Multiple sequence alignment - TraesCS5D01G216100

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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 TraesCS5D01G216100 chr5D 100.000 5013 0 0 1 5013 324972461 324967449 0.000000e+00 9258.0
1 TraesCS5D01G216100 chr5A 91.817 4717 201 52 380 5013 423058284 423053670 0.000000e+00 6401.0
2 TraesCS5D01G216100 chr5B 92.661 4224 187 59 335 4501 377390646 377386489 0.000000e+00 5969.0
3 TraesCS5D01G216100 chr5B 88.218 348 17 13 1 332 377391108 377390769 1.310000e-105 394.0
4 TraesCS5D01G216100 chr5B 81.336 434 23 22 4593 5013 377386447 377386059 2.930000e-77 300.0
5 TraesCS5D01G216100 chr7A 89.333 300 32 0 1858 2157 121992 122291 1.320000e-100 377.0
6 TraesCS5D01G216100 chr7A 91.632 239 18 2 1920 2157 708790353 708790590 3.740000e-86 329.0
7 TraesCS5D01G216100 chr7A 91.176 68 4 2 1730 1797 121929 121994 1.920000e-14 91.6
8 TraesCS5D01G216100 chr2B 89.333 300 32 0 1858 2157 282993821 282993522 1.320000e-100 377.0
9 TraesCS5D01G216100 chr2B 88.235 68 6 2 1730 1797 282993884 282993819 4.160000e-11 80.5
10 TraesCS5D01G216100 chr7B 91.983 237 17 2 1922 2157 568665936 568665701 1.040000e-86 331.0
11 TraesCS5D01G216100 chr3B 91.561 237 18 2 1922 2157 460380578 460380343 4.840000e-85 326.0
12 TraesCS5D01G216100 chr6B 91.558 154 11 2 2005 2157 651217517 651217365 1.410000e-50 211.0
13 TraesCS5D01G216100 chr6D 93.043 115 7 1 1920 2034 364893401 364893514 3.100000e-37 167.0
14 TraesCS5D01G216100 chr6D 95.000 60 3 0 2098 2157 364893515 364893574 1.490000e-15 95.3
15 TraesCS5D01G216100 chr2D 92.373 118 8 1 1920 2037 35055732 35055616 3.100000e-37 167.0


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 TraesCS5D01G216100 chr5D 324967449 324972461 5012 True 9258 9258 100.000 1 5013 1 chr5D.!!$R1 5012
1 TraesCS5D01G216100 chr5A 423053670 423058284 4614 True 6401 6401 91.817 380 5013 1 chr5A.!!$R1 4633
2 TraesCS5D01G216100 chr5B 377386059 377391108 5049 True 2221 5969 87.405 1 5013 3 chr5B.!!$R1 5012

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
116 119 0.031857 CGAATGGCAACTGCAAACCA 59.968 50.0 3.76 0.0 44.36 3.67 F
674 833 0.271005 TAATCTTCCCCCTCCCCTCC 59.729 60.0 0.00 0.0 0.00 4.30 F
1068 1242 0.254107 ACTCCTCCTCCTCCTCCTCT 60.254 60.0 0.00 0.0 0.00 3.69 F
2783 2974 0.033920 AGCACACGAAGCTGTCATCA 59.966 50.0 0.00 0.0 41.61 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1056 1230 1.065053 TCGAACTCAGAGGAGGAGGAG 60.065 57.143 1.53 0.0 45.81 3.69 R
2058 2241 1.656652 CCAACAGCTTGAGGATACCG 58.343 55.000 0.00 0.0 37.17 4.02 R
2849 3040 0.473326 ATGAGATGCCTGCTTCCCTC 59.527 55.000 1.80 0.0 0.00 4.30 R
4507 4766 0.031010 ATCCTACCCTGGACTGGACC 60.031 60.000 0.00 0.0 39.17 4.46 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
30 31 7.518731 TTCAACATATTAAAATTGCGAAGGC 57.481 32.000 0.00 0.00 40.52 4.35
93 96 1.859080 CACGGCTAAACTTATCCGCTC 59.141 52.381 10.78 0.00 43.98 5.03
116 119 0.031857 CGAATGGCAACTGCAAACCA 59.968 50.000 3.76 0.00 44.36 3.67
121 124 2.034878 TGGCAACTGCAAACCATGTAA 58.965 42.857 3.76 0.00 44.36 2.41
122 125 2.432146 TGGCAACTGCAAACCATGTAAA 59.568 40.909 3.76 0.00 44.36 2.01
