Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold198
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: 3915534
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 240068 characters in sequence are not A, C, G, or T
File 13 of 13
Found at i:3825815 original size:20 final size:21
Alignment explanation
Indices: 3825785--3825871 Score: 66
Period size: 20 Copynumber: 4.5 Consensus size: 21
3825775 AACATGAAAA
3825785 TTTTG-AAACACGAGA-TTT-T
1 TTTTGAAAACACGA-ATTTTCT
3825804 TTTTGAAAACACGAATTTTCT
1 TTTTGAAAACACGAATTTTCT
* **
3825825 TTTTG-AAACGCGAA---AAT
1 TTTTGAAAACACGAATTTTCT
*
3825842 TTTT-AAAACACAAATTTT-T
1 TTTTGAAAACACGAATTTTCT
3825861 TTTTGAAAACA
1 TTTTGAAAACA
3825872 TAAAAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
17 12 0.22
19 11 0.20
20 25 0.46
21 6 0.11
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.40
Consensus pattern (21 bp):
TTTTGAAAACACGAATTTTCT
Found at i:3825878 original size:37 final size:38
Alignment explanation
Indices: 3825803--3825881 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
3825793 CACGAGATTT
* * *
3825803 TTTTTGAAAACACGAATTTTCTTTTTGAAACGCGAAAA
1 TTTTTGAAAACACAAATTTTCTTTTTGAAACACAAAAA
*
3825841 TTTTT-AAAACACAAATTTT-TTTTTGAAAACATAAAAA
1 TTTTTGAAAACACAAATTTTCTTTTTG-AAACACAAAAA
3825878 TTTT
1 TTTT
3825882 GATAAAAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 6 0.17
37 25 0.69
38 5 0.14
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.42
Consensus pattern (38 bp):
TTTTTGAAAACACAAATTTTCTTTTTGAAACACAAAAA
Found at i:3825932 original size:17 final size:16
Alignment explanation
Indices: 3825908--3826138 Score: 140
Period size: 17 Copynumber: 12.9 Consensus size: 16
3825898 CGAGGATTTT
3825908 TTTTTGAAACACGAAA
1 TTTTTGAAACACGAAA
*
3825924 TTTTATGAAACACGGTCAA
1 TTTT-TGAAACAC-G-AAA
3825943 TTTTTGAAAACACGAGAA
1 TTTTTG-AAACACGA-AA
*
3825961 TTTTTGAAAGACGAGAA
1 TTTTTGAAACACGA-AA
*
3825978 TTTTTTTAAAACACGGAAA
1 --TTTTTGAAACAC-GAAA
*
3825997 TTTATGAAACACGGAAA
1 TTTTTGAAACAC-GAAA
*
3826014 TCTTTTTTGAAAACAAGAAAA
1 ---TTTTTG-AAACACG-AAA
* *
3826035 TTTTTTAAATACGAGAA
1 TTTTTGAAACACGA-AA
3826052 TTTTTGAAAACACGGGAAA
1 TTTTTG-AAACAC--GAAA
3826071 -TTTTGAAAACACGAAAA
1 TTTTTG-AAACACG-AAA
3826088 TTTTTGAAACACGAGAAA
1 TTTTTGAAACAC--GAAA
*
3826106 TTTTTTGAAAACACAAAAA
1 -TTTTTG-AAACAC-GAAA
*
3826125 TTTTTGAATCACGA
1 TTTTTGAAACACGA
3826139 TTTTTTTAAG
Statistics
Matches: 175, Mismatches: 17, Indels: 46
0.74 0.07 0.19
Matches are distributed among these distances:
16 7 0.04
17 59 0.34
18 48 0.27
19 37 0.21
20 16 0.09
21 8 0.05
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (16 bp):
TTTTTGAAACACGAAA
Found at i:3825962 original size:18 final size:18
Alignment explanation
