Multiple sequence alignment - TraesCS2D01G600400

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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 TraesCS2D01G600400 chr2D 100.000 3208 0 0 1 3208 651071162 651074369 0.000000e+00 5925.0
1 TraesCS2D01G600400 chr2D 82.877 146 18 6 2519 2658 134411700 134411556 1.210000e-24 124.0
2 TraesCS2D01G600400 chr2B 92.083 2223 98 28 1 2219 780016195 780018343 0.000000e+00 3059.0
3 TraesCS2D01G600400 chr2B 93.500 400 23 2 2812 3208 780019738 780020137 2.760000e-165 592.0
4 TraesCS2D01G600400 chr2B 90.870 230 19 2 2212 2441 780019250 780019477 1.120000e-79 307.0
5 TraesCS2D01G600400 chr2B 92.000 175 11 1 2651 2825 780019550 780019721 3.200000e-60 243.0
6 TraesCS2D01G600400 chr2A 92.333 2152 97 22 2 2113 776601043 776598920 0.000000e+00 2998.0
7 TraesCS2D01G600400 chr2A 93.007 143 10 0 2146 2288 776598933 776598791 3.240000e-50 209.0
8 TraesCS2D01G600400 chr7D 83.562 146 16 8 2519 2658 13330438 13330295 2.600000e-26 130.0
9 TraesCS2D01G600400 chr7D 100.000 30 0 0 839 868 60588144 60588173 4.470000e-04 56.5
10 TraesCS2D01G600400 chr7B 84.444 135 17 4 2519 2650 547516719 547516852 2.600000e-26 130.0
11 TraesCS2D01G600400 chr6D 83.562 146 17 6 2519 2658 14177740 14177596 2.600000e-26 130.0
12 TraesCS2D01G600400 chr5B 84.444 135 17 4 2519 2650 491108892 491109025 2.600000e-26 130.0
13 TraesCS2D01G600400 chr3B 83.088 136 17 5 2519 2650 463081756 463081623 5.620000e-23 119.0
14 TraesCS2D01G600400 chr3B 80.822 146 21 7 2518 2658 253976772 253976915 1.220000e-19 108.0
15 TraesCS2D01G600400 chr3B 73.234 269 57 10 377 639 13246545 13246286 2.050000e-12 84.2
16 TraesCS2D01G600400 chr4A 81.379 145 21 6 2519 2658 680482287 680482144 2.620000e-21 113.0
17 TraesCS2D01G600400 chr6B 81.343 134 18 5 2511 2641 33953241 33953370 5.660000e-18 102.0
18 TraesCS2D01G600400 chr3A 72.924 277 59 11 370 639 16009741 16009474 7.380000e-12 82.4
19 TraesCS2D01G600400 chr3D 72.826 276 57 13 370 637 5409705 5409970 9.540000e-11 78.7
20 TraesCS2D01G600400 chr3D 100.000 30 0 0 839 868 573935063 573935092 4.470000e-04 56.5


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 TraesCS2D01G600400 chr2D 651071162 651074369 3207 False 5925.00 5925 100.00000 1 3208 1 chr2D.!!$F1 3207
1 TraesCS2D01G600400 chr2B 780016195 780020137 3942 False 1050.25 3059 92.11325 1 3208 4 chr2B.!!$F1 3207
2 TraesCS2D01G600400 chr2A 776598791 776601043 2252 True 1603.50 2998 92.67000 2 2288 2 chr2A.!!$R1 2286

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
45 46 0.035458 CTTGGAGGAAGCAACGGTCT 59.965 55.000 0.0 0.0 0.0 3.85 F
553 554 1.074775 CCCCCGATGACTTCCCCTA 60.075 63.158 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1229 1256 1.254882 GAGCGCTATCGATCGACATG 58.745 55.0 22.06 14.08 41.41 3.21 R
2365 3324 0.179215 CGAAATTCTGCAGCCGTGAC 60.179 55.0 9.47 0.00 0.00 3.67 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
45 46 0.035458 CTTGGAGGAAGCAACGGTCT 59.965 55.000 0.00 0.00 0.00 3.85
214 215 4.388499 CCTTGGTCACCGTCCCCG 62.388 72.222 0.00 0.00 0.00 5.73
220 221 3.998672 TCACCGTCCCCGCTTCAC 61.999 66.667 0.00 0.00 0.00 3.18
300 301 3.695606 GAGGTGACGCTCAGCCCA 61.696 66.667 11.73 0.00 45.34 5.36
