Multiple sequence alignment - TraesCS3B01G414300

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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 TraesCS3B01G414300 chr3B 100.000 3476 0 0 1 3476 650955508 650952033 0.000000e+00 6420.0
1 TraesCS3B01G414300 chr3B 94.692 1526 78 1 953 2475 651257017 651258542 0.000000e+00 2366.0
2 TraesCS3B01G414300 chr3B 77.412 425 91 4 1960 2383 603452351 603451931 7.450000e-62 248.0
3 TraesCS3B01G414300 chr3B 79.524 210 37 3 2934 3143 690728404 690728607 1.010000e-30 145.0
4 TraesCS3B01G414300 chr3D 91.881 2759 129 38 540 3225 488119753 488117017 0.000000e+00 3766.0
5 TraesCS3B01G414300 chr3D 94.695 1527 76 3 953 2475 488234622 488236147 0.000000e+00 2366.0
6 TraesCS3B01G414300 chr3D 82.087 508 68 8 1 507 488120239 488119754 2.500000e-111 412.0
7 TraesCS3B01G414300 chr3D 77.551 441 80 11 1960 2392 456597287 456596858 7.450000e-62 248.0
8 TraesCS3B01G414300 chr3D 78.800 250 43 4 1 250 48068828 48069067 3.590000e-35 159.0
9 TraesCS3B01G414300 chr3D 76.190 252 49 4 8 259 23158011 23158251 4.710000e-24 122.0
10 TraesCS3B01G414300 chr3A 96.139 1865 48 9 692 2535 631729597 631727736 0.000000e+00 3024.0
11 TraesCS3B01G414300 chr3A 94.892 1527 72 4 953 2475 631775732 631777256 0.000000e+00 2383.0
12 TraesCS3B01G414300 chr3A 86.517 356 24 8 2620 2961 631727468 631727123 1.520000e-98 370.0
13 TraesCS3B01G414300 chr3A 80.952 231 32 11 2916 3143 639658844 639659065 4.610000e-39 172.0
14 TraesCS3B01G414300 chr3A 80.952 231 32 11 2916 3143 639665648 639665869 4.610000e-39 172.0
15 TraesCS3B01G414300 chr3A 92.437 119 8 1 3232 3349 7713808 7713690 5.970000e-38 169.0
16 TraesCS3B01G414300 chr3A 79.821 223 31 10 2921 3141 706643975 706644185 2.160000e-32 150.0
17 TraesCS3B01G414300 chr3A 98.182 55 1 0 2539 2593 631727601 631727547 2.860000e-16 97.1
18 TraesCS3B01G414300 chr5D 83.147 896 143 8 1057 1948 540240497 540239606 0.000000e+00 811.0
19 TraesCS3B01G414300 chr5D 81.450 717 124 9 1424 2134 464457873 464458586 2.330000e-161 579.0
20 TraesCS3B01G414300 chr5D 81.048 248 21 13 3232 3476 46342297 46342073 1.280000e-39 174.0
21 TraesCS3B01G414300 chr5D 80.519 154 28 2 105 258 389815529 389815680 2.190000e-22 117.0
22 TraesCS3B01G414300 chr4A 82.924 896 145 8 1057 1948 628090303 628089412 0.000000e+00 800.0
23 TraesCS3B01G414300 chr5B 82.478 896 149 8 1057 1948 682538799 682537908 0.000000e+00 778.0
24 TraesCS3B01G414300 chr5B 82.542 716 118 7 1424 2134 571535880 571536593 1.060000e-174 623.0
25 TraesCS3B01G414300 chr1A 79.388 621 99 22 1057 1671 490411649 490412246 8.980000e-111 411.0
26 TraesCS3B01G414300 chr1A 90.756 119 10 1 3232 3349 45851139 45851021 1.290000e-34 158.0
27 TraesCS3B01G414300 chr7D 87.097 155 17 3 107 259 542947640 542947487 4.610000e-39 172.0
28 TraesCS3B01G414300 chr7D 90.517 116 9 2 3232 3346 139190541 139190655 6.010000e-33 152.0
29 TraesCS3B01G414300 chr7D 81.295 139 24 2 129 267 14630813 14630677 1.020000e-20 111.0
30 TraesCS3B01G414300 chr7B 82.741 197 28 3 2948 3143 104298342 104298533 1.660000e-38 171.0
31 TraesCS3B01G414300 chr2D 80.816 245 21 13 3235 3476 145676345 145676124 5.970000e-38 169.0
32 TraesCS3B01G414300 chr2D 79.412 136 14 8 2016 2137 26481152 26481287 2.220000e-12 84.2
33 TraesCS3B01G414300 chr5A 91.667 120 9 1 3231 3349 704588936 704588817 7.720000e-37 165.0
34 TraesCS3B01G414300 chr5A 75.397 252 49 4 8 258 314147918 314148157 3.670000e-20 110.0
35 TraesCS3B01G414300 chr5A 94.737 57 1 2 1 56 440281671 440281726 1.720000e-13 87.9
36 TraesCS3B01G414300 chr5A 95.833 48 2 0 8 55 367082678 367082725 1.030000e-10 78.7
37 TraesCS3B01G414300 chr1D 83.333 186 22 6 2946 3129 223794760 223794938 2.780000e-36 163.0
38 TraesCS3B01G414300 chr1D 78.404 213 35 3 5 217 14267282 14267081 1.010000e-25 128.0
39 TraesCS3B01G414300 chr1D 87.273 55 2 5 605 657 448612261 448612210 1.350000e-04 58.4
40 TraesCS3B01G414300 chr7A 91.525 118 7 1 3232 3346 697883375 697883492 3.590000e-35 159.0
41 TraesCS3B01G414300 chr7A 81.122 196 30 7 2937 3131 576192815 576193004 2.160000e-32 150.0
42 TraesCS3B01G414300 chr6B 80.184 217 36 4 2928 3143 92186928 92187138 4.650000e-34 156.0
43 TraesCS3B01G414300 chr6A 90.598 117 9 2 3234 3349 457607607 457607492 1.670000e-33 154.0
44 TraesCS3B01G414300 chr1B 90.000 120 8 2 3229 3346 374331153 374331270 6.010000e-33 152.0
45 TraesCS3B01G414300 chr1B 97.778 45 1 0 11 55 364280282 364280238 1.030000e-10 78.7
46 TraesCS3B01G414300 chr4B 80.095 211 32 8 2937 3146 22697280 22697079 7.770000e-32 148.0
47 TraesCS3B01G414300 chrUn 77.823 248 44 3 11 258 35850509 35850273 3.620000e-30 143.0
48 TraesCS3B01G414300 chrUn 77.823 248 44 3 11 258 339653203 339652967 3.620000e-30 143.0
49 TraesCS3B01G414300 chr2B 83.916 143 23 0 116 258 798206567 798206709 1.680000e-28 137.0
50 TraesCS3B01G414300 chr2B 78.698 169 32 4 101 267 728238091 728238257 3.670000e-20 110.0
51 TraesCS3B01G414300 chr6D 82.014 139 23 2 129 267 417521130 417520994 2.190000e-22 117.0
52 TraesCS3B01G414300 chr4D 82.014 139 23 2 129 267 35334101 35334237 2.190000e-22 117.0


