Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009595.1 Hibiscus syriacus cultivar Beakdansim tig00116974_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1046665
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:374053 original size:14 final size:14
Alignment explanation
Indices: 374011--374078 Score: 64
Period size: 14 Copynumber: 4.9 Consensus size: 14
374001 CAAAATCGGA
* *
374011 TTTATGTTTTAGAG
1 TTTATGATTTATAG
* *
374025 TTTAGGGTTTATAG
1 TTTATGATTTATAG
*
374039 TTTATGATTTGTAG
1 TTTATGATTTATAG
* * *
374053 TTTAAGGTTTATAA
1 TTTATGATTTATAG
374067 TTTATGATTTAT
1 TTTATGATTTAT
374079 TGTAAAGATA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (14 bp):
TTTATGATTTATAG
Found at i:374054 original size:28 final size:28
Alignment explanation
Indices: 374010--374076 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
374000 ACAAAATCGG
* *
374010 ATTTATGTTTTAG-AGTTTAGGGTTTATA
1 ATTTATGATTT-GTAGTTTAAGGTTTATA
*
374038 GTTTATGATTTGTAGTTTAAGGTTTATA
1 ATTTATGATTTGTAGTTTAAGGTTTATA
374066 ATTTATGATTT
1 ATTTATGATTT
374077 ATTGTAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.55
Consensus pattern (28 bp):
ATTTATGATTTGTAGTTTAAGGTTTATA
Found at i:374167 original size:14 final size:14
Alignment explanation
Indices: 374125--374168 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
374115 AGGAGGTAAA
*
374125 TATAATTTAGGGTT
1 TATAATTTATGGTT
* * *
374139 TATAGTTCATAGTT
1 TATAATTTATGGTT
374153 TATAATTTATGGTT
1 TATAATTTATGGTT
374167 TA
1 TA
374169 GGGTTTAAGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.52
Consensus pattern (14 bp):
TATAATTTATGGTT
Found at i:384432 original size:12 final size:11
Alignment explanation
Indices: 384408--384520 Score: 66
Period size: 12 Copynumber: 9.4 Consensus size: 11
384398 TTCAAAGAGG
384408 TTTTAT-TTAA
1 TTTTATATTAA
384418 TTTTATATTATA
1 TTTTATATTA-A
*
384430 TTTTATTTTAA
1 TTTTATATTAA
384441 TTTTAATATTAA
1 TTTT-ATATTAA
* *
384453 TTTTTTAAATAAA
1 --TTTTATATTAA
**
384466 TTAAATATTAATA
1 TTTTATATT-A-A
384479 TTTTAATATTATA
1 TTTT-ATATTA-A
*
384492 TTATAGATATTAA
1 TT-T-TATATTAA
384505 TTTTAATATTAA
1 TTTT-ATATTAA
384517 TTTT
1 TTTT
384521 TTAAATAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
10 6 0.08
11 13 0.16
12 29 0.36
13 16 0.20
14 16 0.20
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (11 bp):
TTTTATATTAA
Found at i:384494 original size:26 final size:27
Alignment explanation
Indices: 384422--384516 Score: 89
Period size: 24 Copynumber: 3.8 Consensus size: 27
384412 ATTTAATTTT
* *
384422 ATATT-ATATTTT-AT-TTTAATTTTA
1 ATATTAATATTTTAATATTAAATTATA
*
384446 ATATTAATTTTTTAA-A-TAAATTA-A
1 ATATTAATATTTTAATATTAAATTATA
*
384470 ATATTAATATTTTAATATTATATTATA
1 ATATTAATATTTTAATATTAAATTATA
384497 GATATT-A-ATTTTAATATTAA
1 -ATATTAATATTTTAATATTAA
384517 TTTTTTAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
24 20 0.34
25 12 0.21
26 19 0.33
27 2 0.03
28 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (27 bp):
ATATTAATATTTTAATATTAAATTATA
Found at i:384516 original size:64 final size:64
Alignment explanation
Indices: 384417--384574 Score: 259
Period size: 64 Copynumber: 2.5 Consensus size: 64
384407 GTTTTATTTA
* *
384417 ATTTT-ATATTATATT-T-TATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
1 ATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
384478 ATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
1 ATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
*
384542 TTTTTAATATTATATTATAGATATTTAATTTTA
1 ATTTTAATATTATATTATAGATA-TTAATTTTA
384575 TATCATATAA
Statistics
Matches: 90, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
61 5 0.06
62 10 0.11
63 1 0.01
64 65 0.72
65 9 0.10
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (64 bp):
ATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
Found at i:384524 original size:40 final size:37
Alignment explanation
Indices: 384469--384557 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 37
384459 AAATAAATTA
*
384469 AATATTAATATTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAATATTTTAA-A-TAAATTA-A-ATATTAATTTTT
*
384509 AATATTAATTTTTTAAATAAATTAAATATTAATTTTTT
1 AATATTAATATTTTAAATAAATTAAATATTAA-TTTTT
384547 AATATT-ATATT
1 AATATTAATATT
384558 ATAGATATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 7 0.16
37 5 0.11
38 16 0.36
39 1 0.02
40 15 0.34
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
AATATTAATATTTTAAATAAATTAAATATTAATTTTT
Found at i:384629 original size:20 final size:19
Alignment explanation
Indices: 384569--384630 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
384559 TAGATATTTA
*
384569 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
384588 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
384606 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
384626 ATTTT
1 ATTTT
384631 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:385150 original size:31 final size:31
Alignment explanation
Indices: 385091--385151 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
385081 GTAGTTGTAT
* * **
385091 AAATTATTTAAATTTTAGTATTGTAAAACTA
1 AAATTATTTAAATATCAGTATTACAAAACTA
385122 AAATTATTTAAATATCAGTATTACAAAACT
1 AAATTATTTAAATATCAGTATTACAAAACT
385152 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (31 bp):
AAATTATTTAAATATCAGTATTACAAAACTA
Found at i:393075 original size:2 final size:2
Alignment explanation
Indices: 393068--393098 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
393058 TTAATACTTT
393068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
393099 TTGTTAGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:395989 original size:24 final size:24
Alignment explanation
Indices: 395962--396034 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
395952 CGTTCATTTA
395962 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
395986 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
396010 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
396034 C
1 C
396035 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:395991 original size:14 final size:14
Alignment explanation
Indices: 395972--396027 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
395962 CGTTCGTGAA
395972 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
395986 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
396000 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
396010 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
396024 CGTT
1 CGTT
396028 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:396044 original size:24 final size:23
Alignment explanation
Indices: 395973--396047 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
395963 GTTCGTGAAC
* *
395973 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
395997 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
396021 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
396045 GTT
1 GTT
396048 TAACCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:396780 original size:10 final size:10
Alignment explanation
Indices: 396765--396839 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
396755 GGATCTCCAA
396765 CGTTTATGTT
1 CGTTTATGTT
396775 CGTTTATGTT
1 CGTTTATGTT
396785 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
396796 ATGTTCGTGTT
1 -CGTTTATGTT
396807 CGTTTATGTT
1 CGTTTATGTT
396817 CG----TGTT
1 CGTTTATGTT
396823 CGTTTATGTT
1 CGTTTATGTT
396833 CGTTTAT
1 CGTTTAT
396840 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:396796 original size:16 final size:16
Alignment explanation
Indices: 396771--396835 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
396761 CCAACGTTTA
396771 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
396787 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
396803 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
396819 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
396835 T
1 T
396836 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:396930 original size:16 final size:16
Alignment explanation
Indices: 396905--396937 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
396895 AAATTTTTTT
396905 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
396921 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
396937 T
1 T
396938 CTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:397308 original size:17 final size:18
Alignment explanation
Indices: 397286--397319 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
397276 TTTAATCATA
397286 TTAGACCT-ATTAAATTG
1 TTAGACCTAATTAAATTG
397303 TTAGACCTAATTAAATT
1 TTAGACCTAATTAAATT
397320 TAAACTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (18 bp):
TTAGACCTAATTAAATTG
Found at i:404716 original size:21 final size:21
Alignment explanation
Indices: 404690--404729 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
404680 CCCCCTTTGA
*
404690 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
404711 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