135 148 5.523438 ACCATGTAAAACAATTCAACGGT 57.477 34.783 0.00 0.00 0.00 4.83
163 176 4.670606 GATGTCCGCGCATCAAAC 57.329 55.556 18.20 0.00 43.38 2.93
192 206 7.064490 ACCAAAGACAAAACTATGTTTGCAAAG 59.936 33.333 13.26 2.86 41.33 2.77
193 207 7.277539 CCAAAGACAAAACTATGTTTGCAAAGA 59.722 33.333 13.26 12.51 41.33 2.52
266 281 7.464358 ACGATAAAATGAAATAGTGTCACTGC 58.536 34.615 16.03 3.28 0.00 4.40
267 282 7.334421 ACGATAAAATGAAATAGTGTCACTGCT 59.666 33.333 16.03 0.00 0.00 4.24
311 327 3.243367 GCTGTTAAACATGTGCCACTTGA 60.243 43.478 16.67 0.00 0.00 3.02
328 344 3.118629 ACTTGATCGAATAGGAGCTGCAA 60.119 43.478 8.35 0.00 0.00 4.08
332 348 0.652592 CGAATAGGAGCTGCAAACCG 59.347 55.000 8.35 1.75 0.00 4.44
339 475 0.512952 GAGCTGCAAACCGTGTAGTG 59.487 55.000 1.02 0.00 41.70 2.74
343 479 2.695359 CTGCAAACCGTGTAGTGGTAT 58.305 47.619 0.00 0.00 39.29 2.73
354 490 7.839907 ACCGTGTAGTGGTATTAGTCAATAAA 58.160 34.615 0.00 0.00 38.15 1.40
355 491 8.313292 ACCGTGTAGTGGTATTAGTCAATAAAA 58.687 33.333 0.00 0.00 38.15 1.52
356 492 9.321562 CCGTGTAGTGGTATTAGTCAATAAAAT 57.678 33.333 0.00 0.00 0.00 1.82
373 509 7.708752 TCAATAAAATCGATGGGGTAAAATTGC 59.291 33.333 0.00 0.00 0.00 3.56
375 511 5.413309 AAATCGATGGGGTAAAATTGCAA 57.587 34.783 0.00 0.00 0.00 4.08
671 830 1.373536 GGATAATCTTCCCCCTCCCC 58.626 60.000 0.00 0.00 0.00 4.81
672 831 1.132036 GGATAATCTTCCCCCTCCCCT 60.132 57.143 0.00 0.00 0.00 4.79
673 832 2.270858 GATAATCTTCCCCCTCCCCTC 58.729 57.143 0.00 0.00 0.00 4.30
674 833 0.271005 TAATCTTCCCCCTCCCCTCC 59.729 60.000 0.00 0.00 0.00 4.30
675 834 2.585523 AATCTTCCCCCTCCCCTCCC 62.586 65.000 0.00 0.00 0.00 4.30
782 945 1.206371 TCCCGATTCCTTCCTTCGTTC 59.794 52.381 0.00 0.00 0.00 3.95
783 946 1.066430 CCCGATTCCTTCCTTCGTTCA 60.066 52.381 0.00 0.00 0.00 3.18
784 947 2.271800 CCGATTCCTTCCTTCGTTCAG 58.728 52.381 0.00 0.00 0.00 3.02
785 948 2.271800 CGATTCCTTCCTTCGTTCAGG 58.728 52.381 0.00 0.00 34.86 3.86
944 1109 3.844211 TGGTGTGGATAGTTAAGAGGCTT 59.156 43.478 0.00 0.00 0.00 4.35
949 1114 5.248477 TGTGGATAGTTAAGAGGCTTTGAGT 59.752 40.000 0.00 0.00 0.00 3.41
952 1117 7.175119 GTGGATAGTTAAGAGGCTTTGAGTTTT 59.825 37.037 0.00 0.00 0.00 2.43
953 1118 7.390718 TGGATAGTTAAGAGGCTTTGAGTTTTC 59.609 37.037 0.00 0.00 0.00 2.29
981 1155 2.035155 TCGTCGGAGGGAAGAGCA 59.965 61.111 0.00 0.00 0.00 4.26
1066 1240 1.529744 CTACTCCTCCTCCTCCTCCT 58.470 60.000 0.00 0.00 0.00 3.69
1067 1241 1.423921 CTACTCCTCCTCCTCCTCCTC 59.576 61.905 0.00 0.00 0.00 3.71
1068 1242 0.254107 ACTCCTCCTCCTCCTCCTCT 60.254 60.000 0.00 0.00 0.00 3.69
1374 1557 4.410400 GTGTTCCAGGGGCCCTCG 62.410 72.222 26.02 18.47 0.00 4.63
1715 1898 1.217882 CGTGGCCCGATTATCACTTC 58.782 55.000 0.00 0.00 39.56 3.01
1739 1922 5.302823 CCCCCTGTTCAATAATTTCTGGATC 59.697 44.000 0.00 0.00 0.00 3.36
1741 1924 6.552350 CCCCTGTTCAATAATTTCTGGATCAT 59.448 38.462 0.00 0.00 0.00 2.45
1742 1925 7.431249 CCCTGTTCAATAATTTCTGGATCATG 58.569 38.462 0.00 0.00 0.00 3.07
1746 1929 9.411189 TGTTCAATAATTTCTGGATCATGATCA 57.589 29.630 31.49 18.85 39.54 2.92
1759 1942 6.925718 TGGATCATGATCACTAAATCTCGTTC 59.074 38.462 31.49 13.18 39.54 3.95
1833 2016 3.853330 CATTGCGTGGAGACGGCG 61.853 66.667 4.80 4.80 46.20 6.46
