Multiple sequence alignment - TraesCS6B01G340400

Loading Multiple Alignment...

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 TraesCS6B01G340400 chr6B 100.000 2240 0 0 1 2240 599692475 599694714 0.000000e+00 4137.0
1 TraesCS6B01G340400 chr6B 97.727 44 1 0 1883 1926 599694313 599694356 2.390000e-10 76.8
2 TraesCS6B01G340400 chr6B 97.727 44 1 0 1839 1882 599694357 599694400 2.390000e-10 76.8
3 TraesCS6B01G340400 chr6A 86.261 1281 92 35 650 1880 546598854 546600100 0.000000e+00 1314.0
4 TraesCS6B01G340400 chr6A 86.019 422 42 9 118 526 546598388 546598805 9.500000e-119 436.0
5 TraesCS6B01G340400 chr6A 90.036 281 15 4 1971 2238 546600114 546600394 3.540000e-93 351.0
6 TraesCS6B01G340400 chr6D 83.954 1396 113 44 550 1901 400650474 400651802 0.000000e+00 1234.0
7 TraesCS6B01G340400 chr6D 93.431 274 14 1 1971 2240 400651794 400652067 9.630000e-109 403.0
8 TraesCS6B01G340400 chr4A 80.592 304 45 9 1349 1645 593487606 593487310 2.900000e-54 222.0
9 TraesCS6B01G340400 chr1B 96.429 112 4 0 1092 1203 727951 728062 3.800000e-43 185.0
10 TraesCS6B01G340400 chr1B 82.941 170 26 2 1328 1496 728145 728312 1.390000e-32 150.0
11 TraesCS6B01G340400 chr7B 82.212 208 25 5 1001 1196 115961879 115962086 3.830000e-38 169.0
12 TraesCS6B01G340400 chr7A 90.179 112 11 0 1085 1196 155951991 155952102 1.790000e-31 147.0
13 TraesCS6B01G340400 chr7D 88.525 122 11 2 1075 1196 153972096 153972214 6.450000e-31 145.0
14 TraesCS6B01G340400 chr7D 100.000 28 0 0 2012 2039 69832124 69832151 4.000000e-03 52.8
15 TraesCS6B01G340400 chr3B 97.500 40 1 0 334 373 826190312 826190273 3.990000e-08 69.4
16 TraesCS6B01G340400 chr4D 100.000 28 0 0 2012 2039 348356846 348356873 4.000000e-03 52.8
17 TraesCS6B01G340400 chr3D 100.000 28 0 0 2012 2039 22169410 22169383 4.000000e-03 52.8


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 TraesCS6B01G340400 chr6B 599692475 599694714 2239 False 1430.200000 4137 98.484667 1 2240 3 chr6B.!!$F1 2239
1 TraesCS6B01G340400 chr6A 546598388 546600394 2006 False 700.333333 1314 87.438667 118 2238 3 chr6A.!!$F1 2120
2 TraesCS6B01G340400 chr6D 400650474 400652067 1593 False 818.500000 1234 88.692500 550 2240 2 chr6D.!!$F1 1690

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
368 374 0.310854 GCACTTGCTGCGGTTTAACT 59.689 50.0 0.0 0.0 35.72 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 1334 0.103208 AGATCGCCCAGTCAATCGAC 59.897 55.0 0.0 0.0 42.95 4.2 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
32 33 7.949903 TTTCATTTGAAGGACAATTGACATG 57.050 32.000 13.59 5.02 43.67 3.21
33 34 6.653526 TCATTTGAAGGACAATTGACATGT 57.346 33.333 13.59 0.00 41.11 3.21
34 35 6.448852 TCATTTGAAGGACAATTGACATGTG 58.551 36.000 13.59 0.00 41.11 3.21
35 36 6.264970 TCATTTGAAGGACAATTGACATGTGA 59.735 34.615 13.59 0.00 41.11 3.58
36 37 6.462552 TTTGAAGGACAATTGACATGTGAA 57.537 33.333 13.59 0.00 38.36 3.18
37 38 6.462552 TTGAAGGACAATTGACATGTGAAA 57.537 33.333 13.59 0.00 33.18 2.69
38 39 6.653526 TGAAGGACAATTGACATGTGAAAT 57.346 33.333 13.59 0.00 0.00 2.17
39 40 7.053316 TGAAGGACAATTGACATGTGAAATT 57.947 32.000 13.59 6.68 0.00 1.82
40 41 7.499292 TGAAGGACAATTGACATGTGAAATTT 58.501 30.769 13.59 0.00 0.00 1.82
41 42 8.637099 TGAAGGACAATTGACATGTGAAATTTA 58.363 29.630 13.59 0.00 0.00 1.40
42 43 9.474920 GAAGGACAATTGACATGTGAAATTTAA 57.525 29.630 13.59 0.00 0.00 1.52
44 45 9.426837 AGGACAATTGACATGTGAAATTTAATG 57.573 29.630 13.59 1.35 0.00 1.90
45 46 9.421806 GGACAATTGACATGTGAAATTTAATGA 57.578 29.630 13.59 0.00 0.00 2.57
96 97 9.838339 AGTACAGTTATTTTGGAATGGATAGAG 57.162 33.333 0.00 0.00 0.00 2.43
97 98 7.573968 ACAGTTATTTTGGAATGGATAGAGC 57.426 36.000 0.00 0.00 0.00 4.09
98 99 7.118723 ACAGTTATTTTGGAATGGATAGAGCA 58.881 34.615 0.00 0.00 0.00 4.26
99 100 7.615365 ACAGTTATTTTGGAATGGATAGAGCAA 59.385 33.333 0.00 0.00 0.00 3.91
100 101 7.917505 CAGTTATTTTGGAATGGATAGAGCAAC 59.082 37.037 0.00 0.00 0.00 4.17
101 102 5.859205 ATTTTGGAATGGATAGAGCAACC 57.141 39.130 0.00 0.00 0.00 3.77
102 103 3.297134 TTGGAATGGATAGAGCAACCC 57.703 47.619 0.00 0.00 0.00 4.11
103 104 2.492025 TGGAATGGATAGAGCAACCCT 58.508 47.619 0.00 0.00 0.00 4.34
104 105 2.173356 TGGAATGGATAGAGCAACCCTG 59.827 50.000 0.00 0.00 0.00 4.45
105 106 2.439507 GGAATGGATAGAGCAACCCTGA 59.560 50.000 0.00 0.00 0.00 3.86
106 107 3.117888 GGAATGGATAGAGCAACCCTGAA 60.118 47.826 0.00 0.00 0.00 3.02
107 108 3.567478 ATGGATAGAGCAACCCTGAAC 57.433 47.619 0.00 0.00 0.00 3.18
108 109 1.207089 TGGATAGAGCAACCCTGAACG 59.793 52.381 0.00 0.00 0.00 3.95
109 110 1.480954 GGATAGAGCAACCCTGAACGA 59.519 52.381 0.00 0.00 0.00 3.85
110 111 2.103263 GGATAGAGCAACCCTGAACGAT 59.897 50.000 0.00 0.00 0.00 3.73
111 112 3.432326 GGATAGAGCAACCCTGAACGATT 60.432 47.826 0.00 0.00 0.00 3.34
