Multiple sequence alignment - TraesCS7D01G169300

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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 TraesCS7D01G169300 chr7D 100.000 4673 0 0 865 5537 120314234 120318906 0.000000e+00 8630.0
1 TraesCS7D01G169300 chr7D 100.000 336 0 0 1 336 120313370 120313705 6.090000e-174 621.0
2 TraesCS7D01G169300 chr7D 91.892 74 6 0 5009 5082 205540693 205540766 2.730000e-18 104.0
3 TraesCS7D01G169300 chr7D 94.118 68 3 1 3896 3963 185353442 185353508 9.810000e-18 102.0
4 TraesCS7D01G169300 chr7B 93.966 2088 60 19 870 2925 81684933 81686986 0.000000e+00 3097.0
5 TraesCS7D01G169300 chr7B 95.009 1643 65 9 3407 5037 81687449 81689086 0.000000e+00 2564.0
6 TraesCS7D01G169300 chr7B 92.757 428 18 7 5119 5537 81689107 81689530 1.710000e-169 606.0
7 TraesCS7D01G169300 chr7B 90.497 463 16 10 2953 3415 81686983 81687417 2.220000e-163 586.0
8 TraesCS7D01G169300 chr7B 85.294 340 36 9 6 335 81684543 81684878 6.870000e-89 339.0
9 TraesCS7D01G169300 chr7B 91.667 72 6 0 5011 5082 194607280 194607209 3.530000e-17 100.0
10 TraesCS7D01G169300 chr7A 92.128 1931 73 33 865 2757 125256645 125258534 0.000000e+00 2651.0
11 TraesCS7D01G169300 chr7A 96.237 1621 46 6 3407 5019 125259239 125260852 0.000000e+00 2641.0
12 TraesCS7D01G169300 chr7A 91.511 483 20 8 2953 3415 125258725 125259206 0.000000e+00 645.0
13 TraesCS7D01G169300 chr7A 90.845 426 23 6 5119 5537 125260891 125261307 1.740000e-154 556.0
14 TraesCS7D01G169300 chr7A 89.535 344 26 5 1 335 125256249 125256591 1.430000e-115 427.0
15 TraesCS7D01G169300 chr7A 88.889 297 22 7 3676 3966 696324841 696324550 6.820000e-94 355.0
16 TraesCS7D01G169300 chr7A 95.556 180 8 0 2746 2925 125258549 125258728 7.020000e-74 289.0
17 TraesCS7D01G169300 chr7A 92.523 107 6 2 3434 3540 696324937 696324833 9.610000e-33 152.0
18 TraesCS7D01G169300 chr7A 96.875 64 2 0 3042 3105 696325032 696324969 2.110000e-19 108.0
19 TraesCS7D01G169300 chr1A 92.337 261 14 3 3702 3961 582876878 582876623 3.150000e-97 366.0
20 TraesCS7D01G169300 chr1A 94.000 100 5 1 3441 3540 582876999 582876901 3.460000e-32 150.0
21 TraesCS7D01G169300 chr1A 96.875 64 2 0 3042 3105 582877099 582877036 2.110000e-19 108.0
22 TraesCS7D01G169300 chr4A 88.776 294 25 5 3676 3966 225615102 225614814 2.450000e-93 353.0
23 TraesCS7D01G169300 chr4A 92.704 233 12 2 3734 3966 700325320 700325093 1.150000e-86 331.0
24 TraesCS7D01G169300 chr4A 96.117 103 4 0 3005 3107 700325476 700325374 9.540000e-38 169.0
25 TraesCS7D01G169300 chr4A 94.059 101 5 1 3440 3540 225615193 225615094 9.610000e-33 152.0
26 TraesCS7D01G169300 chr2D 85.106 141 12 4 5013 5144 498106118 498106258 9.680000e-28 135.0
27 TraesCS7D01G169300 chr3D 92.958 71 5 0 5013 5083 91331069 91330999 2.730000e-18 104.0
28 TraesCS7D01G169300 chr6D 92.958 71 4 1 3896 3966 28132547 28132478 9.810000e-18 102.0
29 TraesCS7D01G169300 chr6D 83.478 115 13 6 5032 5143 91845502 91845613 9.810000e-18 102.0
30 TraesCS7D01G169300 chr6A 91.781 73 6 0 5010 5082 70421220 70421148 9.810000e-18 102.0
