Multiple sequence alignment - TraesCS1D01G292800

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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 TraesCS1D01G292800 chr1D 100.000 4582 0 0 1 4582 392018030 392022611 0.000000e+00 8462.0
1 TraesCS1D01G292800 chr1D 89.163 932 88 10 2529 3454 391984887 391985811 0.000000e+00 1149.0
2 TraesCS1D01G292800 chr1D 84.400 1000 106 21 671 1653 391968845 391969811 0.000000e+00 937.0
3 TraesCS1D01G292800 chr1D 84.689 418 49 7 1647 2060 391969926 391970332 1.990000e-108 403.0
4 TraesCS1D01G292800 chr1D 100.000 37 0 0 143 179 392018140 392018176 8.230000e-08 69.4
5 TraesCS1D01G292800 chr1D 100.000 37 0 0 111 147 392018172 392018208 8.230000e-08 69.4
6 TraesCS1D01G292800 chr1B 92.837 3197 155 37 1435 4578 530659632 530656457 0.000000e+00 4567.0
7 TraesCS1D01G292800 chr1B 88.627 932 61 22 535 1436 530660708 530659792 0.000000e+00 1092.0
8 TraesCS1D01G292800 chr1B 88.158 912 98 9 2548 3454 530666932 530666026 0.000000e+00 1077.0
9 TraesCS1D01G292800 chr1B 83.946 816 109 13 1270 2072 530668587 530667781 0.000000e+00 761.0
10 TraesCS1D01G292800 chr1B 87.580 314 32 2 143 456 530660946 530660640 1.570000e-94 357.0
11 TraesCS1D01G292800 chr1B 94.118 51 3 0 3450 3500 530666012 530665962 1.370000e-10 78.7
12 TraesCS1D01G292800 chr1A 93.863 994 46 6 1113 2091 493274225 493273232 0.000000e+00 1483.0
13 TraesCS1D01G292800 chr1A 91.418 1037 73 10 3558 4582 493271167 493270135 0.000000e+00 1408.0
14 TraesCS1D01G292800 chr1A 85.813 1297 139 26 2548 3820 493281365 493280090 0.000000e+00 1334.0
15 TraesCS1D01G292800 chr1A 86.169 629 76 8 1452 2072 493282861 493282236 0.000000e+00 669.0
16 TraesCS1D01G292800 chr1A 89.918 486 36 8 2529 3005 493272079 493271598 8.430000e-172 614.0
17 TraesCS1D01G292800 chr1A 90.278 360 28 4 877 1235 493284305 493283952 8.980000e-127 464.0
18 TraesCS1D01G292800 chr1A 88.127 379 20 8 2083 2439 493273077 493272702 1.180000e-115 427.0
19 TraesCS1D01G292800 chr1A 92.754 276 13 2 3263 3538 493271606 493271338 4.300000e-105 392.0
20 TraesCS1D01G292800 chr1A 86.747 249 17 8 877 1125 493279659 493279427 3.520000e-66 263.0
21 TraesCS1D01G292800 chr1A 87.234 141 16 2 1270 1409 493283956 493283817 4.740000e-35 159.0
22 TraesCS1D01G292800 chr7D 88.028 142 9 1 2069 2202 228526063 228526204 1.320000e-35 161.0
23 TraesCS1D01G292800 chr7D 92.941 85 4 1 2120 2202 35603231 35603315 6.230000e-24 122.0
24 TraesCS1D01G292800 chr3A 81.046 153 9 5 2070 2203 387286168 387286017 2.250000e-18 104.0
25 TraesCS1D01G292800 chr3A 82.653 98 4 3 2112 2197 80090538 80090634 1.770000e-09 75.0


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 TraesCS1D01G292800 chr1D 392018030 392022611 4581 False 8462.000000 8462 100.000000 1 4582 1 chr1D.!!$F2 4581
1 TraesCS1D01G292800 chr1D 391984887 391985811 924 False 1149.000000 1149 89.163000 2529 3454 1 chr1D.!!$F1 925
2 TraesCS1D01G292800 chr1D 391968845 391970332 1487 False 670.000000 937 84.544500 671 2060 2 chr1D.!!$F3 1389
3 TraesCS1D01G292800 chr1B 530656457 530660946 4489 True 2005.333333 4567 89.681333 143 4578 3 chr1B.!!$R1 4435
4 TraesCS1D01G292800 chr1B 530665962 530668587 2625 True 638.900000 1077 88.740667 1270 3500 3 chr1B.!!$R2 2230
5 TraesCS1D01G292800 chr1A 493270135 493274225 4090 True 864.800000 1483 91.216000 1113 4582 5 chr1A.!!$R1 3469
6 TraesCS1D01G292800 chr1A 493279427 493284305 4878 True 577.800000 1334 87.248200 877 3820 5 chr1A.!!$R2 2943

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
796 805 0.111266 CGCAAAAACGAGTCTCACGG 60.111 55.0 0.00 0.00 34.06 4.94 F
1031 1046 0.107703 GGATTGCCGTCAGACATGGA 60.108 55.0 0.41 0.00 31.73 3.41 F
1518 2633 0.257039 AACATCCCCTTGCAGCTAGG 59.743 55.0 15.51 15.51 0.00 3.02 F
2145 3565 0.400594 AGCGGGCAAGTTTCTAAGGT 59.599 50.0 0.00 0.00 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 3505 0.895530 CGGGTGGTGCTCTCTTTAGA 59.104 55.0 0.0 0.0 0.00 2.10 R
3023 5166 0.250166 CCCGGTGAGTTTTCCGTCTT 60.250 55.0 0.0 0.0 44.51 3.01 R
3024 5167 1.117142 TCCCGGTGAGTTTTCCGTCT 61.117 55.0 0.0 0.0 44.51 4.18 R
4002 6379 0.037590 ATCGGCAGTGTTTAAGGGCA 59.962 50.0 0.0 0.0 0.00 5.36 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
20 21 3.934457 AACAAAATTAAGCCGTCCAGG 57.066 42.857 0.00 0.00 44.97 4.45
21 22 2.871453 ACAAAATTAAGCCGTCCAGGT 58.129 42.857 0.00 0.00 43.70 4.00
