Multiple sequence alignment - TraesCS6D01G335700

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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 TraesCS6D01G335700 chr6D 100.000 4229 0 0 1 4229 436859922 436864150 0.000000e+00 7810.0
1 TraesCS6D01G335700 chr6D 94.286 35 2 0 3706 3740 436863589 436863623 2.000000e-03 54.7
2 TraesCS6D01G335700 chr6D 94.286 35 2 0 3668 3702 436863627 436863661 2.000000e-03 54.7
3 TraesCS6D01G335700 chr6B 91.780 1837 97 15 2376 4197 660645399 660647196 0.000000e+00 2507.0
4 TraesCS6D01G335700 chr6B 95.734 1219 34 5 1175 2376 660643980 660645197 0.000000e+00 1947.0
5 TraesCS6D01G335700 chr6B 92.224 643 36 11 493 1132 660643009 660643640 0.000000e+00 898.0
6 TraesCS6D01G335700 chr6B 83.333 438 48 14 1 429 660642123 660642544 8.580000e-102 381.0
7 TraesCS6D01G335700 chr6B 97.143 35 1 0 3706 3740 660646670 660646704 4.570000e-05 60.2
8 TraesCS6D01G335700 chr6A 97.770 807 18 0 1707 2513 585169471 585170277 0.000000e+00 1391.0
9 TraesCS6D01G335700 chr6A 97.411 811 19 2 1705 2513 585181595 585182405 0.000000e+00 1380.0
10 TraesCS6D01G335700 chr6A 91.425 723 27 12 2578 3269 585170274 585170992 0.000000e+00 959.0
11 TraesCS6D01G335700 chr6A 91.425 723 27 12 2578 3269 585182402 585183120 0.000000e+00 959.0
12 TraesCS6D01G335700 chr6A 94.728 569 13 3 1160 1711 585168601 585169169 0.000000e+00 869.0
13 TraesCS6D01G335700 chr6A 89.371 668 53 11 464 1126 585167950 585168604 0.000000e+00 824.0
14 TraesCS6D01G335700 chr6A 81.818 99 14 4 3886 3982 162307488 162307584 3.510000e-11 80.5
15 TraesCS6D01G335700 chr7A 88.360 189 22 0 3983 4171 310591029 310591217 1.180000e-55 228.0
16 TraesCS6D01G335700 chr7A 83.838 198 30 2 3983 4178 696999373 696999176 2.010000e-43 187.0
17 TraesCS6D01G335700 chr7B 86.243 189 26 0 3983 4171 284953658 284953470 5.540000e-49 206.0
18 TraesCS6D01G335700 chr7B 82.323 198 33 2 3983 4178 115547686 115547883 2.020000e-38 171.0
19 TraesCS6D01G335700 chr5B 85.714 189 27 0 3983 4171 400094666 400094478 2.580000e-47 200.0
20 TraesCS6D01G335700 chr5A 85.638 188 27 0 3983 4170 341136935 341137122 9.270000e-47 198.0
21 TraesCS6D01G335700 chr5A 96.875 32 1 0 324 355 9497586 9497617 2.000000e-03 54.7
22 TraesCS6D01G335700 chr3A 85.714 182 26 0 3983 4164 427767752 427767571 4.320000e-45 193.0
23 TraesCS6D01G335700 chr3A 100.000 32 0 0 2800 2831 194704380 194704411 4.570000e-05 60.2
24 TraesCS6D01G335700 chr4A 82.500 200 30 5 3983 4178 107370446 107370644 2.020000e-38 171.0
25 TraesCS6D01G335700 chr7D 97.222 36 1 0 2796 2831 388038985 388039020 1.270000e-05 62.1
26 TraesCS6D01G335700 chr7D 96.970 33 1 0 327 359 607075516 607075548 5.910000e-04 56.5
27 TraesCS6D01G335700 chr2D 100.000 33 0 0 2799 2831 5730509 5730541 1.270000e-05 62.1
28 TraesCS6D01G335700 chr2D 100.000 32 0 0 2800 2831 550804723 550804754 4.570000e-05 60.2
29 TraesCS6D01G335700 chr2D 96.970 33 1 0 2799 2831 121777058 121777026 5.910000e-04 56.5
30 TraesCS6D01G335700 chr2B 97.059 34 1 0 326 359 8419088 8419121 1.640000e-04 58.4
31 TraesCS6D01G335700 chr5D 97.059 34 0 1 327 360 393987029 393986997 5.910000e-04 56.5
32 TraesCS6D01G335700 chr2A 94.444 36 2 0 2799 2834 637977501 637977466 5.910000e-04 56.5
33 TraesCS6D01G335700 chr4D 96.970 33 0 1 327 358 494484096 494484064 2.000000e-03 54.7


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 TraesCS6D01G335700 chr6D 436859922 436864150 4228 False 2639.80 7810 96.190667 1 4229 3 chr6D.!!$F1 4228
1 TraesCS6D01G335700 chr6B 660642123 660647196 5073 False 1158.64 2507 92.042800 1 4197 5 chr6B.!!$F1 4196
2 TraesCS6D01G335700 chr6A 585181595 585183120 1525 False 1169.50 1380 94.418000 1705 3269 2 chr6A.!!$F3 1564
3 TraesCS6D01G335700 chr6A 585167950 585170992 3042 False 1010.75 1391 93.323500 464 3269 4 chr6A.!!$F2 2805

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
28 29 0.106719 AATCTGTGTATTGGGCCGGG 60.107 55.000 2.18 0.0 0.00 5.73 F
870 1289 0.107643 GACTCTGCTTAGGGGCCATC 59.892 60.000 4.39 0.0 0.00 3.51 F
2109 3150 0.034756 GCATTTCCCCTGCCGTTTTT 59.965 50.000 0.00 0.0 33.44 1.94 F
2115 3156 2.164338 TCCCCTGCCGTTTTTGTATTC 58.836 47.619 0.00 0.0 0.00 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1157 1577 0.111061 AGCATTGGTGGTCTGCTTCA 59.889 50.000 0.00 0.0 43.44 3.02 R
