Multiple sequence alignment - TraesCS3D01G137200

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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 TraesCS3D01G137200 chr3D 100.000 4497 0 0 1467 5963 95946218 95950714 0.000000e+00 8305.0
1 TraesCS3D01G137200 chr3D 100.000 1051 0 0 1 1051 95944752 95945802 0.000000e+00 1941.0
2 TraesCS3D01G137200 chr3D 94.595 111 3 2 5790 5897 95950434 95950544 1.030000e-37 169.0
3 TraesCS3D01G137200 chr3D 94.595 111 3 2 5683 5793 95950541 95950648 1.030000e-37 169.0
4 TraesCS3D01G137200 chr3B 95.124 4061 137 30 1517 5551 146884415 146888440 0.000000e+00 6346.0
5 TraesCS3D01G137200 chr3B 86.335 966 85 23 1 949 146883012 146883947 0.000000e+00 1009.0
6 TraesCS3D01G137200 chr3B 88.288 111 13 0 5853 5963 146888695 146888805 3.750000e-27 134.0
7 TraesCS3D01G137200 chr3B 89.474 95 10 0 5642 5736 146888574 146888668 2.920000e-23 121.0
8 TraesCS3D01G137200 chr3A 91.896 3961 219 55 1517 5424 114041235 114045146 0.000000e+00 5443.0
9 TraesCS3D01G137200 chr3A 87.591 411 25 6 5491 5897 114045166 114045554 2.530000e-123 453.0
10 TraesCS3D01G137200 chr3A 78.517 782 100 41 171 919 114040071 114040817 9.110000e-123 451.0
11 TraesCS3D01G137200 chr3A 89.051 274 18 7 5693 5963 114045456 114045720 4.460000e-86 329.0
12 TraesCS3D01G137200 chr3A 91.089 101 4 2 5790 5889 114045359 114045455 1.350000e-26 132.0
13 TraesCS3D01G137200 chr1B 80.952 462 74 12 2095 2550 191002864 191003317 2.640000e-93 353.0
14 TraesCS3D01G137200 chr1D 80.736 462 75 12 2095 2550 142151248 142150795 1.230000e-91 348.0
15 TraesCS3D01G137200 chr5D 80.645 124 24 0 3269 3392 545212529 545212406 4.920000e-16 97.1


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 TraesCS3D01G137200 chr3D 95944752 95950714 5962 False 2646.0 8305 97.29750 1 5963 4 chr3D.!!$F1 5962
1 TraesCS3D01G137200 chr3B 146883012 146888805 5793 False 1902.5 6346 89.80525 1 5963 4 chr3B.!!$F1 5962
2 TraesCS3D01G137200 chr3A 114040071 114045720 5649 False 1361.6 5443 87.62880 171 5963 5 chr3A.!!$F1 5792

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
710 750 0.100503 GTAATGCATGGCCAACGTCC 59.899 55.0 10.96 0.00 0.00 4.79 F
1556 1627 0.318762 GCTCTTCTCACGGTGGTTCT 59.681 55.0 8.50 0.00 0.00 3.01 F
1755 1826 0.668535 GTTGACCAGAAACAGTGGCC 59.331 55.0 0.00 0.00 38.83 5.36 F
3261 3347 0.769247 AGGTACCTGGTGAACCCAAC 59.231 55.0 15.42 0.53 44.65 3.77 F
3898 3989 0.179018 AACGGGTTGCTCTGCTTTCT 60.179 50.0 0.00 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1855 0.453282 CACACAATTTCTCTGCCGCG 60.453 55.000 0.00 0.00 0.00 6.46 R
2902 2985 2.036958 TGTCCAGTTCCACTGTTGTG 57.963 50.000 3.30 0.00 44.50 3.33 R
3478 3564 3.315191 AGGCTGACAAATACACAACACAC 59.685 43.478 0.00 0.00 0.00 3.82 R
4249 4342 3.674997 TCCTACTTCCACAAAGATGCAC 58.325 45.455 0.00 0.00 38.44 4.57 R
5511 5644 0.036952 TAGCAGCAGACTTCTGTGGC 60.037 55.000 8.04 11.05 45.45 5.01 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 0.748005 ATGCGGGGGTCGAGATTTTG 60.748 55.000 0.00 0.00 42.43 2.44
32 33 1.644786 GCGGGGGTCGAGATTTTGTG 61.645 60.000 0.00 0.00 42.43 3.33
38 39 1.401539 GGTCGAGATTTTGTGCAAGCC 60.402 52.381 0.00 0.00 0.00 4.35
48 49 2.523657 TGCAAGCCATGGGTGCAA 60.524 55.556 27.55 16.68 32.17 4.08
61 62 1.963515 GGGTGCAAGAAAGATGGTGTT 59.036 47.619 0.00 0.00 0.00 3.32
