Multiple sequence alignment - TraesCS7B01G214100

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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 TraesCS7B01G214100 chr7B 100.000 3839 0 0 1 3839 392819218 392815380 0.000000e+00 7090.0
1 TraesCS7B01G214100 chr7D 96.268 3001 89 12 844 3839 393110105 393107123 0.000000e+00 4900.0
2 TraesCS7B01G214100 chr7D 88.989 663 49 10 38 690 393111298 393110650 0.000000e+00 798.0
3 TraesCS7B01G214100 chr7A 94.570 3002 110 14 860 3839 445628196 445625226 0.000000e+00 4591.0
4 TraesCS7B01G214100 chr7A 91.341 358 19 5 351 699 445642067 445641713 2.680000e-131 479.0
5 TraesCS7B01G214100 chr7A 90.476 273 20 2 65 337 445647203 445646937 4.720000e-94 355.0
6 TraesCS7B01G214100 chr6B 97.778 45 1 0 47 91 567899465 567899421 1.140000e-10 78.7
7 TraesCS7B01G214100 chr1D 97.619 42 1 0 47 88 319918665 319918624 5.320000e-09 73.1


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 TraesCS7B01G214100 chr7B 392815380 392819218 3838 True 7090 7090 100.0000 1 3839 1 chr7B.!!$R1 3838
1 TraesCS7B01G214100 chr7D 393107123 393111298 4175 True 2849 4900 92.6285 38 3839 2 chr7D.!!$R1 3801
2 TraesCS7B01G214100 chr7A 445625226 445628196 2970 True 4591 4591 94.5700 860 3839 1 chr7A.!!$R1 2979

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
167 170 0.319727 GCGAGATGAGCCAGGATCTG 60.320 60.0 6.21 0.0 0.00 2.90 F
1376 1784 0.523072 GCATGCATCCAGTTCGTTGT 59.477 50.0 14.21 0.0 0.00 3.32 F
1679 2088 0.957395 AGCATTGTCAGGCTTGTCCG 60.957 55.0 0.00 0.0 36.92 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 2523 0.542333 TTCACAGTTCCGGGACACAA 59.458 50.0 17.22 0.0 0.00 3.33 R
2587 2996 1.828979 AAACACACAAACGACCCACT 58.171 45.0 0.00 0.0 0.00 4.00 R
3524 3951 0.043940 AGGATCCAGCAAGAGGAGGT 59.956 55.0 15.82 0.0 38.83 3.85 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
24 25 6.904498 TGTTTATTTTGTGAGGATTGGTACG 58.096 36.000 0.00 0.00 0.00 3.67
25 26 6.072397 TGTTTATTTTGTGAGGATTGGTACGG 60.072 38.462 0.00 0.00 0.00 4.02
26 27 3.495434 TTTTGTGAGGATTGGTACGGT 57.505 42.857 0.00 0.00 0.00 4.83
27 28 2.754946 TTGTGAGGATTGGTACGGTC 57.245 50.000 0.00 0.00 0.00 4.79
28 29 1.634960 TGTGAGGATTGGTACGGTCA 58.365 50.000 0.00 0.00 0.00 4.02
29 30 1.972075 TGTGAGGATTGGTACGGTCAA 59.028 47.619 0.00 0.00 0.00 3.18
30 31 2.369203 TGTGAGGATTGGTACGGTCAAA 59.631 45.455 0.00 0.00 0.00 2.69
31 32 3.181453 TGTGAGGATTGGTACGGTCAAAA 60.181 43.478 0.00 0.00 0.00 2.44
32 33 4.007659 GTGAGGATTGGTACGGTCAAAAT 58.992 43.478 0.00 0.00 0.00 1.82
33 34 4.457949 GTGAGGATTGGTACGGTCAAAATT 59.542 41.667 0.00 0.00 0.00 1.82
