Multiple sequence alignment - TraesCS2A01G434800

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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 TraesCS2A01G434800 chr2A 100.000 6957 0 0 1 6957 686874028 686880984 0.000000e+00 12848.0
1 TraesCS2A01G434800 chr2B 94.286 4078 164 28 632 4678 650399322 650403361 0.000000e+00 6176.0
2 TraesCS2A01G434800 chr2B 93.173 498 18 6 4586 5083 650403356 650403837 0.000000e+00 717.0
3 TraesCS2A01G434800 chr2B 91.714 350 19 5 5439 5784 650404552 650404895 1.760000e-130 477.0
4 TraesCS2A01G434800 chr2B 83.768 499 58 14 3 498 650356040 650356518 1.060000e-122 451.0
5 TraesCS2A01G434800 chr2B 95.122 205 7 3 5082 5286 650403996 650404197 3.130000e-83 320.0
6 TraesCS2A01G434800 chr2B 92.513 187 12 2 5783 5969 650405062 650405246 4.140000e-67 267.0
7 TraesCS2A01G434800 chr2B 87.500 120 12 1 488 607 650396995 650397111 1.220000e-27 135.0
8 TraesCS2A01G434800 chr2B 100.000 31 0 0 5971 6001 650405271 650405301 2.710000e-04 58.4
9 TraesCS2A01G434800 chr2D 92.297 4336 206 60 429 4678 544664516 544668809 0.000000e+00 6039.0
10 TraesCS2A01G434800 chr2D 90.509 1454 93 24 4586 6027 544668804 544670224 0.000000e+00 1879.0
11 TraesCS2A01G434800 chr2D 89.325 637 53 8 6328 6951 544670772 544671406 0.000000e+00 785.0
12 TraesCS2A01G434800 chr2D 85.101 396 55 2 3 398 544662330 544662721 1.090000e-107 401.0
13 TraesCS2A01G434800 chr2D 89.369 301 18 8 6028 6324 544670280 544670570 3.960000e-97 366.0


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 TraesCS2A01G434800 chr2A 686874028 686880984 6956 False 12848.000000 12848 100.000000 1 6957 1 chr2A.!!$F1 6956
1 TraesCS2A01G434800 chr2B 650396995 650405301 8306 False 1164.342857 6176 93.472571 488 6001 7 chr2B.!!$F2 5513
2 TraesCS2A01G434800 chr2D 544662330 544671406 9076 False 1894.000000 6039 89.320200 3 6951 5 chr2D.!!$F1 6948

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
398 399 0.034616 GCCCGAGAGCTGCATCTTAT 59.965 55.000 1.02 0.00 0.00 1.73 F
803 4761 0.824759 ATTGAGCGGTGGAGAGTACC 59.175 55.000 0.00 0.00 34.81 3.34 F
1299 5264 1.134128 TGCCTTTGAGACTTGAGCACA 60.134 47.619 0.00 0.00 0.00 4.57 F
1307 5272 1.762222 GACTTGAGCACACGCGTGTT 61.762 55.000 40.13 28.22 45.50 3.32 F
2776 6762 2.623915 CGGAGGGGATACGGTAGCG 61.624 68.421 13.69 13.69 37.60 4.26 F
3677 7665 1.402968 TCTCGTAGTGGGAACATACGC 59.597 52.381 0.00 0.00 46.14 4.42 F
5339 9778 1.464608 GTGATGTTACATGTGCTGCGT 59.535 47.619 9.11 0.00 0.00 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 5320 0.321919 ATCACCACGCTTGCATCAGT 60.322 50.0 0.00 0.00 0.00 3.41 R
2452 6435 2.107950 TTTGGGGCAAGACTATCACG 57.892 50.0 0.00 0.00 0.00 4.35 R
2876 6862 2.237143 TCTTGGGCACAGAGTAATCCAG 59.763 50.0 0.00 0.00 0.00 3.86 R
3110 7097 3.223435 AGGACATGACCACCGTAGATAG 58.777 50.0 16.63 0.00 0.00 2.08 R
4117 8106 0.329596 GGTTGACCTCTGAAGCCCAT 59.670 55.0 0.00 0.00 0.00 4.00 R
5441 9883 0.097674 GCTGTATGAAGCTTGTGCGG 59.902 55.0 2.10 2.18 45.42 5.69 R
6717 11649 0.457035 CATGGAGGCATGGGTTTTCG 59.543 55.0 0.00 0.00 0.00 3.46 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
44 45 2.306847 GCCTTCCAGGTTGTGAAGAAA 58.693 47.619 0.00 0.00 40.30 2.52
47 48 2.727123 TCCAGGTTGTGAAGAAAGCA 57.273 45.000 0.00 0.00 0.00 3.91
51 52 2.033801 CAGGTTGTGAAGAAAGCAGTGG 59.966 50.000 0.00 0.00 0.00 4.00
52 53 2.092429 AGGTTGTGAAGAAAGCAGTGGA 60.092 45.455 0.00 0.00 0.00 4.02
67 68 1.284198 AGTGGACTCGGCTTCTAGGTA 59.716 52.381 0.00 0.00 0.00 3.08
76 77 2.287668 CGGCTTCTAGGTATCACTTCCG 60.288 54.545 0.00 0.00 0.00 4.30
80 81 4.142227 GCTTCTAGGTATCACTTCCGAACA 60.142 45.833 0.00 0.00 0.00 3.18
84 85 6.942976 TCTAGGTATCACTTCCGAACAAAAT 58.057 36.000 0.00 0.00 0.00 1.82
90 91 1.265905 ACTTCCGAACAAAATCACCGC 59.734 47.619 0.00 0.00 0.00 5.68
99 100 2.238646 ACAAAATCACCGCCCATCTCTA 59.761 45.455 0.00 0.00 0.00 2.43
113 114 4.705554 CATCTCTATGATGCACGTTGTC 57.294 45.455 0.00 0.00 44.96 3.18
115 116 3.181486 ATCTCTATGATGCACGTTGTCGT 60.181 43.478 0.00 0.00 41.60 4.34
118 119 8.329637 ATCTCTATGATGCACGTTGTCGTACA 62.330 42.308 0.00 0.00 45.41 2.90
119 120 9.694018 ATCTCTATGATGCACGTTGTCGTACAA 62.694 40.741 0.00 0.00 44.68 2.41
130 131 4.209703 CGTTGTCGTACAAACTACACCAAT 59.790 41.667 9.46 0.00 40.15 3.16
135 136 3.122278 CGTACAAACTACACCAATGACCG 59.878 47.826 0.00 0.00 0.00 4.79
142 143 0.320374 ACACCAATGACCGTCATCGT 59.680 50.000 14.42 10.70 35.76 3.73
146 147 2.429250 ACCAATGACCGTCATCGTGATA 59.571 45.455 14.42 0.00 35.76 2.15
152 153 4.131596 TGACCGTCATCGTGATATAGTCA 58.868 43.478 0.00 0.00 35.01 3.41
153 154 4.577283 TGACCGTCATCGTGATATAGTCAA 59.423 41.667 0.00 0.00 38.90 3.18
154 155 4.856664 ACCGTCATCGTGATATAGTCAAC 58.143 43.478 0.00 0.00 38.90 3.18
155 156 4.337274 ACCGTCATCGTGATATAGTCAACA 59.663 41.667 0.00 0.00 38.90 3.33
167 168 7.657761 GTGATATAGTCAACATTAGTGGGGAAG 59.342 40.741 0.00 0.00 38.90 3.46
169 170 3.256704 AGTCAACATTAGTGGGGAAGGA 58.743 45.455 0.00 0.00 0.00 3.36
198 199 6.401047 AGCAATGATTAGGGTGATGATTTG 57.599 37.500 0.00 0.00 0.00 2.32
207 208 2.507471 GGGTGATGATTTGGAGAGGAGT 59.493 50.000 0.00 0.00 0.00 3.85
219 220 2.904434 GGAGAGGAGTAAGGTGGTTTCA 59.096 50.000 0.00 0.00 0.00 2.69
