Multiple sequence alignment - TraesCS2B01G365900

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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 TraesCS2B01G365900 chr2B 100.000 3494 0 0 1 3494 521519137 521515644 0.000000e+00 6453.0
1 TraesCS2B01G365900 chr2B 87.928 555 34 11 869 1422 762186194 762185672 1.060000e-174 623.0
2 TraesCS2B01G365900 chr2B 88.027 451 30 7 869 1318 411179329 411179756 2.410000e-141 512.0
3 TraesCS2B01G365900 chr2B 92.523 107 5 3 2937 3040 357143832 357143938 2.170000e-32 150.0
4 TraesCS2B01G365900 chr2B 94.624 93 4 1 2937 3028 728363306 728363398 3.640000e-30 143.0
5 TraesCS2B01G365900 chr2B 92.308 52 3 1 2928 2978 507916874 507916925 4.840000e-09 73.1
6 TraesCS2B01G365900 chr2B 88.462 52 4 2 2925 2975 198092628 198092678 1.050000e-05 62.1
7 TraesCS2B01G365900 chr2D 92.633 2131 98 31 489 2591 441872763 441870664 0.000000e+00 3011.0
8 TraesCS2B01G365900 chr2D 88.252 349 25 6 2587 2930 441870621 441870284 1.510000e-108 403.0
9 TraesCS2B01G365900 chr2D 90.066 151 14 1 185 334 441874231 441874081 9.900000e-46 195.0
10 TraesCS2B01G365900 chr2D 88.158 76 4 1 433 503 441872853 441872778 6.210000e-13 86.1
11 TraesCS2B01G365900 chr2D 87.692 65 1 5 333 391 617215185 617215248 6.260000e-08 69.4
12 TraesCS2B01G365900 chr2A 94.299 1105 41 11 1500 2591 585741559 585740464 0.000000e+00 1672.0
13 TraesCS2B01G365900 chr2A 89.155 876 44 28 598 1428 585742457 585741588 0.000000e+00 1044.0
14 TraesCS2B01G365900 chr2A 98.592 568 8 0 2927 3494 654744784 654744217 0.000000e+00 1005.0
15 TraesCS2B01G365900 chr2A 97.368 570 13 2 2926 3494 166249102 166248534 0.000000e+00 968.0
16 TraesCS2B01G365900 chr2A 90.090 555 30 8 869 1422 272968412 272967882 0.000000e+00 697.0
17 TraesCS2B01G365900 chr2A 83.586 396 37 9 2587 2967 585740431 585740049 2.580000e-91 346.0
18 TraesCS2B01G365900 chr2A 95.745 47 2 0 330 376 566852086 566852132 3.740000e-10 76.8
19 TraesCS2B01G365900 chr2A 86.885 61 6 1 333 391 649489597 649489537 2.250000e-07 67.6
20 TraesCS2B01G365900 chr7A 97.670 558 13 0 2937 3494 8462425 8461868 0.000000e+00 959.0
21 TraesCS2B01G365900 chr7A 86.949 567 44 16 2936 3491 232337607 232337060 8.290000e-171 610.0
22 TraesCS2B01G365900 chr7A 91.837 49 3 1 328 375 503424521 503424569 2.250000e-07 67.6
23 TraesCS2B01G365900 chr1A 92.751 538 33 3 2936 3467 518027045 518026508 0.000000e+00 773.0
24 TraesCS2B01G365900 chr1A 92.548 416 27 1 3056 3467 561077197 561077612 8.350000e-166 593.0
25 TraesCS2B01G365900 chr1A 82.342 555 35 17 869 1422 346784776 346785268 1.160000e-114 424.0
26 TraesCS2B01G365900 chr7D 90.502 558 26 7 869 1422 556663918 556663384 0.000000e+00 712.0
27 TraesCS2B01G365900 chr7D 86.219 566 44 14 2937 3491 596073922 596074464 1.810000e-162 582.0
28 TraesCS2B01G365900 chr5D 90.270 555 30 6 869 1422 561349252 561348721 0.000000e+00 704.0
29 TraesCS2B01G365900 chr5D 84.058 69 8 1 329 397 561092257 561092192 2.910000e-06 63.9
30 TraesCS2B01G365900 chr3B 90.270 555 22 11 869 1419 740378984 740379510 0.000000e+00 697.0
31 TraesCS2B01G365900 chr3B 86.572 566 46 10 2937 3491 655667108 655667654 6.460000e-167 597.0
32 TraesCS2B01G365900 chr3B 89.354 263 13 5 869 1130 739244316 739244068 2.020000e-82 316.0
33 TraesCS2B01G365900 chr3B 84.672 137 21 0 1539 1675 137750705 137750841 1.690000e-28 137.0
34 TraesCS2B01G365900 chr5A 90.074 544 33 7 2928 3467 690938923 690939449 0.000000e+00 686.0
35 TraesCS2B01G365900 chrUn 91.667 348 14 5 869 1215 67152371 67152704 5.280000e-128 468.0
36 TraesCS2B01G365900 chr6A 81.564 358 64 2 1922 2278 393637966 393638322 9.480000e-76 294.0
37 TraesCS2B01G365900 chr6A 79.284 391 61 16 1030 1404 393637191 393637577 4.480000e-64 255.0
38 TraesCS2B01G365900 chr6A 84.722 144 21 1 1544 1686 393637591 393637734 3.640000e-30 143.0
39 TraesCS2B01G365900 chr6D 78.571 406 67 16 1027 1416 274341580 274341179 2.080000e-62 250.0
40 TraesCS2B01G365900 chr6D 82.877 146 20 5 1544 1686 274341177 274341034 3.660000e-25 126.0
41 TraesCS2B01G365900 chr6D 88.525 61 2 4 336 391 8789962 8790022 6.260000e-08 69.4
42 TraesCS2B01G365900 chr5B 87.429 175 7 5 869 1042 553580204 553580044 1.660000e-43 187.0
43 TraesCS2B01G365900 chr6B 84.722 144 21 1 1544 1686 436709326 436709183 3.640000e-30 143.0
44 TraesCS2B01G365900 chr6B 93.750 48 3 0 329 376 15719412 15719459 4.840000e-09 73.1
45 TraesCS2B01G365900 chr3D 84.672 137 21 0 1539 1675 88352214 88352350 1.690000e-28 137.0
46 TraesCS2B01G365900 chr3A 84.672 137 21 0 1539 1675 105112953 105112817 1.690000e-28 137.0
47 TraesCS2B01G365900 chr4B 90.566 53 5 0 329 381 416641157 416641209 1.740000e-08 71.3
48 TraesCS2B01G365900 chr7B 86.154 65 4 3 332 391 640229898 640229962 8.100000e-07 65.8


