Multiple sequence alignment - TraesCS6D01G151500

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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 TraesCS6D01G151500 chr6D 100.000 2526 0 0 1 2526 124833491 124836016 0.000000e+00 4665
1 TraesCS6D01G151500 chr6D 91.547 556 30 5 1966 2521 124845285 124845823 0.000000e+00 750
2 TraesCS6D01G151500 chr6D 82.143 196 31 4 2098 2291 336967863 336968056 5.590000e-37 165
3 TraesCS6D01G151500 chr6A 90.508 1201 66 17 831 2000 156458659 156457476 0.000000e+00 1543
4 TraesCS6D01G151500 chr6A 87.526 489 49 8 13 496 156459138 156458657 2.840000e-154 555
5 TraesCS6D01G151500 chr6B 91.803 732 38 8 745 1469 222424185 222424901 0.000000e+00 1000
6 TraesCS6D01G151500 chr6B 86.293 642 70 13 1 634 222422991 222423622 0.000000e+00 682
7 TraesCS6D01G151500 chr6B 91.743 327 25 2 1882 2207 222427128 222427453 1.070000e-123 453
8 TraesCS6D01G151500 chr6B 90.034 291 13 6 1475 1751 222424951 222425239 1.850000e-96 363
9 TraesCS6D01G151500 chr6B 88.158 228 26 1 2292 2519 222427615 222427841 1.150000e-68 270
10 TraesCS6D01G151500 chr6B 85.795 176 23 2 2101 2275 638430818 638430644 4.290000e-43 185
11 TraesCS6D01G151500 chr6B 85.227 176 24 2 2101 2275 638419330 638419156 2.000000e-41 180
12 TraesCS6D01G151500 chr6B 98.718 78 1 0 1822 1899 222427044 222427121 3.390000e-29 139
13 TraesCS6D01G151500 chr3D 82.742 423 49 15 2101 2518 390078134 390078537 3.090000e-94 355
14 TraesCS6D01G151500 chr3D 86.705 173 21 2 2104 2275 4502564 4502735 9.220000e-45 191
15 TraesCS6D01G151500 chr5D 79.859 427 54 19 2101 2523 370943210 370943608 1.480000e-72 283
16 TraesCS6D01G151500 chr3B 88.587 184 21 0 2340 2523 20462979 20463162 9.090000e-55 224
17 TraesCS6D01G151500 chr3B 81.746 126 20 3 8 131 686387235 686387359 4.450000e-18 102
18 TraesCS6D01G151500 chr7D 86.813 182 17 3 2341 2521 460113076 460112901 1.980000e-46 196
19 TraesCS6D01G151500 chr7D 85.882 170 18 4 6 171 596112754 596112921 2.580000e-40 176
20 TraesCS6D01G151500 chr7D 85.542 166 21 2 9 171 47386984 47387149 1.200000e-38 171
21 TraesCS6D01G151500 chr5A 86.517 178 22 2 2339 2515 444079271 444079095 7.130000e-46 195
22 TraesCS6D01G151500 chr5A 85.714 175 24 1 2101 2274 168845526 168845700 1.540000e-42 183
23 TraesCS6D01G151500 chr2B 83.168 202 32 2 2101 2300 225812664 225812865 1.540000e-42 183
24 TraesCS6D01G151500 chr2B 81.500 200 33 4 2104 2300 103710782 103710584 7.230000e-36 161
