Multiple sequence alignment - TraesCS1B01G379200

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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 TraesCS1B01G379200 chr1B 100.000 5301 0 0 1 5301 611931499 611926199 0.000000e+00 9790.0
1 TraesCS1B01G379200 chr2A 92.242 4318 190 57 544 4784 69355855 69351606 0.000000e+00 5984.0
2 TraesCS1B01G379200 chr2A 88.443 424 25 8 4834 5257 69351479 69351080 1.720000e-134 490.0
3 TraesCS1B01G379200 chr2D 90.444 3380 194 62 316 3619 69539195 69535869 0.000000e+00 4333.0
4 TraesCS1B01G379200 chr2D 92.790 846 41 5 3792 4618 69535674 69534830 0.000000e+00 1206.0
5 TraesCS1B01G379200 chr2D 90.504 337 17 8 4923 5257 69534575 69534252 1.050000e-116 431.0
6 TraesCS1B01G379200 chr2D 91.139 158 10 2 3541 3698 69535871 69535718 1.500000e-50 211.0
7 TraesCS1B01G379200 chr2D 91.339 127 10 1 169 295 69539310 69539185 7.060000e-39 172.0
8 TraesCS1B01G379200 chr2D 98.077 52 1 0 4733 4784 69534769 69534718 2.030000e-14 91.6
9 TraesCS1B01G379200 chr2B 93.162 2413 119 17 2337 4722 105993710 105991317 0.000000e+00 3500.0
10 TraesCS1B01G379200 chr2B 84.167 720 76 25 1531 2227 105994441 105993737 0.000000e+00 664.0
11 TraesCS1B01G379200 chr2B 92.771 332 21 1 154 482 105998970 105998639 1.340000e-130 477.0
12 TraesCS1B01G379200 chr2B 88.108 370 16 13 739 1089 105995235 105994875 1.060000e-111 414.0
13 TraesCS1B01G379200 chr2B 94.043 235 11 2 5023 5257 105991116 105990885 2.350000e-93 353.0
14 TraesCS1B01G379200 chr2B 90.123 162 15 1 1 162 105999192 105999032 5.380000e-50 209.0
15 TraesCS1B01G379200 chr2B 90.722 97 7 1 4926 5022 105991294 105991200 1.550000e-25 128.0
16 TraesCS1B01G379200 chr4A 81.757 592 94 11 2337 2921 222107592 222108176 2.870000e-132 483.0
17 TraesCS1B01G379200 chr1A 75.339 442 65 29 4782 5219 566410213 566410614 7.060000e-39 172.0
18 TraesCS1B01G379200 chr1A 75.395 443 63 30 4782 5219 566415853 566416254 7.060000e-39 172.0
19 TraesCS1B01G379200 chr1A 87.395 119 10 3 4852 4970 533779298 533779185 1.200000e-26 132.0
20 TraesCS1B01G379200 chr1A 100.000 31 0 0 4130 4160 541812116 541812086 2.060000e-04 58.4
21 TraesCS1B01G379200 chr7D 75.472 318 48 21 4862 5177 549548401 549548690 1.550000e-25 128.0
22 TraesCS1B01G379200 chr1D 88.182 110 10 2 4862 4970 436855983 436855876 1.550000e-25 128.0
23 TraesCS1B01G379200 chr1D 100.000 30 0 0 4130 4159 314938812 314938841 7.420000e-04 56.5
24 TraesCS1B01G379200 chr7B 90.526 95 6 2 4862 4956 285454992 285454901 7.210000e-24 122.0
25 TraesCS1B01G379200 chr6B 91.209 91 4 4 4871 4961 684384643 684384557 2.590000e-23 121.0
26 TraesCS1B01G379200 chr6A 91.209 91 4 4 4871 4961 596161922 596161836 2.590000e-23 121.0
27 TraesCS1B01G379200 chr6A 76.190 147 28 7 2364 2507 614721997 614722139 2.650000e-08 71.3
28 TraesCS1B01G379200 chr5A 100.000 31 0 0 4130 4160 173018631 173018661 2.060000e-04 58.4
29 TraesCS1B01G379200 chr4D 100.000 30 0 0 4130 4159 131721348 131721377 7.420000e-04 56.5
30 TraesCS1B01G379200 chr4D 100.000 30 0 0 4130 4159 222605225 222605196 7.420000e-04 56.5
31 TraesCS1B01G379200 chr4D 100.000 30 0 0 4130 4159 480931440 480931469 7.420000e-04 56.5


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 TraesCS1B01G379200 chr1B 611926199 611931499 5300 True 9790.000000 9790 100.000000 1 5301 1 chr1B.!!$R1 5300
1 TraesCS1B01G379200 chr2A 69351080 69355855 4775 True 3237.000000 5984 90.342500 544 5257 2 chr2A.!!$R1 4713
2 TraesCS1B01G379200 chr2D 69534252 69539310 5058 True 1074.100000 4333 92.382167 169 5257 6 chr2D.!!$R1 5088
3 TraesCS1B01G379200 chr2B 105990885 105999192 8307 True 820.714286 3500 90.442286 1 5257 7 chr2B.!!$R1 5256
4 TraesCS1B01G379200 chr4A 222107592 222108176 584 False 483.000000 483 81.757000 2337 2921 1 chr4A.!!$F1 584

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
535 3979 0.032130 TATGCTCCGATGCTCGTTCC 59.968 55.0 5.15 0.0 38.40 3.62 F
717 4207 0.246635 TGCTAAACCTCTCCACGCTC 59.753 55.0 0.00 0.0 0.00 5.03 F
920 4440 0.251832 TTCTCCCCGCTCTCTCTTGT 60.252 55.0 0.00 0.0 0.00 3.16 F
1122 4643 0.324091 CCTCCCTACCCGTGTAGTGT 60.324 60.0 4.33 0.0 42.49 3.55 F
1129 4650 0.537143 ACCCGTGTAGTGTACGACCA 60.537 55.0 0.00 0.0 43.82 4.02 F
1130 4651 0.597568 CCCGTGTAGTGTACGACCAA 59.402 55.0 0.00 0.0 43.82 3.67 F
1526 5119 0.905357 ATGGTCTGGTCTGTGTAGGC 59.095 55.0 0.00 0.0 0.00 3.93 F
2657 6309 1.059098 TGGAAGCAGAGCTGAAGGAA 58.941 50.0 0.85 0.0 39.62 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 5205 1.069022 CAAGCACCGTTGGTCATTCTG 60.069 52.381 0.00 0.00 31.02 3.02 R
1586 5206 1.238439 CAAGCACCGTTGGTCATTCT 58.762 50.000 0.00 0.00 31.02 2.40 R
2206 5843 1.462616 AGTTTGCAACAGTGAGCACA 58.537 45.000 13.16 5.93 41.05 4.57 R
2657 6309 1.471119 CCATGGAAATGACAGCTGCT 58.529 50.000 15.27 0.00 0.00 4.24 R
2894 6546 2.707791 CTCTGCCCCCAGAATCTGAATA 59.292 50.000 12.53 0.00 46.84 1.75 R
2974 6627 6.665992 ACCAGACATCAAGTTCAACTAGTA 57.334 37.500 0.00 0.00 0.00 1.82 R
3405 7065 2.354805 CCTCCCAAGTTCTTTACCCTCG 60.355 54.545 0.00 0.00 0.00 4.63 R
4304 8056 0.105964 TTTCCGCCATATCTCCGTGG 59.894 55.000 0.00 0.00 38.55 4.94 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
42 43 0.963856 TCCGTGTAGTGATGGCGTCT 60.964 55.000 8.40 0.00 0.00 4.18
47 48 3.262420 GTGTAGTGATGGCGTCTTTCAT 58.738 45.455 8.40 0.00 0.00 2.57