22 23 3.227614 ACAAAATTAAGCCGTCCAGGTT 58.772 40.909 0.00 0.00 43.70 3.50
23 24 3.639561 ACAAAATTAAGCCGTCCAGGTTT 59.360 39.130 0.00 0.00 45.76 3.27
24 25 4.100344 ACAAAATTAAGCCGTCCAGGTTTT 59.900 37.500 0.00 0.00 40.82 2.43
25 26 4.948341 AAATTAAGCCGTCCAGGTTTTT 57.052 36.364 0.00 0.00 40.82 1.94
26 27 4.514781 AATTAAGCCGTCCAGGTTTTTC 57.485 40.909 0.00 0.00 40.82 2.29
27 28 2.642154 TAAGCCGTCCAGGTTTTTCA 57.358 45.000 0.00 0.00 40.82 2.69
28 29 1.770294 AAGCCGTCCAGGTTTTTCAA 58.230 45.000 0.00 0.00 40.82 2.69
29 30 1.318576 AGCCGTCCAGGTTTTTCAAG 58.681 50.000 0.00 0.00 43.70 3.02
30 31 1.029681 GCCGTCCAGGTTTTTCAAGT 58.970 50.000 0.00 0.00 43.70 3.16
31 32 1.001706 GCCGTCCAGGTTTTTCAAGTC 60.002 52.381 0.00 0.00 43.70 3.01
32 33 2.294074 CCGTCCAGGTTTTTCAAGTCA 58.706 47.619 0.00 0.00 34.51 3.41
33 34 2.884639 CCGTCCAGGTTTTTCAAGTCAT 59.115 45.455 0.00 0.00 34.51 3.06
34 35 3.058224 CCGTCCAGGTTTTTCAAGTCATC 60.058 47.826 0.00 0.00 34.51 2.92
35 36 3.363970 CGTCCAGGTTTTTCAAGTCATCG 60.364 47.826 0.00 0.00 0.00 3.84
36 37 2.552315 TCCAGGTTTTTCAAGTCATCGC 59.448 45.455 0.00 0.00 0.00 4.58
37 38 2.293122 CCAGGTTTTTCAAGTCATCGCA 59.707 45.455 0.00 0.00 0.00 5.10
38 39 3.057315 CCAGGTTTTTCAAGTCATCGCAT 60.057 43.478 0.00 0.00 0.00 4.73
39 40 4.549458 CAGGTTTTTCAAGTCATCGCATT 58.451 39.130 0.00 0.00 0.00 3.56
40 41 4.618489 CAGGTTTTTCAAGTCATCGCATTC 59.382 41.667 0.00 0.00 0.00 2.67
41 42 4.520492 AGGTTTTTCAAGTCATCGCATTCT 59.480 37.500 0.00 0.00 0.00 2.40
42 43 4.618489 GGTTTTTCAAGTCATCGCATTCTG 59.382 41.667 0.00 0.00 0.00 3.02
43 44 5.451908 GTTTTTCAAGTCATCGCATTCTGA 58.548 37.500 0.00 0.00 0.00 3.27
44 45 5.885230 TTTTCAAGTCATCGCATTCTGAT 57.115 34.783 0.00 0.00 0.00 2.90
45 46 4.870221 TTCAAGTCATCGCATTCTGATG 57.130 40.909 0.00 0.00 43.62 3.07
46 47 3.865446 TCAAGTCATCGCATTCTGATGT 58.135 40.909 3.21 0.00 42.96 3.06
47 48 5.009854 TCAAGTCATCGCATTCTGATGTA 57.990 39.130 3.21 0.00 42.96 2.29
48 49 5.418676 TCAAGTCATCGCATTCTGATGTAA 58.581 37.500 3.21 0.00 42.96 2.41
49 50 6.051074 TCAAGTCATCGCATTCTGATGTAAT 58.949 36.000 3.21 0.00 42.96 1.89
50 51 6.539826 TCAAGTCATCGCATTCTGATGTAATT 59.460 34.615 3.21 0.00 42.96 1.40
51 52 6.536731 AGTCATCGCATTCTGATGTAATTC 57.463 37.500 3.21 0.00 42.96 2.17
52 53 6.286758 AGTCATCGCATTCTGATGTAATTCT 58.713 36.000 3.21 0.00 42.96 2.40
53 54 7.436933 AGTCATCGCATTCTGATGTAATTCTA 58.563 34.615 3.21 0.00 42.96 2.10
54 55 8.093307 AGTCATCGCATTCTGATGTAATTCTAT 58.907 33.333 3.21 0.00 42.96 1.98
55 56 9.358872 GTCATCGCATTCTGATGTAATTCTATA 57.641 33.333 3.21 0.00 42.96 1.31
58 59 8.189709 TCGCATTCTGATGTAATTCTATATGC 57.810 34.615 0.00 0.00 35.63 3.14
59 60 8.037166 TCGCATTCTGATGTAATTCTATATGCT 58.963 33.333 0.00 0.00 35.63 3.79
60 61 8.663025 CGCATTCTGATGTAATTCTATATGCTT 58.337 33.333 0.00 0.00 35.63 3.91
61 62 9.985318 GCATTCTGATGTAATTCTATATGCTTC 57.015 33.333 0.00 0.00 35.63 3.86
122 123 8.755696 TTTTTGCTTTGACCATACACATATTC 57.244 30.769 0.00 0.00 0.00 1.75
123 124 7.701539 TTTGCTTTGACCATACACATATTCT 57.298 32.000 0.00 0.00 0.00 2.40
124 125 6.925610 TGCTTTGACCATACACATATTCTC 57.074 37.500 0.00 0.00 0.00 2.87
125 126 5.822519 TGCTTTGACCATACACATATTCTCC 59.177 40.000 0.00 0.00 0.00 3.71
126 127 5.822519 GCTTTGACCATACACATATTCTCCA 59.177 40.000 0.00 0.00 0.00 3.86
127 128 6.488006 GCTTTGACCATACACATATTCTCCAT 59.512 38.462 0.00 0.00 0.00 3.41
128 129 7.521099 GCTTTGACCATACACATATTCTCCATG 60.521 40.741 0.00 0.00 0.00 3.66
129 130 5.868454 TGACCATACACATATTCTCCATGG 58.132 41.667 4.97 4.97 37.93 3.66
130 131 5.369404 TGACCATACACATATTCTCCATGGT 59.631 40.000 12.58 3.11 45.52 3.55
131 132 6.556874 TGACCATACACATATTCTCCATGGTA 59.443 38.462 12.58 0.00 43.50 3.25
132 133 7.237471 TGACCATACACATATTCTCCATGGTAT 59.763 37.037 12.58 6.80 43.50 2.73
133 134 7.988937 ACCATACACATATTCTCCATGGTATT 58.011 34.615 12.58 0.89 42.10 1.89
134 135 8.448008 ACCATACACATATTCTCCATGGTATTT 58.552 33.333 12.58 0.00 42.10 1.40
135 136 8.950210 CCATACACATATTCTCCATGGTATTTC 58.050 37.037 12.58 0.00 0.00 2.17
136 137 9.506018 CATACACATATTCTCCATGGTATTTCA 57.494 33.333 12.58 0.00 0.00 2.69
137 138 7.807977 ACACATATTCTCCATGGTATTTCAC 57.192 36.000 12.58 0.00 0.00 3.18
187 188 4.846779 TCACCAAACATACCTTTGCTTC 57.153 40.909 0.00 0.00 30.87 3.86
192 193 6.010219 ACCAAACATACCTTTGCTTCTATGT 58.990 36.000 0.00 0.00 32.35 2.29
