Multiple sequence alignment - TraesCS1D01G226600

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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 TraesCS1D01G226600 chr1D 100.000 5909 0 0 1 5909 314990875 314984967 0.000000e+00 10912
1 TraesCS1D01G226600 chr1D 84.444 270 25 7 5649 5909 313990384 313990645 3.540000e-62 250
2 TraesCS1D01G226600 chr1A 94.484 4333 133 21 1282 5567 395461924 395457651 0.000000e+00 6580
3 TraesCS1D01G226600 chr1A 90.525 591 19 17 586 1158 395462505 395461934 0.000000e+00 747
4 TraesCS1D01G226600 chr1A 87.714 350 22 11 219 561 395462830 395462495 7.180000e-104 388
5 TraesCS1D01G226600 chr1A 96.178 157 6 0 5492 5648 395457659 395457503 2.110000e-64 257
6 TraesCS1D01G226600 chr1A 89.247 186 11 5 1 184 395463099 395462921 2.140000e-54 224
7 TraesCS1D01G226600 chr1A 90.728 151 6 2 5759 5909 395457360 395457218 1.680000e-45 195
8 TraesCS1D01G226600 chr1A 83.684 190 22 5 5649 5829 476074097 476073908 2.830000e-38 171
9 TraesCS1D01G226600 chr1A 84.328 134 13 4 2691 2816 444171812 444171679 2.240000e-24 124
10 TraesCS1D01G226600 chr1A 83.206 131 14 4 2691 2813 575548284 575548154 4.840000e-21 113
11 TraesCS1D01G226600 chr1B 93.868 2805 80 29 651 3395 426687260 426684488 0.000000e+00 4143
12 TraesCS1D01G226600 chr1B 95.700 1651 46 13 3628 5275 426684430 426682802 0.000000e+00 2632
13 TraesCS1D01G226600 chr1B 86.982 338 15 15 219 555 426687619 426687310 2.620000e-93 353
14 TraesCS1D01G226600 chr1B 96.479 142 2 1 2 143 426687783 426687645 1.280000e-56 231
15 TraesCS1D01G226600 chr1B 82.593 270 28 13 5649 5908 502982995 502982735 2.770000e-53 220
16 TraesCS1D01G226600 chr1B 95.161 62 3 0 3591 3652 426684490 426684429 1.360000e-16 99
17 TraesCS1D01G226600 chr4B 85.978 271 20 9 5649 5909 105010736 105010474 2.100000e-69 274
18 TraesCS1D01G226600 chr4B 85.106 141 18 3 5510 5648 105010958 105010819 2.220000e-29 141
19 TraesCS1D01G226600 chr5B 83.704 270 22 11 5649 5909 549677924 549677668 9.900000e-58 235
20 TraesCS1D01G226600 chr5B 82.528 269 30 9 5649 5908 357310532 357310792 2.770000e-53 220
21 TraesCS1D01G226600 chr5B 82.759 261 26 9 5649 5899 138340535 138340786 1.290000e-51 215
22 TraesCS1D01G226600 chr4D 83.395 271 27 8 5649 5909 45307080 45307342 9.900000e-58 235
23 TraesCS1D01G226600 chr3B 82.418 273 25 11 5649 5909 706981673 706981934 3.590000e-52 217
24 TraesCS1D01G226600 chr2B 82.540 252 26 8 5649 5891 159598012 159597770 7.760000e-49 206
25 TraesCS1D01G226600 chr2B 81.609 174 19 5 5741 5909 631210579 631210414 1.340000e-26 132
26 TraesCS1D01G226600 chr3A 85.806 155 9 8 5760 5909 108940021 108939875 1.030000e-32 152
27 TraesCS1D01G226600 chr3A 83.969 131 13 4 2691 2813 698287652 698287782 1.040000e-22 119
28 TraesCS1D01G226600 chr7D 80.184 217 28 6 5697 5908 629492706 629492500 1.330000e-31 148
