Multiple sequence alignment - TraesCS4A01G376300

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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 TraesCS4A01G376300 chr4A 100.000 4478 0 0 1 4478 650656613 650661090 0.000000e+00 8270
1 TraesCS4A01G376300 chr4A 97.154 2951 79 4 781 3731 19533864 19536809 0.000000e+00 4979
2 TraesCS4A01G376300 chr4A 87.884 553 35 11 230 773 19533358 19533887 4.920000e-174 621
3 TraesCS4A01G376300 chr4A 81.389 720 103 16 3776 4477 651203041 651202335 3.910000e-155 558
4 TraesCS4A01G376300 chr3A 96.626 3527 80 16 230 3738 57559730 57563235 0.000000e+00 5818
5 TraesCS4A01G376300 chr3A 94.618 576 22 5 747 1321 714380590 714381157 0.000000e+00 883
6 TraesCS4A01G376300 chr3A 90.044 452 28 9 315 754 714379961 714380407 1.810000e-158 569
7 TraesCS4A01G376300 chr1D 97.661 3206 59 7 539 3736 27684640 27681443 0.000000e+00 5491
8 TraesCS4A01G376300 chr1D 90.270 740 50 10 466 1191 467932539 467931808 0.000000e+00 948
9 TraesCS4A01G376300 chr1A 97.659 2648 47 3 1103 3738 537444684 537447328 0.000000e+00 4532
10 TraesCS4A01G376300 chr1A 84.622 2341 352 4 1144 3483 575539638 575541971 0.000000e+00 2322
11 TraesCS4A01G376300 chr4D 84.000 2500 378 17 1000 3490 301348766 301346280 0.000000e+00 2381
12 TraesCS4A01G376300 chr4D 86.971 307 21 9 3447 3736 435007772 435007468 1.200000e-85 327
13 TraesCS4A01G376300 chr7A 84.665 2341 351 4 1144 3483 722583128 722585461 0.000000e+00 2327
14 TraesCS4A01G376300 chr7A 84.287 2342 358 6 1144 3483 543992943 543990610 0.000000e+00 2278
15 TraesCS4A01G376300 chr7A 84.315 2308 351 7 1178 3483 545679118 545681416 0.000000e+00 2246
16 TraesCS4A01G376300 chr7A 85.131 343 39 9 4013 4347 42699953 42700291 1.540000e-89 340
17 TraesCS4A01G376300 chr6B 93.627 1114 35 11 229 1340 16263724 16264803 0.000000e+00 1631
18 TraesCS4A01G376300 chr5A 93.165 1112 35 13 230 1340 523078751 523079822 0.000000e+00 1594
19 TraesCS4A01G376300 chr5A 91.328 1107 68 12 309 1402 456679938 456678847 0.000000e+00 1487
20 TraesCS4A01G376300 chr3B 88.213 806 71 10 466 1261 766065299 766066090 0.000000e+00 941
21 TraesCS4A01G376300 chr3B 87.828 534 26 14 230 754 750996335 750995832 1.390000e-164 590
22 TraesCS4A01G376300 chr7D 87.957 739 72 12 3736 4460 43076473 43077208 0.000000e+00 856
23 TraesCS4A01G376300 chr7D 91.847 601 44 5 906 1502 634928153 634927554 0.000000e+00 833
24 TraesCS4A01G376300 chr7D 81.806 775 94 26 3736 4478 43067115 43067874 1.380000e-169 606
25 TraesCS4A01G376300 chr7D 93.450 229 14 1 1 229 43076254 43076481 5.550000e-89 339
26 TraesCS4A01G376300 chr2B 92.203 513 30 3 314 816 39937835 39938347 0.000000e+00 717
27 TraesCS4A01G376300 chr6D 90.722 291 17 4 3447 3737 457552408 457552128 3.270000e-101 379
28 TraesCS4A01G376300 chr1B 90.345 290 25 2 3447 3736 15515848 15516134 1.180000e-100 377
