Multiple sequence alignment - TraesCS3A01G475600

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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 TraesCS3A01G475600 chr3A 100.000 3870 0 0 995 4864 707123714 707127583 0.000000e+00 7147.0
1 TraesCS3A01G475600 chr3A 100.000 572 0 0 1 572 707122720 707123291 0.000000e+00 1057.0
2 TraesCS3A01G475600 chr3A 98.889 90 1 0 4398 4487 574288075 574287986 1.400000e-35 161.0
3 TraesCS3A01G475600 chr3A 97.619 42 0 1 3960 4000 489193137 489193178 2.430000e-08 71.3
4 TraesCS3A01G475600 chr3A 95.455 44 0 2 3956 3997 580599700 580599743 8.740000e-08 69.4
5 TraesCS3A01G475600 chr3D 95.274 2878 98 16 995 3861 573118925 573121775 0.000000e+00 4527.0
6 TraesCS3A01G475600 chr3D 91.620 358 28 2 214 570 573118489 573118845 1.220000e-135 494.0
7 TraesCS3A01G475600 chr3D 96.679 271 6 1 4483 4750 573123183 573123453 9.600000e-122 448.0
8 TraesCS3A01G475600 chr3D 88.839 224 23 2 4581 4802 573149661 573149884 1.720000e-69 274.0
9 TraesCS3A01G475600 chr3D 91.837 98 5 2 3863 3959 573122126 573122221 3.050000e-27 134.0
10 TraesCS3A01G475600 chr3D 100.000 35 0 0 3997 4031 573122219 573122253 1.130000e-06 65.8
11 TraesCS3A01G475600 chr3D 87.719 57 4 3 3961 4015 27936602 27936547 4.060000e-06 63.9
12 TraesCS3A01G475600 chr3B 93.940 2987 124 12 999 3960 762306372 762309326 0.000000e+00 4460.0
13 TraesCS3A01G475600 chr3B 95.801 381 13 3 4483 4860 762393521 762393901 3.220000e-171 612.0
14 TraesCS3A01G475600 chr3B 86.063 574 59 9 1 571 762305713 762306268 9.010000e-167 597.0
15 TraesCS3A01G475600 chr3B 89.091 275 16 7 4483 4744 762373508 762373781 3.630000e-86 329.0
16 TraesCS3A01G475600 chr3B 85.246 305 33 10 4083 4380 762309348 762309647 2.200000e-78 303.0
17 TraesCS3A01G475600 chr3B 93.401 197 12 1 4607 4802 762309664 762309860 1.710000e-74 291.0
18 TraesCS3A01G475600 chr3B 100.000 43 0 0 3989 4031 762309322 762309364 4.040000e-11 80.5
19 TraesCS3A01G475600 chr3B 100.000 40 0 0 3960 3999 435816924 435816885 1.880000e-09 75.0
20 TraesCS3A01G475600 chr3B 97.619 42 0 1 3960 4000 478078407 478078448 2.430000e-08 71.3
21 TraesCS3A01G475600 chr1D 92.777 2132 123 17 1738 3861 423059095 423056987 0.000000e+00 3055.0
22 TraesCS3A01G475600 chr1B 92.088 2136 135 21 1735 3861 572310932 572308822 0.000000e+00 2977.0
23 TraesCS3A01G475600 chr1B 86.538 52 5 2 3943 3993 90090322 90090372 6.800000e-04 56.5
24 TraesCS3A01G475600 chr1A 92.553 2041 111 18 1735 3763 518988677 518986666 0.000000e+00 2889.0
25 TraesCS3A01G475600 chr1A 98.876 89 1 0 4400 4488 514886275 514886363 5.040000e-35 159.0
26 TraesCS3A01G475600 chr1A 98.876 89 1 0 4400 4488 515142541 515142629 5.040000e-35 159.0
27 TraesCS3A01G475600 chr1A 96.226 53 1 1 4032 4083 554284235 554284183 8.670000e-13 86.1
28 TraesCS3A01G475600 chr1A 96.226 53 1 1 4032 4083 554289458 554289510 8.670000e-13 86.1
29 TraesCS3A01G475600 chr1A 97.297 37 1 0 3961 3997 131963620 131963584 4.060000e-06 63.9
30 TraesCS3A01G475600 chr1A 96.970 33 1 0 3961 3993 571581109 571581077 6.800000e-04 56.5
31 TraesCS3A01G475600 chr7D 91.553 805 59 5 1888 2684 139369679 139368876 0.000000e+00 1101.0
32 TraesCS3A01G475600 chr7D 98.077 52 0 1 4032 4082 183786001 183786052 6.710000e-14 89.8
33 TraesCS3A01G475600 chr4A 89.095 807 77 6 1888 2684 220627979 220627174 0.000000e+00 992.0
34 TraesCS3A01G475600 chr6A 93.210 162 10 1 2524 2684 395653971 395654132 2.260000e-58 237.0
35 TraesCS3A01G475600 chr2A 91.975 162 12 1 2524 2684 315573675 315573836 4.900000e-55 226.0
36 TraesCS3A01G475600 chr2A 97.872 94 2 0 4400 4493 750532392 750532485 3.900000e-36 163.0
37 TraesCS3A01G475600 chr2A 89.286 112 11 1 4392 4502 771521803 771521914 6.560000e-29 139.0
38 TraesCS3A01G475600 chr2A 93.333 45 3 0 3961 4005 23630434 23630478 3.140000e-07 67.6
39 TraesCS3A01G475600 chr2A 93.333 45 3 0 3960 4004 703709042 703708998 3.140000e-07 67.6
40 TraesCS3A01G475600 chr2A 85.965 57 4 4 3939 3993 690525528 690525474 1.890000e-04 58.4
41 TraesCS3A01G475600 chr6D 97.849 93 2 0 4395 4487 91845508 91845416 1.400000e-35 161.0
42 TraesCS3A01G475600 chr5A 100.000 87 0 0 4400 4486 705821976 705822062 1.400000e-35 161.0
43 TraesCS3A01G475600 chr6B 97.826 92 2 0 4393 4484 459601730 459601639 5.040000e-35 159.0
44 TraesCS3A01G475600 chr6B 96.296 54 1 1 4032 4084 585808026 585808079 2.410000e-13 87.9
45 TraesCS3A01G475600 chr6B 94.340 53 1 2 4031 4082 70569448 70569397 4.040000e-11 80.5
46 TraesCS3A01G475600 chr6B 95.455 44 1 1 3961 4004 551951923 551951965 8.740000e-08 69.4
47 TraesCS3A01G475600 chr2B 94.175 103 4 2 4386 4487 227115930 227115829 6.520000e-34 156.0
48 TraesCS3A01G475600 chr2B 92.857 42 2 1 3961 4001 407242122 407242081 5.260000e-05 60.2
49 TraesCS3A01G475600 chr5D 92.063 63 2 2 4032 4093 225256324 225256384 8.670000e-13 86.1
50 TraesCS3A01G475600 chr4D 96.226 53 1 1 4032 4083 401088629 401088681 8.670000e-13 86.1
