Multiple sequence alignment - TraesCS4A01G490200

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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 TraesCS4A01G490200 chr4A 100.000 3944 0 0 1 3944 740494223 740498166 0.000000e+00 7284.0
1 TraesCS4A01G490200 chr4A 85.207 4002 458 87 4 3944 739606057 739609985 0.000000e+00 3988.0
2 TraesCS4A01G490200 chr4A 87.530 2486 255 29 4 2450 740150551 740148082 0.000000e+00 2822.0
3 TraesCS4A01G490200 chr4A 83.584 3064 415 48 8 3029 742160624 742157607 0.000000e+00 2791.0
4 TraesCS4A01G490200 chr4A 81.224 2908 440 68 799 3660 733805926 733808773 0.000000e+00 2248.0
5 TraesCS4A01G490200 chr4A 84.321 2245 283 29 671 2893 740122887 740120690 0.000000e+00 2132.0
6 TraesCS4A01G490200 chr4A 85.505 2049 246 29 868 2893 742021129 742023149 0.000000e+00 2091.0
7 TraesCS4A01G490200 chr4A 85.615 2009 262 16 1001 2989 739886463 739888464 0.000000e+00 2084.0
8 TraesCS4A01G490200 chr4A 82.668 1529 223 23 1710 3213 741505836 741504325 0.000000e+00 1317.0
9 TraesCS4A01G490200 chr4A 83.776 1319 192 13 1590 2893 741805100 741806411 0.000000e+00 1230.0
10 TraesCS4A01G490200 chr4A 83.266 741 80 30 3224 3944 742023259 742023975 3.320000e-180 641.0
11 TraesCS4A01G490200 chr4A 80.088 914 120 41 2455 3353 740135858 740134992 1.200000e-174 623.0
12 TraesCS4A01G490200 chr4A 88.636 484 43 10 3463 3944 740134293 740133820 2.640000e-161 579.0
13 TraesCS4A01G490200 chr4A 81.616 718 87 33 3250 3944 733822174 733822869 1.600000e-153 553.0
14 TraesCS4A01G490200 chr4A 84.739 249 25 11 2999 3242 733821805 733822045 1.830000e-58 237.0
15 TraesCS4A01G490200 chr4A 81.667 180 24 7 445 615 733800041 733800220 1.480000e-29 141.0
16 TraesCS4A01G490200 chr7A 84.708 3309 384 72 2 3242 3843696 3840442 0.000000e+00 3195.0
17 TraesCS4A01G490200 chr7A 79.719 3417 523 95 2 3343 3155536 3152215 0.000000e+00 2314.0
18 TraesCS4A01G490200 chr7A 84.368 1900 277 10 1007 2893 2800443 2798551 0.000000e+00 1845.0
19 TraesCS4A01G490200 chr7A 82.451 718 73 34 3246 3944 3840303 3839620 2.640000e-161 579.0
20 TraesCS4A01G490200 chr7A 85.654 474 53 11 3478 3944 3801781 3801316 5.930000e-133 484.0
21 TraesCS4A01G490200 chr7A 86.441 413 48 7 3534 3944 2126311 2125905 2.800000e-121 446.0
22 TraesCS4A01G490200 chr7A 86.567 402 53 1 2 402 2805427 2805026 3.620000e-120 442.0
23 TraesCS4A01G490200 chr7A 93.750 48 3 0 2955 3002 114451263 114451310 5.470000e-09 73.1
24 TraesCS4A01G490200 chr7D 84.697 2725 319 58 439 3121 4009771 4007103 0.000000e+00 2632.0
25 TraesCS4A01G490200 chr7D 81.121 3051 480 53 2 3003 2904432 2901429 0.000000e+00 2355.0
26 TraesCS4A01G490200 chr7D 81.074 3017 480 62 2 2972 3552161 3549190 0.000000e+00 2324.0
27 TraesCS4A01G490200 chr7D 86.113 1541 195 9 885 2407 3423787 3422248 0.000000e+00 1642.0
28 TraesCS4A01G490200 chr7D 87.796 844 73 11 1278 2109 2519471 2518646 0.000000e+00 961.0
29 TraesCS4A01G490200 chr7D 82.810 733 88 26 3226 3944 4006760 4006052 4.330000e-174 621.0