224 225 3.974642 AGGAGTAAGGTGGTTTCAAGAGT 59.025 43.478 0.00 0.00 0.00 3.24
227 228 6.958192 AGGAGTAAGGTGGTTTCAAGAGTATA 59.042 38.462 0.00 0.00 0.00 1.47
229 230 6.628185 AGTAAGGTGGTTTCAAGAGTATACG 58.372 40.000 0.00 0.00 0.00 3.06
231 232 5.069501 AGGTGGTTTCAAGAGTATACGAC 57.930 43.478 0.00 0.00 0.00 4.34
252 253 4.315803 ACAAAGATGACGACAGTTAAGGG 58.684 43.478 0.00 0.00 0.00 3.95
255 256 0.892755 ATGACGACAGTTAAGGGCGA 59.107 50.000 9.15 0.00 0.00 5.54
259 260 0.179134 CGACAGTTAAGGGCGAGAGG 60.179 60.000 0.00 0.00 0.00 3.69
265 266 2.465010 TTAAGGGCGAGAGGGGGTGA 62.465 60.000 0.00 0.00 0.00 4.02
277 278 0.624254 GGGGGTGAGGGTAGAAAAGG 59.376 60.000 0.00 0.00 0.00 3.11
297 298 4.799564 GGCAACACCTTCATAATTGGAA 57.200 40.909 0.00 0.00 34.51 3.53
315 316 8.876275 AATTGGAATTTTTATCGATCATGTGG 57.124 30.769 0.00 0.00 0.00 4.17
321 322 2.793278 TATCGATCATGTGGACGTGG 57.207 50.000 0.00 0.00 33.80 4.94
341 342 5.751028 CGTGGAAAACCACATGTTACATTTT 59.249 36.000 17.53 0.70 40.38 1.82
342 343 6.074569 CGTGGAAAACCACATGTTACATTTTC 60.075 38.462 17.53 17.39 40.38 2.29
343 344 5.980116 TGGAAAACCACATGTTACATTTTCG 59.020 36.000 18.23 0.00 37.07 3.46
344 345 6.183360 TGGAAAACCACATGTTACATTTTCGA 60.183 34.615 18.23 14.84 37.07 3.71
345 346 6.866248 GGAAAACCACATGTTACATTTTCGAT 59.134 34.615 18.23 0.00 37.07 3.59
347 348 8.964420 AAAACCACATGTTACATTTTCGATAG 57.036 30.769 0.00 0.00 35.67 2.08
382 383 2.546494 CCAATCCGAGCAATCGCCC 61.546 63.158 0.00 0.00 39.83 6.13
385 386 2.978452 AATCCGAGCAATCGCCCGAG 62.978 60.000 0.00 0.00 42.84 4.63
387 388 2.656651 CGAGCAATCGCCCGAGAG 60.657 66.667 0.00 0.00 42.84 3.20
398 399 0.034616 GCCCGAGAGCTGCATCTTAT 59.965 55.000 1.02 0.00 0.00 1.73
400 401 1.342496 CCCGAGAGCTGCATCTTATCA 59.658 52.381 1.02 0.00 0.00 2.15
401 402 2.028294 CCCGAGAGCTGCATCTTATCAT 60.028 50.000 1.02 0.00 0.00 2.45
402 403 3.556633 CCCGAGAGCTGCATCTTATCATT 60.557 47.826 1.02 0.00 0.00 2.57
404 405 5.233225 CCGAGAGCTGCATCTTATCATTAA 58.767 41.667 1.02 0.00 0.00 1.40
405 406 5.873712 CCGAGAGCTGCATCTTATCATTAAT 59.126 40.000 1.02 0.00 0.00 1.40
406 407 6.370994 CCGAGAGCTGCATCTTATCATTAATT 59.629 38.462 1.02 0.00 0.00 1.40
408 409 8.379161 CGAGAGCTGCATCTTATCATTAATTAC 58.621 37.037 1.02 0.00 0.00 1.89
409 410 9.212641 GAGAGCTGCATCTTATCATTAATTACA 57.787 33.333 1.02 0.00 0.00 2.41
410 411 8.997323 AGAGCTGCATCTTATCATTAATTACAC 58.003 33.333 1.02 0.00 0.00 2.90
411 412 8.915057 AGCTGCATCTTATCATTAATTACACT 57.085 30.769 1.02 0.00 0.00 3.55
412 413 8.997323 AGCTGCATCTTATCATTAATTACACTC 58.003 33.333 1.02 0.00 0.00 3.51
413 414 8.777413 GCTGCATCTTATCATTAATTACACTCA 58.223 33.333 0.00 0.00 0.00 3.41
479 2244 6.435292 AGTAAATATTATGTTCGCCTCCCT 57.565 37.500 0.00 0.00 0.00 4.20
481 2246 4.974645 AATATTATGTTCGCCTCCCTCA 57.025 40.909 0.00 0.00 0.00 3.86
483 2248 1.271856 TTATGTTCGCCTCCCTCACA 58.728 50.000 0.00 0.00 0.00 3.58
485 2250 2.432628 GTTCGCCTCCCTCACACG 60.433 66.667 0.00 0.00 0.00 4.49
486 2251 2.915659 TTCGCCTCCCTCACACGT 60.916 61.111 0.00 0.00 0.00 4.49
510 2280 2.050836 TTGGTCCGGCATGTCACACT 62.051 55.000 0.00 0.00 0.00 3.55
545 2315 1.406219 CTCCGTTGTGTCGCTCATCG 61.406 60.000 5.82 5.82 40.15 3.84
554 2324 2.510012 CGCTCATCGAAGGCAGCA 60.510 61.111 0.00 0.00 41.67 4.41
555 2325 2.102438 CGCTCATCGAAGGCAGCAA 61.102 57.895 0.00 0.00 41.67 3.91
556 2326 1.427020 GCTCATCGAAGGCAGCAAC 59.573 57.895 0.00 0.00 0.00 4.17
580 2350 3.119743 TCGTCGGCTTATTATATCACCGG 60.120 47.826 0.00 0.00 40.95 5.28
591 2361 3.791640 TCACCGGCATGTGAGACT 58.208 55.556 0.00 0.00 40.22 3.24
599 2369 1.949525 GGCATGTGAGACTGTTTGTGT 59.050 47.619 0.00 0.00 0.00 3.72
633 4285 4.313020 AGCCAAAACTCATCTCTCCATT 57.687 40.909 0.00 0.00 0.00 3.16
733 4691 8.890718 AGTTAAGTGTTAAGAGTTGTCCTTTTC 58.109 33.333 3.02 0.00 0.00 2.29
770 4728 4.343814 TGATGTACTGAAGGACTCACACAA 59.656 41.667 0.00 0.00 31.09 3.33
771 4729 4.322080 TGTACTGAAGGACTCACACAAG 57.678 45.455 0.00 0.00 0.00 3.16
803 4761 0.824759 ATTGAGCGGTGGAGAGTACC 59.175 55.000 0.00 0.00 34.81 3.34
910 4872 1.579698 CTGGTCCAGCAGATCGATTG 58.420 55.000 5.79 1.24 0.00 2.67
1075 5040 2.736826 CCGCCTTCTTCCCCCTCTC 61.737 68.421 0.00 0.00 0.00 3.20
1087 5052 2.328589 CCCTCTCCCCCTCTCTCCA 61.329 68.421 0.00 0.00 0.00 3.86
1281 5246 3.875510 AAGGAGCCAGCCCACTTGC 62.876 63.158 0.00 0.00 34.79 4.01
1285 5250 2.919328 GCCAGCCCACTTGCCTTT 60.919 61.111 0.00 0.00 0.00 3.11
1293 5258 1.610522 CCCACTTGCCTTTGAGACTTG 59.389 52.381 0.00 0.00 0.00 3.16
1296 5261 2.031333 CACTTGCCTTTGAGACTTGAGC 60.031 50.000 0.00 0.00 0.00 4.26
1299 5264 1.134128 TGCCTTTGAGACTTGAGCACA 60.134 47.619 0.00 0.00 0.00 4.57
1307 5272 1.762222 GACTTGAGCACACGCGTGTT 61.762 55.000 40.13 28.22 45.50 3.32
1345 5315 4.386652 GCCATGTGCTTGTTGAAATGTTAG 59.613 41.667 0.00 0.00 36.87 2.34
1348 5318 5.574891 TGTGCTTGTTGAAATGTTAGTGT 57.425 34.783 0.00 0.00 0.00 3.55
1350 5320 7.089770 TGTGCTTGTTGAAATGTTAGTGTTA 57.910 32.000 0.00 0.00 0.00 2.41
1352 5322 7.148154 TGTGCTTGTTGAAATGTTAGTGTTACT 60.148 33.333 0.00 0.00 0.00 2.24
1353 5323 7.165812 GTGCTTGTTGAAATGTTAGTGTTACTG 59.834 37.037 0.00 0.00 0.00 2.74
1354 5324 7.066404 TGCTTGTTGAAATGTTAGTGTTACTGA 59.934 33.333 0.00 0.00 0.00 3.41
1355 5325 8.076178 GCTTGTTGAAATGTTAGTGTTACTGAT 58.924 33.333 0.00 0.00 0.00 2.90