Indices: 3825908--3826132 Score: 173
Period size: 18 Copynumber: 12.4 Consensus size: 18
3825898 CGAGGATTTT
3825908 TTTTTG-AAACACGA-AA
1 TTTTTGAAAACACGAGAA
3825924 TTTTATG-AAACACG-GTCAA
1 TTTT-TGAAAACACGAG--AA
3825943 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAGAA
*
3825961 TTTTTG-AAAGACGAGAA
1 TTTTTGAAAACACGAGAA
*
3825978 TTTTTTTAAAACACG-GAAA
1 -TTTTTGAAAACACGAG-AA
*
3825997 TTTATG-AAACACG-GAAA
1 TTTTTGAAAACACGAG-AA
* *
3826014 TCTTTTTTGAAAACAAGAAAA
1 ---TTTTTGAAAACACGAGAA
* *
3826035 TTTTT-TAAATACGAGAA
1 TTTTTGAAAACACGAGAA
*
3826052 TTTTTGAAAACACGGGAA
1 TTTTTGAAAACACGAGAA
* *
3826070 ATTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAGAA
3826088 TTTTTG-AAACACGAGAAA
1 TTTTTGAAAACACGAG-AA
* *
3826106 TTTTTTGAAAACACAAAAA
1 -TTTTTGAAAACACGAGAA
3826125 TTTTTGAA
1 TTTTTGAA
3826133 TCACGATTTT
Statistics
Matches: 169, Mismatches: 22, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
16 4 0.02
17 51 0.30
18 64 0.38
19 29 0.17
20 13 0.08
21 8 0.05
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAGAA
Found at i:3825982 original size:74 final size:74
Alignment explanation
Indices: 3825892--3826129 Score: 206
Period size: 74 Copynumber: 3.2 Consensus size: 74
3825882 GATAAAAAGC
* *
3825892 GAAACACGAGGATTTTTTTTTGAAACAC-GAAATTTTATGAAACACGG-TCAATTTTTGAAAACA
1 GAAACACGAGAATTTTTTTTTAAAACACGGAAA-TTTATGAAACACGGATC-ATTTTTGAAAACA
* *
3825955 CGAGAATTTTT
64 AGAAAATTTTT
* *
3825966 GAAAGACGAGAA--TTTTTTTAAAACACGGAAATTTATGAAACACGGAAATCTTTTTTGAAAACA
1 GAAACACGAGAATTTTTTTTTAAAACACGGAAATTTATGAAACACGG--ATCATTTTTGAAAACA
3826029 AGAAAATTTTT
64 AGAAAATTTTT
* * * **
3826040 TAAATACGAGAA---TTTTTGAAAACACGGGAAATTT-TGAAAACAC-GAAAATTTTTGAAACAC
1 GAAACACGAGAATTTTTTTTTAAAACAC-GGAAATTTATG-AAACACGGATCATTTTTGAAA-AC
* *
3826100 GAGAAATTTTTT
63 AAGAAAATTTTT
* *
3826112 GAAAACACAAAAATTTTT
1 G-AAACACGAGAATTTTT
3826130 GAATCACGAT
Statistics
Matches: 135, Mismatches: 18, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
71 10 0.07
72 39 0.29
73 27 0.20
74 55 0.41
75 2 0.01
76 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (74 bp):
GAAACACGAGAATTTTTTTTTAAAACACGGAAATTTATGAAACACGGATCATTTTTGAAAACAAG
AAAATTTTT
Found at i:3826125 original size:37 final size:37
Alignment explanation
Indices: 3825908--3826138 Score: 157
Period size: 37 Copynumber: 6.4 Consensus size: 37
3825898 CGAGGATTTT
* **
3825908 TTTTTGAAACAC--GAAATTTTATG-AAACACGGTCAA
1 TTTTTGAAACACGAGAAATTTTTTGAAAACAC-GAAAA
**
3825943 TTTTTGAAAACACGAG-AA-TTTTTGAAAGACGA-GAATT
1 TTTTTG-AAACACGAGAAATTTTTTGAAA-AC-ACGAAAA
* * *
3825980 TTTTTAAAACACG-GAAA-TTTATG-AAACACGGAAATCT
1 TTTTTGAAACACGAGAAATTTTTTGAAAACAC-GAAA--A
* * *
3826017 TTTTTGAAA-ACAAGAAAATTTTTT--AAATACGAGAA
1 TTTTTGAAACACGAG-AAATTTTTTGAAAACACGAAAA
