Multiple sequence alignment - TraesCS7A01G244500

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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 TraesCS7A01G244500 chr7A 100.000 3740 0 0 1 3740 221976732 221972993 0.000000e+00 6907.0
1 TraesCS7A01G244500 chr7D 92.532 3696 248 20 55 3740 208836222 208832545 0.000000e+00 5271.0
2 TraesCS7A01G244500 chrUn 91.155 3697 301 21 56 3738 86158423 86162107 0.000000e+00 4992.0
3 TraesCS7A01G244500 chr6D 88.563 3646 382 29 115 3740 326296872 326293242 0.000000e+00 4390.0
4 TraesCS7A01G244500 chr6D 92.754 69 3 2 1 68 284249538 284249605 8.550000e-17 99.0
5 TraesCS7A01G244500 chr6B 88.147 3535 382 26 114 3623 496412092 496415614 0.000000e+00 4172.0
6 TraesCS7A01G244500 chr6B 95.238 63 2 1 1 63 323845471 323845410 8.550000e-17 99.0
7 TraesCS7A01G244500 chr6B 96.491 57 2 0 1 57 9401315 9401371 1.110000e-15 95.3
8 TraesCS7A01G244500 chr3D 98.305 59 1 0 1 59 587955719 587955661 1.840000e-18 104.0
9 TraesCS7A01G244500 chr3D 95.312 64 1 2 1 62 201528433 201528370 2.380000e-17 100.0
10 TraesCS7A01G244500 chr3D 95.238 63 2 1 1 63 324299229 324299290 8.550000e-17 99.0
11 TraesCS7A01G244500 chr3D 91.429 70 4 2 1 69 270189098 270189030 1.110000e-15 95.3
12 TraesCS7A01G244500 chr1D 95.238 63 3 0 1 63 400517509 400517447 2.380000e-17 100.0
13 TraesCS7A01G244500 chr5B 91.429 70 4 2 1 68 327387954 327388023 1.110000e-15 95.3


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 TraesCS7A01G244500 chr7A 221972993 221976732 3739 True 6907 6907 100.000 1 3740 1 chr7A.!!$R1 3739
1 TraesCS7A01G244500 chr7D 208832545 208836222 3677 True 5271 5271 92.532 55 3740 1 chr7D.!!$R1 3685
2 TraesCS7A01G244500 chrUn 86158423 86162107 3684 False 4992 4992 91.155 56 3738 1 chrUn.!!$F1 3682
3 TraesCS7A01G244500 chr6D 326293242 326296872 3630 True 4390 4390 88.563 115 3740 1 chr6D.!!$R1 3625
4 TraesCS7A01G244500 chr6B 496412092 496415614 3522 False 4172 4172 88.147 114 3623 1 chr6B.!!$F2 3509

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
60 61 0.037303 CTTGTGGGTCATCAGGCTGT 59.963 55.0 15.27 0.00 0.00 4.40 F
63 64 0.250901 GTGGGTCATCAGGCTGTTGT 60.251 55.0 21.51 4.96 0.00 3.32 F
94 95 0.734253 CGCGTGAAGCTTCTACTGCT 60.734 55.0 26.09 0.00 45.59 4.24 F
1946 1971 0.460811 GTGCTGGCATCGATGACTCA 60.461 55.0 30.50 23.88 36.54 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1849 1.630878 GGTGAATGGGTGGAGAAGACT 59.369 52.381 0.00 0.00 0.00 3.24 R
1871 1896 2.397754 CGATGTGGATGGTGCGCAA 61.398 57.895 14.00 0.00 30.58 4.85 R
2087 2112 0.250295 CTCCAAAGGTCAGCGGTGAA 60.250 55.000 20.46 0.28 33.27 3.18 R
3655 3688 0.322975 CTGGTGGAACTGAGGGACTG 59.677 60.000 0.00 0.00 35.75 3.51 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
