Multiple sequence alignment - TraesCS7B01G319400

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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 TraesCS7B01G319400 chr7B 100.000 4744 0 0 1 4744 569432781 569437524 0.000000e+00 8761
1 TraesCS7B01G319400 chr7B 95.133 3452 112 18 247 3669 569475902 569479326 0.000000e+00 5393
2 TraesCS7B01G319400 chr7B 89.023 2487 184 47 1878 4305 591052777 591055233 0.000000e+00 2998
3 TraesCS7B01G319400 chr7B 86.116 1887 179 51 3 1843 591050926 591052775 0.000000e+00 1956
4 TraesCS7B01G319400 chr7B 90.403 1042 76 14 2637 3669 633003886 633002860 0.000000e+00 1349
5 TraesCS7B01G319400 chr7B 89.695 1048 79 15 2637 3669 632797787 632798820 0.000000e+00 1310
6 TraesCS7B01G319400 chr7B 87.981 624 43 12 3700 4305 569479329 569479938 0.000000e+00 708
7 TraesCS7B01G319400 chr7B 94.030 335 20 0 4410 4744 530006794 530006460 4.240000e-140 508
8 TraesCS7B01G319400 chr7B 93.433 335 22 0 4410 4744 395640439 395640105 9.170000e-137 497
9 TraesCS7B01G319400 chr7B 91.940 335 27 0 4410 4744 568482738 568483072 2.000000e-128 470
10 TraesCS7B01G319400 chr7B 84.513 226 20 9 4103 4326 632798820 632799032 4.810000e-50 209
11 TraesCS7B01G319400 chr7B 84.513 226 20 9 4103 4326 633002860 633002648 4.810000e-50 209
12 TraesCS7B01G319400 chr7D 89.604 2347 176 35 1876 4177 548329007 548326684 0.000000e+00 2920
13 TraesCS7B01G319400 chr7D 88.275 2371 168 52 1876 4177 548062766 548065095 0.000000e+00 2737
14 TraesCS7B01G319400 chr7D 93.128 1528 71 13 2897 4404 530427841 530429354 0.000000e+00 2209
15 TraesCS7B01G319400 chr7D 86.200 1884 182 45 2 1844 548060921 548062767 0.000000e+00 1967
16 TraesCS7B01G319400 chr7D 86.250 800 79 19 387 1172 548337823 548337041 0.000000e+00 839
17 TraesCS7B01G319400 chr7D 85.654 711 65 18 1159 1844 548329704 548329006 0.000000e+00 713
18 TraesCS7B01G319400 chr7D 91.935 496 38 2 2952 3446 573971593 573971099 0.000000e+00 693
19 TraesCS7B01G319400 chr7D 84.783 368 42 11 3968 4326 573971078 573970716 1.620000e-94 357
20 TraesCS7B01G319400 chr7D 84.783 368 42 11 3968 4326 574248706 574248344 1.620000e-94 357
21 TraesCS7B01G319400 chr7D 84.426 366 33 16 3 363 548338163 548337817 5.880000e-89 339
22 TraesCS7B01G319400 chr7A 89.429 2261 179 31 1955 4177 630675684 630673446 0.000000e+00 2796
23 TraesCS7B01G319400 chr7A 86.430 1776 163 46 3 1743 630677615 630675883 0.000000e+00 1873
24 TraesCS7B01G319400 chr7A 84.599 474 49 10 3643 4095 630623656 630623186 2.600000e-122 449
25 TraesCS7B01G319400 chr5B 94.328 335 19 0 4410 4744 344237652 344237986 9.100000e-142 514
26 TraesCS7B01G319400 chr5B 91.940 335 27 0 4410 4744 106355843 106355509 2.000000e-128 470
27 TraesCS7B01G319400 chr4B 82.788 581 92 8 2484 3057 636976742 636976163 3.270000e-141 512
28 TraesCS7B01G319400 chr4B 82.586 580 94 7 2484 3057 636965504 636964926 5.480000e-139 505
29 TraesCS7B01G319400 chr1B 93.656 331 21 0 4410 4740 6577581 6577911 3.300000e-136 496
30 TraesCS7B01G319400 chr1B 92.239 335 25 1 4410 4744 442182749 442182416 1.550000e-129 473
31 TraesCS7B01G319400 chr1B 91.718 326 27 0 4419 4744 161380606 161380281 2.010000e-123 453
32 TraesCS7B01G319400 chr6A 92.212 321 25 0 4419 4739 102140582 102140262 5.600000e-124 455


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 TraesCS7B01G319400 chr7B 569432781 569437524 4743 False 8761.0 8761 100.0000 1 4744 1 chr7B.!!$F2 4743
1 TraesCS7B01G319400 chr7B 569475902 569479938 4036 False 3050.5 5393 91.5570 247 4305 2 chr7B.!!$F3 4058
2 TraesCS7B01G319400 chr7B 591050926 591055233 4307 False 2477.0 2998 87.5695 3 4305 2 chr7B.!!$F4 4302
3 TraesCS7B01G319400 chr7B 633002648 633003886 1238 True 779.0 1349 87.4580 2637 4326 2 chr7B.!!$R3 1689
4 TraesCS7B01G319400 chr7B 632797787 632799032 1245 False 759.5 1310 87.1040 2637 4326 2 chr7B.!!$F5 1689
5 TraesCS7B01G319400 chr7D 548060921 548065095 4174 False 2352.0 2737 87.2375 2 4177 2 chr7D.!!$F2 4175
6 TraesCS7B01G319400 chr7D 530427841 530429354 1513 False 2209.0 2209 93.1280 2897 4404 1 chr7D.!!$F1 1507
7 TraesCS7B01G319400 chr7D 548326684 548329704 3020 True 1816.5 2920 87.6290 1159 4177 2 chr7D.!!$R2 3018
8 TraesCS7B01G319400 chr7D 548337041 548338163 1122 True 589.0 839 85.3380 3 1172 2 chr7D.!!$R3 1169
9 TraesCS7B01G319400 chr7D 573970716 573971593 877 True 525.0 693 88.3590 2952 4326 2 chr7D.!!$R4 1374
10 TraesCS7B01G319400 chr7A 630673446 630677615 4169 True 2334.5 2796 87.9295 3 4177 2 chr7A.!!$R2 4174
11 TraesCS7B01G319400 chr4B 636976163 636976742 579 True 512.0 512 82.7880 2484 3057 1 chr4B.!!$R2 573
12 TraesCS7B01G319400 chr4B 636964926 636965504 578 True 505.0 505 82.5860 2484 3057 1 chr4B.!!$R1 573

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
965 982 1.075536 GAAGGAAAGGGGCTGGAGAAA 59.924 52.381 0.00 0.0 0.00 2.52 F
1410 1445 0.460311 ACCGCTGTAGACTGCCATAC 59.540 55.000 6.02 0.0 37.50 2.39 F