31 TraesCS7D01G169300 chr5A 91.781 73 6 0 5010 5082 341660119 341660191 9.810000e-18 102.0
32 TraesCS7D01G169300 chr5A 87.654 81 8 1 5002 5082 389715933 389716011 5.910000e-15 93.5
33 TraesCS7D01G169300 chr3B 90.667 75 7 0 5009 5083 805607671 805607745 3.530000e-17 100.0
34 TraesCS7D01G169300 chr3B 88.406 69 6 2 5086 5152 716149040 716149108 1.280000e-11 82.4
35 TraesCS7D01G169300 chr5D 93.220 59 3 1 5086 5143 510094706 510094764 9.880000e-13 86.1
36 TraesCS7D01G169300 chr4B 93.103 58 4 0 5086 5143 527317363 527317420 9.880000e-13 86.1
37 TraesCS7D01G169300 chr6B 88.406 69 7 1 5075 5143 255276405 255276338 1.280000e-11 82.4
38 TraesCS7D01G169300 chr6B 88.406 69 7 1 5075 5143 584034471 584034538 1.280000e-11 82.4
39 TraesCS7D01G169300 chr2B 89.394 66 6 1 5086 5151 184121531 184121467 1.280000e-11 82.4
40 TraesCS7D01G169300 chr1D 89.231 65 7 0 5087 5151 326255636 326255700 1.280000e-11 82.4
41 TraesCS7D01G169300 chr2A 91.379 58 5 0 5086 5143 698191029 698190972 4.600000e-11 80.5


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 TraesCS7D01G169300 chr7D 120313370 120318906 5536 False 4625.5 8630 100.000000 1 5537 2 chr7D.!!$F3 5536
1 TraesCS7D01G169300 chr7B 81684543 81689530 4987 False 1438.4 3097 91.504600 6 5537 5 chr7B.!!$F1 5531
2 TraesCS7D01G169300 chr7A 125256249 125261307 5058 False 1201.5 2651 92.635333 1 5537 6 chr7A.!!$F1 5536

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
973 991 1.100510 GGATTTTACGGTTCTGCCCC 58.899 55.0 0.0 0.0 0.00 5.80 F
2900 2997 0.541863 GTGACCATGTACCTCCCTGG 59.458 60.0 0.0 0.0 42.93 4.45 F
3757 3915 0.185901 ACAGACATGGCAAGTTGGGT 59.814 50.0 0.0 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2955 3052 0.330604 ATGGAGAAGCAGCACCACAT 59.669 50.000 0.00 0.0 35.19 3.21 R
4330 4497 0.370273 CGAAGTATTGCACGGTGAGC 59.630 55.000 13.29 0.0 0.00 4.26 R
4940 5115 1.919308 TGCCAATGCCAGCCCAATT 60.919 52.632 0.00 0.0 36.33 2.32 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
28 29 1.858091 ATCATCACGAATCTCCACGC 58.142 50.000 0.00 0.00 0.00 5.34
37 38 2.355756 CGAATCTCCACGCAAAATCCAT 59.644 45.455 0.00 0.00 0.00 3.41
45 47 3.181497 CCACGCAAAATCCATGAAGTAGG 60.181 47.826 0.00 0.00 0.00 3.18
61 63 9.205719 CATGAAGTAGGAATTAGATGAGACATG 57.794 37.037 0.00 0.00 0.00 3.21
70 72 8.499162 GGAATTAGATGAGACATGGTTATTTCG 58.501 37.037 0.00 0.00 0.00 3.46
84 86 9.914131 CATGGTTATTTCGTATCTAGATGAGAA 57.086 33.333 15.79 15.96 37.85 2.87
92 94 7.949903 TCGTATCTAGATGAGAACTAGTCAC 57.050 40.000 15.79 0.00 37.85 3.67
95 97 6.612247 ATCTAGATGAGAACTAGTCACACG 57.388 41.667 3.89 0.00 37.85 4.49
100 106 4.156664 TGAGAACTAGTCACACGCTAAC 57.843 45.455 0.00 0.00 0.00 2.34
131 137 1.332375 ACAATCGGTTGAACCAACACG 59.668 47.619 16.93 11.48 45.11 4.49
156 162 7.309012 CGCCCTTTCTCATGATTAAATCATCAT 60.309 37.037 0.00 0.00 46.62 2.45
335 352 3.621558 CTTCCTCCAATTACCCACCTTC 58.378 50.000 0.00 0.00 0.00 3.46
973 991 1.100510 GGATTTTACGGTTCTGCCCC 58.899 55.000 0.00 0.00 0.00 5.80
1340 1376 1.682867 TTATTGCGCTGCTCGTGTCG 61.683 55.000 9.73 0.00 41.07 4.35