29 TraesCS4A01G376300 chr5D 94.836 213 11 0 3447 3659 371067543 371067755 2.580000e-87 333
30 TraesCS4A01G376300 chr5D 86.631 187 16 3 3551 3736 525398612 525398790 9.830000e-47 198


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 TraesCS4A01G376300 chr4A 650656613 650661090 4477 False 8270.0 8270 100.0000 1 4478 1 chr4A.!!$F1 4477
1 TraesCS4A01G376300 chr4A 19533358 19536809 3451 False 2800.0 4979 92.5190 230 3731 2 chr4A.!!$F2 3501
2 TraesCS4A01G376300 chr4A 651202335 651203041 706 True 558.0 558 81.3890 3776 4477 1 chr4A.!!$R1 701
3 TraesCS4A01G376300 chr3A 57559730 57563235 3505 False 5818.0 5818 96.6260 230 3738 1 chr3A.!!$F1 3508
4 TraesCS4A01G376300 chr3A 714379961 714381157 1196 False 726.0 883 92.3310 315 1321 2 chr3A.!!$F2 1006
5 TraesCS4A01G376300 chr1D 27681443 27684640 3197 True 5491.0 5491 97.6610 539 3736 1 chr1D.!!$R1 3197
6 TraesCS4A01G376300 chr1D 467931808 467932539 731 True 948.0 948 90.2700 466 1191 1 chr1D.!!$R2 725
7 TraesCS4A01G376300 chr1A 537444684 537447328 2644 False 4532.0 4532 97.6590 1103 3738 1 chr1A.!!$F1 2635
8 TraesCS4A01G376300 chr1A 575539638 575541971 2333 False 2322.0 2322 84.6220 1144 3483 1 chr1A.!!$F2 2339
9 TraesCS4A01G376300 chr4D 301346280 301348766 2486 True 2381.0 2381 84.0000 1000 3490 1 chr4D.!!$R1 2490
10 TraesCS4A01G376300 chr7A 722583128 722585461 2333 False 2327.0 2327 84.6650 1144 3483 1 chr7A.!!$F3 2339
11 TraesCS4A01G376300 chr7A 543990610 543992943 2333 True 2278.0 2278 84.2870 1144 3483 1 chr7A.!!$R1 2339
12 TraesCS4A01G376300 chr7A 545679118 545681416 2298 False 2246.0 2246 84.3150 1178 3483 1 chr7A.!!$F2 2305
13 TraesCS4A01G376300 chr6B 16263724 16264803 1079 False 1631.0 1631 93.6270 229 1340 1 chr6B.!!$F1 1111
14 TraesCS4A01G376300 chr5A 523078751 523079822 1071 False 1594.0 1594 93.1650 230 1340 1 chr5A.!!$F1 1110
15 TraesCS4A01G376300 chr5A 456678847 456679938 1091 True 1487.0 1487 91.3280 309 1402 1 chr5A.!!$R1 1093
16 TraesCS4A01G376300 chr3B 766065299 766066090 791 False 941.0 941 88.2130 466 1261 1 chr3B.!!$F1 795
17 TraesCS4A01G376300 chr3B 750995832 750996335 503 True 590.0 590 87.8280 230 754 1 chr3B.!!$R1 524
18 TraesCS4A01G376300 chr7D 634927554 634928153 599 True 833.0 833 91.8470 906 1502 1 chr7D.!!$R1 596
19 TraesCS4A01G376300 chr7D 43067115 43067874 759 False 606.0 606 81.8060 3736 4478 1 chr7D.!!$F1 742
20 TraesCS4A01G376300 chr7D 43076254 43077208 954 False 597.5 856 90.7035 1 4460 2 chr7D.!!$F2 4459
21 TraesCS4A01G376300 chr2B 39937835 39938347 512 False 717.0 717 92.2030 314 816 1 chr2B.!!$F1 502

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
257 258 0.468771 AGCTTCTGCAAGGCCAAGTT 60.469 50.000 5.01 0.00 42.74 2.66 F
774 987 1.151413 TCCCCTGAACAGAACCTAGGT 59.849 52.381 9.21 9.21 0.00 3.08 F
