Multiple sequence alignment - TraesCS3D01G068400

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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 TraesCS3D01G068400 chr3D 100.000 4626 0 0 1 4626 30088938 30084313 0.000000e+00 8543.0
1 TraesCS3D01G068400 chr3D 82.920 363 50 9 2265 2618 608203284 608202925 2.690000e-82 316.0
2 TraesCS3D01G068400 chr3D 77.247 356 64 13 2292 2636 510649717 510649368 4.720000e-45 193.0
3 TraesCS3D01G068400 chr3D 79.439 214 41 3 2453 2664 95953356 95953144 1.040000e-31 148.0
4 TraesCS3D01G068400 chr3D 100.000 38 0 0 3348 3385 30085555 30085518 2.310000e-08 71.3
5 TraesCS3D01G068400 chr3D 100.000 38 0 0 3384 3421 30085591 30085554 2.310000e-08 71.3
6 TraesCS3D01G068400 chr3D 95.122 41 2 0 361 401 515957005 515957045 1.070000e-06 65.8
7 TraesCS3D01G068400 chr3A 96.953 3413 67 12 1 3385 41654176 41650773 0.000000e+00 5692.0
8 TraesCS3D01G068400 chr3A 97.549 612 14 1 3384 3995 41650810 41650200 0.000000e+00 1046.0
9 TraesCS3D01G068400 chr3A 96.822 409 9 1 3989 4397 41644948 41644544 0.000000e+00 680.0
10 TraesCS3D01G068400 chr3A 96.203 237 9 0 4390 4626 41643205 41642969 5.610000e-104 388.0
11 TraesCS3D01G068400 chr3A 78.149 389 60 18 2274 2650 42195566 42195941 1.670000e-54 224.0
12 TraesCS3D01G068400 chr7A 83.208 399 45 8 2281 2657 11356278 11355880 3.430000e-91 346.0
13 TraesCS3D01G068400 chr7A 75.873 315 62 11 2279 2587 216353704 216353398 1.040000e-31 148.0
14 TraesCS3D01G068400 chr5B 82.482 411 52 16 2265 2664 123767931 123767530 4.430000e-90 342.0
15 TraesCS3D01G068400 chr5B 95.238 42 2 0 364 405 540916202 540916243 2.990000e-07 67.6
16 TraesCS3D01G068400 chr4A 83.642 324 39 13 2347 2661 633052208 633052526 4.530000e-75 292.0
17 TraesCS3D01G068400 chr4A 94.545 55 2 1 1097 1150 734874293 734874239 2.970000e-12 84.2
18 TraesCS3D01G068400 chr4A 94.545 55 2 1 1097 1150 736112588 736112534 2.970000e-12 84.2
19 TraesCS3D01G068400 chr5A 80.914 372 56 10 2262 2626 555595516 555595153 3.520000e-71 279.0
20 TraesCS3D01G068400 chr5A 96.154 52 1 1 1099 1150 601437150 601437100 2.970000e-12 84.2
21 TraesCS3D01G068400 chr1A 79.562 411 65 14 2265 2660 98227461 98227055 4.560000e-70 276.0
22 TraesCS3D01G068400 chr5D 80.429 373 54 13 2262 2626 439979436 439979075 2.740000e-67 267.0
23 TraesCS3D01G068400 chr6A 79.656 349 50 13 2279 2618 403322970 403323306 1.000000e-56 231.0
24 TraesCS3D01G068400 chr6A 96.154 52 2 0 1099 1150 581742973 581742922 8.250000e-13 86.1
25 TraesCS3D01G068400 chr7D 76.368 402 63 14 2265 2661 51452263 51452637 2.200000e-43 187.0
26 TraesCS3D01G068400 chr7D 85.629 167 22 2 2266 2430 428025770 428025604 1.710000e-39 174.0
27 TraesCS3D01G068400 chr7D 78.205 234 33 8 2265 2491 476009948 476010170 2.900000e-27 134.0
