Multiple sequence alignment - TraesCS4D01G313600

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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 TraesCS4D01G313600 chr4D 100.000 3611 0 0 1 3611 479539654 479543264 0.000000e+00 6669.0
1 TraesCS4D01G313600 chr4D 99.371 159 1 0 1 159 479534184 479534342 4.560000e-74 289.0
2 TraesCS4D01G313600 chr4B 96.362 2144 57 8 908 3044 606764618 606766747 0.000000e+00 3507.0
3 TraesCS4D01G313600 chr4B 89.910 555 36 8 160 697 606763483 606764034 0.000000e+00 697.0
4 TraesCS4D01G313600 chr4B 90.395 177 10 3 744 913 606764490 606764666 3.630000e-55 226.0
5 TraesCS4D01G313600 chr4B 80.000 115 21 2 3495 3608 606575041 606575154 2.310000e-12 84.2
6 TraesCS4D01G313600 chr4A 97.027 1749 52 0 908 2656 685834707 685836455 0.000000e+00 2942.0
7 TraesCS4D01G313600 chr4A 85.456 1547 206 15 1015 2553 632989706 632991241 0.000000e+00 1592.0
8 TraesCS4D01G313600 chr4A 85.391 1547 207 15 1015 2553 632999852 632998317 0.000000e+00 1587.0
9 TraesCS4D01G313600 chr4A 77.833 1412 282 23 994 2392 686140135 686138742 0.000000e+00 845.0
10 TraesCS4D01G313600 chr4A 95.070 142 7 0 772 913 685834609 685834750 1.300000e-54 224.0
11 TraesCS4D01G313600 chr4A 100.000 58 0 0 650 707 685834541 685834598 1.370000e-19 108.0
12 TraesCS4D01G313600 chr5D 84.823 1555 218 16 1015 2562 537162874 537161331 0.000000e+00 1548.0
13 TraesCS4D01G313600 chr5D 84.799 1546 218 15 1015 2553 537088077 537089612 0.000000e+00 1537.0
14 TraesCS4D01G313600 chr5D 80.706 1586 256 37 997 2548 512534342 512535911 0.000000e+00 1188.0
15 TraesCS4D01G313600 chr5D 86.117 497 49 10 3005 3484 487522285 487521792 5.340000e-143 518.0
16 TraesCS4D01G313600 chr5D 83.366 505 49 18 3002 3484 486274043 486274534 5.540000e-118 435.0
17 TraesCS4D01G313600 chr5D 98.788 165 1 1 1 164 326411666 326411830 3.530000e-75 292.0
18 TraesCS4D01G313600 chr5D 99.371 159 1 0 1 159 65887827 65887669 4.560000e-74 289.0
19 TraesCS4D01G313600 chr5D 99.371 159 1 0 1 159 73406093 73405935 4.560000e-74 289.0
20 TraesCS4D01G313600 chr5D 90.789 76 5 2 3533 3607 345521989 345521915 2.290000e-17 100.0
21 TraesCS4D01G313600 chr5B 84.729 1552 211 19 1015 2553 677537454 677538992 0.000000e+00 1530.0
22 TraesCS4D01G313600 chr5B 84.472 1552 215 19 1015 2553 677545043 677543505 0.000000e+00 1507.0
23 TraesCS4D01G313600 chr5B 84.725 491 55 7 3011 3484 600103840 600103353 1.170000e-129 473.0
24 TraesCS4D01G313600 chr5B 84.254 489 54 14 3014 3484 326081141 326080658 4.250000e-124 455.0
25 TraesCS4D01G313600 chr5B 82.824 524 67 12 2978 3484 630120766 630121283 7.110000e-122 448.0
26 TraesCS4D01G313600 chr5B 78.074 488 64 25 3012 3484 555059210 555058751 5.940000e-68 268.0
27 TraesCS4D01G313600 chr5A 80.542 1588 256 40 994 2548 640724642 640726209 0.000000e+00 1171.0
28 TraesCS4D01G313600 chr5A 81.264 443 56 16 2954 3373 8743352 8742914 2.080000e-87 333.0
29 TraesCS4D01G313600 chr3D 82.832 565 74 13 2941 3484 523802086 523801524 5.420000e-133 484.0
30 TraesCS4D01G313600 chr3D 97.619 168 4 0 1 168 55747842 55747675 4.560000e-74 289.0
31 TraesCS4D01G313600 chr3D 98.171 164 2 1 1 164 302916764 302916602 5.900000e-73 285.0
32 TraesCS4D01G313600 chr3D 84.706 85 8 5 3530 3611 421702773 421702691 2.990000e-11 80.5
33 TraesCS4D01G313600 chr2B 83.570 493 55 20 3013 3484 698187513 698187026 4.280000e-119 438.0
34 TraesCS4D01G313600 chr2B 83.096 491 59 14 3014 3484 607076263 607076749 3.330000e-115 425.0
35 TraesCS4D01G313600 chr2B 81.308 535 65 19 2974 3484 666175289 666174766 5.620000e-108 401.0
36 TraesCS4D01G313600 chr6A 82.420 529 65 13 2978 3484 398974330 398973808 1.540000e-118 436.0
37 TraesCS4D01G313600 chr3B 81.818 528 65 17 2980 3484 784855463 784854944 7.210000e-112 414.0
38 TraesCS4D01G313600 chr1B 81.698 530 64 16 2980 3484 39638591 39638070 9.330000e-111 411.0
39 TraesCS4D01G313600 chr7D 85.861 389 44 6 3105 3484 504773369 504773755 1.560000e-108 403.0
40 TraesCS4D01G313600 chr6B 87.059 340 33 6 3153 3484 176694524 176694188 1.220000e-99 374.0
41 TraesCS4D01G313600 chr2D 98.765 162 1 1 1 161 576445716 576445877 1.640000e-73 287.0
42 TraesCS4D01G313600 chr2D 97.605 167 3 1 1 166 547024714 547024548 5.900000e-73 285.0
43 TraesCS4D01G313600 chr2D 86.139 101 12 2 3510 3609 555952437 555952338 1.370000e-19 108.0
44 TraesCS4D01G313600 chrUn 97.590 166 4 0 1 166 98017823 98017658 5.900000e-73 285.0
45 TraesCS4D01G313600 chr1D 88.889 126 10 4 3484 3607 483906450 483906327 6.240000e-33 152.0
46 TraesCS4D01G313600 chr1A 85.600 125 12 6 3487 3607 580929283 580929161 3.790000e-25 126.0
47 TraesCS4D01G313600 chr2A 84.615 130 15 4 3484 3609 695451175 695451047 1.360000e-24 124.0
48 TraesCS4D01G313600 chr7B 84.167 120 12 7 3488 3604 746103863 746103978 3.810000e-20 110.0
