC 59.350 38.462 0.00 0.00 33.52 2.73
1495 6644 6.425721 GCAACTAATGTTTGTAGGACAGTACA 59.574 38.462 0.00 0.00 33.52 2.90
1496 6645 7.119262 GCAACTAATGTTTGTAGGACAGTACAT 59.881 37.037 0.00 4.52 37.03 2.29
1497 6646 8.656849 CAACTAATGTTTGTAGGACAGTACATC 58.343 37.037 0.00 0.00 35.54 3.06
1529 6678 2.175878 ATGTCAGGCTTGTGTCACTC 57.824 50.000 4.27 0.00 0.00 3.51
1549 6698 2.980475 GCTGACTCTCTGCTGCCT 59.020 61.111 0.00 0.00 38.17 4.75
1550 6699 1.448189 GCTGACTCTCTGCTGCCTG 60.448 63.158 0.00 0.00 38.17 4.85
1551 6700 1.973760 CTGACTCTCTGCTGCCTGT 59.026 57.895 0.00 0.00 0.00 4.00
1552 6701 0.390078 CTGACTCTCTGCTGCCTGTG 60.390 60.000 0.00 0.00 0.00 3.66
1553 6702 1.117749 TGACTCTCTGCTGCCTGTGT 61.118 55.000 0.00 0.00 0.00 3.72
1554 6703 0.389687 GACTCTCTGCTGCCTGTGTC 60.390 60.000 0.00 0.63 0.00 3.67
1555 6704 1.117749 ACTCTCTGCTGCCTGTGTCA 61.118 55.000 0.00 0.00 0.00 3.58
1556 6705 0.669932 CTCTCTGCTGCCTGTGTCAC 60.670 60.000 0.00 0.00 0.00 3.67
1557 6706 1.117749 TCTCTGCTGCCTGTGTCACT 61.118 55.000 4.27 0.00 0.00 3.41
1558 6707 0.949588 CTCTGCTGCCTGTGTCACTG 60.950 60.000 4.27 3.57 0.00 3.66
1559 6708 1.070275 CTGCTGCCTGTGTCACTGA 59.930 57.895 11.17 0.00 0.00 3.41
1560 6709 0.533531 CTGCTGCCTGTGTCACTGAA 60.534 55.000 11.17 0.00 0.00 3.02
1561 6710 0.107263 TGCTGCCTGTGTCACTGAAA 60.107 50.000 11.17 0.00 0.00 2.69
1562 6711 1.242076 GCTGCCTGTGTCACTGAAAT 58.758 50.000 11.17 0.00 0.00 2.17
1563 6712 1.198637 GCTGCCTGTGTCACTGAAATC 59.801 52.381 11.17 0.00 0.00 2.17
1564 6713 2.497138 CTGCCTGTGTCACTGAAATCA 58.503 47.619 11.17 3.57 0.00 2.57
1588 6737 8.043113 TCAGTATGCAGTTATTCAGAGTTGAAT 58.957 33.333 7.78 7.78 45.41 2.57
1612 6824 4.930963 CAGTATGCACAAACAGTTGGAAA 58.069 39.130 0.00 0.00 39.22 3.13
1651 6865 7.352079 TGAAAGAAAGCAAGGAAAAGAGATT 57.648 32.000 0.00 0.00 0.00 2.40
1653 6867 8.912988 TGAAAGAAAGCAAGGAAAAGAGATTTA 58.087 29.630 0.00 0.00 0.00 1.40
1655 6869 9.920133 AAAGAAAGCAAGGAAAAGAGATTTATC 57.080 29.630 0.00 0.00 0.00 1.75
1656 6870 8.876303 AGAAAGCAAGGAAAAGAGATTTATCT 57.124 30.769 0.00 0.00 40.50 1.98
1657 6871 8.738106 AGAAAGCAAGGAAAAGAGATTTATCTG 58.262 33.333 0.00 0.00 37.25 2.90
1658 6872 8.641498 AAAGCAAGGAAAAGAGATTTATCTGA 57.359 30.769 0.00 0.00 37.25 3.27
1659 6873 8.820153 AAGCAAGGAAAAGAGATTTATCTGAT 57.180 30.769 0.00 0.00 37.25 2.90
1660 6874 8.449251 AGCAAGGAAAAGAGATTTATCTGATC 57.551 34.615 0.00 0.00 37.25 2.92
1661 6875 8.273605 AGCAAGGAAAAGAGATTTATCTGATCT 58.726 33.333 0.00 0.00 37.25 2.75
1662 6876 8.901793 GCAAGGAAAAGAGATTTATCTGATCTT 58.098 33.333 0.00 0.00 37.25 2.40
1664 6878 8.449251 AGGAAAAGAGATTTATCTGATCTTGC 57.551 34.615 0.00 0.00 37.25 4.01
1665 6879 8.273605 AGGAAAAGAGATTTATCTGATCTTGCT 58.726 33.333 0.00 0.00 37.25 3.91
1666 6880 8.558700 GGAAAAGAGATTTATCTGATCTTGCTC 58.441 37.037 0.00 0.00 37.25 4.26
1667 6881 9.328845 GAAAAGAGATTTATCTGATCTTGCTCT 57.671 33.333 0.00 0.74 37.25 4.09
1668 6882 9.683870 AAAAGAGATTTATCTGATCTTGCTCTT 57.316 29.630 14.61 14.61 40.67 2.85
1669 6883 9.683870 AAAGAGATTTATCTGATCTTGCTCTTT 57.316 29.630 20.62 20.62 42.20 2.52
1670 6884 8.891671 AGAGATTTATCTGATCTTGCTCTTTC 57.108 34.615 0.00 0.00 37.25 2.62
1671 6885 7.933033 AGAGATTTATCTGATCTTGCTCTTTCC 59.067 37.037 0.00 0.00 37.25 3.13
1672 6886 7.571919 AGATTTATCTGATCTTGCTCTTTCCA 58.428 34.615 0.00 0.00 35.42 3.53
1673 6887 8.051535 AGATTTATCTGATCTTGCTCTTTCCAA 58.948 33.333 0.00 0.00 35.42 3.53
1674 6888 8.763984 ATTTATCTGATCTTGCTCTTTCCAAT 57.236 30.769 0.00 0.00 0.00 3.16
1675 6889 7.798596 TTATCTGATCTTGCTCTTTCCAATC 57.201 36.000 0.00 0.00 0.00 2.67
1676 6890 5.169992 TCTGATCTTGCTCTTTCCAATCA 57.830 39.130 0.00 0.00 0.00 2.57
