Multiple sequence alignment - TraesCS2B01G074200

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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 TraesCS2B01G074200 chr2B 100.000 5249 0 0 1 5249 40274585 40279833 0.000000e+00 9694.0
1 TraesCS2B01G074200 chr2B 81.420 1437 154 54 3030 4397 40068958 40070350 0.000000e+00 1070.0
2 TraesCS2B01G074200 chr2B 91.383 499 41 2 2024 2521 40067994 40068491 0.000000e+00 682.0
3 TraesCS2B01G074200 chr2B 88.740 373 30 8 2667 3033 40068547 40068913 3.730000e-121 446.0
4 TraesCS2B01G074200 chr2B 92.177 294 18 3 4264 4554 618098097 618098388 1.360000e-110 411.0
5 TraesCS2B01G074200 chr2B 83.146 445 58 14 1125 1565 40067332 40067763 1.770000e-104 390.0
6 TraesCS2B01G074200 chr2B 86.761 355 35 10 168 521 40066017 40066360 8.250000e-103 385.0
7 TraesCS2B01G074200 chr2B 85.000 300 27 8 4793 5088 55914412 55914127 6.650000e-74 289.0
8 TraesCS2B01G074200 chr2B 88.333 240 23 4 1627 1862 40067765 40068003 3.090000e-72 283.0
9 TraesCS2B01G074200 chr2B 89.844 128 8 4 4962 5088 55925137 55925014 5.440000e-35 159.0
10 TraesCS2B01G074200 chr2B 83.654 104 10 7 4430 4531 40070356 40070454 2.010000e-14 91.6
11 TraesCS2B01G074200 chr2D 91.306 3646 205 55 1133 4730 24562187 24558606 0.000000e+00 4874.0
12 TraesCS2B01G074200 chr2D 82.470 1409 163 53 3033 4397 24703336 24701968 0.000000e+00 1157.0
13 TraesCS2B01G074200 chr2D 89.934 606 46 9 2024 2629 24704338 24703748 0.000000e+00 767.0
14 TraesCS2B01G074200 chr2D 87.102 659 55 20 2 647 24563518 24562877 0.000000e+00 719.0
15 TraesCS2B01G074200 chr2D 92.191 461 22 8 4793 5249 24558260 24557810 1.590000e-179 640.0
16 TraesCS2B01G074200 chr2D 91.455 433 26 9 717 1144 24562767 24562341 7.570000e-163 584.0
17 TraesCS2B01G074200 chr2D 88.889 369 30 6 2670 3033 24703746 24703384 1.340000e-120 444.0
18 TraesCS2B01G074200 chr2D 84.615 442 54 11 1132 1566 24704999 24704565 1.350000e-115 427.0
19 TraesCS2B01G074200 chr2D 87.333 300 28 7 4793 5088 33879538 33879245 8.420000e-88 335.0
20 TraesCS2B01G074200 chr2D 86.054 294 28 7 202 492 24706586 24706303 2.380000e-78 303.0
21 TraesCS2B01G074200 chr2D 86.777 242 24 5 1625 1862 24704566 24704329 4.030000e-66 263.0
22 TraesCS2B01G074200 chr2D 87.037 108 9 5 4433 4538 24701959 24701855 3.320000e-22 117.0
23 TraesCS2B01G074200 chr2D 91.139 79 4 3 4705 4781 24558288 24558365 2.590000e-18 104.0
24 TraesCS2B01G074200 chr2A 91.129 3641 216 48 1135 4730 27340365 27343943 0.000000e+00 4835.0
25 TraesCS2B01G074200 chr2A 91.104 607 54 0 2024 2630 27329379 27329985 0.000000e+00 822.0
26 TraesCS2B01G074200 chr2A 87.097 527 49 13 3030 3552 27330394 27330905 3.520000e-161 579.0
27 TraesCS2B01G074200 chr2A 88.409 440 27 10 711 1135 27339770 27340200 4.690000e-140 508.0
28 TraesCS2B01G074200 chr2A 83.158 570 62 18 3832 4397 27331091 27331630 1.700000e-134 490.0
29 TraesCS2B01G074200 chr2A 89.247 372 30 5 2667 3033 27329983 27330349 1.720000e-124 457.0
30 TraesCS2B01G074200 chr2A 84.807 441 54 10 1133 1566 27328715 27329149 1.040000e-116 431.0
31 TraesCS2B01G074200 chr2A 91.582 297 23 2 4954 5249 27344093 27344388 4.890000e-110 409.0
32 TraesCS2B01G074200 chr2A 81.920 448 35 28 92 521 27327354 27327773 2.340000e-88 337.0
33 TraesCS2B01G074200 chr2A 87.552 241 27 2 1625 1862 27329148 27329388 5.180000e-70 276.0
34 TraesCS2B01G074200 chr2A 78.252 469 52 24 280 707 27339119 27339578 6.750000e-64 255.0
35 TraesCS2B01G074200 chr2A 79.894 378 41 18 4899 5249 36671699 36672068 1.460000e-60 244.0
36 TraesCS2B01G074200 chr5B 93.515 293 13 4 4265 4554 49007518 49007229 1.040000e-116 431.0
37 TraesCS2B01G074200 chrUn 86.364 264 22 9 232 491 319885064 319884811 5.180000e-70 276.0
38 TraesCS2B01G074200 chrUn 86.364 264 22 9 232 491 360410286 360410033 5.180000e-70 276.0
39 TraesCS2B01G074200 chr3B 86.364 264 22 9 232 491 803436053 803436306 5.180000e-70 276.0
40 TraesCS2B01G074200 chr3B 85.985 264 23 9 232 491 803434242 803434495 2.410000e-68 270.0
41 TraesCS2B01G074200 chr3B 84.848 264 26 6 232 491 803481319 803481572 2.430000e-63 254.0
42 TraesCS2B01G074200 chr1A 100.000 28 0 0 6 33 500433994 500434021 9.000000e-03 52.8


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 TraesCS2B01G074200 chr2B 40274585 40279833 5248 False 9694.000000 9694 100.000000 1 5249 1 chr2B.!!$F1 5248
1 TraesCS2B01G074200 chr2B 40066017 40070454 4437 False 478.228571 1070 86.205286 168 4531 7 chr2B.!!$F3 4363
2 TraesCS2B01G074200 chr2D 24557810 24563518 5708 True 1704.250000 4874 90.513500 2 5249 4 chr2D.!!$R2 5247
3 TraesCS2B01G074200 chr2D 24701855 24706586 4731 True 496.857143 1157 86.539429 202 4538 7 chr2D.!!$R3 4336