*
3826052 TTTTTGAAAACACGGGAAA--TTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAGAAATTTTTTGAAAACACGAAAA
*
3826088 TTTTTGAAACACGAGAAATTTTTTGAAAACACAAAAA
1 TTTTTGAAACACGAGAAATTTTTTGAAAACACGAAAA
*
3826125 TTTTTGAATCACGA
1 TTTTTGAAACACGA
3826139 TTTTTTTAAG
Statistics
Matches: 155, Mismatches: 21, Indels: 38
0.72 0.10 0.18
Matches are distributed among these distances:
33 1 0.01
34 6 0.04
35 29 0.19
36 48 0.31
37 55 0.35
38 11 0.07
39 5 0.03
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (37 bp):
TTTTTGAAACACGAGAAATTTTTTGAAAACACGAAAA
Found at i:3826271 original size:15 final size:16
Alignment explanation
Indices: 3826255--3826286 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3826245 TGATTCTATT
3826255 AAAACACGAGAATTTAA
1 AAAACACGAGAATTT-A
3826272 AAAACACGAGAATTT
1 AAAACACGAGAATTT
3826287 TAGAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (16 bp):
AAAACACGAGAATTTA
Found at i:3826449 original size:22 final size:23
Alignment explanation
Indices: 3826424--3826474 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
3826414 TATTCGAATT
* *
3826424 TAAAAAATAAAATAAA-ATAAAA
1 TAAAAAAGAAAATAAATACAAAA
*
3826446 TAAAAAAGAACATAAATACAAAA
1 TAAAAAAGAAAATAAATACAAAA
3826469 TAAAAA
1 TAAAAA
3826475 TACTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (23 bp):
TAAAAAAGAAAATAAATACAAAA
Found at i:3826514 original size:21 final size:21
Alignment explanation
Indices: 3826472--3826515 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3826462 TACAAAATAA
* ** *
3826472 AAATACTTAAAAATGTGCAAC
1 AAATACTAAAAAAAATGAAAC
3826493 AAATACTAAAAAAAATGAAAC
1 AAATACTAAAAAAAATGAAAC
3826514 AA
1 AA
3826516 CATTTATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.64, C:0.11, G:0.07, T:0.18
Consensus pattern (21 bp):
AAATACTAAAAAAAATGAAAC
Found at i:3826951 original size:14 final size:14
Alignment explanation
Indices: 3826901--3826951 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
3826891 TTCTTTCCCC
* *
3826901 CTTTCTTCTTCCTT
1 CTTTTTTCTTCTTT
*
3826915 CTTCTTTCTT-TTT
1 CTTTTTTCTTCTTT
3826928 C-TTTTT-TTCTTT
1 CTTTTTTCTTCTTT
3826940 CTTTTTTCTTCT
1 CTTTTTTCTTCT
3826952 CCTTCGTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 2 0.07
12 8 0.27
13 8 0.27
14 12 0.40
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
CTTTTTTCTTCTTT
Found at i:3827482 original size:30 final size:30
Alignment explanation
Indices: 3827448--3827597 Score: 162
Period size: 30 Copynumber: 5.0 Consensus size: 30
3827438 GGGCCGAAAC
*
3827448 GTAATTTTGAGAAAGTTTAAGGGTCCAAAT
1 GTAATTTTGAGAAAGTTTAGGGGTCCAAAT
** *
3827478 GTAATTTCAAGAAAGTTTATGGGT-CAAGAT
1 GTAATTTTGAGAAAGTTTAGGGGTCCAA-AT
* * **
3827508 GTAATTTAGA-AAACTTTAGGGGTTGAAAT
1 GTAATTTTGAGAAAGTTTAGGGGTCCAAAT