30 TraesCS4A01G490200 chr7D 91.932 409 32 1 2 410 4010115 4009708 4.420000e-159 571.0
31 TraesCS4A01G490200 chr7D 87.389 452 46 9 3495 3944 2508416 2507974 3.520000e-140 508.0
32 TraesCS4A01G490200 chr7D 78.286 525 88 22 3162 3676 2678684 2678176 8.230000e-82 315.0
33 TraesCS4A01G490200 chr7D 95.833 48 2 0 2955 3002 618627929 618627976 1.180000e-10 78.7
34 TraesCS4A01G490200 chr7B 95.833 48 2 0 2955 3002 551823412 551823459 1.180000e-10 78.7
35 TraesCS4A01G490200 chr4B 95.833 48 2 0 2955 3002 531453532 531453485 1.180000e-10 78.7
36 TraesCS4A01G490200 chr3A 95.833 48 2 0 2955 3002 160917704 160917751 1.180000e-10 78.7
37 TraesCS4A01G490200 chr2A 95.833 48 2 0 2955 3002 287753921 287753874 1.180000e-10 78.7
38 TraesCS4A01G490200 chr4D 93.750 48 3 0 2955 3002 115697241 115697194 5.470000e-09 73.1
39 TraesCS4A01G490200 chr4D 93.750 48 3 0 2955 3002 437398576 437398623 5.470000e-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 TraesCS4A01G490200 chr4A 740494223 740498166 3943 False 7284.000000 7284 100.000000 1 3944 1 chr4A.!!$F5 3943
1 TraesCS4A01G490200 chr4A 739606057 739609985 3928 False 3988.000000 3988 85.207000 4 3944 1 chr4A.!!$F3 3940
2 TraesCS4A01G490200 chr4A 740148082 740150551 2469 True 2822.000000 2822 87.530000 4 2450 1 chr4A.!!$R2 2446
3 TraesCS4A01G490200 chr4A 742157607 742160624 3017 True 2791.000000 2791 83.584000 8 3029 1 chr4A.!!$R4 3021
4 TraesCS4A01G490200 chr4A 733805926 733808773 2847 False 2248.000000 2248 81.224000 799 3660 1 chr4A.!!$F2 2861
5 TraesCS4A01G490200 chr4A 740120690 740122887 2197 True 2132.000000 2132 84.321000 671 2893 1 chr4A.!!$R1 2222
6 TraesCS4A01G490200 chr4A 739886463 739888464 2001 False 2084.000000 2084 85.615000 1001 2989 1 chr4A.!!$F4 1988
7 TraesCS4A01G490200 chr4A 742021129 742023975 2846 False 1366.000000 2091 84.385500 868 3944 2 chr4A.!!$F8 3076
8 TraesCS4A01G490200 chr4A 741504325 741505836 1511 True 1317.000000 1317 82.668000 1710 3213 1 chr4A.!!$R3 1503
9 TraesCS4A01G490200 chr4A 741805100 741806411 1311 False 1230.000000 1230 83.776000 1590 2893 1 chr4A.!!$F6 1303
10 TraesCS4A01G490200 chr4A 740133820 740135858 2038 True 601.000000 623 84.362000 2455 3944 2 chr4A.!!$R5 1489
11 TraesCS4A01G490200 chr4A 733821805 733822869 1064 False 395.000000 553 83.177500 2999 3944 2 chr4A.!!$F7 945
12 TraesCS4A01G490200 chr7A 3152215 3155536 3321 True 2314.000000 2314 79.719000 2 3343 1 chr7A.!!$R4 3341
13 TraesCS4A01G490200 chr7A 3839620 3843696 4076 True 1887.000000 3195 83.579500 2 3944 2 chr7A.!!$R6 3942
14 TraesCS4A01G490200 chr7A 2798551 2800443 1892 True 1845.000000 1845 84.368000 1007 2893 1 chr7A.!!$R2 1886
15 TraesCS4A01G490200 chr7D 2901429 2904432 3003 True 2355.000000 2355 81.121000 2 3003 1 chr7D.!!$R4 3001
16 TraesCS4A01G490200 chr7D 3549190 3552161 2971 True 2324.000000 2324 81.074000 2 2972 1 chr7D.!!$R6 2970
17 TraesCS4A01G490200 chr7D 3422248 3423787 1539 True 1642.000000 1642 86.113000 885 2407 1 chr7D.!!$R5 1522