49 TraesCS4D01G313600 chr7A 84.524 84 8 5 3526 3606 734535237 734535156 1.070000e-10 78.7


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 TraesCS4D01G313600 chr4D 479539654 479543264 3610 False 6669.000000 6669 100.000000 1 3611 1 chr4D.!!$F2 3610
1 TraesCS4D01G313600 chr4B 606763483 606766747 3264 False 1476.666667 3507 92.222333 160 3044 3 chr4B.!!$F2 2884
2 TraesCS4D01G313600 chr4A 632989706 632991241 1535 False 1592.000000 1592 85.456000 1015 2553 1 chr4A.!!$F1 1538
3 TraesCS4D01G313600 chr4A 632998317 632999852 1535 True 1587.000000 1587 85.391000 1015 2553 1 chr4A.!!$R1 1538
4 TraesCS4D01G313600 chr4A 685834541 685836455 1914 False 1091.333333 2942 97.365667 650 2656 3 chr4A.!!$F2 2006
5 TraesCS4D01G313600 chr4A 686138742 686140135 1393 True 845.000000 845 77.833000 994 2392 1 chr4A.!!$R2 1398
6 TraesCS4D01G313600 chr5D 537161331 537162874 1543 True 1548.000000 1548 84.823000 1015 2562 1 chr5D.!!$R5 1547
7 TraesCS4D01G313600 chr5D 537088077 537089612 1535 False 1537.000000 1537 84.799000 1015 2553 1 chr5D.!!$F4 1538
8 TraesCS4D01G313600 chr5D 512534342 512535911 1569 False 1188.000000 1188 80.706000 997 2548 1 chr5D.!!$F3 1551
9 TraesCS4D01G313600 chr5B 677537454 677538992 1538 False 1530.000000 1530 84.729000 1015 2553 1 chr5B.!!$F2 1538
10 TraesCS4D01G313600 chr5B 677543505 677545043 1538 True 1507.000000 1507 84.472000 1015 2553 1 chr5B.!!$R4 1538
11 TraesCS4D01G313600 chr5B 630120766 630121283 517 False 448.000000 448 82.824000 2978 3484 1 chr5B.!!$F1 506
12 TraesCS4D01G313600 chr5A 640724642 640726209 1567 False 1171.000000 1171 80.542000 994 2548 1 chr5A.!!$F1 1554
13 TraesCS4D01G313600 chr3D 523801524 523802086 562 True 484.000000 484 82.832000 2941 3484 1 chr3D.!!$R4 543
14 TraesCS4D01G313600 chr2B 666174766 666175289 523 True 401.000000 401 81.308000 2974 3484 1 chr2B.!!$R1 510
15 TraesCS4D01G313600 chr6A 398973808 398974330 522 True 436.000000 436 82.420000 2978 3484 1 chr6A.!!$R1 506
16 TraesCS4D01G313600 chr3B 784854944 784855463 519 True 414.000000 414 81.818000 2980 3484 1 chr3B.!!$R1 504
17 TraesCS4D01G313600 chr1B 39638070 39638591 521 True 411.000000 411 81.698000 2980 3484 1 chr1B.!!$R1 504

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
382 385 0.106918 ACCAAAGCCTGTCGAACCAA 60.107 50.0 0.0 0.0 0.0 3.67 F
793 1220 0.391228 TCCGTGCAAGCAACAGACTA 59.609 50.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2568 0.803768 CACGAGCTGGATCCAGAACG 60.804 60.000 40.29 37.82 46.3 3.95 R
2678 3135 2.686405 AGTTCTAGTCACGACACACACA 59.314 45.455 0.00 0.00 0.0 3.72 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
35 36 6.946229 CTGTTTCTACAGCTATTGTTACGT 57.054 37.500 0.00 0.00 44.81 3.57
36 37 6.699895 TGTTTCTACAGCTATTGTTACGTG 57.300 37.500 0.00 0.00 41.29 4.49
37 38 6.218019 TGTTTCTACAGCTATTGTTACGTGT 58.782 36.000 0.00 0.00 41.29 4.49
38 39 6.702723 TGTTTCTACAGCTATTGTTACGTGTT 59.297 34.615 0.00 0.00 41.29 3.32
39 40 7.225145 TGTTTCTACAGCTATTGTTACGTGTTT 59.775 33.333 0.00 0.00 41.29 2.83
40 41 6.699895 TCTACAGCTATTGTTACGTGTTTG 57.300 37.500 0.00 0.00 41.29 2.93
41 42 4.141855 ACAGCTATTGTTACGTGTTTGC 57.858 40.909 0.00 0.00 36.31 3.68
42 43 3.813166 ACAGCTATTGTTACGTGTTTGCT 59.187 39.130 0.00 0.00 36.31 3.91
43 44 4.151070 CAGCTATTGTTACGTGTTTGCTG 58.849 43.478 0.00 5.38 39.16 4.41
44 45 2.908626 GCTATTGTTACGTGTTTGCTGC 59.091 45.455 0.00 0.00 0.00 5.25
45 46 3.364964 GCTATTGTTACGTGTTTGCTGCT 60.365 43.478 0.00 0.00 0.00 4.24
46 47 2.466870 TTGTTACGTGTTTGCTGCTG 57.533 45.000 0.00 0.00 0.00 4.41
47 48 1.374560 TGTTACGTGTTTGCTGCTGT 58.625 45.000 0.00 0.00 0.00 4.40
48 49 1.740585 TGTTACGTGTTTGCTGCTGTT 59.259 42.857 0.00 0.00 0.00 3.16
49 50 2.937149 TGTTACGTGTTTGCTGCTGTTA 59.063 40.909 0.00 0.00 0.00 2.41
50 51 3.562141 TGTTACGTGTTTGCTGCTGTTAT 59.438 39.130 0.00 0.00 0.00 1.89
51 52 2.686558 ACGTGTTTGCTGCTGTTATG 57.313 45.000 0.00 0.00 0.00 1.90
52 53 1.330306 CGTGTTTGCTGCTGTTATGC 58.670 50.000 0.00 0.00 0.00 3.14
53 54 1.334870 CGTGTTTGCTGCTGTTATGCA 60.335 47.619 0.00 0.00 41.05 3.96
54 55 2.669113 CGTGTTTGCTGCTGTTATGCAT 60.669 45.455 3.79 3.79 42.48 3.96
55 56 2.664568 GTGTTTGCTGCTGTTATGCATG 59.335 45.455 10.16 0.00 42.48 4.06
56 57 2.296752 TGTTTGCTGCTGTTATGCATGT 59.703 40.909 10.16 0.00 42.48 3.21
57 58 2.919229 GTTTGCTGCTGTTATGCATGTC 59.081 45.455 10.16 2.63 42.48 3.06
58 59 2.118313 TGCTGCTGTTATGCATGTCT 57.882 45.000 10.16 0.00 42.48 3.41
59 60 2.439409 TGCTGCTGTTATGCATGTCTT 58.561 42.857 10.16 0.00 42.48 3.01
60 61 2.162809 TGCTGCTGTTATGCATGTCTTG 59.837 45.455 10.16 0.00 42.48 3.02
75 76 6.551385 CATGTCTTGCTGTTCTTCTAGTTT 57.449 37.500 0.00 0.00 0.00 2.66
76 77 5.991328 TGTCTTGCTGTTCTTCTAGTTTG 57.009 39.130 0.00 0.00 0.00 2.93
