Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012945.1 Kokia drynarioides strain JFW-HI SEQ_127963, 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: 156324
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:25 original size:2 final size:2
Alignment explanation
Indices: 18--55 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
8 AATTTGATAA
18 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56 ATAAATGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4382 original size:26 final size:26
Alignment explanation
Indices: 4342--4435 Score: 100
Period size: 26 Copynumber: 3.6 Consensus size: 26
4332 TAGGCTTAAT
* *
4342 TCTGGACATGCTCATACAGCGACAAC
1 TCTGGACATGCTCATGCAGCGACAAA
* *
4368 TCTGGACATGTTCATGCAGCGATAAA
1 TCTGGACATGCTCATGCAGCGACAAA
* * *
4394 TCTGGACAAGTTTC-TGCAGCGACAAT
1 TCTGGACATG-CTCATGCAGCGACAAA
*
4420 TCTAGACATGCTCATG
1 TCTGGACATGCTCATG
4436 TAGCAACATT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
25 2 0.04
26 51 0.91
27 3 0.05
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (26 bp):
TCTGGACATGCTCATGCAGCGACAAA
Found at i:13732 original size:55 final size:55
Alignment explanation
Indices: 13673--13797 Score: 171
Period size: 55 Copynumber: 2.3 Consensus size: 55
13663 AATATTATCG
* *
13673 CCGCATCTGATAGCTCACTACATGAGCATATCCAGAATTACGA-CCAGAATTGTCA
1 CCGCATCTGATAGCTCACTACATAAGCATATCCAAAATTAC-ACCCAGAATTGTCA
* * *
13728 CCGCATATGATAGCTCGCTGCATAAGCATATCCAAAATTACACCCAGAATTGTCA
1 CCGCATCTGATAGCTCACTACATAAGCATATCCAAAATTACACCCAGAATTGTCA
* *
13783 TCGCATCTGACAGCT
1 CCGCATCTGATAGCT
13798 ATCCAGATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 1 0.02
55 60 0.98
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (55 bp):
CCGCATCTGATAGCTCACTACATAAGCATATCCAAAATTACACCCAGAATTGTCA
Found at i:28198 original size:22 final size:20
Alignment explanation
Indices: 28162--28205 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
28152 GATTGATTTG
28162 AAGGACAAAAAAAGAAAGCGC
1 AAGGACAAAAAAAG-AAGCGC
*
28183 AAGGATAATAAAAAGAAGCGC
1 AAGGACAA-AAAAAGAAGCGC
28204 AA
1 AA
28206 AGAGGAAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.61, C:0.11, G:0.23, T:0.05
Consensus pattern (20 bp):
AAGGACAAAAAAAGAAGCGC
Found at i:28960 original size:10 final size:11
Alignment explanation
Indices: 28947--28992 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
28937 AAAAAAACAC
28947 AAAAAG-AAAG
1 AAAAAGAAAAG
28957 AAAAAG-AAAG
1 AAAAAGAAAAG
*
28967 AAGAAGAAAAG
1 AAAAAGAAAAG
28978 AGAAAAGAAAAG
1 A-AAAAGAAAAG
28990 AAA
1 AAA
28993 TATATTATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:28970 original size:17 final size:17
Alignment explanation
Indices: 28954--28992 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28944 CACAAAAAGA
28954 AAGAAAA-AGAAAGAAG
1 AAGAAAAGAGAAAGAAG
28970 AAGAAAAGAGAAAAGAA-
1 AAGAAAAGAG-AAAGAAG
28987 AAGAAA
1 AAGAAA
28993 TATATTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 8 0.38
18 6 0.29
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAGAAAGAAG
Found at i:34164 original size:21 final size:21
Alignment explanation
Indices: 34140--34190 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
34130 GCAGGCTCTG
34140 TTTCTTCCTTCTCGTTCTCAT
1 TTTCTTCCTTCTCGTTCTCAT
34161 TTTCTTCCTTCTCGTTCTCAT
1 TTTCTTCCTTCTCGTTCTCAT
34182 TTTCTTCCT
1 TTTCTTCCT
34191 GCTTCTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.04, C:0.33, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTCTTCCTTCTCGTTCTCAT
Found at i:53412 original size:15 final size:15
Alignment explanation
Indices: 53398--53426 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53388 GAGCGCAAGA
53398 AGGAGG-AGAAGAAG
1 AGGAGGAAGAAGAAG
53412 AGGAGGAAGAAGAAG
1 AGGAGGAAGAAGAAG
53427 CACCGTGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (15 bp):
AGGAGGAAGAAGAAG
Found at i:59910 original size:43 final size:43
Alignment explanation
Indices: 59849--59931 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
59839 TTTAGCATGA
** * *
59849 AATTTTTATGTTCTAGAGGTTACATTAAGTATAGATAGAATGT
1 AATTTTTACATTCAAGAGGTAACATTAAGTATAGATAGAATGT
59892 AATTTTTACATTCAAGAGGTAACATTAAGTATAGATAGAA
1 AATTTTTACATTCAAGAGGTAACATTAAGTATAGATAGAA
59932 AGGTAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (43 bp):