1356 5326 9.385902 CTTGTTGAAATGTTAGTGTTACTGATG 57.614 33.333 0.00 0.00 0.00 3.07
1357 5327 7.359595 TGTTGAAATGTTAGTGTTACTGATGC 58.640 34.615 0.00 0.00 0.00 3.91
1358 5328 7.012799 TGTTGAAATGTTAGTGTTACTGATGCA 59.987 33.333 0.00 0.00 0.00 3.96
1359 5329 7.503521 TGAAATGTTAGTGTTACTGATGCAA 57.496 32.000 0.00 0.00 0.00 4.08
1443 5413 3.925090 GCCCGATCCGGTAGGTGG 61.925 72.222 0.00 0.00 46.80 4.61
1484 5456 5.647658 TGTATGATTTGTGCTTGAAGGTAGG 59.352 40.000 0.00 0.00 0.00 3.18
1737 5719 9.520515 AATTAATTGTACCAGTTCAGAAGATGT 57.479 29.630 0.00 0.00 0.00 3.06
1741 5723 6.174720 TGTACCAGTTCAGAAGATGTTCTT 57.825 37.500 1.60 0.00 41.40 2.52
1849 5831 7.216494 TGAAATGCATCTATAACCGAAGATGA 58.784 34.615 14.75 2.83 37.52 2.92
1917 5899 9.356433 GAGGTGACTATTAGAGAAACTACAAAC 57.644 37.037 0.00 0.00 44.43 2.93
2026 6009 7.006509 AGCATTTATGGTTTATATGCAGACCT 58.993 34.615 0.00 0.00 34.35 3.85
2027 6010 7.175641 AGCATTTATGGTTTATATGCAGACCTC 59.824 37.037 0.00 0.00 34.35 3.85
2147 6130 6.473455 GTGAGCAACTATATGTTCCATTTTGC 59.527 38.462 0.00 0.00 36.63 3.68
2452 6435 9.899226 GTTTCCTATTCAACCATAAATATGCTC 57.101 33.333 0.00 0.00 32.40 4.26
2646 6632 4.242475 TCCTGCACAGAGTAAATACAACG 58.758 43.478 0.00 0.00 0.00 4.10
2650 6636 3.181520 GCACAGAGTAAATACAACGCTGG 60.182 47.826 10.86 2.77 45.58 4.85
2776 6762 2.623915 CGGAGGGGATACGGTAGCG 61.624 68.421 13.69 13.69 37.60 4.26
2791 6777 2.787680 GGTAGCGCTATACTGAAACACG 59.212 50.000 21.96 0.00 0.00 4.49
2876 6862 3.057734 CGGTGGAGTAGACTTTGACAAC 58.942 50.000 0.00 0.00 0.00 3.32
2996 6983 5.231779 GTCTTCATCTTGAGTGACATGATCG 59.768 44.000 0.00 0.00 40.03 3.69
3110 7097 5.125257 GTGGAAGTAGAGGTAGTAGTGGTTC 59.875 48.000 0.00 0.00 0.00 3.62
3391 7379 8.418597 AACTAGTAGTCTGGAACTGTTGATTA 57.581 34.615 2.58 0.00 39.11 1.75
3512 7500 4.361451 AACAAAATATCAGGCAGAAGCG 57.639 40.909 0.00 0.00 43.41 4.68
3518 7506 5.984695 AATATCAGGCAGAAGCGACTATA 57.015 39.130 0.00 0.00 43.41 1.31
3677 7665 1.402968 TCTCGTAGTGGGAACATACGC 59.597 52.381 0.00 0.00 46.14 4.42
3755 7743 5.815233 TGGATTTAGGGTTTTGAATTGCA 57.185 34.783 0.00 0.00 0.00 4.08
3966 7955 2.302157 AGGAACCGGAGTAAAAGAGGTG 59.698 50.000 9.46 0.00 35.08 4.00
3984 7973 9.614792 AAAGAGGTGTGTTATTATATCTTGGAC 57.385 33.333 0.00 0.00 0.00 4.02
4021 8010 8.122952 GCAGTAACATGAGGTATTCATTTGTAC 58.877 37.037 0.00 0.00 44.14 2.90
4036 8025 6.098679 TCATTTGTACAATATGCTTGTTGGC 58.901 36.000 9.56 6.53 34.11 4.52
4065 8054 7.545265 GGCTATAGATGATCTTACTTCAAGCAG 59.455 40.741 3.21 0.00 33.94 4.24
4090 8079 4.608170 AGGGGTTGTGGTTGATATGAAT 57.392 40.909 0.00 0.00 0.00 2.57
4117 8106 1.948611 GCGGGAGAATGGCAACTGTTA 60.949 52.381 0.00 0.00 37.61 2.41
4127 8116 1.474077 GGCAACTGTTATGGGCTTCAG 59.526 52.381 0.00 0.00 0.00 3.02
4155 8144 7.753580 GGTCAACCTTTACATAAGCATTACAAC 59.246 37.037 0.00 0.00 30.46 3.32
4184 8173 6.474140 TTTGAGATTTCTATGCATGCCATT 57.526 33.333 16.68 2.45 35.34 3.16
4189 8178 7.120923 AGATTTCTATGCATGCCATTTCTTT 57.879 32.000 16.68 0.00 35.34 2.52
4195 8184 5.664294 ATGCATGCCATTTCTTTTCTGTA 57.336 34.783 16.68 0.00 0.00 2.74
4281 8270 1.680338 AACAAAGCACTCCCAGACAC 58.320 50.000 0.00 0.00 0.00 3.67
4300 8289 8.950210 CCAGACACTTATGAGTAACATCATTTT 58.050 33.333 0.00 0.00 40.40 1.82
4340 8358 9.733556 TTCCAGTAATCATATTGTACAGTTTGT 57.266 29.630 8.30 0.00 0.00 2.83
4405 8423 6.605594 CCAGCCACCCTTATAAAAGAACATAA 59.394 38.462 0.00 0.00 34.37 1.90
4448 8466 7.168972 CAGACCGAGATTGAAGTTATGATTCTC 59.831 40.741 0.00 0.00 0.00 2.87
4467 8485 3.191581 TCTCGCTAGAGTCAAAGAAGGTG 59.808 47.826 0.00 0.00 44.65 4.00
4480 8498 3.515602 AGAAGGTGGATGCTTTTCTGT 57.484 42.857 0.00 0.00 0.00 3.41
4483 8501 5.574188 AGAAGGTGGATGCTTTTCTGTATT 58.426 37.500 0.00 0.00 0.00 1.89
4504 8522 1.656587 TTTGAAGGGCCTGAGAGCTA 58.343 50.000 6.92 0.00 0.00 3.32
4523 8541 9.604626 GAGAGCTAATGCATATTTATGTTTGAC 57.395 33.333 0.00 0.00 42.74 3.18
4532 8550 7.009083 TGCATATTTATGTTTGACGAATGCAAC 59.991 33.333 3.86 0.00 42.83 4.17
4566 8584 6.715280 AGTCATGACTCCTGTTATTCACAAT 58.285 36.000 22.89 0.00 36.92 2.71
4567 8585 7.170965 AGTCATGACTCCTGTTATTCACAATT 58.829 34.615 22.89 0.00 36.92 2.32
4568 8586 7.667219 AGTCATGACTCCTGTTATTCACAATTT 59.333 33.333 22.89 0.00 36.92 1.82
4569 8587 8.299570 GTCATGACTCCTGTTATTCACAATTTT 58.700 33.333 18.83 0.00 33.87 1.82
4762 8870 5.495926 ACTTTAGAGATGGCATATGAGGG 57.504 43.478 6.97 0.00 0.00 4.30
4895 9003 5.030147 TCTCAAGGATTTCCAGGTAAGCTA 58.970 41.667 0.00 0.00 38.89 3.32
4962 9070 2.610374 TGTGTTTCTTGGTACTTGACGC 59.390 45.455 0.00 0.00 0.00 5.19
5075 9183 6.719370 AGGCAACATATGGTAAGTTTGAAGAA 59.281 34.615 7.80 0.00 41.41 2.52
5119 9385 2.443416 TCCTCTCTCGGATCGTTTCAA 58.557 47.619 0.00 0.00 0.00 2.69
5128 9394 2.532193 CGGATCGTTTCAATCGTCAACG 60.532 50.000 0.00 0.00 43.70 4.10
5251 9520 8.561738 ACGGTAATATATTTCCTTAATGCCAG 57.438 34.615 16.44 3.48 0.00 4.85
5330 9769 2.840038 TGCAGGAGAGGTGATGTTACAT 59.160 45.455 0.00 0.00 0.00 2.29
5334 9773 2.939103 GGAGAGGTGATGTTACATGTGC 59.061 50.000 9.11 1.72 0.00 4.57
5339 9778 1.464608 GTGATGTTACATGTGCTGCGT 59.535 47.619 9.11 0.00 0.00 5.24
5340 9779 2.670905 GTGATGTTACATGTGCTGCGTA 59.329 45.455 9.11 0.00 0.00 4.42
5347 9786 3.313012 ACATGTGCTGCGTAAAGACTA 57.687 42.857 0.00 0.00 0.00 2.59