2171 3212 1.612726 GCCTGCTCACTGAATCAACCT 60.613 52.381 0.00 0.0 0.00 3.50 R
3146 4431 0.038892 CAATGCAACACTCCAGCCAC 60.039 55.000 0.00 0.0 0.00 5.01 R
4018 5306 0.107508 GGAGCTTCTGTAGGCATGCA 60.108 55.000 21.36 0.0 0.00 3.96 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
25 26 3.356290 AGTGAAATCTGTGTATTGGGCC 58.644 45.455 0.00 0.00 0.00 5.80
28 29 0.106719 AATCTGTGTATTGGGCCGGG 60.107 55.000 2.18 0.00 0.00 5.73
50 51 1.237285 AAGTCGATTGTGGCCTGTGC 61.237 55.000 3.32 0.00 0.00 4.57
54 55 1.430632 GATTGTGGCCTGTGCGATG 59.569 57.895 3.32 0.00 38.85 3.84
99 100 5.736951 ATCTATAATCTGAGGGTGAGCAC 57.263 43.478 0.00 0.00 0.00 4.40
100 101 2.898729 ATAATCTGAGGGTGAGCACG 57.101 50.000 0.00 0.00 0.00 5.34
101 102 1.847328 TAATCTGAGGGTGAGCACGA 58.153 50.000 0.00 0.00 0.00 4.35
102 103 0.247736 AATCTGAGGGTGAGCACGAC 59.752 55.000 0.00 0.00 0.00 4.34
120 121 2.903855 GATGGCGGCAGATGGTGG 60.904 66.667 19.29 0.00 0.00 4.61
148 149 2.095372 CGTCCTTACGCAAAATTCTCCC 59.905 50.000 0.00 0.00 43.12 4.30
194 201 5.557891 AATGTCTCTATTTGAAGCTGTGC 57.442 39.130 0.00 0.00 0.00 4.57
195 202 4.006780 TGTCTCTATTTGAAGCTGTGCA 57.993 40.909 0.00 0.00 0.00 4.57
198 205 3.943381 TCTCTATTTGAAGCTGTGCATGG 59.057 43.478 0.00 0.00 0.00 3.66
215 222 2.425143 TGGGAGAAAATGCTGCTAGG 57.575 50.000 0.00 0.00 0.00 3.02
227 234 2.233922 TGCTGCTAGGTGGTCTAAGAAC 59.766 50.000 0.00 0.00 0.00 3.01
238 245 6.158695 AGGTGGTCTAAGAACATGGATGTATT 59.841 38.462 0.00 0.00 40.80 1.89
282 289 4.550577 TTGTACTGCCATGATATTTGCG 57.449 40.909 0.00 0.00 0.00 4.85
284 291 1.321474 ACTGCCATGATATTTGCGGG 58.679 50.000 0.00 0.00 34.40 6.13
299 306 1.884235 GCGGGCAGCTTGATATAAGT 58.116 50.000 1.25 0.00 44.04 2.24
301 308 3.399330 GCGGGCAGCTTGATATAAGTTA 58.601 45.455 1.25 0.00 44.04 2.24
302 309 3.186613 GCGGGCAGCTTGATATAAGTTAC 59.813 47.826 1.25 0.00 44.04 2.50
303 310 3.746492 CGGGCAGCTTGATATAAGTTACC 59.254 47.826 0.00 0.00 0.00 2.85
304 311 4.714632 GGGCAGCTTGATATAAGTTACCA 58.285 43.478 0.00 0.00 0.00 3.25
341 348 9.234827 TGCAATCAATAATGAATAGATCGGAAT 57.765 29.630 0.00 0.00 39.49 3.01
350 357 6.287107 TGAATAGATCGGAATTTTTCTCGC 57.713 37.500 0.00 0.00 0.00 5.03
351 358 5.815222 TGAATAGATCGGAATTTTTCTCGCA 59.185 36.000 0.00 0.00 0.00 5.10
352 359 6.315144 TGAATAGATCGGAATTTTTCTCGCAA 59.685 34.615 0.00 0.00 0.00 4.85
355 362 5.954335 AGATCGGAATTTTTCTCGCAAAAT 58.046 33.333 0.00 0.00 37.86 1.82
364 371 7.803079 ATTTTTCTCGCAAAATAAAGAGAGC 57.197 32.000 0.00 0.00 40.33 4.09
371 378 3.611549 GCAAAATAAAGAGAGCAGCAAGC 59.388 43.478 0.00 0.00 46.19 4.01
383 390 1.407989 GCAGCAAGCAGGATAGGAAGT 60.408 52.381 0.00 0.00 44.79 3.01
385 392 2.093288 CAGCAAGCAGGATAGGAAGTGA 60.093 50.000 0.00 0.00 0.00 3.41
394 401 7.406104 AGCAGGATAGGAAGTGATTTTTAACT 58.594 34.615 0.00 0.00 0.00 2.24
515 927 6.351881 GGTCAGTTTTCCTTTTTCTTTCCCTT 60.352 38.462 0.00 0.00 0.00 3.95
518 930 7.125659 TCAGTTTTCCTTTTTCTTTCCCTTGAT 59.874 33.333 0.00 0.00 0.00 2.57
523 935 6.816136 TCCTTTTTCTTTCCCTTGATGAAAC 58.184 36.000 0.00 0.00 0.00 2.78
528 940 8.491331 TTTTCTTTCCCTTGATGAAACAAAAG 57.509 30.769 0.00 0.00 30.12 2.27
540 952 3.312421 TGAAACAAAAGAAGTCCAGCTCG 59.688 43.478 0.00 0.00 0.00 5.03
581 993 3.570559 CTCGCGATTCTATTCCTCTTCC 58.429 50.000 10.36 0.00 0.00 3.46
590 1002 3.964031 TCTATTCCTCTTCCTTCCTCTGC 59.036 47.826 0.00 0.00 0.00 4.26
753 1166 1.467920 GCCCAGATCCAAAAGTGAGG 58.532 55.000 0.00 0.00 0.00 3.86
834 1253 4.917998 TCAGTCTCTTTCATTCTTCGTTCG 59.082 41.667 0.00 0.00 0.00 3.95
835 1254 4.681942 CAGTCTCTTTCATTCTTCGTTCGT 59.318 41.667 0.00 0.00 0.00 3.85
836 1255 5.175856 CAGTCTCTTTCATTCTTCGTTCGTT 59.824 40.000 0.00 0.00 0.00 3.85
837 1256 5.175856 AGTCTCTTTCATTCTTCGTTCGTTG 59.824 40.000 0.00 0.00 0.00 4.10
838 1257 4.084537 TCTCTTTCATTCTTCGTTCGTTGC 60.085 41.667 0.00 0.00 0.00 4.17
843 1262 0.658897 TTCTTCGTTCGTTGCCAACC 59.341 50.000 1.21 0.00 0.00 3.77
853 1272 1.443802 GTTGCCAACCTCAGCTAGAC 58.556 55.000 0.00 0.00 0.00 2.59
859 1278 1.824230 CAACCTCAGCTAGACTCTGCT 59.176 52.381 0.00 0.00 40.54 4.24
870 1289 0.107643 GACTCTGCTTAGGGGCCATC 59.892 60.000 4.39 0.00 0.00 3.51
890 1309 0.753262 ATCCCGACCTTCAGGATTCG 59.247 55.000 0.00 0.00 37.06 3.34
926 1346 1.383803 CCCTTCCTCTAGGCAGCCT 60.384 63.158 20.63 20.63 37.71 4.58