25 TraesCS6D01G151500 chr1A 88.182 110 10 3 58 165 57199345 57199237 7.330000e-26 128
26 TraesCS6D01G151500 chr1D 86.486 111 11 4 57 165 58506944 58506836 4.410000e-23 119
27 TraesCS6D01G151500 chr1D 80.132 151 25 5 17 164 58509835 58509687 9.560000e-20 108


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 TraesCS6D01G151500 chr6D 124833491 124836016 2525 False 4665.0 4665 100.000000 1 2526 1 chr6D.!!$F1 2525
1 TraesCS6D01G151500 chr6D 124845285 124845823 538 False 750.0 750 91.547000 1966 2521 1 chr6D.!!$F2 555
2 TraesCS6D01G151500 chr6A 156457476 156459138 1662 True 1049.0 1543 89.017000 13 2000 2 chr6A.!!$R1 1987
3 TraesCS6D01G151500 chr6B 222422991 222427841 4850 False 484.5 1000 91.124833 1 2519 6 chr6B.!!$F1 2518

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
546 557 0.392461 TGGGTCCGCTGCTGAAATAC 60.392 55.0 0.0 0.0 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2263 4673 0.103572 GCGGCCGGTTTACATCTCTA 59.896 55.0 29.38 0.0 0.0 2.43 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
117 118 7.706179 ACAAACAAGTGAAATGTGAAATGTAGG 59.294 33.333 0.00 0.00 0.00 3.18
366 370 8.716619 TTGATGTTATTTTAAAGGTTTCGACG 57.283 30.769 0.00 0.00 0.00 5.12
387 391 7.065324 TCGACGCAAGGAGTTCAAATATAAATT 59.935 33.333 0.00 0.00 46.39 1.82
488 495 7.633193 ATTGTGTACGAGAAGAGATAGAGTT 57.367 36.000 0.00 0.00 0.00 3.01
504 512 4.346734 AGAGTTGTTCTGCGCATTAATG 57.653 40.909 12.24 11.27 33.93 1.90
508 516 4.156556 AGTTGTTCTGCGCATTAATGTCAT 59.843 37.500 12.24 0.00 0.00 3.06
512 520 4.335400 TCTGCGCATTAATGTCATCCTA 57.665 40.909 12.24 0.00 0.00 2.94
524 532 9.770097 ATTAATGTCATCCTACATGTGAAGTAG 57.230 33.333 9.11 0.00 39.98 2.57
533 541 4.222124 ACATGTGAAGTAGAATGGGTCC 57.778 45.455 0.00 0.00 0.00 4.46
541 552 0.975556 TAGAATGGGTCCGCTGCTGA 60.976 55.000 0.00 0.00 0.00 4.26
546 557 0.392461 TGGGTCCGCTGCTGAAATAC 60.392 55.000 0.00 0.00 0.00 1.89
620 631 0.725117 CGATTGGGTAAGACGTTGCC 59.275 55.000 0.00 0.00 37.70 4.52
665 1112 0.915364 TTTGCTTTGCCCCTGGTTTT 59.085 45.000 0.00 0.00 0.00 2.43
666 1113 0.467804 TTGCTTTGCCCCTGGTTTTC 59.532 50.000 0.00 0.00 0.00 2.29
667 1114 0.398381 TGCTTTGCCCCTGGTTTTCT 60.398 50.000 0.00 0.00 0.00 2.52
668 1115 0.758734 GCTTTGCCCCTGGTTTTCTT 59.241 50.000 0.00 0.00 0.00 2.52
669 1116 1.140852 GCTTTGCCCCTGGTTTTCTTT 59.859 47.619 0.00 0.00 0.00 2.52
670 1117 2.806745 GCTTTGCCCCTGGTTTTCTTTC 60.807 50.000 0.00 0.00 0.00 2.62