*
3827537 GTAATTTTGAGAAAGTTTAGGGGTCGAAAT
1 GTAATTTTGAGAAAGTTTAGGGGTCCAAAT
* *
3827567 GTAATTTT-AGAAAAGTTTAGAGGTCAAAAT
1 GTAATTTTGAG-AAAGTTTAGGGGTCCAAAT
3827597 G
1 G
3827598 AAAAAAATAA
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
29 27 0.26
30 76 0.74
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (30 bp):
GTAATTTTGAGAAAGTTTAGGGGTCCAAAT
Found at i:3827538 original size:29 final size:29
Alignment explanation
Indices: 3827428--3827597 Score: 155
Period size: 30 Copynumber: 5.7 Consensus size: 29
3827418 TAATGGCAAC
* * * * *
3827428 AAAACTTTTGGGGCCGAAACGTAATTTTG
1 AAAAGTTTAGGGGTCGAAATGTAATTTAG
* *
3827457 AGAAAGTTTAAGGGTCCAAATGTAATTTCA-
1 A-AAAGTTTAGGGGTCGAAATGTAATTT-AG
*
3827487 AGAAAGTTTATGGGTC-AAGATGTAATTTAG
1 A-AAAGTTTAGGGGTCGAA-ATGTAATTTAG
* * *
3827517 AAAACTTTAGGGGTTGAAATGTAATTTTG
1 AAAAGTTTAGGGGTCGAAATGTAATTTAG
3827546 AGAAAGTTTAGGGGTCGAAATGTAATTTTAG
1 A-AAAGTTTAGGGGTCGAAATGTAA-TTTAG
* *
3827577 AAAAGTTTAGAGGTCAAAATG
1 AAAAGTTTAGGGGTCGAAATG
3827598 AAAAAAATAA
Statistics
Matches: 117, Mismatches: 17, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
29 26 0.22
30 86 0.74
31 5 0.04
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (29 bp):
AAAAGTTTAGGGGTCGAAATGTAATTTAG
Found at i:3827541 original size:59 final size:60
Alignment explanation
Indices: 3827437--3827586 Score: 171
Period size: 59 Copynumber: 2.5 Consensus size: 60
3827427 CAAAACTTTT
* * * * **
3827437 GGGGCCGAAACGTAATTTT-GAGAAAGTTTAAGGGTCCAAATGTAATTTCAAGAAAGTTTA
1 GGGGTCGAAATGTAATTTTAGA-AAACTTTAGGGGTTGAAATGTAATTTCAAGAAAGTTTA
* **
3827497 TGGGTC-AAGATGTAA-TTTAGAAAACTTTAGGGGTTGAAATGTAATTTTGAGAAAGTTTA
1 GGGGTCGAA-ATGTAATTTTAGAAAACTTTAGGGGTTGAAATGTAATTTCAAGAAAGTTTA
*
3827556 GGGGTCGAAATGTAATTTTAGAAAAGTTTAG
1 GGGGTCGAAATGTAATTTTAGAAAACTTTAG
3827587 AGGTCAAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
59 48 0.64
60 27 0.36
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (60 bp):
GGGGTCGAAATGTAATTTTAGAAAACTTTAGGGGTTGAAATGTAATTTCAAGAAAGTTTA
Found at i:3827582 original size:89 final size:89
Alignment explanation
Indices: 3827428--3827593 Score: 237
Period size: 89 Copynumber: 1.9 Consensus size: 89
3827418 TAATGGCAAC
*
3827428 AAAACTTTTGGGGCCGAAACGTAATTTTGAGAAAGTTTAAGGGTCCAAATGTAATTTCAAGAAAG
1 AAAACTTTAGGGGCCGAAACGTAATTTTGAGAAAGTTTAAGGGTCCAAATGTAATTTCAAGAAAG
3827493 TTTATG-GGTCAAGATGTAATTTAG
66 TTTA-GAGGTCAAGATGTAATTTAG
** * * * *
3827517 AAAACTTTAGGGGTTGAAATGTAATTTTGAGAAAGTTTAGGGGTCGAAATGTAATTT-TAGAAAA
1 AAAACTTTAGGGGCCGAAACGTAATTTTGAGAAAGTTTAAGGGTCCAAATGTAATTTCAAG-AAA
3827581 GTTTAGAGGTCAA
65 GTTTAGAGGTCAA
3827594 AATGAAAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
88 3 0.04
89 65 0.96
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.32