928 1348 1.484065 CCCTTCCTCTAGGCAGCCTAT 60.484 57.143 22.14 0.00 35.36 2.57
952 1372 2.127651 TAGGTTCAACCCCCTTCAGT 57.872 50.000 1.75 0.00 39.75 3.41
965 1385 2.297597 CCCTTCAGTATCCATCGACCTC 59.702 54.545 0.00 0.00 0.00 3.85
1024 1444 2.224548 GGGATAGGTCATTGTAGCCCAC 60.225 54.545 0.00 0.00 43.36 4.61
1039 1459 1.503542 CCACTGTCGAATGCCAAGC 59.496 57.895 0.00 0.00 0.00 4.01
1132 1552 5.001232 GTCTACCCAATGTAAGCTGAAACA 58.999 41.667 0.00 0.00 0.00 2.83
1133 1553 5.472137 GTCTACCCAATGTAAGCTGAAACAA 59.528 40.000 0.00 0.00 0.00 2.83
1134 1554 6.016610 GTCTACCCAATGTAAGCTGAAACAAA 60.017 38.462 0.00 0.00 0.00 2.83
1135 1555 4.944048 ACCCAATGTAAGCTGAAACAAAC 58.056 39.130 0.00 0.00 0.00 2.93
1136 1556 4.649218 ACCCAATGTAAGCTGAAACAAACT 59.351 37.500 0.00 0.00 0.00 2.66
1137 1557 5.830991 ACCCAATGTAAGCTGAAACAAACTA 59.169 36.000 0.00 0.00 0.00 2.24
1138 1558 6.493458 ACCCAATGTAAGCTGAAACAAACTAT 59.507 34.615 0.00 0.00 0.00 2.12
1139 1559 7.015195 ACCCAATGTAAGCTGAAACAAACTATT 59.985 33.333 0.00 0.00 0.00 1.73
1140 1560 7.872483 CCCAATGTAAGCTGAAACAAACTATTT 59.128 33.333 0.00 0.00 0.00 1.40
1141 1561 8.915654 CCAATGTAAGCTGAAACAAACTATTTC 58.084 33.333 0.00 0.00 36.73 2.17
1142 1562 8.915654 CAATGTAAGCTGAAACAAACTATTTCC 58.084 33.333 0.00 0.00 35.57 3.13
1143 1563 7.817418 TGTAAGCTGAAACAAACTATTTCCT 57.183 32.000 0.00 0.00 35.57 3.36
1144 1564 7.871853 TGTAAGCTGAAACAAACTATTTCCTC 58.128 34.615 0.00 0.00 35.57 3.71
1145 1565 5.966742 AGCTGAAACAAACTATTTCCTCC 57.033 39.130 0.00 0.00 35.57 4.30
1146 1566 4.767409 AGCTGAAACAAACTATTTCCTCCC 59.233 41.667 0.00 0.00 35.57 4.30
1147 1567 4.522789 GCTGAAACAAACTATTTCCTCCCA 59.477 41.667 0.00 0.00 35.57 4.37
1148 1568 5.010617 GCTGAAACAAACTATTTCCTCCCAA 59.989 40.000 0.00 0.00 35.57 4.12
1149 1569 6.462347 GCTGAAACAAACTATTTCCTCCCAAA 60.462 38.462 0.00 0.00 35.57 3.28
1150 1570 7.425224 TGAAACAAACTATTTCCTCCCAAAA 57.575 32.000 0.00 0.00 35.57 2.44
1151 1571 7.852263 TGAAACAAACTATTTCCTCCCAAAAA 58.148 30.769 0.00 0.00 35.57 1.94
1183 1900 3.152341 CAGACCACCAATGCTCTCTTTT 58.848 45.455 0.00 0.00 0.00 2.27
1346 2066 5.156608 ACATTGATCTCAGTCATCACACA 57.843 39.130 0.00 0.00 29.70 3.72
1546 2266 3.270027 TGCTCAACTATGCTATTGCGTT 58.730 40.909 0.00 0.00 43.34 4.84
1876 2916 1.856265 GCTTGTTCTGAGTTGCCCGG 61.856 60.000 0.00 0.00 0.00 5.73
1882 2922 0.320374 TCTGAGTTGCCCGGTACTTG 59.680 55.000 0.00 0.00 0.00 3.16
1929 2969 2.672098 CCAGCACTCCACTATAGAGGT 58.328 52.381 14.95 0.00 35.58 3.85
2109 3150 0.034756 GCATTTCCCCTGCCGTTTTT 59.965 50.000 0.00 0.00 33.44 1.94
2115 3156 2.164338 TCCCCTGCCGTTTTTGTATTC 58.836 47.619 0.00 0.00 0.00 1.75
2171 3212 7.890515 TGGTTTCATATTTGTTGTATGCAGAA 58.109 30.769 0.00 0.00 31.22 3.02
2391 3634 8.236586 TGTAGACATGAAGTTGTTTATGATTGC 58.763 33.333 0.00 0.00 34.13 3.56
2496 3748 9.967346 GATTCCCCTAGTTTTAATAAATGAAGC 57.033 33.333 0.00 0.00 0.00 3.86
2515 3767 2.437281 AGCGAGACATGATGGAATTCCT 59.563 45.455 24.73 10.79 36.82 3.36
2556 3808 6.821388 AGGCTAAAATATCGAGTCTTGATGT 58.179 36.000 12.29 3.32 0.00 3.06
2557 3809 6.703607 AGGCTAAAATATCGAGTCTTGATGTG 59.296 38.462 12.29 0.00 0.00 3.21
2558 3810 6.480320 GGCTAAAATATCGAGTCTTGATGTGT 59.520 38.462 12.29 0.00 0.00 3.72
2559 3811 7.652105 GGCTAAAATATCGAGTCTTGATGTGTA 59.348 37.037 12.29 2.70 0.00 2.90
2560 3812 8.695284 GCTAAAATATCGAGTCTTGATGTGTAG 58.305 37.037 12.29 11.24 0.00 2.74
2561 3813 9.952188 CTAAAATATCGAGTCTTGATGTGTAGA 57.048 33.333 12.29 0.00 0.00 2.59
2566 3818 5.822278 TCGAGTCTTGATGTGTAGATAAGC 58.178 41.667 0.00 0.00 0.00 3.09
2567 3819 5.357032 TCGAGTCTTGATGTGTAGATAAGCA 59.643 40.000 0.00 0.00 0.00 3.91
2568 3820 6.039829 TCGAGTCTTGATGTGTAGATAAGCAT 59.960 38.462 0.00 0.00 0.00 3.79
2569 3821 6.143598 CGAGTCTTGATGTGTAGATAAGCATG 59.856 42.308 0.00 0.00 0.00 4.06
2570 3822 5.757320 AGTCTTGATGTGTAGATAAGCATGC 59.243 40.000 10.51 10.51 0.00 4.06
2571 3823 5.757320 GTCTTGATGTGTAGATAAGCATGCT 59.243 40.000 16.30 16.30 0.00 3.79
2572 3824 6.259608 GTCTTGATGTGTAGATAAGCATGCTT 59.740 38.462 33.70 33.70 39.83 3.91
2573 3825 7.439356 GTCTTGATGTGTAGATAAGCATGCTTA 59.561 37.037 35.50 35.50 41.95 3.09
2720 3972 9.117183 CACCCGTGTAGCTTATATGTCTATATA 57.883 37.037 0.00 0.00 31.97 0.86
2721 3973 9.863650 ACCCGTGTAGCTTATATGTCTATATAT 57.136 33.333 0.00 0.00 33.06 0.86
