Multiple sequence alignment - TraesCS1D01G420800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G420800 chr1D 100.000 4753 0 0 1 4753 477181630 477186382 0.000000e+00 8778.0
1 TraesCS1D01G420800 chr1D 87.970 133 15 1 85 216 475277653 475277785 6.370000e-34 156.0
2 TraesCS1D01G420800 chr1D 94.565 92 5 0 2601 2692 415987234 415987143 4.960000e-30 143.0
3 TraesCS1D01G420800 chr1D 94.737 38 0 2 624 661 432998023 432997988 1.850000e-04 58.4
4 TraesCS1D01G420800 chr1B 91.424 2029 123 20 602 2606 664768255 664770256 0.000000e+00 2736.0
5 TraesCS1D01G420800 chr1B 91.602 1286 72 17 3426 4698 664772119 664773381 0.000000e+00 1744.0
6 TraesCS1D01G420800 chr1B 91.785 633 32 11 2739 3359 664771467 664772091 0.000000e+00 863.0
7 TraesCS1D01G420800 chr1B 87.281 228 26 3 223 448 664767853 664768079 1.700000e-64 257.0
8 TraesCS1D01G420800 chr1B 85.268 224 24 5 2 216 664767591 664767814 6.190000e-54 222.0
9 TraesCS1D01G420800 chr1B 97.674 86 2 0 2608 2693 322104631 322104546 1.070000e-31 148.0
10 TraesCS1D01G420800 chr1B 85.714 140 16 2 85 223 486338121 486337985 1.380000e-30 145.0
11 TraesCS1D01G420800 chr1B 100.000 42 0 0 2691 2732 664770255 664770296 1.420000e-10 78.7
12 TraesCS1D01G420800 chr1B 100.000 30 0 0 4719 4748 664773368 664773397 6.640000e-04 56.5
13 TraesCS1D01G420800 chr1A 85.995 2035 149 61 2691 4698 573232279 573234204 0.000000e+00 2054.0
14 TraesCS1D01G420800 chr1A 94.359 1046 46 5 1572 2606 573231237 573232280 0.000000e+00 1592.0
15 TraesCS1D01G420800 chr1A 90.238 1178 80 19 660 1811 573230062 573231230 0.000000e+00 1506.0
16 TraesCS1D01G420800 chr1A 82.439 615 62 30 1 575 573229153 573229761 3.300000e-136 496.0
17 TraesCS1D01G420800 chr1A 92.925 212 15 0 3426 3637 562930203 562929992 4.620000e-80 309.0
18 TraesCS1D01G420800 chr1A 87.302 189 22 2 226 413 7842438 7842625 1.040000e-51 215.0
19 TraesCS1D01G420800 chr1A 98.551 69 1 0 3110 3178 562930401 562930333 6.460000e-24 122.0
20 TraesCS1D01G420800 chr1A 91.667 60 5 0 592 651 573229802 573229861 3.050000e-12 84.2
21 TraesCS1D01G420800 chr5D 92.537 268 20 0 3426 3693 382013041 382012774 7.460000e-103 385.0
22 TraesCS1D01G420800 chr5D 86.331 139 18 1 85 222 371279101 371278963 2.960000e-32 150.0
23 TraesCS1D01G420800 chr5D 85.612 139 19 1 85 222 67952634 67952496 1.380000e-30 145.0
24 TraesCS1D01G420800 chr5D 96.341 82 3 0 3278 3359 382013150 382013069 8.300000e-28 135.0
25 TraesCS1D01G420800 chr3A 92.164 268 21 0 3426 3693 235363916 235364183 3.470000e-101 379.0
26 TraesCS1D01G420800 chr3A 91.481 270 22 1 3426 3694 30183858 30184127 2.090000e-98 370.0
27 TraesCS1D01G420800 chr3A 96.341 82 3 0 3278 3359 30183749 30183830 8.300000e-28 135.0
28 TraesCS1D01G420800 chr3A 98.551 69 1 0 3110 3178 235363718 235363786 6.460000e-24 122.0
29 TraesCS1D01G420800 chr3B 87.435 191 22 2 226 415 4651611 4651422 8.010000e-53 219.0
30 TraesCS1D01G420800 chr3B 84.932 146 18 2 79 223 780286529 780286671 1.380000e-30 145.0
31 TraesCS1D01G420800 chr3B 92.857 42 1 2 624 665 732049057 732049018 5.140000e-05 60.2
32 TraesCS1D01G420800 chr2D 86.432 199 24 3 226 422 102278522 102278719 1.040000e-51 215.0
33 TraesCS1D01G420800 chr2D 86.010 193 25 2 226 417 650950094 650949903 6.230000e-49 206.0
34 TraesCS1D01G420800 chr2B 86.458 192 22 3 226 415 214598101 214597912 1.730000e-49 207.0
35 TraesCS1D01G420800 chr2B 85.864 191 25 2 226 414 77775145 77775335 8.070000e-48 202.0
36 TraesCS1D01G420800 chr4B 85.000 200 23 4 232 429 67560857 67561051 3.750000e-46 196.0
37 TraesCS1D01G420800 chr4B 88.571 140 14 2 85 223 640239218 640239080 8.180000e-38 169.0
38 TraesCS1D01G420800 chr6B 93.878 98 6 0 2596 2693 275935220 275935317 1.070000e-31 148.0
39 TraesCS1D01G420800 chr6B 92.500 40 1 2 623 662 683214148 683214111 6.640000e-04 56.5
40 TraesCS1D01G420800 chr4A 96.591 88 3 0 2605 2692 712733707 712733794 3.830000e-31 147.0
41 TraesCS1D01G420800 chr4A 85.612 139 19 1 85 222 578768174 578768036 1.380000e-30 145.0
42 TraesCS1D01G420800 chr4A 85.612 139 19 1 85 222 579439389 579439251 1.380000e-30 145.0
43 TraesCS1D01G420800 chrUn 95.604 91 3 1 2604 2694 62690467 62690556 1.380000e-30 145.0
44 TraesCS1D01G420800 chr7D 95.556 90 4 0 2603 2692 49828771 49828860 1.380000e-30 145.0
45 TraesCS1D01G420800 chr7D 85.612 139 19 1 85 222 153076177 153076039 1.380000e-30 145.0
46 TraesCS1D01G420800 chr5B 95.556 90 4 0 2604 2693 580683467 580683556 1.380000e-30 145.0
47 TraesCS1D01G420800 chr7A 93.684 95 6 0 2598 2692 129877033 129876939 4.960000e-30 143.0
48 TraesCS1D01G420800 chr7A 89.130 46 2 3 624 668 93133853 93133896 2.000000e-03 54.7