309 310 1.222113 GCTCAGCCCAGGGTAGAAC 59.778 63.158 7.55 0.00 0.00 3.01
483 484 2.425592 CCTTGCCCAGACACGACA 59.574 61.111 0.00 0.00 0.00 4.35
553 554 1.074775 CCCCCGATGACTTCCCCTA 60.075 63.158 0.00 0.00 0.00 3.53
594 595 1.733399 GAGGTCGAGCGTTGTGGTC 60.733 63.158 9.28 0.00 41.76 4.02
883 884 2.737252 GCGACGTCCATCTTTTCTTCTT 59.263 45.455 10.58 0.00 0.00 2.52
1260 1289 1.425694 TAGCGCTCTCTCTCCCTCTA 58.574 55.000 16.34 0.00 0.00 2.43
1277 1306 0.952280 CTATCGGCTTCTACTCGCCA 59.048 55.000 0.00 0.00 46.62 5.69
1280 1309 0.752009 TCGGCTTCTACTCGCCATCT 60.752 55.000 0.00 0.00 46.62 2.90
1328 1357 4.081642 TCAAATTGTAGAGAAGGAGGACGG 60.082 45.833 0.00 0.00 0.00 4.79
1566 1595 1.529244 AAAGAGCAGCGGCAAACCT 60.529 52.632 12.44 0.00 44.61 3.50
1600 1629 2.606587 GGACCATCCACCAGGCAGT 61.607 63.158 0.00 0.00 36.28 4.40
1607 1636 4.969196 CACCAGGCAGTCACGCGT 62.969 66.667 5.58 5.58 0.00 6.01
2075 2120 5.232414 CGTCGTCCTAGAATCTTCCAAAATC 59.768 44.000 0.00 0.00 0.00 2.17
2135 2180 5.652014 ACCATACCATATTGGAACACAGTTG 59.348 40.000 0.00 0.00 40.96 3.16
2136 2181 5.885352 CCATACCATATTGGAACACAGTTGA 59.115 40.000 0.00 0.00 40.96 3.18
2148 2193 5.371115 AACACAGTTGAAATAATCGTGGG 57.629 39.130 0.00 0.00 0.00 4.61
2168 2213 2.353109 GGGTTTAGACACTCCCGTACAC 60.353 54.545 0.00 0.00 0.00 2.90
2204 2249 7.281841 TGGCTCATATTATGACAAATCTCACA 58.718 34.615 2.14 0.00 35.06 3.58
2242 3201 1.343884 ACTTCCTGATCAGAGGAGGGG 60.344 57.143 24.62 6.42 43.26 4.79
2358 3317 9.905713 TCTATATCAATAACCCATTATGCCTTC 57.094 33.333 0.00 0.00 31.07 3.46
2365 3324 1.597742 CCATTATGCCTTCGGGAGTG 58.402 55.000 0.00 0.00 37.25 3.51
2400 3359 2.500509 TTCGTTTGCACAAACCATCC 57.499 45.000 18.01 0.00 45.78 3.51
2401 3360 0.671251 TCGTTTGCACAAACCATCCC 59.329 50.000 18.01 0.00 45.78 3.85
2405 3364 0.179004 TTGCACAAACCATCCCGAGT 60.179 50.000 0.00 0.00 0.00 4.18
2409 3368 2.354821 GCACAAACCATCCCGAGTAATC 59.645 50.000 0.00 0.00 0.00 1.75
2413 3372 5.236478 CACAAACCATCCCGAGTAATCATAC 59.764 44.000 0.00 0.00 0.00 2.39
2417 3376 6.187727 ACCATCCCGAGTAATCATACAAAT 57.812 37.500 0.00 0.00 34.29 2.32
2420 3379 7.234782 ACCATCCCGAGTAATCATACAAATAGA 59.765 37.037 0.00 0.00 34.29 1.98
2464 3423 9.922477 TGTTAGAGAGATCTATTTAAGTGGAGA 57.078 33.333 0.00 0.00 0.00 3.71
2466 3425 9.922477 TTAGAGAGATCTATTTAAGTGGAGACA 57.078 33.333 0.00 0.00 38.70 3.41
2479 3438 3.896648 TGGAGACACGAAGAAAAATGC 57.103 42.857 0.00 0.00 33.40 3.56
2480 3439 3.210227 TGGAGACACGAAGAAAAATGCA 58.790 40.909 0.00 0.00 33.40 3.96
2481 3440 3.820467 TGGAGACACGAAGAAAAATGCAT 59.180 39.130 0.00 0.00 33.40 3.96
2482 3441 4.083324 TGGAGACACGAAGAAAAATGCATC 60.083 41.667 0.00 0.00 33.40 3.91
2483 3442 4.154918 GGAGACACGAAGAAAAATGCATCT 59.845 41.667 0.00 0.00 0.00 2.90
2484 3443 5.288543 AGACACGAAGAAAAATGCATCTC 57.711 39.130 0.00 0.00 0.00 2.75
2485 3444 4.756642 AGACACGAAGAAAAATGCATCTCA 59.243 37.500 0.00 0.00 0.00 3.27
2486 3445 5.413833 AGACACGAAGAAAAATGCATCTCAT 59.586 36.000 0.00 0.00 36.87 2.90
2487 3446 5.396484 ACACGAAGAAAAATGCATCTCATG 58.604 37.500 0.00 0.00 35.13 3.07
2488 3447 5.181811 ACACGAAGAAAAATGCATCTCATGA 59.818 36.000 0.00 0.00 35.13 3.07
2489 3448 5.510674 CACGAAGAAAAATGCATCTCATGAC 59.489 40.000 0.00 0.00 35.13 3.06