28 TraesCS3D01G068400 chr7B 85.315 143 14 6 2291 2430 445664305 445664167 1.740000e-29 141.0
29 TraesCS3D01G068400 chr7B 92.857 56 2 2 1107 1162 165100268 165100215 3.840000e-11 80.5
30 TraesCS3D01G068400 chr4D 81.818 143 23 3 2290 2430 460302705 460302564 2.920000e-22 117.0
31 TraesCS3D01G068400 chr4D 92.857 56 3 1 1096 1150 447129610 447129555 3.840000e-11 80.5
32 TraesCS3D01G068400 chr6D 96.296 54 1 1 1098 1150 382611184 382611131 2.290000e-13 87.9
33 TraesCS3D01G068400 chr6D 88.060 67 5 3 1085 1148 30079493 30079427 4.960000e-10 76.8
34 TraesCS3D01G068400 chr3B 97.826 46 1 0 358 403 758520691 758520736 3.840000e-11 80.5
35 TraesCS3D01G068400 chr3B 97.826 46 1 0 358 403 758524736 758524781 3.840000e-11 80.5
36 TraesCS3D01G068400 chr3B 97.826 46 1 0 358 403 758528783 758528828 3.840000e-11 80.5
37 TraesCS3D01G068400 chr1D 91.228 57 4 1 350 405 387891091 387891035 4.960000e-10 76.8
38 TraesCS3D01G068400 chr6B 95.455 44 2 0 360 403 635069858 635069901 2.310000e-08 71.3
39 TraesCS3D01G068400 chr6B 93.182 44 2 1 364 407 707161243 707161201 3.860000e-06 63.9


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 TraesCS3D01G068400 chr3D 30084313 30088938 4625 True 2895.2 8543 100.0000 1 4626 3 chr3D.!!$R4 4625
1 TraesCS3D01G068400 chr3A 41650200 41654176 3976 True 3369.0 5692 97.2510 1 3995 2 chr3A.!!$R2 3994
2 TraesCS3D01G068400 chr3A 41642969 41644948 1979 True 534.0 680 96.5125 3989 4626 2 chr3A.!!$R1 637

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
573 592 0.039074 CCGATGCGAGTGGACTATCC 60.039 60.000 0.00 0.00 36.96 2.59 F
753 772 0.961019 CTTTGCCTAAAGGTGCAGCA 59.039 50.000 19.63 4.34 39.67 4.41 F
1436 1459 1.006102 CCCGAGCAGAGTTCGTGTT 60.006 57.895 2.82 0.00 36.37 3.32 F
3366 3394 0.035458 CCTTCTTCAGCGGAACAGGT 59.965 55.000 10.42 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2460 2483 0.179150 TTGTGTTCAAACAGCGCACC 60.179 50.000 11.47 0.0 40.05 5.01 R
2519 2542 2.996631 TGGTTGCAAAATTTGGTGCTT 58.003 38.095 14.29 0.0 41.48 3.91 R
3380 3408 0.034896 TGTTCCGCTGAAGAAGGACC 59.965 55.000 0.00 0.0 33.16 4.46 R
4197 4225 0.108041 AACCATTACCACGCCTACCG 60.108 55.000 0.00 0.0 44.21 4.02 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
198 200 3.428862 GCGAATTCCCAATAACAACAGGG 60.429 47.826 0.00 0.00 42.86 4.45
206 208 4.568804 CCCAATAACAACAGGGGTATCACA 60.569 45.833 0.00 0.00 37.66 3.58
238 240 2.277501 CTTGCGCTTGCGCCATAC 60.278 61.111 32.10 9.70 43.34 2.39
250 252 5.512753 TTGCGCCATACATAACAATCAAT 57.487 34.783 4.18 0.00 0.00 2.57
276 278 2.294979 GGACACCGGGTATGAAATTCC 58.705 52.381 6.32 0.00 32.19 3.01
300 302 3.049912 GTGTTTGCACGAATTTCTTCCC 58.950 45.455 0.00 0.00 35.75 3.97
305 307 3.153130 TGCACGAATTTCTTCCCATTGA 58.847 40.909 0.00 0.00 0.00 2.57
556 575 4.201679 TACGCATGGCCGTCTCCG 62.202 66.667 0.00 0.52 42.20 4.63
