Multiple sequence alignment - TraesCS6A01G095900

Loading Multiple Alignment...

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 TraesCS6A01G095900 chr6A 100.000 7621 0 0 1 7621 63098742 63106362 0.000000e+00 14074.0
1 TraesCS6A01G095900 chr6A 96.582 2194 54 12 5311 7495 49776390 49778571 0.000000e+00 3616.0
2 TraesCS6A01G095900 chr6A 93.617 47 2 1 7528 7574 100672176 100672221 1.370000e-07 69.4
3 TraesCS6A01G095900 chr6D 95.383 5913 181 32 988 6860 52285210 52291070 0.000000e+00 9323.0
4 TraesCS6A01G095900 chr6D 85.361 526 74 3 86 609 52284182 52284706 6.730000e-150 542.0
5 TraesCS6A01G095900 chr6D 93.452 336 15 5 6868 7202 52291187 52291516 6.870000e-135 492.0
6 TraesCS6A01G095900 chr6D 86.982 169 19 2 599 767 178849364 178849199 3.630000e-43 187.0
7 TraesCS6A01G095900 chr6D 88.636 88 7 3 832 917 52284766 52284852 3.760000e-18 104.0
8 TraesCS6A01G095900 chr6B 94.091 6109 237 48 70 6128 118954077 118960111 0.000000e+00 9167.0
9 TraesCS6A01G095900 chr6B 90.165 1515 77 34 6113 7621 118967033 118968481 0.000000e+00 1906.0
10 TraesCS6A01G095900 chr6B 86.081 467 55 8 144 607 681079953 681080412 1.910000e-135 494.0
11 TraesCS6A01G095900 chr6B 87.037 162 18 3 601 761 15232347 15232506 6.080000e-41 180.0
12 TraesCS6A01G095900 chr2A 84.203 1380 161 38 4560 5928 516707167 516708500 0.000000e+00 1288.0
13 TraesCS6A01G095900 chr2A 81.729 1434 193 40 1865 3255 516703840 516705247 0.000000e+00 1133.0
14 TraesCS6A01G095900 chr2A 89.464 522 46 3 3989 4503 516706621 516707140 0.000000e+00 651.0
15 TraesCS6A01G095900 chr2A 84.006 644 78 16 3283 3913 516705959 516706590 5.090000e-166 595.0
16 TraesCS6A01G095900 chr2A 83.532 419 44 10 1219 1616 26016840 26017254 1.210000e-97 368.0
17 TraesCS6A01G095900 chr2A 78.967 271 29 10 1612 1882 26025931 26026173 7.920000e-35 159.0
18 TraesCS6A01G095900 chr2A 86.014 143 17 2 6196 6338 516708744 516708883 4.760000e-32 150.0
19 TraesCS6A01G095900 chr2A 91.304 69 4 2 965 1033 209265085 209265151 8.140000e-15 93.5
20 TraesCS6A01G095900 chr2A 92.424 66 3 2 968 1033 546783431 546783368 8.140000e-15 93.5
21 TraesCS6A01G095900 chr2D 82.597 1448 188 37 1878 3276 382337478 382338910 0.000000e+00 1219.0
22 TraesCS6A01G095900 chr2D 83.127 646 82 15 3283 3913 382338954 382339587 1.440000e-156 564.0
23 TraesCS6A01G095900 chr2D 86.910 466 58 3 144 607 222599965 222599501 3.150000e-143 520.0
24 TraesCS6A01G095900 chr2D 79.036 768 107 36 4560 5316 382353249 382353973 1.920000e-130 477.0
25 TraesCS6A01G095900 chr2D 89.655 232 24 0 4249 4480 382352970 382353201 5.780000e-76 296.0
26 TraesCS6A01G095900 chr2D 94.839 155 8 0 3989 4143 382339618 382339772 7.640000e-60 243.0
27 TraesCS6A01G095900 chr2D 86.905 168 19 3 606 772 134301488 134301653 1.310000e-42 185.0
28 TraesCS6A01G095900 chr4D 86.859 624 57 16 3126 3740 489725214 489725821 0.000000e+00 675.0
29 TraesCS6A01G095900 chr5A 86.256 633 53 10 3126 3740 671167902 671168518 0.000000e+00 656.0
30 TraesCS6A01G095900 chr5A 83.235 680 66 21 1219 1882 523021676 523022323 1.430000e-161 580.0
31 TraesCS6A01G095900 chr5A 91.304 69 4 2 965 1033 196304408 196304474 8.140000e-15 93.5
32 TraesCS6A01G095900 chr5A 91.304 69 4 2 965 1033 196305128 196305194 8.140000e-15 93.5
33 TraesCS6A01G095900 chr2B 86.695 466 59 3 144 607 345458693 345458229 1.470000e-141 514.0
34 TraesCS6A01G095900 chr1D 86.111 468 59 4 144 607 10334353 10334818 4.110000e-137 499.0
35 TraesCS6A01G095900 chr3D 86.111 468 58 6 144 607 182049891 182050355 1.480000e-136 497.0
36 TraesCS6A01G095900 chr3D 85.714 168 23 1 606 772 313908601 313908768 7.860000e-40 176.0
37 TraesCS6A01G095900 chr7D 85.653 467 59 7 144 607 257511613 257512074 1.150000e-132 484.0
38 TraesCS6A01G095900 chr7D 92.424 66 3 2 968 1033 507238220 507238157 8.140000e-15 93.5
39 TraesCS6A01G095900 chr3B 84.958 472 60 8 144 607 260319257 260319725 1.160000e-127 468.0
40 TraesCS6A01G095900 chr3B 86.471 170 19 4 606 774 529407950 529407784 4.700000e-42 183.0
41 TraesCS6A01G095900 chr4B 85.942 377 34 10 3126 3487 628065036 628065408 1.200000e-102 385.0
42 TraesCS6A01G095900 chr4B 92.913 254 18 0 3487 3740 628065570 628065823 3.360000e-98 370.0
43 TraesCS6A01G095900 chr5D 89.809 157 16 0 605 761 377988001 377988157 1.300000e-47 202.0