49 50 3.684305 TGTAGTGATGGCGTCTTTCATTG 59.316 43.478 8.40 0.00 0.00 2.82
58 59 2.350772 GCGTCTTTCATTGTGGAAGTGG 60.351 50.000 0.00 0.00 0.00 4.00
62 63 4.580580 GTCTTTCATTGTGGAAGTGGAGTT 59.419 41.667 0.00 0.00 0.00 3.01
73 74 2.281484 TGGAGTTGGCTTGGTCGC 60.281 61.111 0.00 0.00 0.00 5.19
115 116 2.223144 TCGTGCAAGTTGGATCTTTTCG 59.777 45.455 4.75 0.73 0.00 3.46
127 128 0.181587 TCTTTTCGGGCTGGTGACAA 59.818 50.000 0.00 0.00 42.06 3.18
137 138 0.819582 CTGGTGACAATGGCCATTCC 59.180 55.000 28.42 24.50 42.06 3.01
139 140 0.679640 GGTGACAATGGCCATTCCGA 60.680 55.000 28.42 11.59 37.80 4.55
159 160 3.547468 CGAAAAGAGGTGTGCTTTTGTTG 59.453 43.478 6.10 0.00 43.45 3.33
237 308 0.466372 TTGTTTGGGTCGTGCCATCA 60.466 50.000 1.70 0.00 39.65 3.07
242 313 1.378514 GGGTCGTGCCATCATTGGT 60.379 57.895 1.70 0.00 45.57 3.67
249 320 4.515191 GTCGTGCCATCATTGGTGTTATAT 59.485 41.667 0.00 0.00 45.57 0.86
407 481 5.741011 AGGCACTTCGATTAGGTGAATAAA 58.259 37.500 10.87 0.00 27.25 1.40
488 3932 8.329502 ACTACTAAATTACAAAGGCTGATTCCT 58.670 33.333 0.00 0.00 38.31 3.36
490 3934 5.665916 AAATTACAAAGGCTGATTCCTGG 57.334 39.130 0.00 0.00 36.38 4.45
496 3940 4.202253 ACAAAGGCTGATTCCTGGAAAAAC 60.202 41.667 14.03 8.69 36.38 2.43
499 3943 3.966665 AGGCTGATTCCTGGAAAAACAAA 59.033 39.130 14.03 0.00 34.56 2.83
501 3945 4.309933 GCTGATTCCTGGAAAAACAAAGG 58.690 43.478 14.03 4.61 0.00 3.11
502 3946 4.309933 CTGATTCCTGGAAAAACAAAGGC 58.690 43.478 14.03 0.00 0.00 4.35
503 3947 3.966665 TGATTCCTGGAAAAACAAAGGCT 59.033 39.130 14.03 0.00 0.00 4.58
504 3948 3.817709 TTCCTGGAAAAACAAAGGCTG 57.182 42.857 6.68 0.00 0.00 4.85
505 3949 3.025322 TCCTGGAAAAACAAAGGCTGA 57.975 42.857 0.00 0.00 0.00 4.26
508 3952 5.144100 TCCTGGAAAAACAAAGGCTGATTA 58.856 37.500 0.00 0.00 0.00 1.75
509 3953 5.010617 TCCTGGAAAAACAAAGGCTGATTAC 59.989 40.000 0.00 0.00 0.00 1.89
510 3954 5.011023 CCTGGAAAAACAAAGGCTGATTACT 59.989 40.000 0.00 0.00 0.00 2.24
511 3955 5.841810 TGGAAAAACAAAGGCTGATTACTG 58.158 37.500 0.00 0.00 0.00 2.74
515 3959 5.629079 AAACAAAGGCTGATTACTGTAGC 57.371 39.130 0.00 0.00 36.74 3.58
517 3961 5.677319 ACAAAGGCTGATTACTGTAGCTA 57.323 39.130 0.00 0.00 37.58 3.32
518 3962 6.240549 ACAAAGGCTGATTACTGTAGCTAT 57.759 37.500 0.00 0.00 37.58 2.97
519 3963 6.051717 ACAAAGGCTGATTACTGTAGCTATG 58.948 40.000 0.00 0.00 37.58 2.23
520 3964 4.264460 AGGCTGATTACTGTAGCTATGC 57.736 45.455 0.00 0.00 37.58 3.14
521 3965 3.900601 AGGCTGATTACTGTAGCTATGCT 59.099 43.478 0.00 0.00 43.41 3.79
524 3968 4.480541 CTGATTACTGTAGCTATGCTCCG 58.519 47.826 0.00 0.00 40.44 4.63
535 3979 0.032130 TATGCTCCGATGCTCGTTCC 59.968 55.000 5.15 0.00 38.40 3.62
538 4009 1.424493 GCTCCGATGCTCGTTCCTTG 61.424 60.000 5.15 0.00 38.40 3.61
539 4010 0.807667 CTCCGATGCTCGTTCCTTGG 60.808 60.000 5.15 0.00 38.40 3.61
542 4013 1.447838 GATGCTCGTTCCTTGGCGA 60.448 57.895 0.00 0.00 35.70 5.54
559 4030 1.816370 CGAGCTCGACACTGTACATC 58.184 55.000 32.06 0.00 43.02 3.06
582 4053 7.483580 TCTTTTCTTTTTAGGGTTGACCAAA 57.516 32.000 2.12 0.00 43.89 3.28
621 4092 3.041940 CCACGTCGTTGTGAGGCC 61.042 66.667 10.61 0.00 42.55 5.19
668 4149 4.215742 CGATGGAACGGCCCGCTA 62.216 66.667 1.23 0.00 34.97 4.26
669 4150 2.588034 GATGGAACGGCCCGCTAC 60.588 66.667 1.23 0.00 34.97 3.58
670 4151 3.081409 ATGGAACGGCCCGCTACT 61.081 61.111 1.23 0.00 34.97 2.57
671 4152 1.741327 GATGGAACGGCCCGCTACTA 61.741 60.000 1.23 0.00 34.97 1.82
672 4153 2.024590 ATGGAACGGCCCGCTACTAC 62.025 60.000 1.23 0.00 34.97 2.73
673 4154 2.278401 GAACGGCCCGCTACTACG 60.278 66.667 1.23 0.00 0.00 3.51
716 4206 0.247736 CTGCTAAACCTCTCCACGCT 59.752 55.000 0.00 0.00 0.00 5.07
717 4207 0.246635 TGCTAAACCTCTCCACGCTC 59.753 55.000 0.00 0.00 0.00 5.03
718 4208 0.533032 GCTAAACCTCTCCACGCTCT 59.467 55.000 0.00 0.00 0.00 4.09
770 4260 2.351276 GGCCGCCTTCCTTCTTCA 59.649 61.111 0.71 0.00 0.00 3.02
810 4307 1.208706 CCTTTCCTCTCTTCCCCTCC 58.791 60.000 0.00 0.00 0.00 4.30
915 4435 2.042435 CCCTTCTCCCCGCTCTCT 60.042 66.667 0.00 0.00 0.00 3.10
917 4437 1.076339 CCTTCTCCCCGCTCTCTCT 60.076 63.158 0.00 0.00 0.00 3.10
918 4438 0.686112 CCTTCTCCCCGCTCTCTCTT 60.686 60.000 0.00 0.00 0.00 2.85
919 4439 0.459489 CTTCTCCCCGCTCTCTCTTG 59.541 60.000 0.00 0.00 0.00 3.02
920 4440 0.251832 TTCTCCCCGCTCTCTCTTGT 60.252 55.000 0.00 0.00 0.00 3.16
1106 4627 2.416432 CGTTCCCTCCGTCTCCCTC 61.416 68.421 0.00 0.00 0.00 4.30
1109 4630 3.756783 CCCTCCGTCTCCCTCCCT 61.757 72.222 0.00 0.00 0.00 4.20
1110 4631 2.392816 CCCTCCGTCTCCCTCCCTA 61.393 68.421 0.00 0.00 0.00 3.53
1111 4632 1.152715 CCTCCGTCTCCCTCCCTAC 60.153 68.421 0.00 0.00 0.00 3.18
1112 4633 1.152715 CTCCGTCTCCCTCCCTACC 60.153 68.421 0.00 0.00 0.00 3.18
1113 4634 2.123382 CCGTCTCCCTCCCTACCC 60.123 72.222 0.00 0.00 0.00 3.69
1118 4639 0.920763 TCTCCCTCCCTACCCGTGTA 60.921 60.000 0.00 0.00 0.00 2.90
1120 4641 1.217057 TCCCTCCCTACCCGTGTAGT 61.217 60.000 4.33 0.00 42.49 2.73
1121 4642 1.041447 CCCTCCCTACCCGTGTAGTG 61.041 65.000 4.33 0.00 42.49 2.74
1122 4643 0.324091 CCTCCCTACCCGTGTAGTGT 60.324 60.000 4.33 0.00 42.49 3.55
1123 4644 1.064463 CCTCCCTACCCGTGTAGTGTA 60.064 57.143 4.33 0.00 42.49 2.90
1124 4645 2.019984 CTCCCTACCCGTGTAGTGTAC 58.980 57.143 4.33 0.00 42.49 2.90
1126 4647 1.678728 CCCTACCCGTGTAGTGTACGA 60.679 57.143 4.33 0.00 42.49 3.43