4 TraesCS2B01G074200 chr2A 27339119 27344388 5269 False 1501.750000 4835 87.343000 280 5249 4 chr2A.!!$F3 4969
5 TraesCS2B01G074200 chr2A 27327354 27331630 4276 False 484.571429 822 86.412143 92 4397 7 chr2A.!!$F2 4305
6 TraesCS2B01G074200 chr3B 803434242 803436306 2064 False 273.000000 276 86.174500 232 491 2 chr3B.!!$F2 259

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
51 52 0.036765 CTTCCGTTGTCCCGAATCCA 60.037 55.0 0.00 0.0 0.00 3.41 F
1046 2435 0.041238 TCGACCCTCAGAAGACCCAT 59.959 55.0 0.00 0.0 0.00 4.00 F
1369 3016 0.378610 TGTAGATCGAGAGCACTGCG 59.621 55.0 0.00 0.0 0.00 5.18 F
3140 4849 0.809241 CCATCTCCGCAGCTGAGAAC 60.809 60.0 20.43 0.0 41.87 3.01 F
4002 5877 0.111639 TGGTTGGTACCCCTGCTTTC 59.888 55.0 10.07 0.0 44.35 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 3542 0.243907 ACGATCCACAGGAGACAACG 59.756 55.0 0.00 0.0 34.05 4.10 R
2894 4548 0.895530 TACTCAGCCTTTGGACTCCG 59.104 55.0 0.00 0.0 0.00 4.63 R
3363 5074 0.608856 ATCCATCGGTTGCACAGCAA 60.609 50.0 0.00 0.0 46.80 3.91 R
4051 5933 0.110056 GAGCGGTGACACAAATGCAG 60.110 55.0 8.08 0.0 0.00 4.41 R
4943 7131 0.609131 AAAGCGATGACCCCAAGTGG 60.609 55.0 0.00 0.0 0.00 4.00 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
28 29 4.200283 CACGCCTCTCCTCGCCTC 62.200 72.222 0.00 0.00 0.00 4.70
31 32 3.894947 GCCTCTCCTCGCCTCGTC 61.895 72.222 0.00 0.00 0.00 4.20
32 33 3.213402 CCTCTCCTCGCCTCGTCC 61.213 72.222 0.00 0.00 0.00 4.79
33 34 2.124487 CTCTCCTCGCCTCGTCCT 60.124 66.667 0.00 0.00 0.00 3.85
34 35 1.751162 CTCTCCTCGCCTCGTCCTT 60.751 63.158 0.00 0.00 0.00 3.36
35 36 1.720694 CTCTCCTCGCCTCGTCCTTC 61.721 65.000 0.00 0.00 0.00 3.46
36 37 2.754658 TCCTCGCCTCGTCCTTCC 60.755 66.667 0.00 0.00 0.00 3.46
44 45 1.080025 CTCGTCCTTCCGTTGTCCC 60.080 63.158 0.00 0.00 0.00 4.46
51 52 0.036765 CTTCCGTTGTCCCGAATCCA 60.037 55.000 0.00 0.00 0.00 3.41
55 56 0.168128 CGTTGTCCCGAATCCAAAGC 59.832 55.000 0.00 0.00 0.00 3.51
60 61 1.078426 CCCGAATCCAAAGCCGAGT 60.078 57.895 0.00 0.00 0.00 4.18
70 71 0.250770 AAAGCCGAGTCCAAACCCTC 60.251 55.000 0.00 0.00 0.00 4.30
75 76 0.685097 CGAGTCCAAACCCTCTCCAA 59.315 55.000 0.00 0.00 0.00 3.53
79 80 2.335712 CCAAACCCTCTCCAAGCGC 61.336 63.158 0.00 0.00 0.00 5.92
80 81 1.600636 CAAACCCTCTCCAAGCGCA 60.601 57.895 11.47 0.00 0.00 6.09
81 82 1.150536 AAACCCTCTCCAAGCGCAA 59.849 52.632 11.47 0.00 0.00 4.85
159 171 2.391389 CGCCAACTTTCCCTCGCTC 61.391 63.158 0.00 0.00 0.00 5.03
160 172 1.003233 GCCAACTTTCCCTCGCTCT 60.003 57.895 0.00 0.00 0.00 4.09
164 176 0.545548 AACTTTCCCTCGCTCTCCCT 60.546 55.000 0.00 0.00 0.00 4.20
227 239 1.202582 ACATACGCCGATATCCAGAGC 59.797 52.381 0.00 0.00 0.00 4.09
230 242 2.920645 CGCCGATATCCAGAGCCGT 61.921 63.158 0.00 0.00 0.00 5.68
457 485 1.115467 CGGCAGGGTCTAGATCTGTT 58.885 55.000 20.15 0.26 0.00 3.16
460 488 3.536570 GGCAGGGTCTAGATCTGTTTTC 58.463 50.000 20.15 9.04 0.00 2.29
462 490 3.935828 GCAGGGTCTAGATCTGTTTTCAC 59.064 47.826 20.15 0.00 0.00 3.18
493 534 6.418226 GCATCTCAAGCTGATGAAATGAATTC 59.582 38.462 14.88 0.00 42.68 2.17
502 543 8.658619 AGCTGATGAAATGAATTCTAGGACTAT 58.341 33.333 7.05 0.00 38.92 2.12
542 1669 3.711059 CTGCCATGGCTGGGACTCC 62.711 68.421 35.53 5.76 43.36 3.85
555 1689 1.997669 GGACTCCTGTAAAGTCGCAG 58.002 55.000 0.00 0.00 43.33 5.18
587 1723 1.041437 AGTAGCATTCTAGGCCGGTC 58.959 55.000 0.00 0.00 0.00 4.79
588 1724 1.041437 GTAGCATTCTAGGCCGGTCT 58.959 55.000 15.76 15.76 0.00 3.85
597 1733 0.544833 TAGGCCGGTCTGTGGGTTAA 60.545 55.000 21.58 0.00 0.00 2.01
647 1800 1.702957 AGGGTTTGTTGAGGGATTCGA 59.297 47.619 0.00 0.00 0.00 3.71
655 1808 6.925610 TTGTTGAGGGATTCGAGATTATTG 57.074 37.500 0.00 0.00 0.00 1.90
656 1809 6.233905 TGTTGAGGGATTCGAGATTATTGA 57.766 37.500 0.00 0.00 0.00 2.57
658 1811 7.282585 TGTTGAGGGATTCGAGATTATTGATT 58.717 34.615 0.00 0.00 0.00 2.57
660 1813 7.734924 TGAGGGATTCGAGATTATTGATTTG 57.265 36.000 0.00 0.00 0.00 2.32
661 1814 7.282585 TGAGGGATTCGAGATTATTGATTTGT 58.717 34.615 0.00 0.00 0.00 2.83
662 1815 7.775093 TGAGGGATTCGAGATTATTGATTTGTT 59.225 33.333 0.00 0.00 0.00 2.83
663 1816 8.159344 AGGGATTCGAGATTATTGATTTGTTC 57.841 34.615 0.00 0.00 0.00 3.18
699 1860 6.662865 TTGATGACAAATTTGAGGGCTTTA 57.337 33.333 24.64 0.00 32.73 1.85
700 1861 6.024552 TGATGACAAATTTGAGGGCTTTAC 57.975 37.500 24.64 6.52 0.00 2.01
710 1871 2.907458 AGGGCTTTACCTCTTGCAAT 57.093 45.000 0.00 0.00 35.43 3.56
711 1872 2.450476 AGGGCTTTACCTCTTGCAATG 58.550 47.619 0.00 0.00 35.43 2.82
712 1873 2.171003 GGGCTTTACCTCTTGCAATGT 58.829 47.619 0.00 0.28 39.10 2.71
713 1874 2.562738 GGGCTTTACCTCTTGCAATGTT 59.437 45.455 0.00 0.00 39.10 2.71
714 1875 3.761752 GGGCTTTACCTCTTGCAATGTTA 59.238 43.478 0.00 0.00 39.10 2.41
