Multiple sequence alignment - TraesCS5B01G417900

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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 TraesCS5B01G417900 chr5B 100.000 2210 0 0 1 2210 592902278 592900069 0.000000e+00 4082.0
1 TraesCS5B01G417900 chr5B 93.722 446 16 2 1776 2209 481732455 481732010 0.000000e+00 658.0
2 TraesCS5B01G417900 chr5B 93.431 411 13 3 1776 2175 693631153 693631560 4.060000e-167 597.0
3 TraesCS5B01G417900 chr5B 100.000 47 0 0 110 156 642336056 642336010 1.090000e-13 87.9
4 TraesCS5B01G417900 chr7B 94.595 1628 79 8 156 1781 634952243 634950623 0.000000e+00 2510.0
5 TraesCS5B01G417900 chr7B 95.632 435 18 1 1776 2210 634950334 634949901 0.000000e+00 697.0
6 TraesCS5B01G417900 chr7B 93.694 444 17 2 1776 2209 634382397 634381955 0.000000e+00 654.0
7 TraesCS5B01G417900 chr7B 99.083 109 1 0 1 109 121019983 121019875 1.730000e-46 196.0
8 TraesCS5B01G417900 chr7B 99.083 109 1 0 1 109 675132650 675132542 1.730000e-46 196.0
9 TraesCS5B01G417900 chr6A 91.289 1125 72 18 156 1264 571153271 571152157 0.000000e+00 1511.0
10 TraesCS5B01G417900 chr6A 93.468 444 18 4 1776 2209 571152104 571151662 0.000000e+00 649.0
11 TraesCS5B01G417900 chr6A 92.793 444 19 3 1776 2209 72522470 72522030 4.000000e-177 630.0
12 TraesCS5B01G417900 chr6A 92.584 445 21 4 1776 2209 247095892 247095449 1.440000e-176 628.0
13 TraesCS5B01G417900 chr6A 88.699 469 45 4 1317 1781 602710934 602710470 1.150000e-157 566.0
14 TraesCS5B01G417900 chr6A 93.023 387 26 1 156 541 247096939 247096553 4.120000e-157 564.0
15 TraesCS5B01G417900 chr7D 91.101 1135 71 18 157 1268 556903445 556904572 0.000000e+00 1509.0
16 TraesCS5B01G417900 chr7D 93.651 441 16 3 1780 2209 556904619 556905058 0.000000e+00 649.0
17 TraesCS5B01G417900 chr7D 98.077 52 1 0 105 156 612139495 612139444 8.400000e-15 91.6
18 TraesCS5B01G417900 chr7D 96.154 52 2 0 105 156 365278345 365278396 3.910000e-13 86.1
19 TraesCS5B01G417900 chr4A 89.956 1125 87 18 157 1264 573501260 573502375 0.000000e+00 1428.0
20 TraesCS5B01G417900 chr4A 93.919 444 17 1 1776 2209 573502428 573502871 0.000000e+00 662.0
21 TraesCS5B01G417900 chr4A 93.596 406 15 2 1814 2209 525058794 525059198 1.460000e-166 595.0
22 TraesCS5B01G417900 chr4A 100.000 106 0 0 1 106 663157990 663158095 1.730000e-46 196.0
23 TraesCS5B01G417900 chr4A 100.000 106 0 0 1 106 728365842 728365947 1.730000e-46 196.0
24 TraesCS5B01G417900 chr4A 96.154 52 2 0 105 156 455829074 455829125 3.910000e-13 86.1
25 TraesCS5B01G417900 chr5D 92.063 882 50 14 403 1268 43780991 43780114 0.000000e+00 1223.0
26 TraesCS5B01G417900 chr5D 95.455 440 10 1 1780 2209 43780067 43779628 0.000000e+00 693.0
27 TraesCS5B01G417900 chr5D 97.119 243 4 2 1969 2209 339675027 339674786 7.350000e-110 407.0
28 TraesCS5B01G417900 chr5D 96.154 52 2 0 105 156 217054802 217054853 3.910000e-13 86.1
29 TraesCS5B01G417900 chr3A 90.241 953 68 16 333 1268 15883442 15884386 0.000000e+00 1221.0
30 TraesCS5B01G417900 chr3A 92.765 387 27 1 156 541 568299475 568299861 1.920000e-155 558.0
31 TraesCS5B01G417900 chr3A 92.564 390 24 3 156 541 690235815 690236203 2.480000e-154 555.0
32 TraesCS5B01G417900 chr3A 89.231 130 8 3 1554 1683 61628845 61628968 8.170000e-35 158.0
33 TraesCS5B01G417900 chr6D 91.537 898 54 14 388 1268 31276556 31277448 0.000000e+00 1218.0
34 TraesCS5B01G417900 chr6D 91.525 885 56 13 396 1268 128400212 128401089 0.000000e+00 1201.0
35 TraesCS5B01G417900 chr6D 95.455 440 10 1 1780 2209 31277495 31277934 0.000000e+00 693.0
36 TraesCS5B01G417900 chr6D 95.238 441 10 4 1780 2209 128401136 128401576 0.000000e+00 688.0
37 TraesCS5B01G417900 chr6D 95.000 440 12 1 1780 2209 30592618 30593057 0.000000e+00 682.0
38 TraesCS5B01G417900 chr6D 84.652 417 39 12 1374 1781 455890690 455890290 2.060000e-105 392.0
39 TraesCS5B01G417900 chr6D 89.764 127 7 3 1557 1683 283303686 283303566 8.170000e-35 158.0
40 TraesCS5B01G417900 chr1A 89.978 898 68 15 388 1268 471679110 471680002 0.000000e+00 1140.0
41 TraesCS5B01G417900 chr1A 93.694 444 17 4 1776 2209 471680050 471680492 0.000000e+00 654.0
42 TraesCS5B01G417900 chr1A 92.825 446 19 3 1776 2209 475680855 475681299 3.100000e-178 634.0