1363 1399 3.103911 CGTGGTTCTGACGTCCGC 61.104 66.667 14.12 3.20 32.06 5.54
1517 1557 5.111989 GGCTTTGCCTTTATGAAATTCTCC 58.888 41.667 0.73 0.00 46.69 3.71
1524 1564 6.049790 GCCTTTATGAAATTCTCCTCTACGT 58.950 40.000 0.00 0.00 0.00 3.57
1539 1579 5.243060 TCCTCTACGTTGTTTCTCTTGATGA 59.757 40.000 0.00 0.00 0.00 2.92
1548 1588 7.322222 CGTTGTTTCTCTTGATGACAATTCTTC 59.678 37.037 0.00 0.00 33.96 2.87
1549 1589 8.348507 GTTGTTTCTCTTGATGACAATTCTTCT 58.651 33.333 0.00 0.00 33.96 2.85
1550 1590 8.455903 TGTTTCTCTTGATGACAATTCTTCTT 57.544 30.769 0.00 0.00 35.37 2.52
1551 1591 8.347771 TGTTTCTCTTGATGACAATTCTTCTTG 58.652 33.333 0.00 0.00 35.37 3.02
1552 1592 6.492007 TCTCTTGATGACAATTCTTCTTGC 57.508 37.500 0.00 0.00 35.37 4.01
1553 1593 6.236409 TCTCTTGATGACAATTCTTCTTGCT 58.764 36.000 0.00 0.00 35.37 3.91
1554 1594 6.148976 TCTCTTGATGACAATTCTTCTTGCTG 59.851 38.462 0.00 0.00 35.37 4.41
1555 1595 5.182570 TCTTGATGACAATTCTTCTTGCTGG 59.817 40.000 0.00 0.00 35.37 4.85
1556 1596 3.192001 TGATGACAATTCTTCTTGCTGGC 59.808 43.478 0.00 0.00 0.00 4.85
1557 1597 2.585330 TGACAATTCTTCTTGCTGGCA 58.415 42.857 0.00 0.00 0.00 4.92
1558 1598 2.957680 TGACAATTCTTCTTGCTGGCAA 59.042 40.909 7.78 7.78 0.00 4.52
1559 1599 3.575256 TGACAATTCTTCTTGCTGGCAAT 59.425 39.130 8.49 0.00 35.20 3.56
1560 1600 4.039488 TGACAATTCTTCTTGCTGGCAATT 59.961 37.500 8.49 0.00 35.20 2.32
1561 1601 4.563061 ACAATTCTTCTTGCTGGCAATTC 58.437 39.130 8.49 0.00 35.20 2.17
1562 1602 4.282703 ACAATTCTTCTTGCTGGCAATTCT 59.717 37.500 8.49 0.00 35.20 2.40
1563 1603 5.221581 ACAATTCTTCTTGCTGGCAATTCTT 60.222 36.000 8.49 0.00 35.20 2.52
1566 1606 2.291209 TCTTGCTGGCAATTCTTGGA 57.709 45.000 8.49 0.00 35.20 3.53
1581 1621 2.099263 TCTTGGAGAAGGTAGAATCGCG 59.901 50.000 0.00 0.00 0.00 5.87
1632 1672 3.053455 CCGGAAGATACGAGAATTGCTC 58.947 50.000 0.00 0.00 40.38 4.26
1895 1943 8.457261 TGCTGCTGATTTTAAACAACAATTTTT 58.543 25.926 0.00 0.00 0.00 1.94
2133 2198 9.541143 CACAGTTTATTTGGTACAGGAATTTTT 57.459 29.630 0.00 0.00 42.39 1.94
2210 2275 4.514441 CCATATGCTCTTGCTCTTTAGGTG 59.486 45.833 0.00 0.00 40.48 4.00
2242 2307 1.472480 CTTTAATGGTCCCAACAGGCG 59.528 52.381 0.00 0.00 34.51 5.52
2368 2433 7.372260 AGTTGATATTGGACTGATCTAGCTT 57.628 36.000 0.00 0.00 0.00 3.74
2582 2648 3.729108 TCTGTTCTTGATGAGAGGGGAT 58.271 45.455 0.00 0.00 35.37 3.85
2583 2649 4.883759 TCTGTTCTTGATGAGAGGGGATA 58.116 43.478 0.00 0.00 35.37 2.59
2584 2650 5.280499 TCTGTTCTTGATGAGAGGGGATAA 58.720 41.667 0.00 0.00 35.37 1.75
2585 2651 5.129485 TCTGTTCTTGATGAGAGGGGATAAC 59.871 44.000 0.00 0.00 35.37 1.89
2586 2652 4.782691 TGTTCTTGATGAGAGGGGATAACA 59.217 41.667 0.00 0.00 35.37 2.41
2896 2993 3.627395 TTCATGTGACCATGTACCTCC 57.373 47.619 2.91 0.00 46.99 4.30
2900 2997 0.541863 GTGACCATGTACCTCCCTGG 59.458 60.000 0.00 0.00 42.93 4.45
2925 3022 4.678574 GCTTTGCATCTGATGTTGGCATAA 60.679 41.667 18.19 7.12 35.07 1.90
2926 3023 5.597806 CTTTGCATCTGATGTTGGCATAAT 58.402 37.500 18.19 0.00 35.07 1.28
2927 3024 6.712179 TTTGCATCTGATGTTGGCATAATA 57.288 33.333 18.19 0.00 35.07 0.98