3058 4343 4.554134 CGCTTCATATTCTCCACAATGCTG 60.554 45.833 0.00 0.00 0.00 4.41
3146 4431 0.882927 TCGGAAAACCGTCTTGCCAG 60.883 55.000 8.46 0.00 34.52 4.85
3186 4471 7.148306 GCATTGGAATTTCTTTGCAAAGATGAT 60.148 33.333 35.66 28.46 46.84 2.45
3249 4534 3.706086 AGTTGGTCACTGCTTTCCATTTT 59.294 39.130 0.00 0.00 32.83 1.82
3256 4541 0.757512 TGCTTTCCATTTTGCCTGCA 59.242 45.000 0.00 0.00 0.00 4.41
3258 4543 1.735571 GCTTTCCATTTTGCCTGCATG 59.264 47.619 0.00 0.00 0.00 4.06
3314 4599 1.507141 CTTGAGGAAGCCGCGTTGTT 61.507 55.000 4.92 0.00 0.00 2.83
3337 4622 0.606401 ACATGTTCTGAGCCCGTTGG 60.606 55.000 0.00 0.00 0.00 3.77
3338 4623 0.606401 CATGTTCTGAGCCCGTTGGT 60.606 55.000 0.00 0.00 0.00 3.67
3339 4624 0.606401 ATGTTCTGAGCCCGTTGGTG 60.606 55.000 0.00 0.00 0.00 4.17
3340 4625 1.070786 GTTCTGAGCCCGTTGGTGA 59.929 57.895 0.00 0.00 0.00 4.02
3341 4626 1.070786 TTCTGAGCCCGTTGGTGAC 59.929 57.895 0.00 0.00 0.00 3.67
3342 4627 1.691195 TTCTGAGCCCGTTGGTGACA 61.691 55.000 0.00 0.00 39.83 3.58
3357 4642 4.274147 TGGTGACAAGTTGTGGTAAATGT 58.726 39.130 14.57 0.00 37.44 2.71
3358 4643 4.097135 TGGTGACAAGTTGTGGTAAATGTG 59.903 41.667 14.57 0.00 37.44 3.21
3385 4670 6.523840 AGATTTTTGCAAAACCTCATGCTAA 58.476 32.000 23.79 6.11 42.97 3.09
3393 4678 3.567478 AACCTCATGCTAATCTGGACC 57.433 47.619 0.00 0.00 0.00 4.46
3411 4696 3.324117 GACCTCGGTGAAAGTTTAGGAC 58.676 50.000 8.13 0.00 0.00 3.85
3517 4803 6.148811 CACTTGACTAATTATGGTTCAACGGT 59.851 38.462 0.00 0.00 0.00 4.83
3522 4808 8.530311 TGACTAATTATGGTTCAACGGTACTTA 58.470 33.333 0.00 0.00 0.00 2.24
3533 4819 3.705043 ACGGTACTTAATCTACTGCCG 57.295 47.619 0.00 0.00 43.05 5.69
3552 4838 1.805945 GTAAGACTGGCGCACCGAG 60.806 63.158 10.83 1.08 39.70 4.63
3591 4877 6.331369 TCAGTCCCTTCAACAATGAAAATC 57.669 37.500 0.00 0.00 44.64 2.17
3614 4901 6.306987 TCCTAAGCCAAAGAAGACAAGAAAT 58.693 36.000 0.00 0.00 0.00 2.17
3620 4907 7.203218 AGCCAAAGAAGACAAGAAATTGTTAC 58.797 34.615 0.00 0.00 34.90 2.50
3631 4918 6.756542 ACAAGAAATTGTTACAGGAAAACAGC 59.243 34.615 0.00 0.00 38.05 4.40
3642 4929 4.929211 ACAGGAAAACAGCTTTTTGAACAC 59.071 37.500 0.00 0.00 29.21 3.32
3643 4930 4.928615 CAGGAAAACAGCTTTTTGAACACA 59.071 37.500 0.00 0.00 29.21 3.72
3658 4945 8.932945 TTTTGAACACAGTACAATTGCAAATA 57.067 26.923 1.71 0.00 0.00 1.40
3673 4960 6.859420 TTGCAAATACTCATATACACGCAT 57.141 33.333 0.00 0.00 0.00 4.73
3711 4998 2.628972 CGAACATCGTTGCATGCAC 58.371 52.632 22.58 14.60 34.72 4.57
3712 4999 0.110283 CGAACATCGTTGCATGCACA 60.110 50.000 22.58 9.24 34.72 4.57
3713 5000 1.466192 CGAACATCGTTGCATGCACAT 60.466 47.619 22.58 10.06 34.72 3.21
3714 5001 2.222999 CGAACATCGTTGCATGCACATA 60.223 45.455 22.58 8.79 34.72 2.29
3718 5005 1.807139 TCGTTGCATGCACATACACT 58.193 45.000 22.58 0.00 0.00 3.55
3729 5016 4.023291 TGCACATACACTCATCCTACTGA 58.977 43.478 0.00 0.00 0.00 3.41
3731 5018 4.806247 GCACATACACTCATCCTACTGAAC 59.194 45.833 0.00 0.00 0.00 3.18
3755 5042 5.391312 AACATCGCTGAAAAGGCTAAAAT 57.609 34.783 0.00 0.00 0.00 1.82
3756 5043 6.509418 AACATCGCTGAAAAGGCTAAAATA 57.491 33.333 0.00 0.00 0.00 1.40
3761 5048 6.560711 TCGCTGAAAAGGCTAAAATAAATCC 58.439 36.000 0.00 0.00 0.00 3.01
3797 5084 5.296813 AGCTAATGACAAACAATTCCGAC 57.703 39.130 0.00 0.00 0.00 4.79
3800 5087 0.233590 TGACAAACAATTCCGACGCG 59.766 50.000 3.53 3.53 0.00 6.01
3807 5094 0.658829 CAATTCCGACGCGCAACAAA 60.659 50.000 5.73 0.00 0.00 2.83
3821 5108 5.500825 GCGCAACAAAATTTTGAAGATTGT 58.499 33.333 32.20 10.38 40.55 2.71
3843 5130 5.048294 TGTTCTATAGAAAGTCTCACACGCA 60.048 40.000 16.73 3.68 35.58 5.24
3897 5184 0.767375 ATGGTGCTGAGTGTTGACCT 59.233 50.000 0.00 0.00 0.00 3.85
3901 5188 2.610727 GGTGCTGAGTGTTGACCTACTC 60.611 54.545 0.00 0.00 42.77 2.59
3922 5209 7.875327 ACTCAAAGGTAACATGTTAAACAGT 57.125 32.000 19.63 12.29 41.41 3.55
3933 5220 6.292923 ACATGTTAAACAGTTAGGTGTAGCA 58.707 36.000 0.00 0.00 0.00 3.49
3934 5221 6.768861 ACATGTTAAACAGTTAGGTGTAGCAA 59.231 34.615 0.00 0.00 27.60 3.91
3950 5237 1.265568 GCAAAGATGCGCATGTTGAG 58.734 50.000 32.39 27.04 43.83 3.02
3951 5238 1.135603 GCAAAGATGCGCATGTTGAGA 60.136 47.619 32.39 5.04 43.83 3.27
3952 5239 2.479049 GCAAAGATGCGCATGTTGAGAT 60.479 45.455 32.39 18.25 43.83 2.75
3953 5240 3.105937 CAAAGATGCGCATGTTGAGATG 58.894 45.455 30.56 21.25 0.00 2.90