5412 9851 2.674852 CGGGACATTGACTCACTTCATG 59.325 50.000 0.00 0.00 0.00 3.07
5441 9883 4.794248 TCATACATCAATACGCTGTTGC 57.206 40.909 0.00 0.00 0.00 4.17
5464 9935 2.159599 GCACAAGCTTCATACAGCAGTC 60.160 50.000 0.00 0.00 42.84 3.51
5514 9985 5.068460 TCAAAATTCGGGTCACACAGATTTT 59.932 36.000 0.00 0.00 0.00 1.82
5515 9986 5.529581 AAATTCGGGTCACACAGATTTTT 57.470 34.783 0.00 0.00 0.00 1.94
5572 10051 6.316390 CCTGATTTATACACCTCCACTTCAAC 59.684 42.308 0.00 0.00 0.00 3.18
5577 10056 3.470645 ACACCTCCACTTCAACACTAC 57.529 47.619 0.00 0.00 0.00 2.73
5706 10188 0.470766 TTGGTGGCGTACAGTTTCCT 59.529 50.000 0.00 0.00 0.00 3.36
5709 10191 2.104451 TGGTGGCGTACAGTTTCCTTTA 59.896 45.455 0.00 0.00 0.00 1.85
5753 10235 4.966965 TGGAGATCTTGTAAGACTCGAC 57.033 45.455 0.00 0.00 37.98 4.20
5767 10250 1.985895 ACTCGACTCCCATTTCCCTTT 59.014 47.619 0.00 0.00 0.00 3.11
5768 10251 2.375509 ACTCGACTCCCATTTCCCTTTT 59.624 45.455 0.00 0.00 0.00 2.27
5769 10252 3.181433 ACTCGACTCCCATTTCCCTTTTT 60.181 43.478 0.00 0.00 0.00 1.94
5820 10472 4.070630 CCAATTTGTTGGTGGTCATTGT 57.929 40.909 0.00 0.00 37.32 2.71
5823 10475 3.533606 TTTGTTGGTGGTCATTGTTGG 57.466 42.857 0.00 0.00 0.00 3.77
6081 10810 7.572814 TCTCAAATCATTATGTGATACACCCA 58.427 34.615 0.00 0.00 46.80 4.51
6113 10845 7.912778 TTTTCCCTAATTATCATTTCCCCTG 57.087 36.000 0.00 0.00 0.00 4.45
6129 10861 4.215109 TCCCCTGGATTTATGCTTTTAGC 58.785 43.478 0.00 0.00 42.82 3.09
6137 10869 8.396272 TGGATTTATGCTTTTAGCTAGGAATC 57.604 34.615 0.00 5.16 42.97 2.52
6144 10876 8.586879 ATGCTTTTAGCTAGGAATCTTTTTCT 57.413 30.769 0.00 0.00 42.97 2.52
6145 10877 8.045176 TGCTTTTAGCTAGGAATCTTTTTCTC 57.955 34.615 0.00 0.00 42.97 2.87
6146 10878 7.885399 TGCTTTTAGCTAGGAATCTTTTTCTCT 59.115 33.333 0.00 0.00 42.97 3.10
6147 10879 8.180920 GCTTTTAGCTAGGAATCTTTTTCTCTG 58.819 37.037 0.00 0.00 38.45 3.35
6183 10915 2.087646 GAAGAATGCCAAGACCTCCAC 58.912 52.381 0.00 0.00 0.00 4.02
6185 10917 0.038166 GAATGCCAAGACCTCCACCA 59.962 55.000 0.00 0.00 0.00 4.17
6217 10949 7.814264 ATCTTGTTATGACATTCCTCAATCC 57.186 36.000 0.00 0.00 35.29 3.01
6218 10950 5.817296 TCTTGTTATGACATTCCTCAATCCG 59.183 40.000 0.00 0.00 35.29 4.18
6219 10951 3.876914 TGTTATGACATTCCTCAATCCGC 59.123 43.478 0.00 0.00 0.00 5.54
6220 10952 2.715749 ATGACATTCCTCAATCCGCA 57.284 45.000 0.00 0.00 0.00 5.69
6232 10964 2.830923 TCAATCCGCATCCACCAAAAAT 59.169 40.909 0.00 0.00 0.00 1.82
6236 10968 2.099405 CCGCATCCACCAAAAATACCT 58.901 47.619 0.00 0.00 0.00 3.08
6237 10969 2.099098 CCGCATCCACCAAAAATACCTC 59.901 50.000 0.00 0.00 0.00 3.85
6239 10971 2.430694 GCATCCACCAAAAATACCTCCC 59.569 50.000 0.00 0.00 0.00 4.30
6309 11041 6.795144 ATGAAGAATTCCACCATTTGCATA 57.205 33.333 0.65 0.00 46.93 3.14
6314 11046 4.989279 ATTCCACCATTTGCATACACTC 57.011 40.909 0.00 0.00 0.00 3.51
6319 11051 4.261952 CCACCATTTGCATACACTCACAAA 60.262 41.667 0.00 0.00 36.53 2.83
6320 11052 4.919168 CACCATTTGCATACACTCACAAAG 59.081 41.667 0.00 0.00 35.65 2.77
6321 11053 4.826733 ACCATTTGCATACACTCACAAAGA 59.173 37.500 0.00 0.00 35.65 2.52
6322 11054 5.156355 CCATTTGCATACACTCACAAAGAC 58.844 41.667 0.00 0.00 35.65 3.01
6324 11056 5.673337 TTTGCATACACTCACAAAGACTC 57.327 39.130 0.00 0.00 0.00 3.36
6394 11323 0.765135 TCCCAACTCTTTGTCCCGGA 60.765 55.000 0.73 0.00 0.00 5.14
6401 11330 0.974383 TCTTTGTCCCGGAGAGGAAC 59.026 55.000 0.73 0.00 45.00 3.62
6431 11360 6.831976 ACACCCACTTAATCCTTCATCTATC 58.168 40.000 0.00 0.00 0.00 2.08
6442 11371 7.707624 ATCCTTCATCTATCTCTCTTGCTAG 57.292 40.000 0.00 0.00 0.00 3.42
6481 11411 1.702182 TCTTGGCAGCCAATTGTTCA 58.298 45.000 27.55 3.15 43.07 3.18
6484 11414 1.114119 TGGCAGCCAATTGTTCAGCA 61.114 50.000 13.33 0.00 0.00 4.41
6496 11426 7.148373 GCCAATTGTTCAGCAAATATTGACATT 60.148 33.333 4.43 0.00 40.91 2.71
6500 11430 9.715121 ATTGTTCAGCAAATATTGACATTCTTT 57.285 25.926 0.00 0.00 40.91 2.52
6514 11444 6.166279 TGACATTCTTTCCACATACACTCTC 58.834 40.000 0.00 0.00 0.00 3.20
6551 11481 8.632906 TTTTTCAATAATTCCAAACCATGCAT 57.367 26.923 0.00 0.00 0.00 3.96
6608 11538 8.613922 AGGAAAAGGATTGTCCAATAAATGAT 57.386 30.769 1.69 0.00 39.61 2.45
6615 11545 9.305555 AGGATTGTCCAATAAATGATCATTAGG 57.694 33.333 21.00 18.49 39.61 2.69
6651 11582 9.476928 TCTCTTAGTAGTCTAGCATAAAAAGGT 57.523 33.333 0.00 0.00 0.00 3.50
6656 11587 7.736893 AGTAGTCTAGCATAAAAAGGTATGGG 58.263 38.462 0.00 0.00 32.93 4.00
6660 11591 7.939588 AGTCTAGCATAAAAAGGTATGGGATTC 59.060 37.037 0.00 0.00 32.93 2.52
6668 11599 5.896073 AAAGGTATGGGATTCACTAGGAG 57.104 43.478 0.00 0.00 0.00 3.69
6676 11607 3.118592 GGGATTCACTAGGAGGTGTCAAG 60.119 52.174 0.00 0.00 38.28 3.02
6678 11609 1.267121 TCACTAGGAGGTGTCAAGCC 58.733 55.000 0.00 0.00 38.28 4.35
6697 11628 2.170166 CCTGTATTGCCAAAAGAGCCA 58.830 47.619 0.00 0.00 0.00 4.75
6698 11629 2.094545 CCTGTATTGCCAAAAGAGCCAC 60.095 50.000 0.00 0.00 0.00 5.01
6704 11635 4.888326 TTGCCAAAAGAGCCACATTAAT 57.112 36.364 0.00 0.00 0.00 1.40
6705 11636 5.991933 TTGCCAAAAGAGCCACATTAATA 57.008 34.783 0.00 0.00 0.00 0.98
6708 11639 6.945218 TGCCAAAAGAGCCACATTAATAAAT 58.055 32.000 0.00 0.00 0.00 1.40
6709 11640 6.817641 TGCCAAAAGAGCCACATTAATAAATG 59.182 34.615 0.00 0.00 46.66 2.32