AATTTTTACATTCAAGAGGTAACATTAAGTATAGATAGAATGT
Found at i:60792 original size:52 final size:52
Alignment explanation
Indices: 60730--60832 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
60720 AGCAATAATG
60730 CTCCAATGAATTCTTGA-CAATACCAGATCTCCATTTAATCAAGACTCAAGTT
1 CTCCAATGAATTCTT-ACCAATACCAGATCTCCATTTAATCAAGACTCAAGTT
*
60782 CTCCAATGAATTCTTACCAATATCAGATCTCCATTTAATCAAGACTCAAGT
1 CTCCAATGAATTCTTACCAATACCAGATCTCCATTTAATCAAGACTCAAGT
60833 ACCCACAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 1 0.02
52 48 0.98
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (52 bp):
CTCCAATGAATTCTTACCAATACCAGATCTCCATTTAATCAAGACTCAAGTT
Found at i:62785 original size:21 final size:18
Alignment explanation
Indices: 62742--62787 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
62732 TTAACAAAAG
*
62742 AAATGCAATGACAAAATA
1 AAATGCAATGAAAAAATA
62760 AAATGCAATGATAATAAATAA
1 AAATGCAATGA-AA-AAAT-A
62781 AAATGCA
1 AAATGCA
62788 TGCAAACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 11 0.46
19 1 0.04
20 4 0.17
21 8 0.33
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.20
Consensus pattern (18 bp):
AAATGCAATGAAAAAATA
Found at i:79463 original size:18 final size:18
Alignment explanation
Indices: 79440--79498 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
79430 CGGAAGGAGT
*
79440 AGCATACTGACTCGTTAG
1 AGCATACTGGCTCGTTAG
*
79458 AGCATATTGGCTCGTTTA-
1 AGCATACTGGCTCG-TTAG
* *
79476 AGCATACGGGCTCGTAAG
1 AGCATACTGGCTCGTTAG
79494 AGCAT
1 AGCAT
79499 TTCCGGATCG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 2 0.06
18 29 0.85
19 3 0.09
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (18 bp):
AGCATACTGGCTCGTTAG
Found at i:80250 original size:21 final size:21
Alignment explanation
Indices: 80226--80272 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
80216 ACTTGTTTCA
* *
80226 GTAGAACTATCACTCGTATCG
1 GTAGAACTATAACTAGTATCG
* *
80247 GTAGAATTATAAGTAGTATCG
1 GTAGAACTATAACTAGTATCG
80268 GTAGA
1 GTAGA
80273 TGTTTGTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (21 bp):
GTAGAACTATAACTAGTATCG
Found at i:92078 original size:13 final size:14
Alignment explanation
Indices: 92060--92090 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
92050 TCAAAATAGC
92060 AAAAAAAGAAAAA-
1 AAAAAAAGAAAAAG
92073 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
92087 AAAA
1 AAAA
92091 GTGTAGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:94638 original size:8 final size:8
Alignment explanation
Indices: 94625--94649 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
94615 TGATGTGTTT
94625 AATCTTTG
1 AATCTTTG
94633 AATCTTTG
1 AATCTTTG
94641 AATCTTTG
1 AATCTTTG
94649 A
1 A
94650 TGATGCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (8 bp):
AATCTTTG
Found at i:109928 original size:17 final size:18
Alignment explanation
Indices: 109885--109938 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
109875 ATGCATAGCA
*
109885 TTTAGTTGTCATTACATT
1 TTTAGTTGTCACTACATT
* *
109903 TTTAATTGTCACTGCA-T
1 TTTAGTTGTCACTACATT
* *
109920 TTTAGTTGTTAATACATT
1 TTTAGTTGTCACTACATT
109938 T
1 T
109939 GCAATATAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTAGTTGTCACTACATT
Found at i:124461 original size:21 final size:21
Alignment explanation
Indices: 124437--124484 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
124427 AGAGTTTTTA
124437 GTATCGGTAGAA-TAGTCACTT
1 GTATCGGTAGAACTA-TCACTT
124458 GTATCGGTAGAACTATCACTT
1 GTATCGGTAGAACTATCACTT
124479 GTATCG
1 GTATCG
124485 ATTGAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAACTATCACTT
Found at i:135607 original size:41 final size:41
Alignment explanation
Indices: 135507--135736 Score: 262
Period size: 41 Copynumber: 5.5 Consensus size: 41
135497 GGTGTATAAA
* ** * ** *
135507 AAGGAAGACTTATGTCTCGAGTTGAGCATGAGAAATTGTATA
1 AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTG-ATT
135549 AATGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATT
1 AA-GGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATT
* * *
135591 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
1 AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATT
* *
135632 AAGGAAGACTCATGTCTCGAAATGAGAATGAGCTTTTGATC
1 AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATT
** * * *
135673 AAGGAAGACTCATGTCTCGAGTTGAGAATGAGAATATGGTT
1 AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATT
* *
135714 AAAGGAAGACTTATGACTCGAAA
1 -AAGGAAGACTCATGTCTCGAAA
135737 AAGCATAAGG
Statistics
Matches: 160, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
41 106 0.66
42 24 0.15
43 30 0.19
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.27
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATT
Found at i:135659 original size:82 final size:82
Alignment explanation
Indices: 135507--135736 Score: 318
Period size: 82 Copynumber: 2.8 Consensus size: 82
135497 GGTGTATAAA
* * * *
135507 AAGGAAGACTTATGTCTCGAGTTGAGCATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAAA
1 AAGGAAGACTCATGTCTCGAGTTGAGAATGAGATA-TGAATAAA-GGAAGACTCATGTCTCGAAA
*
135572 TGAGAATGAGATTTTGATT
64 TGAGAATGAGATTTTGATC
*
135591 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT-AAGGAAGACTCATGTCTCGAAAT
1 AAGGAAGACTCATGTCTCGAGTTGAGAATGAGA-TATGAATAAAGGAAGACTCATGTCTCGAAAT
*
135655 GAGAATGAGCTTTTGATC
65 GAGAATGAGATTTTGATC
** * *
135673 AAGGAAGACTCATGTCTCGAGTTGAGAATGAGAATATGGTTAAAGGAAGACTTATGACTCGAAA
1 AAGGAAGACTCATGTCTCGAGTTGAGAATGAG-ATATGAATAAAGGAAGACTCATGTCTCGAAA
135737 AAGCATAAGG
Statistics
Matches: 131, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
82 73 0.56
83 23 0.18
84 34 0.26
85 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.27
Consensus pattern (82 bp):
AAGGAAGACTCATGTCTCGAGTTGAGAATGAGATATGAATAAAGGAAGACTCATGTCTCGAAATG
AGAATGAGATTTTGATC
Found at i:140704 original size:28 final size:30
Alignment explanation
Indices: 140638--140721 Score: 81
Period size: 28 Copynumber: 3.0 Consensus size: 30
140628 AATAAGATGA
* *
140638 AATTAAAG-TTGAAA-T-GAAATTTAAATT
1 AATTAGAGTTTGAAATTAGAAATTGAAATT
* *
140665 AATTTATAGTTT-AAATTCGAAATTGAAATT
1 AA-TTAGAGTTTGAAATTAGAAATTGAAATT
140695 AA-TAGAGTTTGAAATTAG-AATTGAAAT
1 AATTAGAGTTTGAAATTAGAAATTGAAAT
140722 AAAATAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
27 2 0.04
28 24 0.50
29 9 0.19
30 13 0.27
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38
Consensus pattern (30 bp):
AATTAGAGTTTGAAATTAGAAATTGAAATT
Found at i:140875 original size:19 final size:18
Alignment explanation
Indices: 140851--140891 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
140841 GTTTAAAGAT
140851 AAATTTAAATTATAGTTTA
1 AAATTTAAATTATAG-TTA
140870 AAATTTAAATTATAGTTA
1 AAATTTAAATTATAGTTA
140888 AAAT
1 AAAT
140892 GAAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
AAATTTAAATTATAGTTA
Found at i:140897 original size:18 final size:19
Alignment explanation
Indices: 140857--140899 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
140847 AGATAAATTT
**
140857 AAATTATAGTTTAAAATTT
1 AAATTATAGTTTAAAATGA
140876 AAATTATAG-TTAAAATGA
1 AAATTATAGTTTAAAATGA
140894 AAATTA
1 AAATTA
140900 AATTTGGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (19 bp):
AAATTATAGTTTAAAATGA
Found at i:141448 original size:24 final size:23
Alignment explanation
Indices: 141416--141491 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 23
141406 CCCAACGGTA
141416 AAAAAATAAATAAATAATTATTTT
1 AAAAAATAAATAAATAA-TATTTT
*
141440 AAAAAATAAAT-AATAATAAATTT
1 AAAAAATAAATAAATAAT-ATTTT
* *
141463 AAATATATATATATAATAA-ATTTT
1 AAA-AAATAAATA-AATAATATTTT
141487 AAAAA
1 AAAAA
141492 TTTTTTAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 1 0.02
23 13 0.30
24 24 0.56
26 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAAAATAAATAAATAATATTTT
Found at i:141696 original size:16 final size:15
Alignment explanation
Indices: 141654--141722 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 15
141644 AACTATTACC
*
141654 AAATTCAAATTAAAA
1 AAATTAAAATTAAAA
*
141669 AACTATTTAAATTAAAA
1 AA--ATTAAAATTAAAA
141686 ATAATTAAAA-TAAATA
1 A-AATTAAAATTAAA-A
*
141702 ATAA-TAAAATTTAAA
1 A-AATTAAAATTAAAA
141717 AAATTA
1 AAATTA
141723 CAAAAAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 2 0.04
15 15 0.33
16 14 0.31
17 13 0.29
18 1 0.02
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTAAAATTAAAA
Found at i:141741 original size:31 final size:31
Alignment explanation
Indices: 141672--141741 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
141662 ATTAAAAAAC
* *
141672 TATTTAAATTAAAAATAATTAAAATAAATAA