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 TraesCS3B01G414300 chr3B 650952033 650955508 3475 True 6420.0 6420 100.000000 1 3476 1 chr3B.!!$R2 3475
1 TraesCS3B01G414300 chr3B 651257017 651258542 1525 False 2366.0 2366 94.692000 953 2475 1 chr3B.!!$F1 1522
2 TraesCS3B01G414300 chr3D 488234622 488236147 1525 False 2366.0 2366 94.695000 953 2475 1 chr3D.!!$F3 1522
3 TraesCS3B01G414300 chr3D 488117017 488120239 3222 True 2089.0 3766 86.984000 1 3225 2 chr3D.!!$R2 3224
4 TraesCS3B01G414300 chr3A 631775732 631777256 1524 False 2383.0 2383 94.892000 953 2475 1 chr3A.!!$F1 1522
5 TraesCS3B01G414300 chr3A 631727123 631729597 2474 True 1163.7 3024 93.612667 692 2961 3 chr3A.!!$R2 2269
6 TraesCS3B01G414300 chr5D 540239606 540240497 891 True 811.0 811 83.147000 1057 1948 1 chr5D.!!$R2 891
7 TraesCS3B01G414300 chr5D 464457873 464458586 713 False 579.0 579 81.450000 1424 2134 1 chr5D.!!$F2 710
8 TraesCS3B01G414300 chr4A 628089412 628090303 891 True 800.0 800 82.924000 1057 1948 1 chr4A.!!$R1 891
9 TraesCS3B01G414300 chr5B 682537908 682538799 891 True 778.0 778 82.478000 1057 1948 1 chr5B.!!$R1 891
10 TraesCS3B01G414300 chr5B 571535880 571536593 713 False 623.0 623 82.542000 1424 2134 1 chr5B.!!$F1 710
11 TraesCS3B01G414300 chr1A 490411649 490412246 597 False 411.0 411 79.388000 1057 1671 1 chr1A.!!$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
33 34 0.254747 CTCCAAGAATAACGCCCCCA 59.745 55.0 0.0 0.0 0.0 4.96 F
927 960 0.321671 CACTCACCACCCACCACTAG 59.678 60.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2013 1.668294 GATCCCCATCACGATCGCT 59.332 57.895 16.60 0.0 0.0 4.93 R
2504 2558 0.788391 CGTACGACAAAACTCCTGCC 59.212 55.000 10.44 0.0 0.0 4.85 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 4.009675 GTCAATGCACACCTCCAAGAATA 58.990 43.478 0.00 0.00 0.00 1.75
33 34 0.254747 CTCCAAGAATAACGCCCCCA 59.745 55.000 0.00 0.00 0.00 4.96
36 37 1.340600 CCAAGAATAACGCCCCCAAGA 60.341 52.381 0.00 0.00 0.00 3.02
59 60 1.326548 GAAACGACACAAGAGCGTTGT 59.673 47.619 0.00 1.96 46.15 3.32
60 61 1.365699 AACGACACAAGAGCGTTGTT 58.634 45.000 4.88 0.00 45.28 2.83
66 67 2.682856 ACACAAGAGCGTTGTTGTCATT 59.317 40.909 11.85 0.00 38.61 2.57
68 69 2.942376 ACAAGAGCGTTGTTGTCATTCA 59.058 40.909 9.01 0.00 36.13 2.57
83 84 6.349973 TGTCATTCAATCGACTGATTTAGC 57.650 37.500 0.00 0.00 42.14 3.09
84 85 5.294306 TGTCATTCAATCGACTGATTTAGCC 59.706 40.000 0.00 0.00 42.14 3.93
85 86 4.816385 TCATTCAATCGACTGATTTAGCCC 59.184 41.667 0.00 0.00 42.14 5.19
86 87 3.194005 TCAATCGACTGATTTAGCCCC 57.806 47.619 0.00 0.00 42.14 5.80
87 88 2.158813 TCAATCGACTGATTTAGCCCCC 60.159 50.000 0.00 0.00 42.14 5.40
119 120 2.427245 CCCAGGTAGCGGACAGAGG 61.427 68.421 4.67 0.00 0.00 3.69
123 124 0.917533 AGGTAGCGGACAGAGGTCTA 59.082 55.000 0.00 0.00 43.77 2.59
127 128 0.621609 AGCGGACAGAGGTCTAGAGT 59.378 55.000 0.00 0.00 43.77 3.24
134 135 4.569015 GGACAGAGGTCTAGAGTTTCTCCT 60.569 50.000 0.00 0.00 43.77 3.69
136 137 3.625764 CAGAGGTCTAGAGTTTCTCCTCG 59.374 52.174 15.49 9.35 44.02 4.63
165 166 1.301401 CAAGAAGGGGACGACGCAA 60.301 57.895 4.20 0.00 33.80 4.85
171 172 1.218316 GGGGACGACGCAAGAGAAT 59.782 57.895 4.20 0.00 43.62 2.40
176 177 2.401195 GACGCAAGAGAATGCCGC 59.599 61.111 0.00 0.00 43.47 6.53
232 233 1.489481 TTCACCTGGATCTGCTCGAT 58.511 50.000 0.00 0.00 34.25 3.59
233 234 0.749049 TCACCTGGATCTGCTCGATG 59.251 55.000 0.00 0.00 30.84 3.84
269 270 1.479730 TCTTGTGCATCTGATCGCTCT 59.520 47.619 11.45 0.00 0.00 4.09
311 312 1.406065 CCGCTCACCCAGATCCAGAT 61.406 60.000 0.00 0.00 0.00 2.90
313 314 1.271934 CGCTCACCCAGATCCAGATAG 59.728 57.143 0.00 0.00 0.00 2.08
317 318 1.983691 CACCCAGATCCAGATAGGCAT 59.016 52.381 0.00 0.00 37.29 4.40
321 322 2.027377 CCAGATCCAGATAGGCATGTCC 60.027 54.545 0.00 0.00 37.29 4.02
337 338 4.485834 CCCGCCGTCGTCGAATCA 62.486 66.667 2.98 0.00 39.71 2.57
338 339 3.245315 CCGCCGTCGTCGAATCAC 61.245 66.667 2.98 0.00 39.71 3.06
341 342 2.578713 CCGTCGTCGAATCACCGG 60.579 66.667 0.00 0.00 39.71 5.28
342 343 3.245315 CGTCGTCGAATCACCGGC 61.245 66.667 0.00 0.00 39.71 6.13
343 344 2.126228 GTCGTCGAATCACCGGCA 60.126 61.111 0.00 0.00 33.10 5.69
344 345 1.735198 GTCGTCGAATCACCGGCAA 60.735 57.895 0.00 0.00 33.10 4.52
345 346 1.735198 TCGTCGAATCACCGGCAAC 60.735 57.895 0.00 0.00 33.10 4.17
346 347 2.736682 CGTCGAATCACCGGCAACC 61.737 63.158 0.00 0.00 33.10 3.77
348 349 4.160635 CGAATCACCGGCAACCGC 62.161 66.667 0.00 0.00 46.86 5.68
349 350 3.053291 GAATCACCGGCAACCGCA 61.053 61.111 0.00 0.00 46.86 5.69
425 426 1.885359 GCCCCAGCCACATCATATCTG 60.885 57.143 0.00 0.00 0.00 2.90
464 465 2.504920 CCATCGGCACAGGAGAGTA 58.495 57.895 0.00 0.00 0.00 2.59
469 470 2.184579 GCACAGGAGAGTACCGGC 59.815 66.667 0.00 0.00 34.73 6.13
485 486 1.997874 GGCCAGTCCATCCCTCTGT 60.998 63.158 0.00 0.00 34.01 3.41
486 487 1.222936 GCCAGTCCATCCCTCTGTG 59.777 63.158 0.00 0.00 0.00 3.66
494 496 0.608130 CATCCCTCTGTGACCGAACA 59.392 55.000 0.00 0.00 0.00 3.18
509 511 3.184736 AACAGGCGTTCAAACCAGT 57.815 47.368 0.00 0.00 0.00 4.00
510 512 1.021968 AACAGGCGTTCAAACCAGTC 58.978 50.000 0.00 0.00 0.00 3.51