112 113 2.100605 AGAGCAACCCTGAACGATTC 57.899 50.000 0.00 0.00 0.00 2.52
113 114 1.347707 AGAGCAACCCTGAACGATTCA 59.652 47.619 0.00 0.00 38.17 2.57
114 115 2.026822 AGAGCAACCCTGAACGATTCAT 60.027 45.455 0.00 0.00 39.30 2.57
115 116 3.197766 AGAGCAACCCTGAACGATTCATA 59.802 43.478 0.00 0.00 39.30 2.15
116 117 3.270877 AGCAACCCTGAACGATTCATAC 58.729 45.455 0.00 0.00 39.30 2.39
117 118 3.055094 AGCAACCCTGAACGATTCATACT 60.055 43.478 0.00 0.00 39.30 2.12
118 119 4.161565 AGCAACCCTGAACGATTCATACTA 59.838 41.667 0.00 0.00 39.30 1.82
119 120 5.057149 GCAACCCTGAACGATTCATACTAT 58.943 41.667 0.00 0.00 39.30 2.12
120 121 5.177696 GCAACCCTGAACGATTCATACTATC 59.822 44.000 0.00 0.00 39.30 2.08
121 122 6.280643 CAACCCTGAACGATTCATACTATCA 58.719 40.000 0.00 0.00 39.30 2.15
122 123 5.844004 ACCCTGAACGATTCATACTATCAC 58.156 41.667 0.00 0.00 39.30 3.06
123 124 5.598830 ACCCTGAACGATTCATACTATCACT 59.401 40.000 0.00 0.00 39.30 3.41
124 125 6.776116 ACCCTGAACGATTCATACTATCACTA 59.224 38.462 0.00 0.00 39.30 2.74
128 129 9.737427 CTGAACGATTCATACTATCACTAAAGT 57.263 33.333 0.00 0.00 39.30 2.66
142 143 6.677781 TCACTAAAGTTCTTGGTTCAACTG 57.322 37.500 0.00 0.00 33.01 3.16
146 147 8.026607 CACTAAAGTTCTTGGTTCAACTGAAAA 58.973 33.333 0.00 0.00 35.58 2.29
212 214 1.433121 GGAGATCCTGCCCAGAAGAT 58.567 55.000 0.00 0.00 0.00 2.40
240 242 2.499289 CACTCCTAGATGCTCACTGGTT 59.501 50.000 0.00 0.00 0.00 3.67
260 262 4.153655 GGTTGATGAACCGTAAACTCCTTC 59.846 45.833 0.00 0.00 42.47 3.46
275 277 4.822026 ACTCCTTCGATAACTTGGTCAAG 58.178 43.478 8.97 8.97 43.79 3.02
333 336 2.435372 TGGGCCAATTCGAAGCTTAT 57.565 45.000 2.13 0.00 0.00 1.73
334 337 3.569194 TGGGCCAATTCGAAGCTTATA 57.431 42.857 2.13 0.00 0.00 0.98
335 338 3.892284 TGGGCCAATTCGAAGCTTATAA 58.108 40.909 2.13 0.00 0.00 0.98
336 339 4.469657 TGGGCCAATTCGAAGCTTATAAT 58.530 39.130 2.13 0.00 0.00 1.28
339 342 6.719370 TGGGCCAATTCGAAGCTTATAATTAT 59.281 34.615 2.13 2.97 0.00 1.28
341 344 8.736244 GGGCCAATTCGAAGCTTATAATTATAA 58.264 33.333 15.47 15.47 0.00 0.98
348 354 7.790000 TCGAAGCTTATAATTATAAACGCCAC 58.210 34.615 18.69 14.09 0.00 5.01
367 373 2.796227 GCACTTGCTGCGGTTTAAC 58.204 52.632 0.00 0.00 35.72 2.01
368 374 0.310854 GCACTTGCTGCGGTTTAACT 59.689 50.000 0.00 0.00 35.72 2.24
372 378 1.231958 TTGCTGCGGTTTAACTCCGG 61.232 55.000 16.58 0.00 46.90 5.14
373 379 2.396157 GCTGCGGTTTAACTCCGGG 61.396 63.158 16.58 0.00 46.90 5.73
374 380 1.294138 CTGCGGTTTAACTCCGGGA 59.706 57.895 16.58 0.00 46.90 5.14
413 422 1.303309 CAGATCAAATCAGGCGACCC 58.697 55.000 0.00 0.00 0.00 4.46
419 428 0.953960 AAATCAGGCGACCCGTTCAC 60.954 55.000 0.00 0.00 35.76 3.18
441 450 2.026522 CCCGTCCGCTGAAACAAAA 58.973 52.632 0.00 0.00 0.00 2.44
445 454 0.318699 GTCCGCTGAAACAAAAGGGC 60.319 55.000 0.00 0.00 0.00 5.19
446 455 0.753479 TCCGCTGAAACAAAAGGGCA 60.753 50.000 0.00 0.00 0.00 5.36
448 457 0.318955 CGCTGAAACAAAAGGGCAGG 60.319 55.000 0.00 0.00 0.00 4.85
449 458 0.752658 GCTGAAACAAAAGGGCAGGT 59.247 50.000 0.00 0.00 0.00 4.00
450 459 1.269778 GCTGAAACAAAAGGGCAGGTC 60.270 52.381 0.00 0.00 0.00 3.85
451 460 2.031120 CTGAAACAAAAGGGCAGGTCA 58.969 47.619 0.00 0.00 0.00 4.02
452 461 1.754226 TGAAACAAAAGGGCAGGTCAC 59.246 47.619 0.00 0.00 0.00 3.67
463 473 0.664767 GCAGGTCACTCTCACGACAC 60.665 60.000 0.00 0.00 33.66 3.67
507 517 1.006832 CAGGCTGTAATTTCGTCCGG 58.993 55.000 6.28 0.00 0.00 5.14
513 523 2.601763 CTGTAATTTCGTCCGGCAGTAC 59.398 50.000 0.00 0.00 0.00 2.73
514 524 2.231964 TGTAATTTCGTCCGGCAGTACT 59.768 45.455 0.00 0.00 0.00 2.73
526 536 3.619929 CCGGCAGTACTAATAACCAACAC 59.380 47.826 0.00 0.00 0.00 3.32
527 537 4.247258 CGGCAGTACTAATAACCAACACA 58.753 43.478 0.00 0.00 0.00 3.72
529 539 5.353123 CGGCAGTACTAATAACCAACACATT 59.647 40.000 0.00 0.00 0.00 2.71
530 540 6.128117 CGGCAGTACTAATAACCAACACATTT 60.128 38.462 0.00 0.00 0.00 2.32
531 541 7.574217 CGGCAGTACTAATAACCAACACATTTT 60.574 37.037 0.00 0.00 0.00 1.82
574 584 3.981211 ACCAACACATTTCATTCAGCAC 58.019 40.909 0.00 0.00 0.00 4.40
575 585 3.243839 ACCAACACATTTCATTCAGCACC 60.244 43.478 0.00 0.00 0.00 5.01
576 586 3.006110 CCAACACATTTCATTCAGCACCT 59.994 43.478 0.00 0.00 0.00 4.00
577 587 3.928727 ACACATTTCATTCAGCACCTG 57.071 42.857 0.00 0.00 0.00 4.00
578 588 3.225104 ACACATTTCATTCAGCACCTGT 58.775 40.909 0.00 0.00 32.61 4.00
579 589 3.005050 ACACATTTCATTCAGCACCTGTG 59.995 43.478 0.00 0.00 38.86 3.66
582 592 1.896220 TTCATTCAGCACCTGTGACC 58.104 50.000 0.51 0.00 32.61 4.02
584 594 1.672356 ATTCAGCACCTGTGACCGC 60.672 57.895 0.51 0.00 32.61 5.68
585 595 4.662961 TCAGCACCTGTGACCGCG 62.663 66.667 0.00 0.00 32.61 6.46
589 599 4.969196 CACCTGTGACCGCGCACT 62.969 66.667 16.12 0.00 39.49 4.40