18 TraesCS4A01G490200 chr7D 4006052 4010115 4063 True 1274.666667 2632 86.479667 2 3944 3 chr7D.!!$R7 3942
19 TraesCS4A01G490200 chr7D 2518646 2519471 825 True 961.000000 961 87.796000 1278 2109 1 chr7D.!!$R2 831
20 TraesCS4A01G490200 chr7D 2678176 2678684 508 True 315.000000 315 78.286000 3162 3676 1 chr7D.!!$R3 514

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
22 23 0.174845 CACGGTTGATCCTCGCCTAA 59.825 55.0 0.00 0.00 0.00 2.69 F
426 430 0.320683 GGGGTTGCATCAAAAGGCAC 60.321 55.0 0.00 0.00 42.83 5.01 F
1837 1898 0.819582 CCAACCTTTGGCTAGCATGG 59.180 55.0 18.24 14.08 45.17 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 1930 2.228059 GGCAACATCTCAGCATAGCAT 58.772 47.619 0.0 0.0 0.00 3.79 R
2202 2278 0.815734 TCGAGTCCCGATCAACTTCC 59.184 55.000 0.0 0.0 43.23 3.46 R
3818 4868 0.397564 TCGGACCCCACTAAACCAAC 59.602 55.000 0.0 0.0 0.00 3.77 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
22 23 0.174845 CACGGTTGATCCTCGCCTAA 59.825 55.000 0.00 0.00 0.00 2.69
89 90 7.394077 TGATTCATTGAATGAGCTAACCAAGAA 59.606 33.333 16.41 0.00 40.94 2.52
106 107 4.386088 CCAAGAAGATGAGTGATGGGGATT 60.386 45.833 0.00 0.00 0.00 3.01
107 108 5.198965 CAAGAAGATGAGTGATGGGGATTT 58.801 41.667 0.00 0.00 0.00 2.17
109 110 5.835582 AGAAGATGAGTGATGGGGATTTTT 58.164 37.500 0.00 0.00 0.00 1.94
203 204 8.454106 CAAAGCAGTGTATGATAAGCTTAAAGT 58.546 33.333 10.85 1.90 41.01 2.66
215 216 9.008965 TGATAAGCTTAAAGTGCAGTTTGATTA 57.991 29.630 26.29 19.43 0.00 1.75
249 250 0.394899 CGGTAGGACGGAACCCTAGT 60.395 60.000 0.00 0.00 36.98 2.57
303 305 7.485418 TGAAATTGACGAGCAAAAGTACTTA 57.515 32.000 8.92 0.00 40.48 2.24
337 339 3.754965 AGGCAGCTAATCAACAAACTCA 58.245 40.909 0.00 0.00 0.00 3.41
426 430 0.320683 GGGGTTGCATCAAAAGGCAC 60.321 55.000 0.00 0.00 42.83 5.01
507 518 8.622572 ACATCAAATAGTAAATGGGGGAAAAT 57.377 30.769 0.00 0.00 0.00 1.82
508 519 9.056799 ACATCAAATAGTAAATGGGGGAAAATT 57.943 29.630 0.00 0.00 0.00 1.82
537 556 8.256605 CCTGAGAAGAAATGAGTTAGAGATGAA 58.743 37.037 0.00 0.00 0.00 2.57
540 559 8.436046 AGAAGAAATGAGTTAGAGATGAATGC 57.564 34.615 0.00 0.00 0.00 3.56
552 571 8.650714 GTTAGAGATGAATGCAAAATTTGGTTC 58.349 33.333 7.89 0.00 0.00 3.62
695 742 3.425758 CGACTTACCCTCGAATTTTTGCC 60.426 47.826 0.00 0.00 32.65 4.52
702 751 2.050691 CTCGAATTTTTGCCGGTGTTG 58.949 47.619 1.90 0.00 0.00 3.33
851 902 3.370276 CTCGTGCATACATGTCTCTCTG 58.630 50.000 0.00 0.00 34.22 3.35
943 1001 7.416664 GCATGCATCCTCTTTTCAAAGGTATTA 60.417 37.037 14.21 0.00 36.67 0.98
944 1002 7.630242 TGCATCCTCTTTTCAAAGGTATTAG 57.370 36.000 0.00 0.00 36.67 1.73
957 1016 9.510062 TTCAAAGGTATTAGGAATACTTAGGGA 57.490 33.333 8.77 0.00 42.63 4.20
1081 1142 3.062774 GGAACTAGTCAAGATCGCTTTGC 59.937 47.826 0.00 0.00 30.14 3.68
1116 1177 3.378427 GTGGAAGCAGGATAATCACAACC 59.622 47.826 0.00 0.00 0.00 3.77
1144 1205 1.660575 CTCGAAGTCGCCACAACGT 60.661 57.895 0.00 0.00 39.60 3.99