404730 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:409115 original size:25 final size:23
Alignment explanation
Indices: 409063--409117 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
409053 ATACATATGC
*
409063 AATATGTGATACTGAACTACATA
1 AATATATGATACTGAACTACATA
* * *
409086 AATATATGATATTGAACTACGTG
1 AATATATGATACTGAACTACATA
409109 AATATATGA
1 AATATATGA
409118 AAAATATGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.33
Consensus pattern (23 bp):
AATATATGATACTGAACTACATA
Found at i:409786 original size:18 final size:18
Alignment explanation
Indices: 409760--409819 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
409750 AATGGGTTAA
*
409760 TGATCATGATATTGATGT
1 TGATAATGATATTGATGT
** **
409778 TGATAATGATAGAGATCA
1 TGATAATGATATTGATGT
*
409796 TGATAATGATATTGACGT
1 TGATAATGATATTGATGT
409814 TGATAA
1 TGATAA
409820 CGATGATATA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (18 bp):
TGATAATGATATTGATGT
Found at i:411769 original size:30 final size:28
Alignment explanation
Indices: 411706--411797 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 28
411696 CATGGATTTA
**
411706 TTTAGTGACCAAATTATAAGATTTTGTAAAG
1 TTTAGTGACCAAA-TAT-A-ATTTTAAAAAG
411737 TTTAGTGACCAAAGTATAATCTTTAAAAAG
1 TTTAGTGACCAAA-TATAAT-TTTAAAAAG
*
411767 TTTAGCGACCAAATAGTAATTTTAAAAAG
1 TTTAGTGACCAAATA-TAATTTTAAAAAG
411796 TT
1 TT
411798 ACAAATGGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
29 15 0.27
30 24 0.44
31 16 0.29
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (28 bp):
TTTAGTGACCAAATATAATTTTAAAAAG
Found at i:414298 original size:17 final size:17
Alignment explanation
Indices: 414276--414308 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
414266 TGAAACAATT
414276 TACGTGATTACATGTAA
1 TACGTGATTACATGTAA
414293 TACGTGATTACATGTA
1 TACGTGATTACATGTA
414309 CATGCACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (17 bp):
TACGTGATTACATGTAA
Found at i:414604 original size:18 final size:18
Alignment explanation
Indices: 414581--414637 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
414571 GTCGAGGGTT
*
414581 AAAGTGATCCTTCGGGAC
1 AAAGTGGTCCTTCGGGAC
414599 AAAGTGGTCCTTCGGGAC
1 AAAGTGGTCCTTCGGGAC
*
414617 ATAGTGGTCCTTCGGGAC
1 AAAGTGGTCCTTCGGGAC
414635 AAA
1 AAA
414638 TGTTCAGTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (18 bp):
AAAGTGGTCCTTCGGGAC
Found at i:415004 original size:18 final size:18
Alignment explanation
Indices: 414981--415081 Score: 89
Period size: 18 Copynumber: 5.6 Consensus size: 18
414971 AATTGGGTTA
414981 ATGATAATGATAGAGATC
1 ATGATAATGATAGAGATC
* *
414999 ATGATAATGATATTA-ATG
1 ATGATAATGATA-GAGATC
* * * *
415017 TTGATAATGATGGAAATT
1 ATGATAATGATAGAGATC
**
415035 ATGATAATGATATTGAT-
1 ATGATAATGATAGAGATC
*
415052 ATGGATAATAATAGAGATC
1 AT-GATAATGATAGAGATC
415071 ATGATAATGAT
1 ATGATAATGAT
415082 GTTGATGTTG
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
17 3 0.05
18 58 0.91
19 3 0.05
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.35
Consensus pattern (18 bp):
ATGATAATGATAGAGATC
Found at i:415039 original size:36 final size:36
Alignment explanation
Indices: 414982--415099 Score: 164
Period size: 36 Copynumber: 3.3 Consensus size: 36
414972 ATTGGGTTAA
*
414982 TGATAATGATAGAGATCATGATAATGATATTAATGT
1 TGATAATGATAGAGATCATGATAATGATATTGATGT
* * * *
415018 TGATAATGATGGAAATTATGATAATGATATTGATAT
1 TGATAATGATAGAGATCATGATAATGATATTGATGT
* * *
415054 GGATAATAATAGAGATCATGATAATGATGTTGATGT
1 TGATAATGATAGAGATCATGATAATGATATTGATGT
415090 TGATAATGAT
1 TGATAATGAT
415100 GATATATGTG
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (36 bp):
TGATAATGATAGAGATCATGATAATGATATTGATGT
Found at i:415093 original size:18 final size:18
Alignment explanation
Indices: 415000--415100 Score: 62
Period size: 18 Copynumber: 5.6 Consensus size: 18
414990 ATAGAGATCA
* *
415000 TGATAATGATATTAATGT
1 TGATAATGATGTTGATGT
***
415018 TGATAATGATGGAAAT-T
1 TGATAATGATGTTGATGT
* *
415035 ATGATAATGATATTGATAT
1 -TGATAATGATGTTGATGT
* * * **
415054 GGATAATAATAG-AGATCA
1 TGATAATGAT-GTTGATGT
415072 TGATAATGATGTTGATGT
1 TGATAATGATGTTGATGT
415090 TGATAATGATG
1 TGATAATGATG
415101 ATATATGTGC
Statistics
Matches: 61, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
17 2 0.03
18 58 0.95
19 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.38
Consensus pattern (18 bp):
TGATAATGATGTTGATGT
Found at i:416146 original size:20 final size:20
Alignment explanation
Indices: 416121--416177 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 20
416111 GTTAACGGGG
416121 GTGTGAGAAGAGAAGAAGAA
1 GTGTGAGAAGAGAAGAAGAA
416141 GTGTGAGAAGAGAAGAAGAAGAA
1 GTGTGAG-A-AG-AGAAGAAGAA
416164 GTGTGAGAAGAGAA
1 GTGTGAGAAGAGAA
416178 ATAGAAGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.32
21 3 0.09
22 3 0.09
23 17 0.50
ACGTcount: A:0.49, C:0.00, G:0.40, T:0.11
Consensus pattern (20 bp):
GTGTGAGAAGAGAAGAAGAA
Found at i:416183 original size:20 final size:19
Alignment explanation
Indices: 416121--416184 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 19
416111 GTTAACGGGG
416121 GTGTGAGAAGAGAAGAAGAA
1 GTGTGAGAAGAGAA-AAGAA
416141 GTGTGAGAAGAGAAGAAGAAGAA
1 GTGTGAG-A-AG-AGAA-AAGAA
416164 GTGTGAGAAGAGAAATAGAA
1 GTGTGAGAAGAGAAA-AGAA
416184 G
1 G
416185 AAGAAGGGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.03
20 16 0.40
21 3 0.08
22 3 0.08
23 17 0.43
ACGTcount: A:0.50, C:0.00, G:0.39, T:0.11
Consensus pattern (19 bp):
GTGTGAGAAGAGAAAAGAA
Found at i:416190 original size:26 final size:23
Alignment explanation
Indices: 416131--416187 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
416121 GTGTGAGAAG
416131 AGAAGAAGAAGTGTGAGAAGAGA
1 AGAAGAAGAAGTGTGAGAAGAGA
416154 AGAAGAAGAAGTGTGAGAAGAGA
1 AGAAGAAGAAGTGTGAGAAGAGA
416177 A-ATAGAAGAAG
1 AGA-AGAAGAAG
416188 AAGGGGGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.54, C:0.00, G:0.37, T:0.09
Consensus pattern (23 bp):
AGAAGAAGAAGTGTGAGAAGAGA
Found at i:422487 original size:9 final size:10
Alignment explanation
Indices: 422473--422519 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 10
422463 ATTATCAATC
422473 AAAAATTTA-
1 AAAAATTTAT
*
422482 AAAAATATAT
1 AAAAATTTAT
* *
422492 CAAAATATAT
1 AAAAATTTAT
422502 AAAAATTTA-
1 AAAAATTTAT
422511 AAAAATTTA
1 AAAAATTTA
422520 GAGGGACAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 17 0.52
10 16 0.48
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:424817 original size:31 final size:31
Alignment explanation
Indices: 424773--424845 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
424763 TAAAACTTGT
* *
424773 AATACAGTCCCCCAACATTTAGT-TCGTTTGC
1 AATACGGTCCCCCAACATTTAATCT-GTTTGC
*
424804 AATATGGTCCCCCAACATTTAATCTGTTTGC
1 AATACGGTCCCCCAACATTTAATCTGTTTGC
424835 AATACGGTCCC
1 AATACGGTCCC
424846 TGACGTTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.32
Consensus pattern (31 bp):
AATACGGTCCCCCAACATTTAATCTGTTTGC
Found at i:426273 original size:32 final size:31
Alignment explanation
Indices: 426205--426295 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 31
426195 GGACCACTGC
*
426205 CCATATGT-TCTGAAGAACATATGTAACCTGT
1 CCATATGTCTC-GAAGAACATAGGTAACCTGT
*
426236 TCATATGTCTCGAATG-ACATAGGTAATCCTGT
1 CCATATGTCTCGAA-GAACATAGGTAA-CCTGT
* *
426268 CCATATATCCCGAAGAACATAGGTAACC
1 CCATATGTCTCGAAGAACATAGGTAACC
426296 CTCGACTCTT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
31 22 0.43
32 29 0.57
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (31 bp):
CCATATGTCTCGAAGAACATAGGTAACCTGT
Found at i:428092 original size:20 final size:20
Alignment explanation
Indices: 428067--428116 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
428057 GATTTTGGGA
428067 CTTTTTCGATCTCGAATTTC
1 CTTTTTCGATCTCGAATTTC
428087 CTTTTTCGATCTCGAATTTC
1 CTTTTTCGATCTCGAATTTC
428107 CTTTTTCGAT
1 CTTTTTCGAT
428117 TCTCTCTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.14, C:0.24, G:0.10, T:0.52
Consensus pattern (20 bp):
CTTTTTCGATCTCGAATTTC
Found at i:429104 original size:170 final size:170
Alignment explanation
Indices: 428822--429161 Score: 680
Period size: 170 Copynumber: 2.0 Consensus size: 170
428812 ATTCAGTGTT
428822 AGTTTTGAACCAAAACCATCTAATTTTCTTTCTTTCTTCTTAATCAAAAATTTTAGTATTCCTTA
1 AGTTTTGAACCAAAACCATCTAATTTTCTTTCTTTCTTCTTAATCAAAAATTTTAGTATTCCTTA
428887 TAAAAGATATTTAGTCCATCAGAATAGAAGTGAAATAGGGTCCTAGCCTAATTTTTTTTTATCTT
66 TAAAAGATATTTAGTCCATCAGAATAGAAGTGAAATAGGGTCCTAGCCTAATTTTTTTTTATCTT
428952 CTTGTTTGGTTTTTCTTTAAATCATGGAATTGGTTGTGAG
131 CTTGTTTGGTTTTTCTTTAAATCATGGAATTGGTTGTGAG
428992 AGTTTTGAACCAAAACCATCTAATTTTCTTTCTTTCTTCTTAATCAAAAATTTTAGTATTCCTTA
1 AGTTTTGAACCAAAACCATCTAATTTTCTTTCTTTCTTCTTAATCAAAAATTTTAGTATTCCTTA
429057 TAAAAGATATTTAGTCCATCAGAATAGAAGTGAAATAGGGTCCTAGCCTAATTTTTTTTTATCTT
66 TAAAAGATATTTAGTCCATCAGAATAGAAGTGAAATAGGGTCCTAGCCTAATTTTTTTTTATCTT
429122 CTTGTTTGGTTTTTCTTTAAATCATGGAATTGGTTGTGAG
131 CTTGTTTGGTTTTTCTTTAAATCATGGAATTGGTTGTGAG
429162 TGTCGACATA
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 170 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (170 bp):