2928 3025 6.904463 TTGCATCTGATGTTGGCATAATAT 57.096 33.333 18.19 0.00 35.07 1.28
2929 3026 7.999450 TTGCATCTGATGTTGGCATAATATA 57.001 32.000 18.19 0.00 35.07 0.86
2930 3027 7.999450 TGCATCTGATGTTGGCATAATATAA 57.001 32.000 18.19 0.00 35.07 0.98
2931 3028 8.406730 TGCATCTGATGTTGGCATAATATAAA 57.593 30.769 18.19 0.00 35.07 1.40
2932 3029 9.027202 TGCATCTGATGTTGGCATAATATAAAT 57.973 29.630 18.19 0.00 35.07 1.40
2942 3039 9.241317 GTTGGCATAATATAAATATCTGCATGC 57.759 33.333 11.82 11.82 35.08 4.06
2943 3040 8.522542 TGGCATAATATAAATATCTGCATGCA 57.477 30.769 21.29 21.29 38.35 3.96
2944 3041 8.968969 TGGCATAATATAAATATCTGCATGCAA 58.031 29.630 22.88 13.05 38.35 4.08
2945 3042 9.459640 GGCATAATATAAATATCTGCATGCAAG 57.540 33.333 22.88 15.46 38.35 4.01
2946 3043 8.965172 GCATAATATAAATATCTGCATGCAAGC 58.035 33.333 22.88 7.04 36.97 4.01
2952 3049 8.752766 ATAAATATCTGCATGCAAGCATAAAC 57.247 30.769 22.88 1.48 44.68 2.01
2953 3050 5.777850 ATATCTGCATGCAAGCATAAACA 57.222 34.783 22.88 5.92 44.68 2.83
2954 3051 4.665833 ATCTGCATGCAAGCATAAACAT 57.334 36.364 22.88 2.23 44.68 2.71
2955 3052 5.777850 ATCTGCATGCAAGCATAAACATA 57.222 34.783 22.88 0.00 44.68 2.29
3072 3169 4.808558 TCATGCCACTTATGAACAAAAGC 58.191 39.130 0.00 0.00 31.98 3.51
3093 3190 4.158394 AGCTGCAGTAAATTGTTGGTATGG 59.842 41.667 16.64 0.00 0.00 2.74
3210 3307 2.091555 ACTTTTGGAGGTTTAGGTGCCA 60.092 45.455 0.00 0.00 0.00 4.92
3243 3340 6.671190 TCAGTTCATTGATGACAATTGTGAC 58.329 36.000 17.58 2.76 43.17 3.67
3272 3369 2.299867 TGGGCAAAGCTTCCAGATTTTC 59.700 45.455 0.00 0.00 30.47 2.29
3573 3730 6.220930 TGGTCTGTGTGTCATAGTTTCTTAC 58.779 40.000 0.00 0.00 0.00 2.34
3657 3815 3.604875 ATGTGGTTTGTAGTCCTACCG 57.395 47.619 2.18 0.00 35.26 4.02
3692 3850 5.135383 ACATGATGGATGGTTGACCTTATG 58.865 41.667 0.00 0.00 36.23 1.90
3757 3915 0.185901 ACAGACATGGCAAGTTGGGT 59.814 50.000 0.00 0.00 0.00 4.51
3806 3964 9.054922 CCAATTTGTTGAAACCACTGAAATAAT 57.945 29.630 0.00 0.00 0.00 1.28
3874 4032 8.690203 TTGGTCATCTATTTTTCTTTGTCTGA 57.310 30.769 0.00 0.00 0.00 3.27
4020 4178 9.396022 TCTAAAGTCTTGATAATTCCACCATTC 57.604 33.333 0.00 0.00 0.00 2.67
4085 4243 2.812011 GTTACTGCAGGAACCATTCGTT 59.188 45.455 28.58 0.21 37.41 3.85
4182 4340 1.448540 GGTCACCTCCATCACAGCG 60.449 63.158 0.00 0.00 0.00 5.18
4278 4444 4.518249 AGAGGCAAGGTAAGCTTAATCAC 58.482 43.478 7.99 0.00 0.00 3.06
4319 4486 4.210120 GCAGCTGGTATTTCAAGTCGATAG 59.790 45.833 17.12 0.00 0.00 2.08
4330 4497 7.582435 TTTCAAGTCGATAGCTTTCTACTTG 57.418 36.000 29.53 29.53 44.54 3.16
4377 4545 1.672356 GCAGCACCGAACTGGATGT 60.672 57.895 0.00 0.00 42.00 3.06
4539 4707 3.886505 TGACCAACTCACATTGTTAACCC 59.113 43.478 2.48 0.00 0.00 4.11
4672 4840 6.810676 CGTAGAATGAATCCATGAGATAGTGG 59.189 42.308 0.00 0.00 33.66 4.00
4725 4894 8.546597 AGAAGAACTTGAGAGCTCTATTTTTC 57.453 34.615 18.25 17.29 28.44 2.29
4954 5129 1.392589 CGACTAATTGGGCTGGCATT 58.607 50.000 2.88 0.00 0.00 3.56
4956 5131 1.410153 GACTAATTGGGCTGGCATTGG 59.590 52.381 2.88 0.00 0.00 3.16
5019 5194 5.243060 CGGATGATACTAACATGTACTCCCA 59.757 44.000 0.00 0.00 0.00 4.37