511 513 0.818040 ACAGGCGTTCAAACCAGTCC 60.818 55.000 0.00 0.00 0.00 3.85
512 514 0.817634 CAGGCGTTCAAACCAGTCCA 60.818 55.000 0.00 0.00 0.00 4.02
513 515 0.535102 AGGCGTTCAAACCAGTCCAG 60.535 55.000 0.00 0.00 0.00 3.86
514 516 1.515521 GGCGTTCAAACCAGTCCAGG 61.516 60.000 0.00 0.00 0.00 4.45
515 517 1.949257 CGTTCAAACCAGTCCAGGC 59.051 57.895 0.00 0.00 0.00 4.85
516 518 1.841663 CGTTCAAACCAGTCCAGGCG 61.842 60.000 0.00 0.00 0.00 5.52
517 519 1.896660 TTCAAACCAGTCCAGGCGC 60.897 57.895 0.00 0.00 0.00 6.53
518 520 3.365265 CAAACCAGTCCAGGCGCC 61.365 66.667 21.89 21.89 0.00 6.53
519 521 3.884774 AAACCAGTCCAGGCGCCA 61.885 61.111 31.54 4.59 0.00 5.69
520 522 3.210012 AAACCAGTCCAGGCGCCAT 62.210 57.895 31.54 11.31 0.00 4.40
521 523 3.628646 AACCAGTCCAGGCGCCATC 62.629 63.158 31.54 15.27 0.00 3.51
589 591 3.749064 TGGCTCGAGCGTGGAGAC 61.749 66.667 29.81 15.23 43.26 3.36
601 603 4.821589 GGAGACGAGCAAGCCCCG 62.822 72.222 0.00 3.48 0.00 5.73
732 757 4.701651 CCCAGCTGTTCAATACATCTTTGA 59.298 41.667 13.81 0.00 35.85 2.69
826 851 2.104267 CATGTCAGCCATGGTCAGC 58.896 57.895 14.67 0.00 46.03 4.26
827 852 0.393944 CATGTCAGCCATGGTCAGCT 60.394 55.000 14.67 0.23 46.03 4.24
831 856 2.673523 AGCCATGGTCAGCTGTCC 59.326 61.111 21.49 21.49 38.11 4.02
832 857 1.922369 AGCCATGGTCAGCTGTCCT 60.922 57.895 26.86 12.51 38.11 3.85
833 858 0.618680 AGCCATGGTCAGCTGTCCTA 60.619 55.000 26.86 15.66 38.11 2.94
834 859 0.471617 GCCATGGTCAGCTGTCCTAT 59.528 55.000 26.86 16.98 0.00 2.57
835 860 1.813092 GCCATGGTCAGCTGTCCTATG 60.813 57.143 26.86 24.48 0.00 2.23
836 861 1.487976 CCATGGTCAGCTGTCCTATGT 59.512 52.381 26.86 10.68 0.00 2.29
845 878 1.202698 GCTGTCCTATGTTAGCTGGGG 60.203 57.143 0.00 0.00 33.53 4.96
927 960 0.321671 CACTCACCACCCACCACTAG 59.678 60.000 0.00 0.00 0.00 2.57
949 989 3.417275 CTCCGGCTAGCGGACACTG 62.417 68.421 22.71 10.16 0.00 3.66
1003 1043 1.560923 CGACCGAAGTAGCAAGATGG 58.439 55.000 0.00 0.00 0.00 3.51
1245 1285 4.918360 TGCTGGGTCACCTGGGGT 62.918 66.667 0.00 0.00 37.76 4.95
1791 1839 3.124921 CCTTACGCCGCCAACCTG 61.125 66.667 0.00 0.00 0.00 4.00
1893 1941 0.984230 TCAAGAAGCCCTCCGTCATT 59.016 50.000 0.00 0.00 0.00 2.57
1998 2046 1.153086 GATCCTGTCCGGCAGCATT 60.153 57.895 17.35 6.72 43.71 3.56
2502 2556 3.494336 CGCTTCGCTTCCTGGCTG 61.494 66.667 0.00 0.00 0.00 4.85
2503 2557 2.359230 GCTTCGCTTCCTGGCTGT 60.359 61.111 0.00 0.00 0.00 4.40
2504 2558 2.684843 GCTTCGCTTCCTGGCTGTG 61.685 63.158 0.00 0.00 0.00 3.66
2505 2559 2.032528 TTCGCTTCCTGGCTGTGG 59.967 61.111 0.00 0.00 0.00 4.17
2506 2560 4.704833 TCGCTTCCTGGCTGTGGC 62.705 66.667 0.00 0.00 37.82 5.01
2532 2592 5.002747 GGAGTTTTGTCGTACGTTTTTGTTG 59.997 40.000 16.05 0.00 0.00 3.33
2593 2786 3.796178 TCATTTTGCTGTTTTTGAGACGC 59.204 39.130 0.00 0.00 0.00 5.19
2628 2873 5.669447 AGAATCTCCCTACCATTTGTCATCT 59.331 40.000 0.00 0.00 0.00 2.90
2643 2888 6.594284 TTGTCATCTGCATTAGAATCTTCG 57.406 37.500 0.00 0.00 39.30 3.79
2657 2902 9.838339 ATTAGAATCTTCGAAGTTTGTATCCAT 57.162 29.630 22.75 12.36 0.00 3.41
2743 2988 4.823442 TCACCATATTGTCAGATTGCCATC 59.177 41.667 0.00 0.00 0.00 3.51
2767 3012 0.847373 TGTGCTTTGTTCCCACCCTA 59.153 50.000 0.00 0.00 0.00 3.53
2805 3075 0.178975 ACTCGCCATTTGGGGTTTGA 60.179 50.000 12.76 0.00 46.93 2.69
2806 3076 0.527565 CTCGCCATTTGGGGTTTGAG 59.472 55.000 12.76 0.46 46.93 3.02
2817 3087 6.491714 TTTGGGGTTTGAGATGAAAATTCA 57.508 33.333 0.00 0.00 42.14 2.57
2826 3096 4.082125 GAGATGAAAATTCAGGTGTGGGT 58.918 43.478 1.98 0.00 41.08 4.51
2856 3126 5.409826 CGATTTTCAAGGAACTGTAGCTTCT 59.590 40.000 0.00 0.00 40.86 2.85
3000 3283 6.427242 TGACAGTACAATACAATAAACGCCAA 59.573 34.615 0.00 0.00 0.00 4.52
3020 3303 8.736244 ACGCCAAAAATAACAATAGTTACATCT 58.264 29.630 0.00 0.00 42.60 2.90
3039 3322 7.589958 ACATCTAGATTTGTAGACCACCTAG 57.410 40.000 1.33 0.00 31.75 3.02
3041 3324 5.516044 TCTAGATTTGTAGACCACCTAGCA 58.484 41.667 0.00 0.00 0.00 3.49
3052 3335 2.029290 ACCACCTAGCAACGACTACAAG 60.029 50.000 0.00 0.00 0.00 3.16
3054 3337 1.893801 ACCTAGCAACGACTACAAGCT 59.106 47.619 0.00 0.00 39.22 3.74
3060 3343 2.800544 GCAACGACTACAAGCTCTCAAA 59.199 45.455 0.00 0.00 0.00 2.69
3074 3357 3.470562 CTCTCAAACGAGCTAAAAACGC 58.529 45.455 0.00 0.00 0.00 4.84
3075 3358 2.867368 TCTCAAACGAGCTAAAAACGCA 59.133 40.909 0.00 0.00 0.00 5.24
3109 3392 4.382541 TCCCTCGCCAGAGCCTGA 62.383 66.667 4.00 0.00 43.05 3.86
3118 3401 1.815408 GCCAGAGCCTGACAAAACTCA 60.815 52.381 4.00 0.00 32.44 3.41
3124 3407 5.239306 CAGAGCCTGACAAAACTCATTGTAA 59.761 40.000 0.00 0.00 43.31 2.41
3150 3433 1.258445 ATCCAGAAGTCGCCGGAGTT 61.258 55.000 5.05 0.00 38.53 3.01
3151 3434 1.738099 CCAGAAGTCGCCGGAGTTG 60.738 63.158 5.05 0.00 35.96 3.16
3152 3435 1.289066 CAGAAGTCGCCGGAGTTGA 59.711 57.895 5.05 0.00 35.96 3.18
3154 3437 2.048127 AAGTCGCCGGAGTTGAGC 60.048 61.111 5.05 0.00 34.53 4.26
3160 3443 0.460284 CGCCGGAGTTGAGCAGTATT 60.460 55.000 5.05 0.00 0.00 1.89
3189 3472 8.624776 AGCTATTTTTCTACCATCACAATAAGC 58.375 33.333 0.00 0.00 0.00 3.09
3195 3478 5.125356 TCTACCATCACAATAAGCCACATG 58.875 41.667 0.00 0.00 0.00 3.21
3199 3482 4.319984 CCATCACAATAAGCCACATGATCG 60.320 45.833 0.00 0.00 0.00 3.69