222 223 5.990996 ACCAAACATGTTATTGCCTTCAAAG 59.009 36.000 12.39 0.00 35.56 2.77
224 225 6.875195 CCAAACATGTTATTGCCTTCAAAGAT 59.125 34.615 12.39 0.00 35.56 2.40
230 231 9.976511 CATGTTATTGCCTTCAAAGATAATCAT 57.023 29.630 0.00 0.00 35.56 2.45
231 232 9.976511 ATGTTATTGCCTTCAAAGATAATCATG 57.023 29.630 0.00 0.00 35.56 3.07
232 233 8.970020 TGTTATTGCCTTCAAAGATAATCATGT 58.030 29.630 0.00 0.00 35.56 3.21
233 234 9.807649 GTTATTGCCTTCAAAGATAATCATGTT 57.192 29.630 0.00 0.00 35.56 2.71
252 253 5.040715 TGTTTTTGTTTTTGCTTGAAGCC 57.959 34.783 15.43 0.00 41.51 4.35
299 300 7.665690 TGTTTTGGTGAACTTATGTATGCAAT 58.334 30.769 0.00 0.00 0.00 3.56
300 301 8.147058 TGTTTTGGTGAACTTATGTATGCAATT 58.853 29.630 0.00 0.00 0.00 2.32
310 311 8.810652 ACTTATGTATGCAATTGTTTTTCGTT 57.189 26.923 7.40 0.00 0.00 3.85
366 367 3.487942 CCCGGTGAACGTTTTTCAAATTC 59.512 43.478 0.46 0.00 42.24 2.17
378 379 7.947830 ACGTTTTTCAAATTCGTGAACTTTTTC 59.052 29.630 0.38 0.00 37.24 2.29
386 387 8.603181 CAAATTCGTGAACTTTTTCCATTCTTT 58.397 29.630 0.00 0.00 0.00 2.52
387 388 9.810545 AAATTCGTGAACTTTTTCCATTCTTTA 57.189 25.926 0.00 0.00 0.00 1.85
472 473 9.585099 TTCAAATTCATGGACATTTACTAATGC 57.415 29.630 0.00 0.00 44.05 3.56
473 474 8.747471 TCAAATTCATGGACATTTACTAATGCA 58.253 29.630 0.00 0.00 44.05 3.96
474 475 9.537192 CAAATTCATGGACATTTACTAATGCAT 57.463 29.630 0.00 0.00 44.05 3.96
475 476 9.537192 AAATTCATGGACATTTACTAATGCATG 57.463 29.630 0.00 0.00 44.05 4.06
476 477 7.878547 TTCATGGACATTTACTAATGCATGA 57.121 32.000 0.00 12.82 42.72 3.07
477 478 7.878547 TCATGGACATTTACTAATGCATGAA 57.121 32.000 0.00 0.00 42.17 2.57
478 479 8.467963 TCATGGACATTTACTAATGCATGAAT 57.532 30.769 0.00 0.00 42.17 2.57
479 480 8.570488 TCATGGACATTTACTAATGCATGAATC 58.430 33.333 0.00 0.00 42.17 2.52
480 481 8.573885 CATGGACATTTACTAATGCATGAATCT 58.426 33.333 0.00 0.00 44.05 2.40
481 482 8.523915 TGGACATTTACTAATGCATGAATCTT 57.476 30.769 0.00 0.00 44.05 2.40
482 483 8.970020 TGGACATTTACTAATGCATGAATCTTT 58.030 29.630 0.00 0.00 44.05 2.52
483 484 9.807649 GGACATTTACTAATGCATGAATCTTTT 57.192 29.630 0.00 0.00 44.05 2.27
489 490 7.801547 ACTAATGCATGAATCTTTTCAAACG 57.198 32.000 0.00 0.00 44.70 3.60
490 491 6.808212 ACTAATGCATGAATCTTTTCAAACGG 59.192 34.615 0.00 0.00 44.70 4.44
491 492 4.844998 TGCATGAATCTTTTCAAACGGA 57.155 36.364 0.00 0.00 44.70 4.69
492 493 5.389859 TGCATGAATCTTTTCAAACGGAT 57.610 34.783 0.00 0.00 44.70 4.18
493 494 5.162794 TGCATGAATCTTTTCAAACGGATG 58.837 37.500 0.00 0.00 44.70 3.51
494 495 5.048154 TGCATGAATCTTTTCAAACGGATGA 60.048 36.000 0.00 0.00 44.70 2.92
495 496 5.514204 GCATGAATCTTTTCAAACGGATGAG 59.486 40.000 0.00 0.00 44.70 2.90
496 497 5.046910 TGAATCTTTTCAAACGGATGAGC 57.953 39.130 0.00 0.00 38.90 4.26
497 498 4.761739 TGAATCTTTTCAAACGGATGAGCT 59.238 37.500 0.00 0.00 38.90 4.09
498 499 5.241506 TGAATCTTTTCAAACGGATGAGCTT 59.758 36.000 0.00 0.00 38.90 3.74
499 500 5.712152 ATCTTTTCAAACGGATGAGCTTT 57.288 34.783 0.00 0.00 0.00 3.51
500 501 5.514274 TCTTTTCAAACGGATGAGCTTTT 57.486 34.783 0.00 0.00 0.00 2.27
501 502 5.901552 TCTTTTCAAACGGATGAGCTTTTT 58.098 33.333 0.00 0.00 0.00 1.94
569 570 3.595709 TGAACTTTTTCTAACGTGCGG 57.404 42.857 0.00 0.00 32.36 5.69
645 646 0.469892 AGTGGTCAAAGCCAAAGGGG 60.470 55.000 0.00 0.00 40.68 4.79
663 664 2.851104 CGACCGAGCGAAACAACC 59.149 61.111 0.00 0.00 0.00 3.77
707 712 3.004734 GCAGTCGCTCGTGCTTGAC 62.005 63.158 7.97 8.44 36.71 3.18
796 805 0.111266 CGCAAAAACGAGTCTCACGG 60.111 55.000 0.00 0.00 34.06 4.94
834 843 0.670546 AACCGAATCAGCACGTCCTG 60.671 55.000 0.00 0.00 0.00 3.86
843 852 4.657824 CACGTCCTGCGAACCCGT 62.658 66.667 0.00 0.00 44.77 5.28
1031 1046 0.107703 GGATTGCCGTCAGACATGGA 60.108 55.000 0.41 0.00 31.73 3.41
1074 1089 2.847234 ACGGAGTCCTGTGGCCAA 60.847 61.111 7.24 0.00 29.74 4.52
1101 1140 3.448686 CGGTGAGCATATCTTTCGTTCT 58.551 45.455 0.00 0.00 0.00 3.01
1102 1141 4.607955 CGGTGAGCATATCTTTCGTTCTA 58.392 43.478 0.00 0.00 0.00 2.10
1103 1142 4.441415 CGGTGAGCATATCTTTCGTTCTAC 59.559 45.833 0.00 0.00 0.00 2.59
1104 1143 4.441415 GGTGAGCATATCTTTCGTTCTACG 59.559 45.833 0.00 0.00 44.19 3.51
1105 1144 4.441415 GTGAGCATATCTTTCGTTCTACGG 59.559 45.833 0.00 0.00 42.81 4.02
1153 1195 4.096311 CAACTAGTCAAGATCACGTACCG 58.904 47.826 0.00 0.00 0.00 4.02
1158 1200 5.171147 AGTCAAGATCACGTACCGATTAG 57.829 43.478 0.00 0.00 0.00 1.73