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 TraesCS2B01G365900 chr2B 521515644 521519137 3493 True 6453.000000 6453 100.000000 1 3494 1 chr2B.!!$R1 3493
1 TraesCS2B01G365900 chr2B 762185672 762186194 522 True 623.000000 623 87.928000 869 1422 1 chr2B.!!$R2 553
2 TraesCS2B01G365900 chr2D 441870284 441874231 3947 True 923.775000 3011 89.777250 185 2930 4 chr2D.!!$R1 2745
3 TraesCS2B01G365900 chr2A 585740049 585742457 2408 True 1020.666667 1672 89.013333 598 2967 3 chr2A.!!$R5 2369
4 TraesCS2B01G365900 chr2A 654744217 654744784 567 True 1005.000000 1005 98.592000 2927 3494 1 chr2A.!!$R4 567
5 TraesCS2B01G365900 chr2A 166248534 166249102 568 True 968.000000 968 97.368000 2926 3494 1 chr2A.!!$R1 568
6 TraesCS2B01G365900 chr2A 272967882 272968412 530 True 697.000000 697 90.090000 869 1422 1 chr2A.!!$R2 553
7 TraesCS2B01G365900 chr7A 8461868 8462425 557 True 959.000000 959 97.670000 2937 3494 1 chr7A.!!$R1 557
8 TraesCS2B01G365900 chr7A 232337060 232337607 547 True 610.000000 610 86.949000 2936 3491 1 chr7A.!!$R2 555
9 TraesCS2B01G365900 chr1A 518026508 518027045 537 True 773.000000 773 92.751000 2936 3467 1 chr1A.!!$R1 531
10 TraesCS2B01G365900 chr7D 556663384 556663918 534 True 712.000000 712 90.502000 869 1422 1 chr7D.!!$R1 553
11 TraesCS2B01G365900 chr7D 596073922 596074464 542 False 582.000000 582 86.219000 2937 3491 1 chr7D.!!$F1 554
12 TraesCS2B01G365900 chr5D 561348721 561349252 531 True 704.000000 704 90.270000 869 1422 1 chr5D.!!$R2 553
13 TraesCS2B01G365900 chr3B 740378984 740379510 526 False 697.000000 697 90.270000 869 1419 1 chr3B.!!$F3 550
14 TraesCS2B01G365900 chr3B 655667108 655667654 546 False 597.000000 597 86.572000 2937 3491 1 chr3B.!!$F2 554
15 TraesCS2B01G365900 chr5A 690938923 690939449 526 False 686.000000 686 90.074000 2928 3467 1 chr5A.!!$F1 539
16 TraesCS2B01G365900 chr6A 393637191 393638322 1131 False 230.666667 294 81.856667 1030 2278 3 chr6A.!!$F1 1248

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
609 1839 0.030638 CAAACACGGAGCCCACAAAG 59.969 55.0 0.0 0.0 0.0 2.77 F
785 2030 0.035630 CACCAAGGGAAGGCAGAGAG 60.036 60.0 0.0 0.0 0.0 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 2797 0.603439 CTTGGCCACCAATTTGTGCC 60.603 55.000 3.88 12.97 43.07 5.01 R
2684 4140 1.135402 GCCAAAGCAAAGTATCCACCG 60.135 52.381 0.00 0.00 39.53 4.94 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
42 43 3.140814 GGAACCCCGAATGGCAGC 61.141 66.667 0.00 0.00 0.00 5.25
43 44 3.140814 GAACCCCGAATGGCAGCC 61.141 66.667 3.66 3.66 0.00 4.85
60 61 4.569180 CGCCAATCCCGAGCCCAT 62.569 66.667 0.00 0.00 0.00 4.00
61 62 2.908940 GCCAATCCCGAGCCCATG 60.909 66.667 0.00 0.00 0.00 3.66
62 63 2.908940 CCAATCCCGAGCCCATGC 60.909 66.667 0.00 0.00 37.95 4.06
63 64 2.124193 CAATCCCGAGCCCATGCA 60.124 61.111 0.00 0.00 41.13 3.96
64 65 2.124151 AATCCCGAGCCCATGCAC 60.124 61.111 0.00 0.00 41.13 4.57
74 75 4.776322 CCATGCACGGCGAAGGGA 62.776 66.667 16.62 3.99 0.00 4.20
75 76 2.514592 CATGCACGGCGAAGGGAT 60.515 61.111 16.62 6.52 0.00 3.85
76 77 2.114670 CATGCACGGCGAAGGGATT 61.115 57.895 16.62 0.00 0.00 3.01
77 78 1.819632 ATGCACGGCGAAGGGATTC 60.820 57.895 16.62 0.00 0.00 2.52
78 79 2.125106 GCACGGCGAAGGGATTCT 60.125 61.111 16.62 0.00 0.00 2.40
79 80 2.464459 GCACGGCGAAGGGATTCTG 61.464 63.158 16.62 0.00 0.00 3.02
80 81 1.815421 CACGGCGAAGGGATTCTGG 60.815 63.158 16.62 0.00 0.00 3.86
81 82 2.203070 CGGCGAAGGGATTCTGGG 60.203 66.667 0.00 0.00 0.00 4.45
82 83 2.193248 GGCGAAGGGATTCTGGGG 59.807 66.667 0.00 0.00 0.00 4.96
83 84 2.375345 GGCGAAGGGATTCTGGGGA 61.375 63.158 0.00 0.00 0.00 4.81
84 85 1.147153 GCGAAGGGATTCTGGGGAG 59.853 63.158 0.00 0.00 0.00 4.30
85 86 1.147153 CGAAGGGATTCTGGGGAGC 59.853 63.158 0.00 0.00 0.00 4.70
86 87 1.147153 GAAGGGATTCTGGGGAGCG 59.853 63.158 0.00 0.00 0.00 5.03
87 88 2.330924 GAAGGGATTCTGGGGAGCGG 62.331 65.000 0.00 0.00 0.00 5.52
88 89 3.878667 GGGATTCTGGGGAGCGGG 61.879 72.222 0.00 0.00 0.00 6.13
89 90 2.768344 GGATTCTGGGGAGCGGGA 60.768 66.667 0.00 0.00 0.00 5.14
90 91 2.375345 GGATTCTGGGGAGCGGGAA 61.375 63.158 0.00 0.00 0.00 3.97
91 92 1.709994 GGATTCTGGGGAGCGGGAAT 61.710 60.000 0.00 0.00 0.00 3.01
92 93 0.250510 GATTCTGGGGAGCGGGAATC 60.251 60.000 0.00 0.00 37.80 2.52
93 94 2.044806 ATTCTGGGGAGCGGGAATCG 62.045 60.000 0.00 0.00 42.76 3.34
94 95 3.154473 CTGGGGAGCGGGAATCGA 61.154 66.667 0.00 0.00 42.43 3.59
95 96 3.447025 CTGGGGAGCGGGAATCGAC 62.447 68.421 0.00 0.00 42.43 4.20
96 97 4.237207 GGGGAGCGGGAATCGACC 62.237 72.222 0.00 0.00 42.43 4.79
102 103 4.143333 CGGGAATCGACCGCCACT 62.143 66.667 0.00 0.00 45.34 4.00
103 104 2.202892 GGGAATCGACCGCCACTC 60.203 66.667 0.00 0.00 0.00 3.51
104 105 2.582498 GGAATCGACCGCCACTCG 60.582 66.667 0.00 0.00 38.08 4.18
105 106 2.488355 GAATCGACCGCCACTCGA 59.512 61.111 0.00 0.00 43.94 4.04
106 107 1.872679 GAATCGACCGCCACTCGAC 60.873 63.158 0.00 0.00 42.69 4.20