2360 2547 1.202604 TCCCACTCGTCAAAGGTGAAC 60.203 52.381 0.00 0.0 34.87 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 2690 0.107800 ATCGCTGCTTCTCATGCACT 60.108 50.000 0.00 0.0 36.37 4.40 R
3207 3409 0.191064 ACCTGAGGGAGGACACAGAA 59.809 55.000 2.38 0.0 46.33 3.02 R
4016 4274 1.518572 GACAGTGTCCCGCCATACG 60.519 63.158 12.54 0.0 43.15 3.06 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
30 32 9.020731 TCCTGTCTTTTGGAAGGAATTAATTAC 57.979 33.333 1.79 1.79 35.88 1.89
35 37 8.726988 TCTTTTGGAAGGAATTAATTACGTGAG 58.273 33.333 3.36 0.00 33.56 3.51
86 88 9.897744 CAGATTAATATTGGTAATTTCGTGCAT 57.102 29.630 0.00 0.00 0.00 3.96
87 89 9.897744 AGATTAATATTGGTAATTTCGTGCATG 57.102 29.630 0.00 0.00 0.00 4.06
90 92 7.754069 AATATTGGTAATTTCGTGCATGTTG 57.246 32.000 5.68 0.00 0.00 3.33
104 106 3.504134 TGCATGTTGTACTAAAATGCCGT 59.496 39.130 20.82 0.00 42.31 5.68
108 110 6.475207 CATGTTGTACTAAAATGCCGTAGAC 58.525 40.000 0.00 0.00 0.00 2.59
110 112 6.167685 TGTTGTACTAAAATGCCGTAGACAT 58.832 36.000 0.00 0.00 0.00 3.06
111 113 6.651643 TGTTGTACTAAAATGCCGTAGACATT 59.348 34.615 0.00 0.00 39.38 2.71
138 141 9.658475 TTTTTCTTACAGATGTACAAAATGTCG 57.342 29.630 12.57 7.42 29.64 4.35
153 156 4.434713 AATGTCGTAATGTTCCTTTGGC 57.565 40.909 0.00 0.00 0.00 4.52
159 162 6.183360 TGTCGTAATGTTCCTTTGGCATAATC 60.183 38.462 0.00 0.00 0.00 1.75
160 163 6.038271 GTCGTAATGTTCCTTTGGCATAATCT 59.962 38.462 0.00 0.00 0.00 2.40
161 164 6.260050 TCGTAATGTTCCTTTGGCATAATCTC 59.740 38.462 0.00 0.00 0.00 2.75
162 165 5.859205 AATGTTCCTTTGGCATAATCTCC 57.141 39.130 0.00 0.00 0.00 3.71
169 172 6.773638 TCCTTTGGCATAATCTCCTCTTATC 58.226 40.000 0.00 0.00 0.00 1.75
176 179 6.876257 GGCATAATCTCCTCTTATCGATTGTT 59.124 38.462 1.71 0.00 0.00 2.83
271 276 6.225981 TCCTGCATATATCGATTGCACTAT 57.774 37.500 17.14 0.64 41.18 2.12
299 304 8.785329 TTTGCTTTATTTTGATTTATGACCCC 57.215 30.769 0.00 0.00 0.00 4.95
300 305 6.883744 TGCTTTATTTTGATTTATGACCCCC 58.116 36.000 0.00 0.00 0.00 5.40
362 368 6.093909 TGCTGAAATACAACTGTGTCATATGG 59.906 38.462 2.13 0.00 39.30 2.74
379 385 6.536582 GTCATATGGCATCGCTTCAGTAATAT 59.463 38.462 1.65 0.00 0.00 1.28
497 505 3.181501 TGGGCGCATTTTTCTTCTTATCG 60.182 43.478 10.83 0.00 0.00 2.92
512 521 3.936453 TCTTATCGGGATTCAACGGTTTG 59.064 43.478 0.00 0.00 0.00 2.93
628 641 5.337491 GCACCCAAATGATACAGGAAACAAT 60.337 40.000 0.00 0.00 0.00 2.71
689 702 2.614057 CGAGAACAAAGATGTATGCCCC 59.386 50.000 0.00 0.00 39.40 5.80
902 919 5.045651 TCTCTCCATTTCTTGCCAGTTGATA 60.046 40.000 0.00 0.00 0.00 2.15
903 920 5.188434 TCTCCATTTCTTGCCAGTTGATAG 58.812 41.667 0.00 0.00 0.00 2.08
965 982 1.075536 GAAGGAAAGGGGCTGGAGAAA 59.924 52.381 0.00 0.00 0.00 2.52
1080 1098 7.064253 GTGTCACTGTGTTGTAGTCTTAGTTTT 59.936 37.037 7.79 0.00 0.00 2.43
1085 1104 9.227777 ACTGTGTTGTAGTCTTAGTTTTCTTTT 57.772 29.630 0.00 0.00 0.00 2.27
1107 1127 4.985413 TGTCTTTCTGTTTGAACTTGCTG 58.015 39.130 0.00 0.00 33.88 4.41
1142 1162 8.610896 CATTGTGTTGTAATGTTGACCATTTTT 58.389 29.630 0.00 0.00 41.01 1.94
1309 1341 4.036262 TCACAGGTGCAACTGACAATTTAC 59.964 41.667 37.55 0.00 40.97 2.01
1335 1367 4.015084 CCCTTCAGAGAATTGCAAGACAT 58.985 43.478 4.94 0.00 0.00 3.06
1410 1445 0.460311 ACCGCTGTAGACTGCCATAC 59.540 55.000 6.02 0.00 37.50 2.39
1683 1748 7.907214 GTGTATTAGAACACCAAGAAGACAT 57.093 36.000 0.00 0.00 43.23 3.06
1830 1895 2.780010 ACCACCCTTATGATAGCTTGCT 59.220 45.455 0.00 0.00 0.00 3.91
1893 1958 8.097038 TGACAAAGCAGTTCAAATACTATCTCT 58.903 33.333 0.00 0.00 0.00 3.10
1982 2149 7.259882 TGCTTACCTGATTTTATGAATGCTTG 58.740 34.615 0.00 0.00 0.00 4.01
1986 2153 6.860080 ACCTGATTTTATGAATGCTTGTCTG 58.140 36.000 0.00 0.00 0.00 3.51
1987 2154 6.435277 ACCTGATTTTATGAATGCTTGTCTGT 59.565 34.615 0.00 0.00 0.00 3.41
1988 2155 7.039504 ACCTGATTTTATGAATGCTTGTCTGTT 60.040 33.333 0.00 0.00 0.00 3.16
1989 2156 8.461222 CCTGATTTTATGAATGCTTGTCTGTTA 58.539 33.333 0.00 0.00 0.00 2.41
2041 2209 4.202050 GCACCACAAGGGAATATGCTTAAG 60.202 45.833 0.00 0.00 41.15 1.85
2139 2307 3.660970 TGCAGGTATTGGGCATTTCTA 57.339 42.857 0.00 0.00 31.58 2.10
2169 2349 6.718912 TCATATCAAGGTGTTGTTTTCCATCA 59.281 34.615 0.00 0.00 34.98 3.07
2360 2547 1.202604 TCCCACTCGTCAAAGGTGAAC 60.203 52.381 0.00 0.00 34.87 3.18
2414 2601 2.778299 GTTGAGTTGCCACCACTATCA 58.222 47.619 0.00 0.00 0.00 2.15
2502 2690 3.509442 AGGGAGAATTGCATGGTTTTCA 58.491 40.909 0.00 0.00 0.00 2.69
2661 2849 6.977213 TGGAAAAGCGGAATAATATTAAGGC 58.023 36.000 0.00 1.45 0.00 4.35
2672 2860 8.821894 GGAATAATATTAAGGCGAGATGATCAC 58.178 37.037 0.00 0.00 0.00 3.06
3207 3409 1.307691 ATGCTGCTTCCCTCCTCCT 60.308 57.895 0.00 0.00 0.00 3.69
3354 3569 7.477494 TCTTTTGAAAAGGTAAAGTGTACTGC 58.523 34.615 16.79 0.00 0.00 4.40
3583 3805 4.158025 AGCATCTGAGCTTTTTCTGGAATG 59.842 41.667 0.00 0.00 43.70 2.67
3689 3916 5.864418 TTACCTCTGTATTCGTTATGGCT 57.136 39.130 0.00 0.00 0.00 4.75
3690 3917 6.964807 TTACCTCTGTATTCGTTATGGCTA 57.035 37.500 0.00 0.00 0.00 3.93
3691 3918 5.455056 ACCTCTGTATTCGTTATGGCTAG 57.545 43.478 0.00 0.00 0.00 3.42