3225 3508 8.947055 AAATTGTTATGATAGTTGGATTTGCC 57.053 30.769 0.00 0.00 37.10 4.52
3226 3509 7.902920 ATTGTTATGATAGTTGGATTTGCCT 57.097 32.000 0.00 0.00 37.63 4.75
3227 3510 6.698008 TGTTATGATAGTTGGATTTGCCTG 57.302 37.500 0.00 0.00 37.63 4.85
3228 3511 6.422333 TGTTATGATAGTTGGATTTGCCTGA 58.578 36.000 0.00 0.00 37.63 3.86
3229 3512 7.062322 TGTTATGATAGTTGGATTTGCCTGAT 58.938 34.615 0.00 0.00 37.63 2.90
3230 3513 7.229306 TGTTATGATAGTTGGATTTGCCTGATC 59.771 37.037 0.00 0.00 37.63 2.92
3231 3514 4.464008 TGATAGTTGGATTTGCCTGATCC 58.536 43.478 3.77 3.77 42.78 3.36
3242 3525 2.989639 CTGATCCAGGGCCGTTGA 59.010 61.111 1.20 1.20 0.00 3.18
3243 3526 1.153289 CTGATCCAGGGCCGTTGAG 60.153 63.158 5.40 0.00 0.00 3.02
3244 3527 2.190578 GATCCAGGGCCGTTGAGG 59.809 66.667 5.40 0.00 44.97 3.86
3245 3528 3.406595 GATCCAGGGCCGTTGAGGG 62.407 68.421 5.40 0.00 41.48 4.30
3255 3538 4.329545 GTTGAGGGGCCTGTGCGA 62.330 66.667 0.84 0.00 38.85 5.10
3256 3539 4.020617 TTGAGGGGCCTGTGCGAG 62.021 66.667 0.84 0.00 38.85 5.03
3284 3567 2.607442 GCACAGGGCCCCCAAAAT 60.607 61.111 21.43 0.00 38.92 1.82
3285 3568 2.659063 GCACAGGGCCCCCAAAATC 61.659 63.158 21.43 0.00 38.92 2.17
3286 3569 1.989508 CACAGGGCCCCCAAAATCC 60.990 63.158 21.43 0.00 38.92 3.01
3287 3570 2.176812 ACAGGGCCCCCAAAATCCT 61.177 57.895 21.43 0.00 38.92 3.24
3288 3571 1.686800 CAGGGCCCCCAAAATCCTG 60.687 63.158 21.43 2.07 38.96 3.86
3289 3572 2.365502 GGGCCCCCAAAATCCTGG 60.366 66.667 12.23 0.00 36.10 4.45
3295 3578 2.365502 CCAAAATCCTGGGGCCCC 60.366 66.667 36.14 36.14 32.32 5.80
3296 3579 2.365502 CAAAATCCTGGGGCCCCC 60.366 66.667 38.81 20.71 45.71 5.40
3305 3588 2.944954 GGGGCCCCCAACTAGGTT 60.945 66.667 33.01 0.00 44.65 3.50
3306 3589 2.554291 GGGGCCCCCAACTAGGTTT 61.554 63.158 33.01 0.00 44.65 3.27
3307 3590 1.000019 GGGCCCCCAACTAGGTTTC 60.000 63.158 12.23 0.00 35.81 2.78
3308 3591 1.771646 GGCCCCCAACTAGGTTTCA 59.228 57.895 0.00 0.00 34.66 2.69
3309 3592 0.335019 GGCCCCCAACTAGGTTTCAT 59.665 55.000 0.00 0.00 34.66 2.57
3310 3593 1.567175 GGCCCCCAACTAGGTTTCATA 59.433 52.381 0.00 0.00 34.66 2.15
3311 3594 2.177016 GGCCCCCAACTAGGTTTCATAT 59.823 50.000 0.00 0.00 34.66 1.78
3312 3595 3.396611 GGCCCCCAACTAGGTTTCATATA 59.603 47.826 0.00 0.00 34.66 0.86
3313 3596 4.395625 GCCCCCAACTAGGTTTCATATAC 58.604 47.826 0.00 0.00 34.66 1.47
3314 3597 4.638304 CCCCCAACTAGGTTTCATATACG 58.362 47.826 0.00 0.00 34.66 3.06
3315 3598 4.102054 CCCCCAACTAGGTTTCATATACGT 59.898 45.833 0.00 0.00 34.66 3.57
3316 3599 5.305128 CCCCCAACTAGGTTTCATATACGTA 59.695 44.000 0.00 0.00 34.66 3.57
3317 3600 6.013984 CCCCCAACTAGGTTTCATATACGTAT 60.014 42.308 13.54 13.54 34.66 3.06
3318 3601 7.178983 CCCCCAACTAGGTTTCATATACGTATA 59.821 40.741 17.24 17.24 34.66 1.47
3319 3602 8.755977 CCCCAACTAGGTTTCATATACGTATAT 58.244 37.037 20.08 20.08 34.66 0.86
3320 3603 9.582431 CCCAACTAGGTTTCATATACGTATATG 57.418 37.037 34.83 34.83 40.31 1.78
3360 3643 5.890334 TCAGTTTTAAGCTGAAAACACTGG 58.110 37.500 31.93 21.01 46.98 4.00
3361 3644 5.417580 TCAGTTTTAAGCTGAAAACACTGGT 59.582 36.000 31.93 14.90 46.98 4.00
3362 3645 5.743872 CAGTTTTAAGCTGAAAACACTGGTC 59.256 40.000 31.93 11.23 46.98 4.02
3363 3646 5.652452 AGTTTTAAGCTGAAAACACTGGTCT 59.348 36.000 31.93 13.69 46.98 3.85
3364 3647 5.499139 TTTAAGCTGAAAACACTGGTCTG 57.501 39.130 0.00 0.00 0.00 3.51
3365 3648 1.972872 AGCTGAAAACACTGGTCTGG 58.027 50.000 0.00 0.00 0.00 3.86
3366 3649 0.954452 GCTGAAAACACTGGTCTGGG 59.046 55.000 0.00 0.00 0.00 4.45
3367 3650 0.954452 CTGAAAACACTGGTCTGGGC 59.046 55.000 0.00 0.00 0.00 5.36
3368 3651 0.467290 TGAAAACACTGGTCTGGGCC 60.467 55.000 0.00 0.00 0.00 5.80
3369 3652 0.178990 GAAAACACTGGTCTGGGCCT 60.179 55.000 4.53 0.00 0.00 5.19
3370 3653 0.261696 AAAACACTGGTCTGGGCCTT 59.738 50.000 4.53 0.00 0.00 4.35
3371 3654 0.178990 AAACACTGGTCTGGGCCTTC 60.179 55.000 4.53 0.00 0.00 3.46
3372 3655 1.062488 AACACTGGTCTGGGCCTTCT 61.062 55.000 4.53 0.00 0.00 2.85
3373 3656 1.062488 ACACTGGTCTGGGCCTTCTT 61.062 55.000 4.53 0.00 0.00 2.52
3374 3657 0.607489 CACTGGTCTGGGCCTTCTTG 60.607 60.000 4.53 0.00 0.00 3.02
3375 3658 1.001641 CTGGTCTGGGCCTTCTTGG 60.002 63.158 4.53 0.00 39.35 3.61
3376 3659 2.356667 GGTCTGGGCCTTCTTGGG 59.643 66.667 4.53 0.00 36.00 4.12
3383 3666 2.124942 GCCTTCTTGGGCCTCGAG 60.125 66.667 5.13 5.13 45.92 4.04
3384 3667 2.124942 CCTTCTTGGGCCTCGAGC 60.125 66.667 6.99 2.33 42.60 5.03
3385 3668 2.665000 CTTCTTGGGCCTCGAGCA 59.335 61.111 6.99 0.00 46.50 4.26
3386 3669 1.003355 CTTCTTGGGCCTCGAGCAA 60.003 57.895 6.99 5.34 46.50 3.91
3387 3670 0.393537 CTTCTTGGGCCTCGAGCAAT 60.394 55.000 6.99 0.00 46.50 3.56
3388 3671 0.908910 TTCTTGGGCCTCGAGCAATA 59.091 50.000 6.99 0.00 46.50 1.90
3389 3672 0.178068 TCTTGGGCCTCGAGCAATAC 59.822 55.000 6.99 0.00 46.50 1.89
3390 3673 1.153449 TTGGGCCTCGAGCAATACG 60.153 57.895 6.99 0.00 46.50 3.06
3391 3674 2.967615 GGGCCTCGAGCAATACGC 60.968 66.667 6.99 3.51 46.50 4.42
3402 3685 2.497107 GCAATACGCTTTGCCATCAT 57.503 45.000 10.87 0.00 44.94 2.45
3403 3686 2.388121 GCAATACGCTTTGCCATCATC 58.612 47.619 10.87 0.00 44.94 2.92