AGTTTTGAACCAAAACCATCTAATTTTCTTTCTTTCTTCTTAATCAAAAATTTTAGTATTCCTTA
TAAAAGATATTTAGTCCATCAGAATAGAAGTGAAATAGGGTCCTAGCCTAATTTTTTTTTATCTT
CTTGTTTGGTTTTTCTTTAAATCATGGAATTGGTTGTGAG
Found at i:430084 original size:31 final size:31
Alignment explanation
Indices: 430049--430123 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
430039 AACGGTCGGG
430049 GACCATATTGCAAACAGAATAAATGTTGGGA
1 GACCATATTGCAAACAGAATAAATGTTGGGA
* *
430080 GACCATATTGCAAACGGACTAAATGTTGGGA
1 GACCATATTGCAAACAGAATAAATGTTGGGA
**
430111 GACTGTATTGCAA
1 GACCATATTGCAA
430124 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (31 bp):
GACCATATTGCAAACAGAATAAATGTTGGGA
Found at i:432740 original size:12 final size:12
Alignment explanation
Indices: 432723--432748 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
432713 TCAGAATCGG
432723 ACCGGTTAGCGA
1 ACCGGTTAGCGA
432735 ACCGGTTAGCGA
1 ACCGGTTAGCGA
432747 AC
1 AC
432749 TGATCATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.27, G:0.31, T:0.15
Consensus pattern (12 bp):
ACCGGTTAGCGA
Found at i:433967 original size:91 final size:92
Alignment explanation
Indices: 433848--434017 Score: 234
Period size: 92 Copynumber: 1.9 Consensus size: 92
433838 GCGAGTTTTC
* *
433848 GAGTCGAGTCGAGCTCAATTTCAGAGTTTTCGAG-TCGAATCGAGCTCAGCAATACTCGAGCTCG
1 GAGTCGAGTCGAGCTCAATTTCAAAGTTTTCAAGTTCGAATCGAGCTCAGCAATACTCGAGCTCG
433912 ACTCGGCTCGTTTACACCCCTAAGTTT
66 ACTCGGCTCGTTTACACCCCTAAGTTT
* * * * * * * *
433939 GAGTCGAGTTGAGCTTACTTTTAAAGTTTTCAAGTTTGAGTCGAGCTCAGCAATACTCGAGTTTG
1 GAGTCGAGTCGAGCTCAATTTCAAAGTTTTCAAGTTCGAATCGAGCTCAGCAATACTCGAGCTCG
*
434004 ACTTGGCTCGTTTA
66 ACTCGGCTCGTTTA
434018 ACAAACGACG
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
91 28 0.42
92 39 0.58
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (92 bp):
GAGTCGAGTCGAGCTCAATTTCAAAGTTTTCAAGTTCGAATCGAGCTCAGCAATACTCGAGCTCG
ACTCGGCTCGTTTACACCCCTAAGTTT
Found at i:442170 original size:3 final size:3
Alignment explanation
Indices: 442164--442269 Score: 63
Period size: 3 Copynumber: 35.7 Consensus size: 3
442154 TCTTGATATA
* * * * *
442164 GAT GAT GAT GAT GAT GAT GAT AAC GAA GAC GAT GAT -ATT GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA-T GAT GAT
* * * * * * *
442209 GAT GAT GAT GA- GAT GAT GAG GAA GAG GGT GAT GAG GAG GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
442256 GAG GAT GAG GAT GA
1 GAT GAT GAT GAT GA
442270 AGGAACTAAG
Statistics
Matches: 79, Mismatches: 21, Indels: 6
0.75 0.20 0.06
Matches are distributed among these distances:
2 3 0.04
3 75 0.95
4 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.39, T:0.22
Consensus pattern (3 bp):
GAT
Found at i:452639 original size:183 final size:183
Alignment explanation
Indices: 452415--452780 Score: 716
Period size: 183 Copynumber: 2.0 Consensus size: 183
452405 CATTTCCTTT
452415 GGAAAATGAAGAGATTGGTACATACAAAATGAAAGGAAAAGACATAAAGAGAAATGCGGGGGGAA
1 GGAAAATGAAGAGATTGGTACATACAAAATGAAAGGAAAAGACATAAAGAGAAATGCGGGGGGAA
452480 ACGCAGCCAAGGGAAGATTCAGAAAAGTAATCGGTCGACTTTCAAAATTCAGAAAATTCAGAAAA
66 ACGCAGCCAAGGGAAGATTCAGAAAAGTAATCGGTCGACTTTCAAAATTCAGAAAATTCAGAAAA
452545 GGTTCAGAAATTTGTTTGAAAAAGAGTCGAGAGAGGGGATGCAATGCATGTTTC
131 GGTTCAGAAATTTGTTTG-AAAAGAGTCGAGAGAGGGGATGCAATGCATGTTTC
452599 GGAAAATGAAGAGA-TGGTACATACAAAATGAAAGGAAAAGACATAAAGAGAAATGCGGGGGGAA
1 GGAAAATGAAGAGATTGGTACATACAAAATGAAAGGAAAAGACATAAAGAGAAATGCGGGGGGAA
452663 ACGCAGCCAAGGGAAGATTCAGAAAAGTAATCGGTCGACTTTCAAAATTCAGAAAATTCAGAAAA
66 ACGCAGCCAAGGGAAGATTCAGAAAAGTAATCGGTCGACTTTCAAAATTCAGAAAATTCAGAAAA
452728 GGTTCAGAAATTTGTTTGAAAAGAGTCGAGAGAGGGGATGCAATGCATGTTTC
131 GGTTCAGAAATTTGTTTGAAAAGAGTCGAGAGAGGGGATGCAATGCATGTTTC
452781 CTTCTTGCCT
Statistics
Matches: 182, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
182 35 0.19
183 133 0.73
184 14 0.08
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.19
Consensus pattern (183 bp):
GGAAAATGAAGAGATTGGTACATACAAAATGAAAGGAAAAGACATAAAGAGAAATGCGGGGGGAA
ACGCAGCCAAGGGAAGATTCAGAAAAGTAATCGGTCGACTTTCAAAATTCAGAAAATTCAGAAAA
GGTTCAGAAATTTGTTTGAAAAGAGTCGAGAGAGGGGATGCAATGCATGTTTC
Found at i:455741 original size:30 final size:30
Alignment explanation
Indices: 455685--455741 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
455675 AAGATTATTT
* *
455685 CAATAAAAAAATTACTAATTTACTAATAGA
1 CAATAAAAAAATGACTAAATTACTAATAGA
*
455715 CAATAAAAAAGATGA-TAAATTGCTAAT
1 CAATAAAAAA-ATGACTAAATTACTAAT
455742 CTATTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 20 0.87
31 3 0.13
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (30 bp):
CAATAAAAAAATGACTAAATTACTAATAGA
Found at i:460683 original size:45 final size:45
Alignment explanation
Indices: 460634--460719 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
460624 AAAATAGCCA
* * *
460634 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGGTATGTGCATCAATGCATAAAATGCACT
*
460679 GAGTGCATCGATGTATGGTATGTGCATCAATGCATAAAATG
1 GAGTGCATCGATGCATGGTATGTGCATCAATGCATAAAATG
460720 AATTCGATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (45 bp):
GAGTGCATCGATGCATGGTATGTGCATCAATGCATAAAATGCACT
Found at i:461463 original size:14 final size:15
Alignment explanation
Indices: 461444--461473 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
461434 TCAGGCATCT
461444 AACAATCCA-AAACA
1 AACAATCCAGAAACA
461458 AACAATCCAGAAACA
1 AACAATCCAGAAACA
461473 A
1 A
461474 CAAAACAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.27, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:463421 original size:64 final size:64
Alignment explanation
Indices: 463339--463492 Score: 184
Period size: 64 Copynumber: 2.4 Consensus size: 64
463329 AGTGTGTATA
* * * * *
463339 GATGCACAGGAAGTGCATCGATGCACCCATTTAAAATGGAAACATCGAATGCAATTAGTGAATC
1 GATGCATAGGTAGTGCATCGATGCACCCACTTAAAATGAAAACATCGAAGGCAATTAGTGAATC
* * ** * *
463403 GATGCATAAGG-AGTGCATCGATGCGCCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGTATC
1 GATGCAT-AGGTAGTGCATCGATGCACCCACTTAAAATGAAAACATCGAAGGCAATTAGTGAATC
*
463467 GATGCATGGGTAGTGCATCGATGCAC
1 GATGCATAGGTAGTGCATCGATGCAC
463493 ATGTTAAAGA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 2 0.03
64 71 0.93
65 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (64 bp):
GATGCATAGGTAGTGCATCGATGCACCCACTTAAAATGAAAACATCGAAGGCAATTAGTGAATC
Found at i:463507 original size:24 final size:20
Alignment explanation
Indices: 463480--463537 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
463470 GCATGGGTAG
463480 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
463504 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
463524 TGCATCGATGCACT
1 TGCATCGATGCACT
463538 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:464602 original size:35 final size:36
Alignment explanation
Indices: 464521--464617 Score: 96
Period size: 35 Copynumber: 2.8 Consensus size: 36
464511 ATAACATTGA
* *
464521 ATAT-AATGTATATGATGT-ATATATGTGTTTTGTG
1 ATATGAATGTATATGATATGATATATGTGTTTAGTG
464555 ATATGAAT-TATATGATATGATATATGTGTGTTAGTG
1 ATATGAATGTATATGATATGATATATGTGT-TTAGTG
* *
464591 AT-T-ATTGTATATGTTATAAGATATATG
1 ATATGAATGTATATG--ATATGATATATG
464618 ATATGAACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
34 15 0.28
35 20 0.38
36 7 0.13
37 11 0.21
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (36 bp):
ATATGAATGTATATGATATGATATATGTGTTTAGTG
Found at i:467944 original size:64 final size:63
Alignment explanation
Indices: 467789--467950 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 63
467779 AATTGTTCAG
* * * * *
467789 TGTGTATAGATGCACAGGAAGTGCATCGATGCACCCATTTAAAATGGAAACATCGAATGCAATT
1 TGTGTATCGATGCATAGG-AGTGCATCGATGCACCCACTTAAAATGAAAACATCGAAGGCAATT
* * * * * * **
467853 AGTGAATCGATGCTTAAGGAGTCCATCGATGCGCCCCCTTAAAATGAAAACATCGAAGGTGATT
1 TGTGTATCGATGCAT-AGGAGTGCATCGATGCACCCACTTAAAATGAAAACATCGAAGGCAATT
*
467917 TGTGTATCGATGCATGGGTAGTGCATCGATGCAC
1 TGTGTATCGATGCATAGG-AGTGCATCGATGCAC
467951 ATGTTAAAGA
Statistics
Matches: 77, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
63 2 0.03
64 72 0.94
65 3 0.04
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (63 bp):
TGTGTATCGATGCATAGGAGTGCATCGATGCACCCACTTAAAATGAAAACATCGAAGGCAATT
Found at i:467965 original size:24 final size:20
Alignment explanation
Indices: 467938--467995 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
467928 GCATGGGTAG
467938 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
467962 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
467982 TGCATCGATGCACT
1 TGCATCGATGCACT
467996 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:470489 original size:23 final size:22
Alignment explanation
Indices: 470454--470533 Score: 92
Period size: 22 Copynumber: 3.6 Consensus size: 22
470444 GCATGGCCTT
470454 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
470476 CGTGCATC-AGTGCACCTTC-ATG
1 -GTGCATCGA-TGCACATTCAAGG
*
470498 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
470520 ATGCATCGATGCAC
1 GTGCATCGATGCAC
470534 TGTTAGGTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 14 0.30
22 18 0.38
23 15 0.32