1262 1304 1.675714 CCGTCAGCTGCCACTATGAAA 60.676 52.381 9.47 0.00 0.00 2.69
1312 1354 1.519455 CACGGGCGATCCACTTCTC 60.519 63.158 0.00 0.00 34.36 2.87
1429 2377 4.141824 GGTGATCCTTTCTCTTCCCACTAG 60.142 50.000 0.00 0.00 0.00 2.57
1439 2548 9.369672 CTTTCTCTTCCCACTAGTACCTATATT 57.630 37.037 0.00 0.00 0.00 1.28
1518 2633 0.257039 AACATCCCCTTGCAGCTAGG 59.743 55.000 15.51 15.51 0.00 3.02
1537 2652 2.096417 AGGAAAGAAAATCGACAACGCG 60.096 45.455 3.53 3.53 39.58 6.01
1549 2664 0.606604 ACAACGCGTGGATAAGGAGT 59.393 50.000 23.00 1.81 0.00 3.85
1552 2667 2.794910 CAACGCGTGGATAAGGAGTATG 59.205 50.000 14.98 0.00 0.00 2.39
1567 2682 3.251571 GAGTATGGTGGAACAGAACGAC 58.748 50.000 0.00 0.00 41.80 4.34
1613 2728 3.376935 CTGCGCCAGGACGAGGATT 62.377 63.158 4.18 0.00 34.06 3.01
2093 3505 4.202182 TGGTTTATAGAGCGGTAAAGCGAT 60.202 41.667 5.64 0.00 39.74 4.58
2100 3512 3.380637 AGAGCGGTAAAGCGATCTAAAGA 59.619 43.478 19.31 0.00 43.00 2.52
2145 3565 0.400594 AGCGGGCAAGTTTCTAAGGT 59.599 50.000 0.00 0.00 0.00 3.50
2151 3571 1.882623 GCAAGTTTCTAAGGTGCTGCT 59.117 47.619 0.00 0.00 32.43 4.24
2230 3655 5.848406 TGGTTCGCAGGATTTTAAAAACAT 58.152 33.333 4.44 0.00 0.00 2.71
2231 3656 6.982852 TGGTTCGCAGGATTTTAAAAACATA 58.017 32.000 4.44 0.00 0.00 2.29
2347 3790 2.134346 GCGCCACATGAAAAACACAAT 58.866 42.857 0.00 0.00 0.00 2.71
2350 3793 4.210120 GCGCCACATGAAAAACACAATAAA 59.790 37.500 0.00 0.00 0.00 1.40
2407 3896 2.894763 TGCATGCAAAATAGGCCATC 57.105 45.000 20.30 0.00 0.00 3.51
2414 3903 3.186909 GCAAAATAGGCCATCGGAAAAC 58.813 45.455 5.01 0.00 0.00 2.43
2432 3922 8.705594 TCGGAAAACTCCTATGATTTCTATTCT 58.294 33.333 0.00 0.00 33.42 2.40
2456 3965 7.395772 TCTCACAAATGGAAACCATAAGCAATA 59.604 33.333 3.64 0.00 44.40 1.90
2653 4786 9.476202 AATTTACTTACTTGAAAGTGGATTTGC 57.524 29.630 5.95 0.00 39.95 3.68
2744 4877 7.014808 TGTCGAGGAATGTACATACCATATGAA 59.985 37.037 9.21 0.00 0.00 2.57
2840 4973 2.254152 TACCTTGAGCTGGATGTCCT 57.746 50.000 0.00 0.00 36.82 3.85
2943 5086 1.552337 AGTGTTGAGGCAGTGATCGAT 59.448 47.619 0.00 0.00 0.00 3.59
2960 5103 2.423892 TCGATGTCTCTGCAGAGGTTAC 59.576 50.000 36.92 28.69 42.30 2.50
3108 5251 6.842676 AGAATTGAAGGTTCAGTTAGAGGTT 58.157 36.000 0.88 0.00 37.27 3.50
3151 5294 3.888930 GACTTTTCAGGGTGGAAATGACA 59.111 43.478 8.07 0.00 36.71 3.58
3225 5368 4.339814 GTGGAGGTGTGTTTTTATCCAACA 59.660 41.667 0.00 0.00 0.00 3.33
3251 5396 2.094906 CCTAAGTCAACCGTCGTGATCA 60.095 50.000 0.00 0.00 0.00 2.92
3286 5431 5.122869 AGTGCTATGCTAGAATGTTTGTGTG 59.877 40.000 0.00 0.00 0.00 3.82
3307 5452 8.962679 TGTGTGTTTAGGAGTTGAATTTAAGTT 58.037 29.630 0.00 0.00 0.00 2.66
3308 5453 9.797556 GTGTGTTTAGGAGTTGAATTTAAGTTT 57.202 29.630 0.00 0.00 0.00 2.66
3450 5647 3.029570 GGTCCAGAACTACGGATAGGTT 58.970 50.000 0.00 0.00 32.83 3.50
3451 5648 4.210331 GGTCCAGAACTACGGATAGGTTA 58.790 47.826 0.00 0.00 32.83 2.85
3452 5649 4.646492 GGTCCAGAACTACGGATAGGTTAA 59.354 45.833 0.00 0.00 32.83 2.01
3453 5650 5.221204 GGTCCAGAACTACGGATAGGTTAAG 60.221 48.000 0.00 0.00 32.83 1.85
3454 5651 4.891756 TCCAGAACTACGGATAGGTTAAGG 59.108 45.833 0.00 0.00 32.08 2.69
3455 5652 4.648307 CCAGAACTACGGATAGGTTAAGGT 59.352 45.833 0.00 0.00 32.08 3.50
3481 5678 2.936498 CTCGTATGTTAAACTGCCAGGG 59.064 50.000 0.00 0.00 0.00 4.45
3704 6055 0.602638 CCACTACGCAGCTGGAAACA 60.603 55.000 17.12 0.00 39.59 2.83
3730 6081 0.745845 CTGGAGACGGAGGCAATTGG 60.746 60.000 7.72 0.00 39.98 3.16
3976 6353 0.619255 TTCAGGGACCGGGCTAATGA 60.619 55.000 7.57 6.38 0.00 2.57
4002 6379 1.492176 CCATAGAGCACCCCAGACAAT 59.508 52.381 0.00 0.00 0.00 2.71
4045 6422 3.853330 CGCTCAACCGTGATGCCG 61.853 66.667 0.00 0.00 31.85 5.69
4047 6424 2.434884 CTCAACCGTGATGCCGCT 60.435 61.111 0.00 0.00 31.85 5.52
4087 6464 4.065789 GTTGGTCTTCTTCGTCTTCCAAT 58.934 43.478 0.00 0.00 36.20 3.16
4094 6471 6.370166 GTCTTCTTCGTCTTCCAATTTCTCAT 59.630 38.462 0.00 0.00 0.00 2.90
4118 6495 1.780503 AAGCAGCCAACAAAGAGGTT 58.219 45.000 0.00 0.00 0.00 3.50
4272 6669 3.841845 TGGTGTTACTAGGTATGTGCCTT 59.158 43.478 0.00 0.00 39.94 4.35
4274 6671 5.484644 TGGTGTTACTAGGTATGTGCCTTTA 59.515 40.000 0.00 0.00 39.94 1.85
4289 6686 1.519408 CTTTACGTTGTCACAGGGGG 58.481 55.000 0.00 0.00 0.00 5.40
4290 6687 0.838608 TTTACGTTGTCACAGGGGGT 59.161 50.000 0.00 0.00 0.00 4.95
4416 6814 0.251297 TTGAGGGACGTACGGGAAGA 60.251 55.000 21.06 0.00 0.00 2.87
