Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014477.1 Kokia drynarioides strain JFW-HI SEQ_129516, 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: 219697
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:4544 original size:51 final size:50
Alignment explanation
Indices: 4471--4597 Score: 173
Period size: 51 Copynumber: 2.5 Consensus size: 50
4461 TGAAAAGGTC
* * *
4471 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAAGTT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATT-AAAGAT
* *
4522 CGATGACTAAGTGTCATTGTGAGTAAATGAATCCATGATGGATTAAAGAT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATTAAAGAT
**
4572 CTGATGACTCCGTGTCATCGTGAGTA
1 C-GATGACTAAGTGTCATCGTGAGTA
4598 TGAATTCCTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 6 0.09
51 61 0.91
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (50 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATTAAAGAT
Found at i:7407 original size:30 final size:31
Alignment explanation
Indices: 7361--7422 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
7351 CTGAAGGAAT
* *
7361 ACAATATGAGTTTTCCAGAAGCAGCATAAGC
1 ACAATATGACTTTTCCAGAAGCAACATAAGC
*
7392 ACAA-ATGACTTTTCCAGATGCAACATAAGC
1 ACAATATGACTTTTCCAGAAGCAACATAAGC
7422 A
1 A
7423 GAGGCACCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (31 bp):
ACAATATGACTTTTCCAGAAGCAACATAAGC
Found at i:8162 original size:14 final size:14
Alignment explanation
Indices: 8143--8169 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8133 ATAGCTTTGG
8143 TTTTTCTTTTGTTA
1 TTTTTCTTTTGTTA
8157 TTTTTCTTTTGTT
1 TTTTTCTTTTGTT
8170 CGTTTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.07, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTGTTA
Found at i:8175 original size:15 final size:14
Alignment explanation
Indices: 8142--8175 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8132 TATAGCTTTG
8142 GTTTTTCTTTTGTT
1 GTTTTTCTTTTGTT
*
8156 ATTTTTCTTTTGTT
1 GTTTTTCTTTTGTT
8170 CGTTTT
1 -GTTTT
8176 AAAATGACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.03, C:0.09, G:0.12, T:0.76
Consensus pattern (14 bp):
GTTTTTCTTTTGTT
Found at i:9250 original size:24 final size:23
Alignment explanation
Indices: 9210--9267 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
9200 TATACATTCT
*
9210 AATTAGAT-TTTATAAATAATTAA
1 AATTA-ATATTTAAAAATAATTAA
* *
9233 TATTAATTATTTAAAAATATTTAA
1 AATTAA-TATTTAAAAATAATTAA
9257 AATTAATATTT
1 AATTAATATTT
9268 CATATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.03
23 10 0.34
24 18 0.62
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTAATATTTAAAAATAATTAA
Found at i:9493 original size:26 final size:26
Alignment explanation
Indices: 9461--9526 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
9451 CTTAAACCAA
*
9461 ACTTTTCAAAAGTACTTCTTAAAAGT
1 ACTTTTCAAAAGTACTTCTTAAAAGC
* *
9487 ACTTTTCCACCAA--ACTTTTTAAAAGC
1 ACTTTT-CA-AAAGTACTTCTTAAAAGC
9513 ACTTTTCAAAAGTA
1 ACTTTTCAAAAGTA
9527 ATGCTATACT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
24 2 0.06
25 2 0.06
26 24 0.75
27 2 0.06
28 2 0.06
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (26 bp):
ACTTTTCAAAAGTACTTCTTAAAAGC
Found at i:24475 original size:12 final size:12
Alignment explanation
Indices: 24454--24482 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24444 GAGATGAAGG
24454 TTTT-GGAGTGT
1 TTTTGGGAGTGT
24465 TTTTGGGAGTGT
1 TTTTGGGAGTGT
24477 TTTTGG
1 TTTTGG
24483 ATGCACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.00, G:0.38, T:0.55
Consensus pattern (12 bp):
TTTTGGGAGTGT
Found at i:36195 original size:41 final size:41
Alignment explanation
Indices: 36138--36220 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
36128 CATTTTCTTA
* *
36138 TTAAATTGTTTTGACATATTGTATCACAGTCTCACAACATT
1 TTAAATTGCTTTGACATATTGTATCACAATCTCACAACATT
36179 TTAAATTGCTTTGACATATTGTATCACAATCTCACAACATT
1 TTAAATTGCTTTGACATATTGTATCACAATCTCACAACATT
36220 T
1 T
36221 GCTTTGACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (41 bp):
TTAAATTGCTTTGACATATTGTATCACAATCTCACAACATT
Found at i:36224 original size:35 final size:37
Alignment explanation
Indices: 36142--36229 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 37
36132 TTCTTATTAA
* *
36142 ATTGTTTTGACATATTGTATCACAGTCTCACAACATTTT
1 ATTGCTTTGACATATTGTATCACAATCTCACAACA--TT
36181 AAATTGCTTTGACATATTGTATCACAATCTCACAACA-T
1 --ATTGCTTTGACATATTGTATCACAATCTCACAACATT
36219 -TTGCTTTGACA
1 ATTGCTTTGACA
36230 ATTTTAATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
35 11 0.24
38 1 0.02
41 33 0.73
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (37 bp):
ATTGCTTTGACATATTGTATCACAATCTCACAACATT
Found at i:49649 original size:18 final size:18
Alignment explanation
Indices: 49612--49649 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
49602 TGTAGTTTGT
*
49612 TGTGACTGCATACGAGCA
1 TGTGACTGCATACGAACA
49630 TGTGACTGCAT-CTGAACA
1 TGTGACTGCATAC-GAACA
49648 TG
1 TG
49650 ATGTGCATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (18 bp):
TGTGACTGCATACGAACA
Found at i:50964 original size:22 final size:21
Alignment explanation
Indices: 50921--50966 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
50911 TAAAACACCT
*
50921 AAAAATAAAAAAAGAGTCAAC
1 AAAAATAAAAAAAAAGTCAAC
50942 AAAAATAAAACAAATAAGT-AAC
1 AAAAATAAAA-AAA-AAGTCAAC
50964 AAA
1 AAA
50967 TAAAAATCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 9 0.41
23 3 0.14
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.11
Consensus pattern (21 bp):
AAAAATAAAAAAAAAGTCAAC
Found at i:62027 original size:17 final size:17
Alignment explanation
Indices: 62007--62041 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
61997 CTGTAGGTAA
62007 AAAGAAGAATCAGAAAG
1 AAAGAAGAATCAGAAAG
62024 AAAGAAGAATCAGAAAG
1 AAAGAAGAATCAGAAAG
62041 A
1 A
62042 CGGACACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.06, G:0.23, T:0.06
Consensus pattern (17 bp):
AAAGAAGAATCAGAAAG
Found at i:68068 original size:24 final size:24
Alignment explanation
Indices: 68004--68069 Score: 62
Period size: 26 Copynumber: 2.7 Consensus size: 24
67994 ATCCATTTTA
*
68004 TATTTTTATA-ATATATTTTTATCT
1 TATTTTTATATAT-TATTTATATCT
* * *
68028 CATTTTTTTGTGAATTATTTATATCT
1 TATTTTTATAT--ATTATTTATATCT