590 600 4.969196 ACCTGTGACCGCGCACTG 62.969 66.667 16.12 15.00 39.49 3.66
591 601 4.969196 CCTGTGACCGCGCACTGT 62.969 66.667 16.12 0.00 39.49 3.55
593 603 2.512745 TGTGACCGCGCACTGTTT 60.513 55.556 16.12 0.00 39.49 2.83
627 639 0.452987 CCACAAGCCCACAATGATCG 59.547 55.000 0.00 0.00 0.00 3.69
628 640 0.452987 CACAAGCCCACAATGATCGG 59.547 55.000 0.00 0.00 0.00 4.18
681 693 4.742201 GCTTCGGACTCGCAGCCA 62.742 66.667 0.00 0.00 46.87 4.75
691 704 4.838152 CGCAGCCAGGCCGTATGT 62.838 66.667 8.22 0.00 0.00 2.29
747 760 0.387622 CGGTCAAAACTGGCATGCAG 60.388 55.000 21.36 16.69 0.00 4.41
748 761 0.668401 GGTCAAAACTGGCATGCAGC 60.668 55.000 21.36 3.15 44.65 5.25
749 762 0.316204 GTCAAAACTGGCATGCAGCT 59.684 50.000 21.36 3.65 44.79 4.24
750 763 0.315886 TCAAAACTGGCATGCAGCTG 59.684 50.000 21.36 10.11 44.79 4.24
751 764 1.005394 AAAACTGGCATGCAGCTGC 60.005 52.632 31.89 31.89 44.79 5.25
752 765 2.758770 AAAACTGGCATGCAGCTGCG 62.759 55.000 32.11 20.58 45.83 5.18
754 767 4.175489 CTGGCATGCAGCTGCGTC 62.175 66.667 30.32 22.52 45.83 5.19
827 850 1.380785 TCCAAGACGTATCCGGCCT 60.381 57.895 0.00 0.00 45.85 5.19
868 893 1.289066 CGCGTGTCTTCTGGAAGGA 59.711 57.895 10.01 0.00 38.88 3.36
870 895 0.670854 GCGTGTCTTCTGGAAGGACC 60.671 60.000 10.01 0.00 38.88 4.46
882 907 1.769716 GAAGGACCATCCCGATCCCC 61.770 65.000 0.00 0.00 37.19 4.81
1020 1046 0.531974 TGGAGCGCAAGAACTCGTTT 60.532 50.000 11.47 0.00 43.02 3.60
1205 1243 1.023513 CAGAAGAAGAAGCAGGGCGG 61.024 60.000 0.00 0.00 0.00 6.13
1238 1279 3.261951 CGCGACTGCCGGGTATTG 61.262 66.667 0.00 0.00 44.85 1.90
1239 1280 2.185867 GCGACTGCCGGGTATTGA 59.814 61.111 2.18 0.00 39.04 2.57
1240 1281 1.227556 GCGACTGCCGGGTATTGAT 60.228 57.895 2.18 0.00 39.04 2.57
1241 1282 0.814010 GCGACTGCCGGGTATTGATT 60.814 55.000 2.18 0.00 39.04 2.57
1252 1293 1.547901 GGTATTGATTAGCCAGGCCCC 60.548 57.143 8.22 0.00 0.00 5.80
1254 1295 1.645402 ATTGATTAGCCAGGCCCCGT 61.645 55.000 8.22 0.00 0.00 5.28
1256 1297 1.526225 GATTAGCCAGGCCCCGTTC 60.526 63.158 8.22 0.00 0.00 3.95
1257 1298 2.960359 GATTAGCCAGGCCCCGTTCC 62.960 65.000 8.22 0.00 0.00 3.62
1281 1322 1.662044 GGCGGATGGAAATGGATGC 59.338 57.895 0.00 0.00 0.00 3.91
1287 1328 3.170717 GGATGGAAATGGATGCATGGAT 58.829 45.455 2.46 0.00 30.89 3.41
1288 1329 3.056107 GGATGGAAATGGATGCATGGATG 60.056 47.826 2.46 0.00 30.89 3.51
1289 1330 3.035055 TGGAAATGGATGCATGGATGT 57.965 42.857 2.46 0.00 0.00 3.06
1293 1334 0.251033 ATGGATGCATGGATGTCCGG 60.251 55.000 2.46 0.00 39.43 5.14
1299 1340 0.532862 GCATGGATGTCCGGTCGATT 60.533 55.000 0.00 0.00 39.43 3.34
1302 1343 0.174845 TGGATGTCCGGTCGATTGAC 59.825 55.000 0.00 4.31 44.72 3.18
1313 1354 0.385751 TCGATTGACTGGGCGATCTC 59.614 55.000 2.60 0.00 0.00 2.75
1317 1358 0.976641 TTGACTGGGCGATCTCTTGT 59.023 50.000 0.00 0.00 0.00 3.16
1320 1361 2.003301 GACTGGGCGATCTCTTGTTTC 58.997 52.381 0.00 0.00 0.00 2.78
1332 1376 6.073980 CGATCTCTTGTTTCCTGTCGTTTAAA 60.074 38.462 0.00 0.00 0.00 1.52
1338 1382 5.823353 TGTTTCCTGTCGTTTAAATGGTTC 58.177 37.500 7.56 0.61 0.00 3.62
1347 1391 8.020861 TGTCGTTTAAATGGTTCTGTACATAC 57.979 34.615 7.56 0.00 0.00 2.39
1373 1421 1.243902 GCCGTTTGATTCAGGGTTGA 58.756 50.000 3.43 0.00 0.00 3.18
1388 1436 1.001633 GGTTGACACCACCACGTAGAT 59.998 52.381 0.00 0.00 43.61 1.98
1393 1444 2.427453 GACACCACCACGTAGATCATCT 59.573 50.000 0.00 0.00 0.00 2.90
1395 1446 3.632604 ACACCACCACGTAGATCATCTAG 59.367 47.826 0.00 0.00 28.01 2.43
1400 1452 3.003482 ACCACGTAGATCATCTAGCGTTC 59.997 47.826 15.42 0.00 35.87 3.95
1428 1480 7.149569 TCTCTGCTTATTGATTGGTTCTTTG 57.850 36.000 0.00 0.00 0.00 2.77
1437 1490 6.391227 TTGATTGGTTCTTTGTTCTTCCTC 57.609 37.500 0.00 0.00 0.00 3.71
1438 1491 5.694995 TGATTGGTTCTTTGTTCTTCCTCT 58.305 37.500 0.00 0.00 0.00 3.69
1472 1525 3.976942 CGATTGATCCGATGAAATTTGCC 59.023 43.478 0.00 0.00 0.00 4.52
1480 1533 2.532723 CGATGAAATTTGCCGCTGATTG 59.467 45.455 0.00 0.00 0.00 2.67
1487 1541 1.169661 TTGCCGCTGATTGGTTCGTT 61.170 50.000 0.00 0.00 0.00 3.85
1501 1555 3.470567 CGTTCACTGACGCTCGCC 61.471 66.667 0.00 0.00 36.12 5.54
1502 1556 3.470567 GTTCACTGACGCTCGCCG 61.471 66.667 0.00 0.00 44.21 6.46
1523 1577 1.587946 GCAGTTGCCTTTGTTTGTTCG 59.412 47.619 0.00 0.00 34.31 3.95
1524 1578 2.192624 CAGTTGCCTTTGTTTGTTCGG 58.807 47.619 0.00 0.00 0.00 4.30
1525 1579 1.136110 AGTTGCCTTTGTTTGTTCGGG 59.864 47.619 0.00 0.00 0.00 5.14
1526 1580 1.135333 GTTGCCTTTGTTTGTTCGGGA 59.865 47.619 0.00 0.00 0.00 5.14
1527 1581 1.475403 TGCCTTTGTTTGTTCGGGAA 58.525 45.000 0.00 0.00 0.00 3.97
1528 1582 1.135333 TGCCTTTGTTTGTTCGGGAAC 59.865 47.619 4.63 4.63 41.50 3.62
1547 1601 4.193334 CGGCGCGTGATCCTCAGA 62.193 66.667 8.43 0.00 0.00 3.27
1553 1607 0.659957 GCGTGATCCTCAGATTTGCC 59.340 55.000 0.00 0.00 30.90 4.52
