Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 61 of 187
Found at i:17883349 original size:28 final size:27
Alignment explanation
Indices: 17883316--17883386 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 27
17883306 TAATGAGATT
17883316 AGCACTAAGTGTGCGAGTTTAATTGA-A
1 AGCACTAAGTGTGCGAGTTTAATT-ATA
*
17883343 ATGCACTAAGTGTGCGAGTTTGATTATTA
1 A-GCACTAAGTGTGCGAGTTTAATTA-TA
17883372 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
17883387 TACTTATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 2 0.05
28 36 0.90
29 2 0.05
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTATA
Found at i:17884392 original size:47 final size:47
Alignment explanation
Indices: 17884323--17884675 Score: 539
Period size: 47 Copynumber: 7.5 Consensus size: 47
17884313 TGTGTTATAA
17884323 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
1 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
*
17884370 ATTTTAATGTATAATGCTGTCCAATTTTCAGTATATTGATGCTGTCC
1 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
17884417 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
1 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
17884464 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
1 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
* * *
17884511 ATTTTAATGTATAATGCTATCCAATTTTGAGTATATTTAAGCTGTCC
1 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
* * *
17884558 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCT
1 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
* * * * *
17884605 AATTTGATGTATAATGCTGTCC-ATTTAGAGCATATT-ATTGCTGTCT
1 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGA-TGCTGTCC
* * *
17884651 AATTTGATGAATAATTGCTGTCCAA
1 ATTTTAATGTATAA-TGCTGTCCAA
17884676 AACAGGGTTG
Statistics
Matches: 290, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
45 1 0.00
46 32 0.11
47 256 0.88
48 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (47 bp):
ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
Found at i:17884670 original size:23 final size:23
Alignment explanation
Indices: 17884598--17884672 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
17884588 GTATATTTAA
*
17884598 GCTGTCTAATTTGATGTATAA-T
1 GCTGTCTAATTTGATGAATAATT
* *
17884620 GCTGTC-CATTTAGA-GCATATTATT
1 GCTGTCTAATTT-GATG-A-ATAATT
17884644 GCTGTCTAATTTGATGAATAATT
1 GCTGTCTAATTTGATGAATAATT
17884667 GCTGTC
1 GCTGTC
17884673 CAAAACAGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
21 5 0.12
22 8 0.19
23 14 0.33
24 10 0.24
25 5 0.12
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (23 bp):
GCTGTCTAATTTGATGAATAATT
Found at i:17893991 original size:2 final size:2
Alignment explanation
Indices: 17893984--17894034 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
17893974 TTCTTGTTGG
17893984 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
17894026 AT AT AT AT A
1 AT AT AT AT A
17894035 AAACAATGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17902365 original size:35 final size:34
Alignment explanation
Indices: 17902324--17902389 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
17902314 ATGTATAGAT
*
17902324 ATGTATATGTTATAATAATAAATAA-AATGAATCTA
1 ATGTATATATTATAAT-AT-AATAATAATGAATCTA
17902359 ATGTATATATTATAATATAATAATAATGAAT
1 ATGTATATATTATAATATAATAATAATGAAT
17902390 GAAATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 9 0.31
35 15 0.52
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.39
Consensus pattern (34 bp):
ATGTATATATTATAATATAATAATAATGAATCTA
Found at i:17909050 original size:79 final size:79
Alignment explanation
Indices: 17908919--17909073 Score: 247
Period size: 79 Copynumber: 2.0 Consensus size: 79
17908909 TGTGATGGTC
*
17908919 GAATATACCAATAGCATGTTTTGATCTGTTAACTATATGTACAATTAGTATGTTCTGATATGTTT
1 GAATATACCAATAGCATGTTTTGATCTGTTAACTATATGTACAACTAGTATGTTCTGATATGTTT
17908984 TATCTGCATATGGG
66 TATCTGCATATGGG
* * * * *
17908998 GAATATGCCAATAGCATGTTTTGATTTGTTAATTATGTGTGCAACTAGTATGTTCTGATATGTTT
1 GAATATACCAATAGCATGTTTTGATCTGTTAACTATATGTACAACTAGTATGTTCTGATATGTTT
*
17909063 TATCTGTATAT
66 TATCTGCATAT
17909074 AAGCATGCCT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (79 bp):
GAATATACCAATAGCATGTTTTGATCTGTTAACTATATGTACAACTAGTATGTTCTGATATGTTT
TATCTGCATATGGG
Found at i:17923392 original size:2 final size:2
Alignment explanation
Indices: 17923387--17923411 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17923377 ATCATTCTAT
17923387 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 T
17923412 GATAAAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17930963 original size:59 final size:57
Alignment explanation
Indices: 17930842--17931010 Score: 173
Period size: 59 Copynumber: 3.0 Consensus size: 57
17930832 ACAAAGACAC
* * *
17930842 CCTTTTAACAGAGATCGCCACAAGGGCTTCCTTTAACAAAGATAACCACAAAGGCTT
1 CCTTTTAATAGAGATTGCCACAAAGGCTTCCTTTAACAAAGATAACCACAAAGGCTT
* * * * **
17930899 TCTTTTAATAGAGATTTCCACAAAAGGCTTCCTTTTAATAGAGATTGCCACAAAGGCTT
1 CCTTTTAATAGAGATTGCCAC-AAAGGCTTCC-TTTAACAAAGATAACCACAAAGGCTT
* * * * *
17930958 CCTTTTAATAGAGATTGTC-TAAAGGCGTCCTTT--CAGAGATAGCCACAAAGGCT
1 CCTTTTAATAGAGATTGCCACAAAGGCTTCCTTTAACAAAGATAACCACAAAGGCT
17931011 CATTTTTATG
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
54 18 0.19
56 3 0.03
57 26 0.28
58 9 0.10
59 38 0.40
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (57 bp):
CCTTTTAATAGAGATTGCCACAAAGGCTTCCTTTAACAAAGATAACCACAAAGGCTT
Found at i:17930990 original size:28 final size:29
Alignment explanation
Indices: 17930842--17930974 Score: 169
Period size: 29 Copynumber: 4.6 Consensus size: 29
17930832 ACAAAGACAC
* * *
17930842 CCTTTTAACAGAGATCGCCACAAGGGCTT
1 CCTTTTAATAGAGATTGCCACAAAGGCTT
* * **
17930871 CC-TTTAACAAAGATAACCACAAAGGCTT
1 CCTTTTAATAGAGATTGCCACAAAGGCTT
* *
17930899 TCTTTTAATAGAGATTTCCACAAAAGGCTT
1 CCTTTTAATAGAGATTGCCAC-AAAGGCTT
17930929 CCTTTTAATAGAGATTGCCACAAAGGCTT
1 CCTTTTAATAGAGATTGCCACAAAGGCTT
17930958 CCTTTTAATAGAGATTG
1 CCTTTTAATAGAGATTG
17930975 TCTAAAGGCG
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
28 23 0.25
29 41 0.45
30 27 0.30
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (29 bp):
CCTTTTAATAGAGATTGCCACAAAGGCTT
Found at i:17932823 original size:9 final size:9
Alignment explanation
Indices: 17932788--17932832 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
17932778 GGTTTTTGGA
17932788 TTTTAGGG-
1 TTTTAGGGT
17932796 -TTTAGGG-
1 TTTTAGGGT
*
17932803 TTTTAAGGT
1 TTTTAGGGT
*
17932812 TTTTAGGAT
1 TTTTAGGGT
17932821 TTTTAGGGT
1 TTTTAGGGT
17932830 TTT
1 TTT
17932833 GGAGAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
7 7 0.23
8 6 0.19
9 18 0.58
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.56
Consensus pattern (9 bp):
TTTTAGGGT
Found at i:17938743 original size:25 final size:25
Alignment explanation
Indices: 17938711--17938792 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
17938701 TTAGATAACC
17938711 TAATAAGATAATTGCATGTGAAAAA
1 TAATAAGATAATTGCATGTGAAAAA
* **
17938736 TAATAAGATACTT--A-GAT-AACCA
1 TAATAAGATAATTGCATG-TGAAAAA
17938758 -AATAAGATAATTGCATGTGAAAAA
1 TAATAAGATAATTGCATGTGAAAAA
17938782 TAATAAGATAA
1 TAATAAGATAA
17938793 ATAAATAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
21 11 0.24
22 4 0.09
23 4 0.09
24 4 0.09
25 22 0.49
ACGTcount: A:0.54, C:0.06, G:0.13, T:0.27
Consensus pattern (25 bp):
TAATAAGATAATTGCATGTGAAAAA
Found at i:17938765 original size:46 final size:46
Alignment explanation
Indices: 17938698--17938791 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
17938688 TTTAATTTAT
*
17938698 TACTTAGATAACCTAATAAGATAATTGCATGTGAAAAATAATAAGA
1 TACTTAGATAACCAAATAAGATAATTGCATGTGAAAAATAATAAGA
17938744 TACTTAGATAACCAAATAAGATAATTGCATGTGAAAAATAATAAGA
1 TACTTAGATAACCAAATAAGATAATTGCATGTGAAAAATAATAAGA
17938790 TA
1 TA
17938792 AATAAATAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (46 bp):
TACTTAGATAACCAAATAAGATAATTGCATGTGAAAAATAATAAGA
Found at i:17944091 original size:33 final size:32
Alignment explanation
Indices: 17944041--17944140 Score: 128
Period size: 33 Copynumber: 3.1 Consensus size: 32
17944031 GAATGTTCTG
*
17944041 TCACCGGCTGTACATTTGTCTCCTGTCCCAAAT
1 TCACCGACTGTACATTTGTCTCCT-TCCCAAAT
* **
17944074 TCACTGGTTGTACATTTGTCTCCTTTCCCAAAT
1 TCACCGACTGTACATTTGTCTCC-TTCCCAAAT
* *
17944107 TCACCGACTGTACATCTGTCTCCTTCTCAAAT
1 TCACCGACTGTACATTTGTCTCCTTCCCAAAT
17944139 TC
1 TC
17944141 TGATCGATCT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
32 10 0.17
33 48 0.81
34 1 0.02
ACGTcount: A:0.19, C:0.32, G:0.12, T:0.37
Consensus pattern (32 bp):
TCACCGACTGTACATTTGTCTCCTTCCCAAAT
Found at i:17953320 original size:21 final size:21
Alignment explanation
Indices: 17953294--17953335 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
17953284 CAAGCCTAAG
*
17953294 CCACACTTGAGACAATGAATA
1 CCACACCTGAGACAATGAATA
17953315 CCACACCTGAGACAATGAATA
1 CCACACCTGAGACAATGAATA
17953336 TCCTGACCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (21 bp):
CCACACCTGAGACAATGAATA
Found at i:17954256 original size:15 final size:15
Alignment explanation
Indices: 17954238--17954267 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17954228 TATATCATTT
*
17954238 CATTATGAATCAAAA
1 CATTATAAATCAAAA
17954253 CATTATAAATCAAAA
1 CATTATAAATCAAAA
17954268 TTTAAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (15 bp):
CATTATAAATCAAAA
Found at i:17962492 original size:16 final size:15