68054 TATTTTTATATATTAT
1 TATTTTTATATATTAT
68070 ACAGTTTACA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
24 12 0.38
26 18 0.56
27 2 0.06
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (24 bp):
TATTTTTATATATTATTTATATCT
Found at i:73166 original size:52 final size:52
Alignment explanation
Indices: 73084--73360 Score: 344
Period size: 52 Copynumber: 5.3 Consensus size: 52
73074 AAAAGGGATC
* * *
73084 GATGAGTATGTGTCATCGTGAGTATCTGAATCCTTTACAAATTATGAGGTCT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCT
73136 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTAC-GAATTATGAGGTCT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAG-ATTATGAGGTCT
* *
73188 AATGACTATGTGTCATCGTGAGTATATGAATCTTTTA-AGGATTATGAGGT-T
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACA-GATTATGAGGTCT
* * * * * *
73239 CGATGACTATATGTCATCGTGGGTATCTGAATCTTTTACGGATTATGATGTCT
1 -GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCT
* * * * * * *
73292 GTTGACTACGTGTCATCATGAGTATGTGAATCCTTTACAGATTGTGGGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCT
73344 GATGACTATGTGTCATC
1 GATGACTATGTGTCATC
73361 ATAAGTACTA
Statistics
Matches: 194, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
51 1 0.01
52 191 0.98
53 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCT
Found at i:86345 original size:17 final size:16
Alignment explanation
Indices: 86319--86352 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
86309 TATTTTTTTC
86319 TTTTTAATTTTGAAAT
1 TTTTTAATTTTGAAAT
*
86335 TTTTATAATTTTTAAAT
1 TTTT-TAATTTTGAAAT
86352 T
1 T
86353 ATTAGTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTTTAATTTTGAAAT
Found at i:88544 original size:41 final size:39
Alignment explanation
Indices: 88497--88596 Score: 98
Period size: 38 Copynumber: 2.6 Consensus size: 39
88487 TCAACCTTGA
** *
88497 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTC-GATAG
* ** *
88537 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGATAG
88574 GTCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
88597 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
36 11 0.24
37 6 0.13
38 12 0.26
39 4 0.09
40 2 0.04
41 11 0.24
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (39 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGATAG
Found at i:90818 original size:24 final size:24
Alignment explanation
Indices: 90789--90839 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
90779 AGAAATAATC
90789 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
90813 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
90837 TTT
1 TTT
90840 GAGTAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:91384 original size:18 final size:18
Alignment explanation
Indices: 91363--91401 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
91353 TTGAAATAGG
91363 TTGTTACTAGG-AAAAAGC
1 TTGTTAC-AGGAAAAAAGC
*
91381 TTGTTACCGGAAAAAAGC
1 TTGTTACAGGAAAAAAGC
91399 TTG
1 TTG
91402 ATAATCTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (18 bp):
TTGTTACAGGAAAAAAGC
Found at i:92825 original size:24 final size:24
Alignment explanation
Indices: 92797--92847 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
92787 AGAAATAATC
*
92797 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
*
92821 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
92845 TTT
1 TTT
92848 GAGTAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:95623 original size:19 final size:19
Alignment explanation
Indices: 95599--95648 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
95589 ATTTCGAATA
95599 AATTAATTGAATCAATTTT
1 AATTAATTGAATCAATTTT
*
95618 AATTAATTCG-ATTAATTTT
1 AATTAATT-GAATCAATTTT
* *
95637 TATTTATTGAAT
1 AATTAATTGAAT
95649 AAAATTAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 24 0.92
20 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (19 bp):
AATTAATTGAATCAATTTT
Found at i:96152 original size:80 final size:80
Alignment explanation
Indices: 96058--96214 Score: 233
Period size: 80 Copynumber: 2.0 Consensus size: 80
96048 TCAAACTATT
* * * *
96058 CAATTTTATCTTTTTTAACTAATGTAAATACAGAAACACCCAAAAATCCAATATAATTGGGTGAC
1 CAATTTTATCTTTTTTAACTAATCTAAAAACAGAAACACACAAAAATCCAAAATAATTGGGTGAC
96123 CAAAAAAGACAATTG
66 CAAAAAAGACAATTG
* * * * *
96138 CAATTTTATCTTTTTTGACTAATCTAAAAATAGAAACACACAAAAATCTAAAATAGTTGGTTGAC
1 CAATTTTATCTTTTTTAACTAATCTAAAAACAGAAACACACAAAAATCCAAAATAATTGGGTGAC
96203 CAAAAAAGACAA
66 CAAAAAAGACAA
96215 AATTAAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (80 bp):
CAATTTTATCTTTTTTAACTAATCTAAAAACAGAAACACACAAAAATCCAAAATAATTGGGTGAC
CAAAAAAGACAATTG
Found at i:97127 original size:22 final size:21
Alignment explanation
Indices: 97101--97141 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
97091 AATTAAATCT
*
97101 AAAAAGATTAGATATCAAATTA
1 AAAAAGATTAAAT-TCAAATTA
*
97123 AAAAATATTAAATTCAAAT
1 AAAAAGATTAAATTCAAAT
97142 ACTAAATTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAAAGATTAAATTCAAATTA
Found at i:98337 original size:3 final size:3
Alignment explanation
Indices: 98329--98359 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
98319 AGGAATTGAA
98329 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
98360 GAATGGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:107078 original size:2 final size:2
Alignment explanation
Indices: 107071--107104 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
107061 CATTAAAATG
107071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
107105 AGAGTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110434 original size:10 final size:10
Alignment explanation
Indices: 110419--110453 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
110409 TAAATTTTGG
110419 AATTTTTATA
1 AATTTTTATA
110429 AATTTTTATA
1 AATTTTTATA
* *
110439 AATATTTAAA
1 AATTTTTATA
110449 AATTT
1 AATTT
110454 AAAAATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
AATTTTTATA
Found at i:110448 original size:18 final size:20
Alignment explanation
Indices: 110427--110490 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
110417 GGAATTTTTA
*
110427 TAAATTTTTATAAA-TA-TT
1 TAAATTTTTAAAAATTATTT
**
110445 TAAAAATTTAAAAATTATTT
1 TAAATTTTTAAAAATTATTT
**
110465 TAAATTTTCGAAAATTATTT
1 TAAATTTTTAAAAATTATTT