6728 11660 2.217750 TGTGAGTCACGAAAACCCATG 58.782 47.619 18.17 0.00 37.14 3.66
6738 11670 1.266867 AAAACCCATGCCTCCATGCC 61.267 55.000 0.00 0.00 45.97 4.40
6780 11721 1.818674 CCCCATGAGTACCTTTTGTGC 59.181 52.381 0.00 0.00 0.00 4.57
6781 11722 2.555227 CCCCATGAGTACCTTTTGTGCT 60.555 50.000 0.00 0.00 43.20 4.40
6800 11741 1.988846 CTTTTCTCCTTCTCCCCCACT 59.011 52.381 0.00 0.00 0.00 4.00
6831 11772 5.292101 CCCTAATCAAATGAGACAAGTCGTC 59.708 44.000 0.00 0.00 45.77 4.20
6857 11798 4.440839 AAAGCAGCGGGAAATCTAAAAG 57.559 40.909 0.00 0.00 0.00 2.27
6911 11852 9.525826 AAATGACAGATTTAATCAAACTCTCCT 57.474 29.630 7.74 0.00 0.00 3.69
6914 11855 8.156820 TGACAGATTTAATCAAACTCTCCTCAA 58.843 33.333 7.74 0.00 0.00 3.02
6919 11860 3.902881 ATCAAACTCTCCTCAATCGCT 57.097 42.857 0.00 0.00 0.00 4.93
6926 11867 4.274147 ACTCTCCTCAATCGCTCTAGAAA 58.726 43.478 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.179158 GGCGACAACAACCAACGTTT 60.179 50.000 0.00 0.00 0.00 3.60
1 2 1.027792 AGGCGACAACAACCAACGTT 61.028 50.000 0.00 0.00 0.00 3.99
5 6 1.529226 CCATAGGCGACAACAACCAA 58.471 50.000 0.00 0.00 0.00 3.67
30 31 2.033801 CCACTGCTTTCTTCACAACCTG 59.966 50.000 0.00 0.00 0.00 4.00
34 35 3.206150 GAGTCCACTGCTTTCTTCACAA 58.794 45.455 0.00 0.00 0.00 3.33
36 37 1.795286 CGAGTCCACTGCTTTCTTCAC 59.205 52.381 0.00 0.00 0.00 3.18
37 38 1.270305 CCGAGTCCACTGCTTTCTTCA 60.270 52.381 0.00 0.00 0.00 3.02
44 45 0.612174 TAGAAGCCGAGTCCACTGCT 60.612 55.000 0.00 0.00 35.08 4.24
47 48 0.039911 ACCTAGAAGCCGAGTCCACT 59.960 55.000 0.00 0.00 0.00 4.00
51 52 3.215975 AGTGATACCTAGAAGCCGAGTC 58.784 50.000 0.00 0.00 0.00 3.36
52 53 3.300239 AGTGATACCTAGAAGCCGAGT 57.700 47.619 0.00 0.00 0.00 4.18
67 68 3.188460 CGGTGATTTTGTTCGGAAGTGAT 59.812 43.478 0.00 0.00 0.00 3.06
76 77 1.818674 AGATGGGCGGTGATTTTGTTC 59.181 47.619 0.00 0.00 0.00 3.18
80 81 3.136443 TCATAGAGATGGGCGGTGATTTT 59.864 43.478 0.00 0.00 33.49 1.82
84 85 2.015456 ATCATAGAGATGGGCGGTGA 57.985 50.000 0.00 0.00 35.06 4.02
108 109 5.234757 TCATTGGTGTAGTTTGTACGACAAC 59.765 40.000 0.00 0.00 44.80 3.32
113 114 3.122278 CGGTCATTGGTGTAGTTTGTACG 59.878 47.826 0.00 0.00 0.00 3.67
115 116 4.202233 TGACGGTCATTGGTGTAGTTTGTA 60.202 41.667 6.76 0.00 0.00 2.41
118 119 3.478857 TGACGGTCATTGGTGTAGTTT 57.521 42.857 6.76 0.00 0.00 2.66
119 120 3.596214 GATGACGGTCATTGGTGTAGTT 58.404 45.455 23.40 0.00 37.20 2.24
120 121 2.416836 CGATGACGGTCATTGGTGTAGT 60.417 50.000 24.68 2.95 37.20 2.73
130 131 4.131596 TGACTATATCACGATGACGGTCA 58.868 43.478 14.01 14.01 44.46 4.02
135 136 8.906693 CACTAATGTTGACTATATCACGATGAC 58.093 37.037 0.00 0.00 36.92 3.06
142 143 7.202093 CCTTCCCCACTAATGTTGACTATATCA 60.202 40.741 0.00 0.00 34.65 2.15
146 147 5.036916 TCCTTCCCCACTAATGTTGACTAT 58.963 41.667 0.00 0.00 0.00 2.12
152 153 3.655777 TGACTTCCTTCCCCACTAATGTT 59.344 43.478 0.00 0.00 0.00 2.71
153 154 3.256704 TGACTTCCTTCCCCACTAATGT 58.743 45.455 0.00 0.00 0.00 2.71
154 155 4.265073 CTTGACTTCCTTCCCCACTAATG 58.735 47.826 0.00 0.00 0.00 1.90
155 156 3.308473 GCTTGACTTCCTTCCCCACTAAT 60.308 47.826 0.00 0.00 0.00 1.73
167 168 4.096984 CACCCTAATCATTGCTTGACTTCC 59.903 45.833 0.00 0.00 37.11 3.46
169 170 4.922206 TCACCCTAATCATTGCTTGACTT 58.078 39.130 0.00 0.00 37.11 3.01
198 199 2.904434 TGAAACCACCTTACTCCTCTCC 59.096 50.000 0.00 0.00 0.00 3.71
207 208 6.209192 TGTCGTATACTCTTGAAACCACCTTA 59.791 38.462 0.56 0.00 0.00 2.69
219 220 6.128090 TGTCGTCATCTTTGTCGTATACTCTT 60.128 38.462 0.56 0.00 36.11 2.85
224 225 5.556355 ACTGTCGTCATCTTTGTCGTATA 57.444 39.130 0.00 0.00 36.11 1.47
227 228 2.795175 ACTGTCGTCATCTTTGTCGT 57.205 45.000 0.00 0.00 36.11 4.34
229 230 4.389077 CCCTTAACTGTCGTCATCTTTGTC 59.611 45.833 0.00 0.00 0.00 3.18
231 232 3.125316 GCCCTTAACTGTCGTCATCTTTG 59.875 47.826 0.00 0.00 0.00 2.77
252 253 3.674050 TACCCTCACCCCCTCTCGC 62.674 68.421 0.00 0.00 0.00 5.03
255 256 0.797579 TTTCTACCCTCACCCCCTCT 59.202 55.000 0.00 0.00 0.00 3.69
259 260 0.034380 GCCTTTTCTACCCTCACCCC 60.034 60.000 0.00 0.00 0.00 4.95
265 266 2.287977 GGTGTTGCCTTTTCTACCCT 57.712 50.000 0.00 0.00 0.00 4.34
277 278 7.671495 AAAATTCCAATTATGAAGGTGTTGC 57.329 32.000 0.00 0.00 0.00 4.17
292 293 7.479980 GTCCACATGATCGATAAAAATTCCAA 58.520 34.615 0.00 0.00 0.00 3.53
294 295 6.136071 CGTCCACATGATCGATAAAAATTCC 58.864 40.000 0.00 0.00 0.00 3.01
297 298 5.007626 CCACGTCCACATGATCGATAAAAAT 59.992 40.000 0.00 0.00 0.00 1.82
307 308 2.159382 GGTTTTCCACGTCCACATGAT 58.841 47.619 0.00 0.00 40.31 2.45
321 322 7.867445 ATCGAAAATGTAACATGTGGTTTTC 57.133 32.000 18.54 18.54 40.96 2.29
329 330 9.773328 ATCAACAACTATCGAAAATGTAACATG 57.227 29.630 0.00 0.00 0.00 3.21
330 331 9.773328 CATCAACAACTATCGAAAATGTAACAT 57.227 29.630 0.00 0.00 0.00 2.71
341 342 4.428615 TCGACACATCAACAACTATCGA 57.571 40.909 0.00 0.00 35.18 3.59
342 343 4.207224 GGATCGACACATCAACAACTATCG 59.793 45.833 0.00 0.00 0.00 2.92
343 344 5.109210 TGGATCGACACATCAACAACTATC 58.891 41.667 0.00 0.00 0.00 2.08
344 345 5.084818 TGGATCGACACATCAACAACTAT 57.915 39.130 0.00 0.00 0.00 2.12
345 346 4.529109 TGGATCGACACATCAACAACTA 57.471 40.909 0.00 0.00 0.00 2.24
347 348 4.437390 GGATTGGATCGACACATCAACAAC 60.437 45.833 0.00 0.00 0.00 3.32
382 383 6.964741 ATTAATGATAAGATGCAGCTCTCG 57.035 37.500 4.22 0.00 0.00 4.04