3404 3687 2.033801 GCAATACGCTTTGCCATCATCT 59.966 45.455 10.87 0.00 44.94 2.90
3405 3688 3.851105 GCAATACGCTTTGCCATCATCTC 60.851 47.826 10.87 0.00 44.94 2.75
3406 3689 1.570813 TACGCTTTGCCATCATCTCG 58.429 50.000 0.00 0.00 0.00 4.04
3407 3690 0.391661 ACGCTTTGCCATCATCTCGT 60.392 50.000 0.00 0.00 0.00 4.18
3408 3691 0.027194 CGCTTTGCCATCATCTCGTG 59.973 55.000 0.00 0.00 0.00 4.35
3409 3692 0.379669 GCTTTGCCATCATCTCGTGG 59.620 55.000 0.00 0.00 38.55 4.94
3410 3693 2.013563 GCTTTGCCATCATCTCGTGGA 61.014 52.381 0.00 0.00 37.72 4.02
3411 3694 2.569059 CTTTGCCATCATCTCGTGGAT 58.431 47.619 0.00 0.00 37.72 3.41
3419 3702 3.615597 ATCTCGTGGATGAGGTGGA 57.384 52.632 0.00 0.00 36.61 4.02
3420 3703 2.094100 ATCTCGTGGATGAGGTGGAT 57.906 50.000 0.00 0.00 36.61 3.41
3421 3704 1.403814 TCTCGTGGATGAGGTGGATC 58.596 55.000 0.00 0.00 36.61 3.36
3422 3705 0.031314 CTCGTGGATGAGGTGGATCG 59.969 60.000 0.00 0.00 32.18 3.69
3423 3706 0.395173 TCGTGGATGAGGTGGATCGA 60.395 55.000 0.00 0.00 0.00 3.59
3424 3707 0.676184 CGTGGATGAGGTGGATCGAT 59.324 55.000 0.00 0.00 0.00 3.59
3425 3708 1.336332 CGTGGATGAGGTGGATCGATC 60.336 57.143 17.36 17.36 0.00 3.69
3441 3724 3.939066 TCGATCCTAGCGATCATAGACA 58.061 45.455 16.59 0.00 46.85 3.41
3442 3725 4.324267 TCGATCCTAGCGATCATAGACAA 58.676 43.478 16.59 0.00 46.85 3.18
3443 3726 4.760204 TCGATCCTAGCGATCATAGACAAA 59.240 41.667 16.59 0.00 46.85 2.83
3444 3727 5.240844 TCGATCCTAGCGATCATAGACAAAA 59.759 40.000 16.59 0.00 46.85 2.44
3445 3728 6.071896 TCGATCCTAGCGATCATAGACAAAAT 60.072 38.462 16.59 0.00 46.85 1.82
3446 3729 6.034363 CGATCCTAGCGATCATAGACAAAATG 59.966 42.308 16.59 0.00 46.85 2.32
3447 3730 6.405278 TCCTAGCGATCATAGACAAAATGA 57.595 37.500 3.98 0.00 37.73 2.57
3448 3731 6.216569 TCCTAGCGATCATAGACAAAATGAC 58.783 40.000 3.98 0.00 36.24 3.06
3449 3732 5.985530 CCTAGCGATCATAGACAAAATGACA 59.014 40.000 3.98 0.00 36.24 3.58
3450 3733 5.980698 AGCGATCATAGACAAAATGACAG 57.019 39.130 0.00 0.00 36.24 3.51
3451 3734 4.272018 AGCGATCATAGACAAAATGACAGC 59.728 41.667 0.00 0.00 38.41 4.40
3452 3735 4.553547 GCGATCATAGACAAAATGACAGCC 60.554 45.833 0.00 0.00 36.24 4.85
3453 3736 4.024556 CGATCATAGACAAAATGACAGCCC 60.025 45.833 0.00 0.00 36.24 5.19
3454 3737 4.299586 TCATAGACAAAATGACAGCCCA 57.700 40.909 0.00 0.00 0.00 5.36
3455 3738 4.264253 TCATAGACAAAATGACAGCCCAG 58.736 43.478 0.00 0.00 0.00 4.45
3456 3739 1.251251 AGACAAAATGACAGCCCAGC 58.749 50.000 0.00 0.00 0.00 4.85
3457 3740 0.961019 GACAAAATGACAGCCCAGCA 59.039 50.000 0.00 0.00 0.00 4.41
3458 3741 0.675633 ACAAAATGACAGCCCAGCAC 59.324 50.000 0.00 0.00 0.00 4.40
3459 3742 0.675083 CAAAATGACAGCCCAGCACA 59.325 50.000 0.00 0.00 0.00 4.57
3460 3743 0.963962 AAAATGACAGCCCAGCACAG 59.036 50.000 0.00 0.00 0.00 3.66
3461 3744 0.178981 AAATGACAGCCCAGCACAGT 60.179 50.000 0.00 0.00 0.00 3.55
3462 3745 0.692476 AATGACAGCCCAGCACAGTA 59.308 50.000 0.00 0.00 0.00 2.74
3463 3746 0.036010 ATGACAGCCCAGCACAGTAC 60.036 55.000 0.00 0.00 0.00 2.73
3464 3747 1.738099 GACAGCCCAGCACAGTACG 60.738 63.158 0.00 0.00 0.00 3.67
3465 3748 2.343758 CAGCCCAGCACAGTACGT 59.656 61.111 0.00 0.00 0.00 3.57
3466 3749 1.301716 CAGCCCAGCACAGTACGTT 60.302 57.895 0.00 0.00 0.00 3.99
3467 3750 1.004918 AGCCCAGCACAGTACGTTC 60.005 57.895 0.00 0.00 0.00 3.95
3468 3751 2.033194 GCCCAGCACAGTACGTTCC 61.033 63.158 0.00 0.00 0.00 3.62
3469 3752 1.736645 CCCAGCACAGTACGTTCCG 60.737 63.158 0.00 0.00 0.00 4.30
3470 3753 1.006571 CCAGCACAGTACGTTCCGT 60.007 57.895 0.00 0.00 44.35 4.69
3471 3754 0.241749 CCAGCACAGTACGTTCCGTA 59.758 55.000 0.00 0.00 41.54 4.02
3472 3755 1.336148 CCAGCACAGTACGTTCCGTAA 60.336 52.381 0.00 0.00 43.95 3.18
3473 3756 1.717645 CAGCACAGTACGTTCCGTAAC 59.282 52.381 0.00 0.00 43.95 2.50
3474 3757 1.610522 AGCACAGTACGTTCCGTAACT 59.389 47.619 0.00 0.00 43.95 2.24
3475 3758 2.035066 AGCACAGTACGTTCCGTAACTT 59.965 45.455 0.00 0.00 43.95 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.655090 TTCTTGGAGGTGTGCATTGA 57.345 45.000 0.00 0.00 0.00 2.57
9 10 1.737793 GGCGTTATTCTTGGAGGTGTG 59.262 52.381 0.00 0.00 0.00 3.82
10 11 1.339727 GGGCGTTATTCTTGGAGGTGT 60.340 52.381 0.00 0.00 0.00 4.16
33 34 2.807108 GCTCTTGTGTCGTTTCCCTCTT 60.807 50.000 0.00 0.00 0.00 2.85
36 37 0.600255 CGCTCTTGTGTCGTTTCCCT 60.600 55.000 0.00 0.00 0.00 4.20
40 41 1.365699 ACAACGCTCTTGTGTCGTTT 58.634 45.000 0.00 0.00 43.45 3.60
43 44 0.650512 ACAACAACGCTCTTGTGTCG 59.349 50.000 0.00 0.00 35.64 4.35
44 45 1.663643 TGACAACAACGCTCTTGTGTC 59.336 47.619 13.61 13.61 35.64 3.67
66 67 2.158813 GGGGGCTAAATCAGTCGATTGA 60.159 50.000 13.38 13.38 41.12 2.57
68 69 2.640316 GGGGGCTAAATCAGTCGATT 57.360 50.000 0.00 0.00 43.94 3.34
101 102 2.427245 CCTCTGTCCGCTACCTGGG 61.427 68.421 0.00 0.00 0.00 4.45
102 103 1.668101 GACCTCTGTCCGCTACCTGG 61.668 65.000 0.00 0.00 35.34 4.45
103 104 0.681564 AGACCTCTGTCCGCTACCTG 60.682 60.000 0.00 0.00 42.81 4.00
119 120 1.064357 CGCCGAGGAGAAACTCTAGAC 59.936 57.143 0.00 0.00 35.33 2.59
123 124 0.457851 CATCGCCGAGGAGAAACTCT 59.542 55.000 0.00 0.00 35.33 3.24
127 128 2.186903 GGCATCGCCGAGGAGAAA 59.813 61.111 1.60 0.00 39.62 2.52