2490 3449 5.413833 ACGAAGAAAAATGCATCTCATGACT 59.586 36.000 0.00 0.00 35.13 3.41
2491 3450 5.737757 CGAAGAAAAATGCATCTCATGACTG 59.262 40.000 0.00 0.00 35.13 3.51
2492 3451 6.402875 CGAAGAAAAATGCATCTCATGACTGA 60.403 38.462 0.00 0.00 35.13 3.41
2493 3452 7.406031 AAGAAAAATGCATCTCATGACTGAT 57.594 32.000 0.00 0.00 35.13 2.90
2494 3453 7.028926 AGAAAAATGCATCTCATGACTGATC 57.971 36.000 0.00 0.00 35.13 2.92
2495 3454 6.602009 AGAAAAATGCATCTCATGACTGATCA 59.398 34.615 0.00 0.00 39.83 2.92
2496 3455 5.752892 AAATGCATCTCATGACTGATCAC 57.247 39.130 0.00 0.00 37.79 3.06
2497 3456 3.189618 TGCATCTCATGACTGATCACC 57.810 47.619 0.00 0.00 37.79 4.02
2498 3457 2.770232 TGCATCTCATGACTGATCACCT 59.230 45.455 0.00 0.00 37.79 4.00
2499 3458 3.181468 TGCATCTCATGACTGATCACCTC 60.181 47.826 0.00 0.00 37.79 3.85
2500 3459 3.803021 GCATCTCATGACTGATCACCTCC 60.803 52.174 0.00 0.00 37.79 4.30
2501 3460 3.105959 TCTCATGACTGATCACCTCCA 57.894 47.619 0.00 0.00 37.79 3.86
2502 3461 3.650948 TCTCATGACTGATCACCTCCAT 58.349 45.455 0.00 0.00 37.79 3.41
2503 3462 3.640498 TCTCATGACTGATCACCTCCATC 59.360 47.826 0.00 0.00 37.79 3.51
2504 3463 3.377573 TCATGACTGATCACCTCCATCA 58.622 45.455 0.00 0.00 37.79 3.07
2505 3464 3.971971 TCATGACTGATCACCTCCATCAT 59.028 43.478 0.00 0.00 37.79 2.45
2506 3465 4.040095 TCATGACTGATCACCTCCATCATC 59.960 45.833 0.00 0.00 37.79 2.92
2507 3466 3.650948 TGACTGATCACCTCCATCATCT 58.349 45.455 0.00 0.00 29.78 2.90
2508 3467 4.808042 TGACTGATCACCTCCATCATCTA 58.192 43.478 0.00 0.00 29.78 1.98
2509 3468 4.586421 TGACTGATCACCTCCATCATCTAC 59.414 45.833 0.00 0.00 29.78 2.59
2510 3469 4.813809 ACTGATCACCTCCATCATCTACT 58.186 43.478 0.00 0.00 29.78 2.57
2511 3470 5.215069 ACTGATCACCTCCATCATCTACTT 58.785 41.667 0.00 0.00 29.78 2.24
2512 3471 6.377080 ACTGATCACCTCCATCATCTACTTA 58.623 40.000 0.00 0.00 29.78 2.24
2513 3472 7.015680 ACTGATCACCTCCATCATCTACTTAT 58.984 38.462 0.00 0.00 29.78 1.73
2514 3473 8.173412 ACTGATCACCTCCATCATCTACTTATA 58.827 37.037 0.00 0.00 29.78 0.98
2515 3474 8.354711 TGATCACCTCCATCATCTACTTATAC 57.645 38.462 0.00 0.00 0.00 1.47
2516 3475 8.173412 TGATCACCTCCATCATCTACTTATACT 58.827 37.037 0.00 0.00 0.00 2.12
2517 3476 9.688091 GATCACCTCCATCATCTACTTATACTA 57.312 37.037 0.00 0.00 0.00 1.82
2531 3490 6.734104 ACTTATACTATAGTAGAACGCCCG 57.266 41.667 17.31 9.53 33.52 6.13
2532 3491 6.234177 ACTTATACTATAGTAGAACGCCCGT 58.766 40.000 17.31 10.08 33.52 5.28
2533 3492 6.148480 ACTTATACTATAGTAGAACGCCCGTG 59.852 42.308 17.31 8.33 33.52 4.94
2534 3493 1.336125 ACTATAGTAGAACGCCCGTGC 59.664 52.381 2.75 0.00 0.00 5.34
2566 3525 3.921257 GCATTGGCAGCTTCCTTTT 57.079 47.368 3.45 0.00 40.72 2.27
2567 3526 2.174363 GCATTGGCAGCTTCCTTTTT 57.826 45.000 3.45 0.00 40.72 1.94
2568 3527 3.317603 GCATTGGCAGCTTCCTTTTTA 57.682 42.857 3.45 0.00 40.72 1.52
2569 3528 2.995939 GCATTGGCAGCTTCCTTTTTAC 59.004 45.455 3.45 0.00 40.72 2.01
2570 3529 3.554752 GCATTGGCAGCTTCCTTTTTACA 60.555 43.478 3.45 0.00 40.72 2.41
2571 3530 4.240096 CATTGGCAGCTTCCTTTTTACAG 58.760 43.478 3.45 0.00 0.00 2.74
2572 3531 2.944129 TGGCAGCTTCCTTTTTACAGT 58.056 42.857 3.45 0.00 0.00 3.55
2573 3532 3.295973 TGGCAGCTTCCTTTTTACAGTT 58.704 40.909 3.45 0.00 0.00 3.16