558 577 4.592192 CGCATGGCCGTCTCCGAT 62.592 66.667 0.00 0.00 35.63 4.18
559 578 2.969238 GCATGGCCGTCTCCGATG 60.969 66.667 0.00 0.00 35.63 3.84
560 579 2.969238 CATGGCCGTCTCCGATGC 60.969 66.667 0.00 0.00 35.63 3.91
561 580 4.592192 ATGGCCGTCTCCGATGCG 62.592 66.667 0.00 0.00 35.63 4.73
563 582 4.933064 GGCCGTCTCCGATGCGAG 62.933 72.222 0.00 0.00 35.63 5.03
573 592 0.039074 CCGATGCGAGTGGACTATCC 60.039 60.000 0.00 0.00 36.96 2.59
589 608 8.809468 TGGACTATCCAATACTACTAGCATAG 57.191 38.462 0.00 0.00 45.00 2.23
590 609 7.339721 TGGACTATCCAATACTACTAGCATAGC 59.660 40.741 0.00 0.00 45.00 2.97
753 772 0.961019 CTTTGCCTAAAGGTGCAGCA 59.039 50.000 19.63 4.34 39.67 4.41
858 877 7.896811 TCTAAGCATCATATAACCATCGTTCT 58.103 34.615 0.00 0.00 33.17 3.01
1063 1082 1.135972 CAAATCGAGCAACACGGGAAG 60.136 52.381 0.00 0.00 0.00 3.46
1117 1136 5.953571 AGGAAAATGTTTGTACTCCCTCTT 58.046 37.500 0.00 0.00 0.00 2.85
1237 1256 3.270877 AGTGTCTTGCTCAACTTTCGTT 58.729 40.909 0.00 0.00 0.00 3.85
1238 1257 4.439057 AGTGTCTTGCTCAACTTTCGTTA 58.561 39.130 0.00 0.00 0.00 3.18
1239 1258 4.270325 AGTGTCTTGCTCAACTTTCGTTAC 59.730 41.667 0.00 0.00 0.00 2.50
1240 1259 3.558418 TGTCTTGCTCAACTTTCGTTACC 59.442 43.478 0.00 0.00 0.00 2.85
1433 1456 2.344203 CCTCCCGAGCAGAGTTCGT 61.344 63.158 2.82 0.00 36.37 3.85
1436 1459 1.006102 CCCGAGCAGAGTTCGTGTT 60.006 57.895 2.82 0.00 36.37 3.32
1441 1464 2.059541 GAGCAGAGTTCGTGTTACACC 58.940 52.381 10.10 0.00 0.00 4.16
1442 1465 1.687123 AGCAGAGTTCGTGTTACACCT 59.313 47.619 10.10 1.06 0.00 4.00
1443 1466 2.102588 AGCAGAGTTCGTGTTACACCTT 59.897 45.455 10.10 0.00 0.00 3.50
1476 1499 7.777910 TCCTTCATTAATTACTGGGTATGGTTG 59.222 37.037 3.27 0.00 0.00 3.77
1511 1534 4.315803 CAACCTGATGAGTTTACTCCGTT 58.684 43.478 7.39 0.61 42.20 4.44
1531 1554 4.674362 CGTTGAATGACGAGGATGTGACTA 60.674 45.833 0.00 0.00 45.47 2.59
1538 1561 7.818997 ATGACGAGGATGTGACTAGTAATAA 57.181 36.000 0.00 0.00 0.00 1.40
1678 1701 6.949352 ATATAGTGAGCCATTCCACAAAAG 57.051 37.500 0.00 0.00 35.84 2.27
1814 1837 2.214376 TCGCTGTGAAATTGGGGATT 57.786 45.000 0.00 0.00 0.00 3.01
1858 1881 3.366374 GCGGAGAAAATCTGGAAAACTGG 60.366 47.826 0.00 0.00 34.56 4.00
1985 2008 6.591750 TGTAAACTTCTGTTGACCCAAAAA 57.408 33.333 0.00 0.00 36.85 1.94
2040 2063 3.756434 TCGCCCGAAAGATTCAGATTTTT 59.244 39.130 0.00 0.00 0.00 1.94
2113 2136 9.162764 TGGTTAAGAGAAATTTTCCTTCTATCG 57.837 33.333 12.97 0.00 33.24 2.92
2221 2244 3.821033 GTGGTCCATAGCTTTGTGACTTT 59.179 43.478 18.09 0.00 0.00 2.66
2329 2352 5.164002 CCCACGCAATAAAACATAGCAAAAC 60.164 40.000 0.00 0.00 0.00 2.43
2406 2429 4.582701 TGCAAAGTTAGGTGGTCAAATG 57.417 40.909 0.00 0.00 0.00 2.32
2429 2452 1.919240 TCCGAGGAGCTCTGTACAAA 58.081 50.000 14.64 0.00 0.00 2.83
2430 2453 2.457598 TCCGAGGAGCTCTGTACAAAT 58.542 47.619 14.64 0.00 0.00 2.32