26 27 8.027771 ACACTCTTACTTATTGAAAGGACTACG 58.972 37.037 0.00 0.00 0.00 3.51
27 28 8.242053 CACTCTTACTTATTGAAAGGACTACGA 58.758 37.037 0.00 0.00 0.00 3.43
28 29 8.968969 ACTCTTACTTATTGAAAGGACTACGAT 58.031 33.333 0.00 0.00 0.00 3.73
29 30 9.804758 CTCTTACTTATTGAAAGGACTACGATT 57.195 33.333 0.00 0.00 0.00 3.34
30 31 9.582431 TCTTACTTATTGAAAGGACTACGATTG 57.418 33.333 0.00 0.00 0.00 2.67
31 32 9.582431 CTTACTTATTGAAAGGACTACGATTGA 57.418 33.333 0.00 0.00 0.00 2.57
33 34 8.649973 ACTTATTGAAAGGACTACGATTGATC 57.350 34.615 0.00 0.00 0.00 2.92
34 35 8.258007 ACTTATTGAAAGGACTACGATTGATCA 58.742 33.333 0.00 0.00 0.00 2.92
35 36 6.910536 ATTGAAAGGACTACGATTGATCAC 57.089 37.500 0.00 0.00 0.00 3.06
36 37 4.755411 TGAAAGGACTACGATTGATCACC 58.245 43.478 0.00 0.00 0.00 4.02
37 38 4.466370 TGAAAGGACTACGATTGATCACCT 59.534 41.667 0.00 0.00 0.00 4.00
38 39 5.655090 TGAAAGGACTACGATTGATCACCTA 59.345 40.000 0.00 0.00 0.00 3.08
39 40 6.323996 TGAAAGGACTACGATTGATCACCTAT 59.676 38.462 0.00 0.00 0.00 2.57
40 41 7.504574 TGAAAGGACTACGATTGATCACCTATA 59.495 37.037 0.00 0.00 0.00 1.31
41 42 6.821031 AGGACTACGATTGATCACCTATAC 57.179 41.667 0.00 0.00 0.00 1.47
42 43 6.544650 AGGACTACGATTGATCACCTATACT 58.455 40.000 0.00 0.00 0.00 2.12
43 44 7.005296 AGGACTACGATTGATCACCTATACTT 58.995 38.462 0.00 0.00 0.00 2.24
44 45 7.040340 AGGACTACGATTGATCACCTATACTTG 60.040 40.741 0.00 0.00 0.00 3.16
45 46 7.255520 GGACTACGATTGATCACCTATACTTGT 60.256 40.741 0.00 0.00 0.00 3.16
46 47 7.426410 ACTACGATTGATCACCTATACTTGTG 58.574 38.462 0.00 0.00 0.00 3.33
47 48 5.601662 ACGATTGATCACCTATACTTGTGG 58.398 41.667 0.00 0.00 33.29 4.17
48 49 4.991056 CGATTGATCACCTATACTTGTGGG 59.009 45.833 0.00 0.00 33.29 4.61
49 50 5.453339 CGATTGATCACCTATACTTGTGGGT 60.453 44.000 0.00 0.00 33.29 4.51
50 51 5.353394 TTGATCACCTATACTTGTGGGTC 57.647 43.478 0.00 0.00 33.29 4.46
51 52 4.358214 TGATCACCTATACTTGTGGGTCA 58.642 43.478 0.00 0.00 33.29 4.02
52 53 4.968719 TGATCACCTATACTTGTGGGTCAT 59.031 41.667 0.00 0.00 33.29 3.06
53 54 5.070446 TGATCACCTATACTTGTGGGTCATC 59.930 44.000 0.00 0.00 33.29 2.92
60 61 0.037303 CTTGTGGGTCATCAGGCTGT 59.963 55.000 15.27 0.00 0.00 4.40
63 64 0.250901 GTGGGTCATCAGGCTGTTGT 60.251 55.000 21.51 4.96 0.00 3.32
94 95 0.734253 CGCGTGAAGCTTCTACTGCT 60.734 55.000 26.09 0.00 45.59 4.24
135 138 6.623549 GCAGAGAGAGATAGATCACATGTAGC 60.624 46.154 0.00 0.00 0.00 3.58
165 168 7.092444 TGAGTTAGAGAAAGAGAGAGAGAGGAT 60.092 40.741 0.00 0.00 0.00 3.24
200 208 1.905637 ATTTTTCTGTCGGGTCCCAC 58.094 50.000 9.12 6.15 0.00 4.61
222 230 3.307199 CGTGTAATTGGTAGAGGTGGGTT 60.307 47.826 0.00 0.00 0.00 4.11