*
110485 TGAATT
1 TAAATT
110491 ATTTTGTAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 11 0.31
19 2 0.06
20 23 0.64
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (20 bp):
TAAATTTTTAAAAATTATTT
Found at i:112921 original size:39 final size:39
Alignment explanation
Indices: 112867--112947 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
112857 AACCAAGATG
112867 TTAGTTTTTTTTTGGTTGATGTAGCTAGTTATAATTCAT
1 TTAGTTTTTTTTTGGTTGATGTAGCTAGTTATAATTCAT
112906 TTAGTTTTTTTTTGGTTGATGTAGCTAGTTATAATTCAT
1 TTAGTTTTTTTTTGGTTGATGTAGCTAGTTATAATTCAT
112945 TTA
1 TTA
112948 CAATAGTATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.21, C:0.05, G:0.17, T:0.57
Consensus pattern (39 bp):
TTAGTTTTTTTTTGGTTGATGTAGCTAGTTATAATTCAT
Found at i:120165 original size:41 final size:41
Alignment explanation
Indices: 120099--120355 Score: 313
Period size: 41 Copynumber: 6.2 Consensus size: 41
120089 ACTTGATGAA
* *
120099 TAAATGGAAGACTCATGTCTTGAGATGAGCATGAGATTATAT
1 TAAA-GGAAGACTCATGACTCGAGATGAGCATGAGATTATAT
*
120141 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATAT
** * *
120182 TAAAGGAAGACTTGTGACTCGAAATTAGCATGAGATTATAT
1 TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATAT
* * *
120223 TAAAGGAAGACTTATGACTCAAAATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATAT
* * *
120264 TAAAGGAAGACTCGTGACTCGGGATGAGTATGAGATTATATT
1 TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATA-T
* * *
120306 TAAAGGAAGACTTATGACTCG-G-TAGAGCATAAGATTGT-T
1 TAAAGGAAGACTCATGACTCGAGAT-GAGCATGAGATTATAT
120345 TAAAAGGAAGA
1 T-AAAGGAAGA
120356 TCTATGATTC
Statistics
Matches: 192, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
39 2 0.01
40 10 0.05
41 156 0.81
42 24 0.12
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.28
Consensus pattern (41 bp):
TAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATAT
Found at i:122175 original size:24 final size:24
Alignment explanation
Indices: 122127--122182 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
122117 TTTTTAATGT
*
122127 AATAGTATATTTATATTTGATAAA
1 AATAATATATTTATATTTGATAAA
*
122151 AATTATATATTTTGATATTT-A-AAA
1 AATAATATA-TTT-ATATTTGATAAA
122175 AATAATAT
1 AATAATAT
122183 TACGATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 17 0.63
25 4 0.15
26 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (24 bp):
AATAATATATTTATATTTGATAAA
Found at i:126151 original size:30 final size:32
Alignment explanation
Indices: 126082--126161 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 32
126072 AGCAAGTAAA
* * *
126082 TGATTGTTTTGTCAC-TTTTCAATAATTTTAG
1 TGATTGTTTTGTTACATTTTCAATAAGTTGAG
*
126113 TGACTGTTTTGTTACATTTTC-A-AAGTTGAG
1 TGATTGTTTTGTTACATTTTCAATAAGTTGAG
*
126143 TGATTGTTTTGTTAAATTT
1 TGATTGTTTTGTTACATTT
126162 AACCGACCAG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 23 0.55
31 14 0.33
32 5 0.12
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.54
Consensus pattern (32 bp):
TGATTGTTTTGTTACATTTTCAATAAGTTGAG
Found at i:129841 original size:21 final size:21
Alignment explanation
Indices: 129800--129842 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
129790 TATTTTAGTC
* *
129800 ATTTAATTATTAATTTCTTTG
1 ATTTAATCATTAACTTCTTTG
129821 ATTTAATCACTTAACTT-TTTG
1 ATTTAATCA-TTAACTTCTTTG
129842 A
1 A
129843 AATTATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (21 bp):
ATTTAATCATTAACTTCTTTG
Found at i:130208 original size:20 final size:19
Alignment explanation
Indices: 130162--130208 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
130152 AAGTGATTTA
*
130162 AAAATATAAAAAAAAATAG
1 AAAATATAAAAAAAAATAC
*
130181 AAATTATAAATAAAAAA-ACC
1 AAAATATAAA-AAAAAATA-C
130201 AAAATATA
1 AAAATATA
130209 TGTATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAATATAAAAAAAAATAC
Found at i:130822 original size:2 final size:2
Alignment explanation
Indices: 130815--130844 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
130805 ATAAAAGGAA
130815 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
130845 TTTTCCCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:132645 original size:15 final size:15
Alignment explanation
Indices: 132625--132658 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
132615 TTTATATTTT
*
132625 CTTTTATTTGTTTCA
1 CTTTTACTTGTTTCA
*
132640 CTTTTACTTGTTTCG
1 CTTTTACTTGTTTCA
132655 CTTT
1 CTTT
132659 AAATTTTACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.65
Consensus pattern (15 bp):
CTTTTACTTGTTTCA
Found at i:136252 original size:23 final size:23
Alignment explanation
Indices: 136226--136273 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
136216 TAAGTGAACT
*
136226 CAAGCTGAAAATACAACTGGAAG
1 CAAGCTGAAAATACAACTGAAAG
*
136249 CAAGCTGAAAATACAGCTGAAAG
1 CAAGCTGAAAATACAACTGAAAG
136272 CA
1 CA
136274 CCAACACAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (23 bp):
CAAGCTGAAAATACAACTGAAAG
Found at i:140786 original size:15 final size:15
Alignment explanation
Indices: 140768--140813 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
140758 GTAACAGGCA
*
140768 AAGATGTAACAAGTG
1 AAGATGCAACAAGTG
*
140783 AAGATGCAATAAGTG
1 AAGATGCAACAAGTG
*
140798 TAGATGCAACAAGTG
1 AAGATGCAACAAGTG
140813 A
1 A
140814 CAATGAAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.20
Consensus pattern (15 bp):
AAGATGCAACAAGTG
Found at i:143683 original size:27 final size:29
Alignment explanation
Indices: 143642--143699 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
143632 GCGTAATATG
*
143642 AAGAACAACCCTTATGGC-TATTTCTGTA
1 AAGAACAACCCTTATGGCTTATCTCTGTA
*
143670 AAGAA-AACCTTTATGGCTTATCTCTGTA
1 AAGAACAACCCTTATGGCTTATCTCTGTA
143698 AA
1 AA
143700 ATGAGCCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (29 bp):
AAGAACAACCCTTATGGCTTATCTCTGTA
Found at i:143730 original size:84 final size:83
Alignment explanation
Indices: 143642--143850 Score: 197
Period size: 83 Copynumber: 2.5 Consensus size: 83
143632 GCGTAATATG
* ** * *
143642 AAGAACAACCCTTATGGCT-ATTTCTG-TAAAGAAAACCTTTATGGCTTATCTCTGTAAAATGAG
1 AAGAA-AACCCTTATGACTGA-TTCTGTTAAAGAAAACCTTTATAACTAATCTCTGTAAAATAAG
143705 CCTTTGTGGCTATCTATTGTT
64 CCTTTGTGGCTATCTA-TGTT
* * * * * *
143726 AAGAAAGCCTTTGTGATTGATTCTGTTAAAGAAAACCTTTGTAACTAATCTCTGTAAAGTAAGCC