51 TraesCS3A01G475600 chr4D 96.154 52 1 1 4032 4082 12449267 12449216 3.120000e-12 84.2
52 TraesCS3A01G475600 chr4D 96.774 31 1 0 4833 4863 477009626 477009656 9.000000e-03 52.8
53 TraesCS3A01G475600 chr2D 96.154 52 1 1 4032 4082 512770254 512770203 3.120000e-12 84.2


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 TraesCS3A01G475600 chr3A 707122720 707127583 4863 False 4102.00 7147 100.000 1 4864 2 chr3A.!!$F3 4863
1 TraesCS3A01G475600 chr3D 573118489 573123453 4964 False 1133.76 4527 95.082 214 4750 5 chr3D.!!$F2 4536
2 TraesCS3A01G475600 chr3B 762305713 762309860 4147 False 1146.30 4460 91.730 1 4802 5 chr3B.!!$F4 4801
3 TraesCS3A01G475600 chr1D 423056987 423059095 2108 True 3055.00 3055 92.777 1738 3861 1 chr1D.!!$R1 2123
4 TraesCS3A01G475600 chr1B 572308822 572310932 2110 True 2977.00 2977 92.088 1735 3861 1 chr1B.!!$R1 2126
5 TraesCS3A01G475600 chr1A 518986666 518988677 2011 True 2889.00 2889 92.553 1735 3763 1 chr1A.!!$R2 2028
6 TraesCS3A01G475600 chr7D 139368876 139369679 803 True 1101.00 1101 91.553 1888 2684 1 chr7D.!!$R1 796
7 TraesCS3A01G475600 chr4A 220627174 220627979 805 True 992.00 992 89.095 1888 2684 1 chr4A.!!$R1 796

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
54 55 0.036388 GAGGATTCGTGCTGGAACCA 60.036 55.000 0.00 0.00 0.00 3.67 F
489 492 0.178987 AGATCCATAGGAGTCGGCGT 60.179 55.000 6.85 0.00 34.05 5.68 F
1344 1379 0.869454 GATCTCGCGAGCTTGGTGAG 60.869 60.000 30.97 18.19 42.06 3.51 F
1516 1551 1.190833 TGCGACCGGGGGTTTAGTTA 61.191 55.000 6.32 0.00 35.25 2.24 F
2162 2207 2.954753 GAGGTCAACAAGTGGCGCG 61.955 63.158 0.00 0.00 29.99 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1079 1082 0.175760 TCACCTACTGCGATTCAGCC 59.824 55.000 0.00 0.00 46.76 4.85 R
1396 1431 0.392336 AAGCAGGATCAGATCTCGGC 59.608 55.000 10.36 11.83 0.00 5.54 R
3300 3353 2.043604 CTCCCATCACTATGCCGGCA 62.044 60.000 34.80 34.80 0.00 5.69 R
3318 3371 2.375174 TGTCCCAGCTGTATTGGAAACT 59.625 45.455 13.81 0.00 37.96 2.66 R
4050 4454 0.039165 GGCACAGTGGTAAAAGCTGC 60.039 55.000 1.84 0.00 33.87 5.25 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
21 22 0.452184 ACTACGATCCACGACAGCTG 59.548 55.000 13.48 13.48 45.77 4.24
22 23 0.867753 CTACGATCCACGACAGCTGC 60.868 60.000 15.27 5.81 45.77 5.25
23 24 1.591504 TACGATCCACGACAGCTGCA 61.592 55.000 15.27 0.00 45.77 4.41
25 26 1.690283 CGATCCACGACAGCTGCAAG 61.690 60.000 15.27 7.92 45.77 4.01
29 30 1.447317 CCACGACAGCTGCAAGGTTT 61.447 55.000 15.27 0.00 46.63 3.27
31 32 0.179045 ACGACAGCTGCAAGGTTTCT 60.179 50.000 15.27 0.00 46.63 2.52
54 55 0.036388 GAGGATTCGTGCTGGAACCA 60.036 55.000 0.00 0.00 0.00 3.67
96 97 4.899239 CCATGGACGGAGAGCGGC 62.899 72.222 5.56 0.00 0.00 6.53
192 193 5.941058 TCACATACGTGGTACCATGATTTTT 59.059 36.000 35.58 18.21 43.79 1.94
228 230 2.859165 AAGGAAGGACGAAGCAATGA 57.141 45.000 0.00 0.00 0.00 2.57
239 241 2.740904 CGAAGCAATGAGAGCAGATCCA 60.741 50.000 0.00 0.00 0.00 3.41
250 252 0.798776 GCAGATCCAACGGTTCACAG 59.201 55.000 0.00 0.00 0.00 3.66
251 253 0.798776 CAGATCCAACGGTTCACAGC 59.201 55.000 0.00 0.00 0.00 4.40
264 266 2.202797 ACAGCAGCCGCATCGTAG 60.203 61.111 0.00 0.00 42.27 3.51
357 360 1.515020 CTTCTCGCAGTGAGGAGGG 59.485 63.158 11.19 0.00 45.42 4.30
489 492 0.178987 AGATCCATAGGAGTCGGCGT 60.179 55.000 6.85 0.00 34.05 5.68
530 533 4.316823 AGCCCTGACCACCTCCGA 62.317 66.667 0.00 0.00 0.00 4.55
537 540 1.606889 GACCACCTCCGAGACCTGT 60.607 63.158 0.00 0.00 0.00 4.00
539 542 2.352032 CCACCTCCGAGACCTGTCC 61.352 68.421 0.00 0.00 0.00 4.02
563 566 1.512694 CGCCTTGCATCCCCTTTTC 59.487 57.895 0.00 0.00 0.00 2.29
571 574 3.296842 ATCCCCTTTTCACCGCCCC 62.297 63.158 0.00 0.00 0.00 5.80
1046 1049 2.342279 GACCACGTAGGCTGTGCA 59.658 61.111 0.00 0.00 43.14 4.57
1062 1065 3.465403 CACCTCCTCTGCCTCCCG 61.465 72.222 0.00 0.00 0.00 5.14
1071 1074 3.976490 CTGCCTCCCGGACCACCTA 62.976 68.421 0.73 0.00 0.00 3.08
1079 1082 1.360551 CGGACCACCTAGCATCTCG 59.639 63.158 0.00 0.00 0.00 4.04
1080 1083 1.742768 GGACCACCTAGCATCTCGG 59.257 63.158 0.00 0.00 0.00 4.63
1088 1091 1.668337 CCTAGCATCTCGGCTGAATCG 60.668 57.143 0.00 0.00 45.44 3.34
1130 1141 8.907222 AAATGCATTTTTCTTTGATTGGTAGT 57.093 26.923 18.99 0.00 0.00 2.73
1131 1142 9.995003 AAATGCATTTTTCTTTGATTGGTAGTA 57.005 25.926 18.99 0.00 0.00 1.82
1132 1143 8.986477 ATGCATTTTTCTTTGATTGGTAGTAC 57.014 30.769 0.00 0.00 0.00 2.73
1133 1144 8.177119 TGCATTTTTCTTTGATTGGTAGTACT 57.823 30.769 0.00 0.00 0.00 2.73
1134 1145 8.081633 TGCATTTTTCTTTGATTGGTAGTACTG 58.918 33.333 5.39 0.00 0.00 2.74
1135 1146 8.082242 GCATTTTTCTTTGATTGGTAGTACTGT 58.918 33.333 5.39 0.00 0.00 3.55
1138 1149 9.841295 TTTTTCTTTGATTGGTAGTACTGTACT 57.159 29.630 22.72 22.72 42.68 2.73
1153 1164 5.551760 ACTGTACTATTTTGCTGTGATGC 57.448 39.130 0.00 0.00 0.00 3.91
1157 1168 2.159476 ACTATTTTGCTGTGATGCGCTG 60.159 45.455 9.73 0.00 35.36 5.18
1240 1273 2.339462 ATTTGGGGTTTGGGGGCTGT 62.339 55.000 0.00 0.00 0.00 4.40