671 1118 2.470057 TTGCCCCTGGTTTTCTTTCT 57.530 45.000 0.00 0.00 0.00 2.52
672 1119 1.703411 TGCCCCTGGTTTTCTTTCTG 58.297 50.000 0.00 0.00 0.00 3.02
673 1120 1.063266 TGCCCCTGGTTTTCTTTCTGT 60.063 47.619 0.00 0.00 0.00 3.41
674 1121 2.039418 GCCCCTGGTTTTCTTTCTGTT 58.961 47.619 0.00 0.00 0.00 3.16
675 1122 2.434336 GCCCCTGGTTTTCTTTCTGTTT 59.566 45.455 0.00 0.00 0.00 2.83
676 1123 3.639561 GCCCCTGGTTTTCTTTCTGTTTA 59.360 43.478 0.00 0.00 0.00 2.01
677 1124 4.500887 GCCCCTGGTTTTCTTTCTGTTTAC 60.501 45.833 0.00 0.00 0.00 2.01
678 1125 4.261447 CCCCTGGTTTTCTTTCTGTTTACG 60.261 45.833 0.00 0.00 0.00 3.18
679 1126 4.577283 CCCTGGTTTTCTTTCTGTTTACGA 59.423 41.667 0.00 0.00 0.00 3.43
680 1127 5.066764 CCCTGGTTTTCTTTCTGTTTACGAA 59.933 40.000 0.00 0.00 0.00 3.85
681 1128 6.404954 CCCTGGTTTTCTTTCTGTTTACGAAA 60.405 38.462 0.00 0.00 0.00 3.46
715 1162 3.287312 ACTGATCCACAAACAAATGCG 57.713 42.857 0.00 0.00 0.00 4.73
716 1163 2.884012 ACTGATCCACAAACAAATGCGA 59.116 40.909 0.00 0.00 0.00 5.10
721 1168 2.685388 TCCACAAACAAATGCGAGACAA 59.315 40.909 0.00 0.00 0.00 3.18
722 1169 3.044986 CCACAAACAAATGCGAGACAAG 58.955 45.455 0.00 0.00 0.00 3.16
723 1170 3.489059 CCACAAACAAATGCGAGACAAGT 60.489 43.478 0.00 0.00 0.00 3.16
727 1174 3.354089 ACAAATGCGAGACAAGTTTGG 57.646 42.857 0.00 0.00 34.10 3.28
728 1175 2.948979 ACAAATGCGAGACAAGTTTGGA 59.051 40.909 0.00 0.00 34.10 3.53
729 1176 3.569701 ACAAATGCGAGACAAGTTTGGAT 59.430 39.130 0.00 0.00 34.10 3.41
730 1177 3.837213 AATGCGAGACAAGTTTGGATG 57.163 42.857 0.00 0.00 0.00 3.51
731 1178 2.542020 TGCGAGACAAGTTTGGATGA 57.458 45.000 0.00 0.00 0.00 2.92
733 1180 2.224281 TGCGAGACAAGTTTGGATGACT 60.224 45.455 0.00 0.00 0.00 3.41
734 1181 2.808543 GCGAGACAAGTTTGGATGACTT 59.191 45.455 0.00 0.00 37.82 3.01
740 1187 1.148310 AGTTTGGATGACTTGCGTCG 58.852 50.000 0.00 0.00 43.21 5.12
741 1188 0.865769 GTTTGGATGACTTGCGTCGT 59.134 50.000 0.00 0.00 43.21 4.34
771 1248 2.185387 TGGAGGTACCTTTAGTGCTCC 58.815 52.381 17.53 10.69 39.86 4.70
786 1263 5.948992 AGTGCTCCAAGAAAAGTATTGTC 57.051 39.130 0.00 0.00 0.00 3.18
823 1300 1.798368 GCGACGTCGTCAATCATCCG 61.798 60.000 35.48 10.05 42.22 4.18
959 1436 4.035208 GCTCCTGTTTATTTCACATACCCG 59.965 45.833 0.00 0.00 0.00 5.28
963 1440 3.942748 TGTTTATTTCACATACCCGGCTC 59.057 43.478 0.00 0.00 0.00 4.70
964 1441 2.519377 TATTTCACATACCCGGCTCG 57.481 50.000 0.00 0.00 0.00 5.03