1188 1249 9.219603 CTACAACCACTTTCTCTTGATTTATCA 57.780 33.333 0.00 0.00 34.44 2.15
1336 1397 5.989168 GCTAATTTGCTTGTTGGTAAACCTT 59.011 36.000 4.53 0.00 35.25 3.50
1378 1439 6.209788 GGTATACACTTCAATTGGTTTTGGGA 59.790 38.462 5.42 0.00 0.00 4.37
1380 1441 5.428184 ACACTTCAATTGGTTTTGGGAAA 57.572 34.783 5.42 0.00 0.00 3.13
1404 1465 6.234177 AGAAGAAAATGAAGACGTGGAGAAT 58.766 36.000 0.00 0.00 0.00 2.40
1451 1512 4.920640 ACTATGATCTACCTTGTCACCG 57.079 45.455 0.00 0.00 0.00 4.94
1465 1526 3.390135 TGTCACCGAAAGACTTGCTTAG 58.610 45.455 0.00 0.00 35.24 2.18
1538 1599 3.119096 GAAGTGGGTCGCCGAAGC 61.119 66.667 0.00 0.00 0.00 3.86
1606 1667 6.038997 AGAGGTACTTCAATGAGTTGGTAC 57.961 41.667 7.82 0.00 41.55 3.34
1664 1725 6.047870 TGTATTTTGGCATGGAAATGTATGC 58.952 36.000 6.00 0.00 46.76 3.14
1687 1748 2.617788 GGCACCATAACTGGATGTCACA 60.618 50.000 0.00 0.00 46.37 3.58
1693 1754 5.369404 ACCATAACTGGATGTCACATCCATA 59.631 40.000 35.02 26.25 46.12 2.74
1837 1898 0.819582 CCAACCTTTGGCTAGCATGG 59.180 55.000 18.24 14.08 45.17 3.66
1862 1923 6.308766 GCAACATTACAAGCAAGGTCATTTAG 59.691 38.462 0.00 0.00 0.00 1.85
1869 1930 4.235079 AGCAAGGTCATTTAGTGCCATA 57.765 40.909 0.00 0.00 35.80 2.74
1906 1967 4.280425 TGTTGCCATCACTTTCATGCTTTA 59.720 37.500 0.00 0.00 0.00 1.85
1986 2050 6.874134 GTCTTGAGCATCTTGGAAAGTTAGTA 59.126 38.462 0.00 0.00 46.34 1.82
2030 2094 1.139654 GAGCATGGGTATCTGTGAGCA 59.860 52.381 0.00 0.00 0.00 4.26
2031 2095 1.773052 AGCATGGGTATCTGTGAGCAT 59.227 47.619 0.00 0.00 0.00 3.79
2092 2168 9.556030 GTAAAAATAGCATAACTGAACTTCCAC 57.444 33.333 0.00 0.00 0.00 4.02
2094 2170 7.759489 AAATAGCATAACTGAACTTCCACAA 57.241 32.000 0.00 0.00 0.00 3.33
2109 2185 3.659786 TCCACAAAGTATTGGTCGACTG 58.340 45.455 16.46 5.56 41.01 3.51
2111 2187 3.432252 CCACAAAGTATTGGTCGACTGAC 59.568 47.826 16.46 8.36 44.72 3.51
2212 2288 5.685728 AGTTATGCCTAAGGGAAGTTGATC 58.314 41.667 0.00 0.00 33.58 2.92
2265 2341 4.636249 AGTTAACAGAGTTGAGGAAGCTG 58.364 43.478 8.61 0.00 0.00 4.24
2276 2352 2.216898 GAGGAAGCTGCGCATTTCTAT 58.783 47.619 24.87 17.57 0.00 1.98
2291 2367 8.030106 GCGCATTTCTATAGGTTTAGATCTAGT 58.970 37.037 0.30 0.00 0.00 2.57
2320 2399 2.102578 GTGCAATGAATAGTTGGGCCT 58.897 47.619 4.53 0.00 0.00 5.19
2321 2400 2.099756 GTGCAATGAATAGTTGGGCCTC 59.900 50.000 4.53 0.00 0.00 4.70
2348 2427 0.449388 GCCAAACTCAGCAAGATCCG 59.551 55.000 0.00 0.00 0.00 4.18
2356 2435 3.894427 ACTCAGCAAGATCCGAGTCATAT 59.106 43.478 0.00 0.00 33.49 1.78
2377 2457 8.498575 TCATATACATTGGTTATGTTTCTGGGA 58.501 33.333 0.00 0.00 45.19 4.37
2473 2559 1.407025 GCTACCAAGAACCTGGGCTAC 60.407 57.143 0.00 0.00 41.16 3.58
2537 2623 8.677300 CCATTTAAAACTGCATGTATACAGTCT 58.323 33.333 11.91 0.00 46.17 3.24
2545 2631 5.445964 TGCATGTATACAGTCTAGACCTGA 58.554 41.667 19.38 5.01 0.00 3.86
2564 2650 4.077822 CTGAAGATCTTTGGCAGTTTCCT 58.922 43.478 9.87 0.00 0.00 3.36
2565 2651 3.822735 TGAAGATCTTTGGCAGTTTCCTG 59.177 43.478 9.87 0.00 41.91 3.86