Alignment explanation
Indices: 17962471--17962539 Score: 56
Period size: 16 Copynumber: 4.7 Consensus size: 15
17962461 TGACATATAA
17962471 GTGAATTAATCACTTT
1 GTGAATTAATCAC-TT
17962487 GTGAATTAATCA-TT
1 GTGAATTAATCACTT
* **
17962501 GAT-AAAT-AT-ACAA
1 G-TGAATTAATCACTT
17962514 GTGAATTAATCACTTT
1 GTGAATTAATCAC-TT
17962530 GTGAATTAAT
1 GTGAATTAAT
17962540 TATTTCTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
12 2 0.05
13 6 0.15
14 8 0.20
15 3 0.07
16 22 0.54
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (15 bp):
GTGAATTAATCACTT
Found at i:17963544 original size:37 final size:36
Alignment explanation
Indices: 17963503--17963574 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
17963493 ATTCCAAAAA
*
17963503 TAATA-TTATTTTAATAGCTTTAATATTAAATTTAATT
1 TAATACTTATCTTAATA-CTTTAATATT-AATTTAATT
* *
17963540 TAATACTTATCTTCATATTTTAATATTAATTTAAT
1 TAATACTTATCTTAATACTTTAATATTAATTTAAT
17963575 AGATTTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 8 0.26
37 14 0.45
38 9 0.29
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (36 bp):
TAATACTTATCTTAATACTTTAATATTAATTTAATT
Found at i:17963581 original size:20 final size:19
Alignment explanation
Indices: 17963503--17963584 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 19
17963493 ATTCCAAAAA
* *
17963503 TAATATTATTTTAATAGCTT
1 TAATATTAATTTAATA-ATT
*
17963523 TAATATTAAATT--TAATT
1 TAATATTAATTTAATAATT
* *
17963540 TAATACTT-ATCTTCATATTT
1 TAATA-TTAAT-TTAATAATT
17963560 TAATATTAATTTAATAGATT
1 TAATATTAATTTAATA-ATT
17963580 TAATA
1 TAATA
17963585 GTAAAGTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
17 8 0.16
18 6 0.12
19 7 0.14
20 28 0.57
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATTAATTTAATAATT
Found at i:17964500 original size:5 final size:5
Alignment explanation
Indices: 17964490--17964519 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
17964480 TTTATAATGT
17964490 TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA
17964520 AGTTTGATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:17966532 original size:37 final size:37
Alignment explanation
Indices: 17966485--17966599 Score: 169
Period size: 37 Copynumber: 3.1 Consensus size: 37
17966475 CAGAATGCAC
*
17966485 ATATACACTTATAC-CTACTTATGCCGAATGCATACAT
1 ATATACACTTATACTC-ACCTATGCCGAATGCATACAT
**
17966522 ATATACACTTATTTTCACCTATGCCGAATGCATACAT
1 ATATACACTTATACTCACCTATGCCGAATGCATACAT
* *
17966559 ATATACCCTTATAGTCACCTATGCCGAATGCATACAT
1 ATATACACTTATACTCACCTATGCCGAATGCATACAT
17966596 ATAT
1 ATAT
17966600 TTTTATCTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
37 70 0.99
38 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33
Consensus pattern (37 bp):
ATATACACTTATACTCACCTATGCCGAATGCATACAT
Found at i:17966867 original size:41 final size:41
Alignment explanation
Indices: 17966821--17966923 Score: 138
Period size: 41 Copynumber: 2.5 Consensus size: 41
17966811 CTCTTGAGCT
*
17966821 TGCTAGACTTATAGTCCG-A-AATGTATCACCGGCATTAAGCC
1 TGCTAGACGTATAGTCCGAATAAT-T-TCACCGGCATTAAGCC
*
17966862 TGCTAGACGTATAGTCTGAATAATTTCACCGGCATTAAGCC
1 TGCTAGACGTATAGTCCGAATAATTTCACCGGCATTAAGCC
* *
17966903 TGCTAGACGTAAAGTCTGAAT
1 TGCTAGACGTATAGTCCGAAT
17966924 TATGTCACTA
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
41 52 0.91
42 2 0.04
43 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (41 bp):
TGCTAGACGTATAGTCCGAATAATTTCACCGGCATTAAGCC
Found at i:17972276 original size:19 final size:19
Alignment explanation
Indices: 17972252--17972289 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17972242 GTAATTGAAC
17972252 TTGAAAATTGGACCTGAGA
1 TTGAAAATTGGACCTGAGA
17972271 TTGAAAATTGGACCTGAGA
1 TTGAAAATTGGACCTGAGA
17972290 ACCCAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (19 bp):
TTGAAAATTGGACCTGAGA
Found at i:17972686 original size:61 final size:58
Alignment explanation
Indices: 17972612--17972737 Score: 171
Period size: 61 Copynumber: 2.1 Consensus size: 58
17972602 ATAATATTGT
* * * *
17972612 TTTAATAGTTTTAATATTTAATTTAATTTAATATTTATCTTATAGATAAATATTCTATTAA
1 TTTAATAGATTTAATATTAAATTTAATCTAATATTTATC---TAGATAAATATTATATTAA
* *
17972673 TTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTCGATAAGTATTATATTAA
1 TTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTAGATAAATATTATATTAA
17972731 TTTAATA
1 TTTAATA
17972738 TTAAATTGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 23 0.39
61 36 0.61
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (58 bp):
TTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTAGATAAATATTATATTAA
Found at i:17972750 original size:58 final size:58
Alignment explanation
Indices: 17972624--17972757 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 58
17972614 TAATAGTTTT
* * * *
17972624 AATATTTAATTTAATTTAATATTTATCTTATAGATAAATATTCTATTAATTTAATAGATTT
1 AATATTAAATTTAATCTAATATTTATC-T-TAGATAAATATTATATTAATTTAATA-ATTA
* *
17972685 AATATTAAATTTAATCTAATATTTATC-TCGATAAGTATTATATTAATTTAAT-ATTA
1 AATATTAAATTTAATCTAATATTTATCTTAGATAAATATTATATTAATTTAATAATTA
*
17972741 AATTGATTAAGTTTAAT
1 AA-T-ATTAAATTTAAT
17972758 AATAGTTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
56 5 0.08
57 1 0.02
58 33 0.52
61 25 0.39
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (58 bp):
AATATTAAATTTAATCTAATATTTATCTTAGATAAATATTATATTAATTTAATAATTA
Found at i:17974184 original size:4 final size:4
Alignment explanation
Indices: 17974177--17974228 Score: 50
Period size: 4 Copynumber: 11.5 Consensus size: 4
17974167 TAGATAGTTT
17974177 ATTA ATTA ATTA ATCCTA ATTA ACTTA ATTA ATCCTA ATTA ACTTA ATTA
1 ATTA ATTA ATTA AT--TA ATTA A-TTA ATTA AT--TA ATTA A-TTA ATTA
17974227 AT
1 AT
17974229 CATAATTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
4 26 0.62
5 8 0.19
6 8 0.19
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (4 bp):
ATTA
Found at i:17974198 original size:10 final size:10
Alignment explanation
Indices: 17974183--17974235 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
17974173 GTTTATTAAT
17974183 TAATTAATCC
1 TAATTAATCC
*
17974193 TAATTAA-CT
1 TAATTAATCC
17974202 TAATTAATCC
1 TAATTAATCC
*
17974212 TAATTAA-CT
1 TAATTAATCC
*
17974221 TAATTAATCA
1 TAATTAATCC
17974231 TAATT
1 TAATT
17974236 TCTTAACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 16 0.43
10 21 0.57
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (10 bp):
TAATTAATCC
Found at i:17974206 original size:19 final size:19
Alignment explanation
Indices: 17974177--17974235 Score: 102
Period size: 19 Copynumber: 3.2 Consensus size: 19
17974167 TAGATAGTTT
17974177 ATTAA-TTAATTAATCCTA
1 ATTAACTTAATTAATCCTA
17974195 ATTAACTTAATTAATCCTA
1 ATTAACTTAATTAATCCTA
*
17974214 ATTAACTTAATTAATCATA
1 ATTAACTTAATTAATCCTA
17974233 ATT
1 ATT
17974236 TCTTAACAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
18 5 0.13
19 34 0.87
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAACTTAATTAATCCTA
Found at i:17982199 original size:22 final size:22
Alignment explanation
Indices: 17982095--17982204 Score: 139
Period size: 22 Copynumber: 5.0 Consensus size: 22
17982085 AAATTCAATA
** *
17982095 TCAATTTTTTTCAAAAGTTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
17982117 TCAATTCCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
17982139 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
* * *
17982161 TCAAATTCCTTCCAAAATCCTC
1 TCAATTTCCTTCAAAAATTCTC
*
17982183 TCAATTTCCTTCAAAAAATCTC
1 TCAATTTCCTTCAAAAATTCTC
17982205 AAAATCCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 76 1.00
ACGTcount: A:0.31, C:0.29, G:0.01, T:0.39
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:17982296 original size:29 final size:29
Alignment explanation
Indices: 17982241--17982296 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
17982231 ATTAAATTTC
17982241 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTT
*
17982270 ATTTTTTTAA-ATAATTTTAAAATTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTT
17982297 AATATTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTT
Found at i:17982304 original size:29 final size:29
Alignment explanation
Indices: 17982241--17982304 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
17982231 ATTAAATTTC
*
17982241 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTA
*
17982270 ATTTTTTTAA-ATAATTTTAAAATTTTTA
1 ATTTTTTTAAGAAAATTTTAAAATTTTTA
*
17982298 ATATTTT
1 ATTTTTT
17982305 CAACAATGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTA
Found at i:17982424 original size:14 final size:15
Alignment explanation
Indices: 17982395--17982428 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17982385 AAATTTTAAA
17982395 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
17982410 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
17982424 TTTTA
1 TTTTA
17982429 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:17984617 original size:23 final size:23
Alignment explanation
Indices: 17984565--17985022 Score: 380
Period size: 23 Copynumber: 18.3 Consensus size: 23
17984555 TTTTGACATT
*
17984565 ATTTGATTAAAAACCCTAACCTTA
1 ATTTAATTAAAAACCCTAACC-TA
*
17984589 ACTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
17984612 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
17984635 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
*
17984658 ACTTAATTGAATTAAAAACCCTAACTTA
1 A--T--TT-AATTAAAAACCCTAACCTA
* *