34 35 4.457603 TGAGGATTGGTACGGTCAAAATTG 59.542 41.667 0.00 0.00 0.00 2.32
35 36 4.403734 AGGATTGGTACGGTCAAAATTGT 58.596 39.130 0.00 0.00 0.00 2.71
36 37 5.562635 AGGATTGGTACGGTCAAAATTGTA 58.437 37.500 0.00 0.00 0.00 2.41
44 45 8.627403 TGGTACGGTCAAAATTGTATGTAAAAA 58.373 29.630 0.00 0.00 0.00 1.94
57 58 5.532779 TGTATGTAAAAAGCCACATGACACA 59.467 36.000 0.00 0.00 36.13 3.72
61 62 4.405116 AAAAAGCCACATGACACATGTT 57.595 36.364 13.58 0.00 0.00 2.71
62 63 3.374220 AAAGCCACATGACACATGTTG 57.626 42.857 13.58 11.79 0.00 3.33
66 69 3.503363 AGCCACATGACACATGTTGTAAG 59.497 43.478 13.58 4.04 39.17 2.34
67 70 3.825308 CCACATGACACATGTTGTAAGC 58.175 45.455 13.58 0.00 39.17 3.09
71 74 5.921976 CACATGACACATGTTGTAAGCAATT 59.078 36.000 13.58 0.00 39.17 2.32
126 129 1.719709 GCAAGGGCGAACGGATAAC 59.280 57.895 0.00 0.00 0.00 1.89
167 170 0.319727 GCGAGATGAGCCAGGATCTG 60.320 60.000 6.21 0.00 0.00 2.90
217 220 1.504359 CGAAAAGTACCGCACCTTCA 58.496 50.000 0.00 0.00 0.00 3.02
225 228 0.670546 ACCGCACCTTCATTCTGTCG 60.671 55.000 0.00 0.00 0.00 4.35
250 253 2.425578 TCGTTGTCGAATGCACAGTA 57.574 45.000 0.00 0.00 43.34 2.74
259 262 2.404215 GAATGCACAGTAGTCACACGT 58.596 47.619 0.00 0.00 0.00 4.49
281 291 4.394439 TTTTTCCCCTGCAACAAACTAC 57.606 40.909 0.00 0.00 0.00 2.73
282 292 1.600023 TTCCCCTGCAACAAACTACG 58.400 50.000 0.00 0.00 0.00 3.51
308 318 1.980765 AGTTTCAGTCTCATCCAGCCA 59.019 47.619 0.00 0.00 0.00 4.75
313 323 0.844660 AGTCTCATCCAGCCATGCAT 59.155 50.000 0.00 0.00 0.00 3.96
343 353 1.059098 AGACATGGTGCCTGTCAGAA 58.941 50.000 16.93 0.00 44.37 3.02
346 356 1.421268 ACATGGTGCCTGTCAGAAGAA 59.579 47.619 0.00 0.00 0.00 2.52
390 400 5.784906 AGGGGAAATGAACATAACCAAACAT 59.215 36.000 0.00 0.00 0.00 2.71
468 482 2.159421 TCTCTCGTTGCCGTCAATAGTC 60.159 50.000 0.00 0.00 34.29 2.59
479 493 2.983136 CGTCAATAGTCATCGCCTGATC 59.017 50.000 0.00 0.00 35.97 2.92
498 512 6.999272 CCTGATCTAGGTAGTACTGTACATGT 59.001 42.308 19.27 2.69 42.00 3.21
511 525 8.904834 AGTACTGTACATGTTCTCTTTATCGAT 58.095 33.333 19.27 2.16 0.00 3.59
546 560 1.084370 ACGATTTGCAGCCGCTAGAC 61.084 55.000 0.00 0.00 39.64 2.59
570 584 7.219322 ACATGCATAATATGACAGCTACAGAA 58.781 34.615 4.14 0.00 0.00 3.02
581 595 3.834813 ACAGCTACAGAAGAATGTCCTGA 59.165 43.478 11.84 0.00 36.72 3.86
598 613 5.300034 TGTCCTGAAACTTCTACAGTTACGA 59.700 40.000 0.00 0.00 45.77 3.43
602 617 7.929785 TCCTGAAACTTCTACAGTTACGATTTT 59.070 33.333 0.00 0.00 45.77 1.82
603 618 8.009974 CCTGAAACTTCTACAGTTACGATTTTG 58.990 37.037 0.00 0.00 45.77 2.44
604 619 8.428186 TGAAACTTCTACAGTTACGATTTTGT 57.572 30.769 0.00 0.00 45.77 2.83
