Multiple sequence alignment - TraesCS7A01G231200

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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 TraesCS7A01G231200 chr7A 100.000 6479 0 0 1 6479 201991447 201984969 0.000000e+00 11965.0
1 TraesCS7A01G231200 chr7A 94.231 156 8 1 4293 4448 206959859 206960013 3.020000e-58 237.0
2 TraesCS7A01G231200 chr7A 94.194 155 8 1 4292 4446 462978586 462978739 1.090000e-57 235.0
3 TraesCS7A01G231200 chr7A 81.301 123 19 4 313 432 573837110 573837231 5.350000e-16 97.1
4 TraesCS7A01G231200 chr7A 80.469 128 23 2 313 439 610151572 610151698 5.350000e-16 97.1
5 TraesCS7A01G231200 chr7D 95.580 5927 204 19 559 6479 192375315 192369441 0.000000e+00 9441.0
6 TraesCS7A01G231200 chr7D 93.939 264 12 3 300 561 192375615 192375354 4.710000e-106 396.0
7 TraesCS7A01G231200 chr7D 94.570 221 7 2 72 291 192376172 192375956 2.890000e-88 337.0
8 TraesCS7A01G231200 chr7D 92.814 167 11 1 4293 4459 197927008 197927173 2.330000e-59 241.0
9 TraesCS7A01G231200 chr7D 93.590 156 8 2 4292 4446 436961794 436961948 1.400000e-56 231.0
10 TraesCS7A01G231200 chr7D 93.000 100 6 1 1 100 192378025 192377927 1.880000e-30 145.0
11 TraesCS7A01G231200 chr7B 94.798 5959 227 37 559 6479 155475045 155469132 0.000000e+00 9210.0
12 TraesCS7A01G231200 chr7B 96.918 292 7 2 1 291 155475879 155475589 7.550000e-134 488.0
13 TraesCS7A01G231200 chr7B 93.233 266 14 2 300 562 155475347 155475083 7.880000e-104 388.0
14 TraesCS7A01G231200 chr7B 93.590 156 8 2 4292 4446 453623289 453623443 1.400000e-56 231.0
15 TraesCS7A01G231200 chr4D 92.147 624 34 3 5856 6479 167197250 167197858 0.000000e+00 867.0
16 TraesCS7A01G231200 chr4D 92.453 53 1 3 445 495 397697297 397697348 9.010000e-09 73.1
17 TraesCS7A01G231200 chr5A 94.118 170 8 2 4285 4454 86662178 86662011 2.320000e-64 257.0
18 TraesCS7A01G231200 chr5A 81.600 125 22 1 314 438 404557262 404557139 1.150000e-17 102.0
19 TraesCS7A01G231200 chr5B 94.805 154 7 1 4293 4446 98663330 98663178 8.400000e-59 239.0
20 TraesCS7A01G231200 chr1A 87.619 105 11 2 313 416 27264132 27264029 3.170000e-23 121.0
21 TraesCS7A01G231200 chr1A 77.540 187 30 6 313 495 7111330 7111508 1.150000e-17 102.0
22 TraesCS7A01G231200 chr2B 87.500 104 12 1 314 416 66962287 66962390 1.140000e-22 119.0
23 TraesCS7A01G231200 chr2A 79.141 163 25 7 313 472 591275637 591275481 3.200000e-18 104.0
24 TraesCS7A01G231200 chr2A 91.304 46 4 0 502 547 126474039 126474084 5.420000e-06 63.9
25 TraesCS7A01G231200 chr4B 79.167 120 25 0 313 432 512542639 512542758 4.160000e-12 84.2
26 TraesCS7A01G231200 chr1D 95.238 42 2 0 506 547 370907342 370907383 4.190000e-07 67.6