49 TraesCS1D01G420800 chr6A 93.684 95 6 0 2598 2692 432513620 432513526 4.960000e-30 143.0
50 TraesCS1D01G420800 chr6D 94.595 37 0 2 624 660 69911732 69911698 6.640000e-04 56.5
51 TraesCS1D01G420800 chr5A 94.595 37 0 2 624 660 136984973 136985007 6.640000e-04 56.5
52 TraesCS1D01G420800 chr2A 94.444 36 0 2 624 659 729162087 729162120 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 TraesCS1D01G420800 chr1D 477181630 477186382 4752 False 8778.000000 8778 100.0000 1 4753 1 chr1D.!!$F2 4752
1 TraesCS1D01G420800 chr1B 664767591 664773397 5806 False 851.028571 2736 92.4800 2 4748 7 chr1B.!!$F1 4746
2 TraesCS1D01G420800 chr1A 573229153 573234204 5051 False 1146.440000 2054 88.9396 1 4698 5 chr1A.!!$F2 4697

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
470 514 0.104304 AGCCTTGTACGATAAGGGCG 59.896 55.0 11.35 0.00 43.9 6.13 F
1259 1595 0.877071 CTCACGCATGCCAAACTCTT 59.123 50.0 13.15 0.00 0.0 2.85 F
1639 1986 0.108945 GCTTGACAAAGGCCATCAGC 60.109 55.0 5.01 5.44 42.6 4.26 F
2557 3160 0.878416 TGACATGCGTAACTTTGCCC 59.122 50.0 0.00 0.00 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1287 1623 0.323908 CGCTACCCAAAATTCCCCCA 60.324 55.0 0.0 0.0 0.0 4.96 R
2675 3278 0.042131 TGTTACTCCCTCCGTCCCAT 59.958 55.0 0.0 0.0 0.0 4.00 R
2676 3279 0.613853 CTGTTACTCCCTCCGTCCCA 60.614 60.0 0.0 0.0 0.0 4.37 R
4527 6321 0.327591 CCTGCTGCCTTCTCCTCTTT 59.672 55.0 0.0 0.0 0.0 2.52 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
66 67 1.448540 CAGAGTTTCTGCGCCCGAT 60.449 57.895 4.18 0.00 37.72 4.18
69 70 2.508439 GTTTCTGCGCCCGATCGA 60.508 61.111 18.66 0.00 0.00 3.59
89 90 4.619227 CGGAAGGTGGGCGTGTGT 62.619 66.667 0.00 0.00 0.00 3.72
90 91 2.668550 GGAAGGTGGGCGTGTGTC 60.669 66.667 0.00 0.00 0.00 3.67
91 92 2.426023 GAAGGTGGGCGTGTGTCT 59.574 61.111 0.00 0.00 0.00 3.41
92 93 1.668151 GAAGGTGGGCGTGTGTCTC 60.668 63.158 0.00 0.00 0.00 3.36
104 113 0.900182 TGTGTCTCCGGCAGATCTGT 60.900 55.000 23.38 0.00 32.08 3.41
114 123 1.457346 GCAGATCTGTCTTTGGTGGG 58.543 55.000 23.38 0.00 30.42 4.61
147 157 3.978855 TCTGTTCGTCATTGTCTACGTTG 59.021 43.478 0.00 0.00 39.99 4.10
156 166 2.787601 TGTCTACGTTGGTGTGTCTC 57.212 50.000 0.00 0.00 0.00 3.36
176 186 1.134491 CCAGGTTGTATCCTTCCGACC 60.134 57.143 0.00 0.00 35.37 4.79
184 194 1.606903 ATCCTTCCGACCTACGCTAG 58.393 55.000 0.00 0.00 41.07 3.42
216 226 1.305219 GCGGTTGCTATTCTGGTGCA 61.305 55.000 0.00 0.00 38.39 4.57
219 229 1.470098 GGTTGCTATTCTGGTGCACTG 59.530 52.381 17.98 10.30 36.37 3.66
222 232 1.073763 TGCTATTCTGGTGCACTGGTT 59.926 47.619 17.98 1.07 0.00 3.67
223 233 1.470098 GCTATTCTGGTGCACTGGTTG 59.530 52.381 17.98 3.00 0.00 3.77
246 287 4.515567 GCTCTACTACAACAAGTTTTGCCT 59.484 41.667 0.00 0.00 0.00 4.75
247 288 5.699458 GCTCTACTACAACAAGTTTTGCCTA 59.301 40.000 0.00 0.00 0.00 3.93
252 293 3.555966 ACAACAAGTTTTGCCTAGCTCT 58.444 40.909 0.00 0.00 0.00 4.09
272 314 3.917760 CGAGGGAGGGGCGATGAC 61.918 72.222 0.00 0.00 0.00 3.06
306 348 1.871039 GGCTCGCTTCAGTGTTTGTAA 59.129 47.619 0.00 0.00 0.00 2.41
374 416 3.729966 TGTTGTTCGTTGTACTGCCATA 58.270 40.909 0.00 0.00 0.00 2.74
376 418 4.024725 TGTTGTTCGTTGTACTGCCATAAC 60.025 41.667 0.00 0.00 0.00 1.89
377 419 2.732500 TGTTCGTTGTACTGCCATAACG 59.267 45.455 7.39 7.39 45.06 3.18
394 436 7.771361 TGCCATAACGGAAGATAAATAGTTTGA 59.229 33.333 0.00 0.00 36.56 2.69
410 454 3.686726 AGTTTGAATGTTTTGCCGCAAAA 59.313 34.783 24.13 24.13 40.41 2.44
463 507 6.870971 TCAGTTTTTAAAGCCTTGTACGAT 57.129 33.333 0.00 0.00 0.00 3.73
468 512 6.746745 TTTTAAAGCCTTGTACGATAAGGG 57.253 37.500 11.35 0.00 43.90 3.95
470 514 0.104304 AGCCTTGTACGATAAGGGCG 59.896 55.000 11.35 0.00 43.90 6.13
495 539 5.945144 TGTAGGTGTCCCTATTCCTTAAC 57.055 43.478 0.00 0.00 45.12 2.01
525 569 4.098349 TCAGTGCATTTTTCAAGCTTCAGT 59.902 37.500 0.00 0.00 0.00 3.41
531 575 4.955925 TTTTTCAAGCTTCAGTGAACGA 57.044 36.364 0.08 0.00 33.58 3.85
553 597 3.002759 ACAAGCAAGCGAAAGAAGAAGAC 59.997 43.478 0.00 0.00 0.00 3.01
821 1121 3.430374 GCTCCCTAAGAAATCGCAGTACA 60.430 47.826 0.00 0.00 0.00 2.90
828 1128 1.331756 GAAATCGCAGTACATGGGCTG 59.668 52.381 12.61 12.61 41.51 4.85
832 1132 1.006832 CGCAGTACATGGGCTGTAAC 58.993 55.000 16.55 3.83 41.93 2.50
838 1138 1.819632 CATGGGCTGTAACGGGCTC 60.820 63.158 0.00 0.00 35.52 4.70
839 1139 3.385749 ATGGGCTGTAACGGGCTCG 62.386 63.158 3.27 3.27 43.02 5.03
840 1140 3.766691 GGGCTGTAACGGGCTCGA 61.767 66.667 15.95 0.00 40.11 4.04
893 1193 7.069950 GGAAGAGTATTGGCCCATTAAGAAAAT 59.930 37.037 0.00 0.00 0.00 1.82
1208 1544 4.752101 GTCCCGTACTACTAGCTTCGATTA 59.248 45.833 0.00 0.00 0.00 1.75
1259 1595 0.877071 CTCACGCATGCCAAACTCTT 59.123 50.000 13.15 0.00 0.00 2.85