302 310 2.910319 AGCAGTGAGGGGTACAAATGTA 59.090 45.455 0.00 0.00 0.00 2.29
303 311 3.523564 AGCAGTGAGGGGTACAAATGTAT 59.476 43.478 0.00 0.00 32.54 2.29
325 333 8.857098 TGTATAAAGAATAGCTCATAGACGGTT 58.143 33.333 0.00 0.00 0.00 4.44
339 347 2.105993 AGACGGTTAAAGGCCTTTGACT 59.894 45.455 37.42 26.21 38.58 3.41
353 361 4.019174 CCTTTGACTAGTGGAAATGGCAT 58.981 43.478 0.00 0.00 0.00 4.40
381 390 3.055891 GCATTTCTGTAAGGCCACCAAAT 60.056 43.478 5.01 0.13 37.57 2.32
402 411 6.388619 AATAGAAGAGGGGCAAACTTAAGA 57.611 37.500 10.09 0.00 0.00 2.10
435 445 7.807977 TTTTTCAAGCTAAAGATGAGAGTGT 57.192 32.000 0.00 0.00 0.00 3.55
449 461 3.371898 TGAGAGTGTGCGCAAATTAGATG 59.628 43.478 14.00 0.00 0.00 2.90
485 498 6.211184 TGTCCCTTTTGAGTTAATGCATTCAT 59.789 34.615 16.86 2.69 33.53 2.57
623 637 6.620678 ACATGATGCACTAATGGTTTTACAC 58.379 36.000 0.00 0.00 0.00 2.90
700 715 8.904099 AATCGATTCTATTTACCGGAGAATTT 57.096 30.769 9.46 0.48 39.46 1.82
701 716 7.941795 TCGATTCTATTTACCGGAGAATTTC 57.058 36.000 9.46 0.88 39.46 2.17
744 759 8.964476 AGAATTTCTTCCTCGAGCAAATAATA 57.036 30.769 6.99 0.00 31.27 0.98
750 765 4.894784 TCCTCGAGCAAATAATATGGTCC 58.105 43.478 6.99 0.00 41.13 4.46
993 1011 2.126603 GTTACCCACCCCTCCCCT 59.873 66.667 0.00 0.00 0.00 4.79
1116 1137 5.137551 CCCTAAACTTGTTCTTCCCTTTCA 58.862 41.667 0.00 0.00 0.00 2.69
1174 1196 2.352805 GAACCAGCCCAGGACCAG 59.647 66.667 0.00 0.00 0.00 4.00
1235 1258 4.856509 TCCCATCGTCTCTTCTAGAAAGA 58.143 43.478 6.63 9.43 35.47 2.52
1244 1267 7.228906 TCGTCTCTTCTAGAAAGAAAGACAAGA 59.771 37.037 23.13 15.94 41.19 3.02
1260 1283 4.895889 AGACAAGATCTCCATCGGACATAA 59.104 41.667 0.00 0.00 33.75 1.90
1275 1298 8.786898 CATCGGACATAAATCATAACCAAATCT 58.213 33.333 0.00 0.00 0.00 2.40
1343 1366 9.646427 AGTCTCCTCGAATTTAGATTATTATGC 57.354 33.333 0.00 0.00 0.00 3.14
1695 1720 1.742880 CACTGTGCATCCCCGTCAG 60.743 63.158 0.00 0.00 0.00 3.51
1697 1722 2.927856 TGTGCATCCCCGTCAGGT 60.928 61.111 0.00 0.00 35.12 4.00
1768 1793 2.170607 CGGATCTAGACACCCACCATTT 59.829 50.000 10.89 0.00 0.00 2.32
1773 1798 1.444933 AGACACCCACCATTTCCTCA 58.555 50.000 0.00 0.00 0.00 3.86
1824 1849 4.693566 GCCATAAGCGCACTAATACCATTA 59.306 41.667 11.47 0.00 0.00 1.90
1871 1896 2.039084 GACCACTGAGTTCCCTTCACAT 59.961 50.000 0.00 0.00 0.00 3.21
1931 1956 0.541392 TATCTGCCATCAACGGTGCT 59.459 50.000 0.00 0.00 0.00 4.40
1946 1971 0.460811 GTGCTGGCATCGATGACTCA 60.461 55.000 30.50 23.88 36.54 3.41
1955 1980 4.502259 GGCATCGATGACTCAACTATTCCT 60.502 45.833 29.20 0.00 31.49 3.36
2052 2077 2.401583 TGTGCAAGCTATCGACCAAT 57.598 45.000 0.00 0.00 0.00 3.16
2087 2112 2.912956 TCTTGACAAGGTTAGAGGCCAT 59.087 45.455 15.13 0.00 0.00 4.40