77 78 4.273480 TGTCTTGCTGTTCTTCTAGTTTGC 59.727 41.667 0.00 0.00 0.00 3.68
78 79 4.513318 GTCTTGCTGTTCTTCTAGTTTGCT 59.487 41.667 0.00 0.00 0.00 3.91
79 80 5.696724 GTCTTGCTGTTCTTCTAGTTTGCTA 59.303 40.000 0.00 0.00 0.00 3.49
80 81 5.928839 TCTTGCTGTTCTTCTAGTTTGCTAG 59.071 40.000 0.00 0.00 44.60 3.42
92 93 6.324819 TCTAGTTTGCTAGATTTTTGCATGC 58.675 36.000 11.82 11.82 46.25 4.06
93 94 5.143376 AGTTTGCTAGATTTTTGCATGCT 57.857 34.783 20.33 0.00 36.55 3.79
94 95 6.271488 AGTTTGCTAGATTTTTGCATGCTA 57.729 33.333 20.33 8.83 36.55 3.49
95 96 6.327934 AGTTTGCTAGATTTTTGCATGCTAG 58.672 36.000 20.33 11.08 36.55 3.42
96 97 5.902613 TTGCTAGATTTTTGCATGCTAGT 57.097 34.783 20.33 1.30 36.55 2.57
97 98 7.121168 AGTTTGCTAGATTTTTGCATGCTAGTA 59.879 33.333 20.33 6.90 36.55 1.82
98 99 7.572523 TTGCTAGATTTTTGCATGCTAGTAT 57.427 32.000 20.33 8.39 36.55 2.12
99 100 7.194607 TGCTAGATTTTTGCATGCTAGTATC 57.805 36.000 20.33 16.15 33.01 2.24
100 101 6.994496 TGCTAGATTTTTGCATGCTAGTATCT 59.006 34.615 20.33 21.34 33.01 1.98
101 102 7.172190 TGCTAGATTTTTGCATGCTAGTATCTC 59.828 37.037 20.33 11.55 33.01 2.75
102 103 7.387397 GCTAGATTTTTGCATGCTAGTATCTCT 59.613 37.037 20.33 13.57 33.01 3.10
103 104 9.270640 CTAGATTTTTGCATGCTAGTATCTCTT 57.729 33.333 20.33 5.44 0.00 2.85
104 105 8.152309 AGATTTTTGCATGCTAGTATCTCTTC 57.848 34.615 20.33 3.24 0.00 2.87
105 106 7.992033 AGATTTTTGCATGCTAGTATCTCTTCT 59.008 33.333 20.33 5.38 0.00 2.85
106 107 9.265901 GATTTTTGCATGCTAGTATCTCTTCTA 57.734 33.333 20.33 0.00 0.00 2.10
107 108 8.654230 TTTTTGCATGCTAGTATCTCTTCTAG 57.346 34.615 20.33 0.00 37.34 2.43
108 109 6.968263 TTGCATGCTAGTATCTCTTCTAGT 57.032 37.500 20.33 0.00 36.84 2.57
109 110 6.567687 TGCATGCTAGTATCTCTTCTAGTC 57.432 41.667 20.33 0.00 36.84 2.59
110 111 6.064717 TGCATGCTAGTATCTCTTCTAGTCA 58.935 40.000 20.33 0.00 36.84 3.41
111 112 6.718912 TGCATGCTAGTATCTCTTCTAGTCAT 59.281 38.462 20.33 0.00 36.84 3.06
112 113 7.028962 GCATGCTAGTATCTCTTCTAGTCATG 58.971 42.308 11.37 19.40 42.65 3.07
113 114 7.094420 GCATGCTAGTATCTCTTCTAGTCATGA 60.094 40.741 23.39 0.00 42.55 3.07
114 115 8.791675 CATGCTAGTATCTCTTCTAGTCATGAA 58.208 37.037 19.20 0.00 42.55 2.57
115 116 8.932434 TGCTAGTATCTCTTCTAGTCATGAAT 57.068 34.615 0.00 0.00 36.84 2.57
116 117 9.360901 TGCTAGTATCTCTTCTAGTCATGAATT 57.639 33.333 0.00 0.00 36.84 2.17
144 145 9.638239 TTTACTGAAATTAATCATGAACTTGCC 57.362 29.630 0.00 0.00 0.00 4.52
145 146 7.472334 ACTGAAATTAATCATGAACTTGCCT 57.528 32.000 0.00 0.00 0.00 4.75
146 147 8.579850 ACTGAAATTAATCATGAACTTGCCTA 57.420 30.769 0.00 0.00 0.00 3.93
147 148 9.023962 ACTGAAATTAATCATGAACTTGCCTAA 57.976 29.630 0.00 0.00 0.00 2.69
154 155 9.639563 TTAATCATGAACTTGCCTAATATTCCA 57.360 29.630 0.00 0.00 0.00 3.53
155 156 8.537728 AATCATGAACTTGCCTAATATTCCAA 57.462 30.769 0.00 0.00 0.00 3.53
156 157 7.333528 TCATGAACTTGCCTAATATTCCAAC 57.666 36.000 0.00 0.00 0.00 3.77
157 158 6.889177 TCATGAACTTGCCTAATATTCCAACA 59.111 34.615 0.00 0.00 0.00 3.33
158 159 7.395772 TCATGAACTTGCCTAATATTCCAACAA 59.604 33.333 0.00 0.00 0.00 2.83
167 168 8.004215 TGCCTAATATTCCAACAAAGATATGGT 58.996 33.333 0.00 0.00 35.66 3.55
204 205 3.327757 TCATGGTGTATAAGGCTCCCATC 59.672 47.826 0.00 0.00 30.47 3.51
213 214 1.207791 AGGCTCCCATCGAGTTTGAT 58.792 50.000 0.00 0.00 41.10 2.57
223 224 5.356751 CCCATCGAGTTTGATTGAACCAATA 59.643 40.000 0.00 0.00 33.90 1.90
294 297 4.321750 CCTTGATCTTTGCTTCAAGTGCAT 60.322 41.667 10.70 0.00 44.70 3.96
297 300 4.278919 TGATCTTTGCTTCAAGTGCATCAA 59.721 37.500 0.00 0.00 40.34 2.57
335 338 7.919690 TGTAGCTTACATGATGCAAAGATAAC 58.080 34.615 11.10 6.63 32.89 1.89
336 339 6.382869 AGCTTACATGATGCAAAGATAACC 57.617 37.500 11.10 0.00 0.00 2.85
341 344 2.016318 TGATGCAAAGATAACCTGGCG 58.984 47.619 0.00 0.00 0.00 5.69
364 367 5.859114 CGTGTGCTAATCTCCAGTATCATAC 59.141 44.000 0.00 0.00 0.00 2.39
368 371 7.147567 TGTGCTAATCTCCAGTATCATACCAAA 60.148 37.037 0.00 0.00 0.00 3.28
369 372 7.386299 GTGCTAATCTCCAGTATCATACCAAAG 59.614 40.741 0.00 0.00 0.00 2.77
371 374 4.689612 TCTCCAGTATCATACCAAAGCC 57.310 45.455 0.00 0.00 0.00 4.35
375 378 4.130118 CCAGTATCATACCAAAGCCTGTC 58.870 47.826 0.00 0.00 0.00 3.51
382 385 0.106918 ACCAAAGCCTGTCGAACCAA 60.107 50.000 0.00 0.00 0.00 3.67
388 391 1.374252 CCTGTCGAACCAACCTCCG 60.374 63.158 0.00 0.00 0.00 4.63
389 392 1.663739 CTGTCGAACCAACCTCCGA 59.336 57.895 0.00 0.00 0.00 4.55
420 423 1.093159 CATCCACAGAAAGAGCCAGC 58.907 55.000 0.00 0.00 0.00 4.85
423 426 0.959372 CCACAGAAAGAGCCAGCCAG 60.959 60.000 0.00 0.00 0.00 4.85
427 430 1.377856 GAAAGAGCCAGCCAGTCCC 60.378 63.158 0.00 0.00 0.00 4.46
466 469 1.541588 GGGAAGGTTGTGAACATGCTC 59.458 52.381 0.00 0.00 0.00 4.26
481 484 3.935203 ACATGCTCTGGTAAACATCTTCG 59.065 43.478 0.00 0.00 0.00 3.79
482 485 3.678056 TGCTCTGGTAAACATCTTCGT 57.322 42.857 0.00 0.00 0.00 3.85