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:470549 original size:20 final size:21
Alignment explanation
Indices: 470458--470552 Score: 79
Period size: 21 Copynumber: 4.4 Consensus size: 21
470448 GGCCTTGTGC
*
470458 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* *
470481 ATC-AGTGCACCTTCATGGTGT
1 ATCGA-TGCACATTCAAGGTGT
*
470502 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
470524 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
470544 ATCGATGCA
1 ATCGATGCA
470553 TTAAGCACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
20 11 0.18
21 21 0.35
22 16 0.27
23 12 0.20
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:477191 original size:19 final size:19
Alignment explanation
Indices: 477167--477212 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
477157 GATAAGCAAA
477167 AAAAGGAAATTCGAGATCG
1 AAAAGGAAATTCGAGATCG
*
477186 AAAAGGAAATTCGAGATTG
1 AAAAGGAAATTCGAGATCG
477205 AAAAGGAA
1 AAAAGGAA
477213 TTTAGGGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.52, C:0.07, G:0.26, T:0.15
Consensus pattern (19 bp):
AAAAGGAAATTCGAGATCG
Found at i:477388 original size:31 final size:31
Alignment explanation
Indices: 477353--477430 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
477343 CGGTTACGTC
* *
477353 GGGGATCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACGAACTAAATGTTG
*
477384 GGGGACCATATTGCAAATGAACTAAATGTTG
1 GGGGACCATATTGCAAACGAACTAAATGTTG
**
477415 GGGGACTGTATTGCAA
1 GGGGACCATATTGCAA
477431 GTTTTAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (31 bp):
GGGGACCATATTGCAAACGAACTAAATGTTG
Found at i:480131 original size:30 final size:30
Alignment explanation
Indices: 480106--480165 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
480096 ATAATTTGAT
*
480106 ACTAAATTTTATATAAAATATTAATTCAACC
1 ACTAAATTTTA-ATAAAATATTAATTTAACC
* *
480137 CCTAAATTTTAGTAAAATATTAATTTAAC
1 ACTAAATTTTAATAAAATATTAATTTAAC
480166 ATCTGATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (30 bp):
ACTAAATTTTAATAAAATATTAATTTAACC
Found at i:487662 original size:18 final size:19
Alignment explanation
Indices: 487620--487663 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
487610 TTTGGTTCAC
* *
487620 GGAATGTAAGATTACCGGTG
1 GGAATATAAGATTACC-GAG
487640 GGAATATAAGATTACC-AG
1 GGAATATAAGATTACCGAG
487658 GGAATA
1 GGAATA
487664 GGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.23
Consensus pattern (19 bp):
GGAATATAAGATTACCGAG
Found at i:490728 original size:21 final size:22
Alignment explanation
Indices: 490688--490728 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
490678 AATCACCCCA
490688 AACCTTAAACACTAAAATAAAT
1 AACCTTAAACACTAAAATAAAT
* *
490710 AACCTTTAA-ACTGAAATAA
1 AACCTTAAACACTAAAATAA
490729 GACTAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.24
Consensus pattern (22 bp):
AACCTTAAACACTAAAATAAAT
Found at i:496846 original size:24 final size:24
Alignment explanation
Indices: 496819--496890 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
496809 GTAAACGGAG
*
496819 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
496843 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
496867 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
496890 A
1 A
496891 GGTAACGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 15 0.36
24 27 0.64
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:496850 original size:12 final size:12
Alignment explanation
Indices: 496823--496914 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
496813 ACGGAGATAT
* *
496823 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
496835 CAGAATTCATAT
1 CAGAATTCAGAA
496847 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
496859 CAGAATCCAGAT
1 CAGAATTCAGAA
496871 CAGAA-TCAGAA
1 CAGAATTCAGAA
496882 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
496896 C-GTA-TCAGAA
1 CAGAATTCAGAA
496906 CAGAATTCA
1 CAGAATTCA
496915 ATTCGAAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:496902 original size:47 final size:48
Alignment explanation
Indices: 496821--496911 Score: 125
Period size: 47 Copynumber: 1.9 Consensus size: 48
496811 AAACGGAGAT
*
496821 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
*
496869 ATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA--TAACAGATATCAGAACAGAAT
496912 TCAATTCGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 30 0.77
48 6 0.15
49 3 0.08
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
Found at i:496907 original size:24 final size:23
Alignment explanation
Indices: 496828--496914 Score: 93
Period size: 24 Copynumber: 3.7 Consensus size: 23
496818 GATATCAGAA
* * *
496828 ATCAAAACAGAATTCATATCAGAT
1 ATCAGAACAGAATTCAGATAAG-T
* * *
496852 ATCAGAACAGAATCCAGATCAGA
1 ATCAGAACAGAATTCAGATAAGT
*
496875 ATCAGAACAGAATTCAGGTAACGT
1 ATCAGAACAGAATTCAGATAA-GT
496899 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
496915 ATTCGAAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 18 0.33
24 36 0.67
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (23 bp):
ATCAGAACAGAATTCAGATAAGT
Found at i:499393 original size:31 final size:31
Alignment explanation
Indices: 499358--499416 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
499348 CAGGTCAACG
*
499358 GTCAACGGGTTGGGTCAACAGGTCGGGTCGA
1 GTCAACGGGTTGGGTAAACAGGTCGGGTCGA
*
499389 GTCAACGGGTTGGGTAAACGGGTCGGGT
1 GTCAACGGGTTGGGTAAACAGGTCGGGT
499417 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.44, T:0.20
Consensus pattern (31 bp):
GTCAACGGGTTGGGTAAACAGGTCGGGTCGA
Found at i:501389 original size:2 final size:2
Alignment explanation
Indices: 501345--501370 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
501335 CAGTAAAAAG
501345 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
501371 TTTAAAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:501579 original size:24 final size:24
Alignment explanation
Indices: 501552--501623 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
501542 GTAAACGGAG
501552 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* * *
501576 ATATCAGATATCATAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTC
* *
501600 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
501623 A
1 A
501624 GGTAACGTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 14 0.34
24 27 0.66
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:501624 original size:12 final size:12
Alignment explanation
Indices: 501556--501647 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
501546 ACGGAGATAT
* *
501556 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
501568 CAGAATTCATAT
1 CAGAATTCAGAA
*
501580 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
501592 CAGAATCCAGAT
1 CAGAATTCAGAA
501604 CAGAA-TCAGAA
1 CAGAATTCAGAA
501615 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
501629 C-GTA-TCAGAA
1 CAGAATTCAGAA
501639 CAGAATTCA
1 CAGAATTCA
501648 ATTCGAAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:501635 original size:47 final size:48
Alignment explanation
Indices: 501554--501644 Score: 116
Period size: 47 Copynumber: 1.9 Consensus size: 48
501544 AAACGGAGAT
* *
501554 ATCAGAAATCAAAACAGAATTCATATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
*
501602 ATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA--TAACAGATATCAGAACAGAAT
501645 TCAATTCGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
47 29 0.76
48 6 0.16
49 3 0.08
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
Found at i:507662 original size:182 final size:185
Alignment explanation
Indices: 507354--507739 Score: 649
Period size: 182 Copynumber: 2.1 Consensus size: 185
507344 TTTTCTAATT
* * *
507354 TATATAA-AAATTAAATA-TTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
507417 TTATAAAATAAAAATTTTAGATAAATTTTTTAATGAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAATTTTAGATAAATTTTTTAATGAATTAATATTGATTTAGGTTTAAAAGTTAT
*
507482 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
131 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
507537 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAAT-A-ATAT-
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAA-AGTTTACAATTAATTTAAATAATATATA
* *
507599 ATTATAAAATAAAAA-TTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 ATTATAAAATAAAAATTTTAGATAAATTTTTTAATGAATTAATATTGATTTAGGTTTAAAAGTTA
*
507663 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGTCTGAGCCCATATGTTA
130 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
507719 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
507740 AATTTCGTTT
Statistics
Matches: 192, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
182 121 0.63
183 22 0.11
184 12 0.06
185 18 0.09
186 19 0.10
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAATTTTAGATAAATTTTTTAATGAATTAATATTGATTTAGGTTTAAAAGTTAT
TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:509126 original size:13 final size:13
Alignment explanation
Indices: 509108--509132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
509098 ATTACAGATG