1287 1623 3.116096 TGGATTACCTGGTAGCAGACT 57.884 47.619 23.31 10.04 37.04 3.24
1293 1629 1.306141 CTGGTAGCAGACTGGGGGA 60.306 63.158 17.08 0.00 0.00 4.81
1370 1706 2.023598 TGATGTCCCTCTCCTGTCATCT 60.024 50.000 0.00 0.00 34.63 2.90
1371 1707 3.205282 TGATGTCCCTCTCCTGTCATCTA 59.795 47.826 0.00 0.00 34.63 1.98
1372 1708 3.304911 TGTCCCTCTCCTGTCATCTAG 57.695 52.381 0.00 0.00 0.00 2.43
1406 1745 6.944862 AGAATGGGGTATATGCTCAGAATTTC 59.055 38.462 0.00 0.00 0.00 2.17
1445 1784 7.380423 AGCACTGTTTCCATTAGGATATACT 57.620 36.000 0.00 0.00 45.26 2.12
1532 1879 6.865205 TGTATTCAGATGCATATCTTGACTCG 59.135 38.462 0.00 0.00 41.71 4.18
1539 1886 3.126858 TGCATATCTTGACTCGGTTTTGC 59.873 43.478 0.00 0.00 0.00 3.68
1548 1895 0.387622 CTCGGTTTTGCATGCCACTG 60.388 55.000 16.68 14.03 0.00 3.66
1639 1986 0.108945 GCTTGACAAAGGCCATCAGC 60.109 55.000 5.01 5.44 42.60 4.26
1664 2011 7.743838 GCGATCAGATTAAATGAACTGCTAATC 59.256 37.037 0.00 0.00 33.02 1.75
1668 2015 9.102757 TCAGATTAAATGAACTGCTAATCTCAC 57.897 33.333 0.00 0.00 38.46 3.51
1704 2051 4.192317 CAAGTAGCCAACTATCAAGTCCC 58.808 47.826 0.00 0.00 37.50 4.46
1720 2067 2.833943 AGTCCCCATCCTTCATTTTTGC 59.166 45.455 0.00 0.00 0.00 3.68
1764 2111 2.489938 ATAACTGACACCAATGCCGT 57.510 45.000 0.00 0.00 0.00 5.68
1803 2394 5.688621 TCAAACGACGACATACCATATTAGC 59.311 40.000 0.00 0.00 0.00 3.09
1827 2427 1.500474 CCAGAGCCCAGAGTCCATTA 58.500 55.000 0.00 0.00 0.00 1.90
1846 2446 9.933723 GTCCATTAAACTACTAAAACAGTCCTA 57.066 33.333 0.00 0.00 38.80 2.94
2051 2652 5.645497 GTCAGTTGGATTTGCTTGAGTAGAT 59.355 40.000 0.00 0.00 0.00 1.98
2102 2703 5.804639 AGAAGCATGTTATGTACTGGTTCA 58.195 37.500 18.72 3.93 40.64 3.18
2103 2704 6.237901 AGAAGCATGTTATGTACTGGTTCAA 58.762 36.000 18.72 0.00 40.64 2.69
2108 2709 4.013728 TGTTATGTACTGGTTCAATGGGC 58.986 43.478 0.00 0.00 0.00 5.36
2151 2752 1.229209 TTGAGAGGAGGAGGGCGTT 60.229 57.895 0.00 0.00 0.00 4.84
2210 2811 1.992557 TCTTCAACCCCCTTATGCTGT 59.007 47.619 0.00 0.00 0.00 4.40
2384 2987 5.843673 TCTCTGTGTTGATCTACTGATCC 57.156 43.478 8.74 0.00 46.34 3.36
2397 3000 9.745880 TGATCTACTGATCCGATTAAAAGTTAC 57.254 33.333 0.00 0.00 46.34 2.50
2398 3001 9.194271 GATCTACTGATCCGATTAAAAGTTACC 57.806 37.037 0.00 0.00 42.35 2.85
2412 3015 3.963428 AGTTACCTCTGCTACTTGGTG 57.037 47.619 0.00 0.00 34.33 4.17
2429 3032 3.527533 TGGTGTTATGTATTCTCCACGC 58.472 45.455 0.00 0.00 0.00 5.34
2445 3048 2.389998 CACGCGCATTTTACTTTTGGT 58.610 42.857 5.73 0.00 0.00 3.67
2455 3058 6.571731 GCATTTTACTTTTGGTCCTACCTTCC 60.572 42.308 0.00 0.00 39.58 3.46
2464 3067 2.026262 GGTCCTACCTTCCAGAATTGCA 60.026 50.000 0.00 0.00 34.73 4.08
2497 3100 2.584835 AGCAAAGTGGTTGGCAGATA 57.415 45.000 0.00 0.00 37.73 1.98
2514 3117 7.988737 TGGCAGATAACATCTTCACAAATTAG 58.011 34.615 0.00 0.00 37.58 1.73
2557 3160 0.878416 TGACATGCGTAACTTTGCCC 59.122 50.000 0.00 0.00 0.00 5.36
2589 3192 2.890808 TGTAGGCAGGAAGCTAATCG 57.109 50.000 0.00 0.00 44.79 3.34
2591 3194 2.362397 TGTAGGCAGGAAGCTAATCGAG 59.638 50.000 0.00 0.00 44.79 4.04
2610 3213 8.988546 AATCGAGCATCCTGATATATAGTACT 57.011 34.615 0.00 0.00 0.00 2.73
2611 3214 8.615878 ATCGAGCATCCTGATATATAGTACTC 57.384 38.462 0.00 0.00 0.00 2.59
2612 3215 6.993308 TCGAGCATCCTGATATATAGTACTCC 59.007 42.308 0.00 0.00 0.00 3.85
2613 3216 6.205853 CGAGCATCCTGATATATAGTACTCCC 59.794 46.154 0.00 0.00 0.00 4.30
2614 3217 7.232552 AGCATCCTGATATATAGTACTCCCT 57.767 40.000 0.00 0.00 0.00 4.20
2615 3218 7.294584 AGCATCCTGATATATAGTACTCCCTC 58.705 42.308 0.00 0.00 0.00 4.30
2616 3219 6.492087 GCATCCTGATATATAGTACTCCCTCC 59.508 46.154 0.00 0.00 0.00 4.30
2617 3220 6.249911 TCCTGATATATAGTACTCCCTCCG 57.750 45.833 0.00 0.00 0.00 4.63
2618 3221 5.730207 TCCTGATATATAGTACTCCCTCCGT 59.270 44.000 0.00 0.00 0.00 4.69
2619 3222 6.056884 CCTGATATATAGTACTCCCTCCGTC 58.943 48.000 0.00 0.00 0.00 4.79
2620 3223 5.999044 TGATATATAGTACTCCCTCCGTCC 58.001 45.833 0.00 0.00 0.00 4.79
2621 3224 5.730207 TGATATATAGTACTCCCTCCGTCCT 59.270 44.000 0.00 0.00 0.00 3.85
2622 3225 6.905215 TGATATATAGTACTCCCTCCGTCCTA 59.095 42.308 0.00 0.00 0.00 2.94
2623 3226 7.571732 TGATATATAGTACTCCCTCCGTCCTAT 59.428 40.741 0.00 0.00 0.00 2.57
2624 3227 9.099071 GATATATAGTACTCCCTCCGTCCTATA 57.901 40.741 0.00 0.00 0.00 1.31
2625 3228 7.761981 ATATAGTACTCCCTCCGTCCTATAA 57.238 40.000 0.00 0.00 0.00 0.98
2626 3229 6.655376 ATAGTACTCCCTCCGTCCTATAAT 57.345 41.667 0.00 0.00 0.00 1.28
2627 3230 4.664392 AGTACTCCCTCCGTCCTATAATG 58.336 47.826 0.00 0.00 0.00 1.90
2628 3231 3.614568 ACTCCCTCCGTCCTATAATGT 57.385 47.619 0.00 0.00 0.00 2.71
2629 3232 4.736611 ACTCCCTCCGTCCTATAATGTA 57.263 45.455 0.00 0.00 0.00 2.29