44 TraesCS6A01G095900 chr5D 91.304 69 4 2 965 1033 90689861 90689927 8.140000e-15 93.5
45 TraesCS6A01G095900 chr3A 86.747 166 17 4 606 767 64291108 64290944 6.080000e-41 180.0
46 TraesCS6A01G095900 chr1B 85.976 164 21 2 599 761 325812539 325812701 2.830000e-39 174.0
47 TraesCS6A01G095900 chrUn 90.909 66 4 2 968 1033 344568162 344568099 3.790000e-13 87.9


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 TraesCS6A01G095900 chr6A 63098742 63106362 7620 False 14074.000000 14074 100.000000 1 7621 1 chr6A.!!$F2 7620
1 TraesCS6A01G095900 chr6A 49776390 49778571 2181 False 3616.000000 3616 96.582000 5311 7495 1 chr6A.!!$F1 2184
2 TraesCS6A01G095900 chr6D 52284182 52291516 7334 False 2615.250000 9323 90.708000 86 7202 4 chr6D.!!$F1 7116
3 TraesCS6A01G095900 chr6B 118954077 118960111 6034 False 9167.000000 9167 94.091000 70 6128 1 chr6B.!!$F2 6058
4 TraesCS6A01G095900 chr6B 118967033 118968481 1448 False 1906.000000 1906 90.165000 6113 7621 1 chr6B.!!$F3 1508
5 TraesCS6A01G095900 chr2A 516703840 516708883 5043 False 763.400000 1288 85.083200 1865 6338 5 chr2A.!!$F4 4473
6 TraesCS6A01G095900 chr2D 382337478 382339772 2294 False 675.333333 1219 86.854333 1878 4143 3 chr2D.!!$F2 2265
7 TraesCS6A01G095900 chr2D 382352970 382353973 1003 False 386.500000 477 84.345500 4249 5316 2 chr2D.!!$F3 1067
8 TraesCS6A01G095900 chr4D 489725214 489725821 607 False 675.000000 675 86.859000 3126 3740 1 chr4D.!!$F1 614
9 TraesCS6A01G095900 chr5A 671167902 671168518 616 False 656.000000 656 86.256000 3126 3740 1 chr5A.!!$F2 614
10 TraesCS6A01G095900 chr5A 523021676 523022323 647 False 580.000000 580 83.235000 1219 1882 1 chr5A.!!$F1 663
11 TraesCS6A01G095900 chr4B 628065036 628065823 787 False 377.500000 385 89.427500 3126 3740 2 chr4B.!!$F1 614

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
892 921 0.179029 AGCCCGCGCCAGTATTATTT 60.179 50.000 0.00 0.0 34.57 1.40 F
1695 2034 0.536006 GCAGACTGCCCAACACTCTT 60.536 55.000 17.01 0.0 37.42 2.85 F
2790 3163 2.494059 ACACAAACGATCCTTGGACTG 58.506 47.619 7.03 0.0 0.00 3.51 F
3752 5043 0.250295 TGGGCAGAAACCTGAAGTCG 60.250 55.000 0.00 0.0 33.56 4.18 F
4232 5537 0.109039 GAGACGAGGAGCTGGTGAAC 60.109 60.000 0.00 0.0 0.00 3.18 F
5057 6412 2.158726 GGTTGGTGACCCAGTTCAGTTA 60.159 50.000 0.00 0.0 43.15 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2805 3178 0.324614 TTCTTGCAGGAGCGGAATGA 59.675 50.000 0.00 0.0 46.23 2.57 R
3314 4412 0.777446 AGCCTGGTTACACCCATGTT 59.223 50.000 0.00 0.0 40.48 2.71 R
4189 5488 0.477204 CATCTGATGCCACCCCAGAT 59.523 55.000 4.47 0.0 45.47 2.90 R
4553 5860 2.559998 ACCTGAAAACAAAGTGCACG 57.440 45.000 12.01 0.0 0.00 5.34 R
6222 7635 2.143925 GCGGAACCTATTACCTGCATC 58.856 52.381 0.00 0.0 0.00 3.91 R
6768 8182 1.065701 AGCTCGCGTAGATGATTCGTT 59.934 47.619 5.77 0.0 0.00 3.85 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
24 25 6.992063 AATAGGTCTGCTCAGTTTACAATG 57.008 37.500 0.00 0.00 0.00 2.82
25 26 3.679389 AGGTCTGCTCAGTTTACAATGG 58.321 45.455 0.00 0.00 0.00 3.16
26 27 2.749621 GGTCTGCTCAGTTTACAATGGG 59.250 50.000 0.00 0.00 0.00 4.00
27 28 2.749621 GTCTGCTCAGTTTACAATGGGG 59.250 50.000 0.00 0.00 0.00 4.96
28 29 2.094675 CTGCTCAGTTTACAATGGGGG 58.905 52.381 0.00 0.00 0.00 5.40
42 43 4.206418 GGGGGAGGGGGAGAAAAT 57.794 61.111 0.00 0.00 0.00 1.82
43 44 2.421317 GGGGGAGGGGGAGAAAATT 58.579 57.895 0.00 0.00 0.00 1.82
44 45 0.261991 GGGGGAGGGGGAGAAAATTC 59.738 60.000 0.00 0.00 0.00 2.17
45 46 1.309876 GGGGAGGGGGAGAAAATTCT 58.690 55.000 0.00 0.00 41.00 2.40
46 47 1.646447 GGGGAGGGGGAGAAAATTCTT 59.354 52.381 0.00 0.00 37.73 2.52
47 48 2.044492 GGGGAGGGGGAGAAAATTCTTT 59.956 50.000 0.00 0.00 37.73 2.52
48 49 3.271225 GGGGAGGGGGAGAAAATTCTTTA 59.729 47.826 0.00 0.00 37.73 1.85
49 50 4.537751 GGGAGGGGGAGAAAATTCTTTAG 58.462 47.826 0.00 0.00 37.73 1.85
50 51 3.954904 GGAGGGGGAGAAAATTCTTTAGC 59.045 47.826 0.00 0.00 37.73 3.09
51 52 3.621558 AGGGGGAGAAAATTCTTTAGCG 58.378 45.455 0.00 0.00 37.73 4.26
52 53 3.265995 AGGGGGAGAAAATTCTTTAGCGA 59.734 43.478 0.00 0.00 37.73 4.93
53 54 3.628032 GGGGGAGAAAATTCTTTAGCGAG 59.372 47.826 0.00 0.00 37.73 5.03
54 55 4.514401 GGGGAGAAAATTCTTTAGCGAGA 58.486 43.478 0.00 0.00 37.73 4.04
55 56 4.333095 GGGGAGAAAATTCTTTAGCGAGAC 59.667 45.833 0.00 0.00 37.73 3.36
56 57 4.033014 GGGAGAAAATTCTTTAGCGAGACG 59.967 45.833 0.00 0.00 37.73 4.18