29 TraesCS1D01G226600 chr6B 83.766 154 15 5 2668 2813 11401323 11401474 2.870000e-28 137
30 TraesCS1D01G226600 chr2A 84.962 133 16 2 5649 5777 768947420 768947288 1.340000e-26 132
31 TraesCS1D01G226600 chr2D 81.765 170 18 8 5745 5909 531363275 531363114 4.810000e-26 130
32 TraesCS1D01G226600 chr6D 85.593 118 9 4 2691 2800 57462882 57462999 3.740000e-22 117
33 TraesCS1D01G226600 chr3D 80.405 148 20 7 5642 5783 496159879 496160023 2.910000e-18 104


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 TraesCS1D01G226600 chr1D 314984967 314990875 5908 True 10912.0 10912 100.000000 1 5909 1 chr1D.!!$R1 5908
1 TraesCS1D01G226600 chr1A 395457218 395463099 5881 True 1398.5 6580 91.479333 1 5909 6 chr1A.!!$R4 5908
2 TraesCS1D01G226600 chr1B 426682802 426687783 4981 True 1491.6 4143 93.638000 2 5275 5 chr1B.!!$R2 5273

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
558 623 0.110010 GTTGCTGCTTCGGCTCTTTC 60.110 55.0 0.00 0.00 42.37 2.62 F
1165 1258 0.036765 CAGCGGCTACAACAGGGTAA 60.037 55.0 0.26 0.00 0.00 2.85 F
1166 1259 0.249398 AGCGGCTACAACAGGGTAAG 59.751 55.0 0.00 0.00 0.00 2.34 F
1168 1261 0.036765 CGGCTACAACAGGGTAAGCA 60.037 55.0 0.00 0.00 0.00 3.91 F
1669 1788 0.620556 TTCCCTGTGCCTTCTCCATC 59.379 55.0 0.00 0.00 0.00 3.51 F
1800 1920 0.708918 GTGAGAGTTTACGCGTGCTC 59.291 55.0 24.59 23.84 0.00 4.26 F
2942 3070 1.833787 TAAAGTCCGGCCAGTGACCC 61.834 60.0 2.24 0.00 31.76 4.46 F
4256 4431 1.760192 AGAACATCATGAAGCTGGCC 58.240 50.0 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2224 2349 0.693092 TGTACCATACCCCTCTGGCC 60.693 60.000 0.00 0.0 37.83 5.36 R
3154 3301 2.238084 TCATCTAGTCTGCCACCACT 57.762 50.000 0.00 0.0 0.00 4.00 R
3276 3427 2.318908 CCCCATAACCCCATTCACATG 58.681 52.381 0.00 0.0 0.00 3.21 R
3466 3617 3.127548 CGCTGCATCCTATTTGAAACACT 59.872 43.478 0.00 0.0 0.00 3.55 R
3477 3628 1.933181 CGAATGTTTCGCTGCATCCTA 59.067 47.619 0.00 0.0 46.97 2.94 R
3496 3647 5.967674 GCTAAATGATTCAGACAATCCAACG 59.032 40.000 0.00 0.0 0.00 4.10 R
4608 4785 1.366319 AAAGATCCCAGTCAGTGCCT 58.634 50.000 0.00 0.0 0.00 4.75 R
5409 5586 0.105964 AGGTGTAGCGCACTGAACAA 59.894 50.000 11.47 0.0 46.86 2.83 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
137 138 1.151899 TAGCCTGTCCAACCACCCT 60.152 57.895 0.00 0.00 0.00 4.34
138 139 0.117541 TAGCCTGTCCAACCACCCTA 59.882 55.000 0.00 0.00 0.00 3.53
152 153 2.245582 CACCCTAACCCTACCCTATCG 58.754 57.143 0.00 0.00 0.00 2.92
154 155 1.203149 CCCTAACCCTACCCTATCGCT 60.203 57.143 0.00 0.00 0.00 4.93
163 164 3.444388 CCTACCCTATCGCTCCTAATCAC 59.556 52.174 0.00 0.00 0.00 3.06
186 215 5.711976 ACTTCAGAAAATTACCACCATGGAG 59.288 40.000 21.47 11.19 40.96 3.86
190 219 6.953520 TCAGAAAATTACCACCATGGAGAATT 59.046 34.615 21.47 14.15 40.96 2.17
244 305 4.664062 CCACTAATGGCTGGTGGG 57.336 61.111 1.82 0.00 44.63 4.61