17984686 ACTTAATTGAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACC-----TA
*
17984714 ATTTAATTAAAAACCCTAACTTA
1 ATTTAATTAAAAACCCTAACCTA
*
17984737 ACTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAA-C---C-TA
17984765 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
*
17984788 TTTTACA-TAAAAACCCTAACCCTAACA
1 ATTTA-ATTAAAAACCCTAA-CCT---A
*
17984815 TATTTTAATTAAAATCCCTAACCTA
1 -A-TTTAATTAAAAACCCTAACCTA
*
17984840 ACTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAA-C---C-TA
*
17984868 ATTTAATTAAAAACCCTAACTTA
1 ATTTAATTAAAAACCCTAACCTA
*
17984891 ACTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAA-C---C-TA
*
17984919 ATTTAATTAAAAATCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
* *
17984942 TTTTACA-TGAAAACCCTAACCCTAACA
1 ATTTA-ATTAAAAACCCTAA-CCT---A
*
17984969 TATTTTAATTAAAATCCCTAACCTA
1 -A-TTTAATTAAAAACCCTAACCTA
*
17984994 ACTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
*
17985017 ACTTAA
1 ATTTAA
17985023 AACCACTAAC
Statistics
Matches: 361, Mismatches: 32, Indels: 83
0.76 0.07 0.17
Matches are distributed among these distances:
23 179 0.50
24 36 0.10
25 3 0.01
27 8 0.02
28 106 0.29
29 29 0.08
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.31
Consensus pattern (23 bp):
ATTTAATTAAAAACCCTAACCTA
Found at i:17984635 original size:28 final size:28
Alignment explanation
Indices: 17984603--17985170 Score: 369
Period size: 23 Copynumber: 21.7 Consensus size: 28
17984593 AATTAAAAAC
17984603 CCTAACCTAATTTAATTAAAAA--C---
1 CCTAACCTAATTTAATTAAAAACCCTAA
17984626 CCTAACCTAATTTAATTAAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
* *
17984654 CCTAACTTAATTGAATTAAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
* *
17984682 -CT----TAACTTAATTGAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
**
17984705 CCTAATTTAATTTAATTAAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
*
17984733 -CT----TAACTTAATTAAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
*
17984756 CCTAACTTAATTTAATTAAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
17984784 CCT-A--T--TTTACA-TAAAAACCCTAA
1 CCTAACCTAATTTA-ATTAAAAACCCTAA
* * *
17984807 CCCTAACATATTTTAATTAAAATCCCTAA
1 -CCTAACCTAATTTAATTAAAAACCCTAA
17984836 CCTAA-C----TTAATTAAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
*
17984859 CCTAACTTAATTTAATTAAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
*
17984887 -CT----TAACTTAATTAAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
*
17984910 CCTAACTTAATTTAATTAAAAA---T--
1 CCTAACCTAATTTAATTAAAAACCCTAA
* *
17984933 CCTAACCTATTTTACA-TGAAAACCCTAA
1 CCTAACCTAATTTA-ATTAAAAACCCTAA
* * *
17984961 CCCTAACATATTTTAATTAAAATCCCTAA
1 -CCTAACCTAATTTAATTAAAAACCCTAA
17984990 CCTAA-C----TTAATTAAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
* *
17985013 CCTAA-C--------TTAAAACCACTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
* *
17985032 CCCTAA-CTATTTTACATGAAAACACTAACCTAA
1 -CCTAACCTAATTTA-ATTAAAA-AC---CCTAA
**
17985065 CCTAATTTAATTTAATTAAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA
* *
17985093 CCCTAACCTATTTTACA-TGAAAACCCTAA
1 -CCTAACCTAATTTA-ATTAAAAACCCTAA
* * *
17985122 CCCTAACCTATTTTAATTAAAATCTCTAA
1 -CCTAACCTAATTTAATTAAAAACCCTAA
17985151 CCCTAACCTAATTTAATTAA
1 -CCTAACCTAATTTAATTAA
17985171 TGTAAAAACC
Statistics
Matches: 447, Mismatches: 39, Indels: 112
0.75 0.07 0.19
Matches are distributed among these distances:
19 11 0.02
20 6 0.01
23 156 0.35
24 11 0.02
25 4 0.01
26 1 0.00
27 8 0.02
28 117 0.26
29 108 0.24
30 2 0.00
31 2 0.00
32 11 0.02
33 10 0.02
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (28 bp):
CCTAACCTAATTTAATTAAAAACCCTAA
Found at i:17984679 original size:51 final size:51
Alignment explanation
Indices: 17984565--17985163 Score: 644
Period size: 51 Copynumber: 11.6 Consensus size: 51
17984555 TTTTGACATT
*
17984565 ATTTGATTAAAAACCCTAACCTTAACTTAATTAAAAACCCTAA-C---C-TA
1 ATTTAATTAAAAACCCTAACC-TAACTTAATTAAAAACCCTAACCTAACTTA
*
17984612 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTA
* * * *
17984663 ATTGAATTAAAAACCCTAACTTAACTTAATTGAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTA
*
17984714 ATTTAATTAAAAACCCTAACTTAACTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTA
** *
17984765 ATTTAATTAAAAACCCTAACCTATTTTACA-TAAAAACCCTAACCCTAACATA
1 ATTTAATTAAAAACCCTAACCTAACTTA-ATTAAAAACCCTAA-CCTAACTTA
* *
17984817 TTTTAATTAAAATCCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTA
*
17984868 ATTTAATTAAAAACCCTAACTTAACTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTA
* ** * *
17984919 ATTTAATTAAAAATCCTAACCTATTTTACA-TGAAAACCCTAACCCTAACATA
1 ATTTAATTAAAAACCCTAACCTAACTTA-ATTAAAAACCCTAA-CCTAACTTA
* *
17984971 TTTTAATTAAAATCCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTA
** ** ** * *
17985022 A---AACCACTAACCCTAA-CTATTTTACATGAAAACACTAACCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA-ATTAAAA-AC---CCTAACCTAACTTA
* * *
17985074 ATTTAATTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA-ATT--A--AAAACCCTAA-CCTAACTTA
* * * *
17985132 TTTTAATTAAAATCTCTAACCCTAACCTAATT
1 ATTTAATTAAAAACCCTAA-CCTAACTTAATT
17985164 TAATTAATGT
Statistics
Matches: 465, Mismatches: 61, Indels: 42
0.82 0.11 0.07
Matches are distributed among these distances:
46 20 0.04
47 27 0.06
48 16 0.03
49 2 0.00
50 1 0.00
51 234 0.50
52 102 0.22
55 11 0.02
57 13 0.03
58 33 0.07
59 1 0.00
60 2 0.00
61 3 0.01
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (51 bp):
ATTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTA
Found at i:17985025 original size:18 final size:19
Alignment explanation
Indices: 17984990--17985039 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
17984980 AAATCCCTAA
*
17984990 CCTAACTTAA-TTAAAAAC
1 CCTAACCTAACTTAAAAAC
17985008 CCTAACCTAACTT-AAAAC
1 CCTAACCTAACTTAAAAAC
17985026 CACTAACCCTAACT
1 C-CTAA-CCTAACT
17985040 ATTTTACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 15 0.54
19 6 0.21
20 7 0.25
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (19 bp):
CCTAACCTAACTTAAAAAC
Found at i:17985110 original size:62 final size:63
Alignment explanation
Indices: 17985021--17985139 Score: 197
Period size: 62 Copynumber: 1.9 Consensus size: 63
17985011 AACCTAACTT
17985021 AAAACCACTAACCCTAACTATTTTACATGAAAACACTAA-CCTAACCTAATTTAATTTAATTA
1 AAAACCACTAACCCTAACTATTTTACATGAAAACACTAACCCTAACCTAATTTAATTTAATTA
* *
17985083 AAAACC-CTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTATTTTAATT
1 AAAACCACTAACCCTAA-CTATTTTACATGAAAACACTAACCCTAACCTAATTTAATT
17985140 AAAATCTCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
61 10 0.19
62 27 0.51
63 16 0.30
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (63 bp):
AAAACCACTAACCCTAACTATTTTACATGAAAACACTAACCCTAACCTAATTTAATTTAATTA
Found at i:17988687 original size:124 final size:125
Alignment explanation
Indices: 17988451--17988715 Score: 381
Period size: 124 Copynumber: 2.1 Consensus size: 125
17988441 CCACGAGGGC
*
17988451 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTATAGC
1 GCGATTTGACACTATTGGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTATAGC
* * * **
17988516 GAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* * * *
17988576 GCGATTTTATACTATTGGCTCAGAAAACGTC-AAAAAAAATTATTTCTTACATGACC-ACTGTAG
1 GCGATTTGACACTATTGGCTCAG-AAACGTCAAAAAAAAATTATTTCCTACATGACCAACTATAG
* *
17988639 TGAAATCGCGTCCACGAGGCCACTATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
65 CGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
**
17988700 GCGATTTCCCACTATT
1 GCGATTTGACACTATT
17988716 TGACCAGATA
Statistics
Matches: 124, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
124 73 0.59
125 44 0.35
126 7 0.06
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (125 bp):
GCGATTTGACACTATTGGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTATAGC
GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:17990206 original size:25 final size:25
Alignment explanation
Indices: 17990161--17990210 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
17990151 TCTGTATTTT
*
17990161 TTTTTTGAAAATTTATTATTTTTAA
1 TTTTTTGAAAATTTATAATTTTTAA
*
17990186 TTTTTT-ATAATTTATAAATTTTTAA
1 TTTTTTGAAAATTTAT-AATTTTTAA
17990211 AACTGTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTTTGAAAATTTATAATTTTTAA
Found at i:17990582 original size:2 final size:2
Alignment explanation
Indices: 17990575--17990612 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17990565 TAACTAGCTT
17990575 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
17990613 ACACCTTCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17997518 original size:15 final size:16
Alignment explanation
Indices: 17997487--17997520 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17997477 AAAACTAAAC
*
17997487 CCCGAAAACTCAAAAA
1 CCCGAAAACTAAAAAA
17997503 CCCGAAAAC-AAAAAA
1 CCCGAAAACTAAAAAA
17997518 CCC
1 CCC
17997521 TTAAAATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.56, C:0.35, G:0.06, T:0.03
Consensus pattern (16 bp):
CCCGAAAACTAAAAAA
Found at i:18012436 original size:28 final size:28
Alignment explanation
Indices: 18012399--18012457 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
18012389 ATTTAGGGGA
18012399 TTTTAAAAGAATTAGAGGTTAAAAAGGT
1 TTTTAAAAGAATTAGAGGTTAAAAAGGT
* *
18012427 TTTTGAAAGAATTAGAGGTTAAAGAGGT
1 TTTTAAAAGAATTAGAGGTTAAAAAGGT
18012455 TTT
1 TTT
18012458 AAGTAATGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36
