Multiple sequence alignment - TraesCS7A01G391400

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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 TraesCS7A01G391400 chr7A 100.000 6030 0 0 1 6030 567507521 567501492 0.000000e+00 11136.0
1 TraesCS7A01G391400 chr7A 100.000 429 0 0 6324 6752 567501198 567500770 0.000000e+00 793.0
2 TraesCS7A01G391400 chr7A 91.879 431 25 4 6324 6752 6958839 6958417 1.620000e-165 593.0
3 TraesCS7A01G391400 chr7A 95.570 158 7 0 5873 6030 685864620 685864777 3.130000e-63 254.0
4 TraesCS7A01G391400 chr7D 94.944 5340 175 37 579 5868 500999257 500993963 0.000000e+00 8277.0
5 TraesCS7A01G391400 chr7D 92.157 153 11 1 5879 6030 10065102 10064950 1.470000e-51 215.0
6 TraesCS7A01G391400 chr7B 95.395 1911 70 14 3128 5032 530002229 530000331 0.000000e+00 3025.0
7 TraesCS7A01G391400 chr7B 91.115 2161 104 35 528 2632 530004981 530002853 0.000000e+00 2846.0
8 TraesCS7A01G391400 chr7B 96.970 429 12 1 2679 3107 530002858 530002431 0.000000e+00 719.0
9 TraesCS7A01G391400 chr7B 92.886 492 25 6 5387 5868 529990813 529990322 0.000000e+00 706.0
10 TraesCS7A01G391400 chr7B 98.061 361 7 0 5030 5390 529991197 529990837 4.440000e-176 628.0
11 TraesCS7A01G391400 chr7B 85.021 474 44 8 65 520 530005564 530005100 2.220000e-124 457.0
12 TraesCS7A01G391400 chr7B 91.875 160 12 1 5871 6030 1816435 1816593 8.810000e-54 222.0
13 TraesCS7A01G391400 chr7B 94.595 74 4 0 1 74 530013518 530013445 1.540000e-21 115.0
14 TraesCS7A01G391400 chr1A 97.436 429 10 1 6324 6752 24351208 24351635 0.000000e+00 730.0
15 TraesCS7A01G391400 chr1A 97.835 231 5 0 5030 5260 33032529 33032299 3.790000e-107 399.0
16 TraesCS7A01G391400 chr1A 94.969 159 8 0 5872 6030 19703203 19703045 4.040000e-62 250.0
17 TraesCS7A01G391400 chr4A 96.970 429 13 0 6324 6752 32062601 32062173 0.000000e+00 721.0
18 TraesCS7A01G391400 chr4A 96.737 429 13 1 6324 6752 476313240 476312813 0.000000e+00 713.0
19 TraesCS7A01G391400 chr4A 94.872 429 22 0 6324 6752 293373491 293373919 0.000000e+00 671.0
20 TraesCS7A01G391400 chr4A 98.268 231 4 0 5030 5260 406151102 406151332 8.150000e-109 405.0
21 TraesCS7A01G391400 chr3B 96.503 429 14 1 6324 6752 419772620 419772193 0.000000e+00 708.0
22 TraesCS7A01G391400 chr3B 100.000 39 0 0 5419 5457 581684489 581684451 9.390000e-09 73.1
23 TraesCS7A01G391400 chr3A 96.253 427 16 0 6324 6750 158201480 158201906 0.000000e+00 701.0
24 TraesCS7A01G391400 chr3A 96.875 160 4 1 5872 6030 158200830 158200989 4.010000e-67 267.0
25 TraesCS7A01G391400 chr3A 78.571 140 25 4 31 168 374080020 374079884 3.350000e-13 87.9
26 TraesCS7A01G391400 chr3A 91.304 46 1 3 421 466 521576966 521577008 7.310000e-05 60.2
27 TraesCS7A01G391400 chr6A 94.872 429 13 1 6324 6752 616107878 616107459 0.000000e+00 662.0
28 TraesCS7A01G391400 chr6A 99.371 159 1 0 5872 6030 616108254 616108096 8.570000e-74 289.0
29 TraesCS7A01G391400 chr5A 94.911 393 20 0 6324 6716 547538913 547538521 3.460000e-172 616.0
30 TraesCS7A01G391400 chr5A 94.969 159 8 0 5872 6030 547539305 547539147 4.040000e-62 250.0
31 TraesCS7A01G391400 chr5A 91.034 145 13 0 1040 1184 681010391 681010247 5.340000e-46 196.0
32 TraesCS7A01G391400 chr5A 83.246 191 24 7 172 360 602260138 602259954 1.160000e-37 169.0
33 TraesCS7A01G391400 chrUn 97.835 231 5 0 5030 5260 242425604 242425834 3.790000e-107 399.0
34 TraesCS7A01G391400 chrUn 97.835 231 5 0 5030 5260 367351498 367351268 3.790000e-107 399.0
35 TraesCS7A01G391400 chrUn 97.835 231 5 0 5030 5260 432439023 432439253 3.790000e-107 399.0
36 TraesCS7A01G391400 chrUn 80.488 123 21 2 32 152 240898172 240898293 2.590000e-14 91.6
37 TraesCS7A01G391400 chrUn 80.488 123 21 2 32 152 270113167 270113288 2.590000e-14 91.6
38 TraesCS7A01G391400 chrUn 80.488 123 21 2 32 152 275229851 275229972 2.590000e-14 91.6
39 TraesCS7A01G391400 chrUn 80.488 123 21 2 32 152 307536044 307535923 2.590000e-14 91.6
40 TraesCS7A01G391400 chr1B 97.835 231 5 0 5030 5260 130982392 130982622 3.790000e-107 399.0
41 TraesCS7A01G391400 chr1B 97.835 231 5 0 5030 5260 416390923 416390693 3.790000e-107 399.0
42 TraesCS7A01G391400 chr2B 94.268 157 9 0 5874 6030 133162399 133162555 2.430000e-59 241.0
43 TraesCS7A01G391400 chr2B 80.952 126 15 7 31 152 776745984 776746104 2.590000e-14 91.6
44 TraesCS7A01G391400 chr4B 91.613 155 13 0 5876 6030 601281042 601280888 1.470000e-51 215.0