1677 6891 5.752650 TCTGATCTTGCTCTTTCCAATCAT 58.247 37.500 0.00 0.00 0.00 2.45
1678 6892 5.821470 TCTGATCTTGCTCTTTCCAATCATC 59.179 40.000 0.00 0.00 0.00 2.92
1679 6893 5.503002 TGATCTTGCTCTTTCCAATCATCA 58.497 37.500 0.00 0.00 0.00 3.07
1680 6894 5.356190 TGATCTTGCTCTTTCCAATCATCAC 59.644 40.000 0.00 0.00 0.00 3.06
1681 6895 4.654915 TCTTGCTCTTTCCAATCATCACA 58.345 39.130 0.00 0.00 0.00 3.58
1682 6896 5.258841 TCTTGCTCTTTCCAATCATCACAT 58.741 37.500 0.00 0.00 0.00 3.21
1683 6897 6.417258 TCTTGCTCTTTCCAATCATCACATA 58.583 36.000 0.00 0.00 0.00 2.29
1699 6914 8.482852 TCATCACATAGATATTCAGAGTTCCA 57.517 34.615 0.00 0.00 34.43 3.53
1700 6915 9.097946 TCATCACATAGATATTCAGAGTTCCAT 57.902 33.333 0.00 0.00 34.43 3.41
1714 6929 3.549794 AGTTCCATATCTTCTTGCTGCC 58.450 45.455 0.00 0.00 0.00 4.85
1715 6930 3.201708 AGTTCCATATCTTCTTGCTGCCT 59.798 43.478 0.00 0.00 0.00 4.75
1716 6931 3.204306 TCCATATCTTCTTGCTGCCTG 57.796 47.619 0.00 0.00 0.00 4.85
1731 6946 1.226686 GCCTGCACTCTGTGTCACTG 61.227 60.000 4.27 3.89 35.75 3.66
1743 6958 4.631377 TCTGTGTCACTGAAACTGAAACTG 59.369 41.667 9.88 0.00 27.51 3.16
1746 7181 5.471797 TGTGTCACTGAAACTGAAACTGAAA 59.528 36.000 4.27 0.00 28.51 2.69
1757 7192 4.748102 ACTGAAACTGAAATTGCATGCTTG 59.252 37.500 20.33 3.71 0.00 4.01
1764 7199 5.359009 ACTGAAATTGCATGCTTGTAGCTAT 59.641 36.000 20.33 0.00 42.97 2.97
1775 7210 7.429633 CATGCTTGTAGCTATTCTGTACTACT 58.570 38.462 0.00 0.00 42.97 2.57
1796 7231 6.313744 ACTGTACATTACTTGAAGCCAAAC 57.686 37.500 0.00 0.00 0.00 2.93
1798 7233 6.017109 ACTGTACATTACTTGAAGCCAAACAG 60.017 38.462 0.00 9.80 37.27 3.16
1799 7234 4.243007 ACATTACTTGAAGCCAAACAGC 57.757 40.909 0.00 0.00 0.00 4.40
1805 7240 1.006922 GAAGCCAAACAGCACCTGC 60.007 57.895 0.00 0.00 42.49 4.85
1808 7243 1.373748 GCCAAACAGCACCTGCATG 60.374 57.895 0.00 0.00 45.16 4.06
1811 7246 1.068895 CCAAACAGCACCTGCATGAAA 59.931 47.619 0.00 0.00 45.16 2.69
1813 7248 2.514205 AACAGCACCTGCATGAAAAC 57.486 45.000 0.00 0.00 45.16 2.43
1824 7259 5.104982 ACCTGCATGAAAACAAGGAAAAGAA 60.105 36.000 0.00 0.00 0.00 2.52
1829 7264 7.984050 TGCATGAAAACAAGGAAAAGAAATACA 59.016 29.630 0.00 0.00 0.00 2.29
1830 7265 8.490355 GCATGAAAACAAGGAAAAGAAATACAG 58.510 33.333 0.00 0.00 0.00 2.74
1831 7266 9.533253 CATGAAAACAAGGAAAAGAAATACAGT 57.467 29.630 0.00 0.00 0.00 3.55
1857 7292 4.704965 TCTGATCTTGCCAATCATCAGAG 58.295 43.478 18.55 3.62 44.05 3.35
1874 7309 6.493115 TCATCAGAGAGATATTCAGAGTTCCC 59.507 42.308 0.00 0.00 34.43 3.97
1876 7311 5.832595 TCAGAGAGATATTCAGAGTTCCCTG 59.167 44.000 0.00 0.00 35.55 4.45
1897 7336 2.665000 GCTGCCTGCACTCACCTA 59.335 61.111 0.00 0.00 42.31 3.08
1904 7343 2.440409 CCTGCACTCACCTAAAATGCT 58.560 47.619 0.00 0.00 37.20 3.79
2082 7688 3.470709 CTGAAGCAGAGAGGAAACAACA 58.529 45.455 0.00 0.00 32.44 3.33
2199 7823 0.960364 TCTGGTTTTGGATCAGCGGC 60.960 55.000 0.00 0.00 0.00 6.53
2214 7838 1.000163 AGCGGCATCGTATTCAGGTAG 60.000 52.381 1.45 0.00 38.89 3.18
2215 7839 1.935300 GCGGCATCGTATTCAGGTAGG 60.935 57.143 0.00 0.00 38.89 3.18
2220 7844 3.808174 GCATCGTATTCAGGTAGGTTTCC 59.192 47.826 0.00 0.00 0.00 3.13
2260 7897 7.859325 TTCCTGTATAAACATGTTTAGGAGC 57.141 36.000 27.47 20.12 35.92 4.70
2261 7898 6.354130 TCCTGTATAAACATGTTTAGGAGCC 58.646 40.000 29.25 17.55 38.30 4.70
2262 7899 6.069905 TCCTGTATAAACATGTTTAGGAGCCA 60.070 38.462 29.25 20.13 38.30 4.75
2263 7900 6.038271 CCTGTATAAACATGTTTAGGAGCCAC 59.962 42.308 29.25 20.18 38.30 5.01
2308 8141 5.163237 TGTCAGGAGCCACTTTTAAGTAACT 60.163 40.000 0.00 0.00 37.08 2.24
2326 8159 8.779354 AAGTAACTCATTCCTTCATTACAGTC 57.221 34.615 0.00 0.00 0.00 3.51
2329 8162 7.678947 AACTCATTCCTTCATTACAGTCTTG 57.321 36.000 0.00 0.00 0.00 3.02