1 TATTAAAATTAAAAATAATTAAAAAAAATAA
* * *
141703 TAATAAAATTTAAAA-AATTACAAAAAAATTA
1 TATTAAAATTAAAAATAATTA-AAAAAAATAA
141734 TATTAAAA
1 TATTAAAA
141742 ATATTTCGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (31 bp):
TATTAAAATTAAAAATAATTAAAAAAAATAA
Found at i:141774 original size:14 final size:12
Alignment explanation
Indices: 141727--141787 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
141717 AAATTACAAA
141727 AAAATTATA-TT
1 AAAATTATATTT
141738 AAAA--ATATTT
1 AAAATTATATTT
**
141748 CGAATT-T-TTT
1 AAAATTATATTT
141758 AAAATACTATATTT
1 AAAAT--TATATTT
141772 AAAATTATATTT
1 AAAATTATATTT
141784 AAAA
1 AAAA
141788 ATGGTAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
9 3 0.08
10 10 0.26
11 5 0.13
12 12 0.31
13 1 0.03
14 8 0.21
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (12 bp):
AAAATTATATTT
Found at i:141936 original size:27 final size:27
Alignment explanation
Indices: 141884--141936 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
141874 CAAATTCAAT
* *
141884 TTAAAAAATTATTTAACTTAAAAATAG
1 TTAAAAAATAATTTAACATAAAAATAG
*
141911 TTAAATAATAATTTAA-ATAAATAATA
1 TTAAAAAATAATTTAACATAAA-AATA
141937 ATAAATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
TTAAAAAATAATTTAACATAAAAATAG
Found at i:142029 original size:10 final size:12
Alignment explanation
Indices: 141989--142031 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
141979 TCGAATATTT
141989 TTTAAAATACTATA
1 TTTAAAAT--TATA
142003 TTTAAAATTATA
1 TTTAAAATTATA
142015 TTTAAAA-TA-A
1 TTTAAAATTATA
142025 TTTAAAA
1 TTTAAAA
142032 ATGATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.28
11 2 0.07
12 11 0.38
14 8 0.28
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTAAAATTATA
Found at i:143503 original size:20 final size:21
Alignment explanation
Indices: 143479--143537 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
143469 TTTTCGAATT
* *
143479 TTTTTAAATATTTTTTTTCTA
1 TTTTCAAATATTTTTTTTATA
143500 TTTTCGAAATA--TTTTTTATA
1 TTTTC-AAATATTTTTTTTATA
143520 TTTTCAAAATATTTTTTT
1 TTTTC-AAATATTTTTTT
143538 ACATATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 18 0.56
21 4 0.12
22 10 0.31
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTCAAATATTTTTTTTATA
Found at i:143534 original size:19 final size:20
Alignment explanation
Indices: 143491--143536 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
143481 TTTAAATATT
* *
143491 TTTTTTCTATTTTCGAAATA
1 TTTTTTATATTTTCAAAATA
143511 TTTTTTATATTTTCAAAATA
1 TTTTTTATATTTTCAAAATA
143531 TTTTTT
1 TTTTTT
143537 TACATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTTATATTTTCAAAATA
Found at i:143549 original size:33 final size:32
Alignment explanation
Indices: 143508--143569 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
143498 TATTTTCGAA
*
143508 ATATTTTTTATATTTTCAAAATATTTTTTTAC
1 ATATTTTTTATATTTTCAAAATAATTTTTTAC
*
143540 ATATATTTTTATATTTTCGAAATAATTTTT
1 ATAT-TTTTTATATTTTCAAAATAATTTTT
143570 AGCTTTTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (32 bp):
ATATTTTTTATATTTTCAAAATAATTTTTTAC
Found at i:143567 original size:20 final size:20
Alignment explanation
Indices: 143492--143580 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
143482 TTAAATATTT
* *
143492 TTTTTCTATTTTCGAAATAT
1 TTTTTATATTTTCGAAATAA
143512 TTTTTATATTTTC--AA-AA
1 TTTTTATATTTTCGAAATAA
* * *
143529 TATTT-T-TTTAC-ATAT-A
1 TTTTTATATTTTCGAAATAA
143545 TTTTTATATTTTCGAAATAA
1 TTTTTATATTTTCGAAATAA
**
143565 TTTTTAGCTTTTCGAA
1 TTTTTATATTTTCGAA
143581 TTTTTTAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
15 4 0.08
16 7 0.13
17 6 0.11
18 6 0.11
19 3 0.06
20 27 0.51
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTTATATTTTCGAAATAA
Found at i:143577 original size:53 final size:54
Alignment explanation
Indices: 143476--143577 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 54
143466 ATATTTTCGA
* * * *
143476 ATTTTTTTAAATATTTTTTTTCTATTTTCGAAATATTTTTTATATTTTCAAAAT
1 ATTTTTTTAAATATTATTTTTATATTTTCGAAATAATTTTTAGATTTTCAAAAT
* *
143530 ATTTTTTTACATA-TATTTTTATATTTTCGAAATAATTTTTAGCTTTTC
1 ATTTTTTTAAATATTATTTTTATATTTTCGAAATAATTTTTAGATTTTC
143578 GAATTTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 30 0.71
54 12 0.29
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (54 bp):