45 TraesCS7A01G391400 chr4B 89.610 154 16 0 1031 1184 643657525 643657372 5.340000e-46 196.0
46 TraesCS7A01G391400 chr4D 91.176 136 12 0 1049 1184 500342942 500342807 1.160000e-42 185.0
47 TraesCS7A01G391400 chr4D 97.297 37 1 0 4053 4089 57027747 57027783 5.650000e-06 63.9
48 TraesCS7A01G391400 chr4D 95.122 41 1 1 426 466 340016997 340016958 5.650000e-06 63.9
49 TraesCS7A01G391400 chr1D 83.432 169 24 3 172 339 192440238 192440073 3.260000e-33 154.0
50 TraesCS7A01G391400 chr1D 97.297 37 1 0 4053 4089 464636389 464636353 5.650000e-06 63.9
51 TraesCS7A01G391400 chr2A 79.032 124 21 4 31 152 374073461 374073341 5.610000e-11 80.5
52 TraesCS7A01G391400 chr2A 97.368 38 1 0 2793 2830 100643887 100643924 1.570000e-06 65.8
53 TraesCS7A01G391400 chr6D 97.297 37 1 0 4053 4089 48150796 48150832 5.650000e-06 63.9
54 TraesCS7A01G391400 chr6D 97.297 37 1 0 4053 4089 289621111 289621075 5.650000e-06 63.9
55 TraesCS7A01G391400 chr3D 97.297 37 1 0 4053 4089 564628522 564628486 5.650000e-06 63.9
56 TraesCS7A01G391400 chr2D 97.297 37 1 0 4053 4089 354810654 354810618 5.650000e-06 63.9


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 TraesCS7A01G391400 chr7A 567500770 567507521 6751 True 5964.50 11136 100.00000 1 6752 2 chr7A.!!$R2 6751
1 TraesCS7A01G391400 chr7D 500993963 500999257 5294 True 8277.00 8277 94.94400 579 5868 1 chr7D.!!$R2 5289
2 TraesCS7A01G391400 chr7B 530000331 530005564 5233 True 1761.75 3025 92.12525 65 5032 4 chr7B.!!$R3 4967
3 TraesCS7A01G391400 chr7B 529990322 529991197 875 True 667.00 706 95.47350 5030 5868 2 chr7B.!!$R2 838
4 TraesCS7A01G391400 chr3A 158200830 158201906 1076 False 484.00 701 96.56400 5872 6750 2 chr3A.!!$F2 878
5 TraesCS7A01G391400 chr6A 616107459 616108254 795 True 475.50 662 97.12150 5872 6752 2 chr6A.!!$R1 880
6 TraesCS7A01G391400 chr5A 547538521 547539305 784 True 433.00 616 94.94000 5872 6716 2 chr5A.!!$R3 844

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
416 435 0.389391 CGGTCCTAGTCATTGGCGAT 59.611 55.000 0.00 0.00 0.00 4.58 F
1339 1518 0.033090 GGTGTTCGACGAAACTCCCT 59.967 55.000 12.67 0.00 37.00 4.20 F
1516 1700 1.135373 GTCAGGAAGCTCGTCGATGAA 60.135 52.381 8.98 0.00 0.00 2.57 F
2367 2560 1.210204 ATGGATGGCACCTGTCCAGT 61.210 55.000 12.66 0.27 44.59 4.00 F
3421 3795 0.822944 TGCCACCAGACAACACATGG 60.823 55.000 0.00 0.00 40.10 3.66 F
4197 4601 0.890996 GGGGTTCTGCAACACTGGAG 60.891 60.000 0.00 0.00 42.15 3.86 F
4565 4969 2.099756 GCAGAGGTAACAATTGATGCCC 59.900 50.000 17.30 10.18 41.41 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1372 1556 0.675083 CACTTGCCAAGTTGCCATGA 59.325 50.000 7.51 0.00 40.46 3.07 R
2515 2708 1.234821 CAGCTGTAACCCGCAAAAGA 58.765 50.000 5.25 0.00 0.00 2.52 R
3094 3287 2.315720 AAAGAGAAAATGCAGCCCCT 57.684 45.000 0.00 0.00 0.00 4.79 R
3658 4062 2.498167 ACTGTTTGCAGGACTTAGCAG 58.502 47.619 4.27 0.79 46.62 4.24 R
4458 4862 0.035458 ACTAGCTTGCTGACCACCAC 59.965 55.000 5.26 0.00 0.00 4.16 R
5638 6072 0.969917 ACTTGCCCGCCATAATGCAA 60.970 50.000 0.00 0.00 41.08 4.08 R
5823 6267 1.448985 TCTTAATCAAGCCACACGCC 58.551 50.000 0.00 0.00 38.78 5.68 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
22 23 5.984695 AAAATCCTTTGCCTCTCTTTACC 57.015 39.130 0.00 0.00 0.00 2.85
23 24 2.762535 TCCTTTGCCTCTCTTTACCG 57.237 50.000 0.00 0.00 0.00 4.02
24 25 1.975680 TCCTTTGCCTCTCTTTACCGT 59.024 47.619 0.00 0.00 0.00 4.83
25 26 2.028385 TCCTTTGCCTCTCTTTACCGTC 60.028 50.000 0.00 0.00 0.00 4.79
26 27 2.347731 CTTTGCCTCTCTTTACCGTCC 58.652 52.381 0.00 0.00 0.00 4.79
27 28 1.344065 TTGCCTCTCTTTACCGTCCA 58.656 50.000 0.00 0.00 0.00 4.02
28 29 1.344065 TGCCTCTCTTTACCGTCCAA 58.656 50.000 0.00 0.00 0.00 3.53
29 30 1.695242 TGCCTCTCTTTACCGTCCAAA 59.305 47.619 0.00 0.00 0.00 3.28
30 31 2.074576 GCCTCTCTTTACCGTCCAAAC 58.925 52.381 0.00 0.00 0.00 2.93
31 32 2.549349 GCCTCTCTTTACCGTCCAAACA 60.549 50.000 0.00 0.00 0.00 2.83
32 33 3.868754 GCCTCTCTTTACCGTCCAAACAT 60.869 47.826 0.00 0.00 0.00 2.71
33 34 3.684788 CCTCTCTTTACCGTCCAAACATG 59.315 47.826 0.00 0.00 0.00 3.21
34 35 4.562757 CCTCTCTTTACCGTCCAAACATGA 60.563 45.833 0.00 0.00 0.00 3.07
35 36 4.963373 TCTCTTTACCGTCCAAACATGAA 58.037 39.130 0.00 0.00 0.00 2.57
36 37 5.369833 TCTCTTTACCGTCCAAACATGAAA 58.630 37.500 0.00 0.00 0.00 2.69