385 386 8.997323 AGTGTAATTAATGATAAGATGCAGCTC 58.003 33.333 4.22 0.00 0.00 4.09
387 388 8.777413 TGAGTGTAATTAATGATAAGATGCAGC 58.223 33.333 0.00 0.00 0.00 5.25
404 405 8.028938 GCCATATTTTTGTCAGTTGAGTGTAAT 58.971 33.333 0.00 0.00 0.00 1.89
405 406 7.013750 TGCCATATTTTTGTCAGTTGAGTGTAA 59.986 33.333 0.00 0.00 0.00 2.41
406 407 6.488344 TGCCATATTTTTGTCAGTTGAGTGTA 59.512 34.615 0.00 0.00 0.00 2.90
408 409 5.771469 TGCCATATTTTTGTCAGTTGAGTG 58.229 37.500 0.00 0.00 0.00 3.51
409 410 6.392354 CATGCCATATTTTTGTCAGTTGAGT 58.608 36.000 0.00 0.00 0.00 3.41
410 411 5.808540 CCATGCCATATTTTTGTCAGTTGAG 59.191 40.000 0.00 0.00 0.00 3.02
411 412 5.245751 ACCATGCCATATTTTTGTCAGTTGA 59.754 36.000 0.00 0.00 0.00 3.18
412 413 5.481105 ACCATGCCATATTTTTGTCAGTTG 58.519 37.500 0.00 0.00 0.00 3.16
413 414 5.743636 ACCATGCCATATTTTTGTCAGTT 57.256 34.783 0.00 0.00 0.00 3.16
450 1718 8.732746 AGGCGAACATAATATTTACTTCAGTT 57.267 30.769 0.00 0.00 0.00 3.16
479 2244 0.038067 CGGACCAACCATACGTGTGA 60.038 55.000 14.51 0.00 38.90 3.58
481 2246 1.294138 CCGGACCAACCATACGTGT 59.706 57.895 0.00 0.00 38.90 4.49
483 2248 1.906105 ATGCCGGACCAACCATACGT 61.906 55.000 5.05 0.00 38.90 3.57
485 2250 0.393808 ACATGCCGGACCAACCATAC 60.394 55.000 5.05 0.00 38.90 2.39
486 2251 0.107410 GACATGCCGGACCAACCATA 60.107 55.000 5.05 0.00 38.90 2.74
510 2280 2.224670 ACGGAGGCAACATTGGTTTCTA 60.225 45.455 0.00 0.00 34.21 2.10
545 2315 2.853914 GACGACGTTGCTGCCTTC 59.146 61.111 0.13 0.00 0.00 3.46
552 2322 1.270971 TAATAAGCCGACGACGTTGC 58.729 50.000 9.87 12.00 37.88 4.17
554 2324 4.913924 GTGATATAATAAGCCGACGACGTT 59.086 41.667 0.13 0.00 37.88 3.99
555 2325 4.470462 GTGATATAATAAGCCGACGACGT 58.530 43.478 0.00 0.00 37.88 4.34
556 2326 3.850273 GGTGATATAATAAGCCGACGACG 59.150 47.826 0.00 0.00 39.43 5.12
580 2350 2.855953 GCACACAAACAGTCTCACATGC 60.856 50.000 0.00 0.00 0.00 4.06
599 2369 5.300539 TGAGTTTTGGCTTACTATGTTTGCA 59.699 36.000 0.00 0.00 0.00 4.08
633 4285 4.768130 TTTCGGGAAATTTTCATACGCA 57.232 36.364 11.09 0.96 0.00 5.24
728 4685 6.809869 ACATCACTTTTTCCTCCTTGAAAAG 58.190 36.000 6.33 6.33 43.09 2.27
733 4691 5.997746 TCAGTACATCACTTTTTCCTCCTTG 59.002 40.000 0.00 0.00 34.26 3.61
770 4728 2.414559 CGCTCAATTTTCATCCAACGCT 60.415 45.455 0.00 0.00 0.00 5.07
771 4729 1.913403 CGCTCAATTTTCATCCAACGC 59.087 47.619 0.00 0.00 0.00 4.84
803 4761 0.875908 CCGTGTACATGCTCCCATCG 60.876 60.000 9.72 0.00 0.00 3.84
980 4942 1.217244 GCGCCCGGTAGAAGAAGAA 59.783 57.895 0.00 0.00 0.00 2.52
981 4943 2.718073 GGCGCCCGGTAGAAGAAGA 61.718 63.158 18.11 0.00 0.00 2.87
982 4944 2.202892 GGCGCCCGGTAGAAGAAG 60.203 66.667 18.11 0.00 0.00 2.85
1075 5040 3.086600 GGTGCTGGAGAGAGGGGG 61.087 72.222 0.00 0.00 0.00 5.40
1281 5246 1.528586 CGTGTGCTCAAGTCTCAAAGG 59.471 52.381 0.00 0.00 0.00 3.11
1285 5250 1.661509 CGCGTGTGCTCAAGTCTCA 60.662 57.895 0.00 0.00 39.65 3.27
1293 5258 2.546321 CAGAACACGCGTGTGCTC 59.454 61.111 42.81 35.09 46.24 4.26
1345 5315 1.135972 CCACGCTTGCATCAGTAACAC 60.136 52.381 0.00 0.00 0.00 3.32
1348 5318 1.155889 CACCACGCTTGCATCAGTAA 58.844 50.000 0.00 0.00 0.00 2.24
1350 5320 0.321919 ATCACCACGCTTGCATCAGT 60.322 50.000 0.00 0.00 0.00 3.41
1352 5322 1.026182 GGATCACCACGCTTGCATCA 61.026 55.000 0.00 0.00 35.97 3.07
1353 5323 1.723870 GGATCACCACGCTTGCATC 59.276 57.895 0.00 0.00 35.97 3.91
1354 5324 2.108514 CGGATCACCACGCTTGCAT 61.109 57.895 0.00 0.00 35.59 3.96
1355 5325 2.741985 CGGATCACCACGCTTGCA 60.742 61.111 0.00 0.00 35.59 4.08
1374 5344 0.610232 GCTTTCCACCTCCTGCACAT 60.610 55.000 0.00 0.00 0.00 3.21
1471 5443 5.499004 AACTCAATACCTACCTTCAAGCA 57.501 39.130 0.00 0.00 0.00 3.91
1498 5470 9.113838 ACAAATATACACTTCCATGAGTTCATC 57.886 33.333 0.00 0.00 33.61 2.92
1503 5475 8.635765 AAACACAAATATACACTTCCATGAGT 57.364 30.769 0.00 0.00 0.00 3.41
1602 5576 5.067674 GCATATCTTCAGTTGTGCCCATTTA 59.932 40.000 0.00 0.00 0.00 1.40
1736 5718 7.011763 ACAAGTAAACTTAAACGGAGGAAGAAC 59.988 37.037 0.00 0.00 34.28 3.01
1737 5719 7.049754 ACAAGTAAACTTAAACGGAGGAAGAA 58.950 34.615 0.00 0.00 34.28 2.52
1741 5723 5.754890 GTGACAAGTAAACTTAAACGGAGGA 59.245 40.000 0.00 0.00 34.28 3.71
1917 5899 5.242171 TGCATGCTAATGGAGGTATTCATTG 59.758 40.000 20.33 0.00 35.50 2.82
1920 5902 4.436113 TGCATGCTAATGGAGGTATTCA 57.564 40.909 20.33 0.00 34.09 2.57
2049 6032 6.818644 GTCTTGTAGTGAATATGAGCTTCCAA 59.181 38.462 0.00 0.00 0.00 3.53
2452 6435 2.107950 TTTGGGGCAAGACTATCACG 57.892 50.000 0.00 0.00 0.00 4.35
2581 6567 6.409704 TCTAGCATGACATTGAAGCTTACTT 58.590 36.000 0.00 0.00 39.43 2.24
2646 6632 8.814038 ATATTGGTCCTCATATTAATTCCAGC 57.186 34.615 0.00 0.00 0.00 4.85
2731 6717 9.595823 GTCTATCCTAAAACACTGTTATTAGCA 57.404 33.333 13.21 5.09 0.00 3.49
2876 6862 2.237143 TCTTGGGCACAGAGTAATCCAG 59.763 50.000 0.00 0.00 0.00 3.86
2996 6983 6.377327 TGTCAAGACCAAGAAGAAAATGAC 57.623 37.500 0.00 0.00 36.19 3.06
3110 7097 3.223435 AGGACATGACCACCGTAGATAG 58.777 50.000 16.63 0.00 0.00 2.08
3317 7305 3.782523 AGCCATCTCTTCCCAACATTCTA 59.217 43.478 0.00 0.00 0.00 2.10
3322 7310 1.988107 AGAAGCCATCTCTTCCCAACA 59.012 47.619 0.41 0.00 42.52 3.33
3512 7500 2.475487 GCGCTTCCCATCGTTTATAGTC 59.525 50.000 0.00 0.00 0.00 2.59
3518 7506 0.451783 GAATGCGCTTCCCATCGTTT 59.548 50.000 9.73 0.00 0.00 3.60