2574 3533 4.465886 TGGCAGCTTCCTTTTTACAGTTA 58.534 39.130 3.45 0.00 0.00 2.24
2583 3542 7.468768 GCTTCCTTTTTACAGTTAAAGCACTCT 60.469 37.037 0.00 0.00 38.16 3.24
2585 3544 8.603242 TCCTTTTTACAGTTAAAGCACTCTAG 57.397 34.615 0.00 0.00 31.54 2.43
2600 3561 5.467063 AGCACTCTAGTTTTCTTCCTTTTCG 59.533 40.000 0.00 0.00 0.00 3.46
2618 3579 7.287235 TCCTTTTCGTTTCCCCAACTAAAATTA 59.713 33.333 0.00 0.00 38.61 1.40
2628 3589 6.826741 TCCCCAACTAAAATTATTTCTCGGAG 59.173 38.462 0.00 0.00 0.00 4.63
2629 3590 6.602009 CCCCAACTAAAATTATTTCTCGGAGT 59.398 38.462 4.69 0.00 0.00 3.85
2630 3591 7.415206 CCCCAACTAAAATTATTTCTCGGAGTG 60.415 40.741 4.69 0.00 0.00 3.51
2631 3592 7.335924 CCCAACTAAAATTATTTCTCGGAGTGA 59.664 37.037 4.69 0.00 0.00 3.41
2632 3593 8.893727 CCAACTAAAATTATTTCTCGGAGTGAT 58.106 33.333 4.69 3.38 0.00 3.06
2637 3598 7.986085 AAATTATTTCTCGGAGTGATATGGG 57.014 36.000 4.69 0.00 0.00 4.00
2638 3599 6.935240 ATTATTTCTCGGAGTGATATGGGA 57.065 37.500 4.69 0.00 0.00 4.37
2639 3600 6.740944 TTATTTCTCGGAGTGATATGGGAA 57.259 37.500 4.69 0.00 0.00 3.97
2640 3601 5.832539 ATTTCTCGGAGTGATATGGGAAT 57.167 39.130 4.69 0.00 0.00 3.01
2641 3602 4.607293 TTCTCGGAGTGATATGGGAATG 57.393 45.455 4.69 0.00 0.00 2.67
2642 3603 2.899900 TCTCGGAGTGATATGGGAATGG 59.100 50.000 4.69 0.00 0.00 3.16
2643 3604 2.899900 CTCGGAGTGATATGGGAATGGA 59.100 50.000 0.00 0.00 0.00 3.41
2644 3605 3.517100 CTCGGAGTGATATGGGAATGGAT 59.483 47.826 0.00 0.00 0.00 3.41
2645 3606 4.683643 TCGGAGTGATATGGGAATGGATA 58.316 43.478 0.00 0.00 0.00 2.59
2646 3607 5.090845 TCGGAGTGATATGGGAATGGATAA 58.909 41.667 0.00 0.00 0.00 1.75
2647 3608 5.546110 TCGGAGTGATATGGGAATGGATAAA 59.454 40.000 0.00 0.00 0.00 1.40
2648 3609 6.215431 TCGGAGTGATATGGGAATGGATAAAT 59.785 38.462 0.00 0.00 0.00 1.40
2649 3610 6.886459 CGGAGTGATATGGGAATGGATAAATT 59.114 38.462 0.00 0.00 0.00 1.82
2650 3611 8.046708 CGGAGTGATATGGGAATGGATAAATTA 58.953 37.037 0.00 0.00 0.00 1.40
2724 3685 9.941325 ACAAATAATAATCCAACATGCAAAGAA 57.059 25.926 0.00 0.00 0.00 2.52
2802 3763 6.850752 ACAAATACCAAATCCCCTACTTTG 57.149 37.500 0.00 0.00 33.20 2.77
2804 3765 7.471890 ACAAATACCAAATCCCCTACTTTGTA 58.528 34.615 0.00 0.00 33.82 2.41
2825 3786 9.658475 TTTGTATTCGTTAATCACTTGAACAAG 57.342 29.630 12.22 12.22 43.79 3.16
2837 3828 3.004734 ACTTGAACAAGCACTTACCATGC 59.995 43.478 13.50 0.00 41.99 4.06
2875 3868 9.965902 AGGATAATGACATATTTAAGGATGACC 57.034 33.333 5.85 0.00 0.00 4.02
2937 3930 2.633481 AGTCTTTCTACGTGGCCTCTTT 59.367 45.455 3.32 0.00 0.00 2.52
2943 3936 2.832129 TCTACGTGGCCTCTTTCAAGAT 59.168 45.455 3.32 0.00 33.93 2.40
3014 4007 6.371389 GTGTAAACTTGCATGAGTAGGTTTC 58.629 40.000 6.60 0.00 38.55 2.78
3034 4028 6.774170 GGTTTCCCAAGAACCTAGTAGAAAAA 59.226 38.462 0.00 0.00 42.58 1.94
3035 4029 7.255381 GGTTTCCCAAGAACCTAGTAGAAAAAC 60.255 40.741 0.00 0.00 42.58 2.43
3094 4088 0.107361 ATACAGCTAAACGCACCCCC 60.107 55.000 0.00 0.00 42.61 5.40
3105 4099 2.982130 CACCCCCTCCTCTTGTCG 59.018 66.667 0.00 0.00 0.00 4.35
3136 4130 4.063998 TGGTATGCTAGACATGCTTCAG 57.936 45.455 12.35 0.00 40.86 3.02
3159 4153 1.352622 AAAGACAGTCTGGGTGCCCA 61.353 55.000 9.90 9.90 45.02 5.36
3182 4176 2.929964 ATGGGTGGCCGGATTGGTT 61.930 57.895 5.05 0.00 41.21 3.67