2122 2147 0.394565 GGAGGGCGATGCTACTTCAT 59.605 55.000 0.00 0.00 0.00 2.57
2134 2159 2.223502 GCTACTTCATGACATCGGACGA 60.224 50.000 0.00 0.00 0.00 4.20
2159 2184 7.788026 ACATGATAATTGCATTGGATTTGACT 58.212 30.769 0.00 0.00 0.00 3.41
2206 2231 2.108168 CCTCCTCGATAAAGACCCACA 58.892 52.381 0.00 0.00 0.00 4.17
2232 2257 6.513806 TGGTGAACCATCATGAAACAATAG 57.486 37.500 0.00 0.00 42.01 1.73
2273 2298 2.740981 GTCCCATGATCGAATGCTCATC 59.259 50.000 0.00 0.00 28.72 2.92
2274 2299 2.369532 TCCCATGATCGAATGCTCATCA 59.630 45.455 0.00 0.00 28.72 3.07
2293 2318 7.954643 CTCATCATGAGGTACCTCTTCGGTAG 61.955 50.000 35.83 23.61 41.08 3.18
2375 2400 2.204463 TCCCATATGGAGGTGCTTGAA 58.796 47.619 24.00 0.00 38.61 2.69
2425 2450 2.824936 CACAACATGGAATTGGTAGCCA 59.175 45.455 0.00 0.00 35.91 4.75
2447 2472 4.403137 GCAGCATTCGTTGGCGCA 62.403 61.111 10.83 0.00 38.14 6.09
2500 2525 2.509548 TCCCTCGGATCATTTCCAATGT 59.490 45.455 0.00 0.00 45.78 2.71
2517 2542 4.876107 CCAATGTGGTGTACCTCAACTATC 59.124 45.833 9.57 0.00 42.06 2.08
2518 2543 5.487433 CAATGTGGTGTACCTCAACTATCA 58.513 41.667 9.57 0.00 42.06 2.15
2529 2554 6.252599 ACCTCAACTATCATATGCAAGGAA 57.747 37.500 0.00 0.00 0.00 3.36
2579 2604 9.547753 TGCTTTGAAGATAAGACAACTATATCC 57.452 33.333 0.00 0.00 0.00 2.59
2584 2609 8.201464 TGAAGATAAGACAACTATATCCGCAAA 58.799 33.333 0.00 0.00 0.00 3.68
2593 2618 6.430000 ACAACTATATCCGCAAAACACTTTCT 59.570 34.615 0.00 0.00 0.00 2.52
2595 2620 6.170506 ACTATATCCGCAAAACACTTTCTCA 58.829 36.000 0.00 0.00 0.00 3.27
2697 2722 9.096823 AGGGATATCGTATGTAAGGTCATAAAA 57.903 33.333 0.00 0.00 33.01 1.52
2724 2749 2.028203 AGTTGTGGCATTTATGGGCAAC 60.028 45.455 5.50 5.50 42.83 4.17
2806 2831 5.361857 AGTTGCATCAATAAAGAATGGGAGG 59.638 40.000 0.00 0.00 0.00 4.30
2933 2960 3.552604 TTTGCTTAATCCGCTTCACAC 57.447 42.857 0.00 0.00 0.00 3.82
2969 2996 7.168219 GGTAATCAAGCCATATCTTACCATCA 58.832 38.462 0.00 0.00 38.51 3.07
3080 3107 6.258287 TGTTTTCACTGCATTTTGGATCTTTG 59.742 34.615 0.00 0.00 0.00 2.77
3177 3204 7.339466 ACTTACATAACATGATTCCTCAAACCC 59.661 37.037 0.00 0.00 34.37 4.11
3341 3373 3.564644 AGGAGTATTCACTATGTCGACGG 59.435 47.826 11.62 6.27 34.21 4.79
3345 3377 0.241749 TTCACTATGTCGACGGCGTT 59.758 50.000 16.19 0.00 38.98 4.84
3348 3380 1.803922 CTATGTCGACGGCGTTGCA 60.804 57.895 22.25 21.44 38.98 4.08
3392 3424 3.222855 CCGCACTTTTGGCCCACA 61.223 61.111 0.00 0.00 0.00 4.17
3411 3443 1.134670 CAACCTACTCACCCAGCTAGC 60.135 57.143 6.62 6.62 0.00 3.42
3414 3446 1.036707 CTACTCACCCAGCTAGCCTC 58.963 60.000 12.13 0.00 0.00 4.70
3423 3455 0.103026 CAGCTAGCCTCGTATGCACA 59.897 55.000 12.13 0.00 0.00 4.57
3434 3466 2.981805 TCGTATGCACAACACGACTAAC 59.018 45.455 9.74 0.00 39.58 2.34