3566 7554 6.478512 ACCTTAAATGGCAAGAACTTGAAA 57.521 33.333 17.19 5.60 42.93 2.69
3677 7665 5.245977 ACATACCTTGTTTCCCCTTGAAATG 59.754 40.000 0.00 0.00 44.44 2.32
3770 7758 2.432510 TCCACCATGGGTTCAACAAAAC 59.567 45.455 18.09 0.00 38.32 2.43
3819 7807 2.617021 GGAGGTCTGGAAAAACCGCATA 60.617 50.000 0.00 0.00 42.61 3.14
3966 7955 6.211515 ACGGACGTCCAAGATATAATAACAC 58.788 40.000 32.80 0.99 35.14 3.32
3984 7973 4.603985 TCATGTTACTGCTATAACGGACG 58.396 43.478 0.00 0.00 37.79 4.79
4021 8010 1.472026 GCCTGGCCAACAAGCATATTG 60.472 52.381 7.01 0.00 36.52 1.90
4036 8025 7.473735 TGAAGTAAGATCATCTATAGCCTGG 57.526 40.000 0.00 0.00 0.00 4.45
4065 8054 4.770010 TCATATCAACCACAACCCCTTTTC 59.230 41.667 0.00 0.00 0.00 2.29
4117 8106 0.329596 GGTTGACCTCTGAAGCCCAT 59.670 55.000 0.00 0.00 0.00 4.00
4155 8144 5.413969 TGCATAGAAATCTCAAATCGCTG 57.586 39.130 0.00 0.00 0.00 5.18
4184 8173 8.562892 CAAGAAATCAAGCTCTACAGAAAAGAA 58.437 33.333 0.00 0.00 0.00 2.52
4189 8178 6.205464 CCAACAAGAAATCAAGCTCTACAGAA 59.795 38.462 0.00 0.00 0.00 3.02
4195 8184 4.464008 TGACCAACAAGAAATCAAGCTCT 58.536 39.130 0.00 0.00 0.00 4.09
4267 8256 2.499289 CTCATAAGTGTCTGGGAGTGCT 59.501 50.000 0.00 0.00 0.00 4.40
4271 8260 5.661056 TGTTACTCATAAGTGTCTGGGAG 57.339 43.478 0.00 0.00 36.92 4.30
4272 8261 5.719563 TGATGTTACTCATAAGTGTCTGGGA 59.280 40.000 0.00 0.00 36.83 4.37
4314 8308 9.733556 ACAAACTGTACAATATGATTACTGGAA 57.266 29.630 0.00 0.00 0.00 3.53
4405 8423 4.632688 CGGTCTGATACCCGTACAATTTTT 59.367 41.667 0.00 0.00 46.62 1.94
4448 8466 2.231478 TCCACCTTCTTTGACTCTAGCG 59.769 50.000 0.00 0.00 0.00 4.26
4483 8501 1.145738 AGCTCTCAGGCCCTTCAAAAA 59.854 47.619 0.00 0.00 0.00 1.94
4494 8512 7.918536 ACATAAATATGCATTAGCTCTCAGG 57.081 36.000 3.54 0.00 42.74 3.86
4504 8522 7.705752 TGCATTCGTCAAACATAAATATGCATT 59.294 29.630 3.54 0.00 40.38 3.56
4523 8541 3.067106 ACTACCAAGTCAGTTGCATTCG 58.933 45.455 0.00 0.00 34.45 3.34
4568 8586 2.037901 TGCATTCAGGACAGCCAAAAA 58.962 42.857 0.00 0.00 36.29 1.94
4569 8587 1.702182 TGCATTCAGGACAGCCAAAA 58.298 45.000 0.00 0.00 36.29 2.44
4576 8594 4.858850 ACCATTAGATTGCATTCAGGACA 58.141 39.130 10.98 0.00 0.00 4.02
4629 8659 6.097129 TGAACCCATTTTCTTAAAACCTTCGT 59.903 34.615 0.00 0.00 32.37 3.85
4630 8660 6.508777 TGAACCCATTTTCTTAAAACCTTCG 58.491 36.000 0.00 0.00 32.37 3.79
4641 8671 7.725844 AGTCAGATAGTTTTGAACCCATTTTCT 59.274 33.333 0.00 0.00 0.00 2.52
4762 8870 1.065636 GCAGTGGAAGTTACCCCTACC 60.066 57.143 0.00 0.00 0.00 3.18
4815 8923 3.677121 CACTCTCACTCTGCACATACAAC 59.323 47.826 0.00 0.00 0.00 3.32
4895 9003 3.134458 CTCGGCTTTTCTGAAGTTCTGT 58.866 45.455 4.17 0.00 0.00 3.41
4962 9070 6.908870 TGGTCTGAATGAATAGTTGATTCG 57.091 37.500 0.00 0.00 46.15 3.34
5107 9373 3.021355 GTTGACGATTGAAACGATCCG 57.979 47.619 0.89 0.00 34.70 4.18
5154 9423 5.421056 TGTACTGACGGAATGGAGTAAAGAT 59.579 40.000 0.00 0.00 0.00 2.40
5251 9520 2.634982 TGCATGTTCGCATTTCCTTC 57.365 45.000 0.00 0.00 36.86 3.46
5330 9769 5.319140 TCTTATAGTCTTTACGCAGCACA 57.681 39.130 0.00 0.00 0.00 4.57
5334 9773 7.919091 TGTACCATTCTTATAGTCTTTACGCAG 59.081 37.037 0.00 0.00 0.00 5.18
5373 9812 6.419791 TGTCCCGATGGTTTAAACATCTATT 58.580 36.000 19.13 0.00 41.91 1.73
5412 9851 7.778386 CAGCGTATTGATGTATGAAAGTAGTC 58.222 38.462 0.00 0.00 0.00 2.59
5441 9883 0.097674 GCTGTATGAAGCTTGTGCGG 59.902 55.000 2.10 2.18 45.42 5.69
5598 10077 7.089770 TCAACACAACATACTTAGCACAAAA 57.910 32.000 0.00 0.00 0.00 2.44
5706 10188 5.627135 ACAAATTCTCCTCCGGTTTCTAAA 58.373 37.500 0.00 0.00 0.00 1.85
5709 10191 3.072476 TGACAAATTCTCCTCCGGTTTCT 59.928 43.478 0.00 0.00 0.00 2.52
5715 10197 3.118629 TCTCCATGACAAATTCTCCTCCG 60.119 47.826 0.00 0.00 0.00 4.63
5774 10257 9.886132 GGTCAGTCCATAACTCTTATCTTTTAA 57.114 33.333 0.00 0.00 35.45 1.52
5775 10258 9.042450 TGGTCAGTCCATAACTCTTATCTTTTA 57.958 33.333 0.00 0.00 41.93 1.52
5776 10259 7.918076 TGGTCAGTCCATAACTCTTATCTTTT 58.082 34.615 0.00 0.00 41.93 2.27
6111 10843 7.807977 TTCCTAGCTAAAAGCATAAATCCAG 57.192 36.000 1.22 0.00 45.56 3.86
6113 10845 8.628630 AGATTCCTAGCTAAAAGCATAAATCC 57.371 34.615 1.22 0.00 45.56 3.01
6129 10861 7.551585 TGACTAGCAGAGAAAAAGATTCCTAG 58.448 38.462 0.00 0.00 0.00 3.02
6137 10869 6.981762 ACATCATGACTAGCAGAGAAAAAG 57.018 37.500 0.00 0.00 0.00 2.27
6142 10874 5.665916 TCAAACATCATGACTAGCAGAGA 57.334 39.130 0.00 0.00 0.00 3.10
6143 10875 6.104665 TCTTCAAACATCATGACTAGCAGAG 58.895 40.000 0.00 0.00 0.00 3.35
6144 10876 6.041423 TCTTCAAACATCATGACTAGCAGA 57.959 37.500 0.00 0.00 0.00 4.26
6145 10877 6.732531 TTCTTCAAACATCATGACTAGCAG 57.267 37.500 0.00 0.00 0.00 4.24
6146 10878 6.403964 GCATTCTTCAAACATCATGACTAGCA 60.404 38.462 0.00 0.00 0.00 3.49
6147 10879 5.970023 GCATTCTTCAAACATCATGACTAGC 59.030 40.000 0.00 0.00 0.00 3.42
6214 10946 2.693074 GGTATTTTTGGTGGATGCGGAT 59.307 45.455 0.00 0.00 0.00 4.18
6215 10947 2.096248 GGTATTTTTGGTGGATGCGGA 58.904 47.619 0.00 0.00 0.00 5.54
6216 10948 2.099098 GAGGTATTTTTGGTGGATGCGG 59.901 50.000 0.00 0.00 0.00 5.69
6217 10949 2.099098 GGAGGTATTTTTGGTGGATGCG 59.901 50.000 0.00 0.00 0.00 4.73
6218 10950 2.430694 GGGAGGTATTTTTGGTGGATGC 59.569 50.000 0.00 0.00 0.00 3.91
6219 10951 3.031013 GGGGAGGTATTTTTGGTGGATG 58.969 50.000 0.00 0.00 0.00 3.51