43 TraesCS5B01G417900 chr1A 92.342 444 22 3 1776 2209 560027857 560027416 2.410000e-174 621.0
44 TraesCS5B01G417900 chr1A 92.746 386 26 2 157 541 475679811 475680195 6.890000e-155 556.0
45 TraesCS5B01G417900 chr1A 92.268 388 25 4 157 541 560028903 560028518 1.490000e-151 545.0
46 TraesCS5B01G417900 chr1A 97.315 149 4 0 1776 1924 516046520 516046668 1.010000e-63 254.0
47 TraesCS5B01G417900 chr1A 89.764 127 7 3 1557 1683 50462511 50462391 8.170000e-35 158.0
48 TraesCS5B01G417900 chr1B 94.607 445 13 2 1776 2209 108095878 108096322 0.000000e+00 678.0
49 TraesCS5B01G417900 chr1B 94.369 444 14 2 1776 2209 121454970 121455412 0.000000e+00 671.0
50 TraesCS5B01G417900 chr2B 94.395 446 13 6 1776 2209 124614716 124614271 0.000000e+00 675.0
51 TraesCS5B01G417900 chr2B 100.000 106 0 0 1 106 473743153 473743048 1.730000e-46 196.0
52 TraesCS5B01G417900 chr2B 99.038 104 1 0 1 104 794161433 794161536 1.040000e-43 187.0
53 TraesCS5B01G417900 chr5A 94.144 444 15 2 1776 2209 663222464 663222906 0.000000e+00 665.0
54 TraesCS5B01G417900 chr3B 93.498 446 17 3 1776 2209 817401087 817400642 0.000000e+00 652.0
55 TraesCS5B01G417900 chr6B 93.065 447 18 2 1776 2209 268614247 268613801 1.850000e-180 641.0
56 TraesCS5B01G417900 chr6B 86.905 420 43 10 1371 1781 693124880 693124464 5.560000e-126 460.0
57 TraesCS5B01G417900 chr6B 88.768 276 31 0 1506 1781 693099116 693098841 2.720000e-89 339.0
58 TraesCS5B01G417900 chr6B 99.099 111 1 0 1 111 85242867 85242977 1.340000e-47 200.0
59 TraesCS5B01G417900 chr6B 100.000 107 0 0 1 107 102524265 102524159 4.810000e-47 198.0
60 TraesCS5B01G417900 chr6B 100.000 107 0 0 1 107 663188832 663188726 4.810000e-47 198.0
61 TraesCS5B01G417900 chr7A 94.832 387 17 3 157 541 638396901 638396516 3.140000e-168 601.0
62 TraesCS5B01G417900 chr7A 93.909 394 22 2 150 541 454750103 454749710 5.250000e-166 593.0
63 TraesCS5B01G417900 chr7A 96.154 52 2 0 105 156 151003387 151003438 3.910000e-13 86.1
64 TraesCS5B01G417900 chr2A 93.782 386 22 2 157 541 122911797 122912181 1.470000e-161 579.0
65 TraesCS5B01G417900 chr2D 89.764 127 7 3 1557 1683 233138727 233138607 8.170000e-35 158.0
66 TraesCS5B01G417900 chr2D 98.077 52 1 0 105 156 568793102 568793153 8.400000e-15 91.6
67 TraesCS5B01G417900 chr2D 96.154 52 2 0 105 156 15753509 15753560 3.910000e-13 86.1
68 TraesCS5B01G417900 chr4B 100.000 48 0 0 109 156 18507749 18507702 3.020000e-14 89.8


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 TraesCS5B01G417900 chr5B 592900069 592902278 2209 True 4082.0 4082 100.0000 1 2210 1 chr5B.!!$R2 2209
1 TraesCS5B01G417900 chr7B 634949901 634952243 2342 True 1603.5 2510 95.1135 156 2210 2 chr7B.!!$R4 2054
2 TraesCS5B01G417900 chr6A 571151662 571153271 1609 True 1080.0 1511 92.3785 156 2209 2 chr6A.!!$R4 2053
3 TraesCS5B01G417900 chr6A 247095449 247096939 1490 True 596.0 628 92.8035 156 2209 2 chr6A.!!$R3 2053
4 TraesCS5B01G417900 chr7D 556903445 556905058 1613 False 1079.0 1509 92.3760 157 2209 2 chr7D.!!$F2 2052
5 TraesCS5B01G417900 chr4A 573501260 573502871 1611 False 1045.0 1428 91.9375 157 2209 2 chr4A.!!$F5 2052
6 TraesCS5B01G417900 chr5D 43779628 43780991 1363 True 958.0 1223 93.7590 403 2209 2 chr5D.!!$R2 1806
7 TraesCS5B01G417900 chr3A 15883442 15884386 944 False 1221.0 1221 90.2410 333 1268 1 chr3A.!!$F1 935
8 TraesCS5B01G417900 chr6D 31276556 31277934 1378 False 955.5 1218 93.4960 388 2209 2 chr6D.!!$F2 1821
9 TraesCS5B01G417900 chr6D 128400212 128401576 1364 False 944.5 1201 93.3815 396 2209 2 chr6D.!!$F3 1813
10 TraesCS5B01G417900 chr1A 471679110 471680492 1382 False 897.0 1140 91.8360 388 2209 2 chr1A.!!$F2 1821
11 TraesCS5B01G417900 chr1A 475679811 475681299 1488 False 595.0 634 92.7855 157 2209 2 chr1A.!!$F3 2052
12 TraesCS5B01G417900 chr1A 560027416 560028903 1487 True 583.0 621 92.3050 157 2209 2 chr1A.!!$R2 2052

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
71 72 0.179092 CGGGACTAAAGGCCCTTACG 60.179 60.0 18.97 1.56 42.4 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 1823 0.401356 TGCAGGGATTCTCTTGTGCA 59.599 50.0 0.0 0.0 38.55 4.57 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 5.485209 GGACTAATGGGTGGAGGTATTAG 57.515 47.826 0.00 0.00 38.46 1.73