1127 4648 1.398390 CCTACCCGTGTAGTGTACGAC 59.602 57.143 4.33 0.00 42.49 4.34
1129 4650 0.537143 ACCCGTGTAGTGTACGACCA 60.537 55.000 0.00 0.00 43.82 4.02
1130 4651 0.597568 CCCGTGTAGTGTACGACCAA 59.402 55.000 0.00 0.00 43.82 3.67
1157 4679 5.237344 TGGTCAAAGGTGTTTGTTTTGTTTG 59.763 36.000 0.00 0.00 43.22 2.93
1158 4680 5.237561 GGTCAAAGGTGTTTGTTTTGTTTGT 59.762 36.000 0.00 0.00 43.22 2.83
1159 4681 6.424207 GGTCAAAGGTGTTTGTTTTGTTTGTA 59.576 34.615 0.00 0.00 43.22 2.41
1160 4682 7.359681 GGTCAAAGGTGTTTGTTTTGTTTGTAG 60.360 37.037 0.00 0.00 43.22 2.74
1161 4683 7.170151 GTCAAAGGTGTTTGTTTTGTTTGTAGT 59.830 33.333 0.00 0.00 43.22 2.73
1162 4684 7.382759 TCAAAGGTGTTTGTTTTGTTTGTAGTC 59.617 33.333 0.00 0.00 43.22 2.59
1163 4685 5.395642 AGGTGTTTGTTTTGTTTGTAGTCG 58.604 37.500 0.00 0.00 0.00 4.18
1164 4686 5.181622 AGGTGTTTGTTTTGTTTGTAGTCGA 59.818 36.000 0.00 0.00 0.00 4.20
1166 4688 6.081693 GTGTTTGTTTTGTTTGTAGTCGACT 58.918 36.000 23.66 23.66 0.00 4.18
1167 4689 7.235777 GTGTTTGTTTTGTTTGTAGTCGACTA 58.764 34.615 21.25 21.25 0.00 2.59
1168 4690 7.745594 GTGTTTGTTTTGTTTGTAGTCGACTAA 59.254 33.333 26.21 11.76 0.00 2.24
1170 4692 8.730427 GTTTGTTTTGTTTGTAGTCGACTAATG 58.270 33.333 26.21 0.00 0.00 1.90
1171 4693 6.950545 TGTTTTGTTTGTAGTCGACTAATGG 58.049 36.000 26.21 0.00 0.00 3.16
1183 4705 1.130561 GACTAATGGTTGCCGTGCTTC 59.869 52.381 0.00 0.00 0.00 3.86
1214 4740 2.290577 GGATCTGTGGAAGGACTTTGCT 60.291 50.000 0.00 0.00 0.00 3.91
1251 4777 4.868172 AGAAAGGTGGGATGATTCATGA 57.132 40.909 3.32 0.00 0.00 3.07
1256 4782 3.784763 AGGTGGGATGATTCATGACTCTT 59.215 43.478 13.56 7.75 0.00 2.85
1257 4783 3.881688 GGTGGGATGATTCATGACTCTTG 59.118 47.826 13.56 0.00 0.00 3.02
1259 4785 4.574013 GTGGGATGATTCATGACTCTTGTC 59.426 45.833 13.56 9.04 43.20 3.18
1260 4786 4.472470 TGGGATGATTCATGACTCTTGTCT 59.528 41.667 13.56 0.00 43.29 3.41
1282 4809 6.708949 GTCTTTTTGAGTTACTCATGGGTGTA 59.291 38.462 16.28 0.00 40.39 2.90
1286 4813 5.909621 TGAGTTACTCATGGGTGTAGTAC 57.090 43.478 11.42 0.00 35.39 2.73
1288 4815 6.724351 TGAGTTACTCATGGGTGTAGTACTA 58.276 40.000 11.42 0.00 35.39 1.82
1289 4816 6.827251 TGAGTTACTCATGGGTGTAGTACTAG 59.173 42.308 11.42 0.00 35.39 2.57
1290 4817 6.729428 AGTTACTCATGGGTGTAGTACTAGT 58.271 40.000 8.99 0.00 0.00 2.57
1291 4818 7.180663 AGTTACTCATGGGTGTAGTACTAGTT 58.819 38.462 8.99 0.00 0.00 2.24
1293 4820 8.960591 GTTACTCATGGGTGTAGTACTAGTTTA 58.039 37.037 8.99 0.00 0.00 2.01
1381 4919 6.619744 TGTTAATGCAGAAACATGTGTATGG 58.380 36.000 12.47 0.00 38.66 2.74
1383 4921 7.122501 TGTTAATGCAGAAACATGTGTATGGAT 59.877 33.333 11.49 11.49 38.66 3.41
1440 4981 3.603965 ACTGGTTCCCCAAATGTTACA 57.396 42.857 0.00 0.00 41.27 2.41
1478 5071 7.375053 TGTTTTTCCAAGCCAGTTATTACATC 58.625 34.615 0.00 0.00 0.00 3.06
1515 5108 6.507900 CATACTGTTGTACTAGATGGTCTGG 58.492 44.000 0.00 0.00 0.00 3.86
1516 5109 4.417437 ACTGTTGTACTAGATGGTCTGGT 58.583 43.478 0.00 1.66 41.27 4.00
1517 5110 4.463186 ACTGTTGTACTAGATGGTCTGGTC 59.537 45.833 0.00 0.00 37.58 4.02
1518 5111 4.673968 TGTTGTACTAGATGGTCTGGTCT 58.326 43.478 0.00 0.00 37.58 3.85
1520 5113 4.317530 TGTACTAGATGGTCTGGTCTGT 57.682 45.455 0.00 0.00 37.58 3.41
1524 5117 4.274147 ACTAGATGGTCTGGTCTGTGTAG 58.726 47.826 0.00 0.00 32.42 2.74
1526 5119 0.905357 ATGGTCTGGTCTGTGTAGGC 59.095 55.000 0.00 0.00 0.00 3.93
1561 5179 1.111277 AGTTTGTGGGTCCTTTGTGC 58.889 50.000 0.00 0.00 0.00 4.57
1568 5188 2.488153 GTGGGTCCTTTGTGCTGTATTC 59.512 50.000 0.00 0.00 0.00 1.75
1585 5205 5.229423 TGTATTCTTTTGCATGTTTCCTGC 58.771 37.500 0.00 0.00 40.10 4.85
1597 5217 2.622942 TGTTTCCTGCAGAATGACCAAC 59.377 45.455 17.39 7.12 39.69 3.77
1621 5242 5.452777 GGTGCTTGTTGTTCTGTTAAGATC 58.547 41.667 0.00 0.00 30.72 2.75
1642 5263 2.421424 CCTTCAGCATTGTCTTGTAGGC 59.579 50.000 0.00 0.00 0.00 3.93
1671 5292 4.927978 TGTTGGTTCATGTTAAGGGTTG 57.072 40.909 0.00 0.00 0.00 3.77
1734 5356 6.205658 GGATTTTATATCAGGTGGTTGAGCTC 59.794 42.308 6.82 6.82 0.00 4.09
1764 5386 7.305993 GCTTTCAACAAGTTTGAAAATACCTCG 60.306 37.037 12.03 2.41 44.67 4.63
2183 5819 1.386533 CACCCAGGATTGTGATGCTC 58.613 55.000 0.00 0.00 34.37 4.26
2206 5843 7.758528 GCTCACTCTGAATTATTTTCATGCTTT 59.241 33.333 0.00 0.00 0.00 3.51
2219 5856 2.033675 TCATGCTTTGTGCTCACTGTTG 59.966 45.455 1.47 0.00 43.37 3.33
2253 5890 7.503566 TGCTCTTATATTTTCTAGCATGCCTTT 59.496 33.333 15.66 0.00 35.20 3.11
2278 5915 1.624336 ATGCTCTTCTTTTGGCTGCA 58.376 45.000 0.50 0.00 0.00 4.41
2657 6309 1.059098 TGGAAGCAGAGCTGAAGGAA 58.941 50.000 0.85 0.00 39.62 3.36
2894 6546 4.281527 AAGCAGCCTGGCAGCACT 62.282 61.111 33.14 19.46 43.44 4.40
3035 6689 4.854399 TGCTTTTGTGGTTGAAGTTATCG 58.146 39.130 0.00 0.00 0.00 2.92
3405 7065 1.289380 AACACGGCTCCGAGTTCTC 59.711 57.895 15.95 0.00 46.67 2.87
3885 7633 8.807581 GTTGAACAATTAGAGTTTGAAACTTGG 58.192 33.333 12.37 0.00 43.03 3.61
3895 7643 5.140454 AGTTTGAAACTTGGCTGACCTTAT 58.860 37.500 4.45 0.00 39.04 1.73
3908 7657 5.863935 GGCTGACCTTATTTTGTTTGTCATC 59.136 40.000 0.00 0.00 32.83 2.92
4096 7845 6.658391 AGAAGAAGAAGAAATCCAAGGACATG 59.342 38.462 0.00 0.00 0.00 3.21
4104 7853 2.575921 TCCAAGGACATGGAGGAGAT 57.424 50.000 0.00 0.00 44.52 2.75
4114 7863 0.619832 TGGAGGAGATTCCAGCAGCT 60.620 55.000 0.00 0.00 42.24 4.24
4129 7878 1.972223 AGCTGTCACCGACGCTAGT 60.972 57.895 10.31 0.00 39.26 2.57