37 38 5.237779 TCTCTTTACCGTCCAAACATGAAAC 59.762 40.000 0.00 0.00 0.00 2.78
38 39 4.276431 TCTTTACCGTCCAAACATGAAACC 59.724 41.667 0.00 0.00 0.00 3.27
39 40 2.358322 ACCGTCCAAACATGAAACCT 57.642 45.000 0.00 0.00 0.00 3.50
40 41 2.661718 ACCGTCCAAACATGAAACCTT 58.338 42.857 0.00 0.00 0.00 3.50
41 42 2.360801 ACCGTCCAAACATGAAACCTTG 59.639 45.455 0.00 0.00 0.00 3.61
42 43 2.621055 CCGTCCAAACATGAAACCTTGA 59.379 45.455 0.00 0.00 0.00 3.02
43 44 3.255642 CCGTCCAAACATGAAACCTTGAT 59.744 43.478 0.00 0.00 0.00 2.57
44 45 4.457603 CCGTCCAAACATGAAACCTTGATA 59.542 41.667 0.00 0.00 0.00 2.15
45 46 5.125417 CCGTCCAAACATGAAACCTTGATAT 59.875 40.000 0.00 0.00 0.00 1.63
46 47 6.350110 CCGTCCAAACATGAAACCTTGATATT 60.350 38.462 0.00 0.00 0.00 1.28
47 48 7.090173 CGTCCAAACATGAAACCTTGATATTT 58.910 34.615 0.00 0.00 0.00 1.40
48 49 7.062138 CGTCCAAACATGAAACCTTGATATTTG 59.938 37.037 0.00 0.00 0.00 2.32
49 50 8.087750 GTCCAAACATGAAACCTTGATATTTGA 58.912 33.333 0.00 0.00 0.00 2.69
50 51 8.814931 TCCAAACATGAAACCTTGATATTTGAT 58.185 29.630 0.00 0.00 0.00 2.57
51 52 9.439500 CCAAACATGAAACCTTGATATTTGATT 57.561 29.630 0.00 0.00 0.00 2.57
55 56 9.807649 ACATGAAACCTTGATATTTGATTAAGC 57.192 29.630 0.00 0.00 0.00 3.09
58 59 9.241919 TGAAACCTTGATATTTGATTAAGCTCA 57.758 29.630 0.00 0.00 0.00 4.26
60 61 9.860898 AAACCTTGATATTTGATTAAGCTCAAC 57.139 29.630 0.00 0.00 34.96 3.18
61 62 8.579850 ACCTTGATATTTGATTAAGCTCAACA 57.420 30.769 0.00 0.00 34.96 3.33
62 63 9.023962 ACCTTGATATTTGATTAAGCTCAACAA 57.976 29.630 0.00 0.00 34.96 2.83
63 64 9.294030 CCTTGATATTTGATTAAGCTCAACAAC 57.706 33.333 0.00 0.00 34.96 3.32
77 78 5.822519 AGCTCAACAACTGTTATTCAACTGA 59.177 36.000 0.00 0.00 37.14 3.41
79 80 6.371809 TCAACAACTGTTATTCAACTGACC 57.628 37.500 0.00 0.00 37.14 4.02
103 104 9.900112 ACCTGATATAACTAGGGTAATCTTCTT 57.100 33.333 0.00 0.00 35.89 2.52
121 122 4.527509 TCTTTGCACACTCCTTAGAGAG 57.472 45.455 0.00 0.00 43.39 3.20
123 124 4.219507 TCTTTGCACACTCCTTAGAGAGAG 59.780 45.833 5.06 0.00 43.39 3.20
127 128 4.588951 TGCACACTCCTTAGAGAGAGAAAA 59.411 41.667 5.06 0.00 43.39 2.29
153 172 5.689383 ATTCTTCATGTTACGTGCAAACT 57.311 34.783 0.00 0.00 0.00 2.66
160 179 5.633601 TCATGTTACGTGCAAACTCTCTTAG 59.366 40.000 0.00 0.00 0.00 2.18
161 180 3.739300 TGTTACGTGCAAACTCTCTTAGC 59.261 43.478 0.00 0.00 0.00 3.09
168 187 5.149977 GTGCAAACTCTCTTAGCATGTTTC 58.850 41.667 0.00 0.00 37.56 2.78
174 193 7.913674 AACTCTCTTAGCATGTTTCTAAAGG 57.086 36.000 0.00 0.00 0.00 3.11
182 201 8.635765 TTAGCATGTTTCTAAAGGTCAGAAAT 57.364 30.769 0.00 0.00 42.35 2.17
305 324 5.582953 TCCTCATGATTTTGGGTTCTCAAT 58.417 37.500 0.00 0.00 0.00 2.57
363 382 8.528044 ACACTTGGTTAACTAATTCAAAAGGA 57.472 30.769 4.74 0.00 0.00 3.36
367 386 9.899226 CTTGGTTAACTAATTCAAAAGGAAGAG 57.101 33.333 4.74 0.00 39.30 2.85
369 388 9.063615 TGGTTAACTAATTCAAAAGGAAGAGAC 57.936 33.333 5.42 0.00 39.30 3.36
391 410 3.294816 GAGTATCTCGATGATGCAGCA 57.705 47.619 7.31 7.31 39.75 4.41
410 429 2.423538 GCAAAATGCGGTCCTAGTCATT 59.576 45.455 0.00 0.00 31.71 2.57
416 435 0.389391 CGGTCCTAGTCATTGGCGAT 59.611 55.000 0.00 0.00 0.00 4.58
419 438 3.391049 GGTCCTAGTCATTGGCGATTAC 58.609 50.000 0.00 0.00 0.00 1.89
424 443 4.386049 CCTAGTCATTGGCGATTACGATTC 59.614 45.833 0.00 0.00 42.66 2.52
425 444 4.060038 AGTCATTGGCGATTACGATTCT 57.940 40.909 0.00 0.00 42.66 2.40
453 472 2.323105 CGTTGCAACGCACGAGTT 59.677 55.556 35.89 0.00 46.06 3.01
466 485 3.661936 CGCACGAGTTCTTTTGCTTAGTC 60.662 47.826 0.00 0.00 32.56 2.59
467 486 3.495001 GCACGAGTTCTTTTGCTTAGTCT 59.505 43.478 0.00 0.00 32.00 3.24
515 534 1.511613 CACTCCACCCTCCATACCAT 58.488 55.000 0.00 0.00 0.00 3.55
520 539 2.057140 CCACCCTCCATACCATGATCA 58.943 52.381 0.00 0.00 0.00 2.92
522 541 2.439135 CACCCTCCATACCATGATCACA 59.561 50.000 0.00 0.00 0.00 3.58
523 542 2.439507 ACCCTCCATACCATGATCACAC 59.560 50.000 0.00 0.00 0.00 3.82
524 543 2.548707 CCCTCCATACCATGATCACACG 60.549 54.545 0.00 0.00 0.00 4.49
525 544 2.365293 CCTCCATACCATGATCACACGA 59.635 50.000 0.00 0.00 0.00 4.35
526 545 3.553715 CCTCCATACCATGATCACACGAG 60.554 52.174 0.00 0.00 0.00 4.18
527 546 3.295973 TCCATACCATGATCACACGAGA 58.704 45.455 0.00 0.00 0.00 4.04
528 547 3.704061 TCCATACCATGATCACACGAGAA 59.296 43.478 0.00 0.00 0.00 2.87
529 548 3.804325 CCATACCATGATCACACGAGAAC 59.196 47.826 0.00 0.00 0.00 3.01