3443 3475 3.181473 ACAACACGACTAACTTGTAGGCA 60.181 43.478 0.00 0.00 30.81 4.75
3489 3521 0.400213 GATAACATGCCCGATCCCCA 59.600 55.000 0.00 0.00 0.00 4.96
3556 3589 2.193865 TTTTGCCAGCGCATGTACCG 62.194 55.000 11.47 0.00 46.67 4.02
3570 3603 2.736826 TACCGCCGCATGATCCCAA 61.737 57.895 0.00 0.00 0.00 4.12
3699 3732 1.826054 CGCAAACCACCCACTTCCA 60.826 57.895 0.00 0.00 0.00 3.53
3702 3735 1.477923 GCAAACCACCCACTTCCACTA 60.478 52.381 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.027771 CGTAGTCCTTTCAATAAGTAAGAGTGT 58.972 37.037 0.00 0.00 0.00 3.55
1 2 8.242053 TCGTAGTCCTTTCAATAAGTAAGAGTG 58.758 37.037 0.00 0.00 0.00 3.51
2 3 8.345724 TCGTAGTCCTTTCAATAAGTAAGAGT 57.654 34.615 0.00 0.00 0.00 3.24
3 4 9.804758 AATCGTAGTCCTTTCAATAAGTAAGAG 57.195 33.333 0.00 0.00 0.00 2.85
4 5 9.582431 CAATCGTAGTCCTTTCAATAAGTAAGA 57.418 33.333 0.00 0.00 0.00 2.10
5 6 9.582431 TCAATCGTAGTCCTTTCAATAAGTAAG 57.418 33.333 0.00 0.00 0.00 2.34
7 8 9.745880 GATCAATCGTAGTCCTTTCAATAAGTA 57.254 33.333 0.00 0.00 0.00 2.24
8 9 8.258007 TGATCAATCGTAGTCCTTTCAATAAGT 58.742 33.333 0.00 0.00 0.00 2.24
9 10 8.543774 GTGATCAATCGTAGTCCTTTCAATAAG 58.456 37.037 0.00 0.00 0.00 1.73
10 11 7.494625 GGTGATCAATCGTAGTCCTTTCAATAA 59.505 37.037 0.00 0.00 0.00 1.40
11 12 6.984474 GGTGATCAATCGTAGTCCTTTCAATA 59.016 38.462 0.00 0.00 0.00 1.90
12 13 5.817816 GGTGATCAATCGTAGTCCTTTCAAT 59.182 40.000 0.00 0.00 0.00 2.57
13 14 5.046591 AGGTGATCAATCGTAGTCCTTTCAA 60.047 40.000 0.00 0.00 0.00 2.69
14 15 4.466370 AGGTGATCAATCGTAGTCCTTTCA 59.534 41.667 0.00 0.00 0.00 2.69
15 16 5.012328 AGGTGATCAATCGTAGTCCTTTC 57.988 43.478 0.00 0.00 0.00 2.62
16 17 6.732896 ATAGGTGATCAATCGTAGTCCTTT 57.267 37.500 0.00 0.00 0.00 3.11
17 18 7.005296 AGTATAGGTGATCAATCGTAGTCCTT 58.995 38.462 0.00 0.00 0.00 3.36
18 19 6.544650 AGTATAGGTGATCAATCGTAGTCCT 58.455 40.000 0.00 0.00 0.00 3.85
19 20 6.821031 AGTATAGGTGATCAATCGTAGTCC 57.179 41.667 0.00 0.00 0.00 3.85
20 21 7.591795 CACAAGTATAGGTGATCAATCGTAGTC 59.408 40.741 0.00 0.00 37.18 2.59
21 22 7.426410 CACAAGTATAGGTGATCAATCGTAGT 58.574 38.462 0.00 0.00 37.18 2.73
22 23 6.863645 CCACAAGTATAGGTGATCAATCGTAG 59.136 42.308 0.00 0.00 37.18 3.51
23 24 6.239204 CCCACAAGTATAGGTGATCAATCGTA 60.239 42.308 0.00 0.00 37.18 3.43
24 25 5.453339 CCCACAAGTATAGGTGATCAATCGT 60.453 44.000 0.00 0.00 37.18 3.73
25 26 4.991056 CCCACAAGTATAGGTGATCAATCG 59.009 45.833 0.00 0.00 37.18 3.34
26 27 5.930135 ACCCACAAGTATAGGTGATCAATC 58.070 41.667 0.00 0.00 37.18 2.67
27 28 5.428457 TGACCCACAAGTATAGGTGATCAAT 59.572 40.000 0.00 0.00 37.18 2.57
28 29 4.780554 TGACCCACAAGTATAGGTGATCAA 59.219 41.667 0.00 0.00 37.18 2.57
29 30 4.358214 TGACCCACAAGTATAGGTGATCA 58.642 43.478 0.00 0.00 37.18 2.92