715 1876 4.402474 GGGCTTTACCTCTTGCAATGTTAT 59.598 41.667 0.00 0.00 39.10 1.89
717 1878 4.800471 GCTTTACCTCTTGCAATGTTATGC 59.200 41.667 0.00 2.80 46.58 3.14
718 1879 5.393461 GCTTTACCTCTTGCAATGTTATGCT 60.393 40.000 0.00 0.00 46.54 3.79
719 1880 5.818136 TTACCTCTTGCAATGTTATGCTC 57.182 39.130 0.00 0.00 46.54 4.26
733 2092 9.688592 CAATGTTATGCTCTTTTCTTCTTCTTT 57.311 29.630 0.00 0.00 0.00 2.52
746 2105 6.808008 TCTTCTTCTTTTGCTCTGTTATGG 57.192 37.500 0.00 0.00 0.00 2.74
758 2117 4.740695 GCTCTGTTATGGAGAATACACGAC 59.259 45.833 0.00 0.00 33.03 4.34
761 2120 6.124340 TCTGTTATGGAGAATACACGACCTA 58.876 40.000 0.00 0.00 0.00 3.08
762 2121 6.262496 TCTGTTATGGAGAATACACGACCTAG 59.738 42.308 0.00 0.00 0.00 3.02
763 2122 5.221130 GTTATGGAGAATACACGACCTAGC 58.779 45.833 0.00 0.00 0.00 3.42
786 2145 3.591196 TTGCAATGCCCTCAAACATAC 57.409 42.857 1.53 0.00 0.00 2.39
797 2156 5.183904 GCCCTCAAACATACTGTGATTCTTT 59.816 40.000 0.00 0.00 0.00 2.52
828 2207 7.372714 TGCTTTCATGAATATCATAACATGGC 58.627 34.615 9.40 9.69 40.00 4.40
840 2219 4.277174 TCATAACATGGCGTCTGTTTTTGT 59.723 37.500 9.52 0.00 37.89 2.83
850 2229 4.712763 CGTCTGTTTTTGTAAGATGGCTC 58.287 43.478 0.00 0.00 0.00 4.70
891 2272 2.285083 TGCGTATCTGCACCATTTACC 58.715 47.619 0.00 0.00 40.62 2.85
946 2332 1.482182 GCCCTTTTATTGCTTCCCTGG 59.518 52.381 0.00 0.00 0.00 4.45
987 2373 1.994467 CGCTCAATCAGTCGACTGC 59.006 57.895 35.48 23.54 43.46 4.40
1045 2434 0.178944 TTCGACCCTCAGAAGACCCA 60.179 55.000 0.00 0.00 0.00 4.51
1046 2435 0.041238 TCGACCCTCAGAAGACCCAT 59.959 55.000 0.00 0.00 0.00 4.00
1095 2484 9.888878 TTAAGTGATATATACAGCGACAGTTAC 57.111 33.333 0.00 0.00 0.00 2.50
1175 2819 5.182760 AGCCTCTTATTGCTTTGAAACAGAG 59.817 40.000 0.00 0.00 32.94 3.35
1210 2854 5.262588 ACCACCTTGTAAAGCAAAAAGAG 57.737 39.130 0.00 0.00 44.44 2.85
1243 2887 4.397481 TCATCTTCTCCACATGCTACAG 57.603 45.455 0.00 0.00 0.00 2.74
1345 2992 4.825546 ATGACAGTGAAGCTTGAAACAG 57.174 40.909 2.10 0.00 0.00 3.16
1358 3005 3.510388 TGAAACAGGAGCTGTAGATCG 57.490 47.619 0.00 0.00 44.62 3.69
1369 3016 0.378610 TGTAGATCGAGAGCACTGCG 59.621 55.000 0.00 0.00 0.00 5.18
1545 3197 7.462731 TGCATCAAAACTGACAAATTTTGTTC 58.537 30.769 15.54 9.66 45.52 3.18
1621 3274 5.123186 TGTGCCGAAATGGAAAATACAGTAG 59.877 40.000 0.00 0.00 42.00 2.57
1693 3346 3.457380 AGATAATGGATGTGGACAGCAGT 59.543 43.478 0.00 0.00 33.17 4.40
1902 3555 2.135933 GAGTTTCCGTTGTCTCCTGTG 58.864 52.381 0.00 0.00 0.00 3.66
1903 3556 1.202651 AGTTTCCGTTGTCTCCTGTGG 60.203 52.381 0.00 0.00 0.00 4.17
2119 3772 1.375908 GAGGTTGTGCAGATGCCGA 60.376 57.895 1.72 0.00 41.18 5.54
2595 4248 6.430962 ACTGGATGTGCAATATCAGATAGT 57.569 37.500 12.65 8.65 35.99 2.12
2630 4283 6.147864 TGAAGAAACACAGGAAATTTCTGG 57.852 37.500 17.42 12.02 40.85 3.86
2653 4306 5.451798 GGTGAAGCTTCAATTTCAACTCCAA 60.452 40.000 29.99 0.00 37.87 3.53
2695 4348 3.426292 GCAAACTAGGGCGTCTGATTTTC 60.426 47.826 0.00 0.00 0.00 2.29
2758 4411 3.142174 CTGTTGTCCAAGAGAAAGGTCC 58.858 50.000 0.00 0.00 33.97 4.46
2877 4531 3.243839 GGAGAAGTTTTGCAATGCTTGGA 60.244 43.478 17.21 0.00 0.00 3.53
2894 4548 4.553547 GCTTGGACTGATATCGATTTGTGC 60.554 45.833 1.71 3.97 0.00 4.57
3068 4777 5.367945 ACCACAGACAGGAAACTTAAGAA 57.632 39.130 10.09 0.00 40.21 2.52
3080 4789 8.983724 CAGGAAACTTAAGAACAGAACTTCTAG 58.016 37.037 10.09 0.00 40.21 2.43
3092 4801 6.827727 ACAGAACTTCTAGCTCCTTTACAAA 58.172 36.000 0.00 0.00 0.00 2.83
3098 4807 7.280356 ACTTCTAGCTCCTTTACAAACAAAGA 58.720 34.615 0.00 0.00 37.66 2.52
3101 4810 5.188327 AGCTCCTTTACAAACAAAGAAGC 57.812 39.130 0.00 0.00 43.85 3.86
3129 4838 1.486310 TCAACAGAATCCCCATCTCCG 59.514 52.381 0.00 0.00 0.00 4.63
3137 4846 2.108566 CCCATCTCCGCAGCTGAG 59.891 66.667 20.43 15.45 0.00 3.35
3140 4849 0.809241 CCATCTCCGCAGCTGAGAAC 60.809 60.000 20.43 0.00 41.87 3.01
3216 4925 6.659668 AGATGCATGATATAGAAAGCATTGCT 59.340 34.615 2.46 5.03 42.18 3.91
3259 4968 5.610398 TGAAGCACATGAGAAGTTTAGTGA 58.390 37.500 0.00 0.00 0.00 3.41
3266 4975 6.846283 CACATGAGAAGTTTAGTGAACGAAAC 59.154 38.462 0.00 10.16 43.20 2.78
3308 5017 6.916360 TTCTTTGCTTCCCAATTCTAACAT 57.084 33.333 0.00 0.00 32.49 2.71
3392 5104 3.565482 GCAACCGATGGATGATACAACAT 59.435 43.478 0.00 0.00 0.00 2.71
3431 5143 6.385649 ACCGTTGTTTGATGAAGTTACATT 57.614 33.333 0.00 0.00 0.00 2.71
3498 5289 7.643764 TGTCTTTCTGCGTTTCTCTAATTTTTG 59.356 33.333 0.00 0.00 0.00 2.44
3502 5293 6.435428 TCTGCGTTTCTCTAATTTTTGTTCC 58.565 36.000 0.00 0.00 0.00 3.62
3503 5294 6.038825 TCTGCGTTTCTCTAATTTTTGTTCCA 59.961 34.615 0.00 0.00 0.00 3.53
3526 5320 9.494271 TCCATTAGCTGCTTCTATTTATAACAG 57.506 33.333 7.79 0.00 0.00 3.16
3644 5466 2.821969 CCATCTGTTGGGACTGAAAAGG 59.178 50.000 0.00 0.00 42.33 3.11
