Multiple sequence alignment - TraesCS5D01G172100

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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 TraesCS5D01G172100 chr5D 100.000 4551 0 0 1 4551 268940091 268935541 0.000000e+00 8405.0
1 TraesCS5D01G172100 chr5D 86.957 437 54 3 4 438 334017782 334017347 5.290000e-134 488.0
2 TraesCS5D01G172100 chr5D 93.023 172 10 2 3841 4010 52112164 52111993 2.720000e-62 250.0
3 TraesCS5D01G172100 chr5D 92.571 175 11 2 3839 4011 491000739 491000565 2.720000e-62 250.0
4 TraesCS5D01G172100 chr5D 95.455 44 2 0 460 503 276308195 276308152 2.270000e-08 71.3
5 TraesCS5D01G172100 chr5B 96.612 1476 23 2 2496 3944 304659427 304657952 0.000000e+00 2423.0
6 TraesCS5D01G172100 chr5B 95.233 944 34 6 2 937 304662262 304661322 0.000000e+00 1483.0
7 TraesCS5D01G172100 chr5B 95.609 911 21 8 935 1844 304661357 304660465 0.000000e+00 1443.0
8 TraesCS5D01G172100 chr5B 93.891 622 36 2 3929 4549 304656777 304656157 0.000000e+00 937.0
9 TraesCS5D01G172100 chr5B 96.019 427 13 3 1800 2222 304660479 304660053 0.000000e+00 691.0
10 TraesCS5D01G172100 chr5B 99.167 240 2 0 2211 2450 304660033 304659794 2.510000e-117 433.0
11 TraesCS5D01G172100 chr5A 91.881 1675 57 35 2206 3842 357079670 357081303 0.000000e+00 2266.0
12 TraesCS5D01G172100 chr5A 90.771 856 43 23 561 1402 357077933 357078766 0.000000e+00 1110.0
13 TraesCS5D01G172100 chr5A 89.236 288 28 2 1526 1813 357079096 357079380 1.560000e-94 357.0
14 TraesCS5D01G172100 chr5A 93.023 172 8 3 3841 4010 12419607 12419776 9.780000e-62 248.0
15 TraesCS5D01G172100 chr5A 89.326 178 18 1 1830 2006 357079367 357079544 5.930000e-54 222.0
16 TraesCS5D01G172100 chrUn 100.000 387 0 0 3324 3710 480444761 480444375 0.000000e+00 715.0
17 TraesCS5D01G172100 chr7A 87.613 444 52 3 1 443 700106704 700106263 3.140000e-141 512.0
18 TraesCS5D01G172100 chr7A 87.244 439 54 2 1 438 61876525 61876088 2.440000e-137 499.0
19 TraesCS5D01G172100 chr3D 87.703 431 52 1 1 430 567489380 567488950 6.800000e-138 501.0
20 TraesCS5D01G172100 chr1D 86.712 444 55 4 1 441 427593685 427594127 1.470000e-134 490.0
21 TraesCS5D01G172100 chr1D 94.611 167 8 1 3841 4006 485716358 485716192 1.620000e-64 257.0
22 TraesCS5D01G172100 chr1A 86.652 442 54 4 1 439 292760966 292760527 6.850000e-133 484.0
23 TraesCS5D01G172100 chr7B 86.621 441 54 4 1 438 21257686 21258124 2.460000e-132 483.0
24 TraesCS5D01G172100 chr1B 85.969 449 60 3 1 448 14660538 14660092 1.150000e-130 477.0
25 TraesCS5D01G172100 chr6D 93.103 174 9 3 3841 4011 27494651 27494478 7.560000e-63 252.0
26 TraesCS5D01G172100 chr6D 92.529 174 11 2 3837 4008 115323185 115323358 9.780000e-62 248.0
27 TraesCS5D01G172100 chr6D 92.899 169 11 1 3838 4005 109240485 109240317 1.260000e-60 244.0