23 24 4.906060 GGACTAATGGGTGGAGGTATTAGT 59.094 45.833 7.88 7.88 44.56 2.24
24 25 6.080009 GGACTAATGGGTGGAGGTATTAGTA 58.920 44.000 0.00 0.00 42.94 1.82
25 26 6.556116 GGACTAATGGGTGGAGGTATTAGTAA 59.444 42.308 0.00 0.00 42.94 2.24
26 27 7.370905 ACTAATGGGTGGAGGTATTAGTAAC 57.629 40.000 0.00 0.00 41.81 2.50
27 28 4.950205 ATGGGTGGAGGTATTAGTAACG 57.050 45.455 0.00 0.00 0.00 3.18
28 29 3.033184 TGGGTGGAGGTATTAGTAACGG 58.967 50.000 0.00 0.00 0.00 4.44
29 30 2.224137 GGGTGGAGGTATTAGTAACGGC 60.224 54.545 0.00 0.00 0.00 5.68
30 31 2.224137 GGTGGAGGTATTAGTAACGGCC 60.224 54.545 0.00 0.00 0.00 6.13
31 32 2.041701 TGGAGGTATTAGTAACGGCCC 58.958 52.381 0.00 0.00 0.00 5.80
32 33 2.041701 GGAGGTATTAGTAACGGCCCA 58.958 52.381 0.00 0.00 0.00 5.36
33 34 2.636403 GGAGGTATTAGTAACGGCCCAT 59.364 50.000 0.00 0.00 0.00 4.00
34 35 3.072038 GGAGGTATTAGTAACGGCCCATT 59.928 47.826 0.00 0.00 0.00 3.16
35 36 4.284234 GGAGGTATTAGTAACGGCCCATTA 59.716 45.833 0.00 0.00 0.00 1.90
36 37 5.476614 GAGGTATTAGTAACGGCCCATTAG 58.523 45.833 0.00 0.00 0.00 1.73
37 38 4.903649 AGGTATTAGTAACGGCCCATTAGT 59.096 41.667 0.00 1.87 0.00 2.24
38 39 5.011431 AGGTATTAGTAACGGCCCATTAGTC 59.989 44.000 0.00 0.00 0.00 2.59
39 40 3.825143 TTAGTAACGGCCCATTAGTCC 57.175 47.619 0.00 0.00 0.00 3.85
40 41 0.835276 AGTAACGGCCCATTAGTCCC 59.165 55.000 0.00 0.00 0.00 4.46
41 42 0.531311 GTAACGGCCCATTAGTCCCG 60.531 60.000 0.00 0.00 45.80 5.14
42 43 1.688269 TAACGGCCCATTAGTCCCGG 61.688 60.000 0.00 0.00 44.70 5.73
43 44 3.476419 CGGCCCATTAGTCCCGGT 61.476 66.667 0.00 0.00 37.21 5.28
44 45 3.004090 GGCCCATTAGTCCCGGTT 58.996 61.111 0.00 0.00 0.00 4.44
45 46 1.153025 GGCCCATTAGTCCCGGTTC 60.153 63.158 0.00 0.00 0.00 3.62
46 47 1.605453 GCCCATTAGTCCCGGTTCA 59.395 57.895 0.00 0.00 0.00 3.18
47 48 0.182775 GCCCATTAGTCCCGGTTCAT 59.817 55.000 0.00 0.00 0.00 2.57
48 49 1.967319 CCCATTAGTCCCGGTTCATG 58.033 55.000 0.00 0.00 0.00 3.07
49 50 1.488812 CCCATTAGTCCCGGTTCATGA 59.511 52.381 0.00 0.00 0.00 3.07
50 51 2.092646 CCCATTAGTCCCGGTTCATGAA 60.093 50.000 3.38 3.38 0.00 2.57
51 52 2.943033 CCATTAGTCCCGGTTCATGAAC 59.057 50.000 27.16 27.16 40.45 3.18
63 64 3.007635 GTTCATGAACCGGGACTAAAGG 58.992 50.000 25.26 0.00 35.36 3.11
64 65 1.065709 TCATGAACCGGGACTAAAGGC 60.066 52.381 6.32 0.00 0.00 4.35
65 66 0.255033 ATGAACCGGGACTAAAGGCC 59.745 55.000 6.32 0.00 0.00 5.19
66 67 1.077930 GAACCGGGACTAAAGGCCC 60.078 63.158 11.29 11.29 41.11 5.80
67 68 1.540617 AACCGGGACTAAAGGCCCT 60.541 57.895 18.97 0.00 42.40 5.19
68 69 1.138228 AACCGGGACTAAAGGCCCTT 61.138 55.000 18.97 4.45 42.40 3.95
69 70 0.252835 ACCGGGACTAAAGGCCCTTA 60.253 55.000 18.97 0.00 42.40 2.69
70 71 0.179702 CCGGGACTAAAGGCCCTTAC 59.820 60.000 18.97 0.00 42.40 2.34
71 72 0.179092 CGGGACTAAAGGCCCTTACG 60.179 60.000 18.97 1.56 42.40 3.18
72 73 1.197812 GGGACTAAAGGCCCTTACGA 58.802 55.000 14.19 0.00 41.31 3.43
73 74 1.556451 GGGACTAAAGGCCCTTACGAA 59.444 52.381 14.19 0.00 41.31 3.85
74 75 2.625737 GGACTAAAGGCCCTTACGAAC 58.374 52.381 0.00 0.00 0.00 3.95
75 76 2.625737 GACTAAAGGCCCTTACGAACC 58.374 52.381 0.00 0.00 0.00 3.62
76 77 1.066645 ACTAAAGGCCCTTACGAACCG 60.067 52.381 0.00 0.00 0.00 4.44
77 78 0.249955 TAAAGGCCCTTACGAACCGG 59.750 55.000 0.00 0.00 0.00 5.28
78 79 2.473891 AAAGGCCCTTACGAACCGGG 62.474 60.000 6.32 0.00 41.06 5.73
79 80 3.393106 GGCCCTTACGAACCGGGA 61.393 66.667 6.32 0.00 40.55 5.14
80 81 2.125391 GCCCTTACGAACCGGGAC 60.125 66.667 6.32 0.00 40.55 4.46
81 82 2.653087 GCCCTTACGAACCGGGACT 61.653 63.158 6.32 0.00 40.55 3.85
82 83 1.322538 GCCCTTACGAACCGGGACTA 61.323 60.000 6.32 0.00 40.55 2.59
83 84 1.406903 CCCTTACGAACCGGGACTAT 58.593 55.000 6.32 0.00 40.55 2.12
84 85 1.758862 CCCTTACGAACCGGGACTATT 59.241 52.381 6.32 0.00 40.55 1.73
85 86 2.958355 CCCTTACGAACCGGGACTATTA 59.042 50.000 6.32 0.00 40.55 0.98
86 87 3.005155 CCCTTACGAACCGGGACTATTAG 59.995 52.174 6.32 0.00 40.55 1.73
87 88 3.005155 CCTTACGAACCGGGACTATTAGG 59.995 52.174 6.32 0.00 0.00 2.69
88 89 2.149973 ACGAACCGGGACTATTAGGT 57.850 50.000 6.32 0.00 38.88 3.08
89 90 1.753073 ACGAACCGGGACTATTAGGTG 59.247 52.381 6.32 0.00 37.03 4.00