605 620 9.531942 TGAAACTTCTACAGTTACGATTTTGTA 57.468 29.630 0.00 0.00 45.77 2.41
606 621 9.789029 GAAACTTCTACAGTTACGATTTTGTAC 57.211 33.333 0.00 0.00 45.77 2.90
607 622 7.558435 ACTTCTACAGTTACGATTTTGTACG 57.442 36.000 0.00 0.00 27.32 3.67
628 643 2.875087 ACTACGTGTGCAGTGTACAA 57.125 45.000 16.05 0.00 0.00 2.41
629 644 2.739292 ACTACGTGTGCAGTGTACAAG 58.261 47.619 21.82 21.82 34.40 3.16
630 645 2.100252 ACTACGTGTGCAGTGTACAAGT 59.900 45.455 28.84 28.84 42.07 3.16
653 668 2.244695 AGAACACTCGATGGTGGTGTA 58.755 47.619 7.70 0.00 42.37 2.90
655 670 3.260884 AGAACACTCGATGGTGGTGTATT 59.739 43.478 7.70 0.00 42.37 1.89
656 671 3.247006 ACACTCGATGGTGGTGTATTC 57.753 47.619 5.66 0.00 41.56 1.75
657 672 2.193447 CACTCGATGGTGGTGTATTCG 58.807 52.381 0.00 0.00 33.95 3.34
658 673 2.097036 ACTCGATGGTGGTGTATTCGA 58.903 47.619 0.00 0.00 0.00 3.71
659 674 2.732366 CTCGATGGTGGTGTATTCGAG 58.268 52.381 6.29 6.29 39.32 4.04
664 679 1.200716 TGGTGGTGTATTCGAGTCGAC 59.799 52.381 16.28 7.70 34.89 4.20
686 701 4.840271 CTGGACTCCCGGTTAGTTATTTT 58.160 43.478 8.02 0.00 34.01 1.82
690 705 3.009805 ACTCCCGGTTAGTTATTTTGGCT 59.990 43.478 0.00 0.00 0.00 4.75
692 707 3.009253 TCCCGGTTAGTTATTTTGGCTGA 59.991 43.478 0.00 0.00 0.00 4.26
694 709 4.401202 CCCGGTTAGTTATTTTGGCTGATT 59.599 41.667 0.00 0.00 0.00 2.57
695 710 5.449999 CCCGGTTAGTTATTTTGGCTGATTC 60.450 44.000 0.00 0.00 0.00 2.52
696 711 5.357032 CCGGTTAGTTATTTTGGCTGATTCT 59.643 40.000 0.00 0.00 0.00 2.40
736 802 3.546002 TTCTTTTTACAATCCGTGGCG 57.454 42.857 0.00 0.00 0.00 5.69
761 827 6.794158 GCAATACGATGCTCAATATTCTGTTC 59.206 38.462 0.00 0.00 43.06 3.18
762 828 7.307632 GCAATACGATGCTCAATATTCTGTTCT 60.308 37.037 0.00 0.00 43.06 3.01
764 830 5.423015 ACGATGCTCAATATTCTGTTCTGT 58.577 37.500 0.00 0.00 0.00 3.41
769 835 4.201891 GCTCAATATTCTGTTCTGTGCTGG 60.202 45.833 0.00 0.00 0.00 4.85
777 843 1.345741 TGTTCTGTGCTGGGAGAGAAG 59.654 52.381 2.30 0.00 0.00 2.85
805 871 1.000145 GACGGATGAGGCGTTTTCTC 59.000 55.000 0.00 0.00 0.00 2.87
812 1184 4.156739 GGATGAGGCGTTTTCTCAGAAAAT 59.843 41.667 15.67 0.00 43.45 1.82
822 1194 7.304066 GTTTTCTCAGAAAATAAAACGGACG 57.696 36.000 15.67 0.00 33.61 4.79
824 1196 5.585500 TCTCAGAAAATAAAACGGACGTG 57.415 39.130 0.00 0.00 0.00 4.49
826 1198 4.378774 TCAGAAAATAAAACGGACGTGGA 58.621 39.130 0.00 0.00 0.00 4.02
827 1199 4.449743 TCAGAAAATAAAACGGACGTGGAG 59.550 41.667 0.00 0.00 0.00 3.86
842 1214 2.434702 CGTGGAGGCCTAATACCTTCTT 59.565 50.000 4.42 0.00 37.77 2.52
911 1317 1.352083 TCTCCAAGTCCACTCAAGGG 58.648 55.000 0.00 0.00 0.00 3.95