Consensus pattern (28 bp):
TTTTAAAAGAATTAGAGGTTAAAAAGGT
Found at i:18013579 original size:20 final size:18
Alignment explanation
Indices: 18013532--18013637 Score: 69
Period size: 18 Copynumber: 5.8 Consensus size: 18
18013522 TTATATAAAC
18013532 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
18013549 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
18013569 ATTAAATTAATAAATACT
1 ATTAAATTAATATTTAAT
18013587 ATTAAGA-TAAGTA-TTAA-
1 ATTAA-ATTAA-TATTTAAT
*
18013604 ATTAAAATTAATATTAAACT
1 ATT-AAATTAATATTTAA-T
*
18013624 ATTAAAATAATATT
1 ATTAAATTAATATT
18013638 ACTTTTGGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
17 14 0.20
18 22 0.31
19 16 0.23
20 18 0.26
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:18013638 original size:36 final size:36
Alignment explanation
Indices: 18013564--18013638 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
18013554 GATAATCACT
*
18013564 TTAATATTAAATTAATAAATACTATTAAGATAAGTA
1 TTAATATTAAATTAATAAATACTATTAAAATAAGTA
18013600 TTAA-ATTAAAATTAATATTAA-ACTATTAAAATAA-TA
1 TTAATATT-AAATTAATA--AATACTATTAAAATAAGTA
18013636 TTA
1 TTA
18013639 CTTTTGGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
35 3 0.09
36 18 0.51
37 12 0.34
38 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (36 bp):
TTAATATTAAATTAATAAATACTATTAAAATAAGTA
Found at i:18015271 original size:16 final size:16
Alignment explanation
Indices: 18015250--18015280 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18015240 CTATGCATGC
*
18015250 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
18015266 AAAATACAAAAGACA
1 AAAATACAAAAGACA
18015281 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:18018299 original size:27 final size:27
Alignment explanation
Indices: 18018269--18018337 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
18018259 ATTAAAAATA
*
18018269 AAAAATTAAGAAAAAATAA-AAT-TTTTT
1 AAAAATTAA-AAAAAA-AAGAATGATTTT
*
18018296 AAAATTTAAAAAAAAAAGAATGATTTT
1 AAAAATTAAAAAAAAAAGAATGATTTT
18018323 AAAAATATAAAAAAA
1 AAAAAT-TAAAAAAA
18018338 TTCCAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.25
27 17 0.47
28 8 0.22
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAAATTAAAAAAAAAAGAATGATTTT
Found at i:18029337 original size:27 final size:28
Alignment explanation
Indices: 18029274--18029335 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
18029264 ATTTTTTGGT
* **
18029274 ATATTTTGATAAATAAAAAAATTTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
18029302 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
18029330 ATATTT
1 ATATTT
18029336 GGGTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:18030896 original size:7 final size:7
Alignment explanation
Indices: 18030884--18030916 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
18030874 TGAGAAATTA
18030884 TTAGGGT
1 TTAGGGT
18030891 TTAGGGT
1 TTAGGGT
*
18030898 TTAGGAT
1 TTAGGGT
18030905 TTAGGGT
1 TTAGGGT
18030912 TTAGG
1 TTAGG
18030917 TATAGGTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.42
Consensus pattern (7 bp):
TTAGGGT
Found at i:18054631 original size:25 final size:25
Alignment explanation
Indices: 18054579--18054631 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
18054569 ATAAAATAAC
* * * *
18054579 TTAAATACTAAAATGGATAGAAAAA
1 TTAAATACCAAAATGAAAACAAAAA
*
18054604 TTAAATACCAAAATGAAAACAAATA
1 TTAAATACCAAAATGAAAACAAAAA
18054629 TTA
1 TTA
18054632 TTCAATGGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.25
Consensus pattern (25 bp):
TTAAATACCAAAATGAAAACAAAAA
Found at i:18058131 original size:211 final size:210
Alignment explanation
Indices: 18057711--18058337 Score: 988
Period size: 211 Copynumber: 3.0 Consensus size: 210
18057701 TATATGAAAA
*
18057711 ACTTAGAAAGGTTTAGCATATCAGTGTTGGACAAATGTCAGCATCCAAGATTGACTTGAGCCTGG
1 ACTTAGAAAGGTTTAGCATATCAGTGTTGGACAAATGTCAGCATCCAAGA-TCACTTGAGCCTGG
* * * *
18057776 GTAACATACCTCATACTGAATGAAGTAAAGAAAAAAAATTG-AAAAACCACATTCAATGGGAAAT
65 GTAACATAGCTCATACCGAATGAAGTAATGAAAACAAATTGAAAAAACCACATTCAATGGGAAAT
*
18057840 AAAGTACATGAAAGAATTGAAGATCATTCTTTTTGCAACCTTGGATTCAACCCAAGCAGTGAAGC
130 AAAGTACATGAAAGAATTGAAGATCATTCTTTTTGCAACATTGGATTCAACCCAAGCAGTGAAGC
18057905 AAACAAATAAAAGATTC
195 AAACAAAT-AAAGATTC
* * *
18057922 ACTTAGAAAGGTTTAGCATACCAGTGTTGGACAAAAGTCAGCATCCAAGAGTCACTTGAGCGTGG
1 ACTTAGAAAGGTTTAGCATATCAGTGTTGGACAAATGTCAGCATCCAAGA-TCACTTGAGCCTGG
* *
18057987 CTAACATAGCTCATACCAAATGAAGTAATGAAAACAAATTGAAAAAACCACATTCAATGGGAAAT
65 GTAACATAGCTCATACCGAATGAAGTAATGAAAACAAATTGAAAAAACCACATTCAATGGGAAAT
* * *
18058052 AAAGTACATGAGAGAACTGAAGATCATTCTTTTTGCAACATTGGATTCAACCCAAGCAGTGACGC
130 AAAGTACATGAAAGAATTGAAGATCATTCTTTTTGCAACATTGGATTCAACCCAAGCAGTGAAGC
18058117 AAACAAATAAAGATTC
195 AAACAAATAAAGATTC
* * * *
18058133 ACTTCGAAAGGTTTACCATATCAGTGTTAGACAAATGTCAGCAACCAAGATCCAC-TGAGCCTGG
1 ACTTAGAAAGGTTTAGCATATCAGTGTTGGACAAATGTCAGCATCCAAGAT-CACTTGAGCCTGG
* * *
18058197 GTAACATAGCTCATACCGAATGATGCAATGAAAACAAATTGAAAAAGCCACATTCAATGGGAAAT
65 GTAACATAGCTCATACCGAATGAAGTAATGAAAACAAATTGAAAAAACCACATTCAATGGGAAAT
* * *
18058262 AAAGTACATGAAAGGATTGAATATCATCCTTTTTGCAACATTGGATTCAACCCAAGCAGTGAAGC
130 AAAGTACATGAAAGAATTGAAGATCATTCTTTTTGCAACATTGGATTCAACCCAAGCAGTGAAGC
18058327 AAACAAATAAA
195 AAACAAATAAA
18058338 AGCTTCTCAT
Statistics
Matches: 381, Mismatches: 33, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
210 139 0.36
211 150 0.39
212 92 0.24
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (210 bp):
ACTTAGAAAGGTTTAGCATATCAGTGTTGGACAAATGTCAGCATCCAAGATCACTTGAGCCTGGG
TAACATAGCTCATACCGAATGAAGTAATGAAAACAAATTGAAAAAACCACATTCAATGGGAAATA
AAGTACATGAAAGAATTGAAGATCATTCTTTTTGCAACATTGGATTCAACCCAAGCAGTGAAGCA
AACAAATAAAGATTC
Found at i:18061028 original size:22 final size:22
Alignment explanation
Indices: 18061003--18061046 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18060993 ATTTTAAATT
18061003 TTAAAAATTTAAAAATAAAGTA
1 TTAAAAATTTAAAAATAAAGTA
** *
18061025 TTAAATCTTTGAAAATAAAGTA
1 TTAAAAATTTAAAAATAAAGTA
18061047 GGGACTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
TTAAAAATTTAAAAATAAAGTA
Found at i:18064067 original size:3 final size:3
Alignment explanation
Indices: 18064059--18064122 Score: 103
Period size: 3 Copynumber: 21.3 Consensus size: 3
18064049 TTTACTTAAG
*
18064059 ATT ATT ATT ATT ATT ATT AATT -TT ATT ATT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
18064104 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
18064123 CTACTACTAC
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:18065280 original size:76 final size:76
Alignment explanation
Indices: 18065128--18065272 Score: 227
Period size: 76 Copynumber: 1.9 Consensus size: 76
18065118 CACTCTCCCC
*
18065128 TATCTTACATTATATACAATATCTTTACATAAAAATCCCTAAACAATAAGTGTCTAAATACACCC
1 TATCTTACATTACATACAATATCTTTACATAAAAATCCCTAAACAATAAGTGTCTAAATACACCC
18065193 CAAACAACTAA
66 CAAACAACTAA
* * * * * *
18065204 TATCTTGCATTACATATAATATCTTTACATAAAAATCCCTAAATAATGAGTGTTTAAATGCACCC
1 TATCTTACATTACATACAATATCTTTACATAAAAATCCCTAAACAATAAGTGTCTAAATACACCC
18065269 CAAA
66 CAAA
18065273 TGGCTAATGA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (76 bp):
TATCTTACATTACATACAATATCTTTACATAAAAATCCCTAAACAATAAGTGTCTAAATACACCC
CAAACAACTAA
Found at i:18068537 original size:91 final size:90
Alignment explanation
Indices: 18068321--18068537 Score: 242
Period size: 89 Copynumber: 2.4 Consensus size: 90
18068311 ACATATCGGA
* * *
18068321 TTGCTCATAAGAGCTTTCCAA-TCGATAACATGCCAGATGCACATAGGAAAAAACTCGTATGCTA
1 TTGCTCATAAGAGCTTTCCAACT-GATAACAAGCCAGATGCACATAGGAAAAAACTCGTAGGCCA
* * *
18068385 AACATTTTCCCTGATAACATGCTAGT
65 AACATTCTCCCCGATAACACGCTAGT
* * * * **
18068411 TT-CTCATAAGAGCTTTCCAACAGATAATAAACCAGATGCACATAGTGCAAAGCCT-GTAGGCCA
1 TTGCTCATAAGAGCTTTCCAACTGATAACAAGCCAGATGCACATAG-GAAAAAACTCGTAGGCCA
* *
18068474 AACATTCTCCCACGGTAACACGTTAGT
65 AACATTCTCCC-CGATAACACGCTAGT
* *
18068501 TTGCTCATAAAAGCTTTCCAACTGATAACACGCCAGA
1 TTGCTCATAAGAGCTTTCCAACTGATAACAAGCCAGA
18068538 ATCTTCAAAG
Statistics
Matches: 104, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
89 54 0.52
90 21 0.20
91 29 0.28
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (90 bp):
TTGCTCATAAGAGCTTTCCAACTGATAACAAGCCAGATGCACATAGGAAAAAACTCGTAGGCCAA
ACATTCTCCCCGATAACACGCTAGT
Found at i:18080113 original size:24 final size:24
Alignment explanation
Indices: 18080081--18080132 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
18080071 TCTTTGGAAT
18080081 TGCCCCTGATGCCGTTACTTATAA
1 TGCCCCTGATGCCGTTACTTATAA
18080105 TGCCCCTGATGCCGTTACTTATAA
1 TGCCCCTGATGCCGTTACTTATAA
18080129 TGCC
1 TGCC
18080133 TTCATGAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (24 bp):
TGCCCCTGATGCCGTTACTTATAA
Found at i:18086597 original size:17 final size:15
Alignment explanation
Indices: 18086561--18086603 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
18086551 TTGATGCATA
*
18086561 AATATAACTAAGAAT
1 AATATAAATAAGAAT
18086576 AATATAAATAAGAAGCT
1 AATATAAATAAGAA--T
*
18086593 AATATATATAA
1 AATATAAATAA
18086604 TTAAATGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.54
17 11 0.46
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (15 bp):
AATATAAATAAGAAT
Found at i:18089095 original size:6 final size:6
Alignment explanation
Indices: 18089083--18089148 Score: 69
Period size: 6 Copynumber: 11.0 Consensus size: 6
18089073 AGAAATATTT
* * * * * * *