3697 3931 6.320418 TCTGTATTCGTTATGGCTAGACTTCA 59.680 38.462 0.00 0.00 0.00 3.02
3739 3974 2.942804 TGGCTTTCACAAACATGAGGA 58.057 42.857 0.00 0.00 0.00 3.71
3746 3981 7.147976 GCTTTCACAAACATGAGGAATAAACT 58.852 34.615 0.00 0.00 0.00 2.66
3747 3982 8.296713 GCTTTCACAAACATGAGGAATAAACTA 58.703 33.333 0.00 0.00 0.00 2.24
3769 4006 8.488651 ACTATGTTAGTTTTTAGATGGAACCG 57.511 34.615 0.00 0.00 34.86 4.44
3850 4090 9.444600 TTTAAGCTTTATAAAGGTCCACTACAG 57.555 33.333 25.71 0.00 45.17 2.74
3926 4167 4.185467 AGTAGACACATCAACTCAGCAG 57.815 45.455 0.00 0.00 0.00 4.24
4049 4311 6.049790 GGACACTGTCTCTAGTTTGAAGTTT 58.950 40.000 9.08 0.00 32.47 2.66
4097 4364 3.778954 AAGGATATAGAGGTGCTTGGC 57.221 47.619 0.00 0.00 0.00 4.52
4110 4380 1.153667 CTTGGCGGTCTCTGCTCTC 60.154 63.158 0.66 0.00 0.00 3.20
4215 4486 5.902613 AATGGAAATCATGTACACCTGTG 57.097 39.130 0.00 0.00 35.99 3.66
4234 4507 8.832521 CACCTGTGAATAGTAGAGTACTTCTAG 58.167 40.741 0.00 0.00 39.05 2.43
4235 4508 8.770322 ACCTGTGAATAGTAGAGTACTTCTAGA 58.230 37.037 0.00 0.00 39.05 2.43
4236 4509 9.616156 CCTGTGAATAGTAGAGTACTTCTAGAA 57.384 37.037 4.81 4.81 39.05 2.10
4283 4562 7.081349 TCGCATTTTGTTCTTTGTAACATAGG 58.919 34.615 0.00 0.00 39.04 2.57
4322 4602 2.028385 ACCTCGCTGTAAACCGAAGAAT 60.028 45.455 0.00 0.00 32.56 2.40
4371 4651 0.623723 ATCATGGTGGGCGTACCTTT 59.376 50.000 10.37 0.00 41.43 3.11
4428 4708 6.484364 AAATCCTTTTGTGGTTTGATCAGT 57.516 33.333 0.00 0.00 0.00 3.41
4429 4709 4.916983 TCCTTTTGTGGTTTGATCAGTG 57.083 40.909 0.00 0.00 0.00 3.66
4430 4710 3.636300 TCCTTTTGTGGTTTGATCAGTGG 59.364 43.478 0.00 0.00 0.00 4.00
4431 4711 3.636300 CCTTTTGTGGTTTGATCAGTGGA 59.364 43.478 0.00 0.00 0.00 4.02
4432 4712 4.281688 CCTTTTGTGGTTTGATCAGTGGAT 59.718 41.667 0.00 0.00 36.13 3.41
4439 4719 4.327885 GATCAGTGGATCGGCGAC 57.672 61.111 13.76 6.32 40.50 5.19
4460 4740 4.394712 CCTCTGTCCGCCCGCTTT 62.395 66.667 0.00 0.00 0.00 3.51
4461 4741 2.815647 CTCTGTCCGCCCGCTTTC 60.816 66.667 0.00 0.00 0.00 2.62
4462 4742 4.388499 TCTGTCCGCCCGCTTTCC 62.388 66.667 0.00 0.00 0.00 3.13
4468 4748 4.530857 CGCCCGCTTTCCCGATCT 62.531 66.667 0.00 0.00 0.00 2.75
4469 4749 2.589159 GCCCGCTTTCCCGATCTC 60.589 66.667 0.00 0.00 0.00 2.75
4470 4750 3.095347 GCCCGCTTTCCCGATCTCT 62.095 63.158 0.00 0.00 0.00 3.10
4471 4751 1.522569 CCCGCTTTCCCGATCTCTT 59.477 57.895 0.00 0.00 0.00 2.85
4472 4752 0.530870 CCCGCTTTCCCGATCTCTTC 60.531 60.000 0.00 0.00 0.00 2.87
4474 4754 1.483424 CGCTTTCCCGATCTCTTCGC 61.483 60.000 0.00 0.00 46.71 4.70
4475 4755 1.154814 GCTTTCCCGATCTCTTCGCC 61.155 60.000 0.00 0.00 46.71 5.54
4476 4756 0.175760 CTTTCCCGATCTCTTCGCCA 59.824 55.000 0.00 0.00 46.71 5.69
4477 4757 0.830648 TTTCCCGATCTCTTCGCCAT 59.169 50.000 0.00 0.00 46.71 4.40
4478 4758 0.830648 TTCCCGATCTCTTCGCCATT 59.169 50.000 0.00 0.00 46.71 3.16
4479 4759 0.104855 TCCCGATCTCTTCGCCATTG 59.895 55.000 0.00 0.00 46.71 2.82
4480 4760 1.502163 CCCGATCTCTTCGCCATTGC 61.502 60.000 0.00 0.00 46.71 3.56
4481 4761 0.811219 CCGATCTCTTCGCCATTGCA 60.811 55.000 0.00 0.00 46.71 4.08
4482 4762 0.580578 CGATCTCTTCGCCATTGCAG 59.419 55.000 0.00 0.00 41.69 4.41
4483 4763 1.661341 GATCTCTTCGCCATTGCAGT 58.339 50.000 0.00 0.00 37.32 4.40
4484 4764 2.012673 GATCTCTTCGCCATTGCAGTT 58.987 47.619 0.00 0.00 37.32 3.16
4485 4765 1.159285 TCTCTTCGCCATTGCAGTTG 58.841 50.000 0.00 0.00 37.32 3.16
4486 4766 1.159285 CTCTTCGCCATTGCAGTTGA 58.841 50.000 0.59 0.00 37.32 3.18
4487 4767 1.741706 CTCTTCGCCATTGCAGTTGAT 59.258 47.619 0.59 0.00 37.32 2.57
4488 4768 1.739466 TCTTCGCCATTGCAGTTGATC 59.261 47.619 0.59 0.00 37.32 2.92
4489 4769 0.810648 TTCGCCATTGCAGTTGATCC 59.189 50.000 0.59 0.00 37.32 3.36
4490 4770 0.035152 TCGCCATTGCAGTTGATCCT 60.035 50.000 0.59 0.00 37.32 3.24
4491 4771 0.379669 CGCCATTGCAGTTGATCCTC 59.620 55.000 0.59 0.00 37.32 3.71
4492 4772 0.379669 GCCATTGCAGTTGATCCTCG 59.620 55.000 0.59 0.00 37.47 4.63
4493 4773 1.019673 CCATTGCAGTTGATCCTCGG 58.980 55.000 0.59 0.00 0.00 4.63
4494 4774 1.019673 CATTGCAGTTGATCCTCGGG 58.980 55.000 0.00 0.00 0.00 5.14
4495 4775 0.620556 ATTGCAGTTGATCCTCGGGT 59.379 50.000 0.00 0.00 0.00 5.28
4496 4776 0.036388 TTGCAGTTGATCCTCGGGTC 60.036 55.000 0.00 0.00 0.00 4.46
4497 4777 0.904865 TGCAGTTGATCCTCGGGTCT 60.905 55.000 0.00 0.00 0.00 3.85
4498 4778 0.179097 GCAGTTGATCCTCGGGTCTC 60.179 60.000 0.00 0.00 0.00 3.36
4499 4779 1.479709 CAGTTGATCCTCGGGTCTCT 58.520 55.000 0.00 0.00 0.00 3.10
4500 4780 1.135915 CAGTTGATCCTCGGGTCTCTG 59.864 57.143 0.00 3.34 0.00 3.35
4501 4781 1.187087 GTTGATCCTCGGGTCTCTGT 58.813 55.000 0.00 0.00 0.00 3.41
4502 4782 1.550976 GTTGATCCTCGGGTCTCTGTT 59.449 52.381 0.00 0.00 0.00 3.16
4503 4783 1.186200 TGATCCTCGGGTCTCTGTTG 58.814 55.000 0.00 0.00 0.00 3.33
4504 4784 1.272480 TGATCCTCGGGTCTCTGTTGA 60.272 52.381 0.00 0.00 0.00 3.18
4505 4785 1.407258 GATCCTCGGGTCTCTGTTGAG 59.593 57.143 0.00 0.00 41.51 3.02
4506 4786 0.404426 TCCTCGGGTCTCTGTTGAGA 59.596 55.000 0.00 0.00 46.13 3.27
4513 4793 3.747735 TCTCTGTTGAGACGGTCCT 57.252 52.632 4.14 0.00 43.73 3.85