2465 2488 4.712122 AATTACCCAAAATGTAGGTGCG 57.288 40.909 0.00 0.00 35.02 5.34
2519 2542 2.103094 CAGAGCTCCCGGATGTCATTTA 59.897 50.000 10.93 0.00 0.00 1.40
2646 2669 2.429930 CACCGAGCTGGGGTTCAA 59.570 61.111 19.90 0.00 44.64 2.69
2649 2672 2.429930 CGAGCTGGGGTTCAACCA 59.570 61.111 9.35 0.00 41.02 3.67
2704 2727 3.206150 TCTCCTGCAGAGTTTGTGTTTC 58.794 45.455 17.39 0.00 43.71 2.78
2837 2860 1.988293 TCGAAAATCCACCTTTGCCA 58.012 45.000 0.00 0.00 0.00 4.92
2875 2898 5.390387 AGTAAGCCATTCCACCAAAAGTAA 58.610 37.500 0.00 0.00 0.00 2.24
3077 3105 2.159787 GCAGATTATATCCAACTGCGCG 60.160 50.000 0.00 0.00 42.92 6.86
3098 3126 5.399301 CGCGAAAAATTCCATGGCTTAATAG 59.601 40.000 6.96 0.00 0.00 1.73
3099 3127 6.273071 GCGAAAAATTCCATGGCTTAATAGT 58.727 36.000 6.96 0.00 0.00 2.12
3131 3159 9.146586 TCCTAAAGGGGATTGATATTTTCATTG 57.853 33.333 0.00 0.00 32.77 2.82
3179 3207 0.037046 AGCATCTGTCATGTCGTGCA 60.037 50.000 13.79 0.00 35.17 4.57
3217 3245 0.609131 CGTTTGGGGATCTTGGCAGT 60.609 55.000 0.00 0.00 0.00 4.40
3264 3292 4.474226 ACTCACGACTCAAAATTGAAGC 57.526 40.909 0.00 0.00 36.64 3.86
3271 3299 6.678663 CACGACTCAAAATTGAAGCGTATTAG 59.321 38.462 17.04 6.78 41.71 1.73
3364 3392 0.321671 TCCCTTCTTCAGCGGAACAG 59.678 55.000 0.00 0.00 0.00 3.16
3365 3393 0.674895 CCCTTCTTCAGCGGAACAGG 60.675 60.000 11.28 11.28 31.86 4.00
3366 3394 0.035458 CCTTCTTCAGCGGAACAGGT 59.965 55.000 10.42 0.00 0.00 4.00
3367 3395 1.275291 CCTTCTTCAGCGGAACAGGTA 59.725 52.381 10.42 0.00 0.00 3.08
3368 3396 2.338500 CTTCTTCAGCGGAACAGGTAC 58.662 52.381 0.00 0.00 0.00 3.34
3369 3397 0.606604 TCTTCAGCGGAACAGGTACC 59.393 55.000 2.73 2.73 0.00 3.34
3370 3398 0.608640 CTTCAGCGGAACAGGTACCT 59.391 55.000 9.21 9.21 0.00 3.08
3371 3399 0.606604 TTCAGCGGAACAGGTACCTC 59.393 55.000 12.84 0.45 0.00 3.85
3372 3400 1.218316 CAGCGGAACAGGTACCTCC 59.782 63.158 12.84 10.17 0.00 4.30
3373 3401 1.988406 AGCGGAACAGGTACCTCCC 60.988 63.158 12.84 12.58 36.75 4.30
3374 3402 1.988406 GCGGAACAGGTACCTCCCT 60.988 63.158 12.84 0.00 36.75 4.20
3375 3403 1.957765 GCGGAACAGGTACCTCCCTC 61.958 65.000 12.84 8.60 36.75 4.30
3376 3404 1.328430 CGGAACAGGTACCTCCCTCC 61.328 65.000 12.84 16.27 36.75 4.30
3377 3405 0.981801 GGAACAGGTACCTCCCTCCC 60.982 65.000 12.84 5.55 36.75 4.30
3378 3406 0.252558 GAACAGGTACCTCCCTCCCA 60.253 60.000 12.84 0.00 36.75 4.37
3379 3407 0.546988 AACAGGTACCTCCCTCCCAC 60.547 60.000 12.84 0.00 36.75 4.61
3380 3408 2.058595 CAGGTACCTCCCTCCCACG 61.059 68.421 12.84 0.00 36.75 4.94
3381 3409 2.762875 GGTACCTCCCTCCCACGG 60.763 72.222 4.06 0.00 0.00 4.94
3382 3410 2.038490 GTACCTCCCTCCCACGGT 59.962 66.667 0.00 0.00 0.00 4.83
3383 3411 2.056815 GTACCTCCCTCCCACGGTC 61.057 68.421 0.00 0.00 0.00 4.79
3384 3412 3.307089 TACCTCCCTCCCACGGTCC 62.307 68.421 0.00 0.00 0.00 4.46
3385 3413 4.400251 CCTCCCTCCCACGGTCCT 62.400 72.222 0.00 0.00 0.00 3.85