2013 2196 7.385267 TCATGGATTTTGACCATTGTTTTAGG 58.615 34.615 0.00 0.00 44.51 2.69
2033 2216 2.554564 GGGGGATTCGGATAATGGGTTC 60.555 54.545 0.00 0.00 0.00 3.62
2039 2222 2.669781 TCGGATAATGGGTTCGGTAGT 58.330 47.619 0.00 0.00 0.00 2.73
2058 2241 6.074994 CGGTAGTTAGTGCATTCGTATTCTTC 60.075 42.308 0.00 0.00 0.00 2.87
2181 2364 5.185635 TGCATTTCCCTTTCACCTTCATTAG 59.814 40.000 0.00 0.00 0.00 1.73
2234 2418 4.873827 TGAAGCCCAACGTATATGACTTTC 59.126 41.667 0.00 0.00 0.00 2.62
2235 2419 4.755266 AGCCCAACGTATATGACTTTCT 57.245 40.909 0.00 0.00 0.00 2.52
2313 2503 8.692110 TTTGCTTTGATCATACTTGCAATAAG 57.308 30.769 16.26 6.99 38.46 1.73
2316 2506 6.976925 GCTTTGATCATACTTGCAATAAGCTT 59.023 34.615 3.48 3.48 45.94 3.74
2323 2513 7.665690 TCATACTTGCAATAAGCTTTCCAAAA 58.334 30.769 3.20 0.00 45.94 2.44
2388 2579 4.079500 TGGCATGGAGTATGGGTTTCAATA 60.080 41.667 0.00 0.00 37.26 1.90
2400 2591 6.443934 TGGGTTTCAATATACCGTTTCATG 57.556 37.500 0.00 0.00 35.19 3.07
2433 2624 2.698274 TCGGCTGCCATGTTCTAATCTA 59.302 45.455 20.29 0.00 0.00 1.98
2443 2634 5.236047 CCATGTTCTAATCTAGCAAGCTGAC 59.764 44.000 4.53 0.00 0.00 3.51
2772 2963 2.430382 GAACCCCGAAGAGCACACGA 62.430 60.000 0.00 0.00 0.00 4.35
2783 2974 0.033920 AGCACACGAAGCTGTCATCA 59.966 50.000 0.00 0.00 41.61 3.07
2849 3040 3.452264 TGGATACACTGGATGAAGGTCTG 59.548 47.826 0.00 0.00 46.17 3.51
2879 3070 5.247792 AGCAGGCATCTCATATCACAATCTA 59.752 40.000 0.00 0.00 0.00 1.98
2936 3127 8.023021 ACTCCAAGATGCAGAAGTATGTATTA 57.977 34.615 0.00 0.00 0.00 0.98
2987 3182 6.979817 TGCAAAATATAGTGATGAACCATTGC 59.020 34.615 0.00 0.00 38.86 3.56
3207 3402 6.364701 TGGGTATGCAGCTTAACTTCAATAT 58.635 36.000 3.51 0.00 0.00 1.28
3222 3417 8.980481 AACTTCAATATATCCATTCGACCTTT 57.020 30.769 0.00 0.00 0.00 3.11
3224 3419 6.801539 TCAATATATCCATTCGACCTTTGC 57.198 37.500 0.00 0.00 0.00 3.68
3227 3422 0.395724 ATCCATTCGACCTTTGCCCC 60.396 55.000 0.00 0.00 0.00 5.80
3228 3423 1.304052 CCATTCGACCTTTGCCCCA 60.304 57.895 0.00 0.00 0.00 4.96
3234 3429 1.976474 GACCTTTGCCCCATTCGCA 60.976 57.895 0.00 0.00 0.00 5.10
3259 3456 2.143008 TTGTGCTGATTTGCTTGCTG 57.857 45.000 0.00 0.00 0.00 4.41
3455 3652 1.241315 GGGTGCTTACGTGGCAATGT 61.241 55.000 17.19 0.00 41.54 2.71
3491 3688 2.420022 GGAACATTCATCGTCCCAAGTG 59.580 50.000 0.00 0.00 0.00 3.16
3501 3698 1.535462 CGTCCCAAGTGAAAAGCGATT 59.465 47.619 0.00 0.00 0.00 3.34
3512 3709 3.826157 TGAAAAGCGATTCCATCAAACCT 59.174 39.130 0.00 0.00 0.00 3.50
3611 3808 5.500645 TCGTCATCTTACTCGAACATGAT 57.499 39.130 0.00 0.00 0.00 2.45
3624 3821 3.181471 CGAACATGATAAGGTGAGAGCCT 60.181 47.826 0.00 0.00 41.41 4.58
3654 3869 3.990469 GGTCGATCGATCACATTGCTAAT 59.010 43.478 23.20 0.00 0.00 1.73
3657 3872 3.431233 CGATCGATCACATTGCTAATGCT 59.569 43.478 24.40 0.00 42.69 3.79
3663 3879 7.322664 TCGATCACATTGCTAATGCTATCATA 58.677 34.615 15.77 7.54 42.69 2.15
3712 3928 4.042062 TCATCCTTGTGGTTTCAGATGTCT 59.958 41.667 0.00 0.00 34.22 3.41
3763 3979 2.742372 GACCTGATGCACCGCGTT 60.742 61.111 4.92 0.00 0.00 4.84
3766 3982 2.741985 CTGATGCACCGCGTTGGA 60.742 61.111 5.60 1.99 42.00 3.53
3802 4018 1.367840 GAGCCCCTACAGCATACCG 59.632 63.158 0.00 0.00 0.00 4.02