506 512 7.602265 CGTGAACATCCCATATATAATGTCACA 59.398 37.037 20.04 15.00 34.04 3.58
525 531 6.073276 TGTCACAATTTCTTTCACATACTCCG 60.073 38.462 0.00 0.00 0.00 4.63
528 534 5.995282 ACAATTTCTTTCACATACTCCGACA 59.005 36.000 0.00 0.00 0.00 4.35
529 535 6.485313 ACAATTTCTTTCACATACTCCGACAA 59.515 34.615 0.00 0.00 0.00 3.18
530 536 7.012894 ACAATTTCTTTCACATACTCCGACAAA 59.987 33.333 0.00 0.00 0.00 2.83
544 550 7.585579 ACTCCGACAAAAACCCTAAATAAAA 57.414 32.000 0.00 0.00 0.00 1.52
570 576 3.927142 GTCCTAGGTTGAAGTTCATGTCG 59.073 47.826 9.08 0.00 0.00 4.35
576 582 3.678548 GGTTGAAGTTCATGTCGTAGGAC 59.321 47.826 6.36 8.63 43.71 3.85
601 607 7.924412 ACTTACTTCAAAGATGAACACGTCTTA 59.076 33.333 0.00 0.00 40.59 2.10
605 611 7.924412 ACTTCAAAGATGAACACGTCTTAGTAA 59.076 33.333 0.00 0.00 40.59 2.24
708 726 3.059884 CAGCACATACGTTGTCTCAAGT 58.940 45.455 0.00 0.00 36.00 3.16
710 728 3.005897 AGCACATACGTTGTCTCAAGTCT 59.994 43.478 0.00 0.00 36.00 3.24
714 732 6.073980 GCACATACGTTGTCTCAAGTCTAAAA 60.074 38.462 0.00 0.00 36.00 1.52
737 755 3.433306 AAAAGGTAGGCAGCACATGTA 57.567 42.857 0.00 0.00 0.00 2.29
738 756 2.403252 AAGGTAGGCAGCACATGTAC 57.597 50.000 0.00 0.00 0.00 2.90
739 757 1.573108 AGGTAGGCAGCACATGTACT 58.427 50.000 0.00 0.00 0.00 2.73
740 758 1.208052 AGGTAGGCAGCACATGTACTG 59.792 52.381 19.97 19.97 36.96 2.74
741 759 1.207089 GGTAGGCAGCACATGTACTGA 59.793 52.381 26.94 6.10 35.90 3.41
743 761 3.069586 GGTAGGCAGCACATGTACTGATA 59.930 47.826 26.94 16.18 35.90 2.15
744 762 4.262635 GGTAGGCAGCACATGTACTGATAT 60.263 45.833 26.94 14.60 35.90 1.63
745 763 4.000331 AGGCAGCACATGTACTGATATC 58.000 45.455 26.94 13.49 35.90 1.63
746 764 2.733552 GGCAGCACATGTACTGATATCG 59.266 50.000 26.94 2.64 35.90 2.92
747 765 3.384668 GCAGCACATGTACTGATATCGT 58.615 45.455 26.94 2.15 35.90 3.73
748 766 3.804325 GCAGCACATGTACTGATATCGTT 59.196 43.478 26.94 0.00 35.90 3.85
793 1220 0.391228 TCCGTGCAAGCAACAGACTA 59.609 50.000 0.00 0.00 0.00 2.59
866 1295 5.630121 TCCCACGCATCCAAATCTATAAAT 58.370 37.500 0.00 0.00 0.00 1.40
914 1343 1.994467 GACAGATCGAAGCAGCACG 59.006 57.895 0.00 0.00 0.00 5.34
915 1344 0.456824 GACAGATCGAAGCAGCACGA 60.457 55.000 15.08 15.08 42.49 4.35
918 1347 4.003534 ATCGAAGCAGCACGATCG 57.996 55.556 14.88 14.88 44.14 3.69
919 1348 2.233654 ATCGAAGCAGCACGATCGC 61.234 57.895 16.60 0.00 44.14 4.58
920 1349 3.918220 CGAAGCAGCACGATCGCC 61.918 66.667 16.60 6.65 0.00 5.54
921 1350 2.815211 GAAGCAGCACGATCGCCA 60.815 61.111 16.60 0.00 0.00 5.69
922 1351 2.806856 GAAGCAGCACGATCGCCAG 61.807 63.158 16.60 6.74 0.00 4.85
923 1352 4.827087 AGCAGCACGATCGCCAGG 62.827 66.667 16.60 3.96 0.00 4.45
981 1418 2.500442 GCACGAGATCTGCGACACG 61.500 63.158 17.60 9.10 0.00 4.49
982 1419 1.869574 CACGAGATCTGCGACACGG 60.870 63.158 17.60 0.00 0.00 4.94
985 1422 3.396911 GAGATCTGCGACACGGCGA 62.397 63.158 16.62 0.00 35.06 5.54
986 1423 3.248171 GATCTGCGACACGGCGAC 61.248 66.667 16.62 3.48 35.06 5.19
987 1424 3.964221 GATCTGCGACACGGCGACA 62.964 63.158 16.62 2.39 35.06 4.35
988 1425 4.994201 TCTGCGACACGGCGACAC 62.994 66.667 16.62 2.68 35.06 3.67
1077 1514 1.079127 CCACTTCAGGGCGATCGTT 60.079 57.895 17.81 0.00 0.00 3.85
1443 1882 1.749638 CGGCGACTACCCTCTGTCT 60.750 63.158 0.00 0.00 0.00 3.41
1458 1897 0.986527 TGTCTGCCACCATCATGTCT 59.013 50.000 0.00 0.00 0.00 3.41
2166 2623 1.586154 CCGTTTTCATGCTCGGCCTT 61.586 55.000 0.00 0.00 36.68 4.35
2584 3041 0.802494 CAACGGCGCCAATAAAGTCT 59.198 50.000 28.98 3.25 0.00 3.24
2703 3160 3.489785 GTGTGTCGTGACTAGAACTTTGG 59.510 47.826 0.00 0.00 0.00 3.28
2780 3238 2.098117 CGCTTGATCTTAGCCAAAAGGG 59.902 50.000 12.74 2.38 40.85 3.95
2796 3254 6.394809 CCAAAAGGGCGACAAAAATATACTT 58.605 36.000 0.00 0.00 0.00 2.24
2835 3293 8.273605 AGGAAGCATCAAGATTTTAGATCTCTT 58.726 33.333 0.00 0.00 0.00 2.85
2875 3334 7.575332 TTGCAAAGAAAAACTTGTGTTACTC 57.425 32.000 0.00 0.00 38.98 2.59
2947 3406 5.554510 CGATTGAACTGTCATTAACGATCGG 60.555 44.000 20.98 0.47 35.13 4.18
2958 3417 0.249073 AACGATCGGGAGAAGATGCG 60.249 55.000 20.98 0.00 45.37 4.73
3000 3461 2.461110 GCGTCGTTTGCGGATGGAT 61.461 57.895 0.00 0.00 38.89 3.41
3030 3497 1.186200 GTTGGGCAAGGGGAGATTTC 58.814 55.000 0.00 0.00 0.00 2.17
3111 3586 3.234353 AGAATCATCTCACGGGATAGCA 58.766 45.455 0.00 0.00 0.00 3.49
3188 3670 7.012327 TGAGAACCTGAAACATAAACTCACAAG 59.988 37.037 0.00 0.00 0.00 3.16
3208 3693 7.602644 TCACAAGGAGAAATAGTGTAATGTGAC 59.397 37.037 0.00 0.00 38.66 3.67
3223 3713 2.546778 TGTGACGTCTTGAACAAGGAC 58.453 47.619 17.92 2.73 38.88 3.85
3236 3726 5.300752 TGAACAAGGACATCTCAAGAAGAC 58.699 41.667 0.00 0.00 36.65 3.01
3248 3741 1.352352 CAAGAAGACACCCCCTGACAT 59.648 52.381 0.00 0.00 0.00 3.06
3257 3750 0.038744 CCCCCTGACATCTGCAAGTT 59.961 55.000 0.00 0.00 33.76 2.66