775 988 1.555533 CCCCTGAACAGAACCTAGGTC 59.444 57.143 16.64 9.02 0.00 3.85 F
2161 2424 1.646912 TCGGGGACAAGGTTATGACA 58.353 50.000 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1805 0.695462 AGCATGGTCCAGAGCCCATA 60.695 55.000 13.84 0.00 39.44 2.74 R
2161 2424 1.406614 GCCTCTCATGTTGCTAGCACT 60.407 52.381 19.17 1.93 0.00 4.40 R
2431 2706 3.245371 TGAATCTGATTTGCCCCTTGTCT 60.245 43.478 4.11 0.00 0.00 3.41 R
3486 3764 1.000060 CATCAGGCAAAGTTGTGTGGG 60.000 52.381 0.00 0.00 0.00 4.61 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
54 55 6.513393 GCGCATAAATAAGGTTGCATTCTAGT 60.513 38.462 0.30 0.00 34.80 2.57
81 82 8.792633 TGGTTAAGAAGGAATTTATGAGTTGTG 58.207 33.333 0.00 0.00 0.00 3.33
106 107 9.899661 TGTGCATATTACTTTTTCCTGTATAGT 57.100 29.630 0.00 0.00 0.00 2.12
153 154 3.874392 AAACATGCCTAGAATTGTGCC 57.126 42.857 0.00 0.00 0.00 5.01
167 168 0.533032 TGTGCCGATCGTGGAACATA 59.467 50.000 15.09 0.00 42.90 2.29
173 174 1.805120 CGATCGTGGAACATACCCCAC 60.805 57.143 7.03 0.00 46.99 4.61
183 184 1.494721 ACATACCCCACCATTAGCAGG 59.505 52.381 0.00 0.00 0.00 4.85
190 191 3.490348 CCCACCATTAGCAGGAATAAGG 58.510 50.000 0.00 0.00 0.00 2.69
200 201 3.073062 AGCAGGAATAAGGTGAACACAGT 59.927 43.478 7.25 0.00 0.00 3.55
201 202 3.189287 GCAGGAATAAGGTGAACACAGTG 59.811 47.826 0.00 0.00 0.00 3.66
202 203 3.753272 CAGGAATAAGGTGAACACAGTGG 59.247 47.826 5.31 0.00 0.00 4.00
203 204 3.394606 AGGAATAAGGTGAACACAGTGGT 59.605 43.478 5.31 0.00 0.00 4.16
217 218 4.858935 CACAGTGGTGTTACAAATGAAGG 58.141 43.478 0.00 0.00 40.24 3.46
218 219 4.578516 CACAGTGGTGTTACAAATGAAGGA 59.421 41.667 0.00 0.00 40.24 3.36
219 220 4.821805 ACAGTGGTGTTACAAATGAAGGAG 59.178 41.667 0.00 0.00 30.30 3.69
220 221 4.216257 CAGTGGTGTTACAAATGAAGGAGG 59.784 45.833 0.00 0.00 0.00 4.30
221 222 4.104102 AGTGGTGTTACAAATGAAGGAGGA 59.896 41.667 0.00 0.00 0.00 3.71
222 223 5.010282 GTGGTGTTACAAATGAAGGAGGAT 58.990 41.667 0.00 0.00 0.00 3.24
223 224 5.009631 TGGTGTTACAAATGAAGGAGGATG 58.990 41.667 0.00 0.00 0.00 3.51
224 225 4.399303 GGTGTTACAAATGAAGGAGGATGG 59.601 45.833 0.00 0.00 0.00 3.51
225 226 5.010282 GTGTTACAAATGAAGGAGGATGGT 58.990 41.667 0.00 0.00 0.00 3.55
226 227 5.009631 TGTTACAAATGAAGGAGGATGGTG 58.990 41.667 0.00 0.00 0.00 4.17
227 228 5.222027 TGTTACAAATGAAGGAGGATGGTGA 60.222 40.000 0.00 0.00 0.00 4.02
236 237 1.841302 GAGGATGGTGACCACTGGCA 61.841 60.000 6.40 0.00 35.80 4.92
257 258 0.468771 AGCTTCTGCAAGGCCAAGTT 60.469 50.000 5.01 0.00 42.74 2.66
363 365 2.674754 CCGGCCCACAACCAGTAT 59.325 61.111 0.00 0.00 0.00 2.12
401 403 2.394708 CCGATACACACATAAGCCTCG 58.605 52.381 0.00 0.00 0.00 4.63
483 488 1.360551 CTGACCGCCGTCTCATAGG 59.639 63.158 6.74 0.00 39.94 2.57
596 611 2.260869 CGGCCACAACCACTCCTTG 61.261 63.158 2.24 0.00 0.00 3.61