4418 6816 0.384669 GAGGGACGTACGGGAAGATG 59.615 60.000 21.06 0.00 0.00 2.90
4419 6817 1.227176 GGGACGTACGGGAAGATGC 60.227 63.158 21.06 1.98 0.00 3.91
4446 6844 0.527565 AATGGCGTGGAATTGAGTGC 59.472 50.000 0.00 0.00 0.00 4.40
4447 6845 0.608856 ATGGCGTGGAATTGAGTGCA 60.609 50.000 0.00 0.00 0.00 4.57
4448 6846 0.608856 TGGCGTGGAATTGAGTGCAT 60.609 50.000 0.00 0.00 0.00 3.96
4527 6929 6.750039 CGGCAAAAGGTAATAAGTTAATGTGG 59.250 38.462 0.00 0.00 0.00 4.17
4563 6965 3.214328 GGGAAGGTGCGATCAAATATGT 58.786 45.455 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.227614 ACCTGGACGGCTTAATTTTGTT 58.772 40.909 0.00 0.00 35.61 2.83
1 2 2.871453 ACCTGGACGGCTTAATTTTGT 58.129 42.857 0.00 0.00 35.61 2.83
2 3 3.934457 AACCTGGACGGCTTAATTTTG 57.066 42.857 0.00 0.00 35.61 2.44
3 4 4.948341 AAAACCTGGACGGCTTAATTTT 57.052 36.364 0.00 0.00 35.61 1.82
4 5 4.342665 TGAAAAACCTGGACGGCTTAATTT 59.657 37.500 0.00 0.00 35.61 1.82
5 6 3.892588 TGAAAAACCTGGACGGCTTAATT 59.107 39.130 0.00 0.00 35.61 1.40
6 7 3.492337 TGAAAAACCTGGACGGCTTAAT 58.508 40.909 0.00 0.00 35.61 1.40
7 8 2.933573 TGAAAAACCTGGACGGCTTAA 58.066 42.857 0.00 0.00 35.61 1.85
8 9 2.642154 TGAAAAACCTGGACGGCTTA 57.358 45.000 0.00 0.00 35.61 3.09
9 10 1.681264 CTTGAAAAACCTGGACGGCTT 59.319 47.619 0.00 0.00 35.61 4.35
10 11 1.318576 CTTGAAAAACCTGGACGGCT 58.681 50.000 0.00 0.00 35.61 5.52
11 12 1.001706 GACTTGAAAAACCTGGACGGC 60.002 52.381 0.00 0.00 35.61 5.68
12 13 2.294074 TGACTTGAAAAACCTGGACGG 58.706 47.619 0.00 0.00 39.35 4.79
13 14 3.363970 CGATGACTTGAAAAACCTGGACG 60.364 47.826 0.00 0.00 0.00 4.79
14 15 3.609409 GCGATGACTTGAAAAACCTGGAC 60.609 47.826 0.00 0.00 0.00 4.02
15 16 2.552315 GCGATGACTTGAAAAACCTGGA 59.448 45.455 0.00 0.00 0.00 3.86
16 17 2.293122 TGCGATGACTTGAAAAACCTGG 59.707 45.455 0.00 0.00 0.00 4.45
17 18 3.624326 TGCGATGACTTGAAAAACCTG 57.376 42.857 0.00 0.00 0.00 4.00
18 19 4.520492 AGAATGCGATGACTTGAAAAACCT 59.480 37.500 0.00 0.00 0.00 3.50
19 20 4.618489 CAGAATGCGATGACTTGAAAAACC 59.382 41.667 0.00 0.00 0.00 3.27
20 21 5.451908 TCAGAATGCGATGACTTGAAAAAC 58.548 37.500 0.00 0.00 34.76 2.43
21 22 5.687770 TCAGAATGCGATGACTTGAAAAA 57.312 34.783 0.00 0.00 34.76 1.94
22 23 5.181811 ACATCAGAATGCGATGACTTGAAAA 59.818 36.000 11.12 0.00 42.39 2.29
23 24 4.696877 ACATCAGAATGCGATGACTTGAAA 59.303 37.500 11.12 0.00 42.39 2.69
24 25 4.256110 ACATCAGAATGCGATGACTTGAA 58.744 39.130 11.12 0.00 42.39 2.69
25 26 3.865446 ACATCAGAATGCGATGACTTGA 58.135 40.909 11.12 0.00 42.39 3.02
26 27 5.723492 TTACATCAGAATGCGATGACTTG 57.277 39.130 11.12 0.00 42.39 3.16
27 28 6.765036 AGAATTACATCAGAATGCGATGACTT 59.235 34.615 11.12 3.57 42.39 3.01
28 29 6.286758 AGAATTACATCAGAATGCGATGACT 58.713 36.000 11.12 0.00 42.39 3.41
29 30 6.536731 AGAATTACATCAGAATGCGATGAC 57.463 37.500 11.12 0.95 42.39 3.06
32 33 8.824781 GCATATAGAATTACATCAGAATGCGAT 58.175 33.333 0.00 0.00 36.26 4.58
33 34 8.037166 AGCATATAGAATTACATCAGAATGCGA 58.963 33.333 0.00 0.00 40.57 5.10
34 35 8.194433 AGCATATAGAATTACATCAGAATGCG 57.806 34.615 0.00 0.00 40.57 4.73
35 36 9.985318 GAAGCATATAGAATTACATCAGAATGC 57.015 33.333 0.00 0.00 36.26 3.56
97 98 8.584157 AGAATATGTGTATGGTCAAAGCAAAAA 58.416 29.630 0.00 0.00 0.00 1.94
98 99 8.121305 AGAATATGTGTATGGTCAAAGCAAAA 57.879 30.769 0.00 0.00 0.00 2.44
99 100 7.148086 GGAGAATATGTGTATGGTCAAAGCAAA 60.148 37.037 0.00 0.00 0.00 3.68
100 101 6.318648 GGAGAATATGTGTATGGTCAAAGCAA 59.681 38.462 0.00 0.00 0.00 3.91
101 102 5.822519 GGAGAATATGTGTATGGTCAAAGCA 59.177 40.000 0.00 0.00 0.00 3.91
102 103 5.822519 TGGAGAATATGTGTATGGTCAAAGC 59.177 40.000 0.00 0.00 0.00 3.51
103 104 7.040892 CCATGGAGAATATGTGTATGGTCAAAG 60.041 40.741 5.56 0.00 31.33 2.77
104 105 6.772233 CCATGGAGAATATGTGTATGGTCAAA 59.228 38.462 5.56 0.00 31.33 2.69
105 106 6.126507 ACCATGGAGAATATGTGTATGGTCAA 60.127 38.462 21.47 0.00 42.09 3.18
106 107 5.369404 ACCATGGAGAATATGTGTATGGTCA 59.631 40.000 21.47 0.00 42.09 4.02
107 108 5.869579 ACCATGGAGAATATGTGTATGGTC 58.130 41.667 21.47 0.00 42.09 4.02
108 109 5.912149 ACCATGGAGAATATGTGTATGGT 57.088 39.130 21.47 0.00 41.28 3.55
109 110 8.868522 AAATACCATGGAGAATATGTGTATGG 57.131 34.615 21.47 0.00 39.49 2.74
110 111 9.506018 TGAAATACCATGGAGAATATGTGTATG 57.494 33.333 21.47 0.00 29.98 2.39
111 112 9.507329 GTGAAATACCATGGAGAATATGTGTAT 57.493 33.333 21.47 0.00 0.00 2.29