28 TraesCS5D01G172100 chr4D 93.529 170 10 1 3837 4005 93336852 93336683 7.560000e-63 252.0


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 TraesCS5D01G172100 chr5D 268935541 268940091 4550 True 8405.00 8405 100.0000 1 4551 1 chr5D.!!$R2 4550
1 TraesCS5D01G172100 chr5B 304656157 304662262 6105 True 1235.00 2423 96.0885 2 4549 6 chr5B.!!$R1 4547
2 TraesCS5D01G172100 chr5A 357077933 357081303 3370 False 988.75 2266 90.3035 561 3842 4 chr5A.!!$F2 3281

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
305 306 0.109086 CGCGATGATAGTGCTAGGGG 60.109 60.0 0.0 0.0 0.0 4.79 F
939 964 0.744281 CCGGCCTCTTTCTCTCTCTC 59.256 60.0 0.0 0.0 0.0 3.20 F
2482 2833 0.669318 TTGCCGTTTCCTCTAGCGTG 60.669 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1624 1877 1.545841 AATCTCGTTCCTTTTGGCCC 58.454 50.000 0.0 0.0 40.12 5.80 R
2755 3479 1.070786 GACGAACTCCACCTTGCCA 59.929 57.895 0.0 0.0 0.00 4.92 R
4173 6099 0.823356 GTGTGGTTGAGCATGTGGGT 60.823 55.000 0.0 0.0 0.00 4.51 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
87 88 1.152440 TGTTGGCCGGGGTGAAAAT 60.152 52.632 2.18 0.00 0.00 1.82
100 101 5.065218 CGGGGTGAAAATCTGTTCTATCTTG 59.935 44.000 0.00 0.00 0.00 3.02
174 175 4.465512 CATTGCCTGTCGTGCGGC 62.466 66.667 0.00 0.00 46.46 6.53
180 181 4.056125 CTGTCGTGCGGCTCCAGA 62.056 66.667 0.00 0.00 0.00 3.86
258 259 3.061848 CGCCGCCTTGAAACCCAT 61.062 61.111 0.00 0.00 0.00 4.00
293 294 2.530177 GACTTCATGTCTTCGCGATGA 58.470 47.619 19.57 19.57 42.21 2.92
305 306 0.109086 CGCGATGATAGTGCTAGGGG 60.109 60.000 0.00 0.00 0.00 4.79
314 315 1.971695 GTGCTAGGGGTGGTGTTGC 60.972 63.158 0.00 0.00 0.00 4.17
317 318 1.675641 CTAGGGGTGGTGTTGCTGC 60.676 63.158 0.00 0.00 0.00 5.25
347 348 4.268644 CGCCTATGTATCTTGTCTTGTGTG 59.731 45.833 0.00 0.00 0.00 3.82
353 354 1.006086 TCTTGTCTTGTGTGTGTGCG 58.994 50.000 0.00 0.00 0.00 5.34
372 373 1.376037 TGTGTTGTGGTGACGTGCA 60.376 52.632 0.00 0.00 0.00 4.57
382 383 1.196808 GGTGACGTGCATTTGTACTGG 59.803 52.381 0.00 0.00 0.00 4.00
726 731 6.775629 ACAAACAAATGGTAAGAAGAGGCTTA 59.224 34.615 0.00 0.00 0.00 3.09
735 740 3.838244 AGAAGAGGCTTACACAACACA 57.162 42.857 0.00 0.00 0.00 3.72
759 768 7.715686 ACAAAAACAAAGAACAAAACCCAGTTA 59.284 29.630 0.00 0.00 0.00 2.24
845 857 1.603678 CCGCAACTACGTACACACCTT 60.604 52.381 0.00 0.00 0.00 3.50
850 862 3.151912 ACTACGTACACACCTTCTCCT 57.848 47.619 0.00 0.00 0.00 3.69
929 954 2.042435 CTCTCTCCCCGGCCTCTT 60.042 66.667 0.00 0.00 0.00 2.85
939 964 0.744281 CCGGCCTCTTTCTCTCTCTC 59.256 60.000 0.00 0.00 0.00 3.20
940 965 1.684869 CCGGCCTCTTTCTCTCTCTCT 60.685 57.143 0.00 0.00 0.00 3.10
941 966 1.676006 CGGCCTCTTTCTCTCTCTCTC 59.324 57.143 0.00 0.00 0.00 3.20
943 968 2.952310 GGCCTCTTTCTCTCTCTCTCTC 59.048 54.545 0.00 0.00 0.00 3.20