253 314 1.676248 TGGCTGGTGGGTAATAAGGT 58.324 50.000 0.00 0.00 0.00 3.50
261 322 1.286553 TGGGTAATAAGGTGCCAAGGG 59.713 52.381 0.00 0.00 0.00 3.95
262 323 1.286849 GGGTAATAAGGTGCCAAGGGT 59.713 52.381 0.00 0.00 0.00 4.34
328 389 1.743958 CAGAAGCAGGCTCATCCAAAG 59.256 52.381 0.00 0.00 37.29 2.77
329 390 0.455005 GAAGCAGGCTCATCCAAAGC 59.545 55.000 0.00 0.00 39.09 3.51
390 452 3.211564 TTTGACCGTCCGTCCGTCC 62.212 63.158 0.00 0.00 41.18 4.79
545 610 1.153289 CCATCTCCCTCCGTTGCTG 60.153 63.158 0.00 0.00 0.00 4.41
555 620 2.740055 CGTTGCTGCTTCGGCTCT 60.740 61.111 0.00 0.00 42.37 4.09
556 621 2.320587 CGTTGCTGCTTCGGCTCTT 61.321 57.895 0.00 0.00 42.37 2.85
557 622 1.845809 CGTTGCTGCTTCGGCTCTTT 61.846 55.000 0.00 0.00 42.37 2.52
558 623 0.110010 GTTGCTGCTTCGGCTCTTTC 60.110 55.000 0.00 0.00 42.37 2.62
559 624 1.237285 TTGCTGCTTCGGCTCTTTCC 61.237 55.000 0.00 0.00 42.37 3.13
560 625 1.376553 GCTGCTTCGGCTCTTTCCT 60.377 57.895 0.00 0.00 42.37 3.36
561 626 1.365368 GCTGCTTCGGCTCTTTCCTC 61.365 60.000 0.00 0.00 42.37 3.71
562 627 0.248843 CTGCTTCGGCTCTTTCCTCT 59.751 55.000 0.00 0.00 42.37 3.69
563 628 0.687354 TGCTTCGGCTCTTTCCTCTT 59.313 50.000 0.00 0.00 42.37 2.85
564 629 1.072331 TGCTTCGGCTCTTTCCTCTTT 59.928 47.619 0.00 0.00 42.37 2.52
565 630 2.155279 GCTTCGGCTCTTTCCTCTTTT 58.845 47.619 0.00 0.00 38.08 2.27
566 631 2.554462 GCTTCGGCTCTTTCCTCTTTTT 59.446 45.455 0.00 0.00 38.08 1.94
607 672 6.561519 TGGCTCTTTCCTTAACTAAGCTAT 57.438 37.500 0.00 0.00 32.02 2.97
608 673 7.670605 TGGCTCTTTCCTTAACTAAGCTATA 57.329 36.000 0.00 0.00 32.02 1.31
632 697 0.892755 TACTAGTCAAGGCCCACACG 59.107 55.000 0.00 0.00 0.00 4.49
695 768 1.063190 TCCCCTCGCTCCATAGAAGAA 60.063 52.381 0.00 0.00 0.00 2.52
733 806 1.790157 TCTCCTCCCCTTCTATCTCCC 59.210 57.143 0.00 0.00 0.00 4.30
763 844 2.362247 TGCTCTGCCGCTCTCTCT 60.362 61.111 0.00 0.00 0.00 3.10
765 846 2.120909 GCTCTGCCGCTCTCTCTCT 61.121 63.158 0.00 0.00 0.00 3.10
766 847 2.024918 CTCTGCCGCTCTCTCTCTC 58.975 63.158 0.00 0.00 0.00 3.20
770 851 2.115911 GCCGCTCTCTCTCTCGGAA 61.116 63.158 3.51 0.00 44.23 4.30
771 852 2.021722 CCGCTCTCTCTCTCGGAAG 58.978 63.158 0.00 0.00 44.23 3.46
772 853 1.355210 CGCTCTCTCTCTCGGAAGC 59.645 63.158 0.00 0.00 0.00 3.86
773 854 1.355210 GCTCTCTCTCTCGGAAGCG 59.645 63.158 0.00 0.00 0.00 4.68
853 942 3.189473 CTGCGCTGCTCTGCTCTG 61.189 66.667 9.73 0.00 0.00 3.35
932 1021 3.797353 GCCGAGCTGATTGGGGGA 61.797 66.667 0.64 0.00 32.21 4.81
933 1022 2.507944 CCGAGCTGATTGGGGGAG 59.492 66.667 0.00 0.00 0.00 4.30
934 1023 2.370445 CCGAGCTGATTGGGGGAGT 61.370 63.158 0.00 0.00 0.00 3.85
1162 1255 2.034879 CACAGCGGCTACAACAGGG 61.035 63.158 0.26 0.00 0.00 4.45
1164 1257 1.189524 ACAGCGGCTACAACAGGGTA 61.190 55.000 0.26 0.00 0.00 3.69
1165 1258 0.036765 CAGCGGCTACAACAGGGTAA 60.037 55.000 0.26 0.00 0.00 2.85