165 166 2.590007 GCGATGGCGGCATTCTCT 60.590 61.111 26.52 3.27 38.16 3.10
232 233 1.210538 AGATGCTGGATTGAGGCTCA 58.789 50.000 14.43 14.43 0.00 4.26
233 234 1.948145 CAAGATGCTGGATTGAGGCTC 59.052 52.381 7.79 7.79 0.00 4.70
256 257 4.241715 GCGGAGAGCGATCAGATG 57.758 61.111 2.38 0.00 35.41 2.90
291 292 2.284625 TGGATCTGGGTGAGCGGT 60.285 61.111 0.00 0.00 30.59 5.68
298 299 1.983691 CATGCCTATCTGGATCTGGGT 59.016 52.381 0.00 0.00 38.35 4.51
321 322 3.245315 GTGATTCGACGACGGCGG 61.245 66.667 24.91 4.56 43.17 6.13
327 328 1.735198 GTTGCCGGTGATTCGACGA 60.735 57.895 1.90 0.00 0.00 4.20
408 409 1.701292 TCCCAGATATGATGTGGCTGG 59.299 52.381 0.00 0.00 42.07 4.85
410 411 1.345741 CGTCCCAGATATGATGTGGCT 59.654 52.381 0.00 0.00 42.07 4.75
415 416 1.066573 GGCCTCGTCCCAGATATGATG 60.067 57.143 0.00 0.00 0.00 3.07
417 418 0.832135 GGGCCTCGTCCCAGATATGA 60.832 60.000 0.84 0.00 45.82 2.15
419 420 4.217112 GGGCCTCGTCCCAGATAT 57.783 61.111 0.84 0.00 45.82 1.63
448 449 2.506065 GGTACTCTCCTGTGCCGAT 58.494 57.895 0.00 0.00 33.37 4.18
449 450 4.013702 GGTACTCTCCTGTGCCGA 57.986 61.111 0.00 0.00 33.37 5.54
455 456 1.668101 GACTGGCCGGTACTCTCCTG 61.668 65.000 19.73 0.69 0.00 3.86
457 458 2.424733 GGACTGGCCGGTACTCTCC 61.425 68.421 20.73 11.75 0.00 3.71
458 459 1.043673 ATGGACTGGCCGGTACTCTC 61.044 60.000 27.60 10.15 40.66 3.20
464 465 4.741239 AGGGATGGACTGGCCGGT 62.741 66.667 19.82 19.82 40.66 5.28
469 470 0.539051 GTCACAGAGGGATGGACTGG 59.461 60.000 0.00 0.00 36.17 4.00
494 496 0.535102 CTGGACTGGTTTGAACGCCT 60.535 55.000 0.00 0.00 0.00 5.52
530 532 3.799755 GATGGCGCGACACCAACC 61.800 66.667 21.63 2.41 41.49 3.77
531 533 3.047280 TGATGGCGCGACACCAAC 61.047 61.111 21.63 11.00 41.49 3.77
532 534 3.047280 GTGATGGCGCGACACCAA 61.047 61.111 21.63 1.73 41.49 3.67
536 538 4.321966 TTGGGTGATGGCGCGACA 62.322 61.111 21.39 21.39 0.00 4.35
537 539 3.799755 GTTGGGTGATGGCGCGAC 61.800 66.667 12.10 8.22 0.00 5.19
571 573 3.749064 TCTCCACGCTCGAGCCAC 61.749 66.667 30.66 5.08 37.91 5.01
577 579 3.610791 TTGCTCGTCTCCACGCTCG 62.611 63.158 0.00 0.00 46.28 5.03
584 586 4.821589 CGGGGCTTGCTCGTCTCC 62.822 72.222 0.00 0.00 0.00 3.71
647 649 3.881019 TTCACGCGTCTCCTCCCCT 62.881 63.158 9.86 0.00 0.00 4.79
649 651 1.668101 ATCTTCACGCGTCTCCTCCC 61.668 60.000 9.86 0.00 0.00 4.30
651 653 2.452105 GTTATCTTCACGCGTCTCCTC 58.548 52.381 9.86 0.00 0.00 3.71
652 654 1.134560 GGTTATCTTCACGCGTCTCCT 59.865 52.381 9.86 0.00 0.00 3.69
653 655 1.134560 AGGTTATCTTCACGCGTCTCC 59.865 52.381 9.86 3.14 0.00 3.71
655 657 3.015327 ACTAGGTTATCTTCACGCGTCT 58.985 45.455 9.86 2.06 0.00 4.18
657 659 2.098770 GGACTAGGTTATCTTCACGCGT 59.901 50.000 5.58 5.58 0.00 6.01
660 662 2.034305 CCGGGACTAGGTTATCTTCACG 59.966 54.545 0.00 0.00 0.00 4.35
661 663 2.223994 GCCGGGACTAGGTTATCTTCAC 60.224 54.545 2.18 0.00 0.00 3.18
662 664 2.037144 GCCGGGACTAGGTTATCTTCA 58.963 52.381 2.18 0.00 0.00 3.02
824 849 1.765314 CCCAGCTAACATAGGACAGCT 59.235 52.381 2.43 2.43 45.01 4.24
825 850 1.202698 CCCCAGCTAACATAGGACAGC 60.203 57.143 0.00 0.00 0.00 4.40
826 851 1.202698 GCCCCAGCTAACATAGGACAG 60.203 57.143 0.00 0.00 35.50 3.51
827 852 0.837272 GCCCCAGCTAACATAGGACA 59.163 55.000 0.00 0.00 35.50 4.02
828 853 0.108774 GGCCCCAGCTAACATAGGAC 59.891 60.000 0.00 0.00 39.73 3.85
829 854 1.407656 CGGCCCCAGCTAACATAGGA 61.408 60.000 0.00 0.00 39.73 2.94
830 855 1.071471 CGGCCCCAGCTAACATAGG 59.929 63.158 0.00 0.00 39.73 2.57
831 856 0.468226 TTCGGCCCCAGCTAACATAG 59.532 55.000 0.00 0.00 39.73 2.23
832 857 0.913205 TTTCGGCCCCAGCTAACATA 59.087 50.000 0.00 0.00 39.73 2.29
833 858 0.039035 TTTTCGGCCCCAGCTAACAT 59.961 50.000 0.00 0.00 39.73 2.71
834 859 0.891904 GTTTTCGGCCCCAGCTAACA 60.892 55.000 0.00 0.00 39.73 2.41
835 860 1.880894 GTTTTCGGCCCCAGCTAAC 59.119 57.895 0.00 0.00 39.73 2.34
836 861 1.673009 CGTTTTCGGCCCCAGCTAA 60.673 57.895 0.00 0.00 39.73 3.09
986 1026 0.460284 CGCCATCTTGCTACTTCGGT 60.460 55.000 0.00 0.00 0.00 4.69
987 1027 0.179111 TCGCCATCTTGCTACTTCGG 60.179 55.000 0.00 0.00 0.00 4.30
1791 1839 3.148279 ACGGCGATGGAGGAGTCC 61.148 66.667 16.62 0.00 44.24 3.85
1965 2013 1.668294 GATCCCCATCACGATCGCT 59.332 57.895 16.60 0.00 0.00 4.93
2491 2545 3.060615 CTGCCACAGCCAGGAAGC 61.061 66.667 0.00 0.00 38.69 3.86
2502 2556 1.529865 GTACGACAAAACTCCTGCCAC 59.470 52.381 0.00 0.00 0.00 5.01
2503 2557 1.870580 CGTACGACAAAACTCCTGCCA 60.871 52.381 10.44 0.00 0.00 4.92
2504 2558 0.788391 CGTACGACAAAACTCCTGCC 59.212 55.000 10.44 0.00 0.00 4.85
2505 2559 1.494824 ACGTACGACAAAACTCCTGC 58.505 50.000 24.41 0.00 0.00 4.85
2506 2560 4.525411 AAAACGTACGACAAAACTCCTG 57.475 40.909 24.41 0.00 0.00 3.86
2507 2561 4.392754 ACAAAAACGTACGACAAAACTCCT 59.607 37.500 24.41 0.00 0.00 3.69
2553 2746 7.253750 GCAAAATGAATAGCTTATTCCACAACG 60.254 37.037 0.00 0.00 43.00 4.10
2628 2873 6.801539 ACAAACTTCGAAGATTCTAATGCA 57.198 33.333 31.08 0.00 35.04 3.96
2682 2927 4.115401 TGTCACAGTATCTGATGTCTGC 57.885 45.455 17.96 8.22 35.18 4.26
2743 2988 2.539476 GTGGGAACAAAGCACAGTTTG 58.461 47.619 0.00 0.00 46.06 2.93
2767 3012 7.123697 TGGCGAGTTTATAGCATATAGGTACAT 59.876 37.037 0.00 0.00 32.12 2.29