965 1442 0.828022 ATTTCACATACCCGGCTCGA 59.172 50.000 0.00 0.00 0.00 4.04
966 1443 0.828022 TTTCACATACCCGGCTCGAT 59.172 50.000 0.00 0.00 0.00 3.59
1045 1522 1.613630 GCCAGGGAGGAGGAAGACA 60.614 63.158 0.00 0.00 41.22 3.41
1054 1531 1.719378 AGGAGGAAGACAAGGAGGAGA 59.281 52.381 0.00 0.00 0.00 3.71
1130 1610 1.276138 TGGTGTTCTGCGTCATCATCT 59.724 47.619 0.00 0.00 0.00 2.90
1134 1614 3.187227 GTGTTCTGCGTCATCATCTTGTT 59.813 43.478 0.00 0.00 0.00 2.83
1166 1646 1.612146 TCCCTGGTCATCTTGGCGA 60.612 57.895 0.00 0.00 0.00 5.54
1212 1692 1.616628 GGGAAGAGGAAGGGAGGCA 60.617 63.158 0.00 0.00 0.00 4.75
1445 1929 2.034879 GCTTGCGCAAGGCTACTCA 61.035 57.895 41.83 12.21 44.05 3.41
1464 1948 4.819088 ACTCAGTTCTTCTTTTTCCTCTGC 59.181 41.667 0.00 0.00 0.00 4.26
1470 1954 4.526970 TCTTCTTTTTCCTCTGCTTGTGT 58.473 39.130 0.00 0.00 0.00 3.72
1482 2010 9.636789 TTCCTCTGCTTGTGTATATTACTACTA 57.363 33.333 0.00 0.00 0.00 1.82
1543 2071 5.010282 ACATGGAGTGTTTTATCTGTTCCC 58.990 41.667 0.00 0.00 38.01 3.97
1570 2098 2.531522 TCATCGATCCATGTGCGATT 57.468 45.000 10.62 0.00 42.23 3.34
1583 2112 2.618241 TGTGCGATTGTTGCTTCTTCTT 59.382 40.909 0.00 0.00 0.00 2.52
1596 2127 4.932200 TGCTTCTTCTTCTACTTTAGCTGC 59.068 41.667 0.00 0.00 0.00 5.25
1604 2135 6.631962 TCTTCTACTTTAGCTGCTAGTTTCC 58.368 40.000 10.12 0.00 0.00 3.13
1674 2213 9.869667 ATATGCTCCTACCGTTCTATATCTATT 57.130 33.333 0.00 0.00 0.00 1.73
1676 2215 9.869667 ATGCTCCTACCGTTCTATATCTATTAT 57.130 33.333 0.00 0.00 0.00 1.28
1765 2327 2.168666 GAAAGTCCGCCGAAGAGGGT 62.169 60.000 0.00 0.00 41.48 4.34
1773 2335 0.390472 GCCGAAGAGGGTGAGACAAG 60.390 60.000 0.00 0.00 41.48 3.16
1775 2337 0.247736 CGAAGAGGGTGAGACAAGGG 59.752 60.000 0.00 0.00 0.00 3.95
1776 2338 1.353091 GAAGAGGGTGAGACAAGGGT 58.647 55.000 0.00 0.00 0.00 4.34
1796 2358 1.623542 GCCCCATCGACCAACTACCT 61.624 60.000 0.00 0.00 0.00 3.08
1820 2382 7.012704 CCTCAATCAATCGATACAAAAGTCCAT 59.987 37.037 0.00 0.00 0.00 3.41
1948 4251 7.753132 GTGTTGAGAATCGTATCCTGATAGATC 59.247 40.741 0.00 0.00 38.61 2.75
2098 4403 2.121832 ACGACAGTGGATCCCCCA 59.878 61.111 9.90 0.00 44.25 4.96
2135 4440 8.805175 TCTCCAATAGAAGATGCAAATTTGAAA 58.195 29.630 22.31 9.27 0.00 2.69
2253 4663 6.389830 TGCAAAAGAGCAACTTCAATAGAA 57.610 33.333 0.00 0.00 42.46 2.10
2254 4664 6.441274 TGCAAAAGAGCAACTTCAATAGAAG 58.559 36.000 3.83 3.83 46.78 2.85
2255 4665 6.262944 TGCAAAAGAGCAACTTCAATAGAAGA 59.737 34.615 11.79 0.00 46.52 2.87