3386 3414 2.284699 CTCCCTCCCACGGTCCTT 60.285 66.667 0.00 0.00 0.00 3.36
3387 3415 2.284405 TCCCTCCCACGGTCCTTC 60.284 66.667 0.00 0.00 0.00 3.46
3388 3416 2.284699 CCCTCCCACGGTCCTTCT 60.285 66.667 0.00 0.00 0.00 2.85
3389 3417 1.918800 CCCTCCCACGGTCCTTCTT 60.919 63.158 0.00 0.00 0.00 2.52
3390 3418 1.597461 CCTCCCACGGTCCTTCTTC 59.403 63.158 0.00 0.00 0.00 2.87
3391 3419 1.192146 CCTCCCACGGTCCTTCTTCA 61.192 60.000 0.00 0.00 0.00 3.02
3392 3420 0.247736 CTCCCACGGTCCTTCTTCAG 59.752 60.000 0.00 0.00 0.00 3.02
3393 3421 1.376037 CCCACGGTCCTTCTTCAGC 60.376 63.158 0.00 0.00 0.00 4.26
3394 3422 1.738099 CCACGGTCCTTCTTCAGCG 60.738 63.158 0.00 0.00 39.40 5.18
3395 3423 1.738099 CACGGTCCTTCTTCAGCGG 60.738 63.158 0.00 0.00 37.83 5.52
3396 3424 1.906824 ACGGTCCTTCTTCAGCGGA 60.907 57.895 0.00 0.00 37.83 5.54
3397 3425 1.292223 CGGTCCTTCTTCAGCGGAA 59.708 57.895 0.00 0.00 0.00 4.30
3398 3426 1.014564 CGGTCCTTCTTCAGCGGAAC 61.015 60.000 0.00 0.00 0.00 3.62
3399 3427 0.034896 GGTCCTTCTTCAGCGGAACA 59.965 55.000 0.00 0.00 34.64 3.18
3437 3465 0.471211 TCCCACGACCCAACTTCTCT 60.471 55.000 0.00 0.00 0.00 3.10
3441 3469 0.178929 ACGACCCAACTTCTCTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
3478 3506 6.234920 CAAACATATATATGTCCCGACCCAA 58.765 40.000 25.01 0.00 45.55 4.12
3535 3563 1.525077 GAACGACTGTGGCACCCAA 60.525 57.895 16.26 0.00 34.18 4.12
3552 3580 5.507650 GCACCCAAAATTTCCACGTAAAGTA 60.508 40.000 0.00 0.00 0.00 2.24
3567 3595 4.214545 CGTAAAGTACTTGGGCAACATCAA 59.785 41.667 9.34 0.00 39.74 2.57
3620 3648 1.369091 CGAATCGCTGGACCCAAAGG 61.369 60.000 0.00 0.00 40.04 3.11
3768 3796 9.212641 CTTTATCATTCTATCGTGTGGATTCAT 57.787 33.333 0.00 0.00 36.55 2.57
3912 3940 6.868622 TGTTTTTACTAATGTGCTTTGTGGT 58.131 32.000 0.00 0.00 0.00 4.16
3925 3953 5.969435 GTGCTTTGTGGTTCTTACTAACAAC 59.031 40.000 0.00 0.00 34.42 3.32
3998 4026 1.202806 CCATCAACACCACACTCCACT 60.203 52.381 0.00 0.00 0.00 4.00
4001 4029 1.134521 TCAACACCACACTCCACTGTC 60.135 52.381 0.00 0.00 0.00 3.51
4011 4039 1.005450 ACTCCACTGTCTCCTCTCCTC 59.995 57.143 0.00 0.00 0.00 3.71
4028 4056 1.004560 TCGCTCTTGCCACTTCCTG 60.005 57.895 0.00 0.00 35.36 3.86
4126 4154 1.324736 CTTCGTTAATCAGGAGCACGC 59.675 52.381 0.00 0.00 0.00 5.34
4197 4225 0.819582 CAATGTCCATTGCCTCCCAC 59.180 55.000 7.05 0.00 41.27 4.61
4288 4316 1.035139 GGGAATCGCTCATGCCAATT 58.965 50.000 0.00 0.00 29.79 2.32
4371 4399 9.980780 CATTGTTGACGTATGTATTTATTGTGA 57.019 29.630 0.00 0.00 0.00 3.58
4427 5801 4.048504 GTTGACTATGCCAAAACCAACAC 58.951 43.478 0.00 0.00 34.35 3.32
4429 5803 1.611491 ACTATGCCAAAACCAACACCG 59.389 47.619 0.00 0.00 0.00 4.94
4430 5804 0.962489 TATGCCAAAACCAACACCGG 59.038 50.000 0.00 0.00 0.00 5.28
4440 5814 1.436195 CCAACACCGGCGATGTATGG 61.436 60.000 7.63 13.97 0.00 2.74