18089083 TATATA GATATA GATATA GAAATA CATACA TACATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
18089131 TATATA TATATA TATATA
1 TATATA TATATA TATATA
18089149 AGAAACAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (6 bp):
TATATA
Found at i:18089123 original size:4 final size:4
Alignment explanation
Indices: 18089083--18089148 Score: 69
Period size: 4 Copynumber: 16.5 Consensus size: 4
18089073 AGAAATATTT
* * * * * * *
18089083 TATA TAGA TATA GATA TAGA AATA CATA CATA CATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
18089131 TATA TATA TATA TATA TA
1 TATA TATA TATA TATA TA
18089149 AGAAACAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (4 bp):
TATA
Found at i:18091842 original size:33 final size:33
Alignment explanation
Indices: 18091800--18091867 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
18091790 TTTATTAAAG
18091800 TTGTCACATGTTATTCTTCGCATTCGCACATGT
1 TTGTCACATGTTATTCTTCGCATTCGCACATGT
*
18091833 TTGTCACATGTTATTCTTCTCATTCGCACATGT
1 TTGTCACATGTTATTCTTCGCATTCGCACATGT
18091866 TT
1 TT
18091868 TAAGACATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.46
Consensus pattern (33 bp):
TTGTCACATGTTATTCTTCGCATTCGCACATGT
Found at i:18094421 original size:27 final size:27
Alignment explanation
Indices: 18094391--18094750 Score: 408
Period size: 27 Copynumber: 13.4 Consensus size: 27
18094381 GGGTATAATA
* *
18094391 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCTTATGGGGGTATTTCG
* * *
18094418 GTCATTCTACCTTAT-AGGGTATTTTG
1 GTCATTTTACCTTATGGGGGTATTTCG
*
18094444 GTCATTTTACCTTGT-GGGGTATTTCG
1 GTCATTTTACCTTATGGGGGTATTTCG
*
18094470 GTCATTCTACCTTAT-GGGGTATTTCG
1 GTCATTTTACCTTATGGGGGTATTTCG
* *
18094496 GTCATTCTACCATA-GAGGGGTATTTCG
1 GTCATTTTACCTTATG-GGGGTATTTCG
* * * *
18094523 GTTAGTTTACCATATGAGGGTATTTCG
1 GTCATTTTACCTTATGGGGGTATTTCG
* *
18094550 GTCATTCTACCTTATGGGGGTATTTCA
1 GTCATTTTACCTTATGGGGGTATTTCG
*
18094577 GTCATTTTATCC-TATGGGGGTATTTCA
1 GTCATTTTA-CCTTATGGGGGTATTTCG
* * * *
18094604 GTCATTGTACCCTATAGGGGTATTTCA
1 GTCATTTTACCTTATGGGGGTATTTCG
* *
18094631 GTTATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCTTATGGGGGTATTTCG
18094658 G-CTATTTTACCTTATGGGGGTATTTCG
1 GTC-ATTTTACCTTATGGGGGTATTTCG
* * *
18094685 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCTTATGGGGGTATTTCG
* *
18094712 GTCATTCTATCTTATGGGGGTATTTCG
1 GTCATTTTACCTTATGGGGGTATTTCG
18094739 GTCATTTTACCT
1 GTCATTTTACCT
18094751 ATTTTAGGGT
Statistics
Matches: 286, Mismatches: 40, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
26 70 0.24
27 212 0.74
28 4 0.01
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCTTATGGGGGTATTTCG
Found at i:18103710 original size:34 final size:32
Alignment explanation
Indices: 18103667--18103760 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 32
18103657 AGATACAAAT
* *
18103667 TTTAGTTTTAGTTAATTTTATTTCAAGTTACTAAG
1 TTTA-TTTTAATTAATTTGATTTCAA--TACTAAG
** *
18103702 TTTATTTTAATTTCTTTGGTTTCAATACTAAG
1 TTTATTTTAATTAATTTGATTTCAATACTAAG
** *
18103734 TTTATTTTAATTTCTTTGGTTTCAATA
1 TTTATTTTAATTAATTTGATTTCAATA
18103761 TGCAACTCGA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
32 34 0.63
34 16 0.30
35 4 0.07
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (32 bp):
TTTATTTTAATTAATTTGATTTCAATACTAAG
Found at i:18103736 original size:32 final size:32
Alignment explanation
Indices: 18103695--18103760 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
18103685 TATTTCAAGT
18103695 TACTAAGTTTATTTTAATTTCTTTGGTTTCAA
1 TACTAAGTTTATTTTAATTTCTTTGGTTTCAA
18103727 TACTAAGTTTATTTTAATTTCTTTGGTTTCAA
1 TACTAAGTTTATTTTAATTTCTTTGGTTTCAA
18103759 TA
1 TA
18103761 TGCAACTCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (32 bp):
TACTAAGTTTATTTTAATTTCTTTGGTTTCAA
Found at i:18105155 original size:17 final size:17
Alignment explanation
Indices: 18105129--18105182 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
18105119 CTAGTTTGGT
18105129 TTTATCTATTTTAGTTA
1 TTTATCTATTTTAGTTA
* *
18105146 TTTGTCTATTTTA-TTG
1 TTTATCTATTTTAGTTA
* *
18105162 TTTATTTAGTTTAGTTA
1 TTTATCTATTTTAGTTA
18105179 TTTA
1 TTTA
18105183 ATTTTTATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.20, C:0.04, G:0.09, T:0.67
Consensus pattern (17 bp):
TTTATCTATTTTAGTTA
Found at i:18113913 original size:2 final size:2
Alignment explanation
Indices: 18113906--18113936 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18113896 TATCCTTAAA
18113906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18113937 CACAGAGCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18115582 original size:13 final size:13
Alignment explanation
Indices: 18115566--18115592 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18115556 CAAGAGGATA
18115566 CTCCCTCTCTTGC
1 CTCCCTCTCTTGC
18115579 CTCCCTCTCTTGC
1 CTCCCTCTCTTGC
18115592 C
1 C
18115593 ACCAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.56, G:0.07, T:0.37
Consensus pattern (13 bp):
CTCCCTCTCTTGC
Found at i:18120241 original size:41 final size:41
Alignment explanation
Indices: 18120172--18120316 Score: 218
Period size: 41 Copynumber: 3.5 Consensus size: 41
18120162 TTTAACATAT
* * *
18120172 TCACAGGCACTTAACCTGCTAAGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* *
18120213 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * *
18120254 TCACTGGCACTTAGCCTGCTAGACTTATAGCCTGTTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
18120295 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
18120317 ACGTAAAGTC
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
Found at i:18121033 original size:114 final size:114
Alignment explanation
Indices: 18120795--18121034 Score: 408
Period size: 114 Copynumber: 2.1 Consensus size: 114
18120785 ATACATATTC
* *
18120795 ATATATACATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTT
1 ATATATATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTC
* *
18120860 ATATACTTTCAATTATAGCTCATCAAATATACAATAGATATACATATAT
66 ATATACTTTCAATTATAGCTCATCAAATATACAATAGATATACACACAT
* *
18120909 ATTTACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTC
1 ATATATATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTC
* *
18120974 ATATATTTTTAATTATAGCTCATCAAATATACAATAGATATACACACAT
66 ATATACTTTCAATTATAGCTCATCAAATATACAATAGATATACACACAT
18121023 ATATATATATAT
1 ATATATATATAT
18121035 ATATGCTGAT
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 116 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (114 bp):
ATATATATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTC
ATATACTTTCAATTATAGCTCATCAAATATACAATAGATATACACACAT
Found at i:18122030 original size:13 final size:13
Alignment explanation
Indices: 18122012--18122036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18122002 CAATCAAATG
18122012 CACACAAAATAAA
1 CACACAAAATAAA
18122025 CACACAAAATAA
1 CACACAAAATAA
18122037 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:18127858 original size:41 final size:41
Alignment explanation
Indices: 18127714--18127860 Score: 224
Period size: 41 Copynumber: 3.6 Consensus size: 41
18127704 TTTAACATAT
*
18127714 TCACCGGCACTTATCCTGCTA-AGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGA-CTTATAGCCTGATTCAGA
** *
18127755 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTCAGA
* *
18127796 TCACCGGCACTTAGCCTGCTAGACTTACAGCCTGTTTCAGA
1 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTCAGA
18127837 TCACCGGCACTTAGCCTGCTAGAC
1 TCACCGGCACTTAGCCTGCTAGAC
18127861 GTAAAGTCTG
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTCAGA
Found at i:18127912 original size:40 final size:40
Alignment explanation
Indices: 18127796--18127919 Score: 99
Period size: 40 Copynumber: 3.1 Consensus size: 40
18127786 CTGATTCAGA
** * ** *
18127796 TCACCGGCACTTAGCCTGCTAGACTTACAGCCTGTTTCAGA-
1 TCACCGGCACTTAGCCTGCTAGACGCAAAGCCTG--AAAAAT
* *
18127837 TCACCGGCACTTAGCCTGCTAGACGTAAAGTCTGAAAAAT
1 TCACCGGCACTTAGCCTGCTAGACGCAAAGCCTGAAAAAT
* ** *
18127877 TCACCGGCA-TTAAGCCTGCTAGGCGCCTAGCCTGAAAATT
1 TCACCGGCACTT-AGCCTGCTAGACGCAAAGCCTGAAAAAT
18127917 TCA
1 TCA
18127920 ATTTCACAGA
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
39 4 0.06
40 34 0.49
41 31 0.45
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
TCACCGGCACTTAGCCTGCTAGACGCAAAGCCTGAAAAAT
Found at i:18128444 original size:114 final size:113
Alignment explanation
Indices: 18128326--18128575 Score: 396
Period size: 114 Copynumber: 2.2 Consensus size: 113
18128316 CTCAAGATCT
18128326 TATACATATTCATATATACATATTCGAACCTCATTTATGCATATATATAACATTCATACTTAACT
1 TATACATATT-ATATATACATATTCGAACCTCATTTATGCATATATATAACATTCATACTTAACT
*
18128391 AATTTCAATTTATATACTTTCAATTATAGCTCATCAAATATACAATAGA
65 AATTTCAATTCATATACTTTCAATTATAGCTCATCAAATATACAATAGA
* *
18128440 TATACATA-TATATTTACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
1 TATACATATTATATATAC--ATATTCGAACCTCATTTATGCATATATATAACATTCATACTTAAC
* *
18128504 TAATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
64 TAATTTCAATTCATATACTTTCAATTATAGCTCATCAAATATACAATAGA
*
18128554 TATACA-ATAGATATATACATAT
1 TATACATAT-TATATATACATAT
18128576 ATATATGCTG
Statistics
Matches: 125, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
112 7 0.06
113 6 0.05
114 105 0.84
115 7 0.06
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.40
Consensus pattern (113 bp):
TATACATATTATATATACATATTCGAACCTCATTTATGCATATATATAACATTCATACTTAACTA
ATTTCAATTCATATACTTTCAATTATAGCTCATCAAATATACAATAGA