4514 4794 1.996798 TCTCTGTTGAGACGGTCCTT 58.003 50.000 4.14 0.00 43.73 3.36
4515 4795 3.150458 TCTCTGTTGAGACGGTCCTTA 57.850 47.619 4.14 0.00 43.73 2.69
4516 4796 3.698289 TCTCTGTTGAGACGGTCCTTAT 58.302 45.455 4.14 0.00 43.73 1.73
4517 4797 4.087182 TCTCTGTTGAGACGGTCCTTATT 58.913 43.478 4.14 0.00 43.73 1.40
4518 4798 4.082190 TCTCTGTTGAGACGGTCCTTATTG 60.082 45.833 4.14 0.00 43.73 1.90
4519 4799 3.830178 TCTGTTGAGACGGTCCTTATTGA 59.170 43.478 4.14 0.00 33.69 2.57
4520 4800 3.921677 TGTTGAGACGGTCCTTATTGAC 58.078 45.455 4.14 0.00 34.42 3.18
4521 4801 3.576982 TGTTGAGACGGTCCTTATTGACT 59.423 43.478 4.14 0.00 35.54 3.41
4522 4802 4.039973 TGTTGAGACGGTCCTTATTGACTT 59.960 41.667 4.14 0.00 35.54 3.01
4523 4803 5.244402 TGTTGAGACGGTCCTTATTGACTTA 59.756 40.000 4.14 0.00 35.54 2.24
4524 4804 5.578005 TGAGACGGTCCTTATTGACTTAG 57.422 43.478 4.14 0.00 35.54 2.18
4525 4805 4.401519 TGAGACGGTCCTTATTGACTTAGG 59.598 45.833 4.14 0.00 35.54 2.69
4526 4806 3.705072 AGACGGTCCTTATTGACTTAGGG 59.295 47.826 4.14 0.00 35.54 3.53
4527 4807 2.169978 ACGGTCCTTATTGACTTAGGGC 59.830 50.000 0.00 0.00 35.54 5.19
4528 4808 2.802057 CGGTCCTTATTGACTTAGGGCG 60.802 54.545 0.00 0.00 34.46 6.13
4529 4809 2.210961 GTCCTTATTGACTTAGGGCGC 58.789 52.381 0.00 0.00 32.39 6.53
4530 4810 1.140252 TCCTTATTGACTTAGGGCGCC 59.860 52.381 21.18 21.18 0.00 6.53
4531 4811 1.141053 CCTTATTGACTTAGGGCGCCT 59.859 52.381 28.56 15.07 37.71 5.52
4532 4812 2.484889 CTTATTGACTTAGGGCGCCTC 58.515 52.381 28.56 16.37 34.61 4.70
4533 4813 0.387929 TATTGACTTAGGGCGCCTCG 59.612 55.000 28.56 14.37 34.61 4.63
4547 4827 4.099170 CTCGCGTTCCGTCGTCCT 62.099 66.667 5.77 0.00 38.35 3.85
4548 4828 3.606065 CTCGCGTTCCGTCGTCCTT 62.606 63.158 5.77 0.00 38.35 3.36
4549 4829 2.732094 CGCGTTCCGTCGTCCTTT 60.732 61.111 0.00 0.00 0.00 3.11
4550 4830 2.713894 CGCGTTCCGTCGTCCTTTC 61.714 63.158 0.00 0.00 0.00 2.62
4551 4831 2.713894 GCGTTCCGTCGTCCTTTCG 61.714 63.158 0.00 0.00 0.00 3.46
4552 4832 2.084681 CGTTCCGTCGTCCTTTCGG 61.085 63.158 0.00 0.00 44.76 4.30
4553 4833 2.048877 TTCCGTCGTCCTTTCGGC 60.049 61.111 0.00 0.00 43.35 5.54
4554 4834 3.578515 TTCCGTCGTCCTTTCGGCC 62.579 63.158 0.00 0.00 43.35 6.13
4556 4836 4.065281 CGTCGTCCTTTCGGCCCT 62.065 66.667 0.00 0.00 31.35 5.19
4557 4837 2.125633 GTCGTCCTTTCGGCCCTC 60.126 66.667 0.00 0.00 0.00 4.30
4558 4838 3.387947 TCGTCCTTTCGGCCCTCC 61.388 66.667 0.00 0.00 0.00 4.30
4559 4839 4.468689 CGTCCTTTCGGCCCTCCC 62.469 72.222 0.00 0.00 0.00 4.30
4577 4857 4.115199 GAAGTGGCCGCCTGGGAT 62.115 66.667 14.07 0.00 38.47 3.85
4578 4858 4.431131 AAGTGGCCGCCTGGGATG 62.431 66.667 14.07 0.00 38.47 3.51
4584 4864 4.883354 CCGCCTGGGATGCCCTTC 62.883 72.222 0.00 0.00 45.70 3.46
4585 4865 3.801997 CGCCTGGGATGCCCTTCT 61.802 66.667 0.00 0.00 45.70 2.85
4586 4866 2.194326 GCCTGGGATGCCCTTCTC 59.806 66.667 0.00 0.00 45.70 2.87
4587 4867 2.922234 CCTGGGATGCCCTTCTCC 59.078 66.667 0.00 0.00 45.70 3.71
4588 4868 2.002977 CCTGGGATGCCCTTCTCCA 61.003 63.158 0.00 0.00 45.70 3.86
4589 4869 1.530771 CTGGGATGCCCTTCTCCAG 59.469 63.158 0.00 0.00 45.70 3.86
4590 4870 1.992519 CTGGGATGCCCTTCTCCAGG 61.993 65.000 0.00 0.00 45.70 4.45
4595 4875 0.842635 ATGCCCTTCTCCAGGACATC 59.157 55.000 0.00 0.00 41.92 3.06
4596 4876 2.922199 ATGCCCTTCTCCAGGACATCG 61.922 57.143 0.00 0.00 41.92 3.84
4608 4888 2.490165 GACATCGTCCTTCTCCCGA 58.510 57.895 0.00 0.00 34.79 5.14
4609 4889 1.033574 GACATCGTCCTTCTCCCGAT 58.966 55.000 0.00 0.00 41.64 4.18
4611 4891 3.515059 ATCGTCCTTCTCCCGATGA 57.485 52.632 0.00 0.00 39.64 2.92
4612 4892 1.323412 ATCGTCCTTCTCCCGATGAG 58.677 55.000 0.00 0.00 39.64 2.90
4613 4893 1.066587 CGTCCTTCTCCCGATGAGC 59.933 63.158 0.00 0.00 41.18 4.26
4614 4894 1.066587 GTCCTTCTCCCGATGAGCG 59.933 63.158 0.00 0.00 41.18 5.03
4615 4895 1.379977 TCCTTCTCCCGATGAGCGT 60.380 57.895 0.00 0.00 41.18 5.07
4616 4896 1.066587 CCTTCTCCCGATGAGCGTC 59.933 63.158 0.00 0.00 41.18 5.19
4617 4897 1.667154 CCTTCTCCCGATGAGCGTCA 61.667 60.000 0.00 0.00 41.18 4.35
4618 4898 0.526524 CTTCTCCCGATGAGCGTCAC 60.527 60.000 0.00 0.00 41.18 3.67
4619 4899 1.945354 TTCTCCCGATGAGCGTCACC 61.945 60.000 0.00 0.00 41.18 4.02
4620 4900 3.758088 CTCCCGATGAGCGTCACCG 62.758 68.421 0.00 0.00 38.67 4.94
4621 4901 3.822192 CCCGATGAGCGTCACCGA 61.822 66.667 3.71 0.00 34.73 4.69
4622 4902 2.579787 CCGATGAGCGTCACCGAC 60.580 66.667 3.71 0.00 34.73 4.79
4642 4922 4.873129 CCCGGACGCCATCTCGTG 62.873 72.222 0.73 0.00 43.42 4.35
4650 4930 2.028190 CCATCTCGTGGCGCCTAG 59.972 66.667 29.70 21.36 42.12 3.02
4651 4931 2.490148 CCATCTCGTGGCGCCTAGA 61.490 63.158 29.70 25.65 42.12 2.43
4652 4932 1.007964 CATCTCGTGGCGCCTAGAG 60.008 63.158 31.96 31.96 0.00 2.43
4653 4933 1.454111 ATCTCGTGGCGCCTAGAGT 60.454 57.895 34.04 24.48 32.90 3.24
4654 4934 1.448922 ATCTCGTGGCGCCTAGAGTC 61.449 60.000 34.04 17.11 32.90 3.36
4655 4935 2.045242 TCGTGGCGCCTAGAGTCT 60.045 61.111 29.70 0.00 0.00 3.24
4656 4936 1.658686 CTCGTGGCGCCTAGAGTCTT 61.659 60.000 30.47 0.00 0.00 3.01