3949 4165 1.274728 GAGGAGATCCAGCGCATGTAT 59.725 52.381 11.47 0.00 38.89 2.29
3958 4174 2.584970 CGCATGTATGACCGCGGT 60.585 61.111 34.89 34.89 43.84 5.68
4046 4274 3.139603 ACCGCAGTGTTAACAAACAAC 57.860 42.857 10.51 0.00 34.01 3.32
4209 4446 4.384940 TGCAAAATGTGTACACTAGCAGA 58.615 39.130 25.60 5.74 0.00 4.26
4215 4454 2.890945 TGTGTACACTAGCAGAGCAGAA 59.109 45.455 25.60 0.00 0.00 3.02
4217 4456 2.231478 TGTACACTAGCAGAGCAGAACC 59.769 50.000 0.00 0.00 0.00 3.62
4225 4464 4.065321 AGCAGAGCAGAACCATGTATAC 57.935 45.455 0.00 0.00 0.00 1.47
4360 4606 1.298993 CAGGTGTGCAGCTCCAGAT 59.701 57.895 0.43 0.00 36.98 2.90
4450 4709 1.677966 CCTTCCCGTGGACGAGAGA 60.678 63.158 0.00 0.00 43.02 3.10
4465 4724 1.135333 GAGAGAATCCTGTCGTGTCCC 59.865 57.143 0.00 0.00 33.66 4.46
4505 4764 2.202703 CGTGGAATCGTCCCGTCC 60.203 66.667 0.00 0.00 44.23 4.79
4507 4766 1.153628 GTGGAATCGTCCCGTCCAG 60.154 63.158 0.00 0.00 44.23 3.86
4508 4767 2.355986 TGGAATCGTCCCGTCCAGG 61.356 63.158 0.00 0.00 44.23 4.45
4509 4768 2.356780 GGAATCGTCCCGTCCAGGT 61.357 63.158 0.00 0.00 38.08 4.00
4510 4769 1.141234 GAATCGTCCCGTCCAGGTC 59.859 63.158 0.00 0.00 38.74 3.85
4511 4770 2.294132 GAATCGTCCCGTCCAGGTCC 62.294 65.000 0.00 0.00 38.74 4.46
4512 4771 3.595428 ATCGTCCCGTCCAGGTCCA 62.595 63.158 0.00 0.00 38.74 4.02
4513 4772 3.760035 CGTCCCGTCCAGGTCCAG 61.760 72.222 0.00 0.00 38.74 3.86
4514 4773 2.603776 GTCCCGTCCAGGTCCAGT 60.604 66.667 0.00 0.00 38.74 4.00
4515 4774 2.283676 TCCCGTCCAGGTCCAGTC 60.284 66.667 0.00 0.00 38.74 3.51
4527 4786 1.123928 GTCCAGTCCAGGGTAGGATG 58.876 60.000 0.00 0.00 40.42 3.51
4528 4787 0.031111 TCCAGTCCAGGGTAGGATGG 60.031 60.000 0.00 0.00 40.42 3.51
4529 4788 0.326618 CCAGTCCAGGGTAGGATGGT 60.327 60.000 0.00 0.00 40.42 3.55
4530 4789 1.062428 CCAGTCCAGGGTAGGATGGTA 60.062 57.143 0.00 0.00 40.42 3.25
4531 4790 2.040178 CAGTCCAGGGTAGGATGGTAC 58.960 57.143 0.00 0.00 40.42 3.34
4532 4791 1.938069 AGTCCAGGGTAGGATGGTACT 59.062 52.381 0.00 0.00 40.42 2.73
4533 4792 3.117246 CAGTCCAGGGTAGGATGGTACTA 60.117 52.174 0.00 0.00 40.42 1.82
4534 4793 3.117208 AGTCCAGGGTAGGATGGTACTAC 60.117 52.174 0.00 0.00 40.42 2.73
4535 4794 3.117208 GTCCAGGGTAGGATGGTACTACT 60.117 52.174 0.00 0.00 40.42 2.57
4536 4795 4.105377 GTCCAGGGTAGGATGGTACTACTA 59.895 50.000 0.00 0.00 40.42 1.82
4537 4796 4.105377 TCCAGGGTAGGATGGTACTACTAC 59.895 50.000 0.00 0.00 40.43 2.73
4554 4813 0.043485 TACCATGGTAGGGTGCTGGA 59.957 55.000 21.05 0.00 39.48 3.86
4587 4846 1.080230 CTCTGGCGTGAGTGAGTGG 60.080 63.158 0.00 0.00 0.00 4.00
4588 4847 1.810606 CTCTGGCGTGAGTGAGTGGT 61.811 60.000 0.00 0.00 0.00 4.16
4589 4848 0.538746 TCTGGCGTGAGTGAGTGGTA 60.539 55.000 0.00 0.00 0.00 3.25
4591 4850 0.538746 TGGCGTGAGTGAGTGGTAGA 60.539 55.000 0.00 0.00 0.00 2.59
4592 4851 0.818296 GGCGTGAGTGAGTGGTAGAT 59.182 55.000 0.00 0.00 0.00 1.98
4593 4852 1.202313 GGCGTGAGTGAGTGGTAGATC 60.202 57.143 0.00 0.00 0.00 2.75
4594 4853 1.746220 GCGTGAGTGAGTGGTAGATCT 59.254 52.381 0.00 0.00 0.00 2.75
4595 4854 2.223386 GCGTGAGTGAGTGGTAGATCTC 60.223 54.545 0.00 0.00 0.00 2.75
4596 4855 2.031068 CGTGAGTGAGTGGTAGATCTCG 59.969 54.545 0.00 0.00 33.88 4.04
4597 4856 2.017782 TGAGTGAGTGGTAGATCTCGC 58.982 52.381 0.00 0.00 40.25 5.03