90 91 1.753073 CGAACCGGGACTATTAGGTGT 59.247 52.381 6.32 0.00 37.03 4.16
91 92 2.167075 CGAACCGGGACTATTAGGTGTT 59.833 50.000 6.32 0.00 37.03 3.32
92 93 3.368739 CGAACCGGGACTATTAGGTGTTT 60.369 47.826 6.32 0.00 37.03 2.83
93 94 4.582869 GAACCGGGACTATTAGGTGTTTT 58.417 43.478 6.32 0.00 37.03 2.43
94 95 4.645863 ACCGGGACTATTAGGTGTTTTT 57.354 40.909 6.32 0.00 35.36 1.94
95 96 4.582869 ACCGGGACTATTAGGTGTTTTTC 58.417 43.478 6.32 0.00 35.36 2.29
96 97 4.287845 ACCGGGACTATTAGGTGTTTTTCT 59.712 41.667 6.32 0.00 35.36 2.52
97 98 5.484998 ACCGGGACTATTAGGTGTTTTTCTA 59.515 40.000 6.32 0.00 35.36 2.10
98 99 5.814188 CCGGGACTATTAGGTGTTTTTCTAC 59.186 44.000 0.00 0.00 0.00 2.59
99 100 6.351626 CCGGGACTATTAGGTGTTTTTCTACT 60.352 42.308 0.00 0.00 0.00 2.57
100 101 7.147846 CCGGGACTATTAGGTGTTTTTCTACTA 60.148 40.741 0.00 0.00 0.00 1.82
101 102 7.919621 CGGGACTATTAGGTGTTTTTCTACTAG 59.080 40.741 0.00 0.00 0.00 2.57
102 103 8.756927 GGGACTATTAGGTGTTTTTCTACTAGT 58.243 37.037 0.00 0.00 35.82 2.57
103 104 9.583765 GGACTATTAGGTGTTTTTCTACTAGTG 57.416 37.037 5.39 0.00 34.37 2.74
104 105 8.999220 ACTATTAGGTGTTTTTCTACTAGTGC 57.001 34.615 5.39 0.00 33.57 4.40
105 106 8.591072 ACTATTAGGTGTTTTTCTACTAGTGCA 58.409 33.333 5.39 0.00 33.57 4.57
106 107 9.601217 CTATTAGGTGTTTTTCTACTAGTGCAT 57.399 33.333 5.39 0.00 0.00 3.96
107 108 7.667043 TTAGGTGTTTTTCTACTAGTGCATG 57.333 36.000 5.39 0.00 0.00 4.06
108 109 5.621193 AGGTGTTTTTCTACTAGTGCATGT 58.379 37.500 5.39 0.00 0.00 3.21
109 110 5.701290 AGGTGTTTTTCTACTAGTGCATGTC 59.299 40.000 5.39 0.00 0.00 3.06
110 111 5.106673 GGTGTTTTTCTACTAGTGCATGTCC 60.107 44.000 5.39 0.00 0.00 4.02
111 112 5.001232 TGTTTTTCTACTAGTGCATGTCCC 58.999 41.667 5.39 0.00 0.00 4.46
112 113 4.901197 TTTTCTACTAGTGCATGTCCCA 57.099 40.909 5.39 0.00 0.00 4.37
113 114 4.901197 TTTCTACTAGTGCATGTCCCAA 57.099 40.909 5.39 0.00 0.00 4.12
114 115 4.901197 TTCTACTAGTGCATGTCCCAAA 57.099 40.909 5.39 0.00 0.00 3.28
115 116 5.435686 TTCTACTAGTGCATGTCCCAAAT 57.564 39.130 5.39 0.00 0.00 2.32
116 117 6.553953 TTCTACTAGTGCATGTCCCAAATA 57.446 37.500 5.39 0.00 0.00 1.40
117 118 6.553953 TCTACTAGTGCATGTCCCAAATAA 57.446 37.500 5.39 0.00 0.00 1.40
118 119 6.346096 TCTACTAGTGCATGTCCCAAATAAC 58.654 40.000 5.39 0.00 0.00 1.89
119 120 3.938963 ACTAGTGCATGTCCCAAATAACG 59.061 43.478 0.00 0.00 0.00 3.18
120 121 3.066291 AGTGCATGTCCCAAATAACGA 57.934 42.857 0.00 0.00 0.00 3.85
121 122 3.620488 AGTGCATGTCCCAAATAACGAT 58.380 40.909 0.00 0.00 0.00 3.73
122 123 4.016444 AGTGCATGTCCCAAATAACGATT 58.984 39.130 0.00 0.00 0.00 3.34
123 124 4.096382 AGTGCATGTCCCAAATAACGATTC 59.904 41.667 0.00 0.00 0.00 2.52
124 125 4.013050 TGCATGTCCCAAATAACGATTCA 58.987 39.130 0.00 0.00 0.00 2.57
125 126 4.460731 TGCATGTCCCAAATAACGATTCAA 59.539 37.500 0.00 0.00 0.00 2.69
126 127 5.126869 TGCATGTCCCAAATAACGATTCAAT 59.873 36.000 0.00 0.00 0.00 2.57
127 128 5.459762 GCATGTCCCAAATAACGATTCAATG 59.540 40.000 0.00 0.00 0.00 2.82
128 129 6.563422 CATGTCCCAAATAACGATTCAATGT 58.437 36.000 0.00 0.00 0.00 2.71
129 130 6.582677 TGTCCCAAATAACGATTCAATGTT 57.417 33.333 0.00 0.00 0.00 2.71
130 131 7.689446 TGTCCCAAATAACGATTCAATGTTA 57.311 32.000 0.00 0.00 35.25 2.41
131 132 8.112016 TGTCCCAAATAACGATTCAATGTTAA 57.888 30.769 0.00 0.00 34.52 2.01
132 133 8.024285 TGTCCCAAATAACGATTCAATGTTAAC 58.976 33.333 0.00 0.00 34.52 2.01
133 134 8.241367 GTCCCAAATAACGATTCAATGTTAACT 58.759 33.333 7.22 0.00 34.52 2.24
134 135 8.240682 TCCCAAATAACGATTCAATGTTAACTG 58.759 33.333 7.22 0.00 34.52 3.16
135 136 7.487829 CCCAAATAACGATTCAATGTTAACTGG 59.512 37.037 7.22 0.17 36.77 4.00
136 137 8.240682 CCAAATAACGATTCAATGTTAACTGGA 58.759 33.333 7.22 0.00 37.94 3.86
137 138 9.277565 CAAATAACGATTCAATGTTAACTGGAG 57.722 33.333 7.22 0.00 34.52 3.86
138 139 5.880054 AACGATTCAATGTTAACTGGAGG 57.120 39.130 7.22 0.00 0.00 4.30
139 140 5.160607 ACGATTCAATGTTAACTGGAGGA 57.839 39.130 7.22 0.00 0.00 3.71
140 141 5.178797 ACGATTCAATGTTAACTGGAGGAG 58.821 41.667 7.22 0.00 0.00 3.69
141 142 5.178797 CGATTCAATGTTAACTGGAGGAGT 58.821 41.667 7.22 0.00 35.94 3.85
142 143 6.070995 ACGATTCAATGTTAACTGGAGGAGTA 60.071 38.462 7.22 0.00 33.09 2.59
143 144 6.816640 CGATTCAATGTTAACTGGAGGAGTAA 59.183 38.462 7.22 0.00 33.09 2.24