3954 5241 2.320745 AGATGCGCATGTTGAGATGA 57.679 45.000 30.76 0.00 0.00 2.92
3956 5243 3.211865 AGATGCGCATGTTGAGATGAAT 58.788 40.909 30.76 0.00 0.00 2.57
3957 5244 2.836479 TGCGCATGTTGAGATGAATG 57.164 45.000 5.66 0.00 0.00 2.67
3958 5245 2.358015 TGCGCATGTTGAGATGAATGA 58.642 42.857 5.66 0.00 0.00 2.57
3959 5246 2.748532 TGCGCATGTTGAGATGAATGAA 59.251 40.909 5.66 0.00 0.00 2.57
3971 5259 3.833650 AGATGAATGAATGGCCACACAAA 59.166 39.130 8.16 2.33 0.00 2.83
3980 5268 0.804989 GGCCACACAAAGAAGGATCG 59.195 55.000 0.00 0.00 0.00 3.69
4001 5289 2.009774 GGTCCAACATTGTCGGAGATG 58.990 52.381 0.00 1.01 40.67 2.90
4002 5290 2.009774 GTCCAACATTGTCGGAGATGG 58.990 52.381 0.00 0.00 40.67 3.51
4005 5293 2.819608 CCAACATTGTCGGAGATGGTTT 59.180 45.455 0.00 0.00 40.67 3.27
4018 5306 4.210331 GAGATGGTTTGGGCATATTCAGT 58.790 43.478 0.00 0.00 0.00 3.41
4044 5332 1.674221 CCTACAGAAGCTCCAGTGCAC 60.674 57.143 9.40 9.40 34.99 4.57
4049 5337 3.169155 AAGCTCCAGTGCACAGCGA 62.169 57.895 21.04 9.85 38.26 4.93
4102 5390 0.884704 TCGGAGCAGACCAAACTTGC 60.885 55.000 0.00 0.00 0.00 4.01
4139 5427 6.037098 CCGTAAAGGAAGATCTGAAGTACTG 58.963 44.000 0.00 0.00 45.00 2.74
4141 5429 6.127703 CGTAAAGGAAGATCTGAAGTACTGGA 60.128 42.308 0.00 0.00 0.00 3.86
4148 5436 8.592809 GGAAGATCTGAAGTACTGGAATATCAT 58.407 37.037 0.00 0.00 0.00 2.45
4164 5452 8.000709 TGGAATATCATCAAAGAACTAGCCATT 58.999 33.333 0.00 0.00 0.00 3.16
4165 5453 8.295288 GGAATATCATCAAAGAACTAGCCATTG 58.705 37.037 0.00 0.00 0.00 2.82
4169 5457 5.645067 TCATCAAAGAACTAGCCATTGACAG 59.355 40.000 5.80 3.57 33.29 3.51
4209 5497 7.189693 TGCAAAGGCTATTGTTCTATTATCG 57.810 36.000 9.90 0.00 41.91 2.92
4210 5498 6.765989 TGCAAAGGCTATTGTTCTATTATCGT 59.234 34.615 9.90 0.00 41.91 3.73
4211 5499 7.282224 TGCAAAGGCTATTGTTCTATTATCGTT 59.718 33.333 9.90 0.00 41.91 3.85
4212 5500 8.129211 GCAAAGGCTATTGTTCTATTATCGTTT 58.871 33.333 9.90 0.00 36.96 3.60
4220 5508 7.868906 TTGTTCTATTATCGTTTTAAGGGGG 57.131 36.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.398554 CCACAATCGACTTGGCCCG 61.399 63.158 0.00 0.00 39.30 6.13
39 40 4.720902 CCCATCGCACAGGCCACA 62.721 66.667 5.01 0.00 36.38 4.17
59 60 9.844257 ATTATAGATATTCTAAGGCAGATTGCC 57.156 33.333 12.07 12.07 46.30 4.52
77 78 4.219507 CGTGCTCACCCTCAGATTATAGAT 59.780 45.833 0.00 0.00 0.00 1.98
79 80 3.570125 TCGTGCTCACCCTCAGATTATAG 59.430 47.826 0.00 0.00 0.00 1.31
80 81 3.318275 GTCGTGCTCACCCTCAGATTATA 59.682 47.826 0.00 0.00 0.00 0.98
81 82 2.101582 GTCGTGCTCACCCTCAGATTAT 59.898 50.000 0.00 0.00 0.00 1.28
83 84 0.247736 GTCGTGCTCACCCTCAGATT 59.752 55.000 0.00 0.00 0.00 2.40
99 100 3.333189 CATCTGCCGCCATCGTCG 61.333 66.667 0.00 0.00 0.00 5.12
100 101 2.969238 CCATCTGCCGCCATCGTC 60.969 66.667 0.00 0.00 0.00 4.20
101 102 3.785859 ACCATCTGCCGCCATCGT 61.786 61.111 0.00 0.00 0.00 3.73
102 103 3.274586 CACCATCTGCCGCCATCG 61.275 66.667 0.00 0.00 0.00 3.84
134 135 2.028130 TGTTGTGGGAGAATTTTGCGT 58.972 42.857 0.00 0.00 0.00 5.24
148 149 5.879237 TGAAGACTTTTAGCTGTTGTTGTG 58.121 37.500 0.00 0.00 0.00 3.33
194 201 2.621998 CCTAGCAGCATTTTCTCCCATG 59.378 50.000 0.00 0.00 0.00 3.66
195 202 2.243221 ACCTAGCAGCATTTTCTCCCAT 59.757 45.455 0.00 0.00 0.00 4.00
198 205 2.019984 CCACCTAGCAGCATTTTCTCC 58.980 52.381 0.00 0.00 0.00 3.71
215 222 7.865706 AAATACATCCATGTTCTTAGACCAC 57.134 36.000 0.00 0.00 41.97 4.16
263 270 2.226437 CCCGCAAATATCATGGCAGTAC 59.774 50.000 0.00 0.00 0.00 2.73
264 271 2.503331 CCCGCAAATATCATGGCAGTA 58.497 47.619 0.00 0.00 0.00 2.74
265 272 1.321474 CCCGCAAATATCATGGCAGT 58.679 50.000 0.00 0.00 0.00 4.40
266 273 0.038892 GCCCGCAAATATCATGGCAG 60.039 55.000 0.00 0.00 38.73 4.85
267 274 0.754587 TGCCCGCAAATATCATGGCA 60.755 50.000 0.00 0.00 45.96 4.92
268 275 0.038892 CTGCCCGCAAATATCATGGC 60.039 55.000 0.00 0.00 39.33 4.40
269 276 0.038892 GCTGCCCGCAAATATCATGG 60.039 55.000 0.00 0.00 38.92 3.66
270 277 0.956633 AGCTGCCCGCAAATATCATG 59.043 50.000 0.00 0.00 42.61 3.07
276 283 1.696063 ATATCAAGCTGCCCGCAAAT 58.304 45.000 0.00 0.00 42.61 2.32
281 288 3.746492 GGTAACTTATATCAAGCTGCCCG 59.254 47.826 0.00 0.00 0.00 6.13
282 289 4.714632 TGGTAACTTATATCAAGCTGCCC 58.285 43.478 0.00 0.00 37.61 5.36
284 291 7.083875 TGTTTGGTAACTTATATCAAGCTGC 57.916 36.000 0.00 0.00 35.24 5.25