4135 7884 0.520404 TCACCGACGCTAGTGAGAAC 59.480 55.000 10.99 0.00 38.07 3.01
4141 7890 3.305964 CGACGCTAGTGAGAACAAGAAA 58.694 45.455 10.99 0.00 0.00 2.52
4144 7893 5.610552 CGACGCTAGTGAGAACAAGAAAAAG 60.611 44.000 10.99 0.00 0.00 2.27
4160 7909 5.934781 AGAAAAAGAAGAAGAGCAAGGAGA 58.065 37.500 0.00 0.00 0.00 3.71
4201 7950 1.372499 CACCGACGGCGAGAAGAAA 60.372 57.895 15.16 0.00 40.82 2.52
4225 7974 5.363979 AAAAGAAGAAGAAATCAGACGCC 57.636 39.130 0.00 0.00 0.00 5.68
4255 8004 0.249073 CCATGGAGATCGACGTGTCC 60.249 60.000 5.56 0.84 32.39 4.02
4258 8007 2.762234 GGAGATCGACGTGTCCGCT 61.762 63.158 0.00 0.00 37.70 5.52
4315 8067 1.364171 GTGAGCGCCACGGAGATAT 59.636 57.895 2.29 0.00 35.86 1.63
4343 8095 6.092748 GGAAATTTGTGGTGTAATGCTGTAG 58.907 40.000 0.00 0.00 0.00 2.74
4351 8103 6.127196 TGTGGTGTAATGCTGTAGTATCATCA 60.127 38.462 0.00 0.00 0.00 3.07
4353 8108 8.088365 GTGGTGTAATGCTGTAGTATCATCATA 58.912 37.037 0.00 0.00 0.00 2.15
4446 8203 2.031258 TCGAAACTTGCAAGTGGTGA 57.969 45.000 31.73 24.09 39.66 4.02
4447 8204 1.939934 TCGAAACTTGCAAGTGGTGAG 59.060 47.619 31.73 20.12 39.66 3.51
4655 8427 7.428472 GCACAACACTTAACTAGACTTTGTTTC 59.572 37.037 0.00 0.00 0.00 2.78
4691 8463 1.469703 CATTGCTGGCAGAATCGAACA 59.530 47.619 20.86 1.07 0.00 3.18
4693 8465 1.159285 TGCTGGCAGAATCGAACAAG 58.841 50.000 20.86 0.00 0.00 3.16
4694 8466 1.160137 GCTGGCAGAATCGAACAAGT 58.840 50.000 20.86 0.00 0.00 3.16
4722 8497 0.250234 TGCCACCACTGAGCATCTAC 59.750 55.000 0.00 0.00 34.92 2.59
4723 8498 0.250234 GCCACCACTGAGCATCTACA 59.750 55.000 0.00 0.00 34.92 2.74
4724 8499 1.741732 GCCACCACTGAGCATCTACAG 60.742 57.143 0.00 0.00 39.65 2.74
4725 8500 1.552337 CCACCACTGAGCATCTACAGT 59.448 52.381 0.00 0.00 46.32 3.55
4726 8501 2.760650 CCACCACTGAGCATCTACAGTA 59.239 50.000 0.00 0.00 44.07 2.74
4727 8502 3.386078 CCACCACTGAGCATCTACAGTAT 59.614 47.826 0.00 0.00 44.07 2.12
4728 8503 4.584743 CCACCACTGAGCATCTACAGTATA 59.415 45.833 0.00 0.00 44.07 1.47
4729 8504 5.244851 CCACCACTGAGCATCTACAGTATAT 59.755 44.000 0.00 0.00 44.07 0.86
4730 8505 6.385843 CACCACTGAGCATCTACAGTATATC 58.614 44.000 0.00 0.00 44.07 1.63
4731 8506 6.208402 CACCACTGAGCATCTACAGTATATCT 59.792 42.308 0.00 0.00 44.07 1.98
4776 8551 3.206150 TCTTCGTTTGCTTCTTCTTGCT 58.794 40.909 0.00 0.00 0.00 3.91
4813 8631 3.474570 CCGAGGGGAGGCTTGAGG 61.475 72.222 0.00 0.00 34.06 3.86
4827 8645 2.420547 GCTTGAGGTGCCTGTATGATGA 60.421 50.000 0.00 0.00 0.00 2.92
4836 8654 4.637534 GTGCCTGTATGATGACATCTTTGT 59.362 41.667 16.25 3.35 39.32 2.83
4837 8655 5.124457 GTGCCTGTATGATGACATCTTTGTT 59.876 40.000 16.25 0.06 35.79 2.83
4838 8656 5.711506 TGCCTGTATGATGACATCTTTGTTT 59.288 36.000 16.25 0.00 35.79 2.83
4840 8658 6.127925 GCCTGTATGATGACATCTTTGTTTCA 60.128 38.462 16.25 5.72 35.79 2.69
4851 8703 7.285172 TGACATCTTTGTTTCATTTCTTCCTGA 59.715 33.333 0.00 0.00 35.79 3.86
4855 8707 9.702494 ATCTTTGTTTCATTTCTTCCTGATTTC 57.298 29.630 0.00 0.00 0.00 2.17
4902 8754 5.770162 CCTTGAAACAATCTTAGGACACCTT 59.230 40.000 0.00 0.00 34.41 3.50
4903 8755 6.265422 CCTTGAAACAATCTTAGGACACCTTT 59.735 38.462 0.00 0.00 34.41 3.11
4904 8756 7.201911 CCTTGAAACAATCTTAGGACACCTTTT 60.202 37.037 0.00 0.00 34.41 2.27
4905 8757 7.038154 TGAAACAATCTTAGGACACCTTTTG 57.962 36.000 0.00 0.00 34.61 2.44
4907 8759 6.635030 AACAATCTTAGGACACCTTTTGAC 57.365 37.500 0.00 0.00 34.61 3.18
4908 8760 5.690865 ACAATCTTAGGACACCTTTTGACA 58.309 37.500 0.00 0.00 34.61 3.58
4909 8761 5.531287 ACAATCTTAGGACACCTTTTGACAC 59.469 40.000 0.00 0.00 34.61 3.67
4910 8762 4.764050 TCTTAGGACACCTTTTGACACA 57.236 40.909 0.00 0.00 34.61 3.72
4911 8763 4.703897 TCTTAGGACACCTTTTGACACAG 58.296 43.478 0.00 0.00 34.61 3.66
4912 8764 4.163458 TCTTAGGACACCTTTTGACACAGT 59.837 41.667 0.00 0.00 34.61 3.55
4913 8765 2.643551 AGGACACCTTTTGACACAGTG 58.356 47.619 0.00 0.00 34.61 3.66
4914 8766 1.065551 GGACACCTTTTGACACAGTGC 59.934 52.381 0.00 0.00 31.58 4.40
4915 8767 1.065551 GACACCTTTTGACACAGTGCC 59.934 52.381 0.00 0.00 31.58 5.01
4916 8768 1.340991 ACACCTTTTGACACAGTGCCT 60.341 47.619 0.00 0.00 31.58 4.75
4917 8769 2.092646 ACACCTTTTGACACAGTGCCTA 60.093 45.455 0.00 0.00 31.58 3.93
4918 8770 3.149196 CACCTTTTGACACAGTGCCTAT 58.851 45.455 0.00 0.00 0.00 2.57
4951 8803 7.663081 TGTGGATGAGAAGGCATTTATATTCTC 59.337 37.037 6.81 6.81 45.07 2.87
4952 8804 7.882271 GTGGATGAGAAGGCATTTATATTCTCT 59.118 37.037 13.23 1.91 45.09 3.10
4962 8814 8.535335 AGGCATTTATATTCTCTGATGATACGT 58.465 33.333 0.00 0.00 0.00 3.57
4963 8815 8.598924 GGCATTTATATTCTCTGATGATACGTG 58.401 37.037 0.00 0.00 0.00 4.49
4973 8825 6.586463 TCTCTGATGATACGTGTTGTTTTCTC 59.414 38.462 0.00 0.00 0.00 2.87
5062 9000 4.026062 CGCAATTGAAGCCAATGATGATTG 60.026 41.667 10.34 0.00 41.84 2.67
5086 9024 5.329493 GCTTTATGTTGGAATTACCGTCAC 58.671 41.667 0.00 0.00 42.61 3.67
5116 9054 2.032799 TGATGACGATATTTTTGCGGCC 59.967 45.455 0.00 0.00 30.53 6.13
5120 9058 1.404035 ACGATATTTTTGCGGCCTTCC 59.596 47.619 0.00 0.00 0.00 3.46
5257 9195 1.040339 TTGTTTCACCGGCCTTGCTT 61.040 50.000 0.00 0.00 0.00 3.91
5258 9196 0.179015 TGTTTCACCGGCCTTGCTTA 60.179 50.000 0.00 0.00 0.00 3.09
5259 9197 0.955905 GTTTCACCGGCCTTGCTTAA 59.044 50.000 0.00 0.00 0.00 1.85
5260 9198 1.544246 GTTTCACCGGCCTTGCTTAAT 59.456 47.619 0.00 0.00 0.00 1.40