65 66 2.819608 TGCAAGAAAGATGGTGTTAGGC 59.180 45.455 0.00 0.00 0.00 3.93
89 90 1.000896 GCATGGTGCAACTAGGGGT 60.001 57.895 2.04 0.00 44.26 4.95
90 91 0.611896 GCATGGTGCAACTAGGGGTT 60.612 55.000 2.04 0.00 44.26 4.11
127 128 5.028678 TGGTATCCCTGGATATGATCACT 57.971 43.478 9.05 0.00 39.04 3.41
181 182 1.635844 CGATCAACGGTTCCGATTGA 58.364 50.000 18.28 20.16 38.46 2.57
207 208 1.603931 CCACGTCGATCATCCTCCATG 60.604 57.143 0.00 0.00 0.00 3.66
215 216 6.108687 GTCGATCATCCTCCATGCAATTATA 58.891 40.000 0.00 0.00 31.70 0.98
217 218 6.070596 TCGATCATCCTCCATGCAATTATAGT 60.071 38.462 0.00 0.00 31.70 2.12
244 245 1.175983 TAAACCCTGCCAGCAAACGG 61.176 55.000 0.00 0.00 0.00 4.44
250 251 1.135402 CCTGCCAGCAAACGGAATTAC 60.135 52.381 0.00 0.00 0.00 1.89
272 273 0.577269 CCTGCTAGCAATACGAACGC 59.423 55.000 19.86 0.00 0.00 4.84
274 275 1.143373 TGCTAGCAATACGAACGCGG 61.143 55.000 16.84 0.00 43.17 6.46
278 279 0.441145 AGCAATACGAACGCGGTTTC 59.559 50.000 12.47 5.07 43.17 2.78
299 301 2.591715 GGAGTTGTGTGGCACGCT 60.592 61.111 29.13 16.38 40.97 5.07
369 371 7.756722 CAGAAAACAAATGCTATCCTCGAAATT 59.243 33.333 0.00 0.00 0.00 1.82
414 417 4.026968 CGTGAACTAAACGTCGTTGGTAAA 60.027 41.667 12.12 3.73 36.31 2.01
417 420 4.794248 ACTAAACGTCGTTGGTAAAACC 57.206 40.909 12.12 0.00 39.22 3.27
430 433 2.729360 GGTAAAACCAATTCAACGCTGC 59.271 45.455 0.00 0.00 38.42 5.25
437 440 0.163788 AATTCAACGCTGCTTCGACG 59.836 50.000 0.00 0.00 0.00 5.12
441 445 2.916052 AACGCTGCTTCGACGGAGA 61.916 57.895 14.70 0.00 0.00 3.71
448 452 3.425625 GCTGCTTCGACGGAGAGATATAG 60.426 52.174 14.70 0.00 0.00 1.31
458 462 9.674824 TCGACGGAGAGATATAGAAAAATAAAC 57.325 33.333 0.00 0.00 0.00 2.01
459 463 9.459640 CGACGGAGAGATATAGAAAAATAAACA 57.540 33.333 0.00 0.00 0.00 2.83
481 485 6.811954 ACATTTCTTCCAAAACATAAACCGT 58.188 32.000 0.00 0.00 0.00 4.83
496 500 1.950472 ACCGTAGTTTAACGTCGACG 58.050 50.000 34.58 34.58 41.27 5.12
499 503 2.523511 CCGTAGTTTAACGTCGACGATG 59.476 50.000 41.52 22.59 41.27 3.84
500 504 2.523511 CGTAGTTTAACGTCGACGATGG 59.476 50.000 41.52 15.70 43.02 3.51
507 511 4.446413 GTCGACGATGGGGCCGTT 62.446 66.667 0.00 0.00 40.67 4.44
529 544 3.886505 TGTTTTGTTTGGCCTATCTCGTT 59.113 39.130 3.32 0.00 0.00 3.85
535 550 1.271840 TGGCCTATCTCGTTGCCCTT 61.272 55.000 3.32 0.00 43.35 3.95
546 561 2.427453 TCGTTGCCCTTAGCTAGAAGAG 59.573 50.000 0.00 0.00 44.23 2.85
558 590 4.139038 AGCTAGAAGAGGGAGTCGAATAC 58.861 47.826 0.00 0.00 0.00 1.89
575 607 9.613428 AGTCGAATACAATCAAATTCCAATAGA 57.387 29.630 0.00 0.00 0.00 1.98
591 623 7.379529 ATTCCAATAGAAAATTAAGCGATTGCG 59.620 33.333 0.00 0.00 41.80 4.85
667 699 3.587923 TCCCACGAAAAACCAGTATACG 58.412 45.455 0.00 0.00 0.00 3.06
668 700 3.006752 TCCCACGAAAAACCAGTATACGT 59.993 43.478 0.00 0.00 0.00 3.57
672 704 6.756074 CCCACGAAAAACCAGTATACGTATAA 59.244 38.462 16.65 0.00 0.00 0.98
710 750 0.100503 GTAATGCATGGCCAACGTCC 59.899 55.000 10.96 0.00 0.00 4.79
739 786 4.720530 CGTAGGTTTATGTTAATCCCGC 57.279 45.455 0.00 0.00 0.00 6.13
787 835 3.708544 CCGTTACCGCTTCCCCCA 61.709 66.667 0.00 0.00 0.00 4.96
789 837 2.045634 GTTACCGCTTCCCCCACC 60.046 66.667 0.00 0.00 0.00 4.61
790 838 2.204029 TTACCGCTTCCCCCACCT 60.204 61.111 0.00 0.00 0.00 4.00
791 839 2.598787 TTACCGCTTCCCCCACCTG 61.599 63.158 0.00 0.00 0.00 4.00