ATTTTTTTAAATATTATTTTTATATTTTCGAAATAATTTTTAGATTTTCAAAAT
Found at i:143619 original size:36 final size:34
Alignment explanation
Indices: 143579--143646 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 34
143569 TAGCTTTTCG
143579 AATTTTTTAAAACTATTTTTTATATCTTCGAAATGA
1 AATTTTTT-AAA-TATTTTTTATATCTTCGAAATGA
* *
143615 AATTTTTTACATATTTTTTATATCTTTGAAAT
1 AATTTTTTAAATATTTTTTATATCTTCGAAAT
143647 ATTAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 20 0.67
35 2 0.07
36 8 0.27
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.54
Consensus pattern (34 bp):
AATTTTTTAAATATTTTTTATATCTTCGAAATGA
Found at i:143705 original size:25 final size:25
Alignment explanation
Indices: 143672--143751 Score: 87
Period size: 25 Copynumber: 3.4 Consensus size: 25
143662 TCCGAAATAT
143672 TTTTTTACAAATTAAAAATCTTATA
1 TTTTTTACAAATTAAAAATCTTATA
** **
143697 TTTTTTACATTTTCGAAA---TAT-
1 TTTTTTACAAATTAAAAATCTTATA
*
143718 TTTTTTATAAATTAAAAATCTTATA
1 TTTTTTACAAATTAAAAATCTTATA
143743 TTTTTTACA
1 TTTTTTACA
143752 TTTTCGAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
21 13 0.32
22 3 0.07
24 3 0.07
25 22 0.54
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (25 bp):
TTTTTTACAAATTAAAAATCTTATA
Found at i:143748 original size:47 final size:46
Alignment explanation
Indices: 143659--143769 Score: 204
Period size: 46 Copynumber: 2.4 Consensus size: 46
143649 TAAAAAATAT
143659 TTTTCCGAAATATTTTTTTACAAATTAAAAATCTTATATTTTTTACA
1 TTTT-CGAAATATTTTTTTACAAATTAAAAATCTTATATTTTTTACA
*
143706 TTTTCGAAATATTTTTTTATAAATTAAAAATCTTATATTTTTTACA
1 TTTTCGAAATATTTTTTTACAAATTAAAAATCTTATATTTTTTACA
143752 TTTTCGAAATATTTTTTT
1 TTTTCGAAATATTTTTTT
143770 TTACAAATGA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
46 59 0.94
47 4 0.06
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (46 bp):
TTTTCGAAATATTTTTTTACAAATTAAAAATCTTATATTTTTTACA
Found at i:144230 original size:24 final size:24
Alignment explanation
Indices: 144203--144250 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
144193 ACGGGATGCC
*
144203 GTTGGTTTTTCTCGGGGAGTATAT
1 GTTGGTTTTTCTCGGGCAGTATAT
144227 GTTGGTTTTTCTCGGGCAGTATAT
1 GTTGGTTTTTCTCGGGCAGTATAT
144251 AAAGGCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.10, G:0.31, T:0.46
Consensus pattern (24 bp):
GTTGGTTTTTCTCGGGCAGTATAT
Found at i:144882 original size:39 final size:38
Alignment explanation
Indices: 144796--144882 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 38
144786 CTCAATTTTG
** * *
144796 ATTTTTTTGTTTATTTTTTAAATTTAATTTGTAATTTC
1 ATTTTTTCATTTATATTTTAAATTTAATTTCTAATTTC
* *
144834 GTTTATTTCATTTATATTTTAAATTTAATTTCTAATTATT
1 ATTT-TTTCATTTATATTTTAAATTTAATTTCTAATT-TC
144874 ATTTTTTCA
1 ATTTTTTCA
144883 AAATTTATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
38 3 0.08
39 33 0.82
40 4 0.10
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (38 bp):
ATTTTTTCATTTATATTTTAAATTTAATTTCTAATTTC
Found at i:145877 original size:57 final size:57
Alignment explanation
Indices: 145789--145899 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
145779 ATTATTCATG
* * * *
145789 GGTGTCGACCATGCCATGAGCGATACTCAAAAAAAGATTTTTTTATCAGATAAAAGA
1 GGTGTCGACCATGCCAAGAGCAACACCCAAAAAAAGATTTTTTTATCAGATAAAAGA
* * *
145846 GGTGTCGACCATGGCAAGTGCAACACCCAAAAAAATATTTTTTTATCAGATAAA
1 GGTGTCGACCATGCCAAGAGCAACACCCAAAAAAAGATTTTTTTATCAGATAAA
145900 GTGGGGTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (57 bp):
GGTGTCGACCATGCCAAGAGCAACACCCAAAAAAAGATTTTTTTATCAGATAAAAGA
Found at i:145942 original size:58 final size:58
Alignment explanation
Indices: 145874--146043 Score: 163
Period size: 58 Copynumber: 3.0 Consensus size: 58
145864 TGCAACACCC
*
145874 AAAA-AAATATTTTTTTATCAGATAAAGTGGGGTGTTAATCATGGCATGAGCG--ACA
1 AAAACAAATATTTTTTTATCAGATAAAGTGGGGTGTTAGTCATGGCATGAGCGACACA
* * * * * **
145929 AAAATATATATATTTTTTATCAGATAAA-TGGAGTG-TCGGCTATGATATGAGCGACACTA
1 AAAACAAATAT-TTTTTTATCAGATAAAGTGGGGTGTTAGTC-ATGGCATGAGCGACAC-A
* * * *
145988 AAAACAAATATTTTTTTATCAGATAAAG-AGGGTGTCAGTCATAGCATAAGCGACAC
1 AAAACAAATATTTTTTTATCAGATAAAGTGGGGTGTTAGTCATGGCATGAGCGACAC
146044 CAAATTTTTT
Statistics
Matches: 89, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
55 6 0.07
56 21 0.24
57 16 0.18
58 34 0.38
59 12 0.13
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (58 bp):