766 979 5.022787 CCCAATTTTATTCCCCTGAACAGA 58.977 41.667 3.19 0.00 32.13 3.41
767 980 5.483583 CCCAATTTTATTCCCCTGAACAGAA 59.516 40.000 3.19 0.00 32.13 3.02
768 981 6.398095 CCAATTTTATTCCCCTGAACAGAAC 58.602 40.000 3.19 0.00 32.13 3.01
769 982 6.398095 CAATTTTATTCCCCTGAACAGAACC 58.602 40.000 3.19 0.00 32.13 3.62
770 983 5.333566 TTTTATTCCCCTGAACAGAACCT 57.666 39.130 3.19 0.00 32.13 3.50
771 984 6.457159 TTTTATTCCCCTGAACAGAACCTA 57.543 37.500 3.19 0.00 32.13 3.08
772 985 5.693769 TTATTCCCCTGAACAGAACCTAG 57.306 43.478 3.19 0.00 32.13 3.02
773 986 1.952621 TCCCCTGAACAGAACCTAGG 58.047 55.000 7.41 7.41 0.00 3.02
774 987 1.151413 TCCCCTGAACAGAACCTAGGT 59.849 52.381 9.21 9.21 0.00 3.08
775 988 1.555533 CCCCTGAACAGAACCTAGGTC 59.444 57.143 16.64 9.02 0.00 3.85
776 989 2.257207 CCCTGAACAGAACCTAGGTCA 58.743 52.381 16.64 6.72 0.00 4.02
777 990 2.840651 CCCTGAACAGAACCTAGGTCAT 59.159 50.000 16.64 3.65 0.00 3.06
778 991 3.118592 CCCTGAACAGAACCTAGGTCATC 60.119 52.174 16.64 10.39 0.00 2.92
779 992 3.429547 CCTGAACAGAACCTAGGTCATCG 60.430 52.174 16.64 9.03 0.00 3.84
780 993 3.162666 TGAACAGAACCTAGGTCATCGT 58.837 45.455 16.64 9.63 0.00 3.73
781 994 3.576982 TGAACAGAACCTAGGTCATCGTT 59.423 43.478 16.64 16.69 0.00 3.85
782 995 3.870633 ACAGAACCTAGGTCATCGTTC 57.129 47.619 16.64 7.96 35.84 3.95
783 996 3.162666 ACAGAACCTAGGTCATCGTTCA 58.837 45.455 16.64 0.00 37.63 3.18
784 997 3.769844 ACAGAACCTAGGTCATCGTTCAT 59.230 43.478 16.64 0.00 37.63 2.57
785 998 4.223032 ACAGAACCTAGGTCATCGTTCATT 59.777 41.667 16.64 0.00 37.63 2.57
786 999 4.806247 CAGAACCTAGGTCATCGTTCATTC 59.194 45.833 16.64 4.78 37.63 2.67
787 1000 3.821421 ACCTAGGTCATCGTTCATTCC 57.179 47.619 9.21 0.00 0.00 3.01
788 1001 2.434702 ACCTAGGTCATCGTTCATTCCC 59.565 50.000 9.21 0.00 0.00 3.97
789 1002 2.700897 CCTAGGTCATCGTTCATTCCCT 59.299 50.000 0.00 0.00 0.00 4.20
790 1003 3.134804 CCTAGGTCATCGTTCATTCCCTT 59.865 47.826 0.00 0.00 0.00 3.95
791 1004 2.991250 AGGTCATCGTTCATTCCCTTG 58.009 47.619 0.00 0.00 0.00 3.61
792 1005 2.571653 AGGTCATCGTTCATTCCCTTGA 59.428 45.455 0.00 0.00 0.00 3.02
793 1006 3.009033 AGGTCATCGTTCATTCCCTTGAA 59.991 43.478 0.00 0.00 33.32 2.69
850 1102 8.502387 GCTGAATATTTCACTGAAGATCATACC 58.498 37.037 0.00 0.00 35.46 2.73
918 1170 2.140717 AGTAGGCAAGTTTCGTTTCCG 58.859 47.619 0.00 0.00 0.00 4.30
1122 1381 3.667360 ACCTTTGCCAATGCTTGAAATC 58.333 40.909 0.00 0.00 38.71 2.17
1542 1805 5.743636 AACATTGTGCATTCTTAACCCAT 57.256 34.783 0.00 0.00 0.00 4.00
1742 2005 2.673368 GTGCTTTTAGAGGACATGACGG 59.327 50.000 0.00 0.00 45.24 4.79
1818 2081 5.595133 TGCTGAATTCAATCCTGATATTGCA 59.405 36.000 9.88 7.92 36.89 4.08
1921 2184 8.929260 TGCATGTAAAATCAGGAATCATATCT 57.071 30.769 0.00 0.00 0.00 1.98
2161 2424 1.646912 TCGGGGACAAGGTTATGACA 58.353 50.000 0.00 0.00 0.00 3.58