5261 9199 1.917872 TTCACCGGCCTTGCTTAATT 58.082 45.000 0.00 0.00 0.00 1.40
5262 9200 2.791347 TCACCGGCCTTGCTTAATTA 57.209 45.000 0.00 0.00 0.00 1.40
5263 9201 2.639065 TCACCGGCCTTGCTTAATTAG 58.361 47.619 0.00 0.00 0.00 1.73
5264 9202 2.026636 TCACCGGCCTTGCTTAATTAGT 60.027 45.455 0.00 0.00 0.00 2.24
5265 9203 3.198200 TCACCGGCCTTGCTTAATTAGTA 59.802 43.478 0.00 0.00 0.00 1.82
5266 9204 3.560068 CACCGGCCTTGCTTAATTAGTAG 59.440 47.826 0.00 0.00 0.00 2.57
5267 9205 3.139077 CCGGCCTTGCTTAATTAGTAGG 58.861 50.000 0.00 0.00 33.47 3.18
5268 9206 3.181458 CCGGCCTTGCTTAATTAGTAGGA 60.181 47.826 0.00 0.00 32.61 2.94
5269 9207 4.505039 CCGGCCTTGCTTAATTAGTAGGAT 60.505 45.833 0.00 0.00 32.61 3.24
5270 9208 5.063880 CGGCCTTGCTTAATTAGTAGGATT 58.936 41.667 0.00 0.00 32.61 3.01
5271 9209 5.049405 CGGCCTTGCTTAATTAGTAGGATTG 60.049 44.000 0.00 0.00 32.61 2.67
5272 9210 5.241728 GGCCTTGCTTAATTAGTAGGATTGG 59.758 44.000 0.00 2.90 32.61 3.16
5273 9211 5.278512 GCCTTGCTTAATTAGTAGGATTGGC 60.279 44.000 0.00 7.49 32.61 4.52
5274 9212 5.827797 CCTTGCTTAATTAGTAGGATTGGCA 59.172 40.000 0.00 0.00 32.61 4.92
5275 9213 6.238759 CCTTGCTTAATTAGTAGGATTGGCAC 60.239 42.308 0.00 0.00 32.61 5.01
5276 9214 6.001449 TGCTTAATTAGTAGGATTGGCACT 57.999 37.500 0.00 0.00 0.00 4.40
5277 9215 5.822519 TGCTTAATTAGTAGGATTGGCACTG 59.177 40.000 0.00 0.00 0.00 3.66
5278 9216 5.823045 GCTTAATTAGTAGGATTGGCACTGT 59.177 40.000 0.00 0.00 0.00 3.55
5279 9217 6.990349 GCTTAATTAGTAGGATTGGCACTGTA 59.010 38.462 0.00 0.00 0.00 2.74
5280 9218 7.497909 GCTTAATTAGTAGGATTGGCACTGTAA 59.502 37.037 0.00 0.00 0.00 2.41
5281 9219 8.726870 TTAATTAGTAGGATTGGCACTGTAAC 57.273 34.615 0.00 0.00 0.00 2.50
5282 9220 3.629142 AGTAGGATTGGCACTGTAACC 57.371 47.619 0.00 0.00 0.00 2.85
5283 9221 3.182152 AGTAGGATTGGCACTGTAACCT 58.818 45.455 0.00 0.00 0.00 3.50
5284 9222 2.496899 AGGATTGGCACTGTAACCTG 57.503 50.000 0.00 0.00 0.00 4.00
5285 9223 1.705186 AGGATTGGCACTGTAACCTGT 59.295 47.619 0.00 0.00 0.00 4.00
5286 9224 2.910319 AGGATTGGCACTGTAACCTGTA 59.090 45.455 0.00 0.00 0.00 2.74
5287 9225 3.329520 AGGATTGGCACTGTAACCTGTAA 59.670 43.478 0.00 0.00 0.00 2.41
5288 9226 3.439129 GGATTGGCACTGTAACCTGTAAC 59.561 47.826 0.00 0.00 0.00 2.50
5289 9227 2.554370 TGGCACTGTAACCTGTAACC 57.446 50.000 1.33 0.00 0.00 2.85
5290 9228 1.769465 TGGCACTGTAACCTGTAACCA 59.231 47.619 1.33 0.00 0.00 3.67
5291 9229 2.373836 TGGCACTGTAACCTGTAACCAT 59.626 45.455 1.33 0.00 0.00 3.55
5292 9230 3.583526 TGGCACTGTAACCTGTAACCATA 59.416 43.478 1.33 0.00 0.00 2.74
5293 9231 4.041815 TGGCACTGTAACCTGTAACCATAA 59.958 41.667 1.33 0.00 0.00 1.90
5294 9232 5.005094 GGCACTGTAACCTGTAACCATAAA 58.995 41.667 0.00 0.00 0.00 1.40
5295 9233 5.106436 GGCACTGTAACCTGTAACCATAAAC 60.106 44.000 0.00 0.00 0.00 2.01
5296 9234 5.106436 GCACTGTAACCTGTAACCATAAACC 60.106 44.000 0.00 0.00 0.00 3.27
5297 9235 5.998981 CACTGTAACCTGTAACCATAAACCA 59.001 40.000 0.00 0.00 0.00 3.67
5298 9236 6.148811 CACTGTAACCTGTAACCATAAACCAG 59.851 42.308 0.00 0.00 0.00 4.00
5299 9237 6.043474 ACTGTAACCTGTAACCATAAACCAGA 59.957 38.462 0.00 0.00 0.00 3.86
5300 9238 6.469410 TGTAACCTGTAACCATAAACCAGAG 58.531 40.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.108804 AAGACGCCATCACTACACGG 60.109 55.000 0.00 0.00 0.00 4.94
26 27 2.683968 TGAAAGACGCCATCACTACAC 58.316 47.619 0.00 0.00 0.00 2.90
42 43 3.636300 CCAACTCCACTTCCACAATGAAA 59.364 43.478 0.00 0.00 0.00 2.69
47 48 0.550914 AGCCAACTCCACTTCCACAA 59.449 50.000 0.00 0.00 0.00 3.33
49 50 0.954452 CAAGCCAACTCCACTTCCAC 59.046 55.000 0.00 0.00 0.00 4.02
73 74 3.006756 ATGAGTGTCGGTGCGAGGG 62.007 63.158 0.00 0.00 36.23 4.30
80 81 1.080501 CACGAGCATGAGTGTCGGT 60.081 57.895 0.00 0.00 35.01 4.69
109 110 1.068333 CATTGTCACCAGCCCGAAAAG 60.068 52.381 0.00 0.00 0.00 2.27
115 116 3.070576 GGCCATTGTCACCAGCCC 61.071 66.667 0.00 0.00 37.66 5.19
127 128 1.005924 ACCTCTTTTCGGAATGGCCAT 59.994 47.619 14.09 14.09 35.94 4.40
137 138 3.420839 ACAAAAGCACACCTCTTTTCG 57.579 42.857 0.00 0.00 40.57 3.46
139 140 4.494484 GACAACAAAAGCACACCTCTTTT 58.506 39.130 0.00 0.00 42.53 2.27
159 160 3.906720 TCCAGGCACAAGTATAAGGAC 57.093 47.619 0.00 0.00 0.00 3.85
237 308 5.129368 AGAAGGCACCATATAACACCAAT 57.871 39.130 0.00 0.00 0.00 3.16
242 313 4.188462 CGTCAAGAAGGCACCATATAACA 58.812 43.478 0.00 0.00 0.00 2.41
249 320 1.444119 GCAACGTCAAGAAGGCACCA 61.444 55.000 0.00 0.00 0.00 4.17
308 379 6.548622 AGCTGCATGTATTTCATTTACTCCAT 59.451 34.615 1.02 0.00 34.09 3.41
314 385 6.261603 CAGGAGAGCTGCATGTATTTCATTTA 59.738 38.462 1.02 0.00 34.09 1.40
488 3932 5.362430 ACAGTAATCAGCCTTTGTTTTTCCA 59.638 36.000 0.00 0.00 0.00 3.53
490 3934 6.582672 GCTACAGTAATCAGCCTTTGTTTTTC 59.417 38.462 0.00 0.00 0.00 2.29
496 3940 5.049818 GCATAGCTACAGTAATCAGCCTTTG 60.050 44.000 0.00 0.00 35.88 2.77
499 3943 3.900601 AGCATAGCTACAGTAATCAGCCT 59.099 43.478 0.00 0.00 36.99 4.58
501 3945 4.241681 GGAGCATAGCTACAGTAATCAGC 58.758 47.826 0.00 0.00 39.71 4.26
502 3946 4.216472 TCGGAGCATAGCTACAGTAATCAG 59.784 45.833 0.00 0.00 39.98 2.90
503 3947 4.142038 TCGGAGCATAGCTACAGTAATCA 58.858 43.478 0.00 0.00 39.98 2.57
504 3948 4.768130 TCGGAGCATAGCTACAGTAATC 57.232 45.455 0.00 0.00 39.98 1.75
505 3949 4.619394 GCATCGGAGCATAGCTACAGTAAT 60.619 45.833 0.00 0.00 39.98 1.89