1344 1379 0.869454 GATCTCGCGAGCTTGGTGAG 60.869 60.000 30.97 18.19 42.06 3.51
1396 1431 4.055360 GTGGAAGTTGGAAAATTTTCGGG 58.945 43.478 21.53 0.00 32.38 5.14
1417 1452 2.233431 GCCGAGATCTGATCCTGCTTAT 59.767 50.000 13.83 0.00 0.00 1.73
1491 1526 5.354234 GGAACCACATGATTACTGTACTTGG 59.646 44.000 0.00 0.00 0.00 3.61
1499 1534 8.458843 ACATGATTACTGTACTTGGTTTATTGC 58.541 33.333 0.00 0.00 0.00 3.56
1504 1539 2.737783 TGTACTTGGTTTATTGCGACCG 59.262 45.455 0.00 0.00 38.81 4.79
1516 1551 1.190833 TGCGACCGGGGGTTTAGTTA 61.191 55.000 6.32 0.00 35.25 2.24
1589 1624 4.693566 TGAGGAAAACACTTAGCATTACGG 59.306 41.667 0.00 0.00 0.00 4.02
1626 1661 7.877097 GGATATGTGTAAGATCAAGCTCAATCT 59.123 37.037 5.24 5.24 33.67 2.40
1684 1719 9.638176 AATCATCTAGATTAGCATGTTTCCTTT 57.362 29.630 1.33 0.00 45.00 3.11
1685 1720 8.668510 TCATCTAGATTAGCATGTTTCCTTTC 57.331 34.615 1.33 0.00 0.00 2.62
1686 1721 8.267183 TCATCTAGATTAGCATGTTTCCTTTCA 58.733 33.333 1.33 0.00 0.00 2.69
1687 1722 9.064706 CATCTAGATTAGCATGTTTCCTTTCAT 57.935 33.333 1.33 0.00 0.00 2.57
1812 1848 7.392673 AGTTTGCATCTCAAGAATAGTTGATGT 59.607 33.333 0.00 0.00 35.88 3.06
1881 1917 7.698506 ATGTAATATTCATGCCCTGATTCAG 57.301 36.000 6.70 6.70 32.72 3.02
2162 2207 2.954753 GAGGTCAACAAGTGGCGCG 61.955 63.158 0.00 0.00 29.99 6.86
2200 2250 3.632145 ACAACACTTTGTGGTTCATCTCC 59.368 43.478 2.72 0.00 44.66 3.71
3106 3159 6.363357 GGTTGCTGATCACTTGATTACAAAAC 59.637 38.462 0.00 0.00 35.49 2.43
3318 3371 1.631071 TTGCCGGCATAGTGATGGGA 61.631 55.000 33.25 8.24 33.26 4.37
3563 3616 4.138290 TCTTTTCTTGTCATTTACGGGCA 58.862 39.130 0.00 0.00 0.00 5.36
3565 3618 2.851263 TCTTGTCATTTACGGGCAGT 57.149 45.000 0.00 0.00 0.00 4.40
3569 3622 1.621317 TGTCATTTACGGGCAGTGAGA 59.379 47.619 0.00 0.00 0.00 3.27
3578 3631 0.755686 GGGCAGTGAGACAGGATAGG 59.244 60.000 0.00 0.00 0.00 2.57
3590 3643 3.640029 GACAGGATAGGAACACGGGAATA 59.360 47.826 0.00 0.00 0.00 1.75
3634 3687 3.500558 TCTGTCAGATTTCAGAGCTCG 57.499 47.619 8.37 3.55 36.04 5.03
3655 3708 2.620115 GGACTGCATCCCACACATATTG 59.380 50.000 4.36 0.00 42.46 1.90
3763 3816 3.782889 GCTGGTTGGCCTATTTACAAG 57.217 47.619 3.32 0.00 35.27 3.16
3798 3851 4.142204 TGTGTAATTTGCTGGGCATACATG 60.142 41.667 7.42 0.00 38.76 3.21
3861 3916 2.031769 TGAATTGTGCAGCAAGAAGTCG 60.032 45.455 0.00 0.00 40.86 4.18
3876 4280 6.626302 CAAGAAGTCGAGAATAGGAGAAGTT 58.374 40.000 0.00 0.00 0.00 2.66
3877 4281 6.844097 AGAAGTCGAGAATAGGAGAAGTTT 57.156 37.500 0.00 0.00 0.00 2.66
3878 4282 7.941431 AGAAGTCGAGAATAGGAGAAGTTTA 57.059 36.000 0.00 0.00 0.00 2.01
3879 4283 8.528044 AGAAGTCGAGAATAGGAGAAGTTTAT 57.472 34.615 0.00 0.00 0.00 1.40
3890 4294 6.734502 AGGAGAAGTTTATAGGAAGCCTAC 57.265 41.667 0.00 0.00 39.10 3.18
3977 4381 9.542462 TGCTATTACAAACGCTCTTATATTTCT 57.458 29.630 0.00 0.00 0.00 2.52
3984 4388 9.431887 ACAAACGCTCTTATATTTCTTTACAGA 57.568 29.630 0.00 0.00 0.00 3.41
3985 4389 9.907576 CAAACGCTCTTATATTTCTTTACAGAG 57.092 33.333 0.00 0.00 0.00 3.35
3986 4390 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
3987 4391 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
3988 4392 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
4040 4444 6.130692 TCATGCATATGAATACCTCATGGT 57.869 37.500 6.97 0.00 44.84 3.55
4041 4445 6.175471 TCATGCATATGAATACCTCATGGTC 58.825 40.000 6.97 0.00 44.84 4.02
4042 4446 5.565455 TGCATATGAATACCTCATGGTCA 57.435 39.130 6.97 0.00 44.78 4.02
4043 4447 5.308014 TGCATATGAATACCTCATGGTCAC 58.692 41.667 6.97 0.00 44.78 3.67
4044 4448 5.163216 TGCATATGAATACCTCATGGTCACA 60.163 40.000 6.97 0.00 44.78 3.58
4045 4449 5.764686 GCATATGAATACCTCATGGTCACAA 59.235 40.000 6.97 0.00 44.78 3.33
4046 4450 6.072838 GCATATGAATACCTCATGGTCACAAG 60.073 42.308 6.97 0.00 44.78 3.16
4047 4451 4.220693 TGAATACCTCATGGTCACAAGG 57.779 45.455 0.00 0.00 44.78 3.61
4048 4452 2.717639 ATACCTCATGGTCACAAGGC 57.282 50.000 0.00 0.00 44.78 4.35
4049 4453 1.357137 TACCTCATGGTCACAAGGCA 58.643 50.000 0.00 0.00 44.78 4.75
4050 4454 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
4051 4455 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
4052 4456 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
4053 4457 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
4054 4458 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
4055 4459 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
4056 4460 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
4057 4461 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
4058 4462 0.386838 GTCACAAGGCAGCAGCTTTT 59.613 50.000 0.00 0.00 38.07 2.27
4059 4463 1.608590 GTCACAAGGCAGCAGCTTTTA 59.391 47.619 0.00 0.00 38.07 1.52
4060 4464 1.608590 TCACAAGGCAGCAGCTTTTAC 59.391 47.619 0.00 0.00 38.07 2.01
4061 4465 0.961753 ACAAGGCAGCAGCTTTTACC 59.038 50.000 0.00 0.00 38.07 2.85
4062 4466 0.961019 CAAGGCAGCAGCTTTTACCA 59.039 50.000 0.00 0.00 38.07 3.25