313 320 9.234827 TCCGATCTATTCATTATTGATTGCAAT 57.765 29.630 12.83 12.83 46.11 3.56
325 332 7.012327 TGCGAGAAAAATTCCGATCTATTCATT 59.988 33.333 0.00 0.00 0.00 2.57
337 344 8.742554 TCTCTTTATTTTGCGAGAAAAATTCC 57.257 30.769 7.05 0.00 39.73 3.01
341 348 6.734137 TGCTCTCTTTATTTTGCGAGAAAAA 58.266 32.000 0.00 0.00 32.65 1.94
343 350 5.617751 GCTGCTCTCTTTATTTTGCGAGAAA 60.618 40.000 0.00 0.00 32.65 2.52
346 353 3.125829 TGCTGCTCTCTTTATTTTGCGAG 59.874 43.478 0.00 0.00 0.00 5.03
348 355 3.476295 TGCTGCTCTCTTTATTTTGCG 57.524 42.857 0.00 0.00 0.00 4.85
349 356 3.611549 GCTTGCTGCTCTCTTTATTTTGC 59.388 43.478 0.00 0.00 38.95 3.68
350 357 4.801891 TGCTTGCTGCTCTCTTTATTTTG 58.198 39.130 0.00 0.00 43.37 2.44
351 358 4.082354 CCTGCTTGCTGCTCTCTTTATTTT 60.082 41.667 0.00 0.00 43.37 1.82
352 359 3.442977 CCTGCTTGCTGCTCTCTTTATTT 59.557 43.478 0.00 0.00 43.37 1.40
355 362 1.625315 TCCTGCTTGCTGCTCTCTTTA 59.375 47.619 0.00 0.00 43.37 1.85
364 371 2.093288 TCACTTCCTATCCTGCTTGCTG 60.093 50.000 0.00 0.00 0.00 4.41
452 695 2.624364 GGCCCACGAGGAAAAGTAAAAA 59.376 45.455 0.00 0.00 38.24 1.94
455 698 1.061546 AGGCCCACGAGGAAAAGTAA 58.938 50.000 0.00 0.00 38.24 2.24
457 700 1.061546 TAAGGCCCACGAGGAAAAGT 58.938 50.000 0.00 0.00 38.24 2.66
458 701 2.420058 ATAAGGCCCACGAGGAAAAG 57.580 50.000 0.00 0.00 38.24 2.27
461 704 1.064979 GGAAATAAGGCCCACGAGGAA 60.065 52.381 0.00 0.00 38.24 3.36
515 927 4.889409 AGCTGGACTTCTTTTGTTTCATCA 59.111 37.500 0.00 0.00 0.00 3.07
518 930 3.312421 CGAGCTGGACTTCTTTTGTTTCA 59.688 43.478 0.00 0.00 0.00 2.69
523 935 2.872245 TGTTCGAGCTGGACTTCTTTTG 59.128 45.455 0.00 0.00 0.00 2.44
528 940 0.039437 TCGTGTTCGAGCTGGACTTC 60.039 55.000 0.00 0.00 41.35 3.01
540 952 1.606350 CGAAGCTCGTGGTCGTGTTC 61.606 60.000 0.00 0.00 38.33 3.18
581 993 1.219393 GGACGGGAAGCAGAGGAAG 59.781 63.158 0.00 0.00 0.00 3.46
714 1127 1.036707 GCTACTGACTGGGAGCCTAG 58.963 60.000 0.00 0.00 0.00 3.02
753 1166 0.179179 GCCGCAGCAAGAACAGAATC 60.179 55.000 0.00 0.00 39.53 2.52
780 1193 5.660460 AGGGTTGAAAATATCGGATTTTGC 58.340 37.500 11.98 0.00 32.03 3.68
792 1205 3.037549 TGACTGGCAAAGGGTTGAAAAT 58.962 40.909 0.00 0.00 36.83 1.82
834 1253 1.002544 AGTCTAGCTGAGGTTGGCAAC 59.997 52.381 21.92 21.92 0.00 4.17
835 1254 1.276421 GAGTCTAGCTGAGGTTGGCAA 59.724 52.381 0.00 0.00 0.00 4.52
836 1255 0.898320 GAGTCTAGCTGAGGTTGGCA 59.102 55.000 0.00 0.00 0.00 4.92
837 1256 1.134848 CAGAGTCTAGCTGAGGTTGGC 60.135 57.143 0.00 0.00 35.39 4.52
838 1257 1.134848 GCAGAGTCTAGCTGAGGTTGG 60.135 57.143 0.00 0.00 35.39 3.77
843 1262 2.622942 CCCTAAGCAGAGTCTAGCTGAG 59.377 54.545 16.40 16.40 41.70 3.35
853 1272 0.769873 ATGATGGCCCCTAAGCAGAG 59.230 55.000 0.00 0.00 0.00 3.35
859 1278 1.074090 TCGGGATGATGGCCCCTAA 60.074 57.895 0.00 0.00 42.92 2.69
890 1309 1.470458 GGGGATTGAACGACCGTAGAC 60.470 57.143 0.00 0.00 0.00 2.59
926 1346 6.214278 TGAAGGGGGTTGAACCTATTAGATA 58.786 40.000 14.87 0.00 38.64 1.98
928 1348 4.440808 TGAAGGGGGTTGAACCTATTAGA 58.559 43.478 14.87 0.00 38.64 2.10
941 1361 1.062428 TCGATGGATACTGAAGGGGGT 60.062 52.381 0.00 0.00 37.61 4.95
942 1362 1.344763 GTCGATGGATACTGAAGGGGG 59.655 57.143 0.00 0.00 37.61 5.40
965 1385 4.552355 GGAAATTGTCCAAAAAGTACCGG 58.448 43.478 0.00 0.00 46.97 5.28
1024 1444 1.298157 TTCCGCTTGGCATTCGACAG 61.298 55.000 9.94 0.00 0.00 3.51
1039 1459 1.094785 CTACCTGGTGGCAATTTCCG 58.905 55.000 10.23 0.00 36.63 4.30
1071 1491 2.155279 GGTTTCCTTCTCTTGGCAGAC 58.845 52.381 0.00 0.00 0.00 3.51
1150 1570 1.683385 GGTGGTCTGCTTCAGCTTTTT 59.317 47.619 0.00 0.00 42.66 1.94
1151 1571 1.322442 GGTGGTCTGCTTCAGCTTTT 58.678 50.000 0.00 0.00 42.66 2.27
1152 1572 0.183492 TGGTGGTCTGCTTCAGCTTT 59.817 50.000 0.00 0.00 42.66 3.51
1153 1573 0.183492 TTGGTGGTCTGCTTCAGCTT 59.817 50.000 0.00 0.00 42.66 3.74
1154 1574 0.403271 ATTGGTGGTCTGCTTCAGCT 59.597 50.000 0.00 0.00 42.66 4.24
1155 1575 0.524862 CATTGGTGGTCTGCTTCAGC 59.475 55.000 0.00 0.00 42.50 4.26
1156 1576 0.524862 GCATTGGTGGTCTGCTTCAG 59.475 55.000 0.00 0.00 33.15 3.02
1157 1577 0.111061 AGCATTGGTGGTCTGCTTCA 59.889 50.000 0.00 0.00 43.44 3.02
1158 1578 0.807496 GAGCATTGGTGGTCTGCTTC 59.193 55.000 0.00 0.00 45.79 3.86
1159 1579 2.952714 GAGCATTGGTGGTCTGCTT 58.047 52.632 0.00 0.00 45.79 3.91
1301 2021 3.102985 CGGCACAACCAAACACGA 58.897 55.556 0.00 0.00 39.03 4.35