508 3952 1.000283 GCATCGGAGCATAGCTACAGT 60.000 52.381 0.00 0.00 39.98 3.55
509 3953 1.271934 AGCATCGGAGCATAGCTACAG 59.728 52.381 0.00 0.00 39.98 2.74
510 3954 1.270826 GAGCATCGGAGCATAGCTACA 59.729 52.381 0.00 0.00 39.98 2.74
511 3955 1.989430 GAGCATCGGAGCATAGCTAC 58.011 55.000 0.00 0.00 39.88 3.58
524 3968 1.447838 TCGCCAAGGAACGAGCATC 60.448 57.895 0.00 0.00 33.69 3.91
535 3979 2.091112 CAGTGTCGAGCTCGCCAAG 61.091 63.158 30.97 17.84 39.60 3.61
538 4009 1.514443 GTACAGTGTCGAGCTCGCC 60.514 63.158 30.97 21.70 39.60 5.54
539 4010 0.179161 ATGTACAGTGTCGAGCTCGC 60.179 55.000 30.97 24.35 39.60 5.03
542 4013 3.944055 AAAGATGTACAGTGTCGAGCT 57.056 42.857 0.00 0.00 0.00 4.09
559 4030 7.441157 GGATTTGGTCAACCCTAAAAAGAAAAG 59.559 37.037 0.00 0.00 31.54 2.27
582 4053 1.109920 CATCACCTCGAGACCCGGAT 61.110 60.000 15.71 6.25 39.14 4.18
621 4092 0.107410 TTGCTGGGCCTGGTATAACG 60.107 55.000 12.70 0.00 0.00 3.18
653 4124 1.759299 TAGTAGCGGGCCGTTCCAT 60.759 57.895 28.82 13.27 36.21 3.41
655 4126 2.105729 GTAGTAGCGGGCCGTTCC 59.894 66.667 28.82 13.36 0.00 3.62
665 4146 0.866483 GCGTTCTGCTCCGTAGTAGC 60.866 60.000 0.00 0.00 41.02 3.58
667 4148 1.426621 CGCGTTCTGCTCCGTAGTA 59.573 57.895 0.00 0.00 43.27 1.82
668 4149 2.178521 CGCGTTCTGCTCCGTAGT 59.821 61.111 0.00 0.00 43.27 2.73
669 4150 3.248171 GCGCGTTCTGCTCCGTAG 61.248 66.667 8.43 0.00 43.27 3.51
728 4218 4.395625 GGTTTTAGGGCTCGGCTTATATT 58.604 43.478 0.00 0.00 0.00 1.28
785 4275 0.176910 GAAGAGAGGAAAGGAGGCGG 59.823 60.000 0.00 0.00 0.00 6.13
841 4350 4.589374 CCTTACCTGTGTATAGGAGGGAAG 59.411 50.000 0.00 0.00 44.61 3.46
842 4351 4.015918 ACCTTACCTGTGTATAGGAGGGAA 60.016 45.833 1.39 0.00 40.42 3.97
843 4352 3.534747 ACCTTACCTGTGTATAGGAGGGA 59.465 47.826 1.39 0.00 40.42 4.20
844 4353 3.924922 ACCTTACCTGTGTATAGGAGGG 58.075 50.000 1.39 3.51 40.42 4.30
915 4435 4.308458 CGCCGGGACACCACAAGA 62.308 66.667 2.18 0.00 36.13 3.02
1109 4630 1.271108 TGGTCGTACACTACACGGGTA 60.271 52.381 0.00 0.00 39.82 3.69
1110 4631 0.537143 TGGTCGTACACTACACGGGT 60.537 55.000 0.00 0.00 39.82 5.28
1111 4632 0.597568 TTGGTCGTACACTACACGGG 59.402 55.000 0.00 0.00 39.82 5.28
1112 4633 2.642139 ATTGGTCGTACACTACACGG 57.358 50.000 0.00 0.00 39.82 4.94
1113 4634 4.039703 CCATATTGGTCGTACACTACACG 58.960 47.826 0.00 0.00 40.72 4.49
1127 4648 5.467035 ACAAACACCTTTGACCATATTGG 57.533 39.130 0.27 0.00 40.83 3.16
1129 4650 7.334858 ACAAAACAAACACCTTTGACCATATT 58.665 30.769 0.27 0.00 39.43 1.28
1130 4651 6.883744 ACAAAACAAACACCTTTGACCATAT 58.116 32.000 0.27 0.00 39.43 1.78
1157 4679 2.190981 CGGCAACCATTAGTCGACTAC 58.809 52.381 24.60 11.20 0.00 2.73
1158 4680 1.820519 ACGGCAACCATTAGTCGACTA 59.179 47.619 21.25 21.25 0.00 2.59
1159 4681 0.606604 ACGGCAACCATTAGTCGACT 59.393 50.000 23.66 23.66 0.00 4.18
1160 4682 0.719465 CACGGCAACCATTAGTCGAC 59.281 55.000 7.70 7.70 0.00 4.20
1161 4683 1.017177 GCACGGCAACCATTAGTCGA 61.017 55.000 0.00 0.00 0.00 4.20
1162 4684 1.019278 AGCACGGCAACCATTAGTCG 61.019 55.000 0.00 0.00 0.00 4.18
1163 4685 1.130561 GAAGCACGGCAACCATTAGTC 59.869 52.381 0.00 0.00 0.00 2.59
1164 4686 1.165270 GAAGCACGGCAACCATTAGT 58.835 50.000 0.00 0.00 0.00 2.24
1166 4688 1.164411 CAGAAGCACGGCAACCATTA 58.836 50.000 0.00 0.00 0.00 1.90
1167 4689 1.526575 CCAGAAGCACGGCAACCATT 61.527 55.000 0.00 0.00 0.00 3.16
1168 4690 1.973281 CCAGAAGCACGGCAACCAT 60.973 57.895 0.00 0.00 0.00 3.55
1170 4692 2.130073 GAACCAGAAGCACGGCAACC 62.130 60.000 0.00 0.00 0.00 3.77
1171 4693 1.282875 GAACCAGAAGCACGGCAAC 59.717 57.895 0.00 0.00 0.00 4.17
1183 4705 0.742281 CCACAGATCCTGCGAACCAG 60.742 60.000 0.00 0.00 41.41 4.00
1214 4740 2.631160 TTCTTGCTTTGTCCGAGGAA 57.369 45.000 0.00 0.00 0.00 3.36
1217 4743 2.031682 CACCTTTCTTGCTTTGTCCGAG 60.032 50.000 0.00 0.00 0.00 4.63
1251 4777 7.227512 CCATGAGTAACTCAAAAAGACAAGAGT 59.772 37.037 0.00 0.00 44.04 3.24
1256 4782 5.530915 CACCCATGAGTAACTCAAAAAGACA 59.469 40.000 0.00 0.00 44.04 3.41
1257 4783 5.531287 ACACCCATGAGTAACTCAAAAAGAC 59.469 40.000 0.00 0.00 44.04 3.01
1259 4785 6.710744 ACTACACCCATGAGTAACTCAAAAAG 59.289 38.462 0.00 0.00 44.04 2.27
1260 4786 6.597562 ACTACACCCATGAGTAACTCAAAAA 58.402 36.000 0.00 0.00 44.04 1.94
1282 4809 6.210185 ACTGGAACCGTGAATAAACTAGTACT 59.790 38.462 0.00 0.00 0.00 2.73
1286 4813 4.092968 GCACTGGAACCGTGAATAAACTAG 59.907 45.833 15.64 0.00 34.35 2.57
1288 4815 2.812011 GCACTGGAACCGTGAATAAACT 59.188 45.455 15.64 0.00 34.35 2.66
1289 4816 2.095415 GGCACTGGAACCGTGAATAAAC 60.095 50.000 15.64 2.33 34.35 2.01
1290 4817 2.156098 GGCACTGGAACCGTGAATAAA 58.844 47.619 15.64 0.00 34.35 1.40
1291 4818 1.349688 AGGCACTGGAACCGTGAATAA 59.650 47.619 15.64 0.00 37.18 1.40
1293 4820 0.110486 AAGGCACTGGAACCGTGAAT 59.890 50.000 15.64 4.68 40.86 2.57
1381 4919 6.874288 ATCAAAGCAGCTACCAGAATAATC 57.126 37.500 0.00 0.00 0.00 1.75
1383 4921 7.829211 ACTTTATCAAAGCAGCTACCAGAATAA 59.171 33.333 0.00 0.00 42.27 1.40
1425 4966 6.546428 TTTTCACTTGTAACATTTGGGGAA 57.454 33.333 0.00 0.00 0.00 3.97
1440 4981 7.279981 GGCTTGGAAAAACAGTAATTTTCACTT 59.720 33.333 11.07 0.00 44.65 3.16
1491 5084 6.096987 ACCAGACCATCTAGTACAACAGTATG 59.903 42.308 0.00 0.00 46.00 2.39
1515 5108 4.440802 CCTCTCACATTAGCCTACACAGAC 60.441 50.000 0.00 0.00 0.00 3.51
1516 5109 3.701542 CCTCTCACATTAGCCTACACAGA 59.298 47.826 0.00 0.00 0.00 3.41