3767 5620 5.693769 TGTTTAGGCTTACCAGAGCTTAT 57.306 39.130 0.00 0.00 42.32 1.73
3838 5713 1.055849 TCACAGCTGCTTCCCAACTA 58.944 50.000 15.27 0.00 0.00 2.24
3845 5720 5.128919 CAGCTGCTTCCCAACTATAATCTT 58.871 41.667 0.00 0.00 0.00 2.40
3858 5733 9.265901 CCAACTATAATCTTGTCAGATACTTGG 57.734 37.037 0.00 0.00 39.00 3.61
3940 5815 3.942115 GGAGAGAACTACAAGGAAATGGC 59.058 47.826 0.00 0.00 0.00 4.40
3992 5867 6.598525 GCTTTTGCAAAATATTGGTTGGTAC 58.401 36.000 24.06 0.00 46.58 3.34
4002 5877 0.111639 TGGTTGGTACCCCTGCTTTC 59.888 55.000 10.07 0.00 44.35 2.62
4009 5884 3.181423 TGGTACCCCTGCTTTCAAGATTT 60.181 43.478 10.07 0.00 0.00 2.17
4010 5885 3.193479 GGTACCCCTGCTTTCAAGATTTG 59.807 47.826 0.00 0.00 0.00 2.32
4011 5886 2.962859 ACCCCTGCTTTCAAGATTTGT 58.037 42.857 0.00 0.00 0.00 2.83
4012 5887 3.308401 ACCCCTGCTTTCAAGATTTGTT 58.692 40.909 0.00 0.00 0.00 2.83
4013 5888 3.711190 ACCCCTGCTTTCAAGATTTGTTT 59.289 39.130 0.00 0.00 0.00 2.83
4014 5889 4.898861 ACCCCTGCTTTCAAGATTTGTTTA 59.101 37.500 0.00 0.00 0.00 2.01
4015 5890 5.365314 ACCCCTGCTTTCAAGATTTGTTTAA 59.635 36.000 0.00 0.00 0.00 1.52
4088 5970 4.273480 CCGCTCACCACTATTAAAATCCTG 59.727 45.833 0.00 0.00 0.00 3.86
4092 5974 7.420800 GCTCACCACTATTAAAATCCTGATTG 58.579 38.462 0.00 0.00 0.00 2.67
4125 6007 0.951558 GAAAGAAGGCTGTTCCGCAA 59.048 50.000 0.00 0.00 40.77 4.85
4180 6062 1.449353 GCGGATGAAGCTGGAGGAT 59.551 57.895 0.00 0.00 0.00 3.24
4253 6135 2.213499 CCAGGGCGAGTTATGAACATC 58.787 52.381 0.00 0.00 0.00 3.06
4258 6140 4.949856 AGGGCGAGTTATGAACATCATTTT 59.050 37.500 0.00 0.00 38.26 1.82
4268 6150 8.408601 GTTATGAACATCATTTTGGCTGATAGT 58.591 33.333 0.00 0.00 38.26 2.12
4296 6178 7.121168 TCAGGCAGTTCTTTCATAATAAGTTGG 59.879 37.037 0.00 0.00 0.00 3.77
4397 6291 3.628257 CCAAGTAATGGGGGAATGCTTCT 60.628 47.826 0.00 0.00 46.27 2.85
4398 6292 3.303351 AGTAATGGGGGAATGCTTCTG 57.697 47.619 0.00 0.00 0.00 3.02
4446 6345 7.492524 TCTTCTAGCAGTGTATGTTTAGATGG 58.507 38.462 0.00 0.00 31.59 3.51
4495 6395 1.747355 CTGTTCCATCAGAATGCCACC 59.253 52.381 0.00 0.00 36.69 4.61
4520 6420 7.359264 CCTGTTGTAGTTTGTAGACAAGAATCG 60.359 40.741 0.00 0.00 37.15 3.34
4531 6431 2.522372 CAAGAATCGACTTGCTGCAG 57.478 50.000 10.11 10.11 40.24 4.41
4559 6459 5.384063 TGTTGCGGTTGATTTGATTGTAT 57.616 34.783 0.00 0.00 0.00 2.29
4560 6460 5.159925 TGTTGCGGTTGATTTGATTGTATG 58.840 37.500 0.00 0.00 0.00 2.39
4640 6540 6.460781 TCTGCTCTACTGTATCTAGCTAGAC 58.539 44.000 25.52 14.88 34.72 2.59
4646 6546 5.279255 ACTGTATCTAGCTAGACGAGTCA 57.721 43.478 25.52 16.93 34.72 3.41
4653 6553 3.337694 AGCTAGACGAGTCAGTGTAGT 57.662 47.619 15.43 5.56 39.37 2.73
4654 6554 3.264104 AGCTAGACGAGTCAGTGTAGTC 58.736 50.000 15.43 10.51 39.37 2.59
4655 6555 3.001414 GCTAGACGAGTCAGTGTAGTCA 58.999 50.000 15.43 0.00 39.37 3.41
4656 6556 3.181518 GCTAGACGAGTCAGTGTAGTCAC 60.182 52.174 15.43 0.00 39.37 3.67
4657 6557 2.152830 AGACGAGTCAGTGTAGTCACC 58.847 52.381 5.99 0.00 44.83 4.02
4672 6572 3.181329 AGTCACCTCACCCATGACATTA 58.819 45.455 6.40 0.00 44.26 1.90
4679 6579 3.941483 CTCACCCATGACATTACAGTTCC 59.059 47.826 0.00 0.00 0.00 3.62
4702 6604 8.908786 TCCATCAGTTTATGAATTACCATCTC 57.091 34.615 0.00 0.00 42.53 2.75
4736 6638 8.717821 TGACATAATTTTTGAGTGTAGTACTGC 58.282 33.333 5.39 4.49 40.53 4.40
4738 6640 9.938280 ACATAATTTTTGAGTGTAGTACTGCTA 57.062 29.630 12.42 0.00 40.53 3.49
4742 6644 7.576750 TTTTTGAGTGTAGTACTGCTATTCG 57.423 36.000 12.42 0.00 40.53 3.34
4743 6645 4.288670 TGAGTGTAGTACTGCTATTCGC 57.711 45.455 12.42 3.45 40.53 4.70
4746 6648 3.114065 GTGTAGTACTGCTATTCGCACC 58.886 50.000 12.42 0.00 45.47 5.01
4747 6649 2.756207 TGTAGTACTGCTATTCGCACCA 59.244 45.455 12.42 0.00 45.47 4.17
4748 6650 3.383505 TGTAGTACTGCTATTCGCACCAT 59.616 43.478 12.42 0.00 45.47 3.55
4749 6651 3.099267 AGTACTGCTATTCGCACCATC 57.901 47.619 0.00 0.00 45.47 3.51
4751 6653 2.698855 ACTGCTATTCGCACCATCTT 57.301 45.000 0.00 0.00 45.47 2.40
4752 6654 3.819564 ACTGCTATTCGCACCATCTTA 57.180 42.857 0.00 0.00 45.47 2.10
4753 6655 4.342862 ACTGCTATTCGCACCATCTTAT 57.657 40.909 0.00 0.00 45.47 1.73
4754 6656 4.310769 ACTGCTATTCGCACCATCTTATC 58.689 43.478 0.00 0.00 45.47 1.75
4755 6657 4.039730 ACTGCTATTCGCACCATCTTATCT 59.960 41.667 0.00 0.00 45.47 1.98
4756 6658 4.560128 TGCTATTCGCACCATCTTATCTC 58.440 43.478 0.00 0.00 45.47 2.75
4757 6659 4.039124 TGCTATTCGCACCATCTTATCTCA 59.961 41.667 0.00 0.00 45.47 3.27
4758 6660 4.991056 GCTATTCGCACCATCTTATCTCAA 59.009 41.667 0.00 0.00 38.92 3.02
4760 6662 6.813649 GCTATTCGCACCATCTTATCTCAATA 59.186 38.462 0.00 0.00 38.92 1.90
4763 6665 8.939201 ATTCGCACCATCTTATCTCAATATAG 57.061 34.615 0.00 0.00 0.00 1.31
4764 6666 6.333416 TCGCACCATCTTATCTCAATATAGC 58.667 40.000 0.00 0.00 0.00 2.97