2630 3233 4.664392 ACTCCCTCCGTCCTATAATGTAG 58.336 47.826 0.00 0.00 0.00 2.74
2631 3234 4.017808 CTCCCTCCGTCCTATAATGTAGG 58.982 52.174 0.00 0.00 36.06 3.18
2632 3235 3.659195 TCCCTCCGTCCTATAATGTAGGA 59.341 47.826 1.33 1.33 41.14 2.94
2686 3289 4.995124 CGTCTTATATTATGGGACGGAGG 58.005 47.826 17.59 0.00 43.69 4.30
2687 3290 4.142227 CGTCTTATATTATGGGACGGAGGG 60.142 50.000 17.59 0.46 43.69 4.30
2688 3291 5.021458 GTCTTATATTATGGGACGGAGGGA 58.979 45.833 0.00 0.00 0.00 4.20
2689 3292 5.127356 GTCTTATATTATGGGACGGAGGGAG 59.873 48.000 0.00 0.00 0.00 4.30
2690 3293 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2691 3294 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2766 4537 7.180229 TCTGTCTATTGTTTCCCTGTCTCATTA 59.820 37.037 0.00 0.00 0.00 1.90
2777 4548 6.973642 TCCCTGTCTCATTATTTCCATTCTT 58.026 36.000 0.00 0.00 0.00 2.52
3092 4863 7.553760 TGCTGATGAAAGCTATGTCAATCTAAA 59.446 33.333 0.00 0.00 43.90 1.85
3183 4957 4.207165 TGATCTTGGGCAGGTAATTAAGC 58.793 43.478 0.00 0.00 0.00 3.09
3190 4964 6.013554 TGGGCAGGTAATTAAGCTAGAAAT 57.986 37.500 0.00 0.00 33.59 2.17
3234 5017 6.476378 ACAGTTGTCATCCTTACTAATTGCT 58.524 36.000 0.00 0.00 0.00 3.91
3256 5039 2.599082 GCCGATACTGTTTCAGTTCGAG 59.401 50.000 22.36 16.96 42.59 4.04
3359 5142 1.827792 TGAAGAGGTTTCCCCCTTGA 58.172 50.000 0.00 0.00 34.03 3.02
3391 5174 7.333528 ACTTGCTTGAATGAGTCAAAGTAAA 57.666 32.000 0.00 0.00 45.67 2.01
3392 5175 7.771183 ACTTGCTTGAATGAGTCAAAGTAAAA 58.229 30.769 0.00 0.00 45.67 1.52
3393 5176 8.250332 ACTTGCTTGAATGAGTCAAAGTAAAAA 58.750 29.630 0.00 0.00 45.67 1.94
3443 5226 7.933396 TCATCATGCTGAAATAAATTCACGAT 58.067 30.769 0.00 0.00 43.08 3.73
3452 5235 7.680982 TGAAATAAATTCACGATTACCAGTCG 58.319 34.615 0.00 0.00 43.08 4.18
3460 5243 2.751259 ACGATTACCAGTCGCTTCTGTA 59.249 45.455 0.00 0.00 42.56 2.74
3461 5244 3.192001 ACGATTACCAGTCGCTTCTGTAA 59.808 43.478 0.00 0.00 42.56 2.41
3465 5248 3.188159 ACCAGTCGCTTCTGTAAAACA 57.812 42.857 4.74 0.00 34.02 2.83
3510 5293 0.948623 TCATTGTGCCGACAGAACCG 60.949 55.000 0.00 0.00 30.92 4.44
3619 5402 2.571653 CACCACATCTCCCTGTTTCCTA 59.428 50.000 0.00 0.00 0.00 2.94
3791 5574 5.238624 ACACTCAGCTGCCATCATATTAT 57.761 39.130 9.47 0.00 0.00 1.28
3812 5595 1.679680 TCGATGTACATCCGAAGTCCC 59.320 52.381 26.33 3.15 34.40 4.46
3840 5624 5.070446 ACATATACCTAGCAAACTAGCAGCA 59.930 40.000 0.00 0.00 44.00 4.41
3875 5659 6.295518 GCTGATTGATGGTCCAGATATAGTCA 60.296 42.308 0.00 0.00 0.00 3.41
3887 5673 0.942252 TATAGTCATCGCTGCGACGT 59.058 50.000 28.41 9.95 39.18 4.34
3910 5696 5.993748 TGTCCATGTAGATGTCACAGTAA 57.006 39.130 0.00 0.00 0.00 2.24
3973 5759 3.621715 CCCCGTTCTGCTATTCTGTAAAC 59.378 47.826 0.00 0.00 0.00 2.01
3989 5775 5.876460 TCTGTAAACCATGTCATCATGTCAG 59.124 40.000 7.30 7.41 46.99 3.51
4037 5823 0.443869 CAATCACTTTCGCCCACTCG 59.556 55.000 0.00 0.00 0.00 4.18
4076 5862 6.466812 TCGCTTTCGAAATAGAAAAGAATCG 58.533 36.000 11.70 0.00 42.44 3.34
4090 5876 7.875971 AGAAAAGAATCGCACTTCTTGTAAAT 58.124 30.769 10.35 0.00 43.05 1.40
4252 6038 1.959282 CAACTTGCCTCAGCCTTTTCT 59.041 47.619 0.00 0.00 38.69 2.52
4253 6039 3.149196 CAACTTGCCTCAGCCTTTTCTA 58.851 45.455 0.00 0.00 38.69 2.10
4254 6040 3.728385 ACTTGCCTCAGCCTTTTCTAT 57.272 42.857 0.00 0.00 38.69 1.98
4255 6041 3.615155 ACTTGCCTCAGCCTTTTCTATC 58.385 45.455 0.00 0.00 38.69 2.08
4256 6042 3.265479 ACTTGCCTCAGCCTTTTCTATCT 59.735 43.478 0.00 0.00 38.69 1.98
4309 6103 2.296480 GCACGTCTCATCGCCGATC 61.296 63.158 0.00 0.00 0.00 3.69
4358 6152 1.135139 CTTCGATGCTTCCTCCTTCGA 59.865 52.381 0.00 0.00 37.19 3.71
4365 6159 1.946745 CTTCCTCCTTCGATCTTGGC 58.053 55.000 0.00 0.00 0.00 4.52
4406 6200 1.364901 GGTCGAGGTTGTCCGTTGA 59.635 57.895 0.00 0.00 39.05 3.18
4480 6274 2.057922 ACACAAGGAAGACATGGACCT 58.942 47.619 0.00 0.00 0.00 3.85
4503 6297 0.462759 GGCTACCAGTCTGACATGCC 60.463 60.000 10.88 11.24 0.00 4.40
4515 6309 1.142667 TGACATGCCACTCACCTGAAA 59.857 47.619 0.00 0.00 0.00 2.69
4517 6311 1.421268 ACATGCCACTCACCTGAAAGA 59.579 47.619 0.00 0.00 34.07 2.52
4525 6319 2.317371 TCACCTGAAAGAGGAGAGCT 57.683 50.000 0.00 0.00 46.33 4.09
4526 6320 1.898472 TCACCTGAAAGAGGAGAGCTG 59.102 52.381 0.00 0.00 46.33 4.24
4527 6321 1.898472 CACCTGAAAGAGGAGAGCTGA 59.102 52.381 0.00 0.00 46.33 4.26
4528 6322 2.301296 CACCTGAAAGAGGAGAGCTGAA 59.699 50.000 0.00 0.00 46.33 3.02
4529 6323 2.975489 ACCTGAAAGAGGAGAGCTGAAA 59.025 45.455 0.00 0.00 46.33 2.69
4530 6324 3.007831 ACCTGAAAGAGGAGAGCTGAAAG 59.992 47.826 0.00 0.00 46.33 2.62
4531 6325 3.260380 CCTGAAAGAGGAGAGCTGAAAGA 59.740 47.826 0.00 0.00 46.33 2.52
4532 6326 4.497300 CTGAAAGAGGAGAGCTGAAAGAG 58.503 47.826 0.00 0.00 30.70 2.85