793 841 4.410400 CCGCTTCCCCCACCTGTC 62.410 72.222 0.00 0.00 0.00 3.51
794 842 4.410400 CGCTTCCCCCACCTGTCC 62.410 72.222 0.00 0.00 0.00 4.02
810 858 2.108566 CCTCCAGAGCGGCATCTG 59.891 66.667 17.20 17.20 45.24 2.90
814 862 4.746361 CAGAGCGGCATCTGGTAG 57.254 61.111 16.67 0.00 42.52 3.18
815 863 2.119009 CAGAGCGGCATCTGGTAGA 58.881 57.895 16.67 0.00 42.52 2.59
949 998 1.108132 CCTCTAGTAGGTGTCCCCGC 61.108 65.000 0.00 0.00 40.94 6.13
950 999 1.445716 CTCTAGTAGGTGTCCCCGCG 61.446 65.000 0.00 0.00 38.74 6.46
951 1000 2.440796 TAGTAGGTGTCCCCGCGG 60.441 66.667 21.04 21.04 38.74 6.46
1037 1086 3.731728 GGAGCCCATGGTGCTGGA 61.732 66.667 26.43 0.00 39.69 3.86
1038 1087 2.439156 GAGCCCATGGTGCTGGAC 60.439 66.667 26.43 12.59 39.69 4.02
1039 1088 4.415150 AGCCCATGGTGCTGGACG 62.415 66.667 22.35 1.85 38.69 4.79
1495 1544 0.321122 CGAAGAGGGTGAGCAGCTTT 60.321 55.000 0.00 0.00 0.00 3.51
1511 1560 2.096218 AGCTTTGCGTGTTCTCGATTTC 60.096 45.455 0.00 0.00 0.00 2.17
1556 1627 0.318762 GCTCTTCTCACGGTGGTTCT 59.681 55.000 8.50 0.00 0.00 3.01
1562 1633 0.679505 CTCACGGTGGTTCTCCTTCA 59.320 55.000 8.50 0.00 34.23 3.02
1713 1784 1.271379 TCGTACAGGAAATCACTGCGT 59.729 47.619 0.00 0.00 39.55 5.24
1755 1826 0.668535 GTTGACCAGAAACAGTGGCC 59.331 55.000 0.00 0.00 38.83 5.36
1797 1870 1.512734 GTGCGCGGCAGAGAAATTG 60.513 57.895 8.83 0.00 40.08 2.32
2080 2157 6.039047 AGTTGATGCAATGCTTATCGAATTCT 59.961 34.615 6.82 0.00 0.00 2.40
2128 2205 2.685106 TGGAGACTGGAGAGACTGTT 57.315 50.000 0.00 0.00 0.00 3.16
2245 2322 1.412710 TGCTTCTTCTCGACCACAAGT 59.587 47.619 0.00 0.00 0.00 3.16
2299 2376 6.275855 TGGAGTATGTCCCTGAGACTCTATAT 59.724 42.308 3.68 0.00 46.31 0.86
2375 2452 5.005779 GTCAAGCTTTACATGTATCAGGTCG 59.994 44.000 6.36 1.76 29.18 4.79
2394 2471 3.565482 GTCGGTGAACCATCATATTGCAT 59.435 43.478 0.00 0.00 38.01 3.96
2540 2621 6.536941 ACCACAAAATGTTTTGGTATGTGTTC 59.463 34.615 19.08 0.00 44.36 3.18
2707 2790 8.827677 CCCCTTAAGAATCAGTAGTTTATTTCG 58.172 37.037 3.36 0.00 0.00 3.46
2902 2985 5.827666 TCACAGCTTAAAGTTGGCTTTAAC 58.172 37.500 8.05 6.46 46.35 2.01
3151 3235 1.880027 CAAGCCTGACCTTGGTTGTAC 59.120 52.381 0.00 0.00 38.78 2.90
3261 3347 0.769247 AGGTACCTGGTGAACCCAAC 59.231 55.000 15.42 0.53 44.65 3.77
3462 3548 8.138928 TGATTAGACTATATTGTCCATGAGGG 57.861 38.462 12.83 0.00 37.66 4.30
3478 3564 2.977580 TGAGGGGATTCTGATCATCCTG 59.022 50.000 12.50 0.00 40.32 3.86
3578 3665 5.062558 GCCTTATGTTTCACATGCAACATTC 59.937 40.000 18.53 7.26 38.40 2.67
3619 3706 4.322650 GCCATGGATGTTTCTTAAAGCCAA 60.323 41.667 18.40 0.00 0.00 4.52
3790 3877 6.487331 TGCATCATGTCATTATACTTGCATGA 59.513 34.615 6.60 15.90 44.14 3.07
3792 3879 7.696872 GCATCATGTCATTATACTTGCATGATC 59.303 37.037 18.94 14.39 46.11 2.92
3819 3906 2.014857 CCACATCTTCTGGCATGTCAG 58.985 52.381 21.57 21.57 30.48 3.51
3875 3966 9.452287 AAATTATGAATTAAAAATGTGCCTGCT 57.548 25.926 0.00 0.00 0.00 4.24
3876 3967 9.452287 AATTATGAATTAAAAATGTGCCTGCTT 57.548 25.926 0.00 0.00 0.00 3.91
3892 3983 1.079503 GCTTCTAACGGGTTGCTCTG 58.920 55.000 0.00 0.00 0.00 3.35
3898 3989 0.179018 AACGGGTTGCTCTGCTTTCT 60.179 50.000 0.00 0.00 0.00 2.52
3899 3990 0.603975 ACGGGTTGCTCTGCTTTCTC 60.604 55.000 0.00 0.00 0.00 2.87
3903 3994 2.498167 GGTTGCTCTGCTTTCTCTTCA 58.502 47.619 0.00 0.00 0.00 3.02
3922 4013 6.467677 TCTTCACTAGATTTTCCACAAGAGG 58.532 40.000 0.00 0.00 0.00 3.69