1 AAGAAAACCCTTATGACTGATTCTGTTAAAGAAAACCTTTATAACTAATCTCTGTAAAATAAGCC
*
143791 TTTGTGTCTATCTATGTT
66 TTTGTGGCTATCTATGTT
* ** * ** * *
143809 AAGAAAGCTTTTGTGGTTGATTATGTTAAAGAAAGCCTTTAT
1 AAGAAAACCCTTATGACTGATTCTGTTAAAGAAAACCTTTAT
143851 GGTTGACTCT
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
83 54 0.51
84 52 0.49
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (83 bp):
AAGAAAACCCTTATGACTGATTCTGTTAAAGAAAACCTTTATAACTAATCTCTGTAAAATAAGCC
TTTGTGGCTATCTATGTT
Found at i:143734 original size:28 final size:29
Alignment explanation
Indices: 143656--144044 Score: 253
Period size: 28 Copynumber: 13.9 Consensus size: 29
143646 ACAACCCTTA
* * *
143656 TGGCT-ATTTCTG-TAAAGAAAACCTTTA
1 TGGCTGATCTCTGTTAAAGAAAGCCTTTG
* *
143683 TGGCTTATCTCTG-TAAA-ATGAGCCTTTG
1 TGGCTGATCTCTGTTAAAGA-AAGCCTTTG
*
143711 TGGCT-ATCTATTGTT-AAGAAAGCCTTTG
1 TGGCTGATCT-CTGTTAAAGAAAGCCTTTG
** *
143739 TGATTGAT-TCTGTTAAAGAAAACCTTTG
1 TGGCTGATCTCTGTTAAAGAAAGCCTTTG
** * *
143767 TAACTAATCTCTG-TAAAGTAAGCCTTTG
1 TGGCTGATCTCTGTTAAAGAAAGCCTTTG
* * *
143795 TGTCT-ATCTATGTT-AAGAAAGCTTTTG
1 TGGCTGATCTCTGTTAAAGAAAGCCTTTG
* * *
143822 TGGTTGAT-TATGTTAAAGAAAGCCTTTA
1 TGGCTGATCTCTGTTAAAGAAAGCCTTTG
* *
143850 TGGTTGA-CTCTGTTAAAGGAAGCCTTTG
1 TGGCTGATCTCTGTTAAAGAAAGCCTTTG
**
143878 TGGCTGA-CTCTGTTAAAGGGAGCCTTTG
1 TGGCTGATCTCTGTTAAAGAAAGCCTTTG
*
143906 TGGTTGAGT-T-TGTTAAAGGAAA-CCTTTG
1 TGGCTGA-TCTCTGTTAAA-GAAAGCCTTTG
** * *
143934 TCACTTAT-TCTGTTAAAGGAAGCCTTTG
1 TGGCTGATCTCTGTTAAAGAAAGCCTTTG
* * * *
143962 TGGCTG-GCTCTGTTGAAG-ATGCCCTTG
1 TGGCTGATCTCTGTTAAAGAAAGCCTTTG
* *
143989 TGG-TGAATCTCTGTTAAAGAATGCCTTTA
1 TGGCTG-ATCTCTGTTAAAGAAAGCCTTTG
* *
144018 TGGC-AACCTCTGTTAAAGGAAAGCCTT
1 TGGCTGATCTCTGTTAAA-GAAAGCCTT
144045 CGTGACTATT
Statistics
Matches: 288, Mismatches: 51, Indels: 44
0.75 0.13 0.11
Matches are distributed among these distances:
26 2 0.01
27 55 0.19
28 202 0.70
29 29 0.10
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (29 bp):
TGGCTGATCTCTGTTAAAGAAAGCCTTTG
Found at i:143932 original size:84 final size:83
Alignment explanation
Indices: 143668--144062 Score: 311
Period size: 84 Copynumber: 4.7 Consensus size: 83
143658 GCTATTTCTG
* * * *
143668 TAAAGAAAACCTTTATGGCTTATCTCTGTAAAATG-AGCCTTTGTGGCTATCTATTGTTAAGAAA
1 TAAAGAAAACCTTTATAG-TTATCTCTGTTAAAGGAAGCCTTTGTGGCTATCT-CTGTTAAGAAA
* *
143732 GCCTTTGTGATTGATTCTGT
64 GCCTTTGTGGTTGATTATGT
* * * * * *
143752 TAAAGAAAACCTTTGTAACTAATCTCTG-TAAAGTAAGCCTTTGTGTCTATCTATGTTAAGAAAG
1 TAAAGAAAACCTTTAT-AGTTATCTCTGTTAAAGGAAGCCTTTGTGGCTATCTCTGTTAAGAAAG
*
143816 CTTTTGTGGTTGATTATGT
65 CCTTTGTGGTTGATTATGT
* * **
143835 TAAAGAAAGCCTTTATGGTTGA-CTCTGTTAAAGGAAGCCTTTGTGGCTGA-CTCTGTTAAAGGG
1 TAAAGAAAACCTTTATAGTT-ATCTCTGTTAAAGGAAGCCTTTGTGGCT-ATCTCTGTT-AAGAA
143898 AGCCTTTGTGGTTGAGTT-TGT
63 AGCCTTTGTGGTTGA-TTATGT
* * * ** *
143919 TAAAGGAAACCTTTGTCACTTAT-TCTGTTAAAGGAAGCCTTTGTGGCTGGCTCTGTTGAAG-AT
1 TAAAGAAAACCTTTAT-AGTTATCTCTGTTAAAGGAAGCCTTTGTGGCTATCTCTGTT-AAGAAA
* *
143982 GCCCTTGTGG-TGAATCTCTGT
64 GCCTTTGTGGTTG-AT-TATGT
** * ** * * * * *
144003 TAAAGAATGCCTTTATGGCAACCTCTGTTAAAGGAAAGCCTTCGTGACTATTTCTATTAA
1 TAAAGAAAACCTTTATAGTTATCTCTGTTAAAGG-AAGCCTTTGTGGCTATCTCTGTTAA
144063 AGGTAATGCC
Statistics
Matches: 248, Mismatches: 48, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
82 9 0.04
83 81 0.33
84 137 0.55
85 21 0.08
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (83 bp):
TAAAGAAAACCTTTATAGTTATCTCTGTTAAAGGAAGCCTTTGTGGCTATCTCTGTTAAGAAAGC
CTTTGTGGTTGATTATGT
Found at i:146189 original size:20 final size:20
Alignment explanation
Indices: 146152--146194 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
146142 GTTACTTTTT
* *
146152 TTTAACTTTTTATATTTAAA
1 TTTAACATTTAATATTTAAA
* *
146172 TTTAACATTTAATTTTTATA
1 TTTAACATTTAATATTTAAA
146192 TTT
1 TTT
146195 TAGCTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTAACATTTAATATTTAAA
Found at i:153757 original size:15 final size:15
Alignment explanation
Indices: 153737--153766 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
153727 TTTTAATCAA
153737 TTGTTGTTGTTGGTT
1 TTGTTGTTGTTGGTT
153752 TTGTTGTTGTTGGTT
1 TTGTTGTTGTTGGTT
153767 CGAGTAGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (15 bp):
TTGTTGTTGTTGGTT
Found at i:154392 original size:18 final size:19
Alignment explanation
Indices: 154370--154421 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 19
154360 AACGATTGAC
154370 CTTCTACTTTTGATTCAAT
1 CTTCTACTTTTGATTCAAT
*
154389 -TTCT-CTTGTCGA--CAAT
1 CTTCTACTT-TTGATTCAAT
154405 CTTCTACTTTTGATTCA
1 CTTCTACTTTTGATTCA
154422 TTTTTCTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
16 4 0.15
17 10 0.38
18 10 0.38
19 2 0.08
ACGTcount: A:0.19, C:0.23, G:0.08, T:0.50
Consensus pattern (19 bp):
CTTCTACTTTTGATTCAAT
Found at i:157158 original size:51 final size:51
Alignment explanation
Indices: 157081--157261 Score: 220
Period size: 51 Copynumber: 3.5 Consensus size: 51
157071 AAACGAAAGG
* *
157081 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTAGAA
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAACCCTTTACAGATTAAAA
*
157132 GTCCGATGACTAAGTGTCATCATGAGTAAATGAACCCTTTACAGATTAAAA
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAACCCTTTACAGATTAAAA
* * * ** * * ** *
157183 GTTCGATGACTGAGTGTCATTGTGAGTAAATGATTCCGTGATGGATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAACCCTTTACAGATTAAAA
*
157234 GTCCGATGACTCCA-TGTCATCGTGAGTA
1 GTCCGATGACT-AAGTGTCATCGTGAGTA
157262 TGAATTCCTA
Statistics
Matches: 112, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
51 111 0.99
52 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (51 bp):
GTCCGATGACTAAGTGTCATCGTGAGTAAATGAACCCTTTACAGATTAAAA
Found at i:160621 original size:20 final size:20
Alignment explanation
Indices: 160596--160634 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
160586 TTTTTCATGA
160596 GATTAATTAAATATAAATAG
1 GATTAATTAAATATAAATAG
*
160616 GATTAATTAAATTTAAATA
1 GATTAATTAAATATAAATA
160635 AATGATTAAT
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
GATTAATTAAATATAAATAG
Found at i:160695 original size:2 final size:2
Alignment explanation
Indices: 160688--160717 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
160678 ATTACCATTA