1166 1259 0.249398 AGCGGCTACAACAGGGTAAG 59.751 55.000 0.00 0.00 0.00 2.34
1168 1261 0.036765 CGGCTACAACAGGGTAAGCA 60.037 55.000 0.00 0.00 0.00 3.91
1192 1302 2.033448 TTGTAACCAGCTGGGCGG 59.967 61.111 35.42 12.27 42.05 6.13
1215 1325 4.395583 GCTCTGTGTGCGCCTTGC 62.396 66.667 4.18 0.00 46.70 4.01
1379 1495 2.934511 AGGGGGTCTCTAAGTCTAACCT 59.065 50.000 0.00 0.00 0.00 3.50
1443 1559 2.747686 GAAGTGGTGGCGGAAGGA 59.252 61.111 0.00 0.00 0.00 3.36
1669 1788 0.620556 TTCCCTGTGCCTTCTCCATC 59.379 55.000 0.00 0.00 0.00 3.51
1702 1821 2.834574 TTCAAAACGTGTTCATGCGT 57.165 40.000 0.00 0.00 43.64 5.24
1703 1822 2.098215 TCAAAACGTGTTCATGCGTG 57.902 45.000 0.00 0.00 41.42 5.34
1747 1867 1.804748 CCGCTGGTTGGTTCTAAAGAC 59.195 52.381 0.00 0.00 0.00 3.01
1800 1920 0.708918 GTGAGAGTTTACGCGTGCTC 59.291 55.000 24.59 23.84 0.00 4.26
2075 2200 7.071572 TGTTAACTAAGATTGGTATAGGGGGTC 59.928 40.741 7.22 0.00 0.00 4.46
2201 2326 5.751586 AGAGAAGTTCCCTTTGTTACAACA 58.248 37.500 0.00 0.00 37.08 3.33
2224 2349 2.124996 TTGGGTGAGGGGGAGAGG 59.875 66.667 0.00 0.00 0.00 3.69
2838 2966 5.817816 TCTCTGACCTCACTTTGTTTTTCTC 59.182 40.000 0.00 0.00 0.00 2.87
2942 3070 1.833787 TAAAGTCCGGCCAGTGACCC 61.834 60.000 2.24 0.00 31.76 4.46
3474 3625 9.571810 GTTCATTATGATTTGCATAGTGTTTCA 57.428 29.630 0.00 0.00 43.68 2.69
3496 3647 4.558538 AATAGGATGCAGCGAAACATTC 57.441 40.909 0.00 0.00 0.00 2.67
3520 3672 5.967674 CGTTGGATTGTCTGAATCATTTAGC 59.032 40.000 0.00 0.00 0.00 3.09
3593 3745 7.806960 CCTCAAAATTTTGTCTTCTGTGATCTC 59.193 37.037 25.98 0.00 39.18 2.75
3613 3765 3.438183 TCTACTTCCCCTAACTGTGGTC 58.562 50.000 0.00 0.00 0.00 4.02
4005 4180 5.815581 TGTTATTTTGACTACAGGCCTGAT 58.184 37.500 39.19 24.04 0.00 2.90
4168 4343 5.104941 TCACCAGTACATATGCAGTAAGCTT 60.105 40.000 3.48 3.48 45.94 3.74
4256 4431 1.760192 AGAACATCATGAAGCTGGCC 58.240 50.000 0.00 0.00 0.00 5.36
4983 5160 2.504367 AGATGGTAATTGCGGCCATAC 58.496 47.619 2.24 0.00 42.48 2.39
5317 5494 3.517602 TGTGTGATAACAGATGCGTACC 58.482 45.455 0.00 0.00 0.00 3.34
5318 5495 2.534349 GTGTGATAACAGATGCGTACCG 59.466 50.000 0.00 0.00 0.00 4.02
5341 5518 3.128938 GCACTTCTCTACTACATCACCGT 59.871 47.826 0.00 0.00 0.00 4.83
5356 5533 7.076842 ACATCACCGTCATTAAAATCTTCTG 57.923 36.000 0.00 0.00 0.00 3.02
5404 5581 4.932911 AATAACCCCTTCCCGAAAGTTA 57.067 40.909 0.00 0.00 32.69 2.24
5405 5582 2.574006 AACCCCTTCCCGAAAGTTAC 57.426 50.000 0.00 0.00 32.69 2.50
5406 5583 0.694771 ACCCCTTCCCGAAAGTTACC 59.305 55.000 0.00 0.00 32.69 2.85
5407 5584 0.989602 CCCCTTCCCGAAAGTTACCT 59.010 55.000 0.00 0.00 32.69 3.08
5409 5586 2.224942 CCCCTTCCCGAAAGTTACCTTT 60.225 50.000 0.00 0.00 43.58 3.11
5410 5587 3.493334 CCCTTCCCGAAAGTTACCTTTT 58.507 45.455 0.00 0.00 40.98 2.27
5411 5588 3.254903 CCCTTCCCGAAAGTTACCTTTTG 59.745 47.826 0.00 0.00 40.98 2.44
5574 5832 3.679980 CACATGAACTAAGTTCTGGACCG 59.320 47.826 0.00 0.00 42.39 4.79