4003 4094 4.420168 GTTGCACTGCTGTAAGTTTTTCA 58.580 39.130 1.98 0.00 35.30 2.69
4063 4155 3.136626 AGTGGCTGGGTGGATAAATACTC 59.863 47.826 0.00 0.00 0.00 2.59
4068 4160 4.520492 GCTGGGTGGATAAATACTCAATGG 59.480 45.833 0.00 0.00 0.00 3.16
4077 4169 7.569485 TGGATAAATACTCAATGGGGTGTACTA 59.431 37.037 0.00 0.00 0.00 1.82
4249 4342 6.538742 TCATTAACGATAAAAGGAGGCTCTTG 59.461 38.462 15.23 0.00 0.00 3.02
4254 4347 2.299326 AAAAGGAGGCTCTTGTGCAT 57.701 45.000 15.23 0.00 34.04 3.96
4397 4491 6.169094 ACTAATGTTGATGAGTCTTGACTGG 58.831 40.000 8.11 0.00 0.00 4.00
4438 4532 8.029642 ACTTTATAGTCACATGTGCTTGTTAC 57.970 34.615 21.38 12.53 0.00 2.50
4506 4600 6.743627 TGTTACTTTAGCTTGAAAACAACGTG 59.256 34.615 0.00 0.00 0.00 4.49
4512 4606 7.485418 TTAGCTTGAAAACAACGTGATCTTA 57.515 32.000 0.00 0.00 0.00 2.10
4513 4607 5.990408 AGCTTGAAAACAACGTGATCTTAG 58.010 37.500 0.00 0.00 0.00 2.18
4651 4745 4.129148 GCCGCCCATTCCCTCCTT 62.129 66.667 0.00 0.00 0.00 3.36
4714 4809 3.067461 TCACGCAGCAACCATTTAAGTTT 59.933 39.130 0.00 0.00 0.00 2.66
4716 4811 4.048504 ACGCAGCAACCATTTAAGTTTTC 58.951 39.130 0.00 0.00 0.00 2.29
4717 4812 4.202111 ACGCAGCAACCATTTAAGTTTTCT 60.202 37.500 0.00 0.00 0.00 2.52
4719 4814 5.569059 CGCAGCAACCATTTAAGTTTTCTAG 59.431 40.000 0.00 0.00 0.00 2.43
5403 5530 0.238289 CCAGTTGTGACGCATGGTTC 59.762 55.000 0.00 0.00 0.00 3.62
5405 5532 1.603802 CAGTTGTGACGCATGGTTCTT 59.396 47.619 0.00 0.00 0.00 2.52
5453 5586 3.373565 CCTTTGACCGCCCAAGGC 61.374 66.667 0.00 0.00 46.75 4.35
5511 5644 1.212688 TCCAAGGCCATGTACATCCTG 59.787 52.381 15.03 10.00 0.00 3.86
5514 5647 1.227102 GGCCATGTACATCCTGCCA 59.773 57.895 25.16 0.00 0.00 4.92
5515 5648 1.103398 GGCCATGTACATCCTGCCAC 61.103 60.000 25.16 8.16 0.00 5.01
5519 5652 2.356022 CCATGTACATCCTGCCACAGAA 60.356 50.000 5.07 0.00 32.44 3.02
5522 5655 2.028112 TGTACATCCTGCCACAGAAGTC 60.028 50.000 0.00 0.00 32.44 3.01
5562 5755 1.380380 GGAGGCAGGTCAATTGGGG 60.380 63.158 5.42 0.00 0.00 4.96
5585 5778 1.152756 AACAAGTTTGCGAGGGCCT 60.153 52.632 5.25 5.25 38.85 5.19
5588 5781 0.318955 CAAGTTTGCGAGGGCCTTTG 60.319 55.000 7.89 4.69 38.85 2.77
5629 5822 2.230660 GAGTGGAAGGAACCAACCAAG 58.769 52.381 9.60 0.00 41.87 3.61
5671 5868 1.611673 CCTTGCGATGAGTTGGACCTT 60.612 52.381 0.00 0.00 0.00 3.50
5702 5899 1.451927 GCTTCGGCCATCATCACCA 60.452 57.895 2.24 0.00 34.32 4.17
5703 5900 0.820891 GCTTCGGCCATCATCACCAT 60.821 55.000 2.24 0.00 34.32 3.55
5704 5901 1.683943 CTTCGGCCATCATCACCATT 58.316 50.000 2.24 0.00 0.00 3.16
5705 5902 1.335810 CTTCGGCCATCATCACCATTG 59.664 52.381 2.24 0.00 0.00 2.82
5706 5903 0.545646 TCGGCCATCATCACCATTGA 59.454 50.000 2.24 0.00 35.73 2.57
5716 5913 1.082169 CACCATTGACAACGGTGCG 60.082 57.895 19.53 0.00 43.43 5.34
5785 5982 2.294512 GGAAGGTGTGAAGCTTTGAAGG 59.705 50.000 0.00 0.00 0.00 3.46
5786 5983 3.214328 GAAGGTGTGAAGCTTTGAAGGA 58.786 45.455 0.00 0.00 0.00 3.36
5787 5984 3.515602 AGGTGTGAAGCTTTGAAGGAT 57.484 42.857 0.00 0.00 0.00 3.24
5788 5985 3.152341 AGGTGTGAAGCTTTGAAGGATG 58.848 45.455 0.00 0.00 0.00 3.51
5789 5986 3.149196 GGTGTGAAGCTTTGAAGGATGA 58.851 45.455 0.00 0.00 0.00 2.92
5790 5987 3.760684 GGTGTGAAGCTTTGAAGGATGAT 59.239 43.478 0.00 0.00 0.00 2.45
5791 5988 4.380233 GGTGTGAAGCTTTGAAGGATGATG 60.380 45.833 0.00 0.00 0.00 3.07