27 TraesCS7A01G231200 chr5D 95.122 41 1 1 506 545 322386713 322386673 5.420000e-06 63.9
28 TraesCS7A01G231200 chr5D 89.796 49 2 3 498 545 496955506 496955460 7.020000e-05 60.2
29 TraesCS7A01G231200 chr2D 93.023 43 3 0 511 553 372800769 372800811 5.420000e-06 63.9
30 TraesCS7A01G231200 chr2D 89.583 48 2 2 514 561 230505102 230505058 2.520000e-04 58.4


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 TraesCS7A01G231200 chr7A 201984969 201991447 6478 True 11965.00 11965 100.00000 1 6479 1 chr7A.!!$R1 6478
1 TraesCS7A01G231200 chr7D 192369441 192378025 8584 True 2579.75 9441 94.27225 1 6479 4 chr7D.!!$R1 6478
2 TraesCS7A01G231200 chr7B 155469132 155475879 6747 True 3362.00 9210 94.98300 1 6479 3 chr7B.!!$R1 6478
3 TraesCS7A01G231200 chr4D 167197250 167197858 608 False 867.00 867 92.14700 5856 6479 1 chr4D.!!$F1 623

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
843 3058 0.179084 GACGGCGAGAATCCATCCAA 60.179 55.000 16.62 0.0 0.00 3.53 F
1013 3228 0.107703 CCTCCAATGGACGCTGCTAA 60.108 55.000 0.00 0.0 0.00 3.09 F
1015 3230 0.392461 TCCAATGGACGCTGCTAACC 60.392 55.000 0.00 0.0 0.00 2.85 F
1624 3839 0.468226 AGCTGAACAAGGTGAACCGA 59.532 50.000 0.00 0.0 42.08 4.69 F
2093 4334 0.694771 TGCTTCTTCATCAGCCAGGT 59.305 50.000 0.00 0.0 34.91 4.00 F
2691 4932 0.978146 GAGGAGCCCTGGTTGAGCTA 60.978 60.000 0.00 0.0 36.87 3.32 F
3364 5605 1.073763 TCACTGGTGCCTTTGTAGCAT 59.926 47.619 0.00 0.0 43.29 3.79 F
3751 5994 2.294233 GTGTCATGTTTGCACACCTGAT 59.706 45.455 13.06 0.0 35.03 2.90 F
4699 6945 4.214971 GCCATGCAGGTATACAAGATTGAG 59.785 45.833 5.01 0.0 40.61 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2783 5024 0.315251 GCAACAAGAGTGCTTTCCCC 59.685 55.000 0.00 0.00 30.14 4.81 R
2880 5121 3.825585 TGTGATAACTTTCAGGCAATGCA 59.174 39.130 7.79 0.00 0.00 3.96 R
3011 5252 8.908903 ACTGTATTGTTGAAAAATACCTTGTCA 58.091 29.630 14.01 0.00 38.97 3.58 R
3554 5797 0.381089 GGCTGAACATGCTGCAGATC 59.619 55.000 20.43 7.38 34.81 2.75 R
3865 6108 2.776536 AGAAGCATCAGCCTCTTATGGT 59.223 45.455 0.00 0.00 38.37 3.55 R
3989 6232 4.149598 AGCAAAGTACCTTGTAAAAGGGG 58.850 43.478 16.40 0.00 44.27 4.79 R
5003 7249 1.202675 TCGTTACGAAGCCAAGGGTTT 60.203 47.619 4.50 0.00 35.84 3.27 R
5384 7634 0.976641 TTCGTTCTCCAGCCTGACAT 59.023 50.000 0.00 0.00 0.00 3.06 R
5854 8104 0.839946 ATCCATGACTGGGCTACCAC 59.160 55.000 0.00 0.00 43.37 4.16 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
111 1894 5.777732 TGACAGCTGGTGGGTAAATTTTTAT 59.222 36.000 19.93 0.00 0.00 1.40
210 1994 1.191535 CTGGGTCCGTAAGTCATCCA 58.808 55.000 0.00 0.00 0.00 3.41
332 2498 8.447924 TGCAATTTGATTCAAAGGATTTTTGA 57.552 26.923 16.34 0.00 35.03 2.69