3260 3753 1.457346 CCTGACATCTGCAAGTTCCC 58.543 55.000 0.00 0.00 33.76 3.97
3288 3781 2.948979 TCGCATACCAATTCCATGAACC 59.051 45.455 0.00 0.00 0.00 3.62
3311 3804 9.753674 AACCTATTTCTGGAATGTAGAATTTGA 57.246 29.630 0.00 0.00 34.42 2.69
3339 3837 9.247861 AGAGGTAAATAAATCAGCAAGATTGTT 57.752 29.630 5.33 2.39 46.09 2.83
3373 3871 7.732222 AACTTGCAAGATATTTATTTCCCCA 57.268 32.000 32.50 0.00 0.00 4.96
3420 3920 6.886178 ACCACTTAGGAGAAATAGGCTTAA 57.114 37.500 0.00 0.00 41.22 1.85
3484 3984 4.692625 ACATGCCGCATTATCTTCATAGAC 59.307 41.667 2.16 0.00 31.99 2.59
3485 3985 4.607293 TGCCGCATTATCTTCATAGACT 57.393 40.909 0.00 0.00 31.99 3.24
3486 3986 4.960938 TGCCGCATTATCTTCATAGACTT 58.039 39.130 0.00 0.00 31.99 3.01
3487 3987 5.368145 TGCCGCATTATCTTCATAGACTTT 58.632 37.500 0.00 0.00 31.99 2.66
3488 3988 5.822519 TGCCGCATTATCTTCATAGACTTTT 59.177 36.000 0.00 0.00 31.99 2.27
3489 3989 6.138761 GCCGCATTATCTTCATAGACTTTTG 58.861 40.000 0.00 0.00 31.99 2.44
3490 3990 6.017934 GCCGCATTATCTTCATAGACTTTTGA 60.018 38.462 0.00 0.00 31.99 2.69
3491 3991 7.467267 GCCGCATTATCTTCATAGACTTTTGAA 60.467 37.037 0.00 1.86 31.99 2.69
3492 3992 8.397906 CCGCATTATCTTCATAGACTTTTGAAA 58.602 33.333 3.12 0.00 31.85 2.69
3493 3993 9.214953 CGCATTATCTTCATAGACTTTTGAAAC 57.785 33.333 3.12 0.00 31.85 2.78
3494 3994 9.508567 GCATTATCTTCATAGACTTTTGAAACC 57.491 33.333 3.12 0.00 31.85 3.27
3498 3998 8.924511 ATCTTCATAGACTTTTGAAACCTCAA 57.075 30.769 3.12 0.00 34.90 3.02
3499 3999 9.354673 ATCTTCATAGACTTTTGAAACCTCAAA 57.645 29.630 0.00 0.00 40.17 2.69
3512 4012 8.641499 TTGAAACCTCAAATACATGAAAACAC 57.359 30.769 0.00 0.00 38.65 3.32
3513 4013 7.776107 TGAAACCTCAAATACATGAAAACACA 58.224 30.769 0.00 0.00 0.00 3.72
3514 4014 8.420222 TGAAACCTCAAATACATGAAAACACAT 58.580 29.630 0.00 0.00 0.00 3.21
3526 4026 6.774084 CATGAAAACACATGTATGTCGATCA 58.226 36.000 0.00 0.22 41.59 2.92
3527 4027 6.983474 TGAAAACACATGTATGTCGATCAT 57.017 33.333 0.00 0.00 39.39 2.45
3528 4028 7.376435 TGAAAACACATGTATGTCGATCATT 57.624 32.000 0.00 0.00 39.39 2.57
3529 4029 7.815641 TGAAAACACATGTATGTCGATCATTT 58.184 30.769 0.00 0.00 39.39 2.32
3530 4030 8.940952 TGAAAACACATGTATGTCGATCATTTA 58.059 29.630 0.00 0.00 39.39 1.40
3531 4031 9.210426 GAAAACACATGTATGTCGATCATTTAC 57.790 33.333 0.00 1.52 39.39 2.01
3532 4032 7.841915 AACACATGTATGTCGATCATTTACA 57.158 32.000 0.00 6.11 39.39 2.41
3533 4033 7.234187 ACACATGTATGTCGATCATTTACAC 57.766 36.000 0.00 0.67 39.39 2.90
3534 4034 6.816140 ACACATGTATGTCGATCATTTACACA 59.184 34.615 0.00 5.28 39.39 3.72
3535 4035 7.495606 ACACATGTATGTCGATCATTTACACAT 59.504 33.333 0.00 6.92 39.39 3.21
3536 4036 8.977505 CACATGTATGTCGATCATTTACACATA 58.022 33.333 0.00 0.00 39.39 2.29
3537 4037 9.541143 ACATGTATGTCGATCATTTACACATAA 57.459 29.630 0.00 0.00 35.87 1.90
3540 4040 9.372369 TGTATGTCGATCATTTACACATAAACA 57.628 29.630 5.94 0.00 37.91 2.83
3543 4043 9.720667 ATGTCGATCATTTACACATAAACAATG 57.279 29.630 0.00 0.00 36.07 2.82
3544 4044 8.940952 TGTCGATCATTTACACATAAACAATGA 58.059 29.630 0.00 0.00 39.07 2.57
3545 4045 9.425893 GTCGATCATTTACACATAAACAATGAG 57.574 33.333 0.00 0.00 39.07 2.90
3546 4046 9.161629 TCGATCATTTACACATAAACAATGAGT 57.838 29.630 0.00 0.00 41.54 3.41
3554 4054 9.984190 TTACACATAAACAATGAGTACTACACA 57.016 29.630 0.00 0.00 40.14 3.72
3555 4055 8.306680 ACACATAAACAATGAGTACTACACAC 57.693 34.615 0.00 0.00 37.59 3.82
3556 4056 7.929245 ACACATAAACAATGAGTACTACACACA 59.071 33.333 0.00 0.00 37.59 3.72
3557 4057 8.769891 CACATAAACAATGAGTACTACACACAA 58.230 33.333 0.00 0.00 39.07 3.33
3558 4058 9.332502 ACATAAACAATGAGTACTACACACAAA 57.667 29.630 0.00 0.00 39.07 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.218019 ACACGTAACAATAGCTGTAGAAACA 58.782 36.000 0.00 0.00 37.23 2.83
14 15 6.701432 ACACGTAACAATAGCTGTAGAAAC 57.299 37.500 0.00 0.00 37.23 2.78
15 16 7.569297 CAAACACGTAACAATAGCTGTAGAAA 58.431 34.615 0.00 0.00 37.23 2.52
16 17 6.347079 GCAAACACGTAACAATAGCTGTAGAA 60.347 38.462 0.00 0.00 37.23 2.10
17 18 5.119588 GCAAACACGTAACAATAGCTGTAGA 59.880 40.000 0.00 0.00 37.23 2.59
18 19 5.120208 AGCAAACACGTAACAATAGCTGTAG 59.880 40.000 0.00 0.00 37.23 2.74
19 20 4.992319 AGCAAACACGTAACAATAGCTGTA 59.008 37.500 0.00 0.00 37.23 2.74
20 21 3.813166 AGCAAACACGTAACAATAGCTGT 59.187 39.130 0.00 0.00 41.27 4.40
21 22 4.151070 CAGCAAACACGTAACAATAGCTG 58.849 43.478 0.00 0.00 40.57 4.24
22 23 3.364964 GCAGCAAACACGTAACAATAGCT 60.365 43.478 0.00 0.00 0.00 3.32
23 24 2.908626 GCAGCAAACACGTAACAATAGC 59.091 45.455 0.00 0.00 0.00 2.97
24 25 4.151070 CAGCAGCAAACACGTAACAATAG 58.849 43.478 0.00 0.00 0.00 1.73
25 26 3.562141 ACAGCAGCAAACACGTAACAATA 59.438 39.130 0.00 0.00 0.00 1.90
26 27 2.357637 ACAGCAGCAAACACGTAACAAT 59.642 40.909 0.00 0.00 0.00 2.71
27 28 1.740585 ACAGCAGCAAACACGTAACAA 59.259 42.857 0.00 0.00 0.00 2.83