4533 6327 3.260380 TGAAAGAGGAGAGCTGAAAGAGG 59.740 47.826 0.00 0.00 34.07 3.69
4534 6328 2.917713 AGAGGAGAGCTGAAAGAGGA 57.082 50.000 0.00 0.00 34.07 3.71
4535 6329 2.738743 AGAGGAGAGCTGAAAGAGGAG 58.261 52.381 0.00 0.00 34.07 3.69
4536 6330 2.311542 AGAGGAGAGCTGAAAGAGGAGA 59.688 50.000 0.00 0.00 34.07 3.71
4537 6331 3.096092 GAGGAGAGCTGAAAGAGGAGAA 58.904 50.000 0.00 0.00 34.07 2.87
4555 6349 2.794820 AAGGCAGCAGGACGAAGCTC 62.795 60.000 0.00 0.00 39.50 4.09
4583 6377 0.246360 TGCAGATGATCGTCACCGTT 59.754 50.000 17.13 0.00 35.01 4.44
4600 6401 0.248743 GTTGATGCCGATGCCACATG 60.249 55.000 0.00 0.00 36.33 3.21
4633 6434 1.737236 TCAATGAAACGAATCTGCGGG 59.263 47.619 0.00 0.00 35.12 6.13
4664 6465 0.524862 GTGTGCTCCCATTCTGCAAG 59.475 55.000 0.00 0.00 38.50 4.01
4666 6467 1.679977 TGCTCCCATTCTGCAAGGC 60.680 57.895 0.00 0.00 33.48 4.35
4678 6479 2.877974 GCAAGGCGTTTCGTCGTGT 61.878 57.895 10.58 0.00 42.23 4.49
4698 6499 0.244450 CAACCATGCCGTCAAATGCT 59.756 50.000 0.00 0.00 0.00 3.79
4699 6500 0.968405 AACCATGCCGTCAAATGCTT 59.032 45.000 0.00 0.00 0.00 3.91
4700 6501 0.527565 ACCATGCCGTCAAATGCTTC 59.472 50.000 0.00 0.00 0.00 3.86
4701 6502 0.813184 CCATGCCGTCAAATGCTTCT 59.187 50.000 0.00 0.00 0.00 2.85
4702 6503 1.203052 CCATGCCGTCAAATGCTTCTT 59.797 47.619 0.00 0.00 0.00 2.52
4703 6504 2.353011 CCATGCCGTCAAATGCTTCTTT 60.353 45.455 0.00 0.00 0.00 2.52
4704 6505 3.319755 CATGCCGTCAAATGCTTCTTTT 58.680 40.909 0.00 0.00 0.00 2.27
4705 6506 3.451141 TGCCGTCAAATGCTTCTTTTT 57.549 38.095 0.00 0.00 0.00 1.94
4727 6528 4.421033 TTTTTGCGTATAATGCCGTCAA 57.579 36.364 0.00 0.00 0.00 3.18
4728 6529 4.421033 TTTTGCGTATAATGCCGTCAAA 57.579 36.364 0.00 0.00 32.51 2.69
4748 6549 7.295201 GTCAAATGCATAGAAAACAGTCGTTA 58.705 34.615 0.00 0.00 33.99 3.18
4749 6550 7.962918 GTCAAATGCATAGAAAACAGTCGTTAT 59.037 33.333 0.00 0.00 33.99 1.89
4750 6551 7.962373 TCAAATGCATAGAAAACAGTCGTTATG 59.038 33.333 0.00 0.00 33.99 1.90
4751 6552 7.609760 AATGCATAGAAAACAGTCGTTATGA 57.390 32.000 0.00 0.00 33.99 2.15
4752 6553 7.609760 ATGCATAGAAAACAGTCGTTATGAA 57.390 32.000 0.00 0.00 33.99 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.153549 GATCGGGCGCAGAAACTCT 60.154 57.895 10.83 0.00 0.00 3.24
83 84 1.517257 GATCTGCCGGAGACACACG 60.517 63.158 5.05 0.00 31.75 4.49
89 90 1.205655 CAAAGACAGATCTGCCGGAGA 59.794 52.381 22.83 5.76 34.48 3.71
90 91 1.649664 CAAAGACAGATCTGCCGGAG 58.350 55.000 22.83 6.65 34.48 4.63
91 92 0.250234 CCAAAGACAGATCTGCCGGA 59.750 55.000 22.83 0.00 34.48 5.14
92 93 0.036010 ACCAAAGACAGATCTGCCGG 60.036 55.000 22.83 16.69 34.48 6.13
95 96 1.271597 ACCCACCAAAGACAGATCTGC 60.272 52.381 22.83 14.86 34.48 4.26
96 97 2.867109 ACCCACCAAAGACAGATCTG 57.133 50.000 21.37 21.37 34.48 2.90
97 98 3.490348 CAAACCCACCAAAGACAGATCT 58.510 45.455 0.00 0.00 36.42 2.75
104 113 0.181587 TCGAGCAAACCCACCAAAGA 59.818 50.000 0.00 0.00 0.00 2.52
147 157 2.354805 GGATACAACCTGGAGACACACC 60.355 54.545 0.00 0.00 35.60 4.16
156 166 1.134491 GGTCGGAAGGATACAACCTGG 60.134 57.143 0.00 0.00 40.49 4.45
176 186 1.660614 CGCCGATGAAGACTAGCGTAG 60.661 57.143 0.00 0.00 38.81 3.51
184 194 4.814294 ACCGCCGCCGATGAAGAC 62.814 66.667 0.00 0.00 36.29 3.01
216 226 4.101119 ACTTGTTGTAGTAGAGCAACCAGT 59.899 41.667 7.89 7.89 42.70 4.00
219 229 6.199393 CAAAACTTGTTGTAGTAGAGCAACC 58.801 40.000 0.00 0.00 42.91 3.77
222 232 4.274950 GGCAAAACTTGTTGTAGTAGAGCA 59.725 41.667 0.00 0.00 0.00 4.26
223 233 4.515567 AGGCAAAACTTGTTGTAGTAGAGC 59.484 41.667 0.00 0.00 0.00 4.09
224 234 6.128526 GCTAGGCAAAACTTGTTGTAGTAGAG 60.129 42.308 0.00 0.00 0.00 2.43
225 235 5.699458 GCTAGGCAAAACTTGTTGTAGTAGA 59.301 40.000 0.00 0.00 0.00 2.59
246 287 2.123683 CCTCCCTCGCCAGAGCTA 60.124 66.667 0.00 0.00 43.05 3.32
255 296 3.917760 GTCATCGCCCCTCCCTCG 61.918 72.222 0.00 0.00 0.00 4.63
282 324 1.222115 AACACTGAAGCGAGCCGAAC 61.222 55.000 0.00 0.00 0.00 3.95
286 328 1.508632 TACAAACACTGAAGCGAGCC 58.491 50.000 0.00 0.00 0.00 4.70
306 348 1.880675 CATAGACCACCTAGCGACGAT 59.119 52.381 0.00 0.00 0.00 3.73
355 397 3.184783 CGTTATGGCAGTACAACGAACAA 59.815 43.478 16.54 0.00 44.85 2.83
361 403 3.592059 TCTTCCGTTATGGCAGTACAAC 58.408 45.455 0.00 0.00 37.80 3.32
440 484 6.870971 ATCGTACAAGGCTTTAAAAACTGA 57.129 33.333 0.00 0.00 0.00 3.41
463 507 1.002315 GGACACCTACAAACGCCCTTA 59.998 52.381 0.00 0.00 0.00 2.69
495 539 5.284660 GCTTGAAAAATGCACTGAATAGACG 59.715 40.000 0.00 0.00 0.00 4.18
525 569 1.003972 CTTTCGCTTGCTTGTCGTTCA 60.004 47.619 0.00 0.00 0.00 3.18
531 575 3.002759 GTCTTCTTCTTTCGCTTGCTTGT 59.997 43.478 0.00 0.00 0.00 3.16
642 748 5.570205 ATCTTATACTCTCTCTCCGTCCA 57.430 43.478 0.00 0.00 0.00 4.02