934 1340 2.585698 CCGGCCCGGCTTAACTAA 59.414 61.111 10.42 0.00 41.17 2.24
1102 1510 2.960170 CGACGAGGTCTCCCGTTT 59.040 61.111 0.00 0.00 39.30 3.60
1225 1633 1.930251 CTCCTTCTCTCAGGTCCACA 58.070 55.000 0.00 0.00 35.15 4.17
1376 1784 0.523072 GCATGCATCCAGTTCGTTGT 59.477 50.000 14.21 0.00 0.00 3.32
1413 1821 2.586258 ATGCCTAGTCGTGCTAGTTG 57.414 50.000 12.97 3.73 44.37 3.16
1418 1826 3.067742 GCCTAGTCGTGCTAGTTGGATTA 59.932 47.826 12.97 0.00 44.37 1.75
1469 1877 6.774170 ACTATCTAATGCTGGAATTGCAATGA 59.226 34.615 13.82 1.88 44.01 2.57
1478 1886 5.410439 GCTGGAATTGCAATGATTTGTTTCT 59.590 36.000 13.82 0.00 35.17 2.52
1551 1960 2.123342 GCAATTTGTTTAGCGTGTGCA 58.877 42.857 0.00 0.00 46.23 4.57
1560 1969 4.092821 TGTTTAGCGTGTGCACATAAGATC 59.907 41.667 24.69 7.86 46.23 2.75
1613 2022 4.965762 GTGTCGTAAAGCTGTTGGTTTTAC 59.034 41.667 0.00 0.00 43.44 2.01
1679 2088 0.957395 AGCATTGTCAGGCTTGTCCG 60.957 55.000 0.00 0.00 36.92 4.79
1692 2101 5.236478 CAGGCTTGTCCGTGGTAAATTATAG 59.764 44.000 0.00 0.00 40.77 1.31
1693 2102 5.104652 AGGCTTGTCCGTGGTAAATTATAGT 60.105 40.000 0.00 0.00 40.77 2.12
1727 2136 3.533606 TTTCTGTCTCTCTGCCTATGC 57.466 47.619 0.00 0.00 38.26 3.14
1923 2332 2.727123 TGGAGAAGACAAGGTTGCAA 57.273 45.000 0.00 0.00 0.00 4.08
1940 2349 6.070309 AGGTTGCAAAATTATTGGGCTCATTA 60.070 34.615 0.00 0.00 0.00 1.90
1943 2352 9.323985 GTTGCAAAATTATTGGGCTCATTATTA 57.676 29.630 0.00 0.00 0.00 0.98
2009 2418 7.284489 TCCAAAATTCACCCTCGGAATATTTAG 59.716 37.037 0.00 0.00 34.02 1.85
2121 2530 7.651304 TGTGTAATGATGAACAAAATTGTGTCC 59.349 33.333 0.63 0.00 41.31 4.02
2123 2532 4.235939 TGATGAACAAAATTGTGTCCCG 57.764 40.909 0.63 0.00 41.31 5.14
2463 2872 9.314501 GACTCGTTCACAACTATTGTTTAATTC 57.685 33.333 0.00 0.00 43.23 2.17
2510 2919 4.083696 CCGCAGTTCCTTAACGTAATGTTT 60.084 41.667 0.00 0.00 42.09 2.83
2516 2925 9.719279 CAGTTCCTTAACGTAATGTTTGTTTTA 57.281 29.630 0.00 0.00 42.09 1.52
2551 2960 7.867921 TGAATCTTAACACTGGGTGGTATTAT 58.132 34.615 2.75 0.00 35.54 1.28
2587 2996 2.169561 TCCAGCCTTGCGTGTATATTGA 59.830 45.455 0.00 0.00 0.00 2.57
2632 3041 6.778834 AATTCATCTTATGTGTGCCATTCA 57.221 33.333 0.00 0.00 34.86 2.57
2669 3078 4.082245 CGCCTACAAATTGAAAAGGTCCAT 60.082 41.667 0.00 0.00 0.00 3.41
2683 3092 4.927267 AGGTCCATGTCAAAATCCTACA 57.073 40.909 0.00 0.00 0.00 2.74
2903 3317 7.405292 TCAGGATGGATCTTGTTTATCTGTTT 58.595 34.615 0.00 0.00 35.61 2.83
2967 3381 2.116827 TGTTTGGTGACTCGGTGTTT 57.883 45.000 0.00 0.00 0.00 2.83
2992 3406 4.322273 GGTGCGTTCTTTAACTAGTAGGGT 60.322 45.833 0.00 0.00 33.15 4.34