28 29 1.374560 ACAGCAGCAAACACGTAACA 58.625 45.000 0.00 0.00 0.00 2.41
29 30 2.468532 AACAGCAGCAAACACGTAAC 57.531 45.000 0.00 0.00 0.00 2.50
30 31 3.608241 GCATAACAGCAGCAAACACGTAA 60.608 43.478 0.00 0.00 0.00 3.18
31 32 2.095969 GCATAACAGCAGCAAACACGTA 60.096 45.455 0.00 0.00 0.00 3.57
32 33 1.334960 GCATAACAGCAGCAAACACGT 60.335 47.619 0.00 0.00 0.00 4.49
33 34 1.330306 GCATAACAGCAGCAAACACG 58.670 50.000 0.00 0.00 0.00 4.49
34 35 2.420628 TGCATAACAGCAGCAAACAC 57.579 45.000 0.00 0.00 40.11 3.32
52 53 6.369005 CAAACTAGAAGAACAGCAAGACATG 58.631 40.000 0.00 0.00 0.00 3.21
53 54 5.049129 GCAAACTAGAAGAACAGCAAGACAT 60.049 40.000 0.00 0.00 0.00 3.06
54 55 4.273480 GCAAACTAGAAGAACAGCAAGACA 59.727 41.667 0.00 0.00 0.00 3.41
55 56 4.513318 AGCAAACTAGAAGAACAGCAAGAC 59.487 41.667 0.00 0.00 0.00 3.01
56 57 4.708177 AGCAAACTAGAAGAACAGCAAGA 58.292 39.130 0.00 0.00 0.00 3.02
69 70 6.327934 AGCATGCAAAAATCTAGCAAACTAG 58.672 36.000 21.98 0.00 46.30 2.57
70 71 6.271488 AGCATGCAAAAATCTAGCAAACTA 57.729 33.333 21.98 0.00 42.15 2.24
71 72 5.143376 AGCATGCAAAAATCTAGCAAACT 57.857 34.783 21.98 0.00 42.15 2.66
72 73 6.095377 ACTAGCATGCAAAAATCTAGCAAAC 58.905 36.000 21.98 0.00 42.15 2.93
73 74 6.271488 ACTAGCATGCAAAAATCTAGCAAA 57.729 33.333 21.98 0.00 42.15 3.68
74 75 5.902613 ACTAGCATGCAAAAATCTAGCAA 57.097 34.783 21.98 0.00 42.15 3.91
75 76 6.994496 AGATACTAGCATGCAAAAATCTAGCA 59.006 34.615 21.98 1.80 43.14 3.49
76 77 7.387397 AGAGATACTAGCATGCAAAAATCTAGC 59.613 37.037 21.98 10.95 32.23 3.42
77 78 8.830201 AGAGATACTAGCATGCAAAAATCTAG 57.170 34.615 21.98 12.95 34.48 2.43
78 79 9.265901 GAAGAGATACTAGCATGCAAAAATCTA 57.734 33.333 21.98 0.00 0.00 1.98
79 80 7.992033 AGAAGAGATACTAGCATGCAAAAATCT 59.008 33.333 21.98 20.35 0.00 2.40
80 81 8.152309 AGAAGAGATACTAGCATGCAAAAATC 57.848 34.615 21.98 16.21 0.00 2.17
81 82 9.270640 CTAGAAGAGATACTAGCATGCAAAAAT 57.729 33.333 21.98 7.90 31.50 1.82
82 83 8.260818 ACTAGAAGAGATACTAGCATGCAAAAA 58.739 33.333 21.98 2.60 39.47 1.94
83 84 7.786030 ACTAGAAGAGATACTAGCATGCAAAA 58.214 34.615 21.98 3.70 39.47 2.44
84 85 7.068716 TGACTAGAAGAGATACTAGCATGCAAA 59.931 37.037 21.98 6.52 39.47 3.68
85 86 6.547510 TGACTAGAAGAGATACTAGCATGCAA 59.452 38.462 21.98 2.20 39.47 4.08
86 87 6.064717 TGACTAGAAGAGATACTAGCATGCA 58.935 40.000 21.98 5.01 39.47 3.96
87 88 6.567687 TGACTAGAAGAGATACTAGCATGC 57.432 41.667 10.51 10.51 39.47 4.06
88 89 8.334263 TCATGACTAGAAGAGATACTAGCATG 57.666 38.462 19.52 19.52 42.96 4.06
89 90 8.932434 TTCATGACTAGAAGAGATACTAGCAT 57.068 34.615 0.00 0.00 39.47 3.79
90 91 8.932434 ATTCATGACTAGAAGAGATACTAGCA 57.068 34.615 0.00 0.00 39.47 3.49
118 119 9.638239 GGCAAGTTCATGATTAATTTCAGTAAA 57.362 29.630 0.00 0.00 0.00 2.01
119 120 9.023962 AGGCAAGTTCATGATTAATTTCAGTAA 57.976 29.630 0.00 0.00 0.00 2.24
120 121 8.579850 AGGCAAGTTCATGATTAATTTCAGTA 57.420 30.769 0.00 0.00 0.00 2.74
121 122 7.472334 AGGCAAGTTCATGATTAATTTCAGT 57.528 32.000 0.00 0.00 0.00 3.41
128 129 9.639563 TGGAATATTAGGCAAGTTCATGATTAA 57.360 29.630 0.00 0.00 0.00 1.40
129 130 9.639563 TTGGAATATTAGGCAAGTTCATGATTA 57.360 29.630 0.00 0.00 0.00 1.75
130 131 8.416329 GTTGGAATATTAGGCAAGTTCATGATT 58.584 33.333 0.00 0.00 0.00 2.57
131 132 7.560991 TGTTGGAATATTAGGCAAGTTCATGAT 59.439 33.333 0.00 0.00 0.00 2.45
132 133 6.889177 TGTTGGAATATTAGGCAAGTTCATGA 59.111 34.615 0.00 0.00 0.00 3.07
133 134 7.099266 TGTTGGAATATTAGGCAAGTTCATG 57.901 36.000 0.00 0.00 0.00 3.07
134 135 7.716799 TTGTTGGAATATTAGGCAAGTTCAT 57.283 32.000 0.00 0.00 0.00 2.57
135 136 7.450014 TCTTTGTTGGAATATTAGGCAAGTTCA 59.550 33.333 0.00 0.00 0.00 3.18
136 137 7.826690 TCTTTGTTGGAATATTAGGCAAGTTC 58.173 34.615 0.00 0.00 0.00 3.01
137 138 7.775053 TCTTTGTTGGAATATTAGGCAAGTT 57.225 32.000 0.00 0.00 0.00 2.66
138 139 7.961326 ATCTTTGTTGGAATATTAGGCAAGT 57.039 32.000 0.00 0.00 0.00 3.16
139 140 9.903682 CATATCTTTGTTGGAATATTAGGCAAG 57.096 33.333 0.00 0.00 0.00 4.01
140 141 8.859090 CCATATCTTTGTTGGAATATTAGGCAA 58.141 33.333 0.00 0.00 31.94 4.52
141 142 8.004215 ACCATATCTTTGTTGGAATATTAGGCA 58.996 33.333 0.00 0.00 34.52 4.75
142 143 8.299570 CACCATATCTTTGTTGGAATATTAGGC 58.700 37.037 0.00 0.00 34.52 3.93
143 144 9.573166 TCACCATATCTTTGTTGGAATATTAGG 57.427 33.333 0.00 0.00 34.52 2.69
145 146 9.066892 GCTCACCATATCTTTGTTGGAATATTA 57.933 33.333 0.00 0.00 34.52 0.98
146 147 7.560991 TGCTCACCATATCTTTGTTGGAATATT 59.439 33.333 0.00 0.00 34.52 1.28
147 148 7.062322 TGCTCACCATATCTTTGTTGGAATAT 58.938 34.615 0.00 0.00 34.52 1.28
148 149 6.422333 TGCTCACCATATCTTTGTTGGAATA 58.578 36.000 0.00 0.00 34.52 1.75
149 150 5.263599 TGCTCACCATATCTTTGTTGGAAT 58.736 37.500 0.00 0.00 34.52 3.01
150 151 4.661222 TGCTCACCATATCTTTGTTGGAA 58.339 39.130 0.00 0.00 34.52 3.53