AAAACAAATATTTTTTTATCAGATAAAGTGGGGTGTTAGTCATGGCATGAGCGACACA
Found at i:146329 original size:22 final size:21
Alignment explanation
Indices: 146286--146331 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
146276 GAGATGATCA
*
146286 TTTAAAATTTTTACTGTTTAT
1 TTTAAAATTTTTACTGTATAT
* *
146307 TTTAAATTATTTTATTGTATAT
1 TTTAAAAT-TTTTACTGTATAT
146329 TTT
1 TTT
146332 TTAACTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTAAAATTTTTACTGTATAT
Found at i:150076 original size:32 final size:31
Alignment explanation
Indices: 150022--150084 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
150012 ATCTTTATGC
* * *
150022 CTTAAATTGAAAATGATTTTTATATAGGGGAG
1 CTTAAATTCAAAATGATCTTTAT-TAAGGGAG
150054 CTTAAATTCAAAATG-TCCTTTATTAAGGGAG
1 CTTAAATTCAAAATGAT-CTTTATTAAGGGAG
150085 TGATCTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (31 bp):
CTTAAATTCAAAATGATCTTTATTAAGGGAG
Found at i:151143 original size:20 final size:19
Alignment explanation
Indices: 151110--151147 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
151100 AAGATAACAA
*
151110 ATAATATGATAATAATATC
1 ATAATATGACAATAATATC
151129 ATAATAATGACAATAATAT
1 ATAAT-ATGACAATAATAT
151148 TAATGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (19 bp):
ATAATATGACAATAATATC
Found at i:152101 original size:29 final size:30
Alignment explanation
Indices: 152070--152438 Score: 315
Period size: 29 Copynumber: 12.5 Consensus size: 30
152060 GCACGGGGGC
* **
152070 AAAATGGTAGTTTTGGAAGGTTCGAAGTCA
1 AAAATGGTATTTTTGGAAGGTTCGGGGTCA
152100 AAAATGAG-ATTTTTGGAA-GTTCGAGGGT--
1 AAAATG-GTATTTTTGGAAGGTTCG-GGGTCA
* *
152128 AAAATGGTAATTTTCGAAAGGTTCGGGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTCGGGGTCA
* * *
152159 AAAATGGGATTTTTGGAAGTTTGGGGGT--
1 AAAATGGTATTTTTGGAAGGTTCGGGGTCA
*
152187 AAAATGGTAATTTTTGAAAGGTTCGGGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTCGGGGTCA
* *
152218 AAAATGGGATTTTTTGAA-GTTCGAGGGT--
1 AAAATGGTATTTTTGGAAGGTTCG-GGGTCA
* *
152246 AAAATGGTGATTCTTAGAAGGTTCGGGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTCGGGGTCA
*
152277 AAAATGGGATTTTTGGAA-GTTCGGGGGT--
1 AAAATGGTATTTTTGGAAGGTTC-GGGGTCA
* ** *
152305 AAAATGGTAAATTTTAAAATGTTCGGGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTCGGGGTCA
*
152336 AAAATGGGATTTTTGGAA-GTTCAGGGGT--
1 AAAATGGTATTTTTGGAAGGTTC-GGGGTCA
*
152364 AAAATGGTAATTTTTAGAAGGTTCGGGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTCGGGGTCA
152395 AAAATGGTAATTTTTGGAA-GTTCGAGGGT--
1 AAAATGGT-ATTTTTGGAAGGTTCG-GGGTCA
152424 AAAATGGTAATTTTT
1 AAAATGGT-ATTTTT
152439 AGAAAGTTTA
Statistics
Matches: 279, Mismatches: 34, Indels: 53
0.76 0.09 0.14
Matches are distributed among these distances:
27 1 0.00
28 34 0.12
29 100 0.36
30 93 0.33
31 51 0.18
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (30 bp):
AAAATGGTATTTTTGGAAGGTTCGGGGTCA
Found at i:152161 original size:59 final size:58
Alignment explanation
Indices: 152070--152437 Score: 524
Period size: 59 Copynumber: 6.2 Consensus size: 58
152060 GCACGGGGGC
* * ** *
152070 AAAATGGTAGTTTTGGAAGGTTCGAAGTCAAAAATGAGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
152128 AAAATGGTAATTTTCGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAATGGTAATTTT-GAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
*
152187 AAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTTGAAGTTCGAGGGT
1 AAAATGGTAA-TTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
152246 AAAATGGTGATTCTT-AGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATT-TTGA-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
152305 AAAATGGTAAATTTTAAAATGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-AGGGGT
1 AAAATGGT-AATTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGT
* *
152364 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGTAATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTGA-AAGGTTCGGGGTCAAAAATGG-GATTTTTGGAAGTTCGAGGGT
152424 AAAATGGTAATTTT
1 AAAATGGTAATTTT
152438 TAGAAAGTTT
Statistics
Matches: 281, Mismatches: 19, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
58 23 0.08
59 217 0.77
60 40 0.14
61 1 0.00
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:154299 original size:17 final size:18
Alignment explanation