2330 8163 7.009179 ACTCATTCCTTCATTACAGTCTTGA 57.991 36.000 0.00 0.00 0.00 3.02
2334 8167 9.770097 TCATTCCTTCATTACAGTCTTGATATC 57.230 33.333 0.00 0.00 0.00 1.63
2338 8187 8.861086 TCCTTCATTACAGTCTTGATATCTACC 58.139 37.037 3.98 0.00 0.00 3.18
2343 8192 9.784531 CATTACAGTCTTGATATCTACCCATTT 57.215 33.333 3.98 0.00 0.00 2.32
2350 8199 4.556233 TGATATCTACCCATTTCTTCGCG 58.444 43.478 0.00 0.00 0.00 5.87
2579 8444 3.817647 GGATCTCAACTCCATAATGCACC 59.182 47.826 0.00 0.00 32.72 5.01
2629 8494 2.039418 TGTACCATTCCAGGATCCTCG 58.961 52.381 12.69 5.44 0.00 4.63
2667 8532 4.655762 TTTATCATAGCGAGACTGCAGT 57.344 40.909 21.88 21.88 37.31 4.40
2701 8566 0.459585 TCGGTTACGGAAGCATGCTC 60.460 55.000 22.93 14.19 41.39 4.26
2731 8596 5.419788 ACATCCATTCAAGCATGCTTCTTAA 59.580 36.000 29.81 22.40 33.42 1.85
2782 8647 3.130340 TGAACAAGTTCAGAGTTTTGGCC 59.870 43.478 11.34 0.00 43.90 5.36
2854 8720 6.640907 GTCAATTTGTTTCTGGGTGAATGTAC 59.359 38.462 0.00 0.00 34.24 2.90
2937 8803 6.612247 TCTTTGTGGTGTTAGTACATGTTG 57.388 37.500 2.30 0.00 36.50 3.33
2939 8805 6.600032 TCTTTGTGGTGTTAGTACATGTTGTT 59.400 34.615 2.30 0.00 36.50 2.83
2988 8856 6.360681 CGTTGTTTTTCTTGGTCAGATCAATC 59.639 38.462 0.00 0.00 0.00 2.67
3049 8922 5.579753 TGTTATAGAGATACTCCCTCCGT 57.420 43.478 0.00 0.00 0.00 4.69
3054 8927 0.108963 AGATACTCCCTCCGTCCGAG 59.891 60.000 0.00 0.00 38.46 4.63
3082 10250 5.824624 ACTTGGTGCTAGATACATCCATTTG 59.175 40.000 0.00 0.00 0.00 2.32
3088 10256 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
3107 10275 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
3191 10359 3.373830 AGAATTCCTGACAGGGAGAGAG 58.626 50.000 21.56 0.00 35.59 3.20
3265 11835 7.067008 CCTTCCCATATTAACTGTCGTTCAAAT 59.933 37.037 0.00 0.00 34.59 2.32
3271 11841 3.559238 AACTGTCGTTCAAATGGATGC 57.441 42.857 0.00 0.00 0.00 3.91
3339 12061 1.133544 GGGACGGAGGGAGTATGTAGT 60.134 57.143 0.00 0.00 0.00 2.73
3340 12062 2.107204 GGGACGGAGGGAGTATGTAGTA 59.893 54.545 0.00 0.00 0.00 1.82
3341 12063 3.245193 GGGACGGAGGGAGTATGTAGTAT 60.245 52.174 0.00 0.00 0.00 2.12
3386 12108 7.492669 CCATACATGACAAACTCTACTGGTTAG 59.507 40.741 0.00 0.00 0.00 2.34
3387 12109 5.238583 ACATGACAAACTCTACTGGTTAGC 58.761 41.667 0.00 0.00 0.00 3.09
3399 12121 2.076863 CTGGTTAGCTAAGCACACACC 58.923 52.381 29.54 16.29 38.60 4.16
3427 12154 4.867608 CCCACAACAAAACAAACCTGTTAG 59.132 41.667 0.00 0.00 45.25 2.34
3454 12181 2.736400 GCTAGTGCACCAAATTGATGGC 60.736 50.000 14.63 1.79 44.75 4.40
3455 12182 0.609662 AGTGCACCAAATTGATGGCC 59.390 50.000 14.63 0.00 44.75 5.36
3466 12193 8.373981 CACCAAATTGATGGCCCAAAATATATA 58.626 33.333 0.00 0.00 44.75 0.86
3507 12234 2.508526 ACAAGAGGACAATCACAAGCC 58.491 47.619 0.00 0.00 0.00 4.35
3576 12319 1.421646 CTTGGTGGAAGTCCTTGGAGT 59.578 52.381 0.00 0.00 36.82 3.85
3593 12336 2.165030 GGAGTCAATCACAGGGCAAATG 59.835 50.000 0.00 0.00 0.00 2.32
3606 12349 5.170748 CAGGGCAAATGTTTGAATTAGACC 58.829 41.667 9.53 0.00 40.55 3.85
3618 12361 0.981183 ATTAGACCACGGCCAAGTGA 59.019 50.000 11.94 0.00 44.43 3.41
3706 12511 3.283751 CTTGTCAACCCCAAACACTGTA 58.716 45.455 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.181503 CCATTATTGCCATATCAGCTCGC 60.182 47.826 0.00 0.00 0.00 5.03
16 17 4.708421 CCTTCCCCATTATTGCCATATCAG 59.292 45.833 0.00 0.00 0.00 2.90
18 19 4.934356 TCCTTCCCCATTATTGCCATATC 58.066 43.478 0.00 0.00 0.00 1.63
19 20 4.607584 TCTCCTTCCCCATTATTGCCATAT 59.392 41.667 0.00 0.00 0.00 1.78
20 21 3.986817 TCTCCTTCCCCATTATTGCCATA 59.013 43.478 0.00 0.00 0.00 2.74
21 22 2.791179 TCTCCTTCCCCATTATTGCCAT 59.209 45.455 0.00 0.00 0.00 4.40
24 25 2.959030 GGTTCTCCTTCCCCATTATTGC 59.041 50.000 0.00 0.00 0.00 3.56