144 145 7.495934 CGATTCAATGTTAACTGGAGGAGTAAT 59.504 37.037 7.22 0.00 33.09 1.89
145 146 7.921786 TTCAATGTTAACTGGAGGAGTAATG 57.078 36.000 7.22 0.00 33.09 1.90
146 147 7.016153 TCAATGTTAACTGGAGGAGTAATGT 57.984 36.000 7.22 0.00 33.09 2.71
147 148 7.458397 TCAATGTTAACTGGAGGAGTAATGTT 58.542 34.615 7.22 0.00 33.09 2.71
148 149 8.598916 TCAATGTTAACTGGAGGAGTAATGTTA 58.401 33.333 7.22 0.00 33.09 2.41
149 150 9.226606 CAATGTTAACTGGAGGAGTAATGTTAA 57.773 33.333 7.22 0.00 33.09 2.01
150 151 9.802039 AATGTTAACTGGAGGAGTAATGTTAAA 57.198 29.630 7.22 0.00 33.57 1.52
151 152 8.842358 TGTTAACTGGAGGAGTAATGTTAAAG 57.158 34.615 7.22 0.00 33.57 1.85
152 153 7.881232 TGTTAACTGGAGGAGTAATGTTAAAGG 59.119 37.037 7.22 0.00 33.57 3.11
153 154 4.844884 ACTGGAGGAGTAATGTTAAAGGC 58.155 43.478 0.00 0.00 30.86 4.35
154 155 4.536489 ACTGGAGGAGTAATGTTAAAGGCT 59.464 41.667 0.00 0.00 30.86 4.58
339 347 1.933812 GATCCACCCCCTTCCCCAA 60.934 63.158 0.00 0.00 0.00 4.12
426 434 4.517952 CAAATGTGCACCATTGGTAAGA 57.482 40.909 15.69 0.00 43.04 2.10
447 459 1.264749 GGGGGAGGTGGGCATTTTTC 61.265 60.000 0.00 0.00 0.00 2.29
496 509 1.100510 CCATTGCTATGTGCTGCACT 58.899 50.000 30.43 19.11 43.37 4.40
580 638 1.490910 GAATCGATCCCCTCCAAACCT 59.509 52.381 0.00 0.00 0.00 3.50
582 640 0.546747 TCGATCCCCTCCAAACCTGT 60.547 55.000 0.00 0.00 0.00 4.00
606 664 1.113517 GCTGCCGTGGACCTCCTATA 61.114 60.000 0.00 0.00 36.82 1.31
822 880 0.689080 TCCACAGCTCTCCATCCCTC 60.689 60.000 0.00 0.00 0.00 4.30
823 881 1.694133 CCACAGCTCTCCATCCCTCC 61.694 65.000 0.00 0.00 0.00 4.30
824 882 1.383803 ACAGCTCTCCATCCCTCCC 60.384 63.158 0.00 0.00 0.00 4.30
825 883 1.074623 CAGCTCTCCATCCCTCCCT 60.075 63.158 0.00 0.00 0.00 4.20
919 978 1.159664 AGGCCAGGGAGACTTCAGT 59.840 57.895 5.01 0.00 0.00 3.41
991 1050 0.853586 ACCAGAGAGGAGGGGAGAGT 60.854 60.000 0.00 0.00 41.22 3.24
1107 1166 4.194720 GTGCTCGACCTCGGCGAT 62.195 66.667 11.27 0.00 40.29 4.58
1192 1251 0.900182 TCCATCTCGTCAGTGCCACT 60.900 55.000 0.00 0.00 0.00 4.00
1210 1269 2.115695 GCACCCAACCCCCGTAAA 59.884 61.111 0.00 0.00 0.00 2.01
1287 1346 0.031314 CTACATCTCGTCAGCGCCAT 59.969 55.000 2.29 0.00 38.14 4.40
1302 1361 4.358841 CATCGCACCCAACCCCCA 62.359 66.667 0.00 0.00 0.00 4.96
1335 1394 2.599973 CTGCTGCTGTTGTTGTTGTTTC 59.400 45.455 0.00 0.00 0.00 2.78
1337 1396 2.992543 GCTGCTGTTGTTGTTGTTTCAA 59.007 40.909 0.00 0.00 0.00 2.69
1360 1419 2.866515 ACCATCCATGTTTACCCCCTA 58.133 47.619 0.00 0.00 0.00 3.53
1364 1423 4.141041 CCATCCATGTTTACCCCCTATCAA 60.141 45.833 0.00 0.00 0.00 2.57
1365 1424 4.788925 TCCATGTTTACCCCCTATCAAG 57.211 45.455 0.00 0.00 0.00 3.02
1371 1430 1.819753 TACCCCCTATCAAGCATGCT 58.180 50.000 16.30 16.30 0.00 3.79
1617 1677 5.048713 GGGACATCAACTACAACTGGAAAAG 60.049 44.000 0.00 0.00 0.00 2.27
1679 1739 2.160219 GCTGAGCACATTCATCGTTCAA 59.840 45.455 0.00 0.00 0.00 2.69
1732 1792 3.350833 AGATCATGGTTCTTTGACCTGC 58.649 45.455 0.00 0.00 40.47 4.85
1749 1809 3.567164 ACCTGCAGACTCAAGAAATTGTG 59.433 43.478 17.39 0.00 0.00 3.33
1750 1810 3.817084 CCTGCAGACTCAAGAAATTGTGA 59.183 43.478 17.39 0.00 0.00 3.58
1758 1818 9.604626 CAGACTCAAGAAATTGTGAGATTAAAC 57.395 33.333 16.78 5.35 43.32 2.01
1765 1825 4.946784 ATTGTGAGATTAAACGGAGTGC 57.053 40.909 0.00 0.00 45.00 4.40
1791 2145 3.135530 AGAGAATCCCTGCAATCTGTACC 59.864 47.826 0.00 0.00 33.66 3.34
1879 2233 7.960738 CCGGAGCCAATATTTGTAATTTATACG 59.039 37.037 0.00 0.00 0.00 3.06
1929 2283 2.670148 AACGATGGCAGGGGAGTCC 61.670 63.158 0.00 0.00 0.00 3.85
2036 2400 0.249280 TCGCAACAAGAGTTCTCGCA 60.249 50.000 0.00 0.00 35.28 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.906060 ACTAATACCTCCACCCATTAGTCC 59.094 45.833 0.00 0.00 39.01 3.85
1 2 7.440198 GTTACTAATACCTCCACCCATTAGTC 58.560 42.308 8.63 0.00 41.17 2.59
2 3 6.041296 CGTTACTAATACCTCCACCCATTAGT 59.959 42.308 9.89 9.89 43.28 2.24
3 4 6.453092 CGTTACTAATACCTCCACCCATTAG 58.547 44.000 0.00 0.00 37.13 1.73
4 5 5.305128 CCGTTACTAATACCTCCACCCATTA 59.695 44.000 0.00 0.00 0.00 1.90
5 6 4.102054 CCGTTACTAATACCTCCACCCATT 59.898 45.833 0.00 0.00 0.00 3.16
6 7 3.644738 CCGTTACTAATACCTCCACCCAT 59.355 47.826 0.00 0.00 0.00 4.00
7 8 3.033184 CCGTTACTAATACCTCCACCCA 58.967 50.000 0.00 0.00 0.00 4.51