945 970 3.879892 GCCTCTTTCTCTCTCTCTCTCTC 59.120 52.174 0.00 0.00 0.00 3.20
946 971 4.384647 GCCTCTTTCTCTCTCTCTCTCTCT 60.385 50.000 0.00 0.00 0.00 3.10
947 972 5.363939 CCTCTTTCTCTCTCTCTCTCTCTC 58.636 50.000 0.00 0.00 0.00 3.20
948 973 5.130145 CCTCTTTCTCTCTCTCTCTCTCTCT 59.870 48.000 0.00 0.00 0.00 3.10
949 974 6.227298 TCTTTCTCTCTCTCTCTCTCTCTC 57.773 45.833 0.00 0.00 0.00 3.20
950 975 5.960811 TCTTTCTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
951 976 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
952 977 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
953 978 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
954 979 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
955 980 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
956 981 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
957 982 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
958 983 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
959 984 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
960 985 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
961 986 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
962 987 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
963 988 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
964 989 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
965 990 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
966 991 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
967 992 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
968 993 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
969 994 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
970 995 3.386078 TCTCTCTCTCTCTCTCTCTCTGC 59.614 52.174 0.00 0.00 0.00 4.26
971 996 2.435805 TCTCTCTCTCTCTCTCTCTGCC 59.564 54.545 0.00 0.00 0.00 4.85
972 997 2.437281 CTCTCTCTCTCTCTCTCTGCCT 59.563 54.545 0.00 0.00 0.00 4.75
973 998 3.643320 CTCTCTCTCTCTCTCTCTGCCTA 59.357 52.174 0.00 0.00 0.00 3.93
974 999 3.643320 TCTCTCTCTCTCTCTCTGCCTAG 59.357 52.174 0.00 0.00 0.00 3.02
975 1000 3.384168 TCTCTCTCTCTCTCTGCCTAGT 58.616 50.000 0.00 0.00 0.00 2.57
976 1001 3.134623 TCTCTCTCTCTCTCTGCCTAGTG 59.865 52.174 0.00 0.00 0.00 2.74
977 1002 1.949525 CTCTCTCTCTCTGCCTAGTGC 59.050 57.143 0.00 0.00 41.77 4.40
978 1003 1.563879 TCTCTCTCTCTGCCTAGTGCT 59.436 52.381 5.06 0.00 42.00 4.40
1023 1048 0.803768 CGAGAAGCCGACAGTCCATG 60.804 60.000 0.00 0.00 0.00 3.66
1266 1291 4.715523 CCCACCGTCCGCCACATT 62.716 66.667 0.00 0.00 0.00 2.71
1375 1400 2.557924 CAGGTATGCACACCACACAATT 59.442 45.455 18.20 0.00 41.40 2.32
1376 1401 2.557924 AGGTATGCACACCACACAATTG 59.442 45.455 18.20 3.24 41.40 2.32
1377 1402 2.295909 GGTATGCACACCACACAATTGT 59.704 45.455 9.93 4.92 38.55 2.71