160688 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
160718 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176565 original size:11 final size:11
Alignment explanation
Indices: 176549--176595 Score: 67
Period size: 11 Copynumber: 4.0 Consensus size: 11
176539 TGATGGATTC
176549 TAATCCTTCTT
1 TAATCCTTCTT
176560 TAATCCTTCTTATT
1 TAATCCTTC---TT
176574 TAATCCTTCTT
1 TAATCCTTCTT
176585 TAATCCTTCTT
1 TAATCCTTCTT
176596 ATTTAATGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 22 0.67
14 11 0.33
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.55
Consensus pattern (11 bp):
TAATCCTTCTT
Found at i:176583 original size:25 final size:25
Alignment explanation
Indices: 176549--176610 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
176539 TGATGGATTC
176549 TAATCCTTCTTTAATCCTTCTTATT
1 TAATCCTTCTTTAATCCTTCTTATT
176574 TAATCCTTCTTTAATCCTTCTTATT
1 TAATCCTTCTTTAATCCTTCTTATT
*
176599 TAATGCTT-TTTA
1 TAATCCTTCTTTA
176611 TCTGTTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 4 0.11
25 32 0.89
ACGTcount: A:0.21, C:0.21, G:0.02, T:0.56
Consensus pattern (25 bp):
TAATCCTTCTTTAATCCTTCTTATT
Found at i:176611 original size:14 final size:14
Alignment explanation
Indices: 176558--176602 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
176548 CTAATCCTTC
176558 TTTAATCCTTCTTA
1 TTTAATCCTTCTTA
176572 TTTAATCCTTC---
1 TTTAATCCTTCTTA
176583 TTTAATCCTTCTTA
1 TTTAATCCTTCTTA
176597 TTTAAT
1 TTTAAT
176603 GCTTTTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 11 0.39
14 17 0.61
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTAATCCTTCTTA
Found at i:177360 original size:52 final size:52
Alignment explanation
Indices: 177260--177360 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
177250 AACGTGATTA
* * *
177260 GTGTCATCGTGAGTATATGAATTCTTTATGGATTATGAGGTTCAATGACTAT
1 GTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCAATGACTAT
*
177312 GTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
1 GTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCAATGAC
177361 ACACCTTTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (52 bp):
GTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCAATGACTAT
Found at i:177368 original size:30 final size:30
Alignment explanation
Indices: 177334--177390 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
177324 GTATATGAAT
177334 CCTTTACGGATTATGAGGTCCGATGACACA
1 CCTTTACGGATTATGAGGTCCGATGACACA
177364 CCTTTACGGATTATGAGGTCCGATGAC
1 CCTTTACGGATTATGAGGTCCGATGAC
177391 TATGTGTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (30 bp):
CCTTTACGGATTATGAGGTCCGATGACACA
Found at i:177421 original size:82 final size:82
Alignment explanation
Indices: 177283--177439 Score: 269
Period size: 82 Copynumber: 1.9 Consensus size: 82
177273 TATATGAATT
* * * *
177283 CTTTATGGATTATGAGGTTCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 CTTTACGGATTATGAGGTCCAATGACTATGTGTCATCATGAGTATATGAATACTTTACGGATTAT
177348 GAGGTCCGATGACACAC
66 GAGGTCCGATGACACAC
*
177365 CTTTACGGATTATGAGGTCCGATGACTATGTGTCATCATGAGTATATGAATACTTTACGGATTAT
1 CTTTACGGATTATGAGGTCCAATGACTATGTGTCATCATGAGTATATGAATACTTTACGGATTAT
177430 GAGGTCCGAT
66 GAGGTCCGAT
177440 AACTATGTGT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (82 bp):
CTTTACGGATTATGAGGTCCAATGACTATGTGTCATCATGAGTATATGAATACTTTACGGATTAT
GAGGTCCGATGACACAC
Found at i:177428 original size:52 final size:52
Alignment explanation
Indices: 177364--177651 Score: 454
Period size: 52 Copynumber: 5.6 Consensus size: 52
177354 CGATGACACA
*
177364 CCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCATGAGTATATGAAT
1 CCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
* *
177416 ACTTTACGGATTATGAGGTCCGATAACTATGTGTCATCGTGAGTATATGAAT
1 CCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
*
177468 CCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTAAGTATATGAAT
1 CCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
*
177520 CCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTCAGTATATGAAT
1 CCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
* * * *
177572 CCTTTATGGATTATGAGGGCCGGTGAC-A-GTGTCATTGTGAGTATATGAAT
1 CCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
** *
177622 TATTTACGGATTACGAGGTCCGATGACTAT
1 CCTTTACGGATTATGAGGTCCGATGACTAT
177652 TAAATAAGAA
Statistics
Matches: 216, Mismatches: 18, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
50 41 0.19
51 2 0.01
52 173 0.80
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (52 bp):
CCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
Found at i:180414 original size:35 final size:38
Alignment explanation
Indices: 180322--180398 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
180312 TGTAATGTCA
180322 TATGCTACTTTTGAAAATCTAATGTAATTATTAAACAT
1 TATGCTACTTTTGAAAATCTAATGTAATTATTAAACAT
180360 TATGCTACTTTTGAAAATCTAATGTAATTATTAAACAT
1 TATGCTACTTTTGAAAATCTAATGTAATTATTAAACAT
180398 T
1 T
180399 CTCCTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (38 bp):
TATGCTACTTTTGAAAATCTAATGTAATTATTAAACAT
Found at i:181305 original size:21 final size:21
Alignment explanation
Indices: 181260--181305 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
181250 AAATGGTAAC
*
181260 AAAATAGTGAAAAAAAACAAG
1 AAAATAGTGAAAAAAAACAAA
181281 AAAATAGT-AACAAAATAA-AAA
1 AAAATAGTGAA-AAAA-AACAAA
181302 AAAA
1 AAAA
181306 CCAAAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 2 0.09
21 18 0.82
22 2 0.09
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAATAGTGAAAAAAAACAAA
Found at i:181324 original size:29 final size:29
Alignment explanation
Indices: 181269--181324 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
181259 CAAAATAGTG
* * *
181269 AAAAAAAACAAGAAAATAGTAACAAAATA
1 AAAAAAAACAAGAAAACAATAAAAAAATA
181298 AAAAAAAACCAA-AAAACAATAAAAAAA
1 AAAAAAAA-CAAGAAAACAATAAAAAAA
181325 AAAGTAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.80, C:0.09, G:0.04, T:0.07
Consensus pattern (29 bp):
AAAAAAAACAAGAAAACAATAAAAAAATA
Found at i:185470 original size:10 final size:9
Alignment explanation
Indices: 185444--185502 Score: 52
Period size: 8 Copynumber: 6.7 Consensus size: 9
185434 CATGTAGTAA
*
185444 AAAAATTAT
1 AAAAATAAT
185453 -AAAA-AAT
1 AAAAATAAT
185460 AAAAATCAAT