530 549 4.432712 CATACCATGATCACACGAGAACA 58.567 43.478 0.00 0.00 0.00 3.18
531 550 2.964740 ACCATGATCACACGAGAACAG 58.035 47.619 0.00 0.00 0.00 3.16
532 551 2.562738 ACCATGATCACACGAGAACAGA 59.437 45.455 0.00 0.00 0.00 3.41
541 671 5.961272 TCACACGAGAACAGATTAGCAATA 58.039 37.500 0.00 0.00 0.00 1.90
577 707 6.299141 TGTATAATGATCAGAAAAGAGGCCC 58.701 40.000 0.00 0.00 0.00 5.80
578 708 5.659849 ATAATGATCAGAAAAGAGGCCCT 57.340 39.130 0.00 0.00 0.00 5.19
581 711 0.998145 ATCAGAAAAGAGGCCCTGCT 59.002 50.000 0.00 0.00 0.00 4.24
611 741 2.395360 GCGAGCAATACCGCCACAA 61.395 57.895 0.00 0.00 45.06 3.33
613 743 1.423845 GAGCAATACCGCCACAACG 59.576 57.895 0.00 0.00 0.00 4.10
624 755 0.996727 GCCACAACGCGACATGAAAC 60.997 55.000 15.93 0.32 0.00 2.78
687 821 1.299089 CACGACGCTCGCCATATCA 60.299 57.895 0.00 0.00 45.12 2.15
717 851 3.434319 CATGCCGTGCACTCCACC 61.434 66.667 16.19 0.00 43.04 4.61
761 895 2.661566 GCCGCATCCATCGATCACG 61.662 63.158 0.00 0.00 41.26 4.35
854 988 2.033448 TCTCCGTTGGCGCCAAAT 59.967 55.556 41.60 0.00 37.70 2.32
858 992 1.136565 CCGTTGGCGCCAAATACAG 59.863 57.895 41.60 27.35 37.70 2.74
901 1036 0.600057 GCTCTGCCACCCTGAAAAAG 59.400 55.000 0.00 0.00 0.00 2.27
981 1126 2.060980 CCTCCTCCCTCTTCCACCG 61.061 68.421 0.00 0.00 0.00 4.94
1208 1355 3.723922 GCCTCCCCCGTTGCCTAA 61.724 66.667 0.00 0.00 0.00 2.69
1228 1395 2.099141 GCTTTTGCCATTCCTTTCCC 57.901 50.000 0.00 0.00 40.15 3.97
1235 1402 2.225343 TGCCATTCCTTTCCCTGTTCAT 60.225 45.455 0.00 0.00 0.00 2.57
1277 1449 2.805671 CACGTACTGGAATCAGCAAACA 59.194 45.455 0.00 0.00 44.59 2.83
1279 1451 3.244078 ACGTACTGGAATCAGCAAACAGA 60.244 43.478 0.00 0.00 44.59 3.41
1280 1452 3.369147 CGTACTGGAATCAGCAAACAGAG 59.631 47.826 0.00 0.00 44.59 3.35
1281 1453 3.498774 ACTGGAATCAGCAAACAGAGT 57.501 42.857 0.00 0.00 44.59 3.24
1292 1471 2.285834 GCAAACAGAGTGTTGTGACTCG 60.286 50.000 0.00 0.00 46.04 4.18
1300 1479 0.736636 TGTTGTGACTCGTGACTCGT 59.263 50.000 0.00 0.00 40.80 4.18
1339 1518 0.033090 GGTGTTCGACGAAACTCCCT 59.967 55.000 12.67 0.00 37.00 4.20
1369 1553 6.642733 ACCACCCTCCCTTATATGATTATG 57.357 41.667 0.00 0.00 0.00 1.90
1370 1554 6.098446 ACCACCCTCCCTTATATGATTATGT 58.902 40.000 0.00 0.00 0.00 2.29
1371 1555 7.260891 ACCACCCTCCCTTATATGATTATGTA 58.739 38.462 0.00 0.00 0.00 2.29
1372 1556 7.912204 ACCACCCTCCCTTATATGATTATGTAT 59.088 37.037 0.00 0.00 0.00 2.29
1373 1557 8.432805 CCACCCTCCCTTATATGATTATGTATC 58.567 40.741 0.00 0.00 0.00 2.24
1374 1558 8.992349 CACCCTCCCTTATATGATTATGTATCA 58.008 37.037 0.00 0.00 46.86 2.15
1399 1583 3.645884 CAACTTGGCAAGTGAAAGGATG 58.354 45.455 31.75 20.24 41.91 3.51
1400 1584 3.228188 ACTTGGCAAGTGAAAGGATGA 57.772 42.857 30.71 0.00 41.01 2.92
1401 1585 3.771216 ACTTGGCAAGTGAAAGGATGAT 58.229 40.909 30.71 2.33 41.01 2.45
1402 1586 4.922206 ACTTGGCAAGTGAAAGGATGATA 58.078 39.130 30.71 0.00 41.01 2.15
1513 1697 1.429825 CGTCAGGAAGCTCGTCGAT 59.570 57.895 0.00 0.00 0.00 3.59
1516 1700 1.135373 GTCAGGAAGCTCGTCGATGAA 60.135 52.381 8.98 0.00 0.00 2.57
1589 1773 4.543590 ACAGAGGTATGCTATATGCCAC 57.456 45.455 0.00 0.00 42.00 5.01
1629 1813 3.059325 GTCGGAGCATGCTATTGATTGTC 60.059 47.826 22.74 4.58 0.00 3.18
1635 1819 3.063861 GCATGCTATTGATTGTCGTGTCA 59.936 43.478 11.37 0.00 0.00 3.58
1671 1855 4.079558 ACCTAGCACCATGAATTCCTTGAT 60.080 41.667 2.27 0.00 0.00 2.57
1949 2142 9.933723 ATGCTTATTTCCAAAAATAGCATATCC 57.066 29.630 16.43 0.00 42.47 2.59
1955 2148 6.199557 TCCAAAAATAGCATATCCTAGCCA 57.800 37.500 0.00 0.00 0.00 4.75
1996 2189 9.883142 AACTTACCATTGATTTTCAAGTTGAAA 57.117 25.926 23.91 23.91 43.84 2.69
2251 2444 3.634448 CACACCAGGTCATTGTTACCAAA 59.366 43.478 0.00 0.00 39.64 3.28
2367 2560 1.210204 ATGGATGGCACCTGTCCAGT 61.210 55.000 12.66 0.27 44.59 4.00
2515 2708 4.529377 AGAATTGACAATGCAGATTGGGTT 59.471 37.500 8.90 0.00 43.00 4.11
2619 2812 4.596212 TGCTCTGAGGGTCATGAATATGAT 59.404 41.667 6.83 0.00 44.62 2.45
2753 2946 1.879380 TGAAAGAAGTTGGTGATGCCG 59.121 47.619 0.00 0.00 41.21 5.69
2909 3102 6.096564 GCAAGGAATTTGGAATCAAGATCTCT 59.903 38.462 0.00 0.00 37.26 3.10
2911 3104 8.529476 CAAGGAATTTGGAATCAAGATCTCTTT 58.471 33.333 0.00 0.00 33.98 2.52
3049 3242 4.945543 TGCACTTGCTGATGAATTGACTAT 59.054 37.500 2.33 0.00 42.66 2.12
3094 3287 3.492102 GGCAACTGGGAGATATTGCTA 57.508 47.619 7.64 0.00 45.37 3.49
3115 3379 2.974794 AGGGGCTGCATTTTCTCTTTTT 59.025 40.909 0.50 0.00 0.00 1.94