8 9 2.224137 GCCGTTACTAATACCTCCACCC 60.224 54.545 0.00 0.00 0.00 4.61
9 10 2.224137 GGCCGTTACTAATACCTCCACC 60.224 54.545 0.00 0.00 0.00 4.61
10 11 2.224137 GGGCCGTTACTAATACCTCCAC 60.224 54.545 0.00 0.00 0.00 4.02
11 12 2.041701 GGGCCGTTACTAATACCTCCA 58.958 52.381 0.00 0.00 0.00 3.86
12 13 2.041701 TGGGCCGTTACTAATACCTCC 58.958 52.381 0.00 0.00 0.00 4.30
13 14 4.347360 AATGGGCCGTTACTAATACCTC 57.653 45.455 9.83 0.00 0.00 3.85
14 15 4.903649 ACTAATGGGCCGTTACTAATACCT 59.096 41.667 14.22 0.00 0.00 3.08
15 16 5.219343 ACTAATGGGCCGTTACTAATACC 57.781 43.478 14.22 0.00 0.00 2.73
16 17 5.233225 GGACTAATGGGCCGTTACTAATAC 58.767 45.833 14.22 0.00 30.75 1.89
17 18 4.284234 GGGACTAATGGGCCGTTACTAATA 59.716 45.833 14.22 0.00 46.52 0.98
18 19 3.072038 GGGACTAATGGGCCGTTACTAAT 59.928 47.826 14.22 0.78 46.52 1.73
19 20 2.435437 GGGACTAATGGGCCGTTACTAA 59.565 50.000 14.22 0.00 46.52 2.24
20 21 2.041701 GGGACTAATGGGCCGTTACTA 58.958 52.381 14.22 0.00 46.52 1.82
21 22 0.835276 GGGACTAATGGGCCGTTACT 59.165 55.000 14.22 5.76 46.52 2.24
22 23 0.531311 CGGGACTAATGGGCCGTTAC 60.531 60.000 14.22 5.89 46.52 2.50
23 24 1.688269 CCGGGACTAATGGGCCGTTA 61.688 60.000 17.04 17.04 46.52 3.18
24 25 2.587889 CGGGACTAATGGGCCGTT 59.412 61.111 16.54 16.54 46.52 4.44
25 26 3.476419 CCGGGACTAATGGGCCGT 61.476 66.667 0.00 0.00 46.52 5.68
26 27 2.935627 GAACCGGGACTAATGGGCCG 62.936 65.000 6.32 0.00 46.52 6.13
27 28 1.153025 GAACCGGGACTAATGGGCC 60.153 63.158 6.32 0.00 44.23 5.80
28 29 0.182775 ATGAACCGGGACTAATGGGC 59.817 55.000 6.32 0.00 0.00 5.36
29 30 1.488812 TCATGAACCGGGACTAATGGG 59.511 52.381 6.32 0.00 0.00 4.00
30 31 2.943033 GTTCATGAACCGGGACTAATGG 59.057 50.000 25.26 0.00 35.36 3.16
42 43 3.007635 CCTTTAGTCCCGGTTCATGAAC 58.992 50.000 27.16 27.16 40.45 3.18
43 44 2.617021 GCCTTTAGTCCCGGTTCATGAA 60.617 50.000 3.38 3.38 0.00 2.57
44 45 1.065709 GCCTTTAGTCCCGGTTCATGA 60.066 52.381 0.00 0.00 0.00 3.07
45 46 1.379527 GCCTTTAGTCCCGGTTCATG 58.620 55.000 0.00 0.00 0.00 3.07
46 47 0.255033 GGCCTTTAGTCCCGGTTCAT 59.745 55.000 0.00 0.00 0.00 2.57
47 48 1.681076 GGCCTTTAGTCCCGGTTCA 59.319 57.895 0.00 0.00 0.00 3.18
48 49 1.077930 GGGCCTTTAGTCCCGGTTC 60.078 63.158 0.84 0.00 32.00 3.62
49 50 3.084304 GGGCCTTTAGTCCCGGTT 58.916 61.111 0.84 0.00 32.00 4.44
53 54 1.197812 TCGTAAGGGCCTTTAGTCCC 58.802 55.000 26.29 5.03 42.94 4.46
54 55 2.625737 GTTCGTAAGGGCCTTTAGTCC 58.374 52.381 26.29 6.64 38.47 3.85
55 56 2.625737 GGTTCGTAAGGGCCTTTAGTC 58.374 52.381 26.29 14.62 38.47 2.59
56 57 1.066645 CGGTTCGTAAGGGCCTTTAGT 60.067 52.381 26.29 1.50 38.47 2.24
57 58 1.648504 CGGTTCGTAAGGGCCTTTAG 58.351 55.000 26.29 18.30 38.47 1.85
58 59 0.249955 CCGGTTCGTAAGGGCCTTTA 59.750 55.000 26.29 2.60 38.47 1.85
59 60 1.002990 CCGGTTCGTAAGGGCCTTT 60.003 57.895 26.29 5.08 38.47 3.11
60 61 2.666812 CCGGTTCGTAAGGGCCTT 59.333 61.111 24.44 24.44 38.47 4.35
61 62 3.396570 CCCGGTTCGTAAGGGCCT 61.397 66.667 0.00 0.00 38.51 5.19
62 63 3.393106 TCCCGGTTCGTAAGGGCC 61.393 66.667 0.00 0.00 44.70 5.80
63 64 1.322538 TAGTCCCGGTTCGTAAGGGC 61.323 60.000 0.00 0.00 44.70 5.19
64 65 1.406903 ATAGTCCCGGTTCGTAAGGG 58.593 55.000 0.00 0.00 46.40 3.95
65 66 3.005155 CCTAATAGTCCCGGTTCGTAAGG 59.995 52.174 0.00 0.00 38.47 2.69
66 67 3.633986 ACCTAATAGTCCCGGTTCGTAAG 59.366 47.826 0.00 0.00 0.00 2.34
67 68 3.381272 CACCTAATAGTCCCGGTTCGTAA 59.619 47.826 0.00 0.00 0.00 3.18
68 69 2.951642 CACCTAATAGTCCCGGTTCGTA 59.048 50.000 0.00 0.00 0.00 3.43
69 70 1.753073 CACCTAATAGTCCCGGTTCGT 59.247 52.381 0.00 0.00 0.00 3.85
70 71 1.753073 ACACCTAATAGTCCCGGTTCG 59.247 52.381 0.00 0.00 0.00 3.95
71 72 3.900966 AACACCTAATAGTCCCGGTTC 57.099 47.619 0.00 0.00 0.00 3.62
72 73 4.645863 AAAACACCTAATAGTCCCGGTT 57.354 40.909 0.00 0.00 0.00 4.44
73 74 4.287845 AGAAAAACACCTAATAGTCCCGGT 59.712 41.667 0.00 0.00 0.00 5.28
74 75 4.840271 AGAAAAACACCTAATAGTCCCGG 58.160 43.478 0.00 0.00 0.00 5.73
75 76 6.637657 AGTAGAAAAACACCTAATAGTCCCG 58.362 40.000 0.00 0.00 0.00 5.14
76 77 8.756927 ACTAGTAGAAAAACACCTAATAGTCCC 58.243 37.037 3.59 0.00 40.55 4.46
77 78 9.583765 CACTAGTAGAAAAACACCTAATAGTCC 57.416 37.037 3.59 0.00 41.76 3.85