57 58 4.863131 GGAGAAAATTCTTTAGCGAGACGA 59.137 41.667 0.00 0.00 37.73 4.20
58 59 5.347907 GGAGAAAATTCTTTAGCGAGACGAA 59.652 40.000 0.00 0.00 37.73 3.85
59 60 6.128634 GGAGAAAATTCTTTAGCGAGACGAAA 60.129 38.462 0.00 0.00 37.73 3.46
60 61 6.822506 AGAAAATTCTTTAGCGAGACGAAAG 58.177 36.000 0.00 0.00 41.03 2.62
61 62 6.645415 AGAAAATTCTTTAGCGAGACGAAAGA 59.355 34.615 0.00 0.00 44.98 2.52
62 63 6.969828 AAATTCTTTAGCGAGACGAAAGAT 57.030 33.333 0.00 0.00 45.64 2.40
63 64 8.475331 AAAATTCTTTAGCGAGACGAAAGATA 57.525 30.769 0.00 0.00 45.64 1.98
64 65 8.649973 AAATTCTTTAGCGAGACGAAAGATAT 57.350 30.769 0.00 0.00 45.64 1.63
65 66 9.745880 AAATTCTTTAGCGAGACGAAAGATATA 57.254 29.630 0.00 0.00 45.64 0.86
66 67 8.730970 ATTCTTTAGCGAGACGAAAGATATAC 57.269 34.615 0.00 0.00 45.64 1.47
67 68 7.493743 TCTTTAGCGAGACGAAAGATATACT 57.506 36.000 0.00 0.00 42.77 2.12
68 69 7.574496 TCTTTAGCGAGACGAAAGATATACTC 58.426 38.462 0.00 0.00 42.77 2.59
75 76 8.605746 GCGAGACGAAAGATATACTCATATAGT 58.394 37.037 0.00 0.00 42.62 2.12
76 77 9.909043 CGAGACGAAAGATATACTCATATAGTG 57.091 37.037 0.00 0.00 39.39 2.74
82 83 8.897457 AAAGATATACTCATATAGTGTTCGCG 57.103 34.615 0.00 0.00 39.39 5.87
151 153 1.963515 CCAAACCAAAGGAGACCAAGG 59.036 52.381 0.00 0.00 0.00 3.61
157 159 1.882623 CAAAGGAGACCAAGGAGCAAC 59.117 52.381 0.00 0.00 0.00 4.17
220 222 2.205074 CTAAAGGCTCGTATGGTGCTG 58.795 52.381 0.00 0.00 35.51 4.41
227 229 2.804572 GCTCGTATGGTGCTGTCATCAT 60.805 50.000 3.90 3.90 45.45 2.45
233 235 5.048713 CGTATGGTGCTGTCATCATAGACTA 60.049 44.000 5.63 0.00 44.46 2.59
234 236 5.876651 ATGGTGCTGTCATCATAGACTAA 57.123 39.130 0.00 0.00 41.99 2.24
257 259 1.067425 TGGTAGATTTGTCACGTCGGG 60.067 52.381 0.00 0.00 0.00 5.14
258 260 1.636988 GTAGATTTGTCACGTCGGGG 58.363 55.000 0.00 0.00 0.00 5.73
259 261 0.533491 TAGATTTGTCACGTCGGGGG 59.467 55.000 0.00 0.00 0.00 5.40
262 264 1.760479 ATTTGTCACGTCGGGGGACA 61.760 55.000 8.16 8.16 39.60 4.02
271 273 0.326927 GTCGGGGGACAGGAAAATCA 59.673 55.000 0.00 0.00 0.00 2.57
341 344 3.821033 GGTCTCAATTGGCAACTACAGTT 59.179 43.478 0.00 0.00 39.12 3.16
391 394 4.283467 CCATAACATCGGGGTGATAGAGAA 59.717 45.833 0.00 0.00 34.83 2.87
403 406 6.830838 GGGGTGATAGAGAAAATGAAGAATGT 59.169 38.462 0.00 0.00 0.00 2.71
424 427 2.304761 TGGGTTGCTCTTTCGGTCTATT 59.695 45.455 0.00 0.00 0.00 1.73
426 429 3.596214 GGTTGCTCTTTCGGTCTATTGA 58.404 45.455 0.00 0.00 0.00 2.57
454 457 9.113838 GACAGTTTTTGATGATATGTATCACCT 57.886 33.333 4.93 0.00 44.66 4.00
468 471 1.838112 TCACCTTGCATGTGATTCCC 58.162 50.000 13.80 0.00 37.80 3.97
469 472 0.819582 CACCTTGCATGTGATTCCCC 59.180 55.000 10.52 0.00 35.74 4.81
515 518 7.540474 TCCTAGAGAGACTAATTGTGTTGTT 57.460 36.000 0.00 0.00 0.00 2.83
615 618 6.631962 ACTCTTGTAAAAGATACTTCCTCCG 58.368 40.000 0.00 0.00 0.00 4.63
628 631 9.022884 AGATACTTCCTCCGTTCCTAAATATAC 57.977 37.037 0.00 0.00 0.00 1.47
635 638 6.982724 CCTCCGTTCCTAAATATACGTCTTTT 59.017 38.462 0.00 0.00 32.45 2.27
709 712 5.645497 AGTCTACATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 0.00 4.70
710 713 5.412594 GTCTACATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 0.00 3.86
715 718 4.906065 TCACTCATTTTGCTCCATATGC 57.094 40.909 0.00 0.00 0.00 3.14
720 723 3.633525 TCATTTTGCTCCATATGCAGTCC 59.366 43.478 0.00 0.00 41.71 3.85
815 818 6.430962 AGTACTATGATGATCACCTTGCAT 57.569 37.500 0.00 0.02 0.00 3.96
825 828 5.188434 TGATCACCTTGCATTAAAGAGGAG 58.812 41.667 6.87 0.00 33.47 3.69
826 829 3.955471 TCACCTTGCATTAAAGAGGAGG 58.045 45.455 6.87 0.26 33.47 4.30
827 830 2.424956 CACCTTGCATTAAAGAGGAGGC 59.575 50.000 6.87 0.00 33.47 4.70
828 831 2.027385 CCTTGCATTAAAGAGGAGGCC 58.973 52.381 0.00 0.00 0.00 5.19
829 832 2.357569 CCTTGCATTAAAGAGGAGGCCT 60.358 50.000 3.86 3.86 36.03 5.19
830 833 3.359950 CTTGCATTAAAGAGGAGGCCTT 58.640 45.455 6.77 0.00 31.76 4.35
890 919 1.004918 GAGCCCGCGCCAGTATTAT 60.005 57.895 0.00 0.00 34.57 1.28
891 920 0.602905 GAGCCCGCGCCAGTATTATT 60.603 55.000 0.00 0.00 34.57 1.40
892 921 0.179029 AGCCCGCGCCAGTATTATTT 60.179 50.000 0.00 0.00 34.57 1.40
1165 1483 3.186047 CCTCCGCGCCAACTAACG 61.186 66.667 0.00 0.00 0.00 3.18
1184 1502 2.530497 GCATCGCAATTACGCCCGA 61.530 57.895 0.00 0.00 0.00 5.14
1205 1523 1.003118 CGGAATCCCTGAACCTTCACA 59.997 52.381 0.00 0.00 32.90 3.58