1555 1609 1.471501 CGTGATCCTCAGATTTGCCGA 60.472 52.381 0.00 0.00 30.90 5.54
1559 1613 0.976641 TCCTCAGATTTGCCGACTGT 59.023 50.000 0.00 0.00 33.93 3.55
1577 1631 0.168128 GTCACCTCCGGCAAATTTCG 59.832 55.000 0.00 0.00 0.00 3.46
1587 1653 2.724174 CGGCAAATTTCGGTTCAGTTTC 59.276 45.455 0.00 0.00 0.00 2.78
1607 1673 8.587950 CAGTTTCGTTATCTGAATTCTGAGTAC 58.412 37.037 18.38 16.14 33.52 2.73
1609 1675 8.587950 GTTTCGTTATCTGAATTCTGAGTACAG 58.412 37.037 18.38 13.77 44.66 2.74
1633 1699 6.038997 ACTACAAAGTCTAGTGGAATGGTC 57.961 41.667 0.00 0.00 0.00 4.02
1674 1744 6.279227 GCATCTAGTACAGTTGCATAGTTG 57.721 41.667 16.69 6.62 45.54 3.16
1700 1771 3.002791 TCGTCCTTCACAGATGAAATGC 58.997 45.455 0.00 0.00 44.28 3.56
1701 1772 2.743664 CGTCCTTCACAGATGAAATGCA 59.256 45.455 0.00 0.00 44.28 3.96
1793 1864 0.667184 CTGTGGGCAATTCAAACGGC 60.667 55.000 0.00 0.00 0.00 5.68
1815 1886 4.500545 GCACTGTATCAGCATAGTAGCACT 60.501 45.833 0.00 0.00 34.37 4.40
1828 1899 6.037610 GCATAGTAGCACTGTTTCAGCTTTAT 59.962 38.462 0.00 0.00 39.68 1.40
1863 1934 5.255687 TGCTCTAAGATTTCAGAAATGGCA 58.744 37.500 13.38 10.03 0.00 4.92
1869 1940 5.988310 AGATTTCAGAAATGGCATGTCAA 57.012 34.783 19.51 5.95 0.00 3.18
1870 1941 5.962433 AGATTTCAGAAATGGCATGTCAAG 58.038 37.500 19.51 11.41 0.00 3.02
1871 1942 4.524316 TTTCAGAAATGGCATGTCAAGG 57.476 40.909 19.51 8.72 0.00 3.61
1872 1943 3.438216 TCAGAAATGGCATGTCAAGGA 57.562 42.857 19.51 10.79 0.00 3.36
1873 1944 3.084039 TCAGAAATGGCATGTCAAGGAC 58.916 45.455 19.51 0.00 0.00 3.85
1874 1945 2.821378 CAGAAATGGCATGTCAAGGACA 59.179 45.455 19.51 1.05 46.90 4.02
1875 1946 3.256383 CAGAAATGGCATGTCAAGGACAA 59.744 43.478 19.51 0.00 45.96 3.18
1876 1947 3.896888 AGAAATGGCATGTCAAGGACAAA 59.103 39.130 19.51 0.00 45.96 2.83
1877 1948 3.947910 AATGGCATGTCAAGGACAAAG 57.052 42.857 3.01 1.06 45.96 2.77
1878 1949 2.363306 TGGCATGTCAAGGACAAAGT 57.637 45.000 0.00 0.00 45.96 2.66
1879 1950 3.500448 TGGCATGTCAAGGACAAAGTA 57.500 42.857 0.00 0.00 45.96 2.24
1880 1951 4.032960 TGGCATGTCAAGGACAAAGTAT 57.967 40.909 0.00 0.00 45.96 2.12
1881 1952 4.009675 TGGCATGTCAAGGACAAAGTATC 58.990 43.478 0.00 0.00 45.96 2.24
1882 1953 3.378427 GGCATGTCAAGGACAAAGTATCC 59.622 47.826 2.87 0.00 45.96 2.59
1890 1961 4.213564 AGGACAAAGTATCCTTGCTCTG 57.786 45.455 0.00 0.00 44.64 3.35
1891 1962 3.840666 AGGACAAAGTATCCTTGCTCTGA 59.159 43.478 0.00 0.00 44.64 3.27
1892 1963 4.081198 AGGACAAAGTATCCTTGCTCTGAG 60.081 45.833 0.00 0.00 44.64 3.35
1893 1964 4.081420 GGACAAAGTATCCTTGCTCTGAGA 60.081 45.833 9.28 0.00 33.03 3.27
1894 1965 5.396213 GGACAAAGTATCCTTGCTCTGAGAT 60.396 44.000 9.28 0.00 33.03 2.75
1895 1966 6.059787 ACAAAGTATCCTTGCTCTGAGATT 57.940 37.500 9.28 0.00 0.00 2.40
1896 1967 6.479884 ACAAAGTATCCTTGCTCTGAGATTT 58.520 36.000 9.28 0.00 0.00 2.17
1897 1968 6.597280 ACAAAGTATCCTTGCTCTGAGATTTC 59.403 38.462 9.28 0.00 0.00 2.17
1898 1969 5.946942 AGTATCCTTGCTCTGAGATTTCA 57.053 39.130 9.28 0.00 0.00 2.69
1911 1982 5.571784 TGAGATTTCAGAAATGGCATGTC 57.428 39.130 13.38 9.77 0.00 3.06
1912 1983 5.011586 TGAGATTTCAGAAATGGCATGTCA 58.988 37.500 19.51 0.60 0.00 3.58
1924 1995 4.032960 TGGCATGTCAAGGACAAAGTAT 57.967 40.909 0.00 0.00 45.96 2.12
1928 1999 5.393962 GCATGTCAAGGACAAAGTATCAAC 58.606 41.667 2.87 0.00 45.96 3.18
1951 2022 3.325870 TCCGTAGAGTTGCAGACATTTG 58.674 45.455 0.00 0.00 0.00 2.32
1952 2023 3.067106 CCGTAGAGTTGCAGACATTTGT 58.933 45.455 0.00 0.00 0.00 2.83
1953 2024 3.498397 CCGTAGAGTTGCAGACATTTGTT 59.502 43.478 0.00 0.00 0.00 2.83
1954 2025 4.024048 CCGTAGAGTTGCAGACATTTGTTT 60.024 41.667 0.00 0.00 0.00 2.83
1955 2026 5.505654 CCGTAGAGTTGCAGACATTTGTTTT 60.506 40.000 0.00 0.00 0.00 2.43
1956 2027 5.971202 CGTAGAGTTGCAGACATTTGTTTTT 59.029 36.000 0.00 0.00 0.00 1.94
2001 2072 7.121759 CAGACATTGTTAGAGATGGTTGGATTT 59.878 37.037 0.00 0.00 0.00 2.17
2086 2158 6.931281 TCAACTCAGAAGAATAAACTCAGTGG 59.069 38.462 0.00 0.00 0.00 4.00
2111 2183 5.583854 CCATTCAACTACTGAGATGGTGAAG 59.416 44.000 13.04 7.41 37.63 3.02
2150 2234 7.042321 CGAACGGTAAAGGATTTAGAATGCATA 60.042 37.037 0.00 0.00 41.97 3.14
2154 2238 7.023575 GGTAAAGGATTTAGAATGCATATGCG 58.976 38.462 22.21 0.00 41.97 4.73
2205 2289 1.908619 TGCTCACAGAAAGCCCATAGA 59.091 47.619 0.00 0.00 39.05 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.995220 CATGTCAATTGTCCTTCAAATGAAAAT 58.005 29.630 5.13 0.00 44.31 1.82
8 9 7.438757 CACATGTCAATTGTCCTTCAAATGAAA 59.561 33.333 5.13 0.00 44.31 2.69
9 10 6.924612 CACATGTCAATTGTCCTTCAAATGAA 59.075 34.615 5.13 0.00 44.31 2.57
10 11 6.264970 TCACATGTCAATTGTCCTTCAAATGA 59.735 34.615 5.13 0.00 41.76 2.57
11 12 6.448852 TCACATGTCAATTGTCCTTCAAATG 58.551 36.000 5.13 1.68 39.62 2.32
12 13 6.653526 TCACATGTCAATTGTCCTTCAAAT 57.346 33.333 5.13 0.00 39.62 2.32