2256 4666 7.040201 TGCAAAAGAGCAACTTCAATAGAAGAT 60.040 33.333 11.79 0.00 46.52 2.40
2322 4745 3.360340 GCGGCTGCTGTTCTGCTT 61.360 61.111 11.21 0.00 39.31 3.91
2323 4746 2.912624 GCGGCTGCTGTTCTGCTTT 61.913 57.895 11.21 0.00 39.31 3.51
2362 4785 3.106054 AGCCCCATTTGCACATTGAATA 58.894 40.909 0.00 0.00 0.00 1.75
2488 4911 9.453572 AATACACATAGACATCACTCAATTTGT 57.546 29.630 0.00 0.00 0.00 2.83
2521 4944 2.233676 TGTCACTAGTGCCATTGTCGAT 59.766 45.455 18.45 0.00 0.00 3.59
2522 4945 2.604914 GTCACTAGTGCCATTGTCGATG 59.395 50.000 18.45 0.00 35.42 3.84
2523 4946 2.495669 TCACTAGTGCCATTGTCGATGA 59.504 45.455 18.45 0.00 38.03 2.92
2524 4947 3.132824 TCACTAGTGCCATTGTCGATGAT 59.867 43.478 18.45 0.00 38.03 2.45
2525 4948 3.246936 CACTAGTGCCATTGTCGATGATG 59.753 47.826 10.54 0.00 38.03 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 6.353323 TCAGTTTCAGAACCTACATTTCACA 58.647 36.000 0.00 0.00 36.39 3.58
156 157 8.918961 AACGTGATTTCAATTAGTTTCACAAA 57.081 26.923 0.00 0.00 34.57 2.83
171 172 7.789302 GCTTGAAATCTTTTCAAACGTGATTTC 59.211 33.333 20.10 20.10 46.14 2.17
178 179 4.970003 ACTCGCTTGAAATCTTTTCAAACG 59.030 37.500 22.63 22.63 44.52 3.60
303 306 6.364261 TCAACCACGTTTAAATACGAATGTG 58.636 36.000 6.69 0.00 43.99 3.21
346 349 6.087159 CCTTGCGTCGAAACCTTTAAAATAAC 59.913 38.462 0.00 0.00 0.00 1.89
350 353 3.626670 TCCTTGCGTCGAAACCTTTAAAA 59.373 39.130 0.00 0.00 0.00 1.52
362 366 5.712217 TTATATTTGAACTCCTTGCGTCG 57.288 39.130 0.00 0.00 0.00 5.12
472 479 5.034152 GCAGAACAACTCTATCTCTTCTCG 58.966 45.833 0.00 0.00 31.12 4.04
488 495 3.065233 GGATGACATTAATGCGCAGAACA 59.935 43.478 18.32 9.26 0.00 3.18
508 516 5.030147 ACCCATTCTACTTCACATGTAGGA 58.970 41.667 0.00 0.00 38.25 2.94
512 520 3.369471 CGGACCCATTCTACTTCACATGT 60.369 47.826 0.00 0.00 0.00 3.21
524 532 0.960364 TTTCAGCAGCGGACCCATTC 60.960 55.000 0.00 0.00 0.00 2.67
533 541 6.498304 AGAAAATATTGGTATTTCAGCAGCG 58.502 36.000 0.00 0.00 39.09 5.18
564 575 9.125026 CCTAGCACCATATATTGTCTTTTCTTT 57.875 33.333 0.00 0.00 0.00 2.52
565 576 8.275040 ACCTAGCACCATATATTGTCTTTTCTT 58.725 33.333 0.00 0.00 0.00 2.52
566 577 7.716998 CACCTAGCACCATATATTGTCTTTTCT 59.283 37.037 0.00 0.00 0.00 2.52
567 578 7.041098 CCACCTAGCACCATATATTGTCTTTTC 60.041 40.741 0.00 0.00 0.00 2.29
568 579 6.772716 CCACCTAGCACCATATATTGTCTTTT 59.227 38.462 0.00 0.00 0.00 2.27
569 580 6.299141 CCACCTAGCACCATATATTGTCTTT 58.701 40.000 0.00 0.00 0.00 2.52
615 626 2.045340 ATGCTACCCACCGGCAAC 60.045 61.111 0.00 0.00 39.46 4.17