1375 1699 1.152839 CGAGGAGGAGGAGGAGGAC 60.153 68.421 0.00 0.00 0.00 3.85
1392 1716 2.597217 CGGTGGGCTTTGCTCCAA 60.597 61.111 0.00 0.00 32.52 3.53
1398 1722 1.466851 GGGCTTTGCTCCAACTTGCT 61.467 55.000 0.00 0.00 0.00 3.91
1409 1733 1.338973 CCAACTTGCTGCTTGTGTGAT 59.661 47.619 0.00 0.00 0.00 3.06
1416 1740 2.950975 TGCTGCTTGTGTGATTTTCTCA 59.049 40.909 0.00 0.00 0.00 3.27
1434 1758 4.074970 TCTCAATTTCTGCCTCTTGGTTC 58.925 43.478 0.00 0.00 35.27 3.62
1568 1901 3.771160 GTGTCCGATGGCCTCCGT 61.771 66.667 3.32 0.00 0.00 4.69
1666 2005 2.310538 CCCCAGCCAATTTAGTGGATC 58.689 52.381 0.00 0.00 41.65 3.36
1678 2017 7.498900 CCAATTTAGTGGATCTTATAGTGTGCA 59.501 37.037 0.00 0.00 41.65 4.57
1686 2025 2.168521 TCTTATAGTGTGCAGACTGCCC 59.831 50.000 25.66 14.20 44.23 5.36
1694 2033 1.072159 GCAGACTGCCCAACACTCT 59.928 57.895 17.01 0.00 37.42 3.24
1695 2034 0.536006 GCAGACTGCCCAACACTCTT 60.536 55.000 17.01 0.00 37.42 2.85
2217 2557 6.597832 AGGGCATGTACTTCTAGATATGAC 57.402 41.667 0.00 0.00 0.00 3.06
2258 2600 4.444022 GGTCAATATCCTCAGATGTGCAGT 60.444 45.833 0.00 0.00 33.67 4.40
2358 2700 5.545588 CTTCTGAGAACAACAGAGATGGAA 58.454 41.667 0.00 0.00 43.67 3.53
2464 2806 5.003214 CAGTTAATGTGAGCGTACTTCGTAC 59.997 44.000 0.00 0.00 42.13 3.67
2641 3013 4.807304 GTCGTTTACCTTGTCAAGTGAGAA 59.193 41.667 11.61 0.00 0.00 2.87
2695 3067 5.847304 TGTATAAGCAGATCTGTGGACATC 58.153 41.667 23.38 5.42 0.00 3.06
2724 3096 4.096984 CCTTAGAAGCATGAACCATTGACC 59.903 45.833 0.00 0.00 0.00 4.02
2790 3163 2.494059 ACACAAACGATCCTTGGACTG 58.506 47.619 7.03 0.00 0.00 3.51
2851 3227 8.540388 TGCAGACTAGGTAATAATCTTCTGTTT 58.460 33.333 0.00 0.00 33.30 2.83
2984 3378 9.448438 AAACATATACACTGTAATCTGCAGAAA 57.552 29.630 22.50 9.42 37.40 2.52
2985 3379 9.618890 AACATATACACTGTAATCTGCAGAAAT 57.381 29.630 22.50 15.23 37.40 2.17
3354 4453 7.718753 CAGGCTTTATCAGAAGGATAAGATTGT 59.281 37.037 0.00 0.00 46.34 2.71
3403 4502 7.007116 TGTATAGTGATCCTTCAGCATCTAGT 58.993 38.462 0.00 0.00 30.85 2.57
3465 4576 1.634702 TTGGTTGCGTTTTCTGTTGC 58.365 45.000 0.00 0.00 0.00 4.17
3542 4833 4.513442 TGTGGAGTTTACATGATAGGCAC 58.487 43.478 0.00 0.00 0.00 5.01
3671 4962 6.765036 TGGTACTCTTCTATACTCGGTAGTTG 59.235 42.308 0.00 0.00 37.15 3.16
3752 5043 0.250295 TGGGCAGAAACCTGAAGTCG 60.250 55.000 0.00 0.00 33.56 4.18
3884 5180 7.201145 GCTCTATGTCATTTGATGCTGAAAAT 58.799 34.615 0.00 0.00 0.00 1.82
3885 5181 7.167635 GCTCTATGTCATTTGATGCTGAAAATG 59.832 37.037 10.45 10.45 42.53 2.32
3888 5184 9.791820 CTATGTCATTTGATGCTGAAAATGTTA 57.208 29.630 14.15 8.17 42.06 2.41
3932 5228 5.297527 TGCATCCATATGTCTGTGATCAAAC 59.702 40.000 0.00 0.00 35.38 2.93
4232 5537 0.109039 GAGACGAGGAGCTGGTGAAC 60.109 60.000 0.00 0.00 0.00 3.18
4280 5586 3.176708 GACGAAGCAGCTATTGTACGAA 58.823 45.455 0.00 0.00 0.00 3.85
4482 5789 5.007136 GTGCATGTTATCTTTCTAGTGGAGC 59.993 44.000 0.00 0.00 0.00 4.70
4483 5790 5.118990 GCATGTTATCTTTCTAGTGGAGCA 58.881 41.667 0.00 0.00 0.00 4.26
4553 5860 8.746922 TTGCAAATTATTTCTGAATCTGACAC 57.253 30.769 0.00 0.00 0.00 3.67
4653 5960 7.982224 TGCAGTCTATTTTTCTCAGATGATTG 58.018 34.615 0.00 0.00 0.00 2.67
4976 6330 8.701895 TGATACCTAAGGTACCTTGAGTATTTG 58.298 37.037 31.66 18.43 41.31 2.32
4982 6337 4.286032 AGGTACCTTGAGTATTTGCTCACA 59.714 41.667 9.21 0.00 44.23 3.58
4994 6349 5.789643 ATTTGCTCACAGTGGTTACATTT 57.210 34.783 0.00 0.00 0.00 2.32
4995 6350 4.566545 TTGCTCACAGTGGTTACATTTG 57.433 40.909 0.00 0.00 0.00 2.32
4996 6351 3.550820 TGCTCACAGTGGTTACATTTGT 58.449 40.909 0.00 0.00 0.00 2.83
4998 6353 5.312895 TGCTCACAGTGGTTACATTTGTAT 58.687 37.500 0.00 0.00 0.00 2.29
4999 6354 5.411361 TGCTCACAGTGGTTACATTTGTATC 59.589 40.000 0.00 0.00 0.00 2.24
5000 6355 5.163754 GCTCACAGTGGTTACATTTGTATCC 60.164 44.000 0.00 9.83 39.61 2.59
5001 6356 6.121776 TCACAGTGGTTACATTTGTATCCT 57.878 37.500 15.41 0.00 39.78 3.24
5002 6357 6.170506 TCACAGTGGTTACATTTGTATCCTC 58.829 40.000 15.41 12.69 39.78 3.71
5003 6358 5.937540 CACAGTGGTTACATTTGTATCCTCA 59.062 40.000 15.41 0.00 39.78 3.86
5004 6359 6.092670 CACAGTGGTTACATTTGTATCCTCAG 59.907 42.308 15.41 12.08 39.78 3.35
5005 6360 6.173339 CAGTGGTTACATTTGTATCCTCAGT 58.827 40.000 15.41 1.54 39.78 3.41
5006 6361 6.655003 CAGTGGTTACATTTGTATCCTCAGTT 59.345 38.462 15.41 0.00 39.78 3.16
5007 6362 7.174946 CAGTGGTTACATTTGTATCCTCAGTTT 59.825 37.037 15.41 0.00 39.78 2.66