25 26 3.214328 CGGTTCTCCTTCCCCATTATTG 58.786 50.000 0.00 0.00 0.00 1.90
26 27 2.422945 GCGGTTCTCCTTCCCCATTATT 60.423 50.000 0.00 0.00 0.00 1.40
66 4418 2.427245 ATCGCTCCCTTCCCTGACG 61.427 63.158 0.00 0.00 0.00 4.35
106 4458 2.284405 ACCTACCACCCTCCACGG 60.284 66.667 0.00 0.00 0.00 4.94
140 4492 1.315981 ATGAGCTCTTCGGCGACTCA 61.316 55.000 24.11 24.11 41.28 3.41
150 4502 3.462021 GGATTTACTCGCATGAGCTCTT 58.538 45.455 16.19 5.66 46.69 2.85
240 4612 6.403855 CGCGGGAAATTTAAAAGAGGTATGAA 60.404 38.462 0.00 0.00 0.00 2.57
278 4650 0.158928 GAGCGACTTGAAACGTCACG 59.841 55.000 0.00 0.00 31.90 4.35
297 4675 6.474364 TGAACGCGTCATCAATTAATACAAG 58.526 36.000 14.44 0.00 0.00 3.16
411 4790 2.491022 GGGAGGTCGACGATGAGGG 61.491 68.421 9.92 0.00 0.00 4.30
412 4791 1.448922 GAGGGAGGTCGACGATGAGG 61.449 65.000 9.92 0.00 0.00 3.86
420 4801 4.816984 GCCGGAGAGGGAGGTCGA 62.817 72.222 5.05 0.00 41.48 4.20
500 4888 8.723942 ATACATGGTATTCTTTGACTTCAGAC 57.276 34.615 0.00 0.00 0.00 3.51
628 5019 8.716646 AATTGGGCAACATTAAATAAAGTAGC 57.283 30.769 0.00 0.00 39.74 3.58
677 5181 8.728088 AAGCAATTTTTCTCACTAATAACACG 57.272 30.769 0.00 0.00 0.00 4.49
701 5513 1.289530 GAAGGAGGAGGAGGAGGAGAA 59.710 57.143 0.00 0.00 0.00 2.87
744 5610 0.258774 AGAGAGAGAGGGCAGAGGAC 59.741 60.000 0.00 0.00 0.00 3.85
783 5667 2.070028 GCTCCGTTCTTCTGTTTCTCC 58.930 52.381 0.00 0.00 0.00 3.71
799 5683 3.503891 GTCTGTCTTTTCTACTCGCTCC 58.496 50.000 0.00 0.00 0.00 4.70
813 5697 1.367840 GGTCGCTGTTGGTCTGTCT 59.632 57.895 0.00 0.00 0.00 3.41
814 5698 2.022129 CGGTCGCTGTTGGTCTGTC 61.022 63.158 0.00 0.00 0.00 3.51
821 5705 2.969443 AAAATTCTCGGTCGCTGTTG 57.031 45.000 0.00 0.00 0.00 3.33
823 5707 2.223377 GTGAAAAATTCTCGGTCGCTGT 59.777 45.455 0.00 0.00 0.00 4.40
825 5709 2.767505 AGTGAAAAATTCTCGGTCGCT 58.232 42.857 0.00 0.00 0.00 4.93
826 5710 3.059188 TCAAGTGAAAAATTCTCGGTCGC 60.059 43.478 0.00 0.00 0.00 5.19
837 5721 3.318839 CACTGCCCATCTCAAGTGAAAAA 59.681 43.478 0.00 0.00 0.00 1.94
838 5722 2.886523 CACTGCCCATCTCAAGTGAAAA 59.113 45.455 0.00 0.00 0.00 2.29
839 5723 2.507484 CACTGCCCATCTCAAGTGAAA 58.493 47.619 0.00 0.00 0.00 2.69
840 5724 1.271543 CCACTGCCCATCTCAAGTGAA 60.272 52.381 3.32 0.00 0.00 3.18
841 5725 0.325933 CCACTGCCCATCTCAAGTGA 59.674 55.000 3.32 0.00 0.00 3.41
842 5726 0.325933 TCCACTGCCCATCTCAAGTG 59.674 55.000 0.00 0.00 0.00 3.16
843 5727 1.067295 TTCCACTGCCCATCTCAAGT 58.933 50.000 0.00 0.00 0.00 3.16
844 5728 2.431954 ATTCCACTGCCCATCTCAAG 57.568 50.000 0.00 0.00 0.00 3.02
845 5729 2.905415 AATTCCACTGCCCATCTCAA 57.095 45.000 0.00 0.00 0.00 3.02
846 5730 2.905415 AAATTCCACTGCCCATCTCA 57.095 45.000 0.00 0.00 0.00 3.27
847 5731 3.511146 TCAAAAATTCCACTGCCCATCTC 59.489 43.478 0.00 0.00 0.00 2.75
848 5732 3.259123 GTCAAAAATTCCACTGCCCATCT 59.741 43.478 0.00 0.00 0.00 2.90
849 5733 3.259123 AGTCAAAAATTCCACTGCCCATC 59.741 43.478 0.00 0.00 0.00 3.51
850 5734 3.242011 AGTCAAAAATTCCACTGCCCAT 58.758 40.909 0.00 0.00 0.00 4.00
851 5735 2.676748 AGTCAAAAATTCCACTGCCCA 58.323 42.857 0.00 0.00 0.00 5.36
852 5736 3.181466 ACAAGTCAAAAATTCCACTGCCC 60.181 43.478 0.00 0.00 0.00 5.36
853 5737 3.803778 CACAAGTCAAAAATTCCACTGCC 59.196 43.478 0.00 0.00 0.00 4.85
854 5738 3.803778 CCACAAGTCAAAAATTCCACTGC 59.196 43.478 0.00 0.00 0.00 4.40
855 5739 5.261209 TCCACAAGTCAAAAATTCCACTG 57.739 39.130 0.00 0.00 0.00 3.66
856 5740 5.835280 AGATCCACAAGTCAAAAATTCCACT 59.165 36.000 0.00 0.00 0.00 4.00
857 5741 5.922544 CAGATCCACAAGTCAAAAATTCCAC 59.077 40.000 0.00 0.00 0.00 4.02
858 5742 5.832595 TCAGATCCACAAGTCAAAAATTCCA 59.167 36.000 0.00 0.00 0.00 3.53
859 5743 6.331369 TCAGATCCACAAGTCAAAAATTCC 57.669 37.500 0.00 0.00 0.00 3.01