13 14 6.462552 TTCACATGTCAATTGTCCTTCAAA 57.537 33.333 5.13 0.00 39.62 2.69
14 15 6.462552 TTTCACATGTCAATTGTCCTTCAA 57.537 33.333 5.13 0.00 40.53 2.69
15 16 6.653526 ATTTCACATGTCAATTGTCCTTCA 57.346 33.333 5.13 0.00 0.00 3.02
16 17 7.951530 AAATTTCACATGTCAATTGTCCTTC 57.048 32.000 11.60 0.00 0.00 3.46
18 19 9.426837 CATTAAATTTCACATGTCAATTGTCCT 57.573 29.630 11.60 2.01 0.00 3.85
19 20 9.421806 TCATTAAATTTCACATGTCAATTGTCC 57.578 29.630 11.60 0.00 0.00 4.02
70 71 9.838339 CTCTATCCATTCCAAAATAACTGTACT 57.162 33.333 0.00 0.00 0.00 2.73
71 72 8.560374 GCTCTATCCATTCCAAAATAACTGTAC 58.440 37.037 0.00 0.00 0.00 2.90
72 73 8.271458 TGCTCTATCCATTCCAAAATAACTGTA 58.729 33.333 0.00 0.00 0.00 2.74
73 74 7.118723 TGCTCTATCCATTCCAAAATAACTGT 58.881 34.615 0.00 0.00 0.00 3.55
74 75 7.572523 TGCTCTATCCATTCCAAAATAACTG 57.427 36.000 0.00 0.00 0.00 3.16
75 76 7.068716 GGTTGCTCTATCCATTCCAAAATAACT 59.931 37.037 0.00 0.00 0.00 2.24
76 77 7.203218 GGTTGCTCTATCCATTCCAAAATAAC 58.797 38.462 0.00 0.00 0.00 1.89
77 78 6.323739 GGGTTGCTCTATCCATTCCAAAATAA 59.676 38.462 0.00 0.00 0.00 1.40
78 79 5.833131 GGGTTGCTCTATCCATTCCAAAATA 59.167 40.000 0.00 0.00 0.00 1.40
79 80 4.651045 GGGTTGCTCTATCCATTCCAAAAT 59.349 41.667 0.00 0.00 0.00 1.82
80 81 4.023291 GGGTTGCTCTATCCATTCCAAAA 58.977 43.478 0.00 0.00 0.00 2.44
81 82 3.269381 AGGGTTGCTCTATCCATTCCAAA 59.731 43.478 0.00 0.00 0.00 3.28
82 83 2.852449 AGGGTTGCTCTATCCATTCCAA 59.148 45.455 0.00 0.00 0.00 3.53
83 84 2.173356 CAGGGTTGCTCTATCCATTCCA 59.827 50.000 0.00 0.00 0.00 3.53
84 85 2.439507 TCAGGGTTGCTCTATCCATTCC 59.560 50.000 0.00 0.00 0.00 3.01
85 86 3.845781 TCAGGGTTGCTCTATCCATTC 57.154 47.619 0.00 0.00 0.00 2.67
86 87 3.682718 CGTTCAGGGTTGCTCTATCCATT 60.683 47.826 0.00 0.00 0.00 3.16
87 88 2.158900 CGTTCAGGGTTGCTCTATCCAT 60.159 50.000 0.00 0.00 0.00 3.41
88 89 1.207089 CGTTCAGGGTTGCTCTATCCA 59.793 52.381 0.00 0.00 0.00 3.41
89 90 1.480954 TCGTTCAGGGTTGCTCTATCC 59.519 52.381 0.00 0.00 0.00 2.59
90 91 2.961526 TCGTTCAGGGTTGCTCTATC 57.038 50.000 0.00 0.00 0.00 2.08
91 92 3.197766 TGAATCGTTCAGGGTTGCTCTAT 59.802 43.478 0.00 0.00 34.08 1.98
92 93 2.565391 TGAATCGTTCAGGGTTGCTCTA 59.435 45.455 0.00 0.00 34.08 2.43
93 94 1.347707 TGAATCGTTCAGGGTTGCTCT 59.652 47.619 0.00 0.00 34.08 4.09
94 95 1.808411 TGAATCGTTCAGGGTTGCTC 58.192 50.000 0.00 0.00 34.08 4.26
95 96 2.496899 ATGAATCGTTCAGGGTTGCT 57.503 45.000 6.59 0.00 43.98 3.91
96 97 3.270877 AGTATGAATCGTTCAGGGTTGC 58.729 45.455 6.59 0.00 43.98 4.17
97 98 6.201044 GTGATAGTATGAATCGTTCAGGGTTG 59.799 42.308 6.59 0.00 43.98 3.77
98 99 6.098409 AGTGATAGTATGAATCGTTCAGGGTT 59.902 38.462 6.59 0.00 43.98 4.11
99 100 5.598830 AGTGATAGTATGAATCGTTCAGGGT 59.401 40.000 6.59 0.00 43.98 4.34
100 101 6.090483 AGTGATAGTATGAATCGTTCAGGG 57.910 41.667 6.59 0.00 43.98 4.45
101 102 9.186323 CTTTAGTGATAGTATGAATCGTTCAGG 57.814 37.037 6.59 0.00 43.98 3.86
102 103 9.737427 ACTTTAGTGATAGTATGAATCGTTCAG 57.263 33.333 6.59 0.00 43.98 3.02
111 112 9.871238 GAACCAAGAACTTTAGTGATAGTATGA 57.129 33.333 0.00 0.00 0.00 2.15
112 113 9.653287 TGAACCAAGAACTTTAGTGATAGTATG 57.347 33.333 0.00 0.00 0.00 2.39
114 115 9.485206 GTTGAACCAAGAACTTTAGTGATAGTA 57.515 33.333 0.00 0.00 0.00 1.82
115 116 8.211629 AGTTGAACCAAGAACTTTAGTGATAGT 58.788 33.333 0.00 0.00 0.00 2.12
116 117 8.499162 CAGTTGAACCAAGAACTTTAGTGATAG 58.501 37.037 0.00 0.00 29.73 2.08
117 118 8.208224 TCAGTTGAACCAAGAACTTTAGTGATA 58.792 33.333 0.00 0.00 29.73 2.15
118 119 7.054124 TCAGTTGAACCAAGAACTTTAGTGAT 58.946 34.615 0.00 0.00 29.73 3.06
119 120 6.411376 TCAGTTGAACCAAGAACTTTAGTGA 58.589 36.000 0.00 0.00 29.73 3.41
120 121 6.677781 TCAGTTGAACCAAGAACTTTAGTG 57.322 37.500 0.00 0.00 29.73 2.74
121 122 7.696992 TTTCAGTTGAACCAAGAACTTTAGT 57.303 32.000 0.00 0.00 33.13 2.24
122 123 8.980143 TTTTTCAGTTGAACCAAGAACTTTAG 57.020 30.769 0.00 0.00 33.13 1.85
146 147 8.329203 TGTGAACCAAAAGCTTTGTTTATTTT 57.671 26.923 13.54 0.00 0.00 1.82
183 185 2.291217 GGCAGGATCTCCCTTCTTGTTT 60.291 50.000 0.00 0.00 44.85 2.83
185 187 0.915364 GGCAGGATCTCCCTTCTTGT 59.085 55.000 0.00 0.00 44.85 3.16
203 205 1.450312 GTGCCGGTCATCTTCTGGG 60.450 63.158 1.90 0.00 32.41 4.45
212 214 1.676678 GCATCTAGGAGTGCCGGTCA 61.677 60.000 1.90 0.00 39.96 4.02
240 242 3.256383 TCGAAGGAGTTTACGGTTCATCA 59.744 43.478 0.00 0.00 0.00 3.07
249 251 6.161381 TGACCAAGTTATCGAAGGAGTTTAC 58.839 40.000 0.00 0.00 0.00 2.01
295 298 2.943033 CCATTTGGAGTCGTGGGATTAC 59.057 50.000 0.00 0.00 37.39 1.89
303 306 0.039618 ATTGGCCCATTTGGAGTCGT 59.960 50.000 0.00 0.00 37.39 4.34
333 336 4.728307 GCAAGTGCGTGGCGTTTATAATTA 60.728 41.667 0.00 0.00 0.00 1.40
334 337 3.753842 CAAGTGCGTGGCGTTTATAATT 58.246 40.909 0.00 0.00 0.00 1.40