5024 5199 2.901839 ACTAACATGTACTCCCACCGTT 59.098 45.455 0.00 0.00 0.00 4.44
5026 5201 0.245539 ACATGTACTCCCACCGTTCG 59.754 55.000 0.00 0.00 0.00 3.95
5027 5202 0.245539 CATGTACTCCCACCGTTCGT 59.754 55.000 0.00 0.00 0.00 3.85
5028 5203 1.473677 CATGTACTCCCACCGTTCGTA 59.526 52.381 0.00 0.00 0.00 3.43
5037 5212 5.127682 ACTCCCACCGTTCGTAAATATAAGT 59.872 40.000 0.00 0.00 0.00 2.24
5038 5213 5.591099 TCCCACCGTTCGTAAATATAAGTC 58.409 41.667 0.00 0.00 0.00 3.01
5039 5214 5.360714 TCCCACCGTTCGTAAATATAAGTCT 59.639 40.000 0.00 0.00 0.00 3.24
5040 5215 6.044682 CCCACCGTTCGTAAATATAAGTCTT 58.955 40.000 0.00 0.00 0.00 3.01
5084 5259 9.838339 AGACTACAAAGGGATGTATAAAGATTG 57.162 33.333 0.00 0.00 35.37 2.67
5085 5260 8.451908 ACTACAAAGGGATGTATAAAGATTGC 57.548 34.615 0.00 0.00 35.37 3.56
5086 5261 6.377327 ACAAAGGGATGTATAAAGATTGCG 57.623 37.500 0.00 0.00 0.00 4.85
5087 5262 5.885912 ACAAAGGGATGTATAAAGATTGCGT 59.114 36.000 0.00 0.00 0.00 5.24
5088 5263 7.051623 ACAAAGGGATGTATAAAGATTGCGTA 58.948 34.615 0.00 0.00 0.00 4.42
5089 5264 7.719633 ACAAAGGGATGTATAAAGATTGCGTAT 59.280 33.333 0.00 0.00 0.00 3.06
5090 5265 9.214957 CAAAGGGATGTATAAAGATTGCGTATA 57.785 33.333 0.00 0.00 0.00 1.47
5091 5266 9.959721 AAAGGGATGTATAAAGATTGCGTATAT 57.040 29.630 0.00 0.00 0.00 0.86
5186 5363 1.915614 GAGGGTGCTGTTCATGTGCG 61.916 60.000 0.00 0.00 0.00 5.34
5191 5368 1.349627 GCTGTTCATGTGCGATCGG 59.650 57.895 18.30 0.00 0.00 4.18
5213 5390 4.155462 GGTACGAGGAAATTTTCAACCTCC 59.845 45.833 14.78 0.90 43.98 4.30
5242 5419 7.014711 AGGAGATCATGTAATTCGTCTACACAT 59.985 37.037 0.00 0.00 32.27 3.21
5284 5461 3.476552 TGTGAGACAAAATGTGGACTCC 58.523 45.455 0.00 0.00 35.37 3.85
5494 5678 7.373493 AGTAACATGAATTTCCTTCTTGCTTG 58.627 34.615 0.00 0.00 40.80 4.01
5509 5693 3.819564 TGCTTGCTATGGTAGTCGAAT 57.180 42.857 0.00 0.00 0.00 3.34
5510 5694 4.137116 TGCTTGCTATGGTAGTCGAATT 57.863 40.909 0.00 0.00 0.00 2.17
5511 5695 4.513442 TGCTTGCTATGGTAGTCGAATTT 58.487 39.130 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 7.345653 ACCATGTCTCATCTAATTCCTACTTCA 59.654 37.037 0.00 0.00 0.00 3.02
45 47 9.046296 ACGAAATAACCATGTCTCATCTAATTC 57.954 33.333 0.00 0.00 0.00 2.17
70 72 7.569297 CGTGTGACTAGTTCTCATCTAGATAC 58.431 42.308 4.54 0.00 38.45 2.24
84 86 6.312918 CCAAATATTGTTAGCGTGTGACTAGT 59.687 38.462 0.00 0.00 0.00 2.57
89 91 4.393680 GTCCCAAATATTGTTAGCGTGTGA 59.606 41.667 0.00 0.00 0.00 3.58
92 94 4.955925 TGTCCCAAATATTGTTAGCGTG 57.044 40.909 0.00 0.00 0.00 5.34
95 97 5.067283 ACCGATTGTCCCAAATATTGTTAGC 59.933 40.000 0.00 0.00 0.00 3.09
100 106 5.574891 TCAACCGATTGTCCCAAATATTG 57.425 39.130 0.00 0.00 37.11 1.90
186 195 3.966979 TGGCTCCATTATTCATGTGTGT 58.033 40.909 0.00 0.00 0.00 3.72
864 881 6.926630 AGGCAGAGGTTATTTATAGGAGAG 57.073 41.667 0.00 0.00 0.00 3.20
865 882 6.270231 GGAAGGCAGAGGTTATTTATAGGAGA 59.730 42.308 0.00 0.00 0.00 3.71
866 883 6.043243 TGGAAGGCAGAGGTTATTTATAGGAG 59.957 42.308 0.00 0.00 0.00 3.69
867 884 5.908831 TGGAAGGCAGAGGTTATTTATAGGA 59.091 40.000 0.00 0.00 0.00 2.94
868 885 6.183361 ACTGGAAGGCAGAGGTTATTTATAGG 60.183 42.308 0.00 0.00 39.30 2.57