4657 4937 1.226717 CGTGGCGCCTAGAGTCTTC 60.227 63.158 29.70 5.65 0.00 2.87
4658 4938 1.142097 GTGGCGCCTAGAGTCTTCC 59.858 63.158 29.70 0.00 0.00 3.46
4659 4939 2.413765 GGCGCCTAGAGTCTTCCG 59.586 66.667 22.15 0.00 0.00 4.30
4660 4940 2.413765 GCGCCTAGAGTCTTCCGG 59.586 66.667 0.00 0.00 0.00 5.14
4661 4941 2.119655 GCGCCTAGAGTCTTCCGGA 61.120 63.158 0.00 0.00 0.00 5.14
4662 4942 1.728672 CGCCTAGAGTCTTCCGGAC 59.271 63.158 1.83 0.00 44.80 4.79
4669 4949 4.480031 GTCTTCCGGACGCTTCTC 57.520 61.111 1.83 0.00 35.07 2.87
4670 4950 1.884444 GTCTTCCGGACGCTTCTCT 59.116 57.895 1.83 0.00 35.07 3.10
4671 4951 1.093159 GTCTTCCGGACGCTTCTCTA 58.907 55.000 1.83 0.00 35.07 2.43
4672 4952 1.093159 TCTTCCGGACGCTTCTCTAC 58.907 55.000 1.83 0.00 0.00 2.59
4673 4953 1.096416 CTTCCGGACGCTTCTCTACT 58.904 55.000 1.83 0.00 0.00 2.57
4674 4954 2.093288 TCTTCCGGACGCTTCTCTACTA 60.093 50.000 1.83 0.00 0.00 1.82
4675 4955 1.950828 TCCGGACGCTTCTCTACTAG 58.049 55.000 0.00 0.00 0.00 2.57
4676 4956 0.945813 CCGGACGCTTCTCTACTAGG 59.054 60.000 0.00 0.00 0.00 3.02
4677 4957 1.666054 CGGACGCTTCTCTACTAGGT 58.334 55.000 0.00 0.00 0.00 3.08
4678 4958 1.598601 CGGACGCTTCTCTACTAGGTC 59.401 57.143 0.00 0.00 0.00 3.85
4679 4959 1.948834 GGACGCTTCTCTACTAGGTCC 59.051 57.143 0.00 0.00 36.11 4.46
4680 4960 2.421811 GGACGCTTCTCTACTAGGTCCT 60.422 54.545 0.00 0.00 39.42 3.85
4681 4961 3.281158 GACGCTTCTCTACTAGGTCCTT 58.719 50.000 0.00 0.00 0.00 3.36
4682 4962 3.018149 ACGCTTCTCTACTAGGTCCTTG 58.982 50.000 0.00 0.00 0.00 3.61
4683 4963 3.018149 CGCTTCTCTACTAGGTCCTTGT 58.982 50.000 10.92 10.92 0.00 3.16
4684 4964 4.197750 CGCTTCTCTACTAGGTCCTTGTA 58.802 47.826 11.97 11.97 0.00 2.41
4685 4965 4.035441 CGCTTCTCTACTAGGTCCTTGTAC 59.965 50.000 8.90 0.00 0.00 2.90
4686 4966 4.035441 GCTTCTCTACTAGGTCCTTGTACG 59.965 50.000 8.90 6.41 0.00 3.67
4687 4967 3.539604 TCTCTACTAGGTCCTTGTACGC 58.460 50.000 8.90 0.00 0.00 4.42
4688 4968 2.283298 TCTACTAGGTCCTTGTACGCG 58.717 52.381 3.53 3.53 0.00 6.01
4689 4969 1.332997 CTACTAGGTCCTTGTACGCGG 59.667 57.143 12.47 0.00 0.00 6.46
4690 4970 1.226888 CTAGGTCCTTGTACGCGGC 60.227 63.158 12.47 3.05 0.00 6.53
4691 4971 2.624437 CTAGGTCCTTGTACGCGGCC 62.624 65.000 12.47 0.00 0.00 6.13
4692 4972 4.382320 GGTCCTTGTACGCGGCCA 62.382 66.667 12.47 2.88 0.00 5.36
4693 4973 2.125269 GTCCTTGTACGCGGCCAT 60.125 61.111 12.47 0.00 0.00 4.40
4694 4974 2.171725 GTCCTTGTACGCGGCCATC 61.172 63.158 12.47 0.00 0.00 3.51
4695 4975 3.261951 CCTTGTACGCGGCCATCG 61.262 66.667 12.47 12.26 42.76 3.84
4729 5009 4.617875 CGAGCCCTTCGGTTTGAT 57.382 55.556 0.00 0.00 45.54 2.57
4730 5010 2.384203 CGAGCCCTTCGGTTTGATC 58.616 57.895 0.00 0.00 45.54 2.92
4731 5011 0.108138 CGAGCCCTTCGGTTTGATCT 60.108 55.000 0.00 0.00 45.54 2.75
4732 5012 1.373570 GAGCCCTTCGGTTTGATCTG 58.626 55.000 0.00 0.00 0.00 2.90
4733 5013 0.035056 AGCCCTTCGGTTTGATCTGG 60.035 55.000 0.00 0.00 0.00 3.86
4734 5014 1.032114 GCCCTTCGGTTTGATCTGGG 61.032 60.000 0.00 0.00 35.98 4.45
4735 5015 0.618458 CCCTTCGGTTTGATCTGGGA 59.382 55.000 0.00 0.00 35.31 4.37
4736 5016 1.212935 CCCTTCGGTTTGATCTGGGAT 59.787 52.381 0.00 0.00 35.31 3.85
4737 5017 2.438021 CCCTTCGGTTTGATCTGGGATA 59.562 50.000 0.00 0.00 35.31 2.59
4738 5018 3.073062 CCCTTCGGTTTGATCTGGGATAT 59.927 47.826 0.00 0.00 35.31 1.63
4739 5019 4.446311 CCCTTCGGTTTGATCTGGGATATT 60.446 45.833 0.00 0.00 35.31 1.28
4740 5020 5.133221 CCTTCGGTTTGATCTGGGATATTT 58.867 41.667 0.00 0.00 0.00 1.40
4741 5021 5.009010 CCTTCGGTTTGATCTGGGATATTTG 59.991 44.000 0.00 0.00 0.00 2.32
4742 5022 3.882888 TCGGTTTGATCTGGGATATTTGC 59.117 43.478 0.00 0.00 0.00 3.68
4743 5023 3.885297 CGGTTTGATCTGGGATATTTGCT 59.115 43.478 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.873591 CCTTCCAAAAGACAGGACACG 59.126 52.381 0.00 0.00 34.14 4.49
30 32 1.442526 GAAGGCATGCATCCCTCACG 61.443 60.000 21.36 0.00 0.00 4.35
35 37 1.884579 CATACTGAAGGCATGCATCCC 59.115 52.381 21.36 0.00 0.00 3.85
73 75 8.716619 TTTTAGTACAACATGCACGAAATTAC 57.283 30.769 0.00 0.00 0.00 1.89
75 77 7.148820 GCATTTTAGTACAACATGCACGAAATT 60.149 33.333 17.05 0.00 40.06 1.82
86 88 5.539979 TGTCTACGGCATTTTAGTACAACA 58.460 37.500 0.00 0.00 0.00 3.33
87 89 6.657836 ATGTCTACGGCATTTTAGTACAAC 57.342 37.500 0.00 0.00 0.00 3.32
138 141 6.547510 AGGAGATTATGCCAAAGGAACATTAC 59.452 38.462 0.00 0.00 0.00 1.89
153 156 7.601886 AGCAACAATCGATAAGAGGAGATTATG 59.398 37.037 0.00 0.00 32.70 1.90
159 162 6.146837 CCAATAGCAACAATCGATAAGAGGAG 59.853 42.308 0.00 0.00 0.00 3.69
160 163 5.991606 CCAATAGCAACAATCGATAAGAGGA 59.008 40.000 0.00 0.00 0.00 3.71
161 164 5.991606 TCCAATAGCAACAATCGATAAGAGG 59.008 40.000 0.00 0.00 0.00 3.69
162 165 7.664082 ATCCAATAGCAACAATCGATAAGAG 57.336 36.000 0.00 0.00 0.00 2.85
169 172 7.250569 ACTTTTGTATCCAATAGCAACAATCG 58.749 34.615 0.00 0.00 34.20 3.34
176 179 7.502226 CCCTTATGACTTTTGTATCCAATAGCA 59.498 37.037 0.00 0.00 34.20 3.49
231 234 3.873952 GCAGGAGGCAGAATACTGTAAAG 59.126 47.826 0.00 0.00 45.04 1.85