1517 5110 3.739519 GCCTCTCACATTAGCCTACACAG 60.740 52.174 0.00 0.00 0.00 3.66
1518 5111 2.168521 GCCTCTCACATTAGCCTACACA 59.831 50.000 0.00 0.00 0.00 3.72
1520 5113 2.752030 AGCCTCTCACATTAGCCTACA 58.248 47.619 0.00 0.00 0.00 2.74
1524 5117 3.828875 ACTAAGCCTCTCACATTAGCC 57.171 47.619 0.00 0.00 0.00 3.93
1526 5119 5.352569 CCACAAACTAAGCCTCTCACATTAG 59.647 44.000 0.00 0.00 0.00 1.73
1561 5179 5.346822 GCAGGAAACATGCAAAAGAATACAG 59.653 40.000 3.59 0.00 43.31 2.74
1585 5205 1.069022 CAAGCACCGTTGGTCATTCTG 60.069 52.381 0.00 0.00 31.02 3.02
1586 5206 1.238439 CAAGCACCGTTGGTCATTCT 58.762 50.000 0.00 0.00 31.02 2.40
1597 5217 3.311322 TCTTAACAGAACAACAAGCACCG 59.689 43.478 0.00 0.00 0.00 4.94
1621 5242 2.421424 GCCTACAAGACAATGCTGAAGG 59.579 50.000 0.00 0.00 0.00 3.46
1642 5263 7.141363 CCTTAACATGAACCAACAAAGAGAAG 58.859 38.462 0.00 0.00 0.00 2.85
1701 5322 6.828273 CCACCTGATATAAAATCCACAACAGA 59.172 38.462 0.00 0.00 0.00 3.41
1706 5327 6.726379 TCAACCACCTGATATAAAATCCACA 58.274 36.000 0.00 0.00 0.00 4.17
1707 5328 6.238759 GCTCAACCACCTGATATAAAATCCAC 60.239 42.308 0.00 0.00 0.00 4.02
1734 5356 6.479095 TTTTCAAACTTGTTGAAAGCCTTG 57.521 33.333 12.50 0.00 45.55 3.61
2183 5819 8.644619 CACAAAGCATGAAAATAATTCAGAGTG 58.355 33.333 0.00 0.00 0.00 3.51
2206 5843 1.462616 AGTTTGCAACAGTGAGCACA 58.537 45.000 13.16 5.93 41.05 4.57
2232 5869 8.305046 ACCAAAAGGCATGCTAGAAAATATAA 57.695 30.769 18.92 0.00 0.00 0.98
2253 5890 4.022068 CAGCCAAAAGAAGAGCATAACCAA 60.022 41.667 0.00 0.00 0.00 3.67
2294 5931 7.391620 AGTTTAGCTTTACTTGCACATAGGTA 58.608 34.615 0.00 0.00 0.00 3.08
2302 5939 9.008965 TCATGAATTAGTTTAGCTTTACTTGCA 57.991 29.630 5.83 0.00 0.00 4.08
2330 5967 2.102420 TCATAGTATCAACCTGGGCACG 59.898 50.000 0.00 0.00 0.00 5.34
2657 6309 1.471119 CCATGGAAATGACAGCTGCT 58.529 50.000 15.27 0.00 0.00 4.24
2666 6318 6.588719 TTAACTTCTGTTCCCATGGAAATG 57.411 37.500 15.22 0.00 43.86 2.32
2755 6407 7.213678 ACTTTTTAGATAGTCATAGAGCTGGC 58.786 38.462 0.00 0.00 0.00 4.85
2894 6546 2.707791 CTCTGCCCCCAGAATCTGAATA 59.292 50.000 12.53 0.00 46.84 1.75
2974 6627 6.665992 ACCAGACATCAAGTTCAACTAGTA 57.334 37.500 0.00 0.00 0.00 1.82
3368 7028 6.198687 CGTGTTTCAAGCTGTTCAAAGATAA 58.801 36.000 0.00 0.00 0.00 1.75
3369 7029 5.277779 CCGTGTTTCAAGCTGTTCAAAGATA 60.278 40.000 0.00 0.00 0.00 1.98
3405 7065 2.354805 CCTCCCAAGTTCTTTACCCTCG 60.355 54.545 0.00 0.00 0.00 4.63
3587 7323 9.829507 CATCTTCCAGTTAAATGAGAACTCTAT 57.170 33.333 4.10 0.00 34.90 1.98
3885 7633 5.569059 CGATGACAAACAAAATAAGGTCAGC 59.431 40.000 0.00 0.00 38.50 4.26
3895 7643 5.811399 AAGTCTGACGATGACAAACAAAA 57.189 34.783 1.52 0.00 36.94 2.44
3908 7657 2.983136 CTGCTGAGTTGTAAGTCTGACG 59.017 50.000 1.52 0.00 31.27 4.35
4096 7845 0.179051 CAGCTGCTGGAATCTCCTCC 60.179 60.000 21.71 0.00 37.46 4.30
4104 7853 2.031012 CGGTGACAGCTGCTGGAA 59.969 61.111 31.00 17.21 35.51 3.53
4114 7863 0.604511 TCTCACTAGCGTCGGTGACA 60.605 55.000 7.30 0.00 37.52 3.58
4129 7878 6.599244 TGCTCTTCTTCTTTTTCTTGTTCTCA 59.401 34.615 0.00 0.00 0.00 3.27
4135 7884 6.261826 TCTCCTTGCTCTTCTTCTTTTTCTTG 59.738 38.462 0.00 0.00 0.00 3.02
4141 7890 3.556004 CGGTCTCCTTGCTCTTCTTCTTT 60.556 47.826 0.00 0.00 0.00 2.52
4144 7893 1.546476 TCGGTCTCCTTGCTCTTCTTC 59.454 52.381 0.00 0.00 0.00 2.87
4160 7909 4.316823 TGCAGGGGTCTCCTCGGT 62.317 66.667 0.00 0.00 46.12 4.69
4255 8004 4.810790 TCTTCTTCTTGTCCTTCTTAGCG 58.189 43.478 0.00 0.00 0.00 4.26
4258 8007 8.251383 TCTTCTTCTTCTTCTTGTCCTTCTTA 57.749 34.615 0.00 0.00 0.00 2.10
4267 8016 4.610231 GCGTGCTTCTTCTTCTTCTTCTTG 60.610 45.833 0.00 0.00 0.00 3.02
4304 8056 0.105964 TTTCCGCCATATCTCCGTGG 59.894 55.000 0.00 0.00 38.55 4.94
4315 8067 1.982660 TACACCACAAATTTCCGCCA 58.017 45.000 0.00 0.00 0.00 5.69
4351 8103 5.475564 ACGGCAAGTACCAAAACTTTCATAT 59.524 36.000 0.00 0.00 37.61 1.78
4353 8108 3.634910 ACGGCAAGTACCAAAACTTTCAT 59.365 39.130 0.00 0.00 37.61 2.57
4366 8121 4.081365 TCCATTCTACATGAACGGCAAGTA 60.081 41.667 0.00 0.00 37.88 2.24
4446 8203 1.003696 GGGCCTCTTAAAGTGACTGCT 59.996 52.381 0.84 0.00 0.00 4.24
4447 8204 1.271379 TGGGCCTCTTAAAGTGACTGC 60.271 52.381 4.53 0.00 0.00 4.40
4553 8310 9.134055 AGTAAGTGTAATGACTAGATAAGGGAC 57.866 37.037 0.00 0.00 0.00 4.46
4601 8363 9.567848 ACAACAACAACAACAAATCTAGTTAAG 57.432 29.630 0.00 0.00 0.00 1.85
4602 8364 9.915629 AACAACAACAACAACAAATCTAGTTAA 57.084 25.926 0.00 0.00 0.00 2.01
4604 8366 7.148656 GCAACAACAACAACAACAAATCTAGTT 60.149 33.333 0.00 0.00 0.00 2.24
4606 8368 6.309980 TGCAACAACAACAACAACAAATCTAG 59.690 34.615 0.00 0.00 0.00 2.43
4607 8369 6.090088 GTGCAACAACAACAACAACAAATCTA 59.910 34.615 0.00 0.00 36.32 1.98
4608 8370 4.993584 TGCAACAACAACAACAACAAATCT 59.006 33.333 0.00 0.00 0.00 2.40
4609 8371 5.078745 GTGCAACAACAACAACAACAAATC 58.921 37.500 0.00 0.00 36.32 2.17
4610 8372 5.028428 GTGCAACAACAACAACAACAAAT 57.972 34.783 0.00 0.00 36.32 2.32
4639 8408 7.618502 TGCAACAAGAAACAAAGTCTAGTTA 57.381 32.000 0.00 0.00 0.00 2.24
4655 8427 2.093625 GCAATGTCATGCATGCAACAAG 59.906 45.455 26.68 20.68 45.70 3.16
4691 8463 4.404073 TCAGTGGTGGCAATGTTTTAACTT 59.596 37.500 0.00 0.00 0.00 2.66
4693 8465 4.298332 CTCAGTGGTGGCAATGTTTTAAC 58.702 43.478 0.00 0.00 0.00 2.01
4694 8466 3.243704 GCTCAGTGGTGGCAATGTTTTAA 60.244 43.478 0.00 0.00 0.00 1.52