5057 6412 2.158726 GGTTGGTGACCCAGTTCAGTTA 60.159 50.000 0.00 0.00 43.15 2.24
5269 6625 3.819337 TCGTATGCATCCAGAGGTAGTAC 59.181 47.826 0.19 0.00 0.00 2.73
5912 7273 3.636300 CCAGAGCTAGATCTGCTGTACTT 59.364 47.826 28.71 0.00 44.47 2.24
6222 7635 5.465935 ACCCAAATAACAAATTAGCGTGTG 58.534 37.500 0.00 0.00 0.00 3.82
6782 8196 1.934589 TGCCCAACGAATCATCTACG 58.065 50.000 0.00 0.00 0.00 3.51
6785 8199 1.535226 CCCAACGAATCATCTACGCGA 60.535 52.381 15.93 0.00 0.00 5.87
6786 8200 1.781429 CCAACGAATCATCTACGCGAG 59.219 52.381 15.93 6.12 0.00 5.03
7026 8548 2.420687 GCTCTTATGGCTTAGGTGCTGT 60.421 50.000 8.62 0.00 0.00 4.40
7082 8604 6.790232 AGGTTTGACAAATTCCAGAAAAGA 57.210 33.333 3.49 0.00 0.00 2.52
7318 8843 5.743636 AATAACCAAATCATGTGCAAGGT 57.256 34.783 0.00 0.00 0.00 3.50
7340 8867 5.241728 GGTATCCATTGAAAGGGTAGCATTC 59.758 44.000 4.24 0.00 39.46 2.67
7348 8875 4.576053 TGAAAGGGTAGCATTCGATCAATG 59.424 41.667 11.35 11.35 44.44 2.82
7350 8877 4.422073 AGGGTAGCATTCGATCAATGAA 57.578 40.909 16.98 3.66 44.40 2.57
7354 8881 6.596888 AGGGTAGCATTCGATCAATGAATATG 59.403 38.462 16.98 0.00 44.40 1.78
7372 8899 5.818136 ATATGGGAAAACAATCTCACACG 57.182 39.130 0.00 0.00 31.26 4.49
7377 8904 4.279659 GGAAAACAATCTCACACGTTCAC 58.720 43.478 0.00 0.00 0.00 3.18
7386 8913 2.878406 CTCACACGTTCACAGGGAAATT 59.122 45.455 0.00 0.00 37.23 1.82
7407 8934 7.427989 AATTTATTCAGACAATGCTCCCAAT 57.572 32.000 0.00 0.00 0.00 3.16
7438 8965 4.437682 AGTTGAACCATCCTTGTCTTCA 57.562 40.909 0.00 0.00 0.00 3.02
7439 8966 4.392940 AGTTGAACCATCCTTGTCTTCAG 58.607 43.478 0.00 0.00 0.00 3.02
7440 8967 2.783135 TGAACCATCCTTGTCTTCAGC 58.217 47.619 0.00 0.00 0.00 4.26
7441 8968 2.087646 GAACCATCCTTGTCTTCAGCC 58.912 52.381 0.00 0.00 0.00 4.85
7442 8969 1.366319 ACCATCCTTGTCTTCAGCCT 58.634 50.000 0.00 0.00 0.00 4.58
7443 8970 1.707427 ACCATCCTTGTCTTCAGCCTT 59.293 47.619 0.00 0.00 0.00 4.35
7444 8971 2.912956 ACCATCCTTGTCTTCAGCCTTA 59.087 45.455 0.00 0.00 0.00 2.69
7447 8974 4.384537 CCATCCTTGTCTTCAGCCTTATGA 60.385 45.833 0.00 0.00 0.00 2.15
7480 9012 8.056407 GGCAACAAGAAACTTAGGAATCTAAT 57.944 34.615 0.00 0.00 35.20 1.73
7564 9096 0.178987 TTGTATTGGTTGGGGTGCGT 60.179 50.000 0.00 0.00 0.00 5.24
7592 9124 4.301505 CAGTAGTGCAACGCCCAT 57.698 55.556 0.00 0.00 45.86 4.00
7607 9139 0.107214 CCCATGCGACACATAAGGGT 60.107 55.000 0.00 0.00 37.26 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.431765 CCATTGTAAACTGAGCAGACCTAT 58.568 41.667 4.21 0.00 0.00 2.57
5 6 2.749621 CCCATTGTAAACTGAGCAGACC 59.250 50.000 4.21 0.00 0.00 3.85
6 7 2.749621 CCCCATTGTAAACTGAGCAGAC 59.250 50.000 4.21 0.00 0.00 3.51
7 8 2.290896 CCCCCATTGTAAACTGAGCAGA 60.291 50.000 4.21 0.00 0.00 4.26
8 9 2.094675 CCCCCATTGTAAACTGAGCAG 58.905 52.381 0.00 0.00 0.00 4.24
9 10 2.214376 CCCCCATTGTAAACTGAGCA 57.786 50.000 0.00 0.00 0.00 4.26
25 26 0.261991 GAATTTTCTCCCCCTCCCCC 59.738 60.000 0.00 0.00 0.00 5.40
26 27 1.309876 AGAATTTTCTCCCCCTCCCC 58.690 55.000 0.00 0.00 29.94 4.81
27 28 3.474798 AAAGAATTTTCTCCCCCTCCC 57.525 47.619 0.00 0.00 31.62 4.30
28 29 3.954904 GCTAAAGAATTTTCTCCCCCTCC 59.045 47.826 0.00 0.00 40.09 4.30
29 30 3.628032 CGCTAAAGAATTTTCTCCCCCTC 59.372 47.826 0.00 0.00 40.09 4.30
30 31 3.265995 TCGCTAAAGAATTTTCTCCCCCT 59.734 43.478 0.00 0.00 40.09 4.79
31 32 3.617284 TCGCTAAAGAATTTTCTCCCCC 58.383 45.455 0.00 0.00 40.09 5.40
32 33 4.333095 GTCTCGCTAAAGAATTTTCTCCCC 59.667 45.833 0.00 0.00 40.09 4.81
33 34 4.033014 CGTCTCGCTAAAGAATTTTCTCCC 59.967 45.833 0.00 0.00 40.09 4.30
34 35 4.863131 TCGTCTCGCTAAAGAATTTTCTCC 59.137 41.667 0.00 0.00 40.09 3.71
35 36 6.390987 TTCGTCTCGCTAAAGAATTTTCTC 57.609 37.500 0.00 0.00 40.09 2.87
36 37 6.645415 TCTTTCGTCTCGCTAAAGAATTTTCT 59.355 34.615 0.00 0.00 40.09 2.52
37 38 6.818416 TCTTTCGTCTCGCTAAAGAATTTTC 58.182 36.000 0.00 0.00 40.09 2.29
38 39 6.780706 TCTTTCGTCTCGCTAAAGAATTTT 57.219 33.333 0.00 0.00 40.09 1.82
39 40 6.969828 ATCTTTCGTCTCGCTAAAGAATTT 57.030 33.333 9.01 0.00 41.24 1.82
40 41 9.182933 GTATATCTTTCGTCTCGCTAAAGAATT 57.817 33.333 9.01 0.00 41.24 2.17
41 42 8.569641 AGTATATCTTTCGTCTCGCTAAAGAAT 58.430 33.333 9.01 7.51 41.24 2.40
42 43 7.928103 AGTATATCTTTCGTCTCGCTAAAGAA 58.072 34.615 9.01 2.75 41.24 2.52
43 44 7.226128 TGAGTATATCTTTCGTCTCGCTAAAGA 59.774 37.037 0.00 0.00 41.89 2.52