4598 4857 1.003331 GAGTGAGTGGTAGATCTCGCG 60.003 57.143 0.00 0.00 43.32 5.87
4599 4858 0.733729 GTGAGTGGTAGATCTCGCGT 59.266 55.000 5.77 0.00 32.82 6.01
4600 4859 0.733150 TGAGTGGTAGATCTCGCGTG 59.267 55.000 5.77 3.13 33.88 5.34
4601 4860 0.733729 GAGTGGTAGATCTCGCGTGT 59.266 55.000 5.77 0.00 0.00 4.49
4663 4923 1.810030 CCTCCGCCGCTTTCTGTAC 60.810 63.158 0.00 0.00 0.00 2.90
4862 5122 2.681778 CCCCTGGTCTCGCTGACT 60.682 66.667 7.99 0.00 44.74 3.41
4867 5127 4.500116 GGTCTCGCTGACTCGCCC 62.500 72.222 7.99 0.00 44.74 6.13
4886 5146 3.451178 GCCCTTGAGTACACTAATCCTCA 59.549 47.826 0.00 0.00 32.38 3.86
4922 5187 9.857656 ATAAGTTTGTCCACTAATCATCATCAT 57.142 29.630 0.00 0.00 0.00 2.45
4988 5259 1.526917 CGCCAAGGCTGGATAAGGG 60.527 63.158 9.73 0.00 46.92 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 6.481976 TCATTGATATTAAACTAGCGTGGTGG 59.518 38.462 0.00 0.00 0.00 4.61
61 62 6.237313 AGTTTAGCCGTGACACTATTTTTC 57.763 37.500 3.68 0.00 0.00 2.29
93 96 0.447406 TTGCAGTTGCCATTCGATCG 59.553 50.000 9.36 9.36 41.18 3.69
116 119 5.776173 TCCACCGTTGAATTGTTTTACAT 57.224 34.783 0.00 0.00 0.00 2.29
121 124 6.642707 TCTTTATCCACCGTTGAATTGTTT 57.357 33.333 0.00 0.00 0.00 2.83
122 125 6.432783 TCATCTTTATCCACCGTTGAATTGTT 59.567 34.615 0.00 0.00 0.00 2.83
135 148 2.754472 CGCGGACATCATCTTTATCCA 58.246 47.619 0.00 0.00 0.00 3.41
163 176 6.237808 GCAAACATAGTTTTGTCTTTGGTGTG 60.238 38.462 0.00 0.00 38.51 3.82
237 252 9.988350 GTGACACTATTTCATTTTATCGTTCAT 57.012 29.630 0.00 0.00 0.00 2.57
238 253 9.214957 AGTGACACTATTTCATTTTATCGTTCA 57.785 29.630 6.24 0.00 0.00 3.18
239 254 9.478019 CAGTGACACTATTTCATTTTATCGTTC 57.522 33.333 8.02 0.00 0.00 3.95
273 288 3.275617 ACAGCGACATTATTTGCCCTA 57.724 42.857 0.00 0.00 0.00 3.53
274 289 2.128771 ACAGCGACATTATTTGCCCT 57.871 45.000 0.00 0.00 0.00 5.19
278 293 7.656468 CACATGTTTAACAGCGACATTATTTG 58.344 34.615 3.63 0.00 32.01 2.32
282 297 4.378978 GGCACATGTTTAACAGCGACATTA 60.379 41.667 3.63 0.00 32.01 1.90
283 298 3.564511 GCACATGTTTAACAGCGACATT 58.435 40.909 3.63 0.00 32.01 2.71
285 300 1.265635 GGCACATGTTTAACAGCGACA 59.734 47.619 3.63 0.00 0.00 4.35
286 301 1.265635 TGGCACATGTTTAACAGCGAC 59.734 47.619 3.63 0.00 0.00 5.19
287 302 1.265635 GTGGCACATGTTTAACAGCGA 59.734 47.619 13.86 0.00 44.52 4.93
288 303 1.266718 AGTGGCACATGTTTAACAGCG 59.733 47.619 21.41 0.00 44.52 5.18
289 304 3.052036 CAAGTGGCACATGTTTAACAGC 58.948 45.455 21.41 1.63 44.52 4.40
311 327 2.565841 GGTTTGCAGCTCCTATTCGAT 58.434 47.619 0.00 0.00 0.00 3.59
328 344 5.726980 TTGACTAATACCACTACACGGTT 57.273 39.130 0.00 0.00 37.99 4.44
339 475 7.664318 ACCCCATCGATTTTATTGACTAATACC 59.336 37.037 0.00 0.00 0.00 2.73
343 479 9.463902 TTTTACCCCATCGATTTTATTGACTAA 57.536 29.630 0.00 0.00 0.00 2.24
354 490 5.413309 TTTGCAATTTTACCCCATCGATT 57.587 34.783 0.00 0.00 0.00 3.34
355 491 5.413309 TTTTGCAATTTTACCCCATCGAT 57.587 34.783 0.00 0.00 0.00 3.59
356 492 4.873746 TTTTGCAATTTTACCCCATCGA 57.126 36.364 0.00 0.00 0.00 3.59
357 493 7.784633 ATTATTTTGCAATTTTACCCCATCG 57.215 32.000 0.00 0.00 0.00 3.84
358 494 9.830975 AGTATTATTTTGCAATTTTACCCCATC 57.169 29.630 0.00 0.00 0.00 3.51