151 152 4.299586 TGCTCACCATATCTTTGTTGGA 57.700 40.909 0.00 0.00 34.52 3.53
152 153 5.389859 TTTGCTCACCATATCTTTGTTGG 57.610 39.130 0.00 0.00 36.56 3.77
153 154 4.860907 GCTTTGCTCACCATATCTTTGTTG 59.139 41.667 0.00 0.00 0.00 3.33
154 155 4.523943 TGCTTTGCTCACCATATCTTTGTT 59.476 37.500 0.00 0.00 0.00 2.83
155 156 4.081406 TGCTTTGCTCACCATATCTTTGT 58.919 39.130 0.00 0.00 0.00 2.83
156 157 4.707030 TGCTTTGCTCACCATATCTTTG 57.293 40.909 0.00 0.00 0.00 2.77
157 158 4.340381 GGATGCTTTGCTCACCATATCTTT 59.660 41.667 0.00 0.00 0.00 2.52
158 159 3.887716 GGATGCTTTGCTCACCATATCTT 59.112 43.478 0.00 0.00 0.00 2.40
167 168 2.097036 CCATGAAGGATGCTTTGCTCA 58.903 47.619 0.00 0.00 41.22 4.26
204 205 4.390603 TCCGTATTGGTTCAATCAAACTCG 59.609 41.667 0.00 0.00 39.52 4.18
213 214 5.240121 GTCTAACCTTCCGTATTGGTTCAA 58.760 41.667 0.00 0.00 42.38 2.69
223 224 1.969862 CGGTGGTCTAACCTTCCGT 59.030 57.895 18.10 0.00 44.55 4.69
294 297 8.572185 TGTAAGCTACAGTTTTTATTGCATTGA 58.428 29.630 0.00 0.00 34.06 2.57
297 300 8.739039 TCATGTAAGCTACAGTTTTTATTGCAT 58.261 29.630 0.00 0.00 42.77 3.96
309 312 6.615264 ATCTTTGCATCATGTAAGCTACAG 57.385 37.500 0.00 0.00 42.77 2.74
335 338 0.811616 GGAGATTAGCACACGCCAGG 60.812 60.000 0.00 0.00 39.83 4.45
336 339 0.108186 TGGAGATTAGCACACGCCAG 60.108 55.000 0.00 0.00 39.83 4.85
341 344 6.159988 GGTATGATACTGGAGATTAGCACAC 58.840 44.000 2.24 0.00 0.00 3.82
364 367 0.310854 GTTGGTTCGACAGGCTTTGG 59.689 55.000 0.00 0.00 0.00 3.28
368 371 1.371558 GAGGTTGGTTCGACAGGCT 59.628 57.895 0.00 0.00 0.00 4.58
369 372 1.671379 GGAGGTTGGTTCGACAGGC 60.671 63.158 0.00 0.00 0.00 4.85
371 374 0.032952 TTCGGAGGTTGGTTCGACAG 59.967 55.000 0.00 0.00 0.00 3.51
375 378 0.601558 TCTCTTCGGAGGTTGGTTCG 59.398 55.000 0.00 0.00 42.08 3.95
382 385 0.615261 GGGTCCTTCTCTTCGGAGGT 60.615 60.000 0.00 0.00 42.08 3.85
388 391 1.909302 TGTGGATGGGTCCTTCTCTTC 59.091 52.381 3.43 0.00 45.32 2.87
389 392 1.912043 CTGTGGATGGGTCCTTCTCTT 59.088 52.381 3.43 0.00 45.32 2.85
466 469 5.163854 GGATGTTCACGAAGATGTTTACCAG 60.164 44.000 0.00 0.00 0.00 4.00
481 484 8.846943 TGTGACATTATATATGGGATGTTCAC 57.153 34.615 18.62 18.62 33.21 3.18
506 512 7.504924 TTTGTCGGAGTATGTGAAAGAAATT 57.495 32.000 0.00 0.00 0.00 1.82
510 516 5.237779 GGTTTTTGTCGGAGTATGTGAAAGA 59.762 40.000 0.00 0.00 0.00 2.52
525 531 9.419297 GGACTCATTTTATTTAGGGTTTTTGTC 57.581 33.333 0.00 0.00 0.00 3.18
529 535 9.475620 CCTAGGACTCATTTTATTTAGGGTTTT 57.524 33.333 1.05 0.00 0.00 2.43
530 536 8.621073 ACCTAGGACTCATTTTATTTAGGGTTT 58.379 33.333 17.98 0.00 32.60 3.27
544 550 5.249393 ACATGAACTTCAACCTAGGACTCAT 59.751 40.000 17.98 9.03 0.00 2.90
570 576 7.148787 CGTGTTCATCTTTGAAGTAAGTCCTAC 60.149 40.741 0.00 0.00 42.41 3.18
576 582 6.771188 AGACGTGTTCATCTTTGAAGTAAG 57.229 37.500 0.00 0.00 42.41 2.34
630 642 2.159099 GGCAGCCCATTAAAAAGGTAGC 60.159 50.000 0.00 0.00 0.00 3.58
631 643 2.430694 GGGCAGCCCATTAAAAAGGTAG 59.569 50.000 27.33 0.00 44.65 3.18
717 735 2.292828 ACATGTGCTGCCTACCTTTT 57.707 45.000 0.00 0.00 0.00 2.27
718 736 2.305927 AGTACATGTGCTGCCTACCTTT 59.694 45.455 16.23 0.00 0.00 3.11
721 739 1.207089 TCAGTACATGTGCTGCCTACC 59.793 52.381 31.96 0.76 42.03 3.18
722 740 2.672961 TCAGTACATGTGCTGCCTAC 57.327 50.000 31.96 11.32 42.03 3.18
723 741 4.321230 CGATATCAGTACATGTGCTGCCTA 60.321 45.833 31.96 25.31 42.03 3.93
724 742 3.553715 CGATATCAGTACATGTGCTGCCT 60.554 47.826 31.96 24.28 42.03 4.75
725 743 2.733552 CGATATCAGTACATGTGCTGCC 59.266 50.000 31.96 20.74 42.03 4.85
726 744 3.384668 ACGATATCAGTACATGTGCTGC 58.615 45.455 31.96 19.89 42.03 5.25
727 745 5.050769 GGAAACGATATCAGTACATGTGCTG 60.051 44.000 31.24 31.24 43.36 4.41
729 747 5.330271 GGAAACGATATCAGTACATGTGC 57.670 43.478 9.11 7.34 0.00 4.57
897 1326 0.174389 ATCGTGCTGCTTCGATCTGT 59.826 50.000 20.52 6.64 41.93 3.41
898 1327 2.969157 ATCGTGCTGCTTCGATCTG 58.031 52.632 20.52 0.00 41.93 2.90
901 1330 2.233654 GCGATCGTGCTGCTTCGAT 61.234 57.895 24.05 24.05 47.00 3.59
902 1331 2.880879 GCGATCGTGCTGCTTCGA 60.881 61.111 17.81 18.41 40.28 3.71
903 1332 3.918220 GGCGATCGTGCTGCTTCG 61.918 66.667 17.81 6.34 34.52 3.79
904 1333 2.806856 CTGGCGATCGTGCTGCTTC 61.807 63.158 17.81 0.00 34.52 3.86
905 1334 2.816958 CTGGCGATCGTGCTGCTT 60.817 61.111 17.81 0.00 34.52 3.91
906 1335 4.827087 CCTGGCGATCGTGCTGCT 62.827 66.667 17.81 0.00 34.52 4.24
926 1355 1.208009 CTTCGATCTCTCGCTGCTGC 61.208 60.000 5.34 5.34 44.65 5.25
927 1356 1.208009 GCTTCGATCTCTCGCTGCTG 61.208 60.000 0.00 0.00 44.65 4.41
928 1357 1.065600 GCTTCGATCTCTCGCTGCT 59.934 57.895 0.00 0.00 44.65 4.24
929 1358 1.208009 CTGCTTCGATCTCTCGCTGC 61.208 60.000 0.00 0.00 44.65 5.25
930 1359 1.208009 GCTGCTTCGATCTCTCGCTG 61.208 60.000 0.00 0.00 44.65 5.18
936 1365 0.368227 CGTGTTGCTGCTTCGATCTC 59.632 55.000 0.00 0.00 0.00 2.75