4063 4467 0.961753 AAGGCAGCAGCTTTTACCAC 59.038 50.000 0.00 0.00 36.57 4.16
4064 4468 0.111253 AGGCAGCAGCTTTTACCACT 59.889 50.000 0.00 0.00 41.70 4.00
4065 4469 0.242017 GGCAGCAGCTTTTACCACTG 59.758 55.000 0.00 0.00 41.70 3.66
4066 4470 0.954452 GCAGCAGCTTTTACCACTGT 59.046 50.000 0.00 0.00 37.91 3.55
4067 4471 1.335324 GCAGCAGCTTTTACCACTGTG 60.335 52.381 0.00 0.00 37.91 3.66
4068 4472 0.954452 AGCAGCTTTTACCACTGTGC 59.046 50.000 1.29 0.00 33.87 4.57
4069 4473 0.039165 GCAGCTTTTACCACTGTGCC 60.039 55.000 1.29 0.00 33.87 5.01
4070 4474 1.317613 CAGCTTTTACCACTGTGCCA 58.682 50.000 1.29 0.00 0.00 4.92
4071 4475 1.680735 CAGCTTTTACCACTGTGCCAA 59.319 47.619 1.29 0.00 0.00 4.52
4072 4476 1.956477 AGCTTTTACCACTGTGCCAAG 59.044 47.619 1.29 2.71 0.00 3.61
4073 4477 1.000274 GCTTTTACCACTGTGCCAAGG 60.000 52.381 1.29 0.00 0.00 3.61
4074 4478 1.000274 CTTTTACCACTGTGCCAAGGC 60.000 52.381 3.61 3.61 42.35 4.35
4075 4479 0.184933 TTTACCACTGTGCCAAGGCT 59.815 50.000 12.96 0.00 42.51 4.58
4076 4480 0.250727 TTACCACTGTGCCAAGGCTC 60.251 55.000 12.96 9.45 42.51 4.70
4077 4481 2.124507 TACCACTGTGCCAAGGCTCC 62.125 60.000 12.96 3.64 42.51 4.70
4078 4482 2.674380 CACTGTGCCAAGGCTCCC 60.674 66.667 12.96 1.13 42.51 4.30
4079 4483 2.856000 ACTGTGCCAAGGCTCCCT 60.856 61.111 12.96 0.00 42.51 4.20
4080 4484 2.437897 CTGTGCCAAGGCTCCCTT 59.562 61.111 12.96 0.00 45.88 3.95
4081 4485 1.676967 CTGTGCCAAGGCTCCCTTC 60.677 63.158 12.96 0.00 42.67 3.46
4082 4486 2.134630 CTGTGCCAAGGCTCCCTTCT 62.135 60.000 12.96 0.00 42.67 2.85
4083 4487 1.377856 GTGCCAAGGCTCCCTTCTC 60.378 63.158 12.96 0.00 42.67 2.87
4084 4488 1.539869 TGCCAAGGCTCCCTTCTCT 60.540 57.895 12.96 0.00 42.67 3.10
4085 4489 1.136329 TGCCAAGGCTCCCTTCTCTT 61.136 55.000 12.96 0.00 42.67 2.85
4086 4490 0.393673 GCCAAGGCTCCCTTCTCTTC 60.394 60.000 3.29 0.00 42.67 2.87
4087 4491 0.987294 CCAAGGCTCCCTTCTCTTCA 59.013 55.000 0.00 0.00 42.67 3.02
4088 4492 1.563410 CCAAGGCTCCCTTCTCTTCAT 59.437 52.381 0.00 0.00 42.67 2.57
4089 4493 2.641305 CAAGGCTCCCTTCTCTTCATG 58.359 52.381 0.00 0.00 42.67 3.07
4090 4494 0.545646 AGGCTCCCTTCTCTTCATGC 59.454 55.000 0.00 0.00 0.00 4.06
4091 4495 0.254178 GGCTCCCTTCTCTTCATGCA 59.746 55.000 0.00 0.00 0.00 3.96
4092 4496 1.133853 GGCTCCCTTCTCTTCATGCAT 60.134 52.381 0.00 0.00 0.00 3.96
4093 4497 2.105477 GGCTCCCTTCTCTTCATGCATA 59.895 50.000 0.00 0.00 0.00 3.14
4094 4498 3.244840 GGCTCCCTTCTCTTCATGCATAT 60.245 47.826 0.00 0.00 0.00 1.78
4095 4499 3.752222 GCTCCCTTCTCTTCATGCATATG 59.248 47.826 0.00 0.00 35.57 1.78
4096 4500 4.504514 GCTCCCTTCTCTTCATGCATATGA 60.505 45.833 6.97 0.00 41.44 2.15
4146 4551 7.838079 TGAATCAAATGGATAAATAGTGGGG 57.162 36.000 0.00 0.00 34.28 4.96
4187 5218 5.893897 ATGCAGTCTTCCTTTTCTGAATC 57.106 39.130 0.00 0.00 0.00 2.52
4203 5234 6.701145 TCTGAATCTCTTTCTGTAGCGTAT 57.299 37.500 0.00 0.00 35.44 3.06
4229 5260 3.058155 TCAGACACGACTTGCTCTCTTAC 60.058 47.826 0.00 0.00 0.00 2.34
4238 5269 5.406780 CGACTTGCTCTCTTACACTTTTCAT 59.593 40.000 0.00 0.00 0.00 2.57
4240 5271 5.471456 ACTTGCTCTCTTACACTTTTCATGG 59.529 40.000 0.00 0.00 0.00 3.66
4244 5275 5.470098 GCTCTCTTACACTTTTCATGGTTCA 59.530 40.000 0.00 0.00 0.00 3.18
4245 5276 6.348050 GCTCTCTTACACTTTTCATGGTTCAG 60.348 42.308 0.00 0.00 0.00 3.02
4247 5278 5.070001 TCTTACACTTTTCATGGTTCAGGG 58.930 41.667 0.00 0.00 0.00 4.45
4248 5279 3.593442 ACACTTTTCATGGTTCAGGGA 57.407 42.857 0.00 0.00 0.00 4.20
4249 5280 3.222603 ACACTTTTCATGGTTCAGGGAC 58.777 45.455 0.00 0.00 0.00 4.46
4250 5281 3.117512 ACACTTTTCATGGTTCAGGGACT 60.118 43.478 0.00 0.00 43.88 3.85
4252 5283 5.070001 CACTTTTCATGGTTCAGGGACTAA 58.930 41.667 0.00 0.00 36.02 2.24
4253 5284 5.048713 CACTTTTCATGGTTCAGGGACTAAC 60.049 44.000 0.00 0.00 36.02 2.34
4254 5285 3.713826 TTCATGGTTCAGGGACTAACC 57.286 47.619 0.00 0.00 40.21 2.85
4255 5286 2.915869 TCATGGTTCAGGGACTAACCT 58.084 47.619 5.88 0.00 40.35 3.50
4256 5287 4.069312 TCATGGTTCAGGGACTAACCTA 57.931 45.455 5.88 0.00 40.35 3.08
4268 5300 5.540719 AGGGACTAACCTATAGTTGCTGATC 59.459 44.000 0.00 0.00 39.65 2.92
4279 5311 2.578683 TGCTGATCGCACTACCAGA 58.421 52.632 7.93 0.00 45.47 3.86
4282 5314 2.294512 TGCTGATCGCACTACCAGATAG 59.705 50.000 7.93 0.00 45.47 2.08
4291 5323 7.526142 TCGCACTACCAGATAGAATATTTCT 57.474 36.000 0.00 0.00 43.72 2.52
4293 5325 8.731605 TCGCACTACCAGATAGAATATTTCTAG 58.268 37.037 3.63 0.00 44.80 2.43
4294 5326 8.516234 CGCACTACCAGATAGAATATTTCTAGT 58.484 37.037 3.63 0.00 44.80 2.57
4312 5344 1.142870 AGTCCCAAAAGTACTGCTGCA 59.857 47.619 0.88 0.88 0.00 4.41
4327 5359 2.342910 CTGCAAGCACCATCTTCAAC 57.657 50.000 0.00 0.00 0.00 3.18
4330 5362 2.294233 TGCAAGCACCATCTTCAACTTC 59.706 45.455 0.00 0.00 0.00 3.01
4331 5363 2.555757 GCAAGCACCATCTTCAACTTCT 59.444 45.455 0.00 0.00 0.00 2.85
4340 5372 5.071788 ACCATCTTCAACTTCTGGTTAGTCA 59.928 40.000 0.00 0.00 36.86 3.41
4344 5377 6.591935 TCTTCAACTTCTGGTTAGTCAATGT 58.408 36.000 0.00 0.00 36.23 2.71