2800 3070 5.922544 CCACACCTGAATTTTCATCTCAAAC 59.077 40.000 0.00 0.00 36.46 2.93
2805 3075 4.118168 ACCCACACCTGAATTTTCATCT 57.882 40.909 0.00 0.00 36.46 2.90
2806 3076 5.975693 TTACCCACACCTGAATTTTCATC 57.024 39.130 0.00 0.00 36.46 2.92
2817 3087 4.645588 TGAAAATCGTTTTTACCCACACCT 59.354 37.500 4.25 0.00 35.20 4.00
2826 3096 7.858879 GCTACAGTTCCTTGAAAATCGTTTTTA 59.141 33.333 4.25 0.00 35.20 1.52
2973 3256 6.905076 GGCGTTTATTGTATTGTACTGTCATG 59.095 38.462 0.00 0.00 0.00 3.07
2974 3257 6.596106 TGGCGTTTATTGTATTGTACTGTCAT 59.404 34.615 0.00 0.00 0.00 3.06
2977 3260 6.804770 TTGGCGTTTATTGTATTGTACTGT 57.195 33.333 0.00 0.00 0.00 3.55
2992 3275 9.699703 ATGTAACTATTGTTATTTTTGGCGTTT 57.300 25.926 3.08 0.00 40.31 3.60
3010 3293 8.910944 GGTGGTCTACAAATCTAGATGTAACTA 58.089 37.037 5.86 4.08 32.05 2.24
3012 3295 7.783042 AGGTGGTCTACAAATCTAGATGTAAC 58.217 38.462 5.86 7.78 32.05 2.50
3020 3303 5.393787 CGTTGCTAGGTGGTCTACAAATCTA 60.394 44.000 0.00 0.00 0.00 1.98
3026 3309 1.542915 GTCGTTGCTAGGTGGTCTACA 59.457 52.381 0.00 0.00 0.00 2.74
3027 3310 1.817447 AGTCGTTGCTAGGTGGTCTAC 59.183 52.381 0.00 0.00 0.00 2.59
3039 3322 2.065993 TGAGAGCTTGTAGTCGTTGC 57.934 50.000 0.00 0.00 0.00 4.17
3041 3324 3.050619 CGTTTGAGAGCTTGTAGTCGTT 58.949 45.455 0.00 0.00 0.00 3.85
3054 3337 2.867368 TGCGTTTTTAGCTCGTTTGAGA 59.133 40.909 0.00 0.00 45.57 3.27
3060 3343 1.857364 CGGTGCGTTTTTAGCTCGT 59.143 52.632 0.00 0.00 35.28 4.18
3067 3350 2.452366 GATGACGGCGGTGCGTTTTT 62.452 55.000 13.24 0.00 0.00 1.94
3101 3384 3.825328 ACAATGAGTTTTGTCAGGCTCT 58.175 40.909 0.00 0.00 34.83 4.09
3124 3407 2.223829 CGGCGACTTCTGGATTGTCTAT 60.224 50.000 0.00 0.00 0.00 1.98
3131 3414 1.258445 AACTCCGGCGACTTCTGGAT 61.258 55.000 9.30 0.00 40.51 3.41
3133 3416 1.738099 CAACTCCGGCGACTTCTGG 60.738 63.158 9.30 0.00 0.00 3.86
3134 3417 0.734253 CTCAACTCCGGCGACTTCTG 60.734 60.000 9.30 0.00 0.00 3.02
3135 3418 1.587054 CTCAACTCCGGCGACTTCT 59.413 57.895 9.30 0.00 0.00 2.85
3172 3455 4.835284 TGTGGCTTATTGTGATGGTAGA 57.165 40.909 0.00 0.00 0.00 2.59
3173 3456 5.125356 TCATGTGGCTTATTGTGATGGTAG 58.875 41.667 0.00 0.00 0.00 3.18
3174 3457 5.109500 TCATGTGGCTTATTGTGATGGTA 57.891 39.130 0.00 0.00 0.00 3.25
3175 3458 3.966979 TCATGTGGCTTATTGTGATGGT 58.033 40.909 0.00 0.00 0.00 3.55
3177 3460 4.512571 TCGATCATGTGGCTTATTGTGATG 59.487 41.667 0.00 0.00 0.00 3.07
3178 3461 4.707105 TCGATCATGTGGCTTATTGTGAT 58.293 39.130 0.00 0.00 0.00 3.06
3179 3462 4.135747 TCGATCATGTGGCTTATTGTGA 57.864 40.909 0.00 0.00 0.00 3.58
3189 3472 8.777413 ACTATCATAACAATTTCGATCATGTGG 58.223 33.333 0.00 0.00 0.00 4.17
3199 3482 9.034544 GGCAAATCCAACTATCATAACAATTTC 57.965 33.333 0.00 0.00 34.01 2.17
3225 3508 1.153289 CTCAACGGCCCTGGATCAG 60.153 63.158 0.00 0.00 0.00 2.90
3226 3509 2.669133 CCTCAACGGCCCTGGATCA 61.669 63.158 0.00 0.00 0.00 2.92
3227 3510 2.190578 CCTCAACGGCCCTGGATC 59.809 66.667 0.00 0.00 0.00 3.36
3228 3511 3.411517 CCCTCAACGGCCCTGGAT 61.412 66.667 0.00 0.00 0.00 3.41
3238 3521 4.329545 TCGCACAGGCCCCTCAAC 62.330 66.667 0.00 0.00 36.38 3.18
3239 3522 4.020617 CTCGCACAGGCCCCTCAA 62.021 66.667 0.00 0.00 36.38 3.02
3267 3550 2.607442 ATTTTGGGGGCCCTGTGC 60.607 61.111 24.38 5.99 40.16 4.57
3268 3551 1.989508 GGATTTTGGGGGCCCTGTG 60.990 63.158 24.38 0.00 36.94 3.66
3269 3552 2.176812 AGGATTTTGGGGGCCCTGT 61.177 57.895 24.38 3.82 36.94 4.00
3270 3553 1.686800 CAGGATTTTGGGGGCCCTG 60.687 63.158 24.38 6.11 38.48 4.45
3271 3554 2.779981 CAGGATTTTGGGGGCCCT 59.220 61.111 24.38 0.28 36.94 5.19
3272 3555 2.365502 CCAGGATTTTGGGGGCCC 60.366 66.667 15.76 15.76 34.46 5.80
3278 3561 2.365502 GGGGCCCCAGGATTTTGG 60.366 66.667 37.61 0.00 38.00 3.28
3279 3562 2.365502 GGGGGCCCCAGGATTTTG 60.366 66.667 41.80 0.00 44.65 2.44
3288 3571 2.509931 GAAACCTAGTTGGGGGCCCC 62.510 65.000 36.02 36.02 45.71 5.80
3289 3572 1.000019 GAAACCTAGTTGGGGGCCC 60.000 63.158 15.76 15.76 41.11 5.80
3290 3573 0.335019 ATGAAACCTAGTTGGGGGCC 59.665 55.000 0.00 0.00 41.11 5.80
3291 3574 3.595190 ATATGAAACCTAGTTGGGGGC 57.405 47.619 0.00 0.00 41.11 5.80
3292 3575 4.102054 ACGTATATGAAACCTAGTTGGGGG 59.898 45.833 0.00 0.00 41.11 5.40
3293 3576 5.286267 ACGTATATGAAACCTAGTTGGGG 57.714 43.478 0.00 0.00 41.11 4.96
3294 3577 9.582431 CATATACGTATATGAAACCTAGTTGGG 57.418 37.037 36.32 14.59 45.23 4.12
3337 3620 5.417580 ACCAGTGTTTTCAGCTTAAAACTGA 59.582 36.000 27.67 12.85 45.43 3.41
3338 3621 5.650543 ACCAGTGTTTTCAGCTTAAAACTG 58.349 37.500 27.67 20.97 45.43 3.16
3339 3622 5.652452 AGACCAGTGTTTTCAGCTTAAAACT 59.348 36.000 27.67 12.91 45.43 2.66
3340 3623 5.743872 CAGACCAGTGTTTTCAGCTTAAAAC 59.256 40.000 23.36 23.36 45.43 2.43
3341 3624 5.163561 CCAGACCAGTGTTTTCAGCTTAAAA 60.164 40.000 1.63 1.63 0.00 1.52
3342 3625 4.338118 CCAGACCAGTGTTTTCAGCTTAAA 59.662 41.667 0.00 0.00 0.00 1.52
3343 3626 3.882888 CCAGACCAGTGTTTTCAGCTTAA 59.117 43.478 0.00 0.00 0.00 1.85
3344 3627 3.476552 CCAGACCAGTGTTTTCAGCTTA 58.523 45.455 0.00 0.00 0.00 3.09
3345 3628 2.301346 CCAGACCAGTGTTTTCAGCTT 58.699 47.619 0.00 0.00 0.00 3.74
3346 3629 1.477558 CCCAGACCAGTGTTTTCAGCT 60.478 52.381 0.00 0.00 0.00 4.24