651 757 7.651607 AGGGCATCTCATATCTTATACTCTCT 58.348 38.462 0.00 0.00 0.00 3.10
652 758 7.896383 AGGGCATCTCATATCTTATACTCTC 57.104 40.000 0.00 0.00 0.00 3.20
653 759 8.677870 AAAGGGCATCTCATATCTTATACTCT 57.322 34.615 0.00 0.00 0.00 3.24
698 997 2.717580 TCGAATGTGCTCTTACACGT 57.282 45.000 0.00 0.00 43.74 4.49
790 1090 6.516860 GCGATTTCTTAGGGAGCAGATAGTAA 60.517 42.308 0.00 0.00 0.00 2.24
794 1094 3.641436 TGCGATTTCTTAGGGAGCAGATA 59.359 43.478 0.00 0.00 0.00 1.98
821 1121 2.590092 GAGCCCGTTACAGCCCAT 59.410 61.111 0.00 0.00 0.00 4.00
828 1128 1.198608 CGATTCGTCGAGCCCGTTAC 61.199 60.000 0.00 0.00 37.05 2.50
838 1138 2.813474 TGCCAAGGCGATTCGTCG 60.813 61.111 8.03 0.00 45.51 5.12
839 1139 2.785258 GTGCCAAGGCGATTCGTC 59.215 61.111 1.60 1.60 45.51 4.20
840 1140 3.118454 CGTGCCAAGGCGATTCGT 61.118 61.111 8.03 0.00 45.51 3.85
1208 1544 0.531311 GGAACGAAACACGACAGGGT 60.531 55.000 0.00 0.00 45.77 4.34
1259 1595 3.992943 ACCAGGTAATCCAATCGACAA 57.007 42.857 0.00 0.00 35.89 3.18
1287 1623 0.323908 CGCTACCCAAAATTCCCCCA 60.324 55.000 0.00 0.00 0.00 4.96
1293 1629 2.752903 CCTTGCTACGCTACCCAAAATT 59.247 45.455 0.00 0.00 0.00 1.82
1311 1647 1.203100 ACTGCCCAAATTCTCTGCCTT 60.203 47.619 0.00 0.00 0.00 4.35
1370 1706 7.287927 GCATATACCCCATTCTAGATGCTACTA 59.712 40.741 0.00 0.00 35.57 1.82
1371 1707 6.098982 GCATATACCCCATTCTAGATGCTACT 59.901 42.308 0.00 0.00 35.57 2.57
1372 1708 6.098982 AGCATATACCCCATTCTAGATGCTAC 59.901 42.308 8.08 0.00 43.06 3.58
1406 1745 1.093159 GTGCTCCTTCTTCCATGCTG 58.907 55.000 0.00 0.00 0.00 4.41
1445 1784 6.796785 TTTGATCTGATCCTGAGTCATACA 57.203 37.500 14.71 0.00 0.00 2.29
1489 1828 8.579850 TGAATACACAATCTGGCTAGAAAATT 57.420 30.769 3.02 0.00 36.32 1.82
1532 1879 0.392336 TTCCAGTGGCATGCAAAACC 59.608 50.000 21.36 1.47 0.00 3.27
1539 1886 3.777478 GTCAATGATTTCCAGTGGCATG 58.223 45.455 3.51 0.00 44.12 4.06
1636 1983 5.007430 AGCAGTTCATTTAATCTGATCGCTG 59.993 40.000 0.00 0.00 0.00 5.18
1639 1986 8.986847 AGATTAGCAGTTCATTTAATCTGATCG 58.013 33.333 5.15 0.00 39.88 3.69
1664 2011 3.502211 ACTTGGCTTTATCAAACCGTGAG 59.498 43.478 0.00 0.00 40.43 3.51
1668 2015 3.181500 GGCTACTTGGCTTTATCAAACCG 60.181 47.826 0.00 0.00 38.32 4.44
1704 2051 5.782047 TGTTGTAGCAAAAATGAAGGATGG 58.218 37.500 0.00 0.00 0.00 3.51
1745 2092 2.083774 CACGGCATTGGTGTCAGTTAT 58.916 47.619 0.00 0.00 0.00 1.89
1764 2111 5.107259 CGTCGTTTGATAGAACACCAAATCA 60.107 40.000 0.00 0.00 33.17 2.57
1803 2394 0.392336 GACTCTGGGCTCTGGCATAG 59.608 60.000 0.00 0.00 40.87 2.23
1827 2427 9.676861 ACAAAAGTAGGACTGTTTTAGTAGTTT 57.323 29.630 0.00 0.00 40.53 2.66
1846 2446 5.643348 CCAGAAAAGAAAAGGCAACAAAAGT 59.357 36.000 0.00 0.00 41.41 2.66
1964 2565 5.068067 GCCTGTACTATCTATAGCTAAGGCC 59.932 48.000 18.12 0.00 39.73 5.19
2051 2652 6.351541 GGTCTAACTGTCATGGTGTTGGTATA 60.352 42.308 0.00 0.00 0.00 1.47
2102 2703 0.695803 CCTACCTCCTCAGGCCCATT 60.696 60.000 0.00 0.00 45.05 3.16
2103 2704 1.074167 CCTACCTCCTCAGGCCCAT 60.074 63.158 0.00 0.00 45.05 4.00
2108 2709 1.234529 CCCTCCCTACCTCCTCAGG 59.765 68.421 0.00 0.00 46.87 3.86
2151 2752 0.771127 CACCAAGAGAAGGACCCCAA 59.229 55.000 0.00 0.00 0.00 4.12
2210 2811 4.234550 AGAGGTCATCTTATGTATGCCCA 58.765 43.478 0.00 0.00 32.99 5.36
2397 3000 4.207891 ACATAACACCAAGTAGCAGAGG 57.792 45.455 0.00 0.00 0.00 3.69
2398 3001 7.268586 AGAATACATAACACCAAGTAGCAGAG 58.731 38.462 0.00 0.00 0.00 3.35
2412 3015 2.198406 TGCGCGTGGAGAATACATAAC 58.802 47.619 8.43 0.00 0.00 1.89
2429 3032 4.457949 AGGTAGGACCAAAAGTAAAATGCG 59.542 41.667 0.00 0.00 41.95 4.73
2445 3048 5.708736 TTATGCAATTCTGGAAGGTAGGA 57.291 39.130 0.00 0.00 0.00 2.94
2455 3058 8.186163 TGCTTCTCAGTTAATTATGCAATTCTG 58.814 33.333 0.00 0.00 35.88 3.02
2464 3067 8.299570 CAACCACTTTGCTTCTCAGTTAATTAT 58.700 33.333 0.00 0.00 0.00 1.28
2497 3100 8.908786 TTCTCACTCTAATTTGTGAAGATGTT 57.091 30.769 9.01 0.00 41.80 2.71
2514 3117 6.144724 CACAACTGCTAGTTAACTTCTCACTC 59.855 42.308 14.49 0.00 36.03 3.51
2557 3160 5.674525 TCCTGCCTACAAGAATACTTCATG 58.325 41.667 0.00 0.00 33.70 3.07
2589 3192 7.294584 AGGGAGTACTATATATCAGGATGCTC 58.705 42.308 0.00 0.00 34.76 4.26
2591 3194 6.492087 GGAGGGAGTACTATATATCAGGATGC 59.508 46.154 0.00 0.00 34.76 3.91
2606 3209 4.405548 ACATTATAGGACGGAGGGAGTAC 58.594 47.826 0.00 0.00 0.00 2.73
2607 3210 4.736611 ACATTATAGGACGGAGGGAGTA 57.263 45.455 0.00 0.00 0.00 2.59
2608 3211 3.614568 ACATTATAGGACGGAGGGAGT 57.385 47.619 0.00 0.00 0.00 3.85
2609 3212 4.017808 CCTACATTATAGGACGGAGGGAG 58.982 52.174 0.00 0.00 36.85 4.30
2610 3213 3.659195 TCCTACATTATAGGACGGAGGGA 59.341 47.826 0.00 0.00 38.71 4.20