Found at i:18128558 original size:11 final size:11
Alignment explanation
Indices: 18128542--18128568 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
18128532 AGCTCATCAA
18128542 ATATACAATAG
1 ATATACAATAG
18128553 ATATACAATAG
1 ATATACAATAG
18128564 ATATA
1 ATATA
18128569 TACATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (11 bp):
ATATACAATAG
Found at i:18130945 original size:27 final size:25
Alignment explanation
Indices: 18130906--18130966 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
18130896 AAAAATATGT
* * *
18130906 TAAAATATGTTATCTTAATAATTAAG
1 TAAAATATATTAT-ATAATAATAAAG
*
18130932 TAAATATATATTATATAATAATAAAT
1 TAAA-ATATATTATATAATAATAAAG
18130958 TAAAATATA
1 TAAAATATA
18130967 ATAATAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 17 0.57
27 8 0.27
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (25 bp):
TAAAATATATTATATAATAATAAAG
Found at i:18131037 original size:4 final size:4
Alignment explanation
Indices: 18131030--18131079 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
18131020 ATTAGAAATT
**
18131030 AGAA AGAA AG-A A-AA AGAA AGAA A-AA TAGAA AGAA AGAA AGGG AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA -AGAA AGAA AGAA AGAA AGAA
18131076 AGAA
1 AGAA
18131080 GAGACGCATG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 6 0.16
4 30 0.79
5 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:18133102 original size:21 final size:21
Alignment explanation
Indices: 18133078--18133117 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18133068 CTAGGATGAT
*
18133078 TGTTTTAGCATGTTTTGAATA
1 TGTTTGAGCATGTTTTGAATA
* *
18133099 TGTTTGATCGTGTTTTGAA
1 TGTTTGAGCATGTTTTGAA
18133118 CAGATTAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.05, G:0.23, T:0.53
Consensus pattern (21 bp):
TGTTTGAGCATGTTTTGAATA
Found at i:18134485 original size:29 final size:27
Alignment explanation
Indices: 18134422--18134474 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
18134412 ATATGTGCCC
*
18134422 ATCAAGTTCATGCAAATATACATGAAA
1 ATCAAGTTCATGCAAATATACATAAAA
*
18134449 ATCAAGTTCATGCAAATATATATAAA
1 ATCAAGTTCATGCAAATATACATAAA
18134475 TAATTGAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.28
Consensus pattern (27 bp):
ATCAAGTTCATGCAAATATACATAAAA
Found at i:18145194 original size:38 final size:38
Alignment explanation
Indices: 18145143--18145219 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
18145133 GTGTGGTGGG
* *
18145143 GGAGTGTTGGAGTGATTTTATGAGGAAAATATGGGATT
1 GGAGTGTTGGAGTGATTTTAGGAGAAAAATATGGGATT
18145181 GGAGTGTTGGAGTGATTTTAGGAGAAAAATATGGGATT
1 GGAGTGTTGGAGTGATTTTAGGAGAAAAATATGGGATT
18145219 G
1 G
18145220 TGGAGTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (38 bp):
GGAGTGTTGGAGTGATTTTAGGAGAAAAATATGGGATT
Found at i:18149399 original size:23 final size:23
Alignment explanation
Indices: 18149372--18149441 Score: 140
Period size: 23 Copynumber: 3.0 Consensus size: 23
18149362 AATATAAGTA
18149372 TAATTCAAGTTTTAAGGTCGATT
1 TAATTCAAGTTTTAAGGTCGATT
18149395 TAATTCAAGTTTTAAGGTCGATT
1 TAATTCAAGTTTTAAGGTCGATT
18149418 TAATTCAAGTTTTAAGGTCGATT
1 TAATTCAAGTTTTAAGGTCGATT
18149441 T
1 T
18149442 TTTATCAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (23 bp):
TAATTCAAGTTTTAAGGTCGATT
Found at i:18149405 original size:45 final size:46
Alignment explanation
Indices: 18149327--18149441 Score: 135
Period size: 46 Copynumber: 2.5 Consensus size: 46
18149317 AGACATGCTT
* *
18149327 TAATTCAAGCTTTAAGGTCGATTTAATGAAAG-TTAAATATA-AGTA
1 TAATTCAAGTTTTAAGGTCGATTTAATGAAAGTTTAAAGATAGA-TA
** * * * *
18149372 TAATTCAAGTTTTAAGGTCGATTTAATTCAAGTTTTAAGGTCGATT
1 TAATTCAAGTTTTAAGGTCGATTTAATGAAAGTTTAAAGATAGATA
18149418 TAATTCAAGTTTTAAGGTCGATTT
1 TAATTCAAGTTTTAAGGTCGATTT
18149442 TTTATCAAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 29 0.48
46 30 0.50
47 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.41
Consensus pattern (46 bp):
TAATTCAAGTTTTAAGGTCGATTTAATGAAAGTTTAAAGATAGATA
Found at i:18163238 original size:31 final size:31
Alignment explanation
Indices: 18163188--18163262 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
18163178 AAAGTTTTCA
* * * * *
18163188 ATTTTGGTTACTAATGTTTTACATTATTTTT
1 ATTTTGGTCACTCACGTTTTACATCATTTAT
* *
18163219 ATTTTGGTCACTCACGTTTTAGATCGTTTAT
1 ATTTTGGTCACTCACGTTTTACATCATTTAT
18163250 ATTTTGGTCACTC
1 ATTTTGGTCACTC
18163263 TCTATTAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (31 bp):
ATTTTGGTCACTCACGTTTTACATCATTTAT
Found at i:18164471 original size:2 final size:2
Alignment explanation
Indices: 18164464--18164508 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
18164454 ATATAATCTC
18164464 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
18164506 TA T
1 TA T
18164509 GGCATCTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18171119 original size:13 final size:13
Alignment explanation
Indices: 18171101--18171125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18171091 ATTGAAAACA
18171101 CTTTTATTTTCTG
1 CTTTTATTTTCTG
18171114 CTTTTATTTTCT
1 CTTTTATTTTCT
18171126 TGCCTATTAT
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:0.08, C:0.16, G:0.04, T:0.72
Consensus pattern (13 bp):
CTTTTATTTTCTG
Found at i:18173694 original size:30 final size:31
Alignment explanation
Indices: 18173644--18173701 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
18173634 TTTCTGAGCC
* *
18173644 TAGGGGCAAAATCATAATTTTTGTAAAACTT
1 TAGGGGAAAAATCATAATTTTTCTAAAACTT
*
18173675 TAGGGGAAAAAT-GTAATTTTTCTAAAA
1 TAGGGGAAAAATCATAATTTTTCTAAAA
18173702 TGTGATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (31 bp):
TAGGGGAAAAATCATAATTTTTCTAAAACTT
Found at i:18173996 original size:50 final size:50
Alignment explanation
Indices: 18173942--18174128 Score: 179
Period size: 50 Copynumber: 3.7 Consensus size: 50
18173932 GATGGTCACG
*
18173942 TGTGTAATACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTTGCA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTTGCA
* * *
18173992 TGTGTAGTACTATGTGCAGGCTACTATGCGTACC-G---GATAGTTTCGATCA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTT-G--CA
* * **
18174041 CGTGTGTAGTACTATGTGCA-GCTACTACGTGTATCGGATAGTGAT-GGTCACA
1 --TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTTGCA
* *
18174093 TGTGTAGTACTATGTGCAGGCTACTATGTGAACCAG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAG
18174129 TATCATTAAT
Statistics
Matches: 111, Mismatches: 14, Indels: 23
0.75 0.09 0.16
Matches are distributed among these distances:
46 7 0.06
47 1 0.01
49 3 0.03
50 61 0.55
51 32 0.29
52 2 0.02
55 2 0.02
56 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTTGCA
Found at i:18174054 original size:101 final size:101
Alignment explanation
Indices: 18173937--18174120 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
18173927 AAAGTGATGG
**
18173937 TCACGTGTGTAATACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTTGCATGTGTAGT
1 TCACGTGTGTAATACTATGTGCA-GCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
18174000 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
64 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
* * *
18174038 TCACGTGTGTAGTACTATGTGCAGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTAC
1 TCACGTGTGTAATACTATGTGCAGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTAC
18174103 TATGTGCAGGCTACTATG
66 TATGTGCAGGCTACTATG
18174121 TGAACCAGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
100 16 0.21
101 56 0.74
102 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (101 bp):
TCACGTGTGTAATACTATGTGCAGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:18174367 original size:16 final size:16
Alignment explanation
Indices: 18174346--18174377 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18174336 TGATTGAAAG
*
18174346 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
18174362 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
18174378 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:18181590 original size:20 final size:21
Alignment explanation
Indices: 18181567--18181622 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
18181557 AATAAATTTG
*
18181567 TAATAATTTATTTAAA-TAAA
1 TAATAATTAATTTAAATTAAA
18181587 TAATAATTAATTTCAAATTAAA
1 TAATAATTAATTT-AAATTAAA
*
18181609 AAAT-ATTAATTTAA
1 TAATAATTAATTTAA
18181623 GTAATTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.44
21 11 0.34
22 7 0.22
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATAATTAATTTAAATTAAA
Found at i:18184132 original size:20 final size:20
Alignment explanation
Indices: 18184107--18184149 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
18184097 ATATAGTAAT
18184107 TAGTTGTAACCCCCTAATTC
1 TAGTTGTAACCCCCTAATTC
* *
18184127 TAGTTGTAATCTCCTAATTC
1 TAGTTGTAACCCCCTAATTC
18184147 TAG
1 TAG
18184150 GATAGTTCCT
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:0.26, C:0.23, G:0.12, T:0.40
Consensus pattern (20 bp):
TAGTTGTAACCCCCTAATTC
Found at i:18191288 original size:15 final size:15
Alignment explanation
Indices: 18191268--18191305 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
18191258 CTTCTTTTAC
*
18191268 TATTATTTTATTCTT
1 TATTATTTTATTATT
*
18191283 TATTATTCTATTATT
1 TATTATTTTATTATT
18191298 T-TTATTTT
1 TATTATTTT
18191306 CTTTAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTATTTTATTATT
Found at i:18191297 original size:26 final size:27