112 113 8.902540 GTGAAATACCATGGAGAATATGTGTA 57.097 34.615 21.47 0.00 0.00 2.90
113 114 7.807977 GTGAAATACCATGGAGAATATGTGT 57.192 36.000 21.47 0.00 0.00 3.72
131 132 8.686334 GGAGAATATGTGTATGTTTGGTGAAAT 58.314 33.333 0.00 0.00 0.00 2.17
132 133 7.667635 TGGAGAATATGTGTATGTTTGGTGAAA 59.332 33.333 0.00 0.00 0.00 2.69
133 134 7.171653 TGGAGAATATGTGTATGTTTGGTGAA 58.828 34.615 0.00 0.00 0.00 3.18
134 135 6.716284 TGGAGAATATGTGTATGTTTGGTGA 58.284 36.000 0.00 0.00 0.00 4.02
135 136 7.420002 CATGGAGAATATGTGTATGTTTGGTG 58.580 38.462 0.00 0.00 0.00 4.17
136 137 6.547141 CCATGGAGAATATGTGTATGTTTGGT 59.453 38.462 5.56 0.00 0.00 3.67
137 138 6.547141 ACCATGGAGAATATGTGTATGTTTGG 59.453 38.462 21.47 0.00 0.00 3.28
138 139 7.572523 ACCATGGAGAATATGTGTATGTTTG 57.427 36.000 21.47 0.00 0.00 2.93
139 140 9.866655 AATACCATGGAGAATATGTGTATGTTT 57.133 29.630 21.47 0.00 29.98 2.83
140 141 9.866655 AAATACCATGGAGAATATGTGTATGTT 57.133 29.630 21.47 0.00 29.98 2.71
141 142 9.507329 GAAATACCATGGAGAATATGTGTATGT 57.493 33.333 21.47 0.00 29.98 2.29
192 193 5.059833 GGCAATAACATGTTTGGTTGGAAA 58.940 37.500 17.78 0.00 0.00 3.13
205 206 9.976511 CATGATTATCTTTGAAGGCAATAACAT 57.023 29.630 0.00 0.00 33.25 2.71
213 214 8.538409 ACAAAAACATGATTATCTTTGAAGGC 57.462 30.769 0.00 0.00 0.00 4.35
224 225 9.985318 CTTCAAGCAAAAACAAAAACATGATTA 57.015 25.926 0.00 0.00 0.00 1.75
230 231 4.516698 TGGCTTCAAGCAAAAACAAAAACA 59.483 33.333 12.53 0.00 44.75 2.83
231 232 5.040715 TGGCTTCAAGCAAAAACAAAAAC 57.959 34.783 12.53 0.00 44.75 2.43
232 233 5.893897 ATGGCTTCAAGCAAAAACAAAAA 57.106 30.435 12.53 0.00 44.75 1.94
233 234 5.893897 AATGGCTTCAAGCAAAAACAAAA 57.106 30.435 12.53 0.00 44.75 2.44
234 235 5.638783 CAAATGGCTTCAAGCAAAAACAAA 58.361 33.333 12.53 0.00 44.75 2.83
235 236 4.438472 GCAAATGGCTTCAAGCAAAAACAA 60.438 37.500 12.53 0.00 44.75 2.83
252 253 5.933463 ACATCAACCAAATTACCAGCAAATG 59.067 36.000 0.00 0.00 0.00 2.32
299 300 6.556212 TCTACATCAGCAAAACGAAAAACAA 58.444 32.000 0.00 0.00 0.00 2.83
300 301 6.125327 TCTACATCAGCAAAACGAAAAACA 57.875 33.333 0.00 0.00 0.00 2.83
310 311 4.511454 GCGGTCATTATCTACATCAGCAAA 59.489 41.667 0.00 0.00 0.00 3.68
354 355 8.224437 TGGAAAAAGTTCACGAATTTGAAAAAC 58.776 29.630 0.00 1.25 37.24 2.43
356 357 7.891183 TGGAAAAAGTTCACGAATTTGAAAA 57.109 28.000 0.00 0.00 37.24 2.29
446 447 9.585099 GCATTAGTAAATGTCCATGAATTTGAA 57.415 29.630 0.00 0.00 43.75 2.69
447 448 8.747471 TGCATTAGTAAATGTCCATGAATTTGA 58.253 29.630 0.00 0.00 43.75 2.69
448 449 8.929827 TGCATTAGTAAATGTCCATGAATTTG 57.070 30.769 0.00 0.00 43.75 2.32
449 450 9.537192 CATGCATTAGTAAATGTCCATGAATTT 57.463 29.630 0.00 0.35 43.75 1.82
450 451 8.916062 TCATGCATTAGTAAATGTCCATGAATT 58.084 29.630 13.98 0.00 43.75 2.17
451 452 8.467963 TCATGCATTAGTAAATGTCCATGAAT 57.532 30.769 13.98 0.00 43.75 2.57
452 453 7.878547 TCATGCATTAGTAAATGTCCATGAA 57.121 32.000 13.98 4.42 43.75 2.57
453 454 7.878547 TTCATGCATTAGTAAATGTCCATGA 57.121 32.000 0.00 13.04 43.75 3.07
454 455 8.573885 AGATTCATGCATTAGTAAATGTCCATG 58.426 33.333 0.00 10.16 43.75 3.66
455 456 8.701908 AGATTCATGCATTAGTAAATGTCCAT 57.298 30.769 0.00 0.00 43.75 3.41
456 457 8.523915 AAGATTCATGCATTAGTAAATGTCCA 57.476 30.769 0.00 0.00 43.75 4.02
457 458 9.807649 AAAAGATTCATGCATTAGTAAATGTCC 57.192 29.630 0.00 0.00 43.75 4.02
463 464 9.340695 CGTTTGAAAAGATTCATGCATTAGTAA 57.659 29.630 0.00 0.00 44.70 2.24
464 465 7.967854 CCGTTTGAAAAGATTCATGCATTAGTA 59.032 33.333 0.00 0.00 44.70 1.82
465 466 6.808212 CCGTTTGAAAAGATTCATGCATTAGT 59.192 34.615 0.00 0.00 44.70 2.24
466 467 7.028962 TCCGTTTGAAAAGATTCATGCATTAG 58.971 34.615 0.00 0.00 44.70 1.73
467 468 6.918626 TCCGTTTGAAAAGATTCATGCATTA 58.081 32.000 0.00 0.00 44.70 1.90
468 469 5.782047 TCCGTTTGAAAAGATTCATGCATT 58.218 33.333 0.00 0.00 44.70 3.56
469 470 5.389859 TCCGTTTGAAAAGATTCATGCAT 57.610 34.783 0.00 0.00 44.70 3.96
470 471 4.844998 TCCGTTTGAAAAGATTCATGCA 57.155 36.364 0.00 0.00 44.70 3.96
471 472 5.401550 TCATCCGTTTGAAAAGATTCATGC 58.598 37.500 0.00 0.00 44.70 4.06
472 473 5.514204 GCTCATCCGTTTGAAAAGATTCATG 59.486 40.000 0.00 0.00 44.70 3.07
473 474 5.416952 AGCTCATCCGTTTGAAAAGATTCAT 59.583 36.000 0.00 0.00 44.70 2.57
474 475 4.761739 AGCTCATCCGTTTGAAAAGATTCA 59.238 37.500 0.00 0.00 43.70 2.57
475 476 5.302357 AGCTCATCCGTTTGAAAAGATTC 57.698 39.130 0.00 0.00 36.04 2.52