335 338 2.477189 GCAAGTGCGTGGCGTTTATAAT 60.477 45.455 0.00 0.00 0.00 1.28
336 339 1.135916 GCAAGTGCGTGGCGTTTATAA 60.136 47.619 0.00 0.00 0.00 0.98
339 342 2.634777 GCAAGTGCGTGGCGTTTA 59.365 55.556 0.00 0.00 0.00 2.01
360 366 1.162698 GCTTGTCCCGGAGTTAAACC 58.837 55.000 0.73 0.00 0.00 3.27
363 369 1.880646 GCTTGCTTGTCCCGGAGTTAA 60.881 52.381 0.73 0.00 0.00 2.01
364 370 0.321298 GCTTGCTTGTCCCGGAGTTA 60.321 55.000 0.73 0.00 0.00 2.24
365 371 1.600916 GCTTGCTTGTCCCGGAGTT 60.601 57.895 0.73 0.00 0.00 3.01
367 373 2.747855 GGCTTGCTTGTCCCGGAG 60.748 66.667 0.73 0.00 0.00 4.63
368 374 3.249189 AGGCTTGCTTGTCCCGGA 61.249 61.111 0.73 0.00 0.00 5.14
371 377 0.037447 AAGAGAGGCTTGCTTGTCCC 59.963 55.000 2.53 0.00 34.93 4.46
372 378 1.163554 CAAGAGAGGCTTGCTTGTCC 58.836 55.000 17.20 0.00 46.67 4.02
395 404 0.179073 CGGGTCGCCTGATTTGATCT 60.179 55.000 0.00 0.00 29.82 2.75
433 442 2.031870 AGTGACCTGCCCTTTTGTTTC 58.968 47.619 0.00 0.00 0.00 2.78
441 450 2.279069 CGTGAGAGTGACCTGCCCT 61.279 63.158 0.00 0.00 0.00 5.19
445 454 0.039074 GGTGTCGTGAGAGTGACCTG 60.039 60.000 0.00 0.00 43.49 4.00
446 455 1.516365 CGGTGTCGTGAGAGTGACCT 61.516 60.000 0.00 0.00 43.49 3.85
448 457 1.081376 CCGGTGTCGTGAGAGTGAC 60.081 63.158 0.00 0.00 43.49 3.67
449 458 1.512996 GACCGGTGTCGTGAGAGTGA 61.513 60.000 14.63 0.00 43.49 3.41
450 459 1.081376 GACCGGTGTCGTGAGAGTG 60.081 63.158 14.63 0.00 43.49 3.51
451 460 0.822532 AAGACCGGTGTCGTGAGAGT 60.823 55.000 14.63 0.00 46.51 3.24
452 461 1.957562 AAGACCGGTGTCGTGAGAG 59.042 57.895 14.63 0.00 46.51 3.20
489 499 0.743345 GCCGGACGAAATTACAGCCT 60.743 55.000 5.05 0.00 0.00 4.58
538 548 8.419076 AATGTGTTGGTTATTTTGTCTCAAAC 57.581 30.769 0.00 0.00 0.00 2.93
539 549 9.092876 GAAATGTGTTGGTTATTTTGTCTCAAA 57.907 29.630 0.00 0.00 0.00 2.69
540 550 8.253810 TGAAATGTGTTGGTTATTTTGTCTCAA 58.746 29.630 0.00 0.00 0.00 3.02
541 551 7.776107 TGAAATGTGTTGGTTATTTTGTCTCA 58.224 30.769 0.00 0.00 0.00 3.27
542 552 8.816640 ATGAAATGTGTTGGTTATTTTGTCTC 57.183 30.769 0.00 0.00 0.00 3.36
543 553 9.260002 GAATGAAATGTGTTGGTTATTTTGTCT 57.740 29.630 0.00 0.00 0.00 3.41
544 554 9.039870 TGAATGAAATGTGTTGGTTATTTTGTC 57.960 29.630 0.00 0.00 0.00 3.18
545 555 8.954950 TGAATGAAATGTGTTGGTTATTTTGT 57.045 26.923 0.00 0.00 0.00 2.83
546 556 8.011106 GCTGAATGAAATGTGTTGGTTATTTTG 58.989 33.333 0.00 0.00 0.00 2.44
547 557 7.714377 TGCTGAATGAAATGTGTTGGTTATTTT 59.286 29.630 0.00 0.00 0.00 1.82
548 558 7.171337 GTGCTGAATGAAATGTGTTGGTTATTT 59.829 33.333 0.00 0.00 0.00 1.40
549 559 6.646240 GTGCTGAATGAAATGTGTTGGTTATT 59.354 34.615 0.00 0.00 0.00 1.40
550 560 6.158598 GTGCTGAATGAAATGTGTTGGTTAT 58.841 36.000 0.00 0.00 0.00 1.89
551 561 5.508825 GGTGCTGAATGAAATGTGTTGGTTA 60.509 40.000 0.00 0.00 0.00 2.85
552 562 4.370917 GTGCTGAATGAAATGTGTTGGTT 58.629 39.130 0.00 0.00 0.00 3.67
553 563 3.243839 GGTGCTGAATGAAATGTGTTGGT 60.244 43.478 0.00 0.00 0.00 3.67
554 564 3.006110 AGGTGCTGAATGAAATGTGTTGG 59.994 43.478 0.00 0.00 0.00 3.77
555 565 3.985279 CAGGTGCTGAATGAAATGTGTTG 59.015 43.478 0.00 0.00 32.44 3.33
558 568 3.253921 TCACAGGTGCTGAATGAAATGTG 59.746 43.478 0.00 0.00 38.46 3.21
574 584 4.969196 ACAGTGCGCGGTCACAGG 62.969 66.667 17.26 11.70 39.35 4.00
575 585 2.534019 AAACAGTGCGCGGTCACAG 61.534 57.895 17.26 12.40 39.35 3.66
576 586 2.512745 AAACAGTGCGCGGTCACA 60.513 55.556 17.26 0.00 39.35 3.58
577 587 2.052237 CAAACAGTGCGCGGTCAC 60.052 61.111 8.83 8.69 37.24 3.67
578 588 2.202946 TCAAACAGTGCGCGGTCA 60.203 55.556 8.83 0.00 0.00 4.02
579 589 2.248431 GTCAAACAGTGCGCGGTC 59.752 61.111 8.83 0.00 0.00 4.79
582 592 3.334751 TCGGTCAAACAGTGCGCG 61.335 61.111 0.00 0.00 0.00 6.86
584 594 1.275657 GTGTCGGTCAAACAGTGCG 59.724 57.895 0.00 0.00 0.00 5.34
585 595 1.275657 CGTGTCGGTCAAACAGTGC 59.724 57.895 0.00 0.00 0.00 4.40
612 624 2.114670 CGCCGATCATTGTGGGCTT 61.115 57.895 5.66 0.00 43.38 4.35
614 626 4.256090 GCGCCGATCATTGTGGGC 62.256 66.667 0.00 0.00 42.14 5.36
615 627 2.823593 TGCGCCGATCATTGTGGG 60.824 61.111 4.18 0.00 0.00 4.61
616 628 2.711311 CTGCGCCGATCATTGTGG 59.289 61.111 4.18 0.00 0.00 4.17
617 629 2.711311 CCTGCGCCGATCATTGTG 59.289 61.111 4.18 0.00 0.00 3.33
618 630 3.204827 GCCTGCGCCGATCATTGT 61.205 61.111 4.18 0.00 0.00 2.71
681 693 0.387929 CACGTCCATACATACGGCCT 59.612 55.000 0.00 0.00 43.25 5.19
691 704 2.889617 CTGCGGTCCACGTCCATA 59.110 61.111 0.00 0.00 46.52 2.74
827 850 2.048877 GGAAACGAACGCGGAGGA 60.049 61.111 12.47 0.00 43.17 3.71
837 862 3.608662 ACGCGTGGGAGGAAACGA 61.609 61.111 12.93 0.00 42.32 3.85
868 893 2.122369 GGAGGGGATCGGGATGGT 60.122 66.667 0.00 0.00 0.00 3.55
870 895 3.314331 CGGGAGGGGATCGGGATG 61.314 72.222 0.00 0.00 0.00 3.51
871 896 3.406113 AACGGGAGGGGATCGGGAT 62.406 63.158 0.00 0.00 0.00 3.85