1378 1403 3.504134 GGTATGCACACCACACAATTGTA 59.496 43.478 9.93 0.00 38.55 2.41
1379 1404 4.157656 GGTATGCACACCACACAATTGTAT 59.842 41.667 9.93 0.00 38.55 2.29
1380 1405 5.355630 GGTATGCACACCACACAATTGTATA 59.644 40.000 9.93 0.00 38.55 1.47
1381 1406 4.757799 TGCACACCACACAATTGTATAC 57.242 40.909 11.53 0.00 33.30 1.47
1382 1407 4.137543 TGCACACCACACAATTGTATACA 58.862 39.130 11.53 0.08 33.30 2.29
1383 1408 4.764308 TGCACACCACACAATTGTATACAT 59.236 37.500 11.53 0.00 33.30 2.29
1384 1409 5.094812 GCACACCACACAATTGTATACATG 58.905 41.667 11.53 5.66 33.30 3.21
1479 1546 9.905713 AGTTATCACCATTTTGCTAGATCTAAA 57.094 29.630 3.57 0.00 0.00 1.85
1817 2070 6.767524 TGAAAGTGAACACCATACTGTTTT 57.232 33.333 1.11 0.00 34.40 2.43
2452 2803 2.775384 ACGGTAGGCTTGGAATTCCATA 59.225 45.455 27.53 14.14 46.97 2.74
2453 2804 3.139077 CGGTAGGCTTGGAATTCCATAC 58.861 50.000 27.53 23.50 46.97 2.39
2454 2805 3.139077 GGTAGGCTTGGAATTCCATACG 58.861 50.000 27.53 18.68 46.97 3.06
2461 2812 1.507141 GGAATTCCATACGCAGCCCG 61.507 60.000 20.04 0.00 38.37 6.13
2475 2826 3.053896 CCCGGTTGCCGTTTCCTC 61.054 66.667 0.00 0.00 46.80 3.71
2480 2831 1.359459 GGTTGCCGTTTCCTCTAGCG 61.359 60.000 0.00 0.00 0.00 4.26
2482 2833 0.669318 TTGCCGTTTCCTCTAGCGTG 60.669 55.000 0.00 0.00 0.00 5.34
2489 2842 4.525686 CGTTTCCTCTAGCGTGTATACTC 58.474 47.826 4.17 0.00 0.00 2.59
2563 3259 8.887036 TTGTCCAATCATGTACACATAGTATC 57.113 34.615 0.00 0.00 34.67 2.24
2686 3410 1.202076 GCTAACACGCTCCATGCTTTC 60.202 52.381 0.00 0.00 40.11 2.62
2701 3425 6.209986 TCCATGCTTTCAAATGATTTCAGTCT 59.790 34.615 0.00 0.00 0.00 3.24
3710 4442 0.033405 TAAGTAGGCGGCTGGTCTCT 60.033 55.000 23.55 8.96 0.00 3.10
3755 4487 4.888239 AGAAACTAGCTTAGAGGTGCGATA 59.112 41.667 0.00 0.00 0.00 2.92
3849 4581 5.485353 TGGAATGTTCTCATGTACTTCCTCT 59.515 40.000 16.71 0.00 34.19 3.69
3854 4586 6.591935 TGTTCTCATGTACTTCCTCTGTTTT 58.408 36.000 0.00 0.00 0.00 2.43
3898 4633 9.507280 GACATTTCAAATGGACTACAACATATG 57.493 33.333 14.70 0.00 0.00 1.78
3899 4634 9.241919 ACATTTCAAATGGACTACAACATATGA 57.758 29.630 14.70 0.00 0.00 2.15
3945 5871 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3957 5883 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
3964 5890 4.034048 GCTCCGTATGTAGTCATTTGTTGG 59.966 45.833 0.00 0.00 35.70 3.77
3975 5901 8.593679 TGTAGTCATTTGTTGGAATCTCTAGAA 58.406 33.333 0.00 0.00 0.00 2.10
4007 5933 6.854091 ATTTAGGAACGGAGGGAGTATATC 57.146 41.667 0.00 0.00 0.00 1.63
4014 5940 5.531753 ACGGAGGGAGTATATCTATGGAA 57.468 43.478 0.00 0.00 0.00 3.53
4048 5974 7.012704 ACCATTCTATTGCAATGTACTCATGAC 59.987 37.037 22.27 0.00 34.19 3.06
4063 5989 3.451526 TCATGACGTGCAAGAGATCATC 58.548 45.455 6.65 0.00 0.00 2.92
4065 5991 3.156511 TGACGTGCAAGAGATCATCTC 57.843 47.619 6.55 6.55 43.70 2.75