4765 6667 6.071391 TCGCACCATCTTATCTCAATATAGCA 60.071 38.462 0.00 0.00 0.00 3.49
4768 6670 7.148340 GCACCATCTTATCTCAATATAGCAACC 60.148 40.741 0.00 0.00 0.00 3.77
4769 6671 7.879677 CACCATCTTATCTCAATATAGCAACCA 59.120 37.037 0.00 0.00 0.00 3.67
4772 6674 6.455647 TCTTATCTCAATATAGCAACCACCG 58.544 40.000 0.00 0.00 0.00 4.94
4773 6675 4.689612 ATCTCAATATAGCAACCACCGT 57.310 40.909 0.00 0.00 0.00 4.83
4774 6676 4.054780 TCTCAATATAGCAACCACCGTC 57.945 45.455 0.00 0.00 0.00 4.79
4776 6678 4.891168 TCTCAATATAGCAACCACCGTCTA 59.109 41.667 0.00 0.00 0.00 2.59
4777 6679 4.940463 TCAATATAGCAACCACCGTCTAC 58.060 43.478 0.00 0.00 0.00 2.59
4779 6681 5.105269 TCAATATAGCAACCACCGTCTACAA 60.105 40.000 0.00 0.00 0.00 2.41
4780 6682 3.688694 ATAGCAACCACCGTCTACAAA 57.311 42.857 0.00 0.00 0.00 2.83
4783 6685 1.944709 GCAACCACCGTCTACAAAACT 59.055 47.619 0.00 0.00 0.00 2.66
4784 6686 3.132925 GCAACCACCGTCTACAAAACTA 58.867 45.455 0.00 0.00 0.00 2.24
4785 6687 3.059393 GCAACCACCGTCTACAAAACTAC 60.059 47.826 0.00 0.00 0.00 2.73
4786 6688 4.374399 CAACCACCGTCTACAAAACTACT 58.626 43.478 0.00 0.00 0.00 2.57
4787 6689 4.248691 ACCACCGTCTACAAAACTACTC 57.751 45.455 0.00 0.00 0.00 2.59
4791 6977 5.508489 CCACCGTCTACAAAACTACTCTCAA 60.508 44.000 0.00 0.00 0.00 3.02
4862 7048 1.967494 GGCGTTAAAACCCAGCCGA 60.967 57.895 0.00 0.00 38.28 5.54
4870 7056 2.871096 AAACCCAGCCGATAAGTTGA 57.129 45.000 0.00 0.00 0.00 3.18
4943 7131 1.789078 CTGGTTCAGCTGGTGTGTGC 61.789 60.000 15.13 0.00 0.00 4.57
4949 7137 1.825191 AGCTGGTGTGTGCCACTTG 60.825 57.895 0.00 0.00 43.94 3.16
5009 7197 2.267426 GAGCGAGCTTCTTCTTCTTCC 58.733 52.381 0.00 0.00 0.00 3.46
5012 7200 2.887337 CGAGCTTCTTCTTCTTCCTCC 58.113 52.381 0.00 0.00 0.00 4.30
5055 7243 8.154649 AGTGTTGAAACAGAGTTAATGTTAGG 57.845 34.615 0.00 0.00 39.91 2.69
5063 7251 1.021968 GTTAATGTTAGGGGCTGGCG 58.978 55.000 0.00 0.00 0.00 5.69
5129 7318 7.493743 AGATTGATGATTTATCACAGCAGAC 57.506 36.000 0.00 0.00 45.22 3.51
5141 7330 1.610522 ACAGCAGACATGGAAAACAGC 59.389 47.619 0.00 0.00 0.00 4.40
5225 7415 8.021973 CCGTTAGCGTTTAGATCTATACAGAAT 58.978 37.037 19.35 7.57 33.21 2.40
5243 7433 5.330295 CAGAATGTCATTTAGCTGACTTGC 58.670 41.667 0.00 0.00 44.73 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.681978 AGGCGTGGCGTGGAGAAC 62.682 66.667 0.00 0.00 0.00 3.01
15 16 3.213402 GGACGAGGCGAGGAGAGG 61.213 72.222 0.00 0.00 0.00 3.69
25 26 1.080025 GGACAACGGAAGGACGAGG 60.080 63.158 0.00 0.00 37.61 4.63
27 28 2.922950 CGGGACAACGGAAGGACGA 61.923 63.158 0.00 0.00 37.61 4.20
28 29 2.424705 TTCGGGACAACGGAAGGACG 62.425 60.000 0.00 0.00 40.31 4.79
29 30 0.036671 ATTCGGGACAACGGAAGGAC 60.037 55.000 0.00 0.00 33.72 3.85
31 32 0.743345 GGATTCGGGACAACGGAAGG 60.743 60.000 0.00 0.00 33.72 3.46
32 33 0.036765 TGGATTCGGGACAACGGAAG 60.037 55.000 0.00 0.00 33.72 3.46
33 34 0.397187 TTGGATTCGGGACAACGGAA 59.603 50.000 0.00 0.00 33.72 4.30
34 35 0.397187 TTTGGATTCGGGACAACGGA 59.603 50.000 0.00 0.00 0.00 4.69
35 36 0.802494 CTTTGGATTCGGGACAACGG 59.198 55.000 0.00 0.00 0.00 4.44
36 37 0.168128 GCTTTGGATTCGGGACAACG 59.832 55.000 0.00 0.00 0.00 4.10
44 45 0.391130 TGGACTCGGCTTTGGATTCG 60.391 55.000 0.00 0.00 0.00 3.34
51 52 0.250770 GAGGGTTTGGACTCGGCTTT 60.251 55.000 0.00 0.00 0.00 3.51
55 56 1.192146 TGGAGAGGGTTTGGACTCGG 61.192 60.000 0.00 0.00 38.72 4.63
60 61 1.374947 CGCTTGGAGAGGGTTTGGA 59.625 57.895 0.00 0.00 33.85 3.53
88 89 1.624487 GAAAAATTTGTAGCGGCCCG 58.376 50.000 0.00 0.00 0.00 6.13
90 91 0.989164 GCGAAAAATTTGTAGCGGCC 59.011 50.000 0.00 0.00 0.00 6.13
91 92 1.911464 GAGCGAAAAATTTGTAGCGGC 59.089 47.619 7.69 0.00 0.00 6.53
92 93 2.515912 GGAGCGAAAAATTTGTAGCGG 58.484 47.619 7.69 0.00 0.00 5.52
94 95 2.492088 AGGGGAGCGAAAAATTTGTAGC 59.508 45.455 5.38 5.38 0.00 3.58
95 96 4.380550 GGAAGGGGAGCGAAAAATTTGTAG 60.381 45.833 0.00 0.00 0.00 2.74
96 97 3.508402 GGAAGGGGAGCGAAAAATTTGTA 59.492 43.478 0.00 0.00 0.00 2.41
97 98 2.299013 GGAAGGGGAGCGAAAAATTTGT 59.701 45.455 0.00 0.00 0.00 2.83
99 100 1.899814 GGGAAGGGGAGCGAAAAATTT 59.100 47.619 0.00 0.00 0.00 1.82
102 107 1.302993 CGGGAAGGGGAGCGAAAAA 60.303 57.895 0.00 0.00 0.00 1.94
103 108 2.349755 CGGGAAGGGGAGCGAAAA 59.650 61.111 0.00 0.00 0.00 2.29
159 171 4.214327 GGCGCGAAGGAGAGGGAG 62.214 72.222 12.10 0.00 0.00 4.30
164 176 4.760047 GGCTTGGCGCGAAGGAGA 62.760 66.667 29.61 0.00 40.44 3.71
227 239 0.608640 AACCCTACTCTGCTTCACGG 59.391 55.000 0.00 0.00 0.00 4.94
230 242 1.902508 CTGGAACCCTACTCTGCTTCA 59.097 52.381 0.00 0.00 0.00 3.02
296 308 1.065782 GGAGGGACTGAAGAAGGAAGC 60.066 57.143 0.00 0.00 41.55 3.86
457 485 3.565482 AGCTTGAGATGCGAAAAGTGAAA 59.435 39.130 0.00 0.00 35.28 2.69
460 488 2.481568 TCAGCTTGAGATGCGAAAAGTG 59.518 45.455 0.00 0.00 35.28 3.16