872 897 4.084147 AACGGGAGGGGATCGGGA 62.084 66.667 0.00 0.00 0.00 5.14
873 898 3.861797 CAACGGGAGGGGATCGGG 61.862 72.222 0.00 0.00 0.00 5.14
882 907 1.883021 GGCAACCAATCAACGGGAG 59.117 57.895 0.00 0.00 0.00 4.30
948 973 1.967535 CTTCTCCTGCGGTCAGTCA 59.032 57.895 0.00 0.00 38.66 3.41
1225 1266 1.202770 GGCTAATCAATACCCGGCAGT 60.203 52.381 0.00 0.00 0.00 4.40
1227 1268 0.840617 TGGCTAATCAATACCCGGCA 59.159 50.000 0.00 0.00 0.00 5.69
1238 1279 1.526225 GAACGGGGCCTGGCTAATC 60.526 63.158 19.68 6.68 0.00 1.75
1239 1280 2.595655 GAACGGGGCCTGGCTAAT 59.404 61.111 19.68 0.53 0.00 1.73
1240 1281 3.723922 GGAACGGGGCCTGGCTAA 61.724 66.667 19.68 0.00 0.00 3.09
1259 1300 3.595758 CATTTCCATCCGCCCGCC 61.596 66.667 0.00 0.00 0.00 6.13
1260 1301 3.595758 CCATTTCCATCCGCCCGC 61.596 66.667 0.00 0.00 0.00 6.13
1262 1303 1.809567 GCATCCATTTCCATCCGCCC 61.810 60.000 0.00 0.00 0.00 6.13
1265 1306 1.271379 CCATGCATCCATTTCCATCCG 59.729 52.381 0.00 0.00 0.00 4.18
1272 1313 1.958579 CGGACATCCATGCATCCATTT 59.041 47.619 0.00 0.00 35.14 2.32
1281 1322 1.202521 TCAATCGACCGGACATCCATG 60.203 52.381 9.46 0.00 35.14 3.66
1287 1328 1.589630 CCAGTCAATCGACCGGACA 59.410 57.895 9.46 0.00 41.62 4.02
1288 1329 1.153628 CCCAGTCAATCGACCGGAC 60.154 63.158 9.46 0.00 41.62 4.79
1289 1330 3.014085 GCCCAGTCAATCGACCGGA 62.014 63.158 9.46 0.00 41.62 5.14
1293 1334 0.103208 AGATCGCCCAGTCAATCGAC 59.897 55.000 0.00 0.00 42.95 4.20
1299 1340 0.976641 AACAAGAGATCGCCCAGTCA 59.023 50.000 0.00 0.00 0.00 3.41
1302 1343 1.065854 AGGAAACAAGAGATCGCCCAG 60.066 52.381 0.00 0.00 0.00 4.45
1306 1347 1.656095 CGACAGGAAACAAGAGATCGC 59.344 52.381 0.00 0.00 0.00 4.58
1313 1354 5.827666 ACCATTTAAACGACAGGAAACAAG 58.172 37.500 0.00 0.00 0.00 3.16
1317 1358 5.591067 ACAGAACCATTTAAACGACAGGAAA 59.409 36.000 0.00 0.00 0.00 3.13
1320 1361 5.467399 TGTACAGAACCATTTAAACGACAGG 59.533 40.000 0.00 0.00 0.00 4.00
1347 1391 2.607771 CCTGAATCAAACGGCAAACCTG 60.608 50.000 0.00 0.00 0.00 4.00
1350 1394 1.339929 ACCCTGAATCAAACGGCAAAC 59.660 47.619 0.00 0.00 0.00 2.93
1354 1398 1.068541 GTCAACCCTGAATCAAACGGC 60.069 52.381 0.00 0.00 31.88 5.68
1355 1399 2.031157 GTGTCAACCCTGAATCAAACGG 60.031 50.000 0.00 0.00 31.88 4.44
1373 1421 2.457598 AGATGATCTACGTGGTGGTGT 58.542 47.619 0.00 0.00 0.00 4.16
1388 1436 3.004210 GCAGAGATCTGAACGCTAGATGA 59.996 47.826 13.98 0.00 46.59 2.92
1393 1444 5.067805 TCAATAAGCAGAGATCTGAACGCTA 59.932 40.000 13.98 0.00 46.59 4.26
1395 1446 4.115516 TCAATAAGCAGAGATCTGAACGC 58.884 43.478 13.98 0.00 46.59 4.84
1400 1452 6.766944 AGAACCAATCAATAAGCAGAGATCTG 59.233 38.462 0.00 5.45 46.40 2.90
1428 1480 4.311606 GAGAACAGGACAAGAGGAAGAAC 58.688 47.826 0.00 0.00 0.00 3.01
1437 1490 3.868077 GGATCAATCGAGAACAGGACAAG 59.132 47.826 0.00 0.00 0.00 3.16
1438 1491 3.676049 CGGATCAATCGAGAACAGGACAA 60.676 47.826 0.00 0.00 0.00 3.18
1472 1525 1.136252 CAGTGAACGAACCAATCAGCG 60.136 52.381 0.00 0.00 0.00 5.18
1480 1533 1.606350 CGAGCGTCAGTGAACGAACC 61.606 60.000 16.04 5.88 45.37 3.62
1507 1561 1.475403 TCCCGAACAAACAAAGGCAA 58.525 45.000 0.00 0.00 0.00 4.52
1513 1567 1.352404 CGCGTTCCCGAACAAACAA 59.648 52.632 0.00 0.00 41.20 2.83
1514 1568 2.535788 CCGCGTTCCCGAACAAACA 61.536 57.895 4.92 0.00 41.20 2.83
1515 1569 2.250190 CCGCGTTCCCGAACAAAC 59.750 61.111 4.92 0.00 41.20 2.93
1530 1584 2.960957 AATCTGAGGATCACGCGCCG 62.961 60.000 5.73 0.00 42.56 6.46
1531 1585 0.811616 AAATCTGAGGATCACGCGCC 60.812 55.000 5.73 0.00 42.56 6.53
1532 1586 0.302890 CAAATCTGAGGATCACGCGC 59.697 55.000 5.73 0.00 42.56 6.86
1533 1587 0.302890 GCAAATCTGAGGATCACGCG 59.697 55.000 3.53 3.53 42.56 6.01
1542 1596 1.728971 GTGACAGTCGGCAAATCTGAG 59.271 52.381 0.00 0.00 33.93 3.35
1547 1601 0.321653 GGAGGTGACAGTCGGCAAAT 60.322 55.000 0.00 0.00 0.00 2.32
1613 1679 4.102524 TGTGACCATTCCACTAGACTTTGT 59.897 41.667 0.00 0.00 35.66 2.83
1616 1682 3.904339 ACTGTGACCATTCCACTAGACTT 59.096 43.478 0.00 0.00 35.66 3.01
1621 1687 5.306937 CCCATATACTGTGACCATTCCACTA 59.693 44.000 0.00 0.00 35.66 2.74
1622 1688 4.103153 CCCATATACTGTGACCATTCCACT 59.897 45.833 0.00 0.00 35.66 4.00
1626 1692 5.552870 ACTCCCATATACTGTGACCATTC 57.447 43.478 0.00 0.00 0.00 2.67
1627 1693 5.975988 AACTCCCATATACTGTGACCATT 57.024 39.130 0.00 0.00 0.00 3.16
1628 1694 5.684704 CAAACTCCCATATACTGTGACCAT 58.315 41.667 0.00 0.00 0.00 3.55
1629 1695 4.625324 GCAAACTCCCATATACTGTGACCA 60.625 45.833 0.00 0.00 0.00 4.02
1630 1696 3.877508 GCAAACTCCCATATACTGTGACC 59.122 47.826 0.00 0.00 0.00 4.02
1632 1698 4.835284 TGCAAACTCCCATATACTGTGA 57.165 40.909 0.00 0.00 0.00 3.58
1633 1699 5.371526 AGATGCAAACTCCCATATACTGTG 58.628 41.667 0.00 0.00 0.00 3.66
1674 1744 3.002791 TCATCTGTGAAGGACGAAATGC 58.997 45.455 0.00 0.00 0.00 3.56