4348 5381 6.260050 TCAACTTCTGGTTAGTCAATGTGTTC 59.740 38.462 0.00 0.00 36.23 3.18
4353 5386 4.141287 TGGTTAGTCAATGTGTTCCAAGG 58.859 43.478 0.00 0.00 0.00 3.61
4380 5413 5.036117 TCCCATTCCTAATGAACTACAGC 57.964 43.478 1.23 0.00 41.46 4.40
4384 5417 1.202371 TCCTAATGAACTACAGCCGCG 60.202 52.381 0.00 0.00 0.00 6.46
4400 5433 1.135199 CCGCGCTTCCACTAACTTCTA 60.135 52.381 5.56 0.00 0.00 2.10
4402 5435 2.415625 CGCGCTTCCACTAACTTCTACT 60.416 50.000 5.56 0.00 0.00 2.57
4403 5436 3.180613 GCGCTTCCACTAACTTCTACTC 58.819 50.000 0.00 0.00 0.00 2.59
4404 5437 3.771798 CGCTTCCACTAACTTCTACTCC 58.228 50.000 0.00 0.00 0.00 3.85
4405 5438 3.429135 CGCTTCCACTAACTTCTACTCCC 60.429 52.174 0.00 0.00 0.00 4.30
4406 5439 3.770388 GCTTCCACTAACTTCTACTCCCT 59.230 47.826 0.00 0.00 0.00 4.20
4407 5440 4.142116 GCTTCCACTAACTTCTACTCCCTC 60.142 50.000 0.00 0.00 0.00 4.30
4408 5441 4.949966 TCCACTAACTTCTACTCCCTCT 57.050 45.455 0.00 0.00 0.00 3.69
4409 5442 4.601084 TCCACTAACTTCTACTCCCTCTG 58.399 47.826 0.00 0.00 0.00 3.35
4410 5443 4.044317 TCCACTAACTTCTACTCCCTCTGT 59.956 45.833 0.00 0.00 0.00 3.41
4411 5444 5.252397 TCCACTAACTTCTACTCCCTCTGTA 59.748 44.000 0.00 0.00 0.00 2.74
4412 5445 5.950549 CCACTAACTTCTACTCCCTCTGTAA 59.049 44.000 0.00 0.00 0.00 2.41
4413 5446 6.436532 CCACTAACTTCTACTCCCTCTGTAAA 59.563 42.308 0.00 0.00 0.00 2.01
4414 5447 7.314393 CACTAACTTCTACTCCCTCTGTAAAC 58.686 42.308 0.00 0.00 0.00 2.01
4415 5448 7.177041 CACTAACTTCTACTCCCTCTGTAAACT 59.823 40.741 0.00 0.00 0.00 2.66
4416 5449 8.389366 ACTAACTTCTACTCCCTCTGTAAACTA 58.611 37.037 0.00 0.00 0.00 2.24
4417 5450 9.240734 CTAACTTCTACTCCCTCTGTAAACTAA 57.759 37.037 0.00 0.00 0.00 2.24
4418 5451 8.667592 AACTTCTACTCCCTCTGTAAACTAAT 57.332 34.615 0.00 0.00 0.00 1.73
4419 5452 9.765295 AACTTCTACTCCCTCTGTAAACTAATA 57.235 33.333 0.00 0.00 0.00 0.98
4420 5453 9.939424 ACTTCTACTCCCTCTGTAAACTAATAT 57.061 33.333 0.00 0.00 0.00 1.28
4426 5459 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
4428 5461 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
4475 5508 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
4476 5509 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
4477 5510 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
4478 5511 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
4479 5512 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
4480 5513 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
4481 5514 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
4500 5533 4.446889 GGGAGTATTTGCCATTCCTCTCAT 60.447 45.833 0.00 0.00 37.22 2.90
4755 5789 2.017138 TGTGTGCTTCAACTCAACGA 57.983 45.000 0.00 0.00 0.00 3.85
4764 5798 1.005037 AACTCAACGATGGCTGCGA 60.005 52.632 6.58 0.00 0.00 5.10
4767 5801 0.807275 CTCAACGATGGCTGCGATGA 60.807 55.000 0.66 10.69 38.05 2.92
4769 5803 1.079197 AACGATGGCTGCGATGACA 60.079 52.632 0.66 0.00 0.00 3.58
4802 5836 9.240734 ACAAAAGCAGATGAGAGATATTTCTTT 57.759 29.630 0.00 0.00 30.30 2.52
4806 5840 9.683870 AAGCAGATGAGAGATATTTCTTTTTCT 57.316 29.630 0.00 0.00 30.30 2.52
4807 5841 9.683870 AGCAGATGAGAGATATTTCTTTTTCTT 57.316 29.630 0.00 0.00 30.30 2.52
4861 5895 4.985044 ACGTAAACAGAAATCTTGTCCG 57.015 40.909 0.00 0.00 0.00 4.79
4862 5896 4.624015 ACGTAAACAGAAATCTTGTCCGA 58.376 39.130 0.00 0.00 0.00 4.55
4863 5897 5.235516 ACGTAAACAGAAATCTTGTCCGAT 58.764 37.500 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.125912 GCAGCTGTCGTGGATCGT 60.126 61.111 16.64 0.00 40.80 3.73
6 7 1.690283 CTTGCAGCTGTCGTGGATCG 61.690 60.000 16.64 0.00 41.41 3.69
17 18 0.106708 TCGTCAGAAACCTTGCAGCT 59.893 50.000 0.00 0.00 0.00 4.24
21 22 2.100605 ATCCTCGTCAGAAACCTTGC 57.899 50.000 0.00 0.00 0.00 4.01
22 23 2.668457 CGAATCCTCGTCAGAAACCTTG 59.332 50.000 0.00 0.00 40.33 3.61
23 24 2.960819 CGAATCCTCGTCAGAAACCTT 58.039 47.619 0.00 0.00 40.33 3.50
46 47 4.785453 GCTCCCCGCTGGTTCCAG 62.785 72.222 13.88 13.88 37.15 3.86
71 72 2.371784 TCCGTCCATGGAGCTTTGA 58.628 52.632 16.81 4.60 33.05 2.69
136 137 4.189580 TAAGCATCGCCAGCCCCC 62.190 66.667 0.00 0.00 0.00 5.40
139 140 2.828128 GCAGTAAGCATCGCCAGCC 61.828 63.158 0.00 0.00 44.79 4.85
140 141 2.711924 GCAGTAAGCATCGCCAGC 59.288 61.111 0.00 0.00 44.79 4.85
170 171 5.941058 TCAAAAATCATGGTACCACGTATGT 59.059 36.000 19.09 3.18 0.00 2.29
211 212 2.275318 CTCTCATTGCTTCGTCCTTCC 58.725 52.381 0.00 0.00 0.00 3.46
228 230 0.976641 TGAACCGTTGGATCTGCTCT 59.023 50.000 0.00 0.00 0.00 4.09
239 241 2.972505 CGGCTGCTGTGAACCGTT 60.973 61.111 0.00 0.00 40.77 4.44
251 253 4.529219 TGCCCTACGATGCGGCTG 62.529 66.667 0.00 0.00 43.42 4.85
311 314 3.168193 CGTTTTGGTTTAGGCTATTGCG 58.832 45.455 0.00 0.00 40.82 4.85
357 360 4.419921 ACCGACGCCATTTCCCCC 62.420 66.667 0.00 0.00 0.00 5.40
519 522 1.596895 GACAGGTCTCGGAGGTGGTC 61.597 65.000 4.96 4.97 0.00 4.02
520 523 1.606889 GACAGGTCTCGGAGGTGGT 60.607 63.158 4.96 0.00 0.00 4.16
526 529 2.680352 GGCAGGACAGGTCTCGGA 60.680 66.667 0.00 0.00 0.00 4.55