Alignment explanation
Indices: 18191268--18191330 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
18191258 CTTCTTTTAC
*
18191268 TATTATTT-TATTCTTTATTATTCTA-T
1 TATTATTTATATTCTTTAATATT-TATT
*
18191294 TATT-TTTATTTTCTTTAATATTTATT
1 TATTATTTATATTCTTTAATATTTATT
18191320 TATTTATTTAT
1 TA-TTATTTAT
18191331 TTATTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 5 0.16
26 19 0.61
27 2 0.06
28 5 0.16
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (27 bp):
TATTATTTATATTCTTTAATATTTATT
Found at i:18191321 original size:4 final size:4
Alignment explanation
Indices: 18191312--18191340 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
18191302 TTTTCTTTAA
18191312 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
18191341 TCCTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:18196626 original size:9 final size:9
Alignment explanation
Indices: 18196603--18196634 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
18196593 GAGTTAAATG
18196603 AATCGAGTT
1 AATCGAGTT
18196612 -ATCGAGTT
1 AATCGAGTT
18196620 AATCGAGTT
1 AATCGAGTT
18196629 AATCGA
1 AATCGA
18196635 ATCAACTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (9 bp):
AATCGAGTT
Found at i:18196713 original size:9 final size:9
Alignment explanation
Indices: 18196687--18196723 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
18196677 TGAGTTTTCA
18196687 AATTTGAAT
1 AATTTGAAT
* *
18196696 AACTCGAAT
1 AATTTGAAT
18196705 AATTTGAAT
1 AATTTGAAT
18196714 AATTTGAAT
1 AATTTGAAT
18196723 A
1 A
18196724 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (9 bp):
AATTTGAAT
Found at i:18196966 original size:30 final size:31
Alignment explanation
Indices: 18196932--18196991 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
18196922 AAACCTTTTA
*
18196932 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
18196962 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
18196992 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:18197260 original size:9 final size:9
Alignment explanation
Indices: 18197246--18197274 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
18197236 AATTTCGTAT
18197246 TTTATATTA
1 TTTATATTA
18197255 TTTATATTA
1 TTTATATTA
18197264 TTTATATTA
1 TTTATATTA
18197273 TT
1 TT
18197275 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:18199315 original size:27 final size:27
Alignment explanation
Indices: 18199256--18199316 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
18199246 ATCAATTATG
18199256 GAATTAAGAAATAAAAATATTGATAATT
1 GAATT-AGAAATAAAAATATTGATAATT
* * *
18199284 AAATTAGAAATAAAATTATTTAGTAA-T
1 GAATTAGAAATAAAAATATTGA-TAATT
18199311 GAATTA
1 GAATTA
18199317 AATAGAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (27 bp):
GAATTAGAAATAAAAATATTGATAATT
Found at i:18202649 original size:27 final size:26
Alignment explanation
Indices: 18202619--18202680 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
18202609 CCTAAAAGGG
* * *
18202619 TAAAATGACCTTAACTCCCTTGTAGGC
1 TAAAATGACCGTAACTCCC-TATAGGA
* *
18202646 TAAAATGATCGTAATTCCCTATAGGA
1 TAAAATGACCGTAACTCCCTATAGGA
18202672 TAAAATGAC
1 TAAAATGAC
18202681 TATTTTACCC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (26 bp):
TAAAATGACCGTAACTCCCTATAGGA
Found at i:18202815 original size:24 final size:24
Alignment explanation
Indices: 18202698--18202831 Score: 153
Period size: 24 Copynumber: 5.6 Consensus size: 24
18202688 CCCCTCAGGG
* *
18202698 TTAAATGATTGATTTGCCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
* * *
18202722 GTAAATGAATGATTTGT-TCGAGAT
1 TTAAATGACTGATTTGTCT-GTGAT
* *
18202746 GTAAATGACTGATTTGTCTATGAT
1 TTAAATGACTGATTTGTCTGTGAT
*
18202770 TTAAATGACTGATTTCTCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
*
18202794 TTAAATGACTGATTTGTTTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
**
18202818 TTGTATGACTGATT
1 TTAAATGACTGATT
18202832 CCGTGCATGG
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.01
24 92 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.45
Consensus pattern (24 bp):
TTAAATGACTGATTTGTCTGTGAT
Found at i:18202951 original size:26 final size:26
Alignment explanation
Indices: 18202922--18202973 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
18202912 TGCCACAATC
*
18202922 ACTGTTACTGGTAGCTTTGCTACGAT
1 ACTGTTACTGGCAGCTTTGCTACGAT
* *
18202948 ACTGTTGCTGGCAGCTTTGCTGCGAT
1 ACTGTTACTGGCAGCTTTGCTACGAT
18202974 GCTACTGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.37
Consensus pattern (26 bp):
ACTGTTACTGGCAGCTTTGCTACGAT
Found at i:18203020 original size:32 final size:32
Alignment explanation
Indices: 18202976--18203306 Score: 307
Period size: 32 Copynumber: 10.4 Consensus size: 32
18202966 GCTGCGATGC
18202976 TACTGATGGCTTTGTGCCGATCATAGTA-TCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACT-GT
* * * *
18203008 TATTGATGGCTTTGTGTCTATCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACTGT
* * * **
18203040 TATTGATGGTTTTGTACCGATCATAGTACCAT
1 TACTGATGGCTTTGTGCCGATCATAGTACTGT
*
18203072 TACTGATGGCTTTGTGTCGATCATAGTA-TCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACT-GT
* * * * *
18203104 TACTGATAGTTTTGTGCTGATCATATTACAGT
1 TACTGATGGCTTTGTGCCGATCATAGTACTGT
* * *
18203136 TACTGATGAG-TGTGTGCCGATCAT-TTCACTAT
1 TACTGATG-GCTTTGTGCCGATCATAGT-ACTGT
* *
18203168 TACTGATGGCTGTGTGCCGATCATA-TCACTGC
1 TACTGATGGCTTTGTGCCGATCATAGT-ACTGT
18203200 TACTGATGGCTTTGTGCCGATCAT-GTTACTGT
1 TACTGATGGCTTTGTGCCGATCATAG-TACTGT
* ** *
18203232 TACTGATGGTTTTGTGCCGATCATAACACTGC
1 TACTGATGGCTTTGTGCCGATCATAGTACTGT
* * *
18203264 TACTGATGGCTTTGTGCCAATCACATTACTG-
1 TACTGATGGCTTTGTGCCGATCATAGTACTGT
*
18203295 TACTTATGGCTT
1 TACTGATGGCTT
18203307 GTAGTCATTC
Statistics
Matches: 249, Mismatches: 40, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
31 14 0.06
32 233 0.94
33 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATAGTACTGT
Found at i:18203143 original size:96 final size:96
Alignment explanation
Indices: 18202976--18203286 Score: 353
Period size: 96 Copynumber: 3.2 Consensus size: 96
18202966 GCTGCGATGC
* * *
18202976 TACTGATGGCTTTGTGCCGATCATAGTATCGTTATTGATGGCTTTGTGTCT-ATCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTATCGTTACTGATGGCTTTGTG-CTGATCATATTACAGT
* * * *
18203040 TATTGATGGTTTTGTACCGATCATAGTACCAT
65 TACTGATGGTTTTGTGCCGATCATAATACTAT
* * *
18203072 TACTGATGGCTTTGTGTCGATCATAGTATCGTTACTGATAGTTTTGTGCTGATCATATTACAGTT
1 TACTGATGGCTTTGTGCCGATCATAGTATCGTTACTGATGGCTTTGTGCTGATCATATTACAGTT
* *
18203137 ACTGATGAG-TGTGTGCCGATCAT-TTCACTAT
66 ACTGATG-GTTTTGTGCCGATCATAAT-ACTAT
* * * * *
18203168 TACTGATGGCTGTGTGCCGATCATA-TCA-CTGCTACTGATGGCTTTGTGCCGATCATGTTACTG
1 TACTGATGGCTTTGTGCCGATCATAGT-ATC-GTTACTGATGGCTTTGTGCTGATCATATTACAG
* **
18203231 TTACTGATGGTTTTGTGCCGATCATAACACTGC
64 TTACTGATGGTTTTGTGCCGATCATAATACTAT
*
18203264 TACTGATGGCTTTGTGCCAATCA
1 TACTGATGGCTTTGTGCCGATCA
18203287 CATTACTGTA
Statistics
Matches: 182, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
95 6 0.03
96 175 0.96
97 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (96 bp):
TACTGATGGCTTTGTGCCGATCATAGTATCGTTACTGATGGCTTTGTGCTGATCATATTACAGTT
ACTGATGGTTTTGTGCCGATCATAATACTAT
Found at i:18203556 original size:28 final size:28
Alignment explanation
Indices: 18203523--18203627 Score: 135
Period size: 28 Copynumber: 3.9 Consensus size: 28
18203513 CATACTGATA
* * *
18203523 CTGTATCGGGCTTAGGTCCACACTGTTT
1 CTGTATTGGGCTAAGGCCCACACTGTTT
* *
18203551 CTGTATTGGTCTAAGGCCCACACTATTT
1 CTGTATTGGGCTAAGGCCCACACTGTTT
18203579 CTGTATTGGGCTAAGGCCCACACTGTTT
1 CTGTATTGGGCTAAGGCCCACACTGTTT
*
18203607 CTATATTGGG--AAGG-CCACACT
1 CTGTATTGGGCTAAGGCCCACACT
18203628 ATACTGTTAC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
25 7 0.10
26 4 0.06
28 58 0.84
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (28 bp):
CTGTATTGGGCTAAGGCCCACACTGTTT
Found at i:18204440 original size:21 final size:21
Alignment explanation
Indices: 18204414--18204454 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18204404 TTCTACCTTA
18204414 ATGTCTCAAAACAACAAGAAC
1 ATGTCTCAAAACAACAAGAAC
* *
18204435 ATGTCTCGATACAACAAGAA
1 ATGTCTCAAAACAACAAGAA
18204455 AATTTTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.12, T:0.17
Consensus pattern (21 bp):
ATGTCTCAAAACAACAAGAAC
Found at i:18222978 original size:2 final size:2
Alignment explanation
Indices: 18222971--18223007 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18222961 TTTCTCACCA
18222971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18223008 AGGAAAGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18223712 original size:18 final size:17
Alignment explanation
Indices: 18223685--18223719 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18223675 TATTATAATT
*
18223685 AAATAAAAATTCATTCA
1 AAATAAAAATTAATTCA
18223702 AAATAAAAAATTAATTCA
1 AAAT-AAAAATTAATTCA
18223720 GGTGATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAAAATTAATTCA
Found at i:18224190 original size:14 final size:15
Alignment explanation
Indices: 18224156--18224194 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
18224146 AAAGTTAGAT
*
18224156 TATATAAATTTATTA
1 TATATAAAATTATTA
*
18224171 TTTATAAAATT-TTA
1 TATATAAAATTATTA
18224185 TATATAAAAT
1 TATATAAAAT
18224195 ATAAAATTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATAAAATTATTA
Found at i:18224854 original size:11 final size:11
Alignment explanation