3148 3522 8.034215 TGATCCATACTGTTTTAATTTTGCAGG 58.966 33.333 0.00 0.00 0.00 4.85
3205 3579 2.086610 ATTGGCCAACACTTCCTTGT 57.913 45.000 23.27 0.00 0.00 3.16
3389 3763 3.640029 CCTTGCGGAGTTATACTAGGGAA 59.360 47.826 0.00 0.00 0.00 3.97
3421 3795 0.822944 TGCCACCAGACAACACATGG 60.823 55.000 0.00 0.00 40.10 3.66
3444 3818 4.798574 CCAACTTTGTAAAGGCATCACTC 58.201 43.478 9.00 0.00 40.31 3.51
3534 3908 1.808512 CGGGAGCTAAACACACACACA 60.809 52.381 0.00 0.00 0.00 3.72
3535 3909 1.602377 GGGAGCTAAACACACACACAC 59.398 52.381 0.00 0.00 0.00 3.82
3550 3954 3.559655 ACACACACACACATACACACATC 59.440 43.478 0.00 0.00 0.00 3.06
3576 3980 6.361899 GCATGTCGCACACAAAAATAAAAAT 58.638 32.000 0.00 0.00 38.97 1.82
3618 4022 8.812513 ATCTGATTTAGATCCATGACACAAAA 57.187 30.769 0.00 0.00 42.54 2.44
3625 4029 6.319048 AGATCCATGACACAAAAGGTAGAT 57.681 37.500 0.00 0.00 0.00 1.98
3628 4032 6.867519 TCCATGACACAAAAGGTAGATAGA 57.132 37.500 0.00 0.00 0.00 1.98
3658 4062 8.612619 TCACTGAACTTTAGATTTTGTTCTGAC 58.387 33.333 14.94 0.00 39.23 3.51
4150 4554 2.220824 TGTGCAACTTGTCTTCGATTCG 59.779 45.455 0.00 0.00 38.04 3.34
4197 4601 0.890996 GGGGTTCTGCAACACTGGAG 60.891 60.000 0.00 0.00 42.15 3.86
4295 4699 6.145048 GGCATCTCACAGTTTTGAAATTCTTG 59.855 38.462 0.00 0.00 0.00 3.02
4458 4862 2.517959 TGTTTTCATTGCTCCAGGGAG 58.482 47.619 11.06 11.06 44.56 4.30
4559 4963 5.947228 TTCTTCTGCAGAGGTAACAATTG 57.053 39.130 23.56 3.24 41.41 2.32
4565 4969 2.099756 GCAGAGGTAACAATTGATGCCC 59.900 50.000 17.30 10.18 41.41 5.36
4581 4985 6.068461 TGATGCCCTAACTGGTTATAACAA 57.932 37.500 17.16 5.18 0.00 2.83
4583 4987 6.545666 TGATGCCCTAACTGGTTATAACAATG 59.454 38.462 17.16 8.65 0.00 2.82
4674 5081 5.164233 GTGTTGACTCGATCATCTCTCAAA 58.836 41.667 0.00 0.00 37.11 2.69
4675 5082 5.061560 GTGTTGACTCGATCATCTCTCAAAC 59.938 44.000 0.00 0.00 37.11 2.93
4870 5277 8.964476 ATTATAATTCGACTCACATCTTGGTT 57.036 30.769 0.00 0.00 0.00 3.67
4901 5308 3.444034 GGAGGCACAAGATTTTAAGGACC 59.556 47.826 0.00 0.00 0.00 4.46
5181 5588 6.073058 GCGAAAATGCATACAGAATGATCCTA 60.073 38.462 0.00 0.00 37.86 2.94
5397 5831 7.937649 ACCAATTAACCAACTCTGAAAGTAAC 58.062 34.615 0.00 0.00 37.17 2.50
5424 5858 4.469227 AGCATCTCCAATTCTGTACTGTCT 59.531 41.667 0.00 0.00 0.00 3.41
5622 6056 4.561213 GTGCTGTGGTTTAACAACAGAAAC 59.439 41.667 30.33 23.09 34.15 2.78
5630 6064 6.533367 TGGTTTAACAACAGAAACAATTCAGC 59.467 34.615 0.00 0.00 37.30 4.26
5638 6072 4.578928 ACAGAAACAATTCAGCTTTACGGT 59.421 37.500 0.00 0.00 38.06 4.83
5683 6117 1.968540 GCCACAGTGGAAGCTGGTC 60.969 63.158 24.96 0.00 40.96 4.02
5698 6132 1.790623 CTGGTCACGTTTACAGGTTCG 59.209 52.381 0.00 0.00 0.00 3.95
5704 6138 1.345415 ACGTTTACAGGTTCGATGGGT 59.655 47.619 0.00 0.00 0.00 4.51
5723 6157 4.062991 GGGTTTTTACAGTGTGTCGAGAT 58.937 43.478 5.88 0.00 0.00 2.75
5743 6177 1.266867 ATGGCCCCTTGACAAATGCC 61.267 55.000 0.00 12.92 39.33 4.40
5770 6214 1.024271 ATGTGTGTGTGTGTGGCTTC 58.976 50.000 0.00 0.00 0.00 3.86
5771 6215 0.035534 TGTGTGTGTGTGTGGCTTCT 60.036 50.000 0.00 0.00 0.00 2.85
5823 6267 9.722056 GAGTTGCTGTGTGGATAATAATTTAAG 57.278 33.333 0.00 0.00 0.00 1.85
5824 6268 8.686334 AGTTGCTGTGTGGATAATAATTTAAGG 58.314 33.333 0.00 0.00 0.00 2.69
5825 6269 7.038154 TGCTGTGTGGATAATAATTTAAGGC 57.962 36.000 0.00 0.00 0.00 4.35
5868 6312 4.280436 TGAGTTGGTGTGTGGGTAATAG 57.720 45.455 0.00 0.00 0.00 1.73
5869 6313 3.007635 GAGTTGGTGTGTGGGTAATAGC 58.992 50.000 0.00 0.00 0.00 2.97
5870 6314 1.735571 GTTGGTGTGTGGGTAATAGCG 59.264 52.381 0.00 0.00 0.00 4.26
6639 7305 2.895680 GATCTCAGTGAGGCGGCA 59.104 61.111 19.99 0.31 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.459337 CGGTAAAGAGAGGCAAAGGATTTT 59.541 41.667 0.00 0.00 35.03 1.82
1 2 4.010349 CGGTAAAGAGAGGCAAAGGATTT 58.990 43.478 0.00 0.00 40.26 2.17
2 3 3.009143 ACGGTAAAGAGAGGCAAAGGATT 59.991 43.478 0.00 0.00 0.00 3.01
3 4 2.572104 ACGGTAAAGAGAGGCAAAGGAT 59.428 45.455 0.00 0.00 0.00 3.24
4 5 1.975680 ACGGTAAAGAGAGGCAAAGGA 59.024 47.619 0.00 0.00 0.00 3.36
5 6 2.347731 GACGGTAAAGAGAGGCAAAGG 58.652 52.381 0.00 0.00 0.00 3.11
6 7 2.289444 TGGACGGTAAAGAGAGGCAAAG 60.289 50.000 0.00 0.00 0.00 2.77
7 8 1.695242 TGGACGGTAAAGAGAGGCAAA 59.305 47.619 0.00 0.00 0.00 3.68
8 9 1.344065 TGGACGGTAAAGAGAGGCAA 58.656 50.000 0.00 0.00 0.00 4.52