509108 TGCATATAAAGAC
1 TGCATATAAAGAC
509121 TGCATATAAAGA
1 TGCATATAAAGA
509133 TTGTCCAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
TGCATATAAAGAC
Found at i:514483 original size:58 final size:58
Alignment explanation
Indices: 514413--514528 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
514403 ATTTGATCCG
514413 AACCAGTGAGGATATGATGTCTAGGAAGTTCCTAATCAGCTTGTGGAAGGATGCTCCA
1 AACCAGTGAGGATATGATGTCTAGGAAGTTCCTAATCAGCTTGTGGAAGGATGCTCCA
514471 AACCAGTGAGGATATGATGTCTAGGAAGTTCCTAATCAGCTTGTGGAAGGATGCTCCA
1 AACCAGTGAGGATATGATGTCTAGGAAGTTCCTAATCAGCTTGTGGAAGGATGCTCCA
514529 TGTTTGGTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (58 bp):
AACCAGTGAGGATATGATGTCTAGGAAGTTCCTAATCAGCTTGTGGAAGGATGCTCCA
Found at i:516082 original size:29 final size:29
Alignment explanation
Indices: 516048--516116 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
516038 TAAAGTATGC
*
516048 AAATGGTCACTAAAGTTT-TAGAAGTTAC-A
1 AAATGGTCACTAAA-TTTATACAA-TTACAA
* *
516077 AAATGGTCATTAAATTTATACCATTACAA
1 AAATGGTCACTAAATTTATACAATTACAA
516106 AAATGGTCACT
1 AAATGGTCACT
516117 GTATATTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 7 0.21
29 27 0.79
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (29 bp):
AAATGGTCACTAAATTTATACAATTACAA
Found at i:518112 original size:2 final size:2
Alignment explanation
Indices: 518105--518159 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
518095 TTCTATTTTC
518105 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
518147 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
518160 TCTTAAATTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:526854 original size:118 final size:118
Alignment explanation
Indices: 526646--526876 Score: 462
Period size: 118 Copynumber: 2.0 Consensus size: 118
526636 GGCGTAGTCA
526646 CAAGCACCGCATTCCCCCCGGGCTATATATCCAGGCCAGTGGCGTCCAATACTCTGGCCATTGAT
1 CAAGCACCGCATTCCCCCCGGGCTATATATCCAGGCCAGTGGCGTCCAATACTCTGGCCATTGAT
526711 CCATTCTTGCCCTTTTCCCATGCTACTCATATCTAAAACTACCGGTTCGTAGT
66 CCATTCTTGCCCTTTTCCCATGCTACTCATATCTAAAACTACCGGTTCGTAGT
526764 CAAGCACCGCATTCCCCCCGGGCTATATATCCAGGCCAGTGGCGTCCAATACTCTGGCCATTGAT
1 CAAGCACCGCATTCCCCCCGGGCTATATATCCAGGCCAGTGGCGTCCAATACTCTGGCCATTGAT
526829 CCATTCTTGCCCTTTTCCCATGCTACTCATATCTAAAACTACCGGTTC
66 CCATTCTTGCCCTTTTCCCATGCTACTCATATCTAAAACTACCGGTTC
526877 ATCACCTTCG
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28
Consensus pattern (118 bp):
CAAGCACCGCATTCCCCCCGGGCTATATATCCAGGCCAGTGGCGTCCAATACTCTGGCCATTGAT
CCATTCTTGCCCTTTTCCCATGCTACTCATATCTAAAACTACCGGTTCGTAGT
Found at i:530490 original size:20 final size:20
Alignment explanation
Indices: 530465--530537 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
530455 GATCAACAAA
530465 TTCGCAACGCGAATTCTAAT
1 TTCGCAACGCGAATTCTAAT
* * *
530485 TTCGCAAC-CCAGTTTTTAAT
1 TTCGCAACGCGA-ATTCTAAT
* *
530505 TTCGCAACGCGAAAGTC-AAA
1 TTCGCAACGCG-AATTCTAAT
530525 TTCGCAACGCGAA
1 TTCGCAACGCGAA
530538 AGTAAAATTC
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.10
20 35 0.83
21 2 0.05
22 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCTAAT
Found at i:530538 original size:20 final size:20
Alignment explanation
Indices: 530505--530552 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
530495 AGTTTTTAAT
*
530505 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTAAAA
530525 TTCGCAACGCGAAAGTAAAA
1 TTCGCAACGCGAAAGTAAAA
*
530545 TTCACAAC
1 TTCGCAAC
530553 TGAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.17
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTAAAA
Found at i:530758 original size:16 final size:14
Alignment explanation
Indices: 530729--530764 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
530719 CTCCATCTCT
530729 ATTTTTTTTATATA
1 ATTTTTTTTATATA
530743 ATTTTATTTCTATATA
1 ATTTT-TTT-TATATA
530759 ATTTTT
1 ATTTTT
530765 CAATGATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 4 0.20
16 11 0.55
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTTTTTATATA
Found at i:531182 original size:86 final size:86
Alignment explanation
Indices: 531087--531259 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
531077 TAGGCTATCT
531087 TATCTGAGAAAAAGTAAAGTTTATTTGTTAATCGACAATGAAGATGTTGAACGATTCATTGCTTA
1 TATCTGAGAAAAAGTAAAGTTTATTTGTTAATCGACAATGAAGATGTTGAACGATTCATTGCTTA
531152 CATTAGTGTTTAGCAAGAGGA
66 CATTAGTGTTTAGCAAGAGGA
531173 TATCTGAGAAAAAGTAAAGTTTATTTGTTAATCGACAATGAAGATGTTGAACGATTCATTGCTTA
1 TATCTGAGAAAAAGTAAAGTTTATTTGTTAATCGACAATGAAGATGTTGAACGATTCATTGCTTA
531238 CATTAGTGTTTAGCAAGAGGA
66 CATTAGTGTTTAGCAAGAGGA
531259 T
1 T
531260 GATGTTACAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (86 bp):
TATCTGAGAAAAAGTAAAGTTTATTTGTTAATCGACAATGAAGATGTTGAACGATTCATTGCTTA
CATTAGTGTTTAGCAAGAGGA
Found at i:531419 original size:12 final size:12
Alignment explanation
Indices: 531398--531431 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
531388 ACCACATTTC
*
531398 CAATACCAAACA
1 CAATATCAAACA
531410 CAATATCAAACA
1 CAATATCAAACA
*
531422 CAATCTCAAA
1 CAATATCAAA
531432 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:531584 original size:24 final size:24
Alignment explanation
Indices: 531557--531610 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
531547 GTATTCAAAA
531557 TTTGATCTTGGTCAAAACCCGGAC
1 TTTGATCTTGGTCAAAACCCGGAC
* * *
531581 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAAAACCCGGAC
531605 TTTGAT
1 TTTGAT
531611 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGTCAAAACCCGGAC
Found at i:532622 original size:70 final size:67
Alignment explanation
Indices: 532492--532625 Score: 241
Period size: 70 Copynumber: 2.0 Consensus size: 67
532482 ATAATTATAA
532492 TTTGTTGATCATTTTGTTAGTTGCATTTCACATTTAATGATTATATTTCTTGTGTATATGATTTA
1 TTTGTTGATCATTTTGTTAGTTGCATTTCACATTTAATGATTATATTTCTTGTGTATATGATTTA
532557 AT
66 AT
532559 TTTGTTGACTCATTTTTGTTAGTTGCATTTCACATTTAAATGATTATATTTCTTGTGTATATGAT
1 TTTGTTGA-TCA-TTTTGTTAGTTGCATTTCACATTT-AATGATTATATTTCTTGTGTATATGAT
532624 TT
63 TT
532626 TGTAGATTCA
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
67 8 0.12
68 3 0.05
69 24 0.38
70 29 0.45
ACGTcount: A:0.23, C:0.08, G:0.13, T:0.55
Consensus pattern (67 bp):
TTTGTTGATCATTTTGTTAGTTGCATTTCACATTTAATGATTATATTTCTTGTGTATATGATTTA
AT
Found at i:534253 original size:20 final size:20
Alignment explanation
Indices: 534225--534267 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
534215 GATCAATGCA
*
534225 AAAGTCAAATTCGCAACGCG
1 AAAGACAAATTCGCAACGCG
*
534245 AAAGACAAATTCGCAACGTG
1 AAAGACAAATTCGCAACGCG
534265 AAA
1 AAA
534268 TAAGCGTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.14
Consensus pattern (20 bp):
AAAGACAAATTCGCAACGCG
Found at i:534387 original size:25 final size:25
Alignment explanation
Indices: 534349--534397 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
534339 AAATCAATTA
*
534349 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
534374 AACATTGTTATGGGTACATTATTT
1 AACATTGTTATGGGTACATTATTT
534398 AGAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:534808 original size:18 final size:18
Alignment explanation
Indices: 534787--534823 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
534777 GTAATTGGAG
534787 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
534805 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
534823 T
1 T
534824 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:534830 original size:24 final size:24
Alignment explanation
Indices: 534779--534831 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
534769 TTTCATATGT
* * *
534779 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
534803 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
534827 AATTT
1 AATTT
534832 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:535176 original size:39 final size:39
Alignment explanation
Indices: 535133--535219 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
535123 TCCGATGCTC
535133 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
535172 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
535211 ATCAAAATC
1 ATCAAAATC
535220 TACAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:539327 original size:19 final size:20
Alignment explanation
Indices: 539305--539347 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
539295 AAATCGCAAC
539305 GCGAT-TTAAGTTTCGCGTT
1 GCGATATTAAGTTTCGCGTT
* * *
539324 GCGATATTCATTTTCTCGTT
1 GCGATATTAAGTTTCGCGTT
539344 GCGA
1 GCGA
539348 ATTTGGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGATATTAAGTTTCGCGTT
Found at i:539808 original size:20 final size:20
Alignment explanation
Indices: 539783--539821 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
539773 GTAAAAACAT
*
539783 TTGACTTTCGCGTTGCGAAC
1 TTGACTATCGCGTTGCGAAC
539803 TTGACTATCGCGTTGCGAA
1 TTGACTATCGCGTTGCGAA
539822 TTTGGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (20 bp):
TTGACTATCGCGTTGCGAAC
Found at i:539898 original size:20 final size:20
Alignment explanation
Indices: 539849--539902 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