3184 4178 2.282887 GGTGGCCGGATTGGTTGT 60.283 61.111 5.05 0.00 41.21 3.32
3188 4182 2.340328 GGCCGGATTGGTTGTGGAC 61.340 63.158 5.05 0.00 41.21 4.02
3196 4190 2.663852 GGTTGTGGACGGTGGTCG 60.664 66.667 0.00 0.00 44.39 4.79
3204 4198 1.814527 GACGGTGGTCGGCTAAGAT 59.185 57.895 0.00 0.00 45.10 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.671742 GAGACCGTTGCTTCCTCCA 59.328 57.895 0.00 0.00 0.00 3.86
45 46 1.990060 GTGCAGCTGGGGAGTAGGA 60.990 63.158 17.12 0.00 0.00 2.94
84 85 3.203487 ACCAAAACCCTGAGAACCTAACA 59.797 43.478 0.00 0.00 0.00 2.41
85 86 3.828921 ACCAAAACCCTGAGAACCTAAC 58.171 45.455 0.00 0.00 0.00 2.34
167 168 2.358737 GCGTCCTTGTCCACTGGG 60.359 66.667 0.00 0.00 0.00 4.45
214 215 2.095252 GGAAGACGAGGCGTGAAGC 61.095 63.158 0.00 0.00 41.37 3.86
220 221 2.125912 CCACTGGAAGACGAGGCG 60.126 66.667 0.00 0.00 37.43 5.52
309 310 0.497265 GTCAACAGACGAACGTCACG 59.503 55.000 25.13 18.51 46.76 4.35
483 484 1.821061 CGCTCAGCCTCGGGGATTAT 61.821 60.000 4.80 0.00 33.58 1.28
647 648 1.338200 GCTTTCTCCATGTCGGACAGT 60.338 52.381 16.84 2.41 39.64 3.55
862 863 2.338500 AGAAGAAAAGATGGACGTCGC 58.662 47.619 9.92 3.20 0.00 5.19
863 864 3.987868 TCAAGAAGAAAAGATGGACGTCG 59.012 43.478 9.92 0.00 0.00 5.12
864 865 5.220303 CGATCAAGAAGAAAAGATGGACGTC 60.220 44.000 7.13 7.13 0.00 4.34
865 866 4.627467 CGATCAAGAAGAAAAGATGGACGT 59.373 41.667 0.00 0.00 0.00 4.34
866 867 4.033358 CCGATCAAGAAGAAAAGATGGACG 59.967 45.833 0.00 0.00 0.00 4.79
867 868 4.938226 ACCGATCAAGAAGAAAAGATGGAC 59.062 41.667 0.00 0.00 0.00 4.02
902 903 4.639959 CCTATATATATCTACTCGCGCGC 58.360 47.826 27.95 23.91 0.00 6.86
908 909 5.163972 CGACGGCGCCTATATATATCTACTC 60.164 48.000 26.68 0.00 0.00 2.59
934 935 9.619316 TGGCCAATAAATAAATTTAATCGATCG 57.381 29.630 9.36 9.36 36.02 3.69
970 994 0.178955 TACCTGGACTCGAACACCCA 60.179 55.000 0.00 0.00 0.00 4.51
1118 1145 9.217278 CGTCGAGGCTACCATATAAGTATATAT 57.783 37.037 0.00 0.00 35.51 0.86
1119 1146 7.658982 CCGTCGAGGCTACCATATAAGTATATA 59.341 40.741 0.00 0.00 0.00 0.86
1120 1147 6.485984 CCGTCGAGGCTACCATATAAGTATAT 59.514 42.308 0.00 0.00 0.00 0.86
1121 1148 5.819379 CCGTCGAGGCTACCATATAAGTATA 59.181 44.000 0.00 0.00 0.00 1.47
1122 1149 4.639310 CCGTCGAGGCTACCATATAAGTAT 59.361 45.833 0.00 0.00 0.00 2.12
1123 1150 4.005650 CCGTCGAGGCTACCATATAAGTA 58.994 47.826 0.00 0.00 0.00 2.24
1124 1151 2.818432 CCGTCGAGGCTACCATATAAGT 59.182 50.000 0.00 0.00 0.00 2.24
1125 1152 3.489180 CCGTCGAGGCTACCATATAAG 57.511 52.381 0.00 0.00 0.00 1.73
1147 1174 1.576527 CGACAAAACAAACGCGCGAG 61.577 55.000 39.36 26.36 0.00 5.03
1229 1256 1.254882 GAGCGCTATCGATCGACATG 58.745 55.000 22.06 14.08 41.41 3.21
1230 1257 3.685459 GAGCGCTATCGATCGACAT 57.315 52.632 22.06 8.35 41.41 3.06
1328 1357 3.797546 GGCTTGACTCTGCTGCGC 61.798 66.667 0.00 0.00 0.00 6.09
1337 1366 3.328931 TCTTGAATCCTCTTGGCTTGACT 59.671 43.478 0.00 0.00 0.00 3.41
1339 1368 3.679389 GTCTTGAATCCTCTTGGCTTGA 58.321 45.455 0.00 0.00 0.00 3.02
1530 1559 2.859165 TTGTAGGCCTTCCACTTGAG 57.141 50.000 12.58 0.00 33.74 3.02
1566 1595 3.089874 CCTGATGAGGCCCCGGAA 61.090 66.667 0.73 0.00 30.52 4.30
1600 1629 1.372004 CGGTCCTTGTAACGCGTGA 60.372 57.895 14.98 0.07 0.00 4.35
1607 1636 3.315949 AGGCGGCGGTCCTTGTAA 61.316 61.111 9.78 0.00 0.00 2.41