1 AAAAAT-AAT
*
185470 AAAAATATT
1 AAAAATAAT
*
185479 AAAATTTAAT
1 AAAA-ATAAT
185489 AAAAAT-AT
1 AAAAATAAT
185497 AAAAAT
1 AAAAAT
185503 TAAAATTAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
7 2 0.05
8 16 0.39
9 7 0.17
10 16 0.39
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATAAT
Found at i:185503 original size:19 final size:19
Alignment explanation
Indices: 185451--185503 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
185441 TAAAAAAATT
185451 ATAAAAA-ATAAAAA-TCA
1 ATAAAAATATAAAAATTCA
* *
185468 ATAAAAATATTAAAATTTA
1 ATAAAAATATAAAAATTCA
185487 ATAAAAATATAAAAATT
1 ATAAAAATATAAAAATT
185504 AAAATTAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 7 0.23
18 6 0.19
19 18 0.58
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAAAAATATAAAAATTCA
Found at i:185506 original size:7 final size:8
Alignment explanation
Indices: 185444--185507 Score: 51
Period size: 10 Copynumber: 7.5 Consensus size: 8
185434 CATGTAGTAA
185444 AAAAATTAT
1 AAAAA-TAT
185453 AAAAA-AT
1 AAAAATAT
185460 AAAAATCAAT
1 AAAAAT--AT
185470 AAAAATATT
1 AAAAATA-T
*
185479 AAAATTTAAT
1 AAAA-AT-AT
185489 AAAAATAT
1 AAAAATAT
185497 AAAAAT-T
1 AAAAATAT
185504 AAAA
1 AAAA
185508 TTAGAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
7 12 0.26
8 9 0.19
9 11 0.23
10 14 0.30
11 1 0.02
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (8 bp):
AAAAATAT
Found at i:185517 original size:25 final size:25
Alignment explanation
Indices: 185467--185520 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
185457 AATAAAAATC
*
185467 AATAAAAATATTAAAATTTAATAAA
1 AATAAAAATATTAAAATTTAAAAAA
*
185492 AATATAAAA-ATTAAAATTAGAAAAAA
1 AATA-AAAATATTAAAATT-TAAAAAA
185518 AAT
1 AAT
185521 TTATAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (25 bp):
AATAAAAATATTAAAATTTAAAAAA
Found at i:189295 original size:83 final size:83
Alignment explanation
Indices: 189156--189325 Score: 322
Period size: 83 Copynumber: 2.0 Consensus size: 83
189146 ACAATCTAAC
*
189156 AGGATGAACAAACTAAATAGTGAAACTGGAAATATCTTGAGAATGAAGAAACTAATAGGAAGCAA
1 AGGATGAACAAACTAAATAGTGAAACTGGAAATATCTTGAGAATGAAGAAACTAATAGGAAACAA
189221 TACAAACAACTAGGCATG
66 TACAAACAACTAGGCATG
*
189239 AGGATGAACAAACTAAATAGTGAACCTGGAAATATCTTGAGAATGAAGAAACTAATAGGAAACAA
1 AGGATGAACAAACTAAATAGTGAAACTGGAAATATCTTGAGAATGAAGAAACTAATAGGAAACAA
189304 TACAAACAACTAGGCATG
66 TACAAACAACTAGGCATG
189322 AGGA
1 AGGA
189326 CTAACCTTGT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 85 1.00
ACGTcount: A:0.49, C:0.12, G:0.21, T:0.18
Consensus pattern (83 bp):
AGGATGAACAAACTAAATAGTGAAACTGGAAATATCTTGAGAATGAAGAAACTAATAGGAAACAA
TACAAACAACTAGGCATG
Found at i:196811 original size:24 final size:24
Alignment explanation
Indices: 196777--196828 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
196767 CTTTTAGAAG
* *
196777 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
196801 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
196825 ATTT
1 ATTT
196829 GACATATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:197450 original size:30 final size:30
Alignment explanation
Indices: 197416--197479 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
197406 TTGATGGAGA
*
197416 AAACATTATCCTTCTTGTAGAAAAGGTTAG
1 AAACATTATCCTTATTGTAGAAAAGGTTAG
*
197446 AAACATTATCCTTATTGTAGAAAATGTTAG
1 AAACATTATCCTTATTGTAGAAAAGGTTAG
197476 AAAC
1 AAAC
197480 TCTTTATGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (30 bp):
AAACATTATCCTTATTGTAGAAAAGGTTAG
Found at i:202281 original size:21 final size:21
Alignment explanation
Indices: 202257--202298 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
202247 GATTTACAAG
*
202257 TATACATAATAAAATAAAATA
1 TATACATAAAAAAATAAAATA
202278 TATACATAAAAAAATAAAATA
1 TATACATAAAAAAATAAAATA
202299 ATAAATTAAA
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:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
TATACATAAAAAAATAAAATA
Found at i:202308 original size:21 final size:21
Alignment explanation
Indices: 202257--202304 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
202247 GATTTACAAG
* *
202257 TATACATAATAAAATAAAATA
1 TATAAATAAAAAAATAAAATA
*
202278 TATACATAAAAAAATAAAATA
1 TATAAATAAAAAAATAAAATA
202299 -ATAAAT
1 TATAAAT
202305 TAAACAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
TATAAATAAAAAAATAAAATA
Found at i:202699 original size:119 final size:118
Alignment explanation
Indices: 202484--202756 Score: 281
Period size: 119 Copynumber: 2.3 Consensus size: 118
202474 GTCAAATTTG
* *
202484 AATTTTTTGAAAGTTTAGGGGTCAAATCAAAATTTTTAGAAAGCTTGGGAGTCAAATTCGAATTT
1 AATTTTTAGAAAGTTTAGGGGTCAAAACAAAATTTTTAGAAAGCTTGGGAGTCAAA-TCGAATTT
* ** * *
202549 TTGGAAAGTTTGAGGTTCAAATTTGAATTTTTGGAAAGTTT-GGCGATCAAATCAT
65 TTGGAAAGTTTAAGGTTCAAAAATGAATTTTTAGAAAGTTTAGG-G-TCAAAACAT
* * * * * *
202604 AATTTTTGGAAAGTTT-GGGGTCAAAACATAATTTTTGGAAAGTTTGGGGGTCAACA-CATAATT
1 AATTTTTAGAAAGTTTAGGGGTCAAAACAAAATTTTTAGAAAGCTTGGGAGTCAA-ATC-GAATT
* *
202667 TTTGGATAGTTTAA-GTGTCAAAAAAT-AGTTTTTAGAAAGTTTAAGGGTCAAAACAT
64 TTTGGAAAGTTTAAGGT-TC-AAAAATGAATTTTTAGAAAGTTT-AGGGTCAAAACAT
202723 AATTTTTAGATAA-TTTAGGGGTCAAAA-AAAATTT
1 AATTTTTAGA-AAGTTTAGGGGTCAAAACAAAATTT
202757 AAAACAAAGT
Statistics
Matches: 129, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
118 3 0.02
119 91 0.71
120 33 0.26
121 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.37
Consensus pattern (118 bp):
AATTTTTAGAAAGTTTAGGGGTCAAAACAAAATTTTTAGAAAGCTTGGGAGTCAAATCGAATTTT
TGGAAAGTTTAAGGTTCAAAAATGAATTTTTAGAAAGTTTAGGGTCAAAACAT
Found at i:202749 original size:30 final size:30
Alignment explanation
Indices: 202484--202749 Score: 231
Period size: 30 Copynumber: 8.9 Consensus size: 30
202474 GTCAAATTTG
* * *
202484 AATTTTTTGAAAGTTTAGGGGTCAAATCAA
1 AATTTTTGGAAAGTTTAGGGGTCAAAACAT
* * * *
202514 AATTTTTAGAAAGCTT-GGGAGTCAAATTC-G
1 AATTTTTGGAAAGTTTAGGG-GTCAAA-ACAT
* **
202544 AATTTTTGGAAAGTTT-GAGGTTC-AAATTT
1 AATTTTTGGAAAGTTTAG-GGGTCAAAACAT
* *
202573 GAATTTTTGGAAAGTTT-GGCGATCAAATCAT
1 -AATTTTTGGAAAGTTTAGG-GGTCAAAACAT
202604 AATTTTTGGAAAGTTT-GGGGTCAAAACAT
1 AATTTTTGGAAAGTTTAGGGGTCAAAACAT
* *
202633 AATTTTTGGAAAGTTTGGGGGTCAACACAT
1 AATTTTTGGAAAGTTTAGGGGTCAAAACAT
* * * *
202663 AATTTTTGGATAGTTTAAGTGTCAAAAAAT