552 555 2.052104 GGGCGGTGAAAAGGGGATG 61.052 63.158 0.00 0.00 0.00 3.51
1027 1030 2.943978 GCACAGCCTACGTGGTCCT 61.944 63.158 0.00 0.00 38.35 3.85
1062 1065 1.742768 CCGAGATGCTAGGTGGTCC 59.257 63.158 0.00 0.00 0.00 4.46
1071 1074 1.593750 GCGATTCAGCCGAGATGCT 60.594 57.895 0.00 0.00 44.00 3.79
1079 1082 0.175760 TCACCTACTGCGATTCAGCC 59.824 55.000 0.00 0.00 46.76 4.85
1080 1083 1.134965 ACTCACCTACTGCGATTCAGC 60.135 52.381 0.00 0.00 46.76 4.26
1109 1113 8.082242 ACAGTACTACCAATCAAAGAAAAATGC 58.918 33.333 0.00 0.00 0.00 3.56
1129 1140 6.478588 GCATCACAGCAAAATAGTACAGTAC 58.521 40.000 2.05 2.05 0.00 2.73
1130 1141 5.290885 CGCATCACAGCAAAATAGTACAGTA 59.709 40.000 0.00 0.00 0.00 2.74
1131 1142 4.093408 CGCATCACAGCAAAATAGTACAGT 59.907 41.667 0.00 0.00 0.00 3.55
1132 1143 4.581493 CGCATCACAGCAAAATAGTACAG 58.419 43.478 0.00 0.00 0.00 2.74
1133 1144 3.181511 GCGCATCACAGCAAAATAGTACA 60.182 43.478 0.30 0.00 0.00 2.90
1134 1145 3.063997 AGCGCATCACAGCAAAATAGTAC 59.936 43.478 11.47 0.00 35.48 2.73
1135 1146 3.063861 CAGCGCATCACAGCAAAATAGTA 59.936 43.478 11.47 0.00 35.48 1.82
1136 1147 2.086869 AGCGCATCACAGCAAAATAGT 58.913 42.857 11.47 0.00 35.48 2.12
1137 1148 2.159476 ACAGCGCATCACAGCAAAATAG 60.159 45.455 11.47 0.00 35.48 1.73
1138 1149 1.811965 ACAGCGCATCACAGCAAAATA 59.188 42.857 11.47 0.00 35.48 1.40
1139 1150 0.599558 ACAGCGCATCACAGCAAAAT 59.400 45.000 11.47 0.00 35.48 1.82
1153 1164 2.865308 CAGCACATCACCACAGCG 59.135 61.111 0.00 0.00 0.00 5.18
1157 1168 0.674581 TAGCAGCAGCACATCACCAC 60.675 55.000 3.17 0.00 45.49 4.16
1240 1273 3.264706 TGATACTCGAAACCCCAAATCCA 59.735 43.478 0.00 0.00 0.00 3.41
1377 1412 3.064207 GGCCCGAAAATTTTCCAACTTC 58.936 45.455 22.15 8.05 33.68 3.01
1381 1416 1.271102 CTCGGCCCGAAAATTTTCCAA 59.729 47.619 22.15 0.00 34.74 3.53
1396 1431 0.392336 AAGCAGGATCAGATCTCGGC 59.608 55.000 10.36 11.83 0.00 5.54
1417 1452 5.682234 TGCACTGATCCTAGAGATTTGAA 57.318 39.130 0.00 0.00 34.42 2.69
1484 1519 2.094734 CCGGTCGCAATAAACCAAGTAC 59.905 50.000 0.00 0.00 35.13 2.73
1485 1520 2.348660 CCGGTCGCAATAAACCAAGTA 58.651 47.619 0.00 0.00 35.13 2.24
1486 1521 1.161843 CCGGTCGCAATAAACCAAGT 58.838 50.000 0.00 0.00 35.13 3.16
1487 1522 0.450184 CCCGGTCGCAATAAACCAAG 59.550 55.000 0.00 0.00 35.13 3.61
1488 1523 0.961358 CCCCGGTCGCAATAAACCAA 60.961 55.000 0.00 0.00 35.13 3.67
1491 1526 0.961857 AACCCCCGGTCGCAATAAAC 60.962 55.000 0.00 0.00 33.12 2.01
1499 1534 0.897621 ACTAACTAAACCCCCGGTCG 59.102 55.000 0.00 0.00 33.12 4.79
1504 1539 4.030314 AGCAAGAACTAACTAAACCCCC 57.970 45.455 0.00 0.00 0.00 5.40
1516 1551 2.648059 ACTCAACTGCAAGCAAGAACT 58.352 42.857 0.00 0.00 37.60 3.01
1589 1624 8.732746 ATCTTACACATATCCTTGTACCAAAC 57.267 34.615 0.00 0.00 0.00 2.93
1626 1661 6.096423 GCCCATCGAGACCTATATTGTATACA 59.904 42.308 0.08 0.08 0.00 2.29
1795 1831 9.307121 CCTACACTAACATCAACTATTCTTGAG 57.693 37.037 0.00 0.00 33.65 3.02
1881 1917 4.865776 ACATCGCTCAGTTAGATCTTAGC 58.134 43.478 0.00 2.29 33.08 3.09
2162 2207 4.932200 AGTGTTGTAGCAGTCTTAATCAGC 59.068 41.667 0.00 0.00 0.00 4.26
2200 2250 5.525012 TCTTCATTCTCGCCATCACTAATTG 59.475 40.000 0.00 0.00 0.00 2.32
3106 3159 5.902681 TGTCTTGGTAACTGATAAGATCCG 58.097 41.667 0.00 0.00 32.44 4.18
3141 3194 3.990959 ACAACAAACCCAATGGTGTTT 57.009 38.095 11.40 11.40 46.13 2.83
3300 3353 2.043604 CTCCCATCACTATGCCGGCA 62.044 60.000 34.80 34.80 0.00 5.69
3318 3371 2.375174 TGTCCCAGCTGTATTGGAAACT 59.625 45.455 13.81 0.00 37.96 2.66
3563 3616 2.755655 CGTGTTCCTATCCTGTCTCACT 59.244 50.000 0.00 0.00 0.00 3.41
3565 3618 2.100197 CCGTGTTCCTATCCTGTCTCA 58.900 52.381 0.00 0.00 0.00 3.27
3569 3622 1.946984 TTCCCGTGTTCCTATCCTGT 58.053 50.000 0.00 0.00 0.00 4.00
3578 3631 6.861065 AATACATGTGATATTCCCGTGTTC 57.139 37.500 9.11 0.00 31.25 3.18
3716 3769 7.601886 CAGCTGGAATAACAGAGTTATAGGATG 59.398 40.741 5.57 1.08 40.97 3.51
3724 3777 2.307098 AGCCAGCTGGAATAACAGAGTT 59.693 45.455 37.21 0.00 40.97 3.01
3798 3851 8.787852 AGGAAAATGACTTACAAAACAGAGATC 58.212 33.333 0.00 0.00 0.00 2.75
3861 3916 8.092068 GGCTTCCTATAAACTTCTCCTATTCTC 58.908 40.741 0.00 0.00 0.00 2.87
3877 4281 9.555411 TGACCATAATATTGTAGGCTTCCTATA 57.445 33.333 0.00 0.00 38.48 1.31
3878 4282 8.449423 TGACCATAATATTGTAGGCTTCCTAT 57.551 34.615 0.00 0.00 38.48 2.57
3879 4283 7.865530 TGACCATAATATTGTAGGCTTCCTA 57.134 36.000 0.00 0.00 34.61 2.94
3914 4318 9.060347 TCTTCATCTTACCTTTGCATATGATTC 57.940 33.333 6.97 0.00 0.00 2.52
3958 4362 9.431887 TCTGTAAAGAAATATAAGAGCGTTTGT 57.568 29.630 0.00 0.00 0.00 2.83
3959 4363 9.907576 CTCTGTAAAGAAATATAAGAGCGTTTG 57.092 33.333 0.00 0.00 0.00 2.93
3960 4364 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
3961 4365 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
3962 4366 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
3963 4367 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
3964 4368 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