5615 5873 0.320073 CTGGCCGAGACCAACGTTAA 60.320 55.000 0.00 0.00 39.86 2.01
5627 5885 4.668289 ACCAACGTTAAAAAGAACTGCTG 58.332 39.130 0.00 0.00 0.00 4.41
5693 6011 2.939103 CGTGTCCTTCCTGATCAAATCC 59.061 50.000 0.00 0.00 0.00 3.01
5695 6013 4.530875 GTGTCCTTCCTGATCAAATCCAT 58.469 43.478 0.00 0.00 0.00 3.41
5742 6060 8.707938 TGTTTCCTAATGCTCATATATGATCG 57.292 34.615 15.71 6.73 36.02 3.69
5743 6061 8.531146 TGTTTCCTAATGCTCATATATGATCGA 58.469 33.333 15.71 3.75 36.02 3.59
5744 6062 9.539825 GTTTCCTAATGCTCATATATGATCGAT 57.460 33.333 15.71 0.00 36.02 3.59
5818 6136 3.037549 ACTTTCCTTGTCCAAATTGGCA 58.962 40.909 7.24 6.10 37.47 4.92
5830 6148 1.915141 AATTGGCAGTTGGAGACAGG 58.085 50.000 0.00 0.00 44.54 4.00
5839 6157 2.147150 GTTGGAGACAGGCTGTTCTTC 58.853 52.381 22.98 17.91 44.54 2.87
5857 6175 2.746277 GTGATCCACCACGCCACC 60.746 66.667 0.00 0.00 0.00 4.61
5858 6176 3.245346 TGATCCACCACGCCACCA 61.245 61.111 0.00 0.00 0.00 4.17
5859 6177 2.272146 GATCCACCACGCCACCAT 59.728 61.111 0.00 0.00 0.00 3.55
5860 6178 2.045045 ATCCACCACGCCACCATG 60.045 61.111 0.00 0.00 0.00 3.66
5861 6179 3.643595 ATCCACCACGCCACCATGG 62.644 63.158 11.19 11.19 41.55 3.66
5862 6180 4.343323 CCACCACGCCACCATGGA 62.343 66.667 21.47 0.00 40.96 3.41
5863 6181 2.747460 CACCACGCCACCATGGAG 60.747 66.667 21.47 11.19 40.96 3.86
5878 6196 3.244700 CCATGGAGGTGATGAGGTTATCC 60.245 52.174 5.56 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 0.402272 AGGGTTAGGGTGGTTGGACA 60.402 55.000 0.00 0.00 0.00 4.02
137 138 1.785208 AGGAGCGATAGGGTAGGGTTA 59.215 52.381 0.00 0.00 0.00 2.85
138 139 0.561680 AGGAGCGATAGGGTAGGGTT 59.438 55.000 0.00 0.00 0.00 4.11
152 153 7.336931 TGGTAATTTTCTGAAGTGATTAGGAGC 59.663 37.037 0.00 0.00 0.00 4.70
154 155 7.610305 GGTGGTAATTTTCTGAAGTGATTAGGA 59.390 37.037 0.00 0.00 0.00 2.94
163 164 5.945784 TCTCCATGGTGGTAATTTTCTGAAG 59.054 40.000 12.58 0.00 39.03 3.02
186 215 1.000163 TCGCTCGCTCTGGGATAATTC 60.000 52.381 0.00 0.00 0.00 2.17
190 219 0.465642 TTCTCGCTCGCTCTGGGATA 60.466 55.000 0.00 0.00 0.00 2.59
244 305 2.093341 TCGACCCTTGGCACCTTATTAC 60.093 50.000 0.00 0.00 0.00 1.89
328 389 1.135660 GCGAGCTTGTTTTTAGGGAGC 60.136 52.381 2.14 0.00 0.00 4.70
329 390 1.468914 GGCGAGCTTGTTTTTAGGGAG 59.531 52.381 2.14 0.00 0.00 4.30
422 484 0.455295 CTCACTCTCGTCGGTTGAGC 60.455 60.000 9.54 0.00 33.41 4.26
450 515 7.382759 ACCTCGAATTTCTAATCTAATCTTCGC 59.617 37.037 0.00 0.00 0.00 4.70
485 550 2.681097 CGAATCTTCCCCCTTTCTCCAC 60.681 54.545 0.00 0.00 0.00 4.02
545 610 1.814793 AAAGAGGAAAGAGCCGAAGC 58.185 50.000 0.00 0.00 40.32 3.86
567 632 3.578282 GAGCCATTTCTGAAGGGGAAAAA 59.422 43.478 12.04 0.00 37.20 1.94
568 633 3.165071 GAGCCATTTCTGAAGGGGAAAA 58.835 45.455 12.04 0.00 37.20 2.29
569 634 2.379907 AGAGCCATTTCTGAAGGGGAAA 59.620 45.455 12.04 0.00 37.20 3.13