868 5805 6.992063 ATGTATGTTTCAGATCCACAAGTC 57.008 37.500 0.00 0.00 0.00 3.01
917 5858 2.302260 GAGCAAATAAAGAGGGGAGGC 58.698 52.381 0.00 0.00 0.00 4.70
920 5861 1.408266 GCCGAGCAAATAAAGAGGGGA 60.408 52.381 0.00 0.00 0.00 4.81
921 5862 1.025041 GCCGAGCAAATAAAGAGGGG 58.975 55.000 0.00 0.00 0.00 4.79
925 5866 1.135803 GCAACGCCGAGCAAATAAAGA 60.136 47.619 0.00 0.00 0.00 2.52
926 5867 1.135689 AGCAACGCCGAGCAAATAAAG 60.136 47.619 8.73 0.00 0.00 1.85
954 5925 0.823460 CACCAACAAAACACCCAGCT 59.177 50.000 0.00 0.00 0.00 4.24
959 5930 3.535280 ACCAATCACCAACAAAACACC 57.465 42.857 0.00 0.00 0.00 4.16
974 5953 1.168714 GCCGCTCTTCTTCAACCAAT 58.831 50.000 0.00 0.00 0.00 3.16
993 5972 1.180029 CCTTCTTCACCATGCCCAAG 58.820 55.000 0.00 0.00 0.00 3.61
994 5973 0.776810 TCCTTCTTCACCATGCCCAA 59.223 50.000 0.00 0.00 0.00 4.12
995 5974 0.329261 CTCCTTCTTCACCATGCCCA 59.671 55.000 0.00 0.00 0.00 5.36
996 5975 0.394899 CCTCCTTCTTCACCATGCCC 60.395 60.000 0.00 0.00 0.00 5.36
1054 6049 6.696411 TGCAGAGAAAAACAAAAAGGAGAAA 58.304 32.000 0.00 0.00 0.00 2.52
1061 6146 5.976458 ACCAGATGCAGAGAAAAACAAAAA 58.024 33.333 0.00 0.00 0.00 1.94
1135 6246 4.112634 GCAACAAACCCTTGAAGAAGAAC 58.887 43.478 0.00 0.00 36.33 3.01
1231 6367 6.173339 GGGTCTGTCTGAATGTTGAGAAATA 58.827 40.000 0.00 0.00 0.00 1.40
1350 6499 6.266558 ACAGTAGTTTCAGATGACAGTCTCTT 59.733 38.462 1.31 0.00 0.00 2.85
1408 6557 5.585047 CACACAGATGATGATGATGACAGTT 59.415 40.000 0.00 0.00 0.00 3.16
1422 6571 2.865119 AGGAATGTGCACACAGATGA 57.135 45.000 24.37 0.00 45.48 2.92
1423 6572 3.752747 TGTTAGGAATGTGCACACAGATG 59.247 43.478 24.37 0.00 45.48 2.90
1424 6573 4.005650 CTGTTAGGAATGTGCACACAGAT 58.994 43.478 24.37 11.55 45.48 2.90
1430 6579 6.106673 AGTACATACTGTTAGGAATGTGCAC 58.893 40.000 10.75 10.75 37.40 4.57
1439 6588 9.962783 GGATAACTGTTAGTACATACTGTTAGG 57.037 37.037 22.11 0.00 39.98 2.69
1449 6598 3.429822 GCTGCCGGATAACTGTTAGTACA 60.430 47.826 5.05 0.19 0.00 2.90
1462 6611 2.128771 AACATTAGTTGCTGCCGGAT 57.871 45.000 5.05 0.00 36.39 4.18
1464 6613 1.269448 ACAAACATTAGTTGCTGCCGG 59.731 47.619 0.00 0.00 38.17 6.13
1465 6614 2.704725 ACAAACATTAGTTGCTGCCG 57.295 45.000 0.00 0.00 38.17 5.69
1466 6615 3.756434 TCCTACAAACATTAGTTGCTGCC 59.244 43.478 0.00 0.00 38.17 4.85
1467 6616 4.215399 TGTCCTACAAACATTAGTTGCTGC 59.785 41.667 0.00 0.00 38.17 5.25
1468 6617 5.470098 ACTGTCCTACAAACATTAGTTGCTG 59.530 40.000 0.00 0.00 38.17 4.41
1469 6618 5.621193 ACTGTCCTACAAACATTAGTTGCT 58.379 37.500 0.00 0.00 38.17 3.91
1470 6619 5.941948 ACTGTCCTACAAACATTAGTTGC 57.058 39.130 0.00 0.00 38.17 4.17
1471 6620 7.956420 TGTACTGTCCTACAAACATTAGTTG 57.044 36.000 0.00 0.00 38.17 3.16
1472 6621 8.594550 AGATGTACTGTCCTACAAACATTAGTT 58.405 33.333 8.33 0.00 35.90 2.24
1473 6622 8.035394 CAGATGTACTGTCCTACAAACATTAGT 58.965 37.037 8.33 0.00 41.30 2.24
1474 6623 8.251026 TCAGATGTACTGTCCTACAAACATTAG 58.749 37.037 8.33 5.82 45.86 1.73
1475 6624 8.129496 TCAGATGTACTGTCCTACAAACATTA 57.871 34.615 8.33 0.00 45.86 1.90
1476 6625 7.004555 TCAGATGTACTGTCCTACAAACATT 57.995 36.000 8.33 0.00 45.86 2.71
1477 6626 6.605471 TCAGATGTACTGTCCTACAAACAT 57.395 37.500 7.17 7.17 45.86 2.71
1478 6627 6.413783 TTCAGATGTACTGTCCTACAAACA 57.586 37.500 0.00 0.00 45.86 2.83
1479 6628 7.724305 TTTTCAGATGTACTGTCCTACAAAC 57.276 36.000 0.00 0.00 45.86 2.93
1480 6629 7.094805 GCATTTTCAGATGTACTGTCCTACAAA 60.095 37.037 0.00 0.00 45.86 2.83
1481 6630 6.371548 GCATTTTCAGATGTACTGTCCTACAA 59.628 38.462 0.00 0.00 45.86 2.41
1482 6631 5.874810 GCATTTTCAGATGTACTGTCCTACA 59.125 40.000 0.00 0.00 45.86 2.74
1483 6632 6.036517 CAGCATTTTCAGATGTACTGTCCTAC 59.963 42.308 0.00 0.00 45.86 3.18