4548 5922 4.937620 TGTTTCTGTCAAGTGATGATAGCC 59.062 41.667 0.00 0.00 44.49 3.93
4584 5958 2.434336 TCACCTATAATGGCTCGTGCTT 59.566 45.455 9.61 0.00 39.59 3.91
4594 5968 0.654683 GCTCGTGCTTGATGACATCC 59.345 55.000 12.90 0.00 36.03 3.51
4616 5990 5.911178 TCCAAAGGGATATTCAGTCTATGGT 59.089 40.000 0.00 0.00 38.64 3.55
4619 5993 7.561356 CCAAAGGGATATTCAGTCTATGGTTTT 59.439 37.037 0.00 0.00 35.59 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 200 7.291411 AGTTCTGGTCTATATGTGTGATACC 57.709 40.000 0.00 0.00 0.00 2.73
206 208 3.133003 AGCGCAAGTTCTGGTCTATATGT 59.867 43.478 11.47 0.00 41.68 2.29
238 240 5.331902 GTGTCCCGTTGATTGATTGTTATG 58.668 41.667 0.00 0.00 0.00 1.90
266 268 3.057174 GTGCAAACACGGGGAATTTCATA 60.057 43.478 0.00 0.00 36.98 2.15
331 333 3.041940 CCGCCGTCCAACACTGTC 61.042 66.667 0.00 0.00 0.00 3.51
362 381 0.173255 CGCAAATTTCCTCCCGCATT 59.827 50.000 0.00 0.00 0.00 3.56
589 608 0.390340 TTCTCATCGTGAGCACTGGC 60.390 55.000 9.34 0.00 43.95 4.85
590 609 1.354040 GTTCTCATCGTGAGCACTGG 58.646 55.000 9.34 0.00 43.95 4.00
789 808 5.102313 GGATTCACCTTTAGCCAATTTTCG 58.898 41.667 0.00 0.00 35.41 3.46
1063 1082 6.072673 CCGGATATGAATTACTTACCTTTGGC 60.073 42.308 0.00 0.00 0.00 4.52
1237 1256 8.694540 CATGATTCATGAAATTTAACCCTGGTA 58.305 33.333 19.84 0.00 43.81 3.25
1238 1257 7.558604 CATGATTCATGAAATTTAACCCTGGT 58.441 34.615 19.84 0.00 43.81 4.00
1239 1258 6.480981 GCATGATTCATGAAATTTAACCCTGG 59.519 38.462 26.94 0.00 43.81 4.45
1240 1259 7.042950 TGCATGATTCATGAAATTTAACCCTG 58.957 34.615 26.94 0.84 43.81 4.45
1295 1318 2.736144 AGAGCGATGTACGTTTTCCA 57.264 45.000 0.00 0.00 44.60 3.53
1511 1534 4.017126 ACTAGTCACATCCTCGTCATTCA 58.983 43.478 0.00 0.00 0.00 2.57
1531 1554 7.172532 TGTTGTTGCTTCGTCTTCATTATTACT 59.827 33.333 0.00 0.00 0.00 2.24
1538 1561 3.466836 TCTGTTGTTGCTTCGTCTTCAT 58.533 40.909 0.00 0.00 0.00 2.57
1619 1642 5.613358 AGCTTTGCAACAGTACTATGTTC 57.387 39.130 0.00 0.00 41.41 3.18
1742 1765 4.005650 AGTGCAACATGAGACGATTTGAT 58.994 39.130 0.00 0.00 41.43 2.57
1814 1837 5.335583 CGCTCAACCACATCCAAAAATTAGA 60.336 40.000 0.00 0.00 0.00 2.10
2040 2063 9.877178 ACAACACTAACAATGGAAAAACAAATA 57.123 25.926 0.00 0.00 0.00 1.40
2113 2136 2.796593 GCAAAACAAGCAACATGGACTC 59.203 45.455 0.00 0.00 0.00 3.36
2221 2244 3.004171 CGACAATTTCGTATGACCCCAA 58.996 45.455 0.00 0.00 43.24 4.12
2255 2278 5.408604 GTGTAGAACAACCACTTCATCGAAT 59.591 40.000 0.00 0.00 0.00 3.34
2406 2429 1.335496 GTACAGAGCTCCTCGGATGTC 59.665 57.143 10.93 0.00 35.36 3.06
2460 2483 0.179150 TTGTGTTCAAACAGCGCACC 60.179 50.000 11.47 0.00 40.05 5.01
2465 2488 6.885735 AATTACAAGTTGTGTTCAAACAGC 57.114 33.333 18.90 0.00 41.98 4.40
2519 2542 2.996631 TGGTTGCAAAATTTGGTGCTT 58.003 38.095 14.29 0.00 41.48 3.91
2613 2636 4.697756 TGCAGCCACGCTACACCC 62.698 66.667 0.00 0.00 36.40 4.61