648 1095 0.398381 AGAAAACCAGGGGCAAAGCA 60.398 50.000 0.00 0.00 0.00 3.91
649 1096 0.758734 AAGAAAACCAGGGGCAAAGC 59.241 50.000 0.00 0.00 0.00 3.51
658 1105 8.370321 GTTTTTCGTAAACAGAAAGAAAACCAG 58.630 33.333 9.83 0.00 39.53 4.00
659 1106 7.866393 TGTTTTTCGTAAACAGAAAGAAAACCA 59.134 29.630 12.35 0.00 39.53 3.67
671 1118 8.842280 AGTTGGAATATCTGTTTTTCGTAAACA 58.158 29.630 14.57 14.57 37.76 2.83
672 1119 9.113876 CAGTTGGAATATCTGTTTTTCGTAAAC 57.886 33.333 8.35 8.35 0.00 2.01
673 1120 9.058174 TCAGTTGGAATATCTGTTTTTCGTAAA 57.942 29.630 0.00 0.00 0.00 2.01
674 1121 8.610248 TCAGTTGGAATATCTGTTTTTCGTAA 57.390 30.769 0.00 0.00 0.00 3.18
675 1122 8.786826 ATCAGTTGGAATATCTGTTTTTCGTA 57.213 30.769 0.00 0.00 0.00 3.43
676 1123 7.148239 GGATCAGTTGGAATATCTGTTTTTCGT 60.148 37.037 0.00 0.00 0.00 3.85
677 1124 7.148255 TGGATCAGTTGGAATATCTGTTTTTCG 60.148 37.037 0.00 0.00 0.00 3.46
678 1125 7.970614 GTGGATCAGTTGGAATATCTGTTTTTC 59.029 37.037 0.00 0.00 0.00 2.29
679 1126 7.451255 TGTGGATCAGTTGGAATATCTGTTTTT 59.549 33.333 0.00 0.00 0.00 1.94
680 1127 6.947733 TGTGGATCAGTTGGAATATCTGTTTT 59.052 34.615 0.00 0.00 0.00 2.43
681 1128 6.484288 TGTGGATCAGTTGGAATATCTGTTT 58.516 36.000 0.00 0.00 0.00 2.83
688 1135 6.968263 TTTGTTTGTGGATCAGTTGGAATA 57.032 33.333 0.00 0.00 0.00 1.75
689 1136 5.867903 TTTGTTTGTGGATCAGTTGGAAT 57.132 34.783 0.00 0.00 0.00 3.01
692 1139 3.742369 GCATTTGTTTGTGGATCAGTTGG 59.258 43.478 0.00 0.00 0.00 3.77
693 1140 3.426191 CGCATTTGTTTGTGGATCAGTTG 59.574 43.478 0.00 0.00 0.00 3.16
694 1141 3.317711 TCGCATTTGTTTGTGGATCAGTT 59.682 39.130 0.00 0.00 0.00 3.16
738 1185 4.351938 CTCCAACGCACCGGACGA 62.352 66.667 24.44 4.93 0.00 4.20
740 1187 2.934570 TACCTCCAACGCACCGGAC 61.935 63.158 9.46 0.00 0.00 4.79
741 1188 2.601067 TACCTCCAACGCACCGGA 60.601 61.111 9.46 0.00 0.00 5.14
742 1189 2.433664 GTACCTCCAACGCACCGG 60.434 66.667 0.00 0.00 0.00 5.28
753 1230 3.514309 TCTTGGAGCACTAAAGGTACCTC 59.486 47.826 16.64 0.75 0.00 3.85
756 1233 5.763698 ACTTTTCTTGGAGCACTAAAGGTAC 59.236 40.000 0.00 0.00 0.00 3.34
771 1248 8.792633 TGTTCCCTAATGACAATACTTTTCTTG 58.207 33.333 0.00 0.00 0.00 3.02
786 1263 3.065371 GTCGCCTGATTTGTTCCCTAATG 59.935 47.826 0.00 0.00 0.00 1.90
815 1292 1.742768 GGCCTCTCGTCGGATGATT 59.257 57.895 0.00 0.00 0.00 2.57
823 1300 3.519930 GGACTCCGGCCTCTCGTC 61.520 72.222 0.00 1.85 0.00 4.20
945 1422 2.033372 TCGAGCCGGGTATGTGAAATA 58.967 47.619 5.91 0.00 0.00 1.40