312 317 0.460811 TCCATGCTACGCAGAAGCTG 60.461 55.000 0.00 0.00 43.65 4.24
379 385 6.096141 GTCTGATTGTGTCCTCTATCTTCAGA 59.904 42.308 0.00 0.00 35.87 3.27
457 465 1.129251 CCATGTCAACAGCTAACGCAG 59.871 52.381 0.00 0.00 39.10 5.18
497 505 7.899178 AAATAAAATCAAACCGTTGAATCCC 57.101 32.000 0.00 0.00 46.66 3.85
614 627 6.260936 CACCCACAGATATTGTTTCCTGTATC 59.739 42.308 0.00 0.00 38.16 2.24
628 641 0.535335 GACTTCGGCACCCACAGATA 59.465 55.000 0.00 0.00 0.00 1.98
965 982 5.245075 CACCACACCCCATAAATTTTAGTGT 59.755 40.000 0.00 6.24 37.46 3.55
1060 1078 9.490663 CAAAAGAAAACTAAGACTACAACACAG 57.509 33.333 0.00 0.00 0.00 3.66
1080 1098 6.586082 GCAAGTTCAAACAGAAAGACAAAAGA 59.414 34.615 0.00 0.00 38.13 2.52
1085 1104 4.458989 ACAGCAAGTTCAAACAGAAAGACA 59.541 37.500 0.00 0.00 38.13 3.41
1107 1127 6.959361 ACATTACAACACAATGAGACAGAAC 58.041 36.000 2.29 0.00 36.95 3.01
1142 1162 3.571590 ACTAATTGTCAAACCCTTGCCA 58.428 40.909 0.00 0.00 32.14 4.92
1206 1226 6.089476 TCACATGGTGCAAAATACAATAACG 58.911 36.000 0.00 0.00 32.98 3.18
1309 1341 3.063510 TGCAATTCTCTGAAGGGTGAG 57.936 47.619 0.00 0.00 0.00 3.51
1435 1474 8.044908 AGAACTTAGTCTTCAACAAAGTAACCA 58.955 33.333 0.00 0.00 36.31 3.67
1590 1647 3.942829 ACAGTGCAGCAACATGTATACT 58.057 40.909 0.00 0.00 0.00 2.12
1796 1861 4.302559 AAGGGTGGTGGAAGAGATAAAC 57.697 45.455 0.00 0.00 0.00 2.01
1830 1895 5.408299 CACAAATCATTTGAGACGTACTGGA 59.592 40.000 17.30 0.00 43.26 3.86
1893 1958 7.259882 CAGAAATTTATCAGCATTGCAACCTA 58.740 34.615 11.91 0.00 0.00 3.08
2041 2209 3.066342 CAGATGATGAACCAAGCCATGAC 59.934 47.826 0.00 0.00 0.00 3.06
2158 2338 5.170021 GCATTTGCTACATGATGGAAAACA 58.830 37.500 0.00 0.00 38.21 2.83
2201 2382 7.656412 TGCAAATTCAAATCTAAGTAAGCACA 58.344 30.769 0.00 0.00 0.00 4.57
2202 2383 8.519492 TTGCAAATTCAAATCTAAGTAAGCAC 57.481 30.769 0.00 0.00 0.00 4.40
2414 2601 3.652869 TGAGGACCTCCAAATCAAGTTCT 59.347 43.478 19.11 0.00 38.89 3.01
2502 2690 0.107800 ATCGCTGCTTCTCATGCACT 60.108 50.000 0.00 0.00 36.37 4.40
2661 2849 6.473778 CCAGTTTTAGTGTAGTGATCATCTCG 59.526 42.308 0.00 0.00 0.00 4.04
2672 2860 6.202954 CCACTCTGTTTCCAGTTTTAGTGTAG 59.797 42.308 0.00 0.00 37.78 2.74
2675 2863 5.123227 TCCACTCTGTTTCCAGTTTTAGTG 58.877 41.667 0.00 0.00 38.55 2.74
2856 3058 0.586319 CACGAAATCAAGCCGTGTGT 59.414 50.000 0.00 0.00 45.79 3.72
3207 3409 0.191064 ACCTGAGGGAGGACACAGAA 59.809 55.000 2.38 0.00 46.33 3.02
3311 3523 8.062065 TCAAAAGAAGGAAACATTTGTACAGT 57.938 30.769 0.00 0.00 33.76 3.55
3354 3569 9.582431 TGTATGATTTACTCCTTTTTACTCGAG 57.418 33.333 11.84 11.84 0.00 4.04
3543 3765 2.786777 TGCTGACGAGAACCTACAGTA 58.213 47.619 0.00 0.00 0.00 2.74
3583 3805 4.725790 AAAGGAAGAATGCTATTGTGCC 57.274 40.909 0.00 0.00 0.00 5.01
3680 3907 4.113354 GGACTTGAAGTCTAGCCATAACG 58.887 47.826 23.06 0.00 44.46 3.18
3684 3911 4.583871 CAAAGGACTTGAAGTCTAGCCAT 58.416 43.478 23.06 0.00 44.46 4.40
3689 3916 7.387948 GTGATAAAGCAAAGGACTTGAAGTCTA 59.612 37.037 23.06 7.13 44.46 2.59
3690 3917 6.205658 GTGATAAAGCAAAGGACTTGAAGTCT 59.794 38.462 23.06 8.16 44.46 3.24
3691 3918 6.205658 AGTGATAAAGCAAAGGACTTGAAGTC 59.794 38.462 16.70 16.70 44.32 3.01
3697 3931 6.515832 CCAAAAGTGATAAAGCAAAGGACTT 58.484 36.000 0.00 0.00 0.00 3.01
3746 3981 7.550196 GTCCGGTTCCATCTAAAAACTAACATA 59.450 37.037 0.00 0.00 0.00 2.29
3747 3982 6.373495 GTCCGGTTCCATCTAAAAACTAACAT 59.627 38.462 0.00 0.00 0.00 2.71
3749 3984 5.702209 TGTCCGGTTCCATCTAAAAACTAAC 59.298 40.000 0.00 0.00 0.00 2.34
3835 4075 9.226606 CATATTTCAAACTGTAGTGGACCTTTA 57.773 33.333 0.00 0.00 0.00 1.85
3836 4076 7.942341 TCATATTTCAAACTGTAGTGGACCTTT 59.058 33.333 0.00 0.00 0.00 3.11
3850 4090 8.375465 GCAGCACAAATTACTCATATTTCAAAC 58.625 33.333 0.00 0.00 0.00 2.93
4016 4274 1.518572 GACAGTGTCCCGCCATACG 60.519 63.158 12.54 0.00 43.15 3.06
4097 4364 2.097629 TGATAAACGAGAGCAGAGACCG 59.902 50.000 0.00 0.00 0.00 4.79
4110 4380 4.000325 TCCATTGTCACCACTGATAAACG 59.000 43.478 0.00 0.00 31.90 3.60
4234 4507 5.986135 AGCTCGTGGTATCTTTCATGTATTC 59.014 40.000 0.00 0.00 0.00 1.75
4235 4508 5.918608 AGCTCGTGGTATCTTTCATGTATT 58.081 37.500 0.00 0.00 0.00 1.89
4236 4509 5.533482 GAGCTCGTGGTATCTTTCATGTAT 58.467 41.667 0.00 0.00 0.00 2.29
4237 4510 4.497507 CGAGCTCGTGGTATCTTTCATGTA 60.498 45.833 27.79 0.00 34.11 2.29
4238 4511 3.735208 CGAGCTCGTGGTATCTTTCATGT 60.735 47.826 27.79 0.00 34.11 3.21
4283 4562 5.631992 CGAGGTATTTCAAAGGAGAAAAGC 58.368 41.667 0.00 0.00 40.54 3.51
4404 4684 7.432869 CACTGATCAAACCACAAAAGGATTTA 58.567 34.615 0.00 0.00 37.28 1.40
4405 4685 6.282930 CACTGATCAAACCACAAAAGGATTT 58.717 36.000 0.00 0.00 42.41 2.17
4406 4686 5.221501 CCACTGATCAAACCACAAAAGGATT 60.222 40.000 0.00 0.00 0.00 3.01
4407 4687 4.281688 CCACTGATCAAACCACAAAAGGAT 59.718 41.667 0.00 0.00 0.00 3.24
4408 4688 3.636300 CCACTGATCAAACCACAAAAGGA 59.364 43.478 0.00 0.00 0.00 3.36
4409 4689 3.636300 TCCACTGATCAAACCACAAAAGG 59.364 43.478 0.00 0.00 0.00 3.11
4410 4690 4.916983 TCCACTGATCAAACCACAAAAG 57.083 40.909 0.00 0.00 0.00 2.27
