Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_18 ID=scaffold_18-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 239776
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.18
Warning! 101276 characters in sequence are not A, C, G, or T
Found at i:12465 original size:15 final size:16
Alignment explanation
Indices: 12444--12482 Score: 71
Period size: 15 Copynumber: 2.5 Consensus size: 16
12434 GTTCGTGAAT
12444 TAAAAAAATTCGTGCA
1 TAAAAAAATTCGTGCA
12460 -AAAAAAATTCGTGCA
1 TAAAAAAATTCGTGCA
12475 TAAAAAAA
1 TAAAAAAA
12483 GAGAGGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.21
Consensus pattern (16 bp):
TAAAAAAATTCGTGCA
Found at i:13463 original size:18 final size:18
Alignment explanation
Indices: 13442--13476 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13432 AGAAAAGAAA
13442 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
13460 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
13477 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:17301 original size:45 final size:45
Alignment explanation
Indices: 17237--17469 Score: 403
Period size: 45 Copynumber: 5.2 Consensus size: 45
17227 CATGAAATTA
*
17237 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
17282 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
17327 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
17372 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
17417 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
17462 AGGAAGCA
1 AGGAAGCA
17470 CCATGGCCGA
Statistics
Matches: 179, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 179 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:24276 original size:10 final size:10
Alignment explanation
Indices: 24261--24302 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
24251 TTTGCAAGTT
24261 TTGAGCTAAA
1 TTGAGCTAAA
* *
24271 TTGAGCTGAT
1 TTGAGCTAAA
*
24281 TTGAGCT-CA
1 TTGAGCTAAA
24290 TTGAGCTAAA
1 TTGAGCTAAA
24300 TTG
1 TTG
24303 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:25944 original size:20 final size:20
Alignment explanation
Indices: 25919--25965 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
25909 TTTTATTTTC
*
25919 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
25939 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
25959 CAGCTCA
1 CAGCTCA
25966 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:32227 original size:18 final size:19
Alignment explanation
Indices: 32193--32229 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
32183 TCCTTTGTGT
*
32193 ATTCAGTATTGAAAAAAAA
1 ATTCAGAATTGAAAAAAAA
32212 ATTCAGAATT-AAAAAAAA
1 ATTCAGAATTGAAAAAAAA
32230 GTGATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.24
Consensus pattern (19 bp):
ATTCAGAATTGAAAAAAAA
Found at i:34273 original size:15 final size:14
Alignment explanation
Indices: 34237--34291 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
34227 TCTATTGAGC
34237 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
34251 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
34265 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
34280 GAAAGAAAAGAA
1 GAGA-AAAAGAA
34292 TGATGAGAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:39635 original size:25 final size:25
Alignment explanation
Indices: 39604--39659 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
39594 ATTAGTAACT
39604 CATTTAGTTTGCATTTCAAACCATG
1 CATTTAGTTTGCATTTCAAACCATG
39629 CATTTAGTTTGCATTTCAAACCATG
1 CATTTAGTTTGCATTTCAAACCATG
39654 CATTTA
1 CATTTA
39660 ATCATCTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.41
Consensus pattern (25 bp):
CATTTAGTTTGCATTTCAAACCATG
Found at i:42839 original size:14 final size:15
Alignment explanation
Indices: 42802--42839 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
42792 AAATTTGAAA
*
42802 AAAATAAAAAAATCG
1 AAAAGAAAAAAATCG
*
42817 AAAAGAAAAAAATTG
1 AAAAGAAAAAAATCG
42832 AAAA-AAAA
1 AAAAGAAAA
42840 TATTGCATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.11