1527 2247 5.469373 TTCAACGCAATAGCATAGTTGAG 57.531 39.130 8.90 0.00 44.00 3.02
1546 2266 0.984230 AATGAGACCCTTCGCCTTCA 59.016 50.000 0.00 0.00 0.00 3.02
1692 2426 6.294176 GGCAAAGCTTAGTGAGATTCTGAAAA 60.294 38.462 0.00 0.00 31.52 2.29
1876 2916 7.328737 ACAATCTAACGTCATGTCTTCAAGTAC 59.671 37.037 0.00 0.00 0.00 2.73
1882 2922 5.168569 TCCACAATCTAACGTCATGTCTTC 58.831 41.667 0.00 0.00 0.00 2.87
2171 3212 1.612726 GCCTGCTCACTGAATCAACCT 60.613 52.381 0.00 0.00 0.00 3.50
2414 3657 6.627243 TCTTTAGCTAAACTATGAGCAACGA 58.373 36.000 14.96 3.86 41.36 3.85
2496 3748 6.925610 TTAAAGGAATTCCATCATGTCTCG 57.074 37.500 26.22 0.00 38.89 4.04
2562 3814 7.378461 GCGCAAATAGTTAAATAAGCATGCTTA 59.622 33.333 35.50 35.50 41.95 3.09
2563 3815 6.198966 GCGCAAATAGTTAAATAAGCATGCTT 59.801 34.615 33.70 33.70 39.83 3.91
2564 3816 5.687285 GCGCAAATAGTTAAATAAGCATGCT 59.313 36.000 16.30 16.30 0.00 3.79
2565 3817 5.458452 TGCGCAAATAGTTAAATAAGCATGC 59.542 36.000 8.16 10.51 0.00 4.06
2566 3818 7.009083 TGTTGCGCAAATAGTTAAATAAGCATG 59.991 33.333 26.87 0.00 0.00 4.06
2567 3819 7.009174 GTGTTGCGCAAATAGTTAAATAAGCAT 59.991 33.333 26.87 0.00 0.00 3.79
2568 3820 6.306837 GTGTTGCGCAAATAGTTAAATAAGCA 59.693 34.615 26.87 10.32 0.00 3.91
2569 3821 6.526674 AGTGTTGCGCAAATAGTTAAATAAGC 59.473 34.615 26.87 7.55 0.00 3.09
2570 3822 9.210426 CTAGTGTTGCGCAAATAGTTAAATAAG 57.790 33.333 26.87 8.95 0.00 1.73
2571 3823 8.723311 ACTAGTGTTGCGCAAATAGTTAAATAA 58.277 29.630 26.87 3.16 31.58 1.40
2572 3824 8.259049 ACTAGTGTTGCGCAAATAGTTAAATA 57.741 30.769 26.87 7.28 31.58 1.40
2573 3825 7.119262 AGACTAGTGTTGCGCAAATAGTTAAAT 59.881 33.333 29.46 19.37 34.15 1.40
3058 4343 2.226437 TCTTCAATGCTTTGAGAACCGC 59.774 45.455 13.97 0.00 42.60 5.68
3146 4431 0.038892 CAATGCAACACTCCAGCCAC 60.039 55.000 0.00 0.00 0.00 5.01
3150 4435 3.947910 AATTCCAATGCAACACTCCAG 57.052 42.857 0.00 0.00 0.00 3.86
3151 4436 3.896888 AGAAATTCCAATGCAACACTCCA 59.103 39.130 0.00 0.00 0.00 3.86
3186 4471 2.027073 GCTGACGACATTGCGGTGA 61.027 57.895 0.00 0.00 35.12 4.02
3249 4534 6.468333 ACAATAAATACATTCATGCAGGCA 57.532 33.333 0.00 0.00 0.00 4.75
3314 4599 1.899814 ACGGGCTCAGAACATGTCTTA 59.100 47.619 0.00 0.00 32.70 2.10
3337 4622 5.243426 ACACATTTACCACAACTTGTCAC 57.757 39.130 0.00 0.00 0.00 3.67
3338 4623 5.906113 AACACATTTACCACAACTTGTCA 57.094 34.783 0.00 0.00 0.00 3.58
3339 4624 7.254227 TCTAACACATTTACCACAACTTGTC 57.746 36.000 0.00 0.00 0.00 3.18
3340 4625 7.817418 ATCTAACACATTTACCACAACTTGT 57.183 32.000 0.00 0.00 0.00 3.16
3341 4626 9.528018 AAAATCTAACACATTTACCACAACTTG 57.472 29.630 0.00 0.00 0.00 3.16
3343 4628 9.528018 CAAAAATCTAACACATTTACCACAACT 57.472 29.630 0.00 0.00 0.00 3.16
3344 4629 8.272866 GCAAAAATCTAACACATTTACCACAAC 58.727 33.333 0.00 0.00 0.00 3.32
3345 4630 7.981789 TGCAAAAATCTAACACATTTACCACAA 59.018 29.630 0.00 0.00 0.00 3.33
3346 4631 7.492524 TGCAAAAATCTAACACATTTACCACA 58.507 30.769 0.00 0.00 0.00 4.17
3347 4632 7.938563 TGCAAAAATCTAACACATTTACCAC 57.061 32.000 0.00 0.00 0.00 4.16
3357 4642 6.202570 GCATGAGGTTTTGCAAAAATCTAACA 59.797 34.615 25.40 18.55 38.72 2.41
3358 4643 6.424812 AGCATGAGGTTTTGCAAAAATCTAAC 59.575 34.615 25.40 12.95 41.35 2.34
3385 4670 1.645710 ACTTTCACCGAGGTCCAGAT 58.354 50.000 0.00 0.00 0.00 2.90
3393 4678 1.725164 GCGTCCTAAACTTTCACCGAG 59.275 52.381 0.00 0.00 0.00 4.63
3473 4759 9.688592 GTCAAGTGAAGATCAAAGAAATTCAAT 57.311 29.630 0.00 0.00 32.13 2.57
3517 4803 6.039047 CAGTCTTACCGGCAGTAGATTAAGTA 59.961 42.308 0.00 0.00 30.92 2.24
3522 4808 2.431057 CCAGTCTTACCGGCAGTAGATT 59.569 50.000 0.00 0.00 30.92 2.40
3527 4813 2.663196 GCCAGTCTTACCGGCAGT 59.337 61.111 0.00 0.00 45.52 4.40
3533 4819 2.813908 CGGTGCGCCAGTCTTACC 60.814 66.667 18.18 2.22 34.09 2.85
3566 4852 5.772825 TTTCATTGTTGAAGGGACTGAAG 57.227 39.130 0.00 0.00 42.60 3.02
3591 4877 6.581171 ATTTCTTGTCTTCTTTGGCTTAGG 57.419 37.500 0.00 0.00 0.00 2.69
3614 4901 6.692486 TCAAAAAGCTGTTTTCCTGTAACAA 58.308 32.000 0.00 0.00 34.64 2.83
3620 4907 4.928615 TGTGTTCAAAAAGCTGTTTTCCTG 59.071 37.500 0.00 0.00 34.64 3.86
3631 4918 6.884096 TGCAATTGTACTGTGTTCAAAAAG 57.116 33.333 7.40 0.00 0.00 2.27
3658 4945 7.448748 TGAGTGTATATGCGTGTATATGAGT 57.551 36.000 1.32 0.00 0.00 3.41
3673 4960 6.600427 TGTTCGTTCAGTAGGATGAGTGTATA 59.400 38.462 0.00 0.00 0.00 1.47