107 108 3.352338 AATCGACCGCCACTCGACC 62.352 63.158 0.00 0.00 42.69 4.79
109 110 4.477975 CGACCGCCACTCGACCTC 62.478 72.222 0.00 0.00 41.67 3.85
110 111 4.477975 GACCGCCACTCGACCTCG 62.478 72.222 0.00 0.00 41.67 4.63
113 114 4.180946 CGCCACTCGACCTCGGAG 62.181 72.222 0.00 0.00 41.67 4.63
114 115 3.827898 GCCACTCGACCTCGGAGG 61.828 72.222 22.40 22.40 42.49 4.30
115 116 3.141488 CCACTCGACCTCGGAGGG 61.141 72.222 26.94 12.18 40.58 4.30
116 117 2.045242 CACTCGACCTCGGAGGGA 60.045 66.667 26.94 14.73 40.58 4.20
117 118 2.115911 CACTCGACCTCGGAGGGAG 61.116 68.421 26.94 23.95 40.58 4.30
118 119 2.299429 ACTCGACCTCGGAGGGAGA 61.299 63.158 27.06 22.82 46.23 3.71
119 120 1.525077 CTCGACCTCGGAGGGAGAG 60.525 68.421 26.94 26.23 46.23 3.20
124 125 2.904866 CTCGGAGGGAGAGGCTCG 60.905 72.222 9.22 0.00 46.23 5.03
125 126 3.707640 CTCGGAGGGAGAGGCTCGT 62.708 68.421 9.22 0.00 46.23 4.18
126 127 3.213402 CGGAGGGAGAGGCTCGTC 61.213 72.222 9.22 7.11 0.00 4.20
127 128 3.213402 GGAGGGAGAGGCTCGTCG 61.213 72.222 9.22 0.00 0.00 5.12
128 129 3.213402 GAGGGAGAGGCTCGTCGG 61.213 72.222 9.22 0.00 0.00 4.79
131 132 3.532155 GGAGAGGCTCGTCGGCAT 61.532 66.667 9.22 0.87 41.46 4.40
132 133 2.026879 GAGAGGCTCGTCGGCATC 59.973 66.667 9.22 10.93 42.40 3.91
133 134 2.755876 AGAGGCTCGTCGGCATCA 60.756 61.111 18.03 0.00 44.17 3.07
134 135 2.184322 GAGGCTCGTCGGCATCAA 59.816 61.111 13.13 0.00 41.80 2.57
135 136 1.880340 GAGGCTCGTCGGCATCAAG 60.880 63.158 13.13 0.00 41.80 3.02
136 137 3.567797 GGCTCGTCGGCATCAAGC 61.568 66.667 7.78 1.07 44.65 4.01
146 147 1.499056 GCATCAAGCCGCGATATGG 59.501 57.895 8.23 0.00 37.23 2.74
147 148 1.915614 GCATCAAGCCGCGATATGGG 61.916 60.000 8.23 0.80 37.23 4.00
157 158 2.899838 GATATGGGGTGCGCGCAA 60.900 61.111 38.24 21.87 0.00 4.85
158 159 2.896801 GATATGGGGTGCGCGCAAG 61.897 63.158 38.24 0.00 43.44 4.01
159 160 3.399105 ATATGGGGTGCGCGCAAGA 62.399 57.895 38.24 18.80 43.02 3.02
171 172 3.706373 GCAAGAGGGGAGCACGGA 61.706 66.667 0.00 0.00 0.00 4.69
172 173 2.581354 CAAGAGGGGAGCACGGAG 59.419 66.667 0.00 0.00 0.00 4.63
173 174 2.685380 AAGAGGGGAGCACGGAGG 60.685 66.667 0.00 0.00 0.00 4.30
174 175 4.787280 AGAGGGGAGCACGGAGGG 62.787 72.222 0.00 0.00 0.00 4.30
194 195 2.277501 GCGTGGACATTGCATCGC 60.278 61.111 0.00 0.00 33.45 4.58
196 197 1.061411 CGTGGACATTGCATCGCAG 59.939 57.895 0.00 0.00 40.61 5.18
206 207 2.126071 CATCGCAGGGTCGAACGT 60.126 61.111 0.00 0.00 42.15 3.99
238 1088 6.096846 ACTCAAATGCGGGCTAAATAAAGAAT 59.903 34.615 0.00 0.00 0.00 2.40
243 1093 3.304726 GCGGGCTAAATAAAGAATCCAGC 60.305 47.826 0.00 0.00 0.00 4.85
267 1117 5.466393 CCGGCTGAAAAATTCAACAGAAATT 59.534 36.000 0.00 0.00 39.58 1.82
268 1118 6.357198 CGGCTGAAAAATTCAACAGAAATTG 58.643 36.000 0.00 0.00 39.58 2.32
270 1120 5.842327 GCTGAAAAATTCAACAGAAATTGCG 59.158 36.000 0.00 0.00 39.58 4.85
298 1148 2.791567 CTCGGACATTCAGAGAGTTCG 58.208 52.381 0.00 0.00 40.43 3.95
303 1153 4.675408 CGGACATTCAGAGAGTTCGAATGA 60.675 45.833 16.00 0.00 41.49 2.57
304 1154 5.171476 GGACATTCAGAGAGTTCGAATGAA 58.829 41.667 16.00 12.18 41.49 2.57
324 1174 4.681025 TGAAAGCGAATTGAAATCACTTGC 59.319 37.500 0.00 0.00 0.00 4.01
331 1181 5.344128 CGAATTGAAATCACTTGCCTGAAAG 59.656 40.000 0.00 0.00 0.00 2.62
332 1182 5.796424 ATTGAAATCACTTGCCTGAAAGT 57.204 34.783 0.00 0.00 41.08 2.66
333 1183 6.899393 ATTGAAATCACTTGCCTGAAAGTA 57.101 33.333 0.00 0.00 38.34 2.24
334 1184 5.689383 TGAAATCACTTGCCTGAAAGTAC 57.311 39.130 0.00 0.00 38.34 2.73
335 1185 5.376625 TGAAATCACTTGCCTGAAAGTACT 58.623 37.500 0.00 0.00 38.34 2.73
336 1186 6.530120 TGAAATCACTTGCCTGAAAGTACTA 58.470 36.000 0.00 0.00 38.34 1.82
337 1187 6.426937 TGAAATCACTTGCCTGAAAGTACTAC 59.573 38.462 0.00 0.00 38.34 2.73
339 1189 5.135508 TCACTTGCCTGAAAGTACTACTC 57.864 43.478 0.00 0.00 38.34 2.59
340 1190 4.021368 TCACTTGCCTGAAAGTACTACTCC 60.021 45.833 0.00 0.00 38.34 3.85
342 1192 3.185880 TGCCTGAAAGTACTACTCCCT 57.814 47.619 0.00 0.00 0.00 4.20
343 1193 3.097614 TGCCTGAAAGTACTACTCCCTC 58.902 50.000 0.00 0.00 0.00 4.30
344 1194 2.431419 GCCTGAAAGTACTACTCCCTCC 59.569 54.545 0.00 0.00 0.00 4.30
345 1195 2.688958 CCTGAAAGTACTACTCCCTCCG 59.311 54.545 0.00 0.00 0.00 4.63
346 1196 3.354467 CTGAAAGTACTACTCCCTCCGT 58.646 50.000 0.00 0.00 0.00 4.69
347 1197 3.762823 CTGAAAGTACTACTCCCTCCGTT 59.237 47.826 0.00 0.00 0.00 4.44
348 1198 3.760684 TGAAAGTACTACTCCCTCCGTTC 59.239 47.826 0.00 0.00 0.00 3.95
349 1199 2.433662 AGTACTACTCCCTCCGTTCC 57.566 55.000 0.00 0.00 0.00 3.62
350 1200 1.921748 AGTACTACTCCCTCCGTTCCT 59.078 52.381 0.00 0.00 0.00 3.36
351 1201 3.118531 AGTACTACTCCCTCCGTTCCTA 58.881 50.000 0.00 0.00 0.00 2.94
352 1202 3.525199 AGTACTACTCCCTCCGTTCCTAA 59.475 47.826 0.00 0.00 0.00 2.69
353 1203 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
354 1204 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