Consensus pattern (15 bp):
AAAAGAAAAAAATCG
Found at i:42902 original size:63 final size:62
Alignment explanation
Indices: 42834--43019 Score: 327
Period size: 63 Copynumber: 3.0 Consensus size: 62
42824 AAAAATTGAA
42834 AAAAAATATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGAAAAAAAAGCAG
1 AAAAAA-ATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGAAAAAAAA-CAG
* *
42898 AAAAAAATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAATAG
1 AAAAAAATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGAAAAAAAACAG
42960 AAAAAAATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAAA
1 AAAAAAATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCG-AAAAAAAA
43020 AAGAGTCTGG
Statistics
Matches: 118, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
62 53 0.45
63 59 0.50
64 6 0.05
ACGTcount: A:0.47, C:0.13, G:0.24, T:0.15
Consensus pattern (62 bp):
AAAAAAATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGAAAAAAAACAG
Found at i:42985 original size:62 final size:63
Alignment explanation
Indices: 42834--43018 Score: 336
Period size: 62 Copynumber: 2.9 Consensus size: 63
42824 AAAAATTGAA
*
42834 AAAAAATATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGAAAAAAAAGCAG
1 AAAAAA-ATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAAGCAG
*
42898 AAAAAAATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAA-TAG
1 AAAAAAATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAAGCAG
42960 AAAAAAATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAA
1 AAAAAAATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAA
43019 AAAGAGTCTG
Statistics
Matches: 119, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
62 61 0.51
63 52 0.44
64 6 0.05
ACGTcount: A:0.47, C:0.14, G:0.24, T:0.15
Consensus pattern (63 bp):
AAAAAAATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAAGCAG
Found at i:43994 original size:18 final size:18
Alignment explanation
Indices: 43973--44007 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43963 AGAAAAGAAA
43973 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
43991 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
44008 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:52634 original size:20 final size:20
Alignment explanation
Indices: 52609--52655 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
52599 AGCTCGTTTC
*
52609 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
52629 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
52649 CAGCTCA
1 CAGCTCA
52656 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:62441 original size:14 final size:14
Alignment explanation
Indices: 62422--62473 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
62412 AAACCGTATA
*
62422 CAATTTTTTTCTTT
1 CAATTTTTTTCTCT
62436 CAATTTTTTTTCTCT
1 CAA-TTTTTTTCTCT
62451 CGAATTTTTTT-TC-
1 C-AATTTTTTTCTCT
*
62464 AAATTTTTTT
1 CAATTTTTTT
62474 TCGAACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 9 0.26
14 5 0.15
15 18 0.53
16 2 0.06
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.67
Consensus pattern (14 bp):
CAATTTTTTTCTCT
Found at i:62446 original size:16 final size:16
Alignment explanation
Indices: 62425--62463 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
62415 CCGTATACAA
*
62425 TTTTTTTCTTTC-AAT
1 TTTTTTTCTCTCGAAT
62440 TTTTTTTCTCTCGAAT
1 TTTTTTTCTCTCGAAT
62456 TTTTTTTC
1 TTTTTTTC
62464 AAATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.10, C:0.15, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTTTCTCTCGAAT
Found at i:62468 original size:12 final size:13
Alignment explanation
Indices: 62453--62487 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
62443 TTTTCTCTCG
62453 AATTTTTTTTC-A
1 AATTTTTTTTCGA
62465 AATTTTTTTTCGA
1 AATTTTTTTTCGA
*
62478 ACTTTTTTTT
1 AATTTTTTTT
62488 ACGTACCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.20, C:0.09, G:0.03, T:0.69
Consensus pattern (13 bp):
AATTTTTTTTCGA
Found at i:66184 original size:12 final size:12
Alignment explanation