483 2652 6.436532 AGCATCCACTCAAATCTCTTGAAAAT 59.563 34.615 0.00 0.00 0.00 1.82
579 2789 8.331740 TCAGGATTCCTATGTTTTCAGAATTCT 58.668 33.333 4.51 0.88 31.90 2.40
586 2796 7.121168 TCCTATGTTTTCAGAATTCTGCGAATT 59.879 33.333 27.45 17.06 43.46 2.17
752 2965 0.984230 TCCAATGGAGTGAGTGACCC 59.016 55.000 0.00 0.00 0.00 4.46
777 2990 5.948162 CCCATCCATCCATCCTATAAAACAG 59.052 44.000 0.00 0.00 0.00 3.16
840 3055 0.671251 AGAGACGGCGAGAATCCATC 59.329 55.000 16.62 0.00 0.00 3.51
841 3056 0.319125 GAGACGGCGAGAATCCATCC 60.319 60.000 16.62 0.00 0.00 3.51
842 3057 1.043116 AGACGGCGAGAATCCATCCA 61.043 55.000 16.62 0.00 0.00 3.41
843 3058 0.179084 GACGGCGAGAATCCATCCAA 60.179 55.000 16.62 0.00 0.00 3.53
844 3059 0.462047 ACGGCGAGAATCCATCCAAC 60.462 55.000 16.62 0.00 0.00 3.77
1009 3224 2.124570 CCCCTCCAATGGACGCTG 60.125 66.667 0.00 0.00 0.00 5.18
1011 3226 2.270205 CCTCCAATGGACGCTGCT 59.730 61.111 0.00 0.00 0.00 4.24
1012 3227 1.522092 CCTCCAATGGACGCTGCTA 59.478 57.895 0.00 0.00 0.00 3.49
1013 3228 0.107703 CCTCCAATGGACGCTGCTAA 60.108 55.000 0.00 0.00 0.00 3.09
1015 3230 0.392461 TCCAATGGACGCTGCTAACC 60.392 55.000 0.00 0.00 0.00 2.85
1029 3244 1.695893 CTAACCCACAGTCGCATGCG 61.696 60.000 33.61 33.61 41.35 4.73
1074 3289 1.140312 TGGCTTCCTTTGAGACACCT 58.860 50.000 0.00 0.00 0.00 4.00
1408 3623 3.670627 GCCTCGTGCAAACTATTTTCCAG 60.671 47.826 0.00 0.00 40.77 3.86
1448 3663 3.389925 TGAGGTTCGTATGTTCCGTTT 57.610 42.857 0.00 0.00 0.00 3.60
1454 3669 3.281341 TCGTATGTTCCGTTTGTACGT 57.719 42.857 0.00 0.00 46.20 3.57
1456 3671 2.979151 CGTATGTTCCGTTTGTACGTGA 59.021 45.455 0.00 0.00 46.20 4.35
1624 3839 0.468226 AGCTGAACAAGGTGAACCGA 59.532 50.000 0.00 0.00 42.08 4.69
1663 3878 4.821589 GAGTTCCTGGAGCGCGGG 62.822 72.222 8.83 0.00 0.00 6.13
1717 3932 4.379243 CTCAAGGCCGCCGTCACT 62.379 66.667 3.05 0.00 0.00 3.41
1786 4001 2.732658 GACCCGTCCGTGTCTTGT 59.267 61.111 0.00 0.00 0.00 3.16
1807 4022 2.470990 TCTATCCTGCATGGTGAGTGT 58.529 47.619 0.00 0.00 37.07 3.55
1808 4023 3.642141 TCTATCCTGCATGGTGAGTGTA 58.358 45.455 0.00 0.00 37.07 2.90
1809 4024 2.698855 ATCCTGCATGGTGAGTGTAC 57.301 50.000 0.00 0.00 37.07 2.90
1810 4025 1.347062 TCCTGCATGGTGAGTGTACA 58.653 50.000 0.00 0.00 37.07 2.90
1811 4026 1.908619 TCCTGCATGGTGAGTGTACAT 59.091 47.619 0.00 0.00 37.07 2.29
1812 4027 3.103742 TCCTGCATGGTGAGTGTACATA 58.896 45.455 0.00 0.00 37.07 2.29
1813 4028 3.118775 TCCTGCATGGTGAGTGTACATAC 60.119 47.826 0.00 0.00 37.07 2.39
2068 4288 8.652810 ATTGAAAGGCATATTTAGTTTCATGC 57.347 30.769 0.00 0.00 42.39 4.06
2075 4316 7.040617 AGGCATATTTAGTTTCATGCTGAGATG 60.041 37.037 5.49 0.00 42.66 2.90