1484 6633 6.070824 TCAGCATTTTCAGATGTACTGTCCTA 60.071 38.462 0.00 0.00 45.86 2.94
1485 6634 4.940046 CAGCATTTTCAGATGTACTGTCCT 59.060 41.667 0.00 0.00 45.86 3.85
1486 6635 4.937620 TCAGCATTTTCAGATGTACTGTCC 59.062 41.667 0.00 0.00 45.86 4.02
1487 6636 6.486253 TTCAGCATTTTCAGATGTACTGTC 57.514 37.500 0.00 0.00 45.86 3.51
1488 6637 6.432162 ACATTCAGCATTTTCAGATGTACTGT 59.568 34.615 0.00 0.00 45.86 3.55
1489 6638 6.849502 ACATTCAGCATTTTCAGATGTACTG 58.150 36.000 0.00 0.00 46.97 2.74
1490 6639 6.656270 TGACATTCAGCATTTTCAGATGTACT 59.344 34.615 0.00 0.00 0.00 2.73
1491 6640 6.845302 TGACATTCAGCATTTTCAGATGTAC 58.155 36.000 0.00 0.00 0.00 2.90
1492 6641 6.094464 CCTGACATTCAGCATTTTCAGATGTA 59.906 38.462 0.00 0.00 42.98 2.29
1493 6642 5.105877 CCTGACATTCAGCATTTTCAGATGT 60.106 40.000 0.00 0.00 42.98 3.06
1494 6643 5.340803 CCTGACATTCAGCATTTTCAGATG 58.659 41.667 0.00 0.00 42.98 2.90
1495 6644 4.142227 GCCTGACATTCAGCATTTTCAGAT 60.142 41.667 0.00 0.00 42.98 2.90
1496 6645 3.192001 GCCTGACATTCAGCATTTTCAGA 59.808 43.478 0.00 0.00 42.98 3.27
1497 6646 3.192844 AGCCTGACATTCAGCATTTTCAG 59.807 43.478 0.00 0.00 42.98 3.02
1529 6678 1.020333 GGCAGCAGAGAGTCAGCTTG 61.020 60.000 0.00 1.43 37.11 4.01
1545 6694 2.497138 CTGATTTCAGTGACACAGGCA 58.503 47.619 8.59 0.00 39.09 4.75
1557 6706 8.043113 ACTCTGAATAACTGCATACTGATTTCA 58.957 33.333 0.00 0.00 0.00 2.69
1558 6707 8.430801 ACTCTGAATAACTGCATACTGATTTC 57.569 34.615 0.00 0.00 0.00 2.17
1559 6708 8.671921 CAACTCTGAATAACTGCATACTGATTT 58.328 33.333 0.00 0.00 0.00 2.17
1560 6709 8.043113 TCAACTCTGAATAACTGCATACTGATT 58.957 33.333 0.00 0.00 0.00 2.57
1561 6710 7.559486 TCAACTCTGAATAACTGCATACTGAT 58.441 34.615 0.00 0.00 0.00 2.90
1562 6711 6.935167 TCAACTCTGAATAACTGCATACTGA 58.065 36.000 0.00 0.00 0.00 3.41
1563 6712 7.601073 TTCAACTCTGAATAACTGCATACTG 57.399 36.000 0.00 0.00 36.62 2.74
1589 6738 2.293122 TCCAACTGTTTGTGCATACTGC 59.707 45.455 0.00 0.00 45.29 4.40
1619 6831 6.976934 TCCTTGCTTTCTTTCAGGTATTTT 57.023 33.333 0.00 0.00 0.00 1.82
1621 6833 6.976934 TTTCCTTGCTTTCTTTCAGGTATT 57.023 33.333 0.00 0.00 0.00 1.89
1622 6834 6.777580 TCTTTTCCTTGCTTTCTTTCAGGTAT 59.222 34.615 0.00 0.00 0.00 2.73
1624 6836 4.956075 TCTTTTCCTTGCTTTCTTTCAGGT 59.044 37.500 0.00 0.00 0.00 4.00
1625 6837 5.300286 TCTCTTTTCCTTGCTTTCTTTCAGG 59.700 40.000 0.00 0.00 0.00 3.86
1636 6849 8.449251 AGATCAGATAAATCTCTTTTCCTTGC 57.551 34.615 0.00 0.00 34.22 4.01
1651 6865 7.341030 TGATTGGAAAGAGCAAGATCAGATAA 58.659 34.615 0.00 0.00 0.00 1.75
1653 6867 5.752650 TGATTGGAAAGAGCAAGATCAGAT 58.247 37.500 0.00 0.00 0.00 2.90
1655 6869 5.589050 TGATGATTGGAAAGAGCAAGATCAG 59.411 40.000 0.00 0.00 0.00 2.90
1656 6870 5.356190 GTGATGATTGGAAAGAGCAAGATCA 59.644 40.000 0.00 0.00 0.00 2.92
1657 6871 5.356190 TGTGATGATTGGAAAGAGCAAGATC 59.644 40.000 0.00 0.00 0.00 2.75
1658 6872 5.258841 TGTGATGATTGGAAAGAGCAAGAT 58.741 37.500 0.00 0.00 0.00 2.40
1659 6873 4.654915 TGTGATGATTGGAAAGAGCAAGA 58.345 39.130 0.00 0.00 0.00 3.02
1660 6874 5.578005 ATGTGATGATTGGAAAGAGCAAG 57.422 39.130 0.00 0.00 0.00 4.01
1661 6875 6.417258 TCTATGTGATGATTGGAAAGAGCAA 58.583 36.000 0.00 0.00 0.00 3.91
1662 6876 5.993055 TCTATGTGATGATTGGAAAGAGCA 58.007 37.500 0.00 0.00 0.00 4.26
1663 6877 8.789825 ATATCTATGTGATGATTGGAAAGAGC 57.210 34.615 0.00 0.00 36.65 4.09
1668 6882 9.939802 CTCTGAATATCTATGTGATGATTGGAA 57.060 33.333 0.00 0.00 36.65 3.53
1669 6883 9.097946 ACTCTGAATATCTATGTGATGATTGGA 57.902 33.333 0.00 0.00 36.65 3.53
1670 6884 9.722184 AACTCTGAATATCTATGTGATGATTGG 57.278 33.333 0.00 0.00 36.65 3.16
1672 6886 9.941325 GGAACTCTGAATATCTATGTGATGATT 57.059 33.333 0.00 0.00 36.65 2.57