2075 2120 6.320494 AGAATCTTGCTATAGGTACGACAG 57.680 41.667 1.04 0.00 0.00 3.51
2119 2164 8.956426 ACGATTATTTCAACTGTGTTCCAATAT 58.044 29.630 0.00 0.00 0.00 1.28
2135 2180 5.878669 AGTGTCTAAACCCCACGATTATTTC 59.121 40.000 0.00 0.00 34.34 2.17
2136 2181 5.812286 AGTGTCTAAACCCCACGATTATTT 58.188 37.500 0.00 0.00 34.34 1.40
2148 2193 2.560105 AGTGTACGGGAGTGTCTAAACC 59.440 50.000 0.00 0.00 46.80 3.27
2168 2213 6.539826 TCATAATATGAGCCAGACAACACAAG 59.460 38.462 0.00 0.00 33.59 3.16
2214 2259 7.877097 CCTCCTCTGATCAGGAAGTTATTAATG 59.123 40.741 22.42 0.00 42.35 1.90
2242 3201 5.766103 TCACCAGGTGCGAGGATACTATTC 61.766 50.000 15.64 0.00 39.68 1.75
2335 3294 6.603201 CCGAAGGCATAATGGGTTATTGATAT 59.397 38.462 0.00 0.00 46.14 1.63
2336 3295 5.943416 CCGAAGGCATAATGGGTTATTGATA 59.057 40.000 0.00 0.00 46.14 2.15
2337 3296 4.766891 CCGAAGGCATAATGGGTTATTGAT 59.233 41.667 0.00 0.00 46.14 2.57
2339 3298 4.503741 CCGAAGGCATAATGGGTTATTG 57.496 45.455 0.00 0.00 46.14 1.90
2365 3324 0.179215 CGAAATTCTGCAGCCGTGAC 60.179 55.000 9.47 0.00 0.00 3.67
2441 3400 9.344772 GTGTCTCCACTTAAATAGATCTCTCTA 57.655 37.037 0.00 0.00 38.61 2.43
2442 3401 7.012894 CGTGTCTCCACTTAAATAGATCTCTCT 59.987 40.741 0.00 0.00 39.55 3.10
2443 3402 7.012515 TCGTGTCTCCACTTAAATAGATCTCTC 59.987 40.741 0.00 0.00 39.55 3.20
2444 3403 6.829298 TCGTGTCTCCACTTAAATAGATCTCT 59.171 38.462 0.00 0.00 39.55 3.10
2445 3404 7.028926 TCGTGTCTCCACTTAAATAGATCTC 57.971 40.000 0.00 0.00 39.55 2.75
2446 3405 7.339721 TCTTCGTGTCTCCACTTAAATAGATCT 59.660 37.037 0.00 0.00 39.55 2.75
2447 3406 7.481642 TCTTCGTGTCTCCACTTAAATAGATC 58.518 38.462 0.00 0.00 39.55 2.75
2449 3408 6.829229 TCTTCGTGTCTCCACTTAAATAGA 57.171 37.500 0.00 0.00 39.55 1.98
2451 3410 8.665643 TTTTTCTTCGTGTCTCCACTTAAATA 57.334 30.769 0.00 0.00 39.55 1.40
2452 3411 7.562454 TTTTTCTTCGTGTCTCCACTTAAAT 57.438 32.000 0.00 0.00 39.55 1.40
2453 3412 6.988622 TTTTTCTTCGTGTCTCCACTTAAA 57.011 33.333 0.00 0.00 39.55 1.52
2454 3413 6.512741 GCATTTTTCTTCGTGTCTCCACTTAA 60.513 38.462 0.00 0.00 39.55 1.85
2455 3414 5.049680 GCATTTTTCTTCGTGTCTCCACTTA 60.050 40.000 0.00 0.00 39.55 2.24
2456 3415 4.261197 GCATTTTTCTTCGTGTCTCCACTT 60.261 41.667 0.00 0.00 39.55 3.16
2457 3416 3.251004 GCATTTTTCTTCGTGTCTCCACT 59.749 43.478 0.00 0.00 39.55 4.00
2458 3417 3.003275 TGCATTTTTCTTCGTGTCTCCAC 59.997 43.478 0.00 0.00 38.27 4.02
2459 3418 3.210227 TGCATTTTTCTTCGTGTCTCCA 58.790 40.909 0.00 0.00 0.00 3.86
2460 3419 3.896648 TGCATTTTTCTTCGTGTCTCC 57.103 42.857 0.00 0.00 0.00 3.71
2461 3420 5.106948 TGAGATGCATTTTTCTTCGTGTCTC 60.107 40.000 0.00 0.00 0.00 3.36
2462 3421 4.756642 TGAGATGCATTTTTCTTCGTGTCT 59.243 37.500 0.00 0.00 0.00 3.41
2463 3422 5.034554 TGAGATGCATTTTTCTTCGTGTC 57.965 39.130 0.00 0.00 0.00 3.67
2464 3423 5.181811 TCATGAGATGCATTTTTCTTCGTGT 59.818 36.000 0.00 0.00 34.15 4.49
2465 3424 5.510674 GTCATGAGATGCATTTTTCTTCGTG 59.489 40.000 0.00 4.71 34.15 4.35
2466 3425 5.413833 AGTCATGAGATGCATTTTTCTTCGT 59.586 36.000 0.00 0.00 34.15 3.85
2467 3426 5.737757 CAGTCATGAGATGCATTTTTCTTCG 59.262 40.000 0.00 0.00 34.15 3.79
2468 3427 6.849502 TCAGTCATGAGATGCATTTTTCTTC 58.150 36.000 0.00 0.00 34.15 2.87