44 45 7.353497 TGAGTATATCTTTCGTCTCGCTAAAG 58.647 38.462 0.00 0.00 0.00 1.85
45 46 7.255491 TGAGTATATCTTTCGTCTCGCTAAA 57.745 36.000 0.00 0.00 0.00 1.85
46 47 6.856135 TGAGTATATCTTTCGTCTCGCTAA 57.144 37.500 0.00 0.00 0.00 3.09
47 48 8.719560 ATATGAGTATATCTTTCGTCTCGCTA 57.280 34.615 0.00 0.00 0.00 4.26
48 49 5.950758 ATGAGTATATCTTTCGTCTCGCT 57.049 39.130 0.00 0.00 0.00 4.93
49 50 8.605746 ACTATATGAGTATATCTTTCGTCTCGC 58.394 37.037 0.00 0.00 36.27 5.03
50 51 9.909043 CACTATATGAGTATATCTTTCGTCTCG 57.091 37.037 0.00 0.00 35.64 4.04
55 56 9.001049 GCGAACACTATATGAGTATATCTTTCG 57.999 37.037 0.00 0.00 35.64 3.46
56 57 9.001049 CGCGAACACTATATGAGTATATCTTTC 57.999 37.037 0.00 0.00 35.64 2.62
57 58 8.512956 ACGCGAACACTATATGAGTATATCTTT 58.487 33.333 15.93 0.00 35.64 2.52
58 59 8.041829 ACGCGAACACTATATGAGTATATCTT 57.958 34.615 15.93 0.00 35.64 2.40
59 60 7.612668 ACGCGAACACTATATGAGTATATCT 57.387 36.000 15.93 0.00 35.64 1.98
60 61 8.670804 AAACGCGAACACTATATGAGTATATC 57.329 34.615 15.93 0.00 35.64 1.63
61 62 9.125906 GAAAACGCGAACACTATATGAGTATAT 57.874 33.333 15.93 0.00 35.64 0.86
62 63 7.592533 GGAAAACGCGAACACTATATGAGTATA 59.407 37.037 15.93 0.00 35.64 1.47
63 64 6.420008 GGAAAACGCGAACACTATATGAGTAT 59.580 38.462 15.93 0.00 35.64 2.12
64 65 5.745294 GGAAAACGCGAACACTATATGAGTA 59.255 40.000 15.93 0.00 35.64 2.59
65 66 4.565564 GGAAAACGCGAACACTATATGAGT 59.434 41.667 15.93 0.00 39.82 3.41
66 67 4.804139 AGGAAAACGCGAACACTATATGAG 59.196 41.667 15.93 0.00 0.00 2.90
67 68 4.751060 AGGAAAACGCGAACACTATATGA 58.249 39.130 15.93 0.00 0.00 2.15
68 69 5.051240 GGTAGGAAAACGCGAACACTATATG 60.051 44.000 15.93 0.00 0.00 1.78
75 76 2.172851 ATGGTAGGAAAACGCGAACA 57.827 45.000 15.93 0.00 0.00 3.18
76 77 5.693104 TCATATATGGTAGGAAAACGCGAAC 59.307 40.000 15.93 0.03 0.00 3.95
151 153 4.389077 ACGTTTAGCTTCACATAGTTGCTC 59.611 41.667 0.00 0.00 35.47 4.26
157 159 4.271049 CCATCCACGTTTAGCTTCACATAG 59.729 45.833 0.00 0.00 0.00 2.23
227 229 8.308931 ACGTGACAAATCTACCATTTTAGTCTA 58.691 33.333 0.00 0.00 0.00 2.59
233 235 4.153475 CCGACGTGACAAATCTACCATTTT 59.847 41.667 0.00 0.00 0.00 1.82
234 236 3.682858 CCGACGTGACAAATCTACCATTT 59.317 43.478 0.00 0.00 0.00 2.32
246 248 3.299977 CTGTCCCCCGACGTGACA 61.300 66.667 0.00 0.00 42.37 3.58
248 250 3.813606 TTCCTGTCCCCCGACGTGA 62.814 63.158 0.00 0.00 42.37 4.35
250 252 1.486145 ATTTTCCTGTCCCCCGACGT 61.486 55.000 0.00 0.00 42.37 4.34
257 259 4.081531 TGCATCAATTGATTTTCCTGTCCC 60.082 41.667 18.41 0.00 31.21 4.46
258 260 5.075858 TGCATCAATTGATTTTCCTGTCC 57.924 39.130 18.41 0.00 31.21 4.02
259 261 6.869913 TCTTTGCATCAATTGATTTTCCTGTC 59.130 34.615 18.41 5.36 31.21 3.51
262 264 7.843490 CATCTTTGCATCAATTGATTTTCCT 57.157 32.000 18.41 0.00 31.21 3.36
341 344 3.895041 TCATCTCTATGCGATTACACCCA 59.105 43.478 0.00 0.00 32.76 4.51
391 394 4.154942 AGAGCAACCCACATTCTTCATTT 58.845 39.130 0.00 0.00 0.00 2.32
403 406 1.344065 TAGACCGAAAGAGCAACCCA 58.656 50.000 0.00 0.00 0.00 4.51
424 427 8.716646 ATACATATCATCAAAAACTGTCGTCA 57.283 30.769 0.00 0.00 0.00 4.35
426 429 8.604035 GTGATACATATCATCAAAAACTGTCGT 58.396 33.333 4.93 0.00 43.82 4.34
454 457 0.683828 ATGCGGGGAATCACATGCAA 60.684 50.000 5.78 0.00 35.78 4.08
466 469 4.582701 TGCTCAAAAATAATATGCGGGG 57.417 40.909 0.00 0.00 0.00 5.73
468 471 5.224888 AGCATGCTCAAAAATAATATGCGG 58.775 37.500 16.30 0.00 42.93 5.69
469 472 5.344128 GGAGCATGCTCAAAAATAATATGCG 59.656 40.000 40.37 0.00 44.40 4.73
515 518 9.383519 CTTCTAACTAGTTTGGCTAAATCATGA 57.616 33.333 14.49 0.00 0.00 3.07
691 694 5.690409 GCATATGGAGCAAAATGAGTGAATG 59.310 40.000 4.56 0.00 0.00 2.67
696 699 4.275810 ACTGCATATGGAGCAAAATGAGT 58.724 39.130 22.77 0.00 42.17 3.41
700 703 3.907221 AGGACTGCATATGGAGCAAAAT 58.093 40.909 22.77 4.09 42.17 1.82
770 773 5.071384 ACTTCCTCCTTTCCTCGTCTAAAAA 59.929 40.000 0.00 0.00 0.00 1.94
771 774 4.591924 ACTTCCTCCTTTCCTCGTCTAAAA 59.408 41.667 0.00 0.00 0.00 1.52
772 775 4.158015 ACTTCCTCCTTTCCTCGTCTAAA 58.842 43.478 0.00 0.00 0.00 1.85
773 776 3.775910 ACTTCCTCCTTTCCTCGTCTAA 58.224 45.455 0.00 0.00 0.00 2.10
774 777 3.453059 ACTTCCTCCTTTCCTCGTCTA 57.547 47.619 0.00 0.00 0.00 2.59
775 778 2.312424 ACTTCCTCCTTTCCTCGTCT 57.688 50.000 0.00 0.00 0.00 4.18
776 779 3.090790 AGTACTTCCTCCTTTCCTCGTC 58.909 50.000 0.00 0.00 0.00 4.20
777 780 3.172471 AGTACTTCCTCCTTTCCTCGT 57.828 47.619 0.00 0.00 0.00 4.18