4411 4691 4.023279 CGATCCACTGATCAAACCACAAAA 60.023 41.667 0.00 0.00 46.50 2.44
4412 4692 3.501828 CGATCCACTGATCAAACCACAAA 59.498 43.478 0.00 0.00 46.50 2.83
4413 4693 3.073678 CGATCCACTGATCAAACCACAA 58.926 45.455 0.00 0.00 46.50 3.33
4414 4694 2.615240 CCGATCCACTGATCAAACCACA 60.615 50.000 0.00 0.00 46.50 4.17
4415 4695 2.009774 CCGATCCACTGATCAAACCAC 58.990 52.381 0.00 0.00 46.50 4.16
4416 4696 1.678728 GCCGATCCACTGATCAAACCA 60.679 52.381 0.00 0.00 46.50 3.67
4417 4697 1.017387 GCCGATCCACTGATCAAACC 58.983 55.000 0.00 0.00 46.50 3.27
4418 4698 0.652592 CGCCGATCCACTGATCAAAC 59.347 55.000 0.00 0.00 46.50 2.93
4419 4699 0.534873 TCGCCGATCCACTGATCAAA 59.465 50.000 0.00 0.00 46.50 2.69
4420 4700 0.179111 GTCGCCGATCCACTGATCAA 60.179 55.000 0.00 0.00 46.50 2.57
4421 4701 1.437573 GTCGCCGATCCACTGATCA 59.562 57.895 0.00 0.00 46.50 2.92
4422 4702 1.658717 CGTCGCCGATCCACTGATC 60.659 63.158 0.00 0.00 43.36 2.92
4423 4703 2.413351 CGTCGCCGATCCACTGAT 59.587 61.111 0.00 0.00 35.63 2.90
4424 4704 4.492160 GCGTCGCCGATCCACTGA 62.492 66.667 5.75 0.00 35.63 3.41
4443 4723 4.394712 AAAGCGGGCGGACAGAGG 62.395 66.667 0.00 0.00 0.00 3.69
4444 4724 2.815647 GAAAGCGGGCGGACAGAG 60.816 66.667 0.00 0.00 0.00 3.35
4445 4725 4.388499 GGAAAGCGGGCGGACAGA 62.388 66.667 0.00 0.00 0.00 3.41
4451 4731 4.530857 AGATCGGGAAAGCGGGCG 62.531 66.667 0.00 0.00 0.00 6.13
4452 4732 2.589159 GAGATCGGGAAAGCGGGC 60.589 66.667 0.00 0.00 0.00 6.13
4453 4733 0.530870 GAAGAGATCGGGAAAGCGGG 60.531 60.000 0.00 0.00 0.00 6.13
4454 4734 2.979130 GAAGAGATCGGGAAAGCGG 58.021 57.895 0.00 0.00 0.00 5.52
4464 4744 1.661341 ACTGCAATGGCGAAGAGATC 58.339 50.000 0.00 0.00 45.35 2.75
4465 4745 1.741706 CAACTGCAATGGCGAAGAGAT 59.258 47.619 0.00 0.00 45.35 2.75
4466 4746 1.159285 CAACTGCAATGGCGAAGAGA 58.841 50.000 0.00 0.00 45.35 3.10
4467 4747 1.159285 TCAACTGCAATGGCGAAGAG 58.841 50.000 0.00 0.00 45.35 2.85
4468 4748 1.739466 GATCAACTGCAATGGCGAAGA 59.261 47.619 0.00 0.00 45.35 2.87
4469 4749 1.202222 GGATCAACTGCAATGGCGAAG 60.202 52.381 0.00 0.00 45.35 3.79
4470 4750 0.810648 GGATCAACTGCAATGGCGAA 59.189 50.000 0.00 0.00 45.35 4.70
4471 4751 0.035152 AGGATCAACTGCAATGGCGA 60.035 50.000 0.00 0.00 45.35 5.54
4472 4752 0.379669 GAGGATCAACTGCAATGGCG 59.620 55.000 0.00 0.00 37.85 5.69
4473 4753 0.379669 CGAGGATCAACTGCAATGGC 59.620 55.000 0.00 0.00 36.05 4.40
4474 4754 1.019673 CCGAGGATCAACTGCAATGG 58.980 55.000 0.00 0.00 33.17 3.16
4475 4755 1.019673 CCCGAGGATCAACTGCAATG 58.980 55.000 0.00 0.00 33.17 2.82
4476 4756 0.620556 ACCCGAGGATCAACTGCAAT 59.379 50.000 0.00 0.00 33.17 3.56
4477 4757 0.036388 GACCCGAGGATCAACTGCAA 60.036 55.000 0.00 0.00 33.17 4.08
4478 4758 0.904865 AGACCCGAGGATCAACTGCA 60.905 55.000 0.00 0.00 33.17 4.41
4479 4759 0.179097 GAGACCCGAGGATCAACTGC 60.179 60.000 0.00 0.00 33.17 4.40
4480 4760 1.135915 CAGAGACCCGAGGATCAACTG 59.864 57.143 0.00 0.00 33.17 3.16
4481 4761 1.272760 ACAGAGACCCGAGGATCAACT 60.273 52.381 0.00 0.00 33.17 3.16
4482 4762 1.187087 ACAGAGACCCGAGGATCAAC 58.813 55.000 0.00 0.00 33.17 3.18
4483 4763 1.550524 CAACAGAGACCCGAGGATCAA 59.449 52.381 0.00 0.00 33.17 2.57
4484 4764 1.186200 CAACAGAGACCCGAGGATCA 58.814 55.000 0.00 0.00 33.17 2.92
4485 4765 1.407258 CTCAACAGAGACCCGAGGATC 59.593 57.143 0.00 0.00 0.00 3.36
4486 4766 1.006043 TCTCAACAGAGACCCGAGGAT 59.994 52.381 0.00 0.00 33.60 3.24
4487 4767 0.404426 TCTCAACAGAGACCCGAGGA 59.596 55.000 0.00 0.00 33.60 3.71
4488 4768 2.962882 TCTCAACAGAGACCCGAGG 58.037 57.895 0.00 0.00 33.60 4.63
4495 4775 1.996798 AAGGACCGTCTCAACAGAGA 58.003 50.000 0.00 0.00 36.10 3.10
4496 4776 4.082190 TCAATAAGGACCGTCTCAACAGAG 60.082 45.833 0.00 0.00 0.00 3.35
4497 4777 3.830178 TCAATAAGGACCGTCTCAACAGA 59.170 43.478 0.00 0.00 0.00 3.41
4498 4778 3.927142 GTCAATAAGGACCGTCTCAACAG 59.073 47.826 0.00 0.00 0.00 3.16
4499 4779 3.576982 AGTCAATAAGGACCGTCTCAACA 59.423 43.478 0.00 0.00 38.59 3.33
4500 4780 4.189639 AGTCAATAAGGACCGTCTCAAC 57.810 45.455 0.00 0.00 38.59 3.18
4501 4781 4.884668 AAGTCAATAAGGACCGTCTCAA 57.115 40.909 0.00 0.00 38.59 3.02
4502 4782 4.401519 CCTAAGTCAATAAGGACCGTCTCA 59.598 45.833 0.00 0.00 38.59 3.27
4503 4783 4.202131 CCCTAAGTCAATAAGGACCGTCTC 60.202 50.000 0.00 0.00 38.59 3.36
4504 4784 3.705072 CCCTAAGTCAATAAGGACCGTCT 59.295 47.826 0.00 0.00 38.59 4.18
4505 4785 3.740452 GCCCTAAGTCAATAAGGACCGTC 60.740 52.174 0.00 0.00 38.59 4.79
4506 4786 2.169978 GCCCTAAGTCAATAAGGACCGT 59.830 50.000 0.00 0.00 38.59 4.83
4507 4787 2.802057 CGCCCTAAGTCAATAAGGACCG 60.802 54.545 0.00 0.00 38.59 4.79
4508 4788 2.835027 CGCCCTAAGTCAATAAGGACC 58.165 52.381 0.00 0.00 38.59 4.46
4509 4789 2.210961 GCGCCCTAAGTCAATAAGGAC 58.789 52.381 0.00 0.00 38.08 3.85
4510 4790 1.140252 GGCGCCCTAAGTCAATAAGGA 59.860 52.381 18.11 0.00 31.64 3.36
4511 4791 1.141053 AGGCGCCCTAAGTCAATAAGG 59.859 52.381 26.15 0.00 28.47 2.69
4512 4792 2.484889 GAGGCGCCCTAAGTCAATAAG 58.515 52.381 26.15 0.00 31.76 1.73