4723 8498 9.757227 CGAGAAAGATTTGGAGAAAGATATACT 57.243 33.333 0.00 0.00 0.00 2.12
4724 8499 8.983724 CCGAGAAAGATTTGGAGAAAGATATAC 58.016 37.037 0.00 0.00 0.00 1.47
4725 8500 7.657761 GCCGAGAAAGATTTGGAGAAAGATATA 59.342 37.037 0.00 0.00 0.00 0.86
4726 8501 6.484977 GCCGAGAAAGATTTGGAGAAAGATAT 59.515 38.462 0.00 0.00 0.00 1.63
4727 8502 5.817816 GCCGAGAAAGATTTGGAGAAAGATA 59.182 40.000 0.00 0.00 0.00 1.98
4728 8503 4.637977 GCCGAGAAAGATTTGGAGAAAGAT 59.362 41.667 0.00 0.00 0.00 2.40
4729 8504 4.003648 GCCGAGAAAGATTTGGAGAAAGA 58.996 43.478 0.00 0.00 0.00 2.52
4730 8505 4.006319 AGCCGAGAAAGATTTGGAGAAAG 58.994 43.478 0.00 0.00 0.00 2.62
4731 8506 3.753272 CAGCCGAGAAAGATTTGGAGAAA 59.247 43.478 0.00 0.00 0.00 2.52
4776 8551 3.505680 CGGATCAAGTGTTGGATTGGAAA 59.494 43.478 0.00 0.00 0.00 3.13
4813 8631 4.637534 ACAAAGATGTCATCATACAGGCAC 59.362 41.667 15.20 0.00 33.41 5.01
4827 8645 7.587037 TCAGGAAGAAATGAAACAAAGATGT 57.413 32.000 0.00 0.00 43.14 3.06
4836 8654 6.875948 TGACGAAATCAGGAAGAAATGAAA 57.124 33.333 0.00 0.00 31.91 2.69
4851 8703 7.203255 TCATCATACGATACTCTGACGAAAT 57.797 36.000 0.00 0.00 0.00 2.17
4855 8707 5.625721 GGTTTCATCATACGATACTCTGACG 59.374 44.000 0.00 0.00 0.00 4.35
4860 8712 8.328864 GTTTCAAGGTTTCATCATACGATACTC 58.671 37.037 0.00 0.00 0.00 2.59
4861 8713 7.822334 TGTTTCAAGGTTTCATCATACGATACT 59.178 33.333 0.00 0.00 0.00 2.12
4902 8754 4.892934 AGGAAAAATAGGCACTGTGTCAAA 59.107 37.500 15.58 2.41 41.52 2.69
4903 8755 4.278170 CAGGAAAAATAGGCACTGTGTCAA 59.722 41.667 15.58 0.00 41.52 3.18
4904 8756 3.820467 CAGGAAAAATAGGCACTGTGTCA 59.180 43.478 15.58 1.07 41.52 3.58
4905 8757 3.821033 ACAGGAAAAATAGGCACTGTGTC 59.179 43.478 3.76 3.76 41.52 3.67
4907 8759 4.164822 CACAGGAAAAATAGGCACTGTG 57.835 45.455 2.76 2.76 46.33 3.66
4908 8760 3.157087 CCACAGGAAAAATAGGCACTGT 58.843 45.455 0.00 0.00 41.52 3.55
4909 8761 3.420893 TCCACAGGAAAAATAGGCACTG 58.579 45.455 0.00 0.00 41.52 3.66
4910 8762 3.806949 TCCACAGGAAAAATAGGCACT 57.193 42.857 0.00 0.00 46.37 4.40
4911 8763 4.016444 TCATCCACAGGAAAAATAGGCAC 58.984 43.478 0.00 0.00 34.34 5.01
4912 8764 4.018506 TCTCATCCACAGGAAAAATAGGCA 60.019 41.667 0.00 0.00 34.34 4.75
4913 8765 4.526970 TCTCATCCACAGGAAAAATAGGC 58.473 43.478 0.00 0.00 34.34 3.93
4914 8766 5.591877 CCTTCTCATCCACAGGAAAAATAGG 59.408 44.000 0.00 0.00 34.34 2.57
4915 8767 5.067023 GCCTTCTCATCCACAGGAAAAATAG 59.933 44.000 0.00 0.00 34.34 1.73
4916 8768 4.949856 GCCTTCTCATCCACAGGAAAAATA 59.050 41.667 0.00 0.00 34.34 1.40
4917 8769 3.766051 GCCTTCTCATCCACAGGAAAAAT 59.234 43.478 0.00 0.00 34.34 1.82
4918 8770 3.157087 GCCTTCTCATCCACAGGAAAAA 58.843 45.455 0.00 0.00 34.34 1.94
4951 8803 5.163854 GGGAGAAAACAACACGTATCATCAG 60.164 44.000 0.00 0.00 0.00 2.90
4952 8804 4.693566 GGGAGAAAACAACACGTATCATCA 59.306 41.667 0.00 0.00 0.00 3.07
4962 8814 4.993029 AAAATGTCGGGAGAAAACAACA 57.007 36.364 0.00 0.00 42.89 3.33
4986 8839 8.020861 ACTATTTCAAAACAATCGCGTTACTA 57.979 30.769 5.77 0.00 0.00 1.82
4992 8845 6.762108 AGACTACTATTTCAAAACAATCGCG 58.238 36.000 0.00 0.00 0.00 5.87
5062 9000 4.396790 TGACGGTAATTCCAACATAAAGCC 59.603 41.667 0.00 0.00 35.57 4.35
5086 9024 8.223769 GCAAAAATATCGTCATCAGGTACTATG 58.776 37.037 0.00 0.00 36.02 2.23
5116 9054 6.226787 AGCTATTGATCATAAACCTCGGAAG 58.773 40.000 0.00 0.00 0.00 3.46
5120 9058 8.993121 ACATTAAGCTATTGATCATAAACCTCG 58.007 33.333 0.00 0.00 0.00 4.63
5214 9152 1.692411 ACAAAACCAGAGCTGTTCCC 58.308 50.000 0.00 0.00 0.00 3.97
5226 9164 4.092237 CCGGTGAAACAAAGAAACAAAACC 59.908 41.667 0.00 0.00 39.98 3.27
5257 9195 7.126726 AGGTTACAGTGCCAATCCTACTAATTA 59.873 37.037 0.00 0.00 0.00 1.40
5258 9196 6.069615 AGGTTACAGTGCCAATCCTACTAATT 60.070 38.462 0.00 0.00 0.00 1.40
5259 9197 5.428783 AGGTTACAGTGCCAATCCTACTAAT 59.571 40.000 0.00 0.00 0.00 1.73
5260 9198 4.781087 AGGTTACAGTGCCAATCCTACTAA 59.219 41.667 0.00 0.00 0.00 2.24
5261 9199 4.161565 CAGGTTACAGTGCCAATCCTACTA 59.838 45.833 0.00 0.00 0.00 1.82
5262 9200 3.055094 CAGGTTACAGTGCCAATCCTACT 60.055 47.826 0.00 0.00 0.00 2.57
5263 9201 3.270877 CAGGTTACAGTGCCAATCCTAC 58.729 50.000 0.00 0.00 0.00 3.18
5264 9202 2.910319 ACAGGTTACAGTGCCAATCCTA 59.090 45.455 0.00 0.00 0.00 2.94
5265 9203 1.705186 ACAGGTTACAGTGCCAATCCT 59.295 47.619 0.00 0.00 0.00 3.24
5266 9204 2.200373 ACAGGTTACAGTGCCAATCC 57.800 50.000 0.00 0.00 0.00 3.01
5267 9205 3.439129 GGTTACAGGTTACAGTGCCAATC 59.561 47.826 0.00 0.00 0.00 2.67
5268 9206 3.181438 TGGTTACAGGTTACAGTGCCAAT 60.181 43.478 0.00 0.00 0.00 3.16
5269 9207 2.172930 TGGTTACAGGTTACAGTGCCAA 59.827 45.455 0.00 0.00 0.00 4.52
5270 9208 1.769465 TGGTTACAGGTTACAGTGCCA 59.231 47.619 0.00 0.00 0.00 4.92
5271 9209 2.554370 TGGTTACAGGTTACAGTGCC 57.446 50.000 0.00 0.00 0.00 5.01
5272 9210 5.106436 GGTTTATGGTTACAGGTTACAGTGC 60.106 44.000 0.00 0.00 0.00 4.40
5273 9211 5.998981 TGGTTTATGGTTACAGGTTACAGTG 59.001 40.000 0.00 0.00 0.00 3.66
5274 9212 6.043474 TCTGGTTTATGGTTACAGGTTACAGT 59.957 38.462 0.00 0.00 0.00 3.55
5275 9213 6.469410 TCTGGTTTATGGTTACAGGTTACAG 58.531 40.000 0.00 0.00 0.00 2.74
5276 9214 6.436738 TCTGGTTTATGGTTACAGGTTACA 57.563 37.500 0.00 0.00 0.00 2.41
5277 9215 6.980051 CTCTGGTTTATGGTTACAGGTTAC 57.020 41.667 0.00 0.00 0.00 2.50


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

AutoCloner maintained by Alex Coulton.