2999 3413 7.448420 GTTCTTTAACTAGTAGGGTTTCCTGT 58.552 38.462 0.00 0.00 36.99 4.00
3017 3431 3.305608 CCTGTTGGCTGAAATGTCCTTTC 60.306 47.826 0.00 0.00 43.05 2.62
3086 3500 7.780008 TCGTTCTTCATGAAGACAAAAGTTA 57.220 32.000 32.80 16.20 46.13 2.24
3170 3584 0.325933 TCTCATGTTGACAGGCCAGG 59.674 55.000 5.01 0.00 0.00 4.45
3172 3586 0.478072 TCATGTTGACAGGCCAGGTT 59.522 50.000 5.01 0.00 0.00 3.50
3173 3587 1.702401 TCATGTTGACAGGCCAGGTTA 59.298 47.619 5.01 0.00 0.00 2.85
3193 3607 3.206211 TTTTTCTGCCGGCTTGCCG 62.206 57.895 29.70 25.17 0.00 5.69
3247 3661 3.568538 GCAGACTGCAACAGGTTTATTG 58.431 45.455 22.62 0.00 44.26 1.90
3299 3713 8.044908 GTCCTACATAATTACCTGTTCCTTTGA 58.955 37.037 0.00 0.00 0.00 2.69
3450 3864 0.965439 TGCCATTTGCCAACTACCAC 59.035 50.000 0.00 0.00 40.16 4.16
3524 3951 1.644509 TCTCCTTCACTTGCTGCCTA 58.355 50.000 0.00 0.00 0.00 3.93
3806 4233 2.639327 GGCTGGCATGGCGTTCTTT 61.639 57.895 15.27 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.072397 CCGTACCAATCCTCACAAAATAAACA 60.072 38.462 0.00 0.00 0.00 2.83
1 2 6.072342 ACCGTACCAATCCTCACAAAATAAAC 60.072 38.462 0.00 0.00 0.00 2.01
2 3 6.005198 ACCGTACCAATCCTCACAAAATAAA 58.995 36.000 0.00 0.00 0.00 1.40
3 4 5.562635 ACCGTACCAATCCTCACAAAATAA 58.437 37.500 0.00 0.00 0.00 1.40
4 5 5.168647 ACCGTACCAATCCTCACAAAATA 57.831 39.130 0.00 0.00 0.00 1.40
5 6 4.007659 GACCGTACCAATCCTCACAAAAT 58.992 43.478 0.00 0.00 0.00 1.82
6 7 3.181453 TGACCGTACCAATCCTCACAAAA 60.181 43.478 0.00 0.00 0.00 2.44
7 8 2.369203 TGACCGTACCAATCCTCACAAA 59.631 45.455 0.00 0.00 0.00 2.83
8 9 1.972075 TGACCGTACCAATCCTCACAA 59.028 47.619 0.00 0.00 0.00 3.33
9 10 1.634960 TGACCGTACCAATCCTCACA 58.365 50.000 0.00 0.00 0.00 3.58
10 11 2.754946 TTGACCGTACCAATCCTCAC 57.245 50.000 0.00 0.00 0.00 3.51
11 12 3.773418 TTTTGACCGTACCAATCCTCA 57.227 42.857 0.00 0.00 0.00 3.86
12 13 4.457949 ACAATTTTGACCGTACCAATCCTC 59.542 41.667 0.00 0.00 0.00 3.71
13 14 4.403734 ACAATTTTGACCGTACCAATCCT 58.596 39.130 0.00 0.00 0.00 3.24
14 15 4.776795 ACAATTTTGACCGTACCAATCC 57.223 40.909 0.00 0.00 0.00 3.01
15 16 6.848451 ACATACAATTTTGACCGTACCAATC 58.152 36.000 0.00 0.00 0.00 2.67
16 17 6.827586 ACATACAATTTTGACCGTACCAAT 57.172 33.333 0.00 0.00 0.00 3.16
17 18 7.741027 TTACATACAATTTTGACCGTACCAA 57.259 32.000 0.00 0.00 0.00 3.67
18 19 7.741027 TTTACATACAATTTTGACCGTACCA 57.259 32.000 0.00 0.00 0.00 3.25
19 20 9.120422 CTTTTTACATACAATTTTGACCGTACC 57.880 33.333 0.00 0.00 0.00 3.34
20 21 8.632551 GCTTTTTACATACAATTTTGACCGTAC 58.367 33.333 0.00 0.00 0.00 3.67
21 22 7.808856 GGCTTTTTACATACAATTTTGACCGTA 59.191 33.333 0.00 0.00 0.00 4.02