4513 4793 1.202486 CGAGGCGCCCTAAGTCAATAA 60.202 52.381 26.15 0.00 31.76 1.40
4514 4794 0.387929 CGAGGCGCCCTAAGTCAATA 59.612 55.000 26.15 0.00 31.76 1.90
4515 4795 1.144057 CGAGGCGCCCTAAGTCAAT 59.856 57.895 26.15 0.00 31.76 2.57
4516 4796 2.577059 CGAGGCGCCCTAAGTCAA 59.423 61.111 26.15 0.00 31.76 3.18
4546 4826 2.125106 CTTCGGGAGGGCCGAAAG 60.125 66.667 0.00 0.00 46.54 2.62
4547 4827 2.926242 ACTTCGGGAGGGCCGAAA 60.926 61.111 0.00 0.00 46.54 3.46
4548 4828 3.702048 CACTTCGGGAGGGCCGAA 61.702 66.667 0.00 0.00 45.45 4.30
4560 4840 4.115199 ATCCCAGGCGGCCACTTC 62.115 66.667 23.09 0.00 0.00 3.01
4561 4841 4.431131 CATCCCAGGCGGCCACTT 62.431 66.667 23.09 0.00 0.00 3.16
4573 4853 2.922234 CCTGGAGAAGGGCATCCC 59.078 66.667 0.00 0.00 45.90 3.85
4589 4869 2.364202 ATCGGGAGAAGGACGATGTCC 61.364 57.143 7.92 7.92 46.86 4.02
4590 4870 1.033574 ATCGGGAGAAGGACGATGTC 58.966 55.000 0.00 0.00 44.66 3.06
4591 4871 3.209091 ATCGGGAGAAGGACGATGT 57.791 52.632 0.00 0.00 44.66 3.06
4602 4882 2.105128 GGTGACGCTCATCGGGAG 59.895 66.667 1.23 1.23 46.93 4.30
4625 4905 4.873129 CACGAGATGGCGTCCGGG 62.873 72.222 17.66 12.20 43.59 5.73
4626 4906 4.873129 CCACGAGATGGCGTCCGG 62.873 72.222 17.66 0.00 43.24 5.14
4634 4914 1.007964 CTCTAGGCGCCACGAGATG 60.008 63.158 30.25 18.03 0.00 2.90
4635 4915 1.448922 GACTCTAGGCGCCACGAGAT 61.449 60.000 36.44 25.35 0.00 2.75
4636 4916 2.045242 ACTCTAGGCGCCACGAGA 60.045 61.111 36.44 28.92 0.00 4.04
4637 4917 1.658686 AAGACTCTAGGCGCCACGAG 61.659 60.000 31.36 31.36 0.00 4.18
4638 4918 1.654954 GAAGACTCTAGGCGCCACGA 61.655 60.000 31.54 22.42 0.00 4.35
4639 4919 1.226717 GAAGACTCTAGGCGCCACG 60.227 63.158 31.54 19.15 0.00 4.94
4640 4920 1.142097 GGAAGACTCTAGGCGCCAC 59.858 63.158 31.54 12.08 0.00 5.01
4641 4921 2.415608 CGGAAGACTCTAGGCGCCA 61.416 63.158 31.54 14.00 0.00 5.69
4642 4922 2.413765 CGGAAGACTCTAGGCGCC 59.586 66.667 21.89 21.89 0.00 6.53
4643 4923 2.119655 TCCGGAAGACTCTAGGCGC 61.120 63.158 0.00 0.00 0.00 6.53
4644 4924 1.728672 GTCCGGAAGACTCTAGGCG 59.271 63.158 5.23 0.00 42.69 5.52
4645 4925 1.728672 CGTCCGGAAGACTCTAGGC 59.271 63.158 12.53 0.00 43.91 3.93
4646 4926 0.748729 AGCGTCCGGAAGACTCTAGG 60.749 60.000 22.33 0.00 43.91 3.02
4647 4927 1.064357 GAAGCGTCCGGAAGACTCTAG 59.936 57.143 22.33 0.00 39.67 2.43
4648 4928 1.093159 GAAGCGTCCGGAAGACTCTA 58.907 55.000 22.33 0.00 39.67 2.43
4649 4929 0.609681 AGAAGCGTCCGGAAGACTCT 60.610 55.000 22.33 17.12 42.42 3.24
4650 4930 0.179158 GAGAAGCGTCCGGAAGACTC 60.179 60.000 22.33 19.34 43.91 3.36
4651 4931 0.609681 AGAGAAGCGTCCGGAAGACT 60.610 55.000 22.33 15.42 43.91 3.24
4652 4932 1.093159 TAGAGAAGCGTCCGGAAGAC 58.907 55.000 22.33 12.20 42.54 3.01
4653 4933 1.093159 GTAGAGAAGCGTCCGGAAGA 58.907 55.000 22.33 0.00 0.00 2.87
4654 4934 1.096416 AGTAGAGAAGCGTCCGGAAG 58.904 55.000 13.59 13.59 0.00 3.46
4655 4935 2.286872 CTAGTAGAGAAGCGTCCGGAA 58.713 52.381 5.23 0.00 0.00 4.30
4656 4936 1.474677 CCTAGTAGAGAAGCGTCCGGA 60.475 57.143 0.00 0.00 0.00 5.14
4657 4937 0.945813 CCTAGTAGAGAAGCGTCCGG 59.054 60.000 0.00 0.00 0.00 5.14
4658 4938 1.598601 GACCTAGTAGAGAAGCGTCCG 59.401 57.143 0.00 0.00 0.00 4.79
4659 4939 1.948834 GGACCTAGTAGAGAAGCGTCC 59.051 57.143 0.00 2.15 0.00 4.79
4660 4940 2.921821 AGGACCTAGTAGAGAAGCGTC 58.078 52.381 0.00 0.00 0.00 5.19
4661 4941 3.018149 CAAGGACCTAGTAGAGAAGCGT 58.982 50.000 0.00 0.00 0.00 5.07
4662 4942 3.018149 ACAAGGACCTAGTAGAGAAGCG 58.982 50.000 0.00 0.00 0.00 4.68
4663 4943 4.035441 CGTACAAGGACCTAGTAGAGAAGC 59.965 50.000 0.00 0.00 0.00 3.86
4664 4944 4.035441 GCGTACAAGGACCTAGTAGAGAAG 59.965 50.000 0.00 0.00 0.00 2.85
4665 4945 3.944015 GCGTACAAGGACCTAGTAGAGAA 59.056 47.826 0.00 0.00 0.00 2.87
4666 4946 3.539604 GCGTACAAGGACCTAGTAGAGA 58.460 50.000 0.00 0.00 0.00 3.10
4667 4947 2.287373 CGCGTACAAGGACCTAGTAGAG 59.713 54.545 0.00 0.00 0.00 2.43
4668 4948 2.283298 CGCGTACAAGGACCTAGTAGA 58.717 52.381 0.00 0.00 0.00 2.59
4669 4949 1.332997 CCGCGTACAAGGACCTAGTAG 59.667 57.143 4.92 0.00 0.00 2.57
4670 4950 1.382522 CCGCGTACAAGGACCTAGTA 58.617 55.000 4.92 0.00 0.00 1.82
4671 4951 1.941999 GCCGCGTACAAGGACCTAGT 61.942 60.000 4.92 0.00 0.00 2.57
4672 4952 1.226888 GCCGCGTACAAGGACCTAG 60.227 63.158 4.92 0.00 0.00 3.02
4673 4953 2.713967 GGCCGCGTACAAGGACCTA 61.714 63.158 4.92 0.00 0.00 3.08
4674 4954 4.078516 GGCCGCGTACAAGGACCT 62.079 66.667 4.92 0.00 0.00 3.85
4675 4955 3.675619 ATGGCCGCGTACAAGGACC 62.676 63.158 4.92 8.09 33.63 4.46
4676 4956 2.125269 ATGGCCGCGTACAAGGAC 60.125 61.111 4.92 5.22 35.66 3.85
4677 4957 2.185867 GATGGCCGCGTACAAGGA 59.814 61.111 4.92 0.00 0.00 3.36
4678 4958 3.261951 CGATGGCCGCGTACAAGG 61.262 66.667 4.92 0.00 0.00 3.61
4718 4998 5.506317 GCAAATATCCCAGATCAAACCGAAG 60.506 44.000 0.00 0.00 0.00 3.79
4719 4999 4.338118 GCAAATATCCCAGATCAAACCGAA 59.662 41.667 0.00 0.00 0.00 4.30
4720 5000 3.882888 GCAAATATCCCAGATCAAACCGA 59.117 43.478 0.00 0.00 0.00 4.69
4721 5001 3.885297 AGCAAATATCCCAGATCAAACCG 59.115 43.478 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.