Consensus pattern (89 bp):
AAAACTTTAGGGGCCGAAACGTAATTTTGAGAAAGTTTAAGGGTCCAAATGTAATTTCAAGAAAG
TTTAGAGGTCAAGATGTAATTTAG
Found at i:3828550 original size:20 final size:20
Alignment explanation
Indices: 3828525--3828569 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3828515 TAAATTCACA
3828525 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
3828545 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
3828565 TAATT
1 TAATT
3828570 CGATTAGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:3829210 original size:24 final size:24
Alignment explanation
Indices: 3829164--3829210 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3829154 GTTGTAAAGT
* *
3829164 TTTATTTTTATTTATATTTATTTA
1 TTTATTTTTACTTATATTAATTTA
3829188 TTTATTTTTACTTAGT-TTAATTT
1 TTTATTTTTACTTA-TATTAATTT
3829211 TTATGTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTATTTTTACTTATATTAATTTA
Found at i:3830753 original size:16 final size:16
Alignment explanation
Indices: 3830732--3830764 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3830722 TCCATTCACG
3830732 ATGTCTAGGTTCGGCC
1 ATGTCTAGGTTCGGCC
*
3830748 ATGTCTAGGTTTGGCC
1 ATGTCTAGGTTCGGCC
3830764 A
1 A
3830765 AAGTGTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.33
Consensus pattern (16 bp):
ATGTCTAGGTTCGGCC
Found at i:3837450 original size:46 final size:44
Alignment explanation
Indices: 3837380--3837471 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 44
3837370 GTTTTAAAGG
* *
3837380 ACCTCGACCCACTATCAACAATGATAGGAACCTTGGTATAAGATGA
1 ACCTCGACCAACAATCAACAATGATAGGAACCTTGGTAT--GATGA
**
3837426 ACCTCGACCAACAATCAAGGATGATAGGAACCTTGGTATGATGA
1 ACCTCGACCAACAATCAACAATGATAGGAACCTTGGTATGATGA
3837470 AC
1 AC
3837472 GCCACACTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 7 0.17
46 35 0.83
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (44 bp):
ACCTCGACCAACAATCAACAATGATAGGAACCTTGGTATGATGA
Found at i:3838835 original size:27 final size:28
Alignment explanation
Indices: 3838805--3838864 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
3838795 ACTTTGGACA
* * *
3838805 ACATTAA-AGCATGCAATAAAATTAGAC
1 ACATTAATAACATGCAATAAAATAAAAC
*
3838832 ACATTAATAACATGCATTAAAATAAAAC
1 ACATTAATAACATGCAATAAAATAAAAC
3838860 ACATT
1 ACATT
3838865 TATCACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (28 bp):
ACATTAATAACATGCAATAAAATAAAAC
Found at i:3840892 original size:791 final size:790
Alignment explanation
Indices: 3839372--3840952 Score: 3029
Period size: 791 Copynumber: 2.0 Consensus size: 790
3839362 TGAGAGATTT
3839372 AAGAATTAGTGAGAATAAGAGAAAAGAAAAAGAAAAGTTATTAATGAAAGAAAAATAGAAGAGAT
1 AAGAATTAGTGAGAATAAGAGAAAAGAAAAAGAAAAGTTATTAATGAAAGAAAAATAGAAGAGAT