78 79 9.085250 GCACTAGTAGAAAAACACCTAATAGTC 57.915 37.037 3.59 0.00 41.76 2.59
79 80 8.591072 TGCACTAGTAGAAAAACACCTAATAGT 58.409 33.333 3.59 0.00 43.34 2.12
80 81 8.997621 TGCACTAGTAGAAAAACACCTAATAG 57.002 34.615 3.59 0.00 38.66 1.73
81 82 9.378551 CATGCACTAGTAGAAAAACACCTAATA 57.621 33.333 3.59 0.00 0.00 0.98
82 83 7.883311 ACATGCACTAGTAGAAAAACACCTAAT 59.117 33.333 3.59 0.00 0.00 1.73
83 84 7.221450 ACATGCACTAGTAGAAAAACACCTAA 58.779 34.615 3.59 0.00 0.00 2.69
84 85 6.765403 ACATGCACTAGTAGAAAAACACCTA 58.235 36.000 3.59 0.00 0.00 3.08
85 86 5.621193 ACATGCACTAGTAGAAAAACACCT 58.379 37.500 3.59 0.00 0.00 4.00
86 87 5.106673 GGACATGCACTAGTAGAAAAACACC 60.107 44.000 3.59 0.00 0.00 4.16
87 88 5.106673 GGGACATGCACTAGTAGAAAAACAC 60.107 44.000 3.59 0.00 0.00 3.32
88 89 5.001232 GGGACATGCACTAGTAGAAAAACA 58.999 41.667 3.59 0.00 0.00 2.83
89 90 5.001232 TGGGACATGCACTAGTAGAAAAAC 58.999 41.667 3.59 0.00 0.00 2.43
90 91 5.235850 TGGGACATGCACTAGTAGAAAAA 57.764 39.130 3.59 0.00 0.00 1.94
91 92 4.901197 TGGGACATGCACTAGTAGAAAA 57.099 40.909 3.59 0.00 0.00 2.29
92 93 4.901197 TTGGGACATGCACTAGTAGAAA 57.099 40.909 3.59 0.00 39.30 2.52
93 94 4.901197 TTTGGGACATGCACTAGTAGAA 57.099 40.909 3.59 0.00 39.30 2.10
94 95 6.346096 GTTATTTGGGACATGCACTAGTAGA 58.654 40.000 3.59 0.00 39.30 2.59
95 96 5.234329 CGTTATTTGGGACATGCACTAGTAG 59.766 44.000 0.00 0.00 39.30 2.57
96 97 5.105269 TCGTTATTTGGGACATGCACTAGTA 60.105 40.000 0.00 0.00 39.30 1.82
97 98 3.938963 CGTTATTTGGGACATGCACTAGT 59.061 43.478 0.00 0.00 39.30 2.57
98 99 4.188462 TCGTTATTTGGGACATGCACTAG 58.812 43.478 0.00 0.00 39.30 2.57
99 100 4.209307 TCGTTATTTGGGACATGCACTA 57.791 40.909 0.00 0.00 39.30 2.74
100 101 3.066291 TCGTTATTTGGGACATGCACT 57.934 42.857 0.00 0.00 39.30 4.40
101 102 4.142491 TGAATCGTTATTTGGGACATGCAC 60.142 41.667 0.00 0.00 39.30 4.57
102 103 4.013050 TGAATCGTTATTTGGGACATGCA 58.987 39.130 0.00 0.00 39.30 3.96
103 104 4.630894 TGAATCGTTATTTGGGACATGC 57.369 40.909 0.00 0.00 39.30 4.06
104 105 6.563422 ACATTGAATCGTTATTTGGGACATG 58.437 36.000 0.00 0.00 39.30 3.21
105 106 6.773976 ACATTGAATCGTTATTTGGGACAT 57.226 33.333 0.00 0.00 39.30 3.06
106 107 6.582677 AACATTGAATCGTTATTTGGGACA 57.417 33.333 0.00 0.00 0.00 4.02
107 108 8.241367 AGTTAACATTGAATCGTTATTTGGGAC 58.759 33.333 8.61 0.00 0.00 4.46
108 109 8.240682 CAGTTAACATTGAATCGTTATTTGGGA 58.759 33.333 8.61 0.00 0.00 4.37
109 110 7.487829 CCAGTTAACATTGAATCGTTATTTGGG 59.512 37.037 8.61 0.00 32.86 4.12
110 111 8.240682 TCCAGTTAACATTGAATCGTTATTTGG 58.759 33.333 8.61 15.10 35.20 3.28
111 112 9.277565 CTCCAGTTAACATTGAATCGTTATTTG 57.722 33.333 8.61 0.00 0.00 2.32
112 113 8.458843 CCTCCAGTTAACATTGAATCGTTATTT 58.541 33.333 8.61 0.00 0.00 1.40
113 114 7.827236 TCCTCCAGTTAACATTGAATCGTTATT 59.173 33.333 8.61 0.00 0.00 1.40
114 115 7.335627 TCCTCCAGTTAACATTGAATCGTTAT 58.664 34.615 8.61 0.00 0.00 1.89
115 116 6.703319 TCCTCCAGTTAACATTGAATCGTTA 58.297 36.000 8.61 0.00 0.00 3.18
116 117 5.556915 TCCTCCAGTTAACATTGAATCGTT 58.443 37.500 8.61 0.00 0.00 3.85
117 118 5.160607 TCCTCCAGTTAACATTGAATCGT 57.839 39.130 8.61 0.00 0.00 3.73
118 119 5.178797 ACTCCTCCAGTTAACATTGAATCG 58.821 41.667 8.61 0.00 26.56 3.34
119 120 8.616076 CATTACTCCTCCAGTTAACATTGAATC 58.384 37.037 8.61 0.00 36.43 2.52
120 121 8.109634 ACATTACTCCTCCAGTTAACATTGAAT 58.890 33.333 8.61 0.00 36.43 2.57
121 122 7.458397 ACATTACTCCTCCAGTTAACATTGAA 58.542 34.615 8.61 0.00 36.43 2.69
122 123 7.016153 ACATTACTCCTCCAGTTAACATTGA 57.984 36.000 8.61 0.20 36.43 2.57
123 124 7.687941 AACATTACTCCTCCAGTTAACATTG 57.312 36.000 8.61 0.00 36.43 2.82
124 125 9.802039 TTTAACATTACTCCTCCAGTTAACATT 57.198 29.630 8.61 0.00 36.43 2.71
125 126 9.449719 CTTTAACATTACTCCTCCAGTTAACAT 57.550 33.333 8.61 0.00 36.43 2.71
126 127 7.881232 CCTTTAACATTACTCCTCCAGTTAACA 59.119 37.037 8.61 0.00 36.43 2.41
127 128 7.148289 GCCTTTAACATTACTCCTCCAGTTAAC 60.148 40.741 0.00 0.00 36.43 2.01
128 129 6.882678 GCCTTTAACATTACTCCTCCAGTTAA 59.117 38.462 0.00 0.00 36.43 2.01
129 130 6.214819 AGCCTTTAACATTACTCCTCCAGTTA 59.785 38.462 0.00 0.00 36.43 2.24
130 131 5.014228 AGCCTTTAACATTACTCCTCCAGTT 59.986 40.000 0.00 0.00 36.43 3.16
131 132 4.536489 AGCCTTTAACATTACTCCTCCAGT 59.464 41.667 0.00 0.00 39.41 4.00