778 781 4.888239 TCATAGTACTTCCTCCTTTCCTCG 59.112 45.833 0.00 0.00 0.00 4.63
779 782 6.551601 TCATCATAGTACTTCCTCCTTTCCTC 59.448 42.308 0.00 0.00 0.00 3.71
780 783 6.444704 TCATCATAGTACTTCCTCCTTTCCT 58.555 40.000 0.00 0.00 0.00 3.36
781 784 6.732896 TCATCATAGTACTTCCTCCTTTCC 57.267 41.667 0.00 0.00 0.00 3.13
782 785 7.870445 GTGATCATCATAGTACTTCCTCCTTTC 59.130 40.741 0.00 0.00 0.00 2.62
815 818 3.134081 CCGATGTAAGGCCTCCTCTTTAA 59.866 47.826 5.23 0.00 30.89 1.52
827 830 2.737881 TTCCCGGCCCGATGTAAGG 61.738 63.158 3.71 0.00 0.00 2.69
828 831 1.523032 GTTCCCGGCCCGATGTAAG 60.523 63.158 3.71 0.00 0.00 2.34
829 832 2.585698 GTTCCCGGCCCGATGTAA 59.414 61.111 3.71 0.00 0.00 2.41
830 833 3.840594 CGTTCCCGGCCCGATGTA 61.841 66.667 3.71 0.00 0.00 2.29
890 919 6.846505 AGAGGAGAGAGAGAGAGAGAGATAAA 59.153 42.308 0.00 0.00 0.00 1.40
891 920 6.385443 AGAGGAGAGAGAGAGAGAGAGATAA 58.615 44.000 0.00 0.00 0.00 1.75
892 921 5.970289 AGAGGAGAGAGAGAGAGAGAGATA 58.030 45.833 0.00 0.00 0.00 1.98
1165 1483 2.331451 GGGCGTAATTGCGATGCC 59.669 61.111 20.50 10.63 46.57 4.40
1168 1486 2.235016 CGTCGGGCGTAATTGCGAT 61.235 57.895 20.50 0.00 35.06 4.58
1169 1487 2.881827 CGTCGGGCGTAATTGCGA 60.882 61.111 20.50 0.00 35.06 5.10
1184 1502 1.003233 GTGAAGGTTCAGGGATTCCGT 59.997 52.381 0.00 0.00 37.98 4.69
1205 1523 1.533711 CGCCCCCAATCAGGAGATT 59.466 57.895 0.00 0.00 45.16 2.40
1375 1699 2.597217 TTGGAGCAAAGCCCACCG 60.597 61.111 0.00 0.00 30.91 4.94
1392 1716 3.382546 AGAAAATCACACAAGCAGCAAGT 59.617 39.130 0.00 0.00 0.00 3.16
1398 1722 6.698329 CAGAAATTGAGAAAATCACACAAGCA 59.302 34.615 0.00 0.00 37.77 3.91
1409 1733 4.895297 ACCAAGAGGCAGAAATTGAGAAAA 59.105 37.500 0.00 0.00 39.06 2.29
1416 1740 7.486407 AATAATGAACCAAGAGGCAGAAATT 57.514 32.000 0.00 0.00 39.06 1.82
1434 1758 7.329226 CCACAAACCAAGAACTGCTTAATAATG 59.671 37.037 0.00 0.00 34.31 1.90
1568 1901 3.814842 GGTCATTCTCACACACAATGTCA 59.185 43.478 0.00 0.00 40.64 3.58
1646 1985 2.091665 AGATCCACTAAATTGGCTGGGG 60.092 50.000 0.00 0.00 36.48 4.96
1686 2025 9.781834 TTAACAACAAAACAGATAAGAGTGTTG 57.218 29.630 11.04 11.04 46.09 3.33
1820 2159 2.885266 TGCTACGTAGATCTGATGGACC 59.115 50.000 26.53 4.26 0.00 4.46
2229 2570 7.417116 GCACATCTGAGGATATTGACCAAAAAT 60.417 37.037 0.00 0.00 0.00 1.82
2258 2600 6.996879 AGTACTCTCGCAGTATGGTAGATAAA 59.003 38.462 0.00 0.00 39.90 1.40
2358 2700 5.389859 TTCCAAGCACGATTTTGATCATT 57.610 34.783 0.00 0.00 0.00 2.57
2464 2806 9.684448 ACTAGATATGACGACAACATCAAATAG 57.316 33.333 12.70 9.19 0.00 1.73
2520 2867 1.065926 TGCCTGCAGGAGACAATACTG 60.066 52.381 37.21 5.32 37.39 2.74
2641 3013 7.334921 CCAGAAAATGCATACATCCAAAATTGT 59.665 33.333 0.00 0.00 34.62 2.71
2695 3067 3.242870 GGTTCATGCTTCTAAGGAATGCG 60.243 47.826 0.00 0.00 32.39 4.73
2724 3096 6.973474 CCTACAAATAAGAGTAGAACTCCACG 59.027 42.308 3.49 0.00 46.18 4.94
2790 3163 2.161211 GGAATGAAGAACAGCACTGAGC 59.839 50.000 4.31 0.00 46.19 4.26
2805 3178 0.324614 TTCTTGCAGGAGCGGAATGA 59.675 50.000 0.00 0.00 46.23 2.57
2985 3379 9.887406 GAAACATTACGACAAAAGAGGAATAAA 57.113 29.630 0.00 0.00 0.00 1.40
3194 3603 4.808414 TCTTGTAACTGCTACATGCTCT 57.192 40.909 0.00 0.00 40.27 4.09
3314 4412 0.777446 AGCCTGGTTACACCCATGTT 59.223 50.000 0.00 0.00 40.48 2.71
3315 4413 0.777446 AAGCCTGGTTACACCCATGT 59.223 50.000 0.00 0.00 43.30 3.21
3354 4453 6.641169 TGATAGTGCAAATGTAAACCACAA 57.359 33.333 0.00 0.00 41.55 3.33
3465 4576 7.525688 TGTAGTAGAATCTTGCAGAATTTCG 57.474 36.000 0.00 0.00 0.00 3.46
3542 4833 2.523015 GATGCTTTCATCCAGTTTGCG 58.477 47.619 0.00 0.00 42.50 4.85
3752 5043 4.565564 ACGATACTTGCGATTGGAACTTAC 59.434 41.667 0.00 0.00 0.00 2.34
3888 5184 9.374838 GGATGCAAGAATACTTTCATTTTGATT 57.625 29.630 0.00 0.00 39.33 2.57
3897 5193 8.288208 CAGACATATGGATGCAAGAATACTTTC 58.712 37.037 7.80 0.00 36.43 2.62
3909 5205 5.297527 TGTTTGATCACAGACATATGGATGC 59.702 40.000 7.80 0.00 36.45 3.91
3932 5228 3.665323 GCACGAGCTCACAAACAATAGTG 60.665 47.826 15.40 10.25 37.91 2.74
3982 5281 8.702438 CCTGAAAACATGCAATAACTTTGTTAG 58.298 33.333 0.00 0.00 30.76 2.34
4171 5470 6.239289 CCCCAGATTGTTTTTGTTGTATCTGT 60.239 38.462 0.00 0.00 38.06 3.41
4189 5488 0.477204 CATCTGATGCCACCCCAGAT 59.523 55.000 4.47 0.00 45.47 2.90
4232 5537 4.942852 AGTGAAGCTCTAATTCGATCCTG 58.057 43.478 0.00 0.00 0.00 3.86