3839437 TGAGACAAAAAAAAGAAAAAGAAATAAAAAGAGAGTGAGTGAGAAAAGAAGTTGTGGAAAAAAAA
66 TGAGACAAAAAAAAGAAAAAGAAATAAAAAGAGAGTGAGTGAGAAAAGAAGTTGTGGAAAAAAAA
3839502 GAATGAAAAAGAATTTGAGCAAGAAAAGAAAATTGAAAAAGAATGCGAGAAAGAAGAATAAGAAA
131 GAATGAAAAAGAATTTGAGCAAGAAAAGAAAATTGAAAAAGAATGCGAGAAAGAAGAATAAGAAA
*
3839567 TTGAGATTGAAGAAATAAAAGCAAGTGTGAGTAATATGAATGACGTTGTTGAAACAAAAAGTGAA
196 TTGAGATTGAAGAAATAAAAACAAGTGTGAGTAATATGAATGACGTTGTTGAAACAAAAAGTGAA
*
3839632 ATTGAAAAGGAGTGTGACAAGGAAATGAGTGTTTTTACTAACCAATATGCAAGTTGTCCTCATTT
261 ATTGAAAAGGAGTGTGACAAGGAAATGAGTGTTTTTACTAACCAACATGCAAGTTGTCCTCATTT
3839697 TGTCTCTTCATTTCAAGTTTCTAATGGTTCATTTGATGAGTTCCAACTTCTTTACTCCACTTTCG
326 TGTCTCTTCATTTCAAGTTTCTAATGGTTCATTTGATGAGTTCCAACTTCTTTACTCCACTTTCG
3839762 AGAGACGGTTCTCTTTAATCAAAAAATGTAAAATAAAAAATGACATTAATCCACAATTTCTTAAA
391 AGAGACGGTTCTCTTTAATCAAAAAATGTAAAATAAAAAATGACATTAATCCACAATTTCTTAAA
3839827 GGTAAGGTAGGTAAGTAATCTTTAGCAATTGAATCAAGACAATCTATTTTAAATATTGTTGATAA
456 GGTAAGGTAGGTAAGTAATCTTTAGCAATTGAATCAAGACAATCTATTTTAAATATTGTTGATAA
3839892 AAATGTCGATGACTTAGTTTTCAAAAGATCTCTTCACAATGTACCAGTTAATTGTCACTCTTTGG
521 AAATGTCGATGACTTAGTTTTCAAAAGATCTCTTCACAATGTACCAGTTAATTGTCACTCTTTGG
3839957 TTGTCATTGATGATTTTGTTTCAGAGAGTGTCAATGTAACCTCCCAAACCCAACCTAGACGTTAT
586 TTGTCATTGATGATTTTGTTTCAGAGAGTGTCAATGTAACCTCCCAAACCCAACCTAGACGTTAT
*
3840022 GGTCGAATCAGGAAGGCCACATTAGCCACCTTAGTGTCGGACCTACCCAACGATAGTTAAAAACC
651 GGTCGAATCAGGAAGGCCACATTAGACACCTTAGTGTCGGACCTACCCAACGATAGTTAAAAACC
3840087 TTCAAGTACTCCTTTTTATAAAATTGTGGTTTCTATTGCTAGCTTTGGAAAACATCCATTTACTT
716 TTCAAGTACTCCTTTTTATAAAATTGTGGTTTCTATTGCTAGCTTTGGAAAACATCCATTTACTT
3840152 AGTCCAACCA
781 AGTCCAACCA
*
3840162 AAGAATTAGTGAGAATAAGAGAAAAGAAAAAGAAAAGTTATTGATGAAAGAAAAATAGAAGAGAT
1 AAGAATTAGTGAGAATAAGAGAAAAGAAAAAGAAAAGTTATTAATGAAAGAAAAATAGAAGAGAT
3840227 TGAGACAAAAAAAAAGAAAAAGAAATAAAAAGAGAGTGAGTGAGAAAAGAAGTTGTGGAAAAAAA
66 TGAGAC-AAAAAAAAGAAAAAGAAATAAAAAGAGAGTGAGTGAGAAAAGAAGTTGTGGAAAAAAA
3840292 AGAATGAAAAAGAATTTGAGCAAGAAAAGAAAATTGAAAAAGAATGCGAGAAAGAAGAATAAGAA
130 AGAATGAAAAAGAATTTGAGCAAGAAAAGAAAATTGAAAAAGAATGCGAGAAAGAAGAATAAGAA
3840357 ATTGAGATTGAAGAAATAAAAACAAGTGTGAGTAATATGAATGACGTTGTTGAAACAAAAAGTGA
195 ATTGAGATTGAAGAAATAAAAACAAGTGTGAGTAATATGAATGACGTTGTTGAAACAAAAAGTGA
3840422 AATTGAAAAGGAGTGTGACAAGGAAATGAGTGTTTTTACTAACCAACATGCAAGTTGTCCTCATT
260 AATTGAAAAGGAGTGTGACAAGGAAATGAGTGTTTTTACTAACCAACATGCAAGTTGTCCTCATT
*
3840487 TTGTCTCTTCATTTCAGGTTTCTAATGGTTCATTTGATGAGTTCCAACTTCTTTACTCCACTTTC
325 TTGTCTCTTCATTTCAAGTTTCTAATGGTTCATTTGATGAGTTCCAACTTCTTTACTCCACTTTC
* *
3840552 GAGAGACGGTTCTCTTTAATCAAAAAATGTTAGAT-AAAAATGACATTAATCCACAATTTCTTAA
390 GAGAGACGGTTCTCTTTAATCAAAAAATGTAAAATAAAAAATGACATTAATCCACAATTTCTTAA
*
3840616 AGGTAAGGTAGGTAAGTAATCTTTAGCAATTGAATCAAGACAATCTATTTTGAATATTGTTGATA