375 511 9.780186 GGAATTCAGGCTGTACTAGTATTATTT 57.220 33.333 15.27 0.00 0.00 1.40
557 706 2.989253 GGGGTTGGGTTGCTTCCG 60.989 66.667 0.00 0.00 0.00 4.30
671 830 2.919043 CGGATTTGGGGAGGGGAG 59.081 66.667 0.00 0.00 0.00 4.30
672 831 3.416880 GCGGATTTGGGGAGGGGA 61.417 66.667 0.00 0.00 0.00 4.81
673 832 2.514516 AAAGCGGATTTGGGGAGGGG 62.515 60.000 0.00 0.00 0.00 4.79
674 833 0.257616 TAAAGCGGATTTGGGGAGGG 59.742 55.000 0.74 0.00 32.01 4.30
675 834 2.364972 ATAAAGCGGATTTGGGGAGG 57.635 50.000 0.74 0.00 32.01 4.30
716 875 1.445942 GAATCGAGGGCGGATGGAA 59.554 57.895 0.00 0.00 38.28 3.53
860 1025 1.153429 CGAACCCGAATCTGGTCCC 60.153 63.158 0.00 0.00 38.22 4.46
861 1026 0.459759 GACGAACCCGAATCTGGTCC 60.460 60.000 0.00 0.00 39.50 4.46
863 1028 0.531200 GAGACGAACCCGAATCTGGT 59.469 55.000 0.00 0.00 39.50 4.00
865 1030 3.347411 GGAGACGAACCCGAATCTG 57.653 57.895 0.00 0.00 39.50 2.90
944 1109 2.993899 GAGCTCGAATCGGAAAACTCAA 59.006 45.455 1.76 0.00 0.00 3.02
949 1114 1.625616 GACGAGCTCGAATCGGAAAA 58.374 50.000 40.58 0.00 44.36 2.29
952 1117 2.707646 CGACGAGCTCGAATCGGA 59.292 61.111 40.58 0.00 46.14 4.55
953 1118 2.352457 CCGACGAGCTCGAATCGG 60.352 66.667 37.49 37.49 46.25 4.18
981 1155 2.122167 GGTCGCCAGAGTCCGAGAT 61.122 63.158 0.00 0.00 33.71 2.75
1041 1215 2.123640 GAGGAGGAGTAGGCGGCT 60.124 66.667 18.33 18.33 0.00 5.52
1056 1230 1.065053 TCGAACTCAGAGGAGGAGGAG 60.065 57.143 1.53 0.00 45.81 3.69
1066 1240 3.379445 GCCCGGGTCGAACTCAGA 61.379 66.667 24.63 0.00 0.00 3.27
1067 1241 3.358076 GAGCCCGGGTCGAACTCAG 62.358 68.421 24.63 0.00 32.08 3.35
1068 1242 3.379445 GAGCCCGGGTCGAACTCA 61.379 66.667 24.63 0.00 32.08 3.41
1715 1898 4.609301 TCCAGAAATTATTGAACAGGGGG 58.391 43.478 0.00 0.00 0.00 5.40
1739 1922 5.043903 ACCGAACGAGATTTAGTGATCATG 58.956 41.667 0.00 0.00 0.00 3.07
1741 1924 4.713824 ACCGAACGAGATTTAGTGATCA 57.286 40.909 0.00 0.00 0.00 2.92
1742 1925 5.347907 ACAAACCGAACGAGATTTAGTGATC 59.652 40.000 0.00 0.00 0.00 2.92
1746 1929 5.295152 AGAACAAACCGAACGAGATTTAGT 58.705 37.500 0.00 0.00 0.00 2.24
1759 1942 3.127895 TCACAGAACCAAAGAACAAACCG 59.872 43.478 0.00 0.00 0.00 4.44
1833 2016 2.362120 ATCTTGGCCAGCAGCACC 60.362 61.111 5.11 0.00 46.50 5.01
2013 2196 2.791655 GAACCCATTATCCGAATCCCC 58.208 52.381 0.00 0.00 0.00 4.81
2033 2216 5.279384 AGAATACGAATGCACTAACTACCG 58.721 41.667 0.00 0.00 0.00 4.02
2039 2222 4.751060 ACCGAAGAATACGAATGCACTAA 58.249 39.130 0.00 0.00 0.00 2.24
2058 2241 1.656652 CCAACAGCTTGAGGATACCG 58.343 55.000 0.00 0.00 37.17 4.02
2080 2263 7.649370 AGATCACAATAATTGCAGTAGATCG 57.351 36.000 0.00 0.00 35.69 3.69
2132 2315 9.850628 CACATGATCATTTGCCTTAAATATAGG 57.149 33.333 5.16 0.00 36.87 2.57
2313 2503 6.482973 TGGTGATTTGAATTCTTTTGGAAAGC 59.517 34.615 7.05 1.35 37.49 3.51
2316 2506 7.123355 AGTGGTGATTTGAATTCTTTTGGAA 57.877 32.000 7.05 0.00 38.41 3.53
2388 2579 4.142469 GCTACCAAAAGCATGAAACGGTAT 60.142 41.667 0.00 0.00 42.30 2.73
2400 2591 1.796796 CAGCCGAGCTACCAAAAGC 59.203 57.895 0.00 0.00 43.11 3.51
2433 2624 2.338577 ACAGAAACTGTCAGCTTGCT 57.661 45.000 0.00 0.00 41.21 3.91
2443 2634 6.226787 ACCTGAACAGATTAGACAGAAACTG 58.773 40.000 3.19 0.00 37.52 3.16