22 23 6.643360 GGCTTTTTACATACAATTTTGACCGT 59.357 34.615 0.00 0.00 0.00 4.83
23 24 6.642950 TGGCTTTTTACATACAATTTTGACCG 59.357 34.615 0.00 0.00 0.00 4.79
24 25 7.439655 TGTGGCTTTTTACATACAATTTTGACC 59.560 33.333 0.00 0.00 0.00 4.02
25 26 8.359060 TGTGGCTTTTTACATACAATTTTGAC 57.641 30.769 0.00 0.00 0.00 3.18
26 27 8.986847 CATGTGGCTTTTTACATACAATTTTGA 58.013 29.630 0.00 0.00 35.86 2.69
27 28 8.986847 TCATGTGGCTTTTTACATACAATTTTG 58.013 29.630 0.00 0.00 35.86 2.44
28 29 8.987890 GTCATGTGGCTTTTTACATACAATTTT 58.012 29.630 0.00 0.00 35.86 1.82
29 30 8.147058 TGTCATGTGGCTTTTTACATACAATTT 58.853 29.630 0.00 0.00 35.86 1.82
30 31 7.598493 GTGTCATGTGGCTTTTTACATACAATT 59.402 33.333 0.00 0.00 35.86 2.32
31 32 7.090173 GTGTCATGTGGCTTTTTACATACAAT 58.910 34.615 0.00 0.00 35.86 2.71
32 33 6.039829 TGTGTCATGTGGCTTTTTACATACAA 59.960 34.615 0.00 0.00 35.86 2.41
33 34 5.532779 TGTGTCATGTGGCTTTTTACATACA 59.467 36.000 0.00 0.00 35.86 2.29
34 35 6.007936 TGTGTCATGTGGCTTTTTACATAC 57.992 37.500 0.00 0.00 35.86 2.39
35 36 6.208402 ACATGTGTCATGTGGCTTTTTACATA 59.792 34.615 13.47 0.00 35.86 2.29
36 37 5.010922 ACATGTGTCATGTGGCTTTTTACAT 59.989 36.000 13.47 0.00 37.99 2.29
44 45 1.985473 ACAACATGTGTCATGTGGCT 58.015 45.000 14.68 0.00 34.38 4.75
87 90 7.821846 CCTTGCTCTCTCTTTTACATCTAACTT 59.178 37.037 0.00 0.00 0.00 2.66
88 91 7.327214 CCTTGCTCTCTCTTTTACATCTAACT 58.673 38.462 0.00 0.00 0.00 2.24
89 92 6.536941 CCCTTGCTCTCTCTTTTACATCTAAC 59.463 42.308 0.00 0.00 0.00 2.34
90 93 6.644347 CCCTTGCTCTCTCTTTTACATCTAA 58.356 40.000 0.00 0.00 0.00 2.10
91 94 5.395768 GCCCTTGCTCTCTCTTTTACATCTA 60.396 44.000 0.00 0.00 33.53 1.98
92 95 4.625083 GCCCTTGCTCTCTCTTTTACATCT 60.625 45.833 0.00 0.00 33.53 2.90
93 96 3.625313 GCCCTTGCTCTCTCTTTTACATC 59.375 47.826 0.00 0.00 33.53 3.06
94 97 3.615155 GCCCTTGCTCTCTCTTTTACAT 58.385 45.455 0.00 0.00 33.53 2.29
126 129 2.546645 ATTGCGAAATGGGTGCTGCG 62.547 55.000 0.00 0.00 0.00 5.18
167 170 3.600909 GCGTACGCGAACTCATTAATTCC 60.601 47.826 26.17 0.00 41.33 3.01
264 267 0.470766 ACGTAGTTTGTTGCAGGGGA 59.529 50.000 0.00 0.00 37.78 4.81
267 270 4.451096 ACTCATTACGTAGTTTGTTGCAGG 59.549 41.667 0.00 0.00 37.78 4.85
313 323 3.193267 GGCACCATGTCTTCTTGCATAAA 59.807 43.478 0.00 0.00 34.76 1.40
322 332 1.002430 TCTGACAGGCACCATGTCTTC 59.998 52.381 10.72 0.00 45.87 2.87
323 333 1.059098 TCTGACAGGCACCATGTCTT 58.941 50.000 10.72 0.00 45.87 3.01
343 353 6.189677 TCAATCGTGTTTTGACTTGTTTCT 57.810 33.333 0.00 0.00 0.00 2.52
346 356 4.202010 CCCTCAATCGTGTTTTGACTTGTT 60.202 41.667 0.00 0.00 0.00 2.83