2670 2759 2.682856 GGTCTTCAAGACACAAGCAACA 59.317 45.455 19.37 0.00 46.79 3.33
2702 2791 0.321122 CAAGAGGGAGATATGCCGGC 60.321 60.000 22.73 22.73 0.00 6.13
2782 2871 5.499004 TGACTTTGACTTTGGTAGCCTAT 57.501 39.130 0.00 0.00 0.00 2.57
2905 2996 1.089481 CAACCGTCCCATCCATCGTG 61.089 60.000 0.00 0.00 0.00 4.35
2908 2999 1.676678 CCGTCCCATCCATCGTGTCT 61.677 60.000 0.00 0.00 0.00 3.41
2916 3007 4.280929 CCCATCCATCGTGTCTTATCACTA 59.719 45.833 0.00 0.00 36.33 2.74
2920 3013 6.961360 TCCATCGTGTCTTATCACTAGATT 57.039 37.500 0.00 0.00 35.67 2.40
3081 3198 0.311165 CTAGCCGTGTATCTCCACCG 59.689 60.000 0.00 0.00 31.47 4.94
3083 3200 2.718073 GCCGTGTATCTCCACCGGT 61.718 63.158 0.00 0.00 34.03 5.28
3140 3369 4.836125 TCATCTGCACCTTGTCTTTTTC 57.164 40.909 0.00 0.00 0.00 2.29
3217 3457 7.982761 AAATCAATTACCAATTTGCACACAT 57.017 28.000 0.00 0.00 0.00 3.21
3274 3653 6.061022 ACCATTGATACTCCACACACATTA 57.939 37.500 0.00 0.00 0.00 1.90
3284 3663 5.247110 ACTCCACACACATTATCTGAGAGTT 59.753 40.000 0.00 0.00 0.00 3.01
3285 3664 6.437477 ACTCCACACACATTATCTGAGAGTTA 59.563 38.462 0.00 0.00 0.00 2.24
3286 3665 6.631016 TCCACACACATTATCTGAGAGTTAC 58.369 40.000 0.00 0.00 0.00 2.50
3391 4366 8.856490 TCTCTTTATTGTCTTTTGAAGCAAAC 57.144 30.769 0.00 0.00 32.79 2.93
3511 4547 7.274250 GCTATGTTTTCTTTTGTTAGCAGATGG 59.726 37.037 0.00 0.00 32.77 3.51
3548 4584 3.924144 AGTGCTTGTTTGCTTTTTGTGA 58.076 36.364 0.00 0.00 0.00 3.58
3558 4594 6.128688 TGTTTGCTTTTTGTGACTTTTGTAGC 60.129 34.615 0.00 0.00 0.00 3.58
3559 4595 4.429108 TGCTTTTTGTGACTTTTGTAGCC 58.571 39.130 0.00 0.00 0.00 3.93
3564 4600 4.647424 TTGTGACTTTTGTAGCCAAAGG 57.353 40.909 0.00 0.00 41.37 3.11
3578 4614 4.898320 AGCCAAAGGAAATGAAAATCACC 58.102 39.130 0.00 0.00 0.00 4.02
3609 4651 9.643693 AAAATTGTTTATCTGCCTTTCATAGTG 57.356 29.630 0.00 0.00 0.00 2.74
3667 4713 3.901844 AGGGTCAAGTAGTCTGTTGCTTA 59.098 43.478 0.00 0.00 0.00 3.09
3714 4760 0.778083 AAGAGGGTCTTGGGGTTTCC 59.222 55.000 0.00 0.00 34.98 3.13
3717 4763 0.482887 AGGGTCTTGGGGTTTCCTTG 59.517 55.000 0.00 0.00 36.20 3.61
3757 4803 3.816523 GTCGTTTGGGTTTGTATCTTGGA 59.183 43.478 0.00 0.00 0.00 3.53
3775 4821 4.656100 TGGATCTTGGTTTTGGAGATCA 57.344 40.909 12.88 0.00 44.76 2.92
3776 4822 4.592942 TGGATCTTGGTTTTGGAGATCAG 58.407 43.478 12.88 0.00 44.76 2.90
3779 4825 2.376518 TCTTGGTTTTGGAGATCAGGCT 59.623 45.455 0.00 0.00 0.00 4.58
3780 4826 2.978156 TGGTTTTGGAGATCAGGCTT 57.022 45.000 0.00 0.00 0.00 4.35
3818 4868 4.629634 GTCTTGTTCTTTGGGTTTTGGTTG 59.370 41.667 0.00 0.00 0.00 3.77
3834 4884 1.958579 GGTTGTTGGTTTAGTGGGGTC 59.041 52.381 0.00 0.00 0.00 4.46
3850 4900 1.975680 GGGTCCGATGTGTATATGGGT 59.024 52.381 0.00 0.00 0.00 4.51
3854 4904 2.143122 CCGATGTGTATATGGGTGTGC 58.857 52.381 0.00 0.00 0.00 4.57
3887 4937 3.121544 GTGTAACTCCGCCTATGCTAAC 58.878 50.000 0.00 0.00 34.43 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.100631 GCGAGGATCAACCGTGGTG 61.101 63.158 0.00 0.00 44.74 4.17
22 23 1.067295 TGGTCCTTGAACAGAGCCAT 58.933 50.000 0.00 0.00 0.00 4.40