9 10 1.344065 TTGGACGGTAAAGAGAGGCA 58.656 50.000 0.00 0.00 0.00 4.75
10 11 2.074576 GTTTGGACGGTAAAGAGAGGC 58.925 52.381 0.00 0.00 0.00 4.70
11 12 3.396260 TGTTTGGACGGTAAAGAGAGG 57.604 47.619 0.00 0.00 0.00 3.69
12 13 4.566004 TCATGTTTGGACGGTAAAGAGAG 58.434 43.478 0.00 0.00 0.00 3.20
13 14 4.610605 TCATGTTTGGACGGTAAAGAGA 57.389 40.909 0.00 0.00 0.00 3.10
14 15 5.449304 GTTTCATGTTTGGACGGTAAAGAG 58.551 41.667 0.00 0.00 0.00 2.85
15 16 4.276431 GGTTTCATGTTTGGACGGTAAAGA 59.724 41.667 0.00 0.00 0.00 2.52
16 17 4.277423 AGGTTTCATGTTTGGACGGTAAAG 59.723 41.667 0.00 0.00 0.00 1.85
17 18 4.208746 AGGTTTCATGTTTGGACGGTAAA 58.791 39.130 0.00 0.00 0.00 2.01
18 19 3.822940 AGGTTTCATGTTTGGACGGTAA 58.177 40.909 0.00 0.00 0.00 2.85
19 20 3.495434 AGGTTTCATGTTTGGACGGTA 57.505 42.857 0.00 0.00 0.00 4.02
20 21 2.358322 AGGTTTCATGTTTGGACGGT 57.642 45.000 0.00 0.00 0.00 4.83
21 22 2.621055 TCAAGGTTTCATGTTTGGACGG 59.379 45.455 0.00 0.00 0.00 4.79
22 23 3.980646 TCAAGGTTTCATGTTTGGACG 57.019 42.857 0.00 0.00 0.00 4.79
23 24 8.087750 TCAAATATCAAGGTTTCATGTTTGGAC 58.912 33.333 0.00 0.00 32.45 4.02
24 25 8.187913 TCAAATATCAAGGTTTCATGTTTGGA 57.812 30.769 0.00 0.00 32.45 3.53
25 26 9.439500 AATCAAATATCAAGGTTTCATGTTTGG 57.561 29.630 0.00 0.00 32.45 3.28
29 30 9.807649 GCTTAATCAAATATCAAGGTTTCATGT 57.192 29.630 0.00 0.00 0.00 3.21
32 33 9.241919 TGAGCTTAATCAAATATCAAGGTTTCA 57.758 29.630 0.00 0.00 0.00 2.69
34 35 9.860898 GTTGAGCTTAATCAAATATCAAGGTTT 57.139 29.630 0.00 0.00 40.72 3.27
35 36 9.023962 TGTTGAGCTTAATCAAATATCAAGGTT 57.976 29.630 0.00 0.00 40.72 3.50
36 37 8.579850 TGTTGAGCTTAATCAAATATCAAGGT 57.420 30.769 0.00 0.00 40.72 3.50
37 38 9.294030 GTTGTTGAGCTTAATCAAATATCAAGG 57.706 33.333 0.00 0.00 40.72 3.61
39 40 9.844790 CAGTTGTTGAGCTTAATCAAATATCAA 57.155 29.630 0.00 0.00 40.72 2.57
40 41 9.013229 ACAGTTGTTGAGCTTAATCAAATATCA 57.987 29.630 0.00 0.00 40.72 2.15
41 42 9.846248 AACAGTTGTTGAGCTTAATCAAATATC 57.154 29.630 0.00 0.00 40.72 1.63
45 46 9.677567 GAATAACAGTTGTTGAGCTTAATCAAA 57.322 29.630 7.73 0.00 40.72 2.69
46 47 8.845227 TGAATAACAGTTGTTGAGCTTAATCAA 58.155 29.630 7.73 0.00 38.90 2.57
47 48 8.389779 TGAATAACAGTTGTTGAGCTTAATCA 57.610 30.769 7.73 0.00 38.90 2.57
48 49 9.118236 GTTGAATAACAGTTGTTGAGCTTAATC 57.882 33.333 7.73 0.00 38.90 1.75
49 50 8.850156 AGTTGAATAACAGTTGTTGAGCTTAAT 58.150 29.630 7.73 0.00 39.30 1.40
50 51 8.128582 CAGTTGAATAACAGTTGTTGAGCTTAA 58.871 33.333 7.73 0.00 39.30 1.85
51 52 7.497579 TCAGTTGAATAACAGTTGTTGAGCTTA 59.502 33.333 7.73 0.00 39.30 3.09
52 53 6.318648 TCAGTTGAATAACAGTTGTTGAGCTT 59.681 34.615 7.73 0.00 39.30 3.74
53 54 5.822519 TCAGTTGAATAACAGTTGTTGAGCT 59.177 36.000 7.73 0.00 39.30 4.09
54 55 5.909610 GTCAGTTGAATAACAGTTGTTGAGC 59.090 40.000 7.73 0.00 39.30 4.26
55 56 6.260936 AGGTCAGTTGAATAACAGTTGTTGAG 59.739 38.462 7.73 0.00 39.30 3.02
56 57 6.038161 CAGGTCAGTTGAATAACAGTTGTTGA 59.962 38.462 7.73 0.00 39.30 3.18
57 58 6.038161 TCAGGTCAGTTGAATAACAGTTGTTG 59.962 38.462 7.73 0.00 39.30 3.33
58 59 6.119536 TCAGGTCAGTTGAATAACAGTTGTT 58.880 36.000 2.75 2.75 39.30 2.83
59 60 5.680619 TCAGGTCAGTTGAATAACAGTTGT 58.319 37.500 0.00 0.00 39.30 3.32
60 61 6.808008 ATCAGGTCAGTTGAATAACAGTTG 57.192 37.500 0.00 0.00 39.30 3.16
62 63 9.601217 GTTATATCAGGTCAGTTGAATAACAGT 57.399 33.333 0.00 0.00 39.30 3.55
63 64 9.823647 AGTTATATCAGGTCAGTTGAATAACAG 57.176 33.333 11.61 0.00 39.30 3.16
77 78 9.900112 AAGAAGATTACCCTAGTTATATCAGGT 57.100 33.333 0.00 0.00 0.00 4.00
103 104 3.767711 TCTCTCTCTAAGGAGTGTGCAA 58.232 45.455 0.00 0.00 40.29 4.08
127 128 8.296713 AGTTTGCACGTAACATGAAGAATATTT 58.703 29.630 0.00 0.00 0.00 1.40
134 153 4.449068 AGAGAGTTTGCACGTAACATGAAG 59.551 41.667 0.00 0.00 0.00 3.02
153 172 7.004555 TGACCTTTAGAAACATGCTAAGAGA 57.995 36.000 0.00 0.00 0.00 3.10
160 179 9.860898 AATTATTTCTGACCTTTAGAAACATGC 57.139 29.630 0.00 0.00 44.29 4.06
222 241 8.824159 TGAATACAACATTGGTGTTTAATTGG 57.176 30.769 13.45 0.00 46.07 3.16
259 278 7.665559 AGGATCATACATTTACACACACAAACT 59.334 33.333 0.00 0.00 0.00 2.66
262 281 7.164803 TGAGGATCATACATTTACACACACAA 58.835 34.615 0.00 0.00 42.56 3.33
331 350 8.434392 TGAATTAGTTAACCAAGTGTAAGGAGT 58.566 33.333 0.88 0.00 0.00 3.85
354 373 7.546250 AGATACTCTGTCTCTTCCTTTTGAA 57.454 36.000 0.00 0.00 0.00 2.69
363 382 5.048782 GCATCATCGAGATACTCTGTCTCTT 60.049 44.000 0.00 0.00 39.92 2.85