963 1440 4.175489 ACGGTCGTGGCGAGATCG 62.175 66.667 12.10 12.10 36.23 3.69
964 1441 2.579787 CACGGTCGTGGCGAGATC 60.580 66.667 14.88 0.00 42.00 2.75
1045 1522 2.739996 CGCCATGGCTCTCCTCCTT 61.740 63.158 33.07 0.00 39.32 3.36
1130 1610 1.225855 GACAGCACGGACATGAACAA 58.774 50.000 0.00 0.00 0.00 2.83
1134 1614 1.913262 AGGGACAGCACGGACATGA 60.913 57.895 0.00 0.00 0.00 3.07
1436 1920 5.072464 AGGAAAAAGAAGAACTGAGTAGCCT 59.928 40.000 0.00 0.00 0.00 4.58
1445 1929 5.067023 CACAAGCAGAGGAAAAAGAAGAACT 59.933 40.000 0.00 0.00 0.00 3.01
1511 2039 2.645838 ACACTCCATGTTCTTGCAGT 57.354 45.000 0.00 0.00 38.98 4.40
1543 2071 5.445540 CGCACATGGATCGATGATTATTCAG 60.446 44.000 22.78 4.84 34.73 3.02
1570 2098 6.425114 CAGCTAAAGTAGAAGAAGAAGCAACA 59.575 38.462 0.00 0.00 0.00 3.33
1583 2112 4.142227 CCGGAAACTAGCAGCTAAAGTAGA 60.142 45.833 3.09 0.00 0.00 2.59
1596 2127 2.676342 CGAACCCAAATCCGGAAACTAG 59.324 50.000 9.01 0.00 0.00 2.57
1604 2135 0.167251 CGAAACCGAACCCAAATCCG 59.833 55.000 0.00 0.00 0.00 4.18
1674 2213 6.295011 CCAACAACTGCCCAACAAAAGATATA 60.295 38.462 0.00 0.00 0.00 0.86
1676 2215 4.202202 CCAACAACTGCCCAACAAAAGATA 60.202 41.667 0.00 0.00 0.00 1.98
1677 2216 3.432046 CCAACAACTGCCCAACAAAAGAT 60.432 43.478 0.00 0.00 0.00 2.40
1680 2219 1.902508 TCCAACAACTGCCCAACAAAA 59.097 42.857 0.00 0.00 0.00 2.44
1751 2293 3.068691 CTCACCCTCTTCGGCGGA 61.069 66.667 7.21 0.00 0.00 5.54
1775 2337 0.743345 GTAGTTGGTCGATGGGGCAC 60.743 60.000 0.00 0.00 0.00 5.01
1776 2338 1.600107 GTAGTTGGTCGATGGGGCA 59.400 57.895 0.00 0.00 0.00 5.36
1782 2344 4.819105 TTGATTGAGGTAGTTGGTCGAT 57.181 40.909 0.00 0.00 0.00 3.59
1796 2358 7.552330 TCATGGACTTTTGTATCGATTGATTGA 59.448 33.333 1.71 0.00 35.99 2.57
1820 2382 2.570415 TGGTTTAGGTGCCGAATTCA 57.430 45.000 6.22 0.00 0.00 2.57
2000 4305 8.377799 AGGAATTTGCTCAAAACCAATTTAGAT 58.622 29.630 17.35 0.80 35.13 1.98
2002 4307 7.967890 AGGAATTTGCTCAAAACCAATTTAG 57.032 32.000 17.35 0.00 35.13 1.85
2003 4308 7.443879 GGAAGGAATTTGCTCAAAACCAATTTA 59.556 33.333 17.35 0.00 35.13 1.40
2009 4314 4.039124 TCTGGAAGGAATTTGCTCAAAACC 59.961 41.667 0.00 6.51 33.56 3.27
2058 4363 0.603569 GAGCTGACACGGAGAAAGGA 59.396 55.000 0.00 0.00 0.00 3.36
2095 4400 3.634397 TTGGAGATGCTCTAAGTTGGG 57.366 47.619 0.00 0.00 0.00 4.12
2098 4403 7.667575 TCTTCTATTGGAGATGCTCTAAGTT 57.332 36.000 0.00 0.00 34.66 2.66
2253 4663 6.260936 CCGGTTTACATCTCTAATTTGCATCT 59.739 38.462 0.00 0.00 0.00 2.90