Indices: 66169--66238 Score: 68
Period size: 12 Copynumber: 5.7 Consensus size: 12
66159 AAAAGAAAAA
66169 GAAAAAGAAGTT
1 GAAAAAGAAGTT
66181 GAAAAAGAAGTT
1 GAAAAAGAAGTT
* *
66193 AAAAAAGAAATT
1 GAAAAAGAAGTT
* ***
66205 AAAAAAGAAAAAAA
1 GAAAAAG--AAGTT
66219 GAAAAAGAAGTT
1 GAAAAAGAAGTT
66231 GAAAAAGA
1 GAAAAAGA
66239 GACTGAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 39 0.81
14 9 0.19
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (12 bp):
GAAAAAGAAGTT
Found at i:66347 original size:21 final size:21
Alignment explanation
Indices: 66306--66348 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
66296 CGAAAGTGTG
**
66306 AGGAAAAAGAGAAGATTGAAA
1 AGGAAAAAGAGAAGAGAGAAA
66327 AGGAAAAAGA-AATGAGAGAAA
1 AGGAAAAAGAGAA-GAGAGAAA
66348 A
1 A
66349 AGAGGCAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.65, C:0.00, G:0.28, T:0.07
Consensus pattern (21 bp):
AGGAAAAAGAGAAGAGAGAAA
Found at i:73890 original size:13 final size:13
Alignment explanation
Indices: 73824--73889 Score: 71
Period size: 13 Copynumber: 5.0 Consensus size: 13
73814 AGACTTTTCA
73824 CTTCTTTTTTTTT
1 CTTCTTTTTTTTT
*
73837 CTTCTTTTTTTTA
1 CTTCTTTTTTTTT
*
73850 CTCCTTTTTTTTT
1 CTTCTTTTTTTTT
* *
73863 GCTCACTTCTTTTTT
1 -CT-TCTTTTTTTTT
73878 -TTCTTTTTTTTT
1 CTTCTTTTTTTTT
73890 TGAATTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
12 9 0.20
13 24 0.55
14 2 0.05
15 9 0.20
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (13 bp):
CTTCTTTTTTTTT
Found at i:75286 original size:66 final size:66
Alignment explanation
Indices: 75180--75311 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
75170 TTTATTGAGA
75180 GGTATCCTCCTATCCTATTTCGTACGAGTCTTGTTCTGACTTATCTAGCTCGCTAGTGGCGTCAA
1 GGTATCCTCCTATCCTATTTCGTACGAGTCTTGTTCTGACTTATCTAGCTCGCTAGTGGCGTCAA
75245 C
66 C
75246 GGTATCCTCCTATCCTATTTCGTACGAGTCTTGTTCTGACTTATCTAGCTCGCTAGTGGCGTCAA
1 GGTATCCTCCTATCCTATTTCGTACGAGTCTTGTTCTGACTTATCTAGCTCGCTAGTGGCGTCAA
75311 C
66 C
75312 TCGACTCCTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (66 bp):
GGTATCCTCCTATCCTATTTCGTACGAGTCTTGTTCTGACTTATCTAGCTCGCTAGTGGCGTCAA
C
Found at i:84409 original size:20 final size:20
Alignment explanation
Indices: 84386--84442 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
84376 AGTTTTTCCC
*
84386 AGCTCGATTTAGCTTACATG
1 AGCTCAATTTAGCTTACATG
* ****
84406 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTTACATG
84426 AGCTCAATTTAGCTTAC
1 AGCTCAATTTAGCTTAC
84443 TTAGCTTGTT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACATG
Found at i:87924 original size:20 final size:20
Alignment explanation
Indices: 87899--87941 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
87889 AAAAGAAAAG
87899 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
87919 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
87939 AAA
1 AAA
87942 ACAAGAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:93409 original size:41 final size:41
Alignment explanation
Indices: 93352--93459 Score: 189
Period size: 41 Copynumber: 2.6 Consensus size: 41
93342 TTTAATATGT
* *
93352 CGAATTTAATGCTGCCACTACATGTTATAAATGTGTCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
93393 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
*
93434 CGAATTTAATGCTGCTACTACATGTT
1 CGAATTTAATGCTGCCACTACATGTT
93460 TGGCCGAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
Found at i:95022 original size:12 final size:11
Alignment explanation
Indices: 95000--95046 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
94990 GTATTATGGT
95000 ATTGTAAAAAAA
1 ATTG-AAAAAAA
95012 ACTTG-AAAAAA
1 A-TTGAAAAAAA
95023 ATTCGAAAAAAA
1 ATT-GAAAAAAA
*
95035 ATTCAAAAAAA
1 ATTGAAAAAAA
95046 A
1 A
95047 GAGTTTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 2 0.06
11 16 0.52
12 10 0.32
13 3 0.10
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (11 bp):
ATTGAAAAAAA
Found at i:95046 original size:11 final size:12
Alignment explanation
Indices: 95005--95046 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