539839 CGATTTACAT
539849 ATTCGCGTTGCGAAATTAGA
1 ATTCGCGTTGCGAAATTAGA
* * *
539869 A-ACTGAGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTAGA
539889 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
539903 TTTGTTAGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTAGA
Found at i:540358 original size:24 final size:23
Alignment explanation
Indices: 540318--540362 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
540308 AATTTTACAC
*
540318 TATATAATTAATTTTTTCATTATA
1 TATATAATTAATATTTT-ATTATA
540342 TATATAATT-ATAATTTTATTA
1 TATATAATTAAT-ATTTTATTA
540363 AATAAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TATATAATTAATATTTTATTATA
Found at i:541862 original size:3 final size:3
Alignment explanation
Indices: 541816--541850 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
541806 AATAAATCAA
*
541816 AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
541851 AAGTAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:543286 original size:37 final size:36
Alignment explanation
Indices: 543202--543387 Score: 118
Period size: 39 Copynumber: 5.1 Consensus size: 36
543192 TAATATATAT
* * * *
543202 AAAACGTTTT-CAAAAAC-ATATAATATAAATTTTT
1 AAAACGTTTTAAAAAAACTATATTATATATATTTTC
*
543236 AAAATGTTTTTTTAAAAAAACTATATTATATATATTTTC
1 AAAACG---TTTTAAAAAAACTATATTATATATATTTTC
* * *
543275 AAAATGGTTTTAAAAATTA-TATATTATATAAATGTTTTC
1 AAAA-CGTTTTAAAAA-AACTATATTATAT--ATATTTTC
* **
543314 ATAACGTTTTCAAAAGTA-TATATTATATATA-TTT-
1 AAAACGTTTT-AAAAAAACTATATTATATATATTTTC
*
543348 AAAACGTTTT-CAAAAACTATA-TATTATATAATTTTC
1 AAAACGTTTTAAAAAAACTATATTA-TATAT-ATTTTC
543384 AAAA
1 AAAA
543388 AAATATTTTC
Statistics
Matches: 121, Mismatches: 16, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
32 5 0.04
33 9 0.07
34 15 0.12
35 6 0.05
36 6 0.05
37 23 0.19
38 24 0.20
39 32 0.26
40 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
AAAACGTTTTAAAAAAACTATATTATATATATTTTC
Found at i:543303 original size:35 final size:35
Alignment explanation
Indices: 543202--543387 Score: 148
Period size: 37 Copynumber: 5.1 Consensus size: 35
543192 TAATATATAT
* *
543202 AAAACGTTTTCAAAAAC-ATATAATATA-AATTTTT
1 AAAACGTTTT-AAAAACTATATATTATATAATTTTC
* *
543236 AAAATGTTTTTTTAAAAA-AACTATATTATATATATTTTC
1 AAAACG---TTTTAAAAACTA-TATATTATATA-ATTTTC
* *
543275 AAAATGGTTTTAAAAATTATATATTATATAAATGTTTTC
1 AAAA-CGTTTTAAAAACTATATATTATAT-AA--TTTTC
* * *
543314 ATAACGTTTTCAAAAGTATATATTATAT-ATATTT-
1 AAAACGTTTTAAAAACTATATATTATATAAT-TTTC
543348 AAAACGTTTTCAAAAACTATATATTATATAATTTTC
1 AAAACGTTTT-AAAAACTATATATTATATAATTTTC
543384 AAAA
1 AAAA
543388 AAATATTTTC
Statistics
Matches: 124, Mismatches: 12, Indels: 30
0.75 0.07 0.18
Matches are distributed among these distances:
34 15 0.12
35 22 0.18
36 13 0.10
37 32 0.26
38 24 0.19
39 17 0.14
40 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (35 bp):
AAAACGTTTTAAAAACTATATATTATATAATTTTC
Found at i:543334 original size:38 final size:36
Alignment explanation
Indices: 543191--543378 Score: 127
Period size: 38 Copynumber: 5.1 Consensus size: 36
543181 AAAATAAATA
*
543191 ATAATATATATAAAACGTTTTCAAAAAC-ATATA--AT
1 ATAA-ATATTTAAAACGTTTTC-AAAACTATATATTAT
* * * **
543226 ATAAATTTTTAAAATGTTTTTTTAAAAAAACTATATTAT
1 ATAAATATTTAAAACG--TTTTCAAAACTA-TATATTAT
* * * *
543265 ATATAT-TTTCAAAATGGTTTTAAAAATTATATATTAT
1 ATAAATATTT-AAAA-CGTTTTCAAAACTATATATTAT
* * *
543302 ATAAATGTTTTCATAACGTTTTCAAAAGTATATATTAT
1 ATAAAT-ATTT-AAAACGTTTTCAAAACTATATATTAT
543340 AT--ATATTTAAAACGTTTTCAAAAACTATATATTAT
1 ATAAATATTTAAAACGTTTTC-AAAACTATATATTAT
543375 ATAA
1 ATAA
543379 TTTTCAAAAA
Statistics
Matches: 122, Mismatches: 18, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
34 19 0.16
35 27 0.22
36 7 0.06
37 17 0.14
38 33 0.27
39 18 0.15
40 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
ATAAATATTTAAAACGTTTTCAAAACTATATATTAT
Found at i:543368 original size:26 final size:24
Alignment explanation
Indices: 543338--543422 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 24
543328 AGTATATATT
543338 ATATATATTTAAAACGTTTTCAAAA
1 ATATATATTTAAAA-GTTTTCAAAA
*
543363 ACTATATATTATATAA-TTTTCAAAA
1 A-TATATATT-TAAAAGTTTTCAAAA
* *
543388 AAATAT-TTTCAAAATGGTTTTTAAAA
1 ATATATATTT-AAAA--GTTTTCAAAA
543414 ATTATATAT
1 A-TATATAT
543423 ATATAAGTGT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
22 1 0.02
23 5 0.11
24 4 0.09
25 11 0.23
26 17 0.36
27 8 0.17
28 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (24 bp):
ATATATATTTAAAAGTTTTCAAAA
Found at i:543397 original size:73 final size:73
Alignment explanation
Indices: 543194--543401 Score: 185
Period size: 73 Copynumber: 2.8 Consensus size: 73
543184 ATAAATAATA
* * * ** * *
543194 ATATATATAAAACGTTTTCAAAAAC-ATATAATATA-AATTTTTAAAATGTTTTTTTAAAAAAAC
1 ATATATTTAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAATATTTTCAAAAAAAC
543257 TATATTAT
66 TATATTAT
* * * **
543265 ATATATTTTCAAAATGGTTTT-AAAAATTATATATTATATAAATGTTTTC--ATAACGTTTTCAA
1 ATATA-TTT-AAAA-CGTTTTCAAAAACTATATATTATAT-AA--TTTTCAAAAAATATTTTCAA
**
543327 AAGTA-TATATTAT
60 AAAAACTATATTAT
543340 ATATATTTAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAAATATTTTCAAAA
1 ATATATTTAAAACGTTTTCAAAAACTATATATTATATAATTTTC-AAAAAATATTTTCAAAA
543402 TGGTTTTTAA
Statistics
Matches: 107, Mismatches: 18, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
70 5 0.05
71 5 0.05
72 9 0.08
73 42 0.39
74 17 0.16
75 13 0.12
76 12 0.11
78 4 0.04
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (73 bp):
ATATATTTAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAATATTTTCAAAAAAAC
TATATTAT
Found at i:543407 original size:123 final size:120
Alignment explanation
Indices: 543267--543521 Score: 424
Period size: 123 Copynumber: 2.1 Consensus size: 120
543257 TATATTATAT
543267 ATATTTTCAAAATGG-TTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
1 ATATTTTCAAAATGGTTTTTAAAAATTATATA-TATATAAATGTTTTCATAACGTTTTCAAAAGT
543331 ATATATTATATATATTT-AAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAA
65 ATATATTATATAT-TTTAAAAACGTTTTCAAAAACTATATA--ATATAATTTTC-AAAAA
*
543390 ATATTTTCAAAATGGTTTTTAAAAATTATATATATATAAGTGTTTTCATAACGTTTTCAAAAGTA
1 ATATTTTCAAAATGGTTTTTAAAAATTATATATATATAAATGTTTTCATAACGTTTTCAAAAGTA
*
543455 TATATTATATATTTTAAAAACGTTTTCAAAAACTATATAATATATTTTTCAAAAA
66 TATATTATATATTTTAAAAACGTTTTCAAAAACTATATAATATAATTTTCAAAAA
*
543510 ATATTTTAAAAA
1 ATATTTTCAAAA
543522 CTATATAATA
Statistics
Matches: 127, Mismatches: 3, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
120 16 0.13
121 10 0.08
122 3 0.02
123 82 0.65
124 16 0.13
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (120 bp):
ATATTTTCAAAATGGTTTTTAAAAATTATATATATATAAATGTTTTCATAACGTTTTCAAAAGTA
TATATTATATATTTTAAAAACGTTTTCAAAAACTATATAATATAATTTTCAAAAA
Found at i:543492 original size:35 final size:35
Alignment explanation
Indices: 543390--543610 Score: 139
Period size: 35 Copynumber: 6.1 Consensus size: 35
543380 TTTCAAAAAA
** * *
543390 ATATTTTCAAAATGGTTTTTAAAAATTATATATATAT
1 ATATTTTCAAAAACG-TTTTCAAAACTATATAT-TAT
* * *
543427 AAGTGTTTTC-ATAACGTTTTCAAAAGTATATATTAT
1 -A-TATTTTCAAAAACGTTTTCAAAACTATATATTAT
*
543463 ATATTTT-AAAAACGTTTTCAAAAACTATATAATAT
1 ATATTTTCAAAAACGTTTTC-AAAACTATATATTAT
** * *
543498 AT-TTTTCAAAAAATATTTTAAAAACTATATAATATAC
1 ATATTTTC-AAAAACGTTTTCAAAACTATAT-AT-TAT
*
543535 ATATTTTCAAAAAATGTTTT--AAACTATATATATAT
1 ATATTTTC-AAAAACGTTTTCAAAACTATATAT-TAT
* * *
543570 ATGTATTTTCAAAAACAATTTGC-AAACTATATAATAT
1 A--TATTTTCAAAAAC-GTTTTCAAAACTATATATTAT
543607 ATAT
1 ATAT
543611 GTGTATATAT
Statistics
Matches: 150, Mismatches: 21, Indels: 27
0.76 0.11 0.14
Matches are distributed among these distances:
34 19 0.13
35 35 0.23
36 27 0.18
37 33 0.22
38 30 0.20
39 6 0.04
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (35 bp):
ATATTTTCAAAAACGTTTTCAAAACTATATATTAT
Found at i:543570 original size:37 final size:36
Alignment explanation
Indices: 543483--543607 Score: 141
Period size: 37 Copynumber: 3.4 Consensus size: 36
543473 AACGTTTTCA
543483 AAAACTATATAATAT-AT-TTTTCAAAAAATATTTT
1 AAAACTATATAATATAATATTTTCAAAAAATATTTT
*
543517 AAAAACTATATAATATACATATTTTCAAAAAATGTTTT
1 -AAAACTATATAATATA-ATATTTTCAAAAAATATTTT
* *
543555 -AAACTATATATATATATGTATTTTCAAAAACA-ATTTG
1 AAAACTATATA-ATATA-ATATTTTCAAAAA-ATATTTT
*
543592 CAAACTATATAATATA
1 AAAACTATATAATATA
543608 TATGTGTATA
Statistics
Matches: 79, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
35 15 0.19
36 10 0.13
37 27 0.34
38 27 0.34
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (36 bp):
AAAACTATATAATATAATATTTTCAAAAAATATTTT
Found at i:544361 original size:84 final size:84
Alignment explanation
Indices: 544216--544978 Score: 820
Period size: 84 Copynumber: 9.2 Consensus size: 84
544206 TTGAATATAA
* * * * *
544216 TCGAACTCGAAGGTC--TT--TAGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATAATGT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* *
544277 GCCTTGGAGCTGAGCGGAT
66 GCCTTGGAGCTGAGCGTAG
** * * * *
544296 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