3347 3630 0.954452 CCCAGACCAGTGTTTTCAGC 59.046 55.000 0.00 0.00 0.00 4.26
3348 3631 0.954452 GCCCAGACCAGTGTTTTCAG 59.046 55.000 0.00 0.00 0.00 3.02
3349 3632 0.467290 GGCCCAGACCAGTGTTTTCA 60.467 55.000 0.00 0.00 0.00 2.69
3350 3633 0.178990 AGGCCCAGACCAGTGTTTTC 60.179 55.000 0.00 0.00 0.00 2.29
3351 3634 0.261696 AAGGCCCAGACCAGTGTTTT 59.738 50.000 0.00 0.00 0.00 2.43
3352 3635 0.178990 GAAGGCCCAGACCAGTGTTT 60.179 55.000 0.00 0.00 0.00 2.83
3353 3636 1.062488 AGAAGGCCCAGACCAGTGTT 61.062 55.000 0.00 0.00 0.00 3.32
3354 3637 1.062488 AAGAAGGCCCAGACCAGTGT 61.062 55.000 0.00 0.00 0.00 3.55
3355 3638 0.607489 CAAGAAGGCCCAGACCAGTG 60.607 60.000 0.00 0.00 0.00 3.66
3356 3639 1.763770 CAAGAAGGCCCAGACCAGT 59.236 57.895 0.00 0.00 0.00 4.00
3357 3640 1.001641 CCAAGAAGGCCCAGACCAG 60.002 63.158 0.00 0.00 0.00 4.00
3358 3641 2.538141 CCCAAGAAGGCCCAGACCA 61.538 63.158 0.00 0.00 35.39 4.02
3359 3642 2.356667 CCCAAGAAGGCCCAGACC 59.643 66.667 0.00 0.00 35.39 3.85
3367 3650 2.124942 GCTCGAGGCCCAAGAAGG 60.125 66.667 15.58 0.00 34.27 3.46
3368 3651 0.393537 ATTGCTCGAGGCCCAAGAAG 60.394 55.000 15.58 0.00 40.92 2.85
3369 3652 0.908910 TATTGCTCGAGGCCCAAGAA 59.091 50.000 15.58 0.37 40.92 2.52
3370 3653 0.178068 GTATTGCTCGAGGCCCAAGA 59.822 55.000 15.58 4.53 40.92 3.02
3371 3654 1.154205 CGTATTGCTCGAGGCCCAAG 61.154 60.000 15.58 0.00 40.92 3.61
3372 3655 1.153449 CGTATTGCTCGAGGCCCAA 60.153 57.895 15.58 10.40 40.92 4.12
3373 3656 2.499205 CGTATTGCTCGAGGCCCA 59.501 61.111 15.58 0.16 40.92 5.36
3374 3657 2.967615 GCGTATTGCTCGAGGCCC 60.968 66.667 15.58 0.00 41.73 5.80
3384 3667 3.605461 CGAGATGATGGCAAAGCGTATTG 60.605 47.826 0.00 0.00 0.00 1.90
3385 3668 2.545526 CGAGATGATGGCAAAGCGTATT 59.454 45.455 0.00 0.00 0.00 1.89
3386 3669 2.138320 CGAGATGATGGCAAAGCGTAT 58.862 47.619 0.00 0.00 0.00 3.06
3387 3670 1.134818 ACGAGATGATGGCAAAGCGTA 60.135 47.619 0.00 0.00 0.00 4.42
3388 3671 0.391661 ACGAGATGATGGCAAAGCGT 60.392 50.000 0.00 0.00 0.00 5.07
3389 3672 0.027194 CACGAGATGATGGCAAAGCG 59.973 55.000 0.00 0.00 0.00 4.68
3390 3673 0.379669 CCACGAGATGATGGCAAAGC 59.620 55.000 0.00 0.00 0.00 3.51
3391 3674 2.028420 TCCACGAGATGATGGCAAAG 57.972 50.000 0.00 0.00 35.81 2.77
3392 3675 2.715749 ATCCACGAGATGATGGCAAA 57.284 45.000 0.00 0.00 35.81 3.68
3401 3684 1.967066 GATCCACCTCATCCACGAGAT 59.033 52.381 0.00 0.00 34.79 2.75
3402 3685 1.403814 GATCCACCTCATCCACGAGA 58.596 55.000 0.00 0.00 34.79 4.04
3403 3686 0.031314 CGATCCACCTCATCCACGAG 59.969 60.000 0.00 0.00 0.00 4.18
3404 3687 0.395173 TCGATCCACCTCATCCACGA 60.395 55.000 0.00 0.00 0.00 4.35
3405 3688 0.676184 ATCGATCCACCTCATCCACG 59.324 55.000 0.00 0.00 0.00 4.94
3406 3689 1.001406 GGATCGATCCACCTCATCCAC 59.999 57.143 34.65 6.83 46.38 4.02
3407 3690 1.342074 GGATCGATCCACCTCATCCA 58.658 55.000 34.65 0.00 46.38 3.41
3423 3706 6.870965 GTCATTTTGTCTATGATCGCTAGGAT 59.129 38.462 0.00 0.00 38.35 3.24
3424 3707 6.183360 TGTCATTTTGTCTATGATCGCTAGGA 60.183 38.462 0.00 0.00 34.75 2.94
3425 3708 5.985530 TGTCATTTTGTCTATGATCGCTAGG 59.014 40.000 0.00 0.00 34.75 3.02
3426 3709 6.346439 GCTGTCATTTTGTCTATGATCGCTAG 60.346 42.308 0.00 0.00 34.75 3.42
3427 3710 5.463392 GCTGTCATTTTGTCTATGATCGCTA 59.537 40.000 0.00 0.00 34.75 4.26
3428 3711 4.272018 GCTGTCATTTTGTCTATGATCGCT 59.728 41.667 0.00 0.00 34.75 4.93
3429 3712 4.521943 GCTGTCATTTTGTCTATGATCGC 58.478 43.478 0.00 0.00 34.75 4.58
3430 3713 4.024556 GGGCTGTCATTTTGTCTATGATCG 60.025 45.833 0.00 0.00 34.75 3.69
3431 3714 4.883585 TGGGCTGTCATTTTGTCTATGATC 59.116 41.667 0.00 0.00 34.75 2.92
3432 3715 4.858850 TGGGCTGTCATTTTGTCTATGAT 58.141 39.130 0.00 0.00 34.75 2.45
3433 3716 4.264253 CTGGGCTGTCATTTTGTCTATGA 58.736 43.478 0.00 0.00 0.00 2.15
3434 3717 3.181493 GCTGGGCTGTCATTTTGTCTATG 60.181 47.826 0.00 0.00 0.00 2.23
3435 3718 3.019564 GCTGGGCTGTCATTTTGTCTAT 58.980 45.455 0.00 0.00 0.00 1.98
3436 3719 2.224744 TGCTGGGCTGTCATTTTGTCTA 60.225 45.455 0.00 0.00 0.00 2.59
3437 3720 1.251251 GCTGGGCTGTCATTTTGTCT 58.749 50.000 0.00 0.00 0.00 3.41
3438 3721 0.961019 TGCTGGGCTGTCATTTTGTC 59.039 50.000 0.00 0.00 0.00 3.18
3439 3722 0.675633 GTGCTGGGCTGTCATTTTGT 59.324 50.000 0.00 0.00 0.00 2.83
3440 3723 0.675083 TGTGCTGGGCTGTCATTTTG 59.325 50.000 0.00 0.00 0.00 2.44
3441 3724 0.963962 CTGTGCTGGGCTGTCATTTT 59.036 50.000 0.00 0.00 0.00 1.82
3442 3725 0.178981 ACTGTGCTGGGCTGTCATTT 60.179 50.000 0.00 0.00 0.00 2.32
3443 3726 0.692476 TACTGTGCTGGGCTGTCATT 59.308 50.000 0.00 0.00 0.00 2.57
3444 3727 0.036010 GTACTGTGCTGGGCTGTCAT 60.036 55.000 0.00 0.00 0.00 3.06
3445 3728 1.371183 GTACTGTGCTGGGCTGTCA 59.629 57.895 0.00 0.00 0.00 3.58
3446 3729 1.738099 CGTACTGTGCTGGGCTGTC 60.738 63.158 0.00 0.00 0.00 3.51
3447 3730 2.040009 AACGTACTGTGCTGGGCTGT 62.040 55.000 0.00 0.00 0.00 4.40
3448 3731 1.291877 GAACGTACTGTGCTGGGCTG 61.292 60.000 0.00 0.00 0.00 4.85
3449 3732 1.004918 GAACGTACTGTGCTGGGCT 60.005 57.895 0.00 0.00 0.00 5.19
3450 3733 2.033194 GGAACGTACTGTGCTGGGC 61.033 63.158 0.00 0.00 0.00 5.36
3451 3734 4.278956 GGAACGTACTGTGCTGGG 57.721 61.111 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.