4234 5539 5.596845 AGAAGTGAAGCTCTAATTCGATCC 58.403 41.667 0.00 0.00 0.00 3.36
4476 5783 4.823989 AGCCTGATAATGTTAATGCTCCAC 59.176 41.667 0.00 0.00 0.00 4.02
4553 5860 2.559998 ACCTGAAAACAAAGTGCACG 57.440 45.000 12.01 0.00 0.00 5.34
4658 5965 9.959721 AAGGTAAACTGCTGAATAAAAGAGATA 57.040 29.630 0.00 0.00 0.00 1.98
4768 6075 2.768253 TACCATCCTGCTGTTGAGTG 57.232 50.000 0.00 0.00 0.00 3.51
4869 6195 4.685056 GTGCGCGTAAACACGTAC 57.315 55.556 8.43 0.00 37.71 3.67
4976 6330 5.163754 GGATACAAATGTAACCACTGTGAGC 60.164 44.000 9.86 0.00 41.46 4.26
4982 6337 6.374417 ACTGAGGATACAAATGTAACCACT 57.626 37.500 18.50 2.84 43.46 4.00
4994 6349 6.892456 AGTGATAGTGAGAAACTGAGGATACA 59.108 38.462 0.00 0.00 40.26 2.29
4995 6350 7.341445 AGTGATAGTGAGAAACTGAGGATAC 57.659 40.000 0.00 0.00 40.26 2.24
4996 6351 7.836685 AGAAGTGATAGTGAGAAACTGAGGATA 59.163 37.037 0.00 0.00 40.26 2.59
4998 6353 6.013379 AGAAGTGATAGTGAGAAACTGAGGA 58.987 40.000 0.00 0.00 40.26 3.71
4999 6354 6.071672 TCAGAAGTGATAGTGAGAAACTGAGG 60.072 42.308 0.00 0.00 40.26 3.86
5000 6355 6.918626 TCAGAAGTGATAGTGAGAAACTGAG 58.081 40.000 0.00 0.00 40.26 3.35
5001 6356 6.901081 TCAGAAGTGATAGTGAGAAACTGA 57.099 37.500 0.00 0.00 40.26 3.41
5002 6357 9.814899 AATATCAGAAGTGATAGTGAGAAACTG 57.185 33.333 1.89 0.00 46.60 3.16
5004 6359 9.809096 TGAATATCAGAAGTGATAGTGAGAAAC 57.191 33.333 0.40 0.00 46.60 2.78
5057 6412 5.594317 AGTCTTTGAAATTACAGTTGCAGGT 59.406 36.000 0.00 0.00 0.00 4.00
5269 6625 3.379372 CAGCTTACATGAATTGAGTGGGG 59.621 47.826 0.00 0.00 0.00 4.96
6222 7635 2.143925 GCGGAACCTATTACCTGCATC 58.856 52.381 0.00 0.00 0.00 3.91
6596 8009 1.206878 CATCACCACCTCCTCCATCA 58.793 55.000 0.00 0.00 0.00 3.07
6758 8172 1.656818 ATGATTCGTTGGGCAAGGCG 61.657 55.000 0.00 0.00 0.00 5.52
6768 8182 1.065701 AGCTCGCGTAGATGATTCGTT 59.934 47.619 5.77 0.00 0.00 3.85
6782 8196 1.233019 AATGTATGCATGGAGCTCGC 58.767 50.000 10.16 6.38 45.94 5.03
6785 8199 4.645863 TCCATAATGTATGCATGGAGCT 57.354 40.909 10.16 0.00 42.55 4.09
6786 8200 4.520111 TGTTCCATAATGTATGCATGGAGC 59.480 41.667 10.16 9.71 46.67 4.70
7067 8589 8.090214 ACAACCACATATCTTTTCTGGAATTTG 58.910 33.333 0.00 0.00 0.00 2.32
7076 8598 7.648142 TCTTGTGAACAACCACATATCTTTTC 58.352 34.615 0.00 0.00 45.31 2.29
7082 8604 8.049117 ACAGATATCTTGTGAACAACCACATAT 58.951 33.333 1.33 0.00 45.31 1.78
7233 8755 2.289694 ACACCGCTGCTCATTCTTAGTT 60.290 45.455 0.00 0.00 0.00 2.24
7318 8843 5.063204 CGAATGCTACCCTTTCAATGGATA 58.937 41.667 0.00 0.00 0.00 2.59
7340 8867 8.355169 AGATTGTTTTCCCATATTCATTGATCG 58.645 33.333 0.00 0.00 0.00 3.69
7348 8875 6.128007 ACGTGTGAGATTGTTTTCCCATATTC 60.128 38.462 0.00 0.00 0.00 1.75
7350 8877 5.253330 ACGTGTGAGATTGTTTTCCCATAT 58.747 37.500 0.00 0.00 0.00 1.78
7354 8881 3.314080 TGAACGTGTGAGATTGTTTTCCC 59.686 43.478 0.00 0.00 0.00 3.97
7372 8899 7.214467 TGTCTGAATAAATTTCCCTGTGAAC 57.786 36.000 0.00 0.00 31.05 3.18
7377 8904 6.870769 AGCATTGTCTGAATAAATTTCCCTG 58.129 36.000 0.00 0.00 0.00 4.45
7386 8913 5.951148 TCAATTGGGAGCATTGTCTGAATAA 59.049 36.000 5.42 0.00 33.91 1.40
7407 8934 5.701224 AGGATGGTTCAACTACCTTTTCAA 58.299 37.500 0.00 0.00 39.04 2.69
7438 8965 0.466922 GCCAGGTGCATCATAAGGCT 60.467 55.000 13.43 0.00 40.77 4.58
7439 8966 2.036236 GCCAGGTGCATCATAAGGC 58.964 57.895 0.00 3.14 40.77 4.35
7459 8986 9.892130 AATCGATTAGATTCCTAAGTTTCTTGT 57.108 29.630 9.39 0.00 45.95 3.16
7535 9067 6.156429 ACCCCAACCAATACAAAGTAAACAAA 59.844 34.615 0.00 0.00 0.00 2.83
7541 9073 3.158676 GCACCCCAACCAATACAAAGTA 58.841 45.455 0.00 0.00 0.00 2.24
7543 9075 1.067915 CGCACCCCAACCAATACAAAG 60.068 52.381 0.00 0.00 0.00 2.77
7548 9080 1.208535 CTAGACGCACCCCAACCAATA 59.791 52.381 0.00 0.00 0.00 1.90
7564 9096 1.330655 GCACTACTGCCCAGGCTAGA 61.331 60.000 10.58 0.00 42.51 2.43
7572 9104 3.431725 GGCGTTGCACTACTGCCC 61.432 66.667 11.14 0.00 43.51 5.36
7587 9119 1.447317 CCCTTATGTGTCGCATGGGC 61.447 60.000 9.20 1.13 35.03 5.36
7590 9122 1.299541 GGACCCTTATGTGTCGCATG 58.700 55.000 9.20 0.00 38.47 4.06
7592 9124 1.600107 GGGACCCTTATGTGTCGCA 59.400 57.895 2.09 0.00 42.21 5.10
7595 9127 2.654863 CCATTGGGACCCTTATGTGTC 58.345 52.381 13.00 0.00 35.59 3.67
7602 9134 1.610379 GCTTGCCATTGGGACCCTT 60.610 57.895 13.00 0.00 35.59 3.95


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

AutoCloner maintained by Alex Coulton.