Indices: 18224838--18224924 Score: 60
Period size: 11 Copynumber: 8.3 Consensus size: 11
18224828 TCAATTATTT
18224838 TCTCAATTTCC
1 TCTCAATTTCC
*
18224849 TCTCAATCTCC
1 TCTCAATTTCC
18224860 TCTCAATTTCC
1 TCTCAATTTCC
18224871 T-TCTAAGTTT-C
1 TCTC-AA-TTTCC
*
18224882 TCTCAA-ATCC
1 TCTCAATTTCC
* **
18224892 -AT--ATTTAA
1 TCTCAATTTCC
*
18224900 TCTCAATTTGC
1 TCTCAATTTCC
18224911 TCTCAATTTCC
1 TCTCAATTTCC
18224922 TCT
1 TCT
18224925 TAAATTTCTC
Statistics
Matches: 57, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 3 0.05
11 44 0.77
12 5 0.09
ACGTcount: A:0.22, C:0.31, G:0.02, T:0.45
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:18224905 original size:51 final size:51
Alignment explanation
Indices: 18224849--18224948 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
18224839 CTCAATTTCC
*
18224849 TCTCAATCTCCTCTCAATTTCCT-TCTAAGTTTCTCTCAAATCCATATTTAA
1 TCTCAATCTCCTCTCAATTTCCTCT-TAAATTTCTCTCAAATCCATATTTAA
* * * *
18224900 TCTCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATCTCCTCTCAATTTCCTCTTAAATTTCTCTCAAATCCATATTT
18224949 TTAATTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.02, T:0.46
Consensus pattern (51 bp):
TCTCAATCTCCTCTCAATTTCCTCTTAAATTTCTCTCAAATCCATATTTAA
Found at i:18227722 original size:36 final size:36
Alignment explanation
Indices: 18227681--18227869 Score: 234
Period size: 36 Copynumber: 5.0 Consensus size: 36
18227671 TAGCTTTAGC
18227681 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
1 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
* *
18227717 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 TACACTTATCTGATCAAGTGAAAAAGTGATAA---GT-G---T
18227760 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
1 ---TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
* *
18227799 TATACTTATCTGATCAAGTGAAAAAGTGATAAGTGC
1 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
* *
18227835 TATACTTATCTGATCAAGTGAGAAAGTGATAAGTG
1 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTG
18227870 GTAGCCTTAG
Statistics
Matches: 136, Mismatches: 7, Indels: 20
0.83 0.04 0.12
Matches are distributed among these distances:
36 98 0.72
39 3 0.02
40 1 0.01
42 1 0.01
43 3 0.02
46 30 0.22
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.30
Consensus pattern (36 bp):
TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
Found at i:18227780 original size:82 final size:81
Alignment explanation
Indices: 18227643--18227958 Score: 366
Period size: 82 Copynumber: 3.9 Consensus size: 81
18227633 TTTGAGTACT
*
18227643 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGAAAAAGT
18227708 GATAAGTGTTACACTTA
65 GATAAGTGTTACACTTA
18227725 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
18227790 GATAAGTGTTATACTTA
65 GATAAGTGTTACACTTA
* * *
18227807 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTATCTGATCAAGTGAGAAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
18227863 ATAAGTGGTAGCCTTAGCTACACTTA
66 ATAA---GT-G---T---TACACTTA
* * * *
18227889 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AG-GGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
18227952 ATAAGTG
66 ATAAGTG
18227959 ATTATACGTA
Statistics
Matches: 205, Mismatches: 10, Indels: 35
0.82 0.04 0.14
Matches are distributed among these distances:
72 28 0.14
74 1 0.00
75 2 0.01
76 3 0.01
78 2 0.01
79 3 0.01
82 132 0.64
85 3 0.01
86 4 0.02
87 2 0.01
89 11 0.05
90 2 0.01
91 12 0.06
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (81 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
ATAAGTGTTACACTTA
Found at i:18227892 original size:118 final size:118
Alignment explanation
Indices: 18227684--18227915 Score: 410
Period size: 118 Copynumber: 2.0 Consensus size: 118
18227674 CTTTAGCTAC
*
18227684 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTACACTTATCTGATCAAGAGACAAAGTGATAA
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAA
*
18227749 GTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
66 GTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
* * *
18227802 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGAGAAAGTGATAA
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAA
*
18227867 GTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
66 GTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTG
18227916 GTAGCCTAGC
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 108 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (118 bp):
ACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAA
GTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
Found at i:18227941 original size:45 final size:46
Alignment explanation
Indices: 18227833--18227958 Score: 204
Period size: 46 Copynumber: 2.8 Consensus size: 46
18227823 AGTGATAAGT
* *
18227833 GCTATACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
18227879 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCC-TA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
*
18227924 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
18227959 ATTATACGTA
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
43 12 0.16
44 5 0.06
45 19 0.25
46 41 0.53
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
Found at i:18228603 original size:24 final size:24
Alignment explanation
Indices: 18228571--18228619 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
18228561 AGCCCATGAA
18228571 CACCCCTAAACCCTAAACTATAAT
1 CACCCCTAAACCCTAAACTATAAT
18228595 CACCCCTAAACCCTAAACTATAAT
1 CACCCCTAAACCCTAAACTATAAT
18228619 C
1 C
18228620 CCTTATACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (24 bp):
CACCCCTAAACCCTAAACTATAAT
Found at i:18229270 original size:6 final size:6
Alignment explanation
Indices: 18229259--18229300 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
18229249 ATAATAATTA
*
18229259 TATATT TATATT TATATT TATATT TATATT TATATT TTTATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT
18229301 GAATTACTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATATT
Found at i:18230274 original size:26 final size:25
Alignment explanation
Indices: 18230227--18230275 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
18230217 ATTAATATAT
* *
18230227 TTAAAAAATTTTAATTCGATTAAAG
1 TTAAAAAATTTCAATTCAATTAAAG
*
18230252 TTAAAAAATATTCAATTTAATTAA
1 TTAAAAAAT-TTCAATTCAATTAA
18230276 TAACCAATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (25 bp):
TTAAAAAATTTCAATTCAATTAAAG
Found at i:18232613 original size:18 final size:18
Alignment explanation
Indices: 18232590--18232625 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18232580 TTCCCTTCTA
18232590 ATTTCTCACTCAAATTTT
1 ATTTCTCACTCAAATTTT
* *
18232608 ATTTCTCTCTCAACTTTT
1 ATTTCTCACTCAAATTTT
18232626 TTTTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTCTCACTCAAATTTT
Found at i:18234703 original size:34 final size:34
Alignment explanation
Indices: 18234660--18234729 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
18234650 GGAGCTAGAA
*
18234660 TTTTATCACATCAGTTTGTTCAATTTAATTTTGT
1 TTTTATCACATAAGTTTGTTCAATTTAATTTTGT
18234694 TTTTATCACATAAGTTTGTTCAATTTAATTTTGT
1 TTTTATCACATAAGTTTGTTCAATTTAATTTTGT
18234728 TT
1 TT
18234730 CTGCTTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.24, C:0.10, G:0.09, T:0.57
Consensus pattern (34 bp):
TTTTATCACATAAGTTTGTTCAATTTAATTTTGT
Found at i:18236686 original size:50 final size:50
Alignment explanation
Indices: 18236611--18236746 Score: 173
Period size: 50 Copynumber: 2.7 Consensus size: 50
18236601 ATTTGGGTAA
* *
18236611 AGAGGTCCCATGTAAGACTATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCACGTAAGACTATGTCTGGGACATGGCATGGGCACCGAGATG
* *
18236661 AGAGGTCCCCCGTAAGACTATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCACGTAAGACTATGTCTGGGACATGGCATGGGCACCGAGATG
** * * * *
18236711 AGAACATCTCATGTAAGACCATGTCTAGGACATGGC
1 AG-AGGTCCCACGTAAGACTATGTCTGGGACATGGC
18236747 TTTGGCATGT
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 48 0.65
51 26 0.35
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCACGTAAGACTATGTCTGGGACATGGCATGGGCACCGAGATG
Found at i:18246407 original size:2 final size:2
Alignment explanation
Indices: 18246402--18246430 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18246392 ATAATAAAGT
18246402 TA TA TA -A 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
18246431 AAATATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:18246418 original size:13 final size:13
Alignment explanation
Indices: 18246389--18246441 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
18246379 TATCAAAGCG
*
18246389 TATATAATAAAGT-
1 TATATAATATA-TA
18246402 TATATAATATATA
1 TATATAATATATA
18246415 TATAT-ATATATA
1 TATATAATATATA
* *
18246427 TATAAAATATGTA
1 TATATAATATATA
18246440 TA
1 TA
18246442 GGCATCTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 12 0.34
13 23 0.66
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (13 bp):
TATATAATATATA
Found at i:18246482 original size:15 final size:17
Alignment explanation
Indices: 18246464--18246500 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
18246454 ATATAGAAAT
*
18246464 AAATACAAATA-AA-CA
1 AAATAAAAATATAAGCA
18246479 AAATAAAAATATAAGCA
1 AAATAAAAATATAAGCA
18246496 AAATA
1 AAATA
18246501 TATTAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 2 0.11
17 7 0.37
ACGTcount: A:0.73, C:0.08, G:0.03, T:0.16
Consensus pattern (17 bp):
AAATAAAAATATAAGCA
Done.