3975 4379 9.198475 CCTTAATAAGTACTCCCTCTGTAAAGA 57.802 37.037 0.00 0.00 0.00 2.52
3976 4380 7.927092 GCCTTAATAAGTACTCCCTCTGTAAAG 59.073 40.741 0.00 0.00 0.00 1.85
3977 4381 7.147602 GGCCTTAATAAGTACTCCCTCTGTAAA 60.148 40.741 0.00 0.00 0.00 2.01
3978 4382 6.325804 GGCCTTAATAAGTACTCCCTCTGTAA 59.674 42.308 0.00 0.00 0.00 2.41
3979 4383 5.837438 GGCCTTAATAAGTACTCCCTCTGTA 59.163 44.000 0.00 0.00 0.00 2.74
3980 4384 4.654724 GGCCTTAATAAGTACTCCCTCTGT 59.345 45.833 0.00 0.00 0.00 3.41
3981 4385 4.902448 AGGCCTTAATAAGTACTCCCTCTG 59.098 45.833 0.00 0.00 0.00 3.35
3982 4386 5.159139 AGGCCTTAATAAGTACTCCCTCT 57.841 43.478 0.00 0.00 0.00 3.69
3983 4387 5.890752 AAGGCCTTAATAAGTACTCCCTC 57.109 43.478 18.87 0.00 0.00 4.30
3984 4388 5.631717 GCAAAGGCCTTAATAAGTACTCCCT 60.632 44.000 20.84 0.00 0.00 4.20
3985 4389 4.579340 GCAAAGGCCTTAATAAGTACTCCC 59.421 45.833 20.84 0.00 0.00 4.30
3986 4390 5.752892 GCAAAGGCCTTAATAAGTACTCC 57.247 43.478 20.84 0.00 0.00 3.85
4032 4436 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
4033 4437 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
4034 4438 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
4035 4439 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
4036 4440 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
4037 4441 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
4038 4442 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
4039 4443 0.386838 AAAAGCTGCTGCCTTGTGAC 59.613 50.000 12.44 0.00 40.80 3.67
4040 4444 1.608590 GTAAAAGCTGCTGCCTTGTGA 59.391 47.619 12.44 0.00 40.80 3.58
4041 4445 1.336240 GGTAAAAGCTGCTGCCTTGTG 60.336 52.381 12.44 0.00 40.80 3.33
4042 4446 0.961753 GGTAAAAGCTGCTGCCTTGT 59.038 50.000 12.44 4.13 40.80 3.16
4043 4447 0.961019 TGGTAAAAGCTGCTGCCTTG 59.039 50.000 12.44 0.00 40.80 3.61
4044 4448 0.961753 GTGGTAAAAGCTGCTGCCTT 59.038 50.000 12.44 8.67 40.80 4.35
4045 4449 0.111253 AGTGGTAAAAGCTGCTGCCT 59.889 50.000 12.44 0.00 40.80 4.75
4046 4450 0.242017 CAGTGGTAAAAGCTGCTGCC 59.758 55.000 12.44 4.43 40.80 4.85
4047 4451 0.954452 ACAGTGGTAAAAGCTGCTGC 59.046 50.000 1.35 7.62 40.05 5.25
4048 4452 1.335324 GCACAGTGGTAAAAGCTGCTG 60.335 52.381 1.35 0.00 33.87 4.41
4049 4453 0.954452 GCACAGTGGTAAAAGCTGCT 59.046 50.000 1.84 0.00 33.87 4.24
4050 4454 0.039165 GGCACAGTGGTAAAAGCTGC 60.039 55.000 1.84 0.00 33.87 5.25
4051 4455 1.317613 TGGCACAGTGGTAAAAGCTG 58.682 50.000 1.84 0.00 36.41 4.24
4052 4456 1.956477 CTTGGCACAGTGGTAAAAGCT 59.044 47.619 1.84 0.00 42.39 3.74
4053 4457 1.000274 CCTTGGCACAGTGGTAAAAGC 60.000 52.381 1.84 0.00 42.39 3.51
4054 4458 1.000274 GCCTTGGCACAGTGGTAAAAG 60.000 52.381 6.79 0.00 42.39 2.27
4055 4459 1.036707 GCCTTGGCACAGTGGTAAAA 58.963 50.000 6.79 0.00 42.39 1.52
4056 4460 0.184933 AGCCTTGGCACAGTGGTAAA 59.815 50.000 14.54 0.00 42.39 2.01
4057 4461 0.250727 GAGCCTTGGCACAGTGGTAA 60.251 55.000 14.54 0.00 42.39 2.85
4058 4462 1.374947 GAGCCTTGGCACAGTGGTA 59.625 57.895 14.54 0.00 42.39 3.25
4059 4463 2.113986 GAGCCTTGGCACAGTGGT 59.886 61.111 14.54 0.00 42.39 4.16
4060 4464 2.674380 GGAGCCTTGGCACAGTGG 60.674 66.667 14.54 0.00 42.39 4.00
4061 4465 2.674380 GGGAGCCTTGGCACAGTG 60.674 66.667 14.54 0.00 42.39 3.66
4062 4466 2.417558 GAAGGGAGCCTTGGCACAGT 62.418 60.000 14.54 0.00 44.82 3.55
4063 4467 1.676967 GAAGGGAGCCTTGGCACAG 60.677 63.158 14.54 0.00 44.82 3.66
4064 4468 2.129555 GAGAAGGGAGCCTTGGCACA 62.130 60.000 14.54 0.00 44.82 4.57
4065 4469 1.377856 GAGAAGGGAGCCTTGGCAC 60.378 63.158 14.54 7.49 44.82 5.01
4066 4470 1.136329 AAGAGAAGGGAGCCTTGGCA 61.136 55.000 14.54 0.00 44.82 4.92
4067 4471 0.393673 GAAGAGAAGGGAGCCTTGGC 60.394 60.000 2.97 2.97 44.82 4.52
4068 4472 0.987294 TGAAGAGAAGGGAGCCTTGG 59.013 55.000 0.00 0.00 44.82 3.61
4069 4473 2.641305 CATGAAGAGAAGGGAGCCTTG 58.359 52.381 0.00 0.00 44.82 3.61
4070 4474 8.878324 CATATGCATGAAGAGAAGGGAGCCTT 62.878 46.154 10.16 0.00 39.47 4.35
4071 4475 0.545646 GCATGAAGAGAAGGGAGCCT 59.454 55.000 0.00 0.00 33.87 4.58
4072 4476 0.254178 TGCATGAAGAGAAGGGAGCC 59.746 55.000 0.00 0.00 0.00 4.70
4073 4477 2.345124 ATGCATGAAGAGAAGGGAGC 57.655 50.000 0.00 0.00 0.00 4.70
4074 4478 5.224821 TCATATGCATGAAGAGAAGGGAG 57.775 43.478 10.16 0.00 38.25 4.30
4075 4479 5.635278 TTCATATGCATGAAGAGAAGGGA 57.365 39.130 10.16 0.00 44.44 4.20
4146 4551 4.570772 TGCATACGCTACAGGAAGATTTTC 59.429 41.667 0.00 0.00 39.64 2.29
4187 5218 6.908284 GTCTGAACTATACGCTACAGAAAGAG 59.092 42.308 0.00 0.00 36.41 2.85
4203 5234 2.885266 AGAGCAAGTCGTGTCTGAACTA 59.115 45.455 0.00 0.00 0.00 2.24
4229 5260 3.490348 AGTCCCTGAACCATGAAAAGTG 58.510 45.455 0.00 0.00 0.00 3.16
4238 5269 5.216665 ACTATAGGTTAGTCCCTGAACCA 57.783 43.478 4.43 0.00 46.41 3.67
4240 5271 5.128991 AGCAACTATAGGTTAGTCCCTGAAC 59.871 44.000 4.43 0.00 36.23 3.18
4244 5275 4.880164 TCAGCAACTATAGGTTAGTCCCT 58.120 43.478 4.43 0.00 36.23 4.20
4245 5276 5.565045 CGATCAGCAACTATAGGTTAGTCCC 60.565 48.000 4.43 0.00 36.23 4.46