2611 3214 4.043608 TCCTACATTATAGGACGGAGGG 57.956 50.000 0.00 0.00 38.71 4.30
2659 3262 7.274447 TCCGTCCCATAATATAAGACGTTTTT 58.726 34.615 17.31 0.00 46.62 1.94
2660 3263 6.819284 TCCGTCCCATAATATAAGACGTTTT 58.181 36.000 17.31 0.00 46.62 2.43
2661 3264 6.409524 TCCGTCCCATAATATAAGACGTTT 57.590 37.500 17.31 0.00 46.62 3.60
2662 3265 5.047519 CCTCCGTCCCATAATATAAGACGTT 60.048 44.000 17.31 0.00 46.62 3.99
2663 3266 4.461781 CCTCCGTCCCATAATATAAGACGT 59.538 45.833 17.31 0.00 46.62 4.34
2665 3268 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
2666 3269 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2667 3270 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2668 3271 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2669 3272 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2670 3273 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2671 3274 4.154942 GTTACTCCCTCCGTCCCATAATA 58.845 47.826 0.00 0.00 0.00 0.98
2672 3275 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
2673 3276 2.292389 TGTTACTCCCTCCGTCCCATAA 60.292 50.000 0.00 0.00 0.00 1.90
2674 3277 1.288633 TGTTACTCCCTCCGTCCCATA 59.711 52.381 0.00 0.00 0.00 2.74
2675 3278 0.042131 TGTTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00
2676 3279 0.613853 CTGTTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
2677 3280 0.614134 ACTGTTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
2678 3281 1.264295 AACTGTTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
2679 3282 2.426381 CCTAACTGTTACTCCCTCCGTC 59.574 54.545 0.00 0.00 0.00 4.79
2680 3283 2.454538 CCTAACTGTTACTCCCTCCGT 58.545 52.381 0.00 0.00 0.00 4.69
2681 3284 1.136500 GCCTAACTGTTACTCCCTCCG 59.864 57.143 0.00 0.00 0.00 4.63
2682 3285 2.168728 CAGCCTAACTGTTACTCCCTCC 59.831 54.545 0.00 0.00 41.86 4.30
2683 3286 2.168728 CCAGCCTAACTGTTACTCCCTC 59.831 54.545 0.00 0.00 45.68 4.30
2684 3287 2.188817 CCAGCCTAACTGTTACTCCCT 58.811 52.381 0.00 0.00 45.68 4.20
2685 3288 1.407025 GCCAGCCTAACTGTTACTCCC 60.407 57.143 0.00 0.00 45.68 4.30
2686 3289 1.278127 TGCCAGCCTAACTGTTACTCC 59.722 52.381 0.00 0.00 45.68 3.85
2687 3290 2.762535 TGCCAGCCTAACTGTTACTC 57.237 50.000 0.00 0.00 45.68 2.59
2688 3291 3.347216 CAATGCCAGCCTAACTGTTACT 58.653 45.455 0.00 0.00 45.68 2.24
2689 3292 2.159379 GCAATGCCAGCCTAACTGTTAC 60.159 50.000 0.00 0.00 45.68 2.50
2690 3293 2.091541 GCAATGCCAGCCTAACTGTTA 58.908 47.619 0.00 0.00 45.68 2.41
2691 3294 0.890683 GCAATGCCAGCCTAACTGTT 59.109 50.000 0.00 0.00 45.68 3.16
2732 3335 8.378565 CAGGGAAACAATAGACAGATACCATAT 58.621 37.037 0.00 0.00 0.00 1.78
2733 3336 7.347222 ACAGGGAAACAATAGACAGATACCATA 59.653 37.037 0.00 0.00 0.00 2.74
2734 3337 6.158695 ACAGGGAAACAATAGACAGATACCAT 59.841 38.462 0.00 0.00 0.00 3.55
2735 3338 5.487488 ACAGGGAAACAATAGACAGATACCA 59.513 40.000 0.00 0.00 0.00 3.25
2743 4514 8.738645 AATAATGAGACAGGGAAACAATAGAC 57.261 34.615 0.00 0.00 0.00 2.59
2766 4537 7.722949 TTCAAGCCTGAATAAGAATGGAAAT 57.277 32.000 0.00 0.00 36.62 2.17
2777 4548 2.499197 TGCGTGTTTCAAGCCTGAATA 58.501 42.857 0.00 0.00 41.22 1.75
3092 4863 9.409839 CCTGCAAACTAGAGATAACAGGACTGT 62.410 44.444 12.70 0.00 45.00 3.55
3183 4957 9.667107 TGACTACCAACAAGGAAATATTTCTAG 57.333 33.333 23.85 17.22 41.22 2.43
3234 5017 2.029739 TCGAACTGAAACAGTATCGGCA 60.030 45.455 22.19 11.34 44.62 5.69
3359 5142 4.042187 ACTCATTCAAGCAAGTAGAAGGGT 59.958 41.667 0.00 0.00 0.00 4.34
3394 5177 9.461312 TGATACTATGCTTTTATCTGGTTTGTT 57.539 29.630 0.00 0.00 0.00 2.83
3424 5207 7.120579 ACTGGTAATCGTGAATTTATTTCAGCA 59.879 33.333 0.00 0.00 44.89 4.41
3443 5226 4.695396 TGTTTTACAGAAGCGACTGGTAA 58.305 39.130 15.27 9.58 41.59 2.85
3452 5235 7.136772 ACCTTCGTTAAATGTTTTACAGAAGC 58.863 34.615 15.39 0.00 33.90 3.86
3461 5244 8.388103 CGATGAGATAACCTTCGTTAAATGTTT 58.612 33.333 0.00 0.00 37.97 2.83
3465 5248 8.361139 AGATCGATGAGATAACCTTCGTTAAAT 58.639 33.333 0.54 0.00 40.26 1.40
3481 5264 1.791204 CGGCACAATGAGATCGATGAG 59.209 52.381 0.54 0.00 0.00 2.90
3482 5265 1.408702 TCGGCACAATGAGATCGATGA 59.591 47.619 0.54 0.00 0.00 2.92
3484 5267 1.136891 TGTCGGCACAATGAGATCGAT 59.863 47.619 0.00 0.00 0.00 3.59
3510 5293 2.303311 ACCCAGACTCTCTGCTTAAACC 59.697 50.000 0.00 0.00 42.98 3.27
3571 5354 3.074412 GACAGGTACCTGAACCATTGTG 58.926 50.000 41.87 17.56 46.30 3.33
3619 5402 1.077716 GGCCGGTAGCTGGAATGTT 60.078 57.895 1.90 0.00 43.05 2.71
3791 5574 2.100252 GGGACTTCGGATGTACATCGAA 59.900 50.000 26.58 26.58 38.69 3.71
3814 5597 6.586844 GCTGCTAGTTTGCTAGGTATATGTAC 59.413 42.308 0.00 0.00 43.69 2.90
3840 5624 6.043590 TGGACCATCAATCAGCTCATAGTTAT 59.956 38.462 0.00 0.00 0.00 1.89
3855 5639 5.336770 GCGATGACTATATCTGGACCATCAA 60.337 44.000 0.00 0.00 31.85 2.57