2084 4325 4.152284 TCATGCTGAGATGCTTCTTCAT 57.848 40.909 3.29 5.58 30.30 2.57
2093 4334 0.694771 TGCTTCTTCATCAGCCAGGT 59.305 50.000 0.00 0.00 34.91 4.00
2137 4378 9.197694 AGTCTTCTATTAGCAATTTAGCATACG 57.802 33.333 0.00 0.00 36.85 3.06
2239 4480 3.735237 TGAGTGAGTTCTTCGAGCTTT 57.265 42.857 0.00 0.00 0.00 3.51
2242 4483 3.648009 AGTGAGTTCTTCGAGCTTTGAG 58.352 45.455 0.00 0.00 0.00 3.02
2465 4706 1.350684 TGCCAACAAGCTGAGGACATA 59.649 47.619 0.00 0.00 0.00 2.29
2526 4767 1.877637 TCAACATTCCAGTCACCACG 58.122 50.000 0.00 0.00 0.00 4.94
2544 4785 1.375523 GCCATCGAGGACCGTGTTT 60.376 57.895 0.00 0.00 41.22 2.83
2617 4858 1.000233 GGGAATGGTGGTGATGGCA 60.000 57.895 0.00 0.00 0.00 4.92
2691 4932 0.978146 GAGGAGCCCTGGTTGAGCTA 60.978 60.000 0.00 0.00 36.87 3.32
2880 5121 2.511218 TGCCAATGCCTCTCTCCTTATT 59.489 45.455 0.00 0.00 36.33 1.40
2912 5153 7.857885 GCCTGAAAGTTATCACATATAAGCAAC 59.142 37.037 0.00 0.00 0.00 4.17
2919 5160 7.279981 AGTTATCACATATAAGCAACGCTGAAA 59.720 33.333 0.00 0.00 39.62 2.69
2920 5161 5.469373 TCACATATAAGCAACGCTGAAAG 57.531 39.130 0.00 0.00 39.62 2.62
2924 5165 5.411361 ACATATAAGCAACGCTGAAAGAACA 59.589 36.000 0.00 0.00 39.62 3.18
2928 5169 3.179048 AGCAACGCTGAAAGAACAAAAC 58.821 40.909 0.00 0.00 37.57 2.43
3029 5270 6.319141 AGCTCTGACAAGGTATTTTTCAAC 57.681 37.500 0.00 0.00 0.00 3.18
3030 5271 5.827797 AGCTCTGACAAGGTATTTTTCAACA 59.172 36.000 0.00 0.00 0.00 3.33
3037 5278 8.908903 TGACAAGGTATTTTTCAACAATACAGT 58.091 29.630 8.38 4.22 38.40 3.55
3038 5279 9.180678 GACAAGGTATTTTTCAACAATACAGTG 57.819 33.333 8.38 7.54 38.40 3.66
3039 5280 8.141268 ACAAGGTATTTTTCAACAATACAGTGG 58.859 33.333 8.38 0.00 38.40 4.00
3040 5281 6.687604 AGGTATTTTTCAACAATACAGTGGC 58.312 36.000 8.38 0.00 38.40 5.01
3058 5299 2.909006 TGGCCTTGAGAAGATCTGAAGT 59.091 45.455 3.32 0.00 36.22 3.01
3061 5302 5.055812 GGCCTTGAGAAGATCTGAAGTATG 58.944 45.833 0.00 0.00 36.22 2.39
3063 5304 6.183360 GGCCTTGAGAAGATCTGAAGTATGTA 60.183 42.308 0.00 0.00 36.22 2.29
3065 5306 7.930865 GCCTTGAGAAGATCTGAAGTATGTAAT 59.069 37.037 0.00 0.00 36.22 1.89
3172 5413 3.376859 TGTTTGTGAGACATTTCGCAAGT 59.623 39.130 2.77 0.00 45.24 3.16
3199 5440 7.147976 GTGACAAAAGGAAAGCAATGAAGTAT 58.852 34.615 0.00 0.00 0.00 2.12
3278 5519 9.793252 ATAGTTGTTTATAAGCTTTGCATTCTG 57.207 29.630 3.20 0.00 0.00 3.02
3291 5532 4.724074 TGCATTCTGTTCCAATTCCATC 57.276 40.909 0.00 0.00 0.00 3.51
3294 5535 5.163488 TGCATTCTGTTCCAATTCCATCATC 60.163 40.000 0.00 0.00 0.00 2.92
3300 5541 6.544931 TCTGTTCCAATTCCATCATCAAGATC 59.455 38.462 0.00 0.00 33.72 2.75
3309 5550 8.941995 ATTCCATCATCAAGATCATTTCAGAT 57.058 30.769 0.00 0.00 33.72 2.90
3353 5594 3.334583 TTCAGGACTATTCACTGGTGC 57.665 47.619 0.00 0.00 33.19 5.01