462 490 3.373130 TCATCAGCTTGAGATGCGAAAAG 59.627 43.478 7.49 0.00 41.98 2.27
493 534 6.547880 ACACCACACAGATCTAATAGTCCTAG 59.452 42.308 0.00 0.00 0.00 3.02
502 543 5.934043 CAGATTCAACACCACACAGATCTAA 59.066 40.000 0.00 0.00 0.00 2.10
555 1689 0.591170 TGCTACTGGCTCGCAAAAAC 59.409 50.000 0.00 0.00 42.39 2.43
562 1696 1.604185 GCCTAGAATGCTACTGGCTCG 60.604 57.143 4.07 0.00 42.39 5.03
567 1701 0.753262 ACCGGCCTAGAATGCTACTG 59.247 55.000 0.00 0.00 0.00 2.74
587 1723 4.273148 ACTGCTAGTCTTTAACCCACAG 57.727 45.455 0.00 0.00 0.00 3.66
588 1724 4.322499 GCTACTGCTAGTCTTTAACCCACA 60.322 45.833 0.00 0.00 36.03 4.17
597 1733 1.480137 CCTGCTGCTACTGCTAGTCTT 59.520 52.381 0.00 0.00 40.48 3.01
631 1783 7.109501 TCAATAATCTCGAATCCCTCAACAAA 58.890 34.615 0.00 0.00 0.00 2.83
647 1800 8.786826 TCAAGTACGGAACAAATCAATAATCT 57.213 30.769 0.00 0.00 0.00 2.40
655 1808 7.129109 TCAATCTTCAAGTACGGAACAAATC 57.871 36.000 0.00 0.00 0.00 2.17
656 1809 7.390440 TCATCAATCTTCAAGTACGGAACAAAT 59.610 33.333 0.00 0.00 0.00 2.32
658 1811 6.147164 GTCATCAATCTTCAAGTACGGAACAA 59.853 38.462 0.00 0.00 0.00 2.83
660 1813 5.637810 TGTCATCAATCTTCAAGTACGGAAC 59.362 40.000 0.00 0.00 0.00 3.62
661 1814 5.789521 TGTCATCAATCTTCAAGTACGGAA 58.210 37.500 3.52 3.52 0.00 4.30
662 1815 5.400066 TGTCATCAATCTTCAAGTACGGA 57.600 39.130 0.00 0.00 0.00 4.69
663 1816 6.480524 TTTGTCATCAATCTTCAAGTACGG 57.519 37.500 0.00 0.00 33.32 4.02
699 1860 3.960571 AGAGCATAACATTGCAAGAGGT 58.039 40.909 4.94 0.85 45.23 3.85
700 1861 4.978083 AAGAGCATAACATTGCAAGAGG 57.022 40.909 4.94 0.00 45.23 3.69
707 1868 9.688592 AAAGAAGAAGAAAAGAGCATAACATTG 57.311 29.630 0.00 0.00 0.00 2.82
709 1870 9.688592 CAAAAGAAGAAGAAAAGAGCATAACAT 57.311 29.630 0.00 0.00 0.00 2.71
710 1871 7.649306 GCAAAAGAAGAAGAAAAGAGCATAACA 59.351 33.333 0.00 0.00 0.00 2.41
711 1872 7.864882 AGCAAAAGAAGAAGAAAAGAGCATAAC 59.135 33.333 0.00 0.00 0.00 1.89
712 1873 7.945134 AGCAAAAGAAGAAGAAAAGAGCATAA 58.055 30.769 0.00 0.00 0.00 1.90
713 1874 7.446625 AGAGCAAAAGAAGAAGAAAAGAGCATA 59.553 33.333 0.00 0.00 0.00 3.14
714 1875 6.264970 AGAGCAAAAGAAGAAGAAAAGAGCAT 59.735 34.615 0.00 0.00 0.00 3.79
715 1876 5.591877 AGAGCAAAAGAAGAAGAAAAGAGCA 59.408 36.000 0.00 0.00 0.00 4.26
717 1878 7.025485 ACAGAGCAAAAGAAGAAGAAAAGAG 57.975 36.000 0.00 0.00 0.00 2.85
718 1879 7.396540 AACAGAGCAAAAGAAGAAGAAAAGA 57.603 32.000 0.00 0.00 0.00 2.52
719 1880 9.178427 CATAACAGAGCAAAAGAAGAAGAAAAG 57.822 33.333 0.00 0.00 0.00 2.27
733 2092 5.105513 TCGTGTATTCTCCATAACAGAGCAA 60.106 40.000 0.00 0.00 0.00 3.91
746 2105 4.025647 GCAATTGCTAGGTCGTGTATTCTC 60.026 45.833 23.21 0.00 38.21 2.87
758 2117 1.068127 GAGGGCATTGCAATTGCTAGG 59.932 52.381 29.37 24.40 42.66 3.02
761 2120 0.978151 TTGAGGGCATTGCAATTGCT 59.022 45.000 29.37 9.23 42.66 3.91
762 2121 1.465777 GTTTGAGGGCATTGCAATTGC 59.534 47.619 23.69 23.69 42.50 3.56
763 2122 2.768698 TGTTTGAGGGCATTGCAATTG 58.231 42.857 9.83 6.84 0.00 2.32
786 2145 6.675026 TGAAAGCATCTTCAAAGAATCACAG 58.325 36.000 0.00 0.00 38.77 3.66
823 2202 4.481930 TCTTACAAAAACAGACGCCATG 57.518 40.909 0.00 0.00 0.00 3.66
828 2207 4.378459 GGAGCCATCTTACAAAAACAGACG 60.378 45.833 0.00 0.00 0.00 4.18
840 2219 5.899547 TCTTCACTAGAATGGAGCCATCTTA 59.100 40.000 1.88 0.00 35.31 2.10
850 2229 6.648310 ACGCATCAATATCTTCACTAGAATGG 59.352 38.462 0.00 0.00 36.22 3.16
946 2332 6.578919 GCGCCTTATTTGTAGCAAAATCTATC 59.421 38.462 0.00 0.00 32.16 2.08
987 2373 2.223340 GCAAGACATCGTGGCTAAATGG 60.223 50.000 0.00 0.00 31.94 3.16
1045 2434 8.575649 AATACACGGGTCTTCTTGAATTTTAT 57.424 30.769 0.00 0.00 0.00 1.40
1046 2435 7.989416 AATACACGGGTCTTCTTGAATTTTA 57.011 32.000 0.00 0.00 0.00 1.52
1095 2484 5.682943 TTAAACTGGTGAAATCCACTTCG 57.317 39.130 0.00 0.00 45.03 3.79
1175 2819 4.663334 ACAAGGTGGTATCTTTTCCTTCC 58.337 43.478 0.00 0.00 36.52 3.46
1243 2887 5.106157 CCTTTGGTGATGTATCAACTGGTTC 60.106 44.000 10.90 0.00 44.70 3.62
1345 2992 1.001815 GTGCTCTCGATCTACAGCTCC 60.002 57.143 7.81 0.00 32.76 4.70
1358 3005 1.513586 GCAATTGCGCAGTGCTCTC 60.514 57.895 30.16 10.52 46.63 3.20
1369 3016 0.901124 TACCCACCAATGGCAATTGC 59.099 50.000 22.47 22.47 45.76 3.56
1442 3090 4.715713 AGTCATGTGGATGATCCTCAATG 58.284 43.478 18.85 15.21 42.50 2.82
1448 3096 4.125703 GACAGAAGTCATGTGGATGATCC 58.874 47.826 4.05 4.05 44.34 3.36
1507 3159 1.473258 TGATGCAAAAAGGATCCCCG 58.527 50.000 8.55 0.00 43.79 5.73
1693 3346 1.496857 TGGTTGGGTGATGAAACCAGA 59.503 47.619 2.45 0.00 46.42 3.86
1781 3434 5.500234 TGGGATCTAGTGAAGAAACATTGG 58.500 41.667 0.00 0.00 37.89 3.16
1786 3439 7.050377 TCATCAATGGGATCTAGTGAAGAAAC 58.950 38.462 5.13 0.00 37.89 2.78
1889 3542 0.243907 ACGATCCACAGGAGACAACG 59.756 55.000 0.00 0.00 34.05 4.10