355 1205 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
356 1206 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
357 1207 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
358 1208 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
359 1209 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
360 1210 6.379579 ACTCCCTCCGTTCCTAAATATAAGA 58.620 40.000 0.00 0.00 0.00 2.10
361 1211 6.267242 ACTCCCTCCGTTCCTAAATATAAGAC 59.733 42.308 0.00 0.00 0.00 3.01
362 1212 5.541484 TCCCTCCGTTCCTAAATATAAGACC 59.459 44.000 0.00 0.00 0.00 3.85
363 1213 5.543020 CCCTCCGTTCCTAAATATAAGACCT 59.457 44.000 0.00 0.00 0.00 3.85
364 1214 6.042897 CCCTCCGTTCCTAAATATAAGACCTT 59.957 42.308 0.00 0.00 0.00 3.50
365 1215 7.419865 CCCTCCGTTCCTAAATATAAGACCTTT 60.420 40.741 0.00 0.00 0.00 3.11
366 1216 7.991460 CCTCCGTTCCTAAATATAAGACCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
369 1219 9.269453 CCGTTCCTAAATATAAGACCTTTTAGG 57.731 37.037 12.11 12.11 46.30 2.69
377 1227 9.916360 AAATATAAGACCTTTTAGGAATTCCGT 57.084 29.630 18.82 9.39 37.67 4.69
378 1228 9.916360 AATATAAGACCTTTTAGGAATTCCGTT 57.084 29.630 18.82 5.13 37.67 4.44
379 1229 5.959618 AAGACCTTTTAGGAATTCCGTTG 57.040 39.130 18.82 8.58 37.67 4.10
380 1230 4.981812 AGACCTTTTAGGAATTCCGTTGT 58.018 39.130 18.82 11.07 37.67 3.32
381 1231 6.117975 AGACCTTTTAGGAATTCCGTTGTA 57.882 37.500 18.82 2.95 37.67 2.41
382 1232 5.936372 AGACCTTTTAGGAATTCCGTTGTAC 59.064 40.000 18.82 7.90 37.67 2.90
383 1233 5.623169 ACCTTTTAGGAATTCCGTTGTACA 58.377 37.500 18.82 0.00 37.67 2.90
384 1234 6.243148 ACCTTTTAGGAATTCCGTTGTACAT 58.757 36.000 18.82 1.33 37.67 2.29
385 1235 7.396418 ACCTTTTAGGAATTCCGTTGTACATA 58.604 34.615 18.82 0.32 37.67 2.29
386 1236 7.335171 ACCTTTTAGGAATTCCGTTGTACATAC 59.665 37.037 18.82 0.00 37.67 2.39
387 1237 6.890663 TTTAGGAATTCCGTTGTACATACG 57.109 37.500 18.82 17.90 42.08 3.06
394 1244 2.486951 CGTTGTACATACGGAGGGAG 57.513 55.000 17.38 0.00 35.47 4.30
395 1245 1.747355 CGTTGTACATACGGAGGGAGT 59.253 52.381 17.38 0.00 35.47 3.85
396 1246 2.945008 CGTTGTACATACGGAGGGAGTA 59.055 50.000 17.38 0.00 35.47 2.59
397 1247 3.242870 CGTTGTACATACGGAGGGAGTAC 60.243 52.174 17.38 0.00 35.47 2.73
398 1248 3.939740 TGTACATACGGAGGGAGTACT 57.060 47.619 0.00 0.00 36.80 2.73
399 1249 3.548770 TGTACATACGGAGGGAGTACTG 58.451 50.000 0.00 0.00 36.80 2.74
400 1250 2.068834 ACATACGGAGGGAGTACTGG 57.931 55.000 0.00 0.00 0.00 4.00
401 1251 0.674534 CATACGGAGGGAGTACTGGC 59.325 60.000 0.00 0.00 0.00 4.85
402 1252 0.260816 ATACGGAGGGAGTACTGGCA 59.739 55.000 0.00 0.00 0.00 4.92
403 1253 0.260816 TACGGAGGGAGTACTGGCAT 59.739 55.000 0.00 0.00 0.00 4.40
404 1254 0.617820 ACGGAGGGAGTACTGGCATT 60.618 55.000 0.00 0.00 0.00 3.56
405 1255 0.179073 CGGAGGGAGTACTGGCATTG 60.179 60.000 0.00 0.00 0.00 2.82
406 1256 0.464554 GGAGGGAGTACTGGCATTGC 60.465 60.000 0.00 0.00 0.00 3.56
407 1257 0.253044 GAGGGAGTACTGGCATTGCA 59.747 55.000 11.39 0.00 0.00 4.08
408 1258 0.254178 AGGGAGTACTGGCATTGCAG 59.746 55.000 11.39 8.54 0.00 4.41
419 1269 4.711355 ACTGGCATTGCAGGTAATTGTATT 59.289 37.500 11.39 0.00 0.00 1.89
428 1278 7.275888 TGCAGGTAATTGTATTGAATGGATC 57.724 36.000 0.00 0.00 0.00 3.36
429 1279 6.265196 TGCAGGTAATTGTATTGAATGGATCC 59.735 38.462 4.20 4.20 0.00 3.36
431 1281 7.039504 GCAGGTAATTGTATTGAATGGATCCAT 60.040 37.037 22.15 22.15 38.46 3.41
453 1650 8.322828 TCCATAAAAAGTTATACCTGCTGTACA 58.677 33.333 0.00 0.00 30.62 2.90
460 1657 1.171308 TACCTGCTGTACAGTCCGAC 58.829 55.000 23.44 7.55 45.68 4.79
529 1759 4.982241 TTCTGAGGAGTTCTGGAAACAT 57.018 40.909 0.00 0.00 41.51 2.71
550 1780 1.457455 CTGGGGCAACAAACTGGGT 60.457 57.895 0.00 0.00 39.74 4.51
556 1786 1.391157 GCAACAAACTGGGTGCAGGA 61.391 55.000 0.00 0.00 34.11 3.86
559 1789 0.550914 ACAAACTGGGTGCAGGAAGA 59.449 50.000 0.00 0.00 0.00 2.87
560 1790 1.242076 CAAACTGGGTGCAGGAAGAG 58.758 55.000 0.00 0.00 0.00 2.85
561 1791 0.111253 AAACTGGGTGCAGGAAGAGG 59.889 55.000 0.00 0.00 0.00 3.69
562 1792 1.783250 AACTGGGTGCAGGAAGAGGG 61.783 60.000 0.00 0.00 0.00 4.30
563 1793 2.935481 TGGGTGCAGGAAGAGGGG 60.935 66.667 0.00 0.00 0.00 4.79
564 1794 4.432741 GGGTGCAGGAAGAGGGGC 62.433 72.222 0.00 0.00 0.00 5.80
565 1795 4.432741 GGTGCAGGAAGAGGGGCC 62.433 72.222 0.00 0.00 0.00 5.80
566 1796 4.785453 GTGCAGGAAGAGGGGCCG 62.785 72.222 0.00 0.00 0.00 6.13
568 1798 4.475135 GCAGGAAGAGGGGCCGAC 62.475 72.222 0.00 0.00 0.00 4.79
569 1799 3.787001 CAGGAAGAGGGGCCGACC 61.787 72.222 0.00 0.00 39.11 4.79
594 1824 2.051345 CGCAACCGCAGTCCAAAC 60.051 61.111 0.00 0.00 38.40 2.93
609 1839 0.030638 CAAACACGGAGCCCACAAAG 59.969 55.000 0.00 0.00 0.00 2.77
615 1845 1.237285 CGGAGCCCACAAAGTCCTTG 61.237 60.000 0.00 0.00 41.19 3.61
624 1854 3.305608 CCACAAAGTCCTTGCATTTCTCC 60.306 47.826 0.00 0.00 38.75 3.71