2646 2669 9.816787 TTAAATTCAAGTAGGGAAAGTAATGGT 57.183 29.630 0.00 0.00 0.00 3.55
2875 2898 5.404946 CCATGCGAATTTCAGAATGTTTCT 58.595 37.500 0.00 0.00 41.70 2.52
2925 2948 6.311815 AGCGATCTCTTCGATTGTCCAAAAA 61.312 40.000 0.00 0.00 45.90 1.94
3050 3078 7.439157 GCAGTTGGATATAATCTGCATGTTA 57.561 36.000 9.99 0.00 46.95 2.41
3059 3087 4.725556 TTTCGCGCAGTTGGATATAATC 57.274 40.909 8.75 0.00 0.00 1.75
3098 3126 9.588096 AATATCAATCCCCTTTAGGATGTTTAC 57.412 33.333 0.00 0.00 46.31 2.01
3364 3392 2.762875 CCGTGGGAGGGAGGTACC 60.763 72.222 2.73 2.73 38.08 3.34
3365 3393 2.038490 ACCGTGGGAGGGAGGTAC 59.962 66.667 0.00 0.00 34.83 3.34
3366 3394 2.361771 GACCGTGGGAGGGAGGTA 59.638 66.667 0.00 0.00 37.07 3.08
3367 3395 4.716977 GGACCGTGGGAGGGAGGT 62.717 72.222 0.00 0.00 40.11 3.85
3368 3396 3.925914 AAGGACCGTGGGAGGGAGG 62.926 68.421 0.00 0.00 35.02 4.30
3369 3397 2.284699 AAGGACCGTGGGAGGGAG 60.285 66.667 0.00 0.00 35.02 4.30
3370 3398 2.284405 GAAGGACCGTGGGAGGGA 60.284 66.667 0.00 0.00 35.02 4.20
3371 3399 1.900545 GAAGAAGGACCGTGGGAGGG 61.901 65.000 0.00 0.00 35.02 4.30
3372 3400 1.192146 TGAAGAAGGACCGTGGGAGG 61.192 60.000 0.00 0.00 37.30 4.30
3373 3401 0.247736 CTGAAGAAGGACCGTGGGAG 59.752 60.000 0.00 0.00 0.00 4.30
3374 3402 1.827399 GCTGAAGAAGGACCGTGGGA 61.827 60.000 0.00 0.00 0.00 4.37
3375 3403 1.376037 GCTGAAGAAGGACCGTGGG 60.376 63.158 0.00 0.00 0.00 4.61
3376 3404 1.738099 CGCTGAAGAAGGACCGTGG 60.738 63.158 0.00 0.00 0.00 4.94
3377 3405 1.738099 CCGCTGAAGAAGGACCGTG 60.738 63.158 0.00 0.00 0.00 4.94
3378 3406 1.469335 TTCCGCTGAAGAAGGACCGT 61.469 55.000 0.00 0.00 33.16 4.83
3379 3407 1.014564 GTTCCGCTGAAGAAGGACCG 61.015 60.000 0.00 0.00 33.16 4.79
3380 3408 0.034896 TGTTCCGCTGAAGAAGGACC 59.965 55.000 0.00 0.00 33.16 4.46
3381 3409 1.433534 CTGTTCCGCTGAAGAAGGAC 58.566 55.000 0.00 0.00 33.16 3.85
3382 3410 0.321671 CCTGTTCCGCTGAAGAAGGA 59.678 55.000 11.95 0.00 37.57 3.36
3383 3411 0.035458 ACCTGTTCCGCTGAAGAAGG 59.965 55.000 14.53 14.53 39.70 3.46
3384 3412 2.338500 GTACCTGTTCCGCTGAAGAAG 58.662 52.381 0.00 0.00 0.00 2.85
3385 3413 1.001633 GGTACCTGTTCCGCTGAAGAA 59.998 52.381 4.06 0.00 0.00 2.52
3386 3414 0.606604 GGTACCTGTTCCGCTGAAGA 59.393 55.000 4.06 0.00 0.00 2.87
3387 3415 0.608640 AGGTACCTGTTCCGCTGAAG 59.391 55.000 15.42 0.00 0.00 3.02
3388 3416 0.606604 GAGGTACCTGTTCCGCTGAA 59.393 55.000 22.10 0.00 0.00 3.02
3389 3417 1.255667 GGAGGTACCTGTTCCGCTGA 61.256 60.000 22.10 0.00 35.41 4.26
3390 3418 1.218316 GGAGGTACCTGTTCCGCTG 59.782 63.158 22.10 0.00 35.41 5.18
3391 3419 1.988406 GGGAGGTACCTGTTCCGCT 60.988 63.158 22.10 0.00 38.98 5.52
3392 3420 1.957765 GAGGGAGGTACCTGTTCCGC 61.958 65.000 22.10 15.41 42.10 5.54
3393 3421 1.328430 GGAGGGAGGTACCTGTTCCG 61.328 65.000 22.10 0.00 42.10 4.30