3364 5605 1.073763 TCACTGGTGCCTTTGTAGCAT 59.926 47.619 0.00 0.00 43.29 3.79
3375 5616 5.154222 GCCTTTGTAGCATTATTTATCGGC 58.846 41.667 0.00 0.00 0.00 5.54
3414 5655 3.386078 ACATAGCTGGGATGTACACTCAG 59.614 47.826 16.48 16.48 35.75 3.35
3540 5783 7.497249 GCTAAAACTCAATGATCCAGTACTGAT 59.503 37.037 24.68 14.86 0.00 2.90
3554 5797 5.862323 CCAGTACTGATATTAAACGATCCCG 59.138 44.000 24.68 0.00 42.50 5.14
3751 5994 2.294233 GTGTCATGTTTGCACACCTGAT 59.706 45.455 13.06 0.00 35.03 2.90
3825 6068 6.712547 GTGCCTTCTTCTGGTATGCTATATTT 59.287 38.462 0.00 0.00 0.00 1.40
3989 6232 5.525378 AGCGATCAGAAACATCATTCTAACC 59.475 40.000 0.00 0.00 37.56 2.85
4070 6314 6.425114 CGGAATCCTATCAAACTCCATACAAG 59.575 42.308 0.00 0.00 0.00 3.16
4185 6431 6.486657 AGCTAAATGTTTGTCAAGTTCAGCTA 59.513 34.615 4.25 0.00 33.01 3.32
4252 6498 8.692710 ACATGAACTGATCAGCATCAATAATTT 58.307 29.630 26.45 12.72 42.53 1.82
4320 6566 6.781014 TCCCTCCGTTCACTATTATAAGATGT 59.219 38.462 0.00 0.00 0.00 3.06
4470 6716 4.621068 ATTACTACAGTGTAGCGCGTAA 57.379 40.909 26.79 18.92 0.00 3.18
4699 6945 4.214971 GCCATGCAGGTATACAAGATTGAG 59.785 45.833 5.01 0.00 40.61 3.02
4703 6949 5.059161 TGCAGGTATACAAGATTGAGCATC 58.941 41.667 5.01 0.00 0.00 3.91
4717 6963 4.492494 TGAGCATCACTTACCACATCAT 57.508 40.909 0.00 0.00 42.56 2.45
5003 7249 6.293698 GGGTCTTCTACAGTTTAACTCCAAA 58.706 40.000 0.00 0.00 0.00 3.28
5318 7568 5.755409 TTGCCAGTGAATCCTAAGTCTTA 57.245 39.130 0.00 0.00 0.00 2.10
5517 7767 0.250234 AGCACGCTCTAGGATTGCAA 59.750 50.000 0.00 0.00 35.57 4.08
5827 8077 4.097892 CCACCCATCTTGTATTTTGGCTAC 59.902 45.833 0.00 0.00 0.00 3.58
5923 8173 8.719648 CAAGGATCAATATGACTAGCAGAATTC 58.280 37.037 0.00 0.00 0.00 2.17
6007 8257 2.789409 AGGCCCACTAAACTAAGCTG 57.211 50.000 0.00 0.00 0.00 4.24
6021 8271 7.703058 AAACTAAGCTGCCAGTATAAAATGT 57.297 32.000 5.09 0.00 0.00 2.71
6047 8297 0.106719 TACAGCAAATAGGGGCCAGC 60.107 55.000 4.39 0.00 0.00 4.85
6051 8301 0.106217 GCAAATAGGGGCCAGCCTTA 60.106 55.000 4.39 2.43 36.10 2.69
6054 8307 2.893489 CAAATAGGGGCCAGCCTTATTC 59.107 50.000 4.39 0.00 36.10 1.75
6120 8373 2.715046 TGCATCCCTAAGCTCAACAAG 58.285 47.619 0.00 0.00 0.00 3.16
6368 8621 6.318648 GCAATGTTCATACTGACCTTCCATTA 59.681 38.462 0.00 0.00 0.00 1.90
6369 8622 7.467811 GCAATGTTCATACTGACCTTCCATTAG 60.468 40.741 0.00 0.00 0.00 1.73
6381 8634 4.263905 ACCTTCCATTAGAGGTTGAATGCA 60.264 41.667 0.00 0.00 32.69 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 1894 1.960417 TGACTTTGCCGTCAATGTGA 58.040 45.000 2.21 0.00 40.69 3.58
163 1947 5.371526 CCATAAGCTGAAAAGAGGCATAGA 58.628 41.667 0.00 0.00 0.00 1.98