667 1908 2.029073 AACACCACACGCGAGAGG 59.971 61.111 15.93 16.90 0.00 3.69
781 2026 1.672356 CGTCACCAAGGGAAGGCAG 60.672 63.158 0.00 0.00 0.00 4.85
782 2027 1.761174 GTCACCAAGGGAAGGCAGA 59.239 57.895 0.00 0.00 0.00 4.26
784 2029 0.473694 TCACCAAGGGAAGGCAGAGA 60.474 55.000 0.00 0.00 0.00 3.10
785 2030 0.035630 CACCAAGGGAAGGCAGAGAG 60.036 60.000 0.00 0.00 0.00 3.20
786 2031 0.178891 ACCAAGGGAAGGCAGAGAGA 60.179 55.000 0.00 0.00 0.00 3.10
844 2101 4.544689 CGCAGAGGAGCCGAGACG 62.545 72.222 0.00 0.00 0.00 4.18
845 2102 3.134792 GCAGAGGAGCCGAGACGA 61.135 66.667 0.00 0.00 0.00 4.20
1457 2771 1.676006 CCGATTAACCCATCAGCCAAC 59.324 52.381 0.00 0.00 0.00 3.77
1458 2772 1.330521 CGATTAACCCATCAGCCAACG 59.669 52.381 0.00 0.00 0.00 4.10
1476 2791 2.438434 GCCCTTATGCCACGCACT 60.438 61.111 0.00 0.00 43.04 4.40
1680 2995 0.036448 ACTTCGACCTCTCCACGAGA 59.964 55.000 0.00 0.00 42.62 4.04
1719 3034 3.966543 CAGGACGCCCCCAAACCT 61.967 66.667 0.00 0.00 34.66 3.50
1794 3112 1.595929 GTGCTTCCGGTTCCGTTCA 60.596 57.895 0.00 0.21 0.00 3.18
1821 3139 4.250305 ACAAAGCCGGCCGTGTCT 62.250 61.111 26.15 15.06 0.00 3.41
1878 3205 1.000771 CTCCTCGTCCTCCACCTCA 60.001 63.158 0.00 0.00 0.00 3.86
1881 3208 0.684479 CCTCGTCCTCCACCTCATCA 60.684 60.000 0.00 0.00 0.00 3.07
2625 4080 7.016661 AGGGATGAGTACATAATTAAGGAGGTG 59.983 40.741 0.00 0.00 36.82 4.00
2626 4081 6.651225 GGATGAGTACATAATTAAGGAGGTGC 59.349 42.308 0.00 0.00 36.82 5.01
2629 4084 7.473511 ATGAGTACATAATTAAGGAGGTGCTCC 60.474 40.741 14.98 0.00 41.70 4.70
2650 4105 3.056749 CCTGTGTTTAGCGGAGTAGAGTT 60.057 47.826 0.00 0.00 0.00 3.01
2651 4106 3.909430 TGTGTTTAGCGGAGTAGAGTTG 58.091 45.455 0.00 0.00 0.00 3.16
2652 4107 3.319972 TGTGTTTAGCGGAGTAGAGTTGT 59.680 43.478 0.00 0.00 0.00 3.32
2653 4108 4.520111 TGTGTTTAGCGGAGTAGAGTTGTA 59.480 41.667 0.00 0.00 0.00 2.41
2654 4109 4.855937 GTGTTTAGCGGAGTAGAGTTGTAC 59.144 45.833 0.00 0.00 0.00 2.90
2655 4110 4.094212 GTTTAGCGGAGTAGAGTTGTACG 58.906 47.826 0.00 0.00 0.00 3.67
2656 4111 1.818642 AGCGGAGTAGAGTTGTACGT 58.181 50.000 0.00 0.00 0.00 3.57
2665 4121 6.044512 AGTAGAGTTGTACGTTTTTGCTTG 57.955 37.500 0.00 0.00 0.00 4.01
2684 4140 4.301628 CTTGGCTTCTTGTCCACATTTTC 58.698 43.478 0.00 0.00 30.97 2.29
2709 4170 0.887933 ATACTTTGCTTTGGCCCGTG 59.112 50.000 0.00 0.00 37.74 4.94
2735 4196 3.564644 ACGAGGATTATTGAGACGATCGT 59.435 43.478 22.97 22.97 36.18 3.73
2754 4215 9.471084 ACGATCGTGTACATAATGAATAATCAA 57.529 29.630 22.06 0.00 39.49 2.57
2782 4243 2.634815 ATTAGGCAGATGAGGTGCAG 57.365 50.000 0.00 0.00 43.12 4.41
2783 4244 0.543277 TTAGGCAGATGAGGTGCAGG 59.457 55.000 0.00 0.00 43.12 4.85
2804 4265 5.519927 CAGGTTGGTCTTGATGTTTGTTTTC 59.480 40.000 0.00 0.00 0.00 2.29
2811 4272 6.202762 GGTCTTGATGTTTGTTTTCCCATTTC 59.797 38.462 0.00 0.00 0.00 2.17
2818 4279 1.268794 TGTTTTCCCATTTCGTGCACG 60.269 47.619 32.76 32.76 41.45 5.34
2840 4301 4.082787 CGGTGACTTTTGGTAAGCATTGAT 60.083 41.667 0.00 0.00 0.00 2.57
2845 4306 7.062255 GTGACTTTTGGTAAGCATTGATTTAGC 59.938 37.037 0.00 0.00 0.00 3.09
3181 4660 6.378661 AGCATCTATGGCAACCATATAGAA 57.621 37.500 6.78 0.00 44.33 2.10
3488 4976 8.311109 TGTGTCATCTAAAGATAAGTGCTTACA 58.689 33.333 0.00 0.00 32.63 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.055227 TGCCATTCGGGGTTCCCC 62.055 66.667 16.52 16.52 41.57 4.81
24 25 2.440247 CTGCCATTCGGGGTTCCC 60.440 66.667 0.00 0.00 41.09 3.97
25 26 3.140814 GCTGCCATTCGGGGTTCC 61.141 66.667 0.00 0.00 37.04 3.62
26 27 3.140814 GGCTGCCATTCGGGGTTC 61.141 66.667 15.17 0.00 37.04 3.62
43 44 4.569180 ATGGGCTCGGGATTGGCG 62.569 66.667 0.00 0.00 0.00 5.69
44 45 2.908940 CATGGGCTCGGGATTGGC 60.909 66.667 0.00 0.00 0.00 4.52
45 46 2.908940 GCATGGGCTCGGGATTGG 60.909 66.667 0.00 0.00 36.96 3.16
46 47 2.124193 TGCATGGGCTCGGGATTG 60.124 61.111 0.00 0.00 41.91 2.67
47 48 2.124151 GTGCATGGGCTCGGGATT 60.124 61.111 0.00 0.00 41.91 3.01
57 58 4.776322 TCCCTTCGCCGTGCATGG 62.776 66.667 21.33 21.33 0.00 3.66
58 59 2.051804 GAATCCCTTCGCCGTGCATG 62.052 60.000 0.00 0.00 0.00 4.06
59 60 1.819632 GAATCCCTTCGCCGTGCAT 60.820 57.895 0.00 0.00 0.00 3.96
60 61 2.435938 GAATCCCTTCGCCGTGCA 60.436 61.111 0.00 0.00 0.00 4.57
61 62 2.125106 AGAATCCCTTCGCCGTGC 60.125 61.111 0.00 0.00 36.45 5.34
62 63 1.815421 CCAGAATCCCTTCGCCGTG 60.815 63.158 0.00 0.00 36.45 4.94
63 64 2.584608 CCAGAATCCCTTCGCCGT 59.415 61.111 0.00 0.00 36.45 5.68
64 65 2.203070 CCCAGAATCCCTTCGCCG 60.203 66.667 0.00 0.00 36.45 6.46
65 66 2.193248 CCCCAGAATCCCTTCGCC 59.807 66.667 0.00 0.00 36.45 5.54
66 67 1.147153 CTCCCCAGAATCCCTTCGC 59.853 63.158 0.00 0.00 36.45 4.70
67 68 1.147153 GCTCCCCAGAATCCCTTCG 59.853 63.158 0.00 0.00 36.45 3.79
68 69 1.147153 CGCTCCCCAGAATCCCTTC 59.853 63.158 0.00 0.00 0.00 3.46
69 70 2.378634 CCGCTCCCCAGAATCCCTT 61.379 63.158 0.00 0.00 0.00 3.95