3394 3422 0.981801 GGGAGGGAGGTACCTGTTCC 60.982 65.000 22.10 21.02 42.10 3.62
3395 3423 0.252558 TGGGAGGGAGGTACCTGTTC 60.253 60.000 22.10 13.29 42.10 3.18
3396 3424 0.546988 GTGGGAGGGAGGTACCTGTT 60.547 60.000 22.10 3.87 42.10 3.16
3397 3425 1.080538 GTGGGAGGGAGGTACCTGT 59.919 63.158 22.10 2.98 42.10 4.00
3398 3426 2.058595 CGTGGGAGGGAGGTACCTG 61.059 68.421 22.10 0.00 42.10 4.00
3399 3427 2.363361 CGTGGGAGGGAGGTACCT 59.637 66.667 16.26 16.26 45.57 3.08
3424 3452 3.375699 TGATAGGGAGAGAAGTTGGGTC 58.624 50.000 0.00 0.00 0.00 4.46
3437 3465 5.601583 TGTTTGCTACGTAATGATAGGGA 57.398 39.130 0.00 0.00 0.00 4.20
3478 3506 4.478206 AGAAACGACATGTCAGGATCAT 57.522 40.909 24.93 4.06 0.00 2.45
3552 3580 0.179004 TCCGTTGATGTTGCCCAAGT 60.179 50.000 0.00 0.00 0.00 3.16
3620 3648 3.259902 ACTTCGGCGATTCCTTTTAGTC 58.740 45.455 11.76 0.00 0.00 2.59
3682 3710 4.540824 GAATGTGAACAGAGCAACCTTTC 58.459 43.478 0.00 0.00 0.00 2.62
3686 3714 1.873591 ACGAATGTGAACAGAGCAACC 59.126 47.619 0.00 0.00 0.00 3.77
3752 3780 5.582269 AGTCAAACATGAATCCACACGATAG 59.418 40.000 0.00 0.00 46.19 2.08
3880 3908 5.623673 GCACATTAGTAAAAACAGAACCACG 59.376 40.000 0.00 0.00 0.00 4.94
3912 3940 6.645790 AGGTCTTCTCGTTGTTAGTAAGAA 57.354 37.500 0.00 0.00 0.00 2.52
3925 3953 3.119316 AGTGCAGATTGTAGGTCTTCTCG 60.119 47.826 0.00 0.00 0.00 4.04
3998 4026 0.329931 AAGAGCGAGGAGAGGAGACA 59.670 55.000 0.00 0.00 0.00 3.41
4001 4029 1.437160 GCAAGAGCGAGGAGAGGAG 59.563 63.158 0.00 0.00 0.00 3.69
4011 4039 0.886490 AACAGGAAGTGGCAAGAGCG 60.886 55.000 0.00 0.00 43.41 5.03
4028 4056 3.338249 TCTCTAGAGCATTGCCACAAAC 58.662 45.455 15.35 0.00 0.00 2.93
4083 4111 2.636830 CAGTTCTTCCCATGTGCCTAG 58.363 52.381 0.00 0.00 0.00 3.02
4084 4112 1.340017 GCAGTTCTTCCCATGTGCCTA 60.340 52.381 0.00 0.00 0.00 3.93
4085 4113 0.610232 GCAGTTCTTCCCATGTGCCT 60.610 55.000 0.00 0.00 0.00 4.75
4086 4114 0.895100 TGCAGTTCTTCCCATGTGCC 60.895 55.000 0.00 0.00 0.00 5.01
4126 4154 1.475682 GATTCTTTCTTGCCCTGCTGG 59.524 52.381 1.89 1.89 37.09 4.85
4197 4225 0.108041 AACCATTACCACGCCTACCG 60.108 55.000 0.00 0.00 44.21 4.02
4288 4316 7.106439 TGCAAAACTTGAGACTTTTGGATAA 57.894 32.000 5.32 0.00 37.68 1.75
4343 4371 8.454894 ACAATAAATACATACGTCAACAATGCA 58.545 29.630 0.00 0.00 0.00 3.96
4371 4399 1.448985 GGACACGTGTGTTGCCATAT 58.551 50.000 28.82 0.00 45.05 1.78
4427 5801 2.327343 CCATGCCATACATCGCCGG 61.327 63.158 0.00 0.00 36.64 6.13
4429 5803 0.534877 TGTCCATGCCATACATCGCC 60.535 55.000 0.00 0.00 36.64 5.54
4430 5804 1.466167 GATGTCCATGCCATACATCGC 59.534 52.381 5.14 0.00 39.90 4.58
4440 5814 6.035843 ACAACAAATTTATCGATGTCCATGC 58.964 36.000 8.54 0.00 0.00 4.06
4548 5922 1.097547 GGTGATGCACAATCTCCCGG 61.098 60.000 0.00 0.00 41.33 5.73
4594 5968 8.408601 CAAAACCATAGACTGAATATCCCTTTG 58.591 37.037 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.