2218 2481 4.792068 TCAAGCTCTTTTCCTCCAAGAAA 58.208 39.130 0.00 0.00 33.98 2.52
2380 2655 3.200483 CGACATGATCAGCTCCATCAAA 58.800 45.455 8.61 0.00 33.94 2.69
2431 2706 6.772360 TTGCTAATGCCAATATTGAGACAA 57.228 33.333 17.23 10.56 38.71 3.18
2729 3005 6.822667 ACAAGATATTGTGAATGCTGTTCA 57.177 33.333 4.61 1.67 33.23 3.18
2840 3116 4.473444 ACAAACCACTCCATTGTCATTCT 58.527 39.130 0.00 0.00 32.02 2.40
3223 3501 0.904649 TCGATGCCTTGTGGAGTCAT 59.095 50.000 0.00 0.00 34.57 3.06
3264 3542 7.250569 TCAATTTGATTGAAAGATTACTCCGC 58.749 34.615 1.10 0.00 45.57 5.54
3465 3743 4.036977 TGCGTGAAGGAACGGAAC 57.963 55.556 0.00 0.00 41.11 3.62
3486 3764 6.238022 GGAACGCTGATTTGTAGTATGTAACC 60.238 42.308 0.00 0.00 0.00 2.85
3639 3917 6.808008 ATTCAATGTGAACAGAAGGTGTAG 57.192 37.500 0.00 0.00 39.45 2.74
3738 4016 0.674581 TTCAAGCTCCGCCACTGATG 60.675 55.000 0.00 0.00 0.00 3.07
3778 4069 3.127030 CCATCCTTGGCGTTTCTCTTTAC 59.873 47.826 0.00 0.00 35.85 2.01
3795 4086 5.919196 TCTTTACGGAATTTGTTAACTCGC 58.081 37.500 7.22 0.00 0.00 5.03
3805 4099 5.927954 TTTGTTAACTCGCCGACTATTTT 57.072 34.783 7.22 0.00 0.00 1.82
3848 4142 2.165845 AGTTTGTAGTAGTGGCTAGGCG 59.834 50.000 12.19 0.00 0.00 5.52
3851 4145 1.341285 TGTAGTAGTGGCTAGGCGGAA 60.341 52.381 12.19 0.00 0.00 4.30
3992 4291 5.298026 TGAATAATTAAGCCAGCGCACAATA 59.702 36.000 11.47 0.00 37.52 1.90
3994 4293 1.378531 TTAAGCCAGCGCACAATAGG 58.621 50.000 11.47 2.16 37.52 2.57
4022 4327 2.137523 CTGGGAGCATTTGTTTTGCAC 58.862 47.619 0.00 0.00 42.62 4.57
4069 4375 8.376889 TGCATCATATTCGCTATGTTTCTTTA 57.623 30.769 5.19 0.00 38.70 1.85
4179 4490 1.378531 TATTGACATGTGCCTTCCGC 58.621 50.000 1.15 0.00 38.31 5.54
4199 4510 4.913376 CGCAAGGTTATCTTCCAATTCAG 58.087 43.478 0.00 0.00 32.41 3.02
4237 4548 4.793071 CAAACTTGCGGTGTTAATCATCA 58.207 39.130 0.00 0.00 0.00 3.07
4240 4551 5.734855 ACTTGCGGTGTTAATCATCATAC 57.265 39.130 0.00 0.00 0.00 2.39
4245 4556 5.293324 TGCGGTGTTAATCATCATACTGTTC 59.707 40.000 0.00 0.00 0.00 3.18
4289 4604 5.976534 CAGGAGACTCTTTGATCTTATCACG 59.023 44.000 1.74 0.00 40.21 4.35
4303 4618 8.960591 TGATCTTATCACGATTGCTAGATATGA 58.039 33.333 0.00 0.00 33.59 2.15
4346 4661 9.077885 ACAACACTATCCATAAATGACAAGTTT 57.922 29.630 0.00 0.00 0.00 2.66
4371 4686 3.438781 CCTAGTTTATTTGCGCCTCAACA 59.561 43.478 4.18 0.00 33.73 3.33
4389 4704 1.202830 ACATGACAAGTAAACGGGCCA 60.203 47.619 4.39 0.00 0.00 5.36
4413 4728 0.324614 ACCTTCCATGACGTGATGCA 59.675 50.000 9.73 0.00 0.00 3.96
4421 4736 2.106477 TGACGTGATGCAATGGCTAA 57.894 45.000 0.00 0.00 41.91 3.09
4426 4741 5.299028 TGACGTGATGCAATGGCTAATTTAT 59.701 36.000 0.00 0.00 41.91 1.40
4460 4776 3.019564 GCTCTACAAATGCCCTGACAAT 58.980 45.455 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.233263 GCAAGCTCTTATCTCGGTCTTTTAG 59.767 44.000 0.00 0.00 0.00 1.85