70 71 2.770048 CCGCTCCCCAGAATCCCT 60.770 66.667 0.00 0.00 0.00 4.20
71 72 3.878667 CCCGCTCCCCAGAATCCC 61.879 72.222 0.00 0.00 0.00 3.85
72 73 1.709994 ATTCCCGCTCCCCAGAATCC 61.710 60.000 0.00 0.00 0.00 3.01
73 74 0.250510 GATTCCCGCTCCCCAGAATC 60.251 60.000 0.00 0.00 38.25 2.52
74 75 1.839894 GATTCCCGCTCCCCAGAAT 59.160 57.895 0.00 0.00 0.00 2.40
75 76 2.731571 CGATTCCCGCTCCCCAGAA 61.732 63.158 0.00 0.00 0.00 3.02
76 77 3.154473 CGATTCCCGCTCCCCAGA 61.154 66.667 0.00 0.00 0.00 3.86
77 78 3.154473 TCGATTCCCGCTCCCCAG 61.154 66.667 0.00 0.00 38.37 4.45
78 79 3.467226 GTCGATTCCCGCTCCCCA 61.467 66.667 0.00 0.00 38.37 4.96
79 80 4.237207 GGTCGATTCCCGCTCCCC 62.237 72.222 0.00 0.00 38.37 4.81
80 81 4.587189 CGGTCGATTCCCGCTCCC 62.587 72.222 0.00 0.00 38.85 4.30
86 87 2.202892 GAGTGGCGGTCGATTCCC 60.203 66.667 0.00 0.00 0.00 3.97
87 88 2.582498 CGAGTGGCGGTCGATTCC 60.582 66.667 2.36 0.00 39.92 3.01
88 89 2.488355 TCGAGTGGCGGTCGATTC 59.512 61.111 6.89 0.00 41.41 2.52
92 93 4.477975 GAGGTCGAGTGGCGGTCG 62.478 72.222 2.12 2.12 41.33 4.79
93 94 4.477975 CGAGGTCGAGTGGCGGTC 62.478 72.222 0.00 0.00 43.02 4.79
96 97 4.180946 CTCCGAGGTCGAGTGGCG 62.181 72.222 0.00 0.00 43.02 5.69
97 98 3.827898 CCTCCGAGGTCGAGTGGC 61.828 72.222 6.24 0.00 43.02 5.01
98 99 3.141488 CCCTCCGAGGTCGAGTGG 61.141 72.222 13.62 2.08 43.02 4.00
99 100 2.045242 TCCCTCCGAGGTCGAGTG 60.045 66.667 13.62 0.00 43.02 3.51
100 101 2.260088 CTCTCCCTCCGAGGTCGAGT 62.260 65.000 13.62 0.00 43.02 4.18
101 102 1.525077 CTCTCCCTCCGAGGTCGAG 60.525 68.421 13.62 12.90 43.02 4.04
102 103 2.590645 CTCTCCCTCCGAGGTCGA 59.409 66.667 13.62 8.00 43.02 4.20
103 104 2.517402 CCTCTCCCTCCGAGGTCG 60.517 72.222 13.62 3.99 42.47 4.79
107 108 2.904866 CGAGCCTCTCCCTCCGAG 60.905 72.222 0.00 0.00 40.30 4.63
108 109 3.700831 GACGAGCCTCTCCCTCCGA 62.701 68.421 0.00 0.00 0.00 4.55
109 110 3.213402 GACGAGCCTCTCCCTCCG 61.213 72.222 0.00 0.00 0.00 4.63
110 111 3.213402 CGACGAGCCTCTCCCTCC 61.213 72.222 0.00 0.00 0.00 4.30
111 112 3.213402 CCGACGAGCCTCTCCCTC 61.213 72.222 0.00 0.00 0.00 4.30
114 115 3.492311 GATGCCGACGAGCCTCTCC 62.492 68.421 0.00 0.00 0.00 3.71
115 116 2.026879 GATGCCGACGAGCCTCTC 59.973 66.667 0.00 0.00 0.00 3.20
116 117 2.290122 CTTGATGCCGACGAGCCTCT 62.290 60.000 0.00 0.00 0.00 3.69
117 118 1.880340 CTTGATGCCGACGAGCCTC 60.880 63.158 0.00 1.64 0.00 4.70
118 119 2.185350 CTTGATGCCGACGAGCCT 59.815 61.111 0.00 0.00 0.00 4.58
119 120 3.567797 GCTTGATGCCGACGAGCC 61.568 66.667 0.00 0.00 38.43 4.70
128 129 1.499056 CCATATCGCGGCTTGATGC 59.501 57.895 6.13 0.00 41.94 3.91
129 130 1.300971 CCCCATATCGCGGCTTGATG 61.301 60.000 6.13 3.03 0.00 3.07
130 131 1.003355 CCCCATATCGCGGCTTGAT 60.003 57.895 6.13 0.00 0.00 2.57
131 132 2.425592 CCCCATATCGCGGCTTGA 59.574 61.111 6.13 0.00 0.00 3.02
132 133 2.111043 ACCCCATATCGCGGCTTG 59.889 61.111 6.13 0.74 0.00 4.01
133 134 2.111043 CACCCCATATCGCGGCTT 59.889 61.111 6.13 0.00 0.00 4.35
134 135 4.626081 GCACCCCATATCGCGGCT 62.626 66.667 6.13 0.00 0.00 5.52
140 141 2.896801 CTTGCGCGCACCCCATATC 61.897 63.158 36.72 0.00 0.00 1.63
141 142 2.901840 CTTGCGCGCACCCCATAT 60.902 61.111 36.72 0.00 0.00 1.78
142 143 4.089239 TCTTGCGCGCACCCCATA 62.089 61.111 36.72 17.84 0.00 2.74
154 155 3.672295 CTCCGTGCTCCCCTCTTGC 62.672 68.421 0.00 0.00 0.00 4.01
155 156 2.581354 CTCCGTGCTCCCCTCTTG 59.419 66.667 0.00 0.00 0.00 3.02
156 157 2.685380 CCTCCGTGCTCCCCTCTT 60.685 66.667 0.00 0.00 0.00 2.85
157 158 4.787280 CCCTCCGTGCTCCCCTCT 62.787 72.222 0.00 0.00 0.00 3.69
169 170 2.670148 AATGTCCACGCTCCCCTCC 61.670 63.158 0.00 0.00 0.00 4.30
170 171 1.450312 CAATGTCCACGCTCCCCTC 60.450 63.158 0.00 0.00 0.00 4.30
171 172 2.671070 CAATGTCCACGCTCCCCT 59.329 61.111 0.00 0.00 0.00 4.79
172 173 3.134127 GCAATGTCCACGCTCCCC 61.134 66.667 0.00 0.00 0.00 4.81
173 174 1.718757 GATGCAATGTCCACGCTCCC 61.719 60.000 0.00 0.00 0.00 4.30
174 175 1.723870 GATGCAATGTCCACGCTCC 59.276 57.895 0.00 0.00 0.00 4.70
175 176 1.349627 CGATGCAATGTCCACGCTC 59.650 57.895 0.00 0.00 0.00 5.03
176 177 2.753966 GCGATGCAATGTCCACGCT 61.754 57.895 0.00 0.00 42.19 5.07
177 178 2.277501 GCGATGCAATGTCCACGC 60.278 61.111 0.00 0.00 39.33 5.34
178 179 1.061411 CTGCGATGCAATGTCCACG 59.939 57.895 0.00 0.00 38.41 4.94
179 180 1.430632 CCTGCGATGCAATGTCCAC 59.569 57.895 0.00 0.00 38.41 4.02
180 181 1.750018 CCCTGCGATGCAATGTCCA 60.750 57.895 0.00 0.00 38.41 4.02
181 182 1.718757 GACCCTGCGATGCAATGTCC 61.719 60.000 0.00 0.00 38.41 4.02
182 183 1.723870 GACCCTGCGATGCAATGTC 59.276 57.895 0.00 5.09 38.41 3.06
183 184 2.108514 CGACCCTGCGATGCAATGT 61.109 57.895 0.00 0.00 38.41 2.71
194 195 1.865788 TTACCGGACGTTCGACCCTG 61.866 60.000 20.12 2.34 0.00 4.45
196 197 1.444383 GTTACCGGACGTTCGACCC 60.444 63.158 20.12 0.00 0.00 4.46
206 207 0.391927 CCCGCATTTGAGTTACCGGA 60.392 55.000 9.46 0.00 38.04 5.14