30 31 5.070446 TGATGACCCACAAGTATAGGTGATC 59.930 44.000 0.00 0.00 41.65 2.92
31 32 4.968719 TGATGACCCACAAGTATAGGTGAT 59.031 41.667 0.00 0.00 37.18 3.06
32 33 4.358214 TGATGACCCACAAGTATAGGTGA 58.642 43.478 0.00 0.00 37.18 4.02
33 34 4.443457 CCTGATGACCCACAAGTATAGGTG 60.443 50.000 0.00 0.00 31.10 4.00
34 35 3.711704 CCTGATGACCCACAAGTATAGGT 59.288 47.826 0.00 0.00 34.57 3.08
35 36 3.495100 GCCTGATGACCCACAAGTATAGG 60.495 52.174 0.00 0.00 0.00 2.57
36 37 3.389329 AGCCTGATGACCCACAAGTATAG 59.611 47.826 0.00 0.00 0.00 1.31
37 38 3.134623 CAGCCTGATGACCCACAAGTATA 59.865 47.826 0.00 0.00 0.00 1.47
38 39 2.092753 CAGCCTGATGACCCACAAGTAT 60.093 50.000 0.00 0.00 0.00 2.12
39 40 1.278985 CAGCCTGATGACCCACAAGTA 59.721 52.381 0.00 0.00 0.00 2.24
40 41 0.037303 CAGCCTGATGACCCACAAGT 59.963 55.000 0.00 0.00 0.00 3.16
41 42 0.037303 ACAGCCTGATGACCCACAAG 59.963 55.000 0.00 0.00 0.00 3.16
42 43 0.478072 AACAGCCTGATGACCCACAA 59.522 50.000 0.00 0.00 0.00 3.33
43 44 0.250858 CAACAGCCTGATGACCCACA 60.251 55.000 0.00 0.00 0.00 4.17
44 45 0.250901 ACAACAGCCTGATGACCCAC 60.251 55.000 9.14 0.00 0.00 4.61
45 46 0.250858 CACAACAGCCTGATGACCCA 60.251 55.000 9.14 0.00 0.00 4.51
46 47 0.962356 CCACAACAGCCTGATGACCC 60.962 60.000 9.14 0.00 0.00 4.46
47 48 0.036732 TCCACAACAGCCTGATGACC 59.963 55.000 9.14 0.00 0.00 4.02
48 49 1.741706 CATCCACAACAGCCTGATGAC 59.258 52.381 9.14 0.00 35.89 3.06
49 50 1.340308 CCATCCACAACAGCCTGATGA 60.340 52.381 9.14 0.00 35.89 2.92
50 51 1.100510 CCATCCACAACAGCCTGATG 58.899 55.000 0.00 0.00 34.10 3.07
51 52 0.033796 CCCATCCACAACAGCCTGAT 60.034 55.000 0.00 0.00 0.00 2.90
52 53 1.379916 CCCATCCACAACAGCCTGA 59.620 57.895 0.00 0.00 0.00 3.86
53 54 2.345760 GCCCATCCACAACAGCCTG 61.346 63.158 0.00 0.00 0.00 4.85
60 61 2.270850 GCGGTAGCCCATCCACAA 59.729 61.111 0.00 0.00 37.42 3.33
63 64 4.155733 CACGCGGTAGCCCATCCA 62.156 66.667 12.47 0.00 41.18 3.41
94 95 1.028130 CTGCTGACCTCATCTCGCTA 58.972 55.000 0.00 0.00 0.00 4.26
135 138 7.770433 TCTCTCTCTCTTTCTCTAACTCATGAG 59.230 40.741 21.37 21.37 0.00 2.90
150 153 5.435041 TCTCCCTTTATCCTCTCTCTCTCTT 59.565 44.000 0.00 0.00 0.00 2.85
200 208 2.235402 ACCCACCTCTACCAATTACACG 59.765 50.000 0.00 0.00 0.00 4.49
303 311 9.745880 CTTTAACCGTCTATGAGCTATTCTTTA 57.254 33.333 0.00 0.00 0.00 1.85
325 333 4.986054 TTCCACTAGTCAAAGGCCTTTA 57.014 40.909 29.94 14.05 0.00 1.85
339 347 2.949963 GCCCTTCATGCCATTTCCACTA 60.950 50.000 0.00 0.00 0.00 2.74
353 361 2.446435 GCCTTACAGAAATGCCCTTCA 58.554 47.619 0.00 0.00 0.00 3.02
381 390 5.072600 TGTTCTTAAGTTTGCCCCTCTTCTA 59.927 40.000 1.63 0.00 0.00 2.10
417 427 3.257393 CGCACACTCTCATCTTTAGCTT 58.743 45.455 0.00 0.00 0.00 3.74