544361 GCCGTT-GAGCTGAGCGTAG
66 GCC-TTGGAGCTGAGCGTAG
* * * * * ** *
544380 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTATTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
544445 GCCTTGGAGCTGAGCGAAG
66 GCCTTGGAGCTGAGCGTAG
*
544464 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * *
544529 GCC-CGCGAAGCTGAGTGTAA
66 GCCTTG-G-AGCTGAGCGTAG
* ** * * * * ** *
544549 TCGAACTTGGGGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTATTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
544614 GCCTTGGAGCTGAGCGAAG
66 GCCTTGGAGCTGAGCGTAG
*
544633 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * *
544698 GCCCTCGAAGCTGAGTGTAA
66 G-CCTTGGAGCTGAGCGTAG
* * ** * *
544718 TCAAACTTGGGGGTC--TT--TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
544779 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * *
544798 TCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGTTAT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * *
544862 GCCCTTGAAGCTGAGTGTAA
66 G-CCTTGGAGCTGAGCGTAG
* * * *
544882 TCGAACT-TAAGGGTC--TT--TGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATG
1 TCGAACTCGAA-GGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
544942 TGCCTTGGAGCTGAGCGTAG
65 TGCCTTGGAGCTGAGCGTAG
*
544962 TCGAACCCGAAGGTCTT
1 TCGAACTCGAAGGTCTT
544979 AGTGGCAGGT
Statistics
Matches: 566, Mismatches: 99, Indels: 34
0.81 0.14 0.05
Matches are distributed among these distances:
80 65 0.11
81 85 0.15
82 2 0.00
83 48 0.08
84 270 0.48
85 95 0.17
86 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:544395 original size:164 final size:165
Alignment explanation
Indices: 544213--544978 Score: 955
Period size: 169 Copynumber: 4.6 Consensus size: 165
544203 AAGTTGAATA
* * * * *
544213 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATAATGTG
1 TAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATACTGCAAATGATGTG
* * * * * *
544278 CCTTGGAGCTGAGCGGATTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTCGACTTAAG
* * * *
544343 TTATGCTGTAAATGATGTGCCGTTG-AGCTGAGCG
131 TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
* ** * * * * * *
544377 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCT-AGACTTAAGTTGTATTGCAAATG
1 TAATCGAACTTGAGGGTC---T-TTGGCAGATAGCCCTTCTCA-ACTTAAGCTATACTGCAAATG
* * *
544441 ATATGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGAC
61 ATGTGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTCGAC
*
544506 TTAAGTTATGCTGCAAATGATGTGCCCGCGAAGCTGAGTG
126 TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
* * * * * *
544546 TAATCGAACTTGGGGGTCTTTTGTTGGCAGACAACCCTTCT-AGACTTAAGTTGTATTGCAAATG
1 TAATCGAACTTGAGGGTC---T-TTGGCAGATAGCCCTTCTCA-ACTTAAGCTATACTGCAAATG
* * *
544610 ATATGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGAC
61 ATGTGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTCGAC
544675 TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
126 TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
* * * *
544715 TAATCAAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATACTGCAAATGATGTG
*
544780 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTCGACTTAAG
66 CCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTCGACTTAAG
* * * *
544844 TTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
131 TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
* * *
544879 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATACTGCAAATGATGTG
* *
544944 CCTTGGAGCTGAGCGTAGTCGAACCCGAAGGTCTT
66 CCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTT
544979 AGTGGCAGGT
Statistics
Matches: 543, Mismatches: 51, Indels: 15
0.89 0.08 0.02
Matches are distributed among these distances:
164 169 0.31
165 70 0.13
166 1 0.00
167 2 0.00
168 113 0.21
169 188 0.35
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (165 bp):
TAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATACTGCAAATGATGTG
CCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTCGACTTAAG
TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
Found at i:550196 original size:3 final size:3
Alignment explanation
Indices: 550150--550184 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
550140 AATAAATCAA
*
550150 AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
550185 AAGTAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:551514 original size:26 final size:25
Alignment explanation
Indices: 551470--551518 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
551460 AATAATAATA
551470 ATATATATATAAACGTTTTCAAAAAC
1 ATATATATATAAACGTTTT-AAAAAC
*
551496 ATATAATATATAAA-TTTTTAAAA
1 ATAT-ATATATAAACGTTTTAAAA
551519 TGTTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 8 0.38
27 9 0.43
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
ATATATATATAAACGTTTTAAAAAC
Found at i:551581 original size:38 final size:37
Alignment explanation
Indices: 551480--551871 Score: 194
Period size: 38 Copynumber: 10.1 Consensus size: 37
551470 ATATATATAT
* * * *
551480 AAACGTTTTCAAAAAC-ATATAATATATAAATTTTTA
1 AAACGTTTTTAAAAACTATATATTATATATATTTTCA
*
551516 AAATGTTTTTTTAAAAAAACTATATATTATATATATTTTCA
1 AAACG--TTTTT--AAAAACTATATATTATATATATTTTCA
* * *
551557 AAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCA
1 AAA-CGTTTTTAAAAACTATATATTATAT--ATATTTTCA
* * *
551597 TAACG-TTTTCAAAAGTATATATTATATATATTTT-A
1 AAACGTTTTTAAAAACTATATATTATATATATTTTCA
*
551632 AAACGTTTTCAAAAAC--TATATTATATA-ATTTTCAAAAAA
1 AAACGTTTTTAAAAACTATATATTATATATATTTTC-----A
* * **
551671 AATATTTTCAAAATGGTTTTTAAAAATTATATATTATATA-AGTGTTTT
1 AA-A----C------GTTTTTAAAAACTATATATTATATATA-TTTTCA
* * *
551719 CATAACG-TTTTCAAAAGTATATATTATATATATTTTAA
1 -A-AACGTTTTTAAAAACTATATATTATATATATTTTCA
* *
551757 AAACGTTTTCAAAAACTATATAATATATA-ATTTTCA
1 AAACGTTTTTAAAAACTATATATTATATATATTTTCA
** * *
551793 AAAAATATTTTAAAAACTATATAATATACATATTTTCA
1 AAACGT-TTTTAAAAACTATATATTATATATATTTTCA
**
551831 AAAAATGTTTT--AAACTATATATTATATATGTATTTTCA
1 AAACGT-TTTTAAAAACTATATATTATATA--TATTTTCA
551869 AAA
1 AAA
551872 ACAATTTGCA
Statistics
Matches: 280, Mismatches: 39, Indels: 72
0.72 0.10 0.18
Matches are distributed among these distances:
33 5 0.02
34 11 0.04
35 5 0.02
36 46 0.16
37 41 0.15
38 93 0.33
39 6 0.02
40 22 0.08
41 20 0.07
42 1 0.00
44 1 0.00
45 1 0.00
49 2 0.01
50 11 0.04
52 12 0.04
53 3 0.01
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
AAACGTTTTTAAAAACTATATATTATATATATTTTCA
Found at i:551651 original size:25 final size:24
Alignment explanation
Indices: 551622--551702 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 24
551612 TATATATTAT
551622 ATATATTTTAAAACGTTTTCAAAAA
1 ATATATTTTAAAA-GTTTTCAAAAA
* * *
551647 CTATATTATATAA-TTTTCAAAAA
1 ATATATTTTAAAAGTTTTCAAAAA
* *
551670 AAATATTTTCAAAATGGTTTTTAAAAA
1 ATATATTTT-AAAA--GTTTTCAAAAA
*
551697 TTATAT
1 ATATAT
551703 ATTATATAAG
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
23 16 0.38
24 3 0.07
25 10 0.24
27 13 0.31
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (24 bp):
ATATATTTTAAAAGTTTTCAAAAA
Found at i:551709 original size:124 final size:126
Alignment explanation
Indices: 551548--551797 Score: 468
Period size: 124 Copynumber: 2.0 Consensus size: 126
551538 TATATTATAT
551548 ATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
1 ATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
551613 ATATATTATATATATTTT-AAAACGTTTTCAAAAACTATAT-TATATAATTTTCAAAAAAA
66 ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATATATAATTTTCAAAAAAA
*
551672 ATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAGTGTTTTCATAACGTTTTCAAAAGT
1 ATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
551737 ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATAATATATAATTTTCAAAAAA
66 ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATAT-ATATATAATTTTCAAAAAA
551798 TATTTTAAAA
Statistics
Matches: 122, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
124 82 0.67
125 22 0.18
127 18 0.15
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (126 bp):
ATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATATATAATTTTCAAAAAAA
Found at i:551900 original size:39 final size:36
Alignment explanation
Indices: 551731--551898 Score: 153
Period size: 37 Copynumber: 4.5 Consensus size: 36
551721 TAACGTTTTC
* * **
551731 AAAAGTATATATTATATATATTTT-AAAAACGTTTTCA
1 AAAACTATATAATATATATATTTTCAAAAA-AATTT-A
551768 AAAACTATATAATATATA-ATTTTCAAAAAATATTTTA
1 AAAACTATATAATATATATATTTTCAAAAAA-A-TTTA
* *
551805 AAAACTATATAATATACATATTTTC-AAAAAATGTTT
1 AAAACTATATAATATATATATTTTCAAAAAAAT-TTA
* * *
551841 TAAACTATATATTATATATGTATTTTCAAAAACAATTTG
1 AAAACTATATA--ATATATATATTTTCAAAAA-AATTTA
*
551880 CAAACTATATAATATATAT
1 AAAACTATATAATATATAT
551899 GTGTATATAT
Statistics
Matches: 110, Mismatches: 12, Indels: 18
0.79 0.09 0.13
Matches are distributed among these distances:
35 1 0.01
36 18 0.16
37 51 0.46
38 21 0.19
39 16 0.15
40 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (36 bp):
AAAACTATATAATATATATATTTTCAAAAAAATTTA
Found at i:554817 original size:10 final size:10