1897 3550 2.455674 TCACAAGAACGATCCACAGG 57.544 50.000 0.00 0.00 0.00 4.00
1902 3555 4.505922 GTCTGATCATCACAAGAACGATCC 59.494 45.833 0.00 0.00 36.58 3.36
1903 3556 5.105063 TGTCTGATCATCACAAGAACGATC 58.895 41.667 0.00 0.00 37.31 3.69
2119 3772 3.784763 AGTGAATCTGATTGACCCTCCAT 59.215 43.478 14.97 0.00 0.00 3.41
2595 4248 6.936900 CCTGTGTTTCTTCAAGATTAGAGGAA 59.063 38.462 4.20 0.00 30.47 3.36
2630 4283 5.186996 TGGAGTTGAAATTGAAGCTTCAC 57.813 39.130 28.46 17.13 36.83 3.18
2653 4306 1.687612 CATCAGTTCCCAGGCAGGT 59.312 57.895 0.00 0.00 34.66 4.00
2758 4411 3.715495 ACATGATTAGAAGAGCTCTGCG 58.285 45.455 19.06 2.76 35.41 5.18
2848 4502 5.350633 CATTGCAAAACTTCTCCTGACAAA 58.649 37.500 1.71 0.00 0.00 2.83
2877 4531 3.181475 ACTCCGCACAAATCGATATCAGT 60.181 43.478 0.00 0.00 0.00 3.41
2894 4548 0.895530 TACTCAGCCTTTGGACTCCG 59.104 55.000 0.00 0.00 0.00 4.63
3012 4673 9.103861 GATCGGTCTTCAAGATTAATCTTTCTT 57.896 33.333 24.94 5.66 44.28 2.52
3068 4777 6.420913 TTGTAAAGGAGCTAGAAGTTCTGT 57.579 37.500 15.90 0.00 0.00 3.41
3092 4801 4.009675 TGTTGACTTGACAGCTTCTTTGT 58.990 39.130 0.00 0.00 0.00 2.83
3098 4807 3.817647 GGATTCTGTTGACTTGACAGCTT 59.182 43.478 0.00 0.00 43.23 3.74
3101 4810 3.077359 GGGGATTCTGTTGACTTGACAG 58.923 50.000 0.00 0.00 44.54 3.51
3137 4846 5.178438 GTGTCCAGAAGAACAGATGAAGTTC 59.822 44.000 0.00 0.00 44.32 3.01
3140 4849 4.689812 CAGTGTCCAGAAGAACAGATGAAG 59.310 45.833 0.00 0.00 0.00 3.02
3154 4863 2.540265 ACAGCTTTCTCAGTGTCCAG 57.460 50.000 0.00 0.00 0.00 3.86
3216 4925 4.847198 TCAAGCTCCTGATAAGATTTGCA 58.153 39.130 0.00 0.00 0.00 4.08
3259 4968 3.303791 GCTTCCGATGACAAAGTTTCGTT 60.304 43.478 0.00 0.00 0.00 3.85
3266 4975 3.438087 AGAATGTGCTTCCGATGACAAAG 59.562 43.478 0.00 0.00 34.11 2.77
3308 5017 3.627395 AATAATGTCTCACCTCGGCAA 57.373 42.857 0.00 0.00 0.00 4.52
3363 5074 0.608856 ATCCATCGGTTGCACAGCAA 60.609 50.000 0.00 0.00 46.80 3.91
3406 5118 5.812652 TGTAACTTCATCAAACAACGGTTC 58.187 37.500 0.00 0.00 35.82 3.62
3460 5251 7.202016 ACGCAGAAAGACAAATCTCAAATAA 57.798 32.000 0.00 0.00 32.34 1.40
3466 5257 5.178438 AGAGAAACGCAGAAAGACAAATCTC 59.822 40.000 0.00 0.00 32.34 2.75
3609 5430 5.707298 CCAACAGATGGTTTACATGAGAACT 59.293 40.000 0.00 0.00 44.85 3.01
3644 5466 6.358118 TCAATAATTGATAAGGCGTGTGAC 57.642 37.500 0.00 0.00 34.08 3.67
3698 5527 5.049828 GCACATACAGGAAAAGCACTTTTT 58.950 37.500 9.59 0.00 42.26 1.94
3699 5528 4.099266 TGCACATACAGGAAAAGCACTTTT 59.901 37.500 8.06 8.06 44.59 2.27
3700 5529 3.636300 TGCACATACAGGAAAAGCACTTT 59.364 39.130 0.00 0.00 0.00 2.66
3701 5530 3.221771 TGCACATACAGGAAAAGCACTT 58.778 40.909 0.00 0.00 0.00 3.16
3702 5531 2.862541 TGCACATACAGGAAAAGCACT 58.137 42.857 0.00 0.00 0.00 4.40
3703 5532 3.855689 ATGCACATACAGGAAAAGCAC 57.144 42.857 0.00 0.00 32.92 4.40
3704 5533 5.973899 TTAATGCACATACAGGAAAAGCA 57.026 34.783 0.00 0.00 34.78 3.91
3705 5534 8.405531 TCTAATTAATGCACATACAGGAAAAGC 58.594 33.333 0.00 0.00 0.00 3.51
3716 5545 6.071952 CCCGCCTAATTCTAATTAATGCACAT 60.072 38.462 13.02 0.00 32.51 3.21
3767 5620 8.929260 AGGTAATTCATGATCTTGCAATATCA 57.071 30.769 24.53 24.53 36.60 2.15
3838 5713 7.129457 TCAGCCAAGTATCTGACAAGATTAT 57.871 36.000 0.00 0.00 40.42 1.28
3845 5720 6.737720 AAGATATCAGCCAAGTATCTGACA 57.262 37.500 5.32 0.00 41.53 3.58
3882 5757 0.388294 CGGATGCTGCTCTCATCTGA 59.612 55.000 13.41 0.00 45.56 3.27
3912 5787 3.323979 TCCTTGTAGTTCTCTCCACCAAC 59.676 47.826 0.00 0.00 0.00 3.77
3913 5788 3.583228 TCCTTGTAGTTCTCTCCACCAA 58.417 45.455 0.00 0.00 0.00 3.67
3914 5789 3.254093 TCCTTGTAGTTCTCTCCACCA 57.746 47.619 0.00 0.00 0.00 4.17
3940 5815 6.623486 TGCAATCCTTGTTCATTATTGACAG 58.377 36.000 0.00 0.00 30.77 3.51
3992 5867 4.341366 AAACAAATCTTGAAAGCAGGGG 57.659 40.909 0.00 0.00 0.00 4.79
4051 5933 0.110056 GAGCGGTGACACAAATGCAG 60.110 55.000 8.08 0.00 0.00 4.41
4088 5970 1.817099 CCCTCCAGCGTCTGCAATC 60.817 63.158 0.00 0.00 46.23 2.67
4092 5974 1.743252 CTTTCCCTCCAGCGTCTGC 60.743 63.158 1.84 0.00 43.24 4.26
4125 6007 2.879233 TTTCCTCGGCGCTTCTGGT 61.879 57.895 7.64 0.00 0.00 4.00
4180 6062 1.067565 CACCTTAACAGAGCAGAGCGA 60.068 52.381 0.00 0.00 0.00 4.93
4268 6150 7.168219 ACTTATTATGAAAGAACTGCCTGACA 58.832 34.615 0.00 0.00 0.00 3.58
4446 6345 3.003480 GCCACTTCACATGGACTCTAAC 58.997 50.000 0.00 0.00 39.87 2.34
4495 6395 7.381408 TCGATTCTTGTCTACAAACTACAACAG 59.619 37.037 0.00 0.00 35.15 3.16
4520 6420 3.047796 CAACATCAAACTGCAGCAAGTC 58.952 45.455 15.27 0.00 0.00 3.01
4531 6431 4.047822 TCAAATCAACCGCAACATCAAAC 58.952 39.130 0.00 0.00 0.00 2.93
4559 6459 3.996363 CCACATCGAGAAACAATCAGTCA 59.004 43.478 0.00 0.00 0.00 3.41
4560 6460 3.372206 CCCACATCGAGAAACAATCAGTC 59.628 47.826 0.00 0.00 0.00 3.51