2759 2950 0.941463 ACAGCTTCGTGTGCTCTTCG 60.941 55.000 0.00 0.00 38.92 3.79
2772 2963 3.503363 TCTGCGAATTTTGATGACAGCTT 59.497 39.130 0.00 0.00 0.00 3.74
2783 2974 5.841810 TCATCAAAGGTTTCTGCGAATTTT 58.158 33.333 0.00 0.00 0.00 1.82
2849 3040 0.473326 ATGAGATGCCTGCTTCCCTC 59.527 55.000 1.80 0.00 0.00 4.30
2879 3070 6.609616 TGTAAAGGTTTTTGTTCCTTCCAGAT 59.390 34.615 0.00 0.00 42.38 2.90
2936 3127 8.378172 AGCATATATAATGCAAACAAGTACGT 57.622 30.769 12.12 0.00 46.77 3.57
2987 3182 8.816640 AAACCAATTAGCAAACATACAGAAAG 57.183 30.769 0.00 0.00 0.00 2.62
3075 3270 2.123589 TCTTCCTCCTTGTCAACCACA 58.876 47.619 0.00 0.00 0.00 4.17
3207 3402 1.133915 GGGGCAAAGGTCGAATGGATA 60.134 52.381 0.00 0.00 0.00 2.59
3222 3417 0.539438 AAACTCTTGCGAATGGGGCA 60.539 50.000 0.00 0.00 38.93 5.36
3224 3419 1.068333 CACAAACTCTTGCGAATGGGG 60.068 52.381 0.00 0.00 35.84 4.96
3227 3422 2.031769 TCAGCACAAACTCTTGCGAATG 60.032 45.455 0.00 0.00 43.87 2.67
3228 3423 2.221169 TCAGCACAAACTCTTGCGAAT 58.779 42.857 0.00 0.00 43.87 3.34
3234 3429 4.365723 CAAGCAAATCAGCACAAACTCTT 58.634 39.130 0.00 0.00 36.85 2.85
3243 3438 4.979204 GCAGCAAGCAAATCAGCA 57.021 50.000 0.00 0.00 44.79 4.41
3259 3456 0.168128 GTGCAATGAACGGTACCTGC 59.832 55.000 10.90 12.25 0.00 4.85
3455 3652 5.068855 TGAATGTTCCTTGTTCAATGCTTCA 59.931 36.000 0.00 0.00 0.00 3.02
3501 3698 0.039618 GGGCAAGGAGGTTTGATGGA 59.960 55.000 0.00 0.00 0.00 3.41
3512 3709 2.856988 AGGGGAAACGGGCAAGGA 60.857 61.111 0.00 0.00 0.00 3.36
3611 3808 2.753452 CGAACACTAGGCTCTCACCTTA 59.247 50.000 0.00 0.00 41.50 2.69
3624 3821 2.282407 TGATCGATCGACCGAACACTA 58.718 47.619 22.06 0.00 42.22 2.74
3663 3879 8.635765 ACAATGTCACATAACTGGAACTAAAT 57.364 30.769 0.00 0.00 0.00 1.40
3679 3895 3.569701 ACCACAAGGATGAACAATGTCAC 59.430 43.478 0.00 0.00 38.69 3.67
3712 3928 1.272092 CCTGCTGGGAATTCTTGGACA 60.272 52.381 5.23 0.00 37.23 4.02
3763 3979 4.020617 CTCGGGCTGTTGGCTCCA 62.021 66.667 0.00 0.00 38.42 3.86
3766 3982 4.335647 CACCTCGGGCTGTTGGCT 62.336 66.667 7.77 0.00 41.46 4.75
3802 4018 4.844420 CGCAGGTCCTCCTTCATC 57.156 61.111 0.00 0.00 43.07 2.92
4000 4222 4.143333 CGGGGTCATCGGCGTCTT 62.143 66.667 6.85 0.00 0.00 3.01
4022 4244 3.242804 TGTTTGTTAACACTGCGGTAAGC 60.243 43.478 8.07 0.00 41.93 3.09
4025 4247 3.065095 GGTTGTTTGTTAACACTGCGGTA 59.935 43.478 8.07 0.00 43.66 4.02
4046 4274 3.507786 TCGAACATCATCGTACAACAGG 58.492 45.455 0.00 0.00 43.19 4.00
4168 4405 2.900106 GCCAAGGCTGGTGGACTCT 61.900 63.158 9.44 0.00 45.53 3.24
4209 4446 6.731292 TGTCATAGTATACATGGTTCTGCT 57.269 37.500 5.50 0.00 0.00 4.24
4215 4454 6.546403 ACGACTCTTGTCATAGTATACATGGT 59.454 38.462 5.50 0.40 43.06 3.55
4217 4456 8.129211 TGAACGACTCTTGTCATAGTATACATG 58.871 37.037 5.50 7.21 43.06 3.21
4225 4464 5.059832 CGAACTTGAACGACTCTTGTCATAG 59.940 44.000 0.00 0.00 43.06 2.23
4248 4487 1.061570 GCAAGCAGAAGCCGAATCG 59.938 57.895 0.00 0.00 43.56 3.34
4343 4589 1.601171 GATCTGGAGCTGCACACCT 59.399 57.895 2.72 0.00 0.00 4.00
4360 4606 1.003580 GATTCAGTTGAGGCCACAGGA 59.996 52.381 5.01 0.99 0.00 3.86
4438 4697 0.811915 ACAGGATTCTCTCGTCCACG 59.188 55.000 0.00 0.00 36.96 4.94
4465 4724 2.508439 ATACGCCTCACCGCAACG 60.508 61.111 0.00 0.00 0.00 4.10