2469 3428 6.829229 TCAGTCATGAGATGCATTTTTCTT 57.171 33.333 0.00 0.00 34.15 2.52
2470 3429 6.602009 TGATCAGTCATGAGATGCATTTTTCT 59.398 34.615 0.00 0.00 39.29 2.52
2471 3430 6.691818 GTGATCAGTCATGAGATGCATTTTTC 59.308 38.462 0.00 0.03 39.29 2.29
2472 3431 6.405508 GGTGATCAGTCATGAGATGCATTTTT 60.406 38.462 0.00 0.00 39.29 1.94
2473 3432 5.067413 GGTGATCAGTCATGAGATGCATTTT 59.933 40.000 0.00 0.00 39.29 1.82
2474 3433 4.579340 GGTGATCAGTCATGAGATGCATTT 59.421 41.667 0.00 0.00 39.29 2.32
2475 3434 4.135306 GGTGATCAGTCATGAGATGCATT 58.865 43.478 0.00 0.00 39.29 3.56
2476 3435 3.391626 AGGTGATCAGTCATGAGATGCAT 59.608 43.478 0.00 0.00 39.29 3.96
2477 3436 2.770232 AGGTGATCAGTCATGAGATGCA 59.230 45.455 0.00 0.00 39.29 3.96
2478 3437 3.391965 GAGGTGATCAGTCATGAGATGC 58.608 50.000 0.00 0.00 39.29 3.91
2479 3438 3.387050 TGGAGGTGATCAGTCATGAGATG 59.613 47.826 0.00 0.00 39.29 2.90
2480 3439 3.650948 TGGAGGTGATCAGTCATGAGAT 58.349 45.455 0.00 0.00 39.29 2.75
2481 3440 3.105959 TGGAGGTGATCAGTCATGAGA 57.894 47.619 0.00 0.00 39.29 3.27
2482 3441 3.387050 TGATGGAGGTGATCAGTCATGAG 59.613 47.826 0.00 0.00 39.29 2.90
2483 3442 3.377573 TGATGGAGGTGATCAGTCATGA 58.622 45.455 0.00 0.00 40.50 3.07
2484 3443 3.832615 TGATGGAGGTGATCAGTCATG 57.167 47.619 0.00 0.00 36.60 3.07
2485 3444 4.232909 AGATGATGGAGGTGATCAGTCAT 58.767 43.478 0.00 0.00 36.69 3.06
2486 3445 3.650948 AGATGATGGAGGTGATCAGTCA 58.349 45.455 0.00 0.00 33.38 3.41
2487 3446 4.832266 AGTAGATGATGGAGGTGATCAGTC 59.168 45.833 0.00 0.00 33.38 3.51
2488 3447 4.813809 AGTAGATGATGGAGGTGATCAGT 58.186 43.478 0.00 0.00 33.38 3.41
2489 3448 5.804944 AAGTAGATGATGGAGGTGATCAG 57.195 43.478 0.00 0.00 33.38 2.90
2490 3449 8.173412 AGTATAAGTAGATGATGGAGGTGATCA 58.827 37.037 0.00 0.00 34.37 2.92
2491 3450 8.588290 AGTATAAGTAGATGATGGAGGTGATC 57.412 38.462 0.00 0.00 0.00 2.92
2506 3465 7.547370 ACGGGCGTTCTACTATAGTATAAGTAG 59.453 40.741 12.98 14.47 44.31 2.57
2507 3466 7.331934 CACGGGCGTTCTACTATAGTATAAGTA 59.668 40.741 12.98 0.00 0.00 2.24
2508 3467 6.148480 CACGGGCGTTCTACTATAGTATAAGT 59.852 42.308 12.98 4.11 0.00 2.24
2509 3468 6.541086 CACGGGCGTTCTACTATAGTATAAG 58.459 44.000 12.98 4.06 0.00 1.73
2510 3469 5.106555 GCACGGGCGTTCTACTATAGTATAA 60.107 44.000 12.98 9.53 0.00 0.98
2511 3470 4.393062 GCACGGGCGTTCTACTATAGTATA 59.607 45.833 12.98 3.51 0.00 1.47
2512 3471 3.190118 GCACGGGCGTTCTACTATAGTAT 59.810 47.826 12.98 0.00 0.00 2.12
2513 3472 2.549754 GCACGGGCGTTCTACTATAGTA 59.450 50.000 12.05 12.05 0.00 1.82
2514 3473 1.336125 GCACGGGCGTTCTACTATAGT 59.664 52.381 10.87 10.87 0.00 2.12
2515 3474 2.047679 GCACGGGCGTTCTACTATAG 57.952 55.000 0.00 0.00 0.00 1.31
2539 3498 3.682885 TGCCAATGCAGCCCGTTG 61.683 61.111 0.00 0.00 44.23 4.10
2548 3507 2.174363 AAAAAGGAAGCTGCCAATGC 57.826 45.000 15.05 0.00 38.26 3.56
2549 3508 4.240096 CTGTAAAAAGGAAGCTGCCAATG 58.760 43.478 15.05 0.00 0.00 2.82
2550 3509 3.897505 ACTGTAAAAAGGAAGCTGCCAAT 59.102 39.130 15.05 0.00 0.00 3.16
2551 3510 3.295973 ACTGTAAAAAGGAAGCTGCCAA 58.704 40.909 15.05 0.00 0.00 4.52
2552 3511 2.944129 ACTGTAAAAAGGAAGCTGCCA 58.056 42.857 15.05 0.00 0.00 4.92
2553 3512 5.447624 TTAACTGTAAAAAGGAAGCTGCC 57.552 39.130 0.73 0.73 0.00 4.85
2554 3513 5.402568 GCTTTAACTGTAAAAAGGAAGCTGC 59.597 40.000 13.98 0.00 34.07 5.25