367 386 4.475028 CTGCATCATCGAGATACTCTGTC 58.525 47.826 0.00 0.00 34.43 3.51
369 388 3.244156 GCTGCATCATCGAGATACTCTG 58.756 50.000 0.00 0.00 34.43 3.35
389 408 1.448985 TGACTAGGACCGCATTTTGC 58.551 50.000 0.00 0.00 40.69 3.68
391 410 3.016736 CCAATGACTAGGACCGCATTTT 58.983 45.455 0.00 0.00 0.00 1.82
402 421 5.223382 AGAATCGTAATCGCCAATGACTAG 58.777 41.667 0.00 0.00 36.96 2.57
437 456 0.027586 AAGAACTCGTGCGTTGCAAC 59.972 50.000 19.89 19.89 41.47 4.17
467 486 9.108284 CGGCACATCCATATGATTATTGTTATA 57.892 33.333 3.65 0.00 36.54 0.98
504 523 2.365293 TCGTGTGATCATGGTATGGAGG 59.635 50.000 0.00 0.00 0.00 4.30
507 526 3.733443 TCTCGTGTGATCATGGTATGG 57.267 47.619 0.00 0.00 0.00 2.74
515 534 4.082245 TGCTAATCTGTTCTCGTGTGATCA 60.082 41.667 0.00 0.00 0.00 2.92
520 539 6.818644 ACAATATTGCTAATCTGTTCTCGTGT 59.181 34.615 15.48 0.00 0.00 4.49
522 541 7.677276 GCAACAATATTGCTAATCTGTTCTCGT 60.677 37.037 15.48 0.00 41.87 4.18
523 542 6.630443 GCAACAATATTGCTAATCTGTTCTCG 59.370 38.462 15.48 0.00 41.87 4.04
524 543 6.914757 GGCAACAATATTGCTAATCTGTTCTC 59.085 38.462 15.48 0.00 44.36 2.87
525 544 6.799512 GGCAACAATATTGCTAATCTGTTCT 58.200 36.000 15.48 0.00 44.36 3.01
577 707 0.167908 TCGCACCGCATTTTAAGCAG 59.832 50.000 0.00 0.00 0.00 4.24
578 708 0.167908 CTCGCACCGCATTTTAAGCA 59.832 50.000 0.00 0.00 0.00 3.91
581 711 0.593618 TTGCTCGCACCGCATTTTAA 59.406 45.000 0.00 0.00 37.22 1.52
611 741 1.599419 GCTTTTGGTTTCATGTCGCGT 60.599 47.619 5.77 0.00 0.00 6.01
613 743 1.000274 AGGCTTTTGGTTTCATGTCGC 60.000 47.619 0.00 0.00 0.00 5.19
624 755 3.652057 TCTTCATAGGGAGGCTTTTGG 57.348 47.619 0.00 0.00 0.00 3.28
674 808 0.799917 CGATCCTGATATGGCGAGCG 60.800 60.000 0.00 0.00 0.00 5.03
743 877 2.661566 CGTGATCGATGGATGCGGC 61.662 63.158 0.54 0.00 39.71 6.53
744 878 2.661566 GCGTGATCGATGGATGCGG 61.662 63.158 0.54 0.00 39.71 5.69
761 895 2.894387 GCTGGCTGATCCGTCTGC 60.894 66.667 4.95 4.95 45.45 4.26
829 963 1.446272 GCCAACGGAGAGGACGAAG 60.446 63.158 0.00 0.00 34.93 3.79
854 988 4.979204 GCAGTGGCGTGTACTGTA 57.021 55.556 14.26 0.00 45.60 2.74
913 1048 3.983420 TGCTTTGGCAGGGGAGGG 61.983 66.667 0.00 0.00 44.28 4.30
945 1090 0.171231 GGAAATCTTGGACAAGCGGC 59.829 55.000 7.18 0.00 38.28 6.53
952 1097 2.171659 GAGGGAGGAGGAAATCTTGGAC 59.828 54.545 0.00 0.00 0.00 4.02
981 1126 3.941657 GAGTGGAGCGGTGGTCAGC 62.942 68.421 0.00 0.00 35.11 4.26
1059 1206 2.946762 GCGAACACCACCTTCAGC 59.053 61.111 0.00 0.00 0.00 4.26
1208 1355 1.625315 GGGAAAGGAATGGCAAAAGCT 59.375 47.619 0.00 0.00 0.00 3.74
1218 1365 3.347216 CGTCATGAACAGGGAAAGGAAT 58.653 45.455 0.00 0.00 0.00 3.01
1220 1367 1.003118 CCGTCATGAACAGGGAAAGGA 59.997 52.381 0.00 0.00 0.00 3.36
1221 1368 1.271379 ACCGTCATGAACAGGGAAAGG 60.271 52.381 15.03 0.00 0.00 3.11
1222 1369 2.185004 ACCGTCATGAACAGGGAAAG 57.815 50.000 15.03 0.00 0.00 2.62
1223 1370 2.226330 CAACCGTCATGAACAGGGAAA 58.774 47.619 15.03 0.00 0.00 3.13
1228 1395 3.961477 TGAAACAACCGTCATGAACAG 57.039 42.857 0.00 0.00 0.00 3.16
1235 1402 1.666700 CTCCGTTTGAAACAACCGTCA 59.333 47.619 8.93 0.00 0.00 4.35
1263 1430 3.213206 ACACTCTGTTTGCTGATTCCA 57.787 42.857 0.00 0.00 0.00 3.53
1266 1433 3.947196 TCACAACACTCTGTTTGCTGATT 59.053 39.130 0.00 0.00 38.77 2.57
1277 1449 2.025155 AGTCACGAGTCACAACACTCT 58.975 47.619 0.00 0.00 40.75 3.24
1279 1451 1.268589 CGAGTCACGAGTCACAACACT 60.269 52.381 2.96 0.00 45.77 3.55
1280 1452 1.121240 CGAGTCACGAGTCACAACAC 58.879 55.000 2.96 0.00 45.77 3.32
1281 1453 0.736636 ACGAGTCACGAGTCACAACA 59.263 50.000 0.00 0.00 45.77 3.33
1292 1471 1.282930 GCCGTTCTTGGACGAGTCAC 61.283 60.000 2.65 0.00 45.47 3.67
1300 1479 2.111999 CTCCAGGTGCCGTTCTTGGA 62.112 60.000 0.00 0.00 0.00 3.53
1339 1518 1.536644 AAGGGAGGGTGGTTTGGTTA 58.463 50.000 0.00 0.00 0.00 2.85
1369 1553 2.493278 ACTTGCCAAGTTGCCATGATAC 59.507 45.455 3.74 0.00 39.04 2.24
1370 1554 2.492881 CACTTGCCAAGTTGCCATGATA 59.507 45.455 7.51 0.00 40.46 2.15
1371 1555 1.274167 CACTTGCCAAGTTGCCATGAT 59.726 47.619 7.51 0.00 40.46 2.45
1372 1556 0.675083 CACTTGCCAAGTTGCCATGA 59.325 50.000 7.51 0.00 40.46 3.07
1373 1557 0.675083 TCACTTGCCAAGTTGCCATG 59.325 50.000 7.51 0.00 40.46 3.66
1374 1558 1.412079 TTCACTTGCCAAGTTGCCAT 58.588 45.000 7.51 0.00 40.46 4.40
1375 1559 1.136695 CTTTCACTTGCCAAGTTGCCA 59.863 47.619 7.51 0.00 40.46 4.92