435 445 4.876125 TCCAAAAACATCTAATTTGCGCA 58.124 34.783 5.66 5.66 33.72 6.09
449 461 6.112734 ACTCAAAAGGGACAATTCCAAAAAC 58.887 36.000 0.00 0.00 44.98 2.43
509 522 1.067060 GAGGGTCAAACAAGCAACCAC 59.933 52.381 0.00 0.00 33.27 4.16
591 605 6.540189 ACCATTAGTGCATCATGTCTAGTTTC 59.460 38.462 0.00 0.00 0.00 2.78
744 759 6.491403 GGTTGCATTAGAATAATCAGGACCAT 59.509 38.462 0.00 0.00 0.00 3.55
750 765 8.246180 ACTTTGTGGTTGCATTAGAATAATCAG 58.754 33.333 0.00 0.00 0.00 2.90
993 1011 3.713288 AGTCACTATTTATAGCGCGCAA 58.287 40.909 35.10 19.45 33.68 4.85
1116 1137 7.781324 AATAGATGTTTGGTGGTGAAAGAAT 57.219 32.000 0.00 0.00 0.00 2.40
1174 1196 4.338379 AAAACAGTGACTAGAGTGGGAC 57.662 45.455 0.00 0.00 0.00 4.46
1199 1222 5.949354 AGACGATGGGAAATTGACCAAATTA 59.051 36.000 5.56 0.00 40.73 1.40
1218 1241 6.879276 TGTCTTTCTTTCTAGAAGAGACGA 57.121 37.500 21.90 15.72 42.96 4.20
1235 1258 3.515502 TGTCCGATGGAGATCTTGTCTTT 59.484 43.478 0.00 0.00 37.29 2.52
1244 1267 7.106239 GGTTATGATTTATGTCCGATGGAGAT 58.894 38.462 0.89 0.89 39.16 2.75
1343 1366 5.750067 GGTATGCAATGGAATTTACTGCAAG 59.250 40.000 4.32 0.00 35.55 4.01
1695 1720 2.232941 TGACATTGAGAAGGGTACGACC 59.767 50.000 0.00 0.00 37.60 4.79
1697 1722 2.232941 GGTGACATTGAGAAGGGTACGA 59.767 50.000 0.00 0.00 0.00 3.43
1824 1849 1.630878 GGTGAATGGGTGGAGAAGACT 59.369 52.381 0.00 0.00 0.00 3.24
1871 1896 2.397754 CGATGTGGATGGTGCGCAA 61.398 57.895 14.00 0.00 30.58 4.85
1931 1956 4.371786 GAATAGTTGAGTCATCGATGCCA 58.628 43.478 20.81 14.39 0.00 4.92
1946 1971 6.874288 ATAACGAGCGTACTAGGAATAGTT 57.126 37.500 0.00 0.00 0.00 2.24
1955 1980 4.129380 TCAGGCTAATAACGAGCGTACTA 58.871 43.478 0.00 0.00 41.06 1.82
2087 2112 0.250295 CTCCAAAGGTCAGCGGTGAA 60.250 55.000 20.46 0.28 33.27 3.18
2122 2147 4.584327 ATTATCATGTCGTCCGATGTCA 57.416 40.909 0.00 0.00 0.00 3.58
2134 2159 7.788026 AGTCAAATCCAATGCAATTATCATGT 58.212 30.769 0.00 0.00 32.46 3.21
2159 2184 2.352561 TATGAGGTTCAACCCCAGGA 57.647 50.000 1.75 0.00 39.75 3.86
2232 2257 5.397221 GGGACCTAACAAGATAGGGGTAAAC 60.397 48.000 8.09 0.00 45.69 2.01
2238 2263 3.973973 TCATGGGACCTAACAAGATAGGG 59.026 47.826 8.09 0.00 45.69 3.53
2359 2384 2.846206 TCCACTTCAAGCACCTCCATAT 59.154 45.455 0.00 0.00 0.00 1.78
2425 2450 0.388907 GCCAACGAATGCTGCACAAT 60.389 50.000 3.57 0.00 0.00 2.71
2447 2472 4.033009 TGGATACCATGACTGTGTGAGAT 58.967 43.478 0.00 0.00 0.00 2.75
2500 2525 5.365314 TGCATATGATAGTTGAGGTACACCA 59.635 40.000 6.97 0.00 38.89 4.17
2517 2542 9.467258 AAAATGACGAAATATTCCTTGCATATG 57.533 29.630 0.00 0.00 0.00 1.78
2518 2543 9.467258 CAAAATGACGAAATATTCCTTGCATAT 57.533 29.630 0.00 0.00 0.00 1.78
2529 2554 4.989279 AGGCAGCAAAATGACGAAATAT 57.011 36.364 0.00 0.00 31.55 1.28