5792 5989 3.192001 TGTGAAGCTTTGAAGGATGATGC 59.808 43.478 0.00 0.00 0.00 3.91
5793 5990 3.442977 GTGAAGCTTTGAAGGATGATGCT 59.557 43.478 0.00 0.00 0.00 3.79
5794 5991 4.082354 GTGAAGCTTTGAAGGATGATGCTT 60.082 41.667 0.00 0.00 41.18 3.91
5795 5992 4.082408 TGAAGCTTTGAAGGATGATGCTTG 60.082 41.667 3.26 0.00 39.04 4.01
5796 5993 3.693807 AGCTTTGAAGGATGATGCTTGA 58.306 40.909 3.26 0.00 0.00 3.02
5797 5994 3.442977 AGCTTTGAAGGATGATGCTTGAC 59.557 43.478 3.26 0.00 0.00 3.18
5819 6016 2.559698 TCATCACCATTGACAACGGT 57.440 45.000 0.00 0.00 33.38 4.83
5913 6213 1.368641 TGCGTGGATTTTCAGGATCG 58.631 50.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.536917 CCCCCGCATCGCTCTGTA 61.537 66.667 0.00 0.00 0.00 2.74
13 14 1.376812 ACAAAATCTCGACCCCCGC 60.377 57.895 0.00 0.00 38.37 6.13
30 31 2.775032 CTTGCACCCATGGCTTGCAC 62.775 60.000 29.43 9.55 35.07 4.57
32 33 1.818959 TTCTTGCACCCATGGCTTGC 61.819 55.000 23.39 23.39 0.00 4.01
38 39 2.094390 CACCATCTTTCTTGCACCCATG 60.094 50.000 0.00 0.00 0.00 3.66
48 49 2.674177 CGACGCCTAACACCATCTTTCT 60.674 50.000 0.00 0.00 0.00 2.52
61 62 2.125713 CACCATGCACGACGCCTA 60.126 61.111 0.00 0.00 41.33 3.93
83 84 4.376225 AAAAAGTCGGATTCAACCCCTA 57.624 40.909 0.00 0.00 0.00 3.53
107 108 6.098838 TGCATAGTGATCATATCCAGGGATAC 59.901 42.308 10.12 0.00 39.56 2.24
108 109 6.204555 TGCATAGTGATCATATCCAGGGATA 58.795 40.000 10.31 10.31 40.80 2.59
109 110 5.034878 TGCATAGTGATCATATCCAGGGAT 58.965 41.667 6.04 6.04 38.54 3.85
110 111 4.428570 TGCATAGTGATCATATCCAGGGA 58.571 43.478 0.00 0.00 0.00 4.20
112 113 5.816258 GTCATGCATAGTGATCATATCCAGG 59.184 44.000 0.00 0.00 0.00 4.45
114 115 5.486419 AGGTCATGCATAGTGATCATATCCA 59.514 40.000 0.00 0.00 0.00 3.41
116 117 6.637657 TGAGGTCATGCATAGTGATCATATC 58.362 40.000 0.00 0.00 0.00 1.63
117 118 6.616237 TGAGGTCATGCATAGTGATCATAT 57.384 37.500 0.00 0.00 0.00 1.78
118 119 6.439692 AGATGAGGTCATGCATAGTGATCATA 59.560 38.462 0.00 0.00 36.57 2.15
119 120 4.968971 TGAGGTCATGCATAGTGATCAT 57.031 40.909 0.00 0.00 0.00 2.45
121 122 4.930405 CAGATGAGGTCATGCATAGTGATC 59.070 45.833 0.00 0.00 36.57 2.92
127 128 2.105306 CCACCAGATGAGGTCATGCATA 59.895 50.000 0.00 0.00 40.77 3.14
215 216 4.462834 GCTGGCAGGGTTTAATTTTAGACT 59.537 41.667 17.64 0.00 0.00 3.24
217 218 4.411927 TGCTGGCAGGGTTTAATTTTAGA 58.588 39.130 17.64 0.00 0.00 2.10
244 245 1.663695 TTGCTAGCAGGGCGTAATTC 58.336 50.000 18.45 0.00 0.00 2.17
250 251 0.529773 TTCGTATTGCTAGCAGGGCG 60.530 55.000 18.45 20.83 0.00 6.13
272 273 1.157870 ACACAACTCCAGCGAAACCG 61.158 55.000 0.00 0.00 0.00 4.44
274 275 0.307760 CCACACAACTCCAGCGAAAC 59.692 55.000 0.00 0.00 0.00 2.78
278 279 2.591429 TGCCACACAACTCCAGCG 60.591 61.111 0.00 0.00 0.00 5.18
279 280 2.896801 CGTGCCACACAACTCCAGC 61.897 63.158 0.00 0.00 33.40 4.85
343 345 5.801350 TCGAGGATAGCATTTGTTTTCTG 57.199 39.130 0.00 0.00 0.00 3.02
362 364 7.637132 GTCAAGAAAACGTTAACTCAATTTCGA 59.363 33.333 0.00 0.00 33.28 3.71
369 371 3.001533 GCCGTCAAGAAAACGTTAACTCA 59.998 43.478 0.00 0.00 38.44 3.41
414 417 1.334960 CGAAGCAGCGTTGAATTGGTT 60.335 47.619 2.38 0.00 35.47 3.67
417 420 1.595609 GTCGAAGCAGCGTTGAATTG 58.404 50.000 2.38 0.00 0.00 2.32
429 432 5.359716 TTTCTATATCTCTCCGTCGAAGC 57.640 43.478 0.00 0.00 0.00 3.86
430 433 9.894783 TTATTTTTCTATATCTCTCCGTCGAAG 57.105 33.333 0.00 0.00 0.00 3.79