1443 1882 0.986527 ACTCAGACATGATGGTGGCA 59.013 50.000 0.00 0.00 34.12 4.92
1458 1897 2.750948 GTCTTCTTGTTGGCGTACTCA 58.249 47.619 0.00 0.00 0.00 3.41
1586 2025 4.814294 CGACCTGGTACGCTGGCC 62.814 72.222 0.00 0.00 0.00 5.36
1710 2149 4.112341 GTGTACCGCGCCGTCTCT 62.112 66.667 4.22 0.00 0.00 3.10
2111 2568 0.803768 CACGAGCTGGATCCAGAACG 60.804 60.000 40.29 37.82 46.30 3.95
2677 3134 3.129813 AGTTCTAGTCACGACACACACAA 59.870 43.478 0.00 0.00 0.00 3.33
2678 3135 2.686405 AGTTCTAGTCACGACACACACA 59.314 45.455 0.00 0.00 0.00 3.72
2679 3136 3.351020 AGTTCTAGTCACGACACACAC 57.649 47.619 0.00 0.00 0.00 3.82
2680 3137 4.109766 CAAAGTTCTAGTCACGACACACA 58.890 43.478 0.00 0.00 0.00 3.72
2681 3138 3.489785 CCAAAGTTCTAGTCACGACACAC 59.510 47.826 0.00 0.00 0.00 3.82
2682 3139 3.491964 CCCAAAGTTCTAGTCACGACACA 60.492 47.826 0.00 0.00 0.00 3.72
2693 3150 6.955851 ACTGTATACACCTACCCAAAGTTCTA 59.044 38.462 0.08 0.00 0.00 2.10
2694 3151 5.783875 ACTGTATACACCTACCCAAAGTTCT 59.216 40.000 0.08 0.00 0.00 3.01
2703 3160 9.439500 TGACAAAATTTACTGTATACACCTACC 57.561 33.333 0.08 0.00 0.00 3.18
2796 3254 7.502226 TCTTGATGCTTCCTTTCTCTAACAAAA 59.498 33.333 0.00 0.00 0.00 2.44
2915 3374 4.492791 TGACAGTTCAATCGTTCGACTA 57.507 40.909 0.00 0.00 0.00 2.59
2923 3382 5.415366 CGATCGTTAATGACAGTTCAATCG 58.585 41.667 7.03 0.00 34.61 3.34
2947 3406 0.806492 GGAACCGACGCATCTTCTCC 60.806 60.000 0.00 0.00 0.00 3.71
3063 3530 4.080807 TGGTCAAGCATAGATTACGGGAAA 60.081 41.667 0.00 0.00 0.00 3.13
3069 3536 8.839310 ATTCTACATGGTCAAGCATAGATTAC 57.161 34.615 0.00 0.00 0.00 1.89
3111 3586 6.882768 AGGAGAACCTTTTGAGATGATAGT 57.117 37.500 0.00 0.00 45.36 2.12
3188 3670 6.331061 AGACGTCACATTACACTATTTCTCC 58.669 40.000 19.50 0.00 0.00 3.71
3191 3674 7.576750 TCAAGACGTCACATTACACTATTTC 57.423 36.000 19.50 0.00 0.00 2.17
3193 3676 6.926826 TGTTCAAGACGTCACATTACACTATT 59.073 34.615 19.50 0.00 0.00 1.73
3208 3693 3.653344 TGAGATGTCCTTGTTCAAGACG 58.347 45.455 13.29 0.00 33.09 4.18
3223 3713 1.912043 AGGGGGTGTCTTCTTGAGATG 59.088 52.381 0.00 0.00 36.61 2.90
3236 3726 0.679002 CTTGCAGATGTCAGGGGGTG 60.679 60.000 0.00 0.00 0.00 4.61
3248 3741 2.783135 GATGACTTGGGAACTTGCAGA 58.217 47.619 0.00 0.00 0.00 4.26
3257 3750 1.199615 TGGTATGCGATGACTTGGGA 58.800 50.000 0.00 0.00 0.00 4.37
3260 3753 3.627123 TGGAATTGGTATGCGATGACTTG 59.373 43.478 0.00 0.00 0.00 3.16
3391 3889 8.168058 AGCCTATTTCTCCTAAGTGGTTTTTAA 58.832 33.333 0.00 0.00 37.07 1.52
3392 3890 7.696017 AGCCTATTTCTCCTAAGTGGTTTTTA 58.304 34.615 0.00 0.00 37.07 1.52
3414 3914 7.976135 ACATCAAGAGTGATATCATTAAGCC 57.024 36.000 9.02 0.00 42.88 4.35
3427 3927 6.185852 TGCAAACATGATACATCAAGAGTG 57.814 37.500 0.00 0.00 40.69 3.51
3487 3987 8.253810 TGTGTTTTCATGTATTTGAGGTTTCAA 58.746 29.630 0.00 0.00 41.44 2.69
3488 3988 7.776107 TGTGTTTTCATGTATTTGAGGTTTCA 58.224 30.769 0.00 0.00 0.00 2.69
3489 3989 8.702438 CATGTGTTTTCATGTATTTGAGGTTTC 58.298 33.333 0.00 0.00 39.93 2.78
3490 3990 8.592105 CATGTGTTTTCATGTATTTGAGGTTT 57.408 30.769 0.00 0.00 39.93 3.27
3502 4002 7.911727 AATGATCGACATACATGTGTTTTCATG 59.088 33.333 9.11 5.53 42.82 3.07
3503 4003 6.983474 TGATCGACATACATGTGTTTTCAT 57.017 33.333 9.11 0.00 41.95 2.57
3504 4004 6.983474 ATGATCGACATACATGTGTTTTCA 57.017 33.333 9.11 4.38 41.95 2.69
3505 4005 9.210426 GTAAATGATCGACATACATGTGTTTTC 57.790 33.333 9.11 0.00 41.95 2.29
3506 4006 8.726068 TGTAAATGATCGACATACATGTGTTTT 58.274 29.630 9.11 0.00 41.95 2.43
3507 4007 8.175069 GTGTAAATGATCGACATACATGTGTTT 58.825 33.333 9.11 0.00 41.95 2.83
3508 4008 7.333174 TGTGTAAATGATCGACATACATGTGTT 59.667 33.333 9.11 0.00 41.95 3.32
3509 4009 6.816140 TGTGTAAATGATCGACATACATGTGT 59.184 34.615 9.11 0.00 41.95 3.72
3510 4010 7.232945 TGTGTAAATGATCGACATACATGTG 57.767 36.000 9.11 0.00 41.95 3.21
3511 4011 9.541143 TTATGTGTAAATGATCGACATACATGT 57.459 29.630 2.69 2.69 45.16 3.21
3514 4014 9.372369 TGTTTATGTGTAAATGATCGACATACA 57.628 29.630 0.00 0.00 38.38 2.29
3517 4017 9.720667 CATTGTTTATGTGTAAATGATCGACAT 57.279 29.630 0.00 0.00 41.45 3.06
3518 4018 8.940952 TCATTGTTTATGTGTAAATGATCGACA 58.059 29.630 0.00 0.00 33.50 4.35
3519 4019 9.425893 CTCATTGTTTATGTGTAAATGATCGAC 57.574 33.333 0.00 0.00 36.83 4.20
3520 4020 9.161629 ACTCATTGTTTATGTGTAAATGATCGA 57.838 29.630 0.00 0.00 38.75 3.59
3528 4028 9.984190 TGTGTAGTACTCATTGTTTATGTGTAA 57.016 29.630 0.00 0.00 41.99 2.41
3529 4029 9.414295 GTGTGTAGTACTCATTGTTTATGTGTA 57.586 33.333 0.00 0.00 40.44 2.90
3530 4030 7.929245 TGTGTGTAGTACTCATTGTTTATGTGT 59.071 33.333 0.00 0.00 42.12 3.72
3531 4031 8.305441 TGTGTGTAGTACTCATTGTTTATGTG 57.695 34.615 0.00 0.00 35.64 3.21
3532 4032 8.896320 TTGTGTGTAGTACTCATTGTTTATGT 57.104 30.769 0.00 0.00 35.64 2.29


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

AutoCloner maintained by Alex Coulton.