4640 6540 2.095668 GTGAGGTGACTACACTGACTCG 60.096 54.545 0.00 0.00 44.43 4.18
4646 6546 1.902508 CATGGGTGAGGTGACTACACT 59.097 52.381 10.89 0.00 44.43 3.55
4653 6553 2.909662 TGTAATGTCATGGGTGAGGTGA 59.090 45.455 0.00 0.00 34.36 4.02
4654 6554 3.273434 CTGTAATGTCATGGGTGAGGTG 58.727 50.000 0.00 0.00 34.36 4.00
4655 6555 2.912956 ACTGTAATGTCATGGGTGAGGT 59.087 45.455 0.00 0.00 34.36 3.85
4656 6556 3.634397 ACTGTAATGTCATGGGTGAGG 57.366 47.619 0.00 0.00 34.36 3.86
4657 6557 3.941483 GGAACTGTAATGTCATGGGTGAG 59.059 47.826 0.00 0.00 34.36 3.51
4672 6572 7.888021 TGGTAATTCATAAACTGATGGAACTGT 59.112 33.333 0.00 0.00 32.72 3.55
4679 6579 8.370493 ACGAGATGGTAATTCATAAACTGATG 57.630 34.615 0.00 0.00 32.72 3.07
4736 6638 8.939201 ATATTGAGATAAGATGGTGCGAATAG 57.061 34.615 0.00 0.00 0.00 1.73
4738 6640 7.493971 GCTATATTGAGATAAGATGGTGCGAAT 59.506 37.037 0.00 0.00 0.00 3.34
4740 6642 6.071391 TGCTATATTGAGATAAGATGGTGCGA 60.071 38.462 0.00 0.00 0.00 5.10
4741 6643 6.101997 TGCTATATTGAGATAAGATGGTGCG 58.898 40.000 0.00 0.00 0.00 5.34
4742 6644 7.148340 GGTTGCTATATTGAGATAAGATGGTGC 60.148 40.741 0.00 0.00 0.00 5.01
4743 6645 7.879677 TGGTTGCTATATTGAGATAAGATGGTG 59.120 37.037 0.00 0.00 0.00 4.17
4744 6646 7.880195 GTGGTTGCTATATTGAGATAAGATGGT 59.120 37.037 0.00 0.00 0.00 3.55
4746 6648 7.063898 CGGTGGTTGCTATATTGAGATAAGATG 59.936 40.741 0.00 0.00 0.00 2.90
4747 6649 7.099764 CGGTGGTTGCTATATTGAGATAAGAT 58.900 38.462 0.00 0.00 0.00 2.40
4748 6650 6.041637 ACGGTGGTTGCTATATTGAGATAAGA 59.958 38.462 0.00 0.00 0.00 2.10
4749 6651 6.223852 ACGGTGGTTGCTATATTGAGATAAG 58.776 40.000 0.00 0.00 0.00 1.73
4751 6653 5.538813 AGACGGTGGTTGCTATATTGAGATA 59.461 40.000 0.00 0.00 0.00 1.98
4752 6654 4.345257 AGACGGTGGTTGCTATATTGAGAT 59.655 41.667 0.00 0.00 0.00 2.75
4753 6655 3.704566 AGACGGTGGTTGCTATATTGAGA 59.295 43.478 0.00 0.00 0.00 3.27
4754 6656 4.060038 AGACGGTGGTTGCTATATTGAG 57.940 45.455 0.00 0.00 0.00 3.02
4755 6657 4.403113 TGTAGACGGTGGTTGCTATATTGA 59.597 41.667 0.00 0.00 0.00 2.57
4756 6658 4.689071 TGTAGACGGTGGTTGCTATATTG 58.311 43.478 0.00 0.00 0.00 1.90
4757 6659 5.347620 TTGTAGACGGTGGTTGCTATATT 57.652 39.130 0.00 0.00 0.00 1.28
4758 6660 5.347620 TTTGTAGACGGTGGTTGCTATAT 57.652 39.130 0.00 0.00 0.00 0.86
4760 6662 3.688694 TTTGTAGACGGTGGTTGCTAT 57.311 42.857 0.00 0.00 0.00 2.97
4762 6664 1.944709 GTTTTGTAGACGGTGGTTGCT 59.055 47.619 0.00 0.00 0.00 3.91
4763 6665 1.944709 AGTTTTGTAGACGGTGGTTGC 59.055 47.619 0.00 0.00 0.00 4.17
4764 6666 4.374399 AGTAGTTTTGTAGACGGTGGTTG 58.626 43.478 0.00 0.00 0.00 3.77
4765 6667 4.343239 AGAGTAGTTTTGTAGACGGTGGTT 59.657 41.667 0.00 0.00 0.00 3.67
4768 6670 5.117355 TGAGAGTAGTTTTGTAGACGGTG 57.883 43.478 0.00 0.00 0.00 4.94
4769 6671 5.779529 TTGAGAGTAGTTTTGTAGACGGT 57.220 39.130 0.00 0.00 0.00 4.83
4772 6674 7.171167 GGGTCTTTTGAGAGTAGTTTTGTAGAC 59.829 40.741 0.00 0.00 0.00 2.59
4773 6675 7.070821 AGGGTCTTTTGAGAGTAGTTTTGTAGA 59.929 37.037 0.00 0.00 0.00 2.59
4774 6676 7.171678 CAGGGTCTTTTGAGAGTAGTTTTGTAG 59.828 40.741 0.00 0.00 0.00 2.74
4776 6678 5.823045 CAGGGTCTTTTGAGAGTAGTTTTGT 59.177 40.000 0.00 0.00 0.00 2.83
4777 6679 5.278022 GCAGGGTCTTTTGAGAGTAGTTTTG 60.278 44.000 0.00 0.00 0.00 2.44
4779 6681 4.141482 TGCAGGGTCTTTTGAGAGTAGTTT 60.141 41.667 0.00 0.00 0.00 2.66
4780 6682 3.391296 TGCAGGGTCTTTTGAGAGTAGTT 59.609 43.478 0.00 0.00 0.00 2.24
4783 6685 4.640771 AATGCAGGGTCTTTTGAGAGTA 57.359 40.909 0.00 0.00 0.00 2.59
4784 6686 3.515602 AATGCAGGGTCTTTTGAGAGT 57.484 42.857 0.00 0.00 0.00 3.24
4785 6687 3.057033 CCAAATGCAGGGTCTTTTGAGAG 60.057 47.826 9.27 0.00 34.78 3.20
4786 6688 2.892852 CCAAATGCAGGGTCTTTTGAGA 59.107 45.455 9.27 0.00 34.78 3.27
4787 6689 2.611224 GCCAAATGCAGGGTCTTTTGAG 60.611 50.000 9.27 2.40 40.77 3.02
4814 7000 5.683876 TCCCAGGAATCTTTTGAGAGTAG 57.316 43.478 0.00 0.00 0.00 2.57
4860 7046 7.024340 TGTACTAGCTACCTTCAACTTATCG 57.976 40.000 0.00 0.00 0.00 2.92
4862 7048 7.764901 GCTTTGTACTAGCTACCTTCAACTTAT 59.235 37.037 11.72 0.00 35.74 1.73
4943 7131 0.609131 AAAGCGATGACCCCAAGTGG 60.609 55.000 0.00 0.00 0.00 4.00
4949 7137 1.084370 CGAGTGAAAGCGATGACCCC 61.084 60.000 0.00 0.00 0.00 4.95
5009 7197 5.353678 CACTTTATTTTCAGCTGAGGAGGAG 59.646 44.000 17.43 13.59 0.00 3.69
5012 7200 6.205464 TCAACACTTTATTTTCAGCTGAGGAG 59.795 38.462 17.43 11.48 0.00 3.69
5063 7251 3.126831 CTCAGTACAGATTTCCATCGCC 58.873 50.000 0.00 0.00 34.17 5.54
5109 7298 5.529800 CCATGTCTGCTGTGATAAATCATCA 59.470 40.000 0.00 0.00 41.52 3.07
5129 7318 2.859538 GTGTTGTGTGCTGTTTTCCATG 59.140 45.455 0.00 0.00 0.00 3.66
5141 7330 9.781834 TTTCTTTAACTAGATTTGTGTTGTGTG 57.218 29.630 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.