458 462 8.079809 ACTACGGTTTATGTTTTGGAAGAAATG 58.920 33.333 0.00 0.00 0.00 2.32
459 463 8.173542 ACTACGGTTTATGTTTTGGAAGAAAT 57.826 30.769 0.00 0.00 0.00 2.17
466 470 7.131565 ACGTTAAACTACGGTTTATGTTTTGG 58.868 34.615 0.00 0.00 44.28 3.28
481 485 2.159393 CCCCATCGTCGACGTTAAACTA 60.159 50.000 34.40 16.30 40.80 2.24
486 490 2.491152 GCCCCATCGTCGACGTTA 59.509 61.111 34.40 19.34 40.80 3.18
490 494 4.446413 AACGGCCCCATCGTCGAC 62.446 66.667 5.18 5.18 40.18 4.20
496 500 0.391228 AACAAAACAACGGCCCCATC 59.609 50.000 0.00 0.00 0.00 3.51
499 503 0.812014 CCAAACAAAACAACGGCCCC 60.812 55.000 0.00 0.00 0.00 5.80
500 504 1.433053 GCCAAACAAAACAACGGCCC 61.433 55.000 0.00 0.00 33.31 5.80
507 511 3.482436 ACGAGATAGGCCAAACAAAACA 58.518 40.909 5.01 0.00 0.00 2.83
529 544 1.291033 TCCCTCTTCTAGCTAAGGGCA 59.709 52.381 19.74 9.01 46.84 5.36
535 550 3.928005 TTCGACTCCCTCTTCTAGCTA 57.072 47.619 0.00 0.00 0.00 3.32
546 561 5.588648 TGGAATTTGATTGTATTCGACTCCC 59.411 40.000 0.00 0.00 32.73 4.30
575 607 5.219633 AGTTCAACGCAATCGCTTAATTTT 58.780 33.333 0.00 0.00 39.84 1.82
628 660 8.574251 TCGTGGGAATTCATATTTATAATGGG 57.426 34.615 7.93 0.00 0.00 4.00
672 704 8.200792 TGCATTACCGCCAGAATTTAATTTATT 58.799 29.630 0.00 0.00 0.00 1.40
684 716 1.823470 GCCATGCATTACCGCCAGA 60.823 57.895 0.00 0.00 0.00 3.86
710 750 3.814005 ACATAAACCTACGGCTACTGG 57.186 47.619 0.00 0.00 0.00 4.00
739 786 1.112113 TAGCTAGCGGAAGGTCAAGG 58.888 55.000 9.55 0.00 44.26 3.61
790 838 2.685017 ATGCCGCTCTGGAGGACA 60.685 61.111 0.00 0.00 42.00 4.02
791 839 2.107953 GATGCCGCTCTGGAGGAC 59.892 66.667 0.00 0.00 42.00 3.85
793 841 2.108566 CAGATGCCGCTCTGGAGG 59.891 66.667 10.37 0.00 42.00 4.30
810 858 1.762957 TGGCTGGCTATGAGTTCTACC 59.237 52.381 2.00 0.00 0.00 3.18
812 860 1.414181 GCTGGCTGGCTATGAGTTCTA 59.586 52.381 2.00 0.00 0.00 2.10
813 861 0.179936 GCTGGCTGGCTATGAGTTCT 59.820 55.000 2.00 0.00 0.00 3.01
814 862 0.817229 GGCTGGCTGGCTATGAGTTC 60.817 60.000 10.74 0.00 38.32 3.01
815 863 1.225704 GGCTGGCTGGCTATGAGTT 59.774 57.895 10.74 0.00 38.32 3.01
858 907 1.228154 GCTTTTGACCGGTCAGGGT 60.228 57.895 34.25 0.00 46.96 4.34
859 908 1.228124 TGCTTTTGACCGGTCAGGG 60.228 57.895 34.25 26.78 46.96 4.45
861 910 1.569493 CGTGCTTTTGACCGGTCAG 59.431 57.895 34.25 24.76 41.13 3.51
1020 1069 3.731728 TCCAGCACCATGGGCTCC 61.732 66.667 20.88 5.16 40.23 4.70
1021 1070 2.439156 GTCCAGCACCATGGGCTC 60.439 66.667 20.88 9.73 41.97 4.70
1022 1071 4.415150 CGTCCAGCACCATGGGCT 62.415 66.667 18.09 18.48 43.11 5.19
1495 1544 2.411748 GACATGAAATCGAGAACACGCA 59.588 45.455 0.00 0.00 0.00 5.24
1511 1560 1.078709 ATTTGACCAGACGCGACATG 58.921 50.000 15.93 8.14 0.00 3.21
1556 1627 2.426522 GCACTAACAGCACATGAAGGA 58.573 47.619 0.00 0.00 0.00 3.36
1562 1633 1.275291 ACTACGGCACTAACAGCACAT 59.725 47.619 0.00 0.00 0.00 3.21
1625 1696 7.991460 AGTAGAACACTGGTTAAAGCTAAACTT 59.009 33.333 10.67 0.00 37.54 2.66
1626 1697 7.506971 AGTAGAACACTGGTTAAAGCTAAACT 58.493 34.615 10.67 0.00 37.36 2.66
1670 1741 1.464722 CCACCAGACCACCCCAAAT 59.535 57.895 0.00 0.00 0.00 2.32
1713 1784 1.289694 CCCGCAAAATCAGCTGCAA 59.710 52.632 9.47 0.00 38.52 4.08
1755 1826 5.289193 CCAAATCGGTTGAACATATGCAAAG 59.711 40.000 1.58 0.00 39.87 2.77
1782 1855 0.453282 CACACAATTTCTCTGCCGCG 60.453 55.000 0.00 0.00 0.00 6.46