210 1994 4.281657 GGTCCCCTTATTTTCAGCTCATT 58.718 43.478 0.00 0.00 0.00 2.57
291 2075 4.877378 ATTGCATGTGGTTGTGATCTTT 57.123 36.364 0.00 0.00 0.00 2.52
292 2076 4.877378 AATTGCATGTGGTTGTGATCTT 57.123 36.364 0.00 0.00 0.00 2.40
293 2077 4.281435 TCAAATTGCATGTGGTTGTGATCT 59.719 37.500 0.00 0.00 0.00 2.75
294 2078 4.558178 TCAAATTGCATGTGGTTGTGATC 58.442 39.130 0.00 0.00 0.00 2.92
295 2079 4.603989 TCAAATTGCATGTGGTTGTGAT 57.396 36.364 0.00 0.00 0.00 3.06
296 2080 4.603989 ATCAAATTGCATGTGGTTGTGA 57.396 36.364 0.00 0.00 0.00 3.58
297 2081 4.750598 TGAATCAAATTGCATGTGGTTGTG 59.249 37.500 0.00 0.00 0.00 3.33
354 2520 8.721133 ACCATTGTAGGAAAAATTTCTAAGGT 57.279 30.769 5.91 0.00 37.35 3.50
507 2676 5.843673 TGCATCACAGGAAAAACAAAGTA 57.156 34.783 0.00 0.00 0.00 2.24
554 2723 8.404000 CAGAATTCTGAAAACATAGGAATCCTG 58.596 37.037 28.13 0.00 46.59 3.86
565 2775 8.864069 TTTTAATTCGCAGAATTCTGAAAACA 57.136 26.923 34.43 17.28 46.59 2.83
579 2789 3.407698 TCAGTGCCTCTTTTAATTCGCA 58.592 40.909 0.00 0.00 0.00 5.10
586 2796 2.825532 GGCCATTTCAGTGCCTCTTTTA 59.174 45.455 0.00 0.00 42.01 1.52
752 2965 5.222316 TGTTTTATAGGATGGATGGATGGGG 60.222 44.000 0.00 0.00 0.00 4.96
755 2968 6.546484 ACCTGTTTTATAGGATGGATGGATG 58.454 40.000 0.00 0.00 38.71 3.51
764 2977 3.981375 GGGAGGGACCTGTTTTATAGGAT 59.019 47.826 0.00 0.00 38.71 3.24
777 2990 3.097162 GGGATGGTGGGAGGGACC 61.097 72.222 0.00 0.00 38.08 4.46
840 3055 1.383248 TTGGGTTGGGTTGGGTTGG 60.383 57.895 0.00 0.00 0.00 3.77
841 3056 1.406860 CCTTGGGTTGGGTTGGGTTG 61.407 60.000 0.00 0.00 0.00 3.77
842 3057 1.074850 CCTTGGGTTGGGTTGGGTT 60.075 57.895 0.00 0.00 0.00 4.11
843 3058 2.612251 CCTTGGGTTGGGTTGGGT 59.388 61.111 0.00 0.00 0.00 4.51
844 3059 2.922503 GCCTTGGGTTGGGTTGGG 60.923 66.667 0.00 0.00 0.00 4.12
1009 3224 1.982073 GCATGCGACTGTGGGTTAGC 61.982 60.000 0.00 0.00 34.24 3.09
1011 3226 1.739929 CGCATGCGACTGTGGGTTA 60.740 57.895 35.82 0.00 42.83 2.85
1012 3227 3.049674 CGCATGCGACTGTGGGTT 61.050 61.111 35.82 0.00 42.83 4.11
1029 3244 4.492611 GGTAAGGCGTACTTATATGAGCC 58.507 47.826 10.35 12.75 43.20 4.70
1299 3514 1.222936 GAGCCTCATCACCCAGTGG 59.777 63.158 0.63 0.63 33.87 4.00
1408 3623 1.464734 TCTCAGTCGACCATCTCACC 58.535 55.000 13.01 0.00 0.00 4.02
1448 3663 0.034756 ACCTGCATTGCTCACGTACA 59.965 50.000 10.49 0.00 0.00 2.90
1624 3839 2.425102 CCCCTCCTTCCTCTCGTAGAAT 60.425 54.545 0.00 0.00 34.09 2.40
1786 4001 2.840038 ACACTCACCATGCAGGATAGAA 59.160 45.455 0.00 0.00 41.22 2.10
2067 4287 2.288458 GCTGATGAAGAAGCATCTCAGC 59.712 50.000 13.05 13.05 43.89 4.26
2068 4288 2.873472 GGCTGATGAAGAAGCATCTCAG 59.127 50.000 0.00 0.00 43.89 3.35
2075 4316 1.093159 CACCTGGCTGATGAAGAAGC 58.907 55.000 0.00 0.00 38.76 3.86