455 AGGTAAGGTAGGTAAGTAATCTTTAGCAATTGAATCAAGACAATCTATTTTAAATATTGTTGATA
*
3840681 AAAATGTCGATGACTTAGTTTTCAAAAGATCTCTTCACAATGTACTAGTTAATTGTCACTCTTTG
520 AAAATGTCGATGACTTAGTTTTCAAAAGATCTCTTCACAATGTACCAGTTAATTGTCACTCTTTG
3840746 GTTGTCATTGATGATTTTGTTTCAGAGAGTGTCAATGTAACCTCCCAAACCCAACCTAGACGTTA
585 GTTGTCATTGATGATTTTGTTTCAGAGAGTGTCAATGTAACCTCCCAAACCCAACCTAGACGTTA
* *
3840811 TGGTCGAATCAGGAAGGCCACATTGGACACCTTAGTGTCGGACCTACCATAACGATAGTTAAAAA
650 TGGTCGAATCAGGAAGGCCACATTAGACACCTTAGTGTCGGACCTACC-CAACGATAGTTAAAAA
3840876 CCTTCAAGTACTCCTTTTTATAAAATTGTGGTTTCTATTGCTAGCTTTGGAAAACATCCATTTAC
714 CCTTCAAGTACTCCTTTTTATAAAATTGTGGTTTCTATTGCTAGCTTTGGAAAACATCCATTTAC
*
3840941 TTTGTCCAACCA
779 TTAGTCCAACCA
3840953 TGCTCAGGTC
Statistics
Matches: 777, Mismatches: 12, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
790 338 0.44
791 439 0.56
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (790 bp):
AAGAATTAGTGAGAATAAGAGAAAAGAAAAAGAAAAGTTATTAATGAAAGAAAAATAGAAGAGAT
TGAGACAAAAAAAAGAAAAAGAAATAAAAAGAGAGTGAGTGAGAAAAGAAGTTGTGGAAAAAAAA
GAATGAAAAAGAATTTGAGCAAGAAAAGAAAATTGAAAAAGAATGCGAGAAAGAAGAATAAGAAA
TTGAGATTGAAGAAATAAAAACAAGTGTGAGTAATATGAATGACGTTGTTGAAACAAAAAGTGAA
ATTGAAAAGGAGTGTGACAAGGAAATGAGTGTTTTTACTAACCAACATGCAAGTTGTCCTCATTT
TGTCTCTTCATTTCAAGTTTCTAATGGTTCATTTGATGAGTTCCAACTTCTTTACTCCACTTTCG
AGAGACGGTTCTCTTTAATCAAAAAATGTAAAATAAAAAATGACATTAATCCACAATTTCTTAAA
GGTAAGGTAGGTAAGTAATCTTTAGCAATTGAATCAAGACAATCTATTTTAAATATTGTTGATAA
AAATGTCGATGACTTAGTTTTCAAAAGATCTCTTCACAATGTACCAGTTAATTGTCACTCTTTGG
TTGTCATTGATGATTTTGTTTCAGAGAGTGTCAATGTAACCTCCCAAACCCAACCTAGACGTTAT
GGTCGAATCAGGAAGGCCACATTAGACACCTTAGTGTCGGACCTACCCAACGATAGTTAAAAACC
TTCAAGTACTCCTTTTTATAAAATTGTGGTTTCTATTGCTAGCTTTGGAAAACATCCATTTACTT
AGTCCAACCA
Found at i:3844131 original size:52 final size:50
Alignment explanation
Indices: 3844067--3844180 Score: 131
Period size: 50 Copynumber: 2.2 Consensus size: 50
3844057 ATGAACAAAT
* *
3844067 GAGTTACTTAATGCAAGAC-TTAATTTAATGTTGCAGACTTAAACTAACATGG
1 GAGTTACATAATGCAAGACATT-ATTT-ATGATGCAGACTT-AACTAACATGG
* * * *
3844119 GAGTTACATAATGCATGTCATTATTTATGATGCATACTTAACTAGCATGG
1 GAGTTACATAATGCAAGACATTATTTATGATGCAGACTTAACTAACATGG
*
3844169 AAGTTACATAAT
1 GAGTTACATAAT
3844181 ACTTTATTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 21 0.39
51 11 0.20
52 20 0.37
53 2 0.04
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (50 bp):
GAGTTACATAATGCAAGACATTATTTATGATGCAGACTTAACTAACATGG
Found at i:3875398 original size:18 final size:19
Alignment explanation
Indices: 3875375--3875421 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
3875365 AGACCGTATA
*
3875375 CAATTTTTTT-CTTTTTTT
1 CAATTTTTTTGATTTTTTT
3875393 CAATTTTTTTGATTTTTTT
1 CAATTTTTTTGATTTTTTT
*