1797 1870 2.202932 ATCGAGCGATGGCCACAC 60.203 61.111 8.16 4.31 41.24 3.82
2080 2157 3.099905 AGCCTACATGTGAGAAGCAGTA 58.900 45.455 9.11 0.00 0.00 2.74
2128 2205 1.246056 GCAGCACCTTCTTGATGGCA 61.246 55.000 0.00 0.00 33.33 4.92
2245 2322 2.501723 GTTCAGGAACAGCTCATCCCTA 59.498 50.000 10.12 0.00 40.84 3.53
2317 2394 2.045708 CCGCTGGTTGGCATTGCTA 61.046 57.895 8.82 0.00 0.00 3.49
2375 2452 4.508861 GCAAATGCAATATGATGGTTCACC 59.491 41.667 0.00 0.00 41.59 4.02
2444 2521 4.202151 CCCTCTAAAAAGCTGCAAACAAGT 60.202 41.667 1.02 0.00 0.00 3.16
2540 2621 4.799678 ACAAGTAGAGATCGTGTTCACAG 58.200 43.478 3.87 0.00 0.00 3.66
2707 2790 6.018016 AGCAATTCAAAACTAAATGCAACACC 60.018 34.615 0.00 0.00 0.00 4.16
2902 2985 2.036958 TGTCCAGTTCCACTGTTGTG 57.963 50.000 3.30 0.00 44.50 3.33
3192 3276 4.215908 CATGGGGTTAGAGCTAGAGTGTA 58.784 47.826 0.00 0.00 0.00 2.90
3462 3548 4.148128 ACACACAGGATGATCAGAATCC 57.852 45.455 5.80 5.80 43.47 3.01
3478 3564 3.315191 AGGCTGACAAATACACAACACAC 59.685 43.478 0.00 0.00 0.00 3.82
3619 3706 5.105635 CCAAGAACCTGCAATAACATCACAT 60.106 40.000 0.00 0.00 0.00 3.21
3790 3877 4.225942 TGCCAGAAGATGTGGACTTAAGAT 59.774 41.667 10.09 0.00 37.23 2.40
3792 3879 3.942829 TGCCAGAAGATGTGGACTTAAG 58.057 45.455 0.00 0.00 37.23 1.85
3819 3906 5.047519 TGGTGTAGAGAAGCTGGTAACTAAC 60.048 44.000 0.00 0.00 37.61 2.34
3875 3966 0.685097 AGCAGAGCAACCCGTTAGAA 59.315 50.000 0.00 0.00 0.00 2.10
3876 3967 0.685097 AAGCAGAGCAACCCGTTAGA 59.315 50.000 0.00 0.00 0.00 2.10
3892 3983 6.428159 TGTGGAAAATCTAGTGAAGAGAAAGC 59.572 38.462 0.00 0.00 37.74 3.51
3898 3989 6.270000 TCCTCTTGTGGAAAATCTAGTGAAGA 59.730 38.462 0.00 0.00 33.97 2.87
3899 3990 6.467677 TCCTCTTGTGGAAAATCTAGTGAAG 58.532 40.000 0.00 0.00 32.39 3.02
3903 3994 5.189180 GCATCCTCTTGTGGAAAATCTAGT 58.811 41.667 0.00 0.00 39.85 2.57
4003 4094 1.269936 GCAATCACAAAGCCAAGCACT 60.270 47.619 0.00 0.00 0.00 4.40
4068 4160 9.730705 AGAGGTAAAATAACTTTTAGTACACCC 57.269 33.333 0.00 0.00 37.47 4.61
4077 4169 8.936070 AAAACGCAAGAGGTAAAATAACTTTT 57.064 26.923 0.00 0.00 43.62 2.27
4107 4199 7.470935 ACCATGTACTAGTATAACACACACA 57.529 36.000 5.75 0.00 0.00 3.72
4108 4200 8.767478 AAACCATGTACTAGTATAACACACAC 57.233 34.615 5.75 0.00 0.00 3.82
4249 4342 3.674997 TCCTACTTCCACAAAGATGCAC 58.325 45.455 0.00 0.00 38.44 4.57
4397 4491 7.498443 ACTATAAAGTTGCACCCACTATCTAC 58.502 38.462 0.00 0.00 29.00 2.59
4506 4600 9.155975 TGAACAGATTGCTAGTTTTCTAAGATC 57.844 33.333 0.00 0.00 31.45 2.75
4512 4606 7.573968 AAACTGAACAGATTGCTAGTTTTCT 57.426 32.000 8.87 0.00 35.52 2.52
4513 4607 9.730420 TTTAAACTGAACAGATTGCTAGTTTTC 57.270 29.630 8.87 0.00 38.72 2.29
4695 4790 4.298332 AGAAAACTTAAATGGTTGCTGCG 58.702 39.130 0.00 0.00 0.00 5.18
4725 4820 6.944096 TGAGACATGTGATCTTCTGATCTTT 58.056 36.000 1.15 0.00 46.84 2.52
4727 4822 6.734502 ATGAGACATGTGATCTTCTGATCT 57.265 37.500 1.15 0.00 46.84 2.75
4728 4823 6.985059 TGAATGAGACATGTGATCTTCTGATC 59.015 38.462 1.15 0.00 46.89 2.92
4729 4824 6.885922 TGAATGAGACATGTGATCTTCTGAT 58.114 36.000 1.15 0.00 35.26 2.90
4730 4825 6.290294 TGAATGAGACATGTGATCTTCTGA 57.710 37.500 1.15 0.00 0.00 3.27
4732 4827 6.944096 TCTTGAATGAGACATGTGATCTTCT 58.056 36.000 1.15 0.00 0.00 2.85
4761 4867 8.494433 ACAGCCTTCCTAATTATTGAACTGATA 58.506 33.333 15.24 0.00 0.00 2.15
5403 5530 1.068333 CACATTTCCCGACTTGCCAAG 60.068 52.381 2.11 2.11 0.00 3.61