Alignment explanation
Indices: 554802--554830 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
554792 AGATCAATAA
554802 AAAATACATT
1 AAAATACATT
554812 AAAATACATT
1 AAAATACATT
554822 AAAATACAT
1 AAAATACAT
554831 AGATCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATACATT
Found at i:554828 original size:39 final size:39
Alignment explanation
Indices: 554733--554855 Score: 162
Period size: 39 Copynumber: 3.1 Consensus size: 39
554723 AGTTCAATAA
*
554733 AAAATACATTAAAATACATAGATCAATAAAAAATTAGATGT
1 AAAATACATTAAAATACATAGATCAATAAAAAA-TACAT-T
*
554774 ACAAGT---TTAAGAATACATAGATCAATAAAAAATACATT
1 A-AAATACATTAA-AATACATAGATCAATAAAAAATACATT
*
554812 AAAATACATTAAAATACATAGATCAATAAAAAATACAAT
1 AAAATACATTAAAATACATAGATCAATAAAAAATACATT
554851 AAAAT
1 AAAAT
554856 TAGATGTACA
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
37 3 0.04
38 2 0.03
39 39 0.53
40 25 0.34
41 1 0.01
42 3 0.04
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.25
Consensus pattern (39 bp):
AAAATACATTAAAATACATAGATCAATAAAAAATACATT
Found at i:554882 original size:27 final size:27
Alignment explanation
Indices: 554847--554914 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
554837 ATAAAAAATA
554847 CAATAAAATTAGATGTACAACATAGAT
1 CAATAAAATTAGATGTACAACATAGAT
*
554874 CACTAAAATTAGATGTACAACATAGAT
1 CAATAAAATTAGATGTACAACATAGAT
*
554901 CAATAAAATGAGAT
1 CAATAAAATTAGAT
554915 ATTGTGTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (27 bp):
CAATAAAATTAGATGTACAACATAGAT
Found at i:555127 original size:26 final size:28
Alignment explanation
Indices: 555106--555164 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 28
555096 TAAGCTCGCG
*
555106 AGTTTTCGAGTCGAGTCGAGCTTCATTTCAA
1 AGTTTTCGAGTCGAGTCGAGC-TC--TGCAA
*
555137 AGTTTTCGAGTCGAGTCGAGCTCAGCAA
1 AGTTTTCGAGTCGAGTCGAGCTCTGCAA
555165 TACTCGAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
30 2 0.08
31 21 0.81
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (28 bp):
AGTTTTCGAGTCGAGTCGAGCTCTGCAA
Found at i:556473 original size:6 final size:6
Alignment explanation
Indices: 556462--556503 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
556452 CCACTGGTGG
556462 GAGGGT GAGGGT GAGGGT GAGGGT GAGGGT G-GGGT GAGGGT G
1 GAGGGT GAGGGT GAGGGT GAGGGT GAGGGT GAGGGT GAGGGT G
556504 TAATTTGGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.14, C:0.00, G:0.69, T:0.17
Consensus pattern (6 bp):
GAGGGT
Found at i:563173 original size:15 final size:15
Alignment explanation
Indices: 563153--563185 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
563143 TGTCACATTA
563153 ACTTTTCAAACCTTG
1 ACTTTTCAAACCTTG
563168 ACTTTTCAAACCTTG
1 ACTTTTCAAACCTTG
563183 ACT
1 ACT
563186 CTTAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.39
Consensus pattern (15 bp):
ACTTTTCAAACCTTG
Found at i:563899 original size:30 final size:30
Alignment explanation
Indices: 563853--563916 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
563843 GAAGGACCTG
* *
563853 TCCAGAGGTTACAAAGAA-CTCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCT-CGGCAACTA
* *
563883 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCTCGGCAACTA
563913 TCCA
1 TCCA
563917 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCTCGGCAACTA
Found at i:564690 original size:64 final size:64
Alignment explanation
Indices: 564585--564727 Score: 182
Period size: 64 Copynumber: 2.2 Consensus size: 64
564575 CAATGAAGAT
* * *
564585 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TCCTTATT-AATGA
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTCTCCTT-TTAAAGGA
* ** * *
564648 GATGCATCGATGCACTCCTTATGCATCGATGCATTGATTGCATTCGATGTTCTTCTTTTAAAGGA
1 -ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTCTCCTTTTAAAGGA
564713 ATGCATCGATGCACT
1 ATGCATCGATGCACT
564728 TATGAATGTG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
64 61 0.88
65 8 0.12
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTCTCCTTTTAAAGGA
Found at i:568869 original size:64 final size:64
Alignment explanation
Indices: 568733--568875 Score: 173
Period size: 64 Copynumber: 2.2 Consensus size: 64
568723 CAATGAAGAT
* * *
568733 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTCCTTATTAATGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTCCTTATTAAGGAG
* ** * *
568797 ATGCATCGATGCACTCCTTATGCATCGATGCATTGATTGCATTCGATGTTCTTCTT-TTAAAGGA
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTT-TCCTTATT-AAGGA
568861 -
64 G
*
568861 ATGTATCGATGCACT
1 ATGCATCGATGCACT
568876 TATGAATGTG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 60 0.88
65 8 0.12
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTCCTTATTAAGGAG
Found at i:577088 original size:6 final size:6
Alignment explanation
Indices: 577077--577117 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
577067 CTGCTCTCTG
577077 CAACTT CAACTT CAACTT CAACTT CAACTT CAACTT CAACT
1 CAACTT CAACTT CAACTT CAACTT CAACTT CAACTT CAACT
577118 CTAGTCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (6 bp):
CAACTT
Found at i:589661 original size:2 final size:2
Alignment explanation
Indices: 589656--589684 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
589646 ATTTGACTTT
589656 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
589685 GATGGGTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:593323 original size:31 final size:30
Alignment explanation
Indices: 593266--593324 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
593256 AATATGGTTG
*
593266 TATCACTAAATTTTAATTTTACAACAATTA
1 TATCACTAAATTTTAATTATACAACAATTA
*
593296 TATCACTAGATTATTAATTAATA-AACAAT
1 TATCACTAAATT-TTAATT-ATACAACAAT
593325 AGGATAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.44
31 12 0.48
32 2 0.08
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.41
Consensus pattern (30 bp):
TATCACTAAATTTTAATTATACAACAATTA
Found at i:598747 original size:20 final size:20
Alignment explanation
Indices: 598722--598837 Score: 144
Period size: 20 Copynumber: 5.8 Consensus size: 20
598712 TGCGAATTTC
*
598722 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
* * *
598742 CAAATTCTCTACGCGAAAAT
1 CAAATTCGCAACGCGAAAGT
* *
598762 CAAATTCGCAACACGATAGT
1 CAAATTCGCAACGCGAAAGT
598782 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* **
598802 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
598821 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
598838 TTTAATTTCG
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
19 16 0.20
20 64 0.80
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:598840 original size:20 final size:20
Alignment explanation
Indices: 598681--598851 Score: 134
Period size: 20 Copynumber: 8.6 Consensus size: 20
598671 AAATGACCAA
* *
598681 CAAATTCACAACGCGAATTC
1 CAAATTCGCAACGCGAATTT
* ***
598701 CAATTTCGCGTTGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
598721 CCAAATTCGCAACGCG-ATAGT
1 -CAAATTCGCAACGCGAAT-TT
* * **
598742 CAAATTCTCTACGCGAAAAT
1 CAAATTCGCAACGCGAATTT
* *
598762 CAAATTCGCAACACG-ATAGT
1 CAAATTCGCAACGCGAAT-TT
**
598782 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAATTT
*
598802 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
598821 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
598841 -AATTTCGCAAC
1 CAAATTCGCAAC
598852 AGGTTTTAGT
Statistics
Matches: 118, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
19 27 0.23
20 77 0.65
21 14 0.12
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:599756 original size:24 final size:24
Alignment explanation
Indices: 599729--599782 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
599719 GTATTTGAAA
599729 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
599753 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
599777 TTTGAT
1 TTTGAT
599783 GATGTGATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:602064 original size:18 final size:18
Alignment explanation
Indices: 602041--602076 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
602031 AAGCAAAAGG
*
602041 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
602059 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
602077 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:602390 original size:20 final size:20
Alignment explanation
Indices: 602362--602405 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
602352 ATGCTACGAT
*
602362 CAACGCAAAAGTCAAATTCG
1 CAACACAAAAGTCAAATTCG
602382 CAACACAAAAGTCAAATTCG
1 CAACACAAAAGTCAAATTCG
602402 CAAC
1 CAAC
602406 GCGAAATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.27, G:0.11, T:0.14
Consensus pattern (20 bp):
CAACACAAAAGTCAAATTCG
Found at i:602585 original size:25 final size:25
Alignment explanation
Indices: 602547--602596 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
602537 AAATCAATTA
*
602547 AACAATGTTGTGGGTACATTATTTG
1 AACAATGTTATGGGTACATTATTTG
*
602572 AACATTGTTATGGGTACATTATTTG
1 AACAATGTTATGGGTACATTATTTG
602597 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (25 bp):
AACAATGTTATGGGTACATTATTTG
Done.