570 635 1.995542 AGAGCCATTTCTGAAGGGGAA 59.004 47.619 12.04 0.00 37.20 3.97
571 636 1.673767 AGAGCCATTTCTGAAGGGGA 58.326 50.000 12.04 0.00 37.20 4.81
572 637 2.521547 AAGAGCCATTTCTGAAGGGG 57.478 50.000 10.85 8.20 37.20 4.79
573 638 2.757314 GGAAAGAGCCATTTCTGAAGGG 59.243 50.000 10.17 5.98 38.86 3.95
574 639 3.694926 AGGAAAGAGCCATTTCTGAAGG 58.305 45.455 10.17 0.00 38.86 3.46
575 640 6.432472 AGTTAAGGAAAGAGCCATTTCTGAAG 59.568 38.462 10.17 0.00 38.86 3.02
576 641 6.306987 AGTTAAGGAAAGAGCCATTTCTGAA 58.693 36.000 10.17 0.00 38.86 3.02
577 642 5.880901 AGTTAAGGAAAGAGCCATTTCTGA 58.119 37.500 10.17 0.00 38.86 3.27
578 643 7.627300 GCTTAGTTAAGGAAAGAGCCATTTCTG 60.627 40.741 10.17 0.00 38.86 3.02
579 644 6.375736 GCTTAGTTAAGGAAAGAGCCATTTCT 59.624 38.462 10.17 0.00 38.86 2.52
580 645 6.375736 AGCTTAGTTAAGGAAAGAGCCATTTC 59.624 38.462 3.24 3.24 38.26 2.17
581 646 6.249192 AGCTTAGTTAAGGAAAGAGCCATTT 58.751 36.000 1.44 0.00 33.95 2.32
582 647 5.821097 AGCTTAGTTAAGGAAAGAGCCATT 58.179 37.500 1.44 0.00 33.95 3.16
583 648 5.443230 AGCTTAGTTAAGGAAAGAGCCAT 57.557 39.130 1.44 0.00 33.95 4.40
584 649 4.910458 AGCTTAGTTAAGGAAAGAGCCA 57.090 40.909 1.44 0.00 33.95 4.75
607 672 2.584031 TGGGCCTTGACTAGTAGTCCTA 59.416 50.000 24.32 13.24 44.44 2.94
608 673 1.361543 TGGGCCTTGACTAGTAGTCCT 59.638 52.381 24.32 0.00 44.44 3.85
733 806 1.105457 CAGAGCAGAGAGAGACAGGG 58.895 60.000 0.00 0.00 0.00 4.45
763 844 2.440430 CTCCTCCCGCTTCCGAGA 60.440 66.667 0.00 0.00 36.29 4.04
765 846 2.440430 CTCTCCTCCCGCTTCCGA 60.440 66.667 0.00 0.00 36.29 4.55
766 847 2.440430 TCTCTCCTCCCGCTTCCG 60.440 66.667 0.00 0.00 0.00 4.30
770 851 1.304217 TTTCGTCTCTCCTCCCGCT 60.304 57.895 0.00 0.00 0.00 5.52
771 852 1.139947 CTTTCGTCTCTCCTCCCGC 59.860 63.158 0.00 0.00 0.00 6.13
772 853 1.139947 GCTTTCGTCTCTCCTCCCG 59.860 63.158 0.00 0.00 0.00 5.14
773 854 0.174617 CTGCTTTCGTCTCTCCTCCC 59.825 60.000 0.00 0.00 0.00 4.30
1162 1255 3.735591 TGGTTACAAGAGTGGTGCTTAC 58.264 45.455 0.00 0.00 0.00 2.34
1164 1257 2.851195 CTGGTTACAAGAGTGGTGCTT 58.149 47.619 0.00 0.00 0.00 3.91
1165 1258 1.543429 GCTGGTTACAAGAGTGGTGCT 60.543 52.381 0.00 0.00 0.00 4.40
1166 1259 0.875059 GCTGGTTACAAGAGTGGTGC 59.125 55.000 0.00 0.00 0.00 5.01
1168 1261 1.072331 CCAGCTGGTTACAAGAGTGGT 59.928 52.381 25.53 0.00 0.00 4.16
1173 1266 1.003839 CGCCCAGCTGGTTACAAGA 60.004 57.895 30.63 0.00 36.04 3.02
1174 1267 2.040544 CCGCCCAGCTGGTTACAAG 61.041 63.158 30.63 15.52 36.04 3.16
1175 1268 2.033448 CCGCCCAGCTGGTTACAA 59.967 61.111 30.63 0.00 36.04 2.41
1176 1269 4.715523 GCCGCCCAGCTGGTTACA 62.716 66.667 30.63 0.00 36.04 2.41
1365 1481 2.613133 CGTCCCGAGGTTAGACTTAGAG 59.387 54.545 0.00 0.00 0.00 2.43
1416 1532 1.059913 CCACCACTTCCTTCAGGACT 58.940 55.000 0.00 0.00 45.39 3.85
1669 1788 9.878599 AACACGTTTTGAATGTATCTAGAAAAG 57.121 29.630 0.00 0.00 0.00 2.27