902 919 1.369692 CTTGAGCGGTGTGGGTGTA 59.630 57.895 0.00 0.00 0.00 2.90
1340 1376 2.213483 CGTCAGAACCACGTGACAC 58.787 57.895 19.30 7.41 42.79 3.67
1502 1542 8.480643 ACAACGTAGAGGAGAATTTCATAAAG 57.519 34.615 0.00 0.00 0.00 1.85
1517 1557 5.920840 TGTCATCAAGAGAAACAACGTAGAG 59.079 40.000 0.00 0.00 0.00 2.43
1524 1564 8.455903 AGAAGAATTGTCATCAAGAGAAACAA 57.544 30.769 0.00 0.00 37.66 2.83
1539 1579 4.282703 AGAATTGCCAGCAAGAAGAATTGT 59.717 37.500 11.21 0.00 39.47 2.71
1557 1597 5.119694 GCGATTCTACCTTCTCCAAGAATT 58.880 41.667 0.00 0.00 38.47 2.17
1558 1598 4.698575 GCGATTCTACCTTCTCCAAGAAT 58.301 43.478 0.00 0.00 40.47 2.40
1559 1599 3.428999 CGCGATTCTACCTTCTCCAAGAA 60.429 47.826 0.00 0.00 32.50 2.52
1560 1600 2.099263 CGCGATTCTACCTTCTCCAAGA 59.901 50.000 0.00 0.00 0.00 3.02
1561 1601 2.464865 CGCGATTCTACCTTCTCCAAG 58.535 52.381 0.00 0.00 0.00 3.61
1562 1602 1.136305 CCGCGATTCTACCTTCTCCAA 59.864 52.381 8.23 0.00 0.00 3.53
1563 1603 0.744874 CCGCGATTCTACCTTCTCCA 59.255 55.000 8.23 0.00 0.00 3.86
1566 1606 0.824759 AAGCCGCGATTCTACCTTCT 59.175 50.000 8.23 0.00 0.00 2.85
1632 1672 2.809601 CGACCTCGGTTCTTGGCG 60.810 66.667 0.00 0.00 35.37 5.69
1924 1972 3.820467 CCTTGTTATCACAGGAGCAAACA 59.180 43.478 0.00 0.00 31.48 2.83
2057 2107 3.455910 TCCATGAGCTACCTACTTTGCAT 59.544 43.478 0.00 0.00 0.00 3.96
2133 2198 4.501571 GCTCACACTGAAACCTCTACAAGA 60.502 45.833 0.00 0.00 0.00 3.02
2144 2209 2.148768 CATGAGCTGCTCACACTGAAA 58.851 47.619 32.54 9.45 43.63 2.69
2210 2275 5.168569 GGACCATTAAAGCTGCTTAAAACC 58.831 41.667 16.31 9.20 0.00 3.27
2242 2307 7.671495 ATTTTAATTCACAAAACTGGGCATC 57.329 32.000 0.00 0.00 0.00 3.91
2368 2433 1.699730 TCGTCCAACTTGACTCAGGA 58.300 50.000 0.00 0.00 32.97 3.86
2501 2567 6.489700 CCATACTGACATGCCCACAATTATTA 59.510 38.462 0.00 0.00 0.00 0.98
2510 2576 0.394216 GTGCCATACTGACATGCCCA 60.394 55.000 0.00 0.00 0.00 5.36
2582 2648 4.616553 TCTAGGCCTCCAGTGTTATGTTA 58.383 43.478 9.68 0.00 0.00 2.41
2583 2649 3.450904 TCTAGGCCTCCAGTGTTATGTT 58.549 45.455 9.68 0.00 0.00 2.71
2584 2650 3.116096 TCTAGGCCTCCAGTGTTATGT 57.884 47.619 9.68 0.00 0.00 2.29
2585 2651 3.900601 AGATCTAGGCCTCCAGTGTTATG 59.099 47.826 9.68 0.00 0.00 1.90
2586 2652 3.900601 CAGATCTAGGCCTCCAGTGTTAT 59.099 47.826 9.68 0.00 0.00 1.89
2896 2993 1.134367 CATCAGATGCAAAGCACCAGG 59.866 52.381 0.00 0.00 43.04 4.45
2900 2997 2.602878 CCAACATCAGATGCAAAGCAC 58.397 47.619 10.59 0.00 43.04 4.40
2926 3023 9.844790 GTTTATGCTTGCATGCAGATATTTATA 57.155 29.630 28.23 13.19 46.71 0.98
2927 3024 8.361889 TGTTTATGCTTGCATGCAGATATTTAT 58.638 29.630 28.23 14.10 46.71 1.40
2928 3025 7.714703 TGTTTATGCTTGCATGCAGATATTTA 58.285 30.769 28.23 14.46 46.71 1.40
2929 3026 6.575267 TGTTTATGCTTGCATGCAGATATTT 58.425 32.000 28.23 15.37 46.71 1.40
2930 3027 6.151663 TGTTTATGCTTGCATGCAGATATT 57.848 33.333 28.23 16.01 46.71 1.28
2931 3028 5.777850 TGTTTATGCTTGCATGCAGATAT 57.222 34.783 28.23 17.15 46.71 1.63
2932 3029 5.777850 ATGTTTATGCTTGCATGCAGATA 57.222 34.783 28.23 18.30 46.71 1.98