1376 1560 1.538849 CCTTTCACTTGCCAAGTTGCC 60.539 52.381 7.51 0.00 40.46 4.52
1377 1561 1.408702 TCCTTTCACTTGCCAAGTTGC 59.591 47.619 7.51 0.00 40.46 4.17
1378 1562 3.318839 TCATCCTTTCACTTGCCAAGTTG 59.681 43.478 7.51 2.06 40.46 3.16
1379 1563 3.565307 TCATCCTTTCACTTGCCAAGTT 58.435 40.909 7.51 0.00 40.46 2.66
1380 1564 3.228188 TCATCCTTTCACTTGCCAAGT 57.772 42.857 3.74 3.74 44.06 3.16
1381 1565 5.902613 TTATCATCCTTTCACTTGCCAAG 57.097 39.130 2.11 2.11 0.00 3.61
1382 1566 6.267471 ACTTTTATCATCCTTTCACTTGCCAA 59.733 34.615 0.00 0.00 0.00 4.52
1402 1586 9.389755 ACTGCAAAAACAATTATGGTTACTTTT 57.610 25.926 0.00 0.00 34.67 2.27
1513 1697 1.890876 CATCCACAAACCGTCCTTCA 58.109 50.000 0.00 0.00 0.00 3.02
1516 1700 1.303317 GGCATCCACAAACCGTCCT 60.303 57.895 0.00 0.00 0.00 3.85
1589 1773 1.369209 CGTGCAAAGCAGAACACCG 60.369 57.895 0.00 0.00 40.08 4.94
1671 1855 0.892755 ATACTCAACGACGGCAAGGA 59.107 50.000 0.00 0.00 0.00 3.36
1738 1922 4.526650 AGGCCCAACCATAACAAAGTAAAG 59.473 41.667 0.00 0.00 43.14 1.85
1746 1930 1.133009 ACCAAAGGCCCAACCATAACA 60.133 47.619 0.00 0.00 43.14 2.41
1752 1936 1.745890 GTCAACCAAAGGCCCAACC 59.254 57.895 0.00 0.00 39.61 3.77
2251 2444 5.486526 TGTTCTGGTTTGTTTGCTGAAATT 58.513 33.333 0.00 0.00 0.00 1.82
2367 2560 4.948341 TCTTGTAGCTTGTGTCCTTGTA 57.052 40.909 0.00 0.00 0.00 2.41
2515 2708 1.234821 CAGCTGTAACCCGCAAAAGA 58.765 50.000 5.25 0.00 0.00 2.52
2619 2812 6.656902 AGCTGATCAAATGTGAGATTCCTAA 58.343 36.000 0.00 0.00 37.14 2.69
2749 2942 4.988065 GCTGTAGTCTTGACGGCA 57.012 55.556 0.00 0.00 46.50 5.69
2753 2946 4.683781 CACTCTTTCTGCTGTAGTCTTGAC 59.316 45.833 0.00 0.00 0.00 3.18
2909 3102 6.447084 AGAATAACTTACTCCCATCCAGGAAA 59.553 38.462 0.00 0.00 41.22 3.13
2911 3104 5.538877 AGAATAACTTACTCCCATCCAGGA 58.461 41.667 0.00 0.00 41.22 3.86
3004 3197 8.848182 GTGCATGTATTAGAGTAGGTAGTTACT 58.152 37.037 0.00 0.00 36.61 2.24
3005 3198 8.848182 AGTGCATGTATTAGAGTAGGTAGTTAC 58.152 37.037 0.00 0.00 0.00 2.50
3094 3287 2.315720 AAAGAGAAAATGCAGCCCCT 57.684 45.000 0.00 0.00 0.00 4.79
3124 3388 7.818930 CACCTGCAAAATTAAAACAGTATGGAT 59.181 33.333 0.00 0.00 43.62 3.41
3205 3579 5.007682 GGTTCTTGGCATTCAGTAAGGTTA 58.992 41.667 0.00 0.00 0.00 2.85
3389 3763 6.128486 TGTCTGGTGGCATATGACATATTTT 58.872 36.000 15.89 0.00 34.33 1.82
3421 3795 3.005791 AGTGATGCCTTTACAAAGTTGGC 59.994 43.478 0.00 0.00 43.49 4.52
3534 3908 3.124578 TGCAGATGTGTGTATGTGTGT 57.875 42.857 0.00 0.00 0.00 3.72
3535 3909 4.011058 CATGCAGATGTGTGTATGTGTG 57.989 45.455 0.00 0.00 36.20 3.82
3576 3980 8.824756 AAATCAGATAGTCTACTGTCAACCTA 57.175 34.615 9.20 0.00 36.68 3.08
3658 4062 2.498167 ACTGTTTGCAGGACTTAGCAG 58.502 47.619 4.27 0.79 46.62 4.24
4001 4405 8.615211 TGAGCTAACAACATTAAAGCATATCTG 58.385 33.333 0.00 0.00 35.63 2.90
4458 4862 0.035458 ACTAGCTTGCTGACCACCAC 59.965 55.000 5.26 0.00 0.00 4.16
4559 4963 6.546034 ACATTGTTATAACCAGTTAGGGCATC 59.454 38.462 13.01 0.00 43.89 3.91
4674 5081 8.601845 TGCGTAGTAGCATCAAAATATTATGT 57.398 30.769 0.00 0.00 42.92 2.29
4901 5308 0.251916 TGCCGATGGGTAACTTCAGG 59.748 55.000 0.00 0.00 34.97 3.86
5181 5588 3.252458 GTGGAGCCAACGTGATTAACTTT 59.748 43.478 0.00 0.00 0.00 2.66
5397 5831 6.765036 ACAGTACAGAATTGGAGATGCTAATG 59.235 38.462 0.00 0.00 0.00 1.90
5622 6056 3.281341 TGCAACCGTAAAGCTGAATTG 57.719 42.857 0.00 0.00 0.00 2.32
5630 6064 2.540769 CCGCCATAATGCAACCGTAAAG 60.541 50.000 0.00 0.00 0.00 1.85
5638 6072 0.969917 ACTTGCCCGCCATAATGCAA 60.970 50.000 0.00 0.00 41.08 4.08
5683 6117 1.730064 CCCATCGAACCTGTAAACGTG 59.270 52.381 0.00 0.00 0.00 4.49
5698 6132 3.810941 TCGACACACTGTAAAAACCCATC 59.189 43.478 0.00 0.00 0.00 3.51
5704 6138 5.350365 GCCATATCTCGACACACTGTAAAAA 59.650 40.000 0.00 0.00 0.00 1.94
5723 6157 1.484038 GCATTTGTCAAGGGGCCATA 58.516 50.000 4.39 0.00 0.00 2.74
5743 6177 4.744137 CCACACACACACACATTAAAATGG 59.256 41.667 7.56 0.00 40.70 3.16
5823 6267 1.448985 TCTTAATCAAGCCACACGCC 58.551 50.000 0.00 0.00 38.78 5.68
5824 6268 3.764885 ATTCTTAATCAAGCCACACGC 57.235 42.857 0.00 0.00 37.98 5.34
5825 6269 7.015226 TCATTATTCTTAATCAAGCCACACG 57.985 36.000 0.00 0.00 0.00 4.49
6639 7305 2.648143 CGGTTGCAATGCCACCCAT 61.648 57.895 20.81 0.00 40.67 4.00
6665 7331 4.720902 CACCGCCCACCAGCATGA 62.721 66.667 0.00 0.00 39.69 3.07


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

AutoCloner maintained by Alex Coulton.