94995 ATGGTATTGT
95005 AAAAAAAACTT-G
1 AAAAAAAA-TTCG
95017 -AAAAAAATTCG
1 AAAAAAAATTCG
95028 AAAAAAAATTC-
1 AAAAAAAATTCG
95039 AAAAAAAA
1 AAAAAAAA
95047 GAGTTTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 10 0.36
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:116638 original size:22 final size:22
Alignment explanation
Indices: 116605--116658 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
116595 TTTAAGTCGA
116605 TTTAAT-TAGTTTATTACA-GCTT
1 TTTAATAT-GTTTATTACATG-TT
* *
116627 TTTAATATGTTTGTTGCATGTT
1 TTTAATATGTTTATTACATGTT
116649 TTTAATATGT
1 TTTAATATGT
116659 CAAGTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.24, C:0.06, G:0.13, T:0.57
Consensus pattern (22 bp):
TTTAATATGTTTATTACATGTT
Found at i:117691 original size:22 final size:22
Alignment explanation
Indices: 117663--117726 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
117653 CCTTTTTGAA
117663 CCATTACCATTTCGTACCAAAT
1 CCATTACCATTTCGTACCAAAT
* **
117685 CCATTACCATTTTGTGTCAAAT
1 CCATTACCATTTCGTACCAAAT
*
117707 CCTTTACCATTTCGTACCAA
1 CCATTACCATTTCGTACCAA
117727 TTCCCAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:124234 original size:16 final size:16
Alignment explanation
Indices: 124215--124248 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
124205 TGAACAACAT
124215 CATTAAACAACAGCAG
1 CATTAAACAACAGCAG
124231 CATTAAACAACAGCAG
1 CATTAAACAACAGCAG
124247 CA
1 CA
124249 AAACACATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.26, G:0.12, T:0.12
Consensus pattern (16 bp):
CATTAAACAACAGCAG
Found at i:125603 original size:52 final size:51
Alignment explanation
Indices: 125521--125625 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 51
125511 TACCATAAGG
* *
125521 AAACATAATGGACAGCAGCTTAAAATCTCATTTCTAGCTCGGTTGAAGCTC
1 AAACATAATGGACAGCAGCTTAAAACCTCATTTCTAGCTCAGTTGAAGCTC
*
125572 AAACAATAATAGG-CAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTC
1 AAAC-ATAAT-GGACAGCAGCTTAAAACCTCATTTCTAGCTCAGTTGAAGCTC
125624 AA
1 AA
125626 TATGTGCATG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
51 4 0.08
52 43 0.88
53 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (51 bp):
AAACATAATGGACAGCAGCTTAAAACCTCATTTCTAGCTCAGTTGAAGCTC
Found at i:132194 original size:20 final size:19
Alignment explanation
Indices: 132171--132235 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
132161 AAGCTCAAAC
132171 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
132191 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
132211 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
132231 GAGCT
1 GAGCT
132236 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:135802 original size:18 final size:18
Alignment explanation
Indices: 135781--135820 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
135771 GATTGAGAGT
* * *
135781 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
135799 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
135817 GAAA
1 GAAA
135821 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:143687 original size:42 final size:42
Alignment explanation
Indices: 143635--143717 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
143625 AATATGTGTG
*
143635 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
1 AAACATTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
143677 AAACATTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
1 AAACATTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
143718 CTTTGAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (42 bp):
AAACATTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
Found at i:144999 original size:13 final size:13
Alignment explanation
Indices: 144981--145008 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
144971 AATAAATTAT
144981 TTAATTTAGTTAG
1 TTAATTTAGTTAG
144994 TTAATTTAGTTAG
1 TTAATTTAGTTAG
145007 TT
1 TT
145009 CAGTTCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (13 bp):
TTAATTTAGTTAG
Found at i:145317 original size:84 final size:84
Alignment explanation