1673 6887 9.097946 TGGAACTCTGAATATCTATGTGATGAT 57.902 33.333 0.00 0.00 36.65 2.45
1674 6888 8.482852 TGGAACTCTGAATATCTATGTGATGA 57.517 34.615 0.00 0.00 36.65 2.92
1714 6929 2.229675 TTCAGTGACACAGAGTGCAG 57.770 50.000 8.59 0.00 36.98 4.41
1715 6930 2.093500 AGTTTCAGTGACACAGAGTGCA 60.093 45.455 11.83 0.00 36.98 4.57
1716 6931 2.286294 CAGTTTCAGTGACACAGAGTGC 59.714 50.000 11.83 0.12 36.98 4.40
1718 6933 4.471904 TTCAGTTTCAGTGACACAGAGT 57.528 40.909 11.83 0.00 0.00 3.24
1719 6934 4.872691 AGTTTCAGTTTCAGTGACACAGAG 59.127 41.667 11.83 1.92 32.22 3.35
1722 6937 4.574892 TCAGTTTCAGTTTCAGTGACACA 58.425 39.130 11.83 0.00 32.22 3.72
1723 6938 5.545658 TTCAGTTTCAGTTTCAGTGACAC 57.454 39.130 0.92 0.92 30.43 3.67
1731 6946 5.464389 AGCATGCAATTTCAGTTTCAGTTTC 59.536 36.000 21.98 0.00 0.00 2.78
1743 6958 6.417044 CAGAATAGCTACAAGCATGCAATTTC 59.583 38.462 21.98 9.02 45.56 2.17
1746 7181 4.885907 ACAGAATAGCTACAAGCATGCAAT 59.114 37.500 21.98 5.17 45.56 3.56
1775 7210 5.278266 GCTGTTTGGCTTCAAGTAATGTACA 60.278 40.000 0.00 0.00 0.00 2.90
1784 7219 1.035139 AGGTGCTGTTTGGCTTCAAG 58.965 50.000 0.00 0.00 0.00 3.02
1790 7225 1.373748 CATGCAGGTGCTGTTTGGC 60.374 57.895 3.18 0.00 42.66 4.52
1791 7226 0.675083 TTCATGCAGGTGCTGTTTGG 59.325 50.000 3.18 0.00 42.66 3.28
1796 7231 2.400399 CTTGTTTTCATGCAGGTGCTG 58.600 47.619 3.18 0.00 42.66 4.41
1798 7233 1.340889 TCCTTGTTTTCATGCAGGTGC 59.659 47.619 0.00 0.00 42.50 5.01
1799 7234 3.731652 TTCCTTGTTTTCATGCAGGTG 57.268 42.857 0.00 0.00 29.95 4.00
1805 7240 9.533253 ACTGTATTTCTTTTCCTTGTTTTCATG 57.467 29.630 0.00 0.00 0.00 3.07
1824 7259 9.664332 GATTGGCAAGATCAGATATACTGTATT 57.336 33.333 5.96 0.00 45.86 1.89
1829 7264 7.914859 TGATGATTGGCAAGATCAGATATACT 58.085 34.615 16.68 0.00 36.99 2.12
1830 7265 8.039538 TCTGATGATTGGCAAGATCAGATATAC 58.960 37.037 31.50 12.97 43.69 1.47
1831 7266 8.142485 TCTGATGATTGGCAAGATCAGATATA 57.858 34.615 31.50 19.77 43.69 0.86
1832 7267 7.017319 TCTGATGATTGGCAAGATCAGATAT 57.983 36.000 31.50 10.87 43.69 1.63
1838 7273 4.958509 TCTCTCTGATGATTGGCAAGATC 58.041 43.478 5.96 10.23 0.00 2.75
1857 7292 4.953940 AGCAGGGAACTCTGAATATCTC 57.046 45.455 5.83 0.00 40.21 2.75
1897 7336 6.592607 CCATGAGCAACAAGATTAAGCATTTT 59.407 34.615 0.00 0.00 0.00 1.82
1904 7343 6.349280 GCAGTTACCATGAGCAACAAGATTAA 60.349 38.462 0.00 0.00 0.00 1.40
2068 7674 6.625960 GCTTTTTCTTGTGTTGTTTCCTCTCT 60.626 38.462 0.00 0.00 0.00 3.10
2082 7688 1.792118 GCGGACGGGCTTTTTCTTGT 61.792 55.000 0.00 0.00 0.00 3.16
2199 7823 4.049186 CGGAAACCTACCTGAATACGATG 58.951 47.826 0.00 0.00 0.00 3.84
2214 7838 8.301720 AGGAAAAATAGAATGTTTACGGAAACC 58.698 33.333 20.37 5.37 43.74 3.27
2215 7839 9.124807 CAGGAAAAATAGAATGTTTACGGAAAC 57.875 33.333 16.63 16.63 44.48 2.78
2258 7895 4.165760 AGGGTAGTACTACAAAAGTGGCT 58.834 43.478 29.38 2.81 39.39 4.75
2259 7896 4.548451 AGGGTAGTACTACAAAAGTGGC 57.452 45.455 29.38 12.72 39.39 5.01
2260 7897 5.861727 ACAAGGGTAGTACTACAAAAGTGG 58.138 41.667 29.38 15.95 39.39 4.00
2261 7898 6.764560 ACAACAAGGGTAGTACTACAAAAGTG 59.235 38.462 29.38 21.21 39.39 3.16
2262 7899 6.892485 ACAACAAGGGTAGTACTACAAAAGT 58.108 36.000 29.38 20.03 42.62 2.66
2263 7900 6.987992 TGACAACAAGGGTAGTACTACAAAAG 59.012 38.462 29.38 19.49 37.78 2.27
2308 8141 9.770097 GATATCAAGACTGTAATGAAGGAATGA 57.230 33.333 0.00 0.00 0.00 2.57
2326 8159 5.119279 CGCGAAGAAATGGGTAGATATCAAG 59.881 44.000 0.00 0.00 0.00 3.02
2329 8162 3.927142 CCGCGAAGAAATGGGTAGATATC 59.073 47.826 8.23 0.00 0.00 1.63
2330 8163 3.576982 TCCGCGAAGAAATGGGTAGATAT 59.423 43.478 8.23 0.00 0.00 1.63
2334 8167 1.933853 CTTCCGCGAAGAAATGGGTAG 59.066 52.381 8.23 0.00 41.71 3.18
2338 8187 1.438651 TCACTTCCGCGAAGAAATGG 58.561 50.000 20.18 4.01 41.71 3.16