1702 1821 3.223394 CGTAGCGCGTACACATACA 57.777 52.632 8.43 0.00 35.54 2.29
1729 1848 4.261614 CCTTTGTCTTTAGAACCAACCAGC 60.262 45.833 0.00 0.00 0.00 4.85
1747 1867 1.981256 AAGCACACTACCCACCTTTG 58.019 50.000 0.00 0.00 0.00 2.77
1800 1920 1.472728 GCCGGCCATACGATTATAGGG 60.473 57.143 18.11 0.00 35.47 3.53
2069 2194 3.012047 ACCTAACCAATTAAAGGACCCCC 59.988 47.826 4.48 0.00 33.16 5.40
2075 2200 8.413229 CCATTATGTCACCTAACCAATTAAAGG 58.587 37.037 0.00 0.00 35.14 3.11
2201 2326 0.996762 TCCCCCTCACCCAACAACTT 60.997 55.000 0.00 0.00 0.00 2.66
2224 2349 0.693092 TGTACCATACCCCTCTGGCC 60.693 60.000 0.00 0.00 37.83 5.36
2358 2483 9.865321 ACGTTCAGAAAGTGCTATATTAAGTTA 57.135 29.630 0.36 0.00 0.00 2.24
2359 2484 8.773404 ACGTTCAGAAAGTGCTATATTAAGTT 57.227 30.769 0.36 0.00 0.00 2.66
2424 2549 3.251571 CGGAAGGCAGTGTCTTTAGTAC 58.748 50.000 12.08 0.00 0.00 2.73
2510 2637 4.202223 ACCTGCTCTGACGTTTTTCTTAGA 60.202 41.667 0.00 0.00 0.00 2.10
2838 2966 3.519510 TGTTTCCTCAGACCTCTATTGGG 59.480 47.826 0.00 0.00 0.00 4.12
2930 3058 4.263572 TGGTTGGGTCACTGGCCG 62.264 66.667 0.00 0.00 0.00 6.13
2942 3070 2.567497 CCAGTGGCTTGGCTGGTTG 61.567 63.158 0.00 0.00 45.28 3.77
3154 3301 2.238084 TCATCTAGTCTGCCACCACT 57.762 50.000 0.00 0.00 0.00 4.00
3276 3427 2.318908 CCCCATAACCCCATTCACATG 58.681 52.381 0.00 0.00 0.00 3.21
3465 3616 4.332543 CGCTGCATCCTATTTGAAACACTA 59.667 41.667 0.00 0.00 0.00 2.74
3466 3617 3.127548 CGCTGCATCCTATTTGAAACACT 59.872 43.478 0.00 0.00 0.00 3.55
3474 3625 4.496341 CGAATGTTTCGCTGCATCCTATTT 60.496 41.667 0.00 0.00 46.97 1.40
3477 3628 1.933181 CGAATGTTTCGCTGCATCCTA 59.067 47.619 0.00 0.00 46.97 2.94
3496 3647 5.967674 GCTAAATGATTCAGACAATCCAACG 59.032 40.000 0.00 0.00 0.00 4.10
3613 3765 9.340695 GAATATTCGAGAGTCAATAGTCATCAG 57.659 37.037 0.00 0.00 32.37 2.90
3866 4041 8.686334 ACAGTTACTCACACAATTTTCATCTTT 58.314 29.630 0.00 0.00 0.00 2.52
4350 4526 4.389890 TTTGCAGCAAGAAACAGTCAAT 57.610 36.364 8.12 0.00 0.00 2.57
4432 4608 6.373186 ACAAGGTCTAAAAGTTAACACAGC 57.627 37.500 8.61 0.00 0.00 4.40
4493 4670 2.094545 GTCAACCATTGTTCATCAGCCC 60.095 50.000 0.00 0.00 30.42 5.19
4608 4785 1.366319 AAAGATCCCAGTCAGTGCCT 58.634 50.000 0.00 0.00 0.00 4.75
4923 5100 8.677870 AACTAGCAGATTTGGAGGAGATATAT 57.322 34.615 0.00 0.00 0.00 0.86
4924 5101 7.179338 GGAACTAGCAGATTTGGAGGAGATATA 59.821 40.741 0.00 0.00 0.00 0.86
4925 5102 6.013812 GGAACTAGCAGATTTGGAGGAGATAT 60.014 42.308 0.00 0.00 0.00 1.63
4926 5103 5.305644 GGAACTAGCAGATTTGGAGGAGATA 59.694 44.000 0.00 0.00 0.00 1.98
4927 5104 4.102367 GGAACTAGCAGATTTGGAGGAGAT 59.898 45.833 0.00 0.00 0.00 2.75
4928 5105 3.452627 GGAACTAGCAGATTTGGAGGAGA 59.547 47.826 0.00 0.00 0.00 3.71
4931 5108 2.743183 CGGGAACTAGCAGATTTGGAGG 60.743 54.545 0.00 0.00 0.00 4.30
5317 5494 3.489398 GGTGATGTAGTAGAGAAGTGCCG 60.489 52.174 0.00 0.00 0.00 5.69