1700 1771 9.604626 GAAACAGAAGTAGATGAAAAATGAGTG 57.395 33.333 0.00 0.00 0.00 3.51
1701 1772 9.342308 TGAAACAGAAGTAGATGAAAAATGAGT 57.658 29.630 0.00 0.00 0.00 3.41
1712 1783 8.682936 ATCTTTGTGTTGAAACAGAAGTAGAT 57.317 30.769 11.56 11.56 42.15 1.98
1765 1836 4.885413 TGAATTGCCCACAGAATTGAAAG 58.115 39.130 0.00 0.00 0.00 2.62
1771 1842 2.029110 CCGTTTGAATTGCCCACAGAAT 60.029 45.455 0.00 0.00 0.00 2.40
1793 1864 4.981054 CAGTGCTACTATGCTGATACAGTG 59.019 45.833 0.00 0.00 33.43 3.66
1889 1960 5.011586 TGACATGCCATTTCTGAAATCTCA 58.988 37.500 12.50 12.82 0.00 3.27
1890 1961 5.571784 TGACATGCCATTTCTGAAATCTC 57.428 39.130 12.50 8.09 0.00 2.75
1891 1962 5.105473 CCTTGACATGCCATTTCTGAAATCT 60.105 40.000 12.50 0.00 0.00 2.40
1892 1963 5.105635 TCCTTGACATGCCATTTCTGAAATC 60.106 40.000 12.50 4.07 0.00 2.17
1893 1964 4.773674 TCCTTGACATGCCATTTCTGAAAT 59.226 37.500 9.76 9.76 0.00 2.17
1894 1965 4.022068 GTCCTTGACATGCCATTTCTGAAA 60.022 41.667 5.15 5.15 32.09 2.69
1895 1966 3.507233 GTCCTTGACATGCCATTTCTGAA 59.493 43.478 0.00 0.00 32.09 3.02
1896 1967 3.084039 GTCCTTGACATGCCATTTCTGA 58.916 45.455 0.00 0.00 32.09 3.27
1897 1968 2.821378 TGTCCTTGACATGCCATTTCTG 59.179 45.455 0.00 0.00 37.67 3.02
1898 1969 3.159213 TGTCCTTGACATGCCATTTCT 57.841 42.857 0.00 0.00 37.67 2.52
1899 1970 3.940209 TTGTCCTTGACATGCCATTTC 57.060 42.857 0.00 0.00 42.40 2.17
1900 1971 3.642848 ACTTTGTCCTTGACATGCCATTT 59.357 39.130 0.00 0.00 42.40 2.32
1901 1972 3.233507 ACTTTGTCCTTGACATGCCATT 58.766 40.909 0.00 0.00 42.40 3.16
1902 1973 2.880443 ACTTTGTCCTTGACATGCCAT 58.120 42.857 0.00 0.00 42.40 4.40
1903 1974 2.363306 ACTTTGTCCTTGACATGCCA 57.637 45.000 0.00 0.00 42.40 4.92
1904 1975 4.009675 TGATACTTTGTCCTTGACATGCC 58.990 43.478 0.00 0.00 42.40 4.40
1905 1976 5.393962 GTTGATACTTTGTCCTTGACATGC 58.606 41.667 0.00 0.00 42.40 4.06
1906 1977 5.707298 AGGTTGATACTTTGTCCTTGACATG 59.293 40.000 0.00 0.00 42.40 3.21
1907 1978 5.880901 AGGTTGATACTTTGTCCTTGACAT 58.119 37.500 0.00 0.00 42.40 3.06
1908 1979 5.304686 AGGTTGATACTTTGTCCTTGACA 57.695 39.130 0.00 0.00 41.09 3.58
1909 1980 4.695928 GGAGGTTGATACTTTGTCCTTGAC 59.304 45.833 0.00 0.00 0.00 3.18
1910 1981 4.562757 CGGAGGTTGATACTTTGTCCTTGA 60.563 45.833 0.00 0.00 0.00 3.02
1911 1982 3.684788 CGGAGGTTGATACTTTGTCCTTG 59.315 47.826 0.00 0.00 0.00 3.61
1912 1983 3.326880 ACGGAGGTTGATACTTTGTCCTT 59.673 43.478 0.00 0.00 0.00 3.36
1924 1995 1.272490 CTGCAACTCTACGGAGGTTGA 59.728 52.381 24.64 13.25 43.46 3.18
1928 1999 0.888619 TGTCTGCAACTCTACGGAGG 59.111 55.000 0.00 0.00 43.46 4.30
1963 2034 9.683069 CTCTAACAATGTCTGCAACTAAAATTT 57.317 29.630 0.00 0.00 0.00 1.82
1964 2035 9.066892 TCTCTAACAATGTCTGCAACTAAAATT 57.933 29.630 0.00 0.00 0.00 1.82
1965 2036 8.621532 TCTCTAACAATGTCTGCAACTAAAAT 57.378 30.769 0.00 0.00 0.00 1.82
1966 2037 8.506437 CATCTCTAACAATGTCTGCAACTAAAA 58.494 33.333 0.00 0.00 0.00 1.52
1967 2038 7.119699 CCATCTCTAACAATGTCTGCAACTAAA 59.880 37.037 0.00 0.00 0.00 1.85
1968 2039 6.595326 CCATCTCTAACAATGTCTGCAACTAA 59.405 38.462 0.00 0.00 0.00 2.24
1969 2040 6.108687 CCATCTCTAACAATGTCTGCAACTA 58.891 40.000 0.00 0.00 0.00 2.24
1970 2041 4.940046 CCATCTCTAACAATGTCTGCAACT 59.060 41.667 0.00 0.00 0.00 3.16
1971 2042 4.697352 ACCATCTCTAACAATGTCTGCAAC 59.303 41.667 0.00 0.00 0.00 4.17
1972 2043 4.910195 ACCATCTCTAACAATGTCTGCAA 58.090 39.130 0.00 0.00 0.00 4.08
1973 2044 4.558226 ACCATCTCTAACAATGTCTGCA 57.442 40.909 0.00 0.00 0.00 4.41
1974 2045 4.095483 CCAACCATCTCTAACAATGTCTGC 59.905 45.833 0.00 0.00 0.00 4.26
1975 2046 5.491070 TCCAACCATCTCTAACAATGTCTG 58.509 41.667 0.00 0.00 0.00 3.51
1976 2047 5.762179 TCCAACCATCTCTAACAATGTCT 57.238 39.130 0.00 0.00 0.00 3.41
1977 2048 7.396540 AAATCCAACCATCTCTAACAATGTC 57.603 36.000 0.00 0.00 0.00 3.06
1978 2049 8.328758 TCTAAATCCAACCATCTCTAACAATGT 58.671 33.333 0.00 0.00 0.00 2.71
1979 2050 8.737168 TCTAAATCCAACCATCTCTAACAATG 57.263 34.615 0.00 0.00 0.00 2.82
1980 2051 9.401058 CTTCTAAATCCAACCATCTCTAACAAT 57.599 33.333 0.00 0.00 0.00 2.71
1981 2052 8.602424 TCTTCTAAATCCAACCATCTCTAACAA 58.398 33.333 0.00 0.00 0.00 2.83
1982 2053 8.146053 TCTTCTAAATCCAACCATCTCTAACA 57.854 34.615 0.00 0.00 0.00 2.41
1983 2054 9.449719 TTTCTTCTAAATCCAACCATCTCTAAC 57.550 33.333 0.00 0.00 0.00 2.34
2039 2111 7.377766 TGAACTTTTGAGTAATGCTCCATAC 57.622 36.000 0.00 0.00 43.48 2.39
2086 2158 3.624861 CACCATCTCAGTAGTTGAATGGC 59.375 47.826 13.42 0.00 42.26 4.40
2111 2183 1.635663 CCGTTCGGATTGCACTGACC 61.636 60.000 5.19 0.00 0.00 4.02
2150 2234 4.384056 AGCATCTTTGTTATCTAGCGCAT 58.616 39.130 11.47 0.00 0.00 4.73
2191 2275 2.424956 GGTTGCTTCTATGGGCTTTCTG 59.575 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.