132 133 5.104259 AGCCTTTAACATTACTCCTCCAG 57.896 43.478 0.00 0.00 0.00 3.86
133 134 5.486063 TGTAGCCTTTAACATTACTCCTCCA 59.514 40.000 0.00 0.00 0.00 3.86
134 135 5.816258 GTGTAGCCTTTAACATTACTCCTCC 59.184 44.000 0.00 0.00 0.00 4.30
135 136 6.641474 AGTGTAGCCTTTAACATTACTCCTC 58.359 40.000 0.00 0.00 0.00 3.71
136 137 6.622427 AGTGTAGCCTTTAACATTACTCCT 57.378 37.500 0.00 0.00 0.00 3.69
137 138 7.554211 AGTAGTGTAGCCTTTAACATTACTCC 58.446 38.462 5.21 0.00 42.19 3.85
138 139 9.733219 CTAGTAGTGTAGCCTTTAACATTACTC 57.267 37.037 12.14 0.00 42.19 2.59
139 140 9.471702 TCTAGTAGTGTAGCCTTTAACATTACT 57.528 33.333 13.01 13.01 45.47 2.24
146 147 9.444600 CCATTTTTCTAGTAGTGTAGCCTTTAA 57.555 33.333 0.00 0.00 0.00 1.52
147 148 7.551617 GCCATTTTTCTAGTAGTGTAGCCTTTA 59.448 37.037 0.00 0.00 0.00 1.85
148 149 6.374613 GCCATTTTTCTAGTAGTGTAGCCTTT 59.625 38.462 0.00 0.00 0.00 3.11
149 150 5.880887 GCCATTTTTCTAGTAGTGTAGCCTT 59.119 40.000 0.00 0.00 0.00 4.35
150 151 5.189934 AGCCATTTTTCTAGTAGTGTAGCCT 59.810 40.000 0.00 0.00 0.00 4.58
151 152 5.429130 AGCCATTTTTCTAGTAGTGTAGCC 58.571 41.667 0.00 0.00 0.00 3.93
152 153 9.413048 CTATAGCCATTTTTCTAGTAGTGTAGC 57.587 37.037 0.00 0.00 0.00 3.58
153 154 9.413048 GCTATAGCCATTTTTCTAGTAGTGTAG 57.587 37.037 14.13 0.00 34.31 2.74
246 253 0.035915 TAACAATGGCGCACCTGCTA 60.036 50.000 10.83 0.00 39.32 3.49
322 329 1.935931 CTTGGGGAAGGGGGTGGAT 60.936 63.158 0.00 0.00 0.00 3.41
339 347 0.251165 AGGTGCGCCATTGGTAAACT 60.251 50.000 20.59 0.00 37.19 2.66
414 422 0.548197 TCCCCCGTCTTACCAATGGT 60.548 55.000 10.81 10.81 40.16 3.55
447 459 1.001020 TGGTGCCCCATTGCTACAG 60.001 57.895 0.00 0.00 35.17 2.74
496 509 3.781307 CCGAATCAGGGCCGGTCA 61.781 66.667 9.07 0.00 38.55 4.02
513 526 5.301805 TCTCTTTTCACCAGACAAAAATCCC 59.698 40.000 0.00 0.00 0.00 3.85
822 880 3.756783 ACGAGGAGGGAGGGAGGG 61.757 72.222 0.00 0.00 0.00 4.30
823 881 2.443016 CACGAGGAGGGAGGGAGG 60.443 72.222 0.00 0.00 0.00 4.30
824 882 3.151022 GCACGAGGAGGGAGGGAG 61.151 72.222 0.00 0.00 0.00 4.30
825 883 4.779733 GGCACGAGGAGGGAGGGA 62.780 72.222 0.00 0.00 0.00 4.20
910 969 0.980423 GAAGGGAGGCACTGAAGTCT 59.020 55.000 0.00 0.00 41.55 3.24
919 978 1.613630 GTCCAGGAGAAGGGAGGCA 60.614 63.158 0.00 0.00 32.85 4.75
991 1050 1.153369 GCAGCAACATCTCCGCCTA 60.153 57.895 0.00 0.00 0.00 3.93
1107 1166 3.259064 GTCGAGGACGGATGAATTGAAA 58.741 45.455 0.00 0.00 40.21 2.69
1192 1251 2.764737 TTTACGGGGGTTGGGTGCA 61.765 57.895 0.00 0.00 0.00 4.57
1210 1269 2.363147 GGGAGAGGAGGCGACTGT 60.363 66.667 0.00 0.00 44.43 3.55
1287 1346 2.204865 CTTATGGGGGTTGGGTGCGA 62.205 60.000 0.00 0.00 0.00 5.10
1320 1379 6.292389 TGGTTTTTGAAACAACAACAACAG 57.708 33.333 13.01 0.00 40.18 3.16
1335 1394 4.564613 GGGGGTAAACATGGATGGTTTTTG 60.565 45.833 0.00 0.00 38.84 2.44
1337 1396 3.178046 GGGGGTAAACATGGATGGTTTT 58.822 45.455 0.00 0.00 38.84 2.43
1397 1457 2.240493 AGTCTGACGGTTTGGTCAAG 57.760 50.000 1.52 0.00 45.59 3.02
1464 1524 9.383519 GAATAGAAGAGTTATTGGATCACAACA 57.616 33.333 0.00 0.00 42.94 3.33
1465 1525 9.606631 AGAATAGAAGAGTTATTGGATCACAAC 57.393 33.333 0.00 0.00 42.94 3.32
1498 1558 6.778834 ACAATGATTCCAATGCAGATTACA 57.221 33.333 0.00 0.00 0.00 2.41
1617 1677 1.754226 TGACCTTGTTTTCCAGCAACC 59.246 47.619 0.00 0.00 0.00 3.77
1679 1739 4.078747 AGGTACCTATACTAGTGCCCAGTT 60.079 45.833 14.41 0.00 39.36 3.16
1732 1792 9.604626 GTTTAATCTCACAATTTCTTGAGTCTG 57.395 33.333 7.88 0.00 40.25 3.51
1749 1809 3.994392 TCTTGTGCACTCCGTTTAATCTC 59.006 43.478 19.41 0.00 0.00 2.75
1750 1810 3.997021 CTCTTGTGCACTCCGTTTAATCT 59.003 43.478 19.41 0.00 0.00 2.40
1758 1818 1.363744 GGATTCTCTTGTGCACTCCG 58.636 55.000 19.41 6.34 0.00 4.63
1763 1823 0.401356 TGCAGGGATTCTCTTGTGCA 59.599 50.000 0.00 0.00 38.55 4.57
1765 1825 3.377485 CAGATTGCAGGGATTCTCTTGTG 59.623 47.826 0.00 0.00 0.00 3.33
1879 2233 9.599866 CATCTCCCTTTTGGAAATATAAAAACC 57.400 33.333 0.00 0.00 44.57 3.27
1929 2283 2.033550 TCAAACGTGACCCGGAAAAATG 59.966 45.455 0.73 0.00 42.24 2.32
2036 2400 2.624838 CCAGAGGCAAACTGAAACACAT 59.375 45.455 7.68 0.00 37.54 3.21


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

AutoCloner maintained by Alex Coulton.