2579 2604 3.617669 ACGATTGAGAAAGTGTTTTGCG 58.382 40.909 0.00 0.00 0.00 4.85
2584 2609 5.334105 CCAATTCGACGATTGAGAAAGTGTT 60.334 40.000 10.71 0.00 38.93 3.32
2593 2618 3.906014 TTTTGCCAATTCGACGATTGA 57.094 38.095 10.71 0.00 38.93 2.57
2595 2620 4.023193 AGAGTTTTTGCCAATTCGACGATT 60.023 37.500 0.00 0.00 0.00 3.34
2765 2790 8.650490 TGATGCAACTACATCTAGGATGAAATA 58.350 33.333 13.51 0.00 45.51 1.40
2806 2831 5.707764 AGTTTTAACATTTGAGAGAGGGAGC 59.292 40.000 0.00 0.00 0.00 4.70
2901 2928 7.229306 AGCGGATTAAGCAAATGATCTATTCAA 59.771 33.333 0.00 0.00 35.92 2.69
2917 2944 4.398549 TTTTCGTGTGAAGCGGATTAAG 57.601 40.909 0.00 0.00 35.06 1.85
2924 2951 2.574322 CAGGAATTTTCGTGTGAAGCG 58.426 47.619 5.13 0.00 38.05 4.68
2933 2960 4.157656 TGGCTTGATTACCAGGAATTTTCG 59.842 41.667 0.00 0.00 0.00 3.46
2969 2996 8.367911 TGGTCATCGACTTAATAGCTAAATCAT 58.632 33.333 0.00 0.00 32.47 2.45
3152 3179 7.467267 CGGGTTTGAGGAATCATGTTATGTAAG 60.467 40.741 0.00 0.00 0.00 2.34
3161 3188 1.462616 TGCGGGTTTGAGGAATCATG 58.537 50.000 0.00 0.00 0.00 3.07
3177 3204 0.390124 ATATTTGCAGCCCCAATGCG 59.610 50.000 0.00 0.00 46.87 4.73
3321 3353 3.298317 GCCGTCGACATAGTGAATACTC 58.702 50.000 17.16 0.00 38.36 2.59
3335 3367 1.348538 CTATTGTGCAACGCCGTCGA 61.349 55.000 0.00 0.00 42.39 4.20
3341 3373 1.606606 GAAGTGCTATTGTGCAACGC 58.393 50.000 0.00 2.39 45.12 4.84
3345 3377 1.825090 CTGGGAAGTGCTATTGTGCA 58.175 50.000 0.00 0.00 41.05 4.57
3348 3380 0.392998 CGGCTGGGAAGTGCTATTGT 60.393 55.000 0.00 0.00 0.00 2.71
3392 3424 1.196012 GCTAGCTGGGTGAGTAGGTT 58.804 55.000 7.70 0.00 0.00 3.50
3411 3443 0.713883 GTCGTGTTGTGCATACGAGG 59.286 55.000 15.41 0.00 46.01 4.63
3414 3446 2.984471 AGTTAGTCGTGTTGTGCATACG 59.016 45.455 8.75 8.75 39.04 3.06
3423 3455 3.738830 TGCCTACAAGTTAGTCGTGTT 57.261 42.857 0.00 0.00 39.30 3.32
3434 3466 9.941325 ATCTTATGAAGATTAGATGCCTACAAG 57.059 33.333 0.00 0.00 45.75 3.16
3462 3494 2.031120 CGGGCATGTTATCCACCATTT 58.969 47.619 0.00 0.00 0.00 2.32
3472 3504 1.836391 CTGGGGATCGGGCATGTTA 59.164 57.895 0.00 0.00 0.00 2.41
3556 3589 1.031571 TGAGTTTGGGATCATGCGGC 61.032 55.000 0.00 0.00 0.00 6.53
3570 3603 1.293924 GCGCTGCATCATACTGAGTT 58.706 50.000 0.00 0.00 0.00 3.01
3654 3687 1.003233 GGTGGAACTGAGGGACTGC 60.003 63.158 0.00 0.00 35.75 4.40
3655 3688 0.322975 CTGGTGGAACTGAGGGACTG 59.677 60.000 0.00 0.00 35.75 3.51
3665 3698 2.617274 GCGAGCAACCTGGTGGAAC 61.617 63.158 5.10 0.00 37.04 3.62
3699 3732 1.005687 AGAGTTGGCTACGGAGGTAGT 59.994 52.381 0.00 0.00 46.42 2.73
3702 3735 1.258445 CCAGAGTTGGCTACGGAGGT 61.258 60.000 0.00 0.00 37.73 3.85


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

AutoCloner maintained by Alex Coulton.