2933 3030 4.665833 ATGTTTATGCTTGCATGCAGAT 57.334 36.364 28.23 17.30 46.71 2.90
2934 3031 5.068067 ACATATGTTTATGCTTGCATGCAGA 59.932 36.000 28.23 22.96 46.71 4.26
2935 3032 5.174943 CACATATGTTTATGCTTGCATGCAG 59.825 40.000 28.23 15.64 46.71 4.41
2937 3034 4.446385 CCACATATGTTTATGCTTGCATGC 59.554 41.667 17.19 17.19 39.09 4.06
2938 3035 5.460748 CACCACATATGTTTATGCTTGCATG 59.539 40.000 17.26 3.09 39.09 4.06
2939 3036 5.593968 CACCACATATGTTTATGCTTGCAT 58.406 37.500 5.37 12.88 39.09 3.96
2940 3037 4.677514 GCACCACATATGTTTATGCTTGCA 60.678 41.667 20.77 0.00 39.09 4.08
2941 3038 3.798337 GCACCACATATGTTTATGCTTGC 59.202 43.478 20.77 12.12 39.09 4.01
2942 3039 5.038683 CAGCACCACATATGTTTATGCTTG 58.961 41.667 25.22 19.06 39.09 4.01
2943 3040 4.440525 GCAGCACCACATATGTTTATGCTT 60.441 41.667 25.22 14.15 39.09 3.91
2944 3041 3.067180 GCAGCACCACATATGTTTATGCT 59.933 43.478 23.34 23.34 39.09 3.79
2945 3042 3.067180 AGCAGCACCACATATGTTTATGC 59.933 43.478 20.59 20.59 39.09 3.14
2946 3043 4.906065 AGCAGCACCACATATGTTTATG 57.094 40.909 5.37 6.04 40.93 1.90
2947 3044 5.195940 AGAAGCAGCACCACATATGTTTAT 58.804 37.500 5.37 0.00 0.00 1.40
2948 3045 4.588899 AGAAGCAGCACCACATATGTTTA 58.411 39.130 5.37 0.00 0.00 2.01
2949 3046 3.424703 AGAAGCAGCACCACATATGTTT 58.575 40.909 5.37 0.00 0.00 2.83
2950 3047 3.012518 GAGAAGCAGCACCACATATGTT 58.987 45.455 5.37 0.00 0.00 2.71
2951 3048 2.636830 GAGAAGCAGCACCACATATGT 58.363 47.619 1.41 1.41 0.00 2.29
2952 3049 1.945394 GGAGAAGCAGCACCACATATG 59.055 52.381 0.00 0.00 0.00 1.78
2953 3050 1.561076 TGGAGAAGCAGCACCACATAT 59.439 47.619 0.00 0.00 0.00 1.78
2954 3051 0.983467 TGGAGAAGCAGCACCACATA 59.017 50.000 0.00 0.00 0.00 2.29
2955 3052 0.330604 ATGGAGAAGCAGCACCACAT 59.669 50.000 0.00 0.00 35.19 3.21
3047 3144 6.202570 GCTTTTGTTCATAAGTGGCATGAAAA 59.797 34.615 0.00 0.00 42.44 2.29
3072 3169 4.704540 TCCCATACCAACAATTTACTGCAG 59.295 41.667 13.48 13.48 0.00 4.41
3210 3307 8.058667 TGTCATCAATGAACTGAGCAAATAAT 57.941 30.769 0.00 0.00 38.75 1.28
3243 3340 2.094545 GGAAGCTTTGCCCACAACTATG 60.095 50.000 0.00 0.00 34.87 2.23
3272 3369 3.771577 ACTGTAGTCACCCCTTGAAAG 57.228 47.619 0.00 0.00 35.39 2.62
3328 3425 9.273016 CGGACTAATCACATAAAAATACTGGAT 57.727 33.333 0.00 0.00 0.00 3.41
3329 3426 8.262227 ACGGACTAATCACATAAAAATACTGGA 58.738 33.333 0.00 0.00 0.00 3.86
3347 3463 7.823799 AGTTCCCGAATAATTAAAACGGACTAA 59.176 33.333 21.40 13.40 45.31 2.24
3366 3482 2.742372 CCGCTTCACCAGTTCCCG 60.742 66.667 0.00 0.00 0.00 5.14
3433 3590 9.533831 ACCTGGAAGTTCAGACATAAAAATAAT 57.466 29.630 0.00 0.00 36.93 1.28
3436 3593 7.004086 TGACCTGGAAGTTCAGACATAAAAAT 58.996 34.615 0.00 0.00 36.93 1.82
3573 3730 4.389992 AGTCTGACAATGACAACGCTAATG 59.610 41.667 10.88 0.00 36.94 1.90
3657 3815 8.225603 ACCATCCATCATGTACTATTTTTCAC 57.774 34.615 0.00 0.00 0.00 3.18
3692 3850 7.390718 TCTTCATAAAAAGAAGTAGGGTTCAGC 59.609 37.037 0.00 0.00 42.35 4.26
3732 3890 3.170791 ACTTGCCATGTCTGTCTATCG 57.829 47.619 0.00 0.00 0.00 2.92
3806 3964 1.651737 TAGCTAGTGCCCCAGTTTCA 58.348 50.000 0.00 0.00 40.80 2.69
3874 4032 3.562176 CCAAGGTCCAGTAAAGGCTGAAT 60.562 47.826 0.00 0.00 38.70 2.57