413 427 8.499162 CCTCCAAAATCGATAACTATGATTGAC 58.501 37.037 0.00 0.00 32.91 3.18
479 493 8.508883 AAGAGAACATGTACAGTACTACCTAG 57.491 38.462 12.07 0.00 0.00 3.02
498 512 3.028850 ACGGTGGGATCGATAAAGAGAA 58.971 45.455 0.00 0.00 0.00 2.87
527 541 1.084370 GTCTAGCGGCTGCAAATCGT 61.084 55.000 21.93 0.00 46.23 3.73
529 543 1.003116 CATGTCTAGCGGCTGCAAATC 60.003 52.381 21.93 8.01 46.23 2.17
546 560 7.601508 TCTTCTGTAGCTGTCATATTATGCATG 59.398 37.037 10.16 0.00 0.00 4.06
570 584 6.426646 ACTGTAGAAGTTTCAGGACATTCT 57.573 37.500 0.00 0.00 34.57 2.40
607 622 3.272439 TGTACACTGCACACGTAGTAC 57.728 47.619 0.00 0.00 41.61 2.73
616 631 4.025979 GTGTTCTACACTTGTACACTGCAC 60.026 45.833 0.00 0.00 45.27 4.57
630 645 2.029380 CACCACCATCGAGTGTTCTACA 60.029 50.000 4.34 0.00 35.93 2.74
659 674 0.962356 TAACCGGGAGTCCAGTCGAC 60.962 60.000 12.30 7.70 42.32 4.20
664 679 4.482952 AAATAACTAACCGGGAGTCCAG 57.517 45.455 12.30 6.97 0.00 3.86
671 686 3.349022 TCAGCCAAAATAACTAACCGGG 58.651 45.455 6.32 0.00 0.00 5.73
673 688 6.436843 AGAATCAGCCAAAATAACTAACCG 57.563 37.500 0.00 0.00 0.00 4.44
686 701 6.491714 AAAGCTAGAGATAAGAATCAGCCA 57.508 37.500 0.00 0.00 31.94 4.75
713 764 4.378978 CGCCACGGATTGTAAAAAGAATGA 60.379 41.667 0.00 0.00 0.00 2.57
736 802 6.233430 ACAGAATATTGAGCATCGTATTGC 57.767 37.500 0.00 0.53 43.09 3.56
749 815 4.264253 TCCCAGCACAGAACAGAATATTG 58.736 43.478 0.00 0.00 0.00 1.90
754 820 1.345741 CTCTCCCAGCACAGAACAGAA 59.654 52.381 0.00 0.00 0.00 3.02
761 827 2.847327 TTTCTTCTCTCCCAGCACAG 57.153 50.000 0.00 0.00 0.00 3.66
762 828 3.576078 TTTTTCTTCTCTCCCAGCACA 57.424 42.857 0.00 0.00 0.00 4.57
789 855 2.386661 TCTGAGAAAACGCCTCATCC 57.613 50.000 0.00 0.00 39.62 3.51
791 857 6.817765 TTATTTTCTGAGAAAACGCCTCAT 57.182 33.333 21.31 7.58 39.62 2.90
805 871 4.378046 CCTCCACGTCCGTTTTATTTTCTG 60.378 45.833 0.00 0.00 0.00 3.02
812 1184 1.004679 GGCCTCCACGTCCGTTTTA 60.005 57.895 0.00 0.00 0.00 1.52
818 1190 0.391966 GGTATTAGGCCTCCACGTCC 59.608 60.000 9.68 1.79 0.00 4.79
819 1191 1.411041 AGGTATTAGGCCTCCACGTC 58.589 55.000 9.68 0.00 0.00 4.34
821 1193 2.040178 AGAAGGTATTAGGCCTCCACG 58.960 52.381 9.68 0.00 34.81 4.94
822 1194 5.625568 TTAAGAAGGTATTAGGCCTCCAC 57.374 43.478 9.68 5.53 34.81 4.02
824 1196 6.062749 CCTTTTAAGAAGGTATTAGGCCTCC 58.937 44.000 9.68 3.68 34.81 4.30
826 1198 5.446860 GCCTTTTAAGAAGGTATTAGGCCT 58.553 41.667 11.78 11.78 40.73 5.19
827 1199 5.769484 GCCTTTTAAGAAGGTATTAGGCC 57.231 43.478 14.16 0.00 40.73 5.19
836 1208 1.077169 ACCCAGGGCCTTTTAAGAAGG 59.923 52.381 1.32 0.00 40.39 3.46
842 1214 2.820105 GCAACTAACCCAGGGCCTTTTA 60.820 50.000 1.32 0.70 0.00 1.52