Indices: 154277--154316 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
154267 GAACTTTATC
* *
154277 TTAAATTT-ATAATAATT
1 TTAAATTTGAAAATAAAT
154294 TTAAATTTGAAAATAAAT
1 TTAAATTTGAAAATAAAT
154312 TTAAA
1 TTAAA
154317 ATTAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TTAAATTTGAAAATAAAT
Found at i:154312 original size:12 final size:11
Alignment explanation
Indices: 154295--154367 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 11
154285 ATAATAATTT
154295 TAAATTTGAAAA
1 TAAATTT-AAAA
154307 TAAATTTAAAA
1 TAAATTTAAAA
154318 TTAAATTTAAAA
1 -TAAATTTAAAA
154330 TTAAAATTTTAACAAA
1 -T-AAA-TTT-A-AAA
*
154346 TTTAATCTTAAAA
1 -TAAAT-TTAAAA
154359 TAAATTTAA
1 TAAATTTAA
154368 GGGGGAGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
11 8 0.15
12 24 0.45
13 6 0.11
14 5 0.09
15 5 0.09
16 5 0.09
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:154314 original size:18 final size:17
Alignment explanation
Indices: 154277--154367 Score: 69
Period size: 17 Copynumber: 5.2 Consensus size: 17
154267 GAACTTTATC
* *
154277 TTAAATTTATAATAATT
1 TTAAATTTAAAATAAAT
154294 TTAAATTTGAAAATAAAT
1 TTAAATTT-AAAATAAAT
* *
154312 TTAAAATTAAATTTAAAAT
1 TTAAATTTAAA-AT-AAAT
* * *
154331 TAAAATTT-TAACAAAT
1 TTAAATTTAAAATAAAT
154347 TT-AATCTTAAAATAAAT
1 TTAAAT-TTAAAATAAAT
154364 TTAA
1 TTAA
154368 GGGGGAGTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
15 3 0.05
16 7 0.12
17 19 0.34
18 17 0.30
19 10 0.18
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:154350 original size:29 final size:27
Alignment explanation
Indices: 154277--154365 Score: 73
Period size: 29 Copynumber: 3.3 Consensus size: 27
154267 GAACTTTATC
*
154277 TTAAATTTATAATAATTTTAAATTTGAAAA
1 TTAAATTT-TAA-AAATTTAAATTT-AAAA
154307 -TAAA-TTT-AAAA-TTAAATTTAAAA
1 TTAAATTTTAAAAATTTAAATTTAAAA
154330 TTAAAATTTTAACAAATTT-AATCTTAAAA
1 TT-AAATTTTAA-AAATTTAAAT-TTAAAA
154359 -TAAATTT
1 TTAAATTT
154366 AAGGGGGAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
23 4 0.08
24 9 0.18
25 5 0.10
26 4 0.08
27 8 0.16
28 9 0.18
29 12 0.24
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (27 bp):
TTAAATTTTAAAAATTTAAATTTAAAA
Found at i:155401 original size:205 final size:207
Alignment explanation
Indices: 154737--155674 Score: 1128
Period size: 206 Copynumber: 4.6 Consensus size: 207
154727 TCTGTGTTTT
* * * * * * * *
154737 ATCAGGAAGACAGATTTGGTCCACTTCTCTGTATCTCATCTGGGAGCTAACCACTTTATTGTTTC
1 ATCAGGAAGACGGACTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTTC
* * * * * *
154802 TACCTGCTT-T-ACGAGTCTTATCAAGAAGCTAGGGATCG-AGGTTTTGCTC-ATATCGAGCAT-
65 GACCTGCTTCTCA-GTGTCTTATCAGGAAGCTAGGGTTCGAAGATTTTGCTCGATATCAAGCATA
* * * * * * *
154862 GAGTTTGATTTGGTCTTCTTCTCAGTATCTCATTAAGAAGATGACTGCATCGTTTGTTTCAA-CT
129 G-GCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGAGATGACCGCATCGCTCGTTTCAATC-
* *
154926 CACTTCTTTGTAACTC
192 CACTTCTCTGTACCTC
* * *
154942 ATCAGGAAGGCGGACTTGGTTTACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGTTTCG
1 ATCAGGAAGACGGACTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
* * * * * *
155007 ACCTGCTTCTCAGTGTCTTATCAGGAAGCTGGGGTTCGAAGATTTTGCCCGCTTTGAA-CGTAGG
66 ACCTGCTTCTCAGTGTCTTATCAGGAAGCTAGGGTTCGAAGATTTTGCTCGATATCAAGCATAGG
*
155071 CTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGAGATGACCGCATCGCTCGTTTCAATCCGCT
131 CTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGAGATGACCGCATCGCTCGTTTCAATCCACT
155136 TCTCTGTACCTC
196 TCTCTGTACCTC
*
155148 ATCAGGAATG-CGGACTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTC
1 ATCAGGAA-GACGGACTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTC
* * * *
155212 GACCTGCTTCTCAGTGTCTTATCAGGAAGTTAGGATTTGAAG-TTTTGCTC-ATATCAAGCATGG
65 GACCTGCTTCTCAGTGTCTTATCAGGAAGCTAGGGTTCGAAGATTTTGCTCGATATCAAGCATAG
* ** * * * * * * * *
155275 GTTTGATTCAGTCTTCTTCTCGGTATTTCAT-TGGGACGATGACTGCGTCGTTTGTTTCAATTCA
130 GCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGA-GATGACCGCATCGCTCGTTTCAATCCA
*
155339 CTTCTCTGTATCTC
194 CTTCTCTGTACCTC
* * * *
155353 ATTAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTTG
1 ATCAGGAAGACGGACTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
* * * * ** *
155418 ACCTGCTTCTCAATGTCTTATCAGGAAGCTGGGGTTCGAAGATTTTAAC-CGCT-TTGAGCGTAG
66 ACCTGCTTCTCAGTGTCTTATCAGGAAGCTAGGGTTCGAAGATTTT-GCTCGATATCAAGCATAG