2125 4366 7.285401 ACCATTCAATTCCTCGTATGCTAAATT 59.715 33.333 0.00 0.00 0.00 1.82
2126 4367 6.772716 ACCATTCAATTCCTCGTATGCTAAAT 59.227 34.615 0.00 0.00 0.00 1.40
2127 4368 6.038161 CACCATTCAATTCCTCGTATGCTAAA 59.962 38.462 0.00 0.00 0.00 1.85
2128 4369 5.527214 CACCATTCAATTCCTCGTATGCTAA 59.473 40.000 0.00 0.00 0.00 3.09
2129 4370 5.056480 CACCATTCAATTCCTCGTATGCTA 58.944 41.667 0.00 0.00 0.00 3.49
2239 4480 3.520290 ATCAATTTCTACGCGACCTCA 57.480 42.857 15.93 0.00 0.00 3.86
2242 4483 4.088648 CACAAATCAATTTCTACGCGACC 58.911 43.478 15.93 0.00 0.00 4.79
2526 4767 1.375523 AAACACGGTCCTCGATGGC 60.376 57.895 0.00 0.00 42.43 4.40
2544 4785 0.396435 ACAGAAGTTCACGGATGGCA 59.604 50.000 5.50 0.00 0.00 4.92
2691 4932 0.924090 GGTACCCCAAGCCCTTGTAT 59.076 55.000 0.00 0.00 38.85 2.29
2783 5024 0.315251 GCAACAAGAGTGCTTTCCCC 59.685 55.000 0.00 0.00 30.14 4.81
2880 5121 3.825585 TGTGATAACTTTCAGGCAATGCA 59.174 39.130 7.79 0.00 0.00 3.96
3011 5252 8.908903 ACTGTATTGTTGAAAAATACCTTGTCA 58.091 29.630 14.01 0.00 38.97 3.58
3025 5266 3.072330 TCTCAAGGCCACTGTATTGTTGA 59.928 43.478 5.01 1.38 0.00 3.18
3029 5270 3.942829 TCTTCTCAAGGCCACTGTATTG 58.057 45.455 5.01 0.00 0.00 1.90
3030 5271 4.472833 AGATCTTCTCAAGGCCACTGTATT 59.527 41.667 5.01 0.00 0.00 1.89
3037 5278 2.909006 ACTTCAGATCTTCTCAAGGCCA 59.091 45.455 5.01 0.00 0.00 5.36
3038 5279 3.625649 ACTTCAGATCTTCTCAAGGCC 57.374 47.619 0.00 0.00 0.00 5.19
3039 5280 5.669477 ACATACTTCAGATCTTCTCAAGGC 58.331 41.667 0.00 0.00 0.00 4.35
3040 5281 9.829507 AATTACATACTTCAGATCTTCTCAAGG 57.170 33.333 0.00 0.00 0.00 3.61
3063 5304 7.553044 CGGAACCTTTGGAGTTCTATTAGAATT 59.447 37.037 9.28 5.35 42.63 2.17
3065 5306 6.211986 TCGGAACCTTTGGAGTTCTATTAGAA 59.788 38.462 1.90 1.90 42.63 2.10
3070 5311 3.838903 ACTCGGAACCTTTGGAGTTCTAT 59.161 43.478 3.89 0.00 42.63 1.98
3071 5312 3.236896 ACTCGGAACCTTTGGAGTTCTA 58.763 45.455 3.89 0.00 42.63 2.10
3073 5314 2.545537 ACTCGGAACCTTTGGAGTTC 57.454 50.000 0.00 0.00 42.36 3.01
3172 5413 3.703556 TCATTGCTTTCCTTTTGTCACCA 59.296 39.130 0.00 0.00 0.00 4.17
3199 5440 5.624159 TCTTCTTTCTGATTTGGCTTCAGA 58.376 37.500 10.08 10.08 45.93 3.27
3277 5518 6.189133 TGATCTTGATGATGGAATTGGAACA 58.811 36.000 0.00 0.00 35.14 3.18
3278 5519 6.704289 TGATCTTGATGATGGAATTGGAAC 57.296 37.500 0.00 0.00 35.14 3.62
3294 5535 7.861372 GTGCATAAGGAATCTGAAATGATCTTG 59.139 37.037 0.00 0.00 0.00 3.02
3300 5541 7.281774 ACAGTAGTGCATAAGGAATCTGAAATG 59.718 37.037 0.00 0.00 0.00 2.32
3309 5550 7.759489 AAATTTGACAGTAGTGCATAAGGAA 57.241 32.000 0.00 0.00 0.00 3.36
3353 5594 6.560253 AGCCGATAAATAATGCTACAAAGG 57.440 37.500 0.00 0.00 0.00 3.11