6220 10952 2.023404 GGGGGAGGTATTTTTGGTGGAT 60.023 50.000 0.00 0.00 0.00 3.41
6239 10971 1.621347 GGGTAAAATGGGGAACTGGGG 60.621 57.143 0.00 0.00 0.00 4.96
6244 10976 2.184533 CCAAGGGGTAAAATGGGGAAC 58.815 52.381 0.00 0.00 0.00 3.62
6287 11019 5.479724 TGTATGCAAATGGTGGAATTCTTCA 59.520 36.000 5.23 2.22 0.00 3.02
6298 11030 4.826733 TCTTTGTGAGTGTATGCAAATGGT 59.173 37.500 0.00 0.00 31.60 3.55
6305 11037 7.436673 CCTATAAGAGTCTTTGTGAGTGTATGC 59.563 40.741 11.40 0.00 0.00 3.14
6309 11041 6.919775 ACCTATAAGAGTCTTTGTGAGTGT 57.080 37.500 11.40 0.00 0.00 3.55
6314 11046 9.632807 GATGCTATACCTATAAGAGTCTTTGTG 57.367 37.037 11.40 1.56 0.00 3.33
6319 11051 7.395617 TCGTGATGCTATACCTATAAGAGTCT 58.604 38.462 0.00 0.00 0.00 3.24
6320 11052 7.201661 CCTCGTGATGCTATACCTATAAGAGTC 60.202 44.444 0.00 0.00 0.00 3.36
6321 11053 6.600032 CCTCGTGATGCTATACCTATAAGAGT 59.400 42.308 0.00 0.00 0.00 3.24
6322 11054 6.038825 CCCTCGTGATGCTATACCTATAAGAG 59.961 46.154 0.00 0.00 0.00 2.85
6324 11056 5.652891 ACCCTCGTGATGCTATACCTATAAG 59.347 44.000 0.00 0.00 0.00 1.73
6359 11288 5.476983 AGTTGGGATGAGGATATGGTTAGA 58.523 41.667 0.00 0.00 0.00 2.10
6367 11296 4.164221 GGACAAAGAGTTGGGATGAGGATA 59.836 45.833 0.00 0.00 39.22 2.59
6394 11323 2.979678 AGTGGGTGTAACATGTTCCTCT 59.020 45.455 15.85 12.84 39.98 3.69
6401 11330 5.943416 TGAAGGATTAAGTGGGTGTAACATG 59.057 40.000 0.00 0.00 39.98 3.21
6481 11411 7.230849 TGTGGAAAGAATGTCAATATTTGCT 57.769 32.000 1.93 0.00 0.00 3.91
6496 11426 3.901222 TGTGGAGAGTGTATGTGGAAAGA 59.099 43.478 0.00 0.00 0.00 2.52
6500 11430 3.195610 GTCATGTGGAGAGTGTATGTGGA 59.804 47.826 0.00 0.00 0.00 4.02
6537 11467 5.999205 AGTAAATCATGCATGGTTTGGAA 57.001 34.783 36.85 21.37 40.97 3.53
6551 11481 4.203226 TCACTGTTGTGGCAAGTAAATCA 58.797 39.130 0.00 0.00 43.94 2.57
6580 11510 9.189156 CATTTATTGGACAATCCTTTTCCTCTA 57.811 33.333 0.03 0.00 37.46 2.43
6582 11512 8.066612 TCATTTATTGGACAATCCTTTTCCTC 57.933 34.615 0.03 0.00 37.46 3.71
6583 11513 8.613922 ATCATTTATTGGACAATCCTTTTCCT 57.386 30.769 0.03 0.00 37.46 3.36
6584 11514 8.477256 TGATCATTTATTGGACAATCCTTTTCC 58.523 33.333 0.03 0.00 37.46 3.13
6590 11520 9.300681 TCCTAATGATCATTTATTGGACAATCC 57.699 33.333 25.26 0.00 32.97 3.01
6639 11570 6.435164 AGTGAATCCCATACCTTTTTATGCT 58.565 36.000 0.00 0.00 0.00 3.79
6641 11572 8.217799 TCCTAGTGAATCCCATACCTTTTTATG 58.782 37.037 0.00 0.00 0.00 1.90
6647 11578 4.235372 CCTCCTAGTGAATCCCATACCTT 58.765 47.826 0.00 0.00 0.00 3.50
6651 11582 4.223953 GACACCTCCTAGTGAATCCCATA 58.776 47.826 0.00 0.00 40.34 2.74
6652 11583 3.041946 GACACCTCCTAGTGAATCCCAT 58.958 50.000 0.00 0.00 40.34 4.00
6653 11584 2.225522 TGACACCTCCTAGTGAATCCCA 60.226 50.000 0.00 0.00 40.34 4.37
6654 11585 2.467880 TGACACCTCCTAGTGAATCCC 58.532 52.381 0.00 0.00 40.34 3.85
6656 11587 3.526534 GCTTGACACCTCCTAGTGAATC 58.473 50.000 0.00 0.00 40.34 2.52
6660 11591 1.066573 CAGGCTTGACACCTCCTAGTG 60.067 57.143 0.00 0.00 43.65 2.74
6668 11599 0.811281 GGCAATACAGGCTTGACACC 59.189 55.000 1.40 0.00 31.65 4.16
6676 11607 1.134995 GGCTCTTTTGGCAATACAGGC 60.135 52.381 0.00 1.98 0.00 4.85
6678 11609 2.557924 TGTGGCTCTTTTGGCAATACAG 59.442 45.455 0.00 0.00 44.02 2.74
6698 11629 9.061610 GGTTTTCGTGACTCACATTTATTAATG 57.938 33.333 9.84 2.94 45.39 1.90
6704 11635 4.452825 TGGGTTTTCGTGACTCACATTTA 58.547 39.130 9.84 0.00 33.40 1.40
6705 11636 3.283751 TGGGTTTTCGTGACTCACATTT 58.716 40.909 9.84 0.00 33.40 2.32
6708 11639 2.217750 CATGGGTTTTCGTGACTCACA 58.782 47.619 9.84 0.00 33.40 3.58
6709 11640 1.069227 GCATGGGTTTTCGTGACTCAC 60.069 52.381 0.00 0.00 28.68 3.51
6710 11641 1.234821 GCATGGGTTTTCGTGACTCA 58.765 50.000 0.00 0.00 30.94 3.41
6711 11642 0.521735 GGCATGGGTTTTCGTGACTC 59.478 55.000 0.00 0.00 0.00 3.36
6717 11649 0.457035 CATGGAGGCATGGGTTTTCG 59.543 55.000 0.00 0.00 0.00 3.46
6728 11660 3.302129 CCAAAAGGGCATGGAGGC 58.698 61.111 0.00 0.00 39.12 4.70
6755 11687 5.069781 CACAAAAGGTACTCATGGGGAAAAA 59.930 40.000 0.00 0.00 38.49 1.94
6756 11688 4.586841 CACAAAAGGTACTCATGGGGAAAA 59.413 41.667 0.00 0.00 38.49 2.29
6757 11689 4.148838 CACAAAAGGTACTCATGGGGAAA 58.851 43.478 0.00 0.00 38.49 3.13
6758 11690 3.761897 CACAAAAGGTACTCATGGGGAA 58.238 45.455 0.00 0.00 38.49 3.97
6759 11691 2.554344 GCACAAAAGGTACTCATGGGGA 60.554 50.000 0.00 0.00 38.49 4.81
6760 11692 1.818674 GCACAAAAGGTACTCATGGGG 59.181 52.381 0.00 0.00 38.49 4.96
6764 11696 5.241728 GGAGAAAAGCACAAAAGGTACTCAT 59.758 40.000 0.00 0.00 38.49 2.90
6765 11697 4.578928 GGAGAAAAGCACAAAAGGTACTCA 59.421 41.667 0.00 0.00 38.49 3.41
6766 11698 4.822350 AGGAGAAAAGCACAAAAGGTACTC 59.178 41.667 0.00 0.00 38.49 2.59
6780 11721 1.988846 AGTGGGGGAGAAGGAGAAAAG 59.011 52.381 0.00 0.00 0.00 2.27
6781 11722 2.133858 AGTGGGGGAGAAGGAGAAAA 57.866 50.000 0.00 0.00 0.00 2.29
6800 11741 8.603898 TTGTCTCATTTGATTAGGGACTACTA 57.396 34.615 0.00 0.00 42.67 1.82
6857 11798 4.150897 TGCCAACTTATGTGATAGGGAC 57.849 45.455 0.00 0.00 0.00 4.46
6911 11852 7.575414 AGAAGTATCTTTCTAGAGCGATTGA 57.425 36.000 10.08 0.00 35.70 2.57
6914 11855 7.575414 TGAAGAAGTATCTTTCTAGAGCGAT 57.425 36.000 9.81 9.81 45.91 4.58


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

AutoCloner maintained by Alex Coulton.