10 11 1.764851 CGAGCAAGCTCTTATCTCGG 58.235 55.000 18.82 0.00 39.23 4.63
42 43 6.430000 TCCTTCTTAACCAACTAGAATGCAAC 59.570 38.462 0.00 0.00 0.00 4.17
54 55 9.362151 ACAACTCATAAATTCCTTCTTAACCAA 57.638 29.630 0.00 0.00 0.00 3.67
93 94 3.767673 AGCTGACCGACTATACAGGAAAA 59.232 43.478 0.00 0.00 0.00 2.29
106 107 3.000684 ACATGTCTAGTAGCTGACCGA 57.999 47.619 0.00 0.00 32.67 4.69
153 154 0.462375 TGGGGTATGTTCCACGATCG 59.538 55.000 14.88 14.88 32.74 3.69
167 168 1.308877 ATTCCTGCTAATGGTGGGGT 58.691 50.000 0.00 0.00 0.00 4.95
173 174 5.066505 GTGTTCACCTTATTCCTGCTAATGG 59.933 44.000 0.00 0.00 0.00 3.16
183 184 4.749245 CACCACTGTGTTCACCTTATTC 57.251 45.455 7.08 0.00 37.72 1.75
200 201 4.715534 TCCTCCTTCATTTGTAACACCA 57.284 40.909 0.00 0.00 0.00 4.17
201 202 4.399303 CCATCCTCCTTCATTTGTAACACC 59.601 45.833 0.00 0.00 0.00 4.16
202 203 5.010282 ACCATCCTCCTTCATTTGTAACAC 58.990 41.667 0.00 0.00 0.00 3.32
203 204 5.009631 CACCATCCTCCTTCATTTGTAACA 58.990 41.667 0.00 0.00 0.00 2.41
204 205 5.123979 GTCACCATCCTCCTTCATTTGTAAC 59.876 44.000 0.00 0.00 0.00 2.50
205 206 5.253330 GTCACCATCCTCCTTCATTTGTAA 58.747 41.667 0.00 0.00 0.00 2.41
206 207 4.324254 GGTCACCATCCTCCTTCATTTGTA 60.324 45.833 0.00 0.00 0.00 2.41
207 208 3.562176 GGTCACCATCCTCCTTCATTTGT 60.562 47.826 0.00 0.00 0.00 2.83
208 209 3.019564 GGTCACCATCCTCCTTCATTTG 58.980 50.000 0.00 0.00 0.00 2.32
209 210 2.649312 TGGTCACCATCCTCCTTCATTT 59.351 45.455 0.00 0.00 0.00 2.32
210 211 2.025887 GTGGTCACCATCCTCCTTCATT 60.026 50.000 0.00 0.00 35.28 2.57
211 212 1.561542 GTGGTCACCATCCTCCTTCAT 59.438 52.381 0.00 0.00 35.28 2.57
212 213 0.984230 GTGGTCACCATCCTCCTTCA 59.016 55.000 0.00 0.00 35.28 3.02
213 214 1.065854 CAGTGGTCACCATCCTCCTTC 60.066 57.143 0.00 0.00 35.28 3.46
214 215 0.987294 CAGTGGTCACCATCCTCCTT 59.013 55.000 0.00 0.00 35.28 3.36
215 216 0.911525 CCAGTGGTCACCATCCTCCT 60.912 60.000 0.00 0.00 35.28 3.69
216 217 1.604378 CCAGTGGTCACCATCCTCC 59.396 63.158 0.00 0.00 35.28 4.30
217 218 1.078143 GCCAGTGGTCACCATCCTC 60.078 63.158 11.74 0.00 35.28 3.71
218 219 1.845627 CTGCCAGTGGTCACCATCCT 61.846 60.000 11.74 0.00 35.28 3.24
219 220 1.377725 CTGCCAGTGGTCACCATCC 60.378 63.158 11.74 0.00 35.28 3.51
220 221 0.392193 CTCTGCCAGTGGTCACCATC 60.392 60.000 11.74 0.00 35.28 3.51
221 222 1.681666 CTCTGCCAGTGGTCACCAT 59.318 57.895 11.74 0.00 35.28 3.55
222 223 3.150949 CTCTGCCAGTGGTCACCA 58.849 61.111 11.74 0.00 0.00 4.17
223 224 2.359230 GCTCTGCCAGTGGTCACC 60.359 66.667 11.74 0.00 0.00 4.02
224 225 0.952984 GAAGCTCTGCCAGTGGTCAC 60.953 60.000 11.74 0.00 0.00 3.67
225 226 1.123861 AGAAGCTCTGCCAGTGGTCA 61.124 55.000 11.74 8.51 0.00 4.02
226 227 0.673022 CAGAAGCTCTGCCAGTGGTC 60.673 60.000 11.74 3.74 37.72 4.02
227 228 1.374190 CAGAAGCTCTGCCAGTGGT 59.626 57.895 11.74 0.00 37.72 4.16
236 237 0.608582 CTTGGCCTTGCAGAAGCTCT 60.609 55.000 3.32 0.00 42.74 4.09