4103 6029 2.768769 GTCCTCCTACCCCTGGGC 60.769 72.222 7.39 0.00 39.32 5.36
4104 6030 2.958739 TCCTCCTACCCCTGGGCT 60.959 66.667 7.39 0.00 39.32 5.19
4220 6146 1.614996 TCTCGCTGATCCTCTCATCC 58.385 55.000 0.00 0.00 32.10 3.51
4241 6167 2.108157 AGCAAGGTTGACGCACGA 59.892 55.556 0.00 0.00 0.00 4.35
4247 6173 0.949105 AGGTTGACGCACGAACATCC 60.949 55.000 0.00 5.68 0.00 3.51
4258 6184 1.523938 GAACATCCACGCCCCTAGC 60.524 63.158 0.00 0.00 38.52 3.42
4362 6288 0.539051 CTCCCGCTCAAGGACAGATT 59.461 55.000 0.00 0.00 0.00 2.40
4407 6333 3.433031 CCGTTGGATCTACATGGGCTTAA 60.433 47.826 0.00 0.00 0.00 1.85
4442 6368 2.191513 CATTGGGCGATGGCAGAGG 61.192 63.158 1.01 0.00 42.47 3.69
4449 6375 2.922234 GATGGCAGAGGGAAGGGG 59.078 66.667 0.00 0.00 0.00 4.79
4455 6381 2.689034 AGAGGGAAGGGGAAGCCG 60.689 66.667 0.00 0.00 0.00 5.52
4501 6427 2.124236 CGCTAGGGAGGAGGACGT 60.124 66.667 0.00 0.00 0.00 4.34
4502 6428 1.753463 CGCTAGGGAGGAGGACGTT 60.753 63.158 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.920112 CCACCGAACGCCACACCA 62.920 66.667 0.00 0.00 0.00 4.17
68 69 1.468506 ATTTTCACCCCGGCCAACAC 61.469 55.000 2.24 0.00 0.00 3.32
87 88 4.141937 CGGTTCATCCCAAGATAGAACAGA 60.142 45.833 0.00 0.00 39.59 3.41
164 165 4.056125 CTCTGGAGCCGCACGACA 62.056 66.667 0.00 0.00 0.00 4.35
174 175 1.410882 GGATCGGAGTTTCCTCTGGAG 59.589 57.143 0.00 0.00 43.24 3.86
176 177 1.490574 AGGATCGGAGTTTCCTCTGG 58.509 55.000 0.00 0.00 43.24 3.86
241 242 3.061848 ATGGGTTTCAAGGCGGCG 61.062 61.111 0.51 0.51 0.00 6.46
242 243 2.573340 CATGGGTTTCAAGGCGGC 59.427 61.111 0.00 0.00 0.00 6.53
293 294 1.559682 CAACACCACCCCTAGCACTAT 59.440 52.381 0.00 0.00 0.00 2.12
347 348 1.226267 CACCACAACACACGCACAC 60.226 57.895 0.00 0.00 0.00 3.82
353 354 1.061887 GCACGTCACCACAACACAC 59.938 57.895 0.00 0.00 0.00 3.82
372 373 6.594788 AATCATCAACAAGCCAGTACAAAT 57.405 33.333 0.00 0.00 0.00 2.32
417 418 3.371285 GCTTATCGAGAAAGGCTTTCGTT 59.629 43.478 28.76 18.54 44.29 3.85
433 434 3.684788 AGTTCACGGTTGTCATGCTTATC 59.315 43.478 0.00 0.00 0.00 1.75
726 731 6.910536 TTGTTCTTTGTTTTTGTGTTGTGT 57.089 29.167 0.00 0.00 0.00 3.72
735 740 8.678593 TTAACTGGGTTTTGTTCTTTGTTTTT 57.321 26.923 0.00 0.00 0.00 1.94
759 768 1.270358 GCTGTCGTTGTCCCTCTTCTT 60.270 52.381 0.00 0.00 0.00 2.52
793 802 2.109425 ACGGAGTATTTTGCTCACCC 57.891 50.000 0.00 0.00 41.94 4.61
845 857 1.120530 GTATTGGCGGGAAGAGGAGA 58.879 55.000 0.00 0.00 0.00 3.71
850 862 4.345547 TGTGTATATGTATTGGCGGGAAGA 59.654 41.667 0.00 0.00 0.00 2.87
929 954 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
939 964 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
940 965 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
941 966 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