32 33 1.273606 CGAGCTCTTTCTGGTCCTTGA 59.726 52.381 12.85 0.00 0.00 3.02
89 90 5.537674 GCATAAAAATCCCCATCACTCATCT 59.462 40.000 0.00 0.00 0.00 2.90
106 107 2.881513 TGAGTTGCTTGGACGCATAAAA 59.118 40.909 0.00 0.00 40.04 1.52
107 108 2.499197 TGAGTTGCTTGGACGCATAAA 58.501 42.857 0.00 0.00 40.04 1.40
109 110 2.076100 CTTGAGTTGCTTGGACGCATA 58.924 47.619 0.00 0.00 40.04 3.14
203 204 4.916983 AAAGCACTGTAATCAAACTGCA 57.083 36.364 0.00 0.00 0.00 4.41
215 216 2.218603 CTACCGGAACAAAAGCACTGT 58.781 47.619 9.46 0.00 0.00 3.55
249 250 7.933577 AGTATGTCATTGAGAACTTTCTTCACA 59.066 33.333 0.00 0.00 37.73 3.58
303 305 1.353694 AGCTGCCTTTCATCCAACTCT 59.646 47.619 0.00 0.00 0.00 3.24
337 339 6.296803 ACCTTTTGTTCTCGAGTAATCCTTT 58.703 36.000 13.13 0.00 0.00 3.11
410 414 0.392336 TGGGTGCCTTTTGATGCAAC 59.608 50.000 0.00 0.00 44.44 4.17
412 416 1.275856 GATTGGGTGCCTTTTGATGCA 59.724 47.619 0.00 0.00 34.54 3.96
414 418 1.545582 ACGATTGGGTGCCTTTTGATG 59.454 47.619 0.00 0.00 0.00 3.07
415 419 1.923356 ACGATTGGGTGCCTTTTGAT 58.077 45.000 0.00 0.00 0.00 2.57
416 420 1.339610 CAACGATTGGGTGCCTTTTGA 59.660 47.619 0.00 0.00 0.00 2.69
417 421 1.339610 TCAACGATTGGGTGCCTTTTG 59.660 47.619 0.00 0.00 0.00 2.44
418 422 1.698506 TCAACGATTGGGTGCCTTTT 58.301 45.000 0.00 0.00 0.00 2.27
426 430 3.319137 TCTCAGAGTTCAACGATTGGG 57.681 47.619 0.00 0.00 0.00 4.12
507 518 7.674348 TCTCTAACTCATTTCTTCTCAGGGTAA 59.326 37.037 0.00 0.00 0.00 2.85
508 519 7.182760 TCTCTAACTCATTTCTTCTCAGGGTA 58.817 38.462 0.00 0.00 0.00 3.69
537 556 4.582701 TGTCTCGAACCAAATTTTGCAT 57.417 36.364 3.50 0.00 0.00 3.96
552 571 6.497785 ACCCTTCTCGTATAATATGTCTCG 57.502 41.667 0.00 0.00 0.00 4.04
566 585 1.279271 AGGACATCCAAACCCTTCTCG 59.721 52.381 0.00 0.00 38.89 4.04
647 669 9.569167 GCAAAGAAGGTATAAAAACTTGATACC 57.431 33.333 5.15 5.15 43.70 2.73
661 683 3.518303 AGGGTAAGTCGCAAAGAAGGTAT 59.482 43.478 0.00 0.00 0.00 2.73
695 742 9.751542 AAGAAGTTCTAGAATATATCAACACCG 57.248 33.333 8.75 0.00 0.00 4.94
851 902 0.684479 GGAAAATGGAGGGGTCCAGC 60.684 60.000 0.00 0.00 43.86 4.85
1081 1142 4.539870 CTGCTTCCACAATTGTTACACAG 58.460 43.478 8.77 9.32 0.00 3.66
1116 1177 2.599377 GGCGACTTCGAGTATACGAGTG 60.599 54.545 2.02 0.00 43.04 3.51
1144 1205 6.395629 GTTGTAGCTTGTATACTTCACTGGA 58.604 40.000 4.17 0.00 0.00 3.86
1316 1377 5.104735 TCCAAAGGTTTACCAACAAGCAAAT 60.105 36.000 1.13 0.00 38.89 2.32
1336 1397 5.486063 TGTATACCTTAGACCAAAGCTCCAA 59.514 40.000 0.00 0.00 0.00 3.53
1378 1439 6.055588 TCTCCACGTCTTCATTTTCTTCTTT 58.944 36.000 0.00 0.00 0.00 2.52
1380 1441 5.215252 TCTCCACGTCTTCATTTTCTTCT 57.785 39.130 0.00 0.00 0.00 2.85
1431 1492 5.515797 TTCGGTGACAAGGTAGATCATAG 57.484 43.478 0.00 0.00 0.00 2.23
1451 1512 6.035542 GCTCAGATACACTAAGCAAGTCTTTC 59.964 42.308 0.00 0.00 39.55 2.62
1465 1526 5.973899 TCAGGATAGATGCTCAGATACAC 57.026 43.478 0.00 0.00 0.00 2.90
1538 1599 4.210331 CCCTGGTTCCTCATGGATAAAAG 58.790 47.826 0.00 0.00 42.81 2.27