476 477 5.712152 AAGCTCATCCGTTTGAAAAGATT 57.288 34.783 0.00 0.00 0.00 2.40
477 478 5.712152 AAAGCTCATCCGTTTGAAAAGAT 57.288 34.783 0.00 0.00 0.00 2.40
478 479 5.514274 AAAAGCTCATCCGTTTGAAAAGA 57.486 34.783 0.00 0.00 0.00 2.52
527 528 9.074443 GTTCATGAATTTGCAAAAATGTTTGTT 57.926 25.926 17.19 2.84 45.06 2.83
528 529 8.460428 AGTTCATGAATTTGCAAAAATGTTTGT 58.540 25.926 17.19 0.00 45.06 2.83
529 530 8.844441 AGTTCATGAATTTGCAAAAATGTTTG 57.156 26.923 17.19 3.80 45.88 2.93
530 531 9.857957 AAAGTTCATGAATTTGCAAAAATGTTT 57.142 22.222 17.19 12.79 0.00 2.83
531 532 9.857957 AAAAGTTCATGAATTTGCAAAAATGTT 57.142 22.222 17.19 5.65 0.00 2.71
532 533 9.857957 AAAAAGTTCATGAATTTGCAAAAATGT 57.142 22.222 17.19 1.73 0.00 2.71
538 539 8.538856 CGTTAGAAAAAGTTCATGAATTTGCAA 58.461 29.630 15.98 0.00 36.09 4.08
539 540 7.704472 ACGTTAGAAAAAGTTCATGAATTTGCA 59.296 29.630 15.98 0.35 36.09 4.08
540 541 7.998212 CACGTTAGAAAAAGTTCATGAATTTGC 59.002 33.333 15.98 10.07 36.09 3.68
541 542 7.998212 GCACGTTAGAAAAAGTTCATGAATTTG 59.002 33.333 15.98 4.78 36.09 2.32
544 545 5.851177 CGCACGTTAGAAAAAGTTCATGAAT 59.149 36.000 12.12 0.00 36.09 2.57
551 552 4.359971 AAACCGCACGTTAGAAAAAGTT 57.640 36.364 0.00 0.00 33.05 2.66
578 579 6.677781 ATTTGAAGAAGTTCACGAGTTCAA 57.322 33.333 11.25 11.25 42.60 2.69
579 580 6.315144 TGAATTTGAAGAAGTTCACGAGTTCA 59.685 34.615 16.50 16.50 42.60 3.18
580 581 6.715464 TGAATTTGAAGAAGTTCACGAGTTC 58.285 36.000 5.50 10.82 42.60 3.01
581 582 6.677781 TGAATTTGAAGAAGTTCACGAGTT 57.322 33.333 5.50 2.29 42.60 3.01
582 583 6.677781 TTGAATTTGAAGAAGTTCACGAGT 57.322 33.333 5.50 0.00 42.60 4.18
583 584 9.831737 AATATTGAATTTGAAGAAGTTCACGAG 57.168 29.630 5.50 0.00 42.60 4.18
622 623 2.301346 CTTTGGCTTTGACCACTGACT 58.699 47.619 0.00 0.00 40.19 3.41
625 626 0.675633 CCCTTTGGCTTTGACCACTG 59.324 55.000 0.00 0.00 40.19 3.66
645 646 2.170273 GTTGTTTCGCTCGGTCGC 59.830 61.111 0.00 0.00 0.00 5.19
663 664 1.588403 CTCAGCTCGCTCGATGGTG 60.588 63.158 11.67 11.67 0.00 4.17
757 766 0.828343 AGAGGTCCTATACAGCGCCC 60.828 60.000 2.29 0.00 0.00 6.13
796 805 2.202756 GTCATGGGAGCGTCCGAC 60.203 66.667 0.00 0.00 37.43 4.79
920 935 3.969250 TTCCACCGATCCAAGCCGC 62.969 63.158 0.00 0.00 0.00 6.53
1000 1015 0.394352 GGCAATCCCAAGTCGGACAT 60.394 55.000 11.27 0.00 36.56 3.06
1031 1046 1.383109 TCCTCCCGCAGATCATGGT 60.383 57.895 0.00 0.00 0.00 3.55
1072 1087 0.732571 ATATGCTCACCGCCGTTTTG 59.267 50.000 0.00 0.00 38.05 2.44
1074 1089 0.178068 AGATATGCTCACCGCCGTTT 59.822 50.000 0.00 0.00 38.05 3.60
1087 1102 7.968956 AGCATATACCGTAGAACGAAAGATATG 59.031 37.037 0.15 8.90 46.05 1.78
1093 1132 6.624352 AGTAGCATATACCGTAGAACGAAA 57.376 37.500 0.15 0.00 46.05 3.46
1101 1140 6.997239 ATCGATCAAGTAGCATATACCGTA 57.003 37.500 0.00 0.00 0.00 4.02
1102 1141 5.899120 ATCGATCAAGTAGCATATACCGT 57.101 39.130 0.00 0.00 0.00 4.83
1103 1142 6.454318 GCAAATCGATCAAGTAGCATATACCG 60.454 42.308 0.00 0.00 0.00 4.02
1104 1143 6.454318 CGCAAATCGATCAAGTAGCATATACC 60.454 42.308 0.00 0.00 41.67 2.73
1105 1144 6.461816 CGCAAATCGATCAAGTAGCATATAC 58.538 40.000 0.00 0.00 41.67 1.47
1153 1195 6.438259 TCTGCACAGTGAGTACTACTAATC 57.562 41.667 4.15 0.00 34.74 1.75
1158 1200 4.859798 GTGATTCTGCACAGTGAGTACTAC 59.140 45.833 4.15 0.00 38.63 2.73
1439 2548 9.926158 TCAATTAACCGTACTATTACTGTTTCA 57.074 29.630 5.58 0.00 37.04 2.69
1456 2565 3.705604 CATCAATGGCGGTCAATTAACC 58.294 45.455 0.00 0.00 35.86 2.85
1518 2633 2.645647 CACGCGTTGTCGATTTTCTTTC 59.354 45.455 10.22 0.00 39.71 2.62
1537 2652 4.163458 TGTTCCACCATACTCCTTATCCAC 59.837 45.833 0.00 0.00 0.00 4.02
1549 2664 3.755112 TTGTCGTTCTGTTCCACCATA 57.245 42.857 0.00 0.00 0.00 2.74
1552 2667 3.120786 CGTATTTGTCGTTCTGTTCCACC 60.121 47.826 0.00 0.00 0.00 4.61
1567 2682 2.019476 CACCGCGCGTCGTATTTG 59.981 61.111 29.95 13.09 36.19 2.32
1613 2728 1.648568 AGGAACAGGAGGGAGATCAGA 59.351 52.381 0.00 0.00 0.00 3.27
1810 3058 6.404708 GCATATCCAAGATCTGAATCAGCTA 58.595 40.000 5.18 0.00 34.07 3.32
1955 3203 2.621526 GGAACGGTTGAAGACATGGTTT 59.378 45.455 0.00 0.00 0.00 3.27
2079 3328 3.703420 TCTTTAGATCGCTTTACCGCTC 58.297 45.455 0.00 0.00 0.00 5.03
2093 3505 0.895530 CGGGTGGTGCTCTCTTTAGA 59.104 55.000 0.00 0.00 0.00 2.10
2135 3555 2.633488 CCCTAGCAGCACCTTAGAAAC 58.367 52.381 0.00 0.00 0.00 2.78
2145 3565 4.783621 CAAGGCGCCCTAGCAGCA 62.784 66.667 26.15 0.00 39.33 4.41