348 350 1.304052 TGCATACTGGTTGTGGGCC 60.304 57.895 0.00 0.00 0.00 5.80
688 709 7.689299 TGTAAGGATTCAGAGAAGGATTTTCA 58.311 34.615 0.00 0.00 0.00 2.69
766 979 3.118371 GGGAATGAACGATGACCTAGGTT 60.118 47.826 17.53 0.00 0.00 3.50
767 980 2.434702 GGGAATGAACGATGACCTAGGT 59.565 50.000 16.26 16.26 0.00 3.08
768 981 2.700897 AGGGAATGAACGATGACCTAGG 59.299 50.000 7.41 7.41 0.00 3.02
769 982 4.122776 CAAGGGAATGAACGATGACCTAG 58.877 47.826 0.00 0.00 0.00 3.02
770 983 3.772572 TCAAGGGAATGAACGATGACCTA 59.227 43.478 0.00 0.00 0.00 3.08
771 984 2.571653 TCAAGGGAATGAACGATGACCT 59.428 45.455 0.00 0.00 0.00 3.85
772 985 2.985896 TCAAGGGAATGAACGATGACC 58.014 47.619 0.00 0.00 0.00 4.02
773 986 4.342352 GTTCAAGGGAATGAACGATGAC 57.658 45.455 4.61 0.00 46.74 3.06
780 993 4.453480 AGGTTCTGTTCAAGGGAATGAA 57.547 40.909 0.00 0.00 36.99 2.57
781 994 4.844085 TCTAGGTTCTGTTCAAGGGAATGA 59.156 41.667 0.00 0.00 35.05 2.57
782 995 5.165961 TCTAGGTTCTGTTCAAGGGAATG 57.834 43.478 0.00 0.00 35.05 2.67
783 996 5.104318 GGATCTAGGTTCTGTTCAAGGGAAT 60.104 44.000 0.00 0.00 35.05 3.01
784 997 4.225267 GGATCTAGGTTCTGTTCAAGGGAA 59.775 45.833 0.00 0.00 0.00 3.97
785 998 3.775316 GGATCTAGGTTCTGTTCAAGGGA 59.225 47.826 0.00 0.00 0.00 4.20
786 999 3.118223 GGGATCTAGGTTCTGTTCAAGGG 60.118 52.174 0.00 0.00 0.00 3.95
787 1000 3.118223 GGGGATCTAGGTTCTGTTCAAGG 60.118 52.174 0.00 0.00 0.00 3.61
788 1001 3.519510 TGGGGATCTAGGTTCTGTTCAAG 59.480 47.826 0.00 0.00 0.00 3.02
789 1002 3.526899 TGGGGATCTAGGTTCTGTTCAA 58.473 45.455 0.00 0.00 0.00 2.69
790 1003 3.199442 TGGGGATCTAGGTTCTGTTCA 57.801 47.619 0.00 0.00 0.00 3.18
791 1004 4.569719 TTTGGGGATCTAGGTTCTGTTC 57.430 45.455 0.00 0.00 0.00 3.18
792 1005 5.536497 ATTTTGGGGATCTAGGTTCTGTT 57.464 39.130 0.00 0.00 0.00 3.16
793 1006 5.510430 GAATTTTGGGGATCTAGGTTCTGT 58.490 41.667 0.00 0.00 0.00 3.41
794 1007 4.889995 GGAATTTTGGGGATCTAGGTTCTG 59.110 45.833 0.00 0.00 0.00 3.02
795 1008 4.079154 GGGAATTTTGGGGATCTAGGTTCT 60.079 45.833 0.00 0.00 0.00 3.01
796 1009 4.215908 GGGAATTTTGGGGATCTAGGTTC 58.784 47.826 0.00 0.00 0.00 3.62
850 1102 2.542595 GTGGACACTTGACACTAAACCG 59.457 50.000 0.00 0.00 32.58 4.44
918 1170 2.624636 CAAGCCCAATTGCTCAATTCC 58.375 47.619 0.00 0.00 41.80 3.01
974 1226 3.644265 TGCCTAGACCTCAACTTGTAACA 59.356 43.478 0.00 0.00 0.00 2.41
1122 1381 1.669115 CTCTGGGTGTGGCTGTTCG 60.669 63.158 0.00 0.00 0.00 3.95
1279 1541 3.055385 TCAGGTTGCATAGGACCTAACAC 60.055 47.826 7.49 0.00 44.28 3.32
1542 1805 0.695462 AGCATGGTCCAGAGCCCATA 60.695 55.000 13.84 0.00 39.44 2.74
1742 2005 5.351740 CCTTTATTCTTTGACTCGGGTCTTC 59.648 44.000 17.97 0.00 42.54 2.87
1818 2081 2.134346 GCATTCGCCAACACACATTTT 58.866 42.857 0.00 0.00 0.00 1.82
1921 2184 5.015178 ACTTAGAATCCCCAATTTCCTCACA 59.985 40.000 0.00 0.00 0.00 3.58