943 968 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
945 970 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
946 971 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
947 972 4.501229 GCAGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
948 973 3.386078 GCAGAGAGAGAGAGAGAGAGAGA 59.614 52.174 0.00 0.00 0.00 3.10
949 974 3.494048 GGCAGAGAGAGAGAGAGAGAGAG 60.494 56.522 0.00 0.00 0.00 3.20
950 975 2.435805 GGCAGAGAGAGAGAGAGAGAGA 59.564 54.545 0.00 0.00 0.00 3.10
951 976 2.437281 AGGCAGAGAGAGAGAGAGAGAG 59.563 54.545 0.00 0.00 0.00 3.20
952 977 2.481441 AGGCAGAGAGAGAGAGAGAGA 58.519 52.381 0.00 0.00 0.00 3.10
953 978 3.389329 ACTAGGCAGAGAGAGAGAGAGAG 59.611 52.174 0.00 0.00 0.00 3.20
954 979 3.134623 CACTAGGCAGAGAGAGAGAGAGA 59.865 52.174 0.00 0.00 0.00 3.10
955 980 3.470709 CACTAGGCAGAGAGAGAGAGAG 58.529 54.545 0.00 0.00 0.00 3.20
956 981 2.421388 GCACTAGGCAGAGAGAGAGAGA 60.421 54.545 0.00 0.00 43.97 3.10
957 982 1.949525 GCACTAGGCAGAGAGAGAGAG 59.050 57.143 0.00 0.00 43.97 3.20
958 983 2.051334 GCACTAGGCAGAGAGAGAGA 57.949 55.000 0.00 0.00 43.97 3.10
969 994 2.932614 CACAACAGTATCAGCACTAGGC 59.067 50.000 0.00 0.00 45.30 3.93
970 995 4.177026 GACACAACAGTATCAGCACTAGG 58.823 47.826 0.00 0.00 0.00 3.02
971 996 4.081972 AGGACACAACAGTATCAGCACTAG 60.082 45.833 0.00 0.00 0.00 2.57
972 997 3.832490 AGGACACAACAGTATCAGCACTA 59.168 43.478 0.00 0.00 0.00 2.74
973 998 2.634940 AGGACACAACAGTATCAGCACT 59.365 45.455 0.00 0.00 0.00 4.40
974 999 2.996621 GAGGACACAACAGTATCAGCAC 59.003 50.000 0.00 0.00 0.00 4.40
975 1000 2.352715 CGAGGACACAACAGTATCAGCA 60.353 50.000 0.00 0.00 0.00 4.41
976 1001 2.263077 CGAGGACACAACAGTATCAGC 58.737 52.381 0.00 0.00 0.00 4.26
977 1002 2.881074 CCGAGGACACAACAGTATCAG 58.119 52.381 0.00 0.00 0.00 2.90
978 1003 1.067142 GCCGAGGACACAACAGTATCA 60.067 52.381 0.00 0.00 0.00 2.15
1014 1039 2.673523 GCCAGGAGCATGGACTGT 59.326 61.111 5.21 0.00 43.57 3.55
1266 1291 2.203640 AGGACGTGCAGGGACAGA 60.204 61.111 10.52 0.00 0.00 3.41
1378 1403 8.892723 CACACCAAAATCTGTATACACATGTAT 58.107 33.333 0.08 9.40 43.15 2.29
1379 1404 7.148323 GCACACCAAAATCTGTATACACATGTA 60.148 37.037 0.08 0.00 33.14 2.29
1380 1405 6.349280 GCACACCAAAATCTGTATACACATGT 60.349 38.462 0.08 0.00 33.14 3.21
1381 1406 6.029607 GCACACCAAAATCTGTATACACATG 58.970 40.000 0.08 0.00 33.14 3.21
1382 1407 5.709631 TGCACACCAAAATCTGTATACACAT 59.290 36.000 0.08 0.00 33.14 3.21
1383 1408 5.049060 GTGCACACCAAAATCTGTATACACA 60.049 40.000 13.17 0.00 0.00 3.72
1384 1409 5.049060 TGTGCACACCAAAATCTGTATACAC 60.049 40.000 17.42 0.00 0.00 2.90
1577 1830 4.404073 TGGTTTCGGCTATGGCAAAAATAT 59.596 37.500 2.58 0.00 40.87 1.28
1624 1877 1.545841 AATCTCGTTCCTTTTGGCCC 58.454 50.000 0.00 0.00 40.12 5.80
1817 2070 4.237976 TGGTGTTCACCCAACTAGAAAA 57.762 40.909 17.78 0.00 35.79 2.29