2343 8192 4.913335 AGTAATATCACTTCCGCGAAGA 57.087 40.909 20.18 3.33 41.71 2.87
2579 8444 6.148480 CCTGAACCAGAACATAACTTCTCTTG 59.852 42.308 0.00 0.00 32.44 3.02
2629 8494 6.732896 TGATAAATCAGTAGGTCTTCCTCC 57.267 41.667 0.00 0.00 37.49 4.30
2667 8532 4.679639 CGTAACCGATCTCAAAGGATCCAA 60.680 45.833 15.82 0.00 38.97 3.53
2701 8566 4.735578 GCATGCTTGAATGGATGTGTAAGG 60.736 45.833 11.37 0.00 37.94 2.69
2782 8647 1.897560 AAAAGGGAGAAGCTGAACCG 58.102 50.000 0.00 0.00 0.00 4.44
2854 8720 4.707030 TTGCTGCCAGAATTGACTAATG 57.293 40.909 0.00 0.00 0.00 1.90
2937 8803 2.095919 GTCGACATGGGCACTGTAAAAC 60.096 50.000 11.55 0.00 0.00 2.43
2939 8805 1.609580 GGTCGACATGGGCACTGTAAA 60.610 52.381 18.91 0.00 0.00 2.01
3049 8922 2.631062 TCTAGCACCAAGTTTTCTCGGA 59.369 45.455 0.00 0.00 0.00 4.55
3054 8927 5.880332 TGGATGTATCTAGCACCAAGTTTTC 59.120 40.000 0.00 0.00 0.00 2.29
3082 10250 1.535896 GTCCGAAAAAGCTTGTCCCTC 59.464 52.381 0.00 0.00 0.00 4.30
3088 10256 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
3107 10275 0.535335 TGATCGCCAACAGGTACTCC 59.465 55.000 0.00 0.00 34.60 3.85
3191 10359 4.178545 ACTGCATAAACTTGGTGCATTC 57.821 40.909 0.00 0.00 46.52 2.67
3271 11841 9.976255 GTATCTAGACGTATTTAGTGCTAGATG 57.024 37.037 20.76 0.00 42.46 2.90
3386 12108 1.301677 GGCTCAGGTGTGTGCTTAGC 61.302 60.000 0.00 0.00 41.91 3.09
3387 12109 0.674895 GGGCTCAGGTGTGTGCTTAG 60.675 60.000 0.07 0.00 41.91 2.18
3399 12121 2.929398 GTTTGTTTTGTTGTGGGCTCAG 59.071 45.455 0.00 0.00 0.00 3.35
3454 12181 9.130661 TGTGTGTCCTTTCATATATATTTTGGG 57.869 33.333 0.00 0.00 0.00 4.12
3466 12193 7.448161 TCTTGTATCAAATGTGTGTCCTTTCAT 59.552 33.333 0.00 0.00 0.00 2.57
3472 12199 5.122396 GTCCTCTTGTATCAAATGTGTGTCC 59.878 44.000 0.00 0.00 0.00 4.02
3545 12288 4.789075 CACCAAGCATGCTGGCGC 62.789 66.667 23.48 0.00 39.27 6.53
3546 12289 4.124351 CCACCAAGCATGCTGGCG 62.124 66.667 23.48 17.44 39.27 5.69
3547 12290 2.221906 CTTCCACCAAGCATGCTGGC 62.222 60.000 23.48 0.00 33.07 4.85
3548 12291 0.896940 ACTTCCACCAAGCATGCTGG 60.897 55.000 23.48 24.74 35.17 4.85
3549 12292 0.524862 GACTTCCACCAAGCATGCTG 59.475 55.000 23.48 12.58 35.17 4.41
3550 12293 0.610232 GGACTTCCACCAAGCATGCT 60.610 55.000 16.30 16.30 35.17 3.79
3551 12294 0.610232 AGGACTTCCACCAAGCATGC 60.610 55.000 10.51 10.51 38.89 4.06
3552 12295 1.542915 CAAGGACTTCCACCAAGCATG 59.457 52.381 0.00 0.00 38.89 4.06
3553 12296 1.548582 CCAAGGACTTCCACCAAGCAT 60.549 52.381 0.00 0.00 38.89 3.79
3554 12297 0.178992 CCAAGGACTTCCACCAAGCA 60.179 55.000 0.00 0.00 38.89 3.91
3555 12298 0.110486 TCCAAGGACTTCCACCAAGC 59.890 55.000 0.00 0.00 38.89 4.01
3556 12299 1.421646 ACTCCAAGGACTTCCACCAAG 59.578 52.381 0.00 0.00 38.89 3.61
3557 12300 1.420138 GACTCCAAGGACTTCCACCAA 59.580 52.381 0.00 0.00 38.89 3.67
3558 12301 1.056660 GACTCCAAGGACTTCCACCA 58.943 55.000 0.00 0.00 38.89 4.17
3559 12302 1.056660 TGACTCCAAGGACTTCCACC 58.943 55.000 0.00 0.00 38.89 4.61
3560 12303 2.930826 TTGACTCCAAGGACTTCCAC 57.069 50.000 0.00 0.00 38.89 4.02
3561 12304 2.978978 TGATTGACTCCAAGGACTTCCA 59.021 45.455 0.00 0.00 38.89 3.53
3562 12305 3.244561 TGTGATTGACTCCAAGGACTTCC 60.245 47.826 0.00 0.00 35.48 3.46
3563 12306 3.999663 CTGTGATTGACTCCAAGGACTTC 59.000 47.826 0.00 0.00 35.48 3.01
3564 12307 3.244700 CCTGTGATTGACTCCAAGGACTT 60.245 47.826 0.00 0.00 35.48 3.01
3576 12319 3.640498 TCAAACATTTGCCCTGTGATTGA 59.360 39.130 0.00 0.00 38.05 2.57
3593 12336 2.156098 TGGCCGTGGTCTAATTCAAAC 58.844 47.619 0.00 0.00 0.00 2.93
3606 12349 1.008538 GTTGCTTCACTTGGCCGTG 60.009 57.895 4.50 4.50 36.25 4.94


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

AutoCloner maintained by Alex Coulton.