Indices: 145143--145319 Score: 221
Period size: 85 Copynumber: 2.1 Consensus size: 84
145133 CTTATTACAT
* * * * * *
145143 CTATTTAATGAGTCCTAGTTCCAGCCGAAATTAATAGCAAGGTCAATGTGTCTTAGTGGCTACCG
1 CTATTTAATGAGTCATAGTTCCAGCCGAAATTAAGAGCAACGTCAAAGTGTCTTAATGGCTACAG
* *
145208 AATTTATTAAATCTTACAT
66 AATTTATTAAATCTCACAG
* * * *
145227 CCATTTAATGTGTCATAGTTCCAGCCGAAATTAAAGAGCAACGTTAAAGTGTCTTAATGGCTGCA
1 CTATTTAATGAGTCATAGTTCCAGCCGAAATT-AAGAGCAACGTCAAAGTGTCTTAATGGCTACA
*
145292 GAATTTATTATATCTCA-AG
65 GAATTTATTAAATCTCACAG
145311 CTATTTAAT
1 CTATTTAAT
145320 TAGCTGTATT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
84 38 0.49
85 40 0.51
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (84 bp):
CTATTTAATGAGTCATAGTTCCAGCCGAAATTAAGAGCAACGTCAAAGTGTCTTAATGGCTACAG
AATTTATTAAATCTCACAG
Found at i:145922 original size:18 final size:16
Alignment explanation
Indices: 145901--145939 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 16
145891 TTTTCTTTCG
145901 TTTCTTTTTCAACTTCTT
1 TTTCTTTTTCAA-TT-TT
145919 TTTCTTTTTCAATTTT
1 TTTCTTTTTCAATTTT
145935 TTTCT
1 TTTCT
145940 CAATCTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 2 0.10
18 12 0.57
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTCTTTTTCAATTTT
Found at i:145970 original size:18 final size:18
Alignment explanation
Indices: 145914--146069 Score: 84
Period size: 18 Copynumber: 8.5 Consensus size: 18
145904 CTTTTTCAAC
* *
145914 TTCTTTTTCTTTTTCAAT
1 TTCTTTTTCATTTTCTAT
* * *
145932 TT-TTTTCTCAATCTCAAT
1 TTCTTTT-TCATTTTCTAT
145950 TTCTTTTTCAATTTTCT-T
1 TTCTTTTTC-ATTTTCTAT
* *
145968 TTCTTCGTTTTCTTTTTCTCT
1 TTC-T--TTTTCATTTTCTAT
** * * *
145989 CACTTTTTTGAGT-TCTTT
1 TTC-TTTTTCATTTTCTAT
* * *
146007 TTCTTTTGCAATTTCTTT
1 TTCTTTTTCATTTTCTAT
*
146025 TTCTTTTTCGTTTTCTAT
1 TTCTTTTTCATTTTCTAT
*
146043 TTCTTTTTCACTTTCTAT
1 TTCTTTTTCATTTTCTAT
146061 TTCTTTTTC
1 TTCTTTTTC
146070 TTATTTTTCA
Statistics
Matches: 106, Mismatches: 24, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
17 10 0.09
18 67 0.63
19 14 0.13
20 6 0.06
21 9 0.08
ACGTcount: A:0.10, C:0.19, G:0.03, T:0.68
Consensus pattern (18 bp):
TTCTTTTTCATTTTCTAT
Found at i:146038 original size:7 final size:6
Alignment explanation
Indices: 146001--146071 Score: 70
Period size: 6 Copynumber: 11.8 Consensus size: 6
145991 CTTTTTTGAG
* ** * *
146001 TTCTTT TTCTTT TGCAAT TTCTTT TTCTTT TTCGTT TTCTAT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
** *
146049 TTCACT TTCTAT TTCTTT TTCTT
1 TTCTTT TTCTTT TTCTTT TTCTT
146072 ATTTTTCATT
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (6 bp):
TTCTTT
Found at i:147413 original size:45 final size:46
Alignment explanation
Indices: 147364--147456 Score: 152
Period size: 45 Copynumber: 2.0 Consensus size: 46
147354 CAAAGAAAAG
147364 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTAT-TGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
** *
147409 ACCTCGACCTTCTATCAAGGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
147455 AC
1 AC
147457 GCCACACTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 36 0.82
46 8 0.18
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
Found at i:148864 original size:22 final size:23
Alignment explanation
Indices: 148825--148876 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
148815 GTATGAAACA
*
148825 GTAAGGGATTTGAAACG-AAATG
1 GTAATGGATTTGAAACGAAAATG
**
148847 GTAATGGATTTGGTACGAAAATG
1 GTAATGGATTTGAAACGAAAATG
*
148870 GAAATGG
1 GTAATGG
148877 TTCAAAAAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.38, C:0.04, G:0.33, T:0.25
Consensus pattern (23 bp):
GTAATGGATTTGAAACGAAAATG
Found at i:150723 original size:20 final size:20
Alignment explanation
Indices: 150698--150755 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
150688 TTTCCATGCG
150698 ATTCAGCTCACTTGAGCTCA
1 ATTCAGCTCACTTGAGCTCA
150718 ATTCAGCTTCCAC--GAGCTCA
1 ATTCAGC-T-CACTTGAGCTCA
*
150738 ATTCAACTCA-TTGAGCTC
1 ATTCAGCTCACTTGAGCTC
150756 GTTATTAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