1961 2248 8.134895 GTGACAATTTATGTTGGTTTTCTCAGA 58.865 33.333 0.00 0.00 44.12 3.27
2051 2338 9.781834 GATGAACGGTTGAAATACATATTTTGA 57.218 29.630 0.00 0.00 36.13 2.69
2072 2365 5.568023 CGGTTTAGATAATAGGGCCGATGAA 60.568 44.000 0.00 0.00 40.27 2.57
2163 2481 2.111043 ACCCACAGCAGAACACCG 59.889 61.111 0.00 0.00 0.00 4.94
2461 2812 1.359459 CGCTAGAGGAAACGGCAACC 61.359 60.000 0.00 0.00 0.00 3.77
2467 2818 4.034858 TGAGTATACACGCTAGAGGAAACG 59.965 45.833 5.50 0.00 0.00 3.60
2475 2826 8.046294 AGATAGGAAATGAGTATACACGCTAG 57.954 38.462 5.50 0.00 0.00 3.42
2489 2842 7.235606 TCCTGTAGGTATGGAAGATAGGAAATG 59.764 40.741 0.00 0.00 36.34 2.32
2686 3410 4.332819 GTCCCGGTAGACTGAAATCATTTG 59.667 45.833 0.00 0.00 33.79 2.32
2755 3479 1.070786 GACGAACTCCACCTTGCCA 59.929 57.895 0.00 0.00 0.00 4.92
2809 3533 3.192844 TCTCCTTGATGGACTTGACGTAC 59.807 47.826 0.00 0.00 40.56 3.67
3755 4487 7.881775 ACAAGACTCCAAAAAGAAACTACAT 57.118 32.000 0.00 0.00 0.00 2.29
3922 4657 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3941 4676 4.034048 CCAACAAATGACTACATACGGAGC 59.966 45.833 0.00 0.00 35.50 4.70
3945 5871 7.492669 AGAGATTCCAACAAATGACTACATACG 59.507 37.037 0.00 0.00 35.50 3.06
3975 5901 8.271398 TCCCTCCGTTCCTAAATATAAATCTT 57.729 34.615 0.00 0.00 0.00 2.40
4007 5933 9.658799 CAATAGAATGGTACCATACTTCCATAG 57.341 37.037 27.58 9.44 39.39 2.23
4014 5940 7.290061 ACATTGCAATAGAATGGTACCATACT 58.710 34.615 27.58 13.47 35.48 2.12
4116 6042 2.666026 CATCCACCAGACGATATCACG 58.334 52.381 3.12 0.00 39.31 4.35
4122 6048 4.941609 GTGCATCCACCAGACGAT 57.058 55.556 0.00 0.00 35.92 3.73
4173 6099 0.823356 GTGTGGTTGAGCATGTGGGT 60.823 55.000 0.00 0.00 0.00 4.51
4220 6146 2.253452 GCGTCAACCTTGCTGCTG 59.747 61.111 0.00 0.00 0.00 4.41
4241 6167 2.590092 GCTAGGGGCGTGGATGTT 59.410 61.111 0.00 0.00 0.00 2.71
4322 6248 4.838152 CGGCTGGTGGGTGATCGG 62.838 72.222 0.00 0.00 0.00 4.18
4328 6254 3.083997 GAGGATCGGCTGGTGGGT 61.084 66.667 0.00 0.00 0.00 4.51
4335 6261 4.841617 TGAGCGGGAGGATCGGCT 62.842 66.667 0.00 0.00 46.19 5.52
4407 6333 4.202243 CCCAATGCATTTTGTCGGGATAAT 60.202 41.667 21.79 0.00 0.00 1.28
4442 6368 3.798511 CCCTCGGCTTCCCCTTCC 61.799 72.222 0.00 0.00 0.00 3.46
4449 6375 3.787001 CACCCCTCCCTCGGCTTC 61.787 72.222 0.00 0.00 0.00 3.86
4478 6404 1.894756 CTCCTCCCTAGCGACTCGG 60.895 68.421 0.00 0.00 0.00 4.63
4487 6413 2.050350 CGCAACGTCCTCCTCCCTA 61.050 63.158 0.00 0.00 0.00 3.53
4490 6416 4.452733 CCCGCAACGTCCTCCTCC 62.453 72.222 0.00 0.00 0.00 4.30
4501 6427 3.338250 AGGATTGAGCCCCCGCAA 61.338 61.111 0.00 0.00 37.52 4.85
4502 6428 4.113815 CAGGATTGAGCCCCCGCA 62.114 66.667 0.00 0.00 37.52 5.69


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

AutoCloner maintained by Alex Coulton.