1693 1754 5.477984 GGCATATCATATCCAACACCATGTT 59.522 40.000 0.00 0.00 42.08 2.71
1699 1760 7.607607 TGACAATAGGCATATCATATCCAACAC 59.392 37.037 0.00 0.00 0.00 3.32
1747 1808 7.875554 TGCATATTGCTCGTTACTATCCAATAA 59.124 33.333 0.75 0.00 45.31 1.40
1837 1898 3.641437 TGACCTTGCTTGTAATGTTGC 57.359 42.857 0.00 0.00 0.00 4.17
1869 1930 2.228059 GGCAACATCTCAGCATAGCAT 58.772 47.619 0.00 0.00 0.00 3.79
1906 1967 2.572290 AGCTAGGACACGCAAAACTTT 58.428 42.857 0.00 0.00 0.00 2.66
2030 2094 3.698040 CAGCAAGAACTTTAGATGCCCAT 59.302 43.478 0.00 0.00 37.73 4.00
2031 2095 3.084039 CAGCAAGAACTTTAGATGCCCA 58.916 45.455 0.00 0.00 37.73 5.36
2062 2138 8.281212 AGTTCAGTTATGCTATTTTTACCCAG 57.719 34.615 0.00 0.00 0.00 4.45
2092 2168 4.556233 TGAGTCAGTCGACCAATACTTTG 58.444 43.478 13.01 1.00 43.73 2.77
2094 2170 4.281182 AGTTGAGTCAGTCGACCAATACTT 59.719 41.667 13.01 0.00 43.73 2.24
2130 2206 7.115663 GGCACTTTAATTTTTGTTTCGCAGATA 59.884 33.333 0.00 0.00 35.04 1.98
2202 2278 0.815734 TCGAGTCCCGATCAACTTCC 59.184 55.000 0.00 0.00 43.23 3.46
2212 2288 1.137513 GTCACAAAGTTCGAGTCCCG 58.862 55.000 0.00 0.00 40.25 5.14
2265 2341 8.030106 ACTAGATCTAAACCTATAGAAATGCGC 58.970 37.037 0.00 0.00 35.64 6.09
2291 2367 7.013559 CCCAACTATTCATTGCACTATCATCAA 59.986 37.037 0.00 0.00 0.00 2.57
2320 2399 1.336887 GCTGAGTTTGGCTACAGACGA 60.337 52.381 0.00 0.00 36.85 4.20
2321 2400 1.071605 GCTGAGTTTGGCTACAGACG 58.928 55.000 0.00 0.00 36.85 4.18
2377 2457 5.104693 TCTCTTCGTGAGTAGAATCTCTCCT 60.105 44.000 7.74 0.00 43.13 3.69
2446 2532 3.307410 CCAGGTTCTTGGTAGCACATGTA 60.307 47.826 0.00 0.00 29.22 2.29
2537 2623 3.840666 ACTGCCAAAGATCTTCAGGTCTA 59.159 43.478 20.69 11.32 0.00 2.59
2564 2650 0.401738 CTGGAGGGAAACAAGCTCCA 59.598 55.000 0.00 0.00 42.00 3.86
2565 2651 0.402121 ACTGGAGGGAAACAAGCTCC 59.598 55.000 0.00 0.00 36.98 4.70
2670 2759 1.543429 CCCTCTTGAAACGAGCCAAGT 60.543 52.381 12.39 0.00 40.32 3.16
2702 2791 3.688673 GCTGAACTCAAGAGATTCAAGGG 59.311 47.826 3.73 1.49 32.41 3.95
2782 2871 3.154827 CTTAAGCAAAGGGAGGTTCCA 57.845 47.619 0.00 0.00 38.64 3.53
2840 2929 2.291217 ACCATTTCCTCAGCCTTCTTCC 60.291 50.000 0.00 0.00 0.00 3.46
2841 2930 2.751806 CACCATTTCCTCAGCCTTCTTC 59.248 50.000 0.00 0.00 0.00 2.87
2916 3007 8.152023 ACCTCTGACTCCAATTACTTAAATCT 57.848 34.615 0.00 0.00 0.00 2.40
2920 3013 8.431910 AGTTACCTCTGACTCCAATTACTTAA 57.568 34.615 0.00 0.00 0.00 1.85
2973 3067 0.975556 TAGCTGCCCGTGGAGATCAA 60.976 55.000 0.00 0.00 0.00 2.57
2995 3091 3.586470 AGGAGATCCGTGAGATACACT 57.414 47.619 0.00 0.00 46.24 3.55
3038 3140 8.284945 AGCTTTGCTCAATCATCTGTTTTATA 57.715 30.769 0.00 0.00 30.62 0.98
3040 3142 6.579666 AGCTTTGCTCAATCATCTGTTTTA 57.420 33.333 0.00 0.00 30.62 1.52
3042 3144 5.392811 GCTAGCTTTGCTCAATCATCTGTTT 60.393 40.000 7.70 0.00 40.44 2.83
3043 3145 4.096081 GCTAGCTTTGCTCAATCATCTGTT 59.904 41.667 7.70 0.00 40.44 3.16
3044 3146 3.626670 GCTAGCTTTGCTCAATCATCTGT 59.373 43.478 7.70 0.00 40.44 3.41