2347 3790 7.789202 TTCCATTGACCCTCATGAAAATTTA 57.211 32.000 0.00 0.00 0.00 1.40
2350 3793 6.879367 ATTTCCATTGACCCTCATGAAAAT 57.121 33.333 0.00 0.00 29.25 1.82
2383 3831 3.181467 TGGCCTATTTTGCATGCAATACC 60.181 43.478 32.27 22.97 35.70 2.73
2432 3922 5.798125 TTGCTTATGGTTTCCATTTGTGA 57.202 34.783 6.59 0.00 42.23 3.58
2652 4785 3.883489 ACTTGTTTAGAACTCAACAGGGC 59.117 43.478 12.88 0.00 35.00 5.19
2653 4786 5.357032 ACAACTTGTTTAGAACTCAACAGGG 59.643 40.000 12.88 8.23 35.00 4.45
2685 4818 2.093341 GTGGCAAGGTAAACGGATCCTA 60.093 50.000 10.75 0.00 0.00 2.94
2840 4973 2.054021 TGAACCCATCCTGTTCTGTGA 58.946 47.619 4.94 0.00 42.04 3.58
2960 5103 1.746615 CTCACATGGCAAGGACGGG 60.747 63.158 0.00 0.00 0.00 5.28
3023 5166 0.250166 CCCGGTGAGTTTTCCGTCTT 60.250 55.000 0.00 0.00 44.51 3.01
3024 5167 1.117142 TCCCGGTGAGTTTTCCGTCT 61.117 55.000 0.00 0.00 44.51 4.18
3151 5294 2.930109 TCAGGGGAGCTAAGAACTCT 57.070 50.000 0.00 0.00 34.46 3.24
3225 5368 4.687464 CGGTTGACTTAGGCCGTT 57.313 55.556 0.00 0.00 39.41 4.44
3251 5396 5.997746 TCTAGCATAGCACTTGTTTTCAACT 59.002 36.000 0.00 0.00 38.99 3.16
3307 5452 6.140377 AGGGACAAAAGGAAATCCAACTAAA 58.860 36.000 1.67 0.00 38.89 1.85
3308 5453 5.711698 AGGGACAAAAGGAAATCCAACTAA 58.288 37.500 1.67 0.00 38.89 2.24
3309 5454 5.321927 GAGGGACAAAAGGAAATCCAACTA 58.678 41.667 1.67 0.00 38.89 2.24
3396 5545 5.065602 GTCATGCATATCTCAAACTTCTGCA 59.934 40.000 0.00 0.00 41.76 4.41
3440 5589 3.952967 GAGTCAGACCTTAACCTATCCGT 59.047 47.826 0.00 0.00 0.00 4.69
3450 5647 7.310664 CAGTTTAACATACGAGTCAGACCTTA 58.689 38.462 0.00 0.00 0.00 2.69
3451 5648 6.157211 CAGTTTAACATACGAGTCAGACCTT 58.843 40.000 0.00 0.00 0.00 3.50
3452 5649 5.710984 CAGTTTAACATACGAGTCAGACCT 58.289 41.667 0.00 0.00 0.00 3.85
3453 5650 4.326548 GCAGTTTAACATACGAGTCAGACC 59.673 45.833 0.00 0.00 0.00 3.85
3454 5651 4.326548 GGCAGTTTAACATACGAGTCAGAC 59.673 45.833 0.00 0.00 0.00 3.51
3455 5652 4.021807 TGGCAGTTTAACATACGAGTCAGA 60.022 41.667 0.00 0.00 0.00 3.27
3481 5678 8.349983 ACACAAAGTATACAACATTTTCAGGTC 58.650 33.333 5.50 0.00 0.00 3.85
3545 5746 5.944007 GCACTGGAACTAAAGGGAAAATAGA 59.056 40.000 0.00 0.00 0.00 1.98
3704 6055 0.977395 CCTCCGTCTCCAGAGGTTTT 59.023 55.000 0.00 0.00 44.01 2.43
3730 6081 4.982916 ACGTCAAACAACACTGATCTAGAC 59.017 41.667 0.00 0.00 0.00 2.59
3874 6248 6.450845 TTCGCTTCATAATTTGCAACTTTG 57.549 33.333 7.39 6.41 0.00 2.77
3878 6252 6.143758 TCTGTTTTCGCTTCATAATTTGCAAC 59.856 34.615 0.00 0.00 0.00 4.17
3879 6253 6.143758 GTCTGTTTTCGCTTCATAATTTGCAA 59.856 34.615 0.00 0.00 0.00 4.08
3880 6254 5.629020 GTCTGTTTTCGCTTCATAATTTGCA 59.371 36.000 0.00 0.00 0.00 4.08
3976 6353 1.132721 TGGGGTGCTCTATGGATAGCT 60.133 52.381 0.00 0.00 39.53 3.32
4002 6379 0.037590 ATCGGCAGTGTTTAAGGGCA 59.962 50.000 0.00 0.00 0.00 5.36
4045 6422 3.209410 ACTATGTATGGAAGCTTGCAGC 58.791 45.455 25.23 19.61 42.84 5.25
4047 6424 3.947196 CCAACTATGTATGGAAGCTTGCA 59.053 43.478 23.56 23.56 39.12 4.08
4087 6464 4.766373 TGTTGGCTGCTTATCAATGAGAAA 59.234 37.500 0.00 0.00 0.00 2.52
4094 6471 3.507233 CCTCTTTGTTGGCTGCTTATCAA 59.493 43.478 0.00 0.00 0.00 2.57
4118 6495 6.380995 GCTTGATCAACATACACAATCAACA 58.619 36.000 3.38 0.00 33.89 3.33
4125 6502 5.431420 AAAACGCTTGATCAACATACACA 57.569 34.783 3.38 0.00 0.00 3.72
4192 6588 3.999663 GACTTCAGTCCTTTCATCACCAG 59.000 47.826 0.00 0.00 39.07 4.00
4219 6615 8.637196 AAATGGGTAAGGAAAACAAAACAAAA 57.363 26.923 0.00 0.00 0.00 2.44
4272 6669 2.530491 ACCCCCTGTGACAACGTAA 58.470 52.632 0.00 0.00 0.00 3.18
4315 6712 7.768240 ACGTCCAAAATCAAAATACTAATCCC 58.232 34.615 0.00 0.00 0.00 3.85
4335 6732 7.170998 CCAGACTACCAAATTATAATGACGTCC 59.829 40.741 14.12 0.00 0.00 4.79
4404 6802 1.880819 AACCGCATCTTCCCGTACGT 61.881 55.000 15.21 0.00 0.00 3.57
4416 6814 0.388391 CACGCCATTTTCAACCGCAT 60.388 50.000 0.00 0.00 0.00 4.73
4418 6816 1.732683 CCACGCCATTTTCAACCGC 60.733 57.895 0.00 0.00 0.00 5.68
4419 6817 0.312416 TTCCACGCCATTTTCAACCG 59.688 50.000 0.00 0.00 0.00 4.44
4446 6844 6.183360 CCTTTTGCAATGACGTGGAATTAATG 60.183 38.462 0.00 0.00 0.00 1.90
4447 6845 5.868801 CCTTTTGCAATGACGTGGAATTAAT 59.131 36.000 0.00 0.00 0.00 1.40
4448 6846 5.221342 ACCTTTTGCAATGACGTGGAATTAA 60.221 36.000 0.00 0.00 0.00 1.40
4527 6929 2.775032 TTCCCAGTACGCCGCTCAAC 62.775 60.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.