238 1088 0.887933 GAATTTTTCAGCCGGCTGGA 59.112 50.000 46.58 41.19 43.75 3.86
243 1093 3.641437 TCTGTTGAATTTTTCAGCCGG 57.359 42.857 0.00 0.00 41.38 6.13
257 1107 0.597568 TCCAGCCGCAATTTCTGTTG 59.402 50.000 0.00 0.00 0.00 3.33
270 1120 1.522580 GAATGTCCGAGCTCCAGCC 60.523 63.158 8.47 0.00 43.38 4.85
298 1148 7.442657 CAAGTGATTTCAATTCGCTTTCATTC 58.557 34.615 5.53 0.00 31.17 2.67
303 1153 3.989817 GGCAAGTGATTTCAATTCGCTTT 59.010 39.130 5.53 0.00 31.17 3.51
304 1154 3.256631 AGGCAAGTGATTTCAATTCGCTT 59.743 39.130 2.82 2.82 31.17 4.68
324 1174 2.688958 CGGAGGGAGTAGTACTTTCAGG 59.311 54.545 0.00 0.00 0.00 3.86
331 1181 2.433662 AGGAACGGAGGGAGTAGTAC 57.566 55.000 0.00 0.00 0.00 2.73
332 1182 4.591321 TTTAGGAACGGAGGGAGTAGTA 57.409 45.455 0.00 0.00 0.00 1.82
333 1183 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
334 1184 7.668886 TCTTATATTTAGGAACGGAGGGAGTAG 59.331 40.741 0.00 0.00 0.00 2.57
335 1185 7.449704 GTCTTATATTTAGGAACGGAGGGAGTA 59.550 40.741 0.00 0.00 0.00 2.59
336 1186 6.267242 GTCTTATATTTAGGAACGGAGGGAGT 59.733 42.308 0.00 0.00 0.00 3.85
337 1187 6.295180 GGTCTTATATTTAGGAACGGAGGGAG 60.295 46.154 0.00 0.00 0.00 4.30
339 1189 5.543020 AGGTCTTATATTTAGGAACGGAGGG 59.457 44.000 0.00 0.00 0.00 4.30
340 1190 6.667558 AGGTCTTATATTTAGGAACGGAGG 57.332 41.667 0.00 0.00 0.00 4.30
351 1201 9.916360 ACGGAATTCCTAAAAGGTCTTATATTT 57.084 29.630 22.05 0.00 36.53 1.40
352 1202 9.916360 AACGGAATTCCTAAAAGGTCTTATATT 57.084 29.630 22.05 0.00 36.53 1.28
353 1203 9.338622 CAACGGAATTCCTAAAAGGTCTTATAT 57.661 33.333 22.05 0.00 36.53 0.86
354 1204 8.323567 ACAACGGAATTCCTAAAAGGTCTTATA 58.676 33.333 22.05 0.00 36.53 0.98
355 1205 7.173032 ACAACGGAATTCCTAAAAGGTCTTAT 58.827 34.615 22.05 0.00 36.53 1.73
356 1206 6.536447 ACAACGGAATTCCTAAAAGGTCTTA 58.464 36.000 22.05 0.00 36.53 2.10
357 1207 5.382616 ACAACGGAATTCCTAAAAGGTCTT 58.617 37.500 22.05 0.15 36.53 3.01
358 1208 4.981812 ACAACGGAATTCCTAAAAGGTCT 58.018 39.130 22.05 1.05 36.53 3.85
359 1209 5.702209 TGTACAACGGAATTCCTAAAAGGTC 59.298 40.000 22.05 6.68 36.53 3.85
360 1210 5.623169 TGTACAACGGAATTCCTAAAAGGT 58.377 37.500 22.05 8.65 36.53 3.50
361 1211 6.753107 ATGTACAACGGAATTCCTAAAAGG 57.247 37.500 22.05 8.00 36.46 3.11
362 1212 7.396419 CGTATGTACAACGGAATTCCTAAAAG 58.604 38.462 22.05 8.72 36.71 2.27
363 1213 7.293402 CGTATGTACAACGGAATTCCTAAAA 57.707 36.000 22.05 1.42 36.71 1.52
364 1214 6.890663 CGTATGTACAACGGAATTCCTAAA 57.109 37.500 22.05 3.48 36.71 1.85
375 1225 1.747355 ACTCCCTCCGTATGTACAACG 59.253 52.381 17.90 17.90 40.01 4.10
376 1226 3.950395 AGTACTCCCTCCGTATGTACAAC 59.050 47.826 0.00 0.00 36.80 3.32
377 1227 3.949754 CAGTACTCCCTCCGTATGTACAA 59.050 47.826 0.00 0.00 36.80 2.41
378 1228 3.548770 CAGTACTCCCTCCGTATGTACA 58.451 50.000 0.00 0.00 36.80 2.90
379 1229 2.883386 CCAGTACTCCCTCCGTATGTAC 59.117 54.545 0.00 0.00 35.18 2.90
380 1230 2.750807 GCCAGTACTCCCTCCGTATGTA 60.751 54.545 0.00 0.00 0.00 2.29
381 1231 2.027949 GCCAGTACTCCCTCCGTATGT 61.028 57.143 0.00 0.00 0.00 2.29
382 1232 0.674534 GCCAGTACTCCCTCCGTATG 59.325 60.000 0.00 0.00 0.00 2.39
383 1233 0.260816 TGCCAGTACTCCCTCCGTAT 59.739 55.000 0.00 0.00 0.00 3.06
384 1234 0.260816 ATGCCAGTACTCCCTCCGTA 59.739 55.000 0.00 0.00 0.00 4.02
385 1235 0.617820 AATGCCAGTACTCCCTCCGT 60.618 55.000 0.00 0.00 0.00 4.69
386 1236 0.179073 CAATGCCAGTACTCCCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
387 1237 0.464554 GCAATGCCAGTACTCCCTCC 60.465 60.000 0.00 0.00 0.00 4.30
388 1238 0.253044 TGCAATGCCAGTACTCCCTC 59.747 55.000 1.53 0.00 0.00 4.30
389 1239 0.254178 CTGCAATGCCAGTACTCCCT 59.746 55.000 1.53 0.00 0.00 4.20
390 1240 0.749454 CCTGCAATGCCAGTACTCCC 60.749 60.000 1.53 0.00 0.00 4.30
391 1241 0.035056 ACCTGCAATGCCAGTACTCC 60.035 55.000 1.53 0.00 0.00 3.85
392 1242 2.691409 TACCTGCAATGCCAGTACTC 57.309 50.000 1.53 0.00 0.00 2.59
393 1243 3.652057 ATTACCTGCAATGCCAGTACT 57.348 42.857 1.53 0.00 0.00 2.73
394 1244 3.443681 ACAATTACCTGCAATGCCAGTAC 59.556 43.478 1.53 0.00 0.00 2.73
395 1245 3.696045 ACAATTACCTGCAATGCCAGTA 58.304 40.909 1.53 1.23 0.00 2.74
396 1246 2.528564 ACAATTACCTGCAATGCCAGT 58.471 42.857 1.53 2.32 0.00 4.00
397 1247 4.924305 ATACAATTACCTGCAATGCCAG 57.076 40.909 1.53 0.00 0.00 4.85
398 1248 4.708909 TCAATACAATTACCTGCAATGCCA 59.291 37.500 1.53 0.00 0.00 4.92
399 1249 5.261209 TCAATACAATTACCTGCAATGCC 57.739 39.130 1.53 0.00 0.00 4.40
400 1250 6.201425 CCATTCAATACAATTACCTGCAATGC 59.799 38.462 0.00 0.00 0.00 3.56
401 1251 7.490840 TCCATTCAATACAATTACCTGCAATG 58.509 34.615 0.00 0.00 0.00 2.82
402 1252 7.658525 TCCATTCAATACAATTACCTGCAAT 57.341 32.000 0.00 0.00 0.00 3.56
403 1253 7.201902 GGATCCATTCAATACAATTACCTGCAA 60.202 37.037 6.95 0.00 0.00 4.08
404 1254 6.265196 GGATCCATTCAATACAATTACCTGCA 59.735 38.462 6.95 0.00 0.00 4.41