3875412 CGATTTTTTT
1 CAATTTTTTT
3875422 TTCAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (19 bp):
CAATTTTTTTGATTTTTTT
Found at i:3875399 original size:10 final size:10
Alignment explanation
Indices: 3875375--3875421 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
3875365 AGACCGTATA
3875375 CAATTTTTTT
1 CAATTTTTTT
3875385 C--TTTTTTT
1 CAATTTTTTT
3875393 CAATTTTTTT
1 CAATTTTTTT
*
3875403 -GATTTTTTT
1 CAATTTTTTT
*
3875412 CGATTTTTTT
1 CAATTTTTTT
3875422 TTCAAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 8 0.24
9 8 0.24
10 17 0.52
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (10 bp):
CAATTTTTTT
Found at i:3889811 original size:52 final size:51
Alignment explanation
Indices: 3889705--3889876 Score: 192
Period size: 50 Copynumber: 3.4 Consensus size: 51
3889695 ATGATGCTTA
* * * *
3889705 AATGCATGATTTAA-TTAA-GATGCAAAC-TAAATGAACA-AATGAGTTACTT
1 AATGCATGACTTAATTTAATGATGCAAACTTAACT-AACATGA-GAGTTACAT
* *
3889754 AATGCATGACTTAATTTAATGATGCAGACTTAAACTAACATGGGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTT-AACTAACATGAGAGTTACAT
* *
3889806 AATGCATGTCATAATTT-ATGATGCAAACTTAACTAACATGAGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGAGAGTTACAT
* *
3889856 AATGCATGACTTTATTAAATG
1 AATGCATGACTTAATTTAATG
3889877 CTGAACACAT
Statistics
Matches: 103, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
49 13 0.13
50 36 0.35
51 23 0.22
52 28 0.27
53 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (51 bp):
AATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGAGAGTTACAT
Found at i:3891443 original size:20 final size:20
Alignment explanation
Indices: 3891420--3891466 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3891410 GGGTTGAGGT
3891420 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
3891440 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
3891460 TGAGCTG
1 TGAGCTG
3891467 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:3914069 original size:19 final size:18
Alignment explanation
Indices: 3914033--3914072 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3914023 TTTCCACTCG
*
3914033 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
3914051 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
3914070 TTT
1 TTT
3914073 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:3915229 original size:9 final size:10
Alignment explanation
Indices: 3915211--3915245 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
3915201 AAAAAATTTC
3915211 GAATTTTTTT
1 GAATTTTTTT
3915221 GAATTTTTTT
1 GAATTTTTTT
3915231 GAATTTTTTT
1 GAATTTTTTT
3915241 CGAAT
1 -GAAT
3915246 ATGCTACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.23, C:0.03, G:0.11, T:0.63
Consensus pattern (10 bp):
GAATTTTTTT
Done.