2555 3514 6.417930 GTGCTTTAACTGTAAAAAGGAAGCTG 59.582 38.462 13.98 0.00 35.26 4.24
2556 3515 6.321435 AGTGCTTTAACTGTAAAAAGGAAGCT 59.679 34.615 13.98 6.23 35.26 3.74
2557 3516 6.504398 AGTGCTTTAACTGTAAAAAGGAAGC 58.496 36.000 13.98 0.00 35.26 3.86
2558 3517 7.931275 AGAGTGCTTTAACTGTAAAAAGGAAG 58.069 34.615 13.98 0.00 35.26 3.46
2559 3518 7.875327 AGAGTGCTTTAACTGTAAAAAGGAA 57.125 32.000 13.98 0.00 35.26 3.36
2560 3519 8.208903 ACTAGAGTGCTTTAACTGTAAAAAGGA 58.791 33.333 13.98 10.17 34.07 3.36
2561 3520 8.379457 ACTAGAGTGCTTTAACTGTAAAAAGG 57.621 34.615 13.98 0.00 34.07 3.11
2565 3524 9.609346 AGAAAACTAGAGTGCTTTAACTGTAAA 57.391 29.630 0.00 0.00 0.00 2.01
2566 3525 9.609346 AAGAAAACTAGAGTGCTTTAACTGTAA 57.391 29.630 0.00 0.00 0.00 2.41
2567 3526 9.257651 GAAGAAAACTAGAGTGCTTTAACTGTA 57.742 33.333 0.00 0.00 0.00 2.74
2568 3527 7.226918 GGAAGAAAACTAGAGTGCTTTAACTGT 59.773 37.037 0.00 0.00 0.00 3.55
2569 3528 7.442666 AGGAAGAAAACTAGAGTGCTTTAACTG 59.557 37.037 0.00 0.00 0.00 3.16
2570 3529 7.510407 AGGAAGAAAACTAGAGTGCTTTAACT 58.490 34.615 0.00 0.00 0.00 2.24
2571 3530 7.731882 AGGAAGAAAACTAGAGTGCTTTAAC 57.268 36.000 0.00 0.00 0.00 2.01
2572 3531 8.747538 AAAGGAAGAAAACTAGAGTGCTTTAA 57.252 30.769 0.00 0.00 0.00 1.52
2573 3532 8.747538 AAAAGGAAGAAAACTAGAGTGCTTTA 57.252 30.769 0.00 0.00 0.00 1.85
2574 3533 7.467403 CGAAAAGGAAGAAAACTAGAGTGCTTT 60.467 37.037 0.00 0.00 0.00 3.51
2583 3542 5.300034 GGGGAAACGAAAAGGAAGAAAACTA 59.700 40.000 0.00 0.00 0.00 2.24
2585 3544 4.142116 TGGGGAAACGAAAAGGAAGAAAAC 60.142 41.667 0.00 0.00 0.00 2.43
2600 3561 7.758076 CCGAGAAATAATTTTAGTTGGGGAAAC 59.242 37.037 0.00 0.00 39.24 2.78
2618 3579 5.513788 CCATTCCCATATCACTCCGAGAAAT 60.514 44.000 1.33 0.00 0.00 2.17
2753 3714 8.929260 TGGAGAGCACAAAATCATATTATCAT 57.071 30.769 0.00 0.00 0.00 2.45
2757 3718 7.936496 TGTTGGAGAGCACAAAATCATATTA 57.064 32.000 0.00 0.00 0.00 0.98
2762 3723 4.998671 TTTGTTGGAGAGCACAAAATCA 57.001 36.364 0.00 0.00 39.40 2.57
2802 3763 7.268447 GTGCTTGTTCAAGTGATTAACGAATAC 59.732 37.037 13.04 0.00 0.00 1.89
2804 3765 6.017109 AGTGCTTGTTCAAGTGATTAACGAAT 60.017 34.615 13.04 0.00 0.00 3.34
2825 3786 4.747810 AGCAATTTTAGCATGGTAAGTGC 58.252 39.130 26.34 26.34 42.81 4.40
2897 3890 8.691661 AAAGACTGACTGGTTATTTGTGTTAT 57.308 30.769 0.00 0.00 0.00 1.89
2943 3936 8.912988 ACCTTGACAGATTTTTGATAGTTTTGA 58.087 29.630 0.00 0.00 0.00 2.69
3014 4007 7.818997 AAAGTTTTTCTACTAGGTTCTTGGG 57.181 36.000 0.00 0.00 0.00 4.12
3094 4088 6.574350 ACCAACTTATTATCGACAAGAGGAG 58.426 40.000 14.59 0.00 0.00 3.69
3105 4099 8.660373 GCATGTCTAGCATACCAACTTATTATC 58.340 37.037 0.00 0.00 35.74 1.75
3136 4130 1.609320 GCACCCAGACTGTCTTTCTCC 60.609 57.143 7.77 0.00 0.00 3.71
3159 4153 1.719063 AATCCGGCCACCCATGCTAT 61.719 55.000 2.24 0.00 0.00 2.97
3167 4161 2.282887 ACAACCAATCCGGCCACC 60.283 61.111 2.24 0.00 39.03 4.61
3173 4167 1.302192 ACCGTCCACAACCAATCCG 60.302 57.895 0.00 0.00 0.00 4.18
3184 4178 2.601067 TTAGCCGACCACCGTCCA 60.601 61.111 0.00 0.00 35.40 4.02
3188 4182 0.389391 ATCATCTTAGCCGACCACCG 59.611 55.000 0.00 0.00 38.18 4.94


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

AutoCloner maintained by Alex Coulton.