*
155481 GCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGAGATGACCGCATCGCTCGTTTCAATCCGC
130 GCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGAGATGACCGCATCGCTCGTTTCAATCCAC
155546 TTCTCTGTACCTC
195 TTCTCTGTACCTC
* * *
155559 ATCAGGAAGGCGGACTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTTG
1 ATCAGGAAGACGGACTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
*
155624 ACCTTCTTCTCAGTGTCTTATCAGGAAGCTAGGGTTCGAAGATTTTGCTCG
66 ACCTGCTTCTCAGTGTCTTATCAGGAAGCTAGGGTTCGAAGATTTTGCTCG
155675 TTTCGAGCCT
Statistics
Matches: 623, Mismatches: 95, Indels: 29
0.83 0.13 0.04
Matches are distributed among these distances:
204 28 0.04
205 232 0.37
206 351 0.56
207 12 0.02
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (207 bp):
ATCAGGAAGACGGACTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
ACCTGCTTCTCAGTGTCTTATCAGGAAGCTAGGGTTCGAAGATTTTGCTCGATATCAAGCATAGG
CTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGAGATGACCGCATCGCTCGTTTCAATCCACT
TCTCTGTACCTC
Found at i:155444 original size:411 final size:411
Alignment explanation
Indices: 154737--155673 Score: 1423
Period size: 411 Copynumber: 2.3 Consensus size: 411
154727 TCTGTGTTTT
* * * * * ** * * *
154737 ATCAGGAAGACAGATTTGGTCCACTTCTCTGTATCTCATCTGGGAGCTAACCACTTTATTGTTTC
1 ATCAGGAAGGCGGACTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACC-TTTTATTGCTTC
* * * * *
154802 TACCTGCTT-T-ACGAGTCTTATCAAGAAGCTAGGGA-TCGAGGTTTTGCTCATATCGAGCATGA
65 GACCTGCTTCTCA-GTGTCTTATCAGGAAGCTA-GGATTCGAAGTTTTGCTCATATCAAGCATGA
**
154864 GTTTGATTTGGTCTTCTTCTCAGTATCTCATTAAGAAGATGACTGCATCGTTTGTTTCAACTCAC
128 GTTTGATTCAGTCTTCTTCTCAGTATCTCATTAAGAAGATGACTGCATCGTTTGTTTCAACTCAC
* * * *
154929 TTCTTTGTAACTCATCAGGAAGGCGGACTTGGTTTACTTCTCAGTATCTCATCAGGAAGCTAACC
193 TTCTCTGTAACTCATCAGGAAGACGAACTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACC
* **
154994 TTTTATTGTTTCGACCTGCTTCTCAGTGTCTTATCAGGAAGCTGGGGTTCGAAGATTTTGCCCGC
258 TTTTATTGTTTCGACCTGCTTCTCAATGTCTTATCAGGAAGCTGGGGTTCGAAGATTTTAACCGC
155059 TTTGAACGTAGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGAGATGACCGCATCGCTCG
323 TTTGAACGTAGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGAGATGACCGCATCGCTCG
155124 TTTCAATCCGCTTCTCTGTACCTC
388 TTTCAATCCGCTTCTCTGTACCTC
*
155148 ATCAGGAATGCGGACTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCG
1 ATCAGGAAGGCGGACTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCG
* * *
155213 ACCTGCTTCTCAGTGTCTTATCAGGAAGTTAGGATTTGAAGTTTTGCTCATATCAAGCATGGGTT
66 ACCTGCTTCTCAGTGTCTTATCAGGAAGCTAGGATTCGAAGTTTTGCTCATATCAAGCATGAGTT
* * ** * * *
155278 TGATTCAGTCTTCTTCTCGGTATTTCATTGGGACGATGACTGCGTCGTTTGTTTCAATTCACTTC
131 TGATTCAGTCTTCTTCTCAGTATCTCATTAAGAAGATGACTGCATCGTTTGTTTCAACTCACTTC
* * *
155343 TCTGTATCTCATTAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTT
196 TCTGTAACTCATCAGGAAGACGAACTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTT
155408 TATTGCTTT-GACCTGCTTCTCAATGTCTTATCAGGAAGCTGGGGTTCGAAGATTTTAACCGCTT
261 TATTG-TTTCGACCTGCTTCTCAATGTCTTATCAGGAAGCTGGGGTTCGAAGATTTTAACCGCTT
*
155472 TGAGCGTAGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGAGATGACCGCATCGCTCGTT
325 TGAACGTAGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGAGATGACCGCATCGCTCGTT
155537 TCAATCCGCTTCTCTGTACCTC
390 TCAATCCGCTTCTCTGTACCTC
*
155559 ATCAGGAAGGCGGACTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTTG
1 ATCAGGAAGGCGGACTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCG
* *
155624 ACCTTCTTCTCAGTGTCTTATCAGGAAGCTAGGGTTCGAAGATTTTGCTC
66 ACCTGCTTCTCAGTGTCTTATCAGGAAGCTAGGATTCGAAG-TTTTGCTC
155674 GTTTCGAGCC
Statistics
Matches: 476, Mismatches: 45, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
410 21 0.04
411 443 0.93
412 12 0.03
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (411 bp):
ATCAGGAAGGCGGACTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCG
ACCTGCTTCTCAGTGTCTTATCAGGAAGCTAGGATTCGAAGTTTTGCTCATATCAAGCATGAGTT
TGATTCAGTCTTCTTCTCAGTATCTCATTAAGAAGATGACTGCATCGTTTGTTTCAACTCACTTC
TCTGTAACTCATCAGGAAGACGAACTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTT
TATTGTTTCGACCTGCTTCTCAATGTCTTATCAGGAAGCTGGGGTTCGAAGATTTTAACCGCTTT
GAACGTAGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGGAGATGACCGCATCGCTCGTTT
CAATCCGCTTCTCTGTACCTC
Done.