18 2 0.06
19 7 0.21
20 20 0.61
21 1 0.03
22 3 0.09
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (20 bp):
ATTCAGCTCACTTGAGCTCA
Found at i:150913 original size:16 final size:15
Alignment explanation
Indices: 150894--150923 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
150884 AGTATCAATT
150894 TTTGATTGGTGATGAC
1 TTTGATTGGT-ATGAC
150910 TTTGATTGGTATGA
1 TTTGATTGGTATGA
150924 TGGATTGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.03, G:0.30, T:0.47
Consensus pattern (15 bp):
TTTGATTGGTATGAC
Found at i:151259 original size:12 final size:12
Alignment explanation
Indices: 151242--151268 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
151232 GACGTCAAGC
151242 CAAGGTGAGTAT
1 CAAGGTGAGTAT
151254 CAAGGTGAGTAT
1 CAAGGTGAGTAT
151266 CAA
1 CAA
151269 ATTGAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (12 bp):
CAAGGTGAGTAT
Found at i:152153 original size:41 final size:41
Alignment explanation
Indices: 152096--152203 Score: 189
Period size: 41 Copynumber: 2.6 Consensus size: 41
152086 TTTAATATGT
* *
152096 CGAATTTAATGCTGCCACTACATGTTATAAATGTGTCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
152137 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
*
152178 CGAATTTAATGCTGCTACTACATGTT
1 CGAATTTAATGCTGCCACTACATGTT
152204 TGGCCGAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
Found at i:154407 original size:19 final size:19
Alignment explanation
Indices: 154379--154425 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
154369 GCGAAAATAC
*
154379 AAAAGAAAAGAAAAATGAAA
1 AAAAG-AAAGAAAAATCAAA
*
154399 AAAAGAAAGAAAATTCAAA
1 AAAAGAAAGAAAAATCAAA
154418 AAAAGAAA
1 AAAAGAAA
154426 ATGAAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (19 bp):
AAAAGAAAGAAAAATCAAA
Found at i:156919 original size:13 final size:13
Alignment explanation
Indices: 156898--156932 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
156888 ATAAATTGTT
* *
156898 GTTAGTTAAATTA
1 GTTAATTAAATAA
156911 GTTAATTAAATAA
1 GTTAATTAAATAA
156924 GTTAATTAA
1 GTTAATTAA
156933 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:161255 original size:18 final size:18
Alignment explanation
Indices: 161199--161258 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
161189 AGTGCGAGCG
161199 AGAAAAAGAAATCGAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
161220 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
161238 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
161256 AGA
1 AGA
161259 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:218033 original size:20 final size:20
Alignment explanation
Indices: 218008--218065 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
217998 TTTCCATGCG
218008 ATTCAGCTCACTTGAGCTCA
1 ATTCAGCTCACTTGAGCTCA
218028 ATTCAGCTTCCAC--GAGCTCA
1 ATTCAGC-T-CACTTGAGCTCA
*
218048 ATTCAACTCA-TTGAGCTC
1 ATTCAGCTCACTTGAGCTC
218066 GTTATTAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
18 2 0.06
19 7 0.21
20 20 0.61
21 1 0.03
22 3 0.09
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (20 bp):
ATTCAGCTCACTTGAGCTCA
Found at i:221534 original size:18 final size:18
Alignment explanation
Indices: 221513--221567 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
221503 CTCACTCTCC
221513 TTTTTTATTTCTTTTTCT
1 TTTTTTATTTCTTTTTCT
** *
221531 TTTTCAATCTCTTTTTCT
1 TTTTTTATTTCTTTTTCT
221549 TTTTCTTCGATTTCTTTTT
1 TTTT-TT--ATTTCTTTTT
221568 TTCGCTCGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 19 0.68
21 9 0.32
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTTTATTTCTTTTTCT
Found at i:224899 original size:30 final size:30
Alignment explanation
Indices: 224863--224922 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
224853 AAATTTACCC
224863 AAGTATAGCCTTAAAACATGATTCATCAAT
1 AAGTATAGCCTTAAAACATGATTCATCAAT
224893 AAGTATAGCCTTAAAACATGATTCATCAAT
1 AAGTATAGCCTTAAAACATGATTCATCAAT
224923 CTCATAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (30 bp):
AAGTATAGCCTTAAAACATGATTCATCAAT
Done.