405 1255 6.265196 TGGATCCATTCAATACAATTACCTGC 59.735 38.462 11.44 0.00 0.00 4.85
406 1256 7.822161 TGGATCCATTCAATACAATTACCTG 57.178 36.000 11.44 0.00 0.00 4.00
428 1278 8.500753 TGTACAGCAGGTATAACTTTTTATGG 57.499 34.615 0.00 0.00 33.76 2.74
453 1650 2.290464 CTTCGGTCTATCTGTCGGACT 58.710 52.381 9.88 0.00 0.00 3.85
460 1657 4.276431 GGAGTAGTTCCTTCGGTCTATCTG 59.724 50.000 0.00 0.00 43.16 2.90
516 1746 3.500343 CCCCAGAAATGTTTCCAGAACT 58.500 45.455 2.04 0.00 37.92 3.01
526 1756 2.102925 CAGTTTGTTGCCCCAGAAATGT 59.897 45.455 0.00 0.00 0.00 2.71
529 1759 1.118838 CCAGTTTGTTGCCCCAGAAA 58.881 50.000 0.00 0.00 0.00 2.52
586 1816 2.430367 GGGCTCCGTGTTTGGACT 59.570 61.111 0.00 0.00 33.48 3.85
594 1824 1.966451 GGACTTTGTGGGCTCCGTG 60.966 63.158 0.00 0.00 0.00 4.94
609 1839 2.496899 TCAGGGAGAAATGCAAGGAC 57.503 50.000 0.00 0.00 0.00 3.85
615 1845 3.320626 GCAGTTTTTCAGGGAGAAATGC 58.679 45.455 0.00 0.00 45.15 3.56
624 1854 0.758685 TGTGGGGGCAGTTTTTCAGG 60.759 55.000 0.00 0.00 0.00 3.86
667 1908 2.126031 GACGGACTGCGGTCTTCC 60.126 66.667 24.48 8.70 41.82 3.46
668 1909 2.504244 CGACGGACTGCGGTCTTC 60.504 66.667 24.48 18.79 40.89 2.87
767 2012 0.178891 TCTCTCTGCCTTCCCTTGGT 60.179 55.000 0.00 0.00 0.00 3.67
781 2026 1.153667 CAACAGGCTCGGCTCTCTC 60.154 63.158 0.00 0.00 0.00 3.20
782 2027 2.977178 CAACAGGCTCGGCTCTCT 59.023 61.111 0.00 0.00 0.00 3.10
784 2029 4.400961 GGCAACAGGCTCGGCTCT 62.401 66.667 0.00 0.00 44.01 4.09
839 2096 1.335142 CCCCGATTCGATTCTCGTCTC 60.335 57.143 7.83 0.00 41.35 3.36
844 2101 3.006537 TGGTATTCCCCGATTCGATTCTC 59.993 47.826 7.83 0.00 0.00 2.87
845 2102 2.969950 TGGTATTCCCCGATTCGATTCT 59.030 45.455 7.83 0.00 0.00 2.40
860 2117 4.202264 TGGTTGCGGTTTGATTTTGGTATT 60.202 37.500 0.00 0.00 0.00 1.89
1482 2797 0.603439 CTTGGCCACCAATTTGTGCC 60.603 55.000 3.88 12.97 43.07 5.01
1484 2799 3.405823 AATCTTGGCCACCAATTTGTG 57.594 42.857 3.88 2.68 43.07 3.33
1491 2806 1.851304 GGATCAAATCTTGGCCACCA 58.149 50.000 3.88 0.00 0.00 4.17
1640 2955 3.945434 CGAGCATGATGTGGCCGC 61.945 66.667 10.11 10.11 0.00 6.53
1680 2995 4.162690 GGCGGCAGAATCGGGAGT 62.163 66.667 3.07 0.00 0.00 3.85
1857 3184 2.363147 GTGGAGGACGAGGAGGCT 60.363 66.667 0.00 0.00 0.00 4.58
1878 3205 2.358247 GCCGTGGTGGTCGTTGAT 60.358 61.111 0.00 0.00 41.21 2.57
2146 3500 4.162690 GAGGCGGGCGATGAGGTT 62.163 66.667 0.00 0.00 0.00 3.50
2384 3738 2.509561 GCTTCTTCTCGTCGCCCC 60.510 66.667 0.00 0.00 0.00 5.80
2388 3745 1.406970 GCGAAGGCTTCTTCTCGTCG 61.407 60.000 23.74 10.81 43.46 5.12
2501 3864 8.785329 AGGAAAAAGTGCTAAAATCTAGAGAG 57.215 34.615 0.00 0.00 0.00 3.20
2503 3866 8.454894 GGAAGGAAAAAGTGCTAAAATCTAGAG 58.545 37.037 0.00 0.00 0.00 2.43
2504 3867 7.393515 GGGAAGGAAAAAGTGCTAAAATCTAGA 59.606 37.037 0.00 0.00 0.00 2.43
2505 3868 7.176690 TGGGAAGGAAAAAGTGCTAAAATCTAG 59.823 37.037 0.00 0.00 0.00 2.43
2578 3945 3.897505 CTCCACCAAATCCCAAAGAAACT 59.102 43.478 0.00 0.00 0.00 2.66
2579 3946 3.006859 CCTCCACCAAATCCCAAAGAAAC 59.993 47.826 0.00 0.00 0.00 2.78
2625 4080 2.755929 CTCCGCTAAACACAGGAGC 58.244 57.895 0.00 0.00 42.99 4.70
2629 4084 3.851976 ACTCTACTCCGCTAAACACAG 57.148 47.619 0.00 0.00 0.00 3.66
2650 4105 2.685897 AGAAGCCAAGCAAAAACGTACA 59.314 40.909 0.00 0.00 0.00 2.90
2651 4106 3.349488 AGAAGCCAAGCAAAAACGTAC 57.651 42.857 0.00 0.00 0.00 3.67
2652 4107 3.129638 ACAAGAAGCCAAGCAAAAACGTA 59.870 39.130 0.00 0.00 0.00 3.57
2653 4108 2.094234 ACAAGAAGCCAAGCAAAAACGT 60.094 40.909 0.00 0.00 0.00 3.99
2654 4109 2.535574 GACAAGAAGCCAAGCAAAAACG 59.464 45.455 0.00 0.00 0.00 3.60
2655 4110 2.866156 GGACAAGAAGCCAAGCAAAAAC 59.134 45.455 0.00 0.00 0.00 2.43
2656 4111 2.499289 TGGACAAGAAGCCAAGCAAAAA 59.501 40.909 0.00 0.00 0.00 1.94
2665 4121 2.351738 CCGAAAATGTGGACAAGAAGCC 60.352 50.000 0.00 0.00 0.00 4.35
2684 4140 1.135402 GCCAAAGCAAAGTATCCACCG 60.135 52.381 0.00 0.00 39.53 4.94
2709 4170 4.795268 TCGTCTCAATAATCCTCGTATGC 58.205 43.478 0.00 0.00 0.00 3.14
2722 4183 6.735130 TCATTATGTACACGATCGTCTCAAT 58.265 36.000 19.84 12.38 0.00 2.57
2728 4189 9.471084 TTGATTATTCATTATGTACACGATCGT 57.529 29.630 16.60 16.60 0.00 3.73
2754 4215 5.900123 ACCTCATCTGCCTAATAGTAACTGT 59.100 40.000 0.00 0.00 0.00 3.55
2761 4222 3.556633 CCTGCACCTCATCTGCCTAATAG 60.557 52.174 0.00 0.00 33.36 1.73
2782 4243 4.808895 GGAAAACAAACATCAAGACCAACC 59.191 41.667 0.00 0.00 0.00 3.77
2783 4244 4.808895 GGGAAAACAAACATCAAGACCAAC 59.191 41.667 0.00 0.00 0.00 3.77
2804 4265 1.963855 TCACCGTGCACGAAATGGG 60.964 57.895 39.10 23.70 43.02 4.00
2811 4272 1.010125 CCAAAAGTCACCGTGCACG 60.010 57.895 31.77 31.77 39.44 5.34
2818 4279 4.846779 TCAATGCTTACCAAAAGTCACC 57.153 40.909 0.00 0.00 0.00 4.02
2840 4301 5.655974 TGATGCCTACAATTTCCATGCTAAA 59.344 36.000 0.00 0.00 0.00 1.85
2845 4306 5.587388 AGTTGATGCCTACAATTTCCATG 57.413 39.130 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.