2098 2361 5.606348 TGGTTGGTTAAAGCAAAACTCAT 57.394 34.783 0.00 0.00 43.13 2.90
2161 2424 1.406614 GCCTCTCATGTTGCTAGCACT 60.407 52.381 19.17 1.93 0.00 4.40
2218 2481 8.166061 ACAATGGACATAATAAGCATATGGACT 58.834 33.333 4.56 0.00 35.51 3.85
2380 2655 6.682861 GCATTTTCAAGTTCAACTAGTTGGGT 60.683 38.462 30.35 15.46 40.78 4.51
2431 2706 3.245371 TGAATCTGATTTGCCCCTTGTCT 60.245 43.478 4.11 0.00 0.00 3.41
2539 2815 4.020751 GGCTGCTATATCTTGGATGACAGA 60.021 45.833 0.00 0.00 0.00 3.41
2729 3005 8.196378 ACACTCTTTAGTTGAGGAGACTAAAT 57.804 34.615 9.18 0.00 44.23 1.40
2840 3116 5.620206 TGATGTAAGCTTCCTCAAAGTCAA 58.380 37.500 0.00 0.00 37.31 3.18
3264 3542 3.356529 ACTGGAAGGGTAATGAGCAAG 57.643 47.619 0.00 0.00 39.30 4.01
3465 3743 4.510340 GGGGTTACATACTACAAATCAGCG 59.490 45.833 0.00 0.00 0.00 5.18
3486 3764 1.000060 CATCAGGCAAAGTTGTGTGGG 60.000 52.381 0.00 0.00 0.00 4.61
3697 3975 4.589675 AAAAGTTGGGCGGGCCGA 62.590 61.111 33.44 11.75 36.85 5.54
3698 3976 3.611674 AAAAAGTTGGGCGGGCCG 61.612 61.111 24.35 24.35 36.85 6.13
3768 4050 8.277713 CGAGTTAACAAATTCCGTAAAGAGAAA 58.722 33.333 8.61 0.00 0.00 2.52
3778 4069 1.727880 TCGGCGAGTTAACAAATTCCG 59.272 47.619 4.99 12.27 37.21 4.30
3795 4086 5.666969 TCACAGTGAACAAAAATAGTCGG 57.333 39.130 0.00 0.00 0.00 4.79
3805 4099 4.717233 AACATTTGCTCACAGTGAACAA 57.283 36.364 14.25 14.25 31.39 2.83
3857 4151 3.349927 TGAATCCTCATGTTGGCTTCTG 58.650 45.455 17.76 0.00 32.66 3.02
3869 4163 4.161295 CGCCGGGCTGAATCCTCA 62.161 66.667 18.34 0.00 0.00 3.86
3914 4211 5.804639 AGATAAATGTGTTGGTGCTACTCA 58.195 37.500 0.00 0.00 0.00 3.41
3964 4263 4.397730 TGCGCTGGCTTAATTATTCAGAAA 59.602 37.500 9.73 0.00 40.82 2.52
3970 4269 4.654091 ATTGTGCGCTGGCTTAATTATT 57.346 36.364 9.73 0.00 40.82 1.40
3992 4291 4.830573 GCTCCCAGCAAAACTCCT 57.169 55.556 0.00 0.00 41.89 3.69
4040 4345 7.603784 AGAAACATAGCGAATATGATGCATGTA 59.396 33.333 2.46 0.00 43.54 2.29
4100 4407 4.065321 AGGAATGCCAAGTTCTAGATCG 57.935 45.455 0.00 0.00 36.29 3.69
4161 4471 2.183409 GCGGAAGGCACATGTCAAT 58.817 52.632 0.00 0.00 42.87 2.57
4199 4510 2.872858 AGTTTGCTCTTCGTCTCCAAAC 59.127 45.455 6.47 6.47 43.21 2.93
4262 4573 8.203485 GTGATAAGATCAAAGAGTCTCCTGAAT 58.797 37.037 8.52 0.00 41.69 2.57
4318 4633 7.665559 ACTTGTCATTTATGGATAGTGTTGTGT 59.334 33.333 0.00 0.00 0.00 3.72
4346 4661 4.834534 TGAGGCGCAAATAAACTAGGTAA 58.165 39.130 10.83 0.00 0.00 2.85
4371 4686 2.279935 TTGGCCCGTTTACTTGTCAT 57.720 45.000 0.00 0.00 0.00 3.06
4389 4704 4.697514 CATCACGTCATGGAAGGTCTATT 58.302 43.478 0.00 0.00 0.00 1.73
4421 4736 9.920946 TTGTAGAGCCTCTAAATGGAAATAAAT 57.079 29.630 2.29 0.00 29.58 1.40
4426 4741 6.095440 GCATTTGTAGAGCCTCTAAATGGAAA 59.905 38.462 22.42 10.67 32.13 3.13


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

AutoCloner maintained by Alex Coulton.