4020 4178 3.315470 CCAAGCATCAGATTCTGGACATG 59.685 47.826 13.59 10.80 31.51 3.21
4085 4243 4.262036 CGGATTTTCTCATCGGGTATCTCA 60.262 45.833 0.00 0.00 0.00 3.27
4182 4340 6.391537 ACGAAAGGAGTAAGAGAGATGAAAC 58.608 40.000 0.00 0.00 0.00 2.78
4278 4444 6.360329 CAGCTGCAAAGCTTAAAATGAAAAG 58.640 36.000 0.00 0.00 43.52 2.27
4319 4486 1.461127 CACGGTGAGCAAGTAGAAAGC 59.539 52.381 0.74 0.00 0.00 3.51
4330 4497 0.370273 CGAAGTATTGCACGGTGAGC 59.630 55.000 13.29 0.00 0.00 4.26
4377 4545 1.374125 CCTCATGCAACCGACGACA 60.374 57.895 0.00 0.00 0.00 4.35
4564 4732 2.830651 ACTAGAATCTGGGAGGACGT 57.169 50.000 0.00 0.00 0.00 4.34
4940 5115 1.919308 TGCCAATGCCAGCCCAATT 60.919 52.632 0.00 0.00 36.33 2.32
4954 5129 5.804639 ACTCATTAAGTTCTATGTGTGCCA 58.195 37.500 5.36 0.00 33.03 4.92
4956 5131 9.098355 TCATTACTCATTAAGTTCTATGTGTGC 57.902 33.333 12.36 0.00 39.55 4.57
5058 5233 9.838339 CAATCTTTATACATCCCTTTGTAGTCT 57.162 33.333 0.00 0.00 35.65 3.24
5059 5234 8.560374 GCAATCTTTATACATCCCTTTGTAGTC 58.440 37.037 0.00 0.00 35.65 2.59
5060 5235 7.226720 CGCAATCTTTATACATCCCTTTGTAGT 59.773 37.037 0.00 0.00 35.65 2.73
5061 5236 7.226720 ACGCAATCTTTATACATCCCTTTGTAG 59.773 37.037 0.00 0.00 35.65 2.74
5062 5237 7.051623 ACGCAATCTTTATACATCCCTTTGTA 58.948 34.615 0.00 0.00 36.57 2.41
5063 5238 5.885912 ACGCAATCTTTATACATCCCTTTGT 59.114 36.000 0.00 0.00 0.00 2.83
5064 5239 6.377327 ACGCAATCTTTATACATCCCTTTG 57.623 37.500 0.00 0.00 0.00 2.77
5065 5240 9.959721 ATATACGCAATCTTTATACATCCCTTT 57.040 29.630 0.00 0.00 0.00 3.11
5112 5287 9.392259 CCTTCCGTTCCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
5113 5288 8.765517 TCCTTCCGTTCCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
5114 5289 8.315220 TCCTTCCGTTCCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
5115 5290 7.564292 ACTCCTTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
5116 5291 7.724287 ACTCCTTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
5117 5292 7.672122 ACTCCTTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
5126 5301 4.038271 TGTCTTACTCCTTCCGTTCCTA 57.962 45.455 0.00 0.00 0.00 2.94
5127 5302 2.885616 TGTCTTACTCCTTCCGTTCCT 58.114 47.619 0.00 0.00 0.00 3.36
5130 5305 5.011738 TCTCAAATGTCTTACTCCTTCCGTT 59.988 40.000 0.00 0.00 0.00 4.44
5136 5311 4.593206 TGTGGTCTCAAATGTCTTACTCCT 59.407 41.667 0.00 0.00 0.00 3.69
5186 5363 5.446875 GGTTGAAAATTTCCTCGTACCGATC 60.447 44.000 3.00 0.00 34.61 3.69
5191 5368 4.155462 GGGAGGTTGAAAATTTCCTCGTAC 59.845 45.833 14.32 6.68 45.04 3.67
5213 5390 4.039730 AGACGAATTACATGATCTCCTGGG 59.960 45.833 0.00 0.00 0.00 4.45
5242 5419 3.737559 AGGACCTGCCATGTTTTATCA 57.262 42.857 0.00 0.00 40.02 2.15
5494 5678 7.921745 ACTAGAGAAAAATTCGACTACCATAGC 59.078 37.037 0.00 0.00 34.02 2.97
5509 5693 9.333724 CCCTACAACTTTTACACTAGAGAAAAA 57.666 33.333 0.00 0.00 0.00 1.94
5510 5694 8.488668 ACCCTACAACTTTTACACTAGAGAAAA 58.511 33.333 0.00 0.00 0.00 2.29
5511 5695 8.026396 ACCCTACAACTTTTACACTAGAGAAA 57.974 34.615 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.