4505 4764 0.978146 CCTACCCTGGACTGGACCTG 60.978 65.000 0.00 0.00 0.00 4.00
4507 4766 0.031010 ATCCTACCCTGGACTGGACC 60.031 60.000 0.00 0.00 39.17 4.46
4508 4767 1.123928 CATCCTACCCTGGACTGGAC 58.876 60.000 0.00 0.00 39.17 4.02
4509 4768 0.031111 CCATCCTACCCTGGACTGGA 60.031 60.000 0.00 0.00 39.17 3.86
4510 4769 0.326618 ACCATCCTACCCTGGACTGG 60.327 60.000 0.00 0.00 39.17 4.00
4511 4770 2.040178 GTACCATCCTACCCTGGACTG 58.960 57.143 0.00 0.00 39.17 3.51
4512 4771 1.938069 AGTACCATCCTACCCTGGACT 59.062 52.381 0.00 0.00 39.17 3.85
4513 4772 2.473576 AGTACCATCCTACCCTGGAC 57.526 55.000 0.00 0.00 39.17 4.02
4514 4773 3.136896 AGTAGTACCATCCTACCCTGGA 58.863 50.000 0.00 0.00 40.82 3.86
4515 4774 3.614568 AGTAGTACCATCCTACCCTGG 57.385 52.381 0.00 0.00 36.30 4.45
4528 4787 3.320256 GCACCCTACCATGGTAGTAGTAC 59.680 52.174 37.95 28.12 44.71 2.73
4529 4788 3.205959 AGCACCCTACCATGGTAGTAGTA 59.794 47.826 37.95 15.58 44.71 1.82
4530 4789 2.023307 AGCACCCTACCATGGTAGTAGT 60.023 50.000 37.95 32.43 44.71 2.73
4531 4790 2.365617 CAGCACCCTACCATGGTAGTAG 59.634 54.545 37.95 31.90 44.71 2.57
4532 4791 2.394632 CAGCACCCTACCATGGTAGTA 58.605 52.381 37.95 16.96 44.71 1.82
4533 4792 1.204146 CAGCACCCTACCATGGTAGT 58.796 55.000 37.95 25.39 44.71 2.73
4534 4793 0.469917 CCAGCACCCTACCATGGTAG 59.530 60.000 35.85 35.85 45.50 3.18
4535 4794 0.043485 TCCAGCACCCTACCATGGTA 59.957 55.000 23.23 23.23 33.84 3.25
4536 4795 0.844661 TTCCAGCACCCTACCATGGT 60.845 55.000 23.55 23.55 36.21 3.55
4537 4796 0.107017 CTTCCAGCACCCTACCATGG 60.107 60.000 11.19 11.19 0.00 3.66
4538 4797 0.107017 CCTTCCAGCACCCTACCATG 60.107 60.000 0.00 0.00 0.00 3.66
4539 4798 0.253160 TCCTTCCAGCACCCTACCAT 60.253 55.000 0.00 0.00 0.00 3.55
4540 4799 0.909610 CTCCTTCCAGCACCCTACCA 60.910 60.000 0.00 0.00 0.00 3.25
4554 4813 1.287739 CCAGAGGTCTCTCTCCTCCTT 59.712 57.143 8.15 0.00 46.79 3.36
4587 4846 0.170561 ACACCACACGCGAGATCTAC 59.829 55.000 15.93 0.00 0.00 2.59
4588 4847 0.170339 CACACCACACGCGAGATCTA 59.830 55.000 15.93 0.00 0.00 1.98
4589 4848 1.080501 CACACCACACGCGAGATCT 60.081 57.895 15.93 0.00 0.00 2.75
4591 4850 2.048222 CCACACCACACGCGAGAT 60.048 61.111 15.93 0.00 0.00 2.75
4592 4851 3.533105 ACCACACCACACGCGAGA 61.533 61.111 15.93 0.00 0.00 4.04
4593 4852 3.337889 CACCACACCACACGCGAG 61.338 66.667 15.93 7.88 0.00 5.03
4594 4853 4.901123 CCACCACACCACACGCGA 62.901 66.667 15.93 0.00 0.00 5.87
4597 4856 4.866224 TGGCCACCACACCACACG 62.866 66.667 0.00 0.00 0.00 4.49
4598 4857 2.441164 TTGGCCACCACACCACAC 60.441 61.111 3.88 0.00 35.10 3.82
4599 4858 2.123939 CTTGGCCACCACACCACA 60.124 61.111 3.88 0.00 35.10 4.17
4600 4859 2.912025 CCTTGGCCACCACACCAC 60.912 66.667 3.88 0.00 35.10 4.16
4601 4860 4.912395 GCCTTGGCCACCACACCA 62.912 66.667 3.88 0.00 30.78 4.17
4650 4910 1.986154 CGTACGTACAGAAAGCGGC 59.014 57.895 24.50 0.00 0.00 6.53
4816 5076 2.032528 CGCTGGAGTTGCAGGGAA 59.967 61.111 11.40 0.00 33.87 3.97
4823 5083 1.342082 CGTAACCGTCGCTGGAGTTG 61.342 60.000 0.00 0.00 0.00 3.16
4862 5122 2.429610 GGATTAGTGTACTCAAGGGCGA 59.570 50.000 0.00 0.00 0.00 5.54
4922 5187 3.057596 CGGTAGTACGGGTTTAAGTGTGA 60.058 47.826 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.