3045 3147 3.003482 GGCTAGCTTTGCTCAATCATCTG 59.997 47.826 15.72 0.00 40.44 2.90
3046 3148 3.212685 GGCTAGCTTTGCTCAATCATCT 58.787 45.455 15.72 0.00 40.44 2.90
3047 3149 2.032204 CGGCTAGCTTTGCTCAATCATC 60.032 50.000 15.72 0.00 40.44 2.92
3048 3150 1.945394 CGGCTAGCTTTGCTCAATCAT 59.055 47.619 15.72 0.00 40.44 2.45
3058 3160 2.108168 TGGAGATACACGGCTAGCTTT 58.892 47.619 15.72 0.00 0.00 3.51
3081 3198 3.463944 CGTACATACCTTGATTCCCACC 58.536 50.000 0.00 0.00 0.00 4.61
3083 3200 2.769663 AGCGTACATACCTTGATTCCCA 59.230 45.455 0.00 0.00 0.00 4.37
3217 3457 9.889128 TGAAATGATGAGAAAGATACATGTACA 57.111 29.630 7.96 0.00 0.00 2.90
3244 3621 7.438459 GTGTGTGGAGTATCAATGGTTACTATC 59.562 40.741 0.00 0.00 36.25 2.08
3284 3663 7.868974 TGCCAGCCTACATATATAGAGTAGTA 58.131 38.462 17.33 4.23 34.78 1.82
3285 3664 6.732487 TGCCAGCCTACATATATAGAGTAGT 58.268 40.000 17.33 4.53 34.78 2.73
3286 3665 6.238897 GCTGCCAGCCTACATATATAGAGTAG 60.239 46.154 5.06 14.07 34.48 2.57
3292 3671 3.096852 ACGCTGCCAGCCTACATATATA 58.903 45.455 11.83 0.00 38.18 0.86
3411 4389 9.777297 AACATAGCAAAATAAAAACAAGTGGAT 57.223 25.926 0.00 0.00 0.00 3.41
3412 4390 9.606631 AAACATAGCAAAATAAAAACAAGTGGA 57.393 25.926 0.00 0.00 0.00 4.02
3474 4509 9.264782 CAAAAGAAAACATAGCAAACAAACAAG 57.735 29.630 0.00 0.00 0.00 3.16
3528 4564 3.679502 AGTCACAAAAAGCAAACAAGCAC 59.320 39.130 0.00 0.00 36.85 4.40
3539 4575 6.035975 CCTTTGGCTACAAAAGTCACAAAAAG 59.964 38.462 0.00 0.00 45.27 2.27
3543 4579 4.274147 TCCTTTGGCTACAAAAGTCACAA 58.726 39.130 0.00 0.00 45.27 3.33
3544 4580 3.892284 TCCTTTGGCTACAAAAGTCACA 58.108 40.909 0.00 0.00 45.27 3.58
3548 4584 6.478512 TTCATTTCCTTTGGCTACAAAAGT 57.521 33.333 0.00 0.00 45.27 2.66
3558 4594 7.565323 TTTTGGTGATTTTCATTTCCTTTGG 57.435 32.000 0.00 0.00 0.00 3.28
3593 4635 5.378230 TTCCATCACTATGAAAGGCAGAT 57.622 39.130 0.00 0.00 34.84 2.90
3638 4684 2.561858 AGACTACTTGACCCTCGAAACC 59.438 50.000 0.00 0.00 0.00 3.27
3643 4689 2.927014 GCAACAGACTACTTGACCCTCG 60.927 54.545 0.00 0.00 0.00 4.63
3667 4713 8.286191 AGAATTCTTTTTCTGAGTGAACAACT 57.714 30.769 0.88 0.00 43.85 3.16
3714 4760 4.630111 ACACACACCAAATAAATGGCAAG 58.370 39.130 0.00 0.00 44.75 4.01
3717 4763 3.241701 CGACACACACCAAATAAATGGC 58.758 45.455 0.00 0.00 44.75 4.40
3757 4803 3.011032 AGCCTGATCTCCAAAACCAAGAT 59.989 43.478 0.00 0.00 32.53 2.40
3775 4821 1.266718 CACACAAACACGCATAAGCCT 59.733 47.619 0.00 0.00 37.52 4.58
3776 4822 1.001815 ACACACAAACACGCATAAGCC 60.002 47.619 0.00 0.00 37.52 4.35
3779 4825 3.375610 ACAAGACACACAAACACGCATAA 59.624 39.130 0.00 0.00 0.00 1.90
3780 4826 2.939756 ACAAGACACACAAACACGCATA 59.060 40.909 0.00 0.00 0.00 3.14
3789 4839 3.426615 ACCCAAAGAACAAGACACACAA 58.573 40.909 0.00 0.00 0.00 3.33
3818 4868 0.397564 TCGGACCCCACTAAACCAAC 59.602 55.000 0.00 0.00 0.00 3.77
3834 4884 2.143122 GCACACCCATATACACATCGG 58.857 52.381 0.00 0.00 0.00 4.18
3854 4904 1.004200 GTTACACCCCCACTCCACG 60.004 63.158 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.