5318 5495 3.489398 CGGTGATGTAGTAGAGAAGTGCC 60.489 52.174 0.00 0.00 0.00 5.01
5341 5518 7.243487 GCATTCGACACAGAAGATTTTAATGA 58.757 34.615 0.00 0.00 33.19 2.57
5404 5581 1.602377 GTAGCGCACTGAACAAAAGGT 59.398 47.619 11.47 0.00 0.00 3.50
5405 5582 1.601903 TGTAGCGCACTGAACAAAAGG 59.398 47.619 11.47 0.00 0.00 3.11
5406 5583 2.602217 GGTGTAGCGCACTGAACAAAAG 60.602 50.000 11.47 0.00 46.86 2.27
5407 5584 1.332375 GGTGTAGCGCACTGAACAAAA 59.668 47.619 11.47 0.00 46.86 2.44
5409 5586 0.105964 AGGTGTAGCGCACTGAACAA 59.894 50.000 11.47 0.00 46.86 2.83
5410 5587 0.105964 AAGGTGTAGCGCACTGAACA 59.894 50.000 11.47 2.57 46.86 3.18
5411 5588 0.512952 CAAGGTGTAGCGCACTGAAC 59.487 55.000 11.47 0.00 46.86 3.18
5497 5687 3.681897 ACAGAAATGACGACTTGCTCATC 59.318 43.478 0.00 0.00 0.00 2.92
5498 5688 3.668447 ACAGAAATGACGACTTGCTCAT 58.332 40.909 0.00 0.00 0.00 2.90
5574 5832 6.477033 CCAGAGTGTGCATTAGTATCTTGTAC 59.523 42.308 0.00 0.00 0.00 2.90
5641 5899 6.292865 CGAGTCTCTGTTGCAATAAGAAACAA 60.293 38.462 16.44 3.28 45.13 2.83
5742 6060 7.113684 CCATCTTTTTCTGACGTCGAGTATATC 59.886 40.741 11.62 0.00 0.00 1.63
5743 6061 6.918569 CCATCTTTTTCTGACGTCGAGTATAT 59.081 38.462 11.62 0.00 0.00 0.86
5744 6062 6.094464 TCCATCTTTTTCTGACGTCGAGTATA 59.906 38.462 11.62 0.00 0.00 1.47
5745 6063 5.103000 CCATCTTTTTCTGACGTCGAGTAT 58.897 41.667 11.62 0.00 0.00 2.12
5746 6064 4.216902 TCCATCTTTTTCTGACGTCGAGTA 59.783 41.667 11.62 0.93 0.00 2.59
5747 6065 3.005472 TCCATCTTTTTCTGACGTCGAGT 59.995 43.478 11.62 0.00 0.00 4.18
5748 6066 3.365220 GTCCATCTTTTTCTGACGTCGAG 59.635 47.826 11.62 9.63 0.00 4.04
5749 6067 3.314553 GTCCATCTTTTTCTGACGTCGA 58.685 45.455 11.62 8.49 0.00 4.20
5750 6068 2.090658 CGTCCATCTTTTTCTGACGTCG 59.909 50.000 11.62 6.07 42.68 5.12
5751 6069 3.706994 CGTCCATCTTTTTCTGACGTC 57.293 47.619 9.11 9.11 42.68 4.34
5754 6072 4.307432 TGAGACGTCCATCTTTTTCTGAC 58.693 43.478 13.01 0.00 0.00 3.51
5755 6073 4.600692 TGAGACGTCCATCTTTTTCTGA 57.399 40.909 13.01 0.00 0.00 3.27
5756 6074 6.758416 TCATATGAGACGTCCATCTTTTTCTG 59.242 38.462 18.79 9.39 0.00 3.02
5757 6075 6.878317 TCATATGAGACGTCCATCTTTTTCT 58.122 36.000 18.79 0.00 0.00 2.52
5818 6136 1.428869 AGAACAGCCTGTCTCCAACT 58.571 50.000 0.00 0.00 0.00 3.16
5830 6148 1.079503 GGTGGATCACGAAGAACAGC 58.920 55.000 0.00 0.00 34.83 4.40
5856 6174 3.244700 GGATAACCTCATCACCTCCATGG 60.245 52.174 4.97 4.97 42.93 3.66
5857 6175 3.649981 AGGATAACCTCATCACCTCCATG 59.350 47.826 0.00 0.00 44.13 3.66
5858 6176 3.946824 AGGATAACCTCATCACCTCCAT 58.053 45.455 0.00 0.00 44.13 3.41
5859 6177 3.421394 AGGATAACCTCATCACCTCCA 57.579 47.619 0.00 0.00 44.13 3.86
5878 6196 3.553508 CCAGGCATTGGTTTGACAAAGAG 60.554 47.826 0.00 0.00 42.41 2.85


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

AutoCloner maintained by Alex Coulton.