5405 5532 1.523154 GCACATTTCCCGACTTGCCA 61.523 55.000 0.00 0.00 0.00 4.92
5472 5605 1.265454 AAGGGGGAGATGGTCACGAC 61.265 60.000 0.00 0.00 0.00 4.34
5473 5606 0.976073 GAAGGGGGAGATGGTCACGA 60.976 60.000 0.00 0.00 0.00 4.35
5474 5607 1.522569 GAAGGGGGAGATGGTCACG 59.477 63.158 0.00 0.00 0.00 4.35
5475 5608 0.914417 TGGAAGGGGGAGATGGTCAC 60.914 60.000 0.00 0.00 0.00 3.67
5476 5609 0.178846 TTGGAAGGGGGAGATGGTCA 60.179 55.000 0.00 0.00 0.00 4.02
5479 5612 1.925888 CCTTGGAAGGGGGAGATGG 59.074 63.158 0.00 0.00 42.66 3.51
5484 5617 2.204448 ATGGCCTTGGAAGGGGGA 60.204 61.111 3.32 0.00 46.56 4.81
5511 5644 0.036952 TAGCAGCAGACTTCTGTGGC 60.037 55.000 8.04 11.05 45.45 5.01
5514 5647 5.049129 GTCAATTTTAGCAGCAGACTTCTGT 60.049 40.000 8.04 0.00 45.45 3.41
5515 5648 5.049198 TGTCAATTTTAGCAGCAGACTTCTG 60.049 40.000 1.56 1.56 46.40 3.02
5519 5652 3.187227 CGTGTCAATTTTAGCAGCAGACT 59.813 43.478 0.00 0.00 0.00 3.24
5522 5655 2.095567 AGCGTGTCAATTTTAGCAGCAG 60.096 45.455 0.00 0.00 0.00 4.24
5562 5755 1.265905 CCCTCGCAAACTTGTTGGTAC 59.734 52.381 0.00 0.00 0.00 3.34
5577 5770 1.675641 CTCAACCCAAAGGCCCTCG 60.676 63.158 0.00 0.00 36.11 4.63
5585 5778 1.631405 CAAGGCCATCTCAACCCAAA 58.369 50.000 5.01 0.00 0.00 3.28
5588 5781 1.000396 AGCAAGGCCATCTCAACCC 60.000 57.895 5.01 0.00 0.00 4.11
5629 5822 0.542805 TACCCGTTCCAACCCATAGC 59.457 55.000 0.00 0.00 0.00 2.97
5641 5838 0.108329 CATCGCAAGGACTACCCGTT 60.108 55.000 0.00 0.00 40.87 4.44
5671 5868 3.133901 TGGCCGAAGCATAGAATAAGTCA 59.866 43.478 0.00 0.00 42.56 3.41
5702 5899 1.841663 GCTCACGCACCGTTGTCAAT 61.842 55.000 0.00 0.00 38.32 2.57
5703 5900 2.530497 GCTCACGCACCGTTGTCAA 61.530 57.895 0.00 0.00 38.32 3.18
5704 5901 2.964925 GCTCACGCACCGTTGTCA 60.965 61.111 0.00 0.00 38.32 3.58
5705 5902 3.712881 GGCTCACGCACCGTTGTC 61.713 66.667 0.00 0.00 38.32 3.18
5724 5921 7.926018 GTGAATGAAACTTGTAGTCCCAAAAAT 59.074 33.333 0.00 0.00 0.00 1.82
5761 5958 3.565307 TCAAAGCTTCACACCTTCCATT 58.435 40.909 0.00 0.00 0.00 3.16
5762 5959 3.228188 TCAAAGCTTCACACCTTCCAT 57.772 42.857 0.00 0.00 0.00 3.41
5786 5983 3.220110 GGTGATGATGGTCAAGCATCAT 58.780 45.455 28.43 28.43 46.82 2.45
5787 5984 2.026075 TGGTGATGATGGTCAAGCATCA 60.026 45.455 22.77 22.77 44.25 3.07
5788 5985 2.646930 TGGTGATGATGGTCAAGCATC 58.353 47.619 13.83 13.83 39.02 3.91
5789 5986 2.812836 TGGTGATGATGGTCAAGCAT 57.187 45.000 0.00 0.00 0.00 3.79
5790 5987 2.756207 CAATGGTGATGATGGTCAAGCA 59.244 45.455 0.00 0.00 0.00 3.91
5791 5988 3.018856 TCAATGGTGATGATGGTCAAGC 58.981 45.455 0.00 0.00 0.00 4.01
5792 5989 4.011698 TGTCAATGGTGATGATGGTCAAG 58.988 43.478 0.00 0.00 35.80 3.02
5793 5990 4.031636 TGTCAATGGTGATGATGGTCAA 57.968 40.909 0.00 0.00 35.80 3.18
5794 5991 3.717452 TGTCAATGGTGATGATGGTCA 57.283 42.857 0.00 0.00 35.80 4.02
5795 5992 3.181507 CGTTGTCAATGGTGATGATGGTC 60.182 47.826 0.00 0.00 35.80 4.02
5796 5993 2.749076 CGTTGTCAATGGTGATGATGGT 59.251 45.455 0.00 0.00 35.80 3.55
5797 5994 2.097954 CCGTTGTCAATGGTGATGATGG 59.902 50.000 14.81 0.00 35.80 3.51
5819 6016 2.668212 CGAAAAGGGGCTCACGCA 60.668 61.111 0.00 0.00 38.10 5.24
5835 6032 4.062293 TGTGAATGAAACTTGTAGTCCCG 58.938 43.478 0.00 0.00 0.00 5.14
5913 6213 3.056035 ACGATTAGGTTGGTGGAGACTTC 60.056 47.826 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.