4268 5300 8.516234 ACTAGAAATATTCTATCTGGTAGTGCG 58.484 37.037 0.00 0.00 41.17 5.34
4272 5304 9.535170 TGGGACTAGAAATATTCTATCTGGTAG 57.465 37.037 0.00 0.00 41.17 3.18
4282 5314 8.613482 GCAGTACTTTTGGGACTAGAAATATTC 58.387 37.037 0.00 0.00 0.00 1.75
4291 5323 2.370519 TGCAGCAGTACTTTTGGGACTA 59.629 45.455 0.00 0.00 0.00 2.59
4293 5325 1.604604 TGCAGCAGTACTTTTGGGAC 58.395 50.000 0.00 0.00 0.00 4.46
4294 5326 2.229792 CTTGCAGCAGTACTTTTGGGA 58.770 47.619 0.00 0.00 0.00 4.37
4312 5344 3.152341 CCAGAAGTTGAAGATGGTGCTT 58.848 45.455 0.00 0.00 0.00 3.91
4316 5348 5.071788 TGACTAACCAGAAGTTGAAGATGGT 59.928 40.000 0.00 0.00 46.05 3.55
4319 5351 7.173907 CACATTGACTAACCAGAAGTTGAAGAT 59.826 37.037 0.00 0.00 39.67 2.40
4320 5352 6.483307 CACATTGACTAACCAGAAGTTGAAGA 59.517 38.462 0.00 0.00 39.67 2.87
4327 5359 5.063204 TGGAACACATTGACTAACCAGAAG 58.937 41.667 0.00 0.00 0.00 2.85
4330 5362 4.216257 CCTTGGAACACATTGACTAACCAG 59.784 45.833 0.00 0.00 39.29 4.00
4331 5363 4.141287 CCTTGGAACACATTGACTAACCA 58.859 43.478 0.00 0.00 39.29 3.67
4340 5372 1.620822 GAGGCACCTTGGAACACATT 58.379 50.000 0.00 0.00 39.29 2.71
4344 5377 1.434513 ATGGGAGGCACCTTGGAACA 61.435 55.000 0.00 0.00 38.98 3.18
4348 5381 1.380380 GGAATGGGAGGCACCTTGG 60.380 63.158 0.00 0.00 38.98 3.61
4353 5386 2.952310 GTTCATTAGGAATGGGAGGCAC 59.048 50.000 0.00 0.00 39.38 5.01
4380 5413 0.389948 AGAAGTTAGTGGAAGCGCGG 60.390 55.000 8.83 0.00 0.00 6.46
4384 5417 3.770388 AGGGAGTAGAAGTTAGTGGAAGC 59.230 47.826 0.00 0.00 0.00 3.86
4400 5433 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
4402 5435 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
4449 5482 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
4450 5483 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
4451 5484 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
4452 5485 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
4453 5486 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
4454 5487 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
4455 5488 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
4456 5489 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
4457 5490 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4462 5495 7.876582 GCAAATACTCCCTCCGTAAACTAATAT 59.123 37.037 0.00 0.00 0.00 1.28
4463 5496 7.212274 GCAAATACTCCCTCCGTAAACTAATA 58.788 38.462 0.00 0.00 0.00 0.98
4464 5497 6.053650 GCAAATACTCCCTCCGTAAACTAAT 58.946 40.000 0.00 0.00 0.00 1.73
4465 5498 5.422145 GCAAATACTCCCTCCGTAAACTAA 58.578 41.667 0.00 0.00 0.00 2.24
4466 5499 4.141869 GGCAAATACTCCCTCCGTAAACTA 60.142 45.833 0.00 0.00 0.00 2.24
4467 5500 3.370209 GGCAAATACTCCCTCCGTAAACT 60.370 47.826 0.00 0.00 0.00 2.66
4468 5501 2.941064 GGCAAATACTCCCTCCGTAAAC 59.059 50.000 0.00 0.00 0.00 2.01
4469 5502 2.572556 TGGCAAATACTCCCTCCGTAAA 59.427 45.455 0.00 0.00 0.00 2.01
4470 5503 2.189676 TGGCAAATACTCCCTCCGTAA 58.810 47.619 0.00 0.00 0.00 3.18
4471 5504 1.868713 TGGCAAATACTCCCTCCGTA 58.131 50.000 0.00 0.00 0.00 4.02
4472 5505 1.213296 ATGGCAAATACTCCCTCCGT 58.787 50.000 0.00 0.00 0.00 4.69
4473 5506 2.222027 GAATGGCAAATACTCCCTCCG 58.778 52.381 0.00 0.00 0.00 4.63
4474 5507 2.175715 AGGAATGGCAAATACTCCCTCC 59.824 50.000 0.00 0.00 0.00 4.30
4475 5508 3.137360 AGAGGAATGGCAAATACTCCCTC 59.863 47.826 11.16 9.54 39.26 4.30
4476 5509 3.126453 AGAGGAATGGCAAATACTCCCT 58.874 45.455 11.16 1.84 0.00 4.20
4477 5510 3.117888 TGAGAGGAATGGCAAATACTCCC 60.118 47.826 11.16 2.13 0.00 4.30
4478 5511 4.156455 TGAGAGGAATGGCAAATACTCC 57.844 45.455 11.16 4.13 0.00 3.85
4479 5512 4.759183 GGATGAGAGGAATGGCAAATACTC 59.241 45.833 7.60 7.60 0.00 2.59
4480 5513 4.414846 AGGATGAGAGGAATGGCAAATACT 59.585 41.667 0.00 0.00 0.00 2.12
4481 5514 4.723309 AGGATGAGAGGAATGGCAAATAC 58.277 43.478 0.00 0.00 0.00 1.89
4630 5663 6.490040 ACGTGCCTTTATATAAGGATGCATTT 59.510 34.615 0.00 0.00 39.81 2.32
4660 5693 1.374758 GGTGAACACTCTCGGCCTG 60.375 63.158 0.00 0.00 0.00 4.85
4755 5789 0.179702 AGATGTGTCATCGCAGCCAT 59.820 50.000 4.44 0.00 40.74 4.40
4764 5798 4.392047 TCTGCTTTTGTGAGATGTGTCAT 58.608 39.130 0.00 0.00 0.00 3.06
4767 5801 4.392047 TCATCTGCTTTTGTGAGATGTGT 58.608 39.130 0.00 0.00 42.48 3.72
4769 5803 4.903054 TCTCATCTGCTTTTGTGAGATGT 58.097 39.130 0.00 0.00 41.40 3.06
4835 5869 8.013378 CGGACAAGATTTCTGTTTACGTTTAAT 58.987 33.333 0.00 0.00 0.00 1.40
4836 5870 7.224362 TCGGACAAGATTTCTGTTTACGTTTAA 59.776 33.333 0.00 0.00 0.00 1.52
4837 5871 6.700960 TCGGACAAGATTTCTGTTTACGTTTA 59.299 34.615 0.00 0.00 0.00 2.01
4838 5872 5.524646 TCGGACAAGATTTCTGTTTACGTTT 59.475 36.000 0.00 0.00 0.00 3.60
4839 5873 5.051816 TCGGACAAGATTTCTGTTTACGTT 58.948 37.500 0.00 0.00 0.00 3.99
4840 5874 4.624015 TCGGACAAGATTTCTGTTTACGT 58.376 39.130 0.00 0.00 0.00 3.57
4841 5875 5.779806 ATCGGACAAGATTTCTGTTTACG 57.220 39.130 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.