3707 4994 4.023291 TCAGTAGGATGAGTGTATGTGCA 58.977 43.478 0.00 0.00 0.00 4.57
3708 4995 4.655762 TCAGTAGGATGAGTGTATGTGC 57.344 45.455 0.00 0.00 0.00 4.57
3709 4996 5.037385 CGTTCAGTAGGATGAGTGTATGTG 58.963 45.833 0.00 0.00 0.00 3.21
3710 4997 4.948004 TCGTTCAGTAGGATGAGTGTATGT 59.052 41.667 0.00 0.00 0.00 2.29
3711 4998 5.500645 TCGTTCAGTAGGATGAGTGTATG 57.499 43.478 0.00 0.00 0.00 2.39
3712 4999 5.417894 TGTTCGTTCAGTAGGATGAGTGTAT 59.582 40.000 0.00 0.00 0.00 2.29
3713 5000 4.763279 TGTTCGTTCAGTAGGATGAGTGTA 59.237 41.667 0.00 0.00 0.00 2.90
3714 5001 3.572682 TGTTCGTTCAGTAGGATGAGTGT 59.427 43.478 0.00 0.00 0.00 3.55
3718 5005 3.733988 GCGATGTTCGTTCAGTAGGATGA 60.734 47.826 0.00 0.00 42.81 2.92
3729 5016 1.069227 GCCTTTTCAGCGATGTTCGTT 60.069 47.619 0.00 0.00 42.81 3.85
3731 5018 0.798776 AGCCTTTTCAGCGATGTTCG 59.201 50.000 0.00 0.00 43.89 3.95
3756 5043 9.003658 CATTAGCTATCGTATTTTCCTGGATTT 57.996 33.333 0.00 0.00 0.00 2.17
3761 5048 7.946655 TGTCATTAGCTATCGTATTTTCCTG 57.053 36.000 0.00 0.00 0.00 3.86
3769 5056 7.042992 CGGAATTGTTTGTCATTAGCTATCGTA 60.043 37.037 0.00 0.00 0.00 3.43
3797 5084 3.832643 TCTTCAAAATTTTGTTGCGCG 57.167 38.095 25.98 0.00 39.18 6.86
3821 5108 5.048294 TGTGCGTGTGAGACTTTCTATAGAA 60.048 40.000 11.24 11.24 0.00 2.10
3829 5116 3.106242 TGTATGTGCGTGTGAGACTTT 57.894 42.857 0.00 0.00 0.00 2.66
3843 5130 7.309805 GGGATTGGCTTAAAAAGTCTTGTATGT 60.310 37.037 0.00 0.00 33.26 2.29
3897 5184 8.967664 ACTGTTTAACATGTTACCTTTGAGTA 57.032 30.769 17.85 0.00 0.00 2.59
3901 5188 8.626526 ACCTAACTGTTTAACATGTTACCTTTG 58.373 33.333 17.85 9.76 0.00 2.77
3916 5203 5.048713 GCATCTTTGCTACACCTAACTGTTT 60.049 40.000 0.00 0.00 45.77 2.83
3933 5220 3.011818 TCATCTCAACATGCGCATCTTT 58.988 40.909 22.51 13.99 0.00 2.52
3934 5221 2.635714 TCATCTCAACATGCGCATCTT 58.364 42.857 22.51 13.30 0.00 2.40
3950 5237 3.872511 TTGTGTGGCCATTCATTCATC 57.127 42.857 9.72 0.00 0.00 2.92
3951 5238 3.833650 TCTTTGTGTGGCCATTCATTCAT 59.166 39.130 9.72 0.00 0.00 2.57
3952 5239 3.229293 TCTTTGTGTGGCCATTCATTCA 58.771 40.909 9.72 0.00 0.00 2.57
3953 5240 3.940209 TCTTTGTGTGGCCATTCATTC 57.060 42.857 9.72 0.00 0.00 2.67
3954 5241 3.007182 CCTTCTTTGTGTGGCCATTCATT 59.993 43.478 9.72 0.00 0.00 2.57
3956 5243 1.962807 CCTTCTTTGTGTGGCCATTCA 59.037 47.619 9.72 8.91 0.00 2.57
3957 5244 2.238521 TCCTTCTTTGTGTGGCCATTC 58.761 47.619 9.72 5.88 0.00 2.67
3958 5245 2.380064 TCCTTCTTTGTGTGGCCATT 57.620 45.000 9.72 0.00 0.00 3.16
3959 5246 2.450476 GATCCTTCTTTGTGTGGCCAT 58.550 47.619 9.72 0.00 0.00 4.40
3980 5268 0.323629 TCTCCGACAATGTTGGACCC 59.676 55.000 18.05 0.00 40.82 4.46
3985 5273 3.366273 CCAAACCATCTCCGACAATGTTG 60.366 47.826 0.00 0.00 0.00 3.33
3991 5279 1.002624 GCCCAAACCATCTCCGACA 60.003 57.895 0.00 0.00 0.00 4.35
4001 5289 1.824230 TGCACTGAATATGCCCAAACC 59.176 47.619 0.00 0.00 42.69 3.27
4002 5290 3.450578 CATGCACTGAATATGCCCAAAC 58.549 45.455 0.00 0.00 42.69 2.93
4005 5293 1.034356 GCATGCACTGAATATGCCCA 58.966 50.000 14.21 0.00 42.69 5.36
4018 5306 0.107508 GGAGCTTCTGTAGGCATGCA 60.108 55.000 21.36 0.00 0.00 3.96
4049 5337 1.519408 ATCAACACGCTTTAGCCGTT 58.481 45.000 0.00 0.00 37.91 4.44
4060 5348 6.020599 CGACCTCTCTTAACATTATCAACACG 60.021 42.308 0.00 0.00 0.00 4.49
4102 5390 2.420129 CCTTTACGGACTCCTCCAATGG 60.420 54.545 0.00 0.00 36.12 3.16
4113 5401 5.074584 ACTTCAGATCTTCCTTTACGGAC 57.925 43.478 0.00 0.00 42.97 4.79
4121 5409 7.786943 TGATATTCCAGTACTTCAGATCTTCCT 59.213 37.037 0.00 0.00 0.00 3.36
4123 5411 9.638239 GATGATATTCCAGTACTTCAGATCTTC 57.362 37.037 0.00 0.00 0.00 2.87
4124 5412 9.152327 TGATGATATTCCAGTACTTCAGATCTT 57.848 33.333 0.00 0.00 0.00 2.40
4129 5417 9.605275 TTCTTTGATGATATTCCAGTACTTCAG 57.395 33.333 0.00 0.00 0.00 3.02
4139 5427 7.992754 ATGGCTAGTTCTTTGATGATATTCC 57.007 36.000 0.00 0.00 0.00 3.01
4141 5429 8.844244 GTCAATGGCTAGTTCTTTGATGATATT 58.156 33.333 14.55 0.00 33.16 1.28
4148 5436 4.202461 ACCTGTCAATGGCTAGTTCTTTGA 60.202 41.667 10.30 10.30 0.00 2.69
4164 5452 0.923358 AAAGGACCACCAACCTGTCA 59.077 50.000 0.00 0.00 38.94 3.58
4165 5453 2.943036 TAAAGGACCACCAACCTGTC 57.057 50.000 0.00 0.00 38.94 3.51
4169 5457 1.917872 TGCATAAAGGACCACCAACC 58.082 50.000 0.00 0.00 38.94 3.77


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

AutoCloner maintained by Alex Coulton.