2254 4664 6.430451 CCGGTTTACATCTCTAATTTGCATC 58.570 40.000 0.00 0.00 0.00 3.91
2255 4665 5.221048 GCCGGTTTACATCTCTAATTTGCAT 60.221 40.000 1.90 0.00 0.00 3.96
2256 4666 4.095782 GCCGGTTTACATCTCTAATTTGCA 59.904 41.667 1.90 0.00 0.00 4.08
2257 4667 4.497507 GGCCGGTTTACATCTCTAATTTGC 60.498 45.833 1.90 0.00 0.00 3.68
2258 4668 4.260620 CGGCCGGTTTACATCTCTAATTTG 60.261 45.833 20.10 0.00 0.00 2.32
2259 4669 3.875134 CGGCCGGTTTACATCTCTAATTT 59.125 43.478 20.10 0.00 0.00 1.82
2260 4670 3.463944 CGGCCGGTTTACATCTCTAATT 58.536 45.455 20.10 0.00 0.00 1.40
2261 4671 2.805657 GCGGCCGGTTTACATCTCTAAT 60.806 50.000 29.38 0.00 0.00 1.73
2262 4672 1.472026 GCGGCCGGTTTACATCTCTAA 60.472 52.381 29.38 0.00 0.00 2.10
2263 4673 0.103572 GCGGCCGGTTTACATCTCTA 59.896 55.000 29.38 0.00 0.00 2.43
2264 4674 1.153429 GCGGCCGGTTTACATCTCT 60.153 57.895 29.38 0.00 0.00 3.10
2265 4675 1.153429 AGCGGCCGGTTTACATCTC 60.153 57.895 26.97 3.63 0.00 2.75
2305 4728 2.793010 GAAAGCAGAACAGCAGCCGC 62.793 60.000 0.00 0.00 36.85 6.53
2308 4731 0.950116 ACTGAAAGCAGAACAGCAGC 59.050 50.000 0.00 0.00 45.17 5.25
2309 4732 3.705043 AAACTGAAAGCAGAACAGCAG 57.295 42.857 0.00 0.00 45.17 4.24
2310 4733 3.003689 GCTAAACTGAAAGCAGAACAGCA 59.996 43.478 0.00 0.00 45.17 4.41
2311 4734 3.559504 GCTAAACTGAAAGCAGAACAGC 58.440 45.455 0.00 0.00 45.17 4.40
2312 4735 3.364366 CGGCTAAACTGAAAGCAGAACAG 60.364 47.826 0.00 0.00 45.17 3.16
2313 4736 2.548057 CGGCTAAACTGAAAGCAGAACA 59.452 45.455 0.00 0.00 45.17 3.18
2314 4737 2.665794 GCGGCTAAACTGAAAGCAGAAC 60.666 50.000 0.00 0.00 45.17 3.01
2315 4738 1.535462 GCGGCTAAACTGAAAGCAGAA 59.465 47.619 0.00 0.00 45.17 3.02
2316 4739 1.156736 GCGGCTAAACTGAAAGCAGA 58.843 50.000 0.00 0.00 45.17 4.26
2318 4741 2.465860 TAGCGGCTAAACTGAAAGCA 57.534 45.000 7.36 0.00 40.61 3.91
2319 4742 3.869246 TGTATAGCGGCTAAACTGAAAGC 59.131 43.478 14.54 0.00 37.60 3.51
2320 4743 4.025647 GCTGTATAGCGGCTAAACTGAAAG 60.026 45.833 14.54 6.37 45.76 2.62
2321 4744 3.869246 GCTGTATAGCGGCTAAACTGAAA 59.131 43.478 14.54 0.00 45.76 2.69
2322 4745 3.454375 GCTGTATAGCGGCTAAACTGAA 58.546 45.455 14.54 0.00 45.76 3.02
2323 4746 3.093717 GCTGTATAGCGGCTAAACTGA 57.906 47.619 14.54 0.00 45.76 3.41
2362 4785 8.121305 TGCACTTTGTTGGTAGAATTATGAAT 57.879 30.769 0.00 0.00 0.00 2.57
2488 4911 3.570125 CACTAGTGACAACAGAGAGGACA 59.430 47.826 18.45 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.