3364 5605 6.816640 GCCATGATACAGTAGCCGATAAATAA 59.183 38.462 0.00 0.00 0.00 1.40
3375 5616 2.223537 TGTGCGCCATGATACAGTAG 57.776 50.000 4.18 0.00 0.00 2.57
3414 5655 3.815401 ACATGTAGACCTTGTTTGACTGC 59.185 43.478 0.00 0.00 0.00 4.40
3540 5783 4.556233 CTGCAGATCGGGATCGTTTAATA 58.444 43.478 8.42 0.00 42.48 0.98
3554 5797 0.381089 GGCTGAACATGCTGCAGATC 59.619 55.000 20.43 7.38 34.81 2.75
3751 5994 7.685481 TGAAGAATACCCTTTGACAATGAGTA 58.315 34.615 2.74 0.82 0.00 2.59
3865 6108 2.776536 AGAAGCATCAGCCTCTTATGGT 59.223 45.455 0.00 0.00 38.37 3.55
3871 6114 5.365025 TGAATAAGTAGAAGCATCAGCCTCT 59.635 40.000 0.00 0.00 43.70 3.69
3952 6195 5.440234 TCTGATCGCTATTAGGAAGTGAC 57.560 43.478 0.00 0.00 36.38 3.67
3989 6232 4.149598 AGCAAAGTACCTTGTAAAAGGGG 58.850 43.478 16.40 0.00 44.27 4.79
4049 6293 9.753674 TTTTTCTTGTATGGAGTTTGATAGGAT 57.246 29.630 0.00 0.00 0.00 3.24
4185 6431 5.185635 TGAGCATTTTGGTTTAAGCTAGCAT 59.814 36.000 18.83 7.77 31.61 3.79
4284 6530 6.134754 AGTGAACGGAGGGAGTAGTAAATAT 58.865 40.000 0.00 0.00 0.00 1.28
4435 6681 6.040504 CACTGTAGTAATATGTACTCCCTGCA 59.959 42.308 0.00 0.00 0.00 4.41
4437 6683 7.584122 ACACTGTAGTAATATGTACTCCCTG 57.416 40.000 0.00 2.81 0.00 4.45
4470 6716 7.388500 CCAAATTAAACACCATCATTGCTTCTT 59.612 33.333 0.00 0.00 0.00 2.52
4699 6945 6.484643 AGACATTATGATGTGGTAAGTGATGC 59.515 38.462 8.00 0.00 46.27 3.91
4703 6949 7.550551 AGAACAGACATTATGATGTGGTAAGTG 59.449 37.037 8.00 0.00 46.27 3.16
4708 6954 6.475504 TGAAGAACAGACATTATGATGTGGT 58.524 36.000 8.00 3.48 46.27 4.16
4765 7011 2.736721 CACTGTCAGGACAACCGTAATG 59.263 50.000 4.53 0.00 41.33 1.90
5003 7249 1.202675 TCGTTACGAAGCCAAGGGTTT 60.203 47.619 4.50 0.00 35.84 3.27
5121 7371 6.552445 AAATGTCAGGCTCTCTGTAAGTAT 57.448 37.500 0.00 0.00 43.76 2.12
5334 7584 6.998673 AGTGTAAATTCAGGCTTGTATATCCC 59.001 38.462 0.00 0.00 0.00 3.85
5384 7634 0.976641 TTCGTTCTCCAGCCTGACAT 59.023 50.000 0.00 0.00 0.00 3.06
5517 7767 4.536765 ACATCTGAACTGTTTGGGAGTTT 58.463 39.130 0.00 0.00 33.71 2.66
5744 7994 5.419155 TCGAGTACTTGGATCTCATGAAGTT 59.581 40.000 10.33 0.00 31.25 2.66
5854 8104 0.839946 ATCCATGACTGGGCTACCAC 59.160 55.000 0.00 0.00 43.37 4.16
5923 8173 8.456904 TGTAAGTAACTTATTAGTCAACTGCG 57.543 34.615 1.84 0.00 33.31 5.18
5982 8232 2.491675 AGTTTAGTGGGCCTTAGCAC 57.508 50.000 4.53 1.47 45.43 4.40
6007 8257 8.283291 GCTGTAATCAGTACATTTTATACTGGC 58.717 37.037 11.23 3.60 46.39 4.85
6021 8271 4.445735 GGCCCCTATTTGCTGTAATCAGTA 60.446 45.833 0.00 0.00 43.05 2.74
6069 8322 2.280552 ACGTCAGCCCGCTTCCTTA 61.281 57.895 0.00 0.00 0.00 2.69
6120 8373 0.863799 ATGTGATGATGCGTGCGATC 59.136 50.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.