3856 5640 4.158579 GCGATGACTATATCTGGACCATCA 59.841 45.833 0.00 0.00 31.85 3.07
3857 5641 4.400884 AGCGATGACTATATCTGGACCATC 59.599 45.833 0.00 0.00 0.00 3.51
3858 5642 4.159321 CAGCGATGACTATATCTGGACCAT 59.841 45.833 0.00 0.00 0.00 3.55
3875 5659 2.809601 GGACAACGTCGCAGCGAT 60.810 61.111 22.72 3.69 38.42 4.58
3887 5673 4.890158 ACTGTGACATCTACATGGACAA 57.110 40.909 0.00 0.00 33.82 3.18
3910 5696 6.177610 TCTACCACAAGTTCTTTTCTGTGTT 58.822 36.000 0.00 0.00 0.00 3.32
3989 5775 1.974236 AGCTAGATCTGGTGGTATGGC 59.026 52.381 5.18 0.00 0.00 4.40
4037 5823 5.907391 TCGAAAGCGATTGTCTTTCTTTTTC 59.093 36.000 19.14 0.00 44.28 2.29
4060 5846 8.017946 ACAAGAAGTGCGATTCTTTTCTATTTC 58.982 33.333 11.99 0.00 45.10 2.17
4207 5993 1.562008 TGTCTGGTGAGGTTTGGTGAA 59.438 47.619 0.00 0.00 0.00 3.18
4309 6103 4.731612 AGTCAGGCACTCGCGCAG 62.732 66.667 8.75 6.77 39.92 5.18
4318 6112 1.664649 CGAACTCGCAAGTCAGGCA 60.665 57.895 0.00 0.00 33.48 4.75
4358 6152 1.827399 AACTGACCGGTCGCCAAGAT 61.827 55.000 28.70 12.87 0.00 2.40
4365 6159 3.048602 AGGTGAACTGACCGGTCG 58.951 61.111 28.70 23.92 41.35 4.79
4406 6200 2.108278 CTGACCGGAAAGGAACCCGT 62.108 60.000 9.46 0.00 45.00 5.28
4469 6263 1.834263 GTAGCCTTGAGGTCCATGTCT 59.166 52.381 0.00 0.00 37.57 3.41
4480 6274 2.009681 TGTCAGACTGGTAGCCTTGA 57.990 50.000 1.81 0.00 0.00 3.02
4515 6309 2.311542 TCTCCTCTTTCAGCTCTCCTCT 59.688 50.000 0.00 0.00 0.00 3.69
4517 6311 2.917713 TCTCCTCTTTCAGCTCTCCT 57.082 50.000 0.00 0.00 0.00 3.69
4524 6318 1.002888 TGCTGCCTTCTCCTCTTTCAG 59.997 52.381 0.00 0.00 0.00 3.02
4525 6319 1.002888 CTGCTGCCTTCTCCTCTTTCA 59.997 52.381 0.00 0.00 0.00 2.69
4526 6320 1.678425 CCTGCTGCCTTCTCCTCTTTC 60.678 57.143 0.00 0.00 0.00 2.62
4527 6321 0.327591 CCTGCTGCCTTCTCCTCTTT 59.672 55.000 0.00 0.00 0.00 2.52
4528 6322 0.546267 TCCTGCTGCCTTCTCCTCTT 60.546 55.000 0.00 0.00 0.00 2.85
4529 6323 1.079987 TCCTGCTGCCTTCTCCTCT 59.920 57.895 0.00 0.00 0.00 3.69
4530 6324 1.220477 GTCCTGCTGCCTTCTCCTC 59.780 63.158 0.00 0.00 0.00 3.71
4531 6325 2.654079 CGTCCTGCTGCCTTCTCCT 61.654 63.158 0.00 0.00 0.00 3.69
4532 6326 2.125350 CGTCCTGCTGCCTTCTCC 60.125 66.667 0.00 0.00 0.00 3.71
4533 6327 0.739112 CTTCGTCCTGCTGCCTTCTC 60.739 60.000 0.00 0.00 0.00 2.87
4534 6328 1.294780 CTTCGTCCTGCTGCCTTCT 59.705 57.895 0.00 0.00 0.00 2.85
4535 6329 2.394563 GCTTCGTCCTGCTGCCTTC 61.395 63.158 0.00 0.00 0.00 3.46
4536 6330 2.359230 GCTTCGTCCTGCTGCCTT 60.359 61.111 0.00 0.00 0.00 4.35
4537 6331 3.308014 GAGCTTCGTCCTGCTGCCT 62.308 63.158 0.00 0.00 39.91 4.75
4555 6349 1.563435 GATCATCTGCACCATCCGCG 61.563 60.000 0.00 0.00 0.00 6.46
4583 6377 1.077572 ACATGTGGCATCGGCATCA 60.078 52.632 0.00 0.00 43.71 3.07
4600 6401 4.436050 CGTTTCATTGATGTGCTACTCCAC 60.436 45.833 0.00 0.00 36.28 4.02
4614 6415 1.737236 TCCCGCAGATTCGTTTCATTG 59.263 47.619 0.00 0.00 0.00 2.82
4633 6434 1.518903 GAGCACACCAGCCAAACCTC 61.519 60.000 0.00 0.00 34.23 3.85
4664 6465 1.083847 GTTGACACGACGAAACGCC 60.084 57.895 0.00 0.00 36.70 5.68
4666 6467 0.856641 ATGGTTGACACGACGAAACG 59.143 50.000 0.00 0.00 39.31 3.60
4678 6479 0.243365 GCATTTGACGGCATGGTTGA 59.757 50.000 0.00 0.00 0.00 3.18
4706 6507 4.421033 TTGACGGCATTATACGCAAAAA 57.579 36.364 0.00 0.00 0.00 1.94
4707 6508 4.421033 TTTGACGGCATTATACGCAAAA 57.579 36.364 0.00 0.00 35.18 2.44
4708 6509 4.346970 CATTTGACGGCATTATACGCAAA 58.653 39.130 0.00 0.00 38.94 3.68
4709 6510 3.790456 GCATTTGACGGCATTATACGCAA 60.790 43.478 0.00 0.00 0.00 4.85
4710 6511 2.286713 GCATTTGACGGCATTATACGCA 60.287 45.455 0.00 0.00 0.00 5.24
4711 6512 2.286713 TGCATTTGACGGCATTATACGC 60.287 45.455 0.00 0.00 34.58 4.42
4712 6513 3.600717 TGCATTTGACGGCATTATACG 57.399 42.857 0.00 0.00 34.58 3.06
4719 6520 3.254411 TGTTTTCTATGCATTTGACGGCA 59.746 39.130 3.54 0.00 45.23 5.69
4720 6521 3.832276 TGTTTTCTATGCATTTGACGGC 58.168 40.909 3.54 0.00 0.00 5.68
4721 6522 5.046910 ACTGTTTTCTATGCATTTGACGG 57.953 39.130 3.54 5.20 0.00 4.79
4722 6523 4.783036 CGACTGTTTTCTATGCATTTGACG 59.217 41.667 3.54 0.00 0.00 4.35
4723 6524 5.689819 ACGACTGTTTTCTATGCATTTGAC 58.310 37.500 3.54 0.00 0.00 3.18
4724 6525 5.940192 ACGACTGTTTTCTATGCATTTGA 57.060 34.783 3.54 0.65 0.00 2.69
4725 6526 7.962373 TCATAACGACTGTTTTCTATGCATTTG 59.038 33.333 3.54 0.00 39.54 2.32
4726 6527 8.039603 TCATAACGACTGTTTTCTATGCATTT 57.960 30.769 3.54 0.00 39.54 2.32
4727 6528 7.609760 TCATAACGACTGTTTTCTATGCATT 57.390 32.000 3.54 0.00 39.54 3.56
4728 6529 7.609760 TTCATAACGACTGTTTTCTATGCAT 57.390 32.000 3.79 3.79 39.54 3.96


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

AutoCloner maintained by Alex Coulton.