934 1340 3.371595 GGAAATGGTGTGTGGGCTACTAT 60.372 47.826 1.79 0.00 0.00 2.12
1225 1633 2.270205 CCCGCCAGCATCTTCACT 59.730 61.111 0.00 0.00 0.00 3.41
1376 1784 9.461312 ACTAGGCATTCAATTATAACAGAAACA 57.539 29.630 5.75 0.00 0.00 2.83
1413 1821 3.801698 TCATCACAAGCAGAGCTAATCC 58.198 45.455 0.00 0.00 38.25 3.01
1418 1826 3.562343 ATCATCATCACAAGCAGAGCT 57.438 42.857 0.00 0.00 42.56 4.09
1469 1877 7.731054 ACTGACTAGTCTCTCAAGAAACAAAT 58.269 34.615 23.01 0.00 31.93 2.32
1478 1886 6.007076 ACATCTCAACTGACTAGTCTCTCAA 58.993 40.000 23.01 2.10 35.69 3.02
1560 1969 8.011673 CGCACCAATGTAATGAACTAATGATAG 58.988 37.037 0.00 0.00 35.14 2.08
1613 2022 4.346418 AGAGGAGAGCCATACATAAACTGG 59.654 45.833 0.00 0.00 36.29 4.00
1727 2136 7.569226 GCTTGCCAAGTACAAAAACATAACATG 60.569 37.037 6.28 0.00 0.00 3.21
2009 2418 7.969536 TTCATATAGCAAAACTGGATAGCTC 57.030 36.000 0.00 0.00 36.80 4.09
2114 2523 0.542333 TTCACAGTTCCGGGACACAA 59.458 50.000 17.22 0.00 0.00 3.33
2121 2530 3.377172 ACTTTCAGTTTTCACAGTTCCGG 59.623 43.478 0.00 0.00 0.00 5.14
2123 2532 7.027778 ACATACTTTCAGTTTTCACAGTTCC 57.972 36.000 0.00 0.00 0.00 3.62
2463 2872 6.480320 GGTAACTCTGTTATTGCATAGAGTGG 59.520 42.308 14.61 2.71 46.61 4.00
2510 2919 8.573035 GTTAAGATTCAAGGTGTCCATAAAACA 58.427 33.333 0.00 0.00 0.00 2.83
2516 2925 5.707298 CAGTGTTAAGATTCAAGGTGTCCAT 59.293 40.000 0.00 0.00 0.00 3.41
2551 2960 2.842208 CTGGAAAACGACAAACAGCA 57.158 45.000 0.00 0.00 0.00 4.41
2587 2996 1.828979 AAACACACAAACGACCCACT 58.171 45.000 0.00 0.00 0.00 4.00
2632 3041 6.380095 TTTGTAGGCGTTTTTGTCTTGTAT 57.620 33.333 0.00 0.00 0.00 2.29
2669 3078 4.698201 TCACCACTGTAGGATTTTGACA 57.302 40.909 3.76 0.00 0.00 3.58
2683 3092 6.248433 AGGAATTGTAAACATGATCACCACT 58.752 36.000 0.00 0.00 0.00 4.00
2721 3130 6.896860 TGAATATCCCAACCAATGAAGAACAT 59.103 34.615 0.00 0.00 41.45 2.71
2903 3317 4.081185 TCGCCAAGCCGAGCATCA 62.081 61.111 0.00 0.00 33.17 3.07
2967 3381 3.756933 ACTAGTTAAAGAACGCACCCA 57.243 42.857 0.00 0.00 40.76 4.51
2992 3406 2.627699 GGACATTTCAGCCAACAGGAAA 59.372 45.455 0.00 0.00 35.27 3.13
3233 3647 8.495148 CCAAATAGAAAACAATAAACCTGTTGC 58.505 33.333 0.00 0.00 37.10 4.17
3235 3649 7.659799 GGCCAAATAGAAAACAATAAACCTGTT 59.340 33.333 0.00 0.00 38.65 3.16
3236 3650 7.158697 GGCCAAATAGAAAACAATAAACCTGT 58.841 34.615 0.00 0.00 0.00 4.00
3247 3661 4.142249 ACATAAGCCGGCCAAATAGAAAAC 60.142 41.667 26.15 0.00 0.00 2.43
3524 3951 0.043940 AGGATCCAGCAAGAGGAGGT 59.956 55.000 15.82 0.00 38.83 3.85
3806 4233 2.978824 GACGGGTAGCTGGCAAGA 59.021 61.111 0.42 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.