1 AATTTTTGGAAAGTTTAGGGGTCAAAACAT
* * *
202693 AGTTTTTAGAAAGTTTAAGGGTCAAAACAT
1 AATTTTTGGAAAGTTTAGGGGTCAAAACAT
*
202723 AATTTTTAGATAA-TTTAGGGGTCAAAA
1 AATTTTTGGA-AAGTTTAGGGGTCAAAA
202750 AAAATTTAAA
Statistics
Matches: 198, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
29 31 0.16
30 158 0.80
31 9 0.05
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.36
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTAGGGGTCAAAACAT
Found at i:202766 original size:60 final size:60
Alignment explanation
Indices: 202642--202766 Score: 135
Period size: 60 Copynumber: 2.1 Consensus size: 60
202632 TAATTTTTGG
** * * * * * ** *
202642 AAAGTTTGGGGGTCAACACATAATTTTTGGATAGTTTAAGTGTCAAAAAATAGTTTTTAG
1 AAAGTTTAAGGGTCAAAACATAATTTTTAGATAATTTAAGGGTCAAAAAATAATTTAAAC
*
202702 AAAGTTTAAGGGTCAAAACATAATTTTTAGATAATTTAGGGGTCAAAAAA-AATTTAAAAC
1 AAAGTTTAAGGGTCAAAACATAATTTTTAGATAATTTAAGGGTCAAAAAATAATTT-AAAC
202762 AAAGT
1 AAAGT
202767 AGGGGCTTCA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
59 4 0.08
60 49 0.92
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (60 bp):
AAAGTTTAAGGGTCAAAACATAATTTTTAGATAATTTAAGGGTCAAAAAATAATTTAAAC
Found at i:204065 original size:12 final size:12
Alignment explanation
Indices: 204048--204079 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
204038 TGAGAAGATA
204048 TCAAAATATTAG
1 TCAAAATATTAG
*
204060 TCAAAACATTAG
1 TCAAAATATTAG
204072 TCAAAATA
1 TCAAAATA
204080 ACAAATGTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (12 bp):
TCAAAATATTAG
Found at i:205709 original size:53 final size:53
Alignment explanation
Indices: 205642--205748 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
205632 ACCAGCCCGA
205642 TAAGTTCCTAGTGTAAATCTTACTTAATATTCTTTGTATATGTATATATGTTG
1 TAAGTTCCTAGTGTAAATCTTACTTAATATTCTTTGTATATGTATATATGTTG
* * *
205695 TAAGTTCGTGGTGTAACTCTTACTTAATATTCTTTGTATATGTATATATGTTG
1 TAAGTTCCTAGTGTAAATCTTACTTAATATTCTTTGTATATGTATATATGTTG
205748 T
1 T
205749 CAATGTACAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (53 bp):
TAAGTTCCTAGTGTAAATCTTACTTAATATTCTTTGTATATGTATATATGTTG
Found at i:210856 original size:102 final size:102
Alignment explanation
Indices: 210696--210884 Score: 342
Period size: 102 Copynumber: 1.9 Consensus size: 102
210686 CGCAATCCAT
* *
210696 TTGCCTAGAATGCTTCTGAGGGTGTAGGGGCAAATTCCTAACAAATCCCTTTGTTCACTCATCCT
1 TTGCCTAGAATGCTTCTGAGGGCGTAGGGGCAAATTACTAACAAATCCCTTTGTTCACTCATCCT
210761 TACGGAAATAGCGCTGATGTTCTCTTCCGTAATTCAG
66 TACGGAAATAGCGCTGATGTTCTCTTCCGTAATTCAG
* *
210798 TTGCCTAGAATGCTTCTGAGGGCGTAGGGGCAAATTACTGACAAATTCCTTTGTTCACTCATCCT
1 TTGCCTAGAATGCTTCTGAGGGCGTAGGGGCAAATTACTAACAAATCCCTTTGTTCACTCATCCT
210863 TACGGAAATAGCGCTGATGTTC
66 TACGGAAATAGCGCTGATGTTC
210885 AAATTCTCCA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 83 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (102 bp):
TTGCCTAGAATGCTTCTGAGGGCGTAGGGGCAAATTACTAACAAATCCCTTTGTTCACTCATCCT
TACGGAAATAGCGCTGATGTTCTCTTCCGTAATTCAG
Found at i:214913 original size:290 final size:290
Alignment explanation
Indices: 214382--214955 Score: 1022
Period size: 290 Copynumber: 2.0 Consensus size: 290
214372 TAATGCTCAG
214382 AGTCTTAATATTTTGAAGGAGACATGCTAACTTTTGGCCTTTATCAGACACTAACTCATACTCTA
1 AGTCTTAATATTTTGAAGGAGACATGCTAACTTTTGGCCTTTATCAGACACTAACTCATACTCTA
* *
214447 TGCTCAAAGCATTTACCTGGACAACTAACTTCTGCAAGTATTCTGTCACTTCTCTCACTTGTGTC
66 TGCTCAAAGCATCTACCTGGACAACTAACTTCTGCAAGTATTCTGCCACTTCTCTCACTTGTGTC
214512 AATGCTTCACCCATGATATGGTCTCGATCTCGAACTTACCTCTGAGAGTGTTAAAGTTGCCTATT
131 AATGCTTCACCCATGATATGGTCTCGATCTCGAACTTACCTCTGAGAGTGTTAAAGTTGCCTATT
* * * *
214577 ACTTGCCTCCAAAGTTCTTTCAAGGAACTCGATCTGAATTTCACAGTTTTGTAATGAAGCTTCAA
196 ACTTGCCTCCAAAGTTCTTTCAAGGAACTCGATCCGAATCTCACAGTTCTATAATGAAGCTTCAA
214642 GTTCTCCAACCCTTCTCTTTAATCTTTTGA
261 GTTCTCCAACCCTTCTCTTTAATCTTTTGA
* *
214672 AGTCTTAATCTTTTGAAGGAGACATGCTAACTTTTGGCCTTTATCAGACACTGACTCATACTCTA
1 AGTCTTAATATTTTGAAGGAGACATGCTAACTTTTGGCCTTTATCAGACACTAACTCATACTCTA
214737 TGCTCAAAGCATCTACCTGGACAACTAACTTCTGCAAGTATTCTGCCACTTCTCTCACTTGTGTC
66 TGCTCAAAGCATCTACCTGGACAACTAACTTCTGCAAGTATTCTGCCACTTCTCTCACTTGTGTC
* * * *
214802 AATGCTTTACTCATGATATGGTCTCGATCTCTAACTTACCTCTGAGAGTGTTAAAGTTTCCTATT
131 AATGCTTCACCCATGATATGGTCTCGATCTCGAACTTACCTCTGAGAGTGTTAAAGTTGCCTATT
*
214867 ACTTGCCTCCAAAGTTCTTTCGAGGAACTCGATCCGAATCTCACAGTTCTATAATGAAGCTTCAA
196 ACTTGCCTCCAAAGTTCTTTCAAGGAACTCGATCCGAATCTCACAGTTCTATAATGAAGCTTCAA
*
214932 GTTCTCCAACCCTTCTTTTTAATC
261 GTTCTCCAACCCTTCTCTTTAATC
214956 CTTCATTCTC
Statistics
Matches: 270, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
290 270 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (290 bp):
AGTCTTAATATTTTGAAGGAGACATGCTAACTTTTGGCCTTTATCAGACACTAACTCATACTCTA
TGCTCAAAGCATCTACCTGGACAACTAACTTCTGCAAGTATTCTGCCACTTCTCTCACTTGTGTC
AATGCTTCACCCATGATATGGTCTCGATCTCGAACTTACCTCTGAGAGTGTTAAAGTTGCCTATT
ACTTGCCTCCAAAGTTCTTTCAAGGAACTCGATCCGAATCTCACAGTTCTATAATGAAGCTTCAA
GTTCTCCAACCCTTCTCTTTAATCTTTTGA
Found at i:218034 original size:18 final size:20
Alignment explanation
Indices: 217998--218040 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
217988 CACATGATTT
217998 ACAA-ATATACATAATAAAA
1 ACAATATATACATAATAAAA
218017 ACAATATATACAT-A-AAAA
1 ACAATATATACATAATAAAA
218035 ACAATA
1 ACAATA
218041 AATTAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
19 5 0.22
20 8 0.35
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (20 bp):
ACAATATATACATAATAAAA
Found at i:218049 original size:18 final size:17
Alignment explanation
Indices: 218008--218050 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
217998 ACAAATATAC
*
218008 ATAAT-AAAAACAATAT
1 ATAATAAAAAACAATAA
218024 ATACATAAAAAACAATAA
1 ATA-ATAAAAAACAATAA
218042 ATTAATAAA
1 A-TAATAAA
218051 TTAAATAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 2 0.09
18 16 0.70
19 2 0.09
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAATAAAAAACAATAA
Found at i:218292 original size:30 final size:30
Alignment explanation
Indices: 218210--218455 Score: 202
Period size: 30 Copynumber: 8.3 Consensus size: 30
218200 ACATTAAAAT
* **
218210 AGGGTCAAATTTGAATTTTTGGAAAGTTCA
1 AGGGTCAAATTTGAATTTTTAGAAAGTTTG
* * ***
218240 AAGGTTAAATCAAAATTTTTTAGAAAGTTTG
1 AGGGTCAAATTTGAA-TTTTTAGAAAGTTTG
*
218271 AGGGTCAAATTTGGATTTTTAGAAAGTTTG
1 AGGGTCAAATTTGAATTTTTAGAAAGTTTG
* *
218301 AGGGTTAAATTTGAATTTTT-GGAAG-TTG
1 AGGGTCAAATTTGAATTTTTAGAAAGTTTG
*
218329 AGGGTCAAATTTGAATTTTTAGAAAGTTTA
1 AGGGTCAAATTTGAATTTTTAGAAAGTTTG
* * *
218359 AGGGTTAAATCAT-AATTTTTGGAAAGTTT-
1 AGGGTCAAAT-TTGAATTTTTAGAAAGTTTG
*
218388 AGGGGTCAAAATAT-AATTTTTAGATAA-TTT-
1 A-GGGTC-AAATTTGAATTTTTAGA-AAGTTTG
* * ** *
218418 AGCGTAAAAAAT-AATTTTTAGAAAGTTTA
1 AGGGTCAAATTTGAATTTTTAGAAAGTTTG
218447 AGGGTCAAA
1 AGGGTCAAA
218456 ACATAATTTT
Statistics
Matches: 177, Mismatches: 30, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
27 2 0.01
28 40 0.23
29 19 0.11
30 88 0.50
31 28 0.16
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (30 bp):
AGGGTCAAATTTGAATTTTTAGAAAGTTTG
Found at i:218351 original size:58 final size:57
Alignment explanation
Indices: 218210--218455 Score: 228
Period size: 58 Copynumber: 4.2 Consensus size: 57
218200 ACATTAAAAT
* * * * *
218210 AGGGTCAAATTTGAATTTTTGGAAAGTTCAAAGGTTAAATCAAAATTTTTTAGAAAGTTTG
1 AGGGTCAAATTTGAATTTTTAGAAAGTTTAAGGGTTAAAT-ATAA-TTTTT-GGAAG-TTG
* * *
218271 AGGGTCAAATTTGGATTTTTAGAAAGTTTGAGGGTTAAATTTGAATTTTTGGAAGTTG
1 AGGGTCAAATTTGAATTTTTAGAAAGTTTAAGGGTTAAATAT-AATTTTTGGAAGTTG
*
218329 AGGGTCAAATTTGAATTTTTAGAAAGTTTAAGGGTTAAATCATAATTTTTGGAAAGTTT
1 AGGGTCAAATTTGAATTTTTAGAAAGTTTAAGGGTTAAAT-ATAATTTTTGG-AAGTTG
* * * * * *
218388 AGGGGTCAAAATAT-AATTTTTAGATAA-TTT-AGCGTAAAAAATAATTTTTAGAAAGTTTA
1 A-GGGTC-AAATTTGAATTTTTAGA-AAGTTTAAGGGTTAAATATAATTTTT-GGAAG-TTG
218447 AGGGTCAAA
1 AGGGTCAAA
218456 ACATAATTTT
Statistics
Matches: 159, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
57 3 0.02
58 67 0.42
59 22 0.14
60 23 0.14
61 44 0.28
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (57 bp):
AGGGTCAAATTTGAATTTTTAGAAAGTTTAAGGGTTAAATATAATTTTTGGAAGTTG
Found at i:218377 original size:88 final size:86
Alignment explanation
Indices: 218209--218485 Score: 243
Period size: 88 Copynumber: 3.1 Consensus size: 86
218199 TACATTAAAA
* * * * *
218209 TAGGGTCAAATTTGAATTTTTGGAAAGTTCAAAGGTTAAATCAAAATTTTTTAGAAAGTTTGAGG
1 TAGGGTTAAATTTGAATTTTTGG-AAGTT-AAGGGTAAAAT-ATAA-TTTTTAGAAAGTTTAAGG
* * *
218274 GTCAAAT-TTGGATTTTTAGAAAGTT
62 GTCAAATCAT-AATTTTTGGAAAGTT
* * *
218299 TGAGGGTTAAATTTGAATTTTTGGAAGTTGAGGGTCAAATTTGAATTTTTAGAAAGTTTAAGGGT
1 T-AGGGTTAAATTTGAATTTTTGGAAGTTAAGGGTAAAATAT-AATTTTTAGAAAGTTTAAGGGT
*
218364 TAAATCATAATTTTTGGAAAGTT
64 CAAATCATAATTTTTGGAAAGTT
* * * * * * *
218387 TAGGGGTCAAAATAT-AATTTTTAGATAATTTAGCGTAAAAAATAATTTTTAGAAAGTTTAAGGG
1 TA-GGGT-TAAATTTGAATTTTTGGA-AGTTAAGGGTAAAATATAATTTTTAGAAAGTTTAAGGG
* *
218451 TCAAAACATAATTTTTGGATAGTTT
63 TCAAATCATAATTTTTGGAAAG-TT
*
218476 TAAGGTTAAA
1 TAGGGTTAAA
218486 AAATAATTTT
Statistics
Matches: 155, Mismatches: 25, Indels: 17
0.79 0.13 0.09
Matches are distributed among these distances:
87 4 0.03
88 93 0.60
89 31 0.20
90 6 0.04
91 21 0.14
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.39
Consensus pattern (86 bp):
TAGGGTTAAATTTGAATTTTTGGAAGTTAAGGGTAAAATATAATTTTTAGAAAGTTTAAGGGTCA
AATCATAATTTTTGGAAAGTT
Found at i:218456 original size:58 final size:60
Alignment explanation
Indices: 218342--218495 Score: 190
Period size: 58 Copynumber: 2.6 Consensus size: 60
218332 GTCAAATTTG
* ** * * *
218342 AATTTTTAGAAAG-TTTAAGGGTTAAATCATAATTTTTGGAAAGTTTAGGGGTCAAAATAT
1 AATTTTTAGATAGATTTAA-GGTTAAAAAATAATTTTTAGAAAGTTTAAGGGTCAAAACAT
218402 AATTTTTAGATA-ATTT-AGCG-TAAAAAATAATTTTTAGAAAGTTTAAGGGTCAAAACAT
1 AATTTTTAGATAGATTTAAG-GTTAAAAAATAATTTTTAGAAAGTTTAAGGGTCAAAACAT
* *
218460 AATTTTTGGATAGTTTTAAGGTTAAAAAATAATTTT
1 AATTTTTAGATAGATTTAAGGTTAAAAAATAATTTT
218496 AAAACAAAGT
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
58 45 0.56
59 6 0.07
60 30 0.37
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.40
Consensus pattern (60 bp):
AATTTTTAGATAGATTTAAGGTTAAAAAATAATTTTTAGAAAGTTTAAGGGTCAAAACAT
Found at i:218464 original size:30 final size:30
Alignment explanation
Indices: 218256--218495 Score: 185
Period size: 30 Copynumber: 8.1 Consensus size: 30
218246 AAATCAAAAT
* * *
218256 TTTTTAGAAAGTTTGAGGGTC-AAATTTGGA
1 TTTTTAGAAAGTTTAAGGGTCAAAATAT-AA
* * *
218286 TTTTTAGAAAGTTTGAGGGT-TAAATTTGAA
1 TTTTTAGAAAGTTTAAGGGTCAAAATAT-AA
* * *
218316 TTTTT-GGAAG-TTGAGGGTC-AAATTTGAA
1 TTTTTAGAAAGTTTAAGGGTCAAAATAT-AA
*
218344 TTTTTAGAAAGTTTAAGGGT-TAAATCATAA
1 TTTTTAGAAAGTTTAAGGGTCAAAAT-ATAA
* *
218374 TTTTTGGAAAGTTTAGGGGTCAAAATATAA
1 TTTTTAGAAAGTTTAAGGGTCAAAATATAA
* *
218404 TTTTTAGATAA-TTT-AGCGT-AAAAAATAA
1 TTTTTAGA-AAGTTTAAGGGTCAAAATATAA
*
218432 TTTTTAGAAAGTTTAAGGGTCAAAACATAA
1 TTTTTAGAAAGTTTAAGGGTCAAAATATAA
* * * *
218462 TTTTTGGATAGTTTTAA-GGTTAAAAAATAA
1 TTTTTAGAAAG-TTTAAGGGTCAAAATATAA
218492 TTTT
1 TTTT
218496 AAAACAAAGT
Statistics
Matches: 180, Mismatches: 18, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.01
28 41 0.23
29 15 0.08
30 110 0.61
31 12 0.07
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (30 bp):
TTTTTAGAAAGTTTAAGGGTCAAAATATAA
Found at i:218965 original size:17 final size:16
Alignment explanation
Indices: 218920--218975 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
218910 TTGGAAATTG
218920 AATTTATTTAAATTTA
1 AATTTATTTAAATTTA
* *
218936 AGTTCATTTTAAATTTA
1 AATTTA-TTTAAATTTA
*
218953 AATTTATTATAAAATTA
1 AATTTATT-TAAATTTA
218970 AATTTA
1 AATTTA
218976 GAAAGTTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
16 6 0.18
17 27 0.82
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
AATTTATTTAAATTTA
Found at i:219056 original size:15 final size:15
Alignment explanation
Indices: 219008--219056 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
218998 AAACAAAGTA
219008 CAATTACAAATGGCC
1 CAATTACAAATGGCC
*
219023 CAAGTACAAATGGCC
1 CAATTACAAATGGCC
*
219038 CAATTACAAACGGCC
1 CAATTACAAATGGCC
219053 CAAT
1 CAAT
219057 GACCCAAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.41, C:0.29, G:0.14, T:0.16
Consensus pattern (15 bp):
CAATTACAAATGGCC
Found at i:219603 original size:3 final size:3
Alignment explanation
Indices: 219595--219633 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
219585 GCTCATAAGT
219595 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
219634 GTAACGTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.